From 2af7f62a8a6466137f69a8daf022708d43d2a11e Mon Sep 17 00:00:00 2001
From: geoffjentry <geoffjentry@gmail.com>
Date: Mon, 4 May 2015 19:59:01 -0400
Subject: [PATCH 001/326] Add license file

---
 LICENSE.txt | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 LICENSE.txt

diff --git a/LICENSE.txt b/LICENSE.txt
new file mode 100644
index 00000000000..2efdb96ebc1
--- /dev/null
+++ b/LICENSE.txt
@@ -0,0 +1,27 @@
+Copyright (c) 2015, Broad Institute, Inc.
+All rights reserved.
+ 
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ 
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+ 
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+ 
+* Neither the name Broad Institute, Inc. nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+ 
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE

From 3677b05ba8f938429b89520b8dd149a65fb479cf Mon Sep 17 00:00:00 2001
From: Scott Frazer <sfrazer@broadinstitute.org>
Date: Mon, 1 Jun 2015 13:50:55 -0400
Subject: [PATCH 002/326] Docker files

---
 .dockerignore     |  1 +
 Dockerfile        | 24 ++++++++++++++++++++++++
 docker/install.sh | 10 ++++++++++
 docker/run.sh     |  5 +++++
 4 files changed, 40 insertions(+)
 create mode 120000 .dockerignore
 create mode 100644 Dockerfile
 create mode 100755 docker/install.sh
 create mode 100755 docker/run.sh

diff --git a/.dockerignore b/.dockerignore
new file mode 120000
index 00000000000..3e4e48b0b5f
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1 @@
+.gitignore
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000000..b11a094e280
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,24 @@
+# http://github.com/broadinstitute/scala-baseimage
+FROM broadinstitute/scala-baseimage
+
+# Cromwell's HTTP Port
+EXPOSE 8000
+
+# Install Cromwell
+ADD . /cromwell
+RUN ["/bin/bash", "-c", "/cromwell/docker/install.sh /cromwell"]
+
+# Add Cromwell as a service (it will start when the container starts)
+RUN mkdir /etc/service/cromwell
+ADD docker/run.sh /etc/service/cromwell/run
+
+# These next 4 commands are for enabling SSH to the container.
+# id_rsa.pub is referenced below, but this should be any public key
+# that you want to be added to authorized_keys for the root user.
+# Copy the public key into this directory because ADD cannot reference
+# Files outside of this directory
+
+#EXPOSE 22
+#RUN rm -f /etc/service/sshd/down
+#ADD id_rsa.pub /tmp/id_rsa.pub
+#RUN cat /tmp/id_rsa.pub >> /root/.ssh/authorized_keys
diff --git a/docker/install.sh b/docker/install.sh
new file mode 100755
index 00000000000..3ea2888203e
--- /dev/null
+++ b/docker/install.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -e
+
+CROMWELL_DIR=$1
+cd $CROMWELL_DIR
+sbt assembly
+CROMWELL_JAR=$(find target | grep 'cromwell.*\.jar')
+mv $CROMWELL_JAR .
+sbt clean
diff --git a/docker/run.sh b/docker/run.sh
new file mode 100755
index 00000000000..c379ba35fe9
--- /dev/null
+++ b/docker/run.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+set -e
+
+java -jar $(find /cromwell | grep 'cromwell.*\.jar') server

From c4e4b45e7e1606ecfc56da2c8bea0bbdd87561b0 Mon Sep 17 00:00:00 2001
From: Thibault Jeandet <tjeandet@broadinstitute.org>
Date: Tue, 26 Jan 2016 15:20:36 -0500
Subject: [PATCH 003/326] adjust yaml file

---
 src/main/resources/swagger/cromwell.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/resources/swagger/cromwell.yaml b/src/main/resources/swagger/cromwell.yaml
index c91796f0eee..83f40a404aa 100644
--- a/src/main/resources/swagger/cromwell.yaml
+++ b/src/main/resources/swagger/cromwell.yaml
@@ -597,12 +597,12 @@ definitions:
     required:
       - valid
     properties:
-      valid:
-        type: boolean
-        description: The validation of the workflow
-      error:
+      status:
+        type: string
+        description: The validation status of the workflow
+      message:
         type: string
-        description: The validation error of the workflow
+        description: Details about the validation
   WorkflowSubmitResponse:
     description: ''
     required:

From 8a48eee787184ee960ec8c580b3b542f8dfae04e Mon Sep 17 00:00:00 2001
From: dgtester <dtester@google.com>
Date: Thu, 21 Jan 2016 16:15:27 -0500
Subject: [PATCH 004/326] Aborts jobs on shutdown.

Added configuration option for abortJobsOnTerminate. Added support for server mode. SingleWorkflowRunnerActor now uses the internal state to determine whether the workflow is done (and not a separately maintained flag).

Added configuration option for abortJobsOnTerminate. Added support for server mode. SingleWorkflowRunnerActor now uses the internal state to determine whether the workflow is done (and not a separately maintained flag).
---
 .../scala/cromwell/engine/CromwellActor.scala | 16 +++++++++++++
 .../workflow/SingleWorkflowRunnerActor.scala  | 12 ++++++++++
 .../workflow/WorkflowManagerActor.scala       | 24 +++++++++++++++++--
 3 files changed, 50 insertions(+), 2 deletions(-)

diff --git a/src/main/scala/cromwell/engine/CromwellActor.scala b/src/main/scala/cromwell/engine/CromwellActor.scala
index 11d19aacc3f..6017d71a75b 100644
--- a/src/main/scala/cromwell/engine/CromwellActor.scala
+++ b/src/main/scala/cromwell/engine/CromwellActor.scala
@@ -1,10 +1,26 @@
 package cromwell.engine
 
 import akka.util.Timeout
+import com.typesafe.config.{ConfigException, ConfigFactory}
 
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
 trait CromwellActor {
   protected implicit val timeout = Timeout(5 seconds)
+
+  /**
+   * Retrieves the configuration option that determines whether this actor should abort all jobs if it receives
+   * a shutdown hook.
+   * @return - The value of the configuration option, or 'false' if the option isn't specified.
+   */
+  def getAbortJobsOnTerminate: Boolean = {
+    val config=ConfigFactory.load.getConfig("backend")
+    try {
+      config.getBoolean("abortJobsOnTerminate")
+    } catch {
+      case _:ConfigException  => false
+    }
+  }
+
 }
diff --git a/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala b/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala
index 0e5457c6d14..8e69829c9fa 100644
--- a/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala
+++ b/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala
@@ -79,6 +79,18 @@ case class SingleWorkflowRunnerActor(source: WorkflowSourceFiles,
     case Event(id: WorkflowId, data) =>
       log.info(s"$tag: workflow ID UUID($id)")
       workflowManager ! SubscribeToWorkflow(id)
+
+      if (getAbortJobsOnTerminate) {
+        Runtime.getRuntime.addShutdownHook(new Thread() {
+          override def run(): Unit = {
+            workflowManager ! WorkflowAbort(id)
+            log.info(s"$tag: Waiting for workflow $id to abort...")
+            while(stateName != Done)
+              Thread.sleep(1000)
+            log.info(s"$tag: Workflow $id aborted.")
+          }
+        })
+      }
       stay using data.copy(id = Option(id))
     case Event(Transition(_, _, WorkflowSucceeded), data) =>
       workflowManager ! WorkflowOutputs(data.id.get)
diff --git a/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala b/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
index 6b5e6dd0380..6a01b80572c 100644
--- a/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
+++ b/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
@@ -14,14 +14,15 @@ import cromwell.engine.db.DataAccess._
 import cromwell.engine.db.ExecutionDatabaseKey
 import cromwell.engine.db.slick._
 import cromwell.engine.workflow.WorkflowActor.{Restart, Start}
+import cromwell.server.CromwellServer
 import cromwell.util.WriteOnceStore
 import cromwell.webservice._
 import org.joda.time.DateTime
 import spray.json._
 import wdl4s._
-
+import wdl4s.values.WdlFile
 import scala.concurrent.ExecutionContext.Implicits.global
-import scala.concurrent.Future
+import scala.concurrent.{Await, Future}
 import scala.concurrent.duration._
 import scala.io.Source
 import scala.language.postfixOps
@@ -68,6 +69,25 @@ class WorkflowManagerActor(backend: Backend) extends Actor with CromwellActor {
 
   private val workflowStore = new WriteOnceStore[WorkflowId, WorkflowActorRef]
 
+  if (getAbortJobsOnTerminate) {
+    Runtime.getRuntime.addShutdownHook(new Thread() {
+      override def run(): Unit = {
+        log.info(s"$tag: Received shutdown signal. Aborting all running workflows...")
+        workflowStore.toMap.foreach{case (id, actor)=>
+          CromwellServer.workflowManagerActor ! WorkflowManagerActor.WorkflowAbort(id)
+        }
+        var numRemaining = -1
+        while(numRemaining != 0) {
+          Thread.sleep(1000)
+          val result = globalDataAccess.getWorkflowsByState(Seq(WorkflowRunning, WorkflowAborting))
+          numRemaining = Await.result(result,Duration.Inf).size
+          log.info(s"$tag: Waiting for all workflows to abort ($numRemaining remaining).")
+        }
+        log.info(s"$tag: All workflows aborted.")
+      }
+    })
+  }
+
   override def preStart() {
     restartIncompleteWorkflows()
   }

From d2b053d7977560498363a0066424767d52a4e135 Mon Sep 17 00:00:00 2001
From: Thibault Jeandet <tjeandet@broadinstitute.org>
Date: Thu, 22 Sep 2016 16:48:32 -0400
Subject: [PATCH 005/326] update version to 0.21

---
 project/Version.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Version.scala b/project/Version.scala
index 99e00f9f622..58c8590e286 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -4,7 +4,7 @@ import sbt._
 
 object Version {
   // Upcoming release, or current if we're on the master branch
-  val cromwellVersion = "0.20"
+  val cromwellVersion = "0.21"
 
   // Adapted from SbtGit.versionWithGit
   def cromwellVersionWithGit: Seq[Setting[_]] =

From fac45fc581f38c0364934f24cf3ffbca342d0cd0 Mon Sep 17 00:00:00 2001
From: Jeff Gentry <geoffjentry@gmail.com>
Date: Fri, 23 Sep 2016 12:46:31 -0400
Subject: [PATCH 006/326] Fix incorrect URL

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 3c5efc0099a..fd1477d503b 100644
--- a/README.md
+++ b/README.md
@@ -76,7 +76,7 @@ A [Workflow Management System](https://en.wikipedia.org/wiki/Workflow_management
   * [GET /api/workflows/:version/:id/metadata](#get-apiworkflowsversionidmetadata)
   * [POST /api/workflows/:version/:id/abort](#post-apiworkflowsversionidabort)
   * [GET /api/workflows/:version/backends](#get-apiworkflowsversionbackends)
-  * [GET /api/workflows/:version/stats](#get-apiworkflowsversionstats)
+  * [GET /api/engine/:version/stats](#get-apiengineversionstats)
   * [Error handling](#error-handling)
 * [Developer](#developer)
   * [Generating table of contents on Markdown files](#generating-table-of-contents-on-markdown-files)
@@ -2501,18 +2501,18 @@ Server: spray-can/1.3.3
 }
 ```
 
-## GET /api/workflows/:version/stats
+## GET /api/engine/:version/stats
 
 This endpoint returns some basic statistics on the current state of the engine. At the moment that includes the number of running workflows and the number of active jobs. 
 
 cURL:
 ```
-$ curl http://localhost:8000/api/workflows/v1/stats
+$ curl http://localhost:8000/api/engine/v1/stats
 ```
 
 HTTPie:
 ```
-$ http http://localhost:8000/api/workflows/v1/stats
+$ http http://localhost:8000/api/engine/v1/stats
 ```
 
 Response:

From 88ff89f0ea378cea46aaaca7d206cb55acec482b Mon Sep 17 00:00:00 2001
From: Ruchi Munshi <rmunshi@broadinstitute.org>
Date: Thu, 13 Oct 2016 10:13:07 -0400
Subject: [PATCH 007/326] release_notes

---
 CHANGELOG.md               | 63 ++++++++++++++++++++++++++++++--------
 project/Dependencies.scala |  4 +--
 2 files changed, 52 insertions(+), 15 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3ff214c551d..eabc031c95b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,22 +1,44 @@
 # Cromwell Change Log
 
-## 0.20
+## 0.22
 
-* The default per-upload bytes size for GCS is now the minumum 256K
-instead of 64M. There is also an undocumented config key
-`google.upload-buffer-bytes` that allows adjusting this internal value.
+* Improved retries for Call Caching and general bug fixes.
+* Now there are configurable caching strategies for the SharedFileSystem backends (i.e. Local). This new "caching"
+  stanza will be nested inside of: backend.{your_SFS_backend}.config.filesystems.local stanza.
+  See below for detailed descriptions of each configurable key.
 
-* Updated Docker Hub hash retriever to parse json with [custom media
-types](https://github.com/docker/distribution/blob/05b0ab0/docs/spec/manifest-v2-1.md).
+```
+caching {
+    duplication-strategy: [
+    "hard-link", "soft-link", "copy"
+    ]
+
+     # Possible values: file, path
+     # "file" will compute an md5 hash of the file content.
+     # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
+     # in order to allow for the original file path to be hashed.
+     hashing-strategy: "file"
+
+     # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
+     # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
+     check-sibling-md5: false
+}
+```
+* Mulitple Input JSON files can now be submitted in server mode through the existing submission endpoint: /api/workflows/:version.
+    This endpoint accepts a POST request with a multipart/form-data encoded body. You can now include multiple keys for workflow inputs.
 
-* Added a `/batch` submit endpoint that accepts a single wdl with
-multiple input files.
+        The keys below can contain optional JSON file(s) of the workflow inputs. A skeleton file can be generated from wdltool using the "inputs" subcommand.
+        NOTE: Each prcoceeding workflowInput file will override any JSON key conflicts.
 
-* The `/query` endpoint now supports querying by `id`, and submitting
-parameters as a HTTP POST.
+        workflowInputs
+        workflowInputs_2
+        workflowInputs_3
+        workflowInputs_4
+        workflowInputs_5
 
-## 0.21
+* Batched status polling of Google Jes for running jobs.
 
+## 0.21
 
 * Warning: Significant database updates when you switch from version 0.19 to 0.21 of Cromwell.
   There may be a long wait period for the migration to finish for large databases.
@@ -71,7 +93,7 @@ task {
     command {
         echo "I'm private !"
     }
-    
+
     runtime {
         docker: "ubuntu:latest"
         noAddress: true
@@ -94,7 +116,7 @@ passed absolute paths for input `File`s.
 * Override the default database configuration by setting the keys
 `database.driver`, `database.db.driver`, `database.db.url`, etc.
 * Override the default database configuration by setting the keys
-`database.driver`, `database.db.driver`, `database.db.url`, etc. 
+`database.driver`, `database.db.driver`, `database.db.url`, etc.
 
 For example:
 ```
@@ -111,3 +133,18 @@ database {
 }
 ```
 
+## 0.20
+
+* The default per-upload bytes size for GCS is now the minumum 256K
+instead of 64M. There is also an undocumented config key
+`google.upload-buffer-bytes` that allows adjusting this internal value.
+
+* Updated Docker Hub hash retriever to parse json with [custom media
+types](https://github.com/docker/distribution/blob/05b0ab0/docs/spec/manifest-v2-1.md).
+
+* Added a `/batch` submit endpoint that accepts a single wdl with
+multiple input files.
+
+* The `/query` endpoint now supports querying by `id`, and submitting
+parameters as a HTTP POST.
+
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index ca5420d5e9b..a902e1b2a20 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -1,8 +1,8 @@
 import sbt._
 
 object Dependencies {
-  lazy val lenthallV = "0.19-882a763-SNAPSHOT"
-  lazy val wdl4sV = "0.6-2964173-SNAPSHOT"
+  lazy val lenthallV = "0.19"
+  lazy val wdl4sV = "0.6"
   lazy val sprayV = "1.3.3"
   /*
   spray-json is an independent project from the "spray suite"

From 06d7f33f2bcd7c47fa714f69ac8daadfce2c77ee Mon Sep 17 00:00:00 2001
From: Ruchi Munshi <rmunshi@broadinstitute.org>
Date: Thu, 13 Oct 2016 11:41:17 -0400
Subject: [PATCH 008/326] typos and reword

---
 CHANGELOG.md | 67 +++++++++++++++++++++++++++++++++++-----------------
 1 file changed, 45 insertions(+), 22 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index eabc031c95b..cf48b60be6b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,32 +3,45 @@
 ## 0.22
 
 * Improved retries for Call Caching and general bug fixes.
-* Now there are configurable caching strategies for the SharedFileSystem backends (i.e. Local). This new "caching"
-  stanza will be nested inside of: backend.{your_SFS_backend}.config.filesystems.local stanza.
+* Users will experience better scalability of status polling for Google JES.
+* Now there are configurable caching strategies for a SharedFileSystem backend (i.e. Local, SFS) in the backend's stanza:
   See below for detailed descriptions of each configurable key.
 
 ```
-caching {
-    duplication-strategy: [
-    "hard-link", "soft-link", "copy"
-    ]
-
-     # Possible values: file, path
-     # "file" will compute an md5 hash of the file content.
-     # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
-     # in order to allow for the original file path to be hashed.
-     hashing-strategy: "file"
-
-     # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
-     # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
-     check-sibling-md5: false
-}
+backend {
+  ...
+  providers {
+    SFS_BackendName {
+      actor-factory = ...
+      config {
+        ...
+        filesystems {
+          local {
+            localization: [
+               ...
+            ]
+            caching {
+              duplication-strategy: [
+                "hard-link", "soft-link", "copy"
+              ]
+              # Possible values: file, path
+              # "file" will compute an md5 hash of the file content.
+              # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
+              # in order to allow for the original file path to be hashed.
+              hashing-strategy: "file"
+
+              # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
+              # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
+              check-sibling-md5: false
+            }
 ```
-* Mulitple Input JSON files can now be submitted in server mode through the existing submission endpoint: /api/workflows/:version.
+* Multiple Input JSON files can now be submitted in server mode through the existing submission endpoint: /api/workflows/:version.
     This endpoint accepts a POST request with a multipart/form-data encoded body. You can now include multiple keys for workflow inputs.
 
-        The keys below can contain optional JSON file(s) of the workflow inputs. A skeleton file can be generated from wdltool using the "inputs" subcommand.
-        NOTE: Each prcoceeding workflowInput file will override any JSON key conflicts.
+        Each key below can contain an optional JSON file of the workflow inputs. A skeleton file can be generated from wdltool using the "inputs" subcommand.
+        NOTE: In case of key conflicts between multiple JSON files, higher values of x in workflowInputs_x override lower values. For example, an input
+        specified in workflowInputs_3 will override an input with the same name that was given in workflowInputs or workflowInputs_2. Similarly, an input
+        specified in workflowInputs_5 will override an input with the same name in any other input file.
 
         workflowInputs
         workflowInputs_2
@@ -36,7 +49,17 @@ caching {
         workflowInputs_4
         workflowInputs_5
 
-* Batched status polling of Google Jes for running jobs.
+* You can now limit the number of concurrent jobs for a backend by specifying the following option in the backend's config stanza:
+```
+backend {
+  ...
+  providers {
+    BackendName {
+      actor-factory = ...
+      config {
+        concurrent-job-limit = 5
+```
+
 
 ## 0.21
 
@@ -135,7 +158,7 @@ database {
 
 ## 0.20
 
-* The default per-upload bytes size for GCS is now the minumum 256K
+* The default per-upload bytes size for GCS is now the minimum 256K
 instead of 64M. There is also an undocumented config key
 `google.upload-buffer-bytes` that allows adjusting this internal value.
 

From f7f068cf59a928471330ae5f37f8bb4401872cb3 Mon Sep 17 00:00:00 2001
From: Jeff Gentry <geoffjentry@gmail.com>
Date: Fri, 2 Dec 2016 20:02:46 -0500
Subject: [PATCH 009/326] Release 23 (#1735)

---
 .travis.yml                                   |  14 +-
 CHANGELOG.md                                  | 119 +++
 MakingABackend.MD                             | 197 ++++
 README.md                                     | 621 ++++++++++++-
 SecurityRecommendations.md                    |  51 ++
 .../backend/BackendCacheHitCopyingActor.scala |   4 +-
 .../backend/BackendJobBreadCrumb.scala        |  14 +
 .../backend/BackendJobExecutionActor.scala    |  15 +-
 .../backend/BackendLifecycleActor.scala       |   6 +-
 .../BackendLifecycleActorFactory.scala        |  26 +-
 .../BackendWorkflowInitializationActor.scala  |  13 +-
 .../cromwell/backend/OutputEvaluator.scala    |  31 -
 .../backend/RuntimeAttributeDefinition.scala  |   4 +-
 .../async/AsyncBackendJobExecutionActor.scala |  10 +-
 .../backend/async/ExecutionHandle.scala       |   6 +-
 .../backend/async/ExecutionResult.scala       |   8 +-
 .../main/scala/cromwell/backend/backend.scala |  30 +-
 .../callcaching/CacheHitDuplicating.scala     |  30 +-
 .../scala/cromwell/backend/io/JobPaths.scala  |  70 +-
 .../backend/io/JobPathsWithDocker.scala       |  39 +
 .../cromwell/backend/io/WorkflowPaths.scala   |  35 +-
 ...rkflowPathsBackendInitializationData.scala |   7 +-
 .../backend/io/WorkflowPathsWithDocker.scala  |  16 +
 .../main/scala/cromwell/backend/package.scala |  12 +-
 .../RuntimeAttributesValidation.scala         |   5 +-
 .../scala/cromwell/backend/wdl/Command.scala  |  31 +
 .../cromwell/backend/wdl/FileSystems.scala    |  30 -
 .../backend/wdl/OutputEvaluator.scala         |  19 +
 .../cromwell/backend/wdl/PureFunctions.scala  |  60 --
 .../backend/wdl/ReadLikeFunctions.scala       |   7 +-
 .../cromwell/backend/wdl/WriteFunctions.scala |  12 +-
 .../DefaultWorkflowFileSystemProvider.scala   |   9 -
 .../wfs/DefaultWorkflowPathBuilder.scala      |   8 +
 .../wfs/WorkflowFileSystemProvider.scala      |  34 -
 .../backend/wfs/WorkflowPathBuilder.scala     |  25 +
 .../scala/cromwell/backend/BackendSpec.scala  |  58 +-
 .../cromwell/backend/io/JobPathsSpec.scala    |  40 +-
 .../cromwell/backend/io/TestWorkflows.scala   |  14 +-
 .../backend/io/WorkflowPathsSpec.scala        |  52 +-
 .../RuntimeAttributesDefaultSpec.scala        |   2 +-
 .../PureStandardLibraryFunctionsSpec.scala    |  30 +
 build.sbt                                     |   1 +
 core/src/main/resources/logback.xml           |  88 ++
 core/src/main/resources/reference.conf        |  38 +-
 .../main/scala/cromwell/core/CallKey.scala    |   7 +
 .../scala/cromwell/core/ExecutionStatus.scala |   2 +-
 .../scala/cromwell/core/ExecutionStore.scala  |  13 -
 .../src/main/scala/cromwell/core/JobKey.scala |   6 +-
 .../scala/cromwell/core/OutputStore.scala     |  40 -
 .../scala/cromwell/core/PathFactory.scala     | 135 ---
 .../cromwell/core/WorkflowMetadataKeys.scala  |   2 +
 .../cromwell/core/WorkflowSourceFiles.scala   |   9 -
 .../core/WorkflowSourceFilesCollection.scala  |  43 +
 .../core/callcaching/CallCachingMode.scala    |   6 +-
 .../cromwell/core/logging/JobLogger.scala     |   2 +-
 .../core/logging/WorkflowLogger.scala         |   8 +-
 .../main/scala/cromwell/core/package.scala    |   2 +-
 .../core/path/CustomRetryParams.scala         |  25 +
 .../core/path/DefaultPathBuilder.scala        |  21 +
 .../core/path/DefaultPathBuilderFactory.scala |   8 +
 .../core/path/JavaWriterImplicits.scala       |  13 +
 .../cromwell/core/path/PathBuilder.scala      |  10 +
 .../core/path/PathBuilderFactory.scala        |  11 +
 .../cromwell/core/{ => path}/PathCopier.scala |  23 +-
 .../cromwell/core/path/PathFactory.scala      |  57 ++
 .../cromwell/core/path/PathImplicits.scala    |  15 +
 .../core/path/PathParsingException.scala      |   5 +
 .../scala/cromwell/core/path/PathWriter.scala |  76 ++
 .../core/path/proxy/FileSystemProxy.scala     |  25 +
 .../cromwell/core/path/proxy/PathProxy.scala  |  44 +
 .../RetryableFileSystemProviderProxy.scala    |  57 ++
 .../scala/cromwell/core/retry/Backoff.scala   |   2 +-
 .../scala/cromwell/core/retry/Retry.scala     |   4 +-
 .../core/simpleton/WdlValueBuilder.scala      |  32 +-
 .../core/simpleton/WdlValueSimpleton.scala    |   2 +
 .../WdlValueJsonFormatter.scala               |   1 +
 .../scala/cromwell/util/PromiseActor.scala    |  38 +-
 .../cromwell/util/StopAndLogSupervisor.scala  |  24 +
 .../main/scala/cromwell/util/TryUtil.scala    |  45 +
 .../path/RetryableFileSystemProxySpec.scala   | 278 ++++++
 .../core/simpleton/WdlValueBuilderSpec.scala  | 129 ++-
 .../test/scala/cromwell/util/SampleWdl.scala  |  19 +-
 .../util/WdlValueJsonFormatterSpec.scala      |  28 +
 .../src/main/resources/changelog.xml          |   5 +
 .../changesets/embiggen_metadata_value.xml    |  50 +
 .../encrypt_and_clear_workflow_options.xml    |  14 +
 .../rename_workflow_options_in_metadata.xml   |  10 +
 .../changesets/sub_workflow_store.xml         |  62 ++
 .../workflow_store_imports_file.xml           |  15 +
 .../migration/src/main/resources/logback.xml  |  36 -
 .../migration/custom/BatchedTaskChange.scala  | 139 +++
 .../custom/MigrationTaskChange.scala          |  48 +
 .../symbol => custom}/QueryPaginator.scala    |   2 +-
 .../symbol => custom}/ResultSetIterator.scala |   2 +-
 .../CallOutputSymbolTableMigration.scala      |   1 -
 .../symbol/InputSymbolTableMigration.scala    |   1 -
 .../table/symbol/MetadataStatement.scala      |   5 +-
 .../table/symbol/SymbolTableMigration.scala   | 109 +--
 .../WorkflowOutputSymbolTableMigration.scala  |   1 -
 .../RenameWorkflowOptionKeysMigration.scala   |  18 +-
 .../ClearMetadataEntryWorkflowOptions.scala   |  15 +
 ...yptWorkflowStoreEntryWorkflowOptions.scala |  14 +
 .../RenameWorkflowOptionsInMetadata.scala     |  38 +
 .../WorkflowOptionsChange.scala               |  69 ++
 .../WorkflowOptionsRenaming.scala             |  21 +
 .../slick/CallCachingSlickDatabase.scala      |   1 +
 .../database/slick/SlickDatabase.scala        |   3 +-
 .../slick/SubWorkflowStoreSlickDatabase.scala |  67 ++
 .../slick/tables/DataAccessComponent.scala    |   6 +-
 .../SubWorkflowStoreEntryComponent.scala      |  62 ++
 .../tables/WorkflowStoreEntryComponent.scala  |   6 +-
 .../cromwell/database/sql/SqlDatabase.scala   |   3 +-
 .../sql/SubWorkflowStoreSqlDatabase.scala     |  21 +
 .../sql/tables/SubWorkflowStoreEntry.scala    |  12 +
 .../sql/tables/WorkflowStoreEntry.scala       |   3 +-
 engine/src/main/resources/logback.xml         |  36 -
 .../src/main/resources/swagger/cromwell.yaml  |  17 +
 .../workflowTimings/workflowTimings.html      | 184 +++-
 .../cromwell/engine/EngineFilesystems.scala   |  47 +-
 .../engine/EngineWorkflowDescriptor.scala     |  26 +-
 .../scala/cromwell/engine/WdlFunctions.scala  |  12 +-
 .../backend/EnhancedWorkflowOptions.scala     |  16 -
 .../workflow/SingleWorkflowRunnerActor.scala  | 258 +++---
 .../engine/workflow/WorkflowActor.scala       |  83 +-
 .../workflow/WorkflowManagerActor.scala       | 102 ++-
 .../lifecycle/CopyWorkflowLogsActor.scala     |   3 +-
 .../lifecycle/CopyWorkflowOutputsActor.scala  |  46 +-
 .../MaterializeWorkflowDescriptorActor.scala  | 152 +++-
 .../lifecycle/WorkflowFinalizationActor.scala |  30 +-
 .../WorkflowInitializationActor.scala         |   4 +-
 .../execution/CallMetadataHelper.scala        | 135 +++
 .../execution/EngineJobExecutionActor.scala   | 137 ++-
 .../lifecycle/execution/ExecutionStore.scala  | 109 +++
 .../execution/JobPreparationActor.scala       | 151 +--
 .../lifecycle/execution/OutputStore.scala     |  98 ++
 .../execution/SubWorkflowExecutionActor.scala | 275 ++++++
 .../lifecycle/execution/WdlLookup.scala       | 106 ---
 .../execution/WorkflowExecutionActor.scala    | 858 +++++++++---------
 .../WorkflowExecutionActorData.scala          | 118 ++-
 .../execution/WorkflowMetadataHelper.scala    |  37 +
 .../execution/callcaching/CallCache.scala     |  10 +-
 .../CallCacheInvalidateActor.scala            |   1 +
 .../callcaching/CallCacheWriteActor.scala     |   6 +-
 .../callcaching/EngineJobHashingActor.scala   |   4 +-
 .../lifecycle/execution/package.scala         |  12 +-
 .../JobExecutionTokenDispenserActor.scala     |   2 +-
 .../workflowstore/InMemoryWorkflowStore.scala |   6 +-
 .../workflowstore/SqlWorkflowStore.scala      |  28 +-
 .../workflowstore/WorkflowStore.scala         |   4 +-
 .../workflowstore/WorkflowStoreActor.scala    |  48 +-
 .../workflowstore/workflowstore_.scala        |   4 +-
 .../jobstore/EmptyJobStoreActor.scala         |  15 +
 .../scala/cromwell/jobstore/jobstore_.scala   |   2 +-
 .../cromwell/server/CromwellRootActor.scala   |  10 +-
 .../cromwell/server/CromwellServer.scala      |   3 +
 .../EmptySubWorkflowStoreActor.scala          |  17 +
 .../SqlSubWorkflowStore.scala                 |  31 +
 .../subworkflowstore/SubWorkflowStore.scala   |  19 +
 .../SubWorkflowStoreActor.scala               |  72 ++
 .../webservice/CromwellApiHandler.scala       |   8 +-
 .../webservice/CromwellApiService.scala       | 122 ++-
 .../webservice/EngineStatsActor.scala         |  10 +-
 .../webservice/WorkflowJsonSupport.scala      |  16 +-
 .../metadata/IndexedJsonValue.scala           |  22 +-
 .../metadata/MetadataBuilderActor.scala       | 122 ++-
 .../cromwell/ArrayOfArrayCoercionSpec.scala   |   4 +-
 .../scala/cromwell/ArrayWorkflowSpec.scala    |  18 +-
 .../cromwell/CallCachingWorkflowSpec.scala    |   2 +-
 .../cromwell/CopyWorkflowOutputsSpec.scala    |   6 +-
 ...itSpec.scala => CromwellTestKitSpec.scala} |  44 +-
 .../cromwell/DeclarationWorkflowSpec.scala    |  12 +-
 .../cromwell/FilePassingWorkflowSpec.scala    |  14 +-
 .../test/scala/cromwell/MapWorkflowSpec.scala |  16 +-
 .../scala/cromwell/MetadataWatchActor.scala   |  20 +-
 ...ultipleFilesWithSameNameWorkflowSpec.scala |   6 +-
 .../cromwell/OptionalParamWorkflowSpec.scala  |  12 +-
 .../PostfixQuantifierWorkflowSpec.scala       |  12 +-
 .../scala/cromwell/RestartWorkflowSpec.scala  |   6 +-
 .../scala/cromwell/ScatterWorkflowSpec.scala  |  40 +-
 .../cromwell/SimpleWorkflowActorSpec.scala    |  32 +-
 .../WdlFunctionsAtWorkflowLevelSpec.scala     |   6 +-
 .../scala/cromwell/WorkflowFailSlowSpec.scala |   2 +-
 .../scala/cromwell/WorkflowOutputsSpec.scala  |  20 +-
 .../cromwell/engine/EngineFunctionsSpec.scala |  12 +-
 .../cromwell/engine/WorkflowAbortSpec.scala   |   4 +-
 .../engine/WorkflowManagerActorSpec.scala     |   6 +-
 .../engine/WorkflowStoreActorSpec.scala       |  81 +-
 .../DefaultBackendJobExecutionActor.scala     |   8 +-
 .../RetryableBackendJobExecutionActor.scala   |   6 +-
 ...etryableBackendLifecycleActorFactory.scala |   4 +-
 .../engine/backend/mock/package.scala         |   2 +-
 .../SingleWorkflowRunnerActorSpec.scala       |  29 +-
 .../engine/workflow/WorkflowActorSpec.scala   |  26 +-
 .../workflow/WorkflowDescriptorBuilder.scala  |  10 +-
 ...terializeWorkflowDescriptorActorSpec.scala |  68 +-
 .../SubWorkflowExecutionActorSpec.scala       | 213 +++++
 .../WorkflowExecutionActorSpec.scala          |  14 +-
 .../EngineJobHashingActorSpec.scala           |  22 +-
 ...jeaBackendIsCopyingCachedOutputsSpec.scala |  39 +-
 .../ejea/EjeaCheckingJobStoreSpec.scala       |  14 +-
 .../execution/ejea/EjeaPreparingJobSpec.scala |  14 +-
 .../EjeaRequestingExecutionTokenSpec.scala    |   4 +-
 .../ejea/EjeaUpdatingJobStoreSpec.scala       |   4 +-
 .../ejea/EngineJobExecutionActorSpec.scala    |   4 +-
 .../EngineJobExecutionActorSpecUtil.scala     |  10 +-
 .../execution/ejea/PerTestHelper.scala        |  83 +-
 .../workflow/mocks/DeclarationMock.scala      |  21 +
 .../engine/workflow/mocks/TaskMock.scala      |  27 +
 .../workflow/mocks/WdlExpressionMock.scala    |  32 +
 .../jobstore/JobStoreServiceSpec.scala        |  13 +-
 .../jobstore/JobStoreWriterSpec.scala         |   4 +-
 .../SubWorkflowStoreSpec.scala                |  87 ++
 .../webservice/CromwellApiServiceSpec.scala   |  14 +-
 .../webservice/EngineStatsActorSpec.scala     |  10 +-
 .../webservice/MetadataBuilderActorSpec.scala | 115 ++-
 .../filesystems/gcs/ContentTypeOption.scala   |  15 -
 .../filesystems/gcs/GcsFileAttributes.scala   |  23 -
 .../filesystems/gcs/GcsFileSystem.scala       |  68 --
 .../gcs/GcsFileSystemProvider.scala           | 295 ------
 .../filesystems/gcs/GcsPathBuilder.scala      | 100 ++
 .../gcs/GcsPathBuilderFactory.scala           |  48 +
 .../filesystems/gcs/GoogleAuthMode.scala      | 186 ----
 .../filesystems/gcs/GoogleConfiguration.scala |  14 +-
 .../cromwell/filesystems/gcs/NioGcsPath.scala | 191 ----
 .../filesystems/gcs/auth/GoogleAuthMode.scala | 187 ++++
 .../auth/RefreshableOAuth2Credentials.scala   |  31 +
 .../cromwell/filesystems/gcs/package.scala    |   6 -
 .../filesystems/gcs/GcsIntegrationTest.scala  |   5 -
 .../filesystems/gcs/GcsPathBuilderSpec.scala  |  31 +
 .../gcs/GoogleConfigurationSpec.scala         |  16 +-
 .../gcs/GoogleCredentialFactorySpec.scala     | 158 ----
 .../gcs/MockGcsFileSystemBuilder.scala        |   9 -
 .../filesystems/gcs/NioGcsPathSpec.scala      | 291 ------
 .../gcs/RefreshTokenModeSpec.scala            |  26 -
 project/Dependencies.scala                    |  53 +-
 project/Merging.scala                         |   5 +
 project/Settings.scala                        |  31 +-
 project/Testing.scala                         |  20 +-
 project/Version.scala                         |   7 +-
 .../services/metadata/CallMetadataKeys.scala  |   2 +
 .../services/metadata/MetadataQuery.scala     |  11 +-
 .../services/metadata/MetadataService.scala   |   3 +-
 .../impl/MetadataDatabaseAccess.scala         |  14 +-
 .../metadata/impl/ReadMetadataActor.scala     |  11 +-
 .../cromwell/services/ServicesStoreSpec.scala |   1 +
 src/bin/travis/afterSuccess.sh                |  20 +
 src/bin/travis/publishSnapshot.sh             |  11 -
 src/bin/travis/resources/centaur.inputs       |  10 +-
 src/bin/travis/resources/centaur.wdl          |   8 +-
 src/bin/travis/resources/local_centaur.conf   |   3 +
 src/bin/travis/test.sh                        |   2 +
 src/bin/travis/testCentaurJes.sh              |   6 +-
 src/bin/travis/testCentaurLocal.sh            |   4 +-
 src/bin/travis/testCheckPublish.sh            |   6 +
 .../scala/cromwell/CromwellCommandLine.scala  |  14 +-
 src/main/scala/cromwell/Main.scala            |  16 +-
 .../cromwell/CromwellCommandLineSpec.scala    |  23 +-
 .../htcondor/HtCondorBackendFactory.scala     |  10 +-
 .../HtCondorInitializationActor.scala         |   6 +-
 .../htcondor/HtCondorJobExecutionActor.scala  |  52 +-
 .../htcondor/HtCondorRuntimeAttributes.scala  |  27 +-
 .../impl/htcondor/HtCondorWrapper.scala       |  27 +-
 .../impl/htcondor/caching/CacheActor.scala    |   6 +-
 .../CachedResultLocalization.scala            |   2 +-
 .../caching/model/CachedExecutionResult.scala |   4 +-
 .../provider/mongodb/MongoCacheActor.scala    |   4 +-
 .../impl/htcondor/HtCondorCommandSpec.scala   |  16 +-
 .../HtCondorInitializationActorSpec.scala     |   8 +-
 .../HtCondorJobExecutionActorSpec.scala       |  48 +-
 .../HtCondorRuntimeAttributesSpec.scala       |  50 +-
 .../CachedResultLocalizationSpec.scala        |   4 +-
 .../mongodb/MongoCacheActorSpec.scala         |   8 +-
 .../backend/impl/jes/GenomicsFactory.scala    |  24 +-
 .../JesAsyncBackendJobExecutionActor.scala    | 276 +++---
 .../backend/impl/jes/JesAttributes.scala      |  24 +-
 .../jes/JesBackendLifecycleActorFactory.scala |  29 +-
 .../impl/jes/JesBackendSingletonActor.scala   |   8 +-
 .../impl/jes/JesCacheHitCopyingActor.scala    |   6 +-
 .../backend/impl/jes/JesCallPaths.scala       |  82 --
 .../backend/impl/jes/JesConfiguration.scala   |  28 +-
 .../impl/jes/JesExpressionFunctions.scala     |  38 +-
 .../impl/jes/JesFinalizationActor.scala       |  31 +-
 .../backend/impl/jes/JesImplicits.scala       |  41 -
 .../impl/jes/JesInitializationActor.scala     |  37 +-
 .../impl/jes/JesJobCachingActorHelper.scala   |  44 +-
 .../impl/jes/JesJobExecutionActor.scala       |  25 +-
 .../backend/impl/jes/JesJobPaths.scala        |  60 ++
 .../backend/impl/jes/JesWorkflowPaths.scala   |  62 +-
 .../scala/cromwell/backend/impl/jes/Run.scala |   7 +-
 .../impl/jes/authentication/JesAuths.scala    |   5 +
 .../jes/authentication/JesCredentials.scala   |   5 -
 .../authentication/JesVMAuthentication.scala  |   2 +-
 .../callcaching/JesBackendFileHashing.scala   |   4 +-
 .../backend/impl/jes/io/package.scala         |   9 +-
 .../statuspolling/JesApiQueryManager.scala    |  22 +-
 .../jes/statuspolling/JesPollingActor.scala   |  46 +-
 .../statuspolling/JesPollingActorClient.scala |   5 +-
 ...JesAsyncBackendJobExecutionActorSpec.scala | 145 ++-
 .../backend/impl/jes/JesAttributesSpec.scala  |  20 +-
 .../backend/impl/jes/JesCallPathsSpec.scala   |  37 +-
 .../impl/jes/JesConfigurationSpec.scala       |  19 +-
 .../impl/jes/JesInitializationActorSpec.scala |  20 +-
 .../impl/jes/JesJobExecutionActorSpec.scala   | 111 +++
 .../backend/impl/jes/JesTestConfig.scala      |   2 +-
 .../impl/jes/JesWorkflowPathsSpec.scala       |  18 +-
 .../backend/impl/jes/MockObjects.scala        |   9 -
 .../cromwell/backend/impl/jes/RunSpec.scala   |   6 +-
 .../JesApiQueryManagerSpec.scala              |  63 +-
 .../statuspolling/JesPollingActorSpec.scala   |  19 +-
 .../config/ConfigAsyncJobExecutionActor.scala |  23 +-
 .../sfs/config/ConfigBackendFileHashing.scala |  12 +-
 .../sfs/config/ConfigHashingStrategy.scala    |  26 +-
 .../impl/sfs/config/ConfigWdlNamespace.scala  |   4 +-
 .../sfs/config/DeclarationValidation.scala    |  18 +-
 .../sfs/GcsWorkflowFileSystemProvider.scala   |  36 -
 .../backend/sfs/SharedFileSystem.scala        |  60 +-
 ...aredFileSystemAsyncJobExecutionActor.scala |  65 +-
 ...leSystemBackendLifecycleActorFactory.scala |  28 +-
 ...SharedFileSystemCacheHitCopyingActor.scala |   7 +-
 .../SharedFileSystemExpressionFunctions.scala |  28 +-
 .../SharedFileSystemInitializationActor.scala |  18 +-
 ...haredFileSystemJobCachingActorHelper.scala |   5 +-
 .../config/ConfigHashingStrategySpec.scala    |  10 +
 ...redFileSystemInitializationActorSpec.scala |  10 +-
 ...haredFileSystemJobExecutionActorSpec.scala |  53 +-
 .../backend/sfs/SharedFileSystemSpec.scala    |  20 +-
 .../sfs/TestLocalAsyncJobExecutionActor.scala |   4 +-
 .../impl/spark/SparkBackendFactory.scala      |  10 +-
 .../impl/spark/SparkInitializationActor.scala |   6 +-
 .../impl/spark/SparkJobExecutionActor.scala   |  44 +-
 .../backend/impl/spark/SparkProcess.scala     |  23 +-
 .../spark/SparkInitializationActorSpec.scala  |   7 +-
 .../spark/SparkJobExecutionActorSpec.scala    |  50 +-
 .../spark/SparkRuntimeAttributesSpec.scala    |  11 +-
 334 files changed, 8400 insertions(+), 4793 deletions(-)
 create mode 100644 MakingABackend.MD
 create mode 100644 SecurityRecommendations.md
 create mode 100644 backend/src/main/scala/cromwell/backend/BackendJobBreadCrumb.scala
 delete mode 100644 backend/src/main/scala/cromwell/backend/OutputEvaluator.scala
 create mode 100644 backend/src/main/scala/cromwell/backend/io/JobPathsWithDocker.scala
 create mode 100644 backend/src/main/scala/cromwell/backend/io/WorkflowPathsWithDocker.scala
 create mode 100644 backend/src/main/scala/cromwell/backend/wdl/Command.scala
 delete mode 100644 backend/src/main/scala/cromwell/backend/wdl/FileSystems.scala
 create mode 100644 backend/src/main/scala/cromwell/backend/wdl/OutputEvaluator.scala
 delete mode 100644 backend/src/main/scala/cromwell/backend/wdl/PureFunctions.scala
 delete mode 100644 backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowFileSystemProvider.scala
 create mode 100644 backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowPathBuilder.scala
 delete mode 100644 backend/src/main/scala/cromwell/backend/wfs/WorkflowFileSystemProvider.scala
 create mode 100644 backend/src/main/scala/cromwell/backend/wfs/WorkflowPathBuilder.scala
 create mode 100644 backend/src/test/scala/cromwell/backend/wdl/PureStandardLibraryFunctionsSpec.scala
 create mode 100644 core/src/main/resources/logback.xml
 create mode 100644 core/src/main/scala/cromwell/core/CallKey.scala
 delete mode 100644 core/src/main/scala/cromwell/core/ExecutionStore.scala
 delete mode 100644 core/src/main/scala/cromwell/core/OutputStore.scala
 delete mode 100644 core/src/main/scala/cromwell/core/PathFactory.scala
 delete mode 100644 core/src/main/scala/cromwell/core/WorkflowSourceFiles.scala
 create mode 100644 core/src/main/scala/cromwell/core/WorkflowSourceFilesCollection.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/CustomRetryParams.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/DefaultPathBuilder.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/JavaWriterImplicits.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/PathBuilder.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
 rename core/src/main/scala/cromwell/core/{ => path}/PathCopier.scala (65%)
 create mode 100644 core/src/main/scala/cromwell/core/path/PathFactory.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/PathImplicits.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/PathParsingException.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/PathWriter.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/proxy/FileSystemProxy.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/proxy/PathProxy.scala
 create mode 100644 core/src/main/scala/cromwell/core/path/proxy/RetryableFileSystemProviderProxy.scala
 create mode 100644 core/src/main/scala/cromwell/util/StopAndLogSupervisor.scala
 create mode 100644 core/src/main/scala/cromwell/util/TryUtil.scala
 create mode 100644 core/src/test/scala/cromwell/core/path/RetryableFileSystemProxySpec.scala
 create mode 100644 core/src/test/scala/cromwell/util/WdlValueJsonFormatterSpec.scala
 create mode 100644 database/migration/src/main/resources/changesets/embiggen_metadata_value.xml
 create mode 100644 database/migration/src/main/resources/changesets/encrypt_and_clear_workflow_options.xml
 create mode 100644 database/migration/src/main/resources/changesets/rename_workflow_options_in_metadata.xml
 create mode 100644 database/migration/src/main/resources/changesets/sub_workflow_store.xml
 create mode 100644 database/migration/src/main/resources/changesets/workflow_store_imports_file.xml
 delete mode 100644 database/migration/src/main/resources/logback.xml
 create mode 100644 database/migration/src/main/scala/cromwell/database/migration/custom/BatchedTaskChange.scala
 create mode 100644 database/migration/src/main/scala/cromwell/database/migration/custom/MigrationTaskChange.scala
 rename database/migration/src/main/scala/cromwell/database/migration/{metadata/table/symbol => custom}/QueryPaginator.scala (88%)
 rename database/migration/src/main/scala/cromwell/database/migration/{metadata/table/symbol => custom}/ResultSetIterator.scala (73%)
 create mode 100644 database/migration/src/main/scala/cromwell/database/migration/workflowoptions/ClearMetadataEntryWorkflowOptions.scala
 create mode 100644 database/migration/src/main/scala/cromwell/database/migration/workflowoptions/EncryptWorkflowStoreEntryWorkflowOptions.scala
 create mode 100644 database/migration/src/main/scala/cromwell/database/migration/workflowoptions/RenameWorkflowOptionsInMetadata.scala
 create mode 100644 database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsChange.scala
 create mode 100644 database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsRenaming.scala
 create mode 100644 database/sql/src/main/scala/cromwell/database/slick/SubWorkflowStoreSlickDatabase.scala
 create mode 100644 database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
 create mode 100644 database/sql/src/main/scala/cromwell/database/sql/SubWorkflowStoreSqlDatabase.scala
 create mode 100644 database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
 delete mode 100644 engine/src/main/resources/logback.xml
 delete mode 100644 engine/src/main/scala/cromwell/engine/backend/EnhancedWorkflowOptions.scala
 create mode 100644 engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/CallMetadataHelper.scala
 create mode 100644 engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/ExecutionStore.scala
 create mode 100644 engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/OutputStore.scala
 create mode 100644 engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala
 delete mode 100644 engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WdlLookup.scala
 create mode 100644 engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowMetadataHelper.scala
 rename engine/src/{test => main}/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala (88%)
 create mode 100644 engine/src/main/scala/cromwell/jobstore/EmptyJobStoreActor.scala
 create mode 100644 engine/src/main/scala/cromwell/subworkflowstore/EmptySubWorkflowStoreActor.scala
 create mode 100644 engine/src/main/scala/cromwell/subworkflowstore/SqlSubWorkflowStore.scala
 create mode 100644 engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStore.scala
 create mode 100644 engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStoreActor.scala
 rename engine/src/test/scala/cromwell/{CromwellTestkitSpec.scala => CromwellTestKitSpec.scala} (94%)
 create mode 100644 engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActorSpec.scala
 create mode 100644 engine/src/test/scala/cromwell/engine/workflow/mocks/DeclarationMock.scala
 create mode 100644 engine/src/test/scala/cromwell/engine/workflow/mocks/TaskMock.scala
 create mode 100644 engine/src/test/scala/cromwell/engine/workflow/mocks/WdlExpressionMock.scala
 create mode 100644 engine/src/test/scala/cromwell/subworkflowstore/SubWorkflowStoreSpec.scala
 delete mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/ContentTypeOption.scala
 delete mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileAttributes.scala
 delete mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileSystem.scala
 delete mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileSystemProvider.scala
 create mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilder.scala
 create mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilderFactory.scala
 delete mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleAuthMode.scala
 delete mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/NioGcsPath.scala
 create mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/auth/GoogleAuthMode.scala
 create mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/auth/RefreshableOAuth2Credentials.scala
 delete mode 100644 filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/package.scala
 delete mode 100644 filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsIntegrationTest.scala
 create mode 100644 filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala
 delete mode 100644 filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GoogleCredentialFactorySpec.scala
 delete mode 100644 filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/MockGcsFileSystemBuilder.scala
 delete mode 100644 filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/NioGcsPathSpec.scala
 delete mode 100644 filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/RefreshTokenModeSpec.scala
 create mode 100755 src/bin/travis/afterSuccess.sh
 delete mode 100755 src/bin/travis/publishSnapshot.sh
 create mode 100755 src/bin/travis/testCheckPublish.sh
 delete mode 100644 supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesCallPaths.scala
 delete mode 100644 supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesImplicits.scala
 create mode 100644 supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobPaths.scala
 create mode 100644 supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesAuths.scala
 delete mode 100644 supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesCredentials.scala
 create mode 100644 supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesJobExecutionActorSpec.scala
 delete mode 100644 supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/MockObjects.scala
 delete mode 100644 supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/GcsWorkflowFileSystemProvider.scala

diff --git a/.travis.yml b/.travis.yml
index 5784eaf62ec..f4d0d9b2eeb 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,14 +6,18 @@ scala:
 jdk:
   - oraclejdk8
 env:
-  # Setting this variable twice will cause the 'script' section to run twice with the respective env var invoked
-  - BUILD_TYPE=sbt
-  - BUILD_TYPE=centaurJes
-  - BUILD_TYPE=centaurLocal
+  global:
+    - CENTAUR_BRANCH=develop
+  matrix:
+    # Setting this variable twice will cause the 'script' section to run twice with the respective env var invoked
+    - BUILD_TYPE=sbt
+    - BUILD_TYPE=checkPublish
+    - BUILD_TYPE=centaurJes
+    - BUILD_TYPE=centaurLocal
 script:
   - src/bin/travis/test.sh
 after_success:
-  - src/bin/travis/publishSnapshot.sh
+  - src/bin/travis/afterSuccess.sh
 deploy:
   provider: script
   script: src/bin/travis/publishRelease.sh
diff --git a/CHANGELOG.md b/CHANGELOG.md
index cf48b60be6b..3f7b649eee6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,124 @@
 # Cromwell Change Log
 
+## 23
+
+* The `meta` and `parameter_meta` blocks are now valid within `workflow` blocks, not just `task`
+* The JES backend configuration now has an option `genomics-api-queries-per-100-seconds` to help tune the rate of batch polling against the JES servers. Users with quotas larger than default should make sure to set this value.
+* Added an option `call-caching.invalidate-bad-cache-results` (default: `true`). If true, Cromwell will invalidate cached results which have failed to copy as part of a cache hit.
+* Timing diagrams and metadata now receive more fine grained workflow states between submission and Running.
+* Support for the Pair WDL type (e.g. `Pair[Int, File] floo = (3, "gs://blar/blaz/qlux.txt")`)
+* Added support for new WDL functions:
+  * `zip: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - align items in the two arrays by index and return them as WDL pairs 
+  * `cross: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - create every possible pair from the two input arrays and return them all as WDL pairs
+  * `transpose: (Array[Array[X]]) => Array[Array[X]]` compute the matrix transpose for a 2D array. Assumes each inner array has the same length.
+* By default, `system.abort-jobs-on-terminate` is false when running `java -jar cromwell.jar server`, and true when running `java -jar cromwell.jar run <wdl> <inputs>`.
+* Enable WDL imports when running in Single Workflow Runner Mode.
+* Support for sub workflows (see [Annex A](#annex-a---workflow-outputs))
+* Enable WDL imports when running in Single Workflow Runner Mode as well as Server Mode
+* Support for WDL imports through an additional imports.zip parameter
+* Support for sub workflows
+* Corrected file globbing in JES to correctly report all generated files. Additionally, file globbing in JES now uses bash-style glob syntax instead of python style glob syntax
+* Support declarations as graph nodes
+* Added the ability to override the default service account that the compute VM is started with via the configuration option `JES.config.genomics.compute-service-account` or through the workflow options parameter `google_compute_service_account`. More details can be found in the README.md
+* Fix bugs related to the behavior of Cromwell in Single Workflow Runner Mode. Cromwell will now exit once a workflow completes in Single Workflow Runner Mode. Additionally, when restarting Cromwell in Single Workflow Runner Mode, Cromwell will no longer restart incomplete workflows from a previous session.
+
+### Annex A - Workflow outputs
+    
+The WDL specification has changed regarding [workflow outputs](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#outputs) to accommodate sub workflows.
+This change is backward compatible in terms of runnable WDLs (WDL files using the deprecated workflow outputs syntax will still run the same). 
+The only visible change lies in the metadata (as well as the console output in single workflow mode, when workflow outputs are printed out at the end of a successful workflow).
+
+TL;DR Unless you are parsing or manipulating the "key" by which workflow outputs are referenced in the metadata (and/or the console output for single workflow mode), you can skip the following explanation.
+
+*Metadata Response*
+```
+{
+  ...
+  outputs {
+    "task_output_1": "hello",
+    "task_output_2": "world"
+            ^
+       If you don't manipulate this part of the metadata, then skip this section
+  }
+}
+```
+
+In order to maintain backward compatibility, workflow outputs expressed with the deprecated syntax are "expanded" to the new syntax. Here is an example:
+
+```
+task t {
+    command {
+        #do something
+    }
+    output {
+        String out1 = "hello"
+        String out2 = "world"
+    }
+}
+```
+
+```
+    workflow old_syntax {
+        call t
+        output {
+            t.*
+        }
+    }
+```
+
+```
+    workflow new_syntax {
+        call t
+        output {
+            String wf_out1 = t.out1
+            String wf_out2 = t.out2
+        }
+    }
+```
+
+The new syntax allows for type checking of the outputs as well as expressions. It also allows for explicitly naming to the outputs.
+The old syntax doesn't give the ability to name workflow outputs. For consistency reasons, Cromwell will generate a "new syntax" workflow output for each task output, and name them.
+Their name will be generated using their FQN, which would give 
+
+```
+output {
+   String w.t.out1 = t.out1
+   String w.t.out2 = t.out2
+}
+```
+        
+However as the FQN separator is `.`, the name itself cannot contain any `.`. 
+For that reason, `.` are replaced with `_` :
+
+*Old syntax expanded to new syntax*
+```
+output {
+   String w_t_out1 = t.out1
+   String w_t_out2 = t.out2
+}
+```
+
+The consequence is that the workflow outputs section of the metadata for `old_syntax` would previously look like 
+ 
+ ```
+    outputs {
+        "w.t.out1": "hello",
+        "w.t.out2": "hello"
+    }
+ ```
+ 
+but it will now look like 
+
+```
+    outputs {
+        "w_t_out1": "hello",
+        "w_t_out2": "hello"
+    }
+```
+
+The same applies for the console output of a workflow run in single workflow mode.
+
+
 ## 0.22
 
 * Improved retries for Call Caching and general bug fixes.
diff --git a/MakingABackend.MD b/MakingABackend.MD
new file mode 100644
index 00000000000..5106b37260c
--- /dev/null
+++ b/MakingABackend.MD
@@ -0,0 +1,197 @@
+# Making a backend
+
+## Part 0: Introduction
+
+- These notes were added while making a new AWS backend for Amazon AWS.
+
+## Part 1 (October 13 2016): The skeleton:
+
+To start with, I just need to create a bunch of boilerplate which will eventually be filled in with all of the lovely AWS details!
+
+### Defining the awsBackend project:
+
+- Added entries to `project/Settings.scala`, `project/Dependencies.scala` and `build.sbt`
+- This was mainly just a copy/paste from existing backend projects. I made a few typos renaming everything and linking the dependencies properly though!
+- E.g. In my first commit I forgot to update the libraryDependencies name for my AWS backend project:
+```
+  val awsBackendSettings = List(
+    name := "cromwell-aws-backend",
+    libraryDependencies ++= awsBackendDependencies
+  ) ++ commonSettings
+```
+- I guessed that I'd need the AWS SDK so I included that immediately in Dependencies.scala:
+```
+  val awsBackendDependencies = List(
+    "com.amazonaws" % "aws-java-sdk" % "1.11.41"
+  )
+```
+- In build.scala I had to also edit the `lazy val root` to include a new `.aggregate(awsBackend)` and a new `.dependsOn(awsBackend)`
+
+### Directory structure:
+
+- This is probably going to be autogenerated for you in the directories specified in the above files. I'd already added my own directory structure and sbt managed to pick it up correctly in `supportedBackends/aws`.
+
+### AWS Job Execution Actor:
+- To run a job, Cromwell needs to instantiate a Job Execution actor. I'll fill in the details later but for now, I'll just add the constructor, props, and an unimplemented method definition for `execute`:
+```
+class AwsJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
+                           override val configurationDescriptor: BackendConfigurationDescriptor) extends BackendJobExecutionActor {
+
+  override def execute: Future[BackendJobExecutionResponse] = ???
+}
+
+object AwsJobExecutionActor {
+  def props(jobDescriptor: BackendJobDescriptor,
+            configurationDescriptor: BackendConfigurationDescriptor): Props = Props(new AwsJobExecutionActor(jobDescriptor, configurationDescriptor))
+}
+```
+
+### Actor factory:
+- This is the class which tells Cromwell which classes represent job execution actors, initialization actors and so on. I'm just adding a skeleton for now, with a constructor of the form the Cromwell expects:
+```
+case class AwsBackendActorFactory(name: String, configurationDescriptor: BackendConfigurationDescriptor) extends BackendLifecycleActorFactory {
+
+  override def jobExecutionActorProps(jobDescriptor: BackendJobDescriptor,
+                                      initializationData: Option[BackendInitializationData],
+                                      serviceRegistryActor: ActorRef,
+                                      backendSingletonActor: Option[ActorRef]): Props = AwsJobExecutionActor.props(jobDescriptor, configurationDescriptor)
+}
+```
+- There are a few other actor definitions that can be added to this file over time. But the only one that Cromwell *requires* to work is the job execution actor.
+
+### Reference conf:
+
+- Reference.conf is a set of reference options which shows people how to enable the backends that they want. So I'll add the initial config which people would add if they wanted the AWS backend (commented out in the reference so it's not enabled by default). This goes below all the other backend references:
+```
+    #AWS {
+    #  actor-factory = "cromwell.backend.impl.aws.AwsBackendActorFactory"
+    #  config {
+    #
+    #  }
+    #}
+```
+
+### Application.conf
+
+- OK so I've now told people how to add this backend... Now I actually add it to my own personal configuration file so I can try it out!
+```
+backend {
+  default = "AWS"
+  providers {
+    AWS {
+      actor-factory = "cromwell.backend.impl.aws.AwsBackendActorFactory"
+      config {
+      
+      }
+    }
+  }
+}
+```
+
+### Trying it out
+So we now have a backend skeleton! What happens when we run it? Well hopefully Cromwell will instantiate the backend far enough to reach the unimplemented execute method and then fall over. Let's give it a go!
+- I fire up cromwell in server mode with my modified application.conf.
+- I create a sample WDL that would sleep for 20 seconds if it actually worked:
+The input WDL:
+```
+task sleep {
+  command { sleep 20 }
+}
+workflow main {
+  call sleep
+}
+```
+- I submit the WDL to the swagger endpoint (http://localhost:8000/swagger/index.html?url=/swagger/cromwell.yaml) and watch the server logs...
+- And as expected:
+```
+2016-10-13 13:14:29,017 cromwell-system-akka.dispatchers.engine-dispatcher-39 INFO  - MaterializeWorkflowDescriptorActor [UUID(ddd827ba)]: Call-to-Backend assignments: main.sleep -> AWS
+2016-10-13 13:14:30,167 cromwell-system-akka.dispatchers.engine-dispatcher-39 INFO  - WorkflowExecutionActor-ddd827ba-091f-4c6f-b98f-cc9825717007 [UUID(ddd827ba)]: Starting calls: main.sleep:NA:1
+2016-10-13 13:14:30,983 cromwell-system-akka.actor.default-dispatcher-5 ERROR - guardian failed, shutting down system
+scala.NotImplementedError: an implementation is missing
+  at scala.Predef$.$qmark$qmark$qmark(Predef.scala:230)
+  at cromwell.backend.impl.aws.AwsJobExecutionActor.execute(AwsJobExecutionActor.scala:12)
+```
+- OK, so now I just need to implement `execute(): Future[JobExecutionResult]` and Cromwell can interface with AWS. How hard can it be!
+
+## Part 2 (October 13 2016): Using Amazon to sleep 20 seconds
+
+### Starting point
+- This was a learning experience after using the Google pipelines service to submit jobs! 
+- To get myself started, I've manually created an ECS cluster which I've called `ecs-t2micro-cluster` via the ECS web console.
+
+### Trial and Error
+
+- I see in the aws sdk docs that there's an AmazonECSAsyncClient class. That sounds promising! Luckily I already added the dependency on AWS SDK in Part 1 so I guess I can just write something basic in my AwsJobExecutionActor class and see what happens:
+
+- I ended up having to add some credentials options to the configuration file. The new `reference.conf` now looks like:
+```
+    #AWS {
+    #  actor-factory = "cromwell.backend.impl.aws.AwsBackendActorFactory"
+    #  config {
+    #    ## These two settings are required to authenticate with the ECS service:
+    #    accessKeyId = "..."
+    #    secretKey = "..."
+    #  }
+    #}
+``` 
+
+- After a little bit of experimentation with the ECS API, I was able to come up with a backend that works but is very limited... It is entirely synchronous in the `execute` method. That's certainly not a final answer but it works OK for running a single task. And we can now run that single `sleep` command successfully on the Amazon EC2 Container Service!
+  - The synchronous `execute` method:
+```
+class AwsJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
+                           override val configurationDescriptor: BackendConfigurationDescriptor) extends BackendJobExecutionActor {
+
+  val awsAccessKeyId = configurationDescriptor.backendConfig.as[String]("accessKeyId")
+  val awsSecretKey = configurationDescriptor.backendConfig.as[String]("secretKey")
+
+  val clusterName = "ecs-t2micro-cluster"
+
+  val credentials = new AWSCredentials {
+    override def getAWSAccessKeyId: String = awsAccessKeyId
+    override def getAWSSecretKey: String = awsSecretKey
+  }
+  val ecsAsyncClient = new AmazonECSAsyncClient(credentials)
+
+  override def execute: Future[BackendJobExecutionResponse] = {
+
+    val commandOverride = new ContainerOverride().withName("simple-app").withCommand(jobDescriptor.call.instantiateCommandLine(Map.empty, OnlyPureFunctions, identity).get)
+
+    val runRequest: RunTaskRequest = new RunTaskRequest()
+      .withCluster(clusterName)
+      .withCount(1)
+      .withTaskDefinition("ubuntuTask:1")
+      .withOverrides(new TaskOverride().withContainerOverrides(commandOverride))
+
+    val submitResultHandler = new AwsSdkAsyncHandler[RunTaskRequest, RunTaskResult]()
+    val _ = ecsAsyncClient.runTaskAsync(runRequest, submitResultHandler)
+
+    submitResultHandler.future map {
+      case AwsSdkAsyncResult(_, result) =>
+        log.info("AWS submission completed:\n{}", result.toString)
+        val taskArn= result.getTasks.asScala.head.getTaskArn
+        val taskDescription = waitUntilDone(taskArn)
+
+        log.info("AWS task completed!\n{}", taskDescription.toString)
+        SucceededResponse(jobDescriptor.key, Option(0), Map.empty, None, Seq.empty)
+    }
+  }
+
+  private def waitUntilDone(taskArn: String): Task = {
+    val describeTasksRequest = new DescribeTasksRequest().withCluster(clusterName).withTasks(List(taskArn).asJava)
+
+    val resultHandler = new AwsSdkAsyncHandler[DescribeTasksRequest, DescribeTasksResult]()
+    val _ = ecsAsyncClient.describeTasksAsync(describeTasksRequest, resultHandler)
+
+    val desribedTasks = Await.result(resultHandler.future, Duration.Inf)
+    val taskDescription = desribedTasks.result.getTasks.asScala.head
+    if (taskDescription.getLastStatus == DesiredStatus.STOPPED.toString) {
+      taskDescription
+    } else {
+      Thread.sleep(200)
+      waitUntilDone(taskArn)
+    }
+  }
+}
+```
+
+
diff --git a/README.md b/README.md
index 1800278e932..ca5c1457610 100644
--- a/README.md
+++ b/README.md
@@ -25,6 +25,7 @@ A [Workflow Management System](https://en.wikipedia.org/wiki/Workflow_management
   * [Workflow Submission](#workflow-submission)
   * [Database](#database)
   * [SIGINT abort handler](#sigint-abort-handler)
+* [Security](#security)
 * [Backends](#backends)
   * [Backend Filesystems](#backend-filesystems)
     * [Shared Local Filesystem](#shared-local-filesystem)
@@ -35,6 +36,7 @@ A [Workflow Management System](https://en.wikipedia.org/wiki/Workflow_management
     * [Caching configuration](#caching-configuration)
     * [Docker](#docker)
     * [CPU, Memory and Disk](#cpu-memory-and-disk)
+    * [Native Specifications](#native-specifications)
   * [Spark Backend](#spark-backend)
     * [Configuring Spark Project](#configuring-spark-project)
     * [Configuring Spark Master and Deploy Mode](#configuring-spark-master-and-deploy-mode)
@@ -63,6 +65,12 @@ A [Workflow Management System](https://en.wikipedia.org/wiki/Workflow_management
 * [Logging](#logging)
 * [Workflow Options](#workflow-options)
 * [Call Caching](#call-caching)
+  * [Configuring Call Caching](#configuring-call-caching)
+  * [Call Caching Workflow Options](#call-caching-workflow-options)
+  * [Local Filesystem Options](#local-filesystem-options)
+* [Imports](#imports)
+* [Sub Workflows](#sub-workflows)
+* [Meta blocks](#meta-blocks)
 * [REST API](#rest-api)
   * [REST API Versions](#rest-api-versions)
   * [POST /api/workflows/:version](#post-apiworkflowsversion)
@@ -124,23 +132,29 @@ See the [migration document](MIGRATION.md) for more details.
 Run the JAR file with no arguments to get the usage message:
 
 ```
+
+
 $ java -jar cromwell.jar
 java -jar cromwell.jar <action> <parameters>
 
 Actions:
-run <WDL file> [<JSON inputs file> [<JSON workflow options>
-  [<OUTPUT workflow metadata>]]]
+run <WDL file> [<JSON inputs file>] [<JSON workflow options>]
+  [<OUTPUT workflow metadata>] [<Zip of WDL Files>]
 
   Given a WDL file and JSON file containing the value of the
   workflow inputs, this will run the workflow locally and
   print out the outputs in JSON format.  The workflow
   options file specifies some runtime configuration for the
   workflow (see README for details).  The workflow metadata
-  output is an optional file path to output the metadata.
+  output is an optional file path to output the metadata. The
+  directory of WDL files is optional. However, it is required
+  if the primary workflow imports workflows that are outside
+  of the root directory of the Cromwell project.
+
   Use a single dash ("-") to skip optional files. Ex:
-    run noinputs.wdl - - metadata.json
+    run noinputs.wdl - - metadata.json -
 
-server
+  server
 
   Starts a web server on port 8000.  See the web server
   documentation for more details about the API endpoints.
@@ -232,6 +246,39 @@ $ cat my_wf.metadata.json
 }
 ```
 
+The fifth, optional parameter to the 'run' subcommand is a zip file which contains WDL source files. This zip file can be passed
+and your primary workflow can import any WDL's from that collection and re-use those tasks.
+
+For example, consider you have a directory of WDL files:
+```
+my_WDLs
+└──cgrep.wdl
+└──ps.wdl
+└──wc.wdl
+```
+
+If you zip that directory to my_WDLs.zip, you have the option to pass it in as the last parameter in your run command
+and be able to reference these WDLs as imports in your primary WDL. For example, your primary WDL can look like this:
+```
+import "ps.wdl" as ps
+import "cgrep.wdl"
+import "wc.wdl" as wordCount
+
+workflow threestep {
+
+call ps.ps as getStatus
+call cgrep.cgrep { input: str = getStatus.x }
+call wordCount { input: str = ... }
+
+}
+
+```
+The command to run this WDL, without needing any inputs, workflow options or metadata files would look like:
+
+```
+$ java -jar cromwell.jar run threestep.wdl - - - /path/to/my_WDLs.zip
+```
+
 ## server
 
 Start a server on port 8000, the API for the server is described in the [REST API](#rest-api) section.
@@ -292,17 +339,14 @@ Then, edit the configuration file `database` stanza, as follows:
 
 ```
 database {
-  config = main.mysql
-
-  main {
-    mysql {
-      db.url = "jdbc:mysql://localhost:3306/cromwell"
-      db.user = "root"
-      db.password = ""
-      db.driver = "com.mysql.jdbc.Driver"
-      db.connectionTimeout = 5000 # NOTE: The default 1000ms is often too short for production mysql use
-      driver = "slick.driver.MySQLDriver$"
-    }
+
+  driver = "slick.driver.MySQLDriver$"
+  db {
+    driver = "com.mysql.jdbc.Driver"
+    url = "jdbc:mysql://host/cromwell"
+    user = "user"
+    password = "pass"
+    connectionTimeout = 5000
   }
 
   test {
@@ -323,6 +367,14 @@ system {
 
 Or, via `-Dsystem.abort-jobs-on-terminate=true` command line option.
 
+By default, this value is false when running `java -jar cromwell.jar server`, and true when running `java -jar cromwell.jar run <wdl> <inputs>`.
+
+# Security
+
+ - Cromwell is NOT on its own a security appliance!
+ - Only YOU are responsible for your own security! 
+ - Some recommendations and suggestions on security can be found in the [SecurityRecommendations.md](SecurityRecommendations.md) document
+
 # Backends
 
 A backend represents a way to run the user's command specified in the `task` section.  Cromwell allows for backends conforming to
@@ -889,6 +941,18 @@ This backend supports CPU, memory and disk size configuration through the use of
 
 It they are not set, HtCondor backend will use default values.
 
+### Native Specifications
+The use of runtime attribute 'nativeSpecs' allows to the user to attach custom HtCondor configuration to tasks.
+An example of this is when there is a need to work with 'requirements' or 'rank' configuration.
+
+```
+"runtimeAttributes": {
+    "nativeSpecs": ["requirements = Arch == \"INTEL\"", "rank = Memory >= 64"]
+}
+```
+
+nativeSpecs attribute needs to be specified as an array of strings to work.
+
 ## Spark Backend
 
 This backend adds support for execution of spark jobs in a workflow using the existing wdl format. 
@@ -1053,6 +1117,7 @@ backend {
       config {
         project = "my-project"
         root = "gs://my-bucket"
+        genomics-api-queries-per-100-seconds = 1000
         .
         .
         .
@@ -1062,6 +1127,8 @@ backend {
 }
 ```
 
+If your project has API quotas other than the defaults set the `genomics-api-queries-per-100-seconds` value to be the lesser of the `Queries per 100 seconds per user` and `Queries per 100 seconds` quotas. This value will be used to help tune Cromwell's rate of interaction with JES.
+
 ### Configuring Authentication
 
 The `google` stanza in the Cromwell configuration file defines how to authenticate to Google.  There are four different
@@ -1139,6 +1206,8 @@ Creating the account will cause the JSON file to be downloaded.  The structure o
 Most importantly, the value of the `client_email` field should go into the `service-account-id` field in the configuration (see below).  The
 `private_key` portion needs to be pulled into its own file (e.g. `my-key.pem`).  The `\n`s in the string need to be converted to newline characters.
 
+While technically not part of Service Account authorization mode, one can also override the default service account that the compute VM is started with via the configuration option `JES.config.genomics.compute-service-account` or through the workflow options parameter `google_compute_service_account`.  It's important that this service account, and the service account specified in `JES.config.genomics.auth` can both read/write the location specified by `JES.config.root`
+
 #### Refresh Token
 
 A **refresh_token** field must be specified in the [workflow options](#workflow-options) when submitting the job.  Omitting this field will cause the workflow to fail.
@@ -1509,7 +1578,8 @@ Valid keys and their meanings:
         * The default is `NoNewCalls` but this can be changed using the `workflow-options.workflow-failure-mode` configuration option.
     * **backend** - Override the default backend specified in the Cromwell configuration for this workflow only.
 * JES Backend Only
-    * **jes_gcs_root** - (JES backend only) Specifies where outputs of the workflow will be written.  Expects this to be a GCS URL (e.g. `gs://my-bucket/workflows`).  If this is not set, this defaults to the value within `backend.jes.root` in the [configuration](#configuring-cromwell).
+    * **jes_gcs_root** - (JES backend only) Specifies where outputs of the workflow will be written.  Expects this to be a GCS URL (e.g. `gs://my-bucket/workflows`).  If this is not set, this defaults to the value within `backend.jes.config.root` in the [configuration](#configuring-cromwell).
+    * **google_compute_service_account** - (JES backend only) Specifies an alternate service account to use on the compute instance (e.g. my-new-svcacct@my-google-project.iam.gserviceaccount.com).  If this is not set, this defaults to the value within `backend.jes.config.genomics.compute-service-account` in the [configuration](#configuring-cromwell) if specified or `default` otherwise.
     * **google_project** - (JES backend only) Specifies which google project to execute this workflow.
     * **refresh_token** - (JES backend only) Only used if `localizeWithRefreshToken` is specified in the [configuration file](#configuring-cromwell).
     * **auth_bucket** - (JES backend only) defaults to the the value in **jes_gcs_root**.  This should represent a GCS URL that only Cromwell can write to.  The Cromwell account is determined by the `google.authScheme` (and the corresponding `google.userAuth` and `google.serviceAuth`)
@@ -1528,16 +1598,20 @@ Cromwell's call cache is maintained in its database.  For best mileage with call
 
 > **Note:** If call caching is enabled, be careful not to change the contents of the output directory for any previously run job.  Doing so might cause cache hits in Cromwell to copy over modified data and Cromwell currently does not check that the contents of the output directory changed.
 
+## Configuring Call Caching
 To enable Call Caching, add the following to your Cromwell [configuration](#configuring-cromwell):
 
 ```
 call-caching {
   enabled = true
+  invalidate-bad-cache-results = true
 }
 ```
 
 When `call-caching.enabled=true` (default: `false`), Cromwell will be able to to copy results from previously run jobs (when appropriate).
+When `invalidate-bad-cache-results=true` (default: `true`), Cromwell will invalidate any cache results which fail to copy during a cache-hit. This is usually desired but might be unwanted if a cache might fail to copy for external reasons, such as a difference in user authentication.
 
+## Call Caching Workflow Options
 Cromwell also accepts two [workflow option](#workflow-options) related to call caching:
 
 * If call caching is enabled, but one wishes to run a workflow but not add any of the calls into the call cache when they finish, the `write_to_cache` option can be set to `false`.  This value defaults to `true`.
@@ -1545,6 +1619,508 @@ Cromwell also accepts two [workflow option](#workflow-options) related to call c
 
 > **Note:** If call caching is disabled, the to workflow options `read_from_cache` and `write_to_cache` will be ignored and the options will be treated as though they were 'false'.
 
+## Local Filesystem Options
+When running a job on the Config (Shared Filesystem) backend, Cromwell provides some additional options in the backend's config section:
+
+```
+      config {
+        ...
+        filesystems {
+          ...
+          local {
+            ...
+            caching {
+              # When copying a cached result, what type of file duplication should occur. Attempted in the order listed below:
+              duplication-strategy: [
+                "hard-link", "soft-link", "copy"
+              ]
+
+              # Possible values: file, path
+              # "file" will compute an md5 hash of the file content.
+              # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
+              # in order to allow for the original file path to be hashed.
+              # Default: file
+              hashing-strategy: "file"
+
+              # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
+              # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
+              # Default: false
+              check-sibling-md5: false
+            }
+          }
+        }
+      }
+```
+# Imports
+
+Import statements inside of a WDL file are supported by Cromwell when running in Server mode as well as Single Workflow Runner Mode.
+
+In Single Workflow Runner Mode, you pass in a zip file which includes the WDL files referenced by the import statements. Cromwell requires the zip file to be passed in as a command line argument, as explained by the section [run](#run).
+
+For example, given a workflow `wf.wdl` and an imports directory `WdlImports.zip`, a sample command would be:
+```
+java -jar cromwell.jar wf.wdl wf.inputs - - WdlImports.zip
+```
+
+In Server Mode, you pass in a zip file using the parameter `wdlDependencies` via the [POST /api/workflows/:version](#post-apiworkflowsversion) endpoint.
+
+
+# Sub Workflows
+
+WDL allows the execution of an entire workflow as a step in a larger workflow (see WDL SPEC for more details), which is what will be referred to as a sub workflow going forward.
+Cromwell supports execution of such workflows. Note that sub workflows can themselves contain sub workflows, etc... There is no limitation as to how deeply workflows can be nested.
+
+## Execution
+
+Sub workflows are executed exactly as a task would be.
+*This means that if another call depends on an output of a sub workflow, this call will run when the whole sub workflow completes (successfully).*
+For example, in the following case :
+
+`main.wdl`
+```
+import "sub_wdl.wdl" as sub
+
+workflow main_workflow {
+
+    call sub.hello_and_goodbye { input: hello_and_goodbye_input = "sub world" }
+    
+    # call myTask { input: hello_and_goodbye.hello_output }
+    
+    output {
+        String main_output = hello_and_goodbye.hello_output
+    }
+}
+```
+
+`sub_wdl.wdl`
+```
+task hello {
+  String addressee
+  command {
+    echo "Hello ${addressee}!"
+  }
+  runtime {
+      docker: "ubuntu:latest"
+  }
+  output {
+    String salutation = read_string(stdout())
+  }
+}
+
+task goodbye {
+  String addressee
+  command {
+    echo "Goodbye ${addressee}!"
+  }
+  runtime {
+      docker: "ubuntu:latest"
+  }
+  output {
+    String salutation = read_string(stdout())
+  }
+}
+
+workflow hello_and_goodbye {
+  String hello_and_goodbye_input
+  
+  call hello {input: addressee = hello_and_goodbye_input }
+  call goodbye {input: addressee = hello_and_goodbye_input }
+  
+  output {
+    String hello_output = hello.salutation
+    String goodbye_output = goodbye.salutation
+  }
+}
+```
+
+`myTask` will start only when hello_and_goodbye completes (which means all of its calls are done), even though `myTask` only needs the output of hello in the hello_and_goodbye sub workflow. 
+If hello_and_goodbye fails, then `myTask` won't be executed.
+Only workflow outputs are visible outside a workflow, which means that references to outputs produced by a sub workflow will only be valid if those outputs are exposed in the workflow output section.
+
+Sub workflows are executed in the context of a main workflow, which means that operations that are normally executed once per workflow (set up, clean up, outputs copying, log copying, etc...)
+will NOT be re-executed for each sub workflow. For instance if a resource is created during workflow initialization, sub workflows will need to share this same resource.
+Workflow outputs will be copied for the main root workflow but not for intermediate sub workflows.
+
+Restarts, aborts, and call-caching work exactly as they would with tasks. 
+All tasks run by a sub workflow are eligible for call caching under the same rules as any other task.
+However, workflows themselves are not cached as such. Which means that running the exact same workflow twice with call caching on will trigger each task to cache individually,
+but not the workflow itself.
+
+The root path for sub workflow execution files (scripts, output files, logs) will be under the parent workflow call directory.
+For example, the execution directory for the above main workflow would look like the following:
+
+```
+cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/ <- main workflow id
+└── call-hello_and_goodbye <- call directory for call hello_and_goodbye in the main workflow
+    └── hello_and_goodbye <- name of the sub workflow 
+        └── a6365f91-c807-465a-9186-a5d3da98fe11 <- sub workflow id
+            ├── call-goodbye
+            │   └── execution
+            │       ├── rc
+            │       ├── script
+            │       ├── script.background
+            │       ├── script.submit
+            │       ├── stderr
+            │       ├── stderr.background
+            │       ├── stdout
+            │       └── stdout.background
+            └── call-hello
+                └── execution
+                    ├── rc
+                    ├── script
+                    ├── script.background
+                    ├── script.submit
+                    ├── stderr
+                    ├── stderr.background
+                    ├── stdout
+                    └── stdout.background
+
+```
+
+## Metadata
+Each sub workflow will have its own workflow ID. This ID will appear in the metadata of the parent workflow, in the call section corresponding to the sub workflow, under the "subWorkflowId" attribute.
+For example, querying the `main_workflow` metadata above (minus the `myTask` call) , could result in something like this:
+
+`GET /api/workflows/v2/1d919bd4-d046-43b0-9918-9964509689dd/metadata`
+
+```
+{
+  "workflowName": "main_workflow",
+  "submittedFiles": {
+    "inputs": "{}",
+    "workflow": "import \"sub_wdl.wdl\" as sub\n\nworkflow main_workflow {\n\n    call sub.hello_and_goodbye { input: hello_and_goodbye_input = \"sub world\" }\n    \n    # call myTask { input: hello_and_goodbye.hello_output }\n    \n    output {\n        String main_output = hello_and_goodbye.hello_output\n    }\n}",
+    "options": "{\n\n}"
+  },
+  "calls": {
+    "main_workflow.hello_and_goodbye": [
+      {
+        "executionStatus": "Done",
+        "shardIndex": -1,
+        "outputs": {
+          "goodbye_output": "Goodbye sub world!",
+          "hello_output": "Hello sub world!"
+        },
+        "inputs": {
+          "hello_and_goodbye_input": "sub world"
+        },
+        "end": "2016-11-17T14:13:41.117-05:00",
+        "attempt": 1,
+        "start": "2016-11-17T14:13:39.236-05:00",
+        "subWorkflowId": "a6365f91-c807-465a-9186-a5d3da98fe11"
+      }
+    ]
+  },
+  "outputs": {
+    "main_output": "Hello sub world!"
+  },
+  "workflowRoot": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd",
+  "id": "1d919bd4-d046-43b0-9918-9964509689dd",
+  "inputs": {},
+  "submission": "2016-11-17T14:13:39.104-05:00",
+  "status": "Succeeded",
+  "end": "2016-11-17T14:13:41.120-05:00",
+  "start": "2016-11-17T14:13:39.204-05:00"
+}
+```
+
+The sub workflow ID can be queried separately:
+
+`GET /api/workflows/v2/a6365f91-c807-465a-9186-a5d3da98fe11/metadata`
+
+```
+{
+  "workflowName": "hello_and_goodbye",
+  "calls": {
+    "sub.hello_and_goodbye.hello": [
+      {
+        "executionStatus": "Done",
+        "stdout": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-hello/execution/stdout",
+        "shardIndex": -1,
+        "outputs": {
+          "salutation": "Hello sub world!"
+        },
+        "runtimeAttributes": {
+          "docker": "ubuntu:latest",
+          "failOnStderr": false,
+          "continueOnReturnCode": "0"
+        },
+        "cache": {
+          "allowResultReuse": true
+        },
+        "Effective call caching mode": "CallCachingOff",
+        "inputs": {
+          "addressee": "sub world"
+        },
+        "returnCode": 0,
+        "jobId": "49830",
+        "backend": "Local",
+        "end": "2016-11-17T14:13:40.712-05:00",
+        "stderr": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-hello/execution/stderr",
+        "callRoot": "/cromwell/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-hello",
+        "attempt": 1,
+        "executionEvents": [
+          {
+            "startTime": "2016-11-17T14:13:39.240-05:00",
+            "description": "Pending",
+            "endTime": "2016-11-17T14:13:39.240-05:00"
+          },
+          {
+            "startTime": "2016-11-17T14:13:39.240-05:00",
+            "description": "RequestingExecutionToken",
+            "endTime": "2016-11-17T14:13:39.240-05:00"
+          },
+          {
+            "startTime": "2016-11-17T14:13:39.240-05:00",
+            "description": "PreparingJob",
+            "endTime": "2016-11-17T14:13:39.243-05:00"
+          },
+          {
+            "startTime": "2016-11-17T14:13:39.243-05:00",
+            "description": "RunningJob",
+            "endTime": "2016-11-17T14:13:40.704-05:00"
+          },
+          {
+            "startTime": "2016-11-17T14:13:40.704-05:00",
+            "description": "UpdatingJobStore",
+            "endTime": "2016-11-17T14:13:40.712-05:00"
+          }
+        ],
+        "start": "2016-11-17T14:13:39.239-05:00"
+      }
+    ],
+    "sub.hello_and_goodbye.goodbye": [
+      {
+        "executionStatus": "Done",
+        "stdout": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-goodbye/execution/stdout",
+        "shardIndex": -1,
+        "outputs": {
+          "salutation": "Goodbye sub world!"
+        },
+        "runtimeAttributes": {
+          "docker": "ubuntu:latest",
+          "failOnStderr": false,
+          "continueOnReturnCode": "0"
+        },
+        "cache": {
+          "allowResultReuse": true
+        },
+        "Effective call caching mode": "CallCachingOff",
+        "inputs": {
+          "addressee": "sub world"
+        },
+        "returnCode": 0,
+        "jobId": "49831",
+        "backend": "Local",
+        "end": "2016-11-17T14:13:41.115-05:00",
+        "stderr": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-goodbye/execution/stderr",
+        "callRoot": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-goodbye",
+        "attempt": 1,
+        "executionEvents": [
+          {
+            "startTime": "2016-11-17T14:13:39.240-05:00",
+            "description": "Pending",
+            "endTime": "2016-11-17T14:13:39.240-05:00"
+          },
+          {
+            "startTime": "2016-11-17T14:13:39.240-05:00",
+            "description": "RequestingExecutionToken",
+            "endTime": "2016-11-17T14:13:39.240-05:00"
+          },
+          {
+            "startTime": "2016-11-17T14:13:39.240-05:00",
+            "description": "PreparingJob",
+            "endTime": "2016-11-17T14:13:39.243-05:00"
+          },
+          {
+            "startTime": "2016-11-17T14:13:39.243-05:00",
+            "description": "RunningJob",
+            "endTime": "2016-11-17T14:13:41.112-05:00"
+          },
+          {
+            "startTime": "2016-11-17T14:13:41.112-05:00",
+            "description": "UpdatingJobStore",
+            "endTime": "2016-11-17T14:13:41.115-05:00"
+          }
+        ],
+        "start": "2016-11-17T14:13:39.239-05:00"
+      }
+    ]
+  },
+  "outputs": {
+    "goodbye_output": "Goodbye sub world!",
+    "hello_output": "Hello sub world!"
+  },
+  "workflowRoot": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11",
+  "id": "a6365f91-c807-465a-9186-a5d3da98fe11",
+  "inputs": {
+    "hello_and_goodbye_input": "sub world"
+  },
+  "status": "Succeeded",
+  "parentWorkflowId": "1d919bd4-d046-43b0-9918-9964509689dd",
+  "end": "2016-11-17T14:13:41.116-05:00",
+  "start": "2016-11-17T14:13:39.236-05:00"
+}
+```
+
+It's also possible to set the URL query parameter `expandSubWorkflows` to `true` to automatically include sub workflows metadata (`false` by default).
+
+`GET api/workflows/v2/1d919bd4-d046-43b0-9918-9964509689dd/metadata?expandSubWorkflows=true`
+
+```
+{
+  "workflowName": "main_workflow",
+  "submittedFiles": {
+    "inputs": "{}",
+    "workflow": "import \"sub_wdl.wdl\" as sub\n\nworkflow main_workflow {\n\n    call sub.hello_and_goodbye { input: hello_and_goodbye_input = \"sub world\" }\n    \n    # call myTask { input: hello_and_goodbye.hello_output }\n    \n    output {\n        String main_output = hello_and_goodbye.hello_output\n    }\n}",
+    "options": "{\n\n}"
+  },
+  "calls": {
+    "main_workflow.hello_and_goodbye": [{
+      "executionStatus": "Done",
+      "subWorkflowMetadata": {
+        "workflowName": "hello_and_goodbye",
+        "calls": {
+          "sub.hello_and_goodbye.hello": [{
+            "executionStatus": "Done",
+            "stdout": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-hello/execution/stdout",
+            "shardIndex": -1,
+            "outputs": {
+              "salutation": "Hello sub world!"
+            },
+            "runtimeAttributes": {
+              "docker": "ubuntu:latest",
+              "failOnStderr": false,
+              "continueOnReturnCode": "0"
+            },
+            "cache": {
+              "allowResultReuse": true
+            },
+            "Effective call caching mode": "CallCachingOff",
+            "inputs": {
+              "addressee": "sub world"
+            },
+            "returnCode": 0,
+            "jobId": "49830",
+            "backend": "Local",
+            "end": "2016-11-17T14:13:40.712-05:00",
+            "stderr": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-hello/execution/stderr",
+            "callRoot": "cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-hello",
+            "attempt": 1,
+            "executionEvents": [{
+              "startTime": "2016-11-17T14:13:39.240-05:00",
+              "description": "Pending",
+              "endTime": "2016-11-17T14:13:39.240-05:00"
+            }, {
+              "startTime": "2016-11-17T14:13:39.240-05:00",
+              "description": "RequestingExecutionToken",
+              "endTime": "2016-11-17T14:13:39.240-05:00"
+            }, {
+              "startTime": "2016-11-17T14:13:39.240-05:00",
+              "description": "PreparingJob",
+              "endTime": "2016-11-17T14:13:39.243-05:00"
+            }, {
+              "startTime": "2016-11-17T14:13:39.243-05:00",
+              "description": "RunningJob",
+              "endTime": "2016-11-17T14:13:40.704-05:00"
+            }, {
+              "startTime": "2016-11-17T14:13:40.704-05:00",
+              "description": "UpdatingJobStore",
+              "endTime": "2016-11-17T14:13:40.712-05:00"
+            }],
+            "start": "2016-11-17T14:13:39.239-05:00"
+          }],
+          "sub.hello_and_goodbye.goodbye": [{
+            "executionStatus": "Done",
+            "stdout": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-goodbye/execution/stdout",
+            "shardIndex": -1,
+            "outputs": {
+              "salutation": "Goodbye sub world!"
+            },
+            "runtimeAttributes": {
+              "docker": "ubuntu:latest",
+              "failOnStderr": false,
+              "continueOnReturnCode": "0"
+            },
+            "cache": {
+              "allowResultReuse": true
+            },
+            "Effective call caching mode": "CallCachingOff",
+            "inputs": {
+              "addressee": "sub world"
+            },
+            "returnCode": 0,
+            "jobId": "49831",
+            "backend": "Local",
+            "end": "2016-11-17T14:13:41.115-05:00",
+            "stderr": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-goodbye/execution/stderr",
+            "callRoot": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11/call-goodbye",
+            "attempt": 1,
+            "executionEvents": [{
+              "startTime": "2016-11-17T14:13:39.240-05:00",
+              "description": "Pending",
+              "endTime": "2016-11-17T14:13:39.240-05:00"
+            }, {
+              "startTime": "2016-11-17T14:13:39.240-05:00",
+              "description": "RequestingExecutionToken",
+              "endTime": "2016-11-17T14:13:39.240-05:00"
+            }, {
+              "startTime": "2016-11-17T14:13:39.240-05:00",
+              "description": "PreparingJob",
+              "endTime": "2016-11-17T14:13:39.243-05:00"
+            }, {
+              "startTime": "2016-11-17T14:13:39.243-05:00",
+              "description": "RunningJob",
+              "endTime": "2016-11-17T14:13:41.112-05:00"
+            }, {
+              "startTime": "2016-11-17T14:13:41.112-05:00",
+              "description": "UpdatingJobStore",
+              "endTime": "2016-11-17T14:13:41.115-05:00"
+            }],
+            "start": "2016-11-17T14:13:39.239-05:00"
+          }]
+        },
+        "outputs": {
+          "goodbye_output": "Goodbye sub world!",
+          "hello_output": "Hello sub world!"
+        },
+        "workflowRoot": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd/call-hello_and_goodbye/hello_and_goodbye/a6365f91-c807-465a-9186-a5d3da98fe11",
+        "id": "a6365f91-c807-465a-9186-a5d3da98fe11",
+        "inputs": {
+          "hello_and_goodbye_input": "sub world"
+        },
+        "status": "Succeeded",
+        "parentWorkflowId": "1d919bd4-d046-43b0-9918-9964509689dd",
+        "end": "2016-11-17T14:13:41.116-05:00",
+        "start": "2016-11-17T14:13:39.236-05:00"
+      },
+      "shardIndex": -1,
+      "outputs": {
+        "goodbye_output": "Goodbye sub world!",
+        "hello_output": "Hello sub world!"
+      },
+      "inputs": {
+        "hello_and_goodbye_input": "sub world"
+      },
+      "end": "2016-11-17T14:13:41.117-05:00",
+      "attempt": 1,
+      "start": "2016-11-17T14:13:39.236-05:00"
+    }]
+  },
+  "outputs": {
+    "main_output": "Hello sub world!"
+  },
+  "workflowRoot": "/cromwell-executions/main_workflow/1d919bd4-d046-43b0-9918-9964509689dd",
+  "id": "1d919bd4-d046-43b0-9918-9964509689dd",
+  "inputs": {
+
+  },
+  "submission": "2016-11-17T14:13:39.104-05:00",
+  "status": "Succeeded",
+  "end": "2016-11-17T14:13:41.120-05:00",
+  "start": "2016-11-17T14:13:39.204-05:00"
+}
+```
+
 # REST API
 
 The `server` subcommand on the executable JAR will start an HTTP server which can accept WDL files to run as well as check status and output of existing workflows.
@@ -1561,7 +2137,18 @@ This endpoint accepts a POST request with a `multipart/form-data` encoded body.
 
 * `wdlSource` - *Required* Contains the WDL file to submit for execution.
 * `workflowInputs` - *Optional* JSON file containing the inputs.  A skeleton file can be generated from [wdltool](https://github.com/broadinstitute/wdltool) using the "inputs" subcommand.
+* `workflowInputs_2` - *Optional* JSON file containing the inputs.
+* `workflowInputs_3` - *Optional* JSON file containing the inputs.
+* `workflowInputs_4` - *Optional* JSON file containing the inputs.
+* `workflowInputs_5` - *Optional* JSON file containing the inputs.
 * `workflowOptions` - *Optional* JSON file containing options for this workflow execution.  See the [run](#run) CLI sub-command for some more information about this.
+* `wdlDependencies` - *Optional* ZIP file containing WDL files that are used to resolve import statements.
+
+Regarding the workflowInputs parameter, in case of key conflicts between multiple input JSON files, higher values of x in workflowInputs_x override lower values. For example, an input specified in workflowInputs_3 will override an input with the same name in workflowInputs or workflowInputs_2.
+Similarly, an input key specified in workflowInputs_5 will override an identical input key in any other input file.
+
+Additionally, although Swagger has a limit of 5 JSON input files, the REST endpoint itself can accept an unlimited number of JSON input files.
+
 
 cURL:
 
diff --git a/SecurityRecommendations.md b/SecurityRecommendations.md
new file mode 100644
index 00000000000..3d980e582af
--- /dev/null
+++ b/SecurityRecommendations.md
@@ -0,0 +1,51 @@
+Security
+========
+
+<!---toc start-->
+* [Firecloud](#firecloud)
+* [Security by sysadmin](#security)
+   * [Multi-tenant](#multi-tenant)
+<!---toc end-->
+
+# Firecloud
+
+TODO
+
+# Security by sysadmin
+__Warning!__
+
+__This section is community-contributed. It is intended as helpful guidance only, and is not endorsed by the Broad Institute.__
+
+Cromwell running in server mode accepts all connections on the configured webservice port. The simplest way to restrict access is by putting an authenticating proxy server in between users and the cromwell server:
+ 1. Configure a firewall rule on the cromwell server host to deny access to the webservice port (e.g. 8000) from all addresses except a secure proxy host.
+ 1. Configure `<YourFavoriteWebProxy>` on the proxy host with `<YourFavoriteAuthMechanism>`, to proxy authenticated traffic from the world to the cromwell server. Using Apache `httpd` web server for example with basic htpassword file-based authentication, the configuration might look something like:
+
+ ```Apache
+<Location /cromwell>
+    Order deny,allow
+    Allow from all
+    AuthType Basic
+    AuthName "Password Required"
+    AuthUserFile /path/to/my/htpasswdfile
+    Require user someone someoneelse
+    ProxyPass http://101.101.234.567:8000     # address of cromwell server web service
+</Location>
+```
+
+ 1. That's it. Users now hit `http://my.proxy.org/cromwell` with authenticated requests, and they're forwarded to port 8000 on the cromwell server host.
+
+## Multi-tenant
+The above scheme extends easily to multiple cromwell instances, for use by different groups within an organization for example. If the instances are running on the same host then each instance should be run as its own dedicated service account user, e.g. `cromwell1`, `cromwell2` etc. so that processes running under one cromwell instance cannot access the files of another; different webservice ports must also be configured. If persistent database storage is being used then each instance should be configured with its own database and database user. The proxy configuration above is extended simply by adding another `Location`:
+
+```Apache
+<Location /cromwell1>
+    Order deny,allow
+    Allow from all
+    AuthType Basic
+    AuthName "Password Required"
+    AuthUserFile /path/to/my/htpasswdfile1
+    Require user stillanotherperson andanother
+    ProxyPass http://101.101.234.567:8001
+</Location>
+```
+
diff --git a/backend/src/main/scala/cromwell/backend/BackendCacheHitCopyingActor.scala b/backend/src/main/scala/cromwell/backend/BackendCacheHitCopyingActor.scala
index 11a95df398c..f1bf383866b 100644
--- a/backend/src/main/scala/cromwell/backend/BackendCacheHitCopyingActor.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendCacheHitCopyingActor.scala
@@ -3,7 +3,7 @@ package cromwell.backend
 import akka.actor.{Actor, ActorLogging}
 import akka.event.LoggingReceive
 import cromwell.backend.BackendCacheHitCopyingActor.CopyOutputsCommand
-import cromwell.backend.BackendJobExecutionActor.{AbortedResponse, BackendJobExecutionResponse, FailedNonRetryableResponse}
+import cromwell.backend.BackendJobExecutionActor.{AbortedResponse, BackendJobExecutionResponse, JobFailedNonRetryableResponse}
 import cromwell.backend.BackendLifecycleActor._
 import cromwell.core.simpleton.WdlValueSimpleton
 
@@ -29,6 +29,6 @@ trait BackendCacheHitCopyingActor extends Actor with ActorLogging with BackendJo
   def abort(): Unit = log.warning("{}: Abort not supported during cache hit copying", jobTag)
 
   private def cachingFailed(t: Throwable) = {
-    FailedNonRetryableResponse(jobKey = jobDescriptor.key, throwable = t, returnCode = None)
+    JobFailedNonRetryableResponse(jobKey = jobDescriptor.key, throwable = t, returnCode = None)
   }
 }
diff --git a/backend/src/main/scala/cromwell/backend/BackendJobBreadCrumb.scala b/backend/src/main/scala/cromwell/backend/BackendJobBreadCrumb.scala
new file mode 100644
index 00000000000..1dbc9ca5090
--- /dev/null
+++ b/backend/src/main/scala/cromwell/backend/BackendJobBreadCrumb.scala
@@ -0,0 +1,14 @@
+package cromwell.backend
+
+import java.nio.file.Path
+
+import cromwell.backend.io.JobPaths
+import cromwell.core.{JobKey, WorkflowId}
+import wdl4s.Workflow
+
+case class BackendJobBreadCrumb(workflow: Workflow, id: WorkflowId, jobKey: JobKey) {
+  def toPath(root: Path): Path = {
+    val workflowPart = root.resolve(workflow.unqualifiedName).resolve(id.toString)
+    JobPaths.callPathBuilder(workflowPart, jobKey)
+  }
+}
diff --git a/backend/src/main/scala/cromwell/backend/BackendJobExecutionActor.scala b/backend/src/main/scala/cromwell/backend/BackendJobExecutionActor.scala
index 60cdc1e02fb..816f43da997 100644
--- a/backend/src/main/scala/cromwell/backend/BackendJobExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendJobExecutionActor.scala
@@ -1,10 +1,13 @@
 package cromwell.backend
 
+import java.nio.file.Path
+
 import akka.actor.ActorLogging
 import akka.event.LoggingReceive
 import cromwell.backend.BackendJobExecutionActor._
 import cromwell.backend.BackendLifecycleActor._
-import cromwell.core.{ExecutionEvent, JobOutputs}
+import cromwell.backend.wdl.OutputEvaluator
+import cromwell.core.{CallOutputs, ExecutionEvent, JobKey}
 import wdl4s.expression.WdlStandardLibraryFunctions
 import wdl4s.values.WdlValue
 
@@ -21,12 +24,12 @@ object BackendJobExecutionActor {
   // Responses
   sealed trait BackendJobExecutionActorResponse extends BackendWorkflowLifecycleActorResponse
 
-  sealed trait BackendJobExecutionResponse extends BackendJobExecutionActorResponse { def jobKey: BackendJobDescriptorKey }
-  case class SucceededResponse(jobKey: BackendJobDescriptorKey, returnCode: Option[Int], jobOutputs: JobOutputs, jobDetritusFiles: Option[Map[String, String]], executionEvents: Seq[ExecutionEvent]) extends BackendJobExecutionResponse
+  sealed trait BackendJobExecutionResponse extends BackendJobExecutionActorResponse { def jobKey: JobKey }
+  case class JobSucceededResponse(jobKey: BackendJobDescriptorKey, returnCode: Option[Int], jobOutputs: CallOutputs, jobDetritusFiles: Option[Map[String, Path]], executionEvents: Seq[ExecutionEvent]) extends BackendJobExecutionResponse
   case class AbortedResponse(jobKey: BackendJobDescriptorKey) extends BackendJobExecutionResponse
   sealed trait BackendJobFailedResponse extends BackendJobExecutionResponse {  def throwable: Throwable; def returnCode: Option[Int] }
-  case class FailedNonRetryableResponse(jobKey: BackendJobDescriptorKey, throwable: Throwable, returnCode: Option[Int]) extends BackendJobFailedResponse
-  case class FailedRetryableResponse(jobKey: BackendJobDescriptorKey, throwable: Throwable, returnCode: Option[Int]) extends BackendJobFailedResponse
+  case class JobFailedNonRetryableResponse(jobKey: JobKey, throwable: Throwable, returnCode: Option[Int]) extends BackendJobFailedResponse
+  case class JobFailedRetryableResponse(jobKey: BackendJobDescriptorKey, throwable: Throwable, returnCode: Option[Int]) extends BackendJobFailedResponse
 }
 
 /**
@@ -45,7 +48,7 @@ trait BackendJobExecutionActor extends BackendJobLifecycleActor with ActorLoggin
 
   // We need this for receive because we can't do `onFailure = ExecutionFailure` directly - because BackendJobDescriptor =/= BackendJobDescriptorKey
   private def executionFailed = (t: Throwable) =>
-    FailedNonRetryableResponse(jobKey = jobDescriptor.key, throwable = t, returnCode = None)
+    JobFailedNonRetryableResponse(jobKey = jobDescriptor.key, throwable = t, returnCode = None)
 
   /**
     * Execute a new job.
diff --git a/backend/src/main/scala/cromwell/backend/BackendLifecycleActor.scala b/backend/src/main/scala/cromwell/backend/BackendLifecycleActor.scala
index 58ef726435f..a6a09cff4a3 100644
--- a/backend/src/main/scala/cromwell/backend/BackendLifecycleActor.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendLifecycleActor.scala
@@ -3,7 +3,7 @@ package cromwell.backend
 import akka.actor.{Actor, ActorRef}
 import cromwell.backend.BackendLifecycleActor._
 import cromwell.core.logging.{JobLogging, WorkflowLogging}
-import wdl4s.Call
+import wdl4s.TaskCall
 
 import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success}
@@ -55,7 +55,7 @@ trait BackendLifecycleActor extends Actor {
 trait BackendWorkflowLifecycleActor extends BackendLifecycleActor with WorkflowLogging {
 
   //For Logging and boilerplate
-  override lazy final val workflowId = workflowDescriptor.id
+  override lazy final val workflowIdForLogging = workflowDescriptor.id
 
   /**
     * The workflow descriptor for the workflow in which this Backend is being used
@@ -65,7 +65,7 @@ trait BackendWorkflowLifecycleActor extends BackendLifecycleActor with WorkflowL
   /**
     * The subset of calls which this backend will be expected to run
     */
-  protected def calls: Seq[Call]
+  protected def calls: Set[TaskCall]
 }
 
 trait BackendJobLifecycleActor extends BackendLifecycleActor with JobLogging {
diff --git a/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala b/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala
index 5a6c5d26823..cb625a78bce 100644
--- a/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala
@@ -6,17 +6,17 @@ import akka.actor.{ActorRef, Props}
 import com.typesafe.config.Config
 import cromwell.backend.callcaching.FileHashingActor
 import cromwell.backend.callcaching.FileHashingActor.FileHashingFunction
-import cromwell.backend.io.WorkflowPaths
+import cromwell.backend.io.WorkflowPathsWithDocker
+import cromwell.core.CallOutputs
 import cromwell.core.JobExecutionToken.JobExecutionTokenType
-import cromwell.core.{ExecutionStore, OutputStore}
-import wdl4s.Call
-import wdl4s.expression.WdlStandardLibraryFunctions
+import wdl4s.TaskCall
+import wdl4s.expression.{PureStandardLibraryFunctions, WdlStandardLibraryFunctions}
 
 
 trait BackendLifecycleActorFactory {
   def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                       calls: Seq[Call],
-                                       serviceRegistryActor: ActorRef): Option[Props]
+                                       calls: Set[TaskCall],
+                                       serviceRegistryActor: ActorRef): Option[Props] = None
 
   def jobExecutionActorProps(jobDescriptor: BackendJobDescriptor,
                              initializationData: Option[BackendInitializationData],
@@ -37,17 +37,21 @@ trait BackendLifecycleActorFactory {
   def backendSingletonActorProps: Option[Props] = None
 
   def workflowFinalizationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                     calls: Seq[Call],
-                                     executionStore: ExecutionStore,
-                                     outputStore: OutputStore,
+                                     calls: Set[TaskCall],
+                                     jobExecutionMap: JobExecutionMap,
+                                     workflowOutputs: CallOutputs,
                                      initializationData: Option[BackendInitializationData]): Option[Props] = None
 
   def expressionLanguageFunctions(workflowDescriptor: BackendWorkflowDescriptor,
                                   jobKey: BackendJobDescriptorKey,
-                                  initializationData: Option[BackendInitializationData]): WdlStandardLibraryFunctions
+                                  initializationData: Option[BackendInitializationData]): WdlStandardLibraryFunctions = PureStandardLibraryFunctions
 
   def getExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor, backendConfig: Config, initializationData: Option[BackendInitializationData]): Path = {
-    new WorkflowPaths(workflowDescriptor, backendConfig).executionRoot
+    new WorkflowPathsWithDocker(workflowDescriptor, backendConfig).executionRoot
+  }
+
+  def getWorkflowExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor, backendConfig: Config, initializationData: Option[BackendInitializationData]): Path = {
+    new WorkflowPathsWithDocker(workflowDescriptor, backendConfig).workflowRoot
   }
 
   def runtimeAttributeDefinitions(initializationDataOption: Option[BackendInitializationData]): Set[RuntimeAttributeDefinition] = Set.empty
diff --git a/backend/src/main/scala/cromwell/backend/BackendWorkflowInitializationActor.scala b/backend/src/main/scala/cromwell/backend/BackendWorkflowInitializationActor.scala
index f98234ce5a2..feaf5720bf0 100644
--- a/backend/src/main/scala/cromwell/backend/BackendWorkflowInitializationActor.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendWorkflowInitializationActor.scala
@@ -4,13 +4,13 @@ import akka.actor.{ActorLogging, ActorRef}
 import akka.event.LoggingReceive
 import cromwell.backend.BackendLifecycleActor._
 import cromwell.backend.BackendWorkflowInitializationActor._
-import cromwell.backend.wdl.OnlyPureFunctions
+import wdl4s.expression.PureStandardLibraryFunctions
 import cromwell.core.{WorkflowMetadataKeys, WorkflowOptions}
 import cromwell.services.metadata.MetadataService.PutMetadataAction
 import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
 import wdl4s.types._
 import wdl4s.values.{WdlArray, WdlBoolean, WdlInteger, WdlString, WdlValue}
-import wdl4s.{Call, NoLookup, Task, WdlExpression}
+import wdl4s._
 
 import scala.concurrent.Future
 import scala.util.{Failure, Success, Try}
@@ -36,7 +36,7 @@ object BackendWorkflowInitializationActor {
 trait BackendWorkflowInitializationActor extends BackendWorkflowLifecycleActor with ActorLogging {
   val serviceRegistryActor: ActorRef
 
-  def calls: Seq[Call]
+  def calls: Set[TaskCall]
 
   /**
     * This method is meant only as a "pre-flight check" validation of runtime attribute expressions during workflow
@@ -53,7 +53,7 @@ trait BackendWorkflowInitializationActor extends BackendWorkflowLifecycleActor w
     wdlExpressionMaybe match {
       case None => !valueRequired
       case Some(wdlExpression: WdlExpression) =>
-        wdlExpression.evaluate(NoLookup, OnlyPureFunctions) map (_.wdlType) match {
+        wdlExpression.evaluate(NoLookup, PureStandardLibraryFunctions) map (_.wdlType) match {
           case Success(wdlType) => predicate(wdlType)
           case Failure(_) => true // If we can't evaluate it, we'll let it pass for now...
         }
@@ -81,7 +81,7 @@ trait BackendWorkflowInitializationActor extends BackendWorkflowLifecycleActor w
     wdlExpressionMaybe match {
       case None => !valueRequired
       case Some(wdlExpression: WdlExpression) =>
-        wdlExpression.evaluate(NoLookup, OnlyPureFunctions) match {
+        wdlExpression.evaluate(NoLookup, PureStandardLibraryFunctions) match {
           case Success(wdlValue) => validateValue(wdlValue)
           case Failure(throwable) => true // If we can't evaluate it, we'll let it pass for now...
         }
@@ -91,6 +91,9 @@ trait BackendWorkflowInitializationActor extends BackendWorkflowLifecycleActor w
 
   protected def runtimeAttributeValidators: Map[String, Option[WdlValue] => Boolean]
 
+  // FIXME: If a workflow executes jobs using multiple backends,
+  // each backend will try to write its own workflow root and override any previous one.
+  // They should be structured differently or at least be prefixed by the backend name
   protected def publishWorkflowRoot(workflowRoot: String) = {
     serviceRegistryActor ! PutMetadataAction(MetadataEvent(MetadataKey(workflowDescriptor.id, None, WorkflowMetadataKeys.WorkflowRoot), MetadataValue(workflowRoot)))
   }
diff --git a/backend/src/main/scala/cromwell/backend/OutputEvaluator.scala b/backend/src/main/scala/cromwell/backend/OutputEvaluator.scala
deleted file mode 100644
index 0c63652651b..00000000000
--- a/backend/src/main/scala/cromwell/backend/OutputEvaluator.scala
+++ /dev/null
@@ -1,31 +0,0 @@
-package cromwell.backend
-
-import cromwell.core.JobOutput
-import wdl4s._
-import wdl4s.expression.WdlStandardLibraryFunctions
-import wdl4s.util.TryUtil
-import wdl4s.values.WdlValue
-
-import scala.util.{Success, Try}
-
-object OutputEvaluator {
-  def evaluateOutputs(jobDescriptor: BackendJobDescriptor,
-                      wdlFunctions: WdlStandardLibraryFunctions,
-                      postMapper: WdlValue => Try[WdlValue] = v => Success(v)) = {
-    val inputs = jobDescriptor.inputs
-    val evaluatedOutputs = jobDescriptor.call.task.outputs.
-      foldLeft(Map.empty[LocallyQualifiedName, Try[JobOutput]])((outputMap, output) => {
-        val currentOutputs = outputMap collect {
-          case (name, value) if value.isSuccess => name -> value.get.wdlValue
-        }
-        def lookup = (currentOutputs ++ inputs).apply _
-        val coerced = output.requiredExpression.evaluate(lookup, wdlFunctions) flatMap output.wdlType.coerceRawValue
-        val jobOutput = output.name -> (coerced flatMap postMapper map JobOutput)
-
-        outputMap + jobOutput
-
-      })
-
-    TryUtil.sequenceMap(evaluatedOutputs, s"Workflow ${jobDescriptor.workflowDescriptor.id} post processing failed.")
-  }
-}
diff --git a/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala b/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala
index 2383091432c..ae9d4b9bf26 100644
--- a/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala
+++ b/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala
@@ -20,8 +20,8 @@ object RuntimeAttributeDefinition {
 
   def evaluateRuntimeAttributes(unevaluated: RuntimeAttributes,
                                 wdlFunctions: WdlStandardLibraryFunctions,
-                                evaluatedInputs: Map[LocallyQualifiedName, WdlValue]): Try[Map[String, WdlValue]] = {
-    val tryInputs = evaluatedInputs map { case (x, y) => x -> Success(y) }
+                                evaluatedInputs: Map[Declaration, WdlValue]): Try[Map[String, WdlValue]] = {
+    val tryInputs = evaluatedInputs map { case (x, y) => x.unqualifiedName -> Success(y) }
     val mapBasedLookup = buildMapBasedLookup(tryInputs) _
     val mapOfTries = unevaluated.attrs mapValues {
       expr => expr.evaluate(mapBasedLookup, wdlFunctions)
diff --git a/backend/src/main/scala/cromwell/backend/async/AsyncBackendJobExecutionActor.scala b/backend/src/main/scala/cromwell/backend/async/AsyncBackendJobExecutionActor.scala
index bbbfbf82b00..759127d6748 100644
--- a/backend/src/main/scala/cromwell/backend/async/AsyncBackendJobExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/async/AsyncBackendJobExecutionActor.scala
@@ -2,7 +2,7 @@ package cromwell.backend.async
 
 import akka.actor.{Actor, ActorLogging, ActorRef}
 import cromwell.backend.BackendJobDescriptor
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, SucceededResponse, _}
+import cromwell.backend.BackendJobExecutionActor._
 import cromwell.backend.async.AsyncBackendJobExecutionActor._
 import cromwell.core.CromwellFatalException
 import cromwell.core.retry.{Retry, SimpleExponentialBackoff}
@@ -60,7 +60,7 @@ trait AsyncBackendJobExecutionActor { this: Actor with ActorLogging =>
   }
 
   private def failAndStop(t: Throwable) = {
-    val responseBuilder = if (retryable) FailedRetryableResponse else FailedNonRetryableResponse
+    val responseBuilder = if (retryable) JobFailedRetryableResponse else JobFailedNonRetryableResponse
     completionPromise.success(responseBuilder.apply(jobDescriptor.key, t, None))
     context.stop(self)
   }
@@ -75,13 +75,13 @@ trait AsyncBackendJobExecutionActor { this: Actor with ActorLogging =>
       context.system.scheduler.scheduleOnce(pollBackOff.backoffMillis.millis, self, IssuePollRequest(handle))
       ()
     case Finish(SuccessfulExecutionHandle(outputs, returnCode, jobDetritusFiles, executionEvents, resultsClonedFrom)) =>
-      completionPromise.success(SucceededResponse(jobDescriptor.key, Some(returnCode), outputs, Option(jobDetritusFiles), executionEvents))
+      completionPromise.success(JobSucceededResponse(jobDescriptor.key, Some(returnCode), outputs, Option(jobDetritusFiles), executionEvents))
       context.stop(self)
     case Finish(FailedNonRetryableExecutionHandle(throwable, returnCode)) =>
-      completionPromise.success(FailedNonRetryableResponse(jobDescriptor.key, throwable, returnCode))
+      completionPromise.success(JobFailedNonRetryableResponse(jobDescriptor.key, throwable, returnCode))
       context.stop(self)
     case Finish(FailedRetryableExecutionHandle(throwable, returnCode)) =>
-      completionPromise.success(FailedRetryableResponse(jobDescriptor.key, throwable, returnCode))
+      completionPromise.success(JobFailedRetryableResponse(jobDescriptor.key, throwable, returnCode))
       context.stop(self)
     case Finish(cromwell.backend.async.AbortedExecutionHandle) =>
       completionPromise.success(AbortedResponse(jobDescriptor.key))
diff --git a/backend/src/main/scala/cromwell/backend/async/ExecutionHandle.scala b/backend/src/main/scala/cromwell/backend/async/ExecutionHandle.scala
index 88232f3b29b..1e4238014d9 100644
--- a/backend/src/main/scala/cromwell/backend/async/ExecutionHandle.scala
+++ b/backend/src/main/scala/cromwell/backend/async/ExecutionHandle.scala
@@ -1,7 +1,9 @@
 package cromwell.backend.async
 
+import java.nio.file.Path
+
 import cromwell.backend.BackendJobDescriptor
-import cromwell.core.{ExecutionEvent, JobOutputs}
+import cromwell.core.{ExecutionEvent, CallOutputs}
 
 /**
  * Trait to encapsulate whether an execution is complete and if so provide a result.  Useful in conjunction
@@ -12,7 +14,7 @@ trait ExecutionHandle {
   def result: ExecutionResult
 }
 
-final case class SuccessfulExecutionHandle(outputs: JobOutputs, returnCode: Int, jobDetritusFiles: Map[String, String], executionEvents: Seq[ExecutionEvent], resultsClonedFrom: Option[BackendJobDescriptor] = None) extends ExecutionHandle {
+final case class SuccessfulExecutionHandle(outputs: CallOutputs, returnCode: Int, jobDetritusFiles: Map[String, Path], executionEvents: Seq[ExecutionEvent], resultsClonedFrom: Option[BackendJobDescriptor] = None) extends ExecutionHandle {
   override val isDone = true
   override val result = SuccessfulExecution(outputs, returnCode, jobDetritusFiles, executionEvents, resultsClonedFrom)
 }
diff --git a/backend/src/main/scala/cromwell/backend/async/ExecutionResult.scala b/backend/src/main/scala/cromwell/backend/async/ExecutionResult.scala
index 267bea8779e..ff972233758 100644
--- a/backend/src/main/scala/cromwell/backend/async/ExecutionResult.scala
+++ b/backend/src/main/scala/cromwell/backend/async/ExecutionResult.scala
@@ -1,7 +1,9 @@
 package cromwell.backend.async
 
+import java.nio.file.Path
+
 import cromwell.backend.BackendJobDescriptor
-import cromwell.core.{ExecutionEvent, JobOutputs}
+import cromwell.core.{ExecutionEvent, CallOutputs}
 
 /**
  * ADT representing the result of an execution of a BackendCall.
@@ -11,9 +13,9 @@ sealed trait ExecutionResult
 /**
  * A successful execution with resolved outputs.
  */
-final case class SuccessfulExecution(outputs: JobOutputs,
+final case class SuccessfulExecution(outputs: CallOutputs,
                                      returnCode: Int,
-                                     jobDetritusFiles: Map[String, String],
+                                     jobDetritusFiles: Map[String, Path],
                                      executionEvents: Seq[ExecutionEvent],
                                      resultsClonedFrom: Option[BackendJobDescriptor] = None) extends ExecutionResult
 
diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index 8ac55a3471f..e1addfe30b1 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -2,20 +2,19 @@ package cromwell.backend
 
 import com.typesafe.config.Config
 import cromwell.core.WorkflowOptions.WorkflowOption
-import cromwell.core.{JobKey, WorkflowId, WorkflowOptions}
+import cromwell.core.{CallKey, WorkflowId, WorkflowOptions}
+import wdl4s._
 import wdl4s.values.WdlValue
-import wdl4s.{Call, NamespaceWithWorkflow, _}
 
 import scala.util.Try
 
 /**
   * For uniquely identifying a job which has been or will be sent to the backend.
   */
-case class BackendJobDescriptorKey(call: Call, index: Option[Int], attempt: Int) extends JobKey {
+case class BackendJobDescriptorKey(call: TaskCall, index: Option[Int], attempt: Int) extends CallKey {
   def scope = call
   private val indexString = index map { _.toString } getOrElse "NA"
   val tag = s"${call.fullyQualifiedName}:$indexString:$attempt"
-  val isShard = index.isDefined
   def mkTag(workflowId: WorkflowId) = s"$workflowId:$this"
 }
 
@@ -25,19 +24,34 @@ case class BackendJobDescriptorKey(call: Call, index: Option[Int], attempt: Int)
 case class BackendJobDescriptor(workflowDescriptor: BackendWorkflowDescriptor,
                                 key: BackendJobDescriptorKey,
                                 runtimeAttributes: Map[LocallyQualifiedName, WdlValue],
-                                inputs: Map[LocallyQualifiedName, WdlValue]) {
+                                inputDeclarations: EvaluatedTaskInputs) {
+  val fullyQualifiedInputs = inputDeclarations map { case (declaration, value) => declaration.fullyQualifiedName -> value }
   val call = key.call
   override val toString = s"${key.mkTag(workflowDescriptor.id)}"
 }
 
+object BackendWorkflowDescriptor {
+  def apply(id: WorkflowId,
+            workflow: Workflow,
+            inputs: Map[FullyQualifiedName, WdlValue],
+            workflowOptions: WorkflowOptions) = {
+    new BackendWorkflowDescriptor(id, workflow, inputs, workflowOptions, List.empty)
+  }
+}
+
 /**
   * For passing to a BackendActor construction time
   */
 case class BackendWorkflowDescriptor(id: WorkflowId,
-                                     workflowNamespace: NamespaceWithWorkflow,
+                                     workflow: Workflow,
                                      inputs: Map[FullyQualifiedName, WdlValue],
-                                     workflowOptions: WorkflowOptions) {
-  override def toString: String = s"[BackendWorkflowDescriptor id=${id.shortString} workflowName=${workflowNamespace.workflow.unqualifiedName}]"
+                                     workflowOptions: WorkflowOptions,
+                                     breadCrumbs: List[BackendJobBreadCrumb]) {
+  
+  val rootWorkflow = breadCrumbs.headOption.map(_.workflow).getOrElse(workflow)
+  val rootWorkflowId = breadCrumbs.headOption.map(_.id).getOrElse(id)
+  
+  override def toString: String = s"[BackendWorkflowDescriptor id=${id.shortString} workflowName=${workflow.unqualifiedName}]"
   def getWorkflowOption(key: WorkflowOption) = workflowOptions.get(key).toOption
 }
 
diff --git a/backend/src/main/scala/cromwell/backend/callcaching/CacheHitDuplicating.scala b/backend/src/main/scala/cromwell/backend/callcaching/CacheHitDuplicating.scala
index c199de6d409..48a6d590eb1 100644
--- a/backend/src/main/scala/cromwell/backend/callcaching/CacheHitDuplicating.scala
+++ b/backend/src/main/scala/cromwell/backend/callcaching/CacheHitDuplicating.scala
@@ -4,12 +4,15 @@ import java.nio.file.Path
 
 import akka.actor.ActorRef
 import cromwell.backend.BackendCacheHitCopyingActor
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, JobSucceededResponse}
 import cromwell.backend.io.JobPaths
-import cromwell.core.PathCopier
+import cromwell.core.path.PathCopier
 import cromwell.core.simpleton.{WdlValueBuilder, WdlValueSimpleton}
 import wdl4s.values.WdlFile
 
+import scala.language.postfixOps
+import scala.util.Try
+
 /**
   * Mixin implementing common functionality for a BackendCacheHitCopyingActor.
   *
@@ -35,7 +38,7 @@ trait CacheHitDuplicating {
     * @param file the string version of the path
     * @return an absolute path to the file with potential credentials embedded within.
     */
-  protected def getPath(file: String): Path
+  protected def getPath(file: String): Try[Path]
 
   protected def destinationCallRootPath: Path
 
@@ -47,9 +50,10 @@ trait CacheHitDuplicating {
   protected def metadataKeyValues: Map[String, Any]
 
   private def lookupSourceCallRootPath(sourceJobDetritusFiles: Map[String, String]): Path = {
-    sourceJobDetritusFiles.get(JobPaths.CallRootPathKey).map(getPath).getOrElse(throw new RuntimeException(
-      s"${JobPaths.CallRootPathKey} wasn't found for call ${jobDescriptor.call.fullyQualifiedName}")
-    )
+    sourceJobDetritusFiles.get(JobPaths.CallRootPathKey).map(getPath).get recover {
+      case failure =>
+        throw new RuntimeException(s"${JobPaths.CallRootPathKey} wasn't found for call ${jobDescriptor.call.fullyQualifiedName}", failure)
+    } get
   }
 
   /**
@@ -59,27 +63,27 @@ trait CacheHitDuplicating {
                              sourceCallRootPath: Path): Seq[WdlValueSimpleton] = {
     wdlValueSimpletons map {
       case WdlValueSimpleton(key, wdlFile: WdlFile) =>
-        val sourcePath = getPath(wdlFile.value)
+        val sourcePath = getPath(wdlFile.value).get
         val destinationPath = PathCopier.getDestinationFilePath(sourceCallRootPath, sourcePath, destinationCallRootPath)
         duplicate(sourcePath, destinationPath)
-        WdlValueSimpleton(key, WdlFile(destinationPath.toString))
+        WdlValueSimpleton(key, WdlFile(destinationPath.toUri.toString))
       case wdlValueSimpleton => wdlValueSimpleton
     }
   }
 
-  private def copyDetritus(sourceJobDetritusFiles: Map[String, String]): Map[String, String] = {
+  private def copyDetritus(sourceJobDetritusFiles: Map[String, String]): Map[String, Path] = {
     val sourceKeys = sourceJobDetritusFiles.keySet
     val destinationKeys = destinationJobDetritusPaths.keySet
     val fileKeys = sourceKeys.intersect(destinationKeys).filterNot(_ == JobPaths.CallRootPathKey)
 
     val destinationJobDetritusFiles = fileKeys map { fileKey =>
-      val sourcePath = getPath(sourceJobDetritusFiles(fileKey))
+      val sourcePath = getPath(sourceJobDetritusFiles(fileKey)).get
       val destinationPath = destinationJobDetritusPaths(fileKey)
       duplicate(sourcePath, destinationPath)
-      (fileKey, destinationPath.toString)
+      (fileKey, destinationPath)
     }
 
-    destinationJobDetritusFiles.toMap + (JobPaths.CallRootPathKey -> destinationCallRootPath.toString)
+    destinationJobDetritusFiles.toMap + (JobPaths.CallRootPathKey -> destinationCallRootPath)
   }
 
   override def copyCachedOutputs(wdlValueSimpletons: Seq[WdlValueSimpleton],
@@ -95,6 +99,6 @@ trait CacheHitDuplicating {
     import cromwell.services.metadata.MetadataService.implicits.MetadataAutoPutter
     serviceRegistryActor.putMetadata(jobDescriptor.workflowDescriptor.id, Option(jobDescriptor.key), metadataKeyValues)
 
-    SucceededResponse(jobDescriptor.key, returnCodeOption, destinationJobOutputs, Option(destinationJobDetritusFiles), Seq.empty)
+    JobSucceededResponse(jobDescriptor.key, returnCodeOption, destinationJobOutputs, Option(destinationJobDetritusFiles), Seq.empty)
   }
 }
diff --git a/backend/src/main/scala/cromwell/backend/io/JobPaths.scala b/backend/src/main/scala/cromwell/backend/io/JobPaths.scala
index c9a5ac120f7..5c3a0c9f7da 100644
--- a/backend/src/main/scala/cromwell/backend/io/JobPaths.scala
+++ b/backend/src/main/scala/cromwell/backend/io/JobPaths.scala
@@ -2,8 +2,7 @@ package cromwell.backend.io
 
 import java.nio.file.Path
 
-import com.typesafe.config.Config
-import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
+import cromwell.core.JobKey
 import cromwell.services.metadata.CallMetadataKeys
 
 object JobPaths {
@@ -15,65 +14,50 @@ object JobPaths {
   val StdErrPathKey = "stderr"
   val ReturnCodePathKey = "returnCode"
   val CallRootPathKey = "callRootPath"
-}
-
-class JobPaths(workflowDescriptor: BackendWorkflowDescriptor,
-               config: Config,
-               jobKey: BackendJobDescriptorKey) extends WorkflowPaths(workflowDescriptor, config) {
-  import JobPaths._
 
-  private def callPathBuilder(root: Path) = {
-    val callName = jobKey.call.fullyQualifiedName.split('.').last
+  def callPathBuilder(root: Path, jobKey: JobKey) = {
+    val callName = jobKey.scope.unqualifiedName
     val call = s"$CallPrefix-$callName"
     val shard = jobKey.index map { s => s"$ShardPrefix-$s" } getOrElse ""
     val retry = if (jobKey.attempt > 1) s"$AttemptPrefix-${jobKey.attempt}" else ""
 
     List(call, shard, retry).foldLeft(root)((path, dir) => path.resolve(dir))
   }
+}
 
-  def toDockerPath(path: Path): Path = {
-    path.toAbsolutePath match {
-      case p if p.startsWith(WorkflowPaths.DockerRoot) => p
-      case p =>
-        /** For example:
-          *
-          * p = /abs/path/to/cromwell-executions/three-step/f00ba4/call-ps/stdout.txt
-          * localExecutionRoot = /abs/path/to/cromwell-executions
-          * subpath = three-step/f00ba4/call-ps/stdout.txt
-          *
-          * return value = /root/three-step/f00ba4/call-ps/stdout.txt
-          *
-          * TODO: this assumes that p.startsWith(localExecutionRoot)
-          */
-        val subpath = p.subpath(executionRoot.getNameCount, p.getNameCount)
-        WorkflowPaths.DockerRoot.resolve(subpath)
-    }
-  }
-
-  val callRoot = callPathBuilder(workflowRoot)
-  val callDockerRoot = callPathBuilder(dockerWorkflowRoot)
-
-  val callExecutionRoot = callRoot.resolve("execution")
-  val callExecutionDockerRoot = callDockerRoot.resolve("execution")
-
-  val callInputsRoot = callRoot.resolve("inputs")
-
-  val stdout = callExecutionRoot.resolve("stdout")
-  val stderr = callExecutionRoot.resolve("stderr")
-  val script = callExecutionRoot.resolve("script")
-  val returnCode = callExecutionRoot.resolve("rc")
+trait JobPaths { this: WorkflowPaths =>
+  import JobPaths._
 
-  lazy val metadataPaths: Map[String, Path] = Map(
+  def returnCodeFilename: String = "rc"
+  def stdoutFilename: String = "stdout"
+  def stderrFilename: String = "stderr"
+  def scriptFilename: String = "script"
+  
+  def jobKey: JobKey
+  lazy val callRoot = callPathBuilder(workflowRoot, jobKey)
+  lazy val callExecutionRoot = callRoot
+  lazy val stdout = callExecutionRoot.resolve(stdoutFilename)
+  lazy val stderr = callExecutionRoot.resolve(stderrFilename)
+  lazy val script = callExecutionRoot.resolve(scriptFilename)
+  lazy val returnCode = callExecutionRoot.resolve(returnCodeFilename)
+
+  private lazy val commonMetadataPaths: Map[String, Path] = Map(
     CallMetadataKeys.CallRoot -> callRoot,
     CallMetadataKeys.Stdout -> stdout,
     CallMetadataKeys.Stderr -> stderr
   )
 
-  lazy val detritusPaths: Map[String, Path] = Map(
+  private lazy val commonDetritusPaths: Map[String, Path] = Map(
     JobPaths.CallRootPathKey -> callRoot,
     JobPaths.ScriptPathKey -> script,
     JobPaths.StdoutPathKey -> stdout,
     JobPaths.StdErrPathKey -> stderr,
     JobPaths.ReturnCodePathKey -> returnCode
   )
+  
+  protected lazy val customMetadataPaths: Map[String, Path] = Map.empty
+  protected lazy val customDetritusPaths: Map[String, Path] = Map.empty
+  
+  lazy val metadataPaths = commonMetadataPaths ++ customMetadataPaths
+  lazy val detritusPaths = commonDetritusPaths ++ customDetritusPaths
 }
diff --git a/backend/src/main/scala/cromwell/backend/io/JobPathsWithDocker.scala b/backend/src/main/scala/cromwell/backend/io/JobPathsWithDocker.scala
new file mode 100644
index 00000000000..49c748e883e
--- /dev/null
+++ b/backend/src/main/scala/cromwell/backend/io/JobPathsWithDocker.scala
@@ -0,0 +1,39 @@
+package cromwell.backend.io
+
+import java.nio.file.Path
+
+import com.typesafe.config.Config
+import cromwell.backend.{BackendWorkflowDescriptor, BackendJobDescriptorKey}
+import cromwell.core.path.PathBuilder
+
+class JobPathsWithDocker(val jobKey: BackendJobDescriptorKey,
+                         workflowDescriptor: BackendWorkflowDescriptor,
+                         config: Config,
+                         pathBuilders: List[PathBuilder] = WorkflowPaths.DefaultPathBuilders) extends WorkflowPathsWithDocker(
+  workflowDescriptor, config, pathBuilders) with JobPaths {
+  import JobPaths._
+  
+  override lazy val callExecutionRoot = { callRoot.resolve("execution") }
+  val callDockerRoot = callPathBuilder(dockerWorkflowRoot, jobKey)
+  val callExecutionDockerRoot = callDockerRoot.resolve("execution")
+  val callInputsRoot = callRoot.resolve("inputs")
+
+  def toDockerPath(path: Path): Path = {
+    path.toAbsolutePath match {
+      case p if p.startsWith(WorkflowPathsWithDocker.DockerRoot) => p
+      case p =>
+        /* For example:
+          *
+          * p = /abs/path/to/cromwell-executions/three-step/f00ba4/call-ps/stdout.txt
+          * localExecutionRoot = /abs/path/to/cromwell-executions
+          * subpath = three-step/f00ba4/call-ps/stdout.txt
+          *
+          * return value = /root/three-step/f00ba4/call-ps/stdout.txt
+          *
+          * TODO: this assumes that p.startsWith(localExecutionRoot)
+          */
+        val subpath = p.subpath(executionRoot.getNameCount, p.getNameCount)
+        WorkflowPathsWithDocker.DockerRoot.resolve(subpath)
+    }
+  }
+}
\ No newline at end of file
diff --git a/backend/src/main/scala/cromwell/backend/io/WorkflowPaths.scala b/backend/src/main/scala/cromwell/backend/io/WorkflowPaths.scala
index 23bdae992a5..be959aec59d 100644
--- a/backend/src/main/scala/cromwell/backend/io/WorkflowPaths.scala
+++ b/backend/src/main/scala/cromwell/backend/io/WorkflowPaths.scala
@@ -1,26 +1,37 @@
 package cromwell.backend.io
 
-import java.nio.file.{FileSystem, FileSystems, Path, Paths}
+import java.nio.file.Path
 
 import com.typesafe.config.Config
 import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
-import cromwell.core.PathFactory
+import cromwell.core.WorkflowOptions.FinalCallLogsDir
+import cromwell.core.path.{DefaultPathBuilder, PathFactory}
 import net.ceedubs.ficus.Ficus._
 
-object WorkflowPaths{
-  val DockerRoot = Paths.get("/root")
-}
+import scala.util.Try
 
-class WorkflowPaths(workflowDescriptor: BackendWorkflowDescriptor, config: Config, val fileSystems: List[FileSystem] = List(FileSystems.getDefault)) extends PathFactory {
-  val executionRoot = Paths.get(config.as[Option[String]]("root").getOrElse("cromwell-executions")).toAbsolutePath
+object WorkflowPaths {
+  val DefaultPathBuilders = List(DefaultPathBuilder)
+}
 
-  private def workflowPathBuilder(root: Path) = {
-    root.resolve(workflowDescriptor.workflowNamespace.workflow.unqualifiedName)
-        .resolve(workflowDescriptor.id.toString)
+trait WorkflowPaths extends PathFactory {
+  def workflowDescriptor: BackendWorkflowDescriptor
+  def config: Config
+  
+  protected lazy val executionRootString = config.as[Option[String]]("root").getOrElse("cromwell-executions")
+  
+  def getPath(url: String): Try[Path] = Try(PathFactory.buildPath(url, pathBuilders))
+  
+  // Rebuild potential intermediate call directories in case of a sub workflow
+  protected def workflowPathBuilder(root: Path) = {
+    workflowDescriptor.breadCrumbs.foldLeft(root)((acc, breadCrumb) => {
+      breadCrumb.toPath(acc)
+    }).resolve(workflowDescriptor.workflow.unqualifiedName).resolve(workflowDescriptor.id.toString + "/")
   }
 
+  lazy val executionRoot = PathFactory.buildPath(executionRootString, pathBuilders).toAbsolutePath
   lazy val workflowRoot = workflowPathBuilder(executionRoot)
-  lazy val dockerWorkflowRoot = workflowPathBuilder(WorkflowPaths.DockerRoot)
+  lazy val finalCallLogsPath = workflowDescriptor.getWorkflowOption(FinalCallLogsDir) map getPath map { _.get }
 
-  def toJobPaths(jobKey: BackendJobDescriptorKey) = new JobPaths(workflowDescriptor, config, jobKey)
+  def toJobPaths(jobKey: BackendJobDescriptorKey): JobPaths
 }
diff --git a/backend/src/main/scala/cromwell/backend/io/WorkflowPathsBackendInitializationData.scala b/backend/src/main/scala/cromwell/backend/io/WorkflowPathsBackendInitializationData.scala
index 6ac8ba96023..b0861d6bbb1 100644
--- a/backend/src/main/scala/cromwell/backend/io/WorkflowPathsBackendInitializationData.scala
+++ b/backend/src/main/scala/cromwell/backend/io/WorkflowPathsBackendInitializationData.scala
@@ -1,8 +1,7 @@
 package cromwell.backend.io
 
-import java.nio.file.FileSystem
-
 import cromwell.backend.BackendInitializationData
+import cromwell.core.path.PathBuilder
 
 /**
   * Extension of backend initialization data that also provides a `WorkflowPaths`, and by proxy its `List[FileSystem]`.
@@ -39,7 +38,7 @@ object WorkflowPathsBackendInitializationData {
     BackendInitializationData.as[WorkflowPathsBackendInitializationData](initializationDataOption).workflowPaths
   }
 
-  def fileSystems(initializationDataOption: Option[BackendInitializationData]): List[FileSystem] = {
-    workflowPaths(initializationDataOption).fileSystems
+  def pathBuilders(initializationDataOption: Option[BackendInitializationData]): List[PathBuilder] = {
+    workflowPaths(initializationDataOption).pathBuilders
   }
 }
diff --git a/backend/src/main/scala/cromwell/backend/io/WorkflowPathsWithDocker.scala b/backend/src/main/scala/cromwell/backend/io/WorkflowPathsWithDocker.scala
new file mode 100644
index 00000000000..c10e66972fd
--- /dev/null
+++ b/backend/src/main/scala/cromwell/backend/io/WorkflowPathsWithDocker.scala
@@ -0,0 +1,16 @@
+package cromwell.backend.io
+
+import java.nio.file.Paths
+
+import com.typesafe.config.Config
+import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
+import cromwell.core.path.PathBuilder
+
+object WorkflowPathsWithDocker {
+  val DockerRoot = Paths.get("/root")
+}
+
+class WorkflowPathsWithDocker(val workflowDescriptor: BackendWorkflowDescriptor, val config: Config, val pathBuilders: List[PathBuilder] = WorkflowPaths.DefaultPathBuilders) extends WorkflowPaths {
+  val dockerWorkflowRoot = workflowPathBuilder(WorkflowPathsWithDocker.DockerRoot)
+  override def toJobPaths(jobKey: BackendJobDescriptorKey): JobPaths = new JobPathsWithDocker(jobKey, workflowDescriptor, config, pathBuilders)
+}
\ No newline at end of file
diff --git a/backend/src/main/scala/cromwell/backend/package.scala b/backend/src/main/scala/cromwell/backend/package.scala
index 3bad6f61f72..132fcf57887 100644
--- a/backend/src/main/scala/cromwell/backend/package.scala
+++ b/backend/src/main/scala/cromwell/backend/package.scala
@@ -1,14 +1,6 @@
 package cromwell
 
-import wdl4s.values.WdlValue
-
-import scala.language.postfixOps
-import scala.util.Success
-
 package object backend {
-  implicit class AugmentedAttemptedLookupSequence(s: Seq[AttemptedLookupResult]) {
-    def toLookupMap: Map[String, WdlValue] = s collect {
-      case AttemptedLookupResult(name, Success(value)) => (name, value)
-    } toMap
-  }
+  /** Represents the jobKeys executed by a (potentially sub-) workflow at a given point in time */
+  type JobExecutionMap = Map[BackendWorkflowDescriptor, List[BackendJobDescriptorKey]]
 }
diff --git a/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala b/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala
index 9e56c71be0f..1ba92527ecd 100644
--- a/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala
@@ -1,9 +1,8 @@
 package cromwell.backend.validation
 
 import cats.syntax.validated._
-import cromwell.backend.wdl.OnlyPureFunctions
+import wdl4s.expression.PureStandardLibraryFunctions
 import cromwell.backend.{MemorySize, RuntimeAttributeDefinition}
-import cromwell.core._
 import cromwell.core.ErrorOr._
 import org.slf4j.Logger
 import wdl4s.WdlExpression
@@ -336,7 +335,7 @@ trait RuntimeAttributesValidation[ValidatedType] {
         For now, if something tries to "lookup" a value, convert it to a WdlString.
          */
         val wdlStringLookup: ScopedLookupFunction = (value: String) => WdlString(value)
-        wdlExpression.evaluate(wdlStringLookup, OnlyPureFunctions) match {
+        wdlExpression.evaluate(wdlStringLookup, PureStandardLibraryFunctions) match {
           case Success(wdlValue) => validateExpression.applyOrElse(wdlValue, (_: Any) => false)
           case Failure(throwable) =>
             throw new RuntimeException(s"Expression evaluation failed due to $throwable: $wdlExpression", throwable)
diff --git a/backend/src/main/scala/cromwell/backend/wdl/Command.scala b/backend/src/main/scala/cromwell/backend/wdl/Command.scala
new file mode 100644
index 00000000000..b0e3c92947e
--- /dev/null
+++ b/backend/src/main/scala/cromwell/backend/wdl/Command.scala
@@ -0,0 +1,31 @@
+package cromwell.backend.wdl
+
+import cromwell.backend.BackendJobDescriptor
+import wdl4s.EvaluatedTaskInputs
+import wdl4s.expression.WdlFunctions
+import wdl4s.values.WdlValue
+
+import scala.util.{Success, Try}
+
+object Command {
+
+  /**
+    * Instantiate the command for this job descriptor.
+    *
+    * @param jobDescriptor jobDescriptor to instantiate the command for
+    * @param callEngineFunction engine functions to use to evaluate expressions inside the command
+    * @param inputsPreProcessor function to be applied to the task inputs before they are used to instantiate the command
+    *                   Typically this is where localization and/or file path transformation work would be done.
+    *                   The return value of the function is the inputs map that will be used to resolve variables in the command line.
+    * @param valueMapper function to apply, during instantiation of the command line, after a variable is resolved
+    * @return
+    */
+  def instantiate(jobDescriptor: BackendJobDescriptor,
+                  callEngineFunction: WdlFunctions[WdlValue],
+                  inputsPreProcessor: EvaluatedTaskInputs => Try[EvaluatedTaskInputs] = (i: EvaluatedTaskInputs) => Success(i),
+                  valueMapper: WdlValue => WdlValue = identity): Try[String] = {
+    inputsPreProcessor(jobDescriptor.inputDeclarations) flatMap { mappedInputs =>
+      jobDescriptor.call.task.instantiateCommand(mappedInputs, callEngineFunction, valueMapper)
+    }
+  }
+}
diff --git a/backend/src/main/scala/cromwell/backend/wdl/FileSystems.scala b/backend/src/main/scala/cromwell/backend/wdl/FileSystems.scala
deleted file mode 100644
index 8919b005805..00000000000
--- a/backend/src/main/scala/cromwell/backend/wdl/FileSystems.scala
+++ /dev/null
@@ -1,30 +0,0 @@
-package cromwell.backend.wdl
-
-import java.nio.file.{FileSystem, Path}
-
-import cromwell.core.PathFactory
-
-trait FileSystems extends PathFactory {
-
-  /**
-    * Ordered list of filesystems to be used to execute wdl functions needing IO.
-    */
-  def fileSystems: List[FileSystem]
-
-  /**
-    * Function applied after a string is successfully resolved to a java.nio.Path
-    */
-  def postMapping(path: Path): Path = path
-
-  /**
-    * Function applied before a string is attempted to be resolved to a java.nio.Path
-    */
-  def preMapping(string: String): String = string
-
-  /**
-    * Use fileSystems in order to try to create a java.nio.Path from path that will be used to perform IO.
-    * If no filesystem is able to construct a Path from the String, an exception will be raised.
-    */
-  protected final def toPath(path: String) = postMapping(buildPath(preMapping(path), fileSystems))
-
-}
diff --git a/backend/src/main/scala/cromwell/backend/wdl/OutputEvaluator.scala b/backend/src/main/scala/cromwell/backend/wdl/OutputEvaluator.scala
new file mode 100644
index 00000000000..ab6c66b0d89
--- /dev/null
+++ b/backend/src/main/scala/cromwell/backend/wdl/OutputEvaluator.scala
@@ -0,0 +1,19 @@
+package cromwell.backend.wdl
+
+import cromwell.backend.BackendJobDescriptor
+import cromwell.core.JobOutput
+import wdl4s.LocallyQualifiedName
+import wdl4s.expression.WdlStandardLibraryFunctions
+import wdl4s.values.WdlValue
+
+import scala.util.{Success, Try}
+
+object OutputEvaluator {
+  def evaluateOutputs(jobDescriptor: BackendJobDescriptor,
+                      wdlFunctions: WdlStandardLibraryFunctions,
+                      postMapper: WdlValue => Try[WdlValue] = v => Success(v)): Try[Map[LocallyQualifiedName, JobOutput]] = {
+    jobDescriptor.call.task.evaluateOutputs(jobDescriptor.inputDeclarations, wdlFunctions, postMapper) map { outputs =>
+      outputs mapValues JobOutput
+    }
+  }
+}
diff --git a/backend/src/main/scala/cromwell/backend/wdl/PureFunctions.scala b/backend/src/main/scala/cromwell/backend/wdl/PureFunctions.scala
deleted file mode 100644
index 9f297d47799..00000000000
--- a/backend/src/main/scala/cromwell/backend/wdl/PureFunctions.scala
+++ /dev/null
@@ -1,60 +0,0 @@
-package cromwell.backend.wdl
-
-import wdl4s.expression.WdlStandardLibraryFunctions
-import wdl4s.types.{WdlArrayType, WdlIntegerType, WdlStringType}
-import wdl4s.values.{WdlArray, WdlFile, WdlFloat, WdlInteger, WdlString, WdlValue}
-
-import scala.util.{Failure, Success, Try}
-
-case object OnlyPureFunctions extends WdlStandardLibraryFunctions with PureFunctions {
-  override def readFile(path: String): String = throw new NotImplementedError("readFile not available in PureNoFunctions.")
-  override def read_json(params: Seq[Try[WdlValue]]): Try[WdlValue] = throw new NotImplementedError("read_json not available in PureNoFunctions.")
-  override def write_json(params: Seq[Try[WdlValue]]): Try[WdlFile] = throw new NotImplementedError("write_json not available in PureNoFunctions.")
-  override def size(params: Seq[Try[WdlValue]]): Try[WdlFloat] = throw new NotImplementedError("size not available in PureNoFunctions.")
-  override def write_tsv(params: Seq[Try[WdlValue]]): Try[WdlFile] = throw new NotImplementedError("write_tsv not available in PureNoFunctions.")
-  override def stdout(params: Seq[Try[WdlValue]]): Try[WdlFile] = throw new NotImplementedError("stdout not available in PureNoFunctions.")
-  override def glob(path: String, pattern: String): Seq[String] = throw new NotImplementedError("glob not available in PureNoFunctions.")
-  override def writeTempFile(path: String, prefix: String, suffix: String, content: String): String = throw new NotImplementedError("writeTempFile not available in PureNoFunctions.")
-  override def stderr(params: Seq[Try[WdlValue]]): Try[WdlFile] = throw new NotImplementedError("stderr not available in PureNoFunctions.")
-}
-
-trait PureFunctions { this: WdlStandardLibraryFunctions =>
-
-  def range(params: Seq[Try[WdlValue]]): Try[WdlArray] = {
-    def extractAndValidateArguments = params.size match {
-      case 1 => validateArguments(params.head)
-      case n => Failure(new IllegalArgumentException(s"Invalid number of parameters for engine function seq: $n. Ensure seq(x: WdlInteger) takes exactly 1 parameters."))
-    }
-
-    def validateArguments(value: Try[WdlValue]) = value match {
-      case Success(intValue: WdlValue) if WdlIntegerType.isCoerceableFrom(intValue.wdlType) =>
-        Integer.valueOf(intValue.valueString) match {
-          case i if i >= 0 => Success(i)
-          case n => Failure(new IllegalArgumentException(s"Parameter to seq must be greater than or equal to 0 (but got $n)"))
-        }
-      case _ => Failure(new IllegalArgumentException(s"Invalid parameter for engine function seq: $value."))
-    }
-
-    extractAndValidateArguments map { intValue => WdlArray(WdlArrayType(WdlIntegerType), (0 until intValue).map(WdlInteger(_))) }
-  }
-
-  override def sub(params: Seq[Try[WdlValue]]): Try[WdlString] = {
-    def extractArguments = params.size match {
-      case 3 => Success((params.head, params(1), params(2)))
-      case n => Failure(new IllegalArgumentException(s"Invalid number of parameters for engine function sub: $n. sub takes exactly 3 parameters."))
-    }
-
-    def validateArguments(values: (Try[WdlValue], Try[WdlValue], Try[WdlValue])) = values match {
-      case (Success(strValue), Success(WdlString(pattern)), Success(replaceValue))
-        if WdlStringType.isCoerceableFrom(strValue.wdlType) &&
-          WdlStringType.isCoerceableFrom(replaceValue.wdlType) =>
-        Success((strValue.valueString, pattern, replaceValue.valueString))
-      case _ => Failure(new IllegalArgumentException(s"Invalid parameters for engine function sub: $values."))
-    }
-
-    for {
-      args <- extractArguments
-      (str, pattern, replace) <- validateArguments(args)
-    } yield WdlString(pattern.r.replaceAllIn(str, replace))
-  }
-}
diff --git a/backend/src/main/scala/cromwell/backend/wdl/ReadLikeFunctions.scala b/backend/src/main/scala/cromwell/backend/wdl/ReadLikeFunctions.scala
index 1f06e10d853..0f3e4679ee5 100644
--- a/backend/src/main/scala/cromwell/backend/wdl/ReadLikeFunctions.scala
+++ b/backend/src/main/scala/cromwell/backend/wdl/ReadLikeFunctions.scala
@@ -1,6 +1,7 @@
 package cromwell.backend.wdl
 
 import cromwell.backend.MemorySize
+import cromwell.core.path.PathFactory
 import wdl4s.expression.WdlStandardLibraryFunctions
 import wdl4s.parser.MemoryUnit
 import wdl4s.types.{WdlArrayType, WdlFileType, WdlObjectType, WdlStringType}
@@ -8,7 +9,7 @@ import wdl4s.values._
 
 import scala.util.{Failure, Success, Try}
 
-trait ReadLikeFunctions extends FileSystems { this: WdlStandardLibraryFunctions =>
+trait ReadLikeFunctions extends PathFactory { this: WdlStandardLibraryFunctions =>
   import better.files._
 
   /**
@@ -27,7 +28,7 @@ trait ReadLikeFunctions extends FileSystems { this: WdlStandardLibraryFunctions
     wdlObjects <- WdlObject.fromTsv(contents)
   } yield wdlObjects
 
-  override def readFile(path: String): String = File(toPath(path)).contentAsString
+  override def readFile(path: String): String = File(buildPath(path)).contentAsString
 
   /**
     * Read all lines from the file referenced by the first parameter and return an Array[String]
@@ -93,7 +94,7 @@ trait ReadLikeFunctions extends FileSystems { this: WdlStandardLibraryFunctions
       for {
         value <- wdlValue
         unit <- convertTo
-      } yield MemorySize(File(toPath(value.valueString)).size.toDouble, MemoryUnit.Bytes).to(unit).amount
+      } yield MemorySize(File(buildPath(value.valueString)).size.toDouble, MemoryUnit.Bytes).to(unit).amount
     }
 
     params match {
diff --git a/backend/src/main/scala/cromwell/backend/wdl/WriteFunctions.scala b/backend/src/main/scala/cromwell/backend/wdl/WriteFunctions.scala
index cb8eea297af..0f602c76e3b 100644
--- a/backend/src/main/scala/cromwell/backend/wdl/WriteFunctions.scala
+++ b/backend/src/main/scala/cromwell/backend/wdl/WriteFunctions.scala
@@ -16,21 +16,17 @@ trait WriteFunctions { this: WdlStandardLibraryFunctions =>
     */
   def writeDirectory: Path
 
-  private lazy val absoluteDirectory = {
-    File(writeDirectory).createDirectories().path
-  }
-
-  override def tempFilePath = absoluteDirectory.toString
+  private lazy val _writeDirectory = File(writeDirectory).createDirectories()
 
   def writeTempFile(path: String,prefix: String,suffix: String,content: String): String = throw new NotImplementedError("This method is not used anywhere and should be removed")
 
   private def writeContent(baseName: String, content: String): Try[WdlFile] = {
-    val fullPath = File(absoluteDirectory)./(s"$baseName${content.md5Sum}.tmp")
+    val tmpFile = _writeDirectory / s"$baseName-${content.md5Sum}.tmp"
 
     Try {
-      if (!fullPath.exists) fullPath.write(content)
+      if (tmpFile.notExists) tmpFile.write(content)
     } map { _ =>
-      WdlFile(fullPath.pathAsString)
+      WdlFile(tmpFile.uri.toString)
     }
   }
 
diff --git a/backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowFileSystemProvider.scala b/backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowFileSystemProvider.scala
deleted file mode 100644
index a10b46a0d5e..00000000000
--- a/backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowFileSystemProvider.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cromwell.backend.wfs
-
-import java.nio.file.FileSystems
-
-object DefaultWorkflowFileSystemProvider extends WorkflowFileSystemProvider {
-  override def fileSystemOption(params: WorkflowFileSystemProviderParams) = {
-    Option(FileSystems.getDefault)
-  }
-}
diff --git a/backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowPathBuilder.scala b/backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowPathBuilder.scala
new file mode 100644
index 00000000000..43af11d8732
--- /dev/null
+++ b/backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowPathBuilder.scala
@@ -0,0 +1,8 @@
+package cromwell.backend.wfs
+
+import cromwell.core.path.DefaultPathBuilder
+
+
+object DefaultWorkflowPathBuilder extends WorkflowPathBuilder {
+  override def pathBuilderOption(params: WorkflowFileSystemProviderParams) = Option(DefaultPathBuilder)
+}
diff --git a/backend/src/main/scala/cromwell/backend/wfs/WorkflowFileSystemProvider.scala b/backend/src/main/scala/cromwell/backend/wfs/WorkflowFileSystemProvider.scala
deleted file mode 100644
index de8272473ed..00000000000
--- a/backend/src/main/scala/cromwell/backend/wfs/WorkflowFileSystemProvider.scala
+++ /dev/null
@@ -1,34 +0,0 @@
-package cromwell.backend.wfs
-
-import java.nio.file.FileSystem
-
-import com.typesafe.config.{Config, ConfigFactory}
-import cromwell.backend.io.WorkflowPaths
-import cromwell.backend.{BackendConfigurationDescriptor, BackendWorkflowDescriptor}
-import cromwell.core.WorkflowOptions
-import net.ceedubs.ficus.Ficus._
-
-import scala.concurrent.ExecutionContext
-
-object WorkflowFileSystemProvider {
-  def workflowPaths(configurationDescriptor: BackendConfigurationDescriptor,
-                    workflowDescriptor: BackendWorkflowDescriptor,
-                    providers: Traversable[WorkflowFileSystemProvider],
-                    fileSystemExecutionContext: ExecutionContext): WorkflowPaths = {
-    val backendConfig = configurationDescriptor.backendConfig
-    val fileSystemConfig = backendConfig.as[Option[Config]]("filesystems").getOrElse(ConfigFactory.empty())
-    val globalConfig = configurationDescriptor.globalConfig
-    val params = WorkflowFileSystemProviderParams(fileSystemConfig, globalConfig, workflowDescriptor.workflowOptions,
-      fileSystemExecutionContext)
-    val fileSystems = providers.flatMap(_.fileSystemOption(params)).toList
-    new WorkflowPaths(workflowDescriptor, configurationDescriptor.backendConfig, fileSystems)
-  }
-}
-
-final case class WorkflowFileSystemProviderParams(fileSystemConfig: Config, globalConfig: Config,
-                                                  workflowOptions: WorkflowOptions,
-                                                  fileSystemExecutionContext: ExecutionContext)
-
-trait WorkflowFileSystemProvider {
-  def fileSystemOption(params: WorkflowFileSystemProviderParams): Option[FileSystem]
-}
diff --git a/backend/src/main/scala/cromwell/backend/wfs/WorkflowPathBuilder.scala b/backend/src/main/scala/cromwell/backend/wfs/WorkflowPathBuilder.scala
new file mode 100644
index 00000000000..bd39ae2c911
--- /dev/null
+++ b/backend/src/main/scala/cromwell/backend/wfs/WorkflowPathBuilder.scala
@@ -0,0 +1,25 @@
+package cromwell.backend.wfs
+
+import com.typesafe.config.Config
+import cromwell.backend.io.{WorkflowPathsWithDocker, WorkflowPaths}
+import cromwell.backend.{BackendConfigurationDescriptor, BackendWorkflowDescriptor}
+import cromwell.core.WorkflowOptions
+import cromwell.core.path.PathBuilder
+
+import scala.concurrent.ExecutionContext
+
+object WorkflowPathBuilder {
+  def workflowPaths(configurationDescriptor: BackendConfigurationDescriptor,
+                    workflowDescriptor: BackendWorkflowDescriptor,
+                    pathBuilders: List[PathBuilder]): WorkflowPaths = {
+    new WorkflowPathsWithDocker(workflowDescriptor, configurationDescriptor.backendConfig, pathBuilders)
+  }
+}
+
+final case class WorkflowFileSystemProviderParams(fileSystemConfig: Config, globalConfig: Config,
+                                                  workflowOptions: WorkflowOptions,
+                                                  fileSystemExecutionContext: ExecutionContext)
+
+trait WorkflowPathBuilder {
+  def pathBuilderOption(params: WorkflowFileSystemProviderParams): Option[PathBuilder]
+}
diff --git a/backend/src/test/scala/cromwell/backend/BackendSpec.scala b/backend/src/test/scala/cromwell/backend/BackendSpec.scala
index c5617ab43ed..7e2354bd515 100644
--- a/backend/src/test/scala/cromwell/backend/BackendSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/BackendSpec.scala
@@ -1,18 +1,20 @@
 package cromwell.backend
 
 import com.typesafe.config.ConfigFactory
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, FailedNonRetryableResponse, FailedRetryableResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, JobFailedNonRetryableResponse, JobFailedRetryableResponse, JobSucceededResponse}
 import cromwell.backend.io.TestWorkflows._
 import cromwell.core.{WorkflowId, WorkflowOptions}
+import wdl4s.util.AggregatedException
 import org.scalatest.Matchers
 import org.scalatest.concurrent.ScalaFutures
 import org.scalatest.time.{Millis, Seconds, Span}
+import org.specs2.mock.Mockito
 import spray.json.{JsObject, JsValue}
 import wdl4s._
 import wdl4s.expression.NoFunctions
 import wdl4s.values.WdlValue
 
-trait BackendSpec extends ScalaFutures with Matchers {
+trait BackendSpec extends ScalaFutures with Matchers with Mockito {
 
   implicit val defaultPatience = PatienceConfig(timeout = Span(5, Seconds), interval = Span(500, Millis))
 
@@ -26,32 +28,44 @@ trait BackendSpec extends ScalaFutures with Matchers {
                               runtime: String = "") = {
     BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(wdl.replaceAll("RUNTIME", runtime)),
+      WdlNamespaceWithWorkflow.load(wdl.replaceAll("RUNTIME", runtime), Seq.empty[ImportResolver]).workflow,
       inputs,
       options
     )
   }
 
+  def fqnMapToDeclarationMap(m: Map[String, WdlValue]): Map[Declaration, WdlValue] = {
+    m map {
+      case (fqn, v) =>
+        val mockDeclaration = mock[Declaration]
+        mockDeclaration.fullyQualifiedName returns fqn
+        mockDeclaration.unqualifiedName returns fqn.split('.').lastOption.getOrElse(fqn)
+        mockDeclaration -> v
+    }
+  }
+
   def jobDescriptorFromSingleCallWorkflow(workflowDescriptor: BackendWorkflowDescriptor,
                                           inputs: Map[String, WdlValue],
                                           options: WorkflowOptions,
                                           runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition]): BackendJobDescriptor = {
-    val call = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val call = workflowDescriptor.workflow.taskCalls.head
     val jobKey = BackendJobDescriptorKey(call, None, 1)
-    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(call.task.runtimeAttributes, NoFunctions, inputs).get // .get is OK here because this is a test
+    val inputDeclarations = call.evaluateTaskInputs(inputs, NoFunctions)
+    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(call.task.runtimeAttributes, NoFunctions, inputDeclarations).get // .get is OK here because this is a test
     val runtimeAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, options)(evaluatedAttributes)
-    BackendJobDescriptor(workflowDescriptor, jobKey, runtimeAttributes, inputs)
+    BackendJobDescriptor(workflowDescriptor, jobKey, runtimeAttributes, inputDeclarations)
   }
 
   def jobDescriptorFromSingleCallWorkflow(wdl: WdlSource,
                                           options: WorkflowOptions,
                                           runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition]): BackendJobDescriptor = {
     val workflowDescriptor = buildWorkflowDescriptor(wdl)
-    val call = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val call = workflowDescriptor.workflow.taskCalls.head
     val jobKey = BackendJobDescriptorKey(call, None, 1)
-    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(call.task.runtimeAttributes, NoFunctions, workflowDescriptor.inputs).get // .get is OK here because this is a test
+    val inputDeclarations = fqnMapToDeclarationMap(workflowDescriptor.inputs)
+    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(call.task.runtimeAttributes, NoFunctions, inputDeclarations).get // .get is OK here because this is a test
     val runtimeAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, options)(evaluatedAttributes)
-    BackendJobDescriptor(workflowDescriptor, jobKey, runtimeAttributes, workflowDescriptor.inputs)
+    BackendJobDescriptor(workflowDescriptor, jobKey, runtimeAttributes, inputDeclarations)
   }
 
   def jobDescriptorFromSingleCallWorkflow(wdl: WdlSource,
@@ -60,16 +74,17 @@ trait BackendSpec extends ScalaFutures with Matchers {
                                           options: WorkflowOptions,
                                           runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition]): BackendJobDescriptor = {
     val workflowDescriptor = buildWorkflowDescriptor(wdl, runtime = runtime)
-    val call = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val call = workflowDescriptor.workflow.taskCalls.head
     val jobKey = BackendJobDescriptorKey(call, None, attempt)
-    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(call.task.runtimeAttributes, NoFunctions, workflowDescriptor.inputs).get // .get is OK here because this is a test
+    val inputDeclarations = fqnMapToDeclarationMap(workflowDescriptor.inputs)
+    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(call.task.runtimeAttributes, NoFunctions, inputDeclarations).get // .get is OK here because this is a test
     val runtimeAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, options)(evaluatedAttributes)
-    BackendJobDescriptor(workflowDescriptor, jobKey, runtimeAttributes, workflowDescriptor.inputs)
+    BackendJobDescriptor(workflowDescriptor, jobKey, runtimeAttributes, inputDeclarations)
   }
 
   def assertResponse(executionResponse: BackendJobExecutionResponse, expectedResponse: BackendJobExecutionResponse) = {
     (executionResponse, expectedResponse) match {
-      case (SucceededResponse(_, _, responseOutputs, _, _), SucceededResponse(_, _, expectedOutputs, _, _)) =>
+      case (JobSucceededResponse(_, _, responseOutputs, _, _), JobSucceededResponse(_, _, expectedOutputs, _, _)) =>
         responseOutputs.size shouldBe expectedOutputs.size
         responseOutputs foreach {
           case (fqn, out) =>
@@ -77,16 +92,23 @@ trait BackendSpec extends ScalaFutures with Matchers {
             expectedOut.isDefined shouldBe true
             expectedOut.get.wdlValue.valueString shouldBe out.wdlValue.valueString
         }
-      case (FailedNonRetryableResponse(_, failure, _), FailedNonRetryableResponse(_, expectedFailure, _)) =>
+      case (JobFailedNonRetryableResponse(_, failure, _), JobFailedNonRetryableResponse(_, expectedFailure, _)) =>
         failure.getClass shouldBe expectedFailure.getClass
-        failure.getMessage should include(expectedFailure.getMessage)
-      case (FailedRetryableResponse(_, failure, _), FailedRetryableResponse(_, expectedFailure, _)) =>
+        concatenateCauseMessages(failure) should include(expectedFailure.getMessage)
+      case (JobFailedRetryableResponse(_, failure, _), JobFailedRetryableResponse(_, expectedFailure, _)) =>
         failure.getClass shouldBe expectedFailure.getClass
       case (response, expectation) =>
         fail(s"Execution response $response wasn't conform to expectation $expectation")
     }
   }
 
+  private def concatenateCauseMessages(t: Throwable): String = t match {
+    case null => ""
+    case ae: AggregatedException => ae.getMessage + ae.exceptions.map(concatenateCauseMessages(_)).mkString + concatenateCauseMessages(ae.getCause)
+    case other: Throwable => other.getMessage + concatenateCauseMessages(t.getCause)
+  }
+
+
   def executeJobAndAssertOutputs(backend: BackendJobExecutionActor, expectedResponse: BackendJobExecutionResponse) = {
     whenReady(backend.execute) { executionResponse =>
       assertResponse(executionResponse, expectedResponse)
@@ -97,13 +119,13 @@ trait BackendSpec extends ScalaFutures with Matchers {
     ConfigFactory.parseString("{}"), ConfigFactory.load())
 
   def firstJobDescriptorKey(workflowDescriptor: BackendWorkflowDescriptor): BackendJobDescriptorKey = {
-    val call = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val call = workflowDescriptor.workflow.taskCalls.head
     BackendJobDescriptorKey(call, None, 1)
   }
 
   def firstJobDescriptor(workflowDescriptor: BackendWorkflowDescriptor,
                          inputs: Map[String, WdlValue] = Map.empty) = {
-    BackendJobDescriptor(workflowDescriptor, firstJobDescriptorKey(workflowDescriptor), Map.empty, inputs)
+    BackendJobDescriptor(workflowDescriptor, firstJobDescriptorKey(workflowDescriptor), Map.empty, fqnMapToDeclarationMap(inputs))
   }
 }
 
diff --git a/backend/src/test/scala/cromwell/backend/io/JobPathsSpec.scala b/backend/src/test/scala/cromwell/backend/io/JobPathsSpec.scala
index f03ca2cf961..dffd648844f 100644
--- a/backend/src/test/scala/cromwell/backend/io/JobPathsSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/io/JobPathsSpec.scala
@@ -6,7 +6,7 @@ import better.files._
 import com.typesafe.config.ConfigFactory
 import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptorKey, BackendSpec}
 import org.scalatest.{FlatSpec, Matchers}
-import wdl4s.Call
+import wdl4s.TaskCall
 
 class JobPathsSpec extends FlatSpec with Matchers with BackendSpec {
 
@@ -32,46 +32,46 @@ class JobPathsSpec extends FlatSpec with Matchers with BackendSpec {
   "JobPaths" should "provide correct paths for a job" in {
 
     val wd = buildWorkflowDescriptor(TestWorkflows.HelloWorld)
-    val call: Call = wd.workflowNamespace.workflow.calls.head
+    val call: TaskCall = wd.workflow.taskCalls.head
     val jobKey = BackendJobDescriptorKey(call, None, 1)
-    val jobPaths = new JobPaths(wd, backendConfig, jobKey)
+    val jobPaths = new JobPathsWithDocker(jobKey, wd, backendConfig)
     val id = wd.id
     jobPaths.callRoot.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id/call-hello").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id/call-hello").pathAsString
     jobPaths.callExecutionRoot.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id/call-hello/execution").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id/call-hello/execution").pathAsString
     jobPaths.returnCode.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id/call-hello/execution/rc").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id/call-hello/execution/rc").pathAsString
     jobPaths.script.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id/call-hello/execution/script").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id/call-hello/execution/script").pathAsString
     jobPaths.stderr.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id/call-hello/execution/stderr").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id/call-hello/execution/stderr").pathAsString
     jobPaths.stdout.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id/call-hello/execution/stdout").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id/call-hello/execution/stdout").pathAsString
     jobPaths.callExecutionRoot.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id/call-hello/execution").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id/call-hello/execution").pathAsString
     jobPaths.callDockerRoot.toString shouldBe
-      File(s"/root/hello/$id/call-hello").pathAsString
+      File(s"/root/wf_hello/$id/call-hello").pathAsString
     jobPaths.callExecutionDockerRoot.toString shouldBe
-      File(s"/root/hello/$id/call-hello/execution").pathAsString
-    jobPaths.toDockerPath(Paths.get(s"local-cromwell-executions/hello/$id/call-hello/execution/stdout")).toString shouldBe
-      File(s"/root/hello/$id/call-hello/execution/stdout").pathAsString
+      File(s"/root/wf_hello/$id/call-hello/execution").pathAsString
+    jobPaths.toDockerPath(Paths.get(s"local-cromwell-executions/wf_hello/$id/call-hello/execution/stdout")).toString shouldBe
+      File(s"/root/wf_hello/$id/call-hello/execution/stdout").pathAsString
     jobPaths.toDockerPath(Paths.get("/root/dock/path")).toString shouldBe
       File("/root/dock/path").pathAsString
 
     val jobKeySharded = BackendJobDescriptorKey(call, Option(0), 1)
-    val jobPathsSharded = new JobPaths(wd, backendConfig, jobKeySharded)
+    val jobPathsSharded = new JobPathsWithDocker(jobKeySharded, wd, backendConfig)
     jobPathsSharded.callExecutionRoot.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id/call-hello/shard-0/execution").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id/call-hello/shard-0/execution").pathAsString
 
     val jobKeyAttempt = BackendJobDescriptorKey(call, None, 2)
-    val jobPathsAttempt = new JobPaths(wd, backendConfig, jobKeyAttempt)
+    val jobPathsAttempt = new JobPathsWithDocker(jobKeyAttempt, wd, backendConfig)
     jobPathsAttempt.callExecutionRoot.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id/call-hello/attempt-2/execution").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id/call-hello/attempt-2/execution").pathAsString
 
     val jobKeyShardedAttempt = BackendJobDescriptorKey(call, Option(0), 2)
-    val jobPathsShardedAttempt = new JobPaths(wd, backendConfig, jobKeyShardedAttempt)
+    val jobPathsShardedAttempt = new JobPathsWithDocker(jobKeyShardedAttempt, wd, backendConfig)
     jobPathsShardedAttempt.callExecutionRoot.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id/call-hello/shard-0/attempt-2/execution").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id/call-hello/shard-0/attempt-2/execution").pathAsString
   }
 }
diff --git a/backend/src/test/scala/cromwell/backend/io/TestWorkflows.scala b/backend/src/test/scala/cromwell/backend/io/TestWorkflows.scala
index 34497e2ef0b..28d35977d69 100644
--- a/backend/src/test/scala/cromwell/backend/io/TestWorkflows.scala
+++ b/backend/src/test/scala/cromwell/backend/io/TestWorkflows.scala
@@ -23,7 +23,7 @@ object TestWorkflows {
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
@@ -39,7 +39,7 @@ object TestWorkflows {
       |  }
       |}
       |
-      |workflow goodbye {
+      |workflow wf_goodbye {
       |  call goodbye
       |}
     """.stripMargin
@@ -61,7 +61,7 @@ object TestWorkflows {
       |  RUNTIME
       |}
       |
-      |workflow localize {
+      |workflow wf_localize {
       |  File workflowFile
       |  call localize { input: inputFileFromCallInputs = workflowFile }
       |}
@@ -76,7 +76,7 @@ object TestWorkflows {
       |  }
       |}
       |
-      |workflow abort {
+      |workflow wf_abort {
       |  call abort
       |}
     """.stripMargin
@@ -93,7 +93,7 @@ object TestWorkflows {
       |  }
       |}
       |
-      |workflow scattering {
+      |workflow wf_scattering {
       |  Array[Int] numbers = [1, 2, 3]
       |  scatter (i in numbers) {
       |     call scattering { input: intNumber = i }
@@ -117,7 +117,7 @@ object TestWorkflows {
       |  }
       |}
       |
-      |workflow localize {
+      |workflow wf_localize {
       |  call localize
       |}
     """.stripMargin
@@ -133,7 +133,7 @@ object TestWorkflows {
       |  }
       |}
       |
-      |workflow localize {
+      |workflow wf_localize {
       |  call localize
       |}
     """.stripMargin
diff --git a/backend/src/test/scala/cromwell/backend/io/WorkflowPathsSpec.scala b/backend/src/test/scala/cromwell/backend/io/WorkflowPathsSpec.scala
index bfae5930da3..36d774bf0b4 100644
--- a/backend/src/test/scala/cromwell/backend/io/WorkflowPathsSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/io/WorkflowPathsSpec.scala
@@ -2,13 +2,13 @@ package cromwell.backend.io
 
 import better.files._
 import com.typesafe.config.Config
-import cromwell.backend.BackendSpec
-import org.mockito.Matchers._
+import cromwell.backend.{BackendJobBreadCrumb, BackendSpec, BackendWorkflowDescriptor}
+import cromwell.core.{JobKey, WorkflowId}
 import org.mockito.Mockito._
-import org.scalatest.mockito.MockitoSugar
 import org.scalatest.{FlatSpec, Matchers}
+import wdl4s.{Call, Workflow}
 
-class WorkflowPathsSpec extends FlatSpec with Matchers with BackendSpec with MockitoSugar {
+class WorkflowPathsSpec extends FlatSpec with Matchers with BackendSpec {
 
   val backendConfig = mock[Config]
 
@@ -16,11 +16,49 @@ class WorkflowPathsSpec extends FlatSpec with Matchers with BackendSpec with Moc
     when(backendConfig.hasPath(any[String])).thenReturn(true)
     when(backendConfig.getString(any[String])).thenReturn("local-cromwell-executions") // This is the folder defined in the config as the execution root dir
     val wd = buildWorkflowDescriptor(TestWorkflows.HelloWorld)
-    val workflowPaths = new WorkflowPaths(wd, backendConfig)
+    val workflowPaths = new WorkflowPathsWithDocker(wd, backendConfig)
     val id = wd.id
     workflowPaths.workflowRoot.toString shouldBe
-      File(s"local-cromwell-executions/hello/$id").pathAsString
+      File(s"local-cromwell-executions/wf_hello/$id").pathAsString
     workflowPaths.dockerWorkflowRoot.toString shouldBe
-      s"/root/hello/$id"
+      s"/root/wf_hello/$id"
+  }
+
+  "WorkflowPaths" should "provide correct paths for a sub workflow" in {
+    when(backendConfig.hasPath(any[String])).thenReturn(true)
+    when(backendConfig.getString(any[String])).thenReturn("local-cromwell-executions") // This is the folder defined in the config as the execution root dir
+    
+    val rootWd = mock[BackendWorkflowDescriptor]
+    val rootWorkflow = mock[Workflow]
+    val rootWorkflowId = WorkflowId.randomId()
+    rootWorkflow.unqualifiedName returns "rootWorkflow"
+    rootWd.workflow returns rootWorkflow
+    rootWd.id returns rootWorkflowId
+
+    val subWd = mock[BackendWorkflowDescriptor]
+    val subWorkflow = mock[Workflow]
+    val subWorkflowId = WorkflowId.randomId()
+    subWorkflow.unqualifiedName returns "subWorkflow"
+    subWd.workflow returns subWorkflow
+    subWd.id returns subWorkflowId
+    
+    val call1 = mock[Call]
+    call1.unqualifiedName returns "call1"
+    val call2 = mock[Call]
+    call2.unqualifiedName returns "call2"
+    
+    val jobKey = new JobKey {
+      override def scope = call1
+      override def tag: String = "tag1"
+      override def index: Option[Int] = Option(1)
+      override def attempt: Int = 2
+    }
+
+    subWd.breadCrumbs returns List(BackendJobBreadCrumb(rootWorkflow, rootWorkflowId, jobKey))
+    subWd.id returns subWorkflowId
+    
+    val workflowPaths = new WorkflowPathsWithDocker(subWd, backendConfig)
+    workflowPaths.workflowRoot.toString shouldBe File(s"local-cromwell-executions/rootWorkflow/$rootWorkflowId/call-call1/shard-1/attempt-2/subWorkflow/$subWorkflowId").pathAsString
+    workflowPaths.dockerWorkflowRoot.toString shouldBe s"/root/rootWorkflow/$rootWorkflowId/call-call1/shard-1/attempt-2/subWorkflow/$subWorkflowId"
   }
 }
diff --git a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesDefaultSpec.scala b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesDefaultSpec.scala
index d1df9d79063..325f874b86d 100644
--- a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesDefaultSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesDefaultSpec.scala
@@ -80,7 +80,7 @@ class RuntimeAttributesDefaultSpec extends FlatSpec with Matchers {
 
     val defaults = workflowOptionsDefault(workflowOptions, coercionMap)
     defaults.isFailure shouldBe true
-    defaults.failed.get.getMessage shouldBe s"Could not parse JsonValue ${map("str")} to valid WdlValue for runtime attribute str"
+    defaults.failed.get.getMessage shouldBe s": RuntimeException: Could not parse JsonValue ${map("str")} to valid WdlValue for runtime attribute str"
   }
 
   it should "fold default values" in {
diff --git a/backend/src/test/scala/cromwell/backend/wdl/PureStandardLibraryFunctionsSpec.scala b/backend/src/test/scala/cromwell/backend/wdl/PureStandardLibraryFunctionsSpec.scala
new file mode 100644
index 00000000000..fb650737784
--- /dev/null
+++ b/backend/src/test/scala/cromwell/backend/wdl/PureStandardLibraryFunctionsSpec.scala
@@ -0,0 +1,30 @@
+package cromwell.backend.wdl
+
+import org.scalatest.{FlatSpec, Matchers}
+import wdl4s.expression.PureStandardLibraryFunctions
+import wdl4s.types.{WdlArrayType, WdlIntegerType}
+import wdl4s.values.{WdlArray, WdlInteger}
+
+import scala.util.Success
+
+
+class PureStandardLibraryFunctionsSpec extends FlatSpec with Matchers {
+
+  behavior of "transpose"
+
+  it should "transpose a 2x3 into a 3x2" in {
+    val inArray = WdlArray(WdlArrayType(WdlArrayType(WdlIntegerType)), List(
+      WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(1), WdlInteger(2), WdlInteger(3))),
+      WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(4), WdlInteger(5), WdlInteger(6)))
+    ))
+
+    val expectedResult = WdlArray(WdlArrayType(WdlArrayType(WdlIntegerType)), List(
+      WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(1), WdlInteger(4))),
+      WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(2), WdlInteger(5))),
+      WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(3), WdlInteger(6)))
+    ))
+
+    PureStandardLibraryFunctions.transpose(Seq(Success(inArray))) should be(Success(expectedResult))
+  }
+
+}
diff --git a/build.sbt b/build.sbt
index 8e666691fc6..bfaae97731e 100644
--- a/build.sbt
+++ b/build.sbt
@@ -9,6 +9,7 @@ lazy val gcsFileSystem = (project in file("filesystems/gcs"))
   .settings(gcsFileSystemSettings:_*)
   .withTestSettings
   .dependsOn(core)
+  .dependsOn(core % "test->test")
 
 lazy val databaseSql = (project in file("database/sql"))
   .settings(databaseSqlSettings:_*)
diff --git a/core/src/main/resources/logback.xml b/core/src/main/resources/logback.xml
new file mode 100644
index 00000000000..e165bc8b2a2
--- /dev/null
+++ b/core/src/main/resources/logback.xml
@@ -0,0 +1,88 @@
+<configuration>
+
+    <!-- default properties for FILEROLLER need to be set upfront -->
+
+    <if condition='property("FILEROLLER_DIR").equals("")'>
+     <then><property name="FILEROLLER_DIR" value="/var/log/cromwell" /></then>
+    </if>
+
+    <if condition='property("FILEROLLER_MAXHISTORY").equals("")'>
+     <then> <property name="FILEROLLER_MAXHISTORY" value="30" /> </then>
+    </if>
+
+    <if condition='property("FILEROLLER_NAME").equals("")'>
+     <then> <property name="FILEROLLER_NAME" value="cromwell.log" /> </then>
+    </if>
+
+  <if condition='property("LOG_MODE").toUpperCase().equals("STANDARD")'>
+    <then>
+      <appender name="STANDARD_APPENDER" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder>
+          <pattern>%date %X{sourceThread} %-5level - %msg%n</pattern>
+        </encoder>
+      </appender>
+    </then>
+    <else>
+      <appender name="STANDARD_APPENDER" class="ch.qos.logback.core.helpers.NOPAppender" />
+    </else>
+  </if>
+
+  <if condition='property("LOG_MODE").toUpperCase().equals("PRETTY")'>
+    <then>
+      <appender name="PRETTY_APPENDER" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder class="ch.qos.logback.core.encoder.LayoutWrappingEncoder">
+          <layout class="cromwell.logging.TerminalLayout" />
+        </encoder>
+      </appender>
+      <logger name="liquibase" level="WARN"/>
+    </then>
+    <else>
+      <appender name="PRETTY_APPENDER" class="ch.qos.logback.core.helpers.NOPAppender" />
+    </else>
+  </if>
+
+  <if condition='property("LOG_MODE").toUpperCase().equals("FILEROLLER")'>
+    <then>
+      <appender name="FILEROLLER_APPENDER" class="ch.qos.logback.core.rolling.RollingFileAppender">
+
+      <file>${FILEROLLER_DIR}/${FILEROLLER_NAME}</file>
+
+      <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
+
+      <if condition='isDefined("FILEROLLER_NAMEPATTERN")'>
+      <then>
+        <fileNamePattern>${FILEROLLER_DIR}/${FILEROLLER_NAMEPATTERN}-${FILEROLLER_NAME}</fileNamePattern>
+      </then>
+      <else>
+         <fileNamePattern>${FILEROLLER_DIR}/%d{yyyyMMdd}-${FILEROLLER_NAME}</fileNamePattern>
+      </else>
+      </if>
+
+      <maxHistory>${FILEROLLER_MAXHISTORY}</maxHistory>
+
+      <if condition='isDefined("FILEROLLER_SIZECAP")'>
+      <then>
+         <totalSizeCap>${FILEROLLER_SIZECAP}</totalSizeCap>
+      </then>
+      </if>
+
+      </rollingPolicy>
+      <encoder>
+        <pattern>%d{yyyy-MM-dd HH:mm:ss,SSS} [%thread] %-5level %logger{35} - %msg%n</pattern>
+      </encoder>
+      </appender>
+    </then>
+    <else>
+      <appender name="FILEROLLER_APPENDER" class="ch.qos.logback.core.helpers.NOPAppender" />
+    </else>
+  </if>
+
+  <root level="${LOG_LEVEL}">
+    <appender-ref ref="STANDARD_APPENDER" />
+    <appender-ref ref="PRETTY_APPENDER" />
+    <appender-ref ref="FILEROLLER_APPENDER" />
+  </root>
+  <logger name="com.zaxxer.hikari" level="ERROR"/>
+  <logger name="HikariPool" level="ERROR"/>
+  <logger name="com.google.cloud.hadoop.gcsio.GoogleCloudStorageReadChannel" level="ERROR"/>
+</configuration>
diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index 9bf2807eaaa..52df9e77121 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -56,7 +56,7 @@ akka {
 
 system {
   # If 'true', a SIGINT will trigger Cromwell to attempt to abort all currently running jobs before exiting
-  abort-jobs-on-terminate = false
+  #abort-jobs-on-terminate = false
 
   # Max number of retries per job that the engine will attempt in case of a retryable failure received from the backend
   max-retries = 10
@@ -97,7 +97,14 @@ workflow-options {
 
 // Optional call-caching configuration.
 call-caching {
+  # Allows re-use of existing results for jobs you've already run
+  # (default: false)
   enabled = false
+
+  # Whether to invalidate a cache result forever if we cannot reuse them. Disable this if you expect some cache copies
+  # to fail for external reasons which should not invalidate the cache (e.g. auth differences between users):
+  # (default: true)
+  invalidate-bad-cache-results = true
 }
 
 google {
@@ -149,7 +156,7 @@ backend {
         run-in-background = true
         runtime-attributes = "String? docker"
         submit = "/bin/bash ${script}"
-        submit-docker = "docker run --rm -v ${cwd}:${docker_cwd} -i ${docker} /bin/bash < ${script}"
+        submit-docker = "docker run --rm -v ${cwd}:${docker_cwd} -i ${docker} /bin/bash ${docker_cwd}/execution/script"
 
         # Root directory where Cromwell writes job results.  This directory must be
         # visible and writeable by the Cromwell process as well as the jobs that Cromwell
@@ -163,6 +170,7 @@ backend {
             ]
 
             caching {
+              # When copying a cached result, what type of file duplication should occur. Attempted in the order listed below:
               duplication-strategy: [
                 "hard-link", "soft-link", "copy"
               ]
@@ -251,7 +259,7 @@ backend {
     #    #6. Job command.
     #    docker {
     #      #Allow soft links in dockerized jobs
-    #      cmd = "docker run -w %s %s %s %s --rm %s %s"
+    #      cmd = "docker run -w %s %s %s %s --rm %s /bin/bash -c \"%s\""
     #      defaultWorkingDir = "/workingDir/"
     #      defaultOutputDir = "/output/"
     #    }
@@ -311,6 +319,15 @@ backend {
     #    # Base bucket for workflow executions
     #    root = "gs://my-cromwell-workflows-bucket"
     #
+    #    # Set this to the lower of the two values "Queries per 100 seconds" and "Queries per 100 seconds per user" for
+    #    # your project.
+    #    #
+    #    # Used to help determine maximum throughput to the Google Genomics API. Setting this value too low will
+    #    # cause a drop in performance. Setting this value too high will cause QPS based locks from Google.
+    #    # 1000 is the default "Queries per 100 seconds per user", 50000 is the default "Queries per 100 seconds"
+    #    # See https://cloud.google.com/genomics/quotas for more information
+    #    genomics-api-queries-per-100-seconds = 1000
+    #
     #    # Polling for completion backs-off gradually for slower-running jobs.
     #    # This is the maximum polling interval (in seconds):
     #    maximum-polling-interval = 600
@@ -325,6 +342,12 @@ backend {
     #      # A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
     #      # Pipelines and manipulate auth JSONs.
     #      auth = "application-default"
+    #
+    #      // alternative service account to use on the launched compute instance
+    #      // NOTE: If combined with service account authorization, both that serivce account and this service account
+    #      // must be able to read and write to the 'root' GCS path
+    #      compute-service-account = "default"
+    #
     #      # Endpoint for APIs, no reason to change this unless directed by Google.
     #      endpoint-url = "https://genomics.googleapis.com/"
     #    }
@@ -338,6 +361,15 @@ backend {
     #  }
     #}
 
+    #AWS {
+    #  actor-factory = "cromwell.backend.impl.aws.AwsBackendActorFactory"
+    #  config {
+    #    ## These two settings are required to authenticate with the ECS service:
+    #    accessKeyId = "..."
+    #    secretKey = "..."
+    #  }
+    #}
+
   }
 }
 
diff --git a/core/src/main/scala/cromwell/core/CallKey.scala b/core/src/main/scala/cromwell/core/CallKey.scala
new file mode 100644
index 00000000000..547eadabde3
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/CallKey.scala
@@ -0,0 +1,7 @@
+package cromwell.core
+
+import wdl4s.Call
+
+trait CallKey extends JobKey {
+  def scope: Call
+}
diff --git a/core/src/main/scala/cromwell/core/ExecutionStatus.scala b/core/src/main/scala/cromwell/core/ExecutionStatus.scala
index 76acb29a4a9..353b44d65a4 100644
--- a/core/src/main/scala/cromwell/core/ExecutionStatus.scala
+++ b/core/src/main/scala/cromwell/core/ExecutionStatus.scala
@@ -2,7 +2,7 @@ package cromwell.core
 
 object ExecutionStatus extends Enumeration {
   type ExecutionStatus = Value
-  val NotStarted, Starting, Running, Failed, Preempted, Done, Aborted = Value
+  val NotStarted, QueuedInCromwell, Starting, Running, Failed, Preempted, Done, Aborted = Value
   val TerminalStatuses = Set(Failed, Done, Aborted, Preempted)
 
   implicit class EnhancedExecutionStatus(val status: ExecutionStatus) extends AnyVal {
diff --git a/core/src/main/scala/cromwell/core/ExecutionStore.scala b/core/src/main/scala/cromwell/core/ExecutionStore.scala
deleted file mode 100644
index 1632061ce3b..00000000000
--- a/core/src/main/scala/cromwell/core/ExecutionStore.scala
+++ /dev/null
@@ -1,13 +0,0 @@
-package cromwell.core
-
-import cromwell.core.ExecutionStatus._
-
-
-object ExecutionStore {
-  def empty = ExecutionStore(Map.empty)
-  type ExecutionStoreEntry = (JobKey, ExecutionStatus)
-}
-
-case class ExecutionStore(store: Map[JobKey, ExecutionStatus]) {
-  def add(values: Map[JobKey, ExecutionStatus]) = this.copy(store = store ++ values)
-}
diff --git a/core/src/main/scala/cromwell/core/JobKey.scala b/core/src/main/scala/cromwell/core/JobKey.scala
index 374e3d0ebc0..9fd22b31ec4 100644
--- a/core/src/main/scala/cromwell/core/JobKey.scala
+++ b/core/src/main/scala/cromwell/core/JobKey.scala
@@ -1,9 +1,9 @@
 package cromwell.core
 
-import wdl4s.Scope
+import wdl4s.{GraphNode, Scope}
 
 trait JobKey {
-  def scope: Scope
+  def scope: Scope with GraphNode
   def index: Option[Int]
   def attempt: Int
   def tag: String
@@ -12,4 +12,6 @@ trait JobKey {
     import ExecutionIndex.IndexEnhancedIndex
     s"${scope.fullyQualifiedName}:${index.fromIndex}:$attempt"
   }
+  
+ def isShard = index.isDefined
 }
diff --git a/core/src/main/scala/cromwell/core/OutputStore.scala b/core/src/main/scala/cromwell/core/OutputStore.scala
deleted file mode 100644
index 38bee68db7b..00000000000
--- a/core/src/main/scala/cromwell/core/OutputStore.scala
+++ /dev/null
@@ -1,40 +0,0 @@
-package cromwell.core
-
-import cromwell.core.ExecutionIndex._
-import cromwell.core.OutputStore.{OutputCallKey, OutputEntry}
-import wdl4s.types.WdlType
-import wdl4s.util.TryUtil
-import wdl4s.values.{WdlCallOutputsObject, WdlValue}
-import wdl4s.{Call, Scope}
-
-import scala.language.postfixOps
-import scala.util.{Failure, Success, Try}
-
-object OutputStore {
-  case class OutputEntry(name: String, wdlType: WdlType, wdlValue: Option[WdlValue])
-  case class OutputCallKey(call: Scope, index: ExecutionIndex)
-  def empty = OutputStore(Map.empty)
-}
-
-case class OutputStore(store: Map[OutputCallKey, Traversable[OutputEntry]]) {
-  def add(values: Map[OutputCallKey, Traversable[OutputEntry]]) = this.copy(store = store ++ values)
-
-  def fetchCallOutputEntries(call: Call, index: ExecutionIndex): Try[WdlCallOutputsObject] = {
-    def outputEntriesToMap(outputs: Traversable[OutputEntry]): Map[String, Try[WdlValue]] = {
-      outputs map { output =>
-        output.wdlValue match {
-          case Some(wdlValue) => output.name -> Success(wdlValue)
-          case None => output.name -> Failure(new RuntimeException(s"Could not retrieve output ${output.name} value"))
-        }
-      } toMap
-    }
-
-    store.get(OutputCallKey(call, index)) match {
-      case Some(outputs) =>
-        TryUtil.sequenceMap(outputEntriesToMap(outputs), s"Output fetching for call ${call.unqualifiedName}") map { outputsMap =>
-          WdlCallOutputsObject(call, outputsMap)
-        }
-      case None => Failure(new RuntimeException(s"Could not find call ${call.unqualifiedName}"))
-    }
-  }
-}
diff --git a/core/src/main/scala/cromwell/core/PathFactory.scala b/core/src/main/scala/cromwell/core/PathFactory.scala
deleted file mode 100644
index f85a05c958f..00000000000
--- a/core/src/main/scala/cromwell/core/PathFactory.scala
+++ /dev/null
@@ -1,135 +0,0 @@
-package cromwell.core
-
-import java.io.Writer
-import java.nio.file.{FileSystem, Path}
-
-import better.files.File
-
-import scala.collection.immutable.Queue
-import scala.util.{Success, Failure, Try}
-
-class FileSystemNotFound(str: String) extends CromwellFatalException(
-  new IllegalArgumentException(s"Could not find suitable filesystem to parse $str")
-)
-
-trait PathFactory {
-  private val schemeMatcher = """([a-z]+://).*""".r
-
-  def findFileSystem(rawString: String, fss: List[FileSystem], mapping: PartialFunction[FileSystem, Try[Path]]) = {
-    fss.toStream collect mapping collectFirst { case Success(p) => p } getOrElse {
-      throw new FileSystemNotFound(rawString)
-    }
-  }
-
-  def buildPath(rawString: String, fileSystems: List[FileSystem]): Path = {
-    findFileSystem(rawString, fileSystems, {
-      case fs: FileSystem =>
-        if (hasWrongScheme(rawString, fs)) {
-          Failure(new IllegalArgumentException(s"$rawString scheme doesn't match ${fs.provider.getScheme}"))
-        } else {
-          Try(fs.getPath(rawString))
-        }
-    })
-  }
-
-  def buildFile(rawString: String, fileSystems: List[FileSystem]): File = File(buildPath(rawString, fileSystems))
-
-  private def hasWrongScheme(rawString: String, fileSystem: FileSystem): Boolean = {
-    schemeMatcher.findFirstMatchIn(rawString) match {
-      case Some(m) => m.group(1) != fileSystem.provider().getScheme
-      case _ => false
-    }
-  }
-}
-
-object PathFactory {
-  def swapExt(filePath: String, oldExt: String, newExt: String): String = {
-    filePath.stripSuffix(oldExt) + newExt
-  }
-
-  implicit class EnhancedPath(val path: Path) extends AnyVal {
-    def swapExt(oldExt: String, newExt: String): Path = {
-      path.getFileSystem.getPath(s"${path.toString.stripSuffix(oldExt)}$newExt")
-    }
-
-    def untailed = UntailedWriter(path)
-
-    def tailed(tailedSize: Int) = TailedWriter(path, tailedSize)
-  }
-
-  implicit class FlushingAndClosingWriter(writer: Writer) {
-    /** Convenience method to flush and close in one shot. */
-    def flushAndClose() = {
-      writer.flush()
-      writer.close()
-    }
-  }
-}
-
-/**
-  * Used with a `ProcessLogger`, writes lines with a newline.
-  */
-trait PathWriter {
-  import better.files._
-
-  val path: Path
-  lazy val writer: Writer = File(path).newBufferedWriter
-
-  /**
-    * Passed to `ProcessLogger` to add a new line.
-    *
-    * @param string Line to add to the logs.
-    */
-  def writeWithNewline(string: String): Unit = {
-    writer.write(string)
-    writer.write("\n")
-  }
-}
-
-/**
-  * Used with a `ProcessLogger`, writes lines with a newline.
-  *
-  * @param path Path to the log file.
-  */
-case class UntailedWriter(path: Path) extends PathWriter
-
-/**
-  * Used with a `ProcessLogger`, queues up the `tailedSize` number of lines.
-  *
-  * @param path Path to the log file.
-  * @param tailedSize Maximum number of lines to save in the internal FIFO queue.
-  */
-case class TailedWriter(path: Path, tailedSize: Int) extends PathWriter {
-  private var isTailed = false
-  private var tailedLines: Queue[String] = Queue.empty
-
-  /**
-    * Passed to `ProcessLogger` to add a new line, and adds the line to the tailed queue.
-    *
-    * @param string Line to add to the logs.
-    */
-  override def writeWithNewline(string: String): Unit = {
-    tailedLines :+= string
-    while (tailedLines.size > tailedSize) {
-      tailedLines = tailedLines.takeRight(tailedSize)
-      isTailed = true
-    }
-    super.writeWithNewline(string)
-  }
-
-  /**
-    * Returns a descriptive tail of the `path` and the last `tailedLines` written.
-    *
-    * @return a descriptive tail of the `path` and the last `tailedLines` written.
-    */
-  def tailString: String = {
-    if (tailedLines.isEmpty) {
-      s"Contents of $path were empty."
-    } else if (isTailed) {
-      s"Last ${tailedLines.size} of $path:\n${tailedLines.mkString("\n")}"
-    } else {
-      s"Contents of $path:\n${tailedLines.mkString("\n")}"
-    }
-  }
-}
-
diff --git a/core/src/main/scala/cromwell/core/WorkflowMetadataKeys.scala b/core/src/main/scala/cromwell/core/WorkflowMetadataKeys.scala
index 80ade0a4da3..922be7ffbc0 100644
--- a/core/src/main/scala/cromwell/core/WorkflowMetadataKeys.scala
+++ b/core/src/main/scala/cromwell/core/WorkflowMetadataKeys.scala
@@ -13,9 +13,11 @@ object WorkflowMetadataKeys {
   val WorkflowLog = "workflowLog"
   val Failures = "failures"
   val WorkflowRoot = "workflowRoot"
+  val ParentWorkflowId = "parentWorkflowId"
 
   val SubmissionSection = "submittedFiles"
   val SubmissionSection_Workflow = "workflow"
   val SubmissionSection_Inputs = "inputs"
   val SubmissionSection_Options = "options"
+  val SubmissionSection_Imports = "imports"
 }
diff --git a/core/src/main/scala/cromwell/core/WorkflowSourceFiles.scala b/core/src/main/scala/cromwell/core/WorkflowSourceFiles.scala
deleted file mode 100644
index ed03f1733d4..00000000000
--- a/core/src/main/scala/cromwell/core/WorkflowSourceFiles.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cromwell.core
-
-import wdl4s.{WdlJson, WdlSource}
-
-/**
-  * Represents the collection of source files that a user submits to run a workflow
-  */
-final case class WorkflowSourceFiles(wdlSource: WdlSource, inputsJson: WdlJson,
-                                     workflowOptionsJson: WorkflowOptionsJson)
diff --git a/core/src/main/scala/cromwell/core/WorkflowSourceFilesCollection.scala b/core/src/main/scala/cromwell/core/WorkflowSourceFilesCollection.scala
new file mode 100644
index 00000000000..ac7a7d6aaa4
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/WorkflowSourceFilesCollection.scala
@@ -0,0 +1,43 @@
+package cromwell.core
+
+import wdl4s.{WdlJson, WdlSource}
+
+/**
+  * Represents the collection of source files that a user submits to run a workflow
+  */
+
+sealed trait WorkflowSourceFilesCollection {
+  def wdlSource: WdlSource
+  def inputsJson: WdlJson
+  def workflowOptionsJson: WorkflowOptionsJson
+  def importsZipFileOption: Option[Array[Byte]] = this match {
+    case _: WorkflowSourceFilesWithoutImports => None
+    case WorkflowSourceFilesWithDependenciesZip(_, _, _, importsZip) => Option(importsZip) // i.e. Some(importsZip) if our wiring is correct
+  }
+
+  def copyOptions(workflowOptions: WorkflowOptionsJson) = this match {
+    case w: WorkflowSourceFilesWithoutImports => WorkflowSourceFilesWithoutImports(w.wdlSource, w.inputsJson, workflowOptions)
+    case w: WorkflowSourceFilesWithDependenciesZip => WorkflowSourceFilesWithDependenciesZip(w.wdlSource, w.inputsJson, workflowOptions, w.importsZip)
+  }
+}
+
+object WorkflowSourceFilesCollection {
+  def apply(wdlSource: WdlSource,
+            inputsJson: WdlJson,
+            workflowOptionsJson: WorkflowOptionsJson,
+            importsFile: Option[Array[Byte]]): WorkflowSourceFilesCollection = importsFile match {
+    case Some(imports) => WorkflowSourceFilesWithDependenciesZip(wdlSource, inputsJson, workflowOptionsJson, imports)
+    case None => WorkflowSourceFilesWithoutImports(wdlSource, inputsJson, workflowOptionsJson)
+  }
+}
+
+final case class WorkflowSourceFilesWithoutImports(wdlSource: WdlSource,
+                                                   inputsJson: WdlJson,
+                                                   workflowOptionsJson: WorkflowOptionsJson) extends WorkflowSourceFilesCollection
+
+final case class WorkflowSourceFilesWithDependenciesZip(wdlSource: WdlSource,
+                                                        inputsJson: WdlJson,
+                                                        workflowOptionsJson: WorkflowOptionsJson,
+                                                        importsZip: Array[Byte]) extends WorkflowSourceFilesCollection {
+  override def toString = s"WorkflowSourceFilesWithDependenciesZip($wdlSource, $inputsJson, $workflowOptionsJson, <<ZIP BINARY CONTENT>>)"
+}
diff --git a/core/src/main/scala/cromwell/core/callcaching/CallCachingMode.scala b/core/src/main/scala/cromwell/core/callcaching/CallCachingMode.scala
index df9fb679ae0..ed939d6aaff 100644
--- a/core/src/main/scala/cromwell/core/callcaching/CallCachingMode.scala
+++ b/core/src/main/scala/cromwell/core/callcaching/CallCachingMode.scala
@@ -19,7 +19,7 @@ case object CallCachingOff extends CallCachingMode {
   override val withoutWrite = this
 }
 
-case class CallCachingActivity(readWriteMode: ReadWriteMode) extends CallCachingMode {
+case class CallCachingActivity(readWriteMode: ReadWriteMode, options: CallCachingOptions = CallCachingOptions(invalidateBadCacheResults = true)) extends CallCachingMode {
   override val readFromCache = readWriteMode.r
   override val writeToCache = readWriteMode.w
   override lazy val withoutRead: CallCachingMode = if (!writeToCache) CallCachingOff else this.copy(readWriteMode = WriteCache)
@@ -35,6 +35,4 @@ case object ReadCache extends ReadWriteMode { override val w = false }
 case object WriteCache extends ReadWriteMode { override val r = false }
 case object ReadAndWriteCache extends ReadWriteMode
 
-sealed trait DockerHashingType
-case object HashDockerName extends DockerHashingType
-case object HashDockerNameAndLookupDockerHash extends DockerHashingType
+final case class CallCachingOptions(invalidateBadCacheResults: Boolean = true)
diff --git a/core/src/main/scala/cromwell/core/logging/JobLogger.scala b/core/src/main/scala/cromwell/core/logging/JobLogger.scala
index 3eb96d4b5d0..1388f5f6b91 100644
--- a/core/src/main/scala/cromwell/core/logging/JobLogger.scala
+++ b/core/src/main/scala/cromwell/core/logging/JobLogger.scala
@@ -9,7 +9,7 @@ trait JobLogging extends ActorLogging { this: Actor =>
   def workflowId: WorkflowId
   def jobTag: String
 
-  lazy val jobLogger: Logger = new JobLogger(self.path.name, workflowId, jobTag, Option(log))
+  lazy val jobLogger = new JobLogger(self.path.name, workflowId, jobTag, Option(log))
 }
 
 /**
diff --git a/core/src/main/scala/cromwell/core/logging/WorkflowLogger.scala b/core/src/main/scala/cromwell/core/logging/WorkflowLogger.scala
index b79e9f7b610..ba339f01136 100644
--- a/core/src/main/scala/cromwell/core/logging/WorkflowLogger.scala
+++ b/core/src/main/scala/cromwell/core/logging/WorkflowLogger.scala
@@ -15,9 +15,9 @@ import org.slf4j.helpers.NOPLogger
 import org.slf4j.{Logger, LoggerFactory}
 
 trait WorkflowLogging extends ActorLogging { this: Actor =>
-  def workflowId: WorkflowId
+  def workflowIdForLogging: WorkflowId
 
-  lazy val workflowLogger = new WorkflowLogger(self.path.name, workflowId, Option(log))
+  lazy val workflowLogger = new WorkflowLogger(self.path.name, workflowIdForLogging, Option(log))
 }
 
 object WorkflowLogger {
@@ -113,10 +113,10 @@ class WorkflowLogger(loggerName: String,
 
   import WorkflowLogger._
 
-  val workflowLogPath = workflowLogConfiguration.map(workflowLogConfigurationActual =>
+  lazy val workflowLogPath = workflowLogConfiguration.map(workflowLogConfigurationActual =>
     File(workflowLogConfigurationActual.dir).createDirectories() / s"workflow.$workflowId.log").map(_.path)
 
-  val fileLogger = workflowLogPath match {
+  lazy val fileLogger = workflowLogPath match {
     case Some(path) => makeFileLogger(path, Level.toLevel(sys.props.getOrElse("LOG_LEVEL", "debug")))
     case None => NOPLogger.NOP_LOGGER
   }
diff --git a/core/src/main/scala/cromwell/core/package.scala b/core/src/main/scala/cromwell/core/package.scala
index 3334bfa246a..def878003a8 100644
--- a/core/src/main/scala/cromwell/core/package.scala
+++ b/core/src/main/scala/cromwell/core/package.scala
@@ -7,7 +7,7 @@ package object core {
   type FullyQualifiedName = String
   type WorkflowOutputs = Map[FullyQualifiedName, JobOutput]
   type WorkflowOptionsJson = String
-  type JobOutputs = Map[LocallyQualifiedName, JobOutput]
+  type CallOutputs = Map[LocallyQualifiedName, JobOutput]
   type HostInputs = Map[String, WdlValue]
   type EvaluatedRuntimeAttributes = Map[String, WdlValue]
 }
diff --git a/core/src/main/scala/cromwell/core/path/CustomRetryParams.scala b/core/src/main/scala/cromwell/core/path/CustomRetryParams.scala
new file mode 100644
index 00000000000..b27b9135ecb
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/CustomRetryParams.scala
@@ -0,0 +1,25 @@
+package cromwell.core.path
+
+import cromwell.core.retry.{Backoff, SimpleExponentialBackoff}
+
+import scala.concurrent.duration.Duration
+import scala.concurrent.duration._
+import scala.language.postfixOps
+
+object CustomRetryParams {
+  val Default = CustomRetryParams(
+    timeout = Duration.Inf,
+    maxRetries = Option(3),
+    backoff = SimpleExponentialBackoff(1 seconds, 3 seconds, 1.5D),
+    isTransient = throwableToFalse,
+    isFatal = throwableToFalse
+  )
+
+  def throwableToFalse(t: Throwable) = false
+}
+
+case class CustomRetryParams(timeout: Duration,
+                             maxRetries: Option[Int],
+                             backoff: Backoff,
+                             isTransient: Throwable => Boolean,
+                             isFatal: Throwable => Boolean)
diff --git a/core/src/main/scala/cromwell/core/path/DefaultPathBuilder.scala b/core/src/main/scala/cromwell/core/path/DefaultPathBuilder.scala
new file mode 100644
index 00000000000..7dc60c1e854
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/DefaultPathBuilder.scala
@@ -0,0 +1,21 @@
+package cromwell.core.path
+
+import java.net.URI
+import java.nio.file.{FileSystems, Path}
+
+import scala.util.Try
+
+/**
+  * PathBuilder using the default FileSystem to attempt to build a Path.
+  */
+case object DefaultPathBuilder extends PathBuilder {
+  override def name = "Default"
+
+  override def build(pathAsString: String): Try[Path] = Try {
+    val uri = URI.create(pathAsString)
+    val host = Option(uri.getHost) getOrElse ""
+    val path = Option(uri.getPath) getOrElse ""
+
+    FileSystems.getDefault.getPath(host, path)
+  }
+}
diff --git a/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala b/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
new file mode 100644
index 00000000000..5339fae3cb8
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
@@ -0,0 +1,8 @@
+package cromwell.core.path
+
+import akka.actor.ActorSystem
+import cromwell.core.WorkflowOptions
+
+case object DefaultPathBuilderFactory extends PathBuilderFactory {
+  override def withOptions(options: WorkflowOptions)(implicit actorSystem: ActorSystem) = DefaultPathBuilder
+}
diff --git a/core/src/main/scala/cromwell/core/path/JavaWriterImplicits.scala b/core/src/main/scala/cromwell/core/path/JavaWriterImplicits.scala
new file mode 100644
index 00000000000..cc1b7f40dde
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/JavaWriterImplicits.scala
@@ -0,0 +1,13 @@
+package cromwell.core.path
+
+import java.io.Writer
+
+object JavaWriterImplicits {
+  implicit class FlushingAndClosingWriter(writer: Writer) {
+    /** Convenience method to flush and close in one shot. */
+    def flushAndClose() = {
+      writer.flush()
+      writer.close()
+    }
+  }
+}
diff --git a/core/src/main/scala/cromwell/core/path/PathBuilder.scala b/core/src/main/scala/cromwell/core/path/PathBuilder.scala
new file mode 100644
index 00000000000..c213101922b
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/PathBuilder.scala
@@ -0,0 +1,10 @@
+package cromwell.core.path
+
+import java.nio.file.Path
+
+import scala.util.Try
+
+trait PathBuilder {
+  def name: String
+  def build(pathAsString: String): Try[Path]
+}
diff --git a/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala b/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
new file mode 100644
index 00000000000..7ee20eb2dec
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
@@ -0,0 +1,11 @@
+package cromwell.core.path
+
+import akka.actor.ActorSystem
+import cromwell.core.WorkflowOptions
+
+/**
+  * Provide a method that can instantiate a path builder with the specified workflow options.
+  */
+trait PathBuilderFactory {
+  def withOptions(options: WorkflowOptions)(implicit actorSystem: ActorSystem): PathBuilder
+}
diff --git a/core/src/main/scala/cromwell/core/PathCopier.scala b/core/src/main/scala/cromwell/core/path/PathCopier.scala
similarity index 65%
rename from core/src/main/scala/cromwell/core/PathCopier.scala
rename to core/src/main/scala/cromwell/core/path/PathCopier.scala
index f90dad60449..58eb290680b 100644
--- a/core/src/main/scala/cromwell/core/PathCopier.scala
+++ b/core/src/main/scala/cromwell/core/path/PathCopier.scala
@@ -1,4 +1,4 @@
-package cromwell.core
+package cromwell.core.path
 
 import java.io.IOException
 import java.nio.file.Path
@@ -8,8 +8,27 @@ import better.files._
 import scala.util.{Failure, Try}
 
 object PathCopier {
+
+  /*
+   * Remove p1 from p2 as long as they match.
+   */
+  private def truncateCommonRoot(p1: Path, p2: Path): String = {
+    def names(p: Path) = 0 until p.getNameCount map p.getName
+
+    val names1 = names(p1)
+
+    val truncated = names(p2).zipWithIndex.dropWhile {
+      case (n1, n2) => n2 < names1.size && n1.equals(names1(n2))
+    } map { _._1 }
+
+    truncated match {
+      case empty if empty.isEmpty => ""
+      case truncs => truncs.reduceLeft(_.resolve(_)).toString
+    }
+  }
+
   def getDestinationFilePath(sourceContextPath: Path, sourceFilePath: Path, destinationDirPath: Path): Path = {
-    val relativeFileString = sourceContextPath.toAbsolutePath.relativize(sourceFilePath.toAbsolutePath).toString
+    val relativeFileString = truncateCommonRoot(sourceContextPath.toAbsolutePath, sourceFilePath.toAbsolutePath)
     destinationDirPath.resolve(relativeFileString)
   }
 
diff --git a/core/src/main/scala/cromwell/core/path/PathFactory.scala b/core/src/main/scala/cromwell/core/path/PathFactory.scala
new file mode 100644
index 00000000000..ff050b55956
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/PathFactory.scala
@@ -0,0 +1,57 @@
+package cromwell.core.path
+
+import java.nio.file.Path
+
+import better.files.File
+
+import scala.util.Success
+
+/**
+  * Convenience trait delegating to the PathFactory singleton
+  */
+trait PathFactory {
+  /**
+    * Path builders to be applied (in order) to attempt to build a java.nio.Path from a string.
+    */
+  def pathBuilders: List[PathBuilder]
+
+  /**
+    * Function applied after a string is successfully resolved to a java.nio.Path
+    */
+  def postMapping(path: Path): Path = path
+
+  /**
+    * Function applied before a string is attempted to be resolved to a java.nio.Path
+    */
+  def preMapping(string: String): String = string
+
+  /**
+    * Attempts to build a java.nio.Path from a String
+    */
+  def buildPath(string: String): Path = PathFactory.buildPath(string, pathBuilders, preMapping, postMapping)
+
+  /**
+    * Attempts to build a better.files.File from a String
+    */
+  def buildFile(string: String): File = PathFactory.buildFile(string, pathBuilders, preMapping, postMapping)
+}
+
+object PathFactory {
+  /**
+    * Attempts to build a java.nio.Path from a String
+    */
+  def buildPath(string: String,
+                pathBuilders: List[PathBuilder],
+                preMapping: String => String = identity[String],
+                postMapping: Path => Path = identity[Path]): Path = {
+    pathBuilders.toStream map { _.build(preMapping(string)) } collectFirst { case Success(p) => postMapping(p) } getOrElse {
+      val pathBuilderNames: String = pathBuilders map { _.name } mkString ", "
+      throw new PathParsingException(s"Could not find suitable filesystem among $pathBuilderNames to parse $string.")
+    }
+  }
+
+  def buildFile(string: String,
+                pathBuilders: List[PathBuilder],
+                preMapping: String => String = identity[String],
+                postMapping: Path => Path = identity[Path]): File = File(buildPath(string, pathBuilders, preMapping, postMapping))
+}
diff --git a/core/src/main/scala/cromwell/core/path/PathImplicits.scala b/core/src/main/scala/cromwell/core/path/PathImplicits.scala
new file mode 100644
index 00000000000..83d4bff7c6a
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/PathImplicits.scala
@@ -0,0 +1,15 @@
+package cromwell.core.path
+
+import java.nio.file.Path
+
+object PathImplicits {
+  implicit class EnhancedPath(val path: Path) extends AnyVal {
+    def swapExt(oldExt: String, newExt: String): Path = {
+      path.getFileSystem.getPath(s"${path.toString.stripSuffix(oldExt)}$newExt")
+    }
+
+    def untailed = UntailedWriter(path)
+
+    def tailed(tailedSize: Int) = TailedWriter(path, tailedSize)
+  }
+}
diff --git a/core/src/main/scala/cromwell/core/path/PathParsingException.scala b/core/src/main/scala/cromwell/core/path/PathParsingException.scala
new file mode 100644
index 00000000000..9bf6b5a7c99
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/PathParsingException.scala
@@ -0,0 +1,5 @@
+package cromwell.core.path
+
+import cromwell.core.CromwellFatalException
+
+case class PathParsingException(message: String) extends CromwellFatalException(new IllegalArgumentException(message))
diff --git a/core/src/main/scala/cromwell/core/path/PathWriter.scala b/core/src/main/scala/cromwell/core/path/PathWriter.scala
new file mode 100644
index 00000000000..e24fb74feb6
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/PathWriter.scala
@@ -0,0 +1,76 @@
+package cromwell.core.path
+
+import java.io.Writer
+import java.nio.file.Path
+
+import scala.collection.immutable.Queue
+
+
+
+/**
+  * Used with a `ProcessLogger`, writes lines with a newline.
+  */
+trait PathWriter {
+  import better.files._
+
+  val path: Path
+  lazy val writer: Writer = File(path).newBufferedWriter
+
+  /**
+    * Passed to `ProcessLogger` to add a new line.
+    *
+    * @param string Line to add to the logs.
+    */
+  def writeWithNewline(string: String): Unit = {
+    writer.write(string)
+    writer.write("\n")
+  }
+}
+
+/**
+  * Used with a `ProcessLogger`, writes lines with a newline.
+  *
+  * @param path Path to the log file.
+  */
+case class UntailedWriter(path: Path) extends PathWriter
+
+/**
+  * Used with a `ProcessLogger`, queues up the `tailedSize` number of lines.
+  *
+  * @param path Path to the log file.
+  * @param tailedSize Maximum number of lines to save in the internal FIFO queue.
+  */
+case class TailedWriter(path: Path, tailedSize: Int) extends PathWriter {
+  private var isTailed = false
+  private var tailedLines: Queue[String] = Queue.empty
+
+  /**
+    * Passed to `ProcessLogger` to add a new line, and adds the line to the tailed queue.
+    *
+    * @param string Line to add to the logs.
+    */
+  override def writeWithNewline(string: String): Unit = {
+    tailedLines :+= string
+    while (tailedLines.size > tailedSize) {
+      tailedLines = tailedLines.takeRight(tailedSize)
+      isTailed = true
+    }
+    super.writeWithNewline(string)
+  }
+
+  /**
+    * Returns a descriptive tail of the `path` and the last `tailedLines` written.
+    *
+    * @return a descriptive tail of the `path` and the last `tailedLines` written.
+    */
+  def tailString: String = {
+    if (tailedLines.isEmpty) {
+      s"Contents of $path were empty."
+    } else if (isTailed) {
+      s"Last ${tailedLines.size} of $path:\n${tailedLines.mkString("\n")}"
+    } else {
+      s"Contents of $path:\n${tailedLines.mkString("\n")}"
+    }
+  }
+}
+
diff --git a/core/src/main/scala/cromwell/core/path/proxy/FileSystemProxy.scala b/core/src/main/scala/cromwell/core/path/proxy/FileSystemProxy.scala
new file mode 100644
index 00000000000..f9e9b581778
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/proxy/FileSystemProxy.scala
@@ -0,0 +1,25 @@
+package cromwell.core.path.proxy
+
+import java.lang.Iterable
+import java.nio.file._
+import java.nio.file.attribute.UserPrincipalLookupService
+import java.nio.file.spi.FileSystemProvider
+import java.util
+
+class FileSystemProxy(delegate: FileSystem, injectedProvider: FileSystemProvider) extends FileSystem {
+
+  override def provider(): FileSystemProvider = injectedProvider
+
+  /* delegated */
+  override def supportedFileAttributeViews(): util.Set[String] = delegate.supportedFileAttributeViews()
+  override def getSeparator: String = delegate.getSeparator
+  override def getRootDirectories: Iterable[Path] = delegate.getRootDirectories
+  override def newWatchService(): WatchService = delegate.newWatchService()
+  override def getFileStores: Iterable[FileStore] = delegate.getFileStores
+  override def isReadOnly: Boolean = delegate.isReadOnly
+  override def getPath(first: String, more: String*): Path = new PathProxy(delegate.getPath(first, more: _*), this)
+  override def isOpen: Boolean = delegate.isOpen
+  override def close(): Unit = delegate.close()
+  override def getPathMatcher(syntaxAndPattern: String): PathMatcher = delegate.getPathMatcher(syntaxAndPattern)
+  override def getUserPrincipalLookupService: UserPrincipalLookupService = delegate.getUserPrincipalLookupService
+}
diff --git a/core/src/main/scala/cromwell/core/path/proxy/PathProxy.scala b/core/src/main/scala/cromwell/core/path/proxy/PathProxy.scala
new file mode 100644
index 00000000000..28428e0a3b4
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/proxy/PathProxy.scala
@@ -0,0 +1,44 @@
+package cromwell.core.path.proxy
+
+import java.io.File
+import java.net.URI
+import java.nio.file.WatchEvent.{Kind, Modifier}
+import java.nio.file._
+import java.util
+
+import scala.util.Try
+
+class PathProxy(delegate: Path, injectedFileSystem: FileSystem) extends Path {
+  def unbox[T](clazz: Class[T]): Try[T] = Try {
+    clazz.cast(delegate)
+  }
+
+  override def getFileSystem: FileSystem = injectedFileSystem
+
+  /* delegated */
+  override def subpath(beginIndex: Int, endIndex: Int): Path = delegate.subpath(beginIndex, endIndex)
+  override def toFile: File = delegate.toFile
+  override def resolveSibling(other: Path): Path = delegate.resolveSibling(other)
+  override def resolveSibling(other: String): Path = delegate.resolveSibling(other)
+  override def isAbsolute: Boolean = delegate.isAbsolute
+  override def getName(index: Int): Path = delegate.getName(index)
+  override def getParent: Path = delegate.getParent
+  override def toAbsolutePath: Path = delegate.toAbsolutePath
+  override def relativize(other: Path): Path = delegate.relativize(other)
+  override def getNameCount: Int = delegate.getNameCount
+  override def toUri: URI = delegate.toUri
+  override def compareTo(other: Path): Int = delegate.compareTo(other)
+  override def register(watcher: WatchService, events: Array[Kind[_]], modifiers: Modifier*): WatchKey = delegate.register(watcher, events, modifiers: _*)
+  override def register(watcher: WatchService, events: Kind[_]*): WatchKey = delegate.register(watcher, events: _*)
+  override def getFileName: Path = delegate.getFileName
+  override def getRoot: Path = delegate.getRoot
+  override def iterator(): util.Iterator[Path] = delegate.iterator()
+  override def normalize(): Path = delegate.normalize()
+  override def endsWith(other: Path): Boolean = delegate.endsWith(other)
+  override def endsWith(other: String): Boolean = delegate.endsWith(other)
+  override def resolve(other: Path): Path = delegate.resolve(other)
+  override def resolve(other: String): Path = delegate.resolve(other)
+  override def startsWith(other: Path): Boolean = delegate.startsWith(other)
+  override def startsWith(other: String): Boolean = delegate.startsWith(other)
+  override def toRealPath(options: LinkOption*): Path = delegate.toRealPath(options: _*)
+}
diff --git a/core/src/main/scala/cromwell/core/path/proxy/RetryableFileSystemProviderProxy.scala b/core/src/main/scala/cromwell/core/path/proxy/RetryableFileSystemProviderProxy.scala
new file mode 100644
index 00000000000..db3975292db
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/path/proxy/RetryableFileSystemProviderProxy.scala
@@ -0,0 +1,57 @@
+package cromwell.core.path.proxy
+
+import java.net.URI
+import java.nio.channels.SeekableByteChannel
+import java.nio.file.DirectoryStream.Filter
+import java.nio.file._
+import java.nio.file.attribute.{BasicFileAttributes, FileAttribute, FileAttributeView}
+import java.nio.file.spi.FileSystemProvider
+import java.util
+
+import akka.actor.ActorSystem
+import cromwell.core.path.CustomRetryParams
+import cromwell.core.retry.Retry
+
+import scala.concurrent.{Await, Future}
+
+class RetryableFileSystemProviderProxy[T <: FileSystemProvider](delegate: T, retryParams: CustomRetryParams = CustomRetryParams.Default)(implicit actorSystem: ActorSystem) extends FileSystemProvider {
+  private val iOExecutionContext = actorSystem.dispatchers.lookup("akka.dispatchers.io-dispatcher")
+
+  // the nio interface is synchronous so we need to wait for the result
+  def withRetry[U](f: () => U): U = Await.result(
+    Retry.withRetry(
+      () => Future(f())(iOExecutionContext),
+      retryParams.maxRetries,
+      retryParams.backoff,
+      retryParams.isTransient,
+      retryParams.isFatal
+    ),
+    retryParams.timeout
+  )
+
+  override def getPath(uri: URI): Path = {
+    val path = delegate.getPath(uri)
+    new PathProxy(path, new FileSystemProxy(path.getFileSystem, this))
+  }
+  override def newFileSystem(uri: URI, env: util.Map[String, _]): FileSystem = {
+    new FileSystemProxy(delegate.newFileSystem(uri, env), this)
+  }
+  override def getScheme: String = delegate.getScheme
+  override def getFileSystem(uri: URI): FileSystem = delegate.getFileSystem(uri)
+  override def getFileStore(path: Path): FileStore = delegate.getFileStore(path)
+
+  /* retried operations */
+  override def move(source: Path, target: Path, options: CopyOption*): Unit = withRetry { () => delegate.move(source, target, options: _*) }
+  override def checkAccess(path: Path, modes: AccessMode*): Unit = withRetry { () => delegate.checkAccess(path, modes: _*) }
+  override def createDirectory(dir: Path, attrs: FileAttribute[_]*): Unit = withRetry { () => delegate.createDirectory(dir, attrs: _*) }
+  override def newByteChannel(path: Path, options: util.Set[_ <: OpenOption], attrs: FileAttribute[_]*): SeekableByteChannel = withRetry { () => delegate.newByteChannel(path, options, attrs: _*) }
+  override def isHidden(path: Path): Boolean = withRetry { () => delegate.isHidden(path) }
+  override def copy(source: Path, target: Path, options: CopyOption*): Unit = withRetry { () => delegate.copy(source, target, options: _*) }
+  override def delete(path: Path): Unit = withRetry { () => delegate.delete(path) }
+  override def newDirectoryStream(dir: Path, filter: Filter[_ >: Path]): DirectoryStream[Path] = withRetry { () => delegate.newDirectoryStream(dir, filter) }
+  override def setAttribute(path: Path, attribute: String, value: scala.Any, options: LinkOption*): Unit = withRetry { () => delegate.setAttribute(path, attribute, value, options: _*) }
+  override def readAttributes[A <: BasicFileAttributes](path: Path, `type`: Class[A], options: LinkOption*): A = withRetry { () => delegate.readAttributes(path, `type`, options: _*) }
+  override def readAttributes(path: Path, attributes: String, options: LinkOption*): util.Map[String, AnyRef] = withRetry { () => delegate.readAttributes(path, attributes, options: _*) }
+  override def isSameFile(path: Path, path2: Path): Boolean = withRetry { () => delegate.isSameFile(path, path2) }
+  override def getFileAttributeView[V <: FileAttributeView](path: Path, `type`: Class[V], options: LinkOption*): V = withRetry { () => delegate.getFileAttributeView(path, `type`, options: _*) }
+}
diff --git a/core/src/main/scala/cromwell/core/retry/Backoff.scala b/core/src/main/scala/cromwell/core/retry/Backoff.scala
index af07de59532..70b3f82f4dc 100644
--- a/core/src/main/scala/cromwell/core/retry/Backoff.scala
+++ b/core/src/main/scala/cromwell/core/retry/Backoff.scala
@@ -4,7 +4,7 @@ import com.google.api.client.util.ExponentialBackOff
 
 import scala.concurrent.duration.{Duration, FiniteDuration}
 
-sealed trait Backoff {
+trait Backoff {
   /** Next interval in millis */
   def backoffMillis: Long
   /** Get the next instance of backoff. This should be called after every call to backoffMillis */
diff --git a/core/src/main/scala/cromwell/core/retry/Retry.scala b/core/src/main/scala/cromwell/core/retry/Retry.scala
index 7ac181129c0..002a8d6e56f 100644
--- a/core/src/main/scala/cromwell/core/retry/Retry.scala
+++ b/core/src/main/scala/cromwell/core/retry/Retry.scala
@@ -25,7 +25,7 @@ object Retry {
     */
   def withRetry[A](f: () => Future[A],
                    maxRetries: Option[Int] = Option(10),
-                   backoff: SimpleExponentialBackoff = SimpleExponentialBackoff(5 seconds, 10 seconds, 1.1D),
+                   backoff: Backoff = SimpleExponentialBackoff(5 seconds, 10 seconds, 1.1D),
                    isTransient: Throwable => Boolean = throwableToFalse,
                    isFatal: Throwable => Boolean = throwableToFalse)
                    (implicit actorSystem: ActorSystem): Future[A] = {
@@ -38,7 +38,7 @@ object Retry {
         case throwable if isFatal(throwable) => Future.failed(new CromwellFatalException(throwable))
         case throwable if !isFatal(throwable) =>
           val retriesLeft = if (isTransient(throwable)) maxRetries else maxRetries map { _ - 1 }
-          after(delay, actorSystem.scheduler)(withRetry(f, backoff = backoff, maxRetries = retriesLeft))
+          after(delay, actorSystem.scheduler)(withRetry(f, backoff = backoff, maxRetries = retriesLeft, isTransient = isTransient, isFatal = isFatal))
       }
     } else f() recoverWith {
       case e: Exception => Future.failed(new CromwellFatalException(e))
diff --git a/core/src/main/scala/cromwell/core/simpleton/WdlValueBuilder.scala b/core/src/main/scala/cromwell/core/simpleton/WdlValueBuilder.scala
index d4e04dd0bba..774c1b5ceb8 100644
--- a/core/src/main/scala/cromwell/core/simpleton/WdlValueBuilder.scala
+++ b/core/src/main/scala/cromwell/core/simpleton/WdlValueBuilder.scala
@@ -1,11 +1,11 @@
 package cromwell.core.simpleton
 
 import wdl4s.TaskOutput
-import wdl4s.types.{WdlArrayType, WdlMapType, WdlPrimitiveType, WdlType}
-import wdl4s.values.{WdlArray, WdlMap, WdlValue}
+import wdl4s.types._
+import wdl4s.values.{WdlArray, WdlMap, WdlOptionalValue, WdlPair, WdlValue}
 
 import scala.language.postfixOps
-import cromwell.core.{JobOutput, JobOutputs}
+import cromwell.core.{CallOutputs, JobOutput}
 import cromwell.core.simpleton.WdlValueSimpleton._
 
 
@@ -73,6 +73,19 @@ object WdlValueBuilder {
       component.path match { case MapElementPattern(key, more) => key.unescapeMeta -> component.copy(path = more)}
     }
 
+    // Returns a tuple of the key into the pair (i.e. left or right) and a `SimpletonComponent` whose path reflects the "descent"
+    // into the pair.  e.g. for a component
+    // SimpletonComponent(":left:foo", someValue) this would return (PairLeft -> SimpletonComponent(":baz", someValue)).
+    sealed trait PairLeftOrRight
+    case object PairLeft extends PairLeftOrRight
+    case object PairRight extends PairLeftOrRight
+    def descendIntoPair(component: SimpletonComponent): (PairLeftOrRight, SimpletonComponent) = {
+      component.path match {
+        case MapElementPattern("left", more) => PairLeft -> component.copy(path = more)
+        case MapElementPattern("right", more) => PairRight -> component.copy(path = more)
+      }
+    }
+
     // Group tuples by key using a Map with key type `K`.
     def group[K](tuples: Traversable[(K, SimpletonComponent)]): Map[K, Traversable[SimpletonComponent]] = {
       tuples groupBy { case (i, _) => i } mapValues { _ map { case (i, s) => s} }
@@ -80,6 +93,12 @@ object WdlValueBuilder {
 
     outputType match {
       case _: WdlPrimitiveType => components collectFirst { case SimpletonComponent(_, v) => v } get
+      case opt: WdlOptionalType =>
+        if (components.isEmpty) {
+          WdlOptionalValue(opt.memberType, None)
+        } else {
+          WdlOptionalValue(toWdlValue(opt.memberType, components))
+        }
       case arrayType: WdlArrayType =>
         val groupedByArrayIndex: Map[Int, Traversable[SimpletonComponent]] = group(components map descendIntoArray)
         WdlArray(arrayType, groupedByArrayIndex.toList.sortBy(_._1) map { case (_, s) => toWdlValue(arrayType.memberType, s) })
@@ -87,6 +106,9 @@ object WdlValueBuilder {
         val groupedByMapKey: Map[String, Traversable[SimpletonComponent]] = group(components map descendIntoMap)
         // map keys are guaranteed by the WDL spec to be primitives, so the "coerceRawValue(..).get" is safe.
         WdlMap(mapType, groupedByMapKey map { case (k, ss) => mapType.keyType.coerceRawValue(k).get -> toWdlValue(mapType.valueType, ss) })
+      case pairType: WdlPairType =>
+        val groupedByLeftOrRight: Map[PairLeftOrRight, Traversable[SimpletonComponent]] = group(components map descendIntoPair)
+        WdlPair(toWdlValue(pairType.leftType, groupedByLeftOrRight(PairLeft)), toWdlValue(pairType.rightType, groupedByLeftOrRight(PairRight)))
     }
   }
 
@@ -107,7 +129,7 @@ object WdlValueBuilder {
     */
   private case class SimpletonComponent(path: String, value: WdlValue)
 
-  def toJobOutputs(taskOutputs: Traversable[TaskOutput], simpletons: Traversable[WdlValueSimpleton]): JobOutputs = {
+  def toJobOutputs(taskOutputs: Traversable[TaskOutput], simpletons: Traversable[WdlValueSimpleton]): CallOutputs = {
     toWdlValues(taskOutputs, simpletons) mapValues JobOutput.apply
   }
 
@@ -119,7 +141,7 @@ object WdlValueBuilder {
 
     // This is meant to "rehydrate" simpletonized WdlValues back to WdlValues.  It is assumed that these WdlValues were
     // "dehydrated" to WdlValueSimpletons correctly. This code is not robust to corrupt input whatsoever.
-    val types = taskOutputs map { o => o.name -> o.wdlType } toMap
+    val types = taskOutputs map { o => o.unqualifiedName -> o.wdlType } toMap
     val simpletonsByOutputName = simpletons groupBy { _.simpletonKey match { case IdentifierAndPathPattern(i, _) => i } }
     val simpletonComponentsByOutputName = simpletonsByOutputName map { case (name, ss) => name -> (ss map simpletonToComponent(name)) }
     types map { case (name, outputType) => name -> toWdlValue(outputType, simpletonComponentsByOutputName(name))}
diff --git a/core/src/main/scala/cromwell/core/simpleton/WdlValueSimpleton.scala b/core/src/main/scala/cromwell/core/simpleton/WdlValueSimpleton.scala
index c417ad3ee0a..1f5e0437554 100644
--- a/core/src/main/scala/cromwell/core/simpleton/WdlValueSimpleton.scala
+++ b/core/src/main/scala/cromwell/core/simpleton/WdlValueSimpleton.scala
@@ -26,8 +26,10 @@ object WdlValueSimpleton {
   implicit class WdlValueSimplifier(wdlValue: WdlValue) {
     def simplify(name: String): Iterable[WdlValueSimpleton] = wdlValue match {
       case prim: WdlPrimitive => List(WdlValueSimpleton(name, prim))
+      case opt: WdlOptionalValue => opt.value.map(_.simplify(name)).getOrElse(Seq.empty)
       case WdlArray(_, arrayValue) => arrayValue.zipWithIndex flatMap { case (arrayItem, index) => arrayItem.simplify(s"$name[$index]") }
       case WdlMap(_, mapValue) => mapValue flatMap { case (key, value) => value.simplify(s"$name:${key.valueString.escapeMeta}") }
+      case WdlPair(left, right) => left.simplify(s"$name:left") ++ right.simplify(s"$name:right")
       case wdlObject: WdlObjectLike => wdlObject.value flatMap { case (key, value) => value.simplify(s"$name:${key.escapeMeta}") }
       case other => throw new Exception(s"Cannot simplify wdl value $other of type ${other.wdlType}")
     }
diff --git a/core/src/main/scala/cromwell/util/JsonFormatting/WdlValueJsonFormatter.scala b/core/src/main/scala/cromwell/util/JsonFormatting/WdlValueJsonFormatter.scala
index 9d8638be0e6..8a997efb0a8 100644
--- a/core/src/main/scala/cromwell/util/JsonFormatting/WdlValueJsonFormatter.scala
+++ b/core/src/main/scala/cromwell/util/JsonFormatting/WdlValueJsonFormatter.scala
@@ -17,6 +17,7 @@ object WdlValueJsonFormatter extends DefaultJsonProtocol {
       case a: WdlArray => new JsArray(a.value.map(write).toVector)
       case m: WdlMap => new JsObject(m.value map {case(k,v) => k.valueString -> write(v)})
       case e: WdlExpression => JsString(e.toWdlString)
+      case q: WdlPair => new JsObject(Map("left" -> write(q.left), "right" -> write(q.right)))
     }
 
     // NOTE: This assumes a map's keys are strings. Since we're coming from JSON this is fine.
diff --git a/core/src/main/scala/cromwell/util/PromiseActor.scala b/core/src/main/scala/cromwell/util/PromiseActor.scala
index 6813a53c7ef..58aea267a03 100644
--- a/core/src/main/scala/cromwell/util/PromiseActor.scala
+++ b/core/src/main/scala/cromwell/util/PromiseActor.scala
@@ -4,6 +4,28 @@ import akka.actor._
 
 import scala.concurrent.{Future, Promise}
 
+private class PromiseActor(promise: Promise[Any], sendTo: ActorRef, msg: Any) extends Actor with ActorLogging {
+
+  context.watch(sendTo)
+  sendTo ! msg
+
+  override def receive = {
+    case Status.Failure(f) =>
+      promise.tryFailure(f)
+      context.stop(self)
+    case Terminated(actorRef) =>
+      if (actorRef == sendTo) {
+        promise.tryFailure(new RuntimeException("Promise-watched actor completed before sending back a message"))
+      } else {
+        log.error("Spooky happenstances! A Terminated({}) message  was sent to a private Promise actor which wasn't watching it!?", actorRef)
+      }
+      context.stop(self)
+    case success =>
+      promise.trySuccess(success)
+      context.stop(self)
+  }
+}
+
 object PromiseActor {
   /**
     * Sends a message to an actor and returns the future associated with the fullfilment of the reply
@@ -16,12 +38,11 @@ object PromiseActor {
     */
   private def askNoTimeout(message: Any, sendTo: ActorRef)(implicit actorRefFactory: ActorRefFactory): Future[Any] = {
     val promise = Promise[Any]()
-    val promiseActor = actorRefFactory.actorOf(props(promise))
-    sendTo.tell(message, promiseActor)
+    val _ = actorRefFactory.actorOf(props(promise, sendTo, message))
     promise.future
   }
 
-  def props(promise: Promise[Any]): Props = Props(new PromiseActor(promise))
+  def props(promise: Promise[Any], sendTo: ActorRef, msg: Any): Props = Props(new PromiseActor(promise, sendTo, msg))
 
   implicit class EnhancedActorRef(val actorRef: ActorRef) extends AnyVal {
     def askNoTimeout(message: Any)(implicit actorRefFactory: ActorRefFactory): Future[Any] = {
@@ -29,14 +50,3 @@ object PromiseActor {
     }
   }
 }
-
-private class PromiseActor(promise: Promise[Any]) extends Actor {
-  override def receive = {
-    case Status.Failure(f) =>
-      promise.tryFailure(f)
-      context.stop(self)
-    case success =>
-      promise.trySuccess(success)
-      context.stop(self)
-  }
-}
diff --git a/core/src/main/scala/cromwell/util/StopAndLogSupervisor.scala b/core/src/main/scala/cromwell/util/StopAndLogSupervisor.scala
new file mode 100644
index 00000000000..4b64e5d8bc0
--- /dev/null
+++ b/core/src/main/scala/cromwell/util/StopAndLogSupervisor.scala
@@ -0,0 +1,24 @@
+package cromwell.util
+
+import akka.actor.SupervisorStrategy.{Decider, Stop}
+import akka.actor.{Actor, ActorRef, OneForOneStrategy, SupervisorStrategy}
+import cromwell.core.logging.WorkflowLogging
+
+trait StopAndLogSupervisor { this: Actor with WorkflowLogging =>
+
+  private var failureLog: Map[ActorRef, Throwable] = Map.empty
+
+  final val stopAndLogStrategy: SupervisorStrategy = {
+    def stoppingDecider: Decider = {
+      case e: Exception =>
+        val failer = sender()
+        failureLog += failer -> e
+        Stop
+    }
+    OneForOneStrategy()(stoppingDecider)
+  }
+
+  final def getFailureCause(actorRef: ActorRef): Option[Throwable] = failureLog.get(actorRef)
+
+  override final val supervisorStrategy = stopAndLogStrategy
+}
diff --git a/core/src/main/scala/cromwell/util/TryUtil.scala b/core/src/main/scala/cromwell/util/TryUtil.scala
new file mode 100644
index 00000000000..18f7ea58a3f
--- /dev/null
+++ b/core/src/main/scala/cromwell/util/TryUtil.scala
@@ -0,0 +1,45 @@
+package cromwell.util
+
+import java.io.{PrintWriter, StringWriter}
+
+import lenthall.exception.ThrowableAggregation
+
+import scala.util.{Success, Failure, Try}
+
+case class AggregatedException(exceptions: Seq[Throwable], prefixError: String = "") extends ThrowableAggregation {
+  override def throwables: Traversable[Throwable] = exceptions
+  override def exceptionContext: String = prefixError
+}
+
+object TryUtil {
+  private def stringifyFailure(failure: Try[Any]): String = {
+    val stringWriter = new StringWriter()
+    val writer = new PrintWriter(stringWriter)
+    failure recover { case e => e.printStackTrace(writer) }
+    writer.flush()
+    writer.close()
+    stringWriter.toString
+  }
+
+  def stringifyFailures[T](possibleFailures: Traversable[Try[T]]): Traversable[String] =
+    possibleFailures.collect { case failure: Failure[T] => stringifyFailure(failure) }
+
+  private def sequenceIterable[T](tries: Iterable[Try[_]], unbox: () => T, prefixErrorMessage: String) = {
+    tries collect { case f: Failure[_] => f } match {
+      case failures if failures.nonEmpty =>
+        val exceptions = failures.toSeq.map(_.exception)
+        Failure(AggregatedException(exceptions, prefixErrorMessage))
+      case _ => Success(unbox())
+    }
+  }
+
+  def sequence[T](tries: Seq[Try[T]], prefixErrorMessage: String = ""): Try[Seq[T]] = {
+    def unbox = tries map { _.get }
+    sequenceIterable(tries, unbox _, prefixErrorMessage)
+  }
+
+  def sequenceMap[T, U](tries: Map[T, Try[U]], prefixErrorMessage: String = ""): Try[Map[T, U]] = {
+    def unbox = tries mapValues { _.get }
+    sequenceIterable(tries.values, unbox _, prefixErrorMessage)
+  }
+}
diff --git a/core/src/test/scala/cromwell/core/path/RetryableFileSystemProxySpec.scala b/core/src/test/scala/cromwell/core/path/RetryableFileSystemProxySpec.scala
new file mode 100644
index 00000000000..88dbf463dca
--- /dev/null
+++ b/core/src/test/scala/cromwell/core/path/RetryableFileSystemProxySpec.scala
@@ -0,0 +1,278 @@
+package cromwell.core.path
+
+import java.io.FileNotFoundException
+import java.nio.channels.SeekableByteChannel
+import java.nio.file.DirectoryStream.Filter
+import java.nio.file.attribute.{BasicFileAttributes, FileAttributeView}
+import java.nio.file.spi.FileSystemProvider
+import java.nio.file.{DirectoryStream, OpenOption, Path, StandardOpenOption}
+import java.util.concurrent.TimeoutException
+
+import cromwell.core.path.proxy.RetryableFileSystemProviderProxy
+import cromwell.core.retry.Backoff
+import cromwell.core.{CromwellFatalException, TestKitSuite}
+import org.mockito.Matchers._
+import org.mockito.Mockito._
+import org.mockito.invocation.InvocationOnMock
+import org.mockito.stubbing.Answer
+import org.scalatest.{FlatSpecLike, Matchers}
+
+import scala.concurrent.duration._
+import scala.language.postfixOps
+
+class RetryableFileSystemProxySpec extends TestKitSuite with FlatSpecLike with Matchers {
+
+  behavior of "RetryableFileSystemProxySpec"
+
+  case class ThrowParams(exception: Exception, nbTimes: Int)
+
+  abstract class FileSystemAnswer[T](delay: Option[Duration] = None,
+                                     throws: Option[ThrowParams] = None) extends Answer[T] {
+
+    var nbThrows = 0
+
+    def delayAndOrThrow() = {
+      delay foreach { d => Thread.sleep(d.toMillis) }
+      throws foreach { e =>
+        if (nbThrows < e.nbTimes) {
+          nbThrows = nbThrows + 1
+          throw e.exception
+        }
+      }
+    }
+  }
+
+  def mockFileSystem(delay: Option[Duration] = None,
+                     throws: Option[ThrowParams] = None): FileSystemProvider =  {
+
+    val provider = mock(classOf[FileSystemProvider])
+
+    def answerUnit: Answer[Unit] = new FileSystemAnswer[Unit](delay, throws) {
+      override def answer(invocation: InvocationOnMock): Unit = delayAndOrThrow()
+    }
+
+    def answerBoolean: Answer[Boolean] = new FileSystemAnswer[Boolean](delay, throws) {
+      override def answer(invocation: InvocationOnMock): Boolean = {
+        delayAndOrThrow()
+        true
+      }
+    }
+
+    def answerSeekableByteChannel: Answer[SeekableByteChannel] = new FileSystemAnswer[SeekableByteChannel](delay, throws) {
+      override def answer(invocation: InvocationOnMock): SeekableByteChannel = {
+        delayAndOrThrow()
+        mock(classOf[SeekableByteChannel])
+      }
+    }
+
+    def answerDirectoryStream: Answer[DirectoryStream[Path]] = new FileSystemAnswer[DirectoryStream[Path]](delay, throws) {
+      override def answer(invocation: InvocationOnMock): DirectoryStream[Path] = {
+        delayAndOrThrow()
+        mock(classOf[DirectoryStream[Path]])
+      }
+    }
+
+    def answerBasicFileAttributes: Answer[BasicFileAttributes] = new FileSystemAnswer[BasicFileAttributes](delay, throws) {
+      override def answer(invocation: InvocationOnMock): BasicFileAttributes = {
+        delayAndOrThrow()
+        mock(classOf[BasicFileAttributes])
+      }
+    }
+
+    def answerMap: Answer[java.util.Map[String, AnyRef]] = new FileSystemAnswer[java.util.Map[String, AnyRef]](delay, throws) {
+      override def answer(invocation: InvocationOnMock): java.util.Map[String, AnyRef] = {
+        delayAndOrThrow()
+        new java.util.HashMap[String, AnyRef]()
+      }
+    }
+
+    def answerFileAttributeView: Answer[FileAttributeView] = new FileSystemAnswer[FileAttributeView](delay, throws) {
+      override def answer(invocation: InvocationOnMock): FileAttributeView = {
+        delayAndOrThrow()
+        mock(classOf[FileAttributeView])
+      }
+    }
+
+    when(provider.move(any[Path], any[Path])).thenAnswer(answerUnit)
+    when(provider.checkAccess(any[Path])).thenAnswer(answerUnit)
+    when(provider.createDirectory(any[Path])).thenAnswer(answerUnit)
+    when(provider.newByteChannel(any[Path], any[java.util.Set[OpenOption]])).thenAnswer(answerSeekableByteChannel)
+    when(provider.isHidden(any[Path])).thenAnswer(answerBoolean)
+    when(provider.copy(any[Path], any[Path])).thenAnswer(answerUnit)
+    when(provider.delete(any[Path])).thenAnswer(answerUnit)
+    when(provider.newDirectoryStream(any[Path], any[Filter[Path]]())).thenAnswer(answerDirectoryStream)
+    when(provider.setAttribute(any[Path], any[String], any[Object])).thenAnswer(answerUnit)
+    when(provider.readAttributes(any[Path], any[String])).thenAnswer(answerMap)
+    when(provider.readAttributes(any[Path], any[Class[BasicFileAttributes]])).thenAnswer(answerBasicFileAttributes)
+    when(provider.isSameFile(any[Path], any[Path])).thenAnswer(answerBoolean)
+    when(provider.getFileAttributeView(any[Path], any[Class[FileAttributeView]])).thenAnswer(answerFileAttributeView)
+
+    provider
+  }
+
+  val testRetryParams = CustomRetryParams.Default.copy(backoff = new Backoff {
+    override def next: Backoff = this
+    override def backoffMillis: Long = 0
+  })
+
+  val pathMock = mock(classOf[Path])
+
+  it should "timeout if the operation takes too long" ignore {
+    val retryParams = testRetryParams.copy(timeout = 100 millis)
+    val mockFs = mockFileSystem(delay = Option(200 millis))
+    val retryableFs = new RetryableFileSystemProviderProxy(mockFs, retryParams)(system)
+
+    a[TimeoutException] shouldBe thrownBy(retryableFs.move(pathMock, pathMock))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.checkAccess(pathMock))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.createDirectory(pathMock))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.newByteChannel(pathMock, mock(classOf[java.util.Set[StandardOpenOption]])))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.isHidden(pathMock))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.copy(pathMock, pathMock))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.delete(pathMock))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.newDirectoryStream(pathMock, mock(classOf[Filter[Path]])))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.setAttribute(pathMock, "", ""))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.readAttributes(pathMock, classOf[BasicFileAttributes]))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.readAttributes(pathMock, ""))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.isSameFile(pathMock, pathMock))
+    a[TimeoutException] shouldBe thrownBy(retryableFs.getFileAttributeView(pathMock, classOf[FileAttributeView]))
+  }
+
+  it should "retry on failure and finally succeed if under retry max" in {
+    val retryParams = testRetryParams.copy(maxRetries = Option(4))
+    val mockFs = mockFileSystem(throws = Option(ThrowParams(new Exception(), nbTimes = 2)))
+    val retryableFs = new RetryableFileSystemProviderProxy(mockFs, retryParams)(system)
+
+    retryableFs.move(pathMock, pathMock)
+    retryableFs.checkAccess(pathMock)
+    retryableFs.createDirectory(pathMock)
+    retryableFs.newByteChannel(pathMock, mock(classOf[java.util.Set[StandardOpenOption]]))
+    retryableFs.isHidden(pathMock)
+    retryableFs.copy(pathMock, pathMock)
+    retryableFs.delete(pathMock)
+    retryableFs.newDirectoryStream(pathMock, mock(classOf[Filter[Path]]))
+    retryableFs.setAttribute(pathMock, "", "")
+    retryableFs.readAttributes(pathMock, classOf[BasicFileAttributes])
+    retryableFs.readAttributes(pathMock, "")
+    retryableFs.isSameFile(pathMock, pathMock)
+    retryableFs.getFileAttributeView(pathMock, classOf[FileAttributeView])
+
+    verify(mockFs, times(3)).move(any[Path], any[Path])
+    verify(mockFs, times(3)).checkAccess(any[Path])
+    verify(mockFs, times(3)).createDirectory(any[Path])
+    verify(mockFs, times(3)).newByteChannel(any[Path], any[java.util.Set[OpenOption]])
+    verify(mockFs, times(3)).isHidden(any[Path])
+    verify(mockFs, times(3)).copy(any[Path], any[Path])
+    verify(mockFs, times(3)).delete(any[Path])
+    verify(mockFs, times(3)).newDirectoryStream(any[Path], any[Filter[Path]]())
+    verify(mockFs, times(3)).setAttribute(any[Path], any[String], any[Object])
+    verify(mockFs, times(3)).readAttributes(any[Path], any[String])
+    verify(mockFs, times(3)).readAttributes(any[Path], any[Class[BasicFileAttributes]])
+    verify(mockFs, times(3)).isSameFile(any[Path], any[Path])
+    verify(mockFs, times(3)).getFileAttributeView(any[Path], any[Class[FileAttributeView]])
+  }
+
+  it should "retry on failure and fail if over retry max" in {
+    val retryParams = testRetryParams.copy(maxRetries = Option(2))
+    val mockFs = mockFileSystem(throws = Option(ThrowParams(new IllegalArgumentException(), nbTimes = 3)))
+    val retryableFs = new RetryableFileSystemProviderProxy(mockFs, retryParams)(system)
+
+    (the [CromwellFatalException] thrownBy retryableFs.move(pathMock, pathMock)).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.checkAccess(pathMock)).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.createDirectory(pathMock)).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.newByteChannel(pathMock, mock(classOf[java.util.Set[StandardOpenOption]]))).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.isHidden(pathMock)).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.copy(pathMock, pathMock)).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.delete(pathMock)).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.newDirectoryStream(pathMock, mock(classOf[Filter[Path]]))).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.setAttribute(pathMock, "", "")).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.readAttributes(pathMock, classOf[BasicFileAttributes])).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.readAttributes(pathMock, "")).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.isSameFile(pathMock, pathMock)).getCause shouldBe a[IllegalArgumentException]
+    (the [CromwellFatalException] thrownBy retryableFs.getFileAttributeView(pathMock, classOf[FileAttributeView])).getCause shouldBe a[IllegalArgumentException]
+
+    verify(mockFs, times(3)).move(any[Path], any[Path])
+    verify(mockFs, times(3)).checkAccess(any[Path])
+    verify(mockFs, times(3)).createDirectory(any[Path])
+    verify(mockFs, times(3)).newByteChannel(any[Path], any[java.util.Set[OpenOption]])
+    verify(mockFs, times(3)).isHidden(any[Path])
+    verify(mockFs, times(3)).copy(any[Path], any[Path])
+    verify(mockFs, times(3)).delete(any[Path])
+    verify(mockFs, times(3)).newDirectoryStream(any[Path], any[Filter[Path]]())
+    verify(mockFs, times(3)).setAttribute(any[Path], any[String], any[Object])
+    verify(mockFs, times(3)).readAttributes(any[Path], any[String])
+    verify(mockFs, times(3)).readAttributes(any[Path], any[Class[BasicFileAttributes]])
+    verify(mockFs, times(3)).isSameFile(any[Path], any[Path])
+    verify(mockFs, times(3)).getFileAttributeView(any[Path], any[Class[FileAttributeView]])
+  }
+
+  it should "ignore transient exceptions" in {
+    def isTransient(t: Throwable) = t.isInstanceOf[FileNotFoundException]
+    val retryParams = testRetryParams.copy(maxRetries = Option(1), isTransient = isTransient)
+    val mockFs = mockFileSystem(throws = Option(ThrowParams(new FileNotFoundException(), nbTimes = 2)))
+    val retryableFs = new RetryableFileSystemProviderProxy(mockFs, retryParams)(system)
+
+    retryableFs.move(pathMock, pathMock)
+    retryableFs.checkAccess(pathMock)
+    retryableFs.createDirectory(pathMock)
+    retryableFs.newByteChannel(pathMock, mock(classOf[java.util.Set[StandardOpenOption]]))
+    retryableFs.isHidden(pathMock)
+    retryableFs.copy(pathMock, pathMock)
+    retryableFs.delete(pathMock)
+    retryableFs.newDirectoryStream(pathMock, mock(classOf[Filter[Path]]))
+    retryableFs.setAttribute(pathMock, "", "")
+    retryableFs.readAttributes(pathMock, classOf[BasicFileAttributes])
+    retryableFs.readAttributes(pathMock, "")
+    retryableFs.isSameFile(pathMock, pathMock)
+    retryableFs.getFileAttributeView(pathMock, classOf[FileAttributeView])
+
+    verify(mockFs, times(3)).move(any[Path], any[Path])
+    verify(mockFs, times(3)).checkAccess(any[Path])
+    verify(mockFs, times(3)).createDirectory(any[Path])
+    verify(mockFs, times(3)).newByteChannel(any[Path], any[java.util.Set[OpenOption]])
+    verify(mockFs, times(3)).isHidden(any[Path])
+    verify(mockFs, times(3)).copy(any[Path], any[Path])
+    verify(mockFs, times(3)).delete(any[Path])
+    verify(mockFs, times(3)).newDirectoryStream(any[Path], any[Filter[Path]]())
+    verify(mockFs, times(3)).setAttribute(any[Path], any[String], any[Object])
+    verify(mockFs, times(3)).readAttributes(any[Path], any[String])
+    verify(mockFs, times(3)).readAttributes(any[Path], any[Class[BasicFileAttributes]])
+    verify(mockFs, times(3)).isSameFile(any[Path], any[Path])
+    verify(mockFs, times(3)).getFileAttributeView(any[Path], any[Class[FileAttributeView]])
+  }
+
+  it should "fail immediately on fatal exceptions" in {
+    def isFatal(t: Throwable) = t.isInstanceOf[FileNotFoundException]
+    val retryParams = testRetryParams.copy(maxRetries = Option(5), isFatal = isFatal)
+    val mockFs = mockFileSystem(throws = Option(ThrowParams(new FileNotFoundException(), nbTimes = 3)))
+    val retryableFs = new RetryableFileSystemProviderProxy(mockFs, retryParams)(system)
+
+    (the [CromwellFatalException] thrownBy retryableFs.move(pathMock, pathMock)).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.checkAccess(pathMock)).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.createDirectory(pathMock)).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.newByteChannel(pathMock, mock(classOf[java.util.Set[StandardOpenOption]]))).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.isHidden(pathMock)).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.copy(pathMock, pathMock)).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.delete(pathMock)).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.newDirectoryStream(pathMock, mock(classOf[Filter[Path]]))).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.setAttribute(pathMock, "", "")).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.readAttributes(pathMock, classOf[BasicFileAttributes])).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.readAttributes(pathMock, "")).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.isSameFile(pathMock, pathMock)).getCause shouldBe a[FileNotFoundException]
+    (the [CromwellFatalException] thrownBy retryableFs.getFileAttributeView(pathMock, classOf[FileAttributeView])).getCause shouldBe a[FileNotFoundException]
+
+    verify(mockFs, times(1)).move(any[Path], any[Path])
+    verify(mockFs, times(1)).checkAccess(any[Path])
+    verify(mockFs, times(1)).createDirectory(any[Path])
+    verify(mockFs, times(1)).newByteChannel(any[Path], any[java.util.Set[OpenOption]])
+    verify(mockFs, times(1)).isHidden(any[Path])
+    verify(mockFs, times(1)).copy(any[Path], any[Path])
+    verify(mockFs, times(1)).delete(any[Path])
+    verify(mockFs, times(1)).newDirectoryStream(any[Path], any[Filter[Path]]())
+    verify(mockFs, times(1)).setAttribute(any[Path], any[String], any[Object])
+    verify(mockFs, times(1)).readAttributes(any[Path], any[String])
+    verify(mockFs, times(1)).readAttributes(any[Path], any[Class[BasicFileAttributes]])
+    verify(mockFs, times(1)).isSameFile(any[Path], any[Path])
+    verify(mockFs, times(1)).getFileAttributeView(any[Path], any[Class[FileAttributeView]])
+  }
+
+}
diff --git a/core/src/test/scala/cromwell/core/simpleton/WdlValueBuilderSpec.scala b/core/src/test/scala/cromwell/core/simpleton/WdlValueBuilderSpec.scala
index eab604c96cb..1e558ceb1dd 100644
--- a/core/src/test/scala/cromwell/core/simpleton/WdlValueBuilderSpec.scala
+++ b/core/src/test/scala/cromwell/core/simpleton/WdlValueBuilderSpec.scala
@@ -2,8 +2,10 @@ package cromwell.core.simpleton
 
 import cromwell.core.simpleton.WdlValueBuilderSpec._
 import org.scalatest.{FlatSpec, Matchers}
+import org.specs2.mock.Mockito
+import wdl4s.parser.WdlParser.Ast
 import wdl4s.types.{WdlArrayType, WdlIntegerType, WdlMapType, WdlStringType}
-import wdl4s.values.{WdlArray, WdlInteger, WdlMap, WdlString}
+import wdl4s.values.{WdlArray, WdlInteger, WdlMap, WdlPair, WdlString, WdlValue}
 import wdl4s.{TaskOutput, WdlExpression}
 
 object WdlValueBuilderSpec {
@@ -11,41 +13,118 @@ object WdlValueBuilderSpec {
   val IgnoredExpression = WdlExpression.fromString(""" "" """)
 }
 
-class WdlValueBuilderSpec extends FlatSpec with Matchers {
+class WdlValueBuilderSpec extends FlatSpec with Matchers with Mockito {
 
-  "Builder" should "build" in {
-
-    val wdlValues = Map(
-      "foo" -> WdlString("none"),
-      "bar" -> WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(1), WdlInteger(2))),
-      "baz" -> WdlArray(WdlArrayType(WdlArrayType(WdlIntegerType)), List(
+  case class SimpletonConversion(name: String, wdlValue: WdlValue, simpletons: Seq[WdlValueSimpleton])
+  val simpletonConversions = List(
+    SimpletonConversion("foo", WdlString("none"), List(WdlValueSimpleton("foo", WdlString("none")))),
+    SimpletonConversion("bar", WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(1), WdlInteger(2))), List(WdlValueSimpleton("bar[0]", WdlInteger(1)), WdlValueSimpleton("bar[1]", WdlInteger(2)))),
+    SimpletonConversion(
+      "baz",
+      WdlArray(WdlArrayType(WdlArrayType(WdlIntegerType)), List(
         WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(0), WdlInteger(1))),
         WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(2), WdlInteger(3))))),
-      "map" -> WdlMap(WdlMapType(WdlStringType, WdlStringType), Map(
+      List(WdlValueSimpleton("baz[0][0]", WdlInteger(0)), WdlValueSimpleton("baz[0][1]", WdlInteger(1)), WdlValueSimpleton("baz[1][0]", WdlInteger(2)), WdlValueSimpleton("baz[1][1]", WdlInteger(3)))
+    ),
+    SimpletonConversion(
+      "map",
+      WdlMap(WdlMapType(WdlStringType, WdlStringType), Map(
         WdlString("foo") -> WdlString("foo"),
-        WdlString("bar") -> WdlString("bar"))
-      ),
-      "map2" -> WdlMap(WdlMapType(WdlStringType, WdlMapType(WdlStringType, WdlStringType)), Map(
-        WdlString("foo") ->
-          WdlMap(WdlMapType(WdlStringType, WdlStringType), Map(WdlString("foo2") -> WdlString("foo"))),
-        WdlString("bar") ->
-          WdlMap(WdlMapType(WdlStringType, WdlStringType), Map(WdlString("bar2") -> WdlString("bar")))
-      )),
-      "map3" -> WdlMap(WdlMapType(WdlStringType, WdlArrayType(WdlIntegerType)), Map(
+        WdlString("bar") -> WdlString("bar"))),
+      List(WdlValueSimpleton("map:foo", WdlString("foo")), WdlValueSimpleton("map:bar", WdlString("bar")))
+    ),
+    SimpletonConversion(
+      "mapOfMaps",
+      WdlMap(WdlMapType(WdlStringType, WdlMapType(WdlStringType, WdlStringType)), Map(
+        WdlString("foo") -> WdlMap(WdlMapType(WdlStringType, WdlStringType), Map(WdlString("foo2") -> WdlString("foo"))),
+        WdlString("bar") ->WdlMap(WdlMapType(WdlStringType, WdlStringType), Map(WdlString("bar2") -> WdlString("bar"))))),
+      List(WdlValueSimpleton("mapOfMaps:foo:foo2", WdlString("foo")), WdlValueSimpleton("mapOfMaps:bar:bar2", WdlString("bar")))
+    ),
+    SimpletonConversion(
+      "simplePair1",
+      WdlPair(WdlInteger(1), WdlString("hello")),
+      List(WdlValueSimpleton("simplePair1:left", WdlInteger(1)), WdlValueSimpleton("simplePair1:right", WdlString("hello")))
+    ),
+    SimpletonConversion(
+      "simplePair2",
+      WdlPair(WdlString("left"), WdlInteger(5)),
+      List(WdlValueSimpleton("simplePair2:left", WdlString("left")), WdlValueSimpleton("simplePair2:right", WdlInteger(5)))
+    ),
+    SimpletonConversion(
+      "pairOfPairs",
+      WdlPair(
+        WdlPair(WdlInteger(1), WdlString("one")),
+        WdlPair(WdlString("two"), WdlInteger(2))),
+      List(
+        WdlValueSimpleton("pairOfPairs:left:left", WdlInteger(1)),
+        WdlValueSimpleton("pairOfPairs:left:right", WdlString("one")),
+        WdlValueSimpleton("pairOfPairs:right:left", WdlString("two")),
+        WdlValueSimpleton("pairOfPairs:right:right", WdlInteger(2)))
+    ),
+    SimpletonConversion(
+      "pairOfArrayAndMap",
+      WdlPair(
+        WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(1), WdlInteger(2))),
+        WdlMap(WdlMapType(WdlStringType, WdlIntegerType), Map(WdlString("left") -> WdlInteger(100), WdlString("right") -> WdlInteger(200)))),
+      List(
+        WdlValueSimpleton("pairOfArrayAndMap:left[0]", WdlInteger(1)),
+        WdlValueSimpleton("pairOfArrayAndMap:left[1]", WdlInteger(2)),
+        WdlValueSimpleton("pairOfArrayAndMap:right:left", WdlInteger(100)),
+        WdlValueSimpleton("pairOfArrayAndMap:right:right", WdlInteger(200)))
+    ),
+    SimpletonConversion(
+      "mapOfArrays",
+      WdlMap(WdlMapType(WdlStringType, WdlArrayType(WdlIntegerType)), Map(
         WdlString("foo") -> WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(0), WdlInteger(1))),
-        WdlString("bar") -> WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(2), WdlInteger(3))))
-      ),
-      "map4" -> WdlMap(WdlMapType(WdlStringType, WdlStringType), Map(
+        WdlString("bar") -> WdlArray(WdlArrayType(WdlIntegerType), List(WdlInteger(2), WdlInteger(3))))),
+      List(WdlValueSimpleton("mapOfArrays:foo[0]", WdlInteger(0)), WdlValueSimpleton("mapOfArrays:foo[1]", WdlInteger(1)),
+        WdlValueSimpleton("mapOfArrays:bar[0]", WdlInteger(2)), WdlValueSimpleton("mapOfArrays:bar[1]", WdlInteger(3)))
+    ),
+    SimpletonConversion(
+      "escapology",
+      WdlMap(WdlMapType(WdlStringType, WdlStringType), Map(
         WdlString("foo[1]") -> WdlString("foo"),
         WdlString("bar[[") -> WdlString("bar"),
-        WdlString("baz:qux") -> WdlString("baz:qux")
-      ))
+        WdlString("baz:qux") -> WdlString("baz:qux"))),
+      List(WdlValueSimpleton("escapology:foo\\[1\\]", WdlString("foo")),
+        WdlValueSimpleton("escapology:bar\\[\\[", WdlString("bar")),
+        WdlValueSimpleton("escapology:baz\\:qux", WdlString("baz:qux")))
     )
+  )
+
+  behavior of "WdlValueSimpleton and WdlValueBuilder"
+
+  simpletonConversions foreach { case SimpletonConversion(name, wdlValue, simpletons) =>
+    it should s"decompose WdlValues into simpletons ($name)" in {
+      import WdlValueSimpleton._
 
-    val taskOutputs = wdlValues map { case (k, wv) => TaskOutput(k, wv.wdlType, IgnoredExpression) }
+      val map = Map(name -> wdlValue)
+      map.simplify should contain theSameElementsAs simpletons
+    }
+
+    it should s"build simpletons back into WdlValues ($name)" in {
+      // The task output is used to tell us the type of output we're expecting:
+      val taskOutputs = List(TaskOutput(name, wdlValue.wdlType, IgnoredExpression, mock[Ast], None))
+      val rebuiltValues = WdlValueBuilder.toWdlValues(taskOutputs, simpletons)
+      rebuiltValues.size should be(1)
+      rebuiltValues(name) should be(wdlValue)
+    }
+
+  }
+
+
+  it should "round trip everything together with no losses" in {
+
+    val wdlValues = (simpletonConversions map { case SimpletonConversion(name, wdlValue, simpletons) => name -> wdlValue }).toMap
+    val taskOutputs = wdlValues map { case (k, wv) => TaskOutput(k, wv.wdlType, IgnoredExpression, mock[Ast], None) }
+    val allSimpletons = simpletonConversions flatMap { case SimpletonConversion(name, wdlValue, simpletons) => simpletons }
 
     import WdlValueSimpleton._
-    val actual = WdlValueBuilder.toWdlValues(taskOutputs, wdlValues.simplify)
+
+    val actualSimpletons = wdlValues.simplify
+    actualSimpletons should contain theSameElementsAs allSimpletons
+
+    val actual = WdlValueBuilder.toWdlValues(taskOutputs, actualSimpletons)
     actual shouldEqual wdlValues
   }
 }
diff --git a/core/src/test/scala/cromwell/util/SampleWdl.scala b/core/src/test/scala/cromwell/util/SampleWdl.scala
index dc2598cf194..2e4d77399df 100644
--- a/core/src/test/scala/cromwell/util/SampleWdl.scala
+++ b/core/src/test/scala/cromwell/util/SampleWdl.scala
@@ -4,7 +4,7 @@ import java.nio.file.{Files, Path}
 import java.util.UUID
 
 import better.files._
-import cromwell.core.WorkflowSourceFiles
+import cromwell.core.{WorkflowSourceFilesWithoutImports}
 import spray.json._
 import wdl4s._
 import wdl4s.types.{WdlArrayType, WdlStringType}
@@ -15,7 +15,7 @@ import scala.language.postfixOps
 trait SampleWdl extends TestFileUtil {
   def wdlSource(runtime: String = ""): WdlSource
   def asWorkflowSources(runtime: String = "", workflowOptions: String = "{}") =
-    WorkflowSourceFiles(wdlSource(runtime), wdlJson, workflowOptions)
+    WorkflowSourceFilesWithoutImports(wdlSource(runtime), wdlJson, workflowOptions)
   val rawInputs: WorkflowRawInputs
 
   def name = getClass.getSimpleName.stripSuffix("$")
@@ -74,14 +74,14 @@ object SampleWdl {
         |  RUNTIME
         |}
         |
-        |workflow hello {
+        |workflow wf_hello {
         |  call hello
         |}
       """.stripMargin.replaceAll("RUNTIME", runtime)
 
-    val Addressee = "hello.hello.addressee"
+    val Addressee = "wf_hello.hello.addressee"
     val rawInputs = Map(Addressee -> "world")
-    val OutputKey = "hello.hello.salutation"
+    val OutputKey = "wf_hello.hello.salutation"
     val OutputValue = "Hello world!"
   }
 
@@ -117,7 +117,7 @@ object SampleWdl {
         |  }
         |}
         |
-        |workflow goodbye {
+        |workflow wf_goodbye {
         |  call goodbye
         |}
       """.stripMargin
@@ -147,9 +147,10 @@ object SampleWdl {
         |  output {
         |    String empty = read_string(stdout())
         |  }
+        |  RUNTIME
         |}
         |
-        |workflow hello {
+        |workflow wf_hello {
         |  call hello
         |  call goodbye {input: emptyInputString=hello.empty }
         |  output {
@@ -509,7 +510,7 @@ object SampleWdl {
         |  RUNTIME
         |}
         |
-        |workflow whereami {
+        |workflow wf_whereami {
         |  call whereami
         |}
       """.stripMargin.replaceAll("RUNTIME", runtime)
@@ -661,7 +662,7 @@ object SampleWdl {
   class ScatterWdl extends SampleWdl {
     val tasks = s"""task A {
       |  command {
-      |    echo -n -e "jeff\nchris\nmiguel\nthibault\nkhalid\nscott"
+      |    echo -n -e "jeff\nchris\nmiguel\nthibault\nkhalid\nruchi"
       |  }
       |  RUNTIME
       |  output {
diff --git a/core/src/test/scala/cromwell/util/WdlValueJsonFormatterSpec.scala b/core/src/test/scala/cromwell/util/WdlValueJsonFormatterSpec.scala
new file mode 100644
index 00000000000..91d678c01d7
--- /dev/null
+++ b/core/src/test/scala/cromwell/util/WdlValueJsonFormatterSpec.scala
@@ -0,0 +1,28 @@
+package cromwell.util
+
+import scala.Vector
+
+import org.scalatest.FlatSpec
+import org.scalatest.Matchers
+
+import JsonFormatting.WdlValueJsonFormatter.WdlValueJsonFormat
+import spray.json.{ JsObject, pimpString }
+import wdl4s.types.{ WdlArrayType, WdlStringType }
+import wdl4s.values.{ WdlArray, WdlPair, WdlString }
+
+class WdlValueJsonFormatterSpec extends FlatSpec with Matchers {
+
+  behavior of "WdlValueJsonFormat"
+
+  it should "write WdlPair to left/right structured JsObject" in {
+    val left = "sanders"
+    val right = Vector("rubio", "carson", "cruz")
+    val wdlPair = WdlPair(WdlString(left), WdlArray(WdlArrayType(WdlStringType), right.map { WdlString(_) }))
+    val ExpectedJson: JsObject =
+      """|{
+         |  "left": "sanders",
+         |  "right": ["rubio", "carson", "cruz"]
+         |}""".stripMargin.parseJson.asJsObject
+    WdlValueJsonFormat.write(wdlPair) should matchPattern { case ExpectedJson => }
+  }
+}
diff --git a/database/migration/src/main/resources/changelog.xml b/database/migration/src/main/resources/changelog.xml
index 251e15d7954..c67137ae073 100644
--- a/database/migration/src/main/resources/changelog.xml
+++ b/database/migration/src/main/resources/changelog.xml
@@ -45,10 +45,15 @@
     <include file="changesets/restart_and_recover_migration.xml" relativeToChangelogFile="true"/>
     <include file="changesets/summary_status_table.xml" relativeToChangelogFile="true"/>
     <include file="changesets/standardize_column_names.xml" relativeToChangelogFile="true" />
+    <include file="changesets/embiggen_metadata_value.xml" relativeToChangelogFile="true" />
     <include file="changesets/metadata_migration.xml" relativeToChangelogFile="true" />
     <include file="changesets/call_caching_job_detritus.xml" relativeToChangelogFile="true"/>
     <include file="changesets/job_store_tinyints.xml" relativeToChangelogFile="true" />
     <include file="changesets/standardize_column_names_again.xml" relativeToChangelogFile="true" />
+    <include file="changesets/rename_workflow_options_in_metadata.xml" relativeToChangelogFile="true" />
+    <include file="changesets/encrypt_and_clear_workflow_options.xml" relativeToChangelogFile="true" />
+    <include file="changesets/sub_workflow_store.xml" relativeToChangelogFile="true" />
+    <include file="changesets/workflow_store_imports_file.xml" relativeToChangelogFile="true" />
 </databaseChangeLog>
 <!--
 
diff --git a/database/migration/src/main/resources/changesets/embiggen_metadata_value.xml b/database/migration/src/main/resources/changesets/embiggen_metadata_value.xml
new file mode 100644
index 00000000000..e0b1ed38d85
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/embiggen_metadata_value.xml
@@ -0,0 +1,50 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <changeSet author="mcovarr" id="entry_or_journal_existence_xor">
+        <preConditions>
+            <or>
+                <and>
+                    <tableExists tableName="METADATA_JOURNAL"/>
+                    <not>
+                        <tableExists tableName="METADATA_ENTRY"/>
+                    </not>
+                </and>
+                <and>
+                    <tableExists tableName="METADATA_ENTRY"/>
+                    <not>
+                        <tableExists tableName="METADATA_JOURNAL"/>
+                    </not>
+                </and>
+            </or>
+        </preConditions>
+        <comment>
+            Either METADATA_JOURNAL or METADATA_ENTRY must exist, but not both (Liquibase doesn't have an xor).
+        </comment>
+    </changeSet>
+
+    <changeSet author="mcovarr" id="embiggen_metadata_entry">
+        <preConditions onFail="MARK_RAN">
+            <tableExists tableName="METADATA_ENTRY"/>
+        </preConditions>
+        <comment>
+            The METADATA_ENTRY version of the embiggener. This should gracefully handle the absence of the table
+            in the event the table is still called METADATA_JOURNAL when this runs.
+        </comment>
+        <modifyDataType tableName="METADATA_ENTRY" columnName="METADATA_VALUE" newDataType="LONGTEXT"/>
+    </changeSet>
+
+    <changeSet author="mcovarr" id="embiggen_metadata_journal">
+        <preConditions onFail="MARK_RAN">
+            <tableExists tableName="METADATA_JOURNAL"/>
+        </preConditions>
+        <comment>
+            The METADATA_JOURNAL version of the embiggener. This should gracefully handle the absence of the table
+            in the event the table has been renamed to METADATA_ENTRY when this runs.
+        </comment>
+        <modifyDataType tableName="METADATA_JOURNAL" columnName="METADATA_VALUE" newDataType="LONGTEXT"/>
+    </changeSet>
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/changesets/encrypt_and_clear_workflow_options.xml b/database/migration/src/main/resources/changesets/encrypt_and_clear_workflow_options.xml
new file mode 100644
index 00000000000..2fe2d766100
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/encrypt_and_clear_workflow_options.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <changeSet author="kshakir" id="encrypt_workflow_store_entry_workflow_options">
+        <customChange class="cromwell.database.migration.workflowoptions.EncryptWorkflowStoreEntryWorkflowOptions"/>
+    </changeSet>
+
+    <changeSet author="kshakir" id="clear_metadata_entry_workflow_options">
+        <customChange class="cromwell.database.migration.workflowoptions.ClearMetadataEntryWorkflowOptions"/>
+    </changeSet>
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/changesets/rename_workflow_options_in_metadata.xml b/database/migration/src/main/resources/changesets/rename_workflow_options_in_metadata.xml
new file mode 100644
index 00000000000..b189e535a8c
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/rename_workflow_options_in_metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <changeSet author="tjeandet" id="rename_workflow_options_in_metadata">
+        <customChange class="cromwell.database.migration.workflowoptions.RenameWorkflowOptionsInMetadata"/>
+    </changeSet>
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/changesets/sub_workflow_store.xml b/database/migration/src/main/resources/changesets/sub_workflow_store.xml
new file mode 100644
index 00000000000..ebde540f1d9
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/sub_workflow_store.xml
@@ -0,0 +1,62 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <property name="clob.type" value="LONGTEXT" dbms="mysql"/>
+    <property name="clob.type" value="LONGVARCHAR" dbms="hsqldb"/>
+
+    <changeSet author="tjeandet" id="SUB_WORKFLOW_STORE_ENTRY">
+        <comment>
+            Temporary storage area for sub workflows which belong to workflows that are still in progress.
+        </comment>
+        <createTable tableName="SUB_WORKFLOW_STORE_ENTRY">
+            <column autoIncrement="true" name="SUB_WORKFLOW_STORE_ENTRY_ID" type="INT">
+                <constraints primaryKey="true" primaryKeyName="PK_SUB_WORKFLOW_STORE_ENTRY"/>
+            </column>
+            <!-- Key fields -->
+            <column name="ROOT_WORKFLOW_ID" type="INT">
+                <constraints nullable="false"/>
+            </column>
+            <column name="PARENT_WORKFLOW_EXECUTION_UUID" type="VARCHAR(255)">
+                <constraints nullable="false"/>
+            </column>
+            <column name="CALL_FULLY_QUALIFIED_NAME" type="VARCHAR(255)">
+                <constraints nullable="false"/>
+            </column>
+            <column name="CALL_INDEX" type="INT">
+                <constraints nullable="false"/>
+            </column>
+            <column name="CALL_ATTEMPT" type="INT">
+                <constraints nullable="false"/>
+            </column>
+            <!-- Value fields -->
+            <column name="SUB_WORKFLOW_EXECUTION_UUID" type="VARCHAR(255)">
+                <constraints nullable="false"/>
+            </column>
+        </createTable>
+        <modifySql dbms="mysql">
+            <append value=" ENGINE=INNODB"/>
+        </modifySql>
+    </changeSet>
+
+    <changeSet author="tjeandet" id="sub_workflow_store_uuid_index">
+        <createIndex indexName="IX_SUB_WORKFLOW_STORE_ENTRY_PWEU"
+                     tableName="SUB_WORKFLOW_STORE_ENTRY">
+            <column name="PARENT_WORKFLOW_EXECUTION_UUID"/>
+        </createIndex>
+    </changeSet>
+
+    <changeSet author="tjeandet" id="sub_workflow_store_jobkey_index">
+        <addUniqueConstraint constraintName="UC_SUB_WORKFLOW_STORE_ENTRY_PWEU_CFQN_CI_CA"
+                     tableName="SUB_WORKFLOW_STORE_ENTRY" columnNames="PARENT_WORKFLOW_EXECUTION_UUID, CALL_FULLY_QUALIFIED_NAME, CALL_INDEX, CALL_ATTEMPT" />
+
+    </changeSet>
+
+    <changeSet author="tjeandet" id="sub_workflow_store_root_workflow_fk">
+    <addForeignKeyConstraint constraintName="FK_SUB_WORKFLOW_STORE_ROOT_WORKFLOW_ID_WORKFLOW_STORE_ENTRY_ID" onDelete="CASCADE"
+                             referencedTableName="WORKFLOW_STORE_ENTRY" referencedColumnNames="WORKFLOW_STORE_ENTRY_ID"
+                             baseTableName="SUB_WORKFLOW_STORE_ENTRY" baseColumnNames="ROOT_WORKFLOW_ID"/>
+     </changeSet>
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/changesets/workflow_store_imports_file.xml b/database/migration/src/main/resources/changesets/workflow_store_imports_file.xml
new file mode 100644
index 00000000000..bd6d3f05106
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/workflow_store_imports_file.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <property name="blob.type" value="LONGBLOB" dbms="mysql"/>
+    <property name="blob.type" value="BLOB" dbms="hsqldb"/>
+
+    <changeSet author="cjllanwarne" id="workflow-store-imports-file">
+        <addColumn
+                tableName="WORKFLOW_STORE_ENTRY">
+            <column name="IMPORTS_ZIP" type="${blob.type}" />
+        </addColumn>
+    </changeSet>
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/logback.xml b/database/migration/src/main/resources/logback.xml
deleted file mode 100644
index fa27b5dde9b..00000000000
--- a/database/migration/src/main/resources/logback.xml
+++ /dev/null
@@ -1,36 +0,0 @@
-<configuration>
-  <if condition='property("LOG_MODE").toUpperCase().equals("STANDARD")'>
-    <then>
-      <appender name="STANDARD_APPENDER" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-          <pattern>%date %X{sourceThread} %-5level - %msg%n</pattern>
-        </encoder>
-      </appender>
-    </then>
-    <else>
-      <appender name="STANDARD_APPENDER" class="ch.qos.logback.core.helpers.NOPAppender" />
-    </else>
-  </if>
-
-  <if condition='property("LOG_MODE").toUpperCase().equals("PRETTY")'>
-    <then>
-      <appender name="PRETTY_APPENDER" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder class="ch.qos.logback.core.encoder.LayoutWrappingEncoder">
-          <layout class="cromwell.logging.TerminalLayout" />
-        </encoder>
-      </appender>
-      <logger name="liquibase" level="WARN"/>
-    </then>
-    <else>
-      <appender name="PRETTY_APPENDER" class="ch.qos.logback.core.helpers.NOPAppender" />
-    </else>
-  </if>
-
-  <root level="${LOG_LEVEL}">
-    <appender-ref ref="STANDARD_APPENDER" />
-    <appender-ref ref="PRETTY_APPENDER" />
-  </root>
-  <logger name="com.zaxxer.hikari" level="ERROR"/>
-  <logger name="HikariPool" level="ERROR"/>
-  <logger name="com.google.cloud.hadoop.gcsio.GoogleCloudStorageReadChannel" level="ERROR"/>
-</configuration>
diff --git a/database/migration/src/main/scala/cromwell/database/migration/custom/BatchedTaskChange.scala b/database/migration/src/main/scala/cromwell/database/migration/custom/BatchedTaskChange.scala
new file mode 100644
index 00000000000..9339dc5d707
--- /dev/null
+++ b/database/migration/src/main/scala/cromwell/database/migration/custom/BatchedTaskChange.scala
@@ -0,0 +1,139 @@
+package cromwell.database.migration.custom
+
+import java.sql.{PreparedStatement, ResultSet}
+
+import liquibase.database.jvm.JdbcConnection
+import liquibase.exception.CustomChangeException
+
+/**
+  * Runs a migration as a series of batches.
+  */
+trait BatchedTaskChange extends MigrationTaskChange {
+  /**
+    * Returns sql to retrieve the maximum primary key for the table.
+    *
+    * Example:
+    * {{{
+    *   SELECT MAX([PRIMARY_KEY])
+    *   FROM [TABLE];
+    * }}}
+    */
+  def readCountQuery: String
+
+  /**
+    * Returns sql to retrieve rows to be passed to migrateBatchRow, batching on a primary key between the half-open
+    * primary key range [start, stop).
+    *
+    * Example:
+    * {{{
+    *   SELECT [COLUMNS]
+    *   FROM [TABLE]
+    *   WHERE [PRIMARY_KEY] >= ? AND [PRIMARY_KEY] < ?;
+    * }}}
+    */
+  def readBatchQuery: String
+
+  /**
+    * Used to prepare the statement that will be passed repeatedly into migrateBatchRow.
+    *
+    * Example:
+    * {{{
+    *   UPDATE [TABLE]
+    *   SET [COLUMNS]
+    *   WHERE [PRIMARY_KEY] = ?;
+    * }}}
+    *
+    * Example:
+    * {{{
+    *   INSERT INTO [TABLE]
+    *   SET [COLUMNS];
+    * }}}
+    */
+  def migrateBatchQuery: String
+
+  /**
+    * Migrate a row.
+    *
+    * Read the values from readRow, update the values, set the updated values on the migrateStatement, and then call
+    * migrateStatement.addBatch(). Return the (estimated) number of rows to be written by this batch.
+    *
+    * @param readRow          The row to migrate
+    * @param migrateStatement The statement to add a new migrated row
+    * @return The number of rows updated
+    */
+  def migrateBatchRow(readRow: ResultSet, migrateStatement: PreparedStatement): Int
+
+  /**
+    * Specify the size of a "page".
+    * For databases with a very large number of rows, selecting all the rows at once can generate a variety of problems.
+    * In order to avoid any issue, the selection is paginated. This value sets how many rows should be retrieved and
+    * processed at a time, before asking for the next page.
+    */
+  private val readBatchSize = config.getInt("database.migration.read-batch-size")
+
+  /**
+    * To keep the size of the insert batch from growing out of control we monitor its size and execute/commit when it
+    * reaches or exceeds writeBatchSize.
+    */
+  private val writeBatchSize = config.getInt("database.migration.write-batch-size")
+
+  override def migrate(connection: JdbcConnection) = {
+
+    logger.info(s"Running migration $migrationName with a read batch size of " +
+      s"$readBatchSize and a write batch size of $writeBatchSize")
+
+    /*
+      * Keep count of the size of the batch.
+      *
+      * @see writeBatchSize
+      */
+    var batchMigrationCounter: Int = 0
+
+    val readCount = getReadCount(connection)
+
+    // So we can display progress
+    val pageCount = Math.max(readCount / readBatchSize, 1)
+
+    val readBatchStatement = connection.prepareStatement(readBatchQuery)
+    val migrateBatchStatement = connection.prepareStatement(migrateBatchQuery)
+
+    val paginator = new QueryPaginator(readBatchStatement, readBatchSize, readCount)
+
+    // Loop over pages
+    paginator.zipWithIndex foreach {
+      case (resultBatch, page) =>
+        // Loop over rows in page
+        new ResultSetIterator(resultBatch).zipWithIndex foreach {
+          case (row, idx) =>
+            batchMigrationCounter += migrateBatchRow(row, migrateBatchStatement)
+            // batchMigrationCounter can actually be bigger than writeBatchSize as wdlValues are processed atomically,
+            // so this is a best effort
+            if (batchMigrationCounter >= writeBatchSize) {
+              migrateBatchStatement.executeBatch()
+              connection.commit()
+              batchMigrationCounter = 0
+            }
+        }
+
+        resultBatch.close()
+
+        val progress = Math.min((page + 1) * 100 / pageCount, 100)
+        logger.info(s"[$migrationName] $progress%")
+    }
+
+    if (batchMigrationCounter != 0) {
+      migrateBatchStatement.executeBatch()
+      connection.commit()
+    }
+  }
+
+  private def getReadCount(connection: JdbcConnection): Int = {
+    val readCountResultSet = connection.createStatement().executeQuery(readCountQuery)
+
+    if (readCountResultSet.next()) {
+      readCountResultSet.getInt(1)
+    } else {
+      throw new CustomChangeException(s"Could not find max value for pagination from sql:\n$readCountQuery")
+    }
+  }
+}
diff --git a/database/migration/src/main/scala/cromwell/database/migration/custom/MigrationTaskChange.scala b/database/migration/src/main/scala/cromwell/database/migration/custom/MigrationTaskChange.scala
new file mode 100644
index 00000000000..4fa7935e632
--- /dev/null
+++ b/database/migration/src/main/scala/cromwell/database/migration/custom/MigrationTaskChange.scala
@@ -0,0 +1,48 @@
+package cromwell.database.migration.custom
+
+import com.typesafe.config.ConfigFactory
+import com.typesafe.scalalogging.LazyLogging
+import liquibase.change.custom.CustomTaskChange
+import liquibase.database.Database
+import liquibase.database.jvm.JdbcConnection
+import liquibase.exception.{CustomChangeException, ValidationErrors}
+import liquibase.resource.ResourceAccessor
+
+/**
+  * Provides a default implementation of a liquibase custom task change.
+  */
+trait MigrationTaskChange extends CustomTaskChange with LazyLogging {
+  lazy val config = ConfigFactory.load
+
+  /** @return name of the migration, defaulting to the class name */
+  def migrationName: String = getClass.getSimpleName
+
+  /**
+    * Performs the migration.
+    *
+    * @param connection the connection to the database
+    */
+  def migrate(connection: JdbcConnection): Unit
+
+  override def execute(database: Database): Unit = {
+    try {
+      val dbConn = database.getConnection.asInstanceOf[JdbcConnection]
+      val autoCommit = dbConn.getAutoCommit
+      dbConn.setAutoCommit(false)
+      migrate(dbConn)
+      dbConn.setAutoCommit(autoCommit)
+    } catch {
+      case customChangeException: CustomChangeException => throw customChangeException
+      case exception: Exception =>
+        throw new CustomChangeException(s"Could not apply migration script for $migrationName", exception)
+    }
+  }
+
+  override def setUp() = {}
+
+  override def getConfirmationMessage = s"$migrationName complete."
+
+  override def validate(database: Database) = new ValidationErrors
+
+  override def setFileOpener(resourceAccessor: ResourceAccessor) = {}
+}
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/QueryPaginator.scala b/database/migration/src/main/scala/cromwell/database/migration/custom/QueryPaginator.scala
similarity index 88%
rename from database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/QueryPaginator.scala
rename to database/migration/src/main/scala/cromwell/database/migration/custom/QueryPaginator.scala
index f7929cea49b..0e6514043c3 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/QueryPaginator.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/custom/QueryPaginator.scala
@@ -1,4 +1,4 @@
-package cromwell.database.migration.metadata.table.symbol
+package cromwell.database.migration.custom
 
 import java.sql.{PreparedStatement, ResultSet}
 
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/ResultSetIterator.scala b/database/migration/src/main/scala/cromwell/database/migration/custom/ResultSetIterator.scala
similarity index 73%
rename from database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/ResultSetIterator.scala
rename to database/migration/src/main/scala/cromwell/database/migration/custom/ResultSetIterator.scala
index 8658a59da50..a9b22962578 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/ResultSetIterator.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/custom/ResultSetIterator.scala
@@ -1,4 +1,4 @@
-package cromwell.database.migration.metadata.table.symbol
+package cromwell.database.migration.custom
 
 import java.sql.ResultSet
 
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/CallOutputSymbolTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/CallOutputSymbolTableMigration.scala
index fbd5529c1f8..09cf42dbff3 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/CallOutputSymbolTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/CallOutputSymbolTableMigration.scala
@@ -6,7 +6,6 @@ import wdl4s.values._
 
 class CallOutputSymbolTableMigration extends SymbolTableMigration {
   override def processSymbol(statement: PreparedStatement,
-                             rowIndex: Int,
                              workflowUuid: String,
                              symbolName: String,
                              symbolScope: String,
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/InputSymbolTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/InputSymbolTableMigration.scala
index 81756d017ae..5740ac3d9f1 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/InputSymbolTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/InputSymbolTableMigration.scala
@@ -7,7 +7,6 @@ import wdl4s.values._
 class InputSymbolTableMigration extends SymbolTableMigration {
 
   override def processSymbol(statement: PreparedStatement,
-                             rowIndex: Int,
                              workflowUuid: String,
                              symbolName: String,
                              symbolScope: String,
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/MetadataStatement.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/MetadataStatement.scala
index a938ebcdf22..311b364fe67 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/MetadataStatement.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/MetadataStatement.scala
@@ -4,7 +4,6 @@ import java.sql.{PreparedStatement, Timestamp, Types}
 import java.time.format.DateTimeFormatter
 import java.time.{OffsetDateTime, ZoneId, ZoneOffset}
 
-import liquibase.database.jvm.JdbcConnection
 import org.slf4j.LoggerFactory
 import wdl4s.values.{WdlBoolean, WdlFloat, WdlInteger, WdlValue}
 
@@ -18,12 +17,12 @@ object MetadataStatement {
   val TimestampIdx = 7
   val ValueTypeIdx = 8
 
-  def makeStatement(connection: JdbcConnection): PreparedStatement = connection.prepareStatement(
+  val InsertSql =
     """
       |INSERT INTO METADATA_JOURNAL
       |(WORKFLOW_EXECUTION_UUID, METADATA_KEY, CALL_FQN, JOB_SCATTER_INDEX, JOB_RETRY_ATTEMPT, METADATA_VALUE, METADATA_TIMESTAMP, METADATA_VALUE_TYPE)
       |VALUES (?, ?, ?, ?, ?, ?, ?, ?)
-    """.stripMargin)
+    """.stripMargin
 
   implicit class OffsetDateTimeToSystemTimestamp(val offsetDateTime: OffsetDateTime) extends AnyVal {
     def toSystemTimestamp = Timestamp.valueOf(offsetDateTime.atZoneSameInstant(ZoneId.systemDefault).toLocalDateTime)
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/SymbolTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/SymbolTableMigration.scala
index a400866a990..19bbc1279da 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/SymbolTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/SymbolTableMigration.scala
@@ -2,15 +2,9 @@ package cromwell.database.migration.metadata.table.symbol
 
 import java.sql.{PreparedStatement, ResultSet}
 
-import com.typesafe.config.ConfigFactory
 import cromwell.core.simpleton.WdlValueSimpleton._
 import cromwell.database.migration.WdlTransformation
-import liquibase.change.custom.CustomTaskChange
-import liquibase.database.Database
-import liquibase.database.jvm.JdbcConnection
-import liquibase.exception.{CustomChangeException, ValidationErrors}
-import liquibase.resource.ResourceAccessor
-import org.slf4j.LoggerFactory
+import cromwell.database.migration.custom.BatchedTaskChange
 import wdl4s.WdlExpression
 import wdl4s.types.WdlType
 import wdl4s.values.WdlValue
@@ -25,42 +19,12 @@ object SymbolTableMigration {
     """.stripMargin
 }
 
-trait SymbolTableMigration extends CustomTaskChange {
-  import SymbolTableMigration._
+trait SymbolTableMigration extends BatchedTaskChange {
   import cromwell.database.migration.WdlTransformation._
 
-  // Nb of rows to retrieve / process in a batch
-  val config = ConfigFactory.load
+  override val readCountQuery = SymbolTableMigration.NbRowsQuery
 
-  /**
-   * Specify the size of a "page".
-   * For databases with a very large number of symbols, selecting all the rows at once can generate a variety of problems.
-   * In order to avoid any issue, the selection is paginated. This value sets how many rows should be retrieved and processed at a time, before asking for the next chunk.
-   */
-  val readBatchSize = config.getInt("database.migration.read-batch-size")
-
-  /**
-   * Because a symbol row can contain any arbitrary wdl value, the amount of metadata rows to insert from a single symbol row can vary from 1 to several thousands (or more).
-   * To keep the size of the insert batch from growing out of control we monitor its size and execute/commit when it reaches or exceeds writeBatchSize.
-   */
-  val writeBatchSize = config.getInt("database.migration.write-batch-size")
-
-  val logger = LoggerFactory.getLogger("LiquibaseMetadataMigration")
-
-  override def execute(database: Database): Unit = {
-    try {
-      val dbConn = database.getConnection.asInstanceOf[JdbcConnection]
-      val autoCommit = dbConn.getAutoCommit
-      dbConn.setAutoCommit(false)
-      migrate(dbConn)
-      dbConn.setAutoCommit(autoCommit)
-    } catch {
-      case t: CustomChangeException => throw t
-      case t: Throwable => throw new CustomChangeException(s"Could not apply migration script for metadata at ${getClass.getSimpleName}", t)
-    }
-  }
-
-  def tmpSymbolPaginatedStatement(connection: JdbcConnection): PreparedStatement = connection.prepareStatement("""
+  override val readBatchQuery = """
       |SELECT
       |    WORKFLOW_EXECUTION_UUID,
       |    SYMBOL_NAME,
@@ -71,64 +35,14 @@ trait SymbolTableMigration extends CustomTaskChange {
       |    WDL_VALUE
       |   FROM TMP_SYMBOL
       |   WHERE TMP_SYMBOL_ID >= ? AND TMP_SYMBOL_ID < ?;
-    """.stripMargin)
-
-  private def migrate(connection: JdbcConnection) = {
-    logger.info(s"Running migration with a read batch size of $readBatchSize and a write batch size of $writeBatchSize")
-
-    /**
-     * Keep count of the size of the batch.
-      *
-      * @see writeBatchSize
-     */
-    var insertsCounter: Int = 0
-
-    // Find the max row id in the TMP_SYMBOL table
-    val tmpSymbolCountRS = connection.createStatement().executeQuery(NbRowsQuery)
-
-    if (tmpSymbolCountRS.next()) {
-      val tmpSymbolCount = tmpSymbolCountRS.getInt("symbol_count")
-
-      // So we can display progress
-      val nbPages = Math.max(tmpSymbolCount / readBatchSize, 1)
-
-      val paginator = new QueryPaginator(tmpSymbolPaginatedStatement(connection), readBatchSize, tmpSymbolCount)
-      val metadataInsertStatement = MetadataStatement.makeStatement(connection)
-
-      // Loop over pages
-      paginator.zipWithIndex foreach {
-        case (resultBatch, page) =>
-          // Loop over rows in page
-          new ResultSetIterator(resultBatch).zipWithIndex foreach {
-            case (row, idx) =>
-              insertsCounter += migrateRow(connection, metadataInsertStatement, row, idx)
-              // insertsCounter can actually be bigger than writeBatchSize as wdlValues are processed atomically, so this is a best effort
-              if (insertsCounter >= writeBatchSize) {
-                metadataInsertStatement.executeBatch()
-                connection.commit()
-                insertsCounter = 0
-              }
-          }
-
-          resultBatch.close()
-
-          val progress = Math.min((page + 1) * 100 / nbPages, 100)
-          logger.info(s"[${getClass.getSimpleName}] $progress%")
-      }
+    """.stripMargin
 
-      if (insertsCounter != 0) {
-        metadataInsertStatement.executeBatch()
-        connection.commit()
-      }
-    } else {
-      throw new CustomChangeException("Could not find max value of symbol id for pagination")
-    }
-  }
+  override val migrateBatchQuery = MetadataStatement.InsertSql
 
   /**
     * Migrate a row to the metadata table
     */
-  protected def migrateRow(connection: JdbcConnection, statement: PreparedStatement, row: ResultSet, idx: Int): Int = {
+  override def migrateBatchRow(row: ResultSet, statement: PreparedStatement): Int = {
     // Try to coerce the value to a WdlValue
     val value = for {
       wdlType <- Try(WdlType.fromWdlString(row.getString("WDL_TYPE")))
@@ -147,7 +61,7 @@ trait SymbolTableMigration extends CustomTaskChange {
 
     value match {
       case Success(wdlValue) =>
-        processSymbol(statement, idx, workflowUuid, symbolName, symbolScope, symbolIndex, symbolAttempt, wdlValue)
+        processSymbol(statement, workflowUuid, symbolName, symbolScope, symbolIndex, symbolAttempt, wdlValue)
       case Failure(f) =>
         logger.error(
           s"""Could not parse symbol of type ${row.getString("WDL_TYPE")}
@@ -157,7 +71,6 @@ trait SymbolTableMigration extends CustomTaskChange {
   }
 
   def processSymbol(statement: PreparedStatement,
-                    idx: Int,
                     workflowUuid: String,
                     symbolName: String,
                     symbolScope: String,
@@ -165,12 +78,6 @@ trait SymbolTableMigration extends CustomTaskChange {
                     symbolAttempt: Option[Int],
                     wdlValue: WdlValue): Int
 
-  override def setUp(): Unit = ()
-
-  override def validate(database: Database): ValidationErrors = new ValidationErrors
-
-  override def setFileOpener(resourceAccessor: ResourceAccessor): Unit = {}
-
   /**
     * Add all necessary statements to the batch for the provided WdlValue.
     */
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/WorkflowOutputSymbolTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/WorkflowOutputSymbolTableMigration.scala
index f188fc0cd4e..269d58a2491 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/WorkflowOutputSymbolTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/WorkflowOutputSymbolTableMigration.scala
@@ -7,7 +7,6 @@ import wdl4s.values._
 class WorkflowOutputSymbolTableMigration extends SymbolTableMigration {
 
   override def processSymbol(statement: PreparedStatement,
-                             rowIndex: Int,
                              workflowUuid: String,
                              symbolName: String,
                              symbolScope: String,
diff --git a/database/migration/src/main/scala/cromwell/database/migration/restart/table/RenameWorkflowOptionKeysMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/restart/table/RenameWorkflowOptionKeysMigration.scala
index 3852750ce8f..c0610ae368b 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/restart/table/RenameWorkflowOptionKeysMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/restart/table/RenameWorkflowOptionKeysMigration.scala
@@ -1,19 +1,11 @@
 package cromwell.database.migration.restart.table
 
+import cromwell.database.migration.workflowoptions.WorkflowOptionsRenaming._
 import cromwell.database.migration.restart.table.RenameWorkflowOptionKeysMigration._
 import liquibase.database.jvm.JdbcConnection
 import spray.json._
 
-
 object RenameWorkflowOptionKeysMigration {
-  private val RenamedOptionKeys = Map(
-    "defaultRuntimeOptions" -> "default_runtime_attributes",
-    "workflowFailureMode" -> "workflow_failure_mode",
-    "workflow_log_dir" -> "final_workflow_log_dir",
-    "outputs_path" -> "final_workflow_outputs_dir",
-    "call_logs_dir" -> "final_call_logs_dir"
-  )
-
   private val QueryWorkflowStore = " SELECT WORKFLOW_STORE_ID, WORKFLOW_OPTIONS FROM WORKFLOW_STORE "
 
   private val UpdateWorkflowStore = " UPDATE WORKFLOW_STORE SET WORKFLOW_OPTIONS = ? WHERE WORKFLOW_STORE_ID = ? "
@@ -25,14 +17,6 @@ class RenameWorkflowOptionKeysMigration extends AbstractRestartMigration {
   override protected def description: String = "Workflow option renaming"
 
   override protected def doMigration(connection: JdbcConnection): Unit = {
-
-    def renameOptionKeys(field: JsField): JsField = {
-      field match {
-        case (oldName, value) if RenamedOptionKeys.contains(oldName) => RenamedOptionKeys(oldName) -> value
-        case noop => noop
-      }
-    }
-
     val query = connection.createStatement()
     lazy val insert = connection.prepareStatement(UpdateWorkflowStore)
     query.execute(QueryWorkflowStore)
diff --git a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/ClearMetadataEntryWorkflowOptions.scala b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/ClearMetadataEntryWorkflowOptions.scala
new file mode 100644
index 00000000000..4d9263491f4
--- /dev/null
+++ b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/ClearMetadataEntryWorkflowOptions.scala
@@ -0,0 +1,15 @@
+package cromwell.database.migration.workflowoptions
+
+import cromwell.core.WorkflowOptions
+
+/**
+  * Clear the values from encrypted keys in METADATA_ENTRY.
+  */
+class ClearMetadataEntryWorkflowOptions extends WorkflowOptionsChange {
+  override val tableName = "METADATA_ENTRY"
+  override val primaryKeyColumn = "METADATA_JOURNAL_ID"
+  override val workflowOptionsColumn = "METADATA_VALUE"
+  override val additionalReadBatchFilters = "AND METADATA_KEY = 'submittedFiles:options'"
+
+  override def migrateWorkflowOptions(workflowOptions: WorkflowOptions) = workflowOptions.clearEncryptedValues
+}
diff --git a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/EncryptWorkflowStoreEntryWorkflowOptions.scala b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/EncryptWorkflowStoreEntryWorkflowOptions.scala
new file mode 100644
index 00000000000..9c3cc74905d
--- /dev/null
+++ b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/EncryptWorkflowStoreEntryWorkflowOptions.scala
@@ -0,0 +1,14 @@
+package cromwell.database.migration.workflowoptions
+
+import cromwell.core.WorkflowOptions
+
+/**
+  * Encrypt the values for encrypted keys in WORKFLOW_STORE_ENTRY.
+  */
+class EncryptWorkflowStoreEntryWorkflowOptions extends WorkflowOptionsChange {
+  override val tableName = "WORKFLOW_STORE_ENTRY"
+  override val primaryKeyColumn = "WORKFLOW_STORE_ENTRY_ID"
+  override val workflowOptionsColumn = "WORKFLOW_OPTIONS"
+
+  override def migrateWorkflowOptions(workflowOptions: WorkflowOptions) = workflowOptions.asPrettyJson
+}
diff --git a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/RenameWorkflowOptionsInMetadata.scala b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/RenameWorkflowOptionsInMetadata.scala
new file mode 100644
index 00000000000..e6842b45951
--- /dev/null
+++ b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/RenameWorkflowOptionsInMetadata.scala
@@ -0,0 +1,38 @@
+package cromwell.database.migration.workflowoptions
+
+import java.sql.{PreparedStatement, ResultSet}
+
+import cromwell.database.migration.custom.BatchedTaskChange
+import cromwell.database.migration.workflowoptions.WorkflowOptionsRenaming._
+import spray.json.{JsObject, _}
+
+class RenameWorkflowOptionsInMetadata extends BatchedTaskChange {
+  val tableName = "METADATA_ENTRY"
+  val primaryKeyColumn = "METADATA_JOURNAL_ID"
+  val workflowOptionsColumn = "METADATA_VALUE"
+  val additionalReadBatchFilters = "AND METADATA_KEY = 'submittedFiles:options'"
+
+  override def readCountQuery = s"SELECT MAX($primaryKeyColumn) FROM $tableName;"
+
+  override def readBatchQuery =
+    s"""|SELECT $primaryKeyColumn, $workflowOptionsColumn
+        |  FROM $tableName
+        |  WHERE $primaryKeyColumn >= ? AND $primaryKeyColumn < ? $additionalReadBatchFilters;
+        |""".stripMargin
+
+  override def migrateBatchQuery = s"UPDATE $tableName SET $workflowOptionsColumn = ? WHERE $primaryKeyColumn = ?;"
+
+  override def migrateBatchRow(readRow: ResultSet, migrateStatement: PreparedStatement): Int = {
+    val rowId = readRow.getInt(1)
+    
+    val migratedJson = readRow.getString(2).parseJson match {
+      case JsObject(fields) => JsObject(fields map renameOptionKeys)
+      case other => other
+    }
+
+    migrateStatement.setString(1, migratedJson.prettyPrint)
+    migrateStatement.setInt(2, rowId)
+    migrateStatement.addBatch()
+    1
+  }
+}
diff --git a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsChange.scala b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsChange.scala
new file mode 100644
index 00000000000..3c1b6b68f6b
--- /dev/null
+++ b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsChange.scala
@@ -0,0 +1,69 @@
+package cromwell.database.migration.workflowoptions
+
+import java.sql.{PreparedStatement, ResultSet}
+
+import cromwell.core.WorkflowOptions
+import cromwell.database.migration.custom.BatchedTaskChange
+import liquibase.database.Database
+
+import scala.util.{Failure, Success}
+
+/**
+  * Edits the workflow options stored in a table.
+  */
+trait WorkflowOptionsChange extends BatchedTaskChange {
+  /** @return name of the table */
+  def tableName: String
+
+  /** @return primary key of the table */
+  def primaryKeyColumn: String
+
+  /** @return column storing the workflow options */
+  def workflowOptionsColumn: String
+
+  /** @return any additional filters to add to the where clause, starting with "AND ..." */
+  def additionalReadBatchFilters: String = ""
+
+  /**
+    * Takes in the workflow options and returns the edited version as a json string.
+    *
+    * @param workflowOptions workflow options object
+    * @return edited workflow object json
+    */
+  def migrateWorkflowOptions(workflowOptions: WorkflowOptions): String
+
+  override def execute(database: Database): Unit = {
+    val configPath = "workflow-options.encrypted-fields"
+    if (config.hasPath(configPath) && !config.getStringList(configPath).isEmpty) {
+      super.execute(database)
+    }
+  }
+
+  override def readCountQuery = s"SELECT MAX($primaryKeyColumn) FROM $tableName;"
+
+  override def readBatchQuery =
+    s"""|SELECT $primaryKeyColumn, $workflowOptionsColumn
+        |  FROM $tableName
+        |  WHERE $primaryKeyColumn >= ? AND $primaryKeyColumn < ? $additionalReadBatchFilters;
+        |""".stripMargin
+
+  override def migrateBatchQuery = s"UPDATE $tableName SET $workflowOptionsColumn = ? WHERE $primaryKeyColumn = ?;"
+
+  override def migrateBatchRow(readRow: ResultSet, migrateStatement: PreparedStatement): Int = {
+    val rowId = readRow.getInt(1)
+    val workflowOptionsJson = readRow.getString(2)
+    WorkflowOptions.fromJsonString(workflowOptionsJson) match {
+      case Success(workflowOptions) =>
+        val migratedJson = migrateWorkflowOptions(workflowOptions)
+        migrateStatement.setString(1, migratedJson)
+        migrateStatement.setInt(2, rowId)
+        migrateStatement.addBatch()
+        1
+      case Failure(exception) =>
+        logger.error(
+          s"Unable to process $tableName pk $rowId\njson:\n$workflowOptionsJson", exception)
+        0
+    }
+  }
+
+}
diff --git a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsRenaming.scala b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsRenaming.scala
new file mode 100644
index 00000000000..d148a570fdf
--- /dev/null
+++ b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsRenaming.scala
@@ -0,0 +1,21 @@
+package cromwell.database.migration.workflowoptions
+
+import spray.json._
+
+object WorkflowOptionsRenaming {
+
+  private val RenamedOptionKeys = Map(
+    "defaultRuntimeOptions" -> "default_runtime_attributes",
+    "workflowFailureMode" -> "workflow_failure_mode",
+    "workflow_log_dir" -> "final_workflow_log_dir",
+    "outputs_path" -> "final_workflow_outputs_dir",
+    "call_logs_dir" -> "final_call_logs_dir"
+  )
+
+  def renameOptionKeys(field: JsField): JsField = {
+    field match {
+      case (oldName, value) if RenamedOptionKeys.contains(oldName) => RenamedOptionKeys(oldName) -> value
+      case noop => noop
+    }
+  }
+}
diff --git a/database/sql/src/main/scala/cromwell/database/slick/CallCachingSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/CallCachingSlickDatabase.scala
index ce40e4e6a87..deb7b6d5e3d 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/CallCachingSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/CallCachingSlickDatabase.scala
@@ -5,6 +5,7 @@ import cromwell.database.sql._
 import cromwell.database.sql.joins.CallCachingJoin
 
 import scala.concurrent.{ExecutionContext, Future}
+import scala.language.postfixOps
 
 trait CallCachingSlickDatabase extends CallCachingSqlDatabase {
   this: SlickDatabase =>
diff --git a/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala
index 80a4413fd17..173de0e89cc 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala
@@ -58,7 +58,8 @@ class SlickDatabase(override val originalDatabaseConfig: Config) extends SqlData
   with JobKeyValueSlickDatabase
   with JobStoreSlickDatabase
   with CallCachingSlickDatabase
-  with SummaryStatusSlickDatabase {
+  with SummaryStatusSlickDatabase
+  with SubWorkflowStoreSlickDatabase {
 
   override val urlKey = SlickDatabase.urlKey(originalDatabaseConfig)
   private val slickConfig = DatabaseConfig.forConfig[JdbcProfile]("", databaseConfig)
diff --git a/database/sql/src/main/scala/cromwell/database/slick/SubWorkflowStoreSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/SubWorkflowStoreSlickDatabase.scala
new file mode 100644
index 00000000000..05d216141d6
--- /dev/null
+++ b/database/sql/src/main/scala/cromwell/database/slick/SubWorkflowStoreSlickDatabase.scala
@@ -0,0 +1,67 @@
+package cromwell.database.slick
+
+import cats.instances.future._
+import cats.syntax.functor._
+import cromwell.database.sql.SubWorkflowStoreSqlDatabase
+import cromwell.database.sql.tables.SubWorkflowStoreEntry
+
+import scala.concurrent.{ExecutionContext, Future}
+import scala.language.postfixOps
+
+trait SubWorkflowStoreSlickDatabase extends SubWorkflowStoreSqlDatabase {
+  this: SlickDatabase =>
+
+  import dataAccess.driver.api._
+
+  def addSubWorkflowStoreEntry(rootWorkflowExecutionUuid: String, 
+                               parentWorkflowExecutionUuid: String,
+                               callFullyQualifiedName: String,
+                               jobIndex: Int,
+                               jobAttempt: Int,
+                               subWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Unit] = {
+    val action = for {
+      workflowStoreEntry <- dataAccess.workflowStoreEntriesForWorkflowExecutionUuid(rootWorkflowExecutionUuid).result.headOption
+      _ <- workflowStoreEntry match {
+        case Some(rootWorkflow) =>
+          dataAccess.subWorkflowStoreEntryIdsAutoInc +=
+            SubWorkflowStoreEntry(
+              rootWorkflow.workflowStoreEntryId,
+              parentWorkflowExecutionUuid,
+              callFullyQualifiedName,
+              jobIndex,
+              jobAttempt,
+              subWorkflowExecutionUuid
+            )
+        case None => DBIO.failed(new IllegalArgumentException(s"Could not find root workflow with UUID $rootWorkflowExecutionUuid"))
+      }
+    } yield ()
+    
+    runTransaction(action) void
+  }
+
+  override def querySubWorkflowStore(parentWorkflowExecutionUuid: String, callFqn: String, jobIndex: Int, jobAttempt: Int)
+                                    (implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]] = {
+    val action = for {
+      subWorkflowStoreEntryOption <- dataAccess.subWorkflowStoreEntriesForJobKey(
+        (parentWorkflowExecutionUuid, callFqn, jobIndex, jobAttempt)
+      ).result.headOption
+    } yield subWorkflowStoreEntryOption
+
+    runTransaction(action)
+  }
+
+  override def removeSubWorkflowStoreEntries(rootWorkflowExecutionUuid: String)
+                                            (implicit ec: ExecutionContext): Future[Int] = {
+    val action = for {
+      workflowStoreEntry <- dataAccess.workflowStoreEntriesForWorkflowExecutionUuid(rootWorkflowExecutionUuid).result.headOption
+      deleted <- workflowStoreEntry match {
+        case Some(rootWorkflow) =>
+          dataAccess.subWorkflowStoreEntriesForRootWorkflowId(rootWorkflow.workflowStoreEntryId.get).delete
+        case None =>
+          DBIO.successful(0)
+      }
+    } yield deleted
+    
+    runTransaction(action)
+  }
+}
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/DataAccessComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/DataAccessComponent.scala
index cdcce5a7a57..b0c70abf351 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/DataAccessComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/DataAccessComponent.scala
@@ -14,7 +14,8 @@ class DataAccessComponent(val driver: JdbcProfile)
     with MetadataEntryComponent
     with SummaryStatusEntryComponent
     with WorkflowMetadataSummaryEntryComponent
-    with WorkflowStoreEntryComponent {
+    with WorkflowStoreEntryComponent
+    with SubWorkflowStoreEntryComponent {
 
   import driver.api._
 
@@ -29,5 +30,6 @@ class DataAccessComponent(val driver: JdbcProfile)
       metadataEntries.schema ++
       summaryStatusEntries.schema ++
       workflowMetadataSummaryEntries.schema ++
-      workflowStoreEntries.schema
+      workflowStoreEntries.schema ++
+      subWorkflowStoreEntries.schema
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
new file mode 100644
index 00000000000..848c60c4b1c
--- /dev/null
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
@@ -0,0 +1,62 @@
+package cromwell.database.slick.tables
+
+import cromwell.database.sql.tables.SubWorkflowStoreEntry
+import slick.model.ForeignKeyAction.Cascade
+
+trait SubWorkflowStoreEntryComponent {
+
+  this: DriverComponent with WorkflowStoreEntryComponent =>
+
+  import driver.api._
+
+  class SubWorkflowStoreEntries(tag: Tag) extends Table[SubWorkflowStoreEntry](tag, "SUB_WORKFLOW_STORE_ENTRY") {
+    def subWorkflowStoreEntryId = column[Int]("SUB_WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
+
+    def rootWorkflowId = column[Int]("ROOT_WORKFLOW_ID")
+    
+    def parentWorkflowExecutionUuid = column[String]("PARENT_WORKFLOW_EXECUTION_UUID")
+
+    def callFullyQualifiedName = column[String]("CALL_FULLY_QUALIFIED_NAME")
+
+    def callIndex = column[Int]("CALL_INDEX")
+
+    def callAttempt = column[Int]("CALL_ATTEMPT")
+
+    def subWorkflowExecutionUuid = column[String]("SUB_WORKFLOW_EXECUTION_UUID")
+
+    override def * = (rootWorkflowId.?, parentWorkflowExecutionUuid, callFullyQualifiedName, callIndex, callAttempt, subWorkflowExecutionUuid, subWorkflowStoreEntryId.?) <> (SubWorkflowStoreEntry.tupled, SubWorkflowStoreEntry.unapply)
+
+    def ucSubWorkflowStoreEntryPweuCfqnJiJa = index("UC_SUB_WORKFLOW_STORE_ENTRY_PWEU_CFQN_CI_CA",
+      (parentWorkflowExecutionUuid, callFullyQualifiedName, callIndex, callAttempt), unique = true)
+
+    def fkSubWorkflowStoreRootWorkflowStoreEntryId = foreignKey("FK_SUB_WORKFLOW_STORE_ROOT_WORKFLOW_ID_WORKFLOW_STORE_ENTRY_ID",
+      rootWorkflowId, workflowStoreEntries)(_.workflowStoreEntryId, onDelete = Cascade)
+
+    def ixSubWorkflowStoreEntryPweu = index("IX_SUB_WORKFLOW_STORE_ENTRY_PWEU", parentWorkflowExecutionUuid, unique = false)
+  }
+
+  protected val subWorkflowStoreEntries = TableQuery[SubWorkflowStoreEntries]
+
+  val subWorkflowStoreEntryIdsAutoInc = subWorkflowStoreEntries returning subWorkflowStoreEntries.map(_.subWorkflowStoreEntryId)
+
+  val subWorkflowStoreEntriesForRootWorkflowId = Compiled(
+    (rootWorkflowId: Rep[Int]) => for {
+      subWorkflowStoreEntry <- subWorkflowStoreEntries
+      if subWorkflowStoreEntry.rootWorkflowId === rootWorkflowId
+    } yield subWorkflowStoreEntry
+  )
+
+  /**
+    * Useful for finding the unique sub workflow entry for a given job key
+    */
+  val subWorkflowStoreEntriesForJobKey = Compiled(
+    (parentWorkflowExecutionUuid: Rep[String], callFullyQualifiedName: Rep[String], jobIndex: Rep[Int],
+     jobAttempt: Rep[Int]) =>
+      for {
+        subWorkflowStoreEntry <- subWorkflowStoreEntries
+        if subWorkflowStoreEntry.parentWorkflowExecutionUuid === parentWorkflowExecutionUuid &&
+          subWorkflowStoreEntry.callFullyQualifiedName === callFullyQualifiedName &&
+          subWorkflowStoreEntry.callIndex === jobIndex && subWorkflowStoreEntry.callAttempt === jobAttempt
+      } yield subWorkflowStoreEntry
+  )
+}
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
index 4a248f803ac..dc896ca3dc4 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
@@ -1,6 +1,6 @@
 package cromwell.database.slick.tables
 
-import java.sql.{Clob, Timestamp}
+import java.sql.{Blob, Clob, Timestamp}
 
 import cromwell.database.sql.tables.WorkflowStoreEntry
 
@@ -25,8 +25,10 @@ trait WorkflowStoreEntryComponent {
 
     def submissionTime = column[Timestamp]("SUBMISSION_TIME")
 
+    def importsZipFile = column[Option[Blob]]("IMPORTS_ZIP")
+
     override def * = (workflowExecutionUuid, workflowDefinition, workflowInputs, workflowOptions, workflowState,
-      submissionTime, workflowStoreEntryId.?) <> (WorkflowStoreEntry.tupled, WorkflowStoreEntry.unapply)
+      submissionTime, importsZipFile, workflowStoreEntryId.?) <> (WorkflowStoreEntry.tupled, WorkflowStoreEntry.unapply)
 
     def ucWorkflowStoreEntryWeu = index("UC_WORKFLOW_STORE_ENTRY_WEU", workflowExecutionUuid, unique = true)
 
diff --git a/database/sql/src/main/scala/cromwell/database/sql/SqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/SqlDatabase.scala
index c6c29479ba0..e1431de761c 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/SqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/SqlDatabase.scala
@@ -10,7 +10,8 @@ trait SqlDatabase extends AutoCloseable
   with CallCachingSqlDatabase
   with JobStoreSqlDatabase
   with MetadataSqlDatabase
-  with WorkflowStoreSqlDatabase {
+  with WorkflowStoreSqlDatabase
+  with SubWorkflowStoreSqlDatabase {
 
   protected val urlKey: String
   protected val originalDatabaseConfig: Config
diff --git a/database/sql/src/main/scala/cromwell/database/sql/SubWorkflowStoreSqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/SubWorkflowStoreSqlDatabase.scala
new file mode 100644
index 00000000000..10707dc9031
--- /dev/null
+++ b/database/sql/src/main/scala/cromwell/database/sql/SubWorkflowStoreSqlDatabase.scala
@@ -0,0 +1,21 @@
+package cromwell.database.sql
+
+import cromwell.database.sql.tables.SubWorkflowStoreEntry
+
+import scala.concurrent.{ExecutionContext, Future}
+
+trait SubWorkflowStoreSqlDatabase {
+  this: SqlDatabase =>
+
+  def addSubWorkflowStoreEntry(rootWorkflowExecutionUuid: String,
+                               parentWorkflowExecutionUuid: String,
+                               callFullyQualifiedName: String,
+                               jobIndex: Int,
+                               jobAttempt: Int,
+                               subWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Unit]
+
+  def querySubWorkflowStore(parentWorkflowExecutionUuid: String, callFqn: String, jobIndex: Int, jobAttempt: Int)
+                    (implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]]
+
+  def removeSubWorkflowStoreEntries(parentWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Int]
+}
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
new file mode 100644
index 00000000000..2e718179a9f
--- /dev/null
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
@@ -0,0 +1,12 @@
+package cromwell.database.sql.tables
+
+case class SubWorkflowStoreEntry
+(
+  rootWorkflowId: Option[Int],
+  parentWorkflowExecutionUuid: String,
+  callFullyQualifiedName: String,
+  jobIndex: Int,
+  jobAttempt: Int,
+  subWorkflowExecutionUuid: String,
+  subWorkflowStoreEntryId: Option[Int] = None
+)
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
index 1154256b559..66cd800851e 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
@@ -1,6 +1,6 @@
 package cromwell.database.sql.tables
 
-import java.sql.{Clob, Timestamp}
+import java.sql.{Blob, Clob, Timestamp}
 
 case class WorkflowStoreEntry
 (
@@ -10,5 +10,6 @@ case class WorkflowStoreEntry
   workflowOptions: Clob,
   workflowState: String,
   submissionTime: Timestamp,
+  importsZipFile: Option[Blob],
   workflowStoreEntryId: Option[Int] = None
 )
diff --git a/engine/src/main/resources/logback.xml b/engine/src/main/resources/logback.xml
deleted file mode 100644
index fa27b5dde9b..00000000000
--- a/engine/src/main/resources/logback.xml
+++ /dev/null
@@ -1,36 +0,0 @@
-<configuration>
-  <if condition='property("LOG_MODE").toUpperCase().equals("STANDARD")'>
-    <then>
-      <appender name="STANDARD_APPENDER" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-          <pattern>%date %X{sourceThread} %-5level - %msg%n</pattern>
-        </encoder>
-      </appender>
-    </then>
-    <else>
-      <appender name="STANDARD_APPENDER" class="ch.qos.logback.core.helpers.NOPAppender" />
-    </else>
-  </if>
-
-  <if condition='property("LOG_MODE").toUpperCase().equals("PRETTY")'>
-    <then>
-      <appender name="PRETTY_APPENDER" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder class="ch.qos.logback.core.encoder.LayoutWrappingEncoder">
-          <layout class="cromwell.logging.TerminalLayout" />
-        </encoder>
-      </appender>
-      <logger name="liquibase" level="WARN"/>
-    </then>
-    <else>
-      <appender name="PRETTY_APPENDER" class="ch.qos.logback.core.helpers.NOPAppender" />
-    </else>
-  </if>
-
-  <root level="${LOG_LEVEL}">
-    <appender-ref ref="STANDARD_APPENDER" />
-    <appender-ref ref="PRETTY_APPENDER" />
-  </root>
-  <logger name="com.zaxxer.hikari" level="ERROR"/>
-  <logger name="HikariPool" level="ERROR"/>
-  <logger name="com.google.cloud.hadoop.gcsio.GoogleCloudStorageReadChannel" level="ERROR"/>
-</configuration>
diff --git a/engine/src/main/resources/swagger/cromwell.yaml b/engine/src/main/resources/swagger/cromwell.yaml
index 7960bb93714..e2e825f8f98 100644
--- a/engine/src/main/resources/swagger/cromwell.yaml
+++ b/engine/src/main/resources/swagger/cromwell.yaml
@@ -93,6 +93,11 @@ paths:
           required: false
           type: file
           in: formData
+        - name: wdlDependencies
+          description: Workflow Options JSON
+          required: false
+          type: file
+          in: formData
       tags:
         - Workflows
       responses:
@@ -134,6 +139,11 @@ paths:
           required: false
           type: file
           in: formData
+        - name: wdlDependencies
+          description: Workflow Options JSON
+          required: false
+          type: file
+          in: formData
       tags:
         - Workflows
       responses:
@@ -386,6 +396,13 @@ paths:
             type: string
           collectionFormat: multi
           in: query
+        - name: expandSubWorkflows
+          description: >
+            When true, metadata for sub workflows will be fetched and inserted automatically in the metadata response.
+          required: false
+          type: boolean
+          default: false
+          in: query
       tags:
         - Workflows
       responses:
diff --git a/engine/src/main/resources/workflowTimings/workflowTimings.html b/engine/src/main/resources/workflowTimings/workflowTimings.html
index bd9de21d647..3e1df152c7a 100644
--- a/engine/src/main/resources/workflowTimings/workflowTimings.html
+++ b/engine/src/main/resources/workflowTimings/workflowTimings.html
@@ -1,40 +1,33 @@
 <html>
 <head>
 
-<script type="text/javascript" src="https://www.google.com/jsapi?autoload={'modules':[{'name':'visualization',
+    <script type="text/javascript" src="https://www.google.com/jsapi?autoload={'modules':[{'name':'visualization',
        'version':'1','packages':['timeline']}]}"></script>
-<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script>
-<script type="text/javascript">
-
-    google.setOnLoadCallback(drawChart);
-    function addDataTableRow(dataTable, callName, callPartName, startDate, endDate) {
-        if (startDate <= endDate) {
-            dataTable.addRow([callName, callPartName, startDate, endDate]);
-        } else {
-            console.error("Unable to add '" + callName + "'s entry: '" + callPartName + "' because start-time '" + startDate + "'' is greater than end-time '" + endDate + "'");
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script>
+    <script type="text/javascript">
+
+        var parentWorkflowNames = [];
+        var expandedParentWorkflows = [];
+        var chartView;
+        
+        google.setOnLoadCallback(drawChart);
+        
+        function addDataTableRow(dataTable, callName, callPartName, startDate, endDate, ancestry) {
+            if (startDate <= endDate) {
+                newRow = dataTable.addRow([callName, callPartName, startDate, endDate]);
+                dataTable.setRowProperty(newRow, "ancestry", ancestry);
+            } else {
+                console.error("Unable to add '" + callName + "'s entry: '" + callPartName + "' because start-time '" + startDate + "'' is greater than end-time '" + endDate + "'");
+            }
         }
-    }
-
-    function drawChart() {
-        var includeKeys = ["start", "end", "executionStatus", "executionEvents"];
-        $.getJSON("./metadata?includeKey=" + includeKeys.join("&includeKey="), function( data ) {
-
-            var container = document.getElementById('chart_div');
-            var chart = new google.visualization.Timeline(container);
 
-            var dataTable = new google.visualization.DataTable();
-            dataTable.addColumn({ type: 'string', id: 'Position' });
-            dataTable.addColumn({ type: 'string', id: 'Name' });
-            dataTable.addColumn({ type: 'date', id: 'Start' });
-            dataTable.addColumn({ type: 'date', id: 'End' });
-
-            var executionCallsCount = 0;
+        function parseMetadata(data, dataTable, ancestry) {
             var workflowName = data.workflowName;
             var workflowEnd = null;
             if (data.hasOwnProperty("end")) {
                 workflowEnd = new Date(data.end);
             }
-
+            var executionCallsCount = 0;
             var callsList = data.calls;
             var sortable = [];
             for (var key in callsList) {
@@ -56,14 +49,21 @@
                     var callStatus = callList[callIndex].executionStatus;
 
                     // add the index of the shard if there is one
-                    var thisCallName = (index == -1 ? callName : callName + "." + index);
+                    var callLqn = (index == -1 ? callName : callName + "." + index);
 
                     // add the retry number, unless this was a successfuly first attempt (for brevity)
-                    thisCallName = ( callStatus == "Done" && attempt == 1 ? thisCallName : thisCallName + ".retry-" + attempt)
+                    callLqn = ( callStatus == "Done" && attempt == 1 ? callLqn : callLqn + ".retry-" + attempt);
 
                     // Remove the workflow name
-                    thisCallName = thisCallName.replace(new RegExp("^" + workflowName + "\\."), "");
+                    callLqn = callLqn.replace(new RegExp("^" + workflowName + "\\."), "");
 
+                    var callFqn;
+                    if (ancestry.length == 0) {
+                        callFqn = callLqn;
+                    } else {
+                        callFqn = ancestry.join("/") + "/" + callLqn;
+                    }
+                    
                     var executionEvents = callList[callIndex].executionEvents;
 
                     var firstEventStart = null;
@@ -85,7 +85,7 @@
                                 finalEventEnd = endDate
                             }
                             // NB: See the column definitions above.
-                            addDataTableRow(dataTable, thisCallName, description, startDate, endDate);
+                            addDataTableRow(dataTable, callFqn, description, startDate, endDate, ancestry);
                         }
 
                         if (callList[callIndex].hasOwnProperty("start")) {
@@ -102,42 +102,126 @@
                         }
 
                         if (firstEventStart == null || finalEventEnd == null) {
-                            addDataTableRow(dataTable, thisCallName, callList[callIndex].executionStatus, callStart, callEnd);
+                            addDataTableRow(dataTable, callFqn, callList[callIndex].executionStatus, callStart, callEnd, ancestry);
                         } else {
-                            if (callStart < firstEventStart) addDataTableRow(dataTable, thisCallName, "cromwell starting overhead", callStart, firstEventStart);
-                            if (callEnd > finalEventEnd) addDataTableRow(dataTable, thisCallName, "cromwell final overhead", finalEventEnd, callEnd);
+                            if (callStart < firstEventStart) addDataTableRow(dataTable, callFqn, "cromwell starting overhead", callStart, firstEventStart, ancestry);
+                            if (callEnd > finalEventEnd) addDataTableRow(dataTable, callFqn, "cromwell final overhead", finalEventEnd, callEnd, ancestry);
                         }
-                    } else if (callList[callIndex].executionStatus == "Running") {
+                    } else if (callList[callIndex].executionStatus == "Running" || callList[callIndex].executionStatus == "QueuedInCromwell" || callList[callIndex].executionStatus == "Starting") {
+                        var status = callList[callIndex].executionStatus
                         executionCallsCount++;
                         var endDate = workflowEnd;
                         if(endDate == null) {
-                            addDataTableRow(dataTable, thisCallName, "Running", new Date(callList[callIndex].start), new Date(Date.now()));
+                            addDataTableRow(dataTable, callFqn, status, new Date(callList[callIndex].start), new Date(Date.now()), ancestry);
                         }
                         else {
-                            addDataTableRow(dataTable, thisCallName, "Still running when workflow ended", new Date(callList[callIndex].start), endDate);
+                            addDataTableRow(dataTable, callFqn, "Still ".concat(status).concat(" when workflow ended"), new Date(callList[callIndex].start), endDate, ancestry);
                         }
                     }
+
+                    if (callList[callIndex].hasOwnProperty("subWorkflowMetadata")) {
+                        var clone = ancestry.slice(0);
+                        clone.push(callLqn);
+                        parentWorkflowNames.push(callFqn);
+                        executionCallsCount += parseMetadata(callList[callIndex].subWorkflowMetadata, dataTable, clone);
+                    }
                 }
             }
+            
+            return executionCallsCount;
+        }
 
-            var options = {
-                colors: ['#33178f', '#c5bc12', '#5e8229', '#9a03f8', '#9e4653', '#4ef2ca', '#2dd801', '#3f7b49', '#763097', '#bc8b28', '#cb716f', '#adce53', '#c3768d', '#fdf92a'],
-                height: executionCallsCount * 18 + 60,
-                timeline: {
-                    avoidOverlappingGridLines: false,
-                    showBarLabels: false,
-                    rowLabelStyle: { fontName: 'Helvetica', fontSize: 10, color: '#603913' },
-                    // Although bar labels are unshown, they still affect the height of each row. So make it small.
-                    barLabelStyle: { fontName: 'Helvetica', fontSize: 5, color: '#603913' },
+        function drawChart() {
+            var includeKeys = ["start", "end", "executionStatus", "executionEvents", "subWorkflowMetadata"];
+            $.getJSON("./metadata?expandSubWorkflows=true&includeKey=" + includeKeys.join("&includeKey="), function(data) {
+                var dataTable = new google.visualization.DataTable();
+                dataTable.addColumn({ type: 'string', id: 'Position' });
+                dataTable.addColumn({ type: 'string', id: 'Name' });
+                dataTable.addColumn({ type: 'date', id: 'Start' });
+                dataTable.addColumn({ type: 'date', id: 'End' });
+
+                var executionCallsCount =  parseMetadata(data, dataTable, []);
+
+                var options = {
+                    colors: ['#33178f', '#c5bc12', '#5e8229', '#9a03f8', '#9e4653', '#4ef2ca', '#2dd801', '#3f7b49', '#763097', '#bc8b28', '#cb716f', '#adce53', '#c3768d', '#fdf92a'],
+                    height: executionCallsCount * 18 + 60,
+                    timeline: {
+                        avoidOverlappingGridLines: false,
+                        showBarLabels: false,
+                        rowLabelStyle: { fontName: 'Helvetica', fontSize: 10, color: '#603913' },
+                        // Although bar labels are unshown, they still affect the height of each row. So make it small.
+                        barLabelStyle: { fontName: 'Helvetica', fontSize: 5, color: '#603913' },
+                    },
+                    tooltip: {isHtml: true}
+                };
+                
+                var container = document.getElementById('chart_div');
+                var chart = new google.visualization.Timeline(container);
+                chartView = hideAllSubWorkflows(dataTable);
+                
+                chart.draw(chartView, options);
+                
+                google.visualization.events.addListener(chart, 'select', selectHandler);
+
+                function selectHandler(e) {
+                    var selectedItem = chart.getSelection()[0];
+                    if (selectedItem) {
+                        chartView = toggleSubWorkflowRows(dataTable, selectedItem.row);
+                        chart.draw(chartView, options);
+                        // For some reason the tooltip gets stuck and doesn't disappear by itself, so remove it explicitly from the DOM
+                        $( ".google-visualization-tooltip" ).remove();
+                    }
                 }
+            });
+        }
+
+        function toggleSubWorkflowRows(dt, selectedRow) {
+            function filterFunction(cell, row, column, table) {
+                var ancestry = table.getRowProperty(row, "ancestry");
+                // Display the row if it's not a sub workflow or if its parent is in the list of workflows to expand.
+                return (ancestry.length == 0 || (expandedParentWorkflows.indexOf(ancestry[ancestry.length - 1]) != -1));
+            }
+    
+            var filter = {
+                test: filterFunction,
+                // Not used because all filtering is done in filterFunction but it's mandatory to have something else than the filter
+                column: 0
             };
-            chart.draw(dataTable, options);
-        });
-    }
-</script>
+            
+            var parentWorkflow;
+            if (selectedRow) parentWorkflow = chartView.getValue(selectedRow, 0);
+
+            var indexOfParentWorkflow = expandedParentWorkflows.indexOf(parentWorkflow);
+
+            if (indexOfParentWorkflow != -1) {
+                // Remove the parent workflow from the list if it's in it
+                expandedParentWorkflows.splice(indexOfParentWorkflow, 1);
+            } else if (parentWorkflow && parentWorkflowNames.indexOf(parentWorkflow) != -1) {
+                // Add it if it's not
+                expandedParentWorkflows.push(parentWorkflow);
+            }
+            
+            var rowsToDisplay = dt.getFilteredRows([filter]);
+            var view = new google.visualization.DataView(dt);
+            view.setRows(rowsToDisplay);
+            return view;
+        }
+        
+        function hideAllSubWorkflows(dt) {
+            var view = new google.visualization.DataView(dt);
+            function filterFunction(cell, row, column, table) {
+                return table.getRowProperty(row, "ancestry").length != 0;
+            }
+
+            view.hideRows(dt.getFilteredRows([{column: 0, test: filterFunction}]));
+            return view;
+        }
+        
+        
+    </script>
+    <title id="title"></title>
 </head>
 <body>
-<title id="title"></title>
 <div id="chart_div"></div>
 </body>
 </html>
diff --git a/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala b/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
index ab9cbceac34..a738984dd96 100644
--- a/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
+++ b/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
@@ -1,18 +1,40 @@
 package cromwell.engine
 
-import java.nio.file.{FileSystem, FileSystems}
-
+import akka.actor.ActorSystem
 import cats.data.Validated.{Invalid, Valid}
+import com.google.api.client.http.HttpResponseException
 import com.typesafe.config.ConfigFactory
 import cromwell.core.WorkflowOptions
-import cromwell.engine.backend.EnhancedWorkflowOptions._
-import cromwell.filesystems.gcs.{GcsFileSystem, GcsFileSystemProvider, GoogleConfiguration}
+import cromwell.core.path.{CustomRetryParams, DefaultPathBuilder, PathBuilder}
+import cromwell.core.retry.SimpleExponentialBackoff
+import cromwell.filesystems.gcs.{GoogleConfiguration, RetryableGcsPathBuilderFactory}
 import lenthall.exception.MessageAggregation
 import net.ceedubs.ficus.Ficus._
 
-import scala.concurrent.ExecutionContext
+import scala.concurrent.duration._
+import scala.language.postfixOps
+
+case class EngineFilesystems(actorSystem: ActorSystem) {
 
-object EngineFilesystems {
+  private def isFatalGcsException(t: Throwable): Boolean = t match {
+    case e: HttpResponseException if e.getStatusCode == 403 => true
+    case e: HttpResponseException if e.getStatusCode == 400 && e.getContent.contains("INVALID_ARGUMENT") => true
+    case _ => false
+  }
+
+  private def isTransientGcsException(t: Throwable): Boolean = t match {
+    // Quota exceeded
+    case e: HttpResponseException if e.getStatusCode == 429 => true
+    case _ => false
+  }
+
+  private val GcsRetryParams = CustomRetryParams(
+    timeout = Duration.Inf,
+    maxRetries = Option(3),
+    backoff = SimpleExponentialBackoff(1 seconds, 3 seconds, 1.5D),
+    isTransient = isTransientGcsException,
+    isFatal = isFatalGcsException
+  )
 
   private val config = ConfigFactory.load
   private val googleConf: GoogleConfiguration = GoogleConfiguration(config)
@@ -26,14 +48,11 @@ object EngineFilesystems {
     }
   }
 
-  def filesystemsForWorkflow(workflowOptions: WorkflowOptions)(implicit ec: ExecutionContext): List[FileSystem] = {
-    def gcsFileSystem: Option[GcsFileSystem] = {
-      googleAuthMode map { mode =>
-        val storage = mode.buildStorage(workflowOptions.toGoogleAuthOptions, googleConf.applicationName)
-        GcsFileSystem(GcsFileSystemProvider(storage))
-      }
-    }
+  private val gcsPathBuilderFactory = googleAuthMode map { mode =>
+    RetryableGcsPathBuilderFactory(mode, customRetryParams = GcsRetryParams)
+  }
 
-    List(gcsFileSystem, Option(FileSystems.getDefault)).flatten
+  def pathBuildersForWorkflow(workflowOptions: WorkflowOptions): List[PathBuilder] = {
+    List(gcsPathBuilderFactory map { _.withOptions(workflowOptions)(actorSystem) }, Option(DefaultPathBuilder)).flatten
   }
 }
diff --git a/engine/src/main/scala/cromwell/engine/EngineWorkflowDescriptor.scala b/engine/src/main/scala/cromwell/engine/EngineWorkflowDescriptor.scala
index c493b41a6a9..d8aa2a44dd2 100644
--- a/engine/src/main/scala/cromwell/engine/EngineWorkflowDescriptor.scala
+++ b/engine/src/main/scala/cromwell/engine/EngineWorkflowDescriptor.scala
@@ -1,20 +1,28 @@
 package cromwell.engine
 
-import java.nio.file.FileSystem
-
 import cromwell.backend.BackendWorkflowDescriptor
 import cromwell.core.WorkflowOptions.WorkflowOption
 import cromwell.core.callcaching.CallCachingMode
+import cromwell.core.path.PathBuilder
 import wdl4s._
 
-final case class EngineWorkflowDescriptor(backendDescriptor: BackendWorkflowDescriptor,
+final case class EngineWorkflowDescriptor(namespace: WdlNamespaceWithWorkflow,
+                                          backendDescriptor: BackendWorkflowDescriptor,
                                           workflowInputs: WorkflowCoercedInputs,
-                                          backendAssignments: Map[Call, String],
+                                          backendAssignments: Map[TaskCall, String],
                                           failureMode: WorkflowFailureMode,
-                                          engineFilesystems: List[FileSystem],
-                                          callCachingMode: CallCachingMode) {
-  def id = backendDescriptor.id
-  def namespace = backendDescriptor.workflowNamespace
-  def name = namespace.workflow.unqualifiedName
+                                          pathBuilders: List[PathBuilder],
+                                          callCachingMode: CallCachingMode,
+                                          parentWorkflow: Option[EngineWorkflowDescriptor] = None) {
+  
+  val rootWorkflow: EngineWorkflowDescriptor = parentWorkflow match {
+    case Some(parent) => parent.rootWorkflow
+    case None => this
+  }
+  
+  val id = backendDescriptor.id
+  lazy val workflow = backendDescriptor.workflow
+  lazy val name = workflow.unqualifiedName
+  val inputs = backendDescriptor.inputs
   def getWorkflowOption(key: WorkflowOption) = backendDescriptor.getWorkflowOption(key)
 }
diff --git a/engine/src/main/scala/cromwell/engine/WdlFunctions.scala b/engine/src/main/scala/cromwell/engine/WdlFunctions.scala
index 3cc8ee1cacd..9fe346c50d9 100644
--- a/engine/src/main/scala/cromwell/engine/WdlFunctions.scala
+++ b/engine/src/main/scala/cromwell/engine/WdlFunctions.scala
@@ -1,17 +1,13 @@
 package cromwell.engine
 
-import java.nio.file.FileSystem
-
-import cromwell.backend.wdl.{PureFunctions, ReadLikeFunctions}
-import wdl4s.expression.WdlStandardLibraryFunctions
+import cromwell.backend.wdl.ReadLikeFunctions
+import wdl4s.expression.PureStandardLibraryFunctionsLike
+import cromwell.core.path.PathBuilder
 import wdl4s.values.{WdlFile, WdlValue}
 
 import scala.util.{Failure, Try}
 
-class WdlFunctions(val fileSystems: List[FileSystem]) extends WdlStandardLibraryFunctions with ReadLikeFunctions with PureFunctions {
-  /**
-    * Ordered list of filesystems to be used to execute WDL functions needing IO.
-    */
+class WdlFunctions(val pathBuilders: List[PathBuilder]) extends PureStandardLibraryFunctionsLike with ReadLikeFunctions {
   private def fail(name: String) = Failure(new NotImplementedError(s"$name() not supported at the workflow level yet"))
 
   override def write_json(params: Seq[Try[WdlValue]]): Try[WdlFile] = fail("write_json")
diff --git a/engine/src/main/scala/cromwell/engine/backend/EnhancedWorkflowOptions.scala b/engine/src/main/scala/cromwell/engine/backend/EnhancedWorkflowOptions.scala
deleted file mode 100644
index e2043cb65bc..00000000000
--- a/engine/src/main/scala/cromwell/engine/backend/EnhancedWorkflowOptions.scala
+++ /dev/null
@@ -1,16 +0,0 @@
-package cromwell.engine.backend
-
-import cromwell.core.WorkflowOptions
-import cromwell.filesystems.gcs.GoogleAuthMode
-import cromwell.filesystems.gcs.GoogleAuthMode.GoogleAuthOptions
-
-import scala.util.Try
-
-object EnhancedWorkflowOptions {
-
-  implicit class GoogleAuthWorkflowOptions(val workflowOptions: WorkflowOptions) extends AnyVal {
-    def toGoogleAuthOptions: GoogleAuthMode.GoogleAuthOptions = new GoogleAuthOptions {
-      override def get(key: String): Try[String] = workflowOptions.get(key)
-    }
-  }
-}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala b/engine/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala
index 8abb0874cab..8a72bc414cc 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala
@@ -9,13 +9,15 @@ import better.files._
 import cats.instances.try_._
 import cats.syntax.functor._
 import cromwell.core.retry.SimpleExponentialBackoff
-import cromwell.core.{ExecutionStore => _, _}
+import cromwell.core._
 import cromwell.engine.workflow.SingleWorkflowRunnerActor._
 import cromwell.engine.workflow.WorkflowManagerActor.RetrieveNewWorkflows
-import cromwell.engine.workflow.workflowstore.WorkflowStoreActor
+import cromwell.engine.workflow.workflowstore.{InMemoryWorkflowStore, WorkflowStoreActor}
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor.SubmitWorkflow
+import cromwell.jobstore.EmptyJobStoreActor
 import cromwell.server.CromwellRootActor
 import cromwell.services.metadata.MetadataService.{GetSingleWorkflowMetadataAction, GetStatus, WorkflowOutputs}
+import cromwell.subworkflowstore.EmptySubWorkflowStoreActor
 import cromwell.webservice.PerRequest.RequestComplete
 import cromwell.webservice.metadata.MetadataBuilderActor
 import spray.http.StatusCodes
@@ -26,160 +28,151 @@ import scala.concurrent.duration._
 import scala.language.postfixOps
 import scala.util.{Failure, Try}
 
-object SingleWorkflowRunnerActor {
-  def props(source: WorkflowSourceFiles, metadataOutputFile: Option[Path]): Props = {
-    Props(new SingleWorkflowRunnerActor(source, metadataOutputFile))
-  }
-
-  sealed trait RunnerMessage
-  // The message to actually run the workflow is made explicit so the non-actor Main can `ask` this actor to do the
-  // running and collect a result.
-  case object RunWorkflow extends RunnerMessage
-  private case object IssuePollRequest extends RunnerMessage
-  private case object IssueReply extends RunnerMessage
-
-  sealed trait RunnerState
-  case object NotStarted extends RunnerState
-  case object RunningWorkflow extends RunnerState
-  case object RequestingOutputs extends RunnerState
-  case object RequestingMetadata extends RunnerState
-  case object Done extends RunnerState
-
-  final case class RunnerData(replyTo: Option[ActorRef] = None,
-                              terminalState: Option[WorkflowState] = None,
-                              id: Option[WorkflowId] = None,
-                              failures: Seq[Throwable] = Seq.empty) {
-
-    def addFailure(message: String): RunnerData = addFailure(new RuntimeException(message))
-
-    def addFailure(e: Throwable): RunnerData = this.copy(failures = e +: failures)
-  }
-
-  implicit class EnhancedJsObject(val jsObject: JsObject) extends AnyVal {
-    def state: WorkflowState = WorkflowState.fromString(jsObject.fields("status").asInstanceOf[JsString].value)
-  }
-
-  private val Tag = "SingleWorkflowRunnerActor"
-}
-
 /**
  * Designed explicitly for the use case of the 'run' functionality in Main. This Actor will start a workflow,
- * print out the outputs when complete and then shut down the actor system. Note that multiple aspects of this
- * are sub-optimal for future use cases where one might want a single workflow being run.
+ * print out the outputs when complete and reply with a result.
  */
-class SingleWorkflowRunnerActor(source: WorkflowSourceFiles, metadataOutputPath: Option[Path])
-  extends CromwellRootActor with LoggingFSM[RunnerState, RunnerData] {
+class SingleWorkflowRunnerActor(source: WorkflowSourceFilesCollection, metadataOutputPath: Option[Path])
+  extends CromwellRootActor with LoggingFSM[RunnerState, SwraData] {
+
+  override val serverMode = false
 
   import SingleWorkflowRunnerActor._
   private val backoff = SimpleExponentialBackoff(1 second, 1 minute, 1.2)
 
-  startWith(NotStarted, RunnerData())
-
-  private def requestMetadata: State = {
-    val metadataBuilder = context.actorOf(MetadataBuilderActor.props(serviceRegistryActor), s"MetadataRequest-Workflow-${stateData.id.get}")
-    metadataBuilder ! GetSingleWorkflowMetadataAction(stateData.id.get, None, None)
-    goto (RequestingMetadata)
-  }
-
-  private def schedulePollRequest(): Unit = {
-    // -Ywarn-value-discard should stash Cancellable to cancel
-    context.system.scheduler.scheduleOnce(backoff.backoffMillis.millis, self, IssuePollRequest)
-    ()
-  }
-
-  private def requestStatus(): Unit = {
-    // This requests status via the metadata service rather than instituting an FSM watch on the underlying workflow actor.
-    // Cromwell's eventual consistency means it isn't safe to use an FSM transition to a terminal state as the signal for
-    // when outputs or metadata have stabilized.
-    val metadataBuilder = context.actorOf(MetadataBuilderActor.props(serviceRegistryActor), s"StatusRequest-Workflow-${stateData.id.get}-request-${UUID.randomUUID()}")
-    metadataBuilder ! GetStatus(stateData.id.get)
-  }
+  override val abortJobsOnTerminate = true
+  override lazy val workflowStore = new InMemoryWorkflowStore()
+  override lazy val jobStoreActor = context.actorOf(EmptyJobStoreActor.props)
+  override lazy val subWorkflowStoreActor = context.actorOf(EmptySubWorkflowStoreActor.props)
 
-  private def issueReply: State = {
-    self ! IssueReply
-    goto (Done)
-  }
+  startWith(NotStarted, EmptySwraData)
 
   when (NotStarted) {
-    case Event(RunWorkflow, data) =>
+    case Event(RunWorkflow, EmptySwraData) =>
       log.info(s"$Tag: Submitting workflow")
       workflowStoreActor ! SubmitWorkflow(source)
-      goto (RunningWorkflow) using data.copy(replyTo = Option(sender()))
+      goto(SubmittedWorkflow) using SubmittedSwraData(sender())
   }
 
-  when (RunningWorkflow) {
-    case Event(WorkflowStoreActor.WorkflowSubmittedToStore(id), data) =>
+  when (SubmittedWorkflow) {
+    case Event(WorkflowStoreActor.WorkflowSubmittedToStore(id), SubmittedSwraData(replyTo)) =>
       log.info(s"$Tag: Workflow submitted UUID($id)")
       // Since we only have a single workflow, force the WorkflowManagerActor's hand in case the polling rate is long
       workflowManagerActor ! RetrieveNewWorkflows
       schedulePollRequest()
-      stay() using data.copy(id = Option(id))
-    case Event(IssuePollRequest, data) =>
-      data.id match {
-        case None => schedulePollRequest()
-        case _ => requestStatus()
-      }
+      goto(RunningWorkflow) using RunningSwraData(replyTo, id)
+  }
+
+  when (RunningWorkflow) {
+    case Event(IssuePollRequest, RunningSwraData(_, id)) =>
+      requestStatus(id)
       stay()
-    case Event(RequestComplete((StatusCodes.OK, jsObject: JsObject)), data) if !jsObject.state.isTerminal =>
+    case Event(RequestComplete((StatusCodes.OK, jsObject: JsObject)), RunningSwraData(_, _)) if !jsObject.state.isTerminal =>
       schedulePollRequest()
       stay()
-    case Event(RequestComplete((StatusCodes.OK, jsObject: JsObject)), data) if jsObject.state == WorkflowSucceeded =>
+    case Event(RequestComplete((StatusCodes.OK, jsObject: JsObject)), RunningSwraData(replyTo, id)) if jsObject.state == WorkflowSucceeded =>
       val metadataBuilder = context.actorOf(MetadataBuilderActor.props(serviceRegistryActor),
-        s"CompleteRequest-Workflow-${stateData.id.get}-request-${UUID.randomUUID()}")
-      metadataBuilder ! WorkflowOutputs(data.id.get)
-      goto(RequestingOutputs) using data.copy(terminalState = Option(WorkflowSucceeded))
-    case Event(RequestComplete((StatusCodes.OK, jsObject: JsObject)), data) if jsObject.state == WorkflowFailed =>
-      val updatedData = data.copy(terminalState = Option(WorkflowFailed)).addFailure(s"Workflow ${data.id.get} transitioned to state Failed")
-      // If there's an output path specified then request metadata, otherwise issue a reply to the original sender.
-      val nextState = if (metadataOutputPath.isDefined) requestMetadata else issueReply
-      nextState using updatedData
+        s"CompleteRequest-Workflow-$id-request-${UUID.randomUUID()}")
+      metadataBuilder ! WorkflowOutputs(id)
+      log.info(s"$Tag workflow finished with status '$WorkflowSucceeded'.")
+      goto(RequestingOutputs) using SucceededSwraData(replyTo, id)
+    case Event(RequestComplete((StatusCodes.OK, jsObject: JsObject)), RunningSwraData(replyTo, id)) if jsObject.state == WorkflowFailed =>
+      log.info(s"$Tag workflow finished with status '$WorkflowFailed'.")
+      requestMetadataOrIssueReply(FailedSwraData(replyTo, id, new RuntimeException(s"Workflow $id transitioned to state $WorkflowFailed")))
+    case Event(RequestComplete((StatusCodes.OK, jsObject: JsObject)), RunningSwraData(replyTo, id)) if jsObject.state == WorkflowAborted =>
+      log.info(s"$Tag workflow finished with status '$WorkflowAborted'.")
+      requestMetadataOrIssueReply(AbortedSwraData(replyTo, id))
   }
 
   when (RequestingOutputs) {
-    case Event(RequestComplete((StatusCodes.OK, outputs: JsObject)), _) =>
+    case Event(RequestComplete((StatusCodes.OK, outputs: JsObject)), data: TerminalSwraData) =>
       outputOutputs(outputs)
-      if (metadataOutputPath.isDefined) requestMetadata else issueReply
+      requestMetadataOrIssueReply(data)
   }
 
   when (RequestingMetadata) {
-    case Event(RequestComplete((StatusCodes.OK, metadata: JsObject)), _) =>
+    case Event(RequestComplete((StatusCodes.OK, metadata: JsObject)), data: TerminalSwraData) =>
       outputMetadata(metadata)
-      issueReply
-  }
-
-  when (Done) {
-    case Event(IssueReply, data) =>
-      data.terminalState foreach { state => log.info(s"$Tag workflow finished with status '$state'.") }
-      data.failures foreach { e => log.error(e, e.getMessage) }
-
-      val message: Any = data.terminalState collect { case WorkflowSucceeded => () } getOrElse Status.Failure(data.failures.head)
-      data.replyTo foreach  { _ ! message }
-      stay()
+      issueReply(data)
   }
 
   onTransition {
     case NotStarted -> RunningWorkflow => schedulePollRequest()
   }
 
-  private def failAndFinish(e: Throwable): State = {
-    log.error(e, s"$Tag received Failure message: ${e.getMessage}")
-    issueReply using stateData.addFailure(e)
-  }
-
   whenUnhandled {
     // Handle failures for all failure responses generically.
-    case Event(r: WorkflowStoreActor.WorkflowAbortFailed, data) => failAndFinish(r.reason)
-    case Event(Failure(e), data) => failAndFinish(e)
-    case Event(Status.Failure(e), data) => failAndFinish(e)
-    case Event(RequestComplete((_, snap)), _) => failAndFinish(new RuntimeException(s"Unexpected API completion message: $snap"))
+    case Event(r: WorkflowStoreActor.WorkflowAbortFailed, data) => failAndFinish(r.reason, data)
+    case Event(Failure(e), data) => failAndFinish(e, data)
+    case Event(Status.Failure(e), data) => failAndFinish(e, data)
+    case Event(RequestComplete((_, snap)), data) => failAndFinish(new RuntimeException(s"Unexpected API completion message: $snap"), data)
     case Event((CurrentState(_, _) | Transition(_, _, _)), _) =>
       // ignore uninteresting current state and transition messages
       stay()
-    case Event(m, _) =>
-      log.warning(s"$Tag: received unexpected message: $m")
+    case Event(m, d) =>
+      log.warning(s"$Tag: received unexpected message: $m in state ${d.getClass.getSimpleName}")
       stay()
   }
 
+  private def requestMetadataOrIssueReply(newData: TerminalSwraData) = if (metadataOutputPath.isDefined) requestMetadata(newData) else issueReply(newData)
+  
+  private def requestMetadata(newData: TerminalSwraData): State = {
+    val metadataBuilder = context.actorOf(MetadataBuilderActor.props(serviceRegistryActor), s"MetadataRequest-Workflow-${newData.id}")
+    metadataBuilder ! GetSingleWorkflowMetadataAction(newData.id, None, None, expandSubWorkflows = true)
+    goto (RequestingMetadata) using newData
+  }
+
+  private def schedulePollRequest(): Unit = {
+    // -Ywarn-value-discard should stash Cancellable to cancel
+    context.system.scheduler.scheduleOnce(backoff.backoffMillis.millis, self, IssuePollRequest)
+    ()
+  }
+
+  private def requestStatus(id: WorkflowId): Unit = {
+    // This requests status via the metadata service rather than instituting an FSM watch on the underlying workflow actor.
+    // Cromwell's eventual consistency means it isn't safe to use an FSM transition to a terminal state as the signal for
+    // when outputs or metadata have stabilized.
+    val metadataBuilder = context.actorOf(MetadataBuilderActor.props(serviceRegistryActor), s"StatusRequest-Workflow-$id-request-${UUID.randomUUID()}")
+    metadataBuilder ! GetStatus(id)
+  }
+
+  private def issueSuccessReply(replyTo: ActorRef): State = {
+    replyTo.tell(msg = (), sender = self) // Because replyTo ! () is the parameterless call replyTo.!()
+    context.stop(self)
+    stay()
+  }
+
+  private def issueFailureReply(replyTo: ActorRef, e: Throwable): State = {
+    replyTo ! Status.Failure(e)
+    context.stop(self)
+    stay()
+  }
+
+  private def issueReply(data: TerminalSwraData) = {
+    data match {
+      case s: SucceededSwraData => issueSuccessReply(s.replyTo)
+      case f: FailedSwraData => issueFailureReply(f.replyTo, f.failure)
+      case a: AbortedSwraData => issueSuccessReply(a.replyTo)
+
+    }
+  }
+
+  private def failAndFinish(e: Throwable, data: SwraData): State = {
+    log.error(e, s"$Tag received Failure message: ${e.getMessage}")
+    data match {
+      case EmptySwraData =>
+        log.error(e, "Cannot issue response. Need a 'replyTo' address to issue the exception response")
+        context.stop(self)
+        stay()
+      case SubmittedSwraData(replyTo) =>
+        issueFailureReply(replyTo, e)
+      case RunningSwraData(replyTo, _) =>
+        issueFailureReply(replyTo, e)
+      case c: TerminalSwraData =>
+        issueFailureReply(c.replyTo, e)
+    }
+  }
+
   /**
     * Outputs the outputs to stdout, and then requests the metadata.
     */
@@ -199,3 +192,44 @@ class SingleWorkflowRunnerActor(source: WorkflowSourceFiles, metadataOutputPath:
     } void
   }
 }
+
+object SingleWorkflowRunnerActor {
+  def props(source: WorkflowSourceFilesCollection, metadataOutputFile: Option[Path]): Props = {
+    Props(new SingleWorkflowRunnerActor(source, metadataOutputFile))
+  }
+
+  sealed trait RunnerMessage
+  // The message to actually run the workflow is made explicit so the non-actor Main can `ask` this actor to do the
+  // running and collect a result.
+  case object RunWorkflow extends RunnerMessage
+  private case object IssuePollRequest extends RunnerMessage
+
+  sealed trait RunnerState
+  case object NotStarted extends RunnerState
+  case object SubmittedWorkflow extends RunnerState
+  case object RunningWorkflow extends RunnerState
+  case object RequestingOutputs extends RunnerState
+  case object RequestingMetadata extends RunnerState
+
+  sealed trait SwraData
+  case object EmptySwraData extends SwraData
+  final case class SubmittedSwraData(replyTo: ActorRef) extends SwraData
+  final case class RunningSwraData(replyTo: ActorRef, id: WorkflowId) extends SwraData
+
+  sealed trait TerminalSwraData extends SwraData { def replyTo: ActorRef; def terminalState: WorkflowState; def id: WorkflowId }
+  final case class SucceededSwraData(replyTo: ActorRef,
+                                     id: WorkflowId) extends TerminalSwraData { override val terminalState = WorkflowSucceeded }
+
+  final case class FailedSwraData(replyTo: ActorRef,
+                                  id: WorkflowId,
+                                  failure: Throwable) extends TerminalSwraData { override val terminalState = WorkflowFailed }
+
+  final case class AbortedSwraData(replyTo: ActorRef,
+                                   id: WorkflowId) extends TerminalSwraData { override val terminalState = WorkflowAborted }
+
+  implicit class EnhancedJsObject(val jsObject: JsObject) extends AnyVal {
+    def state: WorkflowState = WorkflowState.fromString(jsObject.fields("status").asInstanceOf[JsString].value)
+  }
+
+  private val Tag = "SingleWorkflowRunnerActor"
+}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
index 1035872d360..6d2a2ff40a6 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
@@ -1,15 +1,14 @@
 package cromwell.engine.workflow
 
-import java.time.OffsetDateTime
-
 import akka.actor.SupervisorStrategy.Escalate
 import akka.actor._
 import com.typesafe.config.Config
-import cromwell.backend.AllBackendInitializationData
+import cromwell.backend._
 import cromwell.core.Dispatcher.EngineDispatcher
 import cromwell.core.WorkflowOptions.FinalWorkflowLogDir
 import cromwell.core._
 import cromwell.core.logging.{WorkflowLogger, WorkflowLogging}
+import cromwell.core.path.PathFactory
 import cromwell.engine._
 import cromwell.engine.backend.BackendSingletonCollection
 import cromwell.engine.workflow.WorkflowActor._
@@ -17,13 +16,12 @@ import cromwell.engine.workflow.lifecycle.MaterializeWorkflowDescriptorActor.{Ma
 import cromwell.engine.workflow.lifecycle.WorkflowFinalizationActor.{StartFinalizationCommand, WorkflowFinalizationFailedResponse, WorkflowFinalizationSucceededResponse}
 import cromwell.engine.workflow.lifecycle.WorkflowInitializationActor.{StartInitializationCommand, WorkflowInitializationFailedResponse, WorkflowInitializationSucceededResponse}
 import cromwell.engine.workflow.lifecycle._
-import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor
+import cromwell.engine.workflow.lifecycle.execution.{WorkflowExecutionActor, WorkflowMetadataHelper}
 import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor._
 import cromwell.services.metadata.MetadataService._
-import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
+import cromwell.subworkflowstore.SubWorkflowStoreActor.WorkflowComplete
 import cromwell.webservice.EngineStatsActor
-
-import scala.util.Random
+import wdl4s.{LocallyQualifiedName => _}
 
 object WorkflowActor {
 
@@ -135,16 +133,18 @@ object WorkflowActor {
 
   def props(workflowId: WorkflowId,
             startMode: StartMode,
-            wdlSource: WorkflowSourceFiles,
+            wdlSource: WorkflowSourceFilesCollection,
             conf: Config,
             serviceRegistryActor: ActorRef,
             workflowLogCopyRouter: ActorRef,
             jobStoreActor: ActorRef,
+            subWorkflowStoreActor: ActorRef,
             callCacheReadActor: ActorRef,
             jobTokenDispenserActor: ActorRef,
-            backendSingletonCollection: BackendSingletonCollection): Props = {
+            backendSingletonCollection: BackendSingletonCollection,
+            serverMode: Boolean): Props = {
     Props(new WorkflowActor(workflowId, startMode, wdlSource, conf, serviceRegistryActor, workflowLogCopyRouter,
-      jobStoreActor, callCacheReadActor, jobTokenDispenserActor, backendSingletonCollection)).withDispatcher(EngineDispatcher)
+      jobStoreActor, subWorkflowStoreActor, callCacheReadActor, jobTokenDispenserActor, backendSingletonCollection, serverMode)).withDispatcher(EngineDispatcher)
   }
 }
 
@@ -153,30 +153,32 @@ object WorkflowActor {
   */
 class WorkflowActor(val workflowId: WorkflowId,
                     startMode: StartMode,
-                    workflowSources: WorkflowSourceFiles,
+                    workflowSources: WorkflowSourceFilesCollection,
                     conf: Config,
-                    serviceRegistryActor: ActorRef,
+                    override val serviceRegistryActor: ActorRef,
                     workflowLogCopyRouter: ActorRef,
                     jobStoreActor: ActorRef,
+                    subWorkflowStoreActor: ActorRef,
                     callCacheReadActor: ActorRef,
                     jobTokenDispenserActor: ActorRef,
-                    backendSingletonCollection: BackendSingletonCollection)
-  extends LoggingFSM[WorkflowActorState, WorkflowActorData] with WorkflowLogging with PathFactory {
+                    backendSingletonCollection: BackendSingletonCollection,
+                    serverMode: Boolean)
+  extends LoggingFSM[WorkflowActorState, WorkflowActorData] with WorkflowLogging with WorkflowMetadataHelper {
 
   implicit val ec = context.dispatcher
+  override val workflowIdForLogging = workflowId
 
   startWith(WorkflowUnstartedState, WorkflowActorData.empty)
 
-  pushCurrentStateToMetadataService(WorkflowUnstartedState.workflowState)
-
+  pushCurrentStateToMetadataService(workflowId, WorkflowUnstartedState.workflowState)
+  
   override def supervisorStrategy: SupervisorStrategy = OneForOneStrategy() { case _ => Escalate }
 
   when(WorkflowUnstartedState) {
     case Event(StartWorkflowCommand, _) =>
-      val actor = context.actorOf(MaterializeWorkflowDescriptorActor.props(serviceRegistryActor, workflowId),
+      val actor = context.actorOf(MaterializeWorkflowDescriptorActor.props(serviceRegistryActor, workflowId, importLocalFilesystem = !serverMode),
         "MaterializeWorkflowDescriptorActor")
-      val startEvent = MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.StartTime), MetadataValue(OffsetDateTime.now.toString))
-      serviceRegistryActor ! PutMetadataAction(startEvent)
+      pushWorkflowStart(workflowId)
 
       actor ! MaterializeWorkflowDescriptorCommand(workflowSources, conf)
       goto(MaterializingWorkflowDescriptorState) using stateData.copy(currentLifecycleStateActor = Option(actor))
@@ -203,10 +205,11 @@ class WorkflowActor(val workflowId: WorkflowId,
         case RestartExistingWorkflow => true
       }
 
-      val executionActor = context.actorOf(WorkflowExecutionActor.props(workflowId,
+      val executionActor = context.actorOf(WorkflowExecutionActor.props(
         workflowDescriptor,
         serviceRegistryActor,
         jobStoreActor,
+        subWorkflowStoreActor,
         callCacheReadActor,
         jobTokenDispenserActor,
         backendSingletonCollection,
@@ -217,16 +220,16 @@ class WorkflowActor(val workflowId: WorkflowId,
 
       goto(ExecutingWorkflowState) using data.copy(currentLifecycleStateActor = Option(executionActor), initializationData = initializationData)
     case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _)) =>
-      finalizeWorkflow(data, workflowDescriptor, ExecutionStore.empty, OutputStore.empty, Option(reason.toList))
+      finalizeWorkflow(data, workflowDescriptor, Map.empty, Map.empty, Option(reason.toList))
   }
 
   when(ExecutingWorkflowState) {
-    case Event(WorkflowExecutionSucceededResponse(executionStore, outputStore),
+    case Event(WorkflowExecutionSucceededResponse(jobKeys, outputs),
     data @ WorkflowActorData(_, Some(workflowDescriptor), _, _)) =>
-      finalizeWorkflow(data, workflowDescriptor, executionStore, outputStore, None)
-    case Event(WorkflowExecutionFailedResponse(executionStore, outputStore, failures),
+      finalizeWorkflow(data, workflowDescriptor, jobKeys, outputs, None)
+    case Event(WorkflowExecutionFailedResponse(jobKeys, failures),
     data @ WorkflowActorData(_, Some(workflowDescriptor), _, _)) =>
-      finalizeWorkflow(data, workflowDescriptor, executionStore, outputStore, Option(failures.toList))
+      finalizeWorkflow(data, workflowDescriptor, jobKeys, Map.empty, Option(List(failures)))
     case Event(msg @ EngineStatsActor.JobCountQuery, data) =>
       data.currentLifecycleStateActor match {
         case Some(a) => a forward msg
@@ -245,7 +248,7 @@ class WorkflowActor(val workflowId: WorkflowId,
 
   when(WorkflowAbortingState) {
     case Event(x: EngineLifecycleStateCompleteResponse, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _)) =>
-      finalizeWorkflow(data, workflowDescriptor, ExecutionStore.empty, OutputStore.empty, failures = None)
+      finalizeWorkflow(data, workflowDescriptor, Map.empty, Map.empty, failures = None)
     case _ => stay()
   }
 
@@ -278,22 +281,19 @@ class WorkflowActor(val workflowId: WorkflowId,
       // Only publish "External" state to metadata service
       // workflowState maps a state to an "external" state (e.g all states extending WorkflowActorRunningState map to WorkflowRunning)
       if (fromState.workflowState != toState.workflowState) {
-        pushCurrentStateToMetadataService(toState.workflowState)
+        pushCurrentStateToMetadataService(workflowId, toState.workflowState)
       }
   }
 
   onTransition {
     case (oldState, terminalState: WorkflowActorTerminalState) =>
       workflowLogger.debug(s"transition from {} to {}. Stopping self.", arg1 = oldState, arg2 = terminalState)
-      // Add the end time of the workflow in the MetadataService
-      val now = OffsetDateTime.now
-      val metadataEventMsg = MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.EndTime), MetadataValue(now))
-      serviceRegistryActor ! PutMetadataAction(metadataEventMsg)
+      pushWorkflowEnd(workflowId)
+      subWorkflowStoreActor ! WorkflowComplete(workflowId)
       terminalState match {
         case WorkflowFailedState =>
           val failures = nextStateData.lastStateReached.failures.getOrElse(List.empty)
-          val failureEvents = failures flatMap { r => throwableToMetadataEvents(MetadataKey(workflowId, None, s"${WorkflowMetadataKeys.Failures}[${Random.nextInt(Int.MaxValue)}]"), r) }
-          serviceRegistryActor ! PutMetadataAction(failureEvents)
+          pushWorkflowFailures(workflowId, failures)
           context.parent ! WorkflowFailedResponse(workflowId, nextStateData.lastStateReached.state, failures)
         case _ => // The WMA is watching state transitions and needs no further info
       }
@@ -303,7 +303,7 @@ class WorkflowActor(val workflowId: WorkflowId,
         stateData.workflowDescriptor foreach { wd =>
           wd.getWorkflowOption(FinalWorkflowLogDir) match {
             case Some(destinationDir) =>
-              workflowLogCopyRouter ! CopyWorkflowLogsActor.Copy(wd.id, buildPath(destinationDir, wd.engineFilesystems))
+              workflowLogCopyRouter ! CopyWorkflowLogsActor.Copy(wd.id, PathFactory.buildPath(destinationDir, wd.pathBuilders))
             case None if WorkflowLogger.isTemporary => workflowLogger.deleteLogFile()
             case _ =>
           }
@@ -323,24 +323,17 @@ class WorkflowActor(val workflowId: WorkflowId,
     goto(finalState) using data.copy(currentLifecycleStateActor = None)
   }
 
-  private[workflow] def makeFinalizationActor(workflowDescriptor: EngineWorkflowDescriptor, executionStore: ExecutionStore, outputStore: OutputStore) = {
-    context.actorOf(WorkflowFinalizationActor.props(workflowId, workflowDescriptor, executionStore, outputStore, stateData.initializationData), name = s"WorkflowFinalizationActor")
+  private[workflow] def makeFinalizationActor(workflowDescriptor: EngineWorkflowDescriptor, jobExecutionMap: JobExecutionMap, workflowOutputs: CallOutputs) = {
+    context.actorOf(WorkflowFinalizationActor.props(workflowId, workflowDescriptor, jobExecutionMap, workflowOutputs, stateData.initializationData), name = s"WorkflowFinalizationActor")
   }
   /**
     * Run finalization actor and transition to FinalizingWorkflowState.
     */
   private def finalizeWorkflow(data: WorkflowActorData, workflowDescriptor: EngineWorkflowDescriptor,
-                               executionStore: ExecutionStore, outputStore: OutputStore,
+                               jobExecutionMap: JobExecutionMap, workflowOutputs: CallOutputs,
                                failures: Option[List[Throwable]]) = {
-    val finalizationActor = makeFinalizationActor(workflowDescriptor, executionStore, outputStore)
+    val finalizationActor = makeFinalizationActor(workflowDescriptor, jobExecutionMap, workflowOutputs)
     finalizationActor ! StartFinalizationCommand
     goto(FinalizingWorkflowState) using data.copy(lastStateReached = StateCheckpoint(stateName, failures))
   }
-
-  // Update the current State of the Workflow (corresponding to the FSM state) in the Metadata service
-  private def pushCurrentStateToMetadataService(workflowState: WorkflowState): Unit = {
-    val metadataEventMsg = MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.Status),
-      MetadataValue(workflowState))
-    serviceRegistryActor ! PutMetadataAction(metadataEventMsg)
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
index 08bade65454..a19772cd83b 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
@@ -1,6 +1,5 @@
 package cromwell.engine.workflow
 
-
 import akka.actor.FSM.{CurrentState, SubscribeTransitionCallBack, Transition}
 import akka.actor._
 import akka.event.Logging
@@ -16,8 +15,10 @@ import cromwell.jobstore.JobStoreActor.{JobStoreWriteFailure, JobStoreWriteSucce
 import cromwell.services.metadata.MetadataService._
 import cromwell.webservice.EngineStatsActor
 import net.ceedubs.ficus.Ficus._
+import org.apache.commons.lang3.exception.ExceptionUtils
+
 import scala.concurrent.duration._
-import scala.concurrent.{Await, Promise}
+import scala.sys.ShutdownHookThread
 
 object WorkflowManagerActor {
   val DefaultMaxWorkflowsToRun = 5000
@@ -42,12 +43,16 @@ object WorkflowManagerActor {
             serviceRegistryActor: ActorRef,
             workflowLogCopyRouter: ActorRef,
             jobStoreActor: ActorRef,
+            subWorkflowStoreActor: ActorRef,
             callCacheReadActor: ActorRef,
             jobTokenDispenserActor: ActorRef,
-            backendSingletonCollection: BackendSingletonCollection): Props = {
-    Props(new WorkflowManagerActor(
-      workflowStore, serviceRegistryActor, workflowLogCopyRouter, jobStoreActor, callCacheReadActor, jobTokenDispenserActor, backendSingletonCollection)
-    ).withDispatcher(EngineDispatcher)
+            backendSingletonCollection: BackendSingletonCollection,
+            abortJobsOnTerminate: Boolean,
+            serverMode: Boolean): Props = {
+    val params = WorkflowManagerActorParams(ConfigFactory.load, workflowStore, serviceRegistryActor,
+      workflowLogCopyRouter, jobStoreActor, subWorkflowStoreActor, callCacheReadActor, jobTokenDispenserActor, backendSingletonCollection,
+      abortJobsOnTerminate, serverMode)
+    Props(new WorkflowManagerActor(params)).withDispatcher(EngineDispatcher)
   }
 
   /**
@@ -78,24 +83,22 @@ object WorkflowManagerActor {
   }
 }
 
-class WorkflowManagerActor(config: Config,
-                           val workflowStore: ActorRef,
-                           val serviceRegistryActor: ActorRef,
-                           val workflowLogCopyRouter: ActorRef,
-                           val jobStoreActor: ActorRef,
-                           val callCacheReadActor: ActorRef,
-                           val jobTokenDispenserActor: ActorRef,
-                           val backendSingletonCollection: BackendSingletonCollection)
+case class WorkflowManagerActorParams(config: Config,
+                                      workflowStore: ActorRef,
+                                      serviceRegistryActor: ActorRef,
+                                      workflowLogCopyRouter: ActorRef,
+                                      jobStoreActor: ActorRef,
+                                      subWorkflowStoreActor: ActorRef,
+                                      callCacheReadActor: ActorRef,
+                                      jobTokenDispenserActor: ActorRef,
+                                      backendSingletonCollection: BackendSingletonCollection,
+                                      abortJobsOnTerminate: Boolean,
+                                      serverMode: Boolean)
+
+class WorkflowManagerActor(params: WorkflowManagerActorParams)
   extends LoggingFSM[WorkflowManagerState, WorkflowManagerData] {
 
-  def this(workflowStore: ActorRef,
-           serviceRegistryActor: ActorRef,
-           workflowLogCopyRouter: ActorRef,
-           jobStoreActor: ActorRef,
-           callCacheReadActor: ActorRef,
-           jobTokenDispenserActor: ActorRef,
-           backendSingletonCollection: BackendSingletonCollection) = this(
-    ConfigFactory.load, workflowStore, serviceRegistryActor, workflowLogCopyRouter, jobStoreActor, callCacheReadActor, jobTokenDispenserActor, backendSingletonCollection)
+  private val config = params.config
 
   private val maxWorkflowsRunning = config.getConfig("system").as[Option[Int]]("max-concurrent-workflows").getOrElse(DefaultMaxWorkflowsToRun)
   private val maxWorkflowsToLaunch = config.getConfig("system").as[Option[Int]]("max-workflow-launch-count").getOrElse(DefaultMaxWorkflowsToLaunch)
@@ -104,9 +107,8 @@ class WorkflowManagerActor(config: Config,
   private val logger = Logging(context.system, this)
   private val tag = self.path.name
 
-  private val donePromise = Promise[Unit]()
-
   private var abortingWorkflowToReplyTo = Map.empty[WorkflowId, ActorRef]
+  private var shutdownHookThreadOption: Option[ShutdownHookThread] = None
 
   override def preStart(): Unit = {
     addShutdownHook()
@@ -114,18 +116,38 @@ class WorkflowManagerActor(config: Config,
     self ! RetrieveNewWorkflows
   }
 
+  override def postStop() = {
+    // If the actor is stopping, especially during error tests, then there's nothing to wait for later at JVM shutdown.
+    tryRemoveShutdownHook()
+    super.postStop()
+  }
+
   private def addShutdownHook() = {
-    // Only abort jobs on SIGINT if the config explicitly sets system.abortJobsOnTerminate = true.
+    // Only abort jobs on SIGINT if the config explicitly sets system.abort-jobs-on-terminate = true.
     val abortJobsOnTerminate =
-      config.getConfig("system").as[Option[Boolean]]("abort-jobs-on-terminate").getOrElse(false)
+    config.getConfig("system").as[Option[Boolean]]("abort-jobs-on-terminate").getOrElse(params.abortJobsOnTerminate)
 
     if (abortJobsOnTerminate) {
-      sys.addShutdownHook {
-        logger.info(s"$tag: Received shutdown signal. Aborting all running workflows...")
+      val shutdownHookThread = sys.addShutdownHook {
+        logger.info(s"$tag: Received shutdown signal.")
         self ! AbortAllWorkflowsCommand
-        Await.result(donePromise.future, Duration.Inf)
+        while (stateData != null && stateData.workflows.nonEmpty) {
+          log.info(s"Waiting for ${stateData.workflows.size} workflows to abort...")
+          Thread.sleep(1000)
+        }
       }
+      shutdownHookThreadOption = Option(shutdownHookThread)
+    }
+  }
+
+  private def tryRemoveShutdownHook() = {
+    try {
+      shutdownHookThreadOption.foreach(_.remove())
+    } catch {
+      case _: IllegalStateException => /* ignore, we're probably shutting down */
+      case exception: Exception => log.error(exception, "Error while removing shutdown hook: {}", exception.getMessage)
     }
+    shutdownHookThreadOption = None
   }
 
   startWith(Running, WorkflowManagerData(workflows = Map.empty))
@@ -140,7 +162,7 @@ class WorkflowManagerActor(config: Config,
         Determine the number of available workflow slots and request the smaller of that number of maxWorkflowsToLaunch.
        */
       val maxNewWorkflows = maxWorkflowsToLaunch min (maxWorkflowsRunning - stateData.workflows.size)
-      workflowStore ! WorkflowStoreActor.FetchRunnableWorkflows(maxNewWorkflows)
+      params.workflowStore ! WorkflowStoreActor.FetchRunnableWorkflows(maxNewWorkflows)
       stay()
     case Event(WorkflowStoreActor.NoNewWorkflowsToStart, stateData) =>
       log.debug("WorkflowStore provided no new workflows to start")
@@ -178,7 +200,7 @@ class WorkflowManagerActor(config: Config,
      Responses from services
      */
     case Event(WorkflowFailedResponse(workflowId, inState, reasons), data) =>
-      log.error(s"$tag Workflow $workflowId failed (during $inState): ${reasons.mkString("\n")}")
+      log.error(s"$tag Workflow $workflowId failed (during $inState): ${expandFailureReasons(reasons)}")
       stay()
     /*
      Watched transitions
@@ -187,13 +209,13 @@ class WorkflowManagerActor(config: Config,
       log.info(s"$tag ${workflowActor.path.name} is in a terminal state: $toState")
       // This silently fails if idFromActor is None, but data.without call right below will as well
       data.idFromActor(workflowActor) foreach { workflowId =>
-        jobStoreActor ! RegisterWorkflowCompleted(workflowId)
+        params.jobStoreActor ! RegisterWorkflowCompleted(workflowId)
         if (toState.workflowState == WorkflowAborted) {
           val replyTo = abortingWorkflowToReplyTo(workflowId)
           replyTo ! WorkflowStoreActor.WorkflowAborted(workflowId)
           abortingWorkflowToReplyTo -= workflowId
         } else {
-          workflowStore ! WorkflowStoreActor.RemoveWorkflow(workflowId)
+          params.workflowStore ! WorkflowStoreActor.RemoveWorkflow(workflowId)
         }
       }
       stay using data.without(workflowActor)
@@ -242,8 +264,7 @@ class WorkflowManagerActor(config: Config,
 
   onTransition {
     case _ -> Done =>
-      logger.info(s"$tag All workflows finished. Stopping self.")
-      donePromise.trySuccess(())
+      logger.info(s"$tag All workflows finished")
       ()
     case fromState -> toState =>
       logger.debug(s"$tag transitioning from $fromState to $toState")
@@ -264,8 +285,9 @@ class WorkflowManagerActor(config: Config,
       StartNewWorkflow
     }
 
-    val wfProps = WorkflowActor.props(workflowId, startMode, workflow.sources, config, serviceRegistryActor,
-      workflowLogCopyRouter, jobStoreActor, callCacheReadActor, jobTokenDispenserActor, backendSingletonCollection)
+    val wfProps = WorkflowActor.props(workflowId, startMode, workflow.sources, config, params.serviceRegistryActor,
+      params.workflowLogCopyRouter, params.jobStoreActor, params.subWorkflowStoreActor, params.callCacheReadActor, params.jobTokenDispenserActor,
+      params.backendSingletonCollection, params.serverMode)
     val wfActor = context.actorOf(wfProps, name = s"WorkflowActor-$workflowId")
 
     wfActor ! SubscribeTransitionCallBack(self)
@@ -277,4 +299,10 @@ class WorkflowManagerActor(config: Config,
   private def scheduleNextNewWorkflowPoll() = {
     context.system.scheduler.scheduleOnce(newWorkflowPollRate, self, RetrieveNewWorkflows)(context.dispatcher)
   }
+
+  private def expandFailureReasons(reasons: Seq[Throwable]) = {
+    reasons map { reason =>
+      reason.getMessage + "\n" + ExceptionUtils.getStackTrace(reason)
+    } mkString "\n"
+  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/CopyWorkflowLogsActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/CopyWorkflowLogsActor.scala
index aa25fdfb869..55ef429beac 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/CopyWorkflowLogsActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/CopyWorkflowLogsActor.scala
@@ -27,8 +27,7 @@ object CopyWorkflowLogsActor {
 // Which could be used for other copying work (outputs, call logs..)
 class CopyWorkflowLogsActor(serviceRegistryActor: ActorRef)
     extends Actor
-    with ActorLogging
-    with PathFactory {
+    with ActorLogging {
 
   def copyAndClean(src: Path, dest: Path) = {
     File(dest).parent.createDirectories()
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/CopyWorkflowOutputsActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/CopyWorkflowOutputsActor.scala
index a5028e5af91..1dbf8b27069 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/CopyWorkflowOutputsActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/CopyWorkflowOutputsActor.scala
@@ -5,33 +5,33 @@ import java.nio.file.Path
 import akka.actor.Props
 import cromwell.backend.BackendWorkflowFinalizationActor.{FinalizationResponse, FinalizationSuccess}
 import cromwell.backend.{AllBackendInitializationData, BackendConfigurationDescriptor, BackendInitializationData, BackendLifecycleActorFactory}
-import cromwell.core._
 import cromwell.core.Dispatcher.IoDispatcher
 import cromwell.core.WorkflowOptions._
+import cromwell.core._
+import cromwell.core.path.{PathCopier, PathFactory}
 import cromwell.engine.EngineWorkflowDescriptor
 import cromwell.engine.backend.{BackendConfiguration, CromwellBackends}
-import wdl4s.ReportableSymbol
-import wdl4s.values.WdlSingleFile
+import wdl4s.values.{WdlArray, WdlMap, WdlSingleFile, WdlValue}
 
 import scala.concurrent.{ExecutionContext, Future}
 
 object CopyWorkflowOutputsActor {
-  def props(workflowId: WorkflowId, workflowDescriptor: EngineWorkflowDescriptor, outputStore: OutputStore,
+  def props(workflowId: WorkflowId, workflowDescriptor: EngineWorkflowDescriptor, workflowOutputs: CallOutputs,
             initializationData: AllBackendInitializationData) = Props(
-    new CopyWorkflowOutputsActor(workflowId, workflowDescriptor, outputStore, initializationData)
+    new CopyWorkflowOutputsActor(workflowId, workflowDescriptor, workflowOutputs, initializationData)
   ).withDispatcher(IoDispatcher)
 }
 
-class CopyWorkflowOutputsActor(workflowId: WorkflowId, val workflowDescriptor: EngineWorkflowDescriptor, outputStore: OutputStore,
+class CopyWorkflowOutputsActor(workflowId: WorkflowId, val workflowDescriptor: EngineWorkflowDescriptor, workflowOutputs: CallOutputs,
                                initializationData: AllBackendInitializationData)
   extends EngineWorkflowFinalizationActor with PathFactory {
 
-  private def copyWorkflowOutputs(workflowOutputsFilePath: String): Unit = {
-    val workflowOutputsPath = buildPath(workflowOutputsFilePath, workflowDescriptor.engineFilesystems)
+  override val pathBuilders = workflowDescriptor.pathBuilders
 
-    val reportableOutputs = workflowDescriptor.backendDescriptor.workflowNamespace.workflow.outputs
+  private def copyWorkflowOutputs(workflowOutputsFilePath: String): Unit = {
+    val workflowOutputsPath = buildPath(workflowOutputsFilePath)
 
-    val outputFilePaths = getOutputFilePaths(reportableOutputs)
+    val outputFilePaths = getOutputFilePaths
 
     outputFilePaths foreach {
       case (workflowRootPath, srcPath) =>
@@ -40,23 +40,23 @@ class CopyWorkflowOutputsActor(workflowId: WorkflowId, val workflowDescriptor: E
     }
   }
 
-  private def getOutputFilePaths(reportableOutputs: Seq[ReportableSymbol]): Seq[(Path, Path)] = {
+  private def findFiles(values: Seq[WdlValue]): Seq[WdlSingleFile] = {
+    values flatMap {
+      case file: WdlSingleFile => Seq(file)
+      case array: WdlArray => findFiles(array.value)
+      case map: WdlMap => findFiles(map.value.values.toSeq)
+      case _ => Seq.empty
+    }
+  }
+  
+  private def getOutputFilePaths: Seq[(Path, Path)] = {
     for {
-      reportableOutput <- reportableOutputs
       // NOTE: Without .toSeq, outputs in arrays only yield the last output
-      (backend, calls) <- workflowDescriptor.backendAssignments.groupBy(_._2).mapValues(_.keys.toSeq).toSeq
+      backend <- workflowDescriptor.backendAssignments.values.toSeq
       config <- BackendConfiguration.backendConfigurationDescriptor(backend).toOption.toSeq
       rootPath <- getBackendRootPath(backend, config).toSeq
-      call <- calls
-      // NOTE: Without .toSeq, outputs in arrays only yield the last output
-      (outputCallKey, outputEntries) <- outputStore.store.toSeq
-      // Only get paths for the original scatter call, not the indexed entries
-      if outputCallKey.call == call && outputCallKey.index.isEmpty
-      outputEntry <- outputEntries
-      if reportableOutput.fullyQualifiedName == s"${call.fullyQualifiedName}.${outputEntry.name}"
-      wdlValue <- outputEntry.wdlValue.toSeq
-      collected = wdlValue collectAsSeq { case f: WdlSingleFile => f }
-      wdlFile <- collected
+      outputFiles = findFiles(workflowOutputs.values.map(_.wdlValue).toSeq)
+      wdlFile <- outputFiles
       wdlPath = rootPath.getFileSystem.getPath(wdlFile.value)
     } yield (rootPath, wdlPath)
   }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActor.scala
index 1a58b849ac9..74a08a8feee 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActor.scala
@@ -1,8 +1,9 @@
 package cromwell.engine.workflow.lifecycle
 
-import java.nio.file.FileSystem
+import java.nio.file.Files
 
 import akka.actor.{ActorRef, FSM, LoggingFSM, Props}
+import better.files.File
 import cats.data.Validated._
 import cats.instances.list._
 import cats.syntax.cartesian._
@@ -14,12 +15,14 @@ import com.typesafe.scalalogging.LazyLogging
 import cromwell.backend.BackendWorkflowDescriptor
 import cromwell.core.Dispatcher.EngineDispatcher
 import cromwell.core.WorkflowOptions.{ReadFromCache, WorkflowOption, WriteToCache}
+import cromwell.core._
 import cromwell.core.callcaching._
 import cromwell.core.logging.WorkflowLogging
+import cromwell.core.path.PathBuilder
 import cromwell.engine._
 import cromwell.engine.backend.CromwellBackends
 import cromwell.engine.workflow.lifecycle.MaterializeWorkflowDescriptorActor.{MaterializeWorkflowDescriptorActorData, MaterializeWorkflowDescriptorActorState}
-import cromwell.services.metadata.MetadataService._
+import cromwell.services.metadata.MetadataService.{PutMetadataAction, _}
 import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
 import cromwell.core.ErrorOr._
 import net.ceedubs.ficus.Ficus._
@@ -41,15 +44,15 @@ object MaterializeWorkflowDescriptorActor {
   // exception if not initialized yet.
   def cromwellBackends = CromwellBackends.instance.get
 
-  def props(serviceRegistryActor: ActorRef, workflowId: WorkflowId, cromwellBackends: => CromwellBackends = cromwellBackends): Props = {
-    Props(new MaterializeWorkflowDescriptorActor(serviceRegistryActor, workflowId, cromwellBackends)).withDispatcher(EngineDispatcher)
+  def props(serviceRegistryActor: ActorRef, workflowId: WorkflowId, cromwellBackends: => CromwellBackends = cromwellBackends, importLocalFilesystem: Boolean): Props = {
+    Props(new MaterializeWorkflowDescriptorActor(serviceRegistryActor, workflowId, cromwellBackends, importLocalFilesystem)).withDispatcher(EngineDispatcher)
   }
 
   /*
   Commands
    */
   sealed trait MaterializeWorkflowDescriptorActorMessage
-  case class MaterializeWorkflowDescriptorCommand(workflowSourceFiles: WorkflowSourceFiles,
+  case class MaterializeWorkflowDescriptorCommand(workflowSourceFiles: WorkflowSourceFilesCollection,
                                                   conf: Config) extends MaterializeWorkflowDescriptorActorMessage
   case object MaterializeWorkflowDescriptorAbortCommand
 
@@ -90,15 +93,17 @@ object MaterializeWorkflowDescriptorActor {
     }
 
     val enabled = conf.as[Option[Boolean]]("call-caching.enabled").getOrElse(false)
+    val invalidateBadCacheResults = conf.as[Option[Boolean]]("call-caching.invalidate-bad-cache-results").getOrElse(true)
+    val callCachingOptions = CallCachingOptions(invalidateBadCacheResults)
     if (enabled) {
       val readFromCache = readOptionalOption(ReadFromCache)
       val writeToCache = readOptionalOption(WriteToCache)
 
       (readFromCache |@| writeToCache) map {
         case (false, false) => CallCachingOff
-        case (true, false) => CallCachingActivity(ReadCache)
-        case (false, true) => CallCachingActivity(WriteCache)
-        case (true, true) => CallCachingActivity(ReadAndWriteCache)
+        case (true, false) => CallCachingActivity(ReadCache, callCachingOptions)
+        case (false, true) => CallCachingActivity(WriteCache, callCachingOptions)
+        case (true, true) => CallCachingActivity(ReadAndWriteCache, callCachingOptions)
       }
     }
     else {
@@ -107,7 +112,10 @@ object MaterializeWorkflowDescriptorActor {
   }
 }
 
-class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef, val workflowId: WorkflowId, cromwellBackends: => CromwellBackends) extends LoggingFSM[MaterializeWorkflowDescriptorActorState, MaterializeWorkflowDescriptorActorData] with LazyLogging with WorkflowLogging {
+class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
+                                         val workflowIdForLogging: WorkflowId,
+                                         cromwellBackends: => CromwellBackends,
+                                         importLocalFilesystem: Boolean) extends LoggingFSM[MaterializeWorkflowDescriptorActorState, MaterializeWorkflowDescriptorActorData] with LazyLogging with WorkflowLogging {
 
   import MaterializeWorkflowDescriptorActor._
 
@@ -119,7 +127,7 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef, val wor
 
   when(ReadyToMaterializeState) {
     case Event(MaterializeWorkflowDescriptorCommand(workflowSourceFiles, conf), _) =>
-      buildWorkflowDescriptor(workflowId, workflowSourceFiles, conf) match {
+      buildWorkflowDescriptor(workflowIdForLogging, workflowSourceFiles, conf) match {
         case Valid(descriptor) =>
           sender() ! MaterializeWorkflowDescriptorSuccessResponse(descriptor)
           goto(MaterializationSuccessfulState)
@@ -157,57 +165,57 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef, val wor
   }
 
   private def buildWorkflowDescriptor(id: WorkflowId,
-                                      sourceFiles: WorkflowSourceFiles,
+                                      sourceFiles: WorkflowSourceFilesCollection,
                                       conf: Config): ErrorOr[EngineWorkflowDescriptor] = {
-    val namespaceValidation = validateNamespace(sourceFiles.wdlSource)
+    val namespaceValidation = validateNamespace(sourceFiles)
     val workflowOptionsValidation = validateWorkflowOptions(sourceFiles.workflowOptionsJson)
     (namespaceValidation |@| workflowOptionsValidation) map {
       (_, _)
     } flatMap { case (namespace, workflowOptions) =>
       pushWfNameMetadataService(namespace.workflow.unqualifiedName)
-      val engineFileSystems = EngineFilesystems.filesystemsForWorkflow(workflowOptions)(iOExecutionContext)
-      buildWorkflowDescriptor(id, sourceFiles, namespace, workflowOptions, conf, engineFileSystems)
+      val pathBuilders = EngineFilesystems(context.system).pathBuildersForWorkflow(workflowOptions)
+      buildWorkflowDescriptor(id, sourceFiles, namespace, workflowOptions, conf, pathBuilders)
     }
   }
 
 
   private def pushWfNameMetadataService(name: String): Unit = {
     // Workflow name:
-    val nameEvent = MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.Name), MetadataValue(name))
+    val nameEvent = MetadataEvent(MetadataKey(workflowIdForLogging, None, WorkflowMetadataKeys.Name), MetadataValue(name))
 
     serviceRegistryActor ! PutMetadataAction(nameEvent)
   }
 
   private def buildWorkflowDescriptor(id: WorkflowId,
-                                      sourceFiles: WorkflowSourceFiles,
-                                      namespace: NamespaceWithWorkflow,
+                                      sourceFiles: WorkflowSourceFilesCollection,
+                                      namespace: WdlNamespaceWithWorkflow,
                                       workflowOptions: WorkflowOptions,
                                       conf: Config,
-                                      engineFilesystems: List[FileSystem]): ErrorOr[EngineWorkflowDescriptor] = {
+                                      pathBuilders: List[PathBuilder]): ErrorOr[EngineWorkflowDescriptor] = {
     val defaultBackendName = conf.as[Option[String]]("backend.default")
     val rawInputsValidation = validateRawInputs(sourceFiles.inputsJson)
     val failureModeValidation = validateWorkflowFailureMode(workflowOptions, conf)
-    val backendAssignmentsValidation = validateBackendAssignments(namespace.workflow.calls, workflowOptions, defaultBackendName)
+    val backendAssignmentsValidation = validateBackendAssignments(namespace.taskCalls, workflowOptions, defaultBackendName)
     val callCachingModeValidation = validateCallCachingMode(workflowOptions, conf)
 
     (rawInputsValidation |@| failureModeValidation |@| backendAssignmentsValidation |@| callCachingModeValidation ) map {
       (_, _, _, _)
     } flatMap { case (rawInputs, failureMode, backendAssignments, callCachingMode) =>
-      buildWorkflowDescriptor(id, namespace, rawInputs, backendAssignments, workflowOptions, failureMode, engineFilesystems, callCachingMode)
+      buildWorkflowDescriptor(id, namespace, rawInputs, backendAssignments, workflowOptions, failureMode, pathBuilders, callCachingMode)
     }
   }
 
   private def buildWorkflowDescriptor(id: WorkflowId,
-                                      namespace: NamespaceWithWorkflow,
+                                      namespace: WdlNamespaceWithWorkflow,
                                       rawInputs: Map[String, JsValue],
-                                      backendAssignments: Map[Call, String],
+                                      backendAssignments: Map[TaskCall, String],
                                       workflowOptions: WorkflowOptions,
                                       failureMode: WorkflowFailureMode,
-                                      engineFileSystems: List[FileSystem],
+                                      pathBuilders: List[PathBuilder],
                                       callCachingMode: CallCachingMode): ErrorOr[EngineWorkflowDescriptor] = {
 
     def checkTypes(inputs: Map[FullyQualifiedName, WdlValue]): ErrorOr[Map[FullyQualifiedName, WdlValue]] = {
-      val allDeclarations = namespace.workflow.scopedDeclarations ++ namespace.workflow.calls.flatMap(_.scopedDeclarations)
+      val allDeclarations = namespace.workflow.declarations ++ namespace.workflow.calls.flatMap(_.declarations)
       val list: List[ErrorOr[(FullyQualifiedName, WdlValue)]] = inputs.map({ case (k, v) =>
         allDeclarations.find(_.fullyQualifiedName == k) match {
           case Some(decl) if decl.wdlType.coerceRawValue(v).isFailure =>
@@ -223,27 +231,27 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef, val wor
     for {
       coercedInputs <- validateCoercedInputs(rawInputs, namespace)
       _ = pushWfInputsToMetadataService(coercedInputs)
-      declarations <- validateDeclarations(namespace, workflowOptions, coercedInputs, engineFileSystems)
-      declarationsAndInputs <- checkTypes(declarations ++ coercedInputs)
-      backendDescriptor = BackendWorkflowDescriptor(id, namespace, declarationsAndInputs, workflowOptions)
-    } yield EngineWorkflowDescriptor(backendDescriptor, coercedInputs, backendAssignments, failureMode, engineFileSystems, callCachingMode)
+      evaluatedWorkflowsDeclarations <- validateDeclarations(namespace, workflowOptions, coercedInputs, pathBuilders)
+      declarationsAndInputs <- checkTypes(evaluatedWorkflowsDeclarations ++ coercedInputs)
+      backendDescriptor = BackendWorkflowDescriptor(id, namespace.workflow, declarationsAndInputs, workflowOptions)
+    } yield EngineWorkflowDescriptor(namespace, backendDescriptor, coercedInputs, backendAssignments, failureMode, pathBuilders, callCachingMode)
   }
 
   private def pushWfInputsToMetadataService(workflowInputs: WorkflowCoercedInputs): Unit = {
     // Inputs
     val inputEvents = workflowInputs match {
       case empty if empty.isEmpty =>
-        List(MetadataEvent.empty(MetadataKey(workflowId, None,WorkflowMetadataKeys.Inputs)))
+        List(MetadataEvent.empty(MetadataKey(workflowIdForLogging, None,WorkflowMetadataKeys.Inputs)))
       case inputs =>
         inputs flatMap { case (inputName, wdlValue) =>
-          wdlValueToMetadataEvents(MetadataKey(workflowId, None, s"${WorkflowMetadataKeys.Inputs}:$inputName"), wdlValue)
+          wdlValueToMetadataEvents(MetadataKey(workflowIdForLogging, None, s"${WorkflowMetadataKeys.Inputs}:$inputName"), wdlValue)
         }
     }
 
     serviceRegistryActor ! PutMetadataAction(inputEvents)
   }
 
-  private def validateBackendAssignments(calls: Seq[Call], workflowOptions: WorkflowOptions, defaultBackendName: Option[String]): ErrorOr[Map[Call, String]] = {
+  private def validateBackendAssignments(calls: Set[TaskCall], workflowOptions: WorkflowOptions, defaultBackendName: Option[String]): ErrorOr[Map[TaskCall, String]] = {
     val callToBackendMap = Try {
       calls map { call =>
         val backendPriorities = Seq(
@@ -272,7 +280,7 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef, val wor
   /**
     * Map a call to a backend name depending on the runtime attribute key
     */
-  private def assignBackendUsingRuntimeAttrs(call: Call): Option[String] = {
+  private def assignBackendUsingRuntimeAttrs(call: TaskCall): Option[String] = {
     val runtimeAttributesMap = call.task.runtimeAttributes.attrs
     runtimeAttributesMap.get(RuntimeBackendKey) map { wdlExpr => evaluateBackendNameExpression(call.fullyQualifiedName, wdlExpr) }
   }
@@ -287,19 +295,87 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef, val wor
     }
   }
 
-  private def validateDeclarations(namespace: NamespaceWithWorkflow,
+  private def validateDeclarations(namespace: WdlNamespaceWithWorkflow,
                                    options: WorkflowOptions,
                                    coercedInputs: WorkflowCoercedInputs,
-                                   engineFileSystems: List[FileSystem]): ErrorOr[WorkflowCoercedInputs] = {
-    namespace.staticWorkflowDeclarationsRecursive(coercedInputs, new WdlFunctions(engineFileSystems)) match {
+                                   pathBuilders: List[PathBuilder]): ErrorOr[WorkflowCoercedInputs] = {
+    namespace.staticDeclarationsRecursive(coercedInputs, new WdlFunctions(pathBuilders)) match {
       case Success(d) => d.validNel
       case Failure(e) => s"Workflow has invalid declarations: ${e.getMessage}".invalidNel
     }
   }
 
-  private def validateNamespace(source: WdlSource): ErrorOr[NamespaceWithWorkflow] = {
+  private def validateImportsDirectory(zipContents: Array[Byte]): ErrorOr[File] = {
+
+    def makeZipFile(contents: Array[Byte]): Try[File] = Try {
+      val dependenciesPath = Files.createTempFile("", ".zip")
+      Files.write(dependenciesPath, contents)
+    }
+
+    def unZipFile(f: File) = Try {
+      val unzippedFile = f.unzip()
+      val unzippedFileContents = unzippedFile.toJava.listFiles().head
+
+      if (unzippedFileContents.isDirectory) File(unzippedFileContents.getPath)
+      else unzippedFile
+    }
+
+    val importsFile = for {
+      zipFile <- makeZipFile(zipContents)
+      unzipped <- unZipFile(zipFile)
+      _ <- Try(zipFile.delete(swallowIOExceptions = true))
+    } yield unzipped
+
+    importsFile match {
+      case Success(unzippedDirectory: File) => unzippedDirectory.validNel
+      case Failure(t) => t.getMessage.invalidNel
+    }
+  }
+
+  private def validateNamespaceWithImports(w: WorkflowSourceFilesWithDependenciesZip): ErrorOr[WdlNamespaceWithWorkflow] = {
+    def getMetadatae(importsDir: File, prefix: String = ""): Seq[(String, File)] = {
+      importsDir.children.toSeq flatMap {
+        case f: File if f.isDirectory => getMetadatae(f, prefix + f.name + "/")
+        case f: File if f.name.endsWith(".wdl") => Seq((prefix + f.name, f))
+        case _ => Seq.empty
+      }
+    }
+
+    def writeMetadatae(importsDir: File) = {
+      import scala.collection.JavaConverters._
+
+      val wfImportEvents = getMetadatae(importsDir) map { case (name: String, f: File) =>
+        val contents = Files.readAllLines(f.path).asScala.mkString(System.lineSeparator())
+        MetadataEvent(MetadataKey(workflowIdForLogging, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Imports, name), MetadataValue(contents))
+      }
+      serviceRegistryActor ! PutMetadataAction(wfImportEvents)
+    }
+
+    validateImportsDirectory(w.importsZip) flatMap { importsDir =>
+      writeMetadatae(importsDir)
+      val importResolvers: Seq[ImportResolver] = if (importLocalFilesystem) {
+        List(WdlNamespace.directoryResolver(importsDir), WdlNamespace.fileResolver)
+      } else {
+        List(WdlNamespace.directoryResolver(importsDir))
+      }
+      val results = WdlNamespaceWithWorkflow.load(w.wdlSource, importResolvers)
+      importsDir.delete(swallowIOExceptions = true)
+      results.validNel
+    }
+  }
+
+  private def validateNamespace(source: WorkflowSourceFilesCollection): ErrorOr[WdlNamespaceWithWorkflow] = {
     try {
-      NamespaceWithWorkflow.load(source).validNel
+      source match {
+        case w: WorkflowSourceFilesWithDependenciesZip => validateNamespaceWithImports(w)
+        case w: WorkflowSourceFilesWithoutImports =>
+          val importResolvers: Seq[ImportResolver] = if (importLocalFilesystem) {
+            List(WdlNamespace.fileResolver)
+          } else {
+            List.empty
+          }
+          WdlNamespaceWithWorkflow.load(w.wdlSource, importResolvers).validNel
+      }
     } catch {
       case e: Exception => s"Unable to load namespace from workflow: ${e.getMessage}".invalidNel
     }
@@ -314,7 +390,7 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef, val wor
   }
 
   private def validateCoercedInputs(rawInputs: Map[String, JsValue],
-                                    namespace: NamespaceWithWorkflow): ErrorOr[WorkflowCoercedInputs] = {
+                                    namespace: WdlNamespaceWithWorkflow): ErrorOr[WorkflowCoercedInputs] = {
     namespace.coerceRawInputs(rawInputs) match {
       case Success(r) => r.validNel
       case Failure(e: ExceptionWithErrors) => Invalid(e.errors)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowFinalizationActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowFinalizationActor.scala
index 9614696e2e0..5c4b777a50b 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowFinalizationActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowFinalizationActor.scala
@@ -1,14 +1,15 @@
 package cromwell.engine.workflow.lifecycle
 
 import akka.actor.{FSM, Props}
-import cromwell.backend.AllBackendInitializationData
 import cromwell.backend.BackendWorkflowFinalizationActor.{FinalizationFailed, FinalizationSuccess, Finalize}
+import cromwell.backend._
 import cromwell.core.Dispatcher.EngineDispatcher
-import cromwell.core.{ExecutionStore, OutputStore, WorkflowId}
+import cromwell.core.{CallOutputs, WorkflowId}
 import cromwell.engine.EngineWorkflowDescriptor
 import cromwell.engine.backend.CromwellBackends
 import cromwell.engine.workflow.lifecycle.WorkflowFinalizationActor._
 import cromwell.engine.workflow.lifecycle.WorkflowLifecycleActor._
+import wdl4s.TaskCall
 
 import scala.util.{Failure, Success, Try}
 
@@ -37,14 +38,14 @@ object WorkflowFinalizationActor {
   case object WorkflowFinalizationSucceededResponse extends WorkflowLifecycleSuccessResponse
   final case class WorkflowFinalizationFailedResponse(reasons: Seq[Throwable]) extends WorkflowLifecycleFailureResponse
 
-  def props(workflowId: WorkflowId, workflowDescriptor: EngineWorkflowDescriptor, executionStore: ExecutionStore,
-  outputStore: OutputStore, initializationData: AllBackendInitializationData): Props = {
-    Props(new WorkflowFinalizationActor(workflowId, workflowDescriptor, executionStore, outputStore, initializationData)).withDispatcher(EngineDispatcher)
+  def props(workflowId: WorkflowId, workflowDescriptor: EngineWorkflowDescriptor, jobExecutionMap: JobExecutionMap,
+            workflowOutputs: CallOutputs, initializationData: AllBackendInitializationData): Props = {
+    Props(new WorkflowFinalizationActor(workflowId, workflowDescriptor, jobExecutionMap, workflowOutputs, initializationData)).withDispatcher(EngineDispatcher)
   }
 }
 
-case class WorkflowFinalizationActor(workflowId: WorkflowId, workflowDescriptor: EngineWorkflowDescriptor,
-                                     executionStore: ExecutionStore, outputStore: OutputStore, initializationData: AllBackendInitializationData)
+case class WorkflowFinalizationActor(workflowIdForLogging: WorkflowId, workflowDescriptor: EngineWorkflowDescriptor,
+                                     jobExecutionMap: JobExecutionMap, workflowOutputs: CallOutputs, initializationData: AllBackendInitializationData)
   extends WorkflowLifecycleActor[WorkflowFinalizationActorState] {
 
   val tag = self.path.name
@@ -62,16 +63,16 @@ case class WorkflowFinalizationActor(workflowId: WorkflowId, workflowDescriptor:
     case Event(StartFinalizationCommand, _) =>
       val backendFinalizationActors = Try {
         for {
-          (backend, calls) <- workflowDescriptor.backendAssignments.groupBy(_._2).mapValues(_.keys.toSeq)
+          (backend, calls) <- workflowDescriptor.backendAssignments.groupBy(_._2).mapValues(_.keySet)
           props <- CromwellBackends.backendLifecycleFactoryActorByName(backend).map(
-            _.workflowFinalizationActorProps(workflowDescriptor.backendDescriptor, calls, executionStore, outputStore, initializationData.get(backend))
+            _.workflowFinalizationActorProps(workflowDescriptor.backendDescriptor, calls, filterJobExecutionsForBackend(calls), workflowOutputs, initializationData.get(backend))
           ).get
           actor = context.actorOf(props, backend)
         } yield actor
       }
 
       val engineFinalizationActor = Try {
-        context.actorOf(CopyWorkflowOutputsActor.props(workflowId, workflowDescriptor, outputStore, initializationData),
+        context.actorOf(CopyWorkflowOutputsActor.props(workflowIdForLogging, workflowDescriptor, workflowOutputs, initializationData),
           "CopyWorkflowOutputsActor")
       }
 
@@ -95,6 +96,15 @@ case class WorkflowFinalizationActor(workflowId: WorkflowId, workflowDescriptor:
           goto(WorkflowFinalizationFailedState)
       }
   }
+  
+  // Only send to each backend the jobs that it executed
+  private def filterJobExecutionsForBackend(calls: Set[TaskCall]): JobExecutionMap = {
+    jobExecutionMap map {
+      case (wd, executedKeys) => wd -> (executedKeys filter { jobKey => calls.contains(jobKey.call) })
+    } filter {
+      case (wd, keys) => keys.nonEmpty
+    }
+  }
 
   when(FinalizationInProgressState) {
     case Event(FinalizationSuccess, stateData) => checkForDoneAndTransition(stateData.withSuccess(sender))
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowInitializationActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowInitializationActor.scala
index 2fd5d75aa10..14e8a31a49f 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowInitializationActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowInitializationActor.scala
@@ -50,7 +50,7 @@ object WorkflowInitializationActor {
   case class BackendActorAndBackend(actor: ActorRef, backend: String)
 }
 
-case class WorkflowInitializationActor(workflowId: WorkflowId,
+case class WorkflowInitializationActor(workflowIdForLogging: WorkflowId,
                                        workflowDescriptor: EngineWorkflowDescriptor,
                                        serviceRegistryActor: ActorRef)
   extends AbortableWorkflowLifecycleActor[WorkflowInitializationActorState] {
@@ -78,7 +78,7 @@ case class WorkflowInitializationActor(workflowId: WorkflowId,
     case Event(StartInitializationCommand, _) =>
       val backendInitializationActors = Try {
         for {
-          (backend, calls) <- workflowDescriptor.backendAssignments.groupBy(_._2).mapValues(_.keys.toSeq)
+          (backend, calls) <- workflowDescriptor.backendAssignments.groupBy(_._2).mapValues(_.keySet)
           props <- CromwellBackends.backendLifecycleFactoryActorByName(backend).map(factory =>
             factory.workflowInitializationActorProps(workflowDescriptor.backendDescriptor, calls, serviceRegistryActor)
           ).get
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/CallMetadataHelper.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/CallMetadataHelper.scala
new file mode 100644
index 00000000000..80748f6dda7
--- /dev/null
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/CallMetadataHelper.scala
@@ -0,0 +1,135 @@
+package cromwell.engine.workflow.lifecycle.execution
+
+import java.time.OffsetDateTime
+
+import akka.actor.ActorRef
+import cromwell.backend.BackendJobDescriptorKey
+import cromwell.core.ExecutionStatus._
+import cromwell.core._
+import cromwell.services.metadata.MetadataService._
+import cromwell.services.metadata._
+import wdl4s._
+import wdl4s.values.WdlValue
+
+import scala.util.Random
+
+trait CallMetadataHelper {
+  
+  def workflowIdForCallMetadata: WorkflowId
+  def serviceRegistryActor: ActorRef
+
+  def pushNewCallMetadata(callKey: CallKey, backendName: Option[String]) = {
+    val startEvents = List(
+      Option(MetadataEvent(metadataKeyForCall(callKey, CallMetadataKeys.Start), MetadataValue(OffsetDateTime.now))),
+      backendName map { name => MetadataEvent(metadataKeyForCall(callKey, CallMetadataKeys.Backend), MetadataValue(name)) }
+    ).flatten
+
+    serviceRegistryActor ! PutMetadataAction(startEvents)
+  }
+
+  def pushQueuedCallMetadata(diffs: Seq[WorkflowExecutionDiff]) = {
+    val startingEvents = for {
+      diff <- diffs
+      (jobKey, executionState) <- diff.executionStoreChanges if jobKey.isInstanceOf[BackendJobDescriptorKey] && executionState == ExecutionStatus.QueuedInCromwell
+    } yield MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.ExecutionStatus), MetadataValue(ExecutionStatus.QueuedInCromwell))
+    serviceRegistryActor ! PutMetadataAction(startingEvents)
+  }
+
+  def pushStartingCallMetadata(callKey: CallKey) = {
+    val statusChange = MetadataEvent(metadataKeyForCall(callKey, CallMetadataKeys.ExecutionStatus), MetadataValue(ExecutionStatus.Starting))
+    serviceRegistryActor ! PutMetadataAction(statusChange)
+  }
+
+  def pushRunningCallMetadata(key: CallKey, evaluatedInputs: EvaluatedTaskInputs) = {
+    val inputEvents = evaluatedInputs match {
+      case empty if empty.isEmpty =>
+        List(MetadataEvent.empty(metadataKeyForCall(key, s"${CallMetadataKeys.Inputs}")))
+      case inputs =>
+        inputs flatMap {
+          case (inputName, inputValue) =>
+            wdlValueToMetadataEvents(metadataKeyForCall(key, s"${CallMetadataKeys.Inputs}:${inputName.unqualifiedName}"), inputValue)
+        }
+    }
+
+    val runningEvent = List(MetadataEvent(metadataKeyForCall(key, CallMetadataKeys.ExecutionStatus), MetadataValue(ExecutionStatus.Running)))
+
+    serviceRegistryActor ! PutMetadataAction(runningEvent ++ inputEvents)
+  }
+
+  def pushWorkflowOutputMetadata(outputs: Map[LocallyQualifiedName, WdlValue]) = {
+    val events = outputs match {
+      case empty if empty.isEmpty => List(MetadataEvent.empty(MetadataKey(workflowIdForCallMetadata, None, WorkflowMetadataKeys.Outputs)))
+      case _ => outputs flatMap {
+        case (outputName, outputValue) =>
+          wdlValueToMetadataEvents(MetadataKey(workflowIdForCallMetadata, None, s"${WorkflowMetadataKeys.Outputs}:$outputName"), outputValue)
+      }
+    }
+
+    serviceRegistryActor ! PutMetadataAction(events)
+  }
+
+  def pushSuccessfulCallMetadata(jobKey: JobKey, returnCode: Option[Int], outputs: CallOutputs) = {
+    val completionEvents = completedCallMetadataEvents(jobKey, ExecutionStatus.Done, returnCode)
+
+    val outputEvents = outputs match {
+      case empty if empty.isEmpty =>
+        List(MetadataEvent.empty(metadataKeyForCall(jobKey, s"${CallMetadataKeys.Outputs}")))
+      case _ =>
+        outputs flatMap { case (lqn, outputValue) => wdlValueToMetadataEvents(metadataKeyForCall(jobKey, s"${CallMetadataKeys.Outputs}:$lqn"), outputValue.wdlValue) }
+    }
+
+    serviceRegistryActor ! PutMetadataAction(completionEvents ++ outputEvents)
+  }
+
+  def pushFailedCallMetadata(jobKey: JobKey, returnCode: Option[Int], failure: Throwable, retryableFailure: Boolean) = {
+    val failedState = if (retryableFailure) ExecutionStatus.Preempted else ExecutionStatus.Failed
+    val completionEvents = completedCallMetadataEvents(jobKey, failedState, returnCode)
+    val retryableFailureEvent = MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.RetryableFailure), MetadataValue(retryableFailure))
+    val failureEvents = throwableToMetadataEvents(metadataKeyForCall(jobKey, s"${CallMetadataKeys.Failures}[$randomNumberString]"), failure).+:(retryableFailureEvent)
+
+    serviceRegistryActor ! PutMetadataAction(completionEvents ++ failureEvents)
+  }
+
+  def pushExecutionEventsToMetadataService(jobKey: JobKey, eventList: Seq[ExecutionEvent]) = {
+    def metadataEvent(k: String, value: Any) = {
+      val metadataValue = MetadataValue(value)
+      val metadataKey = metadataKeyForCall(jobKey, k)
+      MetadataEvent(metadataKey, metadataValue)
+    }
+    
+    eventList.headOption foreach { firstEvent =>
+      // The final event is only used as the book-end for the final pairing so the name is never actually used...
+      val offset = firstEvent.offsetDateTime.getOffset
+      val now = OffsetDateTime.now.withOffsetSameInstant(offset)
+      val lastEvent = ExecutionEvent("!!Bring Back the Monarchy!!", now)
+      val tailedEventList = eventList :+ lastEvent
+      val events = tailedEventList.sliding(2).zipWithIndex flatMap {
+        case (Seq(eventCurrent, eventNext), index) =>
+          val eventKey = s"executionEvents[$index]"
+          List(
+            metadataEvent(s"$eventKey:description", eventCurrent.name),
+            metadataEvent(s"$eventKey:startTime", eventCurrent.offsetDateTime),
+            metadataEvent(s"$eventKey:endTime", eventNext.offsetDateTime)
+          )
+      }
+
+      serviceRegistryActor ! PutMetadataAction(events.toIterable)
+    }
+  }
+
+  private def completedCallMetadataEvents(jobKey: JobKey, executionStatus: ExecutionStatus, returnCode: Option[Int]) = {
+    val returnCodeEvent = returnCode map { rc =>
+      List(MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.ReturnCode), MetadataValue(rc)))
+    }
+
+    List(
+      MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.ExecutionStatus), MetadataValue(executionStatus)),
+      MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.End), MetadataValue(OffsetDateTime.now))
+    ) ++ returnCodeEvent.getOrElse(List.empty)
+  }
+  
+  private def metadataKeyForCall(jobKey: JobKey, myKey: String) = MetadataKey(workflowIdForCallMetadata, Option(MetadataJobKey(jobKey.scope.fullyQualifiedName, jobKey.index, jobKey.attempt)), myKey)
+
+  private def randomNumberString: String = Random.nextInt.toString.stripPrefix("-")
+  
+}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/EngineJobExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/EngineJobExecutionActor.scala
index 25c1852dc5e..afa48474d78 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/EngineJobExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/EngineJobExecutionActor.scala
@@ -1,7 +1,5 @@
 package cromwell.engine.workflow.lifecycle.execution
 
-import java.time.OffsetDateTime
-
 import akka.actor.{ActorRef, ActorRefFactory, LoggingFSM, Props}
 import akka.routing.RoundRobinPool
 import cats.data.NonEmptyList
@@ -14,8 +12,8 @@ import cromwell.core._
 import cromwell.core.callcaching._
 import cromwell.core.logging.WorkflowLogging
 import cromwell.core.simpleton.WdlValueSimpleton
+import cromwell.engine.workflow.lifecycle.execution.CallPreparationActor.{BackendJobPreparationSucceeded, CallPreparationFailed}
 import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor._
-import cromwell.engine.workflow.lifecycle.execution.JobPreparationActor.{BackendJobPreparationFailed, BackendJobPreparationSucceeded}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.{CacheHit, CacheMiss, CallCacheHashes, HashError}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.FetchCachedResultsActor.{CachedOutputLookupFailed, CachedOutputLookupSucceeded}
 import cromwell.engine.workflow.lifecycle.execution.callcaching._
@@ -23,8 +21,6 @@ import cromwell.engine.workflow.tokens.JobExecutionTokenDispenserActor.{JobExecu
 import cromwell.jobstore.JobStoreActor._
 import cromwell.jobstore.{Pending => _, _}
 import cromwell.services.SingletonServicesStore
-import cromwell.services.metadata.MetadataService.PutMetadataAction
-import cromwell.services.metadata.{MetadataEvent, MetadataJobKey, MetadataKey, MetadataValue}
 import wdl4s.TaskOutput
 
 import scala.concurrent.ExecutionContext
@@ -36,17 +32,18 @@ class EngineJobExecutionActor(replyTo: ActorRef,
                               factory: BackendLifecycleActorFactory,
                               initializationData: Option[BackendInitializationData],
                               restarting: Boolean,
-                              serviceRegistryActor: ActorRef,
+                              val serviceRegistryActor: ActorRef,
                               jobStoreActor: ActorRef,
                               callCacheReadActor: ActorRef,
                               jobTokenDispenserActor: ActorRef,
                               backendSingletonActor: Option[ActorRef],
                               backendName: String,
-                              callCachingMode: CallCachingMode) extends LoggingFSM[EngineJobExecutionActorState, EJEAData] with WorkflowLogging {
+                              callCachingMode: CallCachingMode) extends LoggingFSM[EngineJobExecutionActorState, EJEAData] with WorkflowLogging with CallMetadataHelper {
 
-  override val workflowId = executionData.workflowDescriptor.id
+  override val workflowIdForLogging = executionData.workflowDescriptor.id
+  override val workflowIdForCallMetadata = executionData.workflowDescriptor.id
 
-  val jobTag = s"${workflowId.shortString}:${jobDescriptorKey.call.fullyQualifiedName}:${jobDescriptorKey.index.fromIndex}:${jobDescriptorKey.attempt}"
+  val jobTag = s"${workflowIdForLogging.shortString}:${jobDescriptorKey.call.fullyQualifiedName}:${jobDescriptorKey.index.fromIndex}:${jobDescriptorKey.attempt}"
   val tag = s"EJEA_$jobTag"
 
   // There's no need to check for a cache hit again if we got preempted, or if there's no result copying actor defined
@@ -78,8 +75,9 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   when(RequestingExecutionToken) {
     case Event(JobExecutionTokenDispensed(jobExecutionToken), NoData) =>
       executionToken = Option(jobExecutionToken)
+      replyTo ! JobStarting(jobDescriptorKey)
       if (restarting) {
-        val jobStoreKey = jobDescriptorKey.toJobStoreKey(workflowId)
+        val jobStoreKey = jobDescriptorKey.toJobStoreKey(workflowIdForLogging)
         jobStoreActor ! QueryJobCompletion(jobStoreKey, jobDescriptorKey.call.task.outputs)
         goto(CheckingJobStore)
       } else {
@@ -96,9 +94,9 @@ class EngineJobExecutionActor(replyTo: ActorRef,
       prepareJob()
     case Event(JobComplete(jobResult), NoData) =>
       val response = jobResult match {
-        case JobResultSuccess(returnCode, jobOutputs) => SucceededResponse(jobDescriptorKey, returnCode, jobOutputs, None, Seq.empty)
-        case JobResultFailure(returnCode, reason, false) => FailedNonRetryableResponse(jobDescriptorKey, reason, returnCode)
-        case JobResultFailure(returnCode, reason, true) => FailedRetryableResponse(jobDescriptorKey, reason, returnCode)
+        case JobResultSuccess(returnCode, jobOutputs) => JobSucceededResponse(jobDescriptorKey, returnCode, jobOutputs, None, Seq.empty)
+        case JobResultFailure(returnCode, reason, false) => JobFailedNonRetryableResponse(jobDescriptorKey, reason, returnCode)
+        case JobResultFailure(returnCode, reason, true) => JobFailedRetryableResponse(jobDescriptorKey, reason, returnCode)
       }
       respondAndStop(response)
     case Event(f: JobStoreReadFailure, NoData) =>
@@ -120,8 +118,8 @@ class EngineJobExecutionActor(replyTo: ActorRef,
           runJob(updatedData)
         case CallCachingOff => runJob(updatedData)
       }
-    case Event(response: BackendJobPreparationFailed, NoData) =>
-      forwardAndStop(response)
+    case Event(CallPreparationFailed(jobKey: BackendJobDescriptorKey, throwable), NoData) =>
+      respondAndStop(JobFailedNonRetryableResponse(jobKey, throwable, None))
   }
 
   private val callCachingReadResultMetadataKey = "Call caching read result"
@@ -156,19 +154,16 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
   when(BackendIsCopyingCachedOutputs) {
     // Backend copying response:
-    case Event(response: SucceededResponse, data @ ResponsePendingData(_, _, Some(Success(hashes)), _)) =>
+    case Event(response: JobSucceededResponse, data @ ResponsePendingData(_, _, Some(Success(hashes)), _)) =>
       saveCacheResults(hashes, data.withSuccessResponse(response))
-    case Event(response: SucceededResponse, data @ ResponsePendingData(_, _, None, _)) if effectiveCallCachingMode.writeToCache =>
+    case Event(response: JobSucceededResponse, data @ ResponsePendingData(_, _, None, _)) if effectiveCallCachingMode.writeToCache =>
       // Wait for the CallCacheHashes
       stay using data.withSuccessResponse(response)
-    case Event(response: SucceededResponse, data: ResponsePendingData) => // bad hashes or cache write off
+    case Event(response: JobSucceededResponse, data: ResponsePendingData) => // bad hashes or cache write off
       saveJobCompletionToJobStore(data.withSuccessResponse(response))
     case Event(response: BackendJobExecutionResponse, data @ ResponsePendingData(_, _, _, Some(cacheHit))) =>
       response match {
-        case f: BackendJobFailedResponse =>
-          invalidateCacheHit(cacheHit.cacheResultIds.head)
-          log.error(f.throwable, "Failed copying cache results for job {}, invalidating cache entry.", jobDescriptorKey)
-          goto(InvalidatingCacheEntry)
+        case f: BackendJobFailedResponse => invalidateCacheHitAndTransition(cacheHit.cacheResultIds.head, data, f.throwable)
         case _ => runJob(data)
       }
 
@@ -216,10 +211,10 @@ class EngineJobExecutionActor(replyTo: ActorRef,
       disableCallCaching(t)
       stay using data.copy(hashes = Option(Failure(t)))
 
-    case Event(response: SucceededResponse, data @ ResponsePendingData(_, _, Some(Success(hashes)), _)) if effectiveCallCachingMode.writeToCache =>
+    case Event(response: JobSucceededResponse, data @ ResponsePendingData(_, _, Some(Success(hashes)), _)) if effectiveCallCachingMode.writeToCache =>
       eventList ++= response.executionEvents
       saveCacheResults(hashes, data.withSuccessResponse(response))
-    case Event(response: SucceededResponse, data @ ResponsePendingData(_, _, None, _)) if effectiveCallCachingMode.writeToCache =>
+    case Event(response: JobSucceededResponse, data @ ResponsePendingData(_, _, None, _)) if effectiveCallCachingMode.writeToCache =>
       log.debug(s"Got job result for {}, awaiting hashes", jobTag)
       stay using data.withSuccessResponse(response)
     case Event(response: BackendJobExecutionResponse, data: ResponsePendingData) =>
@@ -240,7 +235,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
     case Event(JobStoreWriteSuccess(_), data: ResponseData) =>
       forwardAndStop(data.response)
     case Event(JobStoreWriteFailure(t), data: ResponseData) =>
-      respondAndStop(FailedNonRetryableResponse(jobDescriptorKey, new Exception(s"JobStore write failure: ${t.getMessage}", t), None))
+      respondAndStop(JobFailedNonRetryableResponse(jobDescriptorKey, new Exception(s"JobStore write failure: ${t.getMessage}", t), None))
   }
 
   onTransition {
@@ -266,7 +261,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   private def forwardAndStop(response: Any): State = {
     replyTo forward response
     returnExecutionToken()
-    tellEventMetadata()
+    pushExecutionEventsToMetadataService(jobDescriptorKey, eventList)
     context stop self
     stay()
   }
@@ -274,7 +269,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   private def respondAndStop(response: Any): State = {
     replyTo ! response
     returnExecutionToken()
-    tellEventMetadata()
+    pushExecutionEventsToMetadataService(jobDescriptorKey, eventList)
     context stop self
     stay()
   }
@@ -286,7 +281,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   }
 
   private def disableCacheWrite(reason: Throwable) = {
-    log.error("{}: Disabling cache writing for this job.", jobTag)
+    log.error(reason, "{}: Disabling cache writing for this job.", jobTag)
     if (effectiveCallCachingMode.writeToCache) {
       effectiveCallCachingMode = effectiveCallCachingMode.withoutWrite
       writeCallCachingModeToMetadata()
@@ -302,7 +297,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
     val jobPreparationActorName = s"BackendPreparationActor_for_$jobTag"
     val jobPrepProps = JobPreparationActor.props(executionData, jobDescriptorKey, factory, initializationData, serviceRegistryActor, backendSingletonActor)
     val jobPreparationActor = createJobPreparationActor(jobPrepProps, jobPreparationActorName)
-    jobPreparationActor ! JobPreparationActor.Start
+    jobPreparationActor ! CallPreparationActor.Start
     goto(PreparingJob)
   }
 
@@ -335,13 +330,13 @@ class EngineJobExecutionActor(replyTo: ActorRef,
         val backendCacheHitCopyingActorProps = propsMaker(data.jobDescriptor, initializationData, serviceRegistryActor)
         val cacheHitCopyActor = context.actorOf(backendCacheHitCopyingActorProps, buildCacheHitCopyingActorName(data.jobDescriptor))
         cacheHitCopyActor ! CopyOutputsCommand(wdlValueSimpletons, jobDetritusFiles, returnCode)
-        replyTo ! JobRunning(data.jobDescriptor, None)
+        replyTo ! JobRunning(data.jobDescriptor.key, data.jobDescriptor.inputDeclarations, None)
         goto(BackendIsCopyingCachedOutputs)
       case None =>
         // This should be impossible with the FSM, but luckily, we CAN recover if some foolish future programmer makes this happen:
         val errorMessage = "Call caching copying should never have even been attempted with no copy actor props! (Programmer error!)"
         log.error(errorMessage)
-        self ! FailedNonRetryableResponse(data.jobDescriptor.key, new RuntimeException(errorMessage), None)
+        self ! JobFailedNonRetryableResponse(data.jobDescriptor.key, new RuntimeException(errorMessage), None)
         goto(BackendIsCopyingCachedOutputs)
     }
   }
@@ -350,7 +345,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
     val backendJobExecutionActor = context.actorOf(data.bjeaProps, buildJobExecutionActorName(data.jobDescriptor))
     val message = if (restarting) RecoverJobCommand else ExecuteJobCommand
     backendJobExecutionActor ! message
-    replyTo ! JobRunning(data.jobDescriptor, Option(backendJobExecutionActor))
+    replyTo ! JobRunning(data.jobDescriptor.key, data.jobDescriptor.inputDeclarations, Option(backendJobExecutionActor))
     goto(RunningJob) using data
   }
 
@@ -371,19 +366,33 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   }
 
   private def buildJobExecutionActorName(jobDescriptor: BackendJobDescriptor) = {
-    s"$workflowId-BackendJobExecutionActor-$jobTag"
+    s"$workflowIdForLogging-BackendJobExecutionActor-$jobTag"
   }
 
   private def buildCacheHitCopyingActorName(jobDescriptor: BackendJobDescriptor) = {
-    s"$workflowId-BackendCacheHitCopyingActor-$jobTag"
+    s"$workflowIdForLogging-BackendCacheHitCopyingActor-$jobTag"
   }
 
-  protected def createSaveCacheResultsActor(hashes: CallCacheHashes, success: SucceededResponse): Unit = {
+  protected def createSaveCacheResultsActor(hashes: CallCacheHashes, success: JobSucceededResponse): Unit = {
     val callCache = new CallCache(SingletonServicesStore.databaseInterface)
-    context.actorOf(CallCacheWriteActor.props(callCache, workflowId, hashes, success), s"CallCacheWriteActor-$tag")
+    context.actorOf(CallCacheWriteActor.props(callCache, workflowIdForLogging, hashes, success), s"CallCacheWriteActor-$tag")
     ()
   }
 
+  private def invalidateCacheHitAndTransition(cacheId: CallCachingEntryId, data: ResponsePendingData, reason: Throwable) = {
+    val invalidationRequired = effectiveCallCachingMode match {
+      case CallCachingOff => throw new RuntimeException("Should not be calling invalidateCacheHit if call caching is off!") // Very unexpected. Fail out of this bad-state EJEA.
+      case activity: CallCachingActivity => activity.options.invalidateBadCacheResults
+    }
+    if (invalidationRequired) {
+      log.error(reason, "Failed copying cache results for job {}, invalidating cache entry.", jobDescriptorKey)
+      invalidateCacheHit(cacheId)
+      goto(InvalidatingCacheEntry)
+    } else {
+      handleCacheInvalidatedResponse(CallCacheInvalidationUnnecessary, data)
+    }
+  }
+
   protected def invalidateCacheHit(cacheId: CallCachingEntryId): Unit = {
     val callCache = new CallCache(SingletonServicesStore.databaseInterface)
     context.actorOf(CallCacheInvalidateActor.props(callCache, cacheId), s"CallCacheInvalidateActor${cacheId.id}-$tag")
@@ -398,71 +407,37 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
   private def saveJobCompletionToJobStore(updatedData: ResponseData) = {
     updatedData.response match {
-      case SucceededResponse(jobKey: BackendJobDescriptorKey, returnCode: Option[Int], jobOutputs: JobOutputs, _, _) => saveSuccessfulJobResults(jobKey, returnCode, jobOutputs)
+      case JobSucceededResponse(jobKey: BackendJobDescriptorKey, returnCode: Option[Int], jobOutputs: CallOutputs, _, _) => saveSuccessfulJobResults(jobKey, returnCode, jobOutputs)
       case AbortedResponse(jobKey: BackendJobDescriptorKey) =>
         log.debug("{}: Won't save aborted job response to JobStore", jobTag)
         forwardAndStop(updatedData.response)
-      case FailedNonRetryableResponse(jobKey: BackendJobDescriptorKey, throwable: Throwable, returnCode: Option[Int]) => saveUnsuccessfulJobResults(jobKey, returnCode, throwable, retryable = false)
-      case FailedRetryableResponse(jobKey: BackendJobDescriptorKey, throwable: Throwable, returnCode: Option[Int]) => saveUnsuccessfulJobResults(jobKey, returnCode, throwable, retryable = true)
+      case JobFailedNonRetryableResponse(jobKey: BackendJobDescriptorKey, throwable: Throwable, returnCode: Option[Int]) => saveUnsuccessfulJobResults(jobKey, returnCode, throwable, retryable = false)
+      case JobFailedRetryableResponse(jobKey: BackendJobDescriptorKey, throwable: Throwable, returnCode: Option[Int]) => saveUnsuccessfulJobResults(jobKey, returnCode, throwable, retryable = true)
     }
     goto(UpdatingJobStore) using updatedData
   }
 
-  private def saveSuccessfulJobResults(jobKey: JobKey, returnCode: Option[Int], outputs: JobOutputs) = {
-    val jobStoreKey = jobKey.toJobStoreKey(workflowId)
+  private def saveSuccessfulJobResults(jobKey: JobKey, returnCode: Option[Int], outputs: CallOutputs) = {
+    val jobStoreKey = jobKey.toJobStoreKey(workflowIdForLogging)
     val jobStoreResult = JobResultSuccess(returnCode, outputs)
     jobStoreActor ! RegisterJobCompleted(jobStoreKey, jobStoreResult)
   }
 
   private def saveUnsuccessfulJobResults(jobKey: JobKey, returnCode: Option[Int], reason: Throwable, retryable: Boolean) = {
-    val jobStoreKey = jobKey.toJobStoreKey(workflowId)
+    val jobStoreKey = jobKey.toJobStoreKey(workflowIdForLogging)
     val jobStoreResult = JobResultFailure(returnCode, reason, retryable)
     jobStoreActor ! RegisterJobCompleted(jobStoreKey, jobStoreResult)
   }
 
   private def writeToMetadata(keyValues: Map[String, String]) = {
     import cromwell.services.metadata.MetadataService.implicits.MetadataAutoPutter
-    serviceRegistryActor.putMetadata(workflowId, Option(jobDescriptorKey), keyValues)
+    serviceRegistryActor.putMetadata(workflowIdForLogging, Option(jobDescriptorKey), keyValues)
   }
 
   private def addHashesAndStay(data: ResponsePendingData, hashes: CallCacheHashes): State = {
     val updatedData = data.copy(hashes = Option(Success(hashes)))
     stay using updatedData
   }
-
-  /**
-    * Fire and forget events to the metadata service
-    */
-  private def tellEventMetadata(): Unit = {
-    eventList.headOption foreach { firstEvent =>
-      // The final event is only used as the book-end for the final pairing so the name is never actually used...
-      val offset = firstEvent.offsetDateTime.getOffset
-      val now = OffsetDateTime.now.withOffsetSameInstant(offset)
-      val lastEvent = ExecutionEvent("!!Bring Back the Monarchy!!", now)
-      val tailedEventList = eventList :+ lastEvent
-      val events = tailedEventList.sliding(2).zipWithIndex flatMap {
-        case (Seq(eventCurrent, eventNext), index) =>
-          val eventKey = s"executionEvents[$index]"
-          List(
-            metadataEvent(s"$eventKey:description", eventCurrent.name),
-            metadataEvent(s"$eventKey:startTime", eventCurrent.offsetDateTime),
-            metadataEvent(s"$eventKey:endTime", eventNext.offsetDateTime)
-          )
-      }
-
-      serviceRegistryActor ! PutMetadataAction(events.toIterable)
-    }
-  }
-
-  private def metadataEvent(key: String, value: Any) = {
-    val metadataValue = MetadataValue(value)
-    MetadataEvent(metadataKey(key), metadataValue)
-  }
-
-  private lazy val metadataJobKey = {
-    MetadataJobKey(jobDescriptorKey.call.fullyQualifiedName, jobDescriptorKey.index, jobDescriptorKey.attempt)
-  }
-  private def metadataKey(key: String) = MetadataKey(workflowId, Option(metadataJobKey), key)
 }
 
 object EngineJobExecutionActor {
@@ -484,8 +459,6 @@ object EngineJobExecutionActor {
   sealed trait EngineJobExecutionActorCommand
   case object Execute extends EngineJobExecutionActorCommand
 
-  final case class JobRunning(jobDescriptor: BackendJobDescriptor, backendJobExecutionActor: Option[ActorRef])
-
   def props(replyTo: ActorRef,
             jobDescriptorKey: BackendJobDescriptorKey,
             executionData: WorkflowExecutionActorData,
@@ -526,10 +499,10 @@ object EngineJobExecutionActor {
                                                     hashes: Option[Try[CallCacheHashes]] = None,
                                                     cacheHit: Option[CacheHit] = None) extends EJEAData {
 
-    def withSuccessResponse(success: SucceededResponse) = SucceededResponseData(success, hashes)
+    def withSuccessResponse(success: JobSucceededResponse) = SucceededResponseData(success, hashes)
 
     def withResponse(response: BackendJobExecutionResponse) = response match {
-      case success: SucceededResponse => SucceededResponseData(success, hashes)
+      case success: JobSucceededResponse => SucceededResponseData(success, hashes)
       case failure => NotSucceededResponseData(failure, hashes)
     }
 
@@ -546,7 +519,7 @@ object EngineJobExecutionActor {
     def hashes: Option[Try[CallCacheHashes]]
   }
 
-  private[execution] case class SucceededResponseData(successResponse: SucceededResponse,
+  private[execution] case class SucceededResponseData(successResponse: JobSucceededResponse,
                                                       hashes: Option[Try[CallCacheHashes]] = None) extends ResponseData {
     override def response = successResponse
   }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/ExecutionStore.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/ExecutionStore.scala
new file mode 100644
index 00000000000..3b9d1af1f56
--- /dev/null
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/ExecutionStore.scala
@@ -0,0 +1,109 @@
+package cromwell.engine.workflow.lifecycle.execution
+
+import cromwell.backend.BackendJobDescriptorKey
+import cromwell.core.ExecutionStatus._
+import cromwell.core.{CallKey, ExecutionStatus, JobKey}
+import cromwell.engine.workflow.lifecycle.execution.ExecutionStore.ExecutionStoreEntry
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{apply => _, _}
+import wdl4s._
+
+
+object ExecutionStore {
+  def empty = ExecutionStore(Map.empty[JobKey, ExecutionStatus])
+  type ExecutionStoreEntry = (JobKey, ExecutionStatus)
+  def apply(workflow: Workflow, workflowCoercedInputs: WorkflowCoercedInputs) = {
+    // Only add direct children to the store, the rest is dynamically created when necessary
+    val keys = workflow.children map {
+      case call: TaskCall => Option(BackendJobDescriptorKey(call, None, 1))
+      case call: WorkflowCall => Option(SubWorkflowKey(call, None, 1))
+      case scatter: Scatter => Option(ScatterKey(scatter))
+      case declaration: Declaration => Option(DeclarationKey(declaration, None, workflowCoercedInputs))
+      case _ => None // Ifs will need to be added here when supported
+    }
+
+    new ExecutionStore(keys.flatten.map(_ -> NotStarted).toMap)
+  }
+}
+
+case class ExecutionStore(store: Map[JobKey, ExecutionStatus]) {
+  def add(values: Map[JobKey, ExecutionStatus]) = this.copy(store = store ++ values)
+
+  // Convert the store to a `List` before `collect`ing to sidestep expensive and pointless hashing of `Scope`s when
+  // assembling the result.
+  def runnableScopes = store.toList collect { case entry if isRunnable(entry) => entry._1 }
+
+  def backendJobKeys = store.keys.toList collect { case k: BackendJobDescriptorKey => k }
+
+  private def isRunnable(entry: ExecutionStoreEntry) = {
+    entry match {
+      case (key, ExecutionStatus.NotStarted) => arePrerequisitesDone(key)
+      case _ => false
+    }
+  }
+
+  def findShardEntries(key: CollectorKey): List[ExecutionStoreEntry] = store.toList filter {
+    case (k: CallKey, v) => k.scope == key.scope && k.isShard
+    case (k: DeclarationKey, v) => k.scope == key.scope && k.isShard
+    case _ => false
+  }
+
+  private def arePrerequisitesDone(key: JobKey): Boolean = {
+    val upstream = key.scope.upstream collect {
+      case n: Call => upstreamEntry(key, n)
+      case n: Scatter => upstreamEntry(key, n)
+      case n: Declaration => upstreamEntry(key, n)
+    }
+
+    val downstream: List[(JobKey, ExecutionStatus)] = key match {
+      case collector: CollectorKey => findShardEntries(collector)
+      case _ => Nil
+    }
+
+    /*
+      * We need to use an "exists" in this case because the execution store can contain a job attempt with the same
+      * fqn and index but a preempted status. We wouldn't want that preempted attempt to count against the completion
+      * of the scatter block.
+      */
+    def isDone(e: JobKey): Boolean = store exists {
+      case (k, s) => k.scope.fullyQualifiedName == e.scope.fullyQualifiedName && k.index == e.index && s == ExecutionStatus.Done
+    }
+
+    val dependencies = upstream.flatten ++ downstream
+    val dependenciesResolved = dependencies forall { case (k, _) => isDone(k) }
+
+    /*
+      * We need to make sure that all prerequisiteScopes have been resolved to some entry before going forward.
+      * If a scope cannot be resolved it may be because it is in a scatter that has not been populated yet,
+      * therefore there is no entry in the executionStore for this scope.
+      * If that's the case this prerequisiteScope has not been run yet, hence the (upstream forall {_.nonEmpty})
+      */
+    (upstream forall { _.nonEmpty }) && dependenciesResolved
+  }
+
+  private def upstreamEntry(entry: JobKey, prerequisiteScope: Scope): Option[ExecutionStoreEntry] = {
+    prerequisiteScope.closestCommonAncestor(entry.scope) match {
+      /*
+        * If this entry refers to a Scope which has a common ancestor with prerequisiteScope
+        * and that common ancestor is a Scatter block, then find the shard with the same index
+        * as 'entry'.  In other words, if you're in the same scatter block as your pre-requisite
+        * scope, then depend on the shard (with same index).
+        *
+        * NOTE: this algorithm was designed for ONE-LEVEL of scattering and probably does not
+        * work as-is for nested scatter blocks
+        */
+      case Some(ancestor: Scatter) =>
+        store find {
+          case (k, _) => k.scope == prerequisiteScope && k.index == entry.index
+        }
+
+      /*
+        * Otherwise, simply refer to the collector entry.  This means that 'entry' depends
+        * on every shard of the pre-requisite scope to finish.
+        */
+      case _ =>
+        store find {
+          case (k, _) => k.scope == prerequisiteScope && k.index.isEmpty
+        }
+    }
+  }
+}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/JobPreparationActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/JobPreparationActor.scala
index 12c719994e5..46743962226 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/JobPreparationActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/JobPreparationActor.scala
@@ -3,88 +3,61 @@ package cromwell.engine.workflow.lifecycle.execution
 import akka.actor.{Actor, ActorRef, Props}
 import cromwell.backend._
 import cromwell.core.logging.WorkflowLogging
-import cromwell.core.{ExecutionStore, JobKey, OutputStore}
+import cromwell.core.{CallKey, JobKey, WorkflowId}
 import cromwell.engine.EngineWorkflowDescriptor
-import cromwell.engine.workflow.lifecycle.execution.JobPreparationActor._
+import cromwell.engine.workflow.lifecycle.execution.CallPreparationActor._
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.SubWorkflowKey
 import wdl4s._
 import wdl4s.expression.WdlStandardLibraryFunctions
-import wdl4s.util.TryUtil
 import wdl4s.values.WdlValue
 
 import scala.util.{Failure, Success, Try}
 
-final case class JobPreparationActor(executionData: WorkflowExecutionActorData,
-                                     jobKey: BackendJobDescriptorKey,
-                                     factory: BackendLifecycleActorFactory,
-                                     initializationData: Option[BackendInitializationData],
-                                     serviceRegistryActor: ActorRef,
-                                     backendSingletonActor: Option[ActorRef])
-  extends Actor with WdlLookup with WorkflowLogging {
-
-  override lazy val workflowDescriptor: EngineWorkflowDescriptor = executionData.workflowDescriptor
-  override lazy val workflowId = workflowDescriptor.id
-  override lazy val executionStore: ExecutionStore = executionData.executionStore
-  override lazy val outputStore: OutputStore = executionData.outputStore
-  override lazy val expressionLanguageFunctions = factory.expressionLanguageFunctions(
-    workflowDescriptor.backendDescriptor, jobKey, initializationData)
-
+abstract class CallPreparationActor(val workflowDescriptor: EngineWorkflowDescriptor,
+                                    val outputStore: OutputStore,
+                                    callKey: CallKey) extends Actor with WorkflowLogging {
+  lazy val workflowIdForLogging = workflowDescriptor.id
+  def expressionLanguageFunctions: WdlStandardLibraryFunctions
+  def prepareExecutionActor(inputEvaluation: Map[Declaration, WdlValue]): CallPreparationActorResponse
+  
   override def receive = {
     case Start =>
-      val response = resolveAndEvaluateInputs(jobKey, expressionLanguageFunctions) map { prepareJobExecutionActor }
-      context.parent ! (response recover { case f => BackendJobPreparationFailed(jobKey, f) }).get
+      val response = resolveAndEvaluateInputs() map { prepareExecutionActor }
+      context.parent ! (response recover { case f => CallPreparationFailed(callKey, f) }).get
       context stop self
 
     case unhandled => workflowLogger.warn(self.path.name + " received an unhandled message: " + unhandled)
   }
 
-  // Split inputs map (= evaluated workflow declarations + coerced json inputs) into [init\.*].last
-  private lazy val splitInputs = workflowDescriptor.backendDescriptor.inputs map { case (fqn, v) => splitFqn(fqn) -> v }
-
-  def resolveAndEvaluateInputs(jobKey: BackendJobDescriptorKey,
-                               wdlFunctions: WdlStandardLibraryFunctions): Try[Map[LocallyQualifiedName, WdlValue]] = {
-    import RuntimeAttributeDefinition.buildMapBasedLookup
+  def resolveAndEvaluateInputs(): Try[Map[Declaration, WdlValue]] = {
     Try {
-      val call = jobKey.call
-      lazy val callInputsFromFile = unqualifiedInputsFromInputFile(call)
-      lazy val workflowScopedLookup = hierarchicalLookup(jobKey.call, jobKey.index) _
-
-      // Try to resolve, evaluate and coerce declarations in order
-      val inputEvaluationAttempt = call.task.declarations.foldLeft(Map.empty[LocallyQualifiedName, Try[WdlValue]])((inputs, declaration) => {
-        val name = declaration.name
-
-        // Try to resolve the declaration, and upon success evaluate the expression
-        // If the declaration is resolved but can't be evaluated this will throw an evaluation exception
-        // If it can't be resolved it's ignored and won't appear in the final input map
-        val evaluated: Option[Try[WdlValue]] = declaration.expression match {
-          // Static expression in the declaration
-          case Some(expr) => Option(expr.evaluate(buildMapBasedLookup(inputs), wdlFunctions))
-          // Expression found in the input mappings
-          case None if call.inputMappings.contains(name) => Option(call.inputMappings(name).evaluate(workflowScopedLookup, wdlFunctions))
-          // Expression found in the input file
-          case None if callInputsFromFile.contains(name) => Option(Success(callInputsFromFile(name)))
-          // Expression can't be found
-          case _ => None
-        }
-
-        // Leave out unresolved declarations
-        evaluated match {
-          case Some(value) =>
-            val coercedValue = value flatMap declaration.wdlType.coerceRawValue
-            inputs + ((name, coercedValue))
-          case None => inputs
-        }
-      })
-
-      TryUtil.sequenceMap(inputEvaluationAttempt, s"Input evaluation for Call ${call.fullyQualifiedName} failed")
-    }.flatten
+      val call = callKey.scope
+      val scatterMap = callKey.index flatMap { i =>
+        // Will need update for nested scatters
+        call.upstream collectFirst { case s: Scatter => Map(s -> i) }
+      } getOrElse Map.empty[Scatter, Int]
+
+      call.evaluateTaskInputs(
+        workflowDescriptor.backendDescriptor.inputs,
+        expressionLanguageFunctions,
+        outputStore.fetchNodeOutputEntries,
+        scatterMap
+      )
+    }
   }
+}
 
-  // Unqualified call inputs for a specific call, from the input json
-  private def unqualifiedInputsFromInputFile(call: Call): Map[LocallyQualifiedName, WdlValue] = splitInputs collect {
-    case((root, inputName), v) if root == call.fullyQualifiedName => inputName -> v
-  }
+final case class JobPreparationActor(executionData: WorkflowExecutionActorData,
+                                     jobKey: BackendJobDescriptorKey,
+                                     factory: BackendLifecycleActorFactory,
+                                     initializationData: Option[BackendInitializationData],
+                                     serviceRegistryActor: ActorRef,
+                                     backendSingletonActor: Option[ActorRef])
+  extends CallPreparationActor(executionData.workflowDescriptor, executionData.outputStore, jobKey) {
 
-  private def prepareJobExecutionActor(inputEvaluation: Map[LocallyQualifiedName, WdlValue]): JobPreparationActorResponse = {
+  override lazy val expressionLanguageFunctions = factory.expressionLanguageFunctions(workflowDescriptor.backendDescriptor, jobKey, initializationData)
+  
+  override def prepareExecutionActor(inputEvaluation: Map[Declaration, WdlValue]): CallPreparationActorResponse = {
     import RuntimeAttributeDefinition.{addDefaultsToAttributes, evaluateRuntimeAttributes}
     val curriedAddDefaultsToAttributes = addDefaultsToAttributes(factory.runtimeAttributeDefinitions(initializationData), workflowDescriptor.backendDescriptor.workflowOptions) _
 
@@ -95,19 +68,45 @@ final case class JobPreparationActor(executionData: WorkflowExecutionActorData,
       jobDescriptor = BackendJobDescriptor(workflowDescriptor.backendDescriptor, jobKey, attributesWithDefault, inputEvaluation)
     } yield BackendJobPreparationSucceeded(jobDescriptor, factory.jobExecutionActorProps(jobDescriptor, initializationData, serviceRegistryActor, backendSingletonActor))) match {
       case Success(s) => s
-      case Failure(f) => BackendJobPreparationFailed(jobKey, f)
+      case Failure(f) => CallPreparationFailed(jobKey, f)
     }
   }
 }
 
-object JobPreparationActor {
-  sealed trait JobPreparationActorCommands
-  case object Start extends JobPreparationActorCommands
+final case class SubWorkflowPreparationActor(executionData: WorkflowExecutionActorData,
+                                             key: SubWorkflowKey,
+                                             subWorkflowId: WorkflowId)
+  extends CallPreparationActor(executionData.workflowDescriptor, executionData.outputStore, key) {
+
+  override lazy val expressionLanguageFunctions = executionData.expressionLanguageFunctions
+
+  override def prepareExecutionActor(inputEvaluation: Map[Declaration, WdlValue]): CallPreparationActorResponse = {
+    val oldBackendDescriptor = workflowDescriptor.backendDescriptor
+    
+    val newBackendDescriptor = oldBackendDescriptor.copy(
+      id = subWorkflowId,
+      workflow = key.scope.calledWorkflow,
+      inputs = workflowDescriptor.inputs ++ (inputEvaluation map { case (k, v) => k.fullyQualifiedName -> v }),
+      breadCrumbs = oldBackendDescriptor.breadCrumbs :+ BackendJobBreadCrumb(workflowDescriptor.workflow, workflowDescriptor.id, key)
+    )
+    val engineDescriptor = workflowDescriptor.copy(backendDescriptor = newBackendDescriptor, parentWorkflow = Option(workflowDescriptor))
+    SubWorkflowPreparationSucceeded(engineDescriptor, inputEvaluation)
+  }
+}
 
-  sealed trait JobPreparationActorResponse
-  case class BackendJobPreparationSucceeded(jobDescriptor: BackendJobDescriptor, bjeaProps: Props) extends JobPreparationActorResponse
-  case class BackendJobPreparationFailed(jobKey: JobKey, throwable: Throwable) extends JobPreparationActorResponse
+object CallPreparationActor {
+  sealed trait CallPreparationActorCommands
+  case object Start extends CallPreparationActorCommands
+
+  sealed trait CallPreparationActorResponse
+  
+  case class BackendJobPreparationSucceeded(jobDescriptor: BackendJobDescriptor, bjeaProps: Props) extends CallPreparationActorResponse
+  case class SubWorkflowPreparationSucceeded(workflowDescriptor: EngineWorkflowDescriptor, inputs: EvaluatedTaskInputs) extends CallPreparationActorResponse
+  case class JobCallPreparationFailed(jobKey: JobKey, throwable: Throwable) extends CallPreparationActorResponse
+  case class CallPreparationFailed(jobKey: JobKey, throwable: Throwable) extends CallPreparationActorResponse
+}
 
+object JobPreparationActor {
   def props(executionData: WorkflowExecutionActorData,
             jobKey: BackendJobDescriptorKey,
             factory: BackendLifecycleActorFactory,
@@ -119,3 +118,13 @@ object JobPreparationActor {
     Props(new JobPreparationActor(executionData, jobKey, factory, initializationData, serviceRegistryActor, backendSingletonActor))
   }
 }
+
+object SubWorkflowPreparationActor {
+  def props(executionData: WorkflowExecutionActorData,
+            key: SubWorkflowKey,
+            subWorkflowId: WorkflowId) = {
+    // Note that JobPreparationActor doesn't run on the engine dispatcher as it mostly executes backend-side code
+    // (WDL expression evaluation using Backend's expressionLanguageFunctions)
+    Props(new SubWorkflowPreparationActor(executionData, key, subWorkflowId))
+  }
+}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/OutputStore.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/OutputStore.scala
new file mode 100644
index 00000000000..02c0bc113e0
--- /dev/null
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/OutputStore.scala
@@ -0,0 +1,98 @@
+package cromwell.engine.workflow.lifecycle.execution
+
+import cromwell.core.ExecutionIndex._
+import cromwell.core._
+import cromwell.engine.workflow.lifecycle.execution.OutputStore.{OutputCallKey, OutputEntry}
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.CollectorKey
+import wdl4s.types.{WdlArrayType, WdlType}
+import wdl4s.util.TryUtil
+import wdl4s.values.{WdlArray, WdlCallOutputsObject, WdlValue}
+import wdl4s.{Call, Declaration, GraphNode, Scope}
+
+import scala.language.postfixOps
+import scala.util.{Failure, Success, Try}
+
+object OutputStore {
+  case class OutputEntry(name: String, wdlType: WdlType, wdlValue: Option[WdlValue])
+  case class OutputCallKey(call: Scope with GraphNode, index: ExecutionIndex)
+  def empty = OutputStore(Map.empty)
+}
+
+case class OutputStore(store: Map[OutputCallKey, List[OutputEntry]]) {
+  def add(values: Map[OutputCallKey, List[OutputEntry]]) = this.copy(store = store ++ values)
+
+  def fetchNodeOutputEntries(node: GraphNode, index: ExecutionIndex): Try[WdlValue] = {
+    def outputEntriesToMap(outputs: List[OutputEntry]): Map[String, Try[WdlValue]] = {
+      outputs map { output =>
+        output.wdlValue match {
+          case Some(wdlValue) => output.name -> Success(wdlValue)
+          case None => output.name -> Failure(new RuntimeException(s"Could not retrieve output ${output.name} value"))
+        }
+      } toMap
+    }
+
+    def callOutputs(call: Call, outputs: List[OutputEntry]) = {
+      TryUtil.sequenceMap(outputEntriesToMap(outputs), s"Output fetching for call ${node.unqualifiedName}") map { outputsMap =>
+        WdlCallOutputsObject(call, outputsMap)
+      }
+    }
+    
+    def declarationOutputs(declaration: Declaration, outputs: List[OutputEntry]) = {
+      outputs match {
+        case OutputEntry(name, _, Some(value)) :: Nil => Success(value)
+        case _ => Failure(new RuntimeException(s"Could not find value for declaration ${declaration.fullyQualifiedName}"))
+      }
+    }
+    
+    store.get(OutputCallKey(node, index)) match {
+      case Some(outputs) =>
+        node match {
+          case call: Call => callOutputs(call, outputs)
+          case declaration: Declaration => declarationOutputs(declaration, outputs)
+          case other =>  Failure(new RuntimeException(s"Only Calls and Declarations are allowed in the OutputStore, found ${other.getClass.getSimpleName}"))
+        }
+      case None => Failure(new RuntimeException(s"Could not find scope ${node.unqualifiedName}"))
+    }
+  }
+  
+  def collectCall(call: Call, sortedShards: Seq[JobKey]) = Try {
+    val shardsOutputs = sortedShards map { e =>
+      fetchNodeOutputEntries(call, e.index) map {
+        case callOutputs: WdlCallOutputsObject => callOutputs.outputs
+        case _ => throw new RuntimeException("Call outputs should be a WdlCallOutputsObject")
+      } getOrElse(throw new RuntimeException(s"Could not retrieve output for shard ${e.scope} #${e.index}"))
+    }
+    
+    call.outputs map { taskOutput =>
+      val wdlValues = shardsOutputs.map(
+        _.getOrElse(taskOutput.unqualifiedName, throw new RuntimeException(s"Could not retrieve output ${taskOutput.unqualifiedName}")))
+      val arrayOfValues = new WdlArray(WdlArrayType(taskOutput.wdlType), wdlValues)
+      taskOutput.unqualifiedName -> JobOutput(arrayOfValues)
+    } toMap
+  }
+  
+  def collectDeclaration(declaration: Declaration, sortedShards: Seq[JobKey]) = Try {
+    val shardsOutputs = sortedShards map { e =>
+      fetchNodeOutputEntries(declaration, e.index) getOrElse {
+        throw new RuntimeException(s"Could not retrieve output for shard ${e.scope} #${e.index}")
+      }
+    }
+    
+    Map(declaration.unqualifiedName -> JobOutput(WdlArray(WdlArrayType(declaration.wdlType), shardsOutputs)))
+  }
+
+  /**
+    * Try to generate output for a collector call, by collecting outputs for all of its shards.
+    * It's fail-fast on shard output retrieval
+    */
+  def generateCollectorOutput(collector: CollectorKey,
+                              shards: Iterable[JobKey]): Try[CallOutputs] = {
+    lazy val sortedShards = shards.toSeq sortBy { _.index.fromIndex }
+    
+    collector.scope match {
+      case call: Call => collectCall(call, sortedShards)
+      case declaration: Declaration => collectDeclaration(declaration, sortedShards)
+      case other => Failure(new RuntimeException(s"Cannot retrieve outputs for ${other.fullyQualifiedName}")) 
+    }
+  }
+}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala
new file mode 100644
index 00000000000..ffac776106f
--- /dev/null
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala
@@ -0,0 +1,275 @@
+package cromwell.engine.workflow.lifecycle.execution
+
+import akka.actor.SupervisorStrategy.Escalate
+import akka.actor.{ActorRef, FSM, LoggingFSM, OneForOneStrategy, Props, SupervisorStrategy}
+import cromwell.backend.{AllBackendInitializationData, BackendLifecycleActorFactory, BackendWorkflowDescriptor}
+import cromwell.core._
+import cromwell.core.logging.JobLogging
+import cromwell.engine.EngineWorkflowDescriptor
+import cromwell.engine.backend.{BackendConfiguration, BackendSingletonCollection}
+import cromwell.engine.workflow.lifecycle.execution.CallPreparationActor.{CallPreparationFailed, Start, SubWorkflowPreparationSucceeded}
+import cromwell.engine.workflow.lifecycle.execution.SubWorkflowExecutionActor._
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor._
+import cromwell.services.metadata.MetadataService._
+import cromwell.services.metadata._
+import cromwell.subworkflowstore.SubWorkflowStoreActor._
+import wdl4s.EvaluatedTaskInputs
+
+class SubWorkflowExecutionActor(key: SubWorkflowKey,
+                                data: WorkflowExecutionActorData,
+                                factories: Map[String, BackendLifecycleActorFactory],
+                                override val serviceRegistryActor: ActorRef,
+                                jobStoreActor: ActorRef,
+                                subWorkflowStoreActor: ActorRef,
+                                callCacheReadActor: ActorRef,
+                                jobTokenDispenserActor: ActorRef,
+                                backendSingletonCollection: BackendSingletonCollection,
+                                initializationData: AllBackendInitializationData,
+                                restarting: Boolean) extends LoggingFSM[SubWorkflowExecutionActorState, SubWorkflowExecutionActorData] with JobLogging with WorkflowMetadataHelper with CallMetadataHelper {
+
+  override def supervisorStrategy: SupervisorStrategy = OneForOneStrategy() { case _ => Escalate }
+
+  private val parentWorkflow = data.workflowDescriptor
+  override val workflowId = parentWorkflow.id
+  override val workflowIdForCallMetadata = parentWorkflow.id
+  override def jobTag: String = key.tag
+
+  startWith(SubWorkflowPendingState, SubWorkflowExecutionActorData.empty)
+  
+  private var eventList: Seq[ExecutionEvent] = Seq(ExecutionEvent(stateName.toString))
+  
+  when(SubWorkflowPendingState) {
+    case Event(Execute, _) =>
+      if (restarting) {
+        subWorkflowStoreActor ! QuerySubWorkflow(parentWorkflow.id, key)
+        goto(SubWorkflowCheckingStoreState)
+      } else {
+        prepareSubWorkflow(createSubWorkflowId())
+      }
+  }
+  
+  when(SubWorkflowCheckingStoreState) {
+    case Event(SubWorkflowFound(entry), _) => 
+      prepareSubWorkflow(WorkflowId.fromString(entry.subWorkflowExecutionUuid))
+    case Event(_: SubWorkflowNotFound, _) =>
+      prepareSubWorkflow(createSubWorkflowId())
+    case Event(SubWorkflowStoreFailure(command, reason), _) =>
+      jobLogger.error(reason, s"SubWorkflowStore failure for command $command, starting sub workflow with fresh ID.")
+      prepareSubWorkflow(createSubWorkflowId())
+  }
+  
+  when(SubWorkflowPreparingState) {
+    case Event(SubWorkflowPreparationSucceeded(subWorkflowEngineDescriptor, inputs), _) =>
+      startSubWorkflow(subWorkflowEngineDescriptor, inputs)
+    case Event(failure: CallPreparationFailed, _) =>
+      context.parent ! SubWorkflowFailedResponse(key, Map.empty, failure.throwable)
+      context stop self
+      stay()
+  }
+  
+  when(SubWorkflowRunningState) {
+    case Event(WorkflowExecutionSucceededResponse(executedJobKeys, outputs), _) =>
+      context.parent ! SubWorkflowSucceededResponse(key, executedJobKeys, outputs)
+      goto(SubWorkflowSucceededState)
+    case Event(WorkflowExecutionFailedResponse(executedJobKeys, reason), _) =>
+      context.parent ! SubWorkflowFailedResponse(key, executedJobKeys, reason)
+      goto(SubWorkflowFailedState)
+    case Event(WorkflowExecutionAbortedResponse(executedJobKeys), _) =>
+      context.parent ! SubWorkflowAbortedResponse(key, executedJobKeys)
+      goto(SubWorkflowAbortedState)
+  }
+  
+  when(SubWorkflowSucceededState) { FSM.NullFunction }
+  when(SubWorkflowFailedState) { FSM.NullFunction }
+  when(SubWorkflowAbortedState) { FSM.NullFunction }
+  
+  whenUnhandled {
+    case Event(SubWorkflowStoreRegisterSuccess(command), _) =>
+      // Nothing to do here
+      stay()
+    case Event(SubWorkflowStoreCompleteSuccess(command), _) =>
+      // Nothing to do here
+      stay()
+    case Event(SubWorkflowStoreFailure(command, reason), _) =>
+      jobLogger.error(reason, s"SubWorkflowStore failure for command $command")
+      stay()
+    case Event(MetadataPutFailed(action, error), _) =>
+      jobLogger.warn(s"Put failed for Metadata action $action", error)
+      stay()
+    case Event(MetadataPutAcknowledgement(_), _) => stay()
+  }
+
+  onTransition {
+    case (fromState, toState) =>
+      stateData.subWorkflowId foreach { id => pushCurrentStateToMetadataService(id, toState.workflowState) } 
+  }
+  
+  onTransition {
+    case (fromState, subWorkflowTerminalState: SubWorkflowTerminalState) =>
+      stateData.subWorkflowId match {
+        case Some(id) => 
+          pushWorkflowEnd(id)
+          pushExecutionEventsToMetadataService(key, eventList)
+        case None => jobLogger.error("Sub workflow completed without a Sub Workflow UUID.")
+      } 
+      context stop self
+  }
+  
+  onTransition {
+    case fromState -> toState => eventList :+= ExecutionEvent(toState.toString)
+  }
+  
+  private def startSubWorkflow(subWorkflowEngineDescriptor: EngineWorkflowDescriptor, inputs: EvaluatedTaskInputs) = {
+    val subWorkflowActor = createSubWorkflowActor(subWorkflowEngineDescriptor)
+    
+    subWorkflowActor ! WorkflowExecutionActor.ExecuteWorkflowCommand
+    context.parent ! JobRunning(key, inputs, Option(subWorkflowActor))
+    pushWorkflowRunningMetadata(subWorkflowEngineDescriptor.backendDescriptor, inputs)
+    
+    goto(SubWorkflowRunningState)
+  }
+  
+  private def prepareSubWorkflow(subWorkflowId: WorkflowId) = {
+    createSubWorkflowPreparationActor(subWorkflowId) ! Start
+    context.parent ! JobStarting(key)
+    pushCurrentStateToMetadataService(subWorkflowId, WorkflowRunning)
+    pushWorkflowStart(subWorkflowId)
+    goto(SubWorkflowPreparingState) using SubWorkflowExecutionActorData(Option(subWorkflowId))
+  }
+  
+  def createSubWorkflowPreparationActor(subWorkflowId: WorkflowId) = {
+    context.actorOf(
+      SubWorkflowPreparationActor.props(data, key, subWorkflowId),
+      s"$subWorkflowId-SubWorkflowPreparationActor-${key.tag}"
+    )
+  }
+  
+  def createSubWorkflowActor(subWorkflowEngineDescriptor: EngineWorkflowDescriptor) = {
+    context.actorOf(
+      WorkflowExecutionActor.props(
+      subWorkflowEngineDescriptor,
+      serviceRegistryActor,
+      jobStoreActor,
+      subWorkflowStoreActor,
+      callCacheReadActor,
+      jobTokenDispenserActor,
+      backendSingletonCollection,
+      initializationData,
+      restarting
+    ),
+      s"${subWorkflowEngineDescriptor.id}-SubWorkflowActor-${key.tag}"
+    )
+  }
+
+  private def pushWorkflowRunningMetadata(subWorkflowDescriptor: BackendWorkflowDescriptor, workflowInputs: EvaluatedTaskInputs) = {
+    val subWorkflowId = subWorkflowDescriptor.id
+    val parentWorkflowMetadataKey = MetadataKey(parentWorkflow.id, Option(MetadataJobKey(key.scope.fullyQualifiedName, key.index, key.attempt)), CallMetadataKeys.SubWorkflowId)
+    
+    val events = List(
+      MetadataEvent(parentWorkflowMetadataKey, MetadataValue(subWorkflowId)),
+      MetadataEvent(MetadataKey(subWorkflowId, None, WorkflowMetadataKeys.Name), MetadataValue(key.scope.callable.unqualifiedName)),
+      MetadataEvent(MetadataKey(subWorkflowId, None, WorkflowMetadataKeys.ParentWorkflowId), MetadataValue(parentWorkflow.id))
+    )
+
+    val inputEvents = workflowInputs match {
+      case empty if empty.isEmpty =>
+        List(MetadataEvent.empty(MetadataKey(subWorkflowId, None,WorkflowMetadataKeys.Inputs)))
+      case inputs =>
+        inputs flatMap { case (inputName, wdlValue) =>
+          wdlValueToMetadataEvents(MetadataKey(subWorkflowId, None, s"${WorkflowMetadataKeys.Inputs}:${inputName.unqualifiedName}"), wdlValue)
+        }
+    }
+
+    val workflowRootEvents = buildWorkflowRootMetadataEvents(subWorkflowDescriptor)
+    
+    serviceRegistryActor ! PutMetadataAction(events ++ inputEvents ++ workflowRootEvents)
+  }
+
+  private def buildWorkflowRootMetadataEvents(subWorkflowDescriptor: BackendWorkflowDescriptor) = {
+    val subWorkflowId = subWorkflowDescriptor.id
+
+    factories flatMap {
+      case (backendName, factory) =>
+        BackendConfiguration.backendConfigurationDescriptor(backendName).toOption map { config =>
+          backendName -> factory.getWorkflowExecutionRootPath(subWorkflowDescriptor, config.backendConfig, initializationData.get(backendName))
+        }
+    } map {
+      case (backend, wfRoot) =>
+        MetadataEvent(MetadataKey(subWorkflowId, None, s"${WorkflowMetadataKeys.WorkflowRoot}[$backend]"), MetadataValue(wfRoot.toAbsolutePath))
+    }
+  }
+  
+  private def createSubWorkflowId() = {
+    val subWorkflowId = WorkflowId.randomId()
+    // Register ID to the sub workflow store
+    subWorkflowStoreActor ! RegisterSubWorkflow(parentWorkflow.rootWorkflow.id, parentWorkflow.id, key, subWorkflowId)
+    subWorkflowId
+  }
+}
+
+object SubWorkflowExecutionActor {
+  sealed trait SubWorkflowExecutionActorState {
+    def workflowState: WorkflowState
+  }
+  sealed trait SubWorkflowTerminalState extends SubWorkflowExecutionActorState
+  
+  case object SubWorkflowPendingState extends SubWorkflowExecutionActorState {
+    override val workflowState = WorkflowRunning
+  }
+  case object SubWorkflowCheckingStoreState extends SubWorkflowExecutionActorState {
+    override val workflowState = WorkflowRunning
+  }
+  case object SubWorkflowPreparingState extends SubWorkflowExecutionActorState {
+    override val workflowState = WorkflowRunning
+  }
+  case object SubWorkflowRunningState extends SubWorkflowExecutionActorState {
+    override val workflowState = WorkflowRunning
+  }
+  case object SubWorkflowAbortingState extends SubWorkflowExecutionActorState {
+    override val workflowState = WorkflowAborting
+  }
+  
+  case object SubWorkflowSucceededState extends SubWorkflowTerminalState {
+    override val workflowState = WorkflowSucceeded
+  }
+  case object SubWorkflowAbortedState extends SubWorkflowTerminalState {
+    override val workflowState = WorkflowAborted
+  }
+  case object SubWorkflowFailedState extends SubWorkflowTerminalState {
+    override val workflowState = WorkflowFailed
+  }
+
+  object SubWorkflowExecutionActorData {
+    def empty = SubWorkflowExecutionActorData(None)
+  }
+  case class SubWorkflowExecutionActorData(subWorkflowId: Option[WorkflowId])
+
+  sealed trait EngineWorkflowExecutionActorCommand
+  case object Execute
+
+  def props(key: SubWorkflowKey,
+            data: WorkflowExecutionActorData,
+            factories: Map[String, BackendLifecycleActorFactory],
+            serviceRegistryActor: ActorRef,
+            jobStoreActor: ActorRef,
+            subWorkflowStoreActor: ActorRef,
+            callCacheReadActor: ActorRef,
+            jobTokenDispenserActor: ActorRef,
+            backendSingletonCollection: BackendSingletonCollection,
+            initializationData: AllBackendInitializationData,
+            restarting: Boolean) = {
+    Props(new SubWorkflowExecutionActor(
+      key,
+      data,
+      factories,
+      serviceRegistryActor,
+      jobStoreActor,
+      subWorkflowStoreActor,
+      callCacheReadActor,
+      jobTokenDispenserActor,
+      backendSingletonCollection,
+      initializationData,
+      restarting)
+    )
+  }
+}
\ No newline at end of file
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WdlLookup.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WdlLookup.scala
deleted file mode 100644
index 8b2af57eac1..00000000000
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WdlLookup.scala
+++ /dev/null
@@ -1,106 +0,0 @@
-package cromwell.engine.workflow.lifecycle.execution
-
-import cromwell.core.{ExecutionIndex, ExecutionStore, OutputStore}
-import cromwell.engine.EngineWorkflowDescriptor
-import ExecutionIndex._
-import wdl4s._
-import wdl4s.expression.WdlStandardLibraryFunctions
-import wdl4s.values.{WdlArray, WdlCallOutputsObject, WdlValue}
-
-import scala.language.postfixOps
-import scala.util.{Failure, Success, Try}
-
-trait WdlLookup {
-
-  def workflowDescriptor: EngineWorkflowDescriptor
-  def executionStore: ExecutionStore
-  def outputStore: OutputStore
-  def expressionLanguageFunctions: WdlStandardLibraryFunctions
-
-  private lazy val splitInputs = workflowDescriptor.backendDescriptor.inputs map {
-    case (fqn, v) => splitFqn(fqn) -> v
-  }
-
-  // Unqualified workflow level inputs
-  private lazy val unqualifiedWorkflowInputs: Map[LocallyQualifiedName, WdlValue] = splitInputs collect {
-    case((root, inputName), v) if root == workflowDescriptor.namespace.workflow.unqualifiedName => inputName -> v
-  }
-
-  /**
-    * Lookup an identifier by
-    * first looking at the completed calls map
-    * and if not found traversing up the scope hierarchy from the scope from which the lookup originated.
-    */
-  def hierarchicalLookup(scope: Scope, index: ExecutionIndex)(identifier: String): WdlValue = {
-    // First lookup calls
-    lookupCall(scope, index, identifier) recoverWith {
-      // Lookup in the same scope (currently no scope support this but say we have scatter declarations, or multiple scatter variables, or nested workflows..)
-      case _: VariableNotFoundException | _: WdlExpressionException => scopedLookup(scope, index, identifier)
-    } recover {
-      // Lookup parent if present
-      case _: VariableNotFoundException | _: WdlExpressionException => scope.parent match {
-        case Some(parent) => hierarchicalLookup(parent, index)(identifier)
-        case None => throw new VariableNotFoundException(s"Can't find $identifier")
-      }
-    } get
-  }
-
-  private def scopedLookup(scope: Scope, index: ExecutionIndex, identifier: String): Try[WdlValue] = {
-    def scopedLookupFunction = scope match {
-      case scatter: Scatter if index.isDefined => lookupScatter(scatter, index.get) _
-      case workflow: Workflow => lookupWorkflowDeclaration _
-      case _ => (_: String) => Failure(new VariableNotFoundException(s"Can't find $identifier in scope $scope"))
-    }
-
-    scopedLookupFunction(identifier)
-  }
-
-  // In this case, the scopedLookup function is effectively equivalent to looking into unqualifiedWorkflowInputs for the value
-  // because the resolution / evaluation / coercion has already happened in the MaterializeWorkflowDescriptorActor
-  private def lookupWorkflowDeclaration(identifier: String) = {
-    unqualifiedWorkflowInputs.get(identifier) match {
-      case Some(value) => Success(value)
-      case None => Failure(new WdlExpressionException(s"Could not resolve variable $identifier as a workflow input"))
-    }
-  }
-
-  private def lookupScatter(scatter: Scatter, index: Int)(identifier: String): Try[WdlValue] = {
-    if (identifier == scatter.item) {
-      // Scatters are not indexed yet (they can't be nested)
-      val scatterLookup = hierarchicalLookup(scatter, None) _
-      scatter.collection.evaluate(scatterLookup, expressionLanguageFunctions) map {
-        case collection: WdlArray if collection.value.isDefinedAt(index) => collection.value(index)
-        case collection: WdlArray => throw new RuntimeException(s"Index $index out of bound in $collection for scatter ${scatter.fullyQualifiedName}")
-        case other => throw new RuntimeException(s"Scatter ${scatter.fullyQualifiedName} collection is not an array: $other")
-      } recover {
-        case e => throw new RuntimeException(s"Failed to evaluate collection for scatter ${scatter.fullyQualifiedName}", e)
-      }
-    } else {
-      Failure(new VariableNotFoundException(identifier))
-    }
-  }
-
-  private def lookupCall(scope: Scope, scopeIndex: ExecutionIndex, identifier: String): Try[WdlCallOutputsObject] = {
-    val calls = executionStore.store.keys.view map { _.scope } collect { case c: Call => c }
-
-    calls find { _.unqualifiedName == identifier } match {
-      case Some(matchedCall) =>
-        /**
-          * After matching the Call, this determines if the `key` depends on a single shard
-          * of a scatter'd job or if it depends on the whole thing.  Right now, the heuristic
-          * is "If we're both in a scatter block together, then I depend on a shard.  If not,
-          * I depend on the collected value"
-          *
-          * TODO: nested-scatter - this will likely not be sufficient for nested scatters
-          */
-        val index: ExecutionIndex = matchedCall.closestCommonAncestor(scope) flatMap {
-          case s: Scatter => scopeIndex
-          case _ => None
-        }
-
-        outputStore.fetchCallOutputEntries(matchedCall, index)
-      case None => Failure(new WdlExpressionException(s"Could not find a call with identifier '$identifier'"))
-    }
-  }
-
-}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala
index b7358296ba1..10f0bf37738 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala
@@ -1,316 +1,76 @@
 package cromwell.engine.workflow.lifecycle.execution
 
-import java.time.OffsetDateTime
-
-import akka.actor.SupervisorStrategy.{Escalate, Stop}
 import akka.actor._
 import cats.data.NonEmptyList
 import com.typesafe.config.ConfigFactory
-import cromwell.backend.BackendJobExecutionActor.{AbortedResponse, FailedNonRetryableResponse, FailedRetryableResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{AbortedResponse, JobFailedNonRetryableResponse, JobFailedRetryableResponse, JobSucceededResponse}
 import cromwell.backend.BackendLifecycleActor.AbortJobCommand
-import cromwell.backend.{AllBackendInitializationData, BackendJobDescriptor, BackendJobDescriptorKey}
-import cromwell.core.Dispatcher.EngineDispatcher
+import cromwell.backend.{AllBackendInitializationData, BackendJobDescriptorKey, JobExecutionMap}
+import cromwell.core.Dispatcher._
 import cromwell.core.ExecutionIndex._
 import cromwell.core.ExecutionStatus._
-import cromwell.core.ExecutionStore.ExecutionStoreEntry
-import cromwell.core.OutputStore.OutputEntry
 import cromwell.core.WorkflowOptions.WorkflowFailureMode
 import cromwell.core._
 import cromwell.core.logging.WorkflowLogging
 import cromwell.engine.backend.{BackendSingletonCollection, CromwellBackends}
-import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor.JobRunning
-import cromwell.engine.workflow.lifecycle.execution.JobPreparationActor.BackendJobPreparationFailed
-import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.WorkflowExecutionActorState
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{apply => _, _}
 import cromwell.engine.workflow.lifecycle.{EngineLifecycleActorAbortCommand, EngineLifecycleActorAbortedResponse}
 import cromwell.engine.{ContinueWhilePossible, EngineWorkflowDescriptor}
-import cromwell.services.metadata.MetadataService._
-import cromwell.services.metadata._
+import cromwell.services.metadata.MetadataService.{MetadataPutAcknowledgement, MetadataPutFailed}
+import cromwell.util.{StopAndLogSupervisor, TryUtil}
 import cromwell.webservice.EngineStatsActor
 import lenthall.exception.ThrowableAggregation
 import net.ceedubs.ficus.Ficus._
-import wdl4s.types.WdlArrayType
-import wdl4s.util.TryUtil
 import wdl4s.values.{WdlArray, WdlValue}
 import wdl4s.{Scope, _}
 
 import scala.annotation.tailrec
 import scala.language.postfixOps
-import scala.util.{Failure, Random, Success, Try}
-
-object WorkflowExecutionActor {
-
-  /**
-    * States
-    */
-  sealed trait WorkflowExecutionActorState { def terminal = false }
-  sealed trait WorkflowExecutionActorTerminalState extends WorkflowExecutionActorState { override val terminal = true }
-
-  case object WorkflowExecutionPendingState extends WorkflowExecutionActorState
-  case object WorkflowExecutionInProgressState extends WorkflowExecutionActorState
-  case object WorkflowExecutionAbortingState extends WorkflowExecutionActorState
-  case object WorkflowExecutionSuccessfulState extends WorkflowExecutionActorTerminalState
-  case object WorkflowExecutionFailedState extends WorkflowExecutionActorTerminalState
-  case object WorkflowExecutionAbortedState extends WorkflowExecutionActorTerminalState
-
-  /**
-    * Commands
-    */
-  sealed trait WorkflowExecutionActorCommand
-  case object ExecuteWorkflowCommand extends WorkflowExecutionActorCommand
-  case object RestartExecutingWorkflowCommand extends WorkflowExecutionActorCommand
-
-  /**
-    * Responses
-    */
-  sealed trait WorkflowExecutionActorResponse {
-    def executionStore: ExecutionStore
-
-    def outputStore: OutputStore
-  }
-
-  case class WorkflowExecutionSucceededResponse(executionStore: ExecutionStore, outputStore: OutputStore)
-    extends WorkflowExecutionActorResponse {
-    override def toString = "WorkflowExecutionSucceededResponse"
-  }
-
-  case class WorkflowExecutionAbortedResponse(executionStore: ExecutionStore, outputStore: OutputStore)
-    extends WorkflowExecutionActorResponse with EngineLifecycleActorAbortedResponse {
-    override def toString = "WorkflowExecutionAbortedResponse"
-  }
-
-  final case class WorkflowExecutionFailedResponse(executionStore: ExecutionStore, outputStore: OutputStore,
-                                                   reasons: Seq[Throwable]) extends WorkflowExecutionActorResponse {
-    override def toString = "WorkflowExecutionFailedResponse"
-  }
-
-  /**
-    * Internal control flow messages
-    */
-  private case class JobInitializationFailed(jobKey: JobKey, throwable: Throwable)
-  private case class ScatterCollectionFailedResponse(collectorKey: CollectorKey, throwable: Throwable)
-  private case class ScatterCollectionSucceededResponse(collectorKey: CollectorKey, outputs: JobOutputs)
-
-  /**
-    * Internal ADTs
-    */
-  case class ScatterKey(scope: Scatter) extends JobKey {
-    override val index = None // When scatters are nested, this might become Some(_)
-    override val attempt = 1
-    override val tag = scope.unqualifiedName
-
-    /**
-      * Creates a sub-ExecutionStore with Starting entries for each of the scoped children.
-      *
-      * @param count Number of ways to scatter the children.
-      * @return ExecutionStore of scattered children.
-      */
-    def populate(count: Int): Map[JobKey, ExecutionStatus.Value] = {
-      val keys = this.scope.children flatMap { explode(_, count) }
-      keys map { _ -> ExecutionStatus.NotStarted } toMap
-    }
-
-    private def explode(scope: Scope, count: Int): Seq[JobKey] = {
-      scope match {
-        case call: Call =>
-          val shards = (0 until count) map { i => BackendJobDescriptorKey(call, Option(i), 1) }
-          shards :+ CollectorKey(call)
-        case scatter: Scatter =>
-          throw new UnsupportedOperationException("Nested Scatters are not supported (yet).")
-        case e =>
-          throw new UnsupportedOperationException(s"Scope ${e.getClass.getName} is not supported.")
-      }
-    }
-  }
-
-  // Represents a scatter collection for a call in the execution store
-  case class CollectorKey(scope: Call) extends JobKey {
-    override val index = None
-    override val attempt = 1
-    override val tag = s"Collector-${scope.unqualifiedName}"
-  }
-
-  case class WorkflowExecutionException[T <: Throwable](exceptions: NonEmptyList[T]) extends ThrowableAggregation {
-    override val throwables = exceptions.toList
-    override val exceptionContext = s"WorkflowExecutionActor"
-  }
-
-  def props(workflowId: WorkflowId,
-            workflowDescriptor: EngineWorkflowDescriptor,
-            serviceRegistryActor: ActorRef,
-            jobStoreActor: ActorRef,
-            callCacheReadActor: ActorRef,
-            jobTokenDispenserActor: ActorRef,
-            backendSingletonCollection: BackendSingletonCollection,
-            initializationData: AllBackendInitializationData,
-            restarting: Boolean): Props = {
-    Props(WorkflowExecutionActor(workflowId, workflowDescriptor, serviceRegistryActor, jobStoreActor,
-      callCacheReadActor, jobTokenDispenserActor, backendSingletonCollection, initializationData, restarting)).withDispatcher(EngineDispatcher)
-  }
-
-  implicit class EnhancedExecutionStore(val executionStore: ExecutionStore) extends AnyVal {
-    // Convert the store to a `List` before `collect`ing to sidestep expensive and pointless hashing of `Scope`s when
-    // assembling the result.
-    def runnableScopes = executionStore.store.toList collect { case entry if isRunnable(entry) => entry._1 }
-
-    private def isRunnable(entry: ExecutionStoreEntry) = {
-      entry match {
-        case (key, ExecutionStatus.NotStarted) => arePrerequisitesDone(key)
-        case _ => false
-      }
-    }
-
-    def findShardEntries(key: CollectorKey): List[ExecutionStoreEntry] = executionStore.store.toList collect {
-      case (k: BackendJobDescriptorKey, v) if k.scope == key.scope && k.isShard => (k, v)
-    }
-
-    private def arePrerequisitesDone(key: JobKey): Boolean = {
-      val upstream = key.scope.prerequisiteScopes.toList.map(s => upstreamEntries(key, s))
-      val downstream = key match {
-        case collector: CollectorKey => findShardEntries(collector)
-        case _ => Nil
-      }
-
-      val dependencies = upstream.flatten ++ downstream
-      val dependenciesResolved = dependencies forall { case (_, s) => s == ExecutionStatus.Done }
-
-      /**
-        * We need to make sure that all prerequisiteScopes have been resolved to some entry before going forward.
-        * If a scope cannot be resolved it may be because it is in a scatter that has not been populated yet,
-        * therefore there is no entry in the executionStore for this scope.
-        * If that's the case this prerequisiteScope has not been run yet, hence the (upstream forall {_.nonEmpty})
-        */
-      (upstream forall { _.nonEmpty }) && dependenciesResolved
-    }
-
-    private def upstreamEntries(entry: JobKey, prerequisiteScope: Scope): Seq[ExecutionStoreEntry] = {
-      prerequisiteScope.closestCommonAncestor(entry.scope) match {
-        /**
-          * If this entry refers to a Scope which has a common ancestor with prerequisiteScope
-          * and that common ancestor is a Scatter block, then find the shard with the same index
-          * as 'entry'.  In other words, if you're in the same scatter block as your pre-requisite
-          * scope, then depend on the shard (with same index).
-          *
-          * NOTE: this algorithm was designed for ONE-LEVEL of scattering and probably does not
-          * work as-is for nested scatter blocks
-          */
-        case Some(ancestor: Scatter) =>
-          executionStore.store filter {
-            case (k, _) => k.scope == prerequisiteScope && k.index == entry.index
-          } toSeq
-
-        /**
-          * Otherwise, simply refer to the entry the collector entry.  This means that 'entry' depends
-          * on every shard of the pre-requisite scope to finish.
-          */
-        case _ =>
-          executionStore.store filter {
-            case (k, _) => k.scope == prerequisiteScope && k.index.isEmpty
-          } toSeq
-      }
-    }
-  }
-
-  implicit class EnhancedOutputStore(val outputStore: OutputStore) extends AnyVal {
-    /**
-      * Try to generate output for a collector call, by collecting outputs for all of its shards.
-      * It's fail-fast on shard output retrieval
-      */
-    def generateCollectorOutput(collector: CollectorKey,
-                                shards: Iterable[BackendJobDescriptorKey]): Try[JobOutputs] = Try {
-      val shardsOutputs = shards.toSeq sortBy { _.index.fromIndex } map { e =>
-        outputStore.fetchCallOutputEntries(e.scope, e.index) map {
-          _.outputs
-        } getOrElse(throw new RuntimeException(s"Could not retrieve output for shard ${e.scope} #${e.index}"))
-      }
-      collector.scope.task.outputs map { taskOutput =>
-        val wdlValues = shardsOutputs.map(
-          _.getOrElse(taskOutput.name, throw new RuntimeException(s"Could not retrieve output ${taskOutput.name}")))
-        val arrayOfValues = new WdlArray(WdlArrayType(taskOutput.wdlType), wdlValues)
-        taskOutput.name -> JobOutput(arrayOfValues)
-      } toMap
-    }
-  }
-}
-
-final case class WorkflowExecutionActor(workflowId: WorkflowId,
-                                        workflowDescriptor: EngineWorkflowDescriptor,
-                                        serviceRegistryActor: ActorRef,
-                                        jobStoreActor: ActorRef,
-                                        callCacheReadActor: ActorRef,
-                                        jobTokenDispenserActor: ActorRef,
-                                        backendSingletonCollection: BackendSingletonCollection,
-                                        initializationData: AllBackendInitializationData,
-                                        restarting: Boolean)
-  extends LoggingFSM[WorkflowExecutionActorState, WorkflowExecutionActorData] with WorkflowLogging {
-
-  import WorkflowExecutionActor._
-
-  override def supervisorStrategy = AllForOneStrategy() {
-    case ex: ActorInitializationException =>
-      context.parent ! WorkflowExecutionFailedResponse(stateData.executionStore, stateData.outputStore, List(ex))
-      context.stop(self)
-      Stop
-    case t => super.supervisorStrategy.decider.applyOrElse(t, (_: Any) => Escalate)
-  }
-
-  val tag = s"WorkflowExecutionActor [UUID(${workflowId.shortString})]"
-  private lazy val DefaultMaxRetriesFallbackValue = 10
-
+import scala.util.{Failure, Success, Try}
+
+case class WorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor,
+                                  serviceRegistryActor: ActorRef,
+                                  jobStoreActor: ActorRef,
+                                  subWorkflowStoreActor: ActorRef,
+                                  callCacheReadActor: ActorRef,
+                                  jobTokenDispenserActor: ActorRef,
+                                  backendSingletonCollection: BackendSingletonCollection,
+                                  initializationData: AllBackendInitializationData,
+                                  restarting: Boolean)
+  extends LoggingFSM[WorkflowExecutionActorState, WorkflowExecutionActorData] with WorkflowLogging with CallMetadataHelper with StopAndLogSupervisor {
+  
   implicit val ec = context.dispatcher
+  
+  override val workflowIdForLogging = workflowDescriptor.id
+  override val workflowIdForCallMetadata = workflowDescriptor.id
 
-  val MaxRetries = ConfigFactory.load().as[Option[Int]]("system.max-retries") match {
+  private val tag = s"WorkflowExecutionActor [UUID(${workflowDescriptor.id.shortString})]"
+  private val MaxRetries = ConfigFactory.load().as[Option[Int]]("system.max-retries") match {
     case Some(value) => value
     case None =>
       workflowLogger.warn(s"Failed to load the max-retries value from the configuration. Defaulting back to a value of '$DefaultMaxRetriesFallbackValue'.")
       DefaultMaxRetriesFallbackValue
   }
-
-  private val factories = TryUtil.sequenceMap(workflowDescriptor.backendAssignments.values.toSet[String] map { backendName =>
+  
+  private val backendFactories = TryUtil.sequenceMap(workflowDescriptor.backendAssignments.values.toSet[String] map { backendName =>
     backendName -> CromwellBackends.backendLifecycleFactoryActorByName(backendName)
   } toMap) recover {
     case e => throw new RuntimeException("Could not instantiate backend factories", e)
   } get
 
-  // Initialize the StateData with ExecutionStore (all calls as NotStarted) and SymbolStore
   startWith(
     WorkflowExecutionPendingState,
     WorkflowExecutionActorData(
       workflowDescriptor,
-      executionStore = buildInitialExecutionStore(),
+      executionStore = ExecutionStore(workflowDescriptor.backendDescriptor.workflow, workflowDescriptor.inputs),
       backendJobExecutionActors = Map.empty,
+      engineCallExecutionActors = Map.empty,
+      subWorkflowExecutionActors = Map.empty,
+      downstreamExecutionMap = Map.empty,
       outputStore = OutputStore.empty
     )
   )
 
-  private def buildInitialExecutionStore(): ExecutionStore = {
-    val workflow = workflowDescriptor.backendDescriptor.workflowNamespace.workflow
-    // Only add direct children to the store, the rest is dynamically created when necessary
-    val keys = workflow.children map {
-      case call: Call => BackendJobDescriptorKey(call, None, 1)
-      case scatter: Scatter => ScatterKey(scatter)
-    }
-
-    ExecutionStore(keys.map(_ -> NotStarted).toMap)
-  }
-
-  private def handleNonRetryableFailure(stateData: WorkflowExecutionActorData, failedJobKey: JobKey, reason: Throwable) = {
-    val mergedStateData = stateData.mergeExecutionDiff(WorkflowExecutionDiff(Map(failedJobKey -> ExecutionStatus.Failed)))
-      .removeBackendJobExecutionActor(failedJobKey)
-
-    if (workflowDescriptor.getWorkflowOption(WorkflowFailureMode).contains(ContinueWhilePossible.toString)) {
-      mergedStateData.workflowCompletionStatus match {
-        case Some(completionStatus) if completionStatus == Failed =>
-          context.parent ! WorkflowExecutionFailedResponse(stateData.executionStore, stateData.outputStore, List(reason))
-          goto(WorkflowExecutionFailedState) using mergedStateData
-        case _ =>
-          stay() using startRunnableScopes(mergedStateData)
-      }
-    } else {
-      context.parent ! WorkflowExecutionFailedResponse(stateData.executionStore, stateData.outputStore, List(reason))
-      goto(WorkflowExecutionFailedState) using mergedStateData
-    }
-  }
-
   when(WorkflowExecutionPendingState) {
     case Event(ExecuteWorkflowCommand, stateData) =>
       val data = startRunnableScopes(stateData)
@@ -318,32 +78,64 @@ final case class WorkflowExecutionActor(workflowId: WorkflowId,
   }
 
   when(WorkflowExecutionInProgressState) {
-    case Event(JobRunning(jobDescriptor, backendJobExecutionActor), stateData) =>
-      pushRunningJobMetadata(jobDescriptor)
+    case Event(JobStarting(jobKey), stateData) =>
+      pushStartingCallMetadata(jobKey)
       stay() using stateData
-        .addBackendJobExecutionActor(jobDescriptor.key, backendJobExecutionActor)
-        .mergeExecutionDiff(WorkflowExecutionDiff(Map(jobDescriptor.key -> ExecutionStatus.Running)))
-    case Event(BackendJobPreparationFailed(jobKey, throwable), stateData) =>
-      pushFailedJobMetadata(jobKey, None, throwable, retryableFailure = false)
-      context.parent ! WorkflowExecutionFailedResponse(stateData.executionStore, stateData.outputStore, List(throwable))
-      goto(WorkflowExecutionFailedState) using stateData.mergeExecutionDiff(WorkflowExecutionDiff(Map(jobKey -> ExecutionStatus.Failed)))
-    case Event(SucceededResponse(jobKey, returnCode, callOutputs, _, _), stateData) =>
-      pushSuccessfulJobMetadata(jobKey, returnCode, callOutputs)
-      handleJobSuccessful(jobKey, callOutputs, stateData)
-    case Event(FailedNonRetryableResponse(jobKey, reason, returnCode), stateData) =>
-      pushFailedJobMetadata(jobKey, returnCode, reason, retryableFailure = false)
-      handleNonRetryableFailure(stateData, jobKey, reason)
-    case Event(FailedRetryableResponse(jobKey, reason, returnCode), stateData) =>
-      workflowLogger.warn(s"Job ${jobKey.tag} failed with a retryable failure: ${reason.getMessage}")
-      pushFailedJobMetadata(jobKey, None, reason, retryableFailure = true)
-      handleRetryableFailure(jobKey, reason, returnCode)
-    case Event(JobInitializationFailed(jobKey, reason), stateData) =>
-      pushFailedJobMetadata(jobKey, None, reason, retryableFailure = false)
-      handleNonRetryableFailure(stateData, jobKey, reason)
+        .mergeExecutionDiff(WorkflowExecutionDiff(Map(jobKey -> ExecutionStatus.Starting)))
+    case Event(JobRunning(key, inputs, callExecutionActor), stateData) =>
+      pushRunningCallMetadata(key, inputs)
+      stay() using stateData
+        .addCallExecutionActor(key, callExecutionActor)
+        .mergeExecutionDiff(WorkflowExecutionDiff(Map(key -> ExecutionStatus.Running)))
+      
+      //Success
+        // Job
+    case Event(JobSucceededResponse(jobKey, returnCode, callOutputs, _, _), stateData) =>
+      pushSuccessfulCallMetadata(jobKey, returnCode, callOutputs)
+      handleCallSuccessful(jobKey, callOutputs, stateData, Map.empty)
+        // Sub Workflow
+    case Event(SubWorkflowSucceededResponse(jobKey, descendantJobKeys, callOutputs), stateData) =>
+      pushSuccessfulCallMetadata(jobKey, None, callOutputs)
+      handleCallSuccessful(jobKey, callOutputs, stateData, descendantJobKeys)
+        // Scatter
     case Event(ScatterCollectionSucceededResponse(jobKey, callOutputs), stateData) =>
-      handleJobSuccessful(jobKey, callOutputs, stateData)
+      handleCallSuccessful(jobKey, callOutputs, stateData, Map.empty)
+        // Declaration
+    case Event(DeclarationEvaluationSucceededResponse(jobKey, callOutputs), stateData) =>
+      handleDeclarationEvaluationSuccessful(jobKey, callOutputs, stateData)
+
+      // Failure
+        // Initialization
+    case Event(JobInitializationFailed(jobKey, reason), stateData) =>
+      pushFailedCallMetadata(jobKey, None, reason, retryableFailure = false)
+      handleNonRetryableFailure(stateData, jobKey, reason, Map.empty)
+      // Job Non Retryable
+    case Event(JobFailedNonRetryableResponse(jobKey, reason, returnCode), stateData) =>
+      pushFailedCallMetadata(jobKey, returnCode, reason, retryableFailure = false)
+      handleNonRetryableFailure(stateData, jobKey, reason, Map.empty)
+      // Job Retryable
+    case Event(JobFailedRetryableResponse(jobKey, reason, returnCode), stateData) =>
+      pushFailedCallMetadata(jobKey, None, reason, retryableFailure = true)
+      handleRetryableFailure(jobKey, reason, returnCode)
+      // Sub Workflow - sub workflow failures are always non retryable
+    case Event(SubWorkflowFailedResponse(jobKey, descendantJobKeys, reason), stateData) =>
+      pushFailedCallMetadata(jobKey, None, reason, retryableFailure = false)
+      handleNonRetryableFailure(stateData, jobKey, reason, descendantJobKeys)
+    case Event(DeclarationEvaluationFailedResponse(jobKey, reason), stateData) =>
+      handleDeclarationEvaluationFailure(jobKey, reason, stateData)
   }
 
+  when(WorkflowExecutionAbortingState) {
+    case Event(AbortedResponse(jobKey), stateData) =>
+      handleCallAborted(stateData, jobKey, Map.empty)
+    case Event(SubWorkflowAbortedResponse(jobKey, executedKeys), stateData) =>
+      handleCallAborted(stateData, jobKey, executedKeys)
+    case Event(SubWorkflowSucceededResponse(subKey, executedKeys, _), stateData) =>
+      handleCallAborted(stateData, subKey, executedKeys)
+    case Event(JobSucceededResponse(jobKey, returnCode, callOutputs, _, _), stateData) =>
+      handleCallAborted(stateData, jobKey, Map.empty)
+  }
+  
   when(WorkflowExecutionSuccessfulState) {
     FSM.NullFunction
   }
@@ -359,51 +151,63 @@ final case class WorkflowExecutionActor(workflowId: WorkflowId,
     */
   private def alreadyFailedMopUp: StateFunction = {
     case Event(JobInitializationFailed(jobKey, reason), stateData) =>
-      pushFailedJobMetadata(jobKey, None, reason, retryableFailure = false)
+      pushFailedCallMetadata(jobKey, None, reason, retryableFailure = false)
       stay
-    case Event(FailedNonRetryableResponse(jobKey, reason, returnCode), stateData) =>
-      pushFailedJobMetadata(jobKey, returnCode, reason, retryableFailure = false)
+    case Event(JobFailedNonRetryableResponse(jobKey, reason, returnCode), stateData) =>
+      pushFailedCallMetadata(jobKey, returnCode, reason, retryableFailure = false)
       stay
-    case Event(FailedRetryableResponse(jobKey, reason, returnCode), stateData) =>
-      pushFailedJobMetadata(jobKey, returnCode, reason, retryableFailure = true)
+    case Event(JobFailedRetryableResponse(jobKey, reason, returnCode), stateData) =>
+      pushFailedCallMetadata(jobKey, returnCode, reason, retryableFailure = true)
       stay
-    case Event(SucceededResponse(jobKey, returnCode, callOutputs, _, _), stateData) =>
-      pushSuccessfulJobMetadata(jobKey, returnCode, callOutputs)
+    case Event(JobSucceededResponse(jobKey, returnCode, callOutputs, _, _), stateData) =>
+      pushSuccessfulCallMetadata(jobKey, returnCode, callOutputs)
       stay
   }
 
-  when(WorkflowExecutionAbortingState) {
-    case Event(AbortedResponse(jobKey), stateData) =>
-      workflowLogger.info(s"$tag job aborted: ${jobKey.tag}")
-      val newStateData = stateData.removeBackendJobExecutionActor(jobKey)
-      if (newStateData.backendJobExecutionActors.isEmpty) {
-        workflowLogger.info(s"$tag all jobs aborted")
-        goto(WorkflowExecutionAbortedState)
-      } else {
-        stay() using newStateData
+
+  def handleTerminated(actorRef: ActorRef) = {
+    // Both of these Should Never Happen (tm), assuming the state data is set correctly on EJEA creation.
+    // If they do, it's a big programmer error and the workflow execution fails.
+    val jobKey = stateData.engineCallExecutionActors.getOrElse(actorRef, throw new RuntimeException("Programmer Error: An EJEA has terminated but was not assigned a jobKey"))
+    val jobStatus = stateData.executionStore.store.getOrElse(jobKey, throw new RuntimeException("Programmer Error: An EJEA representing a jobKey which this workflow is not running has sent up a terminated message."))
+
+    if (!jobStatus.isTerminal) {
+      val terminationException = getFailureCause(actorRef) match {
+        case Some(e) => new RuntimeException("Unexpected failure in EJEA.", e)
+        case None => new RuntimeException("Unexpected failure in EJEA (root cause not captured).")
       }
+      self ! JobFailedNonRetryableResponse(jobKey, terminationException, None)
+    }
+
+    stay
   }
 
   whenUnhandled {
+    case Event(Terminated(actorRef), stateData) => handleTerminated(actorRef) using stateData.removeEngineJobExecutionActor(actorRef)
     case Event(MetadataPutFailed(action, error), _) =>
       // Do something useful here??
-      workflowLogger.warn(s"$tag Put failed for Metadata action $action : ${error.getMessage}")
-      stay
+      workflowLogger.warn(s"$tag Put failed for Metadata action $action", error)
+      stay()
     case Event(MetadataPutAcknowledgement(_), _) => stay()
     case Event(EngineLifecycleActorAbortCommand, stateData) =>
-      if (stateData.backendJobExecutionActors.nonEmpty) {
-        log.info(s"$tag: Abort received. Aborting ${stateData.backendJobExecutionActors.size} EJEAs")
-        stateData.backendJobExecutionActors.values foreach {_ ! AbortJobCommand}
+      if (stateData.hasRunningActors) {
+        log.info(s"$tag: Abort received. " +
+          s"Aborting ${stateData.backendJobExecutionActors.size} Job Execution Actors" +
+          s"and ${stateData.subWorkflowExecutionActors.size} Sub Workflow Execution Actors"
+        )
+        stateData.backendJobExecutionActors.values foreach { _ ! AbortJobCommand }
+        stateData.subWorkflowExecutionActors.values foreach { _ ! EngineLifecycleActorAbortCommand }
         goto(WorkflowExecutionAbortingState)
       } else {
         goto(WorkflowExecutionAbortedState)
       }
     case Event(EngineStatsActor.JobCountQuery, data) =>
       sender ! EngineStatsActor.JobCount(data.backendJobExecutionActors.size)
+      data.subWorkflowExecutionActors.values foreach { _ forward EngineStatsActor.JobCountQuery }
       stay()
     case unhandledMessage =>
       workflowLogger.warn(s"$tag received an unhandled message: ${unhandledMessage.event} in state: $stateName")
-      stay
+      stay()
   }
 
   onTransition {
@@ -415,11 +219,61 @@ final case class WorkflowExecutionActor(workflowId: WorkflowId,
   }
 
   onTransition {
-    case _ -> WorkflowExecutionSuccessfulState =>
-      pushWorkflowOutputMetadata(nextStateData)
-      context.parent ! WorkflowExecutionSucceededResponse(nextStateData.executionStore, nextStateData.outputStore)
     case _ -> WorkflowExecutionAbortedState =>
-      context.parent ! WorkflowExecutionAbortedResponse(nextStateData.executionStore, nextStateData.outputStore)
+      context.parent ! WorkflowExecutionAbortedResponse(nextStateData.jobExecutionMap)
+  }
+
+  private def handleNonRetryableFailure(stateData: WorkflowExecutionActorData, failedJobKey: JobKey, reason: Throwable, jobExecutionMap: JobExecutionMap) = {
+    val newData = stateData
+      .removeCallExecutionActor(failedJobKey)
+      .addExecutions(jobExecutionMap)
+    
+    handleExecutionFailure(failedJobKey, newData, reason, jobExecutionMap)
+  }
+  
+  private def handleDeclarationEvaluationFailure(declarationKey: DeclarationKey, reason: Throwable, stateData: WorkflowExecutionActorData) = {
+    handleExecutionFailure(declarationKey, stateData, reason, Map.empty)
+  }
+  
+  private def handleExecutionFailure(failedJobKey: JobKey, data: WorkflowExecutionActorData, reason: Throwable, jobExecutionMap: JobExecutionMap) = {
+    val newData = data.executionFailed(failedJobKey)
+    
+    if (workflowDescriptor.getWorkflowOption(WorkflowFailureMode).contains(ContinueWhilePossible.toString)) {
+      newData.workflowCompletionStatus match {
+        case Some(completionStatus) if completionStatus == Failed =>
+          context.parent ! WorkflowExecutionFailedResponse(newData.jobExecutionMap, reason)
+          goto(WorkflowExecutionFailedState) using newData
+        case _ =>
+          stay() using startRunnableScopes(newData)
+      }
+    } else {
+      context.parent ! WorkflowExecutionFailedResponse(newData.jobExecutionMap, reason)
+      goto(WorkflowExecutionFailedState) using newData
+    }
+  }
+  
+  private def handleWorkflowSuccessful(data: WorkflowExecutionActorData) = {
+    import cromwell.util.JsonFormatting.WdlValueJsonFormatter._
+    import spray.json._
+    
+     val (response, finalState) = workflowDescriptor.workflow.evaluateOutputs(
+      workflowDescriptor.inputs,
+      data.expressionLanguageFunctions,
+      data.outputStore.fetchNodeOutputEntries
+    ) map { workflowOutputs =>
+       workflowLogger.info(
+         s"""Workflow ${workflowDescriptor.workflow.unqualifiedName} complete. Final Outputs:
+             |${workflowOutputs.toJson.prettyPrint}""".stripMargin
+       )
+       pushWorkflowOutputMetadata(workflowOutputs)
+       (WorkflowExecutionSucceededResponse(data.jobExecutionMap, workflowOutputs mapValues JobOutput.apply), WorkflowExecutionSuccessfulState)
+    } recover {
+       case ex =>
+         (WorkflowExecutionFailedResponse(data.jobExecutionMap, ex), WorkflowExecutionFailedState)
+    } get
+    
+    context.parent ! response
+    goto(finalState) using data
   }
 
   private def handleRetryableFailure(jobKey: BackendJobDescriptorKey, reason: Throwable, returnCode: Option[Int]) = {
@@ -427,103 +281,51 @@ final case class WorkflowExecutionActor(workflowId: WorkflowId,
     if (jobKey.attempt <= MaxRetries) {
       val newJobKey = jobKey.copy(attempt = jobKey.attempt + 1)
       workflowLogger.info(s"Retrying job execution for ${newJobKey.tag}")
-      /** Currently, we update the status of the old key to Preempted, and add a new entry (with the #attempts incremented by 1)
+      /*  Currently, we update the status of the old key to Preempted, and add a new entry (with the #attempts incremented by 1)
         * to the execution store with status as NotStarted. This allows startRunnableCalls to re-execute this job */
       val executionDiff = WorkflowExecutionDiff(Map(jobKey -> ExecutionStatus.Preempted, newJobKey -> ExecutionStatus.NotStarted))
-      val newData = stateData.mergeExecutionDiff(executionDiff)
+      val newData = stateData.mergeExecutionDiff(executionDiff).removeCallExecutionActor(jobKey)
       stay() using startRunnableScopes(newData)
     } else {
       workflowLogger.warn(s"Exhausted maximum number of retries for job ${jobKey.tag}. Failing.")
-      goto(WorkflowExecutionFailedState) using stateData.mergeExecutionDiff(WorkflowExecutionDiff(Map(jobKey -> ExecutionStatus.Failed)))
-    }
-  }
-
-  private def handleJobSuccessful(jobKey: JobKey, outputs: JobOutputs, data: WorkflowExecutionActorData) = {
-    workflowLogger.debug(s"Job ${jobKey.tag} succeeded!")
-    val newData = data.jobExecutionSuccess(jobKey, outputs)
-
-    newData.workflowCompletionStatus match {
-      case Some(ExecutionStatus.Done) =>
-        workflowLogger.info(newData.outputsJson())
-        goto(WorkflowExecutionSuccessfulState) using newData
-      case Some(sts) =>
-        context.parent ! WorkflowExecutionFailedResponse(stateData.executionStore, stateData.outputStore, List(new Exception("One or more jobs failed in fail-slow mode")))
-        goto(WorkflowExecutionFailedState) using newData
-      case _ =>
-        stay() using startRunnableScopes(newData)
+      goto(WorkflowExecutionFailedState) using stateData.mergeExecutionDiff(WorkflowExecutionDiff(Map(jobKey -> ExecutionStatus.Failed))).removeCallExecutionActor(jobKey)
     }
   }
 
-  private def pushWorkflowOutputMetadata(data: WorkflowExecutionActorData) = {
-    val reportableOutputs = workflowDescriptor.backendDescriptor.workflowNamespace.workflow.outputs
-    val keyValues = data.outputStore.store filterKeys {
-      _.index.isEmpty
-    } flatMap {
-      case (key, value) =>
-        value collect {
-          case entry if isReportableOutput(key.call, entry, reportableOutputs) =>
-            s"${key.call.fullyQualifiedName}.${entry.name}" -> entry.wdlValue
-        }
-    } collect {
-      case (key, Some(wdlValue)) => (key, wdlValue)
-    }
-
-    val events = keyValues match {
-      case empty if empty.isEmpty => List(MetadataEvent.empty(MetadataKey(workflowId, None, WorkflowMetadataKeys.Outputs)))
-      case _ => keyValues flatMap {
-        case (outputName, outputValue) =>
-          wdlValueToMetadataEvents(MetadataKey(workflowId, None, s"${WorkflowMetadataKeys.Outputs}:$outputName"), outputValue)
-      }
-    }
-
-    serviceRegistryActor ! PutMetadataAction(events)
+  private def handleCallSuccessful(jobKey: JobKey, outputs: CallOutputs, data: WorkflowExecutionActorData, jobExecutionMap: JobExecutionMap) = {
+    handleExecutionSuccess(data.callExecutionSuccess(jobKey, outputs).addExecutions(jobExecutionMap))
   }
-
-  private def isReportableOutput(scope: Scope, entry: OutputEntry,
-                                 reportableOutputs: Seq[ReportableSymbol]): Boolean = {
-    reportableOutputs exists { reportableOutput =>
-      reportableOutput.fullyQualifiedName == s"${scope.fullyQualifiedName}.${entry.name}"
-    }
+  
+  private def handleDeclarationEvaluationSuccessful(key: DeclarationKey, value: WdlValue, data: WorkflowExecutionActorData) = {
+    handleExecutionSuccess(data.declarationEvaluationSuccess(key, value))
   }
-
-  private def pushSuccessfulJobMetadata(jobKey: JobKey, returnCode: Option[Int], outputs: JobOutputs) = {
-    val completionEvents = completedJobMetadataEvents(jobKey, ExecutionStatus.Done, returnCode)
-
-    val outputEvents = outputs match {
-      case empty if empty.isEmpty =>
-        List(MetadataEvent.empty(metadataKey(jobKey, s"${CallMetadataKeys.Outputs}")))
+  
+  private def handleExecutionSuccess(data: WorkflowExecutionActorData) = {
+    data.workflowCompletionStatus match {
+      case Some(ExecutionStatus.Done) =>
+        handleWorkflowSuccessful(data)
+      case Some(sts) =>
+        context.parent ! WorkflowExecutionFailedResponse(data.jobExecutionMap, new Exception("One or more jobs failed in fail-slow mode"))
+        goto(WorkflowExecutionFailedState) using data
       case _ =>
-        outputs flatMap { case (lqn, value) => wdlValueToMetadataEvents(metadataKey(jobKey, s"${CallMetadataKeys.Outputs}:$lqn"), value.wdlValue) }
+        stay() using startRunnableScopes(data)
     }
-
-    serviceRegistryActor ! PutMetadataAction(completionEvents ++ outputEvents)
-  }
-
-  private def pushFailedJobMetadata(jobKey: JobKey, returnCode: Option[Int], failure: Throwable, retryableFailure: Boolean) = {
-    val failedState = if (retryableFailure) ExecutionStatus.Preempted else ExecutionStatus.Failed
-    val completionEvents = completedJobMetadataEvents(jobKey, failedState, returnCode)
-    val retryableFailureEvent = MetadataEvent(metadataKey(jobKey, CallMetadataKeys.RetryableFailure), MetadataValue(retryableFailure))
-    val failureEvents = throwableToMetadataEvents(metadataKey(jobKey, s"${CallMetadataKeys.Failures}[$randomNumberString]"), failure).+:(retryableFailureEvent)
-
-    serviceRegistryActor ! PutMetadataAction(completionEvents ++ failureEvents)
   }
-
-  private def randomNumberString: String = Random.nextInt.toString.stripPrefix("-")
-
-  private def completedJobMetadataEvents(jobKey: JobKey, executionStatus: ExecutionStatus, returnCode: Option[Int]) = {
-    val returnCodeEvent = returnCode map { rc =>
-      List(MetadataEvent(metadataKey(jobKey, CallMetadataKeys.ReturnCode), MetadataValue(rc)))
+  
+  private def handleCallAborted(data: WorkflowExecutionActorData, jobKey: JobKey, jobExecutionMap: JobExecutionMap) = {
+    workflowLogger.info(s"$tag job aborted: ${jobKey.tag}")
+    val newStateData = data.removeCallExecutionActor(jobKey).addExecutions(jobExecutionMap)
+    if (!newStateData.hasRunningActors) {
+      workflowLogger.info(s"$tag all jobs aborted")
+      goto(WorkflowExecutionAbortedState)
+    } else {
+      stay() using newStateData
     }
-
-    List(
-      MetadataEvent(metadataKey(jobKey, CallMetadataKeys.ExecutionStatus), MetadataValue(executionStatus)),
-      MetadataEvent(metadataKey(jobKey, CallMetadataKeys.End), MetadataValue(OffsetDateTime.now))
-    ) ++ returnCodeEvent.getOrElse(List.empty)
   }
 
   /**
     * Attempt to start all runnable jobs and return updated state data.  This will create a new copy
-    * of the state data including new pending persists.
+    * of the state data.
     */
   @tailrec
   private def startRunnableScopes(data: WorkflowExecutionActorData): WorkflowExecutionActorData = {
@@ -537,6 +339,9 @@ final case class WorkflowExecutionActor(workflowId: WorkflowId,
       case k: BackendJobDescriptorKey => processRunnableJob(k, data)
       case k: ScatterKey => processRunnableScatter(k, data)
       case k: CollectorKey => processRunnableCollector(k, data)
+      case k: SubWorkflowKey => processRunnableSubWorkflow(k, data)
+      case k: StaticDeclarationKey => processRunnableStaticDeclaration(k)
+      case k: DynamicDeclarationKey => processRunnableDynamicDeclaration(k, data)
       case k =>
         val exception = new UnsupportedOperationException(s"Unknown entry in execution store: ${k.tag}")
         self ! JobInitializationFailed(k, exception)
@@ -544,35 +349,42 @@ final case class WorkflowExecutionActor(workflowId: WorkflowId,
     }
 
     TryUtil.sequence(executionDiffs) match {
-      case Success(diffs) if diffs.exists(_.containsNewEntry) => startRunnableScopes(data.mergeExecutionDiffs(diffs))
-      case Success(diffs) => data.mergeExecutionDiffs(diffs)
-      case Failure(e) => data
+      case Success(diffs) =>
+        // Update the metadata for the jobs we just sent to EJEAs (they'll start off queued up waiting for tokens):
+        pushQueuedCallMetadata(diffs)
+        if (diffs.exists(_.containsNewEntry)) {
+          startRunnableScopes(data.mergeExecutionDiffs(diffs))
+        } else {
+          data.mergeExecutionDiffs(diffs)
+        }
+      case Failure(e) => throw new RuntimeException("Unexpected engine failure", e)
     }
   }
 
-  private def pushNewJobMetadata(jobKey: BackendJobDescriptorKey, backendName: String) = {
-    val startEvents = List(
-      MetadataEvent(metadataKey(jobKey, CallMetadataKeys.Start), MetadataValue(OffsetDateTime.now)),
-      MetadataEvent(metadataKey(jobKey, CallMetadataKeys.Backend), MetadataValue(backendName))
-    )
-
-    serviceRegistryActor ! PutMetadataAction(startEvents)
+  def processRunnableStaticDeclaration(declaration: StaticDeclarationKey) = {
+    self ! DeclarationEvaluationSucceededResponse(declaration, declaration.value)
+    Success(WorkflowExecutionDiff(Map(declaration -> ExecutionStatus.Running)))
   }
+  
+  def processRunnableDynamicDeclaration(declaration: DynamicDeclarationKey, data: WorkflowExecutionActorData) = {
+    val scatterMap = declaration.index flatMap { i =>
+      // Will need update for nested scatters
+      declaration.scope.ancestry collectFirst { case s: Scatter => Map(s -> i) }
+    } getOrElse Map.empty[Scatter, Int]
 
-  private def pushRunningJobMetadata(jobDescriptor: BackendJobDescriptor) = {
-    val inputEvents = jobDescriptor.inputs match {
-      case empty if empty.isEmpty =>
-        List(MetadataEvent.empty(metadataKey(jobDescriptor.key, s"${CallMetadataKeys.Inputs}")))
-      case inputs =>
-        inputs flatMap {
-          case (inputName, inputValue) =>
-            wdlValueToMetadataEvents(metadataKey(jobDescriptor.key, s"${CallMetadataKeys.Inputs}:$inputName"), inputValue)
-        }
+    val lookup = declaration.scope.lookupFunction(
+      workflowDescriptor.workflowInputs,
+      data.expressionLanguageFunctions,
+      data.outputStore.fetchNodeOutputEntries,
+      scatterMap
+    )
+    
+    declaration.requiredExpression.evaluate(lookup, data.expressionLanguageFunctions) match {
+      case Success(result) => self ! DeclarationEvaluationSucceededResponse(declaration, result)
+      case Failure(ex) => self ! DeclarationEvaluationFailedResponse(declaration, ex)
     }
 
-    val runningEvent = List(MetadataEvent(metadataKey(jobDescriptor.key, CallMetadataKeys.ExecutionStatus), MetadataValue(ExecutionStatus.Running)))
-
-    serviceRegistryActor ! PutMetadataAction(runningEvent ++ inputEvents)
+    Success(WorkflowExecutionDiff(Map(declaration -> ExecutionStatus.Running)))
   }
 
   private def processRunnableJob(jobKey: BackendJobDescriptorKey, data: WorkflowExecutionActorData): Try[WorkflowExecutionDiff] = {
@@ -583,7 +395,7 @@ final case class WorkflowExecutionActor(workflowId: WorkflowId,
         workflowLogger.error(exception, s"$tag $message")
         throw exception
       case Some(backendName) =>
-        factories.get(backendName) match {
+        backendFactories.get(backendName) match {
           case Some(factory) =>
             val ejeaName = s"${workflowDescriptor.id}-EngineJobExecutionActor-${jobKey.tag}"
             val backendSingleton = backendSingletonCollection.backendSingletonActors(backendName)
@@ -591,32 +403,224 @@ final case class WorkflowExecutionActor(workflowId: WorkflowId,
               self, jobKey, data, factory, initializationData.get(backendName), restarting, serviceRegistryActor,
               jobStoreActor, callCacheReadActor, jobTokenDispenserActor, backendSingleton, backendName, workflowDescriptor.callCachingMode)
             val ejeaRef = context.actorOf(ejeaProps, ejeaName)
-            pushNewJobMetadata(jobKey, backendName)
+            context watch ejeaRef
+            pushNewCallMetadata(jobKey, Option(backendName))
             ejeaRef ! EngineJobExecutionActor.Execute
-            Success(WorkflowExecutionDiff(Map(jobKey -> ExecutionStatus.Starting)))
+            Success(WorkflowExecutionDiff(
+              executionStoreChanges = Map(jobKey -> ExecutionStatus.QueuedInCromwell),
+              engineJobExecutionActorAdditions = Map(ejeaRef -> jobKey)))
           case None =>
             throw WorkflowExecutionException(NonEmptyList.of(new Exception(s"Could not get BackendLifecycleActor for backend $backendName")))
         }
     }
   }
+  
+  private def processRunnableSubWorkflow(key: SubWorkflowKey, data: WorkflowExecutionActorData): Try[WorkflowExecutionDiff] = {
+    val sweaRef = context.actorOf(
+      SubWorkflowExecutionActor.props(key, data, backendFactories, serviceRegistryActor, jobStoreActor, subWorkflowStoreActor,
+        callCacheReadActor, jobTokenDispenserActor, backendSingletonCollection, initializationData, restarting),
+      s"SubWorkflowExecutionActor-${key.tag}"
+    )
+
+    context watch sweaRef
+    pushNewCallMetadata(key, None)
+    sweaRef ! SubWorkflowExecutionActor.Execute
+    
+    Success(WorkflowExecutionDiff(executionStoreChanges = Map(key -> ExecutionStatus.QueuedInCromwell),
+      engineJobExecutionActorAdditions = Map(sweaRef -> key)))
+  }
 
   private def processRunnableScatter(scatterKey: ScatterKey, data: WorkflowExecutionActorData): Try[WorkflowExecutionDiff] = {
-    val lookup = data.hierarchicalLookup(scatterKey.scope, None) _
+    val lookup = scatterKey.scope.lookupFunction(
+      workflowDescriptor.workflowInputs,
+      data.expressionLanguageFunctions,
+      data.outputStore.fetchNodeOutputEntries
+    )
 
     scatterKey.scope.collection.evaluate(lookup, data.expressionLanguageFunctions) map {
-      case a: WdlArray => WorkflowExecutionDiff(scatterKey.populate(a.value.size) + (scatterKey -> ExecutionStatus.Done))
+      case a: WdlArray => WorkflowExecutionDiff(scatterKey.populate(a.value.size, workflowDescriptor.inputs) + (scatterKey -> ExecutionStatus.Done))
       case v: WdlValue => throw new RuntimeException("Scatter collection must evaluate to an array")
     }
   }
 
   private def processRunnableCollector(collector: CollectorKey, data: WorkflowExecutionActorData): Try[WorkflowExecutionDiff] = {
-    val shards = data.executionStore.findShardEntries(collector) collect { case (k: BackendJobDescriptorKey, v) if v == ExecutionStatus.Done => k }
+    val shards = data.executionStore.findShardEntries(collector) collect { 
+      case (k: CallKey, v) if v == ExecutionStatus.Done => k 
+      case (k: DynamicDeclarationKey, v) if v == ExecutionStatus.Done => k 
+    }
     data.outputStore.generateCollectorOutput(collector, shards) match {
       case Failure(e) => Failure(new RuntimeException(s"Failed to collect output shards for call ${collector.tag}"))
       case Success(outputs) => self ! ScatterCollectionSucceededResponse(collector, outputs)
         Success(WorkflowExecutionDiff(Map(collector -> ExecutionStatus.Starting)))
     }
   }
-
-  private def metadataKey(jobKey: JobKey, myKey: String) = MetadataKey(workflowDescriptor.id, Option(MetadataJobKey(jobKey.scope.fullyQualifiedName, jobKey.index, jobKey.attempt)), myKey)
 }
+
+object WorkflowExecutionActor {
+
+  /**
+    * States
+    */
+  sealed trait WorkflowExecutionActorState {
+    def terminal = false
+  }
+
+  sealed trait WorkflowExecutionActorTerminalState extends WorkflowExecutionActorState {
+    override val terminal = true
+  }
+
+  case object WorkflowExecutionPendingState extends WorkflowExecutionActorState
+
+  case object WorkflowExecutionInProgressState extends WorkflowExecutionActorState
+
+  case object WorkflowExecutionAbortingState extends WorkflowExecutionActorState
+
+  case object WorkflowExecutionSuccessfulState extends WorkflowExecutionActorTerminalState
+
+  case object WorkflowExecutionFailedState extends WorkflowExecutionActorTerminalState
+
+  case object WorkflowExecutionAbortedState extends WorkflowExecutionActorTerminalState
+
+  /**
+    * Commands
+    */
+  sealed trait WorkflowExecutionActorCommand
+
+  case object ExecuteWorkflowCommand extends WorkflowExecutionActorCommand
+
+  /**
+    * Responses
+    */
+  sealed trait WorkflowExecutionActorResponse {
+    def jobExecutionMap: JobExecutionMap
+  }
+
+  case class WorkflowExecutionSucceededResponse(jobExecutionMap: JobExecutionMap, outputs: CallOutputs)
+    extends WorkflowExecutionActorResponse {
+    override def toString = "WorkflowExecutionSucceededResponse"
+  }
+
+  case class WorkflowExecutionAbortedResponse(jobExecutionMap: JobExecutionMap)
+    extends WorkflowExecutionActorResponse with EngineLifecycleActorAbortedResponse {
+    override def toString = "WorkflowExecutionAbortedResponse"
+  }
+
+  final case class WorkflowExecutionFailedResponse(jobExecutionMap: JobExecutionMap, reason: Throwable) extends WorkflowExecutionActorResponse {
+    override def toString = "WorkflowExecutionFailedResponse"
+  }
+
+  /**
+    * Internal control flow messages
+    */
+  private case class JobInitializationFailed(jobKey: JobKey, throwable: Throwable)
+
+  private case class ScatterCollectionFailedResponse(collectorKey: CollectorKey, throwable: Throwable)
+
+  private case class ScatterCollectionSucceededResponse(collectorKey: CollectorKey, outputs: CallOutputs)
+  
+  private case class DeclarationEvaluationSucceededResponse(declarationKey: DeclarationKey, value: WdlValue)
+  
+  private case class DeclarationEvaluationFailedResponse(declarationKey: DeclarationKey, reason: Throwable)
+
+  case class SubWorkflowSucceededResponse(key: SubWorkflowKey, jobExecutionMap: JobExecutionMap, outputs: CallOutputs)
+
+  case class SubWorkflowFailedResponse(key: SubWorkflowKey, jobExecutionMap: JobExecutionMap, reason: Throwable)
+
+  case class SubWorkflowAbortedResponse(key: SubWorkflowKey, jobExecutionMap: JobExecutionMap)
+
+  /**
+    * Internal ADTs
+    */
+  case class ScatterKey(scope: Scatter) extends JobKey {
+    override val index = None
+    // When scatters are nested, this might become Some(_)
+    override val attempt = 1
+    override val tag = scope.unqualifiedName
+
+    /**
+      * Creates a sub-ExecutionStore with Starting entries for each of the scoped children.
+      *
+      * @param count Number of ways to scatter the children.
+      * @return ExecutionStore of scattered children.
+      */
+    def populate(count: Int, workflowCoercedInputs: WorkflowCoercedInputs): Map[JobKey, ExecutionStatus.Value] = {
+      val keys = this.scope.children flatMap {
+        explode(_, count, workflowCoercedInputs)
+      }
+      keys map {
+        _ -> ExecutionStatus.NotStarted
+      } toMap
+    }
+
+    private def explode(scope: Scope, count: Int, workflowCoercedInputs: WorkflowCoercedInputs): Seq[JobKey] = {
+      scope match {
+        case call: TaskCall =>
+          val shards = (0 until count) map { i => BackendJobDescriptorKey(call, Option(i), 1) }
+          shards :+ CollectorKey(call)
+        case call: WorkflowCall =>
+          val shards = (0 until count) map { i => SubWorkflowKey(call, Option(i), 1) }
+          shards :+ CollectorKey(call)
+        case declaration: Declaration =>
+          val shards = (0 until count) map { i => DeclarationKey(declaration, Option(i), workflowCoercedInputs) }
+          shards :+ CollectorKey(declaration)
+        case scatter: Scatter =>
+          throw new UnsupportedOperationException("Nested Scatters are not supported (yet) ... but you might try a sub workflow to achieve the same effect!")
+        case e =>
+          throw new UnsupportedOperationException(s"Scope ${e.getClass.getName} is not supported.")
+      }
+    }
+  }
+
+  // Represents a scatter collection for a call in the execution store
+  case class CollectorKey(scope: Scope with GraphNode) extends JobKey {
+    override val index = None
+    override val attempt = 1
+    override val tag = s"Collector-${scope.unqualifiedName}"
+  }
+
+  case class SubWorkflowKey(scope: WorkflowCall, index: ExecutionIndex, attempt: Int) extends CallKey {
+    override val tag = s"SubWorkflow-${scope.unqualifiedName}:${index.fromIndex}:$attempt"
+  }
+
+  object DeclarationKey {
+    def apply(declaration: Declaration, index: ExecutionIndex, inputs: WorkflowCoercedInputs): DeclarationKey = {
+      inputs.find(_._1 == declaration.fullyQualifiedName) match {
+        case Some((_, value)) => StaticDeclarationKey(declaration, index, value)
+        case None => declaration.expression map { expression =>
+          DynamicDeclarationKey(declaration, index, expression)
+        } getOrElse {
+          throw new RuntimeException(s"Found a declaration ${declaration.fullyQualifiedName} without expression and without input value. This should have been a validation error.")
+        }
+      }
+    }
+  }
+    
+  sealed trait DeclarationKey extends JobKey {
+    override val attempt = 1
+    override val tag = s"Declaration-${scope.unqualifiedName}:${index.fromIndex}:$attempt"
+  }
+  
+  case class StaticDeclarationKey(scope: Declaration, index: ExecutionIndex, value: WdlValue) extends DeclarationKey
+  
+  case class DynamicDeclarationKey(scope: Declaration, index: ExecutionIndex, requiredExpression: WdlExpression) extends DeclarationKey
+
+  case class WorkflowExecutionException[T <: Throwable](exceptions: NonEmptyList[T]) extends ThrowableAggregation {
+    override val throwables = exceptions.toList
+    override val exceptionContext = s"WorkflowExecutionActor"
+  }
+
+  private lazy val DefaultMaxRetriesFallbackValue = 10
+
+  def props(workflowDescriptor: EngineWorkflowDescriptor,
+            serviceRegistryActor: ActorRef,
+            jobStoreActor: ActorRef,
+            subWorkflowStoreActor: ActorRef,
+            callCacheReadActor: ActorRef,
+            jobTokenDispenserActor: ActorRef,
+            backendSingletonCollection: BackendSingletonCollection,
+            initializationData: AllBackendInitializationData,
+            restarting: Boolean): Props = {
+    Props(WorkflowExecutionActor(workflowDescriptor, serviceRegistryActor, jobStoreActor, subWorkflowStoreActor,
+      callCacheReadActor, jobTokenDispenserActor, backendSingletonCollection, initializationData, restarting)).withDispatcher(EngineDispatcher)
+  }
+}
\ No newline at end of file
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorData.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorData.scala
index 599c8f1b4a5..4bf2f213cb5 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorData.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorData.scala
@@ -1,55 +1,100 @@
 package cromwell.engine.workflow.lifecycle.execution
 
 import akka.actor.ActorRef
+import cromwell.backend._
 import cromwell.core.ExecutionStatus._
-import cromwell.core.OutputStore.{OutputCallKey, OutputEntry}
 import cromwell.core._
+import cromwell.engine.workflow.lifecycle.execution.OutputStore.{OutputCallKey, OutputEntry}
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{DeclarationKey, SubWorkflowKey}
 import cromwell.engine.{EngineWorkflowDescriptor, WdlFunctions}
 import cromwell.util.JsonFormatting.WdlValueJsonFormatter
-import wdl4s.Scope
-
+import wdl4s.values.WdlValue
+import wdl4s.{GraphNode, Scope}
 
 object WorkflowExecutionDiff {
   def empty = WorkflowExecutionDiff(Map.empty)
 }
 /** Data differential between current execution data, and updates performed in a method that needs to be merged. */
-final case class WorkflowExecutionDiff(executionStore: Map[JobKey, ExecutionStatus]) {
-  def containsNewEntry = executionStore.exists(_._2 == NotStarted)
+final case class WorkflowExecutionDiff(executionStoreChanges: Map[JobKey, ExecutionStatus],
+                                       engineJobExecutionActorAdditions: Map[ActorRef, JobKey] = Map.empty) {
+  def containsNewEntry = executionStoreChanges.exists(_._2 == NotStarted)
+}
+
+object WorkflowExecutionActorData {
+  def empty(workflowDescriptor: EngineWorkflowDescriptor) = {
+    new WorkflowExecutionActorData(
+      workflowDescriptor,
+      ExecutionStore.empty,
+      Map.empty,
+      Map.empty,
+      Map.empty,
+      Map.empty,
+      OutputStore.empty
+    )
+  }
 }
 
 case class WorkflowExecutionActorData(workflowDescriptor: EngineWorkflowDescriptor,
                                       executionStore: ExecutionStore,
                                       backendJobExecutionActors: Map[JobKey, ActorRef],
-                                      outputStore: OutputStore) extends WdlLookup {
+                                      engineCallExecutionActors: Map[ActorRef, JobKey],
+                                      subWorkflowExecutionActors: Map[SubWorkflowKey, ActorRef],
+                                      downstreamExecutionMap: JobExecutionMap,
+                                      outputStore: OutputStore) {
+
+  val expressionLanguageFunctions = new WdlFunctions(workflowDescriptor.pathBuilders)
+
+  def callExecutionSuccess(jobKey: JobKey, outputs: CallOutputs) = {
+    val (newJobExecutionActors, newSubWorkflowExecutionActors) = jobKey match {
+      case jobKey: BackendJobDescriptorKey => (backendJobExecutionActors - jobKey, subWorkflowExecutionActors)
+      case swKey: SubWorkflowKey => (backendJobExecutionActors, subWorkflowExecutionActors - swKey)
+      case _ => (backendJobExecutionActors, subWorkflowExecutionActors)
+    }
 
-  override val expressionLanguageFunctions = new WdlFunctions(workflowDescriptor.engineFilesystems)
+    this.copy(
+      executionStore = executionStore.add(Map(jobKey -> Done)),
+      backendJobExecutionActors = newJobExecutionActors,
+      subWorkflowExecutionActors = newSubWorkflowExecutionActors,
+      outputStore = outputStore.add(updateSymbolStoreEntry(jobKey, outputs))
+    )
+  }
+
+  def declarationEvaluationSuccess(declarationKey: DeclarationKey, value: WdlValue) = {
+    val outputStoreKey = OutputCallKey(declarationKey.scope, declarationKey.index)
+    val outputStoreValue = OutputEntry(declarationKey.scope.unqualifiedName, value.wdlType, Option(value))
+    this.copy(
+      executionStore = executionStore.add(Map(declarationKey -> Done)),
+      outputStore = outputStore.add(Map(outputStoreKey -> List(outputStoreValue)))
+    )
+  }
 
-  def jobExecutionSuccess(jobKey: JobKey, outputs: JobOutputs) = this.copy(
-    executionStore = executionStore.add(Map(jobKey -> Done)),
-    backendJobExecutionActors = backendJobExecutionActors - jobKey,
-    outputStore = outputStore.add(updateSymbolStoreEntry(jobKey, outputs))
-  )
+  def executionFailed(jobKey: JobKey) = mergeExecutionDiff(WorkflowExecutionDiff(Map(jobKey -> ExecutionStatus.Failed)))
 
   /** Add the outputs for the specified `JobKey` to the symbol cache. */
-  private def updateSymbolStoreEntry(jobKey: JobKey, outputs: JobOutputs) = {
+  private def updateSymbolStoreEntry(jobKey: JobKey, outputs: CallOutputs) = {
     val newOutputEntries = outputs map {
       case (name, value) => OutputEntry(name, value.wdlValue.wdlType, Option(value.wdlValue))
     }
 
-    Map(OutputCallKey(jobKey.scope, jobKey.index) -> newOutputEntries)
+    Map(OutputCallKey(jobKey.scope, jobKey.index) -> newOutputEntries.toList)
   }
 
   /** Checks if the workflow is completed by scanning through the executionStore.
     * If complete, this will return Some(finalStatus).  Otherwise, returns None */
   def workflowCompletionStatus: Option[ExecutionStatus] = {
     // `List`ify the `prerequisiteScopes` to avoid expensive hashing of `Scope`s when assembling the result.
-    def upstream(scope: Scope): List[Scope] = scope.prerequisiteScopes.toList ++ scope.prerequisiteScopes.toList.flatMap(upstream)
-    def upstreamFailed(scope: Scope) = upstream(scope) filter { s =>
-      executionStore.store.map({ case (a, b) => a.scope -> b }).get(s).contains(Failed)
+    def upstream(scope: GraphNode): List[Scope] = {
+      val directUpstream: List[Scope with GraphNode] = scope.upstream.toList
+      directUpstream ++ directUpstream.flatMap(upstream)
+    }
+    def upstreamFailed(scope: Scope) = scope match {
+      case node: GraphNode => upstream(node) filter { s =>
+        executionStore.store.exists({ case (key, status) => status == Failed && key.scope == s })
+      }
     }
     // activeJobs is the subset of the executionStore that are either running or will run in the future.
     val activeJobs = executionStore.store.toList filter {
-      case (jobKey, jobStatus) => (jobStatus == NotStarted && upstreamFailed(jobKey.scope).isEmpty) || jobStatus == Starting || jobStatus == Running
+      case (jobKey, jobStatus) => (jobStatus == NotStarted && upstreamFailed(jobKey.scope).isEmpty) || jobStatus == QueuedInCromwell || jobStatus == Starting || jobStatus == Running
     }
 
     activeJobs match {
@@ -63,13 +108,30 @@ case class WorkflowExecutionActorData(workflowDescriptor: EngineWorkflowDescript
     executionStore.store.values.exists(_ == ExecutionStatus.Failed)
   }
 
-  def addBackendJobExecutionActor(jobKey: JobKey, actor: Option[ActorRef]): WorkflowExecutionActorData = actor match {
-      case Some(actorRef) => this.copy(backendJobExecutionActors = backendJobExecutionActors + (jobKey -> actorRef))
+  def removeEngineJobExecutionActor(actorRef: ActorRef) = {
+    this.copy(engineCallExecutionActors = engineCallExecutionActors - actorRef)
+  }
+
+  def addCallExecutionActor(jobKey: JobKey, actor: Option[ActorRef]): WorkflowExecutionActorData = actor match {
+      case Some(actorRef) =>
+        jobKey match {
+          case jobKey: BackendJobDescriptorKey => this.copy(backendJobExecutionActors = backendJobExecutionActors + (jobKey -> actorRef))
+          case swKey: SubWorkflowKey => this.copy(subWorkflowExecutionActors = subWorkflowExecutionActors + (swKey -> actorRef))
+          case _ => this
+        }
       case None => this
   }
 
-  def removeBackendJobExecutionActor(jobKey: JobKey): WorkflowExecutionActorData = {
-    this.copy(backendJobExecutionActors = backendJobExecutionActors - jobKey)
+  def removeCallExecutionActor(jobKey: JobKey): WorkflowExecutionActorData = {
+    jobKey match {
+      case jobKey: BackendJobDescriptorKey => this.copy(backendJobExecutionActors = backendJobExecutionActors - jobKey)
+      case swKey: SubWorkflowKey => this.copy(subWorkflowExecutionActors = subWorkflowExecutionActors - swKey)
+      case _ => this
+    }
+  }
+
+  def addExecutions(jobExecutionMap: JobExecutionMap): WorkflowExecutionActorData = {
+    this.copy(downstreamExecutionMap = downstreamExecutionMap ++ jobExecutionMap)
   }
 
   def outputsJson(): String = {
@@ -86,11 +148,19 @@ case class WorkflowExecutionActorData(workflowDescriptor: EngineWorkflowDescript
   }
 
   def mergeExecutionDiff(diff: WorkflowExecutionDiff): WorkflowExecutionActorData = {
-    this.copy(executionStore = executionStore.add(diff.executionStore))
+    this.copy(
+      executionStore = executionStore.add(diff.executionStoreChanges),
+      engineCallExecutionActors = engineCallExecutionActors ++ diff.engineJobExecutionActorAdditions)
   }
 
   def mergeExecutionDiffs(diffs: Traversable[WorkflowExecutionDiff]): WorkflowExecutionActorData = {
     diffs.foldLeft(this)((newData, diff) => newData.mergeExecutionDiff(diff))
   }
-
+  
+  def jobExecutionMap: JobExecutionMap = {
+    val keys = executionStore.store.collect({case (k: BackendJobDescriptorKey, status) if status != ExecutionStatus.NotStarted => k }).toList
+    downstreamExecutionMap updated (workflowDescriptor.backendDescriptor, keys)
+  }
+  
+  def hasRunningActors = backendJobExecutionActors.nonEmpty || subWorkflowExecutionActors.nonEmpty
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowMetadataHelper.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowMetadataHelper.scala
new file mode 100644
index 00000000000..d569f1faeea
--- /dev/null
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowMetadataHelper.scala
@@ -0,0 +1,37 @@
+package cromwell.engine.workflow.lifecycle.execution
+
+import java.time.OffsetDateTime
+
+import akka.actor.ActorRef
+import cromwell.core.{WorkflowId, WorkflowMetadataKeys, WorkflowState}
+import cromwell.services.metadata.MetadataService._
+import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
+
+import scala.util.Random
+
+trait WorkflowMetadataHelper {
+
+  def serviceRegistryActor: ActorRef
+  
+  def pushWorkflowStart(workflowId: WorkflowId) = {
+    val startEvent = MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.StartTime), MetadataValue(OffsetDateTime.now.toString))
+    serviceRegistryActor ! PutMetadataAction(startEvent)
+  }
+  
+  def pushWorkflowEnd(workflowId: WorkflowId) = {
+    val metadataEventMsg = MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.EndTime), MetadataValue(OffsetDateTime.now.toString))
+    serviceRegistryActor ! PutMetadataAction(metadataEventMsg)
+  }
+  
+  def pushWorkflowFailures(workflowId: WorkflowId, failures: List[Throwable]) = {
+    val failureEvents = failures flatMap { r => throwableToMetadataEvents(MetadataKey(workflowId, None, s"${WorkflowMetadataKeys.Failures}[${Random.nextInt(Int.MaxValue)}]"), r) }
+    serviceRegistryActor ! PutMetadataAction(failureEvents)
+  }
+  
+  def pushCurrentStateToMetadataService(workflowId: WorkflowId, workflowState: WorkflowState): Unit = {
+    val metadataEventMsg = MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.Status),
+      MetadataValue(workflowState))
+    serviceRegistryActor ! PutMetadataAction(metadataEventMsg)
+  }
+  
+}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCache.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCache.scala
index 8c5331c424e..674b1ee88e8 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCache.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCache.scala
@@ -1,7 +1,9 @@
 package cromwell.engine.workflow.lifecycle.execution.callcaching
 
+import java.nio.file.Path
+
 import cats.data.NonEmptyList
-import cromwell.backend.BackendJobExecutionActor.SucceededResponse
+import cromwell.backend.BackendJobExecutionActor.JobSucceededResponse
 import cromwell.core.ExecutionIndex.IndexEnhancedIndex
 import cromwell.core.WorkflowId
 import cromwell.core.callcaching.HashResult
@@ -19,7 +21,7 @@ final case class CallCachingEntryId(id: Int)
   * Given a database-layer CallCacheStore, this accessor can access the database with engine-friendly data types.
   */
 class CallCache(database: CallCachingSqlDatabase) {
-  def addToCache(workflowId: WorkflowId, callCacheHashes: CallCacheHashes, response: SucceededResponse)(implicit ec: ExecutionContext): Future[Unit] = {
+  def addToCache(workflowId: WorkflowId, callCacheHashes: CallCacheHashes, response: JobSucceededResponse)(implicit ec: ExecutionContext): Future[Unit] = {
     val metaInfo = CallCachingEntry(
       workflowExecutionUuid = workflowId.toString,
       callFullyQualifiedName = response.jobKey.call.fullyQualifiedName,
@@ -35,7 +37,7 @@ class CallCache(database: CallCachingSqlDatabase) {
   }
 
   private def addToCache(callCachingEntry: CallCachingEntry, hashes: Set[HashResult],
-                         result: Iterable[WdlValueSimpleton], jobDetritus: Map[String, String])
+                         result: Iterable[WdlValueSimpleton], jobDetritus: Map[String, Path])
                         (implicit ec: ExecutionContext): Future[Unit] = {
 
     val hashesToInsert: Iterable[CallCachingHashEntry] = {
@@ -51,7 +53,7 @@ class CallCache(database: CallCachingSqlDatabase) {
 
     val jobDetritusToInsert: Iterable[CallCachingDetritusEntry] = {
       jobDetritus map {
-        case (fileName, filePath) => CallCachingDetritusEntry(fileName, filePath)
+        case (fileName, filePath) => CallCachingDetritusEntry(fileName, filePath.toUri.toString)
       }
     }
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheInvalidateActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheInvalidateActor.scala
index ef09d32e918..a0ec75fc8cd 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheInvalidateActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheInvalidateActor.scala
@@ -33,4 +33,5 @@ object CallCacheInvalidateActor {
 
 sealed trait CallCacheInvalidatedResponse
 case object CallCacheInvalidatedSuccess extends CallCacheInvalidatedResponse
+case object CallCacheInvalidationUnnecessary extends CallCacheInvalidatedResponse
 case class CallCacheInvalidatedFailure(t: Throwable) extends CallCacheInvalidatedResponse
\ No newline at end of file
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheWriteActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheWriteActor.scala
index f0e9c01864a..c6e42b5cc7d 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheWriteActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheWriteActor.scala
@@ -2,14 +2,14 @@ package cromwell.engine.workflow.lifecycle.execution.callcaching
 
 import akka.actor.{Actor, ActorLogging, Props}
 import cromwell.backend.BackendJobExecutionActor
-import cromwell.backend.BackendJobExecutionActor.SucceededResponse
+import cromwell.backend.BackendJobExecutionActor.JobSucceededResponse
 import cromwell.core.WorkflowId
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.CallCacheHashes
 
 import scala.concurrent.ExecutionContext
 import scala.util.{Failure, Success}
 
-case class CallCacheWriteActor(callCache: CallCache, workflowId: WorkflowId, callCacheHashes: CallCacheHashes, succeededResponse: BackendJobExecutionActor.SucceededResponse) extends Actor with ActorLogging {
+case class CallCacheWriteActor(callCache: CallCache, workflowId: WorkflowId, callCacheHashes: CallCacheHashes, succeededResponse: BackendJobExecutionActor.JobSucceededResponse) extends Actor with ActorLogging {
 
   implicit val ec: ExecutionContext = context.dispatcher
 
@@ -30,7 +30,7 @@ case class CallCacheWriteActor(callCache: CallCache, workflowId: WorkflowId, cal
 }
 
 object CallCacheWriteActor {
-  def props(callCache: CallCache, workflowId: WorkflowId, callCacheHashes: CallCacheHashes, succeededResponse: SucceededResponse): Props =
+  def props(callCache: CallCache, workflowId: WorkflowId, callCacheHashes: CallCacheHashes, succeededResponse: JobSucceededResponse): Props =
     Props(CallCacheWriteActor(callCache, workflowId, callCacheHashes, succeededResponse))
 }
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActor.scala
index b4ad358f54d..053e8a14e72 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActor.scala
@@ -65,7 +65,7 @@ case class EngineJobHashingActor(receiver: ActorRef,
 
     import cromwell.core.simpleton.WdlValueSimpleton._
 
-    val inputSimpletons = jobDescriptor.inputs.simplify
+    val inputSimpletons = jobDescriptor.fullyQualifiedInputs.simplify
     val (fileInputSimpletons, nonFileInputSimpletons) = inputSimpletons partition {
       case WdlValueSimpleton(_, f: WdlFile) => true
       case _ => false
@@ -107,7 +107,7 @@ case class EngineJobHashingActor(receiver: ActorRef,
     }
 
     val outputExpressionHashResults = jobDescriptor.call.task.outputs map { output =>
-      HashResult(HashKey(s"output expression: ${output.wdlType.toWdlString} ${output.name}"), output.requiredExpression.valueString.md5HashValue)
+      HashResult(HashKey(s"output expression: ${output.wdlType.toWdlString} ${output.unqualifiedName}"), output.requiredExpression.valueString.md5HashValue)
     }
 
     // Build these all together for the final set of initial hashes:
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/package.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/package.scala
index 1d3eedd9fae..d0350e66296 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/package.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/package.scala
@@ -1,10 +1,12 @@
 package cromwell.engine.workflow.lifecycle
 
+import akka.actor.ActorRef
 import wdl4s._
 
-package object execution {
-  def splitFqn(fullyQualifiedName: FullyQualifiedName): (String, String) = {
-    val lastIndex = fullyQualifiedName.lastIndexOf(".")
-    (fullyQualifiedName.substring(0, lastIndex), fullyQualifiedName.substring(lastIndex + 1))
-  }
+package execution {
+
+  import cromwell.core.CallKey
+
+  final case class JobRunning(key: CallKey, inputs: EvaluatedTaskInputs, executionActor: Option[ActorRef])
+  final case class JobStarting(callKey: CallKey)
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/tokens/JobExecutionTokenDispenserActor.scala b/engine/src/main/scala/cromwell/engine/workflow/tokens/JobExecutionTokenDispenserActor.scala
index b2afd6b5efd..99d10221dc9 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/tokens/JobExecutionTokenDispenserActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/tokens/JobExecutionTokenDispenserActor.scala
@@ -84,7 +84,7 @@ class JobExecutionTokenDispenserActor extends Actor with ActorLogging {
   private def onTerminate(terminee: ActorRef): Unit = {
     tokenAssignments.get(terminee) match {
       case Some(token) =>
-        log.error("Actor {} stopped without returning its Job Execution Token. Reclaiming it!", terminee)
+        log.debug("Actor {} stopped without returning its Job Execution Token. Reclaiming it!", terminee)
         self.tell(msg = JobExecutionTokenReturn(token), sender = terminee)
       case None =>
         log.debug("Actor {} stopped while we were still watching it... but it doesn't have a token. Removing it from any queues if necessary", terminee)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala
similarity index 88%
rename from engine/src/test/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala
rename to engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala
index a24be2d3259..0f04212f843 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala
@@ -1,7 +1,7 @@
 package cromwell.engine.workflow.workflowstore
 
 import cats.data.NonEmptyList
-import cromwell.core.{WorkflowId, WorkflowSourceFiles}
+import cromwell.core.{WorkflowId, WorkflowSourceFilesCollection}
 import cromwell.engine.workflow.workflowstore.WorkflowStoreState.StartableState
 
 import scala.concurrent.{ExecutionContext, Future}
@@ -14,7 +14,7 @@ class InMemoryWorkflowStore extends WorkflowStore {
     * Adds the requested WorkflowSourceFiles to the store and returns a WorkflowId for each one (in order)
     * for tracking purposes.
     */
-  override def add(sources: NonEmptyList[WorkflowSourceFiles])(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowId]] = {
+  override def add(sources: NonEmptyList[WorkflowSourceFilesCollection])(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowId]] = {
     val submittedWorkflows = sources map { SubmittedWorkflow(WorkflowId.randomId(), _, WorkflowStoreState.Submitted) }
     workflowStore = workflowStore ++ submittedWorkflows.toList
     Future.successful(submittedWorkflows map { _.id })
@@ -44,7 +44,7 @@ class InMemoryWorkflowStore extends WorkflowStore {
   override def initialize(implicit ec: ExecutionContext): Future[Unit] = Future.successful(())
 }
 
-final case class SubmittedWorkflow(id: WorkflowId, sources: WorkflowSourceFiles, state: WorkflowStoreState) {
+final case class SubmittedWorkflow(id: WorkflowId, sources: WorkflowSourceFilesCollection, state: WorkflowStoreState) {
   def toWorkflowToStart: WorkflowToStart = {
     state match {
       case r: StartableState => WorkflowToStart(id, sources, r)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStore.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStore.scala
index 7056137c3af..29190617ee9 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStore.scala
@@ -1,9 +1,12 @@
 package cromwell.engine.workflow.workflowstore
 
 import java.time.OffsetDateTime
+import javax.sql.rowset.serial.SerialBlob
 
 import cats.data.NonEmptyList
-import cromwell.core.{WorkflowId, WorkflowSourceFiles}
+import com.typesafe.config.ConfigFactory
+import net.ceedubs.ficus.Ficus._
+import cromwell.core.{WorkflowId, WorkflowSourceFilesCollection}
 import cromwell.database.sql.SqlConverters._
 import cromwell.database.sql.WorkflowStoreSqlDatabase
 import cromwell.database.sql.tables.WorkflowStoreEntry
@@ -13,9 +16,13 @@ import scala.concurrent.{ExecutionContext, Future}
 
 case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase) extends WorkflowStore {
   override def initialize(implicit ec: ExecutionContext): Future[Unit] = {
-    sqlDatabase.updateWorkflowState(
-      WorkflowStoreState.Running.toString,
-      WorkflowStoreState.Restartable.toString)
+          if (ConfigFactory.load().as[Option[Boolean]]("system.workflow-restart").getOrElse(true)) {
+            sqlDatabase.updateWorkflowState(
+                WorkflowStoreState.Running.toString,
+                WorkflowStoreState.Restartable.toString)
+          } else {
+            Future.successful(())
+          }
   }
 
   override def remove(id: WorkflowId)(implicit ec: ExecutionContext): Future[Boolean] = {
@@ -36,7 +43,7 @@ case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase) extends Workf
     * Adds the requested WorkflowSourceFiles to the store and returns a WorkflowId for each one (in order)
     * for tracking purposes.
     */
-  override def add(sources: NonEmptyList[WorkflowSourceFiles])(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowId]] = {
+  override def add(sources: NonEmptyList[WorkflowSourceFilesCollection])(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowId]] = {
 
     val asStoreEntries = sources map toWorkflowStoreEntry
     val returnValue = asStoreEntries map { workflowStore => WorkflowId.fromString(workflowStore.workflowExecutionUuid) }
@@ -46,24 +53,27 @@ case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase) extends Workf
   }
 
   private def fromWorkflowStoreEntry(workflowStoreEntry: WorkflowStoreEntry): WorkflowToStart = {
-    val sources = WorkflowSourceFiles(
+    val sources = WorkflowSourceFilesCollection(
       workflowStoreEntry.workflowDefinition.toRawString,
       workflowStoreEntry.workflowInputs.toRawString,
-      workflowStoreEntry.workflowOptions.toRawString)
+      workflowStoreEntry.workflowOptions.toRawString,
+      workflowStoreEntry.importsZipFile.map(b => b.getBytes(1, b.length.asInstanceOf[Int]))
+    )
     WorkflowToStart(
       WorkflowId.fromString(workflowStoreEntry.workflowExecutionUuid),
       sources,
       fromDbStateStringToStartableState(workflowStoreEntry.workflowState))
   }
 
-  private def toWorkflowStoreEntry(workflowSourceFiles: WorkflowSourceFiles): WorkflowStoreEntry = {
+  private def toWorkflowStoreEntry(workflowSourceFiles: WorkflowSourceFilesCollection): WorkflowStoreEntry = {
     WorkflowStoreEntry(
       WorkflowId.randomId().toString,
       workflowSourceFiles.wdlSource.toClob,
       workflowSourceFiles.inputsJson.toClob,
       workflowSourceFiles.workflowOptionsJson.toClob,
       WorkflowStoreState.Submitted.toString,
-      OffsetDateTime.now.toSystemTimestamp
+      OffsetDateTime.now.toSystemTimestamp,
+      workflowSourceFiles.importsZipFileOption.map(new SerialBlob(_))
     )
   }
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStore.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStore.scala
index e3d7b44bedc..f4734f7bb73 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStore.scala
@@ -1,7 +1,7 @@
 package cromwell.engine.workflow.workflowstore
 
 import cats.data.NonEmptyList
-import cromwell.core.{WorkflowId, WorkflowSourceFiles}
+import cromwell.core.{WorkflowId, WorkflowSourceFilesCollection}
 import cromwell.engine.workflow.workflowstore.WorkflowStoreState.StartableState
 
 import scala.concurrent.{ExecutionContext, Future}
@@ -14,7 +14,7 @@ trait WorkflowStore {
     * Adds the requested WorkflowSourceFiles to the store and returns a WorkflowId for each one (in order)
     * for tracking purposes.
     */
-  def add(sources: NonEmptyList[WorkflowSourceFiles])(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowId]]
+  def add(sources: NonEmptyList[WorkflowSourceFilesCollection])(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowId]]
 
   /**
     * Retrieves up to n workflows which have not already been pulled into the engine and sets their pickedUp
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreActor.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreActor.scala
index 24cb3a6a7ef..2ecccbce23b 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreActor.scala
@@ -4,7 +4,7 @@ import java.time.OffsetDateTime
 
 import akka.actor.{ActorLogging, ActorRef, LoggingFSM, Props}
 import cats.data.NonEmptyList
-import cromwell.core.{WorkflowId, WorkflowMetadataKeys, WorkflowSourceFiles}
+import cromwell.core._
 import cromwell.engine.workflow.WorkflowManagerActor
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor._
@@ -12,9 +12,10 @@ import cromwell.engine.workflow.workflowstore.WorkflowStoreState.StartableState
 import cromwell.services.metadata.MetadataService.{MetadataPutAcknowledgement, PutMetadataAction}
 import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
 import org.apache.commons.lang3.exception.ExceptionUtils
+import wdl4s.util.TryUtil
 
 import scala.concurrent.{ExecutionContext, Future}
-import scala.util.{Failure, Success}
+import scala.util.{Failure, Success, Try}
 
 case class WorkflowStoreActor(store: WorkflowStore, serviceRegistryActor: ActorRef)
   extends LoggingFSM[WorkflowStoreActorState, WorkflowStoreActorData] with ActorLogging {
@@ -69,14 +70,14 @@ case class WorkflowStoreActor(store: WorkflowStore, serviceRegistryActor: ActorR
   private def startNewWork(command: WorkflowStoreActorCommand, sndr: ActorRef, nextData: WorkflowStoreActorData) = {
     val work: Future[Any] = command match {
       case cmd @ SubmitWorkflow(sourceFiles) =>
-        store.add(NonEmptyList.of(sourceFiles)) map { ids =>
+        storeWorkflowSources(NonEmptyList.of(sourceFiles)) map { ids =>
           val id = ids.head
           registerSubmissionWithMetadataService(id, sourceFiles)
           sndr ! WorkflowSubmittedToStore(id)
           log.info("Workflow {} submitted.", id)
         }
       case cmd @ BatchSubmitWorkflows(sources) =>
-        store.add(sources) map { ids =>
+        storeWorkflowSources(sources) map { ids =>
           val assignedSources = ids.toList.zip(sources.toList)
           assignedSources foreach { case (id, sourceFiles) => registerSubmissionWithMetadataService(id, sourceFiles) }
           sndr ! WorkflowsBatchSubmittedToStore(ids)
@@ -116,6 +117,37 @@ case class WorkflowStoreActor(store: WorkflowStore, serviceRegistryActor: ActorR
     goto(Working) using nextData
   }
 
+  private def storeWorkflowSources(sources: NonEmptyList[WorkflowSourceFilesCollection]): Future[NonEmptyList[WorkflowId]] = {
+    for {
+      processedSources <- Future.fromTry(processSources(sources, _.asPrettyJson))
+      workflowIds <- store.add(processedSources)
+    } yield workflowIds
+  }
+
+  private def processSources(sources: NonEmptyList[WorkflowSourceFilesCollection],
+                             processOptions: WorkflowOptions => WorkflowOptionsJson):
+  Try[NonEmptyList[WorkflowSourceFilesCollection]] = {
+    val nelTries: NonEmptyList[Try[WorkflowSourceFilesCollection]] = sources map processSource(processOptions)
+    val seqTries: Seq[Try[WorkflowSourceFilesCollection]] = nelTries.toList
+    val trySeqs: Try[Seq[WorkflowSourceFilesCollection]] = TryUtil.sequence(seqTries)
+    val tryNel: Try[NonEmptyList[WorkflowSourceFilesCollection]] = trySeqs.map(seq => NonEmptyList.fromList(seq.toList).get)
+    tryNel
+  }
+
+  /**
+    * Runs processing on workflow source files before they are stored.
+    *
+    * @param processOptions How to process the workflow options
+    * @param source         Original workflow source
+    * @return Attempted updated workflow source
+    */
+  private def processSource(processOptions: WorkflowOptions => WorkflowOptionsJson)
+                           (source: WorkflowSourceFilesCollection): Try[WorkflowSourceFilesCollection] = {
+    for {
+      processedWorkflowOptions <- WorkflowOptions.fromJsonString(source.workflowOptionsJson)
+    } yield source.copyOptions(processOptions(processedWorkflowOptions))
+  }
+
   private def addWorkCompletionHooks[A](command: WorkflowStoreActorCommand, work: Future[A]) = {
     work.onComplete {
       case Success(_) =>
@@ -152,7 +184,9 @@ case class WorkflowStoreActor(store: WorkflowStore, serviceRegistryActor: ActorR
   /**
     * Takes the workflow id and sends it over to the metadata service w/ default empty values for inputs/outputs
     */
-  private def registerSubmissionWithMetadataService(id: WorkflowId, sourceFiles: WorkflowSourceFiles): Unit = {
+  private def registerSubmissionWithMetadataService(id: WorkflowId, originalSourceFiles: WorkflowSourceFilesCollection): Unit = {
+    val sourceFiles = processSource(_.clearEncryptedValues)(originalSourceFiles).get
+
     val submissionEvents = List(
       MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionTime), MetadataValue(OffsetDateTime.now.toString)),
       MetadataEvent.empty(MetadataKey(id, None, WorkflowMetadataKeys.Inputs)),
@@ -186,8 +220,8 @@ object WorkflowStoreActor {
   private[workflowstore] case object Idle extends WorkflowStoreActorState
 
   sealed trait WorkflowStoreActorCommand
-  final case class SubmitWorkflow(source: WorkflowSourceFiles) extends WorkflowStoreActorCommand
-  final case class BatchSubmitWorkflows(sources: NonEmptyList[WorkflowSourceFiles]) extends WorkflowStoreActorCommand
+  final case class SubmitWorkflow(source: WorkflowSourceFilesCollection) extends WorkflowStoreActorCommand
+  final case class BatchSubmitWorkflows(sources: NonEmptyList[WorkflowSourceFilesCollection]) extends WorkflowStoreActorCommand
   final case class FetchRunnableWorkflows(n: Int) extends WorkflowStoreActorCommand
   final case class RemoveWorkflow(id: WorkflowId) extends WorkflowStoreActorCommand
   final case class AbortWorkflow(id: WorkflowId, manager: ActorRef) extends WorkflowStoreActorCommand
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/workflowstore_.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/workflowstore_.scala
index 0d9481c47df..61bc37ee0d0 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/workflowstore_.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/workflowstore_.scala
@@ -1,6 +1,6 @@
 package cromwell.engine.workflow.workflowstore
 
-import cromwell.core.{WorkflowId, WorkflowSourceFiles}
+import cromwell.core.{WorkflowId, WorkflowSourceFilesCollection}
 import cromwell.engine.workflow.workflowstore.WorkflowStoreState.StartableState
 
 sealed trait WorkflowStoreState {def isStartable: Boolean}
@@ -12,4 +12,4 @@ object WorkflowStoreState {
   case object Restartable extends StartableState
 }
 
-final case class WorkflowToStart(id: WorkflowId, sources: WorkflowSourceFiles, state: StartableState)
+final case class WorkflowToStart(id: WorkflowId, sources: WorkflowSourceFilesCollection, state: StartableState)
diff --git a/engine/src/main/scala/cromwell/jobstore/EmptyJobStoreActor.scala b/engine/src/main/scala/cromwell/jobstore/EmptyJobStoreActor.scala
new file mode 100644
index 00000000000..a2eb585a395
--- /dev/null
+++ b/engine/src/main/scala/cromwell/jobstore/EmptyJobStoreActor.scala
@@ -0,0 +1,15 @@
+package cromwell.jobstore
+
+import akka.actor.{Actor, Props}
+import cromwell.jobstore.JobStoreActor._
+
+class EmptyJobStoreActor extends Actor {
+  override def receive: Receive = {
+    case w: JobStoreWriterCommand => sender ! JobStoreWriteSuccess(w)
+    case _: QueryJobCompletion => sender ! JobNotComplete
+  }
+}
+
+object EmptyJobStoreActor {
+  def props: Props = Props(new EmptyJobStoreActor())
+}
diff --git a/engine/src/main/scala/cromwell/jobstore/jobstore_.scala b/engine/src/main/scala/cromwell/jobstore/jobstore_.scala
index 7fbdd01079b..921183d3583 100644
--- a/engine/src/main/scala/cromwell/jobstore/jobstore_.scala
+++ b/engine/src/main/scala/cromwell/jobstore/jobstore_.scala
@@ -5,6 +5,6 @@ import cromwell.core.{WorkflowId, _}
 case class JobStoreKey(workflowId: WorkflowId, callFqn: String, index: Option[Int], attempt: Int)
 
 sealed trait JobResult
-case class JobResultSuccess(returnCode: Option[Int], jobOutputs: JobOutputs) extends JobResult
+case class JobResultSuccess(returnCode: Option[Int], jobOutputs: CallOutputs) extends JobResult
 case class JobResultFailure(returnCode: Option[Int], reason: Throwable, retryable: Boolean) extends JobResult
 
diff --git a/engine/src/main/scala/cromwell/server/CromwellRootActor.scala b/engine/src/main/scala/cromwell/server/CromwellRootActor.scala
index cc0f5f4aaf7..37dea81331d 100644
--- a/engine/src/main/scala/cromwell/server/CromwellRootActor.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellRootActor.scala
@@ -13,6 +13,7 @@ import cromwell.engine.workflow.tokens.JobExecutionTokenDispenserActor
 import cromwell.engine.workflow.workflowstore.{SqlWorkflowStore, WorkflowStore, WorkflowStoreActor}
 import cromwell.jobstore.{JobStore, JobStoreActor, SqlJobStore}
 import cromwell.services.{ServiceRegistryActor, SingletonServicesStore}
+import cromwell.subworkflowstore.{SqlSubWorkflowStore, SubWorkflowStoreActor}
 import net.ceedubs.ficus.Ficus._
 /**
   * An actor which serves as the lord protector for the rest of Cromwell, allowing us to have more fine grain
@@ -29,6 +30,7 @@ import net.ceedubs.ficus.Ficus._
 
   private val logger = Logging(context.system, this)
   private val config = ConfigFactory.load()
+  val serverMode: Boolean
 
   lazy val serviceRegistryActor: ActorRef = context.actorOf(ServiceRegistryActor.props(config), "ServiceRegistryActor")
   lazy val numberOfWorkflowLogCopyWorkers = config.getConfig("system").as[Option[Int]]("number-of-workflow-log-copy-workers").getOrElse(DefaultNumberOfWorkflowLogCopyWorkers)
@@ -44,6 +46,9 @@ import net.ceedubs.ficus.Ficus._
   lazy val jobStore: JobStore = new SqlJobStore(SingletonServicesStore.databaseInterface)
   lazy val jobStoreActor = context.actorOf(JobStoreActor.props(jobStore), "JobStoreActor")
 
+  lazy val subWorkflowStore = new SqlSubWorkflowStore(SingletonServicesStore.databaseInterface)
+  lazy val subWorkflowStoreActor = context.actorOf(SubWorkflowStoreActor.props(subWorkflowStore), "SubWorkflowStoreActor")
+
   lazy val callCache: CallCache = new CallCache(SingletonServicesStore.databaseInterface)
   lazy val callCacheReadActor = context.actorOf(RoundRobinPool(25)
     .props(CallCacheReadActor.props(callCache)),
@@ -56,9 +61,12 @@ import net.ceedubs.ficus.Ficus._
 
   lazy val jobExecutionTokenDispenserActor = context.actorOf(JobExecutionTokenDispenserActor.props)
 
+  def abortJobsOnTerminate: Boolean
+
   lazy val workflowManagerActor = context.actorOf(
     WorkflowManagerActor.props(
-      workflowStoreActor, serviceRegistryActor, workflowLogCopyRouter, jobStoreActor, callCacheReadActor, jobExecutionTokenDispenserActor, backendSingletonCollection),
+      workflowStoreActor, serviceRegistryActor, workflowLogCopyRouter, jobStoreActor, subWorkflowStoreActor, callCacheReadActor,
+      jobExecutionTokenDispenserActor, backendSingletonCollection, abortJobsOnTerminate, serverMode),
     "WorkflowManagerActor")
 
   override def receive = {
diff --git a/engine/src/main/scala/cromwell/server/CromwellServer.scala b/engine/src/main/scala/cromwell/server/CromwellServer.scala
index dca31a625d3..36010fb620d 100644
--- a/engine/src/main/scala/cromwell/server/CromwellServer.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellServer.scala
@@ -53,6 +53,9 @@ object CromwellServer {
 class CromwellServerActor(config: Config) extends CromwellRootActor with CromwellApiService with SwaggerService {
   implicit def executionContext = actorRefFactory.dispatcher
 
+  override val serverMode = true
+  override val abortJobsOnTerminate = false
+
   override def actorRefFactory = context
   override def receive = handleTimeouts orElse runRoute(possibleRoutes)
 
diff --git a/engine/src/main/scala/cromwell/subworkflowstore/EmptySubWorkflowStoreActor.scala b/engine/src/main/scala/cromwell/subworkflowstore/EmptySubWorkflowStoreActor.scala
new file mode 100644
index 00000000000..166d7d685bd
--- /dev/null
+++ b/engine/src/main/scala/cromwell/subworkflowstore/EmptySubWorkflowStoreActor.scala
@@ -0,0 +1,17 @@
+package cromwell.subworkflowstore
+
+import akka.actor.{Actor, ActorLogging, Props}
+import cromwell.subworkflowstore.SubWorkflowStoreActor._
+
+class EmptySubWorkflowStoreActor extends Actor with ActorLogging {
+  override def receive: Receive = {
+    case register: RegisterSubWorkflow => sender() ! SubWorkflowStoreRegisterSuccess(register) 
+    case query: QuerySubWorkflow => sender() ! SubWorkflowNotFound(query)
+    case complete: WorkflowComplete =>sender() ! SubWorkflowStoreCompleteSuccess(complete)
+    case unknown => log.error(s"SubWorkflowStoreActor received unknown message: $unknown")
+  }
+}
+
+object EmptySubWorkflowStoreActor {
+  def props: Props = Props(new EmptySubWorkflowStoreActor())
+}
diff --git a/engine/src/main/scala/cromwell/subworkflowstore/SqlSubWorkflowStore.scala b/engine/src/main/scala/cromwell/subworkflowstore/SqlSubWorkflowStore.scala
new file mode 100644
index 00000000000..64f21275ff4
--- /dev/null
+++ b/engine/src/main/scala/cromwell/subworkflowstore/SqlSubWorkflowStore.scala
@@ -0,0 +1,31 @@
+package cromwell.subworkflowstore
+import cromwell.database.sql.SubWorkflowStoreSqlDatabase
+import cromwell.database.sql.tables.SubWorkflowStoreEntry
+
+import scala.concurrent.{ExecutionContext, Future}
+
+class SqlSubWorkflowStore(subWorkflowStoreSqlDatabase: SubWorkflowStoreSqlDatabase) extends SubWorkflowStore {
+  override def addSubWorkflowStoreEntry(rootWorkflowExecutionUuid: String,
+                                        parentWorkflowExecutionUuid: String,
+                                        callFullyQualifiedName: String,
+                                        jobIndex: Int,
+                                        jobAttempt: Int,
+                                        subWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Unit] = {
+    subWorkflowStoreSqlDatabase.addSubWorkflowStoreEntry(
+      rootWorkflowExecutionUuid,
+      parentWorkflowExecutionUuid,
+      callFullyQualifiedName,
+      jobIndex,
+      jobAttempt,
+      subWorkflowExecutionUuid
+    )
+  }
+
+  override def querySubWorkflowStore(parentWorkflowExecutionUuid: String, callFqn: String, jobIndex: Int, jobAttempt: Int)(implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]] = {
+    subWorkflowStoreSqlDatabase.querySubWorkflowStore(parentWorkflowExecutionUuid, callFqn, jobIndex, jobAttempt)
+  }
+
+  override def removeSubWorkflowStoreEntries(parentWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Int] = {
+    subWorkflowStoreSqlDatabase.removeSubWorkflowStoreEntries(parentWorkflowExecutionUuid)
+  }
+}
diff --git a/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStore.scala b/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStore.scala
new file mode 100644
index 00000000000..8ad92fa9bae
--- /dev/null
+++ b/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStore.scala
@@ -0,0 +1,19 @@
+package cromwell.subworkflowstore
+
+import cromwell.database.sql.tables.SubWorkflowStoreEntry
+
+import scala.concurrent.{ExecutionContext, Future}
+
+trait SubWorkflowStore {
+  def addSubWorkflowStoreEntry(rootWorkflowExecutionUuid: String,
+                               parentWorkflowExecutionUuid: String,
+                               callFullyQualifiedName: String,
+                               jobIndex: Int,
+                               jobAttempt: Int,
+                               subWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Unit]
+
+  def querySubWorkflowStore(parentWorkflowExecutionUuid: String, callFqn: String, jobIndex: Int, jobAttempt: Int)
+                           (implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]]
+
+  def removeSubWorkflowStoreEntries(parentWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Int]
+}
diff --git a/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStoreActor.scala b/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStoreActor.scala
new file mode 100644
index 00000000000..cf762408716
--- /dev/null
+++ b/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStoreActor.scala
@@ -0,0 +1,72 @@
+package cromwell.subworkflowstore
+
+import akka.actor.{Actor, ActorLogging, ActorRef, Props}
+import cromwell.core.ExecutionIndex._
+import cromwell.core.{JobKey, WorkflowId}
+import cromwell.database.sql.tables.SubWorkflowStoreEntry
+import cromwell.subworkflowstore.SubWorkflowStoreActor._
+
+import scala.concurrent.ExecutionContext
+import scala.util.{Failure, Success}
+
+class SubWorkflowStoreActor(database: SubWorkflowStore) extends Actor with ActorLogging {
+  
+  implicit val ec: ExecutionContext = context.dispatcher
+
+  override def receive = {
+    case register: RegisterSubWorkflow => registerSubWorkflow(sender(), register)
+    case query: QuerySubWorkflow => querySubWorkflow(sender(), query)
+    case complete: WorkflowComplete => workflowComplete(sender(), complete)
+    case unknown => log.error(s"SubWorkflowStoreActor received unknown message: $unknown")
+  }
+  
+  private def registerSubWorkflow(replyTo: ActorRef, command: RegisterSubWorkflow) = {
+    database.addSubWorkflowStoreEntry(
+      command.rootWorkflowExecutionUuid.toString,
+      command.parentWorkflowExecutionUuid.toString,
+      command.jobKey.scope.fullyQualifiedName,
+      command.jobKey.index.fromIndex,
+      command.jobKey.attempt,
+      command.subWorkflowExecutionUuid.toString
+    ) onComplete { 
+      case Success(_) => replyTo ! SubWorkflowStoreRegisterSuccess(command) 
+      case Failure(ex) => replyTo ! SubWorkflowStoreFailure(command, ex)
+    }
+  }
+
+  private def querySubWorkflow(replyTo: ActorRef, command: QuerySubWorkflow) = {
+    val jobKey = command.jobKey
+    database.querySubWorkflowStore(command.parentWorkflowExecutionUuid.toString, jobKey.scope.fullyQualifiedName, jobKey.index.fromIndex, jobKey.attempt) onComplete {
+      case Success(Some(result)) => replyTo ! SubWorkflowFound(result)
+      case Success(None) => replyTo ! SubWorkflowNotFound(command)
+      case Failure(ex) => replyTo ! SubWorkflowStoreFailure(command, ex)
+    }
+  }
+
+  private def workflowComplete(replyTo: ActorRef, command: WorkflowComplete) = {
+    database.removeSubWorkflowStoreEntries(command.workflowExecutionUuid.toString) onComplete {
+      case Success(_) => replyTo ! SubWorkflowStoreCompleteSuccess(command)
+      case Failure(ex) => replyTo ! SubWorkflowStoreFailure(command, ex)
+    }
+  }
+  
+}
+
+object SubWorkflowStoreActor {
+  sealed trait SubWorkflowStoreActorCommand
+  case class RegisterSubWorkflow(rootWorkflowExecutionUuid: WorkflowId, parentWorkflowExecutionUuid: WorkflowId, jobKey: JobKey, subWorkflowExecutionUuid: WorkflowId) extends SubWorkflowStoreActorCommand
+  case class QuerySubWorkflow(parentWorkflowExecutionUuid: WorkflowId, jobKey: JobKey) extends SubWorkflowStoreActorCommand
+  case class WorkflowComplete(workflowExecutionUuid: WorkflowId) extends SubWorkflowStoreActorCommand
+
+  sealed trait SubWorkflowStoreActorResponse
+  case class SubWorkflowStoreRegisterSuccess(command: RegisterSubWorkflow) extends SubWorkflowStoreActorResponse
+  case class SubWorkflowFound(subWorkflowStoreEntry: SubWorkflowStoreEntry) extends SubWorkflowStoreActorResponse
+  case class SubWorkflowNotFound(command: QuerySubWorkflow) extends SubWorkflowStoreActorResponse
+  case class SubWorkflowStoreCompleteSuccess(command: SubWorkflowStoreActorCommand) extends SubWorkflowStoreActorResponse
+  
+  case class SubWorkflowStoreFailure(command: SubWorkflowStoreActorCommand, failure: Throwable) extends SubWorkflowStoreActorResponse
+  
+  def props(database: SubWorkflowStore) = Props(
+    new SubWorkflowStoreActor(database)
+  )
+}
diff --git a/engine/src/main/scala/cromwell/webservice/CromwellApiHandler.scala b/engine/src/main/scala/cromwell/webservice/CromwellApiHandler.scala
index a2441abb4ac..76ec94d7785 100644
--- a/engine/src/main/scala/cromwell/webservice/CromwellApiHandler.scala
+++ b/engine/src/main/scala/cromwell/webservice/CromwellApiHandler.scala
@@ -21,8 +21,8 @@ object CromwellApiHandler {
 
   sealed trait ApiHandlerMessage
 
-  final case class ApiHandlerWorkflowSubmit(source: WorkflowSourceFiles) extends ApiHandlerMessage
-  final case class ApiHandlerWorkflowSubmitBatch(sources: NonEmptyList[WorkflowSourceFiles]) extends ApiHandlerMessage
+  final case class ApiHandlerWorkflowSubmit(source: WorkflowSourceFilesCollection) extends ApiHandlerMessage
+  final case class ApiHandlerWorkflowSubmitBatch(sources: NonEmptyList[WorkflowSourceFilesCollection]) extends ApiHandlerMessage
   final case class ApiHandlerWorkflowQuery(uri: Uri, parameters: Seq[(String, String)]) extends ApiHandlerMessage
   final case class ApiHandlerWorkflowStatus(id: WorkflowId) extends ApiHandlerMessage
   final case class ApiHandlerWorkflowOutputs(id: WorkflowId) extends ApiHandlerMessage
@@ -66,7 +66,9 @@ class CromwellApiHandler(requestHandlerActor: ActorRef) extends Actor with Workf
     case WorkflowStoreActor.WorkflowSubmittedToStore(id) =>
       context.parent ! RequestComplete((StatusCodes.Created, WorkflowSubmitResponse(id.toString, WorkflowSubmitted.toString)))
 
-    case ApiHandlerWorkflowSubmitBatch(sources) => requestHandlerActor ! WorkflowStoreActor.BatchSubmitWorkflows(sources)
+    case ApiHandlerWorkflowSubmitBatch(sources) => requestHandlerActor !
+      WorkflowStoreActor.BatchSubmitWorkflows(sources.map(x => WorkflowSourceFilesWithoutImports(x.wdlSource,x.inputsJson,x.workflowOptionsJson)))
+
 
     case WorkflowStoreActor.WorkflowsBatchSubmittedToStore(ids) =>
       val responses = ids map { id => WorkflowSubmitResponse(id.toString, WorkflowSubmitted.toString) }
diff --git a/engine/src/main/scala/cromwell/webservice/CromwellApiService.scala b/engine/src/main/scala/cromwell/webservice/CromwellApiService.scala
index 54ddf278660..34fff945b3f 100644
--- a/engine/src/main/scala/cromwell/webservice/CromwellApiService.scala
+++ b/engine/src/main/scala/cromwell/webservice/CromwellApiService.scala
@@ -1,9 +1,9 @@
 package cromwell.webservice
 
 import akka.actor._
-import java.lang.Throwable
+
 import cats.data.NonEmptyList
-import cromwell.core.{WorkflowId, WorkflowSourceFiles}
+import cromwell.core.{WorkflowId, WorkflowOptionsJson, WorkflowSourceFilesCollection}
 import cromwell.engine.backend.BackendConfiguration
 import cromwell.services.metadata.MetadataService._
 import cromwell.webservice.WorkflowJsonSupport._
@@ -14,6 +14,9 @@ import spray.http._
 import spray.httpx.SprayJsonSupport._
 import spray.json._
 import spray.routing._
+import wdl4s.{WdlJson, WdlSource}
+
+import scala.util.{Failure, Success, Try}
 
 trait SwaggerService extends SwaggerUiResourceHttpService {
   override def swaggerServiceName = "cromwell"
@@ -50,8 +53,8 @@ trait CromwellApiService extends HttpService with PerRequestCreator {
       perRequest(requestContext, metadataBuilderProps, message)
   }
 
-  private def failBadRequest(exception: Exception, statusCode: StatusCode = StatusCodes.BadRequest) = respondWithMediaType(`application/json`) {
-    complete((statusCode, APIResponse.fail(exception).toJson.prettyPrint))
+  private def failBadRequest(t: Throwable, statusCode: StatusCode = StatusCodes.BadRequest) = respondWithMediaType(`application/json`) {
+    complete((statusCode, APIResponse.fail(t).toJson.prettyPrint))
   }
 
   val workflowRoutes = queryRoute ~ queryPostRoute ~ workflowOutputsRoute ~ submitRoute ~ submitBatchRoute ~
@@ -124,18 +127,70 @@ trait CromwellApiService extends HttpService with PerRequestCreator {
       }
     }
 
+  case class PartialWorkflowSources(wdlSource: Option[WdlSource], workflowInputs: Seq[WdlJson], workflowInputsAux: Map[Int, WdlJson], workflowOptions: Option[WorkflowOptionsJson], zippedImports: Option[Array[Byte]])
+  object PartialWorkflowSources {
+    private def workflowInputs(bodyPart: BodyPart): Seq[WdlJson] = {
+      import spray.json._
+      bodyPart.entity.data.asString.parseJson match {
+        case JsArray(Seq(x, xs@_*)) => (List(x) ++ xs).map(_.compactPrint)
+        case JsArray(_) => Seq.empty
+        case v: JsValue => Seq(v.compactPrint)
+      }
+    }
+
+    def partialSourcesToSourceCollections(partialSources: Try[PartialWorkflowSources], allowNoInputs: Boolean): Try[Seq[WorkflowSourceFilesCollection]] = {
+      partialSources flatMap {
+        case PartialWorkflowSources(Some(wdlSource), workflowInputs, workflowInputsAux, workflowOptions, wdlDependencies) =>
+          //The order of addition allows for the expected override of colliding keys.
+          val sortedInputAuxes = workflowInputsAux.toSeq.sortBy(_._1).map(x => Option(x._2))
+          val wfInputs: Try[Seq[WdlJson]] = if (workflowInputs.isEmpty) {
+            if (allowNoInputs) Success(Seq("{}")) else Failure(new IllegalArgumentException("No inputs were provided"))
+          } else Success(workflowInputs map { workflowInputSet =>
+            mergeMaps(Seq(Option(workflowInputSet)) ++ sortedInputAuxes).toString
+          })
+          wfInputs.map(_.map(x => WorkflowSourceFilesCollection(wdlSource, x, workflowOptions.getOrElse("{}"), wdlDependencies)))
+        case other => Failure(new IllegalArgumentException(s"Incomplete workflow submission: $other"))
+      }
+    }
+
+    def fromSubmitRoute(formData: MultipartFormData, allowNoInputs: Boolean): Try[Seq[WorkflowSourceFilesCollection]] = {
+      val partialSources = Try(formData.fields.foldLeft(PartialWorkflowSources(None, Seq.empty, Map.empty, None, None)) { (partialSources: PartialWorkflowSources, bodyPart: BodyPart) =>
+        if (bodyPart.name.contains("wdlSource")) {
+          partialSources.copy(wdlSource = Some(bodyPart.entity.data.asString))
+        } else if (bodyPart.name.contains("workflowInputs")) {
+          partialSources.copy(workflowInputs = workflowInputs(bodyPart))
+        } else if (bodyPart.name.forall(_.startsWith("workflowInputs_"))) {
+          val index = bodyPart.name.get.stripPrefix("workflowInputs_").toInt
+          partialSources.copy(workflowInputsAux = partialSources.workflowInputsAux + (index -> bodyPart.entity.data.asString))
+        } else if (bodyPart.name.contains("workflowOptions")) {
+          partialSources.copy(workflowOptions = Some(bodyPart.entity.data.asString))
+        } else if (bodyPart.name.contains("wdlDependencies")) {
+          partialSources.copy(zippedImports = Some(bodyPart.entity.data.toByteArray))
+        } else {
+          throw new IllegalArgumentException(s"Unexpected body part name: ${bodyPart.name.getOrElse("None")}")
+        }
+      })
+      partialSourcesToSourceCollections(partialSources, allowNoInputs)
+    }
+  }
+
   def submitRoute =
     path("workflows" / Segment) { version =>
       post {
-        formFields("wdlSource", "workflowInputs".?, "workflowInputs_2".?, "workflowInputs_3".?,
-          "workflowInputs_4".?, "workflowInputs_5".?, "workflowOptions".?) {
-          (wdlSource, workflowInputs, workflowInputs_2, workflowInputs_3, workflowInputs_4, workflowInputs_5, workflowOptions) =>
-          requestContext =>
-            //The order of addition allows for the expected override of colliding keys.
-            val wfInputs = mergeMaps(Seq(workflowInputs, workflowInputs_2, workflowInputs_3, workflowInputs_4, workflowInputs_5)).toString
-
-            val workflowSourceFiles = WorkflowSourceFiles(wdlSource, wfInputs, workflowOptions.getOrElse("{}"))
-            perRequest(requestContext, CromwellApiHandler.props(workflowStoreActor), CromwellApiHandler.ApiHandlerWorkflowSubmit(workflowSourceFiles))
+        entity(as[MultipartFormData]) { formData =>
+          requestContext => {
+            PartialWorkflowSources.fromSubmitRoute(formData, allowNoInputs = true) match {
+              case Success(workflowSourceFiles) if workflowSourceFiles.size == 1 =>
+                perRequest(requestContext, CromwellApiHandler.props(workflowStoreActor), CromwellApiHandler.ApiHandlerWorkflowSubmit(workflowSourceFiles.head))
+              case Success(workflowSourceFiles) =>
+                failBadRequest(new IllegalArgumentException("To submit more than one workflow at a time, use the batch endpoint."))
+              case Failure(t) =>
+                System.err.println(t)
+                t.printStackTrace(System.err)
+                failBadRequest(t)
+            }
+            ()
+          }
         }
       }
     }
@@ -143,19 +198,18 @@ trait CromwellApiService extends HttpService with PerRequestCreator {
   def submitBatchRoute =
     path("workflows" / Segment / "batch") { version =>
       post {
-        formFields("wdlSource", "workflowInputs", "workflowOptions".?) {
-          (wdlSource, workflowInputs, workflowOptions) =>
-            requestContext =>
-              import spray.json._
-              workflowInputs.parseJson match {
-                case JsArray(Seq(x, xs@_*)) =>
-                  val nelInputses = NonEmptyList.of(x, xs: _*)
-                  val sources = nelInputses.map(inputs => WorkflowSourceFiles(wdlSource, inputs.compactPrint, workflowOptions.getOrElse("{}")))
-                  perRequest(requestContext, CromwellApiHandler.props(workflowStoreActor), CromwellApiHandler.ApiHandlerWorkflowSubmitBatch(sources))
-                case JsArray(_) => failBadRequest(new RuntimeException("Nothing was submitted"))
-                case _ => reject
-              }
-              ()
+        entity(as[MultipartFormData]) { formData =>
+          requestContext => {
+            PartialWorkflowSources.fromSubmitRoute(formData, allowNoInputs = false) match {
+              case Success(workflowSourceFiles) =>
+                perRequest(requestContext, CromwellApiHandler.props(workflowStoreActor), CromwellApiHandler.ApiHandlerWorkflowSubmitBatch(NonEmptyList.fromListUnsafe(workflowSourceFiles.toList)))
+              case Failure(t) =>
+                System.err.println(t)
+                t.printStackTrace(System.err)
+                failBadRequest(t)
+            }
+            ()
+          }
         }
       }
     }
@@ -183,13 +237,21 @@ trait CromwellApiService extends HttpService with PerRequestCreator {
       parameterMultiMap { parameters =>
         val includeKeysOption = NonEmptyList.fromList(parameters.getOrElse("includeKey", List.empty))
         val excludeKeysOption = NonEmptyList.fromList(parameters.getOrElse("excludeKey", List.empty))
-        (includeKeysOption, excludeKeysOption) match {
-          case (Some(_), Some(_)) =>
+        val expandSubWorkflowsOption = {
+          parameters.get("expandSubWorkflows") match {
+            case Some(v :: Nil) => Try(v.toBoolean)
+            case _ => Success(false)
+          }
+        }
+
+        (includeKeysOption, excludeKeysOption, expandSubWorkflowsOption) match {
+          case (Some(_), Some(_), _) =>
             failBadRequest(new IllegalArgumentException("includeKey and excludeKey may not be specified together"))
-          case _ =>
+          case (_, _, Success(expandSubWorkflows)) =>
             withRecognizedWorkflowId(possibleWorkflowId) { id =>
-              handleMetadataRequest(GetSingleWorkflowMetadataAction(id, includeKeysOption, excludeKeysOption))
+              handleMetadataRequest(GetSingleWorkflowMetadataAction(id, includeKeysOption, excludeKeysOption, expandSubWorkflows))
             }
+          case (_, _, Failure(ex)) => failBadRequest(new IllegalArgumentException(ex))
         }
       }
     }
diff --git a/engine/src/main/scala/cromwell/webservice/EngineStatsActor.scala b/engine/src/main/scala/cromwell/webservice/EngineStatsActor.scala
index 3b83955a3cf..047eeccb9ae 100644
--- a/engine/src/main/scala/cromwell/webservice/EngineStatsActor.scala
+++ b/engine/src/main/scala/cromwell/webservice/EngineStatsActor.scala
@@ -19,9 +19,10 @@ final case class EngineStatsActor(workflowActors: List[ActorRef], replyTo: Actor
   private var jobCounts = Map.empty[ActorRef, Int]
 
   /*
-    It's possible that WorkflowActors might disappear behind us and never manage to write us back.
-    Instead of waiting longingly, watching a mailbox which might never receive some love instead wait
-    a specified period of time and assume anything which was going to reply already has
+   * FIXME 
+   * Because of sub workflows there is currently no reliable way to know if we received responses from all running WEAs. 
+   * For now, we always wait for the timeout duration before responding to give a chance to all WEAs to respond (even nested ones).
+   * This could be improved by having WEAs wait for their sub WEAs before sending back the response.
   */
   val scheduledMsg = context.system.scheduler.scheduleOnce(timeout, self, ShutItDown)
 
@@ -31,7 +32,6 @@ final case class EngineStatsActor(workflowActors: List[ActorRef], replyTo: Actor
   override def receive = {
     case JobCount(count) =>
       jobCounts += (sender -> count)
-      if (jobCounts.size == workflowActors.size) reportStats()
     case ShutItDown =>
       reportStats()
     case wompWomp => log.error("Unexpected message to EngineStatsActor: {}", wompWomp)
@@ -59,5 +59,5 @@ object EngineStatsActor {
 
   final case class EngineStats(workflows: Int, jobs: Int)
 
-  val MaxTimeToWait = 30 seconds
+  val MaxTimeToWait = 3 seconds
 }
diff --git a/engine/src/main/scala/cromwell/webservice/WorkflowJsonSupport.scala b/engine/src/main/scala/cromwell/webservice/WorkflowJsonSupport.scala
index a294c58fc9c..b2afe311f65 100644
--- a/engine/src/main/scala/cromwell/webservice/WorkflowJsonSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/WorkflowJsonSupport.scala
@@ -1,13 +1,15 @@
 package cromwell.webservice
 
+import java.nio.file.Paths
 import java.time.OffsetDateTime
 
-import cromwell.core.WorkflowSourceFiles
+import cromwell.core._
 import cromwell.engine._
 import cromwell.services.metadata.MetadataService
 import MetadataService.{WorkflowQueryResponse, WorkflowQueryResult}
 import cromwell.util.JsonFormatting.WdlValueJsonFormatter
 import WdlValueJsonFormatter._
+import better.files.File
 import spray.json.{DefaultJsonProtocol, JsString, JsValue, RootJsonFormat}
 
 object WorkflowJsonSupport extends DefaultJsonProtocol {
@@ -18,7 +20,17 @@ object WorkflowJsonSupport extends DefaultJsonProtocol {
   implicit val callOutputResponseProtocol = jsonFormat3(CallOutputResponse)
   implicit val engineStatsProtocol = jsonFormat2(EngineStatsActor.EngineStats)
   implicit val callAttempt = jsonFormat2(CallAttempt)
-  implicit val workflowSourceData = jsonFormat3(WorkflowSourceFiles)
+  implicit val workflowSourceData = jsonFormat3(WorkflowSourceFilesWithoutImports)
+
+  implicit object fileJsonFormat extends RootJsonFormat[File] {
+    override def write(obj: File) = JsString(obj.path.toAbsolutePath.toString)
+    override def read(json: JsValue): File = json match {
+      case JsString(str) => Paths.get(str)
+      case unknown => throw new NotImplementedError(s"Cannot parse $unknown to a File")
+    }
+  }
+
+  implicit val workflowSourceDataWithImports = jsonFormat4(WorkflowSourceFilesWithDependenciesZip)
   implicit val errorResponse = jsonFormat3(FailureResponse)
   implicit val successResponse = jsonFormat3(SuccessResponse)
 
diff --git a/engine/src/main/scala/cromwell/webservice/metadata/IndexedJsonValue.scala b/engine/src/main/scala/cromwell/webservice/metadata/IndexedJsonValue.scala
index d9ed774383a..f51e64187ca 100644
--- a/engine/src/main/scala/cromwell/webservice/metadata/IndexedJsonValue.scala
+++ b/engine/src/main/scala/cromwell/webservice/metadata/IndexedJsonValue.scala
@@ -4,6 +4,7 @@ import java.time.OffsetDateTime
 
 import cats.{Monoid, Semigroup}
 import cats.instances.map._
+import cromwell.services.metadata.CallMetadataKeys
 import spray.json._
 
 
@@ -30,20 +31,33 @@ object IndexedJsonValue {
 
 /** Customized version of Json data structure, to account for timestamped values and lazy array creation */
 sealed trait TimestampedJsValue {
-  def toJson: JsValue
+  def toJson(expandedValues: Map[String, JsValue]): JsValue
   def timestamp: OffsetDateTime
 }
 
 private case class TimestampedJsList(v: Map[Int, TimestampedJsValue], timestamp: OffsetDateTime) extends TimestampedJsValue {
-  override val toJson = JsArray(v.values.toVector map { _.toJson })
+  override def toJson(expandedValues: Map[String, JsValue]) = JsArray(v.values.toVector map { _.toJson(expandedValues) })
 }
 
 private case class TimestampedJsObject(v: Map[String, TimestampedJsValue], timestamp: OffsetDateTime) extends TimestampedJsValue {
-  override val toJson = JsObject(v mapValues { _.toJson })
+  override def toJson(expandedValues: Map[String, JsValue]) = {
+    val mappedValues = v map {
+      case (key, subWorkflowId: TimestampedJsPrimitive) if key == CallMetadataKeys.SubWorkflowId =>
+        val subId = subWorkflowId.v.asInstanceOf[JsString]
+        expandedValues.get(subId.value) map { subMetadata =>
+           CallMetadataKeys.SubWorkflowMetadata -> subMetadata
+        } getOrElse {
+          key -> subWorkflowId.v
+        }
+      case (key, value) => key -> value.toJson(expandedValues)
+    }
+    
+    JsObject(mappedValues)
+  }
 }
 
 private class TimestampedJsPrimitive(val v: JsValue, val timestamp: OffsetDateTime) extends TimestampedJsValue {
-  override val toJson = v
+  override def toJson(expandedValues: Map[String, JsValue]) = v
 }
 
 private case class TimestampedEmptyJson(override val timestamp: OffsetDateTime) extends TimestampedJsPrimitive(JsObject(Map.empty[String, JsValue]), timestamp)
\ No newline at end of file
diff --git a/engine/src/main/scala/cromwell/webservice/metadata/MetadataBuilderActor.scala b/engine/src/main/scala/cromwell/webservice/metadata/MetadataBuilderActor.scala
index 0653be4256d..272e94c75a5 100644
--- a/engine/src/main/scala/cromwell/webservice/metadata/MetadataBuilderActor.scala
+++ b/engine/src/main/scala/cromwell/webservice/metadata/MetadataBuilderActor.scala
@@ -13,8 +13,8 @@ import cromwell.services.ServiceRegistryActor.ServiceRegistryFailure
 import cromwell.services.metadata.MetadataService._
 import cromwell.services.metadata._
 import cromwell.webservice.PerRequest.{RequestComplete, RequestCompleteWithHeaders}
-import cromwell.webservice.metadata.MetadataBuilderActor.{Idle, MetadataBuilderActorState, WaitingForMetadataService}
-import cromwell.webservice.{APIResponse, WorkflowJsonSupport}
+import cromwell.webservice.metadata.MetadataBuilderActor.{Idle, MetadataBuilderActorData, MetadataBuilderActorState, WaitingForMetadataService, WaitingForSubWorkflows}
+import cromwell.webservice.{APIResponse, PerRequestCreator, WorkflowJsonSupport}
 import org.slf4j.LoggerFactory
 import spray.http.{StatusCodes, Uri}
 import spray.httpx.SprayJsonSupport._
@@ -29,7 +29,21 @@ object MetadataBuilderActor {
   sealed trait MetadataBuilderActorState
   case object Idle extends MetadataBuilderActorState
   case object WaitingForMetadataService extends MetadataBuilderActorState
-
+  case object WaitingForSubWorkflows extends MetadataBuilderActorState
+
+  case class MetadataBuilderActorData(
+                                      originalQuery: MetadataQuery,
+                                      originalEvents: Seq[MetadataEvent],
+                                      subWorkflowsMetadata: Map[String, JsValue],
+                                      waitFor: Int
+                                    ) {
+    def withSubWorkflow(id: String, metadata: JsValue) = {
+      this.copy(subWorkflowsMetadata = subWorkflowsMetadata + ((id, metadata)))
+    }
+    
+    def isComplete = subWorkflowsMetadata.size == waitFor
+  }
+  
   def props(serviceRegistryActor: ActorRef) = {
     Props(new MetadataBuilderActor(serviceRegistryActor)).withDispatcher(ApiDispatcher)
   }
@@ -138,8 +152,8 @@ object MetadataBuilderActor {
     events.toList map { e => keyValueToIndexedJson(e.key.key, e.value, e.offsetDateTime) } combineAll
   }
 
-  private def eventsToAttemptMetadata(attempt: Int, events: Seq[MetadataEvent]) = {
-    val withAttemptField = JsObject(eventsToIndexedJson(events).toJson.asJsObject.fields + (AttemptKey -> JsNumber(attempt)))
+  private def eventsToAttemptMetadata(expandedValues: Map[String, JsValue])(attempt: Int, events: Seq[MetadataEvent]) = {
+    val withAttemptField = JsObject(eventsToIndexedJson(events).toJson(expandedValues).asJsObject.fields + (AttemptKey -> JsNumber(attempt)))
     MetadataForAttempt(attempt, withAttemptField)
   }
 
@@ -160,10 +174,10 @@ object MetadataBuilderActor {
     workflowNonStatusEvents ++ sortedStateEvents.headOption.toList
   }
 
-  private def parseWorkflowEventsToTimestampedJsValue(events: Seq[MetadataEvent], includeCallsIfEmpty: Boolean): JsObject = {
+  private def parseWorkflowEventsToTimestampedJsValue(events: Seq[MetadataEvent], includeCallsIfEmpty: Boolean, expandedValues: Map[String, JsValue]): JsObject = {
     // Partition if sequence of events in a pair of (Workflow level events, Call level events)
     val (workflowLevel, callLevel) = events partition { _.key.jobKey.isEmpty }
-    val foldedWorkflowValues = eventsToIndexedJson(reduceWorkflowEvents(workflowLevel)).toJson.asJsObject
+    val foldedWorkflowValues = eventsToIndexedJson(reduceWorkflowEvents(workflowLevel)).toJson(expandedValues).asJsObject
 
     val callsGroupedByFQN = callLevel groupBy { _.key.jobKey.get.callFqn }
     val callsGroupedByFQNAndIndex = callsGroupedByFQN mapValues { _ groupBy { _.key.jobKey.get.index } }
@@ -171,7 +185,7 @@ object MetadataBuilderActor {
 
     val callsMap = callsGroupedByFQNAndIndexAndAttempt mapValues { eventsForIndex =>
       eventsForIndex mapValues { eventsForAttempt =>
-        eventsForAttempt map Function.tupled(eventsToAttemptMetadata)
+        eventsForAttempt map Function.tupled(eventsToAttemptMetadata(expandedValues))
       } map { Function.tupled(attemptMetadataToIndexMetadata) }
     } mapValues { md => JsArray(md.toVector.sortBy(_.index) flatMap { _.metadata }) }
 
@@ -180,13 +194,13 @@ object MetadataBuilderActor {
     JsObject(foldedWorkflowValues.fields ++ callData)
   }
 
-  private def parseWorkflowEvents(includeCallsIfEmpty: Boolean)(events: Seq[MetadataEvent]): JsObject = parseWorkflowEventsToTimestampedJsValue(events, includeCallsIfEmpty)
+  private def parseWorkflowEvents(includeCallsIfEmpty: Boolean, expandedValues: Map[String, JsValue])(events: Seq[MetadataEvent]): JsObject = parseWorkflowEventsToTimestampedJsValue(events, includeCallsIfEmpty, expandedValues)
 
   /**
     * Parse a Seq of MetadataEvent into a full Json metadata response.
     */
-  private def parse(events: Seq[MetadataEvent]): JsObject = {
-    JsObject(events.groupBy(_.key.workflowId.toString) mapValues parseWorkflowEvents(includeCallsIfEmpty = true))
+  private def parse(events: Seq[MetadataEvent], expandedValues: Map[String, JsValue]): JsObject = {
+    JsObject(events.groupBy(_.key.workflowId.toString) mapValues parseWorkflowEvents(includeCallsIfEmpty = true, expandedValues))
   }
 
   implicit class EnhancedMetadataValue(val value: MetadataValue) extends AnyVal {
@@ -194,12 +208,12 @@ object MetadataBuilderActor {
   }
 }
 
-class MetadataBuilderActor(serviceRegistryActor: ActorRef) extends LoggingFSM[MetadataBuilderActorState, Unit]
+class MetadataBuilderActor(serviceRegistryActor: ActorRef) extends LoggingFSM[MetadataBuilderActorState, Option[MetadataBuilderActorData]]
   with DefaultJsonProtocol with WorkflowQueryPagination {
 
   import WorkflowJsonSupport._
 
-  startWith(Idle, ())
+  startWith(Idle, None)
   val tag = self.path.name
 
   when(Idle) {
@@ -214,9 +228,8 @@ class MetadataBuilderActor(serviceRegistryActor: ActorRef) extends LoggingFSM[Me
   }
 
   when(WaitingForMetadataService) {
-    case Event(MetadataLookupResponse(query, metadata), _) =>
-      context.parent ! RequestComplete((StatusCodes.OK, processMetadataResponse(query, metadata)))
-      allDone
+    case Event(MetadataLookupResponse(query, metadata), None) =>
+      processMetadataResponse(query, metadata)
     case Event(StatusLookupResponse(w, status), _) =>
       context.parent ! RequestComplete((StatusCodes.OK, processStatusResponse(w, status)))
       allDone
@@ -225,7 +238,6 @@ class MetadataBuilderActor(serviceRegistryActor: ActorRef) extends LoggingFSM[Me
       context.parent ! RequestComplete((StatusCodes.InternalServerError, response))
       allDone
     case Event(WorkflowQuerySuccess(uri: Uri, response, metadata), _) =>
-      import WorkflowJsonSupport._
       context.parent ! RequestCompleteWithHeaders(response, generateLinkHeaders(uri, metadata):_*)
       allDone
     case Event(failure: WorkflowQueryFailure, _) =>
@@ -235,10 +247,10 @@ class MetadataBuilderActor(serviceRegistryActor: ActorRef) extends LoggingFSM[Me
       // Add in an empty output event if there aren't already any output events.
       val hasOutputs = events exists { _.key.key.startsWith(WorkflowMetadataKeys.Outputs + ":") }
       val updatedEvents = if (hasOutputs) events else MetadataEvent.empty(MetadataKey(id, None, WorkflowMetadataKeys.Outputs)) +: events
-      context.parent ! RequestComplete((StatusCodes.OK, workflowMetadataResponse(id, updatedEvents, includeCallsIfEmpty = false)))
+      context.parent ! RequestComplete((StatusCodes.OK, workflowMetadataResponse(id, updatedEvents, includeCallsIfEmpty = false, Map.empty)))
       allDone
     case Event(LogsResponse(w, l), _) =>
-      context.parent ! RequestComplete((StatusCodes.OK, workflowMetadataResponse(w, l, includeCallsIfEmpty = false)))
+      context.parent ! RequestComplete((StatusCodes.OK, workflowMetadataResponse(w, l, includeCallsIfEmpty = false, Map.empty)))
       allDone
     case Event(failure: MetadataServiceFailure, _) =>
       context.parent ! RequestComplete((StatusCodes.InternalServerError, APIResponse.error(failure.reason)))
@@ -249,14 +261,76 @@ class MetadataBuilderActor(serviceRegistryActor: ActorRef) extends LoggingFSM[Me
       context stop self
       stay()
   }
+  
+  when(WaitingForSubWorkflows) {
+    case Event(RequestComplete(metadata), Some(data)) =>
+      processSubWorkflowMetadata(metadata, data)
+  }
+  
+  whenUnhandled {
+    case Event(message, data) =>
+      log.error(s"Received unexpected message $message in state $stateName with data $data")
+      stay()
+  }
+  
+  def processSubWorkflowMetadata(metadataResponse: Any, data: MetadataBuilderActorData) = {
+    metadataResponse match {
+      case (StatusCodes.OK, js: JsObject) =>
+        js.fields.get(WorkflowMetadataKeys.Id) match {
+          case Some(subId: JsString) =>
+            val newData = data.withSubWorkflow(subId.value, js)
+            
+            if (newData.isComplete) {
+              buildAndStop(data.originalQuery, data.originalEvents, newData.subWorkflowsMetadata)
+            } else {
+              stay() using Option(newData)
+            }
+          case _ => failAndDie(new RuntimeException("Received unexpected response while waiting for sub workflow metadata."))
+        }
+      case _ => failAndDie(new RuntimeException("Failed to retrieve metadata for a sub workflow."))
+    }
+  }
+  
+  def failAndDie(reason: Throwable) = {
+    context.parent ! RequestComplete((StatusCodes.InternalServerError, APIResponse.error(reason)))
+    context stop self
+    stay()
+  }
+  
+  def buildAndStop(query: MetadataQuery, eventsList: Seq[MetadataEvent], expandedValues: Map[String, JsValue]) = {
+    context.parent ! RequestComplete((StatusCodes.OK, processMetadataEvents(query, eventsList, expandedValues)))
+    allDone
+  }
+  
+  def processMetadataResponse(query: MetadataQuery, eventsList: Seq[MetadataEvent]) = {
+    if (query.expandSubWorkflows) {
+      // Scan events for sub workflow ids
+      val subWorkflowIds = eventsList.collect({
+        case MetadataEvent(key, value, _) if key.key.endsWith(CallMetadataKeys.SubWorkflowId) => value map { _.value }
+      }).flatten
+
+      // If none is found just proceed to build metadata
+      if (subWorkflowIds.isEmpty) buildAndStop(query, eventsList, Map.empty)
+      else {
+        // Otherwise spin up a metadata builder actor for each sub workflow
+        subWorkflowIds foreach { subId =>
+          val subMetadataBuilder = context.actorOf(MetadataBuilderActor.props(serviceRegistryActor), PerRequestCreator.endpointActorName)
+          subMetadataBuilder ! GetMetadataQueryAction(query.copy(workflowId = WorkflowId.fromString(subId)))
+        }
+        goto(WaitingForSubWorkflows) using Option(MetadataBuilderActorData(query, eventsList, Map.empty, subWorkflowIds.size))
+      }
+    } else {
+      buildAndStop(query, eventsList, Map.empty)
+    }
+  }
 
-  def processMetadataResponse(query: MetadataQuery, eventsList: Seq[MetadataEvent]): JsObject = {
+  def processMetadataEvents(query: MetadataQuery, eventsList: Seq[MetadataEvent], expandedValues: Map[String, JsValue]): JsObject = {
     // Should we send back some message ? Or even fail the request instead ?
     if (eventsList.isEmpty) JsObject(Map.empty[String, JsValue])
     else {
       query match {
-        case MetadataQuery(w, _, _, _, _) => workflowMetadataResponse(w, eventsList)
-        case _ => MetadataBuilderActor.parse(eventsList)
+        case MetadataQuery(w, _, _, _, _, _) => workflowMetadataResponse(w, eventsList, includeCallsIfEmpty = true, expandedValues)
+        case _ => MetadataBuilderActor.parse(eventsList, expandedValues)
       }
     }
   }
@@ -268,7 +342,7 @@ class MetadataBuilderActor(serviceRegistryActor: ActorRef) extends LoggingFSM[Me
     ))
   }
 
-  private def workflowMetadataResponse(workflowId: WorkflowId, eventsList: Seq[MetadataEvent], includeCallsIfEmpty: Boolean = true) = {
-    JsObject(MetadataBuilderActor.parseWorkflowEvents(includeCallsIfEmpty)(eventsList).fields + ("id" -> JsString(workflowId.toString)))
+  private def workflowMetadataResponse(workflowId: WorkflowId, eventsList: Seq[MetadataEvent], includeCallsIfEmpty: Boolean, expandedValues: Map[String, JsValue]) = {
+    JsObject(MetadataBuilderActor.parseWorkflowEvents(includeCallsIfEmpty, expandedValues)(eventsList).fields + ("id" -> JsString(workflowId.toString)))
   }
 }
diff --git a/engine/src/test/scala/cromwell/ArrayOfArrayCoercionSpec.scala b/engine/src/test/scala/cromwell/ArrayOfArrayCoercionSpec.scala
index 00a530f31e7..5374409350e 100644
--- a/engine/src/test/scala/cromwell/ArrayOfArrayCoercionSpec.scala
+++ b/engine/src/test/scala/cromwell/ArrayOfArrayCoercionSpec.scala
@@ -6,14 +6,14 @@ import wdl4s.values.{WdlArray, WdlString}
 import cromwell.util.SampleWdl
 
 
-class ArrayOfArrayCoercionSpec extends CromwellTestkitSpec {
+class ArrayOfArrayCoercionSpec extends CromwellTestKitSpec {
   "A workflow that has an Array[Array[File]] input " should {
     "accept an Array[Array[String]] as the value for the input" in {
       runWdlAndAssertOutputs(
         sampleWdl = SampleWdl.ArrayOfArrays,
         eventFilter = EventFilter.info(pattern = "Workflow complete", occurrences = 1),
         expectedOutputs = Map(
-          "wf.subtask.concatenated" -> WdlArray(WdlArrayType(WdlStringType), Seq(
+          "wf_subtask_concatenated" -> WdlArray(WdlArrayType(WdlStringType), Seq(
             WdlString("foo\nbar\nbaz"),
             WdlString("third\nfourth")
           ))
diff --git a/engine/src/test/scala/cromwell/ArrayWorkflowSpec.scala b/engine/src/test/scala/cromwell/ArrayWorkflowSpec.scala
index 843796c1a8a..9c9708307e2 100644
--- a/engine/src/test/scala/cromwell/ArrayWorkflowSpec.scala
+++ b/engine/src/test/scala/cromwell/ArrayWorkflowSpec.scala
@@ -5,15 +5,15 @@ import java.nio.file.Files
 import akka.testkit._
 import better.files._
 import cromwell.util.SampleWdl
-import wdl4s.NamespaceWithWorkflow
+import wdl4s.{ImportResolver, WdlNamespaceWithWorkflow}
 import wdl4s.expression.NoFunctions
 import wdl4s.types.{WdlArrayType, WdlFileType, WdlStringType}
 import wdl4s.values.{WdlArray, WdlFile, WdlInteger, WdlString}
 
 
-class ArrayWorkflowSpec extends CromwellTestkitSpec {
+class ArrayWorkflowSpec extends CromwellTestKitSpec {
   val tmpDir = Files.createTempDirectory("ArrayWorkflowSpec")
-  val ns = NamespaceWithWorkflow.load(SampleWdl.ArrayLiteral(tmpDir).wdlSource(""))
+  val ns = WdlNamespaceWithWorkflow.load(SampleWdl.ArrayLiteral(tmpDir).wdlSource(""), Seq.empty[ImportResolver])
   val expectedArray = WdlArray(WdlArrayType(WdlFileType), Seq(WdlFile("f1"), WdlFile("f2"), WdlFile("f3")))
 
   "A task which contains a parameter " should {
@@ -22,9 +22,9 @@ class ArrayWorkflowSpec extends CromwellTestkitSpec {
         sampleWdl = SampleWdl.ArrayIO,
         eventFilter = EventFilter.info(pattern = "Workflow complete", occurrences = 1),
         expectedOutputs = Map(
-          "wf.count_lines.count" -> WdlInteger(3),
-          "wf.count_lines_array.count" -> WdlInteger(3),
-          "wf.serialize.contents" -> WdlString("str1\nstr2\nstr3")
+          "wf_count_lines_count" -> WdlInteger(3),
+          "wf_count_lines_array_count" -> WdlInteger(3),
+          "wf_serialize_contents" -> WdlString("str1\nstr2\nstr3")
         )
       )
     }
@@ -32,7 +32,7 @@ class ArrayWorkflowSpec extends CromwellTestkitSpec {
 
   "A static Array[File] declaration" should {
     "be a valid declaration" in {
-      val declaration = ns.workflow.declarations.find {_.name == "arr"}.getOrElse {
+      val declaration = ns.workflow.declarations.find {_.unqualifiedName == "arr"}.getOrElse {
         fail("Expected declaration 'arr' to be found")
       }
       val expression = declaration.expression.getOrElse {
@@ -47,14 +47,14 @@ class ArrayWorkflowSpec extends CromwellTestkitSpec {
       val catTask = ns.findTask("cat").getOrElse {
         fail("Expected to find task 'cat'")
       }
-      val command = catTask.instantiateCommand(Map("files" -> expectedArray), NoFunctions).getOrElse {
+      val command = catTask.instantiateCommand(catTask.inputsFromMap(Map("cat.files" -> expectedArray)), NoFunctions).getOrElse {
         fail("Expected instantiation to work")
       }
       command shouldEqual "cat -s f1 f2 f3"
     }
     "Coerce Array[String] to Array[File] when running the workflow" in {
       val outputs = Map(
-        "wf.cat.lines" -> WdlArray(WdlArrayType(WdlStringType), Seq(
+        "wf_cat_lines" -> WdlArray(WdlArrayType(WdlStringType), Seq(
             WdlString("line1"),
             WdlString("line2"),
             WdlString("line3"),
diff --git a/engine/src/test/scala/cromwell/CallCachingWorkflowSpec.scala b/engine/src/test/scala/cromwell/CallCachingWorkflowSpec.scala
index cea47fe8d1c..202dcecf152 100644
--- a/engine/src/test/scala/cromwell/CallCachingWorkflowSpec.scala
+++ b/engine/src/test/scala/cromwell/CallCachingWorkflowSpec.scala
@@ -11,7 +11,7 @@ import wdl4s.types.{WdlArrayType, WdlIntegerType, WdlStringType}
 import wdl4s.values.{WdlArray, WdlFile, WdlInteger, WdlString}
 
 
-class CallCachingWorkflowSpec extends CromwellTestkitSpec {
+class CallCachingWorkflowSpec extends CromwellTestKitSpec {
   def cacheHitMessageForCall(name: String) = s"Call Caching: Cache hit. Using UUID\\(.{8}\\):$name\\.*"
 
   val expectedOutputs = Map(
diff --git a/engine/src/test/scala/cromwell/CopyWorkflowOutputsSpec.scala b/engine/src/test/scala/cromwell/CopyWorkflowOutputsSpec.scala
index c43346330c4..b6465a8acaa 100644
--- a/engine/src/test/scala/cromwell/CopyWorkflowOutputsSpec.scala
+++ b/engine/src/test/scala/cromwell/CopyWorkflowOutputsSpec.scala
@@ -9,7 +9,7 @@ import org.scalatest.prop.Tables.Table
 
 import scala.language.postfixOps
 
-class CopyWorkflowOutputsSpec extends CromwellTestkitSpec {
+class CopyWorkflowOutputsSpec extends CromwellTestKitSpec {
 
   "CopyWorkflowOutputsCall" should {
     "copy workflow outputs" in {
@@ -31,7 +31,7 @@ class CopyWorkflowOutputsSpec extends CromwellTestkitSpec {
           pattern = "transition from FinalizingWorkflowState to WorkflowSucceededState", occurrences = 1),
         runtime = "",
         workflowOptions = s""" { "final_workflow_outputs_dir": "$tmpDir" } """,
-        expectedOutputs = Seq("A.out", "A.out2", "B.outs") map { o => ("wfoutputs." + o) -> CromwellTestkitSpec.AnyValueIsFine } toMap,
+        expectedOutputs = Seq("A_out", "A_out2", "B_outs") map { o => ("wfoutputs_" + o) -> CromwellTestKitSpec.AnyValueIsFine } toMap,
         allowOtherOutputs = false
       )
 
@@ -64,7 +64,7 @@ class CopyWorkflowOutputsSpec extends CromwellTestkitSpec {
           pattern = "transition from FinalizingWorkflowState to WorkflowSucceededState", occurrences = 1),
         runtime = "",
         workflowOptions = s""" { "final_workflow_outputs_dir": "$tmpDir" } """,
-        expectedOutputs = Map("wfoutputs.A.outs" -> CromwellTestkitSpec.AnyValueIsFine),
+        expectedOutputs = Map("wfoutputs_A_outs" -> CromwellTestKitSpec.AnyValueIsFine),
         allowOtherOutputs = false
       )
 
diff --git a/engine/src/test/scala/cromwell/CromwellTestkitSpec.scala b/engine/src/test/scala/cromwell/CromwellTestKitSpec.scala
similarity index 94%
rename from engine/src/test/scala/cromwell/CromwellTestkitSpec.scala
rename to engine/src/test/scala/cromwell/CromwellTestKitSpec.scala
index 090d94fd160..c30488027d9 100644
--- a/engine/src/test/scala/cromwell/CromwellTestkitSpec.scala
+++ b/engine/src/test/scala/cromwell/CromwellTestKitSpec.scala
@@ -2,12 +2,13 @@ package cromwell
 
 import java.nio.file.Paths
 import java.util.UUID
+import java.util.concurrent.atomic.AtomicInteger
 
 import akka.actor.{Actor, ActorRef, ActorSystem, Props, Terminated}
 import akka.pattern.ask
 import akka.testkit._
 import com.typesafe.config.{Config, ConfigFactory}
-import cromwell.CromwellTestkitSpec._
+import cromwell.CromwellTestKitSpec._
 import cromwell.backend._
 import cromwell.core._
 import cromwell.engine.backend.BackendConfigurationEntry
@@ -21,6 +22,7 @@ import cromwell.server.{CromwellRootActor, CromwellSystem}
 import cromwell.services.ServiceRegistryActor
 import cromwell.services.metadata.MetadataQuery
 import cromwell.services.metadata.MetadataService._
+import cromwell.subworkflowstore.EmptySubWorkflowStoreActor
 import cromwell.util.SampleWdl
 import cromwell.webservice.PerRequest.RequestComplete
 import cromwell.webservice.metadata.MetadataBuilderActor
@@ -30,7 +32,7 @@ import org.scalatest.time.{Millis, Seconds, Span}
 import org.scalatest.{BeforeAndAfterAll, Matchers, OneInstancePerTest, WordSpecLike}
 import spray.http.StatusCode
 import spray.json._
-import wdl4s.Call
+import wdl4s.TaskCall
 import wdl4s.expression.{NoFunctions, WdlStandardLibraryFunctions}
 import wdl4s.types._
 import wdl4s.values._
@@ -43,7 +45,7 @@ import scala.util.matching.Regex
 case class TestBackendLifecycleActorFactory(configurationDescriptor: BackendConfigurationDescriptor)
   extends BackendLifecycleActorFactory {
   override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                                calls: Seq[Call],
+                                                calls: Set[TaskCall],
                                                 serviceRegistryActor: ActorRef): Option[Props] = None
 
   override def jobExecutionActorProps(jobDescriptor: BackendJobDescriptor,
@@ -63,7 +65,7 @@ case class TestBackendLifecycleActorFactory(configurationDescriptor: BackendConf
 case class OutputNotFoundException(outputFqn: String, actualOutputs: String) extends RuntimeException(s"Expected output $outputFqn was not found in: '$actualOutputs'")
 case class LogNotFoundException(log: String) extends RuntimeException(s"Expected log $log was not found")
 
-object CromwellTestkitSpec {
+object CromwellTestKitSpec {
   val ConfigText =
     """
       |akka {
@@ -121,9 +123,11 @@ object CromwellTestkitSpec {
 
   val TimeoutDuration = 60 seconds
 
+  private val testWorkflowManagerSystemCount = new AtomicInteger()
+
   class TestWorkflowManagerSystem extends CromwellSystem {
-    override protected def systemName: String = "test-system"
-    override protected def newActorSystem() = ActorSystem(systemName, ConfigFactory.parseString(CromwellTestkitSpec.ConfigText))
+    override protected def systemName: String = "test-system-" + testWorkflowManagerSystemCount.incrementAndGet()
+    override protected def newActorSystem() = ActorSystem(systemName, ConfigFactory.parseString(CromwellTestKitSpec.ConfigText))
     /**
       * Do NOT shut down the test actor system inside the normal flow.
       * The actor system will be externally shutdown outside the block.
@@ -134,18 +138,6 @@ object CromwellTestkitSpec {
     def shutdownTestActorSystem() = super.shutdownActorSystem()
   }
 
-  /**
-    * Loans a test actor system. NOTE: This should be run OUTSIDE of a wait block, never within one.
-    */
-  def withTestWorkflowManagerSystem[T](block: CromwellSystem => T): T = {
-    val testWorkflowManagerSystem = new CromwellTestkitSpec.TestWorkflowManagerSystem
-    try {
-      block(testWorkflowManagerSystem)
-    } finally {
-      TestKit.shutdownActorSystem(testWorkflowManagerSystem.actorSystem, TimeoutDuration)
-    }
-  }
-
   /**
    * Wait for exactly one occurrence of the specified info pattern in the specified block.  The block is in its own
    * parameter list for usage syntax reasons.
@@ -264,9 +256,11 @@ object CromwellTestkitSpec {
   }
 
   class TestCromwellRootActor(config: Config) extends CromwellRootActor {
+    override val serverMode = true
     override lazy val serviceRegistryActor = ServiceRegistryActorInstance
     override lazy val workflowStore = new InMemoryWorkflowStore
-    def submitWorkflow(sources: WorkflowSourceFiles): WorkflowId = {
+    override val abortJobsOnTerminate = false
+    def submitWorkflow(sources: WorkflowSourceFilesWithoutImports): WorkflowId = {
       val submitMessage = WorkflowStoreActor.SubmitWorkflow(sources)
       val result = Await.result(workflowStoreActor.ask(submitMessage)(TimeoutDuration), Duration.Inf).asInstanceOf[WorkflowSubmittedToStore].workflowId
       workflowManagerActor ! RetrieveNewWorkflows
@@ -275,12 +269,12 @@ object CromwellTestkitSpec {
   }
 }
 
-abstract class CromwellTestkitSpec(val twms: TestWorkflowManagerSystem = new CromwellTestkitSpec.TestWorkflowManagerSystem()) extends TestKit(twms.actorSystem)
+abstract class CromwellTestKitSpec(val twms: TestWorkflowManagerSystem = new CromwellTestKitSpec.TestWorkflowManagerSystem()) extends TestKit(twms.actorSystem)
   with DefaultTimeout with ImplicitSender with WordSpecLike with Matchers with BeforeAndAfterAll with ScalaFutures with OneInstancePerTest with Eventually {
 
   override protected def afterAll() = { twms.shutdownTestActorSystem(); () }
 
-  implicit val defaultPatience = PatienceConfig(timeout = Span(30, Seconds), interval = Span(100, Millis))
+  implicit val defaultPatience = PatienceConfig(timeout = Span(200, Seconds), interval = Span(1000, Millis))
   implicit val ec = system.dispatcher
 
   val dummyServiceRegistryActor = system.actorOf(Props.empty)
@@ -336,7 +330,7 @@ abstract class CromwellTestkitSpec(val twms: TestWorkflowManagerSystem = new Cro
              config: Config = DefaultConfig,
              patienceConfig: PatienceConfig = defaultPatience)(implicit ec: ExecutionContext): Map[FullyQualifiedName, WdlValue] = {
     val rootActor = buildCromwellRootActor(config)
-    val sources = WorkflowSourceFiles(sampleWdl.wdlSource(runtime), sampleWdl.wdlJson, workflowOptions)
+    val sources = WorkflowSourceFilesWithoutImports(sampleWdl.wdlSource(runtime), sampleWdl.wdlJson, workflowOptions)
     val workflowId = rootActor.underlyingActor.submitWorkflow(sources)
     eventually { verifyWorkflowState(rootActor.underlyingActor.serviceRegistryActor, workflowId, terminalState) } (config = patienceConfig, pos = implicitly[org.scalactic.source.Position])
     val outcome = getWorkflowOutputsFromMetadata(workflowId, rootActor.underlyingActor.serviceRegistryActor)
@@ -382,7 +376,7 @@ abstract class CromwellTestkitSpec(val twms: TestWorkflowManagerSystem = new Cro
 
   def getWorkflowMetadata(workflowId: WorkflowId, serviceRegistryActor: ActorRef, key: Option[String] = None)(implicit ec: ExecutionContext): JsObject = {
     // MetadataBuilderActor sends its response to context.parent, so we can't just use an ask to talk to it here
-    val message = GetMetadataQueryAction(MetadataQuery(workflowId, None, key, None, None))
+    val message = GetMetadataQueryAction(MetadataQuery(workflowId, None, key, None, None, expandSubWorkflows = false))
     val parentProbe = TestProbe()
 
     TestActorRef(MetadataBuilderActor.props(serviceRegistryActor), parentProbe.ref, s"MetadataActor-${UUID.randomUUID()}") ! message
@@ -444,6 +438,10 @@ class AlwaysHappyJobStoreActor extends Actor {
   }
 }
 
+object AlwaysHappySubWorkflowStoreActor {
+  def props: Props = Props(new EmptySubWorkflowStoreActor)
+}
+
 object AlwaysHappyJobStoreActor {
   def props: Props = Props(new AlwaysHappyJobStoreActor)
 }
diff --git a/engine/src/test/scala/cromwell/DeclarationWorkflowSpec.scala b/engine/src/test/scala/cromwell/DeclarationWorkflowSpec.scala
index d829b84eb90..aeca4777f11 100644
--- a/engine/src/test/scala/cromwell/DeclarationWorkflowSpec.scala
+++ b/engine/src/test/scala/cromwell/DeclarationWorkflowSpec.scala
@@ -1,7 +1,7 @@
 package cromwell
 
 import wdl4s.types.{WdlFileType, WdlStringType}
-import wdl4s.{NamespaceWithWorkflow, WorkflowInput}
+import wdl4s.{ImportResolver, WdlNamespaceWithWorkflow, WorkflowInput}
 import cromwell.util.SampleWdl
 import org.scalatest.{Matchers, WordSpecLike}
 
@@ -9,11 +9,11 @@ import org.scalatest.{Matchers, WordSpecLike}
 class DeclarationWorkflowSpec extends Matchers with WordSpecLike {
   "A workflow with declarations in it" should {
     "compute inputs properly" in {
-      NamespaceWithWorkflow.load(SampleWdl.DeclarationsWorkflow.wdlSource(runtime="")).workflow.inputs shouldEqual Map(
-        "two_step.cat.file" -> WorkflowInput("two_step.cat.file", WdlFileType, postfixQuantifier = None),
-        "two_step.cgrep.str_decl" -> WorkflowInput("two_step.cgrep.str_decl", WdlStringType, postfixQuantifier = None),
-        "two_step.cgrep.pattern" -> WorkflowInput("two_step.cgrep.pattern", WdlStringType, postfixQuantifier = None),
-        "two_step.flags_suffix" -> WorkflowInput("two_step.flags_suffix", WdlStringType, postfixQuantifier = None)
+      WdlNamespaceWithWorkflow.load(SampleWdl.DeclarationsWorkflow.wdlSource(runtime=""), Seq.empty[ImportResolver]).workflow.inputs shouldEqual Map(
+        "two_step.cat.file" -> WorkflowInput("two_step.cat.file", WdlFileType),
+        "two_step.cgrep.str_decl" -> WorkflowInput("two_step.cgrep.str_decl", WdlStringType),
+        "two_step.cgrep.pattern" -> WorkflowInput("two_step.cgrep.pattern", WdlStringType),
+        "two_step.flags_suffix" -> WorkflowInput("two_step.flags_suffix", WdlStringType)
       )
     }
   }
diff --git a/engine/src/test/scala/cromwell/FilePassingWorkflowSpec.scala b/engine/src/test/scala/cromwell/FilePassingWorkflowSpec.scala
index 1aaafaf2fa1..40eb03624bc 100644
--- a/engine/src/test/scala/cromwell/FilePassingWorkflowSpec.scala
+++ b/engine/src/test/scala/cromwell/FilePassingWorkflowSpec.scala
@@ -6,19 +6,19 @@ import wdl4s.values.{WdlFile, WdlString}
 
 import scala.concurrent.duration._
 
-class FilePassingWorkflowSpec extends CromwellTestkitSpec {
+class FilePassingWorkflowSpec extends CromwellTestKitSpec {
   "A workflow that passes files between tasks" should {
     "pass files properly" in {
       runWdlAndAssertOutputs(
         sampleWdl = SampleWdl.FilePassingWorkflow,
         EventFilter.info(pattern = "Workflow complete", occurrences = 1),
         expectedOutputs = Map(
-          "file_passing.a.out" -> WdlFile("out"),
-          "file_passing.a.out_interpolation" -> WdlFile("out"),
-          "file_passing.a.contents" -> WdlString("foo bar baz"),
-          "file_passing.b.out" -> WdlFile("out"),
-          "file_passing.b.out_interpolation" -> WdlFile("out"),
-          "file_passing.b.contents" -> WdlString("foo bar baz")
+          "file_passing_a_out" -> WdlFile("out"),
+          "file_passing_a_out_interpolation" -> WdlFile("out"),
+          "file_passing_a_contents" -> WdlString("foo bar baz"),
+          "file_passing_b_out" -> WdlFile("out"),
+          "file_passing_b_out_interpolation" -> WdlFile("out"),
+          "file_passing_b_contents" -> WdlString("foo bar baz")
         ),
         patienceConfig = PatienceConfig(2.minutes.dilated)
       )
diff --git a/engine/src/test/scala/cromwell/MapWorkflowSpec.scala b/engine/src/test/scala/cromwell/MapWorkflowSpec.scala
index 9a00c115eb8..f13b022c590 100644
--- a/engine/src/test/scala/cromwell/MapWorkflowSpec.scala
+++ b/engine/src/test/scala/cromwell/MapWorkflowSpec.scala
@@ -3,17 +3,17 @@ package cromwell
 import akka.testkit._
 import better.files._
 import cromwell.util.SampleWdl
-import wdl4s.NamespaceWithWorkflow
+import wdl4s.{ImportResolver, WdlNamespaceWithWorkflow}
 import wdl4s.expression.{NoFunctions, WdlFunctions}
 import wdl4s.types.{WdlFileType, WdlIntegerType, WdlMapType, WdlStringType}
 import wdl4s.values._
 
 import scala.util.{Success, Try}
 
-class MapWorkflowSpec extends CromwellTestkitSpec {
+class MapWorkflowSpec extends CromwellTestKitSpec {
   private val pwd = File(".")
   private val sampleWdl = SampleWdl.MapLiteral(pwd.path)
-  val ns = NamespaceWithWorkflow.load(sampleWdl.wdlSource(""))
+  val ns = WdlNamespaceWithWorkflow.load(sampleWdl.wdlSource(""), Seq.empty[ImportResolver])
   val expectedMap = WdlMap(WdlMapType(WdlFileType, WdlStringType), Map(
     WdlFile("f1") -> WdlString("alice"),
     WdlFile("f2") -> WdlString("bob"),
@@ -28,12 +28,12 @@ class MapWorkflowSpec extends CromwellTestkitSpec {
         sampleWdl = sampleWdl,
         EventFilter.info(pattern = "Starting calls: wf.read_map:NA:1, wf.write_map:NA:1", occurrences = 1),
         expectedOutputs = Map(
-          "wf.read_map.out_map" -> WdlMap(WdlMapType(WdlStringType, WdlIntegerType), Map(
+          "wf_read_map_out_map" -> WdlMap(WdlMapType(WdlStringType, WdlIntegerType), Map(
             WdlString("x") -> WdlInteger(500),
             WdlString("y") -> WdlInteger(600),
             WdlString("z") -> WdlInteger(700)
           )),
-          "wf.write_map.contents" -> WdlString("f1\talice\nf2\tbob\nf3\tchuck")
+          "wf_write_map_contents" -> WdlString("f1\talice\nf2\tbob\nf3\tchuck")
         )
       )
       sampleWdl.cleanup()
@@ -42,7 +42,7 @@ class MapWorkflowSpec extends CromwellTestkitSpec {
 
   "A static Map[File, String] declaration" should {
     "be a valid declaration" in {
-      val declaration = ns.workflow.declarations.find {_.name == "map"}.getOrElse {
+      val declaration = ns.workflow.declarations.find {_.unqualifiedName == "map"}.getOrElse {
         fail("Expected declaration 'map' to be found")
       }
       val expression = declaration.expression.getOrElse {
@@ -64,7 +64,7 @@ class MapWorkflowSpec extends CromwellTestkitSpec {
           case _ => throw new UnsupportedOperationException("Only write_map should be called")
         }
       }
-      val command = writeMapTask.instantiateCommand(Map("file_to_name" -> expectedMap), new CannedFunctions).getOrElse {
+      val command = writeMapTask.instantiateCommand(writeMapTask.inputsFromMap(Map("file_to_name" -> expectedMap)), new CannedFunctions).getOrElse {
         fail("Expected instantiation to work")
       }
       command shouldEqual "cat /test/map/path"
@@ -75,7 +75,7 @@ class MapWorkflowSpec extends CromwellTestkitSpec {
         sampleWdl,
         eventFilter = EventFilter.info(pattern = "Starting calls: wf.read_map:NA:1, wf.write_map:NA:1", occurrences = 1),
         expectedOutputs = Map(
-          "wf.read_map.out_map" -> WdlMap(WdlMapType(WdlStringType, WdlIntegerType), Map(
+          "wf_read_map_out_map" -> WdlMap(WdlMapType(WdlStringType, WdlIntegerType), Map(
             WdlString("x") -> WdlInteger(500),
             WdlString("y") -> WdlInteger(600),
             WdlString("z") -> WdlInteger(700)
diff --git a/engine/src/test/scala/cromwell/MetadataWatchActor.scala b/engine/src/test/scala/cromwell/MetadataWatchActor.scala
index 691c4efc58e..c0c29444274 100644
--- a/engine/src/test/scala/cromwell/MetadataWatchActor.scala
+++ b/engine/src/test/scala/cromwell/MetadataWatchActor.scala
@@ -1,7 +1,7 @@
 package cromwell
 
 import akka.actor.{Actor, Props}
-import cromwell.services.metadata.{MetadataEvent, MetadataJobKey, MetadataString}
+import cromwell.services.metadata.{MetadataEvent, MetadataJobKey, MetadataString, MetadataValue}
 import cromwell.services.metadata.MetadataService.PutMetadataAction
 import MetadataWatchActor._
 
@@ -32,26 +32,36 @@ object MetadataWatchActor {
 
   trait Matcher {
     def matches(events: Traversable[MetadataEvent]): Boolean
+    private var _nearMisses: List[String] = List.empty
+    protected def addNearMissInfo(miss: String) = _nearMisses :+= miss
+    def nearMissInformation = _nearMisses
+
+    def checkMetadataValueContains(key: String, actual: MetadataValue, expected: String): Boolean = {
+      val result = actual.value.contains(expected)
+      if (!result) addNearMissInfo(s"Key $key had unexpected value.\nActual value: ${actual.value}\n\nDid not contain: $expected")
+      result
+    }
   }
 
   def metadataKeyAttemptChecker(attempt: Int): Option[MetadataJobKey] => Boolean = {
     case Some(jobKey) => jobKey.attempt == attempt
     case None => false
   }
+
   final case class JobKeyMetadataKeyAndValueContainStringMatcher(jobKeyCheck: Option[MetadataJobKey] => Boolean, key: String, value: String) extends Matcher {
     def matches(events: Traversable[MetadataEvent]): Boolean = {
-      events.exists(e => e.key.key.contains(key) && jobKeyCheck(e.key.jobKey) && e.value.exists { v => v.valueType == MetadataString && v.value.contains(value) })
+      events.exists(e => e.key.key.contains(key) && jobKeyCheck(e.key.jobKey) && e.value.exists { v => v.valueType == MetadataString && checkMetadataValueContains(e.key.key, v, value) })
     }
   }
 
   abstract class KeyMatchesRegexAndValueContainsStringMatcher(keyTemplate: String, value: String) extends Matcher {
     val templateRegex = keyTemplate.r
     def matches(events: Traversable[MetadataEvent]): Boolean = {
-      events.exists(e => templateRegex.findFirstIn(e.key.key).isDefined && e.value.exists { v => v.value.contains(value) })
+      events.exists(e => templateRegex.findFirstIn(e.key.key).isDefined &&
+        e.value.exists { v => checkMetadataValueContains(e.key.key, v, value) })
     }
   }
 
   val failurePattern = """failures\[\d*\].message"""
-  final case class FailureMatcher(value: String) extends KeyMatchesRegexAndValueContainsStringMatcher(failurePattern, value) {
-  }
+  final case class FailureMatcher(value: String) extends KeyMatchesRegexAndValueContainsStringMatcher(failurePattern, value) { }
 }
diff --git a/engine/src/test/scala/cromwell/MultipleFilesWithSameNameWorkflowSpec.scala b/engine/src/test/scala/cromwell/MultipleFilesWithSameNameWorkflowSpec.scala
index f0b7a70af0f..4fc24c56e23 100644
--- a/engine/src/test/scala/cromwell/MultipleFilesWithSameNameWorkflowSpec.scala
+++ b/engine/src/test/scala/cromwell/MultipleFilesWithSameNameWorkflowSpec.scala
@@ -5,15 +5,15 @@ import cromwell.util.SampleWdl
 import wdl4s.values.WdlString
 
 
-class MultipleFilesWithSameNameWorkflowSpec extends CromwellTestkitSpec {
+class MultipleFilesWithSameNameWorkflowSpec extends CromwellTestKitSpec {
   "A workflow with two file inputs that have the same name" should {
     "not clobber one file with the contents of another" in {
       runWdlAndAssertOutputs(
         sampleWdl = SampleWdl.FileClobber,
         EventFilter.info(pattern = "Starting calls: two.x:NA:1, two.y:NA:1", occurrences = 1),
         expectedOutputs = Map(
-          "two.x.out" -> WdlString("first file.txt"),
-          "two.y.out" -> WdlString("second file.txt")
+          "two_x_out" -> WdlString("first file.txt"),
+          "two_y_out" -> WdlString("second file.txt")
         )
       )
     }
diff --git a/engine/src/test/scala/cromwell/OptionalParamWorkflowSpec.scala b/engine/src/test/scala/cromwell/OptionalParamWorkflowSpec.scala
index 919008315bc..73347b7944a 100644
--- a/engine/src/test/scala/cromwell/OptionalParamWorkflowSpec.scala
+++ b/engine/src/test/scala/cromwell/OptionalParamWorkflowSpec.scala
@@ -22,20 +22,20 @@ class OptionalParamWorkflowSpec extends Matchers with WordSpecLike {
          |  call find
          |}
        """.stripMargin
-      val ns = WdlNamespace.load(wf)
+      val ns = WdlNamespace.loadUsingSource(wf, None, None)
       val findTask = ns.findTask("find") getOrElse {
         fail("Expected to find task 'find'")
       }
 
-      val instantiateWithoutValue = findTask.instantiateCommand(Map("root" -> WdlFile("src")), NoFunctions) getOrElse {
+      val instantiateWithoutValue = findTask.instantiateCommand(findTask.inputsFromMap(Map("find.root" -> WdlFile("src"))), NoFunctions) getOrElse {
         fail("Expected instantiation to work")
       }
       instantiateWithoutValue shouldEqual "find src"
 
-      val instantiateWithValue = findTask.instantiateCommand(Map(
-        "root" -> WdlFile("src"),
-        "pattern" -> WdlString("*.java")
-      ), NoFunctions).getOrElse {fail("Expected instantiation to work")}
+      val instantiateWithValue = findTask.instantiateCommand(findTask.inputsFromMap(Map(
+        "find.root" -> WdlFile("src"),
+        "find.pattern" -> WdlString("*.java")
+      )), NoFunctions).getOrElse {fail("Expected instantiation to work")}
       instantiateWithValue shouldEqual "find src -name *.java"
     }
   }
diff --git a/engine/src/test/scala/cromwell/PostfixQuantifierWorkflowSpec.scala b/engine/src/test/scala/cromwell/PostfixQuantifierWorkflowSpec.scala
index 8530dd6d29c..c72d98758d8 100644
--- a/engine/src/test/scala/cromwell/PostfixQuantifierWorkflowSpec.scala
+++ b/engine/src/test/scala/cromwell/PostfixQuantifierWorkflowSpec.scala
@@ -5,27 +5,27 @@ import wdl4s.values.WdlString
 import cromwell.util.SampleWdl
 
 
-class PostfixQuantifierWorkflowSpec extends CromwellTestkitSpec {
+class PostfixQuantifierWorkflowSpec extends CromwellTestKitSpec {
   "A task which contains a parameter with a zero-or-more postfix quantifier" should {
     "accept an array of size 3" in {
       runWdlAndAssertOutputs(
         sampleWdl = SampleWdl.ZeroOrMorePostfixQuantifierWorkflowWithArrayInput,
         EventFilter.info(pattern = "Starting calls: postfix.hello", occurrences = 1),
-        expectedOutputs = Map("postfix.hello.greeting" -> WdlString("hello alice,bob,charles"))
+        expectedOutputs = Map("postfix_hello_greeting" -> WdlString("hello alice,bob,charles"))
       )
     }
     "accept an array of size 1" in {
       runWdlAndAssertOutputs(
         sampleWdl = SampleWdl.ZeroOrMorePostfixQuantifierWorkflowWithOneElementArrayInput,
         EventFilter.info(pattern = "Starting calls: postfix.hello", occurrences = 1),
-        expectedOutputs = Map("postfix.hello.greeting" -> WdlString("hello alice"))
+        expectedOutputs = Map("postfix_hello_greeting" -> WdlString("hello alice"))
       )
     }
     "accept an array of size 0" in {
       runWdlAndAssertOutputs(
         sampleWdl = SampleWdl.ZeroOrMorePostfixQuantifierWorkflowWithZeroElementArrayInput,
         EventFilter.info(pattern = "Starting calls: postfix.hello", occurrences = 1),
-        expectedOutputs = Map("postfix.hello.greeting" -> WdlString("hello"))
+        expectedOutputs = Map("postfix_hello_greeting" -> WdlString("hello"))
       )
     }
   }
@@ -35,14 +35,14 @@ class PostfixQuantifierWorkflowSpec extends CromwellTestkitSpec {
       runWdlAndAssertOutputs(
         sampleWdl = SampleWdl.OneOrMorePostfixQuantifierWorkflowWithArrayInput,
         EventFilter.info(pattern = "Starting calls: postfix.hello", occurrences = 1),
-        expectedOutputs = Map("postfix.hello.greeting" -> WdlString("hello alice,bob,charles"))
+        expectedOutputs = Map("postfix_hello_greeting" -> WdlString("hello alice,bob,charles"))
       )
     }
     "accept a scalar for the value" in {
       runWdlAndAssertOutputs(
         sampleWdl = SampleWdl.OneOrMorePostfixQuantifierWorkflowWithScalarInput,
         EventFilter.info(pattern = "Starting calls: postfix.hello", occurrences = 1),
-        expectedOutputs = Map("postfix.hello.greeting" -> WdlString("hello alice"))
+        expectedOutputs = Map("postfix_hello_greeting" -> WdlString("hello alice"))
       )
     }
   }
diff --git a/engine/src/test/scala/cromwell/RestartWorkflowSpec.scala b/engine/src/test/scala/cromwell/RestartWorkflowSpec.scala
index 6b706fbc6ea..5db1f3ebe3f 100644
--- a/engine/src/test/scala/cromwell/RestartWorkflowSpec.scala
+++ b/engine/src/test/scala/cromwell/RestartWorkflowSpec.scala
@@ -6,11 +6,11 @@ import cromwell.core.Tags._
 import cromwell.core._
 import cromwell.engine.workflow.WorkflowDescriptorBuilder
 
-class RestartWorkflowSpec extends CromwellTestkitSpec with WorkflowDescriptorBuilder {
+class RestartWorkflowSpec extends CromwellTestKitSpec with WorkflowDescriptorBuilder {
 
-  val actorSystem = ActorSystem("RestartWorkflowSpec", ConfigFactory.parseString(CromwellTestkitSpec.ConfigText))
+  val actorSystem = ActorSystem("RestartWorkflowSpec", ConfigFactory.parseString(CromwellTestKitSpec.ConfigText))
   //val localBackend = new OldStyleLocalBackend(CromwellTestkitSpec.DefaultLocalBackendConfigEntry, actorSystem)
-  val sources = WorkflowSourceFiles(
+  val sources = WorkflowSourceFilesWithoutImports(
     wdlSource="""task a {command{}}
                 |workflow w {
                 |  call a
diff --git a/engine/src/test/scala/cromwell/ScatterWorkflowSpec.scala b/engine/src/test/scala/cromwell/ScatterWorkflowSpec.scala
index 0d8847a27b2..c1ca1ad9e94 100644
--- a/engine/src/test/scala/cromwell/ScatterWorkflowSpec.scala
+++ b/engine/src/test/scala/cromwell/ScatterWorkflowSpec.scala
@@ -6,15 +6,15 @@ import wdl4s.types.{WdlArrayType, WdlFileType, WdlIntegerType, WdlStringType}
 import wdl4s.values.{WdlArray, WdlFile, WdlInteger, WdlString}
 import cromwell.util.SampleWdl
 
-class ScatterWorkflowSpec extends CromwellTestkitSpec {
+class ScatterWorkflowSpec extends CromwellTestKitSpec {
   "A workflow with a stand-alone scatter block in it" should {
     "run properly" in {
       runWdlAndAssertOutputs(
         sampleWdl = SampleWdl.SimpleScatterWdl,
         eventFilter = EventFilter.info(pattern = "Workflow complete", occurrences = 1),
         expectedOutputs = Map(
-          "scatter0.outside_scatter.out" -> WdlInteger(8000),
-          "scatter0.inside_scatter.out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(1, 2, 3, 4, 5).map(WdlInteger(_)))
+          "scatter0_outside_scatter_out" -> WdlInteger(8000),
+          "scatter0_inside_scatter_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(1, 2, 3, 4, 5).map(WdlInteger(_)))
         )
       )
     }
@@ -25,11 +25,11 @@ class ScatterWorkflowSpec extends CromwellTestkitSpec {
         sampleWdl = new SampleWdl.ScatterWdl,
         eventFilter = EventFilter.info(pattern = "Workflow complete", occurrences = 1),
         expectedOutputs = Map(
-          "w.E.E_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(9, 9, 9, 9, 9, 9).map(WdlInteger(_))),
-          "w.C.C_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(400, 500, 600, 800, 600, 500).map(WdlInteger(_))),
-          "w.A.A_out" -> WdlArray(WdlArrayType(WdlStringType), Seq("jeff", "chris", "miguel", "thibault", "khalid", "scott").map(WdlString)),
-          "w.D.D_out" -> WdlInteger(34),
-          "w.B.B_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(4, 5, 6, 8, 6, 5).map(WdlInteger(_)))
+          "w_E_E_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(9, 9, 9, 9, 9, 9).map(WdlInteger(_))),
+          "w_C_C_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(400, 500, 600, 800, 600, 500).map(WdlInteger(_))),
+          "w_A_A_out" -> WdlArray(WdlArrayType(WdlStringType), Seq("jeff", "chris", "miguel", "thibault", "khalid", "ruchi").map(WdlString)),
+          "w_D_D_out" -> WdlInteger(34),
+          "w_B_B_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(4, 5, 6, 8, 6, 5).map(WdlInteger(_)))
         )
       )
     }
@@ -40,12 +40,12 @@ class ScatterWorkflowSpec extends CromwellTestkitSpec {
         sampleWdl = SampleWdl.SiblingsScatterWdl,
         eventFilter = EventFilter.info(pattern = "Workflow complete", occurrences = 1),
         expectedOutputs = Map(
-          "w.E.E_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(9, 9, 9, 9, 9, 9).map(WdlInteger(_))),
-          "w.F.B_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(4, 5, 6, 8, 6, 5).map(WdlInteger(_))),
-          "w.C.C_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(400, 500, 600, 800, 600, 500).map(WdlInteger(_))),
-          "w.A.A_out" -> WdlArray(WdlArrayType(WdlStringType), Seq("jeff", "chris", "miguel", "thibault", "khalid", "scott").map(WdlString)),
-          "w.D.D_out" -> WdlInteger(34),
-          "w.B.B_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(4, 5, 6, 8, 6, 5).map(WdlInteger(_)))
+          "w_E_E_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(9, 9, 9, 9, 9, 9).map(WdlInteger(_))),
+          "w_F_B_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(4, 5, 6, 8, 6, 5).map(WdlInteger(_))),
+          "w_C_C_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(400, 500, 600, 800, 600, 500).map(WdlInteger(_))),
+          "w_A_A_out" -> WdlArray(WdlArrayType(WdlStringType), Seq("jeff", "chris", "miguel", "thibault", "khalid", "ruchi").map(WdlString)),
+          "w_D_D_out" -> WdlInteger(34),
+          "w_B_B_out" -> WdlArray(WdlArrayType(WdlIntegerType), Seq(4, 5, 6, 8, 6, 5).map(WdlInteger(_)))
         )
       )
     }
@@ -57,9 +57,9 @@ class ScatterWorkflowSpec extends CromwellTestkitSpec {
         sampleWdl = SampleWdl.PrepareScatterGatherWdl(),
         eventFilter = EventFilter.info(pattern = "Workflow complete", occurrences = 1),
         expectedOutputs = Map(
-          "sc_test.do_gather.sum" -> WdlInteger(11),
-          "sc_test.do_prepare.split_files" -> WdlArray(WdlArrayType(WdlFileType), Seq("temp_aa", "temp_ab", "temp_ac", "temp_ad").map(WdlFile(_))),
-          "sc_test.do_scatter.count_file" -> WdlArray(WdlArrayType(WdlFileType), (1 to 4).map(_ => WdlFile("output.txt")))
+          "sc_test_do_gather_sum" -> WdlInteger(11),
+          "sc_test_do_prepare_split_files" -> WdlArray(WdlArrayType(WdlFileType), Seq("temp_aa", "temp_ab", "temp_ac", "temp_ad").map(WdlFile(_))),
+          "sc_test_do_scatter_count_file" -> WdlArray(WdlArrayType(WdlFileType), (1 to 4).map(_ => WdlFile("output.txt")))
         )
       )
     }
@@ -74,9 +74,9 @@ class ScatterWorkflowSpec extends CromwellTestkitSpec {
                   |}
                   """.stripMargin,
         expectedOutputs = Map(
-          "sc_test.do_gather.sum" -> WdlInteger(11),
-          "sc_test.do_prepare.split_files" -> WdlArray(WdlArrayType(WdlFileType), Seq("temp_aa", "temp_ab", "temp_ac", "temp_ad").map(WdlFile(_))),
-          "sc_test.do_scatter.count_file" -> WdlArray(WdlArrayType(WdlFileType), (1 to 4).map(_ => WdlFile("output.txt")))
+          "sc_test_do_gather_sum" -> WdlInteger(11),
+          "sc_test_do_prepare_split_files" -> WdlArray(WdlArrayType(WdlFileType), Seq("temp_aa", "temp_ab", "temp_ac", "temp_ad").map(WdlFile(_))),
+          "sc_test_do_scatter_count_file" -> WdlArray(WdlArrayType(WdlFileType), (1 to 4).map(_ => WdlFile("output.txt")))
         )
       )
     }
diff --git a/engine/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala b/engine/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
index f327c6da413..3859368d761 100644
--- a/engine/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
+++ b/engine/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
@@ -7,7 +7,7 @@ import akka.testkit._
 import com.typesafe.config.ConfigFactory
 import cromwell.MetadataWatchActor.{FailureMatcher, Matcher}
 import cromwell.SimpleWorkflowActorSpec._
-import cromwell.core.{WorkflowId, WorkflowSourceFiles}
+import cromwell.core.{WorkflowId, WorkflowSourceFilesWithoutImports}
 import cromwell.engine.backend.BackendSingletonCollection
 import cromwell.engine.workflow.WorkflowActor
 import cromwell.engine.workflow.WorkflowActor._
@@ -28,13 +28,13 @@ object SimpleWorkflowActorSpec {
     promise: Promise[Unit])
 }
 
-class SimpleWorkflowActorSpec extends CromwellTestkitSpec with BeforeAndAfter {
+class SimpleWorkflowActorSpec extends CromwellTestKitSpec with BeforeAndAfter {
 
   private def buildWorkflowActor(sampleWdl: SampleWdl,
                                  rawInputsOverride: String,
                                  workflowId: WorkflowId,
                                  matchers: Matcher*): TestableWorkflowActorAndMetadataPromise = {
-    val workflowSources = WorkflowSourceFiles(sampleWdl.wdlSource(), rawInputsOverride, "{}")
+    val workflowSources = WorkflowSourceFilesWithoutImports(sampleWdl.wdlSource(), rawInputsOverride, "{}")
     val promise = Promise[Unit]()
     val watchActor = system.actorOf(MetadataWatchActor.props(promise, matchers: _*), s"service-registry-$workflowId-${UUID.randomUUID()}")
     val supervisor = TestProbe()
@@ -43,9 +43,11 @@ class SimpleWorkflowActorSpec extends CromwellTestkitSpec with BeforeAndAfter {
         serviceRegistryActor = watchActor,
         workflowLogCopyRouter = system.actorOf(Props.empty, s"workflow-copy-log-router-$workflowId-${UUID.randomUUID()}"),
         jobStoreActor = system.actorOf(AlwaysHappyJobStoreActor.props),
+        subWorkflowStoreActor = system.actorOf(AlwaysHappySubWorkflowStoreActor.props),
         callCacheReadActor = system.actorOf(EmptyCallCacheReadActor.props),
         jobTokenDispenserActor = system.actorOf(JobExecutionTokenDispenserActor.props),
-        backendSingletonCollection = BackendSingletonCollection(Map("Local" -> None))),
+        backendSingletonCollection = BackendSingletonCollection(Map("Local" -> None)),
+        serverMode = true),
       supervisor = supervisor.ref,
       name = s"workflow-actor-$workflowId"
     )
@@ -64,7 +66,7 @@ class SimpleWorkflowActorSpec extends CromwellTestkitSpec with BeforeAndAfter {
       val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, _) = buildWorkflowActor(SampleWdl.HelloWorld, SampleWdl.HelloWorld.wdlJson, workflowId)
       val probe = TestProbe()
       probe watch workflowActor
-      startingCallsFilter("hello.hello") {
+      startingCallsFilter("wf_hello.hello") {
         workflowActor ! StartWorkflowCommand
       }
 
@@ -75,7 +77,7 @@ class SimpleWorkflowActorSpec extends CromwellTestkitSpec with BeforeAndAfter {
     }
 
     "fail to construct with missing inputs" in {
-      val expectedError = "Required workflow input 'hello.hello.addressee' not specified."
+      val expectedError = "Required workflow input 'wf_hello.hello.addressee' not specified."
       val failureMatcher = FailureMatcher(expectedError)
       val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) = buildWorkflowActor(SampleWdl.HelloWorld, "{}", workflowId, failureMatcher)
       val probe = TestProbe()
@@ -92,7 +94,7 @@ class SimpleWorkflowActorSpec extends CromwellTestkitSpec with BeforeAndAfter {
     }
 
     "fail to construct with inputs of the wrong type" in {
-      val expectedError = "Could not coerce value for 'hello.hello.addressee' into: WdlStringType"
+      val expectedError = "Could not coerce JsNumber value for 'wf_hello.hello.addressee' (3) into: WdlStringType"
       val failureMatcher = FailureMatcher(expectedError)
       val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) = buildWorkflowActor(SampleWdl.HelloWorld, s""" { "$Addressee" : 3} """,
         workflowId, failureMatcher)
@@ -100,7 +102,13 @@ class SimpleWorkflowActorSpec extends CromwellTestkitSpec with BeforeAndAfter {
       val probe = TestProbe()
       probe watch workflowActor
       workflowActor ! StartWorkflowCommand
-      Await.result(promise.future, TestExecutionTimeout)
+      try {
+        Await.result(promise.future, TestExecutionTimeout)
+      } catch {
+        case e: Throwable =>
+          val info = failureMatcher.nearMissInformation
+          fail(s"We didn't see the expected error message $expectedError within $TestExecutionTimeout. ${info.mkString(", ")}")
+      }
       probe.expectTerminated(workflowActor, AwaitAlmostNothing)
       supervisor.expectMsgPF(AwaitAlmostNothing, "parent should get a failed response") {
         case x: WorkflowFailedResponse =>
@@ -111,12 +119,12 @@ class SimpleWorkflowActorSpec extends CromwellTestkitSpec with BeforeAndAfter {
     }
 
     "fail when a call fails" in {
-      val expectedError = "Call goodbye.goodbye: return code was 1"
+      val expectedError = "Call wf_goodbye.goodbye:NA:1: return code was 1"
       val failureMatcher = FailureMatcher(expectedError)
       val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) = buildWorkflowActor(SampleWdl.GoodbyeWorld, SampleWdl.GoodbyeWorld.wdlJson, workflowId, failureMatcher)
       val probe = TestProbe()
       probe watch workflowActor
-      startingCallsFilter("goodbye.goodbye") {
+      startingCallsFilter("wf_goodbye.goodbye") {
         workflowActor ! StartWorkflowCommand
       }
       Await.result(promise.future, TestExecutionTimeout)
@@ -130,7 +138,7 @@ class SimpleWorkflowActorSpec extends CromwellTestkitSpec with BeforeAndAfter {
     }
 
     "gracefully handle malformed WDL" in {
-      val expectedError = "Input evaluation for Call test1.summary failedVariable 'Can't find bfile' not found"
+      val expectedError = "Input evaluation for Call test1.summary failed.\nVariable 'bfile' not found"
       val failureMatcher = FailureMatcher(expectedError)
       val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) = buildWorkflowActor(SampleWdl.CoercionNotDefined, SampleWdl.CoercionNotDefined.wdlJson, workflowId, failureMatcher)
       val probe = TestProbe()
@@ -148,7 +156,7 @@ class SimpleWorkflowActorSpec extends CromwellTestkitSpec with BeforeAndAfter {
   }
 
   private def startingCallsFilter[T](callNames: String*)(block: => T): T = {
-    import CromwellTestkitSpec.waitForInfo
+    import CromwellTestKitSpec.waitForInfo
     within(TestExecutionTimeout) {
       waitForInfo(s"Starting calls: ${callNames.mkString("", ":NA:1, ", ":NA:1")}$$", 1) {
         block
diff --git a/engine/src/test/scala/cromwell/WdlFunctionsAtWorkflowLevelSpec.scala b/engine/src/test/scala/cromwell/WdlFunctionsAtWorkflowLevelSpec.scala
index 72c618fca52..3052e337041 100644
--- a/engine/src/test/scala/cromwell/WdlFunctionsAtWorkflowLevelSpec.scala
+++ b/engine/src/test/scala/cromwell/WdlFunctionsAtWorkflowLevelSpec.scala
@@ -6,7 +6,7 @@ import wdl4s.types.{WdlMapType, WdlStringType}
 import wdl4s.values.{WdlMap, WdlString}
 
 
-class WdlFunctionsAtWorkflowLevelSpec extends CromwellTestkitSpec {
+class WdlFunctionsAtWorkflowLevelSpec extends CromwellTestKitSpec {
   val outputMap = WdlMap(WdlMapType(WdlStringType, WdlStringType), Map(
     WdlString("k1") -> WdlString("v1"),
     WdlString("k2") -> WdlString("v2"),
@@ -19,8 +19,8 @@ class WdlFunctionsAtWorkflowLevelSpec extends CromwellTestkitSpec {
         sampleWdl = SampleWdl.WdlFunctionsAtWorkflowLevel,
         eventFilter = EventFilter.info(pattern = "Starting calls: w.a", occurrences = 1),
         expectedOutputs = Map(
-          "w.a.x" -> WdlString("one two three four five"),
-          "w.a.y" -> outputMap
+          "w_a_x" -> WdlString("one two three four five"),
+          "w_a_y" -> outputMap
         )
       )
     }
diff --git a/engine/src/test/scala/cromwell/WorkflowFailSlowSpec.scala b/engine/src/test/scala/cromwell/WorkflowFailSlowSpec.scala
index 1cd7a7ef36c..2093cf19848 100644
--- a/engine/src/test/scala/cromwell/WorkflowFailSlowSpec.scala
+++ b/engine/src/test/scala/cromwell/WorkflowFailSlowSpec.scala
@@ -5,7 +5,7 @@ import cromwell.util.SampleWdl
 
 
 // TODO: These tests are (and were) somewhat unsatisfactory. They'd be much better if we use TestFSMRefs and TestProbes to simulate job completions against the WorkflowActor and make sure it only completes the workflow at the appropriate time.
-class WorkflowFailSlowSpec extends CromwellTestkitSpec {
+class WorkflowFailSlowSpec extends CromwellTestKitSpec {
   val FailFastOptions =
     """
       |{
diff --git a/engine/src/test/scala/cromwell/WorkflowOutputsSpec.scala b/engine/src/test/scala/cromwell/WorkflowOutputsSpec.scala
index 18df317959d..0f210fd1e93 100644
--- a/engine/src/test/scala/cromwell/WorkflowOutputsSpec.scala
+++ b/engine/src/test/scala/cromwell/WorkflowOutputsSpec.scala
@@ -2,10 +2,10 @@ package cromwell
 
 import akka.testkit._
 import cromwell.util.SampleWdl
-import cromwell.CromwellTestkitSpec.AnyValueIsFine
+import cromwell.CromwellTestKitSpec.AnyValueIsFine
 
 
-class WorkflowOutputsSpec extends CromwellTestkitSpec {
+class WorkflowOutputsSpec extends CromwellTestKitSpec {
   "Workflow outputs" should {
     "use all outputs if none are specified" in {
       runWdlAndAssertOutputs(
@@ -13,9 +13,9 @@ class WorkflowOutputsSpec extends CromwellTestkitSpec {
         eventFilter = EventFilter.info(pattern = s"is in a terminal state: WorkflowSucceededState", occurrences = 1),
         runtime = "",
         expectedOutputs = Map(
-          "three_step.ps.procs" -> AnyValueIsFine,
-          "three_step.cgrep.count" -> AnyValueIsFine,
-          "three_step.wc.count" -> AnyValueIsFine
+          "three_step_ps_procs" -> AnyValueIsFine,
+          "three_step_cgrep_count" -> AnyValueIsFine,
+          "three_step_wc_count" -> AnyValueIsFine
         ),
         allowOtherOutputs = false
       )
@@ -27,8 +27,8 @@ class WorkflowOutputsSpec extends CromwellTestkitSpec {
         eventFilter = EventFilter.info(pattern = s"is in a terminal state: WorkflowSucceededState", occurrences = 1),
         runtime = "",
         expectedOutputs = Map(
-          "three_step.cgrep.count" -> AnyValueIsFine,
-          "three_step.wc.count" -> AnyValueIsFine
+          "three_step_cgrep_count" -> AnyValueIsFine,
+          "three_step_wc_count" -> AnyValueIsFine
         ),
         allowOtherOutputs = false
       )
@@ -40,8 +40,8 @@ class WorkflowOutputsSpec extends CromwellTestkitSpec {
         eventFilter = EventFilter.info(pattern = s"is in a terminal state: WorkflowSucceededState", occurrences = 1),
         runtime = "",
         expectedOutputs = Map(
-          "scatter0.outside_scatter.out" -> AnyValueIsFine,
-          "scatter0.inside_scatter.out" -> AnyValueIsFine
+          "scatter0_outside_scatter_out" -> AnyValueIsFine,
+          "scatter0_inside_scatter_out" -> AnyValueIsFine
         ),
         allowOtherOutputs = false
       )
@@ -53,7 +53,7 @@ class WorkflowOutputsSpec extends CromwellTestkitSpec {
         eventFilter = EventFilter.info(pattern = s"is in a terminal state: WorkflowSucceededState", occurrences = 1),
         runtime = "",
         expectedOutputs = Map(
-          "scatter0.inside_scatter.out" -> AnyValueIsFine
+          "scatter0_inside_scatter_out" -> AnyValueIsFine
         ),
         allowOtherOutputs = false
       )
diff --git a/engine/src/test/scala/cromwell/engine/EngineFunctionsSpec.scala b/engine/src/test/scala/cromwell/engine/EngineFunctionsSpec.scala
index ec512107e9e..14ccbd6bddb 100644
--- a/engine/src/test/scala/cromwell/engine/EngineFunctionsSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/EngineFunctionsSpec.scala
@@ -1,21 +1,23 @@
 package cromwell.engine
 
-import java.nio.file.{FileSystem, FileSystems, Path}
+import java.nio.file.Path
 
-import cromwell.backend.wdl.{PureFunctions, ReadLikeFunctions, WriteFunctions}
+import cromwell.backend.wdl.{ReadLikeFunctions, WriteFunctions}
+import cromwell.core.path.{DefaultPathBuilder, PathBuilder}
 import org.scalatest.prop.TableDrivenPropertyChecks._
 import org.scalatest.prop.Tables.Table
 import org.scalatest.{FlatSpec, Matchers}
-import wdl4s.expression.{NoFunctions, WdlStandardLibraryFunctions}
+import wdl4s.expression.{NoFunctions, PureStandardLibraryFunctionsLike, WdlStandardLibraryFunctions}
 import wdl4s.values.{WdlFile, WdlInteger, WdlString, WdlValue}
 
 import scala.util.{Failure, Success, Try}
 
 class EngineFunctionsSpec extends FlatSpec with Matchers {
 
-  trait WdlStandardLibraryImpl extends WdlStandardLibraryFunctions with ReadLikeFunctions with WriteFunctions with PureFunctions {
+  trait WdlStandardLibraryImpl extends WdlStandardLibraryFunctions with ReadLikeFunctions with WriteFunctions with PureStandardLibraryFunctionsLike {
     private def fail(name: String) = Failure(new NotImplementedError(s"$name() not implemented yet"))
 
+    override def writeTempFile(path: String, prefix: String, suffix: String, content: String): String = super[WriteFunctions].writeTempFile(path, prefix, suffix, content)
     override def stdout(params: Seq[Try[WdlValue]]): Try[WdlFile] = fail("stdout")
     override def stderr(params: Seq[Try[WdlValue]]): Try[WdlFile] = fail("stderr")
   }
@@ -38,7 +40,7 @@ class EngineFunctionsSpec extends FlatSpec with Matchers {
   "sub" should "replace a string according to a pattern" in {
     class TestEngineFn extends WdlStandardLibraryImpl {
       override def glob(path: String, pattern: String): Seq[String] = ???
-      override def fileSystems: List[FileSystem] = List(FileSystems.getDefault)
+      override def pathBuilders: List[PathBuilder] = List(DefaultPathBuilder)
       override def writeDirectory: Path = ???
     }
 
diff --git a/engine/src/test/scala/cromwell/engine/WorkflowAbortSpec.scala b/engine/src/test/scala/cromwell/engine/WorkflowAbortSpec.scala
index 6a4b0a077ac..37ed641c8a7 100644
--- a/engine/src/test/scala/cromwell/engine/WorkflowAbortSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/WorkflowAbortSpec.scala
@@ -1,8 +1,8 @@
 package cromwell.engine
 
-import cromwell.CromwellTestkitSpec
+import cromwell.CromwellTestKitSpec
 
-class WorkflowAbortSpec extends CromwellTestkitSpec {
+class WorkflowAbortSpec extends CromwellTestKitSpec {
 
   // TODO: When re-enabled, this test also needs to check that child processes have actually been stopped.
   "A WorkflowManagerActor" should {
diff --git a/engine/src/test/scala/cromwell/engine/WorkflowManagerActorSpec.scala b/engine/src/test/scala/cromwell/engine/WorkflowManagerActorSpec.scala
index 55faea29fb8..1d7d313b638 100644
--- a/engine/src/test/scala/cromwell/engine/WorkflowManagerActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/WorkflowManagerActorSpec.scala
@@ -1,11 +1,11 @@
 package cromwell.engine
 
-import cromwell.CromwellTestkitSpec
+import cromwell.CromwellTestKitSpec
 import cromwell.engine.workflow.WorkflowDescriptorBuilder
 import cromwell.util.SampleWdl
 
 
-class WorkflowManagerActorSpec extends CromwellTestkitSpec with WorkflowDescriptorBuilder {
+class WorkflowManagerActorSpec extends CromwellTestKitSpec with WorkflowDescriptorBuilder {
   override implicit val actorSystem = system
 
   "A WorkflowManagerActor" should {
@@ -13,7 +13,7 @@ class WorkflowManagerActorSpec extends CromwellTestkitSpec with WorkflowDescript
     "run workflows in the correct directory" in {
       val outputs = runWdl(sampleWdl = SampleWdl.CurrentDirectory)
 
-      val outputName = "whereami.whereami.pwd"
+      val outputName = "wf_whereami_whereami_pwd"
       val salutation = outputs(outputName)
       val actualOutput = salutation.valueString.trim
       actualOutput should endWith("/call-whereami/execution")
diff --git a/engine/src/test/scala/cromwell/engine/WorkflowStoreActorSpec.scala b/engine/src/test/scala/cromwell/engine/WorkflowStoreActorSpec.scala
index 18460e765fe..d6719fe85ec 100644
--- a/engine/src/test/scala/cromwell/engine/WorkflowStoreActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/WorkflowStoreActorSpec.scala
@@ -1,17 +1,21 @@
 package cromwell.engine
 
 import cats.data.NonEmptyList
-import cromwell.CromwellTestkitSpec
-import cromwell.core.WorkflowId
+import cromwell.CromwellTestKitSpec
+import cromwell.core.{WorkflowId, WorkflowSourceFilesCollection}
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor._
 import cromwell.engine.workflow.workflowstore._
+import cromwell.services.metadata.MetadataQuery
+import cromwell.services.metadata.MetadataService.{GetMetadataQueryAction, MetadataLookupResponse}
+import cromwell.services.metadata.impl.ReadMetadataActor
+import cromwell.util.EncryptionSpec
 import cromwell.util.SampleWdl.HelloWorld
 import org.scalatest.Matchers
 
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-class WorkflowStoreActorSpec extends CromwellTestkitSpec with Matchers {
+class WorkflowStoreActorSpec extends CromwellTestKitSpec with Matchers {
   val helloWorldSourceFiles = HelloWorld.asWorkflowSources()
 
   /**
@@ -31,17 +35,22 @@ class WorkflowStoreActorSpec extends CromwellTestkitSpec with Matchers {
     list.foldLeft((List.empty[WorkflowToStart], true))(folderFunction)._2
   }
 
+  private def prettyOptions(workflowSourceFiles: WorkflowSourceFilesCollection): WorkflowSourceFilesCollection = {
+    import spray.json._
+    workflowSourceFiles.copyOptions(workflowSourceFiles.workflowOptionsJson.parseJson.prettyPrint)
+  }
+
   "The WorkflowStoreActor" should {
     "return an ID for a submitted workflow" in {
       val store = new InMemoryWorkflowStore
-      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestkitSpec.ServiceRegistryActorInstance))
+      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestKitSpec.ServiceRegistryActorInstance))
       storeActor ! SubmitWorkflow(helloWorldSourceFiles)
       expectMsgType[WorkflowSubmittedToStore](10 seconds)
     }
 
     "return 3 IDs for a batch submission of 3" in {
       val store = new InMemoryWorkflowStore
-      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestkitSpec.ServiceRegistryActorInstance))
+      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestKitSpec.ServiceRegistryActorInstance))
       storeActor ! BatchSubmitWorkflows(NonEmptyList.of(helloWorldSourceFiles, helloWorldSourceFiles, helloWorldSourceFiles))
       expectMsgPF(10 seconds) {
         case WorkflowsBatchSubmittedToStore(ids) => ids.toList.size shouldBe 3
@@ -50,7 +59,7 @@ class WorkflowStoreActorSpec extends CromwellTestkitSpec with Matchers {
 
     "fetch exactly N workflows" in {
       val store = new InMemoryWorkflowStore
-      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestkitSpec.ServiceRegistryActorInstance))
+      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestKitSpec.ServiceRegistryActorInstance))
       storeActor ! BatchSubmitWorkflows(NonEmptyList.of(helloWorldSourceFiles, helloWorldSourceFiles, helloWorldSourceFiles))
       val insertedIds = expectMsgType[WorkflowsBatchSubmittedToStore](10 seconds).workflowIds.toList
 
@@ -63,15 +72,65 @@ class WorkflowStoreActorSpec extends CromwellTestkitSpec with Matchers {
           workflowNel map {
             case WorkflowToStart(id, sources, state) =>
               insertedIds.contains(id) shouldBe true
-              sources shouldBe helloWorldSourceFiles
+              sources shouldBe prettyOptions(helloWorldSourceFiles)
               state shouldBe WorkflowStoreState.Submitted
           }
       }
     }
 
+    "fetch encrypted and cleared workflow options" in {
+      EncryptionSpec.assumeAes256Cbc()
+
+      val optionedSourceFiles = HelloWorld.asWorkflowSources(workflowOptions =
+        s"""|{
+            |  "key": "value",
+            |  "refresh_token": "it's a secret"
+            |}
+            |""".stripMargin)
+
+
+      val store = new InMemoryWorkflowStore
+      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestKitSpec.ServiceRegistryActorInstance))
+      val readMetadataActor = system.actorOf(ReadMetadataActor.props())
+      storeActor ! BatchSubmitWorkflows(NonEmptyList.of(optionedSourceFiles))
+      val insertedIds = expectMsgType[WorkflowsBatchSubmittedToStore](10 seconds).workflowIds.toList
+
+      storeActor ! FetchRunnableWorkflows(1)
+      expectMsgPF(10 seconds) {
+        case NewWorkflowsToStart(workflowNel) =>
+          workflowNel.toList.size should be(1)
+          checkDistinctIds(workflowNel.toList) should be(true)
+          workflowNel.toList.foreach {
+            case WorkflowToStart(id, sources, state) =>
+              insertedIds.contains(id) should be(true)
+              sources.wdlSource should be(optionedSourceFiles.wdlSource)
+              sources.inputsJson should be(optionedSourceFiles.inputsJson)
+              state should be(WorkflowStoreState.Submitted)
+
+              import spray.json._
+
+              val encryptedJsObject = sources.workflowOptionsJson.parseJson.asJsObject
+              encryptedJsObject.fields.keys should contain theSameElementsAs Seq("key", "refresh_token")
+              encryptedJsObject.fields("key") should be(JsString("value"))
+              encryptedJsObject.fields("refresh_token").asJsObject.fields.keys should contain theSameElementsAs
+                Seq("iv", "ciphertext")
+
+              readMetadataActor ! GetMetadataQueryAction(MetadataQuery.forWorkflow(id))
+              expectMsgPF(10 seconds) {
+                case MetadataLookupResponse(_, eventList) =>
+                  val optionsEvent = eventList.find(_.key.key == "submittedFiles:options").get
+                  val clearedJsObject = optionsEvent.value.get.value.parseJson.asJsObject
+                  clearedJsObject.fields.keys should contain theSameElementsAs Seq("key", "refresh_token")
+                  clearedJsObject.fields("key") should be(JsString("value"))
+                  clearedJsObject.fields("refresh_token") should be(JsString("cleared"))
+              }
+          }
+      }
+    }
+
     "return only the remaining workflows if N is larger than size" in {
       val store = new InMemoryWorkflowStore
-      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestkitSpec.ServiceRegistryActorInstance))
+      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestKitSpec.ServiceRegistryActorInstance))
       storeActor ! BatchSubmitWorkflows(NonEmptyList.of(helloWorldSourceFiles, helloWorldSourceFiles, helloWorldSourceFiles))
       val insertedIds = expectMsgType[WorkflowsBatchSubmittedToStore](10 seconds).workflowIds.toList
 
@@ -84,7 +143,7 @@ class WorkflowStoreActorSpec extends CromwellTestkitSpec with Matchers {
           workflowNel map {
             case WorkflowToStart(id, sources, state) =>
               insertedIds.contains(id) shouldBe true
-              sources shouldBe helloWorldSourceFiles
+              sources shouldBe prettyOptions(helloWorldSourceFiles)
               state shouldBe WorkflowStoreState.Submitted
           }
       }
@@ -92,7 +151,7 @@ class WorkflowStoreActorSpec extends CromwellTestkitSpec with Matchers {
 
     "remove workflows which exist" in {
       val store = new InMemoryWorkflowStore
-      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestkitSpec.ServiceRegistryActorInstance))
+      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestKitSpec.ServiceRegistryActorInstance))
       storeActor ! SubmitWorkflow(helloWorldSourceFiles)
       val id = expectMsgType[WorkflowSubmittedToStore](10 seconds).workflowId
       storeActor ! RemoveWorkflow(id)
@@ -105,7 +164,7 @@ class WorkflowStoreActorSpec extends CromwellTestkitSpec with Matchers {
 
     "remain responsive if you ask to remove a workflow it doesn't have" in {
       val store = new InMemoryWorkflowStore
-      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestkitSpec.ServiceRegistryActorInstance))
+      val storeActor = system.actorOf(WorkflowStoreActor.props(store, CromwellTestKitSpec.ServiceRegistryActorInstance))
       val id = WorkflowId.randomId()
       storeActor ! RemoveWorkflow(id)
 
diff --git a/engine/src/test/scala/cromwell/engine/backend/mock/DefaultBackendJobExecutionActor.scala b/engine/src/test/scala/cromwell/engine/backend/mock/DefaultBackendJobExecutionActor.scala
index f98fa17bd9a..0763a1c30c0 100644
--- a/engine/src/test/scala/cromwell/engine/backend/mock/DefaultBackendJobExecutionActor.scala
+++ b/engine/src/test/scala/cromwell/engine/backend/mock/DefaultBackendJobExecutionActor.scala
@@ -1,9 +1,9 @@
 package cromwell.engine.backend.mock
 
 import akka.actor.{ActorRef, Props}
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, JobSucceededResponse}
 import cromwell.backend._
-import wdl4s.Call
+import wdl4s.TaskCall
 import wdl4s.expression.{NoFunctions, WdlStandardLibraryFunctions}
 
 import scala.concurrent.Future
@@ -14,7 +14,7 @@ object DefaultBackendJobExecutionActor {
 
 case class DefaultBackendJobExecutionActor(override val jobDescriptor: BackendJobDescriptor, override val configurationDescriptor: BackendConfigurationDescriptor) extends BackendJobExecutionActor {
   override def execute: Future[BackendJobExecutionResponse] = {
-    Future.successful(SucceededResponse(jobDescriptor.key, Some(0), (jobDescriptor.call.task.outputs map taskOutputToJobOutput).toMap, None, Seq.empty))
+    Future.successful(JobSucceededResponse(jobDescriptor.key, Some(0), (jobDescriptor.call.task.outputs map taskOutputToJobOutput).toMap, None, Seq.empty))
   }
 
   override def recover = execute
@@ -25,7 +25,7 @@ case class DefaultBackendJobExecutionActor(override val jobDescriptor: BackendJo
 class DefaultBackendLifecycleActorFactory(name: String, configurationDescriptor: BackendConfigurationDescriptor)
   extends BackendLifecycleActorFactory {
   override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                                calls: Seq[Call],
+                                                calls: Set[TaskCall],
                                                 serviceRegistryActor: ActorRef): Option[Props] = None
 
   override def jobExecutionActorProps(jobDescriptor: BackendJobDescriptor,
diff --git a/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendJobExecutionActor.scala b/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendJobExecutionActor.scala
index 60617f468b7..eaaa04abb52 100644
--- a/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendJobExecutionActor.scala
+++ b/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendJobExecutionActor.scala
@@ -2,7 +2,7 @@ package cromwell.engine.backend.mock
 
 import akka.actor.Props
 import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendJobExecutionActor}
-import cromwell.backend.BackendJobExecutionActor.{FailedRetryableResponse, BackendJobExecutionResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{JobFailedRetryableResponse, BackendJobExecutionResponse, JobSucceededResponse}
 
 import scala.concurrent.Future
 
@@ -16,9 +16,9 @@ case class RetryableBackendJobExecutionActor(override val jobDescriptor: Backend
 
   override def execute: Future[BackendJobExecutionResponse] = {
     if (jobDescriptor.key.attempt < attempts)
-      Future.successful(FailedRetryableResponse(jobDescriptor.key, new RuntimeException("An apparent transient Exception!"), None))
+      Future.successful(JobFailedRetryableResponse(jobDescriptor.key, new RuntimeException("An apparent transient Exception!"), None))
     else
-      Future.successful(SucceededResponse(jobDescriptor.key, Some(0), (jobDescriptor.call.task.outputs map taskOutputToJobOutput).toMap, None, Seq.empty))
+      Future.successful(JobSucceededResponse(jobDescriptor.key, Some(0), (jobDescriptor.call.task.outputs map taskOutputToJobOutput).toMap, None, Seq.empty))
   }
 
   override def recover = execute
diff --git a/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendLifecycleActorFactory.scala b/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendLifecycleActorFactory.scala
index 46f28f44757..c884816108f 100644
--- a/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendLifecycleActorFactory.scala
+++ b/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendLifecycleActorFactory.scala
@@ -2,13 +2,13 @@ package cromwell.engine.backend.mock
 
 import akka.actor.{ActorRef, Props}
 import cromwell.backend._
-import wdl4s.Call
+import wdl4s.TaskCall
 import wdl4s.expression.{NoFunctions, WdlStandardLibraryFunctions}
 
 class RetryableBackendLifecycleActorFactory(name: String, configurationDescriptor: BackendConfigurationDescriptor)
   extends BackendLifecycleActorFactory {
   override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                                calls: Seq[Call],
+                                                calls: Set[TaskCall],
                                                 serviceRegistryActor: ActorRef): Option[Props] = None
 
   override def jobExecutionActorProps(jobDescriptor: BackendJobDescriptor,
diff --git a/engine/src/test/scala/cromwell/engine/backend/mock/package.scala b/engine/src/test/scala/cromwell/engine/backend/mock/package.scala
index 4baeb9c33aa..a2f914121e3 100644
--- a/engine/src/test/scala/cromwell/engine/backend/mock/package.scala
+++ b/engine/src/test/scala/cromwell/engine/backend/mock/package.scala
@@ -9,7 +9,7 @@ package object mock {
 
   // This is used by stubbed backends that are to be used in tests to prepare dummy outputs for job
   def taskOutputToJobOutput(taskOutput: TaskOutput) =
-    taskOutput.name -> JobOutput(sampleValue(taskOutput.wdlType))
+    taskOutput.unqualifiedName -> JobOutput(sampleValue(taskOutput.wdlType))
 
   private def sampleValue(wdlType: WdlType): WdlValue = wdlType match {
     case WdlIntegerType => WdlInteger(3)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/SingleWorkflowRunnerActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/SingleWorkflowRunnerActorSpec.scala
index 540da9863c8..6dec787d546 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/SingleWorkflowRunnerActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/SingleWorkflowRunnerActorSpec.scala
@@ -6,10 +6,11 @@ import java.time.OffsetDateTime
 import akka.actor._
 import akka.pattern.ask
 import akka.testkit.TestKit
+import akka.util.Timeout
 import better.files._
 import com.typesafe.config.ConfigFactory
-import cromwell.CromwellTestkitSpec._
-import cromwell.core.WorkflowSourceFiles
+import cromwell.CromwellTestKitSpec._
+import cromwell.core.{WorkflowSourceFilesCollection}
 import cromwell.engine.backend.BackendSingletonCollection
 import cromwell.engine.workflow.SingleWorkflowRunnerActor.RunWorkflow
 import cromwell.engine.workflow.SingleWorkflowRunnerActorSpec._
@@ -17,7 +18,7 @@ import cromwell.engine.workflow.tokens.JobExecutionTokenDispenserActor
 import cromwell.engine.workflow.workflowstore.{InMemoryWorkflowStore, WorkflowStoreActor}
 import cromwell.util.SampleWdl
 import cromwell.util.SampleWdl.{ExpressionsInInputs, GoodbyeWorld, ThreeStep}
-import cromwell.{AlwaysHappyJobStoreActor, CromwellTestkitSpec, EmptyCallCacheReadActor}
+import cromwell.{AlwaysHappyJobStoreActor, AlwaysHappySubWorkflowStoreActor, CromwellTestKitSpec, EmptyCallCacheReadActor}
 import org.scalatest.prop.{TableDrivenPropertyChecks, TableFor3}
 import spray.json._
 
@@ -45,29 +46,34 @@ object SingleWorkflowRunnerActorSpec {
     def toFields = jsValue.get.asJsObject.fields
   }
 
-  class TestSingleWorkflowRunnerActor(source: WorkflowSourceFiles,
+  class TestSingleWorkflowRunnerActor(source: WorkflowSourceFilesCollection,
                                       metadataOutputPath: Option[Path])
     extends SingleWorkflowRunnerActor(source, metadataOutputPath) {
-    override lazy val serviceRegistryActor = CromwellTestkitSpec.ServiceRegistryActorInstance
+    override lazy val serviceRegistryActor = CromwellTestKitSpec.ServiceRegistryActorInstance
   }
 }
 
-abstract class SingleWorkflowRunnerActorSpec extends CromwellTestkitSpec {
+abstract class SingleWorkflowRunnerActorSpec extends CromwellTestKitSpec {
   private val workflowStore = system.actorOf(WorkflowStoreActor.props(new InMemoryWorkflowStore, dummyServiceRegistryActor))
   private val jobStore = system.actorOf(AlwaysHappyJobStoreActor.props)
+  private val subWorkflowStore = system.actorOf(AlwaysHappySubWorkflowStoreActor.props)
   private val callCacheReadActor = system.actorOf(EmptyCallCacheReadActor.props)
   private val jobTokenDispenserActor = system.actorOf(JobExecutionTokenDispenserActor.props)
 
 
   def workflowManagerActor(): ActorRef = {
-    system.actorOf(Props(new WorkflowManagerActor(ConfigFactory.load(),
+    val params = WorkflowManagerActorParams(ConfigFactory.load(),
       workflowStore,
       dummyServiceRegistryActor,
       dummyLogCopyRouter,
       jobStore,
+      subWorkflowStore,
       callCacheReadActor,
       jobTokenDispenserActor,
-      BackendSingletonCollection(Map.empty))), "WorkflowManagerActor")
+      BackendSingletonCollection(Map.empty),
+      abortJobsOnTerminate = false,
+      serverMode = false)
+    system.actorOf(Props(new WorkflowManagerActor(params)), "WorkflowManagerActor")
   }
   
   def createRunnerActor(sampleWdl: SampleWdl = ThreeStep, managerActor: => ActorRef = workflowManagerActor(),
@@ -78,7 +84,7 @@ abstract class SingleWorkflowRunnerActorSpec extends CromwellTestkitSpec {
   def singleWorkflowActor(sampleWdl: SampleWdl = ThreeStep, managerActor: => ActorRef = workflowManagerActor(),
                           outputFile: => Option[Path] = None): Unit = {
     val actorRef = createRunnerActor(sampleWdl, managerActor, outputFile)
-    val futureResult = actorRef ? RunWorkflow
+    val futureResult = actorRef.ask(RunWorkflow)(timeout = new Timeout(TimeoutDuration))
     Await.ready(futureResult, Duration.Inf)
     ()
   }
@@ -111,9 +117,8 @@ class SingleWorkflowRunnerActorWithMetadataSpec extends SingleWorkflowRunnerActo
       singleWorkflowActor(
         sampleWdl = wdlFile,
         outputFile = Option(metadataFile.path))
+        TestKit.shutdownActorSystem(system, TimeoutDuration)
     }
-    TestKit.shutdownActorSystem(system, TimeoutDuration)
-
     val metadataFileContent = metadataFile.contentAsString
     val metadata = metadataFileContent.parseJson.asJsObject.fields
     metadata.get("id") shouldNot be(empty)
@@ -200,7 +205,7 @@ class SingleWorkflowRunnerActorWithMetadataOnFailureSpec extends SingleWorkflowR
       val calls = metadata.get("calls").toFields
       calls should not be empty
 
-      val callSeq = calls("goodbye.goodbye").asInstanceOf[JsArray].elements
+      val callSeq = calls("wf_goodbye.goodbye").asInstanceOf[JsArray].elements
       callSeq should have size 1
       val call = callSeq.head.asJsObject.fields
       val inputs = call.get("inputs").toFields
diff --git a/engine/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
index b98c5657f95..1301f0e9b15 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
@@ -3,8 +3,8 @@ package cromwell.engine.workflow
 import akka.actor.{Actor, ActorRef}
 import akka.testkit.{TestActorRef, TestFSMRef, TestProbe}
 import com.typesafe.config.{Config, ConfigFactory}
-import cromwell.backend.AllBackendInitializationData
-import cromwell.core.{ExecutionStore, OutputStore, WorkflowId, WorkflowSourceFiles}
+import cromwell.backend.{AllBackendInitializationData, JobExecutionMap}
+import cromwell.core._
 import cromwell.engine.EngineWorkflowDescriptor
 import cromwell.engine.backend.BackendSingletonCollection
 import cromwell.engine.workflow.WorkflowActor._
@@ -13,13 +13,13 @@ import cromwell.engine.workflow.lifecycle.WorkflowFinalizationActor.{StartFinali
 import cromwell.engine.workflow.lifecycle.WorkflowInitializationActor.{WorkflowInitializationAbortedResponse, WorkflowInitializationFailedResponse}
 import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{WorkflowExecutionAbortedResponse, WorkflowExecutionFailedResponse, WorkflowExecutionSucceededResponse}
 import cromwell.util.SampleWdl.ThreeStep
-import cromwell.{AlwaysHappyJobStoreActor, CromwellTestkitSpec, EmptyCallCacheReadActor}
+import cromwell.{AlwaysHappyJobStoreActor, AlwaysHappySubWorkflowStoreActor, CromwellTestKitSpec, EmptyCallCacheReadActor}
 import org.scalatest.BeforeAndAfter
 import org.scalatest.concurrent.Eventually
 
 import scala.concurrent.duration._
 
-class WorkflowActorSpec extends CromwellTestkitSpec with WorkflowDescriptorBuilder with BeforeAndAfter with Eventually {
+class WorkflowActorSpec extends CromwellTestKitSpec with WorkflowDescriptorBuilder with BeforeAndAfter with Eventually {
   override implicit val actorSystem = system
 
   val mockServiceRegistryActor = TestActorRef(new Actor {
@@ -53,6 +53,7 @@ class WorkflowActorSpec extends CromwellTestkitSpec with WorkflowDescriptorBuild
         serviceRegistryActor = mockServiceRegistryActor,
         workflowLogCopyRouter = TestProbe().ref,
         jobStoreActor = system.actorOf(AlwaysHappyJobStoreActor.props),
+        subWorkflowStoreActor = system.actorOf(AlwaysHappySubWorkflowStoreActor.props),
         callCacheReadActor = system.actorOf(EmptyCallCacheReadActor.props),
         jobTokenDispenserActor = TestProbe().ref
       ),
@@ -62,7 +63,7 @@ class WorkflowActorSpec extends CromwellTestkitSpec with WorkflowDescriptorBuild
     actor
   }
 
-  implicit val TimeoutDuration = CromwellTestkitSpec.TimeoutDuration
+  implicit val TimeoutDuration = CromwellTestKitSpec.TimeoutDuration
 
   "WorkflowActor" should {
 
@@ -95,7 +96,7 @@ class WorkflowActorSpec extends CromwellTestkitSpec with WorkflowDescriptorBuild
     "run Finalization if Execution fails" in {
       val actor = createWorkflowActor(ExecutingWorkflowState)
       deathwatch watch actor
-      actor ! WorkflowExecutionFailedResponse(ExecutionStore.empty, OutputStore.empty, Seq(new Exception("Execution Failed")))
+      actor ! WorkflowExecutionFailedResponse(Map.empty, new Exception("Execution Failed"))
       finalizationProbe.expectMsg(StartFinalizationCommand)
       actor.stateName should be(FinalizingWorkflowState)
       actor ! WorkflowFinalizationSucceededResponse
@@ -108,9 +109,9 @@ class WorkflowActorSpec extends CromwellTestkitSpec with WorkflowDescriptorBuild
       deathwatch watch actor
       actor ! AbortWorkflowCommand
       eventually { actor.stateName should be(WorkflowAbortingState) }
-      currentLifecycleActor.expectMsgPF(CromwellTestkitSpec.TimeoutDuration) {
+      currentLifecycleActor.expectMsgPF(CromwellTestKitSpec.TimeoutDuration) {
         case EngineLifecycleActorAbortCommand =>
-          actor ! WorkflowExecutionAbortedResponse(ExecutionStore.empty, OutputStore.empty)
+          actor ! WorkflowExecutionAbortedResponse(Map.empty)
       }
       finalizationProbe.expectMsg(StartFinalizationCommand)
       actor.stateName should be(FinalizingWorkflowState)
@@ -122,7 +123,7 @@ class WorkflowActorSpec extends CromwellTestkitSpec with WorkflowDescriptorBuild
     "run Finalization actor if Execution succeeds" in {
       val actor = createWorkflowActor(ExecutingWorkflowState)
       deathwatch watch actor
-      actor ! WorkflowExecutionSucceededResponse(ExecutionStore.empty, OutputStore.empty)
+      actor ! WorkflowExecutionSucceededResponse(Map.empty, Map.empty)
       finalizationProbe.expectMsg(StartFinalizationCommand)
       actor.stateName should be(FinalizingWorkflowState)
       actor ! WorkflowFinalizationSucceededResponse
@@ -151,13 +152,14 @@ class WorkflowActorSpec extends CromwellTestkitSpec with WorkflowDescriptorBuild
 class MockWorkflowActor(val finalizationProbe: TestProbe,
                         workflowId: WorkflowId,
                         startMode: StartMode,
-                        workflowSources: WorkflowSourceFiles,
+                        workflowSources: WorkflowSourceFilesCollection,
                         conf: Config,
                         serviceRegistryActor: ActorRef,
                         workflowLogCopyRouter: ActorRef,
                         jobStoreActor: ActorRef,
+                        subWorkflowStoreActor: ActorRef,
                         callCacheReadActor: ActorRef,
-                        jobTokenDispenserActor: ActorRef) extends WorkflowActor(workflowId, startMode, workflowSources, conf, serviceRegistryActor, workflowLogCopyRouter, jobStoreActor, callCacheReadActor, jobTokenDispenserActor, BackendSingletonCollection(Map.empty)) {
+                        jobTokenDispenserActor: ActorRef) extends WorkflowActor(workflowId, startMode, workflowSources, conf, serviceRegistryActor, workflowLogCopyRouter, jobStoreActor, subWorkflowStoreActor, callCacheReadActor, jobTokenDispenserActor, BackendSingletonCollection(Map.empty), serverMode = true) {
 
-  override def makeFinalizationActor(workflowDescriptor: EngineWorkflowDescriptor, executionStore: ExecutionStore, outputStore: OutputStore) = finalizationProbe.ref
+  override def makeFinalizationActor(workflowDescriptor: EngineWorkflowDescriptor, jobExecutionMap: JobExecutionMap, worfklowOutputs: CallOutputs) = finalizationProbe.ref
 }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/WorkflowDescriptorBuilder.scala b/engine/src/test/scala/cromwell/engine/workflow/WorkflowDescriptorBuilder.scala
index 73013e71284..e4f5e1350b5 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/WorkflowDescriptorBuilder.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/WorkflowDescriptorBuilder.scala
@@ -2,8 +2,8 @@ package cromwell.engine.workflow
 
 import akka.actor.{ActorSystem, Props}
 import com.typesafe.config.ConfigFactory
-import cromwell.CromwellTestkitSpec
-import cromwell.core.{WorkflowId, WorkflowSourceFiles}
+import cromwell.CromwellTestKitSpec
+import cromwell.core.{WorkflowId, WorkflowSourceFilesCollection}
 import cromwell.engine.EngineWorkflowDescriptor
 import cromwell.engine.workflow.lifecycle.MaterializeWorkflowDescriptorActor
 import cromwell.engine.workflow.lifecycle.MaterializeWorkflowDescriptorActor.{MaterializeWorkflowDescriptorCommand, MaterializeWorkflowDescriptorFailureResponse, MaterializeWorkflowDescriptorSuccessResponse, WorkflowDescriptorMaterializationResult}
@@ -12,16 +12,16 @@ import scala.concurrent.Await
 
 trait WorkflowDescriptorBuilder {
 
-  implicit val awaitTimeout = CromwellTestkitSpec.TimeoutDuration
+  implicit val awaitTimeout = CromwellTestKitSpec.TimeoutDuration
   implicit val actorSystem: ActorSystem
 
-  def createMaterializedEngineWorkflowDescriptor(id: WorkflowId, workflowSources: WorkflowSourceFiles): EngineWorkflowDescriptor = {
+  def createMaterializedEngineWorkflowDescriptor(id: WorkflowId, workflowSources: WorkflowSourceFilesCollection): EngineWorkflowDescriptor = {
     import akka.pattern.ask
     implicit val timeout = akka.util.Timeout(awaitTimeout)
     implicit val ec = actorSystem.dispatcher
 
     val serviceRegistryIgnorer = actorSystem.actorOf(Props.empty)
-    val actor = actorSystem.actorOf(MaterializeWorkflowDescriptorActor.props(serviceRegistryIgnorer, id), "MaterializeWorkflowDescriptorActor-" + id.id)
+    val actor = actorSystem.actorOf(MaterializeWorkflowDescriptorActor.props(serviceRegistryIgnorer, id, importLocalFilesystem = false), "MaterializeWorkflowDescriptorActor-" + id.id)
     val workflowDescriptorFuture = actor.ask(
       MaterializeWorkflowDescriptorCommand(workflowSources, ConfigFactory.load)
     ).mapTo[WorkflowDescriptorMaterializationResult]
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala
index 970bc715694..0715ebeedda 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala
@@ -3,8 +3,8 @@ package cromwell.engine.workflow.lifecycle
 import akka.actor.Props
 import akka.testkit.TestDuration
 import com.typesafe.config.ConfigFactory
-import cromwell.CromwellTestkitSpec
-import cromwell.core.{WorkflowId, WorkflowOptions, WorkflowSourceFiles}
+import cromwell.CromwellTestKitSpec
+import cromwell.core.{WorkflowId, WorkflowOptions, WorkflowSourceFilesWithoutImports}
 import cromwell.engine.backend.{BackendConfigurationEntry, CromwellBackends}
 import cromwell.engine.workflow.lifecycle.MaterializeWorkflowDescriptorActor.{MaterializeWorkflowDescriptorCommand, MaterializeWorkflowDescriptorFailureResponse, MaterializeWorkflowDescriptorSuccessResponse}
 import cromwell.util.SampleWdl.HelloWorld
@@ -16,7 +16,7 @@ import wdl4s.values.{WdlInteger, WdlString}
 
 import scala.concurrent.duration._
 
-class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with BeforeAndAfter with MockitoSugar {
+class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitSpec with BeforeAndAfter with MockitoSugar {
 
   val workflowId = WorkflowId.randomId()
   val minimumConf = ConfigFactory.parseString(
@@ -54,18 +54,18 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
 
   "MaterializeWorkflowDescriptorActor" should {
     "accept valid WDL, inputs and options files" in {
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
-      val sources = WorkflowSourceFiles(wdlSourceNoDocker, validInputsJson, validOptionsFile)
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
+      val sources = WorkflowSourceFilesWithoutImports(wdlSourceNoDocker, validInputsJson, validOptionsFile)
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf)
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorSuccessResponse(wfDesc) =>
             wfDesc.id shouldBe workflowId
-            wfDesc.name shouldBe "hello"
+            wfDesc.name shouldBe "wf_hello"
             wfDesc.namespace.tasks.size shouldBe 1
-            wfDesc.workflowInputs.head shouldBe (("hello.hello.addressee", WdlString("world")))
-            wfDesc.backendDescriptor.inputs.head shouldBe (("hello.hello.addressee", WdlString("world")))
+            wfDesc.workflowInputs.head shouldBe (("wf_hello.hello.addressee", WdlString("world")))
+            wfDesc.backendDescriptor.inputs.head shouldBe (("wf_hello.hello.addressee", WdlString("world")))
             wfDesc.getWorkflowOption(WorkflowOptions.WriteToCache) shouldBe Option("true")
             wfDesc.getWorkflowOption(WorkflowOptions.ReadFromCache) shouldBe None
             // Default backend assignment is "Local":
@@ -73,7 +73,7 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
               case (call, assignment) if call.task.name.equals("hello") => assignment shouldBe "Local"
               case (call, assignment) => fail(s"Unexpected call: ${call.task.name}")
             }
-            wfDesc.engineFilesystems.size shouldBe 1
+            wfDesc.pathBuilders.size shouldBe 1
           case MaterializeWorkflowDescriptorFailureResponse(reason) => fail(s"Materialization failed with $reason")
           case unknown =>
             fail(s"Unexpected materialization response: $unknown")
@@ -99,8 +99,8 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
           |{ "foo.i": "17" }
         """.stripMargin
 
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
-      val sources = WorkflowSourceFiles(wdl, inputs, validOptionsFile)
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
+      val sources = WorkflowSourceFilesWithoutImports(wdl, inputs, validOptionsFile)
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf)
 
       within(Timeout) {
@@ -149,8 +149,8 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
           |  }
           |}
         """.stripMargin
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
-      val sources = WorkflowSourceFiles(wdl, "{}", defaultDocker)
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
+      val sources = WorkflowSourceFilesWithoutImports(wdl, "{}", defaultDocker)
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf)
 
       within(Timeout) {
@@ -196,14 +196,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
       val cromwellBackends = CromwellBackends(fauxBackendEntries)
 
       // Run the test:
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, cromwellBackends))
-      val sources = WorkflowSourceFiles(wdl, "{}", "{}")
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, cromwellBackends, importLocalFilesystem = false))
+      val sources = WorkflowSourceFilesWithoutImports(wdl, "{}", "{}")
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, differentDefaultBackendConf)
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorSuccessResponse(wfDesc) =>
-            wfDesc.namespace.workflow.calls foreach {
+            wfDesc.namespace.workflow.taskCalls foreach {
               case call if call.task.name.equals("a") =>
                 wfDesc.backendAssignments(call) shouldBe "SpecifiedBackend"
               case call if call.task.name.equals("b") =>
@@ -231,8 +231,8 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
           |}
         """.stripMargin
 
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
-      val sources = WorkflowSourceFiles(wdl, "{}", "{}")
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
+      val sources = WorkflowSourceFilesWithoutImports(wdl, "{}", "{}")
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, differentDefaultBackendConf)
 
       within(Timeout) {
@@ -250,8 +250,8 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
     }
 
     "reject an invalid WDL source" in {
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
-      val sources = WorkflowSourceFiles(unstructuredFile, validInputsJson, validOptionsFile)
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
+      val sources = WorkflowSourceFilesWithoutImports(unstructuredFile, validInputsJson, validOptionsFile)
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf)
 
       within(Timeout) {
@@ -274,8 +274,8 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
           |
           |# no workflow foo { ... } block!!
         """.stripMargin
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
-      val sources = WorkflowSourceFiles(noWorkflowWdl, validInputsJson, validOptionsFile)
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
+      val sources = WorkflowSourceFilesWithoutImports(noWorkflowWdl, validInputsJson, validOptionsFile)
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf)
 
       within(Timeout) {
@@ -299,8 +299,8 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
           |
           |workflow foo {  }
         """.stripMargin
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
-      val badWdlSources = WorkflowSourceFiles(noWorkflowWdl, validInputsJson, validOptionsFile)
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
+      val badWdlSources = WorkflowSourceFilesWithoutImports(noWorkflowWdl, validInputsJson, validOptionsFile)
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(badWdlSources, minimumConf)
 
       within(Timeout) {
@@ -318,8 +318,8 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
 
 
     "reject an invalid options file" in {
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
-      val sources = WorkflowSourceFiles(wdlSourceNoDocker, validInputsJson, unstructuredFile)
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
+      val sources = WorkflowSourceFilesWithoutImports(wdlSourceNoDocker, validInputsJson, unstructuredFile)
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf)
 
       within(Timeout) {
@@ -336,8 +336,8 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
     }
 
     "reject an invalid workflow inputs file" in {
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
-      val sources = WorkflowSourceFiles(wdlSourceNoDocker, unstructuredFile, validOptionsFile)
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
+      val sources = WorkflowSourceFilesWithoutImports(wdlSourceNoDocker, unstructuredFile, validOptionsFile)
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf)
 
       within(Timeout) {
@@ -354,15 +354,15 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
     }
 
     "reject requests if any required inputs are missing" in {
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
       val noInputsJson = "{}"
-      val badOptionsSources = WorkflowSourceFiles(wdlSourceNoDocker, noInputsJson, validOptionsFile)
+      val badOptionsSources = WorkflowSourceFilesWithoutImports(wdlSourceNoDocker, noInputsJson, validOptionsFile)
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(badOptionsSources, minimumConf)
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
-            reason.getMessage should startWith("Workflow input processing failed.\nRequired workflow input 'hello.hello.addressee' not specified")
+            reason.getMessage should startWith("Workflow input processing failed.\nRequired workflow input 'wf_hello.hello.addressee' not specified")
           case MaterializeWorkflowDescriptorSuccessResponse(wfDesc) => fail("This materialization should not have succeeded!")
           case unknown =>
             fail(s"Unexpected materialization response: $unknown")
@@ -381,14 +381,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestkitSpec with Be
           |  call bar
           |}
         """.stripMargin
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId))
-      val sources = WorkflowSourceFiles(wdl, "{}", validOptionsFile)
+      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviourActor, workflowId, importLocalFilesystem = false))
+      val sources = WorkflowSourceFilesWithoutImports(wdl, "{}", validOptionsFile)
       materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf)
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
-            reason.getMessage should startWith("Workflow input processing failed.\nInvalid right-side type of 'foo.j'.  Expecting Int, got String")
+            reason.getMessage should startWith("Workflow input processing failed.\nUnable to load namespace from workflow: ERROR: Value for j is not coerceable into a Int")
           case MaterializeWorkflowDescriptorSuccessResponse(wfDesc) => fail("This materialization should not have succeeded!")
           case unknown => fail(s"Unexpected materialization response: $unknown")
         }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActorSpec.scala
new file mode 100644
index 00000000000..1f61772e659
--- /dev/null
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActorSpec.scala
@@ -0,0 +1,213 @@
+package cromwell.engine.workflow.lifecycle.execution
+
+import java.util.UUID
+
+import akka.actor.Props
+import akka.testkit.{TestFSMRef, TestProbe}
+import cromwell.backend.{AllBackendInitializationData, BackendWorkflowDescriptor, JobExecutionMap}
+import cromwell.core._
+import cromwell.core.callcaching.CallCachingOff
+import cromwell.database.sql.tables.SubWorkflowStoreEntry
+import cromwell.engine.backend.BackendSingletonCollection
+import cromwell.engine.workflow.lifecycle.execution.CallPreparationActor.{CallPreparationFailed, SubWorkflowPreparationSucceeded}
+import cromwell.engine.workflow.lifecycle.execution.SubWorkflowExecutionActor._
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor._
+import cromwell.engine.{ContinueWhilePossible, EngineWorkflowDescriptor}
+import cromwell.subworkflowstore.SubWorkflowStoreActor.{QuerySubWorkflow, SubWorkflowFound, SubWorkflowNotFound}
+import org.scalatest.concurrent.Eventually
+import org.scalatest.{FlatSpecLike, Matchers}
+import org.specs2.mock.Mockito
+import wdl4s.{WdlNamespaceWithWorkflow, Workflow, WorkflowCall}
+
+import scala.concurrent.duration._
+import scala.language.postfixOps
+
+class SubWorkflowExecutionActorSpec extends TestKitSuite with FlatSpecLike with Matchers with Mockito with Eventually {
+  
+  behavior of "SubWorkflowExecutionActor"
+
+  val serviceRegistryProbe = TestProbe()
+  val jobStoreProbe = TestProbe()
+  val subWorkflowStoreProbe = TestProbe()
+  val callCacheReadActorProbe = TestProbe()
+  val jobTokenDispenserProbe = TestProbe()
+  val preparationActor = TestProbe()
+  val subWorkflowActor = TestProbe()
+  val deathWatch = TestProbe()
+  val parentProbe = TestProbe()
+  val parentBackendDescriptor = mock[BackendWorkflowDescriptor]
+  val parentWorkflowId: WorkflowId = WorkflowId.randomId()
+  parentBackendDescriptor.id returns parentWorkflowId
+  val parentWorkflowDescriptor = EngineWorkflowDescriptor(
+    mock[WdlNamespaceWithWorkflow],
+    parentBackendDescriptor,
+    Map.empty,
+    Map.empty,
+    ContinueWhilePossible,
+    List.empty,
+    CallCachingOff
+  )
+  val subWorkflow = mock[Workflow]
+  subWorkflow.unqualifiedName returns "sub_wf"
+  val subWorkflowCall = mock[WorkflowCall]
+  subWorkflowCall.fullyQualifiedName returns "foo.bar"
+  subWorkflowCall.callable returns subWorkflow
+  val subKey = SubWorkflowKey(subWorkflowCall, None, 1)
+  
+  val awaitTimeout: FiniteDuration = 10 seconds
+
+  def buildEWEA(restart: Boolean = false) = {
+    new TestFSMRef[SubWorkflowExecutionActorState, SubWorkflowExecutionActorData, SubWorkflowExecutionActor](system, Props(
+      new SubWorkflowExecutionActor(
+        subKey,
+        WorkflowExecutionActorData.empty(parentWorkflowDescriptor),
+        Map.empty,
+        serviceRegistryProbe.ref,
+        jobStoreProbe.ref,
+        subWorkflowStoreProbe.ref,
+        callCacheReadActorProbe.ref,
+        jobTokenDispenserProbe.ref,
+        BackendSingletonCollection(Map.empty),
+        AllBackendInitializationData(Map.empty),
+        restart
+      ) {
+        override def createSubWorkflowPreparationActor(subWorkflowId: WorkflowId) = preparationActor.ref
+        override def createSubWorkflowActor(createSubWorkflowActor: EngineWorkflowDescriptor) = subWorkflowActor.ref
+      }), parentProbe.ref, s"SubWorkflowExecutionActorSpec-${UUID.randomUUID()}")
+  }
+  
+  it should "Check the sub workflow store when restarting" in {
+    val ewea = buildEWEA(restart = true)
+    ewea.setState(SubWorkflowPendingState)
+
+    ewea ! Execute
+    subWorkflowStoreProbe.expectMsg(QuerySubWorkflow(parentWorkflowId, subKey))
+    eventually {
+      ewea.stateName shouldBe SubWorkflowCheckingStoreState
+    }
+  }
+
+  it should "Reuse sub workflow id if found in the store" in {
+    import cromwell.core.ExecutionIndex._
+    
+    val ewea = buildEWEA(restart = true)
+    ewea.setState(SubWorkflowCheckingStoreState)
+    
+    val subWorkflowUuid = WorkflowId.randomId()
+    ewea ! SubWorkflowFound(SubWorkflowStoreEntry(Option(0), parentWorkflowId.toString, subKey.scope.fullyQualifiedName, subKey.index.fromIndex, subKey.attempt, subWorkflowUuid.toString, None))
+    preparationActor.expectMsg(CallPreparationActor.Start)
+    parentProbe.expectMsg(JobStarting(subKey))
+    
+    eventually {
+      ewea.stateName shouldBe SubWorkflowPreparingState
+      ewea.stateData.subWorkflowId shouldBe Some(subWorkflowUuid)
+    }
+  }
+
+  it should "Fall back to a random Id if the sub workflow id is not found in the store" in {
+    val ewea = buildEWEA(restart = true)
+    ewea.setState(SubWorkflowCheckingStoreState)
+
+    ewea ! SubWorkflowNotFound(QuerySubWorkflow(parentWorkflowId, subKey))
+    preparationActor.expectMsg(CallPreparationActor.Start)
+    parentProbe.expectMsg(JobStarting(subKey))
+    
+    eventually {
+      ewea.stateName shouldBe SubWorkflowPreparingState
+      ewea.stateData.subWorkflowId should not be empty
+    }
+  }
+  
+  it should "Prepare a sub workflow" in {
+    val ewea = buildEWEA()
+    ewea.setState(SubWorkflowPendingState)
+    
+    ewea ! Execute
+    preparationActor.expectMsg(CallPreparationActor.Start)
+    parentProbe.expectMsg(JobStarting(subKey))
+    eventually {
+      ewea.stateName shouldBe SubWorkflowPreparingState
+    }
+  }
+
+  it should "Run a sub workflow" in {
+    val ewea = buildEWEA()
+    ewea.setState(SubWorkflowPreparingState, SubWorkflowExecutionActorData(Some(WorkflowId.randomId())))
+
+    val subWorkflowId = WorkflowId.randomId()
+    val subBackendDescriptor = mock[BackendWorkflowDescriptor]
+    subBackendDescriptor.id returns subWorkflowId
+    val subWorkflowDescriptor = EngineWorkflowDescriptor(
+      mock[WdlNamespaceWithWorkflow],
+      subBackendDescriptor,
+      Map.empty,
+      Map.empty,
+      ContinueWhilePossible,
+      List.empty,
+      CallCachingOff
+    )
+    
+    ewea ! SubWorkflowPreparationSucceeded(subWorkflowDescriptor, Map.empty)
+    subWorkflowActor.expectMsg(WorkflowExecutionActor.ExecuteWorkflowCommand)
+    parentProbe.expectMsg(JobRunning(subKey, Map.empty, Option(subWorkflowActor.ref)))
+    eventually {
+      ewea.stateName shouldBe SubWorkflowRunningState
+    }
+  }
+
+  it should "Fail a sub workflow if preparation failed" in {
+    val ewea = buildEWEA()
+    ewea.setState(SubWorkflowPreparingState)
+    deathWatch watch ewea
+
+    val subWorkflowKey = mock[SubWorkflowKey]
+    val throwable: Exception = new Exception("Expected test exception")
+    val preparationFailedMessage: CallPreparationFailed = CallPreparationFailed(subWorkflowKey, throwable)
+    ewea ! preparationFailedMessage
+    parentProbe.expectMsg(SubWorkflowFailedResponse(subKey, Map.empty, throwable))
+    deathWatch.expectTerminated(ewea, awaitTimeout)
+  }
+  
+  it should "Relay Workflow Successful message" in {
+    val ewea = buildEWEA()
+    ewea.setState(SubWorkflowRunningState, SubWorkflowExecutionActorData(Some(WorkflowId.randomId())))
+
+    deathWatch watch ewea
+
+    val jobExecutionMap: JobExecutionMap = Map.empty
+    val outputs: CallOutputs = Map.empty[LocallyQualifiedName, JobOutput]
+    val workflowSuccessfulMessage = WorkflowExecutionSucceededResponse(jobExecutionMap, outputs)
+    ewea ! workflowSuccessfulMessage
+    parentProbe.expectMsg(SubWorkflowSucceededResponse(subKey, jobExecutionMap, outputs))
+    deathWatch.expectTerminated(ewea, awaitTimeout)
+  }
+
+  it should "Relay Workflow Failed message" in {
+    val ewea = buildEWEA()
+    ewea.setState(SubWorkflowRunningState, SubWorkflowExecutionActorData(Some(WorkflowId.randomId())))
+
+    deathWatch watch ewea
+
+    val jobExecutionMap: JobExecutionMap = Map.empty
+    val expectedException: Exception = new Exception("Expected test exception")
+    
+    val workflowSuccessfulMessage = WorkflowExecutionFailedResponse(jobExecutionMap, expectedException)
+    ewea ! workflowSuccessfulMessage
+    parentProbe.expectMsg(SubWorkflowFailedResponse(subKey, jobExecutionMap, expectedException))
+    deathWatch.expectTerminated(ewea, awaitTimeout)
+  }
+
+  it should "Relay Workflow Aborted message" in {
+    val ewea = buildEWEA()
+    ewea.setState(SubWorkflowRunningState, SubWorkflowExecutionActorData(Some(WorkflowId.randomId())))
+
+    deathWatch watch ewea
+
+    val jobExecutionMap: JobExecutionMap = Map.empty
+    val workflowAbortedMessage = WorkflowExecutionAbortedResponse(jobExecutionMap)
+    ewea ! workflowAbortedMessage
+    parentProbe.expectMsg(SubWorkflowAbortedResponse(subKey, jobExecutionMap))
+    deathWatch.expectTerminated(ewea, awaitTimeout)
+  }
+
+}
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorSpec.scala
index 01af65d1aeb..51007a2dfc8 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorSpec.scala
@@ -12,13 +12,13 @@ import cromwell.engine.workflow.tokens.JobExecutionTokenDispenserActor
 import cromwell.services.ServiceRegistryActor
 import cromwell.services.metadata.MetadataService
 import cromwell.util.SampleWdl
-import cromwell.{AlwaysHappyJobStoreActor, CromwellTestkitSpec, EmptyCallCacheReadActor, MetadataWatchActor}
+import cromwell._
 import org.scalatest.BeforeAndAfter
 
-import scala.concurrent.{Await, Promise}
 import scala.concurrent.duration._
+import scala.concurrent.{Await, Promise}
 
-class WorkflowExecutionActorSpec extends CromwellTestkitSpec with BeforeAndAfter with WorkflowDescriptorBuilder {
+class WorkflowExecutionActorSpec extends CromwellTestKitSpec with BeforeAndAfter with WorkflowDescriptorBuilder {
 
   override implicit val actorSystem = system
   implicit val DefaultDuration = 20.seconds.dilated
@@ -53,6 +53,7 @@ class WorkflowExecutionActorSpec extends CromwellTestkitSpec with BeforeAndAfter
       val metadataWatcherProps = Props(MetadataWatchActor(metadataSuccessPromise, requiredMetadataMatchers: _*))
       val serviceRegistryActor = system.actorOf(ServiceRegistryActor.props(ConfigFactory.load(), overrides = Map(MetadataService.MetadataServiceName -> metadataWatcherProps)))
       val jobStoreActor = system.actorOf(AlwaysHappyJobStoreActor.props)
+      val subWorkflowStoreActor = system.actorOf(AlwaysHappySubWorkflowStoreActor.props)
       val jobTokenDispenserActor = system.actorOf(JobExecutionTokenDispenserActor.props)
       val MockBackendConfigEntry = BackendConfigurationEntry(
         name = "Mock",
@@ -66,12 +67,12 @@ class WorkflowExecutionActorSpec extends CromwellTestkitSpec with BeforeAndAfter
       val callCacheReadActor = TestProbe()
 
       val workflowExecutionActor = system.actorOf(
-        WorkflowExecutionActor.props(workflowId, engineWorkflowDescriptor, serviceRegistryActor, jobStoreActor,
+        WorkflowExecutionActor.props(engineWorkflowDescriptor, serviceRegistryActor, jobStoreActor, subWorkflowStoreActor,
           callCacheReadActor.ref, jobTokenDispenserActor, MockBackendSingletonCollection, AllBackendInitializationData.empty, restarting = false),
         "WorkflowExecutionActor")
 
       EventFilter.info(pattern = ".*Final Outputs", occurrences = 1).intercept {
-        EventFilter.info(pattern = "Starting calls: hello.hello", occurrences = 3).intercept {
+        EventFilter.info(pattern = "Starting calls: wf_hello.hello", occurrences = 3).intercept {
           workflowExecutionActor ! ExecuteWorkflowCommand
         }
       }
@@ -86,6 +87,7 @@ class WorkflowExecutionActorSpec extends CromwellTestkitSpec with BeforeAndAfter
     "execute a workflow with scatters" in {
       val serviceRegistry = mockServiceRegistryActor
       val jobStore = system.actorOf(AlwaysHappyJobStoreActor.props)
+      val subWorkflowStoreActor = system.actorOf(AlwaysHappySubWorkflowStoreActor.props)
       val callCacheReadActor = system.actorOf(EmptyCallCacheReadActor.props)
       val jobTokenDispenserActor = system.actorOf(JobExecutionTokenDispenserActor.props)
 
@@ -99,7 +101,7 @@ class WorkflowExecutionActorSpec extends CromwellTestkitSpec with BeforeAndAfter
       val workflowId = WorkflowId.randomId()
       val engineWorkflowDescriptor = createMaterializedEngineWorkflowDescriptor(workflowId, SampleWdl.SimpleScatterWdl.asWorkflowSources(runtime = runtimeSection))
       val workflowExecutionActor = system.actorOf(
-        WorkflowExecutionActor.props(workflowId, engineWorkflowDescriptor, serviceRegistry, jobStore,
+        WorkflowExecutionActor.props(engineWorkflowDescriptor, serviceRegistry, jobStore, subWorkflowStoreActor,
           callCacheReadActor, jobTokenDispenserActor, MockBackendSingletonCollection, AllBackendInitializationData.empty, restarting = false),
         "WorkflowExecutionActor")
 
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActorSpec.scala
index d79a383fbf8..34ac835cd31 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActorSpec.scala
@@ -1,23 +1,23 @@
 package cromwell.engine.workflow.lifecycle.execution.callcaching
 
 import akka.actor.{ActorRef, ActorSystem, Props}
-import akka.testkit.{ImplicitSender, TestKit, TestProbe}
+import akka.testkit.{ImplicitSender, TestProbe}
 import cats.data.NonEmptyList
-import cromwell.CromwellTestkitSpec
+import cromwell.CromwellTestKitSpec
+import cromwell.backend._
 import cromwell.backend.callcaching.FileHashingActor.{FileHashResponse, SingleFileHashRequest}
-import cromwell.backend.{BackendInitializationData, BackendJobDescriptor, BackendJobDescriptorKey, BackendWorkflowDescriptor, RuntimeAttributeDefinition}
 import cromwell.core.callcaching._
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.{CacheHit, CacheMiss, CallCacheHashes}
 import org.scalatest.mockito.MockitoSugar
-import org.scalatest.{BeforeAndAfterAll, Matchers, WordSpecLike}
+import org.scalatest.{Matchers, WordSpecLike}
 import wdl4s._
 import wdl4s.values.{WdlFile, WdlValue}
 
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-class EngineJobHashingActorSpec extends TestKit(new CromwellTestkitSpec.TestWorkflowManagerSystem().actorSystem)
-  with ImplicitSender with WordSpecLike with Matchers with MockitoSugar with BeforeAndAfterAll {
+class EngineJobHashingActorSpec extends CromwellTestKitSpec
+  with ImplicitSender with WordSpecLike with Matchers with MockitoSugar {
 
   import EngineJobHashingActorSpec._
 
@@ -162,13 +162,9 @@ class EngineJobHashingActorSpec extends TestKit(new CromwellTestkitSpec.TestWork
       }
     }
   }
-
-  override def afterAll() = {
-    TestKit.shutdownActorSystem(system)
-  }
 }
 
-object EngineJobHashingActorSpec extends MockitoSugar {
+object EngineJobHashingActorSpec extends BackendSpec {
   import org.mockito.Mockito._
 
   def createEngineJobHashingActor
@@ -198,12 +194,12 @@ object EngineJobHashingActorSpec extends MockitoSugar {
 
   def templateJobDescriptor(inputs: Map[LocallyQualifiedName, WdlValue] = Map.empty) = {
     val task = mock[Task]
-    val call = mock[Call]
+    val call = mock[TaskCall]
     when(task.commandTemplateString).thenReturn("Do the stuff... now!!")
     when(task.outputs).thenReturn(List.empty)
     when(call.task).thenReturn(task)
     val workflowDescriptor = mock[BackendWorkflowDescriptor]
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, BackendJobDescriptorKey(call, None, 1), Map.empty, inputs)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, BackendJobDescriptorKey(call, None, 1), Map.empty, fqnMapToDeclarationMap(inputs))
     jobDescriptor
   }
 
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaBackendIsCopyingCachedOutputsSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaBackendIsCopyingCachedOutputsSpec.scala
index 7aa4ccfda04..b3971175944 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaBackendIsCopyingCachedOutputsSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaBackendIsCopyingCachedOutputsSpec.scala
@@ -3,9 +3,10 @@ package cromwell.engine.workflow.lifecycle.execution.ejea
 import cats.data.NonEmptyList
 import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor._
 import EngineJobExecutionActorSpec._
-import cromwell.core.callcaching.CallCachingMode
+import cromwell.core.callcaching._
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.{CacheHit, CallCacheHashes, EJHAResponse, HashError}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCachingEntryId
+
 import scala.util.{Failure, Success, Try}
 import cromwell.engine.workflow.lifecycle.execution.ejea.HasJobSuccessResponse.SuccessfulCallCacheHashes
 
@@ -97,20 +98,43 @@ class EjeaBackendIsCopyingCachedOutputsSpec extends EngineJobExecutionActorSpec
           }
         }
 
+        if (mode.readFromCache) {
           s"invalidate a call for caching if backend coping failed when it was going to receive $hashComboName, if call caching is $mode" in {
             ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, mode)
             // Send the response from the copying actor
             ejea ! failureNonRetryableResponse
 
             expectInvalidateCallCacheActor(cacheId)
-            eventually { ejea.stateName should be(InvalidatingCacheEntry) }
-            ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper. bjeaProps, initialHashData, cacheHit))
+            eventually {
+              ejea.stateName should be(InvalidatingCacheEntry)
+            }
+            ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, initialHashData, cacheHit))
+          }
+
+          s"not invalidate a call for caching if backend coping failed when invalidation is disabled, when it was going to receive $hashComboName, if call caching is $mode" in {
+            val invalidationDisabledOptions = CallCachingOptions(invalidateBadCacheResults = false)
+            val cacheInvalidationDisabledMode = mode match {
+              case CallCachingActivity(rw, options) => CallCachingActivity(rw, invalidationDisabledOptions)
+              case _ => fail(s"Mode $mode not appropriate for cache invalidation tests")
+            }
+            ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, cacheInvalidationDisabledMode)
+            // Send the response from the copying actor
+            ejea ! failureNonRetryableResponse
+
+            eventually {
+              ejea.stateName should be(RunningJob)
+            }
+            // Make sure we didn't start invalidating anything:
+            helper.invalidateCacheActorCreations.hasExactlyOne should be(false)
+            ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, initialHashData, None))
           }
 
           s"invalidate a call for caching if backend coping failed (preserving and received hashes) when call caching is $mode, the EJEA has $hashComboName and then gets a success result" in {
             ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, mode)
             // Send the response from the EJHA (if there was one!):
-            ejhaResponse foreach { ejea ! _ }
+            ejhaResponse foreach {
+              ejea ! _
+            }
 
             // Nothing should happen here:
             helper.jobStoreProbe.expectNoMsg(awaitAlmostNothing)
@@ -120,9 +144,12 @@ class EjeaBackendIsCopyingCachedOutputsSpec extends EngineJobExecutionActorSpec
             ejea ! failureNonRetryableResponse
 
             expectInvalidateCallCacheActor(cacheId)
-            eventually { ejea.stateName should be(InvalidatingCacheEntry) }
-            ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper. bjeaProps, finalHashData, cacheHit))
+            eventually {
+              ejea.stateName should be(InvalidatingCacheEntry)
+            }
+            ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, finalHashData, cacheHit))
           }
+        }
       }
     }
   }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingJobStoreSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingJobStoreSpec.scala
index a8f2bdf46b5..5a9bb4f5c2a 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingJobStoreSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingJobStoreSpec.scala
@@ -1,9 +1,9 @@
 package cromwell.engine.workflow.lifecycle.execution.ejea
 
-import cromwell.backend.BackendJobExecutionActor.{FailedNonRetryableResponse, FailedRetryableResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{JobFailedNonRetryableResponse, JobFailedRetryableResponse, JobSucceededResponse}
 import cromwell.core._
+import cromwell.engine.workflow.lifecycle.execution.CallPreparationActor
 import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor.{CheckingJobStore, NoData, PreparingJob}
-import cromwell.engine.workflow.lifecycle.execution.JobPreparationActor
 import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec.EnhancedTestEJEA
 import cromwell.jobstore.JobStoreActor.{JobComplete, JobNotComplete}
 import cromwell.jobstore.{JobResultFailure, JobResultSuccess}
@@ -17,12 +17,12 @@ class EjeaCheckingJobStoreSpec extends EngineJobExecutionActorSpec {
       createCheckingJobStoreEjea()
       ejea.setState(CheckingJobStore)
       val returnCode: Option[Int] = Option(0)
-      val jobOutputs: JobOutputs = Map.empty
+      val jobOutputs: CallOutputs = Map.empty
 
       ejea ! JobComplete(JobResultSuccess(returnCode, jobOutputs))
 
       helper.replyToProbe.expectMsgPF(awaitTimeout) {
-        case response: SucceededResponse =>
+        case response: JobSucceededResponse =>
           response.returnCode shouldBe returnCode
           response.jobOutputs shouldBe jobOutputs
       }
@@ -40,11 +40,11 @@ class EjeaCheckingJobStoreSpec extends EngineJobExecutionActorSpec {
         ejea ! JobComplete(JobResultFailure(returnCode, reason, retryable))
 
         helper.replyToProbe.expectMsgPF(awaitTimeout) {
-          case response: FailedNonRetryableResponse =>
+          case response: JobFailedNonRetryableResponse =>
             false should be(retryable)
             response.returnCode shouldBe returnCode
             response.throwable shouldBe reason
-          case response: FailedRetryableResponse =>
+          case response: JobFailedRetryableResponse =>
             true should be(retryable)
             response.returnCode shouldBe returnCode
             response.throwable shouldBe reason
@@ -59,7 +59,7 @@ class EjeaCheckingJobStoreSpec extends EngineJobExecutionActorSpec {
       ejea.setState(CheckingJobStore)
       ejea ! JobNotComplete
 
-      helper.jobPreparationProbe.expectMsg(awaitTimeout, "expecting RecoverJobCommand", JobPreparationActor.Start)
+      helper.jobPreparationProbe.expectMsg(awaitTimeout, "expecting RecoverJobCommand", CallPreparationActor.Start)
       ejea.stateName should be(PreparingJob)
 
       ejea.stop()
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPreparingJobSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPreparingJobSpec.scala
index 1d6f2ccbe5b..bdb426b6037 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPreparingJobSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPreparingJobSpec.scala
@@ -1,9 +1,10 @@
 package cromwell.engine.workflow.lifecycle.execution.ejea
 
-import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor._
-import EngineJobExecutionActorSpec._
+import cromwell.backend.BackendJobExecutionActor.JobFailedNonRetryableResponse
 import cromwell.core.callcaching.CallCachingMode
-import cromwell.engine.workflow.lifecycle.execution.JobPreparationActor.{BackendJobPreparationFailed, BackendJobPreparationSucceeded}
+import cromwell.engine.workflow.lifecycle.execution.CallPreparationActor.{BackendJobPreparationSucceeded, CallPreparationFailed}
+import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor._
+import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec._
 import org.scalatest.concurrent.Eventually
 
 class EjeaPreparingJobSpec extends EngineJobExecutionActorSpec with CanExpectHashingInitialization with Eventually {
@@ -34,10 +35,11 @@ class EjeaPreparingJobSpec extends EngineJobExecutionActorSpec with CanExpectHas
       }
 
       s"Not proceed if Job Preparation fails ($mode)" in {
-        val prepFailedResponse = BackendJobPreparationFailed(helper.jobDescriptorKey, new Exception("The goggles! They do nothing!"))
+        val prepActorResponse = CallPreparationFailed(helper.jobDescriptorKey, new Exception("The goggles! They do nothing!"))
+        val prepFailedEjeaResponse = JobFailedNonRetryableResponse(helper.jobDescriptorKey, prepActorResponse.throwable, None)
         ejea = ejeaInPreparingState(mode)
-        ejea ! prepFailedResponse
-        helper.replyToProbe.expectMsg(prepFailedResponse)
+        ejea ! prepActorResponse
+        helper.replyToProbe.expectMsg(prepFailedEjeaResponse)
         helper.deathwatch.expectTerminated(ejea, awaitTimeout)
       }
     }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingExecutionTokenSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingExecutionTokenSpec.scala
index 83ae088350a..3047de56099 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingExecutionTokenSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingExecutionTokenSpec.scala
@@ -1,7 +1,7 @@
 package cromwell.engine.workflow.lifecycle.execution.ejea
 
+import cromwell.engine.workflow.lifecycle.execution.CallPreparationActor
 import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor._
-import cromwell.engine.workflow.lifecycle.execution.JobPreparationActor
 import cromwell.engine.workflow.tokens.JobExecutionTokenDispenserActor.{JobExecutionTokenDenied, JobExecutionTokenDispensed}
 import cromwell.jobstore.JobStoreActor.QueryJobCompletion
 import org.scalatest.concurrent.Eventually
@@ -45,7 +45,7 @@ class EjeaRequestingExecutionTokenSpec extends EngineJobExecutionActorSpec with
         ejea = helper.buildEJEA(restarting = false)
         ejea ! JobExecutionTokenDispensed(helper.executionToken)
 
-        helper.jobPreparationProbe.expectMsg(max = awaitTimeout, hint = "Awaiting job preparation", JobPreparationActor.Start)
+        helper.jobPreparationProbe.expectMsg(max = awaitTimeout, hint = "Awaiting job preparation", CallPreparationActor.Start)
         helper.jobStoreProbe.expectNoMsg(awaitAlmostNothing)
         ejea.stateName should be(PreparingJob)
       }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingJobStoreSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingJobStoreSpec.scala
index 1b783a69e7b..73a224a004c 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingJobStoreSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingJobStoreSpec.scala
@@ -1,7 +1,7 @@
 package cromwell.engine.workflow.lifecycle.execution.ejea
 
 import EngineJobExecutionActorSpec._
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, FailedNonRetryableResponse}
+import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, JobFailedNonRetryableResponse}
 import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor._
 import cromwell.jobstore.JobStoreActor.{JobStoreWriteFailure, JobStoreWriteSuccess}
 import cromwell.engine.workflow.lifecycle.execution.ejea.HasJobSuccessResponse.SuccessfulCallCacheHashes
@@ -33,7 +33,7 @@ class EjeaUpdatingJobStoreSpec extends EngineJobExecutionActorSpec with HasJobSu
       val exception = new Exception("I loved Ophelia: forty thousand brothers\\ Could not, with all their quantity of love,\\ Make up my sum. What wilt thou do for her?")
       ejea ! JobStoreWriteFailure(exception)
       helper.replyToProbe.expectMsgPF(awaitTimeout) {
-        case FailedNonRetryableResponse(jobDescriptorKey, reason, None) =>
+        case JobFailedNonRetryableResponse(jobDescriptorKey, reason, None) =>
           jobDescriptorKey should be(helper.jobDescriptorKey)
           reason.getCause should be(exception)
       }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpec.scala
index cbba498116c..10577678154 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpec.scala
@@ -4,7 +4,7 @@ import akka.actor.Actor
 import akka.testkit.TestFSMRef
 import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor._
 import cromwell.jobstore.{Pending => _}
-import cromwell.CromwellTestkitSpec
+import cromwell.CromwellTestKitSpec
 import cromwell.backend.BackendJobExecutionActor
 import cromwell.backend.BackendJobExecutionActor.BackendJobExecutionActorCommand
 import cromwell.core.callcaching._
@@ -15,7 +15,7 @@ import scala.concurrent.duration._
 import scala.language.postfixOps
 
 
-trait EngineJobExecutionActorSpec extends CromwellTestkitSpec
+trait EngineJobExecutionActorSpec extends CromwellTestKitSpec
   with Matchers with Mockito with BeforeAndAfterAll with BeforeAndAfter {
 
   // If we WANT something to happen, make sure it happens within this window:
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpecUtil.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpecUtil.scala
index 8ef607c5b80..b6ddb560169 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpecUtil.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpecUtil.scala
@@ -1,6 +1,6 @@
 package cromwell.engine.workflow.lifecycle.execution.ejea
 
-import cromwell.backend.BackendJobExecutionActor.{AbortedResponse, FailedNonRetryableResponse, FailedRetryableResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{AbortedResponse, JobFailedNonRetryableResponse, JobFailedRetryableResponse, JobSucceededResponse}
 import cromwell.core.JobOutput
 import cromwell.core.callcaching._
 import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor.{EJEAData, SucceededResponseData, UpdatingCallCache, UpdatingJobStore}
@@ -23,7 +23,7 @@ private[ejea] trait CanValidateJobStoreKey { self: EngineJobExecutionActorSpec =
 }
 
 private[ejea] trait CanExpectCacheWrites extends Eventually { self: EngineJobExecutionActorSpec =>
-  def expectCacheWrite(expectedResponse: SucceededResponse, expectedCallCacheHashes: CallCacheHashes): Unit = {
+  def expectCacheWrite(expectedResponse: JobSucceededResponse, expectedCallCacheHashes: CallCacheHashes): Unit = {
     eventually { ejea.stateName should be(UpdatingCallCache) }
     ejea.stateData should be(SucceededResponseData(expectedResponse, Some(Success(expectedCallCacheHashes))))
     helper.callCacheWriteActorCreations match {
@@ -83,7 +83,7 @@ private[ejea] trait CanExpectCacheInvalidation extends Eventually { self: Engine
 private[ejea] trait HasJobSuccessResponse { self: EngineJobExecutionActorSpec =>
   val successRc = Option(171)
   val successOutputs = Map("a" -> JobOutput(WdlInteger(3)), "b" -> JobOutput(WdlString("bee")))
-  def successResponse = SucceededResponse(helper.jobDescriptorKey, successRc, successOutputs, None, Seq.empty)
+  def successResponse = JobSucceededResponse(helper.jobDescriptorKey, successRc, successOutputs, None, Seq.empty)
 }
 private[ejea] object HasJobSuccessResponse {
   val SuccessfulCallCacheHashes = CallCacheHashes(Set(HashResult(HashKey("whatever you want"), HashValue("whatever you need"))))
@@ -93,7 +93,7 @@ private[ejea] trait HasJobFailureResponses { self: EngineJobExecutionActorSpec =
   val failedRc = Option(12)
   val failureReason = new Exception("The sixth sheik's sheep is sick!")
   // Need to delay making the response because job descriptors come from the per-test "helper", which is null outside tests!
-  def failureRetryableResponse = FailedRetryableResponse(helper.jobDescriptorKey, failureReason, failedRc)
-  def failureNonRetryableResponse = FailedNonRetryableResponse(helper.jobDescriptorKey, failureReason, Option(12))
+  def failureRetryableResponse = JobFailedRetryableResponse(helper.jobDescriptorKey, failureReason, failedRc)
+  def failureNonRetryableResponse = JobFailedNonRetryableResponse(helper.jobDescriptorKey, failureReason, Option(12))
   def abortedResponse = AbortedResponse(helper.jobDescriptorKey)
 }
\ No newline at end of file
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/PerTestHelper.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/PerTestHelper.scala
index 16274a27508..9389362ad41 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/PerTestHelper.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/PerTestHelper.scala
@@ -4,29 +4,27 @@ import java.util.UUID
 
 import akka.actor.{ActorRef, ActorSystem, Props}
 import akka.testkit.{TestFSMRef, TestProbe}
-import cromwell.backend.BackendJobExecutionActor.SucceededResponse
-import cromwell.backend.{BackendInitializationData, BackendJobDescriptor, BackendJobDescriptorKey, BackendLifecycleActorFactory, BackendWorkflowDescriptor}
+import cromwell.backend.BackendJobExecutionActor.JobSucceededResponse
+import cromwell.backend._
 import cromwell.core.JobExecutionToken.JobExecutionTokenType
 import cromwell.core.callcaching.{CallCachingActivity, CallCachingMode, CallCachingOff}
-import cromwell.core.{ExecutionStore, JobExecutionToken, OutputStore, WorkflowId}
+import cromwell.core.{CallOutputs, JobExecutionToken, WorkflowId}
 import cromwell.engine.EngineWorkflowDescriptor
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCachingEntryId
-import cromwell.engine.workflow.lifecycle.execution.{EngineJobExecutionActor, WorkflowExecutionActorData}
 import cromwell.engine.workflow.lifecycle.execution.EngineJobExecutionActor.{EJEAData, EngineJobExecutionActorState}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCachingEntryId
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.CallCacheHashes
+import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec._
+import cromwell.engine.workflow.lifecycle.execution.{EngineJobExecutionActor, WorkflowExecutionActorData}
+import cromwell.engine.workflow.mocks.{DeclarationMock, TaskMock, WdlExpressionMock}
+import cromwell.util.AkkaTestUtil._
 import org.specs2.mock.Mockito
-import wdl4s.WdlExpression.ScopedLookupFunction
-import wdl4s.expression.{NoFunctions, WdlFunctions, WdlStandardLibraryFunctions}
-import wdl4s.types.{WdlIntegerType, WdlStringType}
-import wdl4s.values.{WdlInteger, WdlString, WdlValue}
 import wdl4s._
-import cromwell.util.AkkaTestUtil._
-import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec._
-
-import scala.util.Success
+import wdl4s.expression.{NoFunctions, WdlStandardLibraryFunctions}
+import wdl4s.parser.WdlParser.Ast
+import wdl4s.types.{WdlIntegerType, WdlStringType}
 
 
-private[ejea] class PerTestHelper(implicit val system: ActorSystem) extends Mockito {
+private[ejea] class PerTestHelper(implicit val system: ActorSystem) extends Mockito with TaskMock with WdlExpressionMock with DeclarationMock {
 
   val workflowId = WorkflowId.randomId()
   val workflowName = "wf"
@@ -37,34 +35,29 @@ private[ejea] class PerTestHelper(implicit val system: ActorSystem) extends Mock
 
   val executionToken = JobExecutionToken(JobExecutionTokenType("test", None), UUID.randomUUID())
 
-  val task = mock[Task]
-  task.declarations returns Seq.empty
-  task.runtimeAttributes returns RuntimeAttributes(Map.empty)
-  task.commandTemplateString returns "!!shazam!!"
-  val stringOutputExpression = mock[WdlExpression]
-  stringOutputExpression.valueString returns "hello"
-  stringOutputExpression.evaluate(any[ScopedLookupFunction], any[ WdlFunctions[WdlValue]]) returns Success(WdlString("hello"))
-  task.outputs returns Seq(TaskOutput("outString", WdlStringType, stringOutputExpression))
-
-  val intInputExpression = mock[WdlExpression]
-  intInputExpression.valueString returns "543"
-  intInputExpression.evaluate(any[ScopedLookupFunction], any[WdlFunctions[WdlValue]]) returns Success(WdlInteger(543))
-
-  val intInputDeclaration = mock[Declaration]
-  intInputDeclaration.name returns "inInt"
-  intInputDeclaration.expression returns Option(intInputExpression)
-  intInputDeclaration.wdlType returns WdlIntegerType
-  task.declarations returns Seq(intInputDeclaration)
-
-  val call: Call = Call(None, jobFqn, task, Set.empty, Map.empty, None)
+  val task = mockTask(
+    taskName,
+    declarations = Seq(mockDeclaration("inInt", WdlIntegerType, mockIntExpression(543))),
+    outputs = Seq(("outString", WdlStringType, mockStringExpression("hello")))
+  )
+
+  val workflow = new Workflow(
+    unqualifiedName = workflowName,
+    workflowOutputWildcards = Seq.empty,
+    wdlSyntaxErrorFormatter = mock[WdlSyntaxErrorFormatter],
+    meta = Map.empty,
+    parameterMeta = Map.empty,
+    ast = mock[Ast])
+  val call: TaskCall = TaskCall(None, task, Map.empty, mock[Ast])
+  call.parent_=(workflow)
   val jobDescriptorKey = BackendJobDescriptorKey(call, jobIndex, jobAttempt)
 
   val backendWorkflowDescriptor = BackendWorkflowDescriptor(workflowId, null, null, null)
-  val backendJobDescriptor = BackendJobDescriptor(backendWorkflowDescriptor, jobDescriptorKey, runtimeAttributes = Map.empty, inputs = Map.empty)
+  val backendJobDescriptor = BackendJobDescriptor(backendWorkflowDescriptor, jobDescriptorKey, runtimeAttributes = Map.empty, inputDeclarations = Map.empty)
 
   var fetchCachedResultsActorCreations: ExpectOne[(CallCachingEntryId, Seq[TaskOutput])] = NothingYet
   var jobHashingInitializations: ExpectOne[(BackendJobDescriptor, CallCachingActivity)] = NothingYet
-  var callCacheWriteActorCreations: ExpectOne[(CallCacheHashes, SucceededResponse)] = NothingYet
+  var callCacheWriteActorCreations: ExpectOne[(CallCacheHashes, JobSucceededResponse)] = NothingYet
   var invalidateCacheActorCreations: ExpectOne[CallCachingEntryId] = NothingYet
 
   val deathwatch = TestProbe()
@@ -94,12 +87,12 @@ private[ejea] class PerTestHelper(implicit val system: ActorSystem) extends Mock
 
     // These two factory methods should never be called from EJEA or any of its descendants:
     override def workflowFinalizationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                                calls: Seq[Call],
-                                                executionStore: ExecutionStore,
-                                                outputStore: OutputStore,
+                                                calls: Set[TaskCall],
+                                                jobExecutionMap: JobExecutionMap,
+                                                workflowOutputs: CallOutputs,
                                                 initializationData: Option[BackendInitializationData]): Option[Props] = throw new UnsupportedOperationException("Unexpected finalization actor creation!")
     override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                                  calls: Seq[Call],
+                                                  calls: Set[TaskCall],
                                                   serviceRegistryActor: ActorRef): Option[Props] = throw new UnsupportedOperationException("Unexpected finalization actor creation!")
   }
 
@@ -108,14 +101,14 @@ private[ejea] class PerTestHelper(implicit val system: ActorSystem) extends Mock
                (implicit startingState: EngineJobExecutionActorState): TestFSMRef[EngineJobExecutionActorState, EJEAData, MockEjea] = {
 
     val factory: BackendLifecycleActorFactory = buildFactory()
-    val descriptor = EngineWorkflowDescriptor(backendWorkflowDescriptor, Map.empty, null, null, null, callCachingMode)
+    val descriptor = EngineWorkflowDescriptor(mock[WdlNamespaceWithWorkflow], backendWorkflowDescriptor, Map.empty, null, null, null, callCachingMode)
 
     val myBrandNewEjea = new TestFSMRef[EngineJobExecutionActorState, EJEAData, MockEjea](system, Props(new MockEjea(
       helper = this,
       jobPreparationProbe = jobPreparationProbe,
       replyTo = replyToProbe.ref,
       jobDescriptorKey = jobDescriptorKey,
-      executionData = WorkflowExecutionActorData(descriptor, ExecutionStore(Map.empty), Map.empty, OutputStore(Map.empty)),
+      executionData = WorkflowExecutionActorData.empty(descriptor),
       factory = factory,
       initializationData = None,
       restarting = restarting,
@@ -149,9 +142,7 @@ private[ejea] class MockEjea(helper: PerTestHelper,
 
   override def makeFetchCachedResultsActor(cacheId: CallCachingEntryId, taskOutputs: Seq[TaskOutput]) = helper.fetchCachedResultsActorCreations = helper.fetchCachedResultsActorCreations.foundOne((cacheId, taskOutputs))
   override def initializeJobHashing(jobDescriptor: BackendJobDescriptor, activity: CallCachingActivity) = helper.jobHashingInitializations = helper.jobHashingInitializations.foundOne((jobDescriptor, activity))
-  override def createSaveCacheResultsActor(hashes: CallCacheHashes, success: SucceededResponse) = helper.callCacheWriteActorCreations = helper.callCacheWriteActorCreations.foundOne((hashes, success))
-  override def invalidateCacheHit(cacheId: CallCachingEntryId): Unit = {
-    helper.invalidateCacheActorCreations = helper.invalidateCacheActorCreations.foundOne(cacheId)
-  }
+  override def createSaveCacheResultsActor(hashes: CallCacheHashes, success: JobSucceededResponse) = helper.callCacheWriteActorCreations = helper.callCacheWriteActorCreations.foundOne((hashes, success))
+  override def invalidateCacheHit(cacheId: CallCachingEntryId): Unit = { helper.invalidateCacheActorCreations = helper.invalidateCacheActorCreations.foundOne(cacheId) }
   override def createJobPreparationActor(jobPrepProps: Props, name: String) = jobPreparationProbe.ref
 }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/mocks/DeclarationMock.scala b/engine/src/test/scala/cromwell/engine/workflow/mocks/DeclarationMock.scala
new file mode 100644
index 00000000000..471d007772d
--- /dev/null
+++ b/engine/src/test/scala/cromwell/engine/workflow/mocks/DeclarationMock.scala
@@ -0,0 +1,21 @@
+package cromwell.engine.workflow.mocks
+
+import org.specs2.mock.Mockito
+import wdl4s.{Declaration, WdlExpression}
+import wdl4s.types.WdlType
+
+object DeclarationMock {
+  type DeclarationMockType = (String, WdlType, WdlExpression)
+}
+
+trait DeclarationMock extends Mockito {
+  def mockDeclaration(name: String,
+                      wdlType: WdlType,
+                      expression: WdlExpression) = {
+    val declaration = mock[Declaration]
+    declaration.unqualifiedName returns name
+    declaration.expression returns Option(expression)
+    declaration.wdlType returns wdlType
+    declaration
+  }
+}
diff --git a/engine/src/test/scala/cromwell/engine/workflow/mocks/TaskMock.scala b/engine/src/test/scala/cromwell/engine/workflow/mocks/TaskMock.scala
new file mode 100644
index 00000000000..4d8ef9c1d29
--- /dev/null
+++ b/engine/src/test/scala/cromwell/engine/workflow/mocks/TaskMock.scala
@@ -0,0 +1,27 @@
+package cromwell.engine.workflow.mocks
+
+import cromwell.engine.workflow.mocks.DeclarationMock.DeclarationMockType
+import org.specs2.mock.Mockito
+import wdl4s._
+import wdl4s.parser.WdlParser.Ast
+
+trait TaskMock extends Mockito {
+  
+  def mockTask(name: String,
+               declarations: Seq[Declaration] = Seq.empty,
+               runtimeAttributes: RuntimeAttributes = new RuntimeAttributes(Map.empty),
+               commandTemplateString: String = "!!shazam!!",
+               outputs: Seq[DeclarationMockType] = Seq.empty
+              ) = {
+    val task = mock[Task]
+    task.declarations returns declarations
+    task.runtimeAttributes returns runtimeAttributes
+    task.commandTemplateString returns commandTemplateString
+    task.name returns name
+    task.unqualifiedName returns name
+    task.outputs returns (outputs map {
+      case (outputName, wdlType, expression) => TaskOutput(outputName, wdlType, expression, mock[Ast], Option(task))
+    })
+    task
+  }
+}
diff --git a/engine/src/test/scala/cromwell/engine/workflow/mocks/WdlExpressionMock.scala b/engine/src/test/scala/cromwell/engine/workflow/mocks/WdlExpressionMock.scala
new file mode 100644
index 00000000000..6bb15b306f5
--- /dev/null
+++ b/engine/src/test/scala/cromwell/engine/workflow/mocks/WdlExpressionMock.scala
@@ -0,0 +1,32 @@
+package cromwell.engine.workflow.mocks
+
+import org.specs2.mock.Mockito
+import wdl4s.WdlExpression
+import wdl4s.WdlExpression._
+import wdl4s.expression.WdlFunctions
+import wdl4s.values.{WdlInteger, WdlString, WdlValue}
+
+import scala.util.Success
+
+trait WdlExpressionMock extends Mockito {
+  val helloStringExpression = {
+    val expression = mock[WdlExpression]
+    expression.valueString returns "hello"
+    expression.evaluate(any[ScopedLookupFunction], any[ WdlFunctions[WdlValue]]) returns Success(WdlString("hello"))
+    expression
+  }
+  
+  def mockStringExpression(value: String) = {
+    val expression = mock[WdlExpression]
+    expression.valueString returns value
+    expression.evaluate(any[ScopedLookupFunction], any[ WdlFunctions[WdlValue]]) returns Success(WdlString(value))
+    expression
+  }
+
+  def mockIntExpression(value: Int) = {
+    val expression = mock[WdlExpression]
+    expression.valueString returns value.toString
+    expression.evaluate(any[ScopedLookupFunction], any[ WdlFunctions[WdlValue]]) returns Success(WdlInteger(value))
+    expression
+  }
+}
diff --git a/engine/src/test/scala/cromwell/jobstore/JobStoreServiceSpec.scala b/engine/src/test/scala/cromwell/jobstore/JobStoreServiceSpec.scala
index fa1cc5067d1..ac84a6c450c 100644
--- a/engine/src/test/scala/cromwell/jobstore/JobStoreServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/jobstore/JobStoreServiceSpec.scala
@@ -1,6 +1,6 @@
 package cromwell.jobstore
 
-import cromwell.CromwellTestkitSpec
+import cromwell.CromwellTestKitSpec
 import cromwell.backend.BackendJobDescriptorKey
 import cromwell.core.{JobOutput, WorkflowId}
 import cromwell.jobstore.JobStoreActor._
@@ -8,9 +8,10 @@ import cromwell.jobstore.JobStoreServiceSpec._
 import cromwell.services.SingletonServicesStore
 import org.scalatest.Matchers
 import org.specs2.mock.Mockito
+import wdl4s.parser.WdlParser.Ast
 import wdl4s.types.WdlStringType
 import wdl4s.values.WdlString
-import wdl4s.{Call, Task, TaskOutput, WdlExpression}
+import wdl4s._
 
 import scala.concurrent.duration._
 import scala.language.postfixOps
@@ -20,7 +21,7 @@ object JobStoreServiceSpec {
   val EmptyExpression = WdlExpression.fromString(""" "" """)
 }
 
-class JobStoreServiceSpec extends CromwellTestkitSpec with Matchers with Mockito {
+class JobStoreServiceSpec extends CromwellTestKitSpec with Matchers with Mockito {
 
   "JobStoreService" should {
     "work" in {
@@ -28,10 +29,10 @@ class JobStoreServiceSpec extends CromwellTestkitSpec with Matchers with Mockito
       val jobStoreService = system.actorOf(JobStoreActor.props(jobStore))
 
       val workflowId = WorkflowId.randomId()
-      val successCall = mock[Call]
+      val successCall = mock[TaskCall]
       successCall.fullyQualifiedName returns "foo.bar"
       val mockTask = mock[Task]
-      mockTask.outputs returns Seq(TaskOutput("baz", WdlStringType, EmptyExpression))
+      mockTask.outputs returns Seq(TaskOutput("baz", WdlStringType, EmptyExpression, mock[Ast], Option(mockTask)))
       successCall.task returns mockTask
 
       val successKey = BackendJobDescriptorKey(successCall, None, 1).toJobStoreKey(workflowId)
@@ -49,7 +50,7 @@ class JobStoreServiceSpec extends CromwellTestkitSpec with Matchers with Mockito
         case JobComplete(JobResultSuccess(Some(0), os)) if os == outputs =>
       }
 
-      val failureCall = mock[Call]
+      val failureCall = mock[TaskCall]
       failureCall.fullyQualifiedName returns "baz.qux"
       val failureKey = BackendJobDescriptorKey(failureCall, None, 1).toJobStoreKey(workflowId)
 
diff --git a/engine/src/test/scala/cromwell/jobstore/JobStoreWriterSpec.scala b/engine/src/test/scala/cromwell/jobstore/JobStoreWriterSpec.scala
index a6e59679aff..eabc86a5e31 100644
--- a/engine/src/test/scala/cromwell/jobstore/JobStoreWriterSpec.scala
+++ b/engine/src/test/scala/cromwell/jobstore/JobStoreWriterSpec.scala
@@ -1,7 +1,7 @@
 package cromwell.jobstore
 
 import akka.testkit.TestFSMRef
-import cromwell.CromwellTestkitSpec
+import cromwell.CromwellTestKitSpec
 import cromwell.core.WorkflowId
 import cromwell.jobstore.JobStoreActor.{JobStoreWriteSuccess, RegisterJobCompleted, RegisterWorkflowCompleted}
 import org.scalatest.{BeforeAndAfter, Matchers}
@@ -11,7 +11,7 @@ import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future, Promise}
 import scala.language.postfixOps
 
-class JobStoreWriterSpec extends CromwellTestkitSpec with Matchers with BeforeAndAfter {
+class JobStoreWriterSpec extends CromwellTestKitSpec with Matchers with BeforeAndAfter {
   
   var database: WriteCountingJobStore = _
   var jobStoreWriter: TestFSMRef[JobStoreWriterState, JobStoreWriterData, JobStoreWriterActor] = _
diff --git a/engine/src/test/scala/cromwell/subworkflowstore/SubWorkflowStoreSpec.scala b/engine/src/test/scala/cromwell/subworkflowstore/SubWorkflowStoreSpec.scala
new file mode 100644
index 00000000000..79e41bd705d
--- /dev/null
+++ b/engine/src/test/scala/cromwell/subworkflowstore/SubWorkflowStoreSpec.scala
@@ -0,0 +1,87 @@
+package cromwell.subworkflowstore
+
+import cromwell.CromwellTestKitSpec
+import cromwell.core.{JobKey, WorkflowId, WorkflowSourceFilesWithoutImports}
+import cromwell.services.SingletonServicesStore
+import cromwell.subworkflowstore.SubWorkflowStoreActor._
+import org.scalatest.Matchers
+import org.specs2.mock.Mockito
+import wdl4s.{TaskCall, WdlExpression}
+import cromwell.core.ExecutionIndex._
+
+import scala.concurrent.duration._
+import SubWorkflowStoreSpec._
+import akka.testkit.TestProbe
+import cromwell.database.sql.tables.SubWorkflowStoreEntry
+import cromwell.engine.workflow.workflowstore.WorkflowStoreActor.{SubmitWorkflow, WorkflowSubmittedToStore}
+import cromwell.engine.workflow.workflowstore.{SqlWorkflowStore, WorkflowStoreActor}
+
+import scala.language.postfixOps
+
+object SubWorkflowStoreSpec {
+  val MaxWait = 5 seconds
+  val EmptyExpression = WdlExpression.fromString(""" "" """)
+}
+
+class SubWorkflowStoreSpec extends CromwellTestKitSpec with Matchers with Mockito {
+  "SubWorkflowStore" should {
+    "work" in {
+      lazy val subWorkflowStore = new SqlSubWorkflowStore(SingletonServicesStore.databaseInterface)
+      val subWorkflowStoreService = system.actorOf(SubWorkflowStoreActor.props(subWorkflowStore))
+
+      lazy val workflowStore = SqlWorkflowStore(SingletonServicesStore.databaseInterface)
+      val workflowStoreService = system.actorOf(WorkflowStoreActor.props(workflowStore, TestProbe().ref))
+
+      val parentWorkflowId = WorkflowId.randomId()
+      val subWorkflowId = WorkflowId.randomId()
+      val subSubWorkflowId = WorkflowId.randomId()
+      val call = mock[TaskCall]
+      call.fullyQualifiedName returns "foo.bar"
+      val jobKey = new JobKey {
+        override def scope = call
+        override def index: Option[Int] = None
+        override def attempt: Int = 0
+        override def tag: String = "foobar"
+      }
+
+      workflowStoreService ! SubmitWorkflow(WorkflowSourceFilesWithoutImports("", "{}", "{}"))
+      val rootWorkflowId = expectMsgType[WorkflowSubmittedToStore](10 seconds).workflowId
+
+      // Query for non existing sub workflow
+      subWorkflowStoreService ! QuerySubWorkflow(parentWorkflowId, jobKey)
+      expectMsgType[SubWorkflowNotFound](MaxWait)
+      
+      // Register sub workflow
+      subWorkflowStoreService ! RegisterSubWorkflow(rootWorkflowId, parentWorkflowId, jobKey, subWorkflowId)
+      expectMsgType[SubWorkflowStoreRegisterSuccess](MaxWait)
+
+      // Query for sub workflow
+      subWorkflowStoreService ! QuerySubWorkflow(parentWorkflowId, jobKey)
+      val subWorkflowEntry = SubWorkflowStoreEntry(Option(0), parentWorkflowId.toString, jobKey.scope.fullyQualifiedName, jobKey.index.fromIndex, jobKey.attempt, subWorkflowId.toString, Some(0))
+      expectMsg[SubWorkflowFound](SubWorkflowFound(subWorkflowEntry))
+
+      // Register sub sub workflow
+      subWorkflowStoreService ! RegisterSubWorkflow(rootWorkflowId, subWorkflowId, jobKey, subSubWorkflowId)
+      expectMsgType[SubWorkflowStoreRegisterSuccess](MaxWait)
+
+      // Query for sub sub workflow
+      subWorkflowStoreService ! QuerySubWorkflow(subWorkflowId, jobKey)
+      val subSubWorkflowEntry = SubWorkflowStoreEntry(Option(0), subWorkflowId.toString, jobKey.scope.fullyQualifiedName, jobKey.index.fromIndex, jobKey.attempt, subSubWorkflowId.toString, Some(1))
+      expectMsg[SubWorkflowFound](SubWorkflowFound(subSubWorkflowEntry))
+      
+      // Delete root workflow
+      subWorkflowStoreService ! WorkflowComplete(rootWorkflowId)
+      expectMsgType[SubWorkflowStoreCompleteSuccess](MaxWait)
+
+      // Verify that everything is gone
+      subWorkflowStoreService ! QuerySubWorkflow(rootWorkflowId, jobKey)
+      expectMsgType[SubWorkflowNotFound](MaxWait)
+
+      subWorkflowStoreService ! QuerySubWorkflow(parentWorkflowId, jobKey)
+      expectMsgType[SubWorkflowNotFound](MaxWait)
+
+      subWorkflowStoreService ! QuerySubWorkflow(subWorkflowId, jobKey)
+      expectMsgType[SubWorkflowNotFound](MaxWait)
+    }
+  }
+}
diff --git a/engine/src/test/scala/cromwell/webservice/CromwellApiServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/CromwellApiServiceSpec.scala
index 9904835dc07..b3fbfee1e8c 100644
--- a/engine/src/test/scala/cromwell/webservice/CromwellApiServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/CromwellApiServiceSpec.scala
@@ -7,7 +7,7 @@ import akka.actor.{Actor, Props}
 import akka.pattern.ask
 import akka.util.Timeout
 import com.typesafe.config.ConfigFactory
-import cromwell.CromwellTestkitSpec
+import cromwell.CromwellTestKitSpec
 import cromwell.core._
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor.{WorkflowAborted => _, _}
@@ -15,7 +15,6 @@ import cromwell.server.{CromwellServerActor, CromwellSystem}
 import cromwell.services.metadata.MetadataService._
 import cromwell.services.metadata._
 import cromwell.services.metadata.impl.MetadataSummaryRefreshActor.MetadataSummarySuccess
-import cromwell.util.SampleWdl.DeclarationsWorkflow._
 import cromwell.util.SampleWdl.HelloWorld
 import org.scalatest.concurrent.{PatienceConfiguration, ScalaFutures}
 import org.scalatest.{FlatSpec, Matchers}
@@ -67,7 +66,7 @@ class CromwellApiServiceSpec extends FlatSpec with CromwellApiService with Scala
   implicit val defaultTimeout = RouteTestTimeout(30.seconds.dilated)
 
   override def actorRefFactory = system
-  override val serviceRegistryActor = CromwellTestkitSpec.ServiceRegistryActorInstance
+  override val serviceRegistryActor = CromwellTestKitSpec.ServiceRegistryActorInstance
 
   override val workflowStoreActor = actorRefFactory.actorOf(Props(new MockWorkflowStoreActor()))
   override val workflowManagerActor = actorRefFactory.actorOf(Props.empty)
@@ -243,7 +242,8 @@ class CromwellApiServiceSpec extends FlatSpec with CromwellApiService with Scala
 
   behavior of "REST API submission endpoint"
   it should "return 201 for a successful workflow submission " in {
-    Post(s"/workflows/$version", FormData(Seq("wdlSource" -> HelloWorld.wdlSource(), "workflowInputs" -> HelloWorld.rawInputs.toJson.toString()))) ~>
+    val bodyParts: Map[String, BodyPart] = Map("wdlSource" -> BodyPart(HelloWorld.wdlSource()), "workflowInputs" -> BodyPart(HelloWorld.rawInputs.toJson.toString()))
+    Post(s"/workflows/$version", MultipartFormData(bodyParts)) ~>
       submitRoute ~>
       check {
         assertResult(
@@ -261,7 +261,7 @@ class CromwellApiServiceSpec extends FlatSpec with CromwellApiService with Scala
   it should "succesfully merge and override multiple input files" in {
 
     val input1 = Map("wf.a1" -> "hello", "wf.a2" -> "world").toJson.toString
-    val input2 = Map.empty.toJson.toString
+    val input2 = Map.empty[String, String].toJson.toString
     val overrideInput1 = Map("wf.a2" -> "universe").toJson.toString
     val allInputs = mergeMaps(Seq(Option(input1), Option(input2), Option(overrideInput1)))
 
@@ -274,9 +274,9 @@ class CromwellApiServiceSpec extends FlatSpec with CromwellApiService with Scala
   behavior of "REST API batch submission endpoint"
   it should "return 200 for a successful workflow submission " in {
     val inputs = HelloWorld.rawInputs.toJson
+    val bodyParts = Map("wdlSource" -> BodyPart(HelloWorld.wdlSource()), "workflowInputs" -> BodyPart(s"[$inputs, $inputs]"))
 
-    Post(s"/workflows/$version/batch",
-      FormData(Seq("wdlSource" -> HelloWorld.wdlSource(), "workflowInputs" -> s"[$inputs, $inputs]"))) ~>
+    Post(s"/workflows/$version/batch", MultipartFormData(bodyParts)) ~>
       submitBatchRoute ~>
       check {
         assertResult(
diff --git a/engine/src/test/scala/cromwell/webservice/EngineStatsActorSpec.scala b/engine/src/test/scala/cromwell/webservice/EngineStatsActorSpec.scala
index 021e4a43c10..b32ceb1c958 100644
--- a/engine/src/test/scala/cromwell/webservice/EngineStatsActorSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/EngineStatsActorSpec.scala
@@ -14,22 +14,22 @@ class EngineStatsActorSpec extends TestKitSuite("EngineStatsActor") with FlatSpe
   behavior of "EngineStatsActor"
 
   val replyTo = TestProbe()
-  val defaultTimeout = 100 millis
+  val defaultTimeout = 500 millis
 
   it should "return double zeros with no WorkflowActors" in {
-    TestActorRef(EngineStatsActor.props(List.empty[ActorRef], replyTo.ref))
+    TestActorRef(EngineStatsActor.props(List.empty[ActorRef], replyTo.ref, timeout = 200 millis))
     replyTo.expectMsg(defaultTimeout, EngineStats(0, 0))
   }
 
   it should "return snakeyes with a single workflow with one job" in {
     val workflowActors = List(Props(FakeWorkflowActor(1))) map { TestActorRef(_) }
-    TestActorRef(EngineStatsActor.props(workflowActors, replyTo.ref))
+    TestActorRef(EngineStatsActor.props(workflowActors, replyTo.ref, timeout = 200 millis))
     replyTo.expectMsg(defaultTimeout, EngineStats(1, 1))
   }
 
   it should "return an unemployed workflow when that's the world it lives in" in {
     val workflowActors = List(Props(FakeWorkflowActor(0))) map { TestActorRef(_) }
-    TestActorRef(EngineStatsActor.props(workflowActors, replyTo.ref))
+    TestActorRef(EngineStatsActor.props(workflowActors, replyTo.ref, timeout = 200 millis))
     replyTo.expectMsg(defaultTimeout, EngineStats(1, 0))
   }
 
@@ -41,7 +41,7 @@ class EngineStatsActorSpec extends TestKitSuite("EngineStatsActor") with FlatSpe
 
   it should "return the summation of jobs for all WorkflowActors" in {
     val workflowActors = List(Props(FakeWorkflowActor(1)), Props(FakeWorkflowActor(2))) map { TestActorRef(_) }
-    TestActorRef(EngineStatsActor.props(workflowActors, replyTo.ref))
+    TestActorRef(EngineStatsActor.props(workflowActors, replyTo.ref, timeout = 200 millis))
     replyTo.expectMsg(defaultTimeout, EngineStats(2, 3))
   }
 }
diff --git a/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala b/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala
index 5ae82221bd4..9ecfeea4292 100644
--- a/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala
@@ -22,15 +22,14 @@ class MetadataBuilderActorSpec extends TestKitSuite("Metadata") with FlatSpecLik
 
   behavior of "MetadataParser"
 
-  val defaultTimeout = 100 millis
+  val defaultTimeout = 200 millis
   val mockServiceRegistry = TestProbe()
-  val parentProbe = TestProbe()
-
 
   def assertMetadataResponse(action: MetadataServiceAction,
                              queryReply: MetadataQuery,
                              events: Seq[MetadataEvent],
                              expectedRes: String) = {
+    val parentProbe = TestProbe()
     val metadataBuilder = TestActorRef(MetadataBuilderActor.props(mockServiceRegistry.ref), parentProbe.ref, s"MetadataActor-${UUID.randomUUID()}")
     metadataBuilder ! action // Ask for everything
     mockServiceRegistry.expectMsg(defaultTimeout, action) // TestActor runs on CallingThreadDispatcher
@@ -96,7 +95,7 @@ class MetadataBuilderActorSpec extends TestKitSuite("Metadata") with FlatSpecLik
         |  "id": "$workflowA"
       |}""".stripMargin
 
-    val mdQuery = MetadataQuery(workflowA, None, None, None, None)
+    val mdQuery = MetadataQuery(workflowA, None, None, None, None, expandSubWorkflows = false)
     val queryAction = GetMetadataQueryAction(mdQuery)
     assertMetadataResponse(queryAction, mdQuery, workflowAEvents, expectedRes)
   }
@@ -113,8 +112,8 @@ class MetadataBuilderActorSpec extends TestKitSuite("Metadata") with FlatSpecLik
     val events = eventList map { e => (e._1, MetadataValue(e._2), e._3) } map Function.tupled(makeEvent(workflow))
     val expectedRes = s"""{ "calls": {}, $expectedJson, "id":"$workflow" }"""
 
-    val mdQuery = MetadataQuery(workflow, None, None, None, None)
-    val queryAction = GetSingleWorkflowMetadataAction(workflow, None, None)
+    val mdQuery = MetadataQuery(workflow, None, None, None, None, expandSubWorkflows = false)
+    val queryAction = GetSingleWorkflowMetadataAction(workflow, None, None, expandSubWorkflows = false)
     assertMetadataResponse(queryAction, mdQuery, events, expectedRes)
   }
 
@@ -305,7 +304,7 @@ class MetadataBuilderActorSpec extends TestKitSuite("Metadata") with FlatSpecLik
           | }
       """.stripMargin
 
-    val mdQuery = MetadataQuery(workflowId, None, None, None, None)
+    val mdQuery = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
     val queryAction = GetMetadataQueryAction(mdQuery)
     assertMetadataResponse(queryAction, mdQuery, events, expectedResponse)
   }
@@ -326,7 +325,7 @@ class MetadataBuilderActorSpec extends TestKitSuite("Metadata") with FlatSpecLik
           |}
       """.stripMargin
 
-    val mdQuery = MetadataQuery(workflowId, None, None, None, None)
+    val mdQuery = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
     val queryAction = GetMetadataQueryAction(mdQuery)
     assertMetadataResponse(queryAction, mdQuery, events, expectedResponse)
   }
@@ -346,14 +345,14 @@ class MetadataBuilderActorSpec extends TestKitSuite("Metadata") with FlatSpecLik
           |}
       """.stripMargin
 
-    val mdQuery = MetadataQuery(workflowId, None, None, None, None)
+    val mdQuery = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
     val queryAction = GetMetadataQueryAction(mdQuery)
     assertMetadataResponse(queryAction, mdQuery, events, expectedResponse)
   }
 
   it should "render empty Json" in {
     val workflowId = WorkflowId.randomId()
-    val mdQuery = MetadataQuery(workflowId, None, None, None, None)
+    val mdQuery = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
     val queryAction = GetMetadataQueryAction(mdQuery)
     val expectedEmptyResponse = """{}"""
     assertMetadataResponse(queryAction, mdQuery, List.empty, expectedEmptyResponse)
@@ -383,7 +382,7 @@ class MetadataBuilderActorSpec extends TestKitSuite("Metadata") with FlatSpecLik
           |}
       """.stripMargin
 
-    val mdQuery = MetadataQuery(workflowId, None, None, None, None)
+    val mdQuery = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
     val queryAction = GetMetadataQueryAction(mdQuery)
     assertMetadataResponse(queryAction, mdQuery, emptyEvents, expectedEmptyResponse)
 
@@ -398,4 +397,98 @@ class MetadataBuilderActorSpec extends TestKitSuite("Metadata") with FlatSpecLik
 
     assertMetadataResponse(queryAction, mdQuery, valueEvents, expectedNonEmptyResponse)
   }
+  
+  it should "expand sub workflow metadata when asked for" in {
+    val mainWorkflowId = WorkflowId.randomId()
+    val subWorkflowId = WorkflowId.randomId()
+    
+    val mainEvents = List(
+      MetadataEvent(MetadataKey(mainWorkflowId, Option(MetadataJobKey("callA", None, 1)), "subWorkflowId"), MetadataValue(subWorkflowId))
+    )
+
+    val subEvents = List(
+      MetadataEvent(MetadataKey(mainWorkflowId, None, "some"), MetadataValue("sub workflow info"))
+    )
+    
+    val mainQuery = MetadataQuery(mainWorkflowId, None, None, None, None, expandSubWorkflows = true)
+    val mainQueryAction = GetMetadataQueryAction(mainQuery)
+    
+    val subQuery = MetadataQuery(subWorkflowId, None, None, None, None, expandSubWorkflows = true)
+    val subQueryAction = GetMetadataQueryAction(subQuery)
+    
+    val parentProbe = TestProbe()
+    val metadataBuilder = TestActorRef(MetadataBuilderActor.props(mockServiceRegistry.ref), parentProbe.ref, s"MetadataActor-${UUID.randomUUID()}")
+    metadataBuilder ! mainQueryAction
+    mockServiceRegistry.expectMsg(defaultTimeout, mainQueryAction)
+    mockServiceRegistry.reply(MetadataLookupResponse(mainQuery, mainEvents))
+    mockServiceRegistry.expectMsg(defaultTimeout, subQueryAction)
+    mockServiceRegistry.reply(MetadataLookupResponse(subQuery, subEvents))
+    
+    val expandedRes =
+      s"""
+         |{
+         |  "calls": {
+         |    "callA": [
+         |      {
+         |        "subWorkflowMetadata": {
+         |          "some": "sub workflow info",
+         |          "calls": {},
+         |          "id": "$subWorkflowId"
+         |         },
+         |         "attempt": 1,
+         |         "shardIndex": -1
+         |      }
+         |    ]
+         |  },
+         |  "id": "$mainWorkflowId"
+         |}
+       """.stripMargin
+
+    parentProbe.expectMsgPF(defaultTimeout) {
+      case response: RequestComplete[(StatusCode, JsObject)] @unchecked =>
+        response.response._1 shouldBe StatusCodes.OK
+        response.response._2 shouldBe expandedRes.parseJson
+    }
+  }
+  
+  it should "NOT expand sub workflow metadata when NOT asked for" in {
+    val mainWorkflowId = WorkflowId.randomId()
+    val subWorkflowId = WorkflowId.randomId()
+
+    val mainEvents = List(
+      MetadataEvent(MetadataKey(mainWorkflowId, Option(MetadataJobKey("callA", None, 1)), "subWorkflowId"), MetadataValue(subWorkflowId))
+    )
+
+    val queryNoExpand = MetadataQuery(mainWorkflowId, None, None, None, None, expandSubWorkflows = false)
+    val queryNoExpandAction = GetMetadataQueryAction(queryNoExpand)
+    
+    val parentProbe = TestProbe()
+    val metadataBuilder = TestActorRef(MetadataBuilderActor.props(mockServiceRegistry.ref), parentProbe.ref, s"MetadataActor-${UUID.randomUUID()}")
+    metadataBuilder ! queryNoExpandAction
+    mockServiceRegistry.expectMsg(defaultTimeout, queryNoExpandAction)
+    mockServiceRegistry.reply(MetadataLookupResponse(queryNoExpand, mainEvents))
+
+
+    val nonExpandedRes =
+      s"""
+         |{
+         |  "calls": {
+         |    "callA": [
+         |      {
+         |        "subWorkflowId": "$subWorkflowId",
+         |        "attempt": 1,
+         |        "shardIndex": -1
+         |      }  
+         |    ]
+         |  },
+         |  "id": "$mainWorkflowId"
+         |}
+       """.stripMargin
+    
+    parentProbe.expectMsgPF(defaultTimeout) {
+      case response: RequestComplete[(StatusCode, JsObject)] @unchecked =>
+        response.response._1 shouldBe StatusCodes.OK
+        response.response._2 shouldBe nonExpandedRes.parseJson
+    }
+  }
 }
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/ContentTypeOption.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/ContentTypeOption.scala
deleted file mode 100644
index e6f83b0e457..00000000000
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/ContentTypeOption.scala
+++ /dev/null
@@ -1,15 +0,0 @@
-package cromwell.filesystems.gcs
-
-import java.nio.file.OpenOption
-
-object ContentTypeOption {
-  sealed trait ContentType
-  case object PlainText extends ContentType with OpenOption {
-    override def toString = "plain/text"
-  }
-  case object Json extends ContentType with OpenOption {
-    override def toString = "application/json"
-  }
-}
-
-
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileAttributes.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileAttributes.scala
deleted file mode 100644
index 5d45641de3b..00000000000
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileAttributes.scala
+++ /dev/null
@@ -1,23 +0,0 @@
-package cromwell.filesystems.gcs
-
-import java.nio.file.attribute.{BasicFileAttributes, FileTime}
-
-import com.google.api.services.storage.Storage
-import com.google.api.services.storage.model.StorageObject
-import org.apache.commons.codec.digest.DigestUtils
-
-class GcsFileAttributes(path: NioGcsPath, storageClient: Storage) extends BasicFileAttributes {
-  override def fileKey(): AnyRef = DigestUtils.md5Hex(path.toString)
-  override def isRegularFile: Boolean = throw new NotImplementedError("To be implemented when/if needed")
-  override def isOther: Boolean = throw new NotImplementedError("To be implemented when/if needed")
-  override def lastModifiedTime(): FileTime = throw new NotImplementedError("To be implemented when/if needed")
-  override def size(): Long = {
-    val getObject = storageClient.objects.get(path.bucket, path.objectName)
-    val storageObject: StorageObject = getObject.execute()
-    storageObject.getSize.longValue()
-  }
-  override def isDirectory: Boolean = path.isDirectory
-  override def isSymbolicLink: Boolean = false
-  override def creationTime(): FileTime = throw new NotImplementedError("To be implemented when/if needed")
-  override def lastAccessTime(): FileTime = throw new NotImplementedError("To be implemented when/if needed")
-}
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileSystem.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileSystem.scala
deleted file mode 100644
index 215b18935bf..00000000000
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileSystem.scala
+++ /dev/null
@@ -1,68 +0,0 @@
-package cromwell.filesystems.gcs
-
-import java.lang.Iterable
-import java.nio.file._
-import java.nio.file.attribute.UserPrincipalLookupService
-import java.nio.file.spi.FileSystemProvider
-import java.util.{Collections, Set => JSet}
-
-
-case class NotAGcsPathException(path: String) extends IllegalArgumentException(s"$path is not a valid GCS path.")
-
-object GcsFileSystem {
-  val Separator = "/"
-  private[gcs] val Scheme = "gs"
-  private[gcs] val Protocol = s"$Scheme://"
-  private val GsUriRegex = s"""$Protocol(.*)""".r
-  private val AttributeViews = Collections.singleton("basic")
-
-  def isAbsoluteGcsPath(str: String) = str match {
-    case GsUriRegex(chunks) => true
-    case _ => false
-  }
-
-  def apply(provider: GcsFileSystemProvider) = new GcsFileSystem(provider)
-}
-
-/**
-  * Implements the java.nio.FileSystem interface for GoogleCloudStorage.
-  */
-class GcsFileSystem private(val gcsFileSystemProvider: GcsFileSystemProvider) extends FileSystem {
-
-  import GcsFileSystem._
-
-  override def supportedFileAttributeViews(): JSet[String] = AttributeViews
-
-  override def getSeparator: String = Separator
-
-  override def getRootDirectories: Iterable[Path] = Collections.emptyList[Path]
-
-  override def newWatchService(): WatchService = throw new NotImplementedError("GCS FS does not support Watch Service at this time")
-
-  override def getFileStores: Iterable[FileStore] = Collections.emptyList()
-
-  override def isReadOnly: Boolean = false
-
-  override def provider(): FileSystemProvider = gcsFileSystemProvider
-
-  override def isOpen: Boolean = true
-
-  override def close(): Unit = throw new UnsupportedOperationException("GCS FS cannot be closed")
-
-  override def getPathMatcher(syntaxAndPattern: String): PathMatcher = FileSystems.getDefault.getPathMatcher(syntaxAndPattern)
-
-  override def getUserPrincipalLookupService: UserPrincipalLookupService = throw new UnsupportedOperationException()
-
-  private def buildPath(first: String, more: Seq[String], forceDirectory: Boolean) = {
-    val directory = forceDirectory || (more.isEmpty && first.endsWith(Separator)) || more.lastOption.exists(_.endsWith(Separator))
-    first match {
-      case GsUriRegex(chunks) => new NioGcsPath(chunks.split(Separator) ++ more.toArray[String], true, directory)(this)
-      case empty if empty.isEmpty => new NioGcsPath(Array.empty[String] ++ more.toArray[String], false, false)(this)
-      case _ => throw NotAGcsPathException(s"$first is not a gcs path")
-    }
-  }
-
-  override def getPath(first: String, more: String*): Path = buildPath(first, more, forceDirectory = false)
-
-  def getPathAsDirectory(first: String, more: String*): Path = buildPath(first, more, forceDirectory = true)
-}
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileSystemProvider.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileSystemProvider.scala
deleted file mode 100644
index 845ec29ef53..00000000000
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsFileSystemProvider.scala
+++ /dev/null
@@ -1,295 +0,0 @@
-package cromwell.filesystems.gcs
-
-import java.io.{FileNotFoundException, OutputStream}
-import java.net.URI
-import java.nio.channels.{Channels, SeekableByteChannel}
-import java.nio.file.DirectoryStream.Filter
-import java.nio.file._
-import java.nio.file.attribute.{BasicFileAttributes, FileAttribute, FileAttributeView}
-import java.nio.file.spi.FileSystemProvider
-import java.util
-import java.util.Collections
-import java.util.concurrent.{AbstractExecutorService, TimeUnit}
-
-import cats.instances.try_._
-import cats.syntax.functor._
-import com.google.api.client.googleapis.json.GoogleJsonResponseException
-import com.google.api.client.googleapis.media.MediaHttpUploader
-import com.google.api.services.storage.Storage
-import com.google.api.services.storage.model.StorageObject
-import com.google.cloud.hadoop.gcsio.{GoogleCloudStorageReadChannel, GoogleCloudStorageWriteChannel, ObjectWriteConditions}
-import com.google.cloud.hadoop.util.{ApiErrorExtractor, AsyncWriteChannelOptions, ClientRequestHelper}
-import com.typesafe.config.{Config, ConfigFactory, ConfigMemorySize}
-import net.ceedubs.ficus.Ficus._
-import net.ceedubs.ficus.readers.ValueReader
-
-import scala.annotation.tailrec
-import scala.collection.JavaConverters._
-import scala.concurrent.duration._
-import scala.concurrent.{ExecutionContext, ExecutionContextExecutorService}
-import scala.language.postfixOps
-import scala.util.{Failure, Success, Try}
-
-object GcsFileSystemProvider {
-  def apply(storageClient: Storage)(implicit ec: ExecutionContext) = {
-    new GcsFileSystemProvider(Success(storageClient), ec)
-  }
-
-  object AcceptAllFilter extends DirectoryStream.Filter[Path] {
-    override def accept(entry: Path): Boolean = true
-  }
-
-  // To choose these numbers I first entered a prolonged period of personal consideration and deep thought.
-  // Then, at the end of this time, I decided to just pick some numbers arbitrarily.
-  private val retryInterval = 500 milliseconds
-  private val retryCount = 3
-
-  def withRetry[A](f: => A, retries: Int = retryCount): A = Try(f) match {
-    case Success(res) => res
-    case Failure(ex: GoogleJsonResponseException)
-      if retries > 0 &&
-        (ex.getStatusCode == 404 || ex.getStatusCode == 500) =>
-      // FIXME remove this sleep
-      Thread.sleep(retryInterval.toMillis)
-      withRetry(f, retries - 1)
-    case Failure(ex) => throw ex
-  }
-
-  // TODO refactor as part of Ficus and submit a PR
-  implicit val configMemorySizeValueReader: ValueReader[ConfigMemorySize] = new ValueReader[ConfigMemorySize] {
-    override def read(config: Config, path: String): ConfigMemorySize = config.getMemorySize(path)
-  }
-}
-
-/**
-  * Converts a Scala ExecutionContext to a Java ExecutorService.
-  * https://groups.google.com/forum/#!topic/scala-user/ZyHrfzD7eX8
-  */
-object ExecutionContextExecutorServiceBridge {
-  def apply(ec: ExecutionContext): ExecutionContextExecutorService = ec match {
-    case null => throw new RuntimeException("Execution context cannot be null")
-    case eces: ExecutionContextExecutorService => eces
-    case executionContext => new AbstractExecutorService with ExecutionContextExecutorService {
-      override def prepare(): ExecutionContext = executionContext
-      override def isShutdown = false
-      override def isTerminated = false
-      override def shutdown() = ()
-      override def shutdownNow() = Collections.emptyList[Runnable]
-      override def execute(runnable: Runnable): Unit = executionContext execute runnable
-      override def reportFailure(t: Throwable): Unit = executionContext reportFailure t
-      override def awaitTermination(length: Long,unit: TimeUnit): Boolean = false
-    }
-  }
-}
-
-/**
-  * Implements java.nio.FileSystemProvider for GoogleCloudStorage
-  * This implementation is not complete and mostly a proof of concept that it's possible to *copy* around files from/to local/gcs.
-  * Copying is the only functionality that has been successfully tested (same and cross filesystems).
-  *
-  * If/when switching to Google's GCS NIO implementation, callers may need to implement various utilities built into
-  * this implementation, including:
-  *
-  * - Minimizing the upload buffer size, assuming the default is also on the order of megabytes of memory per upload
-  * - Automatically retrying transient errors
-  * - etc.
-  *
-  * @param storageClient Google API Storage object
-  * @param executionContext executionContext, will be used to perform async writes to GCS after being converted to a Java execution service
-  */
-class GcsFileSystemProvider private[gcs](storageClient: Try[Storage], val executionContext: ExecutionContext) extends FileSystemProvider {
-  import GcsFileSystemProvider._
-
-  private[this] lazy val config = ConfigFactory.load()
-
-  // We want to throw an exception here if we try to use this class with a failed gcs interface
-  lazy val client = storageClient.get
-  private val executionService = ExecutionContextExecutorServiceBridge(executionContext)
-  private val errorExtractor = new ApiErrorExtractor()
-  def notAGcsPath(path: Path) = throw new IllegalArgumentException(s"$path is not a GCS path.")
-
-  lazy val defaultFileSystem: GcsFileSystem = GcsFileSystem(this)
-
-  private def exists(path: Path): Unit = path match {
-    case gcsPath: NioGcsPath =>
-      val attempt: Try[Any] = Try(withRetry(client.objects.get(gcsPath.bucket, gcsPath.objectName).execute)) recover {
-        case ex: GoogleJsonResponseException
-          if ex.getStatusCode == 404 => if (!gcsPath.isDirectory) throw new FileNotFoundException(path.toString)
-      }
-      attempt.void.get
-    case _ => throw new FileNotFoundException(path.toString)
-  }
-
-  /**
-    * Note: options and attributes are not honored.
-    */
-  override def newByteChannel(path: Path, options: util.Set[_ <: OpenOption], attrs: FileAttribute[_]*): SeekableByteChannel = {
-    def createReadChannel(gcsPath: NioGcsPath) = new GoogleCloudStorageReadChannel(client,
-       gcsPath.bucket,
-       gcsPath.objectName,
-       errorExtractor,
-       new ClientRequestHelper[StorageObject]()
-     )
-    
-    path match {
-      case gcsPath: NioGcsPath => withRetry(createReadChannel(gcsPath))
-      case _ => notAGcsPath(path)
-    }
-  }
-
-  /*
-  For now, default all upload buffers as small as possible, 256K per upload. Without this default the buffers are 64M.
-  In the future, we may possibly be able to pass information to the NioGcsPath with the expected... or Google's GCS NIO
-  implementation will be finished we'll need to revisit this issue again.
-
-  See also:
-  - com.google.cloud.hadoop.util.AbstractGoogleAsyncWriteChannel.setUploadBufferSize
-  - com.google.api.client.googleapis.media.MediaHttpUploader.setContentAndHeadersOnCurrentRequest
-   */
-  private[this] lazy val uploadBufferBytes = {
-    val configBytes = config.as[Option[ConfigMemorySize]]("google.upload-buffer-bytes").map(_.toBytes.toInt)
-    configBytes.getOrElse(MediaHttpUploader.MINIMUM_CHUNK_SIZE)
-  }
-
-  /**
-    * Overrides the default implementation to provide a writable channel (which newByteChannel doesn't).
-    * NOTE: options are not honored.
-    */
-  override def newOutputStream(path: Path, options: OpenOption*): OutputStream = {
-    val contentType = options collectFirst {
-      case e: ContentTypeOption.ContentType => e.toString
-    } getOrElse ContentTypeOption.PlainText.toString
-
-    def initializeOutputStream(gcsPath: NioGcsPath) = {
-      val channel = new GoogleCloudStorageWriteChannel(
-        executionService,
-        client,
-        new ClientRequestHelper[StorageObject](),
-        gcsPath.bucket,
-        gcsPath.objectName,
-        AsyncWriteChannelOptions.newBuilder().setUploadBufferSize(uploadBufferBytes).build(),
-        new ObjectWriteConditions(),
-        Map.empty[String, String].asJava,
-        contentType)
-      channel.initialize()
-      Channels.newOutputStream(channel)
-    }
-
-    path match {
-      case gcsPath: NioGcsPath => withRetry(initializeOutputStream(gcsPath))
-      case _ => notAGcsPath(path)
-    }
-  }
-
-  override def copy(source: Path, target: Path, options: CopyOption*): Unit = {
-    (source, target) match {
-      case (s: NioGcsPath, d: NioGcsPath) =>
-        def innerCopy(): Unit = {
-          val storageObject = client.objects.get(s.bucket, s.objectName).execute
-          client.objects.copy(s.bucket, s.objectName, d.bucket, d.objectName, storageObject).execute
-          ()
-        }
-
-        withRetry(innerCopy())
-      case _ => throw new UnsupportedOperationException(s"Can only copy from GCS to GCS: $source or $target is not a GCS path")
-    }
-  }
-
-  override def delete(path: Path): Unit = {
-    path match {
-      case gcs: NioGcsPath => try {
-        withRetry {
-          client.objects.delete(gcs.bucket, gcs.objectName).execute()
-          ()
-        }
-      } catch {
-        case ex: GoogleJsonResponseException if ex.getStatusCode == 404 => throw new NoSuchFileException(path.toString)
-      }
-      case _ => notAGcsPath(path)
-    }
-  }
-
-  override def readAttributes[A <: BasicFileAttributes](path: Path, `type`: Class[A], options: LinkOption*): A = path match {
-    case gcsPath: NioGcsPath =>
-      exists(path)
-      new GcsFileAttributes(gcsPath, client).asInstanceOf[A]
-    case _ => notAGcsPath(path)
-  }
-
-  override def move(source: Path, target: Path, options: CopyOption*): Unit = {
-    (source, target) match {
-      case (s: NioGcsPath, d: NioGcsPath) =>
-        def moveInner(): Unit = {
-          val storageObject = client.objects.get(s.bucket, s.objectName).execute
-          client.objects.rewrite(s.bucket, s.objectName, d.bucket, d.objectName, storageObject).execute
-          ()
-        }
-
-        withRetry(moveInner())
-      case _ => throw new UnsupportedOperationException(s"Can only move from GCS to GCS: $source or $target is not a GCS path")
-    }
-  }
-
-  def crc32cHash(path: Path) = path match {
-    case gcsDir: NioGcsPath => withRetry(client.objects().get(gcsDir.bucket, gcsDir.objectName).execute().getCrc32c)
-    case _ => notAGcsPath(path)
-  }
-
-  override def checkAccess(path: Path, modes: AccessMode*): Unit = { exists(path); () }
-  override def createDirectory(dir: Path, attrs: FileAttribute[_]*): Unit = {}
-
-  override def getFileSystem(uri: URI): FileSystem = defaultFileSystem
-
-  override def isHidden(path: Path): Boolean = throw new NotImplementedError()
-
-  private[this] lazy val maxResults = config.as[Option[Int]]("google.list-max-results").getOrElse(1000).toLong
-
-  private def list(gcsDir: NioGcsPath) = {
-    val listRequest = client.objects().list(gcsDir.bucket).setMaxResults(maxResults)
-    listRequest.setPrefix(gcsDir.objectName)
-
-    def objectToPath(storageObject: StorageObject): Path = {
-      NioGcsPath(s"$getScheme${storageObject.getBucket}${GcsFileSystem.Separator}${storageObject.getName}")(gcsDir.getFileSystem.asInstanceOf[GcsFileSystem])
-    }
-
-    // Contains a Seq corresponding to the current page of objects, plus a token for the next page of objects, if any.
-    case class ListPageResult(objects: Seq[StorageObject], nextPageToken: Option[String])
-
-    def requestListPage(pageToken: Option[String]): ListPageResult = {
-      val objects = withRetry(listRequest.setPageToken(pageToken.orNull).execute())
-      ListPageResult(objects.getItems.asScala, Option(objects.getNextPageToken))
-    }
-
-    @tailrec
-    def remainingObjects(pageToken: Option[String], acc: Seq[StorageObject]): Seq[StorageObject] = {
-      if (pageToken.isEmpty) acc
-      else {
-        val page = requestListPage(pageToken)
-        remainingObjects(page.nextPageToken, acc ++ page.objects)
-      }
-    }
-
-    val firstPage = requestListPage(pageToken = None)
-    val allObjects = remainingObjects(firstPage.nextPageToken, firstPage.objects)
-
-    new DirectoryStream[Path] {
-      override def iterator(): util.Iterator[Path] = (allObjects map objectToPath).toIterator.asJava
-      override def close(): Unit = {}
-    }
-  }
-
-  override def newDirectoryStream(dir: Path, filter: Filter[_ >: Path]): DirectoryStream[Path] = dir match {
-    case gcsDir: NioGcsPath => list(gcsDir)
-    case _ => notAGcsPath(dir)
-  }
-  override def setAttribute(path: Path, attribute: String, value: scala.Any, options: LinkOption*): Unit = throw new NotImplementedError()
-  override def getPath(uri: URI): Path = throw new NotImplementedError()
-  override def newFileSystem(uri: URI, env: util.Map[String, _]): FileSystem = {
-    throw new UnsupportedOperationException("GcsFileSystem provider doesn't support creation of new FileSystems at this time. Use getFileSystem instead.")
-  }
-  override def readAttributes(path: Path, attributes: String, options: LinkOption*): util.Map[String, AnyRef] = throw new NotImplementedError()
-  override def isSameFile(path: Path, path2: Path): Boolean = throw new NotImplementedError()
-  override def getFileAttributeView[V <: FileAttributeView](path: Path, `type`: Class[V], options: LinkOption*): V = throw new NotImplementedError()
-  override def getFileStore(path: Path): FileStore = throw new NotImplementedError()
-  override def getScheme: String = GcsFileSystem.Protocol
-}
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilder.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilder.scala
new file mode 100644
index 00000000000..0649da9b7b3
--- /dev/null
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilder.scala
@@ -0,0 +1,100 @@
+package cromwell.filesystems.gcs
+
+import java.net.URI
+import java.nio.file.Path
+import java.nio.file.spi.FileSystemProvider
+
+import akka.actor.ActorSystem
+import com.google.api.client.googleapis.javanet.GoogleNetHttpTransport
+import com.google.api.client.json.jackson2.JacksonFactory
+import com.google.cloud.RetryParams
+import com.google.cloud.storage.StorageOptions
+import com.google.cloud.storage.contrib.nio.{CloudStorageConfiguration, CloudStorageFileSystem, CloudStoragePath}
+import com.google.common.base.Preconditions._
+import cromwell.core.WorkflowOptions
+import cromwell.core.path.proxy.{PathProxy, RetryableFileSystemProviderProxy}
+import cromwell.core.path.{CustomRetryParams, PathBuilder}
+import cromwell.filesystems.gcs.auth.GoogleAuthMode
+
+import scala.util.{Failure, Try}
+
+object GcsPathBuilder {
+
+  val JsonFactory = JacksonFactory.getDefaultInstance
+  val HttpTransport = GoogleNetHttpTransport.newTrustedTransport
+
+  def checkValid(uri: URI) = {
+    checkNotNull(uri.getScheme, s"%s does not have a gcs scheme", uri)
+    checkArgument(
+      uri.getScheme.equalsIgnoreCase(CloudStorageFileSystem.URI_SCHEME),
+      "Cloud Storage URIs must have '%s' scheme: %s",
+      CloudStorageFileSystem.URI_SCHEME,
+      uri
+    )
+    checkNotNull(uri.getHost, s"%s does not have a host", uri)
+  }
+
+  def isValidGcsUrl(str: String): Boolean = {
+    Try(checkValid(URI.create(str))).isSuccess
+  }
+
+  def isGcsPath(path: Path): Boolean = {
+    path.getFileSystem.provider().getScheme == CloudStorageFileSystem.URI_SCHEME
+  }
+}
+
+class GcsPathBuilder(authMode: GoogleAuthMode,
+                     retryParams: RetryParams,
+                     cloudStorageConfiguration: CloudStorageConfiguration,
+                     options: WorkflowOptions) extends PathBuilder {
+  authMode.validate(options)
+
+  protected val storageOptions = StorageOptions.builder()
+    .authCredentials(authMode.authCredentials(options))
+    .retryParams(retryParams)
+    .build()
+
+  // The CloudStorageFileSystemProvider constructor is not public. Currently the only way to obtain one is through a CloudStorageFileSystem
+  // Moreover at this point we can use the same provider for all operations as we have usable credentials
+  // In order to avoid recreating a provider with every getPath call, create a dummy FileSystem just to get its provider
+  protected val _provider = CloudStorageFileSystem.forBucket("dummy", cloudStorageConfiguration, storageOptions).provider()
+
+  protected def provider: FileSystemProvider = _provider
+  /*
+   * The StorageService already contains a StorageRpc object that contains a com.google.api.services.storage.Storage object
+   * However it is not accessible from StorageService.
+   * com.google.cloud.storage.Storage has some batching capabilities but not for copying.
+   * In order to support batch copy, we need a com.google.api.services.storage.Storage.
+   */
+  def getHash(path: Path): Try[String] = {
+    path match {
+      case gcsPath: CloudStoragePath => Try(storageOptions.service().get(gcsPath.bucket(), gcsPath.toRealPath().toString).crc32c())
+      case proxy: PathProxy =>
+        val gcsPath = proxy.unbox(classOf[CloudStoragePath]).get
+        Try(storageOptions.service().get(gcsPath.bucket(), gcsPath.toRealPath().toString).crc32c())
+      case other => Failure(new IllegalArgumentException(s"$other is not a CloudStoragePath"))
+    }
+  }
+
+  def build(string: String): Try[Path] = {
+    Try {
+      val uri = URI.create(string)
+      GcsPathBuilder.checkValid(uri)
+      provider.getPath(uri)
+    }
+  }
+
+  override def name: String = "Gcs"
+}
+
+class RetryableGcsPathBuilder(authMode: GoogleAuthMode,
+                              googleRetryParams: RetryParams,
+                              customRetryParams: CustomRetryParams,
+                              cloudStorageConfiguration: CloudStorageConfiguration,
+                              options: WorkflowOptions)(implicit actorSystem: ActorSystem)
+  extends GcsPathBuilder(authMode, googleRetryParams, cloudStorageConfiguration, options) {
+
+  override protected def provider = new RetryableFileSystemProviderProxy(_provider, customRetryParams)
+
+  override def getHash(path: Path) = provider.withRetry(() => super.getHash(path))
+}
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilderFactory.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilderFactory.scala
new file mode 100644
index 00000000000..83aad3ce850
--- /dev/null
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilderFactory.scala
@@ -0,0 +1,48 @@
+package cromwell.filesystems.gcs
+
+import akka.actor.ActorSystem
+import com.google.api.client.googleapis.media.MediaHttpUploader
+import com.google.cloud.RetryParams
+import com.google.cloud.storage.contrib.nio.CloudStorageConfiguration
+import com.typesafe.config.ConfigFactory
+import cromwell.core.WorkflowOptions
+import cromwell.core.path.{CustomRetryParams, PathBuilderFactory}
+import cromwell.filesystems.gcs.auth.GoogleAuthMode
+import net.ceedubs.ficus.Ficus._
+
+object GcsPathBuilderFactory {
+
+  private[this] lazy val UploadBufferBytes = {
+    ConfigFactory.load().as[Option[Int]]("google.upload-buffer-bytes").getOrElse(MediaHttpUploader.MINIMUM_CHUNK_SIZE)
+  }
+
+  val DefaultRetryParams = RetryParams.defaultInstance()
+  val DefaultCloudStorageConfiguration = {
+    CloudStorageConfiguration.builder()
+      .blockSize(UploadBufferBytes)
+      .permitEmptyPathComponents(true)
+      .stripPrefixSlash(true)
+      .usePseudoDirectories(true)
+      .build()
+  }
+}
+
+case class GcsPathBuilderFactory(authMode: GoogleAuthMode,
+                                 retryParams: RetryParams = GcsPathBuilderFactory.DefaultRetryParams,
+                                 cloudStorageConfiguration: CloudStorageConfiguration = GcsPathBuilderFactory.DefaultCloudStorageConfiguration)
+
+  extends PathBuilderFactory {
+
+  def withOptions(options: WorkflowOptions)(implicit actorSystem: ActorSystem) = new GcsPathBuilder(authMode, retryParams, cloudStorageConfiguration, options)
+}
+
+case class RetryableGcsPathBuilderFactory(authMode: GoogleAuthMode,
+                                          googleRetryParams: RetryParams = GcsPathBuilderFactory.DefaultRetryParams,
+                                          customRetryParams: CustomRetryParams = CustomRetryParams.Default,
+                                          cloudStorageConfiguration: CloudStorageConfiguration = GcsPathBuilderFactory.DefaultCloudStorageConfiguration)
+
+
+  extends PathBuilderFactory {
+
+  def withOptions(options: WorkflowOptions)(implicit actorSystem: ActorSystem) = new RetryableGcsPathBuilder(authMode, googleRetryParams, customRetryParams, cloudStorageConfiguration, options)
+}
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleAuthMode.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleAuthMode.scala
deleted file mode 100644
index 2930cc91149..00000000000
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleAuthMode.scala
+++ /dev/null
@@ -1,186 +0,0 @@
-package cromwell.filesystems.gcs
-
-import java.io.{FileNotFoundException, IOException, InputStreamReader}
-import java.nio.file.{Files, Paths}
-
-import com.google.api.client.auth.oauth2.Credential
-import com.google.api.client.extensions.java6.auth.oauth2.AuthorizationCodeInstalledApp
-import com.google.api.client.googleapis.auth.oauth2.{GoogleAuthorizationCodeFlow, GoogleClientSecrets, GoogleCredential}
-import com.google.api.client.googleapis.extensions.java6.auth.oauth2.GooglePromptReceiver
-import com.google.api.client.googleapis.javanet.GoogleNetHttpTransport
-import com.google.api.client.json.JsonFactory
-import com.google.api.client.json.jackson2.JacksonFactory
-import com.google.api.client.util.store.FileDataStoreFactory
-import com.google.api.services.storage.{Storage, StorageScopes}
-import cromwell.filesystems.gcs.GoogleAuthMode.{GcsScopes, GoogleAuthOptions}
-import org.slf4j.LoggerFactory
-
-import scala.collection.JavaConverters._
-import scala.util.{Failure, Success, Try}
-
-object GoogleAuthMode {
-
-  lazy val jsonFactory = JacksonFactory.getDefaultInstance
-  lazy val httpTransport = GoogleNetHttpTransport.newTrustedTransport
-  val RefreshTokenOptionKey = "refresh_token"
-
-  /**
-    * Before it returns the raw credential, checks if the token will expire within 60 seconds.
-    *
-    * TODO: Needs more design / testing around thread safety.
-    * For example, the credential returned is mutable, and may be modified by another thread.
-    *
-    * Most Google clients have the ability to refresh tokens automatically, as they use the standard Google
-    * HttpTransport that automatically triggers credential refreshing via Credential.handleResponse. Since Cromwell
-    * contacts https://gcr.io directly via HTTP requests using spray-client, we need to keep the token fresh ourselves.
-    *
-    * @see Credential#handleResponse(HttpRequest, HttpResponse, boolean)
-    */
-  implicit class EnhancedCredentials(val credential: Credential) extends AnyVal {
-    def freshCredential: Try[Credential] = {
-      val stillValid = Option(credential.getExpiresInSeconds).exists(_ > 60)
-      if (stillValid || credential.refreshToken()) {
-        Success(credential)
-      } else {
-        Failure(new Exception("Unable to refresh token"))
-      }
-    }
-  }
-
-  def buildStorage(credential: Credential, applicationName: String) = {
-    new Storage.Builder(
-      httpTransport,
-      jsonFactory,
-      credential).setApplicationName(applicationName).build()
-  }
-
-  trait GoogleAuthOptions {
-    def get(key: String): Try[String]
-  }
-
-  val GcsScopes = List(
-    StorageScopes.DEVSTORAGE_FULL_CONTROL,
-    StorageScopes.DEVSTORAGE_READ_WRITE
-  )
-}
-
-
-sealed trait GoogleAuthMode {
-  def credential(options: GoogleAuthOptions): Credential
-
-  def assertWorkflowOptions(options: GoogleAuthOptions): Unit = ()
-
-  def name: String
-
-  def requiresAuthFile: Boolean = false
-
-  protected lazy val log = LoggerFactory.getLogger(getClass.getSimpleName)
-
-  protected def validateCredentials(credential: Credential) = {
-    Try(credential.refreshToken()) match {
-      case Failure(ex) => throw new RuntimeException(s"Google credentials are invalid: ${ex.getMessage}")
-      case Success(_) => credential
-    }
-  }
-
-  def buildStorage(options: GoogleAuthOptions, applicationName: String): Storage = {
-    GoogleAuthMode.buildStorage(credential(options), applicationName)
-  }
-}
-
-final case class ServiceAccountMode(override val name: String, accountId: String, pemPath: String, scopes: List[String] = GcsScopes) extends GoogleAuthMode {
-  import GoogleAuthMode._
-
-  private lazy val credentials: Credential = {
-    val pemFile = Paths.get(pemPath).toAbsolutePath
-    if (!Files.exists(pemFile)) {
-      throw new FileNotFoundException(s"PEM file $pemFile does not exist")
-    }
-    validateCredentials(
-      new GoogleCredential.Builder().setTransport(httpTransport)
-      .setJsonFactory(jsonFactory)
-      .setServiceAccountId(accountId)
-      .setServiceAccountScopes(scopes.asJava)
-      .setServiceAccountPrivateKeyFromPemFile(pemFile.toFile)
-      .build()
-    )
-  }
-
-  override def credential(options: GoogleAuthOptions) = credentials
-}
-
-final case class UserMode(override val name: String, user: String, secretsFile: String, datastoreDir: String, scopes: List[String] = GcsScopes) extends GoogleAuthMode {
-  import GoogleAuthMode._
-
-  private def filePathToSecrets(secrets: String, jsonFactory: JsonFactory) = {
-    val secretsPath = Paths.get(secrets).toAbsolutePath
-    if(!Files.isReadable(secretsPath)) {
-      log.warn("Secrets file does not exist or is not readable.")
-    }
-    val secretStream = new InputStreamReader(Files.newInputStream(secretsPath))
-
-    GoogleClientSecrets.load(jsonFactory, secretStream)
-  }
-
-  private lazy val credentials: Credential = {
-    val clientSecrets = filePathToSecrets(secretsFile, jsonFactory)
-    val dataStore = Paths.get(datastoreDir).toAbsolutePath
-    val dataStoreFactory = new FileDataStoreFactory(dataStore.toFile)
-    val flow = new GoogleAuthorizationCodeFlow.Builder(httpTransport,
-      jsonFactory,
-      clientSecrets,
-      scopes.asJava).setDataStoreFactory(dataStoreFactory).build
-    validateCredentials(new AuthorizationCodeInstalledApp(flow, new GooglePromptReceiver).authorize(user))
-  }
-
-  override def credential(options: GoogleAuthOptions) = credentials
-}
-
-// It would be goofy to have multiple auths that are application_default, but Cromwell won't prevent it.
-final case class ApplicationDefaultMode(override val name: String, scopes: List[String] = GcsScopes) extends GoogleAuthMode {
-  import GoogleAuthMode._
-
-  private lazy val credentials: Credential = {
-    try {
-      validateCredentials(GoogleCredential.getApplicationDefault().createScoped(scopes.asJava))
-    } catch {
-      case e: IOException =>
-        log.warn("Failed to get application default credentials", e)
-        throw e
-    }
-  }
-
-  override def credential(options: GoogleAuthOptions) = credentials
-}
-
-final case class RefreshTokenMode(name: String, clientId: String, clientSecret: String) extends GoogleAuthMode with ClientSecrets {
-  import GoogleAuthMode._
-
-  override def requiresAuthFile = true
-
-  /**
-    * Throws if the refresh token is not specified.
-    */
-  override def assertWorkflowOptions(options: GoogleAuthOptions): Unit = { getToken(options); () }
-
-  private def getToken(options: GoogleAuthOptions): String = {
-    options.get(RefreshTokenOptionKey).getOrElse(throw new IllegalArgumentException(s"Missing parameters in workflow options: $RefreshTokenOptionKey"))
-  }
-
-  override def credential(options: GoogleAuthOptions): Credential = {
-    validateCredentials(
-      new GoogleCredential.Builder().setTransport(httpTransport)
-      .setJsonFactory(jsonFactory)
-      .setClientSecrets(clientId, clientSecret)
-      .build()
-      .setRefreshToken(getToken(options))
-    )
-  }
-}
-
-trait ClientSecrets {
-  val clientId: String
-  val clientSecret: String
-}
-
-final case class SimpleClientSecrets(clientId: String, clientSecret: String) extends ClientSecrets
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleConfiguration.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleConfiguration.scala
index 9c557983921..8fa93b61da8 100644
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleConfiguration.scala
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleConfiguration.scala
@@ -7,14 +7,12 @@ import cats.syntax.traverse._
 import cats.syntax.validated._
 import com.google.api.services.storage.StorageScopes
 import com.typesafe.config.Config
+import cromwell.filesystems.gcs.auth._
 import lenthall.config.ConfigValidationException
 import lenthall.config.ValidatedConfig._
 import cromwell.core.ErrorOr._
 import org.slf4j.LoggerFactory
 
-import scala.collection.JavaConverters._
-
-
 final case class GoogleConfiguration private (applicationName: String, authsByName: Map[String, GoogleAuthMode]) {
 
   def auth(name: String): ErrorOr[GoogleAuthMode] = {
@@ -28,15 +26,15 @@ final case class GoogleConfiguration private (applicationName: String, authsByNa
 }
 
 object GoogleConfiguration {
-
+  import scala.collection.JavaConverters._
   private val log = LoggerFactory.getLogger("GoogleConfiguration")
 
-  private val GoogleScopes = List(
+  val GoogleScopes = List(
     StorageScopes.DEVSTORAGE_FULL_CONTROL,
     StorageScopes.DEVSTORAGE_READ_WRITE,
     "https://www.googleapis.com/auth/genomics",
     "https://www.googleapis.com/auth/compute"
-  )
+  ).asJava
 
   def apply(config: Config): GoogleConfiguration = {
 
@@ -55,10 +53,10 @@ object GoogleConfiguration {
       }
 
       def refreshTokenAuth(authConfig: Config, name: String) = authConfig validateAny {
-        cfg => RefreshTokenMode(name, cfg.getString("client-id"), cfg.getString("client-secret"))
+        cfg => RefreshTokenMode(name, cfg.getString("client-id"), cfg.getString("client-secret"), GoogleScopes)
       }
 
-      def applicationDefaultAuth(name: String): ErrorOr[GoogleAuthMode] = ApplicationDefaultMode(name, GoogleScopes).validNel
+      def applicationDefaultAuth(name: String): ErrorOr[GoogleAuthMode] = ApplicationDefaultMode(name).validNel
 
       val name = authConfig.getString("name")
       val scheme = authConfig.getString("scheme")
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/NioGcsPath.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/NioGcsPath.scala
deleted file mode 100644
index 65e148f7787..00000000000
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/NioGcsPath.scala
+++ /dev/null
@@ -1,191 +0,0 @@
-package cromwell.filesystems.gcs
-
-import java.io.File
-import java.net.URI
-import java.nio.file.WatchEvent.{Kind, Modifier}
-import java.nio.file._
-import java.util
-
-import scala.collection.JavaConverters._
-import scala.language.postfixOps
-import scala.util.Try
-
-object NioGcsPath {
-  def apply(path: String)(implicit gcsFileSystem: GcsFileSystem) = gcsFileSystem.getPath(path)
-
-  implicit class PathEnhanced(val path: Path) extends AnyVal {
-    def asGcsPath(implicit gcsFileSystem: GcsFileSystem) = path match {
-      case gcsPath: NioGcsPath => gcsPath
-      case otherPath: Path => getSoftPath(otherPath.toString).asInstanceOf[NioGcsPath]
-      case _ => throw new IllegalArgumentException("Only GcsPaths are supported.")
-    }
-  }
-
-  /** Allow instantiation of a relative gcs path.
-    * Relative GCS paths can only be created via NioGcsPath methods (eg: subpath, getName...) but not through the GcsFileSystem.getPath method
-    * in order to avoid floating paths without root. It also ensures that a relative local path cannot mistakenly be parsed as a GCS path.
-    * */
-  private def getSoftPath(first: String, more: String*)(implicit gcsFs: GcsFileSystem): Path = Try(gcsFs.getPath(first, more: _*)) recover {
-    case e: NotAGcsPathException => new NioGcsPath(first.split(GcsFileSystem.Separator) ++ more.toArray[String], false, first.endsWith(GcsFileSystem.Separator))(gcsFs)
-  } get
-
-  val Protocol = GcsFileSystem.Protocol
-}
-
-/**
-  * NOTE: Currently called NioGcsPath so it can exist alongside the current GcsPath class.
-  *       If this approach was to be validated the current GcsPath class would be replaced by this one.
-  * This class proposes an implementation of the java.nio.Path interface for GoogleCloudStorage.
-  * The following methods are yet to be implemented:
-  *   relativize
-  *   compareTo
-  * @param chunks array containing all parts of the path in between separators - except the protocol (gs://)
-  *               eg: gs://path/to/resource.txt -> chunks = [path, to, resource.txt]
-  * @param absolute true if this path is to be considered absolute.
-  *                 Only absolute GCS paths can be used to actually locate resources.
-  *                 Calling methods on an absolute path can return a relative paths (eg subpath).
-  * @param gcsFileSystem the gcsFileSystem to be used when performing operations on this path
-  */
-class NioGcsPath(private val chunks: Array[String], absolute: Boolean, val isDirectory: Boolean)(implicit gcsFileSystem: GcsFileSystem) extends Path {
-  import NioGcsPath._
-
-  private val separator = GcsFileSystem.Separator
-
-  private val objectChunks = chunks match {
-    case values if isAbsolute && values.nonEmpty => values.tail
-    case _ => chunks
-  }
-
-  private val fullPath = chunksToString(chunks)
-
-  lazy val bucket: String = chunks match {
-    case values if values.isEmpty && isAbsolute => throw new IllegalStateException("An absolute gcs path cannot be empty")
-    case _ => if(isAbsolute) chunks.head else {
-      throw new UnsupportedOperationException("Attached gcs filesystem has no root and is not Absolute. The corresponding bucket is unknown.")
-    }
-  }
-
-  val objectName = chunksToString(objectChunks)
-
-  private def chunksToString(chunksArray: Array[String]): String = chunksArray.mkString(separator)
-
-  override def subpath(beginIndex: Int, endIndex: Int): Path = {
-    val directory = if (endIndex == chunks.length - 1) isDirectory else true
-    new NioGcsPath(chunks.slice(beginIndex, endIndex), isAbsolute && beginIndex == 0, directory)
-  }
-
-  override def toFile: File = throw new UnsupportedOperationException("A GCS path cannot be converted to a File.")
-
-  override def resolveSibling(other: Path): Path = {
-    val otherPath = other.asGcsPath
-    new NioGcsPath(getParent.asGcsPath.chunks ++ otherPath.chunks, isAbsolute, otherPath.isDirectory)
-  }
-
-  override def resolveSibling(other: String): Path = {
-    val otherPath = getSoftPath(other).asGcsPath
-    new NioGcsPath(getParent.asGcsPath.chunks ++ getSoftPath(other).asGcsPath.chunks, isAbsolute, otherPath.isDirectory)
-  }
-
-  override def getFileSystem: FileSystem = gcsFileSystem
-
-  override def getName(index: Int): Path = {
-    val directory = if (index == chunks.length - 1) isDirectory else true
-    new NioGcsPath(Array(chunks(index)), isAbsolute && index == 0, directory)
-  }
-
-  override def getParent: Path = chunks match {
-    case values if values.isEmpty || values.length == 1 => null
-    case values => new NioGcsPath(values.init, isAbsolute, true)
-  }
-
-  override def toAbsolutePath: Path = if (isAbsolute) this else {
-    throw new UnsupportedOperationException(s"Attached gcs filesystem has no root. path $toString can't be converted to an absolute path.")
-  }
-
-  override def relativize(other: Path): Path = other match {
-    case gcs: NioGcsPath => new NioGcsPath(gcs.chunks.diff(this.chunks), false, gcs.isDirectory)
-    case _ => throw new IllegalArgumentException(s"$other is not a GCS path.")
-  }
-
-  override def getNameCount: Int = chunks.length
-
-  override def toUri: URI = new URI(GcsFileSystem.Scheme, bucket, s"/$objectName", null)
-
-  override def compareTo(other: Path): Int = throw new NotImplementedError()
-
-  override def register(watcher: WatchService, events: Array[Kind[_]], modifiers: Modifier*): WatchKey = throw new UnsupportedOperationException()
-
-  override def register(watcher: WatchService, events: Kind[_]*): WatchKey = throw new UnsupportedOperationException()
-
-  override def getFileName: Path = chunks match {
-    case values if values.isEmpty => null
-    case _ => new NioGcsPath(Array(chunks.last), isAbsolute && chunks.length == 1, isDirectory)
-  }
-
-  override def getRoot: Path = new NioGcsPath(Array(bucket), true, true)
-
-  override def iterator(): util.Iterator[Path] = {
-    if (chunks.isEmpty) chunks.map(_.asInstanceOf[Path]).iterator.asJava else {
-      val init = chunks.init map { elt => new NioGcsPath(Array(elt), false, true).asInstanceOf[Path] }
-      val fullIterator = init :+ new NioGcsPath(Array(chunks.last), false, isDirectory).asInstanceOf[Path]
-      fullIterator.iterator.asJava
-    }
-  }
-
-  override def normalize(): Path = if (isAbsolute) this else throw new UnsupportedOperationException("Cannot normalize a relative GCS path.")
-
-  override def endsWith(other: Path): Boolean = {
-    other match {
-      case rel: NioGcsPath if !isAbsolute && rel.isAbsolute => false
-      case _: NioGcsPath => chunks.endsWith(other.asGcsPath.chunks)
-      case _ => false
-    }
-  }
-
-  override def endsWith(other: String): Boolean = {
-    Try(getSoftPath(other)) map {
-      case rel: NioGcsPath if !isAbsolute && rel.isAbsolute => false
-      case path@(_: NioGcsPath) => chunks.endsWith(path.asGcsPath.chunks)
-      case _ => false
-    } getOrElse false
-  }
-
-  override def resolve(other: Path): Path = {
-    if (other.isAbsolute) other
-    else {
-      val otherGcs = other.asGcsPath
-      new NioGcsPath(chunks ++ otherGcs.chunks, isAbsolute, otherGcs.isDirectory)
-    }
-  }
-
-  override def resolve(other: String): Path = {
-    val otherPath = getSoftPath(other).asGcsPath
-    if (otherPath.isAbsolute) otherPath
-    else new NioGcsPath(chunks ++ otherPath.asGcsPath.chunks, isAbsolute, otherPath.isDirectory)
-  }
-
-  override def toRealPath(options: LinkOption*): Path = this
-
-  override def startsWith(other: Path): Boolean = {
-    other match {
-      case rel: NioGcsPath if !isAbsolute && rel.isAbsolute => false
-      case _: NioGcsPath => chunks.startsWith(other.asGcsPath.chunks)
-      case _ => false
-    }
-  }
-
-  override def startsWith(other: String): Boolean = {
-    Try(getSoftPath(other)) map {
-      case rel: NioGcsPath if !isAbsolute && rel.isAbsolute => false
-      case path@(_: NioGcsPath) => chunks.startsWith(path.asGcsPath.chunks)
-      case _ => false
-    } getOrElse false
-  }
-
-  override def toString: String = {
-    if (absolute) s"$Protocol$fullPath"
-    else fullPath
-  }
-
-  override def isAbsolute: Boolean = absolute
-}
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/auth/GoogleAuthMode.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/auth/GoogleAuthMode.scala
new file mode 100644
index 00000000000..26d18833dc3
--- /dev/null
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/auth/GoogleAuthMode.scala
@@ -0,0 +1,187 @@
+package cromwell.filesystems.gcs.auth
+
+import java.io.{FileNotFoundException, InputStreamReader}
+import java.nio.file.Paths
+
+import better.files._
+import com.google.api.client.auth.oauth2.Credential
+import com.google.api.client.extensions.java6.auth.oauth2.AuthorizationCodeInstalledApp
+import com.google.api.client.googleapis.auth.oauth2.{GoogleAuthorizationCodeFlow, GoogleClientSecrets, GoogleCredential}
+import com.google.api.client.googleapis.extensions.java6.auth.oauth2.GooglePromptReceiver
+import com.google.api.client.googleapis.javanet.GoogleNetHttpTransport
+import com.google.api.client.googleapis.testing.auth.oauth2.MockGoogleCredential
+import com.google.api.client.json.jackson2.JacksonFactory
+import com.google.api.client.util.store.FileDataStoreFactory
+import com.google.api.services.storage.StorageScopes
+import com.google.auth.oauth2.{ClientId, ServiceAccountCredentials}
+import com.google.cloud.AuthCredentials
+import cromwell.core.WorkflowOptions
+import cromwell.filesystems.gcs.auth.GoogleAuthMode._
+import org.slf4j.LoggerFactory
+
+import scala.collection.JavaConverters._
+import scala.util.{Failure, Success, Try}
+
+object GoogleAuthMode {
+
+  lazy val jsonFactory = JacksonFactory.getDefaultInstance
+  lazy val httpTransport = GoogleNetHttpTransport.newTrustedTransport
+
+  val RefreshTokenOptionKey = "refresh_token"
+  val GcsScopes = List(
+    StorageScopes.DEVSTORAGE_FULL_CONTROL,
+    StorageScopes.DEVSTORAGE_READ_WRITE
+  ).asJava
+
+  def checkReadable(file: File) = {
+    if (!file.isReadable) throw new FileNotFoundException(s"File $file does not exist or is not readable")
+  }
+
+  case object NoAuthMode extends GoogleAuthMode {
+    override def name = "no_auth"
+
+    override def authCredentials(options: WorkflowOptions): AuthCredentials = AuthCredentials.noAuth()
+    override def credential(options: WorkflowOptions): Credential = new MockGoogleCredential.Builder().build()
+  }
+}
+
+
+sealed trait GoogleAuthMode {
+  protected lazy val log = LoggerFactory.getLogger(getClass.getSimpleName)
+
+  /**
+    * Validate the auth mode against provided options
+    */
+  def validate(options: WorkflowOptions): Unit = {()}
+
+  def name: String
+  // Create an AuthCredentials object from the google-cloud library (https://github.com/GoogleCloudPlatform/google-cloud-java using https://github.com/google/google-auth-library-java under the hood)
+  def authCredentials(options: WorkflowOptions): AuthCredentials
+  // Create a Credential object from the google.api.client.auth library (https://github.com/google/google-api-java-client)
+  def credential(options: WorkflowOptions): Credential
+
+  def requiresAuthFile: Boolean = false
+
+  protected def validateAuthCredentials(authCredentials: AuthCredentials, scopes: java.util.Collection[String]): AuthCredentials = validate(authCredentials, authCredentials.credentials().createScoped(scopes).refresh)
+
+  protected def validateCredential(credential: Credential) = validate(credential, credential.refreshToken)
+
+  private def validate[T](credential: T, validation: () => Any): T = {
+    Try(validation()) match {
+      case Failure(ex) => throw new RuntimeException(s"Google credentials are invalid: ${ex.getMessage}")
+      case Success(_) => credential
+    }
+  }
+}
+
+final case class ServiceAccountMode(override val name: String,
+                                    accountId: String,
+                                    pemPath: String,
+                                    scopes: java.util.List[String]) extends GoogleAuthMode {
+  private val pemFile = File(pemPath)
+  checkReadable(pemFile)
+
+  private lazy val _authCredentials: AuthCredentials = {
+    val saCredentials = ServiceAccountCredentials.fromPkcs8(accountId, accountId, pemFile.contentAsString, null, scopes)
+    validateAuthCredentials(AuthCredentials.createFor(saCredentials.getClientId, saCredentials.getPrivateKey), scopes)
+  }
+
+  private lazy val _credential: Credential = {
+    validateCredential(
+      new GoogleCredential.Builder().setTransport(httpTransport)
+        .setJsonFactory(jsonFactory)
+        .setServiceAccountId(accountId)
+        .setServiceAccountScopes(scopes)
+        .setServiceAccountPrivateKeyFromPemFile(pemFile.toJava)
+        .build()
+    )
+  }
+
+  override def authCredentials(options: WorkflowOptions) = _authCredentials
+
+  override def credential(options: WorkflowOptions): Credential = _credential
+}
+
+final case class UserMode(override val name: String,
+                          user: String,
+                          val secretsPath: String,
+                          datastoreDir: String,
+                          scopes: java.util.List[String]) extends GoogleAuthMode {
+
+  private lazy val secrets = {
+    val secretsFile = File(secretsPath)
+    checkReadable(secretsFile)
+
+    val secretStream = new InputStreamReader(secretsFile.newInputStream)
+
+    GoogleClientSecrets.load(jsonFactory, secretStream)
+  }
+
+  private lazy val _credential: Credential = {
+    val dataStore = Paths.get(datastoreDir).toAbsolutePath
+    val dataStoreFactory = new FileDataStoreFactory(dataStore.toFile)
+    val flow = new GoogleAuthorizationCodeFlow.Builder(httpTransport, jsonFactory, secrets, scopes).setDataStoreFactory(dataStoreFactory).build
+    validateCredential(new AuthorizationCodeInstalledApp(flow, new GooglePromptReceiver).authorize(user))
+  }
+
+  private lazy val _authCredentials: AuthCredentials = {
+    new RefreshableOAuth2Credentials(_credential.getRefreshToken, new ClientId(secrets.getDetails.getClientId, secrets.getDetails.getClientSecret))
+  }
+
+  override def credential(options: WorkflowOptions) = _credential
+
+  override def authCredentials(options: WorkflowOptions) = _authCredentials
+}
+
+private object ApplicationDefault {
+  private [auth] lazy val _AuthCredentials = AuthCredentials.createApplicationDefaults()
+  private [auth] lazy val _Credential: Credential = GoogleCredential.getApplicationDefault()
+}
+
+final case class ApplicationDefaultMode(name: String) extends GoogleAuthMode {
+  override def authCredentials(options: WorkflowOptions) = ApplicationDefault._AuthCredentials
+  override def credential(options: WorkflowOptions) = ApplicationDefault._Credential
+}
+
+final case class RefreshTokenMode(name: String,
+                                  clientId: String,
+                                  clientSecret: String,
+                                  scopes: java.util.List[String]) extends GoogleAuthMode with ClientSecrets {
+  import GoogleAuthMode._
+  override def requiresAuthFile = true
+
+  private def extractRefreshToken(options: WorkflowOptions): String = {
+    options.get(RefreshTokenOptionKey) getOrElse {
+      throw new IllegalArgumentException(s"Missing parameters in workflow options: $RefreshTokenOptionKey")
+    }
+  }
+
+  override def validate(options: WorkflowOptions) = {
+    extractRefreshToken(options)
+
+    ()
+  }
+
+  override def authCredentials(options: WorkflowOptions): AuthCredentials = {
+    val refreshToken = extractRefreshToken(options)
+    validateAuthCredentials(new RefreshableOAuth2Credentials(refreshToken, new ClientId(clientId, clientSecret)), scopes)
+  }
+
+  override def credential(options: WorkflowOptions): Credential = {
+    val refreshToken = extractRefreshToken(options)
+    validateCredential(
+      new GoogleCredential.Builder().setTransport(httpTransport)
+        .setJsonFactory(jsonFactory)
+        .setClientSecrets(clientId, clientSecret)
+        .build()
+        .setRefreshToken(refreshToken)
+    )
+  }
+}
+
+trait ClientSecrets {
+  val clientId: String
+  val clientSecret: String
+}
+
+final case class SimpleClientSecrets(clientId: String, clientSecret: String) extends ClientSecrets
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/auth/RefreshableOAuth2Credentials.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/auth/RefreshableOAuth2Credentials.scala
new file mode 100644
index 00000000000..ae1e32ef526
--- /dev/null
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/auth/RefreshableOAuth2Credentials.scala
@@ -0,0 +1,31 @@
+package cromwell.filesystems.gcs.auth
+
+import java.io.Serializable
+import java.util.Objects
+
+import com.google.auth.oauth2.{ClientId, GoogleCredentials, UserCredentials}
+import com.google.cloud.{AuthCredentials, RestorableState}
+
+class RefreshableOAuth2Credentials(refreshToken: String, clientId: ClientId) extends AuthCredentials {
+  private val _credentials: GoogleCredentials = new UserCredentials(clientId.getClientId, clientId.getClientSecret, refreshToken)
+
+  private class RefreshableOAuth2CredentialsState(val refreshToken: String, val clientId: ClientId) extends RestorableState[AuthCredentials] with Serializable {
+
+    override def restore: AuthCredentials = new RefreshableOAuth2Credentials(refreshToken, clientId)
+
+    override def hashCode: Int = Objects.hash(refreshToken, clientId.getClientId, clientId.getClientSecret)
+
+    override def equals(obj: Any): Boolean = {
+      obj.isInstanceOf[RefreshableOAuth2CredentialsState] && {
+        val other = obj.asInstanceOf[RefreshableOAuth2CredentialsState]
+        Objects.equals(refreshToken, other.refreshToken) &&
+        Objects.equals(clientId.getClientId, other.clientId.getClientId) &&
+        Objects.equals(clientId.getClientSecret, other.clientId.getClientSecret)
+      }
+    }
+  }
+
+  override def credentials: GoogleCredentials = _credentials
+
+  def capture: RestorableState[AuthCredentials] = new RefreshableOAuth2CredentialsState(refreshToken, clientId)
+}
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/package.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/package.scala
deleted file mode 100644
index 0ec2c03168c..00000000000
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/package.scala
+++ /dev/null
@@ -1,6 +0,0 @@
-package cromwell.filesystems
-
-
-package object gcs {
-  type RefreshToken = String
-}
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsIntegrationTest.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsIntegrationTest.scala
deleted file mode 100644
index 3c6a287348b..00000000000
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsIntegrationTest.scala
+++ /dev/null
@@ -1,5 +0,0 @@
-package cromwell.filesystems.gcs
-
-import org.scalatest.Tag
-
-object GcsIntegrationTest extends Tag("GcsIntegrationTest")
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala
new file mode 100644
index 00000000000..598cb546173
--- /dev/null
+++ b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala
@@ -0,0 +1,31 @@
+package cromwell.filesystems.gcs
+
+import com.google.cloud.RetryParams
+import com.google.cloud.storage.contrib.nio.CloudStorageConfiguration
+import cromwell.core.path.CustomRetryParams
+import cromwell.core.path.proxy.RetryableFileSystemProviderProxy
+import cromwell.core.{TestKitSuite, WorkflowOptions}
+import cromwell.filesystems.gcs.auth.GoogleAuthMode
+import org.scalatest.{FlatSpecLike, Matchers}
+
+class GcsPathBuilderSpec extends TestKitSuite with FlatSpecLike with Matchers {
+
+  implicit val as = system
+
+  behavior of "GcsPathBuilderSpec"
+
+  it should "create a path with a retryable provider" in {
+    val retryablePathBuilder = new RetryableGcsPathBuilder(
+      GoogleAuthMode.NoAuthMode,
+      RetryParams.defaultInstance(),
+      CustomRetryParams.Default,
+      CloudStorageConfiguration.DEFAULT,
+      WorkflowOptions.empty
+    )
+
+    val path = retryablePathBuilder.build("gs://bucket/object")
+    path.isSuccess shouldBe true
+    path.get.getFileSystem.provider() shouldBe a[RetryableFileSystemProviderProxy[_]]
+  }
+
+}
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GoogleConfigurationSpec.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GoogleConfigurationSpec.scala
index 3eeeaf56817..cc1c9fd6c36 100644
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GoogleConfigurationSpec.scala
+++ b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GoogleConfigurationSpec.scala
@@ -1,6 +1,8 @@
 package cromwell.filesystems.gcs
 
+import better.files.File
 import com.typesafe.config.{ConfigException, ConfigFactory}
+import cromwell.filesystems.gcs.auth.{ApplicationDefaultMode, RefreshTokenMode, ServiceAccountMode, UserMode}
 import lenthall.config.ConfigValidationException
 import org.scalatest.{FlatSpec, Matchers}
 
@@ -10,8 +12,10 @@ class GoogleConfigurationSpec extends FlatSpec with Matchers {
   behavior of "GoogleConfiguration"
 
   it should "parse all manner of well-formed auths" in {
+    val mockFile = File.newTemporaryFile()
+
     val righteousGoogleConfig =
-      """
+      s"""
         |google {
         |  application-name = "cromwell"
         |
@@ -30,14 +34,14 @@ class GoogleConfigurationSpec extends FlatSpec with Matchers {
         |      name = "name-user"
         |      scheme = "user_account"
         |      user = "me"
-        |      secrets-file = "/very/secret/file.txt"
+        |      secrets-file = "${mockFile.pathAsString}"
         |      data-store-dir = "/where/the/data/at"
         |    },
         |    {
         |      name = "name-service"
         |      scheme = "service_account"
         |      service-account-id = "my-google-account"
-        |      pem-file = "/yonder/file.pem"
+        |      pem-file = "${mockFile.pathAsString}"
         |    }
         |  ]
         |}
@@ -61,13 +65,15 @@ class GoogleConfigurationSpec extends FlatSpec with Matchers {
 
     val user = (auths collectFirst { case a: UserMode => a }).get
     user.name shouldBe "name-user"
-    user.secretsFile shouldBe "/very/secret/file.txt"
+    user.secretsPath shouldBe mockFile.pathAsString
     user.datastoreDir shouldBe "/where/the/data/at"
 
     val service = (auths collectFirst { case a: ServiceAccountMode => a }).get
     service.name shouldBe "name-service"
     service.accountId shouldBe "my-google-account"
-    service.pemPath shouldBe "/yonder/file.pem"
+    service.pemPath shouldBe mockFile.pathAsString
+
+    mockFile.delete(true)
   }
 
 
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GoogleCredentialFactorySpec.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GoogleCredentialFactorySpec.scala
deleted file mode 100644
index 541dc75eb8a..00000000000
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GoogleCredentialFactorySpec.scala
+++ /dev/null
@@ -1,158 +0,0 @@
-package cromwell.filesystems.gcs
-
-import java.nio.file.Paths
-
-import com.google.api.client.auth.oauth2.Credential
-import com.google.api.client.googleapis.auth.oauth2.GoogleCredential
-import com.google.api.client.googleapis.javanet.GoogleNetHttpTransport
-import com.google.api.client.json.jackson2.JacksonFactory
-import com.typesafe.config.ConfigFactory
-import cromwell.filesystems.gcs.GoogleAuthMode.EnhancedCredentials
-import org.scalatest.{FlatSpec, Matchers}
-
-import scala.util.Try
-
-class GoogleCredentialFactorySpec extends FlatSpec with Matchers {
-  import GoogleCredentialFactorySpec._
-
-  behavior of "GoogleCredentialFactory"
-
-  it should "refresh a token using user credentials" taggedAs GcsIntegrationTest in {
-    val credential = UserMode(
-      name = "user",
-      user = secretConf("user"),
-      secretsFile = secretConf("secrets-file"),
-      datastoreDir = secretConf("data-store-dir")).credential(emptyOptions)
-
-    val firstCredentialTry: Try[Credential] = credential.freshCredential
-    assert(firstCredentialTry.isSuccess)
-    val firstCredential = firstCredentialTry.get
-    firstCredential.getAccessToken shouldNot be(empty)
-
-    firstCredential.setExpiresInSeconds(59L)
-
-    val secondCredentialTry: Try[Credential] = firstCredential.freshCredential
-    assert(secondCredentialTry.isSuccess)
-
-    val secondCredential = secondCredentialTry.get
-    secondCredential.getAccessToken shouldNot be(empty)
-    secondCredential.getExpiresInSeconds shouldNot be(null)
-    secondCredential.getExpiresInSeconds.longValue should be > 60L
-  }
-
-  it should "refresh a token using a service account" taggedAs GcsIntegrationTest in {
-    val credential = ServiceAccountMode(
-      name = "service",
-      accountId = secretConf("service-account-id"),
-      pemPath = secretConf("pem-file")).credential(emptyOptions)
-
-    val firstCredentialTry: Try[Credential] = credential.freshCredential
-    assert(firstCredentialTry.isSuccess)
-    val firstCredential = firstCredentialTry.get
-    firstCredential.getAccessToken shouldNot be(empty)
-
-    firstCredential.setExpiresInSeconds(59L)
-
-    val secondCredentialTry: Try[Credential] = firstCredential.freshCredential
-    assert(secondCredentialTry.isSuccess)
-
-    val secondCredential = secondCredentialTry.get
-    secondCredential.getAccessToken shouldNot be(empty)
-    secondCredential.getExpiresInSeconds shouldNot be(null)
-    secondCredential.getExpiresInSeconds.longValue should be > 60L
-  }
-
-  it should "refresh a token using a refresh token" taggedAs GcsIntegrationTest in {
-    val opts = GoogleOptionsMap(Map("refresh_token" -> secretConf("refresh_token")))
-
-    val credential = RefreshTokenMode(name = "refresh",
-      clientId = secretConf("client-id"),
-      clientSecret = secretConf("client-secret")).credential(opts)
-
-    val firstUserCredentialsTry = credential.freshCredential
-
-    assert(firstUserCredentialsTry.isSuccess)
-    val firstUserCredentials = firstUserCredentialsTry.get
-
-    val firstRefreshedUserCredentialsTry: Try[Credential] = firstUserCredentials.freshCredential
-    assert(firstRefreshedUserCredentialsTry.isSuccess)
-    val firstRefreshedUserCredentials = firstRefreshedUserCredentialsTry.get
-    firstRefreshedUserCredentials.getAccessToken shouldNot be(empty)
-
-    firstRefreshedUserCredentials.setExpiresInSeconds(59L)
-
-    val secondRefreshedUserCredentialsTry: Try[Credential] = firstRefreshedUserCredentials.freshCredential
-    assert(secondRefreshedUserCredentialsTry.isSuccess)
-
-    val secondRefreshedUserCredentials = secondRefreshedUserCredentialsTry.get
-    secondRefreshedUserCredentials.getAccessToken shouldNot be(empty)
-    secondRefreshedUserCredentials.getExpiresInSeconds shouldNot be(null)
-    secondRefreshedUserCredentials.getExpiresInSeconds.longValue should be > 60L
-  }
-
-  it should "not refresh an empty token" in {
-
-    val wrongCredentials = new GoogleCredential.Builder()
-      .setTransport(GoogleNetHttpTransport.newTrustedTransport)
-      .setJsonFactory(JacksonFactory.getDefaultInstance)
-      .setClientSecrets("fakeId", "fakeSecret")
-      .build()
-
-    val exception = wrongCredentials.freshCredential.failed.get
-
-    exception.getMessage should be("Unable to refresh token")
-  }
-
-  it should "refresh a token using application default credentials" taggedAs GcsIntegrationTest in {
-    val credential = applicationDefaultCredential
-
-    val firstCredentialTry: Try[Credential] = credential.freshCredential
-    assert(firstCredentialTry.isSuccess)
-    val firstCredential = firstCredentialTry.get
-    firstCredential.getAccessToken shouldNot be(empty)
-
-    firstCredential.setExpiresInSeconds(59L)
-
-    val secondCredentialTry: Try[Credential] = firstCredential.freshCredential
-    assert(secondCredentialTry.isSuccess)
-
-    val secondCredential = secondCredentialTry.get
-    secondCredential.getAccessToken shouldNot be(empty)
-    secondCredential.getExpiresInSeconds shouldNot be(null)
-    secondCredential.getExpiresInSeconds.longValue should be > 60L
-  }
-}
-
-object GoogleCredentialFactorySpec {
-  /*
-
-  To run this integration spec, your cromwell-credentials.conf file should have the following keys for the listed tests:
-
-  // For testing UserMode
-  user = "<user email>"
-  secrets-file = "<path to json secrets for above email>"
-  data-store-dir = "<path to where secrets will be stored>"
-
-  // For testing ServiceAccountMode
-  service-account-id = "<service account id>"
-  pem-file = "<path to the pem file>"
-
-  // For testing RefreshTokenMode
-  client-id = "<service account id, preferably one configured to use the oauth playground>"
-  client-secret = "<secret for the above client-id>"
-  refresh_token = "<refresh token created with the above id/secret and the cloud storage api scopes>"
-
-   */
-
-  private lazy val credentialsConfig = ConfigFactory.parseFile(Paths.get("cromwell-credentials.conf").toFile)
-
-  private def secretConf(path: String) = credentialsConfig.getString(path)
-
-  private val emptyOptions = GoogleOptionsMap(Map.empty)
-
-  def applicationDefaultCredential = ApplicationDefaultMode(name = "default").credential(emptyOptions)
-}
-
-case class GoogleOptionsMap(map: Map[String, String]) extends GoogleAuthMode.GoogleAuthOptions {
-  override def get(key: String): Try[String] = Try { map(key) }
-}
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/MockGcsFileSystemBuilder.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/MockGcsFileSystemBuilder.scala
deleted file mode 100644
index af569d7f0c1..00000000000
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/MockGcsFileSystemBuilder.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cromwell.filesystems.gcs
-
-import scala.util.Failure
-
-object MockGcsFileSystemBuilder {
-  val mockGcsFileSystem = new GcsFileSystemProvider(
-    Failure(new Exception("No Storage object available")),
-    scala.concurrent.ExecutionContext.global).defaultFileSystem
-}
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/NioGcsPathSpec.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/NioGcsPathSpec.scala
deleted file mode 100644
index ccb35efa622..00000000000
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/NioGcsPathSpec.scala
+++ /dev/null
@@ -1,291 +0,0 @@
-package cromwell.filesystems.gcs
-
-import java.nio.file.Path
-
-import org.scalatest.mockito.MockitoSugar
-import org.scalatest.prop.TableDrivenPropertyChecks._
-import org.scalatest.prop.Tables.Table
-import org.scalatest.{FlatSpec, Matchers}
-
-class NioGcsPathSpec extends FlatSpec with Matchers with MockitoSugar {
-
-  behavior of "NioGcsPath"
-
-  implicit val GCSFs = MockGcsFileSystemBuilder.mockGcsFileSystem
-
-  it should "implement toString" in {
-    val absPath1 = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val relPath1 = new NioGcsPath(Array("some", "relative", "path"), false, true)
-
-    absPath1.toString shouldBe "gs://absolute/path/to/somewhere"
-    relPath1.toString shouldBe "some/relative/path"
-  }
-
-  it should "implement subpath" in {
-    val absPath1 = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val relPath1 = new NioGcsPath(Array("some", "relative", "path"), false, true)
-
-    val absSub1 = absPath1.subpath(0, 2)
-    absSub1.isAbsolute shouldBe true
-    absSub1.toString shouldBe "gs://absolute/path"
-
-    val absSub2 = absPath1.subpath(1, 2)
-    absSub2.isAbsolute shouldBe false
-    absSub2.toString shouldBe "path"
-
-    val relSub1 = relPath1.subpath(0, 2)
-    relSub1.isAbsolute shouldBe false
-    relSub1.toString shouldBe "some/relative"
-  }
-
-  it should "implement resolveSibling" in {
-    val absPath1 = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val relPath1 = new NioGcsPath(Array("some", "relative", "path"), false, true)
-    val relPath2 = new NioGcsPath(Array("another", "relative", "resource", "path"), false, true)
-
-    val absSibling = absPath1.resolveSibling("somewhere else")
-    absSibling.isAbsolute shouldBe true
-    absSibling.toString shouldBe "gs://absolute/path/to/somewhere else"
-
-    val absSiblingPath = absPath1.resolveSibling(relPath1)
-    absSiblingPath.isAbsolute shouldBe true
-    absSiblingPath.toString shouldBe "gs://absolute/path/to/some/relative/path"
-
-    val absRel = relPath1.resolveSibling("other path")
-    absRel.isAbsolute shouldBe false
-    absRel.toString shouldBe "some/relative/other path"
-
-    val absRelPath = relPath1.resolveSibling(relPath2)
-    absRelPath.isAbsolute shouldBe false
-    absRelPath.toString shouldBe "some/relative/another/relative/resource/path"
-  }
-
-  it should "implement resolve" in {
-    val absPath1 = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val absPath2 = new NioGcsPath(Array("absolute", "location"), true, true)
-    val relPath1 = new NioGcsPath(Array("some", "relative", "path"), false, true)
-    val relPath2 = new NioGcsPath(Array("another", "relative", "resource", "path"), false, true)
-
-    val absToRel = absPath1.resolve(relPath1)
-    absToRel.isAbsolute shouldBe true
-    absToRel.toString shouldBe "gs://absolute/path/to/somewhere/some/relative/path"
-
-    val absToAbs = absPath1.resolve(absPath2)
-    absToAbs.isAbsolute shouldBe true
-    absToAbs.toString shouldBe "gs://absolute/location"
-
-    val relToAbs = relPath1.resolve(absPath1)
-    relToAbs.isAbsolute shouldBe true
-    relToAbs.toString shouldBe "gs://absolute/path/to/somewhere"
-
-    val relToRel = relPath1.resolve(relPath2)
-    relToRel.isAbsolute shouldBe false
-    relToRel.toString shouldBe "some/relative/path/another/relative/resource/path"
-  }
-
-  it should "implement getName" in {
-    val absPath1 = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val relPath1 = new NioGcsPath(Array("some", "relative", "path"), false, true)
-
-    val nameAbs1 = absPath1.getName(0)
-    nameAbs1.isAbsolute shouldBe true
-    nameAbs1.toString shouldBe "gs://absolute"
-
-    val nameAbs2 = absPath1.getName(1)
-    nameAbs2.isAbsolute shouldBe false
-    nameAbs2.toString shouldBe "path"
-
-    val nameRel1 = relPath1.getName(0)
-    nameRel1.isAbsolute shouldBe false
-    nameRel1.toString shouldBe "some"
-
-    val nameRel2 = relPath1.getName(1)
-    nameRel2.isAbsolute shouldBe false
-    nameRel2.toString shouldBe "relative"
-  }
-
-  it should "implement getParent" in {
-    val empty = new NioGcsPath(Array.empty[String], true, true)
-    val singleton = new NioGcsPath(Array("singleton"), true, true)
-    val absPath1 = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val relPath1 = new NioGcsPath(Array("some", "relative", "path"), false, true)
-
-    val parentAbs1 = absPath1.getParent
-    parentAbs1.isAbsolute shouldBe true
-    parentAbs1.toString shouldBe "gs://absolute/path/to"
-
-    empty.getParent shouldBe null
-    singleton.getParent shouldBe null
-
-    val nameRel1 = relPath1.getParent
-    nameRel1.isAbsolute shouldBe false
-    nameRel1.toString shouldBe "some/relative"
-  }
-
-  it should "implement toAbsolutePath" in {
-    val absPath1 = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val relPath1 = new NioGcsPath(Array("some", "relative", "path"), false, true)
-
-    val abs = absPath1.toAbsolutePath
-    abs.isAbsolute shouldBe true
-    abs.toString shouldBe "gs://absolute/path/to/somewhere"
-
-    an[Exception] shouldBe thrownBy(relPath1.toAbsolutePath)
-  }
-
-  it should "implement getNameCount" in {
-    val empty = new NioGcsPath(Array.empty[String], true, true)
-    val singleton = new NioGcsPath(Array("singleton"), true, true)
-    val absPath1 = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val relPath1 = new NioGcsPath(Array("some", "relative", "path"), false, true)
-
-    absPath1.getNameCount shouldBe 4
-    relPath1.getNameCount shouldBe 3
-    empty.getNameCount shouldBe 0
-    singleton.getNameCount shouldBe 1
-  }
-
-  it should "implement getFileName" in {
-    val empty = new NioGcsPath(Array.empty[String], true, true)
-    val singletonAbs = new NioGcsPath(Array("singleton"), true, true)
-    val singletonRel = new NioGcsPath(Array("singleton"), false, true)
-    val absPath1 = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val relPath1 = new NioGcsPath(Array("some", "relative", "path"), false, true)
-
-    val emptyFileName = empty.getFileName
-    emptyFileName shouldBe null
-
-    val singletonAbsFileName = singletonAbs.getFileName
-    singletonAbsFileName.isAbsolute shouldBe true
-    singletonAbsFileName.toString shouldBe "gs://singleton"
-
-    val singletonRelFileName = singletonRel.getFileName
-    singletonRelFileName.isAbsolute shouldBe false
-    singletonRelFileName.toString shouldBe "singleton"
-
-    val relFileName = relPath1.getFileName
-    relFileName.isAbsolute shouldBe false
-    relFileName.toString shouldBe "path"
-
-    val absFileName = absPath1.getFileName
-    absFileName.isAbsolute shouldBe false
-    absFileName.toString shouldBe "somewhere"
-  }
-
-  it should "implement getIterator" in {
-    val empty = new NioGcsPath(Array.empty[String], true, true)
-    val singletonAbs = new NioGcsPath(Array("singleton"), true, true)
-    val singletonRel = new NioGcsPath(Array("singleton"), false, true)
-    val absPath1 = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val relPath1 = new NioGcsPath(Array("some", "relative", "path"), false, true)
-
-    empty.iterator().hasNext shouldBe false
-
-    val singletonAbsIterator = singletonAbs.iterator()
-    val nextAbsSingleton: Path = singletonAbsIterator.next()
-    nextAbsSingleton.isAbsolute shouldBe false
-    nextAbsSingleton.toString shouldBe "singleton"
-    singletonAbsIterator.hasNext shouldBe false
-
-    val singletonRelIterator = singletonRel.iterator()
-    val nextRelSingleton: Path = singletonRelIterator.next()
-    nextRelSingleton.isAbsolute shouldBe false
-    nextRelSingleton.toString shouldBe "singleton"
-    singletonRelIterator.hasNext shouldBe false
-
-    val relIterator = relPath1.iterator()
-    val nextRel: Path = relIterator.next()
-    nextRel.isAbsolute shouldBe false
-    nextRel.toString shouldBe "some"
-    relIterator.next().toString shouldBe "relative"
-    relIterator.next().toString shouldBe "path"
-    relIterator.hasNext shouldBe false
-
-    val absIterator = absPath1.iterator()
-    val absRel: Path = absIterator.next()
-    absRel.isAbsolute shouldBe false
-    absRel.toString shouldBe "absolute"
-    absIterator.next().toString shouldBe "path"
-    absIterator.next().toString shouldBe "to"
-    absIterator.next().toString shouldBe "somewhere"
-    absIterator.hasNext shouldBe false
-  }
-
-  it should "implement startsWith" in {
-    val empty = new NioGcsPath(Array.empty[String], false, true)
-    val singletonAbs = new NioGcsPath(Array("absolute"), true, true)
-
-    val absPath = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val startsWithAbsPath = new NioGcsPath(Array("absolute", "path", "to"), true, true)
-    val doesntStartsWithAbsPath = new NioGcsPath(Array("absolute", "path", "to", "another", "place"), true, true)
-    val absPathStartingLikeRel = new NioGcsPath(Array("some", "relative", "path"), true, true)
-
-    val relPath = new NioGcsPath(Array("some", "relative", "path"), false, true)
-    val startsWithRelPath = new NioGcsPath(Array("some", "relative"), false, true)
-    val doesntStartsWithRelPath = new NioGcsPath(Array("some", "relative", "other", "path"), false, true)
-    val relPathStartingLikeAbs = new NioGcsPath(Array("absolute", "path", "to"), false, true)
-
-    val paths = Table(
-      ("path1", "path2", "result"),
-      (empty, empty, true),
-      (empty, absPath, false),
-      (singletonAbs, singletonAbs, true),
-      (absPath, startsWithAbsPath, true),
-      (absPath, doesntStartsWithAbsPath, false),
-      (absPath, relPathStartingLikeAbs, true),
-      (absPath, relPath, false),
-      (relPath, startsWithRelPath, true),
-      (relPath, doesntStartsWithRelPath, false),
-      (relPath, absPathStartingLikeRel, false),
-      (relPath, absPath, false)
-    )
-
-    forAll(paths) { (p1, p2, res) =>
-      val startsWith: Boolean = p1.startsWith(p2)
-      startsWith shouldBe res
-      val startsWith1: Boolean = p1.startsWith(p2.toString)
-      startsWith1 shouldBe res
-    }
-  }
-
-  it should "implement endsWith" in {
-    val empty = new NioGcsPath(Array.empty[String], false, true)
-    val singletonAbs = new NioGcsPath(Array("absolute"), true, true)
-
-    val absPath = new NioGcsPath(Array("absolute", "path", "to", "somewhere"), true, true)
-    val doesntEndWithAbsPath = new NioGcsPath(Array("absolute", "path", "to", "another", "place"), true, true)
-    val absPathEndingLikeRel = new NioGcsPath(Array("relative", "path"), true, true)
-
-    val relPath = new NioGcsPath(Array("some", "relative", "path"), false, true)
-    val endsWithRelPath = new NioGcsPath(Array("relative", "path"), false, true)
-    val doesntStartsWithRelPath = new NioGcsPath(Array("relative", "other", "path"), false, true)
-    val relPathEndingLikeAbs = new NioGcsPath(Array("path", "to", "somewhere"), false, true)
-
-    val paths = Table(
-      ("path1", "path2", "result"),
-      (empty, empty, true),
-      (empty, absPath, false),
-      (singletonAbs, singletonAbs, true),
-      (absPath, absPath, true),
-      (absPath, doesntEndWithAbsPath, false),
-      (absPath, relPathEndingLikeAbs, true),
-      (absPath, relPath, false),
-      (relPath, endsWithRelPath, true),
-      (relPath, doesntStartsWithRelPath, false),
-      (relPath, absPathEndingLikeRel, false),
-      (relPath, absPath, false)
-    )
-
-    forAll(paths) { (p1, p2, res) =>
-      p1.endsWith(p2) shouldBe res
-      p1.endsWith(p2.toString) shouldBe res
-    }
-  }
-
-  it should "implement toUri" in {
-    val file = new NioGcsPath(Array("some", "file"), true, false)
-    val uri = file.toUri
-    uri.toString shouldBe "gs://some/file"
-  }
-
-}
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/RefreshTokenModeSpec.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/RefreshTokenModeSpec.scala
deleted file mode 100644
index f959dcad544..00000000000
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/RefreshTokenModeSpec.scala
+++ /dev/null
@@ -1,26 +0,0 @@
-package cromwell.filesystems.gcs
-
-import org.scalatest.{FlatSpec, Matchers}
-
-class RefreshTokenModeSpec extends FlatSpec with Matchers {
-
-  val refreshToken = RefreshTokenMode(name = "bar", clientId = "secret-id", clientSecret = "secret-secret")
-
-  behavior of "RefreshTokenMode"
-
-  it should "assert good workflow options" in {
-    val goodOptions = GoogleOptionsMap(Map("refresh_token" -> "token"))
-    refreshToken.assertWorkflowOptions(goodOptions)
-  }
-
-  it should "fail to assert bad workflow options" in {
-    val badOptions = GoogleOptionsMap(Map("fresh_tokin" -> "broken"))
-    val noOptions = GoogleOptionsMap(Map.empty[String, String])
-
-    List(badOptions, noOptions).foreach { option =>
-      the[IllegalArgumentException] thrownBy {
-        refreshToken.assertWorkflowOptions(option)
-      } should have message s"Missing parameters in workflow options: refresh_token"
-    }
-  }
-}
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index a902e1b2a20..ee130f095d8 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -2,7 +2,7 @@ import sbt._
 
 object Dependencies {
   lazy val lenthallV = "0.19"
-  lazy val wdl4sV = "0.6"
+  lazy val wdl4sV = "0.7"
   lazy val sprayV = "1.3.3"
   /*
   spray-json is an independent project from the "spray suite"
@@ -12,22 +12,37 @@ object Dependencies {
   - http://doc.akka.io/docs/akka/2.4/scala/http/common/json-support.html#akka-http-spray-json
    */
   lazy val sprayJsonV = "1.3.2"
-  lazy val akkaV = "2.4.9"
+  lazy val akkaV = "2.4.12"
   lazy val slickV = "3.1.1"
-  lazy val googleClientApiV = "1.20.0"
+  lazy val googleClientApiV = "1.22.0"
+  lazy val googleGenomicsServicesApiV = "1.20.0"
   lazy val betterFilesV = "2.16.0"
   lazy val catsV = "0.7.2"
 
   // Internal collections of dependencies
 
+  private val catsDependencies = List(
+    "org.typelevel" %% "cats" % "0.7.2",
+    "com.github.benhutchison" %% "mouse" % "0.5"
+  ) map (_
+    /*
+    Exclude test framework cats-laws and its transitive dependency scalacheck.
+    If sbt detects scalacheck, it tries to run it.
+    Explicitly excluding the two problematic artifacts instead of including the three (or four?).
+    https://github.com/typelevel/cats/tree/v0.7.2#getting-started
+    Re "_2.11", see also: https://github.com/sbt/sbt/issues/1518
+     */
+    exclude("org.typelevel", "cats-laws_2.11")
+    exclude("org.typelevel", "cats-kernel-laws_2.11")
+    )
+
   private val baseDependencies = List(
     "org.broadinstitute" %% "lenthall" % lenthallV,
-    "org.typelevel" %% "cats" % catsV,
-    "com.github.benhutchison" %% "mouse" % "0.5",
     "com.iheart" %% "ficus" % "1.3.0",
     "org.scalatest" %% "scalatest" % "3.0.0" % Test,
-    "org.specs2" %% "specs2" % "3.7" % Test
-  )
+    "org.pegdown" % "pegdown" % "1.6.0" % Test,
+    "org.specs2" %% "specs2-mock" % "3.8.5" % Test
+  ) ++ catsDependencies
 
   private val slf4jBindingDependencies = List(
     // http://logback.qos.ch/dependencies.html
@@ -65,10 +80,10 @@ object Dependencies {
   )
 
   private val googleCloudDependencies = List(
-    "com.google.gcloud" % "gcloud-java" % "0.0.9",
-    "com.google.oauth-client" % "google-oauth-client" % googleClientApiV,
-    "com.google.cloud.bigdataoss" % "gcsio" % "1.4.4",
-    "com.google.apis" % "google-api-services-genomics" % ("v1alpha2-rev14-" + googleClientApiV)
+    "com.google.apis" % "google-api-services-genomics" % ("v1alpha2-rev14-" + googleGenomicsServicesApiV),
+    "com.google.cloud" % "google-cloud-nio" % "0.3.0"
+      exclude("com.google.api.grpc", "grpc-google-common-protos")
+      exclude("com.google.cloud.datastore", "datastore-v1-protos")
   )
 
   private val dbmsDependencies = List(
@@ -86,15 +101,12 @@ object Dependencies {
 
   // Sub-project dependencies, added in addition to any dependencies inherited from .dependsOn().
 
-  val gcsFileSystemDependencies = baseDependencies ++ googleApiClientDependencies ++ googleCloudDependencies
+  val gcsFileSystemDependencies = baseDependencies ++ googleApiClientDependencies ++ googleCloudDependencies ++ List (
+    "com.github.pathikrit" %% "better-files" % betterFilesV
+  )
 
   val databaseSqlDependencies = baseDependencies ++ slickDependencies ++ dbmsDependencies
 
-  val databaseMigrationDependencies = List(
-    "org.broadinstitute" %% "wdl4s" % wdl4sV, // Used in migration scripts
-    "com.github.pathikrit" %% "better-files" % betterFilesV % Test
-  ) ++ baseDependencies ++ liquibaseDependencies ++ dbmsDependencies
-
   val coreDependencies = List(
     "com.typesafe.scala-logging" %% "scala-logging" % "3.4.0",
     "org.broadinstitute" %% "wdl4s" % wdl4sV,
@@ -108,6 +120,10 @@ object Dependencies {
     // TODO: We're not using the "F" in slf4j. Core only supports logback, specifically the WorkflowLogger.
     slf4jBindingDependencies
 
+  val databaseMigrationDependencies = List(
+    "com.github.pathikrit" %% "better-files" % betterFilesV % Test
+  ) ++ liquibaseDependencies ++ dbmsDependencies
+
   val htCondorBackendDependencies = List(
     "com.twitter" %% "chill" % "0.8.0",
     "org.mongodb" %% "casbah" % "3.0.0"
@@ -118,12 +134,9 @@ object Dependencies {
   ) ++ sprayServerDependencies
 
   val engineDependencies = List(
-    "com.typesafe.scala-logging" %% "scala-logging" % "3.4.0",
     "org.webjars" % "swagger-ui" % "2.1.1",
     "commons-codec" % "commons-codec" % "1.10",
     "commons-io" % "commons-io" % "2.5",
-    "org.typelevel" %% "cats" % catsV,
-    "com.github.pathikrit" %% "better-files" % betterFilesV,
     "io.swagger" % "swagger-parser" % "1.0.22" % Test,
     "org.yaml" % "snakeyaml" % "1.17" % Test
   ) ++ sprayServerDependencies
diff --git a/project/Merging.scala b/project/Merging.scala
index 0591a09f9e2..2c941a76e65 100644
--- a/project/Merging.scala
+++ b/project/Merging.scala
@@ -25,10 +25,15 @@ object Merging {
           MergeStrategy.filterDistinctLines
         case ("spring.schemas" :: Nil) | ("spring.handlers" :: Nil) =>
           MergeStrategy.filterDistinctLines
+        case "io.netty.versions.properties" :: Nil =>
+          MergeStrategy.first
+        case "maven" :: "com.google.guava" :: xs =>
+          MergeStrategy.first
         case _ => MergeStrategy.deduplicate
       }
     case "asm-license.txt" | "overview.html" | "cobertura.properties" =>
       MergeStrategy.discard
+
     case _ => MergeStrategy.deduplicate
   }
 }
\ No newline at end of file
diff --git a/project/Settings.scala b/project/Settings.scala
index 4a092ce6802..f59d102e840 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -6,8 +6,8 @@ import Version._
 import sbt.Keys._
 import sbt._
 import sbtassembly.AssemblyPlugin.autoImport._
-import sbtrelease.ReleasePlugin
 import sbtdocker.DockerPlugin.autoImport._
+import sbtrelease.ReleasePlugin
 
 object Settings {
 
@@ -48,7 +48,13 @@ object Settings {
     "-Ywarn-numeric-widen",
     "-Ywarn-value-discard",
     "-Ywarn-unused",
-    "-Ywarn-unused-import"
+    "-Ywarn-unused-import",
+    "-Xfatal-warnings"
+  )
+
+  val docSettings = List(
+    // http://stackoverflow.com/questions/31488335/scaladoc-2-11-6-fails-on-throws-tag-with-unable-to-find-any-member-to-link#31497874
+    "-no-link-warnings"
   )
 
   lazy val assemblySettings = Seq(
@@ -58,14 +64,17 @@ object Settings {
     logLevel in assembly := Level.Info,
     assemblyMergeStrategy in assembly := customMergeStrategy
   )
-  
+
   lazy val dockerSettings = Seq(
     imageNames in docker := Seq(
-        ImageName(
-          namespace = Option("broadinstitute"),
-          repository = name.value,
-          tag = Some(s"${version.value}")
-        )
+      ImageName(
+        namespace = Option("broadinstitute"),
+        repository = name.value,
+        tag = Option(cromwellVersion)),
+      ImageName(
+        namespace = Option("broadinstitute"),
+        repository = name.value,
+        tag = Option(version.value))
     ),
     dockerfile in docker := {
       // The assembly task generates a fat JAR file
@@ -77,7 +86,7 @@ object Settings {
         expose(8000)
         add(artifact, artifactTargetPath)
         runRaw(s"ln -s $artifactTargetPath /app/cromwell.jar")
-        
+
         // If you use the 'exec' form for an entry point, shell processing is not performed and 
         // environment variable substitution does not occur.  Thus we have to /bin/bash here
         // and pass along any subsequent command line arguments
@@ -89,8 +98,7 @@ object Settings {
       cache = false,
       removeIntermediateContainers = BuildOptions.Remove.Always
     )
-    )
-  
+  )
 
   val commonSettings = ReleasePlugin.projectSettings ++ testSettings ++ assemblySettings ++
     dockerSettings ++ cromwellVersionWithGit ++ publishingSettings ++ List(
@@ -98,6 +106,7 @@ object Settings {
     scalaVersion := "2.11.8",
     resolvers ++= commonResolvers,
     scalacOptions ++= compilerSettings,
+    scalacOptions in (Compile, doc) ++= docSettings,
     parallelExecution := false
   )
 
diff --git a/project/Testing.scala b/project/Testing.scala
index 82df707d504..46ca8f15575 100644
--- a/project/Testing.scala
+++ b/project/Testing.scala
@@ -10,23 +10,25 @@ object Testing {
   lazy val DbmsTest = config("dbms") extend Test
 
   lazy val DockerTestTag = "DockerTest"
-  lazy val UseDockerTaggedTests = Tests.Argument("-n", DockerTestTag)
-  lazy val DontUseDockerTaggedTests = Tests.Argument("-l", DockerTestTag)
+  lazy val UseDockerTaggedTests = Tests.Argument(TestFrameworks.ScalaTest, "-n", DockerTestTag)
+  lazy val DontUseDockerTaggedTests = Tests.Argument(TestFrameworks.ScalaTest, "-l", DockerTestTag)
 
   lazy val CromwellIntegrationTestTag = "CromwellIntegrationTest"
-  lazy val UseCromwellIntegrationTaggedTests = Tests.Argument("-n", CromwellIntegrationTestTag)
-  lazy val DontUseCromwellIntegrationTaggedTests = Tests.Argument("-l", CromwellIntegrationTestTag)
+  lazy val UseCromwellIntegrationTaggedTests =
+    Tests.Argument(TestFrameworks.ScalaTest, "-n", CromwellIntegrationTestTag)
+  lazy val DontUseCromwellIntegrationTaggedTests =
+    Tests.Argument(TestFrameworks.ScalaTest, "-l", CromwellIntegrationTestTag)
 
   lazy val GcsIntegrationTestTag = "GcsIntegrationTest"
-  lazy val UseGcsIntegrationTaggedTests = Tests.Argument("-n", GcsIntegrationTestTag)
-  lazy val DontUseGcsIntegrationTaggedTests = Tests.Argument("-l", GcsIntegrationTestTag)
+  lazy val UseGcsIntegrationTaggedTests = Tests.Argument(TestFrameworks.ScalaTest, "-n", GcsIntegrationTestTag)
+  lazy val DontUseGcsIntegrationTaggedTests = Tests.Argument(TestFrameworks.ScalaTest, "-l", GcsIntegrationTestTag)
 
   lazy val DbmsTestTag = "DbmsTest"
-  lazy val UseDbmsTaggedTests = Tests.Argument("-n", DbmsTestTag)
-  lazy val DontUseDbmsTaggedTests = Tests.Argument("-l", DbmsTestTag)
+  lazy val UseDbmsTaggedTests = Tests.Argument(TestFrameworks.ScalaTest, "-n", DbmsTestTag)
+  lazy val DontUseDbmsTaggedTests = Tests.Argument(TestFrameworks.ScalaTest, "-l", DbmsTestTag)
 
   lazy val PostMVPTag = "PostMVP"
-  lazy val DontUsePostMVPTaggedTests = Tests.Argument("-l", PostMVPTag)
+  lazy val DontUsePostMVPTaggedTests = Tests.Argument(TestFrameworks.ScalaTest, "-l", PostMVPTag)
 
   lazy val TestReportArgs = Tests.Argument(TestFrameworks.ScalaTest, "-oDSI", "-h", "target/test-reports")
 
diff --git a/project/Version.scala b/project/Version.scala
index e6de0a5cdee..70adedb03b8 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -3,8 +3,8 @@ import sbt.Keys._
 import sbt._
 
 object Version {
-  // Upcoming release, or current if we're on the master branch
-  val cromwellVersion = "0.22"
+  // Upcoming release, or current if we're on a master / hotfix branch
+  val cromwellVersion = "23"
 
   // Adapted from SbtGit.versionWithGit
   def cromwellVersionWithGit: Seq[Setting[_]] =
@@ -39,6 +39,7 @@ object Version {
     // The project isSnapshot string passed in via command line settings, if desired.
     val isSnapshot = sys.props.get("project.isSnapshot").forall(_.toBoolean)
 
-    if (isSnapshot) s"$version-SNAPSHOT" else version
+    // For now, obfuscate SNAPSHOTs from sbt's developers: https://github.com/sbt/sbt/issues/2687#issuecomment-236586241
+    if (isSnapshot) s"$version-SNAP" else version
   }
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/CallMetadataKeys.scala b/services/src/main/scala/cromwell/services/metadata/CallMetadataKeys.scala
index 5284a9a8e2e..bf1df98d9ca 100644
--- a/services/src/main/scala/cromwell/services/metadata/CallMetadataKeys.scala
+++ b/services/src/main/scala/cromwell/services/metadata/CallMetadataKeys.scala
@@ -17,4 +17,6 @@ object CallMetadataKeys {
   val BackendLogsPrefix = "backendLogs"
   val JobId = "jobId"
   val CallRoot = "callRoot"
+  val SubWorkflowId = "subWorkflowId"
+  val SubWorkflowMetadata = "subWorkflowMetadata"
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala b/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala
index 374169d0555..6542c2082a7 100644
--- a/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala
+++ b/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala
@@ -36,7 +36,7 @@ case object MetadataBoolean extends MetadataType { override val typeName = "bool
 
 object MetadataValue {
   def apply(value: Any) = {
-    value match {
+    Option(value).getOrElse("") match {
       case WdlInteger(i) => new MetadataValue(i.toString, MetadataInt)
       case WdlFloat(f) => new MetadataValue(f.toString, MetadataNumber)
       case WdlBoolean(b) => new MetadataValue(b.toString, MetadataBoolean)
@@ -75,16 +75,17 @@ object MetadataQueryJobKey {
 
 case class MetadataQuery(workflowId: WorkflowId, jobKey: Option[MetadataQueryJobKey], key: Option[String],
                          includeKeysOption: Option[NonEmptyList[String]],
-                         excludeKeysOption: Option[NonEmptyList[String]])
+                         excludeKeysOption: Option[NonEmptyList[String]],
+                         expandSubWorkflows: Boolean)
 
 object MetadataQuery {
-  def forWorkflow(workflowId: WorkflowId) = MetadataQuery(workflowId, None, None, None, None)
+  def forWorkflow(workflowId: WorkflowId) = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
 
   def forJob(workflowId: WorkflowId, jobKey: MetadataJobKey) = {
-    MetadataQuery(workflowId, Option(MetadataQueryJobKey.forMetadataJobKey(jobKey)), None, None, None)
+    MetadataQuery(workflowId, Option(MetadataQueryJobKey.forMetadataJobKey(jobKey)), None, None, None, expandSubWorkflows = false)
   }
 
   def forKey(key: MetadataKey) = {
-    MetadataQuery(key.workflowId, key.jobKey map MetadataQueryJobKey.forMetadataJobKey, Option(key.key), None, None)
+    MetadataQuery(key.workflowId, key.jobKey map MetadataQueryJobKey.forMetadataJobKey, Option(key.key), None, None, expandSubWorkflows = false)
   }
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/MetadataService.scala b/services/src/main/scala/cromwell/services/metadata/MetadataService.scala
index 672f68580d1..e2a62c784c3 100644
--- a/services/src/main/scala/cromwell/services/metadata/MetadataService.scala
+++ b/services/src/main/scala/cromwell/services/metadata/MetadataService.scala
@@ -50,7 +50,8 @@ object MetadataService {
 
   case class PutMetadataAction(events: Iterable[MetadataEvent]) extends MetadataServiceAction
   case class GetSingleWorkflowMetadataAction(workflowId: WorkflowId, includeKeysOption: Option[NonEmptyList[String]],
-                                             excludeKeysOption: Option[NonEmptyList[String]])
+                                             excludeKeysOption: Option[NonEmptyList[String]],
+                                             expandSubWorkflows: Boolean)
     extends ReadAction
   case class GetMetadataQueryAction(key: MetadataQuery) extends ReadAction
   case class GetStatus(workflowId: WorkflowId) extends ReadAction
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala b/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala
index 76476d3fddd..5250107b63a 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala
@@ -107,19 +107,19 @@ trait MetadataDatabaseAccess {
     val uuid = query.workflowId.id.toString
 
     val futureMetadata: Future[Seq[MetadataEntry]] = query match {
-      case MetadataQuery(_, None, None, None, None) => databaseInterface.queryMetadataEntries(uuid)
-      case MetadataQuery(_, None, Some(key), None, None) => databaseInterface.queryMetadataEntries(uuid, key)
-      case MetadataQuery(_, Some(jobKey), None, None, None) =>
+      case MetadataQuery(_, None, None, None, None, _) => databaseInterface.queryMetadataEntries(uuid)
+      case MetadataQuery(_, None, Some(key), None, None, _) => databaseInterface.queryMetadataEntries(uuid, key)
+      case MetadataQuery(_, Some(jobKey), None, None, None, _) =>
         databaseInterface.queryMetadataEntries(uuid, jobKey.callFqn, jobKey.index, jobKey.attempt)
-      case MetadataQuery(_, Some(jobKey), Some(key), None, None) =>
+      case MetadataQuery(_, Some(jobKey), Some(key), None, None, _) =>
         databaseInterface.queryMetadataEntries(uuid, key, jobKey.callFqn, jobKey.index, jobKey.attempt)
-      case MetadataQuery(_, None, None, Some(includeKeys), None) =>
+      case MetadataQuery(_, None, None, Some(includeKeys), None, _) =>
         databaseInterface.
           queryMetadataEntriesLikeMetadataKeys(uuid, includeKeys.map(_ + "%"), requireEmptyJobKey = false)
-      case MetadataQuery(_, None, None, None, Some(excludeKeys)) =>
+      case MetadataQuery(_, None, None, None, Some(excludeKeys), _) =>
         databaseInterface.
           queryMetadataEntryNotLikeMetadataKeys(uuid, excludeKeys.map(_ + "%"), requireEmptyJobKey = false)
-      case MetadataQuery(_, None, None, Some(includeKeys), Some(excludeKeys)) => Future.failed(
+      case MetadataQuery(_, None, None, Some(includeKeys), Some(excludeKeys), _) => Future.failed(
         new IllegalArgumentException(
           s"Include/Exclude keys may not be mixed: include = $includeKeys, exclude = $excludeKeys"))
       case invalidQuery => Future.failed(new IllegalArgumentException(
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataActor.scala
index ebdc500de0f..5308d69f255 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataActor.scala
@@ -5,7 +5,7 @@ import cromwell.core.Dispatcher.ApiDispatcher
 import cromwell.core.{WorkflowId, WorkflowSubmitted}
 import cromwell.services.SingletonServicesStore
 import cromwell.services.metadata.MetadataService._
-import cromwell.services.metadata.{MetadataQuery, WorkflowQueryParameters}
+import cromwell.services.metadata.{CallMetadataKeys, MetadataQuery, WorkflowQueryParameters}
 
 import scala.concurrent.Future
 import scala.util.{Failure, Success, Try}
@@ -19,9 +19,12 @@ class ReadMetadataActor extends Actor with ActorLogging with MetadataDatabaseAcc
   implicit val ec = context.dispatcher
 
   def receive = {
-    case GetSingleWorkflowMetadataAction(workflowId, includeKeysOption, excludeKeysOption) =>
-      queryAndRespond(MetadataQuery(workflowId, None, None, includeKeysOption, excludeKeysOption))
-    case GetMetadataQueryAction(query@MetadataQuery(_, _, _, _, _)) => queryAndRespond(query)
+    case GetSingleWorkflowMetadataAction(workflowId, includeKeysOption, excludeKeysOption, expandSubWorkflows) =>
+      val includeKeys = if (expandSubWorkflows) {
+        includeKeysOption map { _.::(CallMetadataKeys.SubWorkflowId) }
+      } else includeKeysOption
+      queryAndRespond(MetadataQuery(workflowId, None, None, includeKeys, excludeKeysOption, expandSubWorkflows))
+    case GetMetadataQueryAction(query@MetadataQuery(_, _, _, _, _, _)) => queryAndRespond(query)
     case GetStatus(workflowId) => queryStatusAndRespond(workflowId)
     case GetLogs(workflowId) => queryLogsAndRespond(workflowId)
     case query: WorkflowQuery[_] => queryWorkflowsAndRespond(query.uri, query.parameters)
diff --git a/services/src/test/scala/cromwell/services/ServicesStoreSpec.scala b/services/src/test/scala/cromwell/services/ServicesStoreSpec.scala
index 291b4198836..7558a398882 100644
--- a/services/src/test/scala/cromwell/services/ServicesStoreSpec.scala
+++ b/services/src/test/scala/cromwell/services/ServicesStoreSpec.scala
@@ -160,6 +160,7 @@ object ServicesStoreSpec {
       s"""
          |db.url = "jdbc:hsqldb:mem:$${uniqueSchema};shutdown=false;hsqldb.tx=mvcc"
          |db.driver = "org.hsqldb.jdbcDriver"
+         |db.connectionTimeout = 3000
          |driver = "slick.driver.HsqldbDriver$$"
          |liquibase.updateSchema = false
          |""".stripMargin)
diff --git a/src/bin/travis/afterSuccess.sh b/src/bin/travis/afterSuccess.sh
new file mode 100755
index 00000000000..e8bd24aae0a
--- /dev/null
+++ b/src/bin/travis/afterSuccess.sh
@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+set -e
+
+echo "BUILD_TYPE='$BUILD_TYPE'"
+echo "TRAVIS_BRANCH='$TRAVIS_BRANCH'"
+echo "TRAVIS_PULL_REQUEST='$TRAVIS_PULL_REQUEST'"
+
+if [ "$BUILD_TYPE" == "sbt" ] && [ "$TRAVIS_PULL_REQUEST" == "false" ]; then
+
+    if [ "$TRAVIS_BRANCH" == "develop" ]; then
+        sbt 'set test in Test := {}' publish
+
+    elif [[ "$TRAVIS_BRANCH" =~ ^[0-9\.]+_hotfix$ ]]; then
+        docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD"
+        sbt 'set test in Test := {}' -Dproject.isSnapshot=false dockerBuildAndPush
+
+    fi
+
+fi
diff --git a/src/bin/travis/publishSnapshot.sh b/src/bin/travis/publishSnapshot.sh
deleted file mode 100755
index 9c18a97fdea..00000000000
--- a/src/bin/travis/publishSnapshot.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-echo "BUILD_TYPE='$BUILD_TYPE'"
-echo "TRAVIS_BRANCH='$TRAVIS_BRANCH'"
-echo "TRAVIS_PULL_REQUEST='$TRAVIS_PULL_REQUEST'"
-
-if [ "$BUILD_TYPE" == "sbt" ] && [ "$TRAVIS_BRANCH" == "develop" ] && [ "$TRAVIS_PULL_REQUEST" == "false" ]; then
-    sbt 'set test in Test := {}' publish
-fi
diff --git a/src/bin/travis/resources/centaur.inputs b/src/bin/travis/resources/centaur.inputs
index c378c0f71a0..544aa8524ff 100644
--- a/src/bin/travis/resources/centaur.inputs
+++ b/src/bin/travis/resources/centaur.inputs
@@ -1,7 +1,7 @@
 {
-  "centaur.centaur.cromwell_jar":"gs://cloud-cromwell-dev/travis-centaur/CROMWELL_JAR",
-  "centaur.centaur.cromwell_branch":"BRANCH",
-  "centaur.centaur.conf":"gs://cloud-cromwell-dev/travis-centaur/multiBackend.conf",
-  "centaur.centaur.pem":"gs://cloud-cromwell-dev/travis-centaur/cromwell-account.pem",
-  "centaur.centaur.token": "gs://cloud-cromwell-dev/travis-centaur/token.txt"
+  "centaur_workflow.centaur.cromwell_jar":"gs://cloud-cromwell-dev/travis-centaur/CROMWELL_JAR",
+  "centaur_workflow.centaur.centaur_branch":"CENTAUR_BRANCH",
+  "centaur_workflow.centaur.conf":"gs://cloud-cromwell-dev/travis-centaur/multiBackend.conf",
+  "centaur_workflow.centaur.pem":"gs://cloud-cromwell-dev/travis-centaur/cromwell-account.pem",
+  "centaur_workflow.centaur.token": "gs://cloud-cromwell-dev/travis-centaur/token.txt"
 }
diff --git a/src/bin/travis/resources/centaur.wdl b/src/bin/travis/resources/centaur.wdl
index 62e13c98c25..230b271aa41 100644
--- a/src/bin/travis/resources/centaur.wdl
+++ b/src/bin/travis/resources/centaur.wdl
@@ -1,5 +1,5 @@
 task centaur {
-    String cromwell_branch
+    String centaur_branch
     File conf
     File pem
     File cromwell_jar
@@ -11,7 +11,9 @@ task centaur {
         export SBT_OPTS=-Dsbt.ivy.home=/cromwell_root/tmp/.ivy2
         git clone https://github.com/broadinstitute/centaur.git
         cd centaur
-        ./test_cromwell.sh -j${cromwell_jar} -c${conf} -r/cromwell_root -t ${secret} -elocaldockertest
+        git checkout ${centaur_branch}
+        cd ..
+        centaur/test_cromwell.sh -j${cromwell_jar} -c${conf} -r/cromwell_root -t ${secret} -elocaldockertest
     >>>
 
     output {
@@ -26,6 +28,6 @@ task centaur {
         failOnStderr: false
     }
 }
-workflow centaur {
+workflow centaur_workflow {
     call centaur
 }
diff --git a/src/bin/travis/resources/local_centaur.conf b/src/bin/travis/resources/local_centaur.conf
index 68ba866bfe0..ef6df397522 100644
--- a/src/bin/travis/resources/local_centaur.conf
+++ b/src/bin/travis/resources/local_centaur.conf
@@ -16,3 +16,6 @@ spray.can {
 call-caching {
   enabled = true
 }
+
+backend.providers.Local.config.filesystems.local.localization = ["soft-link", "copy"]
+backend.providers.Local.config.concurrent-job-limit = 20
diff --git a/src/bin/travis/test.sh b/src/bin/travis/test.sh
index 8730db3af23..9fd024c6924 100755
--- a/src/bin/travis/test.sh
+++ b/src/bin/travis/test.sh
@@ -11,6 +11,8 @@ elif [ "$BUILD_TYPE" = "centaurLocal" ]; then
     "${SCRIPT_DIR}"/testCentaurLocal.sh
 elif [ "$BUILD_TYPE" = "sbt" ]; then
     "${SCRIPT_DIR}"/testSbt.sh
+elif [ "$BUILD_TYPE" = "checkPublish" ]; then
+    "${SCRIPT_DIR}"/testCheckPublish.sh
 else
     echo "Unknown BUILD_TYPE: '$BUILD_TYPE'"
     exit 1
diff --git a/src/bin/travis/testCentaurJes.sh b/src/bin/travis/testCentaurJes.sh
index 04813698d4b..96e5e8e8bf1 100755
--- a/src/bin/travis/testCentaurJes.sh
+++ b/src/bin/travis/testCentaurJes.sh
@@ -54,7 +54,7 @@ echo "RUNNING TRAVIS CENTAUR"
 sbt assembly
 
 # Update the inputs file with stuff specific to this run
-sed -i "s/BRANCH/${TRAVIS_BRANCH}/g" src/bin/travis/resources/centaur.inputs
+sed -i "s/CENTAUR_BRANCH/${CENTAUR_BRANCH}/g" src/bin/travis/resources/centaur.inputs
 CROMWELL_JAR=cromwell_${TRAVIS_BUILD_ID}.jar
 sed -i "s/CROMWELL_JAR/${CROMWELL_JAR}/g" src/bin/travis/resources/centaur.inputs
 
@@ -69,9 +69,9 @@ EXIT_CODE="${PIPESTATUS[0]}"
 export WORKFLOW_ID=`grep "SingleWorkflowRunnerActor: Workflow submitted " log.txt | perl -pe 's/\e\[?.*?[\@-~]//g' | cut -f7 -d" "`
 
 # Grab the Centaur log from GCS and cat it so we see it in the main travis log. 
-export CENTAUR_LOG_PATH="gs://cloud-cromwell-dev/cromwell_execution/travis/centaur/${WORKFLOW_ID}/call-centaur//cromwell_root/logs/centaur.log"
+export CENTAUR_LOG_PATH="gs://cloud-cromwell-dev/cromwell_execution/travis/centaur_workflow/${WORKFLOW_ID}/call-centaur/cromwell_root/logs/centaur.log"
 gsutil cp ${CENTAUR_LOG_PATH} centaur.log
 cat centaur.log
-echo "More logs for this run are available at https://console.cloud.google.com/storage/browser/cloud-cromwell-dev/cromwell_execution/travis/centaur/${WORKFLOW_ID}/call-centaur/"
+echo "More logs for this run are available at https://console.cloud.google.com/storage/browser/cloud-cromwell-dev/cromwell_execution/travis/centaur_workflow/${WORKFLOW_ID}/call-centaur/"
 
 exit "${EXIT_CODE}"
diff --git a/src/bin/travis/testCentaurLocal.sh b/src/bin/travis/testCentaurLocal.sh
index fe77a134718..337c302bff1 100755
--- a/src/bin/travis/testCentaurLocal.sh
+++ b/src/bin/travis/testCentaurLocal.sh
@@ -34,4 +34,6 @@ CROMWELL_JAR=$(find "$(pwd)/target/scala-2.11" -name "cromwell-*.jar")
 LOCAL_CONF="$(pwd)/src/bin/travis/resources/local_centaur.conf"
 git clone https://github.com/broadinstitute/centaur.git
 cd centaur
-./test_cromwell.sh -j"${CROMWELL_JAR}" -c${LOCAL_CONF}
+git checkout ${CENTAUR_BRANCH}
+cd ..
+centaur/test_cromwell.sh -j"${CROMWELL_JAR}" -c${LOCAL_CONF}
diff --git a/src/bin/travis/testCheckPublish.sh b/src/bin/travis/testCheckPublish.sh
new file mode 100755
index 00000000000..541b553850a
--- /dev/null
+++ b/src/bin/travis/testCheckPublish.sh
@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+set -e
+set -x
+
+sbt clean assembly doc
diff --git a/src/main/scala/cromwell/CromwellCommandLine.scala b/src/main/scala/cromwell/CromwellCommandLine.scala
index c52ebbd66de..230045559b6 100644
--- a/src/main/scala/cromwell/CromwellCommandLine.scala
+++ b/src/main/scala/cromwell/CromwellCommandLine.scala
@@ -6,7 +6,7 @@ import better.files._
 import cats.data.Validated._
 import cats.syntax.cartesian._
 import cats.syntax.validated._
-import cromwell.core.WorkflowSourceFiles
+import cromwell.core.{WorkflowSourceFilesWithoutImports, WorkflowSourceFilesCollection, WorkflowSourceFilesWithDependenciesZip}
 import cromwell.util.FileUtil._
 import lenthall.exception.MessageAggregation
 import cromwell.core.ErrorOr._
@@ -17,7 +17,7 @@ sealed abstract class CromwellCommandLine
 case object UsageAndExit extends CromwellCommandLine
 case object RunServer extends CromwellCommandLine
 final case class RunSingle(wdlPath: Path,
-                           sourceFiles: WorkflowSourceFiles,
+                           sourceFiles: WorkflowSourceFilesCollection,
                            inputsPath: Option[Path],
                            optionsPath: Option[Path],
                            metadataPath: Option[Path]) extends CromwellCommandLine
@@ -26,7 +26,7 @@ object CromwellCommandLine {
   def apply(args: Seq[String]): CromwellCommandLine = {
     args.headOption match {
       case Some("server") if args.size == 1 => RunServer
-      case Some("run") if args.size >= 2 && args.size <= 5 => RunSingle(args.tail)
+      case Some("run") if args.size >= 2 && args.size <= 6 => RunSingle(args.tail)
       case _ => UsageAndExit
     }
   }
@@ -38,15 +38,19 @@ object RunSingle {
     val inputsPath = argPath(args, 1, Option(".inputs"), checkDefaultExists = false)
     val optionsPath = argPath(args, 2, Option(".options"), checkDefaultExists = true)
     val metadataPath = argPath(args, 3, None)
+    val importPath = argPath(args, 4, None)
 
     val wdl = readContent("WDL file", wdlPath)
     val inputsJson = readJson("Inputs", inputsPath)
     val optionsJson = readJson("Workflow Options", optionsPath)
 
-    val sourceFiles = (wdl |@| inputsJson |@| optionsJson) map { WorkflowSourceFiles.apply }
+    val sourceFileCollection = importPath match {
+      case Some(p) => (wdl |@| inputsJson |@| optionsJson) map { (w, i, o) => WorkflowSourceFilesWithDependenciesZip.apply(w, i, o, Files.readAllBytes(p)) }
+      case None => (wdl |@| inputsJson |@| optionsJson) map WorkflowSourceFilesWithoutImports.apply
+    }
 
     val runSingle = for {
-      sources <- sourceFiles
+      sources <- sourceFileCollection
       _ <- writeableMetadataPath(metadataPath)
     } yield RunSingle(wdlPath, sources, inputsPath, optionsPath, metadataPath)
 
diff --git a/src/main/scala/cromwell/Main.scala b/src/main/scala/cromwell/Main.scala
index 74a5405c119..c5287557242 100644
--- a/src/main/scala/cromwell/Main.scala
+++ b/src/main/scala/cromwell/Main.scala
@@ -74,11 +74,9 @@ object Main extends App {
 
     import PromiseActor.EnhancedActorRef
 
-    val promise = runner.askNoTimeout(RunWorkflow)
-    waitAndExit(promise, CromwellSystem)
+    waitAndExit(runner.askNoTimeout(RunWorkflow), CromwellSystem)
   }
 
-
   private def waitAndExit(futureResult: Future[Any], workflowManagerSystem: CromwellSystem): Unit = {
     Await.ready(futureResult, Duration.Inf)
 
@@ -100,17 +98,21 @@ object Main extends App {
         |java -jar cromwell.jar <action> <parameters>
         |
         |Actions:
-        |run <WDL file> [<JSON inputs file> [<JSON workflow options>
-        |  [<OUTPUT workflow metadata>]]]
+        |run <WDL file> [<JSON inputs file>] [<JSON workflow options>]
+        |  [<OUTPUT workflow metadata>] [<Zip of WDL Files>]
         |
         |  Given a WDL file and JSON file containing the value of the
         |  workflow inputs, this will run the workflow locally and
         |  print out the outputs in JSON format.  The workflow
         |  options file specifies some runtime configuration for the
         |  workflow (see README for details).  The workflow metadata
-        |  output is an optional file path to output the metadata.
+        |  output is an optional file path to output the metadata. The
+        |  directory of WDL files is optional. However, it is required
+        |  if the primary workflow imports workflows that are outside
+        |  of the root directory of the Cromwell project.
+        |
         |  Use a single dash ("-") to skip optional files. Ex:
-        |    run noinputs.wdl - - metadata.json
+        |    run noinputs.wdl - - metadata.json -
         |
         |server
         |
diff --git a/src/test/scala/cromwell/CromwellCommandLineSpec.scala b/src/test/scala/cromwell/CromwellCommandLineSpec.scala
index 42f03fdfcb4..66c8ee29ce6 100644
--- a/src/test/scala/cromwell/CromwellCommandLineSpec.scala
+++ b/src/test/scala/cromwell/CromwellCommandLineSpec.scala
@@ -1,9 +1,9 @@
 package cromwell
 
 import better.files._
-import cromwell.core.PathFactory._
+import cromwell.core.path.PathImplicits._
 import cromwell.util.SampleWdl
-import cromwell.util.SampleWdl.ThreeStep
+import cromwell.util.SampleWdl.{FileClobber, FilePassingWorkflow, ThreeStep}
 import org.scalatest.{FlatSpec, Matchers}
 
 import scala.util.Try
@@ -30,7 +30,7 @@ class CromwellCommandLineSpec extends FlatSpec with Matchers {
   }
 
   it should "fail with too many arguments to run" in {
-    CromwellCommandLine(List("run", "bork", "bork", "bork", "bork", "bork"))
+    CromwellCommandLine(List("run", "bork", "bork", "bork", "bork", "bork", "blerg"))
   }
 
   it should "RunSingle when supplying wdl and inputs" in {
@@ -76,6 +76,23 @@ class CromwellCommandLineSpec extends FlatSpec with Matchers {
     ccl.isFailure shouldBe true
     ccl.failed.get.getMessage should include("Unable to write to metadata directory:")
   }
+
+  it should "run if imports directory is a .zip file" in {
+    val wdlDir = File.newTemporaryDirectory("wdlDirectory")
+
+    val filePassing = File.newTemporaryFile("filePassing", ".wdl", Option(wdlDir))
+    val fileClobber = File.newTemporaryFile("fileClobber", ".wdl", Option(wdlDir))
+    filePassing write FilePassingWorkflow.wdlSource()
+    fileClobber write FileClobber.wdlSource()
+
+    val zippedDir = wdlDir.zip()
+    val zippedPath = zippedDir.pathAsString
+
+    val ccl = Try(CromwellCommandLine(List("run", filePassing.pathAsString, "-", "-", "-", zippedPath)))
+    ccl.isFailure shouldBe false
+
+    zippedDir.delete(swallowIOExceptions = true)
+  }
 }
 
 object CromwellCommandLineSpec {
diff --git a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorBackendFactory.scala b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorBackendFactory.scala
index 75f2f779a51..3c8e48fd49d 100644
--- a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorBackendFactory.scala
+++ b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorBackendFactory.scala
@@ -5,10 +5,10 @@ import com.typesafe.config.Config
 import com.typesafe.scalalogging.StrictLogging
 import cromwell.backend._
 import cromwell.backend.impl.htcondor.caching.CacheActorFactory
-import cromwell.backend.io.JobPaths
+import cromwell.backend.io.JobPathsWithDocker
 import cromwell.backend.sfs.SharedFileSystemExpressionFunctions
 import cromwell.core.{CallContext, WorkflowOptions}
-import wdl4s.Call
+import wdl4s.TaskCall
 import wdl4s.expression.WdlStandardLibraryFunctions
 
 import scala.util.{Failure, Success, Try}
@@ -17,7 +17,7 @@ case class HtCondorBackendFactory(name: String, configurationDescriptor: Backend
   extends BackendLifecycleActorFactory with StrictLogging {
 
   override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                                calls: Seq[Call],
+                                                calls: Set[TaskCall],
                                                 serviceRegistryActor: ActorRef): Option[Props] = {
     Option(HtCondorInitializationActor.props(workflowDescriptor, calls, configurationDescriptor, serviceRegistryActor))
   }
@@ -32,14 +32,14 @@ case class HtCondorBackendFactory(name: String, configurationDescriptor: Backend
   override def expressionLanguageFunctions(workflowDescriptor: BackendWorkflowDescriptor,
                                            jobKey: BackendJobDescriptorKey,
                                            initializationData: Option[BackendInitializationData]): WdlStandardLibraryFunctions = {
-    val jobPaths = new JobPaths(workflowDescriptor, configurationDescriptor.backendConfig, jobKey)
+    val jobPaths = new JobPathsWithDocker(jobKey, workflowDescriptor, configurationDescriptor.backendConfig)
     val callContext = CallContext(
       jobPaths.callExecutionRoot,
       jobPaths.stdout.toAbsolutePath.toString,
       jobPaths.stderr.toAbsolutePath.toString
     )
 
-    new SharedFileSystemExpressionFunctions(HtCondorJobExecutionActor.fileSystems, callContext)
+    new SharedFileSystemExpressionFunctions(HtCondorJobExecutionActor.pathBuilders, callContext)
   }
 
   private def resolveCacheProviderProps(workflowOptions: WorkflowOptions) = {
diff --git a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorInitializationActor.scala b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorInitializationActor.scala
index b0fdc75b2b8..1212876b677 100644
--- a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorInitializationActor.scala
+++ b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorInitializationActor.scala
@@ -7,9 +7,9 @@ import cromwell.backend.validation.RuntimeAttributesDefault
 import cromwell.backend.validation.RuntimeAttributesKeys._
 import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor, BackendWorkflowInitializationActor}
 import cromwell.core.WorkflowOptions
+import wdl4s.TaskCall
 import wdl4s.types.{WdlBooleanType, WdlIntegerType, WdlStringType}
 import wdl4s.values.WdlValue
-import wdl4s.Call
 
 import scala.concurrent.Future
 import scala.util.Try
@@ -19,14 +19,14 @@ object HtCondorInitializationActor {
     ContinueOnReturnCodeKey, CpuKey, MemoryKey, DiskKey)
 
   def props(workflowDescriptor: BackendWorkflowDescriptor,
-            calls: Seq[Call],
+            calls: Set[TaskCall],
             configurationDescriptor: BackendConfigurationDescriptor,
             serviceRegistryActor: ActorRef): Props =
     Props(new HtCondorInitializationActor(workflowDescriptor, calls, configurationDescriptor, serviceRegistryActor))
 }
 
 class HtCondorInitializationActor(override val workflowDescriptor: BackendWorkflowDescriptor,
-                                  override val calls: Seq[Call],
+                                  override val calls: Set[TaskCall],
                                   override val configurationDescriptor: BackendConfigurationDescriptor,
                                   override val serviceRegistryActor: ActorRef) extends BackendWorkflowInitializationActor {
 
diff --git a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorJobExecutionActor.scala b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorJobExecutionActor.scala
index 400c6a55f03..d005016ca3c 100644
--- a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorJobExecutionActor.scala
+++ b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorJobExecutionActor.scala
@@ -1,20 +1,22 @@
 package cromwell.backend.impl.htcondor
 
-import java.nio.file.FileSystems
 import java.nio.file.attribute.PosixFilePermission
 import java.util.UUID
 
 import akka.actor.{ActorRef, Props}
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, FailedNonRetryableResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, JobFailedNonRetryableResponse, JobSucceededResponse}
 import cromwell.backend._
 import cromwell.backend.impl.htcondor.caching.CacheActor._
 import cromwell.backend.impl.htcondor.caching.localization.CachedResultLocalization
-import cromwell.backend.io.JobPaths
+import cromwell.backend.io.JobPathsWithDocker
 import cromwell.backend.sfs.{SharedFileSystem, SharedFileSystemExpressionFunctions}
+import cromwell.backend.wdl.Command
+import cromwell.core.path.JavaWriterImplicits._
+import cromwell.core.path.{DefaultPathBuilder, PathBuilder}
 import cromwell.services.keyvalue.KeyValueServiceActor._
 import cromwell.services.metadata.CallMetadataKeys
 import org.apache.commons.codec.digest.DigestUtils
-import wdl4s._
+import wdl4s.EvaluatedTaskInputs
 import wdl4s.parser.MemoryUnit
 import wdl4s.types.{WdlArrayType, WdlFileType}
 import wdl4s.util.TryUtil
@@ -27,7 +29,7 @@ import scala.util.{Failure, Success, Try}
 object HtCondorJobExecutionActor {
   val HtCondorJobIdKey = "htCondor_job_id"
 
-  val fileSystems = List(FileSystems.getDefault)
+  val pathBuilders = List(DefaultPathBuilder)
 
   def props(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor, serviceRegistryActor: ActorRef, cacheActorProps: Option[Props]): Props =
     Props(new HtCondorJobExecutionActor(jobDescriptor, configurationDescriptor, serviceRegistryActor, cacheActorProps))
@@ -41,9 +43,9 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
 
   import HtCondorJobExecutionActor._
   import better.files._
-  import cromwell.core.PathFactory._
 
   private val tag = s"CondorJobExecutionActor-${jobDescriptor.call.fullyQualifiedName}:"
+  override val pathBuilders: List[PathBuilder] = HtCondorJobExecutionActor.pathBuilders
 
   implicit val executionContext = context.dispatcher
 
@@ -53,7 +55,7 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
   private val fileSystemsConfig = configurationDescriptor.backendConfig.getConfig("filesystems")
   override val sharedFileSystemConfig = fileSystemsConfig.getConfig("local")
   private val workflowDescriptor = jobDescriptor.workflowDescriptor
-  private val jobPaths = new JobPaths(workflowDescriptor, configurationDescriptor.backendConfig, jobDescriptor.key)
+  private val jobPaths = new JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, configurationDescriptor.backendConfig)
 
   // Files
   private val executionDir = jobPaths.callExecutionRoot
@@ -72,9 +74,9 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
   private lazy val stderrWriter = extProcess.tailedWriter(100, submitFileStderr)
 
   private val call = jobDescriptor.key.call
-  private val callEngineFunction = SharedFileSystemExpressionFunctions(jobPaths, fileSystems)
+  private val callEngineFunction = SharedFileSystemExpressionFunctions(jobPaths, pathBuilders)
 
-  private val lookup = jobDescriptor.inputs.apply _
+  private val lookup = jobDescriptor.fullyQualifiedInputs.apply _
 
   private val runtimeAttributes = {
     val evaluateAttrs = call.task.runtimeAttributes.attrs mapValues (_.evaluate(lookup, callEngineFunction))
@@ -202,18 +204,18 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
             condorJobId = Option(overallJobIdentifier)
             self ! TrackTaskStatus(overallJobIdentifier)
 
-          case _ => self ! JobExecutionResponse(FailedNonRetryableResponse(jobDescriptor.key,
+          case _ => self ! JobExecutionResponse(JobFailedNonRetryableResponse(jobDescriptor.key,
             new IllegalStateException("Failed to retrieve job(id) and cluster id"), Option(condorReturnCode)))
         }
 
       case 0 =>
         log.error(s"Unexpected! Received return code for condor submission as 0, although stderr file is non-empty: {}", File(submitFileStderr).lines)
-        self ! JobExecutionResponse(FailedNonRetryableResponse(jobDescriptor.key,
+        self ! JobExecutionResponse(JobFailedNonRetryableResponse(jobDescriptor.key,
           new IllegalStateException(s"Execution process failed. HtCondor returned zero status code but non empty stderr file: $condorReturnCode"),
           Option(condorReturnCode)))
 
       case nonZeroExitCode: Int =>
-        self ! JobExecutionResponse(FailedNonRetryableResponse(jobDescriptor.key,
+        self ! JobExecutionResponse(JobFailedNonRetryableResponse(jobDescriptor.key,
           new IllegalStateException(s"Execution process failed. HtCondor returned non zero status code: $condorReturnCode"), Option(condorReturnCode)))
     }
   }
@@ -229,16 +231,16 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
         context.system.scheduler.scheduleOnce(pollingInterval.seconds, self, TrackTaskStatus(jobIdentifier))
         ()
       case Success(Some(rc)) if runtimeAttributes.continueOnReturnCode.continueFor(rc) => self ! JobExecutionResponse(processSuccess(rc))
-      case Success(Some(rc)) => self ! JobExecutionResponse(FailedNonRetryableResponse(jobDescriptor.key,
+      case Success(Some(rc)) => self ! JobExecutionResponse(JobFailedNonRetryableResponse(jobDescriptor.key,
         new IllegalStateException("Job exited with invalid return code: " + rc), Option(rc)))
-      case Failure(error) => self ! JobExecutionResponse(FailedNonRetryableResponse(jobDescriptor.key, error, None))
+      case Failure(error) => self ! JobExecutionResponse(JobFailedNonRetryableResponse(jobDescriptor.key, error, None))
     }
   }
 
   private def processSuccess(rc: Int): BackendJobExecutionResponse = {
     evaluateOutputs(callEngineFunction, outputMapper(jobPaths)) match {
       case Success(outputs) =>
-        val succeededResponse = SucceededResponse(jobDescriptor.key, Some(rc), outputs, None, Seq.empty)
+        val succeededResponse = JobSucceededResponse(jobDescriptor.key, Some(rc), outputs, None, Seq.empty)
         log.debug("{} Storing data into cache for hash {}.", tag, jobHash)
         // If cache fails to store data for any reason it should not stop the workflow/task execution but log the issue.
         cacheActor foreach { _ ! StoreExecutionResult(jobHash, succeededResponse) }
@@ -247,12 +249,12 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
         val message = Option(e.getMessage) map {
           ": " + _
         } getOrElse ""
-        FailedNonRetryableResponse(jobDescriptor.key, new Throwable("Failed post processing of outputs" + message, e), Option(rc))
+        JobFailedNonRetryableResponse(jobDescriptor.key, new Throwable("Failed post processing of outputs" + message, e), Option(rc))
     }
   }
 
   private def calculateHash: String = {
-    val cmd = call.task.instantiateCommand(jobDescriptor.inputs, callEngineFunction, identity) match {
+    val cmd = Command.instantiate(jobDescriptor, callEngineFunction) match {
       case Success(command) => command
       case Failure(ex) =>
         val errMsg = s"$tag Cannot instantiate job command for caching purposes due to ${ex.getMessage}."
@@ -276,7 +278,7 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
       executionDir.toString.toFile.createIfNotExists(asDirectory = true, createParents = true)
 
       log.debug("{} Resolving job command", tag)
-      val command = localizeInputs(jobPaths.callInputsRoot, runtimeAttributes.dockerImage.isDefined, fileSystems, jobDescriptor.inputs) flatMap {
+      val command = localizeInputs(jobPaths.callInputsRoot, runtimeAttributes.dockerImage.isDefined)(jobDescriptor.inputDeclarations) flatMap {
         localizedInputs => resolveJobCommand(localizedInputs)
       }
 
@@ -296,7 +298,7 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
           HtCondorRuntimeKeys.Disk -> runtimeAttributes.disk.to(MemoryUnit.KB).amount.toLong
         )
 
-      cmds.generateSubmitFile(submitFilePath, attributes) // This writes the condor submit file
+      cmds.generateSubmitFile(submitFilePath, attributes, runtimeAttributes.nativeSpecs) // This writes the condor submit file
       ()
 
     } catch {
@@ -306,7 +308,7 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
     }
   }
 
-  private def resolveJobCommand(localizedInputs: CallInputs): Try[String] = {
+  private def resolveJobCommand(localizedInputs: EvaluatedTaskInputs): Try[String] = {
     val command = if (runtimeAttributes.dockerImage.isDefined) {
       modifyCommandForDocker(call.task.instantiateCommand(localizedInputs, callEngineFunction, identity), localizedInputs)
     } else {
@@ -329,7 +331,7 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
     serviceRegistryActor.putMetadata(jobDescriptor.workflowDescriptor.id, Option(jobDescriptor.key), metadataKeyValues)
   }
 
-  private def modifyCommandForDocker(jobCmd: Try[String], localizedInputs: CallInputs): Try[String] = {
+  private def modifyCommandForDocker(jobCmd: Try[String], localizedInputs: EvaluatedTaskInputs): Try[String] = {
     Try {
       val dockerInputDataVol = localizedInputs.values.collect {
         case file if file.wdlType == WdlFileType =>
@@ -362,16 +364,16 @@ class HtCondorJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
       createExecutionFolderAndScript()
       executeTask()
     } catch {
-      case e: Exception => self ! JobExecutionResponse(FailedNonRetryableResponse(jobDescriptor.key, e, None))
+      case e: Exception => self ! JobExecutionResponse(JobFailedNonRetryableResponse(jobDescriptor.key, e, None))
     }
   }
 
-  private def localizeCachedResponse(succeededResponse: SucceededResponse): BackendJobExecutionResponse = {
+  private def localizeCachedResponse(succeededResponse: JobSucceededResponse): BackendJobExecutionResponse = {
     Try(localizeCachedOutputs(executionDir, succeededResponse.jobOutputs)) match {
       case Success(outputs) =>
         executionDir.toString.toFile.createIfNotExists(asDirectory = true, createParents = true)
-        SucceededResponse(jobDescriptor.key, succeededResponse.returnCode, outputs, None, Seq.empty)
-      case Failure(exception) => FailedNonRetryableResponse(jobDescriptor.key, exception, None)
+        JobSucceededResponse(jobDescriptor.key, succeededResponse.returnCode, outputs, None, Seq.empty)
+      case Failure(exception) => JobFailedNonRetryableResponse(jobDescriptor.key, exception, None)
     }
   }
 }
diff --git a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorRuntimeAttributes.scala b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorRuntimeAttributes.scala
index f8dd9a59595..758d2dbb4ac 100644
--- a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorRuntimeAttributes.scala
+++ b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorRuntimeAttributes.scala
@@ -12,8 +12,8 @@ import cromwell.backend.validation.RuntimeAttributesValidation._
 import cromwell.core._
 import cromwell.core.ErrorOr._
 import lenthall.exception.MessageAggregation
-import wdl4s.types.{WdlIntegerType, WdlStringType, WdlBooleanType, WdlType}
-import wdl4s.values.{WdlString, WdlBoolean, WdlInteger, WdlValue}
+import wdl4s.types._
+import wdl4s.values.{WdlArray, WdlBoolean, WdlInteger, WdlString, WdlValue}
 
 
 object HtCondorRuntimeAttributes {
@@ -26,6 +26,7 @@ object HtCondorRuntimeAttributes {
   val DockerWorkingDirKey = "dockerWorkingDir"
   val DockerOutputDirKey = "dockerOutputDir"
   val DiskKey = "disk"
+  val NativeSpecsKey = "nativeSpecs"
 
   val staticDefaults = Map(
     FailOnStderrKey -> WdlBoolean(FailOnStderrDefaultValue),
@@ -43,7 +44,8 @@ object HtCondorRuntimeAttributes {
     DockerOutputDirKey -> Set(WdlStringType),
     CpuKey -> Set(WdlIntegerType),
     MemoryKey -> Set(WdlStringType),
-    DiskKey -> Set(WdlStringType)
+    DiskKey -> Set(WdlStringType),
+    NativeSpecsKey -> Set(WdlArrayType(WdlStringType))
   )
 
   def apply(attrs: Map[String, WdlValue], options: WorkflowOptions): HtCondorRuntimeAttributes = {
@@ -59,9 +61,10 @@ object HtCondorRuntimeAttributes {
     val cpu = validateCpu(withDefaultValues.get(CpuKey), noValueFoundFor(CpuKey))
     val memory = validateMemory(withDefaultValues.get(MemoryKey), noValueFoundFor(MemoryKey))
     val disk = validateDisk(withDefaultValues.get(DiskKey), noValueFoundFor(DiskKey))
+    val nativeSpecs = validateNativeSpecs(withDefaultValues.get(NativeSpecsKey), None.validNel)
 
-    (continueOnReturnCode |@| docker |@| dockerWorkingDir |@| dockerOutputDir |@| failOnStderr |@| cpu |@| memory |@| disk) map {
-      new HtCondorRuntimeAttributes(_, _, _, _, _, _, _, _)
+    (continueOnReturnCode |@| docker |@| dockerWorkingDir |@| dockerOutputDir |@| failOnStderr |@| cpu |@| memory |@| disk |@| nativeSpecs) map {
+      new HtCondorRuntimeAttributes(_, _, _, _, _, _, _, _, _)
     } match {
       case Valid(x) => x
       case Invalid(nel) => throw new RuntimeException with MessageAggregation {
@@ -97,6 +100,17 @@ object HtCondorRuntimeAttributes {
       case None => onMissingKey
     }
   }
+
+  private def validateNativeSpecs(value: Option[WdlValue], onMissingKey: => ErrorOr[Option[Array[String]]]): ErrorOr[Option[Array[String]]] = {
+    val nativeSpecsWrongFormatMsg = s"Expecting $NativeSpecsKey runtime attribute to be an Array of Strings. Exception: %s"
+    value match {
+      case Some(ns: WdlArray) if ns.wdlType.memberType.equals(WdlStringType) =>
+        val nsa = ns.value.map { value => value.valueString }.toArray
+        Option(nsa).validNel
+      case Some(_) => String.format(nativeSpecsWrongFormatMsg, "Not supported WDL type value").invalidNel
+      case None => onMissingKey
+    }
+  }
 }
 
 case class HtCondorRuntimeAttributes(continueOnReturnCode: ContinueOnReturnCode,
@@ -106,4 +120,5 @@ case class HtCondorRuntimeAttributes(continueOnReturnCode: ContinueOnReturnCode,
                                      failOnStderr: Boolean,
                                      cpu: Int,
                                      memory: MemorySize,
-                                     disk: MemorySize)
+                                     disk: MemorySize,
+                                     nativeSpecs: Option[Array[String]])
diff --git a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorWrapper.scala b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorWrapper.scala
index 76a81c08a3b..35af6dd1d1b 100644
--- a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorWrapper.scala
+++ b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/HtCondorWrapper.scala
@@ -5,8 +5,9 @@ import java.nio.file.{Files, Path}
 import better.files._
 import com.typesafe.scalalogging.StrictLogging
 import cromwell.backend.impl.htcondor
-import cromwell.core.PathFactory.{EnhancedPath, FlushingAndClosingWriter}
-import cromwell.core.{TailedWriter, UntailedWriter}
+import cromwell.core.path.{TailedWriter, UntailedWriter}
+import cromwell.core.path.PathImplicits._
+import cromwell.core.path.JavaWriterImplicits._
 
 import scala.sys.process._
 
@@ -55,22 +56,28 @@ class HtCondorCommands extends StrictLogging {
     */
   def writeScript(instantiatedCommand: String, filePath: Path, containerRoot: Path): Unit = {
     logger.debug(s"Writing bash script for execution. Command: $instantiatedCommand.")
-    File(filePath).write(
-      s"""#!/bin/sh
-          |cd $containerRoot
-          |$instantiatedCommand
-          |echo $$? > rc
-          |""".stripMargin)
+    val scriptBody = s"""
+
+#!/bin/sh
+cd $containerRoot
+$instantiatedCommand
+echo $$? > rc
+
+""".trim + "\n"
+    File(filePath).write(scriptBody)
     ()
   }
 
-  def generateSubmitFile(path: Path, attributes: Map[String, Any]): String = {
+  def generateSubmitFile(path: Path, attributes: Map[String, Any], nativeSpecs: Option[Array[String]]): String = {
     def htCondorSubmitCommand(filePath: Path) = {
       s"${HtCondorCommands.Submit} ${filePath.toString}"
     }
 
     val submitFileWriter = path.untailed
-    attributes.foreach(attribute => submitFileWriter.writeWithNewline(s"${attribute._1}=${attribute._2}"))
+    attributes.foreach { attribute => submitFileWriter.writeWithNewline(s"${attribute._1}=${attribute._2}") }
+    //Native specs is intended for attaching HtCondor native configuration such as 'requirements' and 'rank' definition
+    //directly to the submit file.
+    nativeSpecs foreach { _.foreach { submitFileWriter.writeWithNewline } }
     submitFileWriter.writeWithNewline(HtCondorRuntimeKeys.Queue)
     submitFileWriter.writer.flushAndClose()
     logger.debug(s"submit file name is : $path")
diff --git a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/CacheActor.scala b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/CacheActor.scala
index 70799bd677a..74fb3ade536 100644
--- a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/CacheActor.scala
+++ b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/CacheActor.scala
@@ -1,7 +1,7 @@
 package cromwell.backend.impl.htcondor.caching
 
 import akka.actor.{Actor, ActorLogging}
-import cromwell.backend.BackendJobExecutionActor.SucceededResponse
+import cromwell.backend.BackendJobExecutionActor.JobSucceededResponse
 import cromwell.backend.impl.htcondor.caching.CacheActor._
 import cromwell.backend.impl.htcondor.caching.exception.{CachedResultAlreadyExistException, CachedResultNotFoundException}
 import cromwell.backend.impl.htcondor.caching.model.CachedExecutionResult
@@ -10,10 +10,10 @@ object CacheActor {
 
   trait CacheActorCommand
   case class ReadExecutionResult(hash: String) extends CacheActorCommand
-  case class StoreExecutionResult(hash: String, succeededResponse: SucceededResponse) extends CacheActorCommand
+  case class StoreExecutionResult(hash: String, succeededResponse: JobSucceededResponse) extends CacheActorCommand
 
   trait CacheActorResponse
-  case class ExecutionResultFound(succeededResponse: SucceededResponse) extends CacheActorResponse
+  case class ExecutionResultFound(succeededResponse: JobSucceededResponse) extends CacheActorResponse
   case object ExecutionResultNotFound extends CacheActorResponse
   case class ExecutionResultStored(hash: String) extends CacheActorResponse
   case object ExecutionResultAlreadyExist extends CacheActorResponse
diff --git a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/localization/CachedResultLocalization.scala b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/localization/CachedResultLocalization.scala
index 2f8254e5c2e..127141c5bc6 100644
--- a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/localization/CachedResultLocalization.scala
+++ b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/localization/CachedResultLocalization.scala
@@ -23,7 +23,7 @@ trait CachedResultLocalization {
     WdlSingleFile(slPath.toString)
   }
 
-  def localizeCachedOutputs(executionPath: Path, outputs: JobOutputs): JobOutputs = {
+  def localizeCachedOutputs(executionPath: Path, outputs: CallOutputs): CallOutputs = {
     outputs map { case (lqn, jobOutput) =>
       jobOutput.wdlValue.wdlType match {
         case WdlFileType => (lqn -> JobOutput(localizeCachedFile(executionPath, jobOutput.wdlValue)))
diff --git a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/model/CachedExecutionResult.scala b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/model/CachedExecutionResult.scala
index fdff708041e..1b023fd410a 100644
--- a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/model/CachedExecutionResult.scala
+++ b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/model/CachedExecutionResult.scala
@@ -1,6 +1,6 @@
 package cromwell.backend.impl.htcondor.caching.model
 
-import cromwell.backend.BackendJobExecutionActor.SucceededResponse
+import cromwell.backend.BackendJobExecutionActor.JobSucceededResponse
 
-case class CachedExecutionResult(hash: String, succeededResponse: SucceededResponse)
+case class CachedExecutionResult(hash: String, succeededResponse: JobSucceededResponse)
 
diff --git a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/provider/mongodb/MongoCacheActor.scala b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/provider/mongodb/MongoCacheActor.scala
index 7f99e1565f2..cf6cf11511c 100644
--- a/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/provider/mongodb/MongoCacheActor.scala
+++ b/supportedBackends/htcondor/src/main/scala/cromwell/backend/impl/htcondor/caching/provider/mongodb/MongoCacheActor.scala
@@ -4,7 +4,7 @@ import com.mongodb.DBObject
 import com.mongodb.casbah.MongoCollection
 import com.mongodb.casbah.commons.{MongoDBObject, TypeImports}
 import com.mongodb.util.JSON
-import cromwell.backend.BackendJobExecutionActor.SucceededResponse
+import cromwell.backend.BackendJobExecutionActor.JobSucceededResponse
 import cromwell.backend.impl.htcondor.caching.CacheActor
 import cromwell.backend.impl.htcondor.caching.exception.{CachedResultAlreadyExistException, CachedResultNotFoundException}
 import cromwell.backend.impl.htcondor.caching.model.CachedExecutionResult
@@ -55,7 +55,7 @@ class MongoCacheActor(collection: MongoCollection,
 
   private def deserializeSucceededResponse(mongoDbObject: TypeImports.DBObject): CachedExecutionResult = {
     val cachedResult = JsonParser(mongoDbObject.toString).convertTo[MongoCachedExecutionResult]
-    val succeededResponse = deserialize(cachedResult.succeededResponse.byteArray, classOf[SucceededResponse])
+    val succeededResponse = deserialize(cachedResult.succeededResponse.byteArray, classOf[JobSucceededResponse])
     CachedExecutionResult(cachedResult.hash, succeededResponse)
   }
 
diff --git a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorCommandSpec.scala b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorCommandSpec.scala
index ce1097f4e79..9a03fecca26 100644
--- a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorCommandSpec.scala
+++ b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorCommandSpec.scala
@@ -5,17 +5,17 @@ import better.files._
 import org.scalatest.{Matchers, WordSpecLike}
 
 class HtCondorCommandSpec extends WordSpecLike with Matchers {
-  val attributes = Map("executable" -> "test.sh", "input" -> "/temp/test", "error"->"stderr")
-  val resultAttributes = List("executable=test.sh","input=/temp/test","error=stderr", "queue")
-  val htCondorCommands = new HtCondorCommands
+  private val attributes = Map("executable" -> "test.sh", "input" -> "/temp/test", "error"->"stderr")
+  private val resultAttributes = List("executable=test.sh","input=/temp/test","error=stderr", "spec1", "spec2", "queue")
+  private val htCondorCommands = new HtCondorCommands
+  private val nativeSpecs = Option(Array("spec1", "spec2"))
 
   "submitCommand method" should {
     "return submit file with content passed to it" in {
-      val dir = File.newTemporaryFile()
-      val command = htCondorCommands.generateSubmitFile(dir.path,attributes)
-      val file = dir
-      resultAttributes shouldEqual  dir.lines.toList
-      dir.delete()
+      val file = File.newTemporaryFile()
+      val command = htCondorCommands.generateSubmitFile(file.path, attributes, nativeSpecs)
+      resultAttributes shouldEqual file.lines.toList
+      file.delete()
       command shouldEqual s"condor_submit ${file.path}"
     }
   }
diff --git a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorInitializationActorSpec.scala b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorInitializationActorSpec.scala
index 9e71d1a1497..29d19d11779 100644
--- a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorInitializationActorSpec.scala
+++ b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorInitializationActorSpec.scala
@@ -5,7 +5,7 @@ import cromwell.backend.BackendWorkflowInitializationActor.Initialize
 import cromwell.backend.{BackendConfigurationDescriptor, BackendSpec, BackendWorkflowDescriptor}
 import cromwell.core.TestKitSuite
 import org.scalatest.{Matchers, WordSpecLike}
-import wdl4s.Call
+import wdl4s.TaskCall
 
 import scala.concurrent.duration._
 
@@ -29,12 +29,12 @@ class HtCondorInitializationActorSpec extends TestKitSuite("HtCondorInitializati
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
 
-  private def getHtCondorBackend(workflowDescriptor: BackendWorkflowDescriptor, calls: Seq[Call], conf: BackendConfigurationDescriptor) = {
+  private def getHtCondorBackend(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[TaskCall], conf: BackendConfigurationDescriptor) = {
     system.actorOf(HtCondorInitializationActor.props(workflowDescriptor, calls, conf, emptyActor))
   }
 
@@ -43,7 +43,7 @@ class HtCondorInitializationActorSpec extends TestKitSuite("HtCondorInitializati
       within(Timeout) {
         EventFilter.warning(message = s"Key/s [proc] is/are not supported by HtCondorBackend. Unsupported attributes will not be part of jobs executions.", occurrences = 1) intercept {
           val workflowDescriptor = buildWorkflowDescriptor(HelloWorld, runtime = """runtime { proc: 1 }""")
-          val backend = getHtCondorBackend(workflowDescriptor, workflowDescriptor.workflowNamespace.workflow.calls,
+          val backend = getHtCondorBackend(workflowDescriptor, workflowDescriptor.workflow.taskCalls,
             emptyBackendConfig)
           backend ! Initialize
         }
diff --git a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorJobExecutionActorSpec.scala b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorJobExecutionActorSpec.scala
index 589554e94d3..33bc5c71c3e 100644
--- a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorJobExecutionActorSpec.scala
+++ b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorJobExecutionActorSpec.scala
@@ -7,15 +7,15 @@ import akka.actor.{Actor, Props}
 import akka.testkit.{ImplicitSender, TestActorRef}
 import better.files._
 import com.typesafe.config.ConfigFactory
-import cromwell.backend.BackendJobExecutionActor.{FailedNonRetryableResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{JobFailedNonRetryableResponse, JobSucceededResponse}
 import cromwell.backend.impl.htcondor.caching.CacheActor
 import cromwell.backend.impl.htcondor.caching.exception.CachedResultNotFoundException
 import cromwell.backend.impl.htcondor.caching.model.CachedExecutionResult
-import cromwell.backend.io.JobPaths
+import cromwell.backend.io.JobPathsWithDocker
 import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendSpec}
 import cromwell.core._
+import cromwell.core.path.{PathWriter, TailedWriter, UntailedWriter}
 import cromwell.services.keyvalue.KeyValueServiceActor.{KvGet, KvPair, KvPut}
-import org.mockito.Matchers._
 import org.mockito.Mockito
 import org.mockito.Mockito._
 import org.scalatest.concurrent.PatienceConfiguration.Timeout
@@ -54,7 +54,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
@@ -73,7 +73,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
@@ -92,7 +92,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
@@ -102,7 +102,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
         |  root = "local-cromwell-executions"
         |
         |  docker {
-        |    cmd = "docker run -w %s %s %s %s --rm %s %s"
+        |    cmd = "docker run -w %s %s %s %s --rm %s /bin/bash -c \\"%s\\""
         |    defaultWorkingDir = "/workingDir/"
         |    defaultOutputDir = "/output/"
         |  }
@@ -147,7 +147,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       }).underlyingActor
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[SucceededResponse]
+        response shouldBe a[JobSucceededResponse]
         verify(htCondorProcess, times(1)).externalProcess(any[Seq[String]], any[ProcessLogger])
         verify(htCondorProcess, times(1)).tailedWriter(any[Int], any[Path])
         verify(htCondorProcess, times(1)).untailedWriter(any[Path])
@@ -179,7 +179,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       }).underlyingActor
 
       whenReady(backend.recover, timeout) { response =>
-        response shouldBe a[SucceededResponse]
+        response shouldBe a[JobSucceededResponse]
       }
 
       cleanUpJob(jobPaths)
@@ -207,7 +207,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       }).underlyingActor
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[SucceededResponse]
+        response shouldBe a[JobSucceededResponse]
         verify(htCondorProcess, times(1)).externalProcess(any[Seq[String]], any[ProcessLogger])
         verify(htCondorProcess, times(1)).tailedWriter(any[Int], any[Path])
         verify(htCondorProcess, times(1)).untailedWriter(any[Path])
@@ -237,8 +237,8 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       when(htCondorProcess.jobReturnCode(any[String], any[Path])).thenReturn(Option(-1))
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[FailedNonRetryableResponse]
-        assert(response.asInstanceOf[FailedNonRetryableResponse].throwable.getMessage.contains("Job exited with invalid return code"))
+        response shouldBe a[JobFailedNonRetryableResponse]
+        assert(response.asInstanceOf[JobFailedNonRetryableResponse].throwable.getMessage.contains("Job exited with invalid return code"))
       }
 
       cleanUpJob(jobPaths)
@@ -271,7 +271,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       when(htCondorProcess.jobReturnCode(any[String], any[Path])).thenReturn(Option(911))
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[SucceededResponse]
+        response shouldBe a[JobSucceededResponse]
       }
 
       cleanUpJob(jobPaths)
@@ -288,7 +288,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
         """.stripMargin
       val jsonInputFile = createCannedFile("testFile", "some content").pathAsString
       val inputs = Map(
-        "inputFile" -> WdlFile(jsonInputFile)
+        "wf_hello.hello.inputFile" -> WdlFile(jsonInputFile)
       )
       val jobDescriptor = prepareJob(helloWorldWdlWithFileInput, runtime, Option(inputs))
       val (job, jobPaths, backendConfigDesc) = (jobDescriptor.jobDescriptor, jobDescriptor.jobPaths, jobDescriptor.backendConfigurationDescriptor)
@@ -310,7 +310,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       when(htCondorProcess.jobReturnCode(any[String], any[Path])).thenReturn(Option(0))
 
       whenReady(backend.execute) { response =>
-        response shouldBe a[SucceededResponse]
+        response shouldBe a[JobSucceededResponse]
       }
 
       val bashScript = Source.fromFile(jobPaths.script.toFile).getLines.mkString
@@ -318,7 +318,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       assert(bashScript.contains("docker run -w /workingDir/ -v"))
       assert(bashScript.contains(":/workingDir/"))
       assert(bashScript.contains(":ro"))
-      assert(bashScript.contains("/call-hello/execution:/outputDir/ --rm ubuntu/latest echo"))
+      assert(bashScript.contains("/call-hello/execution:/outputDir/ --rm ubuntu/latest /bin/bash -c \"echo"))
 
       cleanUpJob(jobPaths)
     }
@@ -346,8 +346,8 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       when(htCondorProcess.jobReturnCode(any[String], any[Path])).thenReturn(Option(-1))
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[FailedNonRetryableResponse]
-        assert(response.asInstanceOf[FailedNonRetryableResponse].throwable.getMessage.contains("Could not write the file."))
+        response shouldBe a[JobFailedNonRetryableResponse]
+        assert(response.asInstanceOf[JobFailedNonRetryableResponse].throwable.getMessage.contains("Could not write the file."))
       }
 
       cleanUpJob(jobPaths)
@@ -372,7 +372,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
       createCannedFile(prefix = "testFile2", contents = "some other content", dir = Some(tempDir2)).pathAsString
 
     val inputs = Map(
-      "inputFiles" -> WdlArray(WdlArrayType(WdlFileType), Seq(WdlFile(jsonInputFile), WdlFile(jsonInputFile2)))
+      "wf_hello.hello.inputFiles" -> WdlArray(WdlArrayType(WdlFileType), Seq(WdlFile(jsonInputFile), WdlFile(jsonInputFile2)))
     )
     val jobDescriptor = prepareJob(helloWorldWdlWithFileArrayInput, runtime, Option(inputs))
     val (job, jobPaths, backendConfigDesc) = (jobDescriptor.jobDescriptor, jobDescriptor.jobPaths, jobDescriptor.backendConfigurationDescriptor)
@@ -394,7 +394,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
     when(htCondorProcess.jobReturnCode(any[String], any[Path])).thenReturn(Option(0))
 
     whenReady(backend.execute) { response =>
-      response shouldBe a[SucceededResponse]
+      response shouldBe a[JobSucceededResponse]
     }
 
     val bashScript = Source.fromFile(jobPaths.script.toFile).getLines.mkString
@@ -403,12 +403,12 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
     assert(bashScript.contains(":/workingDir/"))
     assert(bashScript.contains(tempDir1.toAbsolutePath.toString))
     assert(bashScript.contains(tempDir2.toAbsolutePath.toString))
-    assert(bashScript.contains("/call-hello/execution:/outputDir/ --rm ubuntu/latest echo"))
+    assert(bashScript.contains("/call-hello/execution:/outputDir/ --rm ubuntu/latest /bin/bash -c \"echo"))
 
     cleanUpJob(jobPaths)
   }
 
-  private def cleanUpJob(jobPaths: JobPaths): Unit = {
+  private def cleanUpJob(jobPaths: JobPathsWithDocker): Unit = {
     File(jobPaths.workflowRoot).delete(true)
     ()
   }
@@ -425,7 +425,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
     val backendWorkflowDescriptor = buildWorkflowDescriptor(wdl = source, inputs = inputFiles.getOrElse(Map.empty), runtime = runtimeString)
     val backendConfigurationDescriptor = BackendConfigurationDescriptor(backendConfig, ConfigFactory.load)
     val jobDesc = jobDescriptorFromSingleCallWorkflow(backendWorkflowDescriptor, inputFiles.getOrElse(Map.empty), emptyWorkflowOptions, Set.empty)
-    val jobPaths = new JobPaths(backendWorkflowDescriptor, backendConfig, jobDesc.key)
+    val jobPaths = new JobPathsWithDocker(jobDesc.key, backendWorkflowDescriptor, backendConfig)
     val executionDir = File(jobPaths.callExecutionRoot)
     val stdout = File(executionDir.pathAsString, "stdout")
     stdout.createIfNotExists(asDirectory = false, createParents = true)
@@ -440,7 +440,7 @@ class HtCondorJobExecutionActorSpec extends TestKitSuite("HtCondorJobExecutionAc
     TestJobDescriptor(jobDesc, jobPaths, backendConfigurationDescriptor)
   }
 
-  private case class TestJobDescriptor(jobDescriptor: BackendJobDescriptor, jobPaths: JobPaths, backendConfigurationDescriptor: BackendConfigurationDescriptor)
+  private case class TestJobDescriptor(jobDescriptor: BackendJobDescriptor, jobPaths: JobPathsWithDocker, backendConfigurationDescriptor: BackendConfigurationDescriptor)
 
   trait MockWriter extends Writer {
     var closed = false
diff --git a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorRuntimeAttributesSpec.scala b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorRuntimeAttributesSpec.scala
index db95a999e09..659d700fa42 100644
--- a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorRuntimeAttributesSpec.scala
+++ b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/HtCondorRuntimeAttributesSpec.scala
@@ -30,7 +30,7 @@ class HtCondorRuntimeAttributesSpec extends WordSpecLike with Matchers {
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
@@ -39,7 +39,8 @@ class HtCondorRuntimeAttributesSpec extends WordSpecLike with Matchers {
 
   val memorySize = MemorySize.parse("0.512 GB").get
   val diskSize = MemorySize.parse("1.024 GB").get
-  val staticDefaults = new HtCondorRuntimeAttributes(ContinueOnReturnCodeSet(Set(0)), None, None, None, false, 1, memorySize, diskSize)
+  val staticDefaults = new HtCondorRuntimeAttributes(ContinueOnReturnCodeSet(Set(0)), None, None, None, false, 1,
+    memorySize, diskSize, None)
 
   def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]) = {
     WorkflowOptions(JsObject(Map(
@@ -219,11 +220,16 @@ class HtCondorRuntimeAttributesSpec extends WordSpecLike with Matchers {
       assertHtCondorRuntimeAttributesSuccessfulCreation(runtimeAttributes, shouldBeIgnored, expectedRuntimeAttributes)
     }
 
-    "throw an exception when tries to validate an invalid disk entry" in {
+    "throw an exception when tries to validate an invalid String disk entry" in {
       val runtimeAttributes = createRuntimeAttributes(HelloWorld, """runtime { docker: "ubuntu:latest" disk: "value" }""").head
       assertHtCondorRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting memory runtime attribute to be an Integer or String with format '8 GB'")
     }
 
+    "throw an exception when tries to validate an invalid Integer array disk entry" in {
+      val runtimeAttributes = createRuntimeAttributes(HelloWorld, """runtime { docker: "ubuntu:latest" disk: [1] }""").head
+      assertHtCondorRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting disk runtime attribute to be an Integer or String with format '8 GB'")
+    }
+
     "use workflow options as default if disk key is missing" in {
       val runtimeAttributes = createRuntimeAttributes(HelloWorld, """runtime { }""").head
       val expectedRuntimeAttributes = staticDefaults.copy(disk = MemorySize.parse("65 GB").get)
@@ -237,37 +243,59 @@ class HtCondorRuntimeAttributesSpec extends WordSpecLike with Matchers {
       val shouldBeIgnored = workflowOptionsWithDefaultRA(Map())
       assertHtCondorRuntimeAttributesSuccessfulCreation(runtimeAttributes, shouldBeIgnored, expectedRuntimeAttributes)
     }
+
+    "return an instance of itself when tries to validate a valid native specs entry" in {
+      val expectedRuntimeAttributes = staticDefaults.copy(nativeSpecs = Option(Array("spec1", "spec2")))
+      val runtimeAttributes = createRuntimeAttributes(HelloWorld, """runtime { nativeSpecs: ["spec1", "spec2"] }""").head
+      assertHtCondorRuntimeAttributesSuccessfulCreation(runtimeAttributes, emptyWorkflowOptions, expectedRuntimeAttributes)
+    }
+
+    "throw an exception when tries to validate an invalid native specs entry" in {
+      val runtimeAttributes = createRuntimeAttributes(HelloWorld, """runtime { nativeSpecs: [1, 2] }""").head
+      assertHtCondorRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting nativeSpecs runtime attribute to be an Array of Strings.")
+    }
   }
 
-  private def assertHtCondorRuntimeAttributesSuccessfulCreation(runtimeAttributes: Map[String, WdlValue], workflowOptions: WorkflowOptions, expectedRuntimeAttributes: HtCondorRuntimeAttributes): Unit = {
+  private def assertHtCondorRuntimeAttributesSuccessfulCreation(runtimeAttributes: Map[String, WdlValue],
+                                                                workflowOptions: WorkflowOptions,
+                                                                expectedRuntimeAttributes: HtCondorRuntimeAttributes) = {
     try {
-      assert(HtCondorRuntimeAttributes(runtimeAttributes, workflowOptions) == expectedRuntimeAttributes)
+      val actualRuntimeAttr = HtCondorRuntimeAttributes(runtimeAttributes, workflowOptions)
+      assert(actualRuntimeAttr.cpu == expectedRuntimeAttributes.cpu)
+      assert(actualRuntimeAttr.disk == expectedRuntimeAttributes.disk)
+      assert(actualRuntimeAttr.memory == expectedRuntimeAttributes.memory)
+      assert(actualRuntimeAttr.continueOnReturnCode == expectedRuntimeAttributes.continueOnReturnCode)
+      assert(actualRuntimeAttr.failOnStderr == expectedRuntimeAttributes.failOnStderr)
+      assert(actualRuntimeAttr.dockerWorkingDir == expectedRuntimeAttributes.dockerWorkingDir)
+      assert(actualRuntimeAttr.dockerImage == expectedRuntimeAttributes.dockerImage)
+      assert(actualRuntimeAttr.dockerOutputDir == expectedRuntimeAttributes.dockerOutputDir)
+      expectedRuntimeAttributes.nativeSpecs match {
+        case Some(ns) => assert(ns.deep == expectedRuntimeAttributes.nativeSpecs.get.deep)
+        case None => assert(expectedRuntimeAttributes.nativeSpecs.isEmpty)
+      }
     } catch {
       case ex: RuntimeException => fail(s"Exception was not expected but received: ${ex.getMessage}")
     }
-    ()
   }
 
-  private def assertHtCondorRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WdlValue], exMsg: String): Unit = {
+  private def assertHtCondorRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WdlValue], exMsg: String) = {
     try {
       HtCondorRuntimeAttributes(runtimeAttributes, emptyWorkflowOptions)
       fail("A RuntimeException was expected.")
     } catch {
       case ex: RuntimeException => assert(ex.getMessage.contains(exMsg))
     }
-    ()
   }
 
   private def createRuntimeAttributes(wdlSource: WdlSource, runtimeAttributes: String): Seq[Map[String, WdlValue]] = {
     val workflowDescriptor = buildWorkflowDescriptor(wdlSource, runtime = runtimeAttributes)
 
     def createLookup(call: Call): ScopedLookupFunction = {
-      val declarations = workflowDescriptor.workflowNamespace.workflow.declarations ++ call.task.declarations
       val knownInputs = workflowDescriptor.inputs
-      WdlExpression.standardLookupFunction(knownInputs, declarations, NoFunctions)
+      call.lookupFunction(knownInputs, NoFunctions)
     }
 
-    workflowDescriptor.workflowNamespace.workflow.calls map {
+    workflowDescriptor.workflow.taskCalls.toSeq map {
       call =>
         val ra = call.task.runtimeAttributes.attrs mapValues { _.evaluate(createLookup(call), NoFunctions) }
         TryUtil.sequenceMap(ra, "Runtime attributes evaluation").get
diff --git a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/caching/localization/CachedResultLocalizationSpec.scala b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/caching/localization/CachedResultLocalizationSpec.scala
index c2c4d101ff1..e0e847e567d 100644
--- a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/caching/localization/CachedResultLocalizationSpec.scala
+++ b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/caching/localization/CachedResultLocalizationSpec.scala
@@ -2,7 +2,7 @@ package cromwell.backend.impl.htcondor.caching.localization
 
 import java.nio.file.Files
 
-import cromwell.core.{JobOutput, JobOutputs}
+import cromwell.core.{JobOutput, CallOutputs}
 import org.scalatest.{BeforeAndAfterAll, Matchers, WordSpecLike}
 import wdl4s.types.{WdlArrayType, WdlFileType}
 import wdl4s.values.{WdlArray, WdlSingleFile, WdlString}
@@ -33,7 +33,7 @@ class CachedResultLocalizationSpec extends WordSpecLike with Matchers with Befor
     }
 
     "localize cached job outputs which are WDL files using symbolic link" in {
-      val outputs: JobOutputs = Map("File1" -> JobOutput(WdlSingleFile(defaultCachedFile.toAbsolutePath.toString)))
+      val outputs: CallOutputs = Map("File1" -> JobOutput(WdlSingleFile(defaultCachedFile.toAbsolutePath.toString)))
       val newJobOutputs = cachedResults.localizeCachedOutputs(newTmpDir, outputs)
       newJobOutputs foreach { case (lqn, jobOutput) =>
         assert(jobOutput.wdlValue.valueString == newTmpFile.toString)
diff --git a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/caching/provider/mongodb/MongoCacheActorSpec.scala b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/caching/provider/mongodb/MongoCacheActorSpec.scala
index fa675e758aa..d638b82d94e 100644
--- a/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/caching/provider/mongodb/MongoCacheActorSpec.scala
+++ b/supportedBackends/htcondor/src/test/scala/cromwell/backend/impl/htcondor/caching/provider/mongodb/MongoCacheActorSpec.scala
@@ -8,7 +8,7 @@ import com.mongodb.util.JSON
 import com.mongodb.{DBObject, WriteResult}
 import com.typesafe.config.{Config, ConfigFactory}
 import cromwell.backend.{MemorySize, BackendJobDescriptorKey}
-import cromwell.backend.BackendJobExecutionActor.SucceededResponse
+import cromwell.backend.BackendJobExecutionActor.JobSucceededResponse
 import cromwell.backend.impl.htcondor.HtCondorRuntimeAttributes
 import cromwell.backend.impl.htcondor.caching.CacheActor._
 import cromwell.backend.impl.htcondor.caching.exception.CachedResultNotFoundException
@@ -20,7 +20,7 @@ import org.mockito.Mockito
 import org.mockito.Mockito._
 import org.scalatest.mockito.MockitoSugar
 import org.scalatest.{BeforeAndAfter, BeforeAndAfterAll, MustMatchers, WordSpecLike}
-import wdl4s.Call
+import wdl4s.TaskCall
 import wdl4s.values.WdlString
 
 class MongoCacheActorSpec extends TestKit(ActorSystem("MongoCacheProviderActorSpecSystem")) with WordSpecLike with MustMatchers
@@ -33,10 +33,10 @@ class MongoCacheActorSpec extends TestKit(ActorSystem("MongoCacheProviderActorSp
   val mongoDbCollectionMock = mock[MongoCollection]
   val memorySize = MemorySize.parse("0.512 GB").get
   val diskSize = MemorySize.parse("1.024 GB").get
-  val runtimeConfig = HtCondorRuntimeAttributes(ContinueOnReturnCodeSet(Set(0)), Some("tool-name"), Some("/workingDir"), Some("/outputDir"), true, 1, memorySize, diskSize)
+  val runtimeConfig = HtCondorRuntimeAttributes(ContinueOnReturnCodeSet(Set(0)), Some("tool-name"), Some("/workingDir"), Some("/outputDir"), true, 1, memorySize, diskSize, None)
   val jobHash = "88dde49db10f1551299fb9937f313c10"
   val taskStatus = "done"
-  val succeededResponseMock = SucceededResponse(BackendJobDescriptorKey(Call(None, "TestJob", null, null, null, None), None, 0), None, Map("test" -> JobOutput(WdlString("Test"))), None, Seq.empty)
+  val succeededResponseMock = JobSucceededResponse(BackendJobDescriptorKey(TaskCall(Option("taskName"), null, null, null), None, 0), None, Map("test" -> JobOutput(WdlString("Test"))), None, Seq.empty)
   val serSucceededRespMock = KryoSerializedObject(serialize(succeededResponseMock))
   val cachedExecutionResult = MongoCachedExecutionResult(jobHash, serSucceededRespMock)
   val cachedExecutionResultDbObject = JSON.parse(cachedExecutionResult.toJson.toString).asInstanceOf[DBObject]
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/GenomicsFactory.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/GenomicsFactory.scala
index 7285171b596..574e581533a 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/GenomicsFactory.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/GenomicsFactory.scala
@@ -2,22 +2,22 @@ package cromwell.backend.impl.jes
 
 import java.net.URL
 
-import com.google.api.client.auth.oauth2.Credential
-import com.google.api.client.http.HttpTransport
-import com.google.api.client.json.JsonFactory
 import com.google.api.services.genomics.Genomics
+import cromwell.core.WorkflowOptions
+import cromwell.filesystems.gcs.auth.GoogleAuthMode
 
 
-object GenomicsFactory {
+case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, endpointUrl: URL) {
 
-  def apply(applicationName: String, credential: Credential, endpointUrl: URL): Genomics = {
-    GoogleGenomics.from(applicationName, endpointUrl, credential, credential.getJsonFactory, credential.getTransport)
-  }
+  def withOptions(options: WorkflowOptions) = {
+    val credential = authMode.credential(options)
 
-  // Wrapper object around Google's Genomics class providing a convenience 'from' "method"
-  object GoogleGenomics {
-    def from(applicationName: String, endpointUrl: URL, credential: Credential, jsonFactory: JsonFactory, httpTransport: HttpTransport): Genomics = {
-      new Genomics.Builder(httpTransport, jsonFactory, credential).setApplicationName(applicationName).setRootUrl(endpointUrl.toString).build
-    }
+    new Genomics.Builder(
+      credential.getTransport,
+      credential.getJsonFactory,
+      credential)
+      .setApplicationName(applicationName)
+      .setRootUrl(endpointUrl.toString)
+      .build
   }
 }
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesAsyncBackendJobExecutionActor.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesAsyncBackendJobExecutionActor.scala
index a08be8df959..84da1efbc13 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesAsyncBackendJobExecutionActor.scala
@@ -9,29 +9,26 @@ import better.files._
 import cats.instances.future._
 import cats.syntax.functor._
 import com.google.api.client.googleapis.json.GoogleJsonResponseException
+import com.google.cloud.storage.contrib.nio.CloudStoragePath
 import cromwell.backend.BackendJobExecutionActor.{AbortedResponse, BackendJobExecutionResponse}
 import cromwell.backend.BackendLifecycleActor.AbortJobCommand
 import cromwell.backend.async.AsyncBackendJobExecutionActor.{ExecutionMode, JobId}
 import cromwell.backend.async.{AbortedExecutionHandle, AsyncBackendJobExecutionActor, ExecutionHandle, FailedNonRetryableExecutionHandle, FailedRetryableExecutionHandle, NonRetryableExecution, SuccessfulExecutionHandle}
-import cromwell.backend.impl.jes.JesImplicits.PathString
 import cromwell.backend.impl.jes.JesJobExecutionActor.JesOperationIdKey
 import cromwell.backend.impl.jes.RunStatus.TerminalRunStatus
 import cromwell.backend.impl.jes.io._
 import cromwell.backend.impl.jes.statuspolling.JesPollingActorClient
-import cromwell.backend.{AttemptedLookupResult, BackendJobDescriptor, BackendWorkflowDescriptor, PreemptedException}
+import cromwell.backend.wdl.OutputEvaluator
+import cromwell.backend.{BackendJobDescriptor, BackendWorkflowDescriptor, PreemptedException}
 import cromwell.core.Dispatcher.BackendDispatcher
 import cromwell.core._
 import cromwell.core.logging.JobLogging
+import cromwell.core.path.proxy.PathProxy
 import cromwell.core.retry.{Retry, SimpleExponentialBackoff}
-import cromwell.filesystems.gcs.NioGcsPath
 import cromwell.services.keyvalue.KeyValueServiceActor._
 import cromwell.services.metadata._
-import wdl4s.AstTools._
-import wdl4s.WdlExpression.ScopedLookupFunction
 import wdl4s._
-import wdl4s.command.ParameterCommandPart
 import wdl4s.expression.NoFunctions
-import wdl4s.util.TryUtil
 import wdl4s.values._
 
 import scala.concurrent.duration._
@@ -58,6 +55,7 @@ object JesAsyncBackendJobExecutionActor {
   object WorkflowOptionKeys {
     val MonitoringScript = "monitoring_script"
     val GoogleProject = "google_project"
+    val GoogleComputeServiceAccount = "google_compute_service_account"
   }
 
 
@@ -68,7 +66,7 @@ object JesAsyncBackendJobExecutionActor {
     * ask them for results.
     */
   case class JesPendingExecutionHandle(jobDescriptor: BackendJobDescriptor,
-                                       jesOutputs: Seq[JesFileOutput],
+                                       jesOutputs: Set[JesFileOutput],
                                        run: Run,
                                        previousStatus: Option[RunStatus]) extends ExecutionHandle {
     override val isDone = false
@@ -92,20 +90,20 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
   override val pollingActor = jesBackendSingletonActor
 
   override lazy val pollBackOff = SimpleExponentialBackoff(
-    initialInterval = 30 seconds, maxInterval = 10 minutes, multiplier = 1.1)
+    initialInterval = 30 seconds, maxInterval = jesAttributes.maxPollingInterval seconds, multiplier = 1.1)
 
   override lazy val executeOrRecoverBackOff = SimpleExponentialBackoff(
     initialInterval = 3 seconds, maxInterval = 20 seconds, multiplier = 1.1)
 
-  private lazy val workflowDescriptor = jobDescriptor.workflowDescriptor
+  override lazy val workflowDescriptor = jobDescriptor.workflowDescriptor
 
   private lazy val call = jobDescriptor.key.call
 
   override lazy val retryable = jobDescriptor.key.attempt <= runtimeAttributes.preemptible
   private lazy val cmdInput =
-    JesFileInput(ExecParamName, jesCallPaths.gcsExecPath.toString, Paths.get(jesCallPaths.gcsExecFilename), workingDisk)
+    JesFileInput(ExecParamName, jesCallPaths.script.toUri.toString, Paths.get(jesCallPaths.scriptFilename), workingDisk)
   private lazy val jesCommandLine = s"/bin/bash ${cmdInput.containerPath}"
-  private lazy val rcJesOutput = JesFileOutput(returnCodeFilename, returnCodeGcsPath.toString, Paths.get(returnCodeFilename), workingDisk)
+  private lazy val rcJesOutput = JesFileOutput(returnCodeFilename, returnCodeGcsPath.toUri.toString, Paths.get(returnCodeFilename), workingDisk)
 
   private lazy val standardParameters = Seq(rcJesOutput)
   private lazy val returnCodeContents = Try(File(returnCodeGcsPath).contentAsString)
@@ -129,26 +127,19 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
 
   override def receive: Receive = pollingActorClientReceive orElse jesReceiveBehavior orElse super.receive
 
-  private def globOutputPath(glob: String) = callRootPath.resolve(s"glob-${glob.md5Sum}/")
-
   private def gcsAuthParameter: Option[JesInput] = {
-    if (jesAttributes.gcsFilesystemAuth.requiresAuthFile || dockerConfiguration.isDefined)
-      Option(JesLiteralInput(ExtraConfigParamName, jesCallPaths.gcsAuthFilePath.toString))
+    if (jesAttributes.auths.gcs.requiresAuthFile || dockerConfiguration.isDefined)
+      Option(JesLiteralInput(ExtraConfigParamName, jesCallPaths.gcsAuthFilePath.toUri.toString))
     else None
   }
 
   private lazy val callContext = CallContext(
     callRootPath,
-    jesStdoutFile.toString,
-    jesStderrFile.toString
+    jesStdoutFile.toUri.toString,
+    jesStderrFile.toUri.toString
   )
 
-  private[jes] lazy val callEngineFunctions = new JesExpressionFunctions(List(jesCallPaths.gcsFileSystem), callContext)
-
-  private val lookup: ScopedLookupFunction = {
-    val declarations = workflowDescriptor.workflowNamespace.workflow.declarations ++ call.task.declarations
-    WdlExpression.standardLookupFunction(jobDescriptor.inputs, declarations, callEngineFunctions)
-  }
+  private[jes] lazy val callEngineFunctions = new JesExpressionFunctions(List(jesCallPaths.gcsPathBuilder), callContext)
 
   /**
     * Takes two arrays of remote and local WDL File paths and generates the necessary JesInputs.
@@ -170,43 +161,28 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
     * relativeLocalizationPath("gs://some/bucket/foo.txt") -> "some/bucket/foo.txt"
     */
   private def relativeLocalizationPath(file: WdlFile): WdlFile = {
-    Try(getPath(file.value)) match {
-      case Success(gcsPath: NioGcsPath) => WdlFile(gcsPath.bucket + "/" + gcsPath.objectName, file.isGlob)
-      case Success(gcsPath) => file
-      case Failure(e) => file
+    getPath(file.value) match {
+      case Success(path) =>
+        val value: WdlSource = path.toUri.getHost + path.toUri.getPath
+        WdlFile(value, file.isGlob)
+      case _ => file
     }
   }
 
-  private[jes] def generateJesInputs(jobDescriptor: BackendJobDescriptor): Iterable[JesInput] = {
-    /**
-      * Commands in WDL tasks can also generate input files.  For example: ./my_exec --file=${write_lines(arr)}
-      *
-      * write_lines(arr) would produce a string-ified version of the array stored as a GCS path.  The next block of code
-      * will go through each ${...} expression within the task's command section and find all write_*() ASTs and
-      * evaluate them so the files are written to GCS and the they can be included as inputs to Google's Pipeline object
-      */
-    val commandExpressions = jobDescriptor.key.scope.task.commandTemplate.collect({
-      case x: ParameterCommandPart => x.expression
-    })
-
-    val writeFunctionAsts = commandExpressions.map(_.ast).flatMap(x => AstTools.findAsts(x, "FunctionCall")).collect({
-      case y if y.getAttribute("name").sourceString.startsWith("write_") => y
-    })
+  private[jes] def generateJesInputs(jobDescriptor: BackendJobDescriptor): Set[JesInput] = {
 
-    val evaluatedExpressionMap = writeFunctionAsts map { ast =>
-      val expression = WdlExpression(ast)
-      val value = expression.evaluate(lookup, callEngineFunctions)
-      expression.toWdlString.md5SumShort -> value
-    } toMap
-
-    val writeFunctionFiles = evaluatedExpressionMap collect { case (k, v: Success[_]) => k -> v.get } collect { case (k, v: WdlFile) => k -> Seq(v)}
+    val writeFunctionFiles = call.task.evaluateFilesFromCommand(jobDescriptor.fullyQualifiedInputs, callEngineFunctions) map {
+      case (expression, file) =>  expression.toWdlString.md5SumShort -> Seq(file)
+    }
 
-    /** Collect all WdlFiles from inputs to the call */
-    val callInputFiles: Map[FullyQualifiedName, Seq[WdlFile]] = jobDescriptor.inputs mapValues { _.collectAsSeq { case w: WdlFile => w } }
+    /* Collect all WdlFiles from inputs to the call */
+    val callInputFiles: Map[FullyQualifiedName, Seq[WdlFile]] = jobDescriptor.fullyQualifiedInputs mapValues { _.collectAsSeq { case w: WdlFile => w } }
 
-    (callInputFiles ++ writeFunctionFiles) flatMap {
+    val inputs = (callInputFiles ++ writeFunctionFiles) flatMap {
       case (name, files) => jesInputsFromWdlFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor)
     }
+
+    inputs.toSet
   }
 
   /**
@@ -236,33 +212,56 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
     if (referenceName.length <= 127) referenceName else referenceName.md5Sum
   }
 
-  private[jes] def generateJesOutputs(jobDescriptor: BackendJobDescriptor): Seq[JesFileOutput] = {
-    val wdlFileOutputs = jobDescriptor.key.scope.task.outputs flatMap { taskOutput =>
-      taskOutput.requiredExpression.evaluateFiles(lookup, NoFunctions, taskOutput.wdlType) match {
-        case Success(wdlFiles) => wdlFiles map relativeLocalizationPath
-        case Failure(ex) =>
-          jobLogger.warn(s"Could not evaluate $taskOutput: ${ex.getMessage}", ex)
-          Seq.empty[WdlFile]
-      }
+  private[jes] def findGlobOutputs(jobDescriptor: BackendJobDescriptor): Set[WdlGlobFile] = {
+    val globOutputs = (call.task.findOutputFiles(jobDescriptor.fullyQualifiedInputs, NoFunctions) map relativeLocalizationPath) collect {
+      case glob: WdlGlobFile => glob
     }
+    globOutputs.distinct.toSet
+  }
+
+  private[jes] def generateJesOutputs(jobDescriptor: BackendJobDescriptor): Set[JesFileOutput] = {
+    val wdlFileOutputs = call.task.findOutputFiles(jobDescriptor.fullyQualifiedInputs, NoFunctions) map relativeLocalizationPath
 
-    // Create the mappings. GLOB mappings require special treatment (i.e. stick everything matching the glob in a folder)
-    wdlFileOutputs.distinct map { wdlFile =>
-      val destination = wdlFile match {
-        case WdlSingleFile(filePath) => callRootPath.resolve(filePath).toString
-        case WdlGlobFile(filePath) => globOutputPath(filePath).toString
+    val outputs = wdlFileOutputs.distinct flatMap { wdlFile =>
+      wdlFile match {
+        case singleFile: WdlSingleFile => List(generateJesSingleFileOutputs(singleFile))
+        case globFile: WdlGlobFile => generateJesGlobFileOutputs(globFile)
       }
-      val (relpath, disk) = relativePathAndAttachedDisk(wdlFile.value, runtimeAttributes.disks)
-      JesFileOutput(makeSafeJesReferenceName(wdlFile.value), destination, relpath, disk)
     }
+
+    outputs.toSet
+  }
+
+  private def generateJesSingleFileOutputs(wdlFile: WdlSingleFile): JesFileOutput = {
+    val destination = callRootPath.resolve(wdlFile.value.stripPrefix("/")).toUri.toString
+    val (relpath, disk) = relativePathAndAttachedDisk(wdlFile.value, runtimeAttributes.disks)
+    JesFileOutput(makeSafeJesReferenceName(wdlFile.value), destination, relpath, disk)
+  }
+
+  private def generateJesGlobFileOutputs(wdlFile: WdlGlobFile): List[JesFileOutput] = {
+    val globName = callEngineFunctions.globName(wdlFile.value)
+    val globDirectory = globName + "/"
+    val globListFile = globName + ".list"
+    val gcsGlobDirectoryDestinationPath = callRootPath.resolve(globDirectory).toUri.toString
+    val gcsGlobListFileDestinationPath = callRootPath.resolve(globListFile).toUri.toString
+
+    val (_, globDirectoryDisk) = relativePathAndAttachedDisk(wdlFile.value, runtimeAttributes.disks)
+
+    // We need both the glob directory and the glob list:
+    List(
+      // The glob directory:
+      JesFileOutput(makeSafeJesReferenceName(globDirectory), gcsGlobDirectoryDestinationPath, Paths.get(globDirectory + "*"), globDirectoryDisk),
+      // The glob list file:
+      JesFileOutput(makeSafeJesReferenceName(globListFile), gcsGlobListFileDestinationPath, Paths.get(globListFile), globDirectoryDisk)
+    )
   }
 
   private def instantiateCommand: Try[String] = {
-    val backendInputs = jobDescriptor.inputs mapValues gcsPathToLocal
-    jobDescriptor.call.instantiateCommandLine(backendInputs, callEngineFunctions, gcsPathToLocal)
+    val backendInputs = jobDescriptor.inputDeclarations mapValues gcsPathToLocal
+    jobDescriptor.call.task.instantiateCommand(backendInputs, callEngineFunctions, valueMapper = gcsPathToLocal)
   }
 
-  private def uploadCommandScript(command: String, withMonitoring: Boolean): Future[Unit] = {
+  private def uploadCommandScript(command: String, withMonitoring: Boolean, globFiles: Set[WdlGlobFile]): Future[Unit] = {
     val monitoring = if (withMonitoring) {
       s"""|touch $JesMonitoringLogFile
           |chmod u+x $JesMonitoringScript
@@ -272,6 +271,22 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
     val tmpDir = File(JesWorkingDisk.MountPoint)./("tmp").path
     val rcPath = File(JesWorkingDisk.MountPoint)./(returnCodeFilename).path
 
+    def globManipulation(globFile: WdlGlobFile) = {
+
+      val globDir = callEngineFunctions.globName(globFile.value)
+      val (_, disk) = relativePathAndAttachedDisk(globFile.value, runtimeAttributes.disks)
+      val globDirectory = Paths.get(s"${disk.mountPoint.toAbsolutePath}/$globDir/")
+      val globList = Paths.get(s"${disk.mountPoint.toAbsolutePath}/$globDir.list")
+
+      s"""
+        |mkdir $globDirectory
+        |ln ${globFile.value} $globDirectory
+        |ls -1 $globDirectory > $globList
+      """.stripMargin
+    }
+
+    val globManipulations = globFiles.map(globManipulation).mkString("\n")
+
     val fileContent =
       s"""
          |#!/bin/bash
@@ -281,35 +296,34 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
          |(
          |cd ${JesWorkingDisk.MountPoint}
          |$command
+         |$globManipulations
          |)
          |echo $$? > $rcPath
        """.stripMargin.trim
 
-    def writeScript(): Future[Unit] = Future { File(jesCallPaths.gcsExecPath).write(fileContent) } void
-
-    implicit val system = context.system
-    Retry.withRetry(
-      writeScript,
-      isTransient = isTransientJesException,
-      isFatal = isFatalJesException
-    )
+    Future(File(jesCallPaths.script).write(fileContent)) void
   }
 
   private def googleProject(descriptor: BackendWorkflowDescriptor): String = {
     descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleProject, jesAttributes.project)
   }
 
+  private def computeServiceAccount(descriptor: BackendWorkflowDescriptor): String = {
+    descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleComputeServiceAccount, jesAttributes.computeServiceAccount)
+  }
+
   private def createJesRun(jesParameters: Seq[JesParameter], runIdForResumption: Option[String]): Future[Run] = {
 
     def createRun() = Future(Run(
       runIdForResumption,
       jobDescriptor = jobDescriptor,
       runtimeAttributes = runtimeAttributes,
-      callRootPath = callRootPath.toString,
+      callRootPath = callRootPath.toUri.toString,
       commandLine = jesCommandLine,
       logFileName = jesLogFilename,
       jesParameters,
       googleProject(jobDescriptor.workflowDescriptor),
+      computeServiceAccount(jobDescriptor.workflowDescriptor),
       retryable,
       initializationData.genomics
     ))
@@ -332,8 +346,8 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
   }
 
   protected def runWithJes(command: String,
-                           jesInputs: Seq[JesInput],
-                           jesOutputs: Seq[JesFileOutput],
+                           jesInputs: Set[JesInput],
+                           jesOutputs: Set[JesFileOutput],
                            runIdForResumption: Option[String],
                            withMonitoring: Boolean): Future[ExecutionHandle] = {
 
@@ -342,7 +356,7 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
     val jesParameters = standardParameters ++ gcsAuthParameter ++ jesInputs ++ jesOutputs
 
     val jesJobSetup = for {
-      _ <- uploadCommandScript(command, withMonitoring)
+      _ <- uploadCommandScript(command, withMonitoring, findGlobOutputs(jobDescriptor))
       run <- createJesRun(jesParameters, runIdForResumption)
       _ = tellMetadata(Map(CallMetadataKeys.JobId -> run.runId))
     } yield run
@@ -359,8 +373,8 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
   }
 
   private def startExecuting(monitoringOutput: Option[JesFileOutput], mode: ExecutionMode): Future[ExecutionHandle] = {
-    val jesInputs: Seq[JesInput] = generateJesInputs(jobDescriptor).toSeq ++ monitoringScript :+ cmdInput
-    val jesOutputs: Seq[JesFileOutput] = generateJesOutputs(jobDescriptor) ++ monitoringOutput
+    val jesInputs: Set[JesInput] = generateJesInputs(jobDescriptor) ++ monitoringScript + cmdInput
+    val jesOutputs: Set[JesFileOutput] = generateJesOutputs(jobDescriptor) ++ monitoringOutput
 
     instantiateCommand match {
       case Success(command) => runWithJes(command, jesInputs, jesOutputs, mode.jobId.collectFirst { case j: JesJobId => j.operationId }, monitoringScript.isDefined)
@@ -425,29 +439,7 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
   /**
     * Fire and forget start info to the metadata service
     */
-  private def tellStartMetadata(): Unit = {
-    val runtimeAttributesMetadata: Map[String, Any] = runtimeAttributes.asMap map {
-      case (key, value) => s"runtimeAttributes:$key" -> value
-    }
-
-    var fileMetadata: Map[String, Any] = jesCallPaths.metadataPaths
-    if (monitoringOutput.nonEmpty) {
-      // TODO: Move this to JesCallPaths
-      fileMetadata += JesMetadataKeys.MonitoringLog -> monitoringOutput.get.gcs
-    }
-
-    val otherMetadata: Map[String, Any] = Map(
-      JesMetadataKeys.GoogleProject -> jesAttributes.project,
-      JesMetadataKeys.ExecutionBucket -> jesAttributes.executionBucket,
-      JesMetadataKeys.EndpointUrl -> jesAttributes.endpointUrl,
-      "preemptible" -> preemptible,
-      "cache:allowResultReuse" -> true
-    )
-
-    val metadataKeyValues = runtimeAttributesMetadata ++ fileMetadata ++ otherMetadata
-
-    tellMetadata(metadataKeyValues)
-  }
+  private def tellStartMetadata() = tellMetadata(metadataKeyValues)
 
   /**
     * Fire and forget info to the metadata service
@@ -457,59 +449,32 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
     serviceRegistryActor.putMetadata(jobDescriptor.workflowDescriptor.id, Option(jobDescriptor.key), metadataKeyValues)
   }
 
-  private def customLookupFunction(alreadyGeneratedOutputs: Map[String, WdlValue])(toBeLookedUp: String): WdlValue = alreadyGeneratedOutputs.getOrElse(toBeLookedUp, lookup(toBeLookedUp))
-
-  private[jes] def wdlValueToGcsPath(jesOutputs: Seq[JesFileOutput])(value: WdlValue): WdlValue = {
+  private[jes] def wdlValueToGcsPath(jesOutputs: Set[JesFileOutput])(value: WdlValue): WdlValue = {
     def toGcsPath(wdlFile: WdlFile) = jesOutputs collectFirst {
       case o if o.name == makeSafeJesReferenceName(wdlFile.valueString) => WdlFile(o.gcs)
     } getOrElse value
+
     value match {
       case wdlArray: WdlArray => wdlArray map wdlValueToGcsPath(jesOutputs)
       case wdlMap: WdlMap => wdlMap map {
         case (k, v) => wdlValueToGcsPath(jesOutputs)(k) -> wdlValueToGcsPath(jesOutputs)(v)
       }
-      case file: WdlFile => if (file.value.isGcsUrl) file else toGcsPath(file)
+      case file: WdlFile => toGcsPath(file)
       case other => other
     }
   }
 
-  private def outputLookup(taskOutput: TaskOutput, currentList: Seq[AttemptedLookupResult]) = for {
-  /**
-    * This will evaluate the task output expression and coerces it to the task output's type.
-    * If the result is a WdlFile, then attempt to find the JesOutput with the same path and
-    * return a WdlFile that represents the GCS path and not the local path.  For example,
-    *
-    * <pre>
-    * output {
-    *   File x = "out" + ".txt"
-    * }
-    * </pre>
-    *
-    * "out" + ".txt" is evaluated to WdlString("out.txt") and then coerced into a WdlFile("out.txt")
-    * Then, via wdlFileToGcsPath(), we attempt to find the JesOutput with .name == "out.txt".
-    * If it is found, then WdlFile("gs://some_bucket/out.txt") will be returned.
-    */
-    wdlValue <- taskOutput.requiredExpression.evaluate(customLookupFunction(currentList.toLookupMap), callEngineFunctions)
-    coercedValue <- taskOutput.wdlType.coerceRawValue(wdlValue)
-    value = wdlValueToGcsPath(generateJesOutputs(jobDescriptor))(coercedValue)
-  } yield value
+  private def postProcess: Try[CallOutputs] = {
+    def wdlValueToSuccess(value: WdlValue): Try[WdlValue] = Success(value)
 
-
-  private def outputFoldingFunction: (Seq[AttemptedLookupResult], TaskOutput) => Seq[AttemptedLookupResult] = {
-    (currentList: Seq[AttemptedLookupResult], taskOutput: TaskOutput) => {
-      currentList ++ Seq(AttemptedLookupResult(taskOutput.name, outputLookup(taskOutput, currentList)))
-    }
-  }
-
-  private def postProcess: Try[JobOutputs] = {
-    val outputs = call.task.outputs
-    val outputMappings = outputs.foldLeft(Seq.empty[AttemptedLookupResult])(outputFoldingFunction).map(_.toPair).toMap
-    TryUtil.sequenceMap(outputMappings) map { outputMap =>
-      outputMap mapValues { v => JobOutput(v) }
-    }
+    OutputEvaluator.evaluateOutputs(
+      jobDescriptor,
+      callEngineFunctions,
+      (wdlValueToSuccess _).compose(wdlValueToGcsPath(generateJesOutputs(jobDescriptor)))
+    )
   }
 
-  private def handleSuccess(outputMappings: Try[JobOutputs], returnCode: Int, jobDetritusFiles: Map[String, String], executionHandle: ExecutionHandle, events: Seq[ExecutionEvent]): ExecutionHandle = {
+  private def handleSuccess(outputMappings: Try[CallOutputs], returnCode: Int, jobDetritusFiles: Map[String, Path], executionHandle: ExecutionHandle, events: Seq[ExecutionEvent]): ExecutionHandle = {
     outputMappings match {
       case Success(outputs) => SuccessfulExecutionHandle(outputs, returnCode, jobDetritusFiles, events)
       case Failure(ex: CromwellAggregatedException) if ex.throwables collectFirst { case s: SocketTimeoutException => s } isDefined =>
@@ -588,10 +553,10 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
           FailedNonRetryableExecutionHandle(new RuntimeException(
             s"execution failed: could not parse return code as integer: ${returnCodeContents.get}")).future
         case _: RunStatus.Success if !continueOnReturnCode.continueFor(returnCode.get) =>
-          val badReturnCodeMessage = s"Call ${call.fullyQualifiedName}: return code was ${returnCode.getOrElse("(none)")}"
+          val badReturnCodeMessage = s"Call ${jobDescriptor.key.tag}: return code was ${returnCode.getOrElse("(none)")}"
           FailedNonRetryableExecutionHandle(new RuntimeException(badReturnCodeMessage), returnCode.toOption).future
         case success: RunStatus.Success =>
-          handleSuccess(postProcess, returnCode.get, jesCallPaths.detritusPaths.mapValues(_.toString), handle, success.eventList).future
+          handleSuccess(postProcess, returnCode.get, jesCallPaths.detritusPaths, handle, success.eventList).future
         case RunStatus.Failed(errorCode, errorMessage, _, _, _, _) => handleFailure(errorCode, errorMessage)
       }
     } catch {
@@ -611,8 +576,8 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
     * @param gcsPath The input path
     * @return A path which is unique per input path
     */
-  private def localFilePathFromCloudStoragePath(mountPoint: Path, gcsPath: NioGcsPath): Path = {
-    mountPoint.resolve(gcsPath.bucket).resolve(gcsPath.objectName)
+  private def localFilePathFromCloudStoragePath(mountPoint: Path, gcsPath: CloudStoragePath): Path = {
+    mountPoint.resolve(gcsPath.bucket()).resolve(gcsPath.toUri.getPath.stripPrefix("/"))
   }
 
   /**
@@ -625,11 +590,14 @@ class JesAsyncBackendJobExecutionActor(override val jobDescriptor: BackendJobDes
   private[jes] def gcsPathToLocal(wdlValue: WdlValue): WdlValue = {
     wdlValue match {
       case wdlFile: WdlFile =>
-        Try(getPath(wdlFile.valueString)) match {
-          case Success(gcsPath: NioGcsPath) =>
+        getPath(wdlFile.valueString) match {
+          case Success(gcsPath: CloudStoragePath) =>
             WdlFile(localFilePathFromCloudStoragePath(workingDisk.mountPoint, gcsPath).toString, wdlFile.isGlob)
-          case Success(otherPath) => wdlValue
-          case Failure(e) => wdlValue
+          case Success(proxy: PathProxy) =>
+            proxy.unbox(classOf[CloudStoragePath]) map { gcsPath =>
+              WdlFile(localFilePathFromCloudStoragePath(workingDisk.mountPoint, gcsPath).toString, wdlFile.isGlob)
+            } getOrElse wdlValue
+          case _ => wdlValue
         }
       case wdlArray: WdlArray => wdlArray map gcsPathToLocal
       case wdlMap: WdlMap => wdlMap map { case (k, v) => gcsPathToLocal(k) -> gcsPathToLocal(v) }
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesAttributes.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesAttributes.scala
index 2e1d00b0e43..ac2475e6430 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesAttributes.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesAttributes.scala
@@ -6,30 +6,29 @@ import cats.data._
 import cats.data.Validated._
 import cats.syntax.cartesian._
 import com.typesafe.config.Config
-import cromwell.backend.impl.jes.JesImplicits.GoogleAuthWorkflowOptions
-import cromwell.core.WorkflowOptions
-import cromwell.filesystems.gcs.{GoogleAuthMode, GoogleConfiguration}
+import cromwell.backend.impl.jes.authentication.JesAuths
+import cromwell.core.ErrorOr._
+import cromwell.filesystems.gcs.GoogleConfiguration
 import lenthall.config.ValidatedConfig._
 import net.ceedubs.ficus.Ficus._
-import cromwell.core.ErrorOr._
 import wdl4s.ExceptionWithErrors
 
 case class JesAttributes(project: String,
-                         genomicsAuth: GoogleAuthMode,
-                         gcsFilesystemAuth: GoogleAuthMode,
+                         computeServiceAccount: String,
+                         auths: JesAuths,
                          executionBucket: String,
                          endpointUrl: URL,
-                         maxPollingInterval: Int) {
-  def genomicsCredential(options: WorkflowOptions) = genomicsAuth.credential(options.toGoogleAuthOptions)
-  def gcsCredential(options: WorkflowOptions) = gcsFilesystemAuth.credential(options.toGoogleAuthOptions)
-}
+                         maxPollingInterval: Int,
+                         qps: Int)
 
 object JesAttributes {
+  val GenomicsApiDefaultQps = 1000
 
   private val jesKeys = Set(
     "project",
     "root",
     "maximum-polling-interval",
+    "compute-service-account",
     "dockerhub",
     "genomics",
     "filesystems",
@@ -47,14 +46,17 @@ object JesAttributes {
     val executionBucket: ValidatedNel[String, String] = backendConfig.validateString("root")
     val endpointUrl: ErrorOr[URL] = backendConfig.validateURL("genomics.endpoint-url")
     val maxPollingInterval: Int = backendConfig.as[Option[Int]]("maximum-polling-interval").getOrElse(600)
+    val computeServiceAccount: String = backendConfig.as[Option[String]]("genomics.compute-service-account").getOrElse("default")
     val genomicsAuthName: ErrorOr[String] = backendConfig.validateString("genomics.auth")
     val gcsFilesystemAuthName: ErrorOr[String] = backendConfig.validateString("filesystems.gcs.auth")
 
+    val qps = backendConfig.as[Option[Int]]("genomics-api-queries-per-100-seconds").getOrElse(GenomicsApiDefaultQps) / 100
+
     (project |@| executionBucket |@| endpointUrl |@| genomicsAuthName |@| gcsFilesystemAuthName) map {
       (_, _, _, _, _)
     } flatMap { case (p, b, u, genomicsName, gcsName) =>
       (googleConfig.auth(genomicsName) |@| googleConfig.auth(gcsName)) map { case (genomicsAuth, gcsAuth) =>
-        JesAttributes(p, genomicsAuth, gcsAuth, b, u, maxPollingInterval)
+        JesAttributes(p, computeServiceAccount, JesAuths(genomicsAuth, gcsAuth), b, u, maxPollingInterval, qps)
       }
     } match {
       case Valid(r) => r
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesBackendLifecycleActorFactory.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesBackendLifecycleActorFactory.scala
index 92f653c1079..f61769379d6 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesBackendLifecycleActorFactory.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesBackendLifecycleActorFactory.scala
@@ -8,9 +8,9 @@ import cromwell.backend._
 import cromwell.backend.callcaching.FileHashingActor.FileHashingFunction
 import cromwell.backend.impl.jes.callcaching.JesBackendFileHashing
 import cromwell.backend.validation.RuntimeAttributesKeys
+import cromwell.core.CallOutputs
 import cromwell.core.Dispatcher.BackendDispatcher
-import cromwell.core.{ExecutionStore, OutputStore}
-import wdl4s.Call
+import wdl4s.TaskCall
 import wdl4s.expression.WdlStandardLibraryFunctions
 
 
@@ -21,7 +21,7 @@ case class JesBackendLifecycleActorFactory(name: String, configurationDescriptor
   val jesConfiguration = new JesConfiguration(configurationDescriptor)
 
   override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                                calls: Seq[Call],
+                                                calls: Set[TaskCall],
                                                 serviceRegistryActor: ActorRef): Option[Props] = {
     Option(JesInitializationActor.props(workflowDescriptor, calls, jesConfiguration, serviceRegistryActor).withDispatcher(BackendDispatcher))
   }
@@ -46,15 +46,15 @@ case class JesBackendLifecycleActorFactory(name: String, configurationDescriptor
   }
 
   override def workflowFinalizationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                              calls: Seq[Call],
-                                              executionStore: ExecutionStore,
-                                              outputStore: OutputStore,
+                                              calls: Set[TaskCall],
+                                              jobExecutionMap: JobExecutionMap,
+                                              workflowOutputs: CallOutputs,
                                               initializationData: Option[BackendInitializationData]) = {
     // The `JesInitializationActor` will only return a non-`Empty` `JesBackendInitializationData` from a successful `beforeAll`
     // invocation.  HOWEVER, the finalization actor is created regardless of whether workflow initialization was successful
     // or not.  So the finalization actor must be able to handle an empty `JesBackendInitializationData` option, and there is no
     // `.get` on the initialization data as there is with the execution or cache hit copying actor methods.
-    Option(JesFinalizationActor.props(workflowDescriptor, calls, jesConfiguration, executionStore, outputStore, initializationData.toJes).withDispatcher(BackendDispatcher))
+    Option(JesFinalizationActor.props(workflowDescriptor, calls, jesConfiguration, jobExecutionMap, workflowOutputs, initializationData.toJes).withDispatcher(BackendDispatcher))
   }
 
   override def runtimeAttributeDefinitions(initializationDataOption: Option[BackendInitializationData]) = staticRuntimeAttributeDefinitions
@@ -63,16 +63,21 @@ case class JesBackendLifecycleActorFactory(name: String, configurationDescriptor
                                            jobKey: BackendJobDescriptorKey,
                                            initializationData: Option[BackendInitializationData]): WdlStandardLibraryFunctions = {
 
-    val jesCallPaths = initializationData.toJes.get.workflowPaths.toJesCallPaths(jobKey)
-    new JesExpressionFunctions(List(jesCallPaths.gcsFileSystem), jesCallPaths.callContext)
+    val jesCallPaths = initializationData.toJes.get.workflowPaths.toJobPaths(jobKey)
+    new JesExpressionFunctions(List(jesCallPaths.gcsPathBuilder), jesCallPaths.callContext)
   }
 
   override def getExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor, backendConfig: Config,
                                     initializationData: Option[BackendInitializationData]): Path = {
-    initializationData.toJes.get.workflowPaths.rootPath
+    initializationData.toJes.get.workflowPaths.executionRoot
   }
 
-  override def backendSingletonActorProps = Option(JesBackendSingletonActor.props())
+  override def getWorkflowExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor, backendConfig: Config,
+                                    initializationData: Option[BackendInitializationData]): Path = {
+    initializationData.toJes.get.workflowPaths.workflowRoot
+  }
+
+  override def backendSingletonActorProps = Option(JesBackendSingletonActor.props(jesConfiguration.qps))
 
   override lazy val fileHashingFunction: Option[FileHashingFunction] = Option(FileHashingFunction(JesBackendFileHashing.getCrc32c))
 }
@@ -86,8 +91,8 @@ object JesBackendLifecycleActorFactory {
   }
 
   val staticRuntimeAttributeDefinitions = {
-    import RuntimeAttributesKeys._
     import JesRuntimeAttributes._
+    import RuntimeAttributesKeys._
 
     Set(
       RuntimeAttributeDefinition(DockerKey, None, usedInCallCaching = true),
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesBackendSingletonActor.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesBackendSingletonActor.scala
index 3b830107a1e..5c1275ae149 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesBackendSingletonActor.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesBackendSingletonActor.scala
@@ -1,12 +1,12 @@
 package cromwell.backend.impl.jes
 
 import akka.actor.{Actor, ActorLogging, Props}
-import cromwell.backend.impl.jes.statuspolling.{JesApiQueryManager}
+import cromwell.backend.impl.jes.statuspolling.JesApiQueryManager
 import cromwell.backend.impl.jes.statuspolling.JesApiQueryManager.DoPoll
 
-class JesBackendSingletonActor extends Actor with ActorLogging {
+final case class JesBackendSingletonActor(qps: Int) extends Actor with ActorLogging {
 
-  val pollingActor = context.actorOf(JesApiQueryManager.props)
+  val pollingActor = context.actorOf(JesApiQueryManager.props(qps))
 
   override def receive = {
     case poll: DoPoll =>
@@ -16,5 +16,5 @@ class JesBackendSingletonActor extends Actor with ActorLogging {
 }
 
 object JesBackendSingletonActor {
-  def props(): Props = Props(new JesBackendSingletonActor())
+  def props(qps: Int): Props = Props(JesBackendSingletonActor(qps))
 }
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesCacheHitCopyingActor.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesCacheHitCopyingActor.scala
index 078e2e081f4..a77dd66c7f6 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesCacheHitCopyingActor.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesCacheHitCopyingActor.scala
@@ -5,7 +5,7 @@ import java.nio.file.Path
 import akka.actor.{ActorRef, Props}
 import cromwell.backend.callcaching.CacheHitDuplicating
 import cromwell.backend.{BackendCacheHitCopyingActor, BackendJobDescriptor}
-import cromwell.core.PathCopier
+import cromwell.core.path.PathCopier
 import cromwell.core.logging.JobLogging
 
 case class JesCacheHitCopyingActor(override val jobDescriptor: BackendJobDescriptor,
@@ -15,9 +15,11 @@ case class JesCacheHitCopyingActor(override val jobDescriptor: BackendJobDescrip
   extends BackendCacheHitCopyingActor with CacheHitDuplicating with JesJobCachingActorHelper with JobLogging {
   override protected def duplicate(source: Path, destination: Path) = PathCopier.copy(source, destination).get
 
-  override protected def destinationCallRootPath = jesCallPaths.callRootPath
+  override protected def destinationCallRootPath = jesCallPaths.callExecutionRoot
 
   override protected def destinationJobDetritusPaths = jesCallPaths.detritusPaths
+  
+  override val workflowDescriptor = jobDescriptor.workflowDescriptor
 }
 
 object JesCacheHitCopyingActor {
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesCallPaths.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesCallPaths.scala
deleted file mode 100644
index f18daecaa5c..00000000000
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesCallPaths.scala
+++ /dev/null
@@ -1,82 +0,0 @@
-package cromwell.backend.impl.jes
-
-import java.nio.file.Path
-
-import cromwell.backend.impl.jes.authentication.JesCredentials
-import cromwell.backend.io.JobPaths
-import cromwell.backend.io.JobPaths._
-import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
-import cromwell.core.CallContext
-import cromwell.services.metadata.CallMetadataKeys
-
-import scala.concurrent.ExecutionContext
-
-object JesCallPaths {
-  def apply(jobKey: BackendJobDescriptorKey, workflowDescriptor: BackendWorkflowDescriptor,
-            jesConfiguration: JesConfiguration,
-            credentials: JesCredentials)(implicit ec: ExecutionContext): JesCallPaths = {
-    new JesCallPaths(jobKey, workflowDescriptor, jesConfiguration, credentials)
-  }
-
-  val JesLogPathKey = "jesLog"
-  val GcsExecPathKey = "gcsExec"
-}
-
-class JesCallPaths(jobKey: BackendJobDescriptorKey, workflowDescriptor: BackendWorkflowDescriptor,
-                   jesConfiguration: JesConfiguration,
-                   credentials: JesCredentials)(implicit ec: ExecutionContext) extends
-  JesWorkflowPaths(workflowDescriptor, jesConfiguration, credentials)(ec) {
-
-  val jesLogBasename = {
-    val index = jobKey.index.map(s => s"-$s").getOrElse("")
-    s"${jobKey.scope.unqualifiedName}$index"
-  }
-
-  val callRootPath: Path = {
-    val callName = jobKey.call.fullyQualifiedName.split('.').last
-    val call = s"$CallPrefix-$callName"
-    val shard = jobKey.index map { s => s"$ShardPrefix-$s" } getOrElse ""
-    val retry = if (jobKey.attempt > 1) s"$AttemptPrefix-${jobKey.attempt}" else ""
-
-    List(call, shard, retry).foldLeft(workflowRootPath)((path, dir) => path.resolve(dir))
-  }
-
-  val returnCodeFilename: String = s"$jesLogBasename-rc.txt"
-  val stdoutFilename: String = s"$jesLogBasename-stdout.log"
-  val stderrFilename: String = s"$jesLogBasename-stderr.log"
-  val jesLogFilename: String = s"$jesLogBasename.log"
-  val gcsExecFilename: String = "exec.sh"
-
-  lazy val returnCodePath: Path = callRootPath.resolve(returnCodeFilename)
-  lazy val stdoutPath: Path = callRootPath.resolve(stdoutFilename)
-  lazy val stderrPath: Path = callRootPath.resolve(stderrFilename)
-  lazy val jesLogPath: Path = callRootPath.resolve(jesLogFilename)
-  lazy val gcsExecPath: Path = callRootPath.resolve(gcsExecFilename)
-  lazy val callContext = CallContext(callRootPath, stdoutFilename, stderrFilename)
-
-  /*
-  TODO: Move various monitoring files path generation here.
-
-  "/cromwell_root" is a well known path, called in the regular JobPaths callDockerRoot.
-  This JesCallPaths should know about that root, and be able to create the monitoring file paths.
-  Instead of the AsyncActor creating the paths, the paths could then be shared with the CachingActor.
-
-  Those monitoring paths could then be returned by metadataFiles and detritusFiles.
-   */
-
-  lazy val metadataPaths: Map[String, Path] = Map(
-    CallMetadataKeys.CallRoot -> callRootPath,
-    CallMetadataKeys.Stdout -> stdoutPath,
-    CallMetadataKeys.Stderr -> stderrPath,
-    CallMetadataKeys.BackendLogsPrefix + ":log" -> jesLogPath
-  )
-
-  lazy val detritusPaths: Map[String, Path] = Map(
-    JobPaths.CallRootPathKey -> callRootPath,
-    JesCallPaths.GcsExecPathKey -> gcsExecPath,
-    JesCallPaths.JesLogPathKey -> jesLogPath,
-    JobPaths.StdoutPathKey -> stdoutPath,
-    JobPaths.StdErrPathKey -> stderrPath,
-    JobPaths.ReturnCodePathKey -> returnCodePath
-  )
-}
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesConfiguration.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesConfiguration.scala
index 6657250b081..20ec8130d9b 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesConfiguration.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesConfiguration.scala
@@ -2,14 +2,36 @@ package cromwell.backend.impl.jes
 
 import cromwell.backend.BackendConfigurationDescriptor
 import cromwell.backend.impl.jes.authentication.JesDockerCredentials
+import cromwell.backend.impl.jes.io._
 import cromwell.core.DockerConfiguration
-import cromwell.filesystems.gcs.GoogleConfiguration
+import cromwell.core.path.CustomRetryParams
+import cromwell.core.retry.SimpleExponentialBackoff
+import cromwell.filesystems.gcs.{GoogleConfiguration, RetryableGcsPathBuilderFactory}
+
+import scala.concurrent.duration._
+import scala.language.postfixOps
+
+object JesConfiguration {
+  val GcsRetryParams = CustomRetryParams(
+    timeout = Duration.Inf,
+    maxRetries = Option(3),
+    backoff = SimpleExponentialBackoff(1 seconds, 3 seconds, 1.5D),
+    isTransient = isTransientJesException,
+    isFatal = isFatalJesException
+  )
+}
 
 class JesConfiguration(val configurationDescriptor: BackendConfigurationDescriptor) {
 
+  private val googleConfig = GoogleConfiguration(configurationDescriptor.globalConfig)
+
   val root = configurationDescriptor.backendConfig.getString("root")
-  val googleConfig = GoogleConfiguration(configurationDescriptor.globalConfig)
   val jesAttributes = JesAttributes(googleConfig, configurationDescriptor.backendConfig)
+  val jesAuths = jesAttributes.auths
+  val jesComputeServiceAccount = jesAttributes.computeServiceAccount
+  val gcsPathBuilderFactory = RetryableGcsPathBuilderFactory(jesAuths.gcs, customRetryParams = JesConfiguration.GcsRetryParams)
+  val genomicsFactory = GenomicsFactory(googleConfig.applicationName, jesAuths.genomics, jesAttributes.endpointUrl)
   val dockerCredentials = DockerConfiguration.build(configurationDescriptor.backendConfig).dockerCredentials map JesDockerCredentials.apply
-  val needAuthFileUpload = jesAttributes.gcsFilesystemAuth.requiresAuthFile || dockerCredentials.isDefined
+  val needAuthFileUpload = jesAuths.gcs.requiresAuthFile || dockerCredentials.isDefined
+  val qps = jesAttributes.qps
 }
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesExpressionFunctions.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesExpressionFunctions.scala
index 823108ca81f..bf29a387fdb 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesExpressionFunctions.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesExpressionFunctions.scala
@@ -1,42 +1,38 @@
 package cromwell.backend.impl.jes
 
-import java.nio.file.{FileSystem, Path}
+import java.nio.file.{Files, Path}
 
-import better.files._
-import cromwell.backend.wdl.{PureFunctions, ReadLikeFunctions, WriteFunctions}
-import cromwell.backend.impl.jes.JesImplicits.PathString
+import cromwell.backend.wdl.{ReadLikeFunctions, WriteFunctions}
 import cromwell.core.CallContext
-import cromwell.filesystems.gcs.GcsFileSystem
-import wdl4s.expression.WdlStandardLibraryFunctions
+import cromwell.core.path.PathBuilder
+import cromwell.filesystems.gcs.GcsPathBuilder
+import wdl4s.expression.{PureStandardLibraryFunctionsLike, WdlStandardLibraryFunctions}
 import wdl4s.values._
 
-import scala.language.postfixOps
+import scala.collection.JavaConverters._
 import scala.util.{Success, Try}
 
-class JesExpressionFunctions(override val fileSystems: List[FileSystem],
-                             context: CallContext
-                             ) extends WdlStandardLibraryFunctions with PureFunctions with ReadLikeFunctions with WriteFunctions {
-  import JesExpressionFunctions.EnhancedPath
+class JesExpressionFunctions(override val pathBuilders: List[PathBuilder], context: CallContext)
+  extends WdlStandardLibraryFunctions with PureStandardLibraryFunctionsLike with ReadLikeFunctions with WriteFunctions {
 
-  private def globDirectory(glob: String): String = s"glob-${glob.md5Sum}/"
+  override def writeTempFile(path: String, prefix: String, suffix: String, content: String): String = super[WriteFunctions].writeTempFile(path, prefix, suffix, content)
+  private[jes] def globDirectory(glob: String): String = globName(glob) + "/"
+  private[jes] def globName(glob: String) = s"glob-${glob.md5Sum}"
 
   override def globPath(glob: String): String = context.root.resolve(globDirectory(glob)).toString
 
   override def glob(path: String, pattern: String): Seq[String] = {
-    File(path.toAbsolutePath(fileSystems).asDirectory).
-      glob("**/*") map { _.pathAsString } filterNot { _.toString == path } toSeq
+    val name = globName(pattern)
+    val listFile = context.root.resolve(s"$name.list").toRealPath()
+    Files.readAllLines(listFile).asScala map { fileName => context.root.resolve(s"$name/$fileName").toUri.toString }
   }
 
-  override def preMapping(str: String): String = if (!GcsFileSystem.isAbsoluteGcsPath(str)) context.root.resolve(str).toString else str
+  override def preMapping(str: String): String = if (!GcsPathBuilder.isValidGcsUrl(str)) {
+    context.root.resolve(str.stripPrefix("/")).toUri.toString
+  } else str
 
   override def stdout(params: Seq[Try[WdlValue]]) = Success(WdlFile(context.stdout))
   override def stderr(params: Seq[Try[WdlValue]]) = Success(WdlFile(context.stderr))
 
   override val writeDirectory: Path = context.root
 }
-
-object JesExpressionFunctions {
-  implicit class EnhancedPath(val path: Path) extends AnyVal {
-    def asDirectory = path.toString.toDirectory(path.getFileSystem)
-  }
-}
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesFinalizationActor.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesFinalizationActor.scala
index 038c615ddfd..fc2d141bebf 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesFinalizationActor.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesFinalizationActor.scala
@@ -6,25 +6,26 @@ import akka.actor.Props
 import better.files._
 import cats.instances.future._
 import cats.syntax.functor._
-import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor, BackendWorkflowFinalizationActor}
+import cromwell.backend.{BackendWorkflowDescriptor, BackendWorkflowFinalizationActor, JobExecutionMap}
+import cromwell.core.CallOutputs
 import cromwell.core.Dispatcher.IoDispatcher
-import cromwell.core.{ExecutionStore, OutputStore, PathCopier}
-import wdl4s.Call
+import cromwell.core.path.PathCopier
+import wdl4s.TaskCall
 
 import scala.concurrent.Future
 import scala.language.postfixOps
 
 object JesFinalizationActor {
-  def props(workflowDescriptor: BackendWorkflowDescriptor, calls: Seq[Call], jesConfiguration: JesConfiguration,
-            executionStore: ExecutionStore, outputStore: OutputStore, initializationData: Option[JesBackendInitializationData]) = {
-    Props(new JesFinalizationActor(workflowDescriptor, calls, jesConfiguration, executionStore, outputStore, initializationData))
+  def props(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[TaskCall], jesConfiguration: JesConfiguration,
+            jobExecutionMap: JobExecutionMap, workflowOutputs: CallOutputs, initializationData: Option[JesBackendInitializationData]) = {
+    Props(new JesFinalizationActor(workflowDescriptor, calls, jesConfiguration, jobExecutionMap, workflowOutputs, initializationData))
   }
 }
 
 class JesFinalizationActor (override val workflowDescriptor: BackendWorkflowDescriptor,
-                            override val calls: Seq[Call],
-                            jesConfiguration: JesConfiguration, executionStore: ExecutionStore,
-                            outputStore: OutputStore,
+                            override val calls: Set[TaskCall],
+                            jesConfiguration: JesConfiguration, jobExecutionMap: JobExecutionMap,
+                            workflowOutputs: CallOutputs,
                             initializationData: Option[JesBackendInitializationData]) extends BackendWorkflowFinalizationActor {
 
   override val configurationDescriptor = jesConfiguration.configurationDescriptor
@@ -68,19 +69,19 @@ class JesFinalizationActor (override val workflowDescriptor: BackendWorkflowDesc
   }
 
   private lazy val logPaths: Seq[Path] = {
-    val allCallPaths = executionStore.store.toSeq collect {
-      case (backendJobDescriptorKey: BackendJobDescriptorKey, _) =>
-        initializationData map { _.workflowPaths.toJesCallPaths(backendJobDescriptorKey) }
+    val allCallPaths = jobExecutionMap flatMap {
+      case (backendJobDescriptor, keys) =>
+        keys map { JesWorkflowPaths(backendJobDescriptor, jesConfiguration)(context.system).toJobPaths(_) }
     }
 
-    allCallPaths.flatten flatMap { callPaths =>
-      Seq(callPaths.stdoutPath, callPaths.stderrPath, callPaths.jesLogPath)
+    allCallPaths.toSeq flatMap { callPaths =>
+      Seq(callPaths.stdout, callPaths.stderr, callPaths.jesLogPath)
     }
   }
 
   private def copyLogs(callLogsDirPath: Path, logPaths: Seq[Path]): Unit = {
     workflowPaths match {
-      case Some(paths) => logPaths.foreach(PathCopier.copy(paths.rootPath, _, callLogsDirPath))
+      case Some(paths) => logPaths.foreach(PathCopier.copy(paths.executionRoot, _, callLogsDirPath))
       case None =>
     }
   }
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesImplicits.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesImplicits.scala
deleted file mode 100644
index 6c722c756a9..00000000000
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesImplicits.scala
+++ /dev/null
@@ -1,41 +0,0 @@
-package cromwell.backend.impl.jes
-
-import java.nio.file.{FileSystem, Path}
-
-import cromwell.core.{PathFactory, WorkflowOptions}
-import cromwell.filesystems.gcs.GoogleAuthMode.GoogleAuthOptions
-import cromwell.filesystems.gcs.{GcsFileSystem, GoogleAuthMode}
-
-import scala.util.Try
-
-object JesImplicits {
-  implicit class GoogleAuthWorkflowOptions(val workflowOptions: WorkflowOptions) extends AnyVal {
-    def toGoogleAuthOptions: GoogleAuthMode.GoogleAuthOptions = new GoogleAuthOptions {
-      override def get(key: String): Try[String] = workflowOptions.get(key)
-    }
-  }
-
-  object PathBuilder extends PathFactory
-
-  implicit class PathString(val str: String) extends AnyVal {
-    def isGcsUrl: Boolean = str.startsWith("gs://")
-    def isUriWithProtocol: Boolean = "^[a-z]+://".r.findFirstIn(str).nonEmpty
-
-    def toPath(fss: List[FileSystem]): Path = PathBuilder.buildPath(str, fss)
-    def toPath(fs: FileSystem): Path = str.toPath(List(fs))
-
-    def toAbsolutePath(fss: List[FileSystem]): Path = str.toPath(fss).toAbsolutePath
-    def toAbsolutePath(fs: FileSystem): Path = str.toAbsolutePath(List(fs))
-
-    def toDirectory(fss: List[FileSystem]): Path = buildPathAsDirectory(str, fss)
-    def toDirectory(fs: FileSystem): Path = str.toDirectory(List(fs))
-
-    // TODO this needs to go away because it's gcs specific. Replacing gcs FS with google implementation (when available) will take care of it
-    private def buildPathAsDirectory(rawString: String, fileSystems: List[FileSystem]): Path = {
-      PathBuilder.findFileSystem(rawString, fileSystems, {
-        case fs: GcsFileSystem => Try(fs.getPathAsDirectory(rawString))
-        case fs => Try(fs.getPath(rawString))
-      })
-    }
-  }
-}
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesInitializationActor.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesInitializationActor.scala
index e76a62e9da3..03cae0dff30 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesInitializationActor.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesInitializationActor.scala
@@ -7,21 +7,20 @@ import cats.instances.future._
 import cats.syntax.functor._
 import com.google.api.services.genomics.Genomics
 import cromwell.backend.impl.jes.JesInitializationActor._
-import cromwell.backend.impl.jes.authentication.{GcsLocalizing, JesAuthInformation, JesCredentials}
+import cromwell.backend.impl.jes.authentication.{GcsLocalizing, JesAuthInformation}
 import cromwell.backend.impl.jes.io._
 import cromwell.backend.validation.RuntimeAttributesDefault
 import cromwell.backend.validation.RuntimeAttributesKeys._
 import cromwell.backend.{BackendInitializationData, BackendWorkflowDescriptor, BackendWorkflowInitializationActor}
-import cromwell.core.Dispatcher.IoDispatcher
 import cromwell.core.WorkflowOptions
-import cromwell.core.retry.Retry
-import cromwell.filesystems.gcs.{ClientSecrets, GoogleAuthMode}
+import cromwell.filesystems.gcs.auth.{ClientSecrets, GoogleAuthMode}
 import spray.json.JsObject
-import wdl4s.Call
+import wdl4s.TaskCall
 import wdl4s.types.{WdlBooleanType, WdlFloatType, WdlIntegerType, WdlStringType}
 import wdl4s.values.WdlValue
 
 import scala.concurrent.Future
+import scala.language.postfixOps
 import scala.util.Try
 
 object JesInitializationActor {
@@ -29,14 +28,14 @@ object JesInitializationActor {
     JesRuntimeAttributes.PreemptibleKey, JesRuntimeAttributes.BootDiskSizeKey, JesRuntimeAttributes.DisksKey)
 
   def props(workflowDescriptor: BackendWorkflowDescriptor,
-            calls: Seq[Call],
+            calls: Set[TaskCall],
             jesConfiguration: JesConfiguration,
             serviceRegistryActor: ActorRef): Props =
     Props(new JesInitializationActor(workflowDescriptor, calls, jesConfiguration, serviceRegistryActor: ActorRef))
 }
 
 class JesInitializationActor(override val workflowDescriptor: BackendWorkflowDescriptor,
-                             override val calls: Seq[Call],
+                             override val calls: Set[TaskCall],
                              private[jes] val jesConfiguration: JesConfiguration,
                              override val serviceRegistryActor: ActorRef)
   extends BackendWorkflowInitializationActor {
@@ -58,14 +57,11 @@ class JesInitializationActor(override val workflowDescriptor: BackendWorkflowDes
 
   private[jes] lazy val refreshTokenAuth: Option[JesAuthInformation] = {
     for {
-      clientSecrets <- List(jesConfiguration.jesAttributes.gcsFilesystemAuth) collectFirst { case s: ClientSecrets => s }
+      clientSecrets <- List(jesConfiguration.jesAttributes.auths.gcs) collectFirst { case s: ClientSecrets => s }
       token <- workflowDescriptor.workflowOptions.get(GoogleAuthMode.RefreshTokenOptionKey).toOption
     } yield GcsLocalizing(clientSecrets, token)
   }
 
-  private val iOExecutionContext = context.system.dispatchers.lookup(IoDispatcher)
-
-
   override protected def coerceDefaultRuntimeAttributes(options: WorkflowOptions): Try[Map[String, WdlValue]] = {
     RuntimeAttributesDefault.workflowOptionsDefault(options, JesRuntimeAttributes.coercionMap)
   }
@@ -75,32 +71,25 @@ class JesInitializationActor(override val workflowDescriptor: BackendWorkflowDes
     */
   override def beforeAll(): Future[Option[BackendInitializationData]] = {
 
-    val genomicsCredential = jesConfiguration.jesAttributes.genomicsCredential(workflowDescriptor.workflowOptions)
-    val gcsCredential = jesConfiguration.jesAttributes.gcsCredential(workflowDescriptor.workflowOptions)
-
-    val jesCredentials = JesCredentials(genomicsCredential = genomicsCredential, gcsCredential = gcsCredential)
     def buildGenomics: Future[Genomics] = Future {
-      GenomicsFactory(jesConfiguration.googleConfig.applicationName, genomicsCredential, jesConfiguration.jesAttributes.endpointUrl)
+      jesConfiguration.genomicsFactory.withOptions(workflowDescriptor.workflowOptions)
     }
 
     for {
-      // generate single filesystem and genomics instances
       genomics <- buildGenomics
-      workflowPaths = new JesWorkflowPaths(workflowDescriptor, jesConfiguration, jesCredentials)(iOExecutionContext)
+      workflowPaths = new JesWorkflowPaths(workflowDescriptor, jesConfiguration)(context.system)
       _ <- if (jesConfiguration.needAuthFileUpload) writeAuthenticationFile(workflowPaths) else Future.successful(())
-      _ = publishWorkflowRoot(workflowPaths.workflowRootPath.toString)
+      _ = publishWorkflowRoot(workflowPaths.workflowRoot.toString)
     } yield Option(JesBackendInitializationData(workflowPaths, genomics))
   }
 
   private def writeAuthenticationFile(workflowPath: JesWorkflowPaths): Future[Unit] = {
     generateAuthJson(jesConfiguration.dockerCredentials, refreshTokenAuth) map { content =>
       val path = workflowPath.gcsAuthFilePath
-      val upload = () => Future(path.writeAsJson(content))
-
-      workflowLogger.info(s"Creating authentication file for workflow ${workflowDescriptor.id} at \n ${path.toString}")
-      Retry.withRetry(upload, isFatal = isFatalJesException, isTransient = isTransientJesException)(context.system).void.recoverWith {
+      workflowLogger.info(s"Creating authentication file for workflow ${workflowDescriptor.id} at \n ${path.toUri}")
+      Future(path.writeAsJson(content)).void.recoverWith {
         case failure => Future.failed(new IOException("Failed to upload authentication file", failure))
-      }
+      } void
     } getOrElse Future.successful(())
   }
 
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobCachingActorHelper.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobCachingActorHelper.scala
index 4ded3e9d14b..fe39df8402a 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobCachingActorHelper.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobCachingActorHelper.scala
@@ -4,12 +4,12 @@ import java.nio.file.Path
 
 import akka.actor.{Actor, ActorRef}
 import better.files._
+import cromwell.backend.BackendWorkflowDescriptor
 import cromwell.backend.callcaching.JobCachingActorHelper
-import cromwell.backend.impl.jes.JesAsyncBackendJobExecutionActor.WorkflowOptionKeys
 import cromwell.backend.impl.jes.io.{JesAttachedDisk, JesWorkingDisk}
 import cromwell.core.logging.JobLogging
 
-import scala.language.postfixOps
+import scala.util.Try
 
 trait JesJobCachingActorHelper extends JobCachingActorHelper {
   this: Actor with JobLogging =>
@@ -25,23 +25,33 @@ trait JesJobCachingActorHelper extends JobCachingActorHelper {
   def initializationData: JesBackendInitializationData
 
   def serviceRegistryActor: ActorRef
+  
+  def workflowDescriptor: BackendWorkflowDescriptor
 
-  def getPath(str: String) = jesCallPaths.gcsFileSystem.getPath(str)
+  def getPath(str: String): Try[Path] = jesCallPaths.getPath(str)
 
   override lazy val configurationDescriptor = jesConfiguration.configurationDescriptor
 
-  lazy val jesCallPaths = initializationData.workflowPaths.toJesCallPaths(jobDescriptor.key)
+  lazy val jesCallPaths = {
+    val workflowPaths = if (workflowDescriptor.breadCrumbs.isEmpty) {
+      initializationData.workflowPaths
+    } else {
+      new JesWorkflowPaths(workflowDescriptor, jesConfiguration)(context.system)
+    }
+    
+    workflowPaths.toJobPaths(jobDescriptor.key)
+  }
 
   lazy val runtimeAttributes = JesRuntimeAttributes(jobDescriptor.runtimeAttributes, jobLogger)
 
   lazy val retryable = jobDescriptor.key.attempt <= runtimeAttributes.preemptible
   lazy val workingDisk: JesAttachedDisk = runtimeAttributes.disks.find(_.name == JesWorkingDisk.Name).get
 
-  lazy val callRootPath: Path = jesCallPaths.callRootPath
+  lazy val callRootPath: Path = jesCallPaths.callExecutionRoot
   lazy val returnCodeFilename = jesCallPaths.returnCodeFilename
-  lazy val returnCodeGcsPath = jesCallPaths.returnCodePath
-  lazy val jesStdoutFile = jesCallPaths.stdoutPath
-  lazy val jesStderrFile = jesCallPaths.stderrPath
+  lazy val returnCodeGcsPath = jesCallPaths.returnCode
+  lazy val jesStdoutFile = jesCallPaths.stdout
+  lazy val jesStderrFile = jesCallPaths.stderr
   lazy val jesLogFilename = jesCallPaths.jesLogFilename
   lazy val defaultMonitoringOutputPath = callRootPath.resolve(JesMonitoringLogFile)
 
@@ -49,28 +59,22 @@ trait JesJobCachingActorHelper extends JobCachingActorHelper {
   lazy val preemptible: Boolean = jobDescriptor.key.attempt <= maxPreemption
 
   lazy val jesAttributes = jesConfiguration.jesAttributes
-  // TODO: Move monitoring paths to JesCallPaths
   lazy val monitoringScript: Option[JesInput] = {
-    jobDescriptor.workflowDescriptor.workflowOptions.get(WorkflowOptionKeys.MonitoringScript) map { path =>
-      JesFileInput(s"$MonitoringParamName-in", getPath(path).toString,
+    jesCallPaths.monitoringPath map { path =>
+      JesFileInput(s"$MonitoringParamName-in", path.toUri.toString,
         JesWorkingDisk.MountPoint.resolve(JesMonitoringScript), workingDisk)
-    } toOption
+    }
   }
   lazy val monitoringOutput = monitoringScript map { _ => JesFileOutput(s"$MonitoringParamName-out",
     defaultMonitoringOutputPath.toString, File(JesMonitoringLogFile).path, workingDisk)
   }
 
+  // Implements CacheHitDuplicating.metadataKeyValues
   lazy val metadataKeyValues: Map[String, Any] = {
     val runtimeAttributesMetadata: Map[String, Any] = runtimeAttributes.asMap map {
       case (key, value) => s"runtimeAttributes:$key" -> value
     }
-
-    var fileMetadata: Map[String, Any] = jesCallPaths.metadataPaths
-    if (monitoringOutput.nonEmpty) {
-      // TODO: Move this to JesCallPaths
-      fileMetadata += JesMetadataKeys.MonitoringLog -> monitoringOutput.get.gcs
-    }
-
+    
     val otherMetadata: Map[String, Any] = Map(
       JesMetadataKeys.GoogleProject -> jesAttributes.project,
       JesMetadataKeys.ExecutionBucket -> jesAttributes.executionBucket,
@@ -79,6 +83,6 @@ trait JesJobCachingActorHelper extends JobCachingActorHelper {
       "cache:allowResultReuse" -> true
     )
 
-    runtimeAttributesMetadata ++ fileMetadata ++ otherMetadata
+    runtimeAttributesMetadata ++ jesCallPaths.metadataPaths ++ otherMetadata
   }
 }
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobExecutionActor.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobExecutionActor.scala
index b1a8ba8d6a6..476ee04aa2b 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobExecutionActor.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobExecutionActor.scala
@@ -1,6 +1,7 @@
 package cromwell.backend.impl.jes
 
-import akka.actor.{ActorRef, Props}
+import akka.actor.SupervisorStrategy.{Decider, Stop}
+import akka.actor.{ActorRef, OneForOneStrategy, Props}
 import akka.event.LoggingReceive
 import cromwell.backend.BackendJobExecutionActor.{AbortedResponse, BackendJobExecutionResponse}
 import cromwell.backend.BackendLifecycleActor.AbortJobCommand
@@ -62,13 +63,15 @@ case class JesJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
 
   private var executor: Option[ActorRef] = None
 
+  private[jes] def jabjeaProps = JesAsyncBackendJobExecutionActor.props(jobDescriptor,
+    completionPromise,
+    jesConfiguration,
+    initializationData,
+    serviceRegistryActor,
+    jesBackendSingletonActor)
+
   private def launchExecutor: Future[Unit] = Future {
-    val executionProps = JesAsyncBackendJobExecutionActor.props(jobDescriptor,
-      completionPromise,
-      jesConfiguration,
-      initializationData,
-      serviceRegistryActor,
-      jesBackendSingletonActor)
+    val executionProps = jabjeaProps
     val executorRef = context.actorOf(executionProps, "JesAsyncBackendJobExecutionActor")
     executor = Option(executorRef)
     ()
@@ -95,4 +98,12 @@ case class JesJobExecutionActor(override val jobDescriptor: BackendJobDescriptor
   }
 
   override def abort(): Unit = {}
+
+  // Supervision strategy: if the JABJEA throws an exception, stop the actor and fail the job.
+  def jobFailingDecider: Decider = {
+    case e: Exception =>
+      completionPromise.tryFailure(new RuntimeException("JesAsyncBackendJobExecutionActor failed and didn't catch its exception.", e))
+      Stop
+  }
+  override val supervisorStrategy = OneForOneStrategy()(jobFailingDecider)
 }
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobPaths.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobPaths.scala
new file mode 100644
index 00000000000..fdbdb1dc7fe
--- /dev/null
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesJobPaths.scala
@@ -0,0 +1,60 @@
+package cromwell.backend.impl.jes
+
+import java.nio.file.Path
+
+import akka.actor.ActorSystem
+import cromwell.backend.io.JobPaths
+import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
+import cromwell.core.CallContext
+import cromwell.services.metadata.CallMetadataKeys
+
+object JesJobPaths {
+  def apply(jobKey: BackendJobDescriptorKey, workflowDescriptor: BackendWorkflowDescriptor,
+            jesConfiguration: JesConfiguration)(implicit actorSystem: ActorSystem): JesJobPaths = {
+    new JesJobPaths(jobKey, workflowDescriptor, jesConfiguration)
+  }
+
+  val JesLogPathKey = "jesLog"
+  val GcsExecPathKey = "gcsExec"
+}
+
+class JesJobPaths(val jobKey: BackendJobDescriptorKey, workflowDescriptor: BackendWorkflowDescriptor,
+                  jesConfiguration: JesConfiguration)(implicit actorSystem: ActorSystem) extends
+  JesWorkflowPaths(workflowDescriptor, jesConfiguration)(actorSystem) with JobPaths {
+
+  val jesLogBasename = {
+    val index = jobKey.index.map(s => s"-$s").getOrElse("")
+    s"${jobKey.scope.unqualifiedName}$index"
+  }
+
+  override val returnCodeFilename: String = s"$jesLogBasename-rc.txt"
+  override val stdoutFilename: String = s"$jesLogBasename-stdout.log"
+  override val stderrFilename: String = s"$jesLogBasename-stderr.log"
+  override val scriptFilename: String = "exec.sh"
+
+  val jesLogFilename: String = s"$jesLogBasename.log"
+  lazy val jesLogPath: Path = callExecutionRoot.resolve(jesLogFilename)
+  
+  lazy val callContext = CallContext(callExecutionRoot, stdoutFilename, stderrFilename)
+
+  /*
+  TODO: Move various monitoring files path generation here.
+
+  "/cromwell_root" is a well known path, called in the regular JobPaths callDockerRoot.
+  This JesCallPaths should know about that root, and be able to create the monitoring file paths.
+  Instead of the AsyncActor creating the paths, the paths could then be shared with the CachingActor.
+
+  Those monitoring paths could then be returned by metadataFiles and detritusFiles.
+   */
+
+  override lazy val customMetadataPaths = Map(
+    CallMetadataKeys.BackendLogsPrefix + ":log" -> jesLogPath
+  ) ++ (
+    monitoringPath map { p => Map(JesMetadataKeys.MonitoringLog -> p) } getOrElse Map.empty  
+  )
+
+  override lazy val customDetritusPaths: Map[String, Path] = Map(
+    JesJobPaths.GcsExecPathKey -> script,
+    JesJobPaths.JesLogPathKey -> jesLogPath
+  )
+}
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesWorkflowPaths.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesWorkflowPaths.scala
index 9b39c869abd..a7ac5e50ab1 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesWorkflowPaths.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/JesWorkflowPaths.scala
@@ -2,51 +2,61 @@ package cromwell.backend.impl.jes
 
 import java.nio.file.Path
 
-import cromwell.backend.impl.jes.authentication.JesCredentials
+import akka.actor.ActorSystem
+import com.typesafe.config.Config
+import cromwell.backend.impl.jes.JesAsyncBackendJobExecutionActor.WorkflowOptionKeys
+import cromwell.backend.io.WorkflowPaths
 import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
-import cromwell.core.WorkflowOptions.FinalCallLogsDir
-import cromwell.filesystems.gcs.{GcsFileSystem, GcsFileSystemProvider, GoogleAuthMode}
+import cromwell.core.WorkflowOptions
+import cromwell.core.path.PathBuilder
+import cromwell.filesystems.gcs.{GcsPathBuilderFactory, RetryableGcsPathBuilder}
 
-import scala.concurrent.ExecutionContext
+import scala.language.postfixOps
 
 object JesWorkflowPaths {
   private val GcsRootOptionKey = "jes_gcs_root"
   private val AuthFilePathOptionKey = "auth_bucket"
 
   def apply(workflowDescriptor: BackendWorkflowDescriptor,
-            jesConfiguration: JesConfiguration,
-            credentials: JesCredentials)(implicit ec: ExecutionContext) = {
-    new JesWorkflowPaths(workflowDescriptor, jesConfiguration, credentials)
+            jesConfiguration: JesConfiguration)(implicit actorSystem: ActorSystem) = {
+    new JesWorkflowPaths(workflowDescriptor, jesConfiguration)
   }
 }
 
-class JesWorkflowPaths(workflowDescriptor: BackendWorkflowDescriptor,
-                       jesConfiguration: JesConfiguration,
-                       credentials: JesCredentials)(implicit ec: ExecutionContext) {
+class JesWorkflowPaths(val workflowDescriptor: BackendWorkflowDescriptor,
+                       jesConfiguration: JesConfiguration)(implicit actorSystem: ActorSystem) extends WorkflowPaths {
 
-  private val gcsStorage = GoogleAuthMode.buildStorage(credentials.gcsCredential, jesConfiguration.googleConfig.applicationName)
-  val gcsFileSystemProvider: GcsFileSystemProvider = GcsFileSystemProvider(gcsStorage)(ec)
-  val gcsFileSystem = GcsFileSystem(gcsFileSystemProvider)
+  override lazy val executionRootString = workflowDescriptor.workflowOptions.getOrElse(JesWorkflowPaths.GcsRootOptionKey, jesConfiguration.root)
+  private val workflowOptions: WorkflowOptions = workflowDescriptor.workflowOptions
+  val gcsPathBuilder: RetryableGcsPathBuilder = jesConfiguration.gcsPathBuilderFactory.withOptions(workflowOptions)
 
-  val rootPath: Path =
-    gcsFileSystem.getPath(workflowDescriptor.workflowOptions.getOrElse(JesWorkflowPaths.GcsRootOptionKey, jesConfiguration.root))
-
-  val workflowRootPath: Path = rootPath.resolve(workflowDescriptor.workflowNamespace.workflow.unqualifiedName)
-    .resolve(workflowDescriptor.id.toString)
-
-  val finalCallLogsPath = workflowDescriptor.getWorkflowOption(FinalCallLogsDir) map { gcsFileSystem.getPath(_) }
+  def getHash(gcsUrl: Path) = gcsPathBuilder.getHash(gcsUrl)
 
   val gcsAuthFilePath: Path = {
     /*
      * This is an "exception". The filesystem used here is built from genomicsAuth
      * unlike everywhere else where the filesystem used is built from gcsFileSystemAuth
      */
-    val genomicsStorage = GoogleAuthMode.buildStorage(credentials.genomicsCredential, jesConfiguration.googleConfig.applicationName)
-    val fileSystemWithGenomicsAuth = GcsFileSystem(GcsFileSystemProvider(genomicsStorage)(ec))
-    val bucket = workflowDescriptor.workflowOptions.get(JesWorkflowPaths.AuthFilePathOptionKey) getOrElse workflowRootPath.toString
-
-    fileSystemWithGenomicsAuth.getPath(bucket).resolve(s"${workflowDescriptor.id}_auth.json")
+    val genomicsCredentials = jesConfiguration.jesAuths.genomics
+    
+    // The default auth file bucket is always at the root of the root workflow
+    val defaultBucket = executionRoot.resolve(workflowDescriptor.rootWorkflow.unqualifiedName).resolve(workflowDescriptor.rootWorkflowId.toString)
+    
+    val bucket = workflowDescriptor.workflowOptions.get(JesWorkflowPaths.AuthFilePathOptionKey) getOrElse defaultBucket.toUri.toString
+    val authBucket = GcsPathBuilderFactory(genomicsCredentials).withOptions(workflowOptions).build(bucket) recover {
+      case ex => throw new Exception(s"Invalid gcs auth_bucket path $bucket", ex)
+    } get
+
+    authBucket.resolve(s"${workflowDescriptor.rootWorkflowId}_auth.json")
+  }
+  
+  
+  val monitoringPath = workflowOptions.get(WorkflowOptionKeys.MonitoringScript).toOption map { path =>
+    // Fail here if the path exists but can't be built
+    getPath(path).get
   }
 
-  def toJesCallPaths(jobKey: BackendJobDescriptorKey) = JesCallPaths(jobKey, workflowDescriptor, jesConfiguration, credentials)(ec)
+  override def toJobPaths(jobKey: BackendJobDescriptorKey) = JesJobPaths(jobKey, workflowDescriptor, jesConfiguration)
+  override def config: Config = jesConfiguration.configurationDescriptor.backendConfig
+  override def pathBuilders: List[PathBuilder] = List(gcsPathBuilder)
 }
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/Run.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/Run.scala
index b5a8b5f9f7b..05078c7f2cc 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/Run.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/Run.scala
@@ -21,7 +21,6 @@ object Run {
     "https://www.googleapis.com/auth/compute"
   ).asJava
 
-  private val JesServiceAccount = new ServiceAccount().setEmail("default").setScopes(GenomicsScopes)
   private val AcceptableEvents = Set("start", "pulling-image", "localizing-files", "running-docker", "delocalizing-files", "ok", "fail", "start-shutdown", "preempted")
 
   val NoAddressFieldName = "noAddress"
@@ -36,6 +35,7 @@ object Run {
             logFileName: String,
             jesParameters: Seq[JesParameter],
             projectId: String,
+            computeServiceAccount: String,
             preemptible: Boolean,
             genomicsInterface: Genomics): Run = {
     val logger = new JobLogger("JesRun", jobDescriptor.workflowDescriptor.id, jobDescriptor.key.tag, None, Set(slf4jLogger))
@@ -48,7 +48,7 @@ object Run {
              .setProjectId(projectId)
              .setDocker(pipelineInfo.docker)
              .setResources(pipelineInfo.resources)
-             .setName(workflow.workflowNamespace.workflow.unqualifiedName)
+             .setName(workflow.workflow.unqualifiedName)
              .setInputParameters(jesParameters.collect({ case i: JesInput => i.toGooglePipelineParameter }).toVector.asJava)
              .setOutputParameters(jesParameters.collect({ case i: JesFileOutput => i.toGooglePipelineParameter }).toVector.asJava)
 
@@ -60,7 +60,8 @@ object Run {
     }
 
     def runPipeline: String = {
-      val rpargs = new RunPipelineArgs().setProjectId(projectId).setServiceAccount(JesServiceAccount).setResources(runtimePipelineResources)
+      val svcAccount = new ServiceAccount().setEmail(computeServiceAccount).setScopes(GenomicsScopes)
+      val rpargs = new RunPipelineArgs().setProjectId(projectId).setServiceAccount(svcAccount).setResources(runtimePipelineResources)
 
       rpargs.setInputs(jesParameters.collect({ case i: JesInput => i.name -> i.toGoogleRunParameter }).toMap.asJava)
       logger.debug(s"Inputs:\n${stringifyMap(rpargs.getInputs.asScala.toMap)}")
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesAuths.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesAuths.scala
new file mode 100644
index 00000000000..bb6b048c4f9
--- /dev/null
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesAuths.scala
@@ -0,0 +1,5 @@
+package cromwell.backend.impl.jes.authentication
+
+import cromwell.filesystems.gcs.auth.GoogleAuthMode
+
+case class JesAuths(genomics: GoogleAuthMode, gcs: GoogleAuthMode)
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesCredentials.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesCredentials.scala
deleted file mode 100644
index b4316fde355..00000000000
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesCredentials.scala
+++ /dev/null
@@ -1,5 +0,0 @@
-package cromwell.backend.impl.jes.authentication
-
-import com.google.api.client.auth.oauth2.Credential
-
-case class JesCredentials(genomicsCredential: Credential, gcsCredential: Credential)
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesVMAuthentication.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesVMAuthentication.scala
index 67ddd1df3cb..9c92b380ae8 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesVMAuthentication.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/authentication/JesVMAuthentication.scala
@@ -1,7 +1,7 @@
 package cromwell.backend.impl.jes.authentication
 
 import cromwell.core.DockerCredentials
-import cromwell.filesystems.gcs.ClientSecrets
+import cromwell.filesystems.gcs.auth.ClientSecrets
 import spray.json.{JsString, JsValue}
 
 /**
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/callcaching/JesBackendFileHashing.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/callcaching/JesBackendFileHashing.scala
index 5c7cf4a8a01..42cf8f7bee2 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/callcaching/JesBackendFileHashing.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/callcaching/JesBackendFileHashing.scala
@@ -9,8 +9,8 @@ import scala.util.{Failure, Try}
 private[jes] object JesBackendFileHashing {
   def getCrc32c(singleFileHashRequest: SingleFileHashRequest, log: LoggingAdapter): Try[String] = {
     def usingJesInitData(jesInitData: JesBackendInitializationData) = for {
-      path <- Try(jesInitData.workflowPaths.gcsFileSystem.getPath(singleFileHashRequest.file.valueString))
-      crc32c <- Try(jesInitData.workflowPaths.gcsFileSystemProvider.crc32cHash(path))
+      path <- jesInitData.workflowPaths.getPath(singleFileHashRequest.file.valueString)
+      crc32c <- jesInitData.workflowPaths.getHash(path)
     } yield crc32c
 
     singleFileHashRequest.initializationData match {
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/io/package.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/io/package.scala
index 24d417c99e3..2a2ae8ac25c 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/io/package.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/io/package.scala
@@ -3,19 +3,14 @@ package cromwell.backend.impl.jes
 import java.nio.file.{Files, Path}
 
 import com.google.api.client.http.HttpResponseException
-import cromwell.filesystems.gcs._
+import com.google.cloud.storage.contrib.nio.CloudStorageOptions
 
 package object io {
   implicit class PathEnhanced(val path: Path) extends AnyVal {
     import better.files._
 
-    def hash = path match {
-      case gcs: NioGcsPath => gcs.getFileSystem.provider().asInstanceOf[GcsFileSystemProvider].crc32cHash(gcs)
-      case _ => File(path).md5
-    }
-
     def writeAsJson(content: String): File = {
-      Files.write(path, content.getBytes, ContentTypeOption.Json)
+      Files.write(path, content.getBytes, CloudStorageOptions.withMimeType("application/json"))
     }
   }
 
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesApiQueryManager.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesApiQueryManager.scala
index f3a7739ac67..12fe055dc84 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesApiQueryManager.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesApiQueryManager.scala
@@ -11,15 +11,19 @@ import scala.collection.immutable.Queue
   * Currently, just holds a set of JES status poll requests until a PollingActor pulls the work.
   * TODO: Could eventually move all of the JES queries into a single work-pulling model.
   */
-class JesApiQueryManager extends Actor with ActorLogging {
+class JesApiQueryManager(val qps: Int) extends Actor with ActorLogging {
 
-  private var workQueue: Queue[JesStatusPollQuery] = Queue.empty
+  // workQueue is protected for the unit tests, not intended to be generally overridden
+  protected[statuspolling] var workQueue: Queue[JesStatusPollQuery] = Queue.empty
   private var workInProgress: Map[ActorRef, JesPollingWorkBatch] = Map.empty
 
   // If the statusPoller dies, we want to stop it and handle the termination ourselves.
   override val supervisorStrategy = SupervisorStrategy.stoppingStrategy
-  private def statusPollerProps = JesPollingActor.props(self)
-  private var statusPoller: ActorRef = _
+  private def statusPollerProps = JesPollingActor.props(self, qps)
+
+  // statusPoller is protected for the unit tests, not intended to be generally overridden
+  protected[statuspolling] var statusPoller: ActorRef = _
+
   resetStatusPoller()
 
   override def receive = {
@@ -70,15 +74,17 @@ class JesApiQueryManager extends Actor with ActorLogging {
     // Currently we can assume this is a polling actor. Might change in a future update:
     workInProgress.get(terminee) match {
       case Some(work) =>
-        // Ouch. We should tell all of its clients that it fell over. And then start a new one.
-        log.error(s"The JES polling actor $terminee unexpectedly terminated while conducting ${work.workBatch.tail.size + 1} polls. Making a new one...")
-        work.workBatch.toList foreach { _.requester ! JesPollingActor.JesPollError }
+        // Most likely due to an unexpected HTTP error, push the work back on the queue and keep going
+        log.info(s"The JES polling actor $terminee unexpectedly terminated while conducting ${work.workBatch.tail.size + 1} polls. Making a new one...")
+        workInProgress -= terminee
+        workQueue = workQueue ++ work.workBatch.toList
       case None =>
         // It managed to die while doing absolutely nothing...!?
         // Maybe it deserves an entry in https://en.wikipedia.org/wiki/List_of_unusual_deaths
         // Oh well, in the mean time don't do anything, just start a new one
         log.error(s"The JES polling actor $terminee managed to unexpectedly terminate whilst doing absolutely nothing. This is probably a programming error. Making a new one...")
     }
+
     resetStatusPoller()
   }
 
@@ -93,7 +99,7 @@ class JesApiQueryManager extends Actor with ActorLogging {
 
 object JesApiQueryManager {
 
-  def props: Props = Props(new JesApiQueryManager)
+  def props(qps: Int): Props = Props(new JesApiQueryManager(qps))
 
   /**
     * Poll the job represented by the Run.
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActor.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActor.scala
index 4152d393333..31a9d114a0c 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActor.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActor.scala
@@ -7,7 +7,7 @@ import com.google.api.client.googleapis.batch.json.JsonBatchCallback
 import com.google.api.client.googleapis.json.GoogleJsonError
 import com.google.api.client.http.HttpHeaders
 import com.google.api.services.genomics.model.Operation
-import cromwell.backend.impl.jes.Run
+import cromwell.backend.impl.jes.{JesAttributes, Run}
 import cromwell.backend.impl.jes.statuspolling.JesApiQueryManager.{JesPollingWorkBatch, JesStatusPollQuery, NoWorkToDo}
 import cromwell.backend.impl.jes.statuspolling.JesPollingActor._
 
@@ -19,12 +19,11 @@ import scala.concurrent.duration._
 /**
   * Polls JES for status. Pipes the results back (so expect either a RunStatus or a akka.actor.Status.Failure).
   */
-class JesPollingActor(pollingManager: ActorRef) extends Actor with ActorLogging {
+class JesPollingActor(val pollingManager: ActorRef, val qps: Int) extends Actor with ActorLogging {
+  // The interval to delay between submitting each batch
+  lazy val batchInterval = determineBatchInterval(determineEffectiveQps(qps))
+  log.debug("JES batch polling interval is {}", batchInterval)
 
-  // We want to query at just under our fixed JES QPS limit of 20 per second. That should hopefully allow some room at the edges
-  // for things like new calls, etc.
-  val MaxBatchSize = 100
-  val BatchInterval = 5.5.seconds
   self ! NoWorkToDo // Starts the check-for-work cycle
 
   implicit val ec: ExecutionContext = context.dispatcher
@@ -109,14 +108,43 @@ class JesPollingActor(pollingManager: ActorRef) extends Actor with ActorLogging
     * Warning: Only use this from inside a receive method.
     */
   private def scheduleCheckForWork(): Unit = {
-    context.system.scheduler.scheduleOnce(BatchInterval) { pollingManager ! JesApiQueryManager.RequestJesPollingWork(MaxBatchSize) }
+    context.system.scheduler.scheduleOnce(batchInterval) { pollingManager ! JesApiQueryManager.RequestJesPollingWork(MaxBatchSize) }
     ()
   }
+
+  /**
+    * We don't want to allow non-positive QPS values. Catch these instances and replace them with a sensible default.
+    * Here we're using the default value coming from JES itself
+    */
+  private def determineEffectiveQps(qps: Int): Int = {
+    if (qps > 0) qps
+    else {
+      val defaultQps = JesAttributes.GenomicsApiDefaultQps
+      log.warning("Supplied QPS for Google Genomics API was not positive, value was {} using {} instead", qps, defaultQps)
+      defaultQps
+    }
+  }
 }
 
 object JesPollingActor {
-  def props(pollingManager: ActorRef) = Props(new JesPollingActor(pollingManager))
+  def props(pollingManager: ActorRef, qps: Int) = Props(new JesPollingActor(pollingManager, qps))
+
+  // The Batch API limits us to 100 at a time
+  val MaxBatchSize = 100
+
+  /**
+    * Given the Genomics API queries per 100 seconds and given MaxBatchSize will determine a batch interval which
+    * is at 90% of the quota. The (still crude) delta is to provide some room at the edges for things like new
+    * calls, etc.
+    *
+    * Forcing the minimum value to be 1 second, for now it seems unlikely to matter and it makes testing a bit
+    * easier
+    */
+  def determineBatchInterval(qps: Int): FiniteDuration = {
+    val maxInterval = MaxBatchSize / qps.toDouble // Force this to be floating point in case the value is < 1
+    val interval = Math.max(maxInterval * 0.9, 1)
+    interval.seconds
+  }
 
   final case class JesPollFailed(e: GoogleJsonError, responseHeaders: HttpHeaders)
-  case object JesPollError
 }
diff --git a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActorClient.scala b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActorClient.scala
index 1bf7328f83a..9070378c338 100644
--- a/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActorClient.scala
+++ b/supportedBackends/jes/src/main/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActorClient.scala
@@ -3,7 +3,7 @@ package cromwell.backend.impl.jes.statuspolling
 import java.io.IOException
 
 import akka.actor.{Actor, ActorLogging, ActorRef}
-import cromwell.backend.impl.jes.statuspolling.JesPollingActor.{JesPollError, JesPollFailed}
+import cromwell.backend.impl.jes.statuspolling.JesPollingActor.JesPollFailed
 import cromwell.backend.impl.jes.{Run, RunStatus}
 
 import scala.concurrent.{Future, Promise}
@@ -28,9 +28,6 @@ trait JesPollingActorClient { this: Actor with ActorLogging =>
     case JesPollFailed(e, responseHeaders) =>
       log.debug("JES poll failed! Sad.")
       completePromise(Failure(new IOException(s"Google request failed: ${e.toPrettyString}")))
-    case JesPollError =>
-      log.debug("JES poll failed when polling actor died unexpectedly! Sad.")
-      completePromise(Failure(new RuntimeException("Unexpected actor death!")))
   }
 
   private def completePromise(runStatus: Try[RunStatus]) = {
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesAsyncBackendJobExecutionActorSpec.scala
index 5601e1ebbbc..40078cac614 100644
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesAsyncBackendJobExecutionActorSpec.scala
@@ -4,19 +4,20 @@ import java.nio.file.Paths
 import java.util.UUID
 
 import akka.actor.{ActorRef, Props}
-import akka.event.LoggingAdapter
 import akka.testkit.{ImplicitSender, TestActorRef, TestDuration, TestProbe}
+import com.google.cloud.storage.contrib.nio.CloudStoragePath
 import cromwell.backend.BackendJobExecutionActor.BackendJobExecutionResponse
+import cromwell.backend._
 import cromwell.backend.async.AsyncBackendJobExecutionActor.{Execute, ExecutionMode}
 import cromwell.backend.async.{AbortedExecutionHandle, ExecutionHandle, FailedNonRetryableExecutionHandle, FailedRetryableExecutionHandle}
 import cromwell.backend.impl.jes.JesAsyncBackendJobExecutionActor.JesPendingExecutionHandle
-import cromwell.backend.impl.jes.MockObjects._
 import cromwell.backend.impl.jes.RunStatus.Failed
 import cromwell.backend.impl.jes.io.{DiskType, JesWorkingDisk}
-import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendJobDescriptorKey, BackendWorkflowDescriptor, PreemptedException, RuntimeAttributeDefinition}
-import cromwell.core.logging.LoggerWrapper
+import cromwell.backend.impl.jes.statuspolling.JesApiQueryManager.DoPoll
+import cromwell.core.logging.JobLogger
 import cromwell.core.{WorkflowId, WorkflowOptions, _}
-import cromwell.filesystems.gcs._
+import cromwell.filesystems.gcs.GcsPathBuilderFactory
+import cromwell.filesystems.gcs.auth.GoogleAuthMode.NoAuthMode
 import cromwell.util.SampleWdl
 import org.scalatest._
 import org.scalatest.prop.Tables.Table
@@ -25,16 +26,16 @@ import org.specs2.mock.Mockito
 import spray.json.{JsObject, JsValue}
 import wdl4s.types.{WdlArrayType, WdlFileType, WdlMapType, WdlStringType}
 import wdl4s.values.{WdlArray, WdlFile, WdlMap, WdlString, WdlValue}
-import wdl4s.{Call, LocallyQualifiedName, NamespaceWithWorkflow}
+import wdl4s.{LocallyQualifiedName, FullyQualifiedName => _, _}
 
 import scala.concurrent.duration._
 import scala.concurrent.{Await, ExecutionContext, Future, Promise}
 import scala.util.{Success, Try}
-import cromwell.backend.impl.jes.MockObjects._
-import cromwell.backend.impl.jes.statuspolling.JesApiQueryManager.DoPoll
 
 class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackendJobExecutionActorSpec")
-  with FlatSpecLike with Matchers with ImplicitSender with Mockito {
+  with FlatSpecLike with Matchers with ImplicitSender with Mockito with BackendSpec {
+
+  val mockPathBuilder = GcsPathBuilderFactory(NoAuthMode).withOptions(mock[WorkflowOptions])
 
   import JesTestConfig._
 
@@ -56,7 +57,7 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
       |  }
       |}
       |
-      |workflow sup {
+      |workflow wf_sup {
       |  call sup
       |}
     """.stripMargin
@@ -65,16 +66,14 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
 
   val NoOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))
 
-  val TestableCallContext = CallContext(MockGcsFileSystemBuilder.mockGcsFileSystem.getPath("gs://root"), "out", "err")
+  val TestableCallContext = CallContext(mockPathBuilder.build("gs://root").get, "out", "err")
 
   val TestableJesExpressionFunctions = {
-    new JesExpressionFunctions(List(MockGcsFileSystemBuilder.mockGcsFileSystem), TestableCallContext)
+    new JesExpressionFunctions(List(mockPathBuilder), TestableCallContext)
   }
 
   private def buildInitializationData(jobDescriptor: BackendJobDescriptor, configuration: JesConfiguration) = {
-    val workflowPaths = JesWorkflowPaths(jobDescriptor.workflowDescriptor,
-      configuration,
-      mockCredentials)(scala.concurrent.ExecutionContext.global)
+    val workflowPaths = JesWorkflowPaths(jobDescriptor.workflowDescriptor, configuration)(system)
     JesBackendInitializationData(workflowPaths, null)
   }
 
@@ -85,12 +84,9 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
                                      jesSingletonActor: ActorRef = emptyActor)
     extends JesAsyncBackendJobExecutionActor(jobDescriptor, promise, jesConfiguration, buildInitializationData(jobDescriptor, jesConfiguration), emptyActor, jesSingletonActor) {
 
-    override lazy val jobLogger = new LoggerWrapper {
-      override def akkaLogger: Option[LoggingAdapter] = Option(log)
-
+    override lazy val jobLogger = new JobLogger("TestLogger", workflowId, jobTag, akkaLogger = Option(log)) {
       override def tag: String = s"$name [UUID(${workflowId.shortString})$jobTag]"
-
-      override def slf4jLoggers: Set[Logger] = Set.empty
+      override val slf4jLoggers: Set[Logger] = Set.empty
     }
 
     override lazy val callEngineFunctions = functions
@@ -110,15 +106,15 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
   private def buildPreemptibleJobDescriptor(attempt: Int, preemptible: Int): BackendJobDescriptor = {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(YoSup.replace("[PREEMPTIBLE]", s"preemptible: $preemptible")),
+      WdlNamespaceWithWorkflow.load(YoSup.replace("[PREEMPTIBLE]", s"preemptible: $preemptible"), Seq.empty[ImportResolver]).workflow,
       Inputs,
       NoOptions
     )
 
-    val job = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val job = workflowDescriptor.workflow.taskCalls.head
     val key = BackendJobDescriptorKey(job, None, attempt)
     val runtimeAttributes = makeRuntimeAttributes(job)
-    BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Inputs)
+    BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnMapToDeclarationMap(Inputs))
   }
 
   private def executionActor(jobDescriptor: BackendJobDescriptor,
@@ -128,7 +124,7 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
 
     // Mock/stub out the bits that would reach out to JES.
     val run = mock[Run]
-    val handle = JesPendingExecutionHandle(jobDescriptor, Seq.empty, run, None)
+    val handle = JesPendingExecutionHandle(jobDescriptor, Set.empty, run, None)
 
     class ExecuteOrRecoverActor extends TestableJesJobExecutionActor(jobDescriptor, promise, jesConfiguration, jesSingletonActor = jesSingletonActor) {
       override def executeOrRecover(mode: ExecutionMode)(implicit ec: ExecutionContext): Future[ExecutionHandle] = Future.successful(handle)
@@ -187,8 +183,8 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
     expectations foreach { case (attempt, preemptible, errorCode, innerErrorCode, shouldRetry) =>
       it should s"handle call failures appropriately with respect to preemption (attempt=$attempt, preemptible=$preemptible, errorCode=$errorCode, innerErrorCode=$innerErrorCode)" in {
         runAndFail(attempt, preemptible, errorCode, innerErrorCode).getClass.getSimpleName match {
-          case "FailedNonRetryableResponse" => false shouldBe shouldRetry
-          case "FailedRetryableResponse" => true shouldBe shouldRetry
+          case "JobFailedNonRetryableResponse" => false shouldBe shouldRetry
+          case "JobFailedRetryableResponse" => true shouldBe shouldRetry
           case huh => fail(s"Unexpected response class name: '$huh'")
         }
       }
@@ -284,21 +280,21 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(YoSup.replace("[PREEMPTIBLE]", "")),
+      WdlNamespaceWithWorkflow.load(YoSup.replace("[PREEMPTIBLE]", ""), Seq.empty[ImportResolver]).workflow,
       inputs,
       NoOptions
     )
 
-    val call = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val call = workflowDescriptor.workflow.taskCalls.head
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, inputs)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnMapToDeclarationMap(inputs))
 
     val props = Props(new TestableJesJobExecutionActor(jobDescriptor, Promise(), jesConfiguration))
     val testActorRef = TestActorRef[TestableJesJobExecutionActor](
       props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
 
-    val mappedInputs = jobDescriptor.inputs mapValues testActorRef.underlyingActor.gcsPathToLocal
+    val mappedInputs = jobDescriptor.fullyQualifiedInputs mapValues testActorRef.underlyingActor.gcsPathToLocal
 
     mappedInputs(stringKey) match {
       case WdlString(v) => assert(v.equalsIgnoreCase(stringVal.value))
@@ -338,15 +334,15 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(SampleWdl.CurrentDirectory.asWorkflowSources(DockerAndDiskRuntime).wdlSource),
+      WdlNamespaceWithWorkflow.load(SampleWdl.CurrentDirectory.asWorkflowSources(DockerAndDiskRuntime).wdlSource, Seq.empty[ImportResolver]).workflow,
       inputs,
       NoOptions
     )
 
-    val job = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val job = workflowDescriptor.workflow.taskCalls.head
     val runtimeAttributes = makeRuntimeAttributes(job)
     val key = BackendJobDescriptorKey(job, None, 1)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, inputs)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnMapToDeclarationMap(inputs))
 
     val props = Props(new TestableJesJobExecutionActor(jobDescriptor, Promise(), jesConfiguration))
     val testActorRef = TestActorRef[TestableJesJobExecutionActor](
@@ -377,15 +373,15 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
   TestActorRef[TestableJesJobExecutionActor] = {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(sampleWdl.asWorkflowSources(DockerAndDiskRuntime).wdlSource),
+      WdlNamespaceWithWorkflow.load(sampleWdl.asWorkflowSources(DockerAndDiskRuntime).wdlSource, Seq.empty[ImportResolver]).workflow,
       inputs,
       NoOptions
     )
 
-    val call = workflowDescriptor.workflowNamespace.workflow.findCallByName(callName).get
+    val call = workflowDescriptor.workflow.findCallByName(callName).get.asInstanceOf[TaskCall]
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, inputs)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnMapToDeclarationMap(inputs))
 
     val props = Props(new TestableJesJobExecutionActor(jobDescriptor, Promise(), jesConfiguration, functions))
     TestActorRef[TestableJesJobExecutionActor](props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
@@ -393,14 +389,14 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
 
   it should "generate correct JesOutputs" in {
     val inputs = Map(
-      "in" -> WdlFile("gs://a/b/c.txt")
+      "in" -> WdlFile("gs://blah/b/c.txt")
     )
     val jesBackend = makeJesActorRef(SampleWdl.FilePassingWorkflow, "a", inputs).underlyingActor
     val jobDescriptor = jesBackend.jobDescriptor
     val workflowId = jesBackend.workflowId
     val jesInputs = jesBackend.generateJesInputs(jobDescriptor)
     jesInputs should have size 1
-    jesInputs should contain(JesFileInput("in-0", "gs://a/b/c.txt", Paths.get("a/b/c.txt"), workingDisk))
+    jesInputs should contain(JesFileInput("in-0", "gs://blah/b/c.txt", Paths.get("blah/b/c.txt"), workingDisk))
     val jesOutputs = jesBackend.generateJesOutputs(jobDescriptor)
     jesOutputs should have size 1
     jesOutputs should contain(JesFileOutput("out",
@@ -413,7 +409,7 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
     )
 
     class TestJesExpressionFunctions extends JesExpressionFunctions(
-      List(MockGcsFileSystemBuilder.mockGcsFileSystem), TestableCallContext) {
+      List(mockPathBuilder), TestableCallContext) {
       override def write_lines(params: Seq[Try[WdlValue]]): Try[WdlFile] = {
         Success(WdlFile(s"gs://some/path/file.txt"))
       }
@@ -438,15 +434,15 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(SampleWdl.CurrentDirectory.asWorkflowSources(DockerAndDiskRuntime).wdlSource),
+      WdlNamespaceWithWorkflow.load(SampleWdl.CurrentDirectory.asWorkflowSources(DockerAndDiskRuntime).wdlSource, Seq.empty[ImportResolver]).workflow,
       inputs,
       NoOptions
     )
 
-    val job = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val job = workflowDescriptor.workflow.taskCalls.head
     val runtimeAttributes = makeRuntimeAttributes(job)
     val key = BackendJobDescriptorKey(job, None, 1)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, inputs)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnMapToDeclarationMap(inputs))
 
     val props = Props(new TestableJesJobExecutionActor(jobDescriptor, Promise(), jesConfiguration))
     val testActorRef = TestActorRef[TestableJesJobExecutionActor](
@@ -466,15 +462,15 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(SampleWdl.CurrentDirectory.asWorkflowSources(DockerAndDiskRuntime).wdlSource),
+      WdlNamespaceWithWorkflow.load(SampleWdl.CurrentDirectory.asWorkflowSources(DockerAndDiskRuntime).wdlSource, Seq.empty[ImportResolver]).workflow,
       inputs,
       NoOptions
     )
 
-    val job = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val job = workflowDescriptor.workflow.taskCalls.head
     val runtimeAttributes = makeRuntimeAttributes(job)
     val key = BackendJobDescriptorKey(job, None, 1)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, inputs)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnMapToDeclarationMap(inputs))
 
     val props = Props(new TestableJesJobExecutionActor(jobDescriptor, Promise(), jesConfiguration))
     val testActorRef = TestActorRef[TestableJesJobExecutionActor](
@@ -487,7 +483,7 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
   }
 
   it should "convert local Paths back to corresponding GCS paths in JesOutputs" in {
-    val jesOutputs = Seq(
+    val jesOutputs = Set(
       JesFileOutput("/cromwell_root/path/to/file1", "gs://path/to/file1",
         Paths.get("/cromwell_root/path/to/file1"), workingDisk),
       JesFileOutput("/cromwell_root/path/to/file2", "gs://path/to/file2",
@@ -510,12 +506,12 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).wdlSource),
+      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).wdlSource, Seq.empty[ImportResolver]).workflow,
       Map.empty,
       NoOptions
     )
 
-    val call = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val call = workflowDescriptor.workflow.taskCalls.head
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
     val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty)
@@ -538,12 +534,12 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
   it should "create a JesFileInput for the monitoring script, when specified" in {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).wdlSource),
+      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).wdlSource, Seq.empty[ImportResolver]).workflow,
       Map.empty,
       WorkflowOptions.fromJsonString("""{"monitoring_script": "gs://path/to/script"}""").get
     )
 
-    val job = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val job = workflowDescriptor.workflow.taskCalls.head
     val runtimeAttributes = makeRuntimeAttributes(job)
     val key = BackendJobDescriptorKey(job, None, 1)
     val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty)
@@ -559,12 +555,12 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
   it should "not create a JesFileInput for the monitoring script, when not specified" in {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).wdlSource),
+      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).wdlSource, Seq.empty[ImportResolver]).workflow,
       Map.empty,
       NoOptions
     )
 
-    val job = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val job = workflowDescriptor.workflow.taskCalls.head
     val key = BackendJobDescriptorKey(job, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(job)
     val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty)
@@ -579,13 +575,13 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
   it should "return JES log paths for non-scattered call" in {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId(UUID.fromString("e6236763-c518-41d0-9688-432549a8bf7c")),
-      NamespaceWithWorkflow.load(
-        SampleWdl.HelloWorld.asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).wdlSource),
+      WdlNamespaceWithWorkflow.load(
+        SampleWdl.HelloWorld.asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).wdlSource, Seq.empty[ImportResolver]).workflow,
       Map.empty,
       WorkflowOptions.fromJsonString(""" {"jes_gcs_root": "gs://path/to/gcs_root"} """).get
     )
 
-    val call = workflowDescriptor.workflowNamespace.workflow.findCallByName("hello").get
+    val call = workflowDescriptor.workflow.findCallByName("hello").get.asInstanceOf[TaskCall]
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
     val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty)
@@ -596,28 +592,27 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
 
     val jesBackend = testActorRef.underlyingActor
 
-    // TODO: NioGcsPath.equals not implemented, so use toString instead
-    jesBackend.jesCallPaths.stdoutPath should be(a[NioGcsPath])
-    jesBackend.jesCallPaths.stdoutPath.toString shouldBe
-      "gs://path/to/gcs_root/hello/e6236763-c518-41d0-9688-432549a8bf7c/call-hello/hello-stdout.log"
-    jesBackend.jesCallPaths.stderrPath should be(a[NioGcsPath])
-    jesBackend.jesCallPaths.stderrPath.toString shouldBe
-      "gs://path/to/gcs_root/hello/e6236763-c518-41d0-9688-432549a8bf7c/call-hello/hello-stderr.log"
-    jesBackend.jesCallPaths.jesLogPath should be(a[NioGcsPath])
-    jesBackend.jesCallPaths.jesLogPath.toString shouldBe
-      "gs://path/to/gcs_root/hello/e6236763-c518-41d0-9688-432549a8bf7c/call-hello/hello.log"
+    jesBackend.jesCallPaths.stdout should be(a[CloudStoragePath])
+    jesBackend.jesCallPaths.stdout.toUri.toString shouldBe
+      "gs://path/to/gcs_root/wf_hello/e6236763-c518-41d0-9688-432549a8bf7c/call-hello/hello-stdout.log"
+    jesBackend.jesCallPaths.stderr should be(a[CloudStoragePath])
+    jesBackend.jesCallPaths.stderr.toUri.toString shouldBe
+      "gs://path/to/gcs_root/wf_hello/e6236763-c518-41d0-9688-432549a8bf7c/call-hello/hello-stderr.log"
+    jesBackend.jesCallPaths.jesLogPath should be(a[CloudStoragePath])
+    jesBackend.jesCallPaths.jesLogPath.toUri.toString shouldBe
+      "gs://path/to/gcs_root/wf_hello/e6236763-c518-41d0-9688-432549a8bf7c/call-hello/hello.log"
   }
 
   it should "return JES log paths for scattered call" in {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId(UUID.fromString("e6236763-c518-41d0-9688-432549a8bf7d")),
-      NamespaceWithWorkflow.load(
-        new SampleWdl.ScatterWdl().asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).wdlSource),
+      WdlNamespaceWithWorkflow.load(
+        new SampleWdl.ScatterWdl().asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).wdlSource, Seq.empty[ImportResolver]).workflow,
       Map.empty,
       WorkflowOptions.fromJsonString(""" {"jes_gcs_root": "gs://path/to/gcs_root"} """).get
     )
 
-    val call = workflowDescriptor.workflowNamespace.workflow.findCallByName("B").get
+    val call = workflowDescriptor.workflow.findCallByName("B").get.asInstanceOf[TaskCall]
     val key = BackendJobDescriptorKey(call, Option(2), 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
     val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty)
@@ -628,14 +623,14 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
 
     val jesBackend = testActorRef.underlyingActor
 
-    jesBackend.jesCallPaths.stdoutPath should be(a[NioGcsPath])
-    jesBackend.jesCallPaths.stdoutPath.toString shouldBe
+    jesBackend.jesCallPaths.stdout should be(a[CloudStoragePath])
+    jesBackend.jesCallPaths.stdout.toUri.toString shouldBe
       "gs://path/to/gcs_root/w/e6236763-c518-41d0-9688-432549a8bf7d/call-B/shard-2/B-2-stdout.log"
-    jesBackend.jesCallPaths.stderrPath should be(a[NioGcsPath])
-    jesBackend.jesCallPaths.stderrPath.toString shouldBe
+    jesBackend.jesCallPaths.stderr should be(a[CloudStoragePath])
+    jesBackend.jesCallPaths.stderr.toUri.toString shouldBe
       "gs://path/to/gcs_root/w/e6236763-c518-41d0-9688-432549a8bf7d/call-B/shard-2/B-2-stderr.log"
-    jesBackend.jesCallPaths.jesLogPath should be(a[NioGcsPath])
-    jesBackend.jesCallPaths.jesLogPath.toString shouldBe
+    jesBackend.jesCallPaths.jesLogPath should be(a[CloudStoragePath])
+    jesBackend.jesCallPaths.jesLogPath.toUri.toString shouldBe
       "gs://path/to/gcs_root/w/e6236763-c518-41d0-9688-432549a8bf7d/call-B/shard-2/B-2.log"
   }
 
@@ -662,7 +657,7 @@ class JesAsyncBackendJobExecutionActorSpec extends TestKitSuite("JesAsyncBackend
     descriptorWithMax2AndKey2.preemptible shouldBe true
   }
 
-  private def makeRuntimeAttributes(job: Call) = {
+  private def makeRuntimeAttributes(job: TaskCall) = {
     val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(job.task.runtimeAttributes, TestableJesExpressionFunctions, Map.empty)
     RuntimeAttributeDefinition.addDefaultsToAttributes(JesBackendLifecycleActorFactory.staticRuntimeAttributeDefinitions, NoOptions)(evaluatedAttributes.get) // Fine to throw the exception if this "get" fails. This is a test after all!
   }
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesAttributesSpec.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesAttributesSpec.scala
index 17c33d0ded8..0eec23cbe40 100644
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesAttributesSpec.scala
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesAttributesSpec.scala
@@ -16,18 +16,19 @@ class JesAttributesSpec extends FlatSpec with Matchers {
 
   it should "parse correct JES config" taggedAs IntegrationTest in {
     val googleConfig = GoogleConfiguration(JesGlobalConfig)
-    val backendConfig = ConfigFactory.parseString(configString.replace("[PREEMPTIBLE]", ""))
+    val backendConfig = ConfigFactory.parseString(configString())
 
     val jesAttributes = JesAttributes(googleConfig, backendConfig)
     jesAttributes.endpointUrl should be(new URL("http://myEndpoint"))
     jesAttributes.project should be("myProject")
     jesAttributes.executionBucket should be("gs://myBucket")
     jesAttributes.maxPollingInterval should be(600)
+    jesAttributes.computeServiceAccount should be("default")
   }
 
   it should "parse correct preemptible config" taggedAs IntegrationTest in {
     val googleConfig = GoogleConfiguration(JesGlobalConfig)
-    val backendConfig = ConfigFactory.parseString(configString.replace("[PREEMPTIBLE]", "preemptible = 3"))
+    val backendConfig = ConfigFactory.parseString(configString(preemptible = "preemptible = 3"))
 
     val jesAttributes = JesAttributes(googleConfig, backendConfig)
     jesAttributes.endpointUrl should be(new URL("http://myEndpoint"))
@@ -36,6 +37,14 @@ class JesAttributesSpec extends FlatSpec with Matchers {
     jesAttributes.maxPollingInterval should be(600)
   }
 
+  it should "parse compute service account" taggedAs IntegrationTest in {
+    val googleConfig = GoogleConfiguration(JesGlobalConfig)
+    val backendConfig = ConfigFactory.parseString(configString(genomics = """compute-service-account = "testing" """))
+
+    val jesAttributes = JesAttributes(googleConfig, backendConfig)
+    jesAttributes.computeServiceAccount should be("testing")
+  }
+
   it should "not parse invalid config" taggedAs IntegrationTest in {
     val nakedConfig =
       ConfigFactory.parseString(
@@ -60,17 +69,18 @@ class JesAttributesSpec extends FlatSpec with Matchers {
     errorsList should contain("no protocol: myEndpoint")
   }
 
-  val configString =
-    """
+  def configString(preemptible: String = "", genomics: String = "") =
+    s"""
       |{
       |   project = "myProject"
       |   root = "gs://myBucket"
       |   maximum-polling-interval = 600
-      |   [PREEMPTIBLE]
+      |   $preemptible
       |   genomics {
       |     // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
       |     // Pipelines and manipulate auth JSONs.
       |     auth = "application-default"
+      |    $genomics
       |     endpoint-url = "http://myEndpoint"
       |   }
       |
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesCallPathsSpec.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesCallPathsSpec.scala
index d2732870634..58841f75664 100644
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesCallPathsSpec.scala
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesCallPathsSpec.scala
@@ -1,13 +1,12 @@
 package cromwell.backend.impl.jes
 
 import cromwell.backend.BackendSpec
+import cromwell.core.TestKitSuite
 import cromwell.util.SampleWdl
-import org.scalatest.{FlatSpec, Matchers}
+import org.scalatest.{FlatSpecLike, Matchers}
 import org.specs2.mock.Mockito
-import scala.concurrent.ExecutionContext.Implicits.global
-import cromwell.backend.impl.jes.MockObjects._
 
-class JesCallPathsSpec extends FlatSpec with Matchers with Mockito {
+class JesCallPathsSpec extends TestKitSuite with FlatSpecLike with Matchers with Mockito {
 
   import BackendSpec._
   import JesTestConfig._
@@ -19,8 +18,8 @@ class JesCallPathsSpec extends FlatSpec with Matchers with Mockito {
     val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
     val jesConfiguration = new JesConfiguration(JesBackendConfigurationDescriptor)
 
-    val callPaths = JesCallPaths(jobDescriptorKey, workflowDescriptor,
-      jesConfiguration, mockCredentials)
+    val callPaths = JesJobPaths(jobDescriptorKey, workflowDescriptor,
+      jesConfiguration)
     callPaths.returnCodeFilename should be("hello-rc.txt")
     callPaths.stderrFilename should be("hello-stderr.log")
     callPaths.stdoutFilename should be("hello-stdout.log")
@@ -32,16 +31,15 @@ class JesCallPathsSpec extends FlatSpec with Matchers with Mockito {
     val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
     val jesConfiguration = new JesConfiguration(JesBackendConfigurationDescriptor)
 
-    val callPaths = JesCallPaths(jobDescriptorKey, workflowDescriptor, jesConfiguration,
-      mockCredentials)
-    callPaths.returnCodePath.toString should
-      be(s"gs://my-cromwell-workflows-bucket/hello/${workflowDescriptor.id}/call-hello/hello-rc.txt")
-    callPaths.stdoutPath.toString should
-      be(s"gs://my-cromwell-workflows-bucket/hello/${workflowDescriptor.id}/call-hello/hello-stdout.log")
-    callPaths.stderrPath.toString should
-      be(s"gs://my-cromwell-workflows-bucket/hello/${workflowDescriptor.id}/call-hello/hello-stderr.log")
-    callPaths.jesLogPath.toString should
-      be(s"gs://my-cromwell-workflows-bucket/hello/${workflowDescriptor.id}/call-hello/hello.log")
+    val callPaths = JesJobPaths(jobDescriptorKey, workflowDescriptor, jesConfiguration)
+    callPaths.returnCode.toUri.toString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello/hello-rc.txt")
+    callPaths.stdout.toUri.toString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello/hello-stdout.log")
+    callPaths.stderr.toUri.toString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello/hello-stderr.log")
+    callPaths.jesLogPath.toUri.toString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello/hello.log")
   }
 
   it should "map the correct call context" in {
@@ -49,10 +47,9 @@ class JesCallPathsSpec extends FlatSpec with Matchers with Mockito {
     val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
     val jesConfiguration = new JesConfiguration(JesBackendConfigurationDescriptor)
 
-    val callPaths = JesCallPaths(jobDescriptorKey, workflowDescriptor, jesConfiguration,
-      mockCredentials)
-    callPaths.callContext.root.toString should
-      be(s"gs://my-cromwell-workflows-bucket/hello/${workflowDescriptor.id}/call-hello")
+    val callPaths = JesJobPaths(jobDescriptorKey, workflowDescriptor, jesConfiguration)
+    callPaths.callContext.root.toUri.toString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello")
     callPaths.callContext.stdout should be("hello-stdout.log")
     callPaths.callContext.stderr should be("hello-stderr.log")
   }
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesConfigurationSpec.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesConfigurationSpec.scala
index c2b77d38cfb..46068343c3f 100644
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesConfigurationSpec.scala
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesConfigurationSpec.scala
@@ -1,16 +1,25 @@
 package cromwell.backend.impl.jes
 
+import better.files.File
 import com.typesafe.config.{ConfigValueFactory, ConfigFactory}
 import cromwell.backend.BackendConfigurationDescriptor
 import org.scalatest.prop.TableDrivenPropertyChecks
-import org.scalatest.{FlatSpec, Matchers}
+import org.scalatest.{BeforeAndAfterAll, FlatSpec, Matchers}
 
-class JesConfigurationSpec extends FlatSpec with Matchers with TableDrivenPropertyChecks {
+class JesConfigurationSpec extends FlatSpec with Matchers with TableDrivenPropertyChecks with BeforeAndAfterAll {
 
   behavior of "JesConfigurationSpec"
 
+  val mockFile = File.newTemporaryFile()
+
+  override def afterAll(): Unit = {
+    mockFile.delete(true)
+
+    ()
+  }
+
   val globalConfig = ConfigFactory.parseString(
-    """
+    s"""
       |google {
       |
       |  application-name = "cromwell"
@@ -24,13 +33,13 @@ class JesConfigurationSpec extends FlatSpec with Matchers with TableDrivenProper
       |      name = "user-via-refresh"
       |      scheme = "refresh_token"
       |      client-id = "secret_id"
-      |      client-secret = "secret_secret"
+      |      client-secret = "${mockFile.pathAsString}"
       |    },
       |    {
       |      name = "service-account"
       |      scheme = "service_account"
       |      service-account-id = "my-service-account"
-      |      pem-file = "/path/to/file.pem"
+      |      pem-file = "${mockFile.pathAsString}"
       |    }
       |  ]
       |}
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesInitializationActorSpec.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesInitializationActorSpec.scala
index 4699402bcb8..73b8cb6de04 100644
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesInitializationActorSpec.scala
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesInitializationActorSpec.scala
@@ -7,14 +7,16 @@ import com.typesafe.config.{Config, ConfigFactory}
 import cromwell.backend.BackendWorkflowInitializationActor.{InitializationFailed, InitializationSuccess, Initialize}
 import cromwell.backend.impl.jes.authentication.GcsLocalizing
 import cromwell.backend.{BackendConfigurationDescriptor, BackendSpec, BackendWorkflowDescriptor}
+import cromwell.core.Tags.IntegrationTest
 import cromwell.core.logging.LoggingTest._
 import cromwell.core.{TestKitSuite, WorkflowOptions}
-import cromwell.filesystems.gcs.{RefreshTokenMode, SimpleClientSecrets}
+import cromwell.filesystems.gcs.GoogleConfiguration
+import cromwell.filesystems.gcs.auth.{RefreshTokenMode, SimpleClientSecrets}
 import cromwell.util.{EncryptionSpec, SampleWdl}
 import org.scalatest.{FlatSpecLike, Matchers}
 import org.specs2.mock.Mockito
 import spray.json._
-import wdl4s.Call
+import wdl4s.TaskCall
 
 import scala.concurrent.duration._
 
@@ -38,7 +40,7 @@ class JesInitializationActorSpec extends TestKitSuite("JesInitializationActorSpe
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
@@ -136,17 +138,17 @@ class JesInitializationActorSpec extends TestKitSuite("JesInitializationActorSpe
 
   val refreshTokenConfig = ConfigFactory.parseString(refreshTokenConfigTemplate)
 
-  private def getJesBackend(workflowDescriptor: BackendWorkflowDescriptor, calls: Seq[Call], conf: BackendConfigurationDescriptor) = {
+  private def getJesBackend(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[TaskCall], conf: BackendConfigurationDescriptor) = {
     system.actorOf(JesInitializationActor.props(workflowDescriptor, calls, new JesConfiguration(conf), emptyActor))
   }
 
   behavior of "JesInitializationActor"
 
-  it should "log a warning message when there are unsupported runtime attributes" in {
+  it should "log a warning message when there are unsupported runtime attributes" taggedAs IntegrationTest in {
     within(Timeout) {
       val workflowDescriptor = buildWorkflowDescriptor(HelloWorld,
         runtime = """runtime { docker: "ubuntu/latest" test: true }""")
-      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.workflowNamespace.workflow.calls,
+      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.workflow.taskCalls,
         defaultBackendConfig)
       val eventPattern =
         "Key/s [test] is/are not supported by JesBackend. Unsupported attributes will not be part of jobs executions."
@@ -163,7 +165,7 @@ class JesInitializationActorSpec extends TestKitSuite("JesInitializationActorSpe
   it should "return InitializationFailed when docker runtime attribute key is not present" in {
     within(Timeout) {
       val workflowDescriptor = buildWorkflowDescriptor(HelloWorld, runtime = """runtime { }""")
-      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.workflowNamespace.workflow.calls,
+      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.workflow.taskCalls,
         defaultBackendConfig)
       backend ! Initialize
       expectMsgPF() {
@@ -182,7 +184,7 @@ class JesInitializationActorSpec extends TestKitSuite("JesInitializationActorSpe
   private def buildJesInitializationTestingBits(backendConfig: Config = dockerBackendConfig): TestingBits = {
     val workflowOptions = WorkflowOptions.fromMap(Map("refresh_token" -> "mytoken")).get
     val workflowDescriptor = buildWorkflowDescriptor(SampleWdl.HelloWorld.wdlSource(), options = workflowOptions)
-    val calls = workflowDescriptor.workflowNamespace.workflow.calls
+    val calls = workflowDescriptor.workflow.taskCalls
     val backendConfigurationDescriptor = BackendConfigurationDescriptor(backendConfig, globalConfig)
     val jesConfiguration = new JesConfiguration(backendConfigurationDescriptor)
 
@@ -197,7 +199,7 @@ class JesInitializationActorSpec extends TestKitSuite("JesInitializationActorSpe
 
     val TestingBits(actorRef, _) = buildJesInitializationTestingBits(refreshTokenConfig)
     val actor = actorRef.underlyingActor
-    actor.refreshTokenAuth should be(Some(GcsLocalizing(RefreshTokenMode("user-via-refresh", "secret_id", "secret_secret"), "mytoken")))
+    actor.refreshTokenAuth should be(Some(GcsLocalizing(RefreshTokenMode("user-via-refresh", "secret_id", "secret_secret", GoogleConfiguration.GoogleScopes),  "mytoken")))
   }
 
   it should "generate the correct json content for no docker token and no refresh token" in {
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesJobExecutionActorSpec.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesJobExecutionActorSpec.scala
new file mode 100644
index 00000000000..2c085371816
--- /dev/null
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesJobExecutionActorSpec.scala
@@ -0,0 +1,111 @@
+package cromwell.backend.impl.jes
+
+import akka.actor.{Actor, ActorRef, Props}
+import akka.testkit.{TestActorRef, TestProbe}
+import cromwell.backend.BackendJobDescriptor
+import cromwell.core.TestKitSuite
+import org.scalatest.{FlatSpecLike, Matchers}
+import org.specs2.mock.Mockito
+
+import scala.concurrent.duration._
+import akka.testkit._
+import cromwell.backend.BackendJobExecutionActor.{ExecuteJobCommand, JobFailedNonRetryableResponse}
+import cromwell.backend.impl.jes.ControllableFailingJabjea.JabjeaExplode
+
+import scala.concurrent.{ExecutionContext, Promise}
+
+class JesJobExecutionActorSpec extends TestKitSuite("JesJobExecutionActorSpec") with FlatSpecLike with Matchers with Mockito {
+
+  behavior of "JesJobExecutionActor"
+
+  private val AwaitAlmostNothing = 100.milliseconds.dilated
+  private val TimeoutDuration = 10.seconds.dilated
+  implicit val ec: ExecutionContext = system.dispatcher
+
+  it should "catch failures in JABJEA initialization and fail the job accordingly" in {
+    val jobDescriptor = mock[BackendJobDescriptor]
+    val jesWorkflowInfo = mock[JesConfiguration]
+    val initializationData = mock[JesBackendInitializationData]
+    val serviceRegistryActor = system.actorOf(Props.empty)
+    val jesBackendSingletonActor = Option(system.actorOf(Props.empty))
+
+    val parent = TestProbe()
+    val deathwatch = TestProbe()
+    val testJJEA = TestActorRef[TestJesJobExecutionActor](
+      props = Props(new TestJesJobExecutionActor(jobDescriptor, jesWorkflowInfo, initializationData, serviceRegistryActor, jesBackendSingletonActor, Props(new ConstructorFailingJABJEA))),
+      supervisor = parent.ref)
+    deathwatch watch testJJEA
+
+    // Nothing happens:
+    parent.expectNoMsg(max = AwaitAlmostNothing)
+    deathwatch.expectNoMsg(max = AwaitAlmostNothing)
+
+    testJJEA.tell(msg = ExecuteJobCommand, sender = parent.ref)
+
+    parent.expectMsgPF(max = TimeoutDuration) {
+      case JobFailedNonRetryableResponse(jobKey, e, errorCode) =>
+        e.getMessage should be("JesAsyncBackendJobExecutionActor failed and didn't catch its exception.")
+    }
+  }
+
+  it should "catch failures at a random point during JABJEA processing and fail the job accordingly" in {
+    val jobDescriptor = mock[BackendJobDescriptor]
+    val jesWorkflowInfo = mock[JesConfiguration]
+    val initializationData = mock[JesBackendInitializationData]
+    val serviceRegistryActor = system.actorOf(Props.empty)
+    val jesBackendSingletonActor = Option(system.actorOf(Props.empty))
+
+    val parent = TestProbe()
+    val deathwatch = TestProbe()
+    val jabjeaConstructionPromise = Promise[ActorRef]()
+    val testJJEA = TestActorRef[TestJesJobExecutionActor](
+      props = Props(new TestJesJobExecutionActor(jobDescriptor, jesWorkflowInfo, initializationData, serviceRegistryActor, jesBackendSingletonActor, Props(new ControllableFailingJabjea(jabjeaConstructionPromise)))),
+      supervisor = parent.ref)
+    deathwatch watch testJJEA
+
+    // Nothing happens:
+    parent.expectNoMsg(max = AwaitAlmostNothing)
+    deathwatch.expectNoMsg(max = AwaitAlmostNothing)
+
+    testJJEA.tell(msg = ExecuteJobCommand, sender = parent.ref)
+
+    // Wait for the JABJEA to be spawned. Then kill it:
+    parent.expectNoMsg(max = AwaitAlmostNothing)
+    deathwatch.expectNoMsg(max = AwaitAlmostNothing)
+    jabjeaConstructionPromise.future foreach { _ ! JabjeaExplode }
+
+    parent.expectMsgPF(max = TimeoutDuration) {
+      case JobFailedNonRetryableResponse(jobKey, e, errorCode) =>
+        e.getMessage should be("JesAsyncBackendJobExecutionActor failed and didn't catch its exception.")
+    }
+  }
+}
+
+class TestJesJobExecutionActor(jobDescriptor: BackendJobDescriptor,
+                               jesWorkflowInfo: JesConfiguration,
+                               initializationData: JesBackendInitializationData,
+                               serviceRegistryActor: ActorRef,
+                               jesBackendSingletonActor: Option[ActorRef],
+                               fakeJabjeaProps: Props) extends JesJobExecutionActor(jobDescriptor, jesWorkflowInfo, initializationData, serviceRegistryActor, jesBackendSingletonActor) {
+  override def jabjeaProps: Props = fakeJabjeaProps
+}
+
+class ConstructorFailingJABJEA extends ControllableFailingJabjea(Promise[ActorRef]()) {
+  // Explode immediately in the constructor:
+  explode()
+}
+
+class ControllableFailingJabjea(constructionPromise: Promise[ActorRef]) extends Actor {
+  def explode() = {
+    val boom = 1 == 1
+    if (boom) throw new RuntimeException("Test Exception! Don't panic if this appears during a test run!")
+  }
+  constructionPromise.trySuccess(self)
+  override def receive = {
+    case JabjeaExplode => explode()
+  }
+}
+
+object ControllableFailingJabjea {
+  case object JabjeaExplode
+}
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesTestConfig.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesTestConfig.scala
index 03f17d65be2..25f06138753 100644
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesTestConfig.scala
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesTestConfig.scala
@@ -48,5 +48,5 @@ object JesTestConfig {
 
   val JesBackendConfig = ConfigFactory.parseString(JesBackendConfigString)
   val JesGlobalConfig = ConfigFactory.parseString(JesGlobalConfigString)
-  val JesBackendConfigurationDescriptor = new BackendConfigurationDescriptor(JesBackendConfig, JesGlobalConfig)
+  val JesBackendConfigurationDescriptor = BackendConfigurationDescriptor(JesBackendConfig, JesGlobalConfig)
 }
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesWorkflowPathsSpec.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesWorkflowPathsSpec.scala
index 3f1dea365a5..48dd3d74c6e 100644
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesWorkflowPathsSpec.scala
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/JesWorkflowPathsSpec.scala
@@ -1,12 +1,12 @@
 package cromwell.backend.impl.jes
 
 import cromwell.backend.BackendSpec
+import cromwell.core.TestKitSuite
 import cromwell.util.SampleWdl
-import org.scalatest.{FlatSpec, Matchers}
+import org.scalatest.{FlatSpecLike, Matchers}
 import org.specs2.mock.Mockito
-import cromwell.backend.impl.jes.MockObjects._
 
-class JesWorkflowPathsSpec extends FlatSpec with Matchers with Mockito {
+class JesWorkflowPathsSpec extends TestKitSuite with FlatSpecLike with Matchers with Mockito {
   import BackendSpec._
   import JesTestConfig._
 
@@ -16,11 +16,11 @@ class JesWorkflowPathsSpec extends FlatSpec with Matchers with Mockito {
     val workflowDescriptor = buildWorkflowDescriptor(SampleWdl.HelloWorld.wdlSource())
     val jesConfiguration = new JesConfiguration(JesBackendConfigurationDescriptor)
 
-    val workflowPaths = JesWorkflowPaths(workflowDescriptor, jesConfiguration, mockCredentials)(scala.concurrent.ExecutionContext.global)
-    workflowPaths.rootPath.toString should be("gs://my-cromwell-workflows-bucket")
-    workflowPaths.workflowRootPath.toString should
-      be(s"gs://my-cromwell-workflows-bucket/hello/${workflowDescriptor.id}")
-    workflowPaths.gcsAuthFilePath.toString should
-      be(s"gs://my-cromwell-workflows-bucket/hello/${workflowDescriptor.id}/${workflowDescriptor.id}_auth.json")
+    val workflowPaths = JesWorkflowPaths(workflowDescriptor, jesConfiguration)(system)
+    workflowPaths.executionRoot.toUri.toString should be("gs://my-cromwell-workflows-bucket/")
+    workflowPaths.workflowRoot.toUri.toString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/")
+    workflowPaths.gcsAuthFilePath.toUri.toString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/${workflowDescriptor.id}_auth.json")
   }
 }
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/MockObjects.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/MockObjects.scala
deleted file mode 100644
index 1cde38c4736..00000000000
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/MockObjects.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cromwell.backend.impl.jes
-
-import com.google.api.client.googleapis.testing.auth.oauth2.MockGoogleCredential
-import cromwell.backend.impl.jes.authentication.JesCredentials
-
-object MockObjects {
-  val mockCredential = new MockGoogleCredential.Builder().build()
-  val mockCredentials = JesCredentials(mockCredential, mockCredential)
-}
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/RunSpec.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/RunSpec.scala
index 39430abb22b..5398ed66c35 100644
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/RunSpec.scala
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/RunSpec.scala
@@ -3,13 +3,11 @@ package cromwell.backend.impl.jes
 import java.time.OffsetDateTime
 import java.util
 
-import com.google.api.client.googleapis.testing.auth.oauth2.MockGoogleCredential
 import com.google.api.client.util.ArrayMap
-import com.google.api.services.genomics.Genomics
 import com.google.api.services.genomics.model.Operation
+import cromwell.core.ExecutionEvent
 import org.scalatest.{FlatSpec, Matchers}
 import org.specs2.mock.{Mockito => MockitoTrait}
-import cromwell.core.ExecutionEvent
 
 import scala.collection.JavaConverters._
 
@@ -36,8 +34,6 @@ class RunSpec extends FlatSpec with Matchers with MockitoTrait {
 
     op.setMetadata(metadata.asJava)
 
-    val mockedCredentials = new MockGoogleCredential.Builder().build()
-    val genomics = new Genomics(mockedCredentials.getTransport, mockedCredentials.getJsonFactory, mockedCredentials)
     val list = Run.getEventList(op)
     list should contain theSameElementsAs List(
       ExecutionEvent("waiting for quota", OffsetDateTime.parse("2015-12-05T00:00:00+00:00")),
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/statuspolling/JesApiQueryManagerSpec.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/statuspolling/JesApiQueryManagerSpec.scala
index 1eaa422977a..c7434419a40 100644
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/statuspolling/JesApiQueryManagerSpec.scala
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/statuspolling/JesApiQueryManagerSpec.scala
@@ -2,7 +2,7 @@ package cromwell.backend.impl.jes.statuspolling
 
 import akka.actor.{ActorRef, Props}
 import akka.testkit.{TestActorRef, TestProbe}
-import cromwell.backend.impl.jes.Run
+import cromwell.backend.impl.jes.{JesConfiguration, Run}
 import cromwell.core.TestKitSuite
 import org.scalatest.{FlatSpecLike, Matchers}
 
@@ -65,49 +65,35 @@ class JesApiQueryManagerSpec extends TestKitSuite("JesApiQueryManagerSpec") with
   }
 
   AkkaTestUtil.actorDeathMethods(system) foreach { case (name, stopMethod) =>
-    it should s"catch polling actors if they $name and then recreate them" in {
-
+    /*
+      This test creates two statusPoller ActorRefs which are handed to the TestJesApiQueryManager. Work is added to that query
+      manager and then the first statusPoller requests work and is subsequently killed. The expectation is that:
+
+      - The work will return to the workQueue of the query manager
+      - The query manager will have registered a new statusPoller
+      - That statusPoller is the second ActorRef (and artifact of TestJesApiQueryManager)
+     */
+    it should s"catch polling actors if they $name, recreate them and add work back to the queue" in {
       val statusPoller1 = TestActorRef(Props(new AkkaTestUtil.DeathTestActor()), TestActorRef(new AkkaTestUtil.StoppingSupervisor()))
-      val statusPoller2 = TestActorRef(Props(new AkkaTestUtil.DeathTestActor()))
+      val statusPoller2 = TestActorRef(Props(new AkkaTestUtil.DeathTestActor()), TestActorRef(new AkkaTestUtil.StoppingSupervisor()))
       val jaqmActor: TestActorRef[TestJesApiQueryManager] = TestActorRef(TestJesApiQueryManager.props(statusPoller1, statusPoller2))
 
-      val statusRequesters = ((0 until BatchSize * 2) map { i => i -> TestProbe(name = s"StatusRequester_$i") }).toMap
+      val emptyActor = system.actorOf(Props.empty)
 
-      // Send a few status poll requests:
+       // Send a few status poll requests:
       BatchSize indexedTimes { index =>
-        val probe = statusRequesters(index)
-        jaqmActor.tell(msg = JesApiQueryManager.DoPoll(Run(index.toString, null)), sender = probe.ref)
-      }
-      BatchSize indexedTimes { i =>
-        val index = i + BatchSize // For the second half of the statusRequester set
-        val probe = statusRequesters(index)
-        jaqmActor.tell(msg = JesApiQueryManager.DoPoll(Run(index.toString, null)), sender = probe.ref)
+        jaqmActor.tell(msg = JesApiQueryManager.DoPoll(Run(index.toString, null)), sender = emptyActor)
       }
 
-      // Request a set of work from the middle of the queue:
-      val batchOffset = 2
-      jaqmActor.tell(msg = JesApiQueryManager.RequestJesPollingWork(batchOffset), sender = statusPoller1)
       jaqmActor.tell(msg = JesApiQueryManager.RequestJesPollingWork(BatchSize), sender = statusPoller1)
 
-      // Kill the original status poller:
       stopMethod(statusPoller1)
 
-      // Only the appropriate requesters get an error:
-      (0 until batchOffset) foreach { index =>
-        val probe = statusRequesters(index)
-        probe.expectNoMsg(max = AwaitAlmostNothing)
-      }
-      (batchOffset until batchOffset + BatchSize) foreach { index =>
-        val probe = statusRequesters(index)
-        probe.expectMsg(max = TestExecutionTimeout, hint = s"Polling error to requester #$index", obj = JesPollingActor.JesPollError)
-      }
-      (batchOffset + BatchSize until 2 * BatchSize) foreach { index =>
-        val probe = statusRequesters(index)
-        probe.expectNoMsg(max = AwaitAlmostNothing)
+      eventually {
+        jaqmActor.underlyingActor.testPollerCreations should be (2)
+        jaqmActor.underlyingActor.queueSize should be (BatchSize)
+        jaqmActor.underlyingActor.statusPollerEquals(statusPoller2) should be (true)
       }
-
-      // Check the next status poller gets created:
-      eventually { jaqmActor.underlyingActor.testPollerCreations should be(2) }
     }
   }
 }
@@ -122,8 +108,7 @@ object JesApiQueryManagerSpec {
 /**
   * This test class allows us to hook into the JesApiQueryManager's makeStatusPoller and provide our own TestProbes instead
   */
-class TestJesApiQueryManager(statusPollerProbes: ActorRef*) extends JesApiQueryManager {
-
+class TestJesApiQueryManager(qps: Int, statusPollerProbes: ActorRef*) extends JesApiQueryManager(qps) {
   var testProbes: Queue[ActorRef] = _
   var testPollerCreations: Int = _
 
@@ -133,7 +118,7 @@ class TestJesApiQueryManager(statusPollerProbes: ActorRef*) extends JesApiQueryM
   }
 
   override private[statuspolling] def makeStatusPoller(): ActorRef = {
-    // Initialise the queue, if necessary:
+    // Initialize the queue, if necessary:
     if (testProbes == null) {
       init()
     }
@@ -146,8 +131,14 @@ class TestJesApiQueryManager(statusPollerProbes: ActorRef*) extends JesApiQueryM
     testProbes = newQueue
     probe
   }
+
+  def queueSize = workQueue.size
+  def statusPollerEquals(otherStatusPoller: ActorRef) = statusPoller == otherStatusPoller
 }
 
 object TestJesApiQueryManager {
-  def props(statusPollers: ActorRef*): Props = Props(new TestJesApiQueryManager(statusPollers: _*))
+  import cromwell.backend.impl.jes.JesTestConfig.JesBackendConfigurationDescriptor
+  val jesConfiguration = new JesConfiguration(JesBackendConfigurationDescriptor)
+
+  def props(statusPollers: ActorRef*): Props = Props(new TestJesApiQueryManager(jesConfiguration.qps, statusPollers: _*))
 }
diff --git a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActorSpec.scala b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActorSpec.scala
index b861cbf0f51..aa29b0df382 100644
--- a/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActorSpec.scala
+++ b/supportedBackends/jes/src/test/scala/cromwell/backend/impl/jes/statuspolling/JesPollingActorSpec.scala
@@ -13,7 +13,7 @@ import com.google.api.client.googleapis.batch.BatchRequest
 import com.google.api.client.googleapis.batch.json.JsonBatchCallback
 import com.google.api.client.googleapis.json.GoogleJsonError
 import com.google.api.services.genomics.model.Operation
-import cromwell.backend.impl.jes.{Run, RunStatus}
+import cromwell.backend.impl.jes.{JesConfiguration, Run, RunStatus}
 import cromwell.backend.impl.jes.statuspolling.JesApiQueryManager.JesStatusPollQuery
 import cromwell.backend.impl.jes.statuspolling.JesPollingActor.JesPollFailed
 import cromwell.backend.impl.jes.statuspolling.TestJesPollingActor.{CallbackFailure, CallbackSuccess, JesBatchCallbackResponse}
@@ -29,9 +29,17 @@ class JesPollingActorSpec extends TestKitSuite("JesPollingActor") with FlatSpecL
   implicit val DefaultPatienceConfig = PatienceConfig(TestExecutionTimeout)
   val AwaitAlmostNothing = 30.milliseconds.dilated
 
+  import cromwell.backend.impl.jes.JesTestConfig.JesBackendConfigurationDescriptor
+  val jesConfiguration = new JesConfiguration(JesBackendConfigurationDescriptor)
+
   var managerProbe: TestProbe = _
   var jpActor: TestActorRef[TestJesPollingActor] = _
 
+  it should "correctly calculate batch intervals" in {
+    JesPollingActor.determineBatchInterval(10) shouldBe 9.seconds
+    JesPollingActor.determineBatchInterval(100) shouldBe 1.second
+  }
+
   it should "query for work and wait for a reply" in {
     managerProbe.expectMsgClass(max = TestExecutionTimeout, c = classOf[JesApiQueryManager.RequestJesPollingWork])
     managerProbe.expectNoMsg(max = AwaitAlmostNothing)
@@ -77,7 +85,7 @@ class JesPollingActorSpec extends TestKitSuite("JesPollingActor") with FlatSpecL
 
   before {
     managerProbe = TestProbe()
-    jpActor = TestActorRef(TestJesPollingActor.props(managerProbe.ref), managerProbe.ref)
+    jpActor = TestActorRef(TestJesPollingActor.props(managerProbe.ref, jesConfiguration), managerProbe.ref)
   }
 }
 
@@ -94,8 +102,9 @@ object JesPollingActorSpec extends Mockito {
   * - Mocks out the methods which actually call out to JES, and allows the callbacks to be triggered in a testable way
   * - Also waits a **lot** less time before polls!
   */
-class TestJesPollingActor(manager: ActorRef) extends JesPollingActor(manager) with Mockito {
-  override val BatchInterval = 10.milliseconds
+class TestJesPollingActor(manager: ActorRef, qps: Int) extends JesPollingActor(manager, qps) with Mockito {
+
+  override lazy val batchInterval = 10.milliseconds
 
   var operationStatusResponses: Queue[RunStatus] = Queue.empty
   var resultHandlers: Queue[JsonBatchCallback[Operation]] = Queue.empty
@@ -123,7 +132,7 @@ class TestJesPollingActor(manager: ActorRef) extends JesPollingActor(manager) wi
 }
 
 object TestJesPollingActor {
-  def props(manager: ActorRef) = Props(new TestJesPollingActor(manager))
+  def props(manager: ActorRef, jesConfiguration: JesConfiguration) = Props(new TestJesPollingActor(manager, jesConfiguration.qps))
 
   sealed trait JesBatchCallbackResponse
   case object CallbackSuccess extends JesBatchCallbackResponse
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala
index ad9761bca10..a47209c20ea 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala
@@ -48,15 +48,20 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
     * @param taskName The name of the task to retrieve from the precomputed wdl namespace.
     * @param inputs   The customized inputs to this task.
     */
-  def writeTaskScript(script: File, taskName: String, inputs: CallInputs): Unit = {
+  def writeTaskScript(script: File, taskName: String, inputs: WorkflowCoercedInputs): Unit = {
     val task = configInitializationData.wdlNamespace.findTask(taskName).
       getOrElse(throw new RuntimeException(s"Unable to find task $taskName"))
-    val command = task.instantiateCommand(inputs, NoFunctions).get
+    val inputsWithFqns = inputs map { case (k, v) => s"$taskName.$k" -> v }
+    val command = task.instantiateCommand(task.inputsFromMap(inputsWithFqns), NoFunctions).get
     jobLogger.info(s"executing: $command")
-    script.write(
-      s"""|#!/bin/bash
-          |$command
-          |""".stripMargin)
+    val scriptBody =
+      s"""
+
+#!/bin/bash
+$command
+
+""".trim + "\n"
+    script.write(scriptBody)
     ()
   }
 
@@ -64,7 +69,7 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
     * The inputs that are not specified by the config, that will be passed into a command for both submit and
     * submit-docker.
     */
-  private lazy val standardInputs: CallInputs = {
+  private lazy val standardInputs: WorkflowCoercedInputs = {
     Map(
       JobNameInput -> WdlString(jobName),
       CwdInput -> WdlString(jobPaths.callRoot.toString),
@@ -77,7 +82,7 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
   /**
     * Extra arguments if this is a submit-docker command, or Map.empty.
     */
-  private lazy val dockerInputs: CallInputs = {
+  private lazy val dockerInputs: WorkflowCoercedInputs = {
     if (isDockerRun) {
       Map(
         DockerCwdInput -> WdlString(jobPaths.callDockerRoot.toString)
@@ -91,7 +96,7 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
     * The arguments generated from the backend config's list of attributes. These will include things like CPU, memory,
     * and other custom arguments like "backend_queue_name", "backend_billing_project", etc.
     */
-  private lazy val runtimeAttributeInputs: CallInputs = {
+  private lazy val runtimeAttributeInputs: WorkflowCoercedInputs = {
     val declarationValidations = configInitializationData.declarationValidations
     val inputOptions = declarationValidations map { declarationValidation =>
       declarationValidation.extractWdlValueOption(validatedRuntimeAttributes) map { wdlValue =>
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashing.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashing.scala
index 0fc377aac55..f8ff92cfd3b 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashing.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashing.scala
@@ -3,13 +3,21 @@ package cromwell.backend.impl.sfs.config
 import akka.event.LoggingAdapter
 import better.files._
 import cromwell.backend.callcaching.FileHashingActor.SingleFileHashRequest
+import cromwell.core.path.DefaultPathBuilder
 import cromwell.util.TryWithResource._
 
+import scala.language.postfixOps
 import scala.util.Try
 
 private[config] object ConfigBackendFileHashing {
-  def getMd5Result(request: SingleFileHashRequest, log: LoggingAdapter): Try[String] =
-    tryWithResource(() => File(request.file.valueString).newInputStream) { inputStream =>
+  def getMd5Result(request: SingleFileHashRequest, log: LoggingAdapter): Try[String] ={
+    val path = DefaultPathBuilder.build(request.file.valueString) recover {
+      case failure => throw new RuntimeException("Failed to construct path to hash", failure)
+    } get
+
+    tryWithResource(() => File(path).newInputStream) { inputStream =>
       org.apache.commons.codec.digest.DigestUtils.md5Hex(inputStream)
     }
+  }
+
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategy.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategy.scala
index 6261e65c96d..f453cf315db 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategy.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategy.scala
@@ -4,13 +4,15 @@ import akka.event.LoggingAdapter
 import better.files.File
 import com.typesafe.config.Config
 import cromwell.backend.callcaching.FileHashingActor.SingleFileHashRequest
+import cromwell.backend.sfs.SharedFileSystemBackendInitializationData
+import cromwell.core.path.PathFactory
 import cromwell.util.TryWithResource._
 import cromwell.util.FileUtil._
 import net.ceedubs.ficus.Ficus._
 import org.apache.commons.codec.digest.DigestUtils
 import org.slf4j.LoggerFactory
 
-import scala.util.Try
+import scala.util.{Failure, Try}
 
 object ConfigHashingStrategy {
   val logger = LoggerFactory.getLogger(getClass)
@@ -37,14 +39,22 @@ abstract class ConfigHashingStrategy {
   protected lazy val checkSiblingMessage = if (checkSiblingMd5) "Check first for sibling md5 and if not found " else ""
 
   def getHash(request: SingleFileHashRequest, log: LoggingAdapter): Try[String] = {
-    val file = File(request.file.valueString).followSymlinks
+    def usingSFSInitData(initData: SharedFileSystemBackendInitializationData) = {
+      val pathBuilders = initData.workflowPaths.pathBuilders
+      val file = PathFactory.buildFile(request.file.valueString, pathBuilders).followSymlinks
 
-    if (checkSiblingMd5) {
-      precomputedMd5(file) match {
-        case Some(md5) => Try(md5.contentAsString)
-        case None => hash(file)
-      }
-    } else hash(file)
+      if (checkSiblingMd5) {
+        precomputedMd5(file) match {
+          case Some(md5) => Try(md5.contentAsString)
+          case None => hash(file)
+        }
+      } else hash(file)
+    }
+
+    request.initializationData match {
+      case Some(initData: SharedFileSystemBackendInitializationData) => usingSFSInitData(initData)
+      case _ => Failure(new IllegalArgumentException("Need SharedFileSystemBackendInitializationData to calculate hash."))
+    }
   }
 
   private def precomputedMd5(file: File): Option[File] = {
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigWdlNamespace.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigWdlNamespace.scala
index cb56e35a082..161768da1c6 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigWdlNamespace.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigWdlNamespace.scala
@@ -44,7 +44,7 @@ class ConfigWdlNamespace(backendConfig: Config) {
     */
   val wdlNamespace = {
     try {
-      WdlNamespace.load(wdlSource)
+      WdlNamespace.loadUsingSource(wdlSource, None, None)
     } catch {
       case exception: Exception =>
         throw new RuntimeException(s"Error parsing generated wdl:\n$wdlSource".stripMargin, exception)
@@ -74,7 +74,7 @@ object ConfigWdlNamespace {
 
   private def makeTask(taskName: String, command: String, declarations: String): Task = {
     val wdlSource = makeWdlSource(taskName, command, declarations)
-    val wdlNamespace = WdlNamespace.load(wdlSource)
+    val wdlNamespace = WdlNamespace.loadUsingSource(wdlSource, None, None)
     wdlNamespace.findTask(taskName).getOrElse(throw new RuntimeException(s"Couldn't find task $taskName"))
   }
 
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala
index ec3aecbf76d..37a42a5c38a 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala
@@ -24,7 +24,7 @@ object DeclarationValidation {
     * @return The DeclarationValidation object for the declaration.
     */
   def fromDeclaration(declaration: Declaration): DeclarationValidation = {
-    declaration.name match {
+    declaration.unqualifiedName match {
       // Docker and CPU are special keys understood by cromwell.
       case DockerValidation.key => new DeclarationValidation(declaration, DockerValidation.instance)
       case CpuValidation.key => new DeclarationValidation(declaration, CpuValidation.default)
@@ -34,11 +34,11 @@ object DeclarationValidation {
       // All other declarations must be a Boolean, Float, Integer, or String.
       case _ =>
         val validator: PrimitiveRuntimeAttributesValidation[_] = declaration.wdlType match {
-          case WdlBooleanType => new BooleanRuntimeAttributesValidation(declaration.name)
-          case WdlFloatType => new FloatRuntimeAttributesValidation(declaration.name)
-          case WdlIntegerType => new IntRuntimeAttributesValidation(declaration.name)
-          case WdlStringType => new StringRuntimeAttributesValidation(declaration.name)
-          case other => throw new RuntimeException(s"Unsupported config runtime attribute $other ${declaration.name}")
+          case WdlBooleanType => new BooleanRuntimeAttributesValidation(declaration.unqualifiedName)
+          case WdlFloatType => new FloatRuntimeAttributesValidation(declaration.unqualifiedName)
+          case WdlIntegerType => new IntRuntimeAttributesValidation(declaration.unqualifiedName)
+          case WdlStringType => new StringRuntimeAttributesValidation(declaration.unqualifiedName)
+          case other => throw new RuntimeException(s"Unsupported config runtime attribute $other ${declaration.unqualifiedName}")
         }
         new DeclarationValidation(declaration, validator)
     }
@@ -52,7 +52,7 @@ object DeclarationValidation {
   * @param instanceValidation A basic instance validation for the declaration.
   */
 class DeclarationValidation(declaration: Declaration, instanceValidation: RuntimeAttributesValidation[_]) {
-  val key = declaration.name
+  val key = declaration.unqualifiedName
 
   /**
     * Creates a validation, by adding on defaults if they're specified in the declaration, and then making the
@@ -74,7 +74,7 @@ class DeclarationValidation(declaration: Declaration, instanceValidation: Runtim
     val validationDefault = if (declaration.expression.isDefined)
       default(instanceValidation, declaration.expression.get)
     else instanceValidation
-    if (declaration.postfixQuantifier.contains("?")) validationDefault.optional else validationDefault
+    if (declaration.wdlType.isInstanceOf[WdlOptionalType]) validationDefault.optional else validationDefault
   }
 
   /**
@@ -151,7 +151,7 @@ class MemoryDeclarationValidation(declaration: Declaration)
   }
 
   private lazy val declarationMemoryUnit: MemoryUnit = {
-    val suffix = memoryUnitSuffix(declaration.name)
+    val suffix = memoryUnitSuffix(declaration.unqualifiedName)
     val memoryUnitOption = MemoryUnit.values.find(_.suffixes.map(_.toLowerCase).contains(suffix.toLowerCase))
     memoryUnitOption match {
       case Some(memoryUnit) => memoryUnit
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/GcsWorkflowFileSystemProvider.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/GcsWorkflowFileSystemProvider.scala
deleted file mode 100644
index d96140014f3..00000000000
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/GcsWorkflowFileSystemProvider.scala
+++ /dev/null
@@ -1,36 +0,0 @@
-package cromwell.backend.sfs
-
-import cats.data.Validated.{Invalid, Valid}
-import cromwell.backend.wfs.{WorkflowFileSystemProvider, WorkflowFileSystemProviderParams}
-import cromwell.filesystems.gcs.GoogleAuthMode.GoogleAuthOptions
-import cromwell.filesystems.gcs.{GcsFileSystem, GcsFileSystemProvider, GoogleConfiguration}
-import net.ceedubs.ficus.Ficus._
-import wdl4s.ValidationException
-
-import scala.util.Try
-
-object GcsWorkflowFileSystemProvider extends WorkflowFileSystemProvider {
-  override def fileSystemOption(params: WorkflowFileSystemProviderParams): Option[GcsFileSystem] = {
-    params.fileSystemConfig.as[Option[String]]("gcs.auth") map gcsFileSystem(params)
-  }
-
-  private def gcsFileSystem(params: WorkflowFileSystemProviderParams)(gcsAuthName: String): GcsFileSystem = {
-    val workflowOptions = params.workflowOptions
-    val globalConfig = params.globalConfig
-    val googleConfig = GoogleConfiguration(globalConfig)
-    val googleAuthModeValidation = googleConfig.auth(gcsAuthName)
-
-    val gcsAuthMode = googleAuthModeValidation match {
-      case Valid(googleAuthMode) => googleAuthMode
-      case Invalid(errors) =>
-        throw new ValidationException("Could not create gcs filesystem from configuration", errors)
-    }
-
-    val authOptions = new GoogleAuthOptions {
-      override def get(key: String): Try[String] = workflowOptions.get(key)
-    }
-
-    val storage = gcsAuthMode.buildStorage(authOptions, googleConfig.applicationName)
-    GcsFileSystem(GcsFileSystemProvider(storage)(params.fileSystemExecutionContext))
-  }
-}
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystem.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystem.scala
index 20c8c3d39bc..188391c450b 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystem.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystem.scala
@@ -1,22 +1,24 @@
 package cromwell.backend.sfs
 
-import java.nio.file.{FileSystem, Path, Paths}
+import java.nio.file.{Path, Paths}
 
 import cats.instances.try_._
 import cats.syntax.functor._
 import com.typesafe.config.Config
+import com.typesafe.scalalogging.StrictLogging
 import cromwell.backend.io.JobPaths
 import cromwell.core._
-import wdl4s.CallInputs
+import cromwell.core.path.PathFactory
+import cromwell.util.TryUtil
+import wdl4s.EvaluatedTaskInputs
 import wdl4s.types.{WdlArrayType, WdlMapType}
-import wdl4s.util.TryUtil
 import wdl4s.values._
 
 import scala.collection.JavaConverters._
 import scala.language.postfixOps
 import scala.util.{Failure, Success, Try}
 
-object SharedFileSystem {
+object SharedFileSystem extends StrictLogging {
   import better.files._
 
   final case class AttemptedLookupResult(name: String, value: Try[WdlValue]) {
@@ -42,31 +44,38 @@ object SharedFileSystem {
   }
 
   private def localizePathViaCopy(originalPath: File, executionPath: File): Try[Unit] = {
-    executionPath.parent.createDirectories()
-    val executionTmpPath = pathPlusSuffix(executionPath, ".tmp")
-    Try(originalPath.copyTo(executionTmpPath, overwrite = true).moveTo(executionPath, overwrite = true)).void
+    val action = Try {
+      executionPath.parent.createDirectories()
+      val executionTmpPath = pathPlusSuffix(executionPath, ".tmp")
+      originalPath.copyTo(executionTmpPath, overwrite = true).moveTo(executionPath, overwrite = true)
+    }.void
+    logOnFailure(action, "copy")
   }
 
   private def localizePathViaHardLink(originalPath: File, executionPath: File): Try[Unit] = {
-    executionPath.parent.createDirectories()
-    // link.linkTo(target) returns target,
-    // however we want to return the link, not the target, so map the result back to executionPath
-
-    // -Ywarn-value-discard
-    // Try(executionPath.linkTo(originalPath, symbolic = false)) map { _ => executionPath }
-    Try { executionPath.linkTo(originalPath, symbolic = false) } void
+    val action = Try {
+      executionPath.parent.createDirectories()
+      executionPath.linkTo(originalPath, symbolic = false)
+    }.void
+    logOnFailure(action, "hard link")
   }
 
   private def localizePathViaSymbolicLink(originalPath: File, executionPath: File): Try[Unit] = {
       if (originalPath.isDirectory) Failure(new UnsupportedOperationException("Cannot localize directory with symbolic links"))
       else {
-        executionPath.parent.createDirectories()
-        // -Ywarn-value-discard
-        // Try(executionPath.linkTo(originalPath, symbolic = true)) map { _ => executionPath }
-        Try { executionPath.linkTo(originalPath, symbolic = true) } void
+        val action = Try {
+          executionPath.parent.createDirectories()
+          executionPath.linkTo(originalPath, symbolic = true)
+        }.void
+        logOnFailure(action, "symbolic link")
       }
   }
 
+  private def logOnFailure(action: Try[Unit], actionLabel: String): Try[Unit] = {
+    if (action.isFailure) logger.warn(s"Localization via $actionLabel has failed: ${action.failed.get.getMessage}")
+    action
+  }
+
   private def duplicate(description: String, source: File, dest: File, strategies: Stream[DuplicationStrategy]) = {
     import cromwell.util.FileUtil._
 
@@ -134,6 +143,9 @@ trait SharedFileSystem extends PathFactory {
       case array: WdlArray =>
         val mappedArray = array.value map outputMapper(job)
         TryUtil.sequence(mappedArray) map { WdlArray(array.wdlType, _) }
+      case map: WdlMap =>
+        val mappedMap = map.value mapValues outputMapper(job)
+        TryUtil.sequenceMap(mappedMap) map { WdlMap(map.wdlType, _) }
       case other => Success(other)
     }
   }
@@ -145,11 +157,8 @@ trait SharedFileSystem extends PathFactory {
   /**
    * Return a possibly altered copy of inputs reflecting any localization of input file paths that might have
    * been performed for this `Backend` implementation.
-   * NOTE: This ends up being a backdoor implementation of Backend.adjustInputPaths as both LocalBackend and SgeBackend
-   *    end up with this implementation and thus use it to satisfy their contract with Backend.
-   *    This is yuck-tastic and I consider this a FIXME, but not for this refactor
    */
-  def localizeInputs(inputsRoot: Path, docker: Boolean, filesystems: List[FileSystem], inputs: CallInputs): Try[CallInputs] = {
+  def localizeInputs(inputsRoot: Path, docker: Boolean)(inputs: EvaluatedTaskInputs): Try[EvaluatedTaskInputs] = {
     val strategies = if (docker) DockerLocalizers else Localizers
 
     // Use URI to identify protocol scheme and strip it out
@@ -161,12 +170,13 @@ trait SharedFileSystem extends PathFactory {
       host map { h => Paths.get(h, uriPath) } getOrElse Paths.get(uriPath)
     }
 
-    /**
+    /*
       * Transform an original input path to a path in the call directory.
       * The new path matches the original path, it only "moves" the root to be the call directory.
       */
+
     def toCallPath(path: String): Try[PairOfFiles] = Try {
-      val src = buildFile(path, filesystems)
+      val src = buildFile(path)
       // Strip out potential prefix protocol
       val localInputPath = stripProtocolScheme(src.path)
       val dest = if (File(inputsRoot).isParentOf(localInputPath)) File(localInputPath)
@@ -181,7 +191,7 @@ trait SharedFileSystem extends PathFactory {
     // Optional function to adjust the path to "docker path" if the call runs in docker
     val localizeFunction = localizeWdlValue(toCallPath, strategies.toStream) _
     val localizedValues = inputs.toSeq map {
-      case (name, value) => localizeFunction(value) map { name -> _ }
+      case (declaration, value) => localizeFunction(value) map { declaration -> _ }
     }
 
     TryUtil.sequence(localizedValues, "Failures during localization").map(_.toMap) recover {
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemAsyncJobExecutionActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemAsyncJobExecutionActor.scala
index 3013b12af94..ef5ef5e89f5 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemAsyncJobExecutionActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemAsyncJobExecutionActor.scala
@@ -1,6 +1,6 @@
 package cromwell.backend.sfs
 
-import java.nio.file.{FileAlreadyExistsException, Path, Paths}
+import java.nio.file.{FileAlreadyExistsException, Path}
 
 import akka.actor.{Actor, ActorLogging, ActorRef}
 import akka.event.LoggingReceive
@@ -12,9 +12,11 @@ import cromwell.backend.async.{AbortedExecutionHandle, AsyncBackendJobExecutionA
 import cromwell.backend.io.WorkflowPathsBackendInitializationData
 import cromwell.backend.sfs.SharedFileSystem._
 import cromwell.backend.validation._
-import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendJobDescriptor, OutputEvaluator}
-import cromwell.core.JobOutputs
+import cromwell.backend.wdl.{OutputEvaluator, Command}
+import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendJobDescriptor}
+import cromwell.core.CallOutputs
 import cromwell.core.logging.JobLogging
+import cromwell.core.path.DefaultPathBuilder
 import cromwell.core.retry.SimpleExponentialBackoff
 import cromwell.services.keyvalue.KeyValueServiceActor._
 import wdl4s.values.{WdlArray, WdlFile, WdlMap, WdlValue}
@@ -135,11 +137,13 @@ trait SharedFileSystemAsyncJobExecutionActor
 
   override lazy val backendInitializationDataOption = params.backendInitializationDataOption
 
-  def toDockerPath(path: WdlValue): WdlValue = {
+  def toUnixPath(docker: Boolean)(path: WdlValue): WdlValue = {
     path match {
-      case file: WdlFile => WdlFile(jobPaths.toDockerPath(Paths.get(path.valueString)).toString)
-      case array: WdlArray => WdlArray(array.wdlType, array.value map toDockerPath)
-      case map: WdlMap => WdlMap(map.wdlType, map.value mapValues toDockerPath)
+      case file: WdlFile =>
+        val cleanPath = DefaultPathBuilder.build(path.valueString).get
+        WdlFile(if (docker) jobPaths.toDockerPath(cleanPath).toString else cleanPath.toString)
+      case array: WdlArray => WdlArray(array.wdlType, array.value map toUnixPath(docker))
+      case map: WdlMap => WdlMap(map.wdlType, map.value mapValues toUnixPath(docker))
       case wdlValue => wdlValue
     }
   }
@@ -150,8 +154,8 @@ trait SharedFileSystemAsyncJobExecutionActor
 
   lazy val workflowDescriptor = jobDescriptor.workflowDescriptor
   lazy val call = jobDescriptor.key.call
-  lazy val fileSystems = WorkflowPathsBackendInitializationData.fileSystems(backendInitializationDataOption)
-  lazy val callEngineFunction = SharedFileSystemExpressionFunctions(jobPaths, fileSystems)
+  lazy val pathBuilders = WorkflowPathsBackendInitializationData.pathBuilders(backendInitializationDataOption)
+  lazy val callEngineFunction = SharedFileSystemExpressionFunctions(jobPaths, pathBuilders)
   override lazy val workflowId = jobDescriptor.workflowDescriptor.id
   override lazy val jobTag = jobDescriptor.key.tag
 
@@ -165,12 +169,18 @@ trait SharedFileSystemAsyncJobExecutionActor
   }
 
   def instantiatedScript: String = {
-    val pathTransformFunction: WdlValue => WdlValue = if (isDockerRun) toDockerPath else identity
-    val tryCommand = sharedFileSystem.localizeInputs(jobPaths.callInputsRoot,
-      isDockerRun, fileSystems, jobDescriptor.inputs) flatMap { localizedInputs =>
-      call.task.instantiateCommand(localizedInputs, callEngineFunction, pathTransformFunction)
+    val pathTransformFunction = toUnixPath(isDockerRun) _
+    val localizer = sharedFileSystem.localizeInputs(jobPaths.callInputsRoot, isDockerRun) _
+    
+    Command.instantiate(
+      jobDescriptor, 
+      callEngineFunction,
+      localizer,
+      pathTransformFunction
+    ) match {
+      case Success(command) => command
+      case Failure(ex) => throw new RuntimeException("Failed to instantiate command line", ex)
     }
-    tryCommand.get
   }
 
   override def executeOrRecover(mode: ExecutionMode)(implicit ec: ExecutionContext) = {
@@ -244,14 +254,19 @@ trait SharedFileSystemAsyncJobExecutionActor
     val rcPath = if (isDockerRun) jobPaths.toDockerPath(jobPaths.returnCode) else jobPaths.returnCode
     val rcTmpPath = s"$rcPath.tmp"
 
-    File(jobPaths.script).write(
-      s"""#!/bin/sh
-          |(
-          | cd $cwd
-          | $instantiatedCommand
-          |)
-          |echo $$? > $rcTmpPath
-          |mv $rcTmpPath $rcPath""".stripMargin)
+    val scriptBody = s"""
+
+#!/bin/sh
+(
+ cd $cwd
+ $instantiatedCommand
+)
+echo $$? > $rcTmpPath
+mv $rcTmpPath $rcPath
+
+""".trim + "\n"
+
+    File(jobPaths.script).write(scriptBody)
   }
 
   /**
@@ -313,7 +328,7 @@ trait SharedFileSystemAsyncJobExecutionActor
   def processReturnCode()(implicit ec: ExecutionContext): Future[ExecutionHandle] = {
     val returnCodeTry = Try(File(jobPaths.returnCode).contentAsString.stripLineEnd.toInt)
 
-    lazy val badReturnCodeMessage = s"Call ${call.fullyQualifiedName}: return code was ${returnCodeTry.getOrElse("(none)")}"
+    lazy val badReturnCodeMessage = s"Call ${jobDescriptor.key.tag}: return code was ${returnCodeTry.getOrElse("(none)")}"
 
     lazy val badReturnCodeResponse = Future.successful(
       FailedNonRetryableExecutionHandle(new Exception(badReturnCodeMessage), returnCodeTry.toOption))
@@ -323,7 +338,7 @@ trait SharedFileSystemAsyncJobExecutionActor
     def processSuccess(returnCode: Int) = {
       val successfulFuture = for {
         outputs <- Future.fromTry(processOutputs())
-      } yield SuccessfulExecutionHandle(outputs, returnCode, jobPaths.detritusPaths.mapValues(_.toString), Seq.empty)
+      } yield SuccessfulExecutionHandle(outputs, returnCode, jobPaths.detritusPaths, Seq.empty)
 
       successfulFuture recover {
         case failed: Throwable =>
@@ -371,7 +386,7 @@ trait SharedFileSystemAsyncJobExecutionActor
     }
   }
 
-  private def processOutputs(): Try[JobOutputs] = {
+  private def processOutputs(): Try[CallOutputs] = {
     OutputEvaluator.evaluateOutputs(jobDescriptor, callEngineFunction, sharedFileSystem.outputMapper(jobPaths))
   }
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemBackendLifecycleActorFactory.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemBackendLifecycleActorFactory.scala
index edacd530311..1ac3093dce1 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemBackendLifecycleActorFactory.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemBackendLifecycleActorFactory.scala
@@ -1,11 +1,16 @@
 package cromwell.backend.sfs
 
 import akka.actor.{ActorRef, Props}
+import cats.data.Validated.{Invalid, Valid}
 import cromwell.backend.BackendJobExecutionActor.BackendJobExecutionResponse
 import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendJobDescriptor, BackendJobDescriptorKey, BackendLifecycleActorFactory, BackendWorkflowDescriptor}
 import cromwell.core.Dispatcher
 import cromwell.core.Dispatcher._
-import wdl4s.Call
+import cromwell.core.path.{DefaultPathBuilderFactory, PathBuilderFactory}
+import cromwell.filesystems.gcs.{GcsPathBuilderFactory, GoogleConfiguration}
+import lenthall.exception.MessageAggregation
+import net.ceedubs.ficus.Ficus._
+import wdl4s.TaskCall
 import wdl4s.expression.WdlStandardLibraryFunctions
 
 import scala.concurrent.Promise
@@ -17,6 +22,23 @@ import scala.concurrent.Promise
   */
 trait SharedFileSystemBackendLifecycleActorFactory extends BackendLifecycleActorFactory {
 
+  /**
+    * If the backend sets a gcs authentication mode, try to create a PathBuilderFactory with it.
+    */
+  lazy val gcsPathBuilderFactory: Option[GcsPathBuilderFactory] = {
+    configurationDescriptor.backendConfig.as[Option[String]]("filesystems.gcs.auth") map { configAuth =>
+      GoogleConfiguration(configurationDescriptor.globalConfig).auth(configAuth) match {
+        case Valid(auth) => GcsPathBuilderFactory(auth)
+        case Invalid(error) => throw new MessageAggregation {
+          override def exceptionContext: String = "Failed to parse gcs auth configuration"
+          override def errorMessages: Traversable[String] = error.toList
+        }
+      }
+    }
+  }
+
+  lazy val pathBuilderFactories: List[PathBuilderFactory] = List(gcsPathBuilderFactory, Option(DefaultPathBuilderFactory)).flatten
+
   /**
     * Config values for the backend, and a pointer to the global config.
     *
@@ -41,10 +63,10 @@ trait SharedFileSystemBackendLifecycleActorFactory extends BackendLifecycleActor
     */
   def asyncJobExecutionActorClass: Class[_ <: SharedFileSystemAsyncJobExecutionActor]
 
-  override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor, calls: Seq[Call],
+  override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[TaskCall],
                                                 serviceRegistryActor: ActorRef) = {
     val params = SharedFileSystemInitializationActorParams(serviceRegistryActor, workflowDescriptor,
-      configurationDescriptor, calls)
+      configurationDescriptor, calls, pathBuilderFactories)
     Option(Props(initializationActorClass, params).withDispatcher(Dispatcher.BackendDispatcher))
   }
 
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemCacheHitCopyingActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemCacheHitCopyingActor.scala
index 62dc98b0781..6ba44914da9 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemCacheHitCopyingActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemCacheHitCopyingActor.scala
@@ -1,10 +1,13 @@
 package cromwell.backend.sfs
 
-import java.nio.file.{Path, Paths}
+import java.nio.file.Path
 
 import akka.actor.ActorRef
 import cromwell.backend.callcaching.CacheHitDuplicating
 import cromwell.backend.{BackendCacheHitCopyingActor, BackendConfigurationDescriptor, BackendInitializationData, BackendJobDescriptor}
+import cromwell.core.path.PathFactory
+
+import scala.util.Try
 
 class SharedFileSystemCacheHitCopyingActor(override val jobDescriptor: BackendJobDescriptor,
                                            override val configurationDescriptor: BackendConfigurationDescriptor,
@@ -17,7 +20,7 @@ class SharedFileSystemCacheHitCopyingActor(override val jobDescriptor: BackendJo
 
   override lazy val destinationJobDetritusPaths = jobPaths.detritusPaths
 
-  override protected def getPath(file: String) = Paths.get(file)
+  override protected def getPath(file: String) = Try(PathFactory.buildPath(file, jobPaths.pathBuilders))
 
   override protected def duplicate(source: Path, destination: Path) = {
     // -Ywarn-value-discard
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemExpressionFunctions.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemExpressionFunctions.scala
index 1f73cac3838..7dc5172ba91 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemExpressionFunctions.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemExpressionFunctions.scala
@@ -1,12 +1,13 @@
 package cromwell.backend.sfs
 
-import java.nio.file.{FileSystem, Path}
+import java.nio.file.Path
 
-import cromwell.backend.io.{JobPaths, WorkflowPathsBackendInitializationData}
+import cromwell.backend.io.{JobPaths, JobPathsWithDocker, WorkflowPathsBackendInitializationData}
 import cromwell.backend.wdl._
 import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendJobDescriptorKey, BackendWorkflowDescriptor}
 import cromwell.core.CallContext
-import wdl4s.expression.WdlStandardLibraryFunctions
+import cromwell.core.path.PathBuilder
+import wdl4s.expression.PureStandardLibraryFunctionsLike
 import wdl4s.values.{WdlFile, WdlValue}
 
 import scala.language.postfixOps
@@ -20,49 +21,50 @@ object SharedFileSystemExpressionFunctions {
   def apply(workflowDescriptor: BackendWorkflowDescriptor,
             jobKey: BackendJobDescriptorKey,
             configurationDescriptor: BackendConfigurationDescriptor,
-            fileSystems: List[FileSystem]): SharedFileSystemExpressionFunctions = {
-    val jobPaths = new JobPaths(workflowDescriptor, configurationDescriptor.backendConfig, jobKey)
+            pathBuilders: List[PathBuilder]): SharedFileSystemExpressionFunctions = {
+    val jobPaths = new JobPathsWithDocker(jobKey, workflowDescriptor, configurationDescriptor.backendConfig)
     val callContext = CallContext(
       jobPaths.callExecutionRoot,
       jobPaths.stdout.toString,
       jobPaths.stderr.toString
     )
-    new SharedFileSystemExpressionFunctions(fileSystems, callContext)
+    new SharedFileSystemExpressionFunctions(pathBuilders, callContext)
   }
 
-  def apply(jobPaths: JobPaths, fileSystems: List[FileSystem]): SharedFileSystemExpressionFunctions = {
+  def apply(jobPaths: JobPaths, pathBuilders: List[PathBuilder]): SharedFileSystemExpressionFunctions = {
     val callContext = CallContext(
       jobPaths.callExecutionRoot,
       jobPaths.stdout.toString,
       jobPaths.stderr.toString
     )
-    new SharedFileSystemExpressionFunctions(fileSystems, callContext)
+    new SharedFileSystemExpressionFunctions(pathBuilders, callContext)
   }
 
   def apply(workflowDescriptor: BackendWorkflowDescriptor,
             configurationDescriptor: BackendConfigurationDescriptor,
             jobKey: BackendJobDescriptorKey,
             initializationData: Option[BackendInitializationData]) = {
-    val jobPaths = new JobPaths(workflowDescriptor, configurationDescriptor.backendConfig, jobKey)
+    val jobPaths = new JobPathsWithDocker(jobKey, workflowDescriptor, configurationDescriptor.backendConfig)
     val callContext = CallContext(
       jobPaths.callExecutionRoot,
       jobPaths.stdout.toString,
       jobPaths.stderr.toString
     )
 
-    new SharedFileSystemExpressionFunctions(WorkflowPathsBackendInitializationData.fileSystems(initializationData), callContext)
+    new SharedFileSystemExpressionFunctions(WorkflowPathsBackendInitializationData.pathBuilders(initializationData), callContext)
   }
 }
 
-class SharedFileSystemExpressionFunctions(override val fileSystems: List[FileSystem],
+class SharedFileSystemExpressionFunctions(override val pathBuilders: List[PathBuilder],
                                           context: CallContext
-                                 ) extends WdlStandardLibraryFunctions with PureFunctions with ReadLikeFunctions with WriteFunctions {
+                                 ) extends PureStandardLibraryFunctionsLike with ReadLikeFunctions with WriteFunctions {
   import SharedFileSystemExpressionFunctions._
   import better.files._
 
+  override def writeTempFile(path: String, prefix: String, suffix: String, content: String): String = super[WriteFunctions].writeTempFile(path, prefix, suffix, content)
   override def globPath(glob: String) = context.root.toString
   override def glob(path: String, pattern: String): Seq[String] = {
-    File(toPath(path)).glob(s"**/$pattern") map { _.pathAsString } toSeq
+    File(context.root).glob(s"**/$pattern") map { _.pathAsString } toSeq
   }
 
   override val writeDirectory = context.root
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemInitializationActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemInitializationActor.scala
index 54a370b3993..52c8fbeaf72 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemInitializationActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemInitializationActor.scala
@@ -4,10 +4,11 @@ import akka.actor.ActorRef
 import better.files._
 import cromwell.backend.io.{WorkflowPaths, WorkflowPathsBackendInitializationData}
 import cromwell.backend.validation.RuntimeAttributesDefault
-import cromwell.backend.wfs.{DefaultWorkflowFileSystemProvider, WorkflowFileSystemProvider}
+import cromwell.backend.wfs.WorkflowPathBuilder
 import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor, BackendWorkflowInitializationActor}
-import cromwell.core.{Dispatcher, WorkflowOptions}
-import wdl4s.Call
+import cromwell.core.WorkflowOptions
+import cromwell.core.path.PathBuilderFactory
+import wdl4s.TaskCall
 import wdl4s.values.WdlValue
 
 import scala.concurrent.Future
@@ -18,7 +19,8 @@ case class SharedFileSystemInitializationActorParams
   serviceRegistryActor: ActorRef,
   workflowDescriptor: BackendWorkflowDescriptor,
   configurationDescriptor: BackendConfigurationDescriptor,
-  calls: Seq[Call]
+  calls: Set[TaskCall],
+  pathBuilderFactories: List[PathBuilderFactory]
 )
 
 class SharedFileSystemBackendInitializationData
@@ -37,7 +39,7 @@ class SharedFileSystemInitializationActor(params: SharedFileSystemInitialization
 
   override lazy val workflowDescriptor: BackendWorkflowDescriptor = params.workflowDescriptor
   override lazy val configurationDescriptor: BackendConfigurationDescriptor = params.configurationDescriptor
-  override lazy val calls: Seq[Call] = params.calls
+  override lazy val calls: Set[TaskCall] = params.calls
   override lazy val serviceRegistryActor: ActorRef = params.serviceRegistryActor
 
   def runtimeAttributesBuilder: SharedFileSystemValidatedRuntimeAttributesBuilder =
@@ -49,11 +51,9 @@ class SharedFileSystemInitializationActor(params: SharedFileSystemInitialization
     ).toMap
   }
 
-  val providers = Seq(GcsWorkflowFileSystemProvider, DefaultWorkflowFileSystemProvider)
-  val ioDispatcher = context.system.dispatchers.lookup(Dispatcher.IoDispatcher)
+  val pathBuilders = params.pathBuilderFactories map { _.withOptions(workflowDescriptor.workflowOptions)(context.system) }
 
-  val workflowPaths = WorkflowFileSystemProvider.workflowPaths(configurationDescriptor, workflowDescriptor,
-    providers, ioDispatcher)
+  val workflowPaths = WorkflowPathBuilder.workflowPaths(configurationDescriptor, workflowDescriptor, pathBuilders)
 
   override def beforeAll(): Future[Option[BackendInitializationData]] = {
     Future.fromTry(Try {
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemJobCachingActorHelper.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemJobCachingActorHelper.scala
index d9d4f42137d..54453ab756e 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemJobCachingActorHelper.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemJobCachingActorHelper.scala
@@ -4,7 +4,7 @@ import akka.actor.{Actor, ActorRef}
 import com.typesafe.config.{Config, ConfigFactory}
 import cromwell.backend.BackendInitializationData
 import cromwell.backend.callcaching.JobCachingActorHelper
-import cromwell.backend.io.JobPaths
+import cromwell.backend.io.{JobPathsWithDocker, WorkflowPathsBackendInitializationData}
 import cromwell.backend.validation.{RuntimeAttributesValidation, ValidatedRuntimeAttributes}
 import cromwell.core.logging.JobLogging
 import net.ceedubs.ficus.Ficus._
@@ -17,7 +17,7 @@ trait SharedFileSystemJobCachingActorHelper extends JobCachingActorHelper {
   def serviceRegistryActor: ActorRef
 
   lazy val jobPaths =
-    new JobPaths(jobDescriptor.workflowDescriptor, configurationDescriptor.backendConfig, jobDescriptor.key)
+    new JobPathsWithDocker(jobDescriptor.key, jobDescriptor.workflowDescriptor, configurationDescriptor.backendConfig)
 
   lazy val initializationData = BackendInitializationData.
     as[SharedFileSystemBackendInitializationData](backendInitializationDataOption)
@@ -37,6 +37,7 @@ trait SharedFileSystemJobCachingActorHelper extends JobCachingActorHelper {
   }
 
   lazy val sharedFileSystem = new SharedFileSystem {
+    override val pathBuilders = WorkflowPathsBackendInitializationData.pathBuilders(backendInitializationDataOption)
     override lazy val sharedFileSystemConfig = {
       configurationDescriptor.backendConfig.as[Option[Config]]("filesystems.local").getOrElse(ConfigFactory.empty())
     }
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategySpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategySpec.scala
index 81edb6f6062..bd25dfc5183 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategySpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategySpec.scala
@@ -6,6 +6,9 @@ import akka.event.LoggingAdapter
 import better.files._
 import com.typesafe.config.{ConfigFactory, ConfigValueFactory}
 import cromwell.backend.callcaching.FileHashingActor.SingleFileHashRequest
+import cromwell.backend.io.WorkflowPaths
+import cromwell.backend.sfs.SharedFileSystemBackendInitializationData
+import cromwell.core.path.DefaultPathBuilder
 import org.apache.commons.codec.digest.DigestUtils
 import org.scalatest.prop.TableDrivenPropertyChecks
 import org.scalatest.{BeforeAndAfterAll, FlatSpec, Matchers}
@@ -43,7 +46,14 @@ class ConfigHashingStrategySpec extends FlatSpec with Matchers with TableDrivenP
       symLink
     } else file
 
+    val workflowPaths = mock[WorkflowPaths]
+    workflowPaths.pathBuilders returns List(DefaultPathBuilder)
+
+    val initData = mock[SharedFileSystemBackendInitializationData]
+    initData.workflowPaths returns workflowPaths
+
     request.file returns WdlFile(requestFile.pathAsString)
+    request.initializationData returns Option(initData)
 
     request
   }
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemInitializationActorSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemInitializationActorSpec.scala
index 64dbfa9d73b..1cbfd2cfeee 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemInitializationActorSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemInitializationActorSpec.scala
@@ -8,7 +8,7 @@ import cromwell.backend.{BackendConfigurationDescriptor, BackendWorkflowDescript
 import cromwell.core.TestKitSuite
 import cromwell.core.logging.LoggingTest._
 import org.scalatest.{Matchers, WordSpecLike}
-import wdl4s.Call
+import wdl4s.TaskCall
 
 import scala.concurrent.duration._
 
@@ -30,14 +30,14 @@ class SharedFileSystemInitializationActorSpec extends TestKitSuite("SharedFileSy
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
 
-  private def getActorRef(workflowDescriptor: BackendWorkflowDescriptor, calls: Seq[Call],
+  private def getActorRef(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[TaskCall],
                           conf: BackendConfigurationDescriptor) = {
-    val params = SharedFileSystemInitializationActorParams(emptyActor, workflowDescriptor, conf, calls)
+    val params = SharedFileSystemInitializationActorParams(emptyActor, workflowDescriptor, conf, calls, List.empty)
     val props = Props(new SharedFileSystemInitializationActor(params))
     system.actorOf(props, "SharedFileSystemInitializationActor")
   }
@@ -47,7 +47,7 @@ class SharedFileSystemInitializationActorSpec extends TestKitSuite("SharedFileSy
       within(Timeout) {
         val workflowDescriptor = buildWorkflowDescriptor(HelloWorld, runtime = """runtime { unsupported: 1 }""")
         val conf = emptyBackendConfig
-        val backend = getActorRef(workflowDescriptor, workflowDescriptor.workflowNamespace.workflow.calls, conf)
+        val backend = getActorRef(workflowDescriptor, workflowDescriptor.workflow.taskCalls, conf)
         val pattern = "Key/s [unsupported] is/are not supported by backend. " +
           "Unsupported attributes will not be part of jobs executions."
         EventFilter.warning(pattern = escapePattern(pattern), occurrences = 1) intercept {
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
index f697a7f4b11..cd573576620 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
@@ -5,17 +5,16 @@ import java.nio.file.{Files, Paths}
 import akka.testkit.TestDuration
 import better.files._
 import com.typesafe.config.ConfigFactory
-import cromwell.backend.BackendJobExecutionActor.{AbortedResponse, FailedNonRetryableResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{AbortedResponse, JobFailedNonRetryableResponse, JobSucceededResponse}
 import cromwell.backend.BackendLifecycleActor.AbortJobCommand
 import cromwell.backend.io.TestWorkflows._
-import cromwell.backend.io.{JobPaths, TestWorkflows}
+import cromwell.backend.io.{JobPathsWithDocker, TestWorkflows}
 import cromwell.backend.sfs.TestLocalAsyncJobExecutionActor._
 import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendJobDescriptorKey, BackendSpec, RuntimeAttributeDefinition}
 import cromwell.core.Tags._
 import cromwell.core._
 import cromwell.services.keyvalue.KeyValueServiceActor.{KvJobKey, KvPair, ScopedKey}
 import org.scalatest.concurrent.PatienceConfiguration.Timeout
-import org.scalatest.mockito.MockitoSugar
 import org.scalatest.prop.TableDrivenPropertyChecks
 import org.scalatest.{FlatSpecLike, OptionValues}
 import wdl4s.types._
@@ -25,17 +24,17 @@ import wdl4s.values._
 import scala.concurrent.duration._
 
 class SharedFileSystemJobExecutionActorSpec extends TestKitSuite("SharedFileSystemJobExecutionActorSpec")
-  with FlatSpecLike with BackendSpec with MockitoSugar with TableDrivenPropertyChecks with OptionValues {
+  with FlatSpecLike with BackendSpec with TableDrivenPropertyChecks with OptionValues {
 
   behavior of "SharedFileSystemJobExecutionActor"
 
   lazy val runtimeAttributeDefinitions = SharedFileSystemValidatedRuntimeAttributesBuilder.default.definitions.toSet
 
   def executeSpec(docker: Boolean) = {
-    val expectedOutputs: JobOutputs = Map(
+    val expectedOutputs: CallOutputs = Map(
       "salutation" -> JobOutput(WdlString("Hello you !"))
     )
-    val expectedResponse = SucceededResponse(mock[BackendJobDescriptorKey], Some(0), expectedOutputs, None, Seq.empty)
+    val expectedResponse = JobSucceededResponse(mock[BackendJobDescriptorKey], Some(0), expectedOutputs, None, Seq.empty)
     val runtime = if (docker) """runtime { docker: "ubuntu:latest" }""" else ""
     val workflowDescriptor = buildWorkflowDescriptor(HelloWorld, runtime = runtime)
     val workflow = TestWorkflow(workflowDescriptor, emptyBackendConfig, expectedResponse)
@@ -52,7 +51,7 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite("SharedFileSyst
   }
 
   it should "send back an execution failure if the task fails" in {
-    val expectedResponse = FailedNonRetryableResponse(mock[BackendJobDescriptorKey], new Exception(""), Option(1))
+    val expectedResponse = JobFailedNonRetryableResponse(mock[BackendJobDescriptorKey], new Exception(""), Option(1))
     val workflow = TestWorkflow(buildWorkflowDescriptor(GoodbyeWorld), emptyBackendConfig, expectedResponse)
     val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor, Map.empty, WorkflowOptions.empty, runtimeAttributeDefinitions), workflow.config)
     testWorkflow(workflow, backend)
@@ -82,11 +81,11 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite("SharedFileSyst
     val jsonInputFile = createCannedFile("localize", "content from json inputs").pathAsString
     val callInputFile = createCannedFile("localize", "content from call inputs").pathAsString
     val inputs = Map(
-      "inputFileFromCallInputs" -> WdlFile(callInputFile),
-      "inputFileFromJson" -> WdlFile(jsonInputFile)
+      "wf_localize.localize.inputFileFromCallInputs" -> WdlFile(callInputFile),
+      "wf_localize.localize.inputFileFromJson" -> WdlFile(jsonInputFile)
     )
 
-    val expectedOutputs: JobOutputs = Map(
+    val expectedOutputs: CallOutputs = Map(
       "out" -> JobOutput(WdlArray(WdlArrayType(WdlStringType),
         Array(
           WdlString("content from json inputs"),
@@ -106,10 +105,10 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite("SharedFileSyst
       val runtime = if (docker) """runtime { docker: "ubuntu:latest" } """ else ""
       val workflowDescriptor = buildWorkflowDescriptor(InputFiles, inputs, runtime = runtime)
       val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflowDescriptor, inputs, WorkflowOptions.empty, runtimeAttributeDefinitions), conf)
-      val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor, Map.empty, WorkflowOptions.empty, runtimeAttributeDefinitions)
-      val expectedResponse = SucceededResponse(jobDescriptor.key, Some(0), expectedOutputs, None, Seq.empty)
+      val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor, inputs, WorkflowOptions.empty, runtimeAttributeDefinitions)
+      val expectedResponse = JobSucceededResponse(jobDescriptor.key, Some(0), expectedOutputs, None, Seq.empty)
 
-      val jobPaths = new JobPaths(workflowDescriptor, conf.backendConfig, jobDescriptor.key)
+      val jobPaths = new JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, conf.backendConfig)
 
       whenReady(backend.execute) { executionResponse =>
         assertResponse(executionResponse, expectedResponse)
@@ -157,7 +156,7 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite("SharedFileSyst
     val backendRef = createBackendRef(jobDescriptor, emptyBackendConfig)
     val backend = backendRef.underlyingActor
 
-    val jobPaths = new JobPaths(workflowDescriptor, ConfigFactory.empty, jobDescriptor.key)
+    val jobPaths = new JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, ConfigFactory.empty)
     File(jobPaths.callExecutionRoot).createDirectories()
     File(jobPaths.stdout).write("Hello stubby ! ")
     File(jobPaths.stderr).touch()
@@ -189,13 +188,13 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite("SharedFileSyst
 
     whenReady(execute, Timeout(10.seconds.dilated)) { executionResponse =>
       if (writeReturnCode) {
-        executionResponse should be(a[SucceededResponse])
-        val succeededResponse = executionResponse.asInstanceOf[SucceededResponse]
+        executionResponse should be(a[JobSucceededResponse])
+        val succeededResponse = executionResponse.asInstanceOf[JobSucceededResponse]
         succeededResponse.returnCode.value should be(0)
         succeededResponse.jobOutputs should be(Map("salutation" -> JobOutput(WdlString("Hello stubby !"))))
       } else {
-        executionResponse should be(a[FailedNonRetryableResponse])
-        val failedResponse = executionResponse.asInstanceOf[FailedNonRetryableResponse]
+        executionResponse should be(a[JobFailedNonRetryableResponse])
+        val failedResponse = executionResponse.asInstanceOf[JobFailedNonRetryableResponse]
         failedResponse.returnCode should be(empty)
         failedResponse.throwable should be(a[RuntimeException])
         failedResponse.throwable.getMessage should startWith("Unable to determine that 0 is alive, and")
@@ -219,20 +218,20 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite("SharedFileSyst
   it should "execute shards from a scatter" in {
     val workflowDescriptor = buildWorkflowDescriptor(TestWorkflows.Scatter)
 
-    val call = workflowDescriptor.workflowNamespace.workflow.calls.head
+    val call = workflowDescriptor.workflow.taskCalls.head
 
     0 to 2 foreach { shard =>
       // This assumes that engine will give us the evaluated value of the scatter item at the correct index
       // If this is not the case, more context/logic will need to be moved to the backend so it can figure it out by itself
-      val symbolMaps: Map[LocallyQualifiedName, WdlInteger] = Map("intNumber" -> WdlInteger(shard))
+      val symbolMaps: Map[LocallyQualifiedName, WdlInteger] = Map("scattering.intNumber" -> WdlInteger(shard))
 
       val runtimeAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, WorkflowOptions.empty)(call.task.runtimeAttributes.attrs)
 
       val jobDescriptor: BackendJobDescriptor =
-        BackendJobDescriptor(workflowDescriptor, BackendJobDescriptorKey(call, Option(shard), 1), runtimeAttributes, symbolMaps)
+        BackendJobDescriptor(workflowDescriptor, BackendJobDescriptorKey(call, Option(shard), 1), runtimeAttributes, fqnMapToDeclarationMap(symbolMaps))
       val backend = createBackend(jobDescriptor, emptyBackendConfig)
       val response =
-        SucceededResponse(mock[BackendJobDescriptorKey], Some(0), Map("out" -> JobOutput(WdlInteger(shard))), None, Seq.empty)
+        JobSucceededResponse(mock[BackendJobDescriptorKey], Some(0), Map("out" -> JobOutput(WdlInteger(shard))), None, Seq.empty)
       executeJobAndAssertOutputs(backend, response)
     }
   }
@@ -240,12 +239,12 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite("SharedFileSyst
   it should "post process outputs" in {
     val inputFile = createCannedFile("localize", "content from json inputs").pathAsString
     val inputs = Map {
-      "inputFile" -> WdlFile(inputFile)
+      "wf_localize.localize.inputFile" -> WdlFile(inputFile)
     }
     val workflowDescriptor = buildWorkflowDescriptor(OutputProcess, inputs)
     val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor, inputs, WorkflowOptions.empty, runtimeAttributeDefinitions)
     val backend = createBackend(jobDescriptor, emptyBackendConfig)
-    val jobPaths = new JobPaths(workflowDescriptor, emptyBackendConfig.backendConfig, jobDescriptor.key)
+    val jobPaths = new JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, emptyBackendConfig.backendConfig)
     val expectedA = WdlFile(jobPaths.callExecutionRoot.resolve("a").toAbsolutePath.toString)
     val expectedB = WdlFile(jobPaths.callExecutionRoot.resolve("dir").toAbsolutePath.resolve("b").toString)
     val expectedOutputs = Map(
@@ -253,13 +252,13 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite("SharedFileSyst
       "o2" -> JobOutput(WdlArray(WdlArrayType(WdlFileType), Seq(expectedA, expectedB))),
       "o3" -> JobOutput(WdlFile(inputFile))
     )
-    val expectedResponse = SucceededResponse(jobDescriptor.key, Some(0), expectedOutputs, None, Seq.empty)
+    val expectedResponse = JobSucceededResponse(jobDescriptor.key, Some(0), expectedOutputs, None, Seq.empty)
 
     executeJobAndAssertOutputs(backend, expectedResponse)
   }
 
-  it should "fail post processing if an output fail is not found" in {
-    val expectedResponse = FailedNonRetryableResponse(mock[BackendJobDescriptorKey],
+  it should "fail post processing if an output file is not found" in {
+    val expectedResponse = JobFailedNonRetryableResponse(mock[BackendJobDescriptorKey],
       AggregatedException(Seq.empty, "Could not process output, file not found"), Option(0))
     val workflow = TestWorkflow(buildWorkflowDescriptor(MissingOutputProcess), emptyBackendConfig, expectedResponse)
     val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor, Map.empty, WorkflowOptions.empty, runtimeAttributeDefinitions), workflow.config)
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemSpec.scala
index c3874a14ae8..d7c39924ce7 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemSpec.scala
@@ -1,22 +1,24 @@
 package cromwell.backend.sfs
 
-import java.nio.file.{FileSystems, Files}
+import java.nio.file.Files
 
 import better.files._
 import com.typesafe.config.{Config, ConfigFactory}
+import cromwell.core.path.DefaultPathBuilder
+import cromwell.backend.BackendSpec
 import org.scalatest.prop.TableDrivenPropertyChecks
 import org.scalatest.{FlatSpec, Matchers}
 import org.specs2.mock.Mockito
 import wdl4s.values.WdlFile
 
-class SharedFileSystemSpec extends FlatSpec with Matchers with Mockito with TableDrivenPropertyChecks {
+class SharedFileSystemSpec extends FlatSpec with Matchers with Mockito with TableDrivenPropertyChecks with BackendSpec {
 
   behavior of "SharedFileSystem"
 
   val defaultLocalization = ConfigFactory.parseString(""" localization: [copy, hard-link, soft-link] """)
   val hardLinkLocalization = ConfigFactory.parseString(""" localization: [hard-link] """)
   val softLinkLocalization = ConfigFactory.parseString(""" localization: [soft-link] """)
-  val localFS = List(FileSystems.getDefault)
+  val localPathBuilder = List(DefaultPathBuilder)
 
 
   def localizationTest(config: Config,
@@ -34,12 +36,16 @@ class SharedFileSystemSpec extends FlatSpec with Matchers with Mockito with Tabl
       dest.touch()
     }
 
-    val inputs = Map("input" -> WdlFile(orig.pathAsString))
-    val sharedFS = new SharedFileSystem { override val sharedFileSystemConfig = config }
-    val result = sharedFS.localizeInputs(callDir.path, docker = docker, localFS, inputs)
+    val inputs = fqnMapToDeclarationMap(Map("input" -> WdlFile(orig.pathAsString)))
+    val sharedFS = new SharedFileSystem {
+      override val pathBuilders = localPathBuilder
+      override val sharedFileSystemConfig = config
+    }
+    val localizedinputs = Map(inputs.head._1 -> WdlFile(dest.pathAsString))
+    val result = sharedFS.localizeInputs(callDir.path, docker = docker)(inputs)
 
     result.isSuccess shouldBe true
-    result.get should contain theSameElementsAs Map("input" -> WdlFile(dest.pathAsString))
+    result.get should contain theSameElementsAs localizedinputs
 
     dest.exists shouldBe true
     countLinks(dest) should be(linkNb)
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/TestLocalAsyncJobExecutionActor.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/TestLocalAsyncJobExecutionActor.scala
index 0ae09136744..72d2c6e9993 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/TestLocalAsyncJobExecutionActor.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/TestLocalAsyncJobExecutionActor.scala
@@ -3,7 +3,7 @@ package cromwell.backend.sfs
 import akka.actor.{ActorSystem, Props}
 import akka.testkit.TestActorRef
 import cromwell.backend.BackendJobExecutionActor.BackendJobExecutionResponse
-import cromwell.backend.io.WorkflowPaths
+import cromwell.backend.io.WorkflowPathsWithDocker
 import cromwell.backend.validation.{DockerValidation, RuntimeAttributesValidation}
 import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor}
 
@@ -34,7 +34,7 @@ object TestLocalAsyncJobExecutionActor {
   def createBackendRef(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor)
                       (implicit system: ActorSystem): TestActorRef[SharedFileSystemJobExecutionActor] = {
     val emptyActor = system.actorOf(Props.empty)
-    val workflowPaths = new WorkflowPaths(jobDescriptor.workflowDescriptor, configurationDescriptor.backendConfig)
+    val workflowPaths = new WorkflowPathsWithDocker(jobDescriptor.workflowDescriptor, configurationDescriptor.backendConfig)
     val initializationData = new SharedFileSystemBackendInitializationData(workflowPaths,
       SharedFileSystemValidatedRuntimeAttributesBuilder.default.withValidation(DockerValidation.optional))
 
diff --git a/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkBackendFactory.scala b/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkBackendFactory.scala
index ef01c9985f9..6fd75323e4a 100644
--- a/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkBackendFactory.scala
+++ b/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkBackendFactory.scala
@@ -2,14 +2,14 @@ package cromwell.backend.impl.spark
 
 import akka.actor.{ActorRef, ActorSystem, Props}
 import cromwell.backend._
+import cromwell.backend.io.JobPathsWithDocker
 import cromwell.backend.sfs.SharedFileSystemExpressionFunctions
-import cromwell.backend.io.JobPaths
 import cromwell.core.CallContext
-import wdl4s.Call
+import wdl4s.TaskCall
 import wdl4s.expression.WdlStandardLibraryFunctions
 
 case class SparkBackendFactory(name: String, configurationDescriptor: BackendConfigurationDescriptor, actorSystem: ActorSystem) extends BackendLifecycleActorFactory {
-  override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor, calls: Seq[Call], serviceRegistryActor: ActorRef): Option[Props] = {
+  override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[TaskCall], serviceRegistryActor: ActorRef): Option[Props] = {
     Option(SparkInitializationActor.props(workflowDescriptor, calls, configurationDescriptor, serviceRegistryActor))
   }
 
@@ -22,13 +22,13 @@ case class SparkBackendFactory(name: String, configurationDescriptor: BackendCon
 
   override def expressionLanguageFunctions(workflowDescriptor: BackendWorkflowDescriptor, jobKey: BackendJobDescriptorKey,
                                            initializationData: Option[BackendInitializationData]): WdlStandardLibraryFunctions = {
-    val jobPaths = new JobPaths(workflowDescriptor, configurationDescriptor.backendConfig, jobKey)
+    val jobPaths = new JobPathsWithDocker(jobKey, workflowDescriptor, configurationDescriptor.backendConfig)
     val callContext = new CallContext(
       jobPaths.callExecutionRoot,
       jobPaths.stdout.toAbsolutePath.toString,
       jobPaths.stderr.toAbsolutePath.toString
     )
 
-    new SharedFileSystemExpressionFunctions(SparkJobExecutionActor.DefaultFileSystems, callContext)
+    new SharedFileSystemExpressionFunctions(SparkJobExecutionActor.DefaultPathBuilders, callContext)
   }
 }
diff --git a/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkInitializationActor.scala b/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkInitializationActor.scala
index 2c4b5f94f76..1ff66aa2474 100644
--- a/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkInitializationActor.scala
+++ b/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkInitializationActor.scala
@@ -6,7 +6,7 @@ import cromwell.backend.validation.RuntimeAttributesDefault
 import cromwell.backend.validation.RuntimeAttributesKeys._
 import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor, BackendWorkflowInitializationActor}
 import cromwell.core.WorkflowOptions
-import wdl4s.Call
+import wdl4s.TaskCall
 import wdl4s.types.{WdlBooleanType, WdlIntegerType, WdlStringType}
 import wdl4s.values.WdlValue
 
@@ -18,14 +18,14 @@ object SparkInitializationActor {
     SparkRuntimeAttributes.NumberOfExecutorsKey, SparkRuntimeAttributes.AppMainClassKey)
 
   def props(workflowDescriptor: BackendWorkflowDescriptor,
-            calls: Seq[Call],
+            calls: Set[TaskCall],
             configurationDescriptor: BackendConfigurationDescriptor,
             serviceRegistryActor: ActorRef): Props =
     Props(new SparkInitializationActor(workflowDescriptor, calls, configurationDescriptor, serviceRegistryActor))
 }
 
 class SparkInitializationActor(override val workflowDescriptor: BackendWorkflowDescriptor,
-                               override val calls: Seq[Call],
+                               override val calls: Set[TaskCall],
                                override val configurationDescriptor: BackendConfigurationDescriptor,
                                override val serviceRegistryActor: ActorRef) extends BackendWorkflowInitializationActor {
 
diff --git a/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkJobExecutionActor.scala b/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkJobExecutionActor.scala
index c793338eb0b..927ac7d45ec 100644
--- a/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkJobExecutionActor.scala
+++ b/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkJobExecutionActor.scala
@@ -1,15 +1,16 @@
 package cromwell.backend.impl.spark
 
-import java.nio.file.FileSystems
 import java.nio.file.attribute.PosixFilePermission
 
 import akka.actor.Props
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, FailedNonRetryableResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, JobFailedNonRetryableResponse, JobSucceededResponse}
 import cromwell.backend.impl.spark.SparkClusterProcess._
-import cromwell.backend.io.JobPaths
+import cromwell.backend.io.JobPathsWithDocker
 import cromwell.backend.sfs.{SharedFileSystem, SharedFileSystemExpressionFunctions}
+import cromwell.backend.wdl.Command
 import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendJobExecutionActor}
-import cromwell.core.{TailedWriter, UntailedWriter}
+import cromwell.core.path.JavaWriterImplicits._
+import cromwell.core.path.{DefaultPathBuilder, TailedWriter, UntailedWriter}
 import wdl4s.parser.MemoryUnit
 import wdl4s.util.TryUtil
 
@@ -18,7 +19,7 @@ import scala.sys.process.ProcessLogger
 import scala.util.{Failure, Success, Try}
 
 object SparkJobExecutionActor {
-  val DefaultFileSystems = List(FileSystems.getDefault)
+  val DefaultPathBuilders = List(DefaultPathBuilder)
 
   def props(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor): Props =
     Props(new SparkJobExecutionActor(jobDescriptor, configurationDescriptor))
@@ -29,8 +30,8 @@ class SparkJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
 
   import SparkJobExecutionActor._
   import better.files._
-  import cromwell.core.PathFactory._
 
+  override val pathBuilders = DefaultPathBuilders
   private val tag = s"SparkJobExecutionActor-${jobDescriptor.key.tag}:"
 
   lazy val cmds = new SparkCommands
@@ -43,7 +44,7 @@ class SparkJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
   private val sparkDeployMode = configurationDescriptor.backendConfig.getString("deployMode").toLowerCase
   override val sharedFileSystemConfig = fileSystemsConfig.getConfig("local")
   private val workflowDescriptor = jobDescriptor.workflowDescriptor
-  private val jobPaths = new JobPaths(workflowDescriptor, configurationDescriptor.backendConfig, jobDescriptor.key)
+  private val jobPaths = new JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, configurationDescriptor.backendConfig)
 
   // Files
   private val executionDir = jobPaths.callExecutionRoot
@@ -58,9 +59,9 @@ class SparkJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
   private lazy val isClusterMode = isSparkClusterMode(sparkDeployMode, sparkMaster)
 
   private val call = jobDescriptor.key.call
-  private val callEngineFunction = SharedFileSystemExpressionFunctions(jobPaths, DefaultFileSystems)
+  private val callEngineFunction = SharedFileSystemExpressionFunctions(jobPaths, DefaultPathBuilders)
 
-  private val lookup = jobDescriptor.inputs.apply _
+  private val lookup = jobDescriptor.fullyQualifiedInputs.apply _
 
   private val executionResponse = Promise[BackendJobExecutionResponse]()
 
@@ -107,12 +108,12 @@ class SparkJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
   private def resolveExecutionResult(jobReturnCode: Try[Int], failedOnStderr: Boolean): Future[BackendJobExecutionResponse] = {
     (jobReturnCode, failedOnStderr) match {
       case (Success(0), true) if File(jobPaths.stderr).lines.toList.nonEmpty =>
-        Future.successful(FailedNonRetryableResponse(jobDescriptor.key,
+        Future.successful(JobFailedNonRetryableResponse(jobDescriptor.key,
         new IllegalStateException(s"Execution process failed although return code is zero but stderr is not empty"), Option(0)))
       case (Success(0), _) => resolveExecutionProcess
-      case (Success(rc), _) => Future.successful(FailedNonRetryableResponse(jobDescriptor.key,
+      case (Success(rc), _) => Future.successful(JobFailedNonRetryableResponse(jobDescriptor.key,
         new IllegalStateException(s"Execution process failed. Spark returned non zero status code: $rc"), Option(rc)))
-      case (Failure(error), _) => Future.successful(FailedNonRetryableResponse(jobDescriptor.key, error, None))
+      case (Failure(error), _) => Future.successful(JobFailedNonRetryableResponse(jobDescriptor.key, error, None))
     }
 
   }
@@ -122,9 +123,9 @@ class SparkJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
       case true =>
         clusterExtProcess.startMonitoringSparkClusterJob(jobPaths.callExecutionRoot, SubmitJobJson.format(sparkDeployMode)) collect {
           case Finished => processSuccess(0)
-          case Failed(error: Throwable) => FailedNonRetryableResponse(jobDescriptor.key, error, None)
+          case Failed(error: Throwable) => JobFailedNonRetryableResponse(jobDescriptor.key, error, None)
         } recover {
-          case error: Throwable => FailedNonRetryableResponse(jobDescriptor.key, error, None)
+          case error: Throwable => JobFailedNonRetryableResponse(jobDescriptor.key, error, None)
         }
       case false => Future.successful(processSuccess(0))
     }
@@ -132,12 +133,12 @@ class SparkJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
 
   private def processSuccess(rc: Int) = {
     evaluateOutputs(callEngineFunction, outputMapper(jobPaths)) match {
-      case Success(outputs) => SucceededResponse(jobDescriptor.key, Some(rc), outputs, None, Seq.empty)
+      case Success(outputs) => JobSucceededResponse(jobDescriptor.key, Some(rc), outputs, None, Seq.empty)
       case Failure(e) =>
         val message = Option(e.getMessage) map {
           ": " + _
         } getOrElse ""
-        FailedNonRetryableResponse(jobDescriptor.key, new Throwable("Failed post processing of outputs" + message, e), Option(rc))
+        JobFailedNonRetryableResponse(jobDescriptor.key, new Throwable("Failed post processing of outputs" + message, e), Option(rc))
     }
   }
 
@@ -155,9 +156,12 @@ class SparkJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
       executionDir.toString.toFile.createIfNotExists(asDirectory = true, createParents = true)
 
       log.debug("{} Resolving job command", tag)
-      val command = localizeInputs(jobPaths.callInputsRoot, docker = false, DefaultFileSystems, jobDescriptor.inputs) flatMap {
-        localizedInputs => call.task.instantiateCommand(localizedInputs, callEngineFunction, identity)
-      }
+
+      val command = Command.instantiate(
+        jobDescriptor,
+        callEngineFunction,
+        localizeInputs(jobPaths.callInputsRoot, docker = false)
+      )
 
       log.debug("{} Creating bash script for executing command: {}", tag, command)
       // TODO: we should use shapeless Heterogeneous list here not good to have generic map
@@ -202,7 +206,7 @@ class SparkJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
         case false => executionResponse completeWith executeTask(extProcess, stdoutWriter, stderrWriter)
       }
     } recover {
-      case exception => executionResponse success FailedNonRetryableResponse(jobDescriptor.key, exception, None)
+      case exception => executionResponse success JobFailedNonRetryableResponse(jobDescriptor.key, exception, None)
     }
   }
 
diff --git a/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkProcess.scala b/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkProcess.scala
index 60f3992186f..01d22116108 100644
--- a/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkProcess.scala
+++ b/supportedBackends/spark/src/main/scala/cromwell/backend/impl/spark/SparkProcess.scala
@@ -2,12 +2,12 @@ package cromwell.backend.impl.spark
 
 import java.nio.file.Path
 
+import better.files._
 import com.typesafe.scalalogging.StrictLogging
-import cromwell.core.{TailedWriter, UntailedWriter}
-import cromwell.core.PathFactory.EnhancedPath
+import cromwell.core.path.PathImplicits._
+import cromwell.core.path.{TailedWriter, UntailedWriter}
 
 import scala.sys.process._
-import better.files._
 import scala.util.{Failure, Success, Try}
 
 object SparkCommands {
@@ -29,12 +29,17 @@ class SparkCommands extends StrictLogging {
     * as some extra shell code for monitoring jobs
     */
   def writeScript(instantiatedCommand: String, filePath: Path, containerRoot: Path) = {
-    File(filePath).write(
-      s"""#!/bin/sh
-          |cd $containerRoot
-          |$instantiatedCommand
-          |echo $$? > rc
-          |""".stripMargin)
+
+    val scriptBody =
+      s"""
+
+#!/bin/sh
+cd $containerRoot
+$instantiatedCommand
+echo $$? > rc
+
+       """.trim + "\n"
+    File(filePath).write(scriptBody)
   }
 
   def sparkSubmitCommand(attributes: Map[String, Any]): String = {
diff --git a/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkInitializationActorSpec.scala b/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkInitializationActorSpec.scala
index f8aba1a4bb4..de58b7c0633 100644
--- a/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkInitializationActorSpec.scala
+++ b/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkInitializationActorSpec.scala
@@ -7,6 +7,7 @@ import cromwell.backend.{BackendConfigurationDescriptor, BackendWorkflowDescript
 import cromwell.core.TestKitSuite
 import org.scalatest.{BeforeAndAfterAll, Matchers, WordSpecLike}
 import wdl4s._
+
 import scala.concurrent.duration._
 
 class SparkInitializationActorSpec  extends  TestKitSuite("SparkInitializationActorSpec")
@@ -27,12 +28,12 @@ class SparkInitializationActorSpec  extends  TestKitSuite("SparkInitializationAc
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
 
-  private def getSparkBackend(workflowDescriptor: BackendWorkflowDescriptor, calls: Seq[Call], conf: BackendConfigurationDescriptor) = {
+  private def getSparkBackend(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[TaskCall], conf: BackendConfigurationDescriptor) = {
     system.actorOf(SparkInitializationActor.props(workflowDescriptor, calls, conf, emptyActor))
   }
 
@@ -41,7 +42,7 @@ class SparkInitializationActorSpec  extends  TestKitSuite("SparkInitializationAc
       within(Timeout) {
         EventFilter.warning(message = s"Key/s [memory] is/are not supported by SparkBackend. Unsupported attributes will not be part of jobs executions.", occurrences = 1) intercept {
           val workflowDescriptor = buildWorkflowDescriptor(HelloWorld, runtime = """runtime { memory: 1 %s: "%s"}""".format("appMainClass", "test"))
-          val backend = getSparkBackend(workflowDescriptor, workflowDescriptor.workflowNamespace.workflow.calls, emptyBackendConfig)
+          val backend = getSparkBackend(workflowDescriptor, workflowDescriptor.workflow.taskCalls, emptyBackendConfig)
           backend ! Initialize
         }
       }
diff --git a/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkJobExecutionActorSpec.scala b/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkJobExecutionActorSpec.scala
index aa4400ac8fa..3a7873fc5fa 100644
--- a/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkJobExecutionActorSpec.scala
+++ b/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkJobExecutionActorSpec.scala
@@ -6,12 +6,12 @@ import java.nio.file.Path
 import akka.testkit.{ImplicitSender, TestActorRef}
 import better.files._
 import com.typesafe.config.ConfigFactory
-import cromwell.backend.BackendJobExecutionActor.{FailedNonRetryableResponse, SucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{JobFailedNonRetryableResponse, JobSucceededResponse}
 import cromwell.backend.impl.spark.SparkClusterProcess._
 import cromwell.backend.io._
 import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendSpec}
-import cromwell.core.{PathWriter, TailedWriter, TestKitSuite, UntailedWriter, _}
-import org.mockito.Matchers._
+import cromwell.core.{TestKitSuite, WorkflowOptions}
+import cromwell.core.path.{PathWriter, TailedWriter, UntailedWriter}
 import org.mockito.Mockito
 import org.mockito.Mockito._
 import org.scalatest.concurrent.PatienceConfiguration.Timeout
@@ -50,7 +50,7 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
@@ -68,7 +68,7 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       | RUNTIME
       |}
       |
-      |workflow helloClusterMode {
+      |workflow wf_helloClusterMode {
       |   call helloClusterMode
       |}
     """.stripMargin
@@ -171,7 +171,7 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       when(sparkClusterProcess.startMonitoringSparkClusterJob(any[Path], any[String])).thenReturn(Future.successful(Finished))
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[SucceededResponse]
+        response shouldBe a[JobSucceededResponse]
         verify(sparkClusterProcess, times(1)).externalProcess(any[Seq[String]], any[ProcessLogger])
         verify(sparkClusterProcess, times(1)).tailedWriter(any[Int], any[Path])
         verify(sparkClusterProcess, times(1)).untailedWriter(any[Path])
@@ -201,8 +201,8 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       when(sparkClusterProcess.startMonitoringSparkClusterJob(any[Path], any[String])).thenReturn(Future.successful(Failed(new Throwable("failed to monitor"))))
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[FailedNonRetryableResponse]
-        assert(response.asInstanceOf[FailedNonRetryableResponse].throwable.getMessage.contains("failed to monitor"))
+        response shouldBe a[JobFailedNonRetryableResponse]
+        assert(response.asInstanceOf[JobFailedNonRetryableResponse].throwable.getMessage.contains("failed to monitor"))
         verify(sparkClusterProcess, times(1)).externalProcess(any[Seq[String]], any[ProcessLogger])
         verify(sparkClusterProcess, times(1)).tailedWriter(any[Int], any[Path])
         verify(sparkClusterProcess, times(1)).untailedWriter(any[Path])
@@ -232,8 +232,8 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       when(sparkClusterProcess.startMonitoringSparkClusterJob(any[Path], any[String])).thenReturn(Future.failed(new IllegalStateException("failed to start monitoring process")))
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[FailedNonRetryableResponse]
-        assert(response.asInstanceOf[FailedNonRetryableResponse].throwable.getMessage.contains("failed to start monitoring process"))
+        response shouldBe a[JobFailedNonRetryableResponse]
+        assert(response.asInstanceOf[JobFailedNonRetryableResponse].throwable.getMessage.contains("failed to start monitoring process"))
         verify(sparkClusterProcess, times(1)).externalProcess(any[Seq[String]], any[ProcessLogger])
         verify(sparkClusterProcess, times(1)).tailedWriter(any[Int], any[Path])
         verify(sparkClusterProcess, times(1)).untailedWriter(any[Path])
@@ -263,8 +263,8 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       when(sparkClusterProcess.processStderr).thenReturn(sampleSubmissionResponse)
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[FailedNonRetryableResponse]
-        assert(response.asInstanceOf[FailedNonRetryableResponse].throwable.getMessage.contains(s"Execution process failed although return code is zero but stderr is not empty"))
+        response shouldBe a[JobFailedNonRetryableResponse]
+        assert(response.asInstanceOf[JobFailedNonRetryableResponse].throwable.getMessage.contains(s"Execution process failed although return code is zero but stderr is not empty"))
         verify(sparkClusterProcess, times(1)).externalProcess(any[Seq[String]], any[ProcessLogger])
         verify(sparkClusterProcess, times(1)).tailedWriter(any[Int], any[Path])
         verify(sparkClusterProcess, times(1)).untailedWriter(any[Path])
@@ -292,8 +292,8 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       when(sparkClusterProcess.processStderr).thenReturn(stderrResult)
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[FailedNonRetryableResponse]
-        assert(response.asInstanceOf[FailedNonRetryableResponse].throwable.getMessage.contains(s"Execution process failed. Spark returned non zero status code:"))
+        response shouldBe a[JobFailedNonRetryableResponse]
+        assert(response.asInstanceOf[JobFailedNonRetryableResponse].throwable.getMessage.contains(s"Execution process failed. Spark returned non zero status code:"))
       }
       cleanUpJob(jobPaths)
     }
@@ -318,8 +318,8 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       when(sparkClusterProcess.processStderr).thenReturn(stderrResult)
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[FailedNonRetryableResponse]
-        assert(response.asInstanceOf[FailedNonRetryableResponse].throwable.getMessage.contains(s"submit job process exitValue method failed"))
+        response shouldBe a[JobFailedNonRetryableResponse]
+        assert(response.asInstanceOf[JobFailedNonRetryableResponse].throwable.getMessage.contains(s"submit job process exitValue method failed"))
       }
       cleanUpJob(jobPaths)
     }
@@ -347,7 +347,7 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       }).underlyingActor
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[SucceededResponse]
+        response shouldBe a[JobSucceededResponse]
         verify(sparkProcess, times(1)).externalProcess(any[Seq[String]], any[ProcessLogger])
         verify(sparkProcess, times(1)).tailedWriter(any[Int], any[Path])
         verify(sparkProcess, times(1)).untailedWriter(any[Path])
@@ -376,8 +376,8 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       when(sparkProcess.processStderr).thenReturn(stderrResult)
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[FailedNonRetryableResponse]
-        assert(response.asInstanceOf[FailedNonRetryableResponse].throwable.getMessage.contains(s"Execution process failed. Spark returned non zero status code:"))
+        response shouldBe a[JobFailedNonRetryableResponse]
+        assert(response.asInstanceOf[JobFailedNonRetryableResponse].throwable.getMessage.contains(s"Execution process failed. Spark returned non zero status code:"))
       }
 
       cleanUpJob(jobPaths)
@@ -402,8 +402,8 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       when(sparkProcess.untailedWriter(any[Path])).thenReturn(stubUntailed)
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[FailedNonRetryableResponse]
-        assert(response.asInstanceOf[FailedNonRetryableResponse].throwable.getMessage.contains(s"Execution process failed although return code is zero but stderr is not empty"))
+        response shouldBe a[JobFailedNonRetryableResponse]
+        assert(response.asInstanceOf[JobFailedNonRetryableResponse].throwable.getMessage.contains(s"Execution process failed although return code is zero but stderr is not empty"))
       }
 
       cleanUpJob(jobPaths)
@@ -427,7 +427,7 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
       when(sparkProcess.untailedWriter(any[Path])).thenReturn(stubUntailed)
 
       whenReady(backend.execute, timeout) { response =>
-        response shouldBe a[SucceededResponse]
+        response shouldBe a[JobSucceededResponse]
         verify(sparkProcess, times(1)).externalProcess(any[Seq[String]], any[ProcessLogger])
         verify(sparkProcess, times(1)).tailedWriter(any[Int], any[Path])
         verify(sparkProcess, times(1)).untailedWriter(any[Path])
@@ -438,7 +438,7 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
 
   }
 
-  private def cleanUpJob(jobPaths: JobPaths): Unit = {
+  private def cleanUpJob(jobPaths: JobPathsWithDocker): Unit = {
     File(jobPaths.workflowRoot).delete(true)
     ()
   }
@@ -447,7 +447,7 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
     val backendWorkflowDescriptor = buildWorkflowDescriptor(wdl = wdlSource, inputs = inputFiles.getOrElse(Map.empty), runtime = runtimeString)
     val backendConfigurationDescriptor = if (isCluster) BackendConfigurationDescriptor(backendClusterConfig, ConfigFactory.load) else BackendConfigurationDescriptor(backendClientConfig, ConfigFactory.load)
     val jobDesc = jobDescriptorFromSingleCallWorkflow(backendWorkflowDescriptor, inputFiles.getOrElse(Map.empty), WorkflowOptions.empty, Set.empty)
-    val jobPaths = if (isCluster) new JobPaths(backendWorkflowDescriptor, backendClusterConfig, jobDesc.key) else new JobPaths(backendWorkflowDescriptor, backendClientConfig, jobDesc.key)
+    val jobPaths = if (isCluster) new JobPathsWithDocker(jobDesc.key, backendWorkflowDescriptor, backendClusterConfig) else new JobPathsWithDocker(jobDesc.key, backendWorkflowDescriptor, backendClientConfig)
     val executionDir = jobPaths.callExecutionRoot
     val stdout = File(executionDir.toString, "stdout")
     stdout.createIfNotExists(asDirectory = false, createParents = true)
@@ -456,7 +456,7 @@ class SparkJobExecutionActorSpec extends TestKitSuite("SparkJobExecutionActor")
     TestJobDescriptor(jobDesc, jobPaths, backendConfigurationDescriptor)
   }
 
-  private case class TestJobDescriptor(jobDescriptor: BackendJobDescriptor, jobPaths: JobPaths, backendConfigurationDescriptor: BackendConfigurationDescriptor)
+  private case class TestJobDescriptor(jobDescriptor: BackendJobDescriptor, jobPaths: JobPathsWithDocker, backendConfigurationDescriptor: BackendConfigurationDescriptor)
 
   trait MockWriter extends Writer {
     var closed = false
diff --git a/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkRuntimeAttributesSpec.scala b/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkRuntimeAttributesSpec.scala
index 33724cb6dac..6167f0fd75a 100644
--- a/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkRuntimeAttributesSpec.scala
+++ b/supportedBackends/spark/src/test/scala/cromwell/backend/impl/spark/SparkRuntimeAttributesSpec.scala
@@ -9,7 +9,7 @@ import wdl4s.WdlExpression._
 import wdl4s.expression.NoFunctions
 import wdl4s.util.TryUtil
 import wdl4s.values.WdlValue
-import wdl4s.{Call, WdlExpression, _}
+import wdl4s.{Call, _}
 
 class SparkRuntimeAttributesSpec extends WordSpecLike with Matchers {
 
@@ -26,7 +26,7 @@ class SparkRuntimeAttributesSpec extends WordSpecLike with Matchers {
       |  RUNTIME
       |}
       |
-      |workflow hello {
+      |workflow wf_hello {
       |  call hello
       |}
     """.stripMargin
@@ -90,7 +90,7 @@ class SparkRuntimeAttributesSpec extends WordSpecLike with Matchers {
                                       runtime: String) = {
     BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      NamespaceWithWorkflow.load(wdl.replaceAll("RUNTIME", runtime.format("appMainClass", "com.test.spark"))),
+      WdlNamespaceWithWorkflow.load(wdl.replaceAll("RUNTIME", runtime.format("appMainClass", "com.test.spark")), Seq.empty[ImportResolver]).workflow,
       inputs,
       options
     )
@@ -100,12 +100,11 @@ class SparkRuntimeAttributesSpec extends WordSpecLike with Matchers {
     val workflowDescriptor = buildWorkflowDescriptor(wdlSource, runtime = runtimeAttributes)
 
     def createLookup(call: Call): ScopedLookupFunction = {
-      val declarations = workflowDescriptor.workflowNamespace.workflow.declarations ++ call.task.declarations
       val knownInputs = workflowDescriptor.inputs
-      WdlExpression.standardLookupFunction(knownInputs, declarations, NoFunctions)
+      call.lookupFunction(knownInputs, NoFunctions)
     }
 
-    workflowDescriptor.workflowNamespace.workflow.calls map {
+    workflowDescriptor.workflow.taskCalls map {
       call =>
         val ra = call.task.runtimeAttributes.attrs mapValues { _.evaluate(createLookup(call), NoFunctions) }
         TryUtil.sequenceMap(ra, "Runtime attributes evaluation").get

From 22fe86033fb7d7ef7589ad3f3e2c60dbed1b22e0 Mon Sep 17 00:00:00 2001
From: Ruchi Munshi <rmunshi@broadinstitute.org>
Date: Tue, 11 Apr 2017 16:19:10 -0400
Subject: [PATCH 010/326] Pin release to centaur branch

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 1be54097a31..44ffb177240 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -19,7 +19,7 @@ before_install:
   - openssl aes-256-cbc -K "$encrypted_5ebd3ff04788_key" -iv "$encrypted_5ebd3ff04788_iv" -in src/bin/travis/resources/jesConf.tar.enc -out jesConf.tar -d || true
 env:
   global:
-    - CENTAUR_BRANCH=develop
+    - CENTAUR_BRANCH=40dff9cade6170d691dae383003d60fecfe24bd2
   matrix:
     # Setting this variable twice will cause the 'script' section to run twice with the respective env var invoked
     - BUILD_TYPE=sbt

From a6bcebb091de9da092603eebfe8a0e288b4c8175 Mon Sep 17 00:00:00 2001
From: Thibault Jeandet <tjeandet@broadinstitute.org>
Date: Tue, 30 May 2017 14:03:37 -0400
Subject: [PATCH 011/326] Pin release to centaur branch

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 44ffb177240..d617bdb877a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -19,7 +19,7 @@ before_install:
   - openssl aes-256-cbc -K "$encrypted_5ebd3ff04788_key" -iv "$encrypted_5ebd3ff04788_iv" -in src/bin/travis/resources/jesConf.tar.enc -out jesConf.tar -d || true
 env:
   global:
-    - CENTAUR_BRANCH=40dff9cade6170d691dae383003d60fecfe24bd2
+    - CENTAUR_BRANCH=989e3d73ca72567398fd2c9fb03dad57d9cb69f5
   matrix:
     # Setting this variable twice will cause the 'script' section to run twice with the respective env var invoked
     - BUILD_TYPE=sbt

From 4480026ca849cc06962381b24062d1b701747ee5 Mon Sep 17 00:00:00 2001
From: Thibault Jeandet <tjeandet@broadinstitute.org>
Date: Fri, 30 Jun 2017 14:21:29 -0400
Subject: [PATCH 012/326] Point centaur to develop

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index d617bdb877a..1be54097a31 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -19,7 +19,7 @@ before_install:
   - openssl aes-256-cbc -K "$encrypted_5ebd3ff04788_key" -iv "$encrypted_5ebd3ff04788_iv" -in src/bin/travis/resources/jesConf.tar.enc -out jesConf.tar -d || true
 env:
   global:
-    - CENTAUR_BRANCH=989e3d73ca72567398fd2c9fb03dad57d9cb69f5
+    - CENTAUR_BRANCH=develop
   matrix:
     # Setting this variable twice will cause the 'script' section to run twice with the respective env var invoked
     - BUILD_TYPE=sbt

From 4521fd490dedf5ed287df7ed7e0147f8d7da6680 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 2 Oct 2018 12:10:33 -0400
Subject: [PATCH 013/326] Fix release mishap - version number

---
 project/Version.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Version.scala b/project/Version.scala
index c7885ad009d..e56538c415a 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -5,7 +5,7 @@ import sbt._
 
 object Version {
   // Upcoming release, or current if we're on a master / hotfix branch
-  val cromwellVersion = "36"
+  val cromwellVersion = "35"
 
   // Adapted from SbtGit.versionWithGit
   def cromwellVersionWithGit: Seq[Setting[_]] =

From ee8cfd4aa6e2e3c1ce0a77416f21886be8e78826 Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Fri, 28 Feb 2020 13:04:10 -0500
Subject: [PATCH 014/326] Fix missing pig in docs (#5435) [no JIRA]

---
 docs/tutorials/MetadataEndpoint.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/tutorials/MetadataEndpoint.md b/docs/tutorials/MetadataEndpoint.md
index 2883c1e0528..fd463f270f4 100644
--- a/docs/tutorials/MetadataEndpoint.md
+++ b/docs/tutorials/MetadataEndpoint.md
@@ -25,4 +25,4 @@ After completing this tutorial you might find the following page interesting:
 _Drop us a line in the [Forum](https://gatkforums.broadinstitute.org/wdl/categories/ask-the-wdl-team) if you have a question._
 
 \*\*\* **UNDER CONSTRUCTION** \*\*\*  
-[![Pennywell pig in red wellies - Richard Austin Images](http://www.richardaustinimages.com/wp-content/uploads/2015/04/fluffyAustin_Pigets_Wellies-500x395.jpg)](http://www.richardaustinimages.com/product/pennywell-pigs-under-umbrella-2/)
+[![Pennywell pig in red wellies - Richard Austin Images](https://static.wixstatic.com/media/b0d56a_6b627e45766d44fa8b2714f5d7860c84~mv2.jpg/v1/fill/w_787,h_551,al_c,q_50,usm_0.66_1.00_0.01/b0d56a_6b627e45766d44fa8b2714f5d7860c84~mv2.jpg)

From fa44f36a53234929deed13ad51edff8a568edb23 Mon Sep 17 00:00:00 2001
From: Marissa <30879508+mepowers@users.noreply.github.com>
Date: Wed, 3 Jun 2020 15:55:29 -0700
Subject: [PATCH 015/326] Update Google.md (#5529)

Thanks!
---
 docs/backends/Google.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/backends/Google.md b/docs/backends/Google.md
index 7c0c492b829..82320340a55 100644
--- a/docs/backends/Google.md
+++ b/docs/backends/Google.md
@@ -11,7 +11,7 @@ The instructions below assume you have created a Google Cloud Storage bucket and
 
 **Configuring Authentication**
 
-The `google` stanza in the Cromwell configuration file defines how to authenticate to Google.  There are four different
+The `google` stanza in the Cromwell configuration file defines how to authenticate to Google.  There are five different
 authentication schemes that might be used:
 
 * `application_default` (default, recommended) - Use [application default](https://developers.google.com/identity/protocols/application-default-credentials) credentials.
@@ -55,7 +55,7 @@ the `genomics` and `filesystems.gcs` sections within a Google configuration bloc
 The auth for the `genomics` section governs the interactions with Google itself, while `filesystems.gcs` governs the localization
 of data into and out of GCE VMs.
 
-**Application Default Credentials**
+***Application Default Credentials***
 
 By default, application default credentials will be used.  Only `name` and `scheme` are required for application default credentials.
 
@@ -66,7 +66,7 @@ $ gcloud auth login
 $ gcloud config set project my-project
 ```
 
-**Service Account**
+***Service Account***
 
 First create a new service account through the [API Credentials](https://console.developers.google.com/apis/credentials) page.  Go to **Create credentials -> Service account key**.  Then in the **Service account** dropdown select **New service account**.  Fill in a name (e.g. `my-account`), and select key type of JSON.
 

From 0963109d8fffae1b567d2b4f74a4fb896d69d0dc Mon Sep 17 00:00:00 2001
From: Kyle Vernest <34135227+kv076@users.noreply.github.com>
Date: Tue, 15 Dec 2020 13:51:26 -0500
Subject: [PATCH 016/326] Update LanguageSupport.md

reference our Jira documentation rather than github with the provided link
---
 docs/LanguageSupport.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/LanguageSupport.md b/docs/LanguageSupport.md
index 74f5ab238f6..d14d6751a42 100644
--- a/docs/LanguageSupport.md
+++ b/docs/LanguageSupport.md
@@ -26,7 +26,7 @@ As well as the changes to the WDL spec between draft-2 and 1.0, Cromwell also su
 ### CWL 1.0
 
 Cromwell provides support for Common Workflow Language (CWL), beginning with the core spec, and most heavily used requirements.
-If you spot a CWL feature that Cromwell doesn't support, please notify us using an issue on our github page!
+If you spot a CWL feature that Cromwell doesn't support, please notify us using an issue on our [Jira page](https://broadworkbench.atlassian.net/secure/RapidBoard.jspa?rapidView=39&view=planning.nodetail&issueLimit=100)!
 
 
 ## Future Language Support

From ef30230346c318bc60e95ef0c023e97a92ed8fb8 Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Tue, 13 Jul 2021 16:18:22 -0400
Subject: [PATCH 017/326] check buckets for region and ensure client has
 correct region

---
 .../java/org/lerch/s3fs/AmazonS3Factory.java  | 14 +++----
 .../org/lerch/s3fs/S3AccessControlList.java   |  8 ++--
 .../java/org/lerch/s3fs/S3FileChannel.java    | 20 ++++-----
 .../main/java/org/lerch/s3fs/S3FileStore.java | 42 ++++++++++++++-----
 .../java/org/lerch/s3fs/S3FileSystem.java     | 30 ++++++-------
 .../org/lerch/s3fs/S3FileSystemProvider.java  | 29 +++++++------
 .../main/java/org/lerch/s3fs/S3Iterator.java  | 22 ++++------
 .../src/main/java/org/lerch/s3fs/S3Path.java  |  4 +-
 .../org/lerch/s3fs/S3SeekableByteChannel.java | 28 ++++++-------
 .../s3fs/attribute/S3BasicFileAttributes.java |  4 +-
 .../s3fs/attribute/S3PosixFileAttributes.java |  2 -
 .../java/org/lerch/s3fs/util/S3Utils.java     | 25 ++++-------
 12 files changed, 114 insertions(+), 114 deletions(-)

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java b/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
index 987e8d71c6a..9d525587642 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
@@ -1,20 +1,16 @@
 package org.lerch.s3fs;
- 
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import software.amazon.awssdk.auth.credentials.AwsCredentialsProvider;
-import software.amazon.awssdk.auth.credentials.StaticCredentialsProvider;
-import software.amazon.awssdk.auth.credentials.DefaultCredentialsProvider;
-import software.amazon.awssdk.auth.credentials.AwsCredentials;
-import software.amazon.awssdk.auth.credentials.AwsBasicCredentials;
+import software.amazon.awssdk.auth.credentials.*;
+import software.amazon.awssdk.core.client.config.ClientOverrideConfiguration;
+import software.amazon.awssdk.http.SdkHttpClient;
+import software.amazon.awssdk.http.apache.ApacheHttpClient;
 import software.amazon.awssdk.regions.Region;
 import software.amazon.awssdk.regions.providers.DefaultAwsRegionProviderChain;
 import software.amazon.awssdk.services.s3.S3Client;
 import software.amazon.awssdk.services.s3.S3ClientBuilder;
 import software.amazon.awssdk.services.s3.S3Configuration;
-import software.amazon.awssdk.http.SdkHttpClient;
-import software.amazon.awssdk.http.apache.ApacheHttpClient;
-import software.amazon.awssdk.core.client.config.ClientOverrideConfiguration;
 
 import java.net.URI;
 import java.util.Properties;
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3AccessControlList.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3AccessControlList.java
index 0d908001ed3..1f219164707 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3AccessControlList.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3AccessControlList.java
@@ -1,14 +1,14 @@
 package org.lerch.s3fs;
 
-import static java.lang.String.format;
+import software.amazon.awssdk.services.s3.model.Grant;
+import software.amazon.awssdk.services.s3.model.Owner;
+import software.amazon.awssdk.services.s3.model.Permission;
 
 import java.nio.file.AccessDeniedException;
 import java.nio.file.AccessMode;
 import java.util.EnumSet;
 
-import software.amazon.awssdk.services.s3.model.Grant;
-import software.amazon.awssdk.services.s3.model.Owner;
-import software.amazon.awssdk.services.s3.model.Permission;
+import static java.lang.String.format;
 
 public class S3AccessControlList {
     private String fileStoreName;
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileChannel.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileChannel.java
index 2f8bd41ff8c..e849294791d 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileChannel.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileChannel.java
@@ -1,8 +1,15 @@
 package org.lerch.s3fs;
 
 import org.apache.tika.Tika;
+import software.amazon.awssdk.core.ResponseInputStream;
+import software.amazon.awssdk.core.sync.RequestBody;
+import software.amazon.awssdk.services.s3.model.GetObjectRequest;
+import software.amazon.awssdk.services.s3.model.GetObjectResponse;
+import software.amazon.awssdk.services.s3.model.PutObjectRequest;
 
-import java.io.*;
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.io.InputStream;
 import java.nio.ByteBuffer;
 import java.nio.MappedByteBuffer;
 import java.nio.channels.FileChannel;
@@ -14,13 +21,6 @@
 import java.util.HashSet;
 import java.util.Set;
 
-import software.amazon.awssdk.core.sync.RequestBody;
-import software.amazon.awssdk.core.ResponseInputStream;
-import software.amazon.awssdk.services.s3.model.GetObjectRequest;
-import software.amazon.awssdk.services.s3.model.GetObjectResponse;
-import software.amazon.awssdk.services.s3.model.PutObjectRequest;
-import software.amazon.awssdk.services.s3.model.S3Object;
-
 import static java.lang.String.format;
 
 public class S3FileChannel extends FileChannel implements S3Channel {
@@ -46,7 +46,7 @@ else if (!exists && !this.options.contains(StandardOpenOption.CREATE_NEW) &&
         boolean removeTempFile = true;
         try {
             if (exists) {
-                try (ResponseInputStream<GetObjectResponse> byteStream = path.getFileSystem()
+                try (ResponseInputStream<GetObjectResponse> byteStream = path.getFileStore()
                         .getClient()
                         .getObject(GetObjectRequest
                                        .builder()
@@ -171,7 +171,7 @@ protected void sync() throws IOException {
                    .contentLength(length)
                    .contentType(new Tika().detect(stream, path.getFileName().toString()));
 
-            path.getFileSystem().getClient().putObject(builder.build(), RequestBody.fromInputStream(stream, length));
+            path.getFileStore().getClient().putObject(builder.build(), RequestBody.fromInputStream(stream, length));
         }
     }
 }
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
index d8082d0605b..6f3c879bc4d 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
@@ -1,28 +1,35 @@
 package org.lerch.s3fs;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import software.amazon.awssdk.regions.Region;
+import software.amazon.awssdk.services.s3.S3Client;
+import software.amazon.awssdk.services.s3.S3Configuration;
+import software.amazon.awssdk.services.s3.model.*;
+
 import java.io.IOException;
+import java.net.URI;
 import java.nio.file.FileStore;
 import java.nio.file.attribute.FileAttributeView;
 import java.nio.file.attribute.FileStoreAttributeView;
 import java.util.Date;
 
-import software.amazon.awssdk.services.s3.S3Client;
-import software.amazon.awssdk.services.s3.model.Bucket;
-import software.amazon.awssdk.services.s3.model.GetBucketAclRequest;
-import software.amazon.awssdk.services.s3.model.HeadBucketRequest;
-import software.amazon.awssdk.services.s3.model.ListBucketsRequest;
-import software.amazon.awssdk.services.s3.model.NoSuchBucketException;
-import software.amazon.awssdk.services.s3.model.Owner;
-import com.google.common.collect.ImmutableList;
-
+/**
+ * In S3 a filestore translates to a bucket
+ */
 public class S3FileStore extends FileStore implements Comparable<S3FileStore> {
 
     private S3FileSystem fileSystem;
     private String name;
+    private S3Client defaultClient;
+    private S3Client bucketSpecificClient;
+    private Logger logger = LoggerFactory.getLogger("S3FileStore");
 
     public S3FileStore(S3FileSystem s3FileSystem, String name) {
         this.fileSystem = s3FileSystem;
         this.name = name;
+        // the default client can be used for getBucketLocation operations
+        this.defaultClient = S3Client.builder().endpointOverride(URI.create("https://s3.us-east-1.amazonaws.com")).region(Region.US_EAST_1).build();
     }
 
     @Override
@@ -121,8 +128,21 @@ public S3Path getRootDirectory() {
         return new S3Path(fileSystem, "/" + this.name());
     }
 
-    private S3Client getClient() {
-        return fileSystem.getClient();
+    /**
+     * Gets a client suitable for this FileStore (bucket) including configuring the correct region endpoint. If no client
+     * exists one will be constructed and cached.
+     * @return a client
+     */
+    public S3Client getClient() {
+        if (bucketSpecificClient == null) {
+            String bucketLocation = defaultClient.getBucketLocation(builder -> builder.bucket(this.name)).locationConstraintAsString();
+            logger.debug("Bucket location is '{}'", bucketLocation);
+
+            Region region = bucketLocation.trim().equals("") ? Region.US_EAST_1 : Region.of(bucketLocation);
+            bucketSpecificClient = S3Client.builder().region(region).build();
+        }
+
+        return bucketSpecificClient;
     }
 
     public Owner getOwner() {
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystem.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystem.java
index 4fadae9518b..0038a787c64 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystem.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystem.java
@@ -1,20 +1,16 @@
 package org.lerch.s3fs;
 
-import static org.lerch.s3fs.S3Path.PATH_SEPARATOR;
+import com.google.common.collect.ImmutableList;
+import com.google.common.collect.ImmutableSet;
+import software.amazon.awssdk.services.s3.S3Client;
+import software.amazon.awssdk.services.s3.model.Bucket;
 
 import java.io.IOException;
-import java.nio.file.FileStore;
-import java.nio.file.FileSystem;
-import java.nio.file.Path;
-import java.nio.file.PathMatcher;
-import java.nio.file.WatchService;
+import java.nio.file.*;
 import java.nio.file.attribute.UserPrincipalLookupService;
 import java.util.Set;
 
-import software.amazon.awssdk.services.s3.S3Client;
-import software.amazon.awssdk.services.s3.model.Bucket;
-import com.google.common.collect.ImmutableList;
-import com.google.common.collect.ImmutableSet;
+import static org.lerch.s3fs.S3Path.PATH_SEPARATOR;
 
 /**
  * S3FileSystem with a concrete client configured and ready to use.
@@ -63,7 +59,7 @@ public boolean isReadOnly() {
 
     @Override
     public String getSeparator() {
-        return S3Path.PATH_SEPARATOR;
+        return PATH_SEPARATOR;
     }
 
     @Override
@@ -113,9 +109,15 @@ public WatchService newWatchService() throws IOException {
         throw new UnsupportedOperationException();
     }
 
-    public S3Client getClient() {
-        return client;
-    }
+//    /**
+//     * Deprecated: since SDKv2 many S3 operations need to be signed with a client using the same Region as the location
+//     * of the bucket. Prefer S3Path.client() instead.
+//     * @return
+//     */
+//    @Deprecated
+//    public S3Client getClient() {
+//        return client;
+//    }
 
     /**
      * get the endpoint associated with this fileSystem.
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystemProvider.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystemProvider.java
index 0095e372a43..e3fdf0065a5 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystemProvider.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystemProvider.java
@@ -1,11 +1,11 @@
 package org.lerch.s3fs;
 
-import org.apache.commons.lang3.tuple.ImmutablePair;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Preconditions;
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.ImmutableSet;
 import com.google.common.collect.Sets;
+import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.lerch.s3fs.attribute.S3BasicFileAttributeView;
 import org.lerch.s3fs.attribute.S3BasicFileAttributes;
 import org.lerch.s3fs.attribute.S3PosixFileAttributeView;
@@ -36,7 +36,8 @@
 
 import static com.google.common.collect.Sets.difference;
 import static java.lang.String.format;
-import static java.lang.Thread.*;
+import static java.lang.Thread.currentThread;
+import static java.lang.Thread.sleep;
 import static org.lerch.s3fs.AmazonS3Factory.*;
 
 /**
@@ -286,7 +287,10 @@ public S3FileSystem getFileSystem(URI uri) {
         if (fileSystems.containsKey(key)) {
             return fileSystems.get(key);
         } else {
-            throw new FileSystemNotFoundException("S3 filesystem not yet created. Use newFileSystem() instead");
+            final String scheme = uri.getScheme();
+            final String uriString = uri.toString();
+            uriString.replace(scheme, "https://");
+            return (S3FileSystem) newFileSystem(uri, Collections.<String, String>emptyMap());
         }
     }
 
@@ -337,7 +341,7 @@ public InputStream newInputStream(Path path, OpenOption... options) throws IOExc
 
         try {
             ResponseInputStream<GetObjectResponse> res = s3Path
-                    .getFileSystem()
+                    .getFileStore()
                     .getClient()
                     .getObject(GetObjectRequest
                             .builder()
@@ -384,7 +388,7 @@ public void createDirectory(Path dir, FileAttribute<?>... attrs) throws IOExcept
         Bucket bucket = s3Path.getFileStore().getBucket();
         String bucketName = s3Path.getFileStore().name();
         if (bucket == null) {
-            s3Path.getFileSystem().getClient().createBucket(CreateBucketRequest.builder().bucket(bucketName).build());
+            s3Path.getFileStore().getClient().createBucket(CreateBucketRequest.builder().bucket(bucketName).build());
         }
         // create the object as directory
         PutObjectRequest.Builder builder = PutObjectRequest.builder();
@@ -392,7 +396,7 @@ public void createDirectory(Path dir, FileAttribute<?>... attrs) throws IOExcept
         builder.bucket(bucketName)
                 .key(directoryKey)
                 .contentLength(0L);
-        s3Path.getFileSystem().getClient().putObject(builder.build(), RequestBody.fromBytes(new byte[0]));
+        s3Path.getFileStore().getClient().putObject(builder.build(), RequestBody.fromBytes(new byte[0]));
     }
 
     @Override
@@ -405,9 +409,9 @@ public void delete(Path path) throws IOException {
 
         String key = s3Path.getKey();
         String bucketName = s3Path.getFileStore().name();
-        s3Path.getFileSystem().getClient().deleteObject(DeleteObjectRequest.builder().bucket(bucketName).key(key).build());
+        s3Path.getFileStore().getClient().deleteObject(DeleteObjectRequest.builder().bucket(bucketName).key(key).build());
         // we delete the two objects (sometimes exists the key '/' and sometimes not)
-        s3Path.getFileSystem().getClient().deleteObject(DeleteObjectRequest.builder().bucket(bucketName).key(key + "/").build());
+        s3Path.getFileStore().getClient().deleteObject(DeleteObjectRequest.builder().bucket(bucketName).key(key + "/").build());
     }
 
     @Override
@@ -437,7 +441,8 @@ public void copy(Path source, Path target, CopyOption... options) throws IOExcep
             String keySource = s3Source.getKey();
             String bucketNameTarget = s3Target.getFileStore().name();
             String keyTarget = s3Target.getKey();
-            s3Source.getFileSystem()
+            // for a cross region copy the client must be for the target (region) not the source region
+            s3Target.getFileStore()
                     .getClient()
                     .copyObject(CopyObjectRequest.builder()
                             .copySource(bucketNameOrigin + "/" + keySource)
@@ -458,7 +463,7 @@ public void copy(Path source, Path target, CopyOption... options) throws IOExcep
     private void multiPartCopy(S3Path source, long objectSize, S3Path target, CopyOption... options) {
         log.info(() -> "Attempting multipart copy as part of call cache hit: source = " + source + ", objectSize = " + objectSize + ", target = " + target + ", options = " + Arrays.deepToString(options));
 
-        S3Client s3Client = target.getFileSystem().getClient();
+        S3Client s3Client = target.getFileStore().getClient();
 
         final CreateMultipartUploadRequest createMultipartUploadRequest = CreateMultipartUploadRequest.builder()
                 .bucket(target.getFileStore().name())
@@ -594,7 +599,7 @@ private void multiPartCopy(S3Path source, long objectSize, S3Path target, CopyOp
      */
     private long objectSize(S3Path object) {
 
-        S3Client s3Client = object.getFileSystem().getClient();
+        S3Client s3Client = object.getFileStore().getClient();
         final String bucket = object.getFileStore().name();
         final String key = object.getKey();
         final HeadObjectResponse headObjectResponse = s3Client.headObject(HeadObjectRequest.builder()
@@ -656,7 +661,7 @@ public void checkAccess(Path path, AccessMode... modes) throws IOException {
         String key = s3Utils.getS3ObjectSummary(s3Path).key();
         String bucket = s3Path.getFileStore().name();
         S3AccessControlList accessControlList =
-                new S3AccessControlList(bucket, key, s3Path.getFileSystem().getClient().getObjectAcl(GetObjectAclRequest.builder().bucket(bucket).key(key).build()).grants(), s3Path.getFileStore().getOwner());
+                new S3AccessControlList(bucket, key, s3Path.getFileStore().getClient().getObjectAcl(GetObjectAclRequest.builder().bucket(bucket).key(key).build()).grants(), s3Path.getFileStore().getOwner());
 
         accessControlList.checkAccess(modes);
     }
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3Iterator.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3Iterator.java
index 3d8f5cb8072..803b5275892 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3Iterator.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3Iterator.java
@@ -1,21 +1,15 @@
 package org.lerch.s3fs;
 
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.NoSuchElementException;
-import java.util.Set;
-
+import com.google.common.collect.Lists;
+import com.google.common.collect.Sets;
+import org.lerch.s3fs.util.S3Utils;
 import software.amazon.awssdk.services.s3.model.CommonPrefix;
 import software.amazon.awssdk.services.s3.model.ListObjectsRequest;
 import software.amazon.awssdk.services.s3.model.ListObjectsResponse;
 import software.amazon.awssdk.services.s3.model.S3Object;
-import com.google.common.collect.Lists;
-import com.google.common.collect.Sets;
-import org.lerch.s3fs.util.S3Utils;
+
+import java.nio.file.Path;
+import java.util.*;
 
 /**
  * S3 iterator over folders at first level.
@@ -50,7 +44,7 @@ public S3Iterator(S3FileStore fileStore, String key, boolean incremental) {
         this.fileStore = fileStore;
         this.fileSystem = fileStore.getFileSystem();
         this.key = key;
-        this.current = fileSystem.getClient().listObjects(listObjectsRequest);
+        this.current = fileStore.getClient().listObjects(listObjectsRequest);
         this.incremental = incremental;
         loadObjects();
     }
@@ -69,7 +63,7 @@ public S3Path next() {
                                                    .marker(current.nextMarker())
                                                    .build();
 
-            this.current = fileSystem.getClient().listObjects(request);
+            this.current = fileStore.getClient().listObjects(request);
             loadObjects();
         }
         if (cursor == size)
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3Path.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3Path.java
index 271a1b31e72..1382c16c3ad 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3Path.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3Path.java
@@ -4,19 +4,19 @@
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Lists;
 import org.lerch.s3fs.attribute.S3BasicFileAttributes;
+import software.amazon.awssdk.services.s3.S3Client;
 
 import java.io.File;
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.net.URI;
-import java.net.URL;
 import java.net.URLDecoder;
 import java.nio.file.*;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Map;
 
 import static com.google.common.collect.Iterables.*;
+import static com.google.common.collect.Iterables.concat;
 import static java.lang.String.format;
 
 public class S3Path implements Path {
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3SeekableByteChannel.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3SeekableByteChannel.java
index 31318d85c25..5f0ff571521 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3SeekableByteChannel.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3SeekableByteChannel.java
@@ -1,8 +1,11 @@
 package org.lerch.s3fs;
 
-import static java.lang.String.format;
+import org.apache.tika.Tika;
+import software.amazon.awssdk.core.sync.RequestBody;
+import software.amazon.awssdk.services.s3.S3Client;
+import software.amazon.awssdk.services.s3.model.GetObjectRequest;
+import software.amazon.awssdk.services.s3.model.PutObjectRequest;
 
-import java.io.ByteArrayInputStream;
 import java.io.BufferedInputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -13,21 +16,14 @@
 import java.util.HashSet;
 import java.util.Set;
 
-import org.apache.tika.Tika;
-
-import software.amazon.awssdk.core.sync.RequestBody;
-import software.amazon.awssdk.services.s3.S3Client;
-import software.amazon.awssdk.services.s3.model.GetObjectResponse;
-import software.amazon.awssdk.services.s3.model.GetObjectRequest;
-import software.amazon.awssdk.services.s3.model.PutObjectRequest;
-import software.amazon.awssdk.services.s3.model.S3Object;
+import static java.lang.String.format;
 
 public class S3SeekableByteChannel implements SeekableByteChannel, S3Channel {
 
-    private S3Path path;
-    private Set<? extends OpenOption> options;
-    private SeekableByteChannel seekable;
-    private Path tempFile;
+    private final S3Path path;
+    private final Set<? extends OpenOption> options;
+    private final SeekableByteChannel seekable;
+    private final Path tempFile;
 
     /**
      * Open or creates a file, returning a seekable byte channel
@@ -52,7 +48,7 @@ else if (!exists && !this.options.contains(StandardOpenOption.CREATE_NEW) &&
         boolean removeTempFile = true;
         try {
             if (exists) {
-                try (InputStream byteStream = path.getFileSystem().getClient()
+                try (InputStream byteStream = path.getFileStore().getClient()
                       .getObject(GetObjectRequest.builder().bucket(path.getFileStore().getBucket().name()).key(key).build())) {
                    Files.copy(byteStream, tempFile, StandardCopyOption.REPLACE_EXISTING);
                 }
@@ -115,7 +111,7 @@ protected void sync() throws IOException {
             builder.bucket(path.getFileStore().name());
             builder.key(path.getKey());
 
-            S3Client client = path.getFileSystem().getClient();
+            S3Client client = path.getFileStore().getClient();
 
             client.putObject(builder.build(), RequestBody.fromInputStream(stream, length));
         }
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/attribute/S3BasicFileAttributes.java b/filesystems/s3/src/main/java/org/lerch/s3fs/attribute/S3BasicFileAttributes.java
index 40e02b17abb..895f5109fb2 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/attribute/S3BasicFileAttributes.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/attribute/S3BasicFileAttributes.java
@@ -1,10 +1,10 @@
 package org.lerch.s3fs.attribute;
 
-import static java.lang.String.format;
-
 import java.nio.file.attribute.BasicFileAttributes;
 import java.nio.file.attribute.FileTime;
 
+import static java.lang.String.format;
+
 public class S3BasicFileAttributes implements BasicFileAttributes {
     private final FileTime lastModifiedTime;
     private final long size;
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/attribute/S3PosixFileAttributes.java b/filesystems/s3/src/main/java/org/lerch/s3fs/attribute/S3PosixFileAttributes.java
index fbe5efac57c..6ffdee62f20 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/attribute/S3PosixFileAttributes.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/attribute/S3PosixFileAttributes.java
@@ -3,8 +3,6 @@
 import java.nio.file.attribute.*;
 import java.util.Set;
 
-import static java.lang.String.format;
-
 public class S3PosixFileAttributes extends S3BasicFileAttributes implements PosixFileAttributes  {
 
     private UserPrincipal userPrincipal;
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3Utils.java b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3Utils.java
index e8586ef4d97..73e25a53b04 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3Utils.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3Utils.java
@@ -1,22 +1,12 @@
 package org.lerch.s3fs.util;
 
-import software.amazon.awssdk.services.s3.S3Client;
-import software.amazon.awssdk.services.s3.model.HeadObjectRequest;
-import software.amazon.awssdk.services.s3.model.HeadObjectResponse;
-import software.amazon.awssdk.services.s3.model.GetObjectAclRequest;
-import software.amazon.awssdk.services.s3.model.GetObjectAclResponse;
-import software.amazon.awssdk.services.s3.model.Grant;
-import software.amazon.awssdk.services.s3.model.ListObjectsV2Request;
-import software.amazon.awssdk.services.s3.model.ListObjectsV2Response;
-import software.amazon.awssdk.services.s3.model.Owner;
-import software.amazon.awssdk.services.s3.model.Permission;
-import software.amazon.awssdk.services.s3.model.S3Object;
-import software.amazon.awssdk.services.s3.model.S3Exception;
 import com.google.common.collect.Sets;
-import org.lerch.s3fs.attribute.S3BasicFileAttributes;
 import org.lerch.s3fs.S3Path;
+import org.lerch.s3fs.attribute.S3BasicFileAttributes;
 import org.lerch.s3fs.attribute.S3PosixFileAttributes;
 import org.lerch.s3fs.attribute.S3UserPrincipal;
+import software.amazon.awssdk.services.s3.S3Client;
+import software.amazon.awssdk.services.s3.model.*;
 
 import java.nio.file.NoSuchFileException;
 import java.nio.file.attribute.FileTime;
@@ -24,7 +14,6 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
-import java.util.concurrent.TimeUnit;
 
 /**
  * Utilities to work with Amazon S3 Objects.
@@ -41,7 +30,7 @@ public class S3Utils {
     public S3Object getS3ObjectSummary(S3Path s3Path) throws NoSuchFileException {
         String key = s3Path.getKey();
         String bucketName = s3Path.getFileStore().name();
-        S3Client client = s3Path.getFileSystem().getClient();
+        S3Client client = s3Path.getFileStore().getClient();
         // try to find the element with the current key (maybe with end slash or maybe not.)
         try {
             HeadObjectResponse metadata = client.headObject(HeadObjectRequest.builder().bucket(bucketName).key(key).build());
@@ -63,9 +52,9 @@ public S3Object getS3ObjectSummary(S3Path s3Path) throws NoSuchFileException {
         }
 
         // if not found (404 err) with the original key.
-        // try to find the elment as a directory.
+        // try to find the element as a directory.
         try {
-            // is a virtual directory
+            // is a virtual directory (S3 prefix)
             ListObjectsV2Request.Builder request = ListObjectsV2Request.builder();
             request.bucket(bucketName);
             String keyFolder = key;
@@ -111,7 +100,7 @@ public S3PosixFileAttributes getS3PosixFileAttributes(S3Path s3Path) throws NoSu
         Set<PosixFilePermission> permissions = null;
 
         if (!attrs.isDirectory()) {
-            S3Client client = s3Path.getFileSystem().getClient();
+            S3Client client = s3Path.getFileStore().getClient();
             GetObjectAclResponse acl = client.getObjectAcl(GetObjectAclRequest.builder().bucket(bucketName).key(key).build());
             Owner owner = acl.owner();
 

From 7675fd94fd79ab93222376af21b26a9bbf579aac Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Thu, 22 Jul 2021 14:34:27 -0400
Subject: [PATCH 018/326] handle redirects and objects that don't allow read
 access to their ACL

---
 .../main/java/org/lerch/s3fs/S3FileStore.java | 39 +++++++++++++++----
 1 file changed, 32 insertions(+), 7 deletions(-)

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
index 6f3c879bc4d..5a38a882ee3 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
@@ -2,6 +2,8 @@
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import software.amazon.awssdk.awscore.exception.AwsServiceException;
+import software.amazon.awssdk.core.exception.SdkClientException;
 import software.amazon.awssdk.regions.Region;
 import software.amazon.awssdk.services.s3.S3Client;
 import software.amazon.awssdk.services.s3.S3Configuration;
@@ -118,8 +120,8 @@ private boolean hasBucket(String bucketName) {
         // model as HeadBucket is now required
         boolean bucket = false;
         try {
-          getClient().headBucket(HeadBucketRequest.builder().bucket(bucketName).build());
-          bucket = true;
+            getClient().headBucket(HeadBucketRequest.builder().bucket(bucketName).build());
+            bucket = true;
         }catch(NoSuchBucketException nsbe) {}
         return bucket;
     }
@@ -135,16 +137,39 @@ public S3Path getRootDirectory() {
      */
     public S3Client getClient() {
         if (bucketSpecificClient == null) {
-            String bucketLocation = defaultClient.getBucketLocation(builder -> builder.bucket(this.name)).locationConstraintAsString();
-            logger.debug("Bucket location is '{}'", bucketLocation);
-
-            Region region = bucketLocation.trim().equals("") ? Region.US_EAST_1 : Region.of(bucketLocation);
-            bucketSpecificClient = S3Client.builder().region(region).build();
+            try {
+                logger.debug("Determining bucket location with getBucketLocation");
+                String bucketLocation = defaultClient.getBucketLocation(builder -> builder.bucket(this.name)).locationConstraintAsString();
+
+                bucketSpecificClient = this.clientForRegion(bucketLocation);
+
+            } catch (S3Exception e) {
+                if(e.statusCode() == 403) {
+                    logger.info("Cannot determine bucket location directly. Attempting to obtain bucket location with headBucket operation");
+                    try {
+                        final HeadBucketResponse headBucketResponse = defaultClient.headBucket(builder -> builder.bucket(this.name));
+                        bucketSpecificClient = this.clientForRegion(headBucketResponse.sdkHttpResponse().firstMatchingHeader("x-amz-bucket-region").orElseThrow());
+                    } catch (S3Exception e2) {
+                        if (e2.statusCode() == 301) {
+                            bucketSpecificClient = this.clientForRegion(e2.awsErrorDetails().sdkHttpResponse().firstMatchingHeader("x-amz-bucket-region").orElseThrow());
+                        }
+                    }
+                } else {
+                    logger.warn("Cannot determine location of {}, falling back to default s3 client for the current profile", this.name);
+                    bucketSpecificClient = S3Client.create();
+                }
+            }
         }
 
         return bucketSpecificClient;
     }
 
+    private S3Client clientForRegion(String regionString){
+        Region region = regionString.equals("") ? Region.US_EAST_1 : Region.of(regionString);
+        logger.debug("Bucket region is: '{}'", region.id());
+        return S3Client.builder().region(region).build();
+    }
+
     public Owner getOwner() {
         if (hasBucket(name))
             return getClient().getBucketAcl(GetBucketAclRequest.builder().bucket(name).build()).owner();

From 08d95b8a0c6ecbb53337433b6c1c095d74f022ae Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Thu, 22 Jul 2021 14:34:59 -0400
Subject: [PATCH 019/326] added retry and size verification to s3 object
 localization

---
 .../backend/impl/aws/AwsBatchJob.scala        | 71 ++++++++++++-------
 1 file changed, 45 insertions(+), 26 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 2378c48c8ef..3903fe8a786 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -30,8 +30,6 @@
  */
 package cromwell.backend.impl.aws
 
-import java.security.MessageDigest
-
 import cats.data.ReaderT._
 import cats.data.{Kleisli, ReaderT}
 import cats.effect.{Async, Timer}
@@ -55,10 +53,11 @@ import software.amazon.awssdk.services.s3.S3Client
 import software.amazon.awssdk.services.s3.model.{GetObjectRequest, HeadObjectRequest, NoSuchKeyException, PutObjectRequest}
 import wdl4s.parser.MemoryUnit
 
+import java.security.MessageDigest
 import scala.collection.JavaConverters._
 import scala.concurrent.duration._
 import scala.language.higherKinds
-import scala.util.{Random, Try}
+import scala.util.Try
 
 /**
   *  The actual job for submission in AWS batch. `AwsBatchJob` is the primary interface to AWS Batch. It creates the
@@ -85,18 +84,12 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                              optAwsAuthMode: Option[AwsAuthMode] = None
                             ) {
 
-  // values for container environment
-  val AWS_MAX_ATTEMPTS: String = "AWS_MAX_ATTEMPTS"
-  val AWS_MAX_ATTEMPTS_DEFAULT_VALUE: String = "14"
-  val AWS_RETRY_MODE: String = "AWS_RETRY_MODE"
-  val AWS_RETRY_MODE_DEFAULT_VALUE: String = "adaptive"
 
   val Log: Logger = LoggerFactory.getLogger(AwsBatchJob.getClass)
 
   //this will be the "folder" that scripts will live in (underneath the script bucket)
   val scriptKeyPrefix = "scripts/"
 
-  // TODO: Auth, endpoint
   lazy val batchClient: BatchClient = {
     val builder = BatchClient.builder()
     configureClient(builder, optAwsAuthMode, configRegion)
@@ -119,26 +112,25 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     */
   lazy val reconfiguredScript: String = {
     //this is the location of the aws cli mounted into the container by the ec2 launch template
-    val s3Cmd = "/usr/local/aws-cli/v2/current/bin/aws s3"
+    val awsCmd = "/usr/local/aws-cli/v2/current/bin/aws "
     //internal to the container, therefore not mounted
     val workDir = "/tmp/scratch"
     //working in a mount will cause collisions in long running workers
     val replaced = commandScript.replaceAllLiterally(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
     val insertionPoint = replaced.indexOf("\n", replaced.indexOf("#!")) +1 //just after the new line after the shebang!
 
-    /* generate a series of s3 copy statements to copy any s3 files into the container. We randomize the order
-       so that large scatters don't all attempt to copy the same thing at the same time. */
-    val inputCopyCommand = Random.shuffle(inputs.map {
+    /* generate a series of s3 copy statements to copy any s3 files into the container. */
+    val inputCopyCommand = inputs.map {
       case input: AwsBatchFileInput if input.s3key.startsWith("s3://") && input.s3key.endsWith(".tmp") =>
         //we are localizing a tmp file which may contain workdirectory paths that need to be reconfigured
         s"""
-           |$s3Cmd cp --no-progress ${input.s3key} $workDir/${input.local}
+           |_s3_localize_with_retry ${input.s3key} $workDir/${input.local}
            |sed -i 's#${AwsBatchWorkingDisk.MountPoint.pathAsString}#$workDir#g' $workDir/${input.local}
            |""".stripMargin
 
 
       case input: AwsBatchFileInput if input.s3key.startsWith("s3://") =>
-        s"$s3Cmd cp --no-progress ${input.s3key} ${input.mount.mountPoint.pathAsString}/${input.local}"
+        s"_s3_localize_with_retry ${input.s3key} ${input.mount.mountPoint.pathAsString}/${input.local}"
           .replaceAllLiterally(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
 
       case input: AwsBatchFileInput =>
@@ -149,11 +141,40 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         s"test -e $filePath || echo 'input file: $filePath does not exist' && exit 1"
 
       case _ => ""
-    }.toList).mkString("\n")
+    }.toList.mkString("\n")
 
     // this goes at the start of the script after the #!
     val preamble =
       s"""
+         |function _s3_localize_with_retry() {
+         |  local s3_path=$$1
+         |  # destination must be the path to a file and not just the directory you want the file in
+         |  local destination=$$2
+         |
+         |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
+         |      bucket="$${BASH_REMATCH[1]}"
+         |      key="$${BASH_REMATCH[2]}"
+         |      content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength')
+         |  else
+         |    echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+         |    exit 1
+         |  fi
+         |
+         |
+         |  for i in {1..5};
+         |  do
+         |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination" &&
+         |    [[ $$(LC_ALL=C ls -dn -- "$$destination" | awk '{print $$5; exit}') -eq "$$content_length" ]] && break ||
+         |    echo "attempt $$i to copy $$s3_path failed";
+         |
+         |    if [ "$$i" -eq 5 ]; then
+         |        echo "failed to copy $$s3_path after $$i attempts. aborting"
+         |        exit 2
+         |    fi
+         |    sleep $$((7 * "$$i"))
+         |  done
+         |}
+         |
          |{
          |set -e
          |echo '*** LOCALIZING INPUTS ***'
@@ -183,24 +204,24 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          */
         s"""
            |touch ${output.name}
-           |$s3Cmd cp --no-progress ${output.name} ${output.s3key}
-           |if [ -e $globDirectory ]; then $s3Cmd cp --no-progress $globDirectory $s3GlobOutDirectory --recursive --exclude "cromwell_glob_control_file"; fi
+           |$awsCmd s3 cp --no-progress ${output.name} ${output.s3key}
+           |if [ -e $globDirectory ]; then $awsCmd s3 cp --no-progress $globDirectory $s3GlobOutDirectory --recursive --exclude "cromwell_glob_control_file"; fi
            |""".stripMargin
 
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
         //output is on working disk mount
         s"""
-           |$s3Cmd cp --no-progress $workDir/${output.local.pathAsString} ${output.s3key}
+           |$awsCmd s3 cp --no-progress $workDir/${output.local.pathAsString} ${output.s3key}
            |""".stripMargin
       case output: AwsBatchFileOutput =>
         //output on a different mount
-        s"$s3Cmd cp --no-progress ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
+        s"$awsCmd s3 cp --no-progress ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
       case _ => ""
     }.mkString("\n") + "\n" +
       s"""
-         |if [ -f $workDir/${jobPaths.returnCodeFilename} ]; then $s3Cmd cp --no-progress $workDir/${jobPaths.returnCodeFilename} ${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename} ; fi\n
-         |if [ -f $stdErr ]; then $s3Cmd cp --no-progress $stdErr ${jobPaths.standardPaths.error.pathAsString}; fi
-         |if [ -f $stdOut ]; then $s3Cmd cp --no-progress $stdOut ${jobPaths.standardPaths.output.pathAsString}; fi
+         |if [ -f $workDir/${jobPaths.returnCodeFilename} ]; then $awsCmd s3 cp --no-progress $workDir/${jobPaths.returnCodeFilename} ${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename} ; fi\n
+         |if [ -f $stdErr ]; then $awsCmd s3 cp --no-progress $stdErr ${jobPaths.standardPaths.error.pathAsString}; fi
+         |if [ -f $stdOut ]; then $awsCmd s3 cp --no-progress $stdOut ${jobPaths.standardPaths.output.pathAsString}; fi
          |""".stripMargin
 
 
@@ -221,8 +242,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
   }
 
   private def generateEnvironmentKVPairs(scriptBucketName: String, scriptKeyPrefix: String, scriptKey: String): List[KeyValuePair] = {
-    List(buildKVPair(AWS_MAX_ATTEMPTS, AWS_MAX_ATTEMPTS_DEFAULT_VALUE),
-      buildKVPair(AWS_RETRY_MODE, AWS_RETRY_MODE_DEFAULT_VALUE),
+    List(
       buildKVPair("BATCH_FILE_TYPE", "script"),
       buildKVPair("BATCH_FILE_S3_URL",batch_file_s3_url(scriptBucketName,scriptKeyPrefix,scriptKey)))
   }
@@ -442,7 +462,6 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
   } yield runStatus
 
   def detail(jobId: String): JobDetail = {
-    //TODO: This client call should be wrapped in a cats Effect
     val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(jobId).build)
 
     val jobDetail = describeJobsResponse.jobs.asScala.headOption.

From 986ab318221148443c5ba51ea52b9f1b5b4055d1 Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Fri, 23 Jul 2021 16:33:14 -0400
Subject: [PATCH 020/326] removed need to have object acl access

---
 .../src/main/java/org/lerch/s3fs/util/S3Utils.java  | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3Utils.java b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3Utils.java
index 73e25a53b04..4f4a3d24996 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3Utils.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3Utils.java
@@ -5,6 +5,8 @@
 import org.lerch.s3fs.attribute.S3BasicFileAttributes;
 import org.lerch.s3fs.attribute.S3PosixFileAttributes;
 import org.lerch.s3fs.attribute.S3UserPrincipal;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import software.amazon.awssdk.services.s3.S3Client;
 import software.amazon.awssdk.services.s3.model.*;
 
@@ -19,6 +21,7 @@
  * Utilities to work with Amazon S3 Objects.
  */
 public class S3Utils {
+    Logger log = LoggerFactory.getLogger("S3Utils");
 
     /**
      * Get the {@link S3Object} that represent this Path or her first child if this path not exists
@@ -34,14 +37,20 @@ public S3Object getS3ObjectSummary(S3Path s3Path) throws NoSuchFileException {
         // try to find the element with the current key (maybe with end slash or maybe not.)
         try {
             HeadObjectResponse metadata = client.headObject(HeadObjectRequest.builder().bucket(bucketName).key(key).build());
-            GetObjectAclResponse acl = client.getObjectAcl(GetObjectAclRequest.builder().bucket(bucketName).key(key).build());
+            Owner objectOwner = Owner.builder().build();
+            try {
+                GetObjectAclResponse acl = client.getObjectAcl(GetObjectAclRequest.builder().bucket(bucketName).key(key).build());
+                objectOwner = acl.owner();
+            } catch (S3Exception e2){
+                log.warn("Unable to determine the owner of object: '{}', setting owner as empty", s3Path);
+            }
             S3Object.Builder builder = S3Object.builder();
 
             builder
                 .key(key)
                 .lastModified(metadata.lastModified())
                 .eTag(metadata.eTag())
-                .owner(acl.owner())
+                .owner(objectOwner)
                 .size(metadata.contentLength())
                 .storageClass(metadata.storageClassAsString());
 

From e171e9139273f50117e969e0acb34144786f1b55 Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Sat, 31 Jul 2021 15:23:42 -0400
Subject: [PATCH 021/326] cache s3 clients and vend from S3ClientStore

---
 .../main/java/org/lerch/s3fs/S3FileStore.java | 34 +-------
 .../org/lerch/s3fs/util/S3ClientStore.java    | 87 +++++++++++++++++++
 2 files changed, 89 insertions(+), 32 deletions(-)
 create mode 100644 filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
index 5a38a882ee3..93f9faf3cba 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
@@ -1,5 +1,6 @@
 package org.lerch.s3fs;
 
+import org.lerch.s3fs.util.S3ClientStore;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import software.amazon.awssdk.awscore.exception.AwsServiceException;
@@ -136,38 +137,7 @@ public S3Path getRootDirectory() {
      * @return a client
      */
     public S3Client getClient() {
-        if (bucketSpecificClient == null) {
-            try {
-                logger.debug("Determining bucket location with getBucketLocation");
-                String bucketLocation = defaultClient.getBucketLocation(builder -> builder.bucket(this.name)).locationConstraintAsString();
-
-                bucketSpecificClient = this.clientForRegion(bucketLocation);
-
-            } catch (S3Exception e) {
-                if(e.statusCode() == 403) {
-                    logger.info("Cannot determine bucket location directly. Attempting to obtain bucket location with headBucket operation");
-                    try {
-                        final HeadBucketResponse headBucketResponse = defaultClient.headBucket(builder -> builder.bucket(this.name));
-                        bucketSpecificClient = this.clientForRegion(headBucketResponse.sdkHttpResponse().firstMatchingHeader("x-amz-bucket-region").orElseThrow());
-                    } catch (S3Exception e2) {
-                        if (e2.statusCode() == 301) {
-                            bucketSpecificClient = this.clientForRegion(e2.awsErrorDetails().sdkHttpResponse().firstMatchingHeader("x-amz-bucket-region").orElseThrow());
-                        }
-                    }
-                } else {
-                    logger.warn("Cannot determine location of {}, falling back to default s3 client for the current profile", this.name);
-                    bucketSpecificClient = S3Client.create();
-                }
-            }
-        }
-
-        return bucketSpecificClient;
-    }
-
-    private S3Client clientForRegion(String regionString){
-        Region region = regionString.equals("") ? Region.US_EAST_1 : Region.of(regionString);
-        logger.debug("Bucket region is: '{}'", region.id());
-        return S3Client.builder().region(region).build();
+        return S3ClientStore.getInstance().getClientForBucketName(this.name);
     }
 
     public Owner getOwner() {
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
new file mode 100644
index 00000000000..61c0286e229
--- /dev/null
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
@@ -0,0 +1,87 @@
+package org.lerch.s3fs.util;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import software.amazon.awssdk.regions.Region;
+import software.amazon.awssdk.services.s3.S3Client;
+import software.amazon.awssdk.services.s3.model.HeadBucketResponse;
+import software.amazon.awssdk.services.s3.model.S3Exception;
+
+import java.net.URI;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * A Singleton cache of clients for buckets configured for the region of those buckets
+ */
+public class S3ClientStore {
+
+    private static final S3ClientStore instance = new S3ClientStore();
+
+    public static final S3Client DEFAULT_CLIENT = S3Client.builder().endpointOverride(URI.create("https://s3.us-east-1.amazonaws.com")).region(Region.US_EAST_1).build();
+
+    private final Map<String, S3Client> bucketToClientMap = Collections.synchronizedMap(new HashMap<>());
+
+    Logger logger = LoggerFactory.getLogger("S3ClientStore");
+
+
+    private S3ClientStore(){}
+
+    public static S3ClientStore getInstance(){
+        return instance;
+    }
+
+    public S3Client getClientForBucketName( String bucketName ) {
+        logger.info("obtaining client for bucket '{}'", bucketName);
+        if (bucketName == null || bucketName.trim().equals("")) {
+            return DEFAULT_CLIENT;
+        }
+
+        return bucketToClientMap.computeIfAbsent(bucketName, this::generateClient);
+    }
+
+    private S3Client generateClient (String name) {
+        logger.info("generating client for bucket: '{}'", name);
+        S3Client bucketSpecificClient;
+        try {
+            logger.info("determining bucket location with getBucketLocation");
+            String bucketLocation = DEFAULT_CLIENT.getBucketLocation(builder -> builder.bucket(name)).locationConstraintAsString();
+
+            bucketSpecificClient = this.clientForRegion(bucketLocation);
+
+        } catch (S3Exception e) {
+            if(e.statusCode() == 403) {
+                logger.info("Cannot determine bucket location directly. Attempting to obtain bucket location with headBucket operation");
+                try {
+                    final HeadBucketResponse headBucketResponse = DEFAULT_CLIENT.headBucket(builder -> builder.bucket(name));
+                    bucketSpecificClient = this.clientForRegion(headBucketResponse.sdkHttpResponse().firstMatchingHeader("x-amz-bucket-region").orElseThrow());
+                } catch (S3Exception e2) {
+                    if (e2.statusCode() == 301) {
+                        bucketSpecificClient = this.clientForRegion(e2.awsErrorDetails().sdkHttpResponse().firstMatchingHeader("x-amz-bucket-region").orElseThrow());
+                    } else {
+                        throw e2;
+                    }
+                }
+            } else {
+                throw e;
+            }
+        }
+
+        if (bucketSpecificClient == null) {
+            logger.warn("Unable to determine the region of bucket: '{}'", name);
+            logger.warn("Generating a client for the current region");
+            bucketSpecificClient = S3Client.create();
+        }
+
+        return bucketSpecificClient;
+    }
+
+    private S3Client clientForRegion(String regionString){
+        // It may be useful to further cache clients for regions although at some point clients for buckets may need to be
+        // specialized beyond just region end points.
+        Region region = regionString.equals("") ? Region.US_EAST_1 : Region.of(regionString);
+        logger.info("bucket region is: '{}'", region.id());
+        return S3Client.builder().region(region).build();
+    }
+}

From 48257ac7b37d7004ac7462bcc7e551eb46c587d3 Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Mon, 2 Aug 2021 16:55:13 -0400
Subject: [PATCH 022/326] updated _s3_localize_with_retry so that the attempt
 to obtain the size of the object is moved within the retry loop

---
 .../backend/impl/aws/AwsBatchJob.scala         | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 3903fe8a786..64228132fb9 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -151,18 +151,16 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  # destination must be the path to a file and not just the directory you want the file in
          |  local destination=$$2
          |
-         |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
-         |      bucket="$${BASH_REMATCH[1]}"
-         |      key="$${BASH_REMATCH[2]}"
-         |      content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength')
-         |  else
-         |    echo "$$s3_path is not an S3 path with a bucket and key. aborting"
-         |    exit 1
-         |  fi
-         |
-         |
          |  for i in {1..5};
          |  do
+         |    if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
+         |        bucket="$${BASH_REMATCH[1]}"
+         |        key="$${BASH_REMATCH[2]}"
+         |        content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength')
+         |    else
+         |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+         |      exit 1
+         |    fi
          |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination" &&
          |    [[ $$(LC_ALL=C ls -dn -- "$$destination" | awk '{print $$5; exit}') -eq "$$content_length" ]] && break ||
          |    echo "attempt $$i to copy $$s3_path failed";

From 4fcc41658894f07633dd469aee3ce184555c06e3 Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Tue, 3 Aug 2021 15:07:03 -0400
Subject: [PATCH 023/326] Increased metadata endpoint retries

---
 .../s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java  | 5 ++---
 .../main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala   | 3 +++
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
index 61c0286e229..a3720d3bab8 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
@@ -52,7 +52,7 @@ private S3Client generateClient (String name) {
 
         } catch (S3Exception e) {
             if(e.statusCode() == 403) {
-                logger.info("Cannot determine bucket location directly. Attempting to obtain bucket location with headBucket operation");
+                logger.info("Cannot determine location of '{}' bucket directly. Attempting to obtain bucket location with headBucket operation", name);
                 try {
                     final HeadBucketResponse headBucketResponse = DEFAULT_CLIENT.headBucket(builder -> builder.bucket(name));
                     bucketSpecificClient = this.clientForRegion(headBucketResponse.sdkHttpResponse().firstMatchingHeader("x-amz-bucket-region").orElseThrow());
@@ -69,8 +69,7 @@ private S3Client generateClient (String name) {
         }
 
         if (bucketSpecificClient == null) {
-            logger.warn("Unable to determine the region of bucket: '{}'", name);
-            logger.warn("Generating a client for the current region");
+            logger.warn("Unable to determine the region of bucket: '{}'. Generating a client for the current region.", name);
             bucketSpecificClient = S3Client.create();
         }
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 64228132fb9..7df82c99ea7 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -146,6 +146,9 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     // this goes at the start of the script after the #!
     val preamble =
       s"""
+         |export AWS_METADATA_SERVICE_TIMEOUT=10
+         |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
+         |
          |function _s3_localize_with_retry() {
          |  local s3_path=$$1
          |  # destination must be the path to a file and not just the directory you want the file in

From 2eb86cf95ad9a8313b2575a9e9e86064777752bd Mon Sep 17 00:00:00 2001
From: henriqueribeiro <henriqueribeiro@users.noreply.github.com>
Date: Wed, 4 Aug 2021 18:56:35 +0100
Subject: [PATCH 024/326] feat: implement aws batch retries (#1)

* add awsBatchRetryAttempts as a runtime attribute

* exit reconfigure-script with same exit code as rc file

* add awsBatchRetryAttempts to AwsBatchJobSpec test

* add documentation for awsBatchRetryAttempts

* create ulimits runtime attribute

* add 'ulimits' runtime attribute

* add ulimits to docs

* add ulimits to test; missing proper tests
---
 .../main/scala/cromwell/backend/backend.scala |   2 +
 docs/RuntimeAttributes.md                     |  53 +++++++-
 .../metadata/impl/MetadataServiceActor.scala  |   2 +-
 ...wsBatchAsyncBackendJobExecutionActor.scala |  16 ++-
 .../backend/impl/aws/AwsBatchAttributes.scala |   9 +-
 .../backend/impl/aws/AwsBatchJob.scala        |  11 +-
 .../impl/aws/AwsBatchJobDefinition.scala      | 107 ++++++++++------
 .../impl/aws/AwsBatchRuntimeAttributes.scala  | 118 +++++++++++++++++-
 .../backend/impl/aws/AwsBatchJobSpec.scala    |   2 +
 .../aws/AwsBatchRuntimeAttributesSpec.scala   |  33 ++++-
 .../backend/impl/aws/AwsBatchTestConfig.scala |   2 +
 .../values/EngineFunctionEvaluators.scala     |   2 +-
 12 files changed, 301 insertions(+), 56 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index 601207362ef..30317d0684c 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -141,6 +141,8 @@ object CommonBackendConfigurationAttributes {
     "default-runtime-attributes.noAddress",
     "default-runtime-attributes.docker",
     "default-runtime-attributes.queueArn",
+    "default-runtime-attributes.awsBatchRetryAttempts",
+    "default-runtime-attributes.ulimits",
     "default-runtime-attributes.failOnStderr",
     "slow-job-warning-time",
     "dockerhub",
diff --git a/docs/RuntimeAttributes.md b/docs/RuntimeAttributes.md
index 7675cc767f4..1bce8a7b306 100644
--- a/docs/RuntimeAttributes.md
+++ b/docs/RuntimeAttributes.md
@@ -56,6 +56,9 @@ There are a number of additional runtime attributes that apply to the Google Clo
 - [useDockerImageCache](#usedockerimagecache)
 
 
+### AWS Specific Attributes
+- [awsBatchRetryAttempts](#awsBatchRetryAttempts)
+- [ulimits](#ulimits)
 
 ## Expression support
 
@@ -323,8 +326,6 @@ runtime {
 ```
 
 
-
-
 ### `bootDiskSizeGb`
 
 In addition to working disks, Google Cloud allows specification of a boot disk size. This is the disk where the docker image itself is booted (**not the working directory of your task on the VM**).
@@ -373,6 +374,54 @@ runtime {
 }
 ```
 
+
+### `awsBatchRetryAttempts`
+
+*Default: _0_*
+
+This runtime attribute adds support to [*AWS Batch Automated Job Retries*](https://docs.aws.amazon.com/batch/latest/userguide/job_retries.html) which makes it possible to tackle transient job failures. For example, if a task fails due to a timeout from accessing an external service, then this option helps re-run the failed the task without having to re-run the entire workflow. It takes an Int, between 1 and 10, as a value that indicates the maximum number of times AWS Batch should retry a failed task. If the value 0 is passed, the [*Retry Strategy*](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#retryStrategy) will not be added to the job definiton and the task will run just once.
+
+```
+runtime {
+  awsBatchRetryAttempts: integer
+}
+```
+
+
+### `ulimits`
+
+*Default: _empty_*
+
+A list of [`ulimits`](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#containerProperties) values to set in the container. This parameter maps to `Ulimits` in the [Create a container](https://docs.docker.com/engine/api/v1.38/) section of the [Docker Remote API](https://docs.docker.com/engine/api/v1.38/) and the `--ulimit` option to [docker run](https://docs.docker.com/engine/reference/commandline/run/).
+
+```
+"ulimits": [
+  {
+    "name": string,
+    "softLimit": integer,
+    "hardLimit": integer
+  }
+  ...
+]
+```
+Parameter description:
+
+- `name`
+  - The `type` of the `ulimit`.
+  - Type: String
+  - Required: Yes, when `ulimits` is used.
+
+- `softLimit`
+  - The soft limit for the `ulimit` type.
+  - Type: Integer
+  - Required: Yes, when `ulimits` is used.
+
+- `hardLimit`
+  - The hard limit for the `ulimit` type.
+  - Type: Integer
+  - Required: Yes, when `ulimits` is used.
+
+
 #### How to Setup
 
 Configure your Google network to use "Private Google Access". This will allow your VMs to access Google Services including Google Container Registry, as well as Dockerhub images.
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala
index a3c4f5fa569..954f5f355f8 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala
@@ -56,7 +56,7 @@ case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, ser
   private val metadataReadTimeout: Duration =
     serviceConfig.getOrElse[Duration]("metadata-read-query-timeout", Duration.Inf)
   private val metadataReadRowNumberSafetyThreshold: Int =
-    serviceConfig.getOrElse[Int]("metadata-read-row-number-safety-threshold", 1000000)
+    serviceConfig.getOrElse[Int]("metadata-read-row-number-safety-threshold", 3000000)
 
   def readMetadataWorkerActorProps(): Props =
     ReadDatabaseMetadataWorkerActor
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 7a36946e78d..4ceb0c8295e 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -202,10 +202,18 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   private def inputsFromWomFiles(namePrefix: String,
                                     remotePathArray: Seq[WomFile],
                                     localPathArray: Seq[WomFile],
-                                    jobDescriptor: BackendJobDescriptor): Iterable[AwsBatchInput] = {
+                                    jobDescriptor: BackendJobDescriptor,
+                                    flag: Boolean): Iterable[AwsBatchInput] = {
+
     (remotePathArray zip localPathArray zipWithIndex) flatMap {
       case ((remotePath, localPath), index) =>
-        Seq(AwsBatchFileInput(s"$namePrefix-$index", remotePath.valueString, DefaultPathBuilder.get(localPath.valueString), workingDisk))
+        var localPathString = localPath.valueString
+        if (localPathString.startsWith("s3://")){
+          localPathString = localPathString.replace("s3://", "")
+        }else if (localPathString.startsWith("s3:/")) {
+          localPathString = localPathString.replace("s3:/", "")
+        }
+        Seq(AwsBatchFileInput(s"$namePrefix-$index", remotePath.valueString, DefaultPathBuilder.get(localPathString), workingDisk))
     }
   }
 
@@ -237,7 +245,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     val writeFunctionFiles = instantiatedCommand.createdFiles map { f => f.file.value.md5SumShort -> List(f) } toMap
 
     val writeFunctionInputs = writeFunctionFiles flatMap {
-      case (name, files) => inputsFromWomFiles(name, files.map(_.file), files.map(localizationPath), jobDescriptor)
+      case (name, files) => inputsFromWomFiles(name, files.map(_.file), files.map(localizationPath), jobDescriptor, false)
     }
 
     // Collect all WomFiles from inputs to the call.
@@ -257,7 +265,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     }
 
     val callInputInputs = callInputFiles flatMap {
-      case (name, files) => inputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor)
+      case (name, files) => inputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor, true)
     }
 
     val scriptInput: AwsBatchInput = AwsBatchFileInput(
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index 26f69c4e79a..dffcb983235 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -71,7 +71,14 @@ object AwsBatchAttributes {
     "filesystems.local.auth",
     "filesystems.s3.auth",
     "filesystems.s3.caching.duplication-strategy",
-    "filesystems.local.caching.duplication-strategy"
+    "filesystems.local.caching.duplication-strategy",
+    "auth",
+    "numCreateDefinitionAttempts",
+    "filesystems.s3.duplication-strategy",
+    "numSubmitAttempts",
+    "default-runtime-attributes.scriptBucketName",
+    "awsBatchRetryAttempts",
+    "ulimits"
   )
 
   private val deprecatedAwsBatchKeys: Map[String, String] = Map(
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 7df82c99ea7..1e2efaa2d5c 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -234,6 +234,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |echo '*** DELOCALIZING OUTPUTS ***'
          |$outputCopyCommand
          |echo '*** COMPLETED DELOCALIZATION ***'
+         |echo '*** EXITING WITH RC CODE ***'
+         |exit $$(head -n 1 $workDir/${jobPaths.returnCodeFilename})
          |}
          |""".stripMargin
   }
@@ -409,16 +411,19 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         // See:
         //
         // http://aws-java-sdk-javadoc.s3-website-us-west-2.amazonaws.com/latest/software/amazon/awssdk/services/batch/model/RegisterJobDefinitionRequest.Builder.html
-        val definitionRequest = RegisterJobDefinitionRequest.builder
+        var definitionRequest = RegisterJobDefinitionRequest.builder
           .containerProperties(jobDefinition.containerProperties)
           .jobDefinitionName(jobDefinitionName)
           // See https://stackoverflow.com/questions/24349517/scala-method-named-type
           .`type`(JobDefinitionType.CONTAINER)
-          .build
+
+        if (jobDefinitionContext.runtimeAttributes.awsBatchRetryAttempts != 0){
+          definitionRequest = definitionRequest.retryStrategy(jobDefinition.retryStrategy)
+        }
 
         Log.debug(s"Submitting definition request: $definitionRequest")
 
-        val response: RegisterJobDefinitionResponse = batchClient.registerJobDefinition(definitionRequest)
+        val response: RegisterJobDefinitionResponse = batchClient.registerJobDefinition(definitionRequest.build)
         Log.info(s"Definition created: $response")
         response.jobDefinitionArn()
       }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index 137cce9a4ef..876a23c32c0 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -35,7 +35,7 @@ import scala.language.postfixOps
 import scala.collection.mutable.ListBuffer
 import cromwell.backend.BackendJobDescriptor
 import cromwell.backend.io.JobPaths
-import software.amazon.awssdk.services.batch.model.{ContainerProperties, Host, KeyValuePair, MountPoint, Volume}
+import software.amazon.awssdk.services.batch.model.{ContainerProperties, Host, KeyValuePair, MountPoint, RetryStrategy, Volume, Ulimit}
 import cromwell.backend.impl.aws.io.AwsBatchVolume
 
 import scala.collection.JavaConverters._
@@ -62,12 +62,14 @@ import wdl4s.parser.MemoryUnit
   */
 sealed trait AwsBatchJobDefinition {
   def containerProperties: ContainerProperties
+  def retryStrategy: RetryStrategy 
   def name: String
 
   override def toString: String = {
     new ToStringBuilder(this, ToStringStyle.JSON_STYLE)
       .append("name", name)
       .append("containerProperties", containerProperties)
+      .append("retryStrategy", retryStrategy)
       .build
   }
 }
@@ -78,23 +80,13 @@ trait AwsBatchJobDefinitionBuilder {
 
   /** Gets a builder, seeded with appropriate portions of the container properties
    *
-   *  @param dockerImage docker image with which to run
-   *  @return ContainerProperties builder ready for modification
+   *  @param context AwsBatchJobDefinitionContext with all the runtime attributes
+   *  @return ContainerProperties builder ready for modification and name
    *
    */
-  def builder(dockerImage: String): ContainerProperties.Builder =
-    ContainerProperties.builder().image(dockerImage)
-
-
-  def buildResources(builder: ContainerProperties.Builder,
-                     context: AwsBatchJobDefinitionContext): (ContainerProperties.Builder, String) = {
-    // The initial buffer should only contain one item - the hostpath of the
-    // local disk mount point, which will be needed by the docker container
-    // that copies data around
-
-    val environment = List.empty[KeyValuePair]
-
-
+  def containerPropertiesBuilder(context: AwsBatchJobDefinitionContext): (ContainerProperties.Builder, String) = {
+    
+    
     def buildVolumes(disks: Seq[AwsBatchVolume]): List[Volume] = {
 
       //all the configured disks plus the fetch and run volume and the aws-cli volume
@@ -111,6 +103,7 @@ trait AwsBatchJobDefinitionBuilder {
       )
     }
 
+
     def buildMountPoints(disks: Seq[AwsBatchVolume]): List[MountPoint] = {
 
       //all the configured disks plus the fetch and run mount point and the AWS cli mount point
@@ -130,45 +123,63 @@ trait AwsBatchJobDefinitionBuilder {
       )
     }
 
-    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair]): String = {
-      val str = s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}"
 
-      val sha1 = MessageDigest.getInstance("SHA-1")
-            .digest( str.getBytes("UTF-8") )
-            .map("%02x".format(_)).mkString
-
-      val prefix = s"cromwell_$imageName".slice(0,88) // will be joined to a 40 character SHA1 for total length of 128
+    def buildUlimits(ulimits: Seq[Map[String, String]]): List[Ulimit] = {
 
-      sanitize(prefix + sha1)
+      ulimits.filter(_.nonEmpty).map(u =>
+        Ulimit.builder()
+          .name(u("name"))
+          .softLimit(u("softLimit").toInt)
+          .hardLimit(u("hardLimit").toInt)
+          .build()
+      ).toList
     }
 
 
+    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit]): String = {
+      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}"
+    }
+    
+
+    val environment = List.empty[KeyValuePair]
     val cmdName = context.runtimeAttributes.fileSystem match {
-       case AWSBatchStorageSystems.s3 => "/var/scratch/fetch_and_run.sh"
-       case _ =>  context.commandText
+      case AWSBatchStorageSystems.s3 => "/var/scratch/fetch_and_run.sh"
+      case _ =>  context.commandText
     }
     val packedCommand = packCommand("/bin/bash", "-c", cmdName)
     val volumes =  buildVolumes( context.runtimeAttributes.disks )
     val mountPoints = buildMountPoints( context.runtimeAttributes.disks)
-    val jobDefinitionName = buildName(
+    val ulimits = buildUlimits( context.runtimeAttributes.ulimits)
+    val containerPropsName = buildName(
       context.runtimeAttributes.dockerImage,
       packedCommand.mkString(","),
       volumes,
       mountPoints,
-      environment
+      environment,
+      ulimits
     )
 
-    (builder
-       .command(packedCommand.asJava)
-        .memory(context.runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt)
-        .vcpus(context.runtimeAttributes.cpu##)
-        .volumes( volumes.asJava)
-        .mountPoints( mountPoints.asJava)
-        .environment(environment.asJava),
+    (ContainerProperties.builder()
+      .image(context.runtimeAttributes.dockerImage)
+      .command(packedCommand.asJava)
+      .memory(context.runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt)
+      .vcpus(context.runtimeAttributes.cpu##)
+      .volumes(volumes.asJava)
+      .mountPoints(mountPoints.asJava)
+      .environment(environment.asJava)
+      .ulimits(ulimits.asJava),
+     containerPropsName)
+  }
 
-      jobDefinitionName)
+  def retryStrategyBuilder(context: AwsBatchJobDefinitionContext): (RetryStrategy.Builder, String) = {
+    // We can add here the 'evaluateOnExit' statement
+    
+    (RetryStrategy.builder()
+      .attempts(context.runtimeAttributes.awsBatchRetryAttempts),
+     context.runtimeAttributes.awsBatchRetryAttempts.toString)
   }
 
+
   private def packCommand(shell: String, options: String, mainCommand: String): Seq[String] = {
     val rc = new ListBuffer[String]()
     val lim = 1024
@@ -189,15 +200,29 @@ trait AwsBatchJobDefinitionBuilder {
 
 object StandardAwsBatchJobDefinitionBuilder extends AwsBatchJobDefinitionBuilder {
   def build(context: AwsBatchJobDefinitionContext): AwsBatchJobDefinition = {
-    //instantiate a builder with the name of the docker image
-    val builderInst = builder(context.runtimeAttributes.dockerImage)
-    val (b, name) = buildResources(builderInst, context)
+    
+    val (containerPropsInst, containerPropsName) = containerPropertiesBuilder(context)
+    val (retryStrategyInst, retryStrategyName) = retryStrategyBuilder(context)
 
-    new StandardAwsBatchJobDefinitionBuilder(b.build, name)
+    val name = buildName(context.runtimeAttributes.dockerImage, containerPropsName, retryStrategyName)
+
+    new StandardAwsBatchJobDefinitionBuilder(containerPropsInst.build, retryStrategyInst.build, name)
   }
+
+  def buildName(imageName: String, containerPropsName: String, retryStrategyName: String): String = {
+      val str = s"$imageName:$containerPropsName:$retryStrategyName"
+
+      val sha1 = MessageDigest.getInstance("SHA-1")
+            .digest( str.getBytes("UTF-8") )
+            .map("%02x".format(_)).mkString
+
+      val prefix = s"cromwell_${imageName}_".slice(0,88) // will be joined to a 40 character SHA1 for total length of 128
+
+      sanitize(prefix + sha1)
+    }
 }
 
-case class StandardAwsBatchJobDefinitionBuilder private(containerProperties: ContainerProperties, name: String) extends AwsBatchJobDefinition
+case class StandardAwsBatchJobDefinitionBuilder private(containerProperties: ContainerProperties, retryStrategy: RetryStrategy, name: String) extends AwsBatchJobDefinition
 
 object AwsBatchJobDefinitionContext
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index c6fc2a5f51f..8296eefd42a 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -60,6 +60,8 @@ import scala.util.matching.Regex
  * @param noAddress is there no address
  * @param scriptS3BucketName the s3 bucket where the execution command or script will be written and, from there, fetched into the container and executed
  * @param fileSystem the filesystem type, default is "s3"
+ * @param awsBatchRetryAttempts number of attempts that AWS Batch will retry the task if it fails
+ * @param ulimits ulimit values to be passed to the container
  */
 case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      zones: Vector[String],
@@ -71,7 +73,9 @@ case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      continueOnReturnCode: ContinueOnReturnCode,
                                      noAddress: Boolean,
                                      scriptS3BucketName: String,
-                                     fileSystem:String= "s3")
+                                     awsBatchRetryAttempts: Int,
+                                     ulimits: Vector[Map[String, String]],
+                                     fileSystem: String= "s3")
 
 object AwsBatchRuntimeAttributes {
 
@@ -79,6 +83,8 @@ object AwsBatchRuntimeAttributes {
 
   val scriptS3BucketKey = "scriptBucketName"
 
+  val awsBatchRetryAttemptsKey = "awsBatchRetryAttempts"
+
   val ZonesKey = "zones"
   private val ZonesDefaultValue = WomString("us-east-1a")
 
@@ -92,6 +98,9 @@ object AwsBatchRuntimeAttributes {
 
   private val MemoryDefaultValue = "2 GB"
 
+  val UlimitsKey = "ulimits"
+  private val UlimitsDefaultValue = WomArray(WomArrayType(WomMapType(WomStringType,WomStringType)), Vector(WomMap(Map.empty[WomValue, WomValue])))
+
   private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] = CpuValidation.instance
     .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
@@ -134,6 +143,14 @@ object AwsBatchRuntimeAttributes {
     QueueArnValidation.withDefault(QueueArnValidation.configDefaultWomValue(runtimeConfig) getOrElse
       (throw new RuntimeException("queueArn is required")))
 
+  private def awsBatchRetryAttemptsValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = {
+    AwsBatchRetryAttemptsValidation(awsBatchRetryAttemptsKey).withDefault(AwsBatchRetryAttemptsValidation(awsBatchRetryAttemptsKey)
+    .configDefaultWomValue(runtimeConfig).getOrElse(WomInteger(0)))
+  }
+
+  private def ulimitsValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[Map[String, String]]] =
+   UlimitsValidation.withDefault(UlimitsValidation.configDefaultWomValue(runtimeConfig) getOrElse UlimitsDefaultValue)
+
   def runtimeAttributesBuilder(configuration: AwsBatchConfiguration): StandardValidatedRuntimeAttributesBuilder = {
     val runtimeConfig = configuration.runtimeConfig
     def validationsS3backend = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
@@ -146,7 +163,9 @@ object AwsBatchRuntimeAttributes {
                         noAddressValidation(runtimeConfig),
                         dockerValidation,
                         queueArnValidation(runtimeConfig),
-                        scriptS3BucketNameValidation(runtimeConfig)
+                        scriptS3BucketNameValidation(runtimeConfig),
+                        awsBatchRetryAttemptsValidation(runtimeConfig),
+                        ulimitsValidation(runtimeConfig),
                       )
    def validationsLocalBackend  = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
       cpuValidation(runtimeConfig),
@@ -181,6 +200,8 @@ object AwsBatchRuntimeAttributes {
        case AWSBatchStorageSystems.s3 => RuntimeAttributesValidation.extract(scriptS3BucketNameValidation(runtimeAttrsConfig) , validatedRuntimeAttributes)
        case _ => ""
      }
+    val awsBatchRetryAttempts: Int = RuntimeAttributesValidation.extract(awsBatchRetryAttemptsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val ulimits: Vector[Map[String, String]] = RuntimeAttributesValidation.extract(ulimitsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
 
 
     new AwsBatchRuntimeAttributes(
@@ -194,6 +215,8 @@ object AwsBatchRuntimeAttributes {
       continueOnReturnCode,
       noAddress,
       scriptS3BucketName,
+      awsBatchRetryAttempts,
+      ulimits,
       fileSystem
     )
   }
@@ -372,3 +395,94 @@ object DisksValidation extends RuntimeAttributesValidation[Seq[AwsBatchVolume]]
   override protected def missingValueMessage: String =
     s"Expecting $key runtime attribute to be a comma separated String or Array[String]"
 }
+
+object AwsBatchRetryAttemptsValidation {
+  def apply(key: String): AwsBatchRetryAttemptsValidation = new AwsBatchRetryAttemptsValidation(key)
+}
+
+class AwsBatchRetryAttemptsValidation(key: String) extends IntRuntimeAttributesValidation(key) {
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[Int]] = {
+    case womValue if WomIntegerType.coerceRawValue(womValue).isSuccess =>
+      WomIntegerType.coerceRawValue(womValue).get match {
+        case WomInteger(value) =>
+          if (value.toInt < 0)
+            s"Expecting $key runtime attribute value greater than or equal to 0".invalidNel
+          else if (value.toInt > 10)
+            s"Expecting $key runtime attribute value lower than or equal to 10".invalidNel
+          else
+            value.toInt.validNel
+      }
+  }
+
+  override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Integer"
+}
+
+
+object UlimitsValidation
+    extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
+  override def key: String = AwsBatchRuntimeAttributes.UlimitsKey
+
+  override def coercion: Traversable[WomType] =
+    Set(WomStringType, WomArrayType(WomMapType(WomStringType, WomStringType)))
+
+  var accepted_keys = Set("name", "softLimit", "hardLimit")
+
+  override protected def validateValue
+      : PartialFunction[WomValue, ErrorOr[Vector[Map[String, String]]]] = {
+    case WomArray(womType, value)
+        if womType.memberType == WomMapType(WomStringType, WomStringType) =>
+      check_maps(value.toVector)
+    case WomMap(_, _) => "!!! ERROR1".invalidNel
+
+  }
+
+  private def check_maps(
+      maps: Vector[WomValue]
+  ): ErrorOr[Vector[Map[String, String]]] = {
+    val entryNels: Vector[ErrorOr[Map[String, String]]] = maps.map {
+      case WomMap(_, value) => check_keys(value)
+      case _                 => "!!! ERROR2".invalidNel
+    }
+    val sequenced: ErrorOr[Vector[Map[String, String]]] = sequenceNels(
+      entryNels
+    )
+    sequenced
+  }
+
+  private def check_keys(
+      dict: Map[WomValue, WomValue]
+  ): ErrorOr[Map[String, String]] = {
+    val map_keys = dict.keySet.map(_.valueString).toSet
+    val unrecognizedKeys =
+      accepted_keys.diff(map_keys) union map_keys.diff(accepted_keys)
+
+    if (!dict.nonEmpty){
+      Map.empty[String, String].validNel  
+    }else if (unrecognizedKeys.nonEmpty) {
+      s"Invalid keys in $key runtime attribute. Refer to 'ulimits' section on https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#containerProperties".invalidNel
+    } else {
+      dict
+        .collect { case (WomString(k), WomString(v)) =>
+          (k, v)
+        // case _ => "!!! ERROR3".invalidNel
+        }
+        .toMap
+        .validNel
+    }
+  }
+
+  private def sequenceNels(
+      nels: Vector[ErrorOr[Map[String, String]]]
+  ): ErrorOr[Vector[Map[String, String]]] = {
+    val emptyNel: ErrorOr[Vector[Map[String, String]]] =
+      Vector.empty[Map[String, String]].validNel
+    val seqNel: ErrorOr[Vector[Map[String, String]]] =
+      nels.foldLeft(emptyNel) { (acc, v) =>
+        (acc, v) mapN { (a, v) => a :+ v }
+      }
+    seqNel
+  }
+
+  override protected def missingValueMessage: String =
+    s"Expecting $key runtime attribute to be an Array[Map[String, String]]"
+}
\ No newline at end of file
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index 5037fc21051..4a7ea041b10 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -113,6 +113,8 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
       continueOnReturnCode = ContinueOnReturnCodeFlag(false),
       noAddress = false,
       scriptS3BucketName = "script-bucket",
+      awsBatchRetryAttempts = 1,
+      ulimits = Vector(Map.empty[String, String]),
       fileSystem = "s3")
 
   private def generateBasicJob: AwsBatchJob = {
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
index 09e1ee94351..f8c009f95ed 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
@@ -65,7 +65,9 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     false,
     ContinueOnReturnCodeSet(Set(0)),
     false,
-    "my-stuff")
+    "my-stuff",
+    1,
+    Vector(Map.empty[String, String]))
 
   val expectedDefaultsLocalFS = new AwsBatchRuntimeAttributes(refineMV[Positive](1), Vector("us-east-1a", "us-east-1b"),
 
@@ -76,6 +78,8 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     ContinueOnReturnCodeSet(Set(0)),
     false,
     "",
+    1,
+    Vector(Map.empty[String, String]),
     "local")
 
   "AwsBatchRuntimeAttributes" should {
@@ -339,6 +343,33 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
       val expectedRuntimeAttributes = expectedDefaults.copy(cpu = refineMV[Positive](4))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes, workflowOptions)
     }
+
+    "validate a valid awsBatchRetryAttempts entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "awsBatchRetryAttempts" -> WomInteger(9), "scriptBucketName" -> WomString("my-stuff"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(awsBatchRetryAttempts = 9)
+      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate with -1 as awsBatchRetryAttempts" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "awsBatchRetryAttempts" -> WomInteger(-1), "scriptBucketName" -> WomString("my-stuff"))
+      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting awsBatchRetryAttempts runtime attribute value greater than or equal to 0")
+    }
+
+    "fail to validate with 12 as awsBatchRetryAttempts" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "awsBatchRetryAttempts" -> WomInteger(12), "scriptBucketName" -> WomString("my-stuff"))
+      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting awsBatchRetryAttempts runtime attribute value lower than or equal to 10")
+    }
+
+    "fail to validate with a string as  awsBatchRetryAttempts" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "awsBatchRetryAttempts" -> WomString("test"), "scriptBucketName" -> WomString("my-stuff"))
+      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting awsBatchRetryAttempts runtime attribute to be an Integer")
+    }
+
+    "validate zero as awsBatchRetryAttempts entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "awsBatchRetryAttempts" -> WomInteger(0), "scriptBucketName" -> WomString("my-stuff"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(awsBatchRetryAttempts = 0)
+      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
   }
 
   private def assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes: Map[String, WomValue],
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
index 38545c7e472..682714b225c 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
@@ -61,6 +61,7 @@ object AwsBatchTestConfig {
       |    zones:["us-east-1a", "us-east-1b"]
       |    queueArn: "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue"
       |    scriptBucketName: "my-bucket"
+      |    awsBatchRetryAttempts: 1
       |}
       |
       |""".stripMargin
@@ -140,6 +141,7 @@ object AwsBatchTestConfigForLocalFS {
       |    zones:["us-east-1a", "us-east-1b"]
       |    queueArn: "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue"
       |    scriptBucketName: ""
+      |    awsBatchRetryAttempts: 1
       |}
       |
       |""".stripMargin
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
index 0a2bf3b998a..21f6f7516a5 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
@@ -51,7 +51,7 @@ object EngineFunctionEvaluators {
       EvaluatedValue(WomSingleFile(ioFunctionSet.pathFunctions.stderr), Seq.empty).validNel
   }
 
-  private val ReadWaitTimeout = 60.seconds
+  private val ReadWaitTimeout = 300.seconds
   private def readFile(fileToRead: WomSingleFile, ioFunctionSet: IoFunctionSet, sizeLimit: Int) = {
     Try(Await.result(ioFunctionSet.readFile(fileToRead.value, Option(sizeLimit), failOnOverflow = true), ReadWaitTimeout))
   }

From e977d082e54605f4c938474c29d41913710282a2 Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Mon, 23 Aug 2021 17:52:33 -0400
Subject: [PATCH 025/326] Improved cross region object access and better handle
 permission restrictions

---
 .../main/java/org/lerch/s3fs/S3FileStore.java |  3 +--
 .../org/lerch/s3fs/util/S3ClientStore.java    |  2 +-
 .../s3/batch/S3BatchCommandBuilder.scala      | 27 ++++++++++++++++++-
 .../backend/impl/aws/AwsBatchJob.scala        |  6 +++--
 4 files changed, 32 insertions(+), 6 deletions(-)

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
index 93f9faf3cba..8e15999180a 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
@@ -25,8 +25,7 @@ public class S3FileStore extends FileStore implements Comparable<S3FileStore> {
     private S3FileSystem fileSystem;
     private String name;
     private S3Client defaultClient;
-    private S3Client bucketSpecificClient;
-    private Logger logger = LoggerFactory.getLogger("S3FileStore");
+    private final Logger logger = LoggerFactory.getLogger("S3FileStore");
 
     public S3FileStore(S3FileSystem s3FileSystem, String name) {
         this.fileSystem = s3FileSystem;
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
index a3720d3bab8..78a139d3f18 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
@@ -33,7 +33,7 @@ public static S3ClientStore getInstance(){
     }
 
     public S3Client getClientForBucketName( String bucketName ) {
-        logger.info("obtaining client for bucket '{}'", bucketName);
+        logger.debug("obtaining client for bucket '{}'", bucketName);
         if (bucketName == null || bucketName.trim().equals("")) {
             return DEFAULT_CLIENT;
         }
diff --git a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
index 8058d897975..645600d1613 100644
--- a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
+++ b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
@@ -30,9 +30,11 @@
  */
 package cromwell.filesystems.s3.batch
 
-import cromwell.core.io.{IoCommandBuilder, PartialIoCommandBuilder}
+import cromwell.core.io.{IoCommandBuilder, IoContentAsStringCommand, IoIsDirectoryCommand, IoReadLinesCommand, IoWriteCommand, PartialIoCommandBuilder}
+import cromwell.core.path.BetterFileMethods.OpenOptions
 import cromwell.core.path.Path
 import cromwell.filesystems.s3.S3Path
+import org.slf4j.{Logger, LoggerFactory}
 
 import scala.util.Try
 
@@ -40,6 +42,29 @@ import scala.util.Try
   * Generates commands for IO operations on S3
   */
 private case object PartialS3BatchCommandBuilder extends PartialIoCommandBuilder {
+  val Log: Logger = LoggerFactory.getLogger(PartialS3BatchCommandBuilder.getClass)
+
+
+  override def contentAsStringCommand: PartialFunction[(Path, Option[Int], Boolean), Try[IoContentAsStringCommand]] = {
+    Log.debug("call to contentAsStringCommand but PartialFunction not implemented, falling back to super")
+    super.contentAsStringCommand
+  }
+
+  override def writeCommand: PartialFunction[(Path, String, OpenOptions, Boolean), Try[IoWriteCommand]] = {
+    Log.debug("call to writeCommand but PartialFunction not implemented, falling back to super")
+    super.writeCommand
+  }
+
+  override def isDirectoryCommand: PartialFunction[Path, Try[IoIsDirectoryCommand]] = {
+    Log.debug("call to isDirectoryCommand but PartialFunction not implemented, falling back to super")
+    super.isDirectoryCommand
+  }
+
+  override def readLinesCommand: PartialFunction[Path, Try[IoReadLinesCommand]] = {
+    Log.debug("call to readLinesCommand but PartialFunction not implemented, falling back to super")
+    super.readLinesCommand
+  }
+
   override def sizeCommand: PartialFunction[Path, Try[S3BatchSizeCommand]] = {
     case path: S3Path => Try(S3BatchSizeCommand(path))
   }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 1e2efaa2d5c..5068c4a9784 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -234,8 +234,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |echo '*** DELOCALIZING OUTPUTS ***'
          |$outputCopyCommand
          |echo '*** COMPLETED DELOCALIZATION ***'
-         |echo '*** EXITING WITH RC CODE ***'
-         |exit $$(head -n 1 $workDir/${jobPaths.returnCodeFilename})
+         |echo '*** EXITING WITH RETURN CODE ***'
+         |rc=$$(head -n 1 $workDir/${jobPaths.returnCodeFilename})
+         |echo $$rc
+         |exit $$rc
          |}
          |""".stripMargin
   }

From 155ed46caee71167d3abd061f42632082b078094 Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Tue, 5 Oct 2021 12:28:44 -0400
Subject: [PATCH 026/326] Improved testing

---
 .../main/scala/cloud/nio/spi/UnixPath.scala   |   2 +-
 .../org/lerch/s3fs/util/S3ClientStore.java    |  32 +++-
 .../lerch/s3fs/util/S3ClientStoreTest.java    | 167 ++++++++++++++++++
 .../backend/impl/aws/AwsBatchJobSpec.scala    | 126 +++++++++++--
 4 files changed, 299 insertions(+), 28 deletions(-)
 create mode 100644 filesystems/s3/src/test/scala/org/lerch/s3fs/util/S3ClientStoreTest.java

diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
index 306afa44cc7..a5d0770bc56 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
@@ -69,7 +69,7 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
 
   def isAbsolute: Boolean = UnixPath.isAbsolute(path)
 
-  def isEmpty: Boolean = path.isEmpty
+  override def isEmpty: Boolean = path.isEmpty
 
   def hasTrailingSeparator: Boolean = UnixPath.hasTrailingSeparator(path)
 
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
index 78a139d3f18..818a0004a3e 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
@@ -28,9 +28,7 @@ public class S3ClientStore {
 
     private S3ClientStore(){}
 
-    public static S3ClientStore getInstance(){
-        return instance;
-    }
+    public static S3ClientStore getInstance() { return instance; }
 
     public S3Client getClientForBucketName( String bucketName ) {
         logger.debug("obtaining client for bucket '{}'", bucketName);
@@ -41,20 +39,35 @@ public S3Client getClientForBucketName( String bucketName ) {
         return bucketToClientMap.computeIfAbsent(bucketName, this::generateClient);
     }
 
-    private S3Client generateClient (String name) {
-        logger.info("generating client for bucket: '{}'", name);
+    /**
+     * Generate a client for the named bucket using a default client to determine the location of the named client
+     * @param bucketName the named of the bucket to make the client for
+     * @return an S3 client appropriate for the region of the named bucket
+     */
+    protected S3Client generateClient(String bucketName){
+        return this.generateClient(bucketName, DEFAULT_CLIENT);
+    }
+
+    /**
+     * Generate a client for the named bucket using a default client to determine the location of the named client
+     * @param bucketName the named of the bucket to make the client for
+     * @param locationClient the client used to determine the location of the named bucket, recommend using DEFAULT_CLIENT
+     * @return an S3 client appropriate for the region of the named bucket
+     */
+    protected S3Client generateClient (String bucketName, S3Client locationClient) {
+        logger.info("generating client for bucket: '{}'", bucketName);
         S3Client bucketSpecificClient;
         try {
             logger.info("determining bucket location with getBucketLocation");
-            String bucketLocation = DEFAULT_CLIENT.getBucketLocation(builder -> builder.bucket(name)).locationConstraintAsString();
+            String bucketLocation = locationClient.getBucketLocation(builder -> builder.bucket(bucketName)).locationConstraintAsString();
 
             bucketSpecificClient = this.clientForRegion(bucketLocation);
 
         } catch (S3Exception e) {
             if(e.statusCode() == 403) {
-                logger.info("Cannot determine location of '{}' bucket directly. Attempting to obtain bucket location with headBucket operation", name);
+                logger.info("Cannot determine location of '{}' bucket directly. Attempting to obtain bucket location with headBucket operation", bucketName);
                 try {
-                    final HeadBucketResponse headBucketResponse = DEFAULT_CLIENT.headBucket(builder -> builder.bucket(name));
+                    final HeadBucketResponse headBucketResponse = locationClient.headBucket(builder -> builder.bucket(bucketName));
                     bucketSpecificClient = this.clientForRegion(headBucketResponse.sdkHttpResponse().firstMatchingHeader("x-amz-bucket-region").orElseThrow());
                 } catch (S3Exception e2) {
                     if (e2.statusCode() == 301) {
@@ -69,7 +82,7 @@ private S3Client generateClient (String name) {
         }
 
         if (bucketSpecificClient == null) {
-            logger.warn("Unable to determine the region of bucket: '{}'. Generating a client for the current region.", name);
+            logger.warn("Unable to determine the region of bucket: '{}'. Generating a client for the current region.", bucketName);
             bucketSpecificClient = S3Client.create();
         }
 
@@ -83,4 +96,5 @@ private S3Client clientForRegion(String regionString){
         logger.info("bucket region is: '{}'", region.id());
         return S3Client.builder().region(region).build();
     }
+
 }
diff --git a/filesystems/s3/src/test/scala/org/lerch/s3fs/util/S3ClientStoreTest.java b/filesystems/s3/src/test/scala/org/lerch/s3fs/util/S3ClientStoreTest.java
new file mode 100644
index 00000000000..6f419d0c335
--- /dev/null
+++ b/filesystems/s3/src/test/scala/org/lerch/s3fs/util/S3ClientStoreTest.java
@@ -0,0 +1,167 @@
+package org.lerch.s3fs.util;
+
+import junit.framework.TestCase;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.InOrder;
+import org.mockito.Mock;
+import static org.mockito.Mockito.*;
+
+import org.mockito.Spy;
+import org.mockito.junit.MockitoJUnitRunner;
+import software.amazon.awssdk.awscore.exception.AwsErrorDetails;
+import software.amazon.awssdk.http.SdkHttpResponse;
+import software.amazon.awssdk.services.s3.S3Client;
+import software.amazon.awssdk.services.s3.model.GetBucketLocationResponse;
+import software.amazon.awssdk.services.s3.model.HeadBucketResponse;
+import software.amazon.awssdk.services.s3.model.S3Exception;
+
+import java.util.NoSuchElementException;
+import java.util.function.Consumer;
+
+@RunWith(MockitoJUnitRunner.class)
+public class S3ClientStoreTest extends TestCase {
+
+    S3ClientStore instance;
+
+    @Mock
+    S3Client mockClient;
+
+    @Spy
+    final S3ClientStore spyInstance = S3ClientStore.getInstance();
+
+    @Before
+    public void setUp() throws Exception {
+        super.setUp();
+        instance = S3ClientStore.getInstance();
+    }
+
+    @Test
+    public void testGetInstanceReturnsSingleton() {
+        assertSame(S3ClientStore.getInstance(), instance);
+    }
+
+    @Test
+    public void testGetClientForNullBucketName() {
+        assertEquals(S3ClientStore.DEFAULT_CLIENT, instance.getClientForBucketName(null));
+    }
+
+    @Test
+    public void testGetClientForEmptyBucketName() {
+        assertEquals(S3ClientStore.DEFAULT_CLIENT, instance.getClientForBucketName(""));
+        assertEquals(S3ClientStore.DEFAULT_CLIENT, instance.getClientForBucketName(" "));
+    }
+
+    @Test
+    public void testGenerateClientWithNoErrors() {
+        when(mockClient.getBucketLocation(any(Consumer.class)))
+                .thenReturn(GetBucketLocationResponse.builder().locationConstraint("us-west-2").build());
+        final S3Client s3Client = instance.generateClient("test-bucket", mockClient);
+        assertNotNull(s3Client);
+
+        ;
+    }
+
+    @Test
+    public void testGenerateClientWith403Response() {
+        // when you get a forbidden response from getBucketLocation
+        when(mockClient.getBucketLocation(any(Consumer.class))).thenThrow(
+                S3Exception.builder().statusCode(403).build()
+        );
+        // you should fall back to a head bucket attempt
+        when(mockClient.headBucket(any(Consumer.class)))
+                .thenReturn((HeadBucketResponse) HeadBucketResponse.builder()
+                        .sdkHttpResponse(SdkHttpResponse.builder()
+                                .putHeader("x-amz-bucket-region", "us-west-2")
+                                .build())
+                        .build());
+
+        // which should get you a client
+        final S3Client s3Client = instance.generateClient("test-bucket", mockClient);
+        assertNotNull(s3Client);
+
+        final InOrder inOrder = inOrder(mockClient);
+        inOrder.verify(mockClient).getBucketLocation(any(Consumer.class));
+        inOrder.verify(mockClient).headBucket(any(Consumer.class));
+        inOrder.verifyNoMoreInteractions();
+    }
+
+    @Test
+    public void testGenerateClientWith403Then301Responses(){
+        // when you get a forbidden response from getBucketLocation
+        when(mockClient.getBucketLocation(any(Consumer.class))).thenThrow(
+                S3Exception.builder().statusCode(403).build()
+        );
+        // and you get a 301 response on headBucket
+        when(mockClient.headBucket(any(Consumer.class))).thenThrow(
+                S3Exception.builder()
+                        .statusCode(301)
+                        .awsErrorDetails(AwsErrorDetails.builder()
+                                .sdkHttpResponse(SdkHttpResponse.builder()
+                                        .putHeader("x-amz-bucket-region", "us-west-2")
+                                        .build())
+                                .build())
+                        .build()
+        );
+
+        // then you should be able to get a client as long as the error response header contains the region
+        final S3Client s3Client = instance.generateClient("test-bucket", mockClient);
+        assertNotNull(s3Client);
+
+        final InOrder inOrder = inOrder(mockClient);
+        inOrder.verify(mockClient).getBucketLocation(any(Consumer.class));
+        inOrder.verify(mockClient).headBucket(any(Consumer.class));
+        inOrder.verifyNoMoreInteractions();
+    }
+
+    @Test
+    public void testGenerateClientWith403Then301ResponsesNoHeader(){
+        // when you get a forbidden response from getBucketLocation
+        when(mockClient.getBucketLocation(any(Consumer.class))).thenThrow(
+                S3Exception.builder().statusCode(403).build()
+        );
+        // and you get a 301 response on headBucket but no header for region
+        when(mockClient.headBucket(any(Consumer.class))).thenThrow(
+                S3Exception.builder()
+                        .statusCode(301)
+                        .awsErrorDetails(AwsErrorDetails.builder()
+                                .sdkHttpResponse(SdkHttpResponse.builder()
+                                        .build())
+                                .build())
+                        .build()
+        );
+
+        // then you should get a NoSuchElement exception when you try to get the header
+        try {
+            instance.generateClient("test-bucket", mockClient);
+        } catch (Exception e) {
+            assertEquals(NoSuchElementException.class, e.getClass());
+        }
+
+        final InOrder inOrder = inOrder(mockClient);
+        inOrder.verify(mockClient).getBucketLocation(any(Consumer.class));
+        inOrder.verify(mockClient).headBucket(any(Consumer.class));
+        inOrder.verifyNoMoreInteractions();
+    }
+
+    @Test
+    public void testCaching() {
+        S3Client client = S3Client.create();
+        doReturn(client).when(spyInstance).generateClient("test-bucket");
+
+        final S3Client client1 = spyInstance.getClientForBucketName("test-bucket");
+        verify(spyInstance).generateClient("test-bucket");
+        assertSame(client1, client);
+
+        S3Client differentClient = S3Client.create();
+        assertNotSame(client, differentClient);
+
+        lenient().doReturn(differentClient).when(spyInstance).generateClient("test-bucket");
+        final S3Client client2 = spyInstance.getClientForBucketName("test-bucket");
+        // same instance because second is cached.
+        assertSame(client1, client2);
+        assertSame(client2, client);
+        assertNotSame(client2, differentClient);
+    }
+}
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index 4a7ea041b10..80d17688a65 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -34,7 +34,9 @@ package cromwell.backend.impl.aws
 import common.collections.EnhancedCollections._
 import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
 import cromwell.backend.BackendSpec._
+import cromwell.backend.impl.aws.io.AwsBatchWorkingDisk
 import cromwell.backend.validation.ContinueOnReturnCodeFlag
+import cromwell.core.path.{DefaultPathBuilder}
 import cromwell.core.TestKitSuite
 import cromwell.util.SampleWdl
 import eu.timepit.refined.api.Refined
@@ -84,7 +86,7 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
                  |
                  |
                  |)
-                 |mv /cromwell_root/hello-rc.txt.tmp /cromwell_root/hello-rc.txt"""
+                 |mv /cromwell_root/hello-rc.txt.tmp /cromwell_root/hello-rc.txt""".stripMargin
 
   val workFlowDescriptor: BackendWorkflowDescriptor = buildWdlWorkflowDescriptor(
     SampleWdl.HelloWorld.workflowSource(),
@@ -100,6 +102,8 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
   val call: CommandCallNode = workFlowDescriptor.callable.taskCallNodes.head
   val jobKey: BackendJobDescriptorKey = BackendJobDescriptorKey(call, None, 1)
   val jobPaths: AwsBatchJobPaths = AwsBatchJobPaths(workflowPaths, jobKey)
+  val s3Inputs: Set[AwsBatchInput] = Set(AwsBatchFileInput("foo", "s3://bucket/foo", DefaultPathBuilder.get("foo"), AwsBatchWorkingDisk()))
+  val s3Outputs: Set[AwsBatchFileOutput] = Set(AwsBatchFileOutput("baa", "s3://bucket/somewhere/baa", DefaultPathBuilder.get("baa"), AwsBatchWorkingDisk()))
 
   val cpu: Int Refined Positive = 2
   val runtimeAttributes: AwsBatchRuntimeAttributes = new AwsBatchRuntimeAttributes(
@@ -131,29 +135,22 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
       jobPaths, Seq.empty[AwsBatchParameter], None)
     job
   }
+  private def generateJobWithS3InOut: AwsBatchJob = {
+    val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
+      "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
+      s3Inputs, s3Outputs,
+      jobPaths, Seq.empty[AwsBatchParameter], None)
+    job
+  }
 
   // TESTS BEGIN HERE
   behavior of "AwsBatchJob"
-
-  it should "have correctly named AWS constants" in {
-
-    val job: AwsBatchJob = generateBasicJob
-
-    job.AWS_RETRY_MODE should be ("AWS_RETRY_MODE")
-    job.AWS_RETRY_MODE_DEFAULT_VALUE should be ("adaptive")
-    job.AWS_MAX_ATTEMPTS should be ("AWS_MAX_ATTEMPTS")
-    job.AWS_MAX_ATTEMPTS_DEFAULT_VALUE should be ("14")
-  }
-
   it should "generate appropriate KV pairs for the container environment for S3" in {
     val job = generateBasicJob
     val generateEnvironmentKVPairs = PrivateMethod[List[KeyValuePair]]('generateEnvironmentKVPairs)
 
     // testing a private method see https://www.scalatest.org/user_guide/using_PrivateMethodTester
     val kvPairs = job invokePrivate generateEnvironmentKVPairs("script-bucket", "prefix-", "key")
-
-    kvPairs should contain (buildKVPair(job.AWS_MAX_ATTEMPTS, job.AWS_MAX_ATTEMPTS_DEFAULT_VALUE))
-    kvPairs should contain (buildKVPair(job.AWS_RETRY_MODE, "adaptive"))
     kvPairs should contain (buildKVPair("BATCH_FILE_TYPE", "script"))
     kvPairs should contain (buildKVPair("BATCH_FILE_S3_URL", "s3://script-bucket/prefix-key"))
   }
@@ -164,10 +161,103 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
 
     // testing a private method see https://www.scalatest.org/user_guide/using_PrivateMethodTester
     val kvPairs = job invokePrivate generateEnvironmentKVPairs("script-bucket", "prefix-", "key")
-
-    kvPairs should contain (buildKVPair(job.AWS_MAX_ATTEMPTS, job.AWS_MAX_ATTEMPTS_DEFAULT_VALUE))
-    kvPairs should contain (buildKVPair(job.AWS_RETRY_MODE, "adaptive"))
     kvPairs should contain (buildKVPair("BATCH_FILE_TYPE", "script"))
     kvPairs should contain (buildKVPair("BATCH_FILE_S3_URL", ""))
   }
+
+  it should "contain expected command script in reconfigured script" in {
+    val job = generateBasicJob
+    job.reconfiguredScript should include (script.replace("/cromwell_root", "/tmp/scratch"))
+  }
+
+  it should "add metadata environment variables to reconfigured script" in {
+    val job = generateJobWithS3InOut
+    job.reconfiguredScript should include ("export AWS_METADATA_SERVICE_TIMEOUT=10\n")
+    job.reconfiguredScript should include ("export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10\n")
+  }
+
+  it should "add s3 localize with retry function to reconfigured script" in {
+    val job = generateBasicJob
+    val retryFunctionText = s"""
+                              |function _s3_localize_with_retry() {
+                              |  local s3_path=$$1
+                              |  # destination must be the path to a file and not just the directory you want the file in
+                              |  local destination=$$2
+                              |
+                              |  for i in {1..5};
+                              |  do
+                              |    if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
+                              |        bucket="$${BASH_REMATCH[1]}"
+                              |        key="$${BASH_REMATCH[2]}"
+                              |        content_length=$$(/usr/local/aws-cli/v2/current/bin/aws  s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength')
+                              |    else
+                              |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+                              |      exit 1
+                              |    fi
+                              |    /usr/local/aws-cli/v2/current/bin/aws  s3 cp --no-progress "$$s3_path" "$$destination" &&
+                              |    [[ $$(LC_ALL=C ls -dn -- "$$destination" | awk '{print $$5; exit}') -eq "$$content_length" ]] && break ||
+                              |    echo "attempt $$i to copy $$s3_path failed";
+                              |
+                              |    if [ "$$i" -eq 5 ]; then
+                              |        echo "failed to copy $$s3_path after $$i attempts. aborting"
+                              |        exit 2
+                              |    fi
+                              |    sleep $$((7 * "$$i"))
+                              |  done
+                              |}
+                              |""".stripMargin
+
+    job.reconfiguredScript should include (retryFunctionText)
+  }
+
+  it should "generate postscript with output copy command in reconfigured script" in {
+    val job = generateJobWithS3InOut
+    val postscript =
+      s"""
+         |{
+         |set -e
+         |echo '*** DELOCALIZING OUTPUTS ***'
+         |
+         |/usr/local/aws-cli/v2/current/bin/aws  s3 cp --no-progress /tmp/scratch/baa s3://bucket/somewhere/baa
+         |
+         |
+         |if [ -f /tmp/scratch/hello-rc.txt ]; then /usr/local/aws-cli/v2/current/bin/aws  s3 cp --no-progress /tmp/scratch/hello-rc.txt ${job.jobPaths.returnCode} ; fi
+         |
+         |if [ -f /tmp/scratch/hello-stderr.log ]; then /usr/local/aws-cli/v2/current/bin/aws  s3 cp --no-progress /tmp/scratch/hello-stderr.log ${job.jobPaths.standardPaths.error}; fi
+         |if [ -f /tmp/scratch/hello-stdout.log ]; then /usr/local/aws-cli/v2/current/bin/aws  s3 cp --no-progress /tmp/scratch/hello-stdout.log ${job.jobPaths.standardPaths.output}; fi
+         |
+         |echo '*** COMPLETED DELOCALIZATION ***'
+         |echo '*** EXITING WITH RETURN CODE ***'
+         |rc=$$(head -n 1 /tmp/scratch/hello-rc.txt)
+         |echo $$rc
+         |exit $$rc
+         |}
+         |""".stripMargin
+    job.reconfiguredScript should include (postscript)
+  }
+
+  it should "generate preamble with input copy command in reconfigured script" in {
+    val job = generateJobWithS3InOut
+    val preamble =
+      s"""
+         |{
+         |set -e
+         |echo '*** LOCALIZING INPUTS ***'
+         |if [ ! -d /tmp/scratch ]; then mkdir /tmp/scratch && chmod 777 /tmp/scratch; fi
+         |cd /tmp/scratch
+         |_s3_localize_with_retry s3://bucket/foo /tmp/scratch/foo
+         |echo '*** COMPLETED LOCALIZATION ***'
+         |set +e
+         |}
+         |""".stripMargin
+
+    job.reconfiguredScript should include (preamble)
+  }
+
+  it should "contain AWS Service clients" in {
+    val job = generateBasicJob
+    job.batchClient should not be null
+    job.s3Client should not be null
+    job.cloudWatchLogsClient should not be null
+  }
 }

From 5ac92609b30e8ee9c002c1b4722c1c66cc31d5d2 Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Tue, 19 Oct 2021 10:59:13 -0400
Subject: [PATCH 027/326] Improved testing

---
 .../backend/impl/aws/AwsBatchJobSpec.scala    | 24 ++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index 80d17688a65..12e933ab959 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -36,7 +36,7 @@ import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
 import cromwell.backend.BackendSpec._
 import cromwell.backend.impl.aws.io.AwsBatchWorkingDisk
 import cromwell.backend.validation.ContinueOnReturnCodeFlag
-import cromwell.core.path.{DefaultPathBuilder}
+import cromwell.core.path.DefaultPathBuilder
 import cromwell.core.TestKitSuite
 import cromwell.util.SampleWdl
 import eu.timepit.refined.api.Refined
@@ -47,7 +47,7 @@ import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import org.specs2.mock.Mockito
 import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider
-import software.amazon.awssdk.services.batch.model.KeyValuePair
+import software.amazon.awssdk.services.batch.model.{ContainerDetail, JobDetail, KeyValuePair}
 import spray.json.{JsObject, JsString}
 import wdl4s.parser.MemoryUnit
 import wom.format.MemorySize
@@ -58,7 +58,7 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
 
   System.setProperty("aws.region", "us-east-1")
 
-  val script = """
+  val script: String = """
                  |tmpDir=mkdir -p "/cromwell-aws/cromwell-execution/wf_hello/2422ea26-2578-48b0-86e9-50cbdda7d70a/call-hello/tmp.39397e83" && echo "/cromwell-aws/cromwell-execution/wf_hello/2422ea26-2578-48b0-86e9-50cbdda7d70a/call-hello/tmp.39397e83"
                  |chmod 777 "$tmpDir"
                  |export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
@@ -121,6 +121,9 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
       ulimits = Vector(Map.empty[String, String]),
       fileSystem = "s3")
 
+  val containerDetail: ContainerDetail = ContainerDetail.builder().exitCode(0).build()
+  val jobDetail: JobDetail = JobDetail.builder().container(containerDetail).build
+
   private def generateBasicJob: AwsBatchJob = {
     val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
@@ -260,4 +263,19 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     job.s3Client should not be null
     job.cloudWatchLogsClient should not be null
   }
+
+  it should "have correct script prefix" in {
+    val job = generateBasicJob
+    job.scriptKeyPrefix should equal("scripts/")
+  }
+
+  it should "return correct RC code given Batch Job Detail" in {
+    val containerDetail: ContainerDetail = ContainerDetail.builder().exitCode(0).build
+    val jobDetail: JobDetail = JobDetail.builder().container(containerDetail).build
+    val job = generateBasicJob
+    job.rc(jobDetail) should be (0)
+  }
+
+
+
 }

From 94a720dcf146f573e35b700ecdfdb5ba1d558a2f Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Tue, 19 Oct 2021 13:31:01 -0400
Subject: [PATCH 028/326] remove unnecessary method

---
 .../backend/impl/aws/AwsBatchJob.scala        | 37 -------------------
 1 file changed, 37 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 5068c4a9784..ee6b95b06c2 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -464,8 +464,6 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     */
   def status(jobId: String): Try[RunStatus] = for {
     statusString <- Try(detail(jobId).status)
-    batchJobContainerContext <- Try(batchJobContainerContext(jobId))
-    _ <- Try(Log.debug(s"Task ${jobDescriptor.key.call.fullyQualifiedName + "-" + jobDescriptor.key.index + "-" + jobDescriptor.key.attempt} in container context $batchJobContainerContext"))
     runStatus <- RunStatus.fromJobStatus(statusString, jobId)
   } yield runStatus
 
@@ -478,41 +476,6 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     jobDetail
   }
 
-  /**
-    * Return information about the container, ECS Cluster and EC2 instance that is (or was) hosting this job
-    * @param jobId the id of the job for which you want the context
-    * @return the context
-    */
-  def batchJobContainerContext(jobId: String): BatchJobContainerContext ={
-    if (jobId == null) return BatchJobContainerContext("","",Seq.empty, Seq.empty)
-
-    val containerInstanceArn = detail(jobId).container().containerInstanceArn()
-    if(containerInstanceArn == null || containerInstanceArn.isEmpty) return BatchJobContainerContext(jobId,"",Seq.empty, Seq.empty)
-
-    val describeJobQueuesResponse = batchClient.describeJobQueues( DescribeJobQueuesRequest.builder().jobQueues( runtimeAttributes.queueArn ).build())
-    val computeEnvironments = describeJobQueuesResponse.jobQueues().asScala.head.computeEnvironmentOrder().asScala.map(_.computeEnvironment())
-    val describeComputeEnvironmentsResponse = batchClient.describeComputeEnvironments( DescribeComputeEnvironmentsRequest.builder().computeEnvironments(computeEnvironments.asJava).build())
-    val ecsClusterArns = describeComputeEnvironmentsResponse.computeEnvironments().asScala.map(_.ecsClusterArn())
-
-    val ecsClient = configureClient(EcsClient.builder(), optAwsAuthMode, configRegion)
-
-    val instanceIds: Seq[String] = ecsClusterArns.map(containerArn => ecsClient.describeContainerInstances(DescribeContainerInstancesRequest.builder().containerInstances(containerInstanceArn).cluster(containerArn).build()))
-      .map(r => r.containerInstances().asScala).flatMap(_.map(_.ec2InstanceId()))
-
-    BatchJobContainerContext(jobId, containerInstanceArn, ecsClusterArns, instanceIds)
-  }
-
-  case class BatchJobContainerContext(jobId: String, containerInstanceArn: String, ecsClusterArns: Seq[String], ec2InstanceIds: Seq[String]) {
-    override def toString: String = {
-      new ToStringBuilder(this, ToStringStyle.JSON_STYLE)
-        .append("jobId", this.jobId)
-        .append("containerInstanceArn", containerInstanceArn)
-        .append("ecsClusterArns", ecsClusterArns)
-        .append("ec2InstanceIds", ec2InstanceIds)
-        .build()
-    }
-  }
-
   def rc(detail: JobDetail): Integer = {
     detail.container.exitCode
   }

From 19461a398deca98d854c4c71fb87a58b3fc02263 Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Fri, 22 Oct 2021 17:32:53 -0400
Subject: [PATCH 029/326] enable hashing of ECR and ECR public fix deprecation
 in job definition creation

---
 .../main/scala/cloud/nio/spi/UnixPath.scala   |  2 +-
 core/src/main/resources/reference.conf        |  2 +
 .../cromwell/docker/DockerInfoActor.scala     |  5 ++-
 .../registryv2/DockerRegistryV2Abstract.scala | 16 +++----
 .../registryv2/flows/aws/AmazonEcr.scala      | 42 +++++++++++++++++++
 .../flows/aws/AmazonEcrAbstract.scala         | 41 ++++++++++++++++++
 .../flows/aws/AmazonEcrPublic.scala           | 36 ++++++++++++++++
 .../registryv2/flows/aws/EcrUtils.scala       |  9 ++++
 .../flows/aws/AmazonEcrPublicSpec.scala       | 25 +++++++++++
 project/Dependencies.scala                    | 10 +++--
 project/Merging.scala                         | 23 ++++++++--
 .../backend/impl/aws/AwsBatchJob.scala        | 10 ++---
 .../impl/aws/AwsBatchJobDefinition.scala      | 10 ++---
 13 files changed, 204 insertions(+), 27 deletions(-)
 create mode 100644 dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcr.scala
 create mode 100644 dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrAbstract.scala
 create mode 100644 dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublic.scala
 create mode 100644 dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/EcrUtils.scala
 create mode 100644 dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala

diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
index a5d0770bc56..306afa44cc7 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
@@ -69,7 +69,7 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
 
   def isAbsolute: Boolean = UnixPath.isAbsolute(path)
 
-  override def isEmpty: Boolean = path.isEmpty
+  def isEmpty: Boolean = path.isEmpty
 
   def hasTrailingSeparator: Boolean = UnixPath.hasTrailingSeparator(path)
 
diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index 709753e3fb8..e436d85c89f 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -388,6 +388,8 @@ docker {
     dockerhub.num-threads = 10
     quay.num-threads = 10
     alibabacloudcr.num-threads = 10
+    ecr.num-threads = 10
+    ecr-public.num-threads = 10
   }
 }
 
diff --git a/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala b/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala
index faa3cd4c36a..3a56294bccf 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala
@@ -15,6 +15,7 @@ import cromwell.core.{Dispatcher, DockerConfiguration}
 import cromwell.docker.DockerInfoActor._
 import cromwell.docker.registryv2.flows.alibabacloudcrregistry._
 import cromwell.docker.registryv2.DockerRegistryV2Abstract
+import cromwell.docker.registryv2.flows.aws.{AmazonEcr, AmazonEcrPublic}
 import cromwell.docker.registryv2.flows.dockerhub.DockerHubRegistry
 import cromwell.docker.registryv2.flows.gcr.GcrRegistry
 import cromwell.docker.registryv2.flows.quay.QuayRegistry
@@ -240,7 +241,9 @@ object DockerInfoActor {
       ("dockerhub", { c: DockerRegistryConfig => new DockerHubRegistry(c) }),
       ("gcr", gcrConstructor),
       ("quay", { c: DockerRegistryConfig => new QuayRegistry(c) }),
-      ("alibabacloudcr", {c: DockerRegistryConfig => new AlibabaCloudCRRegistry(c)})
+      ("alibabacloudcr", {c: DockerRegistryConfig => new AlibabaCloudCRRegistry(c)}),
+      ("ecr", {c: DockerRegistryConfig => new AmazonEcr(c)}),
+      ("ecr-public", {c: DockerRegistryConfig => new AmazonEcrPublic(c)})
     ).traverse[ErrorOr, DockerRegistry]({
       case (configPath, constructor) => DockerRegistryConfig.fromConfig(config.as[Config](configPath)).map(constructor)
     }).unsafe("Docker registry configuration")
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
index e03b3bee3c5..b4ae630751b 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
@@ -60,7 +60,7 @@ object DockerRegistryV2Abstract {
           )
       })
   }
-  
+
   // Placeholder exceptions that can be carried through IO before being converted to a DockerInfoFailedResponse
   private class Unauthorized() extends Exception
   private class NotFound() extends Exception
@@ -76,6 +76,8 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
   implicit val cs = IO.contextShift(ec)
   implicit val timer = IO.timer(ec)
 
+  protected val authorizationScheme: AuthScheme = AuthScheme.Bearer
+
   /**
     * This is the main function. Given a docker context and an http client, retrieve information about the docker image.
     */
@@ -204,7 +206,7 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * Request to get the manifest, using the auth token if provided
     */
   private def manifestRequest(token: Option[String], imageId: DockerImageIdentifier): IO[Request[IO]] = {
-    val authorizationHeader = token.map(t => Authorization(Credentials.Token(AuthScheme.Bearer, t)))
+    val authorizationHeader = token.map(t => Authorization(Credentials.Token(authorizationScheme, t)))
     val request = Method.GET(
       buildManifestUri(imageId),
       List(
@@ -235,13 +237,13 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * The response can be of 2 sorts:
     * - A manifest (https://docs.docker.com/registry/spec/manifest-v2-2/#image-manifest-field-descriptions)
     * - A manifest list which contains a list of pointers to other manifests (https://docs.docker.com/registry/spec/manifest-v2-2/#manifest-list)
-    * 
+    *
     * When a manifest list is returned, we need to pick one of the manifest pointers and make another request for that manifest.
-    * 
+    *
     * Because the different manifests in the list are (supposed to be) variations of the same image over different platforms,
     * we simply pick the first one here since we only care about the approximate size, and we don't expect it to change drastically
     * between platforms.
-    * If that assumption turns out to be incorrect, a smarter decision may need to be made to choose the manifest to lookup. 
+    * If that assumption turns out to be incorrect, a smarter decision may need to be made to choose the manifest to lookup.
     */
   private def parseManifest(dockerImageIdentifier: DockerImageIdentifier, token: Option[String])(response: Response[IO])(implicit client: Client[IO]): IO[Option[DockerManifest]] = response match {
     case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(ManifestV2MediaType)) =>
@@ -268,14 +270,14 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     }
   }
 
-  private def getDigestFromResponse(response: Response[IO]): IO[DockerHashResult] = response match {
+  protected def getDigestFromResponse(response: Response[IO]): IO[DockerHashResult] = response match {
     case Status.Successful(r) => extractDigestFromHeaders(r.headers)
     case Status.Unauthorized(_) => IO.raiseError(new Unauthorized)
     case Status.NotFound(_) => IO.raiseError(new NotFound)
     case failed => failed.as[String].flatMap(body => IO.raiseError(new Exception(s"Failed to get manifest: $body"))
     )
   }
-  
+
   private def extractDigestFromHeaders(headers: Headers) = {
     headers.find(a => a.toRaw.name.equals(DigestHeaderName)) match {
       case Some(digest) => IO.fromEither(DockerHashResult.fromString(digest.value).toEither)
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcr.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcr.scala
new file mode 100644
index 00000000000..a073b9f4eb2
--- /dev/null
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcr.scala
@@ -0,0 +1,42 @@
+package cromwell.docker.registryv2.flows.aws
+
+import cats.effect.IO
+import cromwell.docker.{DockerImageIdentifier, DockerInfoActor, DockerRegistryConfig}
+import org.http4s.AuthScheme
+import org.http4s.client.Client
+import software.amazon.awssdk.services.ecr.EcrClient
+
+import scala.compat.java8.OptionConverters._
+import scala.concurrent.Future
+
+class AmazonEcr(override val config: DockerRegistryConfig, ecrClient: EcrClient = EcrClient.create()) extends AmazonEcrAbstract(config) {
+
+  override protected val authorizationScheme: AuthScheme = AuthScheme.Basic
+
+  /**
+    * e.g 123456789012.dkr.ecr.us-east-1.amazonaws.com
+    */
+  override protected def registryHostName(dockerImageIdentifier: DockerImageIdentifier): String = {
+    var hostname = dockerImageIdentifier.hostAsString
+    if (hostname.lastIndexOf("/").equals(hostname.length -1)) {
+      hostname = hostname.substring(0, hostname.length -1)
+    }
+    hostname
+  }
+  /**
+    * Returns true if this flow is able to process this docker image,
+    * false otherwise
+    */
+  override def accepts(dockerImageIdentifier: DockerImageIdentifier): Boolean = dockerImageIdentifier.hostAsString.contains("amazonaws.com")
+
+  override protected def getToken(dockerInfoContext: DockerInfoActor.DockerInfoContext)(implicit client: Client[IO]): IO[Option[String]] = {
+    val eventualMaybeToken = Future(ecrClient.getAuthorizationToken
+      .authorizationData()
+      .stream()
+      .findFirst()
+      .asScala
+      .map(_.authorizationToken()))
+
+    IO.fromFuture(IO(eventualMaybeToken))
+  }
+}
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrAbstract.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrAbstract.scala
new file mode 100644
index 00000000000..bc9ea61fd74
--- /dev/null
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrAbstract.scala
@@ -0,0 +1,41 @@
+package cromwell.docker.registryv2.flows.aws
+
+import cats.effect.IO
+import cromwell.docker.{DockerHashResult, DockerImageIdentifier, DockerInfoActor, DockerRegistryConfig}
+import cromwell.docker.registryv2.DockerRegistryV2Abstract
+import cromwell.docker.registryv2.flows.aws.EcrUtils.{EcrForbidden, EcrNotFound, EcrUnauthorized}
+import org.apache.commons.codec.digest.DigestUtils
+import org.http4s.{Header, Response, Status}
+
+abstract class AmazonEcrAbstract(override val config: DockerRegistryConfig) extends DockerRegistryV2Abstract(config) {
+
+  /**
+    * Not used as getToken is overridden
+    */
+  override protected def authorizationServerHostName(dockerImageIdentifier: DockerImageIdentifier): String = ""
+
+  /**
+    * Not used as getToken is overridden
+    */
+  override protected def buildTokenRequestHeaders(dockerInfoContext: DockerInfoActor.DockerInfoContext): List[Header] = List.empty
+
+  /**
+    * Amazon ECR repositories don't have a digest header in responses so we must made it from the manifest body
+    */
+  override protected def getDigestFromResponse(response: Response[IO]): IO[DockerHashResult] = response match {
+    case Status.Successful(r) => digestManifest(r.bodyText)
+    case Status.Unauthorized(_) => IO.raiseError(new EcrUnauthorized)
+    case Status.NotFound(_) => IO.raiseError(new EcrNotFound)
+    case Status.Forbidden(_) => IO.raiseError(new EcrForbidden)
+    case failed => failed.as[String].flatMap(body => IO.raiseError(new Exception(s"Failed to get manifest: $body")))
+  }
+
+  private def digestManifest(bodyText: fs2.Stream[IO, String]): IO[DockerHashResult] = {
+    bodyText
+      .compile
+      .string
+      .map(data => "sha256:"+DigestUtils.sha256Hex(data))
+      .map(DockerHashResult.fromString)
+      .flatMap(IO.fromTry)
+  }
+}
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublic.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublic.scala
new file mode 100644
index 00000000000..797d4b70703
--- /dev/null
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublic.scala
@@ -0,0 +1,36 @@
+package cromwell.docker.registryv2.flows.aws
+
+import cats.effect.IO
+import cromwell.docker.{DockerImageIdentifier, DockerInfoActor, DockerRegistryConfig}
+import org.http4s.client.Client
+import software.amazon.awssdk.services.ecrpublic.EcrPublicClient
+import software.amazon.awssdk.services.ecrpublic.model.GetAuthorizationTokenRequest
+
+import scala.concurrent.Future
+
+
+class AmazonEcrPublic(override val config: DockerRegistryConfig, ecrClient: EcrPublicClient = EcrPublicClient.create()) extends AmazonEcrAbstract(config) {
+  /**
+    * public.ecr.aws
+    */
+  override protected def registryHostName(dockerImageIdentifier: DockerImageIdentifier): String = "public.ecr.aws"
+
+  /**
+    * Returns true if this flow is able to process this docker image,
+    * false otherwise
+    */
+  override def accepts(dockerImageIdentifier: DockerImageIdentifier): Boolean = dockerImageIdentifier.hostAsString.contains("public.ecr.aws")
+
+
+  override protected def getToken(dockerInfoContext: DockerInfoActor.DockerInfoContext)(implicit client: Client[IO]): IO[Option[String]] = {
+
+    val eventualMaybeToken: Future[Option[String]] = Future(
+      Option(ecrClient
+        .getAuthorizationToken(GetAuthorizationTokenRequest.builder().build())
+        .authorizationData.authorizationToken()
+      )
+    )
+
+    IO.fromFuture(IO(eventualMaybeToken))
+  }
+}
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/EcrUtils.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/EcrUtils.scala
new file mode 100644
index 00000000000..9da904c8adc
--- /dev/null
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/EcrUtils.scala
@@ -0,0 +1,9 @@
+package cromwell.docker.registryv2.flows.aws
+
+object EcrUtils {
+
+  case class EcrUnauthorized() extends Exception
+  case class EcrNotFound() extends Exception
+  case class EcrForbidden() extends Exception
+
+}
diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
new file mode 100644
index 00000000000..7d76aff61a5
--- /dev/null
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
@@ -0,0 +1,25 @@
+package cromwell.docker.registryv2.flows.aws
+
+import cromwell.core.TestKitSuite
+import cromwell.docker.{DockerImageIdentifier, DockerRegistryConfig}
+import org.scalatest.BeforeAndAfter
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.matchers.should.Matchers
+import org.scalatestplus.mockito.MockitoSugar
+
+class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with MockitoSugar with BeforeAndAfter{
+  val goodUri = "public.ecr.aws/amazonlinux/amazonlinux:latest"
+  val badUri = "ubuntu:latest"
+  val registry = new AmazonEcrPublic(DockerRegistryConfig.default)
+
+
+  it should "Accept good URI" in {
+    val dockerImageIdentifier = DockerImageIdentifier.fromString(goodUri).get
+    registry.accepts(dockerImageIdentifier) shouldEqual(true)
+  }
+
+  it should "NOT accept bad URI" in {
+    val dockerImageIdentifier = DockerImageIdentifier.fromString(badUri).get
+    registry.accepts(dockerImageIdentifier) shouldEqual(false)
+  }
+}
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index ed80d57b886..31cafa994d3 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -11,7 +11,7 @@ object Dependencies {
   private val ammoniteOpsV = "2.3.8"
   private val apacheCommonNetV = "3.7.2"
   private val apacheHttpClientV = "4.5.13"
-  private val awsSdkV = "2.15.41"
+  private val awsSdkV = "2.17.66"
   private val betterFilesV = "3.9.1"
   private val catsEffectV = "2.3.0"
   private val catsV = "2.3.0"
@@ -56,7 +56,7 @@ object Dependencies {
   private val heterodonV = "1.0.0-beta3"
   private val hsqldbV = "2.5.1"
   private val http4sVersion = "0.21.7" // scala-steward:off (CROM-6678)
-  private val jacksonV = "2.12.2"
+  private val jacksonV = "2.12.5"
   private val jacksonJqV = "1.0.0-preview.20201123"
   private val janinoV = "3.1.2"
   private val javaxActivationV = "1.2.0"
@@ -311,7 +311,9 @@ object Dependencies {
     "cloudwatchlogs",
     "s3",
     "sts",
-    "ecs"
+    "ecs",
+    "ecr",
+    "ecrpublic",
   ).map(artifactName => "software.amazon.awssdk" % artifactName % awsSdkV)
 
   private val googleCloudDependencies = List(
@@ -502,7 +504,7 @@ object Dependencies {
 
   val databaseMigrationDependencies = liquibaseDependencies ++ dbmsDependencies
 
-  val dockerHashingDependencies = http4sDependencies ++ circeDependencies ++ aliyunCrDependencies
+  val dockerHashingDependencies = http4sDependencies ++ circeDependencies ++ aliyunCrDependencies ++ awsCloudDependencies
 
   val cromwellApiClientDependencies = List(
     "org.scalaz" %% "scalaz-core" % scalazV,
diff --git a/project/Merging.scala b/project/Merging.scala
index 964d342a234..53135adce26 100644
--- a/project/Merging.scala
+++ b/project/Merging.scala
@@ -4,8 +4,8 @@ import sbtassembly.{MergeStrategy, PathList}
 
 object Merging {
   val customMergeStrategy: Def.Initialize[String => MergeStrategy] = Def.setting {
-    case PathList(ps@_*) if ps.last == "project.properties" =>
-      // Merge/Filter project.properties files from Google jars that otherwise collide at merge time.
+    case PathList(ps@_*) if Set("project.properties", "execution.interceptors").contains(ps.last) =>
+      // Merge/Filter files from AWS/Google jars that otherwise collide at merge time.
       MergeStrategy.filterDistinctLines
     case PathList(ps@_*) if ps.last == "logback.xml" =>
       MergeStrategy.first
@@ -16,12 +16,27 @@ object Merging {
       path map {
         _.toLowerCase
       } match {
-        case "spring.tooling" :: xs =>
+        case "spring.tooling" :: _ =>
           MergeStrategy.discard
         case "io.netty.versions.properties" :: Nil =>
           MergeStrategy.first
-        case "maven" :: "com.google.guava" :: xs =>
+        case "maven" :: "com.google.guava" :: _ =>
           MergeStrategy.first
+        case "native-image" :: _ if Set("native-image.properties", "reflection-config.json").contains(path.last) =>
+          /*
+          Discard GraalVM configuration files.
+          grpc-netty-shaded 1.39.0 tried to put the netty classes into a different package, but left the shaded version
+          of the config file with the same name as the unshaded netty library. Thus when merging the shaded and
+          unshaded netty jars we end up with assembly conflicts.
+
+          However, we're not using GraalVM for execution so just discard the configuration files.
+
+          See also:
+          - https://www.graalvm.org/reference-manual/native-image/BuildConfiguration/#configuration-file-format
+          - https://github.com/grpc/grpc-java/issues/7540
+          - https://github.com/grpc/grpc-java/releases/tag/v1.39.0
+           */
+          MergeStrategy.discard
         case _ =>
           val oldStrategy = (assembly / assemblyMergeStrategy).value
           oldStrategy(x)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index ee6b95b06c2..3102f678aa6 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -47,8 +47,6 @@ import software.amazon.awssdk.services.batch.BatchClient
 import software.amazon.awssdk.services.batch.model._
 import software.amazon.awssdk.services.cloudwatchlogs.CloudWatchLogsClient
 import software.amazon.awssdk.services.cloudwatchlogs.model.{GetLogEventsRequest, OutputLogEvent}
-import software.amazon.awssdk.services.ecs.EcsClient
-import software.amazon.awssdk.services.ecs.model.DescribeContainerInstancesRequest
 import software.amazon.awssdk.services.s3.S3Client
 import software.amazon.awssdk.services.s3.model.{GetObjectRequest, HeadObjectRequest, NoSuchKeyException, PutObjectRequest}
 import wdl4s.parser.MemoryUnit
@@ -289,11 +287,13 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
             .containerOverrides(
               ContainerOverrides.builder
                 .environment(
-
                   generateEnvironmentKVPairs(runtimeAttributes.scriptS3BucketName, scriptKeyPrefix, scriptKey): _*
                 )
-                .memory(runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt)
-                .vcpus(runtimeAttributes.cpu.##).build
+                .resourceRequirements(
+                  ResourceRequirement.builder().`type`(ResourceType.VCPU).value(runtimeAttributes.cpu.##.toString).build(),
+                  ResourceRequirement.builder().`type`(ResourceType.MEMORY).value(runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString).build()
+                )
+                .build()
             )
             .jobQueue(runtimeAttributes.queueArn)
             .jobDefinition(definitionArn)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index 876a23c32c0..b8ac5cb229a 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -31,16 +31,14 @@
 
 package cromwell.backend.impl.aws
 
-import scala.language.postfixOps
 import scala.collection.mutable.ListBuffer
 import cromwell.backend.BackendJobDescriptor
 import cromwell.backend.io.JobPaths
-import software.amazon.awssdk.services.batch.model.{ContainerProperties, Host, KeyValuePair, MountPoint, RetryStrategy, Volume, Ulimit}
+import software.amazon.awssdk.services.batch.model.{ContainerProperties, Host, KeyValuePair, MountPoint, ResourceRequirement, ResourceType, RetryStrategy, Ulimit, Volume}
 import cromwell.backend.impl.aws.io.AwsBatchVolume
 
 import scala.collection.JavaConverters._
 import java.security.MessageDigest
-
 import org.apache.commons.lang3.builder.{ToStringBuilder, ToStringStyle}
 import org.slf4j.{Logger, LoggerFactory}
 import wdl4s.parser.MemoryUnit
@@ -162,8 +160,10 @@ trait AwsBatchJobDefinitionBuilder {
     (ContainerProperties.builder()
       .image(context.runtimeAttributes.dockerImage)
       .command(packedCommand.asJava)
-      .memory(context.runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt)
-      .vcpus(context.runtimeAttributes.cpu##)
+      .resourceRequirements(
+        ResourceRequirement.builder().`type`(ResourceType.VCPU).value(context.runtimeAttributes.cpu.##.toString).build(),
+        ResourceRequirement.builder().`type`(ResourceType.MEMORY).value(context.runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString).build()
+      )
       .volumes(volumes.asJava)
       .mountPoints(mountPoints.asJava)
       .environment(environment.asJava)

From 29e403937d5b4614038bb4da0bc8f313307a9f0e Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Tue, 26 Oct 2021 15:34:20 -0400
Subject: [PATCH 030/326] improve test coverage for AmazonEcr and
 AmazonEcrPublic

---
 .../flows/aws/AmazonEcrPublicSpec.scala       | 62 +++++++++++++---
 .../registryv2/flows/aws/AmazonEcrSpec.scala  | 72 +++++++++++++++++++
 2 files changed, 125 insertions(+), 9 deletions(-)
 create mode 100644 dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala

diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
index 7d76aff61a5..18a0a23232e 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
@@ -1,25 +1,69 @@
 package cromwell.docker.registryv2.flows.aws
 
+import cats.effect.{IO, Resource}
 import cromwell.core.TestKitSuite
-import cromwell.docker.{DockerImageIdentifier, DockerRegistryConfig}
-import org.scalatest.BeforeAndAfter
+import cromwell.docker.registryv2.DockerRegistryV2Abstract
+import cromwell.docker.{DockerImageIdentifier, DockerInfoActor, DockerInfoRequest, DockerRegistryConfig}
+import org.http4s.{Header, Headers, MediaType, Request, Response}
+import org.http4s.client.Client
+import org.http4s.headers.`Content-Type`
+import org.mockito.ArgumentMatchers.any
+import org.mockito.Mockito._
+import org.scalatest.{BeforeAndAfter, PrivateMethodTester}
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import org.scalatestplus.mockito.MockitoSugar
+import software.amazon.awssdk.services.ecrpublic.model.{AuthorizationData, GetAuthorizationTokenRequest, GetAuthorizationTokenResponse}
+import software.amazon.awssdk.services.ecrpublic.EcrPublicClient
+
+class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with MockitoSugar with BeforeAndAfter with PrivateMethodTester {
+  behavior of "AmazonEcrPublic"
 
-class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with MockitoSugar with BeforeAndAfter{
   val goodUri = "public.ecr.aws/amazonlinux/amazonlinux:latest"
-  val badUri = "ubuntu:latest"
-  val registry = new AmazonEcrPublic(DockerRegistryConfig.default)
+  val otherUri = "ubuntu:latest"
+
+
+  val mediaType: MediaType = MediaType.parse(DockerRegistryV2Abstract.ManifestV2MediaType).right.get
+  val contentType: Header = `Content-Type`(mediaType)
+  val mockEcrClient: EcrPublicClient = mock[EcrPublicClient]
+  implicit val mockIOClient: Client[IO] = Client({ _: Request[IO] =>
+    // This response will have an empty body, so we need to be explicit about the typing:
+    Resource.pure[IO, Response[IO]](Response(headers = Headers.of(contentType))) : Resource[IO, Response[IO]]
+  })
 
+  val registry = new AmazonEcrPublic(DockerRegistryConfig.default, mockEcrClient)
 
   it should "Accept good URI" in {
     val dockerImageIdentifier = DockerImageIdentifier.fromString(goodUri).get
-    registry.accepts(dockerImageIdentifier) shouldEqual(true)
+    registry.accepts(dockerImageIdentifier) shouldEqual true
+  }
+
+  it should "NOT accept other URI" in {
+    val dockerImageIdentifier = DockerImageIdentifier.fromString(otherUri).get
+    registry.accepts(dockerImageIdentifier) shouldEqual false
   }
 
-  it should "NOT accept bad URI" in {
-    val dockerImageIdentifier = DockerImageIdentifier.fromString(badUri).get
-    registry.accepts(dockerImageIdentifier) shouldEqual(false)
+  it should "have public.ecr.aws as registryHostName" in {
+    val registryHostNameMethod = PrivateMethod[String]('registryHostName)
+    registry invokePrivate registryHostNameMethod(DockerImageIdentifier.fromString(goodUri).get) shouldEqual "public.ecr.aws"
+  }
+
+  it should "return expected auth token" in {
+    val token = "auth-token"
+    val imageId = DockerImageIdentifier.fromString(goodUri).get
+    val dockerInfoRequest = DockerInfoRequest(imageId)
+    val context = DockerInfoActor.DockerInfoContext(request = dockerInfoRequest, replyTo =  emptyActor)
+
+    when(mockEcrClient.getAuthorizationToken(any[GetAuthorizationTokenRequest]()))
+      .thenReturn(GetAuthorizationTokenResponse
+        .builder()
+        .authorizationData(AuthorizationData
+          .builder()
+          .authorizationToken(token)
+          .build())
+        .build)
+
+    val getTokenMethod = PrivateMethod[IO[Option[String]]]('getToken)
+    registry invokePrivate getTokenMethod(context, mockIOClient) ensuring(io => io.unsafeRunSync().get == token)
   }
 }
diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala
new file mode 100644
index 00000000000..5ddf98c7ffa
--- /dev/null
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala
@@ -0,0 +1,72 @@
+package cromwell.docker.registryv2.flows.aws
+
+import cats.effect.{IO, Resource}
+import cromwell.core.TestKitSuite
+import cromwell.docker.registryv2.DockerRegistryV2Abstract
+import cromwell.docker.{DockerImageIdentifier, DockerInfoActor, DockerInfoRequest, DockerRegistryConfig}
+import org.http4s.{AuthScheme, Header, Headers, MediaType, Request, Response}
+import org.http4s.client.Client
+import org.http4s.headers.`Content-Type`
+import org.mockito.Mockito._
+import org.scalatest.{BeforeAndAfter, PrivateMethodTester}
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.matchers.should.Matchers
+import org.scalatestplus.mockito.MockitoSugar
+import software.amazon.awssdk.services.ecr.EcrClient
+import software.amazon.awssdk.services.ecr.model.{AuthorizationData, GetAuthorizationTokenResponse}
+
+class AmazonEcrSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with MockitoSugar with BeforeAndAfter with PrivateMethodTester{
+  behavior of "AmazonEcr"
+
+  val goodUri = "123456789012.dkr.ecr.us-east-1.amazonaws.com/amazonlinux/amazonlinux:latest"
+  val otherUri = "ubuntu:latest"
+
+  val mediaType: MediaType = MediaType.parse(DockerRegistryV2Abstract.ManifestV2MediaType).right.get
+  val contentType: Header = `Content-Type`(mediaType)
+  val mockEcrClient: EcrClient = mock[EcrClient]
+  implicit val mockIOClient: Client[IO] = Client({ _: Request[IO] =>
+    // This response will have an empty body, so we need to be explicit about the typing:
+    Resource.pure[IO, Response[IO]](Response(headers = Headers.of(contentType))) : Resource[IO, Response[IO]]
+  })
+
+  val registry = new AmazonEcr(DockerRegistryConfig.default, mockEcrClient)
+
+  it should "accept good URI" in {
+    val dockerImageIdentifier = DockerImageIdentifier.fromString(goodUri).get
+    registry.accepts(dockerImageIdentifier) shouldEqual true
+  }
+
+  it should "NOT accept other URI" in {
+    val dockerImageIdentifier = DockerImageIdentifier.fromString(otherUri).get
+    registry.accepts(dockerImageIdentifier) shouldEqual false
+  }
+
+  it should "use Basic Auth Scheme" in {
+    val authSchemeMethod = PrivateMethod[AuthScheme]('authorizationScheme)
+    registry invokePrivate authSchemeMethod() shouldEqual AuthScheme.Basic
+  }
+
+  it should "return 123456789012.dkr.ecr.us-east-1.amazonaws.com as registryHostName" in {
+    val registryHostNameMethod = PrivateMethod[String]('registryHostName)
+    registry invokePrivate registryHostNameMethod(DockerImageIdentifier.fromString(goodUri).get) shouldEqual "123456789012.dkr.ecr.us-east-1.amazonaws.com"
+  }
+
+  it should "return expected auth token" in {
+    val token = "auth-token"
+    val imageId = DockerImageIdentifier.fromString(goodUri).get
+    val dockerInfoRequest = DockerInfoRequest(imageId)
+    val context = DockerInfoActor.DockerInfoContext(request = dockerInfoRequest, replyTo =  emptyActor)
+
+    when(mockEcrClient.getAuthorizationToken)
+      .thenReturn(GetAuthorizationTokenResponse
+        .builder()
+        .authorizationData(AuthorizationData
+          .builder()
+          .authorizationToken(token)
+          .build())
+        .build)
+
+    val getTokenMethod = PrivateMethod[IO[Option[String]]]('getToken)
+    registry invokePrivate getTokenMethod(context, mockIOClient) ensuring(io => io.unsafeRunSync().get == token)
+  }
+}

From ca1dba36abd29f75b77546243985ef175e4ec4a0 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Thu, 30 Dec 2021 12:54:53 +0000
Subject: [PATCH 031/326] working version of local filesystem with fsx too

---
 ...wsBatchAsyncBackendJobExecutionActor.scala | 26 ++++++++++++---
 .../backend/impl/aws/AwsBatchAttributes.scala | 19 +++++++++--
 .../impl/aws/AwsBatchConfiguration.scala      |  4 +--
 .../backend/impl/aws/AwsBatchJob.scala        |  9 ++++--
 .../aws/AwsBatchJobCachingActorHelper.scala   | 26 +++++++++++++--
 .../impl/aws/AwsBatchJobDefinition.scala      | 32 +++++++++++++++----
 6 files changed, 95 insertions(+), 21 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 7a36946e78d..49602106660 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -124,8 +124,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   override lazy val dockerImageUsed: Option[String] = Option(jobDockerImage)
 
   private lazy val execScript =
-    s"""|#!$jobShell
-        |${jobPaths.script.pathWithoutScheme}
+    s"""|${jobPaths.script.pathWithoutScheme}
         |""".stripMargin
 
 
@@ -178,7 +177,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       generateAwsBatchOutputs(jobDescriptor),
       jobPaths, Seq.empty[AwsBatchParameter],
       configuration.awsConfig.region,
-      Option(configuration.awsAuth))
+      Option(configuration.awsAuth),
+      configuration.fsxFileSystem)
   }
   /* Tries to abort the job in flight
    *
@@ -281,14 +281,30 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     def getAbsolutePath(path: Path) = {
       configuration.fileSystem match {
         case AWSBatchStorageSystems.s3 => AwsBatchWorkingDisk.MountPoint.resolve(path)
-        case _ => DefaultPathBuilder.get(configuration.root).resolve(path)
+        // case _ => DefaultPathBuilder.get(configuration.root).resolve(path)
+        case _ => AwsBatchWorkingDisk.MountPoint.resolve(path)
       }
-  }
+    }
+
+    val p = DefaultPathBuilder.get(path)
+    println("!!!!!!!!!!!!!!!!!!!!!!!!! relativePathAndVolume")
+    println(p.toString())
+    println(p.isAbsolute)
+    println(getAbsolutePath(p).toString())
+    println(configuration.root)
+    println(DefaultPathBuilder.get(configuration.root).toString())
+
     val absolutePath = DefaultPathBuilder.get(path) match {
       case p if !p.isAbsolute => getAbsolutePath(p)
       case p => p
     }
 
+    println(absolutePath.toString())
+    disks.map(x=>{
+      println(x.mountPoint.toString())
+      println("--------------")
+    })
+
     disks.find(d => absolutePath.startsWith(d.mountPoint)) match {
       case Some(disk) => (disk.mountPoint.relativize(absolutePath), disk)
       case None =>
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index 26f69c4e79a..55da57c90e2 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -59,7 +59,8 @@ case class AwsBatchAttributes(fileSystem: String,
                               executionBucket: String,
                               duplicationStrategy: AwsBatchCacheHitDuplicationStrategy,
                               submitAttempts: Int Refined Positive,
-                              createDefinitionAttempts: Int Refined Positive)
+                              createDefinitionAttempts: Int Refined Positive,
+                              fsxFileSystem: Option[List[String]])
 
 object AwsBatchAttributes {
   lazy val Logger = LoggerFactory.getLogger(this.getClass)
@@ -90,6 +91,14 @@ object AwsBatchAttributes {
       deprecatedKeys foreach { key => logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}") }
     }
 
+    def parseFSx(backendConfig: Config): Option[List[String]] = {
+      val fsxConfig = backendConfig.getStringList("filesystems.fsx")
+      fsxConfig.isEmpty match {
+        case true => None
+        case false => Some(fsxConfig.asScala.toList)
+      }
+    }
+
     warnDeprecated(configKeys, deprecatedAwsBatchKeys, context, Logger)
 
     val executionBucket: ErrorOr[String] = validate { backendConfig.as[String]("root") }
@@ -123,6 +132,11 @@ object AwsBatchAttributes {
             case other => throw new IllegalArgumentException(s"Unrecognized caching duplication strategy: $other. Supported strategies are copy and reference. See reference.conf for more details.")
           }
       }
+    
+    val fsx: ErrorOr[Option[List[String]]] = validate {backendConfig.hasPath("filesystems.fsx") match {
+      case true => parseFSx(backendConfig)
+      case false => None
+    }}
 
     (
       fileSysStr,
@@ -130,7 +144,8 @@ object AwsBatchAttributes {
       executionBucket,
       duplicationStrategy,
       backendConfig.as[ErrorOr[Int Refined Positive]]("numSubmitAttempts"),
-      backendConfig.as[ErrorOr[Int Refined Positive]]("numCreateDefinitionAttempts")
+      backendConfig.as[ErrorOr[Int Refined Positive]]("numCreateDefinitionAttempts"),
+      fsx
     ).tupled.map((AwsBatchAttributes.apply _).tupled) match {
       case Valid(r) => r
       case Invalid(f) =>
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
index 2bc76d4bb0b..b9278485305 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
@@ -53,9 +53,9 @@ class AwsBatchConfiguration(val configurationDescriptor: BackendConfigurationDes
   }
   val pathBuilderFactory = configurationDescriptor.backendConfig.hasPath("filesystems.s3") match {
     case true => S3PathBuilderFactory(configurationDescriptor.globalConfig, configurationDescriptor.backendConfig)
-    case false =>
-    PathBuilderFactory
+    case false => PathBuilderFactory
   }
+  val fsxFileSystem = batchAttributes.fsxFileSystem
 }
 
 object AWSBatchStorageSystems {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 90f1918b9da..eb4680662a2 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -31,6 +31,7 @@
 package cromwell.backend.impl.aws
 
 import java.security.MessageDigest
+import java.nio.file.attribute.PosixFilePermission
 
 import cats.data.ReaderT._
 import cats.data.{Kleisli, ReaderT}
@@ -82,7 +83,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                              jobPaths: JobPaths, // Based on config, calculated in Job Paths, key to all things outside container
                              parameters: Seq[AwsBatchParameter],
                              configRegion: Option[Region],
-                             optAwsAuthMode: Option[AwsAuthMode] = None
+                             optAwsAuthMode: Option[AwsAuthMode] = None,
+                             fsxFileSystem: Option[List[String]]
                             ) {
 
   // values for container environment
@@ -241,6 +243,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
        val regex = "s3://([^/]*)/(.*)".r
        val regex(bucketName, key) = jobPaths.callExecutionRoot.toString
        writeReconfiguredScriptForAudit(reconfiguredScript, bucketName, key+"/reconfigured-script.sh")
+    }else{
+      jobPaths.script.addPermission(PosixFilePermission.OTHERS_EXECUTE)
     }
 
 
@@ -367,7 +371,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         jobDescriptor = jobDescriptor,
         jobPaths = jobPaths,
         inputs = inputs,
-        outputs = outputs)
+        outputs = outputs,
+        fsxFileSystem = fsxFileSystem)
 
       val jobDefinitionBuilder = StandardAwsBatchJobDefinitionBuilder
       val jobDefinition = jobDefinitionBuilder.build(jobDefinitionContext)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
index 903f88a1cc4..a9c416563d3 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
@@ -55,12 +55,32 @@ trait AwsBatchJobCachingActorHelper extends StandardCachingActorHelper {
 
   lazy val runtimeAttributes: AwsBatchRuntimeAttributes = AwsBatchRuntimeAttributes(validatedRuntimeAttributes, configuration.runtimeConfig, configuration.fileSystem)
 
+  println("!!!!!!!!!!!!!!!!!!! DISKS")
+  println(runtimeAttributes.disks)
+  runtimeAttributes.disks.map(x =>{
+    println(x.fsType)
+    println(x.mountPoint)
+    println(x.name)
+  })
+
   lazy val workingDisk: AwsBatchVolume = runtimeAttributes.disks.find(x => configuration.fileSystem match {
-    case AWSBatchStorageSystems.s3 => x.name == AwsBatchWorkingDisk.Name
-    case _ =>  configuration.root.startsWith(x.mountPoint.pathAsString)
+    case AWSBatchStorageSystems.s3 => {
+      println("!!!!!!!!!!!!!!!!!! S3")
+      println(x.name)
+      println(AwsBatchWorkingDisk.Name)
+     x.name == AwsBatchWorkingDisk.Name
+    }
+    case _ =>  {
+      println("!!!!!!!!!!!!!!!!!! LOCAL")
+      println(configuration.root)
+      println(x.mountPoint.pathAsString)
+      println(AwsBatchWorkingDisk.toString())
+      println(AwsBatchWorkingDisk.Name)
+      // configuration.root.startsWith(x.mountPoint.pathAsString)
+      x.name == AwsBatchWorkingDisk.Name
+    }
   }).get
 
-
   lazy val callRootPath: Path = callPaths.callExecutionRoot
   lazy val returnCodeFilename: String = callPaths.returnCodeFilename
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index ae356b89772..10b617580d4 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -93,7 +93,15 @@ trait AwsBatchJobDefinitionBuilder {
     val environment = List.empty[KeyValuePair]
 
 
-    def buildVolumes(disks: Seq[AwsBatchVolume]): List[Volume] = {
+    def buildVolumes(disks: Seq[AwsBatchVolume], fsx: Option[List[String]]): List[Volume] = {
+
+      val fsx_volumes = fsx.isDefined match {
+        case true => fsx.get.map(mnt => Volume.builder().name(mnt).host(Host.builder().sourcePath(s"/$mnt").build()).build())
+        case false => List()
+      }
+
+      println("FSX!!!!!!!!!!!!!!!!")
+      println(fsx_volumes)
 
       //all the configured disks plus the fetch and run volume and the aws-cli volume
       disks.map(d => d.toVolume()).toList ++ List(
@@ -106,10 +114,18 @@ trait AwsBatchJobDefinitionBuilder {
           .name("awsCliHome")
           .host(Host.builder().sourcePath("/usr/local/aws-cli").build())
           .build()
-      )
+      ) ++ fsx_volumes
     }
 
-    def buildMountPoints(disks: Seq[AwsBatchVolume]): List[MountPoint] = {
+    def buildMountPoints(disks: Seq[AwsBatchVolume], fsx: Option[List[String]]): List[MountPoint] = {
+
+      val fsx_disks = fsx.isDefined match {
+        case true => fsx.get.map(mnt => MountPoint.builder().readOnly(false).sourceVolume(mnt).containerPath(s"/$mnt").build())
+        case false => List()
+      }
+
+      println("FSX!!!!!!!!!!!!!!!!")
+      println(fsx_disks)
 
       //all the configured disks plus the fetch and run mount point and the AWS cli mount point
       disks.map(_.toMountPoint).toList ++ List(
@@ -125,7 +141,7 @@ trait AwsBatchJobDefinitionBuilder {
           //where the aws-cli will be on the container
           .containerPath("/usr/local/aws-cli")
           .build()
-      )
+      ) ++ fsx_disks
     }
 
     def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair]): String = {
@@ -146,8 +162,8 @@ trait AwsBatchJobDefinitionBuilder {
        case _ =>  context.commandText
     }
     val packedCommand = packCommand("/bin/bash", "-c", cmdName)
-    val volumes =  buildVolumes( context.runtimeAttributes.disks )
-    val mountPoints = buildMountPoints( context.runtimeAttributes.disks)
+    val volumes =  buildVolumes( context.runtimeAttributes.disks, context.fsxFileSystem)
+    val mountPoints = buildMountPoints( context.runtimeAttributes.disks, context.fsxFileSystem)
     val jobDefinitionName = buildName(
       context.runtimeAttributes.dockerImage,
       packedCommand.mkString(","),
@@ -216,7 +232,8 @@ case class AwsBatchJobDefinitionContext(
             jobDescriptor: BackendJobDescriptor,
             jobPaths: JobPaths,
             inputs: Set[AwsBatchInput],
-            outputs: Set[AwsBatchFileOutput]){
+            outputs: Set[AwsBatchFileOutput],
+            fsxFileSystem: Option[List[String]]){
 
   override def toString: String = {
     new ToStringBuilder(this, ToStringStyle.JSON_STYLE)
@@ -229,6 +246,7 @@ case class AwsBatchJobDefinitionContext(
       .append("jobPaths", jobPaths)
       .append("inputs", inputs)
       .append("outputs", outputs)
+      .append("fsxFileSystem", fsxFileSystem)
       .build
   }
 }

From c639ed1fefc115d03c8cadbe0e931dbae4281864 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Wed, 5 Jan 2022 10:21:02 +0000
Subject: [PATCH 032/326] add ulimits and aws batch retries

---
 .../main/scala/cromwell/backend/backend.scala |   2 +
 .../StandardAsyncExecutionActor.scala         |   2 +
 ...wsBatchAsyncBackendJobExecutionActor.scala |  14 --
 .../backend/impl/aws/AwsBatchAttributes.scala |   9 +-
 .../backend/impl/aws/AwsBatchJob.scala        |  10 +-
 .../aws/AwsBatchJobCachingActorHelper.scala   |  20 +--
 .../impl/aws/AwsBatchJobDefinition.scala      |  99 ++++++++------
 .../impl/aws/AwsBatchRuntimeAttributes.scala  | 123 +++++++++++++++++-
 8 files changed, 196 insertions(+), 83 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index ea413c10367..18718f0e76f 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -139,6 +139,8 @@ object CommonBackendConfigurationAttributes {
     "default-runtime-attributes.noAddress",
     "default-runtime-attributes.docker",
     "default-runtime-attributes.queueArn",
+    "default-runtime-attributes.awsBatchRetryAttempts",
+    "default-runtime-attributes.ulimits",
     "default-runtime-attributes.failOnStderr",
     "slow-job-warning-time",
     "dockerhub",
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 96adb8c07b5..67e05464d54 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -449,8 +449,10 @@ trait StandardAsyncExecutionActor
         |tee $stderrRedirection < "$$$err" >&2 &
         |(
         |cd ${cwd.pathAsString}
+        |set -x
         |ENVIRONMENT_VARIABLES
         |INSTANTIATED_COMMAND
+        |set +x
         |) $stdinRedirection > "$$$out" 2> "$$$err"
         |echo $$? > $rcTmpPath
         |$emptyDirectoryFillCommand
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 49602106660..4b04f4cf1f5 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -286,25 +286,11 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       }
     }
 
-    val p = DefaultPathBuilder.get(path)
-    println("!!!!!!!!!!!!!!!!!!!!!!!!! relativePathAndVolume")
-    println(p.toString())
-    println(p.isAbsolute)
-    println(getAbsolutePath(p).toString())
-    println(configuration.root)
-    println(DefaultPathBuilder.get(configuration.root).toString())
-
     val absolutePath = DefaultPathBuilder.get(path) match {
       case p if !p.isAbsolute => getAbsolutePath(p)
       case p => p
     }
 
-    println(absolutePath.toString())
-    disks.map(x=>{
-      println(x.mountPoint.toString())
-      println("--------------")
-    })
-
     disks.find(d => absolutePath.startsWith(d.mountPoint)) match {
       case Some(disk) => (disk.mountPoint.relativize(absolutePath), disk)
       case None =>
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index 55da57c90e2..9236b8342db 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -72,7 +72,14 @@ object AwsBatchAttributes {
     "filesystems.local.auth",
     "filesystems.s3.auth",
     "filesystems.s3.caching.duplication-strategy",
-    "filesystems.local.caching.duplication-strategy"
+    "filesystems.local.caching.duplication-strategy",
+    "auth",
+    "numCreateDefinitionAttempts",
+    "filesystems.s3.duplication-strategy",
+    "numSubmitAttempts",
+    "default-runtime-attributes.scriptBucketName",
+    "awsBatchRetryAttempts",
+    "ulimits"
   )
 
   private val deprecatedAwsBatchKeys: Map[String, String] = Map(
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index eb4680662a2..352a07f6cd1 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -402,16 +402,20 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         // See:
         //
         // http://aws-java-sdk-javadoc.s3-website-us-west-2.amazonaws.com/latest/software/amazon/awssdk/services/batch/model/RegisterJobDefinitionRequest.Builder.html
-        val definitionRequest = RegisterJobDefinitionRequest.builder
+        var definitionRequest = RegisterJobDefinitionRequest.builder
           .containerProperties(jobDefinition.containerProperties)
           .jobDefinitionName(jobDefinitionName)
           // See https://stackoverflow.com/questions/24349517/scala-method-named-type
           .`type`(JobDefinitionType.CONTAINER)
-          .build
+          //.build
+
+        if (jobDefinitionContext.runtimeAttributes.awsBatchRetryAttempts != 0){
+          definitionRequest = definitionRequest.retryStrategy(jobDefinition.retryStrategy)
+        }
 
         Log.debug(s"Submitting definition request: $definitionRequest")
 
-        val response: RegisterJobDefinitionResponse = batchClient.registerJobDefinition(definitionRequest)
+        val response: RegisterJobDefinitionResponse = batchClient.registerJobDefinition(definitionRequest.build)
         Log.info(s"Definition created: $response")
         response.jobDefinitionArn()
       }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
index a9c416563d3..a3c693855be 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
@@ -55,27 +55,9 @@ trait AwsBatchJobCachingActorHelper extends StandardCachingActorHelper {
 
   lazy val runtimeAttributes: AwsBatchRuntimeAttributes = AwsBatchRuntimeAttributes(validatedRuntimeAttributes, configuration.runtimeConfig, configuration.fileSystem)
 
-  println("!!!!!!!!!!!!!!!!!!! DISKS")
-  println(runtimeAttributes.disks)
-  runtimeAttributes.disks.map(x =>{
-    println(x.fsType)
-    println(x.mountPoint)
-    println(x.name)
-  })
-
   lazy val workingDisk: AwsBatchVolume = runtimeAttributes.disks.find(x => configuration.fileSystem match {
-    case AWSBatchStorageSystems.s3 => {
-      println("!!!!!!!!!!!!!!!!!! S3")
-      println(x.name)
-      println(AwsBatchWorkingDisk.Name)
-     x.name == AwsBatchWorkingDisk.Name
-    }
+    case AWSBatchStorageSystems.s3 => x.name == AwsBatchWorkingDisk.Name
     case _ =>  {
-      println("!!!!!!!!!!!!!!!!!! LOCAL")
-      println(configuration.root)
-      println(x.mountPoint.pathAsString)
-      println(AwsBatchWorkingDisk.toString())
-      println(AwsBatchWorkingDisk.Name)
       // configuration.root.startsWith(x.mountPoint.pathAsString)
       x.name == AwsBatchWorkingDisk.Name
     }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index 10b617580d4..db06a9a4c8d 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -34,7 +34,7 @@ package cromwell.backend.impl.aws
 import scala.collection.mutable.ListBuffer
 import cromwell.backend.BackendJobDescriptor
 import cromwell.backend.io.JobPaths
-import software.amazon.awssdk.services.batch.model.{ContainerProperties, Host, KeyValuePair, MountPoint, ResourceRequirement, ResourceType, Volume}
+import software.amazon.awssdk.services.batch.model.{ContainerProperties, Host, KeyValuePair, MountPoint, ResourceRequirement, ResourceType, Volume, RetryStrategy, Ulimit}
 import cromwell.backend.impl.aws.io.AwsBatchVolume
 
 import scala.collection.JavaConverters._
@@ -60,12 +60,14 @@ import wdl4s.parser.MemoryUnit
   */
 sealed trait AwsBatchJobDefinition {
   def containerProperties: ContainerProperties
+  def retryStrategy: RetryStrategy
   def name: String
 
   override def toString: String = {
     new ToStringBuilder(this, ToStringStyle.JSON_STYLE)
       .append("name", name)
       .append("containerProperties", containerProperties)
+      .append("retryStrategy", retryStrategy)
       .build
   }
 }
@@ -76,21 +78,11 @@ trait AwsBatchJobDefinitionBuilder {
 
   /** Gets a builder, seeded with appropriate portions of the container properties
    *
-   *  @param dockerImage docker image with which to run
-   *  @return ContainerProperties builder ready for modification
+   *  @param context AwsBatchJobDefinitionContext with all the runtime attributes
+   *  @return ContainerProperties builder ready for modification and name
    *
    */
-  def builder(dockerImage: String): ContainerProperties.Builder =
-    ContainerProperties.builder().image(dockerImage)
-
-
-  def buildResources(builder: ContainerProperties.Builder,
-                     context: AwsBatchJobDefinitionContext): (ContainerProperties.Builder, String) = {
-    // The initial buffer should only contain one item - the hostpath of the
-    // local disk mount point, which will be needed by the docker container
-    // that copies data around
-
-    val environment = List.empty[KeyValuePair]
+  def containerPropertiesBuilder(context: AwsBatchJobDefinitionContext): (ContainerProperties.Builder, String) = {
 
 
     def buildVolumes(disks: Seq[AwsBatchVolume], fsx: Option[List[String]]): List[Volume] = {
@@ -100,9 +92,6 @@ trait AwsBatchJobDefinitionBuilder {
         case false => List()
       }
 
-      println("FSX!!!!!!!!!!!!!!!!")
-      println(fsx_volumes)
-
       //all the configured disks plus the fetch and run volume and the aws-cli volume
       disks.map(d => d.toVolume()).toList ++ List(
         Volume.builder()
@@ -124,9 +113,6 @@ trait AwsBatchJobDefinitionBuilder {
         case false => List()
       }
 
-      println("FSX!!!!!!!!!!!!!!!!")
-      println(fsx_disks)
-
       //all the configured disks plus the fetch and run mount point and the AWS cli mount point
       disks.map(_.toMountPoint).toList ++ List(
         MountPoint.builder()
@@ -144,36 +130,42 @@ trait AwsBatchJobDefinitionBuilder {
       ) ++ fsx_disks
     }
 
-    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair]): String = {
-      val str = s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}"
+    def buildUlimits(ulimits: Seq[Map[String, String]]): List[Ulimit] = {
 
-      val sha1 = MessageDigest.getInstance("SHA-1")
-            .digest( str.getBytes("UTF-8") )
-            .map("%02x".format(_)).mkString
-
-      val prefix = s"cromwell_$imageName".slice(0,88) // will be joined to a 40 character SHA1 for total length of 128
-
-      sanitize(prefix + sha1)
+      ulimits.filter(_.nonEmpty).map(u =>
+        Ulimit.builder()
+          .name(u("name"))
+          .softLimit(u("softLimit").toInt)
+          .hardLimit(u("hardLimit").toInt)
+          .build()
+      ).toList
     }
 
+    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit]): String = {
+      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}"
+    }
 
+    val environment = List.empty[KeyValuePair]
     val cmdName = context.runtimeAttributes.fileSystem match {
-       case AWSBatchStorageSystems.s3 => "/var/scratch/fetch_and_run.sh"
-       case _ =>  context.commandText
+      case AWSBatchStorageSystems.s3 => "/var/scratch/fetch_and_run.sh"
+      case _ =>  context.commandText
     }
     val packedCommand = packCommand("/bin/bash", "-c", cmdName)
     val volumes =  buildVolumes( context.runtimeAttributes.disks, context.fsxFileSystem)
     val mountPoints = buildMountPoints( context.runtimeAttributes.disks, context.fsxFileSystem)
-    val jobDefinitionName = buildName(
+    val ulimits = buildUlimits( context.runtimeAttributes.ulimits)
+    val containerPropsName = buildName(
       context.runtimeAttributes.dockerImage,
       packedCommand.mkString(","),
       volumes,
       mountPoints,
-      environment
+      environment,
+      ulimits
     )
 
-    (builder
-       .command(packedCommand.asJava)
+    (ContainerProperties.builder()
+      .image(context.runtimeAttributes.dockerImage)
+      .command(packedCommand.asJava)
       .resourceRequirements(
         ResourceRequirement.builder()
           .`type`(ResourceType.MEMORY)
@@ -186,9 +178,18 @@ trait AwsBatchJobDefinitionBuilder {
       )
         .volumes( volumes.asJava)
         .mountPoints( mountPoints.asJava)
-        .environment(environment.asJava),
+        .environment(environment.asJava)
+        .ulimits(ulimits.asJava),
 
-      jobDefinitionName)
+      containerPropsName)
+  }
+
+  def retryStrategyBuilder(context: AwsBatchJobDefinitionContext): (RetryStrategy.Builder, String) = {
+    // We can add here the 'evaluateOnExit' statement
+
+    (RetryStrategy.builder()
+      .attempts(context.runtimeAttributes.awsBatchRetryAttempts),
+     context.runtimeAttributes.awsBatchRetryAttempts.toString)
   }
 
   private def packCommand(shell: String, options: String, mainCommand: String): Seq[String] = {
@@ -211,15 +212,29 @@ trait AwsBatchJobDefinitionBuilder {
 
 object StandardAwsBatchJobDefinitionBuilder extends AwsBatchJobDefinitionBuilder {
   def build(context: AwsBatchJobDefinitionContext): AwsBatchJobDefinition = {
-    //instantiate a builder with the name of the docker image
-    val builderInst = builder(context.runtimeAttributes.dockerImage)
-    val (b, name) = buildResources(builderInst, context)
 
-    new StandardAwsBatchJobDefinitionBuilder(b.build, name)
+    val (containerPropsInst, containerPropsName) = containerPropertiesBuilder(context)
+    val (retryStrategyInst, retryStrategyName) = retryStrategyBuilder(context)
+
+    val name = buildName(context.runtimeAttributes.dockerImage, containerPropsName, retryStrategyName)
+
+    new StandardAwsBatchJobDefinitionBuilder(containerPropsInst.build, retryStrategyInst.build, name)
+  }
+
+  def buildName(imageName: String, containerPropsName: String, retryStrategyName: String): String = {
+    val str = s"$imageName:$containerPropsName:$retryStrategyName"
+
+    val sha1 = MessageDigest.getInstance("SHA-1")
+          .digest( str.getBytes("UTF-8") )
+          .map("%02x".format(_)).mkString
+
+    val prefix = s"cromwell_${imageName}_".slice(0,88) // will be joined to a 40 character SHA1 for total length of 128
+
+    sanitize(prefix + sha1)
   }
 }
 
-case class StandardAwsBatchJobDefinitionBuilder private(containerProperties: ContainerProperties, name: String) extends AwsBatchJobDefinition
+case class StandardAwsBatchJobDefinitionBuilder private(containerProperties: ContainerProperties, retryStrategy: RetryStrategy, name: String) extends AwsBatchJobDefinition
 
 object AwsBatchJobDefinitionContext
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index c6fc2a5f51f..d563b7435cc 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -60,6 +60,8 @@ import scala.util.matching.Regex
  * @param noAddress is there no address
  * @param scriptS3BucketName the s3 bucket where the execution command or script will be written and, from there, fetched into the container and executed
  * @param fileSystem the filesystem type, default is "s3"
+ * @param awsBatchRetryAttempts number of attempts that AWS Batch will retry the task if it fails
+ * @param ulimits ulimit values to be passed to the container
  */
 case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      zones: Vector[String],
@@ -71,6 +73,8 @@ case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      continueOnReturnCode: ContinueOnReturnCode,
                                      noAddress: Boolean,
                                      scriptS3BucketName: String,
+                                     awsBatchRetryAttempts: Int,
+                                     ulimits: Vector[Map[String, String]],
                                      fileSystem:String= "s3")
 
 object AwsBatchRuntimeAttributes {
@@ -79,6 +83,8 @@ object AwsBatchRuntimeAttributes {
 
   val scriptS3BucketKey = "scriptBucketName"
 
+  val awsBatchRetryAttemptsKey = "awsBatchRetryAttempts"
+
   val ZonesKey = "zones"
   private val ZonesDefaultValue = WomString("us-east-1a")
 
@@ -92,6 +98,9 @@ object AwsBatchRuntimeAttributes {
 
   private val MemoryDefaultValue = "2 GB"
 
+  val UlimitsKey = "ulimits"
+  private val UlimitsDefaultValue = WomArray(WomArrayType(WomMapType(WomStringType,WomStringType)), Vector(WomMap(Map.empty[WomValue, WomValue])))
+
   private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] = CpuValidation.instance
     .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
@@ -134,6 +143,14 @@ object AwsBatchRuntimeAttributes {
     QueueArnValidation.withDefault(QueueArnValidation.configDefaultWomValue(runtimeConfig) getOrElse
       (throw new RuntimeException("queueArn is required")))
 
+  private def awsBatchRetryAttemptsValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = {
+    AwsBatchRetryAttemptsValidation(awsBatchRetryAttemptsKey).withDefault(AwsBatchRetryAttemptsValidation(awsBatchRetryAttemptsKey)
+    .configDefaultWomValue(runtimeConfig).getOrElse(WomInteger(0)))
+  }
+
+  private def ulimitsValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[Map[String, String]]] =
+    UlimitsValidation.withDefault(UlimitsValidation.configDefaultWomValue(runtimeConfig) getOrElse UlimitsDefaultValue)
+
   def runtimeAttributesBuilder(configuration: AwsBatchConfiguration): StandardValidatedRuntimeAttributesBuilder = {
     val runtimeConfig = configuration.runtimeConfig
     def validationsS3backend = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
@@ -146,7 +163,9 @@ object AwsBatchRuntimeAttributes {
                         noAddressValidation(runtimeConfig),
                         dockerValidation,
                         queueArnValidation(runtimeConfig),
-                        scriptS3BucketNameValidation(runtimeConfig)
+                        scriptS3BucketNameValidation(runtimeConfig),
+                        awsBatchRetryAttemptsValidation(runtimeConfig),
+                        ulimitsValidation(runtimeConfig)
                       )
    def validationsLocalBackend  = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
       cpuValidation(runtimeConfig),
@@ -157,7 +176,9 @@ object AwsBatchRuntimeAttributes {
       memoryMinValidation(runtimeConfig),
       noAddressValidation(runtimeConfig),
       dockerValidation,
-      queueArnValidation(runtimeConfig)
+      queueArnValidation(runtimeConfig),
+      awsBatchRetryAttemptsValidation(runtimeConfig),
+      ulimitsValidation(runtimeConfig)
     )
 
     configuration.fileSystem match  {
@@ -180,8 +201,9 @@ object AwsBatchRuntimeAttributes {
     val scriptS3BucketName = fileSystem match  {
        case AWSBatchStorageSystems.s3 => RuntimeAttributesValidation.extract(scriptS3BucketNameValidation(runtimeAttrsConfig) , validatedRuntimeAttributes)
        case _ => ""
-     }
-
+    }
+    val awsBatchRetryAttempts: Int = RuntimeAttributesValidation.extract(awsBatchRetryAttemptsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val ulimits: Vector[Map[String, String]] = RuntimeAttributesValidation.extract(ulimitsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
 
     new AwsBatchRuntimeAttributes(
       cpu,
@@ -194,6 +216,8 @@ object AwsBatchRuntimeAttributes {
       continueOnReturnCode,
       noAddress,
       scriptS3BucketName,
+      awsBatchRetryAttempts,
+      ulimits,
       fileSystem
     )
   }
@@ -372,3 +396,94 @@ object DisksValidation extends RuntimeAttributesValidation[Seq[AwsBatchVolume]]
   override protected def missingValueMessage: String =
     s"Expecting $key runtime attribute to be a comma separated String or Array[String]"
 }
+
+object AwsBatchRetryAttemptsValidation {
+  def apply(key: String): AwsBatchRetryAttemptsValidation = new AwsBatchRetryAttemptsValidation(key)
+}
+
+class AwsBatchRetryAttemptsValidation(key: String) extends IntRuntimeAttributesValidation(key) {
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[Int]] = {
+    case womValue if WomIntegerType.coerceRawValue(womValue).isSuccess =>
+      WomIntegerType.coerceRawValue(womValue).get match {
+        case WomInteger(value) =>
+          if (value.toInt < 0)
+            s"Expecting $key runtime attribute value greater than or equal to 0".invalidNel
+          else if (value.toInt > 10)
+            s"Expecting $key runtime attribute value lower than or equal to 10".invalidNel
+          else
+            value.toInt.validNel
+      }
+  }
+
+  override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Integer"
+}
+
+
+object UlimitsValidation
+    extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
+  override def key: String = AwsBatchRuntimeAttributes.UlimitsKey
+
+  override def coercion: Traversable[WomType] =
+    Set(WomStringType, WomArrayType(WomMapType(WomStringType, WomStringType)))
+
+  var accepted_keys = Set("name", "softLimit", "hardLimit")
+
+  override protected def validateValue
+      : PartialFunction[WomValue, ErrorOr[Vector[Map[String, String]]]] = {
+    case WomArray(womType, value)
+        if womType.memberType == WomMapType(WomStringType, WomStringType) =>
+      check_maps(value.toVector)
+    case WomMap(_, _) => "!!! ERROR1".invalidNel
+
+  }
+
+  private def check_maps(
+      maps: Vector[WomValue]
+  ): ErrorOr[Vector[Map[String, String]]] = {
+    val entryNels: Vector[ErrorOr[Map[String, String]]] = maps.map {
+      case WomMap(_, value) => check_keys(value)
+      case _                 => "!!! ERROR2".invalidNel
+    }
+    val sequenced: ErrorOr[Vector[Map[String, String]]] = sequenceNels(
+      entryNels
+    )
+    sequenced
+  }
+
+  private def check_keys(
+      dict: Map[WomValue, WomValue]
+  ): ErrorOr[Map[String, String]] = {
+    val map_keys = dict.keySet.map(_.valueString).toSet
+    val unrecognizedKeys =
+      accepted_keys.diff(map_keys) union map_keys.diff(accepted_keys)
+
+    if (!dict.nonEmpty){
+      Map.empty[String, String].validNel  
+    }else if (unrecognizedKeys.nonEmpty) {
+      s"Invalid keys in $key runtime attribute. Refer to 'ulimits' section on https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#containerProperties".invalidNel
+    } else {
+      dict
+        .collect { case (WomString(k), WomString(v)) =>
+          (k, v)
+        // case _ => "!!! ERROR3".invalidNel
+        }
+        .toMap
+        .validNel
+    }
+  }
+
+  private def sequenceNels(
+      nels: Vector[ErrorOr[Map[String, String]]]
+  ): ErrorOr[Vector[Map[String, String]]] = {
+    val emptyNel: ErrorOr[Vector[Map[String, String]]] =
+      Vector.empty[Map[String, String]].validNel
+    val seqNel: ErrorOr[Vector[Map[String, String]]] =
+      nels.foldLeft(emptyNel) { (acc, v) =>
+        (acc, v) mapN { (a, v) => a :+ v }
+      }
+    seqNel
+  }
+
+  override protected def missingValueMessage: String =
+    s"Expecting $key runtime attribute to be an Array[Map[String, String]]"
+}

From 66b29b4fb23d0d2aa4ba476c198f0553b0e96131 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Mon, 10 Jan 2022 16:36:01 +0000
Subject: [PATCH 033/326] add exit to end of script

---
 .../backend/standard/StandardAsyncExecutionActor.scala         | 1 +
 .../impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala       | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 67e05464d54..8693e1a0c4a 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -463,6 +463,7 @@ trait StandardAsyncExecutionActor
         |${directoryScripts(directoryOutputs)}
         |)
         |mv $rcTmpPath $rcPath
+        |exit $$(head -n 1 $rcPath)
         |""".stripMargin
       .replace("SCRIPT_PREAMBLE", scriptPreamble)
       .replace("ENVIRONMENT_VARIABLES", environmentVariables)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 4b04f4cf1f5..d869a423f74 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -124,7 +124,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   override lazy val dockerImageUsed: Option[String] = Option(jobDockerImage)
 
   private lazy val execScript =
-    s"""|${jobPaths.script.pathWithoutScheme}
+    s"""|ls -lah ${jobPaths.script.pathWithoutScheme}
+        |${jobPaths.script.pathWithoutScheme}
         |""".stripMargin
 
 

From 02150b2bf20bbb12f0e548cfdd0822df5793c297 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Mon, 31 Jan 2022 16:40:07 +0000
Subject: [PATCH 034/326] add script closure

---
 .../standard/StandardAsyncExecutionActor.scala | 12 ++++++++----
 ...AwsBatchAsyncBackendJobExecutionActor.scala | 18 +++++++++++++++++-
 .../backend/impl/aws/AwsBatchJob.scala         | 12 +++++++-----
 3 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 8693e1a0c4a..d4c74730a48 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -329,6 +329,9 @@ trait StandardAsyncExecutionActor
   /** Any custom code that should be run within commandScriptContents before the instantiated command. */
   def scriptPreamble: String = ""
 
+  /** Any custom code that should be run within commandScriptContents right before exiting. */
+  def scriptClosure: String = ""
+
   def cwd: Path = commandDirectory
   def rcPath: Path = cwd./(jobPaths.returnCodeFilename)
 
@@ -447,14 +450,14 @@ trait StandardAsyncExecutionActor
         |touch $stdoutRedirection $stderrRedirection
         |tee $stdoutRedirection < "$$$out" &
         |tee $stderrRedirection < "$$$err" >&2 &
+        |set -x
         |(
         |cd ${cwd.pathAsString}
-        |set -x
         |ENVIRONMENT_VARIABLES
         |INSTANTIATED_COMMAND
-        |set +x
         |) $stdinRedirection > "$$$out" 2> "$$$err"
         |echo $$? > $rcTmpPath
+        |set +x
         |$emptyDirectoryFillCommand
         |(
         |cd ${cwd.pathAsString}
@@ -463,13 +466,14 @@ trait StandardAsyncExecutionActor
         |${directoryScripts(directoryOutputs)}
         |)
         |mv $rcTmpPath $rcPath
-        |exit $$(head -n 1 $rcPath)
+        |SCRIPT_CLOSURE
         |""".stripMargin
       .replace("SCRIPT_PREAMBLE", scriptPreamble)
       .replace("ENVIRONMENT_VARIABLES", environmentVariables)
       .replace("INSTANTIATED_COMMAND", commandString)
       .replace("SCRIPT_EPILOGUE", scriptEpilogue)
-      .replace("DOCKER_OUTPUT_DIR_LINK", dockerOutputDir))
+      .replace("DOCKER_OUTPUT_DIR_LINK", dockerOutputDir)
+      .replace("SCRIPT_CLOSURE", scriptClosure))
   }
 
   def runtimeEnvironmentPathMapper(env: RuntimeEnvironment): RuntimeEnvironment = {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index d869a423f74..5b6639344fa 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -124,7 +124,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   override lazy val dockerImageUsed: Option[String] = Option(jobDockerImage)
 
   private lazy val execScript =
-    s"""|ls -lah ${jobPaths.script.pathWithoutScheme}
+    s"""|df -h
+        |ls -lah ${jobPaths.script.pathWithoutScheme}
         |${jobPaths.script.pathWithoutScheme}
         |""".stripMargin
 
@@ -399,6 +400,21 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     case _ =>  jobPaths.callExecutionRoot
   }
 
+  override def scriptPreamble: String = {
+    configuration.fileSystem match {
+      case  AWSBatchStorageSystems.s3 => ""
+      case _ => s"""|# clean directory in case of multiple retries
+                    |ls | grep -v script | xargs rm -rf""".stripMargin
+    }
+  }
+
+  override def scriptClosure: String = {
+    configuration.fileSystem match {
+      case  AWSBatchStorageSystems.s3 => ""
+      case _ => s"exit $$(head -n 1 $rcPath)"
+    }
+  }
+
   override def globParentDirectory(womGlobFile: WomGlobFile): Path =
     configuration.fileSystem match {
       case  AWSBatchStorageSystems.s3 =>
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 352a07f6cd1..50f1ca0fec7 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -186,21 +186,19 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         s"""
            |touch ${output.name}
            |$s3Cmd cp --no-progress ${output.name} ${output.s3key}
-           |if [ -e $globDirectory ]; then $s3Cmd cp --no-progress $globDirectory $s3GlobOutDirectory --recursive --exclude "cromwell_glob_control_file"; fi
-           |""".stripMargin
+           |if [ -e $globDirectory ]; then $s3Cmd cp --no-progress $globDirectory $s3GlobOutDirectory --recursive --exclude "cromwell_glob_control_file"; fi""".stripMargin
 
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
         //output is on working disk mount
         s"""
-           |$s3Cmd cp --no-progress $workDir/${output.local.pathAsString} ${output.s3key}
-           |""".stripMargin
+           |$s3Cmd cp --no-progress $workDir/${output.local.pathAsString} ${output.s3key}""".stripMargin
       case output: AwsBatchFileOutput =>
         //output on a different mount
         s"$s3Cmd cp --no-progress ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
       case _ => ""
     }.mkString("\n") + "\n" +
       s"""
-         |if [ -f $workDir/${jobPaths.returnCodeFilename} ]; then $s3Cmd cp --no-progress $workDir/${jobPaths.returnCodeFilename} ${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename} ; fi\n
+         |if [ -f $workDir/${jobPaths.returnCodeFilename} ]; then $s3Cmd cp --no-progress $workDir/${jobPaths.returnCodeFilename} ${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename} ; fi
          |if [ -f $stdErr ]; then $s3Cmd cp --no-progress $stdErr ${jobPaths.standardPaths.error.pathAsString}; fi
          |if [ -f $stdOut ]; then $s3Cmd cp --no-progress $stdOut ${jobPaths.standardPaths.output.pathAsString}; fi
          |""".stripMargin
@@ -214,6 +212,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |echo '*** DELOCALIZING OUTPUTS ***'
          |$outputCopyCommand
          |echo '*** COMPLETED DELOCALIZATION ***'
+         |echo '*** EXITING WITH RETURN CODE ***'
+         |rc=$$(head -n 1 $workDir/${jobPaths.returnCodeFilename})
+         |echo $$rc
+         |exit $$rc
          |}
          |""".stripMargin
   }

From 2f434e1462bd053530f2f3c5a0dcfbcd4aaa5aea Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 1 Mar 2022 12:04:47 +0000
Subject: [PATCH 035/326] clean preamble; do not gzip batch command

---
 .../AwsBatchAsyncBackendJobExecutionActor.scala |  6 ++++--
 .../impl/aws/AwsBatchJobDefinition.scala        | 17 +++++++++--------
 2 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 2ffca40e71d..9e65e819988 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -123,9 +123,12 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
   override lazy val dockerImageUsed: Option[String] = Option(jobDockerImage)
 
+  // |cd ${jobPaths.script.parent.pathWithoutScheme}; ls | grep -v script | xargs rm -rf; cd -
+
   private lazy val execScript =
     s"""|df -h
         |ls -lah ${jobPaths.script.pathWithoutScheme}
+        |find ${jobPaths.script.parent.pathWithoutScheme} -group root | grep -v script | xargs rm -vrf
         |${jobPaths.script.pathWithoutScheme}
         |""".stripMargin
 
@@ -411,8 +414,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   override def scriptPreamble: String = {
     configuration.fileSystem match {
       case  AWSBatchStorageSystems.s3 => ""
-      case _ => s"""|# clean directory in case of multiple retries
-                    |ls | grep -v script | xargs rm -rf""".stripMargin
+      case _ => s""
     }
   }
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index 2adb27df5a8..3b8470c6c29 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -186,14 +186,15 @@ trait AwsBatchJobDefinitionBuilder {
 
   private def packCommand(shell: String, options: String, mainCommand: String): Seq[String] = {
     val rc = new ListBuffer[String]()
-    val lim = 1024
-    val packedCommand = mainCommand.length() match {
-      case len if len <= lim => mainCommand
-      case len if len > lim => {
-        rc += "gzipdata" // This is hard coded in our agent and must be the first item
-        gzip(mainCommand)
-      }
-    }
+    // val lim = 1024
+    // val packedCommand = mainCommand.length() match {
+    //   case len if len <= lim => mainCommand
+    //   case len if len > lim => {
+    //     rc += "gzipdata" // This is hard coded in our agent and must be the first item
+    //     gzip(mainCommand)
+    //   }
+    // }
+    val packedCommand = mainCommand
     rc += shell
     rc += options
     rc += packedCommand

From 1d20031e5ac9a58c0b856a7651a875dde620fe93 Mon Sep 17 00:00:00 2001
From: Mark Schreiber <mrschre@amazon.com>
Date: Mon, 14 Mar 2022 11:36:56 -0400
Subject: [PATCH 036/326] improved logging

---
 .../registryv2/flows/aws/AmazonEcr.scala      |  3 ++
 .../flows/aws/AmazonEcrAbstract.scala         | 18 +++++--
 .../flows/aws/AmazonEcrPublic.scala           |  6 ++-
 .../registryv2/flows/aws/EcrUtils.scala       |  2 +-
 .../backend/impl/aws/AwsBatchJob.scala        | 53 ++++++++++---------
 5 files changed, 51 insertions(+), 31 deletions(-)

diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcr.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcr.scala
index a073b9f4eb2..f1174009669 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcr.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcr.scala
@@ -4,12 +4,14 @@ import cats.effect.IO
 import cromwell.docker.{DockerImageIdentifier, DockerInfoActor, DockerRegistryConfig}
 import org.http4s.AuthScheme
 import org.http4s.client.Client
+import org.slf4j.{Logger, LoggerFactory}
 import software.amazon.awssdk.services.ecr.EcrClient
 
 import scala.compat.java8.OptionConverters._
 import scala.concurrent.Future
 
 class AmazonEcr(override val config: DockerRegistryConfig, ecrClient: EcrClient = EcrClient.create()) extends AmazonEcrAbstract(config) {
+  private val logger: Logger = LoggerFactory.getLogger(this.getClass)
 
   override protected val authorizationScheme: AuthScheme = AuthScheme.Basic
 
@@ -30,6 +32,7 @@ class AmazonEcr(override val config: DockerRegistryConfig, ecrClient: EcrClient
   override def accepts(dockerImageIdentifier: DockerImageIdentifier): Boolean = dockerImageIdentifier.hostAsString.contains("amazonaws.com")
 
   override protected def getToken(dockerInfoContext: DockerInfoActor.DockerInfoContext)(implicit client: Client[IO]): IO[Option[String]] = {
+    logger.info("obtaining access token for '{}'", dockerInfoContext.dockerImageID.fullName)
     val eventualMaybeToken = Future(ecrClient.getAuthorizationToken
       .authorizationData()
       .stream()
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrAbstract.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrAbstract.scala
index bc9ea61fd74..f30f11fb971 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrAbstract.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrAbstract.scala
@@ -6,31 +6,41 @@ import cromwell.docker.registryv2.DockerRegistryV2Abstract
 import cromwell.docker.registryv2.flows.aws.EcrUtils.{EcrForbidden, EcrNotFound, EcrUnauthorized}
 import org.apache.commons.codec.digest.DigestUtils
 import org.http4s.{Header, Response, Status}
+import org.slf4j.{Logger, LoggerFactory}
 
 abstract class AmazonEcrAbstract(override val config: DockerRegistryConfig) extends DockerRegistryV2Abstract(config) {
+  private val logger: Logger = LoggerFactory.getLogger(this.getClass)
+
 
   /**
     * Not used as getToken is overridden
     */
-  override protected def authorizationServerHostName(dockerImageIdentifier: DockerImageIdentifier): String = ""
+  override protected def authorizationServerHostName(dockerImageIdentifier: DockerImageIdentifier): String = {
+    logger.warn("A call has been made to authorizationServerHostName for an ECR container but ECR auth should be done via SDK. This call will be ignored")
+    ""
+  }
 
   /**
     * Not used as getToken is overridden
     */
-  override protected def buildTokenRequestHeaders(dockerInfoContext: DockerInfoActor.DockerInfoContext): List[Header] = List.empty
+  override protected def buildTokenRequestHeaders(dockerInfoContext: DockerInfoActor.DockerInfoContext): List[Header] = {
+    logger.warn("A call has been made to buildTokenRequestHeaders for an ECR container but ECR auth should be done via SDK. This call will be ignored")
+    List.empty
+  }
 
   /**
-    * Amazon ECR repositories don't have a digest header in responses so we must made it from the manifest body
+    * Amazon ECR repositories don't have a digest header in responses so we must make it from the manifest body
     */
   override protected def getDigestFromResponse(response: Response[IO]): IO[DockerHashResult] = response match {
     case Status.Successful(r) => digestManifest(r.bodyText)
-    case Status.Unauthorized(_) => IO.raiseError(new EcrUnauthorized)
+    case Status.Unauthorized(_) => IO.raiseError(new EcrUnauthorized("Not authorized to obtain a digest from this registry. Your token may be invalid"))
     case Status.NotFound(_) => IO.raiseError(new EcrNotFound)
     case Status.Forbidden(_) => IO.raiseError(new EcrForbidden)
     case failed => failed.as[String].flatMap(body => IO.raiseError(new Exception(s"Failed to get manifest: $body")))
   }
 
   private def digestManifest(bodyText: fs2.Stream[IO, String]): IO[DockerHashResult] = {
+    logger.info("computing sha256 digest for container manifest")
     bodyText
       .compile
       .string
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublic.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublic.scala
index 797d4b70703..edff304a810 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublic.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublic.scala
@@ -3,6 +3,7 @@ package cromwell.docker.registryv2.flows.aws
 import cats.effect.IO
 import cromwell.docker.{DockerImageIdentifier, DockerInfoActor, DockerRegistryConfig}
 import org.http4s.client.Client
+import org.slf4j.{Logger, LoggerFactory}
 import software.amazon.awssdk.services.ecrpublic.EcrPublicClient
 import software.amazon.awssdk.services.ecrpublic.model.GetAuthorizationTokenRequest
 
@@ -10,6 +11,9 @@ import scala.concurrent.Future
 
 
 class AmazonEcrPublic(override val config: DockerRegistryConfig, ecrClient: EcrPublicClient = EcrPublicClient.create()) extends AmazonEcrAbstract(config) {
+ private val logger: Logger = LoggerFactory.getLogger(this.getClass)
+
+
   /**
     * public.ecr.aws
     */
@@ -23,7 +27,7 @@ class AmazonEcrPublic(override val config: DockerRegistryConfig, ecrClient: EcrP
 
 
   override protected def getToken(dockerInfoContext: DockerInfoActor.DockerInfoContext)(implicit client: Client[IO]): IO[Option[String]] = {
-
+    logger.info("obtaining access token for '{}'", dockerInfoContext.dockerImageID.fullName)
     val eventualMaybeToken: Future[Option[String]] = Future(
       Option(ecrClient
         .getAuthorizationToken(GetAuthorizationTokenRequest.builder().build())
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/EcrUtils.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/EcrUtils.scala
index 9da904c8adc..405c22076e4 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/EcrUtils.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/aws/EcrUtils.scala
@@ -2,7 +2,7 @@ package cromwell.docker.registryv2.flows.aws
 
 object EcrUtils {
 
-  case class EcrUnauthorized() extends Exception
+  case class EcrUnauthorized(msg: String) extends Exception
   case class EcrNotFound() extends Exception
   case class EcrForbidden() extends Exception
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 3102f678aa6..0db547242c1 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -390,12 +390,11 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
 
 
       //check if there is already a suitable definition based on the calculated job definition name
-      val jobDefinitionName = jobDefinition.name
 
-      Log.debug(s"Checking for existence of job definition called: $jobDefinitionName")
+      Log.debug(s"Checking for existence of job definition called: ${jobDefinition.name}")
 
       val describeJobDefinitionRequest = DescribeJobDefinitionsRequest.builder()
-        .jobDefinitionName( jobDefinitionName )
+        .jobDefinitionName( jobDefinition.name )
         .status("ACTIVE")
         .build()
 
@@ -403,30 +402,19 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
 
       if ( !describeJobDefinitionResponse.jobDefinitions.isEmpty ) {
         //sort the definitions so that the latest revision is at the head
-        val definitions = describeJobDefinitionResponse.jobDefinitions().asScala.toList.sortWith(_.revision > _.revision)
-
-        //return the arn of the job
-        definitions.head.jobDefinitionArn()
-      } else {
-        Log.debug(s"No job definition found. Creating job definition: $jobDefinitionName")
-
-        // See:
-        //
-        // http://aws-java-sdk-javadoc.s3-website-us-west-2.amazonaws.com/latest/software/amazon/awssdk/services/batch/model/RegisterJobDefinitionRequest.Builder.html
-        var definitionRequest = RegisterJobDefinitionRequest.builder
-          .containerProperties(jobDefinition.containerProperties)
-          .jobDefinitionName(jobDefinitionName)
-          // See https://stackoverflow.com/questions/24349517/scala-method-named-type
-          .`type`(JobDefinitionType.CONTAINER)
-
-        if (jobDefinitionContext.runtimeAttributes.awsBatchRetryAttempts != 0){
-          definitionRequest = definitionRequest.retryStrategy(jobDefinition.retryStrategy)
+        val existingDefinition = describeJobDefinitionResponse.jobDefinitions().asScala.toList.sortWith(_.revision > _.revision).head
+
+        //TODO test this
+        if (existingDefinition.containerProperties().memory() != null || existingDefinition.containerProperties().vcpus() != null) {
+          Log.warn("the job definition '{}' has deprecated configuration for memory and vCPU and will be replaced", existingDefinition.jobDefinitionName())
+          registerJobDefinition(jobDefinition, jobDefinitionContext).jobDefinitionArn()
+        } else {
+          existingDefinition.jobDefinitionArn()
         }
+      } else {
+        Log.debug(s"No job definition found. Creating job definition: ${jobDefinition.name}")
 
-        Log.debug(s"Submitting definition request: $definitionRequest")
-
-        val response: RegisterJobDefinitionResponse = batchClient.registerJobDefinition(definitionRequest.build)
-        Log.info(s"Definition created: $response")
+        val response: RegisterJobDefinitionResponse = registerJobDefinition(jobDefinition, jobDefinitionContext)
         response.jobDefinitionArn()
       }
     })
@@ -455,6 +443,21 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     }
   }
 
+  def registerJobDefinition(jobDefinition: AwsBatchJobDefinition, jobDefinitionContext: AwsBatchJobDefinitionContext): RegisterJobDefinitionResponse = {
+    // See:
+    //
+    // http://aws-java-sdk-javadoc.s3-website-us-west-2.amazonaws.com/latest/software/amazon/awssdk/services/batch/model/RegisterJobDefinitionRequest.Builder.html
+    var definitionRequest = RegisterJobDefinitionRequest.builder
+      .containerProperties(jobDefinition.containerProperties)
+      .jobDefinitionName(jobDefinition.name)
+      // See https://stackoverflow.com/questions/24349517/scala-method-named-type
+      .`type`(JobDefinitionType.CONTAINER)
+
+    if (jobDefinitionContext.runtimeAttributes.awsBatchRetryAttempts != 0){
+      definitionRequest = definitionRequest.retryStrategy(jobDefinition.retryStrategy)
+    }
+    batchClient.registerJobDefinition(definitionRequest.build)
+  }
 
   /** Gets the status of a job by its Id, converted to a RunStatus
     *

From 60cd8dba265a88b1dcb31aa0dd62ae948ffb8818 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 15 Mar 2022 10:47:49 +0000
Subject: [PATCH 037/326] dump

---
 ...wsBatchAsyncBackendJobExecutionActor.scala |  2 +-
 .../backend/impl/aws/AwsBatchAttributes.scala | 26 ++++++++++---------
 .../impl/aws/AwsBatchConfiguration.scala      |  2 +-
 .../backend/impl/aws/AwsBatchJob.scala        |  4 +--
 .../impl/aws/AwsBatchJobDefinition.scala      |  8 +++---
 5 files changed, 22 insertions(+), 20 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 9e65e819988..9fb5ba7ca9f 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -183,7 +183,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       jobPaths, Seq.empty[AwsBatchParameter],
       configuration.awsConfig.region,
       Option(configuration.awsAuth),
-      configuration.fsxFileSystem)
+      configuration.fsxMntPoint)
   }
   /* Tries to abort the job in flight
    *
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index 9236b8342db..f1fd47c8ddd 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -60,7 +60,7 @@ case class AwsBatchAttributes(fileSystem: String,
                               duplicationStrategy: AwsBatchCacheHitDuplicationStrategy,
                               submitAttempts: Int Refined Positive,
                               createDefinitionAttempts: Int Refined Positive,
-                              fsxFileSystem: Option[List[String]])
+                              fsxMntPoint: Option[List[String]])
 
 object AwsBatchAttributes {
   lazy val Logger = LoggerFactory.getLogger(this.getClass)
@@ -70,12 +70,14 @@ object AwsBatchAttributes {
     "root",
     "filesystems",
     "filesystems.local.auth",
+    "filesystems.local.fsx",
+    "filesystems.local.localization",
+    "filesystems.local.caching.hashing-strategy",
+    "filesystems.local.caching.duplication-strategy",
     "filesystems.s3.auth",
     "filesystems.s3.caching.duplication-strategy",
-    "filesystems.local.caching.duplication-strategy",
     "auth",
     "numCreateDefinitionAttempts",
-    "filesystems.s3.duplication-strategy",
     "numSubmitAttempts",
     "default-runtime-attributes.scriptBucketName",
     "awsBatchRetryAttempts",
@@ -98,11 +100,10 @@ object AwsBatchAttributes {
       deprecatedKeys foreach { key => logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}") }
     }
 
-    def parseFSx(backendConfig: Config): Option[List[String]] = {
-      val fsxConfig = backendConfig.getStringList("filesystems.fsx")
-      fsxConfig.isEmpty match {
+    def parseFSx(config: List[String]): Option[List[String]] = {
+      config.isEmpty match {
         case true => None
-        case false => Some(fsxConfig.asScala.toList)
+        case false => Some(config)
       }
     }
 
@@ -140,10 +141,11 @@ object AwsBatchAttributes {
           }
       }
     
-    val fsx: ErrorOr[Option[List[String]]] = validate {backendConfig.hasPath("filesystems.fsx") match {
-      case true => parseFSx(backendConfig)
-      case false => None
-    }}
+    val fsxMntPoint: ErrorOr[Option[List[String]]] = validate {backendConfig.hasPath("filesystems.local.fsx") match {
+        case true => parseFSx(backendConfig.getStringList("filesystems.local.fsx").asScala.toList)
+        case false => None
+      }
+    }
 
     (
       fileSysStr,
@@ -152,7 +154,7 @@ object AwsBatchAttributes {
       duplicationStrategy,
       backendConfig.as[ErrorOr[Int Refined Positive]]("numSubmitAttempts"),
       backendConfig.as[ErrorOr[Int Refined Positive]]("numCreateDefinitionAttempts"),
-      fsx
+      fsxMntPoint
     ).tupled.map((AwsBatchAttributes.apply _).tupled) match {
       case Valid(r) => r
       case Invalid(f) =>
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
index b9278485305..0dea4e0e167 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
@@ -55,7 +55,7 @@ class AwsBatchConfiguration(val configurationDescriptor: BackendConfigurationDes
     case true => S3PathBuilderFactory(configurationDescriptor.globalConfig, configurationDescriptor.backendConfig)
     case false => PathBuilderFactory
   }
-  val fsxFileSystem = batchAttributes.fsxFileSystem
+  val fsxMntPoint = batchAttributes.fsxMntPoint
 }
 
 object AWSBatchStorageSystems {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 0c501774180..d7bbfc62271 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -84,7 +84,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                              parameters: Seq[AwsBatchParameter],
                              configRegion: Option[Region],
                              optAwsAuthMode: Option[AwsAuthMode] = None,
-                             fsxFileSystem: Option[List[String]]
+                             fsxMntPoint: Option[List[String]]
                             ) {
 
 
@@ -390,7 +390,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         jobPaths = jobPaths,
         inputs = inputs,
         outputs = outputs,
-        fsxFileSystem = fsxFileSystem)
+        fsxMntPoint = fsxMntPoint)
 
       val jobDefinitionBuilder = StandardAwsBatchJobDefinitionBuilder
       val jobDefinition = jobDefinitionBuilder.build(jobDefinitionContext)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index 3b8470c6c29..3e674255b95 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -150,8 +150,8 @@ trait AwsBatchJobDefinitionBuilder {
       case _ =>  context.commandText
     }
     val packedCommand = packCommand("/bin/bash", "-c", cmdName)
-    val volumes =  buildVolumes( context.runtimeAttributes.disks, context.fsxFileSystem)
-    val mountPoints = buildMountPoints( context.runtimeAttributes.disks, context.fsxFileSystem)
+    val volumes =  buildVolumes( context.runtimeAttributes.disks, context.fsxMntPoint)
+    val mountPoints = buildMountPoints( context.runtimeAttributes.disks, context.fsxMntPoint)
     val ulimits = buildUlimits( context.runtimeAttributes.ulimits)
     val containerPropsName = buildName(
       context.runtimeAttributes.dockerImage,
@@ -240,7 +240,7 @@ case class AwsBatchJobDefinitionContext(
             jobPaths: JobPaths,
             inputs: Set[AwsBatchInput],
             outputs: Set[AwsBatchFileOutput],
-            fsxFileSystem: Option[List[String]]){
+            fsxMntPoint: Option[List[String]]){
 
   override def toString: String = {
     new ToStringBuilder(this, ToStringStyle.JSON_STYLE)
@@ -253,7 +253,7 @@ case class AwsBatchJobDefinitionContext(
       .append("jobPaths", jobPaths)
       .append("inputs", inputs)
       .append("outputs", outputs)
-      .append("fsxFileSystem", fsxFileSystem)
+      .append("fsxMntPoint", fsxMntPoint)
       .build
   }
 }

From bb37a716ed83f9ad6209122eb324469af2b6d72c Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 15 Mar 2022 12:25:10 +0000
Subject: [PATCH 038/326] add aws batch preamble; increase the character limit
 for job definition command

---
 .../AwsBatchAsyncBackendJobExecutionActor.scala |  6 ++----
 .../impl/aws/AwsBatchJobDefinition.scala        | 17 ++++++++---------
 2 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 9fb5ba7ca9f..8d44fd84d36 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -126,9 +126,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   // |cd ${jobPaths.script.parent.pathWithoutScheme}; ls | grep -v script | xargs rm -rf; cd -
 
   private lazy val execScript =
-    s"""|df -h
-        |ls -lah ${jobPaths.script.pathWithoutScheme}
-        |find ${jobPaths.script.parent.pathWithoutScheme} -group root | grep -v script | xargs rm -vrf
+    s"""|#!$jobShell
         |${jobPaths.script.pathWithoutScheme}
         |""".stripMargin
 
@@ -414,7 +412,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   override def scriptPreamble: String = {
     configuration.fileSystem match {
       case  AWSBatchStorageSystems.s3 => ""
-      case _ => s""
+      case _ => s"find ${jobPaths.script.parent.pathWithoutScheme} -group root | grep -v script | xargs rm -vrf"
     }
   }
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index 3e674255b95..0bdc9e00cc1 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -186,15 +186,14 @@ trait AwsBatchJobDefinitionBuilder {
 
   private def packCommand(shell: String, options: String, mainCommand: String): Seq[String] = {
     val rc = new ListBuffer[String]()
-    // val lim = 1024
-    // val packedCommand = mainCommand.length() match {
-    //   case len if len <= lim => mainCommand
-    //   case len if len > lim => {
-    //     rc += "gzipdata" // This is hard coded in our agent and must be the first item
-    //     gzip(mainCommand)
-    //   }
-    // }
-    val packedCommand = mainCommand
+    val lim = 20480
+    val packedCommand = mainCommand.length() match {
+      case len if len <= lim => mainCommand
+      case len if len > lim => {
+        rc += "gzipdata" // This is hard coded in our agent and must be the first item
+        gzip(mainCommand)
+      }
+    }
     rc += shell
     rc += options
     rc += packedCommand

From 0b40de32cb0ead900116ab86da39c213d5b78c11 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 15 Mar 2022 13:10:19 +0000
Subject: [PATCH 039/326] add dockerhub authentication

---
 project/Dependencies.scala                    |  1 +
 .../impl/aws/AwsBatchConfiguration.scala      |  3 +-
 .../aws/AwsBatchInitializationActor.scala     | 65 +++++++++++++++++++
 .../scala/cromwell/backend/impl/aws/README.md | 14 ++++
 4 files changed, 82 insertions(+), 1 deletion(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 9b7103a48df..51de922881a 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -323,6 +323,7 @@ object Dependencies {
     "ecs",
     "ecr",
     "ecrpublic",
+    "secretsmanager",
   ).map(artifactName => "software.amazon.awssdk" % artifactName % awsSdkV)
 
   private val googleCloudDependencies = List(
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
index 0dea4e0e167..78bbb2d1a51 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
@@ -45,7 +45,6 @@ class AwsBatchConfiguration(val configurationDescriptor: BackendConfigurationDes
   val runtimeConfig = configurationDescriptor.backendRuntimeAttributesConfig
   val batchAttributes = AwsBatchAttributes.fromConfigs(awsConfig, configurationDescriptor.backendConfig)
   val awsAuth = batchAttributes.auth
-  val dockerCredentials = BackendDockerConfiguration.build(configurationDescriptor.backendConfig).dockerCredentials
   val fileSystem =
     configurationDescriptor.backendConfig.hasPath("filesystems.s3") match {
       case true =>  "s3"
@@ -55,6 +54,8 @@ class AwsBatchConfiguration(val configurationDescriptor: BackendConfigurationDes
     case true => S3PathBuilderFactory(configurationDescriptor.globalConfig, configurationDescriptor.backendConfig)
     case false => PathBuilderFactory
   }
+  val dockerCredentials = BackendDockerConfiguration.build(configurationDescriptor.backendConfig).dockerCredentials
+  val dockerToken: Option[String] = dockerCredentials map { _.token }
   val fsxMntPoint = batchAttributes.fsxMntPoint
 }
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
index 93f06cd3477..347e697e55b 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
@@ -35,6 +35,8 @@ import java.io.IOException
 
 import akka.actor.ActorRef
 import software.amazon.awssdk.auth.credentials.AwsCredentialsProvider
+import software.amazon.awssdk.services.secretsmanager.SecretsManagerClient
+import software.amazon.awssdk.services.secretsmanager.model.{CreateSecretRequest, SecretsManagerException, SecretListEntry, UpdateSecretRequest}
 import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
 import cromwell.backend.standard.{StandardInitializationActor, StandardInitializationActorParams, StandardValidatedRuntimeAttributesBuilder}
 import cromwell.backend.{BackendConfigurationDescriptor, BackendWorkflowDescriptor, BackendInitializationData}
@@ -42,8 +44,12 @@ import cromwell.core.io.DefaultIoCommandBuilder
 import cromwell.core.io.AsyncIoActorClient
 import cromwell.core.path.Path
 import wom.graph.CommandCallNode
+import org.apache.commons.codec.binary.Base64
+import spray.json.{JsObject, JsString}
+import org.slf4j.{Logger, LoggerFactory}
 
 import scala.concurrent.Future
+import scala.collection.JavaConverters._
 
 case class AwsBatchInitializationActorParams
 (
@@ -65,6 +71,8 @@ object AwsBatchInitializationActor {
 class AwsBatchInitializationActor(params: AwsBatchInitializationActorParams)
   extends StandardInitializationActor(params) with AsyncIoActorClient {
 
+  val Log: Logger = LoggerFactory.getLogger(AwsBatchInitializationActor.getClass)
+
   override lazy val ioActor = params.ioActor
   private val configuration = params.configuration
   override implicit val system = context.system
@@ -87,6 +95,63 @@ class AwsBatchInitializationActor(params: AwsBatchInitializationActorParams)
   private lazy val provider: Future[AwsCredentialsProvider] =
     Future { configuration.awsAuth.provider() }
 
+  lazy val secretsClient: SecretsManagerClient = {
+    val builder = SecretsManagerClient.builder()
+    configureClient(builder, Option(configuration.awsAuth), configuration.awsConfig.region)
+  }
+
+  private def storePrivateDockerToken(token: String) = {
+    try {
+
+      val secretName: String = "cromwell/credentials/dockerhub"
+
+      // Check if secret already exists
+      // If exists, update it otherwise create it
+      val secretsList: List[SecretListEntry] = secretsClient.listSecrets().secretList().asScala.toList
+
+      if(secretsList.exists(_.name == secretName)){
+        val secretRequest: UpdateSecretRequest = UpdateSecretRequest.builder()
+          .secretId(secretName)
+          .secretString(token)
+          .build();
+
+        secretsClient.updateSecret(secretRequest);
+
+        Log.info(s"Secret '$secretName' was updated.")
+      } else {
+        val secretRequest: CreateSecretRequest = CreateSecretRequest.builder()
+          .name(secretName)
+          .secretString(token)
+          .build()
+
+        secretsClient.createSecret(secretRequest)
+
+        Log.info(s"Secret '$secretName' was created.")
+      }
+    }
+    catch {
+      case e: SecretsManagerException => Log.warn(e.awsErrorDetails().errorMessage())
+    }
+  }
+
+  val privateDockerUnencryptedToken: Option[String] = configuration.dockerToken flatMap { dockerToken =>
+    new String(Base64.decodeBase64(dockerToken)).split(':') match {
+      case Array(username, password) =>
+        // unencrypted tokens are base64-encoded username:password
+        Option(JsObject(
+          Map(
+            "username" -> JsString(username),
+            "password" -> JsString(password)
+          )).compactPrint)
+      case _ => throw new RuntimeException(s"provided dockerhub token '$dockerToken' is not a base64-encoded username:password")
+    }
+  }
+
+  privateDockerUnencryptedToken match {
+    case Some(token) => storePrivateDockerToken(token)
+    case None => Log.debug("No docker token was passed")
+  }
+
   override lazy val workflowPaths: Future[AwsBatchWorkflowPaths] = for {
     prov <- provider
   } yield new AwsBatchWorkflowPaths(workflowDescriptor, prov, configuration)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index f0c2ee2eb03..62206005546 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -379,6 +379,20 @@ the AWS Services involved in the processing of the work.
 NOTE: ECS Agent permissions currently must use the permissions as outlined
       in the AmazonEC2ContainerServiceForEC2Role managed policy.
 
+Features
+---------------------
+### Docker Hub Authentication
+
+Docker Hub authentication for AWS Backend enable users to access and use private Docker containers.
+
+1. Create an access token in Docker Hub;
+2. Encode the following string as base64: `<dockerhub-username>:<dockerhub-acess-token>`
+3. Place the following snippet into `cromwell.conf` file under `config`:
+```
+dockerhub { token = "<enconded-string-from-point-2>" }
+```
+
+
 Future considerations
 ---------------------
 

From cb134359e3871ace7fb19da04634d58d81ac3d17 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 15 Mar 2022 13:12:24 +0000
Subject: [PATCH 040/326] move features section to top

---
 .../scala/cromwell/backend/impl/aws/README.md | 27 ++++++++++---------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 62206005546..b766002af1c 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -29,6 +29,20 @@ defined.
 This infrastructure and all the associated configuration still exists; however,
 it is moved out of the Cromwell configuration.
 
+Features
+---------------------
+### Docker Hub Authentication
+
+Docker Hub authentication for AWS Backend enable users to access and use private Docker containers.
+
+1. Create an access token in Docker Hub;
+2. Encode the following string as base64: `<dockerhub-username>:<dockerhub-acess-token>`
+3. Place the following snippet into `cromwell.conf` file under `config`:
+```
+dockerhub { token = "<enconded-string-from-point-2>" }
+```
+
+
 AWS Batch
 ---------
 
@@ -379,19 +393,6 @@ the AWS Services involved in the processing of the work.
 NOTE: ECS Agent permissions currently must use the permissions as outlined
       in the AmazonEC2ContainerServiceForEC2Role managed policy.
 
-Features
----------------------
-### Docker Hub Authentication
-
-Docker Hub authentication for AWS Backend enable users to access and use private Docker containers.
-
-1. Create an access token in Docker Hub;
-2. Encode the following string as base64: `<dockerhub-username>:<dockerhub-acess-token>`
-3. Place the following snippet into `cromwell.conf` file under `config`:
-```
-dockerhub { token = "<enconded-string-from-point-2>" }
-```
-
 
 Future considerations
 ---------------------

From b42341e28615107f083fa5e003947432d14b927c Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 15 Mar 2022 14:23:57 +0000
Subject: [PATCH 041/326] update diagram1

---
 .../scala/cromwell/backend/impl/aws/README.md | 53 +++++--------------
 1 file changed, 14 insertions(+), 39 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index b766002af1c..07023224cff 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -42,7 +42,6 @@ Docker Hub authentication for AWS Backend enable users to access and use private
 dockerhub { token = "<enconded-string-from-point-2>" }
 ```
 
-
 AWS Batch
 ---------
 
@@ -83,47 +82,23 @@ will auto-expand,
 generated shell scripts from S3 that contain the instructions of the workflow
 task 
 
-```text
-                  +-------------+
-                  |             |
-                  |  AWS Batch  |
-                  |             |
-                  +------+------+
-                         |
-                         |
-                         |
-                         |
-                         |
-        +----------------v------------------+
-        |                                   |
-        |  Elastic Container Service (ECS)  |
-        |                                   |
-        +----------------+------------------+
-                         |
-                         |
-                         |
-                         |
-                         |
-+------------------------v-------------------------+
-|                                                  |
-|  AutoScaling Group                               |
-|                                                  |
-| +---------------------------------+              |
-| |                                 |              |
-| |  EC2 Instance                   |              |
-| |                                 |              |
-| |  +--------------------+         |              |
-| |  |                    |         |              |
-| |  |  Docker Container  |         |              |
-| |  |                    |         |              |
-| |  +--------------------+  ...    |              |
-| |                                 |              |
-| +---------------------------------+     ...      |
-|                                                  |
-+--------------------------------------------------+
 
+```mermaid
+  flowchart LR
+    subgraph auto ["AutoScaling Group"]
+      direction RL
+      subgraph ec2_1 ["EC2 Instance"]
+          docker_1["Docker Container"]
+      end
+      subgraph ec2_2 ["EC2 Instance"]
+          docker_2["Docker Container"]
+      end
+    end
+    batch["AWS Batch"]-->ecs["Elastic Container Service (ECS)"];
+    ecs-->auto;
 ```
 
+
 Cromwell AWS Batch Backend
 --------------------------
 

From d4dc38d505e42d430019f14cacadbc7639c1af7e Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 15 Mar 2022 14:31:09 +0000
Subject: [PATCH 042/326] update diagram 2 and 3

---
 .../scala/cromwell/backend/impl/aws/README.md | 78 +++++--------------
 1 file changed, 18 insertions(+), 60 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 07023224cff..52d43f01d88 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -106,32 +106,14 @@ There are several scala classes as part of the AWS Batch Backend, but
 the primary classes involved in running the backend are shown below. The
 arrows represent the flow of job submission.
 
-```text
-    +----------------------------------------+
-    |                                        |
-    |  AwsBatchBackendLifecycleActorFactory  |
-    |                                        |
-    +------------------+---------------------+
-                       |
-                       |
-                       |
-                       |
-                       |
-    +------------------v----------------------+
-    |                                         |
-    |  AwsBatchAsyncBackendJobExecutionActor  |
-    |                                         |
-    +------------------+----------------------+
-                       |
-                       |
-                       |
-                       |
-                       |
-               +-------v-------+                 +-------------------------+
-               |               |                 |                         |
-               |  AwsBatchJob  +----------------->  AwsBatchJobDefinition  |
-               |               |                 |                         |
-               +---------------+                 +-------------------------+
+```mermaid
+  flowchart TD;
+    factory[AwsBatchBackendLifecycleActorFactory]
+    execution[AwsBatchAsyncBackendJobExecutionActor]
+    job[AwsBatchJob]
+    definition[AwsBatchJobDefinition]
+    
+    factory-->execution-->job-->definition;
 ```
 
 1. The `AwsBatchBackendLifecycleActorFactory` class is configured by the user
@@ -150,41 +132,17 @@ arrows represent the flow of job submission.
 
 AWS Batch Job Instantiation
 ---------------------------
-```text
-             +--------------------+
-             |                    |
-             |  Cromwell Backend  |
-             |                    |
-             +---------+----------+
-                       |
-                       |
-                   SubmitJob
-                       |
-                       |
-                +------v------+
-                |             |
-                |  AWS Batch  |
-                |             |
-                +------^------+
-                       |
-                       |
-                     Polls
-                       |
-                       |
-                +------+------+
-                |             |
-                |  ECS Agent  |
-                |             |
-                +------+------+
-                       |
-           Creates, Launches and Monitors
-                       |
-              +--------v---------+ 
-              |                  |
-              |  Task Container  |
-              |                  |
-              +------------------+
 
+```mermaid
+  flowchart TD;
+    cromwell[Cromwell Backend]
+    batch[AWS Batch]
+    ecs[ECS Agent]
+    task[Task Container]
+    
+    cromwell-- SubmitJob -->batch
+    batch-- Polls -->ecs
+    ecs-- Creates, Launches and Monitors -->task
 ```
 
 When a Cromwell task begins, the Cromwell backend will call the SubmitJob

From 355648388fcac88d61a68e087d384edc7a9fb5d7 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 15 Mar 2022 15:14:47 +0000
Subject: [PATCH 043/326] last diagram

---
 .../scala/cromwell/backend/impl/aws/README.md | 116 +++++++++---------
 1 file changed, 60 insertions(+), 56 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 52d43f01d88..a898a61e4e4 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -134,11 +134,11 @@ AWS Batch Job Instantiation
 ---------------------------
 
 ```mermaid
-  flowchart TD;
-    cromwell[Cromwell Backend]
-    batch[AWS Batch]
-    ecs[ECS Agent]
-    task[Task Container]
+  flowchart TD
+    cromwell["Cromwell Backend"]
+    batch["AWS Batch"]
+    ecs["ECS Agent"]
+    task["Task Container"]
     
     cromwell-- SubmitJob -->batch
     batch-- Polls -->ecs
@@ -252,58 +252,62 @@ The flow described below represents the permissions needed by each stage, from
 Cromwell server through the task running. This includes the permissions needed for
 the AWS Services involved in the processing of the work.
 
-```text
-+----------------------------+
-|                            |  s3:GetObject on bucket for workflow and script bucket
-|                            |  s3:ListObjects on script bucket
-|                            |  s3:PutObject on script bucket
-|          Cromwell          |  batch:RegisterTaskDefinition
-|                            |  batch:SubmitJob
-|                            |  batch:DescribeJobs
-|                            |  batch:DescribeJobDefinitions
-+-------------+--------------+
-              |
-              |
-              |
-+-------------v--------------+
-|                            |  AWSBatchServiceRole managed policy - described at:
-|          AWS Batch         |
-|                            |     https://docs.aws.amazon.com/batch/latest/userguide/service_IAM_role.html
-+-------------+--------------+
-              |
-              |
-              |
-+-------------v--------------+
-|                            |  AWSServiceRoleForECS Service-linked role, documented at:
-|                            |
-| Elastic Container Service  |     https://docs.aws.amazon.com/AmazonECS/latest/developerguide/using-service-linked-roles.html
-|                            |
-|  (See discussion #1 below) |  AmazonEC2ContainerServiceAutoscaleRole managed policy - described at:
-|                            |
-|                            |     https://docs.aws.amazon.com/AmazonECS/latest/developerguide/autoscale_IAM_role.html
-+-------------+--------------+
-              |
-              |
-              |
-+-------------v--------------+
-|                            |
-|                            |  AmazonEC2ContainerServiceforEC2Role managed policy, described at:
-| ECS Agent (running on EC2) |     https://docs.aws.amazon.com/AmazonECS/latest/developerguide/instance_IAM_role.html (EC2)
-|                            |    OR
-|                            |  AmazonECSTaskExecutionRolePolicy managed policy, described at:  
-|                            |     https://docs.aws.amazon.com/AmazonECS/latest/developerguide/task_execution_IAM_role.html (Fargate)
-+-------------+--------------+ 
-              |
-              |
-              |
-+-------------v--------------+
-|                            |  Task Role permissions. These are user defined, but ecs-tasks.amazon.com must have sts:AssumeRole trust relationship defined. Documentation:
-|       Task Container       |
-|                            |     https://docs.aws.amazon.com/AmazonECS/latest/developerguide/task_IAM_role.html
-|                            |  s3:GetObject, s3:PutObject, s3:ListObjects
-+----------------------------+
-```
+```mermaid
+  flowchart TD
+    cromwell["Cromwell"]
+    batch["AWS Batch"]
+    ecs["Elastic Container Service\n\n(See discussion #1 below)"]
+    ec2["ECS Agent (running on EC2)"]
+    task["Task Container"]
+
+    cromwell_desc["s3:GetObject on bucket for workflow and script bucket
+                   s3:ListObjects on script bucket
+                   s3:PutObject on script bucket
+                   batch:RegisterTaskDefinition
+                   batch:SubmitJob
+                   batch:DescribeJobs
+                   batch:DescribeJobDefinitions"]
+
+    batch_desc["AWSBatchServiceRole managed policy, described <a href='https://docs.aws.amazon.com/batch/latest/userguide/service_IAM_role.html'>here</a>"]
+
+    ecs_desc["AWSServiceRoleForECS Service-linked role, described <a href='https://docs.aws.amazon.com/AmazonECS/latest/developerguide/using-service-linked-roles.html'>here</a>
+    
+              AmazonEC2ContainerServiceAutoscaleRole managed policy, described <a href='https://docs.aws.amazon.com/AmazonECS/latest/developerguide/autoscale_IAM_role.html'>here</a>"]
+
+    ec2_desc["(EC2) AmazonEC2ContainerServiceforEC2Role managed policy, described <a href='https://docs.aws.amazon.com/AmazonECS/latest/developerguide/instance_IAM_role.html'>here</a>
+    
+              (Fargate) AmazonECSTaskExecutionRolePolicy managed policy, described <a href='https://docs.aws.amazon.com/AmazonECS/latest/developerguide/task_execution_IAM_role.html'>here</a>"]
+
+    task_desc["Task Role permissions.
+              These are user defined, but ecs-tasks.amazon.com must have sts:AssumeRole trust relationship defined.
+              Documentation <a href='https://docs.aws.amazon.com/AmazonECS/latest/developerguide/task_IAM_role.html'>here</a>
+              s3:GetObject
+              s3:PutObject
+              s3:ListObjects"]
 
+    subgraph 1 [" "]
+      direction RL
+      cromwell_desc-->cromwell
+    end
+    subgraph 2 [" "]
+      direction RL
+      batch_desc-->batch
+    end
+    subgraph 3 [" "]
+      direction RL
+      ecs_desc-->ecs
+    end
+    subgraph 4 [" "]
+      direction RL
+      ec2_desc-->ec2
+    end
+    subgraph 5 [" "]
+      direction RL
+      task_desc-->task
+    end
+
+    1-->2-->3-->4-->5
+```
 
 1. ECS has several sets of permissions for various items. AWS Batch, however,
    does not take advantage of certain features of ECS, most importantly

From 26089fed992605ce709770442133bbdbf5241061 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 15 Mar 2022 15:20:45 +0000
Subject: [PATCH 044/326] add documentation

---
 docs/RuntimeAttributes.md                     |  4 +-
 .../scala/cromwell/backend/impl/aws/README.md | 47 +++++++++++++++++++
 2 files changed, 50 insertions(+), 1 deletion(-)

diff --git a/docs/RuntimeAttributes.md b/docs/RuntimeAttributes.md
index c31b6fbbf41..1f16e125eff 100644
--- a/docs/RuntimeAttributes.md
+++ b/docs/RuntimeAttributes.md
@@ -379,7 +379,9 @@ runtime {
 
 *Default: _0_*
 
-This runtime attribute adds support to [*AWS Batch Automated Job Retries*](https://docs.aws.amazon.com/batch/latest/userguide/job_retries.html) which makes it possible to tackle transient job failures. For example, if a task fails due to a timeout from accessing an external service, then this option helps re-run the failed the task without having to re-run the entire workflow. It takes an Int, between 1 and 10, as a value that indicates the maximum number of times AWS Batch should retry a failed task. If the value 0 is passed, the [*Retry Strategy*](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#retryStrategy) will not be added to the job definiton and the task will run just once.
+This runtime attribute adds support to [*AWS Batch Automated Job Retries*](https://docs.aws.amazon.com/batch/latest/userguide/job_retries.html) which makes it possible to tackle transient job failures. For example, if a task fails due to a timeout from accessing an external service, then this option helps re-run the failed the task without having to re-run the entire workflow. This option is also very useful when using SPOT instances.
+
+It takes an Int, between 1 and 10, as a value that indicates the maximum number of times AWS Batch should retry a failed task. If the value 0 is passed, the [*Retry Strategy*](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#retryStrategy) will not be added to the job definiton and the task will run just once.
 
 ```
 runtime {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index a898a61e4e4..4cb7e67bb4b 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -42,6 +42,53 @@ Docker Hub authentication for AWS Backend enable users to access and use private
 dockerhub { token = "<enconded-string-from-point-2>" }
 ```
 
+### `awsBatchRetryAttempts`
+
+*Default: _0_*
+
+This runtime attribute adds support to [*AWS Batch Automated Job Retries*](https://docs.aws.amazon.com/batch/latest/userguide/job_retries.html) which makes it possible to tackle transient job failures. For example, if a task fails due to a timeout from accessing an external service, then this option helps re-run the failed the task without having to re-run the entire workflow. This option is also very useful when using SPOT instances.
+
+It takes an Int, between 1 and 10, as a value that indicates the maximum number of times AWS Batch should retry a failed task. If the value 0 is passed, the [*Retry Strategy*](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#retryStrategy) will not be added to the job definiton and the task will run just once.
+
+```
+runtime {
+  awsBatchRetryAttempts: integer
+}
+```
+
+### `ulimits`
+
+*Default: _empty_*
+
+A list of [`ulimits`](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#containerProperties) values to set in the container. This parameter maps to `Ulimits` in the [Create a container](https://docs.docker.com/engine/api/v1.38/) section of the [Docker Remote API](https://docs.docker.com/engine/api/v1.38/) and the `--ulimit` option to [docker run](https://docs.docker.com/engine/reference/commandline/run/).
+
+```
+"ulimits": [
+  {
+    "name": string,
+    "softLimit": integer,
+    "hardLimit": integer
+  }
+  ...
+]
+```
+Parameter description:
+
+- `name`
+  - The `type` of the `ulimit`.
+  - Type: String
+  - Required: Yes, when `ulimits` is used.
+
+- `softLimit`
+  - The soft limit for the `ulimit` type.
+  - Type: Integer
+  - Required: Yes, when `ulimits` is used.
+
+- `hardLimit`
+  - The hard limit for the `ulimit` type.
+  - Type: Integer
+  - Required: Yes, when `ulimits` is used.
+
 AWS Batch
 ---------
 

From 2971fa696e9cdea42c063bd1903fe3205de2ef84 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 15 Mar 2022 15:33:09 +0000
Subject: [PATCH 045/326] update readme

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 2f053f1a821..bb313473f58 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,9 @@
 [![Build Status](https://travis-ci.com/broadinstitute/cromwell.svg?branch=develop)](https://travis-ci.com/broadinstitute/cromwell?branch=develop)
 [![codecov](https://codecov.io/gh/broadinstitute/cromwell/branch/develop/graph/badge.svg)](https://codecov.io/gh/broadinstitute/cromwell)
 
-## Welcome to Cromwell
+## Welcome to "AWS-friendly" Cromwell
+
+More information regarding AWS features can be found [here](https://github.com/henriqueribeiro/cromwell/tree/master/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws)
 
 Cromwell is an open-source Workflow Management System for bioinformatics. Licensing is [BSD 3-Clause](LICENSE.txt).
 

From 600df43845cb3a47374179a4dc3926116d29abbd Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Wed, 16 Mar 2022 18:47:07 +0000
Subject: [PATCH 046/326] move rm command to the batch command

---
 .../impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala       | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 8d44fd84d36..34334449587 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -127,6 +127,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
   private lazy val execScript =
     s"""|#!$jobShell
+        |find ${jobPaths.script.parent.pathWithoutScheme} -group root | grep -v script | xargs rm -vrf
         |${jobPaths.script.pathWithoutScheme}
         |""".stripMargin
 
@@ -412,7 +413,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   override def scriptPreamble: String = {
     configuration.fileSystem match {
       case  AWSBatchStorageSystems.s3 => ""
-      case _ => s"find ${jobPaths.script.parent.pathWithoutScheme} -group root | grep -v script | xargs rm -vrf"
+      case _ => ""
     }
   }
 

From 2773507423742c5ece540fcc9e748e16ef07be83 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Fri, 18 Mar 2022 15:04:51 +0100
Subject: [PATCH 047/326] Feature/ecr private (#2)

* correct pull identifier for local docker hashing on ECR private

* removed check for deprecated attributes, causing assembly to fail

* catch missing RC file and retry job after 5min sleep instead of failing WF
---
 .../StandardAsyncExecutionActor.scala         | 32 ++++++++++++++++---
 .../cromwell/docker/local/DockerCliFlow.scala | 30 ++++++++++-------
 .../backend/impl/aws/AwsBatchJob.scala        | 26 +++++++++------
 3 files changed, 63 insertions(+), 25 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index ea07651e825..df20a8b318f 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -1232,8 +1232,10 @@ trait StandardAsyncExecutionActor
     */
   def handleExecutionResult(status: StandardAsyncRunState,
                             oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
-
+    
+    // get the memory retry code.
     def memoryRetryRC: Future[Boolean] = {
+      // convert int to boolean
       def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
         codeAsOption match {
           case Some(codeAsString) =>
@@ -1250,14 +1252,14 @@ trait StandardAsyncExecutionActor
           case None => false
         }
       }
-
+      // read if the file exists
       def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] = {
         if (fileExists)
           asyncIo.contentAsStringAsync(jobPaths.memoryRetryRC, None, failOnOverflow = false).map(Option(_))
         else
           Future.successful(None)
       }
-
+      //finally : assign the yielded variable
       for {
         fileExists <- asyncIo.existsAsync(jobPaths.memoryRetryRC)
         retryCheckRCAsOption <- readMemoryRetryRCFile(fileExists)
@@ -1265,11 +1267,31 @@ trait StandardAsyncExecutionActor
       } yield retryWithMoreMemory
     }
 
+    // get the exit code of the job.
+    def JobExitCode: Future[String] = {
+      
+      // read if the file exists
+      def readRCFile(fileExists: Boolean): Future[String] = {
+        if (fileExists)
+          asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
+        else
+          jobLogger.warn("RC file not found. Setting job to failed & waiting 5m before retry.")
+          Thread.sleep(300000)
+          Future("1")
+      }
+      //finally : assign the yielded variable
+      for {
+        fileExists <- asyncIo.existsAsync(jobPaths.returnCode)
+        jobRC <- readRCFile(fileExists)
+      } yield jobRC
+    }
+
+    // get path to sderr
     val stderr = jobPaths.standardPaths.error
     lazy val stderrAsOption: Option[Path] = Option(stderr)
-
+    // get the three needed variables, using functions above or direct assignment.
     val stderrSizeAndReturnCodeAndMemoryRetry = for {
-      returnCodeAsString <- asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
+      returnCodeAsString <- JobExitCode
       // Only check stderr size if we need to, otherwise this results in a lot of unnecessary I/O that
       // may fail due to race conditions on quickly-executing jobs.
       stderrSize <- if (failOnStdErr) asyncIo.sizeAsync(stderr) else Future.successful(0L)
diff --git a/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliFlow.scala b/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliFlow.scala
index f6bf6e96d4c..9be67d87de2 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliFlow.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliFlow.scala
@@ -109,17 +109,25 @@ object DockerCliFlow {
   /** Utility for converting the flow image id to the format output by the docker cli. */
   private def cliKeyFromImageId(context: DockerInfoContext): DockerCliKey = {
     val imageId = context.dockerImageID
-    (imageId.host, imageId.repository) match {
-      case (None, None) =>
-        // For docker hub images (host == None), and don't include "library".
-        val repository = imageId.image
-        val tag = imageId.reference
-        DockerCliKey(repository, tag)
-      case _ =>
-        // For all other images, include the host and repository.
-        val repository = s"${imageId.hostAsString}${imageId.nameWithDefaultRepository}"
-        val tag = imageId.reference
-        DockerCliKey(repository, tag)
+    // private aws ECR does not have library, check for ECR in docker host.
+    if ( imageId.hostAsString.matches(raw"\d+\.dkr\.ecr\..+\.amazonaws\.com/") ) {
+       val repository = s"${imageId.hostAsString}${imageId.image}"
+       val tag = imageId.reference
+       DockerCliKey(repository, tag)
+    } else {
+      (imageId.host, imageId.repository) match {
+        case (None, None) =>
+          // For docker hub images (host == None), and don't include "library".
+          val repository = imageId.image
+          val tag = imageId.reference
+          DockerCliKey(repository, tag)
+        case _ =>
+          // For all other images, include the host and repository.
+          val repository = s"${imageId.hostAsString}${imageId.nameWithDefaultRepository}"
+          val tag = imageId.reference
+          DockerCliKey(repository, tag)
+      
+       }
     }
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 0db547242c1..95aaef26a05 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -405,12 +405,12 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         val existingDefinition = describeJobDefinitionResponse.jobDefinitions().asScala.toList.sortWith(_.revision > _.revision).head
 
         //TODO test this
-        if (existingDefinition.containerProperties().memory() != null || existingDefinition.containerProperties().vcpus() != null) {
-          Log.warn("the job definition '{}' has deprecated configuration for memory and vCPU and will be replaced", existingDefinition.jobDefinitionName())
-          registerJobDefinition(jobDefinition, jobDefinitionContext).jobDefinitionArn()
-        } else {
-          existingDefinition.jobDefinitionArn()
-        }
+        //if (existingDefinition.containerProperties().memory() != null || existingDefinition.containerProperties().vcpus() != null) {
+        //  Log.warn("the job definition '{}' has deprecated configuration for memory and vCPU and will be replaced", existingDefinition.jobDefinitionName())
+        //  registerJobDefinition(jobDefinition, jobDefinitionContext).jobDefinitionArn()
+        //} else {
+        existingDefinition.jobDefinitionArn()
+        //}
       } else {
         Log.debug(s"No job definition found. Creating job definition: ${jobDefinition.name}")
 
@@ -479,10 +479,18 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     jobDetail
   }
 
-  def rc(detail: JobDetail): Integer = {
-    detail.container.exitCode
+  // code didn't get into the null block, so possibly not needed.
+  def rc(detail: JobDetail): Integer =  {
+    if (detail.container.exitCode == null) {
+        // if exitCode is not present, return failed ( exitCode == 127 for command not found)
+        Log.info("rc value missing. Setting to failed and sleeping for 30s...")
+        Thread.sleep(30000)
+        127
+    } else {
+        Log.info("rc value found. Setting to '{}'",detail.container.exitCode.toString())
+        detail.container.exitCode
+    }
   }
-
   def output(detail: JobDetail): String = {
     val events: Seq[OutputLogEvent] = cloudWatchLogsClient.getLogEvents(GetLogEventsRequest.builder
       // http://aws-java-sdk-javadoc.s3-website-us-west-2.amazonaws.com/latest/software/amazon/awssdk/services/batch/model/ContainerDetail.html#logStreamName--

From bad8e112480d1d2c24cec580b0dab7a92a740de7 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Sun, 20 Mar 2022 07:35:57 +0100
Subject: [PATCH 048/326] Corrected Syntax on retunCode Checking

---
 .../backend/standard/StandardAsyncExecutionActor.scala         | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index df20a8b318f..8ec3de54487 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -1274,10 +1274,11 @@ trait StandardAsyncExecutionActor
       def readRCFile(fileExists: Boolean): Future[String] = {
         if (fileExists)
           asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
-        else
+        else {
           jobLogger.warn("RC file not found. Setting job to failed & waiting 5m before retry.")
           Thread.sleep(300000)
           Future("1")
+        }
       }
       //finally : assign the yielded variable
       for {

From 0f1a23624ad666cc457ca4609890323778a614fc Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Sun, 20 Mar 2022 17:39:15 +0100
Subject: [PATCH 049/326] Corrected Syntax on retunCode Checking (#3)

---
 .../backend/standard/StandardAsyncExecutionActor.scala         | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index df20a8b318f..8ec3de54487 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -1274,10 +1274,11 @@ trait StandardAsyncExecutionActor
       def readRCFile(fileExists: Boolean): Future[String] = {
         if (fileExists)
           asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
-        else
+        else {
           jobLogger.warn("RC file not found. Setting job to failed & waiting 5m before retry.")
           Thread.sleep(300000)
           Future("1")
+        }
       }
       //finally : assign the yielded variable
       for {

From 8f6525cab264ab98445e23c0f54fde7080d9541d Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Thu, 24 Mar 2022 14:41:55 +0100
Subject: [PATCH 050/326] Added documentation for ECR Call Caching

---
 .../scala/cromwell/backend/impl/aws/README.md | 339 ++++++++++--------
 1 file changed, 189 insertions(+), 150 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index f0c2ee2eb03..fbbd7d50d67 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -29,6 +29,106 @@ defined.
 This infrastructure and all the associated configuration still exists; however,
 it is moved out of the Cromwell configuration.
 
+Features
+---------------------
+### Docker Hub Authentication
+
+Docker Hub authentication for AWS Backend enable users to access and use private Docker containers.
+
+1. Create an access token in Docker Hub;
+2. Encode the following string as base64: `<dockerhub-username>:<dockerhub-acess-token>`
+3. Place the following snippet into `cromwell.conf` file under `config`:
+```
+dockerhub { token = "<enconded-string-from-point-2>" }
+```
+
+### `awsBatchRetryAttempts`
+
+*Default: _0_*
+
+This runtime attribute adds support to [*AWS Batch Automated Job Retries*](https://docs.aws.amazon.com/batch/latest/userguide/job_retries.html) which makes it possible to tackle transient job failures. For example, if a task fails due to a timeout from accessing an external service, then this option helps re-run the failed the task without having to re-run the entire workflow. This option is also very useful when using SPOT instances.
+
+It takes an Int, between 1 and 10, as a value that indicates the maximum number of times AWS Batch should retry a failed task. If the value 0 is passed, the [*Retry Strategy*](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#retryStrategy) will not be added to the job definiton and the task will run just once.
+
+```
+runtime {
+  awsBatchRetryAttempts: integer
+}
+```
+
+### `ulimits`
+
+*Default: _empty_*
+
+A list of [`ulimits`](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#containerProperties) values to set in the container. This parameter maps to `Ulimits` in the [Create a container](https://docs.docker.com/engine/api/v1.38/) section of the [Docker Remote API](https://docs.docker.com/engine/api/v1.38/) and the `--ulimit` option to [docker run](https://docs.docker.com/engine/reference/commandline/run/).
+
+```
+"ulimits": [
+  {
+    "name": string,
+    "softLimit": integer,
+    "hardLimit": integer
+  }
+  ...
+]
+```
+Parameter description:
+
+- `name`
+  - The `type` of the `ulimit`.
+  - Type: String
+  - Required: Yes, when `ulimits` is used.
+
+- `softLimit`
+  - The soft limit for the `ulimit` type.
+  - Type: Integer
+  - Required: Yes, when `ulimits` is used.
+
+- `hardLimit`
+  - The hard limit for the `ulimit` type.
+  - Type: Integer
+  - Required: Yes, when `ulimits` is used.
+
+### Call Caching with ECR private
+
+AWS ECR is a private container registry, for which access can be regulated using IAM. Call caching is possible by setting up the following configuration:
+
+1. Setup a user with pull-access to ECR, then use this role to run cromwell
+
+profile default region must be setup in ~/.aws/config: 
+```
+[profile MyECR-user]
+region = eu-west-1
+```
+Provide the profile when launching cromwell:
+```
+AWS_PROFILE=MyECR-user java .... -jar cromwell.jar run .... 
+```
+
+Other methods to provide the profile might also work, but are not tested (Environment, roles, ...)
+
+2. Enable call caching in the cromwell configuration
+
+The following statement enable call caching, with "local" hash checking:
+
+```
+call-caching {
+  enabled = true
+  invalidate-bad-cache-results = true
+}
+docker {
+   hash-lookup {
+       method = "local"
+   }
+}
+```
+
+Notes:
+- local hashing means that all used containers are pulled. Make sure you have enough storage
+- enable a database to make the cache persistent over cromwell restarts
+
+
+
 AWS Batch
 ---------
 
@@ -69,47 +169,23 @@ will auto-expand,
 generated shell scripts from S3 that contain the instructions of the workflow
 task 
 
-```text
-                  +-------------+
-                  |             |
-                  |  AWS Batch  |
-                  |             |
-                  +------+------+
-                         |
-                         |
-                         |
-                         |
-                         |
-        +----------------v------------------+
-        |                                   |
-        |  Elastic Container Service (ECS)  |
-        |                                   |
-        +----------------+------------------+
-                         |
-                         |
-                         |
-                         |
-                         |
-+------------------------v-------------------------+
-|                                                  |
-|  AutoScaling Group                               |
-|                                                  |
-| +---------------------------------+              |
-| |                                 |              |
-| |  EC2 Instance                   |              |
-| |                                 |              |
-| |  +--------------------+         |              |
-| |  |                    |         |              |
-| |  |  Docker Container  |         |              |
-| |  |                    |         |              |
-| |  +--------------------+  ...    |              |
-| |                                 |              |
-| +---------------------------------+     ...      |
-|                                                  |
-+--------------------------------------------------+
 
+```mermaid
+  flowchart LR
+    subgraph auto ["AutoScaling Group"]
+      direction RL
+      subgraph ec2_1 ["EC2 Instance"]
+          docker_1["Docker Container"]
+      end
+      subgraph ec2_2 ["EC2 Instance"]
+          docker_2["Docker Container"]
+      end
+    end
+    batch["AWS Batch"]-->ecs["Elastic Container Service (ECS)"];
+    ecs-->auto;
 ```
 
+
 Cromwell AWS Batch Backend
 --------------------------
 
@@ -117,32 +193,14 @@ There are several scala classes as part of the AWS Batch Backend, but
 the primary classes involved in running the backend are shown below. The
 arrows represent the flow of job submission.
 
-```text
-    +----------------------------------------+
-    |                                        |
-    |  AwsBatchBackendLifecycleActorFactory  |
-    |                                        |
-    +------------------+---------------------+
-                       |
-                       |
-                       |
-                       |
-                       |
-    +------------------v----------------------+
-    |                                         |
-    |  AwsBatchAsyncBackendJobExecutionActor  |
-    |                                         |
-    +------------------+----------------------+
-                       |
-                       |
-                       |
-                       |
-                       |
-               +-------v-------+                 +-------------------------+
-               |               |                 |                         |
-               |  AwsBatchJob  +----------------->  AwsBatchJobDefinition  |
-               |               |                 |                         |
-               +---------------+                 +-------------------------+
+```mermaid
+  flowchart TD;
+    factory[AwsBatchBackendLifecycleActorFactory]
+    execution[AwsBatchAsyncBackendJobExecutionActor]
+    job[AwsBatchJob]
+    definition[AwsBatchJobDefinition]
+    
+    factory-->execution-->job-->definition;
 ```
 
 1. The `AwsBatchBackendLifecycleActorFactory` class is configured by the user
@@ -161,41 +219,17 @@ arrows represent the flow of job submission.
 
 AWS Batch Job Instantiation
 ---------------------------
-```text
-             +--------------------+
-             |                    |
-             |  Cromwell Backend  |
-             |                    |
-             +---------+----------+
-                       |
-                       |
-                   SubmitJob
-                       |
-                       |
-                +------v------+
-                |             |
-                |  AWS Batch  |
-                |             |
-                +------^------+
-                       |
-                       |
-                     Polls
-                       |
-                       |
-                +------+------+
-                |             |
-                |  ECS Agent  |
-                |             |
-                +------+------+
-                       |
-           Creates, Launches and Monitors
-                       |
-              +--------v---------+ 
-              |                  |
-              |  Task Container  |
-              |                  |
-              +------------------+
 
+```mermaid
+  flowchart TD
+    cromwell["Cromwell Backend"]
+    batch["AWS Batch"]
+    ecs["ECS Agent"]
+    task["Task Container"]
+    
+    cromwell-- SubmitJob -->batch
+    batch-- Polls -->ecs
+    ecs-- Creates, Launches and Monitors -->task
 ```
 
 When a Cromwell task begins, the Cromwell backend will call the SubmitJob
@@ -305,59 +339,63 @@ The flow described below represents the permissions needed by each stage, from
 Cromwell server through the task running. This includes the permissions needed for
 the AWS Services involved in the processing of the work.
 
-```text
-+----------------------------+
-|                            |  s3:GetObject on bucket for workflow and script bucket
-|                            |  s3:ListObjects on script bucket
-|                            |  s3:PutObject on script bucket
-|          Cromwell          |  batch:RegisterTaskDefinition
-|                            |  batch:SubmitJob
-|                            |  batch:DescribeJobs
-|                            |  batch:DescribeJobDefinitions
-+-------------+--------------+
-              |
-              |
-              |
-+-------------v--------------+
-|                            |  AWSBatchServiceRole managed policy - described at:
-|          AWS Batch         |
-|                            |     https://docs.aws.amazon.com/batch/latest/userguide/service_IAM_role.html
-+-------------+--------------+
-              |
-              |
-              |
-+-------------v--------------+
-|                            |  AWSServiceRoleForECS Service-linked role, documented at:
-|                            |
-| Elastic Container Service  |     https://docs.aws.amazon.com/AmazonECS/latest/developerguide/using-service-linked-roles.html
-|                            |
-|  (See discussion #1 below) |  AmazonEC2ContainerServiceAutoscaleRole managed policy - described at:
-|                            |
-|                            |     https://docs.aws.amazon.com/AmazonECS/latest/developerguide/autoscale_IAM_role.html
-+-------------+--------------+
-              |
-              |
-              |
-+-------------v--------------+
-|                            |
-|                            |  AmazonEC2ContainerServiceforEC2Role managed policy, described at:
-| ECS Agent (running on EC2) |     https://docs.aws.amazon.com/AmazonECS/latest/developerguide/instance_IAM_role.html (EC2)
-|                            |    OR
-|                            |  AmazonECSTaskExecutionRolePolicy managed policy, described at:  
-|                            |     https://docs.aws.amazon.com/AmazonECS/latest/developerguide/task_execution_IAM_role.html (Fargate)
-+-------------+--------------+ 
-              |
-              |
-              |
-+-------------v--------------+
-|                            |  Task Role permissions. These are user defined, but ecs-tasks.amazon.com must have sts:AssumeRole trust relationship defined. Documentation:
-|       Task Container       |
-|                            |     https://docs.aws.amazon.com/AmazonECS/latest/developerguide/task_IAM_role.html
-|                            |  s3:GetObject, s3:PutObject, s3:ListObjects
-+----------------------------+
+```mermaid
+  flowchart TD
+    cromwell["Cromwell"]
+    batch["AWS Batch"]
+    ecs["Elastic Container Service\n\n(See discussion #1 below)"]
+    ec2["ECS Agent (running on EC2)"]
+    task["Task Container"]
+
+    cromwell_desc["s3:GetObject on bucket for workflow and script bucket
+                   s3:ListObjects on script bucket
+                   s3:PutObject on script bucket
+                   batch:RegisterTaskDefinition
+                   batch:SubmitJob
+                   batch:DescribeJobs
+                   batch:DescribeJobDefinitions"]
+
+    batch_desc["AWSBatchServiceRole managed policy, described <a href='https://docs.aws.amazon.com/batch/latest/userguide/service_IAM_role.html'>here</a>"]
+
+    ecs_desc["AWSServiceRoleForECS Service-linked role, described <a href='https://docs.aws.amazon.com/AmazonECS/latest/developerguide/using-service-linked-roles.html'>here</a>
+    
+              AmazonEC2ContainerServiceAutoscaleRole managed policy, described <a href='https://docs.aws.amazon.com/AmazonECS/latest/developerguide/autoscale_IAM_role.html'>here</a>"]
+
+    ec2_desc["(EC2) AmazonEC2ContainerServiceforEC2Role managed policy, described <a href='https://docs.aws.amazon.com/AmazonECS/latest/developerguide/instance_IAM_role.html'>here</a>
+    
+              (Fargate) AmazonECSTaskExecutionRolePolicy managed policy, described <a href='https://docs.aws.amazon.com/AmazonECS/latest/developerguide/task_execution_IAM_role.html'>here</a>"]
+
+    task_desc["Task Role permissions.
+              These are user defined, but ecs-tasks.amazon.com must have sts:AssumeRole trust relationship defined.
+              Documentation <a href='https://docs.aws.amazon.com/AmazonECS/latest/developerguide/task_IAM_role.html'>here</a>
+              s3:GetObject
+              s3:PutObject
+              s3:ListObjects"]
+
+    subgraph 1 [" "]
+      direction RL
+      cromwell_desc-->cromwell
+    end
+    subgraph 2 [" "]
+      direction RL
+      batch_desc-->batch
+    end
+    subgraph 3 [" "]
+      direction RL
+      ecs_desc-->ecs
+    end
+    subgraph 4 [" "]
+      direction RL
+      ec2_desc-->ec2
+    end
+    subgraph 5 [" "]
+      direction RL
+      task_desc-->task
+    end
+
+    1-->2-->3-->4-->5
 ```
 
-
 1. ECS has several sets of permissions for various items. AWS Batch, however,
    does not take advantage of certain features of ECS, most importantly
    ECS Services are out of scope of AWS Batch. ECS services require things
@@ -379,6 +417,7 @@ the AWS Services involved in the processing of the work.
 NOTE: ECS Agent permissions currently must use the permissions as outlined
       in the AmazonEC2ContainerServiceForEC2Role managed policy.
 
+
 Future considerations
 ---------------------
 
@@ -422,4 +461,4 @@ Cromwell
 * There is a significant amount of dependent libraries (with more added by
   the introduction of the S3 filesystem and the AWS SDK). Dependency management
   is challenging as a result. Adding significant new functionality is relatively
-  painful when new dependencies are needed.
+  painful when new dependencies are needed.
\ No newline at end of file

From 5cac2b2ab979be3b5646277ba7bad837a8bc87b3 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Fri, 25 Mar 2022 05:27:57 +0100
Subject: [PATCH 051/326] revised localization functions to improve stability

---
 .../backend/impl/aws/AwsBatchJob.scala        | 108 ++++++++++++++----
 .../backend/impl/aws/AwsBatchJobSpec.scala    | 103 ++++++++++++++---
 2 files changed, 175 insertions(+), 36 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index c81bc75fe2b..e79a948377b 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -149,7 +149,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     // this goes at the start of the script after the #!
     val preamble =
       s"""
-         |export AWS_METADATA_SERVICE_TIMEOUT=10
+          |export AWS_METADATA_SERVICE_TIMEOUT=10
          |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
          |
          |function _s3_localize_with_retry() {
@@ -157,28 +157,96 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  # destination must be the path to a file and not just the directory you want the file in
          |  local destination=$$2
          |
-         |  for i in {1..5};
+         |  for i in {1..6};
          |  do
-         |    if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
-         |        bucket="$${BASH_REMATCH[1]}"
-         |        key="$${BASH_REMATCH[2]}"
-         |        content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength')
-         |    else
+         |    # abort if tries are exhausted
+         |    if [ "$$i" -eq 6 ]; then
+         |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts. aborting"
+         |        exit 2
+         |    fi
+         |    # check validity of source path
+         |    if ! [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
          |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
          |      exit 1
          |    fi
-         |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination" &&
-         |    [[ $$(LC_ALL=C ls -dn -- "$$destination" | awk '{print $$5; exit}') -eq "$$content_length" ]] && break ||
-         |    echo "attempt $$i to copy $$s3_path failed";
+         |    # copy  
+         |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination"  ||
+         |        ( echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue)
+         |    # check data integrity
+         |    _check_data_integrity $$destination $$s3_path || 
+         |       (echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
+         |    # copy succeeded
+         |    break
+         |  done
+         |}
          |
-         |    if [ "$$i" -eq 5 ]; then
-         |        echo "failed to copy $$s3_path after $$i attempts. aborting"
+         |function _s3_delocalize_with_retry() {
+         |  local local_path=$$1
+         |  # destination must be the path to a file and not just the directory you want the file in
+         |  local destination=$$2
+         |
+         |  for i in {1..6};
+         |  do
+         |    # if tries exceeded : abort
+         |    if [ "$$i" -eq 6 ]; then
+         |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts. aborting"
          |        exit 2
          |    fi
-         |    sleep $$((7 * "$$i"))
+         |    # if destination is not a bucket : abort
+         |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then 
+         |     echo "$$destination is not an S3 path with a bucket and key. aborting"
+         |      exit 1
+         |    fi
+         |    # copy ok or try again.
+         |    if [[ -d "$$local_path" ]]; then
+         |       # make sure to strip the trailing / in destination 
+         |       destination=$${destination%/}
+         |       # glob directory. do recursive copy
+         |       $awsCmd s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" || 
+         |         ( echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
+         |       # check integrity for each of the files
+         |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
+         |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE || 
+         |               ( echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2)
+         |       done
+         |    else 
+         |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" || 
+         |         ( echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
+         |      # check content length for data integrity
+         |      _check_data_integrity $$local_path $$destination || 
+         |         ( echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
+         |    fi
+         |    # copy succeeded
+         |    break
          |  done
          |}
          |
+         |function _check_data_integrity() {
+         |  local local_path=$$1
+         |  local s3_path=$$2
+         |  
+         |  # remote : use content_length
+         |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then 
+         |        bucket="$${BASH_REMATCH[1]}"
+         |        key="$${BASH_REMATCH[2]}"
+         |  else
+         |      # this is already checked in the caller function
+         |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+         |      exit 1
+         |  fi
+         |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
+         |        ( echo "Attempt to get head of object failed for $$s3_path." && return 1 )
+         |  # local
+         |  local_content_length=$$(LC_ALL=C ls -dn -- "$$local_path" | awk '{print $$5; exit}' ) || 
+         |        ( echo "Attempt to get local content length failed for $$_local_path." && return 1 )   
+         |  # compare
+         |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
+         |       true
+         |  else
+         |       false  
+         |  fi
+         |}
+         |
          |{
          |set -e
          |echo '*** LOCALIZING INPUTS ***'
@@ -208,23 +276,23 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          */
         s"""
            |touch ${output.name}
-           |$awsCmd s3 cp --no-progress ${output.name} ${output.s3key}
-           |if [ -e $globDirectory ]; then $awsCmd s3 cp --no-progress $globDirectory $s3GlobOutDirectory --recursive --exclude "cromwell_glob_control_file"; fi""".stripMargin
+           |_s3_delocalize_with_retry ${output.name} ${output.s3key}
+           |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory "; fi""".stripMargin
 
 
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
         //output is on working disk mount
-        s"""$awsCmd s3 cp --no-progress $workDir/${output.local.pathAsString} ${output.s3key}""".stripMargin
+        s"""_s3_delocalize_with_retry $workDir/${output.local.pathAsString} ${output.s3key}""".stripMargin
 
       case output: AwsBatchFileOutput =>
         //output on a different mount
-        s"$awsCmd s3 cp --no-progress ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
+        s"_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
       case _ => ""
     }.mkString("\n") + "\n" +
       s"""
-         |if [ -f $workDir/${jobPaths.returnCodeFilename} ]; then $awsCmd s3 cp --no-progress $workDir/${jobPaths.returnCodeFilename} ${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename} ; fi
-         |if [ -f $stdErr ]; then $awsCmd s3 cp --no-progress $stdErr ${jobPaths.standardPaths.error.pathAsString}; fi
-         |if [ -f $stdOut ]; then $awsCmd s3 cp --no-progress $stdOut ${jobPaths.standardPaths.output.pathAsString}; fi
+         |if [ -f $workDir/${jobPaths.returnCodeFilename} ]; then _s3_delocalize_with_retry $workDir/${jobPaths.returnCodeFilename} ${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename} ; fi
+         |if [ -f $stdErr ]; then _s3_delocalize_with_retry $stdErr ${jobPaths.standardPaths.error.pathAsString}; fi
+         |if [ -f $stdOut ]; then _s3_delocalize_with_retry $stdOut ${jobPaths.standardPaths.output.pathAsString}; fi
          |""".stripMargin
 
 
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index 12e933ab959..2a55f63be1c 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -182,32 +182,103 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
   it should "add s3 localize with retry function to reconfigured script" in {
     val job = generateBasicJob
     val retryFunctionText = s"""
+                              |export AWS_METADATA_SERVICE_TIMEOUT=10
+                              |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
+                              |
                               |function _s3_localize_with_retry() {
                               |  local s3_path=$$1
                               |  # destination must be the path to a file and not just the directory you want the file in
                               |  local destination=$$2
                               |
-                              |  for i in {1..5};
+                              |  for i in {1..6};
                               |  do
-                              |    if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
-                              |        bucket="$${BASH_REMATCH[1]}"
-                              |        key="$${BASH_REMATCH[2]}"
-                              |        content_length=$$(/usr/local/aws-cli/v2/current/bin/aws  s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength')
-                              |    else
+                              |    # abort if tries are exhausted
+                              |    if [ "$$i" -eq 6 ]; then
+                              |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts. aborting"
+                              |        exit 2
+                              |    fi
+                              |    # check validity of source path
+                              |    if ! [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
                               |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
                               |      exit 1
                               |    fi
-                              |    /usr/local/aws-cli/v2/current/bin/aws  s3 cp --no-progress "$$s3_path" "$$destination" &&
-                              |    [[ $$(LC_ALL=C ls -dn -- "$$destination" | awk '{print $$5; exit}') -eq "$$content_length" ]] && break ||
-                              |    echo "attempt $$i to copy $$s3_path failed";
+                              |    # copy  
+                              |    /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$s3_path" "$$destination"  ||
+                              |        ( echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue)
+                              |    # check data integrity
+                              |    _check_data_integrity $$destination $$s3_path || 
+                              |       (echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
+                              |    # copy succeeded
+                              |    break
+                              |  done
+                              |}
+                              |
+                              |function _s3_delocalize_with_retry() {
+                              |  local local_path=$$1
+                              |  # destination must be the path to a file and not just the directory you want the file in
+                              |  local destination=$$2
                               |
-                              |    if [ "$$i" -eq 5 ]; then
-                              |        echo "failed to copy $$s3_path after $$i attempts. aborting"
+                              |  for i in {1..6};
+                              |  do
+                              |    # if tries exceeded : abort
+                              |    if [ "$$i" -eq 6 ]; then
+                              |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts. aborting"
                               |        exit 2
                               |    fi
-                              |    sleep $$((7 * "$$i"))
+                              |    # if destination is not a bucket : abort
+                              |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then 
+                              |     echo "$$destination is not an S3 path with a bucket and key. aborting"
+                              |      exit 1
+                              |    fi
+                              |    # copy ok or try again.
+                              |    if [[ -d "$$local_path" ]]; then
+                              |       # make sure to strip the trailing / in destination 
+                              |       destination=$${destination%/}
+                              |       # glob directory. do recursive copy
+                              |       /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" || 
+                              |         ( echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
+                              |       # check integrity for each of the files
+                              |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
+                              |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE || 
+                              |               ( echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2)
+                              |       done
+                              |    else 
+                              |      /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$local_path" "$$destination" || 
+                              |         ( echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
+                              |      # check content length for data integrity
+                              |      _check_data_integrity $$local_path $$destination || 
+                              |         ( echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
+                              |    fi
+                              |    # copy succeeded
+                              |    break
                               |  done
                               |}
+                              |
+                              |function _check_data_integrity() {
+                              |  local local_path=$$1
+                              |  local s3_path=$$2
+                              |  
+                              |  # remote : use content_length
+                              |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then 
+                              |        bucket="$${BASH_REMATCH[1]}"
+                              |        key="$${BASH_REMATCH[2]}"
+                              |  else
+                              |      # this is already checked in the caller function
+                              |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+                              |      exit 1
+                              |  fi
+                              |  s3_content_length=$$(/usr/local/aws-cli/v2/current/bin/aws s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
+                              |        ( echo "Attempt to get head of object failed for $$s3_path." && return 1 )
+                              |  # local
+                              |  local_content_length=$$(LC_ALL=C ls -dn -- "$$local_path" | awk '{print $$5; exit}' ) || 
+                              |        ( echo "Attempt to get local content length failed for $$_local_path." && return 1 )   
+                              |  # compare
+                              |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
+                              |       true
+                              |  else
+                              |       false  
+                              |  fi
+                              |}
                               |""".stripMargin
 
     job.reconfiguredScript should include (retryFunctionText)
@@ -221,13 +292,13 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
          |set -e
          |echo '*** DELOCALIZING OUTPUTS ***'
          |
-         |/usr/local/aws-cli/v2/current/bin/aws  s3 cp --no-progress /tmp/scratch/baa s3://bucket/somewhere/baa
+         |_s3_delocalize_with_retry /tmp/scratch/baa s3://bucket/somewhere/baa
          |
          |
-         |if [ -f /tmp/scratch/hello-rc.txt ]; then /usr/local/aws-cli/v2/current/bin/aws  s3 cp --no-progress /tmp/scratch/hello-rc.txt ${job.jobPaths.returnCode} ; fi
+         |if [ -f /tmp/scratch/hello-rc.txt ]; then _s3_delocalize_with_retry /tmp/scratch/hello-rc.txt ${job.jobPaths.returnCode} ; fi
          |
-         |if [ -f /tmp/scratch/hello-stderr.log ]; then /usr/local/aws-cli/v2/current/bin/aws  s3 cp --no-progress /tmp/scratch/hello-stderr.log ${job.jobPaths.standardPaths.error}; fi
-         |if [ -f /tmp/scratch/hello-stdout.log ]; then /usr/local/aws-cli/v2/current/bin/aws  s3 cp --no-progress /tmp/scratch/hello-stdout.log ${job.jobPaths.standardPaths.output}; fi
+         |if [ -f /tmp/scratch/hello-stderr.log ]; then _s3_delocalize_with_retrys /tmp/scratch/hello-stderr.log ${job.jobPaths.standardPaths.error}; fi
+         |if [ -f /tmp/scratch/hello-stdout.log ]; then _s3_delocalize_with_retry /tmp/scratch/hello-stdout.log ${job.jobPaths.standardPaths.output}; fi
          |
          |echo '*** COMPLETED DELOCALIZATION ***'
          |echo '*** EXITING WITH RETURN CODE ***'

From 7a4ec48c9a9503dac87d3a7bf6a410df6421ecfb Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Fri, 25 Mar 2022 11:17:39 +0000
Subject: [PATCH 052/326] fix tests

---
 .../scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala   | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index 2a55f63be1c..3de115e4f97 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -128,21 +128,21 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       Seq.empty[AwsBatchInput].toSet, Seq.empty[AwsBatchFileOutput].toSet,
-      jobPaths, Seq.empty[AwsBatchParameter], None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None)
     job
   }
   private def generateBasicJobForLocalFS: AwsBatchJob = {
     val job = AwsBatchJob(null, runtimeAttributes.copy(fileSystem="local"), "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       Seq.empty[AwsBatchInput].toSet, Seq.empty[AwsBatchFileOutput].toSet,
-      jobPaths, Seq.empty[AwsBatchParameter], None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None)
     job
   }
   private def generateJobWithS3InOut: AwsBatchJob = {
     val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       s3Inputs, s3Outputs,
-      jobPaths, Seq.empty[AwsBatchParameter], None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None)
     job
   }
 

From 2d447df86baa986396c76bbf05dfbe54e7f8cc48 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Wed, 30 Mar 2022 19:50:31 +0100
Subject: [PATCH 053/326] update readme

---
 README.md                                              |  4 +++-
 .../src/main/scala/cromwell/backend/impl/aws/README.md | 10 ++++++++--
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index bb313473f58..adecd7d31fd 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,12 @@
 [![Build Status](https://travis-ci.com/broadinstitute/cromwell.svg?branch=develop)](https://travis-ci.com/broadinstitute/cromwell?branch=develop)
 [![codecov](https://codecov.io/gh/broadinstitute/cromwell/branch/develop/graph/badge.svg)](https://codecov.io/gh/broadinstitute/cromwell)
 
-## Welcome to "AWS-friendly" Cromwell
+## Welcome to the "AWS-friendly" Cromwell
 
 More information regarding AWS features can be found [here](https://github.com/henriqueribeiro/cromwell/tree/master/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws)
 
+Contact: henrique [at] loka [dot] com 
+
 Cromwell is an open-source Workflow Management System for bioinformatics. Licensing is [BSD 3-Clause](LICENSE.txt).
 
 The [Cromwell documentation has a dedicated site](https://cromwell.readthedocs.io/en/stable).
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index b692e356cc1..62a0495c1be 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -42,6 +42,8 @@ Docker Hub authentication for AWS Backend enable users to access and use private
 dockerhub { token = "<enconded-string-from-point-2>" }
 ```
 
+Stack must be deployed through https://github.com/aws-samples/aws-genomics-workflows.
+
 ### `awsBatchRetryAttempts`
 
 *Default: _0_*
@@ -50,6 +52,8 @@ This runtime attribute adds support to [*AWS Batch Automated Job Retries*](https
 
 It takes an Int, between 1 and 10, as a value that indicates the maximum number of times AWS Batch should retry a failed task. If the value 0 is passed, the [*Retry Strategy*](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#retryStrategy) will not be added to the job definiton and the task will run just once.
 
+This configuration should be passed in the `options.json` file when launching the pipeline.
+
 ```
 runtime {
   awsBatchRetryAttempts: integer
@@ -62,6 +66,8 @@ runtime {
 
 A list of [`ulimits`](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#containerProperties) values to set in the container. This parameter maps to `Ulimits` in the [Create a container](https://docs.docker.com/engine/api/v1.38/) section of the [Docker Remote API](https://docs.docker.com/engine/api/v1.38/) and the `--ulimit` option to [docker run](https://docs.docker.com/engine/reference/commandline/run/).
 
+This configuration should be passed in the `options.json` file when launching the pipeline.
+
 ```
 "ulimits": [
   {
@@ -95,7 +101,7 @@ AWS ECR is a private container registry, for which access can be regulated using
 
 1. Setup a user with pull-access to ECR, then use this role to run cromwell
 
-profile default region must be setup in ~/.aws/config: 
+profile default region must be setup in `~/.aws/config`: 
 ```
 [profile MyECR-user]
 region = eu-west-1
@@ -459,4 +465,4 @@ Cromwell
 * There is a significant amount of dependent libraries (with more added by
   the introduction of the S3 filesystem and the AWS SDK). Dependency management
   is challenging as a result. Adding significant new functionality is relatively
-  painful when new dependencies are needed.
\ No newline at end of file
+  painful when new dependencies are needed.

From a85b6f66acad2e9633a0ed9334e7616786d8b85e Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Mon, 4 Apr 2022 08:39:38 +0200
Subject: [PATCH 054/326] Corrected braces in localization scripts to enable
 loop control

---
 .../cromwell/backend/impl/aws/AwsBatchJob.scala  | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index e79a948377b..3bcdb2de5de 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -171,10 +171,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |    fi
          |    # copy  
          |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination"  ||
-         |        ( echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue)
+         |        { echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue; }
          |    # check data integrity
          |    _check_data_integrity $$destination $$s3_path || 
-         |       (echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
+         |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # copy succeeded
          |    break
          |  done
@@ -203,18 +203,18 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |       destination=$${destination%/}
          |       # glob directory. do recursive copy
          |       $awsCmd s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" || 
-         |         ( echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
+         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
          |       # check integrity for each of the files
          |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
          |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE || 
-         |               ( echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2)
+         |               { echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2; }
          |       done
          |    else 
          |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" || 
-         |         ( echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
+         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
          |      # check content length for data integrity
          |      _check_data_integrity $$local_path $$destination || 
-         |         ( echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
+         |         { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    fi
          |    # copy succeeded
          |    break
@@ -235,10 +235,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |      exit 1
          |  fi
          |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
-         |        ( echo "Attempt to get head of object failed for $$s3_path." && return 1 )
+         |        { echo "Attempt to get head of object failed for $$s3_path." && return 1 ; }
          |  # local
          |  local_content_length=$$(LC_ALL=C ls -dn -- "$$local_path" | awk '{print $$5; exit}' ) || 
-         |        ( echo "Attempt to get local content length failed for $$_local_path." && return 1 )   
+         |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }   
          |  # compare
          |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
          |       true

From 7462b6865635da8fdd8ceac48e3a1ea99a4e7b91 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Mon, 4 Apr 2022 08:40:48 +0200
Subject: [PATCH 055/326] Added support for Retry in case of time-out errors

---
 .../engine/io/RetryableRequestSupport.scala   | 26 ++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala b/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
index 03ef9224b7d..9efa3e7c767 100644
--- a/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
+++ b/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
@@ -26,7 +26,7 @@ object RetryableRequestSupport {
     case _: SocketException => true
     case _: SocketTimeoutException => true
     case ioE: IOException if Option(ioE.getMessage).exists(_.contains("Error getting access token for service account")) => true
-    case ioE: IOException => isGcs500(ioE) || isGcs503(ioE) || isGcs504(ioE)
+    case ioE: IOException => isGcs500(ioE) || isGcs503(ioE) || isGcs504(ioE) || isAws504(ioE)
     case other =>
       // Infinitely retryable is a subset of retryable
       isInfinitelyRetryable(other)
@@ -86,4 +86,28 @@ object RetryableRequestSupport {
       msg.contains("504 Gateway Timeout")
     )
   }
+  // AWS timeout error
+  def isAws504(failure: Throwable): Boolean = {
+    Option(failure.getMessage).exists(msg =>
+      ( 
+        // timeout in reading form s3. 
+        msg.contains("Could not read from s3") && 
+        msg.contains("Timeout waiting for connection") 
+      ) || (
+        // reading in cromwell wdl (read_lines() etc)
+        msg.contains("Failed to evaluate") &&
+        msg.contains("s3://") && 
+        msg.contains("Timed out after")
+      )
+    )
+  }
+  // General AWS IO error : all items unreadable except rc.txt files (might be missing)
+  //   => mainly for testing. will retry mis-specified s3 paths as well... 
+  def isAwsIO(failure:Throwable): Boolean = {
+    Option(failure.getMessage).exists(msg =>
+      msg.contains("Could not read from s3") && 
+      ! msg.contains("-rc.txt") 
+    )
+  }
+
 }

From 40adf36b3e73fdea1bb0b0354e9c419a16dc9889 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Mon, 4 Apr 2022 08:41:40 +0200
Subject: [PATCH 056/326] Enabled support for retryWithMoreMemory for AWS/Batch

---
 .../StandardAsyncExecutionActor.scala         | 128 ++++++++++--------
 ...wsBatchAsyncBackendJobExecutionActor.scala |  37 ++++-
 2 files changed, 107 insertions(+), 58 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 9b21871b538..2ef8b7bd5b7 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -1265,70 +1265,16 @@ trait StandardAsyncExecutionActor
   def handleExecutionResult(status: StandardAsyncRunState,
                             oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
     
-    // get the memory retry code.
-    def memoryRetryRC: Future[Boolean] = {
-      // convert int to boolean
-      def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
-        codeAsOption match {
-          case Some(codeAsString) =>
-            Try(codeAsString.trim.toInt) match {
-              case Success(code) => code match {
-                case StderrContainsRetryKeysCode => true
-                case _ => false
-              }
-              case Failure(e) =>
-                log.error(s"'CheckingForMemoryRetry' action exited with code '$codeAsString' which couldn't be " +
-                  s"converted to an Integer. Task will not be retried with more memory. Error: ${ExceptionUtils.getMessage(e)}")
-                false
-            }
-          case None => false
-        }
-      }
-      // read if the file exists
-      def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] = {
-        if (fileExists)
-          asyncIo.contentAsStringAsync(jobPaths.memoryRetryRC, None, failOnOverflow = false).map(Option(_))
-        else
-          Future.successful(None)
-      }
-      //finally : assign the yielded variable
-      for {
-        fileExists <- asyncIo.existsAsync(jobPaths.memoryRetryRC)
-        retryCheckRCAsOption <- readMemoryRetryRCFile(fileExists)
-        retryWithMoreMemory = returnCodeAsBoolean(retryCheckRCAsOption)
-      } yield retryWithMoreMemory
-    }
-
-    // get the exit code of the job.
-    def JobExitCode: Future[String] = {
-      
-      // read if the file exists
-      def readRCFile(fileExists: Boolean): Future[String] = {
-        if (fileExists)
-          asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
-        else {
-          jobLogger.warn("RC file not found. Setting job to failed & waiting 5m before retry.")
-          Thread.sleep(300000)
-          Future("1")
-        }
-      }
-      //finally : assign the yielded variable
-      for {
-        fileExists <- asyncIo.existsAsync(jobPaths.returnCode)
-        jobRC <- readRCFile(fileExists)
-      } yield jobRC
-    }
-
     // get path to sderr
     val stderr = jobPaths.standardPaths.error
     lazy val stderrAsOption: Option[Path] = Option(stderr)
-    // get the three needed variables, using functions above or direct assignment.
+    // get the three needed variables, using helper functions below, or direct assignment.
     val stderrSizeAndReturnCodeAndMemoryRetry = for {
       returnCodeAsString <- JobExitCode
       // Only check stderr size if we need to, otherwise this results in a lot of unnecessary I/O that
       // may fail due to race conditions on quickly-executing jobs.
       stderrSize <- if (failOnStdErr) asyncIo.sizeAsync(stderr) else Future.successful(0L)
-      retryWithMoreMemory <- memoryRetryRC
+      retryWithMoreMemory <- memoryRetryRC(oldHandle.pendingJob)
     } yield (stderrSize, returnCodeAsString, retryWithMoreMemory)
 
     stderrSizeAndReturnCodeAndMemoryRetry flatMap {
@@ -1337,25 +1283,36 @@ trait StandardAsyncExecutionActor
 
         if (isDone(status)) {
           tryReturnCodeAsInt match {
+            // stderr not empty : retry
             case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
-            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
+            // job was aborted (cancelled by user?) 
+            // on AWS OOM kill are code 137 : check retryWithMoreMemory here 
+            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) && !retryWithMoreMemory =>
+              jobLogger.debug(s"Job was aborted, code was : '${returnCodeAsString}'")
               Future.successful(AbortedExecutionHandle)
+            // job considered ok by accepted exit code
             case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
               handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
+            // job failed on out-of-memory : retry
             case Success(returnCodeAsInt) if retryWithMoreMemory  =>
+              jobLogger.warn(s"Retrying job due to OOM with exit code : '${returnCodeAsString}' ")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle, retryWithMoreMemory)
+            // unaccepted return code : retry.
             case Success(returnCodeAsInt) =>
+              jobLogger.debug(s"Retrying with wrong exit code : '${returnCodeAsString}'")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
             case Failure(_) =>
+              jobLogger.warn(s"General failure of job with exit code : '${returnCodeAsString}'")
               Future.successful(FailedNonRetryableExecutionHandle(ReturnCodeIsNotAnInt(jobDescriptor.key.tag, returnCodeAsString, stderrAsOption), kvPairsToSave = None))
           }
         } else {
           tryReturnCodeAsInt match {
             case Success(returnCodeAsInt) if retryWithMoreMemory && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
+              jobLogger.debug(s"job not done but retrying already? : ${status.toString()}")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle, retryWithMoreMemory)
             case _ =>
@@ -1373,6 +1330,63 @@ trait StandardAsyncExecutionActor
     }
   }
 
+  // helper function for handleExecutionResult : get the exit code of the job.
+  def JobExitCode: Future[String] = {
+      
+    // read if the file exists
+    def readRCFile(fileExists: Boolean): Future[String] = {
+      if (fileExists)
+        asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
+      else {
+        jobLogger.warn("RC file not found. Setting job to failed & retry.")
+        //Thread.sleep(300000)
+        Future("1")
+      }
+    }
+    //finally : assign the yielded variable
+    for {
+      fileExists <- asyncIo.existsAsync(jobPaths.returnCode)
+      jobRC <- readRCFile(fileExists)
+    } yield jobRC
+  }
+
+  // helper function for handleExecutionResult : get the memory retry code.
+  def memoryRetryRC(job: StandardAsyncJob): Future[Boolean] = {
+    // job is used in aws override version. use here to prevent compilation error.
+    log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
+    // convert int to boolean
+    def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
+      codeAsOption match {
+        case Some(codeAsString) =>
+          Try(codeAsString.trim.toInt) match {
+            case Success(code) => code match {
+              case StderrContainsRetryKeysCode => true
+              case _ => false
+            }
+            case Failure(e) =>
+              log.error(s"'CheckingForMemoryRetry' action exited with code '$codeAsString' which couldn't be " +
+                s"converted to an Integer. Task will not be retried with more memory. Error: ${ExceptionUtils.getMessage(e)}")
+              false
+          }
+        case None => false
+      }
+    }
+    // read if the file exists
+    def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] = {
+      if (fileExists)
+        asyncIo.contentAsStringAsync(jobPaths.memoryRetryRC, None, failOnOverflow = false).map(Option(_))
+      else
+        Future.successful(None)
+    }
+    //finally : assign the yielded variable
+    for {
+      fileExists <- asyncIo.existsAsync(jobPaths.memoryRetryRC)
+      retryCheckRCAsOption <- readMemoryRetryRCFile(fileExists)
+      retryWithMoreMemory = returnCodeAsBoolean(retryCheckRCAsOption)
+    } yield retryWithMoreMemory
+  }
+
+
   /**
     * Send the job id of the running job to the key value store.
     *
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 34334449587..a534ae2b8da 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -57,7 +57,10 @@ import cromwell.filesystems.s3.S3Path
 import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
 import cromwell.services.keyvalue.KvClient
 import org.slf4j.{Logger, LoggerFactory}
-import software.amazon.awssdk.services.batch.model.{BatchException, SubmitJobResponse}
+import software.amazon.awssdk.services.batch.BatchClient
+//import software.amazon.awssdk.services.batch.model.{BatchException, SubmitJobResponse}
+import software.amazon.awssdk.services.batch.model._
+
 import wom.callable.Callable.OutputDefinition
 import wom.core.FullyQualifiedName
 import wom.expression.NoIoFunctionSet
@@ -184,6 +187,13 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       Option(configuration.awsAuth),
       configuration.fsxMntPoint)
   }
+
+  // setup batch client to query job container info
+  lazy val batchClient: BatchClient = {
+    val builder = BatchClient.builder()
+    configureClient(builder, batchJob.optAwsAuthMode, batchJob.configRegion)
+  }
+
   /* Tries to abort the job in flight
    *
    * @param job A StandardAsyncJob object (has jobId value) to cancel
@@ -514,6 +524,31 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     } yield guaranteedAnswer
   }
 
+  // new OOM detection 
+  override def memoryRetryRC(job: StandardAsyncJob): Future[Boolean] = Future {
+      Log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
+      val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(job.jobId).build)
+      val jobDetail = describeJobsResponse.jobs.get(0) //OrElse(throw new RuntimeException(s"Could not get job details for job '${job.jobId}'"))
+      val nrAttempts = jobDetail.attempts.size
+      val lastattempt = jobDetail.attempts.get(nrAttempts-1)
+      val containerRC = lastattempt.container.exitCode
+      // if not zero => get reason, else set retry to false.
+      containerRC.toString() match {
+        case "0" => 
+            Log.debug("container exit code was zero")
+            false
+        case _ => 
+            val containerStatusReason = lastattempt.container.reason 
+            Log.warn(s"Job failed with Container status reason : '${containerStatusReason}'")
+            val RetryMemoryKeys = memoryRetryErrorKeys.toList.flatten
+            val retry = RetryMemoryKeys.exists(containerStatusReason.contains)
+            Log.debug(s"Retry job based on provided keys : '${retry}'")
+            retry
+      }
+        
+        
+    }
+ 
   // Despite being a "runtime" exception, BatchExceptions for 429 (too many requests) are *not* fatal:
   override def isFatal(throwable: Throwable): Boolean = throwable match {
     case be: BatchException => !be.getMessage.contains("Status Code: 429")

From 0e25349bb8dca295e5ec1c08afce449939441724 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Mon, 4 Apr 2022 14:04:35 +0200
Subject: [PATCH 057/326] bugfix : removed incorrect quote

---
 .../src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 3bcdb2de5de..757c7ab7b87 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -277,7 +277,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         s"""
            |touch ${output.name}
            |_s3_delocalize_with_retry ${output.name} ${output.s3key}
-           |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory "; fi""".stripMargin
+           |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi""".stripMargin
 
 
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>

From 320208f2d0e53658057e7e40dfa12158f44729fa Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Mon, 4 Apr 2022 14:17:53 +0200
Subject: [PATCH 058/326] added memory-retry documentation

---
 .../scala/cromwell/backend/impl/aws/README.md | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 62a0495c1be..df83472bdc2 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -133,6 +133,48 @@ Notes:
 - local hashing means that all used containers are pulled. Make sure you have enough storage
 - enable a database to make the cache persistent over cromwell restarts
 
+### Retry with more memory
+
+Cromwell can be configured to retry jobs with more allocated memory, under a defined set of conditions. To enable this, set the following parameters:
+
+cromwell configuration: `cromwell.config`:
+```
+// set the maximal amount of retries.
+// backend.providers.AWSBatch.config.default-runtime-attribues.maxRetries
+backend {
+  providers {
+    AWSBatch {
+      config {
+        default-runtime-attributes {
+          maxRetries: 6 
+        }
+      }
+    }
+  }
+}
+
+// set the keys for Out-Of-Memory killing. 
+// system.io.memory-retry-error-keys
+system{
+    io{
+        memory-retry-error-keys = ["OutOfMemory","Killed"]
+    }
+}
+```
+
+Workflow specific runtime options : `workflow_options.json`:
+```
+{
+    "memory_retry_multiplier" : 1.5
+}
+```
+
+When providing the options.json file during workflow submission, jobs that were terminated due to insufficient memory will be retried 6 times, with increasing memory allocation. For example 4Gb => 6Gb => 9Gb => 13.5Gb => ... 
+
+Note: Retries of jobs using the `awsBatchRetryAttempts` counter do *not* increase memory allocation. 
+
+
+
 AWS Batch
 ---------
 

From 22bc5d7dcc4a85a02de3319180c4bab197ccd1d8 Mon Sep 17 00:00:00 2001
From: henriqueribeiro <henriqueribeiro@users.noreply.github.com>
Date: Mon, 4 Apr 2022 18:18:40 +0100
Subject: [PATCH 059/326] Revert "Extra failure handling for Batch"

---
 .../StandardAsyncExecutionActor.scala         | 128 ++++++++----------
 .../engine/io/RetryableRequestSupport.scala   |  26 +---
 ...wsBatchAsyncBackendJobExecutionActor.scala |  37 +----
 .../backend/impl/aws/AwsBatchJob.scala        |  18 +--
 .../scala/cromwell/backend/impl/aws/README.md |  42 ------
 5 files changed, 68 insertions(+), 183 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 2ef8b7bd5b7..9b21871b538 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -1265,16 +1265,70 @@ trait StandardAsyncExecutionActor
   def handleExecutionResult(status: StandardAsyncRunState,
                             oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
     
+    // get the memory retry code.
+    def memoryRetryRC: Future[Boolean] = {
+      // convert int to boolean
+      def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
+        codeAsOption match {
+          case Some(codeAsString) =>
+            Try(codeAsString.trim.toInt) match {
+              case Success(code) => code match {
+                case StderrContainsRetryKeysCode => true
+                case _ => false
+              }
+              case Failure(e) =>
+                log.error(s"'CheckingForMemoryRetry' action exited with code '$codeAsString' which couldn't be " +
+                  s"converted to an Integer. Task will not be retried with more memory. Error: ${ExceptionUtils.getMessage(e)}")
+                false
+            }
+          case None => false
+        }
+      }
+      // read if the file exists
+      def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] = {
+        if (fileExists)
+          asyncIo.contentAsStringAsync(jobPaths.memoryRetryRC, None, failOnOverflow = false).map(Option(_))
+        else
+          Future.successful(None)
+      }
+      //finally : assign the yielded variable
+      for {
+        fileExists <- asyncIo.existsAsync(jobPaths.memoryRetryRC)
+        retryCheckRCAsOption <- readMemoryRetryRCFile(fileExists)
+        retryWithMoreMemory = returnCodeAsBoolean(retryCheckRCAsOption)
+      } yield retryWithMoreMemory
+    }
+
+    // get the exit code of the job.
+    def JobExitCode: Future[String] = {
+      
+      // read if the file exists
+      def readRCFile(fileExists: Boolean): Future[String] = {
+        if (fileExists)
+          asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
+        else {
+          jobLogger.warn("RC file not found. Setting job to failed & waiting 5m before retry.")
+          Thread.sleep(300000)
+          Future("1")
+        }
+      }
+      //finally : assign the yielded variable
+      for {
+        fileExists <- asyncIo.existsAsync(jobPaths.returnCode)
+        jobRC <- readRCFile(fileExists)
+      } yield jobRC
+    }
+
     // get path to sderr
     val stderr = jobPaths.standardPaths.error
     lazy val stderrAsOption: Option[Path] = Option(stderr)
-    // get the three needed variables, using helper functions below, or direct assignment.
+    // get the three needed variables, using functions above or direct assignment.
     val stderrSizeAndReturnCodeAndMemoryRetry = for {
       returnCodeAsString <- JobExitCode
       // Only check stderr size if we need to, otherwise this results in a lot of unnecessary I/O that
       // may fail due to race conditions on quickly-executing jobs.
       stderrSize <- if (failOnStdErr) asyncIo.sizeAsync(stderr) else Future.successful(0L)
-      retryWithMoreMemory <- memoryRetryRC(oldHandle.pendingJob)
+      retryWithMoreMemory <- memoryRetryRC
     } yield (stderrSize, returnCodeAsString, retryWithMoreMemory)
 
     stderrSizeAndReturnCodeAndMemoryRetry flatMap {
@@ -1283,36 +1337,25 @@ trait StandardAsyncExecutionActor
 
         if (isDone(status)) {
           tryReturnCodeAsInt match {
-            // stderr not empty : retry
             case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
-            // job was aborted (cancelled by user?) 
-            // on AWS OOM kill are code 137 : check retryWithMoreMemory here 
-            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) && !retryWithMoreMemory =>
-              jobLogger.debug(s"Job was aborted, code was : '${returnCodeAsString}'")
+            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
               Future.successful(AbortedExecutionHandle)
-            // job considered ok by accepted exit code
             case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
               handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
-            // job failed on out-of-memory : retry
             case Success(returnCodeAsInt) if retryWithMoreMemory  =>
-              jobLogger.warn(s"Retrying job due to OOM with exit code : '${returnCodeAsString}' ")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle, retryWithMoreMemory)
-            // unaccepted return code : retry.
             case Success(returnCodeAsInt) =>
-              jobLogger.debug(s"Retrying with wrong exit code : '${returnCodeAsString}'")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
             case Failure(_) =>
-              jobLogger.warn(s"General failure of job with exit code : '${returnCodeAsString}'")
               Future.successful(FailedNonRetryableExecutionHandle(ReturnCodeIsNotAnInt(jobDescriptor.key.tag, returnCodeAsString, stderrAsOption), kvPairsToSave = None))
           }
         } else {
           tryReturnCodeAsInt match {
             case Success(returnCodeAsInt) if retryWithMoreMemory && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
-              jobLogger.debug(s"job not done but retrying already? : ${status.toString()}")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle, retryWithMoreMemory)
             case _ =>
@@ -1330,63 +1373,6 @@ trait StandardAsyncExecutionActor
     }
   }
 
-  // helper function for handleExecutionResult : get the exit code of the job.
-  def JobExitCode: Future[String] = {
-      
-    // read if the file exists
-    def readRCFile(fileExists: Boolean): Future[String] = {
-      if (fileExists)
-        asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
-      else {
-        jobLogger.warn("RC file not found. Setting job to failed & retry.")
-        //Thread.sleep(300000)
-        Future("1")
-      }
-    }
-    //finally : assign the yielded variable
-    for {
-      fileExists <- asyncIo.existsAsync(jobPaths.returnCode)
-      jobRC <- readRCFile(fileExists)
-    } yield jobRC
-  }
-
-  // helper function for handleExecutionResult : get the memory retry code.
-  def memoryRetryRC(job: StandardAsyncJob): Future[Boolean] = {
-    // job is used in aws override version. use here to prevent compilation error.
-    log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
-    // convert int to boolean
-    def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
-      codeAsOption match {
-        case Some(codeAsString) =>
-          Try(codeAsString.trim.toInt) match {
-            case Success(code) => code match {
-              case StderrContainsRetryKeysCode => true
-              case _ => false
-            }
-            case Failure(e) =>
-              log.error(s"'CheckingForMemoryRetry' action exited with code '$codeAsString' which couldn't be " +
-                s"converted to an Integer. Task will not be retried with more memory. Error: ${ExceptionUtils.getMessage(e)}")
-              false
-          }
-        case None => false
-      }
-    }
-    // read if the file exists
-    def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] = {
-      if (fileExists)
-        asyncIo.contentAsStringAsync(jobPaths.memoryRetryRC, None, failOnOverflow = false).map(Option(_))
-      else
-        Future.successful(None)
-    }
-    //finally : assign the yielded variable
-    for {
-      fileExists <- asyncIo.existsAsync(jobPaths.memoryRetryRC)
-      retryCheckRCAsOption <- readMemoryRetryRCFile(fileExists)
-      retryWithMoreMemory = returnCodeAsBoolean(retryCheckRCAsOption)
-    } yield retryWithMoreMemory
-  }
-
-
   /**
     * Send the job id of the running job to the key value store.
     *
diff --git a/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala b/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
index 9efa3e7c767..03ef9224b7d 100644
--- a/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
+++ b/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
@@ -26,7 +26,7 @@ object RetryableRequestSupport {
     case _: SocketException => true
     case _: SocketTimeoutException => true
     case ioE: IOException if Option(ioE.getMessage).exists(_.contains("Error getting access token for service account")) => true
-    case ioE: IOException => isGcs500(ioE) || isGcs503(ioE) || isGcs504(ioE) || isAws504(ioE)
+    case ioE: IOException => isGcs500(ioE) || isGcs503(ioE) || isGcs504(ioE)
     case other =>
       // Infinitely retryable is a subset of retryable
       isInfinitelyRetryable(other)
@@ -86,28 +86,4 @@ object RetryableRequestSupport {
       msg.contains("504 Gateway Timeout")
     )
   }
-  // AWS timeout error
-  def isAws504(failure: Throwable): Boolean = {
-    Option(failure.getMessage).exists(msg =>
-      ( 
-        // timeout in reading form s3. 
-        msg.contains("Could not read from s3") && 
-        msg.contains("Timeout waiting for connection") 
-      ) || (
-        // reading in cromwell wdl (read_lines() etc)
-        msg.contains("Failed to evaluate") &&
-        msg.contains("s3://") && 
-        msg.contains("Timed out after")
-      )
-    )
-  }
-  // General AWS IO error : all items unreadable except rc.txt files (might be missing)
-  //   => mainly for testing. will retry mis-specified s3 paths as well... 
-  def isAwsIO(failure:Throwable): Boolean = {
-    Option(failure.getMessage).exists(msg =>
-      msg.contains("Could not read from s3") && 
-      ! msg.contains("-rc.txt") 
-    )
-  }
-
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index a534ae2b8da..34334449587 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -57,10 +57,7 @@ import cromwell.filesystems.s3.S3Path
 import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
 import cromwell.services.keyvalue.KvClient
 import org.slf4j.{Logger, LoggerFactory}
-import software.amazon.awssdk.services.batch.BatchClient
-//import software.amazon.awssdk.services.batch.model.{BatchException, SubmitJobResponse}
-import software.amazon.awssdk.services.batch.model._
-
+import software.amazon.awssdk.services.batch.model.{BatchException, SubmitJobResponse}
 import wom.callable.Callable.OutputDefinition
 import wom.core.FullyQualifiedName
 import wom.expression.NoIoFunctionSet
@@ -187,13 +184,6 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       Option(configuration.awsAuth),
       configuration.fsxMntPoint)
   }
-
-  // setup batch client to query job container info
-  lazy val batchClient: BatchClient = {
-    val builder = BatchClient.builder()
-    configureClient(builder, batchJob.optAwsAuthMode, batchJob.configRegion)
-  }
-
   /* Tries to abort the job in flight
    *
    * @param job A StandardAsyncJob object (has jobId value) to cancel
@@ -524,31 +514,6 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     } yield guaranteedAnswer
   }
 
-  // new OOM detection 
-  override def memoryRetryRC(job: StandardAsyncJob): Future[Boolean] = Future {
-      Log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
-      val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(job.jobId).build)
-      val jobDetail = describeJobsResponse.jobs.get(0) //OrElse(throw new RuntimeException(s"Could not get job details for job '${job.jobId}'"))
-      val nrAttempts = jobDetail.attempts.size
-      val lastattempt = jobDetail.attempts.get(nrAttempts-1)
-      val containerRC = lastattempt.container.exitCode
-      // if not zero => get reason, else set retry to false.
-      containerRC.toString() match {
-        case "0" => 
-            Log.debug("container exit code was zero")
-            false
-        case _ => 
-            val containerStatusReason = lastattempt.container.reason 
-            Log.warn(s"Job failed with Container status reason : '${containerStatusReason}'")
-            val RetryMemoryKeys = memoryRetryErrorKeys.toList.flatten
-            val retry = RetryMemoryKeys.exists(containerStatusReason.contains)
-            Log.debug(s"Retry job based on provided keys : '${retry}'")
-            retry
-      }
-        
-        
-    }
- 
   // Despite being a "runtime" exception, BatchExceptions for 429 (too many requests) are *not* fatal:
   override def isFatal(throwable: Throwable): Boolean = throwable match {
     case be: BatchException => !be.getMessage.contains("Status Code: 429")
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 757c7ab7b87..e79a948377b 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -171,10 +171,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |    fi
          |    # copy  
          |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination"  ||
-         |        { echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue; }
+         |        ( echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue)
          |    # check data integrity
          |    _check_data_integrity $$destination $$s3_path || 
-         |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+         |       (echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
          |    # copy succeeded
          |    break
          |  done
@@ -203,18 +203,18 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |       destination=$${destination%/}
          |       # glob directory. do recursive copy
          |       $awsCmd s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" || 
-         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
+         |         ( echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
          |       # check integrity for each of the files
          |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
          |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE || 
-         |               { echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2; }
+         |               ( echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2)
          |       done
          |    else 
          |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" || 
-         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
+         |         ( echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
          |      # check content length for data integrity
          |      _check_data_integrity $$local_path $$destination || 
-         |         { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+         |         ( echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
          |    fi
          |    # copy succeeded
          |    break
@@ -235,10 +235,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |      exit 1
          |  fi
          |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
-         |        { echo "Attempt to get head of object failed for $$s3_path." && return 1 ; }
+         |        ( echo "Attempt to get head of object failed for $$s3_path." && return 1 )
          |  # local
          |  local_content_length=$$(LC_ALL=C ls -dn -- "$$local_path" | awk '{print $$5; exit}' ) || 
-         |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }   
+         |        ( echo "Attempt to get local content length failed for $$_local_path." && return 1 )   
          |  # compare
          |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
          |       true
@@ -277,7 +277,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         s"""
            |touch ${output.name}
            |_s3_delocalize_with_retry ${output.name} ${output.s3key}
-           |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi""".stripMargin
+           |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory "; fi""".stripMargin
 
 
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index df83472bdc2..62a0495c1be 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -133,48 +133,6 @@ Notes:
 - local hashing means that all used containers are pulled. Make sure you have enough storage
 - enable a database to make the cache persistent over cromwell restarts
 
-### Retry with more memory
-
-Cromwell can be configured to retry jobs with more allocated memory, under a defined set of conditions. To enable this, set the following parameters:
-
-cromwell configuration: `cromwell.config`:
-```
-// set the maximal amount of retries.
-// backend.providers.AWSBatch.config.default-runtime-attribues.maxRetries
-backend {
-  providers {
-    AWSBatch {
-      config {
-        default-runtime-attributes {
-          maxRetries: 6 
-        }
-      }
-    }
-  }
-}
-
-// set the keys for Out-Of-Memory killing. 
-// system.io.memory-retry-error-keys
-system{
-    io{
-        memory-retry-error-keys = ["OutOfMemory","Killed"]
-    }
-}
-```
-
-Workflow specific runtime options : `workflow_options.json`:
-```
-{
-    "memory_retry_multiplier" : 1.5
-}
-```
-
-When providing the options.json file during workflow submission, jobs that were terminated due to insufficient memory will be retried 6 times, with increasing memory allocation. For example 4Gb => 6Gb => 9Gb => 13.5Gb => ... 
-
-Note: Retries of jobs using the `awsBatchRetryAttempts` counter do *not* increase memory allocation. 
-
-
-
 AWS Batch
 ---------
 

From 1d225d5599511a508a929ec24d3f99161c8726cd Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Tue, 5 Apr 2022 09:22:51 +0200
Subject: [PATCH 060/326] catch the fact that not all failed batch jobs have a
 status reason

---
 .../AwsBatchAsyncBackendJobExecutionActor.scala   | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index a534ae2b8da..06d9d4dce35 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -538,8 +538,19 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
             Log.debug("container exit code was zero")
             false
         case _ => 
-            val containerStatusReason = lastattempt.container.reason 
-            Log.warn(s"Job failed with Container status reason : '${containerStatusReason}'")
+            // not every failed job has a container exit reason.
+            val containerStatusReason:String = {
+               var lastReason =  lastattempt.container.reason
+               // cast null to empty-string to prevent nullpointer execption.
+               if (lastReason == null || lastReason.isEmpty) {
+                   lastReason = ""
+                   log.debug("No exit reason found for container.")
+               } else {
+                   Log.warn(s"Job failed with Container status reason : '${lastReason}'")
+               }
+               lastReason
+            }
+            // check the list of OOM-keys against the exit reason.
             val RetryMemoryKeys = memoryRetryErrorKeys.toList.flatten
             val retry = RetryMemoryKeys.exists(containerStatusReason.contains)
             Log.debug(s"Retry job based on provided keys : '${retry}'")

From 039d808be67ac357f291834ef4c487152966c09c Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Tue, 5 Apr 2022 10:15:31 +0200
Subject: [PATCH 061/326] recommit changes rejected in last PR

---
 .../StandardAsyncExecutionActor.scala         | 128 ++++++++++--------
 .../engine/io/RetryableRequestSupport.scala   |  26 +++-
 ...wsBatchAsyncBackendJobExecutionActor.scala |  12 +-
 .../backend/impl/aws/AwsBatchJob.scala        |  18 +--
 .../scala/cromwell/backend/impl/aws/README.md |  42 ++++++
 5 files changed, 158 insertions(+), 68 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 9b21871b538..2ef8b7bd5b7 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -1265,70 +1265,16 @@ trait StandardAsyncExecutionActor
   def handleExecutionResult(status: StandardAsyncRunState,
                             oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
     
-    // get the memory retry code.
-    def memoryRetryRC: Future[Boolean] = {
-      // convert int to boolean
-      def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
-        codeAsOption match {
-          case Some(codeAsString) =>
-            Try(codeAsString.trim.toInt) match {
-              case Success(code) => code match {
-                case StderrContainsRetryKeysCode => true
-                case _ => false
-              }
-              case Failure(e) =>
-                log.error(s"'CheckingForMemoryRetry' action exited with code '$codeAsString' which couldn't be " +
-                  s"converted to an Integer. Task will not be retried with more memory. Error: ${ExceptionUtils.getMessage(e)}")
-                false
-            }
-          case None => false
-        }
-      }
-      // read if the file exists
-      def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] = {
-        if (fileExists)
-          asyncIo.contentAsStringAsync(jobPaths.memoryRetryRC, None, failOnOverflow = false).map(Option(_))
-        else
-          Future.successful(None)
-      }
-      //finally : assign the yielded variable
-      for {
-        fileExists <- asyncIo.existsAsync(jobPaths.memoryRetryRC)
-        retryCheckRCAsOption <- readMemoryRetryRCFile(fileExists)
-        retryWithMoreMemory = returnCodeAsBoolean(retryCheckRCAsOption)
-      } yield retryWithMoreMemory
-    }
-
-    // get the exit code of the job.
-    def JobExitCode: Future[String] = {
-      
-      // read if the file exists
-      def readRCFile(fileExists: Boolean): Future[String] = {
-        if (fileExists)
-          asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
-        else {
-          jobLogger.warn("RC file not found. Setting job to failed & waiting 5m before retry.")
-          Thread.sleep(300000)
-          Future("1")
-        }
-      }
-      //finally : assign the yielded variable
-      for {
-        fileExists <- asyncIo.existsAsync(jobPaths.returnCode)
-        jobRC <- readRCFile(fileExists)
-      } yield jobRC
-    }
-
     // get path to sderr
     val stderr = jobPaths.standardPaths.error
     lazy val stderrAsOption: Option[Path] = Option(stderr)
-    // get the three needed variables, using functions above or direct assignment.
+    // get the three needed variables, using helper functions below, or direct assignment.
     val stderrSizeAndReturnCodeAndMemoryRetry = for {
       returnCodeAsString <- JobExitCode
       // Only check stderr size if we need to, otherwise this results in a lot of unnecessary I/O that
       // may fail due to race conditions on quickly-executing jobs.
       stderrSize <- if (failOnStdErr) asyncIo.sizeAsync(stderr) else Future.successful(0L)
-      retryWithMoreMemory <- memoryRetryRC
+      retryWithMoreMemory <- memoryRetryRC(oldHandle.pendingJob)
     } yield (stderrSize, returnCodeAsString, retryWithMoreMemory)
 
     stderrSizeAndReturnCodeAndMemoryRetry flatMap {
@@ -1337,25 +1283,36 @@ trait StandardAsyncExecutionActor
 
         if (isDone(status)) {
           tryReturnCodeAsInt match {
+            // stderr not empty : retry
             case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
-            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
+            // job was aborted (cancelled by user?) 
+            // on AWS OOM kill are code 137 : check retryWithMoreMemory here 
+            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) && !retryWithMoreMemory =>
+              jobLogger.debug(s"Job was aborted, code was : '${returnCodeAsString}'")
               Future.successful(AbortedExecutionHandle)
+            // job considered ok by accepted exit code
             case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
               handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
+            // job failed on out-of-memory : retry
             case Success(returnCodeAsInt) if retryWithMoreMemory  =>
+              jobLogger.warn(s"Retrying job due to OOM with exit code : '${returnCodeAsString}' ")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle, retryWithMoreMemory)
+            // unaccepted return code : retry.
             case Success(returnCodeAsInt) =>
+              jobLogger.debug(s"Retrying with wrong exit code : '${returnCodeAsString}'")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
             case Failure(_) =>
+              jobLogger.warn(s"General failure of job with exit code : '${returnCodeAsString}'")
               Future.successful(FailedNonRetryableExecutionHandle(ReturnCodeIsNotAnInt(jobDescriptor.key.tag, returnCodeAsString, stderrAsOption), kvPairsToSave = None))
           }
         } else {
           tryReturnCodeAsInt match {
             case Success(returnCodeAsInt) if retryWithMoreMemory && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
+              jobLogger.debug(s"job not done but retrying already? : ${status.toString()}")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle, retryWithMoreMemory)
             case _ =>
@@ -1373,6 +1330,63 @@ trait StandardAsyncExecutionActor
     }
   }
 
+  // helper function for handleExecutionResult : get the exit code of the job.
+  def JobExitCode: Future[String] = {
+      
+    // read if the file exists
+    def readRCFile(fileExists: Boolean): Future[String] = {
+      if (fileExists)
+        asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
+      else {
+        jobLogger.warn("RC file not found. Setting job to failed & retry.")
+        //Thread.sleep(300000)
+        Future("1")
+      }
+    }
+    //finally : assign the yielded variable
+    for {
+      fileExists <- asyncIo.existsAsync(jobPaths.returnCode)
+      jobRC <- readRCFile(fileExists)
+    } yield jobRC
+  }
+
+  // helper function for handleExecutionResult : get the memory retry code.
+  def memoryRetryRC(job: StandardAsyncJob): Future[Boolean] = {
+    // job is used in aws override version. use here to prevent compilation error.
+    log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
+    // convert int to boolean
+    def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
+      codeAsOption match {
+        case Some(codeAsString) =>
+          Try(codeAsString.trim.toInt) match {
+            case Success(code) => code match {
+              case StderrContainsRetryKeysCode => true
+              case _ => false
+            }
+            case Failure(e) =>
+              log.error(s"'CheckingForMemoryRetry' action exited with code '$codeAsString' which couldn't be " +
+                s"converted to an Integer. Task will not be retried with more memory. Error: ${ExceptionUtils.getMessage(e)}")
+              false
+          }
+        case None => false
+      }
+    }
+    // read if the file exists
+    def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] = {
+      if (fileExists)
+        asyncIo.contentAsStringAsync(jobPaths.memoryRetryRC, None, failOnOverflow = false).map(Option(_))
+      else
+        Future.successful(None)
+    }
+    //finally : assign the yielded variable
+    for {
+      fileExists <- asyncIo.existsAsync(jobPaths.memoryRetryRC)
+      retryCheckRCAsOption <- readMemoryRetryRCFile(fileExists)
+      retryWithMoreMemory = returnCodeAsBoolean(retryCheckRCAsOption)
+    } yield retryWithMoreMemory
+  }
+
+
   /**
     * Send the job id of the running job to the key value store.
     *
diff --git a/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala b/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
index 03ef9224b7d..9efa3e7c767 100644
--- a/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
+++ b/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
@@ -26,7 +26,7 @@ object RetryableRequestSupport {
     case _: SocketException => true
     case _: SocketTimeoutException => true
     case ioE: IOException if Option(ioE.getMessage).exists(_.contains("Error getting access token for service account")) => true
-    case ioE: IOException => isGcs500(ioE) || isGcs503(ioE) || isGcs504(ioE)
+    case ioE: IOException => isGcs500(ioE) || isGcs503(ioE) || isGcs504(ioE) || isAws504(ioE)
     case other =>
       // Infinitely retryable is a subset of retryable
       isInfinitelyRetryable(other)
@@ -86,4 +86,28 @@ object RetryableRequestSupport {
       msg.contains("504 Gateway Timeout")
     )
   }
+  // AWS timeout error
+  def isAws504(failure: Throwable): Boolean = {
+    Option(failure.getMessage).exists(msg =>
+      ( 
+        // timeout in reading form s3. 
+        msg.contains("Could not read from s3") && 
+        msg.contains("Timeout waiting for connection") 
+      ) || (
+        // reading in cromwell wdl (read_lines() etc)
+        msg.contains("Failed to evaluate") &&
+        msg.contains("s3://") && 
+        msg.contains("Timed out after")
+      )
+    )
+  }
+  // General AWS IO error : all items unreadable except rc.txt files (might be missing)
+  //   => mainly for testing. will retry mis-specified s3 paths as well... 
+  def isAwsIO(failure:Throwable): Boolean = {
+    Option(failure.getMessage).exists(msg =>
+      msg.contains("Could not read from s3") && 
+      ! msg.contains("-rc.txt") 
+    )
+  }
+
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index d5a32cb2b3f..06d9d4dce35 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -57,7 +57,10 @@ import cromwell.filesystems.s3.S3Path
 import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
 import cromwell.services.keyvalue.KvClient
 import org.slf4j.{Logger, LoggerFactory}
-import software.amazon.awssdk.services.batch.model.{BatchException, SubmitJobResponse}
+import software.amazon.awssdk.services.batch.BatchClient
+//import software.amazon.awssdk.services.batch.model.{BatchException, SubmitJobResponse}
+import software.amazon.awssdk.services.batch.model._
+
 import wom.callable.Callable.OutputDefinition
 import wom.core.FullyQualifiedName
 import wom.expression.NoIoFunctionSet
@@ -184,6 +187,13 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       Option(configuration.awsAuth),
       configuration.fsxMntPoint)
   }
+
+  // setup batch client to query job container info
+  lazy val batchClient: BatchClient = {
+    val builder = BatchClient.builder()
+    configureClient(builder, batchJob.optAwsAuthMode, batchJob.configRegion)
+  }
+
   /* Tries to abort the job in flight
    *
    * @param job A StandardAsyncJob object (has jobId value) to cancel
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index e79a948377b..757c7ab7b87 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -171,10 +171,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |    fi
          |    # copy  
          |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination"  ||
-         |        ( echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue)
+         |        { echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue; }
          |    # check data integrity
          |    _check_data_integrity $$destination $$s3_path || 
-         |       (echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
+         |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # copy succeeded
          |    break
          |  done
@@ -203,18 +203,18 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |       destination=$${destination%/}
          |       # glob directory. do recursive copy
          |       $awsCmd s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" || 
-         |         ( echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
+         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
          |       # check integrity for each of the files
          |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
          |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE || 
-         |               ( echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2)
+         |               { echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2; }
          |       done
          |    else 
          |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" || 
-         |         ( echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
+         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
          |      # check content length for data integrity
          |      _check_data_integrity $$local_path $$destination || 
-         |         ( echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
+         |         { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    fi
          |    # copy succeeded
          |    break
@@ -235,10 +235,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |      exit 1
          |  fi
          |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
-         |        ( echo "Attempt to get head of object failed for $$s3_path." && return 1 )
+         |        { echo "Attempt to get head of object failed for $$s3_path." && return 1 ; }
          |  # local
          |  local_content_length=$$(LC_ALL=C ls -dn -- "$$local_path" | awk '{print $$5; exit}' ) || 
-         |        ( echo "Attempt to get local content length failed for $$_local_path." && return 1 )   
+         |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }   
          |  # compare
          |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
          |       true
@@ -277,7 +277,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         s"""
            |touch ${output.name}
            |_s3_delocalize_with_retry ${output.name} ${output.s3key}
-           |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory "; fi""".stripMargin
+           |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi""".stripMargin
 
 
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 62a0495c1be..df83472bdc2 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -133,6 +133,48 @@ Notes:
 - local hashing means that all used containers are pulled. Make sure you have enough storage
 - enable a database to make the cache persistent over cromwell restarts
 
+### Retry with more memory
+
+Cromwell can be configured to retry jobs with more allocated memory, under a defined set of conditions. To enable this, set the following parameters:
+
+cromwell configuration: `cromwell.config`:
+```
+// set the maximal amount of retries.
+// backend.providers.AWSBatch.config.default-runtime-attribues.maxRetries
+backend {
+  providers {
+    AWSBatch {
+      config {
+        default-runtime-attributes {
+          maxRetries: 6 
+        }
+      }
+    }
+  }
+}
+
+// set the keys for Out-Of-Memory killing. 
+// system.io.memory-retry-error-keys
+system{
+    io{
+        memory-retry-error-keys = ["OutOfMemory","Killed"]
+    }
+}
+```
+
+Workflow specific runtime options : `workflow_options.json`:
+```
+{
+    "memory_retry_multiplier" : 1.5
+}
+```
+
+When providing the options.json file during workflow submission, jobs that were terminated due to insufficient memory will be retried 6 times, with increasing memory allocation. For example 4Gb => 6Gb => 9Gb => 13.5Gb => ... 
+
+Note: Retries of jobs using the `awsBatchRetryAttempts` counter do *not* increase memory allocation. 
+
+
+
 AWS Batch
 ---------
 

From ad8f194c87f99f191fe7e3e8be7bb4c984a39461 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Sat, 9 Apr 2022 19:10:14 +0200
Subject: [PATCH 062/326] fix nullPointer Exception in new retryfunction in
 case of spot kills

---
 ...wsBatchAsyncBackendJobExecutionActor.scala | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 06d9d4dce35..c6a9ed3aae3 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -526,22 +526,33 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
   // new OOM detection 
   override def memoryRetryRC(job: StandardAsyncJob): Future[Boolean] = Future {
+      // STATUS LOGIC:
+      //   - success : container exit code is zero
+      //   - command failure: container exit code > 0, no statusReason in container
+      //   - OOM kill : container exit code > 0, statusReason contains "OutOfMemory"
+      //   - spot kill : no container exit code set. statusReason of ATTEMPT (not container) says "host EC2 (...) terminated"
+
       Log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
       val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(job.jobId).build)
       val jobDetail = describeJobsResponse.jobs.get(0) //OrElse(throw new RuntimeException(s"Could not get job details for job '${job.jobId}'"))
       val nrAttempts = jobDetail.attempts.size
       val lastattempt = jobDetail.attempts.get(nrAttempts-1)
-      val containerRC = lastattempt.container.exitCode
+      var containerRC = lastattempt.container.exitCode
+      // if missing, set to failed.
+      if (containerRC == null ) {
+          Log.debug(s"No RC found for job '${job.jobId}', most likely a spot kill")
+          containerRC = 1
+      }
       // if not zero => get reason, else set retry to false.
       containerRC.toString() match {
         case "0" => 
-            Log.debug("container exit code was zero")
+            Log.debug("container exit code was zero. job succeeded")
             false
         case _ => 
-            // not every failed job has a container exit reason.
+            // failed job due to command errors (~ user errors) don't have a container exit reason.
             val containerStatusReason:String = {
                var lastReason =  lastattempt.container.reason
-               // cast null to empty-string to prevent nullpointer execption.
+               // cast null to empty-string to prevent nullpointer exception.
                if (lastReason == null || lastReason.isEmpty) {
                    lastReason = ""
                    log.debug("No exit reason found for container.")

From d4cca503e7470a00a6d1fe6926f3cd5c3e34efe0 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Tue, 12 Jul 2022 14:33:49 +0200
Subject: [PATCH 063/326] add multipart upload configuration to job script and
 streamline with internal cromwell call cache copy procedures

---
 .../org/lerch/s3fs/S3FileSystemProvider.java  | 37 +++++++++++++------
 .../backend/impl/aws/AwsBatchJob.scala        | 33 ++++++++++++++++-
 .../scala/cromwell/backend/impl/aws/README.md | 23 ++++++++++++
 3 files changed, 80 insertions(+), 13 deletions(-)

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystemProvider.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystemProvider.java
index 208db86d1ba..b8a3b44aa08 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystemProvider.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystemProvider.java
@@ -40,6 +40,9 @@
 import static java.lang.Thread.currentThread;
 import static java.lang.Thread.sleep;
 import static org.lerch.s3fs.AmazonS3Factory.*;
+import com.typesafe.config.Config;
+import com.typesafe.config.ConfigFactory;
+
 
 /**
  *
@@ -82,7 +85,7 @@ public class S3FileSystemProvider extends FileSystemProvider {
     private Cache cache = new Cache();
 
     private final Logger log = Logger.getLogger(this.getClass().getName());
-
+     
     @Override
     public String getScheme() {
         return "s3";
@@ -422,6 +425,12 @@ public void copy(Path source, Path target, CopyOption... options) throws IOExcep
 
         final S3Path s3Source = toS3Path(source);
         final S3Path s3Target = toS3Path(target);
+        log.fine("Starting copy of "+source);
+        // get/set threshold for multipart uploads.
+        final Config conf = ConfigFactory.load();
+        Long threshold = conf.hasPath("engine.filesystems.s3.MultipartThreshold") ? conf.getMemorySize("engine.filesystems.s3.MultipartThreshold").toBytes() : 5L * 1024L * 1024L * 1024L; 
+        log.fine("MultiPart Threshold during S3 copy: "+threshold+ " bytes");
+
 
         final ImmutableSet<CopyOption> actualOptions = ImmutableSet.copyOf(options);
         verifySupportedOptions(EnumSet.of(StandardCopyOption.REPLACE_EXISTING), actualOptions);
@@ -429,15 +438,17 @@ public void copy(Path source, Path target, CopyOption... options) throws IOExcep
         if (exists(s3Target) && !actualOptions.contains(StandardCopyOption.REPLACE_EXISTING)) {
             throw new FileAlreadyExistsException(format("target already exists: %s", target));
         }
-
         long objectSize = this.objectSize(s3Source);
-        long threshold = 5L * 1024L * 1024L * 1024L; //5GB
         if (objectSize >= threshold) {
             // large file, do a multipart copy
+            log.fine("Doing multipart copy for "+s3Source+" to "+s3Target);
             multiPartCopy(s3Source, objectSize, s3Target, options);
+            log.fine("MP copy finished for : "+source);
 
         } else {
             //do a normal copy
+            log.fine("Doing normal copy for "+s3Source+" to "+s3Target);
+
             String bucketNameOrigin = s3Source.getFileStore().name();
             String keySource = s3Source.getKey();
             String bucketNameTarget = s3Target.getFileStore().name();
@@ -451,6 +462,7 @@ public void copy(Path source, Path target, CopyOption... options) throws IOExcep
                             .destinationBucket(bucketNameTarget)
                             .destinationKey(keyTarget)
                             .build());
+            log.fine("Copy finished : "+source);
         }
     }
 
@@ -463,7 +475,7 @@ public void copy(Path source, Path target, CopyOption... options) throws IOExcep
      * @param options copy options
      */
     private void multiPartCopy(S3Path source, long objectSize, S3Path target, CopyOption... options) {
-        log.info(() -> "Attempting multipart copy as part of call cache hit: source = " + source + ", objectSize = " + objectSize + ", target = " + target + ", options = " + Arrays.deepToString(options));
+        log.fine(() -> "Attempting multipart copy as part of call cache hit: source = " + source + ", objectSize = " + objectSize + ", target = " + target + ", options = " + Arrays.deepToString(options));
 
         S3Client s3Client = target.getFileStore().getClient();
 
@@ -482,10 +494,13 @@ private void multiPartCopy(S3Path source, long objectSize, S3Path target, CopyOp
         List<CompletableFuture<UploadPartCopyResponse>> uploadFutures = new ArrayList<>();
 
         /* if you set this number to a larger value then ensure the HttpClient has sufficient
-           maxConnections (see org.lerch.s3fsAmazonS3Factory.getHttpClient)  */
-        int THREADS = 500;
+           maxConnections (see org.lerch.s3fsAmazonS3Factory.getHttpClient)  :
+             default value == 500   */
+        final Config conf = ConfigFactory.load();
+        // override max connections if set.
+        final int THREADS = conf.hasPath("engine.filesystems.s3.threads") ? Integer.parseInt(conf.getString("engine.filesystems.s3.threads")) : 500; 
 
-        log.info(() -> "Allocating work stealing pool with "+THREADS+" threads");
+        log.fine(() -> "Allocating work stealing pool with "+THREADS+" threads");
         final ExecutorService MULTIPART_OPERATION_EXECUTOR_SERVICE = Executors.newWorkStealingPool(THREADS);
 
 
@@ -535,7 +550,7 @@ private void multiPartCopy(S3Path source, long objectSize, S3Path target, CopyOp
                 log.severe("Max Memory = "+runtime.maxMemory());
 
                 // clean up so we don't get zombie threads
-                log.info(() -> "Shutting down work stealing pool");
+                log.fine(() -> "Shutting down work stealing pool");
                 MULTIPART_OPERATION_EXECUTOR_SERVICE.shutdown();
 
                 log.throwing(S3FileSystemProvider.class.getName(), "multiPartCopy", e);
@@ -562,7 +577,7 @@ private void multiPartCopy(S3Path source, long objectSize, S3Path target, CopyOp
                         .build())
                 .collect(Collectors.toList());
 
-        log.info(() -> "Shutting down work stealing pool");
+        log.fine(() -> "Shutting down work stealing pool");
         MULTIPART_OPERATION_EXECUTOR_SERVICE.shutdown();
 
         // build a request to complete the upload
@@ -579,7 +594,7 @@ private void multiPartCopy(S3Path source, long objectSize, S3Path target, CopyOp
             // make a request to complete the multipart upload
             final CompleteMultipartUploadResponse completeMultipartUploadResponse = s3Client.completeMultipartUpload(completeMultipartUploadRequest);
 
-            log.info(() -> "Multipart copy complete with status code: "+completeMultipartUploadResponse.sdkHttpResponse().statusCode());
+            log.fine(() -> "Multipart copy complete with status code: "+completeMultipartUploadResponse.sdkHttpResponse().statusCode());
         } catch (AwsServiceException | SdkClientException e) {
             log.warning(() -> "An "+e.getClass().getName()+" with message "+e.getMessage()+
                     " occurred while completing the multipart upload. Will try again.");
@@ -590,7 +605,7 @@ private void multiPartCopy(S3Path source, long objectSize, S3Path target, CopyOp
             }
 
             final CompleteMultipartUploadResponse completeMultipartUploadResponse = s3Client.completeMultipartUpload(completeMultipartUploadRequest);
-            log.info(() -> "Multipart copy complete with status code: "+completeMultipartUploadResponse.sdkHttpResponse().statusCode());
+            log.fine(() -> "Multipart copy complete with status code: "+completeMultipartUploadResponse.sdkHttpResponse().statusCode());
         }
     }
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 757c7ab7b87..7ad344f91e5 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -60,6 +60,8 @@ import scala.collection.JavaConverters._
 import scala.concurrent.duration._
 import scala.language.higherKinds
 import scala.util.Try
+import com.typesafe.config.Config
+import com.typesafe.config.ConfigFactory
 
 /**
   *  The actual job for submission in AWS batch. `AwsBatchJob` is the primary interface to AWS Batch. It creates the
@@ -146,10 +148,15 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
       case _ => ""
     }.toList.mkString("\n")
 
+    // get multipart threshold from config.
+    val conf : Config = ConfigFactory.load();
+    val mp_threshold : Long = if (conf.hasPath("engine.filesystems.s3.MultipartThreshold") ) conf.getMemorySize("engine.filesystems.s3.MultipartThreshold").toBytes() else 5L * 1024L * 1024L * 1024L; 
+    Log.info(s"MultiPart Threshold for delocalizing is $mp_threshold")
+
     // this goes at the start of the script after the #!
     val preamble =
       s"""
-          |export AWS_METADATA_SERVICE_TIMEOUT=10
+         |export AWS_METADATA_SERVICE_TIMEOUT=10
          |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
          |
          |function _s3_localize_with_retry() {
@@ -171,7 +178,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |    fi
          |    # copy  
          |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination"  ||
-         |        { echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue; }
+         |        { echo "attempt $$i to copy $$s3_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # check data integrity
          |    _check_data_integrity $$destination $$s3_path || 
          |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
@@ -181,10 +188,20 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |}
          |
          |function _s3_delocalize_with_retry() {
+         |  # input variables
          |  local local_path=$$1
          |  # destination must be the path to a file and not just the directory you want the file in
          |  local destination=$$2
          |
+         |  # get the multipart chunk size
+         |  chunk_size=$$(_get_multipart_chunk_size $$local_path)
+         |  echo "chunk size : $$chunk_size bytes"
+         |  local MP_THRESHOLD=${mp_threshold}
+         |  # then set them 
+         |  $awsCmd configure set default.s3.multipart_threshold $$MP_THRESHOLD
+         |  $awsCmd configure set default.s3.multipart_chunksize $$chunk_size
+         |
+         |  # try & validate upload 5 times
          |  for i in {1..6};
          |  do
          |    # if tries exceeded : abort
@@ -221,6 +238,18 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  done
          |}
          |
+         |function _get_multipart_chunk_size() {
+         |  local file_path=$$1
+         |  # file size
+         |  file_size=$$(stat --printf="%s" $$file_path) 
+         |  # chunk_size : you can have at most 10K parts with at least one 5MB part
+         |  # this reflects the formula in s3-copy commands of cromwell (S3FileSystemProvider.java) 
+         |  #   => long partSize = Math.max((objectSize / 10000L) + 1, 5 * 1024 * 1024);
+         |  a=$$(( ( file_size / 10000) + 1 ))
+         |  b=$$(( 5 * 1024 * 1024 ))
+         |  chunk_size=$$(( a > b ? a : b ))
+         |  echo $$chunk_size
+         }
          |function _check_data_integrity() {
          |  local local_path=$$1
          |  local s3_path=$$2
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index df83472bdc2..2003e0f9ef3 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -173,6 +173,29 @@ When providing the options.json file during workflow submission, jobs that were
 
 Note: Retries of jobs using the `awsBatchRetryAttempts` counter do *not* increase memory allocation. 
 
+### Multipart copy settings
+
+Multipart copying is a technology to increase upload performance by splitting the file in parallel processes. The awscli client does this automatically for all files over 8Mb. If a file was uploaded using MultiPart uploads, this is reflected in the ETAG value by a trailing '-\d+', where '\d+' reflects the number of parts. 
+
+Cromwell uses a default threshold of 5Gb for multipart copying during cache-copy processes, and tries to create as much parts as possible (minimal size 5Mb, max parts 10K). Although the default settings are fine, this threshold can be adjusted to reflect ETAG-expectations in for examples upstream/downstream applications. If the treshold changes, the ETAGs will differ after copying the data. 
+
+s3 multipart specific options: `cromwell.config`:
+```
+// activate s3 as a supported filesystem
+engine {
+  filesystems {
+    s3 {
+        auth = "default",
+        enabled: true,
+        # at what size should we start using multipart uploads ?
+        MultipartThreshold = "4G",
+        # multipart copying threads : if you set this number to a larger value then ensure the HttpClient has sufficient
+        #   maxConnections (see org.lerch.s3fsAmazonS3Factory.getHttpClient). Default : 500
+        threads = 50
+    }
+  }
+}
+```
 
 
 AWS Batch

From 2bcf564ad7cd8611ba3a8ae7932e9baab2f5bb1c Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Tue, 12 Jul 2022 14:34:09 +0200
Subject: [PATCH 064/326] reduce logging a bit

---
 .../s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
index 818a0004a3e..7cfd648e7a7 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
@@ -55,10 +55,10 @@ protected S3Client generateClient(String bucketName){
      * @return an S3 client appropriate for the region of the named bucket
      */
     protected S3Client generateClient (String bucketName, S3Client locationClient) {
-        logger.info("generating client for bucket: '{}'", bucketName);
+        logger.debug("generating client for bucket: '{}'", bucketName);
         S3Client bucketSpecificClient;
         try {
-            logger.info("determining bucket location with getBucketLocation");
+            logger.debug("determining bucket location with getBucketLocation");
             String bucketLocation = locationClient.getBucketLocation(builder -> builder.bucket(bucketName)).locationConstraintAsString();
 
             bucketSpecificClient = this.clientForRegion(bucketLocation);
@@ -93,7 +93,7 @@ private S3Client clientForRegion(String regionString){
         // It may be useful to further cache clients for regions although at some point clients for buckets may need to be
         // specialized beyond just region end points.
         Region region = regionString.equals("") ? Region.US_EAST_1 : Region.of(regionString);
-        logger.info("bucket region is: '{}'", region.id());
+        logger.debug("bucket region is: '{}'", region.id());
         return S3Client.builder().region(region).build();
     }
 

From b3dea498201caa047e78b75e4fa69a84016bf4bc Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Tue, 12 Jul 2022 14:34:41 +0200
Subject: [PATCH 065/326] take httpClient max-connections from config if 
 present

---
 .../java/org/lerch/s3fs/AmazonS3Factory.java   | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java b/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
index 9d525587642..c45c1b08574 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
@@ -14,7 +14,8 @@
 
 import java.net.URI;
 import java.util.Properties;
-
+import com.typesafe.config.Config;
+import com.typesafe.config.ConfigFactory;
 
 /**
  * Factory base class to create a new AmazonS3 instance.
@@ -99,7 +100,20 @@ protected AwsCredentials getAWSCredentials(Properties props) {
 
     protected SdkHttpClient getHttpClient(Properties props) {
         // TODO: custom http configuration based on properties
-        return ApacheHttpClient.builder().maxConnections(1024).build();
+        ApacheHttpClient.Builder httpClientBuilder = ApacheHttpClient.builder();
+        // override max connections if set in cromwell.config : engine.filesystems.
+        final Config conf = ConfigFactory.load();
+        log.fine("trying to override some settings in httpclient.");
+        if (conf.hasPath("akka.http.server.max-connections") ) {
+            log.debug("Overriding maxconnections to "+conf.getString("akka.http.server.max-connections"));
+            httpClientBuilder = httpClientBuilder.maxConnections(Integer.parseInt(conf.getString("akka.http.server.max-connections")));
+        }
+        else {
+            log.debug("MaxConnections not found in config. Using default value of 1024");
+            httpClientBuilder = httpClientBuilder.maxConnections(1024);
+        }
+        //return ApacheHttpClient.builder().maxConnections(1024).build();
+        return httpClientBuilder.build();
     }
 
     protected S3Configuration getServiceConfiguration(Properties props) {

From 258279ad2e0c97c01832789b8307406805c26def Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Tue, 12 Jul 2022 19:23:46 +0200
Subject: [PATCH 066/326] move more logging to debug channel

---
 .../cromwell/backend/standard/StandardAsyncExecutionActor.scala | 2 +-
 .../s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java        | 2 +-
 .../src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 2ef8b7bd5b7..8a032a02faa 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -385,7 +385,7 @@ trait StandardAsyncExecutionActor
   def commandScriptContents: ErrorOr[String] = {
     val commandString = instantiatedCommand.commandString
     val commandStringAbbreviated = StringUtils.abbreviateMiddle(commandString, "...", abbreviateCommandLength)
-    jobLogger.info(s"`$commandStringAbbreviated`")
+    jobLogger.debug(s"`$commandStringAbbreviated`")
     tellMetadata(Map(CallMetadataKeys.CommandLine -> commandStringAbbreviated))
 
     val cwd = commandDirectory
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java b/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
index c45c1b08574..08ad1abafa5 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
@@ -103,7 +103,7 @@ protected SdkHttpClient getHttpClient(Properties props) {
         ApacheHttpClient.Builder httpClientBuilder = ApacheHttpClient.builder();
         // override max connections if set in cromwell.config : engine.filesystems.
         final Config conf = ConfigFactory.load();
-        log.fine("trying to override some settings in httpclient.");
+        log.debug("trying to override some settings in httpclient.");
         if (conf.hasPath("akka.http.server.max-connections") ) {
             log.debug("Overriding maxconnections to "+conf.getString("akka.http.server.max-connections"));
             httpClientBuilder = httpClientBuilder.maxConnections(Integer.parseInt(conf.getString("akka.http.server.max-connections")));
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 7ad344f91e5..b13e58e2b91 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -151,7 +151,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     // get multipart threshold from config.
     val conf : Config = ConfigFactory.load();
     val mp_threshold : Long = if (conf.hasPath("engine.filesystems.s3.MultipartThreshold") ) conf.getMemorySize("engine.filesystems.s3.MultipartThreshold").toBytes() else 5L * 1024L * 1024L * 1024L; 
-    Log.info(s"MultiPart Threshold for delocalizing is $mp_threshold")
+    Log.debug(s"MultiPart Threshold for delocalizing is $mp_threshold")
 
     // this goes at the start of the script after the #!
     val preamble =

From 4b501ee8c5f03d12f9d2bcb1014d60d652bf4537 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Fri, 19 Aug 2022 10:40:16 +0200
Subject: [PATCH 067/326] more logging reduction

---
 .../lifecycle/execution/job/EngineJobExecutionActor.scala     | 2 +-
 .../main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
index 891a5b6dd26..3402bc7c085 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
@@ -262,7 +262,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
         log.info(template, jobTag, data.failedCopyAttempts, callCachingParameters.maxFailedCopyAttempts, data.aggregatedHashString)
       } else {
         log.info(s"BT-322 {} cache hit copying nomatch: could not find a suitable cache hit.", jobTag)
-        workflowLogger.info("Could not copy a suitable cache hit for {}. No copy attempts were made.", jobTag)
+        workflowLogger.debug("Could not copy a suitable cache hit for {}. No copy attempts were made.", jobTag)
       }
 
       runJob(data)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index b13e58e2b91..f0aeab3fbbd 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -195,7 +195,6 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |
          |  # get the multipart chunk size
          |  chunk_size=$$(_get_multipart_chunk_size $$local_path)
-         |  echo "chunk size : $$chunk_size bytes"
          |  local MP_THRESHOLD=${mp_threshold}
          |  # then set them 
          |  $awsCmd configure set default.s3.multipart_threshold $$MP_THRESHOLD
@@ -378,7 +377,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     //calls the client to submit the job
     def callClient(definitionArn: String, awsBatchAttributes: AwsBatchAttributes): Aws[F, SubmitJobResponse] = {
 
-      Log.info(s"Submitting taskId: $taskId, job definition : $definitionArn, script: $batch_script")
+      Log.debug(s"Submitting taskId: $taskId, job definition : $definitionArn, script: $batch_script")
+      Log.info(s"Submitting taskId: $taskId, script: $batch_script")
 
       val submit: F[SubmitJobResponse] =
         async.delay(batchClient.submitJob(

From 517a6158774315b28f78e3d099792e89c3d740d3 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Fri, 19 Aug 2022 10:43:21 +0200
Subject: [PATCH 068/326] handle jobs terminated before first attempt in retry
 logic

---
 ...wsBatchAsyncBackendJobExecutionActor.scala | 77 +++++++++++++++++--
 1 file changed, 69 insertions(+), 8 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index c6a9ed3aae3..d1c774ce806 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -37,11 +37,16 @@ import java.io.FileNotFoundException
 import akka.actor.ActorRef
 import akka.pattern.AskSupport
 import akka.util.Timeout
+
+import cats.implicits._
+
+import common.exception.MessageAggregation
 import common.collections.EnhancedCollections._
 import common.util.StringUtil._
 import common.validation.Validation._
+
 import cromwell.backend._
-import cromwell.backend.async.{ExecutionHandle, PendingExecutionHandle}
+import cromwell.backend.async._ //{ExecutionHandle, PendingExecutionHandle}
 import cromwell.backend.impl.aws.IntervalLimitedAwsJobSubmitActor.SubmitAwsJobRequest
 import cromwell.backend.impl.aws.OccasionalStatusPollingActor.{NotifyOfStatus, WhatsMyStatus}
 import cromwell.backend.impl.aws.RunStatus.{Initializing, TerminalRunStatus}
@@ -49,16 +54,21 @@ import cromwell.backend.impl.aws.io._
 import cromwell.backend.io.DirectoryFunctions
 import cromwell.backend.io.JobPaths
 import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
+import cromwell.backend.OutputEvaluator._
+
 import cromwell.core._
+import cromwell.core.path.Path
 import cromwell.core.path.{DefaultPathBuilder, Path, PathBuilder, PathFactory}
 import cromwell.core.io.{DefaultIoCommandBuilder, IoCommandBuilder}
 import cromwell.core.retry.SimpleExponentialBackoff
+
 import cromwell.filesystems.s3.S3Path
 import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
+
 import cromwell.services.keyvalue.KvClient
+
 import org.slf4j.{Logger, LoggerFactory}
 import software.amazon.awssdk.services.batch.BatchClient
-//import software.amazon.awssdk.services.batch.model.{BatchException, SubmitJobResponse}
 import software.amazon.awssdk.services.batch.model._
 
 import wom.callable.Callable.OutputDefinition
@@ -67,7 +77,7 @@ import wom.expression.NoIoFunctionSet
 import wom.types.{WomArrayType, WomSingleFileType}
 import wom.values._
 
-import scala.concurrent.{Future, Promise}
+import scala.concurrent._
 import scala.concurrent.duration._
 import scala.language.postfixOps
 import scala.util.control.NoStackTrace
@@ -510,7 +520,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       case NotifyOfStatus(_, _, Some(value)) =>
         Future.successful(value)
       case NotifyOfStatus(_, _, None) =>
-        jobLogger.info("Having to fall back to AWS query for status")
+        jobLogger.debug("Having to fall back to AWS query for status")
         Future.fromTry(job.status(jobId))
       case other =>
         val message = s"Programmer Error (please report this): Received an unexpected message from the OccasionalPollingActor: $other"
@@ -536,8 +546,24 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(job.jobId).build)
       val jobDetail = describeJobsResponse.jobs.get(0) //OrElse(throw new RuntimeException(s"Could not get job details for job '${job.jobId}'"))
       val nrAttempts = jobDetail.attempts.size
-      val lastattempt = jobDetail.attempts.get(nrAttempts-1)
-      var containerRC = lastattempt.container.exitCode
+      // if job is terminated/cancelled before starting, there are no attempts. 
+      val lastattempt = 
+          try {
+              jobDetail.attempts.get(nrAttempts-1)
+          } catch {
+              case _ : Throwable => null
+          }
+      if (lastattempt == null ) {
+        Log.info(s"No attempts were made for job '${job.jobId}'. no memory-related retry needed.")
+        false
+      }
+
+      var containerRC = 
+          try {
+              lastattempt.container.exitCode
+          } catch {
+              case _ : Throwable => null
+          }
       // if missing, set to failed.
       if (containerRC == null ) {
           Log.debug(s"No RC found for job '${job.jobId}', most likely a spot kill")
@@ -621,8 +647,9 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   override def getTerminalEvents(runStatus: RunStatus): Seq[ExecutionEvent] = {
     runStatus match {
       case successStatus: RunStatus.Succeeded => successStatus.eventList
-      case unknown =>
-        throw new RuntimeException(s"handleExecutionSuccess not called with RunStatus.Success. Instead got $unknown")
+      case unknown => {
+            throw new RuntimeException(s"handleExecutionSuccess not called with RunStatus.Success. Instead got $unknown")
+      }
     }
   }
 
@@ -642,4 +669,38 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       }
     )
   }
+    
+  override def handleExecutionSuccess(runStatus: StandardAsyncRunState,
+                             handle: StandardAsyncPendingExecutionHandle,
+                             returnCode: Int)(implicit ec: ExecutionContext): Future[ExecutionHandle] = {
+    evaluateOutputs() map {
+      case ValidJobOutputs(outputs) =>
+        // Need to make sure the paths are up to date before sending the detritus back in the response
+        updateJobPaths()
+        // If instance is terminated while copying stdout/stderr : status is failed while jobs outputs are ok
+        //   => Retryable 
+        if (runStatus.toString().equals("Failed")) {
+            jobLogger.warn("Got Failed RunStatus for success Execution")
+
+            val exception = new MessageAggregation {
+              override def exceptionContext: String = "Got Failed RunStatus for success Execution"
+              override def errorMessages: Traversable[String] = Array("Got Failed RunStatus for success Execution")
+            }
+            FailedNonRetryableExecutionHandle(exception, kvPairsToSave = None)
+        } else {
+            SuccessfulExecutionHandle(outputs, returnCode, jobPaths.detritusPaths, getTerminalEvents(runStatus))
+        }
+      case InvalidJobOutputs(errors) =>
+        val exception = new MessageAggregation {
+          override def exceptionContext: String = "Failed to evaluate job outputs"
+          override def errorMessages: Traversable[String] = errors.toList
+        }
+        FailedNonRetryableExecutionHandle(exception, kvPairsToSave = None)
+      case JobOutputsEvaluationException(exception: Exception) if retryEvaluateOutputsAggregated(exception) =>
+        // Return the execution handle in this case to retry the operation
+        handle
+      case JobOutputsEvaluationException(ex) => FailedNonRetryableExecutionHandle(ex, kvPairsToSave = None)
+    }
+  }
+
 }

From 808767272796f9b40d50bbce1cd73b46119e4f93 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Fri, 19 Aug 2022 10:44:20 +0200
Subject: [PATCH 069/326] handle spot kills AFTER RC.txt file uploaded as a
 regular spot kill and allow retry

---
 .../backend/async/KnownJobFailureException.scala |  4 ++++
 .../standard/StandardAsyncExecutionActor.scala   | 16 ++++++++++------
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/async/KnownJobFailureException.scala b/backend/src/main/scala/cromwell/backend/async/KnownJobFailureException.scala
index 8dd9aef3544..97b76c77f5e 100644
--- a/backend/src/main/scala/cromwell/backend/async/KnownJobFailureException.scala
+++ b/backend/src/main/scala/cromwell/backend/async/KnownJobFailureException.scala
@@ -13,6 +13,10 @@ final case class WrongReturnCode(jobTag: String, returnCode: Int, stderrPath: Op
   override def getMessage = s"Job $jobTag exited with return code $returnCode which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
 }
 
+final case class UnExpectedStatus(jobTag: String, returnCode: Int, jobStatus: String, stderrPath: Option[Path]) extends KnownJobFailureException {
+  override def getMessage = s"Job $jobTag exited with success code '$returnCode' but failed status '$jobStatus'. Suspecting spot kill and retrying."
+}
+
 final case class ReturnCodeIsNotAnInt(jobTag: String, returnCode: String, stderrPath: Option[Path]) extends KnownJobFailureException {
   override def getMessage = {
     if (returnCode.isEmpty)
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 8a032a02faa..38d9a821f7e 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -364,7 +364,7 @@ trait StandardAsyncExecutionActor
    * to re-do this before sending the response.
    */
   private var jobPathsUpdated: Boolean = false
-  private def updateJobPaths(): Unit = if (!jobPathsUpdated) {
+  def updateJobPaths(): Unit = if (!jobPathsUpdated) {
     // .get's are safe on stdout and stderr after falling back to default names above.
     jobPaths.standardPaths = StandardPaths(
       output = hostPathFromContainerPath(executionStdout),
@@ -1161,7 +1161,7 @@ trait StandardAsyncExecutionActor
         configurationDescriptor.slowJobWarningAfter foreach { duration => self ! WarnAboutSlownessAfter(handle.pendingJob.jobId, duration) }
 
         tellKvJobId(handle.pendingJob) map { _ =>
-          if (logJobIds) jobLogger.info(s"job id: ${handle.pendingJob.jobId}")
+          if (logJobIds) jobLogger.debug(s"job id: ${handle.pendingJob.jobId}")
           tellMetadata(Map(CallMetadataKeys.JobId -> handle.pendingJob.jobId))
           /*
           NOTE: Because of the async nature of the Scala Futures, there is a point in time where we have submitted this or
@@ -1280,7 +1280,7 @@ trait StandardAsyncExecutionActor
     stderrSizeAndReturnCodeAndMemoryRetry flatMap {
       case (stderrSize, returnCodeAsString, retryWithMoreMemory) =>
         val tryReturnCodeAsInt = Try(returnCodeAsString.trim.toInt)
-
+        jobLogger.debug(s"Handling execution Result with status '${status.toString()}' and returnCode ${returnCodeAsString}")
         if (isDone(status)) {
           tryReturnCodeAsInt match {
             // stderr not empty : retry
@@ -1292,12 +1292,17 @@ trait StandardAsyncExecutionActor
             case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) && !retryWithMoreMemory =>
               jobLogger.debug(s"Job was aborted, code was : '${returnCodeAsString}'")
               Future.successful(AbortedExecutionHandle)
+            // if instance killed after RC.txt creation : edge case with status == Failed AND returnCode == [accepted values] => retry.
+            case Success(returnCodeAsInt) if status.toString() == "Failed" && continueOnReturnCode.continueFor(returnCodeAsInt) =>
+                jobLogger.debug(s"Suspected spot kill due to status/RC mismatch")
+                val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(UnExpectedStatus(jobDescriptor.key.tag, returnCodeAsInt, status.toString(), stderrAsOption), Option(returnCodeAsInt), None))
+                retryElseFail(executionHandle)
             // job considered ok by accepted exit code
             case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
               handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
             // job failed on out-of-memory : retry
             case Success(returnCodeAsInt) if retryWithMoreMemory  =>
-              jobLogger.warn(s"Retrying job due to OOM with exit code : '${returnCodeAsString}' ")
+              jobLogger.info(s"Retrying job due to OOM with exit code : '${returnCodeAsString}' ")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle, retryWithMoreMemory)
             // unaccepted return code : retry.
@@ -1338,8 +1343,7 @@ trait StandardAsyncExecutionActor
       if (fileExists)
         asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
       else {
-        jobLogger.warn("RC file not found. Setting job to failed & retry.")
-        //Thread.sleep(300000)
+        jobLogger.debug("RC file not found. Setting job to failed.")
         Future("1")
       }
     }

From 56d927eeb530247973cfd7fd9fc4df7596972ab8 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Fri, 19 Aug 2022 11:34:36 +0100
Subject: [PATCH 070/326] fix depecrated

---
 .../backend/impl/aws/AwsBatchInitializationActor.scala      | 2 +-
 .../main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala  | 6 ++----
 .../backend/impl/aws/AwsBatchRuntimeAttributes.scala        | 2 +-
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
index d608c162be0..16241dbb8ce 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
@@ -49,7 +49,7 @@ import spray.json.{JsObject, JsString}
 import org.slf4j.{Logger, LoggerFactory}
 
 import scala.concurrent.Future
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 
 case class AwsBatchInitializationActorParams
 (
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 5c97886130f..72469f75475 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -55,10 +55,8 @@ import software.amazon.awssdk.services.s3.S3Client
 import software.amazon.awssdk.services.s3.model.{GetObjectRequest, HeadObjectRequest, NoSuchKeyException, PutObjectRequest}
 import wdl4s.parser.MemoryUnit
 
-import java.security.MessageDigest
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 import scala.concurrent.duration._
-import scala.language.higherKinds
 import scala.util.Try
 import com.typesafe.config.Config
 import com.typesafe.config.ConfigFactory
@@ -136,7 +134,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
 
       case input: AwsBatchFileInput if input.s3key.startsWith("s3://") =>
         s"_s3_localize_with_retry ${input.s3key} ${input.mount.mountPoint.pathAsString}/${input.local}"
-          .replaceAllLiterally(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
+          .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
 
       case input: AwsBatchFileInput =>
         //here we don't need a copy command but the centaurTests expect us to verify the existence of the file
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index 7a3b4fdc150..c6dcd6aecfa 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -423,7 +423,7 @@ object UlimitsValidation
     extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
   override def key: String = AwsBatchRuntimeAttributes.UlimitsKey
 
-  override def coercion: Traversable[WomType] =
+  override def coercion: Iterable[WomType] =
     Set(WomStringType, WomArrayType(WomMapType(WomStringType, WomStringType)))
 
   var accepted_keys = Set("name", "softLimit", "hardLimit")

From 87cffaa651242d2bb4affb9164e1a89f79aeec5e Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Fri, 19 Aug 2022 12:01:59 +0100
Subject: [PATCH 071/326] fix deprecated libraries

---
 .../lifecycle/execution/job/EngineJobExecutionActor.scala    | 2 +-
 .../impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala     | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
index f2bd2dd4b3d..0f9eec73ef4 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
@@ -262,7 +262,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
         log.info(template, jobTag, data.failedCopyAttempts, callCachingParameters.maxFailedCopyAttempts, data.aggregatedHashString)
       } else {
         log.info(s"BT-322 {} cache hit copying nomatch: could not find a suitable cache hit.", jobTag)
-        workflowLogger.debug("Could not copy a suitable cache hit for {}. No copy attempts were made.", arg = jobTag)
+        workflowLogger.debug(s"Could not copy a suitable cache hit for {$jobTag}. No copy attempts were made.")
       }
 
       runJob(data)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 4ccc6272fc0..af9d95f8b66 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -57,7 +57,6 @@ import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardAsyncExec
 import cromwell.backend.OutputEvaluator._
 
 import cromwell.core._
-import cromwell.core.path.Path
 import cromwell.core.path.{DefaultPathBuilder, Path, PathBuilder, PathFactory}
 import cromwell.core.io.{DefaultIoCommandBuilder, IoCommandBuilder}
 import cromwell.core.retry.SimpleExponentialBackoff
@@ -684,7 +683,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
             val exception = new MessageAggregation {
               override def exceptionContext: String = "Got Failed RunStatus for success Execution"
-              override def errorMessages: Traversable[String] = Array("Got Failed RunStatus for success Execution")
+              override def errorMessages: Iterable[String] = Array("Got Failed RunStatus for success Execution")
             }
             FailedNonRetryableExecutionHandle(exception, kvPairsToSave = None)
         } else {
@@ -693,7 +692,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       case InvalidJobOutputs(errors) =>
         val exception = new MessageAggregation {
           override def exceptionContext: String = "Failed to evaluate job outputs"
-          override def errorMessages: Traversable[String] = errors.toList
+          override def errorMessages: Iterable[String] = errors.toList
         }
         FailedNonRetryableExecutionHandle(exception, kvPairsToSave = None)
       case JobOutputsEvaluationException(exception: Exception) if retryEvaluateOutputsAggregated(exception) =>

From e802f29549d15d807bff65d661d86883c940336e Mon Sep 17 00:00:00 2001
From: Katrina P <68349264+kpierre13@users.noreply.github.com>
Date: Wed, 24 Aug 2022 13:09:32 -0400
Subject: [PATCH 072/326] BW-1206 - Combine all Wes Endpoints & add Tests
 (#6833)

* Add tests, getting frid of WesRunRoutes.scala

* wesWorkflowId fix, ec implicits errors gone

* Refactoring path for GET /runs

* Indentation fix

* Commit to rollback

* Revert "Indentation fix"

This reverts commit 63fc4842c9d4eff68ec9cb7c3ef19e110696598b.

* PR trigger

* Optimize imports

* Missed import
---
 .../cromwell/server/CromwellServer.scala      |   4 +-
 .../routes/CromwellApiService.scala           | 164 +++++++++---------
 .../routes/WesCromwellRouteSupport.scala      |   1 +
 .../routes/wes/WesRouteSupport.scala          | 152 +++++++++++-----
 .../webservice/routes/wes/WesRunRoutes.scala  |  94 ----------
 .../routes/CromwellApiServiceSpec.scala       |  21 ++-
 .../routes/wes/WesRouteSupportSpec.scala      |  70 +++++++-
 7 files changed, 266 insertions(+), 240 deletions(-)
 delete mode 100644 engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala

diff --git a/engine/src/main/scala/cromwell/server/CromwellServer.scala b/engine/src/main/scala/cromwell/server/CromwellServer.scala
index b5705b91dae..76f784875fc 100644
--- a/engine/src/main/scala/cromwell/server/CromwellServer.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellServer.scala
@@ -11,7 +11,6 @@ import cromwell.services.instrumentation.CromwellInstrumentationActor
 import cromwell.webservice.SwaggerService
 import cromwell.webservice.routes.CromwellApiService
 import cromwell.webservice.routes.wes.WesRouteSupport
-import cromwell.webservice.routes.wes.WesRunRoutes
 
 import scala.concurrent.Future
 import scala.util.{Failure, Success}
@@ -37,7 +36,6 @@ class CromwellServerActor(cromwellSystem: CromwellSystem, gracefulShutdown: Bool
     with CromwellApiService
     with CromwellInstrumentationActor
     with WesRouteSupport
-    with WesRunRoutes
     with SwaggerService
     with ActorLogging {
   implicit val actorSystem = context.system
@@ -53,7 +51,7 @@ class CromwellServerActor(cromwellSystem: CromwellSystem, gracefulShutdown: Bool
     * cromwell.yaml is broken unless the swagger index.html is patched. Copy/paste the code from rawls or cromiam if
     * actual cromwell+swagger+oauth+/api support is needed.
     */
-  val apiRoutes: Route = pathPrefix("api")(concat(workflowRoutes, womtoolRoutes, wesRoutes, runRoutes))
+  val apiRoutes: Route = pathPrefix("api")(concat(workflowRoutes, womtoolRoutes, wesRoutes))
   val nonApiRoutes: Route = concat(engineRoutes, swaggerUiResourceRoute)
   val allRoutes: Route = concat(apiRoutes, nonApiRoutes)
 
diff --git a/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala b/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
index 47aa8b57b5c..637509cc4fd 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
@@ -38,11 +38,9 @@ import scala.io.Source
 import scala.util.{Failure, Success, Try}
 
 trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport with WomtoolRouteSupport with WebServiceUtils with WesCromwellRouteSupport {
-
   import CromwellApiService._
 
   implicit def actorRefFactory: ActorRefFactory
-
   implicit val materializer: ActorMaterializer
   implicit val ec: ExecutionContext
 
@@ -57,9 +55,7 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
       }
     },
     path("engine" / Segment / "version") { _ =>
-      get {
-        complete(versionResponse)
-      }
+      get { complete(versionResponse) }
     },
     path("engine" / Segment / "status") { _ =>
       onComplete(serviceRegistryActor.ask(GetCurrentStatus).mapTo[StatusCheckResponse]) {
@@ -74,11 +70,7 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
 
   val workflowRoutes =
     path("workflows" / Segment / "backends") { _ =>
-      get {
-        instrumentRequest {
-          complete(ToResponseMarshallable(backendResponse))
-        }
-      }
+      get { instrumentRequest { complete(ToResponseMarshallable(backendResponse)) } }
     } ~
       path("workflows" / Segment / "callcaching" / "diff") { _ =>
         parameterSeq { parameters =>
@@ -144,7 +136,7 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
             val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor) flatMap { workflowId =>
               workflowStoreActor.ask(WorkflowStoreActor.WorkflowOnHoldToSubmittedCommand(workflowId)).mapTo[WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedResponse]
             }
-            onComplete(response) {
+            onComplete(response){
               case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e: NotInOnHoldStateException)) => e.errorRequest(StatusCodes.Forbidden)
               case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e)) => e.errorRequest(StatusCodes.InternalServerError)
               case Success(r: WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedSuccess) => completeResponse(StatusCodes.OK, toResponse(r.workflowId, WorkflowSubmitted), Seq.empty)
@@ -180,93 +172,93 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
       case Failure(e) => e.failRequest(StatusCodes.InternalServerError)
     }
   }
-}
 
-  object CromwellApiService {
+}
 
-    import spray.json._
+object CromwellApiService {
+  import spray.json._
 
-    /**
-      * Sends a request to abort the workflow. Provides configurable success & error handlers to allow
-      * for different API endpoints to provide different effects in the appropriate situations, e.g. HTTP codes
-      * and error messages
-      */
-    def abortWorkflow(possibleWorkflowId: String,
-                      workflowStoreActor: ActorRef,
-                      workflowManagerActor: ActorRef,
-                      successHandler: PartialFunction[SuccessfulAbortResponse, Route] = standardAbortSuccessHandler,
-                      errorHandler: PartialFunction[Throwable, Route] = standardAbortErrorHandler)
-                     (implicit timeout: Timeout): Route = {
-      handleExceptions(ExceptionHandler(errorHandler)) {
-        Try(WorkflowId.fromString(possibleWorkflowId)) match {
-          case Success(workflowId) =>
-            val response = workflowStoreActor.ask(WorkflowStoreActor.AbortWorkflowCommand(workflowId)).mapTo[AbortResponse]
-            onComplete(response) {
-              case Success(x: SuccessfulAbortResponse) => successHandler(x)
-              case Success(x: WorkflowAbortFailureResponse) => throw x.failure
-              case Failure(e) => throw e
-            }
-          case Failure(_) => throw InvalidWorkflowException(possibleWorkflowId)
-        }
+  /**
+    * Sends a request to abort the workflow. Provides configurable success & error handlers to allow
+    * for different API endpoints to provide different effects in the appropriate situations, e.g. HTTP codes
+    * and error messages
+    */
+  def abortWorkflow(possibleWorkflowId: String,
+                    workflowStoreActor: ActorRef,
+                    workflowManagerActor: ActorRef,
+                    successHandler: PartialFunction[SuccessfulAbortResponse, Route] = standardAbortSuccessHandler,
+                    errorHandler: PartialFunction[Throwable, Route] = standardAbortErrorHandler)
+                   (implicit timeout: Timeout): Route = {
+    handleExceptions(ExceptionHandler(errorHandler)) {
+      Try(WorkflowId.fromString(possibleWorkflowId)) match {
+        case Success(workflowId) =>
+          val response = workflowStoreActor.ask(WorkflowStoreActor.AbortWorkflowCommand(workflowId)).mapTo[AbortResponse]
+          onComplete(response) {
+            case Success(x: SuccessfulAbortResponse) => successHandler(x)
+            case Success(x: WorkflowAbortFailureResponse) => throw x.failure
+            case Failure(e) => throw e
+          }
+        case Failure(_) => throw InvalidWorkflowException(possibleWorkflowId)
       }
     }
+  }
 
-    /**
-      * The abort success handler for typical cases, i.e. cromwell's API.
-      */
-    private def standardAbortSuccessHandler: PartialFunction[SuccessfulAbortResponse, Route] = {
-      case WorkflowAbortedResponse(id) => complete(ToResponseMarshallable(WorkflowAbortResponse(id.toString, WorkflowAborted.toString)))
-      case WorkflowAbortRequestedResponse(id) => complete(ToResponseMarshallable(WorkflowAbortResponse(id.toString, WorkflowAborting.toString)))
-    }
+  /**
+    * The abort success handler for typical cases, i.e. cromwell's API.
+    */
+  private def standardAbortSuccessHandler: PartialFunction[SuccessfulAbortResponse, Route] = {
+    case WorkflowAbortedResponse(id) => complete(ToResponseMarshallable(WorkflowAbortResponse(id.toString, WorkflowAborted.toString)))
+    case WorkflowAbortRequestedResponse(id) => complete(ToResponseMarshallable(WorkflowAbortResponse(id.toString, WorkflowAborting.toString)))
+  }
 
-    /**
-      * The abort error handler for typical cases, i.e. cromwell's API
-      */
-    private def standardAbortErrorHandler: PartialFunction[Throwable, Route] = {
-      case e: InvalidWorkflowException => e.failRequest(StatusCodes.BadRequest)
-      case e: WorkflowNotFoundException => e.errorRequest(StatusCodes.NotFound)
-      case _: AskTimeoutException if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
-      case e: TimeoutException => e.failRequest(StatusCodes.ServiceUnavailable)
-      case e: Exception => e.errorRequest(StatusCodes.InternalServerError)
-    }
+  /**
+    * The abort error handler for typical cases, i.e. cromwell's API
+    */
+  private def standardAbortErrorHandler: PartialFunction[Throwable, Route] = {
+    case e: InvalidWorkflowException => e.failRequest(StatusCodes.BadRequest)
+    case e: WorkflowNotFoundException => e.errorRequest(StatusCodes.NotFound)
+    case _: AskTimeoutException if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
+    case e: TimeoutException => e.failRequest(StatusCodes.ServiceUnavailable)
+    case e: Exception => e.errorRequest(StatusCodes.InternalServerError)
+  }
 
-    def validateWorkflowIdInMetadata(possibleWorkflowId: String,
-                                     serviceRegistryActor: ActorRef)
-                                    (implicit timeout: Timeout, executor: ExecutionContext): Future[WorkflowId] = {
-      Try(WorkflowId.fromString(possibleWorkflowId)) match {
-        case Success(w) =>
-          serviceRegistryActor.ask(ValidateWorkflowIdInMetadata(w)).mapTo[WorkflowValidationResponse] flatMap {
-            case RecognizedWorkflowId => Future.successful(w)
-            case UnrecognizedWorkflowId => validateWorkflowIdInMetadataSummaries(possibleWorkflowId, serviceRegistryActor)
-            case FailedToCheckWorkflowId(t) => Future.failed(t)
-          }
-        case Failure(_) => Future.failed(InvalidWorkflowException(possibleWorkflowId))
-      }
+  def validateWorkflowIdInMetadata(possibleWorkflowId: String,
+                                   serviceRegistryActor: ActorRef)
+                                  (implicit timeout: Timeout, executor: ExecutionContext): Future[WorkflowId] = {
+    Try(WorkflowId.fromString(possibleWorkflowId)) match {
+      case Success(w) =>
+        serviceRegistryActor.ask(ValidateWorkflowIdInMetadata(w)).mapTo[WorkflowValidationResponse] flatMap {
+          case RecognizedWorkflowId => Future.successful(w)
+          case UnrecognizedWorkflowId => validateWorkflowIdInMetadataSummaries(possibleWorkflowId, serviceRegistryActor)
+          case FailedToCheckWorkflowId(t) => Future.failed(t)
+        }
+      case Failure(_) => Future.failed(InvalidWorkflowException(possibleWorkflowId))
     }
+  }
 
-    def validateWorkflowIdInMetadataSummaries(possibleWorkflowId: String,
-                                              serviceRegistryActor: ActorRef)
-                                             (implicit timeout: Timeout, executor: ExecutionContext): Future[WorkflowId] = {
-      Try(WorkflowId.fromString(possibleWorkflowId)) match {
-        case Success(w) =>
-          serviceRegistryActor.ask(ValidateWorkflowIdInMetadataSummaries(w)).mapTo[WorkflowValidationResponse] map {
-            case RecognizedWorkflowId => w
-            case UnrecognizedWorkflowId => throw UnrecognizedWorkflowException(w)
-            case FailedToCheckWorkflowId(t) => throw t
-          }
-        case Failure(_) => Future.failed(InvalidWorkflowException(possibleWorkflowId))
-      }
+  def validateWorkflowIdInMetadataSummaries(possibleWorkflowId: String,
+                                            serviceRegistryActor: ActorRef)
+                                           (implicit timeout: Timeout, executor: ExecutionContext): Future[WorkflowId] = {
+    Try(WorkflowId.fromString(possibleWorkflowId)) match {
+      case Success(w) =>
+        serviceRegistryActor.ask(ValidateWorkflowIdInMetadataSummaries(w)).mapTo[WorkflowValidationResponse] map {
+          case RecognizedWorkflowId => w
+          case UnrecognizedWorkflowId => throw UnrecognizedWorkflowException(w)
+          case FailedToCheckWorkflowId(t) => throw t
+        }
+      case Failure(_) => Future.failed(InvalidWorkflowException(possibleWorkflowId))
     }
+  }
 
-    final case class BackendResponse(supportedBackends: List[String], defaultBackend: String)
+  final case class BackendResponse(supportedBackends: List[String], defaultBackend: String)
 
-    final case class UnrecognizedWorkflowException(id: WorkflowId) extends Exception(s"Unrecognized workflow ID: $id")
+  final case class UnrecognizedWorkflowException(id: WorkflowId) extends Exception(s"Unrecognized workflow ID: $id")
 
-    final case class InvalidWorkflowException(possibleWorkflowId: String) extends Exception(s"Invalid workflow ID: '$possibleWorkflowId'.")
+  final case class InvalidWorkflowException(possibleWorkflowId: String) extends Exception(s"Invalid workflow ID: '$possibleWorkflowId'.")
 
-    val cromwellVersion = VersionUtil.getVersion("cromwell-engine")
-    val swaggerUiVersion = VersionUtil.getVersion("swagger-ui", VersionUtil.sbtDependencyVersion("swaggerUi"))
-    val backendResponse = BackendResponse(BackendConfiguration.AllBackendEntries.map(_.name).sorted, BackendConfiguration.DefaultBackendEntry.name)
-    val versionResponse = JsObject(Map("cromwell" -> cromwellVersion.toJson))
-    val serviceShuttingDownResponse = new Exception("Cromwell service is shutting down.").failRequest(StatusCodes.ServiceUnavailable)
-  }
+  val cromwellVersion = VersionUtil.getVersion("cromwell-engine")
+  val swaggerUiVersion = VersionUtil.getVersion("swagger-ui", VersionUtil.sbtDependencyVersion("swaggerUi"))
+  val backendResponse = BackendResponse(BackendConfiguration.AllBackendEntries.map(_.name).sorted, BackendConfiguration.DefaultBackendEntry.name)
+  val versionResponse = JsObject(Map("cromwell" -> cromwellVersion.toJson))
+  val serviceShuttingDownResponse = new Exception("Cromwell service is shutting down.").failRequest(StatusCodes.ServiceUnavailable)
+}
\ No newline at end of file
diff --git a/engine/src/main/scala/cromwell/webservice/routes/WesCromwellRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/WesCromwellRouteSupport.scala
index 95cde16cd22..349d36a9251 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/WesCromwellRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/WesCromwellRouteSupport.scala
@@ -31,6 +31,7 @@ trait WesCromwellRouteSupport extends WebServiceUtils {
   implicit val timeout: Timeout = duration
 
   implicit def actorRefFactory: ActorRefFactory
+
   implicit val materializer: ActorMaterializer
   implicit val ec: ExecutionContext
 
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
index e4969702460..7ec56e3317a 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
@@ -1,31 +1,38 @@
 package cromwell.webservice.routes.wes
 
 import akka.actor.ActorRef
+import akka.http.scaladsl.model.{StatusCode, StatusCodes}
 import akka.http.scaladsl.server.Directives._
-import akka.http.scaladsl.server.Route
+import akka.http.scaladsl.server.directives.RouteDirectives.complete
+import akka.http.scaladsl.server.{Directive1, Route}
 import akka.pattern.{AskTimeoutException, ask}
 import akka.util.Timeout
+import com.typesafe.config.ConfigFactory
+import cromwell.core.WorkflowId
+import cromwell.core.abort.SuccessfulAbortResponse
 import cromwell.engine.instrumentation.HttpInstrumentation
-import cromwell.services.metadata.MetadataService.{GetStatus, MetadataServiceResponse, StatusLookupFailed}
-import cromwell.webservice.routes.CromwellApiService.{UnrecognizedWorkflowException, validateWorkflowIdInMetadata}
+import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
+import cromwell.server.CromwellShutdown
+import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, GetSingleWorkflowMetadataAction, GetStatus, MetadataServiceResponse, StatusLookupFailed}
+import cromwell.services.{FailedMetadataJsonResponse, SuccessfulMetadataJsonResponse}
 import cromwell.webservice.WebServiceUtils.EnhancedThrowable
+import cromwell.webservice.routes.CromwellApiService.{UnrecognizedWorkflowException, validateWorkflowIdInMetadata}
+import cromwell.webservice.routes.MetadataRouteSupport.{metadataBuilderActorRequest, metadataQueryRequest}
+import cromwell.webservice.routes.wes.WesResponseJsonSupport._
+import cromwell.webservice.routes.wes.WesRouteSupport._
+import cromwell.webservice.routes.{CromwellApiService, WesCromwellRouteSupport}
+import net.ceedubs.ficus.Ficus._
 
-import scala.concurrent.ExecutionContext
+import scala.concurrent.duration.FiniteDuration
+import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success}
-import WesResponseJsonSupport._
-import akka.http.scaladsl.model.{StatusCode, StatusCodes}
-import akka.http.scaladsl.server.directives.RouteDirectives.complete
-import WesRouteSupport._
-import cromwell.core.abort.SuccessfulAbortResponse
-import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
-import cromwell.server.CromwellShutdown
-import cromwell.services.SuccessfulMetadataJsonResponse
-import cromwell.webservice.routes.CromwellApiService
 
-trait WesRouteSupport extends HttpInstrumentation {
+
+
+trait WesRouteSupport extends HttpInstrumentation with WesCromwellRouteSupport {
+
   val serviceRegistryActor: ActorRef
   val workflowManagerActor: ActorRef
-  val workflowStoreActor: ActorRef
 
   implicit val ec: ExecutionContext
   implicit val timeout: Timeout
@@ -49,36 +56,53 @@ trait WesRouteSupport extends HttpInstrumentation {
         pathPrefix("ga4gh" / "wes" / "v1") {
           concat(
             path("service-info") {
-              complete(ServiceInfo.toWesResponse(workflowStoreActor))
+              get {
+                complete(ServiceInfo.toWesResponse(workflowStoreActor))
+              }
             },
-            pathPrefix("runs") {
-              concat(
-                path(Segment / "status") { possibleWorkflowId =>
-                  val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor).flatMap(w => serviceRegistryActor.ask(GetStatus(w)).mapTo[MetadataServiceResponse])
-                  // WES can also return a 401 or a 403 but that requires user auth knowledge which Cromwell doesn't currently have
-                  onComplete(response) {
-                    case Success(SuccessfulMetadataJsonResponse(_, jsObject)) =>
-                      val wesState = WesState.fromCromwellStatusJson(jsObject)
-                      complete(WesRunStatus(possibleWorkflowId, wesState))
-                    case Success(r: StatusLookupFailed) => r.reason.errorRequest(StatusCodes.InternalServerError)
-                    case Success(m: MetadataServiceResponse) =>
-                      // This should never happen, but ....
-                      val error = new IllegalStateException("Unexpected response from Metadata service: " + m)
-                      error.errorRequest(StatusCodes.InternalServerError)
-                    case Failure(_: UnrecognizedWorkflowException) => complete(NotFoundError)
-                    case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
-                  }
-                },
-                path(Segment / "cancel") { possibleWorkflowId =>
-                  post {
-                    CromwellApiService.abortWorkflow(possibleWorkflowId,
-                      workflowStoreActor,
-                      workflowManagerActor,
-                      successHandler = WesAbortSuccessHandler,
-                      errorHandler = WesAbortErrorHandler)
+            path("runs") {
+              get {
+                parameters(("page_size".as[Int].?, "page_token".?)) { (pageSize, pageToken) =>
+                  completeCromwellResponse(listRuns(pageSize, pageToken, serviceRegistryActor))
+                }
+              } ~
+                post {
+                  extractSubmission() { submission =>
+                    submitRequest(submission.entity,
+                      isSingleSubmission = true)
                   }
                 }
-              )
+            },
+            path("runs" / Segment) { workflowId =>
+              get {
+                // this is what it was like in code found in the project… it perhaps isn’t ideal but doesn’t seem to hurt, so leaving it like this for now.
+                completeCromwellResponse(runLog(workflowId, (w: WorkflowId) => GetSingleWorkflowMetadataAction(w, None, None, expandSubWorkflows = false), serviceRegistryActor))
+              }
+            },
+            path("runs" / Segment / "status") { possibleWorkflowId =>
+              val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor).flatMap(w => serviceRegistryActor.ask(GetStatus(w)).mapTo[MetadataServiceResponse])
+              // WES can also return a 401 or a 403 but that requires user auth knowledge which Cromwell doesn't currently have
+              onComplete(response) {
+                case Success(SuccessfulMetadataJsonResponse(_, jsObject)) =>
+                  val wesState = WesState.fromCromwellStatusJson(jsObject)
+                  complete(WesRunStatus(possibleWorkflowId, wesState))
+                case Success(r: StatusLookupFailed) => r.reason.errorRequest(StatusCodes.InternalServerError)
+                case Success(m: MetadataServiceResponse) =>
+                  // This should never happen, but ....
+                  val error = new IllegalStateException("Unexpected response from Metadata service: " + m)
+                  error.errorRequest(StatusCodes.InternalServerError)
+                case Failure(_: UnrecognizedWorkflowException) => complete(NotFoundError)
+                case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
+              }
+            },
+            path("runs" / Segment / "cancel") { possibleWorkflowId =>
+              post {
+                CromwellApiService.abortWorkflow(possibleWorkflowId,
+                  workflowStoreActor,
+                  workflowManagerActor,
+                  successHandler = WesAbortSuccessHandler,
+                  errorHandler = WesAbortErrorHandler)
+              }
             }
           )
         }
@@ -86,7 +110,15 @@ trait WesRouteSupport extends HttpInstrumentation {
     }
 }
 
+
+
 object WesRouteSupport {
+  import WesResponseJsonSupport._
+
+  implicit lazy val duration: FiniteDuration = ConfigFactory.load().as[FiniteDuration]("akka.http.server.request-timeout")
+  implicit lazy val timeout: Timeout = duration
+  import scala.concurrent.ExecutionContext.Implicits.global
+
   val NotFoundError = WesErrorResponse("The requested workflow run wasn't found", StatusCodes.NotFound.intValue)
 
   def WesAbortSuccessHandler: PartialFunction[SuccessfulAbortResponse, Route] = {
@@ -104,4 +136,38 @@ object WesRouteSupport {
   private def respondWithWesError(errorMsg: String, status: StatusCode): Route = {
     complete((status, WesErrorResponse(errorMsg, status.intValue)))
   }
-}
+
+  def extractSubmission(): Directive1[WesSubmission] = {
+    formFields((
+      "workflow_params".?,
+      "workflow_type".?,
+      "workflow_type_version".?,
+      "tags".?,
+      "workflow_engine_parameters".?,
+      "workflow_url".?,
+      "workflow_attachment".as[String].*
+    )).as(WesSubmission)
+  }
+
+  def completeCromwellResponse(future: => Future[WesResponse]): Route = {
+    onComplete(future) {
+      case Success(response: WesResponse) => complete(response)
+      case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
+    }
+  }
+
+  def listRuns(pageSize: Option[Int], pageToken: Option[String], serviceRegistryActor: ActorRef): Future[WesResponse] = {
+    // FIXME: to handle - page_size, page_token
+    // FIXME: How to handle next_page_token in response?
+    metadataQueryRequest(Seq.empty[(String, String)], serviceRegistryActor).map(RunListResponse.fromMetadataQueryResponse)
+  }
+
+  def runLog(workflowId: String, request: WorkflowId => BuildMetadataJsonAction, serviceRegistryActor: ActorRef): Future[WesResponse] = {
+    val metadataJsonResponse = metadataBuilderActorRequest(workflowId, request, serviceRegistryActor)
+
+    metadataJsonResponse.map {
+      case SuccessfulMetadataJsonResponse(_, responseJson) => WesResponseWorkflowMetadata(WesRunLog.fromJson(responseJson.toString()))
+      case FailedMetadataJsonResponse(_, reason) => WesErrorResponse(reason.getMessage, StatusCodes.InternalServerError.intValue)
+    }
+  }
+}
\ No newline at end of file
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala
deleted file mode 100644
index 6ecbac4bdfa..00000000000
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala
+++ /dev/null
@@ -1,94 +0,0 @@
-package cromwell.webservice.routes.wes
-
-import akka.actor.ActorRef
-import akka.http.scaladsl.model.StatusCodes
-import akka.http.scaladsl.server.Directives._
-import akka.http.scaladsl.server.directives.RouteDirectives.complete
-import akka.http.scaladsl.server.{Directive1, Route}
-import akka.util.Timeout
-import com.typesafe.config.ConfigFactory
-import cromwell.core.WorkflowId
-import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, GetSingleWorkflowMetadataAction}
-import cromwell.services.{FailedMetadataJsonResponse, SuccessfulMetadataJsonResponse}
-import cromwell.webservice.routes.MetadataRouteSupport.{metadataBuilderActorRequest, metadataQueryRequest}
-import cromwell.webservice.routes.WesCromwellRouteSupport
-import cromwell.webservice.routes.wes.WesRunRoutes.{completeCromwellResponse, extractSubmission, runLog}
-import net.ceedubs.ficus.Ficus._
-
-import scala.concurrent.ExecutionContext.Implicits.global
-import scala.concurrent.Future
-import scala.concurrent.duration.FiniteDuration
-import scala.util.{Failure, Success}
-
-trait WesRunRoutes extends WesCromwellRouteSupport {
-
-  val serviceRegistryActor: ActorRef
-
-  lazy val runRoutes: Route =
-    pathPrefix("ga4gh" / "wes" / "v1") {
-      concat(
-        path("runs") {
-          get {
-            parameters(("page_size".as[Int].?, "page_token".?)) { (pageSize, pageToken) =>
-              WesRunRoutes.completeCromwellResponse(WesRunRoutes.listRuns(pageSize, pageToken, serviceRegistryActor))
-            }
-          } ~
-          post {
-            extractSubmission() { submission =>
-              submitRequest(submission.entity,
-                isSingleSubmission = true,
-              )
-            }
-          }
-        },
-        path("runs" / Segment) { workflowId =>
-          get {
-            // this is what it was like in code found in the project… it perhaps isn’t ideal but doesn’t seem to hurt, so leaving it like this for now.
-            completeCromwellResponse(runLog(workflowId, (w: WorkflowId) => GetSingleWorkflowMetadataAction(w, None, None, expandSubWorkflows = false), serviceRegistryActor))
-          }
-      }
-      )
-    }
-}
-
-object WesRunRoutes {
-
-  import WesResponseJsonSupport._
-
-  implicit lazy val duration: FiniteDuration = ConfigFactory.load().as[FiniteDuration]("akka.http.server.request-timeout")
-  implicit lazy val timeout: Timeout = duration
-
-  def extractSubmission(): Directive1[WesSubmission] = {
-    formFields((
-      "workflow_params".?,
-      "workflow_type".?,
-      "workflow_type_version".?,
-      "tags".?,
-      "workflow_engine_parameters".?,
-      "workflow_url".?,
-      "workflow_attachment".as[String].*
-    )).as(WesSubmission)
-  }
-
-  def completeCromwellResponse(future: => Future[WesResponse]): Route = {
-    onComplete(future) {
-      case Success(response: WesResponse) => complete(response)
-      case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
-    }
-  }
-
-  def listRuns(pageSize: Option[Int], pageToken: Option[String], serviceRegistryActor: ActorRef): Future[WesResponse] = {
-    // FIXME: to handle - page_size, page_token
-    // FIXME: How to handle next_page_token in response?
-    metadataQueryRequest(Seq.empty[(String, String)], serviceRegistryActor).map(RunListResponse.fromMetadataQueryResponse)
-  }
-
-  def runLog(workflowId: String, request: WorkflowId => BuildMetadataJsonAction, serviceRegistryActor: ActorRef): Future[WesResponse] = {
-    val metadataJsonResponse = metadataBuilderActorRequest(workflowId, request, serviceRegistryActor)
-
-    metadataJsonResponse.map {
-      case SuccessfulMetadataJsonResponse(_, responseJson) => WesResponseWorkflowMetadata(WesRunLog.fromJson(responseJson.toString()))
-      case FailedMetadataJsonResponse(_, reason) => WesErrorResponse(reason.getMessage, StatusCodes.InternalServerError.intValue)
-    }
-  }
-}
diff --git a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
index 2a3b11a41c5..c40c84397f7 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
@@ -1,7 +1,5 @@
 package cromwell.webservice.routes
 
-import java.time.OffsetDateTime
-
 import akka.actor.{Actor, ActorLogging, ActorSystem, Props}
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
 import akka.http.scaladsl.model.ContentTypes._
@@ -17,13 +15,13 @@ import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor._
 import cromwell.engine.workflow.workflowstore.WorkflowStoreEngineActor.{WorkflowOnHoldToSubmittedFailure, WorkflowOnHoldToSubmittedSuccess}
 import cromwell.engine.workflow.workflowstore.WorkflowStoreSubmitActor.{WorkflowSubmittedToStore, WorkflowsBatchSubmittedToStore}
+import cromwell.services._
 import cromwell.services.healthmonitor.ProtoHealthMonitorServiceActor.{GetCurrentStatus, StatusCheckResponse, SubsystemStatus}
 import cromwell.services.instrumentation.InstrumentationService.InstrumentationServiceMessage
 import cromwell.services.metadata.MetadataArchiveStatus._
 import cromwell.services.metadata.MetadataService._
 import cromwell.services.metadata._
 import cromwell.services.metadata.impl.builder.MetadataBuilderActor
-import cromwell.services._
 import cromwell.services.womtool.WomtoolServiceMessages.{DescribeFailure, DescribeRequest, DescribeSuccess}
 import cromwell.services.womtool.models.WorkflowDescription
 import cromwell.util.SampleWdl.HelloWorld
@@ -34,6 +32,7 @@ import org.scalatest.flatspec.AsyncFlatSpec
 import org.scalatest.matchers.should.Matchers
 import spray.json._
 
+import java.time.OffsetDateTime
 import scala.concurrent.duration._
 
 class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with Matchers {
@@ -529,6 +528,7 @@ object CromwellApiServiceSpec {
   val WorkflowIdExistingOnlyInSummaryTable = WorkflowId.fromString("f0000000-0000-0000-0000-000000000011")
   val ArchivedWorkflowId = WorkflowId.fromString("c4c6339c-2145-47fb-acc5-b5cb8d2809f5")
   val ArchivedAndDeletedWorkflowId = WorkflowId.fromString("abc1234d-2145-47fb-acc5-b5cb8d2809f5")
+  val wesWorkflowId = WorkflowId.randomId()
   val SummarizedWorkflowIds = Set(
     SummarizedWorkflowId,
     WorkflowIdExistingOnlyInSummaryTable,
@@ -545,7 +545,8 @@ object CromwellApiServiceSpec {
     FailedWorkflowId,
     SummarizedWorkflowId,
     ArchivedWorkflowId,
-    ArchivedAndDeletedWorkflowId
+    ArchivedAndDeletedWorkflowId,
+    wesWorkflowId
   )
 
   class MockApiService()(implicit val system: ActorSystem) extends CromwellApiService {
@@ -564,13 +565,21 @@ object CromwellApiServiceSpec {
       List(
         MetadataEvent(MetadataKey(workflowId, None, "testKey1a"), MetadataValue("myValue1a", MetadataString)),
         MetadataEvent(MetadataKey(workflowId, None, "testKey1b"), MetadataValue("myValue1b", MetadataString)),
-        MetadataEvent(MetadataKey(workflowId, None, "testKey2a"), MetadataValue("myValue2a", MetadataString))
+        MetadataEvent(MetadataKey(workflowId, None, "testKey2a"), MetadataValue("myValue2a", MetadataString)),
+      )
+    }
+    private def wesFullMetadataResponse(workflowId: WorkflowId) = {
+      List(
+        MetadataEvent(MetadataKey(workflowId, None, "status"), MetadataValue("Running", MetadataString)),
+        MetadataEvent(MetadataKey(workflowId, None, "submittedFiles:workflow"), MetadataValue("myValue2a", MetadataString)),
+
       )
     }
 
     def responseMetadataValues(workflowId: WorkflowId, withKeys: List[String], withoutKeys: List[String]): JsObject = {
       def keyFilter(keys: List[String])(m: MetadataEvent) = keys.exists(k => m.key.key.startsWith(k))
-      val events = fullMetadataResponse(workflowId)
+      val metadataEvents = if (workflowId == wesWorkflowId) wesFullMetadataResponse(workflowId) else fullMetadataResponse(workflowId)
+      val events = metadataEvents
         .filter(m => withKeys.isEmpty || keyFilter(withKeys)(m))
         .filter(m => withoutKeys.isEmpty || !keyFilter(withoutKeys)(m))
 
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
index 0c0fe1c8054..c8306088ded 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
@@ -1,22 +1,27 @@
 package cromwell.webservice.routes.wes
 
 import akka.actor.Props
-import akka.http.scaladsl.model.StatusCodes
 import akka.http.scaladsl.model.HttpMethods.POST
-import akka.http.scaladsl.testkit.ScalatestRouteTest
+import akka.http.scaladsl.model._
+import akka.http.scaladsl.server.MethodRejection
+import akka.http.scaladsl.testkit.{RouteTestTimeout, ScalatestRouteTest}
+import cromwell.util.SampleWdl.HelloWorld
 import cromwell.webservice.routes.CromwellApiServiceSpec
-
-import scala.concurrent.duration._
 import cromwell.webservice.routes.CromwellApiServiceSpec.{MockServiceRegistryActor, MockWorkflowManagerActor, MockWorkflowStoreActor}
+import cromwell.webservice.routes.wes.WesResponseJsonSupport._
 import org.scalatest.flatspec.AsyncFlatSpec
 import org.scalatest.matchers.should.Matchers
-import WesResponseJsonSupport._
-import akka.http.scaladsl.server.MethodRejection
+import spray.json._
+
+import scala.concurrent.duration._
 
 class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Matchers with WesRouteSupport {
+
   val actorRefFactory = system
   override implicit val ec = system.dispatcher
-  override implicit val timeout = 5.seconds
+  override val timeout = routeTestTimeout.duration
+  implicit def routeTestTimeout = RouteTestTimeout(5.seconds)
+
 
   override val workflowStoreActor = actorRefFactory.actorOf(Props(new MockWorkflowStoreActor()))
   override val serviceRegistryActor = actorRefFactory.actorOf(Props(new MockServiceRegistryActor()))
@@ -149,4 +154,53 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
         rejection shouldEqual MethodRejection(POST)
       }
   }
-}
+
+  behavior of "WES API /runs POST endpoint"
+  it should "return 201 for a successful workflow submission" in {
+    val workflowSource = Multipart.FormData.BodyPart("workflow_url", HttpEntity(MediaTypes.`application/json`, "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"))
+    val workflowInputs = Multipart.FormData.BodyPart("workflow_params", HttpEntity(MediaTypes.`application/json`, HelloWorld.rawInputs.toJson.toString()))
+    val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
+    Post(s"/ga4gh/wes/$version/runs", formData) ~>
+      wesRoutes ~>
+      check {
+        assertResult(
+          s"""{
+             |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
+             |  "status": "Submitted"
+             |}""".stripMargin) {
+          responseAs[String].parseJson.prettyPrint
+        }
+        assertResult(StatusCodes.Created) {
+          status
+        }
+        headers should be(Seq.empty)
+      }
+  }
+
+
+  behavior of "WES API /runs GET endpoint"
+  it should "return results for a good query" in {
+    Get(s"/ga4gh/wes/v1/runs") ~>
+      wesRoutes ~>
+      check {
+        status should be(StatusCodes.OK)
+        contentType should be(ContentTypes.`application/json`)
+        val results = responseAs[JsObject].fields("runs").convertTo[Seq[JsObject]]
+        results.head.fields("run_id") should be(JsString(CromwellApiServiceSpec.ExistingWorkflowId.toString))
+        results.head.fields("state") should be(JsString("COMPLETE"))
+      }
+  }
+
+  behavior of "WES API /runs/{run_id} endpoint"
+  it should "return valid metadata when supplied a run_id" in {
+    Get(s"/ga4gh/wes/v1/runs/${CromwellApiServiceSpec.wesWorkflowId}") ~>
+      wesRoutes ~>
+      check {
+        status should be(StatusCodes.OK)
+        val result = responseAs[JsObject].fields("workflowLog").asJsObject()
+        result.fields.keys should contain allOf("request", "run_id", "state")
+        result.fields("state") should be(JsString("RUNNING"))
+        result.fields("run_id") should be(JsString(CromwellApiServiceSpec.wesWorkflowId.toString))
+      }
+  }
+}
\ No newline at end of file

From 79afa2997f91718cbbacc3aa68ca4ee086b6d7f8 Mon Sep 17 00:00:00 2001
From: Katrina P <68349264+kpierre13@users.noreply.github.com>
Date: Thu, 25 Aug 2022 15:15:55 -0400
Subject: [PATCH 073/326] BW-1354 - Porting CBAS preliminary step (#6837)

* Getting rid of shared utility file; Adding/Updating WES version of submit.

* Edit spec file

* Adding Wes-like error
---
 .../routes/CromwellApiService.scala           | 79 ++++++++++++++--
 .../routes/WesCromwellRouteSupport.scala      | 90 -------------------
 .../routes/wes/WesRouteSupport.scala          | 78 ++++++++++++++--
 .../routes/wes/WesRouteSupportSpec.scala      |  3 +-
 4 files changed, 141 insertions(+), 109 deletions(-)
 delete mode 100644 engine/src/main/scala/cromwell/webservice/routes/WesCromwellRouteSupport.scala

diff --git a/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala b/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
index 637509cc4fd..a1c4f023135 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
@@ -1,10 +1,13 @@
 package cromwell.webservice.routes
 
+import java.util.UUID
+
 import akka.actor.{ActorRef, ActorRefFactory}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheDiffActorJsonFormatting.successfulResponseJsonFormatter
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
 import akka.http.scaladsl.marshalling.ToResponseMarshallable
-import akka.http.scaladsl.model.ContentTypes._
 import akka.http.scaladsl.model._
+import akka.http.scaladsl.model.ContentTypes._
 import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server.{ExceptionHandler, Route}
 import akka.pattern.{AskTimeoutException, ask}
@@ -12,6 +15,7 @@ import akka.stream.ActorMaterializer
 import akka.util.Timeout
 import cats.data.NonEmptyList
 import cats.data.Validated.{Invalid, Valid}
+import com.typesafe.config.ConfigFactory
 import common.exception.AggregatedMessageException
 import common.util.VersionUtil
 import cromwell.core.abort._
@@ -20,24 +24,25 @@ import cromwell.engine.backend.BackendConfiguration
 import cromwell.engine.instrumentation.HttpInstrumentation
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheDiffActor.{CachedCallNotFoundException, CallCacheDiffActorResponse, FailedCallCacheDiffResponse, SuccessfulCallCacheDiffResponse}
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheDiffActorJsonFormatting.successfulResponseJsonFormatter
 import cromwell.engine.workflow.lifecycle.execution.callcaching.{CallCacheDiffActor, CallCacheDiffQueryParameter}
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.NotInOnHoldStateException
-import cromwell.engine.workflow.workflowstore.{WorkflowStoreActor, WorkflowStoreEngineActor}
+import cromwell.engine.workflow.workflowstore.{WorkflowStoreActor, WorkflowStoreEngineActor, WorkflowStoreSubmitActor}
 import cromwell.server.CromwellShutdown
-import cromwell.services._
 import cromwell.services.healthmonitor.ProtoHealthMonitorServiceActor.{GetCurrentStatus, StatusCheckResponse}
 import cromwell.services.metadata.MetadataService._
-import cromwell.webservice.WebServiceUtils.EnhancedThrowable
-import cromwell.webservice.WorkflowJsonSupport._
 import cromwell.webservice._
+import cromwell.services._
+import cromwell.webservice.WorkflowJsonSupport._
+import cromwell.webservice.WebServiceUtils
+import cromwell.webservice.WebServiceUtils.EnhancedThrowable
+import net.ceedubs.ficus.Ficus._
 
-import java.util.UUID
+import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future, TimeoutException}
 import scala.io.Source
 import scala.util.{Failure, Success, Try}
 
-trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport with WomtoolRouteSupport with WebServiceUtils with WesCromwellRouteSupport {
+trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport with WomtoolRouteSupport with WebServiceUtils {
   import CromwellApiService._
 
   implicit def actorRefFactory: ActorRefFactory
@@ -48,6 +53,10 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
   val workflowManagerActor: ActorRef
   val serviceRegistryActor: ActorRef
 
+  // Derive timeouts (implicit and not) from akka http's request timeout since there's no point in being higher than that
+  implicit val duration = ConfigFactory.load().as[FiniteDuration]("akka.http.server.request-timeout")
+  implicit val timeout: Timeout = duration
+
   val engineRoutes = concat(
     path("engine" / Segment / "stats") { _ =>
       get {
@@ -173,6 +182,58 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
     }
   }
 
+  private def toResponse(workflowId: WorkflowId, workflowState: WorkflowState): WorkflowSubmitResponse = {
+    WorkflowSubmitResponse(workflowId.toString, workflowState.toString)
+  }
+
+  private def submitRequest(formData: Multipart.FormData, isSingleSubmission: Boolean): Route = {
+
+    def getWorkflowState(workflowOnHold: Boolean): WorkflowState = {
+      if (workflowOnHold)
+        WorkflowOnHold
+      else WorkflowSubmitted
+    }
+
+    def askSubmit(command: WorkflowStoreActor.WorkflowStoreActorSubmitCommand, warnings: Seq[String], workflowState: WorkflowState): Route = {
+      // NOTE: Do not blindly copy the akka-http -to- ask-actor pattern below without knowing the pros and cons.
+      onComplete(workflowStoreActor.ask(command).mapTo[WorkflowStoreSubmitActor.WorkflowStoreSubmitActorResponse]) {
+        case Success(w) =>
+          w match {
+            case WorkflowStoreSubmitActor.WorkflowSubmittedToStore(workflowId, _) =>
+              completeResponse(StatusCodes.Created, toResponse(workflowId, workflowState), warnings)
+            case WorkflowStoreSubmitActor.WorkflowsBatchSubmittedToStore(workflowIds, _) =>
+              completeResponse(StatusCodes.Created, workflowIds.toList.map(toResponse(_, workflowState)), warnings)
+            case WorkflowStoreSubmitActor.WorkflowSubmitFailed(throwable) =>
+              throwable.failRequest(StatusCodes.BadRequest, warnings)
+          }
+        case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
+        case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
+        case Failure(e) => e.failRequest(StatusCodes.InternalServerError, warnings)
+      }
+    }
+
+    onComplete(materializeFormData(formData)) {
+      case Success(data) =>
+        PartialWorkflowSources.fromSubmitRoute(data, allowNoInputs = isSingleSubmission) match {
+          case Success(workflowSourceFiles) if isSingleSubmission && workflowSourceFiles.size == 1 =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            askSubmit(WorkflowStoreActor.SubmitWorkflow(workflowSourceFiles.head), warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+          // Catches the case where someone has gone through the single submission endpoint w/ more than one workflow
+          case Success(workflowSourceFiles) if isSingleSubmission =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            val e = new IllegalArgumentException("To submit more than one workflow at a time, use the batch endpoint.")
+            e.failRequest(StatusCodes.BadRequest, warnings)
+          case Success(workflowSourceFiles) =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            askSubmit(
+              WorkflowStoreActor.BatchSubmitWorkflows(NonEmptyList.fromListUnsafe(workflowSourceFiles.toList)),
+              warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+          case Failure(t) => t.failRequest(StatusCodes.BadRequest)
+        }
+      case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
+      case Failure(e) => e.failRequest(StatusCodes.InternalServerError)
+    }
+  }
 }
 
 object CromwellApiService {
@@ -261,4 +322,4 @@ object CromwellApiService {
   val backendResponse = BackendResponse(BackendConfiguration.AllBackendEntries.map(_.name).sorted, BackendConfiguration.DefaultBackendEntry.name)
   val versionResponse = JsObject(Map("cromwell" -> cromwellVersion.toJson))
   val serviceShuttingDownResponse = new Exception("Cromwell service is shutting down.").failRequest(StatusCodes.ServiceUnavailable)
-}
\ No newline at end of file
+}
diff --git a/engine/src/main/scala/cromwell/webservice/routes/WesCromwellRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/WesCromwellRouteSupport.scala
deleted file mode 100644
index 349d36a9251..00000000000
--- a/engine/src/main/scala/cromwell/webservice/routes/WesCromwellRouteSupport.scala
+++ /dev/null
@@ -1,90 +0,0 @@
-package cromwell.webservice.routes
-
-
-import akka.actor.{ActorRef, ActorRefFactory}
-import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
-import akka.http.scaladsl.model.{Multipart, StatusCodes}
-import akka.http.scaladsl.server.Directives.onComplete
-import akka.http.scaladsl.server.Route
-import akka.pattern.{AskTimeoutException, ask}
-import akka.stream.ActorMaterializer
-import akka.util.Timeout
-import cats.data.NonEmptyList
-import com.typesafe.config.ConfigFactory
-import cromwell.core.{WorkflowId, WorkflowOnHold, WorkflowState, WorkflowSubmitted, path => _}
-import cromwell.engine.workflow.workflowstore.{WorkflowStoreActor, WorkflowStoreSubmitActor}
-import cromwell.server.CromwellShutdown
-import cromwell.webservice.WebServiceUtils.EnhancedThrowable
-import cromwell.webservice.WorkflowJsonSupport._
-import cromwell.webservice.{PartialWorkflowSources, WebServiceUtils, WorkflowSubmitResponse}
-import net.ceedubs.ficus.Ficus._
-
-import scala.concurrent.duration.FiniteDuration
-import scala.concurrent.{ExecutionContext, TimeoutException}
-import scala.util.{Failure, Success}
-
-trait WesCromwellRouteSupport extends WebServiceUtils {
-
-  val workflowStoreActor: ActorRef
-
-  implicit val duration = ConfigFactory.load().as[FiniteDuration]("akka.http.server.request-timeout")
-  implicit val timeout: Timeout = duration
-
-  implicit def actorRefFactory: ActorRefFactory
-
-  implicit val materializer: ActorMaterializer
-  implicit val ec: ExecutionContext
-
-  def toResponse(workflowId: WorkflowId, workflowState: WorkflowState): WorkflowSubmitResponse = {
-    WorkflowSubmitResponse(workflowId.toString, workflowState.toString)
-  }
-
-  def submitRequest(formData: Multipart.FormData, isSingleSubmission: Boolean): Route = {
-
-    def getWorkflowState(workflowOnHold: Boolean): WorkflowState = {
-      if (workflowOnHold)
-        WorkflowOnHold
-      else WorkflowSubmitted
-    }
-
-    def sendToWorkflowStore(command: WorkflowStoreActor.WorkflowStoreActorSubmitCommand, warnings: Seq[String], workflowState: WorkflowState): Route = {
-      // NOTE: Do not blindly copy the akka-http -to- ask-actor pattern below without knowing the pros and cons.
-      onComplete(workflowStoreActor.ask(command).mapTo[WorkflowStoreSubmitActor.WorkflowStoreSubmitActorResponse]) {
-        case Success(w) =>
-          w match {
-            case WorkflowStoreSubmitActor.WorkflowSubmittedToStore(workflowId, _) =>
-              completeResponse(StatusCodes.Created, toResponse(workflowId, workflowState), warnings)
-            case WorkflowStoreSubmitActor.WorkflowsBatchSubmittedToStore(workflowIds, _) =>
-              completeResponse(StatusCodes.Created, workflowIds.toList.map(toResponse(_, workflowState)), warnings)
-            case WorkflowStoreSubmitActor.WorkflowSubmitFailed(throwable) =>
-              throwable.failRequest(StatusCodes.BadRequest, warnings)
-          }
-        case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => CromwellApiService.serviceShuttingDownResponse
-        case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
-        case Failure(e) => e.failRequest(StatusCodes.InternalServerError, warnings)
-      }
-    }
-
-    onComplete(materializeFormData(formData)) {
-      case Success(data) =>
-        PartialWorkflowSources.fromSubmitRoute(data, allowNoInputs = isSingleSubmission) match {
-          case Success(workflowSourceFiles) if isSingleSubmission && workflowSourceFiles.size == 1 =>
-            val warnings = workflowSourceFiles.flatMap(_.warnings)
-            sendToWorkflowStore(WorkflowStoreActor.SubmitWorkflow(workflowSourceFiles.head), warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
-          // Catches the case where someone has gone through the single submission endpoint w/ more than one workflow
-          case Success(workflowSourceFiles) if isSingleSubmission =>
-            val warnings = workflowSourceFiles.flatMap(_.warnings)
-            val e = new IllegalArgumentException("To submit more than one workflow at a time, use the batch endpoint.")
-            e.failRequest(StatusCodes.BadRequest, warnings)
-          case Success(workflowSourceFiles) =>
-            val warnings = workflowSourceFiles.flatMap(_.warnings)
-            sendToWorkflowStore(
-              WorkflowStoreActor.BatchSubmitWorkflows(NonEmptyList.fromListUnsafe(workflowSourceFiles.toList)),
-              warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
-          case Failure(t) => t.failRequest(StatusCodes.BadRequest)
-        }
-      case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
-      case Failure(e) => e.failRequest(StatusCodes.InternalServerError)
-    }
-  }
-}
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
index 7ec56e3317a..ba6546fb3e3 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
@@ -1,41 +1,47 @@
 package cromwell.webservice.routes.wes
 
 import akka.actor.ActorRef
-import akka.http.scaladsl.model.{StatusCode, StatusCodes}
+import akka.http.scaladsl.model.{Multipart, StatusCode, StatusCodes}
 import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server.directives.RouteDirectives.complete
 import akka.http.scaladsl.server.{Directive1, Route}
 import akka.pattern.{AskTimeoutException, ask}
+import akka.stream.ActorMaterializer
 import akka.util.Timeout
+import cats.data.NonEmptyList
 import com.typesafe.config.ConfigFactory
-import cromwell.core.WorkflowId
 import cromwell.core.abort.SuccessfulAbortResponse
+import cromwell.core.{WorkflowId, WorkflowOnHold, WorkflowState, WorkflowSubmitted}
 import cromwell.engine.instrumentation.HttpInstrumentation
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
+import cromwell.engine.workflow.workflowstore.{WorkflowStoreActor, WorkflowStoreSubmitActor}
 import cromwell.server.CromwellShutdown
 import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, GetSingleWorkflowMetadataAction, GetStatus, MetadataServiceResponse, StatusLookupFailed}
 import cromwell.services.{FailedMetadataJsonResponse, SuccessfulMetadataJsonResponse}
-import cromwell.webservice.WebServiceUtils.EnhancedThrowable
+import cromwell.webservice.PartialWorkflowSources
+import cromwell.webservice.WebServiceUtils.{EnhancedThrowable, completeResponse, materializeFormData}
+import cromwell.webservice.routes.CromwellApiService
 import cromwell.webservice.routes.CromwellApiService.{UnrecognizedWorkflowException, validateWorkflowIdInMetadata}
 import cromwell.webservice.routes.MetadataRouteSupport.{metadataBuilderActorRequest, metadataQueryRequest}
 import cromwell.webservice.routes.wes.WesResponseJsonSupport._
-import cromwell.webservice.routes.wes.WesRouteSupport._
-import cromwell.webservice.routes.{CromwellApiService, WesCromwellRouteSupport}
+import cromwell.webservice.routes.wes.WesRouteSupport.{respondWithWesError, _}
 import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.duration.FiniteDuration
-import scala.concurrent.{ExecutionContext, Future}
+import scala.concurrent.{ExecutionContext, Future, TimeoutException}
 import scala.util.{Failure, Success}
 
 
 
-trait WesRouteSupport extends HttpInstrumentation with WesCromwellRouteSupport {
+trait WesRouteSupport extends HttpInstrumentation {
 
   val serviceRegistryActor: ActorRef
   val workflowManagerActor: ActorRef
+  val workflowStoreActor: ActorRef
 
   implicit val ec: ExecutionContext
   implicit val timeout: Timeout
+  implicit val materializer: ActorMaterializer
 
   /*
     Defines routes intended to sit alongside the primary Cromwell REST endpoints. For instance, we'll now have:
@@ -68,7 +74,7 @@ trait WesRouteSupport extends HttpInstrumentation with WesCromwellRouteSupport {
               } ~
                 post {
                   extractSubmission() { submission =>
-                    submitRequest(submission.entity,
+                    wesSubmitRequest(submission.entity,
                       isSingleSubmission = true)
                   }
                 }
@@ -108,6 +114,62 @@ trait WesRouteSupport extends HttpInstrumentation with WesCromwellRouteSupport {
         }
       )
     }
+
+  def toWesResponse(workflowId: WorkflowId, workflowState: WorkflowState):  WesRunStatus = {
+    WesRunStatus(workflowId.toString, WesState.fromCromwellStatus(workflowState))
+  }
+
+  def toWesResponseId(workflowId: WorkflowId): WesRunId ={
+    WesRunId(workflowId.toString)
+  }
+
+  def wesSubmitRequest(formData: Multipart.FormData, isSingleSubmission: Boolean): Route = {
+    def getWorkflowState(workflowOnHold: Boolean): WorkflowState = {
+      if (workflowOnHold)
+        WorkflowOnHold
+      else WorkflowSubmitted
+    }
+
+    def sendToWorkflowStore(command: WorkflowStoreActor.WorkflowStoreActorSubmitCommand, warnings: Seq[String], workflowState: WorkflowState): Route = {
+      // NOTE: Do not blindly copy the akka-http -to- ask-actor pattern below without knowing the pros and cons.
+      onComplete(workflowStoreActor.ask(command).mapTo[WorkflowStoreSubmitActor.WorkflowStoreSubmitActorResponse]) {
+        case Success(w) =>
+          w match {
+            case WorkflowStoreSubmitActor.WorkflowSubmittedToStore(workflowId, _) =>
+              completeResponse(StatusCodes.Created, toWesResponseId(workflowId), warnings)
+            case WorkflowStoreSubmitActor.WorkflowsBatchSubmittedToStore(workflowIds, _) =>
+              completeResponse(StatusCodes.Created, workflowIds.toList.map(toWesResponse(_, workflowState)), warnings)
+            case WorkflowStoreSubmitActor.WorkflowSubmitFailed(throwable) =>
+              respondWithWesError(throwable.getLocalizedMessage, StatusCodes.BadRequest)
+          }
+        case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => respondWithWesError("Cromwell service is shutting down", StatusCodes.InternalServerError)
+        case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
+        case Failure(e) => e.failRequest(StatusCodes.InternalServerError, warnings)
+      }
+    }
+
+    onComplete(materializeFormData(formData)) {
+      case Success(data) =>
+        PartialWorkflowSources.fromSubmitRoute(data, allowNoInputs = isSingleSubmission) match {
+          case Success(workflowSourceFiles) if isSingleSubmission && workflowSourceFiles.size == 1 =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            sendToWorkflowStore(WorkflowStoreActor.SubmitWorkflow(workflowSourceFiles.head), warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+          // Catches the case where someone has gone through the single submission endpoint w/ more than one workflow
+          case Success(workflowSourceFiles) if isSingleSubmission =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            val e = new IllegalArgumentException("To submit more than one workflow at a time, use the batch endpoint.")
+            e.failRequest(StatusCodes.BadRequest, warnings)
+          case Success(workflowSourceFiles) =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            sendToWorkflowStore(
+              WorkflowStoreActor.BatchSubmitWorkflows(NonEmptyList.fromListUnsafe(workflowSourceFiles.toList)),
+              warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+          case Failure(t) => t.failRequest(StatusCodes.BadRequest)
+        }
+      case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
+      case Failure(e) => respondWithWesError(e.getLocalizedMessage, StatusCodes.InternalServerError)
+    }
+  }
 }
 
 
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
index c8306088ded..6e9a390ad4a 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
@@ -165,8 +165,7 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
       check {
         assertResult(
           s"""{
-             |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
-             |  "status": "Submitted"
+             |  "run_id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}"
              |}""".stripMargin) {
           responseAs[String].parseJson.prettyPrint
         }

From 4d8ef27265748c1c79b3c9ffbfd68f5342dabc68 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Fri, 26 Aug 2022 18:27:48 +0100
Subject: [PATCH 074/326] Actors to push metadata to AWS SNS @markjschreiber

---
 project/Dependencies.scala                    |   1 +
 .../HybridSnsMetadataServiceActor.scala.scala |  86 +++++++++++++
 .../AwsSnsMetadataServiceActor.scala.scala    | 114 ++++++++++++++++++
 .../sns/AwsSnsMetadataServiceActorSpec.scala  |  60 +++++++++
 4 files changed, 261 insertions(+)
 create mode 100644 services/src/main/scala/cromwell/services/metadata/impl/hybridsns/HybridSnsMetadataServiceActor.scala.scala
 create mode 100644 services/src/main/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActor.scala.scala
 create mode 100644 services/src/test/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActorSpec.scala

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 1c2c4460c8e..55f2b316db7 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -312,6 +312,7 @@ object Dependencies {
     "ecr",
     "ecrpublic",
     "secretsmanager",
+    "sns",
   ).map(artifactName => "software.amazon.awssdk" % artifactName % awsSdkV)
 
   private val googleCloudDependencies = List(
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/hybridsns/HybridSnsMetadataServiceActor.scala.scala b/services/src/main/scala/cromwell/services/metadata/impl/hybridsns/HybridSnsMetadataServiceActor.scala.scala
new file mode 100644
index 00000000000..a173b1d9855
--- /dev/null
+++ b/services/src/main/scala/cromwell/services/metadata/impl/hybridsns/HybridSnsMetadataServiceActor.scala.scala
@@ -0,0 +1,86 @@
+/*
+ * Copyright 2020 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package cromwell.services.metadata.impl.sns
+
+import akka.actor.{Actor, ActorLogging, ActorRef}
+import com.typesafe.config.Config
+import cromwell.services.metadata.MetadataService.{PutMetadataAction, PutMetadataActionAndRespond}
+import cromwell.services.metadata.impl.MetadataServiceActor
+
+
+/**
+  * A metadata service implementation which will function as a standard metadata service but also push all metadata
+  * events to AWS SNS (Simple Notification Service). This class closely follows the pattern established in the
+  * HybridPubSubMetadataServiceActor
+  *
+  * Under the hood it maintains its own MetadataServiceActor and AwsSnsMetadataServiceActor. All messages are routed
+  * to the MetadataServiceActor. PutMetadataActions are also sent to the AwsSnsMetadataServiceActor. PutMetadataActionAndRespond
+  * messages will be sent to the SnsMetadataServiceActor as a standard PutMetadataAction, i.e. only the standard
+  * metadata service will be ACKing the request.
+  *
+  * To use this actor something similar to the following should be present in the cromwell.conf file:
+  * <pre>
+  * services {
+  *   MetadataService {
+  *     class="cromwell.services.metadata.impl.sns.HybridSnsMetadataServiceActor"
+  *     config {
+  *       aws {
+  *         application-name = "cromwell"
+  *         auths = [{
+  *           name = "default"
+  *           scheme = "default"
+  *         }]
+  *         region = "us-east-1"
+  *         topicArn = "arn:aws:sns:us-east-1:1111111111111:cromwell-metadata"
+  *       }
+  *     }
+  *   }
+  * }
+  * </pre>
+  *
+  * @see cromwell.services.metadata.impl.sns.AwsSnsMetadataServiceActor
+  */
+class HybridSnsMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor with ActorLogging  {
+  val standardMetadataActor: ActorRef = context.actorOf(MetadataServiceActor.props(serviceConfig, globalConfig, serviceRegistryActor))
+  val awsSnsMetadataActor: ActorRef = context.actorOf(AwsSnsMetadataServiceActor.props(serviceConfig, globalConfig, serviceRegistryActor))
+
+  override def receive = {
+    case action: PutMetadataAction =>
+      standardMetadataActor forward action
+      awsSnsMetadataActor forward action
+    case action: PutMetadataActionAndRespond =>
+      standardMetadataActor forward action
+      awsSnsMetadataActor forward PutMetadataAction(action.events)
+    case anythingElse => standardMetadataActor forward anythingElse
+  }
+}
+
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActor.scala.scala b/services/src/main/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActor.scala.scala
new file mode 100644
index 00000000000..10f9caaba35
--- /dev/null
+++ b/services/src/main/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActor.scala.scala
@@ -0,0 +1,114 @@
+/*
+ * Copyright 2022 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package cromwell.services.metadata.impl.sns
+
+import akka.actor.{Actor, ActorLogging, ActorRef, Props}
+import com.typesafe.config.Config
+import cromwell.cloudsupport.aws.AwsConfiguration
+import cromwell.core.Dispatcher.ServiceDispatcher
+import cromwell.services.metadata.MetadataEvent
+import cromwell.services.metadata.MetadataService.{MetadataWriteFailure, MetadataWriteSuccess, PutMetadataAction, PutMetadataActionAndRespond}
+import software.amazon.awssdk.auth.credentials.AwsCredentialsProviderChain
+import software.amazon.awssdk.regions.Region
+import software.amazon.awssdk.services.sns.SnsClient
+import software.amazon.awssdk.services.sns.model.PublishRequest
+import spray.json.enrichAny
+
+import scala.concurrent.{ExecutionContextExecutor, Future}
+import scala.util.{Failure, Success}
+
+
+/**
+  * An actor that publishes metadata events to AWS SNS
+  * @param serviceConfig the source of service config information
+  * @param globalConfig the source of global config information
+  * @param serviceRegistryActor the actor for registering services
+  * @see cromwell.services.metadata.impl.sns.HybridSnsMetadataServiceActor
+  */
+class AwsSnsMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor with ActorLogging {
+  implicit val ec: ExecutionContextExecutor = context.dispatcher
+
+  //setup sns client
+  val topicArn: String = serviceConfig.getString("aws.topicArn")
+
+  val awsConfig: AwsConfiguration = AwsConfiguration(globalConfig)
+  val credentialsProviderChain: AwsCredentialsProviderChain =
+    AwsCredentialsProviderChain.of(awsConfig.authsByName.values.map(_.provider()).toSeq :_*)
+
+  lazy val snsClient: SnsClient = SnsClient.builder()
+    .region(awsConfig.region.getOrElse(Region.US_EAST_1))
+    .credentialsProvider(credentialsProviderChain)
+    .build()
+
+  def publishMessages(events: Iterable[MetadataEvent]): Future[Unit] = {
+    import AwsSnsMetadataServiceActor.EnhancedMetadataEvents
+
+    val eventsJson = events.toJson
+    //if there are no events then don't publish anything
+    if( eventsJson.length < 1) { return Future(())}
+    log.debug("Publishing to " + topicArn + ": " + eventsJson)
+
+    Future {
+      snsClient.publish(PublishRequest.builder()
+        .message("[" + eventsJson.mkString(",") + "]")
+        .topicArn(topicArn)
+        .subject("cromwell-metadata-event")
+        .build())
+      () //return unit
+    }
+  }
+
+  override def receive: Receive = {
+    case action: PutMetadataAction =>
+      publishMessages(action.events).failed foreach { e =>
+        log.error(e, "Failed to post metadata: " + action.events)
+      }
+    case action: PutMetadataActionAndRespond =>
+      publishMessages(action.events) onComplete {
+        case Success(_) => action.replyTo ! MetadataWriteSuccess(action.events)
+        case Failure(e) => action.replyTo ! MetadataWriteFailure(e, action.events)
+      }
+  }
+}
+
+object AwsSnsMetadataServiceActor {
+  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef): Props = {
+    Props(new AwsSnsMetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor)).withDispatcher(ServiceDispatcher)
+  }
+
+  implicit class EnhancedMetadataEvents(val e: Iterable[MetadataEvent]) extends AnyVal {
+    import cromwell.services.metadata.MetadataJsonSupport._
+
+    def toJson: Seq[String] = e.map(_.toJson.toString()).toSeq
+  }
+}
+
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActorSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActorSpec.scala
new file mode 100644
index 00000000000..028a1b5fac5
--- /dev/null
+++ b/services/src/test/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActorSpec.scala
@@ -0,0 +1,60 @@
+package cromwell.services.metadata.impl.sns
+
+import java.time.OffsetDateTime
+
+import akka.actor.{ActorInitializationException, ActorRef, Props}
+import akka.testkit.{EventFilter, TestProbe}
+import com.typesafe.config.{Config, ConfigFactory}
+import cromwell.core.WorkflowId
+import cromwell.services.ServicesSpec
+import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
+
+
+class AwsSnsMetadataServiceActorSpec extends ServicesSpec {
+  import AwsSnsMetadataServiceActorSpec._
+
+  val registryProbe: ActorRef = TestProbe().ref
+
+  "An AwsSnsMetadataActor with an empty serviceConfig" should {
+    "fail to build" in {
+      EventFilter[ActorInitializationException](occurrences = 1) intercept {
+        system.actorOf(Props(new AwsSnsMetadataServiceActor(emptyConfig, emptyConfig, registryProbe)))
+      }
+    }
+  }
+
+  "An AwsSnsMetadataActor with a topic and configuration" should {
+    "successfully build" in {
+      system.actorOf(Props(new AwsSnsMetadataServiceActor(configWithTopic, emptyConfig, registryProbe)))
+    }
+
+    "process an event" in {
+      val actor = system.actorOf(Props(new AwsSnsMetadataServiceActor(configWithTopic, emptyConfig, registryProbe)))
+      actor ! event
+    }
+  }
+}
+
+object AwsSnsMetadataServiceActorSpec {
+
+  // This doesn't include a topic so should be a failure
+  val emptyConfig: Config = ConfigFactory.empty()
+
+  val configWithTopic: Config = ConfigFactory.parseString(
+    """
+      |aws {
+      |  application-name = "cromwell"
+      |  auths = [{
+      |    name = "default"
+      |    scheme = "default"
+      |  }]
+      |  region = "us-east-1"
+      |  topicArn = "arn:aws:sns:us-east-1:1111111111111:cromwell-metadata"
+      |}
+    """.stripMargin
+  )
+
+  val event: MetadataEvent = MetadataEvent(MetadataKey(WorkflowId.randomId(), None, "key"),
+    Option(MetadataValue("value")), OffsetDateTime.now)
+}
+

From 3b0856d080349c1b73bd6f8da4993fc3cc1ead4e Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Mon, 29 Aug 2022 17:24:38 +0100
Subject: [PATCH 075/326] - support fifo and non-fifo sns topics - support for
 eventbridge

---
 project/Dependencies.scala                    |   1 +
 .../aws/EventBridgeMetadataServiceActor.scala | 122 ++++++++++++++++++
 .../SnsMetadataServiceActor.scala}            |  22 +++-
 ...ybridEventBridgeMetadataServiceActor.scala |  86 ++++++++++++
 .../HybridSnsMetadataServiceActor.scala}      |   2 +-
 .../EventBridgeMetadataServiceActorSpec.scala |  60 +++++++++
 .../SnsMetadataServiceActorSpec.scala}        |   2 +-
 7 files changed, 287 insertions(+), 8 deletions(-)
 create mode 100644 services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala
 rename services/src/main/scala/cromwell/services/metadata/impl/{sns/AwsSnsMetadataServiceActor.scala.scala => aws/SnsMetadataServiceActor.scala} (90%)
 create mode 100644 services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala
 rename services/src/main/scala/cromwell/services/metadata/impl/{hybridsns/HybridSnsMetadataServiceActor.scala.scala => hybridaws/HybridSnsMetadataServiceActor.scala} (98%)
 create mode 100644 services/src/test/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActorSpec.scala
 rename services/src/test/scala/cromwell/services/metadata/impl/{sns/AwsSnsMetadataServiceActorSpec.scala => aws/SnsMetadataServiceActorSpec.scala} (97%)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 55f2b316db7..519c13d4c37 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -313,6 +313,7 @@ object Dependencies {
     "ecrpublic",
     "secretsmanager",
     "sns",
+    "eventbridge",
   ).map(artifactName => "software.amazon.awssdk" % artifactName % awsSdkV)
 
   private val googleCloudDependencies = List(
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala
new file mode 100644
index 00000000000..20c41ca8c28
--- /dev/null
+++ b/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala
@@ -0,0 +1,122 @@
+/*
+ * Copyright 2022 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package cromwell.services.metadata.impl.aws
+
+import akka.actor.{Actor, ActorLogging, ActorRef, Props}
+import com.typesafe.config.Config
+import cromwell.cloudsupport.aws.AwsConfiguration
+import cromwell.core.Dispatcher.ServiceDispatcher
+import cromwell.services.metadata.MetadataEvent
+import cromwell.services.metadata.MetadataService.{MetadataWriteFailure, MetadataWriteSuccess, PutMetadataAction, PutMetadataActionAndRespond}
+import software.amazon.awssdk.auth.credentials.AwsCredentialsProviderChain
+import software.amazon.awssdk.regions.Region
+import software.amazon.awssdk.services.eventbridge.EventBridgeClient
+import software.amazon.awssdk.services.eventbridge.model.PutEventsRequest
+import software.amazon.awssdk.services.eventbridge.model.PutEventsRequestEntry
+import spray.json.enrichAny
+
+import scala.concurrent.{ExecutionContextExecutor, Future}
+import scala.util.{Failure, Success}
+
+
+/**
+  * An actor that publishes metadata events to AWS EventBridge
+  * @param serviceConfig the source of service config information
+  * @param globalConfig the source of global config information
+  * @param serviceRegistryActor the actor for registering services
+  * @see cromwell.services.metadata.impl.aws.HybridEventBridgeMetadataServiceActor
+  */
+class AwsEventBridgeMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor with ActorLogging {
+  implicit val ec: ExecutionContextExecutor = context.dispatcher
+
+  //setup EB client
+  val busName: String = serviceConfig.getString("aws.busName")
+
+  val awsConfig: AwsConfiguration = AwsConfiguration(globalConfig)
+  val credentialsProviderChain: AwsCredentialsProviderChain =
+    AwsCredentialsProviderChain.of(awsConfig.authsByName.values.map(_.provider()).toSeq :_*)
+
+  lazy val eventBrClient : EventBridgeClient = EventBridgeClient.builder()
+    .region(awsConfig.region.getOrElse(Region.US_EAST_1))
+    .credentialsProvider(credentialsProviderChain)
+    .build();
+
+  def publishMessages(events: Iterable[MetadataEvent]): Future[Unit] = {
+    import AwsEventBridgeMetadataServiceActor.EnhancedMetadataEvents
+
+    val eventsJson = events.toJson
+    //if there are no events then don't publish anything
+    if( eventsJson.length < 1) { return Future(())}
+    log.debug(f"Publishing to $busName : $eventsJson")
+
+    val reqEntry = PutEventsRequestEntry.builder()
+      .eventBusName(busName)
+      .source("cromwell")
+      .detailType("cromwell-metadata-event")
+      .detail(eventsJson.mkString(","))
+      .build()
+
+    val eventsRequest = PutEventsRequest.builder()
+      .entries(reqEntry)
+      .build()
+
+    Future {
+      eventBrClient.putEvents(eventsRequest)
+      () //return unit
+    }
+  }
+
+  override def receive: Receive = {
+    case action: PutMetadataAction =>
+      publishMessages(action.events).failed foreach { e =>
+        log.error(e, "Failed to post metadata: " + action.events)
+      }
+    case action: PutMetadataActionAndRespond =>
+      publishMessages(action.events) onComplete {
+        case Success(_) => action.replyTo ! MetadataWriteSuccess(action.events)
+        case Failure(e) => action.replyTo ! MetadataWriteFailure(e, action.events)
+      }
+  }
+}
+
+object AwsEventBridgeMetadataServiceActor {
+  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef): Props = {
+    Props(new AwsEventBridgeMetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor)).withDispatcher(ServiceDispatcher)
+  }
+
+  implicit class EnhancedMetadataEvents(val e: Iterable[MetadataEvent]) extends AnyVal {
+    import cromwell.services.metadata.MetadataJsonSupport._
+
+    def toJson: Seq[String] = e.map(_.toJson.toString()).toSeq
+  }
+}
+
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActor.scala.scala b/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
similarity index 90%
rename from services/src/main/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActor.scala.scala
rename to services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
index 10f9caaba35..da66ae4f7f4 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActor.scala.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
@@ -29,7 +29,9 @@
  *  POSSIBILITY OF SUCH DAMAGE.
  */
 
-package cromwell.services.metadata.impl.sns
+package cromwell.services.metadata.impl.aws
+
+import java.util.UUID
 
 import akka.actor.{Actor, ActorLogging, ActorRef, Props}
 import com.typesafe.config.Config
@@ -75,13 +77,21 @@ class AwsSnsMetadataServiceActor(serviceConfig: Config, globalConfig: Config, se
     val eventsJson = events.toJson
     //if there are no events then don't publish anything
     if( eventsJson.length < 1) { return Future(())}
-    log.debug("Publishing to " + topicArn + ": " + eventsJson)
+    log.debug(f"Publishing to $topicArn : $eventsJson")
+
+    val message = PublishRequest.builder()
+      .message("[" + eventsJson.mkString(",") + "]")
+      .topicArn(topicArn)
+      .subject("cromwell-metadata-event")
+
+    if (topicArn.endsWith(".fifo")) {
+      message
+        .messageGroupId("cromwell")
+        .messageDeduplicationId(UUID.randomUUID().toString())
+    }
 
     Future {
-      snsClient.publish(PublishRequest.builder()
-        .message("[" + eventsJson.mkString(",") + "]")
-        .topicArn(topicArn)
-        .subject("cromwell-metadata-event")
+      snsClient.publish(message
         .build())
       () //return unit
     }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala
new file mode 100644
index 00000000000..d5b011df176
--- /dev/null
+++ b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala
@@ -0,0 +1,86 @@
+/*
+ * Copyright 2020 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package cromwell.services.metadata.impl.aws
+
+import akka.actor.{Actor, ActorLogging, ActorRef}
+import com.typesafe.config.Config
+import cromwell.services.metadata.MetadataService.{PutMetadataAction, PutMetadataActionAndRespond}
+import cromwell.services.metadata.impl.MetadataServiceActor
+
+
+/**
+  * A metadata service implementation which will function as a standard metadata service but also push all metadata
+  * events to AWS EventBridge. This class closely follows the pattern established in the
+  * HybridPubSubMetadataServiceActor
+  *
+  * Under the hood it maintains its own MetadataServiceActor and AwsEventBridgeMetadataServiceActor. All messages are routed
+  * to the MetadataServiceActor. PutMetadataActions are also sent to the AwsEventBridgeMetadataServiceActor. PutMetadataActionAndRespond
+  * messages will be sent to the EventBridgeMetadataServiceActor as a standard PutMetadataAction, i.e. only the standard
+  * metadata service will be ACKing the request.
+  *
+  * To use this actor something similar to the following should be present in the cromwell.conf file:
+  * <pre>
+  * services {
+  *   MetadataService {
+  *     class="cromwell.services.metadata.impl.aws.HybridEventBridgeMetadataServiceActor"
+  *     config {
+  *       aws {
+  *         application-name = "cromwell"
+  *         auths = [{
+  *           name = "default"
+  *           scheme = "default"
+  *         }]
+  *         region = "us-east-1"
+  *         busName = "cromwell-metadata"
+  *       }
+  *     }
+  *   }
+  * }
+  * </pre>
+  *
+  * @see cromwell.services.metadata.impl.aws.AwsEventBridgeMetadataServiceActor
+  */
+class HybridEventBridgeMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor with ActorLogging  {
+  val standardMetadataActor: ActorRef = context.actorOf(MetadataServiceActor.props(serviceConfig, globalConfig, serviceRegistryActor))
+  val awsEventBridgeMetadataActor: ActorRef = context.actorOf(AwsEventBridgeMetadataServiceActor.props(serviceConfig, globalConfig, serviceRegistryActor))
+
+  override def receive = {
+    case action: PutMetadataAction =>
+      standardMetadataActor forward action
+      awsEventBridgeMetadataActor forward action
+    case action: PutMetadataActionAndRespond =>
+      standardMetadataActor forward action
+      awsEventBridgeMetadataActor forward PutMetadataAction(action.events)
+    case anythingElse => standardMetadataActor forward anythingElse
+  }
+}
+
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/hybridsns/HybridSnsMetadataServiceActor.scala.scala b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala
similarity index 98%
rename from services/src/main/scala/cromwell/services/metadata/impl/hybridsns/HybridSnsMetadataServiceActor.scala.scala
rename to services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala
index a173b1d9855..26c2e3f70ca 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/hybridsns/HybridSnsMetadataServiceActor.scala.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala
@@ -29,7 +29,7 @@
  *  POSSIBILITY OF SUCH DAMAGE.
  */
 
-package cromwell.services.metadata.impl.sns
+package cromwell.services.metadata.impl.aws
 
 import akka.actor.{Actor, ActorLogging, ActorRef}
 import com.typesafe.config.Config
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActorSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActorSpec.scala
new file mode 100644
index 00000000000..ecfab9dc00a
--- /dev/null
+++ b/services/src/test/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActorSpec.scala
@@ -0,0 +1,60 @@
+package cromwell.services.metadata.impl.aws
+
+import java.time.OffsetDateTime
+
+import akka.actor.{ActorInitializationException, ActorRef, Props}
+import akka.testkit.{EventFilter, TestProbe}
+import com.typesafe.config.{Config, ConfigFactory}
+import cromwell.core.WorkflowId
+import cromwell.services.ServicesSpec
+import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
+
+
+class AwsEventBridgeMetadataServiceActorSpec extends ServicesSpec {
+  import AwsEventBridgeMetadataServiceActorSpec._
+
+  val registryProbe: ActorRef = TestProbe().ref
+
+  "An AwsEventBridgeMetadataActor with an empty serviceConfig" should {
+    "fail to build" in {
+      EventFilter[ActorInitializationException](occurrences = 1) intercept {
+        system.actorOf(Props(new AwsEventBridgeMetadataServiceActor(emptyConfig, emptyConfig, registryProbe)))
+      }
+    }
+  }
+
+  "An AwsEventBridgeMetadataActor with a bus name and configuration" should {
+    "successfully build" in {
+      system.actorOf(Props(new AwsEventBridgeMetadataServiceActor(configWithBus, emptyConfig, registryProbe)))
+    }
+
+    "process an event" in {
+      val actor = system.actorOf(Props(new AwsEventBridgeMetadataServiceActor(configWithBus, emptyConfig, registryProbe)))
+      actor ! event
+    }
+  }
+}
+
+object AwsSnsMetadataServiceActorSpec {
+
+  // This doesn't include a topic so should be a failure
+  val emptyConfig: Config = ConfigFactory.empty()
+
+  val configWithBus: Config = ConfigFactory.parseString(
+    """
+      |aws {
+      |  application-name = "cromwell"
+      |  auths = [{
+      |    name = "default"
+      |    scheme = "default"
+      |  }]
+      |  region = "us-east-1"
+      |  busName = "cromwell-metadata"
+      |}
+    """.stripMargin
+  )
+
+  val event: MetadataEvent = MetadataEvent(MetadataKey(WorkflowId.randomId(), None, "key"),
+    Option(MetadataValue("value")), OffsetDateTime.now)
+}
+
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActorSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActorSpec.scala
similarity index 97%
rename from services/src/test/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActorSpec.scala
rename to services/src/test/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActorSpec.scala
index 028a1b5fac5..26347136655 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/sns/AwsSnsMetadataServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActorSpec.scala
@@ -1,4 +1,4 @@
-package cromwell.services.metadata.impl.sns
+package cromwell.services.metadata.impl.aws
 
 import java.time.OffsetDateTime
 

From b5ef39aa652c607e5c370f1e8c0e7705a3fa8ff6 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 29 Aug 2022 19:48:55 -0400
Subject: [PATCH 076/326] BW-1378 Addl CromIAM user enablement checks (#6826)

---
 CHANGELOG.md                                  | 14 +++++
 .../CromIamInstrumentation.scala              |  1 +
 .../main/scala/cromiam/sam/SamClient.scala    | 33 ++++++++++++
 .../webservice/CromIamApiService.scala        | 16 +++---
 .../cromiam/webservice/QuerySupport.scala     |  2 +-
 .../cromiam/webservice/RequestSupport.scala   | 26 ++++++++-
 .../webservice/SubmissionSupport.scala        |  2 +-
 .../webservice/WomtoolRouteSupport.scala      | 10 ++--
 .../webservice/CromIamApiServiceSpec.scala    | 38 ++++++++++++-
 .../cromiam/webservice/MockClients.scala      |  9 ++++
 .../webservice/WomtoolRouteSupportSpec.scala  | 54 ++++++++++++++++++-
 11 files changed, 184 insertions(+), 21 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0c40f47b651..e1158be3ca4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,19 @@
 # Cromwell Change Log
 
+## 84 Release Notes
+
+### CromIAM enabled user checks
+
+For Cromwell instances utilizing the optional CromIAM identity and access management component, the following endpoints now verify that the calling user is enabled before forwarding the request.
+* `/api/workflows/v1/backends`
+* `/api/womtool/v1/describe`
+
+This change makes the above endpoints consistent with the existing behavior of all the other endpoints in the `/api/` path of CromIAM. 
+
+## 83 Release Notes
+
+* Changes the type of several primary key columns in call caching tables from int to bigint. The database migration may be lengthy if your database contains a large amount of call caching data.
+
 ## 82 Release Notes
 
  * Restored missing example configuration file
diff --git a/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala b/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
index 63f48073146..65b164f00f6 100644
--- a/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
+++ b/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
@@ -20,6 +20,7 @@ trait CromIamInstrumentation extends CromwellInstrumentation {
 
   val samPrefix: NonEmptyList[String] = NonEmptyList.one("sam")
   val getWhitelistPrefix = NonEmptyList.one("get-whitelist")
+  val getUserEnabledPrefix = NonEmptyList.one("get-user-enabled")
   val userCollectionPrefix = NonEmptyList.one("user-collection")
   val authCollectionPrefix = NonEmptyList.one("auth-collection")
   val registerCollectionPrefix = NonEmptyList.one("register-collection")
diff --git a/CromIAM/src/main/scala/cromiam/sam/SamClient.scala b/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
index f289251a2fb..d6a315f8241 100644
--- a/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
+++ b/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
@@ -18,6 +18,7 @@ import cromiam.sam.SamResourceJsonSupport._
 import cromiam.server.status.StatusCheckedSubsystem
 import cromwell.api.model._
 import mouse.boolean._
+import spray.json.RootJsonFormat
 
 import scala.concurrent.ExecutionContextExecutor
 
@@ -73,6 +74,33 @@ class SamClient(scheme: String,
     } yield whitelisted
   }
 
+  def isUserEnabledSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+    val request = HttpRequest(
+      method = HttpMethods.GET,
+      uri = samUserStatusUri,
+      headers = List[HttpHeader](user.authorization)
+    )
+
+    for {
+      response <- instrumentRequest(
+        () => Http().singleRequest(request).asFailureResponseOrT,
+        cromIamRequest,
+        instrumentationPrefixForSam(getUserEnabledPrefix)
+      )
+      userEnabled <- response.status match {
+        case StatusCodes.OK =>
+          val unmarshal: IO[UserStatusInfo] = IO.fromFuture(IO(Unmarshal(response.entity).to[UserStatusInfo]))
+          FailureResponseOrT.right[HttpResponse](unmarshal).map { userInfo =>
+            if (!userInfo.enabled) log.info("Access denied for user {}", user.userId)
+            userInfo.enabled
+          }
+        case _ =>
+          log.error("Could not verify access with Sam for user {}, error was {} {}", user.userId, response.status, response.toString().take(100))
+          FailureResponseOrT.pure[IO, HttpResponse](false)
+      }
+    } yield userEnabled
+  }
+
   def collectionsForUser(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[List[Collection]] = {
     val request = HttpRequest(method = HttpMethods.GET, uri = samBaseCollectionUri, headers = List[HttpHeader](user.authorization))
 
@@ -170,6 +198,7 @@ class SamClient(scheme: String,
   private lazy val samBaseResourceUri = s"$samBaseUri/api/resource"
   private lazy val samBaseCollectionUri = s"$samBaseResourceUri/workflow-collection"
   private lazy val samSubmitWhitelistUri = s"$samBaseResourceUri/caas/submit/action/get_whitelist"
+  private lazy val samUserStatusUri = s"$samBaseUri/register/user/v2/self/info"
 
 }
 
@@ -188,4 +217,8 @@ object SamClient {
 
   def SamRegisterCollectionExceptionResp(statusCode: StatusCode) = HttpResponse(status = statusCode, entity = SamRegisterCollectionException(statusCode).getMessage)
 
+  case class UserStatusInfo(adminEnabled: Boolean, enabled: Boolean, userEmail: String, userSubjectId: String)
+
+  implicit val UserStatusInfoFormat: RootJsonFormat[UserStatusInfo] = jsonFormat4(UserStatusInfo)
+
 }
diff --git a/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala b/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
index 63694599476..7a16e5ea797 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
@@ -81,7 +81,7 @@ trait CromIamApiService extends RequestSupport
 
   def abortRoute: Route = path("api" / "workflows" / Segment / Segment / Abort) { (_, workflowId) =>
     post {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserWorkflowAction(user, workflowId, Abort)
         complete {
           authorizeAbortThenForwardToCromwell(user, workflowId, req).asHttpResponse
@@ -93,7 +93,7 @@ trait CromIamApiService extends RequestSupport
   //noinspection MutatorLikeMethodIsParameterless
   def releaseHoldRoute: Route =  path("api" / "workflows" / Segment / Segment / ReleaseHold) { (_, workflowId) =>
     post {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserWorkflowAction(user, workflowId, ReleaseHold)
         complete {
           authorizeUpdateThenForwardToCromwell(user, workflowId, req).asHttpResponse
@@ -112,7 +112,7 @@ trait CromIamApiService extends RequestSupport
   def labelPatchRoute: Route = {
     path("api" / "workflows" / Segment / Segment / Labels) { (_, workflowId) =>
       patch {
-        extractUserAndRequest { (user, req) =>
+        extractUserAndStrictRequest { (user, req) =>
           entity(as[String]) { labels =>
             logUserWorkflowAction(user, workflowId, Labels)
             validateLabels(Option(labels)) { _ => // Not using the labels, just using this to verify they didn't specify labels we don't want them to
@@ -130,7 +130,7 @@ trait CromIamApiService extends RequestSupport
 
   def callCacheDiffRoute: Route = path("api" / "workflows" / Segment / "callcaching" / "diff") { _ =>
     get {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserAction(user, "call caching diff")
         parameterSeq { parameters =>
           val paramMap = parameters.toMap
@@ -150,11 +150,9 @@ trait CromIamApiService extends RequestSupport
     */
   private def workflowGetRoute(urlSuffix: String): Route = path("api" / "workflows" / Segment / urlSuffix) { _ =>
     get {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserAction(user, urlSuffix)
-        complete {
-          cromwellClient.forwardToCromwell(req).asHttpResponse
-        }
+        forwardIfUserEnabled(user, req, cromwellClient, samClient)
       }
     }
   }
@@ -166,7 +164,7 @@ trait CromIamApiService extends RequestSupport
 
   private def workflowRoute(urlSuffix: String, method: Directive0): Route = path("api" / "workflows" / Segment / Segment / urlSuffix) { (_, workflowId) =>
     method {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserWorkflowAction(user, workflowId, urlSuffix)
         complete {
           authorizeReadThenForwardToCromwell(user, List(workflowId), req).asHttpResponse
diff --git a/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala b/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
index cddabe74a57..e9397605c6a 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
@@ -55,7 +55,7 @@ trait QuerySupport extends RequestSupport {
     * directive
     */
   private def preprocessQuery: Directive[(User, List[Collection], HttpRequest)] = {
-    extractUserAndRequest tflatMap { case (user, cromIamRequest) =>
+    extractUserAndStrictRequest tflatMap { case (user, cromIamRequest) =>
       log.info("Received query " + cromIamRequest.method.value + " request for user " + user.userId)
 
       onComplete(samClient.collectionsForUser(user, cromIamRequest).value.unsafeToFuture()) flatMap {
diff --git a/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
index 12b231485f7..c9b6a196368 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
@@ -6,6 +6,13 @@ import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server._
 import cromiam.auth.User
 import org.broadinstitute.dsde.workbench.model.WorkbenchUserId
+import akka.http.scaladsl.model.HttpResponse
+import akka.http.scaladsl.server.Directives.{authorize, complete, onComplete}
+import akka.http.scaladsl.server.Route
+import cromiam.cromwell.CromwellClient
+import cromiam.sam.SamClient
+
+import scala.util.{Failure, Success}
 
 trait RequestSupport {
   def extractStrictRequest: Directive1[HttpRequest] = {
@@ -26,10 +33,27 @@ trait RequestSupport {
     }
   }
 
-  def extractUserAndRequest: Directive[(User, HttpRequest)] = {
+  def extractUserAndStrictRequest: Directive[(User, HttpRequest)] = {
     for {
       user <- extractUser
       request <- extractStrictRequest
     } yield (user, request)
   }
+
+  def forwardIfUserEnabled(user: User, req: HttpRequest, cromwellClient: CromwellClient, samClient: SamClient): Route = {
+    import cromwell.api.model.EnhancedFailureResponseOrHttpResponseT
+
+    onComplete(samClient.isUserEnabledSam(user, req).value.unsafeToFuture()) {
+      case Success(Left(httpResponse: HttpResponse)) => complete(httpResponse)
+      case Success(Right(isEnabled: Boolean)) =>
+        authorize(isEnabled) {
+          complete {
+            cromwellClient.forwardToCromwell(req).asHttpResponse
+          }
+        }
+      case Failure(e) =>
+        val message = s"Unable to look up enablement status for user ${user.userId}: ${e.getMessage}. Please try again later."
+        throw new RuntimeException(message, e)
+    }
+  }
 }
diff --git a/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
index c1f5477475b..52a05d1cdc7 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
@@ -31,7 +31,7 @@ trait SubmissionSupport extends RequestSupport {
   // FIXME - getting pathPrefix to shrink this keeps hosing up, there's gotta be some way to do this
   def submitRoute: Route = (path("api" / "workflows" / Segment) | path("api" / "workflows" / Segment / "batch")) { _ =>
     post {
-      extractUserAndRequest { (user, request) =>
+      extractUserAndStrictRequest { (user, request) =>
         log.info("Received submission request from user " + user.userId)
         onComplete(samClient.isSubmitWhitelisted(user, request).value.unsafeToFuture()) {
           case Success(Left(httpResponse)) => complete(httpResponse)
diff --git a/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala
index 671d4a76543..a6098b1fae0 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala
@@ -2,20 +2,18 @@ package cromiam.webservice
 
 import akka.http.scaladsl.server.Directives._
 import cromiam.cromwell.CromwellClient
-import cromwell.api.model._
+import cromiam.sam.SamClient
 
 trait WomtoolRouteSupport extends RequestSupport {
   // When this trait is mixed into `CromIamApiService` the value of `cromwellClient` is the reader (non-abort) address
   val cromwellClient: CromwellClient
+  val samClient: SamClient
 
   val womtoolRoutes =
     path("api" / "womtool" / Segment / "describe") { _ =>
       post {
-        extractStrictRequest { req =>
-          complete {
-            // This endpoint requires authn which it gets for free from the proxy, does not care about authz
-            cromwellClient.forwardToCromwell(req).asHttpResponse
-          }
+        extractUserAndStrictRequest { (user, req) =>
+          forwardIfUserEnabled(user, req, cromwellClient, samClient)
         }
       }
     }
diff --git a/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
index 5ad6a976204..89945c5bfcb 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
@@ -4,7 +4,8 @@ import akka.event.NoLogging
 import akka.http.scaladsl.model.StatusCodes._
 import akka.http.scaladsl.model.headers.{Authorization, OAuth2BearerToken, RawHeader}
 import akka.http.scaladsl.model.{ContentTypes, HttpEntity, HttpHeader}
-import akka.http.scaladsl.server.MissingHeaderRejection
+import akka.http.scaladsl.server.Route.seal
+import akka.http.scaladsl.server.{AuthorizationFailedRejection, MissingHeaderRejection}
 import akka.http.scaladsl.testkit.ScalatestRouteTest
 import com.typesafe.config.Config
 import common.assertion.CromwellTimeoutSpec
@@ -303,12 +304,45 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-  it should "reject request if it doesn't contain OIDC_CLAIM_user_id in header" in {
+  it should "reject request if it doesn't contain OIDC_CLAIM_user_id or token" in {
     Get(s"/api/workflows/$version/backends") ~> allRoutes ~> check {
       rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
     }
   }
 
+  it should "return 403 when we request with a disabled user" in {
+    Get(
+      s"/api/workflows/$version/backends"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")), RawHeader("OIDC_CLAIM_user_id", "disabled@example.com"))
+    ) ~> allRoutes ~> check {
+      rejection shouldEqual AuthorizationFailedRejection
+    }
+  }
+
+  it should "reject request if it contains a token and no OIDC_CLAIM_user_id in header" in {
+    Get(
+      s"/api/workflows/$version/backends"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")))
+    ) ~> allRoutes ~> check {
+      rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
+    }
+  }
+
+  it should "return 404 when no auth token provided" in {
+    Get(
+      s"/api/workflows/$version/backends"
+    ).withHeaders(
+      List(RawHeader("OIDC_CLAIM_user_id", "enabled@example.com"))
+      // "[An] explicit call on the Route.seal method is needed in test code, but in your application code it is not necessary."
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/testkit.html#testing-sealed-routes
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/routes.html#sealing-a-route
+    ) ~> seal(allRoutes) ~> check {
+      responseAs[String] shouldEqual "The requested resource could not be found."
+      status shouldBe NotFound
+    }
+  }
 
   behavior of "ReleaseHold endpoint"
   it should "return 200 for authorized user who has collection associated with root workflow" in {
diff --git a/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala b/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
index 3fb9689e5cc..59e75347159 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
@@ -141,6 +141,15 @@ class MockSamClient(checkSubmitWhitelist: Boolean = true)
     FailureResponseOrT.pure(!user.userId.value.equalsIgnoreCase(NotWhitelistedUser))
   }
 
+  override def isUserEnabledSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+    if (user.userId.value == "enabled@example.com" || user.userId.value == MockSamClient.AuthorizedUserCollectionStr)
+      FailureResponseOrT.pure(true)
+    else if (user.userId.value == "disabled@example.com")
+      FailureResponseOrT.pure(false)
+    else
+      throw new Exception("Misconfigured test")
+  }
+
   override def requestAuth(authorizationRequest: CollectionAuthorizationRequest,
                            cromIamRequest: HttpRequest): FailureResponseOrT[Unit] = {
     authorizationRequest.user.userId.value match {
diff --git a/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
index 7ba1c495f23..785c887c374 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
@@ -2,6 +2,9 @@ package cromiam.webservice
 
 import akka.http.scaladsl.model.ContentTypes
 import akka.http.scaladsl.model.StatusCodes._
+import akka.http.scaladsl.model.headers.{Authorization, OAuth2BearerToken, RawHeader}
+import akka.http.scaladsl.server.Route.seal
+import akka.http.scaladsl.server.{AuthorizationFailedRejection, MissingHeaderRejection}
 import akka.http.scaladsl.testkit.ScalatestRouteTest
 import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
@@ -11,15 +14,64 @@ import org.scalatest.matchers.should.Matchers
 class WomtoolRouteSupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with WomtoolRouteSupport with ScalatestRouteTest {
 
   override lazy val cromwellClient = new MockCromwellClient()
+  override lazy val samClient = new MockSamClient()
 
   behavior of "Womtool endpoint routes"
 
   it should "return 200 when we request to the right path" in {
-    Post(s"/api/womtool/v1/describe") ~> womtoolRoutes ~> check {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")), RawHeader("OIDC_CLAIM_user_id", "enabled@example.com"))
+    ) ~> womtoolRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Hey there, workflow describer"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
+  it should "return 403 when we request with a disabled user" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")), RawHeader("OIDC_CLAIM_user_id", "disabled@example.com"))
+    ) ~> womtoolRoutes ~> check {
+      rejection shouldEqual AuthorizationFailedRejection
+    }
+  }
+
+  it should "bail out with no user ID" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")))
+    ) ~> womtoolRoutes ~> check {
+      rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
+    }
+  }
+
+  it should "return 404 when no auth token provided" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(RawHeader("OIDC_CLAIM_user_id", "enabled@example.com"))
+      // "[An] explicit call on the Route.seal method is needed in test code, but in your application code it is not necessary."
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/testkit.html#testing-sealed-routes
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/routes.html#sealing-a-route
+    ) ~> seal(womtoolRoutes) ~> check {
+      responseAs[String] shouldEqual "The requested resource could not be found."
+      status shouldBe NotFound
+    }
+  }
+
+  it should "bail out with no headers" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List.empty
+    ) ~> womtoolRoutes ~> check {
+      rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
+    }
+  }
+
 }

From 8abf84ceeed1c0e5131ed4883357f90b0ad33c82 Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Tue, 30 Aug 2022 16:34:33 +0100
Subject: [PATCH 077/326] - remove "licensing" - add docs

---
 .../aws/EventBridgeMetadataServiceActor.scala | 31 -----------
 .../impl/aws/SnsMetadataServiceActor.scala    | 31 -----------
 ...ybridEventBridgeMetadataServiceActor.scala | 31 -----------
 .../HybridSnsMetadataServiceActor.scala       | 31 -----------
 .../scala/cromwell/backend/impl/aws/README.md | 54 +++++++++++++++++++
 5 files changed, 54 insertions(+), 124 deletions(-)

diff --git a/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala
index 20c41ca8c28..b22fccb5170 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala
@@ -1,34 +1,3 @@
-/*
- * Copyright 2022 Amazon.com, Inc. or its affiliates.
- *
- *  Redistribution and use in source and binary forms, with or without
- *  modification, are permitted provided that the following conditions are met:
- *
- *  1. Redistributions of source code must retain the above copyright notice,
- *  this list of conditions and the following disclaimer.
- *
- *  2. Redistributions in binary form must reproduce the above copyright
- *  notice, this list of conditions and the following disclaimer in the
- *  documentation and/or other materials provided with the distribution.
- *
- *  3. Neither the name of the copyright holder nor the names of its
- *  contributors may be used to endorse or promote products derived from
- *  this software without specific prior written permission.
- *
- *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
- *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
- *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
- *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
- *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
- *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *  POSSIBILITY OF SUCH DAMAGE.
- */
-
 package cromwell.services.metadata.impl.aws
 
 import akka.actor.{Actor, ActorLogging, ActorRef, Props}
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
index da66ae4f7f4..724f0af6c03 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
@@ -1,34 +1,3 @@
-/*
- * Copyright 2022 Amazon.com, Inc. or its affiliates.
- *
- *  Redistribution and use in source and binary forms, with or without
- *  modification, are permitted provided that the following conditions are met:
- *
- *  1. Redistributions of source code must retain the above copyright notice,
- *  this list of conditions and the following disclaimer.
- *
- *  2. Redistributions in binary form must reproduce the above copyright
- *  notice, this list of conditions and the following disclaimer in the
- *  documentation and/or other materials provided with the distribution.
- *
- *  3. Neither the name of the copyright holder nor the names of its
- *  contributors may be used to endorse or promote products derived from
- *  this software without specific prior written permission.
- *
- *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
- *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
- *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
- *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
- *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
- *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *  POSSIBILITY OF SUCH DAMAGE.
- */
-
 package cromwell.services.metadata.impl.aws
 
 import java.util.UUID
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala
index d5b011df176..fc76207ba9d 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala
@@ -1,34 +1,3 @@
-/*
- * Copyright 2020 Amazon.com, Inc. or its affiliates.
- *
- *  Redistribution and use in source and binary forms, with or without
- *  modification, are permitted provided that the following conditions are met:
- *
- *  1. Redistributions of source code must retain the above copyright notice,
- *  this list of conditions and the following disclaimer.
- *
- *  2. Redistributions in binary form must reproduce the above copyright
- *  notice, this list of conditions and the following disclaimer in the
- *  documentation and/or other materials provided with the distribution.
- *
- *  3. Neither the name of the copyright holder nor the names of its
- *  contributors may be used to endorse or promote products derived from
- *  this software without specific prior written permission.
- *
- *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
- *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
- *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
- *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
- *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
- *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *  POSSIBILITY OF SUCH DAMAGE.
- */
-
 package cromwell.services.metadata.impl.aws
 
 import akka.actor.{Actor, ActorLogging, ActorRef}
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala
index 26c2e3f70ca..d1a05e46924 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala
@@ -1,34 +1,3 @@
-/*
- * Copyright 2020 Amazon.com, Inc. or its affiliates.
- *
- *  Redistribution and use in source and binary forms, with or without
- *  modification, are permitted provided that the following conditions are met:
- *
- *  1. Redistributions of source code must retain the above copyright notice,
- *  this list of conditions and the following disclaimer.
- *
- *  2. Redistributions in binary form must reproduce the above copyright
- *  notice, this list of conditions and the following disclaimer in the
- *  documentation and/or other materials provided with the distribution.
- *
- *  3. Neither the name of the copyright holder nor the names of its
- *  contributors may be used to endorse or promote products derived from
- *  this software without specific prior written permission.
- *
- *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
- *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
- *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
- *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
- *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
- *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- *  POSSIBILITY OF SUCH DAMAGE.
- */
-
 package cromwell.services.metadata.impl.aws
 
 import akka.actor.{Actor, ActorLogging, ActorRef}
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 2003e0f9ef3..61bb351c7e9 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -197,6 +197,60 @@ engine {
 }
 ```
 
+### Metadata notifications
+
+Cromwell has a feature that allows it to send metadata notifications to you. These notifications are mostly state transitions (task start, task end, workflow succeeded, workflow failed, etc) but also task descriptions. 
+
+In the AWS backend those notifications can be send to **SNS Topic** or **EventBridge Bus** and you can use them to trigger some post run jobs. Below you can find information on how to setup it.
+
+#### AWS SNS
+
+1. Create an SNS topic, add the following to your `cromwell.conf` file and replace `topicArn` with the topic's ARN you just created:
+
+```
+services {
+    MetadataService {
+        class="cromwell.services.metadata.impl.aws.HybridSnsMetadataServiceActor"
+        config {
+            aws {
+                application-name = "cromwell"
+                auths = [{
+                    name = "default"
+                    scheme = "default"
+                }]
+                region = "us-east-1"
+                topicArn = "<topicARN>"
+            }
+        }
+    }
+}
+```
+2. Add `sns:Publish` IAM policy to your Cromwell server IAM role. 
+
+#### AWS EventBridge
+
+1. Create an EventBridge bus, add the following to your `cromwell.conf` file and replace `busName` with the name of the bus you just created:
+
+```
+services {
+    MetadataService {
+        class="cromwell.services.metadata.impl.aws.HybridEventBridgeMetadataServiceActor"
+        config {
+            aws {
+                application-name = "cromwell"
+                auths = [{
+                    name = "default"
+                    scheme = "default"
+                }]
+                region = "us-east-1"
+                busName = "<busName>"
+            }
+        }
+    }
+}
+```
+2. Add `events:PutEvents` IAM policy to your Cromwell server IAM role. 
+
 
 AWS Batch
 ---------

From 6afc7fc5ecc74e3b19c011f6a40e7a5967af48e7 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 30 Aug 2022 17:06:14 +0000
Subject: [PATCH 078/326] Update cromwell version from 84 to 85

---
 project/Version.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Version.scala b/project/Version.scala
index 1d21894dfb0..c0bdb0b3453 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -5,7 +5,7 @@ import sbt._
 
 object Version {
   // Upcoming release, or current if we're on a master / hotfix branch
-  val cromwellVersion = "84"
+  val cromwellVersion = "85"
 
   /**
     * Returns true if this project should be considered a snapshot.

From 16ea7b3f6a3bf0e363872028aeac74f2ec1a6d5c Mon Sep 17 00:00:00 2001
From: Henrique Silva <henrique.rd.silva@gmail.com>
Date: Wed, 31 Aug 2022 10:17:57 +0100
Subject: [PATCH 079/326] - add licensing - fix tests

---
 .../aws/EventBridgeMetadataServiceActor.scala | 31 +++++++++++++++++
 .../impl/aws/SnsMetadataServiceActor.scala    | 31 +++++++++++++++++
 ...ybridEventBridgeMetadataServiceActor.scala | 31 +++++++++++++++++
 .../HybridSnsMetadataServiceActor.scala       | 31 +++++++++++++++++
 .../EventBridgeMetadataServiceActorSpec.scala | 33 ++++++++++++++++++-
 .../aws/SnsMetadataServiceActorSpec.scala     | 31 +++++++++++++++++
 6 files changed, 187 insertions(+), 1 deletion(-)

diff --git a/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala
index b22fccb5170..20c41ca8c28 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActor.scala
@@ -1,3 +1,34 @@
+/*
+ * Copyright 2022 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+
 package cromwell.services.metadata.impl.aws
 
 import akka.actor.{Actor, ActorLogging, ActorRef, Props}
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
index 724f0af6c03..da66ae4f7f4 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
@@ -1,3 +1,34 @@
+/*
+ * Copyright 2022 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+
 package cromwell.services.metadata.impl.aws
 
 import java.util.UUID
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala
index fc76207ba9d..1cde14f7212 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridEventBridgeMetadataServiceActor.scala
@@ -1,3 +1,34 @@
+/*
+ * Copyright 2022 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+
 package cromwell.services.metadata.impl.aws
 
 import akka.actor.{Actor, ActorLogging, ActorRef}
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala
index d1a05e46924..f5a7b486327 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/hybridaws/HybridSnsMetadataServiceActor.scala
@@ -1,3 +1,34 @@
+/*
+ * Copyright 2022 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+
 package cromwell.services.metadata.impl.aws
 
 import akka.actor.{Actor, ActorLogging, ActorRef}
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActorSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActorSpec.scala
index ecfab9dc00a..ab85ad525fa 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/aws/EventBridgeMetadataServiceActorSpec.scala
@@ -1,3 +1,34 @@
+/*
+ * Copyright 2022 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+
 package cromwell.services.metadata.impl.aws
 
 import java.time.OffsetDateTime
@@ -35,7 +66,7 @@ class AwsEventBridgeMetadataServiceActorSpec extends ServicesSpec {
   }
 }
 
-object AwsSnsMetadataServiceActorSpec {
+object AwsEventBridgeMetadataServiceActorSpec {
 
   // This doesn't include a topic so should be a failure
   val emptyConfig: Config = ConfigFactory.empty()
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActorSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActorSpec.scala
index 26347136655..6c6803b39cb 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActorSpec.scala
@@ -1,3 +1,34 @@
+/*
+ * Copyright 2022 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+
 package cromwell.services.metadata.impl.aws
 
 import java.time.OffsetDateTime

From 54fed3e172e2138cd956c0b9663c05a8a5d34dbc Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Wed, 31 Aug 2022 18:45:43 -0400
Subject: [PATCH 080/326] BW-1393 Release doc updates (#6839)

---
 processes/release_processes/README.MD |  3 ++-
 publish/publish_inputs.json           | 10 +++++-----
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/processes/release_processes/README.MD b/processes/release_processes/README.MD
index d16f97fddef..d23d601b747 100644
--- a/processes/release_processes/README.MD
+++ b/processes/release_processes/README.MD
@@ -45,7 +45,8 @@ The release WDL uses a github token to perform actions on your behalf.
 Make or copy the following files into a temporary `release/` directory outside the Cromwell repository. This removes any chance of committing your token.
 
 * A copy of the workflow file to run (https://github.com/broadinstitute/cromwell/blob/develop/publish/publish_workflow.wdl)
-* An inputs json like this:
+* An inputs json like this one.
+  * `publishHomebrew` is `false` due to Homebrew taking on this part themselves. Homebrew remains an active distribution channel. 
 
 ```json
 {
diff --git a/publish/publish_inputs.json b/publish/publish_inputs.json
index e9c54b9f3d6..ea877b9c34e 100644
--- a/publish/publish_inputs.json
+++ b/publish/publish_inputs.json
@@ -1,7 +1,7 @@
 {
-  "publish_workflow.githubToken": "<<REQUIRED: GithubAPIToken (value, not path)>>",
-  "publish_workflow.organization": "<<REQUIRED: broadinstitute for a real release, your github username if testing>>",
-  "publish_workflow.publishDocker": <<OPTIONAL: the docker image to use for publishing, default broadinstitute/cromwell-publish:latest>>,
-  "publish_workflow.majorRelease": <<OPTIONAL: true for a major release, false for a minor release, default true>>,
-  "publish_workflow.publishHomebrew": <<OPTIONAL: true to publish release to homebrew, false to skip, default true>>
+  "publish_workflow.githubToken": "<<GITHUB TOKEN VALUE>>",
+  "publish_workflow.majorRelease": true,
+  "publish_workflow.publishHomebrew": false,
+  "publish_workflow.publishDocker": "broadinstitute/cromwell-publish:latest",
+  "publish_workflow.organization": "broadinstitute"
 }

From f289382eb20181c8631bd90bf1fb219f46553478 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 9 Sep 2022 09:13:58 -0400
Subject: [PATCH 081/326] BT-732 Checksum validation for blobs read by engine
 (#6838)

* Draft support for optional FileHash

* Draft getMd5 for BlobPath

* Resolve non-parallel IO to fix tests

* Checksum validation for BlobPath

* Nicer error message

* Test for missing Blob hash

* Break attr acquisition into separate method

* Cleanup, comments

* In-progress tests of blob hash command

* Remove test

* Remove unused import
---
 .../cromwell/engine/io/nio/NioFlow.scala      | 47 ++++++++++++++-----
 .../cromwell/engine/io/nio/NioFlowSpec.scala  | 39 ++++++++++++++-
 .../filesystems/blob/BlobPathBuilder.scala    | 19 +++++++-
 3 files changed, 91 insertions(+), 14 deletions(-)

diff --git a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
index 0598e154f2d..012e771b5a0 100644
--- a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
+++ b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
@@ -12,6 +12,7 @@ import cromwell.core.path.Path
 import cromwell.engine.io.IoActor._
 import cromwell.engine.io.RetryableRequestSupport.{isInfinitelyRetryable, isRetryable}
 import cromwell.engine.io.{IoAttempts, IoCommandContext, IoCommandStalenessBackpressuring}
+import cromwell.filesystems.blob.BlobPath
 import cromwell.filesystems.drs.DrsPath
 import cromwell.filesystems.gcs.GcsPath
 import cromwell.filesystems.s3.S3Path
@@ -128,21 +129,33 @@ class NioFlow(parallelism: Int,
 
     def readFileAndChecksum: IO[String] = {
       for {
-        fileHash <- getHash(command.file)
+        fileHash <- getStoredHash(command.file)
         uncheckedValue <- readFile
-        checksumResult <- checkHash(uncheckedValue, fileHash)
+        checksumResult <- fileHash match {
+          case Some(hash) => checkHash(uncheckedValue, hash)
+          // If there is no stored checksum, don't attempt to validate.
+          // If the missing checksum is itself an error condition, that
+          // should be detected by the code that gets the FileHash.
+          case None => IO.pure(ChecksumSkipped())
+        }
         verifiedValue <- checksumResult match {
           case _: ChecksumSkipped => IO.pure(uncheckedValue)
           case _: ChecksumSuccess => IO.pure(uncheckedValue)
           case failure: ChecksumFailure => IO.raiseError(
             ChecksumFailedException(
-              s"Failed checksum for '${command.file}'. Expected '${fileHash.hashType}' hash of '${fileHash.hash}'. Calculated hash '${failure.calculatedHash}'"))
+              fileHash match {
+                case Some(hash) => s"Failed checksum for '${command.file}'. Expected '${hash.hashType}' hash of '${hash.hash}'. Calculated hash '${failure.calculatedHash}'"
+                case None => s"Failed checksum for '${command.file}'. Couldn't find stored file hash." // This should never happen
+              }
+            )
+          )
         }
       } yield verifiedValue
     }
 
     val fileContentIo = command.file match {
-      case _: DrsPath => readFileAndChecksum
+      case _: DrsPath  => readFileAndChecksum
+      case _: BlobPath => readFileAndChecksum
       case _ => readFile
     }
     fileContentIo.map(_.replaceAll("\\r\\n", "\\\n"))
@@ -153,19 +166,27 @@ class NioFlow(parallelism: Int,
   }
 
   private def hash(hash: IoHashCommand): IO[String] = {
-    getHash(hash.file).map(_.hash)
+    // If there is no hash accessible from the file storage system,
+    // we'll read the file and generate the hash ourselves.
+    getStoredHash(hash.file).flatMap {
+      case Some(storedHash) => IO.pure(storedHash)
+      case None => generateMd5FileHashForPath(hash.file)
+    }.map(_.hash)
   }
 
-  private def getHash(file: Path): IO[FileHash] = {
+  private def getStoredHash(file: Path): IO[Option[FileHash]] = {
     file match {
-      case gcsPath: GcsPath => getFileHashForGcsPath(gcsPath)
+      case gcsPath: GcsPath => getFileHashForGcsPath(gcsPath).map(Option(_))
+      case blobPath: BlobPath => getFileHashForBlobPath(blobPath)
       case drsPath: DrsPath => IO {
+        // We assume all DRS files have a stored hash; this will throw
+        // if the file does not.
         drsPath.getFileHash
-      }
+      }.map(Option(_))
       case s3Path: S3Path => IO {
-        FileHash(HashType.S3Etag, s3Path.eTag)
+        Option(FileHash(HashType.S3Etag, s3Path.eTag))
       }
-      case path => getMd5FileHashForPath(path)
+      case _ => IO.pure(None)
     }
   }
 
@@ -201,7 +222,11 @@ class NioFlow(parallelism: Int,
     gcsPath.objectBlobId.map(id => FileHash(HashType.GcsCrc32c, gcsPath.cloudStorage.get(id).getCrc32c))
   }
 
-  private def getMd5FileHashForPath(path: Path): IO[FileHash] = delayedIoFromTry {
+  private def getFileHashForBlobPath(blobPath: BlobPath): IO[Option[FileHash]] = delayedIoFromTry {
+    blobPath.md5HexString.map(md5 => md5.map(FileHash(HashType.Md5, _)))
+  }
+
+  private def generateMd5FileHashForPath(path: Path): IO[FileHash] = delayedIoFromTry {
     tryWithResource(() => path.newInputStream) { inputStream =>
       FileHash(HashType.Md5, org.apache.commons.codec.digest.DigestUtils.md5Hex(inputStream))
     }
diff --git a/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala b/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
index 4b3461ae7d3..b01d52eece0 100644
--- a/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
@@ -20,13 +20,14 @@ import org.mockito.Mockito.{times, verify, when}
 import org.scalatest.flatspec.AsyncFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import common.mock.MockSugar
+import cromwell.filesystems.blob.BlobPath
 
 import java.nio.file.NoSuchFileException
 import java.util.UUID
 import scala.concurrent.ExecutionContext
 import scala.concurrent.duration._
 import scala.language.postfixOps
-import scala.util.Failure
+import scala.util.{Failure, Success, Try}
 import scala.util.control.NoStackTrace
 
 class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with MockSugar {
@@ -127,6 +128,23 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     }
   }
 
+  it should "get hash from a BlobPath when stored hash exists" in {
+    val testPath = mock[BlobPath]
+    val hashString = "2d01d5d9c24034d54fe4fba0ede5182d" // echo "hello there" | md5sum
+    testPath.md5HexString returns Try(Option(hashString))
+
+    val context = DefaultCommandContext(hashCommand(testPath).get, replyTo)
+    val testSource = Source.single(context)
+
+    val stream = testSource.via(flow).toMat(readSink)(Keep.right)
+
+    stream.run() map {
+      case (success: IoSuccess[_], _) => assert(success.result.asInstanceOf[String] == hashString)
+      case (ack, _) =>
+        fail(s"read returned an unexpected message:\n$ack\n\n")
+    }
+  }
+
   it should "fail if DrsPath hash doesn't match checksum" in {
     val testPath = mock[DrsPath]
     when(testPath.limitFileContent(any[Option[Int]], any[Boolean])(any[ExecutionContext])).thenReturn("hello".getBytes)
@@ -171,6 +189,25 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     }
   }
 
+  it should "succeed if a BlobPath is missing a stored hash" in {
+    val testPath = mock[BlobPath]
+    when(testPath.limitFileContent(any[Option[Int]], any[Boolean])(any[ExecutionContext]))
+      .thenReturn("hello there".getBytes)
+    when(testPath.md5HexString)
+      .thenReturn(Success(None))
+
+    val context = DefaultCommandContext(contentAsStringCommand(testPath, Option(100), failOnOverflow = true).get, replyTo)
+    val testSource = Source.single(context)
+
+    val stream = testSource.via(flow).toMat(readSink)(Keep.right)
+
+    stream.run() map {
+      case (success: IoSuccess[_], _) => assert(success.result.asInstanceOf[String] == "hello there")
+      case (ack, _) =>
+        fail(s"read returned an unexpected message:\n$ack\n\n")
+    }
+  }
+
   it should "copy Nio paths" in {
     val testPath = DefaultPathBuilder.createTempFile()
     val testCopyPath = testPath.sibling(UUID.randomUUID().toString)
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 69a21c90eda..b89a335b9de 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -1,13 +1,13 @@
 package cromwell.filesystems.blob
 
 import com.azure.core.credential.AzureSasCredential
-import com.azure.storage.blob.nio.AzureFileSystem
+import com.azure.storage.blob.nio.{AzureBlobFileAttributes, AzureFileSystem}
 import com.google.common.net.UrlEscapers
 import cromwell.core.path.{NioPath, Path, PathBuilder}
 import cromwell.filesystems.blob.BlobPathBuilder._
 
 import java.net.{MalformedURLException, URI}
-import java.nio.file.{FileSystem, FileSystemNotFoundException, FileSystems}
+import java.nio.file.{FileSystem, FileSystemNotFoundException, FileSystems, Files}
 import scala.jdk.CollectionConverters._
 import scala.language.postfixOps
 import scala.util.{Failure, Try}
@@ -90,4 +90,19 @@ case class BlobPath private[blob](nioPath: NioPath, endpoint: String, container:
   override def pathAsString: String = List(endpoint, container, nioPath.toString()).mkString("/")
 
   override def pathWithoutScheme: String = parseURI(endpoint).getHost + "/" + container + "/" + nioPath.toString()
+
+  def blobFileAttributes: Try[AzureBlobFileAttributes] =
+    Try(Files.readAttributes(nioPath, classOf[AzureBlobFileAttributes]))
+
+  def md5HexString: Try[Option[String]] = {
+    blobFileAttributes.map(h =>
+      Option(h.blobHttpHeaders().getContentMd5) match {
+        case None => None
+        case Some(arr) if arr.isEmpty => None
+        // Convert the bytes to a hex-encoded string. Note that this value
+        // is rendered in base64 in the Azure web portal.
+        case Some(bytes) => Option(bytes.map("%02x".format(_)).mkString)
+      }
+    )
+  }
 }

From 01d63af33fec14ff00076753c96075ca931c0c77 Mon Sep 17 00:00:00 2001
From: Christian Freitas <christian.j.freitas@gmail.com>
Date: Mon, 12 Sep 2022 16:18:51 -0400
Subject: [PATCH 082/326] BT-711 Refresh SAS token for filesystem on expiry
 (#6831)

* BT-711 Refresh SAS token for filesystem on expiry

* Rough cut of token refresh using exceptions

* Ignore tests, and minor cleanup

* Remove stray line

* Draft of manager class for handling expiring file systems

* Style fixes

* Refactor of blobfilesystemManager and tests covering its functionality

* Refined tests to validate close filesystem as separate unit

* Ignore connected tests

* Clean up of some things

* Refactor BlobFileSystemManager to separate file, and some other cleanup

* Some additional scala-ifying

* Small cleanup

* Correcting imports

* trigger tests

* trigger tests
---
 .../blob/BlobFileSystemManager.scala          | 140 ++++++++++++++
 .../filesystems/blob/BlobPathBuilder.scala    |  79 ++++----
 .../blob/BlobPathBuilderFactory.scala         | 111 ++---------
 .../blob/BlobPathBuilderFactorySpec.scala     | 179 +++++++++++++++++-
 .../blob/BlobPathBuilderSpec.scala            |  68 ++++---
 5 files changed, 406 insertions(+), 171 deletions(-)
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
new file mode 100644
index 00000000000..3b8f5149055
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -0,0 +1,140 @@
+package cromwell.filesystems.blob
+
+import com.azure.core.credential.AzureSasCredential
+import com.azure.core.management.AzureEnvironment
+import com.azure.core.management.profile.AzureProfile
+import com.azure.identity.DefaultAzureCredentialBuilder
+import com.azure.resourcemanager.AzureResourceManager
+import com.azure.storage.blob.nio.AzureFileSystem
+import com.azure.storage.blob.sas.{BlobContainerSasPermission, BlobServiceSasSignatureValues}
+import com.azure.storage.blob.{BlobContainerClient, BlobContainerClientBuilder}
+import com.azure.storage.common.StorageSharedKeyCredential
+
+import java.net.URI
+import java.nio.file.{FileSystem, FileSystemNotFoundException, FileSystems}
+import java.time.temporal.ChronoUnit
+import java.time.{Duration, Instant, OffsetDateTime}
+import scala.jdk.CollectionConverters._
+import scala.util.{Failure, Success, Try}
+import com.azure.resourcemanager.storage.models.StorageAccountKey
+
+case class FileSystemAPI() {
+  def getFileSystem(uri: URI): Try[FileSystem] = Try(FileSystems.getFileSystem(uri))
+  def newFileSystem(uri: URI, config: Map[String, Object]): FileSystem = FileSystems.newFileSystem(uri, config.asJava)
+  def closeFileSystem(uri: URI): Option[Unit] = getFileSystem(uri).toOption.map(_.close)
+}
+
+object BlobFileSystemManager {
+  def parseTokenExpiry(token: AzureSasCredential): Option[Instant] = for {
+    expiryString <- token.getSignature.split("&").find(_.startsWith("se")).map(_.replaceFirst("se=","")).map(_.replace("%3A", ":"))
+    instant = Instant.parse(expiryString)
+  } yield instant
+
+  def buildConfigMap(credential: AzureSasCredential, container: BlobContainerName): Map[String, Object] = {
+    Map((AzureFileSystem.AZURE_STORAGE_SAS_TOKEN_CREDENTIAL, credential),
+      (AzureFileSystem.AZURE_STORAGE_FILE_STORES, container.value),
+      (AzureFileSystem.AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK, java.lang.Boolean.TRUE))
+  }
+  def hasTokenExpired(tokenExpiry: Instant, buffer: Duration): Boolean = Instant.now.plus(buffer).isAfter(tokenExpiry)
+  def uri(endpoint: EndpointURL) = new URI("azb://?endpoint=" + endpoint)
+}
+case class BlobFileSystemManager(
+    container: BlobContainerName,
+    endpoint: EndpointURL,
+    expiryBufferMinutes: Long,
+    blobTokenGenerator: BlobTokenGenerator,
+    fileSystemAPI: FileSystemAPI = FileSystemAPI(),
+    private val initialExpiration: Option[Instant] = None) {
+  private var expiry: Option[Instant] = initialExpiration
+  val buffer: Duration = Duration.of(expiryBufferMinutes, ChronoUnit.MINUTES)
+
+  def getExpiry: Option[Instant] = expiry
+  def uri: URI = BlobFileSystemManager.uri(endpoint)
+  def isTokenExpired: Boolean = expiry.exists(BlobFileSystemManager.hasTokenExpired(_, buffer))
+  def shouldReopenFilesystem: Boolean = isTokenExpired || expiry.isEmpty
+  def retrieveFilesystem(): Try[FileSystem] = {
+    synchronized {
+      shouldReopenFilesystem match {
+        case false => fileSystemAPI.getFileSystem(uri).recoverWith {
+          // If no filesystem already exists, this will create a new connection, with the provided configs
+          case _: FileSystemNotFoundException => blobTokenGenerator.generateAccessToken.flatMap(generateFilesystem(uri, container, _))
+        }
+        // If the token has expired, OR there is no token record, try to close the FS and regenerate
+        case true =>
+          fileSystemAPI.closeFileSystem(uri)
+          blobTokenGenerator.generateAccessToken.flatMap(generateFilesystem(uri, container, _))
+      }
+    }
+  }
+
+  private def generateFilesystem(uri: URI, container: BlobContainerName, token: AzureSasCredential): Try[FileSystem] = {
+    expiry = BlobFileSystemManager.parseTokenExpiry(token)
+    if (expiry.isEmpty) return Failure(new Exception("Could not reopen filesystem, no expiration found"))
+    Try(fileSystemAPI.newFileSystem(uri, BlobFileSystemManager.buildConfigMap(token, container)))
+  }
+
+}
+
+sealed trait BlobTokenGenerator {def generateAccessToken: Try[AzureSasCredential]}
+object BlobTokenGenerator {
+  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[String]): BlobTokenGenerator = {
+    createBlobTokenGenerator(container, endpoint, None, None, subscription)
+  }
+  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: Option[WorkspaceId], workspaceManagerURL: Option[WorkspaceManagerURL], subscription: Option[String]): BlobTokenGenerator = {
+     (container: BlobContainerName, endpoint: EndpointURL, workspaceId, workspaceManagerURL) match {
+       case (container, endpoint, None, None) =>
+         NativeBlobTokenGenerator(container, endpoint, subscription)
+       case (container, endpoint, Some(workspaceId), Some(workspaceManagerURL)) =>
+         WSMBlobTokenGenerator(container, endpoint, workspaceId, workspaceManagerURL)
+       case _ =>
+         throw new Exception("Arguments provided do not match any available BlobTokenGenerator implementation.")
+     }
+  }
+  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL): BlobTokenGenerator = createBlobTokenGenerator(container, endpoint, None)
+  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: Option[WorkspaceId], workspaceManagerURL: Option[WorkspaceManagerURL]): BlobTokenGenerator =
+      createBlobTokenGenerator(container, endpoint, workspaceId, workspaceManagerURL, None)
+
+}
+
+case class WSMBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: WorkspaceId, workspaceManagerURL: WorkspaceManagerURL) extends BlobTokenGenerator {
+  def generateAccessToken: Try[AzureSasCredential] = Failure(new NotImplementedError)
+}
+
+case class NativeBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[String] = None) extends BlobTokenGenerator {
+
+  private val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
+  private def azureCredentialBuilder = new DefaultAzureCredentialBuilder()
+      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
+      .build
+  private def authenticateWithSubscription(sub: String) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub)
+  private def authenticateWithDefaultSubscription = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withDefaultSubscription()
+  private def azure = subscription.map(authenticateWithSubscription(_)).getOrElse(authenticateWithDefaultSubscription)
+
+  private def findAzureStorageAccount(name: StorageAccountName) = azure.storageAccounts.list.asScala.find(_.name.equals(name.value))
+      .map(Success(_)).getOrElse(Failure(new Exception("Azure Storage Account not found")))
+  private def buildBlobContainerClient(credential: StorageSharedKeyCredential, endpoint: EndpointURL, container: BlobContainerName): BlobContainerClient = {
+    new BlobContainerClientBuilder()
+        .credential(credential)
+        .endpoint(endpoint.value)
+        .containerName(container.value)
+        .buildClient()
+  }
+  private val bcsp = new BlobContainerSasPermission()
+    .setReadPermission(true)
+    .setCreatePermission(true)
+    .setListPermission(true)
+
+
+  def generateAccessToken: Try[AzureSasCredential] = for {
+    uri <- BlobPathBuilder.parseURI(endpoint.value)
+    configuredAccount <- BlobPathBuilder.parseStorageAccount(uri)
+    azureAccount <- findAzureStorageAccount(configuredAccount)
+    keys = azureAccount.getKeys.asScala
+    key <- keys.headOption.fold[Try[StorageAccountKey]](Failure(new Exception("Storage account has no keys")))(Success(_))
+    first = key.value
+    sskc = new StorageSharedKeyCredential(configuredAccount.value, first)
+    bcc = buildBlobContainerClient(sskc, endpoint, container)
+    bsssv = new BlobServiceSasSignatureValues(OffsetDateTime.now.plusDays(1), bcsp)
+    asc = new AzureSasCredential(bcc.generateSas(bsssv))
+  } yield asc
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index b89a335b9de..3e69ce2a7bd 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -1,16 +1,14 @@
 package cromwell.filesystems.blob
 
-import com.azure.core.credential.AzureSasCredential
-import com.azure.storage.blob.nio.{AzureBlobFileAttributes, AzureFileSystem}
+import com.azure.storage.blob.nio.{AzureBlobFileAttributes}
 import com.google.common.net.UrlEscapers
 import cromwell.core.path.{NioPath, Path, PathBuilder}
 import cromwell.filesystems.blob.BlobPathBuilder._
 
 import java.net.{MalformedURLException, URI}
-import java.nio.file.{FileSystem, FileSystemNotFoundException, FileSystems, Files}
-import scala.jdk.CollectionConverters._
 import scala.language.postfixOps
-import scala.util.{Failure, Try}
+import scala.util.{Failure, Success, Try}
+import java.nio.file.Files
 
 object BlobPathBuilder {
 
@@ -18,9 +16,10 @@ object BlobPathBuilder {
   case class ValidBlobPath(path: String) extends BlobPathValidation
   case class UnparsableBlobPath(errorMessage: Throwable) extends BlobPathValidation
 
-  def invalidBlobPathMessage(container: String, endpoint: String) = s"Malformed Blob URL for this builder. Expecting a URL for a container $container and endpoint $endpoint"
-  def parseURI(string: String) = URI.create(UrlEscapers.urlFragmentEscaper().escape(string))
-  def parseStorageAccount(uri: URI) = uri.getHost().split("\\.").filter(!_.isEmpty()).headOption
+  def invalidBlobPathMessage(container: BlobContainerName, endpoint: EndpointURL) = s"Malformed Blob URL for this builder. Expecting a URL for a container $container and endpoint $endpoint"
+  def parseURI(string: String): Try[URI] = Try(URI.create(UrlEscapers.urlFragmentEscaper().escape(string)))
+  def parseStorageAccount(uri: URI): Try[StorageAccountName] = uri.getHost.split("\\.").find(_.nonEmpty).map(StorageAccountName(_))
+      .map(Success(_)).getOrElse(Failure(new Exception("Could not parse storage account")))
 
   /**
     * Validates a that a path from a string is a valid BlobPath of the format:
@@ -40,56 +39,50 @@ object BlobPathBuilder {
     *
     * If the configured container and storage account do not match, the string is considered unparsable
     */
-  def validateBlobPath(string: String, container: String, endpoint: String): BlobPathValidation = {
-    Try {
-      val uri = parseURI(string)
-      val storageAccount = parseStorageAccount(parseURI(endpoint))
-      val hasContainer = uri.getPath().split("/").filter(!_.isEmpty()).headOption.contains(container)
-      def hasEndpoint = parseStorageAccount(uri).contains(storageAccount.get)
-      if (hasContainer && !storageAccount.isEmpty && hasEndpoint) {
-        ValidBlobPath(uri.getPath.replaceFirst("/" + container, ""))
-      } else {
-        UnparsableBlobPath(new MalformedURLException(invalidBlobPathMessage(container, endpoint)))
+  def validateBlobPath(string: String, container: BlobContainerName, endpoint: EndpointURL): BlobPathValidation = {
+    val blobValidation = for {
+      testUri <- parseURI(string)
+      endpointUri <- parseURI(endpoint.value)
+      testStorageAccount <- parseStorageAccount(testUri)
+      endpointStorageAccount <- parseStorageAccount(endpointUri)
+      hasContainer = testUri.getPath.split("/").find(_.nonEmpty).contains(container.value)
+      hasEndpoint = testStorageAccount.equals(endpointStorageAccount)
+      blobPathValidation = (hasContainer && hasEndpoint) match {
+        case true => ValidBlobPath(testUri.getPath.replaceFirst("/" + container, ""))
+        case false => UnparsableBlobPath(new MalformedURLException(invalidBlobPathMessage(container, endpoint)))
       }
-    } recover { case t => UnparsableBlobPath(t) } get
+    } yield blobPathValidation
+    blobValidation recover { case t => UnparsableBlobPath(t) } get
   }
 }
 
-class BlobPathBuilder(blobTokenGenerator: BlobTokenGenerator, container: String, endpoint: String) extends PathBuilder {
-
-  val credential: AzureSasCredential = new AzureSasCredential(blobTokenGenerator.getAccessToken)
-  val fileSystemConfig: Map[String, Object] = Map((AzureFileSystem.AZURE_STORAGE_SAS_TOKEN_CREDENTIAL, credential),
-                                                  (AzureFileSystem.AZURE_STORAGE_FILE_STORES, container),
-                                                  (AzureFileSystem.AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK, java.lang.Boolean.TRUE))
-
-  def retrieveFilesystem(uri: URI): Try[FileSystem] = {
-    Try(FileSystems.getFileSystem(uri)) recover {
-      // If no filesystem already exists, this will create a new connection, with the provided configs
-      case _: FileSystemNotFoundException => FileSystems.newFileSystem(uri, fileSystemConfig.asJava)
-    }
-  }
+class BlobPathBuilder(container: BlobContainerName, endpoint: EndpointURL)(private val fsm: BlobFileSystemManager) extends PathBuilder {
 
   def build(string: String): Try[BlobPath] = {
     validateBlobPath(string, container, endpoint) match {
-      case ValidBlobPath(path) => for {
-            fileSystem <- retrieveFilesystem(new URI("azb://?endpoint=" + endpoint))
-            nioPath <- Try(fileSystem.getPath(path))
-            blobPath = BlobPath(nioPath, endpoint, container)
-          } yield blobPath
+      case ValidBlobPath(path) => Try(BlobPath(path, endpoint, container)(fsm))
       case UnparsableBlobPath(errorMessage: Throwable) => Failure(errorMessage)
     }
   }
-
   override def name: String = "Azure Blob Storage"
 }
 
-// Add args for container, storage account name
-case class BlobPath private[blob](nioPath: NioPath, endpoint: String, container: String) extends Path {
-  override protected def newPath(nioPath: NioPath): Path = BlobPath(nioPath, endpoint, container)
+case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, container: BlobContainerName)(private val fsm: BlobFileSystemManager) extends Path {
+  override def nioPath: NioPath = findNioPath(pathString)
+
+  override protected def newPath(nioPath: NioPath): Path = BlobPath(nioPath.toString, endpoint, container)(fsm)
+
+  override def pathAsString: String = List(endpoint, container, nioPath.toString).mkString("/")
 
-  override def pathAsString: String = List(endpoint, container, nioPath.toString()).mkString("/")
+  //This is purposefully an unprotected get because if the endpoint cannot be parsed this should fail loudly rather than quietly
+  override def pathWithoutScheme: String = parseURI(endpoint.value).map(_.getHost + "/" + container + "/" + nioPath.toString).get
 
-  override def pathWithoutScheme: String = parseURI(endpoint).getHost + "/" + container + "/" + nioPath.toString()
+  private def findNioPath(path: String): NioPath = (for {
+    fileSystem <- fsm.retrieveFilesystem()
+    nioPath = fileSystem.getPath(path)
+  // This is purposefully an unprotected get because the NIO API needing an unwrapped path object.
+  // If an error occurs the api expects a thrown exception
+  } yield nioPath).get
 
   def blobFileAttributes: Try[AzureBlobFileAttributes] =
     Try(Files.readAttributes(nioPath, classOf[AzureBlobFileAttributes]))
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index b12abf5cc34..c93f751b706 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -1,114 +1,35 @@
 package cromwell.filesystems.blob
 
 import akka.actor.ActorSystem
-import com.azure.core.management.AzureEnvironment
-import com.azure.core.management.profile.AzureProfile
-import com.azure.identity.DefaultAzureCredentialBuilder
-import com.azure.resourcemanager.AzureResourceManager
-import com.azure.storage.blob.BlobContainerClientBuilder
-import com.azure.storage.blob.sas.{BlobContainerSasPermission, BlobServiceSasSignatureValues}
-import com.azure.storage.common.StorageSharedKeyCredential
 import com.typesafe.config.Config
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.PathBuilderFactory
 import net.ceedubs.ficus.Ficus._
 
-import java.time.OffsetDateTime
-import scala.concurrent.ExecutionContext
-import scala.concurrent.Future
-import scala.jdk.CollectionConverters._
+import scala.concurrent.{ExecutionContext, Future}
 
 final case class BlobFileSystemConfig(config: Config)
+
+final case class BlobContainerName(value: String) {override def toString: String = value}
+final case class StorageAccountName(value: String) {override def toString: String = value}
+final case class EndpointURL(value: String) {override def toString: String = value}
+final case class WorkspaceId(value: String) {override def toString: String = value}
+final case class WorkspaceManagerURL(value: String) {override def toString: String = value}
 final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, singletonConfig: BlobFileSystemConfig) extends PathBuilderFactory {
-  val container: String = instanceConfig.as[String]("store")
-  val endpoint: String = instanceConfig.as[String]("endpoint")
-  val workspaceId: Option[String] = instanceConfig.as[Option[String]]("workspace-id")
-  val workspaceManagerURL: Option[String] = singletonConfig.config.as[Option[String]]("workspace-manager-url")
+  val subscription: Option[String] = instanceConfig.as[Option[String]]("subscription")
+  val container: BlobContainerName = BlobContainerName(instanceConfig.as[String]("container"))
+  val endpoint: EndpointURL = EndpointURL(instanceConfig.as[String]("endpoint"))
+  val workspaceId: Option[WorkspaceId] = instanceConfig.as[Option[String]]("workspace-id").map(WorkspaceId(_))
+  val expiryBufferMinutes: Long = instanceConfig.as[Option[Long]]("expiry-buffer-minutes").getOrElse(10)
+  val workspaceManagerURL: Option[WorkspaceManagerURL] = singletonConfig.config.as[Option[String]]("workspace-manager-url").map(WorkspaceManagerURL(_))
 
   val blobTokenGenerator: BlobTokenGenerator = BlobTokenGenerator.createBlobTokenGenerator(
-    container, endpoint, workspaceId, workspaceManagerURL)
+    container, endpoint, workspaceId, workspaceManagerURL, subscription)
+  val fsm: BlobFileSystemManager = BlobFileSystemManager(container, endpoint, expiryBufferMinutes, blobTokenGenerator)
 
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[BlobPathBuilder] = {
     Future {
-      new BlobPathBuilder(blobTokenGenerator, container, endpoint)
+      new BlobPathBuilder(container, endpoint)(fsm)
     }
   }
 }
-
-sealed trait BlobTokenGenerator {
-  def getAccessToken: String
-}
-
-object BlobTokenGenerator {
-  def createBlobTokenGenerator(container: String, endpoint: String): BlobTokenGenerator = {
-    createBlobTokenGenerator(container, endpoint, None, None)
-  }
-  def createBlobTokenGenerator(container: String, endpoint: String, workspaceId: Option[String], workspaceManagerURL: Option[String]): BlobTokenGenerator = {
-     (container: String, endpoint: String, workspaceId, workspaceManagerURL) match {
-       case (container, endpoint, None, None) =>
-         NativeBlobTokenGenerator(container, endpoint)
-       case (container, endpoint, Some(workspaceId), Some(workspaceManagerURL)) =>
-         WSMBlobTokenGenerator(container, endpoint, workspaceId, workspaceManagerURL)
-       case _ =>
-         throw new Exception("Arguments provided do not match any available BlobTokenGenerator implementation.")
-     }
-  }
-}
-
-case class WSMBlobTokenGenerator(container: String, endpoint: String, workspaceId: String, workspaceManagerURL: String) extends BlobTokenGenerator {
-  def getAccessToken: String = {
-    throw new NotImplementedError
-  }
-}
-
-case class NativeBlobTokenGenerator(container: String, endpoint: String) extends BlobTokenGenerator {
-  def getAccessToken: String = {
-    val storageAccountName = BlobPathBuilder.parseStorageAccount(BlobPathBuilder.parseURI(endpoint)) match {
-      case Some(storageAccountName) => storageAccountName
-      case _ => throw new Exception("Storage account could not be parsed from endpoint")
-    }
-
-    val profile = new AzureProfile(AzureEnvironment.AZURE)
-    val azureCredential = new DefaultAzureCredentialBuilder()
-      .authorityHost(profile.getEnvironment.getActiveDirectoryEndpoint)
-      .build
-    val azure = AzureResourceManager.authenticate(azureCredential, profile).withDefaultSubscription
-
-    val storageAccounts = azure.storageAccounts()
-    val storageAccount = storageAccounts
-      .list()
-      .asScala
-      .find(_.name == storageAccountName)
-
-    val storageAccountKeys = storageAccount match {
-      case Some(value) => value.getKeys.asScala.map(_.value())
-      case _ => throw new Exception("Storage Account not found")
-    }
-
-    val storageAccountKey = storageAccountKeys.headOption match {
-      case Some(value) => value
-      case _ => throw new Exception("Storage Account has no keys")
-    }
-
-    val keyCredential = new StorageSharedKeyCredential(
-      storageAccountName,
-      storageAccountKey
-    )
-    val blobContainerClient = new BlobContainerClientBuilder()
-      .credential(keyCredential)
-      .endpoint(endpoint)
-      .containerName(container)
-      .buildClient()
-
-    val blobContainerSasPermission = new BlobContainerSasPermission()
-      .setReadPermission(true)
-      .setCreatePermission(true)
-      .setListPermission(true)
-    val blobServiceSasSignatureValues = new BlobServiceSasSignatureValues(
-      OffsetDateTime.now.plusDays(1),
-      blobContainerSasPermission
-    )
-
-    blobContainerClient.generateSas(blobServiceSasSignatureValues)
-  }
-}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
index 08efd534056..f5b71a06ead 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
@@ -1,28 +1,189 @@
 package cromwell.filesystems.blob
 
+import com.azure.core.credential.AzureSasCredential
 import com.typesafe.config.ConfigFactory
+import common.mock.MockSugar
+import org.mockito.Mockito._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers {
+import java.nio.file.{FileSystem, FileSystemNotFoundException}
+import java.time.format.DateTimeFormatter
+import java.time.temporal.ChronoUnit
+import java.time.{Duration, Instant, ZoneId}
+import scala.util.{Failure, Try}
 
+
+object BlobPathBuilderFactorySpec {
+  def buildExampleSasToken(expiry: Instant): AzureSasCredential = {
+    val formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd").withZone(ZoneId.systemDefault())
+    val sv = formatter.format(expiry)
+    val se = expiry.toString().replace(":","%3A")
+    new AzureSasCredential(s"sv=$sv&se=$se&sr=c&sp=rcl")
+  }
+}
+class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSugar {
+  def generateTokenExpiration(minutes: Long) = Instant.now.plus(minutes, ChronoUnit.MINUTES)
   it should "parse configs for a functioning factory" in {
-    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
-    val store = "inputs"
-    val workspaceId = "mockWorkspaceId"
-    val workspaceManagerURL = "https://test.ws.org"
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val container = BlobContainerName("storageContainer")
+    val workspaceId = WorkspaceId("mockWorkspaceId")
+    val workspaceManagerURL = WorkspaceManagerURL("https://test.ws.org")
     val instanceConfig = ConfigFactory.parseString(
       s"""
-      |store = "$store"
+      |container = "$container"
+
       |endpoint = "$endpoint"
+      |expiry-buffer-minutes = "10"
       |workspace-id = "$workspaceId"
       """.stripMargin)
     val singletonConfig = ConfigFactory.parseString(s"""workspace-manager-url = "$workspaceManagerURL" """)
     val globalConfig = ConfigFactory.parseString("""""")
     val factory = BlobPathBuilderFactory(globalConfig, instanceConfig, new BlobFileSystemConfig(singletonConfig))
-    factory.container should equal(store)
+    factory.container should equal(container)
     factory.endpoint should equal(endpoint)
-    factory.workspaceId should equal(Some(workspaceId))
-    factory.workspaceManagerURL should equal(Some(workspaceManagerURL))
+    factory.expiryBufferMinutes should equal(10L)
+    factory.workspaceId should contain(workspaceId)
+    factory.workspaceManagerURL should contain(workspaceManagerURL)
+  }
+
+  it should "build an example sas token of the correct format" in {
+    val testToken = BlobPathBuilderFactorySpec.buildExampleSasToken(Instant.ofEpochMilli(1603794041000L))
+    val sourceToken = "sv=2020-10-27&se=2020-10-27T10%3A20%3A41Z&sr=c&sp=rcl"
+    testToken.getSignature should equal(sourceToken)
+  }
+
+  it should "parse an expiration time from a sas token" in {
+    val expiryTime = generateTokenExpiration(20L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(expiryTime)
+    val expiry = BlobFileSystemManager.parseTokenExpiry(sasToken)
+    expiry should contain(expiryTime)
+  }
+
+  it should "verify an unexpired token will be processed as unexpired" in {
+    val expiryTime = generateTokenExpiration(11L)
+    val expired = BlobFileSystemManager.hasTokenExpired(expiryTime, Duration.ofMinutes(10L))
+    expired shouldBe false
+  }
+
+  it should "test an expired token will be processed as expired" in {
+    val expiryTime = generateTokenExpiration(9L)
+    val expired = BlobFileSystemManager.hasTokenExpired(expiryTime, Duration.ofMinutes(10L))
+    expired shouldBe true
+  }
+
+  it should "test that a filesystem gets closed correctly" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+    val fileSystems = mock[FileSystemAPI]
+    val fileSystem = mock[FileSystem]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(fileSystem))
+    when(fileSystems.closeFileSystem(azureUri)).thenCallRealMethod()
+
+    fileSystems.closeFileSystem(azureUri)
+    verify(fileSystem, times(1)).close()
+  }
+
+  it should "test retrieveFileSystem with expired filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val expiredToken = generateTokenExpiration(9L)
+    val refreshedToken = generateTokenExpiration(69L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+
+    val fileSystems = mock[FileSystemAPI]
+    val blobTokenGenerator = mock[BlobTokenGenerator]
+    when(blobTokenGenerator.generateAccessToken).thenReturn(Try(sasToken))
+
+    val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(expiredToken))
+    fsm.getExpiry should contain(expiredToken)
+    fsm.isTokenExpired shouldBe true
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(refreshedToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, never()).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
+    verify(fileSystems, times(1)).closeFileSystem(azureUri)
+  }
+
+  it should "test retrieveFileSystem with an unexpired fileSystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val initialToken = generateTokenExpiration(11L)
+    val refreshedToken = generateTokenExpiration(71L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+    // Need a fake filesystem to supply the getFileSystem simulated try
+    val dummyFileSystem = mock[FileSystem]
+
+    val fileSystems = mock[FileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(dummyFileSystem))
+
+    val blobTokenGenerator = mock[BlobTokenGenerator]
+    when(blobTokenGenerator.generateAccessToken).thenReturn(Try(sasToken))
+
+    val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(initialToken))
+    fsm.getExpiry should contain(initialToken)
+    fsm.isTokenExpired shouldBe false
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(initialToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, times(1)).getFileSystem(azureUri)
+    verify(fileSystems, never()).newFileSystem(azureUri, configMap)
+    verify(fileSystems, never()).closeFileSystem(azureUri)
+  }
+
+  it should "test retrieveFileSystem with an uninitialized filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val refreshedToken = generateTokenExpiration(71L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+
+    val fileSystems = mock[FileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Failure(new FileSystemNotFoundException))
+    val blobTokenGenerator = mock[BlobTokenGenerator]
+    when(blobTokenGenerator.generateAccessToken).thenReturn(Try(sasToken))
+
+    val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(refreshedToken))
+    fsm.getExpiry.isDefined shouldBe true
+    fsm.isTokenExpired shouldBe false
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(refreshedToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, times(1)).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
+    verify(fileSystems, never()).closeFileSystem(azureUri)
+  }
+
+  it should "test retrieveFileSystem with an unknown filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val refreshedToken = generateTokenExpiration(71L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+
+    val fileSystems = mock[FileSystemAPI]
+    val blobTokenGenerator = mock[BlobTokenGenerator]
+    when(blobTokenGenerator.generateAccessToken).thenReturn(Try(sasToken))
+
+    val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems)
+    fsm.getExpiry.isDefined shouldBe false
+    fsm.isTokenExpired shouldBe false
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(refreshedToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, never()).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
+    verify(fileSystems, times(1)).closeFileSystem(azureUri)
   }
 }
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index 69cec235aff..9975065a3e2 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -1,19 +1,22 @@
 package cromwell.filesystems.blob
+import common.mock.MockSugar
+import org.mockito.Mockito.when
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
-import java.nio.file.Files
+
+import scala.util.{Failure, Try}
 
 object BlobPathBuilderSpec {
-  def buildEndpoint(storageAccount: String) = s"https://$storageAccount.blob.core.windows.net"
+  def buildEndpoint(storageAccount: String) = EndpointURL(s"https://$storageAccount.blob.core.windows.net")
 }
 
-class BlobPathBuilderSpec extends AnyFlatSpec with Matchers{
-
+class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
+  // ValidateBlobPath
   it should "parse a URI into a path" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = "container"
+    val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
-    val testString = endpoint + "/" + container + evalPath
+    val testString = endpoint.value + "/" + container + evalPath
     BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
       case BlobPathBuilder.ValidBlobPath(path) => path should equal(evalPath)
       case BlobPathBuilder.UnparsableBlobPath(errorMessage) => fail(errorMessage)
@@ -22,53 +25,70 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers{
 
   it should "bad storage account fails causes URI to fail parse into a path" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = "container"
+    val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
-    val testString = BlobPathBuilderSpec.buildEndpoint("badStorageAccount") + container + evalPath
+    val testString = BlobPathBuilderSpec.buildEndpoint("badStorageAccount").value + container.value + evalPath
     BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
       case BlobPathBuilder.ValidBlobPath(path) => fail(s"Valid path: $path found when verifying mismatched storage account")
-      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage() should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
+      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
     }
   }
 
   it should "bad container fails causes URI to fail parse into a path" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = "container"
+    val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
-    val testString = endpoint + "badContainer" + evalPath
+    val testString = endpoint.value + "badContainer" + evalPath
     BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
       case BlobPathBuilder.ValidBlobPath(path) => fail(s"Valid path: $path found when verifying mismatched container")
-      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage() should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
+      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
     }
   }
 
+  it should "provide a readable error when getting an illegal nioPath" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val container = BlobContainerName("container")
+    val evalPath = "/path/to/file"
+    val exception = new Exception("Failed to do the thing")
+    val fsm = mock[BlobFileSystemManager]
+    when(fsm.retrieveFilesystem()).thenReturn(Failure(exception))
+    val path = BlobPath(evalPath, endpoint, container)(fsm)
+    val testException = Try(path.nioPath).failed.toOption
+    testException should contain(exception)
+  }
+
   ignore should "build a blob path from a test string and read a file" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
-    val endpointHost = BlobPathBuilder.parseURI(endpoint).getHost
-    val store = "inputs"
+    val endpointHost = BlobPathBuilder.parseURI(endpoint.value).map(_.getHost).getOrElse(fail("Could not parse URI"))
+    val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
-    val blobTokenGenerator: BlobTokenGenerator = BlobTokenGenerator.createBlobTokenGenerator(store, endpoint)
-    val testString = endpoint + "/" + store + evalPath
-    val blobPath: BlobPath = new BlobPathBuilder(blobTokenGenerator, store, endpoint) build testString getOrElse fail()
+    val blobTokenGenerator = NativeBlobTokenGenerator(store, endpoint)
+    val fsm: BlobFileSystemManager = BlobFileSystemManager(store, endpoint, 10L, blobTokenGenerator)
+    val testString = endpoint.value + "/" + store + evalPath
+    val blobPath: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
 
     blobPath.container should equal(store)
     blobPath.endpoint should equal(endpoint)
     blobPath.pathAsString should equal(testString)
     blobPath.pathWithoutScheme should equal(endpointHost + "/" + store + evalPath)
-
-    val is = Files.newInputStream(blobPath.nioPath)
+    val is = blobPath.newInputStream()
     val fileText = (is.readAllBytes.map(_.toChar)).mkString
     fileText should include ("This is my test file!!!! Did it work?")
   }
 
   ignore should "build duplicate blob paths in the same filesystem" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
-    val store = "inputs"
+    val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
-    val blobTokenGenerator: BlobTokenGenerator = BlobTokenGenerator.createBlobTokenGenerator(store, endpoint)
-    val testString = endpoint + "/" + store + evalPath
-    val blobPath1: BlobPath = new BlobPathBuilder(blobTokenGenerator, store, endpoint) build testString getOrElse fail()
-    val blobPath2: BlobPath = new BlobPathBuilder(blobTokenGenerator, store, endpoint) build testString getOrElse fail()
+    val blobTokenGenerator = NativeBlobTokenGenerator(store, endpoint)
+    val fsm: BlobFileSystemManager = BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
+    val testString = endpoint.value + "/" + store + evalPath
+    val blobPath1: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
+    blobPath1.nioPath.getFileSystem.close()
+    val blobPath2: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
     blobPath1 should equal(blobPath2)
+    val is = blobPath1.newInputStream()
+    val fileText = (is.readAllBytes.map(_.toChar)).mkString
+    fileText should include ("This is my test file!!!! Did it work?")
   }
 }

From 664de52e74a893b43169525baa5bcd5b0a9fd632 Mon Sep 17 00:00:00 2001
From: Christian Freitas <christian.j.freitas@gmail.com>
Date: Mon, 12 Sep 2022 16:19:11 -0400
Subject: [PATCH 083/326] Batch 1 of scala steward updates (#6903)

* Batch 1 of scala steward updates

* Rollback snakeYAML

* Attempt 3, with only the passing dependancies

* Revert google API and Big Query udpates

* Winding back other google deps

* rollback remaining google updates

* trigger tests

* trigger tests
---
 project/Dependencies.scala | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index a6cc50eb351..fadd662d2f3 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -10,9 +10,9 @@ object Dependencies {
   // We would like to use the BOM to manage Azure SDK versions, but SBT doesn't support it.
   // https://github.com/Azure/azure-sdk-for-java/tree/main/sdk/boms/azure-sdk-bom
   // https://github.com/sbt/sbt/issues/4531
-  private val azureStorageBlobNioV = "12.0.0-beta.18"
-  private val azureIdentitySdkV = "1.4.2"
-  private val azureKeyVaultSdkV = "4.3.7"
+  private val azureStorageBlobNioV = "12.0.0-beta.19"
+  private val azureIdentitySdkV = "1.4.6"
+  private val azureKeyVaultSdkV = "4.3.8"
   private val betterFilesV = "3.9.1"
   /*
   cats-effect, fs2, http4s, and sttp (also to v3) should all be upgraded at the same time to use cats-effect 3.x.
@@ -34,7 +34,7 @@ object Dependencies {
   private val configsV = "0.6.1"
   private val delightRhinoSandboxV = "0.0.15"
   private val diffsonSprayJsonV = "4.1.1"
-  private val ficusV = "1.5.1"
+  private val ficusV = "1.5.2"
   private val fs2V = "2.5.9" // scala-steward:off (CROM-6564)
   private val googleApiClientV = "1.33.2"
   private val googleCloudBigQueryV = "2.10.0"
@@ -75,8 +75,8 @@ object Dependencies {
   private val metrics4ScalaV = "4.2.8"
   private val metrics3StatsdV = "4.2.0"
   private val mockFtpServerV = "3.0.0"
-  private val mockitoV = "3.11.2"
-  private val mockserverNettyV = "5.11.2"
+  private val mockitoV = "3.12.4"
+  private val mockserverNettyV = "5.14.0"
   private val mouseV = "1.0.10"
   /*
   Newer version 8.0.29 fails `Control characters should work with metadata` Centaur tests, has charset changes mentioned in release notes
@@ -88,7 +88,7 @@ object Dependencies {
   private val postgresV = "42.3.3"
   private val pprintV = "0.7.1"
   private val rdf4jV = "3.7.1"
-  private val refinedV = "0.9.28"
+  private val refinedV = "0.9.29"
   private val rhinoV = "1.7.13"
   private val scalaCollectionCompatV = "2.5.0"
   private val scalaGraphV = "1.13.1"
@@ -98,9 +98,9 @@ object Dependencies {
   private val scalameterV = "0.19"
   private val scalatestV = "3.2.10"
   private val scalatestScalacheckV = scalatestV + ".0"
-  private val scoptV = "4.0.1"
+  private val scoptV = "4.1.0"
   private val sentryLogbackV = "5.2.4"
-  private val shapelessV = "2.3.7"
+  private val shapelessV = "2.3.9"
   private val simulacrumV = "1.0.1"
   private val slf4jV = "1.7.32"
   private val slickCatsV = "0.10.4"
@@ -191,8 +191,8 @@ object Dependencies {
     "com.azure" % "azure-security-keyvault-secrets" % azureKeyVaultSdkV
       exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
       exclude("jakarta.activation", "jakarta.activation-api"),
-    "com.azure" % "azure-core-management" % "1.7.0",
-    "com.azure.resourcemanager" % "azure-resourcemanager" % "2.17.0"
+    "com.azure" % "azure-core-management" % "1.7.1",
+    "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0"
   )
 
   val implFtpDependencies = List(

From 4884f735a7f3bd8863acf763bdac15b76fac9b2a Mon Sep 17 00:00:00 2001
From: Saloni Shah <salonipshah11@gmail.com>
Date: Fri, 16 Sep 2022 15:07:59 -0400
Subject: [PATCH 084/326] [BW-1398] Migrate PKs to BIGINT (#6907)

---
 CHANGELOG.md                                  | 10 +++
 .../src/main/resources/changelog.xml          |  3 +
 .../enlarge_docker_hash_store_entry_id.xml    | 41 ++++++++++
 .../enlarge_sub_workflow_store_entry_id.xml   | 41 ++++++++++
 .../enlarge_workflow_store_entry_id.xml       | 82 +++++++++++++++++++
 .../DockerHashStoreEntryComponent.scala       |  2 +-
 .../SubWorkflowStoreEntryComponent.scala      |  6 +-
 .../tables/WorkflowStoreEntryComponent.scala  |  2 +-
 .../sql/tables/DockerHashStoreEntry.scala     |  2 +-
 .../sql/tables/SubWorkflowStoreEntry.scala    |  4 +-
 .../sql/tables/WorkflowStoreEntry.scala       |  2 +-
 11 files changed, 186 insertions(+), 9 deletions(-)
 create mode 100644 database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml
 create mode 100644 database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml
 create mode 100644 database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e1158be3ca4..4dcab0dfa3f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,15 @@
 # Cromwell Change Log
 
+## 85 Release Notes
+
+### Migration of PKs to BIGINT
+
+The PK of below tables will be migrated from INT to BIGINT. Also, since `ROOT_WORKFLOW_ID` in `SUB_WORKFLOW_STORE_ENTRY` is a FK to `WORKFLOW_STORE_ENTRY_ID` in `WORKFLOW_STORE_ENTRY` 
+it is also being migrated from INT to BIGINT.
+* DOCKER_HASH_STORE_ENTRY
+* WORKFLOW_STORE_ENTRY
+* SUB_WORKFLOW_STORE_ENTRY
+
 ## 84 Release Notes
 
 ### CromIAM enabled user checks
diff --git a/database/migration/src/main/resources/changelog.xml b/database/migration/src/main/resources/changelog.xml
index 5d711061c31..49d568766b3 100644
--- a/database/migration/src/main/resources/changelog.xml
+++ b/database/migration/src/main/resources/changelog.xml
@@ -87,6 +87,9 @@
     <include file="changesets/enlarge_call_caching_detritus_entry_id.xml" relativeToChangelogFile="true" />
     <include file="changesets/enlarge_call_caching_simpleton_entry_id.xml" relativeToChangelogFile="true" />
     <include file="changesets/reset_call_caching_hash_entry_id_autoincrement.xml" relativeToChangelogFile="true" />
+    <include file="changesets/enlarge_docker_hash_store_entry_id.xml" relativeToChangelogFile="true" />
+    <include file="changesets/enlarge_workflow_store_entry_id.xml" relativeToChangelogFile="true" />
+    <include file="changesets/enlarge_sub_workflow_store_entry_id.xml" relativeToChangelogFile="true" />
     <!-- REMINDER!
       Before appending here, did you remember to include the 'objectQuotingStrategy="QUOTE_ALL_OBJECTS"' line in your changeset/xyz.xml...?
     -->
diff --git a/database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml b/database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml
new file mode 100644
index 00000000000..fc7992268e6
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- BEGIN DOCKER_HASH_STORE_ENTRY_ID PK widening -->
+    <!-- For Postgresql there are 2 changesets: one for modifying the table column type, and another one for altering the autoincrementing sequence.
+         The other DBs can be refactored similarly with a single addAutoIncrement changeset. -->
+    <changeSet author="sshah" id="enlarge_docker_hash_store_entry_id" dbms="mysql,hsqldb,mariadb">
+        <addAutoIncrement
+                columnName="DOCKER_HASH_STORE_ENTRY_ID"
+                columnDataType="BIGINT"
+                incrementBy="1"
+                tableName="DOCKER_HASH_STORE_ENTRY"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_docker_hash_store_entry_id" dbms="postgresql">
+        <modifyDataType
+                columnName="DOCKER_HASH_STORE_ENTRY_ID"
+                tableName="DOCKER_HASH_STORE_ENTRY"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_docker_hash_store_entry_id_seq" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- idempotency check (noop if the sequence is present and already consistent what the alter would do) -->
+            <sqlCheck expectedResult="0">
+                SELECT count(*)
+                FROM information_schema.sequences
+                WHERE sequence_name = 'DOCKER_HASH_STORE_ENTRY_DOCKER_HASH_STORE_ENTRY_ID_seq'
+                AND data_type = 'bigint';
+            </sqlCheck>
+        </preConditions>
+        <sql>alter sequence "DOCKER_HASH_STORE_ENTRY_DOCKER_HASH_STORE_ENTRY_ID_seq" as bigint;</sql>
+    </changeSet>
+    <!-- END DOCKER_HASH_STORE_ENTRY_ID PK widening -->
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml b/database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml
new file mode 100644
index 00000000000..57894db824b
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- BEGIN SUB_WORKFLOW_STORE_ENTRY_ID PK widening -->
+    <!-- For Postgresql there are 2 changesets: one for modifying the table column type, and another one for altering the autoincrementing sequence.
+         The other DBs can be refactored similarly with a single addAutoIncrement changeset. -->
+    <changeSet author="sshah" id="enlarge_sub_workflow_store_entry_id" dbms="mysql,hsqldb,mariadb">
+        <addAutoIncrement
+                columnName="SUB_WORKFLOW_STORE_ENTRY_ID"
+                columnDataType="BIGINT"
+                incrementBy="1"
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_sub_workflow_store_entry_id" dbms="postgresql">
+        <modifyDataType
+                columnName="SUB_WORKFLOW_STORE_ENTRY_ID"
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_sub_workflow_store_entry_id_seq" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- idempotency check (noop if the sequence is present and already consistent what the alter would do) -->
+            <sqlCheck expectedResult="0">
+                SELECT count(*)
+                FROM information_schema.sequences
+                WHERE sequence_name = 'SUB_WORKFLOW_STORE_ENTRY_SUB_WORKFLOW_STORE_ENTRY_ID_seq'
+                AND data_type = 'bigint';
+            </sqlCheck>
+        </preConditions>
+        <sql>alter sequence "SUB_WORKFLOW_STORE_ENTRY_SUB_WORKFLOW_STORE_ENTRY_ID_seq" as bigint;</sql>
+    </changeSet>
+    <!-- END SUB_WORKFLOW_STORE_ENTRY_ID PK widening -->
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml b/database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml
new file mode 100644
index 00000000000..ea2b498fd51
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml
@@ -0,0 +1,82 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- Drop the foreign key constraint from SUB_WORKFLOW_STORE_ENTRY to WORKFLOW_STORE_ENTRY to allow for the latter's PK to be widened. -->
+    <changeSet author="sshah" id="drop_sub_workflow_store_entry_root_workflow_id_fk" dbms="mysql,hsqldb,postgresql,mariadb">
+        <dropForeignKeyConstraint
+                baseTableName="SUB_WORKFLOW_STORE_ENTRY"
+                constraintName="FK_SUB_WORKFLOW_STORE_ENTRY_ROOT_WORKFLOW_ID"
+        />
+    </changeSet>
+
+    <!-- BEGIN WORKFLOW_STORE_ENTRY_ID PK widening -->
+    <!-- For Postgresql there are 2 changesets: one for modifying the table column type, and another one for altering the autoincrementing sequence.
+         The other DBs can be refactored similarly with a single addAutoIncrement changeset. -->
+    <changeSet author="sshah" id="enlarge_workflow_store_entry_id" dbms="mysql,hsqldb,mariadb">
+        <addAutoIncrement
+                columnName="WORKFLOW_STORE_ENTRY_ID"
+                columnDataType="BIGINT"
+                incrementBy="1"
+                tableName="WORKFLOW_STORE_ENTRY"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_workflow_store_entry_id" dbms="postgresql">
+        <modifyDataType
+                columnName="WORKFLOW_STORE_ENTRY_ID"
+                tableName="WORKFLOW_STORE_ENTRY"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_workflow_store_entry_id_seq" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- idempotency check (noop if the sequence is present and already consistent what the alter would do) -->
+            <sqlCheck expectedResult="0">
+                SELECT count(*)
+                FROM information_schema.sequences
+                WHERE sequence_name = 'WORKFLOW_STORE_ENTRY_WORKFLOW_STORE_ENTRY_ID_seq'
+                AND data_type = 'bigint';
+            </sqlCheck>
+        </preConditions>
+        <sql>alter sequence "WORKFLOW_STORE_ENTRY_WORKFLOW_STORE_ENTRY_ID_seq" as bigint;</sql>
+    </changeSet>
+    <!-- END WORKFLOW_STORE_ENTRY_ID PK widening -->
+
+    <!-- BEGIN widening FK to match PK -->
+    <changeSet author="sshah" id="enlarge_sub_workflow_store_entry_fk" dbms="mysql,hsqldb,postgresql,mariadb">
+        <modifyDataType
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+                columnName="ROOT_WORKFLOW_ID"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+    <!-- END widening FK to match PK -->
+
+    <!-- MariaDB's FK NotNull constraint does not survive the widening above and must be recreated explicitly. -->
+    <!-- BEGIN Restoring FK NotNull constraint -->
+    <changeSet author="sshah" id="mariadb_not_null_constraint_sub_workflow_store_entry_fk" dbms="mariadb,mysql">
+        <addNotNullConstraint
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+                columnName="ROOT_WORKFLOW_ID"
+                columnDataType="BIGINT"
+        />
+    </changeSet>
+    <!-- END Restoring FK NotNull constraint -->
+
+    <!-- Restoring the FK -->
+    <changeSet author="sshah" id="recreate_sub_workflow_store_entry_root_workflow_id_fk" dbms="mysql,hsqldb,postgresql,mariadb">
+        <addForeignKeyConstraint
+                constraintName="FK_SUB_WORKFLOW_STORE_ENTRY_ROOT_WORKFLOW_ID"
+                baseColumnNames="ROOT_WORKFLOW_ID"
+                baseTableName="SUB_WORKFLOW_STORE_ENTRY"
+                referencedTableName="WORKFLOW_STORE_ENTRY"
+                referencedColumnNames="WORKFLOW_STORE_ENTRY_ID"
+                onDelete="CASCADE"
+        />
+    </changeSet>
+
+</databaseChangeLog>
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
index e258b40f3b7..5929b2e5a6a 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
@@ -9,7 +9,7 @@ trait DockerHashStoreEntryComponent {
   import driver.api._
 
   class DockerHashStoreEntries(tag: Tag) extends Table[DockerHashStoreEntry](tag, "DOCKER_HASH_STORE_ENTRY") {
-    def dockerHashStoreEntryId = column[Int]("DOCKER_HASH_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
+    def dockerHashStoreEntryId = column[Long]("DOCKER_HASH_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def workflowExecutionUuid = column[String]("WORKFLOW_EXECUTION_UUID", O.Length(255))
 
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
index 2ea7b36782c..11fa2191cb2 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
@@ -10,9 +10,9 @@ trait SubWorkflowStoreEntryComponent {
   import driver.api._
 
   class SubWorkflowStoreEntries(tag: Tag) extends Table[SubWorkflowStoreEntry](tag, "SUB_WORKFLOW_STORE_ENTRY") {
-    def subWorkflowStoreEntryId = column[Int]("SUB_WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
+    def subWorkflowStoreEntryId = column[Long]("SUB_WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
-    def rootWorkflowId = column[Int]("ROOT_WORKFLOW_ID")
+    def rootWorkflowId = column[Long]("ROOT_WORKFLOW_ID")
     
     def parentWorkflowExecutionUuid = column[String]("PARENT_WORKFLOW_EXECUTION_UUID", O.Length(255))
 
@@ -40,7 +40,7 @@ trait SubWorkflowStoreEntryComponent {
   val subWorkflowStoreEntryIdsAutoInc = subWorkflowStoreEntries returning subWorkflowStoreEntries.map(_.subWorkflowStoreEntryId)
 
   val subWorkflowStoreEntriesForRootWorkflowId = Compiled(
-    (rootWorkflowId: Rep[Int]) => for {
+    (rootWorkflowId: Rep[Long]) => for {
       subWorkflowStoreEntry <- subWorkflowStoreEntries
       if subWorkflowStoreEntry.rootWorkflowId === rootWorkflowId
     } yield subWorkflowStoreEntry
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
index 0e29cee651f..847fa862405 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
@@ -11,7 +11,7 @@ trait WorkflowStoreEntryComponent {
   import driver.api._
 
   class WorkflowStoreEntries(tag: Tag) extends Table[WorkflowStoreEntry](tag, "WORKFLOW_STORE_ENTRY") {
-    def workflowStoreEntryId = column[Int]("WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
+    def workflowStoreEntryId = column[Long]("WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def workflowExecutionUuid = column[String]("WORKFLOW_EXECUTION_UUID", O.Length(255))
 
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
index a4a5b1247ee..542558324f5 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
@@ -6,5 +6,5 @@ case class DockerHashStoreEntry
   dockerTag: String,
   dockerHash: String,
   dockerSize: Option[Long],
-  dockerHashStoreEntryId: Option[Int] = None
+  dockerHashStoreEntryId: Option[Long] = None
 )
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
index 96ac39aa672..4cf89381ad0 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
@@ -2,11 +2,11 @@ package cromwell.database.sql.tables
 
 case class SubWorkflowStoreEntry
 (
-  rootWorkflowId: Option[Int],
+  rootWorkflowId: Option[Long],
   parentWorkflowExecutionUuid: String,
   callFullyQualifiedName: String,
   callIndex: Int,
   callAttempt: Int,
   subWorkflowExecutionUuid: String,
-  subWorkflowStoreEntryId: Option[Int] = None
+  subWorkflowStoreEntryId: Option[Long] = None
 )
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
index 6c03db87014..efb594444d4 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
@@ -21,5 +21,5 @@ case class WorkflowStoreEntry
   cromwellId: Option[String],
   heartbeatTimestamp: Option[Timestamp],
   hogGroup: Option[String],
-  workflowStoreEntryId: Option[Int] = None
+  workflowStoreEntryId: Option[Long] = None
 )

From e3f1ad0335b763056e598d97c64cc7f0186c68f8 Mon Sep 17 00:00:00 2001
From: Christian Freitas <christian.j.freitas@gmail.com>
Date: Tue, 20 Sep 2022 08:19:10 -0400
Subject: [PATCH 085/326] BT-745  Batch 2 of scala steward updates (#6906)

* Update SBT to 2.0.0

* Fix sbt-git import

* Update mouse to 1.0.11

* Update rhino 1.7.14
---
 project/Dependencies.scala | 6 ++++--
 project/Version.scala      | 3 ++-
 project/plugins.sbt        | 2 +-
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index fadd662d2f3..21c50b77e10 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -77,7 +77,8 @@ object Dependencies {
   private val mockFtpServerV = "3.0.0"
   private val mockitoV = "3.12.4"
   private val mockserverNettyV = "5.14.0"
-  private val mouseV = "1.0.10"
+  private val mouseV = "1.0.11"
+
   /*
   Newer version 8.0.29 fails `Control characters should work with metadata` Centaur tests, has charset changes mentioned in release notes
   https://dev.mysql.com/doc/relnotes/mysql/8.0/en/news-8-0-29.html#mysqld-8-0-29-charset
@@ -89,7 +90,8 @@ object Dependencies {
   private val pprintV = "0.7.1"
   private val rdf4jV = "3.7.1"
   private val refinedV = "0.9.29"
-  private val rhinoV = "1.7.13"
+  private val rhinoV = "1.7.14"
+
   private val scalaCollectionCompatV = "2.5.0"
   private val scalaGraphV = "1.13.1"
   private val scalaLoggingV = "3.9.4"
diff --git a/project/Version.scala b/project/Version.scala
index c0bdb0b3453..dbe795e6f0c 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -1,7 +1,8 @@
 import Dependencies._
-import com.typesafe.sbt.SbtGit._
+import com.github.sbt.git.SbtGit._
 import sbt.Keys._
 import sbt._
+import com.github.sbt.git.SbtGit
 
 object Version {
   // Upcoming release, or current if we're on a master / hotfix branch
diff --git a/project/plugins.sbt b/project/plugins.sbt
index 51289a45e53..cef75cd05b3 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1,5 +1,5 @@
 addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.9.0")
 addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.0")
-addSbtPlugin("com.typesafe.sbt" % "sbt-git" % "1.0.2")
+addSbtPlugin("com.github.sbt" % "sbt-git" % "2.0.0")
 addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.9.3")
 addDependencyTreePlugin

From 68949364c7ffab8450116baa8e2a4e276bb16d70 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 23 Sep 2022 11:08:10 -0400
Subject: [PATCH 086/326] SUP-692 Retry with more memory after RC 137 (#6912)

* Reorder execution result checks so 137 can retry with more memory

* Test for memory retry after 137 RC

* Fix test expectations

* Make memory retry checks consistent

* Revert changes to existing test

* Rename retryWithMoreMemory to outOfMemoryDetected
---
 .../StandardAsyncExecutionActor.scala         | 23 +++++++++++--------
 .../retry_with_more_memory_after_137.wdl      | 22 ++++++++++++++++++
 .../retry_with_more_memory_after_137.test     | 21 +++++++++++++++++
 3 files changed, 57 insertions(+), 9 deletions(-)
 create mode 100644 centaur/src/main/resources/standardTestCases/retry_with_more_memory/retry_with_more_memory_after_137.wdl
 create mode 100644 centaur/src/main/resources/standardTestCases/retry_with_more_memory_after_137.test

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 0f1e2c931a8..c98e429c63d 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -244,6 +244,8 @@ trait StandardAsyncExecutionActor
     }
   }
 
+  lazy val memoryRetryRequested: Boolean = memoryRetryFactor.nonEmpty
+
   /**
     * Returns the shell scripting for finding all files listed within a directory.
     *
@@ -1259,6 +1261,7 @@ trait StandardAsyncExecutionActor
   def handleExecutionResult(status: StandardAsyncRunState,
                             oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
 
+    // Returns true if the task has written an RC file that indicates OOM, false otherwise
     def memoryRetryRC: Future[Boolean] = {
       def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
         codeAsOption match {
@@ -1299,11 +1302,11 @@ trait StandardAsyncExecutionActor
       // Only check stderr size if we need to, otherwise this results in a lot of unnecessary I/O that
       // may fail due to race conditions on quickly-executing jobs.
       stderrSize <- if (failOnStdErr) asyncIo.sizeAsync(stderr) else Future.successful(0L)
-      retryWithMoreMemory <- memoryRetryRC
-    } yield (stderrSize, returnCodeAsString, retryWithMoreMemory)
+      outOfMemoryDetected <- memoryRetryRC
+    } yield (stderrSize, returnCodeAsString, outOfMemoryDetected)
 
     stderrSizeAndReturnCodeAndMemoryRetry flatMap {
-      case (stderrSize, returnCodeAsString, retryWithMoreMemory) =>
+      case (stderrSize, returnCodeAsString, outOfMemoryDetected) =>
         val tryReturnCodeAsInt = Try(returnCodeAsString.trim.toInt)
 
         if (isDone(status)) {
@@ -1311,13 +1314,15 @@ trait StandardAsyncExecutionActor
             case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
-            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
-              Future.successful(AbortedExecutionHandle)
             case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
               handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
-            case Success(returnCodeAsInt) if retryWithMoreMemory  =>
+            // It's important that we check retryWithMoreMemory case before isAbort. RC could be 137 in either case;
+            // if it was caused by OOM killer, want to handle as OOM and not job abort.
+            case Success(returnCodeAsInt) if outOfMemoryDetected && memoryRetryRequested  =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
-              retryElseFail(executionHandle, retryWithMoreMemory)
+              retryElseFail(executionHandle, outOfMemoryDetected)
+            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
+              Future.successful(AbortedExecutionHandle)
             case Success(returnCodeAsInt) =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
@@ -1326,9 +1331,9 @@ trait StandardAsyncExecutionActor
           }
         } else {
           tryReturnCodeAsInt match {
-            case Success(returnCodeAsInt) if retryWithMoreMemory && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
+            case Success(returnCodeAsInt) if outOfMemoryDetected && memoryRetryRequested && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
-              retryElseFail(executionHandle, retryWithMoreMemory)
+              retryElseFail(executionHandle, outOfMemoryDetected)
             case _ =>
               val failureStatus = handleExecutionFailure(status, tryReturnCodeAsInt.toOption)
               retryElseFail(failureStatus)
diff --git a/centaur/src/main/resources/standardTestCases/retry_with_more_memory/retry_with_more_memory_after_137.wdl b/centaur/src/main/resources/standardTestCases/retry_with_more_memory/retry_with_more_memory_after_137.wdl
new file mode 100644
index 00000000000..2fe434475c6
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/retry_with_more_memory/retry_with_more_memory_after_137.wdl
@@ -0,0 +1,22 @@
+version 1.0
+
+task imitate_oom_error {
+  command {
+    printf "Exception in thread "main" java.lang.OutOfMemoryError: testing\n\tat Test.main(Test.java:1)\n" >&2
+    touch foo
+    exit 137
+  }
+  output {
+    File foo = "foo"
+  }
+  runtime {
+    docker: "python:latest"
+    memory: "1 GB"
+    maxRetries: 2
+    backend: "Papiv2"
+  }
+}
+
+workflow retry_with_more_memory_after_137 {
+  call imitate_oom_error
+}
diff --git a/centaur/src/main/resources/standardTestCases/retry_with_more_memory_after_137.test b/centaur/src/main/resources/standardTestCases/retry_with_more_memory_after_137.test
new file mode 100644
index 00000000000..a69290ca511
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/retry_with_more_memory_after_137.test
@@ -0,0 +1,21 @@
+name: retry_with_more_memory_after_137
+testFormat: workflowfailure
+backends: [Papiv2]
+
+files {
+  workflow: retry_with_more_memory/retry_with_more_memory_after_137.wdl
+  options: retry_with_more_memory/retry_with_more_memory.options
+}
+
+metadata {
+  workflowName: retry_with_more_memory_after_137
+  status: Failed
+  "failures.0.message": "Workflow failed"
+  "failures.0.causedBy.0.message": "stderr for job `retry_with_more_memory_after_137.imitate_oom_error:NA:3` contained one of the `memory-retry-error-keys: [OutOfMemory,Killed]` specified in the Cromwell config. Job might have run out of memory."
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.1.executionStatus": "RetryableFailure"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.1.runtimeAttributes.memory": "1 GB"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.2.executionStatus": "RetryableFailure"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.2.runtimeAttributes.memory": "1.1 GB"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.3.executionStatus": "Failed"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.3.runtimeAttributes.memory": "1.2100000000000002 GB"
+}

From 6227be973ea81759381066f44b5193752ac81c3c Mon Sep 17 00:00:00 2001
From: Christian Freitas <christian.j.freitas@gmail.com>
Date: Tue, 27 Sep 2022 15:02:04 -0400
Subject: [PATCH 087/326] Scala steward updates batch 3 (#6913)

* Scala steward updates batch 3
---
 project/Dependencies.scala        | 8 ++++----
 project/GenerateRestApiDocs.scala | 9 ++++-----
 project/swagger2markup.sbt        | 2 +-
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 21c50b77e10..7a8f34daf51 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -65,7 +65,7 @@ object Dependencies {
   private val kindProjectorV = "0.13.2"
   private val kittensV = "2.3.2"
   private val liquibaseV = "4.8.0"
-  private val logbackV = "1.2.10"
+  private val logbackV = "1.2.11"
   private val lz4JavaV = "1.8.0"
   private val mariadbV = "2.7.4"
   /*
@@ -87,14 +87,14 @@ object Dependencies {
   private val nettyV = "4.1.72.Final"
   private val owlApiV = "5.1.19"
   private val postgresV = "42.3.3"
-  private val pprintV = "0.7.1"
+  private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
   private val refinedV = "0.9.29"
   private val rhinoV = "1.7.14"
 
   private val scalaCollectionCompatV = "2.5.0"
   private val scalaGraphV = "1.13.1"
-  private val scalaLoggingV = "3.9.4"
+  private val scalaLoggingV = "3.9.5"
   private val scalaPoolV = "0.4.3"
   private val scalacticV = "3.2.10"
   private val scalameterV = "0.19"
@@ -123,7 +123,7 @@ object Dependencies {
   private val sttpV = "1.7.2"
   private val swaggerParserV = "1.0.56"
   private val swaggerUiV = "4.5.0"
-  private val testContainersScalaV = "0.40.2"
+  private val testContainersScalaV = "0.40.10"
   private val tikaV = "2.3.0"
   private val typesafeConfigV = "1.4.1"
   private val workbenchGoogleV = "0.21-5c9c4f6" // via: https://github.com/broadinstitute/workbench-libs/blob/develop/google/CHANGELOG.md
diff --git a/project/GenerateRestApiDocs.scala b/project/GenerateRestApiDocs.scala
index afb1168fa5c..9173a25c3c5 100644
--- a/project/GenerateRestApiDocs.scala
+++ b/project/GenerateRestApiDocs.scala
@@ -1,13 +1,12 @@
-import java.time.OffsetDateTime
-import java.time.format.DateTimeFormatter
-
-import io.github.swagger2markup.Swagger2MarkupConverter
 import io.github.swagger2markup.builder.Swagger2MarkupConfigBuilder
-import io.github.swagger2markup.markup.builder.MarkupLanguage
+import io.github.swagger2markup.{MarkupLanguage, Swagger2MarkupConverter}
 import org.apache.commons.lang3.{ClassUtils, StringUtils}
 import sbt.Keys._
 import sbt._
 
+import java.time.OffsetDateTime
+import java.time.format.DateTimeFormatter
+
 /**
   * Provides a task to generate the REST API markdown from the Swagger YAML.
   *
diff --git a/project/swagger2markup.sbt b/project/swagger2markup.sbt
index 96f836bcc72..1fa882328f1 100644
--- a/project/swagger2markup.sbt
+++ b/project/swagger2markup.sbt
@@ -14,7 +14,7 @@ val jacksonV = "2.8.4"
 val javaslangV = "2.0.5"
 val plexusUtilsV = "3.0.22"
 val slf4jV = "1.7.21"
-val swagger2markupV = "1.3.3"
+val swagger2markupV = "1.3.4"
 
 resolvers ++= List(
   "JCenter" at "https://jcenter.bintray.com"

From f052c788ebe7adcef9d44677953957602777b514 Mon Sep 17 00:00:00 2001
From: Christian Freitas <christian.j.freitas@gmail.com>
Date: Fri, 30 Sep 2022 09:31:06 -0400
Subject: [PATCH 088/326] WX-745 Batch 4 scala steward updates (#6916)

---
 project/Dependencies.scala | 18 +++++++++---------
 project/plugins.sbt        |  2 +-
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 7a8f34daf51..e85188a2ff1 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -6,7 +6,7 @@ object Dependencies {
   private val akkaV = "2.5.32" // scala-steward:off (CROM-6637)
   private val ammoniteOpsV = "2.4.1"
   private val apacheHttpClientV = "4.5.13"
-  private val awsSdkV = "2.17.194"
+  private val awsSdkV = "2.17.265"
   // We would like to use the BOM to manage Azure SDK versions, but SBT doesn't support it.
   // https://github.com/Azure/azure-sdk-for-java/tree/main/sdk/boms/azure-sdk-bom
   // https://github.com/sbt/sbt/issues/4531
@@ -43,7 +43,7 @@ object Dependencies {
   private val googleCloudMonitoringV = "3.2.5"
   private val googleCloudNioV = "0.124.8"
   private val googleCloudStorageV = "2.9.2"
-  private val googleGaxGrpcV = "2.12.2"
+  private val googleGaxGrpcV = "2.19.0"
   // latest date via: https://mvnrepository.com/artifact/com.google.apis/google-api-services-genomics
   private val googleGenomicsServicesV2Alpha1ApiV = "v2alpha1-rev20210811-1.32.1"
   private val googleHttpClientApacheV = "2.1.2"
@@ -53,13 +53,13 @@ object Dependencies {
   private val googleOauth2V = "1.5.3"
   private val googleOauthClientV = "1.33.1"
   private val googleCloudResourceManagerV = "1.2.5"
-  private val grpcV = "1.45.0"
+  private val grpcV = "1.45.1"
   private val guavaV = "31.0.1-jre"
   private val heterodonV = "1.0.0-beta3"
   private val hsqldbV = "2.6.1"
   private val http4sV = "0.21.31" // this release is EOL. We need to upgrade further for cats3. https://http4s.org/versions/
   private val jacksonV = "2.13.3"
-  private val janinoV = "3.1.6"
+  private val janinoV = "3.1.7"
   private val jsr305V = "3.0.2"
   private val junitV = "4.13.2"
   private val kindProjectorV = "0.13.2"
@@ -96,12 +96,12 @@ object Dependencies {
   private val scalaGraphV = "1.13.1"
   private val scalaLoggingV = "3.9.5"
   private val scalaPoolV = "0.4.3"
-  private val scalacticV = "3.2.10"
-  private val scalameterV = "0.19"
+  private val scalacticV = "3.2.13"
+  private val scalameterV = "0.21"
   private val scalatestV = "3.2.10"
   private val scalatestScalacheckV = scalatestV + ".0"
   private val scoptV = "4.1.0"
-  private val sentryLogbackV = "5.2.4"
+  private val sentryLogbackV = "5.7.4"
   private val shapelessV = "2.3.9"
   private val simulacrumV = "1.0.1"
   private val slf4jV = "1.7.32"
@@ -122,10 +122,10 @@ object Dependencies {
   private val sprayJsonV = "1.3.6"
   private val sttpV = "1.7.2"
   private val swaggerParserV = "1.0.56"
-  private val swaggerUiV = "4.5.0"
+  private val swaggerUiV = "4.5.2"
   private val testContainersScalaV = "0.40.10"
   private val tikaV = "2.3.0"
-  private val typesafeConfigV = "1.4.1"
+  private val typesafeConfigV = "1.4.2"
   private val workbenchGoogleV = "0.21-5c9c4f6" // via: https://github.com/broadinstitute/workbench-libs/blob/develop/google/CHANGELOG.md
   private val workbenchModelV = "0.15-f9f0d4c" // via: https://github.com/broadinstitute/workbench-libs/blob/develop/model/CHANGELOG.md
   private val workbenchUtilV = "0.6-65bba14" // via: https://github.com/broadinstitute/workbench-libs/blob/develop/util/CHANGELOG.md
diff --git a/project/plugins.sbt b/project/plugins.sbt
index cef75cd05b3..dd6a98e1b9b 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1,5 +1,5 @@
 addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.9.0")
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.0")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.1")
 addSbtPlugin("com.github.sbt" % "sbt-git" % "2.0.0")
 addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.9.3")
 addDependencyTreePlugin

From 443a6fc265ed5cae3d697eac0bec79d31eadb7be Mon Sep 17 00:00:00 2001
From: Brian Reilly <breilly@broadinstitute.org>
Date: Fri, 30 Sep 2022 14:36:50 -0400
Subject: [PATCH 089/326] WX-746 Localize all DRS inputs in a single Action
 (#6914)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 CHANGELOG.md                                  | 22 +++++
 .../drs/localizer/CommandLineParser.scala     | 39 ++++++--
 .../drs/localizer/DrsLocalizerMain.scala      | 25 ++++-
 .../AzureB2CAccessTokenStrategy.scala         |  2 +-
 .../drs/localizer/CommandLineParserSpec.scala | 71 +++++++++++++-
 project/Dependencies.scala                    |  1 +
 ...inesApiAsyncBackendJobExecutionActor.scala |  4 +
 .../common/PipelinesApiJobPaths.scala         |  1 +
 ...inesApiAsyncBackendJobExecutionActor.scala | 28 +++++-
 .../PipelinesParameterConversions.scala       | 23 +----
 .../pipelines/v2beta/api/Localization.scala   | 53 +++++++++-
 ...ApiAsyncBackendJobExecutionActorSpec.scala | 49 ++++++++++
 .../v2beta/PipelinesConversionsSpec.scala     | 96 -------------------
 .../v2beta/api/LocalizationSpec.scala         | 67 +++++++++++++
 14 files changed, 351 insertions(+), 130 deletions(-)
 delete mode 100644 supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala
 create mode 100644 supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4dcab0dfa3f..351adccf651 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,28 @@ it is also being migrated from INT to BIGINT.
 * WORKFLOW_STORE_ENTRY
 * SUB_WORKFLOW_STORE_ENTRY
 
+### Improvement to "retry with more memory" behavior
+
+Cromwell will now retry a task with more memory after it fails with return code 137, provided all
+the other requirements for retrying with more memory are met.
+
+### Support for invoking `CromwellDRSLocalizer` with manifest file
+
+`CromwellDRSLocalizer` can now handle multiple file localizations in a single invocation. Users can provide a 
+manifest file containing multiple (DRS id, local container path) pairs in CSV format, and they will be localized in 
+sequence, with the program exiting if any fail.
+```
+java -jar /path/to/localizer.jar [options] -m /local/path/to/manifest/file.txt
+```
+
+The previous method of passing in a single DRS file and container destination using positional arguments is still 
+supported.
+
+### Improvement to DRS localization in GCP papiv2beta backend
+
+All DRS inputs to a task are now localized in a single PAPI action, which should improve speed and resolve
+failures observed when attempting to localize a large number of DRS files.
+
 ## 84 Release Notes
 
 ### CromIAM enabled user checks
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
index df0f7c2eba6..b200d4b18de 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
@@ -14,15 +14,25 @@ class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage)
 
   head("cromwell-drs-localizer", localizerVersion)
 
-  arg[String]("drs-object-id").text("DRS object ID").required().
+  arg[String]("drs-object-id").text("DRS object ID").optional().
     action((s, c) =>
       c.copy(drsObject = Option(s)))
-  arg[String]("container-path").text("Container path").required().
+  arg[String]("container-path").text("Container path").optional().
     action((s, c) =>
       c.copy(containerPath = Option(s)))
-  arg[String]("requester-pays-project").text("Requester pays project").optional().
+  arg[String]("requester-pays-project").text(s"Requester pays project (only valid with '$Google' auth strategy)").optional().
     action((s, c) =>
       c.copy(googleRequesterPaysProject = Option(s)))
+  opt[String]('m', "manifest-path").text("File path of manifest containing multiple files to localize").
+    action((s, c) =>
+      c.copy(manifestPath = Option(s)))
+  opt[String]('r', "requester-pays-project").text(s"Requester pays project (only valid with '$Google' auth strategy)").optional().
+    action((s, c) => {
+      c.copy(
+        googleRequesterPaysProject = Option(s),
+        googleRequesterPaysProjectConflict = c.googleRequesterPaysProject.exists(_ != s)
+      )
+    })
   opt[String]('t', "access-token-strategy").text(s"Access token strategy, must be one of '$Azure' or '$Google' (default '$Google')").
     action((s, c) =>
       c.copy(accessTokenStrategy = Option(s.toLowerCase())))
@@ -35,6 +45,11 @@ class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage)
   opt[String]('i', "identity-client-id").text("Azure identity client id").
     action((s, c) =>
       c.copy(azureIdentityClientId = Option(s)))
+  checkConfig(c =>
+    if (c.googleRequesterPaysProjectConflict)
+      failure("Requester pays project differs between positional argument and option flag")
+    else success
+  )
   checkConfig(c =>
     c.accessTokenStrategy match {
       case Some(Azure) if c.googleRequesterPaysProject.nonEmpty =>
@@ -48,6 +63,13 @@ class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage)
       case None => Left("Programmer error, access token strategy should not be None")
     }
   )
+  checkConfig(c =>
+    (c.drsObject, c.containerPath, c.manifestPath) match {
+      case (Some(_), Some(_), None) => Right(())
+      case (None, None, Some(_)) => Right(())
+      case _ => Left("Must provide either DRS path and container path, OR manifest file (-m).")
+    }
+  )
 }
 
 object CommandLineParser {
@@ -64,9 +86,12 @@ object CommandLineParser {
   val Usage =
     s"""
 Usage:
-    java -jar /path/to/localizer.jar [options] drs://provider/object /local/path/to/file.txt [requester pays project]
 
-    Note that the <requester pays project> optional argument is only valid with access token strategy 'Google'.
+    Can be run to localize a single file with DRS id and local container path provided in args:
+    java -jar /path/to/localizer.jar [options] drs://provider/object /local/path/to/file.txt
+
+    Can also be used to localize multiple files in one invocation with manifest file provided in args:
+    java -jar /path/to/localizer.jar [options] -m /local/path/to/manifest/file
     """
 
 }
@@ -77,4 +102,6 @@ case class CommandLineArguments(accessTokenStrategy: Option[String] = Option(Goo
                                 googleRequesterPaysProject: Option[String] = None,
                                 azureVaultName: Option[String] = None,
                                 azureSecretName: Option[String] = None,
-                                azureIdentityClientId: Option[String] = None)
+                                azureIdentityClientId: Option[String] = None,
+                                manifestPath: Option[String] = None,
+                                googleRequesterPaysProjectConflict: Boolean = false)
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
index c7ecdd3f3e4..05ecf0ce48c 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
@@ -2,6 +2,7 @@ package drs.localizer
 
 import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO, IOApp}
+import cats.implicits._
 import cloud.nio.impl.drs.DrsPathResolver.{FatalRetryDisposition, RegularRetryDisposition}
 import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsPathResolver, MarthaField}
 import cloud.nio.spi.{CloudNioBackoff, CloudNioSimpleExponentialBackoff}
@@ -10,8 +11,12 @@ import drs.localizer.CommandLineParser.AccessTokenStrategy.{Azure, Google}
 import drs.localizer.accesstokens.{AccessTokenStrategy, AzureB2CAccessTokenStrategy, GoogleAccessTokenStrategy}
 import drs.localizer.downloaders.AccessUrlDownloader.Hashes
 import drs.localizer.downloaders._
+import org.apache.commons.csv.{CSVFormat, CSVParser}
 
+import java.io.File
+import java.nio.charset.Charset
 import scala.concurrent.duration._
+import scala.jdk.CollectionConverters._
 import scala.language.postfixOps
 
 object DrsLocalizerMain extends IOApp with StrictLogging {
@@ -51,8 +56,24 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
   }
 
   def runLocalizer(commandLineArguments: CommandLineArguments, accessTokenStrategy: AccessTokenStrategy): IO[ExitCode] = {
-    val drsObject = commandLineArguments.drsObject.get
-    val containerPath = commandLineArguments.containerPath.get
+    commandLineArguments.manifestPath match {
+      case Some(manifestPath) =>
+        val manifestFile = new File(manifestPath)
+        val csvParser = CSVParser.parse(manifestFile, Charset.defaultCharset(), CSVFormat.DEFAULT)
+        val exitCodes: IO[List[ExitCode]] = csvParser.asScala.map(record => {
+          val drsObject = record.get(0)
+          val containerPath = record.get(1)
+          localizeFile(commandLineArguments, accessTokenStrategy, drsObject, containerPath)
+        }).toList.sequence
+        exitCodes.map(_.find(_ != ExitCode.Success).getOrElse(ExitCode.Success))
+      case None =>
+        val drsObject = commandLineArguments.drsObject.get
+        val containerPath = commandLineArguments.containerPath.get
+        localizeFile(commandLineArguments, accessTokenStrategy, drsObject, containerPath)
+    }
+  }
+
+  private def localizeFile(commandLineArguments: CommandLineArguments, accessTokenStrategy: AccessTokenStrategy, drsObject: String, containerPath: String) = {
     new DrsLocalizerMain(drsObject, containerPath, accessTokenStrategy, commandLineArguments.googleRequesterPaysProject).
       resolveAndDownloadWithRetries(downloadRetries = 3, checksumRetries = 1, defaultDownloaderFactory, Option(defaultBackoff)).map(_.exitCode)
   }
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
index cf83171adf0..1634815d1f4 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
@@ -10,7 +10,7 @@ import drs.localizer.CommandLineArguments
 case class AzureB2CAccessTokenStrategy(commandLineArguments: CommandLineArguments) extends AccessTokenStrategy {
   override def getAccessToken(): ErrorOr[String] = {
     commandLineArguments match {
-      case CommandLineArguments(_, _, _, _, Some(vault), Some(secret), clientId) =>
+      case CommandLineArguments(_, _, _, _, Some(vault), Some(secret), clientId, _, _) =>
         AzureKeyVaultClient(vault, clientId) flatMap { _.getSecret(secret) }
       case invalid => s"Invalid command line arguments: $invalid".invalidNel
     }
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
index 3f7b96f5edc..349b2d6887b 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
@@ -16,6 +16,7 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   private val azureVaultName = "Kwikset"
   private val azureSecretName = "shhh"
   private val azureIdentityClientId = "itme@azure.com"
+  private val manifestPath = "/my/manifest.txt"
 
   behavior of "DRS Localizer command line parser"
 
@@ -41,10 +42,36 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.azureVaultName shouldBe empty
     args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
   it should "successfully parse with three arguments" in {
     val args = parser.parse(Array(drsObject, containerPath, requesterPaysProject), CommandLineArguments()).get
+    args.drsObject.get shouldBe drsObject
+    args.containerPath.get shouldBe containerPath
+    args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
+    args.googleRequesterPaysProject.get shouldBe requesterPaysProject
+    args.azureVaultName shouldBe empty
+    args.azureSecretName shouldBe empty
+    args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
+  }
+
+  it should "successfully parse requester pays project" in {
+    val args = parser.parse(Array(drsObject, containerPath, "-r", requesterPaysProject), CommandLineArguments()).get
+
+    args.drsObject.get shouldBe drsObject
+    args.containerPath.get shouldBe containerPath
+    args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
+    args.googleRequesterPaysProject.get shouldBe requesterPaysProject
+    args.azureVaultName shouldBe empty
+    args.azureSecretName shouldBe empty
+    args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
+  }
+
+  it should "successfully parse with three arguments and requester pays project" in {
+    val args = parser.parse(Array(drsObject, containerPath, requesterPaysProject, "-r", requesterPaysProject), CommandLineArguments()).get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
@@ -53,10 +80,43 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.azureVaultName shouldBe empty
     args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
+  }
+
+  it should "fail if requester pays argument and flag specify different projects" in {
+    parser.parse(Array(drsObject, containerPath, requesterPaysProject, "-r", "boom!"), CommandLineArguments()) shouldBe None
+  }
+
+  it should "successfully parse args with a manifest file" in {
+    val args = parser.parse(Array("-m", manifestPath), CommandLineArguments()).get
+
+    args.drsObject shouldBe empty
+    args.containerPath shouldBe empty
+    args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
+    args.googleRequesterPaysProject shouldBe empty
+    args.azureVaultName shouldBe empty
+    args.azureSecretName shouldBe empty
+    args.azureIdentityClientId shouldBe empty
+    args.manifestPath.get shouldBe manifestPath
+  }
+
+  it should "fail to parse with a manifest file and one single-file arg" in {
+    val args = parser.parse(Array(drsObject, "--manifest-path", manifestPath), CommandLineArguments())
+    args shouldBe None
   }
 
-  it should "successfully parse an explicit Google access token strategy invocation" in {
-    val args = parser.parse(Array("--access-token-strategy", "google", drsObject, containerPath, requesterPaysProject), CommandLineArguments()).get
+  it should "fail to parse with a manifest file and two single-file args" in {
+    val args = parser.parse(Array(drsObject, containerPath, "--manifest-path", manifestPath), CommandLineArguments())
+    args shouldBe None
+  }
+
+  it should "successfully parse an explicit Google access token stregy invocation" in {
+    val args = parser.parse(Array(
+      "--access-token-strategy", "google",
+      drsObject,
+      containerPath,
+      "--requester-pays-project", requesterPaysProject
+    ), CommandLineArguments()).get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
@@ -65,6 +125,7 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.azureVaultName shouldBe empty
     args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
   it should "fail to parse an Azure invocation missing vault name and secret name" in {
@@ -98,7 +159,9 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
       "--access-token-strategy", AccessTokenStrategy.Azure,
       "--secret-name", azureSecretName,
       "--vault-name", azureVaultName,
-      drsObject, containerPath, requesterPaysProject), CommandLineArguments())
+      drsObject,
+      containerPath,
+      "--requester-pays-project", requesterPaysProject), CommandLineArguments())
 
     args shouldBe None
   }
@@ -117,6 +180,7 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.azureVaultName.get shouldBe azureVaultName
     args.azureSecretName.get shouldBe azureSecretName
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
   it should "successfully parse an Azure invocation with all the trimmings" in {
@@ -134,6 +198,7 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.azureVaultName.get shouldBe azureVaultName
     args.azureSecretName.get shouldBe azureSecretName
     args.azureIdentityClientId.get shouldBe azureIdentityClientId
+    args.manifestPath shouldBe empty
   }
 
   it should "fail to parse with an unrecognized access token strategy" in {
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index e85188a2ff1..50c76893e80 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -564,6 +564,7 @@ object Dependencies {
     "com.iheart" %% "ficus" % ficusV,
     "com.softwaremill.sttp" %% "circe" % sttpV,
     "com.github.scopt" %% "scopt" % scoptV,
+    "org.apache.commons" % "commons-csv" % commonsCsvV,
   ) ++ circeDependencies ++ catsDependencies ++ slf4jBindingDependencies ++ languageFactoryDependencies ++ azureDependencies
 
   val allProjectDependencies: List[ModuleID] =
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
index e79ef867a54..c1c68b7dd39 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -542,6 +542,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     Future.successful(PendingExecutionHandle(jobDescriptor, jobForResumption, Option(Run(jobForResumption)), previousState = None))
   }
 
+  protected def uploadDrsLocalizationManifest(createPipelineParameters: CreatePipelineParameters, cloudPath: Path): Future[Unit] = Future.successful(())
+
   protected def uploadGcsTransferLibrary(createPipelineParameters: CreatePipelineParameters, cloudPath: Path, gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = Future.successful(())
 
   protected def uploadGcsLocalizationScript(createPipelineParameters: CreatePipelineParameters,
@@ -639,6 +641,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
       customLabels <- Future.fromTry(GoogleLabels.fromWorkflowOptions(workflowDescriptor.workflowOptions))
       jesParameters <- generateInputOutputParameters
       createParameters = createPipelineParameters(jesParameters, customLabels)
+      drsLocalizationManifestCloudPath = jobPaths.callExecutionRoot / PipelinesApiJobPaths.DrsLocalizationManifestName
+      _ <- uploadDrsLocalizationManifest(createParameters, drsLocalizationManifestCloudPath)
       gcsTransferConfiguration = initializationData.papiConfiguration.papiAttributes.gcsTransferConfiguration
       gcsTransferLibraryCloudPath = jobPaths.callExecutionRoot / PipelinesApiJobPaths.GcsTransferLibraryName
       transferLibraryContainerPath = createParameters.commandScriptContainerPath.sibling(GcsTransferLibraryName)
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
index 0fc9a8ff49d..ae047187825 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
@@ -13,6 +13,7 @@ object PipelinesApiJobPaths {
   val GcsTransferLibraryName = "gcs_transfer.sh"
   val GcsLocalizationScriptName = "gcs_localization.sh"
   val GcsDelocalizationScriptName = "gcs_delocalization.sh"
+  val DrsLocalizationManifestName = "drs_manifest"
 }
 
 // Non-`final` as this is mocked for testing since using a real instance proved too difficult.
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
index 77370cabc92..aa49c385ba6 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -12,14 +12,19 @@ import cromwell.backend.google.pipelines.common.io.PipelinesApiWorkingDisk
 import cromwell.backend.google.pipelines.v2beta.PipelinesApiAsyncBackendJobExecutionActor._
 import cromwell.backend.standard.StandardAsyncExecutionActorParams
 import cromwell.core.path.{DefaultPathBuilder, Path}
+import cromwell.filesystems.drs.DrsPath
 import cromwell.filesystems.gcs.GcsPathBuilder.ValidFullGcsPath
 import cromwell.filesystems.gcs.{GcsPath, GcsPathBuilder}
 import org.apache.commons.codec.digest.DigestUtils
+import org.apache.commons.csv.{CSVFormat, CSVPrinter}
+import org.apache.commons.io.output.ByteArrayOutputStream
 import wom.core.FullyQualifiedName
 import wom.expression.FileEvaluation
 import wom.values.{GlobFunctions, WomFile, WomGlobFile, WomMaybeListedDirectory, WomMaybePopulatedFile, WomSingleFile, WomUnlistedDirectory}
 
-import java.io.FileNotFoundException
+import java.nio.charset.Charset
+
+import java.io.{FileNotFoundException, OutputStreamWriter}
 import scala.concurrent.Future
 import scala.io.Source
 import scala.language.postfixOps
@@ -174,6 +179,14 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
 
   import mouse.all._
 
+  override def uploadDrsLocalizationManifest(createPipelineParameters: CreatePipelineParameters, cloudPath: Path): Future[Unit] = {
+    val content = generateDrsLocalizerManifest(createPipelineParameters.inputOutputParameters.fileInputParameters)
+    if (content.nonEmpty)
+      asyncIo.writeAsync(cloudPath, content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+    else
+      Future.unit
+  }
+
   private def generateGcsLocalizationScript(inputs: List[PipelinesApiInput],
                                             referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]])
                                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
@@ -396,4 +409,17 @@ object PipelinesApiAsyncBackendJobExecutionActor {
       }
     } combineAll
   }
+
+  private [v2beta] def generateDrsLocalizerManifest(inputs: List[PipelinesApiInput]): String = {
+    val outputStream = new ByteArrayOutputStream()
+    val csvPrinter = new CSVPrinter(new OutputStreamWriter(outputStream), CSVFormat.DEFAULT)
+    val drsFileInputs = inputs collect {
+      case drsInput@PipelinesApiFileInput(_, drsPath: DrsPath, _, _) => (drsInput, drsPath)
+    }
+    drsFileInputs foreach { case (drsInput, drsPath) =>
+      csvPrinter.printRecord(drsPath.pathAsString, drsInput.containerPath.pathAsString)
+    }
+    csvPrinter.close(true)
+    outputStream.toString(Charset.defaultCharset())
+  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
index 505c23edb9c..64365fe404f 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
@@ -1,6 +1,5 @@
 package cromwell.backend.google.pipelines.v2beta
 
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, DrsConfig}
 import com.google.api.services.lifesciences.v2beta.model.{Action, Mount}
 import com.typesafe.config.ConfigFactory
 import cromwell.backend.google.pipelines.common.action.ActionCommands._
@@ -27,25 +26,6 @@ trait PipelinesParameterConversions {
 
       val labels = ActionBuilder.parameterLabels(fileInput)
       fileInput.cloudPath match {
-        case drsPath: DrsPath =>
-
-          import scala.jdk.CollectionConverters._
-
-          val drsFileSystemProvider = drsPath.drsPath.getFileSystem.provider.asInstanceOf[DrsCloudNioFileSystemProvider]
-
-          val drsDockerImage = config.getString("drs.localization.docker-image")
-          // Note: Don't ShellPath.escape the paths as we are directly invoking the localizer and NOT launching a shell.
-          val drsCommand =
-            List(fileInput.cloudPath.pathAsString, fileInput.containerPath.pathAsString) ++
-              drsPath.requesterPaysProjectIdOption.toList
-          val marthaEnv = DrsConfig.toEnv(drsFileSystemProvider.drsConfig)
-          val localizationAction = ActionBuilder
-            .withImage(drsDockerImage)
-            .withCommand(drsCommand: _*)
-            .withMounts(mounts)
-            .setEnvironment(marthaEnv.asJava)
-            .withLabels(labels)
-          List(ActionBuilder.describeParameter(fileInput, labels), localizationAction)
         case sraPath: SraPath =>
           val sraConfig = config.getConfig("filesystems.sra")
 
@@ -78,6 +58,9 @@ trait PipelinesParameterConversions {
         case _: GcsPath =>
           // GCS paths will be localized with a separate localization script.
           Nil
+        case _: DrsPath =>
+          // DRS paths will be localized with a single call to cromwell-drs-localizer with a manifest
+          Nil
       }
     }
   }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
index 4aa52f89801..8e8065fe679 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
@@ -1,14 +1,21 @@
 package cromwell.backend.google.pipelines.v2beta.api
 
+import cloud.nio.impl.drs.DrsConfig
 import com.google.api.services.lifesciences.v2beta.model.{Action, Mount}
+import com.typesafe.config.ConfigFactory
 import cromwell.backend.google.pipelines.common.action.ActionCommands.localizeFile
 import cromwell.backend.google.pipelines.common.action.ActionLabels._
 import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.pipelines.common.PipelinesApiFileInput
 import cromwell.backend.google.pipelines.common.PipelinesApiJobPaths._
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.CreatePipelineParameters
 import cromwell.backend.google.pipelines.v2beta.PipelinesConversions._
 import cromwell.backend.google.pipelines.v2beta.ToParameter.ops._
-import cromwell.backend.google.pipelines.v2beta.api.ActionBuilder.cloudSdkShellAction
+import cromwell.backend.google.pipelines.v2beta.api.ActionBuilder.{EnhancedAction, cloudSdkShellAction}
+import cromwell.core.path.Path
+import cromwell.filesystems.drs.DrsPath
+
+import scala.jdk.CollectionConverters._
 
 
 trait Localization {
@@ -34,15 +41,59 @@ trait Localization {
     val runGcsLocalizationScript = cloudSdkShellAction(
       s"/bin/bash $gcsLocalizationContainerPath")(mounts = mounts, labels = localizationLabel)
 
+    val drsInputs: List[DrsPath] = createPipelineParameters.inputOutputParameters.fileInputParameters.collect {
+      case PipelinesApiFileInput(_, drsPath: DrsPath, _, _) => drsPath
+    }
+
+    val drsLocalizationActions = if (drsInputs.nonEmpty) {
+      val drsLocalizationManifestContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(DrsLocalizationManifestName)
+      val localizeDrsLocalizationManifest = cloudSdkShellAction(localizeFile(
+        cloudPath = createPipelineParameters.cloudCallRoot / DrsLocalizationManifestName,
+        containerPath = drsLocalizationManifestContainerPath))(mounts = mounts, labels = localizationLabel)
+
+      // Requester pays project id is stored on each DrsPath, but will be the same for all DRS inputs to a
+      // particular workflow because it's determined by the Google project set in workflow options.
+      val requesterPaysProjectId: Option[String] = drsInputs.flatMap(_.requesterPaysProjectIdOption).headOption
+      val runDrsLocalization = Localization.drsAction(drsLocalizationManifestContainerPath, mounts, localizationLabel, requesterPaysProjectId)
+      List(localizeDrsLocalizationManifest, runDrsLocalization)
+    } else List[Action]()
+
     // Any "classic" PAPI v2 one-at-a-time localizations for non-GCS inputs.
     val singletonLocalizations = createPipelineParameters.inputOutputParameters.fileInputParameters.flatMap(_.toActions(mounts).toList)
 
     val localizations =
       localizeGcsTransferLibrary ::
         localizeGcsLocalizationScript :: runGcsLocalizationScript ::
+        drsLocalizationActions :::
         localizeGcsDelocalizationScript ::
         singletonLocalizations
 
     ActionBuilder.annotateTimestampedActions("localization", Value.Localization)(localizations)
   }
 }
+
+object Localization {
+
+  def drsAction(manifestPath: Path,
+                mounts: List[Mount],
+                labels: Map[String, String],
+                requesterPaysProjectId: Option[String]
+               ): Action = {
+    val config = ConfigFactory.load
+    val marthaConfig = config.getConfig("filesystems.drs.global.config.martha")
+    val drsConfig = DrsConfig.fromConfig(marthaConfig)
+    val drsDockerImage = config.getString("drs.localization.docker-image")
+
+    val manifestArg = List("-m", manifestPath.pathAsString)
+    val requesterPaysArg = requesterPaysProjectId.map(r => List("-r", r)).getOrElse(List.empty)
+    val drsCommand = manifestArg ++ requesterPaysArg
+
+    val marthaEnv = DrsConfig.toEnv(drsConfig)
+    ActionBuilder
+      .withImage(drsDockerImage)
+      .withCommand(drsCommand: _*)
+      .withMounts(mounts)
+      .setEnvironment(marthaEnv.asJava)
+      .withLabels(labels)
+  }
+}
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
index 9b93a976e22..093ecd3fa27 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
@@ -2,14 +2,22 @@ package cromwell.backend.google.pipelines.v2beta
 
 import java.nio.file.Paths
 import cats.data.NonEmptyList
+import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import com.google.cloud.NoCredentials
+import com.typesafe.config.{Config, ConfigFactory}
 import common.assertion.CromwellTimeoutSpec
 import common.mock.MockSugar
 import cromwell.backend.google.pipelines.common.PipelinesApiFileInput
+import cromwell.backend.google.pipelines.common.io.{DiskType, PipelinesApiWorkingDisk}
 import cromwell.core.path.DefaultPathBuilder
+import cromwell.filesystems.drs.DrsPathBuilder
 import org.mockito.Mockito._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
+import scala.concurrent.duration.DurationInt
+
 class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   with MockSugar {
   behavior of "PipelinesParameterConversions"
@@ -44,4 +52,45 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Cro
 
     PipelinesApiAsyncBackendJobExecutionActor.groupParametersByGcsBucket(inputs) shouldEqual expected
   }
+
+  it should "generate a CSV manifest for DRS inputs, ignoring non-DRS inputs" in {
+    def makeDrsPathBuilder: DrsPathBuilder = {
+      val marthaConfig: Config = ConfigFactory.parseString(
+        """martha {
+          |   url = "http://martha-url"
+          |}
+          |""".stripMargin
+      )
+
+      val fakeCredentials = NoCredentials.getInstance
+
+      val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
+        throw new UnsupportedOperationException("PipelinesApiAsyncBackendJobExecutionActorSpec doesn't need to use drs read interpreter.")
+
+      DrsPathBuilder(
+        new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+        None,
+      )
+    }
+
+    val mount = PipelinesApiWorkingDisk(DiskType.LOCAL, 1)
+
+    def makeDrsInput(name: String, drsUri: String, containerPath: String): PipelinesApiFileInput = {
+      val drsPath = makeDrsPathBuilder.build(drsUri).get
+      val containerRelativePath = DefaultPathBuilder.get(containerPath)
+      PipelinesApiFileInput(name, drsPath, containerRelativePath, mount)
+    }
+
+    val nonDrsInput: PipelinesApiFileInput = PipelinesApiFileInput("nnn",
+      DefaultPathBuilder.get("/local/nnn.bai"), DefaultPathBuilder.get("/path/to/nnn.bai"), mount)
+
+    val inputs = List(
+      makeDrsInput("aaa", "drs://drs.example.org/aaa", "path/to/aaa.bai"),
+      nonDrsInput,
+      makeDrsInput("bbb", "drs://drs.example.org/bbb", "path/to/bbb.bai")
+    )
+
+    PipelinesApiAsyncBackendJobExecutionActor.generateDrsLocalizerManifest(inputs) shouldEqual
+      "drs://drs.example.org/aaa,/cromwell_root/path/to/aaa.bai\r\ndrs://drs.example.org/bbb,/cromwell_root/path/to/bbb.bai\r\n"
+  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala
deleted file mode 100644
index c3ed9d27b02..00000000000
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala
+++ /dev/null
@@ -1,96 +0,0 @@
-package cromwell.backend.google.pipelines.v2beta
-
-import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
-import com.google.cloud.NoCredentials
-import com.typesafe.config.{Config, ConfigFactory}
-import common.assertion.CromwellTimeoutSpec
-import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.GcsTransferConfiguration
-import cromwell.backend.google.pipelines.common.PipelinesApiFileInput
-import cromwell.backend.google.pipelines.common.action.ActionUtils
-import cromwell.backend.google.pipelines.common.io.{DiskType, PipelinesApiWorkingDisk}
-import cromwell.core.path.DefaultPathBuilder
-import cromwell.filesystems.drs.DrsPathBuilder
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-import scala.jdk.CollectionConverters._
-import scala.concurrent.duration.DurationInt
-
-class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "PipelinesConversions"
-  implicit val gcsTransferConfiguration: GcsTransferConfiguration =
-    GcsTransferConfiguration(transferAttempts = refineMV(1), parallelCompositeUploadThreshold = "0")
-
-  private val marthaConfig: Config = ConfigFactory.parseString(
-    """martha {
-      |   url = "http://martha-url"
-      |}
-      |""".stripMargin
-  )
-
-  private lazy val fakeCredentials = NoCredentials.getInstance
-
-  private val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
-    throw new UnsupportedOperationException("Currently PipelinesConversionsSpec doesn't need to use drs read interpreter.")
-
-  it should "create a DRS input parameter" in {
-
-    val drsPathBuilder = DrsPathBuilder(
-      new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
-      None,
-    )
-    val drsPath = drsPathBuilder.build("drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba").get
-    val containerRelativePath = DefaultPathBuilder.get("path/to/file.bai")
-    val mount = PipelinesApiWorkingDisk(DiskType.LOCAL, 1)
-    val input = PipelinesApiFileInput("example", drsPath, containerRelativePath, mount)
-    val actions = PipelinesConversions.inputToParameter.toActions(input, Nil)
-    actions.size should be(2)
-
-    val logging = actions.head
-
-    logging.keySet.asScala should contain theSameElementsAs
-      Set("entrypoint", "commands", "imageUri", "labels", "mounts", "timeout")
-
-    logging.get("commands") should be(a[java.util.List[_]])
-    logging.get("commands").asInstanceOf[java.util.List[_]] should contain(
-      """printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" """ +
-        """Localizing\ input\ drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba\ """ +
-        """-\>\ /cromwell_root/path/to/file.bai"""
-    )
-
-    logging.get("mounts") should be(a[java.util.List[_]])
-    logging.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
-
-    logging.get("imageUri") should be(ActionUtils.CloudSdkImage)
-
-    val loggingLabels = logging.get("labels").asInstanceOf[java.util.Map[_, _]]
-    loggingLabels.keySet.asScala should contain theSameElementsAs List("logging", "inputName")
-    loggingLabels.get("logging") should be("Localization")
-    loggingLabels.get("inputName") should be("example")
-
-    val action = actions.tail.head
-
-    action.keySet.asScala should contain theSameElementsAs
-      Set("commands", "environment", "imageUri", "labels", "mounts")
-
-    action.get("commands") should be(a[java.util.List[_]])
-    action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
-      "drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba",
-      "/cromwell_root/path/to/file.bai"
-    )
-
-    action.get("mounts") should be(a[java.util.List[_]])
-    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
-
-    action.get("imageUri") should be("somerepo/drs-downloader:tagged")
-
-    val actionLabels = action.get("labels").asInstanceOf[java.util.Map[_, _]]
-    actionLabels.keySet.asScala should contain theSameElementsAs List("tag", "inputName")
-    actionLabels.get("tag") should be("Localization")
-    actionLabels.get("inputName") should be("example")
-  }
-
-}
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala
new file mode 100644
index 00000000000..f815ceebd14
--- /dev/null
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala
@@ -0,0 +1,67 @@
+package cromwell.backend.google.pipelines.v2beta.api
+
+import common.assertion.CromwellTimeoutSpec
+import cromwell.backend.google.pipelines.common.PipelinesApiJobPaths.DrsLocalizationManifestName
+import cromwell.core.path.DefaultPathBuilder
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import scala.jdk.CollectionConverters._
+
+class LocalizationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  behavior of "Localization"
+
+  it should "create the right action to localize DRS files using a manifest" in {
+
+    val manifestPathString = s"path/to/${DrsLocalizationManifestName}"
+    val manifestPath = DefaultPathBuilder.get(manifestPathString)
+    val tagKey = "tag"
+    val tagLabel = "myLabel"
+
+    val action = Localization.drsAction(manifestPath, Nil, Map(tagKey -> tagLabel), None)
+    action.keySet.asScala should contain theSameElementsAs
+      Set("commands", "environment", "imageUri", "labels", "mounts")
+
+    action.get("commands") should be(a[java.util.List[_]])
+    action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
+      "-m", manifestPathString
+    )
+
+    action.get("mounts") should be(a[java.util.List[_]])
+    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+
+    action.get("imageUri") should be("somerepo/drs-downloader:tagged")
+
+    val actionLabels = action.get("labels").asInstanceOf[java.util.Map[_, _]]
+    actionLabels.keySet.asScala should contain theSameElementsAs List("tag")
+    actionLabels.get(tagKey) should be(tagLabel)
+  }
+
+  it should "create the right action to localize DRS files using a manifest with requester pays" in {
+
+    val manifestPathString = s"path/to/${DrsLocalizationManifestName}"
+    val manifestPath = DefaultPathBuilder.get(manifestPathString)
+    val tagKey = "tag"
+    val tagLabel = "myLabel"
+    val requesterPaysProjectId = "123"
+
+    val action = Localization.drsAction(manifestPath, Nil, Map(tagKey -> tagLabel), Option(requesterPaysProjectId))
+    action.keySet.asScala should contain theSameElementsAs
+      Set("commands", "environment", "imageUri", "labels", "mounts")
+
+    action.get("commands") should be(a[java.util.List[_]])
+    action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
+      "-m", manifestPathString, "-r", requesterPaysProjectId
+    )
+
+    action.get("mounts") should be(a[java.util.List[_]])
+    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+
+    action.get("imageUri") should be("somerepo/drs-downloader:tagged")
+
+    val actionLabels = action.get("labels").asInstanceOf[java.util.Map[_, _]]
+    actionLabels.keySet.asScala should contain theSameElementsAs List("tag")
+    actionLabels.get(tagKey) should be(tagLabel)
+  }
+}

From f4a19ba925d498a7c01645e897915f0aa7061ac6 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 3 Oct 2022 14:11:14 -0400
Subject: [PATCH 090/326] WX-755 Build all images instead of just Cromwell
 (#6919)

---
 .github/workflows/chart_update_on_merge.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index 9e847bc17eb..81a7c3a8259 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -48,12 +48,12 @@ jobs:
       with:
         username: dsdejenkins
         password: ${{ secrets.DSDEJENKINS_PASSWORD }}
+    # Build & push `cromwell`, `womtool`, `cromiam`, and `cromwell-drs-localizer`
     - name: Build Cromwell Docker
       run: |
         set -e
         cd cromwell
-        sbt server/docker
-        docker push broadinstitute/cromwell:$CROMWELL_SNAP_VERSION
+        sbt dockerBuildAndPush
     - name: Edit & push chart
       env:
         BROADBOT_GITHUB_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}

From 07d4a7472def7220ca644016d19e142b9268b972 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 4 Oct 2022 11:16:41 -0400
Subject: [PATCH 091/326] WX-755 Add `isRelease` option for Docker builds
 (#6923)

---
 .github/workflows/chart_update_on_merge.yml |  2 +-
 project/Publishing.scala                    | 15 ++++++++++++++-
 project/Version.scala                       | 13 ++++++++++++-
 3 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index 81a7c3a8259..f87b48d484e 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -53,7 +53,7 @@ jobs:
       run: |
         set -e
         cd cromwell
-        sbt dockerBuildAndPush
+        sbt -Dproject.isSnapshot=false -Dproject.isRelease=false dockerBuildAndPush
     - name: Edit & push chart
       env:
         BROADBOT_GITHUB_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
diff --git a/project/Publishing.scala b/project/Publishing.scala
index 150c30ca293..1b798780086 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -36,7 +36,20 @@ object Publishing {
       ArrayBuffer(broadinstitute/cromwell:dev, broadinstitute/cromwell:develop)
     */
     dockerTags := {
-      val versionsCsv = if (Version.isSnapshot) version.value else s"$cromwellVersion,${version.value}"
+      val versionsCsv = if (Version.isSnapshot) {
+        // Tag looks like `85-443a6fc-SNAP`
+        version.value
+      } else {
+        if (Version.isRelease) {
+          // Tags look like `85`, `85-443a6fc`
+          s"$cromwellVersion,${version.value}"
+        } else {
+          // Tag looks like `85-443a6fc`
+          version.value
+        }
+      }
+
+      // Travis applies (as of 10/22) the `dev` and `develop` tags on merge to `develop`
       sys.env.getOrElse("CROMWELL_SBT_DOCKER_TAGS", versionsCsv).split(",")
     },
     docker / imageNames := dockerTags.value map { tag =>
diff --git a/project/Version.scala b/project/Version.scala
index dbe795e6f0c..ca782b990e2 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -13,8 +13,19 @@ object Version {
     *
     * The value is read in directly from the system property `project.isSnapshot` as there were confusing issues with
     * the multi-project and sbt.Keys#isSnapshot().
+    *
+    * Default `true`.
+    */
+  val isSnapshot: Boolean = sys.props.get("project.isSnapshot").forall(_.toBoolean)
+
+  /**
+    * Returns `true` if this project should tag a release like `85` in addition to a hash like `85-443a6fc`.
+    *
+    * Has no effect when `isSnapshot` is `true`.
+    *
+    * Default `true`.
     */
-  val isSnapshot = sys.props.get("project.isSnapshot").forall(_.toBoolean)
+  val isRelease: Boolean = sys.props.get("project.isRelease").forall(_.toBoolean)
 
   // Adapted from SbtGit.versionWithGit
   def cromwellVersionWithGit: Seq[Setting[_]] =

From dd40e08c5d1cb4ccac371a7c645b3a522f0c7df1 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Wed, 5 Oct 2022 10:19:36 -0400
Subject: [PATCH 092/326] WX-755 Cromwell/CromIAM automatically board train
 (#6924)

---
 .github/workflows/chart_update_on_merge.yml | 22 +++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index f87b48d484e..1d5d0bd7864 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -41,7 +41,7 @@ jobs:
         echo "CROMWELL_NUMBER=$((previous_version + 1))" >> $GITHUB_ENV
     - name: Save complete image ID
       run: |
-        echo "CROMWELL_SNAP_VERSION=`echo "$CROMWELL_NUMBER-$CROMWELL_SHORT_SHA-SNAP"`" >> $GITHUB_ENV
+        echo "CROMWELL_VERSION=`echo "$CROMWELL_NUMBER-$CROMWELL_SHORT_SHA"`" >> $GITHUB_ENV
     # `DSDEJENKINS_PASSWORD` auto syncs from vault with https://github.com/broadinstitute/terraform-ap-deployments/pull/614
     - name: Login to Docker Hub
       uses: docker/login-action@v1
@@ -54,6 +54,20 @@ jobs:
         set -e
         cd cromwell
         sbt -Dproject.isSnapshot=false -Dproject.isRelease=false dockerBuildAndPush
+    - name: Deploy to dev and board release train (Cromwell)
+      uses: broadinstitute/repository-dispatch@master
+      with:
+        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+        repository: broadinstitute/terra-helmfile
+        event-type: update-service
+        client-payload: '{"service": "cromwell", "version": "$CROMWELL_VERSION", "dev_only": false}'
+    - name: Deploy to dev and board release train (CromIAM)
+      uses: broadinstitute/repository-dispatch@master
+      with:
+        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+        repository: broadinstitute/terra-helmfile
+        event-type: update-service
+        client-payload: '{"service": "cromiam", "version": "$CROMWELL_VERSION", "dev_only": false}'
     - name: Edit & push chart
       env:
         BROADBOT_GITHUB_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
@@ -62,10 +76,10 @@ jobs:
         cd cromwhelm
         git checkout main
         ls -la
-        sed -i "s/appVersion.*/appVersion: \"$CROMWELL_SNAP_VERSION\"/" cromwell-helm/Chart.yaml
-        sed -i "s/image: broadinstitute\/cromwell.*/image: broadinstitute\/cromwell:$CROMWELL_SNAP_VERSION/" cromwell-helm/templates/cromwell.yaml
+        sed -i "s/appVersion.*/appVersion: \"$CROMWELL_VERSION\"/" cromwell-helm/Chart.yaml
+        sed -i "s/image: broadinstitute\/cromwell.*/image: broadinstitute\/cromwell:$CROMWELL_VERSION/" cromwell-helm/templates/cromwell.yaml
         git diff
         git config --global user.name "broadbot"
         git config --global user.email "broadbot@broadinstitute.org"
-        git commit -am "Auto update to Cromwell $CROMWELL_SNAP_VERSION"
+        git commit -am "Auto update to Cromwell $CROMWELL_VERSION"
         git push https://broadbot:$BROADBOT_GITHUB_TOKEN@github.com/broadinstitute/cromwhelm.git main

From 980d4100d4ce7454e4259166bbe95f41a4f06660 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Wed, 5 Oct 2022 13:55:22 -0400
Subject: [PATCH 093/326] WX-755 Fix environment variable syntax (#6926)

---
 .github/workflows/chart_update_on_merge.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index 1d5d0bd7864..aa7a2c9c9ad 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -60,14 +60,14 @@ jobs:
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
         repository: broadinstitute/terra-helmfile
         event-type: update-service
-        client-payload: '{"service": "cromwell", "version": "$CROMWELL_VERSION", "dev_only": false}'
+        client-payload: '{"service": "cromwell", "version": "${{ env.CROMWELL_VERSION }}", "dev_only": false}'
     - name: Deploy to dev and board release train (CromIAM)
       uses: broadinstitute/repository-dispatch@master
       with:
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
         repository: broadinstitute/terra-helmfile
         event-type: update-service
-        client-payload: '{"service": "cromiam", "version": "$CROMWELL_VERSION", "dev_only": false}'
+        client-payload: '{"service": "cromiam", "version": "${{ env.CROMWELL_VERSION }}", "dev_only": false}'
     - name: Edit & push chart
       env:
         BROADBOT_GITHUB_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}

From 7ad40b195ea67e8e6b3c62d935bdc5ece277c887 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Thu, 6 Oct 2022 15:22:41 -0400
Subject: [PATCH 094/326] WX-743 Enable TES task creation with BlobPaths
 (#6921)

* Give blob SAS tokens write permission

* Case class wrapper for subscription id

* Resolve duplicate container name in absolute BlobPath

* Ignored test demonstrating correct absolute path generation

* Update filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala

Co-authored-by: Brian Reilly <breilly@broadinstitute.org>

* PR feedback

Co-authored-by: Brian Reilly <breilly@broadinstitute.org>
---
 .../blob/BlobFileSystemManager.scala          | 14 ++++++---
 .../filesystems/blob/BlobPathBuilder.scala    | 29 ++++++++++++++++---
 .../blob/BlobPathBuilderFactory.scala         |  7 +++--
 .../blob/BlobPathBuilderSpec.scala            | 13 +++++++++
 4 files changed, 52 insertions(+), 11 deletions(-)

diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index 3b8f5149055..a3e6f33572a 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -77,10 +77,15 @@ case class BlobFileSystemManager(
 
 sealed trait BlobTokenGenerator {def generateAccessToken: Try[AzureSasCredential]}
 object BlobTokenGenerator {
-  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[String]): BlobTokenGenerator = {
+  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId]): BlobTokenGenerator = {
     createBlobTokenGenerator(container, endpoint, None, None, subscription)
   }
-  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: Option[WorkspaceId], workspaceManagerURL: Option[WorkspaceManagerURL], subscription: Option[String]): BlobTokenGenerator = {
+  def createBlobTokenGenerator(container: BlobContainerName,
+                               endpoint: EndpointURL,
+                               workspaceId: Option[WorkspaceId],
+                               workspaceManagerURL: Option[WorkspaceManagerURL],
+                               subscription: Option[SubscriptionId]
+                              ): BlobTokenGenerator = {
      (container: BlobContainerName, endpoint: EndpointURL, workspaceId, workspaceManagerURL) match {
        case (container, endpoint, None, None) =>
          NativeBlobTokenGenerator(container, endpoint, subscription)
@@ -100,13 +105,13 @@ case class WSMBlobTokenGenerator(container: BlobContainerName, endpoint: Endpoin
   def generateAccessToken: Try[AzureSasCredential] = Failure(new NotImplementedError)
 }
 
-case class NativeBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[String] = None) extends BlobTokenGenerator {
+case class NativeBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId] = None) extends BlobTokenGenerator {
 
   private val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
   private def azureCredentialBuilder = new DefaultAzureCredentialBuilder()
       .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
       .build
-  private def authenticateWithSubscription(sub: String) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub)
+  private def authenticateWithSubscription(sub: SubscriptionId) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub.value)
   private def authenticateWithDefaultSubscription = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withDefaultSubscription()
   private def azure = subscription.map(authenticateWithSubscription(_)).getOrElse(authenticateWithDefaultSubscription)
 
@@ -123,6 +128,7 @@ case class NativeBlobTokenGenerator(container: BlobContainerName, endpoint: Endp
     .setReadPermission(true)
     .setCreatePermission(true)
     .setListPermission(true)
+    .setWritePermission(true)
 
 
   def generateAccessToken: Try[AzureSasCredential] = for {
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 3e69ce2a7bd..1be6bb8e13b 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -67,19 +67,40 @@ class BlobPathBuilder(container: BlobContainerName, endpoint: EndpointURL)(priva
   override def name: String = "Azure Blob Storage"
 }
 
+object BlobPath {
+  // The Azure NIO library uses `{containerName}:` as the root of the path.
+  // This doesn't work well for our need to easily transfer back and forth
+  // to and from the blob URL format. This method removes anything up to and including
+  // the first colon, to create a path string useful for working with BlobPath.
+  // This is safe because the NIO library enforces no colons except to mark
+  // the root container name.
+  private def nioPathString(nioPath: NioPath): String = {
+    val pathStr = nioPath.toString
+    pathStr.substring(pathStr.indexOf(":")+1)
+  }
+
+  def apply(nioPath: NioPath,
+            endpoint: EndpointURL,
+            container: BlobContainerName,
+            fsm: BlobFileSystemManager): BlobPath = {
+    BlobPath(nioPathString(nioPath), endpoint, container)(fsm)
+  }
+}
+
 case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, container: BlobContainerName)(private val fsm: BlobFileSystemManager) extends Path {
   override def nioPath: NioPath = findNioPath(pathString)
 
-  override protected def newPath(nioPath: NioPath): Path = BlobPath(nioPath.toString, endpoint, container)(fsm)
+  override protected def newPath(nioPath: NioPath): Path = BlobPath(nioPath, endpoint, container, fsm)
 
-  override def pathAsString: String = List(endpoint, container, nioPath.toString).mkString("/")
+  override def pathAsString: String = List(endpoint, container, pathString.stripPrefix("/")).mkString("/")
 
   //This is purposefully an unprotected get because if the endpoint cannot be parsed this should fail loudly rather than quietly
-  override def pathWithoutScheme: String = parseURI(endpoint.value).map(_.getHost + "/" + container + "/" + nioPath.toString).get
+  override def pathWithoutScheme: String = parseURI(endpoint.value).map(u => List(u.getHost, container, pathString).mkString("/")).get
 
   private def findNioPath(path: String): NioPath = (for {
     fileSystem <- fsm.retrieveFilesystem()
-    nioPath = fileSystem.getPath(path)
+    // The Azure NIO library uses `{container}:` to represent the root of the path
+    nioPath = fileSystem.getPath(s"${container.value}:", path)
   // This is purposefully an unprotected get because the NIO API needing an unwrapped path object.
   // If an error occurs the api expects a thrown exception
   } yield nioPath).get
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index c93f751b706..e6d269a07b0 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -10,18 +10,19 @@ import scala.concurrent.{ExecutionContext, Future}
 
 final case class BlobFileSystemConfig(config: Config)
 
+final case class SubscriptionId(value: String) {override def toString: String = value}
 final case class BlobContainerName(value: String) {override def toString: String = value}
 final case class StorageAccountName(value: String) {override def toString: String = value}
 final case class EndpointURL(value: String) {override def toString: String = value}
 final case class WorkspaceId(value: String) {override def toString: String = value}
 final case class WorkspaceManagerURL(value: String) {override def toString: String = value}
 final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, singletonConfig: BlobFileSystemConfig) extends PathBuilderFactory {
-  val subscription: Option[String] = instanceConfig.as[Option[String]]("subscription")
+  val subscription: Option[SubscriptionId] = instanceConfig.as[Option[String]]("subscription").map(SubscriptionId)
   val container: BlobContainerName = BlobContainerName(instanceConfig.as[String]("container"))
   val endpoint: EndpointURL = EndpointURL(instanceConfig.as[String]("endpoint"))
-  val workspaceId: Option[WorkspaceId] = instanceConfig.as[Option[String]]("workspace-id").map(WorkspaceId(_))
+  val workspaceId: Option[WorkspaceId] = instanceConfig.as[Option[String]]("workspace-id").map(WorkspaceId)
   val expiryBufferMinutes: Long = instanceConfig.as[Option[Long]]("expiry-buffer-minutes").getOrElse(10)
-  val workspaceManagerURL: Option[WorkspaceManagerURL] = singletonConfig.config.as[Option[String]]("workspace-manager-url").map(WorkspaceManagerURL(_))
+  val workspaceManagerURL: Option[WorkspaceManagerURL] = singletonConfig.config.as[Option[String]]("workspace-manager-url").map(WorkspaceManagerURL)
 
   val blobTokenGenerator: BlobTokenGenerator = BlobTokenGenerator.createBlobTokenGenerator(
     container, endpoint, workspaceId, workspaceManagerURL, subscription)
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index 9975065a3e2..671e7b2d35b 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -91,4 +91,17 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val fileText = (is.readAllBytes.map(_.toChar)).mkString
     fileText should include ("This is my test file!!!! Did it work?")
   }
+
+  ignore should "resolve a path without duplicating container name" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
+    val store = BlobContainerName("inputs")
+    val blobTokenGenerator = NativeBlobTokenGenerator(store, endpoint)
+    val fsm: BlobFileSystemManager = BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
+
+    val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
+    val blobRoot: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build rootString getOrElse fail()
+    blobRoot.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution")
+    val otherFile = blobRoot.resolve("test/inputFile.txt")
+    otherFile.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
+  }
 }

From 18fbb14a6dc4e8813cde24c88b725bcb51640ad1 Mon Sep 17 00:00:00 2001
From: Brian Reilly <breilly@broadinstitute.org>
Date: Fri, 7 Oct 2022 10:36:04 -0400
Subject: [PATCH 095/326] [WX-765] Update snakeyaml to 1.33 (#6927)

* update snakeyaml to 1.33

* Don't use deprecated no-arg Constructor constructor

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .../test/scala/cromiam/webservice/SwaggerServiceSpec.scala | 7 ++++---
 .../scala/cromwell/webservice/SwaggerServiceSpec.scala     | 6 +++---
 project/Dependencies.scala                                 | 2 +-
 wom/src/main/scala/wom/util/YamlUtils.scala                | 6 ++++--
 4 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
index c0277fd92c0..838a523f4eb 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
@@ -12,7 +12,7 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 import org.yaml.snakeyaml.constructor.Constructor
 import org.yaml.snakeyaml.error.YAMLException
 import org.yaml.snakeyaml.nodes.MappingNode
-import org.yaml.snakeyaml.{Yaml => SnakeYaml}
+import org.yaml.snakeyaml.{LoaderOptions, Yaml => SnakeYaml}
 
 import scala.jdk.CollectionConverters._
 
@@ -21,6 +21,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
   with TableDrivenPropertyChecks {
   def actorRefFactory = system
   override def oauthConfig: SwaggerOauthConfig = SwaggerOauthConfig("clientId", "realm", "appName")
+  val yamlLoaderOptions = new LoaderOptions
 
   behavior of "SwaggerService"
 
@@ -32,7 +33,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
         contentType should be(ContentTypes.`application/octet-stream`)
 
         val body = responseAs[String]
-        val yaml = new SnakeYaml(new UniqueKeyConstructor()).loadAs(body, classOf[java.util.Map[String, AnyRef]])
+        val yaml = new SnakeYaml(new UniqueKeyConstructor(new LoaderOptions)).loadAs(body, classOf[java.util.Map[String, AnyRef]])
 
         yaml.get("swagger") should be("2.0")
       }
@@ -109,7 +110,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
   * Adapted from:
   * https://bitbucket.org/asomov/snakeyaml/src/e9cd9f5e8d76c61eb983e29b3dc039c1fac9c393/src/test/java/org/yaml/snakeyaml/issues/issue139/UniqueKeyTest.java?fileviewer=file-view-default#UniqueKeyTest.java-43:62
   */
-class UniqueKeyConstructor extends Constructor {
+class UniqueKeyConstructor(val loaderOptions: LoaderOptions) extends Constructor(loaderOptions) {
 
   import java.util.{Map => JMap}
 
diff --git a/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
index ed4e588cfd1..24cce8ae932 100644
--- a/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
@@ -11,7 +11,7 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 import org.yaml.snakeyaml.constructor.Constructor
 import org.yaml.snakeyaml.error.YAMLException
 import org.yaml.snakeyaml.nodes.MappingNode
-import org.yaml.snakeyaml.{Yaml => SnakeYaml}
+import org.yaml.snakeyaml.{LoaderOptions, Yaml => SnakeYaml}
 
 import scala.jdk.CollectionConverters._
 
@@ -28,7 +28,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
         status should be(StatusCodes.OK)
 
         val body = responseAs[String]
-        val yaml = new SnakeYaml(new UniqueKeyConstructor()).loadAs(body, classOf[java.util.Map[String, AnyRef]])
+        val yaml = new SnakeYaml(new UniqueKeyConstructor(new LoaderOptions)).loadAs(body, classOf[java.util.Map[String, AnyRef]])
 
         yaml.get("swagger") should be("2.0")
       }
@@ -100,7 +100,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
   * Adapted from:
   * https://bitbucket.org/asomov/snakeyaml/src/e9cd9f5e8d76c61eb983e29b3dc039c1fac9c393/src/test/java/org/yaml/snakeyaml/issues/issue139/UniqueKeyTest.java?fileviewer=file-view-default#UniqueKeyTest.java-43:62
   */
-class UniqueKeyConstructor extends Constructor {
+class UniqueKeyConstructor(val loaderOptions: LoaderOptions) extends Constructor(loaderOptions) {
 
   import java.util.{Map => JMap}
 
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 50c76893e80..ebb4b1c0d69 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -118,7 +118,7 @@ object Dependencies {
     * https://github.com/slick/slick/pull/2201
   */
   private val slickV = "3.4.0-M1"
-  private val snakeyamlV = "1.30"
+  private val snakeyamlV = "1.33"
   private val sprayJsonV = "1.3.6"
   private val sttpV = "1.7.2"
   private val swaggerParserV = "1.0.56"
diff --git a/wom/src/main/scala/wom/util/YamlUtils.scala b/wom/src/main/scala/wom/util/YamlUtils.scala
index b4e0f063c9b..50dffc0457d 100644
--- a/wom/src/main/scala/wom/util/YamlUtils.scala
+++ b/wom/src/main/scala/wom/util/YamlUtils.scala
@@ -38,7 +38,7 @@ object YamlUtils {
             maxDepth: Int Refined NonNegative = defaultMaxDepth
            ): Either[ParsingFailure, Json] = {
     try {
-      val yamlConstructor = new SafeConstructor()
+      val yamlConstructor = new SafeConstructor(loaderOptions)
       val yamlComposer = new MaxDepthComposer(yaml, maxDepth)
       yamlConstructor.setComposer(yamlComposer)
       val parsed = yamlConstructor.getSingleData(classOf[AnyRef])
@@ -76,12 +76,14 @@ object YamlUtils {
   // org.yaml.snakeyaml.error.YAMLException: Number of aliases for non-scalar nodes exceeds the specified max=50
   // that comes from the SnakeYAML library.
   private val loaderOptions = new LoaderOptions()
+  loaderOptions.setAllowRecursiveKeys(true)
+  loaderOptions.setNestingDepthLimit(1000)
   loaderOptions.setMaxAliasesForCollections(Integer.MAX_VALUE)
 
   /** Extends SnakeYaml's Composer checking for a maximum depth before a StackOverflowError occurs. */
   private class MaxDepthComposer(yaml: String, maxDepth: Int Refined NonNegative)
     extends Composer(
-      new ParserImpl(new StreamReader(new StringReader(yaml))),
+      new ParserImpl(new StreamReader(new StringReader(yaml)), loaderOptions),
       new Resolver(),
       loaderOptions
     ) {

From c5994261f40c529fcad02fc4577db9aad6ade79e Mon Sep 17 00:00:00 2001
From: Katrina P <68349264+kpierre13@users.noreply.github.com>
Date: Tue, 11 Oct 2022 09:43:42 -0400
Subject: [PATCH 096/326] WM-1414 Refactoring WesRunLog to omit Cromwell's
 "workflowLog" object (#6925)

---
 .../webservice/routes/wes/WesResponse.scala      | 16 ++++++++++++++--
 .../webservice/routes/wes/WesRouteSupport.scala  |  2 +-
 .../webservice/routes/wes/WesRunLog.scala        | 13 -------------
 .../routes/wes/WesRouteSupportSpec.scala         |  2 +-
 4 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
index 32e221272e0..58313cb5946 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
@@ -2,8 +2,7 @@ package cromwell.webservice.routes.wes
 
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport
 import cromwell.webservice.routes.wes.WesState.WesState
-import spray.json.{DefaultJsonProtocol, RootJsonFormat}
-import cromwell.webservice.routes.wes.WesRunLog
+import spray.json.{DefaultJsonProtocol, JsObject, RootJsonFormat}
 
 sealed trait WesResponse extends Product with Serializable
 final case class WesErrorResponse(msg: String, status_code: Int) extends WesResponse
@@ -12,6 +11,18 @@ final case class WesRunStatus(run_id: String, state: WesState) extends WesRespon
 final case class WesResponseRunList(runs: List[WesRunStatus]) extends WesResponse
 final case class WesResponseWorkflowMetadata(workflowLog: WesRunLog) extends WesResponse
 
+final case class WesRunLog(run_id: String,
+                           request: WesRunRequest,
+                           state: WesState,
+                           run_log: Option[WesLog],
+                           task_logs: Option[List[WesLog]],
+                           outputs: Option[JsObject]
+                          ) extends WesResponse
+
+object WesRunLog {
+  def fromJson(json: String): WesRunLog = CromwellMetadata.fromJson(json).wesRunLog
+}
+
 
 final case class WesStatusInfoResponse(workflow_type_version: Map[String, Iterable[String]],
                                     supported_wes_versions: Iterable[String],
@@ -48,6 +59,7 @@ object WesResponseJsonSupport extends SprayJsonSupport with DefaultJsonProtocol
         case i: WesStatusInfoResponse => i.toJson
         case l: WesResponseRunList => l.toJson
         case m: WesResponseWorkflowMetadata => m.toJson
+        case w: WesRunLog => w.toJson
       }
     }
 
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
index ba6546fb3e3..41973bb8981 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
@@ -228,7 +228,7 @@ object WesRouteSupport {
     val metadataJsonResponse = metadataBuilderActorRequest(workflowId, request, serviceRegistryActor)
 
     metadataJsonResponse.map {
-      case SuccessfulMetadataJsonResponse(_, responseJson) => WesResponseWorkflowMetadata(WesRunLog.fromJson(responseJson.toString()))
+      case SuccessfulMetadataJsonResponse(_, responseJson) => WesRunLog.fromJson(responseJson.toString())
       case FailedMetadataJsonResponse(_, reason) => WesErrorResponse(reason.getMessage, StatusCodes.InternalServerError.intValue)
     }
   }
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
index 344498e51ab..c882ebf4f8b 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
@@ -1,6 +1,5 @@
 package cromwell.webservice.routes.wes
 
-import cromwell.webservice.routes.wes.WesState.WesState
 import spray.json.JsObject
 
 
@@ -20,15 +19,3 @@ final case class WesRunRequest(workflow_params: Option[JsObject],
                                workflow_engine_parameters: Option[JsObject],
                                workflow_url: Option[String]
                               )
-
-final case class WesRunLog(run_id: String,
-                           request: WesRunRequest,
-                           state: WesState,
-                           run_log: Option[WesLog],
-                           task_logs: Option[List[WesLog]],
-                           outputs: Option[JsObject]
-                          )
-
-object WesRunLog {
-  def fromJson(json: String): WesRunLog = CromwellMetadata.fromJson(json).wesRunLog
-}
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
index 6e9a390ad4a..00a361a3174 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
@@ -196,7 +196,7 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
       wesRoutes ~>
       check {
         status should be(StatusCodes.OK)
-        val result = responseAs[JsObject].fields("workflowLog").asJsObject()
+        val result = responseAs[JsObject]
         result.fields.keys should contain allOf("request", "run_id", "state")
         result.fields("state") should be(JsString("RUNNING"))
         result.fields("run_id") should be(JsString(CromwellApiServiceSpec.wesWorkflowId.toString))

From b0a254112bf0589ebe22dea7abf520ba2c78c973 Mon Sep 17 00:00:00 2001
From: Christian Freitas <christian.j.freitas@gmail.com>
Date: Fri, 14 Oct 2022 09:34:13 -0400
Subject: [PATCH 097/326] Upgrade Postgres to 42.4.1 (#6932)

---
 project/Dependencies.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index ebb4b1c0d69..675c0f7c7dd 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -86,7 +86,7 @@ object Dependencies {
   private val mysqlV = "8.0.28"
   private val nettyV = "4.1.72.Final"
   private val owlApiV = "5.1.19"
-  private val postgresV = "42.3.3"
+  private val postgresV = "42.4.1"
   private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
   private val refinedV = "0.9.29"

From 622c8e6b79b4ce123912ace0ed37b28f1c461324 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 14 Oct 2022 10:19:51 -0400
Subject: [PATCH 098/326] WX-735 Fix incorrect and/or nondeterministic
 filesystem ordering (#6930)

---
 .../core/path/DefaultPathBuilderFactory.scala |  3 +++
 .../core/path/PathBuilderFactory.scala        | 21 ++++++++++++-------
 .../cromwell/engine/EngineFilesystems.scala   | 14 ++++++++-----
 .../blob/BlobPathBuilderFactory.scala         |  3 +++
 4 files changed, 28 insertions(+), 13 deletions(-)

diff --git a/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala b/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
index 91f05b10ef7..20a2afdd5ce 100644
--- a/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
+++ b/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
@@ -2,6 +2,7 @@ package cromwell.core.path
 
 import akka.actor.ActorSystem
 import cromwell.core.WorkflowOptions
+import cromwell.core.path.PathBuilderFactory.PriorityDefault
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -9,4 +10,6 @@ case object DefaultPathBuilderFactory extends PathBuilderFactory {
   override def withOptions(options: WorkflowOptions)(implicit actorSystem: ActorSystem, ec: ExecutionContext) = Future.successful(DefaultPathBuilder)
   val name = "local"
   val tuple = name -> this
+
+  override def priority: Int = PriorityDefault
 }
diff --git a/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala b/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
index 1f215ba2933..79adaae4d6b 100644
--- a/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
+++ b/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
@@ -5,6 +5,7 @@ import cromwell.core.{Dispatcher, WorkflowOptions}
 import cats.syntax.traverse._
 import cats.instances.list._
 import cats.instances.future._
+import cromwell.core.path.PathBuilderFactory.PriorityStandard
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -12,16 +13,13 @@ object PathBuilderFactory {
   // Given a list of factories, instantiates the corresponding path builders
   def instantiatePathBuilders(factories: List[PathBuilderFactory], workflowOptions: WorkflowOptions)(implicit as: ActorSystem): Future[List[PathBuilder]] = {
     implicit val ec: ExecutionContext = as.dispatchers.lookup(Dispatcher.IoDispatcher)
-    // The DefaultPathBuilderFactory always needs to be last.
-    // The reason is path builders are tried in order, and the default one is very generous in terms of paths it "thinks" it supports
-    // For instance, it will return a Path for a gcs url even though it doesn't really support it
-    val sortedFactories = factories.sortWith({
-      case (_, DefaultPathBuilderFactory) => true
-      case (DefaultPathBuilderFactory, _) => false
-      case (a, b) => factories.indexOf(a) < factories.indexOf(b)
-    })
+    val sortedFactories = factories.sortBy(_.priority)
     sortedFactories.traverse(_.withOptions(workflowOptions))
   }
+
+  val PriorityBlob     = 100   // High priority to evaluate first, because blob files may inadvertently match other filesystems
+  val PriorityStandard = 1000
+  val PriorityDefault  = 10000 // "Default" is a fallback, evaluate last
 }
 
 /**
@@ -29,4 +27,11 @@ object PathBuilderFactory {
   */
 trait PathBuilderFactory {
   def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder]
+
+  /**
+    * Candidate filesystems are considered in a stable order, as some requests may match multiple filesystems.
+    * To customize this order, the priority of a filesystem may be adjusted. Lower number == higher priority.
+    * @return This filesystem's priority
+    */
+  def priority: Int = PriorityStandard
 }
diff --git a/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala b/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
index 296d227d39f..c648261a7f4 100644
--- a/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
+++ b/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
@@ -8,19 +8,23 @@ import cromwell.core.filesystem.CromwellFileSystems
 import cromwell.core.path.{DefaultPathBuilderFactory, PathBuilder, PathBuilderFactory}
 import net.ceedubs.ficus.Ficus._
 
+import scala.collection.immutable.SortedMap
 import scala.concurrent.Future
 
 object EngineFilesystems {
   private val config: Config = ConfigFactory.load
 
-  private val defaultFileSystemFactory: Map[String, PathBuilderFactory] =
+  private val defaultFileSystemFactory: SortedMap[String, PathBuilderFactory] =
     Option(DefaultPathBuilderFactory.tuple)
       .filter(_ => config.as[Boolean]("engine.filesystems.local.enabled"))
-      .toMap
+      .to(collection.immutable.SortedMap)
 
-  private val pathBuilderFactories: Map[String, PathBuilderFactory] = {
-    CromwellFileSystems.instance.factoriesFromConfig(config.as[Config]("engine"))
-      .unsafe("Failed to instantiate engine filesystem") ++ defaultFileSystemFactory
+  private val pathBuilderFactories: SortedMap[String, PathBuilderFactory] = {
+    // Unordered maps are a classical source of randomness injection into a system
+    (
+      CromwellFileSystems.instance.factoriesFromConfig(config.as[Config]("engine"))
+        .unsafe("Failed to instantiate engine filesystem") ++ defaultFileSystemFactory
+    ).to(collection.immutable.SortedMap)
   }
 
   def configuredPathBuilderFactories: List[PathBuilderFactory] = pathBuilderFactories.values.toList
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index e6d269a07b0..1a9df21b0f2 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -4,6 +4,7 @@ import akka.actor.ActorSystem
 import com.typesafe.config.Config
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.PathBuilderFactory
+import cromwell.core.path.PathBuilderFactory.PriorityBlob
 import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.{ExecutionContext, Future}
@@ -33,4 +34,6 @@ final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Co
       new BlobPathBuilder(container, endpoint)(fsm)
     }
   }
+
+  override def priority: Int = PriorityBlob
 }

From 1a3889689060dcff2b6706a98ae69fd2fa9f70ef Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 17 Oct 2022 16:18:09 -0400
Subject: [PATCH 099/326] WX-772 Update Scala to 2.13.9 (#6928)

* Update Scala to 2.13.9

* Try updating sbt-scoverage

* Does this version exist anywhere we can see?

* This version actually exists

* Update library version to remove conflict

* Codegen version

* Fix fun new 2.13.9 compiler errors

* Resolve warnings

* Newest Scala?

* I guess not

* Does this please Travis?

* force ci

* Back out changes to generated code

Co-authored-by: Adam Nichols <aednichols@gmail.com>
---
 CHANGELOG.md                                  |  5 +++++
 .../standard/StandardCachingActorHelper.scala |  2 +-
 .../RootWorkflowFileHashCacheActor.scala      |  2 +-
 .../centaur/reporting/BigQueryReporter.scala  |  2 +-
 codegen_java/build.sbt                        |  2 +-
 .../main/scala/common/util/TerminalUtil.scala |  4 ++--
 .../collections/EnhancedCollectionsSpec.scala |  6 +++---
 .../cromwell/core/io/IoClientHelperSpec.scala |  4 ++--
 .../cromwell/core/retry/BackoffSpec.scala     |  2 +-
 .../callcaching/FetchCachedResultsActor.scala |  2 +-
 .../job/EngineJobExecutionActor.scala         |  2 +-
 .../ValidatingCachingConfigSpec.scala         |  2 +-
 project/Dependencies.scala                    |  8 ++++---
 project/Settings.scala                        |  2 +-
 project/plugins.sbt                           |  2 +-
 ...ectiveTsvInstrumentationServiceActor.scala |  2 +-
 .../impl/MetadataDatabaseAccessSpec.scala     |  2 +-
 .../PipelinesApiJobCachingActorHelper.scala   |  2 +-
 ...inesApiAsyncBackendJobExecutionActor.scala |  4 ++--
 .../v2alpha1/api/DeserializationSpec.scala    |  6 +++---
 ...inesApiAsyncBackendJobExecutionActor.scala |  4 ++--
 .../v2beta/api/DeserializationSpec.scala      |  6 +++---
 .../scala/wdl/draft2/model/AstTools.scala     |  4 ++--
 .../scala/wom/types/WomFileTypeSpec.scala     |  2 +-
 .../test/scala/wom/types/WomTypeSpec.scala    | 21 ++++++++++---------
 25 files changed, 54 insertions(+), 46 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 351adccf651..1e44012027c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -32,6 +32,11 @@ supported.
 All DRS inputs to a task are now localized in a single PAPI action, which should improve speed and resolve
 failures observed when attempting to localize a large number of DRS files.
 
+### Security Patching
+
+Updates to dependencies to fix security vulnerabilities.
+
+
 ## 84 Release Notes
 
 ### CromIAM enabled user checks
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala b/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
index dd4254c8439..a64c6a5439c 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
@@ -78,7 +78,7 @@ trait StandardCachingActorHelper extends JobCachingActorHelper {
 
     val fileMetadata = jobPaths.metadataPaths
 
-    runtimeAttributesMetadata ++ fileMetadata ++ nonStandardMetadata
+    nonStandardMetadata ++ runtimeAttributesMetadata ++ fileMetadata
   }
 
   /**
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
index e33625741b3..c3d1452660e 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
@@ -48,7 +48,7 @@ class RootWorkflowFileHashCacheActor private[callcaching](override val ioActor:
           // hash to become available.
           cache.put(key, FileHashValueRequested(requesters = requester :: requesters))
         case FileHashSuccess(value) =>
-          sender() ! Tuple2(hashCommand.fileHashContext, IoSuccess(requester.ioCommand, value))
+          sender() ! Tuple2[Any, Any](hashCommand.fileHashContext, IoSuccess(requester.ioCommand, value))
         case FileHashFailure(error) =>
           sender() ! Tuple2(hashCommand.fileHashContext, IoFailure(requester.ioCommand, new IOException(error)))
       }
diff --git a/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala b/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
index 16463742632..9a88a9ac109 100644
--- a/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
+++ b/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
@@ -189,7 +189,7 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
   }
 
   private def toJobKeyValueRow(jobKeyValueEntry: JobKeyValueEntry): RowToInsert = {
-    RowToInsert of Map(
+    RowToInsert of Map[String, Any](
       "call_fully_qualified_name" -> jobKeyValueEntry.callFullyQualifiedName,
       "job_attempt" -> jobKeyValueEntry.jobAttempt,
       "job_index" -> jobKeyValueEntry.jobIndex,
diff --git a/codegen_java/build.sbt b/codegen_java/build.sbt
index 2ba35a693c3..0ad461a66b8 100644
--- a/codegen_java/build.sbt
+++ b/codegen_java/build.sbt
@@ -6,7 +6,7 @@ lazy val root = (project in file(".")).
     Seq(organization := "org.broadinstitute.cromwell",
     name := "cromwell-client",
     version := createVersion("0.1"),
-    scalaVersion := "2.13.8",
+    scalaVersion := "2.13.9",
     scalacOptions ++= Seq("-feature"),
     compile / javacOptions ++= Seq("-Xlint:deprecation"),
     Compile / packageDoc / publishArtifact := false,
diff --git a/common/src/main/scala/common/util/TerminalUtil.scala b/common/src/main/scala/common/util/TerminalUtil.scala
index dab7fb9ce17..cb7c980aecb 100644
--- a/common/src/main/scala/common/util/TerminalUtil.scala
+++ b/common/src/main/scala/common/util/TerminalUtil.scala
@@ -6,10 +6,10 @@ object TerminalUtil {
     def maxWidth(lengths: Seq[Seq[Int]], column: Int) = lengths.map { length => length(column) }.max
     val widths = (rows :+ header).map { row => row.map { s => s.length } }
     val maxWidths = widths.head.indices.map { column => maxWidth(widths, column) }
-    val tableHeader = header.indices.map { i => header(i).padTo(maxWidths(i), " ").mkString("") }.mkString("|")
+    val tableHeader = header.indices.map { i => header(i).padTo(maxWidths(i), ' ').mkString("") }.mkString("|")
     val tableDivider = header.indices.map { i => "-" * maxWidths(i) }.mkString("|")
     val tableRows = rows.map { row =>
-      val mdRow = row.indices.map { i => row(i).padTo(maxWidths(i), " ").mkString("") }.mkString("|")
+      val mdRow = row.indices.map { i => row(i).padTo(maxWidths(i), ' ').mkString("") }.mkString("|")
       s"|$mdRow|"
     }
     s"|$tableHeader|\n|$tableDivider|\n${tableRows.mkString("\n")}\n"
diff --git a/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala b/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala
index 12dba2e15d9..d2e0a38878c 100644
--- a/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala
+++ b/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala
@@ -11,7 +11,7 @@ class EnhancedCollectionsSpec extends AsyncFlatSpec with Matchers {
   behavior of "EnhancedCollections"
 
   it should "filter a List by type and return a List" in {
-    val objectList = List("hello", 3, None, "world")
+    val objectList = List[Any]("hello", 3, None, "world")
     val stringList = objectList.filterByType[String]
 
     stringList should be(List("hello", "world"))
@@ -28,14 +28,14 @@ class EnhancedCollectionsSpec extends AsyncFlatSpec with Matchers {
   }
 
   it should "filter a Set by type and return a Set" in {
-    val objectSet = Set("hello", 3, None, "world")
+    val objectSet = Set[Any]("hello", 3, None, "world")
     val intSet: Set[Int] = objectSet.filterByType[Int]
 
     intSet should be(Set(3))
   }
 
   it should "find the first Int in a List" in {
-    val objectSet = List("hello", 3, None, 4, "world")
+    val objectSet = List[Any]("hello", 3, None, 4, "world")
     objectSet.firstByType[Int] should be(Some(3))
   }
 
diff --git a/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala b/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
index f77df6fa011..06132ba152b 100644
--- a/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
+++ b/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
@@ -27,7 +27,7 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
     val testActor = TestActorRef(new IoClientHelperTestActor(ioActorProbe.ref, delegateProbe.ref, backoff, noResponseTimeout))
 
     val command = DefaultIoSizeCommand(mock[Path])
-    val response = IoSuccess(command, 5)
+    val response = IoSuccess(command, 5L)
 
     // Send the command
     testActor.underlyingActor.sendMessage(command)
@@ -58,7 +58,7 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
 
     val commandContext = "context"
     val command = DefaultIoSizeCommand(mock[Path])
-    val response = IoSuccess(command, 5)
+    val response = IoSuccess(command, 5L)
 
     // Send the command
     testActor.underlyingActor.sendMessageWithContext(commandContext, command)
diff --git a/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala b/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
index 58fa597dc03..c6a008feb02 100644
--- a/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
+++ b/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
@@ -54,7 +54,7 @@ class BackoffSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   it should "parse config" in {
     val config = ConfigFactory.parseMap(
-      Map(
+      Map[String, Any](
         "min" -> "5 seconds",
         "max" -> "30 seconds",
         "multiplier" -> 6D,
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
index 0eef565caf2..89745e6523d 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
@@ -37,7 +37,7 @@ class FetchCachedResultsActor(cacheResultId: CallCachingEntryId, replyTo: ActorR
 
         val sourceCacheDetails = Seq(result.callCachingEntry.workflowExecutionUuid,
           result.callCachingEntry.callFullyQualifiedName,
-          result.callCachingEntry.jobIndex).mkString(":")
+          result.callCachingEntry.jobIndex.toString).mkString(":")
 
         CachedOutputLookupSucceeded(simpletons, jobDetritusFiles.toMap,
           result.callCachingEntry.returnCode,
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
index 3bbdb5eb1f2..4423de202cc 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
@@ -753,7 +753,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
   private def logCacheHitSuccessAndNotifyMetadata(data: ResponsePendingData): Unit = {
 
-    val metadataMap = Map(callCachingHitResultMetadataKey -> true) ++ data.ejeaCacheHit.flatMap(_.details).map(details => callCachingReadResultMetadataKey -> s"Cache Hit: $details").toMap
+    val metadataMap = Map[String, Any](callCachingHitResultMetadataKey -> true) ++ data.ejeaCacheHit.flatMap(_.details).map(details => callCachingReadResultMetadataKey -> s"Cache Hit: $details").toMap
 
     writeToMetadata(metadataMap)
 
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
index 40b628a700d..095721569e7 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
@@ -11,7 +11,7 @@ import scala.util.{Failure, Success, Try}
 class ValidatingCachingConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
 
     it should "run config tests" in {
-      val cases = Table(
+      val cases = Table[String, Any](
         ("config"                 , "exceptionMessage"                                                              ),
         ("enabled = not-a-boolean", "String: 1: enabled has type STRING rather than BOOLEAN"                        ),
         ("enabled = true"         , true                                                                            ),
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 675c0f7c7dd..0a0dee70cfa 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -89,7 +89,7 @@ object Dependencies {
   private val postgresV = "42.4.1"
   private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
-  private val refinedV = "0.9.29"
+  private val refinedV = "0.10.1"
   private val rhinoV = "1.7.14"
 
   private val scalaCollectionCompatV = "2.5.0"
@@ -480,7 +480,8 @@ object Dependencies {
   val coreDependencies: List[ModuleID] = List(
     "com.google.auth" % "google-auth-library-oauth2-http" % googleOauth2V,
     "com.chuusai" %% "shapeless" % shapelessV,
-    "com.storm-enroute" %% "scalameter" % scalameterV % Test,
+    "com.storm-enroute" %% "scalameter" % scalameterV % Test
+      exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.github.scopt" %% "scopt" % scoptV,
   ) ++ akkaStreamDependencies ++ configDependencies ++ catsDependencies ++ circeDependencies ++
     googleApiClientDependencies ++ statsDDependencies ++ betterFilesDependencies ++
@@ -509,7 +510,8 @@ object Dependencies {
     "com.storm-enroute" %% "scalameter" % scalameterV
       exclude("com.fasterxml.jackson.core", "jackson-databind")
       exclude("com.fasterxml.jackson.module", "jackson-module-scala")
-      exclude("org.scala-tools.testing", "test-interface"),
+      exclude("org.scala-tools.testing", "test-interface")
+      exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.fasterxml.jackson.core" % "jackson-databind" % jacksonV,
     "io.github.andrebeat" %% "scala-pool" % scalaPoolV
   ) ++ swaggerUiDependencies ++ akkaHttpDependencies ++ akkaHttpCirceIntegrationDependency ++ circeDependencies ++
diff --git a/project/Settings.scala b/project/Settings.scala
index 951b1fc8fe6..797d7917dd9 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -70,7 +70,7 @@ object Settings {
     assembly / assemblyMergeStrategy := customMergeStrategy.value,
   )
 
-  val Scala2_13Version = "2.13.8"
+  val Scala2_13Version = "2.13.9"
   private val ScalaVersion: String = Scala2_13Version
   private val sharedSettings: Seq[Setting[_]] =
     cromwellVersionWithGit ++ publishingSettings ++ List(
diff --git a/project/plugins.sbt b/project/plugins.sbt
index dd6a98e1b9b..34bccb47a0a 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1,5 +1,5 @@
 addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.9.0")
 addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.1")
 addSbtPlugin("com.github.sbt" % "sbt-git" % "2.0.0")
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.9.3")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.4")
 addDependencyTreePlugin
diff --git a/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala b/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
index fd1864d45f0..4df3f966db6 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
@@ -143,7 +143,7 @@ object SelectiveTsvInstrumentationServiceActor {
 
       val header = (List("timestamp") ++ interestingFields).mkString("\t")
       val rows = stateHistory.map { case (timestamp, fieldMap) =>
-        (Vector(timestamp.toString) ++ interestingFields.map(f => fieldMap.getOrElse(f, 0))).mkString("\t")
+        (Vector(timestamp.toString) ++ interestingFields.map(f => fieldMap.getOrElse(f, 0).toString)).mkString("\t")
       }
       Vector(header) ++ rows
     }
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
index 8e6029140e9..2a812419775 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
@@ -287,7 +287,7 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         }
         // Filter by workflow id within random Ids
         _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          (randomIds :+ workflow1Id).map(id => WorkflowQueryKey.Id.name -> id.toString))) map { case (response, _) =>
+          (randomIds :+ workflow1Id.toString).map(id => WorkflowQueryKey.Id.name -> id))) map { case (response, _) =>
           val resultsById = response.results groupBy {
             _.name
           }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
index 2e6682c2e69..353e33a5019 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
@@ -75,7 +75,7 @@ trait PipelinesApiJobCachingActorHelper extends StandardCachingActorHelper {
       .get(WorkflowOptionKeys.GoogleProject)
       .getOrElse(jesAttributes.project)
 
-    Map(
+    Map[String, Any](
       PipelinesApiMetadataKeys.GoogleProject -> googleProject,
       PipelinesApiMetadataKeys.ExecutionBucket -> initializationData.workflowPaths.executionRootString,
       PipelinesApiMetadataKeys.EndpointUrl -> jesAttributes.endpointUrl,
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
index a0f899a26ff..2da04c65e92 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -141,9 +141,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       }
 
       val optional = Option(output) collectFirst { case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
-      val contentType = output.contentType.getOrElse("")
+      val contentType = output.contentType.map(_.toString).getOrElse("")
 
-      List(kind, output.cloudPath, output.containerPath, optional, contentType)
+      List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
     } mkString("\"", "\"\n|  \"", "\"")
 
     val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
index 1c936e76317..7f10580b700 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
@@ -82,9 +82,9 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
-          "virtualMachine" -> Map(
+          "virtualMachine" -> Map[String, Any](
             "machineType" -> "custom-1-1024",
             "preemptible" -> false
           ).asJava
@@ -117,7 +117,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
           "virtualMachine" -> Map(
             "machineType" -> "custom-1-1024",
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
index aa49c385ba6..fb6c8d425f7 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -146,9 +146,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       }
 
       val optional = Option(output) collectFirst { case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
-      val contentType = output.contentType.getOrElse("")
+      val contentType = output.contentType.map(_.toString).getOrElse("")
 
-      List(kind, output.cloudPath, output.containerPath, optional, contentType)
+      List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
     } mkString("\"", "\"\n|  \"", "\"")
 
     val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
index 37020b0b0d6..6afd75adbd6 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
@@ -81,9 +81,9 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
-          "virtualMachine" -> Map(
+          "virtualMachine" -> Map[String, Any](
             "machineType" -> "custom-1-1024",
             "preemptible" -> false
           ).asJava
@@ -115,7 +115,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
           "virtualMachine" -> Map(
             "machineType" -> "custom-1-1024",
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
index c1f3c18242b..24194807f17 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
@@ -196,7 +196,7 @@ object AstTools {
           val pairType = womType.asInstanceOf[WomPairType]
           WomPair(subElements.head.womValue(pairType.leftType, wdlSyntaxErrorFormatter), subElements(1).womValue(pairType.rightType, wdlSyntaxErrorFormatter))
         } else {
-          throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).getOrElse("No AST").toString})")
+          throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})")
         }
       }
 
@@ -224,7 +224,7 @@ object AstTools {
         case a: Ast if a.getName == "TupleLiteral" => astTupleToValue(a)
         case a: Ast if a.getName == "MapLiteral" && womType.isInstanceOf[WomMapType] => astToMap(a)
         case a: Ast if a.getName == "ObjectLiteral" && womType == WomObjectType => astToObject(a)
-        case _ => throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).getOrElse("No AST").toString})")
+        case _ => throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})")
       }
     }
   }
diff --git a/wom/src/test/scala/wom/types/WomFileTypeSpec.scala b/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
index 217c15964cc..c4a90fadb07 100644
--- a/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
@@ -65,7 +65,7 @@ class WomFileTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     }
   }
 
-  lazy val failedCoercionTests = Table(
+  lazy val failedCoercionTests = Table[String, WomType, Any, String](
     ("description", "womFileType", "value", "expected"),
 
     ("a double to a dir", WomUnlistedDirectoryType, 6.28318,
diff --git a/wom/src/test/scala/wom/types/WomTypeSpec.scala b/wom/src/test/scala/wom/types/WomTypeSpec.scala
index 01c5030806d..4d3c7befeb5 100644
--- a/wom/src/test/scala/wom/types/WomTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomTypeSpec.scala
@@ -10,6 +10,7 @@ import wom.values._
 
 import scala.runtime.ScalaRunTime
 import scala.util.Random
+import scala.util.matching.Regex
 
 
 class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
@@ -32,7 +33,7 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     WomSingleFileType.stableName shouldEqual "File"
   }
 
-  val rawValuesCoercedToType = Table(
+  val rawValuesCoercedToType = Table[Any, WomType, Any, Regex](
     (
       "Raw Value",
       "WomType",
@@ -43,33 +44,33 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       WomString("hello"),
       WomIntegerType,
       classOf[NumberFormatException],
-      "For input string: \"hello\""
+      "For input string: \"hello\"".r
     ),
     (
       WomInteger(0),
       WomBooleanType,
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '0' of type 'Int' to 'Boolean'."""
+      """No coercion defined from wom value\(s\) '0' of type 'Int' to 'Boolean'.""".r
     ),
     (
       0,
       WomBooleanType,
       classOf[IllegalArgumentException],
-      "No coercion defined from '0' of type 'java.lang.Integer' to 'Boolean'."
+      "No coercion defined from '0' of type 'java.lang.Integer' to 'Boolean'.".r
     ),
     (
       Array(0, 1, 2, 3, 4),
       WomBooleanType,
       classOf[IllegalArgumentException],
-      """No coercion defined from 'Array\(0, 1, 2\)' of type 'int\[\]' to 'Boolean'."""
+      """No coercion defined from 'Array\(0, 1, 2\)' of type 'int\[\]' to 'Boolean'.""".r
     ),
     (
       new AnyRef {},
       WomBooleanType,
       classOf[IllegalArgumentException],
-      "No coercion defined from" +
+      ("No coercion defined from" +
         """ 'wom.types.WomTypeSpec\$\$anon\$(.*)@.*' of type""" +
-        """ 'wom.types.WomTypeSpec\$\$anon\$\1' to 'Boolean'."""
+        """ 'wom.types.WomTypeSpec\$\$anon\$\1' to 'Boolean'.""").r
     ),
     (
       WomArray(WomArrayType(WomOptionalType(WomIntegerType)), Seq(
@@ -81,19 +82,19 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       ),
       WomOptionalType(WomMaybeEmptyArrayType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '\[0, 1, 2\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'."""
+      """No coercion defined from wom value\(s\) '\[0, 1, 2\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'.""".r
     ),
     (
       WomArray(WomArrayType(WomOptionalType(WomIntegerType)), Seq(WomOptionalValue.none(WomIntegerType))),
       WomOptionalType(WomMaybeEmptyArrayType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '\[null\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'."""
+      """No coercion defined from wom value\(s\) '\[null\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'.""".r
     ),
     (
       WomOptionalValue.none(WomArrayType(WomIntegerType)),
       WomMaybeEmptyArrayType(WomOptionalType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) 'null' of type 'Array\[Int\]\?' to 'Array\[Int\?\]'."""
+      """No coercion defined from wom value\(s\) 'null' of type 'Array\[Int\]\?' to 'Array\[Int\?\]'.""".r
     )
   )
 

From d602cef3486892155de77ec4cae2298d87bc60c0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 19 Oct 2022 10:37:44 -0400
Subject: [PATCH 100/326] WX-781 Bump jackson-databind in
 /CromwellRefdiskManifestCreator (#6935)

Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.13.2.2 to 2.13.4.1.
- [Release notes](https://github.com/FasterXML/jackson/releases)
- [Commits](https://github.com/FasterXML/jackson/commits)

---
updated-dependencies:
- dependency-name: com.fasterxml.jackson.core:jackson-databind
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 CromwellRefdiskManifestCreator/pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CromwellRefdiskManifestCreator/pom.xml b/CromwellRefdiskManifestCreator/pom.xml
index 987aad421be..829f64b5fd3 100644
--- a/CromwellRefdiskManifestCreator/pom.xml
+++ b/CromwellRefdiskManifestCreator/pom.xml
@@ -48,7 +48,7 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>2.13.2.2</version>
+            <version>2.13.4.1</version>
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>

From 34e358867ac8d9c1c9ac3cb462188f5a256cf2b6 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 21 Oct 2022 17:59:25 -0400
Subject: [PATCH 101/326] WX-808 Host allowlist for HTTP imports (#6938)

* `hostAllowlist` that allows everything

* Refactor

* Stick allow list in HttpResolver

* Better default config

* Allow list tests

* Make it build

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 core/src/main/resources/reference.conf        |  4 ++
 .../languages/util/ImportResolver.scala       | 53 +++++++++++++++----
 .../languages/util/ImportResolverSpec.scala   | 43 +++++++++++++--
 .../NamespaceCacheSpec.scala                  |  2 +-
 4 files changed, 85 insertions(+), 17 deletions(-)

diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index c58eda5bc9f..8034409dbf5 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -439,6 +439,10 @@ engine {
 languages {
   default: WDL
   WDL {
+    http-allow-list {
+      enabled: false
+      allowed-http-hosts: []
+    }
     versions {
       default: "draft-2"
       "draft-2" {
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
index 01c5db23084..f7fd70cfc56 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
@@ -9,12 +9,14 @@ import cats.syntax.either._
 import cats.syntax.validated._
 import com.softwaremill.sttp._
 import com.softwaremill.sttp.asynchttpclient.cats.AsyncHttpClientCatsBackend
+import com.typesafe.config.ConfigFactory
 import common.Checked
 import common.transforms.CheckedAtoB
 import common.validation.ErrorOr._
 import common.validation.Checked._
 import common.validation.Validation._
 import cromwell.core.path.{DefaultPathBuilder, Path}
+import net.ceedubs.ficus.Ficus._
 
 import java.nio.file.{Path => NioPath}
 import java.security.MessageDigest
@@ -157,7 +159,9 @@ object ImportResolver {
     }
   }
 
-  case class HttpResolver(relativeTo: Option[String] = None, headers: Map[String, String] = Map.empty) extends ImportResolver {
+  case class HttpResolver(relativeTo: Option[String],
+                          headers: Map[String, String],
+                          hostAllowlist: Option[List[String]]) extends ImportResolver {
     import HttpResolver._
 
     override def name: String = relativeTo match {
@@ -169,7 +173,7 @@ object ImportResolver {
     def newResolverList(newRoot: String): List[ImportResolver] = {
       val rootWithoutFilename = newRoot.split('/').init.mkString("", "/", "/")
       List(
-        HttpResolver(relativeTo = Some(canonicalize(rootWithoutFilename)), headers)
+        HttpResolver(relativeTo = Some(canonicalize(rootWithoutFilename)), headers, hostAllowlist)
       )
     }
 
@@ -183,18 +187,20 @@ object ImportResolver {
         else "Relative path".invalidNelCheck
     }
 
+    def isAllowed(uri: Uri): Boolean = hostAllowlist match {
+      case Some(hosts) => hosts.contains(uri.host)
+      case None => true
+    }
+
     override def innerResolver(str: String, currentResolvers: List[ImportResolver]): Checked[ResolvedImportBundle] = {
-      pathToLookup(str) flatMap { toLookup =>
+      pathToLookup(str) flatMap { toLookup: WorkflowSource =>
         (Try {
-          implicit val sttpBackend = HttpResolver.sttpBackend()
-          val responseIO: IO[Response[String]] = sttp.get(uri"$toLookup").headers(headers).send()
-
-          // temporary situation to get functionality working before
-          // starting in on async-ifying the entire WdlNamespace flow
-          val result: Checked[String] = Await.result(responseIO.unsafeToFuture(), 15.seconds).body.leftMap { e => NonEmptyList(e.toString.trim, List.empty) }
+          val uri: Uri = uri"$toLookup"
 
-          result map {
-            ResolvedImportBundle(_, newResolverList(toLookup), ResolvedImportRecord(toLookup))
+          if (isAllowed(uri)) {
+            getUri(toLookup)
+          } else {
+            s"Disallowed domain in URI. ${uri.toString()}".invalidNelCheck
           }
         } match {
           case Success(result) => result
@@ -203,6 +209,19 @@ object ImportResolver {
       }
     }
 
+    private def getUri(toLookup: WorkflowSource): Either[NonEmptyList[WorkflowSource], ResolvedImportBundle] = {
+      implicit val sttpBackend = HttpResolver.sttpBackend()
+      val responseIO: IO[Response[WorkflowSource]] = sttp.get(uri"$toLookup").headers(headers).send()
+
+      // temporary situation to get functionality working before
+      // starting in on async-ifying the entire WdlNamespace flow
+      val result: Checked[WorkflowSource] = Await.result(responseIO.unsafeToFuture(), 15.seconds).body.leftMap { e => NonEmptyList(e.toString.trim, List.empty) }
+
+      result map {
+        ResolvedImportBundle(_, newResolverList(toLookup), ResolvedImportRecord(toLookup))
+      }
+    }
+
     override def cleanupIfNecessary(): ErrorOr[Unit] = ().validNel
 
     override def hashKey: ErrorOr[String] = relativeTo.toString.md5Sum.validNel
@@ -213,6 +232,18 @@ object ImportResolver {
     import common.util.IntrospectableLazy
     import common.util.IntrospectableLazy._
 
+    def apply(relativeTo: Option[String] = None,
+              headers: Map[String, String] = Map.empty): HttpResolver = {
+      val config = ConfigFactory.load().getConfig("languages.WDL.http-allow-list")
+      val allowListEnabled = config.as[Option[Boolean]]("enabled").getOrElse(false)
+      val allowList: Option[List[String]] =
+        if (allowListEnabled)
+          config.as[Option[List[String]]]("allowed-http-hosts")
+        else None
+
+      new HttpResolver(relativeTo, headers, allowList)
+    }
+
     val sttpBackend: IntrospectableLazy[SttpBackend[IO, Nothing]] = lazily {
       // 2.13 Beginning with sttp 1.6.x a `ContextShift` parameter is now required to construct an
       // `AsyncHttpClientCatsBackend`. There may be a more appropriate choice for backing this than the global
diff --git a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
index 26249b02da1..813a688a573 100644
--- a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
+++ b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
@@ -1,7 +1,8 @@
 package cromwell.languages.util
 
-import java.nio.file.{Files, Paths}
+import com.softwaremill.sttp._
 
+import java.nio.file.{Files, Paths}
 import common.assertion.CromwellTimeoutSpec
 import common.assertion.ErrorOrAssertions._
 import cromwell.core.WorkflowId
@@ -41,13 +42,13 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   it should "resolve a path from no initial root" in {
-    val resolver = HttpResolver()
+    val resolver = HttpResolver(None, Map.empty, None)
     val toResolve = resolver.pathToLookup("http://abc.com:8000/blah1/blah2.wdl")
     toResolve shouldBeValid "http://abc.com:8000/blah1/blah2.wdl"
   }
 
   it should "resolve a path and store the import in ResolvedImportRecord" in {
-    val resolver = HttpResolver()
+    val resolver = HttpResolver(None, Map.empty, None)
     val importUri = "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.wdl"
     val resolvedBundle = resolver.innerResolver(importUri, List(resolver))
 
@@ -57,10 +58,42 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     }
   }
 
+  behavior of "HttpResolver with allowList"
+
+  val allowList = Option(List("my.favorite.wdls.com", "anotherwdlsite.org"))
+  val pathEnd = "bob/loblaw/blah/blah.wdl"
+
+  it should "allow any import when there is no allow list" in {
+    val resolver = HttpResolver(None, Map.empty, None)
+    resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"http://some-garbage.whatever.eu/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"localhost:8080/my/secrets") shouldBe true
+  }
+
+  it should "allow any import that's on the allow list" in {
+    val resolver = HttpResolver(None, Map.empty, allowList)
+    resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"http://anotherwdlsite.org/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"https://yetanotherwdlsite.org/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://FOO.my.favorite.wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"localhost:8080/my/secrets") shouldBe false
+  }
+
+  it should "allow nothing with an empty allow list" in {
+    val resolver = HttpResolver(None, Map.empty, Option(List.empty))
+    resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"http://anotherwdlsite.org/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://yetanotherwdlsite.org/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://FOO.my.favorite.wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"localhost:8080/my/secrets") shouldBe false
+  }
+
   behavior of "HttpResolver with a 'relativeTo' value"
 
-  val relativeHttpResolver = HttpResolver(relativeTo = Some("http://abc.com:8000/blah1/blah2/"))
-  val relativeToGithubHttpResolver = HttpResolver(relativeTo = Some(relativeToGithubRoot))
+  val relativeHttpResolver = HttpResolver(relativeTo = Some("http://abc.com:8000/blah1/blah2/"), Map.empty, None)
+  val relativeToGithubHttpResolver = HttpResolver(relativeTo = Some(relativeToGithubRoot), Map.empty, None)
 
   it should "resolve an absolute path from a different initial root" in {
     val pathToLookup = relativeHttpResolver.pathToLookup("http://def.org:8080/blah3.wdl")
diff --git a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
index df87f2fa644..b96cfa5c2f6 100644
--- a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
+++ b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
@@ -61,7 +61,7 @@ class NamespaceCacheSpec extends AnyFlatSpec with CromwellTimeoutSpec with Befor
     )
 
     var lookupCount = 0
-    val countingResolver = new HttpResolver() {
+    val countingResolver = new HttpResolver(None, Map.empty, None) {
       override def pathToLookup(str: String): Checked[String] = {
         lookupCount = lookupCount + 1
         super.pathToLookup(str)

From f64b2c45c38426e495a46d6630348fb8dec56e18 Mon Sep 17 00:00:00 2001
From: Christian Freitas <christian.j.freitas@gmail.com>
Date: Mon, 24 Oct 2022 14:09:56 -0400
Subject: [PATCH 102/326] Update commons text to 1.10.0 (#6937)

---
 project/Dependencies.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 0a0dee70cfa..8906e010531 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -30,7 +30,7 @@ object Dependencies {
   private val commonsLang3V = "3.12.0"
   private val commonsMathV = "3.6.1"
   private val commonNetV = "3.8.0" // via: https://commons.apache.org/proper/commons-net/
-  private val commonsTextV = "1.9"
+  private val commonsTextV = "1.10.0"
   private val configsV = "0.6.1"
   private val delightRhinoSandboxV = "0.0.15"
   private val diffsonSprayJsonV = "4.1.1"

From c775ddd94d32be35911b7faa345322fd67481d40 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 28 Oct 2022 09:32:35 -0400
Subject: [PATCH 103/326] WX-751 Token refresh signal for monitoring (#6939)

* Log messages

* `DEBUG` -> `INFO`
---
 .../cromwell/filesystems/blob/BlobFileSystemManager.scala | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index a3e6f33572a..3ebce4db878 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -17,6 +17,7 @@ import java.time.{Duration, Instant, OffsetDateTime}
 import scala.jdk.CollectionConverters._
 import scala.util.{Failure, Success, Try}
 import com.azure.resourcemanager.storage.models.StorageAccountKey
+import com.typesafe.scalalogging.LazyLogging
 
 case class FileSystemAPI() {
   def getFileSystem(uri: URI): Try[FileSystem] = Try(FileSystems.getFileSystem(uri))
@@ -44,7 +45,7 @@ case class BlobFileSystemManager(
     expiryBufferMinutes: Long,
     blobTokenGenerator: BlobTokenGenerator,
     fileSystemAPI: FileSystemAPI = FileSystemAPI(),
-    private val initialExpiration: Option[Instant] = None) {
+    private val initialExpiration: Option[Instant] = None) extends LazyLogging {
   private var expiry: Option[Instant] = initialExpiration
   val buffer: Duration = Duration.of(expiryBufferMinutes, ChronoUnit.MINUTES)
 
@@ -57,10 +58,13 @@ case class BlobFileSystemManager(
       shouldReopenFilesystem match {
         case false => fileSystemAPI.getFileSystem(uri).recoverWith {
           // If no filesystem already exists, this will create a new connection, with the provided configs
-          case _: FileSystemNotFoundException => blobTokenGenerator.generateAccessToken.flatMap(generateFilesystem(uri, container, _))
+          case _: FileSystemNotFoundException =>
+            logger.info(s"Creating new blob filesystem for URI $uri")
+            blobTokenGenerator.generateAccessToken.flatMap(generateFilesystem(uri, container, _))
         }
         // If the token has expired, OR there is no token record, try to close the FS and regenerate
         case true =>
+          logger.info(s"Closing & regenerating token for existing blob filesystem at URI $uri")
           fileSystemAPI.closeFileSystem(uri)
           blobTokenGenerator.generateAccessToken.flatMap(generateFilesystem(uri, container, _))
       }

From 8485284a52adcf9163b5fd2a60e95bd0e1ce012e Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Tue, 1 Nov 2022 10:14:30 -0400
Subject: [PATCH 104/326] WX-744 Optionally rewrite blob paths to appear as
 local paths (#6941)

* Modify blob paths for TES

* Make blob transformation configurable

* Update supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Apply PR feedback in second place

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 build.sbt                                     |  1 +
 .../TesAsyncBackendJobExecutionActor.scala    | 10 +++++++-
 .../cromwell/backend/impl/tes/TesTask.scala   | 22 ++++++++++++++---
 .../backend/impl/tes/TesTaskSpec.scala        | 24 +++++++++++++++++++
 4 files changed, 53 insertions(+), 4 deletions(-)

diff --git a/build.sbt b/build.sbt
index 3b255d0e0e5..948d18039ab 100644
--- a/build.sbt
+++ b/build.sbt
@@ -245,6 +245,7 @@ lazy val tesBackend = (project in backendRoot / "tes")
   .dependsOn(sfsBackend)
   .dependsOn(ftpFileSystem)
   .dependsOn(drsFileSystem)
+  .dependsOn(azureBlobFileSystem)
   .dependsOn(backend % "test->test")
   .dependsOn(common % "test->test")
 
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 1fe5b743465..63b43ddbcf5 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -80,6 +80,14 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
 
   private val tesEndpoint = workflowDescriptor.workflowOptions.getOrElse("endpoint", tesConfiguration.endpointURL)
 
+  // Temporary support for configuring the format we use to send BlobPaths to TES.
+  // Added 10/2022 as a workaround for the CromwellOnAzure TES server expecting
+  // blob containers to be mounted via blobfuse rather than addressed natively.
+  private val transformBlobToLocalPaths: Boolean =
+    configurationDescriptor.backendConfig
+      .getAs[Boolean]("transform-blob-to-local-path")
+      .getOrElse(false)
+
   override lazy val jobTag: String = jobDescriptor.key.tag
 
   private val outputMode = validate {
@@ -148,7 +156,7 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
         mode)
     })
 
-    tesTask.map(TesTask.makeTask)
+    tesTask.map(TesTask.makeTask(_, transformBlobToLocalPaths))
   }
 
   def writeScriptFile(): Future[Unit] = {
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index 52fdd7c3fce..719ad36942b 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -258,14 +258,16 @@ object TesTask {
     )
   }
 
-  def makeTask(tesTask: TesTask): Task = {
+  def makeTask(tesTask: TesTask, transformBlobToLocalPath: Boolean = false): Task = {
+    val inputs = if (transformBlobToLocalPath) transformInputs(tesTask.inputs) else tesTask.inputs
+    val outputs = if (transformBlobToLocalPath) transformOutputs(tesTask.outputs) else tesTask.outputs
     Task(
       id = None,
       state = None,
       name = Option(tesTask.name),
       description = Option(tesTask.description),
-      inputs = Option(tesTask.inputs),
-      outputs = Option(tesTask.outputs),
+      inputs = Option(inputs),
+      outputs = Option(outputs),
       resources = Option(tesTask.resources),
       executors = tesTask.executors,
       volumes = None,
@@ -273,6 +275,20 @@ object TesTask {
       logs = None
     )
   }
+
+  def transformInputs(inputs: Seq[Input]): Seq[Input] = inputs.map(i =>
+    i.copy(url=i.url.map(transformBlobString))
+  )
+
+  def transformOutputs(outputs: Seq[Output]): Seq[Output] = outputs.map(i =>
+    i.copy(url=i.url.map(transformBlobString))
+  )
+
+  val blobSegment = ".blob.core.windows.net"
+  def transformBlobString(s: String): String = if (s.contains(blobSegment)) {
+    s.replaceFirst("https:/", "").replaceFirst(blobSegment, "")
+  } else s
+
 }
 
 // Field requirements in classes below based off GA4GH schema
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index 0e8440f2a1d..c2ee68e0068 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -88,4 +88,28 @@ class TesTaskSpec
 
     task.tags shouldBe Option(Map("foo" -> "bar"))
   }
+
+  it should "apply the correct transformation to a blob path" in {
+    val orig = "https://coaexternalstorage.blob.core.windows.net/cromwell/mydir/myfile.txt"
+    TesTask.transformBlobString(orig) shouldBe "/coaexternalstorage/cromwell/mydir/myfile.txt"
+  }
+
+  it should "not transform a non-blob path" in {
+    val orig = "https://some-bogus-url.test/cromwell/mydir/myfile.txt"
+    TesTask.transformBlobString(orig) shouldBe orig
+  }
+
+  it should "transform inputs" in {
+    val baseInput = Input(
+      Option("name"),
+      Option("descr"),
+      Option("https://coaexternalstorage.blob.core.windows.net/cromwell/mydir/myfile.txt"),
+      "path",
+      Option("type"),
+      Option("content"),
+    )
+    val inputs = Option(Seq(baseInput))
+    val outcome = inputs.map(TesTask.transformInputs)
+    outcome.get.head.url.get shouldBe "/coaexternalstorage/cromwell/mydir/myfile.txt"
+  }
 }

From 269089cb8e51298f65c7ed875d749f40b640be32 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Thu, 3 Nov 2022 16:12:24 -0400
Subject: [PATCH 105/326] Update changelog for wdl http allow list (#6944)

---
 CHANGELOG.md | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1e44012027c..1bba52ebded 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,6 +36,24 @@ failures observed when attempting to localize a large number of DRS files.
 
 Updates to dependencies to fix security vulnerabilities.
 
+### Allow list for HTTP WDL resolution
+
+Administrators can now configure Cromwell with an allow list that limits the domains from which WDLs can be resolved and imported. 
+Default behavior is unchanged (Cromwell attempts to resolve WDL files from any URI). Example configuration:
+```
+languages {
+  WDL {
+    http-allow-list {
+      enabled: true
+      allowed-http-hosts: [
+        "my.wdl.repo.org",
+        "raw.githubusercontent.com"
+      ]
+    }
+  }
+}
+```
+
 
 ## 84 Release Notes
 

From 4a6ad8e13a74ba278f05c99bf5fef27e064805d8 Mon Sep 17 00:00:00 2001
From: Katrina P <68349264+kpierre13@users.noreply.github.com>
Date: Mon, 7 Nov 2022 10:55:22 -0500
Subject: [PATCH 106/326] WM-1491 Fixing Cromwell-client (#6943)

* More updated client for use in cbas

* Removing excess code
---
 docs/api/RESTAPI.md                           | 20 +++++------
 .../src/main/resources/swagger/cromwell.yaml  | 35 ++++++++-----------
 2 files changed, 24 insertions(+), 31 deletions(-)

diff --git a/docs/api/RESTAPI.md b/docs/api/RESTAPI.md
index f1713bc831a..9eaedd4a3a5 100644
--- a/docs/api/RESTAPI.md
+++ b/docs/api/RESTAPI.md
@@ -1,5 +1,5 @@
 <!--
-This file was generated by `sbt generateRestApiDocs` on Thu, 4 Aug 2022 13:39:32 -0400
+This file was generated by `sbt generateRestApiDocs` on Wed, 2 Nov 2022 12:56:53 -0400
 
 !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
 
@@ -909,9 +909,9 @@ Call level metadata
 |**backendLogs**  <br>*optional*|Paths to backend specific logs for this call|object|
 |**backendStatus**  <br>*optional*|Status in backend-specific terms.  Currently this will only be defined for the JES backend.|string|
 |**end**  <br>*optional*|End datetime of the call execution in ISO8601 format with milliseconds|string (date-time)|
-|**executionStatus**  <br>*required*|Status in Cromwell execution terms.|string|
-|**failures**  <br>*optional*||[FailureMessage](#failuremessage)|
-|**inputs**  <br>*required*|Mapping of input fully qualified names to stringified values|object|
+|**executionStatus**  <br>*optional*|Status in Cromwell execution terms.|string|
+|**failures**  <br>*optional*||< [FailureMessage](#failuremessage) > array|
+|**inputs**  <br>*optional*|Mapping of input fully qualified names to stringified values|object|
 |**jobId**  <br>*optional*|Backend-specific job ID|string|
 |**returnCode**  <br>*optional*|Call execution return code|integer|
 |**start**  <br>*optional*|Start datetime of the call execution in ISO8601 format with milliseconds|string (date-time)|
@@ -956,8 +956,8 @@ Failure messages
 
 |Name|Description|Schema|
 |---|---|---|
-|**failure**  <br>*required*|The failure message|string|
-|**timestamp**  <br>*required*|The time at which this failure occurred|string (date-time)|
+|**causedBy**  <br>*optional*||< [FailureMessage](#failuremessage) > array|
+|**message**  <br>*optional*|The failure message|string|
 
 
 <a name="labelsresponse"></a>
@@ -1275,13 +1275,13 @@ Workflow and call level metadata
 |---|---|---|
 |**calls**  <br>*optional*||[CallMetadata](#callmetadata)|
 |**end**  <br>*optional*|End datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
-|**failures**  <br>*optional*||[FailureMessage](#failuremessage)|
-|**id**  <br>*required*|The identifier of the workflow|string|
+|**failures**  <br>*optional*||< [FailureMessage](#failuremessage) > array|
+|**id**  <br>*optional*|The identifier of the workflow|string|
 |**inputs**  <br>*optional*|Map of input keys to input values|object|
 |**outputs**  <br>*optional*|Map of output keys to output values|object|
 |**start**  <br>*optional*|Start datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
-|**status**  <br>*required*|The status of the workflow|string|
-|**submission**  <br>*required*|Submission datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
+|**status**  <br>*optional*|The status of the workflow|string|
+|**submission**  <br>*optional*|Submission datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
 
 
 <a name="workflowqueryparameter"></a>
diff --git a/engine/src/main/resources/swagger/cromwell.yaml b/engine/src/main/resources/swagger/cromwell.yaml
index e992f4c5e15..28dd9f6466b 100644
--- a/engine/src/main/resources/swagger/cromwell.yaml
+++ b/engine/src/main/resources/swagger/cromwell.yaml
@@ -607,7 +607,7 @@ paths:
         '400':
           $ref: '#/responses/BadRequest'
         '404':
-           description: No matching cache entry. Cromwell versions prior to 28 will not have recorded information necessary for this endpoint and thus will also appear to not exist.
+          description: No matching cache entry. Cromwell versions prior to 28 will not have recorded information necessary for this endpoint and thus will also appear to not exist.
         '500':
           $ref: '#/responses/ServerError'
   '/api/workflows/{version}/backends':
@@ -1035,10 +1035,6 @@ definitions:
         example: Submitted
   WorkflowMetadataResponse:
     description: Workflow and call level metadata
-    required:
-      - id
-      - status
-      - submission
     properties:
       id:
         type: string
@@ -1067,12 +1063,11 @@ definitions:
       calls:
         $ref: '#/definitions/CallMetadata'
       failures:
-        $ref: '#/definitions/FailureMessage'
+        type: array
+        items:
+          $ref: '#/definitions/FailureMessage'
   CallMetadata:
     description: Call level metadata
-    required:
-      - inputs
-      - executionStatus
     properties:
       inputs:
         type: object
@@ -1098,7 +1093,9 @@ definitions:
         type: string
         description: Backend-specific job ID
       failures:
-        $ref: '#/definitions/FailureMessage'
+        type: array
+        items:
+          $ref: '#/definitions/FailureMessage'
       returnCode:
         type: integer
         description: Call execution return code
@@ -1113,17 +1110,14 @@ definitions:
         description: Paths to backend specific logs for this call
   FailureMessage:
     description: Failure messages
-    required:
-      - failure
-      - timestamp
     properties:
-      failure:
+      message:
         type: string
         description: The failure message
-      timestamp:
-        type: string
-        format: date-time
-        description: The time at which this failure occurred
+      causedBy:
+        type: array
+        items:
+          $ref: '#/definitions/FailureMessage'
   WorkflowDescription:
     required:
       - valid
@@ -1212,9 +1206,9 @@ definitions:
               typeName: Pair
               pairTypes:
                 - leftType:
-                  -  typeName: Int
+                    -  typeName: Int
                 - rightType:
-                  -  typeName: String
+                    -  typeName: String
             optional: false
             default: null
             typeDisplayName: Pair[Int, String]
@@ -1959,4 +1953,3 @@ definitions:
           are also allowed. The version should be changed whenever the service
           is updated.
         example: 1.0.0
-

From d475d5a5b1d97d04f36552eb3c5ef09560831989 Mon Sep 17 00:00:00 2001
From: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Date: Mon, 7 Nov 2022 14:01:37 -0500
Subject: [PATCH 107/326] Fix client build script (#6945)

---
 scripts/gen_java_client.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/gen_java_client.sh b/scripts/gen_java_client.sh
index 409af51a83f..59642098b1d 100755
--- a/scripts/gen_java_client.sh
+++ b/scripts/gen_java_client.sh
@@ -4,6 +4,7 @@ BASE_PACKAGE="cromwell.client"
 
 ORIGINAL_API_YAML=engine/src/main/resources/swagger/cromwell.yaml
 API_YAML=codegen_java/cromwell.nofile.yaml
+OPENAPI_DOCKER="openapitools/openapi-generator-cli@sha256:ddd1b01cbe8f494c6612c548e91f983938164ab713a4d18d099a1fc4a77c651d"
 
 # Cromwell doesn't specify the OAuth configuration in its swagger, and
 # without it the client doesn't support authentication.
@@ -37,7 +38,7 @@ cat $ORIGINAL_API_YAML | sed s/type:\ file/type:\ string/g >> $API_YAML
 # generator's build.sbt with ours.
 # 1. Hide our build.sbt
 mv codegen_java/build.sbt codegen_java/build.sbt.bak
-docker run --rm -v ${PWD}:/local openapitools/openapi-generator-cli generate \
+docker run --rm -v ${PWD}:/local ${OPENAPI_DOCKER} generate \
   -i /local/$API_YAML \
   -g java \
   -o /local/codegen_java \

From 432e72f26423bdff892a16e6301f03a7aacce476 Mon Sep 17 00:00:00 2001
From: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Date: Thu, 17 Nov 2022 08:03:09 -0500
Subject: [PATCH 108/326] WX-837: Remove CWL references from documentation
 (#6949)

* wx-837 removed cwl references in markdown doc files

* wx-837 removed cwlParsingOverview.md, updated mkdocs.yml

* wx-837 updated cromwell.yaml, generated new RESTAPI file
---
 docs/LanguageSupport.md                       |  7 --
 docs/RuntimeAttributes.md                     | 15 -----
 docs/WOMtool.md                               |  4 +-
 docs/api/RESTAPI.md                           | 25 ++++---
 docs/cromwell_features/HogFactors.md          |  2 +-
 docs/developers/CwlParsing.md                 | 66 -------------------
 .../workflowParsing/cwlParsingOverview.md     |  1 -
 .../workflowParsing/wdlParsingOverview.md     |  4 +-
 docs/filesystems/Filesystems.md               |  5 --
 docs/tutorials/Containers.md                  | 22 +------
 docs/wf_options/Overview.md                   |  4 +-
 .../src/main/resources/swagger/cromwell.yaml  | 25 +++----
 mkdocs.yml                                    |  2 -
 13 files changed, 29 insertions(+), 153 deletions(-)
 delete mode 100644 docs/developers/CwlParsing.md
 delete mode 100644 docs/developers/bitesize/workflowParsing/cwlParsingOverview.md

diff --git a/docs/LanguageSupport.md b/docs/LanguageSupport.md
index 74f5ab238f6..ff7a64164f9 100644
--- a/docs/LanguageSupport.md
+++ b/docs/LanguageSupport.md
@@ -22,13 +22,6 @@ Cromwell also supports WDL version 1.0.
 
 As well as the changes to the WDL spec between draft-2 and 1.0, Cromwell also supports nested scatters and the [localization_optional](optimizations/FileLocalization.md) optimization in WDL 1.0.  
 
-
-### CWL 1.0
-
-Cromwell provides support for Common Workflow Language (CWL), beginning with the core spec, and most heavily used requirements.
-If you spot a CWL feature that Cromwell doesn't support, please notify us using an issue on our github page!
-
-
 ## Future Language Support
 
 ### WDL 'development'
diff --git a/docs/RuntimeAttributes.md b/docs/RuntimeAttributes.md
index 70485339b3e..ffac8a705d5 100644
--- a/docs/RuntimeAttributes.md
+++ b/docs/RuntimeAttributes.md
@@ -153,15 +153,6 @@ runtime {
 }
 ```
 
-
-#### CWL
-
-CWL splits the `cpu` requirement into `cpuMin` and `cpuMax`. If one of them is provided, `cpu` will inherit this value. If both of them are provided, `cpu` will take the value of `cpuMin`.
-If none is provided, `cpu` will default to its default value.
-
-Note: If provided, `cpuMin` and/or `cpuMax` will be available to the [HPC runtime attribute configuration](/tutorials/HPCIntro.md#specifying-the-runtime-attributes-for-your-hpc-tasks).
-
-
 ### `memory`
 *Default: "2G"*
 
@@ -180,12 +171,6 @@ runtime {
 
 Within the SFS backend, you can additionally specify `memory_mb` or `memory_gb` as runtime attributes within the configuration. More information can be found [here](https://cromwell.readthedocs.io/en/stable/tutorials/HPCIntro/#specifying-the-runtime-attributes-for-your-hpc-tasks).
 
-#### CWL
-
-CWL splits the `memory` requirement into `ramMin` and `ramMax`. If one of them is provided, `memory` will inherit this value. If both of them are provided, `memory` will take the value of `ramMin`. If none is provided, `memory` will default to its default value.
-
-Note: If provided, `ramMin` and/or `ramMax` will be available to the [HPC runtime attribute configuration](/tutorials/HPCIntro.md#specifying-the-runtime-attributes-for-your-hpc-tasks).
-
 
 ### `disks`
 
diff --git a/docs/WOMtool.md b/docs/WOMtool.md
index fc8c16c7897..5b88e5a21a6 100644
--- a/docs/WOMtool.md
+++ b/docs/WOMtool.md
@@ -59,9 +59,9 @@ graph <WDL file>
   otherwise. Note that graph currently DOES NOT WORK on
   version 1.0 workflows.
 
-womgraph <WDL or CWL file> [ancillary files]
+womgraph <WDL file> [ancillary files]
 
-  Reads a WDL or CWL file from the first argument and
+  Reads a WDL file from the first argument and
   converts it to a WOM representation then prints out a graph
   of the WOM produced.
   Any imported files can be supplied as subsequent arguments.
diff --git a/docs/api/RESTAPI.md b/docs/api/RESTAPI.md
index 9eaedd4a3a5..42eb3969d5d 100644
--- a/docs/api/RESTAPI.md
+++ b/docs/api/RESTAPI.md
@@ -1,5 +1,5 @@
 <!--
-This file was generated by `sbt generateRestApiDocs` on Wed, 2 Nov 2022 12:56:53 -0400
+This file was generated by `sbt generateRestApiDocs` on Tue, 15 Nov 2022 14:26:23 -0500
 
 !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
 
@@ -48,7 +48,7 @@ The `workflow_url` is either an absolute URL to a workflow file that is accessib
 
 The `workflow_params` JSON object specifies input parameters, such as input files.  The exact format of the JSON object depends on the conventions of the workflow language being used.  Input files should either be absolute URLs, or relative URLs corresponding to files uploaded using `workflow_attachment`.  The WES endpoint must understand and be able to access URLs supplied in the input.  This is implementation specific.
 
-The `workflow_type` is the type of workflow language and must be "CWL" or "WDL" currently (or another alternative  supported by this WES instance).
+The `workflow_type` is the type of workflow language and must be "WDL" currently (or another alternative supported by this WES instance).
 
 The `workflow_type_version` is the version of the workflow language submitted and must be one supported by this WES instance.
 
@@ -264,8 +264,8 @@ POST /api/womtool/{version}/describe
 |**Path**|**version**  <br>*required*|Cromwell API Version|string|`"v1"`|
 |**FormData**|**workflowInputs**  <br>*optional*|JSON or YAML file containing the inputs as an object.|file||
 |**FormData**|**workflowSource**  <br>*optional*|The workflow source file to submit for execution. Either workflow source or workflow url is required.|file||
-|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.|enum (WDL, CWL)||
-|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.|enum (draft-2, 1.0, v1.0)||
+|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL.|enum (WDL)||
+|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.|enum (draft-2, 1.0)||
 |**FormData**|**workflowUrl**  <br>*optional*|URL which points to the workflow. Either workflow source or workflow url is required.|string||
 
 
@@ -312,10 +312,9 @@ Submits a workflow to Cromwell. Note that this endpoint can accept an unlimited
 |**FormData**|**workflowInputs_5**  <br>*optional*|A fifth JSON or YAML file containing inputs.|file||
 |**FormData**|**workflowOnHold**  <br>*optional*|Put workflow on hold upon submission. By default, it is taken as false.|boolean||
 |**FormData**|**workflowOptions**  <br>*optional*|JSON file containing configuration options for the execution of this workflow.|file||
-|**FormData**|**workflowRoot**  <br>*optional*|The root object to be run. Only necessary for CWL submissions containing multiple objects (in an array).|string||
 |**FormData**|**workflowSource**  <br>*optional*|The workflow source file to submit for execution. Either workflow source or workflow url is required.|file||
-|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.|enum (WDL, CWL)||
-|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.|enum (draft-2, 1.0, v1.0)||
+|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL.|enum (WDL)||
+|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.|enum (draft-2, 1.0)||
 |**FormData**|**workflowUrl**  <br>*optional*|URL which points to the workflow. Either workflow source or workflow url is required.|string||
 
 
@@ -391,8 +390,8 @@ In instances where you want to run the same workflow multiple times with varying
 |**FormData**|**workflowOnHold**  <br>*optional*|Put workflow on hold upon submission. By default, it is taken as false.|boolean||
 |**FormData**|**workflowOptions**  <br>*optional*|JSON file containing configuration options for the execution of this workflow.|file||
 |**FormData**|**workflowSource**  <br>*optional*|The workflow source file to submit for execution. Either workflow source or workflow url is required.|file||
-|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.|enum (WDL, CWL)||
-|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.|enum (draft-2, 1.0, v1.0)||
+|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL.|enum (WDL)||
+|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.|enum (draft-2, 1.0)||
 |**FormData**|**workflowUrl**  <br>*optional*|URL which points to the workflow. Either workflow source or workflow url is required.|string||
 
 
@@ -933,9 +932,9 @@ A message that allows one to describe default parameters for a workflow engine.
 
 <a name="descriptortype"></a>
 ### DescriptorType
-One from a list of descriptor type strings (e.g. CWL, WDL). Note that these files can also include associated Docker/container files and test parameters that further describe a version of a tool
+One from a list of descriptor type strings (e.g. WDL). Note that these files can also include associated Docker/container files and test parameters that further describe a version of a tool
 
-*Type* : enum (CWL, WDL)
+*Type* : enum (WDL)
 
 
 <a name="descriptortypeandversion"></a>
@@ -1038,9 +1037,9 @@ To execute a workflow, send a run request including all the details needed to be
 |**tags**  <br>*optional*||< string, string > map|
 |**workflow_engine_parameters**  <br>*optional*||< string, string > map|
 |**workflow_params**  <br>*optional*|REQUIRED The workflow run parameterizations (JSON encoded), including input and output file locations|object|
-|**workflow_type**  <br>*optional*|REQUIRED The workflow descriptor type, must be "CWL" or "WDL" currently (or another alternative supported by this WES instance)|string|
+|**workflow_type**  <br>*optional*|REQUIRED The workflow descriptor type, must be "WDL" currently (or another alternative supported by this WES instance)|string|
 |**workflow_type_version**  <br>*optional*|REQUIRED The workflow descriptor type version, must be one supported by this WES instance|string|
-|**workflow_url**  <br>*optional*|REQUIRED The workflow CWL or WDL document. When `workflow_attachments` is used to attach files, the `workflow_url` may be a relative path to one of the attachments.|string|
+|**workflow_url**  <br>*optional*|REQUIRED The workflow WDL document. When `workflow_attachments` is used to attach files, the `workflow_url` may be a relative path to one of the attachments.|string|
 
 
 <a name="runstatus"></a>
diff --git a/docs/cromwell_features/HogFactors.md b/docs/cromwell_features/HogFactors.md
index c2d5f1b968f..aed82d5ebc9 100644
--- a/docs/cromwell_features/HogFactors.md
+++ b/docs/cromwell_features/HogFactors.md
@@ -2,7 +2,7 @@
 
 ## Introduction
 
-Cromwell has only a finite amount of resources at its disposal. WDL and CWL workflows allow scattered tasks to be
+Cromwell has only a finite amount of resources at its disposal. WDL workflows allow scattered tasks to be
 run a huge number of times with very simple syntax.
 This makes it easy for a very small number of workflows to hog all of the resources of Cromwell, forcing all other 
 workflows (even a simple 'hello_world') to wait in line behind them. 
diff --git a/docs/developers/CwlParsing.md b/docs/developers/CwlParsing.md
deleted file mode 100644
index c3982f784e5..00000000000
--- a/docs/developers/CwlParsing.md
+++ /dev/null
@@ -1,66 +0,0 @@
-# How CWL is Parsed
-
-The ultimate entry point to parsing CWL is in `CwlV1_0LanguageFactory.validateNamespace`. 
-
-Within that method, the process of parsing CWL can be thought of as performing these 4 steps:
-
-1. Produce a canonical one-file representation of the CWL as a JSON object in memory
-    - For the entrypoint into this process, see `CwlPreprocessor.preProcessCwl`
-2. Use Circe to turn that representation into scala case classes
-3. Convert the case classes into an appropriate WOM representations
-4. Mix in inputs to produce a WOM Executable.
-
-## Getting a canonical flat file
-
-### From a source file and dependencies zip:
-
-Note that the recursive implementation of `SALAD and flatten` in code can be found in: `CwlPreprocessor.preProcessCwl`.
-
-The process looks like:
-
-1. Write the workflow source file to disk
-2. Make sure the dependencies are unzipped next to it
-3. `SALAD and flatten` (see `CwlCanonicalizer.getCanonicalCwl`):
-    - Run `cwltool --print-pre` against the source file to get a canonicalize JSON representation (aka `SALAD`) it.
-        - NB: `cwltool --print-pre` must be able to resolve dependencies but it does not flatten them into the file.
-    - Recursively `SALAD and flatten` any references into their own JSON representations of the contents.
-    - Replace every reference in-place with the expanded JSON content.
-4. At the end of this process we will have:
-    - A single flat JSON 
-    - Every imported step expanded to contain an in-line description
-    - No more external references - everything required is provided in-line
-
-### From a workflow URL:
-
-The process looks similar to "source file and dependencies" except we never write anything locally:
-
-1. `SALAD and flatten`:
-    - Run `cwltool --print-pre` against the URL to get a canonicalize JSON representation (aka `SALAD`) it.
-        - NB: `cwltool --print-pre` must be able to resolve dependencies but it does not flatten them into the file.
-    - Recursively `SALAD and flatten` any references into their own JSON representations of the contents.
-    - Replace every reference in-place with the expanded JSON content.
-2. At the end of this process we will have:
-    - A single flat JSON 
-    - Every imported step expanded to contain an in-line description
-    - No more external references - everything required is provided in-line
-
-
-## Using Circe to get case classes
-
-This process is more or less automatic - the case classes define the fields which they anticipate existing in the JSON.
-and Circe does the rest.
-    - Optional fields in case classes are allowed to not exist in the JSON
-    - All fields in the JSON must be represented by fields in the appropriate case classes
-    - In cases where the JSON may be structured in one of several ways, we use Shapeless coproducts to specify "one of" many options.
-
-If a file is failing to parse the first stop should always be to double-check that the case classes accurately represent
-the range of possible CWL JSON.
-
-## Convert the case classes into WOM representations
-
-- This is a recursive process of examining the CWL case classes and creating WOM values instead.
-- Note that the CWL Language Factory (at least as of November 2018) does not implement the provision of WOM Bundles for 
-imports. Instead, CWL Language Factory implements only the all-in-one method of converting CWL source and inputs files 
-together into a WOM Executable.
-    - Pragmatically, this just means that using the CWL language factory to process an import statement in a WDL file 
-    is currently impossible (ie we cannot import CWL from WDL... yet).
diff --git a/docs/developers/bitesize/workflowParsing/cwlParsingOverview.md b/docs/developers/bitesize/workflowParsing/cwlParsingOverview.md
deleted file mode 100644
index 3ba5b13c494..00000000000
--- a/docs/developers/bitesize/workflowParsing/cwlParsingOverview.md
+++ /dev/null
@@ -1 +0,0 @@
-Coming soon.
diff --git a/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md b/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md
index 178ec2f3e8f..666e331334d 100644
--- a/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md
+++ b/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md
@@ -31,7 +31,7 @@ You can think of WDL parsing in Cromwell in terms of the following major steps:
         * Including custom type references, variable references, task calls, subworkflow calls 
 * **WOM Bundle**:
     * A set of tasks, workflows and custom types, and the fully qualified names by which they can be referenced.
-    * In Cromwell's WOM format (the WOM format is the ultimate destination for _all_ languages, including WDL and CWL)
+    * In Cromwell's WOM format (the WOM format is the ultimate destination for _all_ languages, including WDL)
 * **Validated WOM Namespace**:
     * The conjunction of a WOM bundle with an input set.
-    * The entry point workflow (or sometimes task, in CWL) is known.
+    * The entry point workflow is known.
diff --git a/docs/filesystems/Filesystems.md b/docs/filesystems/Filesystems.md
index d5a66de7eba..67f663650ca 100644
--- a/docs/filesystems/Filesystems.md
+++ b/docs/filesystems/Filesystems.md
@@ -150,11 +150,6 @@ engine {
 }
 ```
 
-#### Engine filesystems and CWL
-
-Note that CWL *always* needs to access file attributes from within the engine, so if you are using CWL, please make sure
-that **every filesystem you might use** is added to the `engine.filesystems` stanza.
-
 ### Backend Filesystems
 
 Similarly to the engine, you can also configure backend filesystems individually. Some backends might require the use of a specific filesystem.
diff --git a/docs/tutorials/Containers.md b/docs/tutorials/Containers.md
index 3934f7a4579..595f8305acc 100644
--- a/docs/tutorials/Containers.md
+++ b/docs/tutorials/Containers.md
@@ -2,7 +2,7 @@
 
 Containers are encapsulated environments that include an operating system, libraries, and software. For example, if you have a host machine running Centos, you can run an isolated container with Ubuntu 18.04. At a high level, it's useful to think of a container as a program or binary.
  
-To promote reproducibility and portability, it's considered best practice to define containers for a WDL and CWL task to run in - this ensures that running the same task on a different system will run the exact same software. 
+To promote reproducibility and portability, it's considered best practice to define containers for a WDL task to run in - this ensures that running the same task on a different system will run the exact same software. 
 
 Docker images are the most common container format, but it is not advisable for certain systems to run Docker itself, and for this reason Cromwell can be configured to support a number of alternatives.
 
@@ -71,26 +71,6 @@ workflow hello {
 }
 ```
 
-Similarly in CWL, you can specify a [`DockerRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#DockerRequirement) inside the requirements section:
-
-```cwl
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-inputs:
-    name:
-        type: string
-        default: "World"
-        inputBinding:
-          prefix: "Hello, "
-outputs:
-    out: stdout
-
-requirements:
-    DockerRequirement:
-        dockerPull: "ubuntu:latest"
-``` 
-___
 ### Docker
 
 [Docker](https://www.docker.com) is a popular container technology that is natively supported by Cromwell and WDL.
diff --git a/docs/wf_options/Overview.md b/docs/wf_options/Overview.md
index 17ef2dd9f5f..9fcd7317eea 100644
--- a/docs/wf_options/Overview.md
+++ b/docs/wf_options/Overview.md
@@ -11,7 +11,7 @@ You provide workflow options to Cromwell in a JSON format. This can be supplied
 }
 ```
 
-Unless otherwise specified you can expect workflow options to override any hard-coded defaults in Cromwell or defaults provided in the [configuration file](../Configuring.md), but to be overridden by any values provided in the workflow definition file itself (WDL or CWL).
+Unless otherwise specified you can expect workflow options to override any hard-coded defaults in Cromwell or defaults provided in the [configuration file](../Configuring.md), but to be overridden by any values provided in the workflow definition file itself (WDL).
 
 Some workflow options apply only to tasks running on the [Google Pipelines API backend](Google).
 
@@ -27,7 +27,7 @@ Some options allow you to override or set defaults for runtime attributes.
 
 You can supply a default for any [Runtime Attributes](../RuntimeAttributes.md) by adding a `default_runtime_attributes` map to your workflow options file. Use the key to provide the attribute name and the value to supply the default. 
 
-These defaults replace any defaults in the Cromwell configuration file but are themselves replaced by any values explicitly provided by the task in the WDL or CWL file.
+These defaults replace any defaults in the Cromwell configuration file but are themselves replaced by any values explicitly provided by the task in the WDL file.
 
 Example `options.json`:
 ```json
diff --git a/engine/src/main/resources/swagger/cromwell.yaml b/engine/src/main/resources/swagger/cromwell.yaml
index 28dd9f6466b..f3230b3c171 100644
--- a/engine/src/main/resources/swagger/cromwell.yaml
+++ b/engine/src/main/resources/swagger/cromwell.yaml
@@ -71,11 +71,6 @@ paths:
           type: file
           in: formData
         - $ref: '#/parameters/workflowTypeParam'
-        - name: workflowRoot
-          description: The root object to be run. Only necessary for CWL submissions containing multiple objects (in an array).
-          required: false
-          type: string
-          in: formData
         - $ref: '#/parameters/workflowTypeVersionParam'
         - name: labels
           description: JSON object of labels to apply to this workflow.
@@ -788,9 +783,8 @@ paths:
         implementation specific.
         
         
-        The `workflow_type` is the type of workflow language and must be "CWL"
-        or "WDL" currently (or another alternative  supported by this WES
-        instance).
+        The `workflow_type` is the type of workflow language and must be "WDL"
+        currently (or another alternative supported by this WES instance).
         
         
         The `workflow_type_version` is the version of the workflow language
@@ -988,16 +982,16 @@ parameters:
   workflowTypeParam:
     name: workflowType
     type: string
-    description: The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.
-    enum: [WDL, CWL]
+    description: The workflow language for the file you submitted. Cromwell currently supports WDL.
+    enum: [WDL]
     required: false
     in: formData
   workflowTypeVersionParam:
     name: workflowTypeVersion
-    description: The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.
+    description: The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.
     required: false
     type: string
-    enum: ["draft-2", "1.0", "v1.0"]
+    enum: ["draft-2", "1.0"]
     in: formData
   versionParam:
     name: version
@@ -1374,12 +1368,11 @@ definitions:
   DescriptorType:
     type: string
     description: >-
-      One from a list of descriptor type strings (e.g. CWL, WDL).
+      One from a list of descriptor type strings (e.g. WDL).
       Note that these files can also include associated Docker/container files
       and test parameters that further describe a version of a tool
     example: "WDL"
     enum:
-      - CWL
       - WDL
   WorkflowQueryParameter:
     description: Workflow query parameters
@@ -1778,7 +1771,7 @@ definitions:
         type: string
         description: >-
           REQUIRED
-          The workflow descriptor type, must be "CWL" or "WDL" currently (or
+          The workflow descriptor type, must be "WDL" currently (or
           another alternative supported by this WES instance)
       workflow_type_version:
         type: string
@@ -1798,7 +1791,7 @@ definitions:
         type: string
         description: >-
           REQUIRED
-          The workflow CWL or WDL document. When `workflow_attachments` is
+          The workflow WDL document. When `workflow_attachments` is
           used to attach files, the `workflow_url` may be a relative path to
           one of the attachments.
     description: >-
diff --git a/mkdocs.yml b/mkdocs.yml
index 68e73560774..7aea4302d34 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -79,7 +79,6 @@ nav:
     - Integration tests: developers/Centaur.md
     - Security: developers/Security.md
     - Contribute to docs: developers/Contribute.md
-    - CWL Parsing: developers/CwlParsing.md
     - Bitesize Design Docs:
         - Workflow Parsing & Graph Construction:
             - What is WOM?: developers/bitesize/workflowParsing/whatIsWom.md
@@ -87,7 +86,6 @@ nav:
                 - Overview: developers/bitesize/workflowParsing/wdlParsingOverview.md
                 - From WDL to WDLOM: developers/bitesize/workflowParsing/wdlToWdlom.md
                 - Adding new WDL Engine Functions: developers/bitesize/workflowParsing/engineFunctionAddition.md
-            - From CWL Source to WOM: developers/bitesize/workflowParsing/cwlParsingOverview.md
         - Cromwell Actor System:
             - High level view: developers/bitesize/majorActorSystem/5000FtActorSystem.md
             - Workflow Execution:

From 95e44492209a55326c36341c538763be169bb094 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 21 Nov 2022 13:06:52 -0500
Subject: [PATCH 109/326] WX-728 Add configurable WSM client to Cromwell
 (#6948)

* Dependencies

* Compiles but no tests

* Formatting

* Moar exclusions

* Update to latest WSM

* Add additional dependency

* We need some UUID here to make the request

* Formatting

* Clarify what is fake

* Formatting

* Use our own version of Jersey and Jackson stuff

* Port-in Khalid's changes (thank you!)

Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>

* Test longevity

Don't break the test if someone decides to add a cert to `ws.org`

* Cleanup

* Cleanup

* Cleanup

* Adjust TES config file for CI

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>
---
 .../blob_md5/blob_md5.inputs.json             |   3 +
 .../standardTestCases/blob_md5/blob_md5.wdl   |  20 ++++
 .../blob/BlobFileSystemManager.scala          |  43 +++----
 .../blob/BlobPathBuilderFactory.scala         |  12 +-
 .../WorkspaceManagerApiClientProvider.scala   |  32 +++++
 .../blob/BlobPathBuilderFactorySpec.scala     |   4 +-
 project/Dependencies.scala                    | 112 +++++++++++++++++-
 project/Publishing.scala                      |   5 +
 ...Repo template_ Cromwell server TES.run.xml |  21 ++++
 src/ci/resources/tes_application.conf         |  51 ++++++++
 10 files changed, 275 insertions(+), 28 deletions(-)
 create mode 100644 centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json
 create mode 100644 centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
 create mode 100644 runConfigurations/Repo template_ Cromwell server TES.run.xml

diff --git a/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json
new file mode 100644
index 00000000000..f004c8be647
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json
@@ -0,0 +1,3 @@
+{
+  "fileChecksum.inputFile": "https://<storage-account>.blob.core.windows.net/cromwell/user-inputs/inputFile.txt"
+}
diff --git a/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl
new file mode 100644
index 00000000000..b482f80d6e4
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl
@@ -0,0 +1,20 @@
+task md5 {
+    File inputFile
+    command {
+        echo "`date`: Running checksum on ${inputFile}..."
+        md5sum ${inputFile} > md5sum.txt
+        echo "`date`: Checksum is complete."
+    }
+    output {
+        File result = "md5sum.txt"
+    }
+    runtime {
+        docker: 'ubuntu:18.04'
+        preemptible: true
+    }
+}
+
+workflow fileChecksum {
+    File inputFile
+    call md5 { input: inputFile=inputFile}
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index 3ebce4db878..877cefdfab5 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -19,6 +19,8 @@ import scala.util.{Failure, Success, Try}
 import com.azure.resourcemanager.storage.models.StorageAccountKey
 import com.typesafe.scalalogging.LazyLogging
 
+import java.util.UUID
+
 case class FileSystemAPI() {
   def getFileSystem(uri: URI): Try[FileSystem] = Try(FileSystems.getFileSystem(uri))
   def newFileSystem(uri: URI, config: Map[String, Object]): FileSystem = FileSystems.newFileSystem(uri, config.asJava)
@@ -82,31 +84,32 @@ case class BlobFileSystemManager(
 sealed trait BlobTokenGenerator {def generateAccessToken: Try[AzureSasCredential]}
 object BlobTokenGenerator {
   def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId]): BlobTokenGenerator = {
-    createBlobTokenGenerator(container, endpoint, None, None, subscription)
+    NativeBlobTokenGenerator(container, endpoint, subscription)
   }
-  def createBlobTokenGenerator(container: BlobContainerName,
-                               endpoint: EndpointURL,
-                               workspaceId: Option[WorkspaceId],
-                               workspaceManagerURL: Option[WorkspaceManagerURL],
-                               subscription: Option[SubscriptionId]
-                              ): BlobTokenGenerator = {
-     (container: BlobContainerName, endpoint: EndpointURL, workspaceId, workspaceManagerURL) match {
-       case (container, endpoint, None, None) =>
-         NativeBlobTokenGenerator(container, endpoint, subscription)
-       case (container, endpoint, Some(workspaceId), Some(workspaceManagerURL)) =>
-         WSMBlobTokenGenerator(container, endpoint, workspaceId, workspaceManagerURL)
-       case _ =>
-         throw new Exception("Arguments provided do not match any available BlobTokenGenerator implementation.")
-     }
+  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: WorkspaceId, workspaceManagerClient: WorkspaceManagerApiClientProvider): BlobTokenGenerator = {
+    WSMBlobTokenGenerator(container, endpoint, workspaceId, workspaceManagerClient)
   }
-  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL): BlobTokenGenerator = createBlobTokenGenerator(container, endpoint, None)
-  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: Option[WorkspaceId], workspaceManagerURL: Option[WorkspaceManagerURL]): BlobTokenGenerator =
-      createBlobTokenGenerator(container, endpoint, workspaceId, workspaceManagerURL, None)
 
 }
 
-case class WSMBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: WorkspaceId, workspaceManagerURL: WorkspaceManagerURL) extends BlobTokenGenerator {
-  def generateAccessToken: Try[AzureSasCredential] = Failure(new NotImplementedError)
+case class WSMBlobTokenGenerator(
+  container: BlobContainerName,
+  endpoint: EndpointURL,
+  workspaceId: WorkspaceId,
+  wsmClient: WorkspaceManagerApiClientProvider) extends BlobTokenGenerator {
+
+  def generateAccessToken: Try[AzureSasCredential] = Try {
+    val token = wsmClient.getControlledAzureResourceApi.createAzureStorageContainerSasToken(
+      UUID.fromString(workspaceId.value),
+      UUID.fromString("00001111-2222-3333-aaaa-bbbbccccdddd"),
+      null,
+      null,
+      null,
+      null
+    ).getToken // TODO `null` items may be required, investigate in WX-696
+
+    new AzureSasCredential(token) // TODO Does `signature` actually mean token? save for WX-696
+  }
 }
 
 case class NativeBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId] = None) extends BlobTokenGenerator {
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index 1a9df21b0f2..e0f7c992bb6 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -24,9 +24,17 @@ final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Co
   val workspaceId: Option[WorkspaceId] = instanceConfig.as[Option[String]]("workspace-id").map(WorkspaceId)
   val expiryBufferMinutes: Long = instanceConfig.as[Option[Long]]("expiry-buffer-minutes").getOrElse(10)
   val workspaceManagerURL: Option[WorkspaceManagerURL] = singletonConfig.config.as[Option[String]]("workspace-manager-url").map(WorkspaceManagerURL)
+  val b2cToken: Option[String] = instanceConfig.as[Option[String]]("b2cToken")
+
+  val blobTokenGenerator: BlobTokenGenerator = (workspaceManagerURL, b2cToken, workspaceId) match {
+    case (Some(url), Some(token), Some(workspaceId)) =>
+      val wsmClient: WorkspaceManagerApiClientProvider = new HttpWorkspaceManagerClientProvider(url, token)
+      // parameterizing client instead of URL to make injecting mock client possible
+      BlobTokenGenerator.createBlobTokenGenerator(container, endpoint, workspaceId, wsmClient)
+    case _ =>
+      BlobTokenGenerator.createBlobTokenGenerator(container, endpoint, subscription)
+  }
 
-  val blobTokenGenerator: BlobTokenGenerator = BlobTokenGenerator.createBlobTokenGenerator(
-    container, endpoint, workspaceId, workspaceManagerURL, subscription)
   val fsm: BlobFileSystemManager = BlobFileSystemManager(container, endpoint, expiryBufferMinutes, blobTokenGenerator)
 
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[BlobPathBuilder] = {
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
new file mode 100644
index 00000000000..c083d262151
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
@@ -0,0 +1,32 @@
+package cromwell.filesystems.blob
+
+import bio.terra.workspace.api.ControlledAzureResourceApi
+import bio.terra.workspace.client.ApiClient
+
+/**
+  * Represents a way to get various workspace manager clients
+  *
+  * Pared down from `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.WorkspaceManagerApiClientProvider`
+  *
+  * For testing, create an anonymous subclass as in `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.HttpWorkspaceManagerDAOSpec`
+  */
+trait WorkspaceManagerApiClientProvider {
+  def getApiClient: ApiClient
+
+  def getControlledAzureResourceApi: ControlledAzureResourceApi
+
+}
+
+class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManagerURL, token: String) extends WorkspaceManagerApiClientProvider {
+  def getApiClient: ApiClient = {
+    val client: ApiClient = new ApiClient()
+    client.setBasePath(baseWorkspaceManagerUrl.value)
+    client.setAccessToken(token)
+
+    client
+  }
+
+  def getControlledAzureResourceApi: ControlledAzureResourceApi =
+    new ControlledAzureResourceApi(getApiClient)
+
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
index f5b71a06ead..0cad162c860 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
@@ -27,8 +27,8 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
   it should "parse configs for a functioning factory" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
     val container = BlobContainerName("storageContainer")
-    val workspaceId = WorkspaceId("mockWorkspaceId")
-    val workspaceManagerURL = WorkspaceManagerURL("https://test.ws.org")
+    val workspaceId = WorkspaceId("B0BAFE77-0000-0000-0000-000000000000")
+    val workspaceManagerURL = WorkspaceManagerURL("https://wsm.example.com")
     val instanceConfig = ConfigFactory.parseString(
       s"""
       |container = "$container"
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 8906e010531..d3ba06edd55 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -59,7 +59,12 @@ object Dependencies {
   private val hsqldbV = "2.6.1"
   private val http4sV = "0.21.31" // this release is EOL. We need to upgrade further for cats3. https://http4s.org/versions/
   private val jacksonV = "2.13.3"
+  private val jakartaActivationV = "1.2.1"
+  private val jakartaAnnotationV = "1.3.5"
+  private val jakartaInjectV = "2.6.1"
+  private val jakartaXmlBindApiV = "2.3.2"
   private val janinoV = "3.1.7"
+  private val jerseyV = "2.32" // Use a jersey compatible with WSM. See notes in wsmDependencies below.
   private val jsr305V = "3.0.2"
   private val junitV = "4.13.2"
   private val kindProjectorV = "0.13.2"
@@ -172,6 +177,16 @@ object Dependencies {
     "com.google.api-client" % "google-api-client-jackson2" % googleApiClientV
       exclude("com.google.guava", "guava-jdk5"),
     "com.google.cloud" % "google-cloud-resourcemanager" % googleCloudResourceManagerV,
+    /*
+    The google-cloud-java dependencies have similar issues with using an older javax.* vs. jakarta.* as guice.
+    google-cloud-java is still using javax.annotation and guice is sticking with javax.inject:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/google-cloud-java/blob/v0.201.0/google-cloud-jar-parent/pom.xml#L131-L136
+
+     Globally use of jakarta instead of javax until Google does themselves.
+     The javax.annotation exclusion is below in cromwellExcludeDependencies.
+     */
+    "jakarta.annotation" % "jakarta.annotation-api" % jakartaAnnotationV,
   )
 
   val spiDependencies: List[ModuleID] = List(
@@ -197,6 +212,36 @@ object Dependencies {
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0"
   )
 
+  val wsmDependencies: List[ModuleID] = List(
+    "bio.terra" % "workspace-manager-client" % "0.254.452-SNAPSHOT"
+      exclude("com.sun.activation", "jakarta.activation"),
+    /*
+    1. WSM is looking for the rs-api under javax.*.
+
+    Jersey 3.x switched to jakarta.ws.rs-api 3.x. If one uses jakarta's rs-api, 3.x will automatically evict 2.x.
+
+    However, jakarta's rs-api 2.x provides packages javax.* while 3.x provides jakarta.* instead.
+     - https://javadoc.io/doc/jakarta.ws.rs/jakarta.ws.rs-api/2.1.6/javax/ws/rs/package-summary.html
+     - https://javadoc.io/doc/jakarta.ws.rs/jakarta.ws.rs-api/3.1.0/jakarta.ws.rs/module-summary.html
+
+    TODO: Perhaps coordinate with the WSM team to use the jakarta 3.x rs-api and jakarta.* instead of javax.*.
+
+    2. Use the exact version of jersey that WSM is using.
+
+    Jersey libraries cannot be mixed and matched as the various modules cannot be mixed and matched.
+    For example jersey-client 2.32 is not compatible with jersey-common 2.37.
+
+    If needed one may also explicitly enumerate the list of jersey artifacts and explicitly set the versions similar to
+    catsDepeendencies, akkaHttpDependencies, etc.
+     - https://broadinstitute.jfrog.io/ui/repos/tree/PomView/libs-snapshot-local/bio/terra/workspace-manager-client/0.254.452-SNAPSHOT/workspace-manager-client-0.254.452-20221114.190249-1.pom
+     - https://github.com/eclipse-ee4j/jersey/blob/2.32/core-client/src/main/java/org/glassfish/jersey/client/ClientExecutorProvidersConfigurator.java#L139
+     - https://github.com/eclipse-ee4j/jersey/blob/2.37/core-client/src/main/java/org/glassfish/jersey/client/ClientExecutorProvidersConfigurator.java#L136-L137
+     */
+    "org.glassfish.jersey.inject" % "jersey-hk2" % jerseyV
+      exclude("com.sun.activation", "jakarta.activation"),
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
+  )
+
   val implFtpDependencies = List(
     "commons-net" % "commons-net" % commonNetV,
     "io.github.andrebeat" %% "scala-pool" % scalaPoolV,
@@ -256,7 +301,11 @@ object Dependencies {
   )
 
   private val liquibaseDependencies = List(
+    // The XML bind API replacement below may be removed when this ticket is addressed:
+    // https://github.com/liquibase/liquibase/issues/2991
     "org.liquibase" % "liquibase-core" % liquibaseV
+      exclude("javax.xml.bind", "jaxb-api"),
+    "jakarta.xml.bind" % "jakarta.xml.bind-api" % jakartaXmlBindApiV,
   )
 
   private val akkaDependencies = List(
@@ -323,15 +372,24 @@ object Dependencies {
   private val googleCloudDependencies = List(
     "io.grpc" % "grpc-core" % grpcV,
     "com.google.guava" % "guava" % guavaV,
+    /*
+    The google-cloud-nio has the same problems with an ancient inject as guice:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/java-storage-nio/blob/v0.124.20/google-cloud-nio/pom.xml#L49-L53
+
+     Force use of jakarta instead of javax until Google does themselves.
+     */
     "com.google.cloud" % "google-cloud-nio" % googleCloudNioV
       exclude("com.google.api.grpc", "grpc-google-common-protos")
       exclude("com.google.cloud.datastore", "datastore-v1-protos")
+      exclude("javax.inject", "javax.inject")
       exclude("org.apache.httpcomponents", "httpclient"),
     "org.broadinstitute.dsde.workbench" %% "workbench-google" % workbenchGoogleV
       exclude("com.google.apis", "google-api-services-genomics"),
     "org.apache.httpcomponents" % "httpclient" % apacheHttpClientV,
     "com.google.apis" % "google-api-services-cloudkms" % googleCloudKmsV
-      exclude("com.google.guava", "guava-jdk5")
+      exclude("com.google.guava", "guava-jdk5"),
+    "org.glassfish.hk2.external" % "jakarta.inject" % jakartaInjectV,
   ) ++ googleGenomicsV2Alpha1Dependency ++ googleLifeSciencesV2BetaDependency
 
   private val dbmsDependencies = List(
@@ -407,7 +465,7 @@ object Dependencies {
     List("scalatest", "mysql", "mariadb", "postgresql")
       .map(name => "com.dimafeng" %% s"testcontainers-scala-$name" % testContainersScalaV % Test)
 
-  val blobFileSystemDependencies: List[ModuleID] = azureDependencies
+  val blobFileSystemDependencies: List[ModuleID] = azureDependencies ++ wsmDependencies
 
   val s3FileSystemDependencies: List[ModuleID] = junitDependencies
 
@@ -431,6 +489,8 @@ object Dependencies {
   val languageFactoryDependencies = List(
     "com.softwaremill.sttp" %% "core" % sttpV,
     "com.softwaremill.sttp" %% "async-http-client-backend-cats" % sttpV
+      exclude("com.sun.activation", "javax.activation"),
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
   )
 
   val draft2LanguageFactoryDependencies = List(
@@ -452,10 +512,16 @@ object Dependencies {
   - https://www.slf4j.org/legacy.html#jclOverSLF4J
    */
   val owlApiDependencies = List(
+    // This whole section (incl. javax->jakarta issues) is probably going to be removed when CWL support is removed
+    // For now, replace javax usage with jakarta.
     "net.sourceforge.owlapi" % "owlapi-distribution" % owlApiV
+      exclude("javax.inject", "javax.inject")
+      exclude("javax.xml.bind", "jaxb-api")
       exclude("org.apache.httpcomponents", "httpclient-osgi")
       exclude("org.apache.httpcomponents", "httpcore-osgi")
       exclude("org.slf4j", "jcl-over-slf4j"),
+    "org.glassfish.hk2.external" % "jakarta.inject" % jakartaInjectV,
+    "jakarta.xml.bind" % "jakarta.xml.bind-api" % jakartaXmlBindApiV,
     "org.apache.httpcomponents" % "httpclient-cache" % apacheHttpClientV,
     "org.apache.httpcomponents" % "httpclient" % apacheHttpClientV
   )
@@ -480,7 +546,9 @@ object Dependencies {
   val coreDependencies: List[ModuleID] = List(
     "com.google.auth" % "google-auth-library-oauth2-http" % googleOauth2V,
     "com.chuusai" %% "shapeless" % shapelessV,
+    // NOTE: See scalameter comment under engineDependencies
     "com.storm-enroute" %% "scalameter" % scalameterV % Test
+      exclude("com.fasterxml.jackson.module", "jackson-module-scala_2.13")
       exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.github.scopt" %% "scopt" % scoptV,
   ) ++ akkaStreamDependencies ++ configDependencies ++ catsDependencies ++ circeDependencies ++
@@ -507,9 +575,22 @@ object Dependencies {
   val engineDependencies: List[ModuleID] = List(
     "commons-codec" % "commons-codec" % commonsCodecV,
     "commons-io" % "commons-io" % commonsIoV,
+    /*
+    Maybe ScalaMeter should be used, but is anyone?
+
+    For now keep its dependencies from breaking jackson for other libraries. If someone wants to use it they can
+    re-fight with dependency-hell at that point.
+
+    Avoid:
+    "com.fasterxml.jackson.databind.JsonMappingException: Scala module 2.11.3 requires Jackson Databind
+    version >= 2.11.0 and < 2.12.0":
+     - https://scalameter.github.io/home/gettingstarted/0.7/sbt/index.html
+     - https://github.com/FasterXML/jackson-module-scala/blob/jackson-module-scala-2.11.3/src/main/scala/com/fasterxml/jackson/module/scala/JacksonModule.scala#L53-L62
+     */
     "com.storm-enroute" %% "scalameter" % scalameterV
       exclude("com.fasterxml.jackson.core", "jackson-databind")
       exclude("com.fasterxml.jackson.module", "jackson-module-scala")
+      exclude("com.fasterxml.jackson.module", "jackson-module-scala_2.13")
       exclude("org.scala-tools.testing", "test-interface")
       exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.fasterxml.jackson.core" % "jackson-databind" % jacksonV,
@@ -525,11 +606,24 @@ object Dependencies {
   val serverDependencies: List[ModuleID] = slf4jBindingDependencies
 
   val cromiamDependencies: List[ModuleID] = List(
+    /*
+    sttp 1.x was last released in 2019
+    See above comment regarding "cats-effect, fs2, http4s, and sttp" all needing to update together.
+    For now, replace sttp 1.x's com.sun.activation usage with the jakarta version.
+
+    NOTE when upgrading: sttp 3.x no longer requires an async-http-client-backend-future so jakarta.activation can
+    probably be removed from the dependencies:
+     - https://sttp.softwaremill.com/en/v3/backends/future.html#using-async-http-client
+     - https://sttp.softwaremill.com/en/v2/backends/future.html#using-async-http-client
+     - https://sttp.softwaremill.com/en/v1/backends/asynchttpclient.html
+     */
     "com.softwaremill.sttp" %% "core" % sttpV,
-    "com.softwaremill.sttp" %% "async-http-client-backend-future" % sttpV,
+    "com.softwaremill.sttp" %% "async-http-client-backend-future" % sttpV
+      exclude("com.sun.activation", "javax.activation"),
     "com.typesafe.scala-logging" %% "scala-logging" % scalaLoggingV,
     "org.broadinstitute.dsde.workbench" %% "workbench-model" % workbenchModelV,
-    "org.broadinstitute.dsde.workbench" %% "workbench-util" % workbenchUtilV
+    "org.broadinstitute.dsde.workbench" %% "workbench-util" % workbenchUtilV,
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
   ) ++ akkaHttpDependencies ++ swaggerUiDependencies ++ slf4jBindingDependencies
 
   val wes2cromwellDependencies: List[ModuleID] = coreDependencies ++ akkaHttpDependencies
@@ -736,5 +830,15 @@ object Dependencies {
   val cromwellExcludeDependencies: List[ExclusionRule] = List(
     // Replaced with jcl-over-slf4j
     ExclusionRule("commons-logging", "commons-logging"),
+    /*
+    The google-cloud-java dependencies have similar issues with using an older javax.* vs. jakarta.* as guice.
+    google-cloud-java is still using javax.annotation and guice is sticking with javax.inject:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/google-cloud-java/blob/v0.201.0/google-cloud-jar-parent/pom.xml#L131-L136
+
+     Globally use of jakarta instead of javax until Google does themselves.
+     The jakarta.annotation inclusion is above in googleApiClientDependencies.
+     */
+    ExclusionRule("javax.annotation", "javax.annotation-api"),
   )
 }
diff --git a/project/Publishing.scala b/project/Publishing.scala
index 1b798780086..1d4143fc13e 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -150,6 +150,10 @@ object Publishing {
     "Broad Artifactory" at
       "https://broadinstitute.jfrog.io/broadinstitute/libs-release/"
 
+  private val broadArtifactoryResolverSnap: Resolver =
+    "Broad Artifactory Snapshots" at
+      "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot-local/"
+
   // https://stackoverflow.com/questions/9819965/artifactory-snapshot-filename-handling
   private val buildTimestamp = System.currentTimeMillis() / 1000
 
@@ -159,6 +163,7 @@ object Publishing {
 
   val additionalResolvers = List(
     broadArtifactoryResolver,
+    broadArtifactoryResolverSnap,
     Resolver.sonatypeRepo("releases")
   )
 
diff --git a/runConfigurations/Repo template_ Cromwell server TES.run.xml b/runConfigurations/Repo template_ Cromwell server TES.run.xml
new file mode 100644
index 00000000000..9cb1818a004
--- /dev/null
+++ b/runConfigurations/Repo template_ Cromwell server TES.run.xml	
@@ -0,0 +1,21 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="Repo template: Cromwell server TES" type="Application" factoryName="Application">
+    <option name="ALTERNATIVE_JRE_PATH" value="$USER_HOME$/.sdkman/candidates/java/current" />
+    <envs>
+      <env name="CROMWELL_BUILD_CENTAUR_SLICK_PROFILE" value="slick.jdbc.MySQLProfile$" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_DRIVER" value="com.mysql.cj.jdbc.Driver" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_URL" value="jdbc:mysql://localhost:3306/cromwell_test?allowPublicKeyRetrieval=true&amp;useSSL=false&amp;rewriteBatchedStatements=true&amp;serverTimezone=UTC&amp;useInformationSchema=true" />
+      <env name="CROMWELL_BUILD_RESOURCES_DIRECTORY" value="target/ci/resources" />
+      <env name="CROMWELL_BUILD_PAPI_JSON_FILE" value="target/ci/resources/cromwell-centaur-service-account.json" />
+      <env name="CROMWELL_BUILD_CENTAUR_READ_LINES_LIMIT" value="128000" />
+      <env name="CROMWELL_BUILD_CENTAUR_256_BITS_KEY" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA=" />
+    </envs>
+    <option name="MAIN_CLASS_NAME" value="cromwell.CromwellApp" />
+    <module name="cromwell" />
+    <option name="PROGRAM_PARAMETERS" value="server" />
+    <option name="VM_PARAMETERS" value="-Dconfig.file=target/ci/resources/tes_application.conf" />
+    <method v="2">
+      <option name="Make" enabled="true" />
+    </method>
+  </configuration>
+</component>
\ No newline at end of file
diff --git a/src/ci/resources/tes_application.conf b/src/ci/resources/tes_application.conf
index 018c13829d8..e6595c8e941 100644
--- a/src/ci/resources/tes_application.conf
+++ b/src/ci/resources/tes_application.conf
@@ -1,16 +1,67 @@
 include required(classpath("application.conf"))
 include "build_application.inc.conf"
 
+filesystems {
+  blob {
+    class = "cromwell.filesystems.blob.BlobPathBuilderFactory"
+    global {
+      class = "cromwell.filesystems.blob.BlobFileSystemConfig"
+      config {
+        workspace-manager-url: "https://workspace.dsde-dev.broadinstitute.org"
+      }
+    }
+  }
+}
+
+engine {
+  filesystems {
+    local {
+      enabled: true
+    }
+    http {
+      enabled: true
+    }
+    blob {
+      enabled: false
+      container: "cromwell"
+      endpoint: "https://<storage-account>.blob.core.windows.net"
+      subscription: "00001111-2222-3333-aaaa-bbbbccccdddd"
+      workspace-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
+      b2cToken: "Zardoz"
+    }
+  }
+}
+
+
 backend {
   default = "TES"
   providers {
     TES {
       actor-factory = "cromwell.backend.impl.tes.TesBackendLifecycleActorFactory"
       config {
+        # Use for running on blob storage
+        #root = "https://<storage-account>.blob.core.windows.net/cromwell/cromwell-executions"
         root = "cromwell-executions"
         dockerRoot = "/cromwell-executions"
         endpoint = "http://127.0.0.1:9000/v1/tasks"
         concurrent-job-limit = 1000
+        transform-blob-to-local-path = false
+        filesystems {
+          blob {
+            enabled: false
+            container: "cromwell"
+            endpoint: "https://<storage-account>.blob.core.windows.net"
+            subscription: "00001111-2222-3333-aaaa-bbbbccccdddd"
+            workspace-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
+            b2cToken: "Zardoz"
+          }
+          local {
+            enabled: true
+          }
+          http {
+            enabled: true
+          }
+        }
       }
 
       # Have the engine (maybe) authenticate to docker.io. See BT-141 for more info.

From 001957bebcc560ce56b07ff4a549503f90127abf Mon Sep 17 00:00:00 2001
From: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Date: Tue, 22 Nov 2022 10:26:25 -0500
Subject: [PATCH 110/326] CROM-6554: Removed PAPIv1 references from doc (#6950)

* crom-6554 removed references to PAPI v1 from doc

* crom-6554 pr feedback, reworded doc to use example conf as a starting point
---
 docs/tutorials/PipelinesApi101.md | 23 +++--------------------
 1 file changed, 3 insertions(+), 20 deletions(-)

diff --git a/docs/tutorials/PipelinesApi101.md b/docs/tutorials/PipelinesApi101.md
index 6cc7bf72db4..ef94d111d04 100644
--- a/docs/tutorials/PipelinesApi101.md
+++ b/docs/tutorials/PipelinesApi101.md
@@ -2,22 +2,11 @@
 
 ## Pipelines API v2
 
-### Basic Information
-
-Initial support for Google [Pipelines API version 2](https://cloud.google.com/genomics/reference/rest/) was added in Cromwell 32.
-Expect feature parity with v1 except:
-
-* PAPI v2 private Docker support is equivalent to that in PAPI v1 but the configuration differs, please see [Docker configuration](http://cromwell.readthedocs.io/en/develop/filesystems/Google#Docker) for more details.
-* The "refresh token" authentication mode is **NOT** supported on PAPI V2.
-
-In addition, the following changes are to be expected:
-
-* Error messages for failed jobs might differ from V1
-* The Pipelines API log file content might differ from V1
-
 ### Setting up PAPIv2
 
-For now the easiest way to try PAPIv2 is to migrate an existing set up from PAPIv1 (see below). After that, copy the PAPIv2 sample configuration in [cromwell.examples.conf](https://github.com/broadinstitute/cromwell/blob/develop/cromwell.example.backends/PAPIv2.conf) in place of the PAPIv1 backend.
+For now the easiest way to try PAPIv2 is to start with the sample configuration in
+[cromwell.examples.conf](https://github.com/broadinstitute/cromwell/blob/develop/cromwell.example.backends/PAPIv2.conf)
+and adjust it to fit your needs.
 
 #### Permissions:
 
@@ -49,12 +38,6 @@ gsutil acl ch -u "$EMAIL":W gs://"$RANDOM_BUCKET_NAME"
 gcloud iam service-accounts keys create sa.json --iam-account "$EMAIL"
 ```
 
-## Pipelines API v1
-
-### Deprecation warning
-
-Please note that Google intends to deprecate PAPIv1 in the near future (circa mid 2019 or perhaps earlier). 
-
 ### Prerequisites
 
 This tutorial page relies on completing the previous tutorial:

From e0c8dd07bdce9ae825be35953efd626bd9348e3e Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Tue, 22 Nov 2022 14:12:08 -0500
Subject: [PATCH 111/326] WX-833 Real Azure DRS Credentials (#6952)

* Remove B2C reference from name

* Get token for current user rather than getting from KeyVault

* Remove KeyVault config for engine

* Remove KeyVault config for DRSLocalizer

* Remove KeyVault dependency

* Remove KeyVault support from localizer repo template

* Cleaned up and working Azure token acquisition for engine

* Collapse localizer's AccessTokenStrategy into DrsCredentials

* Cleanup
---
 .../cloud/nio/impl/drs/DrsCredentials.scala   | 90 ++++++++++++++-----
 .../drs/DrsCloudNioFileProviderSpec.scala     |  2 +-
 .../MockDrsCloudNioFileSystemProvider.scala   |  2 +-
 .../impl/drs/MockEngineDrsPathResolver.scala  |  2 +-
 .../drs/localizer/CommandLineParser.scala     | 15 +---
 .../DrsLocalizerDrsPathResolver.scala         |  7 +-
 .../drs/localizer/DrsLocalizerMain.scala      | 21 +++--
 .../accesstokens/AccessTokenStrategy.scala    |  7 --
 .../AzureB2CAccessTokenStrategy.scala         | 40 ---------
 .../GoogleAccessTokenStrategy.scala           | 28 ------
 .../drs/localizer/CommandLineParserSpec.scala | 54 +----------
 .../drs/localizer/DrsLocalizerMainSpec.scala  |  8 +-
 .../drs/DrsPathBuilderFactory.scala           | 16 ++--
 .../filesystems/drs/DrsPathBuilderSpec.scala  |  4 +-
 project/Dependencies.scala                    |  4 -
 ...o template_ Cromwell DRS Localizer.run.xml |  2 +-
 .../v2alpha1/PipelinesConversionsSpec.scala   |  4 +-
 ...ApiAsyncBackendJobExecutionActorSpec.scala |  4 +-
 18 files changed, 109 insertions(+), 201 deletions(-)
 delete mode 100644 cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AccessTokenStrategy.scala
 delete mode 100644 cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
 delete mode 100644 cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala

diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
index 66a89fe4014..9fae8552fa7 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
@@ -1,25 +1,32 @@
 package cloud.nio.impl.drs
 
 import cats.syntax.validated._
+import com.azure.core.credential.TokenRequestContext
+import com.azure.core.management.AzureEnvironment
+import com.azure.core.management.profile.AzureProfile
 import com.azure.identity.DefaultAzureCredentialBuilder
-import com.azure.security.keyvault.secrets.{SecretClient, SecretClientBuilder}
-import com.google.auth.oauth2.{AccessToken, OAuth2Credentials}
+import com.google.auth.oauth2.{AccessToken, GoogleCredentials, OAuth2Credentials}
 import com.typesafe.config.Config
-import common.validation.ErrorOr
 import common.validation.ErrorOr.ErrorOr
 import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.duration._
+import scala.jdk.DurationConverters._
+import scala.util.{Failure, Success, Try}
 
 /**
   * This trait allows us to abstract away different token attainment strategies
   * for different cloud environments.
   **/
-sealed trait DrsCredentials {
+trait DrsCredentials {
   def getAccessToken: ErrorOr[String]
 }
 
-case class GoogleDrsCredentials(credentials: OAuth2Credentials, acceptableTTL: Duration) extends DrsCredentials {
+/**
+  * Strategy for obtaining an access token from an existing OAuth credential. This class
+  * is designed for use within the Cromwell engine.
+  */
+case class GoogleOauthDrsCredentials(credentials: OAuth2Credentials, acceptableTTL: Duration) extends DrsCredentials {
   //Based on method from GoogleRegistry
   def getAccessToken: ErrorOr[String] = {
     def accessTokenTTLIsAcceptable(accessToken: AccessToken): Boolean = {
@@ -39,25 +46,68 @@ case class GoogleDrsCredentials(credentials: OAuth2Credentials, acceptableTTL: D
   }
 }
 
-object GoogleDrsCredentials {
-  def apply(credentials: OAuth2Credentials, config: Config): GoogleDrsCredentials =
-    GoogleDrsCredentials(credentials, config.as[FiniteDuration]("access-token-acceptable-ttl"))
+object GoogleOauthDrsCredentials {
+  def apply(credentials: OAuth2Credentials, config: Config): GoogleOauthDrsCredentials =
+    GoogleOauthDrsCredentials(credentials, config.as[FiniteDuration]("access-token-acceptable-ttl"))
+}
+
+
+/**
+  * Strategy for obtaining an access token from Google Application Default credentials that are assumed to already exist
+  * in the environment. This class is designed for use by standalone executables running in environments
+  * that have direct access to a Google identity (ex. CromwellDrsLocalizer).
+  */
+case object GoogleAppDefaultTokenStrategy extends DrsCredentials {
+  private final val UserInfoEmailScope = "https://www.googleapis.com/auth/userinfo.email"
+  private final val UserInfoProfileScope = "https://www.googleapis.com/auth/userinfo.profile"
+
+  def getAccessToken: ErrorOr[String] = {
+    Try {
+      val scopedCredentials = GoogleCredentials.getApplicationDefault().createScoped(UserInfoEmailScope, UserInfoProfileScope)
+      scopedCredentials.refreshAccessToken().getTokenValue
+    } match {
+      case Success(null) => "null token value attempting to refresh access token".invalidNel
+      case Success(value) => value.validNel
+      case Failure(e) => s"Failed to refresh access token: ${e.getMessage}".invalidNel
+    }
+  }
 }
 
-case class AzureDrsCredentials(identityClientId: Option[String], vaultName: String, secretName: String) extends DrsCredentials {
+/**
+  * Strategy for obtaining an access token in an environment with available Azure identity.
+  * If you need to disambiguate among multiple active user-assigned managed identities, pass
+  * in the client id of the identity that should be used.
+  */
+case class AzureDrsCredentials(identityClientId: Option[String]) extends DrsCredentials {
+
+  final val tokenAcquisitionTimeout = 30.seconds
 
-  lazy val secretClient: ErrorOr[SecretClient] = ErrorOr {
-    val defaultCreds = identityClientId.map(identityId =>
-      new DefaultAzureCredentialBuilder().managedIdentityClientId(identityId)
-    ).getOrElse(
-      new DefaultAzureCredentialBuilder()
-    ).build()
+  val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
+  val tokenScope = "https://management.azure.com/.default"
 
-    new SecretClientBuilder()
-      .vaultUrl(s"https://${vaultName}.vault.azure.net")
-      .credential(defaultCreds)
-      .buildClient()
+  def tokenRequestContext: TokenRequestContext = {
+    val trc = new TokenRequestContext()
+    trc.addScopes(tokenScope)
+    trc
   }
 
-  def getAccessToken: ErrorOr[String] = secretClient.map(_.getSecret(secretName).getValue)
+  def defaultCredentialBuilder: DefaultAzureCredentialBuilder =
+    new DefaultAzureCredentialBuilder()
+      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
+
+  def getAccessToken: ErrorOr[String] = {
+    val credentials = identityClientId.foldLeft(defaultCredentialBuilder) {
+      (builder, clientId) => builder.managedIdentityClientId(clientId)
+    }.build()
+
+    Try(
+      credentials
+        .getToken(tokenRequestContext)
+        .block(tokenAcquisitionTimeout.toJava)
+    ) match {
+      case Success(null) => "null token value attempting to obtain access token".invalidNel
+      case Success(token) => token.getToken.validNel
+      case Failure(error) => s"Failed to refresh access token: ${error.getMessage}".invalidNel
+    }
+  }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
index fd7b71ef4ee..405f22b3b20 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
@@ -33,7 +33,7 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
     val fileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = config)
     fileSystemProvider.drsConfig.marthaUrl should be("https://from.config")
     fileSystemProvider.drsCredentials match {
-      case GoogleDrsCredentials(_, ttl) => ttl should be(1.minute)
+      case GoogleOauthDrsCredentials(_, ttl) => ttl should be(1.minute)
       case error => fail(s"Expected GoogleDrsCredentials, found $error")
     }
     fileSystemProvider.fileProvider should be(a[DrsCloudNioFileProvider])
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
index 025d7c6d543..08683a6d820 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
@@ -17,7 +17,7 @@ class MockDrsCloudNioFileSystemProvider(config: Config = mockConfig,
                                           ),
                                         mockResolver: Option[EngineDrsPathResolver] = None,
                                        )
-  extends DrsCloudNioFileSystemProvider(config, GoogleDrsCredentials(NoCredentials.getInstance, config), drsReadInterpreter) {
+  extends DrsCloudNioFileSystemProvider(config, GoogleOauthDrsCredentials(NoCredentials.getInstance, config), drsReadInterpreter) {
 
   override lazy val drsPathResolver: EngineDrsPathResolver = {
     mockResolver getOrElse
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
index 116155753f1..8395233ce4d 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
@@ -14,7 +14,7 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
                                 httpClientBuilderOverride: Option[HttpClientBuilder] = None,
                                 accessTokenAcceptableTTL: Duration = Duration.Inf,
                                )
-  extends EngineDrsPathResolver(drsConfig, GoogleDrsCredentials(NoCredentials.getInstance, accessTokenAcceptableTTL)) {
+  extends EngineDrsPathResolver(drsConfig, GoogleOauthDrsCredentials(NoCredentials.getInstance, accessTokenAcceptableTTL)) {
 
   override protected lazy val httpClientBuilder: HttpClientBuilder =
     httpClientBuilderOverride getOrElse MockSugar.mock[HttpClientBuilder]
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
index b200d4b18de..3b7be2b38bd 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
@@ -36,12 +36,6 @@ class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage)
   opt[String]('t', "access-token-strategy").text(s"Access token strategy, must be one of '$Azure' or '$Google' (default '$Google')").
     action((s, c) =>
       c.copy(accessTokenStrategy = Option(s.toLowerCase())))
-  opt[String]('v', "vault-name").text("Azure vault name").
-    action((s, c) =>
-      c.copy(azureVaultName = Option(s)))
-  opt[String]('s', "secret-name").text("Azure secret name").
-    action((s, c) =>
-      c.copy(azureSecretName = Option(s)))
   opt[String]('i', "identity-client-id").text("Azure identity client id").
     action((s, c) =>
       c.copy(azureIdentityClientId = Option(s)))
@@ -54,11 +48,10 @@ class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage)
     c.accessTokenStrategy match {
       case Some(Azure) if c.googleRequesterPaysProject.nonEmpty =>
         Left(s"Requester pays project is only valid with access token strategy '$Google'")
-      case Some(Azure) if List(c.azureVaultName, c.azureSecretName).exists(_.isEmpty) =>
-        Left(s"Both vault name and secret name must be specified for access token strategy $Azure")
+      case Some(Google) if c.azureIdentityClientId.nonEmpty =>
+        Left(s"Identity client id is only valid with access token strategy '$Azure'")
       case Some(Azure) => Right(())
-      case Some(Google) if List(c.azureSecretName, c.azureVaultName, c.azureIdentityClientId).forall(_.isEmpty) => Right(())
-      case Some(Google) => Left(s"One or more specified options are only valid with access token strategy '$Azure'")
+      case Some(Google) => Right(())
       case Some(huh) => Left(s"Unrecognized access token strategy '$huh'")
       case None => Left("Programmer error, access token strategy should not be None")
     }
@@ -100,8 +93,6 @@ case class CommandLineArguments(accessTokenStrategy: Option[String] = Option(Goo
                                 drsObject: Option[String] = None,
                                 containerPath: Option[String] = None,
                                 googleRequesterPaysProject: Option[String] = None,
-                                azureVaultName: Option[String] = None,
-                                azureSecretName: Option[String] = None,
                                 azureIdentityClientId: Option[String] = None,
                                 manifestPath: Option[String] = None,
                                 googleRequesterPaysProjectConflict: Boolean = false)
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
index ac27367b932..944d418acbb 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
@@ -1,10 +1,9 @@
 package drs.localizer
 
-import cloud.nio.impl.drs.{DrsConfig, DrsPathResolver}
+import cloud.nio.impl.drs.{DrsConfig, DrsCredentials, DrsPathResolver}
 import common.validation.ErrorOr.ErrorOr
-import drs.localizer.accesstokens.AccessTokenStrategy
 
 
-class DrsLocalizerDrsPathResolver(drsConfig: DrsConfig, accessTokenStrategy: AccessTokenStrategy) extends DrsPathResolver(drsConfig) {
-  override def getAccessToken: ErrorOr[String] = accessTokenStrategy.getAccessToken()
+class DrsLocalizerDrsPathResolver(drsConfig: DrsConfig, drsCredentials: DrsCredentials) extends DrsPathResolver(drsConfig) {
+  override def getAccessToken: ErrorOr[String] = drsCredentials.getAccessToken
 }
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
index 05ecf0ce48c..df184efae92 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
@@ -4,11 +4,10 @@ import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO, IOApp}
 import cats.implicits._
 import cloud.nio.impl.drs.DrsPathResolver.{FatalRetryDisposition, RegularRetryDisposition}
-import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsPathResolver, MarthaField}
+import cloud.nio.impl.drs._
 import cloud.nio.spi.{CloudNioBackoff, CloudNioSimpleExponentialBackoff}
 import com.typesafe.scalalogging.StrictLogging
 import drs.localizer.CommandLineParser.AccessTokenStrategy.{Azure, Google}
-import drs.localizer.accesstokens.{AccessTokenStrategy, AzureB2CAccessTokenStrategy, GoogleAccessTokenStrategy}
 import drs.localizer.downloaders.AccessUrlDownloader.Hashes
 import drs.localizer.downloaders._
 import org.apache.commons.csv.{CSVFormat, CSVParser}
@@ -29,8 +28,8 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
     val localize: Option[IO[ExitCode]] = for {
       pa <- parsedArgs
       run <- pa.accessTokenStrategy.collect {
-        case Azure => runLocalizer(pa, AzureB2CAccessTokenStrategy(pa))
-        case Google => runLocalizer(pa, GoogleAccessTokenStrategy)
+        case Azure => runLocalizer(pa, AzureDrsCredentials(pa.azureIdentityClientId))
+        case Google => runLocalizer(pa, GoogleAppDefaultTokenStrategy)
       }
     } yield run
 
@@ -55,7 +54,7 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
     IO.pure(ExitCode.Error)
   }
 
-  def runLocalizer(commandLineArguments: CommandLineArguments, accessTokenStrategy: AccessTokenStrategy): IO[ExitCode] = {
+  def runLocalizer(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials): IO[ExitCode] = {
     commandLineArguments.manifestPath match {
       case Some(manifestPath) =>
         val manifestFile = new File(manifestPath)
@@ -63,31 +62,31 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
         val exitCodes: IO[List[ExitCode]] = csvParser.asScala.map(record => {
           val drsObject = record.get(0)
           val containerPath = record.get(1)
-          localizeFile(commandLineArguments, accessTokenStrategy, drsObject, containerPath)
+          localizeFile(commandLineArguments, drsCredentials, drsObject, containerPath)
         }).toList.sequence
         exitCodes.map(_.find(_ != ExitCode.Success).getOrElse(ExitCode.Success))
       case None =>
         val drsObject = commandLineArguments.drsObject.get
         val containerPath = commandLineArguments.containerPath.get
-        localizeFile(commandLineArguments, accessTokenStrategy, drsObject, containerPath)
+        localizeFile(commandLineArguments, drsCredentials, drsObject, containerPath)
     }
   }
 
-  private def localizeFile(commandLineArguments: CommandLineArguments, accessTokenStrategy: AccessTokenStrategy, drsObject: String, containerPath: String) = {
-    new DrsLocalizerMain(drsObject, containerPath, accessTokenStrategy, commandLineArguments.googleRequesterPaysProject).
+  private def localizeFile(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials, drsObject: String, containerPath: String) = {
+    new DrsLocalizerMain(drsObject, containerPath, drsCredentials, commandLineArguments.googleRequesterPaysProject).
       resolveAndDownloadWithRetries(downloadRetries = 3, checksumRetries = 1, defaultDownloaderFactory, Option(defaultBackoff)).map(_.exitCode)
   }
 }
 
 class DrsLocalizerMain(drsUrl: String,
                        downloadLoc: String,
-                       accessTokenStrategy: AccessTokenStrategy,
+                       drsCredentials: DrsCredentials,
                        requesterPaysProjectIdOption: Option[String]) extends StrictLogging {
 
   def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] = {
     IO {
       val drsConfig = DrsConfig.fromEnv(sys.env)
-      new DrsLocalizerDrsPathResolver(drsConfig, accessTokenStrategy)
+      new DrsLocalizerDrsPathResolver(drsConfig, drsCredentials)
     }
   }
 
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AccessTokenStrategy.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AccessTokenStrategy.scala
deleted file mode 100644
index 756f5371c0f..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AccessTokenStrategy.scala
+++ /dev/null
@@ -1,7 +0,0 @@
-package drs.localizer.accesstokens
-
-import common.validation.ErrorOr.ErrorOr
-
-trait AccessTokenStrategy {
-  def getAccessToken(): ErrorOr[String]
-}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
deleted file mode 100644
index 1634815d1f4..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
+++ /dev/null
@@ -1,40 +0,0 @@
-package drs.localizer.accesstokens
-
-import cats.syntax.validated._
-import com.azure.identity.DefaultAzureCredentialBuilder
-import com.azure.security.keyvault.secrets.{SecretClient, SecretClientBuilder}
-import common.validation.ErrorOr
-import common.validation.ErrorOr.{ErrorOr,ShortCircuitingFlatMap}
-import drs.localizer.CommandLineArguments
-
-case class AzureB2CAccessTokenStrategy(commandLineArguments: CommandLineArguments) extends AccessTokenStrategy {
-  override def getAccessToken(): ErrorOr[String] = {
-    commandLineArguments match {
-      case CommandLineArguments(_, _, _, _, Some(vault), Some(secret), clientId, _, _) =>
-        AzureKeyVaultClient(vault, clientId) flatMap { _.getSecret(secret) }
-      case invalid => s"Invalid command line arguments: $invalid".invalidNel
-    }
-  }
-}
-
-// Note: The AzureKeyVaultClient code here is basically a copy/paste of the code temporarily living in the TES backend.
-// All the current KeyVault interaction in Cromwell is temporary, but the code in the TES backend might be even more
-// temporary than this.
-class AzureKeyVaultClient(client: SecretClient) {
-  def getSecret(secretName: String): ErrorOr[String] = ErrorOr(client.getSecret(secretName).getValue)
-}
-
-object AzureKeyVaultClient {
-  def apply(vaultName: String, identityClientId: Option[String]): ErrorOr[AzureKeyVaultClient] = ErrorOr {
-    val credentialBuilder = identityClientId.foldLeft(new DefaultAzureCredentialBuilder()) {
-      (builder, clientId) => builder.managedIdentityClientId(clientId)
-    }
-
-    val client = new SecretClientBuilder()
-      .vaultUrl(s"https://${vaultName}.vault.azure.net")
-      .credential(credentialBuilder.build())
-      .buildClient()
-
-    new AzureKeyVaultClient(client)
-  }
-}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala
deleted file mode 100644
index 5af2b8af441..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala
+++ /dev/null
@@ -1,28 +0,0 @@
-package drs.localizer.accesstokens
-
-import cats.syntax.validated._
-import com.google.auth.oauth2.GoogleCredentials
-import common.validation.ErrorOr.ErrorOr
-
-import scala.jdk.CollectionConverters._
-import scala.util.{Failure, Success, Try}
-
-/**
- * Strategy for obtaining an access token from Google Application Default credentials that are assumed to already exist.
- */
-case object GoogleAccessTokenStrategy extends AccessTokenStrategy {
-  private final val UserInfoEmailScope = "https://www.googleapis.com/auth/userinfo.email"
-  private final val UserInfoProfileScope = "https://www.googleapis.com/auth/userinfo.profile"
-  private final val UserInfoScopes = List(UserInfoEmailScope, UserInfoProfileScope)
-
-  override def getAccessToken(): ErrorOr[String] = {
-    Try {
-      val scopedCredentials = GoogleCredentials.getApplicationDefault().createScoped(UserInfoScopes.asJava)
-      scopedCredentials.refreshAccessToken().getTokenValue
-    } match {
-      case Success(null) => "null token value attempting to refresh access token".invalidNel
-      case Success(value) => value.validNel
-      case Failure(e) => s"Failed to refresh access token: ${e.getMessage}".invalidNel
-    }
-  }
-}
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
index 349b2d6887b..7be30be8ac0 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
@@ -13,8 +13,6 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   private val drsObject = "drs://provider/object"
   private val containerPath = "/cromwell_root/my.bam"
   private val requesterPaysProject = "i_heart_egress"
-  private val azureVaultName = "Kwikset"
-  private val azureSecretName = "shhh"
   private val azureIdentityClientId = "itme@azure.com"
   private val manifestPath = "/my/manifest.txt"
 
@@ -39,8 +37,6 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject shouldBe empty
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
     args.manifestPath shouldBe empty
   }
@@ -51,8 +47,6 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject.get shouldBe requesterPaysProject
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
     args.manifestPath shouldBe empty
   }
@@ -64,8 +58,6 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject.get shouldBe requesterPaysProject
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
     args.manifestPath shouldBe empty
   }
@@ -77,8 +69,6 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject.get shouldBe requesterPaysProject
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
     args.manifestPath shouldBe empty
   }
@@ -94,8 +84,6 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath shouldBe empty
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject shouldBe empty
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
     args.manifestPath.get shouldBe manifestPath
   }
@@ -110,7 +98,7 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args shouldBe None
   }
 
-  it should "successfully parse an explicit Google access token stregy invocation" in {
+  it should "successfully parse an explicit Google access token strategy invocation" in {
     val args = parser.parse(Array(
       "--access-token-strategy", "google",
       drsObject,
@@ -122,43 +110,13 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject.get shouldBe requesterPaysProject
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
     args.manifestPath shouldBe empty
   }
 
-  it should "fail to parse an Azure invocation missing vault name and secret name" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      drsObject, containerPath), CommandLineArguments())
-
-    args shouldBe None
-  }
-
-  it should "fail to parse an Azure invocation missing vault name" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--secret-name", azureSecretName,
-      drsObject, containerPath), CommandLineArguments())
-
-    args shouldBe None
-  }
-
-  it should "fail to parse an Azure invocation missing secret name" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--vault-name", azureVaultName,
-      drsObject, containerPath), CommandLineArguments())
-
-    args shouldBe None
-  }
-
   it should "fail to parse an Azure invocation that specifies requester pays" in {
     val args = parser.parse(Array(
       "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--secret-name", azureSecretName,
-      "--vault-name", azureVaultName,
       drsObject,
       containerPath,
       "--requester-pays-project", requesterPaysProject), CommandLineArguments())
@@ -169,25 +127,19 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   it should "successfully parse an Azure invocation" in {
     val args = parser.parse(Array(
       "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--secret-name", azureSecretName,
-      "--vault-name", azureVaultName,
       drsObject, containerPath), CommandLineArguments()).get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Azure
     args.googleRequesterPaysProject shouldBe empty
-    args.azureVaultName.get shouldBe azureVaultName
-    args.azureSecretName.get shouldBe azureSecretName
     args.azureIdentityClientId shouldBe empty
     args.manifestPath shouldBe empty
   }
 
-  it should "successfully parse an Azure invocation with all the trimmings" in {
+  it should "successfully parse an Azure invocation with identity" in {
     val args = parser.parse(Array(
       "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--vault-name", azureVaultName,
-      "--secret-name", azureSecretName,
       "--identity-client-id", azureIdentityClientId,
       drsObject, containerPath), CommandLineArguments()).get
 
@@ -195,8 +147,6 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Azure
     args.googleRequesterPaysProject shouldBe empty
-    args.azureVaultName.get shouldBe azureVaultName
-    args.azureSecretName.get shouldBe azureSecretName
     args.azureIdentityClientId.get shouldBe azureIdentityClientId
     args.manifestPath shouldBe empty
   }
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
index 84b407cec41..b306c0a3a94 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
@@ -4,10 +4,10 @@ import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO}
 import cats.syntax.validated._
 import cloud.nio.impl.drs.DrsPathResolver.FatalRetryDisposition
-import cloud.nio.impl.drs.{AccessUrl, DrsConfig, MarthaField, MarthaResponse}
+import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsCredentials, MarthaField, MarthaResponse}
 import common.assertion.CromwellTimeoutSpec
+import common.validation.ErrorOr.ErrorOr
 import drs.localizer.MockDrsLocalizerDrsPathResolver.{FakeAccessTokenStrategy, FakeHashes}
-import drs.localizer.accesstokens.AccessTokenStrategy
 import drs.localizer.downloaders.AccessUrlDownloader.Hashes
 import drs.localizer.downloaders._
 import org.scalatest.flatspec.AnyFlatSpec
@@ -341,5 +341,7 @@ class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig) extends
 
 object MockDrsLocalizerDrsPathResolver {
   val FakeHashes: Option[Map[String, String]] = Option(Map("md5" -> "abc123", "crc32c" -> "34fd67"))
-  val FakeAccessTokenStrategy: AccessTokenStrategy = () => "testing code: do not call me".invalidNel
+  val FakeAccessTokenStrategy: DrsCredentials = new DrsCredentials {
+    override def getAccessToken: ErrorOr[String] = "testing code: do not call me".invalidNel
+  }
 }
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
index bc7fb598a81..ae49cf0b5e4 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
@@ -2,13 +2,12 @@ package cromwell.filesystems.drs
 
 import akka.actor.ActorSystem
 import cats.data.Validated.{Invalid, Valid}
-import cloud.nio.impl.drs.{AzureDrsCredentials, DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import cloud.nio.impl.drs.{AzureDrsCredentials, DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.api.services.oauth2.Oauth2Scopes
 import com.typesafe.config.Config
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.{PathBuilder, PathBuilderFactory}
-import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -24,10 +23,8 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
   private lazy val googleConfiguration: GoogleConfiguration = GoogleConfiguration(globalConfig)
   private lazy val scheme = instanceConfig.getString("auth")
 
-  // For Azure support
+  // For Azure support - this should be the UAMI client id
   private val dataAccessIdentityKey = "data_access_identity"
-  private lazy val azureKeyVault = instanceConfig.as[Option[String]]("azure-keyvault-name")
-  private lazy val azureSecretName = instanceConfig.as[Option[String]]("azure-token-secret")
 
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] = {
     Future {
@@ -37,13 +34,12 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
         Oauth2Scopes.USERINFO_PROFILE
       )
 
-      val (googleAuthMode, drsCredentials) = (scheme, azureKeyVault, azureSecretName) match {
-        case ("azure", Some(vaultName), Some(secretName)) => (None, AzureDrsCredentials(options.get(dataAccessIdentityKey).toOption, vaultName, secretName))
-        case ("azure", _, _) => throw new RuntimeException(s"Error while instantiating DRS path builder factory. Couldn't find azure-keyvault-name and azure-token-secret in config.")
-        case (googleAuthScheme, _, _) => googleConfiguration.auth(googleAuthScheme) match {
+      val (googleAuthMode, drsCredentials) = scheme match {
+        case "azure" => (None, AzureDrsCredentials(options.get(dataAccessIdentityKey).toOption))
+        case googleAuthScheme => googleConfiguration.auth(googleAuthScheme) match {
           case Valid(auth) => (
             Option(auth),
-            GoogleDrsCredentials(auth.credentials(options.get(_).get, marthaScopes), singletonConfig.config)
+            GoogleOauthDrsCredentials(auth.credentials(options.get(_).get, marthaScopes), singletonConfig.config)
           )
           case Invalid(error) => throw new RuntimeException(s"Error while instantiating DRS path builder factory. Errors: ${error.toString}")
         }
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
index 242b662d5ea..bc556c9bdf3 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
@@ -1,7 +1,7 @@
 package cromwell.filesystems.drs
 
 import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.cloud.NoCredentials
 import com.typesafe.config.{Config, ConfigFactory}
 import cromwell.core.TestKitSuite
@@ -387,7 +387,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   private lazy val fakeCredentials = NoCredentials.getInstance
 
   private lazy val drsPathBuilder = DrsPathBuilder(
-    new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+    new DrsCloudNioFileSystemProvider(marthaConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
     None,
   )
 }
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index d3ba06edd55..3aac8c77c8c 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -12,7 +12,6 @@ object Dependencies {
   // https://github.com/sbt/sbt/issues/4531
   private val azureStorageBlobNioV = "12.0.0-beta.19"
   private val azureIdentitySdkV = "1.4.6"
-  private val azureKeyVaultSdkV = "4.3.8"
   private val betterFilesV = "3.9.1"
   /*
   cats-effect, fs2, http4s, and sttp (also to v3) should all be upgraded at the same time to use cats-effect 3.x.
@@ -205,9 +204,6 @@ object Dependencies {
     "com.azure" % "azure-identity" % azureIdentitySdkV
       exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
       exclude("jakarta.activation", "jakarta.activation-api"),
-    "com.azure" % "azure-security-keyvault-secrets" % azureKeyVaultSdkV
-      exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
-      exclude("jakarta.activation", "jakarta.activation-api"),
     "com.azure" % "azure-core-management" % "1.7.1",
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0"
   )
diff --git a/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml b/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml
index 1ca941fbfa9..c718d7ff1f1 100644
--- a/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml	
+++ b/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml	
@@ -5,7 +5,7 @@
     </envs>
     <option name="MAIN_CLASS_NAME" value="drs.localizer.DrsLocalizerMain" />
     <module name="cromwell-drs-localizer" />
-    <option name="PROGRAM_PARAMETERS" value="--access-token-strategy azure drs://jade.datarepo-dev.broadinstitute.org/v1_f3c32ddd-20eb-4033-9716-46866521a3a4_8d651e95-38ce-4bc8-a8a4-8a4cd9513db1 $USER_HOME$/Downloads/NA12878_PLUMBING_wgs.g.vcf.gz.tbi --vault-name vault --secret-name secret --identity-client-id identity" />
+    <option name="PROGRAM_PARAMETERS" value="--access-token-strategy azure drs://jade.datarepo-dev.broadinstitute.org/v1_f3c32ddd-20eb-4033-9716-46866521a3a4_8d651e95-38ce-4bc8-a8a4-8a4cd9513db1 $USER_HOME$/Downloads/NA12878_PLUMBING_wgs.g.vcf.gz.tbi --identity-client-id identity" />
     <method v="2">
       <option name="Make" enabled="true" />
     </method>
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
index 3535f1db8d8..d9fe26e7c0c 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
@@ -1,7 +1,7 @@
 package cromwell.backend.google.pipelines.v2alpha1
 
 import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.cloud.NoCredentials
 import com.typesafe.config.{Config, ConfigFactory}
 import common.assertion.CromwellTimeoutSpec
@@ -39,7 +39,7 @@ class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   it should "create a DRS input parameter" in {
 
     val drsPathBuilder = DrsPathBuilder(
-      new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+      new DrsCloudNioFileSystemProvider(marthaConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
       None,
     )
     val drsPath = drsPathBuilder.build("drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba").get
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
index 093ecd3fa27..5764bbbc2e4 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
@@ -3,7 +3,7 @@ package cromwell.backend.google.pipelines.v2beta
 import java.nio.file.Paths
 import cats.data.NonEmptyList
 import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.cloud.NoCredentials
 import com.typesafe.config.{Config, ConfigFactory}
 import common.assertion.CromwellTimeoutSpec
@@ -68,7 +68,7 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Cro
         throw new UnsupportedOperationException("PipelinesApiAsyncBackendJobExecutionActorSpec doesn't need to use drs read interpreter.")
 
       DrsPathBuilder(
-        new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+        new DrsCloudNioFileSystemProvider(marthaConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
         None,
       )
     }

From 2be07871ac0eebc222f7a51c656403e69cbc3bc0 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 1 Dec 2022 14:00:30 -0500
Subject: [PATCH 112/326] WX-853 Remove most CWL (#6955)

---
 CHANGELOG.md                                  |     5 +
 build.sbt                                     |    27 -
 .../bcbio_joint_gvcf.test                     |    23 -
 .../integrationTestCases/bcbio_prealign.test  |    20 -
 .../integrationTestCases/bcbio_rnaseq.test    |    19 -
 .../integrationTestCases/bcbio_somatic.test   |    22 -
 .../integrationTestCases/bcbio_svcall.test    |    22 -
 .../bcbio_wes-chr21-test-workflow.test        |    22 -
 .../cwl/bcbio/bcbio.options                   |     5 -
 .../main-gvcf-joint-samples.json              |   615 -
 .../gvcf-joint-workflow/main-gvcf-joint.cwl   |   794 -
 .../steps/alignment_to_rec.cwl                |   198 -
 .../steps/batch_for_jointvc.cwl               |   329 -
 .../steps/batch_for_variantcall.cwl           |   401 -
 .../steps/combine_sample_regions.cwl          |    99 -
 .../steps/compare_to_rm.cwl                   |   337 -
 .../steps/concat_batch_variantcalls.cwl       |   196 -
 .../concat_batch_variantcalls_jointvc.cwl     |   209 -
 .../steps/finalize_jointvc.cwl                |   331 -
 .../steps/get_parallel_regions.cwl            |   171 -
 .../steps/get_parallel_regions_jointvc.cwl    |   184 -
 .../steps/merge_split_alignments.cwl          |   168 -
 .../steps/multiqc_summary.cwl                 |    95 -
 .../steps/pipeline_summary.cwl                |   219 -
 .../steps/postprocess_alignment.cwl           |   223 -
 .../steps/postprocess_alignment_to_rec.cwl    |   233 -
 .../steps/postprocess_variants.cwl            |   195 -
 .../steps/prep_align_inputs.cwl               |   142 -
 .../steps/prep_samples.cwl                    |    95 -
 .../steps/prep_samples_to_rec.cwl             |    85 -
 .../steps/process_alignment.cwl               |   198 -
 .../gvcf-joint-workflow/steps/qc_to_rec.cwl   |   295 -
 .../gvcf-joint-workflow/steps/run_jointvc.cwl |   203 -
 .../steps/summarize_vc.cwl                    |   225 -
 .../steps/variantcall_batch_region.cwl        |   266 -
 .../gvcf-joint-workflow/wf-alignment.cwl      |   143 -
 .../gvcf-joint-workflow/wf-jointcall.cwl      |   360 -
 .../gvcf-joint-workflow/wf-variantcall.cwl    |   329 -
 .../main-prealign-samples.json                |   526 -
 .../bcbio/prealign-workflow/main-prealign.cwl |   672 -
 .../steps/batch_for_variantcall.cwl           |   407 -
 .../steps/combine_sample_regions.cwl          |   101 -
 .../prealign-workflow/steps/compare_to_rm.cwl |   315 -
 .../steps/concat_batch_variantcalls.cwl       |   199 -
 .../steps/get_parallel_regions.cwl            |   174 -
 .../steps/multiqc_summary.cwl                 |    95 -
 .../steps/organize_noalign.cwl                |    59 -
 .../steps/pipeline_summary.cwl                |   221 -
 .../steps/postprocess_alignment.cwl           |   221 -
 .../steps/postprocess_alignment_to_rec.cwl    |   229 -
 .../steps/postprocess_variants.cwl            |   183 -
 .../prealign-workflow/steps/prep_samples.cwl  |    93 -
 .../steps/prep_samples_to_rec.cwl             |    81 -
 .../prealign-workflow/steps/qc_to_rec.cwl     |   299 -
 .../prealign-workflow/steps/summarize_vc.cwl  |   198 -
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 .../main-somatic-samples.json                 |   680 -
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 .../svcall-workflow/steps/batch_for_sv.cwl    |   359 -
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 ...InitialWorkDirRequirement.inline_file.test |    16 -
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 .../cwl_cache_between_workflows.test          |    19 -
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 .../cwl_disk_resources_papiv2.test            |    17 -
 .../standardTestCases/cwl_docker_size.test    |    21 -
 .../cwl_docker_size/cwl_docker_size.cwl       |    40 -
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 .../cwl_format/cwl_format.cwl                 |    25 -
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 ..._inputdir_zero_doesnt_localize_papiv2.test |    17 -
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 .../cwl_prefix_for_array/prefix_for_array.cwl |    23 -
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 .../cwl_recursive_link_directories.test       |    18 -
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 .../cwl_relative_imports/cwl_glob_sort.cwl    |    16 -
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 .../cwl_inputdir_zero_doesnt_localize.cwl     |   129 -
 .../cwl_resources/cwl_resources.cwl           |    27 -
 .../cwl_resources_papiv2.test                 |    17 -
 .../cwl_restart/cwl_restart.cwl               |   117 -
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 .../standardTestCases/cwl_run/1st-tool.cwl    |     9 -
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 .../cwl_secondary_files.test                  |    21 -
 .../cwl_secondary_files/bam.txt               |     0
 .../cwl_secondary_files/bam.txt.also          |     0
 .../cwl_secondary_files/bar.txt               |     0
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 core/src/main/resources/reference.conf        |    23 -
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 .../scala/cwl/ArgumentToCommandPart.scala     |    26 -
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 cwl/src/main/scala/cwl/CommandLineTool.scala  |   439 -
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 cwl/src/main/scala/cwl/CwlCodecs.scala        |   153 -
 cwl/src/main/scala/cwl/CwlDecoder.scala       |    84 -
 .../scala/cwl/CwlExecutableValidation.scala   |    38 -
 .../scala/cwl/CwlExpressionCommandPart.scala  |   146 -
 .../CwlJsonToDelayedCoercionFunction.scala    |    90 -
 cwl/src/main/scala/cwl/CwlToRun.scala         |    11 -
 cwl/src/main/scala/cwl/CwlType.scala          |   284 -
 cwl/src/main/scala/cwl/CwlVersion.scala       |     7 -
 cwl/src/main/scala/cwl/CwlWomExpression.scala |   260 -
 cwl/src/main/scala/cwl/CwltoolRunner.scala    |    71 -
 cwl/src/main/scala/cwl/EnumSchema.scala       |    35 -
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 cwl/src/main/scala/cwl/ExpressionTool.scala   |   136 -
 cwl/src/main/scala/cwl/FileParameter.scala    |   150 -
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 cwl/src/main/scala/cwl/GlobEvaluator.scala    |    67 -
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 cwl/src/main/scala/cwl/InputParameter.scala   |   190 -
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 cwl/src/main/scala/cwl/OutputParameter.scala  |    62 -
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 cwl/src/main/scala/cwl/ParameterContext.scala |    17 -
 .../main/scala/cwl/RequirementsAndHints.scala |     9 -
 .../main/scala/cwl/RunOutputsToTypeMap.scala  |    45 -
 cwl/src/main/scala/cwl/RunToEmbeddedCwl.scala |    36 -
 .../main/scala/cwl/RunToInputTypeMap.scala    |    37 -
 cwl/src/main/scala/cwl/ScatterLogic.scala     |   263 -
 cwl/src/main/scala/cwl/ScatterMethod.scala    |     9 -
 .../cwl/StringOrStringArrayToStringList.scala |    12 -
 cwl/src/main/scala/cwl/Tool.scala             |   189 -
 cwl/src/main/scala/cwl/TypeAliases.scala      |   115 -
 cwl/src/main/scala/cwl/Workflow.scala         |   246 -
 cwl/src/main/scala/cwl/WorkflowStep.scala     |   537 -
 .../main/scala/cwl/WorkflowStepInput.scala    |   155 -
 .../cwl/WorkflowStepInputExpression.scala     |    51 -
 .../WorkflowStepInputMergeExpression.scala    |    84 -
 .../main/scala/cwl/command/ParentName.scala   |    10 -
 .../scala/cwl/command/StringCommandPart.scala |    18 -
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 .../cwl/internal/CwlEcmaScriptDecoder.scala   |   124 -
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 .../cwl/internal/EnhancedRhinoSandbox.scala   |   167 -
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 cwl/src/main/scala/cwl/model.scala            |   310 -
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 cwl/src/main/scala/cwl/ontology/Schema.scala  |   180 -
 cwl/src/main/scala/cwl/package.scala          |   154 -
 .../cwl/preprocessor/CwlCanonicalizer.scala   |   249 -
 .../cwl/preprocessor/CwlPreProcessor.scala    |   236 -
 .../scala/cwl/preprocessor/CwlReference.scala |    82 -
 .../RequirementToAttributeMap.scala           |    79 -
 .../ResourceRequirementToWomExpression.scala  |    15 -
 cwl/src/test/resources/1st-tool.cwl           |     9 -
 cwl/src/test/resources/1st-workflow.cwl       |    23 -
 cwl/src/test/resources/application.conf       |    14 -
 cwl/src/test/resources/arguments.cwl          |    22 -
 cwl/src/test/resources/bad.cwl                |     1 -
 cwl/src/test/resources/bad2.cwl               |     1 -
 cwl/src/test/resources/brokenlinks.cwl        |    23 -
 cwl/src/test/resources/cwl/lodash.js          | 17112 ------
 cwl/src/test/resources/cwl/ontology/EDAM.owl  | 51294 ----------------
 .../test/resources/cwl/ontology/gx_edam.ttl   |     7 -
 .../complex_workflow/expected_result.json     |   204 -
 .../complex_workflow/root_workflow.cwl        |    41 -
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 .../deep_nesting/parseInt-tool.cwl            |    14 -
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 .../simple_workflow/root_workflow.cwl         |    23 -
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 cwl/src/test/resources/dir_example.cwl        |    17 -
 cwl/src/test/resources/env.cwl                |    10 -
 cwl/src/test/resources/exampledir/example.txt |     1 -
 cwl/src/test/resources/file_example.cwl       |    17 -
 cwl/src/test/resources/file_size_example.cwl  |    18 -
 cwl/src/test/resources/links_dont_parse.cwl   |    23 -
 cwl/src/test/resources/logback-test.xml       |    17 -
 cwl/src/test/resources/nestedworkflows.cwl    |    52 -
 cwl/src/test/resources/tar-param.cwl          |    17 -
 cwl/src/test/resources/three_step.cwl         |   112 -
 .../test/scala/cwl/CommandLineToolSpec.scala  |   279 -
 .../cwl/CommandOutputExpressionSpec.scala     |    57 -
 cwl/src/test/scala/cwl/CwlDecoderSpec.scala   |    48 -
 .../scala/cwl/CwlEcmaScriptDecoderSpec.scala  |    77 -
 .../scala/cwl/CwlEcmaScriptEncoderSpec.scala  |    35 -
 .../cwl/CwlExpressionCommandPartSpec.scala    |    34 -
 .../scala/cwl/CwlInputValidationSpec.scala    |   203 -
 .../test/scala/cwl/CwlWorkflowWomSpec.scala   |   216 -
 cwl/src/test/scala/cwl/DirectorySpec.scala    |    41 -
 .../test/scala/cwl/ExportCwlSamplesSpec.scala |   146 -
 .../scala/cwl/ExpressionEvaluatorSpec.scala   |    24 -
 .../cwl/ExpressionInterpolatorSpec.scala      |   121 -
 cwl/src/test/scala/cwl/FileSpec.scala         |    54 -
 .../scala/cwl/FullyQualifiedNameSpec.scala    |    27 -
 .../test/scala/cwl/LocalIoFunctionSet.scala   |    48 -
 .../test/scala/cwl/ParseBigThreeSpec.scala    |    34 -
 cwl/src/test/scala/cwl/ParsingSpec.scala      |    63 -
 cwl/src/test/scala/cwl/ScatterLogicSpec.scala |   140 -
 cwl/src/test/scala/cwl/TestSetup.scala        |     9 -
 .../scala/cwl/WomTypeConversionSpec.scala     |   134 -
 .../scala/cwl/WomValueJsonFormatter.scala     |    27 -
 .../cwl/WorkflowStepInputExpressionSpec.scala |    59 -
 .../scala/cwl/WorkflowStepInputSpec.scala     |   109 -
 .../cwl/internal/EcmaScriptUtilSpec.scala     |    96 -
 .../internal/EnhancedRhinoSandboxSpec.scala   |   141 -
 .../test/scala/cwl/ontology/SchemaSpec.scala  |   114 -
 .../preprocessor/CwlPreProcessorSpec.scala    |   125 -
 .../cwl/preprocessor/CwlReferenceSpec.scala   |    79 -
 .../routes/wes/ServiceInfoSpec.scala          |     2 +-
 project/Dependencies.scala                    |    49 +-
 project/plugins.sbt                           |     1 +
 .../scala/cromwell/CommandLineArguments.scala |    44 +-
 server/src/test/resources/cwl_glob_sort.cwl   |    16 -
 .../cromwell/CromwellCommandLineSpec.scala    |    26 -
 src/ci/bin/testSingleWorkflowRunner.sh        |    23 -
 .../main/scala/womtool/graph/WomGraph.scala   |    22 +-
 .../scala/womtool/input/WomGraphMaker.scala   |     4 +-
 429 files changed, 14 insertions(+), 120546 deletions(-)
 delete mode 100644 centaur/src/main/resources/integrationTestCases/bcbio_joint_gvcf.test
 delete mode 100644 centaur/src/main/resources/integrationTestCases/bcbio_prealign.test
 delete mode 100644 centaur/src/main/resources/integrationTestCases/bcbio_rnaseq.test
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diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1bba52ebded..408660d8953 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -54,6 +54,11 @@ languages {
 }
 ```
 
+### CWL implementation removed
+
+This release removes the `cwl` top-level artifact. Some nonfunctional references may remain, and will be addressed over time. 
+
+For more information, see the [Cromwell 79 release notes](https://github.com/broadinstitute/cromwell/releases/tag/79). 
 
 ## 84 Release Notes
 
diff --git a/build.sbt b/build.sbt
index 948d18039ab..e2e0c490767 100644
--- a/build.sbt
+++ b/build.sbt
@@ -74,12 +74,6 @@ lazy val wdlTransformsBiscayne = (project in wdlTransformsRoot / "biscayne")
   .dependsOn(common % "test->test")
   .dependsOn(wom % "test->test")
 
-lazy val cwl = project
-  .withLibrarySettings("cromwell-cwl", cwlDependencies)
-  .dependsOn(wom)
-  .dependsOn(wom % "test->test")
-  .dependsOn(common % "test->test")
-
 lazy val core = project
   .withLibrarySettings("cromwell-core", coreDependencies)
   .dependsOn(wom)
@@ -183,7 +177,6 @@ lazy val services = project
   .dependsOn(wdlDraft2LanguageFactory % "test->test") // because the WaaS tests init language config with all languages
   .dependsOn(wdlDraft3LanguageFactory % "test->test")
   .dependsOn(wdlBiscayneLanguageFactory % "test->test")
-  .dependsOn(cwlV1_0LanguageFactory % "test->test")
   .dependsOn(core % "test->test")
   .dependsOn(ftpFileSystem % "test->test")
   .dependsOn(common % "test->test")
@@ -264,7 +257,6 @@ lazy val engine = project
   .dependsOn(azureBlobFileSystem % "test->test")
   .dependsOn(`cloud-nio-spi`)
   .dependsOn(languageFactoryCore)
-  .dependsOn(cwlV1_0LanguageFactory % "test->test")
   .dependsOn(wdlDraft2LanguageFactory % "test->test")
   .dependsOn(wdlDraft3LanguageFactory % "test->test")
   .dependsOn(wdlBiscayneLanguageFactory % "test->test")
@@ -279,20 +271,11 @@ lazy val engine = project
 
 // Executables
 
-lazy val centaurCwlRunner = project
-  .withExecutableSettings("centaur-cwl-runner", centaurCwlRunnerDependencies, buildDocker = false)
-  .dependsOn(cwl)
-  .dependsOn(centaur)
-  .dependsOn(gcsFileSystem)
-  .dependsOn(ftpFileSystem)
-  .dependsOn(common % "test->test")
-
 lazy val womtool = project
   .withExecutableSettings("womtool", womtoolDependencies)
   .dependsOn(wdlDraft2LanguageFactory)
   .dependsOn(wdlDraft3LanguageFactory)
   .dependsOn(wdlBiscayneLanguageFactory)
-  .dependsOn(cwlV1_0LanguageFactory)
   .dependsOn(wom % "test->test")
   .dependsOn(common % "test->test")
 
@@ -338,12 +321,6 @@ lazy val wdlBiscayneLanguageFactory = (project in languageFactoryRoot / "wdl-bis
   .dependsOn(wdlTransformsBiscayne)
   .dependsOn(common % "test->test")
 
-lazy val cwlV1_0LanguageFactory = (project in languageFactoryRoot / "cwl-v1-0")
-  .withLibrarySettings("cwl-v1-0")
-  .dependsOn(languageFactoryCore)
-  .dependsOn(cwl)
-  .dependsOn(common % "test->test")
-
 lazy val `cloud-nio-spi` = (project in cloudNio / "cloud-nio-spi")
   .withLibrarySettings(libraryName = "cloud-nio-spi", dependencies = spiDependencies)
   .dependsOn(common % "test->test")
@@ -386,7 +363,6 @@ lazy val server = project
   .dependsOn(wdlDraft2LanguageFactory)
   .dependsOn(wdlDraft3LanguageFactory)
   .dependsOn(wdlBiscayneLanguageFactory)
-  .dependsOn(cwlV1_0LanguageFactory)
   .dependsOn(engine % "test->test")
   .dependsOn(common % "test->test")
 
@@ -403,14 +379,11 @@ lazy val root = (project in file("."))
   .aggregate(azureBlobFileSystem)
   .aggregate(backend)
   .aggregate(centaur)
-  .aggregate(centaurCwlRunner)
   .aggregate(cloudSupport)
   .aggregate(common)
   .aggregate(core)
   .aggregate(cromiam)
   .aggregate(cromwellApiClient)
-  .aggregate(cwl)
-  .aggregate(cwlV1_0LanguageFactory)
   .aggregate(databaseMigration)
   .aggregate(databaseSql)
   .aggregate(dockerHashing)
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_joint_gvcf.test b/centaur/src/main/resources/integrationTestCases/bcbio_joint_gvcf.test
deleted file mode 100644
index ef32cbc7d7c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_joint_gvcf.test
+++ /dev/null
@@ -1,23 +0,0 @@
-name: bcbio_joint_gvcf
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-
-files {
-  workflow: cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl
-  inputs: cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json
-  imports: [
-    cwl/bcbio/gvcf-joint-workflow/steps,
-    cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl,
-    cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl,
-    cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_prealign.test b/centaur/src/main/resources/integrationTestCases/bcbio_prealign.test
deleted file mode 100644
index 2c4a6db3f45..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_prealign.test
+++ /dev/null
@@ -1,20 +0,0 @@
-name: bcbio_prealign
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/prealign-workflow/main-prealign.cwl
-  inputs: cwl/bcbio/prealign-workflow/main-prealign-samples.json
-    imports: [
-      cwl/bcbio/prealign-workflow/steps,
-      cwl/bcbio/prealign-workflow/wf-variantcall.cwl
-    ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_rnaseq.test b/centaur/src/main/resources/integrationTestCases/bcbio_rnaseq.test
deleted file mode 100644
index 64ac876c568..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_rnaseq.test
+++ /dev/null
@@ -1,19 +0,0 @@
-name: bcbio_rnaseq
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl
-  inputs: cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json
-  imports: [
-    cwl/bcbio/rnaseq-workflow/steps
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_somatic.test b/centaur/src/main/resources/integrationTestCases/bcbio_somatic.test
deleted file mode 100644
index 440099f280e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_somatic.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: bcbio_somatic
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/somatic-workflow/main-somatic.cwl
-  inputs: cwl/bcbio/somatic-workflow/main-somatic-samples.json
-  imports: [
-    cwl/bcbio/somatic-workflow/steps,
-    cwl/bcbio/somatic-workflow/wf-alignment.cwl,
-    cwl/bcbio/somatic-workflow/wf-svcall.cwl,
-    cwl/bcbio/somatic-workflow/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_svcall.test b/centaur/src/main/resources/integrationTestCases/bcbio_svcall.test
deleted file mode 100644
index 9116814fe6d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_svcall.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: bcbio_svcall
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/svcall-workflow/main-svcall.cwl
-  inputs: cwl/bcbio/svcall-workflow/main-svcall-samples.json
-  imports: [
-    cwl/bcbio/svcall-workflow/steps,
-    cwl/bcbio/svcall-workflow/wf-alignment.cwl,
-    cwl/bcbio/svcall-workflow/wf-svcall.cwl,
-    cwl/bcbio/svcall-workflow/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_wes-chr21-test-workflow.test b/centaur/src/main/resources/integrationTestCases/bcbio_wes-chr21-test-workflow.test
deleted file mode 100644
index 1969d6bef66..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_wes-chr21-test-workflow.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: wes_chr21_test-workflow
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
-  inputs: cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json
-  imports: [
-    cwl/bcbio/wes_chr21_test-workflow-gcp/steps,
-    cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl,
-    cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl,
-    cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/bcbio.options b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/bcbio.options
deleted file mode 100644
index 1340bda7f1c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/bcbio.options
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-  "default_runtime_attributes": {
-    "bootDiskSizeGb": 20
-  }
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json
deleted file mode 100644
index b7080e81448..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json
+++ /dev/null
@@ -1,615 +0,0 @@
-{
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__adapters": [
-        [
-            "polyx"
-        ],
-        [
-            "polyx"
-        ]
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
-        },
-        null
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants"
-        ],
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "gvcf"
-        ],
-        [
-            "gvcf"
-        ]
-    ],
-    "config__algorithm__trim_reads": [
-        "read_through",
-        "False"
-    ],
-    "config__algorithm__validate": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/7_100326_FC6107FAAXX-grade.vcf"
-        },
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__variantcaller": [
-        [
-            "gatk-haplotype",
-            "strelka2"
-        ],
-        [
-            "gatk-haplotype",
-            "strelka2"
-        ]
-    ],
-    "config__algorithm__vcfanno": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ]
-    ],
-    "description": [
-        "Test1",
-        "Test2"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX.bam"
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        "b1",
-        "b1"
-    ],
-    "metadata__phenotype": [
-        "",
-        ""
-    ],
-    "reference__bwa__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__lb": [
-        null,
-        null
-    ],
-    "rgnames__pl": [
-        "illumina",
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__rg": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__sample": [
-        "Test1",
-        "Test2"
-    ],
-    "vrn_file": [
-        null,
-        null
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl
deleted file mode 100644
index a798100dc12..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl
+++ /dev/null
@@ -1,794 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: config__algorithm__coverage
-    source: config__algorithm__coverage
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: batch_for_jointvc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: jointvc_batch_rec
-  run: steps/batch_for_jointvc.cwl
-- id: jointcall
-  in:
-  - id: jointvc_batch_rec
-    source: batch_for_jointvc/jointvc_batch_rec
-  out:
-  - id: jointvc_rec
-  - id: vrn_file_joint
-  run: wf-jointcall.cwl
-  scatter:
-  - jointvc_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: jointvc_rec
-    source: jointcall/jointvc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/alignment_to_rec.cwl
deleted file mode 100644
index 1379c575535..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-          items: string
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: rgnames__pu
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_jointvc.cwl
deleted file mode 100644
index 523567ed191..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_jointvc.cwl
+++ /dev/null
@@ -1,329 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=jointvc_batch_rec:resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: jointvc_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index ca40e5b30cf..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,401 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 2048
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index d876db22bd2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index 06152084c58..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,337 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index d486086c79e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,196 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl
deleted file mode 100644
index dbb0f54be94..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl
+++ /dev/null
@@ -1,209 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file_joint
-- sentinel_inputs=jointvc_batch_rec:record,region:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: region
-  type:
-    items: string
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/finalize_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/finalize_jointvc.cwl
deleted file mode 100644
index fd1e04762e4..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/finalize_jointvc.cwl
+++ /dev/null
@@ -1,331 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=jointvc_rec:resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions;vrn_file_joint
-- sentinel_inputs=jointvc_batch_rec:record,vrn_file_joint:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- finalize_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: jointvc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      - name: vrn_file_joint
-        type: File
-      name: jointvc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index 18e635c4006..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,171 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 2048
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl
deleted file mode 100644
index fac484f75ca..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl
+++ /dev/null
@@ -1,184 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region
-- sentinel_inputs=jointvc_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-outputs:
-- id: region
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/merge_split_alignments.cwl
deleted file mode 100644
index 66e17dc7aa9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,168 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1035
-  ramMin: 4096
-  tmpdirMin: 6
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 45a90274381..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 2048
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index 75e0c7a35d5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,219 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 4096
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index 09728af2814..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,223 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1033
-  ramMin: 4096
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 813f3fed737..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,233 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;config__algorithm__coverage;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index a300aa5be18..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,195 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file_joint
-- sentinel_inputs=jointvc_batch_rec:record,vrn_file_joint:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: vrn_file_joint_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_align_inputs.cwl
deleted file mode 100644
index 8179e185e8b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,142 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples.cwl
deleted file mode 100644
index 244502016fb..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 830e65f0404..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__coverage;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=config__algorithm__coverage:var,rgnames__sample:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/process_alignment.cwl
deleted file mode 100644
index b12a9946b5c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 4096
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 7
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 53e0a326097..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,295 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;config__algorithm__coverage;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/run_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/run_jointvc.cwl
deleted file mode 100644
index 897c1e02ca8..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/run_jointvc.cwl
+++ /dev/null
@@ -1,203 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region
-- sentinel_inputs=jointvc_batch_rec:record,region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- run_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: gvcfgenotyper
-    specs:
-    - https://anaconda.org/bioconda/gvcfgenotyper
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: region_toolinput
-  type: string
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region
-  type: string
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index 85b8a8f01e0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,225 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=jointvc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: jointvc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        - name: vrn_file_joint
-          type: File
-        name: jointvc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index eb58aa47177..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,266 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 4096
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl
deleted file mode 100644
index 27c76c747c5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl
+++ /dev/null
@@ -1,143 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl
deleted file mode 100644
index 3091d1de370..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl
+++ /dev/null
@@ -1,360 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-outputs:
-- id: jointvc_rec
-  outputSource: finalize_jointvc/jointvc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      - name: vrn_file_joint
-        type: File
-      name: jointvc_rec
-      type: record
-    type: array
-- id: vrn_file_joint
-  outputSource: postprocess_variants/vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  out:
-  - id: region
-  run: steps/get_parallel_regions_jointvc.cwl
-- id: run_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: region_toolinput
-    source: get_parallel_regions_jointvc/region
-  out:
-  - id: vrn_file_region
-  - id: region
-  run: steps/run_jointvc.cwl
-  scatter:
-  - region_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: region
-    source: run_jointvc/region
-  - id: vrn_file_region
-    source: run_jointvc/vrn_file_region
-  out:
-  - id: vrn_file_joint
-  run: steps/concat_batch_variantcalls_jointvc.cwl
-- id: postprocess_variants
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: vrn_file_joint_toolinput
-    source: concat_batch_variantcalls_jointvc/vrn_file_joint
-  out:
-  - id: vrn_file_joint
-  run: steps/postprocess_variants.cwl
-- id: finalize_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: vrn_file_joint
-    source: postprocess_variants/vrn_file_joint
-  out:
-  - id: jointvc_rec
-  run: steps/finalize_jointvc.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl
deleted file mode 100644
index ffabd7e9f1e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,329 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign-samples.json
deleted file mode 100644
index 3e1234addda..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign-samples.json
+++ /dev/null
@@ -1,526 +0,0 @@
-{
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__coverage": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
-        }
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "qualimap",
-            "samtools",
-            "variants"
-        ],
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "qualimap",
-            "samtools",
-            "variants"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "qualimap_full"
-        ],
-        [
-            "qualimap_full"
-        ]
-    ],
-    "config__algorithm__validate": [
-        null,
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        null,
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__variantcaller": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__vcfanno": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ]
-    ],
-    "description": [
-        "Test1",
-        "Test2"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX.bam"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX_2.bam"
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        null,
-        null
-    ],
-    "metadata__phenotype": [
-        "",
-        ""
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__sample": [
-        "Test1",
-        "Test2"
-    ],
-    "vrn_file": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test1-gatk-haplotype.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test1-gatk-haplotype.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test2-gatk-haplotype.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test2-gatk-haplotype.vcf.gz.tbi"
-                }
-            ]
-        }
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign.cwl
deleted file mode 100644
index 535082448ed..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign.cwl
+++ /dev/null
@@ -1,672 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: organize_noalign
-  in:
-  - id: files
-    source: files
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/organize_noalign.cwl
-  scatter:
-  - files
-  - resources
-  - description
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: config__algorithm__coverage
-    source: config__algorithm__coverage
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: organize_noalign/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 1ad9465444b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,407 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type:
-          - boolean
-          - 'null'
-          - string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type: File
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index 2df313f7a8f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,101 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index ab4909659ca..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,315 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index ae12d21651d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,199 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index c4e3997bca4..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,174 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 82ce9f97a43..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/organize_noalign.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/organize_noalign.cwl
deleted file mode 100644
index 370f2ccf982..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/organize_noalign.cwl
+++ /dev/null
@@ -1,59 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=files:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- organize_noalign
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1024
-  ramMin: 3072
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-inputs:
-- id: files
-  type:
-    items: File
-    type: array
-- id: resources
-  type: string
-- id: description
-  type: string
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type: File
-- id: work_bam_plus__disc
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index c0e41e5ba62..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type:
-      - 'null'
-      - string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index 6a261c205af..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1033
-  ramMin: 6144
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type: File
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index e61b71f4d28..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,229 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;config__algorithm__coverage;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type: File
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index dd7e67c7d61..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,183 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1025
-  ramMin: 6144
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples.cwl
deleted file mode 100644
index f473b969345..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,93 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage
-      type: File
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 54f7781bb21..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,81 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__coverage;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=config__algorithm__coverage:var,rgnames__sample:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: config__algorithm__coverage
-  type:
-    items: File
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage
-        type: File
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 3de03a1a1a8..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,299 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;config__algorithm__coverage;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index e9fde20378c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type:
-          - boolean
-          - 'null'
-          - string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index e9192828e62..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,269 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/wf-variantcall.cwl
deleted file mode 100644
index b48a8254984..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,316 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json
deleted file mode 100644
index 3e67d52727e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json
+++ /dev/null
@@ -1,111 +0,0 @@
-{
-    "analysis": [
-        "RNA-seq"
-    ],
-    "config__algorithm__aligner": [
-        "hisat2"
-    ],
-    "config__algorithm__coverage_interval": [
-        null
-    ],
-    "config__algorithm__expression_caller": [
-        [
-            "salmon",
-            "kallisto"
-        ]
-    ],
-    "config__algorithm__fusion_caller": [
-        [
-            "pizzly"
-        ]
-    ],
-    "config__algorithm__qc": [
-        [
-            "fastqc",
-            "qualimap_rnaseq",
-            "samtools"
-        ]
-    ],
-    "config__algorithm__quality_format": [
-        "standard"
-    ],
-    "config__algorithm__tools_off": [
-        []
-    ],
-    "config__algorithm__tools_on": [
-        []
-    ],
-    "description": [
-        "Test1"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbio-cromwell-dev-test/test_bcbio_cwl/testdata/test_fusion/fusion-1_1.fq.gz"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbio-cromwell-dev-test/test_bcbio_cwl/testdata/test_fusion/fusion-1_2.fq.gz"
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19"
-    ],
-    "genome_resources__rnaseq__transcripts": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.gtf",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.gtf.db"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__hisat2__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/hisat2-wf.tar.gz"
-        }
-    ],
-    "resources": [
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test1"
-    ],
-    "rgnames__lb": [
-        null
-    ],
-    "rgnames__pl": [
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test1"
-    ],
-    "rgnames__rg": [
-        "Test1"
-    ],
-    "rgnames__sample": [
-        "Test1"
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl
deleted file mode 100644
index 2dd258ac786..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl
+++ /dev/null
@@ -1,304 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: config__algorithm__expression_caller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: reference__hisat2__indexes
-  type:
-    items: File
-    type: array
-- id: config__algorithm__fusion_caller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__rnaseq__transcripts
-  secondaryFiles:
-  - .db
-  type:
-    items: File
-    type: array
-- id: config__algorithm__quality_format
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: process_alignment/align_bam
-  type:
-    items: File
-    type: array
-- id: quant__tsv
-  outputSource: rnaseq_quantitate/quant__tsv
-  type:
-    items: File
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prepare_sample
-  in:
-  - id: files
-    source: files
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: genome_build
-    source: genome_build
-  - id: genome_resources__rnaseq__transcripts
-    source: genome_resources__rnaseq__transcripts
-  - id: analysis
-    source: analysis
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__hisat2__indexes
-    source: reference__hisat2__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__expression_caller
-    source: config__algorithm__expression_caller
-  - id: config__algorithm__fusion_caller
-    source: config__algorithm__fusion_caller
-  - id: config__algorithm__quality_format
-    source: config__algorithm__quality_format
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_rec
-  run: steps/prepare_sample.cwl
-  scatter:
-  - files
-  - rgnames__sample
-  - reference__fasta__base
-  - genome_build
-  - genome_resources__rnaseq__transcripts
-  - analysis
-  - rgnames__pl
-  - rgnames__pu
-  - rgnames__lane
-  - rgnames__rg
-  - rgnames__lb
-  - reference__hisat2__indexes
-  - config__algorithm__aligner
-  - config__algorithm__expression_caller
-  - config__algorithm__fusion_caller
-  - config__algorithm__quality_format
-  - resources
-  - description
-  scatterMethod: dotproduct
-- id: trim_sample
-  in:
-  - id: prep_rec
-    source: prepare_sample/prep_rec
-  out:
-  - id: trim_rec
-  run: steps/trim_sample.cwl
-  scatter:
-  - prep_rec
-  scatterMethod: dotproduct
-- id: process_alignment
-  in:
-  - id: trim_rec
-    source: trim_sample/trim_rec
-  out:
-  - id: align_bam
-  run: steps/process_alignment.cwl
-  scatter:
-  - trim_rec
-  scatterMethod: dotproduct
-- id: rnaseq_quantitate
-  in:
-  - id: trim_rec
-    source: trim_sample/trim_rec
-  - id: align_bam
-    source: process_alignment/align_bam
-  out:
-  - id: count_file
-  - id: quant__tsv
-  - id: quant__hdf5
-  - id: quant__fusion
-  run: steps/rnaseq_quantitate.cwl
-  scatter:
-  - trim_rec
-  - align_bam
-  scatterMethod: dotproduct
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: process_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: genome_resources__rnaseq__transcripts
-    source: genome_resources__rnaseq__transcripts
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  run: steps/multiqc_summary.cwl
-- id: detect_fusions
-  in:
-  - id: quant__fusion
-    source: rnaseq_quantitate/quant__fusion
-  - id: quant__hdf5
-    source: rnaseq_quantitate/quant__hdf5
-  - id: trim_rec
-    source: trim_sample/trim_rec
-  out:
-  - id: fusion__fasta
-  - id: fusion__json
-  run: steps/detect_fusions.cwl
-  scatter:
-  - quant__fusion
-  - quant__hdf5
-  - trim_rec
-  scatterMethod: dotproduct
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/detect_fusions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/detect_fusions.cwl
deleted file mode 100644
index 8803c214f31..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/detect_fusions.cwl
+++ /dev/null
@@ -1,97 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=fusion__fasta,fusion__json
-- sentinel_inputs=quant__fusion:var,quant__hdf5:var,trim_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_fusions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: pizzly
-    specs:
-    - https://anaconda.org/bioconda/pizzly
-inputs:
-- id: quant__fusion
-  type: File
-- id: quant__hdf5
-  type: File
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-outputs:
-- id: fusion__fasta
-  type: File
-- id: fusion__json
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 604f9291df7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,96 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__rnaseq__transcripts
-        type: File
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type: File
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index 230b84afc66..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,155 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_build;genome_resources__rnaseq__transcripts;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;align_bam
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=4
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=4
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_build
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type: File
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_build
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type: File
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/prepare_sample.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/prepare_sample.cwl
deleted file mode 100644
index e5b8cdf645e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/prepare_sample.cwl
+++ /dev/null
@@ -1,146 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=prep_rec:resources;description;files;reference__fasta__base;config__algorithm__expression_caller;rgnames__lb;rgnames__rg;reference__hisat2__indexes;config__algorithm__fusion_caller;config__algorithm__aligner;rgnames__pl;genome_build;rgnames__pu;genome_resources__rnaseq__transcripts;config__algorithm__quality_format;analysis;rgnames__sample;rgnames__lane
-- sentinel_inputs=files:var,rgnames__sample:var,reference__fasta__base:var,genome_build:var,genome_resources__rnaseq__transcripts:var,analysis:var,rgnames__pl:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__hisat2__indexes:var,config__algorithm__aligner:var,config__algorithm__expression_caller:var,config__algorithm__fusion_caller:var,config__algorithm__quality_format:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prepare_sample
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-inputs:
-- id: files
-  type:
-    items: File
-    type: array
-- id: rgnames__sample
-  type: string
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type: File
-- id: genome_build
-  type: string
-- id: genome_resources__rnaseq__transcripts
-  secondaryFiles:
-  - .db
-  type: File
-- id: analysis
-  type: string
-- id: rgnames__pl
-  type: string
-- id: rgnames__pu
-  type: string
-- id: rgnames__lane
-  type: string
-- id: rgnames__rg
-  type: string
-- id: rgnames__lb
-  type:
-  - 'null'
-  - string
-- id: reference__hisat2__indexes
-  type: File
-- id: config__algorithm__aligner
-  type: string
-- id: config__algorithm__expression_caller
-  type:
-    items: string
-    type: array
-- id: config__algorithm__fusion_caller
-  type:
-    items: string
-    type: array
-- id: config__algorithm__quality_format
-  type: string
-- id: resources
-  type: string
-- id: description
-  type: string
-outputs:
-- id: prep_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: prep_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/process_alignment.cwl
deleted file mode 100644
index 88af1224f95..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,108 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=align_bam
-- sentinel_inputs=trim_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: star
-    specs:
-    - https://anaconda.org/bioconda/star
-  - package: hisat2
-    specs:
-    - https://anaconda.org/bioconda/hisat2
-  - package: tophat
-    specs:
-    - https://anaconda.org/bioconda/tophat
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-inputs:
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 5ff5b2f10e0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,135 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_build;genome_resources__rnaseq__transcripts;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;align_bam
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,genome_resources__rnaseq__transcripts:var,genome_build:var,config__algorithm__coverage_interval:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__qc:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items: File
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: genome_resources__rnaseq__transcripts
-  secondaryFiles:
-  - .db
-  type:
-    items: File
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__rnaseq__transcripts
-        type: File
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type: File
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/rnaseq_quantitate.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/rnaseq_quantitate.cwl
deleted file mode 100644
index 05d2ec813ae..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/rnaseq_quantitate.cwl
+++ /dev/null
@@ -1,123 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=count_file,quant__tsv,quant__hdf5,quant__fusion
-- sentinel_inputs=trim_rec:record,align_bam:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- rnaseq_quantitate
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1025
-  ramMin: 4096
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: sailfish
-    specs:
-    - https://anaconda.org/bioconda/sailfish
-  - package: salmon
-    specs:
-    - https://anaconda.org/bioconda/salmon
-  - package: kallisto>
-    specs:
-    - https://anaconda.org/bioconda/kallisto>
-    version:
-    - 0.43.1
-  - package: subread
-    specs:
-    - https://anaconda.org/bioconda/subread
-  - package: gffread
-    specs:
-    - https://anaconda.org/bioconda/gffread
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-wasabi
-    specs:
-    - https://anaconda.org/bioconda/r-wasabi
-inputs:
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type: File
-outputs:
-- id: count_file
-  type: File
-- id: quant__tsv
-  type: File
-- id: quant__hdf5
-  type: File
-- id: quant__fusion
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/trim_sample.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/trim_sample.cwl
deleted file mode 100644
index 14124636cec..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/trim_sample.cwl
+++ /dev/null
@@ -1,140 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=trim_rec:resources;description;files;reference__fasta__base;config__algorithm__expression_caller;rgnames__lb;rgnames__rg;reference__hisat2__indexes;config__algorithm__fusion_caller;config__algorithm__aligner;rgnames__pl;genome_build;rgnames__pu;genome_resources__rnaseq__transcripts;config__algorithm__quality_format;analysis;rgnames__sample;rgnames__lane
-- sentinel_inputs=prep_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- trim_sample
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-inputs:
-- id: prep_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: prep_rec
-    type: record
-outputs:
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic-samples.json
deleted file mode 100644
index cbafda3641d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic-samples.json
+++ /dev/null
@@ -1,680 +0,0 @@
-{
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__adapters": [
-        [],
-        []
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants",
-            "viral"
-        ],
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants",
-            "viral"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__svcaller": [
-        [
-            "manta"
-        ],
-        [
-            "manta"
-        ]
-    ],
-    "config__algorithm__svprioritize": [
-        null,
-        null
-    ],
-    "config__algorithm__svvalidate": [
-        null,
-        null
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [],
-        []
-    ],
-    "config__algorithm__trim_reads": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__validate": [
-        null,
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/Test1-grade.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/Test1-grade.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "config__algorithm__validate_regions": [
-        null,
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__variant_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__variantcaller": [
-        [
-            "vardict"
-        ],
-        [
-            "vardict"
-        ]
-    ],
-    "config__algorithm__vcfanno": [
-        [],
-        []
-    ],
-    "description": [
-        "Test2",
-        "Test1"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX.bam"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gc_profile": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/gc/GC_profile.1000bp.cnp"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/gc/GC_profile.1000bp.cnp"
-        }
-    ],
-    "genome_resources__variation__germline_het_pon": [
-        null,
-        null
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        "b1",
-        "b1"
-    ],
-    "metadata__phenotype": [
-        "normal",
-        "tumor"
-    ],
-    "reference__bwa__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "reference__viral": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.sa"
-                }
-            ]
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test2",
-        "Test1"
-    ],
-    "rgnames__lb": [
-        null,
-        null
-    ],
-    "rgnames__pl": [
-        "illumina",
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test2",
-        "Test1"
-    ],
-    "rgnames__rg": [
-        "Test2",
-        "Test1"
-    ],
-    "rgnames__sample": [
-        "Test2",
-        "Test1"
-    ],
-    "vrn_file": [
-        null,
-        null
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic.cwl
deleted file mode 100644
index 699d99a4690..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic.cwl
+++ /dev/null
@@ -1,973 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__calls
-  outputSource: summarize_sv/sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  outputSource: summarize_sv/svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: sv__prioritize__tsv
-  outputSource: summarize_sv/sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  outputSource: summarize_sv/sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  outputSource: summarize_sv/sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: calculate_sv_bins
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__seq2c_bed_ready
-    source: postprocess_alignment/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: sv_bin_rec
-  run: steps/calculate_sv_bins.cwl
-- id: calculate_sv_coverage
-  in:
-  - id: sv_bin_rec
-    source: calculate_sv_bins/sv_bin_rec
-  out:
-  - id: sv_rawcoverage_rec
-  run: steps/calculate_sv_coverage.cwl
-  scatter:
-  - sv_bin_rec
-  scatterMethod: dotproduct
-- id: normalize_sv_coverage
-  in:
-  - id: sv_rawcoverage_rec
-    source: calculate_sv_coverage/sv_rawcoverage_rec
-  out:
-  - id: sv_coverage_rec
-  run: steps/normalize_sv_coverage.cwl
-- id: batch_for_sv
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: work_bam_plus__disc
-    source: alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr
-    source: alignment/work_bam_plus__sr
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__svprioritize
-    source: config__algorithm__svprioritize
-  - id: config__algorithm__svvalidate
-    source: config__algorithm__svvalidate
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: genome_resources__variation__gc_profile
-    source: genome_resources__variation__gc_profile
-  - id: genome_resources__variation__germline_het_pon
-    source: genome_resources__variation__germline_het_pon
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: sv_coverage_rec
-    source: normalize_sv_coverage/sv_coverage_rec
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  out:
-  - id: sv_batch_rec
-  run: steps/batch_for_sv.cwl
-- id: svcall
-  in:
-  - id: sv_batch_rec
-    source: batch_for_sv/sv_batch_rec
-  out:
-  - id: sv_rec
-  run: wf-svcall.cwl
-  scatter:
-  - sv_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_sv
-  in:
-  - id: sv_rec
-    source: svcall/sv_rec
-  out:
-  - id: sv__calls
-  - id: sv__supplemental
-  - id: sv__prioritize__tsv
-  - id: sv__prioritize__raw
-  - id: svvalidate__grading_summary
-  - id: svvalidate__grading_plots
-  run: steps/summarize_sv.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: reference__viral
-    source: reference__viral
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/alignment_to_rec.cwl
deleted file mode 100644
index 11cd9fc8d40..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,200 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: rgnames__pu
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_sv.cwl
deleted file mode 100644
index 16b905acacf..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_sv.cwl
+++ /dev/null
@@ -1,375 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=sv_batch_rec:resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;reference__snpeff__hg19;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;work_bam_plus__disc;work_bam_plus__sr;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,work_bam_plus__disc:var,work_bam_plus__sr:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__svprioritize:var,config__algorithm__svvalidate:var,regions__sample_callable:var,genome_resources__variation__gc_profile:var,genome_resources__variation__germline_het_pon:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,sv_coverage_rec:record,variants__samples:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10240
-  ramMin: 6144
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-outputs:
-- id: sv_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: work_bam_plus__disc
-          type:
-          - File
-          - 'null'
-        - name: work_bam_plus__sr
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 60af6c4469e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,407 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;genome_resources__variation__1000g;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10246
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_bins.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_bins.cwl
deleted file mode 100644
index 40bd035478a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_bins.cwl
+++ /dev/null
@@ -1,225 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_bin_rec:regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;resources;description;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=align_bam:var,reference__fasta__base:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__svcaller:var,depth__variant_regions__regions:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__rnaseq__gene_bed:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_bins
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: sv_bin_rec
-  type:
-    items:
-      fields:
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_bin_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_coverage.cwl
deleted file mode 100644
index fc75d2c1b71..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_coverage.cwl
+++ /dev/null
@@ -1,218 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=sv_rawcoverage_rec:depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;resources;description;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_bin_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-inputs:
-- id: sv_bin_rec
-  type:
-    fields:
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_bin_rec
-    type: record
-outputs:
-- id: sv_rawcoverage_rec
-  type:
-    fields:
-    - name: depth__bins__target
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__seq2c
-      type:
-      - File
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_rawcoverage_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index 5a8f8a3c6cb..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index d6b910b7f9e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,311 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index ef31b2ffe4f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/detect_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/detect_sv.cwl
deleted file mode 100644
index 234bcc60d69..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/detect_sv.cwl
+++ /dev/null
@@ -1,414 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=sv_rec:sv__variantcaller;sv__vrn_file;sv__supplemental;svvalidate__summary;resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: delly
-    specs:
-    - https://anaconda.org/bioconda/delly
-  - package: duphold
-    specs:
-    - https://anaconda.org/bioconda/duphold
-  - package: extract-sv-reads
-    specs:
-    - https://anaconda.org/bioconda/extract-sv-reads
-  - package: lumpy-sv
-    specs:
-    - https://anaconda.org/bioconda/lumpy-sv
-  - package: manta
-    specs:
-    - https://anaconda.org/bioconda/manta
-  - package: break-point-inspector
-    specs:
-    - https://anaconda.org/bioconda/break-point-inspector
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: smoove
-    specs:
-    - https://anaconda.org/bioconda/smoove
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-  - package: simple_sv_annotation
-    specs:
-    - https://anaconda.org/bioconda/simple_sv_annotation
-  - package: survivor
-    specs:
-    - https://anaconda.org/bioconda/survivor
-  - package: svtools
-    specs:
-    - https://anaconda.org/bioconda/svtools
-  - package: svtyper
-    specs:
-    - https://anaconda.org/bioconda/svtyper
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: xorg-libxt
-    specs:
-    - https://anaconda.org/bioconda/xorg-libxt
-  - package: vawk
-    specs:
-    - https://anaconda.org/bioconda/vawk
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index 48e5f050eb3..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,173 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10246
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/merge_split_alignments.cwl
deleted file mode 100644
index 029b704bbb2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,169 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10251
-  ramMin: 6144
-  tmpdirMin: 6
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 9d65504ba6b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,96 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10246
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/normalize_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/normalize_sv_coverage.cwl
deleted file mode 100644
index 1bdc8dbc3b8..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/normalize_sv_coverage.cwl
+++ /dev/null
@@ -1,236 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_coverage_rec:depth__bins__normalized;depth__bins__background;resources;description;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_rawcoverage_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- normalize_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_rawcoverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rawcoverage_rec
-      type: record
-    type: array
-outputs:
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index 89f6372949c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,223 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: reference__viral
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index 8585bfb3074..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,224 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10249
-  ramMin: 6144
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 9d93ac8f1db..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,235 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index 6fba055bcd7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,182 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10241
-  ramMin: 6144
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_align_inputs.cwl
deleted file mode 100644
index c40a38fc01a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,143 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples.cwl
deleted file mode 100644
index 4e62820988d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 9268efdafcb..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__svcaller;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=rgnames__sample:var,config__algorithm__svcaller:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/process_alignment.cwl
deleted file mode 100644
index 45b58d1ab98..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,199 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 7
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index eccc8330618..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,310 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;metadata__phenotype;config__algorithm__tools_off;reference__viral;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,reference__viral:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__viral
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_sv.cwl
deleted file mode 100644
index be7b4a8c87f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_sv.cwl
+++ /dev/null
@@ -1,242 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv__calls,sv__supplemental,sv__prioritize__tsv,sv__prioritize__raw,svvalidate__grading_summary,svvalidate__grading_plots
-- sentinel_inputs=sv_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10243
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcbio-prioritize
-    specs:
-    - https://anaconda.org/bioconda/bcbio-prioritize
-inputs:
-- id: sv_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: sv__variantcaller
-          type:
-          - string
-          - 'null'
-        - name: sv__vrn_file
-          type:
-          - File
-          - 'null'
-        - name: sv__supplemental
-          type:
-            items:
-            - File
-            type: array
-        - name: svvalidate__summary
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: svvalidate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index 62c64099b31..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,195 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - File
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index 1dc7a6e7128..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,268 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-alignment.cwl
deleted file mode 100644
index c2ce73cfc61..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-alignment.cwl
+++ /dev/null
@@ -1,144 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-svcall.cwl
deleted file mode 100644
index db9522935a1..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-svcall.cwl
+++ /dev/null
@@ -1,328 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  outputSource: detect_sv/sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: detect_sv
-  in:
-  - id: sv_batch_rec
-    source: sv_batch_rec
-  out:
-  - id: sv_rec
-  run: steps/detect_sv.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-variantcall.cwl
deleted file mode 100644
index da6bab7ac21..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,312 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall-samples.json
deleted file mode 100644
index 28826670c5c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall-samples.json
+++ /dev/null
@@ -1,707 +0,0 @@
-{
-    "analysis": [
-        "variant",
-        "variant"
-    ],
-    "config__algorithm__adapters": [
-        [],
-        []
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "samtools"
-        ],
-        [
-            "samtools"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__sv_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__svcaller": [
-        [
-            "cnvkit",
-            "manta",
-            "lumpy"
-        ],
-        [
-            "cnvkit",
-            "manta",
-            "lumpy"
-        ]
-    ],
-    "config__algorithm__svprioritize": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__svvalidate": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/Test1-grade.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/Test1-grade.vcf.gz.tbi"
-                }
-            ]
-        },
-        null
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "coverage_perbase"
-        ],
-        [
-            "coverage_perbase"
-        ]
-    ],
-    "config__algorithm__trim_reads": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__validate": [
-        null,
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        null,
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        null,
-        null
-    ],
-    "config__algorithm__variantcaller": [
-        [
-            "vardict"
-        ],
-        [
-            "vardict"
-        ]
-    ],
-    "config__algorithm__vcfanno": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/somatic.conf"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ]
-    ],
-    "description": [
-        "Test1",
-        "Test2"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gc_profile": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/gc/GC_profile.1000bp.cnp"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/gc/GC_profile.1000bp.cnp"
-        }
-    ],
-    "genome_resources__variation__germline_het_pon": [
-        null,
-        null
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        "b1",
-        "b1"
-    ],
-    "metadata__phenotype": [
-        "tumor",
-        "normal"
-    ],
-    "reference__bwa__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "reference__viral": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.sa"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.bwt"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.sa"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.bwt"
-                }
-            ]
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__lb": [
-        null,
-        null
-    ],
-    "rgnames__pl": [
-        "illumina",
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__rg": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__sample": [
-        "Test1",
-        "Test2"
-    ],
-    "vrn_file": [
-        null,
-        null
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall.cwl
deleted file mode 100644
index ec310cc54cd..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall.cwl
+++ /dev/null
@@ -1,975 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__sv_regions
-  type:
-    items: File
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__svvalidate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__calls
-  outputSource: summarize_sv/sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  outputSource: summarize_sv/svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: sv__prioritize__tsv
-  outputSource: summarize_sv/sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  outputSource: summarize_sv/sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  outputSource: summarize_sv/sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: calculate_sv_bins
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__sv_regions
-    source: config__algorithm__sv_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: sv_bin_rec
-  run: steps/calculate_sv_bins.cwl
-- id: calculate_sv_coverage
-  in:
-  - id: sv_bin_rec
-    source: calculate_sv_bins/sv_bin_rec
-  out:
-  - id: sv_rawcoverage_rec
-  run: steps/calculate_sv_coverage.cwl
-  scatter:
-  - sv_bin_rec
-  scatterMethod: dotproduct
-- id: normalize_sv_coverage
-  in:
-  - id: sv_rawcoverage_rec
-    source: calculate_sv_coverage/sv_rawcoverage_rec
-  out:
-  - id: sv_coverage_rec
-  run: steps/normalize_sv_coverage.cwl
-- id: batch_for_sv
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: work_bam_plus__disc
-    source: alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr
-    source: alignment/work_bam_plus__sr
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__svprioritize
-    source: config__algorithm__svprioritize
-  - id: config__algorithm__svvalidate
-    source: config__algorithm__svvalidate
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: genome_resources__variation__gc_profile
-    source: genome_resources__variation__gc_profile
-  - id: genome_resources__variation__germline_het_pon
-    source: genome_resources__variation__germline_het_pon
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: sv_coverage_rec
-    source: normalize_sv_coverage/sv_coverage_rec
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  out:
-  - id: sv_batch_rec
-  run: steps/batch_for_sv.cwl
-- id: svcall
-  in:
-  - id: sv_batch_rec
-    source: batch_for_sv/sv_batch_rec
-  out:
-  - id: sv_rec
-  run: wf-svcall.cwl
-  scatter:
-  - sv_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_sv
-  in:
-  - id: sv_rec
-    source: svcall/sv_rec
-  out:
-  - id: sv__calls
-  - id: sv__supplemental
-  - id: sv__prioritize__tsv
-  - id: sv__prioritize__raw
-  - id: svvalidate__grading_summary
-  - id: svvalidate__grading_plots
-  run: steps/summarize_sv.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: reference__viral
-    source: reference__viral
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/alignment_to_rec.cwl
deleted file mode 100644
index 8208a1f1eed..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,206 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: rgnames__pu
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - 'null'
-        - string
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_sv.cwl
deleted file mode 100644
index 5c725369def..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_sv.cwl
+++ /dev/null
@@ -1,359 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=sv_batch_rec:resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;reference__snpeff__hg19;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;work_bam_plus__disc;work_bam_plus__sr;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,work_bam_plus__disc:var,work_bam_plus__sr:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__svprioritize:var,config__algorithm__svvalidate:var,regions__sample_callable:var,genome_resources__variation__gc_profile:var,genome_resources__variation__germline_het_pon:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,sv_coverage_rec:record,variants__samples:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 6144
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items: File
-    type: array
-- id: config__algorithm__svvalidate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-outputs:
-- id: sv_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type: File
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: work_bam_plus__disc
-          type:
-          - File
-          - 'null'
-        - name: work_bam_plus__sr
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__sv_regions
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 1a04f1e6887..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,401 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;genome_resources__variation__1000g;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_bins.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_bins.cwl
deleted file mode 100644
index 34683452f0d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_bins.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_bin_rec:regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;resources;description;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=align_bam:var,reference__fasta__base:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__sv_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__svcaller:var,depth__variant_regions__regions:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__rnaseq__gene_bed:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_bins
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__sv_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: sv_bin_rec
-  type:
-    items:
-      fields:
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_bin_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_coverage.cwl
deleted file mode 100644
index 79ba8e7eaf5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_coverage.cwl
+++ /dev/null
@@ -1,207 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=sv_rawcoverage_rec:depth__bins__target;depth__bins__antitarget;resources;description;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_bin_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_bin_rec
-  type:
-    fields:
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__sv_regions
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_bin_rec
-    type: record
-outputs:
-- id: sv_rawcoverage_rec
-  type:
-    fields:
-    - name: depth__bins__target
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__sv_regions
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_rawcoverage_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index 434161e89da..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index 142a0d44ce9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,307 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index b8cd24d68bc..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,196 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/detect_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/detect_sv.cwl
deleted file mode 100644
index 4aab2c1343b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/detect_sv.cwl
+++ /dev/null
@@ -1,396 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=sv_rec:sv__variantcaller;sv__vrn_file;sv__supplemental;svvalidate__summary;resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: delly
-    specs:
-    - https://anaconda.org/bioconda/delly
-  - package: duphold
-    specs:
-    - https://anaconda.org/bioconda/duphold
-  - package: extract-sv-reads
-    specs:
-    - https://anaconda.org/bioconda/extract-sv-reads
-  - package: lumpy-sv
-    specs:
-    - https://anaconda.org/bioconda/lumpy-sv
-  - package: manta
-    specs:
-    - https://anaconda.org/bioconda/manta
-  - package: break-point-inspector
-    specs:
-    - https://anaconda.org/bioconda/break-point-inspector
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: smoove
-    specs:
-    - https://anaconda.org/bioconda/smoove
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-  - package: simple_sv_annotation
-    specs:
-    - https://anaconda.org/bioconda/simple_sv_annotation
-  - package: survivor
-    specs:
-    - https://anaconda.org/bioconda/survivor
-  - package: svtools
-    specs:
-    - https://anaconda.org/bioconda/svtools
-  - package: svtyper
-    specs:
-    - https://anaconda.org/bioconda/svtyper
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: xorg-libxt
-    specs:
-    - https://anaconda.org/bioconda/xorg-libxt
-  - package: vawk
-    specs:
-    - https://anaconda.org/bioconda/vawk
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index 71ac417a4ce..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,171 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/merge_split_alignments.cwl
deleted file mode 100644
index afe6f73cfc2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,171 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1035
-  ramMin: 6144
-  tmpdirMin: 6
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 82ce9f97a43..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/normalize_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/normalize_sv_coverage.cwl
deleted file mode 100644
index 813a2a21a63..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/normalize_sv_coverage.cwl
+++ /dev/null
@@ -1,224 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_coverage_rec:depth__bins__normalized;depth__bins__background;resources;description;depth__bins__target;depth__bins__antitarget;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_rawcoverage_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- normalize_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_rawcoverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rawcoverage_rec
-      type: record
-    type: array
-outputs:
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index d320e1afb86..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: reference__viral
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index ccdfc8e177e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,223 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1033
-  ramMin: 6144
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 1f033c9d3c7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,233 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index dd40cf1d9a4..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,180 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1025
-  ramMin: 6144
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_align_inputs.cwl
deleted file mode 100644
index cd325c5f774..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,145 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples.cwl
deleted file mode 100644
index 63d24367261..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,93 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index da7b1d7f2b0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,79 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=rgnames__sample:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - 'null'
-        - string
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/process_alignment.cwl
deleted file mode 100644
index af6768e2f88..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,201 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 7
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 4565b513de7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,308 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;metadata__phenotype;config__algorithm__tools_off;reference__viral;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,reference__viral:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__viral
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_sv.cwl
deleted file mode 100644
index 87f503d9117..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_sv.cwl
+++ /dev/null
@@ -1,228 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv__calls,sv__supplemental,sv__prioritize__tsv,sv__prioritize__raw,svvalidate__grading_summary,svvalidate__grading_plots
-- sentinel_inputs=sv_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1027
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: sv_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: sv__variantcaller
-          type:
-          - string
-          - 'null'
-        - name: sv__vrn_file
-          type:
-          - File
-          - 'null'
-        - name: sv__supplemental
-          type:
-            items:
-            - File
-            type: array
-        - name: svvalidate__summary
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type: File
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__sv_regions
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: svvalidate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index c560affeded..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,193 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index 7e8f1574bfc..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,266 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-alignment.cwl
deleted file mode 100644
index 3785183a8df..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-alignment.cwl
+++ /dev/null
@@ -1,146 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-svcall.cwl
deleted file mode 100644
index 01ae7b07f7a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-svcall.cwl
+++ /dev/null
@@ -1,310 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  outputSource: detect_sv/sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: detect_sv
-  in:
-  - id: sv_batch_rec
-    source: sv_batch_rec
-  out:
-  - id: sv_rec
-  run: steps/detect_sv.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-variantcall.cwl
deleted file mode 100644
index f7dd3955627..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,308 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json
deleted file mode 100644
index 1439ccade50..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json
+++ /dev/null
@@ -1,1059 +0,0 @@
-{
-    "expected_validation":
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/grading-summary-combined-expected.csv"
-        },
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__adapters": [
-        [
-            "polyx"
-        ],
-        [
-            "polyx"
-        ]
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__archive": [
-        null,
-        null
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        "{\"numpass\": 2}",
-        "{\"numpass\": 2}"
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants",
-            "viral"
-        ],
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants",
-            "viral"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__svcaller": [
-        [
-            "cnvkit"
-        ],
-        [
-            "cnvkit"
-        ]
-    ],
-    "config__algorithm__svprioritize": [
-        null,
-        null
-    ],
-    "config__algorithm__svvalidate": [
-        null,
-        null
-    ],
-    "config__algorithm__tools_off": [
-        [
-            "gemini"
-        ],
-        [
-            "gemini"
-        ]
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "gatk4",
-            "break-point-inspector",
-            "noalt_calling"
-        ],
-        [
-            "gatk4",
-            "break-point-inspector",
-            "noalt_calling"
-        ]
-    ],
-    "config__algorithm__trim_reads": [
-        "atropos",
-        "atropos"
-    ],
-    "config__algorithm__validate": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/wes-ensemble-annotated_exome_chr21_noAnnot_somatic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/wes_agha_test/wes-ensemble-annotated_exome_chr21_noAnnot_somatic.vcf.gz.tbi"
-                }
-            ]
-        },
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/Exome-Agilent_V6_chr21.bed"
-        },
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/Exome-Agilent_V6_chr21.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/Exome-Agilent_V6_chr21.bed"
-        }
-    ],
-    "config__algorithm__variantcaller": [
-        [
-            "germline:vardict",
-            "germline:strelka2",
-            "germline:gatk-haplotype",
-            "somatic:vardict",
-            "somatic:strelka2",
-            "somatic:mutect2"
-        ],
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-                "class": "File",
-                "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/low_complexity_51to200bp.bed.gz",
-                "secondaryFiles": [
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-                        "class": "File",
-                        "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/low_complexity_51to200bp.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/low_complexity_gt200bp.bed.gz",
-                "secondaryFiles": [
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-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/repeats/polyx.bed.gz",
-                "secondaryFiles": [
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-                        "class": "File",
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-            },
-            {
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-                "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/self_chain.bed.gz",
-                "secondaryFiles": [
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-                        "class": "File",
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-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/ENCODE/wgEncodeDacMapabilityConsensusExcludable.bed.gz",
-                "secondaryFiles": [
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-                        "class": "File",
-                        "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/ENCODE/wgEncodeDacMapabilityConsensusExcludable.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/rtg--GRCh37.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/rtg--GRCh37.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__GRCh37_75": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/snpeff--GRCh37.75-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/snpeff--GRCh37.75-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/versions.csv"
-        }
-    ],
-    "reference__viral": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.sa"
-                }
-            ]
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__lane": [
-        "NA12878_chr21",
-        "NA24385_chr21"
-    ],
-    "rgnames__lb": [
-        null,
-        null
-    ],
-    "rgnames__pl": [
-        "illumina",
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "NA12878_chr21",
-        "NA24385_chr21"
-    ],
-    "rgnames__rg": [
-        "NA12878_chr21",
-        "NA24385_chr21"
-    ],
-    "rgnames__sample": [
-        "NA12878_chr21",
-        "NA24385_chr21"
-    ],
-    "vrn_file": [
-        null,
-        null
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
deleted file mode 100644
index c325ecade0b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
+++ /dev/null
@@ -1,997 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: reference__snpeff__GRCh37_75
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .fai
-  - .ann
-  - .sa
-  - .pac
-  - .amb
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: config__algorithm__archive
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__calls
-  outputSource: summarize_sv/sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  outputSource: summarize_sv/svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: sv__prioritize__tsv
-  outputSource: summarize_sv/sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  outputSource: summarize_sv/sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  outputSource: summarize_sv/sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__archive
-    source: config__algorithm__archive
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__GRCh37_75
-    source: reference__snpeff__GRCh37_75
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: batch_for_ensemble
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: ensemble_prep_rec
-  run: steps/batch_for_ensemble.cwl
-- id: combine_calls
-  in:
-  - id: ensemble_prep_rec
-    source: batch_for_ensemble/ensemble_prep_rec
-  out:
-  - id: ensemble_rec
-  run: steps/combine_calls.cwl
-  scatter:
-  - ensemble_prep_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  - id: ensemble_rec
-    source: combine_calls/ensemble_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: calculate_sv_bins
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__seq2c_bed_ready
-    source: postprocess_alignment/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: sv_bin_rec
-  run: steps/calculate_sv_bins.cwl
-- id: calculate_sv_coverage
-  in:
-  - id: sv_bin_rec
-    source: calculate_sv_bins/sv_bin_rec
-  out:
-  - id: sv_rawcoverage_rec
-  run: steps/calculate_sv_coverage.cwl
-  scatter:
-  - sv_bin_rec
-  scatterMethod: dotproduct
-- id: normalize_sv_coverage
-  in:
-  - id: sv_rawcoverage_rec
-    source: calculate_sv_coverage/sv_rawcoverage_rec
-  out:
-  - id: sv_coverage_rec
-  run: steps/normalize_sv_coverage.cwl
-- id: batch_for_sv
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: work_bam_plus__disc
-    source: alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr
-    source: alignment/work_bam_plus__sr
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__svprioritize
-    source: config__algorithm__svprioritize
-  - id: config__algorithm__svvalidate
-    source: config__algorithm__svvalidate
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: genome_resources__variation__gc_profile
-    source: genome_resources__variation__gc_profile
-  - id: genome_resources__variation__germline_het_pon
-    source: genome_resources__variation__germline_het_pon
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__GRCh37_75
-    source: reference__snpeff__GRCh37_75
-  - id: sv_coverage_rec
-    source: normalize_sv_coverage/sv_coverage_rec
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  out:
-  - id: sv_batch_rec
-  run: steps/batch_for_sv.cwl
-- id: svcall
-  in:
-  - id: sv_batch_rec
-    source: batch_for_sv/sv_batch_rec
-  out:
-  - id: sv_rec
-  run: wf-svcall.cwl
-  scatter:
-  - sv_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_sv
-  in:
-  - id: sv_rec
-    source: svcall/sv_rec
-  out:
-  - id: sv__calls
-  - id: sv__supplemental
-  - id: sv__prioritize__tsv
-  - id: sv__prioritize__raw
-  - id: svvalidate__grading_summary
-  - id: svvalidate__grading_plots
-  run: steps/summarize_sv.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: reference__viral
-    source: reference__viral
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl
deleted file mode 100644
index 506764917f5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,194 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions;rgnames__pu
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items: string
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-          items: string
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      - name: rgnames__pu
-        type: string
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl
deleted file mode 100644
index df553e9e92f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl
+++ /dev/null
@@ -1,273 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=ensemble_prep_rec:batch_id;variants__calls;variants__variantcallers;resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__snpeff__GRCh37_75;reference__genome_context;reference__rtg;config__algorithm__validate;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_ensemble
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10240
-  ramMin: 3072
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__ensemble
-          type: string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: ensemble_prep_rec
-  type:
-    items:
-      fields:
-      - name: batch_id
-        type: string
-      - name: variants__calls
-        type:
-          items: File
-          type: array
-      - name: variants__variantcallers
-        type:
-          items: string
-          type: array
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: ensemble_prep_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl
deleted file mode 100644
index c25d67e007b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl
+++ /dev/null
@@ -1,363 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=sv_batch_rec:resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;reference__snpeff__GRCh37_75;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;work_bam_plus__disc;work_bam_plus__sr;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,work_bam_plus__disc:var,work_bam_plus__sr:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__svprioritize:var,config__algorithm__svvalidate:var,regions__sample_callable:var,genome_resources__variation__gc_profile:var,genome_resources__variation__germline_het_pon:var,genome_resources__aliases__snpeff:var,reference__snpeff__GRCh37_75:var,sv_coverage_rec:record,variants__samples:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10240
-  ramMin: 49152
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 3656
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__GRCh37_75
-  type:
-    items: File
-    type: array
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-outputs:
-- id: sv_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: work_bam_plus__disc
-          type:
-          - File
-          - 'null'
-        - name: work_bam_plus__sr
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type: File
-        - name: genome_resources__variation__encode_blacklist
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 6504ed26811..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,395 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;reference__snpeff__GRCh37_75;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;reference__rtg;config__algorithm__validate;genome_resources__variation__1000g;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__GRCh37_75:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10477
-  ramMin: 3072
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items: string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__GRCh37_75
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type: File
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type: File
-        - name: genome_resources__variation__encode_blacklist
-          type: File
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type: string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl
deleted file mode 100644
index bee219164db..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl
+++ /dev/null
@@ -1,219 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_bin_rec:regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;resources;description;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=align_bam:var,reference__fasta__base:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__svcaller:var,depth__variant_regions__regions:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__rnaseq__gene_bed:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_bins
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: sv_bin_rec
-  type:
-    items:
-      fields:
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_bin_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl
deleted file mode 100644
index 330224b83db..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl
+++ /dev/null
@@ -1,206 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=sv_rawcoverage_rec:depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;resources;description;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_bin_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-inputs:
-- id: sv_bin_rec
-  type:
-    fields:
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type: File
-    - name: genome_resources__variation__encode_blacklist
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_bin_rec
-    type: record
-outputs:
-- id: sv_rawcoverage_rec
-  type:
-    fields:
-    - name: depth__bins__target
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__seq2c
-      type:
-      - File
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type: File
-    - name: genome_resources__variation__encode_blacklist
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_rawcoverage_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl
deleted file mode 100644
index 7730a2a3223..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl
+++ /dev/null
@@ -1,180 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=ensemble_rec:ensemble__vrn_file;ensemble__validate__summary;ensemble__batch_samples;ensemble__batch_id
-- sentinel_inputs=ensemble_prep_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_calls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10240
-  ramMin: 49152
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4687
-- class: SoftwareRequirement
-  packages:
-  - package: bcbio-variation-recall
-    specs:
-    - https://anaconda.org/bioconda/bcbio-variation-recall
-inputs:
-- id: ensemble_prep_rec
-  type:
-    fields:
-    - name: batch_id
-      type: string
-    - name: variants__calls
-      type:
-        items: File
-        type: array
-    - name: variants__variantcallers
-      type:
-        items: string
-        type: array
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: batch_samples
-      type:
-      - 'null'
-      - items: string
-        type: array
-    - name: validate__summary
-      type:
-      - File
-      - 'null'
-    - name: validate__tp
-      type:
-      - File
-      - 'null'
-    - name: validate__fp
-      type:
-      - File
-      - 'null'
-    - name: validate__fn
-      type:
-      - File
-      - 'null'
-    - name: vrn_file
-      type: File
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__vcfanno
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__variantcaller
-      type: string
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: config__algorithm__min_allele_fraction
-      type: double
-    - name: reference__snpeff__GRCh37_75
-      type: File
-    - name: reference__genome_context
-      type:
-        items: File
-        type: array
-    - name: reference__rtg
-      type: File
-    - name: config__algorithm__validate
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__validate_regions
-      type:
-      - File
-      - 'null'
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__aliases__human
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__tools_off
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__ensemble
-      type: string
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__effects
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: genome_resources__aliases__ensembl
-      type: string
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: genome_resources__aliases__snpeff
-      type: string
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: regions__sample_callable
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: ensemble_prep_rec
-    type: record
-outputs:
-- id: ensemble_rec
-  type:
-    fields:
-    - name: ensemble__vrn_file
-      type:
-      - File
-      - 'null'
-    - name: ensemble__validate__summary
-      type:
-      - File
-      - 'null'
-    - name: ensemble__batch_samples
-      type:
-        items: string
-        type: array
-    - name: ensemble__batch_id
-      type: string
-    name: ensemble_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl
deleted file mode 100644
index e59fc89683e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10299
-  ramMin: 3072
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 3008
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl
deleted file mode 100644
index ed7c9b1e0b1..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,299 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__snpeff__GRCh37_75;reference__genome_context;reference__rtg;config__algorithm__validate;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index a5d59d661a0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,190 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl
deleted file mode 100644
index 66d592642d7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl
+++ /dev/null
@@ -1,402 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=sv_rec:sv__variantcaller;sv__vrn_file;sv__supplemental;svvalidate__summary;resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 3656
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: delly
-    specs:
-    - https://anaconda.org/bioconda/delly
-  - package: duphold
-    specs:
-    - https://anaconda.org/bioconda/duphold
-  - package: extract-sv-reads
-    specs:
-    - https://anaconda.org/bioconda/extract-sv-reads
-  - package: lumpy-sv
-    specs:
-    - https://anaconda.org/bioconda/lumpy-sv
-  - package: manta
-    specs:
-    - https://anaconda.org/bioconda/manta
-  - package: break-point-inspector
-    specs:
-    - https://anaconda.org/bioconda/break-point-inspector
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: smoove
-    specs:
-    - https://anaconda.org/bioconda/smoove
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-  - package: simple_sv_annotation
-    specs:
-    - https://anaconda.org/bioconda/simple_sv_annotation
-  - package: survivor
-    specs:
-    - https://anaconda.org/bioconda/survivor
-  - package: svtools
-    specs:
-    - https://anaconda.org/bioconda/svtools
-  - package: svtyper
-    specs:
-    - https://anaconda.org/bioconda/svtyper
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: xorg-libxt
-    specs:
-    - https://anaconda.org/bioconda/xorg-libxt
-  - package: vawk
-    specs:
-    - https://anaconda.org/bioconda/vawk
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl
deleted file mode 100644
index 71c08911610..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,165 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10477
-  ramMin: 3072
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl
deleted file mode 100644
index 4e139a4d748..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,165 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10655
-  ramMin: 49152
-  tmpdirMin: 208
-- class: dx:InputResourceRequirement
-  indirMin: 3127
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl
deleted file mode 100644
index 96036a07fc2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,94 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10477
-  ramMin: 3072
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: reference__versions
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl
deleted file mode 100644
index af33573637d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl
+++ /dev/null
@@ -1,224 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_coverage_rec:depth__bins__normalized;depth__bins__background;resources;description;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_rawcoverage_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- normalize_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_rawcoverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rawcoverage_rec
-      type: record
-    type: array
-outputs:
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl
deleted file mode 100644
index 4ffe2646ec9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,219 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;genome_build;config__algorithm__tools_off;reference__versions;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 3010
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-        items: string
-        type: array
-    - name: reference__versions
-      type: File
-    - name: reference__viral
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-        items: string
-        type: array
-    - name: reference__versions
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl
deleted file mode 100644
index 92f4acb8c7f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10596
-  ramMin: 49152
-  tmpdirMin: 178
-- class: dx:InputResourceRequirement
-  indirMin: 18018
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type: File
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type: File
-    - name: genome_resources__variation__encode_blacklist
-      type: File
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__archive
-      type:
-      - 'null'
-      - string
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 926d37e91df..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,237 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__archive;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__archive:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__archive
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__archive
-        type:
-        - 'null'
-        - string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl
deleted file mode 100644
index 5151f1520c6..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,174 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10299
-  ramMin: 49152
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl
deleted file mode 100644
index 5c392bdb350..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,139 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3127
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl
deleted file mode 100644
index 8e6d9500406..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10299
-  ramMin: 3072
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 3008
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 9ccaa591fde..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__svcaller;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=rgnames__sample:var,config__algorithm__svcaller:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10299
-  ramMin: 3072
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl
deleted file mode 100644
index 718e2cd14e0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl
+++ /dev/null
@@ -1,195 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 3246
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl
deleted file mode 100644
index 0336669ad83..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,307 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;metadata__batch;genome_build;metadata__phenotype;config__algorithm__tools_off;reference__versions;reference__viral;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,reference__viral:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .fai
-  - .ann
-  - .sa
-  - .pac
-  - .amb
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: reference__versions
-        type: File
-      - name: reference__viral
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl
deleted file mode 100644
index c5f8047d69a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl
+++ /dev/null
@@ -1,236 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv__calls,sv__supplemental,sv__prioritize__tsv,sv__prioritize__raw,svvalidate__grading_summary,svvalidate__grading_plots
-- sentinel_inputs=sv_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10358
-  ramMin: 3072
-  tmpdirMin: 59
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: bcbio-prioritize
-    specs:
-    - https://anaconda.org/bioconda/bcbio-prioritize
-inputs:
-- id: sv_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: sv__variantcaller
-          type:
-          - string
-          - 'null'
-        - name: sv__vrn_file
-          type:
-          - File
-          - 'null'
-        - name: sv__supplemental
-          type:
-            items:
-            - File
-            type: array
-        - name: svvalidate__summary
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type: File
-        - name: genome_resources__variation__encode_blacklist
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: svvalidate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl
deleted file mode 100644
index 48ec1cd601a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,212 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record,ensemble_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1000000
-  ramMin: 3072
-  tmpdirMin: 1000000
-- class: dx:InputResourceRequirement
-  indirMin: 1000000
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__ensemble
-          type: string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-- id: ensemble_rec
-  type:
-    items:
-      fields:
-      - name: ensemble__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: ensemble__validate__summary
-        type:
-        - File
-        - 'null'
-      - name: ensemble__batch_samples
-        type:
-          items: string
-          type: array
-      - name: ensemble__batch_id
-        type: string
-      name: ensemble_rec
-      type: record
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl
deleted file mode 100644
index a4fadb20991..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,260 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl
deleted file mode 100644
index 0f1dfd3dd81..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl
+++ /dev/null
@@ -1,140 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl
deleted file mode 100644
index f8724f9b0b9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl
+++ /dev/null
@@ -1,316 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  outputSource: detect_sv/sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: detect_sv
-  in:
-  - id: sv_batch_rec
-    source: sv_batch_rec
-  out:
-  - id: sv_rec
-  run: steps/detect_sv.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl
deleted file mode 100644
index fc5066d386e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl
+++ /dev/null
@@ -1,300 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file.test
deleted file mode 100644
index 98ddd1a832e..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: inline_file
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_inline_file
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/inline_file.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_inline_file.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file_custom_entryname.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file_custom_entryname.test
deleted file mode 100644
index 1164b6fdf2f..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file_custom_entryname.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: inline_file_custom_entryname
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_inline_file
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/inline_file_custom_entryname.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_inline_file.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string.test
deleted file mode 100644
index 4ec70064ffc..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: iwdr_input_string
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_input_string
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/input_string.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_input_string.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string_function.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string_function.test
deleted file mode 100644
index 1c7973b96d6..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string_function.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: iwdr_input_string_function
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_input_string_function
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/input_string_function.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_input_string_function.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/file_array_listing.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/file_array_listing.cwl
deleted file mode 100644
index 86fb7c060a3..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/file_array_listing.cwl
+++ /dev/null
@@ -1,26 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: iwdr_array_listing
-  class: CommandLineTool
-  baseCommand: ['ls']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing: $(inputs.files)
-
-  stdout: file_list
-  inputs:
-      - id: files
-        type:
-          type: array
-          items: File
-        default: [ "/Users/chrisl/Downloads/cwl/allRequirements.txt" ]
-  arguments: [ "*.txt" ]
-  outputs:
-      - id: file_list
-        type: string
-        outputBinding:
-          glob: file_list
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file.cwl
deleted file mode 100644
index 1980beb52d8..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file.cwl
+++ /dev/null
@@ -1,43 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_inline_file
-  class: CommandLineTool
-  baseCommand: ['python3', 'prime_sieve.py', '100']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: 'prime_sieve.py'
-              entry: |
-                  import sys
-                  import math
-
-                  limit = int(sys.argv[1])
-                  sieve = [True for i in range(limit)]
-                  for i in range(2, math.floor(limit / 2)):
-                      if sieve[i]:
-                          for j in range(i * 2, limit, i):
-                              sieve[j] = False
-
-                  result = "["
-                  for i in range(2, limit):
-                      if sieve[i]:
-                          if result != "[":
-                              result += ", "
-                          result += str(i)
-                  result += "]"
-
-                  print(result)
-
-  stdout: "primes"
-  inputs: []
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file_custom_entryname.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file_custom_entryname.cwl
deleted file mode 100644
index bff672a7e8a..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file_custom_entryname.cwl
+++ /dev/null
@@ -1,47 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_inline_file
-  class: CommandLineTool
-  baseCommand: ['python3']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: $(inputs.script_name)
-              entry: |
-                  import sys
-                  import math
-
-                  limit = int(sys.argv[1])
-                  sieve = [True for i in range(limit)]
-                  for i in range(2, math.floor(limit / 2)):
-                      if sieve[i]:
-                          for j in range(i * 2, limit, i):
-                              sieve[j] = False
-
-                  result = "["
-                  for i in range(2, limit):
-                      if sieve[i]:
-                          if result != "[":
-                              result += ", "
-                          result += str(i)
-                  result += "]"
-
-                  print(result)
-
-  stdout: "primes"
-  inputs:
-      - id: script_name
-        type: string
-        default: "astounding.py"
-  arguments: [ $(inputs.script_name), '100' ]
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string.cwl
deleted file mode 100644
index 286f6b7aedc..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string.cwl
+++ /dev/null
@@ -1,50 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_input_string
-  class: CommandLineTool
-  baseCommand: ['python3', 'prime_sieve.py', '100']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: $(inputs.script_name)
-              entry: $(inputs.script)
-
-  stdout: "primes"
-  inputs:
-      - id: script
-        type: string
-        default: |
-          import sys
-          import math
-
-          limit = int(sys.argv[1])
-          sieve = [True for i in range(limit)]
-          for i in range(2, math.floor(limit / 2)):
-              if sieve[i]:
-                  for j in range(i * 2, limit, i):
-                      sieve[j] = False
-
-          result = "["
-          for i in range(2, limit):
-              if sieve[i]:
-                  if result != "[":
-                      result += ", "
-                  result += str(i)
-          result += "]"
-
-          print(result)
-      - id: script_name
-        type: string
-        default: "prime_sieve.py"
-  arguments: [ $(inputs.script_name), '100' ]
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string_function.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string_function.cwl
deleted file mode 100644
index f70cd7bf8b9..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string_function.cwl
+++ /dev/null
@@ -1,49 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_input_string_function
-  class: CommandLineTool
-  baseCommand: ['python3']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: ${var result = inputs.script_name + ".py"; return result;}
-              entry: ${var scr = inputs.script; return scr + "print(result);"}
-
-  stdout: "primes"
-  inputs:
-      - id: script
-        type: string
-        default: |
-          import sys
-          import math
-
-          limit = int(sys.argv[1])
-          sieve = [True for i in range(limit)]
-          for i in range(2, math.floor(limit / 2)):
-              if sieve[i]:
-                  for j in range(i * 2, limit, i):
-                      sieve[j] = False
-
-          result = "["
-          for i in range(2, limit):
-              if sieve[i]:
-                  if result != "[":
-                      result += ", "
-                  result += str(i)
-          result += "]"
-
-      - id: script_name
-        type: string
-        default: "prime_sieve.py"
-  arguments: [ '${var result = inputs.script_name + ".py"; return result;}', '100' ]
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test.aws.test b/centaur/src/main/resources/standardTestCases/ad_hoc_file_test.aws.test
deleted file mode 100644
index 8016f90f665..00000000000
--- a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test.aws.test
+++ /dev/null
@@ -1,14 +0,0 @@
-name: ad_hoc_file_test.aws
-testFormat: workflowsuccess
-backends: [ AWSBATCH ]
-
-files {
-  workflow: ad_hoc_file_test/workflow.cwl
-  imports: [
-    ad_hoc_file_test/cwl-test.cwl
-  ]
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/cwl-test.cwl b/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/cwl-test.cwl
deleted file mode 100644
index 7ac312f6f3a..00000000000
--- a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/cwl-test.cwl
+++ /dev/null
@@ -1,21 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-baseCommand: ["sh", "example.sh"]
-hints:
-  DockerRequirement:
-    dockerPull: ubuntu:latest
-inputs: []
-
-requirements:
-  InitialWorkDirRequirement:
-    listing:
-      - entryname: example.sh
-        entry: |-
-          PREFIX='Message is:'
-          MSG="\${PREFIX} Hello world!"
-          echo \${MSG}
-
-outputs:
-  example_out:
-    type: stdout
-stdout: output.txt
diff --git a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/workflow.cwl b/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/workflow.cwl
deleted file mode 100644
index 678132165b2..00000000000
--- a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/workflow.cwl
+++ /dev/null
@@ -1,10 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs: []
-outputs: []
-
-steps:
-  test:
-    run: cwl-test.cwl
-    in: []
-    out: []
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows.test b/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows.test
deleted file mode 100644
index e5381017829..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows.test
+++ /dev/null
@@ -1,19 +0,0 @@
-name: cwl_cache_between_workflows
-testFormat: runtwiceexpectingcallcaching
-workflowRoot: cwl-cache-between-workflows
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_cache_between_workflows/cwl_cache_between_workflows.cwl
-  inputs: cwl_cache_between_workflows/cwl_cache_between_workflows.json
-}
-
-metadata {
-  status: Succeeded
-  "calls.cwl-cache-between-workflows.step-average.callCaching.result": "Cache Hit: <<CACHE_HIT_UUID>>:cwl-cache-between-workflows.step-average:-1"
-  "calls.cwl-cache-between-workflows.step-product.callCaching.result": "Cache Hit: <<CACHE_HIT_UUID>>:cwl-cache-between-workflows.step-product:-1"
-  "outputs.cwl-cache-between-workflows.trapezoidalArea": 77.0,
-  "outputs.cwl-cache-between-workflows.baseAverage": 11.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.cwl b/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.cwl
deleted file mode 100644
index d48e74cd935..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.cwl
+++ /dev/null
@@ -1,79 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: average
-  class: CommandLineTool
-
-  inputs:
-    base1:
-      type: int
-      default: 9
-    base2:
-      type: int
-      default: 13
-
-  outputs:
-    baseAverage:
-      type: float
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseFloat(self[0].contents))
-
-  arguments:
-  - valueFrom: "echo $((inputs.base1 + inputs.base2) / 2)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-- id: height-product
-  class: CommandLineTool
-
-  inputs:
-    baseAverage: float
-    height:
-      type: float
-      default: 7.0
-
-  outputs:
-    trapezoidalArea:
-      type: long
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseFloat(self[0].contents))
-
-  arguments:
-  - valueFrom: "echo $(inputs.baseAverage * inputs.height)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-- id: cwl-cache-between-workflows
-  class: Workflow
-
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  - class: ShellCommandRequirement
-
-  inputs: []
-
-  outputs:
-    baseAverage:
-      type: float
-      outputSource: step-average/baseAverage
-    trapezoidalArea:
-      type: long
-      outputSource: step-product/trapezoidalArea
-
-  steps:
-    step-average:
-      run: "#average"
-      in: []
-      out: [baseAverage]
-
-    step-product:
-      run: "#height-product"
-      in:
-        baseAverage: step-average/baseAverage
-      out: [trapezoidalArea]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.json b/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.json
deleted file mode 100644
index 0967ef424bc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.json
+++ /dev/null
@@ -1 +0,0 @@
-{}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow.test b/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow.test
deleted file mode 100644
index 8ef753b494d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow.test
+++ /dev/null
@@ -1,26 +0,0 @@
-name: cwl_cache_within_workflow
-testFormat: workflowsuccess
-workflowRoot: cwl-cache-within-workflow
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_cache_within_workflow/cwl_cache_within_workflow.cwl
-  inputs: cwl_cache_within_workflow/cwl_cache_within_workflow.json
-}
-
-metadata {
-  status: Succeeded
-  "calls.cwl-cache-within-workflow.foo.callCaching.result": "Cache Miss"
-  "calls.cwl-cache-within-workflow.bar.callCaching.result": "Cache Miss"
-  "calls.cwl-cache-within-workflow.re-bar.callCaching.result": "Cache Hit: <<UUID>>:cwl-cache-within-workflow.bar:-1"
-  "calls.cwl-cache-within-workflow.bar.inputs.pi": 3.14159
-  "calls.cwl-cache-within-workflow.bar.inputs.rSquared": 16.23381791021144
-  "calls.cwl-cache-within-workflow.bar.outputs.area": 51
-  "calls.cwl-cache-within-workflow.bar.outputs.rSquaredCopy": 16.23381791021144
-  "calls.cwl-cache-within-workflow.re-bar.inputs.pi": 3.14159
-  "calls.cwl-cache-within-workflow.re-bar.inputs.rSquared": 16.23381791021144
-  "calls.cwl-cache-within-workflow.re-bar.outputs.area": 51
-  "calls.cwl-cache-within-workflow.re-bar.outputs.rSquaredCopy": 16.23381791021144
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.cwl b/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.cwl
deleted file mode 100644
index 15b1fd79a01..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.cwl
+++ /dev/null
@@ -1,129 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: one
-  class: CommandLineTool
-
-  inputs:
-    r:
-      type: float
-
-  outputs:
-    rSquared:
-      type: float
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseFloat(self[0].contents))
-    rCopy:
-      type: float
-      outputBinding:
-        outputEval: $(inputs.r)
-
-  arguments:
-  - valueFrom: "echo $(inputs.r * inputs.r)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-- id: two
-  class: CommandLineTool
-
-  inputs:
-    rSquared: float
-    pi: float
-
-  outputs:
-    area:
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    rSquaredCopy:
-      outputBinding:
-        outputEval: $(inputs.rSquared)
-      type: float
-
-  arguments:
-  - valueFrom: "echo $(inputs.rSquared * inputs.pi)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-# Throwing in some ExpressionTools for fun. Currently these not only don't cache but aren't even listed in the metadata
-# except in the original workflow blob (see #3499). The current thinking is that these should appear in metadata with a
-# call-like presentation but that they don't need to be eligible for caching since ExpressionTools are supposed to be
-# very lightweight and not worth the expense of hashing and potential cache hit copying.
-- id: three
-  class: ExpressionTool
-
-  inputs:
-    rSquared: float
-    pi: float
-
-  outputs:
-    area: int
-    rSquaredCopy: float
-
-  expression: |
-    ${
-    return {"area": parseInt(inputs.pi * inputs.rSquared),
-            "rSquaredCopy": inputs.rSquared };
-    }
-
-
-- id: cwl-cache-within-workflow
-  class: Workflow
-
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  - class: ShellCommandRequirement
-
-  inputs:
-    radius: float
-    pi: float
-
-  outputs:
-    area:
-      type: int
-      outputSource: re-bar/area
-    area-expression:
-      type: int
-      outputSource: re-baz/area
-
-  steps:
-    foo:
-      run: "#one"
-      in:
-        r: radius
-        pi: pi
-      out: [rSquared, rCopy]
-
-    bar:
-      run: "#two"
-      in:
-        rSquared: "foo/rSquared"
-        pi: pi
-      out: [area, rSquaredCopy]
-
-    re-bar:
-      run: "#two"
-      in:
-        rSquared: "bar/rSquaredCopy"
-        pi: pi
-      out: [area, rSquaredCopy]
-
-    baz:
-      run: "#three"
-      in:
-        rSquared: "foo/rSquared"
-        pi: pi
-      out: [area, rSquaredCopy]
-
-    re-baz:
-      run: "#three"
-      in:
-        rSquared: "baz/rSquaredCopy"
-        pi: pi
-      out: [area, rSquaredCopy]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.json b/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.json
deleted file mode 100644
index 563f2413547..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "radius": 4.029121233,
-  "pi": 3.14159
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_disk_resources_papiv2.test b/centaur/src/main/resources/standardTestCases/cwl_disk_resources_papiv2.test
deleted file mode 100644
index 8677bcf711e..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_disk_resources_papiv2.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_disk_resources_papiv2
-testFormat: workflowsuccess
-backends: [Papiv2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_resources/cwl_disk_resources.cwl
-}
-
-metadata {
-  status: Succeeded
-  "outputs.diskSizeTool.disk_size": 30
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: diskSizeTool
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size.test b/centaur/src/main/resources/standardTestCases/cwl_docker_size.test
deleted file mode 100644
index ca700d5cd9d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_docker_files
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_docker_size/cwl_docker_size.cwl
-  inputs: cwl_docker_size/cwl_docker_size.yaml
-  options: cwl_docker_size/cwl_docker_size.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.main.stdout_output": "execute order=66"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.cwl b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.cwl
deleted file mode 100644
index 5383bccb484..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.cwl
+++ /dev/null
@@ -1,40 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: main
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: INPUT
-      type: File[]
-  stdout: stdout
-  outputs:
-    stdout_output:
-      type: string
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: $(self[0].contents.trim())
-  arguments:
-    - valueFrom: |
-        ${
-          if (inputs.INPUT.length == 0) {
-            var cmd = ['echo', "no inputs"];
-            return cmd
-          }
-          else {
-            var cmd = ["echo", "execute"];
-            var use_input = [];
-            for (var i = 0; i < inputs.INPUT.length; i++) {
-              var filesize = inputs.INPUT[i].size;
-              use_input.push("order=".concat(filesize));
-            }
-
-            var run_cmd = cmd.concat(use_input);
-            return run_cmd
-          }
-
-        }
-  out: stdout
-  baseCommand: []
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.options b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.yaml b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.yaml
deleted file mode 100644
index 097e69e8590..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-INPUT:
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt
deleted file mode 100644
index 1a6374205aa..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt
+++ /dev/null
@@ -1 +0,0 @@
-And you people, you're all astronauts, on some kind of star trek.
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir.test b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir.test
deleted file mode 100644
index 57a69084c62..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir.test
+++ /dev/null
@@ -1,20 +0,0 @@
-name: cwl_dynamic_initial_workdir
-testFormat: workflowsuccess
-ignore: false
-workflowRoot: main
-workflowType: CWL
-workflowTypeVersion: v1.0
-backendsMode: "only"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl
-  inputs: cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs
-}
-
-metadata {
-  status: Succeeded
-  "outputs.main.sha": "13cda8661796ae241da3a18668fb552161a72592\n"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl
deleted file mode 100644
index 6012854d0b7..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl
+++ /dev/null
@@ -1,29 +0,0 @@
-cwlVersion: v1.0
-$graph:
-  id: main
-  class: CommandLineTool
-  cwlVersion: v1.0
-  requirements:
-    - class: ShellCommandRequirement
-    - class: InitialWorkDirRequirement
-      listing: $(inputs.indir.listing)
-    - class: DockerRequirement
-      dockerPull: "ubuntu:latest"
-  inputs:
-    indir: Directory
-  outputs:
-    sha:
-      type: string
-      outputBinding:
-        glob: output.txt
-        loadContents: true
-        outputEval: $(self[0].contents)
-  arguments: ["find", "-L", ".", "-name", "?",
-    {shellQuote: false, valueFrom: "|"},
-    "sort",
-    {shellQuote: false, valueFrom: "|"},
-    "sha1sum",
-    {shellQuote: false, valueFrom: "|"},
-    "cut", "-c", "1-40"
-  ]
-  stdout: output.txt
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs
deleted file mode 100644
index f37fed14367..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs
+++ /dev/null
@@ -1,3 +0,0 @@
-indir:
-  class: Directory
-  location: centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/a b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/a
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/b b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/b
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/c/d b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/c/d
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.cwl b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.cwl
deleted file mode 100644
index c2079a82721..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.cwl
+++ /dev/null
@@ -1,25 +0,0 @@
-cwlVersion: v1.0
-$namespaces:
-  edam: http://edamontology.org/
-  gx: http://galaxyproject.org/formats/
-$schemas:
-  - file:./cwl/src/test/resources/cwl/ontology/EDAM.owl
-  - file:./cwl/src/test/resources/cwl/ontology/gx_edam.ttl
-$graph:
-- id: main
-  class: CommandLineTool
-  cwlVersion: v1.0
-  inputs:
-    - id: reference
-      type: File
-      format: gx:fasta
-      inputBinding: { position: 2 }
-  outputs:
-    - id: lineCount
-      type: int
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: "$(parseInt(self[0].contents))"
-  baseCommand: ["wc", "-l"]
-  stdout: stdout
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.options b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_invalid.yaml b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_invalid.yaml
deleted file mode 100644
index 6e75ae34f28..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_invalid.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Try to pass a fastq in as a fasta
-reference:
-  class: File
-  format: edam:format_1930
-  path: "centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_missing.yaml b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_missing.yaml
deleted file mode 100644
index 4e8a35cb2e9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_missing.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Pass a fastq in as a fasta, but without passing the format
-reference:
-  class: File
-  #format: edam:format_1930
-  path: "centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl
deleted file mode 100644
index b85bf8d2434..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl
+++ /dev/null
@@ -1,27 +0,0 @@
-cwlVersion: v1.0
-$namespaces:
-  edam: http://edamontology.org/
-  gx: http://galaxyproject.org/formats/
-$schemas:
-  # Relative path:
-  - ../../../../../../cwl/src/test/resources/cwl/ontology/EDAM.owl
-  # Absolute (remote) path:
-  - https://raw.githubusercontent.com/broadinstitute/cromwell/develop/cwl/src/test/resources/cwl/ontology/gx_edam.ttl
-$graph:
-- id: main
-  class: CommandLineTool
-  cwlVersion: v1.0
-  inputs:
-    - id: reference
-      type: File
-      format: gx:fasta
-      inputBinding: { position: 2 }
-  outputs:
-    - id: lineCount
-      type: int
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: "$(parseInt(self[0].contents))"
-  baseCommand: ["wc", "-l"]
-  stdout: stdout
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_valid.yaml b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_valid.yaml
deleted file mode 100644
index b598f92b7e1..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_valid.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Pass in a valid input file format
-reference:
-  class: File
-  format: edam:format_1929
-  path: "centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta b/centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta
deleted file mode 100644
index e91d1521810..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->sequence #1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq b/centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq
deleted file mode 100644
index 5ecec0ebec8..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq
+++ /dev/null
@@ -1,4 +0,0 @@
-@SEQ_ID
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
-+
-!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_invalid.test b/centaur/src/main/resources/standardTestCases/cwl_format_invalid.test
deleted file mode 100644
index 43962bb5bfc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_invalid.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_invalid
-testFormat: workflowfailure
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_format/cwl_format.cwl
-  inputs: cwl_format/cwl_format_invalid.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "failures.0.message": "Workflow input processing failed"
-  "failures.0.causedBy.0.message": "Failed to evaluate input 'reference' (reason 1 of 1): edam:format_1930 is not compatible with http://galaxyproject.org/formats/fasta"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_missing.test b/centaur/src/main/resources/standardTestCases/cwl_format_missing.test
deleted file mode 100644
index a7b626f69e4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_missing.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_missing
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_format/cwl_format.cwl
-  inputs: cwl_format/cwl_format_missing.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "workflowName": "main"
-  "outputs.main.lineCount": "4"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_valid.test b/centaur/src/main/resources/standardTestCases/cwl_format_valid.test
deleted file mode 100644
index 6a6452deff5..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_valid.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_valid
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_format/cwl_format.cwl
-  inputs: cwl_format/cwl_format_valid.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "workflowName": "main"
-  "outputs.main.lineCount": "2"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_valid_with_workflow_url.test b/centaur/src/main/resources/standardTestCases/cwl_format_valid_with_workflow_url.test
deleted file mode 100644
index e587dbfe6d6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_valid_with_workflow_url.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_valid_with_workflow_url
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflowUrl: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl"
-  inputs: cwl_format/cwl_format_valid.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "workflowName": "main"
-  "outputs.main.lineCount": "2"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_glob_sort.test b/centaur/src/main/resources/standardTestCases/cwl_glob_sort.test
deleted file mode 100644
index 04856ab66b9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_glob_sort.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: cwl_glob_sort
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: globSort
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_glob_sort/cwl_glob_sort.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.globSort.letters": "a b c w x y z"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl b/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl
deleted file mode 100644
index 8d54af1c040..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl
+++ /dev/null
@@ -1,19 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: globSort
-  cwlVersion: v1.0
-  class: CommandLineTool
-  requirements:
-    - class: InlineJavascriptRequirement
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs: []
-  baseCommand: [touch, z, y, x, w, c, b, a]
-  outputs:
-    letters:
-      type: string
-      outputBinding:
-        glob: '?'
-        outputEval: |
-          ${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(" ") }
diff --git a/centaur/src/main/resources/standardTestCases/cwl_glob_sort_with_workflow_url.test b/centaur/src/main/resources/standardTestCases/cwl_glob_sort_with_workflow_url.test
deleted file mode 100644
index 6e7ed2b1dd2..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_glob_sort_with_workflow_url.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: cwl_glob_sort_with_workflow_url
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: globSort
-skipDescribeEndpointValidation: true
-
-files {
-  workflowUrl: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl"
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.globSort.letters": "a b c w x y z"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type.test b/centaur/src/main/resources/standardTestCases/cwl_import_type.test
deleted file mode 100644
index 9e530a95469..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type.test
+++ /dev/null
@@ -1,14 +0,0 @@
-name: cwl_import_type
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_import_type/test_wf.cwl
-  inputs: cwl_import_type/test_wf_inputs.json
-  imports: [
-    cwl_import_type/capture_kit.yml,
-    cwl_import_type/touch.cwl
-  ]
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/capture_kit.yml b/centaur/src/main/resources/standardTestCases/cwl_import_type/capture_kit.yml
deleted file mode 100644
index 4323dd90f6d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/capture_kit.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-- name: capture_kit
-  type: record
-  fields:
-    - name: bait
-      type: string
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf.cwl b/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf.cwl
deleted file mode 100644
index 3658ab127d0..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf.cwl
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
-
-class: Workflow
-
-requirements:
-  - class: SchemaDefRequirement
-    types:
-      - $import: capture_kit.yml
-
-inputs:
-  - id: bam
-    type: string
-  - id: capture_kit
-    type: capture_kit.yml#capture_kit
-
-outputs:
-  - id: output_bam
-    type: File
-    outputSource: touch_bam/output
-
-steps:
-  - id: touch_bam
-    run: touch.cwl
-    in:
-      - id: input
-        source: bam
-    out:
-      - id: output
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf_inputs.json b/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf_inputs.json
deleted file mode 100644
index 55141261811..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf_inputs.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "bam": "a.bam",
-    "capture_kit": {
-        "bait": "abait"
-    }
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/touch.cwl b/centaur/src/main/resources/standardTestCases/cwl_import_type/touch.cwl
deleted file mode 100644
index 8a0be057c42..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/touch.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
-
-requirements:
-  - class: DockerRequirement
-    dockerPull: ubuntu:bionic-20180426
-
-class: CommandLineTool
-
-inputs:
-  - id: input
-    type: string
-    inputBinding:
-      position: 0
-
-outputs:
-  - id: output
-    type: File
-    outputBinding:
-      glob: $(inputs.input)
-      
-baseCommand: [touch]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed.test b/centaur/src/main/resources/standardTestCases/cwl_import_type_packed.test
deleted file mode 100644
index 0a3fd7c20a4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed.test
+++ /dev/null
@@ -1,11 +0,0 @@
-name: cwl_import_type_packed
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_import_type_packed/test_pack.cwl
-  inputs: cwl_import_type_packed/test_wf_inputs.json
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_pack.cwl b/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_pack.cwl
deleted file mode 100644
index 4150b5a5796..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_pack.cwl
+++ /dev/null
@@ -1,91 +0,0 @@
-{
-    "cwlVersion": "v1.0", 
-    "$graph": [
-        {
-            "inputs": [
-                {
-                    "type": "string", 
-                    "id": "#main/bam"
-                }, 
-                {
-                    "type": "#capture_kit.yml/capture_kit", 
-                    "id": "#main/capture_kit"
-                }
-            ], 
-            "requirements": [
-                {
-                    "class": "SchemaDefRequirement", 
-                    "types": [
-                        {
-                            "fields": [
-                                {
-                                    "type": "string", 
-                                    "name": "#capture_kit.yml/capture_kit/bait"
-                                }
-                            ], 
-                            "type": "record", 
-                            "name": "#capture_kit.yml/capture_kit"
-                        }
-                    ]
-                }
-            ], 
-            "outputs": [
-                {
-                    "outputSource": "#main/touch_bam/output", 
-                    "type": "File", 
-                    "id": "#main/output_bam"
-                }
-            ], 
-            "class": "Workflow", 
-            "steps": [
-                {
-                    "out": [
-                        {
-                            "id": "#main/touch_bam/output"
-                        }
-                    ], 
-                    "run": "#touch.cwl", 
-                    "id": "#main/touch_bam", 
-                    "in": [
-                        {
-                            "source": "#main/bam", 
-                            "id": "#main/touch_bam/input"
-                        }
-                    ]
-                }
-            ], 
-            "id": "#main"
-        }, 
-        {
-            "inputs": [
-                {
-                    "inputBinding": {
-                        "position": 0
-                    }, 
-                    "type": "string", 
-                    "id": "#touch.cwl/input"
-                }
-            ], 
-            "requirements": [
-                {
-                    "dockerPull": "ubuntu:bionic-20180426", 
-                    "class": "DockerRequirement"
-                }
-            ], 
-            "outputs": [
-                {
-                    "outputBinding": {
-                        "glob": "$(inputs.input)"
-                    }, 
-                    "type": "File", 
-                    "id": "#touch.cwl/output"
-                }
-            ], 
-            "baseCommand": [
-                "touch"
-            ], 
-            "class": "CommandLineTool", 
-            "id": "#touch.cwl"
-        }
-    ]
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_wf_inputs.json b/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_wf_inputs.json
deleted file mode 100644
index 55141261811..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_wf_inputs.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "bam": "a.bam",
-    "capture_kit": {
-        "bait": "abait"
-    }
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression.test b/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression.test
deleted file mode 100644
index 0e39f78ce78..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_input_binding_expression
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_input_binding_expression
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_input_binding_expression/cwl_input_binding_expression.cwl
-  inputs: cwl_input_binding_expression/cwl_input_binding_expression.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.cwl_input_binding_expression.b": "hello world"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.cwl b/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.cwl
deleted file mode 100644
index f534adfaa36..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.cwl
+++ /dev/null
@@ -1,25 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: cwl_input_binding_expression
-  class: CommandLineTool
-  requirements:
-    - class: InlineJavascriptRequirement
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: hello
-      type: string
-      inputBinding:
-        valueFrom: $(self + " world")
-        position: 1
-  outputs:
-    b:
-      type: string
-      outputBinding:
-        loadContents: true
-        glob: stdout
-        outputEval: $(self[0].contents.trim())
-  stdout: stdout
-  baseCommand: []
-  arguments: [echo]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.json b/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.json
deleted file mode 100644
index 8920ee8d630..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "hello": "hello"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_json.test b/centaur/src/main/resources/standardTestCases/cwl_input_json.test
deleted file mode 100644
index 1dd81ba8260..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_json.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_input_json
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-backendsMode: "only"
-workflowRoot: cwl_input_json
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_input_json/cwl_input_json.yaml
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_json/cwl_input_json.yaml b/centaur/src/main/resources/standardTestCases/cwl_input_json/cwl_input_json.yaml
deleted file mode 100644
index f6e5616c6c4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_json/cwl_input_json.yaml
+++ /dev/null
@@ -1,70 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: cwl_input_json
-  class: Workflow
-  inputs: []
-  outputs:
-    final_output:
-      type: File
-      outputSource: round/output_file
-  steps:
-    make:
-      run: "#makefile"
-      in: []
-      out: [fileoutput]
-    round:
-      run: "#roundtrip"
-      in:
-        input_record: 
-          source: "make/fileoutput"
-      out: [output_file]
-          
-- id: makefile
-  class: CommandLineTool
-  requirements:
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  inputs: []
-  outputs:
-    fileoutput:
-      type:
-        fields:
-        - name: input_file
-          type: File
-        name: input_record
-        type: record
-  arguments:
-    - valueFrom: >
-         echo foo > foo && echo '{ "fileoutput": { "input_file": {"path": "$(runtime.outdir)/foo", "class": "File"} } }' > cwl.output.json
-      shellQuote: false
-
-- id: roundtrip
-  class: CommandLineTool
-  hints:
-  - class: DockerRequirement
-    dockerPull: "stedolan/jq:latest"
-  inputs:
-  - id: input_record
-    type:
-      fields:
-      - name: input_file
-        type: File
-      name: input_record
-      type: record
-  outputs:
-  - id: output_file
-    type: File
-  requirements:
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: InitialWorkDirRequirement
-    listing:
-    - entry: $(JSON.stringify(inputs))
-      entryname: cwl.inputs.json
-  arguments:
-  # Round-trips the file referenced in cwl.input.json to cwl.output.json. Also ls it in the command to make sure it's there.
-    - valueFrom: >
-         INPUT_FILE=\$(cat cwl.inputs.json | jq -r '.. | .path? // empty') && ls $INPUT_FILE && echo "{\"output_file\": {\"path\": \"\$INPUT_FILE\", \"class\": \"File\"} }" > cwl.output.json
-      shellQuote: false
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray.test b/centaur/src/main/resources/standardTestCases/cwl_input_typearray.test
deleted file mode 100644
index a87bcbf9f65..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_typearray.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_input_typearray
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: input_typearray
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_input_typearray/input_typearray.cwl
-  inputs: cwl_input_typearray/input_typearray.yml
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.input_typearray.response_f": "input.txt"
-  "outputs.input_typearray.response_s": "nonexistent_path.txt"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input.txt b/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.cwl b/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.cwl
deleted file mode 100644
index 897b74822e8..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.cwl
+++ /dev/null
@@ -1,42 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: input_typearray
-  cwlVersion: v1.0
-  class: CommandLineTool
-  baseCommand: ['/bin/echo']
-  stdout: "response.txt"
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  - class: InlineJavascriptRequirement
-  arguments:
-      - position: 3
-        valueFrom: "sentinel"
-  inputs:
-    value_f:
-      type:
-        - string
-        - File
-      inputBinding:
-        position: 1
-      doc: "an input to test with a File value"
-    value_s:
-      type:
-        - string
-        - File
-      inputBinding:
-        position: 2
-      doc: "an input to test with a string value"
-  outputs:
-    response_f:
-      type: string
-      outputBinding:
-        glob: response.txt
-        loadContents: true
-        outputEval: $(self[0].contents.split(" ")[0].split("/").slice(-1)[0])
-    response_s:
-      type: string
-      outputBinding:
-        glob: response.txt
-        loadContents: true
-        outputEval: $(self[0].contents.split(" ")[1].split("/").slice(-1)[0])
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.yml b/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.yml
deleted file mode 100644
index 421402d9289..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-value_f:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_input_typearray/input.txt"
-value_s: "centaur/src/main/resources/standardTestCases/cwl_input_typearray/nonexistent_path.txt"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_inputdir_zero_doesnt_localize_papiv2.test b/centaur/src/main/resources/standardTestCases/cwl_inputdir_zero_doesnt_localize_papiv2.test
deleted file mode 100644
index 564633779a7..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_inputdir_zero_doesnt_localize_papiv2.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_inputdir_zero_doesnt_localize_papiv2
-testFormat: workflowsuccess
-backends: [Papiv2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl
-}
-
-metadata {
-  status: Succeeded
-  "outputs.inputdir_zero_doesnt_localize.errors": ""
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: inputdir_zero_doesnt_localize
diff --git a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings.test b/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings.test
deleted file mode 100644
index 89399e2e8fc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_interpolated_strings
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: interpolatedStrings
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_interpolated_strings/cwl_interpolated_strings.cwl
-  inputs: cwl_interpolated_strings/cwl_interpolated_strings.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.interpolatedStrings.rfc3092": "foo bar baz qux quux"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.cwl b/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.cwl
deleted file mode 100644
index e650061a5cc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.cwl
+++ /dev/null
@@ -1,25 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: interpolatedStrings
-  class: CommandLineTool
-  cwlVersion: v1.0
-  requirements:
-    - class: ShellCommandRequirement
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-
-  inputs:
-    - id: bar
-      type: string
-    - id: qux
-      type: string
-
-  outputs:
-    - id: rfc3092
-      type: string
-
-  arguments:
-     - valueFrom: >
-         echo '{ "rfc3092": "foo $(inputs.bar) baz $(inputs.qux) quux" }' > cwl.output.json
-       shellQuote: false
diff --git a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.json b/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.json
deleted file mode 100644
index 3f1bcedd11f..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.json
+++ /dev/null
@@ -1 +0,0 @@
-{"bar": "bar", "qux": "qux"}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_optionals.test b/centaur/src/main/resources/standardTestCases/cwl_optionals.test
deleted file mode 100644
index 2d945f36ee0..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_optionals.test
+++ /dev/null
@@ -1,13 +0,0 @@
-name: cwl_optionals
-testFormat: workflowsuccess
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_optionals/cwl_optionals.cwl
-  inputs: cwl_optionals/cwl_optionals.json
-}
-
-metadata {
-  "actualWorkflowLanguage": CWL
-  "actualWorkflowLanguageVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.cwl b/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.cwl
deleted file mode 100755
index 592227bf025..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.cwl
+++ /dev/null
@@ -1,12 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-hints:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-baseCommand: echo
-inputs:
-  message:
-    type: string[]?
-  unsupplied_optional:
-    type: string[]?
-outputs: []
diff --git a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.json b/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.json
deleted file mode 100644
index c76e98d49c3..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.json
+++ /dev/null
@@ -1 +0,0 @@
-{"message": ["foo","bar"]}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.cwl b/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.cwl
deleted file mode 100644
index 406301e7ecb..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.cwl
+++ /dev/null
@@ -1,34 +0,0 @@
-cwlVersion: v1.0
-$graph:  
-- id: outputJson
-  # slightly modified version of conformance test #2 to remove the default File that doesn't work on PAPI
-  # It is instead being passed as an input through the input json file
-  class: CommandLineTool
-  cwlVersion: v1.0
-  hints:
-    - class: DockerRequirement
-      dockerPull: python:2-slim
-  inputs:
-    - id: reference
-      type: File
-      inputBinding: { position: 2 }
-  
-    - id: reads
-      type:
-        type: array
-        items: File
-        inputBinding: { prefix: "-YYY" }
-      inputBinding: { position: 3, prefix: "-XXX" }
-  
-    - id: "args.py"
-      type: File
-      inputBinding:
-        position: -1
-  
-  outputs:
-    # note the absence of any sort of valueFrom.
-    # The output value is generated from the "cwl.output.json" file created by the python script
-    args: string[]
-  
-  baseCommand: python
-  arguments: ["bwa", "mem"]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.inputs b/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.inputs
deleted file mode 100644
index d83a30872a9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.inputs
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-    "args.py": {
-      "class": "File",
-      "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/args.py"
-    },
-    "reference": {
-        "class": "File",
-        "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/chr20.fa",
-        "size": 123,
-        "checksum": "sha1$hash"
-    },
-    "reads": [
-        {
-            "class": "File",
-            "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/example_human_Illumina.pe_1.fastq"
-        },
-        {
-            "class": "File",
-            "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/example_human_Illumina.pe_2.fastq"
-        }
-    ]
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_output_json_jes.test b/centaur/src/main/resources/standardTestCases/cwl_output_json_jes.test
deleted file mode 100644
index c7ddf584bd4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_output_json_jes.test
+++ /dev/null
@@ -1,25 +0,0 @@
-name: cwl_output_json_jes
-testFormat: workflowsuccess
-backends: [Papi]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_output_json/cwl_output_json.cwl
-  inputs: cwl_output_json/cwl_output_json.inputs
-}
-
-metadata {
-  status: Succeeded
-  "outputs.outputJson.args.0": "bwa"
-  "outputs.outputJson.args.1": "mem"
-  "outputs.outputJson.args.2": "chr20.fa"
-  "outputs.outputJson.args.3": "-XXX"
-  "outputs.outputJson.args.4": "-YYY"
-  "outputs.outputJson.args.5": "example_human_Illumina.pe_1.fastq"
-  "outputs.outputJson.args.6": "-YYY"
-  "outputs.outputJson.args.7": "example_human_Illumina.pe_2.fastq"
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: outputJson
diff --git a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array.test b/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array.test
deleted file mode 100644
index cea66a37026..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_prefix_for_array
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: prefix-for-array
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_prefix_for_array/prefix_for_array.cwl
-  inputs: cwl_prefix_for_array/prefix_for_array.yml
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.prefix-for-array.out": "--bonus first second\n"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.cwl b/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.cwl
deleted file mode 100644
index ca9044e5c61..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: prefix-for-array
-  cwlVersion: v1.0
-  class: CommandLineTool
-  baseCommand: ['/bin/echo']
-  stdout: "hello.txt"
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  inputs:
-      bonus:
-          type: string[]
-          inputBinding:
-              prefix: "--bonus"
-  outputs:
-    out:
-      type: string
-      outputBinding:
-        glob: hello.txt
-        loadContents: true
-        outputEval: $(self[0].contents)
-
diff --git a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.yml b/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.yml
deleted file mode 100644
index 6a3badb824c..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.yml
+++ /dev/null
@@ -1 +0,0 @@
-bonus: ["first", "second"]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories.test b/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories.test
deleted file mode 100644
index 390c1d66409..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_recursive_link_directories
-testFormat: workflowsuccess
-backends: [Local]
-backendsMode: only
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_recursive_link_directories/cwl_recursive_link_directories.cwl
-}
-
-metadata {
-  status: Succeeded
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_recursive_link_directories
diff --git a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories/cwl_recursive_link_directories.cwl b/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories/cwl_recursive_link_directories.cwl
deleted file mode 100644
index a4a19fd6a5d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories/cwl_recursive_link_directories.cwl
+++ /dev/null
@@ -1,19 +0,0 @@
-cwlVersion: v1.0
-$graph:  
-- id: cwl_recursive_link_directories
-  class: CommandLineTool
-  requirements:
-    - class: ShellCommandRequirement
-  cwlVersion: v1.0
-  hints:
-    - class: DockerRequirement
-      dockerPull: ubuntu:latest
-  inputs: []
-  outputs:
-    output_dir:
-        type: Directory
-        outputBinding:
-          glob: work_dir
-  arguments:
-    - shellQuote: false
-      valueFrom: "mkdir work_dir && ln -s .. work_dir/link"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/cwl_glob_sort.cwl b/centaur/src/main/resources/standardTestCases/cwl_relative_imports/cwl_glob_sort.cwl
deleted file mode 100644
index 330c896eea6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/cwl_glob_sort.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-requirements:
-  - class: InlineJavascriptRequirement
-hints:
-  DockerRequirement:
-    dockerPull: "debian:stretch-slim"
-inputs: []
-baseCommand: [touch, z, y, x, w, c, b, a]
-outputs:
-  letters:
-    type: string
-    outputBinding:
-      glob: '?'
-      outputEval: |
-        ${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(" ") }
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl b/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl
deleted file mode 100644
index 0ba8fc7236d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: relative_imports
-  class: Workflow
-
-  inputs: []
-  outputs:
-    letters:
-      type: string
-      outputSource: globSort/letters
-
-  steps:
-    globSort:
-      in: []
-      run: cwl_glob_sort.cwl
-      out: [letters]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_url.test b/centaur/src/main/resources/standardTestCases/cwl_relative_imports_url.test
deleted file mode 100644
index eabd10754f6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_url.test
+++ /dev/null
@@ -1,20 +0,0 @@
-name: cwl_relative_imports_url
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: relative_imports
-skipDescribeEndpointValidation: true
-# This test has experienced sporadic failures, and CWL is not fully supported. Therefore the test is being disabled.
-ignore: true
-
-files {
-  workflowUrl: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl"
-}
-
-metadata {
-  status: Succeeded
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.relative_imports.globSort.outputs.letters": "a b c w x y z"
-  "outputs.relative_imports.letters": "a b c w x y z"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_zip.test b/centaur/src/main/resources/standardTestCases/cwl_relative_imports_zip.test
deleted file mode 100644
index deccb8d73a3..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_zip.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_relative_imports_zip
-testFormat: workflowsuccess
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_relative_imports/workflow.cwl
-  imports: [
-    cwl_relative_imports/cwl_glob_sort.cwl
-  ]
-}
-
-metadata {
-  status: Succeeded
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.relative_imports.globSort.outputs.letters": "a b c w x y z"
-  "outputs.relative_imports.letters": "a b c w x y z"
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: relative_imports
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_disk_resources.cwl b/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_disk_resources.cwl
deleted file mode 100644
index 683dd5b17e6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_disk_resources.cwl
+++ /dev/null
@@ -1,38 +0,0 @@
-cwlVersion: v1.0
-# Asks for 10 GB (~=10240 MB) of output dir, tmp dir and input dir.
-# Unfortunately the internal metadata from the VM, despite having some information about the disks doesn't give their size.
-# To avoid possibly unreliable computations based on free or other tool, instead use the GCE API directly to look up the disk info.
-# To do that we need project name, zone and name of the disk which we all obtain via the internal metadata
-# Of importance is the assumption that <disk name> == <instance name>-1
-# Note the "-1" after the instance name. That is because the disk just named <instance name> is the boot disk. The working disk has a "-1" suffix
-# The test expectation ensures that the output is 30, which means all 3 resources have been taken into account.
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-$graph:  
-- id: diskSizeTool
-  class: CommandLineTool
-  cwlVersion: v1.0
-  doc: "Asks for disk minimums"
-  requirements:
-    ResourceRequirement:
-      outdirMin: 10240
-      tmpdirMin: 10240
-  hints:
-  - class: ShellCommandRequirement
-  - class: DockerRequirement
-    dockerPull: gcr.io/google.com/cloudsdktool/cloud-sdk:slim
-  - class: dx:InputResourceRequirement
-    indirMin: 10240
-  inputs: []
-  outputs:
-    disk_size:
-      type: int
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents.trim()))
-  arguments:
-    - valueFrom: >
-        apt-get install --assume-yes jq > /dev/null && NAME=`curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/name` && ZONE=`basename \`curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/zone\`` && PROJECT=`curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/project/project-id` && curl -s -H "Authorization: Bearer `gcloud auth print-access-token`" "https://www.googleapis.com/compute/v1/projects/${PROJECT}/zones/${ZONE}/disks/${NAME}-1?fields=sizeGb" | jq -r '.sizeGb'
-      shellQuote: false
-  stdout: stdout
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl b/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl
deleted file mode 100644
index d874ee0bffb..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl
+++ /dev/null
@@ -1,129 +0,0 @@
-cwlVersion: v1.0
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-$graph:
-- id: inputdir_zero_doesnt_localize
-  class: Workflow
-  hints:
-  - class: ShellCommandRequirement
-  - class: DockerRequirement
-    dockerPull: gcr.io/google.com/cloudsdktool/cloud-sdk:slim
-  - class: dx:InputResourceRequirement
-    indirMin: 0
-  inputs: []
-  outputs:
-  - id: errors
-    type: File
-    outputSource: findFile/errors
-  steps:
-  - id: echo
-    in: []
-    out:
-    - id: echoOut
-    - id: echoArrayOut
-    - id: echoRecordOut
-    - id: echoMaybeOut
-    run:
-      class: CommandLineTool
-      inputs: []
-      outputs:
-      - id: echoOut
-        outputBinding:
-          glob: lonely_file
-        type: File
-        secondaryFiles: [.also]
-      - id: echoArrayOut
-        outputBinding:
-          glob: '*.txt*'
-          outputEval: $([self[0]])  
-        type:
-          items: File
-          type: array
-      - id: echoRecordOut
-        secondaryFiles: [.also]
-        type:
-          type: record
-          name: foo
-          fields:
-            - name: a
-              type: File
-              outputBinding:
-                glob: file_in_object
-      - id: echoMaybeOut
-        type: 
-        - File
-        - 'null'
-        secondaryFiles: [.also]
-        outputBinding:
-          glob: maybe_file
-      arguments:
-       - valueFrom: |
-           echo "lonely_file" > lonely_file
-           echo "lonely_file.also" > lonely_file.also
-           echo "file_in_array.txt" > file_in_array.txt
-           echo "file_in_array.txt.also" > file_in_array.txt.also
-           echo "file_in_object" > file_in_object
-           echo "file_in_object.also" > file_in_object.also
-           echo "maybe_file" > maybe_file
-           echo "maybe_file.also" > maybe_file.also
-         shellQuote: false
-  - id: findFile
-    in:
-    - id: f
-      source: "#inputdir_zero_doesnt_localize/echo/echoOut"
-    - id: g
-      source: "#inputdir_zero_doesnt_localize/echo/echoArrayOut"
-    - id: h
-      source: "#inputdir_zero_doesnt_localize/echo/echoRecordOut"
-    - id: i
-      source: "#inputdir_zero_doesnt_localize/echo/echoMaybeOut"
-    out:
-    - id: errors
-    run:
-      inputs:
-      - id: f
-        type: File
-        secondaryFiles: [.also]
-      - id: i
-        type: File?
-        secondaryFiles: [.also]
-      - id: g
-        type:
-          type: array
-          items: File
-        secondaryFiles: [.also]
-      - id: h
-        secondaryFiles: [.also]
-        type:
-          type: record
-          name: foo
-          fields:
-            - name: a
-              type: File
-      outputs:
-      - id: errors
-        type: string
-        outputBinding:
-          glob: errors.txt
-          loadContents: true
-          outputEval: $(self[0].contents)
-      class: CommandLineTool
-      requirements:
-      - class: ShellCommandRequirement
-      - class: InlineJavascriptRequirement
-      arguments:
-      # Unfortunately we can't use the same trick as in draft3_nio_file_papi1 because in papi 2 the instance metadata doesn't seem to contain
-      # the PAPI operation ID. So instead simply check that the input files are not there. This is not as neat as the PAPI1 version
-      # but should check the right thing as long as the files are localized (in general, but not here) somewhere in the same directory as where the command
-      # runs. If that changes then the directory where "find" searches should be updated 
-        - valueFrom: |
-            touch errors.txt
-            find . -name lonely_file >> errors.txt
-            find . -name lonely_file.also >> errors.txt
-            find . -name file_in_array >> errors.txt
-            find . -name file_in_array.also >> errors.txt
-            find . -name file_in_object >> errors.txt
-            find . -name file_in_object.also >> errors.txt
-            find . -name maybe_file >> errors.txt
-            find . -name maybe_file.also >> errors.txt
-          shellQuote: false
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_resources.cwl b/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_resources.cwl
deleted file mode 100644
index 295302acc2e..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_resources.cwl
+++ /dev/null
@@ -1,27 +0,0 @@
-cwlVersion: v1.0
-$graph:  
-- id: machineTypeTool
-  class: CommandLineTool
-  cwlVersion: v1.0
-  doc: "Asks for CPU and Memory minimums"
-  requirements:
-    ResourceRequirement:
-      coresMin: 2
-      coresMax: 2
-      ramMin: 7GB
-      ramMax: 7GB
-  hints:
-    DockerRequirement:
-      dockerPull: python:latest
-  inputs: []
-  outputs:
-    machine_type:
-      type: string
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: $(self[0].contents.trim())
-  baseCommand: ['curl', 'http://metadata.google.internal/computeMetadata/v1/instance/machine-type', '-H', 'Metadata-Flavor: Google']
-  stdout: stdout
-
-
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources_papiv2.test b/centaur/src/main/resources/standardTestCases/cwl_resources_papiv2.test
deleted file mode 100644
index ccb4f0ad534..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources_papiv2.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_resources_papiv2
-testFormat: workflowsuccess
-backends: [Papiv2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_resources/cwl_resources.cwl
-}
-
-metadata {
-  status: Succeeded
-  "outputs.machineTypeTool.machine_type": "projects/1005074806481/machineTypes/custom-2-7168"
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: machineTypeTool
diff --git a/centaur/src/main/resources/standardTestCases/cwl_restart/cwl_restart.cwl b/centaur/src/main/resources/standardTestCases/cwl_restart/cwl_restart.cwl
deleted file mode 100644
index 82664f739b1..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_restart/cwl_restart.cwl
+++ /dev/null
@@ -1,117 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-id: cwl_restart
-# Workflow-level DockerRequirement
-requirements:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-inputs: []
-outputs:
-- id: flag
-  outputSource: "#third_step/flag"
-  type: boolean
-steps:
-- id: first_step
-  in: []
-  out:
-  - id: firstfoofile
-  # A dash is not valid in a WDL identifier and would have broken older `IdentifierAndPathPattern` parsing.
-  - id: first-bar-file
-  run:
-    inputs: []
-    outputs:
-    - id: firstfoofile
-      outputBinding:
-        glob: out.txt
-      type: File
-    - id: first-bar-file
-      outputBinding:
-        glob: out.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    arguments:
-    - valueFrom: echo
-    - valueFrom: "I have a bad feeling about this"
-    - valueFrom: ">"
-      shellQuote: false
-    - valueFrom: "out.txt"
-- id: cromwell_killer
-  in:
-  - id: fooinput
-    source: "#first_step/firstfoofile"
-  - id: bar-input
-    source: "#first_step/first-bar-file"
-  out:
-  - id: "footxt"
-  - id: "bar-txt"
-  run:
-    inputs:
-    - id: fooinput
-      type: File
-    - id: bar-input
-      type: File
-    outputs:
-    - id: "footxt"
-      outputBinding:
-        glob: foo.txt
-      type: File
-    - id: "bar-txt"
-      outputBinding:
-        glob: bar.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    arguments:
-    - valueFrom: sleep
-    - valueFrom: "60"
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: foo
-    - valueFrom: ">"
-      shellQuote: false
-    - valueFrom: "foo.txt"
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: bar
-    - valueFrom: ">"
-      shellQuote: false
-    - valueFrom: "bar.txt"
-- id: third_step
-  in:
-  - id: foo
-    source: "#cromwell_killer/footxt"
-  - id: bar
-    source: "#cromwell_killer/bar-txt"
-  out:
-  - id: flag
-  run:
-    inputs:
-    - id: foo
-      type: File
-    - id: bar
-      type: File
-    outputs:
-    - id: flag
-      outputBinding:
-        outputEval: $(true)
-      type: boolean
-    class: CommandLineTool
-    requirements:
-    - class: InlineJavascriptRequirement
-    - class: ShellCommandRequirement
-    arguments:
-    - valueFrom: echo
-    - valueFrom: "Are we alive???"
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: $(inputs.foo)
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: $(inputs.bar)
diff --git a/centaur/src/main/resources/standardTestCases/cwl_restart_local_with_recover.test b/centaur/src/main/resources/standardTestCases/cwl_restart_local_with_recover.test
deleted file mode 100644
index a45e97769cd..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_restart_local_with_recover.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_restart_local_with_recover
-testFormat: CromwellRestartWithRecover
-callMark: cromwell_killer
-backendsMode: "only"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_restart/cwl_restart.cwl
-}
-
-metadata {
-  status: Succeeded
-  "calls.first_step.executionStatus": Done
-  "calls.cromwell_killer.executionStatus": Done
-  "calls.third_step.executionStatus": Done
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
diff --git a/centaur/src/main/resources/standardTestCases/cwl_run/1st-tool.cwl b/centaur/src/main/resources/standardTestCases/cwl_run/1st-tool.cwl
deleted file mode 100644
index af0c4de297d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_run/1st-tool.cwl
+++ /dev/null
@@ -1,9 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-inputs:
-  message:
-    type: string
-    inputBinding:
-      position: 1
-outputs: []
diff --git a/centaur/src/main/resources/standardTestCases/cwl_run/echo-job.yml b/centaur/src/main/resources/standardTestCases/cwl_run/echo-job.yml
deleted file mode 100644
index 913ff438103..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_run/echo-job.yml
+++ /dev/null
@@ -1 +0,0 @@
-message: Hello CWL!
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files.test b/centaur/src/main/resources/standardTestCases/cwl_secondary_files.test
deleted file mode 100644
index 2c8f861e1e9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_secondary_files
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_secondary_files/cwl_secondary_files.cwl
-  inputs: cwl_secondary_files/cwl_secondary_files.yaml
-  options: cwl_secondary_files/cwl_secondary_files.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.main.the_answer": "$(42)"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.cwl b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.cwl
deleted file mode 100644
index 123a7b574a1..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.cwl
+++ /dev/null
@@ -1,44 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: main
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: command
-      type: string
-    - id: f
-      type: File
-      inputBinding:
-        position: 2
-      secondaryFiles: [.also]
-    - id: of
-      type: File?
-      inputBinding:
-        position: 3
-      secondaryFiles: [.also]
-    - id: fs
-      type:
-        type: array
-        items: File
-        inputBinding:
-          position: 4
-      secondaryFiles: [.also]
-    - id: fr
-      secondaryFiles: [.also]
-      type:
-        type: record
-        name: foo
-        fields:
-          - name: a
-            type: File
-            inputBinding:
-              position: 5
-  outputs:
-    the_answer:
-      type: string
-      outputBinding:
-        outputEval: ${ return "$(" + 42 + ")"; }
-  baseCommand: []
-  arguments: ["bash", "-c", $(inputs.command)]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.options b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.yaml b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.yaml
deleted file mode 100644
index 928cfb8cbb3..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.yaml
+++ /dev/null
@@ -1,17 +0,0 @@
-# This command will stat the secondaryFiles and if they're missing bad times
-command: stat $(echo $* | sed 's/.txt/.txt.also/g') > /dev/null
-f:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt"
-of:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt"
-fs:
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt"
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt"
-fr:
-  a:
-    class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt"
\ No newline at end of file
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow.test b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow.test
deleted file mode 100644
index f6dff3fb727..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_secondary_files_workflow
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_secondary_files_workflow
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl
-  inputs: cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml
-  options: cwl_secondary_files_workflow/cwl_secondary_files_workflow.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.cwl_secondary_files_workflow.the_answer": "$(42)"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl
deleted file mode 100644
index d5f9dc3f8c9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl
+++ /dev/null
@@ -1,55 +0,0 @@
-cwlVersion: v1.0
-$graph:
-# The inputs of the workflow specify secondary files but NOT of the tool
-# Verify that they are still propagated through
-- id: cwl_secondary_files_workflow
-  class: Workflow
-  inputs:
-  - id: command
-    type: string
-  - id: wf_file_input
-    type: File
-    secondaryFiles: [.also]
-  - id: wf_file_input_array
-    type:
-      type: array
-      items: File
-    secondaryFiles: [.also]
-  outputs:
-  - id: the_answer
-    type: string
-    outputSource: run_tool/the_answer
-  steps:
-  - id: run_tool
-    run: "#cwl_secondary_files_workflow_tool"
-    in:
-      command: command
-      f: wf_file_input
-      fs: wf_file_input_array
-    out:
-    - id: the_answer
-- id: cwl_secondary_files_workflow_tool
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: command
-      type: string
-    - id: f
-      type: File
-      inputBinding:
-        position: 2
-    - id: fs
-      type:
-        type: array
-        items: File
-        inputBinding:
-          position: 3
-  outputs:
-    the_answer:
-      type: string
-      outputBinding:
-        outputEval: ${ return "$(" + 42 + ")"; }
-  baseCommand: []
-  arguments: ["bash", "-c", $(inputs.command)]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.options b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml
deleted file mode 100644
index e0cf43d4b1a..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-# This command will stat the secondaryFiles and if they're missing bad times
-command: stat $(echo $* | sed 's/.txt/.txt.also/g') > /dev/null
-wf_file_input:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt"
-wf_file_input_array:
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt"
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.cwl b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.cwl
deleted file mode 100644
index b49ec9b1134..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: cwl_stdout_expression
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: foo
-      type: string
-    - id: bar
-      type: string
-  outputs:
-    b: stdout
-  stdout: "stdout-$(inputs.foo)-$(inputs.bar).txt"
-  baseCommand: []
-  arguments: [echo, $(inputs.foo), $(inputs.bar)]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.json b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.json
deleted file mode 100644
index 82e0295d318..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "foo": "baz",
-  "bar": "qux"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_local.test b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_local.test
deleted file mode 100644
index 13bfbb68e24..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_local.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_stdout_expression_local
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_stdout_expression
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_stdout_expression/cwl_stdout_expression.cwl
-  inputs: cwl_stdout_expression/cwl_stdout_expression.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.cwl_stdout_expression.stdout": "<<WORKFLOW_ROOT>>/call-cwl_stdout_expression/execution/stdout-baz-qux.txt"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_papi.test b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_papi.test
deleted file mode 100644
index b48a0effa79..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_papi.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_stdout_expression_papi
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_stdout_expression
-backends: [Papi2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_stdout_expression/cwl_stdout_expression.cwl
-  inputs: cwl_stdout_expression/cwl_stdout_expression.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.cwl_stdout_expression.stdout": "<<WORKFLOW_ROOT>>call-cwl_stdout_expression/stdout-baz-qux.txt"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwls/scatter-job1.json b/centaur/src/main/resources/standardTestCases/cwls/scatter-job1.json
deleted file mode 100644
index b3ab2751243..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwls/scatter-job1.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "inp": ["one", "two", "three", "four"],
-  "inp2": "yeahhh"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwls/scatter-wf1.cwl b/centaur/src/main/resources/standardTestCases/cwls/scatter-wf1.cwl
deleted file mode 100644
index dc46aa7da4a..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwls/scatter-wf1.cwl
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: string[]
-  inp2: string
-outputs:
-  out:
-    type: string[]
-    outputSource: step1/echo_out
-
-requirements:
-  - class: ScatterFeatureRequirement
-  - class: DockerRequirement
-    dockerPull: ubuntu:latest
-
-steps:
-  step1:
-    in:
-      echo_in: inp
-      echo_in2: inp2
-    out: [echo_out]
-    scatter: echo_in
-    run:
-      class: CommandLineTool
-      inputs:
-        echo_in:
-          type: string
-          inputBinding: {}
-        echo_in2:
-          type: string
-          inputBinding: {}
-      outputs:
-        echo_out:
-          type: string
-          outputBinding:
-            glob: "step1_out"
-            loadContents: true
-            outputEval: $(self[0].contents)
-      baseCommand: "echo"
-      arguments:
-        - "-n"
-        - "foo"
-      stdout: "step1_out"
diff --git a/centaur/src/main/resources/standardTestCases/expressionLib.test b/centaur/src/main/resources/standardTestCases/expressionLib.test
deleted file mode 100644
index 74299af9bc6..00000000000
--- a/centaur/src/main/resources/standardTestCases/expressionLib.test
+++ /dev/null
@@ -1,15 +0,0 @@
-name: expression_lib_cwl
-cwlVersion: 1.0
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: expressionLib/expressionLib.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/expressionLib/expressionLib.cwl b/centaur/src/main/resources/standardTestCases/expressionLib/expressionLib.cwl
deleted file mode 100644
index fe8df12b4b0..00000000000
--- a/centaur/src/main/resources/standardTestCases/expressionLib/expressionLib.cwl
+++ /dev/null
@@ -1,14 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-requirements:
-  InlineJavascriptRequirement:
-    expressionLib:
-      - "function foo() { return 2; }"
-inputs: []
-outputs:
-  out: stdout
-arguments: [echo, $(foo())]
-stdout: whatever.txt
diff --git a/centaur/src/main/resources/standardTestCases/hello_cwl.test b/centaur/src/main/resources/standardTestCases/hello_cwl.test
deleted file mode 100644
index 18712fd5404..00000000000
--- a/centaur/src/main/resources/standardTestCases/hello_cwl.test
+++ /dev/null
@@ -1,12 +0,0 @@
-name: hello_cwl
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: hello
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: hello_cwl/hello.cwl
-  inputs: hello_cwl/hello.inputs
-  "outputs.hello.salutation": "Hello m'Lord!"
-}
diff --git a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.cwl b/centaur/src/main/resources/standardTestCases/hello_cwl/hello.cwl
deleted file mode 100644
index deb1e4d1f4a..00000000000
--- a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.cwl
+++ /dev/null
@@ -1,21 +0,0 @@
-cwlVersion: v1.0
-$graph:
-  id: hello
-  class: CommandLineTool
-  requirements:
-    - class: DockerRequirement
-      dockerPull: ubuntu:latest
-  baseCommand: echo
-  inputs:
-    message:
-      type: string
-      inputBinding:
-        position: 1
-  stdout: hello-stdout.txt
-  outputs:
-    - id: salutation
-      type: string
-      outputBinding:
-        glob: hello-stdout.txt
-        loadContents: true
-        outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.inputs b/centaur/src/main/resources/standardTestCases/hello_cwl/hello.inputs
deleted file mode 100644
index 11888b548ad..00000000000
--- a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.inputs
+++ /dev/null
@@ -1,3 +0,0 @@
-# Seemingly innocuous but this particular message actually tests proper shell quoting of
-# spaces, single quotes, and exclamation points.
-message: Hello m'Lord!
diff --git a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs.cwl b/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs.cwl
deleted file mode 100644
index e476be06d12..00000000000
--- a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs.cwl
+++ /dev/null
@@ -1,49 +0,0 @@
-cwlVersion: v1.0
-$graph:
-  - id: http_inputs
-    class: Workflow
-    inputs:
-    - id: jamie
-      type: File
-    outputs:
-    - id: md5
-      outputSource: "#http_inputs/sum/md5"
-      type: int
-    steps:
-    - id: sum
-      in:
-      - id: jamie
-        source: "#http_inputs/jamie"
-      out:
-      - id: md5
-      # Workflow step-level DockerRequirement
-      requirements:
-        DockerRequirement:
-          dockerPull: "ubuntu:latest"
-      run:
-        inputs:
-        - id: jamie
-          type: File
-        outputs:
-        - id: md5
-          outputBinding:
-            glob: md5-stdOut.txt
-            loadContents: true
-            outputEval: $(self[0].contents)
-          type: string
-        class: CommandLineTool
-        requirements:
-        - class: ShellCommandRequirement
-        - class: InlineJavascriptRequirement
-        arguments:
-        - valueFrom: "/usr/bin/md5sum"
-          shellQuote: false
-        - valueFrom: $(inputs.jamie)
-          shellQuote: true
-        - valueFrom: '|'
-          shellQuote: false
-        - valueFrom: cut
-          shellQuote: false
-        - valueFrom: -c1-32
-          shellQuote: false
-        stdout: md5-stdOut.txt
diff --git a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs_cwl.inputs b/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs_cwl.inputs
deleted file mode 100644
index 9a7137d1bf9..00000000000
--- a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs_cwl.inputs
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "jamie": "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/docs/jamie_the_cromwell_pig.png",
-}
diff --git a/centaur/src/main/resources/standardTestCases/http_inputs_cwl.test b/centaur/src/main/resources/standardTestCases/http_inputs_cwl.test
deleted file mode 100644
index 7ed111e3ec7..00000000000
--- a/centaur/src/main/resources/standardTestCases/http_inputs_cwl.test
+++ /dev/null
@@ -1,15 +0,0 @@
-name: http_inputs_cwl
-backends: [Local, Papiv2]
-testFormat: workflowsuccess
-workflowRoot: http_inputs
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: http_inputs/http_inputs.cwl
-  inputs: http_inputs/http_inputs_cwl.inputs
-}
-
-metadata {
-  status: Succeeded
-  "outputs.http_inputs.md5": "602d0a4c1d54b7302e2d245a66a1b609\n"
-}
diff --git a/centaur/src/main/resources/standardTestCases/scatter-wf1.test b/centaur/src/main/resources/standardTestCases/scatter-wf1.test
deleted file mode 100644
index 397b94710a3..00000000000
--- a/centaur/src/main/resources/standardTestCases/scatter-wf1.test
+++ /dev/null
@@ -1,11 +0,0 @@
-name: cwl_scatter_wf1
-testFormat: workflowsuccess
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwls/scatter-wf1.cwl
-  inputs: cwls/scatter-job1.json
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
diff --git a/centaur/src/main/resources/standardTestCases/three_step.test b/centaur/src/main/resources/standardTestCases/three_step.test
deleted file mode 100644
index b24e649ecce..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: three_step_cwl
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: three_step/three_step.cwl
-  inputs: three_step/inputs.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.wc.executionStatus": Done
-  "calls.ps.executionStatus": Done
-  "calls.cgrep.executionStatus": Done
-  "calls.ps.runtimeAttributes.docker": "ubuntu:bionic"
-  "calls.wc.runtimeAttributes.docker": "ubuntu:latest"
-  "calls.cgrep.runtimeAttributes.docker": "debian:jessie"
-}
diff --git a/centaur/src/main/resources/standardTestCases/three_step/inputs.json b/centaur/src/main/resources/standardTestCases/three_step/inputs.json
deleted file mode 100644
index 8dac4768fff..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step/inputs.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "pattern": "java"
-}
diff --git a/centaur/src/main/resources/standardTestCases/three_step/three_step.cwl b/centaur/src/main/resources/standardTestCases/three_step/three_step.cwl
deleted file mode 100644
index e328003eab1..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step/three_step.cwl
+++ /dev/null
@@ -1,114 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-id: three_step
-# Workflow-level DockerRequirement
-hints:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-inputs:
-- id: pattern
-  type: string
-outputs:
-- id: cgrep-count
-  outputSource: "#cgrep/cgrep-count"
-  type: int
-- id: wc-count
-  outputSource: "#wc/wc-count"
-  type: int
-steps:
-- id: ps
-  in: []
-  out:
-  - id: ps-stdOut
-  run:
-    inputs: []
-    outputs:
-    - id: ps-stdOut
-      outputBinding:
-        glob: ps-stdOut.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-      # Command line tool-level DockerRequirement
-      # Check it: this DockerRequirement does not use the `class` formatting but should still parse
-      # thanks to the magic of SALAD.
-      DockerRequirement:
-        dockerPull: "ubuntu:bionic"
-    baseCommand: ps
-    stdout: ps-stdOut.txt
-- id: cgrep
-  in:
-  - id: pattern
-    source: "#pattern"
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: cgrep-count
-  # Workflow step-level DockerRequirement
-  requirements:
-    DockerRequirement:
-      dockerPull: "debian:jessie"
-  run:
-    inputs:
-    - id: pattern
-      type: string
-    - id: file
-      type: File
-    outputs:
-    - id: cgrep-count
-      outputBinding:
-        glob: cgrep-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: grep
-      shellQuote: false
-    - valueFrom: $(inputs.pattern)
-      shellQuote: false
-    - valueFrom: ${return inputs.file}
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: cgrep-stdOut.txt
-- id: wc
-  in:
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: wc-count
-  run:
-    inputs:
-    - id: file
-      type: File
-    outputs:
-    - id: wc-count
-      outputBinding:
-        glob: wc-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: cat
-      shellQuote: false
-    - valueFrom: $(inputs.file)
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: wc-stdOut.txt
diff --git a/centaur/src/main/resources/standardTestCases/three_step/three_step_caller_wf.cwl b/centaur/src/main/resources/standardTestCases/three_step/three_step_caller_wf.cwl
deleted file mode 100644
index ab5d8ddc458..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step/three_step_caller_wf.cwl
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env cwl-runner
-class: Workflow
-cwlVersion: v1.0
-
-inputs:
-- id: pin
-  type: string
-  default: "v"
-
-outputs:
-    count_output:
-      type: int
-      outputSource: threestep/wc-count
-
-requirements:
-  - class: SubworkflowFeatureRequirement
-
-steps:
-  threestep:
-    run: three_step.cwl
-    in:
-    - id: pattern
-      source: pin
-    out: [wc-count]
diff --git a/centaur/src/main/resources/standardTestCases/three_step_subworkflow.test b/centaur/src/main/resources/standardTestCases/three_step_subworkflow.test
deleted file mode 100644
index 6ae478035b7..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step_subworkflow.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: three_step__subwf_cwl
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-
-files {
-  workflow: three_step/three_step_caller_wf.cwl,
-  imports: [
-    three_step/three_step.cwl
-  ]
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/workflow_type_and_version_cwl.test b/centaur/src/main/resources/standardTestCases/workflow_type_and_version_cwl.test
deleted file mode 100644
index 14ba92c588f..00000000000
--- a/centaur/src/main/resources/standardTestCases/workflow_type_and_version_cwl.test
+++ /dev/null
@@ -1,16 +0,0 @@
-ignore: true
-name: workflow_type_and_version_cwl
-testFormat: workflowsuccess
-
-files {
-  workflow: workflow_type_and_version_cwl/workflow_type_and_version_cwl.wdl
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-
-metadata {
-  workflowName: workflow_type_and_version_cwl
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index 8034409dbf5..b5573e0249f 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -470,29 +470,6 @@ languages {
       }
     }
   }
-  CWL {
-    versions {
-      default: "v1.0"
-      "v1.0" {
-        language-factory = "languages.cwl.CwlV1_0LanguageFactory"
-        config {
-          strict-validation: false
-          enabled: true
-
-          # Optional section to define a command returning paths to output files that
-          # can only be known after the user's command has been run
-          output-runtime-extractor {
-            # Optional docker image on which the command should be run - Must have bash if provided
-            docker-image = "stedolan/jq@sha256:a61ed0bca213081b64be94c5e1b402ea58bc549f457c2682a86704dd55231e09"
-            # Single line command executed after the tool has run.
-            # It should write to stdout the file paths that are referenced in the cwl.output.json (or any other file path
-            # not already defined in the outputs of the tool and therefore unknown when the tool is run)
-            command = "cat cwl.output.json 2>/dev/null | jq -r '.. | .path? // .location? // empty'"
-          }
-        }
-      }
-    }
-  }
 }
 
 ontology {
diff --git a/cromwell.example.backends/cromwell.examples.conf b/cromwell.example.backends/cromwell.examples.conf
index 49b676a2c7c..4ca250d1202 100644
--- a/cromwell.example.backends/cromwell.examples.conf
+++ b/cromwell.example.backends/cromwell.examples.conf
@@ -308,17 +308,6 @@ languages {
       }
     }
   }
-  CWL {
-    versions {
-      "v1.0" {
-        # language-factory = "languages.cwl.CwlV1_0LanguageFactory"
-        # config {
-        #   strict-validation: false
-        #   enabled: true
-        # }
-      }
-    }
-  }
 }
 
 # Here is where you can define the backend providers that Cromwell understands.
diff --git a/cwl/src/main/resources/reference.conf b/cwl/src/main/resources/reference.conf
deleted file mode 100644
index 0d0d8a980f9..00000000000
--- a/cwl/src/main/resources/reference.conf
+++ /dev/null
@@ -1,3 +0,0 @@
-cwltool-runner {
-  class = "cwl.CwltoolHeterodon"
-}
diff --git a/cwl/src/main/scala/cwl/ArgumentToCommandPart.scala b/cwl/src/main/scala/cwl/ArgumentToCommandPart.scala
deleted file mode 100644
index ca67eaa7ab3..00000000000
--- a/cwl/src/main/scala/cwl/ArgumentToCommandPart.scala
+++ /dev/null
@@ -1,26 +0,0 @@
-package cwl
-
-import cwl.command.StringCommandPart
-import shapeless._
-import wom.CommandPart
-
-object ArgumentToCommandPart extends Poly1 {
-  type MakeCommandPart = (Boolean, ExpressionLib) => CommandPart
-  implicit def caseStringOrExpression: Case.Aux[StringOrExpression, MakeCommandPart] = at {
-    _.fold(this)
-  }
-
-  implicit def caseExpression: Case.Aux[Expression, MakeCommandPart] = at {
-    CwlExpressionCommandPart.apply
-  }
-
-  implicit def caseString: Case.Aux[String, MakeCommandPart] = at {
-    string =>
-      (_, _) =>
-        StringCommandPart(string)
-  }
-
-  implicit def caseCommandLineBinding: Case.Aux[ArgumentCommandLineBinding, MakeCommandPart] = at {
-    ArgumentCommandLineBindingCommandPart.apply
-  }
-}
diff --git a/cwl/src/main/scala/cwl/BaseCommandToCommandParts.scala b/cwl/src/main/scala/cwl/BaseCommandToCommandParts.scala
deleted file mode 100644
index 2f597918082..00000000000
--- a/cwl/src/main/scala/cwl/BaseCommandToCommandParts.scala
+++ /dev/null
@@ -1,11 +0,0 @@
-package cwl
-
-import cwl.command.StringCommandPart
-import shapeless.Poly1
-import wom.CommandPart
-
-object BaseCommandToCommandParts extends Poly1 {
-  implicit def one = at[String] { Seq(_).map(StringCommandPart.apply): Seq[CommandPart] }
-
-  implicit def many = at[Array[String]] { _.toSeq.map(StringCommandPart.apply): Seq[CommandPart] }
-}
diff --git a/cwl/src/main/scala/cwl/CommandLineTool.scala b/cwl/src/main/scala/cwl/CommandLineTool.scala
deleted file mode 100644
index 49a2de8c861..00000000000
--- a/cwl/src/main/scala/cwl/CommandLineTool.scala
+++ /dev/null
@@ -1,439 +0,0 @@
-package cwl
-
-import cats.data.{NonEmptyList, OptionT}
-import cats.syntax.apply._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cats.instances.future._
-import common.Checked
-import common.validation.ErrorOr._
-import cwl.CommandLineTool._
-import cwl.CwlVersion._
-import cwl.internal.CommandPartSortingAlgorithm
-import io.circe.Json
-import shapeless.syntax.singleton._
-import shapeless.{:+:, CNil, Coproduct, Poly1, Witness}
-import wom.callable.CommandTaskDefinition.{EvaluatedOutputs, OutputFunctionResponse}
-import wom.callable.{Callable, CallableTaskDefinition, ContainerizedInputExpression}
-import wom.expression.{IoFunctionSet, ValueAsAnExpression, WomExpression}
-import wom.graph.GraphNodePort.OutputPort
-import wom.types.{WomArrayType, WomIntegerType, WomOptionalType}
-import wom.util.YamlUtils
-import wom.values.{WomArray, WomEvaluatedCallInputs, WomGlobFile, WomInteger, WomString, WomValue}
-import wom.{CommandPart, RuntimeAttributes, RuntimeAttributesKeys}
-
-import scala.concurrent.{ExecutionContext, Future}
-import scala.math.Ordering
-
-/**
-  * @param `class` This _should_ always be "CommandLineTool," however the spec does not -er- specify this.
-  */
-case class CommandLineTool private(
-                                    inputs: Array[CommandInputParameter],
-                                    outputs: Array[CommandOutputParameter],
-                                    `class`: Witness.`"CommandLineTool"`.T,
-                                    id: String,
-                                    requirements: Option[Array[Requirement]],
-                                    hints: Option[Array[Hint]],
-                                    label: Option[String],
-                                    doc: Option[String],
-                                    cwlVersion: Option[CwlVersion],
-                                    baseCommand: Option[BaseCommand],
-                                    arguments: Option[Array[CommandLineTool.Argument]],
-                                    stdin: Option[StringOrExpression],
-                                    stderr: Option[StringOrExpression],
-                                    stdout: Option[StringOrExpression],
-                                    successCodes: Option[Array[Int]],
-                                    temporaryFailCodes: Option[Array[Int]],
-                                    permanentFailCodes: Option[Array[Int]],
-                                    `$namespaces`: Option[Map[String, String]],
-                                    `$schemas`: Option[Array[String]]
-                                  ) extends Tool {
-
-  def asCwl: Cwl = Coproduct[Cwl](this)
-
-  lazy val baseCommandPart: List[CommandPart] = baseCommand.toList.flatMap(_.fold(BaseCommandToCommandParts))
-
-  /*
-   * The command template is built following the rules described here: http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-   * - The baseCommand goes first
-   * - Then the arguments are assigned a sorting key and transformed into a CommandPart
-   * - Finally the inputs are folded one by one into a CommandPartsList
-   * - arguments and inputs CommandParts are sorted according to their sort key
-   */
-  private [cwl] def buildCommandTemplate: CommandPartExpression[List[CommandPart]] =
-    (
-      CommandPartSortingAlgorithm.inputBindingsCommandParts(inputs),
-      CommandPartSortingAlgorithm.argumentCommandParts(arguments)
-    ).mapN ( _ ++ _ ).
-      //sort the highest level, then recursively pull in the nested (and sorted) command parts within each SortKeyAndCommandPart
-      map{ _.sorted.flatMap(_.sortedCommandParts) }.
-      map(baseCommandPart ++ _)
-
-  // This seems like it makes sense only for CommandLineTool and hence is not abstracted in Tool. If this assumption is wrong it could be moved up.
-  private def environmentDefs(requirementsAndHints: List[Requirement], expressionLib: ExpressionLib): ErrorOr[Map[String, WomExpression]] = {
-    // For environment variables we need to make sure that we aren't being asked to evaluate expressions from a containing
-    // workflow step or its containing workflow or anything containing the workflow. The current structure of this code
-    // is not prepared to evaluate those expressions. Actually this is true for attributes too and we're totally not
-    // checking for this condition there. Blurgh.
-    // TODO CWL: for runtime attributes, detect unevaluatable expressions in the containment hierarchy.
-
-    // This traverses all `EnvironmentDef`s within all `EnvVarRequirement`s. The spec doesn't appear to say how to handle
-    // duplicate `envName` keys in a single array of `EnvironmentDef`s; this code gives precedence to the last occurrence.
-    val allEnvVarDefs = for {
-      req <- requirementsAndHints
-      envVarReq <- req.select[EnvVarRequirement].toList
-      // Reverse the defs within an env var requirement so that when we fold from the right below the later defs
-      // will take precedence over the earlier defs.
-      envDef <- envVarReq.envDef.toList.reverse
-    } yield envDef
-
-    // Compact the `EnvironmentDef`s. Don't convert to `WomExpression`s yet, the `StringOrExpression`s need to be
-    // compared to the `EnvVarRequirement`s that were defined on this tool.
-    val effectiveEnvironmentDefs = allEnvVarDefs.foldRight(Map.empty[String, StringOrExpression]) {
-      case (envVarReq, envVarMap) => envVarMap + (envVarReq.envName -> envVarReq.envValue)
-    }
-
-    // These are the effective environment defs irrespective of where they were found in the
-    // Run / WorkflowStep / Workflow containment hierarchy.
-    val effectiveExpressionEnvironmentDefs = effectiveEnvironmentDefs filter { case (_, expr) => expr.select[Expression].isDefined }
-
-    // These are only the environment defs defined on this tool.
-    val cltRequirements = requirements.toList.flatten ++ hints.toList.flatten.flatMap(_.select[Requirement])
-    val cltEnvironmentDefExpressions = (for {
-      cltEnvVarRequirement <- cltRequirements flatMap {
-        _.select[EnvVarRequirement]
-      }
-      cltEnvironmentDef <- cltEnvVarRequirement.envDef.toList
-      expr <- cltEnvironmentDef.envValue.select[Expression].toList
-    } yield expr).toSet
-
-    // If there is an expression in an effective environment def that wasn't defined on this tool then error out since
-    // there isn't currently a way of evaluating it.
-    val unevaluatableEnvironmentDefs = for {
-      (name, stringOrExpression) <- effectiveExpressionEnvironmentDefs.toList
-      expression <- stringOrExpression.select[Expression].toList
-      if !cltEnvironmentDefExpressions.contains(expression)
-    } yield name
-
-    unevaluatableEnvironmentDefs match {
-      case Nil =>
-        // No unevaluatable environment defs => keep on truckin'
-        effectiveEnvironmentDefs.foldRight(Map.empty[String, WomExpression]) { case ((envName, envValue), acc) =>
-          acc + (envName -> envValue.fold(StringOrExpressionToWomExpression).apply(inputNames, expressionLib))
-        }.validNel
-      case xs =>
-        s"Could not evaluate environment variable expressions defined in the call hierarchy of tool $id: ${xs.mkString(", ")}.".invalidNel
-    }
-  }
-
-  /*
-    * Custom evaluation of the outputs of the command line tool (custom as in bypasses the engine provided default implementation).
-    * This is needed because the output of a CWL tool might be defined by the presence of a cwl.output.json file in the output directory.
-    * In that case, the content of the file should be used as output. This means that otherwise provided output expressions should not be evaluated.
-    * This method checks for the existence of this file, and optionally return a Map[OutputPort, WomValue] if the file was found.
-    * It ensures all the output ports of the corresponding WomCallNode get a WomValue which is needed for the engine to keep running the workflow properly.
-    * If the json file happens to be missing values for one or more output ports, it's a failure.
-    * If the file is not present, an empty value is returned and the engine will execute its own output evaluation logic.
-    *
-    * TODO: use IO instead of Future ?
-   */
-  final private def outputEvaluationJsonFunction(outputPorts: Set[OutputPort],
-                                                 inputs: Map[String, WomValue],
-                                                 ioFunctionSet: IoFunctionSet,
-                                                 executionContext: ExecutionContext): OutputFunctionResponse = {
-    implicit val ec = executionContext
-    import cats.syntax.either._
-
-    // Convert the parsed json to Wom-usable output values
-    def jsonToOutputs(json: Map[String, Json]): Checked[List[(OutputPort, WomValue)]] = {
-
-      outputPorts.toList.traverse[ErrorOr, (OutputPort, WomValue)]({ outputPort =>
-        // If the type is optional, then we can set the value to none if there's nothing in the json
-        def emptyValue = outputPort.womType match {
-          case optional: WomOptionalType => Option((outputPort -> optional.none).validNel)
-          case _ => None
-        }
-
-        json.get(outputPort.internalName)
-          .map(
-            _.foldWith(CwlJsonToDelayedCoercionFunction).apply(outputPort.womType)
-              .map(outputPort -> _)
-          )
-          .orElse(emptyValue)
-          .getOrElse(s"Cannot find a value for output ${outputPort.internalName} in output json $json".invalidNel)
-      }).toEither
-    }
-
-    // Parse content as json and return output values for each output port
-    def parseContent(content: String): EvaluatedOutputs = {
-      val yaml = YamlUtils.parse(content)
-      for {
-        parsed <- yaml.flatMap(_.as[Map[String, Json]]).leftMap(error => NonEmptyList.one(error.getMessage))
-        jobOutputsMap <- jsonToOutputs(parsed)
-      } yield jobOutputsMap.toMap
-    }
-
-    for {
-      // Glob for "cwl.output.json"
-      outputJsonGlobs <- OptionT.liftF { ioFunctionSet.glob(CwlOutputJson) }
-      // There can only be 0 or 1, so try to take the head of the list
-      outputJsonFile <- OptionT.fromOption[Future] { outputJsonGlobs.headOption }
-      // Read the content using the ioFunctionSet.readFile function
-      content <- OptionT.liftF { ioFunctionSet.readFile(outputJsonFile, None, failOnOverflow = false) }
-      // parse the content and validate it
-      outputs = parseContent(content)
-    } yield outputs
-  }
-
-  override protected def toolAttributes: Map[String, WomExpression] = {
-    val codes: List[Int] = successCodes match {
-      case Some(c) => c.toList // Use the provided list of success codes.
-      case None => List(0) // Default to allowing only 0 for a success code.
-    }
-
-    val arr = WomArray(WomArrayType(WomIntegerType), codes map WomInteger.apply)
-    Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> ValueAsAnExpression(arr))
-  }
-
-  override def buildTaskDefinition(taskName: String,
-                          inputDefinitions: List[_ <: Callable.InputDefinition],
-                          outputDefinitions: List[Callable.OutputDefinition],
-                          runtimeAttributes: RuntimeAttributes,
-                          requirementsAndHints: List[cwl.Requirement],
-                          expressionLib: ExpressionLib): ErrorOr[CallableTaskDefinition] = {
-
-    def redirect(soe: Option[StringOrExpression]): Option[WomExpression] = soe map {
-      _.fold(StringOrExpressionToWomExpression).apply(inputNames, expressionLib)
-    }
-
-    // This seems like it makes sense only for CommandLineTool and hence is not abstracted in Tool. If this assumption is wrong it could be moved up.
-    val adHocFileCreations: Set[ContainerizedInputExpression] = (for {
-      requirements <- requirements.getOrElse(Array.empty[Requirement])
-      initialWorkDirRequirement <- requirements.select[InitialWorkDirRequirement].toArray
-      listing <- initialWorkDirRequirement.listings
-    } yield InitialWorkDirFileGeneratorExpression(listing, expressionLib)).toSet[ContainerizedInputExpression]
-
-    val dockerOutputDirectory = requirementsAndHints
-      .flatMap(_.select[DockerRequirement])
-      .flatMap(_.dockerOutputDirectory)
-      .headOption
-
-    def inputsToCommandParts(inputs: WomEvaluatedCallInputs) : ErrorOr[Seq[CommandPart]] =
-     buildCommandTemplate.run((RequirementsAndHints(requirementsAndHints), expressionLib, inputs))
-
-    environmentDefs(requirementsAndHints, expressionLib) map { environmentExpressions =>
-      CallableTaskDefinition(
-        taskName,
-        inputsToCommandParts,
-        runtimeAttributes,
-        Map.empty,
-        Map.empty,
-        outputDefinitions,
-        inputDefinitions,
-        adHocFileCreation = adHocFileCreations,
-        environmentExpressions = environmentExpressions,
-        // TODO: This doesn't work in all cases and it feels clunky anyway - find a way to sort that out
-        prefixSeparator = "#",
-        commandPartSeparator = " ",
-        stdinRedirection = redirect(stdin),
-        stdoutOverride = redirect(stdout),
-        stderrOverride = redirect(stderr),
-        additionalGlob = Option(WomGlobFile(CwlOutputJson)),
-        customizedOutputEvaluation = outputEvaluationJsonFunction,
-        homeOverride = Option(_.outputPath),
-        dockerOutputDirectory = dockerOutputDirectory,
-        sourceLocation = None
-      )
-    }
-  }
-}
-
-object CommandLineTool {
-  val CwlOutputJson = "cwl.output.json"
-
-  val DefaultPosition = Coproduct[StringOrInt](0)
-
-  // Elements of the sorting key can be either Strings or Ints
-  type StringOrInt = String :+: Int :+: CNil
-  object StringOrInt {
-    object String { def unapply(stringOrInt: StringOrInt): Option[String] = stringOrInt.select[String] }
-    object Int { def unapply(stringOrInt: StringOrInt): Option[Int] = stringOrInt.select[Int] }
-  }
-
-  /*
-   * The algorithm described here http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding to sort the command line parts
-   * uses a sorting key assigned to each binding. This class represents such a key
-   */
-  object CommandBindingSortingKey {
-    def empty = CommandBindingSortingKey(List.empty, List.empty)
-  }
-  case class CommandBindingSortingKey(head: List[StringOrInt],
-                                      tail: List[StringOrInt] = List.empty) {
-    val value = head ++ tail
-
-    def append(binding: Option[CommandLineBinding], name: StringOrInt): CommandBindingSortingKey = binding match {
-      // If there's an input binding, add the position to the key (or 0)
-      case Some(b) =>
-        // The spec is inconsistent about this as it says "If position is not specified, it is not added to the sorting key"
-        // but also that the position defaults to 0. cwltool uses 0 when there's no position so we'll do that too.
-        val position = b.position.map(Coproduct[StringOrInt](_)) getOrElse DefaultPosition
-        copy(head = head :+ position, tail = tail :+ name)
-      // Otherwise do nothing
-      case None => this
-    }
-
-    /**
-      * Creates a new key with head and tail combined into the new head.
-      */
-    def asNewKey = CommandBindingSortingKey(value)
-  }
-
-  // Maps a sorting key to its (sorted) bindings
-  case class SortKeyAndCommandPart(
-    sortingKey: CommandBindingSortingKey,
-    commandPart: CommandPart,
-    nestedCommandParts: List[SortKeyAndCommandPart] = List.empty) {
-      def sortedCommandParts:List[CommandPart] =
-        List(commandPart) ++ nestedCommandParts.sorted.flatMap(_.sortedCommandParts)
-    }
-
-  type CommandPartsList = List[SortKeyAndCommandPart]
-
-  // Ordering for CommandBindingSortingKeyElement
-  implicit val SortingKeyTypeOrdering: Ordering[StringOrInt] = Ordering.fromLessThan[StringOrInt]({
-    // String comparison
-    case (StringOrInt.String(s1), StringOrInt.String(s2)) => s1 < s2
-    // Int comparison
-    case (StringOrInt.Int(i1), StringOrInt.Int(i2)) => i1 < i2
-    // Int < String (from the spec: "Numeric entries sort before strings.")
-    case (StringOrInt.Int(_), StringOrInt.String(_)) => true
-    // String > Int
-    case (StringOrInt.String(_), StringOrInt.Int(_)) => false
-    case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-  })
-
-  // https://github.com/scala/bug/issues/4097#issuecomment-292388627
-  implicit def IterableSubclass[CC[X] <: Iterable[X], T: Ordering] : Ordering[CC[T]] = {
-    new Ordering[CC[T]] {
-      val ord = implicitly[Ordering[T]]
-      def compare(x: CC[T], y: CC[T]): Int = {
-        val xe = x.iterator
-        val ye = y.iterator
-
-        while (xe.hasNext && ye.hasNext) {
-          val res = ord.compare(xe.next(), ye.next())
-          if (res != 0) return res
-        }
-
-        Ordering.Boolean.compare(xe.hasNext, ye.hasNext)
-      }
-    }
-  }
-
-  // Ordering for a CommandBindingSortingKey
-  implicit val SortingKeyOrdering: Ordering[CommandBindingSortingKey] = Ordering.by(_.value)
-
-  // Ordering for a CommandPartSortMapping: order by sorting key
-  implicit val SortKeyAndCommandPartOrdering: Ordering[SortKeyAndCommandPart] = Ordering.by(_.sortingKey)
-
-  def apply(inputs: Array[CommandInputParameter] = Array.empty,
-            outputs: Array[CommandOutputParameter] = Array.empty,
-            id: String,
-            requirements: Option[Array[Requirement]] = None,
-            hints: Option[Array[Hint]] = None,
-            label: Option[String] = None,
-            doc: Option[String] = None,
-            cwlVersion: Option[CwlVersion] = Option(CwlVersion.Version1),
-            baseCommand: Option[BaseCommand] = None,
-            arguments: Option[Array[CommandLineTool.Argument]] = None,
-            stdin: Option[StringOrExpression] = None,
-            stderr: Option[StringOrExpression] = None,
-            stdout: Option[StringOrExpression] = None,
-            successCodes: Option[Array[Int]] = None,
-            temporaryFailCodes: Option[Array[Int]] = None,
-            permanentFailCodes: Option[Array[Int]] = None,
-            namespaces: Option[Map[String, String]] = None,
-            schemas: Option[Array[String]] = None
-           ): CommandLineTool = {
-    CommandLineTool(
-      inputs,
-      outputs,
-      "CommandLineTool".narrow,
-      id,
-      requirements,
-      hints,
-      label,
-      doc,
-      cwlVersion,
-      baseCommand,
-      arguments,
-      stdin,
-      stderr,
-      stdout,
-      successCodes,
-      temporaryFailCodes,
-      permanentFailCodes,
-      namespaces,
-      schemas
-    )
-  }
-
-  type BaseCommand = SingleOrArrayOfStrings
-
-  type Argument = ArgumentCommandLineBinding :+: StringOrExpression :+: CNil
-
-  case class CommandInputParameter(
-                                    id: String,
-                                    label: Option[String] = None,
-                                    secondaryFiles: Option[SecondaryFiles] = None,
-                                    format: Option[InputParameterFormat] = None, //only valid when type: File
-                                    streamable: Option[Boolean] = None, //only valid when type: File
-                                    doc: Option[Doc] = None,
-                                    inputBinding: Option[InputCommandLineBinding] = None,
-                                    default: Option[CwlAny] = None,
-                                    `type`: Option[MyriadInputType] = None) extends InputParameter
-
-  case class CommandOutputParameter(
-                                     id: String,
-                                     label: Option[String] = None,
-                                     secondaryFiles: Option[SecondaryFiles] = None,
-                                     format: Option[OutputParameterFormat] = None, //only valid when type: File
-                                     streamable: Option[Boolean] = None, //only valid when type: File
-                                     doc: Option[Doc] = None,
-                                     outputBinding: Option[CommandOutputBinding] = None,
-                                     `type`: Option[MyriadOutputType] = None) extends OutputParameter {
-
-    /** Overridden to strip off the intentionally uniquified bits and leave only the stuff that we want to look
-      * at for the purposes of determining cache hits.
-      *
-      * before:
-      *
-      * CommandOutputParameter(file:///var/folders/qh/vvrlr2q92mvb9bb45sttxll4y3gg2g/T/e17762d1-9921-46c5-833e-cb47e3c3bdfd.temp.1197611185902619026/e17762d1-9921-46c5-833e-cb47e3c3bdfd.cwl#ps/ea5165fc-8948-43ae-8dec-3c0468b56bcb/ps-stdOut,None,None,None,None,None,Some(CommandOutputBinding(Some(Inl(Inr(Inl(ps-stdOut.txt)))),None,None)),Some(Inl(Inl(File))))
-      *
-      * after:
-      *
-      * CommandOutputParameter(ps-stdOut,None,None,None,None,None,Some(CommandOutputBinding(Some(Inl(Inr(Inl(ps-stdOut.txt)))),None,None)),Some(Inl(Inl(File))))
-      *
-      * This is possibly too strict (i.e. some of these fields may be irrelevant for cache hit determination), but preferable
-      * to having false positives.
-      * Also two coproduct types that can be either single or Arrays have custom stringifying folds for arrays. */
-    override def cacheString: String = {
-      val cacheableId: String = id.substring(id.lastIndexOf('/') + 1)
-      val cacheableSecondaryFiles = secondaryFiles map { _.fold(SecondaryFilesCacheableString)}
-      val cacheableType: Option[String] = `type`.map(_.fold(MyriadOutputTypeCacheableString))
-      s"CommandOutputParameter($cacheableId,$label,$cacheableSecondaryFiles,$format,$streamable,$doc,$outputBinding,$cacheableType)"
-    }
-  }
-}
-
-object StringOrExpressionToWomExpression extends Poly1 {
-  implicit def string: Case.Aux[String, (Set[String], ExpressionLib) => WomExpression] = at[String] { s => (inputNames, expressionLib) =>
-    ValueAsAnExpression(WomString(s))
-  }
-
-  implicit def expression: Case.Aux[Expression, (Set[String], ExpressionLib) => WomExpression] = at[Expression] { e => (inputNames, expressionLib) =>
-    cwl.ECMAScriptWomExpression(e, inputNames, expressionLib)
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CommandOutputBinding.scala b/cwl/src/main/scala/cwl/CommandOutputBinding.scala
deleted file mode 100644
index bab616f2995..00000000000
--- a/cwl/src/main/scala/cwl/CommandOutputBinding.scala
+++ /dev/null
@@ -1,295 +0,0 @@
-package cwl
-
-import cats.effect.IO
-import cats.effect.IO._
-import cats.syntax.functor._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.syntax.parallel._
-import cats.instances.list._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import wom.expression.IoFunctionSet.{IoDirectory, IoFile}
-import wom.expression.{FileEvaluation, IoFunctionSet}
-import wom.types._
-import wom.values._
-
-/** @see <a href="http://www.commonwl.org/v1.0/Workflow.html#CommandOutputBinding">CommandOutputBinding</a> */
-case class CommandOutputBinding(glob: Option[Glob] = None,
-                                loadContents: Option[Boolean] = None,
-                                outputEval: Option[StringOrExpression] = None)
-
-object CommandOutputBinding {
-  /**
-    * TODO: WOM: WOMFILE: Need to support returning globs for primary and secondary.
-    *
-    * Right now, when numerous glob files are created, the backends place each glob result into a different subdirectory.
-    * Later, when the secondary files are being generated each of their globs are in different sub-directories.
-    * Unfortunately, the secondary file resolution assumes that the secondaries are _next to_ the primaries, not in
-    * sibling directories.
-    *
-    * While this is being worked on, instead of looking up globs return regular files until this can be fixed.
-    */
-  def isRegularFile(path: String): Boolean = {
-    path match {
-      case _ if path.contains("*") => false
-      case _ if path.contains("?") => false
-      case _ => true
-    }
-  }
-
-  /**
-    * Returns all the primary and secondary files that _will be_ created by this command output binding.
-    */
-  def getOutputWomFiles(inputValues: Map[String, WomValue],
-                        outputWomType: WomType,
-                        commandOutputBinding: CommandOutputBinding,
-                        secondaryFilesOption: Option[SecondaryFiles],
-                        ioFunctionSet: IoFunctionSet,
-                        expressionLib: ExpressionLib): IOChecked[Set[FileEvaluation]] = {
-    val parameterContext = ParameterContext(ioFunctionSet, expressionLib, inputs = inputValues)
-
-    /*
-    CWL can output two types of "glob" path types:
-    - File will be a glob path
-    - Directory is a path that will be searched for files. It's assumed that it will not be a glob, but the spec is
-      unclear and doesn't specifically say how Directories are listed. If the backend uses a POSIX
-      `find <dir> -type f`, then a globbed path should still work.
-
-    Either way create one of the two types as a return type that the backend should be looking for when the command
-    completes.
-
-    UPDATE:
-    It turns out that secondary files can be directories. TODO: WOM: WOMFILE: Not sure what to do with that yet.
-    https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/search.cwl#L42
-    https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/index.py#L36-L37
-     */
-    def primaryPathsToWomFiles(primaryPaths: List[String]): ErrorOr[List[WomFile]] = {
-      validate {
-        primaryPaths map { primaryPath =>
-          val outputWomFlatType = outputWomType match {
-            case WomMaybeListedDirectoryType => WomUnlistedDirectoryType
-            case WomArrayType(WomMaybeListedDirectoryType) => WomUnlistedDirectoryType
-            case _ if isRegularFile(primaryPath) => WomSingleFileType
-            case _ => WomGlobFileType
-          }
-
-          WomFile(outputWomFlatType, primaryPath)
-        }
-      }
-    }
-
-    def secondaryFilesToWomFiles(primaryWomFiles: List[WomFile], ioFunctionSet: IoFunctionSet): IOChecked[List[WomFile]] = {
-      primaryWomFiles.flatTraverse[IOChecked, WomFile] { primaryWomFile =>
-        FileParameter.secondaryFiles(primaryWomFile,
-          primaryWomFile.womFileType, secondaryFilesOption, parameterContext, expressionLib, ioFunctionSet)
-      }
-    }
-
-    for {
-      primaryPaths <- GlobEvaluator.globs(commandOutputBinding.glob, parameterContext, expressionLib).toIOChecked
-      primaryWomFiles <- primaryPathsToWomFiles(primaryPaths).toIOChecked
-      // This sets optional = false arbitrarily for now as this code doesn't have the context to make that determination,
-      // the caller can change this if necessary.
-      primaryEvaluations = primaryWomFiles map { FileEvaluation(_, optional = false, secondary = false) }
-      secondaryWomFiles <- secondaryFilesToWomFiles(primaryWomFiles, ioFunctionSet)
-      secondaryEvaluations = secondaryWomFiles map { FileEvaluation(_, optional = false, secondary = true) }
-    } yield (primaryEvaluations ++ secondaryEvaluations).toSet
-  }
-
-  /**
-    * Generates an output wom value based on the specification in command output binding.
-    *
-    * Depending on the outputWomType, the following steps will be applied as specified in the CWL spec:
-    * 1. glob: get a list the globbed files as our primary files
-    * 2. loadContents: load the contents of the primary files
-    * 3. outputEval: pass in the primary files to an expression to generate our return value
-    * 4. secondaryFiles: just before returning the value, fill in the secondary files on the return value
-    *
-    * The result type will be coerced to the output type.
-    */
-  def generateOutputWomValue(inputValues: Map[String, WomValue],
-                             ioFunctionSet: IoFunctionSet,
-                             outputWomType: WomType,
-                             commandOutputBinding: CommandOutputBinding,
-                             secondaryFilesCoproduct: Option[SecondaryFiles],
-                             formatCoproduct: Option[StringOrExpression],
-                             expressionLib: ExpressionLib): IOChecked[WomValue] = {
-    import ioFunctionSet.cs
-
-    val parameterContext = ParameterContext(ioFunctionSet, expressionLib, inputs = inputValues)
-
-    // 3. outputEval: pass in the primary files to an expression to generate our return value
-    def evaluateWomValue(womFilesArray: WomArray): ErrorOr[WomValue] = {
-      commandOutputBinding.outputEval match {
-        case Some(StringOrExpression.String(string)) => WomString(string).valid
-        case Some(StringOrExpression.Expression(expression)) =>
-          val outputEvalParameterContext = parameterContext.copy(self = womFilesArray)
-          ExpressionEvaluator.eval(expression, outputEvalParameterContext)
-        case None =>
-          womFilesArray.valid
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-    }
-
-    // Used to retrieve the file format to be injected into a file result.
-    def formatOptionErrorOr = OutputParameter.format(formatCoproduct, parameterContext, expressionLib)
-
-    // 4. secondaryFiles: just before returning the value, fill in the secondary files on the return value
-    def populateSecondaryFiles(evaluatedWomValue: WomValue): IOChecked[WomValue] = {
-      for {
-        formatOption <- formatOptionErrorOr.toIOChecked
-        womValue <- FileParameter.populateSecondaryFiles(
-          evaluatedWomValue,
-          secondaryFilesCoproduct,
-          formatOption,
-          parameterContext,
-          expressionLib,
-          ioFunctionSet
-        )
-      } yield womValue
-    }
-
-    // CWL tells us the type this output is expected to be. Attempt to coerce the actual output into this type.
-    def coerceWomValue(populatedWomValue: WomValue): ErrorOr[WomValue] = {
-      (outputWomType, populatedWomValue) match {
-
-        case (womType: WomArrayType, womValue: WomArray) =>
-          // Array -from- Array then coerce normally
-          // NOTE: this evaluates to the same as the last case, but guards against the next cases accidentally matching
-          womType.coerceRawValue(womValue).toErrorOr
-
-        case (womType: WomArrayType, womValue) =>
-          // Array -from- Single then coerce a single value to an array
-          womType.coerceRawValue(womValue).toErrorOr.map(value => WomArray(womType, List(value)))
-
-        case (womType, womValue: WomArray) if womValue.value.lengthCompare(1) == 0 =>
-          // Single -from- Array then coerce the head (if there's only a head)
-          womType.coerceRawValue(womValue.value.head).toErrorOr
-
-        case (womType, womValue) =>
-          // <other> to <other> then coerce normally
-          womType.coerceRawValue(womValue).toErrorOr
-
-      }
-    }
-
-    for {
-      // 1. glob: get a list the globbed files as our primary files
-      primaryPaths <- GlobEvaluator.globs(commandOutputBinding.glob, parameterContext, expressionLib).toIOChecked
-
-      // 2. loadContents: load the contents of the primary files
-      primaryAsDirectoryOrFiles <- primaryPaths.parTraverse[IOChecked, List[WomFile]] {
-        loadPrimaryWithContents(ioFunctionSet, outputWomType, commandOutputBinding)
-      } map (_.flatten)
-
-      // Make globbed files absolute paths by prefixing them with the output dir if necessary
-      absolutePaths = primaryAsDirectoryOrFiles.map(_.mapFile(ioFunctionSet.pathFunctions.relativeToHostCallRoot))
-
-      // Load file size
-      withFileSizes <- absolutePaths.parTraverse[IOChecked, WomFile](_.withSize(ioFunctionSet).to[IOChecked])
-
-      womFilesArray = WomArray(withFileSizes)
-
-      // 3. outputEval: pass in the primary files to an expression to generate our return value
-      evaluatedWomValue <- evaluateWomValue(womFilesArray).toIOChecked
-
-      // 4. secondaryFiles: just before returning the value, fill in the secondary files on the return value
-      populatedWomValue <- populateSecondaryFiles(evaluatedWomValue)
-
-      // CWL tells us the type this output is expected to be. Attempt to coerce the actual output into this type.
-      coercedWomValue <- coerceWomValue(populatedWomValue).toIOChecked
-    } yield coercedWomValue
-  }
-
-  /**
-    * Given a cwl glob path and an output type, gets the listing using the ioFunctionSet, and optionally loads the
-    * contents of the file(s).
-    */
-  private def loadPrimaryWithContents(ioFunctionSet: IoFunctionSet,
-                                      outputWomType: WomType,
-                                      commandOutputBinding: CommandOutputBinding)
-                                     (cwlPath: String): IOChecked[List[WomFile]] = {
-    import ioFunctionSet.cs
-
-    /*
-    For each file matched in glob, read up to the first 64 KiB of text from the file and place it in the contents field
-    of the file object for manipulation by outputEval.
-     */
-    val womMaybeListedDirectoryOrFileType = outputWomType match {
-      case WomMaybeListedDirectoryType => WomMaybeListedDirectoryType
-      case WomArrayType(WomMaybeListedDirectoryType) => WomMaybeListedDirectoryType
-      case _ => WomMaybePopulatedFileType
-    }
-    womMaybeListedDirectoryOrFileType match {
-      case WomMaybeListedDirectoryType =>
-        // Even if multiple directories are _somehow_ requested, a single flattened directory is returned.
-        loadDirectoryWithListing(ioFunctionSet, commandOutputBinding)(cwlPath).map(List(_))
-      case WomMaybePopulatedFileType if isRegularFile(cwlPath) =>
-        loadFileWithContents(ioFunctionSet, commandOutputBinding)(cwlPath).to[IOChecked].map(List(_))
-      case WomMaybePopulatedFileType =>
-        //TODO: HACK ALERT - DB: I am starting on ticket https://github.com/broadinstitute/cromwell/issues/3092 which will redeem me of this mortal sin.
-        val detritusFiles = List(
-          "docker_cid",
-          "gcs_delocalization.sh",
-          "gcs_localization.sh",
-          "gcs_transfer.sh",
-          "rc.tmp",
-          "script",
-          "script.background",
-          "script.submit",
-          "stderr",
-          "stderr.background",
-          "stdout",
-          "stdout.background",
-        )
-        val globs: IOChecked[Seq[String]] =
-          ioFunctionSet.glob(cwlPath).toIOChecked
-              .map({
-                _
-                .filterNot{ s =>
-                  detritusFiles exists s.endsWith
-                }
-              })
-
-        globs.flatMap({ files =>
-          files.toList.parTraverse[IOChecked, WomFile](v => loadFileWithContents(ioFunctionSet, commandOutputBinding)(v).to[IOChecked])
-        })
-      case other => s"Program error: $other type was not expected".invalidIOChecked
-    }
-  }
-
-  /**
-    * Loads a directory with the files listed, each file with contents populated.
-    */
-  private def loadDirectoryWithListing(ioFunctionSet: IoFunctionSet,
-                                       commandOutputBinding: CommandOutputBinding)(path: String, visited: Vector[String] = Vector.empty): IOChecked[WomMaybeListedDirectory] = {
-    import ioFunctionSet.cs
-
-    for {
-      listing <- IO.fromFuture(IO { ioFunctionSet.listDirectory(path)(visited) }).to[IOChecked]
-      loadedListing <- listing.toList.parTraverse[IOChecked, WomFile]({
-        case IoFile(p) => loadFileWithContents(ioFunctionSet, commandOutputBinding)(p).to[IOChecked]
-        case IoDirectory(p) => loadDirectoryWithListing(ioFunctionSet, commandOutputBinding)(p, visited :+ path).widen
-      })
-    } yield WomMaybeListedDirectory(valueOption = Option(path), listingOption = Option(loadedListing))
-  }
-
-  /**
-    * Loads a file at path reading 64KiB of data into the contents.
-    */
-  private def loadFileWithContents(ioFunctionSet: IoFunctionSet,
-                                   commandOutputBinding: CommandOutputBinding)(path: String): IO[WomFile] = {
-    val contentsOptionErrorOr = {
-      if (commandOutputBinding.loadContents getOrElse false) {
-        FileParameter.load64KiB(path, ioFunctionSet) map Option.apply
-      } else {
-        IO.pure(None)
-      }
-    }
-    contentsOptionErrorOr map { contentsOption =>
-      WomMaybePopulatedFile(valueOption = Option(path), contentsOption = contentsOption)
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlCodecs.scala b/cwl/src/main/scala/cwl/CwlCodecs.scala
deleted file mode 100644
index d7010494bca..00000000000
--- a/cwl/src/main/scala/cwl/CwlCodecs.scala
+++ /dev/null
@@ -1,153 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import cats.syntax.show._
-import common.Checked
-import common.validation.Checked._
-import cwl.CommandLineTool.{CommandInputParameter, CommandOutputParameter}
-import cwl.CwlType.CwlType
-import cwl.CwlVersion.CwlVersion
-import cwl.ExpressionTool.{ExpressionToolInputParameter, ExpressionToolOutputParameter}
-import cwl.InitialWorkDirRequirement.IwdrListingArrayEntry
-import cwl.LinkMergeMethod.LinkMergeMethod
-import cwl.ScatterMethod.ScatterMethod
-import cwl.SchemaDefRequirement.SchemaDefTypes
-import cwl.Workflow.{WorkflowInputParameter, WorkflowOutputParameter}
-import io.circe.DecodingFailure._
-import io.circe.Json._
-import io.circe._
-import io.circe.generic.semiauto._
-import io.circe.literal._
-import io.circe.refined._
-import io.circe.shapes._
-import shapeless.Coproduct
-
-object CwlCodecs {
-  /*
-  Semi-auto codecs for the Cwl types
-  https://circe.github.io/circe/codecs/semiauto-derivation.html
-
-  Some types, such as BaseCommand are not listed, as they are actually one-for-one type aliases. Having two exact
-  implicits for the same type will confuse the compiler, leading to cryptic error messages elsewhere.
-
-  For example, a duplicated decoder such as:
-
-  ```
-  implicit lazy val decodeSingleOrArrayOfStrings: Decoder[SingleOrArrayOfStrings] = decodeCCons
-  implicit lazy val decodeBaseCommand: Decoder[BaseCommand] = decodeCCons
-  ```
-
-  causes cryptic errors such as:
-
-  ```
-  [error] cwl/src/main/scala/cwl/CwlCodecs.scala:123:456: could not find Lazy implicit value of type io.circe.generic.decoding.DerivedDecoder[A]
-  [error]   implicit lazy val decodeCommandInputParameter: Decoder[CommandInputParameter] = deriveDecoder
-
-  (etc. etc. etc.)
-  ```
-   */
-
-  // Semi-Automatically derived codecs
-  implicit lazy val codecArgumentCommandLineBinding: Codec[ArgumentCommandLineBinding] = deriveCodec
-  implicit lazy val codecCommandInputParameter: Codec[CommandInputParameter] = deriveCodec
-  implicit lazy val codecCommandLineTool: Codec[CommandLineTool] = deriveCodec
-  implicit lazy val codecCommandOutputBinding: Codec[CommandOutputBinding] = deriveCodec
-  implicit lazy val codecCommandOutputParameter: Codec[CommandOutputParameter] = deriveCodec
-  implicit lazy val codecCwlType: Codec[CwlType] = Codec.codecForEnumeration(CwlType)
-  implicit lazy val codecCwlVersion: Codec[CwlVersion] = Codec.codecForEnumeration(CwlVersion)
-  implicit lazy val codecDirectory: Codec[Directory] = deriveCodec
-  implicit lazy val codecDockerRequirement: Codec[DockerRequirement] = deriveCodec
-  implicit lazy val codecEnvVarRequirement: Codec[EnvVarRequirement] = deriveCodec
-  implicit lazy val codecEnvironmentDef: Codec[EnvironmentDef] = deriveCodec
-  implicit lazy val codecExpressionDirent: Codec[ExpressionDirent] = deriveCodec
-  implicit lazy val codecExpressionTool: Codec[ExpressionTool] = deriveCodec
-  implicit lazy val codecExpressionToolInputParameter: Codec[ExpressionToolInputParameter] = deriveCodec
-  implicit lazy val codecExpressionToolOutputParameter: Codec[ExpressionToolOutputParameter] = deriveCodec
-  implicit lazy val codecFile: Codec[File] = deriveCodec
-  implicit lazy val codecInitialWorkDirRequirement: Codec[InitialWorkDirRequirement] = deriveCodec
-  implicit lazy val codecInlineJavascriptRequirement: Codec[InlineJavascriptRequirement] = deriveCodec
-  implicit lazy val codecInputArraySchema: Codec[InputArraySchema] = deriveCodec
-  implicit lazy val codecInputBinding: Codec[InputBinding] = deriveCodec
-  implicit lazy val codecInputCommandLineBinding: Codec[InputCommandLineBinding] = deriveCodec
-  implicit lazy val codecInputEnumSchema: Codec[InputEnumSchema] = deriveCodec
-  implicit lazy val codecInputRecordField: Codec[InputRecordField] = deriveCodec
-  implicit lazy val codecInputRecordSchema: Codec[InputRecordSchema] = deriveCodec
-  implicit lazy val codecInputResourceRequirement: Codec[DnaNexusInputResourceRequirement] = deriveCodec
-  implicit lazy val codecLinkMergeMethod: Codec[LinkMergeMethod] = Codec.codecForEnumeration(LinkMergeMethod)
-  implicit lazy val codecMultipleInputFeatureRequirement: Codec[MultipleInputFeatureRequirement] = deriveCodec
-  implicit lazy val codecOutputArraySchema: Codec[OutputArraySchema] = deriveCodec
-  implicit lazy val codecOutputEnumSchema: Codec[OutputEnumSchema] = deriveCodec
-  implicit lazy val codecOutputRecordField: Codec[OutputRecordField] = deriveCodec
-  implicit lazy val codecOutputRecordSchema: Codec[OutputRecordSchema] = deriveCodec
-  implicit lazy val codecResourceRequirement: Codec[ResourceRequirement] = deriveCodec
-  implicit lazy val codecScatterFeatureRequirement: Codec[ScatterFeatureRequirement] = deriveCodec
-  implicit lazy val codecScatterMethod: Codec[ScatterMethod] = Codec.codecForEnumeration(ScatterMethod)
-  implicit lazy val codecSchemaDefRequirement: Codec[SchemaDefRequirement] = deriveCodec
-  implicit lazy val codecShellCommandRequirement: Codec[ShellCommandRequirement] = deriveCodec
-  implicit lazy val codecSoftwarePackage: Codec[SoftwarePackage] = deriveCodec
-  implicit lazy val codecSoftwareRequirement: Codec[SoftwareRequirement] = deriveCodec
-  implicit lazy val codecStepInputExpressionRequirement: Codec[StepInputExpressionRequirement] = deriveCodec
-  implicit lazy val codecStringDirent: Codec[StringDirent] = deriveCodec
-  implicit lazy val codecSubworkflowFeatureRequirement: Codec[SubworkflowFeatureRequirement] = deriveCodec
-  implicit lazy val codecWorkflow: Codec[Workflow] = deriveCodec
-  implicit lazy val codecWorkflowInputParameter: Codec[WorkflowInputParameter] = deriveCodec
-  implicit lazy val codecWorkflowOutputParameter: Codec[WorkflowOutputParameter] = deriveCodec
-  implicit lazy val codecWorkflowStep: Codec[WorkflowStep] = deriveCodec
-  implicit lazy val codecWorkflowStepInput: Codec[WorkflowStepInput] = deriveCodec
-  implicit lazy val codecWorkflowStepOutput: Codec[WorkflowStepOutput] = deriveCodec
-
-  // Encoders and decoders for Coproduct-based types must be explicitly derived
-  implicit lazy val decodeCwlAny: Decoder[CwlAny] = decodeCCons
-  implicit lazy val decodeExpression: Decoder[Expression] = decodeCCons
-  implicit lazy val decodeFileOrDirectory: Decoder[FileOrDirectory] = decodeCCons
-  implicit lazy val decodeGlob: Decoder[Glob] = decodeCCons
-  implicit lazy val decodeHint: Decoder[Hint] = decodeCCons
-  implicit lazy val decodeIwdrListingArrayEntry: Decoder[IwdrListingArrayEntry] = decodeCCons
-  implicit lazy val decodeMyriadInputInnerType: Decoder[MyriadInputInnerType] = decodeCCons
-  implicit lazy val decodeMyriadInputType: Decoder[MyriadInputType] = decodeCCons
-  implicit lazy val decodeMyriadOutputType: Decoder[MyriadOutputType] = decodeCCons
-  implicit lazy val decodeRequirement: Decoder[Requirement] = decodeCCons
-  implicit lazy val decodeResourceRequirementType: Decoder[ResourceRequirementType] = decodeCCons
-  implicit lazy val decodeSchemaDefTypes: Decoder[SchemaDefTypes] = decodeCCons
-  implicit lazy val decodeSecondaryFiles: Decoder[SecondaryFiles] = decodeCCons
-  implicit lazy val decodeSingleOrArrayOfStrings: Decoder[SingleOrArrayOfStrings] = decodeCCons
-  implicit lazy val decodeStringOrExpression: Decoder[StringOrExpression] = decodeCCons
-
-  implicit lazy val encodeCwlAny: Encoder[CwlAny] = encodeCCons
-  implicit lazy val encodeExpression: Encoder[Expression] = encodeCCons
-  implicit lazy val encodeFileOrDirectory: Encoder[FileOrDirectory] = encodeCCons
-  implicit lazy val encodeGlob: Encoder[Glob] = encodeCCons
-  implicit lazy val encodeHint: Encoder[Hint] = encodeCCons
-  implicit lazy val encodeIwdrListingArrayEntry: Encoder[IwdrListingArrayEntry] = encodeCCons
-  implicit lazy val encodeMyriadInputInnerType: Encoder[MyriadInputInnerType] = encodeCCons
-  implicit lazy val encodeMyriadInputType: Encoder[MyriadInputType] = encodeCCons
-  implicit lazy val encodeMyriadOutputType: Encoder[MyriadOutputType] = encodeCCons
-  implicit lazy val encodeRequirement: Encoder[Requirement] = encodeCCons
-  implicit lazy val encodeResourceRequirementType: Encoder[ResourceRequirementType] = encodeCCons
-  implicit lazy val encodeSchemaDefTypes: Encoder[SchemaDefTypes] = encodeCCons
-  implicit lazy val encodeSecondaryFiles: Encoder[SecondaryFiles] = encodeCCons
-  implicit lazy val encodeSingleOrArrayOfStrings: Encoder[SingleOrArrayOfStrings] = encodeCCons
-  implicit lazy val encodeStringOrExpression: Encoder[StringOrExpression] = encodeCCons
-
-  def decodeCwl(json: Json): Checked[Cwl] = {
-    findClass(json) match {
-      case Some("Workflow") => decodeWithErrorStringsJson[Workflow](json).map(Coproduct[Cwl].apply(_))
-      case Some("CommandLineTool") => decodeWithErrorStringsJson[CommandLineTool](json).map(Coproduct[Cwl].apply(_))
-      case Some("ExpressionTool") => decodeWithErrorStringsJson[ExpressionTool](json).map(Coproduct[Cwl].apply(_))
-      case Some(other) => s"Class field was declared incorrectly: $other is not one of Workflow, CommandLineTool, or ExpressionTool! as seen in ${json.show}".invalidNelCheck
-      case None => s"Class field was omitted in ${json.show}".invalidNelCheck
-    }
-  }
-
-  private def decodeWithErrorStringsJson[A](in: Json)(implicit d: Codec[A]): Checked[A] =
-    in.as[A].leftMap(_.show).leftMap(NonEmptyList.one)
-
-  private def findClass(json: Json): Option[String] =
-    for {
-      obj <- json.asObject
-      map = obj.toMap
-      classObj <- map.get("class")
-      classString <- classObj.asString
-    } yield classString
-}
diff --git a/cwl/src/main/scala/cwl/CwlDecoder.scala b/cwl/src/main/scala/cwl/CwlDecoder.scala
deleted file mode 100644
index b7a4125e5a3..00000000000
--- a/cwl/src/main/scala/cwl/CwlDecoder.scala
+++ /dev/null
@@ -1,84 +0,0 @@
-package cwl
-
-import better.files.{File => BFile}
-import cats.data.EitherT._
-import cats.effect.IO
-import cats.syntax.either._
-import cats.{Applicative, Monad}
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.preprocessor.{CwlFileReference, CwlPreProcessor, CwlReference}
-import io.circe.Json
-
-import scala.util.Try
-
-object CwlDecoder {
-
-  implicit val composedApplicative = Applicative[IO] compose Applicative[ErrorOr]
-
-  def saladCwlFile(reference: CwlReference): IOChecked[String] = {
-    val cwlToolResult =
-      Try(CwltoolRunner.instance.salad(reference))
-        .toCheckedWithContext(s"run cwltool on file ${reference.pathAsString}", throwableToStringFunction = t => t.toString)
-
-    fromEither[IO](cwlToolResult)
-  }
-
-  private lazy val cwlPreProcessor = new CwlPreProcessor()
-
-  // TODO: WOM: During conformance testing the saladed-CWLs are referring to files in the temp directory.
-  // Thus we can't delete the temp directory until after the workflow is complete, like the workflow logs.
-  // All callers to this method should be fixed around the same time.
-  // https://github.com/broadinstitute/cromwell/issues/3186
-  def todoDeleteCwlFileParentDirectory(cwlFile: BFile): IOChecked[Unit] = {
-    goIOChecked {
-      //cwlFile.parent.delete(swallowIOExceptions = true)
-    }
-  }
-
-  def parseJson(json: Json, from: String): IOChecked[Cwl] = fromEither[IO](CwlCodecs.decodeCwl(json).contextualizeErrors(s"parse '$from'"))
-
-  /**
-    * Notice it gives you one instance of Cwl.  This has transformed all embedded files into scala object state
-    */
-  def decodeCwlReference(reference: CwlReference)(implicit processor: CwlPreProcessor = cwlPreProcessor): IOChecked[Cwl] = {
-    def makeStandaloneWorkflow(): IOChecked[Json] = processor.preProcessCwl(reference)
-
-    for {
-      standaloneWorkflow <- makeStandaloneWorkflow()
-      parsedCwl <- parseJson(standaloneWorkflow, reference.pathAsString)
-    } yield parsedCwl
-  }
-
-  def decodeCwlFile(file: BFile, workflowRoot: Option[String] = None) = {
-    decodeCwlReference(CwlFileReference(file, workflowRoot))
-  }
-
-  def decodeCwlString(cwl: String,
-                      zipOption: Option[BFile] = None,
-                      rootName: Option[String] = None,
-                      cwlFilename: String = "cwl_temp_file"): IOChecked[Cwl] = {
-    for {
-      parentDir <- goIOChecked(BFile.newTemporaryDirectory("cwl_temp_dir_")) // has a random long appended like `cwl_temp_dir_100000000000`
-      file <- fromEither[IO](parentDir./(cwlFilename + ".cwl").write(cwl).asRight) // serves as the basis for the output directory name; must remain stable across restarts
-      _ <- zipOption match {
-        case Some(zip) => goIOChecked(zip.unzipTo(parentDir))
-        case None => Monad[IOChecked].unit
-      }
-      out <- decodeCwlFile(file, rootName)
-      _ <- todoDeleteCwlFileParentDirectory(file)
-    } yield out
-  }
-
-  //This is used when traversing over Cwl and replacing links w/ embedded data
-  private[cwl] def decodeCwlAsValidated(fileName: String): IOCheckedValidated[(String, Cwl)] = {
-    //The SALAD preprocess step puts "file://" as a prefix to all filenames.  Better files doesn't like this.
-    val bFileName = fileName.stripPrefix("file://")
-
-    decodeCwlReference(CwlFileReference(BFile(bFileName), None)).
-      map(fileName.toString -> _).
-      value.
-      map(_.toValidated)
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlExecutableValidation.scala b/cwl/src/main/scala/cwl/CwlExecutableValidation.scala
deleted file mode 100644
index f6f8237c5ff..00000000000
--- a/cwl/src/main/scala/cwl/CwlExecutableValidation.scala
+++ /dev/null
@@ -1,38 +0,0 @@
-package cwl
-
-import common.Checked
-import common.validation.Checked._
-import io.circe.Json
-import wom.callable.{ExecutableCallable, TaskDefinition}
-import wom.executable.Executable
-import wom.executable.Executable.{InputParsingFunction, ParsedInputMap}
-import wom.expression.IoFunctionSet
-import wom.util.YamlUtils
-
-object CwlExecutableValidation {
-
-  // Decodes the input file, and build the ParsedInputMap
-  private val inputCoercionFunction: InputParsingFunction =
-    inputFile => {
-      val yaml = YamlUtils.parse(inputFile)
-      yaml.flatMap(_.as[Map[String, Json]]) match {
-        case Left(error) => error.getMessage.invalidNelCheck[ParsedInputMap]
-        case Right(inputValue) => inputValue.map({ case (key, value) => key -> value.foldWith(CwlJsonToDelayedCoercionFunction) }).validNelCheck
-      }
-    }
-
-  def buildWomExecutableCallable(callable: Checked[ExecutableCallable], inputFile: Option[String], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    for {
-      womDefinition <- callable
-      executable <- Executable.withInputs(womDefinition, inputCoercionFunction, inputFile, ioFunctions, strictValidation)
-    } yield executable
-  }
-
-  def buildWomExecutable(callableTaskDefinition: Checked[TaskDefinition], inputFile: Option[String], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    for {
-      taskDefinition <- callableTaskDefinition
-      executableTaskDefinition = taskDefinition.toExecutable.toEither
-      executable <- CwlExecutableValidation.buildWomExecutableCallable(executableTaskDefinition, inputFile, ioFunctions, strictValidation)
-    } yield executable
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlExpressionCommandPart.scala b/cwl/src/main/scala/cwl/CwlExpressionCommandPart.scala
deleted file mode 100644
index f323c74dbd2..00000000000
--- a/cwl/src/main/scala/cwl/CwlExpressionCommandPart.scala
+++ /dev/null
@@ -1,146 +0,0 @@
-package cwl
-
-import cats.syntax.either._
-import cats.syntax.validated._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import wom.callable.RuntimeEnvironment
-import wom.expression.IoFunctionSet
-import wom.graph.LocalName
-import wom.values._
-import wom.{CommandPart, InstantiatedCommand}
-
-import scala.language.postfixOps
-
-case class CwlExpressionCommandPart(expr: Expression)(hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib) extends CommandPart {
-  override def instantiate(inputsMap: Map[LocalName, WomValue],
-                           functions: IoFunctionSet,
-                           valueMapper: (WomValue) => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] = {
-    val stringKeyMap = inputsMap map {
-      case (LocalName(localName), value) => localName -> valueMapper(value)
-    }
-    val parameterContext = ParameterContext(
-      functions,
-      expressionLib,
-      inputs = stringKeyMap, runtimeOption = Option(runtimeEnvironment)
-    )
-    ExpressionEvaluator.eval(expr, parameterContext) map { womValue =>
-      List(InstantiatedCommand(valueMapper(womValue).valueString.shellQuote))
-    }
-  }
-}
-
-/**
-  * Generates command parts from a CWL Binding
-  */
-abstract class CommandLineBindingCommandPart(commandLineBinding: CommandLineBinding)(hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib) extends CommandPart {
-
-
-  private lazy val prefixAsString = commandLineBinding.prefix.getOrElse("")
-  private lazy val prefixAsList = commandLineBinding.prefix.toList
-  private lazy val separate = commandLineBinding.effectiveSeparate
-
-  def handlePrefix(value: String) = {
-    if (separate) prefixAsList :+ value else List(s"$prefixAsString$value")
-  }
-
-  /**
-    * Value bound to this command part.
-    * InputCommandLineBindingCommandPart has one
-    * ArgumentCommandLineBindingCommandPart does not
-    */
-  def boundValue: Option[WomValue]
-
-  // If the bound value is defined but contains an empty optional value, we should not evaluate the valueFrom
-  // Conformance test "stage-unprovided-file" tests this behavior
-  private lazy val evaluateValueFrom = boundValue.forall {
-    case WomOptionalValue(_, None) => false
-    case _ => true
-  }
-
-  override def instantiate(inputsMap: Map[LocalName, WomValue],
-                           functions: IoFunctionSet,
-                           valueMapper: (WomValue) => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] = {
-      val stringInputsMap = inputsMap map {
-        case (LocalName(localName), value) => localName -> valueMapper(value)
-      }
-    val parameterContext = ParameterContext(
-      functions,
-      expressionLib,
-      inputs = stringInputsMap,
-      runtimeOption = Option(runtimeEnvironment),
-      self = boundValue.getOrElse(ParameterContext.EmptySelf)
-    )
-
-    val evaluatedValueFrom = commandLineBinding.optionalValueFrom flatMap {
-      case StringOrExpression.Expression(expression) if evaluateValueFrom => Option(ExpressionEvaluator.eval(expression, parameterContext) map valueMapper)
-      case StringOrExpression.String(string) if evaluateValueFrom => Option(WomString(string).validNel)
-      case _ => None
-    }
-
-    val evaluatedWomValue: Checked[WomValue] = evaluatedValueFrom.orElse(boundValue.map(_.validNel)) match {
-      case Some(womValue) => womValue.map(valueMapper).toEither
-      case None => "Command line binding has no valueFrom field and no bound value".invalidNelCheck
-    }
-
-    def applyShellQuote(value: String): String = commandLineBinding.shellQuote match {
-      // Only honor shellQuote = false if ShellCommandRequirement is enabled.
-      // Conformance test "Test that shell directives are not interpreted."
-      case Some(false) if hasShellCommandRequirement => value
-      case _ => value.shellQuote
-    }
-
-    def processValue(womValue: WomValue): List[String] = womValue match {
-      case WomOptionalValue(_, Some(value)) => processValue(valueMapper(value))
-      case WomOptionalValue(_, None) => List.empty
-      case _: WomString | _: WomInteger | _: WomFile | _: WomLong | _: WomFloat => handlePrefix(valueMapper(womValue).valueString)
-      // For boolean values, use the value of the boolean to choose whether to print the prefix or not
-      case WomBoolean(false) => List.empty
-      case WomBoolean(true) => prefixAsList
-      case WomArray(_, values) => commandLineBinding.itemSeparator match {
-        case Some(_) if values.isEmpty => List.empty
-        case Some(itemSeparator) => handlePrefix(values.map(valueMapper(_).valueString).mkString(itemSeparator))
-
-        /*
-        via: http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding
-
-        > If itemSeparator is specified, add prefix and the join the array into a single string with itemSeparator
-        > separating the items. Otherwise first add prefix, then recursively process individual elements.
-
-        Not 100% sure if this is conformant, as we are only recurse the head into `processValue` here... However the
-        conformance test "Test InlineJavascriptRequirement with multiple expressions in the same tool" is happy with the
-        behavior.
-         */
-        // InstantiatedCommand elements are generated here when there exists an optionalValueFrom
-        case None if commandLineBinding.optionalValueFrom.isDefined => values.toList match {
-          case head :: tail => processValue(head) ++ tail.map(valueMapper(_).valueString)
-          case Nil => prefixAsList
-        }
-
-        // When there is no optionalValueFrom the InstantiatedCommand elements for the womValue are appended elsewhere
-        case _ => prefixAsList
-      }
-      case _: WomObjectLike => prefixAsList
-      case WomEnumerationValue(_, value) => handlePrefix(value)
-      case WomCoproductValue(_, value) => processValue(value)
-      case w => throw new RuntimeException(s"Unhandled CwlExpressionCommandPart value '$w' of type ${w.womType.stableName}")
-    }
-
-    evaluatedWomValue map { v => processValue(v) map applyShellQuote map (InstantiatedCommand(_)) } toValidated
-  }
-}
-
-case class InputCommandLineBindingCommandPart(commandLineBinding: InputCommandLineBinding, associatedValue: WomValue)
-                                             (hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib)
-  extends CommandLineBindingCommandPart(commandLineBinding)(hasShellCommandRequirement, expressionLib) {
-  override lazy val boundValue = Option(associatedValue)
-}
-
-case class ArgumentCommandLineBindingCommandPart(commandLineBinding: ArgumentCommandLineBinding)
-                                                (hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib)
-  extends CommandLineBindingCommandPart(commandLineBinding)(hasShellCommandRequirement, expressionLib) {
-  override lazy val boundValue = None
-}
diff --git a/cwl/src/main/scala/cwl/CwlJsonToDelayedCoercionFunction.scala b/cwl/src/main/scala/cwl/CwlJsonToDelayedCoercionFunction.scala
deleted file mode 100644
index 55dc7f9e3ba..00000000000
--- a/cwl/src/main/scala/cwl/CwlJsonToDelayedCoercionFunction.scala
+++ /dev/null
@@ -1,90 +0,0 @@
-package cwl
-
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import cwl.CwlCodecs._
-import io.circe.{Json, JsonNumber, JsonObject}
-import wom.executable.Executable.DelayedCoercionFunction
-import wom.types._
-import wom.values._
-
-// With recursive types we could let circe parse it for us, but until we figure that out just parse it as Json and
-// manually check for File / Directory structures
-private [cwl] object CwlJsonToDelayedCoercionFunction extends Json.Folder[DelayedCoercionFunction] {
-  private def simpleCoercion(value: Any)(womType: WomType): ErrorOr[WomValue] = womType.coerceRawValue(value).toErrorOr
-
-  override def onNull: DelayedCoercionFunction = WomOptionalValue.none(_).validNel
-
-  override def onBoolean(value: Boolean): DelayedCoercionFunction = simpleCoercion(value)
-
-  override def onNumber(value: JsonNumber): DelayedCoercionFunction = {
-    case WomFloatType => WomFloat(value.toDouble).validNel
-    case WomIntegerType => value.toInt.map(WomInteger.apply).toValidNel(s"$value is not a valid Int")
-    case WomLongType => value.toLong.map(WomLong.apply).toValidNel(s"$value is not a valid Long")
-    case other => other.coerceRawValue(value.toString).toErrorOr
-  }
-
-  override def onString(value: String): DelayedCoercionFunction = simpleCoercion(value)
-
-  override def onArray(value: Vector[Json]): DelayedCoercionFunction = {
-    case womArrayType: WomArrayType =>
-      value.toList
-        .traverse(_.foldWith(this).apply(womArrayType.memberType))
-        .map {
-          WomArray(womArrayType, _)
-        }
-
-    case WomOptionalType(otherType) =>
-      onArray(value).apply(otherType)
-    case WomCoproductType(types) =>
-      val attempts: List[ErrorOr[WomValue]] = types.toList.map(onArray(value)(_))
-      attempts.find(_.isValid).getOrElse(attempts.sequence[ErrorOr, WomValue].map(_.head))
-    case WomAnyType =>
-      // Make an array of WomAny
-      value.toList
-        .traverse(_.foldWith(this).apply(WomAnyType))
-        .map {
-          WomArray(WomArrayType(WomAnyType), _)
-        }
-    case other => s"Cannot convert an array input value into a non array type: $other".invalidNel
-  }
-
-  override def onObject(value: JsonObject): DelayedCoercionFunction = {
-    // CWL files are represented as Json objects, so this could be a file 
-    case WomSingleFileType | WomMaybePopulatedFileType if value.toMap.get("class").flatMap(_.asString).contains("File") =>
-      Json.fromJsonObject(value).as[File] match {
-        case Left(errors) => errors.message.invalidNel
-        case Right(file) => file.asWomValue
-      }
-    case WomMaybeListedDirectoryType | WomUnlistedDirectoryType if value.toMap.get("class").flatMap(_.asString).contains("Directory") =>
-      Json.fromJsonObject(value).as[Directory] match {
-        case Left(errors) => errors.message.invalidNel
-        case Right(directory) => directory.asWomValue
-      }
-    case composite: WomCompositeType =>
-      val foldedMap = value.toList.traverse[ErrorOr, (String, WomValue)]({
-        case (k, v) =>
-          composite.typeMap.get(k).map({ valueType =>
-            v.foldWith(this).apply(valueType).map(k -> _)
-          }).getOrElse(s"Input field $k is not defined in the composite input type $composite".invalidNel)
-      }).map(_.toMap[String, WomValue])
-
-      foldedMap.map(WomObject.withTypeUnsafe(_, composite))
-    case WomObjectType =>
-      val foldedMap = value.toList.traverse[ErrorOr, (String, WomValue)]({
-        case (k, v) => v.foldWith(this).apply(WomAnyType).map(k -> _)
-      }).map(_.toMap[String, WomValue])
-
-      foldedMap.map(WomObject.apply)
-    case WomOptionalType(otherType) => onObject(value).apply(otherType)
-    case WomCoproductType(types) =>
-      val attempts: List[ErrorOr[WomValue]] = types.toList.map(onObject(value)(_))
-      //these are all Invalid, just taking head to satisfy required type of WomValue instead of List[WomValue]
-      attempts.find(_.isValid).getOrElse(attempts.sequence[ErrorOr, WomValue].map(_.head))
-    case other => s"Cannot convert an object value $value into a non array type: $other".invalidNel
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlToRun.scala b/cwl/src/main/scala/cwl/CwlToRun.scala
deleted file mode 100644
index 1571958abb5..00000000000
--- a/cwl/src/main/scala/cwl/CwlToRun.scala
+++ /dev/null
@@ -1,11 +0,0 @@
-package cwl
-
-import shapeless._
-
-object CwlToRun extends Poly1 {
-  implicit def commandLineTool = at[CommandLineTool] { Coproduct[WorkflowStep.Run](_) }
-  implicit def workflow = at[Workflow] { Coproduct[WorkflowStep.Run](_) }
-  implicit def expressionTool = at[ExpressionTool] { Coproduct[WorkflowStep.Run](_) }
-}
-
-
diff --git a/cwl/src/main/scala/cwl/CwlType.scala b/cwl/src/main/scala/cwl/CwlType.scala
deleted file mode 100644
index 7ec171d97fb..00000000000
--- a/cwl/src/main/scala/cwl/CwlType.scala
+++ /dev/null
@@ -1,284 +0,0 @@
-package cwl
-
-import cats.instances.list._
-import cats.instances.option._
-import cats.syntax.functor._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import eu.timepit.refined._
-import mouse.all._
-import shapeless.Poly1
-import shapeless.syntax.singleton._
-import wom.expression.IoFunctionSet.{IoDirectory, IoFile}
-import wom.expression.{IoFunctionSet, PathFunctionSet}
-import wom.types.WomFileType
-import wom.values._
-
-import scala.annotation.tailrec
-
-object CwlType extends Enumeration {
-  type CwlType = Value
-
-  val Any = Value("Any")
-  val Null = Value("null")
-  val Boolean = Value("boolean")
-  val Int = Value("int")
-  val Long = Value("long")
-  val Float = Value("float")
-  val Double = Value("double")
-  val String = Value("string")
-  val File = Value("File")
-  val Directory = Value("Directory")
-}
-
-case class File private
-(
-  `class`: W.`"File"`.T,
-  location: Option[String], //TODO refine w/ regex  of IRI
-  path: Option[String],
-  basename: Option[String],
-  checksum: Option[String],
-  size: Option[Long],
-  secondaryFiles: Option[Array[FileOrDirectory]],
-  format: Option[String],
-  contents: Option[String]
-) {
-  lazy val effectivePath = path.orElse(location)
-
-  lazy val errorOrSecondaryFiles: ErrorOr[List[WomFile]] = {
-    val dirsOrFiles: List[FileOrDirectory] = secondaryFiles.getOrElse(Array.empty).toList
-    dirsOrFiles.traverse{
-      _.fold(CwlDirectoryOrFileAsWomSingleDirectoryOrFile)
-    }
-  }
-
-  lazy val asWomValue: ErrorOr[WomMaybePopulatedFile] = {
-    errorOrSecondaryFiles flatMap { secondaryFiles =>
-      val valueOption = location.orElse(path)
-      (valueOption, contents) match {
-        case (None, None) =>
-          "Cannot convert CWL File to WomValue without either a location, a path, or contents".invalidNel
-        case (None, Some(content)) =>
-          val initializeFunction: WomMaybePopulatedFile => IoFunctionSet => IOChecked[WomValue] = { file =>ioFunctionSet =>
-            val name = basename.getOrElse(content.hashCode.toString)
-            ioFunctionSet.writeFile(name, content).toIOChecked(ioFunctionSet.cs) map { writtenFile =>
-              file.copy(valueOption = Option(writtenFile.value))
-            }
-          }
-
-          new WomMaybePopulatedFile(None, checksum, size, format, contents, initializeFunction = initializeFunction).valid
-        case (_, _) =>
-          WomMaybePopulatedFile(valueOption, checksum, size, format, contents, secondaryFiles).valid
-      }
-    }
-  }
-}
-
-object File {
-  def apply(
-             location: Option[String] = None, //TODO refine w/ regex  of IRI
-             path: Option[String] = None,
-             basename: Option[String] = None,
-             checksum: Option[String] = None,
-             size: Option[Long] = None,
-             secondaryFiles: Option[Array[FileOrDirectory]] = None,
-             format: Option[String] = None,
-             contents: Option[String] = None): File = {
-    new cwl.File(
-      "File".narrow,
-      location,
-      path,
-      basename,
-      checksum,
-      size,
-      secondaryFiles,
-      format,
-      contents
-    )
-  }
-
-  def dirname(value: String): String = {
-    val index = value.lastIndexOf('/')
-    if (index >= 0) {
-      value.substring(0, index)
-    } else {
-      ""
-    }
-  }
-
-  def basename(value: String): String = value.substring(value.lastIndexOf('/') + 1)
-
-  def nameroot(value: String): String = basename(value).stripSuffix(nameext(value))
-
-  def nameext(value: String): String = {
-    val base = basename(value)
-    val index = base.lastIndexOf('.')
-    if (index >= 0) {
-      base.substring(index)
-    } else {
-      ""
-    }
-  }
-
-  def recursivelyBuildDirectory(directory: String, ioFunctions: IoFunctionSet)(visited: Vector[String] = Vector.empty): IOChecked[WomMaybeListedDirectory] = {
-    for {
-      listing <- ioFunctions.listDirectory(directory)(visited).toIOChecked(ioFunctions.cs)
-      fileListing <- listing.toList.traverse[IOChecked, WomFile]({
-        case IoDirectory(e) => recursivelyBuildDirectory(e, ioFunctions)(visited :+ directory).widen
-        case IoFile(e) => WomMaybePopulatedFile(e).validIOChecked.widen
-      })
-    } yield WomMaybeListedDirectory(Option(directory), Option(fileListing))
-  }
-
-  private def asAbsoluteSiblingOfPrimary(primary: WomFile, pathFunctions: PathFunctionSet)(path: String) = {
-    pathFunctions.absoluteSibling(primary.value, path)
-  }
-
-  def secondaryStringFile(primaryWomFile: WomFile,
-                          stringWomFileType: WomFileType,
-                          secondaryValue: String,
-                          ioFunctions: IoFunctionSet): IOChecked[WomFile] = {
-    val secondaryRelativeFileName = File.relativeFileName(primaryWomFile.value, secondaryValue)
-
-    // If the primary file is an absolute path, and the secondary is not, make the secondary file an absolute path and a sibling of the primary
-    // http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter
-    val filePath = asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions)(secondaryRelativeFileName)
-
-    // If the secondary file is in fact a directory, look into it and build its listing
-    for {
-      isDirectory <- ioFunctions.isDirectory(filePath).toIOChecked(ioFunctions.cs)
-      file <- if (isDirectory) recursivelyBuildDirectory(filePath, ioFunctions)() else WomFile(stringWomFileType, filePath).validIOChecked
-    } yield file
-  }
-
-  def secondaryExpressionFiles(primaryWomFile: WomFile,
-                               stringWomFileType: WomFileType,
-                               expression: Expression,
-                               parameterContext: ParameterContext,
-                               expressionLib: ExpressionLib,
-                               ioFunctions: IoFunctionSet): ErrorOr[List[WomFile]] = {
-
-    /*
-    If the value is an expression, the value of self in the expression must be the primary input or output File object
-    to which this binding applies.
-     */
-    val secondaryParameterContext = parameterContext.copy(self = primaryWomFile)
-
-    /*
-    The expression must return a filename string relative to the path to the primary File, a File or Directory object
-    with either path or location and basename fields set, or an array consisting of strings or File or Directory
-    objects.
-     */
-    def parseResult(nestedLevel: Int)(womValue: WomValue): ErrorOr[List[WomFile]] = {
-      womValue match {
-        case womString: WomString =>
-          List(WomFile(stringWomFileType, womString.value |> asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions))).valid
-        case womMaybeListedDirectory: WomMaybeListedDirectory =>
-          List(womMaybeListedDirectory.mapFile(asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions))).valid
-        case womMaybePopulatedFile: WomMaybePopulatedFile =>
-          List(womMaybePopulatedFile.mapFile(asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions))).valid
-        case womArray: WomArray if nestedLevel == 0 =>
-          womArray.value.toList flatTraverse parseResult(nestedLevel + 1)
-        case other => s"Not a valid secondary file: $other".invalidNel
-      }
-    }
-
-    val possibleArrayErrorOr: ErrorOr[WomValue] = ExpressionEvaluator.eval(expression, secondaryParameterContext)
-    possibleArrayErrorOr.flatMap(parseResult(nestedLevel = 0))
-  }
-
-  def relativeFileName(primary: String, secondary: String): String = {
-    /*
-    If a value in secondaryFiles is a string that is not an expression, it specifies that the following pattern should
-    be applied to the path of the primary file to yield a filename relative to the primary File:
-
-    1. If string begins with one or more caret ^ characters, for each caret, remove the last file extension from the
-    path (the last period . and all following characters). If there are no file extensions, the path is unchanged.
-
-    2. Append the remainder of the string to the end of the file path.
-     */
-    if (secondary.startsWith("^")) {
-      @tailrec
-      def stripCaret(primaryAcc: String, secondaryAcc: String): (String, String) = {
-        if (secondaryAcc.startsWith("^")) {
-          val idx = primaryAcc.lastIndexOf('.')
-          if (idx < 0) {
-            (primaryAcc, secondaryAcc.dropWhile(_ == '^'))
-          } else {
-            val primaryNext = primaryAcc.substring(0, idx)
-            val secondaryNext = secondaryAcc.drop(1)
-            stripCaret(primaryNext, secondaryNext)
-          }
-        } else {
-          (primaryAcc, secondaryAcc)
-        }
-      }
-
-      val (prefix, suffix) = stripCaret(primary, secondary)
-      prefix + suffix
-    } else {
-      primary + secondary
-    }
-
-  }
-}
-
-case class Directory private
-(
-  `class`: W.`"Directory"`.T,
-  location: Option[String],
-  path: Option[String],
-  basename: Option[String],
-  listing: Option[Array[FileOrDirectory]]
-) {
-  lazy val errorOrListingOption: ErrorOr[Option[List[WomFile]]] = {
-    val maybeErrorOrList: Option[ErrorOr[List[WomFile]]] =
-      listing map {
-        _.toList.traverse {
-          _.fold(CwlDirectoryOrFileAsWomSingleDirectoryOrFile)
-        }
-      }
-    maybeErrorOrList.sequence[ErrorOr, List[WomFile]]
-  }
-
-  lazy val asWomValue: ErrorOr[WomFile] = {
-    errorOrListingOption flatMap { listingOption =>
-      path.orElse(location) map { value =>
-        WomMaybeListedDirectory(Option(value), listingOption, basename).valid
-      } getOrElse {
-        val initializeFunction: WomMaybeListedDirectory => IoFunctionSet => IOChecked[WomValue] = { dir =>ioFunctionSet =>
-          ioFunctionSet.createTemporaryDirectory(basename).toIOChecked(ioFunctionSet.cs) map { tempDir =>
-            dir.copy(valueOption = Option(tempDir))
-          }
-        }
-        new WomMaybeListedDirectory(None, listingOption, basename, initializeFunction = initializeFunction).valid
-      }
-    }
-  }
-}
-
-object Directory {
-  def apply(location: Option[String] = None,
-            path: Option[String] = None,
-            basename: Option[String] = None,
-            listing: Option[Array[FileOrDirectory]] = None
-           ): Directory =
-    new cwl.Directory("Directory".narrow, location, path, basename, listing)
-
-  def basename(value: String): String = {
-    val stripped = value.stripSuffix("/")
-    stripped.substring(stripped.lastIndexOf('/') + 1)
-  }
-}
-
-private[cwl] object CwlDirectoryOrFileAsWomSingleDirectoryOrFile extends Poly1 {
-  implicit def caseFile: Case.Aux[File, ErrorOr[WomFile]] = at {
-    _.asWomValue
-  }
-
-  implicit def caseDirectory: Case.Aux[Directory, ErrorOr[WomFile]] = at {
-    _.asWomValue
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlVersion.scala b/cwl/src/main/scala/cwl/CwlVersion.scala
deleted file mode 100644
index 12336b1cceb..00000000000
--- a/cwl/src/main/scala/cwl/CwlVersion.scala
+++ /dev/null
@@ -1,7 +0,0 @@
-package cwl
-
-object CwlVersion extends Enumeration {
-  type CwlVersion = Value
-
-  val Version1 = Value("v1.0")
-}
diff --git a/cwl/src/main/scala/cwl/CwlWomExpression.scala b/cwl/src/main/scala/cwl/CwlWomExpression.scala
deleted file mode 100644
index 5d77370ba49..00000000000
--- a/cwl/src/main/scala/cwl/CwlWomExpression.scala
+++ /dev/null
@@ -1,260 +0,0 @@
-package cwl
-
-import cats.instances.list._
-import cats.syntax.functor._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import common.validation.ErrorOr.{ErrorOr, ShortCircuitingFlatMap}
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import cwl.InitialWorkDirFileGeneratorExpression._
-import cwl.InitialWorkDirRequirement.IwdrListingArrayEntry
-import shapeless.Poly1
-import wom.callable.{AdHocValue, ContainerizedInputExpression}
-import wom.expression.IoFunctionSet.{IoDirectory, IoFile}
-import wom.expression.{FileEvaluation, IoFunctionSet, WomExpression}
-import wom.types._
-import wom.values._
-
-import scala.concurrent.Await
-import scala.concurrent.duration.Duration
-
-trait CwlWomExpression extends WomExpression {
-
-  def cwlExpressionType: WomType
-
-  override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] = cwlExpressionType.validNel
-
-  def expressionLib: ExpressionLib
-
-  def evaluate(inputs: Map[String, WomValue], parameterContext: ParameterContext, expression: Expression): ErrorOr[WomValue] =
-    expression.
-      fold(EvaluateExpression).
-      apply(parameterContext)
-}
-
-case class ECMAScriptWomExpression(expression: Expression,
-                                   override val inputs: Set[String],
-                                   override val expressionLib: ExpressionLib) extends CwlWomExpression {
-  val cwlExpressionType = WomAnyType
-
-  override def sourceString = expression match {
-    case Expression.ECMAScriptExpression(s) => s.value
-    case Expression.ECMAScriptFunction(s) => s.value
-    case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-  }
-
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet) = {
-    val pc = ParameterContext(ioFunctionSet, expressionLib, inputValues)
-    evaluate(inputValues, pc, expression)
-  }
-
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType) = Set.empty[FileEvaluation].validNel
-}
-
-final case class InitialWorkDirFileGeneratorExpression(entry: IwdrListingArrayEntry, expressionLib: ExpressionLib) extends ContainerizedInputExpression {
-
-  def evaluate(inputValues: Map[String, WomValue], mappedInputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): IOChecked[List[AdHocValue]] = {
-    def recursivelyBuildDirectory(directory: String): IOChecked[WomMaybeListedDirectory] = {
-      import cats.syntax.traverse._
-      for {
-        listing <- ioFunctionSet.listDirectory(directory)().toIOChecked(ioFunctionSet.cs)
-        fileListing <- listing.toList.traverse[IOChecked, WomFile] {
-          case IoDirectory(e) => recursivelyBuildDirectory(e).widen
-          case IoFile(e) => WomSingleFile(e).validIOChecked.widen
-        }
-      } yield WomMaybeListedDirectory(Option(directory), Option(fileListing))
-    }
-
-    inputValues.toList.traverse[IOChecked, (String, WomValue)]({
-      case (k, v: WomMaybeListedDirectory) =>
-        val absolutePathString = ioFunctionSet.pathFunctions.relativeToHostCallRoot(v.value)
-        recursivelyBuildDirectory(absolutePathString).contextualizeErrors(s"Error building directory $absolutePathString") map { k -> _ }
-      case kv => kv.validIOChecked
-    }).map(_.toMap)
-      .flatMap({ updatedValues =>
-        val unmappedParameterContext = ParameterContext(ioFunctionSet, expressionLib, updatedValues)
-        entry.fold(InitialWorkDirFilePoly).apply(unmappedParameterContext, mappedInputValues).toIOChecked
-      })
-  }
-}
-
-object InitialWorkDirFileGeneratorExpression {
-  type InitialWorkDirFileEvaluator = (ParameterContext, Map[String, WomValue]) => ErrorOr[List[AdHocValue]]
-
-  /**
-    * Converts an InitialWorkDir.
-    *
-    * TODO: Review against the spec. Especially for Dirent values. For example:
-    *
-    * "If the value is an expression that evaluates to a Dirent object, this indicates that the File or Directory in
-    * entry should be added to the designated output directory with the name in entryname."
-    *
-    * - http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement
-    * - http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent
-    */
-  object InitialWorkDirFilePoly extends Poly1 {
-    implicit val caseExpressionDirent: Case.Aux[ExpressionDirent, InitialWorkDirFileEvaluator] = {
-      at { expressionDirent =>
-        (unmappedParameterContext, mappedInputValues) => {
-
-          val mutableInputOption = expressionDirent.entry.fold(ExpressionToMutableInputOptionPoly)
-
-          val entryEvaluation =
-            expressionDirent.entry match {
-                //we need to catch this special case to feed in "value-mapped" input values
-              case expr@Expression.ECMAScriptExpression(exprString) if exprString.value.trim() == "$(JSON.stringify(inputs))" =>
-                val specialParameterContext = ParameterContext(
-                  unmappedParameterContext.ioFunctionSet,
-                  unmappedParameterContext.expressionLib,
-                  mappedInputValues
-                )
-                ExpressionEvaluator.eval(expr, specialParameterContext)
-              case _ => ExpressionEvaluator.eval(expressionDirent.entry, unmappedParameterContext)
-            }
-
-          val womValueErrorOr: ErrorOr[AdHocValue] = entryEvaluation flatMap {
-            case womFile: WomFile =>
-              val errorOrEntryName: ErrorOr[Option[String]] = expressionDirent.entryname match {
-                case Some(actualEntryName) => actualEntryName.fold(EntryNamePoly).apply(unmappedParameterContext).map(Option.apply)
-                case None => None.valid
-              }
-              errorOrEntryName map { entryName =>
-                AdHocValue(womFile, entryName, inputName = mutableInputOption)
-              }
-            case other => for {
-              coerced <- WomStringType.coerceRawValue(other).toErrorOr
-              contentString = coerced.asInstanceOf[WomString].value
-              // We force the entryname to be specified, and then evaluate it:
-              entryNameStringOrExpression <- expressionDirent.entryname.toErrorOr(
-                "Invalid dirent: Entry was a string but no file name was supplied")
-              entryName <- entryNameStringOrExpression.fold(EntryNamePoly).apply(unmappedParameterContext)
-              writeFile = unmappedParameterContext.ioFunctionSet.writeFile(entryName, contentString)
-              writtenFile <- validate(Await.result(writeFile, Duration.Inf))
-            } yield AdHocValue(writtenFile, alternativeName = None, inputName = mutableInputOption)
-          }
-
-          womValueErrorOr.map(List(_))
-        }
-      }
-    }
-
-    implicit val caseStringDirent: Case.Aux[StringDirent, InitialWorkDirFileEvaluator] = {
-      at {
-        stringDirent => {
-          (unmappedParameterContext, _) =>
-            val womValueErrorOr = for {
-              entryName <- stringDirent.entryname.fold(EntryNamePoly).apply(unmappedParameterContext)
-              contentString = stringDirent.entry
-              writeFile = unmappedParameterContext.ioFunctionSet.writeFile(entryName, contentString)
-              writtenFile <- validate(Await.result(writeFile, Duration.Inf))
-            } yield writtenFile
-
-            womValueErrorOr.map(AdHocValue(_, alternativeName = None, inputName = None)).map(List(_))
-        }
-      }
-    }
-
-    implicit val caseExpression: Case.Aux[Expression, InitialWorkDirFileEvaluator] = {
-      at { expression =>
-        (unmappedParameterContext, _) => {
-          // A single expression which must evaluate to an array of Files
-          val expressionEvaluation = ExpressionEvaluator.eval(expression, unmappedParameterContext)
-
-          expressionEvaluation flatMap {
-            case array: WomArray if array.value.forall(_.isInstanceOf[WomFile]) =>
-              array.value.toList.map(_.asInstanceOf[WomFile]).map(AdHocValue(_, alternativeName = None, inputName = None)).validNel
-            case file: WomFile =>
-              List(AdHocValue(file, alternativeName = None, inputName = None)).validNel
-            case other =>
-              val error = "InitialWorkDirRequirement listing expression must be File or Array[File] but got %s: %s"
-                .format(other, other.womType.stableName)
-              error.invalidNel
-          }
-        }
-      }
-    }
-
-    implicit val caseString: Case.Aux[String, InitialWorkDirFileEvaluator] = {
-      at { string =>
-        (_, _) => {
-          List(AdHocValue(WomSingleFile(string), alternativeName = None, inputName = None)).valid
-        }
-      }
-    }
-
-    implicit val caseStringOrExpression: Case.Aux[StringOrExpression, InitialWorkDirFileEvaluator] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit val caseFile: Case.Aux[File, InitialWorkDirFileEvaluator] = {
-      at { file =>
-        (_, _) => {
-          file.asWomValue.map(AdHocValue(_, alternativeName = None, inputName = None)).map(List(_))
-        }
-      }
-    }
-
-    implicit val caseDirectory: Case.Aux[Directory, InitialWorkDirFileEvaluator] = {
-      at { directory =>
-        (_, _) => {
-          directory.asWomValue.map(AdHocValue(_, alternativeName = None, inputName = None)).map(List(_))
-        }
-      }
-    }
-
-  }
-
-  type EntryNameEvaluator = ParameterContext => ErrorOr[String]
-
-  object EntryNamePoly extends Poly1 {
-    implicit val caseString: Case.Aux[String, EntryNameEvaluator] = {
-      at {
-        string => {
-          _ =>
-            string.valid
-        }
-      }
-    }
-
-    implicit val caseExpression: Case.Aux[Expression, EntryNameEvaluator] = {
-      at {
-        expression => {
-          parameterContext =>
-            for {
-              entryNameExpressionEvaluated <- ExpressionEvaluator.eval(expression, parameterContext)
-              entryNameValidated <- mustBeString(entryNameExpressionEvaluated)
-            } yield entryNameValidated
-        }
-      }
-    }
-
-    private def mustBeString(womValue: WomValue): ErrorOr[String] = {
-      womValue match {
-        case WomString(s) => s.valid
-        case other => WomStringType.coerceRawValue(other).map(_.asInstanceOf[WomString].value).toErrorOr
-      }
-    }
-  }
-
-  /**
-    * Searches for ECMAScript expressions that mutate input paths.
-    *
-    * @see [[AdHocValue]]
-    */
-  object ExpressionToMutableInputOptionPoly extends Poly1 {
-    private val MutableInputRegex = """(?s)\s*\$\(\s*inputs\.(\w+)\s*\)\s*""".r
-    implicit val caseECMAScriptExpression: Case.Aux[ECMAScriptExpression, Option[String]] = {
-      at { eCMAScriptExpression =>
-        eCMAScriptExpression.value match {
-          case MutableInputRegex(mutableInput) => Option(mutableInput)
-          case _ => None
-        }
-      }
-    }
-    implicit val caseECMAScriptFunction: Case.Aux[ECMAScriptFunction, Option[String]] = at { _ => None }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwltoolRunner.scala b/cwl/src/main/scala/cwl/CwltoolRunner.scala
deleted file mode 100644
index 834c9d80b23..00000000000
--- a/cwl/src/main/scala/cwl/CwltoolRunner.scala
+++ /dev/null
@@ -1,71 +0,0 @@
-package cwl
-
-import ammonite.ops.ImplicitWd._
-import ammonite.ops._
-import com.typesafe.config.ConfigFactory
-import cwl.preprocessor.CwlReference
-import org.broadinstitute.heterodon.ExecAndEval
-
-/**
-  * Interface for running cwltool.
-  */
-sealed trait CwltoolRunner {
-  def salad(reference: CwlReference): String
-}
-
-object CwltoolRunner {
-  private lazy val config = ConfigFactory.load
-
-  lazy val instance: CwltoolRunner = {
-    val runnerClass = config.getString("cwltool-runner.class")
-    Class.forName(runnerClass).getDeclaredConstructor().newInstance().asInstanceOf[CwltoolRunner]
-  }
-}
-
-/**
-  * Runs cwltool as an external process.
-  */
-final class CwltoolProcess extends CwltoolRunner {
-  override def salad(reference: CwlReference): String = {
-    val commandResult: CommandResult = %%("cwltool", "--quiet", "--print-pre", reference.pathAsString)
-    commandResult.exitCode match {
-      case 0 => commandResult.out.string
-      case error =>
-        throw new RuntimeException(
-          s"running CwlTool on file ${reference.pathAsString} resulted in exit code $error and stderr ${commandResult.err.string}")
-    }
-  }
-}
-
-/**
-  * Runs cwltool via heterodon.
-  *
-  * https://github.com/broadinstitute/heterodon
-  */
-final class CwltoolHeterodon extends CwltoolRunner {
-  // Trimmed down version of
-  // https://github.com/common-workflow-language/cwltool/blob/1a839255795882894b4bbfea6d909a74cacb1d6a/cwltool/main.py#L355
-  private val cwltoolSaladExecScript =
-  """|import json
-     |import logging
-     |
-     |from cwltool.load_tool import fetch_document, resolve_tool_uri, validate_document
-     |from cwltool.loghandler import _logger
-     |
-     |
-     |def cwltool_salad(path):
-     |    _logger.setLevel(logging.WARN)
-     |    uri, tool_file_uri = resolve_tool_uri(path)
-     |    document_loader, workflowobj, uri = fetch_document(uri)
-     |    document_loader, avsc_names, processobj, metadata, uri \
-     |        = validate_document(document_loader, workflowobj, uri, preprocess_only=True)
-     |    return json.dumps(processobj, indent=4)
-     |""".stripMargin
-
-  private def cwltoolSaladEvalStatement(reference: CwlReference): String = s"cwltool_salad('${reference.pathAsString}')"
-
-  def salad(reference: CwlReference): String = {
-    val execAndEval = new ExecAndEval()
-    execAndEval.apply(cwltoolSaladExecScript, cwltoolSaladEvalStatement(reference)).asInstanceOf[String]
-  }
-}
diff --git a/cwl/src/main/scala/cwl/EnumSchema.scala b/cwl/src/main/scala/cwl/EnumSchema.scala
deleted file mode 100644
index 83ff1b05813..00000000000
--- a/cwl/src/main/scala/cwl/EnumSchema.scala
+++ /dev/null
@@ -1,35 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import shapeless.Witness
-import wom.types.WomEnumerationType
-
-trait EnumSchema {
-
-  val name: Option[String]
-  val symbols: Array[String]
-  val `type`: Witness.`"enum"`.T
-  val label: Option[String]
-
-  def toWomEnumerationType: WomEnumerationType = {
-    val symbolIds = symbols.toList.map{
-      s => s.substring(s.lastIndexOf("/") + 1)
-    }
-    WomEnumerationType(NonEmptyList.fromListUnsafe(symbolIds))
-  }
-}
-
-case class InputEnumSchema(
-  name: Option[String],
-  symbols: Array[String],
-  `type`: Witness.`"enum"`.T = Witness("enum").value,
-  label: Option[String] = None,
-  inputBinding: Option[InputCommandLineBinding] = None) extends EnumSchema
-
-case class OutputEnumSchema(
-  name: Option[String],
-  symbols: Array[String],
-  `type`: Witness.`"enum"`.T,
-  label: Option[String],
-  outputBinding: Option[CommandOutputBinding]) extends EnumSchema
-
diff --git a/cwl/src/main/scala/cwl/EvaluateExpression.scala b/cwl/src/main/scala/cwl/EvaluateExpression.scala
deleted file mode 100644
index 00036d49de4..00000000000
--- a/cwl/src/main/scala/cwl/EvaluateExpression.scala
+++ /dev/null
@@ -1,20 +0,0 @@
-package cwl
-
-import common.validation.ErrorOr.ErrorOr
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import shapeless.Poly1
-import wom.values.WomValue
-
-object EvaluateExpression extends Poly1 {
-  implicit val script: Case.Aux[ECMAScriptExpression, ParameterContext => ErrorOr[WomValue]] = {
-    at {
-      ExpressionEvaluator.evalExpression
-    }
-  }
-
-  implicit val function: Case.Aux[ECMAScriptFunction, ParameterContext => ErrorOr[WomValue]] = {
-    at {
-      ExpressionEvaluator.evalFunction
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ExpressionEvaluator.scala b/cwl/src/main/scala/cwl/ExpressionEvaluator.scala
deleted file mode 100644
index a3ed2c7a7c4..00000000000
--- a/cwl/src/main/scala/cwl/ExpressionEvaluator.scala
+++ /dev/null
@@ -1,101 +0,0 @@
-package cwl
-
-import cats.syntax.validated._
-import common.validation.ErrorOr._
-import cwl.internal.{CwlEcmaScriptDecoder, EcmaScriptEncoder, EcmaScriptUtil}
-import eu.timepit.refined.api.Refined
-import eu.timepit.refined.string.MatchesRegex
-import shapeless.Witness
-import wom.callable.RuntimeEnvironment
-import wom.values.{WomFloat, WomInteger, WomString, WomValue}
-
-// http://www.commonwl.org/v1.0/CommandLineTool.html#Expressions
-object ExpressionEvaluator {
-  // A code fragment wrapped in the $(...) syntax must be evaluated as a ECMAScript expression.
-  /*
-  There are several places in cwltool where a simple contains check is used:
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/builder.py#L157
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/command_line_tool.py#L669
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/expression.py#L219
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/process.py#L645
-   */
-  val ECMAScriptExpressionWitness = Witness("""(?s).*\$\(.*""")
-  val ECMAScriptExpressionRegex = ECMAScriptExpressionWitness.value.r
-  type MatchesECMAScriptExpression = MatchesRegex[ECMAScriptExpressionWitness.T]
-  type ECMAScriptExpression = String Refined MatchesECMAScriptExpression
-
-  // A code fragment wrapped in the ${...} syntax must be evaluated as a ECMAScript function body for an anonymous,
-  // zero-argument function.
-  val ECMAScriptFunctionWitness = Witness("""(?s)\s*\$\{(.*)\}\s*""")
-  val ECMAScriptFunctionRegex = ECMAScriptFunctionWitness.value.r
-  type MatchesECMAScriptFunction = MatchesRegex[ECMAScriptFunctionWitness.T]
-  type ECMAScriptFunction = String Refined MatchesECMAScriptFunction
-
-  def eval(expr: Expression, parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    expr.fold(EvaluateExpression).apply(parameterContext)
-  }
-
-  def evalExpression(expression: ECMAScriptExpression)(parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    def evaluator(string: String): ErrorOr[WomValue] = {
-      eval(string, parameterContext)
-    }
-
-    ExpressionInterpolator.interpolate(expression.value, evaluator, strip_whitespace = false)
-  }
-
-  def evalFunction(function: ECMAScriptFunction)(parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    function.value match {
-      case ECMAScriptFunctionRegex(script) =>
-
-        val functionExpression =
-          s"""|(function() {
-              |FUNCTION_BODY
-              |})();
-              |""".stripMargin.replace("FUNCTION_BODY", script)
-
-        eval(functionExpression, parameterContext)
-      case unmatched =>
-        s"Expression '$unmatched' was unable to be matched to regex '${ECMAScriptFunctionWitness.value}'".invalidNel
-    }
-  }
-
-  private lazy val cwlJsDecoder = new CwlEcmaScriptDecoder()
-
-  def eval(expr: String, parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    val script = if (parameterContext.expressionLib.isEmpty) {
-      expr
-    } else {
-      parameterContext.expressionLib.mkString("", ";", s";$expr")
-    }
-    val (rawVals, mapVals) = paramValues(parameterContext)
-    EcmaScriptUtil.evalStructish(
-      script,
-      rawVals,
-      mapVals,
-      new EcmaScriptEncoder(),
-      cwlJsDecoder
-    )
-  }
-
-  def paramValues(parameterContext: ParameterContext): ((String, WomValue), Map[String, Map[String, WomValue]]) = {
-    (
-        "self" -> parameterContext.self
-      ,
-      Map(
-        "inputs" -> parameterContext.inputs,
-        "runtime" -> parameterContext.runtimeOption.map(cwlMap).getOrElse(Map.empty)
-      )
-    )
-  }
-
-  def cwlMap(runtime: RuntimeEnvironment): Map[String, WomValue] = {
-    Map(
-      "outdir" -> WomString(runtime.outputPath),
-      "tmpdir" -> WomString(runtime.tempPath),
-      "cores" -> WomInteger(runtime.cores.value),
-      "ram" -> WomFloat(runtime.ram),
-      "outdirSize" -> WomFloat(runtime.outputPathSize.toDouble),
-      "tmpdirSize" -> WomFloat(runtime.tempPathSize.toDouble)
-    )
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ExpressionInterpolator.scala b/cwl/src/main/scala/cwl/ExpressionInterpolator.scala
deleted file mode 100644
index 9a40ee8e06f..00000000000
--- a/cwl/src/main/scala/cwl/ExpressionInterpolator.scala
+++ /dev/null
@@ -1,173 +0,0 @@
-package cwl
-
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.validation.ErrorOr._
-import wom.types.WomNothingType
-import wom.values._
-
-import scala.jdk.CollectionConverters._
-
-/**
-  * Partial copy-port of cwltool's expression.py.
-  *
-  * Minimizes refactor so that as expression.py continues to update the updates may be manually copied here also.
-  *
-  * Current omissions in `def interpolate`:
-  * - `def evaluator`
-  *   - Utility not copy-ported.
-  *   - `def interpolate` instead ignores absence of InlineJavascriptRequirement and instead always uses fullJS=True
-  * - `leaf = json.dumps(e, sort_keys=True)`
-  *   - When the interpolated string is not just-a-single-expression there is undefined behavior of rendering
-  *     non-WomPrimitive values into json.
-  *   - Even if it did, does not sort the keys.
-  *   - Thus we do not currently return character-for-character equality for these expressions with cwltool, however
-  *     these cases are not explicitly defined in the CWL spec as far as I know.
-  *
-  * @see https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/expression.py
-  */
-//noinspection ZeroIndexToHead,RemoveRedundantReturn
-object ExpressionInterpolator {
-
-  class SubstitutionException(message: String) extends RuntimeException(message)
-
-  /**
-    * Copy-port of expression.py's scanner.
-    */
-  private def scanner(scan: String): List[Int] = {
-    val DEFAULT = 0
-    val DOLLAR = 1
-    val PAREN = 2
-    val BRACE = 3
-    val SINGLE_QUOTE = 4
-    val DOUBLE_QUOTE = 5
-    val BACKSLASH = 6
-
-    var i = 0
-    val stack = new java.util.Stack[Int]
-    stack.push(DEFAULT)
-    var start = 0
-    while (i < scan.length) {
-      val state = stack.peek
-      val c = scan(i)
-
-      if (state == DEFAULT) {
-        if (c == '$') {
-          stack.push(DOLLAR)
-        } else if (c == '\\') {
-          stack.push(BACKSLASH)
-        }
-      } else if (state == BACKSLASH) {
-        stack.pop()
-        if (stack.peek == DEFAULT) {
-          return List(i - 1, i + 1)
-        }
-      } else if (state == DOLLAR) {
-        if (c == '(') {
-          start = i - 1
-          stack.push(PAREN)
-        } else if (c == '{') {
-          start = i - 1
-          stack.push(BRACE)
-        } else {
-          stack.pop()
-        }
-      } else if (state == PAREN) {
-        if (c == '(') {
-          stack.push(PAREN)
-        } else if (c == ')') {
-          stack.pop()
-          if (stack.peek == DOLLAR) {
-            return List(start, i + 1)
-          }
-        } else if (c == '\'') {
-          stack.push(SINGLE_QUOTE)
-        } else if (c == '"') {
-          stack.push(DOUBLE_QUOTE)
-        }
-      } else if (state == BRACE) {
-        if (c == '{') {
-          stack.push(BRACE)
-        } else if (c == '}') {
-          stack.pop()
-          if (stack.peek == DOLLAR) {
-            return List(start, i + 1)
-          }
-        } else if (c == '\'') {
-          stack.push(SINGLE_QUOTE)
-        } else if (c == '"') {
-          stack.push(DOUBLE_QUOTE)
-        }
-      } else if (state == SINGLE_QUOTE) {
-        if (c == '\'') {
-          stack.pop()
-        } else if (c == '\\') {
-          stack.push(BACKSLASH)
-        }
-      } else if (state == DOUBLE_QUOTE) {
-        if (c == '"') {
-          stack.pop()
-        } else if (c == '\\') {
-          stack.push(BACKSLASH)
-        }
-      }
-      i += 1
-    }
-    if (stack.size > 1) {
-      throw new SubstitutionException(
-        "Substitution error, unfinished block starting at position %s: %s".format(start, scan.drop(start)))
-    } else {
-      return null
-    }
-  }
-
-  /**
-    * Copy-port of expression.py's interpolate.
-    */
-  def interpolate(scanParam: String,
-                  evaluator: String => ErrorOr[WomValue],
-                  strip_whitespace: Boolean = true): ErrorOr[WomValue] = {
-    var scan = scanParam
-    if (strip_whitespace) {
-      scan = scan.trim
-    }
-    val parts = new java.util.Stack[ErrorOr[WomValue]]
-    var w = scanner(scan)
-    while (w != null) {
-      parts.push(WomString(scan.slice(0, w(0))).valid)
-
-      if (scan(w(0)) == '$') {
-        val e = evaluator(scan.slice(w(0) + 1, w(1)))
-        if (w(0) == 0 && w(1) == scan.length && parts.size <= 1) {
-          return e
-        }
-        /*
-        Original-ish:
-          var leaf = json.dumps(e, sort_keys=True)
-          if (leaf(0) == '"') {
-            leaf = leaf.drop(1).dropRight(1)
-          }
-        Instead, push the raw WomValue. WomString's won't have been quoted as python's json.dumps does.
-        Other WomPrimitive's should be fine. CWL using other structures (Maps, Arrays, etc.) may have problems.
-         */
-        val leaf = e
-        parts.push(leaf)
-      } else if (scan(w(0)) == '\\') {
-        val e = scan(w(1) - 1)
-        parts.push(WomString(e.toString).valid)
-      }
-
-      scan = scan.drop(w(1))
-      w = scanner(scan)
-    }
-    parts.push(WomString(scan).valid)
-    return parts.asScala.toList.sequence[ErrorOr, WomValue] map { list =>
-      WomString(list.map{
-        //we represent nulls as this type because Wom doesn't have a "null" value, but it does have a nothing type
-        case WomOptionalValue(WomNothingType, None) => "null"
-        case other => other.valueString
-      }.mkString(""))
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ExpressionTool.scala b/cwl/src/main/scala/cwl/ExpressionTool.scala
deleted file mode 100644
index 53c8a675a4c..00000000000
--- a/cwl/src/main/scala/cwl/ExpressionTool.scala
+++ /dev/null
@@ -1,136 +0,0 @@
-package cwl
-
-import cats.syntax.either._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import cwl.CwlVersion._
-import cwl.ExpressionTool.{ExpressionToolInputParameter, ExpressionToolOutputParameter}
-import shapeless.{Coproduct, Witness}
-import wom.RuntimeAttributes
-import wom.callable.{Callable, CallableExpressionTaskDefinition}
-import wom.expression.{IoFunctionSet, ValueAsAnExpression}
-import wom.graph.GraphNodePort.OutputPort
-import wom.types.{WomMapType, WomStringType, WomType}
-import wom.values.{WomMap, WomObject, WomString, WomValue}
-
-case class ExpressionTool(
-                           inputs: Array[ExpressionToolInputParameter] = Array.empty,
-                           outputs: Array[ExpressionToolOutputParameter] = Array.empty,
-                           `class`: Witness.`"ExpressionTool"`.T,
-                           expression: StringOrExpression,
-                           id: String,
-                           requirements: Option[Array[Requirement]] = None,
-                           hints: Option[Array[Hint]] = None,
-                           label: Option[String] = None,
-                           doc: Option[String] = None,
-                           cwlVersion: Option[CwlVersion] = None,
-                           `$namespaces`: Option[Map[String, String]] = None,
-                           `$schemas`: Option[Array[String]] = None
-                         ) extends Tool {
-
-  def asCwl: Cwl = Coproduct[Cwl](this)
-
-  def castWomValueAsMap(evaluatedExpression: WomValue): Checked[Map[String, WomValue]] = {
-    evaluatedExpression match {
-      case WomMap(WomMapType(WomStringType, _), map) =>  map.map{
-        case (WomString(key), value) => key -> value
-        case (key, _) => throw new RuntimeException(s"saw a non-string value $key in wom map $evaluatedExpression typed with string keys ")
-      }.asRight
-      case obj: WomObject => obj.values.asRight
-      case _ => s"Could not cast value $evaluatedExpression to a Map[String, WomValue]".invalidNelCheck
-    }
-  }
-
-  def buildTaskDefinition(taskName: String,
-                          inputDefinitions: List[_ <: Callable.InputDefinition],
-                          outputDefinitions: List[Callable.OutputDefinition],
-                          runtimeAttributes: RuntimeAttributes,
-                          requirementsAndHints: List[cwl.Requirement],
-                          expressionLib: ExpressionLib): ErrorOr[CallableExpressionTaskDefinition] = {
-
-    def evaluate(inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, outputPorts: List[OutputPort]): Checked[Map[OutputPort, WomValue]] = {
-      val womExpression = expression match {
-        case StringOrExpression.String(str) => ValueAsAnExpression(WomString(str))
-        case StringOrExpression.Expression(expr) => ECMAScriptWomExpression(expr, inputNames, expressionLib)
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-
-      // If we expect a certain type for
-      def coerce(womValue: WomValue, womType: WomType): Checked[WomValue] = womType.coerceRawValue(womValue).toChecked
-
-      /*
-        * Look in the object (the result of the expression evaluation) for values to match output each port.
-        * Ideally we'd want to find a value for each output port declared by the tool.
-        * However since the spec is not clear on this and cwltool seems to ignore entirely the outputs declaration,
-        * we'll do the same for now, meaning we'll assign a value to the output port iff the result of the expression has one for them,
-        * otherwise we'll remove the port for the final map.
-        * If there are fields in the expression's result that do not have a matching declared output port, they won't be added either,
-        * because we'd have to create an output port for them now which would be useless anyway since nothing could point to it.
-       */
-      def mapPortsToValues(values: Map[String, WomValue]): Checked[Map[OutputPort, WomValue]] = {
-        import cats.syntax.traverse._
-
-        val coercedValues: List[ErrorOr[(OutputPort, WomValue)]] = for {
-          outputPort <- outputPorts
-          value <- values.get(outputPort.internalName)
-          coerced = coerce(value, outputPort.womType).toValidated
-        } yield coerced.map(outputPort -> _)
-
-        coercedValues.sequence[ErrorOr, (OutputPort, WomValue)].map(_.toMap).toEither
-      }
-
-      for {
-        // Evaluate the expression
-        evaluatedExpression <- womExpression.evaluateValue(inputs, ioFunctionSet).toEither
-        /*
-          * We expect the result to be an object of the form:
-          * {
-          *   "outputName": value,
-          *   ...
-          * }
-         */
-        womMap <- castWomValueAsMap(evaluatedExpression)
-
-        mappedValues <- mapPortsToValues(womMap)
-      } yield mappedValues
-    }
-
-    CallableExpressionTaskDefinition(
-      taskName,
-      evaluate,
-      runtimeAttributes,
-      Map.empty,
-      Map.empty,
-      outputDefinitions,
-      inputDefinitions,
-      // TODO: This doesn't work in all cases and it feels clunky anyway - find a way to sort that out
-      prefixSeparator = "#"
-    ).validNel
-  }
-}
-
-object ExpressionTool {
-
-  case class ExpressionToolInputParameter(id: String,
-                                          label: Option[String] = None,
-                                          secondaryFiles: Option[SecondaryFiles] = None,
-                                          format: Option[InputParameterFormat] = None,
-                                          streamable: Option[Boolean] = None,
-                                          doc: Option[Doc] = None,
-                                          inputBinding: Option[InputCommandLineBinding] = None,
-                                          default: Option[CwlAny] = None,
-                                          `type`: Option[MyriadInputType] = None) extends InputParameter
-
-  case class ExpressionToolOutputParameter(id: String,
-                                           label: Option[String] = None,
-                                           secondaryFiles: Option[SecondaryFiles] = None,
-                                           format: Option[OutputParameterFormat] = None,
-                                           streamable: Option[Boolean] = None,
-                                           doc: Option[Doc] = None,
-                                           outputBinding: Option[CommandOutputBinding] = None,
-                                           `type`: Option[MyriadOutputType] = None) extends OutputParameter
-}
diff --git a/cwl/src/main/scala/cwl/FileParameter.scala b/cwl/src/main/scala/cwl/FileParameter.scala
deleted file mode 100644
index 2413d9d7c02..00000000000
--- a/cwl/src/main/scala/cwl/FileParameter.scala
+++ /dev/null
@@ -1,150 +0,0 @@
-package cwl
-
-import cats.effect.IO
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.ontology.Schema
-import shapeless.Poly1
-import wom.expression.IoFunctionSet
-import wom.types.{WomFileType, WomMaybePopulatedFileType}
-import wom.values.{WomArray, WomFile, WomMaybePopulatedFile, WomValue}
-
-object FileParameter {
-  private val ReadLimit = Option(64 * 1024)
-
-  def populateSecondaryFiles(womValue: WomValue,
-                             secondaryFilesCoproduct: Option[SecondaryFiles],
-                             formatOption: Option[String],
-                             parameterContext: ParameterContext,
-                             expressionLib: ExpressionLib,
-                             ioFunctions: IoFunctionSet): IOChecked[WomValue] = {
-
-    womValue match {
-
-      case womMaybePopulatedFile: WomMaybePopulatedFile =>
-        val secondaryFilesErrorOr = FileParameter.secondaryFiles(
-          womMaybePopulatedFile,
-          WomMaybePopulatedFileType,
-          secondaryFilesCoproduct,
-          parameterContext,
-          expressionLib,
-          ioFunctions
-        )
-
-        secondaryFilesErrorOr map { secondaryFiles =>
-          womMaybePopulatedFile.copy(secondaryFiles = secondaryFiles, formatOption = formatOption)
-        }
-
-      case womArray: WomArray =>
-        womArray.value.toList.traverse(
-          populateSecondaryFiles(_, secondaryFilesCoproduct, formatOption, parameterContext, expressionLib, ioFunctions)
-        ).map(WomArray(_))
-
-      case womValue: WomValue => womValue.validIOChecked
-    }
-  }
-
-  /**
-    * Checks if the file is compatible with a format.
-    */
-  def checkFormat(womMaybePopulatedFile: WomMaybePopulatedFile,
-                  formatsOption: Option[List[String]],
-                  schemaOption: Option[Schema]): ErrorOr[Unit] = {
-    validate {
-      for {
-        schema <- schemaOption
-        fileFormat <- womMaybePopulatedFile.formatOption
-        formats <- formatsOption
-      } yield {
-        if (!formats.exists(schema.isSubClass(fileFormat, _)))
-          throw new RuntimeException(s"$fileFormat is not compatible with ${formats.mkString(", ")}")
-      }
-      ()
-    }
-  }
-
-  /**
-    * Populates the contents if they aren't loaded already.
-    */
-  def maybeLoadContents(womMaybePopulatedFile: WomMaybePopulatedFile,
-                        ioFunctionSet: IoFunctionSet,
-                        loadContents: Boolean): IO[Option[String]] = {
-    womMaybePopulatedFile.contentsOption match {
-      case someContents@Some(_) => IO.pure(someContents)
-      case None if !loadContents => IO.pure(None)
-      case _ => FileParameter.load64KiB(womMaybePopulatedFile.value, ioFunctionSet).map(Option(_))
-    }
-  }
-
-  def load64KiB(path: String, ioFunctionSet: IoFunctionSet): IO[String] = {
-    implicit val ec = IO.contextShift(ioFunctionSet.ec)
-    IO.fromFuture(IO { ioFunctionSet.readFile(path, ReadLimit, failOnOverflow = false) })
-  }
-
-  /**
-    * Returns the list of secondary files for the primary file.
-    */
-  def secondaryFiles(primaryWomFile: WomFile,
-                     stringWomFileType: WomFileType,
-                     secondaryFilesOption: Option[SecondaryFiles],
-                     parameterContext: ParameterContext,
-                     expressionLib: ExpressionLib,
-                     ioFunctions: IoFunctionSet): IOChecked[List[WomFile]] = {
-    secondaryFilesOption
-      .map(secondaryFiles(primaryWomFile, stringWomFileType, _, parameterContext, expressionLib, ioFunctions))
-      .getOrElse(List.empty[WomFile].validIOChecked)
-  }
-
-  /**
-    * Returns the list of secondary files for the primary file.
-    */
-  def secondaryFiles(primaryWomFile: WomFile,
-                     stringWomFileType: WomFileType,
-                     secondaryFiles: SecondaryFiles,
-                     parameterContext: ParameterContext,
-                     expressionLib: ExpressionLib,
-                     ioFunctions: IoFunctionSet): IOChecked[List[WomFile]] = {
-    secondaryFiles
-      .fold(SecondaryFilesPoly)
-      .apply(primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions)
-  }
-
-  type SecondaryFilesFunction = (WomFile, WomFileType, ParameterContext, ExpressionLib, IoFunctionSet) => IOChecked[List[WomFile]]
-
-  object SecondaryFilesPoly extends Poly1 {
-    implicit def caseStringOrExpression: Case.Aux[StringOrExpression, SecondaryFilesFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseExpression: Case.Aux[Expression, SecondaryFilesFunction] = {
-      at {
-        expression =>
-          (primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions) =>
-            File.secondaryExpressionFiles(primaryWomFile, stringWomFileType, expression, parameterContext, expressionLib, ioFunctions).toIOChecked
-      }
-    }
-
-    implicit def caseString: Case.Aux[String, SecondaryFilesFunction] = {
-      at {
-        string =>
-          (primaryWomFile, stringWomFileType, _, _, ioFunctions) =>
-            File.secondaryStringFile(primaryWomFile, stringWomFileType, string, ioFunctions).map(List(_))
-      }
-    }
-
-    implicit def caseArray: Case.Aux[Array[StringOrExpression], SecondaryFilesFunction] = {
-      at {
-        array =>
-          (primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions) =>
-            val functions: List[SecondaryFilesFunction] = array.toList.map(_.fold(this))
-            functions.flatTraverse(_ (primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions))
-      }
-    }
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/FullyQualifiedName.scala b/cwl/src/main/scala/cwl/FullyQualifiedName.scala
deleted file mode 100644
index faabfa44fc4..00000000000
--- a/cwl/src/main/scala/cwl/FullyQualifiedName.scala
+++ /dev/null
@@ -1,61 +0,0 @@
-package cwl
-
-import cwl.command.ParentName
-
-/**
-  * All of these classes decompose a "fully qualified" id into its constituent parts.  They have unique types as
-  * they are seen in different parts of a CWL document and they differ in content.
-  *
-  * The fully qualified names are created by the Schema salad preprocessing step.
-  *
-  * @see <a href="http://www.commonwl.org/v1.0/SchemaSalad.html#Identifier_resolution">Schema salad Identifier Resolution</a>
-  */
-trait FullyQualifiedName {
-  def fileName: String
-  def id: String
-  def parent: Option[String]
-}
-
-case class FileAndId private(fileName: String, parent: Option[String], id: String) extends FullyQualifiedName
-
-object FileAndId {
-  def apply(in: String)(implicit parent: ParentName): FileAndId = {
-    val Array(fileName, id) = in.split("#")
-    val cleanID = parent.stripParent(id)
-    FileAndId(fileName, parent.value, cleanID)
-  }
-}
-
-case class FileStepAndId private(fileName: String, parent: Option[String], stepId: String, id: String) extends FullyQualifiedName
-
-object FileStepAndId {
-  def apply(in: String)(implicit parent: ParentName): FileStepAndId = {
-    val Array(fileName, id) = in.split("#")
-    val cleanID = parent.stripParent(id)
-    val Array(stepId, outputId) = cleanID.split("/")
-    FileStepAndId(fileName, parent.value, stepId, outputId)
-  }
-}
-
-case class ArbitrarilyNested(fileName: String, parent: Option[String], id: String) extends FullyQualifiedName
-
-case class FileStepUUID(fileName: String, parent: Option[String], id: String, uuid: String, stepId: String) extends FullyQualifiedName
-
-object FullyQualifiedName {
-  def apply(in: String)(implicit parent: ParentName): FullyQualifiedName = maybeApply(in)(parent).getOrElse(throw new Exception(s"malformed FQN: $in"))
-
-  def maybeApply(in: String)(implicit parent: ParentName): Option[FullyQualifiedName] = {
-
-    in.split("#") match {
-      case Array(file, after) =>
-        val cleanAfter = parent.stripParent(after)
-        cleanAfter.split("/").toList match {
-          case step :: uuid :: id :: Nil => Option(FileStepUUID(file, parent.value, id, uuid, step))
-          case step :: id :: Nil => Option(FileStepAndId(file, parent.value, step, id))
-          case id :: Nil => Option(FileAndId(file, parent.value, id))
-          case many => Option(ArbitrarilyNested(file, parent.value, many.last))
-        }
-      case _ => None
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/GlobEvaluator.scala b/cwl/src/main/scala/cwl/GlobEvaluator.scala
deleted file mode 100644
index d50b154da2c..00000000000
--- a/cwl/src/main/scala/cwl/GlobEvaluator.scala
+++ /dev/null
@@ -1,67 +0,0 @@
-package cwl
-
-import cats.syntax.validated._
-import common.validation.ErrorOr._
-import shapeless._
-import wom.types.{WomArrayType, WomStringType}
-import wom.values._
-
-/*
-CommandOutputBinding.glob:
-Find files relative to the output directory, using POSIX glob(3) pathname matching. If an array is provided, find
-files that match any pattern in the array. If an expression is provided, the expression must return a string or an
-array of strings, which will then be evaluated as one or more glob patterns. Must only match and return files which
-actually exist.
-
-http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding
- */
-object GlobEvaluator {
-
-  type GlobEvaluatorFunction = (ParameterContext, ExpressionLib) => ErrorOr[List[String]]
-
-  def globs(globOption: Option[Glob], parameterContext: ParameterContext, expressionLib: ExpressionLib): ErrorOr[List[String]] = {
-    globOption map {
-      globs(_, parameterContext, expressionLib)
-    } getOrElse {
-      Nil.valid
-    }
-  }
-
-  def globs(glob: Glob, parameterContext: ParameterContext, expressionLib: ExpressionLib): ErrorOr[List[String]] = {
-    glob.fold(GlobEvaluator.GlobEvaluatorPoly).apply(parameterContext, expressionLib)
-  }
-
-  object GlobEvaluatorPoly extends Poly1 {
-    implicit def caseStringOrExpression: Case.Aux[StringOrExpression, GlobEvaluatorFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseExpression: Case.Aux[Expression, GlobEvaluatorFunction] = {
-      at {
-        expression =>
-          (parameterContext, expressionLib) => {
-            ExpressionEvaluator.eval(expression, parameterContext) flatMap {
-              case WomArray(_, values) if values.isEmpty => Nil.valid
-              case WomString(value) => List(value).valid
-              case WomArray(WomArrayType(WomStringType), values) => values.toList.map(_.valueString).valid
-              case womValue =>
-                val message = s"Unexpected expression result: $womValue while evaluating expression '$expression' " +
-                  s"using inputs '$parameterContext'"
-                message.invalidNel
-            }
-          }
-      }
-    }
-
-    implicit def caseArrayString: Case.Aux[Array[String], GlobEvaluatorFunction] = {
-      at { array => (_, _) => array.toList.valid }
-    }
-
-    implicit def caseString: Case.Aux[String, GlobEvaluatorFunction] = {
-      at { string => (_, _) => List(string).valid }
-    }
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/InitialWorkDirRequirement.scala b/cwl/src/main/scala/cwl/InitialWorkDirRequirement.scala
deleted file mode 100644
index 28e49fe71d9..00000000000
--- a/cwl/src/main/scala/cwl/InitialWorkDirRequirement.scala
+++ /dev/null
@@ -1,63 +0,0 @@
-package cwl
-
-import cwl.InitialWorkDirRequirement._
-import eu.timepit.refined.W
-import shapeless.{:+:, CNil, _}
-
-final case class InitialWorkDirRequirement(
-                                            `class`: W.`"InitialWorkDirRequirement"`.T,
-                                            listing: IwdrListing
-                                          ) {
-  val listings: Array[IwdrListingArrayEntry] = listing.fold(IwdrListingArrayPoly)
-
-  override def toString: WorkflowStepInputId =
-    s"""InitialWorkDirRequirement(
-      |  ${listings.mkString(System.lineSeparator + "  ")}
-      |)""".stripMargin
-}
-
-/**
-  *  Short for "Directory Entry"
-  *  @see <a href="http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent">Dirent Specification</a>
-  *
-  *  Split into two cases because entryName is only optional if entry is an Expression
-  */
-trait Dirent {
-  def writable: Option[Boolean]
-  def writableWithDefault = writable.getOrElse(false)
-}
-
-final case class ExpressionDirent(
-                                   entry: Expression,
-                                   entryname: Option[StringOrExpression],
-                                   writable: Option[Boolean]
-                                 ) extends Dirent
-
-final case class StringDirent(
-                               entry: String,
-                               entryname: StringOrExpression,
-                               writable: Option[Boolean]
-                             ) extends Dirent
-
-object InitialWorkDirRequirement {
-
-  // "ExpressionDirent" has to come before StringDirent because expressions are matched by "String" first if we do it the
-  // other way round.
-  final type IwdrListingArrayEntry = File :+: Directory :+: ExpressionDirent :+: StringDirent :+: StringOrExpression :+: CNil
-  final type IwdrListing = Array[IwdrListingArrayEntry] :+: StringOrExpression :+: CNil
-
-  object IwdrListingArrayPoly extends Poly1 {
-    implicit val caseArrayIwdrListingArrayEntry: Case.Aux[Array[IwdrListingArrayEntry], Array[IwdrListingArrayEntry]] = {
-      at {
-        identity
-      }
-    }
-
-    implicit val caseStringOrExpression: Case.Aux[StringOrExpression, Array[IwdrListingArrayEntry]] = {
-      at {
-        stringOrExpression =>
-          Array(Coproduct[IwdrListingArrayEntry](stringOrExpression))
-      }
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/InputParameter.scala b/cwl/src/main/scala/cwl/InputParameter.scala
deleted file mode 100644
index d8b1579dcef..00000000000
--- a/cwl/src/main/scala/cwl/InputParameter.scala
+++ /dev/null
@@ -1,190 +0,0 @@
-package cwl
-
-import cats.syntax.functor._
-import cats.syntax.parallel._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cats.instances.option._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.FileParameter._
-import cwl.ontology.Schema
-import shapeless.Poly1
-import wom.callable.Callable.InputDefinition.InputValueMapper
-import wom.expression.IoFunctionSet
-import wom.types.{WomSingleFileType, WomType}
-import wom.values.{WomArray, WomMaybeListedDirectory, WomMaybePopulatedFile, WomObject, WomObjectLike, WomOptionalValue, WomValue}
-
-trait InputParameter {
-  def id: String
-  def label: Option[String]
-  def secondaryFiles: Option[SecondaryFiles]
-  def format: Option[InputParameterFormat]
-  def streamable: Option[Boolean]
-  def doc: Option[Doc]
-  def inputBinding: Option[InputCommandLineBinding]
-  def default: Option[CwlAny]
-  def `type`: Option[MyriadInputType]
-  def loadContents = inputBinding.flatMap(_.loadContents).getOrElse(false)
-}
-
-object InputParameter {
-  object IdDefaultAndType {
-    def unapply(arg: InputParameter): Option[(String, CwlAny, MyriadInputType)] = (arg.default, arg.`type`) match {
-      case (Some(default), Some(tpe)) => Option((arg.id, default, tpe))
-      case _ => None
-    }
-  }
-
-  object IdAndType {
-    def unapply(arg: InputParameter): Option[(String, MyriadInputType)] = (arg.default, arg.`type`) match {
-      case (None, Some(tpe)) => Option((arg.id, tpe))
-      case _ => None
-    }
-  }
-
-  type DefaultToWomValueFunction = WomType => ErrorOr[WomValue]
-
-  object DefaultToWomValuePoly extends Poly1 {
-    implicit def caseFileOrDirectory: Case.Aux[FileOrDirectory, DefaultToWomValueFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseFileOrDirectoryArray: Case.Aux[Array[FileOrDirectory], DefaultToWomValueFunction] = {
-      at {
-        fileOrDirectoryArray =>
-          womType =>
-            fileOrDirectoryArray
-              .toList
-              .traverse(_.fold(this).apply(womType))
-              .map(WomArray(_))
-      }
-    }
-
-    implicit def caseFile: Case.Aux[File, DefaultToWomValueFunction] = {
-      at {
-        file =>
-          womType =>
-            file.asWomValue.flatMap(womType.coerceRawValue(_).toErrorOr)
-      }
-    }
-
-    implicit def caseDirectory: Case.Aux[Directory, DefaultToWomValueFunction] = {
-      at {
-        directory =>
-          womType =>
-            directory.asWomValue.flatMap(womType.coerceRawValue(_).toErrorOr)
-      }
-    }
-
-    implicit def caseJson: Case.Aux[io.circe.Json, DefaultToWomValueFunction] = {
-      at {
-        circeJson =>
-          womType =>
-            val stringJson = circeJson.noSpaces
-            import spray.json._
-            val sprayJson = stringJson.parseJson
-            womType.coerceRawValue(sprayJson).toErrorOr
-      }
-    }
-  }
-
-  object InputParameterFormatPoly extends Poly1 {
-    implicit val caseExpression: Case.Aux[Expression, ParameterContext => ErrorOr[List[String]]] = {
-      at { expression =>
-        parameterContext =>
-          ExpressionEvaluator.eval(expression, parameterContext) map {
-            case WomArray(_, values) => values.toList.map(_.valueString)
-            case womValue => List(womValue.valueString)
-          }
-      }
-    }
-
-    implicit val caseString: Case.Aux[String, ParameterContext => ErrorOr[List[String]]] = {
-      at { string =>
-        _ =>
-          List(string).valid
-      }
-    }
-
-    implicit val caseArrayString: Case.Aux[Array[String], ParameterContext => ErrorOr[List[String]]] = {
-      at { array =>
-        _ =>
-          array.toList.valid
-      }
-    }
-  }
-
-  /**
-    * Yet another value mapper. This one is needed because in CWL we might need to "augment" inputs which we can only do
-    * once they have been linked to a WomValue. This input value mapper encapsulates logic to be applied once that is
-    * done. For now, if the inputParameter has an input binding with loadContents = true, load the content of the file.
-    *
-    * This is based on the spec in http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-    *
-    * NOTE: There may be _many_ cases not implemented here that need to be fixed.
-    */
-  def inputValueMapper(inputParameter: InputParameter,
-                       inputType: MyriadInputType,
-                       expressionLib: ExpressionLib,
-                       schemaOption: Option[Schema]): InputValueMapper = {
-    ioFunctionSet: IoFunctionSet => {
-      import ioFunctionSet.cs
-
-      def populateFiles(womValue: WomValue): IOChecked[WomValue] = {
-        womValue match {
-          case womMaybePopulatedFile: WomMaybePopulatedFile =>
-            // Don't include the secondary files in the self variables
-            val parameterContext = ParameterContext(ioFunctionSet, expressionLib, self = womMaybePopulatedFile.copy(secondaryFiles = List.empty))
-            val secondaryFilesFromInputParameter = inputParameter.secondaryFiles
-            val secondaryFilesFromType = inputType.fold(MyriadInputTypeToSecondaryFiles)
-            val secondaryFiles = secondaryFilesFromInputParameter orElse secondaryFilesFromType
-            val inputFormatsErrorOr = inputParameter.format
-                .traverse(_.fold(InputParameterFormatPoly).apply(parameterContext))
-
-            for {
-              inputFormatsOption <- inputFormatsErrorOr.toIOChecked
-              _ <- checkFormat(womMaybePopulatedFile, inputFormatsOption, schemaOption).toIOChecked
-              contentsOption <- FileParameter.maybeLoadContents(
-                womMaybePopulatedFile,
-                ioFunctionSet,
-                inputParameter.loadContents
-              ).to[IOChecked]
-              withSize <- womMaybePopulatedFile.withSize(ioFunctionSet).to[IOChecked]
-              loaded = withSize.copy(contentsOption = contentsOption)
-              secondaries <- FileParameter.secondaryFiles(
-                loaded,
-                WomSingleFileType,
-                secondaryFiles,
-                parameterContext,
-                expressionLib,
-                ioFunctionSet
-              )
-              updated = loaded.copy(secondaryFiles = loaded.secondaryFiles ++  secondaries)
-            } yield updated
-          case womMaybeListedDirectory: WomMaybeListedDirectory => womMaybeListedDirectory.withSize(ioFunctionSet).to[IOChecked].widen
-          case WomArray(_, values) => values.toList.parTraverse[IOChecked, WomValue](populateFiles).map(WomArray(_))
-          case WomOptionalValue(_, Some(innerValue)) => populateFiles(innerValue).map(WomOptionalValue(_))
-          case obj: WomObjectLike =>
-            // Map the values
-            val populated: IOChecked[WomObject] = obj.values.toList.parTraverse[IOChecked, (String, WomValue)]({
-              case (key, value) => populateFiles(value).map(key -> _)
-            })
-            .map(_.toMap)
-            // Validate new types are still valid w.r.t the object
-            .flatMap(WomObject.withTypeChecked(_, obj.womObjectTypeLike).toIOChecked)
-            
-            populated.widen[WomValue]
-          case womValue: WomValue =>
-            pure(womValue)
-        }
-      }
-
-      womValue => populateFiles(womValue)
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/LinkMergeMethod.scala b/cwl/src/main/scala/cwl/LinkMergeMethod.scala
deleted file mode 100644
index bd54ca6b56a..00000000000
--- a/cwl/src/main/scala/cwl/LinkMergeMethod.scala
+++ /dev/null
@@ -1,8 +0,0 @@
-package cwl
-
-object LinkMergeMethod extends Enumeration {
-  type LinkMergeMethod = Value
-
-  val MergeNested = Value("merge_nested")
-  val MergeFlattened = Value("merge_flattened")
-}
diff --git a/cwl/src/main/scala/cwl/MyriadInputTypeToSecondaryFiles.scala b/cwl/src/main/scala/cwl/MyriadInputTypeToSecondaryFiles.scala
deleted file mode 100644
index 4ddc09625d3..00000000000
--- a/cwl/src/main/scala/cwl/MyriadInputTypeToSecondaryFiles.scala
+++ /dev/null
@@ -1,25 +0,0 @@
-package cwl
-
-import cwl.CwlType.CwlType
-import shapeless.Poly1
-
-// IAS.secondaryFiles are NOT listed in 1.0 spec, but according to jgentry they will be, maybe
-object MyriadInputTypeToSecondaryFiles extends Poly1 {
-  implicit val caseMyriadInputInnerType: Case.Aux[MyriadInputInnerType, Option[SecondaryFiles]] = at {
-    _.fold(MyriadInputInnerTypeToSecondaryFiles)
-  }
-
-  implicit val caseArrayMyriadInputInnerType: Case.Aux[Array[MyriadInputInnerType], Option[SecondaryFiles]] = at {
-    _.to(LazyList).flatMap(_.fold(MyriadInputInnerTypeToSecondaryFiles)).headOption
-  }
-}
-
-object MyriadInputInnerTypeToSecondaryFiles extends Poly1 {
-  implicit val caseCwlType: Case.Aux[CwlType, Option[SecondaryFiles]] = at { _ => None }
-  implicit val caseInputRecordSchema: Case.Aux[InputRecordSchema, Option[SecondaryFiles]] = at { _ => None }
-  implicit val caseInputEnumSchema: Case.Aux[InputEnumSchema, Option[SecondaryFiles]] = at { _ => None }
-  implicit val caseInputArraySchema: Case.Aux[InputArraySchema, Option[SecondaryFiles]] = at {
-    inputArraySchema => inputArraySchema.secondaryFiles
-  }
-  implicit val caseString: Case.Aux[String, Option[SecondaryFiles]] = at { _ => None }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadInputTypeToSortedCommandParts.scala b/cwl/src/main/scala/cwl/MyriadInputTypeToSortedCommandParts.scala
deleted file mode 100644
index 498e97c016f..00000000000
--- a/cwl/src/main/scala/cwl/MyriadInputTypeToSortedCommandParts.scala
+++ /dev/null
@@ -1,254 +0,0 @@
-package cwl
-
-import cwl.CommandLineTool.{CommandBindingSortingKey, CommandPartsList, SortKeyAndCommandPart, StringOrInt}
-import cwl.CwlType.CwlType
-import cwl.SchemaDefRequirement.SchemaDefTypes
-import cwl.command.ParentName
-import shapeless.{Coproduct, Poly1}
-import wom.values.{WomArray, WomCoproductValue, WomObjectLike, WomOptionalValue, WomValue}
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.instances.list._
-import cats.instances.option._
-
-/**
-  * Poly1 to fold over a MyriadInputType and create a List of SortingKeyAndCommandPart based on the rules described here:
-  * http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-  */
-object MyriadInputTypeToSortedCommandParts extends Poly1 {
-  import Case._
-
-  /**
-    * CommandLineBinding: binding of the element being processed.
-    *   It's possible for an input not to have an "inputBinding", but to have a complex type which itself has inputBindings for its fields or items.
-    *   e.g:
-    *     - id: arrayInput
-    *       type:
-    *         type: array
-    *         items: File
-    *         inputBinding: { prefix: "-YYY" }
-    *
-    * Here the array type has an inputBinding but the input itself (arrayInput) does not.
-    * This would yield on the command line something like "-YYY arrayItem0 -YYY arrayItem1 ..."
-    *
-    * On the other hand:
-    *     - id: arrayInput
-    *       type:
-    *         type: array
-    *         items: File
-    *         inputBinding: { prefix: "-YYY" }
-    *       inputBinding: { prefix: "-XXX" }
-    *
-    * In this case the input itself has a binding as well, which would yield something like "-XXX -YYY arrayItem0 -YYY arrayItem1 ..."
-    *
-    * For arrays specifically, the presence of an "itemSeparator" and / or "valueFrom" in the input binding will change the way the array is processed,
-    * which is why we need to know about it in this Poly1 that folds over the input types.
-    *
-    * WomValue: value bound to the element (in the cases above it would be the WomArray)
-    * CommandBindingSortingKey: The current sorting key. Because we might need to recurse in nested types we need to propagate the key as we do.
-    */
-  type CommandPartBuilder = (Option[InputCommandLineBinding], WomValue, CommandBindingSortingKey, Boolean, ExpressionLib, SchemaDefRequirement) => CommandPartsList
-
-  implicit def m: Aux[MyriadInputInnerType, CommandPartBuilder] = {
-    at {
-      innerType => {
-        (binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-          innerType
-            .fold(MyriadInputInnerTypeToSortedCommandParts)
-            .apply(binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement).fold(
-              throw new RuntimeException(s"inner type to command part failed!  on type $innerType w/ womValue $womValue"))(identity)
-      }
-    }
-  }
-
-  implicit def am: Aux[Array[MyriadInputInnerType], CommandPartBuilder] = {
-    at {
-      types => {
-        (binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-          def lookupTypes(innerTypes: Array[MyriadInputInnerType]) = {
-            innerTypes.toList.map{
-              _.fold(MyriadInputInnerTypeToSortedCommandParts)
-                .apply(binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-            }.reduce(_ orElse _)
-          }
-          val result: Option[CommandPartsList] =
-            types.partition(_.select[CwlType].contains(CwlType.Null)) match {
-              case (Array(_), types) => lookupTypes(types) orElse Some(List.empty[SortKeyAndCommandPart])
-              case (Array(), types) => lookupTypes(types)
-            }
-         result.fold(
-            throw new RuntimeException(s"could not produce command line parts from input $womValue and types $types"))(
-            identity
-          )
-      }
-    }
-  }
-}
-
-object MyriadInputInnerTypeToSortedCommandParts extends Poly1 {
-
-  type CommandPartBuilder = (Option[InputCommandLineBinding], WomValue, CommandBindingSortingKey, Boolean, ExpressionLib, SchemaDefRequirement) => Option[CommandPartsList]
-
-  import Case._
-
-  // Primitive type: we just need to create a command part from the binding if there's one here.
-  implicit def ct: Aux[CwlType, CommandPartBuilder] = {
-    at {
-      cwlType => {
-        case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-        case (inputBinding, womValue, key, hasShellCommandRequirement, expressionLib, _) => {
-          (cwlType, womValue) match {
-            case (CwlType.Null, _) => List.empty.some
-            case (_, WomOptionalValue(_, None)) => List.empty.some
-            case (_,_) => inputBinding.toList.map(_.toCommandPart(key, womValue, hasShellCommandRequirement, expressionLib)).some
-          }
-        }
-      }
-    }
-  }
-
-  implicit def irs: Aux[InputRecordSchema, CommandPartBuilder] = at[InputRecordSchema] { irs => {
-    def go: CommandPartBuilder = {
-
-      //If the value is optional and is supplied, recurse over the value provided
-      case (inputBinding, WomCoproductValue(_, value), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        go(inputBinding, value, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-
-      //If the value is optional and is supplied, recurse over the value provided
-      case (inputBinding, WomOptionalValue(_, Some(value)), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        go(inputBinding, value, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-
-      // If it's optional and there's no value, do nothing
-      case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-
-      // If there's no input binding and no input bindings within the irs, do nothing
-      case (None, _, _, _, _, _) if !irs.fields.exists(_.exists(_.inputBinding.isDefined)) => List.empty.some
-
-      case (inputBinding, objectLike: WomObjectLike, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        // If there's an input binding, make a SortKeyAndCommandPart for it
-        val sortingKeyFromInputBindingFromInputParameter: Option[SortKeyAndCommandPart] =
-          inputBinding.map(_.toCommandPart(sortingKey, objectLike, hasShellCommandRequirement, expressionLib))
-
-        // iterate through the fields and fold over their type
-        val partsFromFields:Option[CommandPartsList] =
-          irs.fields.toList.flatten.
-            flatTraverse{
-              case InputRecordField(name, tpe, _, inputBinding, _) =>
-                // Parse the name to get a clean id
-                val parsedName = FullyQualifiedName(name)(ParentName.empty).id
-
-                // The field name needs to be added to the key after the input binding (as per the spec)
-                // Also start from the key from the input binding if there was one
-                val fieldSortingKey =
-                  sortingKeyFromInputBindingFromInputParameter.
-                    map(_.sortingKey).
-                    getOrElse(sortingKey).
-                    append(inputBinding, Coproduct[StringOrInt](parsedName))
-
-                val innerValueOption: Option[WomValue] = objectLike.values.get(parsedName)
-
-                val folded = innerValueOption.map(tpe.fold(MyriadInputTypeToSortedCommandParts).
-                  apply(inputBinding, _, fieldSortingKey.asNewKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement))
-                folded
-            }
-
-        sortingKeyFromInputBindingFromInputParameter.fold(
-          partsFromFields )(
-          sortingKeyFromInputBindingFromInputParameter =>
-            partsFromFields.map{k => List(sortingKeyFromInputBindingFromInputParameter.copy(nestedCommandParts = k)) }
-        )
-      case (_, other, _, _, _, _) => throw new RuntimeException(s"Value $other cannot be used for an input of type InputRecordSchema")
-    }
-
-    go
-  }}
-
-  implicit def ies: Aux[InputEnumSchema, CommandPartBuilder] = at[InputEnumSchema] { inputEnumSchema =>
-    def go: CommandPartBuilder = {
-      case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-      case (inputBinding, value, sortingKey, hasShellCommandRequirement, expressionLib, _) =>
-        // If there's an input binding, make a SortKeyAndCommandPart for it
-        val fromInputBinding =
-          inputBinding.map(_.toCommandPart(sortingKey, value, hasShellCommandRequirement, expressionLib)).toList
-
-        val fromIes = inputEnumSchema.inputBinding.map(_.toCommandPart(sortingKey, value, hasShellCommandRequirement, expressionLib)).toList
-
-        (fromInputBinding ++ fromIes).some
-    }
-    go
-  }
-
-  implicit def ias: Aux[InputArraySchema, CommandPartBuilder] = at[InputArraySchema] { ias =>
-    def go: CommandPartBuilder = {
-      case (inputBindingFromInputParameterParent, WomOptionalValue(_, Some(value)), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        go(inputBindingFromInputParameterParent, value, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-
-      //If it's optional and there's no value, do nothing
-      case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-
-      // If there's no input binding and no input bindings for the ias, do nothing
-      case (None, _, _, _, _, _) if ias.inputBinding.isEmpty => List.empty.some
-
-      case (inputBinding, WomArray.WomArrayLike(womArray: WomArray), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-
-
-        // If there's an input binding, make a SortKeyAndCommandPart for it
-        val sortKeyFromInputBindingFromInputerParameterParent: Option[SortKeyAndCommandPart] =
-          inputBinding.
-            map(_.toCommandPart(sortingKey, womArray, hasShellCommandRequirement, expressionLib))
-
-        // Now depending on whether we have an itemSeparator and/or valueFrom or not, we're going to recurse over each element of the array (or not).
-        // See http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding
-        if (inputBinding.flatMap(_.itemSeparator).isDefined || inputBinding.flatMap(_.valueFrom).isDefined) {
-          // If there's an item separator or a valueFrom we can stop here.
-          // When the command part is instantiated (see CommandLineBindingCommandPart) it will evaluate the valueFrom (if defined) and join the items together (if there's an itemSeparator).
-          sortKeyFromInputBindingFromInputerParameterParent.toList.some
-        } else {
-          // If neither valueFrom nor itemSeparator were defined, we need to process each item of the array
-          val fromArray: Option[CommandPartsList] = womArray.value.zipWithIndex.toList.flatTraverse({
-            case (item, index) =>
-              // Update the sorting key with the binding position (if any), add the index
-              val itemSortingKey = {
-
-              // The index needs to be added to the key after the input binding (as per the spec)
-              // Also start from the key from the input binding if there was one
-                val sortKey = sortKeyFromInputBindingFromInputerParameterParent.fold(sortingKey)(_.sortingKey)
-
-                sortKey.append(ias.inputBinding, Coproduct[StringOrInt](index))
-              }
-
-              // Even if the item doesn't have an explicit input binding, it should appear in the command so create a default empty one
-              //there is an explicit input binding!
-              val arrayItemInputBinding =
-                ias.
-                  inputBinding.
-                  orElse(Option(InputCommandLineBinding.default))
-
-              // Fold over the item type of each array element
-              Option(ias.items.fold(MyriadInputTypeToSortedCommandParts).apply(arrayItemInputBinding, item, itemSortingKey.asNewKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement))
-          })
-          sortKeyFromInputBindingFromInputerParameterParent.fold(fromArray){
-            sortKeyFromInputBindingFromInputerParameterParent =>
-              fromArray.map{k => List(sortKeyFromInputBindingFromInputerParameterParent.copy(nestedCommandParts = k)) }
-          }
-        }
-
-      case (_, other, _, _, _, _) => throw new RuntimeException(s"Value $other cannot be used for an input of type InputArraySchema")
-    }
-
-    go
-  }
-
-  implicit def s: Aux[String, CommandPartBuilder] = {
-    at {
-      s => {
-        case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-        case (commandLineBindingFromInput, womValue, sortingKey, boolean, expressionLib, schemaDefRequirement) => {
-          val womType: SchemaDefTypes = schemaDefRequirement.lookupCwlType(s).getOrElse(throw new RuntimeException(s"Looked for type $s in custom types $schemaDefRequirement but no match was found!"))
-
-          womType.fold(this).apply(commandLineBindingFromInput, womValue, sortingKey, boolean, expressionLib, schemaDefRequirement)
-        }
-      }
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadInputTypeToWomType.scala b/cwl/src/main/scala/cwl/MyriadInputTypeToWomType.scala
deleted file mode 100644
index d3be698bd33..00000000000
--- a/cwl/src/main/scala/cwl/MyriadInputTypeToWomType.scala
+++ /dev/null
@@ -1,95 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cwl.CwlType.CwlType
-import cwl.MyriadInputTypeToWomType.SchemaLookup
-import cwl.command.ParentName
-import mouse.all._
-import shapeless.Poly1
-import wom.types._
-
-object MyriadInputInnerTypeToString extends Poly1 {
-  implicit def ct = at[CwlType]{ _.toString }
-  implicit def irs = at[InputRecordSchema]{_.toString}
-  implicit def ies = at[InputEnumSchema]{ _.toString }
-  implicit def ias = at[InputArraySchema]{ _.toString}
-  implicit def s = at[String]{identity}
-}
-
-object MyriadInputTypeToWomType extends Poly1 {
-
-  import Case._
-
-  type SchemaLookup = SchemaDefRequirement => WomType
-
-  implicit def m:Aux[MyriadInputInnerType, SchemaLookup]= at[MyriadInputInnerType] {_.fold(MyriadInputInnerTypeToWomType)}
-
-  // An array of type means "this input value can be in any of those types."
-  // Currently we only accept single types or [null, X] to mean Optional[X]
-  implicit def am: Aux[Array[MyriadInputInnerType], SchemaLookup] = at[Array[MyriadInputInnerType]] {
-    types =>
-      schemaLookup =>
-        types.partition(_.select[CwlType].contains(CwlType.Null)) match {
-          // If there's a single non null type, use that
-          case (Array(), Array(singleNonNullType)) =>
-            singleNonNullType.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup)
-          case (Array(), array: Array[MyriadInputInnerType]) if array.length > 1  =>
-            val types = array.map(_.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup))
-            WomCoproductType(NonEmptyList.fromListUnsafe(types.toList))
-          // If there's a null type and a single non null type, it's a WomOptionalType
-          case (Array(_), Array(singleNonNullType)) =>
-            WomOptionalType(singleNonNullType.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup))
-          case (Array(_), array: Array[MyriadInputInnerType]) if array.length > 1  =>
-            val types = array.map(_.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup))
-            WomOptionalType(WomCoproductType(NonEmptyList.fromListUnsafe(types.toList)))
-          case (Array(_), _) =>
-            val readableTypes = types.map(_.fold(MyriadInputInnerTypeToString)).mkString(", ")
-            throw new UnsupportedOperationException(s"Cromwell only supports single types or optionals (as indicated by [null, X]). Instead we saw: $readableTypes")
-    }
-  }
-}
-
-object MyriadInputInnerTypeToWomType extends Poly1 {
-  import Case._
-
-  def ex(component: String) = throw new RuntimeException(s"input type $component not yet suported by WOM!")
-
-  implicit def ct: Aux[CwlType, SchemaLookup] = at[CwlType]{
-    ct =>
-      cwl.cwlTypeToWomType(ct) |> Function.const
-  }
-
-  def inputRecordSchemaToWomType(irs: InputRecordSchema): SchemaLookup = { schemaLookup: SchemaDefRequirement =>
-    irs match {
-      case InputRecordSchema(_,  Some(fields), _, _) =>
-        val typeMap = fields.map({ field =>
-          FullyQualifiedName(field.name)(ParentName.empty).id -> field.`type`.fold(MyriadInputTypeToWomType).apply(schemaLookup)
-        }).toMap
-        WomCompositeType(typeMap)
-      case irs => irs.toString |> ex
-    }
-  }
-
-  implicit def irs: Aux[InputRecordSchema, SchemaLookup] = at[InputRecordSchema]{
-    inputRecordSchemaToWomType
-  }
-
-  implicit def ies: Aux[InputEnumSchema, SchemaLookup] = at[InputEnumSchema]{
-    ies =>
-      ies.toWomEnumerationType |> Function.const
-  }
-
-  implicit def ias: Aux[InputArraySchema, SchemaLookup] = at[InputArraySchema]{
-    ias =>
-      lookup =>
-        val arrayType: WomType = ias.items.fold(MyriadInputTypeToWomType).apply(lookup)
-        WomArrayType(arrayType)
-  }
-
-  implicit def s: Aux[String, SchemaLookup] = at[String]{
-    string =>
-      schemaReq =>
-        schemaReq.lookupType(string).getOrElse(throw new RuntimeException(s"Custom type $string was referred to but not found in schema def ${schemaReq}."))
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomFiles.scala b/cwl/src/main/scala/cwl/MyriadOutputTypeToWomFiles.scala
deleted file mode 100644
index 7c007d07d46..00000000000
--- a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomFiles.scala
+++ /dev/null
@@ -1,66 +0,0 @@
-package cwl
-
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.validation.IOChecked._
-import cwl.CwlType.CwlType
-import cwl.MyriadOutputTypeToWomFiles.EvaluationFunction
-import mouse.all._
-import shapeless.Poly1
-import wom.expression.FileEvaluation
-
-object MyriadOutputTypeToWomFiles extends Poly1 {
-
-  type EvaluationFunction = CommandOutputBinding => IOChecked[Set[FileEvaluation]]
-
-  import Case._
-
-  implicit def cwlType: Aux[MyriadOutputInnerType, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[MyriadOutputInnerType]{
-    _.fold(MyriadOutputInnerTypeToWomFiles)
-  }
-
-  implicit def acwl: Aux[Array[MyriadOutputInnerType], EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[Array[MyriadOutputInnerType]] { types =>
-    evalFunction =>
-      types.toList.traverse(_.fold(MyriadOutputInnerTypeToWomFiles).apply(evalFunction)).map(_.toSet.flatten)
-  }
-}
-
-object MyriadOutputInnerTypeToWomFiles extends Poly1 {
-
-  import Case._
-
-  def ex(component: String) = throw new RuntimeException(s"output type $component cannot yield wom files")
-
-  implicit def cwlType: Aux[CwlType, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[CwlType] { _ =>_ =>
-    Set.empty[FileEvaluation].validIOChecked
-  }
-
-  implicit def ors: Aux[OutputRecordSchema, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[OutputRecordSchema] {
-    case OutputRecordSchema(_, Some(fields), _) =>
-      evalFunction =>
-        fields.toList.traverse[IOChecked, Set[FileEvaluation]]({ field =>
-          field.outputBinding match {
-            case Some(binding) => evalFunction(binding)
-            case None => field.`type`.fold(MyriadOutputTypeToWomFiles).apply(evalFunction)
-          }
-        }).map(_.toSet.flatten)
-    case ors => ors.toString |> ex
-  }
-
-  implicit def oes: Aux[OutputEnumSchema, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[OutputEnumSchema]{ oes =>_ =>
-    oes.toString |> ex
-  }
-
-  implicit def oas: Aux[OutputArraySchema, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[OutputArraySchema]{ oas =>
-    evalFunction =>
-      import cats.syntax.apply._
-      def fromBinding: IOChecked[Set[FileEvaluation]] = oas.outputBinding.map(evalFunction).getOrElse(Set.empty[FileEvaluation].validIOChecked)
-      def fromType: IOChecked[Set[FileEvaluation]] = oas.items.fold(MyriadOutputTypeToWomFiles).apply(evalFunction)
-
-      (fromBinding, fromType) mapN (_ ++ _)
-  }
-
-  implicit def s: Aux[String, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[String]{ _ =>_ =>
-    Set.empty[FileEvaluation].validIOChecked
-  }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomType.scala b/cwl/src/main/scala/cwl/MyriadOutputTypeToWomType.scala
deleted file mode 100644
index 61107143006..00000000000
--- a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomType.scala
+++ /dev/null
@@ -1,105 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cwl.CwlType.CwlType
-import cwl.command.ParentName
-import mouse.all._
-import shapeless.Poly1
-import wom.types._
-
-object MyriadOutputInnerTypeToString extends Poly1 {
-
-  implicit def cwlType = at[CwlType] {
-    _.toString
-  }
-
-  implicit def ors = at[OutputRecordSchema] {
-    _.toString
-  }
-
-  implicit def oes = at[OutputEnumSchema] {
-    _.toString
-  }
-
-  implicit def oas = at[OutputArraySchema] {
-    _.toString
-  }
-
-  implicit def s = at[String] {
-    identity
-  }
-}
-
-object MyriadOutputTypeToWomType extends Poly1{
-
-  import Case._
-
-  type SchemaDefToWomType = SchemaDefRequirement => WomType
-
-  implicit def cwlType: Aux[MyriadOutputInnerType, SchemaDefToWomType] = at[MyriadOutputInnerType]{ moit => schemaDefRequirement =>
-    moit.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement)
-  }
-
-  implicit def acwl: Aux[Array[MyriadOutputInnerType], SchemaDefToWomType] = at[Array[MyriadOutputInnerType]] { types => schemaDefRequirement =>
-    types.partition(_.select[CwlType].contains(CwlType.Null)) match {
-      // If there's a single non null type, use that
-      case (Array(), Array(singleNonNullType)) =>
-        singleNonNullType.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement)
-      case (Array(), array: Array[MyriadOutputInnerType]) if array.size > 1  =>
-        val types = array.map(_.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement))
-        WomCoproductType(NonEmptyList.fromListUnsafe(types.toList))
-      // If there's a null type and a single non null type, it's a WomOptionalType
-      case (Array(_), Array(singleNonNullType)) =>
-        WomOptionalType(singleNonNullType.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement))
-      case (Array(_), array: Array[MyriadOutputInnerType]) if array.size > 1  =>
-        val types = array.map(_.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement))
-        WomOptionalType(WomCoproductType(NonEmptyList.fromListUnsafe(types.toList)))
-      case _ =>
-        val readableTypes = types.map(_.fold(MyriadOutputInnerTypeToString)).mkString(", ")
-        throw new UnsupportedOperationException(s"Cromwell only supports single types or optionals (as indicated by [null, X]). Instead we saw: $readableTypes")
-    }
-  }
-}
-
-object MyriadOutputInnerTypeToWomType extends Poly1 {
-
-  import Case._
-  import MyriadOutputTypeToWomType.SchemaDefToWomType
-
-  implicit def cwlType: Aux[CwlType, SchemaDefToWomType] =
-    at[CwlType]{
-      cwl.cwlTypeToWomType andThen Function.const
-    }
-
-  implicit def ors: Aux[OutputRecordSchema, SchemaDefToWomType] = at[OutputRecordSchema] {
-    ors => schemaDefRequirement =>
-      ors.fields.fold(
-        WomCompositeType(Map.empty))(
-        {fields =>
-          val typeMap = fields.map({ field =>
-            val parsedName = FullyQualifiedName(field.name)(ParentName.empty).id
-            parsedName -> field.`type`.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-          }).toMap
-          WomCompositeType(typeMap)
-        }
-      )
-  }
-
-  implicit def oes: Aux[OutputEnumSchema, MyriadOutputTypeToWomType.SchemaDefToWomType] =
-    at[OutputEnumSchema] {
-      oes => oes.toWomEnumerationType |> Function.const
-    }
-
-  implicit def oas: Aux[OutputArraySchema, MyriadOutputTypeToWomType.SchemaDefToWomType] =
-    at[OutputArraySchema] {
-      oas => schemaDefRequirement =>
-        val arrayType: WomType = oas.items.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-        WomArrayType(arrayType)
-    }
-
-  implicit def s: Aux[String, MyriadOutputTypeToWomType.SchemaDefToWomType] =
-    at[String] {
-      string => schemaReq =>
-        schemaReq.lookupType(string).getOrElse(throw new RuntimeException(s"Custom type $string was referred to but not found in schema def ${schemaReq.types.mkString(", ")}."))
-    }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomValue.scala b/cwl/src/main/scala/cwl/MyriadOutputTypeToWomValue.scala
deleted file mode 100644
index 332e4ab3888..00000000000
--- a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomValue.scala
+++ /dev/null
@@ -1,100 +0,0 @@
-package cwl
-
-import cats.data.Validated.Valid
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.validation.IOChecked.IOChecked
-import common.validation.IOChecked._
-import cwl.CwlType.CwlType
-import cwl.command.ParentName
-import mouse.all._
-import shapeless.Poly1
-import wom.types._
-import wom.values.{WomObject, WomValue}
-
-/**
-  * Folds a MyriadOutputType into a WomValue
-  * This is needed because the type might define the structure of the final output value (for OutputRecordSchemas for example)
-  */
-object MyriadOutputTypeToWomValue extends Poly1 {
-
-  // We pass in a function that can evaluate a CommandOutputBinding and produce a WomValue. This allows us to recurse into the
-  // MyriadOutputTypes and evaluate values as we do.
-  type EvaluationFunction = (CommandOutputBinding, WomType) => IOChecked[WomValue]
-
-  //Our overall return type gives us the evaluator function and custom types; returns WomValues
-  type Output = (EvaluationFunction, SchemaDefRequirement) => IOChecked[WomValue]
-
-  import Case._
-
-  implicit def cwlType: Aux[MyriadOutputInnerType, Output] = at[MyriadOutputInnerType]{
-    moit => (evalFunction, schemaDefRequirement) => moit.fold(MyriadOutputInnerTypeToWomValue).apply(evalFunction, schemaDefRequirement)
-  }
-
-  // TODO: Not sure what the right thing to do is here, for now go over the list of types and use the first evaluation that yields success
-  implicit def acwl: Aux[Array[MyriadOutputInnerType], Output] = at[Array[MyriadOutputInnerType]] { types =>
-    (evalFunction,schemaDefRequirement) =>
-      types.toList.map(_.fold(MyriadOutputInnerTypeToWomValue).apply(evalFunction, schemaDefRequirement)).map(_.toErrorOr).collectFirst({
-        case Valid(validValue) => validValue
-      }).toValidNel(s"Cannot find a suitable type to build a WomValue from in ${types.mkString(", ")}").toIOChecked
-  }
-}
-
-object MyriadOutputInnerTypeToWomValue extends Poly1 {
-
-  import Case._
-  import MyriadOutputTypeToWomValue.Output
-
-  def ex(component: String) = throw new RuntimeException(s"output type $component cannot yield a wom value")
-
-  implicit def cwlType: Aux[CwlType, Output] = at[CwlType] { _ => (_,_) =>
-    "No output binding is defined. Are you expecting the output to be inferred from a cwl.output.json file ? If so please make sure the file was effectively created.".invalidIOChecked
-  }
-
-  implicit def ors: Aux[OutputRecordSchema, Output] = at[OutputRecordSchema] { ors => (evalFunction, schemaDefRequirement) => ors match {
-    case OutputRecordSchema(_, Some(fields), _) =>
-        // Go over each field and evaluate the binding if there's one, otherwise keep folding over field types
-        def evaluateValues = fields.toList.traverse[IOChecked, ((String, WomValue), (String, WomType))]({ field =>
-          val womType = field.`type`.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-          val womValue: IOChecked[WomValue] = field.outputBinding match {
-            case Some(binding) => evalFunction(binding, womType)
-            case None => field.`type`.fold(MyriadOutputTypeToWomValue).apply(evalFunction, schemaDefRequirement)
-          }
-
-          // TODO: ParentName might need to be passed in here ?
-          // return the value and the type with a clean parsedName
-          womValue map { value =>
-            val parsedName = FullyQualifiedName(field.name)(ParentName.empty).id
-            (parsedName -> value) -> (parsedName -> womType)
-          }
-        })
-
-        evaluateValues map { evaluatedValues =>
-          val (valueMap, typeMap) = evaluatedValues.unzip
-          // Create a typed WomObject from the values and the typeMap
-          WomObject.withTypeUnsafe(valueMap.toMap, WomCompositeType(typeMap.toMap))
-        }
-    case ors => ors.toString |> ex
-  }}
-
-  implicit def oes: Aux[OutputEnumSchema, Output] = at[OutputEnumSchema]{
-    //DB: I tried to do a pattern match as the overall function here but the compiler exploded
-    oes => (f, schemaDefRequirement) => oes match {
-      case oes@OutputEnumSchema(_, _, _, _, Some(outputBinding)) => f(outputBinding, oes.toWomEnumerationType)
-      case _ => s"The enumeration type $oes requires an outputbinding to be evaluated.".invalidIOChecked
-    }
-  }
-
-  implicit def oas: Aux[OutputArraySchema, Output] = at[OutputArraySchema]{ oas => (evalFunction, schemaDefRequirement) => oas match {
-    case OutputArraySchema(itemsType, _, _, outputBinding) =>
-      lazy val itemsWomType = itemsType.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-      def fromBinding = outputBinding.map(evalFunction(_, WomArrayType(itemsWomType)))
-      def fromTypes = itemsType.fold(MyriadOutputTypeToWomValue).apply(evalFunction, schemaDefRequirement)
-      fromBinding.getOrElse(fromTypes)
-  }}
-
-  implicit def s: Aux[String, Output] = at[String]{ s => (_, _) =>
-    s.toString |> ex
-  }
-}
diff --git a/cwl/src/main/scala/cwl/OutputParameter.scala b/cwl/src/main/scala/cwl/OutputParameter.scala
deleted file mode 100644
index 274469da7ee..00000000000
--- a/cwl/src/main/scala/cwl/OutputParameter.scala
+++ /dev/null
@@ -1,62 +0,0 @@
-package cwl
-
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.option._
-import common.validation.ErrorOr._
-import shapeless.{:+:, CNil, Poly1}
-import wom.values.{WomString, WomValue}
-
-trait OutputParameter {
-  def id: String
-  def label: Option[String]
-  def secondaryFiles: Option[SecondaryFiles]
-  def format: Option[OutputParameterFormat]
-  def streamable: Option[Boolean]
-  def doc: Option[String :+: Array[String] :+: CNil]
-  def outputBinding: Option[CommandOutputBinding]
-  def `type`: Option[MyriadOutputType]
-  def cacheString: String = toString
-}
-
-object OutputParameter {
-  object IdAndType {
-    def unapply(arg: OutputParameter): Option[(String, MyriadOutputType)] = arg.`type`.map((arg.id, _))
-  }
-
-  def format(formatOption: Option[StringOrExpression],
-             parameterContext: ParameterContext,
-             expressionLib: ExpressionLib): ErrorOr[Option[String]] = {
-    formatOption.traverse{
-      format(_, parameterContext, expressionLib)
-    }
-  }
-
-  def format(format: StringOrExpression, parameterContext: ParameterContext, expressionLib: ExpressionLib): ErrorOr[String] = {
-    format.fold(OutputParameter.FormatPoly).apply(parameterContext, expressionLib)
-  }
-
-  type FormatFunction = (ParameterContext, ExpressionLib) => ErrorOr[String]
-
-  object FormatPoly extends Poly1 {
-    implicit def caseStringOrExpression: Case.Aux[StringOrExpression, FormatFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseExpression: Case.Aux[Expression, FormatFunction] = {
-      at {
-        expression =>
-          (parameterContext, expressionLib) =>
-            val result: ErrorOr[WomValue] = ExpressionEvaluator.eval(expression, parameterContext)
-            result flatMap {
-              case womString: WomString => womString.value.valid
-              case other => s"Not a valid file format: $other".invalidNel
-            }
-      }
-    }
-
-    implicit def caseString: Case.Aux[String, FormatFunction] = at { string => (_,_) => string.valid }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/OutputParameterExpression.scala b/cwl/src/main/scala/cwl/OutputParameterExpression.scala
deleted file mode 100644
index b044bc36077..00000000000
--- a/cwl/src/main/scala/cwl/OutputParameterExpression.scala
+++ /dev/null
@@ -1,115 +0,0 @@
-package cwl
-
-import common.validation.ErrorOr.ErrorOr
-import common.validation.IOChecked.{IOChecked, _}
-import cwl.CwlType.CwlType
-import shapeless.Poly1
-import wom.expression.{EmptyIoFunctionSet, FileEvaluation, IoFunctionSet}
-import wom.types._
-import wom.values.WomValue
-
-import scala.Function.const
-import scala.concurrent.{ExecutionContext, Future}
-
-case class OutputParameterExpression(parameter: OutputParameter,
-                                     override val cwlExpressionType: WomType,
-                                     override val inputs: Set[String],
-                                     override val expressionLib: ExpressionLib,
-                                     schemaDefRequirement: SchemaDefRequirement) extends CwlWomExpression {
-
-  override def sourceString = parameter.toString
-
-  override def cacheString: String = parameter.cacheString
-
-  private def evaluateOutputBinding(inputValues: Map[String, WomValue],
-                                    ioFunctionSet: IoFunctionSet,
-                                    secondaryFilesOption: Option[SecondaryFiles],
-                                    formatOption: Option[StringOrExpression]
-                                   )(outputBinding: CommandOutputBinding,
-                                    cwlExpressionType: WomType): IOChecked[WomValue] = {
-    CommandOutputBinding.generateOutputWomValue(
-      inputValues,
-      ioFunctionSet,
-      cwlExpressionType,
-      outputBinding,
-      secondaryFilesOption,
-      formatOption,
-      expressionLib
-    )
-  }
-
-  private def evaluateOutputBindingFiles(inputValues: Map[String, WomValue],
-                                    ioFunctionSet: IoFunctionSet,
-                                    secondaryFilesOption: Option[SecondaryFiles],
-                                    coerceTo: WomType
-                                   )(outputBinding: CommandOutputBinding): IOChecked[Set[FileEvaluation]] = {
-    CommandOutputBinding.getOutputWomFiles(
-      inputValues,
-      coerceTo,
-      outputBinding,
-      secondaryFilesOption,
-      ioFunctionSet,
-      expressionLib
-    )
-  }
-  
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
-    def fromOutputBinding =
-      parameter.outputBinding.map(evaluateOutputBinding(inputValues, ioFunctionSet, parameter.secondaryFiles, parameter.format)(_, cwlExpressionType))
-
-    def fromType =
-      parameter.`type`.map(_.fold(MyriadOutputTypeToWomValue).apply(
-        evaluateOutputBinding(inputValues, ioFunctionSet, parameter.secondaryFiles, parameter.format),
-        schemaDefRequirement
-      ))
-
-    fromOutputBinding.orElse(fromType).getOrElse(s"Cannot evaluate ${parameter.toString}".invalidIOChecked).toErrorOr
-  }
-
-  /**
-    * Returns the list of files that _will be_ output after the command is run, unless they are optional and if so _may be_.
-    *
-    * In CWL, a list of outputs is specified as glob, say `*.bam`, plus a list of secondary files that may be in the
-    * form of paths or specified using carets such as `^.bai`.
-    *
-    * The coerceTo may be one of four different values:
-    * - WomMaybePopulatedFileType
-    * - WomArrayType(WomMaybePopulatedFileType)
-    * - WomMaybeListedDirectoryType
-    * - WomArrayType(WomMaybeListedDirectoryType) (Possible according to the way the spec is written, but not likely?)
-    */
-  override def evaluateFiles(inputs: Map[String, WomValue], unused: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
-    import cats.syntax.apply._
-
-    // Ignore the supplied ioFunctionSet and use a custom stubbed IoFunctionSet. This is better than a real I/O function set
-    // because in the context of file evaluation we don't care about the results of these operations. The NoIoFunctionSet
-    // that otherwise would be used throws for all of its operations which doesn't fly for the way our CWL evaluation works.
-    val stubbedIoFunctionSet = new EmptyIoFunctionSet {
-      override def size(path: String): Future[Long] = Future.successful(0L)
-      override def isDirectory(path: String): Future[Boolean] = Future.successful(false)
-      override def ec: ExecutionContext = scala.concurrent.ExecutionContext.global
-    }
-    def fromOutputBinding: IOChecked[Set[FileEvaluation]] = parameter
-      .outputBinding
-      .map(evaluateOutputBindingFiles(inputs, stubbedIoFunctionSet, parameter.secondaryFiles, coerceTo))
-      .getOrElse(Set.empty[FileEvaluation].validIOChecked)
-
-    def fromType: IOChecked[Set[FileEvaluation]] = parameter
-      .`type`
-      .map(_.fold(MyriadOutputTypeToWomFiles).apply(evaluateOutputBindingFiles(inputs, stubbedIoFunctionSet, parameter.secondaryFiles, coerceTo)))
-      .getOrElse(Set.empty[FileEvaluation].validIOChecked)
-
-    val optional: Boolean = parameter.`type`.exists(_.fold(OutputTypeIsOptional))
-
-    ((fromOutputBinding, fromType) mapN (_ ++ _) map { _ map { _.copy(optional = optional) } }).toErrorOr
-  }
-}
-
-object OutputTypeIsOptional extends Poly1 {
-  implicit val one: Case.Aux[MyriadOutputInnerType, Boolean] = at[MyriadOutputInnerType] { const(false) }
-
-  implicit val arr: Case.Aux[Array[MyriadOutputInnerType], Boolean] = at[Array[MyriadOutputInnerType]] {
-    // Possibly too broad, would return true for just single 'null'.
-    _.exists(_.select[CwlType].contains(CwlType.Null))
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ParameterContext.scala b/cwl/src/main/scala/cwl/ParameterContext.scala
deleted file mode 100644
index 4bcb4d132d5..00000000000
--- a/cwl/src/main/scala/cwl/ParameterContext.scala
+++ /dev/null
@@ -1,17 +0,0 @@
-package cwl
-
-import wom.callable.RuntimeEnvironment
-import wom.expression.IoFunctionSet
-import wom.types.WomNothingType
-import wom.values.{WomOptionalValue, WomValue}
-
-object ParameterContext {
-  val EmptySelf = WomOptionalValue(WomNothingType, None)
-}
-
-case class ParameterContext(
-                            ioFunctionSet: IoFunctionSet,
-                            expressionLib: ExpressionLib,
-                            inputs: Map[String, WomValue] = Map.empty,
-                            self: WomValue = ParameterContext.EmptySelf,
-                            runtimeOption: Option[RuntimeEnvironment] = None)
diff --git a/cwl/src/main/scala/cwl/RequirementsAndHints.scala b/cwl/src/main/scala/cwl/RequirementsAndHints.scala
deleted file mode 100644
index 46b5c52e410..00000000000
--- a/cwl/src/main/scala/cwl/RequirementsAndHints.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cwl
-
-case class RequirementsAndHints(list: List[Requirement]) {
-
-  lazy val hasShellCommandRequirement: Boolean = list.exists(_.select[ShellCommandRequirement].nonEmpty)
-
-  //Should we add up all the types instead?  This would mean subworkflows can inherit their parent schemas
-  lazy val schemaDefRequirement = list.flatMap(_.select[SchemaDefRequirement]).headOption.getOrElse(SchemaDefRequirement())
-}
diff --git a/cwl/src/main/scala/cwl/RunOutputsToTypeMap.scala b/cwl/src/main/scala/cwl/RunOutputsToTypeMap.scala
deleted file mode 100644
index f327b5b03ea..00000000000
--- a/cwl/src/main/scala/cwl/RunOutputsToTypeMap.scala
+++ /dev/null
@@ -1,45 +0,0 @@
-package cwl
-
-import shapeless.Poly1
-import wom.types.WomType
-
-object RunOutputsToTypeMap extends Poly1 {
-
-  import Case.Aux
-
-  type SchemaDefToTypeMap = SchemaDefRequirement => WomTypeMap
-
-  def handleOutputParameters[A <: OutputParameter](outputs: Array[A], schemaDefRequirement: SchemaDefRequirement): Map[String, WomType] = {
-    outputs.toList.foldLeft(Map.empty[String, WomType]) {
-      (acc, out) =>
-        acc ++
-          out.
-            `type`.
-            map(_.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)).
-            map(out.id -> _).
-            toList.
-            toMap
-    }
-  }
-
-  implicit def commandLineTool : Aux[CommandLineTool, SchemaDefToTypeMap] =
-    at[CommandLineTool] {
-      clt => handleOutputParameters(clt.outputs, _)
-    }
-
-  implicit def string: Aux[String, SchemaDefToTypeMap] = at[String] {
-    _ => _ =>
-      Map.empty[String, WomType] //should never happen because we dereference/embed CWL subworkflows into one object from the original string references
-  }
-
-  implicit def expressionTool: Aux[ExpressionTool, SchemaDefToTypeMap] = at[ExpressionTool] {
-    et =>
-      handleOutputParameters(et.outputs, _)
-  }
-
-  implicit def workflow: Aux[Workflow, SchemaDefToTypeMap] = at[Workflow] {
-    wf =>
-      handleOutputParameters(wf.outputs, _)
-  }
-}
-
diff --git a/cwl/src/main/scala/cwl/RunToEmbeddedCwl.scala b/cwl/src/main/scala/cwl/RunToEmbeddedCwl.scala
deleted file mode 100644
index 2547b6333a4..00000000000
--- a/cwl/src/main/scala/cwl/RunToEmbeddedCwl.scala
+++ /dev/null
@@ -1,36 +0,0 @@
-package cwl
-
-import shapeless._
-import WorkflowStep.Run
-
-object RunToEmbeddedCwl extends Poly1 {
-  implicit def commandLineTool =
-    at[CommandLineTool] {
-      clt =>
-        (_: Map[String, Cwl]) =>
-         Coproduct[Run](clt)
-    }
-
-  implicit def string = at[String] {
-    fileName =>
-      (cwlMap: Map[String, Cwl]) => {
-        val cwl = cwlMap(fileName)
-        cwl.fold(CwlToRun)
-      }
-  }
-
-
-  implicit def expressionTool = at[ExpressionTool] {
-    et =>
-      (_: Map[String, Cwl]) =>
-        Coproduct[Run](et)
-  }
-
-  implicit def workflow = at[Workflow] {
-    wf =>
-      (_: Map[String, Cwl]) =>
-        Coproduct[Run](wf)
-  }
-}
-
-
diff --git a/cwl/src/main/scala/cwl/RunToInputTypeMap.scala b/cwl/src/main/scala/cwl/RunToInputTypeMap.scala
deleted file mode 100644
index 7111e389050..00000000000
--- a/cwl/src/main/scala/cwl/RunToInputTypeMap.scala
+++ /dev/null
@@ -1,37 +0,0 @@
-package cwl
-
-import cwl.command.ParentName
-import shapeless.Poly1
-
-object RunToInputTypeMap extends Poly1 {
-
-  type MyriadInputTypeMap = Map[String, Option[MyriadInputType]]
-
-  type OutputType = ParentName => MyriadInputTypeMap
-
-  import Case.Aux
-
-  implicit def s: Aux[String, OutputType] =
-    at[String] {
-      run =>  _ => throw new RuntimeException(s"Run field $run was not inlined as expected")
-    }
-
-  implicit def clt: Aux[CommandLineTool, OutputType] =
-    at[CommandLineTool]{clt => parentName => clt.inputs.map{
-      input =>
-          FullyQualifiedName(input.id)(parentName).id -> input.`type`
-    }.toMap}
-
-  implicit def et: Aux[ExpressionTool, OutputType] =
-    at[ExpressionTool]{et => parentName => et.inputs.map{
-      input =>
-        FullyQualifiedName(input.id)(parentName).id -> input.`type`
-    }.toMap}
-
-  implicit def wf: Aux[Workflow, OutputType] =
-    at[Workflow]{ wf => parentName => wf.inputs.map{
-      input =>
-        FullyQualifiedName(input.id)(parentName).id -> input.`type`
-    }.toMap}
-
-}
diff --git a/cwl/src/main/scala/cwl/ScatterLogic.scala b/cwl/src/main/scala/cwl/ScatterLogic.scala
deleted file mode 100644
index 97d87daf6df..00000000000
--- a/cwl/src/main/scala/cwl/ScatterLogic.scala
+++ /dev/null
@@ -1,263 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.instances.list._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import cwl.ScatterMethod.ScatterMethod
-import shapeless.Poly1
-import wom.graph.CallNode.CallNodeAndNewNodes
-import wom.graph.GraphNodePort.ScatterGathererPort
-import wom.graph.ScatterNode._
-import wom.graph._
-import wom.graph.expression.ExpressionNode
-import wom.types.{WomArrayType, WomMaybeEmptyArrayType, WomType}
-import wom.values.{WomArray, WomValue}
-
-import scala.annotation.tailrec
-
-/**
-  * Contains methods used to implement the scatter related logic for CWL workflows.
-  * The general idea is as follows:
-  *
-  * See WorkflowStep for an example of WOM graph for scatters.
-  * 
-  * # Scattering over multiple variables
-  *
-  * When several variables are being scattered over, a scatter method is mandatory to specify how the elements must be combined.
-  * Let's use the following 2 arrays as an example:
-  *
-  * a1: ["one", "two"], a2: ["three", "four"]
-  *
-  * * DotProduct:
-  * DotProduct only works if all the arrays have the same length.
-  *
-  * Shard 0: "one" - "three"
-  * Shard 1: "two" - "four"
-  *
-  * * CrossProduct (nested or flat):
-  * Both cross product methods generate the same shards, the difference is in how they are collected at the end
-  *
-  * Shard 0: "one" - "three"
-  * Shard 1: "one" - "four"
-  * Shard 2: "two" - "three"
-  * Shard 3: "two" - "four"
-  *
-  * To support this, each SVN will have a method which given a shard index will return the index at which the value should be looked up in the array.
-  *
-  * For dot product, this function is the same for all SVN and will be the identity[Int] function.
-  * For cross product, this function depends on the number of elements in each array, which is known at runtime.
-  *   When we do have this information we update each SVN with it in the ScatterProcessingFunction and returns the number of shards to be generated.
-  */
-object ScatterLogic {
-  case class ScatterFunctions(processing: ScatterProcessingFunction, collection: ScatterCollectionFunctionBuilder)
-
-  object ScatterVariablesPoly extends Poly1 {
-    implicit def fromString: Case.Aux[String, List[String]] = at[String] { s: String => List(s) }
-    implicit def fromStringList: Case.Aux[Array[String], List[String]] = at[Array[String]] { l: Array[String] => l.toList }
-  }
-
-  // Validate that the scatter expression is an ArrayLike and return the member type
-  private [cwl] def scatterExpressionItemType(expressionNode: ExpressionNode) = {
-    expressionNode.womType match {
-      case WomArrayType(itemType) => itemType.validNelCheck // Covers maps because this is a custom unapply (see WomArrayType)
-      case other => s"Cannot scatter over a non-traversable type ${other.stableName}".invalidNelCheck
-    }
-  }
-
-  def scatterGatherPortTypeFunction(scatterMethod: Option[ScatterMethod], scatterVariables: NonEmptyList[_]): WomType => WomArrayType = scatterMethod match {
-    case Some(ScatterMethod.NestedCrossProduct) =>
-      innerType: WomType =>
-        scatterVariables.tail.foldLeft(WomArrayType(innerType))({ case (t, _) => WomArrayType(t) })
-    case _ => innerType: WomType => WomArrayType(innerType)
-  }
-
-  // Build a map (potentially empty) of scatterered input steps with their corresponding SVN node.
-  def buildScatterVariableNodes(scatter: ScatterVariables, stepInputMappings: Map[WorkflowStepInput, ExpressionNode], stepId: String): Checked[Map[WorkflowStepInput, ScatterVariableNode]] = {
-    import cats.syntax.all._
-
-    def buildScatterVariable(scatterVariableName: String): ErrorOr[(WorkflowStepInput, ScatterVariableNode)] = {
-      // Assume the variable is a step input (is that always true ??). Find the corresponding expression node
-
-      stepInputMappings.find({ case (stepInput, _) => stepInput.id == scatterVariableName }) match {
-        case Some((stepInput, expressionNode)) =>
-          scatterExpressionItemType(expressionNode).toValidated map { itemType =>
-            // create a scatter variable node for other scattered nodes to point to
-            stepInput -> ScatterVariableNode(WomIdentifier(scatterVariableName), expressionNode, itemType)
-          }
-        case None => s"Could not find a variable $scatterVariableName in the workflow step input to scatter over. Please make sure $scatterVariableName is an input of step $stepId".invalidNel
-      }
-    }
-    // Take the scatter field defining the (list of) input(s) to be scattered over
-    scatter
-      // Fold them so we have a List[String] no matter what (a single scattered input becomes a single element list)
-      .map(_.fold(ScatterVariablesPoly))
-      // If there's no scatter make it an empty list
-      .getOrElse(List.empty)
-      // Traverse the list to create ScatterVariableNodes that will be used later on to create the ScatterNode
-      .traverse(buildScatterVariable)
-      .toEither
-      .map(_.toMap)
-  }
-
-  // Prepare the nodes to be returned if this call is being scattered
-  def buildScatterNode(callNodeAndNewNodes: CallNodeAndNewNodes,
-                       scatterVariableNodes: NonEmptyList[ScatterVariableNode],
-                       ogins: Set[OuterGraphInputNode],
-                       stepExpressionNodes: Set[ExpressionNode],
-                       scatterMethod: Option[ScatterMethod]): Checked[ScatterNode] = {
-
-    val scatterProcessingFunctionCheck = (scatterVariableNodes.size, scatterMethod) match {
-      // If we scatter over one variable only, the default processing method can handle it
-      case (1, _) => ScatterFunctions(ScatterNode.DefaultScatterProcessingFunction, ScatterNode.DefaultScatterCollectionFunctionBuilder).validNelCheck
-      case (_, Some(method)) => ScatterFunctions(processingFunction(method), collectingFunctionBuilder(method)).validNelCheck
-      case (_, None) => "When scattering over multiple variables, a scatter method needs to be defined. See http://www.commonwl.org/v1.0/Workflow.html#WorkflowStep".invalidNelCheck
-    }
-
-    val callNode = callNodeAndNewNodes.node
-
-    // We need to generate PBGONs for every output port of the call, so that they can be linked outside the scatter graph
-    val portBasedGraphOutputNodes = callNode.outputPorts.map(op => PortBasedGraphOutputNode(op.identifier, op.womType, op))
-
-    def buildScatterNode(innerGraph: Graph, scatterFunctions: ScatterFunctions) = {
-      val scatterNodeBuilder = new ScatterNodeBuilder
-      val outputPorts: Set[ScatterGathererPort] = innerGraph.nodes.collect { case gon: PortBasedGraphOutputNode =>
-        scatterNodeBuilder.makeOutputPort(scatterGatherPortTypeFunction(scatterMethod, scatterVariableNodes)(gon.womType), gon)
-      }
-
-      scatterNodeBuilder.build(innerGraph, outputPorts, scatterVariableNodes.toList, scatterFunctions.processing, scatterFunctions.collection)
-    }
-    
-    for {
-      scatterProcessingFunctionAndBuilder <- scatterProcessingFunctionCheck
-      graph <- Graph.validateAndConstruct(
-        Set(callNodeAndNewNodes.node) ++
-          ogins ++
-          stepExpressionNodes ++
-          scatterVariableNodes.toList ++
-          portBasedGraphOutputNodes
-      ).toEither
-      scatterNode = buildScatterNode(graph, scatterProcessingFunctionAndBuilder)
-    } yield scatterNode.node
-  }
-
-  /*
-   * Processing function for cross products. Logic is as follows:
-   * We want 1) know how many shards should be created (which this function will return)
-   *         2) update each SVN with their relative index length (see ScatterVariableNode for more detail)
-   *         
-   * We are going to multiply all the array sizes (which will give us 1) at the end)
-   * Along the way we will update the relative index length for each SVN.
-   * To do so, we start at the end of the list and recurse.
-   */
-  private [cwl] val CrossProductScatterProcessingFunction: ScatterProcessingFunction = { nodesAndValues: List[ScatterVariableAndValue] =>
-    @tailrec
-    def updateIndexLengthRec(currentList: List[ScatterVariableAndValue], combinedArraySize: Int): Int = currentList match {
-      case Nil => combinedArraySize
-      case ScatterVariableAndValue(variableNode, arrayValue) :: tail =>
-        variableNode.withRelativeIndexLength(combinedArraySize)
-        updateIndexLengthRec(tail, combinedArraySize * arrayValue.size)
-    }
-
-    // Reverse the list so that we start from the last variable and make our way back to the first one
-    updateIndexLengthRec(nodesAndValues.reverse, 1).validNelCheck
-  }
-
-  private [cwl] val DotProductScatterProcessingFunction: ScatterProcessingFunction = ScatterNode.DefaultScatterProcessingFunction
-
-  // Recursively nest shard results appropriately based on the size of the scatter variable arrays
-  private [cwl] val NestedCrossProductScatterCollectionFunctionBuilder: ScatterCollectionFunctionBuilder = { arraySizes: List[Int] =>
-    (sortedShards: List[WomValue], valueType: WomArrayType) =>
-
-      @tailrec
-      def buildCollectorArrayRec(currentList: List[Int], currentWomValues: List[WomValue], currentWomType: WomType): WomArray = {
-        /*  We stop right before the last element because it will necessarily be the number of elements in currentWomValues (provided the list is non empty).
-          * e.g if currentList is (2, 3, 2), then currentWomValues will have 2 * 3 * 2 = 12 elements (this is a cross product)
-          * As we recurse, we keep grouping currentWomValues by the numbers in currentList:
-          * 
-          * group by 2: [[_, _], [_, _], [_, _], [_, _], [_, _], [_, _]]
-          * group by 3: [
-          *   [[_, _], [_, _], [_, _]],
-          *   [[_, _], [_, _], [_, _]]
-          * ]
-          * This list has necessarily 2 elements already because 12 / 2 / 3 = 2. So we can make the final WomArray out of that
-        */
-        currentList match {
-          case _ :: Nil | Nil =>
-            WomArray(WomMaybeEmptyArrayType(currentWomType), currentWomValues)
-          case head :: tail =>
-            val arrayType = WomMaybeEmptyArrayType(currentWomType)
-            val womArrays = currentWomValues.grouped(head).toList map { WomArray(arrayType, _) }
-            buildCollectorArrayRec(tail, womArrays, arrayType)
-        }
-      }
-
-      def mostInnerType(tpe: WomType): WomType = tpe match {
-        case WomArrayType(t) => mostInnerType(t)
-        case other => other
-      }
-
-      def buildEmptyArrays(arraySizeList: List[Int], womType: WomType, womValues: List[WomValue]): WomArray = arraySizeList match {
-        case Nil => womType match {
-          case arrayType: WomArrayType => WomArray(arrayType, womValues)
-          case _ =>
-            // This would mean arraySizeList was empty to begin with (otherwise we would have wrapped womType in a WomArrayType at least once)
-            // which should be impossible since it would mean there was no scatter variables, so we shouldn't even be here
-            throw new RuntimeException("Programmer error ! We should not be collecting scatter nodes if there was no scatter !")
-        }
-        case 0 :: tail =>
-          buildEmptyArrays(tail, WomArrayType(womType), List.empty)
-        case head :: tail =>
-          val arrayType = womType match {
-            case array: WomArrayType => array
-            case nonArray => WomArrayType(nonArray)
-          }
-          val womArrays = (0 until head).toList map { _ => WomArray(arrayType, womValues) }
-          buildEmptyArrays(tail, WomArrayType(womType), womArrays)
-      }
-
-      /*
-       * There are 2 distinct cases.
-       * If we have no shards, it means that at least one of the scatter expressions evaluated to an empty array.
-       * In that case we want to create an array structure of empty arrays reflecting the scatter array sizes.
-       * e.g:
-       * 
-       * scatter array sizes   |   collected result
-       *        [0]                       []
-       *       [0, 2]                     [] 
-       *       [2, 0]                   [[], []]
-       *      [2, 0, 3]                 [[], []]
-       *      [2, 3, 0]                [[[], [], []], [[], [], []]] 
-       *
-       * Note that as soon as we reach a size 0, we return an empty array.
-       * 
-       * If we have shards, we successively group the shards list to build arrays of the right size.
-       * 
-       * In both cases we reverse the list so that we can left recurse while still building the result starting from the most nested arrays
-       */
-      if (sortedShards.isEmpty) {
-        buildEmptyArrays(arraySizes.reverse, mostInnerType(valueType), List.empty)
-      } else {
-        // 
-        buildCollectorArrayRec(arraySizes.reverse, sortedShards, mostInnerType(valueType))
-      }
-  }
-
-  // select a processing function based on the scatter method
-  private def processingFunction(scatterMethod: ScatterMethod) = scatterMethod match {
-    case ScatterMethod.DotProduct => DotProductScatterProcessingFunction
-    // Both cross product methods use the same processing function, the difference is in how we collect results (see collectingFunctionBuilder)
-    case ScatterMethod.FlatCrossProduct => CrossProductScatterProcessingFunction
-    case ScatterMethod.NestedCrossProduct => CrossProductScatterProcessingFunction
-  }
-
-  // select a collecting function builder based on the scatter method
-  private def collectingFunctionBuilder(scatterMethod: ScatterMethod) = scatterMethod match {
-    // dot product and flat cross product output a flat array, which is the default behavior
-    case ScatterMethod.DotProduct => ScatterNode.DefaultScatterCollectionFunctionBuilder
-    case ScatterMethod.FlatCrossProduct => ScatterNode.DefaultScatterCollectionFunctionBuilder
-    // nested cross product uses a special collecting function to build nested arrays
-    case ScatterMethod.NestedCrossProduct => NestedCrossProductScatterCollectionFunctionBuilder
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ScatterMethod.scala b/cwl/src/main/scala/cwl/ScatterMethod.scala
deleted file mode 100644
index 0a60575e0cb..00000000000
--- a/cwl/src/main/scala/cwl/ScatterMethod.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cwl
-
-object ScatterMethod extends Enumeration {
-  type ScatterMethod = Value
-
-  val DotProduct = Value("dotproduct")
-  val NestedCrossProduct = Value("nested_crossproduct")
-  val FlatCrossProduct = Value("flat_crossproduct")
-}
diff --git a/cwl/src/main/scala/cwl/StringOrStringArrayToStringList.scala b/cwl/src/main/scala/cwl/StringOrStringArrayToStringList.scala
deleted file mode 100644
index 73afab205b7..00000000000
--- a/cwl/src/main/scala/cwl/StringOrStringArrayToStringList.scala
+++ /dev/null
@@ -1,12 +0,0 @@
-package cwl
-
-import shapeless.Poly1
-
-/**
-  * From a logic standpoint it's easier to treat sources as a list of strings.
-  */
-object StringOrStringArrayToStringList extends Poly1{
-  import Case._
-  implicit def string: Aux[String, List[String]] = at[String]{List(_)}
-  implicit def array: Aux[Array[String], List[String]] = at[Array[String]]{_.toList}
-}
diff --git a/cwl/src/main/scala/cwl/Tool.scala b/cwl/src/main/scala/cwl/Tool.scala
deleted file mode 100644
index d31b7368aee..00000000000
--- a/cwl/src/main/scala/cwl/Tool.scala
+++ /dev/null
@@ -1,189 +0,0 @@
-package cwl
-
-import java.nio.file.Paths
-
-import cats.instances.list._
-import common.Checked
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import cwl.CwlVersion.CwlVersion
-import cwl.Tool.inlineJavascriptRequirements
-import cwl.command.ParentName
-import cwl.requirement.RequirementToAttributeMap
-import shapeless.Inl
-import wom.callable.Callable.{OverridableInputDefinitionWithDefault, OptionalInputDefinition, OutputDefinition, RequiredInputDefinition}
-import wom.callable.MetaValueElement.{MetaValueElementBoolean, MetaValueElementObject}
-import wom.callable.{Callable, MetaValueElement, TaskDefinition}
-import wom.executable.Executable
-import wom.expression.{IoFunctionSet, ValueAsAnExpression, WomExpression}
-import wom.types.WomOptionalType
-import wom.values.{WomInteger, WomLong, WomString}
-import wom.{RuntimeAttributes, RuntimeAttributesKeys}
-
-import scala.util.Try
-
-object Tool {
-  def inlineJavascriptRequirements(allRequirementsAndHints: Seq[Requirement]): Vector[String] = {
-    val inlineJavscriptRequirements: Seq[InlineJavascriptRequirement] = allRequirementsAndHints.toList.collect {
-      case Inl(ijr:InlineJavascriptRequirement) => ijr
-    }
-
-    inlineJavscriptRequirements.flatMap(_.expressionLib.toList.flatten).toVector
-  }
-}
-
-/**
-  * Abstraction over a Tool (CommandLineTool or ExpressionTool)
-  * Contains common logic to both, mostly to build the wom task definition.
-  */
-trait Tool {
-  def inputs: Array[_ <: InputParameter]
-  def outputs: Array[_ <: OutputParameter]
-  def `class`: String
-  def id: String
-  def requirements: Option[Array[Requirement]]
-  def hints: Option[Array[Hint]]
-  def label: Option[String]
-  def doc: Option[String]
-  def cwlVersion: Option[CwlVersion]
-
-  def asCwl: Cwl
-
-  /** Builds an `Executable` directly from a `Tool` CWL with no parent workflow. */
-  def womExecutable(validator: RequirementsValidator, inputFile: Option[String] = None, ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    val taskDefinition = buildTaskDefinition(validator, Vector.empty)
-    CwlExecutableValidation.buildWomExecutable(taskDefinition, inputFile, ioFunctions, strictValidation)
-  }
-
-  protected def buildTaskDefinition(taskName: String,
-                                    inputDefinitions: List[_ <: Callable.InputDefinition],
-                                    outputDefinitions: List[Callable.OutputDefinition],
-                                    runtimeAttributes: RuntimeAttributes,
-                                    requirementsAndHints: List[cwl.Requirement],
-                                    expressionLib: ExpressionLib): ErrorOr[TaskDefinition]
-
-  private [cwl] implicit val explicitWorkflowName = ParentName(id)
-  protected val inputNames: Set[String] = this.inputs.map(i => FullyQualifiedName(i.id).id).toSet
-
-  // Circe can't create bidirectional links between workflow steps and runs (including `CommandLineTool`s) so this
-  // ugly var is here to link back to a possible parent workflow step. This is needed to navigate upward for finding
-  // requirements in the containment hierarchy. There isn't always a containing workflow step so this is an `Option`.
-  private[cwl] var parentWorkflowStep: Option[WorkflowStep] = None
-
-
-  private def validateRequirementsAndHints(validator: RequirementsValidator): ErrorOr[List[Requirement]] = {
-    import cats.syntax.traverse._
-
-    val allRequirements = requirements.toList.flatten ++ parentWorkflowStep.toList.flatMap(_.allRequirements.list)
-    // All requirements must validate or this fails.
-    val errorOrValidatedRequirements: ErrorOr[List[Requirement]] = allRequirements traverse validator
-
-    errorOrValidatedRequirements map { validRequirements =>
-      // Only Requirement hints, everything else is thrown out.
-      // TODO CWL don't throw them out but pass them back to the caller to do with as the caller pleases.
-      val hintRequirements = hints.toList.flatten.flatMap { _.select[Requirement] }
-      val parentHintRequirements = parentWorkflowStep.toList.flatMap(_.allHints)
-
-      // Throw out invalid Requirement hints.
-      // TODO CWL pass invalid hints back to the caller to do with as the caller pleases.
-      val validHints = (hintRequirements ++ parentHintRequirements).collect { case req if validator(req).isValid => req }
-      validRequirements ++ validHints
-    }
-  }
-
-  private def processRequirement(requirement: Requirement, expressionLib: ExpressionLib): Map[String, WomExpression] = {
-    requirement.fold(RequirementToAttributeMap).apply(inputNames, expressionLib)
-  }
-
-  protected def toolAttributes: Map[String, WomExpression] = Map.empty
-
-  def buildTaskDefinition(validator: RequirementsValidator, parentExpressionLib: ExpressionLib): Checked[TaskDefinition] = {
-    def build(requirementsAndHints: Seq[cwl.Requirement]) = {
-      val id = this.id
-
-      val expressionLib: ExpressionLib = parentExpressionLib ++ inlineJavascriptRequirements(requirementsAndHints)
-
-      // This is basically doing a `foldMap` but can't actually be a `foldMap` because:
-      // - There is no monoid instance for `WomExpression`s.
-      // - We want to fold from the right so the hints and requirements with the lowest precedence are processed first
-      //   and later overridden if there are duplicate hints or requirements of the same type with higher precedence.
-      val attributesMap: Map[String, WomExpression] = requirementsAndHints.foldRight(Map.empty[String, WomExpression])({
-        case (requirement, acc) => acc ++ processRequirement(requirement, expressionLib)
-      })
-
-      val runtimeAttributes: RuntimeAttributes = RuntimeAttributes(attributesMap ++ toolAttributes)
-
-      val schemaDefRequirement: SchemaDefRequirement = requirementsAndHints.flatMap{
-        _.select[SchemaDefRequirement].toList
-      }.headOption.getOrElse(SchemaDefRequirement())
-
-      lazy val localizationOptionalMetaObject: MetaValueElement = MetaValueElementObject(
-        Map(
-          "localization_optional" -> MetaValueElementBoolean(true)
-        )
-      )
-
-      // If input dir min == 0 that's a signal not to localize the input files
-      // https://github.com/dnanexus/dx-cwl/blob/fca163d825beb62f8a3004f2e0a6742805e6218c/dx-cwl#L426
-      val localizationOptional = runtimeAttributes.attributes.get(RuntimeAttributesKeys.DnaNexusInputDirMinKey) match {
-        case Some(ValueAsAnExpression(WomInteger(0))) => Option(localizationOptionalMetaObject)
-        case Some(ValueAsAnExpression(WomLong(0L))) => Option(localizationOptionalMetaObject)
-        case Some(ValueAsAnExpression(WomString("0"))) => Option(localizationOptionalMetaObject)
-        case _ => None
-      }
-
-      val inputDefinitions: List[_ <: Callable.InputDefinition] =
-        this.inputs.map {
-          case input @ InputParameter.IdDefaultAndType(inputId, default, tpe) =>
-            val inputType = tpe.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement)
-            val inputName = FullyQualifiedName(inputId).id
-            val defaultWomValue = default.fold(InputParameter.DefaultToWomValuePoly).apply(inputType).toTry.get
-            OverridableInputDefinitionWithDefault(
-              inputName,
-              inputType,
-              ValueAsAnExpression(defaultWomValue),
-              InputParameter.inputValueMapper(input, tpe, expressionLib, asCwl.schemaOption),
-              localizationOptional
-            )
-          case input @ InputParameter.IdAndType(inputId, tpe) =>
-            val inputType = tpe.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement)
-            val inputName = FullyQualifiedName(inputId).id
-            inputType match {
-              case optional: WomOptionalType =>
-                OptionalInputDefinition(
-                  inputName,
-                  optional,
-                  InputParameter.inputValueMapper(input, tpe, expressionLib, asCwl.schemaOption),
-                  localizationOptional
-                )
-              case _ =>
-                RequiredInputDefinition(
-                  inputName,
-                  inputType,
-                  InputParameter.inputValueMapper(input, tpe, expressionLib, asCwl.schemaOption),
-                  localizationOptional
-                )
-            }
-          case other => throw new UnsupportedOperationException(s"command input parameters such as $other are not yet supported")
-        }.toList
-
-      val outputDefinitions: List[Callable.OutputDefinition] = this.outputs.map {
-        case p @ OutputParameter.IdAndType(cop_id, tpe) =>
-          val womType = tpe.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-          OutputDefinition(FullyQualifiedName(cop_id).id, womType, OutputParameterExpression(p, womType, inputNames, expressionLib, schemaDefRequirement))
-        case other => throw new UnsupportedOperationException(s"Command output parameters such as $other are not yet supported")
-      }.toList
-
-      // The try will succeed if this is a task within a step. If it's a standalone file, the ID will be the file,
-      // so the filename is the fallback.
-      def taskName = Try(FullyQualifiedName(id).id).getOrElse(Paths.get(id).getFileName.toString)
-
-      buildTaskDefinition(taskName, inputDefinitions, outputDefinitions, runtimeAttributes, requirementsAndHints.toList, expressionLib).toEither
-    }
-
-    validateRequirementsAndHints(validator).toEither match {
-      case Right(requirementsAndHints: Seq[cwl.Requirement]) => build(requirementsAndHints)
-      case Left(errors) => Left(errors)
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/TypeAliases.scala b/cwl/src/main/scala/cwl/TypeAliases.scala
deleted file mode 100644
index abbfc9e81e0..00000000000
--- a/cwl/src/main/scala/cwl/TypeAliases.scala
+++ /dev/null
@@ -1,115 +0,0 @@
-package cwl
-
-import cwl.CwlType.CwlType
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import io.circe.Json
-import shapeless.{:+:, CNil}
-import wom.types.WomType
-
-trait TypeAliases {
-
-  type Expression = ECMAScriptFunction :+: ECMAScriptExpression :+: CNil
-
-  // http://www.commonwl.org/v1.0/Workflow.html#InputParameter
-  // http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter
-  type InputParameterFormat = Expression :+: String :+: Array[String] :+: CNil
-  
-  // http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter
-  // http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter
-  type OutputParameterFormat = StringOrExpression
-  
-  type Doc = String :+: Array[String] :+: CNil
-
-  type StringOrExpression = Expression :+: String :+: CNil
-
-  type CwlAny =
-    FileOrDirectory :+:
-      Array[FileOrDirectory] :+:
-      Json :+:
-      CNil
-
-  type WorkflowStepInputId = String
-
-  type Requirement =
-    InlineJavascriptRequirement :+:
-      SchemaDefRequirement :+:
-      DockerRequirement :+:
-      SoftwareRequirement :+:
-      InitialWorkDirRequirement :+:
-      EnvVarRequirement :+:
-      ShellCommandRequirement :+:
-      ResourceRequirement :+:
-      SubworkflowFeatureRequirement :+:
-      ScatterFeatureRequirement :+:
-      MultipleInputFeatureRequirement :+:
-      StepInputExpressionRequirement :+:
-      DnaNexusInputResourceRequirement :+:
-      CNil
-
-  type Hint =
-    Requirement :+:
-      CwlAny :+:
-      CNil
-
-  type MyriadInputType =
-    MyriadInputInnerType :+:
-      Array[MyriadInputInnerType] :+:
-      CNil
-
-  type MyriadInputInnerType =
-    CwlType :+:
-      InputRecordSchema :+:
-      InputEnumSchema :+:
-      InputArraySchema :+:
-      String :+:
-      CNil
-
-  type MyriadOutputType =
-    MyriadOutputInnerType :+:
-      Array[MyriadOutputInnerType] :+:
-      CNil
-
-  type MyriadOutputInnerType =
-    CwlType :+:
-      OutputRecordSchema :+:
-      OutputEnumSchema :+:
-      OutputArraySchema :+:
-      String :+:
-      CNil
-
-  type ResourceRequirementType = Long :+: Expression :+: String :+: CNil
-
-  type SingleOrArrayOfStrings = String :+: Array[String] :+: CNil
-
-  type ScatterVariables = Option[SingleOrArrayOfStrings]
-
-  type FileOrDirectory = File :+: Directory :+: CNil
-
-  type Glob = StringOrExpression :+: Array[String] :+: CNil
-
-  type SecondaryFiles = StringOrExpression :+: Array[StringOrExpression] :+: CNil
-}
-
-object MyriadInputType {
-
-  object InputArraySchema {
-    def unapply(m: MyriadInputType): Option[InputArraySchema] = m.select[MyriadInputInnerType].flatMap(_.select[InputArraySchema])
-  }
-
-  object InputArray {
-    def unapply(m: MyriadInputType): Option[Array[MyriadInputInnerType]] = m.select[Array[MyriadInputInnerType]]
-  }
-
-  object CwlType {
-    def unapply(m: MyriadInputType): Option[CwlType] = {
-      m.select[MyriadInputInnerType].flatMap(_.select[CwlType])
-    }
-  }
-
-  object WomType {
-    def unapply(m: MyriadInputType): Option[WomType] = m match {
-      case CwlType(c) => Option(cwl.cwlTypeToWomType(c))
-      case _ => None
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/Workflow.scala b/cwl/src/main/scala/cwl/Workflow.scala
deleted file mode 100644
index 22b30019ff1..00000000000
--- a/cwl/src/main/scala/cwl/Workflow.scala
+++ /dev/null
@@ -1,246 +0,0 @@
-package cwl
-
-import java.nio.file.Paths
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.Checked
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.CwlVersion._
-import cwl.LinkMergeMethod.LinkMergeMethod
-import cwl.Workflow.{WorkflowInputParameter, WorkflowOutputParameter}
-import cwl.command.ParentName
-import shapeless._
-import shapeless.syntax.singleton._
-import wom.SourceFileLocation
-import wom.callable.{MetaValueElement, WorkflowDefinition}
-import wom.executable.Executable
-import wom.expression.{IoFunctionSet, ValueAsAnExpression}
-import wom.graph.GraphNodePort.{GraphNodeOutputPort, OutputPort}
-import wom.graph._
-import wom.types.{WomOptionalType, WomType}
-
-case class Workflow private(
-                             cwlVersion: Option[CwlVersion],
-                             `class`: Witness.`"Workflow"`.T,
-                             id: String,
-                             inputs: Array[WorkflowInputParameter],
-                             outputs: Array[WorkflowOutputParameter],
-                             steps: Array[WorkflowStep],
-                             requirements: Option[Array[Requirement]],
-                             hints: Option[Array[Hint]],
-                             `$namespaces`: Option[Map[String, String]],
-                             `$schemas`: Option[Array[String]]
-                           ) {
-
-  steps.foreach { _.parentWorkflow = this }
-
-  /** Builds an `Executable` from a `Workflow` CWL with no parent `Workflow` */
-  def womExecutable(validator: RequirementsValidator, inputFile: Option[String] = None, ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    CwlExecutableValidation.buildWomExecutableCallable(womDefinition(validator, Vector.empty), inputFile, ioFunctions, strictValidation)
-  }
-
-  /* Circe can't create bidirectional links between workflow steps and runs (including `Workflow`s) so this
-   * ugly var is here to link back to a possible parent workflow step. This is needed to navigate upward for finding
-   * requirements in the containment hierarchy. There isn't always a containing workflow step so this is an `Option`.
-   */
-  private[cwl] var parentWorkflowStep: Option[WorkflowStep] = None
-
-  val allRequirements: RequirementsAndHints = RequirementsAndHints(requirements.toList.flatten ++ parentWorkflowStep.toList.flatMap { _.allRequirements.list })
-
-  private [cwl] implicit val explicitWorkflowName = ParentName(id)
-
-  lazy val womFqn: Option[wom.graph.FullyQualifiedName] = {
-    explicitWorkflowName.value map { workflowName =>
-      /* Sometimes the workflow name is of the form "parentWorkflowStepName/UUID"
-       * In that case, we don't want the fqn to look like "parentWorkflowStepName.parentWorkflowStepName/UUID"
-       * To avoid that, strip the parentWorkflowStepName from the workflowName
-       */
-      val cleanWorkflowName = parentWorkflowStep
-        .map(_.womFqn.value + "/")
-        .map(workflowName.stripPrefix)
-        .getOrElse(workflowName)
-
-      parentWorkflowStep.map(_.womFqn.combine(cleanWorkflowName))
-        .getOrElse(wom.graph.FullyQualifiedName(cleanWorkflowName))
-    }
-  }
-
-  lazy val allHints: List[Requirement] = {
-    // Just ignore any hint that isn't a Requirement.
-    val requirementHints = hints.toList.flatten.flatMap { _.select[Requirement] }
-    requirementHints ++ parentWorkflowStep.toList.flatMap { _.allHints }
-  }
-
-  val fileNames: List[String] = steps.toList.flatMap(_.run.select[String].toList)
-
-  def outputsTypeMap: WomTypeMap = steps.foldLeft(Map.empty[String, WomType]) {
-    /* Not implemented as a `foldMap` because there is no semigroup instance for `WomType`s.  `foldMap` doesn't know that
-     * we don't need a semigroup instance since the map keys should be unique and therefore map values would never need
-     * to be combined under the same key.
-     */
-    (acc, s) => acc ++ s.typedOutputs
-  }
-
-  def womGraph(workflowName: String, validator: RequirementsValidator, expressionLib: ExpressionLib): Checked[Graph] = {
-    val workflowNameIdentifier = explicitWorkflowName.value.map(WomIdentifier.apply).getOrElse(WomIdentifier(workflowName))
-
-    def womTypeForInputParameter(input: InputParameter): Option[WomType] = {
-      input.`type`.map(_.fold(MyriadInputTypeToWomType).apply(allRequirements.schemaDefRequirement))
-    }
-
-    val typeMap: WomTypeMap =
-      outputsTypeMap ++
-        /* Note this is only looking at the workflow inputs and not recursing into steps, because our current thinking
-         * is that in CWL graph inputs can only be defined at the workflow level.  It's possible that's not actually
-         * correct, but that's the assumption being made here.
-         */
-        inputs.toList.flatMap { i =>
-          womTypeForInputParameter(i).map(i.id -> _).toList
-        }.toMap
-
-    val externalGraphInputNodes: Set[ExternalGraphInputNode] = inputs.map { wip =>
-      val womType: WomType = womTypeForInputParameter(wip).get
-      val parsedInputId = FileAndId(wip.id).id
-      val womId = WomIdentifier(parsedInputId, wip.id)
-      val valueMapper =
-        InputParameter.inputValueMapper(wip, wip.`type`.get, expressionLib, asCwl.schemaOption)
-
-      def optionalWithDefault(memberType: WomType): OptionalGraphInputNodeWithDefault = {
-        val defaultValue = wip.default.get.fold(InputParameter.DefaultToWomValuePoly).apply(womType).toTry.get
-        OptionalGraphInputNodeWithDefault(womId, memberType, ValueAsAnExpression(defaultValue), parsedInputId, valueMapper)
-      }
-
-      womType match {
-        case WomOptionalType(memberType) if wip.default.isDefined => optionalWithDefault(memberType)
-        case _ if wip.default.isDefined => optionalWithDefault(womType)
-        case optional @ WomOptionalType(_) => OptionalGraphInputNode(womId, optional, parsedInputId, valueMapper)
-        case _ => RequiredGraphInputNode(womId, womType, parsedInputId, valueMapper)
-      }
-    }.toSet
-
-    val workflowInputs: Map[String, GraphNodeOutputPort] =
-      externalGraphInputNodes.map { egin =>
-        egin.localName -> egin.singleOutputPort
-      }.toMap
-
-    val graphFromSteps: Checked[Set[GraphNode]] =
-      steps.
-        toList.
-        foldLeft((Set.empty[GraphNode] ++ externalGraphInputNodes).asRight[NonEmptyList[String]])(
-          (nodes, step) => nodes.flatMap(step.callWithInputs(typeMap, this, _, workflowInputs, validator, expressionLib)))
-
-    val graphFromOutputs: Checked[Set[GraphNode]] =
-      outputs.toList.traverse[ErrorOr, GraphNode] {
-        case WorkflowOutputParameter(id, _, _, _, _, _, _, Some(Inl(outputSource: String)), _, Some(tpe)) =>
-          val womType: WomType = tpe.fold(MyriadOutputTypeToWomType).apply(allRequirements.schemaDefRequirement)
-
-          val parsedWorkflowOutput = FileAndId(id)
-          val parsedOutputSource = cwl.FullyQualifiedName(outputSource)
-
-          // Try to find an output port for this cwl output in the set of available nodes
-          def lookupOutputSource(fqn: cwl.FullyQualifiedName): Checked[OutputPort] = {
-            def isRightOutputPort(op: GraphNodePort.OutputPort) = cwl.FullyQualifiedName.maybeApply(op.name) match {
-              case Some(f) => f.id == fqn.id
-              case None => op.internalName == fqn.id
-            }
-
-            def sourceNode(graph: Set[GraphNode]): Checked[GraphNode] = {
-              val findSource: PartialFunction[GraphNode, GraphNode] = fqn match {
-                // A step output becoming a workflow output.
-                case fsi: FileStepAndId => {
-                  case callNode: CallNode if callNode.localName == fsi.stepId => callNode
-                  case scatterNode: ScatterNode if scatterNode.innerGraph.calls.exists(_.localName == fsi.stepId) => scatterNode
-                }
-                // A workflow input recycled back to be an output.
-                case fi: FileAndId => {
-                  case gin: ExternalGraphInputNode if gin.nameInInputSet == fi.id => gin
-                }
-              }
-              graph collectFirst findSource toRight NonEmptyList.one(s"Call Node by name $fqn was not found in set $graph")
-            }
-
-            for {
-              set <- graphFromSteps
-              node <- sourceNode(set)
-              output <- node.outputPorts.find(isRightOutputPort).toChecked(s"looking for ${fqn.id} in call $node output ports ${node.outputPorts}")
-            } yield output
-          }
-
-          lookupOutputSource(parsedOutputSource).map({ port =>
-            val localName = LocalName(parsedWorkflowOutput.id)
-            val fullyQualifiedName = workflowNameIdentifier.fullyQualifiedName.combine(parsedWorkflowOutput.id)
-            val outputIdentifier = WomIdentifier(localName, fullyQualifiedName)
-            PortBasedGraphOutputNode(outputIdentifier, womType, port)
-          }).toValidated
-        case wop => throw new UnsupportedOperationException(s"Workflow output parameters such as $wop are not supported.")
-      }.map(_.toSet).toEither
-
-    for {
-      outputs <- graphFromOutputs
-      steps <- graphFromSteps
-      ret <- Graph.validateAndConstruct(steps ++ externalGraphInputNodes ++ outputs).toEither
-    } yield ret
-  }
-
-  def womDefinition(validator: RequirementsValidator, expressionLib: ExpressionLib): Checked[WorkflowDefinition] = {
-    val name: String = Paths.get(id).getFileName.toString
-    val meta: Map[String, MetaValueElement.MetaValueElementString] = Map.empty
-    val paramMeta: Map[String, MetaValueElement.MetaValueElementString] = Map.empty
-    val lexInfo : Option[SourceFileLocation] = None
-
-    womGraph(name, validator, expressionLib).map(graph =>
-      WorkflowDefinition(
-        name,
-        graph,
-        meta,
-        paramMeta,
-        lexInfo
-      )
-    )
-  }
-
-  def asCwl = Coproduct[Cwl](this)
-}
-object Workflow {
-
-  case class WorkflowInputParameter(id: String,
-                                    label: Option[String] = None,
-                                    secondaryFiles: Option[SecondaryFiles] = None,
-                                    format: Option[InputParameterFormat] = None,
-                                    streamable: Option[Boolean] = None,
-                                    doc: Option[Doc] = None,
-                                    inputBinding: Option[InputCommandLineBinding] = None,
-                                    default: Option[CwlAny] = None,
-                                    `type`: Option[MyriadInputType] = None) extends InputParameter
-
-  case class WorkflowOutputParameter(
-                                      id: String,
-                                      label: Option[String] = None,
-                                      secondaryFiles: Option[SecondaryFiles] = None,
-                                      format: Option[OutputParameterFormat] = None,
-                                      streamable: Option[Boolean] = None,
-                                      doc: Option[Doc] = None,
-                                      outputBinding: Option[CommandOutputBinding] = None,
-                                      outputSource: Option[WorkflowOutputParameter#OutputSource] = None,
-                                      linkMerge: Option[LinkMergeMethod] = None,
-                                      `type`: Option[MyriadOutputType] = None) extends OutputParameter {
-
-    type OutputSource = String :+: Array[String] :+: CNil
-  }
-
-  def apply(cwlVersion: Option[CwlVersion] = Option(CwlVersion.Version1),
-            id: String,
-            inputs: Array[WorkflowInputParameter] = Array.empty,
-            outputs: Array[WorkflowOutputParameter] = Array.empty,
-            steps: Array[WorkflowStep] = Array.empty,
-            requirements: Option[Array[Requirement]] = None,
-            hints: Option[Array[Hint]] = None,
-            namespaces: Option[Map[String, String]] = None,
-            schemas: Option[Array[String]] = None
-           ): Workflow  =
-    Workflow(cwlVersion, "Workflow".narrow, id, inputs, outputs, steps, requirements, hints, namespaces, schemas)
-}
diff --git a/cwl/src/main/scala/cwl/WorkflowStep.scala b/cwl/src/main/scala/cwl/WorkflowStep.scala
deleted file mode 100644
index cf39f261bae..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStep.scala
+++ /dev/null
@@ -1,537 +0,0 @@
-package cwl
-
-import cats.Monoid
-import cats.data.NonEmptyList
-import cats.data.Validated._
-import cats.syntax.either._
-import cats.syntax.foldable._
-import cats.syntax.monoid._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import cwl.ScatterLogic.ScatterVariablesPoly
-import cwl.ScatterMethod._
-import cwl.WorkflowStep.{WorkflowStepInputFold, _}
-import cwl.WorkflowStepInput._
-import cwl.command.ParentName
-import shapeless.{:+:, CNil, _}
-import wom.callable.Callable
-import wom.callable.Callable._
-import wom.graph.CallNode._
-import wom.graph.GraphNodePort.{GraphNodeOutputPort, OutputPort}
-import wom.graph._
-import wom.graph.expression.ExpressionNode
-import wom.types.WomType
-import wom.values.WomValue
-import wom.graph.{FullyQualifiedName => WomFullyQualifiedName}
-
-/**
-  * An individual job to run.
-  *
-  * @see <a href="http://www.commonwl.org/v1.0/Workflow.html#WorkflowStep">CWL Spec | Workflow Step</a>
-  * @param run Purposefully not defaulted as it's required in the specification and it is unreasonable to not have something to run.
-  */
-case class WorkflowStep(
-                         id: String,
-                         in: Array[WorkflowStepInput] = Array.empty,
-                         out: WorkflowStepOutputType,
-                         run: Run,
-                         requirements: Option[Array[Requirement]] = None,
-                         hints: Option[Array[Hint]] = None,
-                         label: Option[String] = None,
-                         doc: Option[String] = None,
-                         scatter: ScatterVariables = None,
-                         scatterMethod: Option[ScatterMethod] = None) {
-
-  run.select[Workflow].foreach(_.parentWorkflowStep = Option(this))
-  run.select[CommandLineTool].foreach(_.parentWorkflowStep = Option(this))
-  run.select[ExpressionTool].foreach(_.parentWorkflowStep = Option(this))
-
-  // We're scattering if scatter is defined, and if it's a list of variables the list needs to be non empty
-  private val isScattered: Boolean = scatter exists { _.select[Array[String]].forall(_.nonEmpty) }
-
-  // Circe can't create bidirectional links between workflows and workflow steps so this ugly var is here to link
-  // back to the parent workflow. This is needed to navigate upward for finding requirements in the containment
-  // hierarchy. There is always a workflow containing a workflow step so this is not an `Option`.
-  private[cwl] var parentWorkflow: Workflow = _
-
-  lazy val allRequirements = RequirementsAndHints(requirements.toList.flatten ++ parentWorkflow.allRequirements.list)
-
-  lazy val womFqn: WomFullyQualifiedName = {
-    implicit val parentName = parentWorkflow.explicitWorkflowName
-    val localFqn = cwl.FullyQualifiedName.maybeApply(id).map(_.id).getOrElse(id)
-    parentWorkflow.womFqn.map(_.combine(localFqn)).getOrElse(wom.graph.FullyQualifiedName(localFqn))
-  }
-
-  lazy val allHints: List[Requirement] = {
-    // Just ignore any hint that isn't a Requirement.
-    val requirementHints = hints.toList.flatten.flatMap { _.select[Requirement] }
-    requirementHints ++ parentWorkflow.allHints
-  }
-
-  // If the step is being scattered over, apply the necessary transformation to get the final output array type.
-  lazy val scatterTypeFunction: WomType => WomType = scatter.map(_.fold(ScatterVariablesPoly)) match {
-    case Some(Nil) => identity[WomType]
-    case Some(nonEmpty) => ScatterLogic.scatterGatherPortTypeFunction(scatterMethod, NonEmptyList.fromListUnsafe(nonEmpty))
-    case _ =>  identity[WomType]
-  }
-
-  def typedOutputs: WomTypeMap = {
-    implicit val parentName = ParentName(id)
-    // Find the type of the outputs of the run section
-    val runOutputTypes = run.fold(RunOutputsToTypeMap).apply(allRequirements.schemaDefRequirement)
-      .map({
-        case (runOutputId, womType) => cwl.FullyQualifiedName(runOutputId).id -> womType
-      })
-    // Use them to find get the final type of the workflow outputs, and only the workflow outputs
-    out.map({ stepOutput =>
-      val stepOutputValue = stepOutput.select[WorkflowStepOutput].map(_.id).getOrElse(stepOutput.select[String].get)
-      val stepOutputId = cwl.FullyQualifiedName(stepOutputValue)
-      stepOutputValue -> scatterTypeFunction(runOutputTypes(stepOutputId.id))
-    }).toMap
-  }
-
-  def fileName: Option[String] = run.select[String]
-
-  /**
-    * Generates all GraphNodes necessary to represent call nodes and input nodes
-    * Recursive because dependencies are discovered as we iterate through inputs and corresponding
-    * upstream nodes need to be generated on the fly.
-    *
-    * Example:
-    *
-    * CWL:
-    * inputs:
-    *   
-id: workflow_input_A

-    *    type: string[]
-    *   -id: workflow_input_B

-    *    type: string[]
-    *   
-id: workflow_input_C

-    *    type: string


-    * steps:

-    *   -id: echo
-    *    run: echo.cwl
-    *    scatter: input0
-    *    in:
-    *      -id:input0
-    *       source:
-    *         - "#workflow_input_A"
-    *         - "#workflow_input_B"

-    *       valueFrom:"bonjour"
-    *
-    *      -id: input1
-    *   
    source: "#workflow_input_C"
-    *       valueFrom:"$(inputs.input0)"
-    *
-    * WOM Diagram:
-    *
-    *  +------------+   +------------+   +------------+
-    *  | WF Input A |   | WF Input B |   | WF Input C |
-    *  +--------+---+ +-+------------+   +------+-----+
-    *           |     |                         |
-    *           |     |                         |
-    *     +-----v-----v+                 +------v-----+
-    *     | StepInput0 |                 | StepInput1 |
-    *     | MergeLogic |                 | MergeLogic |
-    *     +-----+------+                 +----+-------+
-    *           |                             |
-    *  +----------------------------------------------+
-    *  |        |                             |       |
-    *  | +------v----------+              +---v--+    |
-    *  | | ScatterVariable +------------+ | OGIN |    |
-    *  | +-----+-----------+            | +--+-+-+    |
-    *  |       |                        |    | |      |
-    *  | +-----v----+                   |    | |      |
-    *  | |StepInput0<------------------------+ |      |
-    *  | |Expression|                   |      |      |
-    *  | +----+-----+                +--v------v+     |
-    *  |      |                      |StepInput1|     |
-    *  |      |                      |Expression|     |
-    *  |      |                      +------+---+     |
-    *  |      |    +-----------+            |         |
-    *  |      +----> Call Node <------------+         |
-    *  |           +-----------+                      |
-    *  |                                 Scatter Node |
-    *  +----------------------------------------------+
-    *
-    * MergeNode: If the step input has one or more sources, a merge node will be created and responsible for merging
-    *   those input sources together. It will NOT evaluate the valueFrom field of the input.
-    *
-    * ScatterVariableNode: If the step input is being scattered over, a scatter variable node will be created and will
-    *   act as a proxy inside the scatter graph for the shards of the scatter. It depends on an upstream merge node outputing an array
-    *   and will provide at runtime shard values for other nodes of the scatter graph.
-    *
-    * OGIN: If the step has at least one input being scattered over, there will be a scatter node created.
-    *   For inputs that are NOT being scattered over but still have one or more input sources (and hence a merge node), an OGIN
-    *   will be created to act as a proxy to the merge node outside the scatter graph.
-    *
-    * ExpressionNode: If an input has a valueFrom field, an expression node will be created to evaluate the expression.
-    *   An important fact to note is that the expression needs access to all other input values
-    *   AFTER their source, default value and shard number has been determined but
-    *   BEFORE their (potential) valueFrom is evaluated (see http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)
-    *   This is why on the above diagram, StepInput0Expression depends on the OGIN, and StepInput1Expression depends on the scatter variable.
-    */
-  def callWithInputs(typeMap: WomTypeMap,
-                     workflow: Workflow,
-                     knownNodes: Set[GraphNode],
-                     workflowInputs: Map[String, GraphNodeOutputPort],
-                     validator: RequirementsValidator,
-                     expressionLib: ExpressionLib): Checked[Set[GraphNode]] = {
-
-    implicit val parentName = workflow.explicitWorkflowName
-
-    val scatterLookupSet =
-      scatter.toList.
-        flatMap(_.fold(StringOrStringArrayToStringList)).
-        map(id => cwl.FullyQualifiedName(id).id)
-
-    def isStepScattered(workflowStepInputId: String) = scatterLookupSet.contains(workflowStepInputId)
-
-    val unqualifiedStepId: WomIdentifier = {
-      cwl.FullyQualifiedName.maybeApply(id).map({ fqn =>
-        WomIdentifier(LocalName(fqn.id), womFqn)
-      }).getOrElse(WomIdentifier(id))
-    }
-
-    def typedRunInputs: Map[String, Option[MyriadInputType]] = run.fold(RunToInputTypeMap).apply(parentName)
-
-    def allIdentifiersRecursively(nodes: Set[GraphNode]): Set[WomIdentifier] = nodes.flatMap({
-      case w: WorkflowCallNode=> Set(w.identifier)
-      case c: CommandCallNode => Set(c.identifier)
-      case e: ExpressionCallNode => Set(e.identifier)
-      // When a node a call node is being scattered over, it is wrapped inside a scatter node. We still don't want to
-      // duplicate it though so look inside scatter nodes to see if it's there.
-      case scatter: ScatterNode => allIdentifiersRecursively(scatter.innerGraph.nodes)
-      case _ => Set.empty[WomIdentifier]
-    })
-
-    // To avoid duplicating nodes, return immediately if we've already covered this node
-    val haveWeSeenThisStep: Boolean = allIdentifiersRecursively(knownNodes).contains(unqualifiedStepId)
-
-    if (haveWeSeenThisStep) Right(knownNodes)
-    else {
-      val callable: Checked[Callable] = run match {
-        case Run.CommandLineTool(clt) => clt.buildTaskDefinition(validator, expressionLib)
-        case Run.Workflow(wf) => wf.womDefinition(validator, expressionLib)
-        case Run.ExpressionTool(et) => et.buildTaskDefinition(validator, expressionLib)
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-
-      val callNodeBuilder = new CallNode.CallNodeBuilder()
-
-      /*
-       * Method used to fold over the list of inputs declared by this step.
-       * Note that because we work on saladed CWL, all ids are fully qualified at this point (e.g: file:///path/to/file/three_step.cwl#cgrep/pattern
-       * The goal of this method is two fold (pardon the pun):
-       *   1) link each input of the step to an output port (which at this point can be from a different step or from a workflow input)
-       *   2) accumulate the nodes created along the way to achieve 1)
-       */
-      def foldStepInput(currentFold: Checked[WorkflowStepInputFold], workflowStepInput: WorkflowStepInput): Checked[WorkflowStepInputFold] = currentFold flatMap {
-        fold =>
-          /*
-            * Try to find in the given set an output port named stepOutputId in a call node named stepId
-            * This is useful when we've determined that the input points to an output of a different step and we want
-            * to get the corresponding output port.
-           */
-          def findThisInputInSet(set: Set[GraphNode], stepId: String, stepOutputId: String): Checked[OutputPort] = {
-            for {
-              // We only care for outputPorts of call nodes or scatter nodes
-              call <- set.collectFirst {
-                case callNode: CallNode if callNode.localName == stepId => callNode
-                case scatterNode: ScatterNode if scatterNode.innerGraph.calls.exists(_.localName == stepId) => scatterNode
-              }.
-                toRight(NonEmptyList.one(s"stepId $stepId not found in known Nodes $set"))
-              output <- call.outputPorts.find(_.internalName == stepOutputId).
-                toRight(NonEmptyList.one(s"step output id $stepOutputId not found in ${call.outputPorts}"))
-            } yield output
-          }
-
-          /*
-           * Build a wom node for the given step and return the newly created nodes
-           * This is useful when we've determined that the input belongs to an upstream step that we haven't covered yet
-           */
-          def buildUpstreamNodes(upstreamStepId: String, accumulatedNodes: Set[GraphNode]): Checked[Set[GraphNode]] =
-          // Find the step corresponding to this upstreamStepId in the set of all the steps of this workflow
-            for {
-              step <- workflow.steps.find { step => cwl.FullyQualifiedName(step.id).id == upstreamStepId }.
-                toRight(NonEmptyList.one(s"no step of id $upstreamStepId found in ${workflow.steps.map(_.id).toList}"))
-              call <- step.callWithInputs(typeMap, workflow, accumulatedNodes, workflowInputs, validator, expressionLib)
-            } yield call
-
-          def fromWorkflowInput(inputName: String): Checked[Map[String, OutputPort]] = {
-            // Try to find it in the workflow inputs map, if we can't it's an error
-            workflowInputs.collectFirst {
-              case (inputId, port) if inputName == inputId => Map(inputId -> port).asRight[NonEmptyList[String]]
-            } getOrElse s"Can't find workflow input for $inputName".invalidNelCheck[Map[String, OutputPort]]
-          }
-
-          def fromStepOutput(stepId: String, stepOutputId: String, accumulatedNodes: Set[GraphNode]): Checked[(Map[String, OutputPort], Set[GraphNode])] = {
-            // First check if we've already built the WOM node for this step, and if so return the associated output port
-            findThisInputInSet(accumulatedNodes, stepId, stepOutputId).map(outputPort => (Map(s"$stepId/$stepOutputId" -> outputPort), accumulatedNodes))
-              .orElse {
-                // Otherwise build the upstream nodes and look again in those newly created nodes
-                for {
-                  newNodes <- buildUpstreamNodes(stepId, accumulatedNodes)
-                  sourceMappings <- findThisInputInSet(newNodes, stepId, stepOutputId).map(outputPort => Map(s"$stepId/$stepOutputId" -> outputPort))
-                } yield (sourceMappings, newNodes ++ accumulatedNodes)
-              }
-          }
-
-          lazy val workflowStepInputId = cwl.FullyQualifiedName(workflowStepInput.id).id
-
-          def updateFold(sourceMappings: Map[String, OutputPort], newNodes: Set[GraphNode]): Checked[WorkflowStepInputFold] = {
-            val typeExpectedByRunInput: Option[cwl.MyriadInputType] = typedRunInputs.get(workflowStepInputId).flatten
-
-            val isThisStepScattered = isStepScattered(workflowStepInputId)
-
-            workflowStepInput.toMergeNode(sourceMappings, expressionLib, typeExpectedByRunInput, isThisStepScattered, allRequirements.schemaDefRequirement) match {
-              // If the input needs a merge node, build it and add it to the input fold
-              case Some(mergeNode) =>
-                mergeNode.toEither.map({ node =>
-                  fold |+| WorkflowStepInputFold(
-                    mergeNodes = Map(workflowStepInput -> node),
-                    generatedNodes = newNodes
-                  )
-                })
-              case None => (fold |+| WorkflowStepInputFold(generatedNodes = newNodes)).validNelCheck
-            }
-          }
-
-          /*
-           * We intend to validate that all of these sources point to a WOM Outputport that we know about.
-           *
-           * If we don't know about them, we find upstream nodes and build them (see "buildUpstreamNodes").
-           */
-          val baseCase = (Map.empty[String, OutputPort], fold.generatedNodes).asRight[NonEmptyList[String]]
-          val inputMappingsAndGraphNodes: Checked[(Map[String, OutputPort], Set[GraphNode])] =
-            workflowStepInput.sources.foldLeft(baseCase) {
-              case (Right((sourceMappings, graphNodes)), inputSource) =>
-                /*
-                 * Parse the inputSource (what this input is pointing to)
-                 * 2 cases:
-                 *   - points to a workflow input
-                 *   - points to an upstream step
-                 */
-                cwl.FullyQualifiedName(inputSource) match {
-                  // The source points to a workflow input, which means it should be in the workflowInputs map
-                  case FileAndId(_, _, inputId) => fromWorkflowInput(inputId).map(newMap => (sourceMappings ++ newMap, graphNodes))
-                  // The source points to an output from a different step
-                  case FileStepAndId(_, _, stepId, stepOutputId) => fromStepOutput(stepId, stepOutputId, graphNodes).map({ case (newMap, newNodes) => (sourceMappings ++ newMap, newNodes) })
-                }
-              case (other, _) => other
-            }
-
-          inputMappingsAndGraphNodes.flatMap((updateFold _).tupled)
-      }
-
-      /*
-       * Folds over input definitions and build an InputDefinitionFold
-       */
-      def foldInputDefinition(pointerNode: Map[String, GraphNodeWithSingleOutputPort])
-                             (inputDefinition: InputDefinition): ErrorOr[InputDefinitionFold] = {
-        inputDefinition match {
-          case _ if pointerNode.contains(inputDefinition.name) =>
-            val expressionNode = pointerNode(inputDefinition.name)
-            InputDefinitionFold(
-              mappings = List(inputDefinition -> expressionNode.inputDefinitionPointer),
-              callInputPorts = Set(callNodeBuilder.makeInputPort(inputDefinition, expressionNode.singleOutputPort))
-            ).validNel
-
-          // No expression node mapping, use the default
-          case withDefault @ OverridableInputDefinitionWithDefault(_, _, expression, _, _) =>
-            InputDefinitionFold(
-              mappings = List(withDefault -> Coproduct[InputDefinitionPointer](expression))
-            ).validNel
-
-          // Required input without default value and without mapping, this is a validation error
-          case RequiredInputDefinition(requiredName, _, _, _) =>
-            s"Input ${requiredName.value} is required and is not bound to any value".invalidNel
-
-          // Optional input without mapping, defaults to empty value
-          case optional: OptionalInputDefinition =>
-            InputDefinitionFold(
-              mappings = List(optional -> Coproduct[InputDefinitionPointer](optional.womType.none: WomValue))
-            ).validNel
-          case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-        }
-      }
-
-      /*
-        If the step is being scattered over, then merge nodes can't directly be referenced because they will be outside the scatter graph.
-        For inputs that are being scattered over, a scatter variable has already been created, but for the others we need
-        an OGIN to link the merge node to the inner scatter graph.
-       */
-      def buildOGINs(mergeNodes: Map[WorkflowStepInput, ExpressionNode],
-                     scatterVariables: Map[WorkflowStepInput, ScatterVariableNode]): Map[WorkflowStepInput, OuterGraphInputNode] = if (isScattered) {
-        mergeNodes
-          .collect({
-            case (input, mergeNode) if !scatterVariables.contains(input) =>
-              val ogin = OuterGraphInputNode(
-                WomIdentifier(input.parsedId).combine("OGIN"),
-                mergeNode.singleOutputPort,
-                preserveScatterIndex = false
-              )
-              input -> ogin
-          })
-      } else Map.empty
-
-      /*
-        * For inputs that have a valueFrom field, create an ExpressionNode responsible for evaluating the expression.
-        * Note that this expression might need access to the other input values, so make each expression node depend on all other
-        * inputs.
-       */
-      def buildStepInputValueFromNodes(sharedInputNodes: Map[WorkflowStepInput, GraphNodeWithSingleOutputPort]): Checked[Map[String, ExpressionNode]] = {
-        // Add new information to the typeMap from the shard input nodes.
-        lazy val updatedTypeMap = sharedInputNodes.map({
-          // If the input node is a scatter variable, make sure the type is the item type, not the array type, as the expression node
-          // will operate on shards not on the whole scattered array.
-          case (stepInput, scatter: ScatterVariableNode) => stepInput.parsedId -> scatter.womType
-          case (stepInput, node) => stepInput.parsedId -> node.singleOutputPort.womType
-        }) ++ typeMap
-
-        // Go over each step input and create an expression node for those which have a valueFrom
-        in.toList.collect({
-          case stepInput @ WorkflowStepInput(_, _, _, _, Some(valueFrom)) =>
-            // Transform the shared inputs map into a usable map to create the expression.
-            lazy val sharedInputMap: Map[String, OutputPort] = sharedInputNodes.map({
-              case (siblingStepInput, graphNode) => siblingStepInput.parsedId -> graphNode.singleOutputPort
-            })
-            val typeExpectedByRunInput: Option[cwl.MyriadInputType] = typedRunInputs.get(stepInput.parsedId).flatten
-            val isThisStepScattered = isStepScattered(stepInput.parsedId)
-
-            stepInput.toExpressionNode(valueFrom, typeExpectedByRunInput, isThisStepScattered, sharedInputMap, updatedTypeMap, expressionLib, allRequirements.schemaDefRequirement).map(stepInput.parsedId -> _)
-        })
-          .sequence[ErrorOr, (String, ExpressionNode)]
-          .toEither
-          .map(_.toMap)
-      }
-
-      //inputs base case consist of the nodes we already know about
-      val baseCase = WorkflowStepInputFold(generatedNodes = knownNodes).asRight[NonEmptyList[String]]
-
-      // WorkflowStepInputFold contains the mappings from step input to ExpressionNode as well as all created nodes
-      val stepInputFoldCheck: Checked[WorkflowStepInputFold] = in.foldLeft(baseCase)(foldStepInput)
-
-      /*
-        * This (big) flatMap builds nodes from top to bottom in the diagram above.
-        * If necessary, the scatter node is built last as it wraps some of the other nodes.
-       */
-      for {
-        /* ************************************ */
-        /* ************ Merge Nodes *********** */
-        /* ************************************ */
-        // Build merge nodes and recursively generates other call nodes that we haven't seen so far
-        stepInputFold <- stepInputFoldCheck
-        // Extract the merge nodes from the fold
-        mergeNodes = stepInputFold.mergeNodes
-
-        /* ************************************ */
-        /* ****** Scatter Variable Nodes ****** */
-        /* ************************************ */
-        scatterVariableNodes <- ScatterLogic.buildScatterVariableNodes(scatter, mergeNodes, unqualifiedStepId.localName.value)
-
-        /* ************************************ */
-        /* *************** OGINS ************** */
-        /* ************************************ */
-        ogins = buildOGINs(mergeNodes, scatterVariableNodes)
-
-        /* ************************************ */
-        /* ********* Expression Nodes ********* */
-        /* ************************************ */
-        // Aggregate the generated nodes so far. This map will be used to generate expression nodes, so the order of aggregation matters:
-        // scatter variables and ogins take precedence over merge nodes (see diagram)
-        aggregatedMapForValueFromNodes = mergeNodes ++ scatterVariableNodes ++ ogins
-        // Build expression nodes for inputs that have a valueFrom field
-        stepInputValueFromNodes <- buildStepInputValueFromNodes(aggregatedMapForValueFromNodes)
-
-        /* ************************************ */
-        /* ************* Call Node ************ */
-        /* ************************************ */
-        // Get the callable object for this step
-        checkedCallable <- callable
-        // Aggregate again by adding generated expression nodes. Again order matters here, expression nodes override other nodes.
-        aggregatedMapForInputDefinitions = aggregatedMapForValueFromNodes.asIdentifierMap ++ stepInputValueFromNodes
-        // Assign each of the callable's input definition to an output port from the pointer map
-        inputDefinitionFold <- checkedCallable.inputs.foldMap(foldInputDefinition(aggregatedMapForInputDefinitions)).toEither
-        // Build the call node
-        callAndNodes = callNodeBuilder.build(unqualifiedStepId, checkedCallable, inputDefinitionFold, Set.empty, None)
-        // Depending on whether the step is being scattered, invoke the scatter node builder or not
-
-        /* ************************************ */
-        /* ************ Scatter Node ********** */
-        /* ************************************ */
-        scatterNodeOrExposedNodes <- if (isScattered) {
-          ScatterLogic.buildScatterNode(
-            callAndNodes,
-            NonEmptyList.fromListUnsafe(scatterVariableNodes.values.toList),
-            ogins.values.toSet,
-            stepInputValueFromNodes.values.toSet,
-            scatterMethod).map(Set(_))
-        } else {
-          // If there's no scatter node then we need to return the expression nodes and the call node explicitly
-          // as they won't be contained in the scatter inner graph
-          (stepInputValueFromNodes.values.toSet + callAndNodes.node).validNelCheck
-        }
-
-        /*
-          * Return all the nodes that need to be made available to the workflow graph:
-          * knownNodes: this method is used to fold over steps so we don't want to forget to accumulate known nodes
-          * mergeNodes: they're always outside of the scatter so always return them
-          * generatedNodes: nodes generated recursively to build this node
-          * scatterNodeOrExposedNodes: see explanation above
-         */
-        allNodes = knownNodes ++ mergeNodes.values.toSet ++ stepInputFold.generatedNodes ++ scatterNodeOrExposedNodes
-      } yield allNodes
-    }
-  }
-}
-
-/**
-  * @see <a href="http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepOutput">WorkflowstepOutput</a>
-  */
-case class WorkflowStepOutput(id: String)
-
-object WorkflowStep {
-
-  // A monoid can't be derived automatically for this class because it contains a Map[String, ExpressionNode],
-  // and there's no monoid defined over ExpressionNode
-  implicit val workflowStepInputFoldMonoid: Monoid[WorkflowStepInputFold] = new Monoid[WorkflowStepInputFold] {
-    override def empty: WorkflowStepInputFold = WorkflowStepInputFold()
-    override def combine(x: WorkflowStepInputFold, y: WorkflowStepInputFold): WorkflowStepInputFold = {
-      WorkflowStepInputFold(
-        mergeNodes = x.mergeNodes ++ y.mergeNodes,
-        generatedNodes = x.generatedNodes ++ y.generatedNodes
-      )
-    }
-  }
-
-  private [cwl] case class WorkflowStepInputFold(mergeNodes: Map[WorkflowStepInput, ExpressionNode] = Map.empty,
-                                                 generatedNodes: Set[GraphNode] = Set.empty)
-
-  /**
-    * Maps input variable (to be scattered over) to their scatter variable node
-    */
-  type ScatterMappings = Map[ExpressionNode, ScatterVariableNode]
-
-  val emptyOutputs: WorkflowStepOutputType = Array.empty
-
-  type Run =
-    String :+:
-      CommandLineTool :+:
-      ExpressionTool :+:
-      Workflow :+:
-      CNil
-
-  object Run {
-    object String { def unapply(run: Run): Option[String] = run.select[String] }
-    object Workflow { def unapply(run: Run): Option[Workflow] = run.select[Workflow] }
-    object CommandLineTool { def unapply(run: Run): Option[CommandLineTool] = run.select[CommandLineTool] }
-    object ExpressionTool { def unapply(run: Run): Option[ExpressionTool] = run.select[ExpressionTool] }
-  }
-
-  type WorkflowStepOutputInnerType = String :+: WorkflowStepOutput :+: CNil
-  type WorkflowStepOutputType = Array[WorkflowStepOutputInnerType]
-}
diff --git a/cwl/src/main/scala/cwl/WorkflowStepInput.scala b/cwl/src/main/scala/cwl/WorkflowStepInput.scala
deleted file mode 100644
index a3d028dbdd6..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStepInput.scala
+++ /dev/null
@@ -1,155 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import cwl.InputParameter.DefaultToWomValuePoly
-import cwl.LinkMergeMethod.LinkMergeMethod
-import cwl.WorkflowStepInput.InputSource
-import cwl.command.ParentName
-import shapeless.{:+:, CNil}
-import wom.expression.ValueAsAnExpression
-import wom.graph.GraphNodePort.OutputPort
-import wom.graph.WomIdentifier
-import wom.graph.expression.{AnonymousExpressionNode, ExposedExpressionNode, ExpressionNode, PlainAnonymousExpressionNode}
-import wom.types._
-
-case class WorkflowStepInput(
-                              id: String,
-                              source: Option[InputSource] = None,
-                              linkMerge: Option[LinkMergeMethod] = None,
-                              default: Option[CwlAny] = None,
-                              valueFrom: Option[StringOrExpression] = None) {
-
-  def parsedId(implicit parentName: ParentName) = FullyQualifiedName(id).id
-
-  def toExpressionNode(valueFromExpression: StringOrExpression,
-                       runInputExpectedType: Option[cwl.MyriadInputType],
-                       isScattered: Boolean,
-                       sourceMappings:Map[String, OutputPort],
-                       outputTypeMap: Map[String, WomType],
-                       expressionLib: ExpressionLib,
-                       schemaDefRequirement: SchemaDefRequirement
-                      )(implicit parentName: ParentName): ErrorOr[ExpressionNode] = {
-    val inputs = sourceMappings.keySet
-    val upstreamMergeType = outputTypeMap.get(parsedId)
-
-    (for {
-      // we may have several sources, we make sure to have a type common to all of them.
-      // In the case where there's no input source, we currently wrap the valueFrom value in a WomString (see WorkflowStepInputExpression)
-      inputType <- WorkflowStepInput.determineValueFromType(upstreamMergeType, runInputExpectedType, isScattered, schemaDefRequirement)
-      womExpression = WorkflowStepInputExpression(parsedId, valueFromExpression, inputType, inputs, expressionLib)
-      identifier = WomIdentifier(id).combine("expression")
-      ret <- ExposedExpressionNode.fromInputMapping(identifier, womExpression, inputType, sourceMappings).toEither
-    } yield ret).toValidated
-  }
-
-  /**
-    *
-    * @param sourceMappings The outputports to which this source refers
-    * @param matchingRunInputType This input matches an input declared in the workflowstep's "run".  This is that step's declared type
-    * @return
-    */
-  def toMergeNode(sourceMappings: Map[String, OutputPort],
-                  expressionLib: ExpressionLib,
-                  matchingRunInputType: Option[MyriadInputType],
-                  isScattered: Boolean,
-                  schemaDefRequirement: SchemaDefRequirement
-                 ): Option[ErrorOr[ExpressionNode]] = {
-
-    val identifier = WomIdentifier(id).combine("merge")
-    val mapType = sourceMappings.map({ case (k, v) => k -> v.womType })
-
-    val maybeMatchingRunInputWomType: Option[WomType] = matchingRunInputType.map(_.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement))
-
-    def makeNode(head: (String, OutputPort), tail: List[(String, OutputPort)]) = for {
-      inputType <- determineMergeType(mapType, maybeMatchingRunInputWomType)
-      womExpression = WorkflowStepInputMergeExpression(this, inputType, NonEmptyList.of(head, tail: _*), expressionLib)
-      node <- AnonymousExpressionNode.fromInputMapping(identifier, womExpression, sourceMappings, PlainAnonymousExpressionNode.apply).toEither
-    } yield node
-
-    val matchingRunInputWomType: WomType = maybeMatchingRunInputWomType.getOrElse(WomAnyType)
-    lazy val defaultValue = default.map { _.fold(DefaultToWomValuePoly).apply(matchingRunInputWomType) }
-
-    sourceMappings.toList match {
-      case head :: tail => Option(makeNode(head, tail).toValidated)
-      case Nil =>
-        defaultValue map { _ map { d =>
-            PlainAnonymousExpressionNode(identifier, ValueAsAnExpression(d), matchingRunInputWomType, Map.empty)
-        } }
-    }
-  }
-
-  def determineMergeType(sources: Map[String, WomType], expectedTypeAsWom: Option[WomType]): Checked[WomType] = {
-    WorkflowStepInput.determineMergeType(sources, linkMerge, expectedTypeAsWom, default.isDefined)
-  }
-
-  lazy val sources: List[String] = source.toList.flatMap(_.fold(StringOrStringArrayToStringList))
-
-  lazy val effectiveLinkMerge: LinkMergeMethod = linkMerge.getOrElse(LinkMergeMethod.MergeNested)
-}
-
-object WorkflowStepInput {
-  type InputSource = String :+: Array[String] :+: CNil
-
-  implicit class EnhancedStepInputMap[A](val map: Map[WorkflowStepInput, A]) extends AnyVal {
-    def asIdentifierMap(implicit parentName: ParentName): Map[String, A] = {
-      map.map({ case (stepInput, value) => stepInput.parsedId -> value })
-    }
-  }
-
-  def determineValueFromType(mergedSourcesType: Option[WomType],
-                             expectedType: Option[MyriadInputType],
-                             isScattered: Boolean,
-                             schemaDefRequirement: SchemaDefRequirement): Checked[WomType] = {
-    val expectedTypeAsWom: Option[WomType] = expectedType.map(_.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement))
-
-    expectedTypeAsWom.getOrElse(WomStringType).asRight
-  }
-
-  def determineMergeType(sources: Map[String, WomType],
-                         linkMerge: Option[LinkMergeMethod],
-                         expectedTypeAsWom: Option[WomType],
-                         hasDefault: Boolean): Checked[WomType] = {
-
-    (sources.toList, expectedTypeAsWom, linkMerge) match {
-      // If there is a single source and no explicit merge method, use the type of the source (unpacked if it's optional
-      // and there's a default since the default would be used if there's no supplied value).
-      case (List((_, WomOptionalType(sourceType))), _, None) if hasDefault => sourceType.asRight
-      case (List((_, opt @ WomOptionalType(_))), _, None) => opt.asRight
-      case (List((_, sourceType)), _, None) => sourceType.asRight
-      // If there is a single source and merge nested is specified, wrap it into an array
-      case (List((_, sourceType)), _, Some(LinkMergeMethod.MergeNested)) => WomArrayType(sourceType).asRight
-      // If there are multiple sources and either no merge method or merge nested, find the closest common type.
-      // TODO: This is technically not enough, cwltool supports sources with totally different types, creating an array with multiple types
-      // Maybe WomCoproduct can help
-      case (_, _, Some(LinkMergeMethod.MergeNested) | None) => WomArrayType(WomType.homogeneousTypeFromTypes(sources.values)).asRight
-
-      //If sink parameter is an array and merge_flattened is used, must validate input & output types are equivalent before proceeding
-      case (_, Some(arrayType @ WomArrayType(itemType)), Some(LinkMergeMethod.MergeFlattened)) if typesToItemMatch(sources.values, itemType) => arrayType.asRight
-      // If sink parameter is not an array and merge flattened is used, validate that the sources types matche the sink type
-      case (_, Some(targetType), Some(LinkMergeMethod.MergeFlattened)) if typesToItemMatch(sources.values, targetType) => WomArrayType(targetType).asRight
-      // If the types are not compatible, fail
-      case (_, Some(targetType), Some(LinkMergeMethod.MergeFlattened)) =>
-        s"could not verify that types $sources and the items type of the run's InputArraySchema $targetType were compatible".invalidNelCheck
-
-      //We don't have type information from the run input so we gather up the sources and try to determine a common type amongst them.
-      case _ => WomType.homogeneousTypeFromTypes(sources.values).asRight
-    }
-  }
-
-  def typesToItemMatch(lst: Iterable[WomType], target: WomType): Boolean = {
-    val effectiveInputType = WomType.homogeneousTypeFromTypes(lst)
-
-    typeToItemMatch(effectiveInputType, target)
-  }
-
-  def typeToItemMatch(upstream: WomType, downstream: WomType): Boolean = {
-    upstream match {
-      case WomType.RecursiveType(innerType) => typeToItemMatch(innerType, downstream)
-      case other => other == downstream
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/WorkflowStepInputExpression.scala b/cwl/src/main/scala/cwl/WorkflowStepInputExpression.scala
deleted file mode 100644
index 476d7f44ef5..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStepInputExpression.scala
+++ /dev/null
@@ -1,51 +0,0 @@
-package cwl
-
-import cats.syntax.validated._
-import wom.expression.{FileEvaluation, IoFunctionSet}
-import wom.types._
-import wom.values._
-
-final case class WorkflowStepInputExpression(inputName: String,
-                                             valueFrom: StringOrExpression,
-                                             override val cwlExpressionType: WomType,
-                                             inputs: Set[String],
-                                             override val expressionLib: ExpressionLib) extends CwlWomExpression {
-
-  override def sourceString = inputName
-
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet) = {
-    valueFrom match {
-      // If valueFrom is a constant string value, use this as the value for this input parameter.
-      // TODO: need to handle case where this is a parameter reference, it currently looks like a String to us!
-      case StringOrExpression.String(value) => WomString(value).validNel
-
-      /*
-       * If valueFrom is a parameter reference or expression, it must be evaluated to yield the actual value to be assiged to the input field.
-       *
-       * The self value of in the parameter reference or expression must be the value of the parameter(s) specified in the source field,
-       * or null if there is no source field.
-       *
-       * The value of inputs in the parameter reference or expression must be the input object to the workflow step after
-       * assigning the source values, applying default, and then scattering. The order of evaluating valueFrom among step
-       * input parameters is undefined and the result of evaluating valueFrom on a parameter must not be visible to
-       * evaluation of valueFrom on other parameters.
-       */
-      case StringOrExpression.Expression(expression) =>
-        //used to determine the value of "self" as expected by CWL Spec
-        def selfValue = inputValues.get(inputName) match {
-          case Some(value) => value
-          case None => WomOptionalValue(WomNothingType, None)
-        }
-
-        val parameterContext = ParameterContext(ioFunctionSet, expressionLib, inputValues, selfValue)
-
-        expression.fold(EvaluateExpression).apply(parameterContext)
-      case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-    }
-  }
-
-  //this is input, so not producing any output files
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType) =
-    Set.empty[FileEvaluation].validNel
-}
-
diff --git a/cwl/src/main/scala/cwl/WorkflowStepInputMergeExpression.scala b/cwl/src/main/scala/cwl/WorkflowStepInputMergeExpression.scala
deleted file mode 100644
index bc7d4f43d75..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStepInputMergeExpression.scala
+++ /dev/null
@@ -1,84 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.Checked
-import common.validation.ErrorOr.ErrorOr
-import cwl.InputParameter.DefaultToWomValuePoly
-import wom.expression.{FileEvaluation, IoFunctionSet}
-import wom.graph.GraphNodePort.OutputPort
-import wom.types.WomType
-import wom.values.{WomArray, WomFile, WomOptionalValue, WomValue}
-
-final case class WorkflowStepInputMergeExpression(input: WorkflowStepInput,
-                                                  cwlExpressionType: WomType,
-                                                  stepInputMappingHead: NonEmptyList[(String, OutputPort)],
-                                                  override val expressionLib: ExpressionLib) extends CwlWomExpression {
-
-  private val allStepInputMappings = stepInputMappingHead.toList
-  private val allStepInputSources = allStepInputMappings.map(_._1)
-
-  override def sourceString: String = s"${input.id}-Merge-Expression"
-  override def inputs: Set[String] = allStepInputSources.toSet
-
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
-    def lookupValue(key: String): ErrorOr[WomValue] =
-      inputValues.
-        get(key).
-        toValidNel(s"source value $key not found in input values ${inputValues.mkString("\n")} and no default value provided.  Graph Inputs were ${allStepInputSources.mkString("\n")}")
-
-    def validateSources(sources: List[String]): ErrorOr[List[WomValue]] =
-      sources.
-        traverse(lookupValue)
-
-    def isEmptyOptionalValue(womValue: WomValue): Boolean = womValue match {
-      case WomOptionalValue(_, None) => true
-      case _ => false
-    }
-
-    (allStepInputSources, input.effectiveLinkMerge, input.default) match {
-      // When we have a single source but no value was provided for it and there's a default.
-      case (List(source), LinkMergeMethod.MergeNested, Some(default)) if isEmptyOptionalValue(inputValues(source)) =>
-        default.fold(DefaultToWomValuePoly).apply(cwlExpressionType)
-
-      case (List(source), LinkMergeMethod.MergeNested, _) => lookupValue(source)
-
-      //When we have several sources, validate they are all present and provide them as a nested array
-      case (sources, LinkMergeMethod.MergeNested, _) => validateSources(sources).map(WomArray.apply)
-
-      case (sources, LinkMergeMethod.MergeFlattened, _) =>
-        val validatedSourceValues: Checked[List[WomValue]] =
-          validateSources(sources).toEither
-
-        def flatten: WomValue => List[WomValue] = {
-          case WomArray(_, value) => value.toList
-          case WomOptionalValue(_, Some(value)) => flatten(value)
-          case other => List(other)
-        }
-
-        //This is the meat of "merge_flattened," where we find arrays and concatenate them to form one array
-        val flattenedValidatedSourceValues: Checked[List[WomValue]] = validatedSourceValues.map(_.flatMap(flatten))
-
-        flattenedValidatedSourceValues.map(list => WomArray(list)).toValidated
-
-      case (List(id), _, _) => lookupValue(id)
-      case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-    }
-  }
-
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
-    if (allStepInputMappings.size > 1) {
-      // TODO add MultipleInputFeatureRequirement logic in here
-      "MultipleInputFeatureRequirement not supported yet".invalidNel
-    } else {
-      val (inputName, _) = allStepInputMappings.head
-      inputTypes(inputName).collectAsSeq({
-        case file: WomFile => file
-      }).toSet[WomFile].map(FileEvaluation.requiredFile).validNel
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/command/ParentName.scala b/cwl/src/main/scala/cwl/command/ParentName.scala
deleted file mode 100644
index 6e34096d4f3..00000000000
--- a/cwl/src/main/scala/cwl/command/ParentName.scala
+++ /dev/null
@@ -1,10 +0,0 @@
-package cwl.command
-
-object ParentName {
-  def empty: ParentName = ParentName(None)
-  def apply(id: String): ParentName = ParentName(id.split("#").tail.headOption)
-}
-
-case class ParentName(value: Option[String]) {
-  def stripParent(in: String) = value.map(v => in.stripPrefix(s"$v/")).getOrElse(in)
-}
diff --git a/cwl/src/main/scala/cwl/command/StringCommandPart.scala b/cwl/src/main/scala/cwl/command/StringCommandPart.scala
deleted file mode 100644
index 9ec668231fb..00000000000
--- a/cwl/src/main/scala/cwl/command/StringCommandPart.scala
+++ /dev/null
@@ -1,18 +0,0 @@
-package cwl.command
-
-import cats.syntax.validated._
-import common.validation.ErrorOr.ErrorOr
-import wom._
-import wom.callable.RuntimeEnvironment
-import wom.expression.IoFunctionSet
-import wom.graph.LocalName
-import wom.values._
-
-case class StringCommandPart(literal: String) extends CommandPart {
-  override def instantiate(inputsMap: Map[LocalName, WomValue],
-                           functions: IoFunctionSet,
-                           valueMapper: (WomValue) => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] =
-    // TODO CWL shellquotes by default, but this shellquotes everything. Only shellquote what should be shellquoted.
-    List(InstantiatedCommand(literal.shellQuote)).validNel
-}
diff --git a/cwl/src/main/scala/cwl/internal/CommandPartSortingAlgorithm.scala b/cwl/src/main/scala/cwl/internal/CommandPartSortingAlgorithm.scala
deleted file mode 100644
index eb6ed0410ce..00000000000
--- a/cwl/src/main/scala/cwl/internal/CommandPartSortingAlgorithm.scala
+++ /dev/null
@@ -1,71 +0,0 @@
-package cwl.internal
-
-import cats.data.Kleisli._
-import cats.data.ReaderT
-import cats.data.Validated._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cwl.CommandLineTool._
-import cwl.command.ParentName
-import cwl.{ArgumentCommandLineBinding, ArgumentToCommandPart, CommandLineTool, CommandPartExpression, FullyQualifiedName, InputParameter, MyriadInputTypeToSortedCommandParts, MyriadInputTypeToWomType}
-import shapeless.Coproduct
-import wom.types.WomStringType
-
-object CommandPartSortingAlgorithm {
-  def argumentCommandParts(arguments: Option[Array[CommandLineTool.Argument]]): CommandPartExpression[List[SortKeyAndCommandPart]] =
-      // arguments is an Option[Array[Argument]], the toList.flatten gives a List[Argument]
-    arguments.toList.flatten
-      // zip the index because we need it in the sorting key
-      .zipWithIndex.flatTraverse(argumentToCommandPart.tupled)
-
-  def argumentToCommandPart: (Argument, Int) => CommandPartExpression[List[SortKeyAndCommandPart]] = (argument, index) => ReaderT {
-    case ((requirementsAndHints, expressionLib, _)) =>
-      val part = argument.fold(ArgumentToCommandPart).apply(requirementsAndHints.hasShellCommandRequirement, expressionLib)
-      // Get the position from the binding if there is one
-      val position = argument.select[ArgumentCommandLineBinding].flatMap(_.position)
-        .map(Coproduct[StringOrInt](_)).getOrElse(CommandLineTool.DefaultPosition)
-
-      // The key consists of the position followed by the index
-      val sortingKey = CommandBindingSortingKey(List(position, Coproduct[StringOrInt](index)))
-
-      List(SortKeyAndCommandPart(sortingKey, part)).validNel
-
-  }
-
-  def inputBindingsCommandParts(inputs: Array[CommandInputParameter]): CommandPartExpression[List[SortKeyAndCommandPart]] =
-    inputs.toList.flatTraverse(inputBindingsCommandPart)
-
-  def inputBindingsCommandPart(inputParameter: CommandInputParameter): CommandPartExpression[List[SortKeyAndCommandPart]] =
-    ReaderT{ case ((hintsAndRequirements, expressionLib, inputValues)) =>
-      val parsedName = FullyQualifiedName(inputParameter.id)(ParentName.empty).id
-
-      val womType = inputParameter.`type`.map(_.fold(MyriadInputTypeToWomType).apply(hintsAndRequirements.schemaDefRequirement)).getOrElse(WomStringType)
-
-      val defaultValue = inputParameter.default.map(_.fold(InputParameter.DefaultToWomValuePoly).apply(womType))
-
-      inputValues
-        .collectFirst({ case (inputDefinition, womValue) if inputDefinition.name == parsedName => womValue.validNel })
-        .orElse(defaultValue) match {
-        case Some(Valid(value)) =>
-          // See http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-          lazy val initialKey = CommandBindingSortingKey.empty
-            .append(inputParameter.inputBinding, Coproduct[StringOrInt](parsedName))
-
-          inputParameter.`type`.toList.
-            flatMap{
-              _.fold(MyriadInputTypeToSortedCommandParts).
-                apply(
-                  inputParameter.inputBinding,
-                  value,
-                  initialKey.asNewKey,
-                  hintsAndRequirements.hasShellCommandRequirement,
-                  expressionLib,
-                  hintsAndRequirements.schemaDefRequirement)
-            }.validNel
-        case Some(Invalid(errors)) => Invalid(errors)
-        case None => s"Could not find an input value for input $parsedName in ${inputValues.prettyString}".invalidNel
-      }
-    }
-
-}
diff --git a/cwl/src/main/scala/cwl/internal/CwlEcmaScriptDecoder.scala b/cwl/src/main/scala/cwl/internal/CwlEcmaScriptDecoder.scala
deleted file mode 100644
index f7f54d3db1c..00000000000
--- a/cwl/src/main/scala/cwl/internal/CwlEcmaScriptDecoder.scala
+++ /dev/null
@@ -1,124 +0,0 @@
-package cwl.internal
-
-import cats.syntax.apply._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cats.instances.option._
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.{Directory, File, FileOrDirectory}
-import org.mozilla.javascript.{ConsString, NativeArray, NativeObject}
-import shapeless.Coproduct
-import wom.types.WomNothingType
-import wom.values._
-
-import scala.jdk.CollectionConverters._
-
-class CwlEcmaScriptDecoder {
-
-  def decode(value: AnyRef): ErrorOr[WomValue] =
-    value match {
-      case map: NativeObject if map.get("class") == "File" => decodeFile(map.asScala.toMap).flatMap(_.asWomValue)
-      case map: NativeObject if map.get("class") == "Directory" => decodeDirectory(map.asScala.toMap).flatMap(_.asWomValue)
-
-      case map: NativeObject => decodeMap(map.asScala.toMap)
-      case array: NativeArray =>
-        val anyList = array.asScala.toList
-        val anyRefArray = anyList.asInstanceOf[List[AnyRef]]
-        anyRefArray.traverse(decode).map(WomArray.apply)
-
-      //we represent nulls as this type because Wom doesn't have a "null" value, but it does have a nothing type
-      //If you wish this to be otherwise please tidy up the Expression interpolator as well
-      case null => WomOptionalValue(WomNothingType, None).valid
-
-      case string: String => WomString(string).valid
-      case consString: ConsString => WomString(consString.toString).valid
-      case int: java.lang.Integer => WomInteger(int).valid
-      case long: java.lang.Long => WomLong(long).valid
-      case double: java.lang.Double if double == double.doubleValue.floor && !double.isInfinite =>
-        WomInteger(double.intValue).valid
-      case double: java.lang.Double => WomFloat(double).valid
-      case boolean: java.lang.Boolean => WomBoolean(boolean).valid
-      case unknown => s"While decoding the output $value of the Javascript interpreter, we encountered $unknown and were unable to reify it.".invalidNel
-    }
-
-  def decodeMap(map: Map[Any, Any]): ErrorOr[WomValue] = {
-    val realMap: Map[AnyRef, AnyRef] = map.asInstanceOf[Map[AnyRef, AnyRef]]
-
-    val tupleList = realMap.toList.traverse{
-      case (k,v) => (k.toString.validNel: ErrorOr[String], decode(v)).tupled
-    }
-    val mapWomValues =  tupleList.map(_.toMap)
-    mapWomValues.map(WomObject.apply)
-  }
-
-  /**
-    * Called to decode a cwl File or Directory.
-    */
-  def decodeDirectoryOrFile(value: Any): ErrorOr[FileOrDirectory] = {
-    val invalidValue = s"Not a valid CWL map or directory: $value".invalidNel
-
-    value match {
-      case map: NativeObject if map.get("class") == "File" => decodeFile(map.asScala.toMap).map(Coproduct[FileOrDirectory](_))
-      case map: NativeObject if map.get("class") == "Directory" => decodeDirectory(map.asScala.toMap).map(Coproduct[FileOrDirectory](_))
-      case _ => invalidValue
-    }
-  }
-
-  /**
-    * Called to decode an array of cwl File or Directory instances.
-    */
-  def decodeDirectoryOrFiles(value: Any): ErrorOr[Array[FileOrDirectory]] = {
-    value match {
-      case na: NativeArray => na.asScala.toList.traverse(decodeDirectoryOrFile).map(_.toArray)
-    }
-  }
-
-  /**
-    * Called to decode a map value using a supplied function.
-    */
-  def decodeMapValue[A](map: Map[Any, Any], key: String, f: Any => A): ErrorOr[Option[A]] = {
-    map.get(key).traverse(anyRef => validate(f(anyRef)))
-  }
-
-  /**
-    * Called to decode an array of files or directories from a map value.
-    */
-  def decodeMapDirectoryOrFiles(map: Map[Any, Any],
-                                key: String): ErrorOr[Option[Array[FileOrDirectory]]] = {
-    map.get(key).traverse(decodeDirectoryOrFiles)
-  }
-
-  /**
-    * Called to decode a cwl File.
-    */
-  def decodeFile(map: Map[Any, Any]): ErrorOr[File] = {
-    val location = decodeMapValue(map, "location", _.toString)
-    val path = decodeMapValue(map, "path", _.toString)
-    val basename = decodeMapValue(map, "basename", _.toString)
-    val checksum = decodeMapValue(map, "checksum", _.toString)
-    val size = decodeMapValue(map, "size", _.toString.toDouble.toLong)
-    val secondaryFiles = decodeMapDirectoryOrFiles(map, "secondaryFiles")
-    val format = decodeMapValue(map, "format", _.toString)
-    val contents = decodeMapValue(map, "contents", _.toString)
-
-    (location, path, basename, checksum, size, secondaryFiles, format, contents).mapN(
-      File(_, _, _, _, _, _, _, _)
-    )
-  }
-
-  /**
-    * Called to decode a cwl Directory.
-    */
-  def decodeDirectory(map: Map[Any, Any]): ErrorOr[Directory] = {
-    val location = decodeMapValue(map, "location", _.toString)
-    val path = decodeMapValue(map, "path", _.toString)
-    val basename = decodeMapValue(map, "basename", _.toString)
-    val listing = decodeMapDirectoryOrFiles(map, "listing")
-
-    (location, path, basename, listing).mapN(
-      Directory(_, _, _, _)
-    )
-  }
-}
diff --git a/cwl/src/main/scala/cwl/internal/EcmaScriptEncoder.scala b/cwl/src/main/scala/cwl/internal/EcmaScriptEncoder.scala
deleted file mode 100644
index e4aed51e215..00000000000
--- a/cwl/src/main/scala/cwl/internal/EcmaScriptEncoder.scala
+++ /dev/null
@@ -1,123 +0,0 @@
-package cwl.internal
-
-import cats.data.Validated.Valid
-import common.validation.ErrorOr.ErrorOr
-import cwl.internal.EcmaScriptUtil.{ECMAScriptVariable, ESArray, ESObject, ESPrimitive}
-import cwl.{Directory, File}
-import mouse.all._
-import wom.values._
-
-/**
-  * Converts a WomValue into a javascript compatible value.
-  */
-class EcmaScriptEncoder {
-
-  /**
-    * Base implementation converts any WomPrimitive (except WomFile) into a javascript compatible value.
-    *
-    * Inputs, and returned output must be one of:
-    * - WomString
-    * - WomBoolean
-    * - WomFloat
-    * - WomInteger
-    * - WomMap
-    * - WomArray
-    * - A "WomNull" equal to WomOptionalValue(WomNothingType, None)
-    *
-    * The WomMap keys and values, and WomArray elements must be the one of the above, recursively.
-    *
-    * Instances of WomFile are not permitted, and must be already converted to one of the above types.
-    *
-    * @param value A WOM value.
-    * @return The javascript equivalent.
-    */
-  def encode(value: WomValue): ECMAScriptVariable = {
-    value match {
-      case file: WomFile => encodeFileOrDirectory(file)
-      case WomOptionalValue(_, None) => ESPrimitive(null)
-      case WomOptionalValue(_, Some(innerValue)) => encode(innerValue)
-      case WomString(string) => string |> ESPrimitive
-      case WomInteger(int) => Int.box(int) |> ESPrimitive
-      case WomLong(long) => Long.box(long) |> ESPrimitive
-      case WomFloat(double) => Double.box(double) |> ESPrimitive
-      case WomBoolean(boolean) => Boolean.box(boolean) |> ESPrimitive
-      case WomArray(_, array) => array.toList.map(encode).toArray |> ESArray
-      case WomMap(_, map) => map.map{
-        case (mapKey, mapValue) => (encodeString(mapKey), encode(mapValue))
-      } |> ESObject
-      case objectLike: WomObjectLike => objectLike.values.map{
-        case (key, innerValue) => (key, encode(innerValue))
-      } |> ESObject
-      case WomCoproductValue(_, womValue) => encode(womValue)
-      case WomEnumerationValue(_, womValue) => womValue |> ESPrimitive
-      case _ => throw new RuntimeException(s"$getClass is unable to encode value: $value")
-    }
-  }
-
-  def encodeString(value: WomValue): String = {
-    encode(value) match {
-      case ESPrimitive(string: String) => string
-
-      //In the case of a non-string, we evaluate a small snippet of Ecma script meant to coerce the object to a string
-      // http://2ality.com/2012/03/converting-to-string.html
-      case _ =>
-        val jsString: ErrorOr[WomValue] = EcmaScriptUtil.evalStructish(""""" + other""","other" -> value, encoder = this)
-        jsString match {
-          case Valid(WomString(string)) => string
-          case unexpected => throw new RuntimeException(s"Expected to convert '$value' to a String but ended up with '$unexpected'")
-        }
-    }
-  }
-
-  /**
-    * Encodes a sequence of wom file or directory values.
-    */
-  def encodeFileOrDirectories(values: Seq[WomFile]): ESArray = {
-    ESArray(values.toList.map(encodeFileOrDirectory).toArray)
-  }
-
-  /**
-    * Encodes a wom file or directory value.
-    */
-  def encodeFileOrDirectory(value: WomFile): ECMAScriptVariable = {
-    value match {
-      case directory: WomUnlistedDirectory => encodeDirectory(WomMaybeListedDirectory(directory.value))
-      case file: WomSingleFile => encodeFile(WomMaybePopulatedFile(file.value))
-      case glob: WomGlobFile => encodeFile(WomMaybePopulatedFile(glob.value))
-      case directory: WomMaybeListedDirectory => encodeDirectory(directory)
-      case file: WomMaybePopulatedFile => encodeFile(file)
-    }
-  }
-
-  /**
-    * Encodes a wom file.
-    */
-  def encodeFile(file: WomMaybePopulatedFile): ECMAScriptVariable =
-    List(
-      Option("class" -> ESPrimitive("File")),
-      file.valueOption.map("location" -> ESPrimitive(_)),
-      file.valueOption.map("path" -> ESPrimitive(_)),
-      Option("basename" -> (File.basename(file.value) |> ESPrimitive)),
-      Option("dirname" -> (File.dirname(file.value) |> ESPrimitive)),
-      Option("nameroot" -> (File.nameroot(file.value) |> ESPrimitive)),
-      Option("nameext" -> (File.nameext(file.value) |> ESPrimitive)),
-      file.checksumOption.map("checksum" -> ESPrimitive(_)),
-      file.sizeOption.map(Long.box).map("size" -> ESPrimitive(_)),
-      Option("secondaryFiles" -> encodeFileOrDirectories(file.secondaryFiles)),
-      file.formatOption.map("format" -> ESPrimitive(_)),
-      file.contentsOption.map("contents" -> ESPrimitive(_))
-    ).flatten.toMap |> ESObject
-
-  /**
-    * Encodes a wom directory.
-    */
-  def encodeDirectory(directory: WomMaybeListedDirectory): ESObject = {
-    List(
-      Option("class" -> ESPrimitive("Directory")),
-      directory.valueOption.map("location" -> ESPrimitive(_)),
-      Option(directory.value).map("path" -> ESPrimitive(_)),
-      Option("basename" -> ESPrimitive(Directory.basename(directory.value))),
-      directory.listingOption.map(encodeFileOrDirectories).map("listing" -> _)
-    ).flatten.toMap |> ESObject
-  }
-}
diff --git a/cwl/src/main/scala/cwl/internal/EcmaScriptUtil.scala b/cwl/src/main/scala/cwl/internal/EcmaScriptUtil.scala
deleted file mode 100644
index d2c5def745f..00000000000
--- a/cwl/src/main/scala/cwl/internal/EcmaScriptUtil.scala
+++ /dev/null
@@ -1,128 +0,0 @@
-package cwl.internal
-
-import common.collections.EnhancedCollections._
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import org.mozilla.javascript._
-import wom.values._
-
-import scala.concurrent.duration._
-import scala.util.Try
-
-/**
-  * This implementation depends on Mozilla Rhino.
-  *
-  * Previously we attempted to use Nashorn which is built into the JDK, but we encountered at least 2 situations where
-  * it didn't work and we found no workarounds to satisfy the use cases.  Namely, JSON.stringify of a Map and calling "sort" on an array.
-  */
-//noinspection VariablePatternShadow
-object EcmaScriptUtil {
-  def writeValue(value: ECMAScriptVariable)(context: Context, scope: Scriptable): AnyRef =
-    value match {
-      case ESObject(fields) =>
-        val newObj = context.newObject(scope)
-
-        fields.toList.foreach{
-          case (name, value) =>
-            val newerObj = writeValue(value)(context, scope)
-            ScriptableObject.putProperty(newObj, name, newerObj)
-        }
-        newObj
-
-      case ESArray(array) =>
-        val newObj = context.newArray(scope, array.length)
-
-        array.toList.zipWithIndex.foreach {
-          case (js, index) =>
-
-            val newerObj = writeValue(js)(context, scope)
-            ScriptableObject.putProperty(newObj, index, newerObj)
-
-        }
-        newObj
-
-      case ESPrimitive(obj) => obj
-    }
-
-  /**
-    * Runs ECMAScript as JS1.8 (aka ES5)
-    *
-    * Uses RhinoSandbox to reduce chances injected JS wreaks havoc on the JVM.
-    *
-    * @see https://en.wikipedia.org/wiki/ECMAScript#Version_correspondence
-    */
-  def evalRaw(expr: String)(block: (Context, Scriptable) => Unit): AnyRef = {
-    // TODO: Parameterize and update callers to pass in source name, max duration, max instructions, etc.?
-    // For now, be very liberal with scripts giving 60 seconds of unrestricted CPU usage and unlimited instructions.
-    val sourceName = "<ecmascript>"
-    val maxDuration: Duration = 60.seconds
-    val maxInstructionsOption: Option[Int] = None
-    val strict = true
-    val languageVersionOption = Option(Context.VERSION_1_8)
-
-    val sandbox = new EnhancedRhinoSandbox(strict, languageVersionOption)
-    if (maxDuration.isFinite) {
-      sandbox.setMaxDuration(maxDuration.toMillis.toInt)
-    }
-    maxInstructionsOption foreach sandbox.setInstructionLimit
-    sandbox.setUseSafeStandardObjects(true)
-    sandbox.setUseSealedScope(true)
-
-    sandbox.eval(sourceName, expr)(block)
-  }
-
-  sealed trait ECMAScriptVariable
-
-  case class ESObject(fields: Map[String, ECMAScriptVariable]) extends ECMAScriptVariable
-  case class ESArray(array: Array[ECMAScriptVariable]) extends ECMAScriptVariable {
-    override def toString: String = s"ESArray(${array.toList})"
-  }
-  case class ESPrimitive(anyRef: AnyRef) extends ECMAScriptVariable
-
-  /**
-    * Evaluates a javascript expression using maps of WOM values.
-    *
-    * TODO: Once custom types are supported as WomValue, this custom method won't be required.
-    *
-    * @param expr      The javascript expression.
-    * @param rawValues A map filled with WOM values.
-    * @param mapValues A map of maps filled with WOM values of various types.
-    * @param encoder   Encodes wom values to javascript.
-    * @param decoder   Decodes wom values from javascript.
-    * @return The result of the expression.
-    */
-  def evalStructish(expr: String,
-                    rawValues: (String, WomValue),
-                    mapValues: Map[String, Map[String, WomValue]] = Map.empty,
-                    encoder: EcmaScriptEncoder,
-                    decoder: CwlEcmaScriptDecoder = new CwlEcmaScriptDecoder): ErrorOr[WomValue] = {
-    def evaluate = evalRaw(expr) { (context, scope) =>
-
-      val (key, value) = rawValues
-
-      val jsValue = encoder.encode(value)
-      val field = writeValue(jsValue)(context, scope)
-      ScriptableObject.putProperty(scope, key, field)
-
-      val jsMap = mapValues.safeMapValues{ _.safeMapValues(encoder.encode) }
-
-      jsMap foreach {
-        case (scopeId, nestedMap) =>
-
-          val newObj = context.newObject(scope)
-          nestedMap.toList foreach {
-            case (key, value) =>
-              val newerObj = writeValue(value)(context, scope)
-              ScriptableObject.putProperty(newObj, key, newerObj)
-          }
-          ScriptableObject.putProperty(scope, scopeId, newObj)
-      }
-
-    }
-    
-    for {
-      evaluated <- Try(evaluate).toErrorOr
-      decoded <- decoder.decode(evaluated)
-    } yield decoded
-  }
-}
diff --git a/cwl/src/main/scala/cwl/internal/EnhancedRhinoSandbox.scala b/cwl/src/main/scala/cwl/internal/EnhancedRhinoSandbox.scala
deleted file mode 100644
index 405c04fdaa2..00000000000
--- a/cwl/src/main/scala/cwl/internal/EnhancedRhinoSandbox.scala
+++ /dev/null
@@ -1,167 +0,0 @@
-package cwl.internal
-
-import cwl.internal.EnhancedRhinoSandbox._
-import delight.rhinosandox.internal._
-import org.mozilla.javascript._
-
-import scala.jdk.CollectionConverters._
-import scala.reflect._
-
-/**
-  * Extends the RhinoSandboxImpl with some fixes and enhancements using java reflection.
-  *
-  * @param strict Should evaluation be strict.
-  * @param languageVersionOption The optional language version to set.
-  */
-class EnhancedRhinoSandbox(strict: Boolean = true, languageVersionOption: Option[Int] = None) extends RhinoSandboxImpl {
-
-  // Allows easier reflection access to private fields
-  private lazy val sandboxImpl: RhinoSandboxImpl = this
-
-  /**
-    * Similar to RhinoSandbox.eval but passes back the context and scope for mutating before evaluation.
-    *
-    * With the original RhinoSandbox.eval not sure how to:
-    * - Create (nested) arrays
-    * - Create (nested) maps
-    * - Set JS/ES version
-    *
-    * So this uses a copy-port of the original, using reflection to read some of RhinoSandbox's private variables.
-    *
-    * Instead of hiding the context and scope as in RhinoSandbox.eval, both are passed back through the block.
-    *
-    * TODO: Ask RhinoSandbox if hacks are even needed, and if so contrib back patches so that reflection isn't required.
-    * - Is there a way to pass nested maps/arrays via a `java.util.Map[String, Object]`, or must we use our `block`?
-    * - Additionally: can we skip passing `context` to a block as a thread may just call `Context.getCurrentContext()`?
-    *
-    * @see https://maxrohde.com/2015/08/06/sandboxing-javascript-in-java-app-link-collection/
-    * @see https://github.com/javadelight/delight-rhino-sandbox/blob/9f5a073/src/main/java/delight/rhinosandox/internal/RhinoSandboxImpl.java#L100-L123
-    * @see delight.rhinosandox.internal.RhinoSandboxImpl#assertContextFactory()
-    */
-  def eval(sourceName: String, js: String)(block: (Context, Scriptable) => Unit): AnyRef = {
-    assertContextFactory()
-    val sandboxImpl_contextFactory = PrivateField(sandboxImpl, "contextFactory").as[ContextFactory]
-    // RhinoSandbox diff: eval has enterContext inside the try, but Rhino docs say it belongs outside.
-    // https://www-archive.mozilla.org/rhino/apidocs/org/mozilla/javascript/ContextFactory.html#enterContext%28%29
-    val context = sandboxImpl_contextFactory.enterContext
-    try {
-      // RhinoSandbox diff: allow setting the language version
-      languageVersionOption foreach context.setLanguageVersion
-      assertSafeScope(context)
-      val sandboxImpl_globalScope = PrivateField(sandboxImpl, "globalScope").as[ScriptableObject]
-      val sandboxImpl_sealScope = PrivateField(sandboxImpl, "sealScope").as[Boolean]
-      if (sandboxImpl_sealScope) {
-        sandboxImpl_globalScope.sealObject()
-      }
-      val sandboxImpl_safeScope = PrivateField(sandboxImpl, "safeScope").as[ScriptableObject]
-      val instanceScope = context.newObject(sandboxImpl_safeScope)
-      instanceScope.setPrototype(sandboxImpl_safeScope)
-      instanceScope.setParentScope(null)
-
-      block(context, instanceScope)
-
-      // RhinoSandbox diff: allow strict JS/ES evaluation
-      // See note at top assertContextFactory as to why we have to put 'use strict'; here.
-      // All on one line to avoid off-by-one error for javascript error messages that report line numbers.
-      // Could also pass zero as the line number, but the RhinoSandbox passes hard codes line number one also.
-      val script = if (strict) s"'use strict';$js" else js
-      context.evaluateString(instanceScope, script, sourceName, 1, null)
-    } finally {
-      Context.exit()
-    }
-  }
-
-  /**
-    * Stricter context factory modified from RhinoSandboxImpl.assertContextFactory().
-    *
-    * ContextFactory.initGlobal() is called within a static synchronized block.
-    * The globalScope initialized via initSafeStandardObjects instead of initStandardObjects.
-    *
-    * The default implementation uses a SafeContext that allows non-strict JS/ES. We would ideally set
-    * FEATURE_STRICT_MODE to true but that only produces warnings and doesn't return an error. Unfortunately when
-    * FEATURE_WARNING_AS_ERROR is enabled then non-strict Rhino warnings like "missing ;" throw errors. Instead,
-    * "'use strict';" is injected before scripts.
-    */
-  override def assertContextFactory(): Unit = {
-    if (PrivateField(sandboxImpl, "contextFactory").as[ContextFactory] != null) {
-      return
-    }
-
-    val _safeContext = new SafeContext
-    PrivateField(sandboxImpl, "contextFactory") := _safeContext
-    val _hasExplicitGlobal = ContextFactory.hasExplicitGlobal
-    val _not = !_hasExplicitGlobal
-    // RhinoSandbox diff: the global does not like to be initialized twice. Synchronize initialization.
-    val sandboxImpl_contextFactory = PrivateField(sandboxImpl, "contextFactory").as[SafeContext]
-    if (_not) initGlobalSynchronized(sandboxImpl_contextFactory)
-
-    val sandboxImpl_instructionLimit = PrivateField(sandboxImpl, "instructionLimit").as[Int]
-    PrivateField(sandboxImpl_contextFactory, "maxInstructions") := sandboxImpl_instructionLimit
-    val sandboxImpl_maxDuration = PrivateField(sandboxImpl, "maxDuration").as[Long]
-    PrivateField(sandboxImpl_contextFactory, "maxRuntimeInMs") := sandboxImpl_maxDuration
-    // RhinoSandbox diff: assertContextFactory has enterContext inside the try, but Rhino docs say it belongs outside.
-    // https://www-archive.mozilla.org/rhino/apidocs/org/mozilla/javascript/ContextFactory.html#enterContext%28%29
-    val context = sandboxImpl_contextFactory.enterContext
-    try {
-      // RhinoSandbox diff: Default globalScope is created via initStandardObjects instead of initSafeStandardObjects.
-      // initStandardObjects would add the various java packages into the global scope, including `java.io.File`, etc.
-      PrivateField(sandboxImpl, "globalScope") := context.initSafeStandardObjects(null, false)
-      val sandboxImpl_inScope = PrivateField(sandboxImpl, "inScope").as[java.util.Map[String, AnyRef]]
-      val _entrySet = sandboxImpl_inScope.entrySet
-      val sandboxImpl_globalScope = PrivateField(sandboxImpl, "globalScope").as[ScriptableObject]
-      for (entry <- _entrySet.asScala) {
-        sandboxImpl_globalScope.put(
-          entry.getKey,
-          sandboxImpl_globalScope,
-          Context.toObject(entry.getValue, sandboxImpl_globalScope))
-      }
-      val parameters = Array(classOf[String])
-      val dealMethod = classOf[RhinoEvalDummy].getMethod("eval", parameters: _*)
-      val _rhinoEval = new RhinoEval("eval", dealMethod, sandboxImpl_globalScope)
-      sandboxImpl_globalScope.defineProperty("eval", _rhinoEval, ScriptableObject.DONTENUM)
-    } finally {
-      Context.exit()
-    }
-  }
-
-}
-
-object EnhancedRhinoSandbox {
-
-  /**
-    * Get or sets a private field.
-    *
-    * @param obj  The instance to retrieve the field from.
-    * @param name The name of the field.
-    * @tparam A The class to retrieve the value from. The field MUST exist on this class, and not a superclass.
-    */
-  final case class PrivateField[A: ClassTag](obj: A, name: String) {
-    private[this] def field = {
-      val field = classTag[A].runtimeClass.getDeclaredField(name)
-      field.setAccessible(true)
-      field
-    }
-
-    def as[B]: B = {
-      field.get(obj).asInstanceOf[B]
-    }
-
-    def :=(value: Any): Unit = {
-      field.set(obj, value)
-    }
-  }
-
-  /**
-    * Call ContextFactory.initGlobal in a static synchronized block.
-    *
-    * @see [[cwl.internal.EnhancedRhinoSandbox.assertContextFactory]]
-    */
-  private def initGlobalSynchronized(sandboxImpl_contextFactory: ContextFactory) = {
-    synchronized {
-      val _hasExplicitGlobal = ContextFactory.hasExplicitGlobal
-      val _not = !_hasExplicitGlobal
-      if (_not) ContextFactory.initGlobal(sandboxImpl_contextFactory)
-    }
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/internal/GigabytesToBytes.scala b/cwl/src/main/scala/cwl/internal/GigabytesToBytes.scala
deleted file mode 100644
index 7e45aeec5ba..00000000000
--- a/cwl/src/main/scala/cwl/internal/GigabytesToBytes.scala
+++ /dev/null
@@ -1,26 +0,0 @@
-package cwl.internal
-
-import shapeless.{Coproduct, Poly1}
-
-object GigabytesToBytes extends Poly1 {
-  val toMebibytesMultiplier = Math.pow(2, 20).toLong
-
-  implicit def long = at[Long] {
-    l =>
-      val value = l * toMebibytesMultiplier
-      Coproduct[cwl.ResourceRequirementType](value)
-  }
-
-  implicit def string = at[String] {
-    s =>
-      //TODO: Scale this by multiplier https://github.com/broadinstitute/cromwell/issues/3382
-      Coproduct[cwl.ResourceRequirementType](s)
-  }
-
-  implicit def expression = at[cwl.Expression] {
-    e =>
-      //TODO: Scale this by multiplier https://github.com/broadinstitute/cromwell/issues/3382
-      Coproduct[cwl.ResourceRequirementType](e)
-  }
-}
-
diff --git a/cwl/src/main/scala/cwl/model.scala b/cwl/src/main/scala/cwl/model.scala
deleted file mode 100644
index 838ee66a98c..00000000000
--- a/cwl/src/main/scala/cwl/model.scala
+++ /dev/null
@@ -1,310 +0,0 @@
-package cwl
-
-import cwl.CommandLineTool.{CommandBindingSortingKey, SortKeyAndCommandPart}
-import cwl.SchemaDefRequirement.{AsInputEnumSchema, AsInputRecordSchema, SchemaDefTypes}
-import cwl.CwlType.CwlType
-import cwl.WorkflowStepInput.InputSource
-import cwl.command.ParentName
-import cwl.internal.GigabytesToBytes
-import eu.timepit.refined._
-import eu.timepit.refined.api.Refined
-import eu.timepit.refined.string.MatchesRegex
-import shapeless.syntax.singleton._
-import shapeless.{:+:, CNil, Coproduct, Poly1, Witness}
-import wom.types.WomType
-import wom.values.WomValue
-import mouse.all._
-
-object WorkflowStepInputSource {
-  object String {
-    def unapply(arg: InputSource): Option[String] = arg.select[String]
-  }
-  object StringArray {
-    def unapply(arg: InputSource): Option[Array[String]] = arg.select[Array[String]]
-  }
-}
-
-/**
-  * Describes a bespoke type.
-  *
-  * @param name This field actually does _not_ appear in the v1.0 schema, but it is used anyway in the conformance tests.
-  *             After some consideration it was determined that we should close our eyes and pretend it is in the spec.  It
-  *             makes its formal appearance as a required field in v1.1.
-  */
-case class InputRecordSchema(
-  name: String,
-  fields: Option[Array[InputRecordField]] = None,
-  `type`: W.`"record"`.T = W("record").value,
-  label: Option[String] = None) {
-
-}
-
-case class InputRecordField(
-  name: String,
-  `type`: MyriadInputType,
-  doc: Option[String] = None,
-  inputBinding: Option[InputCommandLineBinding],
-  label: Option[String] = None)
-
-case class InputArraySchema
-(
-  items: MyriadInputType,
-  `type`: W.`"array"`.T = Witness("array").value,
-  label: Option[String] = None,
-  inputBinding: Option[InputCommandLineBinding] = None,
-  // IAS.secondaryFiles are NOT listed in 1.0 spec, but according to jgentry they will be, maybe
-  secondaryFiles: Option[SecondaryFiles] = None
-)
-
-trait CommandLineBinding {
-  def loadContents: Option[Boolean]
-  def position: Option[Int]
-  def prefix: Option[String]
-  def separate: Option[Boolean]
-  def itemSeparator: Option[String]
-  def optionalValueFrom: Option[StringOrExpression]
-  def shellQuote: Option[Boolean]
-  // separate defaults to true
-  def effectiveSeparate = separate.getOrElse(true)
-}
-
-object InputCommandLineBinding {
-  def default = InputCommandLineBinding()
-}
-
-case class InputCommandLineBinding(
-                               loadContents: Option[Boolean] = None,
-                               position: Option[Int] = None,
-                               prefix: Option[String] = None,
-                               separate: Option[Boolean] = None,
-                               itemSeparator: Option[String] = None,
-                               valueFrom: Option[StringOrExpression] = None,
-                               shellQuote: Option[Boolean] = None) extends CommandLineBinding {
-  override val optionalValueFrom = valueFrom
-
-  def toCommandPart(sortingKey: CommandBindingSortingKey, boundValue: WomValue, hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib) = {
-    SortKeyAndCommandPart(sortingKey, InputCommandLineBindingCommandPart(this, boundValue)(hasShellCommandRequirement, expressionLib))
-  }
-}
-
-// valueFrom is required for command line bindings in the argument section: http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding
-case class ArgumentCommandLineBinding(
-                               valueFrom: StringOrExpression,
-                               loadContents: Option[Boolean] = None,
-                               position: Option[Int] = None,
-                               prefix: Option[String] = None,
-                               separate: Option[Boolean] = None,
-                               itemSeparator: Option[String] = None,
-                               shellQuote: Option[Boolean] = None) extends CommandLineBinding {
-  override val optionalValueFrom = Option(valueFrom)
-}
-
-case class InputBinding(position: Int, prefix: String)
-
-object MyriadOutputInnerTypeCacheableString extends Poly1 {
-  import Case._
-
-  private def cacheableOutputRecordFieldString(field: OutputRecordField): String = {
-    val fieldType = field.`type`.fold(MyriadOutputTypeCacheableString)
-    val lqn = field.name.substring(field.name.lastIndexOf('#') + 1)
-    s"OutputRecordField($lqn,$fieldType,${field.doc},${field.outputBinding})"
-  }
-
-  implicit def recordSchema: Aux[OutputRecordSchema, String] = at[OutputRecordSchema] {
-    s =>
-      val t = s.`type`
-      s"OutputRecordSchema($t,${s.fields.map(a => "Array(" + a.map(cacheableOutputRecordFieldString).mkString(",") + ")" )},${s.label})"
-  }
-
-  implicit def arraySchema: Aux[OutputArraySchema, String] = at[OutputArraySchema] {
-    a =>
-      val is: String = a.items.fold(MyriadOutputTypeCacheableString)
-      val t = a.`type`
-      s"OutputArraySchema($is,$t,${a.label},${a.outputBinding})"
-  }
-
-  implicit def enumSchema: Aux[OutputEnumSchema, String] = at[OutputEnumSchema] { _.toString }
-  implicit def cwlType: Aux[CwlType, String] = at[CwlType] { _.toString }
-  implicit def string: Aux[String, String] = at[String] { identity }
-}
-
-
-object MyriadOutputTypeCacheableString extends Poly1 {
-  import Case._
-
-  implicit def one: Aux[MyriadOutputInnerType, String] = at[MyriadOutputInnerType] {
-    _.fold(MyriadOutputInnerTypeCacheableString)
-  }
-
-  implicit def many: Aux[Array[MyriadOutputInnerType], String] = at[Array[MyriadOutputInnerType]] { a =>
-    val strings: Array[String] = a.map(_.fold(MyriadOutputInnerTypeCacheableString))
-    "Array(" + strings.mkString(",") + ")"
-  }
-}
-
-object SecondaryFilesCacheableString extends Poly1 {
-  import Case._
-
-  implicit def one: Aux[StringOrExpression, String] = at[StringOrExpression] {
-    _.toString
-  }
-
-  implicit def array: Aux[Array[StringOrExpression], String] = at[Array[StringOrExpression]] {
-    _.mkString("Array(", ",", ")")
-  }
-
-}
-
-case class OutputRecordSchema(
-  `type`: W.`"record"`.T,
-  fields: Option[Array[OutputRecordField]],
-  label: Option[String])
-
-case class OutputRecordField(
-  name: String,
-  `type`: MyriadOutputType,
-  doc: Option[String],
-  outputBinding: Option[CommandOutputBinding])
-
-case class OutputArraySchema(
-  items: MyriadOutputType,
-  `type`: W.`"array"`.T = Witness("array").value,
-  label: Option[String] = None,
-  outputBinding: Option[CommandOutputBinding] = None)
-
-case class InlineJavascriptRequirement(
-  `class`: W.`"InlineJavascriptRequirement"`.T = "InlineJavascriptRequirement".narrow,
-  expressionLib: Option[Array[String]] = None)
-
-case class SchemaDefRequirement(
-  types: Array[SchemaDefTypes] = Array.empty,
-  `class`: W.`"SchemaDefRequirement"`.T = Witness("SchemaDefRequirement").value) {
-
-  def lookupType(tpe: String): Option[WomType] =
-    lookupCwlType(tpe).flatMap{
-      case AsInputRecordSchema(inputRecordSchema: InputRecordSchema) => MyriadInputInnerTypeToWomType.inputRecordSchemaToWomType(inputRecordSchema).apply(this) |> Option.apply
-      case _ => None
-    }
-
-  //Currently only InputRecordSchema has a name in the spec, so it is the only thing that can be referenced via string
-  def lookupCwlType(tpe: String): Option[SchemaDefTypes] = {
-
-    def matchesType(inputEnumSchema: InputEnumSchema): Boolean = {
-      inputEnumSchema.name.fold(false){name => FileAndId(name)(ParentName.empty).id equalsIgnoreCase FileAndId(tpe)(ParentName.empty).id}
-    }
-
-    types.toList.flatMap {
-      case AsInputRecordSchema(inputRecordSchema: InputRecordSchema) if FileAndId(inputRecordSchema.name)(ParentName.empty).id equalsIgnoreCase FileAndId(tpe)(ParentName.empty).id =>
-        List(Coproduct[SchemaDefTypes](inputRecordSchema))
-      case AsInputEnumSchema(inputEnumSchema: InputEnumSchema) if matchesType(inputEnumSchema) =>
-        List(Coproduct[SchemaDefTypes](inputEnumSchema))
-      case _ =>
-        List()
-    }.headOption
-  }
-}
-
-object SchemaDefRequirement {
-  type SchemaDefTypes = InputRecordSchema :+: InputEnumSchema :+: InputArraySchema :+: CNil
-
-  object AsInputRecordSchema {
-    def unapply(arg: SchemaDefTypes): Option[InputRecordSchema] = arg.select[InputRecordSchema]
-  }
-
-  object AsInputEnumSchema {
-    def unapply(arg: SchemaDefTypes): Option[InputEnumSchema] = arg.select[InputEnumSchema]
-  }
-
-  object AsInputArraySchema {
-    def unapply(arg: SchemaDefTypes): Option[InputArraySchema] = arg.select[InputArraySchema]
-  }
-}
-
-//There is a large potential for regex refinements on these string types
-case class DockerRequirement(
-  `class`: W.`"DockerRequirement"`.T,
-  dockerPull: Option[String], //TODO Refine to match a docker image regex?
-  dockerLoad: Option[String],
-  dockerFile: Option[String],
-  dockerImport: Option[String],
-  dockerImageId: Option[String],
-  dockerOutputDirectory: Option[String]
-  )
-
-case class SoftwareRequirement(
-  `class`: W.`"SoftwareRequirement"`.T,
-  packages: Array[SoftwarePackage] = Array.empty
-  )
-
-case class SoftwarePackage(
-  `package`: String,
-  version: Option[Array[String]],
-  specs: Option[Array[String]] // This could be refined to match a regex for IRI.
-  ) {
-  type Package = String
-  type Specs = Array[String]
-}
-
-case class EnvVarRequirement(
-                              `class`: EnvVarRequirement.ClassType = EnvVarRequirement.`class`,
-                              envDef: Array[EnvironmentDef]
-                            )
-
-object EnvVarRequirement {
-  type ClassType = Witness.`"EnvVarRequirement"`.T
-
-  val `class`: ClassType = "EnvVarRequirement".asInstanceOf[ClassType]
-}
-
-case class EnvironmentDef(envName: String, envValue: StringOrExpression) {
-  type EnvName = String
-  type EnvValue = String
-}
-
-
-case class ShellCommandRequirement(`class`: W.`"ShellCommandRequirement"`.T = "ShellCommandRequirement".narrow)
-
-case class ResourceRequirement(
-                                `class`: W.`"ResourceRequirement"`.T,
-                                coresMin: Option[ResourceRequirementType],
-                                coresMax: Option[ResourceRequirementType],
-                                ramMin: Option[ResourceRequirementType],
-                                ramMax: Option[ResourceRequirementType],
-                                tmpdirMin: Option[ResourceRequirementType],
-                                tmpdirMax: Option[ResourceRequirementType],
-                                outdirMin: Option[ResourceRequirementType],
-                                outdirMax: Option[ResourceRequirementType]) {
-  def effectiveCoreMin = coresMin.orElse(coresMax)
-  def effectiveCoreMax = coresMax.orElse(coresMin)
-
-  def effectiveRamMin = ramMin.orElse(ramMax).map(_.fold(GigabytesToBytes))
-  def effectiveRamMax = ramMax.orElse(ramMin).map(_.fold(GigabytesToBytes))
-
-  def effectiveTmpdirMin = tmpdirMin.orElse(tmpdirMax)
-  def effectiveTmpdirMax = tmpdirMax.orElse(tmpdirMin)
-
-  def effectiveOutdirMin = outdirMin.orElse(outdirMax)
-  def effectiveOutdirMax = outdirMax.orElse(outdirMin)
-}
-
-/**
-  * This promotes DNA Nexus InputResourceRequirement to a first class citizen requirement, which it really isn't.
-  * Since it's the only one for now it's not a big deal but if more of these pop up we might want to treat custom requirements
-  * in a different way
-  */
-case class DnaNexusInputResourceRequirement(
-                                     `class`: String Refined MatchesRegex[W.`".*InputResourceRequirement"`.T],
-                                     indirMin: Option[Long]
-                                   )
-
-case class SubworkflowFeatureRequirement(
-  `class`: W.`"SubworkflowFeatureRequirement"`.T)
-
-case class ScatterFeatureRequirement(
-  `class`: W.`"ScatterFeatureRequirement"`.T)
-
-case class MultipleInputFeatureRequirement(
-  `class`: W.`"MultipleInputFeatureRequirement"`.T)
-
-case class StepInputExpressionRequirement(
-  `class`: W.`"StepInputExpressionRequirement"`.T)
diff --git a/cwl/src/main/scala/cwl/ontology/CacheConfiguration.scala b/cwl/src/main/scala/cwl/ontology/CacheConfiguration.scala
deleted file mode 100644
index cb82d9db591..00000000000
--- a/cwl/src/main/scala/cwl/ontology/CacheConfiguration.scala
+++ /dev/null
@@ -1,15 +0,0 @@
-package cwl.ontology
-
-import com.typesafe.config.Config
-import common.validation.Validation._
-import net.ceedubs.ficus.Ficus._
-
-case class CacheConfiguration(maxSize: Long)
-
-object CacheConfiguration {
-  def apply(config: Config): CacheConfiguration = {
-    validate(config.getAs[Long]("max-size").getOrElse(0L))
-      .map(new CacheConfiguration(_))
-      .unsafe("Ontology cache configuration")
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ontology/OntologyConfiguration.scala b/cwl/src/main/scala/cwl/ontology/OntologyConfiguration.scala
deleted file mode 100644
index 5382ac35b91..00000000000
--- a/cwl/src/main/scala/cwl/ontology/OntologyConfiguration.scala
+++ /dev/null
@@ -1,27 +0,0 @@
-package cwl.ontology
-
-import cats.syntax.apply._
-import com.typesafe.config.Config
-import common.util.Backoff
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import net.ceedubs.ficus.Ficus._
-
-import scala.concurrent.duration.FiniteDuration
-
-case class OntologyConfiguration(retries: Option[Int], backoff: Backoff, poolSize: Int)
-
-object OntologyConfiguration {
-  def apply(config: Config): OntologyConfiguration = {
-    val retries = validate { Option(config.as[Int]("retries")) }
-    val backoff = validate {
-      Backoff.staticBackoff(
-        config.as[FiniteDuration]("backoff-time")
-      )
-    }
-    val poolSize = validate { config.as[Int]("pool-size") }
-
-    val validated: ErrorOr[OntologyConfiguration] = (retries, backoff, poolSize).mapN(OntologyConfiguration.apply)
-    validated.unsafe("Ontology configuration")
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ontology/Schema.scala b/cwl/src/main/scala/cwl/ontology/Schema.scala
deleted file mode 100644
index a2ed13d7bf3..00000000000
--- a/cwl/src/main/scala/cwl/ontology/Schema.scala
+++ /dev/null
@@ -1,180 +0,0 @@
-package cwl.ontology
-
-import java.util.concurrent.Executors
-
-import cats.effect.IO
-import cats.syntax.traverse._
-import cats.instances.list._
-import com.google.common.cache.{Cache, CacheBuilder}
-import com.typesafe.config.{Config, ConfigFactory}
-import com.typesafe.scalalogging.Logger
-import common.util.IORetry
-import common.util.IORetry.StatefulIoError
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.ontology.Schema._
-import mouse.all._
-import net.ceedubs.ficus.Ficus._
-import org.semanticweb.owlapi.apibinding.OWLManager
-import org.semanticweb.owlapi.model._
-import org.semanticweb.owlapi.model.parameters.OntologyCopy
-import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory
-import org.semanticweb.owlapi.reasoner.{OWLReasoner, OWLReasonerFactory}
-import org.semanticweb.owlapi.util.OWLAPIStreamUtils
-import org.slf4j.LoggerFactory
-
-import scala.jdk.CollectionConverters._
-import scala.concurrent.ExecutionContext
-import scala.util.Try
-
-/**
-  * OWL/RDF Schema lookup.
-  *
-  * @param schemaIris IRI paths to OWL/RDF schemas.
-  * @param namespaces Additional/Override namespace prefixes.
-  */
-case class Schema(schemaIris: Seq[String],
-                  namespaces: Map[String, String],
-                  ontologyManager: OWLOntologyManager = OWLManager.createOWLOntologyManager,
-                  reasonerFactory: OWLReasonerFactory = new StructuralReasonerFactory) {
-
-  /**
-    * Returns a full IRI based on a full or abbreviated IRI.
-    *
-    * A full IRI wrapped in < and > will not be checked for abbreviations but will be returned without the wrapper.
-    *
-    * @see https://www.w3.org/TR/owl2-syntax/#IRIs
-    */
-  def fullIri(name: String): String = getIri(name).getIRIString
-
-  /**
-    * Returns true if child is an equivalent of ancestor, and if not then recursively checks if any of the child's
-    * super classes are an equivalent of ancestor.
-    */
-  def isSubClass(child: String, ancestor: String): Boolean = {
-    val childIri: IRI = getIri(child)
-    val ancestorIri: IRI = getIri(ancestor)
-    val childClass: OWLClass = dataFactory.getOWLClass(childIri)
-    val ancestorClass: OWLClass = dataFactory.getOWLClass(ancestorIri)
-    val schemaReasoner: OWLReasoner = reasonerFactory.createReasoner(schemaOntology)
-    try {
-      Schema.isSubClass(schemaReasoner, childClass, ancestorClass)
-    } finally {
-      schemaReasoner.dispose()
-    }
-  }
-
-  private val dataFactory: OWLDataFactory = ontologyManager.getOWLDataFactory
-  private val schemaOntology: OWLOntology = ontologyManager.createOntology()
-  private val schemaPrefixManager: PrefixManager =
-    ontologyManager.getOntologyFormat(schemaOntology).asPrefixOWLDocumentFormat
-
-  {
-    def addToSchema(originalOntology: OWLOntology): Unit = {
-      schemaOntology.addAxioms(originalOntology.axioms())
-      val originalOntologyFormat: OWLDocumentFormat = ontologyManager.getOntologyFormat(originalOntology)
-      if (originalOntologyFormat.isPrefixOWLDocumentFormat)
-        schemaPrefixManager.copyPrefixesFrom(originalOntologyFormat.asPrefixOWLDocumentFormat)
-    }
-
-    val errorOr: ErrorOr[Unit] = for {
-      ontologies <- schemaIris.toList.traverse(loadOntologyFromIri(ontologyManager))
-      _ = ontologies.foreach(addToSchema)
-    } yield ()
-    errorOr.toTry("Error loading schemas").get
-
-    // Add any namespace overrides
-    namespaces foreach {
-      case (prefixName, prefix) => schemaPrefixManager.setPrefix(prefixName, prefix)
-    }
-  }
-
-  /**
-    * Returns the full IRI for the name using the prefixManager.
-    *
-    * TODO: Not 100% sure why you can't ask owl-api for an iri-with-prefix and have it looked up automatically.
-    *
-    * There does seem to be a difference between abbreviated and full IRIs in the official spec, where full IRIs are
-    * wrapped in < >. But this doesn't seem to be the format used by CWL nor owl-api.
-    *
-    * Please update this comment if/when one knows the correct behavior.
-    *
-    * @see https://www.w3.org/TR/owl2-syntax/#IRIs
-    */
-  private def getIri(name: String): IRI = {
-    Try(schemaPrefixManager.getIRI(name)).getOrElse(IRI.create(name))
-  }
-}
-
-object Schema {
-  // Extending StrictLogging creates a circular dependency here for some reason, so making the logger ourselves
-  private val logger: Logger = Logger(LoggerFactory.getLogger(getClass.getName))
-  private [ontology] val ontologyConfig = ConfigFactory.load.as[Config]("ontology")
-  private val ontologyConfiguration = OntologyConfiguration(ontologyConfig)
-  private [ontology] val cacheConfig = ontologyConfig.getAs[Config]("cache")
-
-  // Simple cache to avoid reloading the same ontologies too often
-  private val ontologyCache = cacheConfig.map(makeOntologyCache)
-
-  private implicit val statefulIoError = StatefulIoError.noop[Unit]
-  private implicit val timer = cats.effect.IO.timer(ExecutionContext.fromExecutor(Executors.newFixedThreadPool(ontologyConfiguration.poolSize)))
-
-  private [ontology] def makeOntologyCache(config: Config): Cache[IRI, OWLOntology] = {
-    val cacheConfig = CacheConfiguration(config)
-    logger.info(s"Ontology cache size: ${cacheConfig.maxSize}")
-    CacheBuilder.newBuilder()
-      .maximumSize(cacheConfig.maxSize)
-      .build[IRI, OWLOntology]()
-  }
-
-  /**
-    * Returns the absolute path for a file, possibly relative to parent.
-    */
-  def getIriPath(parent: String, path: String): String = IRI.create(parent).resolve(path).getIRIString
-
-  /**
-    * Load an ontology either from an IRI.
-    */
-  private [ontology] def loadOntologyFromIri(ontologyManager: OWLOntologyManager, cache: Option[Cache[IRI, OWLOntology]] = ontologyCache)(schemaIri: String): ErrorOr[OWLOntology] = {
-    validate {
-      val iri = IRI.create(schemaIri)
-      cache.flatMap(_.getIfPresent(iri) |> Option.apply) match {
-        case Some(ontology) =>
-          ontologyManager.copyOntology(ontology, OntologyCopy.DEEP)
-        case _ =>
-          logger.info(s"Loading ${iri.toURI.toString}")
-          val ontology = loadOntologyFromIri(ontologyManager, iri)
-          cache.foreach(_.put(iri, ontology))
-          ontology
-      }
-    }
-  }
-
-  // Loading the ontology can fail transiently, so put retires around it. See https://github.com/protegeproject/webprotege/issues/298
-  private [ontology] def loadOntologyFromIri(ontologyManager: OWLOntologyManager, iri: IRI): OWLOntology = {
-    val load = IO { ontologyManager.loadOntologyFromOntologyDocument(iri) }
-    IORetry.withRetry[OWLOntology, Unit](load, (), ontologyConfiguration.retries, ontologyConfiguration.backoff).unsafeRunSync()
-  }
-
-  /**
-    * Returns true if child is an equivalent of ancestor, and if not then recursively checks if any of the child's
-    * super classes are an equivalent of ancestor.
-    */
-  private def isSubClass(reasoner: OWLReasoner, childClass: OWLClass, ancestorClass: OWLClass): Boolean = {
-    val equivalent: Set[OWLClass] = reasoner.getEquivalentClasses(childClass).asScala.toSet + childClass
-    if (equivalent.contains(ancestorClass)) {
-      true
-    } else {
-      val parentClasses: Set[OWLClass] = for {
-        equivalentClass <- equivalent
-        parentClass <- OWLAPIStreamUtils
-          .asSet(reasoner.getSuperClasses(equivalentClass).entities)
-          .asScala
-          .toSet[OWLClass]
-      } yield parentClass
-      parentClasses.collect({
-        case superClass: OWLClass if isSubClass(reasoner, superClass, ancestorClass) => superClass
-      }).nonEmpty
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/package.scala b/cwl/src/main/scala/cwl/package.scala
deleted file mode 100644
index 96796712f1e..00000000000
--- a/cwl/src/main/scala/cwl/package.scala
+++ /dev/null
@@ -1,154 +0,0 @@
-
-import cats.data.ReaderT
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr._
-import cwl.CwlType._
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import cwl.command.ParentName
-import cwl.ontology.Schema
-import shapeless._
-import wom.executable.Executable
-import wom.expression.IoFunctionSet
-import wom.types._
-import wom.values.WomEvaluatedCallInputs
-
-import scala.util.{Failure, Success, Try}
-
-/**
- * This package is intended to parse all CWL files.
- *
- * It makes heavy use of Circe YAML/Json auto derivation feature and
- * Circe modules that support the Scala libraries shapeless and Refined.
- *
- * The [[https://oss.sonatype.org/service/local/repositories/releases/archive/com/chuusai/shapeless_2.12/2.3.2/shapeless_2.12-2.3.2-javadoc.jar/!/shapeless/Coproduct.html shapeless.coproduct]] feature allows us to specify a large
- * number of potential types to be parsed.  A.k.a. a "disjunction" or "OR" relationship amongst these types.
- *
- * The [[https://github.com/fthomas/refined/blob/master/modules/core/shared/src/main/scala/eu/timepit/refined/string.scala MatchesRegex]] "refined type" is used
- * to enforce structure upon String values in the CWL Yaml.  Shapeless' Witness type
- * is used to declare a type containing a String literal.
- *
- * @see <a href="http://www.commonwl.org/v1.0/">CWL Specification</a>
- * @see <a href="https://github.com/circe/circe">circe</a>
- * @see <a href="https://github.com/circe/circe-yaml">circe-yaml</a>
- * @see <a href="https://github.com/fthomas/refined">Refined</a>
- * @see <a href="https://github.com/milessabin/shapeless">Shapeless</a>
- */
-package object cwl extends TypeAliases {
-
-  type CwlFile = Array[Cwl] :+: Cwl :+: CNil
-  type Cwl = Workflow :+: CommandLineTool :+: ExpressionTool :+: CNil
-
-  object Cwl {
-    object Workflow { def unapply(cwl: Cwl): Option[Workflow] = cwl.select[Workflow] }
-    object CommandLineTool { def unapply(cwl: Cwl): Option[CommandLineTool] = cwl.select[CommandLineTool] }
-    object ExpressionTool { def unapply(cwl: Cwl): Option[ExpressionTool] = cwl.select[ExpressionTool] }
-  }
-
-  def cwlTypeToWomType : CwlType => WomType = {
-    case CwlType.Any => WomAnyType
-    case Null => WomNothingType
-    case Boolean => WomBooleanType
-    case Int => WomIntegerType
-    case Long => WomLongType
-    case Float => WomFloatType
-    case Double => WomFloatType
-    case String => WomStringType
-    case CwlType.File => WomMaybePopulatedFileType
-    case CwlType.Directory => WomMaybeListedDirectoryType
-  }
-
-  object StringOrExpression {
-    object String {
-      def unapply(soe: StringOrExpression): Option[String] = soe.select[String]
-    }
-    object Expression {
-      def unapply(soe: StringOrExpression): Option[Expression] = soe.select[Expression]
-    }
-    object ECMAScriptExpression {
-      def unapply(soe: StringOrExpression): Option[ECMAScriptExpression] = soe.select[Expression].flatMap(_.select[ECMAScriptExpression])
-    }
-    object ECMAScriptFunction {
-      def unapply(soe: StringOrExpression): Option[ECMAScriptFunction] = soe.select[Expression].flatMap(_.select[ECMAScriptFunction])
-    }
-  }
-
-  object Expression {
-    object ECMAScriptExpression {
-      def unapply(soe: Expression): Option[ECMAScriptExpression] = soe.select[ECMAScriptExpression]
-    }
-    object ECMAScriptFunction {
-      def unapply(soe: Expression): Option[ECMAScriptFunction] = soe.select[ECMAScriptFunction]
-    }
-  }
-
-  type WomTypeMap = Map[String, WomType]
-
-  type RequirementsValidator = Requirement => ErrorOr[Requirement]
-  import cats.syntax.validated._
-  val AcceptAllRequirements: RequirementsValidator = _.validNel
-
-  implicit class CwlHelper(val cwl: Cwl) extends AnyVal {
-    def womExecutable(validator: RequirementsValidator, inputsFile: Option[String], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-      def executable = cwl match {
-        case Cwl.Workflow(w) => w.womExecutable(validator, inputsFile, ioFunctions, strictValidation)
-        case Cwl.CommandLineTool(clt) => clt.womExecutable(validator, inputsFile, ioFunctions, strictValidation)
-        case Cwl.ExpressionTool(et) => et.womExecutable(validator, inputsFile, ioFunctions, strictValidation)
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-      Try(executable) match {
-        case Success(s) => s
-        case Failure(f) => f.getMessage.invalidNelCheck
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-    }
-
-    def requiredInputs: Map[String, WomType] = {
-      implicit val parent = ParentName.empty
-
-      cwl match {
-        case Cwl.Workflow(w) => selectWomTypeInputs(w.inputs collect {
-          case i if i.`type`.isDefined => FullyQualifiedName(i.id).id -> i.`type`.get
-        })
-        case Cwl.CommandLineTool(clt) => selectWomTypeInputs(clt.inputs collect {
-          case i if i.`type`.isDefined => FullyQualifiedName(i.id).id -> i.`type`.get
-        })
-        case Cwl.ExpressionTool(et) => selectWomTypeInputs(et.inputs collect {
-          case i if i.`type`.isDefined => FullyQualifiedName(i.id).id -> i.`type`.get
-        })
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-    }
-
-    def schemaOption: Option[Schema] = cwl.fold(CwlSchemaOptionPoly)
-
-    private def selectWomTypeInputs(myriadInputMap: Array[(String, MyriadInputType)]): Map[String, WomType] = {
-      (myriadInputMap collect {
-        case (key, MyriadInputType.WomType(w)) => key -> w
-      }).toMap
-    }
-  }
-
-  object CwlSchemaOptionPoly extends Poly1 {
-    implicit val caseWorkflow: Case.Aux[Workflow, Option[Schema]] = at {
-      workflow => getSchema(workflow.`$schemas`, workflow.`$namespaces`)
-    }
-    implicit val caseCommandLineTool: Case.Aux[CommandLineTool, Option[Schema]] = at {
-      commandLineTool => getSchema(commandLineTool.`$schemas`, commandLineTool.`$namespaces`)
-    }
-    implicit val caseExpressionTool: Case.Aux[ExpressionTool, Option[Schema]] = at {
-      expressionTool => getSchema(expressionTool.`$schemas`, expressionTool.`$namespaces`)
-    }
-
-    private def getSchema(schemasOption: Option[Array[String]],
-                          namespacesOption: Option[Map[String, String]]): Option[Schema] = {
-      schemasOption.map(a => Schema(a.toIndexedSeq, namespacesOption getOrElse Map.empty))
-    }
-  }
-
-  type ExpressionLib = Vector[String]
-
-  type Inputs = (RequirementsAndHints, ExpressionLib, WomEvaluatedCallInputs)
-
-  type CommandPartExpression[A] = ReaderT[ErrorOr, Inputs, A]
-}
diff --git a/cwl/src/main/scala/cwl/preprocessor/CwlCanonicalizer.scala b/cwl/src/main/scala/cwl/preprocessor/CwlCanonicalizer.scala
deleted file mode 100644
index b369d404c18..00000000000
--- a/cwl/src/main/scala/cwl/preprocessor/CwlCanonicalizer.scala
+++ /dev/null
@@ -1,249 +0,0 @@
-package cwl.preprocessor
-
-import cats.effect.{ContextShift, IO}
-import cats.syntax.parallel._
-import cats.instances.list._
-import common.validation.ErrorOr.ErrorOr
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.preprocessor.CwlReference.EnhancedCwlId
-import cwl.preprocessor.CwlPreProcessor._
-import io.circe.Json
-import io.circe.optics.JsonPath._
-import cwl.preprocessor.CwlCanonicalizer._
-
-/**
-  * The real guts of the CWL pre-processor is taking a CWL reference and producing a single, self-contained JSON from it.
-  */
-private [preprocessor] class CwlCanonicalizer(saladFunction: SaladFunction)(implicit cs: ContextShift[IO]) {
-
-  def getCanonicalCwl(reference: CwlReference,
-                      namespacesJsonOption: Option[Json] = None,
-                      schemasJsonOption: Option[Json] = None): IOChecked[Json] = {
-    flattenCwlReferenceInner(
-      reference,
-      Map.empty,
-      Map.empty,
-      Set.empty,
-      namespacesJsonOption,
-      schemasJsonOption).map(_.processedJson)
-  }
-
-  /**
-    * Flatten the cwl reference given already known processed references.
-    */
-  private def flattenCwlReferenceInner(cwlReference: CwlReference,
-                                       unProcessedReferences: UnProcessedReferences,
-                                       processedReferences: ProcessedReferences,
-                                       breadCrumbs: Set[CwlReference],
-                                       namespacesJsonOption: Option[Json],
-                                       schemasJsonOption: Option[Json]): IOChecked[ProcessedJsonAndDependencies] = {
-    /*
-     * Salad and parse from a CWL reference into a Json object
-     */
-    def saladAndParse(ref: CwlReference): IOChecked[Json] =  for {
-      saladed <- saladFunction(ref)
-      saladedJson <- parseJson(saladed)
-    } yield saladedJson
-
-    for {
-      // parse the file containing the reference
-      parsed <- saladAndParse(cwlReference)
-      // Get a Map[CwlReference, Json] from the parsed file. If the file is a JSON object and only contains one node, the map will only have 1 element
-      newUnProcessedReferences = mapIdToContent(parsed).toMap
-      // The reference json in the file
-      referenceJson <- newUnProcessedReferences
-        .collectFirst({ case (ref, json) if ref.pointerWithinFile == cwlReference.pointerWithinFile => json })
-        .toIOChecked(s"Cannot find a tool or workflow with ID '${cwlReference.pointerWithinFile}' in file ${cwlReference.pathAsString}'s set: [${newUnProcessedReferences.keySet.mkString(", ")}]")
-      // Process the reference json
-      processed <- flattenJson(
-        referenceJson,
-        newUnProcessedReferences ++ unProcessedReferences,
-        processedReferences,
-        breadCrumbs + cwlReference,
-        namespacesJsonOption,
-        schemasJsonOption
-      )
-    } yield processed
-  }
-
-  /**
-    * Given a Json representing a tool or workflow, flattens it and return the other processed references that were generated.
-    *
-    * NB: Flatten here means two things:
-    *  - Find references within the CWL and convert them into 'local' links
-    *  - Create a map of canonical links to JSON CWL content
-    *
-    * @param saladedJson           json to process
-    * @param unProcessedReferences references that have been parsed and saladed (we have the json), but not flattened yet
-    * @param processedReferences   references that are fully flattened
-    * @param breadCrumbs           list of references that brought us here
-    * @param namespacesJsonOption  Namespaces from the original json
-    * @param schemasJsonOption     Schemas from the original json
-    */
-  private def flattenJson(saladedJson: Json,
-                          unProcessedReferences: UnProcessedReferences,
-                          processedReferences: ProcessedReferences,
-                          breadCrumbs: Set[CwlReference],
-                          namespacesJsonOption: Option[Json],
-                          schemasJsonOption: Option[Json]): IOChecked[ProcessedJsonAndDependencies] = {
-    /*
-     * Given a reference from a step's run field, flattens it and return it
-     * @param unProcessedReferences references that have been parsed and saladed (we have the json), but not flattened yet.
-     * @param checkedProcessedReferences references that are fully processed
-     * @param cwlReference reference being processed
-     * @return a new ProcessedReferences Map including this cwlReference processed along with all the dependencies
-     *         that might have been processed recursively.
-     */
-    def processCwlRunReference(checkedProcessedReferences: IOChecked[ProcessedReferences],
-                               cwlReference: CwlReference): IOChecked[ProcessedReferences] = {
-      def processReference(processedReferences: ProcessedReferences) = {
-
-        val result: IOChecked[ProcessedJsonAndDependencies] = unProcessedReferences.get(cwlReference) match {
-          case Some(unProcessedReferenceJson) =>
-            // Found the json in the unprocessed map, no need to reparse the file, just flatten this json
-            flattenJson(
-              unProcessedReferenceJson,
-              unProcessedReferences,
-              processedReferences,
-              breadCrumbs,
-              namespacesJsonOption,
-              schemasJsonOption
-            )
-          case None =>
-            // This is the first time we're seeing this reference, we need to parse its file and flatten it
-            flattenCwlReferenceInner(
-              cwlReference,
-              unProcessedReferences,
-              processedReferences,
-              breadCrumbs,
-              namespacesJsonOption,
-              schemasJsonOption
-            )
-        }
-
-        result map {
-          // Return everything we've got (the previously known "processedReferences" + our new processed reference + everything that was processed to get to it)
-          case ProcessedJsonAndDependencies(processed, newReferences) => processedReferences ++ newReferences + (cwlReference -> processed)
-        }
-      }
-
-      def processIfNeeded(processedReferences: ProcessedReferences): IOChecked[ProcessedReferences] = {
-        // If the reference has already been processed, no need to do anything
-        if (processedReferences.contains(cwlReference)) processedReferences.validIOChecked
-        // If the reference is in the bread crumbs it means we circled back to it: fail the pre-processing
-        else if (breadCrumbs.contains(cwlReference)) s"Found a circular dependency on $cwlReference".invalidIOChecked
-        // Otherwise let's see if we already have the json for it or if we need to process the file
-        else processReference(processedReferences)
-      }
-
-      for {
-        processedReferences <- checkedProcessedReferences
-        newReferences <- processIfNeeded(processedReferences)
-      } yield newReferences
-    }
-
-    def addJsonKeyValue(originalJson: Json, key: String, valueOption: Option[Json]): Json = {
-      valueOption match {
-        case Some(value) => originalJson.mapObject(_.add(key, value))
-        case None => originalJson
-      }
-    }
-
-    val namespacesJson = addJsonKeyValue(saladedJson, JsonKeyNamespaces, namespacesJsonOption)
-    val schemasJson = addJsonKeyValue(namespacesJson, JsonKeySchemas, schemasJsonOption)
-
-    import cats.syntax.apply._
-
-    // Take the processed runs and inject them in the json
-    def inlineProcessedJsons(newKnownReferences: ProcessedReferences, inlinedRunWorkflows: Map[String, ProcessedJsonAndDependencies]) = {
-      // Provide a function to swap the run reference with its json content
-      val lookupFunction: Json => Json = {
-        json: Json => {
-          val fromRunReferenceMap = for {
-            asString <- json.asString
-            reference <- asString.asReference
-            embeddedJson <- newKnownReferences.get(reference)
-          } yield embeddedJson
-
-          val fromInlinedWorkflow = for {
-            asObject <- json.asObject
-            id <- asObject.kleisli("id")
-            idAsString <- id.asString
-            embeddedJson <- inlinedRunWorkflows.get(idAsString)
-          } yield embeddedJson.processedJson
-
-          fromRunReferenceMap.orElse(fromInlinedWorkflow).getOrElse(json)
-        }
-      }
-
-      val flattenedJson = root.steps.each.run.json.modify(lookupFunction)(schemasJson)
-
-      ProcessedJsonAndDependencies(flattenedJson, newKnownReferences ++ inlinedRunWorkflows.values.flatMap(_.processedDependencies))
-    }
-
-    /*
-     * Given a json, collects all "steps.run" values that are JSON Strings, and convert them to CwlReferences.
-     * A saladed JSON is assumed.
-     */
-    def findRunReferences(json: Json): List[CwlReference] = {
-      json.asArray match {
-        case Some(cwls) => cwls.toList.flatMap(findRunReferences)
-        case _ => root.steps.each.run.string.getAll(json).flatMap(_.asReference).distinct
-      }
-    }
-
-    /*
-     * Given a json, collects all "steps.run" values that are JSON Objects representing a workflow.
-     * A saladed JSON is assumed.
-     * @return a Map[String, Json], where the key is the cwl id of the workflow, and the value its content
-     */
-    def findRunInlinedWorkflows(json: Json): ErrorOr[Map[String, Json]] = {
-      import cats.syntax.traverse._
-
-      json.asArray match {
-        case Some(cwls) => cwls.toList
-          .flatTraverse(findRunInlinedWorkflows(_).map(_.toList))
-          .map(_.toMap)
-        case _ =>
-          // Look for all the "run" steps that are json objects
-          root.steps.each.run.obj.getAll(json)
-            .map(Json.fromJsonObject)
-            // Only keep the workflows (CommandLineTools don't have steps so no need to process them)
-            .filter(root.`class`.string.exist(_.equalsIgnoreCase("Workflow")))
-            .traverse[ErrorOr, (String, Json)]( obj =>
-              // Find the id of the workflow
-              root.id.string.getOption(obj)
-                .toErrorOr("Programmer error: Workflow did not contain an id. Make sure the cwl has been saladed")
-                .map(_ -> obj)
-            ).map(_.toMap)
-      }
-    }
-
-    // Recursively process the run references (where run is a string pointing to another Workflow / Tool)
-    // TODO: it would be nice to accumulate failures here somehow (while still folding and be able to re-use
-    // successfully processed references, so I don't know if ErrorOr would work)
-    val processedRunReferences: IOChecked[ProcessedReferences] = findRunReferences(schemasJson).foldLeft(processedReferences.validIOChecked)(processCwlRunReference)
-
-    // Recursively process the inlined run workflows (where run is a Json object representing a workflow)
-    val processedInlineReferences: IOChecked[Map[String, ProcessedJsonAndDependencies]] = (for {
-      inlineWorkflowReferences <- findRunInlinedWorkflows(saladedJson).toIOChecked
-      flattenedWorkflows <- inlineWorkflowReferences.toList.parTraverse[IOChecked, (String, ProcessedJsonAndDependencies)]({
-        case (id, value) => flattenJson(value, unProcessedReferences, processedReferences, breadCrumbs, namespacesJsonOption, schemasJsonOption).map(id -> _)
-      })
-    } yield flattenedWorkflows).map(_.toMap)
-
-    // Replace the unprocessed runs with their processed value
-    (processedRunReferences, processedInlineReferences).tupled.map(Function.tupled(inlineProcessedJsons))
-  }
-}
-
-private object CwlCanonicalizer {
-  /**
-    * A Cwl json that has been processed (saladed and flattened), as well as its processed dependencies.
-    */
-  final case class ProcessedJsonAndDependencies(processedJson: Json, processedDependencies: ProcessedReferences)
-
-  final type UnProcessedReferences = Map[CwlReference, Json]
-  final type ProcessedReferences = Map[CwlReference, Json]
-}
diff --git a/cwl/src/main/scala/cwl/preprocessor/CwlPreProcessor.scala b/cwl/src/main/scala/cwl/preprocessor/CwlPreProcessor.scala
deleted file mode 100644
index 9855ee73953..00000000000
--- a/cwl/src/main/scala/cwl/preprocessor/CwlPreProcessor.scala
+++ /dev/null
@@ -1,236 +0,0 @@
-package cwl.preprocessor
-
-import java.util.concurrent.Executors
-
-import cats.data.NonEmptyList
-import cats.effect.{ContextShift, IO}
-import cats.syntax.either._
-import common.validation.IOChecked._
-import cwl.CwlDecoder
-import cwl.ontology.Schema
-import cwl.preprocessor.CwlPreProcessor._
-import cwl.preprocessor.CwlReference.EnhancedCwlId
-import io.circe.optics.JsonPath._
-import io.circe.{Json, JsonNumber, JsonObject}
-import mouse.all._
-import org.slf4j.LoggerFactory
-import wom.util.YamlUtils
-
-import scala.concurrent.ExecutionContext
-
-/**
-  * Class to create a standalone version of a CWL file.
-  *
-  * NB: Want to use the pre-processor? Use preProcessCwl(ref: CwlReference)
-  *
-  * @param saladFunction function that takes a file and produce a saladed version of the content
-  */
-class CwlPreProcessor(saladFunction: SaladFunction = saladCwlFile) {
-
-  private val ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(5))
-  private implicit val cs = IO.contextShift(ec)
-
-  /**
-    * This is THE main entry point into the CWL pre-processor. Takes a CWL reference and
-    * returns a canonical JSON version with all references resolved.
-    *
-    * @param ref The reference to the CWL to pre-process
-    * @return A canonical JSON representation of the CWL with all internal references expanded in-place
-    */
-  def preProcessCwl(ref: CwlReference): IOChecked[Json] = ref match {
-    case file: CwlFileReference => preProcessCwlFile(file)
-    case other => preProcessRemoteCwl(other)
-  }
-
-  /**
-    * Convenience method to get the processed workflow as a string.
-    */
-  def preProcessCwlToString(cwlReference: CwlReference): IOChecked[String] = preProcessCwl(cwlReference).map(_.printCompact)
-
-  def preProcessInputFiles(inputContent: String, mappingFunction: String => String): IOChecked[String] = for {
-    parsed <- parseYaml(inputContent)
-    mapped = parsed |> mapFilesAndDirectories(mappingFunction) |> mapNumbers
-  } yield mapped.printCompact
-
-  /**
-    * Pre-process a CWL file and create a standalone, runnable (given proper inputs), inlined version of its content.
-    *
-    * The general idea is to work on CwlReferences, starting from the one coming to this function in the form of file and optional root.
-    * The goal is to look at the steps in this workflow that point to other references, and recursively flatten them until we can replace the step with
-    * its flat version.
-    *
-    * There are 3 pieces of information that are carried around during this process:
-    *  1) ProcessedReferences: A Map[CwlReference, Json] of CwlReference for which we have the fully processed (saladed AND flattened) Json value.
-    *
-    *  2) UnProcessedReferences: A Map[CwlReference, Json] of CwlReference for which we have the saladed but NOT flattened Json value.
-    *     This can happen because a file can contain multiple tools / workflows. When we salad / parse this file, we get (CwlReference, Json) pairs
-    *     for all the workflow / tools in the file, but they are not flattened yet.
-    *     We keep this to avoid having to re-salad / re-parse files unnecessarily.
-    *
-    *  3) BreadCrumb: A Set[CwlReference] used to follow the trail of CwlReferences that we are processing as we recurse down.
-    *     This is used to be able to detect circular dependencies (if the cwlReference being processed is in that set, then we have a circular dependency) .
-    *
-    */
-  private def preProcessCwlFile(reference: CwlFileReference): IOChecked[Json] = {
-
-    def absoluteSchemaPaths(json: Json): Json = {
-      json mapArray {
-        _ map absoluteSchemaPaths
-      } mapString {
-        Schema.getIriPath(reference.fullReference, _)
-      }
-    }
-
-    // NB the JSON here is only used to decide whether or not to flatten. If we do decide to flatten we throw away the
-    // json and request a canonical version from the CwlCanonicalizer.
-    def flattenOrByPass(json: Json): IOChecked[Json] = {
-      def flatten(json: Json): IOChecked[Json] = {
-        val cwlReferenceFlattener = new CwlCanonicalizer(saladFunction)
-        val namespacesJsonOption: Option[Json] = json.asObject.flatMap(_.kleisli(JsonKeyNamespaces))
-        val schemasJsonOption: Option[Json] = json.asObject.flatMap(_.kleisli(JsonKeySchemas)).map(absoluteSchemaPaths)
-
-        cwlReferenceFlattener.getCanonicalCwl(
-          reference,
-          namespacesJsonOption,
-          schemasJsonOption
-        )
-      }
-
-      def bypass(alreadyCanonicalJson: Json): IOChecked[Json] = alreadyCanonicalJson.validIOChecked
-
-      val fileContentReference = for {
-        asObject <- json.asObject
-        fileContentId <- asObject.kleisli("id")
-        stringId <- fileContentId.asString
-        fileContentReference <- CwlReference.fromString(stringId)
-      } yield fileContentReference
-
-      fileContentReference match {
-        // This by passes the pre-processing if the file already has an id for which the file part doesn't match the path of the file
-        // passed to this function, as this would indicate that it has already been saladed and pre-processed.
-        case Some(CwlFileReference(file, _)) if !file.equals(reference.file) => bypass(json)
-        case _ => flatten(json)
-      }
-    }
-
-    for {
-      original <- parseYaml(reference.file.contentAsString)
-      flattened <- flattenOrByPass(original)
-    } yield flattened
-  }
-
-  // Like 'File', except that we don't read any contents before passing the path over to cwltool to canonicalize.
-  private def preProcessRemoteCwl(reference: CwlReference)(implicit cs: ContextShift[IO]): IOChecked[Json] = {
-    val cwlCanonicalizer = new CwlCanonicalizer(saladFunction)
-    cwlCanonicalizer.getCanonicalCwl(reference)
-  }
-}
-
-object CwlPreProcessor {
-  private val Log = LoggerFactory.getLogger("CwlPreProcessor")
-
-  private [preprocessor] type SaladFunction = CwlReference => IOChecked[String]
-  private [preprocessor] val JsonKeyNamespaces = s"$$namespaces"
-  private [preprocessor] val JsonKeySchemas = s"$$schemas"
-
-  private def saladSpinner(doLogging: Boolean): SaladFunction = ref => {
-    if (doLogging) {
-      Log.info(s"Pre-Processing ${ref.pathAsString}")
-    }
-
-    CwlDecoder.saladCwlFile(ref)
-  }
-
-  private [preprocessor] val saladCwlFile: SaladFunction = saladSpinner(true)
-  private val saladCwlFileWithoutLogging: SaladFunction = saladSpinner(false)
-
-  implicit class PrintableJson(val json: Json) extends AnyVal {
-    def printCompact = io.circe.Printer.noSpaces.print(json)
-  }
-
-  def noLogging = new CwlPreProcessor(saladCwlFileWithoutLogging)
-
-  // Fold over a json recursively and prefix all files
-  def mapFilesAndDirectories(mappingFunction: String => String)(json: Json): Json = {
-    // Function to check if the given json has the provided key / value pair
-    def hasKeyValue(key: String, value: String): Json => Boolean = {
-      root.selectDynamic(key).string.exist(_.equalsIgnoreCase(value))
-    }
-
-    // Return true if the given json object represents a File
-    def isFile(obj: JsonObject) = hasKeyValue("class", "File")(Json.fromJsonObject(obj))
-
-    // Return true if the given json object represents a Directory
-    def isDirectory(obj: JsonObject) = hasKeyValue("class", "Directory")(Json.fromJsonObject(obj))
-
-    // Modify the string at "key" using the mappingFunction
-    def mapStringValue(key: String, mappingFunction: String => String): Json => Json = root.selectDynamic(key).string.modify(mappingFunction)
-
-    // Map "location" and "default"
-    def prefix(mappingFunction: String => String): Json => Json = mapStringValue("location", mappingFunction).compose(mapStringValue("path", mappingFunction))
-
-    // Prefix the location or path in the json object if it's a file or directory, otherwise recurse over its fields
-    def prefixObject(mappingFunction: String => String)(obj: JsonObject): Json = {
-      // If the object is file or a directory, prefix it with the gcs prefix
-      if (isFile(obj) || isDirectory(obj)) {
-        prefix(mappingFunction)(Json.fromJsonObject(obj))
-          // Even if it's a file it may have secondary files. So keep recursing on its fields
-          .mapObject(_.mapValues(mapFilesAndDirectories(mappingFunction)))
-      }
-      // Otherwise recursively process its fields
-      else Json.fromJsonObject(obj.mapValues(mapFilesAndDirectories(mappingFunction)))
-    }
-
-    json.fold(
-      jsonNull = json,
-      jsonBoolean = _ => json,
-      jsonNumber = _ => json,
-      jsonString = _ => json,
-      jsonObject = prefixObject(mappingFunction),
-      jsonArray = arr => Json.arr(arr.map(mapFilesAndDirectories(mappingFunction)): _*)
-    )
-  }
-
-  private [preprocessor] def mapNumbers(json: Json): Json = {
-    // Circumvent Circe's scientific format for numbers: convert to a JSON String without exponential notation.
-    def nonScientificNumberFormatting(jsonNumber: JsonNumber): Json = {
-      val conversions = LazyList[JsonNumber => Option[Any]](
-        _.toBigInt.map(_.longValue),
-        _.toBigDecimal.map(_.doubleValue),
-        Function.const(Option("null")))
-
-      // The `get` is safe because `Option("null")` guarantees a match even if the other two Stream elements
-      // do not satisfy the predicate.
-      conversions.map(_.apply(jsonNumber)).find(_.isDefined).flatten.get.toString |> Json.fromString
-    }
-
-    json.fold(
-      jsonNull = json,
-      jsonBoolean = _ => json,
-      jsonNumber = nonScientificNumberFormatting,
-      jsonString = _ => json,
-      jsonObject = _.mapValues(mapNumbers) |> Json.fromJsonObject,
-      jsonArray = _.map(mapNumbers) |> Json.fromValues
-    )
-  }
-
-  private [preprocessor] def parseJson(in: String): IOChecked[Json] = {
-    io.circe.parser.parse(in).leftMap(error => NonEmptyList.one(error.message)).toIOChecked
-  }
-
-  private [preprocessor] def parseYaml(in: String): IOChecked[Json] = {
-    val yaml = YamlUtils.parse(in)
-    yaml.leftMap(error => NonEmptyList.one(error.message)).toIOChecked
-  }
-
-  /**
-    * Given a json, collect all tools or workflows and map them with their reference id.
-    * A saladed JSON is assumed.
-    */
-  private [preprocessor] def mapIdToContent(json: Json): List[(CwlReference, Json)] = {
-    json.asArray match {
-      case Some(cwls) => cwls.toList.flatMap(mapIdToContent)
-      case None => root.id.string.getOption(json).flatMap(_.asReference).map(_ -> json).toList
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/preprocessor/CwlReference.scala b/cwl/src/main/scala/cwl/preprocessor/CwlReference.scala
deleted file mode 100644
index badddf028b4..00000000000
--- a/cwl/src/main/scala/cwl/preprocessor/CwlReference.scala
+++ /dev/null
@@ -1,82 +0,0 @@
-package cwl.preprocessor
-
-import better.files.{File => BFile}
-import cwl.preprocessor.CwlReference._
-import cwl.{FileAndId, FullyQualifiedName}
-import cwl.command.ParentName
-
-sealed trait CwlReference {
-  def pathAsString: String
-  def pointerWithinFile: Option[String]
-  def changePointer(to: Option[String]): CwlReference
-
-  private def pointerWithHash: String = pointerWithinFile.map(p => s"#$p").getOrElse("")
-  lazy val fullReference: String = s"$pathAsString$pointerWithHash"
-
-  override def toString: String = fullReference
-}
-
-/**
-  * Saladed CWLs reference other local CWL "node" (workflow or tool) using a URI as follow:
-  * file:///path/to/file/containing/node.cwl[#pointer_to_node]
-  * #pointer_to_node to node is optional, and will specify which workflow or tool is being targeted in the file.
-  *
-  * e.g:
-  *   {
-  *     "class": "Workflow",
-  *     "id": "file:///path/to/workflow/workflow.cwl",
-  *     ...
-  *     "steps": [
-  *       {
-  *         "run": "file:///path/to/workflow/multi_tools.cwl#my_tool",
-  *         ...
-  *       }
-  *     ]
-  *   }
-  *
-  * This snippet contains 2 references, one that is the ID of this workflow, the other one is the run step pointing to "my_tool" in "/path/to/workflow/multi_tools.cwl"
-  *
-  */
-final case class CwlFileReference(file: BFile, pointerWithinFile: Option[String]) extends CwlReference {
-  override val pathAsString: String = s"$LocalScheme${file.toString}"
-  override def changePointer(to: Option[String]): CwlReference = this.copy(pointerWithinFile = to)
-}
-
-final case class CwlHttpReference(pathAsString: String, pointerWithinFile: Option[String]) extends CwlReference {
-  override def changePointer(to: Option[String]): CwlReference = this.copy(pointerWithinFile = to)
-}
-
-object CwlReference {
-  val LocalScheme = "file://"
-  val HttpScheme = "http://"
-  val HttpsScheme = "https://"
-
-  implicit class EnhancedCwlId(val id: String) extends AnyVal {
-    def asReference: Option[CwlReference] = CwlReference.fromString(id)
-    def stripFilePrefix = id.stripPrefix(LocalScheme)
-  }
-
-  val ReferenceRegex = "(.*://)?([^#]*)(#(.*))?".r
-
-  def fromString(in: String): Option[CwlReference] = {
-    in match {
-      case ReferenceRegex(scheme, path, _, pointerWithinFile) =>
-        if (scheme == LocalScheme) {
-          FullyQualifiedName.maybeApply(in)(ParentName.empty) match {
-            case Some(FileAndId(file, _, _)) => Option(CwlFileReference(BFile(file.stripFilePrefix), Option(pointerWithinFile)))
-            case _ => Option(CwlFileReference(BFile(in.stripFilePrefix), Option(pointerWithinFile)))
-          }
-        } else if (scheme == HttpScheme || scheme == HttpsScheme) {
-          Option(CwlHttpReference(s"$scheme$path", Option(pointerWithinFile)))
-        } else {
-          None
-        }
-    }
-  }
-}
-
-object CwlFileReference {
-  def apply(file: BFile, pointer: Option[String]) = {
-    new CwlFileReference(file, pointer)
-  }
-}
diff --git a/cwl/src/main/scala/cwl/requirement/RequirementToAttributeMap.scala b/cwl/src/main/scala/cwl/requirement/RequirementToAttributeMap.scala
deleted file mode 100644
index 1a727837172..00000000000
--- a/cwl/src/main/scala/cwl/requirement/RequirementToAttributeMap.scala
+++ /dev/null
@@ -1,79 +0,0 @@
-package cwl.requirement
-
-import cwl._
-import shapeless.Poly1
-import wom.RuntimeAttributesKeys._
-import wom.expression.{ValueAsAnExpression, WomExpression}
-import wom.values.{WomLong, WomString}
-
-object RequirementToAttributeMap extends Poly1 {
-  type ResourcesToExpressionMap = (Set[String], ExpressionLib) => Map[String, WomExpression]
-  implicit def fromJs: Case.Aux[InlineJavascriptRequirement, ResourcesToExpressionMap] = at[InlineJavascriptRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromSchemaDef: Case.Aux[SchemaDefRequirement, ResourcesToExpressionMap] = at[SchemaDefRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromDocker: Case.Aux[DockerRequirement, ResourcesToExpressionMap] = at[DockerRequirement] {
-    docker => (_,_) => docker.dockerPull.orElse(docker.dockerImageId).map({ pull =>
-      DockerKey -> ValueAsAnExpression(WomString(pull))
-    }).toMap
-  }
-
-  implicit def fromSoftware: Case.Aux[SoftwareRequirement, ResourcesToExpressionMap] = at[SoftwareRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromInitialWorkDir: Case.Aux[InitialWorkDirRequirement, ResourcesToExpressionMap] = at[InitialWorkDirRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromEnvVar: Case.Aux[EnvVarRequirement, ResourcesToExpressionMap] = at[EnvVarRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromShellCommand: Case.Aux[ShellCommandRequirement, ResourcesToExpressionMap] = at[ShellCommandRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromResource: Case.Aux[ResourceRequirement, ResourcesToExpressionMap] = at[ResourceRequirement] {
-    resource => (inputNames, expressionLib) =>
-      def toExpression(resourceRequirement: ResourceRequirementType) =
-        resourceRequirement.fold(ResourceRequirementToWomExpression).apply(inputNames, expressionLib)
-
-      List(
-        // Map cpuMin to both cpuMin and cpu keys
-        resource.effectiveCoreMin.toList.map(toExpression).flatMap(min => List(CpuMinKey -> min, CpuKey -> min)),
-        resource.effectiveCoreMax.toList.map(toExpression).map(CpuMaxKey -> _),
-        // Map ramMin to both memoryMin and memory keys
-        resource.effectiveRamMin.toList.map(toExpression).flatMap(min => List(MemoryMinKey -> min, MemoryKey -> min)),
-        resource.effectiveRamMax.toList.map(toExpression).map(MemoryMaxKey -> _),
-        resource.effectiveTmpdirMin.toList.map(toExpression).map(TmpDirMinKey -> _),
-        resource.effectiveTmpdirMax.toList.map(toExpression).map(TmpDirMaxKey -> _),
-        resource.effectiveOutdirMin.toList.map(toExpression).map(OutDirMinKey -> _),
-        resource.effectiveOutdirMax.toList.map(toExpression).map(OutDirMaxKey -> _)
-      ).flatten.toMap
-  }
-
-  implicit def fromInputResourceRequirement: Case.Aux[DnaNexusInputResourceRequirement, ResourcesToExpressionMap] = at[DnaNexusInputResourceRequirement] {
-    case DnaNexusInputResourceRequirement(_, indirMin) => (_, _) => indirMin.map(value => ValueAsAnExpression(WomLong(value))).map(DnaNexusInputDirMinKey -> _).toMap
-  }
-
-  implicit def fromSubWorkflow: Case.Aux[SubworkflowFeatureRequirement, ResourcesToExpressionMap] = at[SubworkflowFeatureRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromScatter: Case.Aux[ScatterFeatureRequirement, ResourcesToExpressionMap] = at[ScatterFeatureRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromMultipleInput: Case.Aux[MultipleInputFeatureRequirement, ResourcesToExpressionMap] = at[MultipleInputFeatureRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromStepInput: Case.Aux[StepInputExpressionRequirement, ResourcesToExpressionMap] = at[StepInputExpressionRequirement] {
-    _ => (_,_) => Map.empty
-  }
-}
diff --git a/cwl/src/main/scala/cwl/requirement/ResourceRequirementToWomExpression.scala b/cwl/src/main/scala/cwl/requirement/ResourceRequirementToWomExpression.scala
deleted file mode 100644
index 74727947657..00000000000
--- a/cwl/src/main/scala/cwl/requirement/ResourceRequirementToWomExpression.scala
+++ /dev/null
@@ -1,15 +0,0 @@
-package cwl.requirement
-
-import cwl.{Expression, ExpressionLib}
-import shapeless.Poly1
-import wom.expression.{ValueAsAnExpression, WomExpression}
-import wom.values.{WomLong, WomString}
-
-object ResourceRequirementToWomExpression extends Poly1 {
-  type ResourceRequirementStringSetToWomExpression = (Set[String], ExpressionLib) => WomExpression
-  implicit def fromLong: Case.Aux[Long, ResourceRequirementStringSetToWomExpression] = at[Long] { l => (_, _) => ValueAsAnExpression(WomLong(l)) }
-  implicit def fromString: Case.Aux[String, ResourceRequirementStringSetToWomExpression] = at[String] { s =>  (_, _) => ValueAsAnExpression(WomString(s)) }
-  implicit def fromExpression: Case.Aux[Expression, ResourceRequirementStringSetToWomExpression] = at[Expression] { e => (inputs, expressionLib) =>
-    cwl.ECMAScriptWomExpression(e, inputs, expressionLib)
-  }
-}
diff --git a/cwl/src/test/resources/1st-tool.cwl b/cwl/src/test/resources/1st-tool.cwl
deleted file mode 100755
index af0c4de297d..00000000000
--- a/cwl/src/test/resources/1st-tool.cwl
+++ /dev/null
@@ -1,9 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-inputs:
-  message:
-    type: string
-    inputBinding:
-      position: 1
-outputs: []
diff --git a/cwl/src/test/resources/1st-workflow.cwl b/cwl/src/test/resources/1st-workflow.cwl
deleted file mode 100644
index ce4b4b0bd71..00000000000
--- a/cwl/src/test/resources/1st-workflow.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: File
-  ex: string
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classfile
-
-steps:
-  untar:
-    run: tar-param.cwl
-    in:
-      tarfile: inp
-      extractfile: ex
-    out: [example_out]
-
-  compile:
-    run: arguments.cwl
-    in:
-      src: untar/example_out
-    out: [classfile]
diff --git a/cwl/src/test/resources/application.conf b/cwl/src/test/resources/application.conf
deleted file mode 100644
index 8d12b670cd3..00000000000
--- a/cwl/src/test/resources/application.conf
+++ /dev/null
@@ -1,14 +0,0 @@
-akka {
-  log-dead-letters = "off"
-  loggers = ["akka.event.slf4j.Slf4jLogger"]
-}
-
-ontology {
-  # Uncomment to enable caching of ontologies. Improves performance when loading ontologies from remote IRIs.
-  #cache {
-  #  max-size = 20
-  #}
-  retries = 3
-  pool-size = 3
-  backoff-time = 2 seconds
-}
diff --git a/cwl/src/test/resources/arguments.cwl b/cwl/src/test/resources/arguments.cwl
deleted file mode 100644
index 730030e7437..00000000000
--- a/cwl/src/test/resources/arguments.cwl
+++ /dev/null
@@ -1,22 +0,0 @@
-cwlVersion: "v1.0"
-class: "CommandLineTool"
-label: "Example trivial wrapper for Java 7 compiler"
-hints: 
-  - dockerPull: "java:7-jdk"
-    class: "DockerRequirement"
-baseCommand: "javac"
-arguments: 
-  - "-d"
-  - "$(runtime.outdir)"
-inputs: 
-  - type: "File"
-    inputBinding: 
-      position: 1
-    id: "file:///home/dan/wdl4s/arguments.cwl#src"
-outputs: 
-  - type: "File"
-    outputBinding: 
-      glob: "*.class"
-    id: "file:///home/dan/wdl4s/arguments.cwl#classfile"
-id: "file:///home/dan/wdl4s/arguments.cwl"
-name: "file:///home/dan/wdl4s/arguments.cwl"
diff --git a/cwl/src/test/resources/bad.cwl b/cwl/src/test/resources/bad.cwl
deleted file mode 100644
index d38ed298731..00000000000
--- a/cwl/src/test/resources/bad.cwl
+++ /dev/null
@@ -1 +0,0 @@
-gibberish
diff --git a/cwl/src/test/resources/bad2.cwl b/cwl/src/test/resources/bad2.cwl
deleted file mode 100644
index d38ed298731..00000000000
--- a/cwl/src/test/resources/bad2.cwl
+++ /dev/null
@@ -1 +0,0 @@
-gibberish
diff --git a/cwl/src/test/resources/brokenlinks.cwl b/cwl/src/test/resources/brokenlinks.cwl
deleted file mode 100644
index c710358ce61..00000000000
--- a/cwl/src/test/resources/brokenlinks.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: File
-  ex: string
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classfile
-
-steps:
-  untar:
-    run: wrong.cwl
-    in:
-      tarfile: inp
-      extractfile: ex
-    out: [example_out]
-
-  compile:
-    run: wrong2.cwl
-    in:
-      src: untar/example_out
-    out: [classfile]
diff --git a/cwl/src/test/resources/cwl/lodash.js b/cwl/src/test/resources/cwl/lodash.js
deleted file mode 100644
index 9b95dfefe87..00000000000
--- a/cwl/src/test/resources/cwl/lodash.js
+++ /dev/null
@@ -1,17112 +0,0 @@
-/**
- * @license
- * Lodash <https://lodash.com/>
- * Copyright OpenJS Foundation and other contributors <https://openjsf.org/>
- * Released under MIT license <https://lodash.com/license>
- * Based on Underscore.js 1.8.3 <http://underscorejs.org/LICENSE>
- * Copyright Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
- */
-;(function() {
-
-  /** Used as a safe reference for `undefined` in pre-ES5 environments. */
-  var undefined;
-
-  /** Used as the semantic version number. */
-  var VERSION = '4.17.15';
-
-  /** Used as the size to enable large array optimizations. */
-  var LARGE_ARRAY_SIZE = 200;
-
-  /** Error message constants. */
-  var CORE_ERROR_TEXT = 'Unsupported core-js use. Try https://npms.io/search?q=ponyfill.',
-      FUNC_ERROR_TEXT = 'Expected a function';
-
-  /** Used to stand-in for `undefined` hash values. */
-  var HASH_UNDEFINED = '__lodash_hash_undefined__';
-
-  /** Used as the maximum memoize cache size. */
-  var MAX_MEMOIZE_SIZE = 500;
-
-  /** Used as the internal argument placeholder. */
-  var PLACEHOLDER = '__lodash_placeholder__';
-
-  /** Used to compose bitmasks for cloning. */
-  var CLONE_DEEP_FLAG = 1,
-      CLONE_FLAT_FLAG = 2,
-      CLONE_SYMBOLS_FLAG = 4;
-
-  /** Used to compose bitmasks for value comparisons. */
-  var COMPARE_PARTIAL_FLAG = 1,
-      COMPARE_UNORDERED_FLAG = 2;
-
-  /** Used to compose bitmasks for function metadata. */
-  var WRAP_BIND_FLAG = 1,
-      WRAP_BIND_KEY_FLAG = 2,
-      WRAP_CURRY_BOUND_FLAG = 4,
-      WRAP_CURRY_FLAG = 8,
-      WRAP_CURRY_RIGHT_FLAG = 16,
-      WRAP_PARTIAL_FLAG = 32,
-      WRAP_PARTIAL_RIGHT_FLAG = 64,
-      WRAP_ARY_FLAG = 128,
-      WRAP_REARG_FLAG = 256,
-      WRAP_FLIP_FLAG = 512;
-
-  /** Used as default options for `_.truncate`. */
-  var DEFAULT_TRUNC_LENGTH = 30,
-      DEFAULT_TRUNC_OMISSION = '...';
-
-  /** Used to detect hot functions by number of calls within a span of milliseconds. */
-  var HOT_COUNT = 800,
-      HOT_SPAN = 16;
-
-  /** Used to indicate the type of lazy iteratees. */
-  var LAZY_FILTER_FLAG = 1,
-      LAZY_MAP_FLAG = 2,
-      LAZY_WHILE_FLAG = 3;
-
-  /** Used as references for various `Number` constants. */
-  var INFINITY = 1 / 0,
-      MAX_SAFE_INTEGER = 9007199254740991,
-      MAX_INTEGER = 1.7976931348623157e+308,
-      NAN = 0 / 0;
-
-  /** Used as references for the maximum length and index of an array. */
-  var MAX_ARRAY_LENGTH = 4294967295,
-      MAX_ARRAY_INDEX = MAX_ARRAY_LENGTH - 1,
-      HALF_MAX_ARRAY_LENGTH = MAX_ARRAY_LENGTH >>> 1;
-
-  /** Used to associate wrap methods with their bit flags. */
-  var wrapFlags = [
-    ['ary', WRAP_ARY_FLAG],
-    ['bind', WRAP_BIND_FLAG],
-    ['bindKey', WRAP_BIND_KEY_FLAG],
-    ['curry', WRAP_CURRY_FLAG],
-    ['curryRight', WRAP_CURRY_RIGHT_FLAG],
-    ['flip', WRAP_FLIP_FLAG],
-    ['partial', WRAP_PARTIAL_FLAG],
-    ['partialRight', WRAP_PARTIAL_RIGHT_FLAG],
-    ['rearg', WRAP_REARG_FLAG]
-  ];
-
-  /** `Object#toString` result references. */
-  var argsTag = '[object Arguments]',
-      arrayTag = '[object Array]',
-      asyncTag = '[object AsyncFunction]',
-      boolTag = '[object Boolean]',
-      dateTag = '[object Date]',
-      domExcTag = '[object DOMException]',
-      errorTag = '[object Error]',
-      funcTag = '[object Function]',
-      genTag = '[object GeneratorFunction]',
-      mapTag = '[object Map]',
-      numberTag = '[object Number]',
-      nullTag = '[object Null]',
-      objectTag = '[object Object]',
-      promiseTag = '[object Promise]',
-      proxyTag = '[object Proxy]',
-      regexpTag = '[object RegExp]',
-      setTag = '[object Set]',
-      stringTag = '[object String]',
-      symbolTag = '[object Symbol]',
-      undefinedTag = '[object Undefined]',
-      weakMapTag = '[object WeakMap]',
-      weakSetTag = '[object WeakSet]';
-
-  var arrayBufferTag = '[object ArrayBuffer]',
-      dataViewTag = '[object DataView]',
-      float32Tag = '[object Float32Array]',
-      float64Tag = '[object Float64Array]',
-      int8Tag = '[object Int8Array]',
-      int16Tag = '[object Int16Array]',
-      int32Tag = '[object Int32Array]',
-      uint8Tag = '[object Uint8Array]',
-      uint8ClampedTag = '[object Uint8ClampedArray]',
-      uint16Tag = '[object Uint16Array]',
-      uint32Tag = '[object Uint32Array]';
-
-  /** Used to match empty string literals in compiled template source. */
-  var reEmptyStringLeading = /\b__p \+= '';/g,
-      reEmptyStringMiddle = /\b(__p \+=) '' \+/g,
-      reEmptyStringTrailing = /(__e\(.*?\)|\b__t\)) \+\n'';/g;
-
-  /** Used to match HTML entities and HTML characters. */
-  var reEscapedHtml = /&(?:amp|lt|gt|quot|#39);/g,
-      reUnescapedHtml = /[&<>"']/g,
-      reHasEscapedHtml = RegExp(reEscapedHtml.source),
-      reHasUnescapedHtml = RegExp(reUnescapedHtml.source);
-
-  /** Used to match template delimiters. */
-  var reEscape = /<%-([\s\S]+?)%>/g,
-      reEvaluate = /<%([\s\S]+?)%>/g,
-      reInterpolate = /<%=([\s\S]+?)%>/g;
-
-  /** Used to match property names within property paths. */
-  var reIsDeepProp = /\.|\[(?:[^[\]]*|(["'])(?:(?!\1)[^\\]|\\.)*?\1)\]/,
-      reIsPlainProp = /^\w*$/,
-      rePropName = /[^.[\]]+|\[(?:(-?\d+(?:\.\d+)?)|(["'])((?:(?!\2)[^\\]|\\.)*?)\2)\]|(?=(?:\.|\[\])(?:\.|\[\]|$))/g;
-
-  /**
-   * Used to match `RegExp`
-   * [syntax characters](http://ecma-international.org/ecma-262/7.0/#sec-patterns).
-   */
-  var reRegExpChar = /[\\^$.*+?()[\]{}|]/g,
-      reHasRegExpChar = RegExp(reRegExpChar.source);
-
-  /** Used to match leading and trailing whitespace. */
-  var reTrim = /^\s+|\s+$/g,
-      reTrimStart = /^\s+/,
-      reTrimEnd = /\s+$/;
-
-  /** Used to match wrap detail comments. */
-  var reWrapComment = /\{(?:\n\/\* \[wrapped with .+\] \*\/)?\n?/,
-      reWrapDetails = /\{\n\/\* \[wrapped with (.+)\] \*/,
-      reSplitDetails = /,? & /;
-
-  /** Used to match words composed of alphanumeric characters. */
-  var reAsciiWord = /[^\x00-\x2f\x3a-\x40\x5b-\x60\x7b-\x7f]+/g;
-
-  /** Used to match backslashes in property paths. */
-  var reEscapeChar = /\\(\\)?/g;
-
-  /**
-   * Used to match
-   * [ES template delimiters](http://ecma-international.org/ecma-262/7.0/#sec-template-literal-lexical-components).
-   */
-  var reEsTemplate = /\$\{([^\\}]*(?:\\.[^\\}]*)*)\}/g;
-
-  /** Used to match `RegExp` flags from their coerced string values. */
-  var reFlags = /\w*$/;
-
-  /** Used to detect bad signed hexadecimal string values. */
-  var reIsBadHex = /^[-+]0x[0-9a-f]+$/i;
-
-  /** Used to detect binary string values. */
-  var reIsBinary = /^0b[01]+$/i;
-
-  /** Used to detect host constructors (Safari). */
-  var reIsHostCtor = /^\[object .+?Constructor\]$/;
-
-  /** Used to detect octal string values. */
-  var reIsOctal = /^0o[0-7]+$/i;
-
-  /** Used to detect unsigned integer values. */
-  var reIsUint = /^(?:0|[1-9]\d*)$/;
-
-  /** Used to match Latin Unicode letters (excluding mathematical operators). */
-  var reLatin = /[\xc0-\xd6\xd8-\xf6\xf8-\xff\u0100-\u017f]/g;
-
-  /** Used to ensure capturing order of template delimiters. */
-  var reNoMatch = /($^)/;
-
-  /** Used to match unescaped characters in compiled string literals. */
-  var reUnescapedString = /['\n\r\u2028\u2029\\]/g;
-
-  /** Used to compose unicode character classes. */
-  var rsAstralRange = '\\ud800-\\udfff',
-      rsComboMarksRange = '\\u0300-\\u036f',
-      reComboHalfMarksRange = '\\ufe20-\\ufe2f',
-      rsComboSymbolsRange = '\\u20d0-\\u20ff',
-      rsComboRange = rsComboMarksRange + reComboHalfMarksRange + rsComboSymbolsRange,
-      rsDingbatRange = '\\u2700-\\u27bf',
-      rsLowerRange = 'a-z\\xdf-\\xf6\\xf8-\\xff',
-      rsMathOpRange = '\\xac\\xb1\\xd7\\xf7',
-      rsNonCharRange = '\\x00-\\x2f\\x3a-\\x40\\x5b-\\x60\\x7b-\\xbf',
-      rsPunctuationRange = '\\u2000-\\u206f',
-      rsSpaceRange = ' \\t\\x0b\\f\\xa0\\ufeff\\n\\r\\u2028\\u2029\\u1680\\u180e\\u2000\\u2001\\u2002\\u2003\\u2004\\u2005\\u2006\\u2007\\u2008\\u2009\\u200a\\u202f\\u205f\\u3000',
-      rsUpperRange = 'A-Z\\xc0-\\xd6\\xd8-\\xde',
-      rsVarRange = '\\ufe0e\\ufe0f',
-      rsBreakRange = rsMathOpRange + rsNonCharRange + rsPunctuationRange + rsSpaceRange;
-
-  /** Used to compose unicode capture groups. */
-  var rsApos = "['\u2019]",
-      rsAstral = '[' + rsAstralRange + ']',
-      rsBreak = '[' + rsBreakRange + ']',
-      rsCombo = '[' + rsComboRange + ']',
-      rsDigits = '\\d+',
-      rsDingbat = '[' + rsDingbatRange + ']',
-      rsLower = '[' + rsLowerRange + ']',
-      rsMisc = '[^' + rsAstralRange + rsBreakRange + rsDigits + rsDingbatRange + rsLowerRange + rsUpperRange + ']',
-      rsFitz = '\\ud83c[\\udffb-\\udfff]',
-      rsModifier = '(?:' + rsCombo + '|' + rsFitz + ')',
-      rsNonAstral = '[^' + rsAstralRange + ']',
-      rsRegional = '(?:\\ud83c[\\udde6-\\uddff]){2}',
-      rsSurrPair = '[\\ud800-\\udbff][\\udc00-\\udfff]',
-      rsUpper = '[' + rsUpperRange + ']',
-      rsZWJ = '\\u200d';
-
-  /** Used to compose unicode regexes. */
-  var rsMiscLower = '(?:' + rsLower + '|' + rsMisc + ')',
-      rsMiscUpper = '(?:' + rsUpper + '|' + rsMisc + ')',
-      rsOptContrLower = '(?:' + rsApos + '(?:d|ll|m|re|s|t|ve))?',
-      rsOptContrUpper = '(?:' + rsApos + '(?:D|LL|M|RE|S|T|VE))?',
-      reOptMod = rsModifier + '?',
-      rsOptVar = '[' + rsVarRange + ']?',
-      rsOptJoin = '(?:' + rsZWJ + '(?:' + [rsNonAstral, rsRegional, rsSurrPair].join('|') + ')' + rsOptVar + reOptMod + ')*',
-      rsOrdLower = '\\d*(?:1st|2nd|3rd|(?![123])\\dth)(?=\\b|[A-Z_])',
-      rsOrdUpper = '\\d*(?:1ST|2ND|3RD|(?![123])\\dTH)(?=\\b|[a-z_])',
-      rsSeq = rsOptVar + reOptMod + rsOptJoin,
-      rsEmoji = '(?:' + [rsDingbat, rsRegional, rsSurrPair].join('|') + ')' + rsSeq,
-      rsSymbol = '(?:' + [rsNonAstral + rsCombo + '?', rsCombo, rsRegional, rsSurrPair, rsAstral].join('|') + ')';
-
-  /** Used to match apostrophes. */
-  var reApos = RegExp(rsApos, 'g');
-
-  /**
-   * Used to match [combining diacritical marks](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks) and
-   * [combining diacritical marks for symbols](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks_for_Symbols).
-   */
-  var reComboMark = RegExp(rsCombo, 'g');
-
-  /** Used to match [string symbols](https://mathiasbynens.be/notes/javascript-unicode). */
-  var reUnicode = RegExp(rsFitz + '(?=' + rsFitz + ')|' + rsSymbol + rsSeq, 'g');
-
-  /** Used to match complex or compound words. */
-  var reUnicodeWord = RegExp([
-    rsUpper + '?' + rsLower + '+' + rsOptContrLower + '(?=' + [rsBreak, rsUpper, '$'].join('|') + ')',
-    rsMiscUpper + '+' + rsOptContrUpper + '(?=' + [rsBreak, rsUpper + rsMiscLower, '$'].join('|') + ')',
-    rsUpper + '?' + rsMiscLower + '+' + rsOptContrLower,
-    rsUpper + '+' + rsOptContrUpper,
-    rsOrdUpper,
-    rsOrdLower,
-    rsDigits,
-    rsEmoji
-  ].join('|'), 'g');
-
-  /** Used to detect strings with [zero-width joiners or code points from the astral planes](http://eev.ee/blog/2015/09/12/dark-corners-of-unicode/). */
-  var reHasUnicode = RegExp('[' + rsZWJ + rsAstralRange  + rsComboRange + rsVarRange + ']');
-
-  /** Used to detect strings that need a more robust regexp to match words. */
-  var reHasUnicodeWord = /[a-z][A-Z]|[A-Z]{2}[a-z]|[0-9][a-zA-Z]|[a-zA-Z][0-9]|[^a-zA-Z0-9 ]/;
-
-  /** Used to assign default `context` object properties. */
-  var contextProps = [
-    'Array', 'Buffer', 'DataView', 'Date', 'Error', 'Float32Array', 'Float64Array',
-    'Function', 'Int8Array', 'Int16Array', 'Int32Array', 'Map', 'Math', 'Object',
-    'Promise', 'RegExp', 'Set', 'String', 'Symbol', 'TypeError', 'Uint8Array',
-    'Uint8ClampedArray', 'Uint16Array', 'Uint32Array', 'WeakMap',
-    '_', 'clearTimeout', 'isFinite', 'parseInt', 'setTimeout'
-  ];
-
-  /** Used to make template sourceURLs easier to identify. */
-  var templateCounter = -1;
-
-  /** Used to identify `toStringTag` values of typed arrays. */
-  var typedArrayTags = {};
-  typedArrayTags[float32Tag] = typedArrayTags[float64Tag] =
-  typedArrayTags[int8Tag] = typedArrayTags[int16Tag] =
-  typedArrayTags[int32Tag] = typedArrayTags[uint8Tag] =
-  typedArrayTags[uint8ClampedTag] = typedArrayTags[uint16Tag] =
-  typedArrayTags[uint32Tag] = true;
-  typedArrayTags[argsTag] = typedArrayTags[arrayTag] =
-  typedArrayTags[arrayBufferTag] = typedArrayTags[boolTag] =
-  typedArrayTags[dataViewTag] = typedArrayTags[dateTag] =
-  typedArrayTags[errorTag] = typedArrayTags[funcTag] =
-  typedArrayTags[mapTag] = typedArrayTags[numberTag] =
-  typedArrayTags[objectTag] = typedArrayTags[regexpTag] =
-  typedArrayTags[setTag] = typedArrayTags[stringTag] =
-  typedArrayTags[weakMapTag] = false;
-
-  /** Used to identify `toStringTag` values supported by `_.clone`. */
-  var cloneableTags = {};
-  cloneableTags[argsTag] = cloneableTags[arrayTag] =
-  cloneableTags[arrayBufferTag] = cloneableTags[dataViewTag] =
-  cloneableTags[boolTag] = cloneableTags[dateTag] =
-  cloneableTags[float32Tag] = cloneableTags[float64Tag] =
-  cloneableTags[int8Tag] = cloneableTags[int16Tag] =
-  cloneableTags[int32Tag] = cloneableTags[mapTag] =
-  cloneableTags[numberTag] = cloneableTags[objectTag] =
-  cloneableTags[regexpTag] = cloneableTags[setTag] =
-  cloneableTags[stringTag] = cloneableTags[symbolTag] =
-  cloneableTags[uint8Tag] = cloneableTags[uint8ClampedTag] =
-  cloneableTags[uint16Tag] = cloneableTags[uint32Tag] = true;
-  cloneableTags[errorTag] = cloneableTags[funcTag] =
-  cloneableTags[weakMapTag] = false;
-
-  /** Used to map Latin Unicode letters to basic Latin letters. */
-  var deburredLetters = {
-    // Latin-1 Supplement block.
-    '\xc0': 'A',  '\xc1': 'A', '\xc2': 'A', '\xc3': 'A', '\xc4': 'A', '\xc5': 'A',
-    '\xe0': 'a',  '\xe1': 'a', '\xe2': 'a', '\xe3': 'a', '\xe4': 'a', '\xe5': 'a',
-    '\xc7': 'C',  '\xe7': 'c',
-    '\xd0': 'D',  '\xf0': 'd',
-    '\xc8': 'E',  '\xc9': 'E', '\xca': 'E', '\xcb': 'E',
-    '\xe8': 'e',  '\xe9': 'e', '\xea': 'e', '\xeb': 'e',
-    '\xcc': 'I',  '\xcd': 'I', '\xce': 'I', '\xcf': 'I',
-    '\xec': 'i',  '\xed': 'i', '\xee': 'i', '\xef': 'i',
-    '\xd1': 'N',  '\xf1': 'n',
-    '\xd2': 'O',  '\xd3': 'O', '\xd4': 'O', '\xd5': 'O', '\xd6': 'O', '\xd8': 'O',
-    '\xf2': 'o',  '\xf3': 'o', '\xf4': 'o', '\xf5': 'o', '\xf6': 'o', '\xf8': 'o',
-    '\xd9': 'U',  '\xda': 'U', '\xdb': 'U', '\xdc': 'U',
-    '\xf9': 'u',  '\xfa': 'u', '\xfb': 'u', '\xfc': 'u',
-    '\xdd': 'Y',  '\xfd': 'y', '\xff': 'y',
-    '\xc6': 'Ae', '\xe6': 'ae',
-    '\xde': 'Th', '\xfe': 'th',
-    '\xdf': 'ss',
-    // Latin Extended-A block.
-    '\u0100': 'A',  '\u0102': 'A', '\u0104': 'A',
-    '\u0101': 'a',  '\u0103': 'a', '\u0105': 'a',
-    '\u0106': 'C',  '\u0108': 'C', '\u010a': 'C', '\u010c': 'C',
-    '\u0107': 'c',  '\u0109': 'c', '\u010b': 'c', '\u010d': 'c',
-    '\u010e': 'D',  '\u0110': 'D', '\u010f': 'd', '\u0111': 'd',
-    '\u0112': 'E',  '\u0114': 'E', '\u0116': 'E', '\u0118': 'E', '\u011a': 'E',
-    '\u0113': 'e',  '\u0115': 'e', '\u0117': 'e', '\u0119': 'e', '\u011b': 'e',
-    '\u011c': 'G',  '\u011e': 'G', '\u0120': 'G', '\u0122': 'G',
-    '\u011d': 'g',  '\u011f': 'g', '\u0121': 'g', '\u0123': 'g',
-    '\u0124': 'H',  '\u0126': 'H', '\u0125': 'h', '\u0127': 'h',
-    '\u0128': 'I',  '\u012a': 'I', '\u012c': 'I', '\u012e': 'I', '\u0130': 'I',
-    '\u0129': 'i',  '\u012b': 'i', '\u012d': 'i', '\u012f': 'i', '\u0131': 'i',
-    '\u0134': 'J',  '\u0135': 'j',
-    '\u0136': 'K',  '\u0137': 'k', '\u0138': 'k',
-    '\u0139': 'L',  '\u013b': 'L', '\u013d': 'L', '\u013f': 'L', '\u0141': 'L',
-    '\u013a': 'l',  '\u013c': 'l', '\u013e': 'l', '\u0140': 'l', '\u0142': 'l',
-    '\u0143': 'N',  '\u0145': 'N', '\u0147': 'N', '\u014a': 'N',
-    '\u0144': 'n',  '\u0146': 'n', '\u0148': 'n', '\u014b': 'n',
-    '\u014c': 'O',  '\u014e': 'O', '\u0150': 'O',
-    '\u014d': 'o',  '\u014f': 'o', '\u0151': 'o',
-    '\u0154': 'R',  '\u0156': 'R', '\u0158': 'R',
-    '\u0155': 'r',  '\u0157': 'r', '\u0159': 'r',
-    '\u015a': 'S',  '\u015c': 'S', '\u015e': 'S', '\u0160': 'S',
-    '\u015b': 's',  '\u015d': 's', '\u015f': 's', '\u0161': 's',
-    '\u0162': 'T',  '\u0164': 'T', '\u0166': 'T',
-    '\u0163': 't',  '\u0165': 't', '\u0167': 't',
-    '\u0168': 'U',  '\u016a': 'U', '\u016c': 'U', '\u016e': 'U', '\u0170': 'U', '\u0172': 'U',
-    '\u0169': 'u',  '\u016b': 'u', '\u016d': 'u', '\u016f': 'u', '\u0171': 'u', '\u0173': 'u',
-    '\u0174': 'W',  '\u0175': 'w',
-    '\u0176': 'Y',  '\u0177': 'y', '\u0178': 'Y',
-    '\u0179': 'Z',  '\u017b': 'Z', '\u017d': 'Z',
-    '\u017a': 'z',  '\u017c': 'z', '\u017e': 'z',
-    '\u0132': 'IJ', '\u0133': 'ij',
-    '\u0152': 'Oe', '\u0153': 'oe',
-    '\u0149': "'n", '\u017f': 's'
-  };
-
-  /** Used to map characters to HTML entities. */
-  var htmlEscapes = {
-    '&': '&amp;',
-    '<': '&lt;',
-    '>': '&gt;',
-    '"': '&quot;',
-    "'": '&#39;'
-  };
-
-  /** Used to map HTML entities to characters. */
-  var htmlUnescapes = {
-    '&amp;': '&',
-    '&lt;': '<',
-    '&gt;': '>',
-    '&quot;': '"',
-    '&#39;': "'"
-  };
-
-  /** Used to escape characters for inclusion in compiled string literals. */
-  var stringEscapes = {
-    '\\': '\\',
-    "'": "'",
-    '\n': 'n',
-    '\r': 'r',
-    '\u2028': 'u2028',
-    '\u2029': 'u2029'
-  };
-
-  /** Built-in method references without a dependency on `root`. */
-  var freeParseFloat = parseFloat,
-      freeParseInt = parseInt;
-
-  /** Detect free variable `global` from Node.js. */
-  var freeGlobal = typeof global == 'object' && global && global.Object === Object && global;
-
-  /** Detect free variable `self`. */
-  var freeSelf = typeof self == 'object' && self && self.Object === Object && self;
-
-  /** Used as a reference to the global object. */
-  var root = freeGlobal || freeSelf || Function('return this')();
-
-  /** Detect free variable `exports`. */
-  var freeExports = typeof exports == 'object' && exports && !exports.nodeType && exports;
-
-  /** Detect free variable `module`. */
-  var freeModule = freeExports && typeof module == 'object' && module && !module.nodeType && module;
-
-  /** Detect the popular CommonJS extension `module.exports`. */
-  var moduleExports = freeModule && freeModule.exports === freeExports;
-
-  /** Detect free variable `process` from Node.js. */
-  var freeProcess = moduleExports && freeGlobal.process;
-
-  /** Used to access faster Node.js helpers. */
-  var nodeUtil = (function() {
-    try {
-      // Use `util.types` for Node.js 10+.
-      var types = freeModule && freeModule.require && freeModule.require('util').types;
-
-      if (types) {
-        return types;
-      }
-
-      // Legacy `process.binding('util')` for Node.js < 10.
-      return freeProcess && freeProcess.binding && freeProcess.binding('util');
-    } catch (e) {}
-  }());
-
-  /* Node.js helper references. */
-  var nodeIsArrayBuffer = nodeUtil && nodeUtil.isArrayBuffer,
-      nodeIsDate = nodeUtil && nodeUtil.isDate,
-      nodeIsMap = nodeUtil && nodeUtil.isMap,
-      nodeIsRegExp = nodeUtil && nodeUtil.isRegExp,
-      nodeIsSet = nodeUtil && nodeUtil.isSet,
-      nodeIsTypedArray = nodeUtil && nodeUtil.isTypedArray;
-
-  /*--------------------------------------------------------------------------*/
-
-  /**
-   * A faster alternative to `Function#apply`, this function invokes `func`
-   * with the `this` binding of `thisArg` and the arguments of `args`.
-   *
-   * @private
-   * @param {Function} func The function to invoke.
-   * @param {*} thisArg The `this` binding of `func`.
-   * @param {Array} args The arguments to invoke `func` with.
-   * @returns {*} Returns the result of `func`.
-   */
-  function apply(func, thisArg, args) {
-    switch (args.length) {
-      case 0: return func.call(thisArg);
-      case 1: return func.call(thisArg, args[0]);
-      case 2: return func.call(thisArg, args[0], args[1]);
-      case 3: return func.call(thisArg, args[0], args[1], args[2]);
-    }
-    return func.apply(thisArg, args);
-  }
-
-  /**
-   * A specialized version of `baseAggregator` for arrays.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} setter The function to set `accumulator` values.
-   * @param {Function} iteratee The iteratee to transform keys.
-   * @param {Object} accumulator The initial aggregated object.
-   * @returns {Function} Returns `accumulator`.
-   */
-  function arrayAggregator(array, setter, iteratee, accumulator) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      var value = array[index];
-      setter(accumulator, value, iteratee(value), array);
-    }
-    return accumulator;
-  }
-
-  /**
-   * A specialized version of `_.forEach` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns `array`.
-   */
-  function arrayEach(array, iteratee) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (iteratee(array[index], index, array) === false) {
-        break;
-      }
-    }
-    return array;
-  }
-
-  /**
-   * A specialized version of `_.forEachRight` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns `array`.
-   */
-  function arrayEachRight(array, iteratee) {
-    var length = array == null ? 0 : array.length;
-
-    while (length--) {
-      if (iteratee(array[length], length, array) === false) {
-        break;
-      }
-    }
-    return array;
-  }
-
-  /**
-   * A specialized version of `_.every` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} predicate The function invoked per iteration.
-   * @returns {boolean} Returns `true` if all elements pass the predicate check,
-   *  else `false`.
-   */
-  function arrayEvery(array, predicate) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (!predicate(array[index], index, array)) {
-        return false;
-      }
-    }
-    return true;
-  }
-
-  /**
-   * A specialized version of `_.filter` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} predicate The function invoked per iteration.
-   * @returns {Array} Returns the new filtered array.
-   */
-  function arrayFilter(array, predicate) {
-    var index = -1,
-        length = array == null ? 0 : array.length,
-        resIndex = 0,
-        result = [];
-
-    while (++index < length) {
-      var value = array[index];
-      if (predicate(value, index, array)) {
-        result[resIndex++] = value;
-      }
-    }
-    return result;
-  }
-
-  /**
-   * A specialized version of `_.includes` for arrays without support for
-   * specifying an index to search from.
-   *
-   * @private
-   * @param {Array} [array] The array to inspect.
-   * @param {*} target The value to search for.
-   * @returns {boolean} Returns `true` if `target` is found, else `false`.
-   */
-  function arrayIncludes(array, value) {
-    var length = array == null ? 0 : array.length;
-    return !!length && baseIndexOf(array, value, 0) > -1;
-  }
-
-  /**
-   * This function is like `arrayIncludes` except that it accepts a comparator.
-   *
-   * @private
-   * @param {Array} [array] The array to inspect.
-   * @param {*} target The value to search for.
-   * @param {Function} comparator The comparator invoked per element.
-   * @returns {boolean} Returns `true` if `target` is found, else `false`.
-   */
-  function arrayIncludesWith(array, value, comparator) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (comparator(value, array[index])) {
-        return true;
-      }
-    }
-    return false;
-  }
-
-  /**
-   * A specialized version of `_.map` for arrays without support for iteratee
-   * shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns the new mapped array.
-   */
-  function arrayMap(array, iteratee) {
-    var index = -1,
-        length = array == null ? 0 : array.length,
-        result = Array(length);
-
-    while (++index < length) {
-      result[index] = iteratee(array[index], index, array);
-    }
-    return result;
-  }
-
-  /**
-   * Appends the elements of `values` to `array`.
-   *
-   * @private
-   * @param {Array} array The array to modify.
-   * @param {Array} values The values to append.
-   * @returns {Array} Returns `array`.
-   */
-  function arrayPush(array, values) {
-    var index = -1,
-        length = values.length,
-        offset = array.length;
-
-    while (++index < length) {
-      array[offset + index] = values[index];
-    }
-    return array;
-  }
-
-  /**
-   * A specialized version of `_.reduce` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @param {*} [accumulator] The initial value.
-   * @param {boolean} [initAccum] Specify using the first element of `array` as
-   *  the initial value.
-   * @returns {*} Returns the accumulated value.
-   */
-  function arrayReduce(array, iteratee, accumulator, initAccum) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    if (initAccum && length) {
-      accumulator = array[++index];
-    }
-    while (++index < length) {
-      accumulator = iteratee(accumulator, array[index], index, array);
-    }
-    return accumulator;
-  }
-
-  /**
-   * A specialized version of `_.reduceRight` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @param {*} [accumulator] The initial value.
-   * @param {boolean} [initAccum] Specify using the last element of `array` as
-   *  the initial value.
-   * @returns {*} Returns the accumulated value.
-   */
-  function arrayReduceRight(array, iteratee, accumulator, initAccum) {
-    var length = array == null ? 0 : array.length;
-    if (initAccum && length) {
-      accumulator = array[--length];
-    }
-    while (length--) {
-      accumulator = iteratee(accumulator, array[length], length, array);
-    }
-    return accumulator;
-  }
-
-  /**
-   * A specialized version of `_.some` for arrays without support for iteratee
-   * shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} predicate The function invoked per iteration.
-   * @returns {boolean} Returns `true` if any element passes the predicate check,
-   *  else `false`.
-   */
-  function arraySome(array, predicate) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (predicate(array[index], index, array)) {
-        return true;
-      }
-    }
-    return false;
-  }
-
-  /**
-   * Gets the size of an ASCII `string`.
-   *
-   * @private
-   * @param {string} string The string inspect.
-   * @returns {number} Returns the string size.
-   */
-  var asciiSize = baseProperty('length');
-
-  /**
-   * Converts an ASCII `string` to an array.
-   *
-   * @private
-   * @param {string} string The string to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function asciiToArray(string) {
-    return string.split('');
-  }
-
-  /**
-   * Splits an ASCII `string` into an array of its words.
-   *
-   * @private
-   * @param {string} The string to inspect.
-   * @returns {Array} Returns the words of `string`.
-   */
-  function asciiWords(string) {
-    return string.match(reAsciiWord) || [];
-  }
-
-  /**
-   * The base implementation of methods like `_.findKey` and `_.findLastKey`,
-   * without support for iteratee shorthands, which iterates over `collection`
-   * using `eachFunc`.
-   *
-   * @private
-   * @param {Array|Object} collection The collection to inspect.
-   * @param {Function} predicate The function invoked per iteration.
-   * @param {Function} eachFunc The function to iterate over `collection`.
-   * @returns {*} Returns the found element or its key, else `undefined`.
-   */
-  function baseFindKey(collection, predicate, eachFunc) {
-    var result;
-    eachFunc(collection, function(value, key, collection) {
-      if (predicate(value, key, collection)) {
-        result = key;
-        return false;
-      }
-    });
-    return result;
-  }
-
-  /**
-   * The base implementation of `_.findIndex` and `_.findLastIndex` without
-   * support for iteratee shorthands.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {Function} predicate The function invoked per iteration.
-   * @param {number} fromIndex The index to search from.
-   * @param {boolean} [fromRight] Specify iterating from right to left.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function baseFindIndex(array, predicate, fromIndex, fromRight) {
-    var length = array.length,
-        index = fromIndex + (fromRight ? 1 : -1);
-
-    while ((fromRight ? index-- : ++index < length)) {
-      if (predicate(array[index], index, array)) {
-        return index;
-      }
-    }
-    return -1;
-  }
-
-  /**
-   * The base implementation of `_.indexOf` without `fromIndex` bounds checks.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function baseIndexOf(array, value, fromIndex) {
-    return value === value
-      ? strictIndexOf(array, value, fromIndex)
-      : baseFindIndex(array, baseIsNaN, fromIndex);
-  }
-
-  /**
-   * This function is like `baseIndexOf` except that it accepts a comparator.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @param {Function} comparator The comparator invoked per element.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function baseIndexOfWith(array, value, fromIndex, comparator) {
-    var index = fromIndex - 1,
-        length = array.length;
-
-    while (++index < length) {
-      if (comparator(array[index], value)) {
-        return index;
-      }
-    }
-    return -1;
-  }
-
-  /**
-   * The base implementation of `_.isNaN` without support for number objects.
-   *
-   * @private
-   * @param {*} value The value to check.
-   * @returns {boolean} Returns `true` if `value` is `NaN`, else `false`.
-   */
-  function baseIsNaN(value) {
-    return value !== value;
-  }
-
-  /**
-   * The base implementation of `_.mean` and `_.meanBy` without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} array The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {number} Returns the mean.
-   */
-  function baseMean(array, iteratee) {
-    var length = array == null ? 0 : array.length;
-    return length ? (baseSum(array, iteratee) / length) : NAN;
-  }
-
-  /**
-   * The base implementation of `_.property` without support for deep paths.
-   *
-   * @private
-   * @param {string} key The key of the property to get.
-   * @returns {Function} Returns the new accessor function.
-   */
-  function baseProperty(key) {
-    return function(object) {
-      return object == null ? undefined : object[key];
-    };
-  }
-
-  /**
-   * The base implementation of `_.propertyOf` without support for deep paths.
-   *
-   * @private
-   * @param {Object} object The object to query.
-   * @returns {Function} Returns the new accessor function.
-   */
-  function basePropertyOf(object) {
-    return function(key) {
-      return object == null ? undefined : object[key];
-    };
-  }
-
-  /**
-   * The base implementation of `_.reduce` and `_.reduceRight`, without support
-   * for iteratee shorthands, which iterates over `collection` using `eachFunc`.
-   *
-   * @private
-   * @param {Array|Object} collection The collection to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @param {*} accumulator The initial value.
-   * @param {boolean} initAccum Specify using the first or last element of
-   *  `collection` as the initial value.
-   * @param {Function} eachFunc The function to iterate over `collection`.
-   * @returns {*} Returns the accumulated value.
-   */
-  function baseReduce(collection, iteratee, accumulator, initAccum, eachFunc) {
-    eachFunc(collection, function(value, index, collection) {
-      accumulator = initAccum
-        ? (initAccum = false, value)
-        : iteratee(accumulator, value, index, collection);
-    });
-    return accumulator;
-  }
-
-  /**
-   * The base implementation of `_.sortBy` which uses `comparer` to define the
-   * sort order of `array` and replaces criteria objects with their corresponding
-   * values.
-   *
-   * @private
-   * @param {Array} array The array to sort.
-   * @param {Function} comparer The function to define sort order.
-   * @returns {Array} Returns `array`.
-   */
-  function baseSortBy(array, comparer) {
-    var length = array.length;
-
-    array.sort(comparer);
-    while (length--) {
-      array[length] = array[length].value;
-    }
-    return array;
-  }
-
-  /**
-   * The base implementation of `_.sum` and `_.sumBy` without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} array The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {number} Returns the sum.
-   */
-  function baseSum(array, iteratee) {
-    var result,
-        index = -1,
-        length = array.length;
-
-    while (++index < length) {
-      var current = iteratee(array[index]);
-      if (current !== undefined) {
-        result = result === undefined ? current : (result + current);
-      }
-    }
-    return result;
-  }
-
-  /**
-   * The base implementation of `_.times` without support for iteratee shorthands
-   * or max array length checks.
-   *
-   * @private
-   * @param {number} n The number of times to invoke `iteratee`.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns the array of results.
-   */
-  function baseTimes(n, iteratee) {
-    var index = -1,
-        result = Array(n);
-
-    while (++index < n) {
-      result[index] = iteratee(index);
-    }
-    return result;
-  }
-
-  /**
-   * The base implementation of `_.toPairs` and `_.toPairsIn` which creates an array
-   * of key-value pairs for `object` corresponding to the property names of `props`.
-   *
-   * @private
-   * @param {Object} object The object to query.
-   * @param {Array} props The property names to get values for.
-   * @returns {Object} Returns the key-value pairs.
-   */
-  function baseToPairs(object, props) {
-    return arrayMap(props, function(key) {
-      return [key, object[key]];
-    });
-  }
-
-  /**
-   * The base implementation of `_.unary` without support for storing metadata.
-   *
-   * @private
-   * @param {Function} func The function to cap arguments for.
-   * @returns {Function} Returns the new capped function.
-   */
-  function baseUnary(func) {
-    return function(value) {
-      return func(value);
-    };
-  }
-
-  /**
-   * The base implementation of `_.values` and `_.valuesIn` which creates an
-   * array of `object` property values corresponding to the property names
-   * of `props`.
-   *
-   * @private
-   * @param {Object} object The object to query.
-   * @param {Array} props The property names to get values for.
-   * @returns {Object} Returns the array of property values.
-   */
-  function baseValues(object, props) {
-    return arrayMap(props, function(key) {
-      return object[key];
-    });
-  }
-
-  /**
-   * Checks if a `cache` value for `key` exists.
-   *
-   * @private
-   * @param {Object} cache The cache to query.
-   * @param {string} key The key of the entry to check.
-   * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-   */
-  function cacheHas(cache, key) {
-    return cache.has(key);
-  }
-
-  /**
-   * Used by `_.trim` and `_.trimStart` to get the index of the first string symbol
-   * that is not found in the character symbols.
-   *
-   * @private
-   * @param {Array} strSymbols The string symbols to inspect.
-   * @param {Array} chrSymbols The character symbols to find.
-   * @returns {number} Returns the index of the first unmatched string symbol.
-   */
-  function charsStartIndex(strSymbols, chrSymbols) {
-    var index = -1,
-        length = strSymbols.length;
-
-    while (++index < length && baseIndexOf(chrSymbols, strSymbols[index], 0) > -1) {}
-    return index;
-  }
-
-  /**
-   * Used by `_.trim` and `_.trimEnd` to get the index of the last string symbol
-   * that is not found in the character symbols.
-   *
-   * @private
-   * @param {Array} strSymbols The string symbols to inspect.
-   * @param {Array} chrSymbols The character symbols to find.
-   * @returns {number} Returns the index of the last unmatched string symbol.
-   */
-  function charsEndIndex(strSymbols, chrSymbols) {
-    var index = strSymbols.length;
-
-    while (index-- && baseIndexOf(chrSymbols, strSymbols[index], 0) > -1) {}
-    return index;
-  }
-
-  /**
-   * Gets the number of `placeholder` occurrences in `array`.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} placeholder The placeholder to search for.
-   * @returns {number} Returns the placeholder count.
-   */
-  function countHolders(array, placeholder) {
-    var length = array.length,
-        result = 0;
-
-    while (length--) {
-      if (array[length] === placeholder) {
-        ++result;
-      }
-    }
-    return result;
-  }
-
-  /**
-   * Used by `_.deburr` to convert Latin-1 Supplement and Latin Extended-A
-   * letters to basic Latin letters.
-   *
-   * @private
-   * @param {string} letter The matched letter to deburr.
-   * @returns {string} Returns the deburred letter.
-   */
-  var deburrLetter = basePropertyOf(deburredLetters);
-
-  /**
-   * Used by `_.escape` to convert characters to HTML entities.
-   *
-   * @private
-   * @param {string} chr The matched character to escape.
-   * @returns {string} Returns the escaped character.
-   */
-  var escapeHtmlChar = basePropertyOf(htmlEscapes);
-
-  /**
-   * Used by `_.template` to escape characters for inclusion in compiled string literals.
-   *
-   * @private
-   * @param {string} chr The matched character to escape.
-   * @returns {string} Returns the escaped character.
-   */
-  function escapeStringChar(chr) {
-    return '\\' + stringEscapes[chr];
-  }
-
-  /**
-   * Gets the value at `key` of `object`.
-   *
-   * @private
-   * @param {Object} [object] The object to query.
-   * @param {string} key The key of the property to get.
-   * @returns {*} Returns the property value.
-   */
-  function getValue(object, key) {
-    return object == null ? undefined : object[key];
-  }
-
-  /**
-   * Checks if `string` contains Unicode symbols.
-   *
-   * @private
-   * @param {string} string The string to inspect.
-   * @returns {boolean} Returns `true` if a symbol is found, else `false`.
-   */
-  function hasUnicode(string) {
-    return reHasUnicode.test(string);
-  }
-
-  /**
-   * Checks if `string` contains a word composed of Unicode symbols.
-   *
-   * @private
-   * @param {string} string The string to inspect.
-   * @returns {boolean} Returns `true` if a word is found, else `false`.
-   */
-  function hasUnicodeWord(string) {
-    return reHasUnicodeWord.test(string);
-  }
-
-  /**
-   * Converts `iterator` to an array.
-   *
-   * @private
-   * @param {Object} iterator The iterator to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function iteratorToArray(iterator) {
-    var data,
-        result = [];
-
-    while (!(data = iterator.next()).done) {
-      result.push(data.value);
-    }
-    return result;
-  }
-
-  /**
-   * Converts `map` to its key-value pairs.
-   *
-   * @private
-   * @param {Object} map The map to convert.
-   * @returns {Array} Returns the key-value pairs.
-   */
-  function mapToArray(map) {
-    var index = -1,
-        result = Array(map.size);
-
-    map.forEach(function(value, key) {
-      result[++index] = [key, value];
-    });
-    return result;
-  }
-
-  /**
-   * Creates a unary function that invokes `func` with its argument transformed.
-   *
-   * @private
-   * @param {Function} func The function to wrap.
-   * @param {Function} transform The argument transform.
-   * @returns {Function} Returns the new function.
-   */
-  function overArg(func, transform) {
-    return function(arg) {
-      return func(transform(arg));
-    };
-  }
-
-  /**
-   * Replaces all `placeholder` elements in `array` with an internal placeholder
-   * and returns an array of their indexes.
-   *
-   * @private
-   * @param {Array} array The array to modify.
-   * @param {*} placeholder The placeholder to replace.
-   * @returns {Array} Returns the new array of placeholder indexes.
-   */
-  function replaceHolders(array, placeholder) {
-    var index = -1,
-        length = array.length,
-        resIndex = 0,
-        result = [];
-
-    while (++index < length) {
-      var value = array[index];
-      if (value === placeholder || value === PLACEHOLDER) {
-        array[index] = PLACEHOLDER;
-        result[resIndex++] = index;
-      }
-    }
-    return result;
-  }
-
-  /**
-   * Converts `set` to an array of its values.
-   *
-   * @private
-   * @param {Object} set The set to convert.
-   * @returns {Array} Returns the values.
-   */
-  function setToArray(set) {
-    var index = -1,
-        result = Array(set.size);
-
-    set.forEach(function(value) {
-      result[++index] = value;
-    });
-    return result;
-  }
-
-  /**
-   * Converts `set` to its value-value pairs.
-   *
-   * @private
-   * @param {Object} set The set to convert.
-   * @returns {Array} Returns the value-value pairs.
-   */
-  function setToPairs(set) {
-    var index = -1,
-        result = Array(set.size);
-
-    set.forEach(function(value) {
-      result[++index] = [value, value];
-    });
-    return result;
-  }
-
-  /**
-   * A specialized version of `_.indexOf` which performs strict equality
-   * comparisons of values, i.e. `===`.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function strictIndexOf(array, value, fromIndex) {
-    var index = fromIndex - 1,
-        length = array.length;
-
-    while (++index < length) {
-      if (array[index] === value) {
-        return index;
-      }
-    }
-    return -1;
-  }
-
-  /**
-   * A specialized version of `_.lastIndexOf` which performs strict equality
-   * comparisons of values, i.e. `===`.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function strictLastIndexOf(array, value, fromIndex) {
-    var index = fromIndex + 1;
-    while (index--) {
-      if (array[index] === value) {
-        return index;
-      }
-    }
-    return index;
-  }
-
-  /**
-   * Gets the number of symbols in `string`.
-   *
-   * @private
-   * @param {string} string The string to inspect.
-   * @returns {number} Returns the string size.
-   */
-  function stringSize(string) {
-    return hasUnicode(string)
-      ? unicodeSize(string)
-      : asciiSize(string);
-  }
-
-  /**
-   * Converts `string` to an array.
-   *
-   * @private
-   * @param {string} string The string to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function stringToArray(string) {
-    return hasUnicode(string)
-      ? unicodeToArray(string)
-      : asciiToArray(string);
-  }
-
-  /**
-   * Used by `_.unescape` to convert HTML entities to characters.
-   *
-   * @private
-   * @param {string} chr The matched character to unescape.
-   * @returns {string} Returns the unescaped character.
-   */
-  var unescapeHtmlChar = basePropertyOf(htmlUnescapes);
-
-  /**
-   * Gets the size of a Unicode `string`.
-   *
-   * @private
-   * @param {string} string The string inspect.
-   * @returns {number} Returns the string size.
-   */
-  function unicodeSize(string) {
-    var result = reUnicode.lastIndex = 0;
-    while (reUnicode.test(string)) {
-      ++result;
-    }
-    return result;
-  }
-
-  /**
-   * Converts a Unicode `string` to an array.
-   *
-   * @private
-   * @param {string} string The string to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function unicodeToArray(string) {
-    return string.match(reUnicode) || [];
-  }
-
-  /**
-   * Splits a Unicode `string` into an array of its words.
-   *
-   * @private
-   * @param {string} The string to inspect.
-   * @returns {Array} Returns the words of `string`.
-   */
-  function unicodeWords(string) {
-    return string.match(reUnicodeWord) || [];
-  }
-
-  /*--------------------------------------------------------------------------*/
-
-  /**
-   * Create a new pristine `lodash` function using the `context` object.
-   *
-   * @static
-   * @memberOf _
-   * @since 1.1.0
-   * @category Util
-   * @param {Object} [context=root] The context object.
-   * @returns {Function} Returns a new `lodash` function.
-   * @example
-   *
-   * _.mixin({ 'foo': _.constant('foo') });
-   *
-   * var lodash = _.runInContext();
-   * lodash.mixin({ 'bar': lodash.constant('bar') });
-   *
-   * _.isFunction(_.foo);
-   * // => true
-   * _.isFunction(_.bar);
-   * // => false
-   *
-   * lodash.isFunction(lodash.foo);
-   * // => false
-   * lodash.isFunction(lodash.bar);
-   * // => true
-   *
-   * // Create a suped-up `defer` in Node.js.
-   * var defer = _.runInContext({ 'setTimeout': setImmediate }).defer;
-   */
-  var runInContext = (function runInContext(context) {
-    context = context == null ? root : _.defaults(root.Object(), context, _.pick(root, contextProps));
-
-    /** Built-in constructor references. */
-    var Array = context.Array,
-        Date = context.Date,
-        Error = context.Error,
-        Function = context.Function,
-        Math = context.Math,
-        Object = context.Object,
-        RegExp = context.RegExp,
-        String = context.String,
-        TypeError = context.TypeError;
-
-    /** Used for built-in method references. */
-    var arrayProto = Array.prototype,
-        funcProto = Function.prototype,
-        objectProto = Object.prototype;
-
-    /** Used to detect overreaching core-js shims. */
-    var coreJsData = context['__core-js_shared__'];
-
-    /** Used to resolve the decompiled source of functions. */
-    var funcToString = funcProto.toString;
-
-    /** Used to check objects for own properties. */
-    var hasOwnProperty = objectProto.hasOwnProperty;
-
-    /** Used to generate unique IDs. */
-    var idCounter = 0;
-
-    /** Used to detect methods masquerading as native. */
-    var maskSrcKey = (function() {
-      var uid = /[^.]+$/.exec(coreJsData && coreJsData.keys && coreJsData.keys.IE_PROTO || '');
-      return uid ? ('Symbol(src)_1.' + uid) : '';
-    }());
-
-    /**
-     * Used to resolve the
-     * [`toStringTag`](http://ecma-international.org/ecma-262/7.0/#sec-object.prototype.tostring)
-     * of values.
-     */
-    var nativeObjectToString = objectProto.toString;
-
-    /** Used to infer the `Object` constructor. */
-    var objectCtorString = funcToString.call(Object);
-
-    /** Used to restore the original `_` reference in `_.noConflict`. */
-    var oldDash = root._;
-
-    /** Used to detect if a method is native. */
-    var reIsNative = RegExp('^' +
-      funcToString.call(hasOwnProperty).replace(reRegExpChar, '\\$&')
-      .replace(/hasOwnProperty|(function).*?(?=\\\()| for .+?(?=\\\])/g, '$1.*?') + '$'
-    );
-
-    /** Built-in value references. */
-    var Buffer = moduleExports ? context.Buffer : undefined,
-        Symbol = context.Symbol,
-        Uint8Array = context.Uint8Array,
-        allocUnsafe = Buffer ? Buffer.allocUnsafe : undefined,
-        getPrototype = overArg(Object.getPrototypeOf, Object),
-        objectCreate = Object.create,
-        propertyIsEnumerable = objectProto.propertyIsEnumerable,
-        splice = arrayProto.splice,
-        spreadableSymbol = Symbol ? Symbol.isConcatSpreadable : undefined,
-        symIterator = Symbol ? Symbol.iterator : undefined,
-        symToStringTag = Symbol ? Symbol.toStringTag : undefined;
-
-    var defineProperty = (function() {
-      try {
-        var func = getNative(Object, 'defineProperty');
-        func({}, '', {});
-        return func;
-      } catch (e) {}
-    }());
-
-    /** Mocked built-ins. */
-    var ctxClearTimeout = context.clearTimeout !== root.clearTimeout && context.clearTimeout,
-        ctxNow = Date && Date.now !== root.Date.now && Date.now,
-        ctxSetTimeout = context.setTimeout !== root.setTimeout && context.setTimeout;
-
-    /* Built-in method references for those with the same name as other `lodash` methods. */
-    var nativeCeil = Math.ceil,
-        nativeFloor = Math.floor,
-        nativeGetSymbols = Object.getOwnPropertySymbols,
-        nativeIsBuffer = Buffer ? Buffer.isBuffer : undefined,
-        nativeIsFinite = context.isFinite,
-        nativeJoin = arrayProto.join,
-        nativeKeys = overArg(Object.keys, Object),
-        nativeMax = Math.max,
-        nativeMin = Math.min,
-        nativeNow = Date.now,
-        nativeParseInt = context.parseInt,
-        nativeRandom = Math.random,
-        nativeReverse = arrayProto.reverse;
-
-    /* Built-in method references that are verified to be native. */
-    var DataView = getNative(context, 'DataView'),
-        Map = getNative(context, 'Map'),
-        Promise = getNative(context, 'Promise'),
-        Set = getNative(context, 'Set'),
-        WeakMap = getNative(context, 'WeakMap'),
-        nativeCreate = getNative(Object, 'create');
-
-    /** Used to store function metadata. */
-    var metaMap = WeakMap && new WeakMap;
-
-    /** Used to lookup unminified function names. */
-    var realNames = {};
-
-    /** Used to detect maps, sets, and weakmaps. */
-    var dataViewCtorString = toSource(DataView),
-        mapCtorString = toSource(Map),
-        promiseCtorString = toSource(Promise),
-        setCtorString = toSource(Set),
-        weakMapCtorString = toSource(WeakMap);
-
-    /** Used to convert symbols to primitives and strings. */
-    var symbolProto = Symbol ? Symbol.prototype : undefined,
-        symbolValueOf = symbolProto ? symbolProto.valueOf : undefined,
-        symbolToString = symbolProto ? symbolProto.toString : undefined;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a `lodash` object which wraps `value` to enable implicit method
-     * chain sequences. Methods that operate on and return arrays, collections,
-     * and functions can be chained together. Methods that retrieve a single value
-     * or may return a primitive value will automatically end the chain sequence
-     * and return the unwrapped value. Otherwise, the value must be unwrapped
-     * with `_#value`.
-     *
-     * Explicit chain sequences, which must be unwrapped with `_#value`, may be
-     * enabled using `_.chain`.
-     *
-     * The execution of chained methods is lazy, that is, it's deferred until
-     * `_#value` is implicitly or explicitly called.
-     *
-     * Lazy evaluation allows several methods to support shortcut fusion.
-     * Shortcut fusion is an optimization to merge iteratee calls; this avoids
-     * the creation of intermediate arrays and can greatly reduce the number of
-     * iteratee executions. Sections of a chain sequence qualify for shortcut
-     * fusion if the section is applied to an array and iteratees accept only
-     * one argument. The heuristic for whether a section qualifies for shortcut
-     * fusion is subject to change.
-     *
-     * Chaining is supported in custom builds as long as the `_#value` method is
-     * directly or indirectly included in the build.
-     *
-     * In addition to lodash methods, wrappers have `Array` and `String` methods.
-     *
-     * The wrapper `Array` methods are:
-     * `concat`, `join`, `pop`, `push`, `shift`, `sort`, `splice`, and `unshift`
-     *
-     * The wrapper `String` methods are:
-     * `replace` and `split`
-     *
-     * The wrapper methods that support shortcut fusion are:
-     * `at`, `compact`, `drop`, `dropRight`, `dropWhile`, `filter`, `find`,
-     * `findLast`, `head`, `initial`, `last`, `map`, `reject`, `reverse`, `slice`,
-     * `tail`, `take`, `takeRight`, `takeRightWhile`, `takeWhile`, and `toArray`
-     *
-     * The chainable wrapper methods are:
-     * `after`, `ary`, `assign`, `assignIn`, `assignInWith`, `assignWith`, `at`,
-     * `before`, `bind`, `bindAll`, `bindKey`, `castArray`, `chain`, `chunk`,
-     * `commit`, `compact`, `concat`, `conforms`, `constant`, `countBy`, `create`,
-     * `curry`, `debounce`, `defaults`, `defaultsDeep`, `defer`, `delay`,
-     * `difference`, `differenceBy`, `differenceWith`, `drop`, `dropRight`,
-     * `dropRightWhile`, `dropWhile`, `extend`, `extendWith`, `fill`, `filter`,
-     * `flatMap`, `flatMapDeep`, `flatMapDepth`, `flatten`, `flattenDeep`,
-     * `flattenDepth`, `flip`, `flow`, `flowRight`, `fromPairs`, `functions`,
-     * `functionsIn`, `groupBy`, `initial`, `intersection`, `intersectionBy`,
-     * `intersectionWith`, `invert`, `invertBy`, `invokeMap`, `iteratee`, `keyBy`,
-     * `keys`, `keysIn`, `map`, `mapKeys`, `mapValues`, `matches`, `matchesProperty`,
-     * `memoize`, `merge`, `mergeWith`, `method`, `methodOf`, `mixin`, `negate`,
-     * `nthArg`, `omit`, `omitBy`, `once`, `orderBy`, `over`, `overArgs`,
-     * `overEvery`, `overSome`, `partial`, `partialRight`, `partition`, `pick`,
-     * `pickBy`, `plant`, `property`, `propertyOf`, `pull`, `pullAll`, `pullAllBy`,
-     * `pullAllWith`, `pullAt`, `push`, `range`, `rangeRight`, `rearg`, `reject`,
-     * `remove`, `rest`, `reverse`, `sampleSize`, `set`, `setWith`, `shuffle`,
-     * `slice`, `sort`, `sortBy`, `splice`, `spread`, `tail`, `take`, `takeRight`,
-     * `takeRightWhile`, `takeWhile`, `tap`, `throttle`, `thru`, `toArray`,
-     * `toPairs`, `toPairsIn`, `toPath`, `toPlainObject`, `transform`, `unary`,
-     * `union`, `unionBy`, `unionWith`, `uniq`, `uniqBy`, `uniqWith`, `unset`,
-     * `unshift`, `unzip`, `unzipWith`, `update`, `updateWith`, `values`,
-     * `valuesIn`, `without`, `wrap`, `xor`, `xorBy`, `xorWith`, `zip`,
-     * `zipObject`, `zipObjectDeep`, and `zipWith`
-     *
-     * The wrapper methods that are **not** chainable by default are:
-     * `add`, `attempt`, `camelCase`, `capitalize`, `ceil`, `clamp`, `clone`,
-     * `cloneDeep`, `cloneDeepWith`, `cloneWith`, `conformsTo`, `deburr`,
-     * `defaultTo`, `divide`, `each`, `eachRight`, `endsWith`, `eq`, `escape`,
-     * `escapeRegExp`, `every`, `find`, `findIndex`, `findKey`, `findLast`,
-     * `findLastIndex`, `findLastKey`, `first`, `floor`, `forEach`, `forEachRight`,
-     * `forIn`, `forInRight`, `forOwn`, `forOwnRight`, `get`, `gt`, `gte`, `has`,
-     * `hasIn`, `head`, `identity`, `includes`, `indexOf`, `inRange`, `invoke`,
-     * `isArguments`, `isArray`, `isArrayBuffer`, `isArrayLike`, `isArrayLikeObject`,
-     * `isBoolean`, `isBuffer`, `isDate`, `isElement`, `isEmpty`, `isEqual`,
-     * `isEqualWith`, `isError`, `isFinite`, `isFunction`, `isInteger`, `isLength`,
-     * `isMap`, `isMatch`, `isMatchWith`, `isNaN`, `isNative`, `isNil`, `isNull`,
-     * `isNumber`, `isObject`, `isObjectLike`, `isPlainObject`, `isRegExp`,
-     * `isSafeInteger`, `isSet`, `isString`, `isUndefined`, `isTypedArray`,
-     * `isWeakMap`, `isWeakSet`, `join`, `kebabCase`, `last`, `lastIndexOf`,
-     * `lowerCase`, `lowerFirst`, `lt`, `lte`, `max`, `maxBy`, `mean`, `meanBy`,
-     * `min`, `minBy`, `multiply`, `noConflict`, `noop`, `now`, `nth`, `pad`,
-     * `padEnd`, `padStart`, `parseInt`, `pop`, `random`, `reduce`, `reduceRight`,
-     * `repeat`, `result`, `round`, `runInContext`, `sample`, `shift`, `size`,
-     * `snakeCase`, `some`, `sortedIndex`, `sortedIndexBy`, `sortedLastIndex`,
-     * `sortedLastIndexBy`, `startCase`, `startsWith`, `stubArray`, `stubFalse`,
-     * `stubObject`, `stubString`, `stubTrue`, `subtract`, `sum`, `sumBy`,
-     * `template`, `times`, `toFinite`, `toInteger`, `toJSON`, `toLength`,
-     * `toLower`, `toNumber`, `toSafeInteger`, `toString`, `toUpper`, `trim`,
-     * `trimEnd`, `trimStart`, `truncate`, `unescape`, `uniqueId`, `upperCase`,
-     * `upperFirst`, `value`, and `words`
-     *
-     * @name _
-     * @constructor
-     * @category Seq
-     * @param {*} value The value to wrap in a `lodash` instance.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var wrapped = _([1, 2, 3]);
-     *
-     * // Returns an unwrapped value.
-     * wrapped.reduce(_.add);
-     * // => 6
-     *
-     * // Returns a wrapped value.
-     * var squares = wrapped.map(square);
-     *
-     * _.isArray(squares);
-     * // => false
-     *
-     * _.isArray(squares.value());
-     * // => true
-     */
-    function lodash(value) {
-      if (isObjectLike(value) && !isArray(value) && !(value instanceof LazyWrapper)) {
-        if (value instanceof LodashWrapper) {
-          return value;
-        }
-        if (hasOwnProperty.call(value, '__wrapped__')) {
-          return wrapperClone(value);
-        }
-      }
-      return new LodashWrapper(value);
-    }
-
-    /**
-     * The base implementation of `_.create` without support for assigning
-     * properties to the created object.
-     *
-     * @private
-     * @param {Object} proto The object to inherit from.
-     * @returns {Object} Returns the new object.
-     */
-    var baseCreate = (function() {
-      function object() {}
-      return function(proto) {
-        if (!isObject(proto)) {
-          return {};
-        }
-        if (objectCreate) {
-          return objectCreate(proto);
-        }
-        object.prototype = proto;
-        var result = new object;
-        object.prototype = undefined;
-        return result;
-      };
-    }());
-
-    /**
-     * The function whose prototype chain sequence wrappers inherit from.
-     *
-     * @private
-     */
-    function baseLodash() {
-      // No operation performed.
-    }
-
-    /**
-     * The base constructor for creating `lodash` wrapper objects.
-     *
-     * @private
-     * @param {*} value The value to wrap.
-     * @param {boolean} [chainAll] Enable explicit method chain sequences.
-     */
-    function LodashWrapper(value, chainAll) {
-      this.__wrapped__ = value;
-      this.__actions__ = [];
-      this.__chain__ = !!chainAll;
-      this.__index__ = 0;
-      this.__values__ = undefined;
-    }
-
-    /**
-     * By default, the template delimiters used by lodash are like those in
-     * embedded Ruby (ERB) as well as ES2015 template strings. Change the
-     * following template settings to use alternative delimiters.
-     *
-     * @static
-     * @memberOf _
-     * @type {Object}
-     */
-    lodash.templateSettings = {
-
-      /**
-       * Used to detect `data` property values to be HTML-escaped.
-       *
-       * @memberOf _.templateSettings
-       * @type {RegExp}
-       */
-      'escape': reEscape,
-
-      /**
-       * Used to detect code to be evaluated.
-       *
-       * @memberOf _.templateSettings
-       * @type {RegExp}
-       */
-      'evaluate': reEvaluate,
-
-      /**
-       * Used to detect `data` property values to inject.
-       *
-       * @memberOf _.templateSettings
-       * @type {RegExp}
-       */
-      'interpolate': reInterpolate,
-
-      /**
-       * Used to reference the data object in the template text.
-       *
-       * @memberOf _.templateSettings
-       * @type {string}
-       */
-      'variable': '',
-
-      /**
-       * Used to import variables into the compiled template.
-       *
-       * @memberOf _.templateSettings
-       * @type {Object}
-       */
-      'imports': {
-
-        /**
-         * A reference to the `lodash` function.
-         *
-         * @memberOf _.templateSettings.imports
-         * @type {Function}
-         */
-        '_': lodash
-      }
-    };
-
-    // Ensure wrappers are instances of `baseLodash`.
-    lodash.prototype = baseLodash.prototype;
-    lodash.prototype.constructor = lodash;
-
-    LodashWrapper.prototype = baseCreate(baseLodash.prototype);
-    LodashWrapper.prototype.constructor = LodashWrapper;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a lazy wrapper object which wraps `value` to enable lazy evaluation.
-     *
-     * @private
-     * @constructor
-     * @param {*} value The value to wrap.
-     */
-    function LazyWrapper(value) {
-      this.__wrapped__ = value;
-      this.__actions__ = [];
-      this.__dir__ = 1;
-      this.__filtered__ = false;
-      this.__iteratees__ = [];
-      this.__takeCount__ = MAX_ARRAY_LENGTH;
-      this.__views__ = [];
-    }
-
-    /**
-     * Creates a clone of the lazy wrapper object.
-     *
-     * @private
-     * @name clone
-     * @memberOf LazyWrapper
-     * @returns {Object} Returns the cloned `LazyWrapper` object.
-     */
-    function lazyClone() {
-      var result = new LazyWrapper(this.__wrapped__);
-      result.__actions__ = copyArray(this.__actions__);
-      result.__dir__ = this.__dir__;
-      result.__filtered__ = this.__filtered__;
-      result.__iteratees__ = copyArray(this.__iteratees__);
-      result.__takeCount__ = this.__takeCount__;
-      result.__views__ = copyArray(this.__views__);
-      return result;
-    }
-
-    /**
-     * Reverses the direction of lazy iteration.
-     *
-     * @private
-     * @name reverse
-     * @memberOf LazyWrapper
-     * @returns {Object} Returns the new reversed `LazyWrapper` object.
-     */
-    function lazyReverse() {
-      if (this.__filtered__) {
-        var result = new LazyWrapper(this);
-        result.__dir__ = -1;
-        result.__filtered__ = true;
-      } else {
-        result = this.clone();
-        result.__dir__ *= -1;
-      }
-      return result;
-    }
-
-    /**
-     * Extracts the unwrapped value from its lazy wrapper.
-     *
-     * @private
-     * @name value
-     * @memberOf LazyWrapper
-     * @returns {*} Returns the unwrapped value.
-     */
-    function lazyValue() {
-      var array = this.__wrapped__.value(),
-          dir = this.__dir__,
-          isArr = isArray(array),
-          isRight = dir < 0,
-          arrLength = isArr ? array.length : 0,
-          view = getView(0, arrLength, this.__views__),
-          start = view.start,
-          end = view.end,
-          length = end - start,
-          index = isRight ? end : (start - 1),
-          iteratees = this.__iteratees__,
-          iterLength = iteratees.length,
-          resIndex = 0,
-          takeCount = nativeMin(length, this.__takeCount__);
-
-      if (!isArr || (!isRight && arrLength == length && takeCount == length)) {
-        return baseWrapperValue(array, this.__actions__);
-      }
-      var result = [];
-
-      outer:
-      while (length-- && resIndex < takeCount) {
-        index += dir;
-
-        var iterIndex = -1,
-            value = array[index];
-
-        while (++iterIndex < iterLength) {
-          var data = iteratees[iterIndex],
-              iteratee = data.iteratee,
-              type = data.type,
-              computed = iteratee(value);
-
-          if (type == LAZY_MAP_FLAG) {
-            value = computed;
-          } else if (!computed) {
-            if (type == LAZY_FILTER_FLAG) {
-              continue outer;
-            } else {
-              break outer;
-            }
-          }
-        }
-        result[resIndex++] = value;
-      }
-      return result;
-    }
-
-    // Ensure `LazyWrapper` is an instance of `baseLodash`.
-    LazyWrapper.prototype = baseCreate(baseLodash.prototype);
-    LazyWrapper.prototype.constructor = LazyWrapper;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a hash object.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function Hash(entries) {
-      var index = -1,
-          length = entries == null ? 0 : entries.length;
-
-      this.clear();
-      while (++index < length) {
-        var entry = entries[index];
-        this.set(entry[0], entry[1]);
-      }
-    }
-
-    /**
-     * Removes all key-value entries from the hash.
-     *
-     * @private
-     * @name clear
-     * @memberOf Hash
-     */
-    function hashClear() {
-      this.__data__ = nativeCreate ? nativeCreate(null) : {};
-      this.size = 0;
-    }
-
-    /**
-     * Removes `key` and its value from the hash.
-     *
-     * @private
-     * @name delete
-     * @memberOf Hash
-     * @param {Object} hash The hash to modify.
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function hashDelete(key) {
-      var result = this.has(key) && delete this.__data__[key];
-      this.size -= result ? 1 : 0;
-      return result;
-    }
-
-    /**
-     * Gets the hash value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf Hash
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function hashGet(key) {
-      var data = this.__data__;
-      if (nativeCreate) {
-        var result = data[key];
-        return result === HASH_UNDEFINED ? undefined : result;
-      }
-      return hasOwnProperty.call(data, key) ? data[key] : undefined;
-    }
-
-    /**
-     * Checks if a hash value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf Hash
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function hashHas(key) {
-      var data = this.__data__;
-      return nativeCreate ? (data[key] !== undefined) : hasOwnProperty.call(data, key);
-    }
-
-    /**
-     * Sets the hash `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf Hash
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the hash instance.
-     */
-    function hashSet(key, value) {
-      var data = this.__data__;
-      this.size += this.has(key) ? 0 : 1;
-      data[key] = (nativeCreate && value === undefined) ? HASH_UNDEFINED : value;
-      return this;
-    }
-
-    // Add methods to `Hash`.
-    Hash.prototype.clear = hashClear;
-    Hash.prototype['delete'] = hashDelete;
-    Hash.prototype.get = hashGet;
-    Hash.prototype.has = hashHas;
-    Hash.prototype.set = hashSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an list cache object.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function ListCache(entries) {
-      var index = -1,
-          length = entries == null ? 0 : entries.length;
-
-      this.clear();
-      while (++index < length) {
-        var entry = entries[index];
-        this.set(entry[0], entry[1]);
-      }
-    }
-
-    /**
-     * Removes all key-value entries from the list cache.
-     *
-     * @private
-     * @name clear
-     * @memberOf ListCache
-     */
-    function listCacheClear() {
-      this.__data__ = [];
-      this.size = 0;
-    }
-
-    /**
-     * Removes `key` and its value from the list cache.
-     *
-     * @private
-     * @name delete
-     * @memberOf ListCache
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function listCacheDelete(key) {
-      var data = this.__data__,
-          index = assocIndexOf(data, key);
-
-      if (index < 0) {
-        return false;
-      }
-      var lastIndex = data.length - 1;
-      if (index == lastIndex) {
-        data.pop();
-      } else {
-        splice.call(data, index, 1);
-      }
-      --this.size;
-      return true;
-    }
-
-    /**
-     * Gets the list cache value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf ListCache
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function listCacheGet(key) {
-      var data = this.__data__,
-          index = assocIndexOf(data, key);
-
-      return index < 0 ? undefined : data[index][1];
-    }
-
-    /**
-     * Checks if a list cache value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf ListCache
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function listCacheHas(key) {
-      return assocIndexOf(this.__data__, key) > -1;
-    }
-
-    /**
-     * Sets the list cache `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf ListCache
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the list cache instance.
-     */
-    function listCacheSet(key, value) {
-      var data = this.__data__,
-          index = assocIndexOf(data, key);
-
-      if (index < 0) {
-        ++this.size;
-        data.push([key, value]);
-      } else {
-        data[index][1] = value;
-      }
-      return this;
-    }
-
-    // Add methods to `ListCache`.
-    ListCache.prototype.clear = listCacheClear;
-    ListCache.prototype['delete'] = listCacheDelete;
-    ListCache.prototype.get = listCacheGet;
-    ListCache.prototype.has = listCacheHas;
-    ListCache.prototype.set = listCacheSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a map cache object to store key-value pairs.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function MapCache(entries) {
-      var index = -1,
-          length = entries == null ? 0 : entries.length;
-
-      this.clear();
-      while (++index < length) {
-        var entry = entries[index];
-        this.set(entry[0], entry[1]);
-      }
-    }
-
-    /**
-     * Removes all key-value entries from the map.
-     *
-     * @private
-     * @name clear
-     * @memberOf MapCache
-     */
-    function mapCacheClear() {
-      this.size = 0;
-      this.__data__ = {
-        'hash': new Hash,
-        'map': new (Map || ListCache),
-        'string': new Hash
-      };
-    }
-
-    /**
-     * Removes `key` and its value from the map.
-     *
-     * @private
-     * @name delete
-     * @memberOf MapCache
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function mapCacheDelete(key) {
-      var result = getMapData(this, key)['delete'](key);
-      this.size -= result ? 1 : 0;
-      return result;
-    }
-
-    /**
-     * Gets the map value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf MapCache
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function mapCacheGet(key) {
-      return getMapData(this, key).get(key);
-    }
-
-    /**
-     * Checks if a map value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf MapCache
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function mapCacheHas(key) {
-      return getMapData(this, key).has(key);
-    }
-
-    /**
-     * Sets the map `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf MapCache
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the map cache instance.
-     */
-    function mapCacheSet(key, value) {
-      var data = getMapData(this, key),
-          size = data.size;
-
-      data.set(key, value);
-      this.size += data.size == size ? 0 : 1;
-      return this;
-    }
-
-    // Add methods to `MapCache`.
-    MapCache.prototype.clear = mapCacheClear;
-    MapCache.prototype['delete'] = mapCacheDelete;
-    MapCache.prototype.get = mapCacheGet;
-    MapCache.prototype.has = mapCacheHas;
-    MapCache.prototype.set = mapCacheSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     *
-     * Creates an array cache object to store unique values.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [values] The values to cache.
-     */
-    function SetCache(values) {
-      var index = -1,
-          length = values == null ? 0 : values.length;
-
-      this.__data__ = new MapCache;
-      while (++index < length) {
-        this.add(values[index]);
-      }
-    }
-
-    /**
-     * Adds `value` to the array cache.
-     *
-     * @private
-     * @name add
-     * @memberOf SetCache
-     * @alias push
-     * @param {*} value The value to cache.
-     * @returns {Object} Returns the cache instance.
-     */
-    function setCacheAdd(value) {
-      this.__data__.set(value, HASH_UNDEFINED);
-      return this;
-    }
-
-    /**
-     * Checks if `value` is in the array cache.
-     *
-     * @private
-     * @name has
-     * @memberOf SetCache
-     * @param {*} value The value to search for.
-     * @returns {number} Returns `true` if `value` is found, else `false`.
-     */
-    function setCacheHas(value) {
-      return this.__data__.has(value);
-    }
-
-    // Add methods to `SetCache`.
-    SetCache.prototype.add = SetCache.prototype.push = setCacheAdd;
-    SetCache.prototype.has = setCacheHas;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a stack cache object to store key-value pairs.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function Stack(entries) {
-      var data = this.__data__ = new ListCache(entries);
-      this.size = data.size;
-    }
-
-    /**
-     * Removes all key-value entries from the stack.
-     *
-     * @private
-     * @name clear
-     * @memberOf Stack
-     */
-    function stackClear() {
-      this.__data__ = new ListCache;
-      this.size = 0;
-    }
-
-    /**
-     * Removes `key` and its value from the stack.
-     *
-     * @private
-     * @name delete
-     * @memberOf Stack
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function stackDelete(key) {
-      var data = this.__data__,
-          result = data['delete'](key);
-
-      this.size = data.size;
-      return result;
-    }
-
-    /**
-     * Gets the stack value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf Stack
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function stackGet(key) {
-      return this.__data__.get(key);
-    }
-
-    /**
-     * Checks if a stack value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf Stack
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function stackHas(key) {
-      return this.__data__.has(key);
-    }
-
-    /**
-     * Sets the stack `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf Stack
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the stack cache instance.
-     */
-    function stackSet(key, value) {
-      var data = this.__data__;
-      if (data instanceof ListCache) {
-        var pairs = data.__data__;
-        if (!Map || (pairs.length < LARGE_ARRAY_SIZE - 1)) {
-          pairs.push([key, value]);
-          this.size = ++data.size;
-          return this;
-        }
-        data = this.__data__ = new MapCache(pairs);
-      }
-      data.set(key, value);
-      this.size = data.size;
-      return this;
-    }
-
-    // Add methods to `Stack`.
-    Stack.prototype.clear = stackClear;
-    Stack.prototype['delete'] = stackDelete;
-    Stack.prototype.get = stackGet;
-    Stack.prototype.has = stackHas;
-    Stack.prototype.set = stackSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an array of the enumerable property names of the array-like `value`.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @param {boolean} inherited Specify returning inherited property names.
-     * @returns {Array} Returns the array of property names.
-     */
-    function arrayLikeKeys(value, inherited) {
-      var isArr = isArray(value),
-          isArg = !isArr && isArguments(value),
-          isBuff = !isArr && !isArg && isBuffer(value),
-          isType = !isArr && !isArg && !isBuff && isTypedArray(value),
-          skipIndexes = isArr || isArg || isBuff || isType,
-          result = skipIndexes ? baseTimes(value.length, String) : [],
-          length = result.length;
-
-      for (var key in value) {
-        if ((inherited || hasOwnProperty.call(value, key)) &&
-            !(skipIndexes && (
-               // Safari 9 has enumerable `arguments.length` in strict mode.
-               key == 'length' ||
-               // Node.js 0.10 has enumerable non-index properties on buffers.
-               (isBuff && (key == 'offset' || key == 'parent')) ||
-               // PhantomJS 2 has enumerable non-index properties on typed arrays.
-               (isType && (key == 'buffer' || key == 'byteLength' || key == 'byteOffset')) ||
-               // Skip index properties.
-               isIndex(key, length)
-            ))) {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * A specialized version of `_.sample` for arrays.
-     *
-     * @private
-     * @param {Array} array The array to sample.
-     * @returns {*} Returns the random element.
-     */
-    function arraySample(array) {
-      var length = array.length;
-      return length ? array[baseRandom(0, length - 1)] : undefined;
-    }
-
-    /**
-     * A specialized version of `_.sampleSize` for arrays.
-     *
-     * @private
-     * @param {Array} array The array to sample.
-     * @param {number} n The number of elements to sample.
-     * @returns {Array} Returns the random elements.
-     */
-    function arraySampleSize(array, n) {
-      return shuffleSelf(copyArray(array), baseClamp(n, 0, array.length));
-    }
-
-    /**
-     * A specialized version of `_.shuffle` for arrays.
-     *
-     * @private
-     * @param {Array} array The array to shuffle.
-     * @returns {Array} Returns the new shuffled array.
-     */
-    function arrayShuffle(array) {
-      return shuffleSelf(copyArray(array));
-    }
-
-    /**
-     * This function is like `assignValue` except that it doesn't assign
-     * `undefined` values.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {string} key The key of the property to assign.
-     * @param {*} value The value to assign.
-     */
-    function assignMergeValue(object, key, value) {
-      if ((value !== undefined && !eq(object[key], value)) ||
-          (value === undefined && !(key in object))) {
-        baseAssignValue(object, key, value);
-      }
-    }
-
-    /**
-     * Assigns `value` to `key` of `object` if the existing value is not equivalent
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {string} key The key of the property to assign.
-     * @param {*} value The value to assign.
-     */
-    function assignValue(object, key, value) {
-      var objValue = object[key];
-      if (!(hasOwnProperty.call(object, key) && eq(objValue, value)) ||
-          (value === undefined && !(key in object))) {
-        baseAssignValue(object, key, value);
-      }
-    }
-
-    /**
-     * Gets the index at which the `key` is found in `array` of key-value pairs.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {*} key The key to search for.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     */
-    function assocIndexOf(array, key) {
-      var length = array.length;
-      while (length--) {
-        if (eq(array[length][0], key)) {
-          return length;
-        }
-      }
-      return -1;
-    }
-
-    /**
-     * Aggregates elements of `collection` on `accumulator` with keys transformed
-     * by `iteratee` and values set by `setter`.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} setter The function to set `accumulator` values.
-     * @param {Function} iteratee The iteratee to transform keys.
-     * @param {Object} accumulator The initial aggregated object.
-     * @returns {Function} Returns `accumulator`.
-     */
-    function baseAggregator(collection, setter, iteratee, accumulator) {
-      baseEach(collection, function(value, key, collection) {
-        setter(accumulator, value, iteratee(value), collection);
-      });
-      return accumulator;
-    }
-
-    /**
-     * The base implementation of `_.assign` without support for multiple sources
-     * or `customizer` functions.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @returns {Object} Returns `object`.
-     */
-    function baseAssign(object, source) {
-      return object && copyObject(source, keys(source), object);
-    }
-
-    /**
-     * The base implementation of `_.assignIn` without support for multiple sources
-     * or `customizer` functions.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @returns {Object} Returns `object`.
-     */
-    function baseAssignIn(object, source) {
-      return object && copyObject(source, keysIn(source), object);
-    }
-
-    /**
-     * The base implementation of `assignValue` and `assignMergeValue` without
-     * value checks.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {string} key The key of the property to assign.
-     * @param {*} value The value to assign.
-     */
-    function baseAssignValue(object, key, value) {
-      if (key == '__proto__' && defineProperty) {
-        defineProperty(object, key, {
-          'configurable': true,
-          'enumerable': true,
-          'value': value,
-          'writable': true
-        });
-      } else {
-        object[key] = value;
-      }
-    }
-
-    /**
-     * The base implementation of `_.at` without support for individual paths.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {string[]} paths The property paths to pick.
-     * @returns {Array} Returns the picked elements.
-     */
-    function baseAt(object, paths) {
-      var index = -1,
-          length = paths.length,
-          result = Array(length),
-          skip = object == null;
-
-      while (++index < length) {
-        result[index] = skip ? undefined : get(object, paths[index]);
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.clamp` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {number} number The number to clamp.
-     * @param {number} [lower] The lower bound.
-     * @param {number} upper The upper bound.
-     * @returns {number} Returns the clamped number.
-     */
-    function baseClamp(number, lower, upper) {
-      if (number === number) {
-        if (upper !== undefined) {
-          number = number <= upper ? number : upper;
-        }
-        if (lower !== undefined) {
-          number = number >= lower ? number : lower;
-        }
-      }
-      return number;
-    }
-
-    /**
-     * The base implementation of `_.clone` and `_.cloneDeep` which tracks
-     * traversed objects.
-     *
-     * @private
-     * @param {*} value The value to clone.
-     * @param {boolean} bitmask The bitmask flags.
-     *  1 - Deep clone
-     *  2 - Flatten inherited properties
-     *  4 - Clone symbols
-     * @param {Function} [customizer] The function to customize cloning.
-     * @param {string} [key] The key of `value`.
-     * @param {Object} [object] The parent object of `value`.
-     * @param {Object} [stack] Tracks traversed objects and their clone counterparts.
-     * @returns {*} Returns the cloned value.
-     */
-    function baseClone(value, bitmask, customizer, key, object, stack) {
-      var result,
-          isDeep = bitmask & CLONE_DEEP_FLAG,
-          isFlat = bitmask & CLONE_FLAT_FLAG,
-          isFull = bitmask & CLONE_SYMBOLS_FLAG;
-
-      if (customizer) {
-        result = object ? customizer(value, key, object, stack) : customizer(value);
-      }
-      if (result !== undefined) {
-        return result;
-      }
-      if (!isObject(value)) {
-        return value;
-      }
-      var isArr = isArray(value);
-      if (isArr) {
-        result = initCloneArray(value);
-        if (!isDeep) {
-          return copyArray(value, result);
-        }
-      } else {
-        var tag = getTag(value),
-            isFunc = tag == funcTag || tag == genTag;
-
-        if (isBuffer(value)) {
-          return cloneBuffer(value, isDeep);
-        }
-        if (tag == objectTag || tag == argsTag || (isFunc && !object)) {
-          result = (isFlat || isFunc) ? {} : initCloneObject(value);
-          if (!isDeep) {
-            return isFlat
-              ? copySymbolsIn(value, baseAssignIn(result, value))
-              : copySymbols(value, baseAssign(result, value));
-          }
-        } else {
-          if (!cloneableTags[tag]) {
-            return object ? value : {};
-          }
-          result = initCloneByTag(value, tag, isDeep);
-        }
-      }
-      // Check for circular references and return its corresponding clone.
-      stack || (stack = new Stack);
-      var stacked = stack.get(value);
-      if (stacked) {
-        return stacked;
-      }
-      stack.set(value, result);
-
-      if (isSet(value)) {
-        value.forEach(function(subValue) {
-          result.add(baseClone(subValue, bitmask, customizer, subValue, value, stack));
-        });
-      } else if (isMap(value)) {
-        value.forEach(function(subValue, key) {
-          result.set(key, baseClone(subValue, bitmask, customizer, key, value, stack));
-        });
-      }
-
-      var keysFunc = isFull
-        ? (isFlat ? getAllKeysIn : getAllKeys)
-        : (isFlat ? keysIn : keys);
-
-      var props = isArr ? undefined : keysFunc(value);
-      arrayEach(props || value, function(subValue, key) {
-        if (props) {
-          key = subValue;
-          subValue = value[key];
-        }
-        // Recursively populate clone (susceptible to call stack limits).
-        assignValue(result, key, baseClone(subValue, bitmask, customizer, key, value, stack));
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.conforms` which doesn't clone `source`.
-     *
-     * @private
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {Function} Returns the new spec function.
-     */
-    function baseConforms(source) {
-      var props = keys(source);
-      return function(object) {
-        return baseConformsTo(object, source, props);
-      };
-    }
-
-    /**
-     * The base implementation of `_.conformsTo` which accepts `props` to check.
-     *
-     * @private
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {boolean} Returns `true` if `object` conforms, else `false`.
-     */
-    function baseConformsTo(object, source, props) {
-      var length = props.length;
-      if (object == null) {
-        return !length;
-      }
-      object = Object(object);
-      while (length--) {
-        var key = props[length],
-            predicate = source[key],
-            value = object[key];
-
-        if ((value === undefined && !(key in object)) || !predicate(value)) {
-          return false;
-        }
-      }
-      return true;
-    }
-
-    /**
-     * The base implementation of `_.delay` and `_.defer` which accepts `args`
-     * to provide to `func`.
-     *
-     * @private
-     * @param {Function} func The function to delay.
-     * @param {number} wait The number of milliseconds to delay invocation.
-     * @param {Array} args The arguments to provide to `func`.
-     * @returns {number|Object} Returns the timer id or timeout object.
-     */
-    function baseDelay(func, wait, args) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      return setTimeout(function() { func.apply(undefined, args); }, wait);
-    }
-
-    /**
-     * The base implementation of methods like `_.difference` without support
-     * for excluding multiple arrays or iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {Array} values The values to exclude.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     */
-    function baseDifference(array, values, iteratee, comparator) {
-      var index = -1,
-          includes = arrayIncludes,
-          isCommon = true,
-          length = array.length,
-          result = [],
-          valuesLength = values.length;
-
-      if (!length) {
-        return result;
-      }
-      if (iteratee) {
-        values = arrayMap(values, baseUnary(iteratee));
-      }
-      if (comparator) {
-        includes = arrayIncludesWith;
-        isCommon = false;
-      }
-      else if (values.length >= LARGE_ARRAY_SIZE) {
-        includes = cacheHas;
-        isCommon = false;
-        values = new SetCache(values);
-      }
-      outer:
-      while (++index < length) {
-        var value = array[index],
-            computed = iteratee == null ? value : iteratee(value);
-
-        value = (comparator || value !== 0) ? value : 0;
-        if (isCommon && computed === computed) {
-          var valuesIndex = valuesLength;
-          while (valuesIndex--) {
-            if (values[valuesIndex] === computed) {
-              continue outer;
-            }
-          }
-          result.push(value);
-        }
-        else if (!includes(values, computed, comparator)) {
-          result.push(value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.forEach` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     */
-    var baseEach = createBaseEach(baseForOwn);
-
-    /**
-     * The base implementation of `_.forEachRight` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     */
-    var baseEachRight = createBaseEach(baseForOwnRight, true);
-
-    /**
-     * The base implementation of `_.every` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} predicate The function invoked per iteration.
-     * @returns {boolean} Returns `true` if all elements pass the predicate check,
-     *  else `false`
-     */
-    function baseEvery(collection, predicate) {
-      var result = true;
-      baseEach(collection, function(value, index, collection) {
-        result = !!predicate(value, index, collection);
-        return result;
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of methods like `_.max` and `_.min` which accepts a
-     * `comparator` to determine the extremum value.
-     *
-     * @private
-     * @param {Array} array The array to iterate over.
-     * @param {Function} iteratee The iteratee invoked per iteration.
-     * @param {Function} comparator The comparator used to compare values.
-     * @returns {*} Returns the extremum value.
-     */
-    function baseExtremum(array, iteratee, comparator) {
-      var index = -1,
-          length = array.length;
-
-      while (++index < length) {
-        var value = array[index],
-            current = iteratee(value);
-
-        if (current != null && (computed === undefined
-              ? (current === current && !isSymbol(current))
-              : comparator(current, computed)
-            )) {
-          var computed = current,
-              result = value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.fill` without an iteratee call guard.
-     *
-     * @private
-     * @param {Array} array The array to fill.
-     * @param {*} value The value to fill `array` with.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns `array`.
-     */
-    function baseFill(array, value, start, end) {
-      var length = array.length;
-
-      start = toInteger(start);
-      if (start < 0) {
-        start = -start > length ? 0 : (length + start);
-      }
-      end = (end === undefined || end > length) ? length : toInteger(end);
-      if (end < 0) {
-        end += length;
-      }
-      end = start > end ? 0 : toLength(end);
-      while (start < end) {
-        array[start++] = value;
-      }
-      return array;
-    }
-
-    /**
-     * The base implementation of `_.filter` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} predicate The function invoked per iteration.
-     * @returns {Array} Returns the new filtered array.
-     */
-    function baseFilter(collection, predicate) {
-      var result = [];
-      baseEach(collection, function(value, index, collection) {
-        if (predicate(value, index, collection)) {
-          result.push(value);
-        }
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.flatten` with support for restricting flattening.
-     *
-     * @private
-     * @param {Array} array The array to flatten.
-     * @param {number} depth The maximum recursion depth.
-     * @param {boolean} [predicate=isFlattenable] The function invoked per iteration.
-     * @param {boolean} [isStrict] Restrict to values that pass `predicate` checks.
-     * @param {Array} [result=[]] The initial result value.
-     * @returns {Array} Returns the new flattened array.
-     */
-    function baseFlatten(array, depth, predicate, isStrict, result) {
-      var index = -1,
-          length = array.length;
-
-      predicate || (predicate = isFlattenable);
-      result || (result = []);
-
-      while (++index < length) {
-        var value = array[index];
-        if (depth > 0 && predicate(value)) {
-          if (depth > 1) {
-            // Recursively flatten arrays (susceptible to call stack limits).
-            baseFlatten(value, depth - 1, predicate, isStrict, result);
-          } else {
-            arrayPush(result, value);
-          }
-        } else if (!isStrict) {
-          result[result.length] = value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `baseForOwn` which iterates over `object`
-     * properties returned by `keysFunc` and invokes `iteratee` for each property.
-     * Iteratee functions may exit iteration early by explicitly returning `false`.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @param {Function} keysFunc The function to get the keys of `object`.
-     * @returns {Object} Returns `object`.
-     */
-    var baseFor = createBaseFor();
-
-    /**
-     * This function is like `baseFor` except that it iterates over properties
-     * in the opposite order.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @param {Function} keysFunc The function to get the keys of `object`.
-     * @returns {Object} Returns `object`.
-     */
-    var baseForRight = createBaseFor(true);
-
-    /**
-     * The base implementation of `_.forOwn` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     */
-    function baseForOwn(object, iteratee) {
-      return object && baseFor(object, iteratee, keys);
-    }
-
-    /**
-     * The base implementation of `_.forOwnRight` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     */
-    function baseForOwnRight(object, iteratee) {
-      return object && baseForRight(object, iteratee, keys);
-    }
-
-    /**
-     * The base implementation of `_.functions` which creates an array of
-     * `object` function property names filtered from `props`.
-     *
-     * @private
-     * @param {Object} object The object to inspect.
-     * @param {Array} props The property names to filter.
-     * @returns {Array} Returns the function names.
-     */
-    function baseFunctions(object, props) {
-      return arrayFilter(props, function(key) {
-        return isFunction(object[key]);
-      });
-    }
-
-    /**
-     * The base implementation of `_.get` without support for default values.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the property to get.
-     * @returns {*} Returns the resolved value.
-     */
-    function baseGet(object, path) {
-      path = castPath(path, object);
-
-      var index = 0,
-          length = path.length;
-
-      while (object != null && index < length) {
-        object = object[toKey(path[index++])];
-      }
-      return (index && index == length) ? object : undefined;
-    }
-
-    /**
-     * The base implementation of `getAllKeys` and `getAllKeysIn` which uses
-     * `keysFunc` and `symbolsFunc` to get the enumerable property names and
-     * symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Function} keysFunc The function to get the keys of `object`.
-     * @param {Function} symbolsFunc The function to get the symbols of `object`.
-     * @returns {Array} Returns the array of property names and symbols.
-     */
-    function baseGetAllKeys(object, keysFunc, symbolsFunc) {
-      var result = keysFunc(object);
-      return isArray(object) ? result : arrayPush(result, symbolsFunc(object));
-    }
-
-    /**
-     * The base implementation of `getTag` without fallbacks for buggy environments.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @returns {string} Returns the `toStringTag`.
-     */
-    function baseGetTag(value) {
-      if (value == null) {
-        return value === undefined ? undefinedTag : nullTag;
-      }
-      return (symToStringTag && symToStringTag in Object(value))
-        ? getRawTag(value)
-        : objectToString(value);
-    }
-
-    /**
-     * The base implementation of `_.gt` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is greater than `other`,
-     *  else `false`.
-     */
-    function baseGt(value, other) {
-      return value > other;
-    }
-
-    /**
-     * The base implementation of `_.has` without support for deep paths.
-     *
-     * @private
-     * @param {Object} [object] The object to query.
-     * @param {Array|string} key The key to check.
-     * @returns {boolean} Returns `true` if `key` exists, else `false`.
-     */
-    function baseHas(object, key) {
-      return object != null && hasOwnProperty.call(object, key);
-    }
-
-    /**
-     * The base implementation of `_.hasIn` without support for deep paths.
-     *
-     * @private
-     * @param {Object} [object] The object to query.
-     * @param {Array|string} key The key to check.
-     * @returns {boolean} Returns `true` if `key` exists, else `false`.
-     */
-    function baseHasIn(object, key) {
-      return object != null && key in Object(object);
-    }
-
-    /**
-     * The base implementation of `_.inRange` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {number} number The number to check.
-     * @param {number} start The start of the range.
-     * @param {number} end The end of the range.
-     * @returns {boolean} Returns `true` if `number` is in the range, else `false`.
-     */
-    function baseInRange(number, start, end) {
-      return number >= nativeMin(start, end) && number < nativeMax(start, end);
-    }
-
-    /**
-     * The base implementation of methods like `_.intersection`, without support
-     * for iteratee shorthands, that accepts an array of arrays to inspect.
-     *
-     * @private
-     * @param {Array} arrays The arrays to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of shared values.
-     */
-    function baseIntersection(arrays, iteratee, comparator) {
-      var includes = comparator ? arrayIncludesWith : arrayIncludes,
-          length = arrays[0].length,
-          othLength = arrays.length,
-          othIndex = othLength,
-          caches = Array(othLength),
-          maxLength = Infinity,
-          result = [];
-
-      while (othIndex--) {
-        var array = arrays[othIndex];
-        if (othIndex && iteratee) {
-          array = arrayMap(array, baseUnary(iteratee));
-        }
-        maxLength = nativeMin(array.length, maxLength);
-        caches[othIndex] = !comparator && (iteratee || (length >= 120 && array.length >= 120))
-          ? new SetCache(othIndex && array)
-          : undefined;
-      }
-      array = arrays[0];
-
-      var index = -1,
-          seen = caches[0];
-
-      outer:
-      while (++index < length && result.length < maxLength) {
-        var value = array[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        value = (comparator || value !== 0) ? value : 0;
-        if (!(seen
-              ? cacheHas(seen, computed)
-              : includes(result, computed, comparator)
-            )) {
-          othIndex = othLength;
-          while (--othIndex) {
-            var cache = caches[othIndex];
-            if (!(cache
-                  ? cacheHas(cache, computed)
-                  : includes(arrays[othIndex], computed, comparator))
-                ) {
-              continue outer;
-            }
-          }
-          if (seen) {
-            seen.push(computed);
-          }
-          result.push(value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.invert` and `_.invertBy` which inverts
-     * `object` with values transformed by `iteratee` and set by `setter`.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} setter The function to set `accumulator` values.
-     * @param {Function} iteratee The iteratee to transform values.
-     * @param {Object} accumulator The initial inverted object.
-     * @returns {Function} Returns `accumulator`.
-     */
-    function baseInverter(object, setter, iteratee, accumulator) {
-      baseForOwn(object, function(value, key, object) {
-        setter(accumulator, iteratee(value), key, object);
-      });
-      return accumulator;
-    }
-
-    /**
-     * The base implementation of `_.invoke` without support for individual
-     * method arguments.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the method to invoke.
-     * @param {Array} args The arguments to invoke the method with.
-     * @returns {*} Returns the result of the invoked method.
-     */
-    function baseInvoke(object, path, args) {
-      path = castPath(path, object);
-      object = parent(object, path);
-      var func = object == null ? object : object[toKey(last(path))];
-      return func == null ? undefined : apply(func, object, args);
-    }
-
-    /**
-     * The base implementation of `_.isArguments`.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an `arguments` object,
-     */
-    function baseIsArguments(value) {
-      return isObjectLike(value) && baseGetTag(value) == argsTag;
-    }
-
-    /**
-     * The base implementation of `_.isArrayBuffer` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array buffer, else `false`.
-     */
-    function baseIsArrayBuffer(value) {
-      return isObjectLike(value) && baseGetTag(value) == arrayBufferTag;
-    }
-
-    /**
-     * The base implementation of `_.isDate` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a date object, else `false`.
-     */
-    function baseIsDate(value) {
-      return isObjectLike(value) && baseGetTag(value) == dateTag;
-    }
-
-    /**
-     * The base implementation of `_.isEqual` which supports partial comparisons
-     * and tracks traversed objects.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @param {boolean} bitmask The bitmask flags.
-     *  1 - Unordered comparison
-     *  2 - Partial comparison
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @param {Object} [stack] Tracks traversed `value` and `other` objects.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     */
-    function baseIsEqual(value, other, bitmask, customizer, stack) {
-      if (value === other) {
-        return true;
-      }
-      if (value == null || other == null || (!isObjectLike(value) && !isObjectLike(other))) {
-        return value !== value && other !== other;
-      }
-      return baseIsEqualDeep(value, other, bitmask, customizer, baseIsEqual, stack);
-    }
-
-    /**
-     * A specialized version of `baseIsEqual` for arrays and objects which performs
-     * deep comparisons and tracks traversed objects enabling objects with circular
-     * references to be compared.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} [stack] Tracks traversed `object` and `other` objects.
-     * @returns {boolean} Returns `true` if the objects are equivalent, else `false`.
-     */
-    function baseIsEqualDeep(object, other, bitmask, customizer, equalFunc, stack) {
-      var objIsArr = isArray(object),
-          othIsArr = isArray(other),
-          objTag = objIsArr ? arrayTag : getTag(object),
-          othTag = othIsArr ? arrayTag : getTag(other);
-
-      objTag = objTag == argsTag ? objectTag : objTag;
-      othTag = othTag == argsTag ? objectTag : othTag;
-
-      var objIsObj = objTag == objectTag,
-          othIsObj = othTag == objectTag,
-          isSameTag = objTag == othTag;
-
-      if (isSameTag && isBuffer(object)) {
-        if (!isBuffer(other)) {
-          return false;
-        }
-        objIsArr = true;
-        objIsObj = false;
-      }
-      if (isSameTag && !objIsObj) {
-        stack || (stack = new Stack);
-        return (objIsArr || isTypedArray(object))
-          ? equalArrays(object, other, bitmask, customizer, equalFunc, stack)
-          : equalByTag(object, other, objTag, bitmask, customizer, equalFunc, stack);
-      }
-      if (!(bitmask & COMPARE_PARTIAL_FLAG)) {
-        var objIsWrapped = objIsObj && hasOwnProperty.call(object, '__wrapped__'),
-            othIsWrapped = othIsObj && hasOwnProperty.call(other, '__wrapped__');
-
-        if (objIsWrapped || othIsWrapped) {
-          var objUnwrapped = objIsWrapped ? object.value() : object,
-              othUnwrapped = othIsWrapped ? other.value() : other;
-
-          stack || (stack = new Stack);
-          return equalFunc(objUnwrapped, othUnwrapped, bitmask, customizer, stack);
-        }
-      }
-      if (!isSameTag) {
-        return false;
-      }
-      stack || (stack = new Stack);
-      return equalObjects(object, other, bitmask, customizer, equalFunc, stack);
-    }
-
-    /**
-     * The base implementation of `_.isMap` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a map, else `false`.
-     */
-    function baseIsMap(value) {
-      return isObjectLike(value) && getTag(value) == mapTag;
-    }
-
-    /**
-     * The base implementation of `_.isMatch` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property values to match.
-     * @param {Array} matchData The property names, values, and compare flags to match.
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @returns {boolean} Returns `true` if `object` is a match, else `false`.
-     */
-    function baseIsMatch(object, source, matchData, customizer) {
-      var index = matchData.length,
-          length = index,
-          noCustomizer = !customizer;
-
-      if (object == null) {
-        return !length;
-      }
-      object = Object(object);
-      while (index--) {
-        var data = matchData[index];
-        if ((noCustomizer && data[2])
-              ? data[1] !== object[data[0]]
-              : !(data[0] in object)
-            ) {
-          return false;
-        }
-      }
-      while (++index < length) {
-        data = matchData[index];
-        var key = data[0],
-            objValue = object[key],
-            srcValue = data[1];
-
-        if (noCustomizer && data[2]) {
-          if (objValue === undefined && !(key in object)) {
-            return false;
-          }
-        } else {
-          var stack = new Stack;
-          if (customizer) {
-            var result = customizer(objValue, srcValue, key, object, source, stack);
-          }
-          if (!(result === undefined
-                ? baseIsEqual(srcValue, objValue, COMPARE_PARTIAL_FLAG | COMPARE_UNORDERED_FLAG, customizer, stack)
-                : result
-              )) {
-            return false;
-          }
-        }
-      }
-      return true;
-    }
-
-    /**
-     * The base implementation of `_.isNative` without bad shim checks.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a native function,
-     *  else `false`.
-     */
-    function baseIsNative(value) {
-      if (!isObject(value) || isMasked(value)) {
-        return false;
-      }
-      var pattern = isFunction(value) ? reIsNative : reIsHostCtor;
-      return pattern.test(toSource(value));
-    }
-
-    /**
-     * The base implementation of `_.isRegExp` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a regexp, else `false`.
-     */
-    function baseIsRegExp(value) {
-      return isObjectLike(value) && baseGetTag(value) == regexpTag;
-    }
-
-    /**
-     * The base implementation of `_.isSet` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a set, else `false`.
-     */
-    function baseIsSet(value) {
-      return isObjectLike(value) && getTag(value) == setTag;
-    }
-
-    /**
-     * The base implementation of `_.isTypedArray` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a typed array, else `false`.
-     */
-    function baseIsTypedArray(value) {
-      return isObjectLike(value) &&
-        isLength(value.length) && !!typedArrayTags[baseGetTag(value)];
-    }
-
-    /**
-     * The base implementation of `_.iteratee`.
-     *
-     * @private
-     * @param {*} [value=_.identity] The value to convert to an iteratee.
-     * @returns {Function} Returns the iteratee.
-     */
-    function baseIteratee(value) {
-      // Don't store the `typeof` result in a variable to avoid a JIT bug in Safari 9.
-      // See https://bugs.webkit.org/show_bug.cgi?id=156034 for more details.
-      if (typeof value == 'function') {
-        return value;
-      }
-      if (value == null) {
-        return identity;
-      }
-      if (typeof value == 'object') {
-        return isArray(value)
-          ? baseMatchesProperty(value[0], value[1])
-          : baseMatches(value);
-      }
-      return property(value);
-    }
-
-    /**
-     * The base implementation of `_.keys` which doesn't treat sparse arrays as dense.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     */
-    function baseKeys(object) {
-      if (!isPrototype(object)) {
-        return nativeKeys(object);
-      }
-      var result = [];
-      for (var key in Object(object)) {
-        if (hasOwnProperty.call(object, key) && key != 'constructor') {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.keysIn` which doesn't treat sparse arrays as dense.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     */
-    function baseKeysIn(object) {
-      if (!isObject(object)) {
-        return nativeKeysIn(object);
-      }
-      var isProto = isPrototype(object),
-          result = [];
-
-      for (var key in object) {
-        if (!(key == 'constructor' && (isProto || !hasOwnProperty.call(object, key)))) {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.lt` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is less than `other`,
-     *  else `false`.
-     */
-    function baseLt(value, other) {
-      return value < other;
-    }
-
-    /**
-     * The base implementation of `_.map` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Array} Returns the new mapped array.
-     */
-    function baseMap(collection, iteratee) {
-      var index = -1,
-          result = isArrayLike(collection) ? Array(collection.length) : [];
-
-      baseEach(collection, function(value, key, collection) {
-        result[++index] = iteratee(value, key, collection);
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.matches` which doesn't clone `source`.
-     *
-     * @private
-     * @param {Object} source The object of property values to match.
-     * @returns {Function} Returns the new spec function.
-     */
-    function baseMatches(source) {
-      var matchData = getMatchData(source);
-      if (matchData.length == 1 && matchData[0][2]) {
-        return matchesStrictComparable(matchData[0][0], matchData[0][1]);
-      }
-      return function(object) {
-        return object === source || baseIsMatch(object, source, matchData);
-      };
-    }
-
-    /**
-     * The base implementation of `_.matchesProperty` which doesn't clone `srcValue`.
-     *
-     * @private
-     * @param {string} path The path of the property to get.
-     * @param {*} srcValue The value to match.
-     * @returns {Function} Returns the new spec function.
-     */
-    function baseMatchesProperty(path, srcValue) {
-      if (isKey(path) && isStrictComparable(srcValue)) {
-        return matchesStrictComparable(toKey(path), srcValue);
-      }
-      return function(object) {
-        var objValue = get(object, path);
-        return (objValue === undefined && objValue === srcValue)
-          ? hasIn(object, path)
-          : baseIsEqual(srcValue, objValue, COMPARE_PARTIAL_FLAG | COMPARE_UNORDERED_FLAG);
-      };
-    }
-
-    /**
-     * The base implementation of `_.merge` without support for multiple sources.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @param {number} srcIndex The index of `source`.
-     * @param {Function} [customizer] The function to customize merged values.
-     * @param {Object} [stack] Tracks traversed source values and their merged
-     *  counterparts.
-     */
-    function baseMerge(object, source, srcIndex, customizer, stack) {
-      if (object === source) {
-        return;
-      }
-      baseFor(source, function(srcValue, key) {
-        stack || (stack = new Stack);
-        if (isObject(srcValue)) {
-          baseMergeDeep(object, source, key, srcIndex, baseMerge, customizer, stack);
-        }
-        else {
-          var newValue = customizer
-            ? customizer(safeGet(object, key), srcValue, (key + ''), object, source, stack)
-            : undefined;
-
-          if (newValue === undefined) {
-            newValue = srcValue;
-          }
-          assignMergeValue(object, key, newValue);
-        }
-      }, keysIn);
-    }
-
-    /**
-     * A specialized version of `baseMerge` for arrays and objects which performs
-     * deep merges and tracks traversed objects enabling objects with circular
-     * references to be merged.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @param {string} key The key of the value to merge.
-     * @param {number} srcIndex The index of `source`.
-     * @param {Function} mergeFunc The function to merge values.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @param {Object} [stack] Tracks traversed source values and their merged
-     *  counterparts.
-     */
-    function baseMergeDeep(object, source, key, srcIndex, mergeFunc, customizer, stack) {
-      var objValue = safeGet(object, key),
-          srcValue = safeGet(source, key),
-          stacked = stack.get(srcValue);
-
-      if (stacked) {
-        assignMergeValue(object, key, stacked);
-        return;
-      }
-      var newValue = customizer
-        ? customizer(objValue, srcValue, (key + ''), object, source, stack)
-        : undefined;
-
-      var isCommon = newValue === undefined;
-
-      if (isCommon) {
-        var isArr = isArray(srcValue),
-            isBuff = !isArr && isBuffer(srcValue),
-            isTyped = !isArr && !isBuff && isTypedArray(srcValue);
-
-        newValue = srcValue;
-        if (isArr || isBuff || isTyped) {
-          if (isArray(objValue)) {
-            newValue = objValue;
-          }
-          else if (isArrayLikeObject(objValue)) {
-            newValue = copyArray(objValue);
-          }
-          else if (isBuff) {
-            isCommon = false;
-            newValue = cloneBuffer(srcValue, true);
-          }
-          else if (isTyped) {
-            isCommon = false;
-            newValue = cloneTypedArray(srcValue, true);
-          }
-          else {
-            newValue = [];
-          }
-        }
-        else if (isPlainObject(srcValue) || isArguments(srcValue)) {
-          newValue = objValue;
-          if (isArguments(objValue)) {
-            newValue = toPlainObject(objValue);
-          }
-          else if (!isObject(objValue) || isFunction(objValue)) {
-            newValue = initCloneObject(srcValue);
-          }
-        }
-        else {
-          isCommon = false;
-        }
-      }
-      if (isCommon) {
-        // Recursively merge objects and arrays (susceptible to call stack limits).
-        stack.set(srcValue, newValue);
-        mergeFunc(newValue, srcValue, srcIndex, customizer, stack);
-        stack['delete'](srcValue);
-      }
-      assignMergeValue(object, key, newValue);
-    }
-
-    /**
-     * The base implementation of `_.nth` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {Array} array The array to query.
-     * @param {number} n The index of the element to return.
-     * @returns {*} Returns the nth element of `array`.
-     */
-    function baseNth(array, n) {
-      var length = array.length;
-      if (!length) {
-        return;
-      }
-      n += n < 0 ? length : 0;
-      return isIndex(n, length) ? array[n] : undefined;
-    }
-
-    /**
-     * The base implementation of `_.orderBy` without param guards.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function[]|Object[]|string[]} iteratees The iteratees to sort by.
-     * @param {string[]} orders The sort orders of `iteratees`.
-     * @returns {Array} Returns the new sorted array.
-     */
-    function baseOrderBy(collection, iteratees, orders) {
-      var index = -1;
-      iteratees = arrayMap(iteratees.length ? iteratees : [identity], baseUnary(getIteratee()));
-
-      var result = baseMap(collection, function(value, key, collection) {
-        var criteria = arrayMap(iteratees, function(iteratee) {
-          return iteratee(value);
-        });
-        return { 'criteria': criteria, 'index': ++index, 'value': value };
-      });
-
-      return baseSortBy(result, function(object, other) {
-        return compareMultiple(object, other, orders);
-      });
-    }
-
-    /**
-     * The base implementation of `_.pick` without support for individual
-     * property identifiers.
-     *
-     * @private
-     * @param {Object} object The source object.
-     * @param {string[]} paths The property paths to pick.
-     * @returns {Object} Returns the new object.
-     */
-    function basePick(object, paths) {
-      return basePickBy(object, paths, function(value, path) {
-        return hasIn(object, path);
-      });
-    }
-
-    /**
-     * The base implementation of  `_.pickBy` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The source object.
-     * @param {string[]} paths The property paths to pick.
-     * @param {Function} predicate The function invoked per property.
-     * @returns {Object} Returns the new object.
-     */
-    function basePickBy(object, paths, predicate) {
-      var index = -1,
-          length = paths.length,
-          result = {};
-
-      while (++index < length) {
-        var path = paths[index],
-            value = baseGet(object, path);
-
-        if (predicate(value, path)) {
-          baseSet(result, castPath(path, object), value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * A specialized version of `baseProperty` which supports deep paths.
-     *
-     * @private
-     * @param {Array|string} path The path of the property to get.
-     * @returns {Function} Returns the new accessor function.
-     */
-    function basePropertyDeep(path) {
-      return function(object) {
-        return baseGet(object, path);
-      };
-    }
-
-    /**
-     * The base implementation of `_.pullAllBy` without support for iteratee
-     * shorthands.
-     *
-     * @private
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns `array`.
-     */
-    function basePullAll(array, values, iteratee, comparator) {
-      var indexOf = comparator ? baseIndexOfWith : baseIndexOf,
-          index = -1,
-          length = values.length,
-          seen = array;
-
-      if (array === values) {
-        values = copyArray(values);
-      }
-      if (iteratee) {
-        seen = arrayMap(array, baseUnary(iteratee));
-      }
-      while (++index < length) {
-        var fromIndex = 0,
-            value = values[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        while ((fromIndex = indexOf(seen, computed, fromIndex, comparator)) > -1) {
-          if (seen !== array) {
-            splice.call(seen, fromIndex, 1);
-          }
-          splice.call(array, fromIndex, 1);
-        }
-      }
-      return array;
-    }
-
-    /**
-     * The base implementation of `_.pullAt` without support for individual
-     * indexes or capturing the removed elements.
-     *
-     * @private
-     * @param {Array} array The array to modify.
-     * @param {number[]} indexes The indexes of elements to remove.
-     * @returns {Array} Returns `array`.
-     */
-    function basePullAt(array, indexes) {
-      var length = array ? indexes.length : 0,
-          lastIndex = length - 1;
-
-      while (length--) {
-        var index = indexes[length];
-        if (length == lastIndex || index !== previous) {
-          var previous = index;
-          if (isIndex(index)) {
-            splice.call(array, index, 1);
-          } else {
-            baseUnset(array, index);
-          }
-        }
-      }
-      return array;
-    }
-
-    /**
-     * The base implementation of `_.random` without support for returning
-     * floating-point numbers.
-     *
-     * @private
-     * @param {number} lower The lower bound.
-     * @param {number} upper The upper bound.
-     * @returns {number} Returns the random number.
-     */
-    function baseRandom(lower, upper) {
-      return lower + nativeFloor(nativeRandom() * (upper - lower + 1));
-    }
-
-    /**
-     * The base implementation of `_.range` and `_.rangeRight` which doesn't
-     * coerce arguments.
-     *
-     * @private
-     * @param {number} start The start of the range.
-     * @param {number} end The end of the range.
-     * @param {number} step The value to increment or decrement by.
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Array} Returns the range of numbers.
-     */
-    function baseRange(start, end, step, fromRight) {
-      var index = -1,
-          length = nativeMax(nativeCeil((end - start) / (step || 1)), 0),
-          result = Array(length);
-
-      while (length--) {
-        result[fromRight ? length : ++index] = start;
-        start += step;
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.repeat` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {string} string The string to repeat.
-     * @param {number} n The number of times to repeat the string.
-     * @returns {string} Returns the repeated string.
-     */
-    function baseRepeat(string, n) {
-      var result = '';
-      if (!string || n < 1 || n > MAX_SAFE_INTEGER) {
-        return result;
-      }
-      // Leverage the exponentiation by squaring algorithm for a faster repeat.
-      // See https://en.wikipedia.org/wiki/Exponentiation_by_squaring for more details.
-      do {
-        if (n % 2) {
-          result += string;
-        }
-        n = nativeFloor(n / 2);
-        if (n) {
-          string += string;
-        }
-      } while (n);
-
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.rest` which doesn't validate or coerce arguments.
-     *
-     * @private
-     * @param {Function} func The function to apply a rest parameter to.
-     * @param {number} [start=func.length-1] The start position of the rest parameter.
-     * @returns {Function} Returns the new function.
-     */
-    function baseRest(func, start) {
-      return setToString(overRest(func, start, identity), func + '');
-    }
-
-    /**
-     * The base implementation of `_.sample`.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to sample.
-     * @returns {*} Returns the random element.
-     */
-    function baseSample(collection) {
-      return arraySample(values(collection));
-    }
-
-    /**
-     * The base implementation of `_.sampleSize` without param guards.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to sample.
-     * @param {number} n The number of elements to sample.
-     * @returns {Array} Returns the random elements.
-     */
-    function baseSampleSize(collection, n) {
-      var array = values(collection);
-      return shuffleSelf(array, baseClamp(n, 0, array.length));
-    }
-
-    /**
-     * The base implementation of `_.set`.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {*} value The value to set.
-     * @param {Function} [customizer] The function to customize path creation.
-     * @returns {Object} Returns `object`.
-     */
-    function baseSet(object, path, value, customizer) {
-      if (!isObject(object)) {
-        return object;
-      }
-      path = castPath(path, object);
-
-      var index = -1,
-          length = path.length,
-          lastIndex = length - 1,
-          nested = object;
-
-      while (nested != null && ++index < length) {
-        var key = toKey(path[index]),
-            newValue = value;
-
-        if (index != lastIndex) {
-          var objValue = nested[key];
-          newValue = customizer ? customizer(objValue, key, nested) : undefined;
-          if (newValue === undefined) {
-            newValue = isObject(objValue)
-              ? objValue
-              : (isIndex(path[index + 1]) ? [] : {});
-          }
-        }
-        assignValue(nested, key, newValue);
-        nested = nested[key];
-      }
-      return object;
-    }
-
-    /**
-     * The base implementation of `setData` without support for hot loop shorting.
-     *
-     * @private
-     * @param {Function} func The function to associate metadata with.
-     * @param {*} data The metadata.
-     * @returns {Function} Returns `func`.
-     */
-    var baseSetData = !metaMap ? identity : function(func, data) {
-      metaMap.set(func, data);
-      return func;
-    };
-
-    /**
-     * The base implementation of `setToString` without support for hot loop shorting.
-     *
-     * @private
-     * @param {Function} func The function to modify.
-     * @param {Function} string The `toString` result.
-     * @returns {Function} Returns `func`.
-     */
-    var baseSetToString = !defineProperty ? identity : function(func, string) {
-      return defineProperty(func, 'toString', {
-        'configurable': true,
-        'enumerable': false,
-        'value': constant(string),
-        'writable': true
-      });
-    };
-
-    /**
-     * The base implementation of `_.shuffle`.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to shuffle.
-     * @returns {Array} Returns the new shuffled array.
-     */
-    function baseShuffle(collection) {
-      return shuffleSelf(values(collection));
-    }
-
-    /**
-     * The base implementation of `_.slice` without an iteratee call guard.
-     *
-     * @private
-     * @param {Array} array The array to slice.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns the slice of `array`.
-     */
-    function baseSlice(array, start, end) {
-      var index = -1,
-          length = array.length;
-
-      if (start < 0) {
-        start = -start > length ? 0 : (length + start);
-      }
-      end = end > length ? length : end;
-      if (end < 0) {
-        end += length;
-      }
-      length = start > end ? 0 : ((end - start) >>> 0);
-      start >>>= 0;
-
-      var result = Array(length);
-      while (++index < length) {
-        result[index] = array[index + start];
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.some` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} predicate The function invoked per iteration.
-     * @returns {boolean} Returns `true` if any element passes the predicate check,
-     *  else `false`.
-     */
-    function baseSome(collection, predicate) {
-      var result;
-
-      baseEach(collection, function(value, index, collection) {
-        result = predicate(value, index, collection);
-        return !result;
-      });
-      return !!result;
-    }
-
-    /**
-     * The base implementation of `_.sortedIndex` and `_.sortedLastIndex` which
-     * performs a binary search of `array` to determine the index at which `value`
-     * should be inserted into `array` in order to maintain its sort order.
-     *
-     * @private
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {boolean} [retHighest] Specify returning the highest qualified index.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     */
-    function baseSortedIndex(array, value, retHighest) {
-      var low = 0,
-          high = array == null ? low : array.length;
-
-      if (typeof value == 'number' && value === value && high <= HALF_MAX_ARRAY_LENGTH) {
-        while (low < high) {
-          var mid = (low + high) >>> 1,
-              computed = array[mid];
-
-          if (computed !== null && !isSymbol(computed) &&
-              (retHighest ? (computed <= value) : (computed < value))) {
-            low = mid + 1;
-          } else {
-            high = mid;
-          }
-        }
-        return high;
-      }
-      return baseSortedIndexBy(array, value, identity, retHighest);
-    }
-
-    /**
-     * The base implementation of `_.sortedIndexBy` and `_.sortedLastIndexBy`
-     * which invokes `iteratee` for `value` and each element of `array` to compute
-     * their sort ranking. The iteratee is invoked with one argument; (value).
-     *
-     * @private
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {Function} iteratee The iteratee invoked per element.
-     * @param {boolean} [retHighest] Specify returning the highest qualified index.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     */
-    function baseSortedIndexBy(array, value, iteratee, retHighest) {
-      value = iteratee(value);
-
-      var low = 0,
-          high = array == null ? 0 : array.length,
-          valIsNaN = value !== value,
-          valIsNull = value === null,
-          valIsSymbol = isSymbol(value),
-          valIsUndefined = value === undefined;
-
-      while (low < high) {
-        var mid = nativeFloor((low + high) / 2),
-            computed = iteratee(array[mid]),
-            othIsDefined = computed !== undefined,
-            othIsNull = computed === null,
-            othIsReflexive = computed === computed,
-            othIsSymbol = isSymbol(computed);
-
-        if (valIsNaN) {
-          var setLow = retHighest || othIsReflexive;
-        } else if (valIsUndefined) {
-          setLow = othIsReflexive && (retHighest || othIsDefined);
-        } else if (valIsNull) {
-          setLow = othIsReflexive && othIsDefined && (retHighest || !othIsNull);
-        } else if (valIsSymbol) {
-          setLow = othIsReflexive && othIsDefined && !othIsNull && (retHighest || !othIsSymbol);
-        } else if (othIsNull || othIsSymbol) {
-          setLow = false;
-        } else {
-          setLow = retHighest ? (computed <= value) : (computed < value);
-        }
-        if (setLow) {
-          low = mid + 1;
-        } else {
-          high = mid;
-        }
-      }
-      return nativeMin(high, MAX_ARRAY_INDEX);
-    }
-
-    /**
-     * The base implementation of `_.sortedUniq` and `_.sortedUniqBy` without
-     * support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     */
-    function baseSortedUniq(array, iteratee) {
-      var index = -1,
-          length = array.length,
-          resIndex = 0,
-          result = [];
-
-      while (++index < length) {
-        var value = array[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        if (!index || !eq(computed, seen)) {
-          var seen = computed;
-          result[resIndex++] = value === 0 ? 0 : value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.toNumber` which doesn't ensure correct
-     * conversions of binary, hexadecimal, or octal string values.
-     *
-     * @private
-     * @param {*} value The value to process.
-     * @returns {number} Returns the number.
-     */
-    function baseToNumber(value) {
-      if (typeof value == 'number') {
-        return value;
-      }
-      if (isSymbol(value)) {
-        return NAN;
-      }
-      return +value;
-    }
-
-    /**
-     * The base implementation of `_.toString` which doesn't convert nullish
-     * values to empty strings.
-     *
-     * @private
-     * @param {*} value The value to process.
-     * @returns {string} Returns the string.
-     */
-    function baseToString(value) {
-      // Exit early for strings to avoid a performance hit in some environments.
-      if (typeof value == 'string') {
-        return value;
-      }
-      if (isArray(value)) {
-        // Recursively convert values (susceptible to call stack limits).
-        return arrayMap(value, baseToString) + '';
-      }
-      if (isSymbol(value)) {
-        return symbolToString ? symbolToString.call(value) : '';
-      }
-      var result = (value + '');
-      return (result == '0' && (1 / value) == -INFINITY) ? '-0' : result;
-    }
-
-    /**
-     * The base implementation of `_.uniqBy` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     */
-    function baseUniq(array, iteratee, comparator) {
-      var index = -1,
-          includes = arrayIncludes,
-          length = array.length,
-          isCommon = true,
-          result = [],
-          seen = result;
-
-      if (comparator) {
-        isCommon = false;
-        includes = arrayIncludesWith;
-      }
-      else if (length >= LARGE_ARRAY_SIZE) {
-        var set = iteratee ? null : createSet(array);
-        if (set) {
-          return setToArray(set);
-        }
-        isCommon = false;
-        includes = cacheHas;
-        seen = new SetCache;
-      }
-      else {
-        seen = iteratee ? [] : result;
-      }
-      outer:
-      while (++index < length) {
-        var value = array[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        value = (comparator || value !== 0) ? value : 0;
-        if (isCommon && computed === computed) {
-          var seenIndex = seen.length;
-          while (seenIndex--) {
-            if (seen[seenIndex] === computed) {
-              continue outer;
-            }
-          }
-          if (iteratee) {
-            seen.push(computed);
-          }
-          result.push(value);
-        }
-        else if (!includes(seen, computed, comparator)) {
-          if (seen !== result) {
-            seen.push(computed);
-          }
-          result.push(value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.unset`.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The property path to unset.
-     * @returns {boolean} Returns `true` if the property is deleted, else `false`.
-     */
-    function baseUnset(object, path) {
-      path = castPath(path, object);
-      object = parent(object, path);
-      return object == null || delete object[toKey(last(path))];
-    }
-
-    /**
-     * The base implementation of `_.update`.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to update.
-     * @param {Function} updater The function to produce the updated value.
-     * @param {Function} [customizer] The function to customize path creation.
-     * @returns {Object} Returns `object`.
-     */
-    function baseUpdate(object, path, updater, customizer) {
-      return baseSet(object, path, updater(baseGet(object, path)), customizer);
-    }
-
-    /**
-     * The base implementation of methods like `_.dropWhile` and `_.takeWhile`
-     * without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to query.
-     * @param {Function} predicate The function invoked per iteration.
-     * @param {boolean} [isDrop] Specify dropping elements instead of taking them.
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Array} Returns the slice of `array`.
-     */
-    function baseWhile(array, predicate, isDrop, fromRight) {
-      var length = array.length,
-          index = fromRight ? length : -1;
-
-      while ((fromRight ? index-- : ++index < length) &&
-        predicate(array[index], index, array)) {}
-
-      return isDrop
-        ? baseSlice(array, (fromRight ? 0 : index), (fromRight ? index + 1 : length))
-        : baseSlice(array, (fromRight ? index + 1 : 0), (fromRight ? length : index));
-    }
-
-    /**
-     * The base implementation of `wrapperValue` which returns the result of
-     * performing a sequence of actions on the unwrapped `value`, where each
-     * successive action is supplied the return value of the previous.
-     *
-     * @private
-     * @param {*} value The unwrapped value.
-     * @param {Array} actions Actions to perform to resolve the unwrapped value.
-     * @returns {*} Returns the resolved value.
-     */
-    function baseWrapperValue(value, actions) {
-      var result = value;
-      if (result instanceof LazyWrapper) {
-        result = result.value();
-      }
-      return arrayReduce(actions, function(result, action) {
-        return action.func.apply(action.thisArg, arrayPush([result], action.args));
-      }, result);
-    }
-
-    /**
-     * The base implementation of methods like `_.xor`, without support for
-     * iteratee shorthands, that accepts an array of arrays to inspect.
-     *
-     * @private
-     * @param {Array} arrays The arrays to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of values.
-     */
-    function baseXor(arrays, iteratee, comparator) {
-      var length = arrays.length;
-      if (length < 2) {
-        return length ? baseUniq(arrays[0]) : [];
-      }
-      var index = -1,
-          result = Array(length);
-
-      while (++index < length) {
-        var array = arrays[index],
-            othIndex = -1;
-
-        while (++othIndex < length) {
-          if (othIndex != index) {
-            result[index] = baseDifference(result[index] || array, arrays[othIndex], iteratee, comparator);
-          }
-        }
-      }
-      return baseUniq(baseFlatten(result, 1), iteratee, comparator);
-    }
-
-    /**
-     * This base implementation of `_.zipObject` which assigns values using `assignFunc`.
-     *
-     * @private
-     * @param {Array} props The property identifiers.
-     * @param {Array} values The property values.
-     * @param {Function} assignFunc The function to assign values.
-     * @returns {Object} Returns the new object.
-     */
-    function baseZipObject(props, values, assignFunc) {
-      var index = -1,
-          length = props.length,
-          valsLength = values.length,
-          result = {};
-
-      while (++index < length) {
-        var value = index < valsLength ? values[index] : undefined;
-        assignFunc(result, props[index], value);
-      }
-      return result;
-    }
-
-    /**
-     * Casts `value` to an empty array if it's not an array like object.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @returns {Array|Object} Returns the cast array-like object.
-     */
-    function castArrayLikeObject(value) {
-      return isArrayLikeObject(value) ? value : [];
-    }
-
-    /**
-     * Casts `value` to `identity` if it's not a function.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @returns {Function} Returns cast function.
-     */
-    function castFunction(value) {
-      return typeof value == 'function' ? value : identity;
-    }
-
-    /**
-     * Casts `value` to a path array if it's not one.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @param {Object} [object] The object to query keys on.
-     * @returns {Array} Returns the cast property path array.
-     */
-    function castPath(value, object) {
-      if (isArray(value)) {
-        return value;
-      }
-      return isKey(value, object) ? [value] : stringToPath(toString(value));
-    }
-
-    /**
-     * A `baseRest` alias which can be replaced with `identity` by module
-     * replacement plugins.
-     *
-     * @private
-     * @type {Function}
-     * @param {Function} func The function to apply a rest parameter to.
-     * @returns {Function} Returns the new function.
-     */
-    var castRest = baseRest;
-
-    /**
-     * Casts `array` to a slice if it's needed.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {number} start The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns the cast slice.
-     */
-    function castSlice(array, start, end) {
-      var length = array.length;
-      end = end === undefined ? length : end;
-      return (!start && end >= length) ? array : baseSlice(array, start, end);
-    }
-
-    /**
-     * A simple wrapper around the global [`clearTimeout`](https://mdn.io/clearTimeout).
-     *
-     * @private
-     * @param {number|Object} id The timer id or timeout object of the timer to clear.
-     */
-    var clearTimeout = ctxClearTimeout || function(id) {
-      return root.clearTimeout(id);
-    };
-
-    /**
-     * Creates a clone of  `buffer`.
-     *
-     * @private
-     * @param {Buffer} buffer The buffer to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Buffer} Returns the cloned buffer.
-     */
-    function cloneBuffer(buffer, isDeep) {
-      if (isDeep) {
-        return buffer.slice();
-      }
-      var length = buffer.length,
-          result = allocUnsafe ? allocUnsafe(length) : new buffer.constructor(length);
-
-      buffer.copy(result);
-      return result;
-    }
-
-    /**
-     * Creates a clone of `arrayBuffer`.
-     *
-     * @private
-     * @param {ArrayBuffer} arrayBuffer The array buffer to clone.
-     * @returns {ArrayBuffer} Returns the cloned array buffer.
-     */
-    function cloneArrayBuffer(arrayBuffer) {
-      var result = new arrayBuffer.constructor(arrayBuffer.byteLength);
-      new Uint8Array(result).set(new Uint8Array(arrayBuffer));
-      return result;
-    }
-
-    /**
-     * Creates a clone of `dataView`.
-     *
-     * @private
-     * @param {Object} dataView The data view to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Object} Returns the cloned data view.
-     */
-    function cloneDataView(dataView, isDeep) {
-      var buffer = isDeep ? cloneArrayBuffer(dataView.buffer) : dataView.buffer;
-      return new dataView.constructor(buffer, dataView.byteOffset, dataView.byteLength);
-    }
-
-    /**
-     * Creates a clone of `regexp`.
-     *
-     * @private
-     * @param {Object} regexp The regexp to clone.
-     * @returns {Object} Returns the cloned regexp.
-     */
-    function cloneRegExp(regexp) {
-      var result = new regexp.constructor(regexp.source, reFlags.exec(regexp));
-      result.lastIndex = regexp.lastIndex;
-      return result;
-    }
-
-    /**
-     * Creates a clone of the `symbol` object.
-     *
-     * @private
-     * @param {Object} symbol The symbol object to clone.
-     * @returns {Object} Returns the cloned symbol object.
-     */
-    function cloneSymbol(symbol) {
-      return symbolValueOf ? Object(symbolValueOf.call(symbol)) : {};
-    }
-
-    /**
-     * Creates a clone of `typedArray`.
-     *
-     * @private
-     * @param {Object} typedArray The typed array to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Object} Returns the cloned typed array.
-     */
-    function cloneTypedArray(typedArray, isDeep) {
-      var buffer = isDeep ? cloneArrayBuffer(typedArray.buffer) : typedArray.buffer;
-      return new typedArray.constructor(buffer, typedArray.byteOffset, typedArray.length);
-    }
-
-    /**
-     * Compares values to sort them in ascending order.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {number} Returns the sort order indicator for `value`.
-     */
-    function compareAscending(value, other) {
-      if (value !== other) {
-        var valIsDefined = value !== undefined,
-            valIsNull = value === null,
-            valIsReflexive = value === value,
-            valIsSymbol = isSymbol(value);
-
-        var othIsDefined = other !== undefined,
-            othIsNull = other === null,
-            othIsReflexive = other === other,
-            othIsSymbol = isSymbol(other);
-
-        if ((!othIsNull && !othIsSymbol && !valIsSymbol && value > other) ||
-            (valIsSymbol && othIsDefined && othIsReflexive && !othIsNull && !othIsSymbol) ||
-            (valIsNull && othIsDefined && othIsReflexive) ||
-            (!valIsDefined && othIsReflexive) ||
-            !valIsReflexive) {
-          return 1;
-        }
-        if ((!valIsNull && !valIsSymbol && !othIsSymbol && value < other) ||
-            (othIsSymbol && valIsDefined && valIsReflexive && !valIsNull && !valIsSymbol) ||
-            (othIsNull && valIsDefined && valIsReflexive) ||
-            (!othIsDefined && valIsReflexive) ||
-            !othIsReflexive) {
-          return -1;
-        }
-      }
-      return 0;
-    }
-
-    /**
-     * Used by `_.orderBy` to compare multiple properties of a value to another
-     * and stable sort them.
-     *
-     * If `orders` is unspecified, all values are sorted in ascending order. Otherwise,
-     * specify an order of "desc" for descending or "asc" for ascending sort order
-     * of corresponding values.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {boolean[]|string[]} orders The order to sort by for each property.
-     * @returns {number} Returns the sort order indicator for `object`.
-     */
-    function compareMultiple(object, other, orders) {
-      var index = -1,
-          objCriteria = object.criteria,
-          othCriteria = other.criteria,
-          length = objCriteria.length,
-          ordersLength = orders.length;
-
-      while (++index < length) {
-        var result = compareAscending(objCriteria[index], othCriteria[index]);
-        if (result) {
-          if (index >= ordersLength) {
-            return result;
-          }
-          var order = orders[index];
-          return result * (order == 'desc' ? -1 : 1);
-        }
-      }
-      // Fixes an `Array#sort` bug in the JS engine embedded in Adobe applications
-      // that causes it, under certain circumstances, to provide the same value for
-      // `object` and `other`. See https://github.com/jashkenas/underscore/pull/1247
-      // for more details.
-      //
-      // This also ensures a stable sort in V8 and other engines.
-      // See https://bugs.chromium.org/p/v8/issues/detail?id=90 for more details.
-      return object.index - other.index;
-    }
-
-    /**
-     * Creates an array that is the composition of partially applied arguments,
-     * placeholders, and provided arguments into a single array of arguments.
-     *
-     * @private
-     * @param {Array} args The provided arguments.
-     * @param {Array} partials The arguments to prepend to those provided.
-     * @param {Array} holders The `partials` placeholder indexes.
-     * @params {boolean} [isCurried] Specify composing for a curried function.
-     * @returns {Array} Returns the new array of composed arguments.
-     */
-    function composeArgs(args, partials, holders, isCurried) {
-      var argsIndex = -1,
-          argsLength = args.length,
-          holdersLength = holders.length,
-          leftIndex = -1,
-          leftLength = partials.length,
-          rangeLength = nativeMax(argsLength - holdersLength, 0),
-          result = Array(leftLength + rangeLength),
-          isUncurried = !isCurried;
-
-      while (++leftIndex < leftLength) {
-        result[leftIndex] = partials[leftIndex];
-      }
-      while (++argsIndex < holdersLength) {
-        if (isUncurried || argsIndex < argsLength) {
-          result[holders[argsIndex]] = args[argsIndex];
-        }
-      }
-      while (rangeLength--) {
-        result[leftIndex++] = args[argsIndex++];
-      }
-      return result;
-    }
-
-    /**
-     * This function is like `composeArgs` except that the arguments composition
-     * is tailored for `_.partialRight`.
-     *
-     * @private
-     * @param {Array} args The provided arguments.
-     * @param {Array} partials The arguments to append to those provided.
-     * @param {Array} holders The `partials` placeholder indexes.
-     * @params {boolean} [isCurried] Specify composing for a curried function.
-     * @returns {Array} Returns the new array of composed arguments.
-     */
-    function composeArgsRight(args, partials, holders, isCurried) {
-      var argsIndex = -1,
-          argsLength = args.length,
-          holdersIndex = -1,
-          holdersLength = holders.length,
-          rightIndex = -1,
-          rightLength = partials.length,
-          rangeLength = nativeMax(argsLength - holdersLength, 0),
-          result = Array(rangeLength + rightLength),
-          isUncurried = !isCurried;
-
-      while (++argsIndex < rangeLength) {
-        result[argsIndex] = args[argsIndex];
-      }
-      var offset = argsIndex;
-      while (++rightIndex < rightLength) {
-        result[offset + rightIndex] = partials[rightIndex];
-      }
-      while (++holdersIndex < holdersLength) {
-        if (isUncurried || argsIndex < argsLength) {
-          result[offset + holders[holdersIndex]] = args[argsIndex++];
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Copies the values of `source` to `array`.
-     *
-     * @private
-     * @param {Array} source The array to copy values from.
-     * @param {Array} [array=[]] The array to copy values to.
-     * @returns {Array} Returns `array`.
-     */
-    function copyArray(source, array) {
-      var index = -1,
-          length = source.length;
-
-      array || (array = Array(length));
-      while (++index < length) {
-        array[index] = source[index];
-      }
-      return array;
-    }
-
-    /**
-     * Copies properties of `source` to `object`.
-     *
-     * @private
-     * @param {Object} source The object to copy properties from.
-     * @param {Array} props The property identifiers to copy.
-     * @param {Object} [object={}] The object to copy properties to.
-     * @param {Function} [customizer] The function to customize copied values.
-     * @returns {Object} Returns `object`.
-     */
-    function copyObject(source, props, object, customizer) {
-      var isNew = !object;
-      object || (object = {});
-
-      var index = -1,
-          length = props.length;
-
-      while (++index < length) {
-        var key = props[index];
-
-        var newValue = customizer
-          ? customizer(object[key], source[key], key, object, source)
-          : undefined;
-
-        if (newValue === undefined) {
-          newValue = source[key];
-        }
-        if (isNew) {
-          baseAssignValue(object, key, newValue);
-        } else {
-          assignValue(object, key, newValue);
-        }
-      }
-      return object;
-    }
-
-    /**
-     * Copies own symbols of `source` to `object`.
-     *
-     * @private
-     * @param {Object} source The object to copy symbols from.
-     * @param {Object} [object={}] The object to copy symbols to.
-     * @returns {Object} Returns `object`.
-     */
-    function copySymbols(source, object) {
-      return copyObject(source, getSymbols(source), object);
-    }
-
-    /**
-     * Copies own and inherited symbols of `source` to `object`.
-     *
-     * @private
-     * @param {Object} source The object to copy symbols from.
-     * @param {Object} [object={}] The object to copy symbols to.
-     * @returns {Object} Returns `object`.
-     */
-    function copySymbolsIn(source, object) {
-      return copyObject(source, getSymbolsIn(source), object);
-    }
-
-    /**
-     * Creates a function like `_.groupBy`.
-     *
-     * @private
-     * @param {Function} setter The function to set accumulator values.
-     * @param {Function} [initializer] The accumulator object initializer.
-     * @returns {Function} Returns the new aggregator function.
-     */
-    function createAggregator(setter, initializer) {
-      return function(collection, iteratee) {
-        var func = isArray(collection) ? arrayAggregator : baseAggregator,
-            accumulator = initializer ? initializer() : {};
-
-        return func(collection, setter, getIteratee(iteratee, 2), accumulator);
-      };
-    }
-
-    /**
-     * Creates a function like `_.assign`.
-     *
-     * @private
-     * @param {Function} assigner The function to assign values.
-     * @returns {Function} Returns the new assigner function.
-     */
-    function createAssigner(assigner) {
-      return baseRest(function(object, sources) {
-        var index = -1,
-            length = sources.length,
-            customizer = length > 1 ? sources[length - 1] : undefined,
-            guard = length > 2 ? sources[2] : undefined;
-
-        customizer = (assigner.length > 3 && typeof customizer == 'function')
-          ? (length--, customizer)
-          : undefined;
-
-        if (guard && isIterateeCall(sources[0], sources[1], guard)) {
-          customizer = length < 3 ? undefined : customizer;
-          length = 1;
-        }
-        object = Object(object);
-        while (++index < length) {
-          var source = sources[index];
-          if (source) {
-            assigner(object, source, index, customizer);
-          }
-        }
-        return object;
-      });
-    }
-
-    /**
-     * Creates a `baseEach` or `baseEachRight` function.
-     *
-     * @private
-     * @param {Function} eachFunc The function to iterate over a collection.
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new base function.
-     */
-    function createBaseEach(eachFunc, fromRight) {
-      return function(collection, iteratee) {
-        if (collection == null) {
-          return collection;
-        }
-        if (!isArrayLike(collection)) {
-          return eachFunc(collection, iteratee);
-        }
-        var length = collection.length,
-            index = fromRight ? length : -1,
-            iterable = Object(collection);
-
-        while ((fromRight ? index-- : ++index < length)) {
-          if (iteratee(iterable[index], index, iterable) === false) {
-            break;
-          }
-        }
-        return collection;
-      };
-    }
-
-    /**
-     * Creates a base function for methods like `_.forIn` and `_.forOwn`.
-     *
-     * @private
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new base function.
-     */
-    function createBaseFor(fromRight) {
-      return function(object, iteratee, keysFunc) {
-        var index = -1,
-            iterable = Object(object),
-            props = keysFunc(object),
-            length = props.length;
-
-        while (length--) {
-          var key = props[fromRight ? length : ++index];
-          if (iteratee(iterable[key], key, iterable) === false) {
-            break;
-          }
-        }
-        return object;
-      };
-    }
-
-    /**
-     * Creates a function that wraps `func` to invoke it with the optional `this`
-     * binding of `thisArg`.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createBind(func, bitmask, thisArg) {
-      var isBind = bitmask & WRAP_BIND_FLAG,
-          Ctor = createCtor(func);
-
-      function wrapper() {
-        var fn = (this && this !== root && this instanceof wrapper) ? Ctor : func;
-        return fn.apply(isBind ? thisArg : this, arguments);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a function like `_.lowerFirst`.
-     *
-     * @private
-     * @param {string} methodName The name of the `String` case method to use.
-     * @returns {Function} Returns the new case function.
-     */
-    function createCaseFirst(methodName) {
-      return function(string) {
-        string = toString(string);
-
-        var strSymbols = hasUnicode(string)
-          ? stringToArray(string)
-          : undefined;
-
-        var chr = strSymbols
-          ? strSymbols[0]
-          : string.charAt(0);
-
-        var trailing = strSymbols
-          ? castSlice(strSymbols, 1).join('')
-          : string.slice(1);
-
-        return chr[methodName]() + trailing;
-      };
-    }
-
-    /**
-     * Creates a function like `_.camelCase`.
-     *
-     * @private
-     * @param {Function} callback The function to combine each word.
-     * @returns {Function} Returns the new compounder function.
-     */
-    function createCompounder(callback) {
-      return function(string) {
-        return arrayReduce(words(deburr(string).replace(reApos, '')), callback, '');
-      };
-    }
-
-    /**
-     * Creates a function that produces an instance of `Ctor` regardless of
-     * whether it was invoked as part of a `new` expression or by `call` or `apply`.
-     *
-     * @private
-     * @param {Function} Ctor The constructor to wrap.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createCtor(Ctor) {
-      return function() {
-        // Use a `switch` statement to work with class constructors. See
-        // http://ecma-international.org/ecma-262/7.0/#sec-ecmascript-function-objects-call-thisargument-argumentslist
-        // for more details.
-        var args = arguments;
-        switch (args.length) {
-          case 0: return new Ctor;
-          case 1: return new Ctor(args[0]);
-          case 2: return new Ctor(args[0], args[1]);
-          case 3: return new Ctor(args[0], args[1], args[2]);
-          case 4: return new Ctor(args[0], args[1], args[2], args[3]);
-          case 5: return new Ctor(args[0], args[1], args[2], args[3], args[4]);
-          case 6: return new Ctor(args[0], args[1], args[2], args[3], args[4], args[5]);
-          case 7: return new Ctor(args[0], args[1], args[2], args[3], args[4], args[5], args[6]);
-        }
-        var thisBinding = baseCreate(Ctor.prototype),
-            result = Ctor.apply(thisBinding, args);
-
-        // Mimic the constructor's `return` behavior.
-        // See https://es5.github.io/#x13.2.2 for more details.
-        return isObject(result) ? result : thisBinding;
-      };
-    }
-
-    /**
-     * Creates a function that wraps `func` to enable currying.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {number} arity The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createCurry(func, bitmask, arity) {
-      var Ctor = createCtor(func);
-
-      function wrapper() {
-        var length = arguments.length,
-            args = Array(length),
-            index = length,
-            placeholder = getHolder(wrapper);
-
-        while (index--) {
-          args[index] = arguments[index];
-        }
-        var holders = (length < 3 && args[0] !== placeholder && args[length - 1] !== placeholder)
-          ? []
-          : replaceHolders(args, placeholder);
-
-        length -= holders.length;
-        if (length < arity) {
-          return createRecurry(
-            func, bitmask, createHybrid, wrapper.placeholder, undefined,
-            args, holders, undefined, undefined, arity - length);
-        }
-        var fn = (this && this !== root && this instanceof wrapper) ? Ctor : func;
-        return apply(fn, this, args);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a `_.find` or `_.findLast` function.
-     *
-     * @private
-     * @param {Function} findIndexFunc The function to find the collection index.
-     * @returns {Function} Returns the new find function.
-     */
-    function createFind(findIndexFunc) {
-      return function(collection, predicate, fromIndex) {
-        var iterable = Object(collection);
-        if (!isArrayLike(collection)) {
-          var iteratee = getIteratee(predicate, 3);
-          collection = keys(collection);
-          predicate = function(key) { return iteratee(iterable[key], key, iterable); };
-        }
-        var index = findIndexFunc(collection, predicate, fromIndex);
-        return index > -1 ? iterable[iteratee ? collection[index] : index] : undefined;
-      };
-    }
-
-    /**
-     * Creates a `_.flow` or `_.flowRight` function.
-     *
-     * @private
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new flow function.
-     */
-    function createFlow(fromRight) {
-      return flatRest(function(funcs) {
-        var length = funcs.length,
-            index = length,
-            prereq = LodashWrapper.prototype.thru;
-
-        if (fromRight) {
-          funcs.reverse();
-        }
-        while (index--) {
-          var func = funcs[index];
-          if (typeof func != 'function') {
-            throw new TypeError(FUNC_ERROR_TEXT);
-          }
-          if (prereq && !wrapper && getFuncName(func) == 'wrapper') {
-            var wrapper = new LodashWrapper([], true);
-          }
-        }
-        index = wrapper ? index : length;
-        while (++index < length) {
-          func = funcs[index];
-
-          var funcName = getFuncName(func),
-              data = funcName == 'wrapper' ? getData(func) : undefined;
-
-          if (data && isLaziable(data[0]) &&
-                data[1] == (WRAP_ARY_FLAG | WRAP_CURRY_FLAG | WRAP_PARTIAL_FLAG | WRAP_REARG_FLAG) &&
-                !data[4].length && data[9] == 1
-              ) {
-            wrapper = wrapper[getFuncName(data[0])].apply(wrapper, data[3]);
-          } else {
-            wrapper = (func.length == 1 && isLaziable(func))
-              ? wrapper[funcName]()
-              : wrapper.thru(func);
-          }
-        }
-        return function() {
-          var args = arguments,
-              value = args[0];
-
-          if (wrapper && args.length == 1 && isArray(value)) {
-            return wrapper.plant(value).value();
-          }
-          var index = 0,
-              result = length ? funcs[index].apply(this, args) : value;
-
-          while (++index < length) {
-            result = funcs[index].call(this, result);
-          }
-          return result;
-        };
-      });
-    }
-
-    /**
-     * Creates a function that wraps `func` to invoke it with optional `this`
-     * binding of `thisArg`, partial application, and currying.
-     *
-     * @private
-     * @param {Function|string} func The function or method name to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @param {Array} [partials] The arguments to prepend to those provided to
-     *  the new function.
-     * @param {Array} [holders] The `partials` placeholder indexes.
-     * @param {Array} [partialsRight] The arguments to append to those provided
-     *  to the new function.
-     * @param {Array} [holdersRight] The `partialsRight` placeholder indexes.
-     * @param {Array} [argPos] The argument positions of the new function.
-     * @param {number} [ary] The arity cap of `func`.
-     * @param {number} [arity] The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createHybrid(func, bitmask, thisArg, partials, holders, partialsRight, holdersRight, argPos, ary, arity) {
-      var isAry = bitmask & WRAP_ARY_FLAG,
-          isBind = bitmask & WRAP_BIND_FLAG,
-          isBindKey = bitmask & WRAP_BIND_KEY_FLAG,
-          isCurried = bitmask & (WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG),
-          isFlip = bitmask & WRAP_FLIP_FLAG,
-          Ctor = isBindKey ? undefined : createCtor(func);
-
-      function wrapper() {
-        var length = arguments.length,
-            args = Array(length),
-            index = length;
-
-        while (index--) {
-          args[index] = arguments[index];
-        }
-        if (isCurried) {
-          var placeholder = getHolder(wrapper),
-              holdersCount = countHolders(args, placeholder);
-        }
-        if (partials) {
-          args = composeArgs(args, partials, holders, isCurried);
-        }
-        if (partialsRight) {
-          args = composeArgsRight(args, partialsRight, holdersRight, isCurried);
-        }
-        length -= holdersCount;
-        if (isCurried && length < arity) {
-          var newHolders = replaceHolders(args, placeholder);
-          return createRecurry(
-            func, bitmask, createHybrid, wrapper.placeholder, thisArg,
-            args, newHolders, argPos, ary, arity - length
-          );
-        }
-        var thisBinding = isBind ? thisArg : this,
-            fn = isBindKey ? thisBinding[func] : func;
-
-        length = args.length;
-        if (argPos) {
-          args = reorder(args, argPos);
-        } else if (isFlip && length > 1) {
-          args.reverse();
-        }
-        if (isAry && ary < length) {
-          args.length = ary;
-        }
-        if (this && this !== root && this instanceof wrapper) {
-          fn = Ctor || createCtor(fn);
-        }
-        return fn.apply(thisBinding, args);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a function like `_.invertBy`.
-     *
-     * @private
-     * @param {Function} setter The function to set accumulator values.
-     * @param {Function} toIteratee The function to resolve iteratees.
-     * @returns {Function} Returns the new inverter function.
-     */
-    function createInverter(setter, toIteratee) {
-      return function(object, iteratee) {
-        return baseInverter(object, setter, toIteratee(iteratee), {});
-      };
-    }
-
-    /**
-     * Creates a function that performs a mathematical operation on two values.
-     *
-     * @private
-     * @param {Function} operator The function to perform the operation.
-     * @param {number} [defaultValue] The value used for `undefined` arguments.
-     * @returns {Function} Returns the new mathematical operation function.
-     */
-    function createMathOperation(operator, defaultValue) {
-      return function(value, other) {
-        var result;
-        if (value === undefined && other === undefined) {
-          return defaultValue;
-        }
-        if (value !== undefined) {
-          result = value;
-        }
-        if (other !== undefined) {
-          if (result === undefined) {
-            return other;
-          }
-          if (typeof value == 'string' || typeof other == 'string') {
-            value = baseToString(value);
-            other = baseToString(other);
-          } else {
-            value = baseToNumber(value);
-            other = baseToNumber(other);
-          }
-          result = operator(value, other);
-        }
-        return result;
-      };
-    }
-
-    /**
-     * Creates a function like `_.over`.
-     *
-     * @private
-     * @param {Function} arrayFunc The function to iterate over iteratees.
-     * @returns {Function} Returns the new over function.
-     */
-    function createOver(arrayFunc) {
-      return flatRest(function(iteratees) {
-        iteratees = arrayMap(iteratees, baseUnary(getIteratee()));
-        return baseRest(function(args) {
-          var thisArg = this;
-          return arrayFunc(iteratees, function(iteratee) {
-            return apply(iteratee, thisArg, args);
-          });
-        });
-      });
-    }
-
-    /**
-     * Creates the padding for `string` based on `length`. The `chars` string
-     * is truncated if the number of characters exceeds `length`.
-     *
-     * @private
-     * @param {number} length The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padding for `string`.
-     */
-    function createPadding(length, chars) {
-      chars = chars === undefined ? ' ' : baseToString(chars);
-
-      var charsLength = chars.length;
-      if (charsLength < 2) {
-        return charsLength ? baseRepeat(chars, length) : chars;
-      }
-      var result = baseRepeat(chars, nativeCeil(length / stringSize(chars)));
-      return hasUnicode(chars)
-        ? castSlice(stringToArray(result), 0, length).join('')
-        : result.slice(0, length);
-    }
-
-    /**
-     * Creates a function that wraps `func` to invoke it with the `this` binding
-     * of `thisArg` and `partials` prepended to the arguments it receives.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {*} thisArg The `this` binding of `func`.
-     * @param {Array} partials The arguments to prepend to those provided to
-     *  the new function.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createPartial(func, bitmask, thisArg, partials) {
-      var isBind = bitmask & WRAP_BIND_FLAG,
-          Ctor = createCtor(func);
-
-      function wrapper() {
-        var argsIndex = -1,
-            argsLength = arguments.length,
-            leftIndex = -1,
-            leftLength = partials.length,
-            args = Array(leftLength + argsLength),
-            fn = (this && this !== root && this instanceof wrapper) ? Ctor : func;
-
-        while (++leftIndex < leftLength) {
-          args[leftIndex] = partials[leftIndex];
-        }
-        while (argsLength--) {
-          args[leftIndex++] = arguments[++argsIndex];
-        }
-        return apply(fn, isBind ? thisArg : this, args);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a `_.range` or `_.rangeRight` function.
-     *
-     * @private
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new range function.
-     */
-    function createRange(fromRight) {
-      return function(start, end, step) {
-        if (step && typeof step != 'number' && isIterateeCall(start, end, step)) {
-          end = step = undefined;
-        }
-        // Ensure the sign of `-0` is preserved.
-        start = toFinite(start);
-        if (end === undefined) {
-          end = start;
-          start = 0;
-        } else {
-          end = toFinite(end);
-        }
-        step = step === undefined ? (start < end ? 1 : -1) : toFinite(step);
-        return baseRange(start, end, step, fromRight);
-      };
-    }
-
-    /**
-     * Creates a function that performs a relational operation on two values.
-     *
-     * @private
-     * @param {Function} operator The function to perform the operation.
-     * @returns {Function} Returns the new relational operation function.
-     */
-    function createRelationalOperation(operator) {
-      return function(value, other) {
-        if (!(typeof value == 'string' && typeof other == 'string')) {
-          value = toNumber(value);
-          other = toNumber(other);
-        }
-        return operator(value, other);
-      };
-    }
-
-    /**
-     * Creates a function that wraps `func` to continue currying.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {Function} wrapFunc The function to create the `func` wrapper.
-     * @param {*} placeholder The placeholder value.
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @param {Array} [partials] The arguments to prepend to those provided to
-     *  the new function.
-     * @param {Array} [holders] The `partials` placeholder indexes.
-     * @param {Array} [argPos] The argument positions of the new function.
-     * @param {number} [ary] The arity cap of `func`.
-     * @param {number} [arity] The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createRecurry(func, bitmask, wrapFunc, placeholder, thisArg, partials, holders, argPos, ary, arity) {
-      var isCurry = bitmask & WRAP_CURRY_FLAG,
-          newHolders = isCurry ? holders : undefined,
-          newHoldersRight = isCurry ? undefined : holders,
-          newPartials = isCurry ? partials : undefined,
-          newPartialsRight = isCurry ? undefined : partials;
-
-      bitmask |= (isCurry ? WRAP_PARTIAL_FLAG : WRAP_PARTIAL_RIGHT_FLAG);
-      bitmask &= ~(isCurry ? WRAP_PARTIAL_RIGHT_FLAG : WRAP_PARTIAL_FLAG);
-
-      if (!(bitmask & WRAP_CURRY_BOUND_FLAG)) {
-        bitmask &= ~(WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG);
-      }
-      var newData = [
-        func, bitmask, thisArg, newPartials, newHolders, newPartialsRight,
-        newHoldersRight, argPos, ary, arity
-      ];
-
-      var result = wrapFunc.apply(undefined, newData);
-      if (isLaziable(func)) {
-        setData(result, newData);
-      }
-      result.placeholder = placeholder;
-      return setWrapToString(result, func, bitmask);
-    }
-
-    /**
-     * Creates a function like `_.round`.
-     *
-     * @private
-     * @param {string} methodName The name of the `Math` method to use when rounding.
-     * @returns {Function} Returns the new round function.
-     */
-    function createRound(methodName) {
-      var func = Math[methodName];
-      return function(number, precision) {
-        number = toNumber(number);
-        precision = precision == null ? 0 : nativeMin(toInteger(precision), 292);
-        if (precision && nativeIsFinite(number)) {
-          // Shift with exponential notation to avoid floating-point issues.
-          // See [MDN](https://mdn.io/round#Examples) for more details.
-          var pair = (toString(number) + 'e').split('e'),
-              value = func(pair[0] + 'e' + (+pair[1] + precision));
-
-          pair = (toString(value) + 'e').split('e');
-          return +(pair[0] + 'e' + (+pair[1] - precision));
-        }
-        return func(number);
-      };
-    }
-
-    /**
-     * Creates a set object of `values`.
-     *
-     * @private
-     * @param {Array} values The values to add to the set.
-     * @returns {Object} Returns the new set.
-     */
-    var createSet = !(Set && (1 / setToArray(new Set([,-0]))[1]) == INFINITY) ? noop : function(values) {
-      return new Set(values);
-    };
-
-    /**
-     * Creates a `_.toPairs` or `_.toPairsIn` function.
-     *
-     * @private
-     * @param {Function} keysFunc The function to get the keys of a given object.
-     * @returns {Function} Returns the new pairs function.
-     */
-    function createToPairs(keysFunc) {
-      return function(object) {
-        var tag = getTag(object);
-        if (tag == mapTag) {
-          return mapToArray(object);
-        }
-        if (tag == setTag) {
-          return setToPairs(object);
-        }
-        return baseToPairs(object, keysFunc(object));
-      };
-    }
-
-    /**
-     * Creates a function that either curries or invokes `func` with optional
-     * `this` binding and partially applied arguments.
-     *
-     * @private
-     * @param {Function|string} func The function or method name to wrap.
-     * @param {number} bitmask The bitmask flags.
-     *    1 - `_.bind`
-     *    2 - `_.bindKey`
-     *    4 - `_.curry` or `_.curryRight` of a bound function
-     *    8 - `_.curry`
-     *   16 - `_.curryRight`
-     *   32 - `_.partial`
-     *   64 - `_.partialRight`
-     *  128 - `_.rearg`
-     *  256 - `_.ary`
-     *  512 - `_.flip`
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @param {Array} [partials] The arguments to be partially applied.
-     * @param {Array} [holders] The `partials` placeholder indexes.
-     * @param {Array} [argPos] The argument positions of the new function.
-     * @param {number} [ary] The arity cap of `func`.
-     * @param {number} [arity] The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createWrap(func, bitmask, thisArg, partials, holders, argPos, ary, arity) {
-      var isBindKey = bitmask & WRAP_BIND_KEY_FLAG;
-      if (!isBindKey && typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      var length = partials ? partials.length : 0;
-      if (!length) {
-        bitmask &= ~(WRAP_PARTIAL_FLAG | WRAP_PARTIAL_RIGHT_FLAG);
-        partials = holders = undefined;
-      }
-      ary = ary === undefined ? ary : nativeMax(toInteger(ary), 0);
-      arity = arity === undefined ? arity : toInteger(arity);
-      length -= holders ? holders.length : 0;
-
-      if (bitmask & WRAP_PARTIAL_RIGHT_FLAG) {
-        var partialsRight = partials,
-            holdersRight = holders;
-
-        partials = holders = undefined;
-      }
-      var data = isBindKey ? undefined : getData(func);
-
-      var newData = [
-        func, bitmask, thisArg, partials, holders, partialsRight, holdersRight,
-        argPos, ary, arity
-      ];
-
-      if (data) {
-        mergeData(newData, data);
-      }
-      func = newData[0];
-      bitmask = newData[1];
-      thisArg = newData[2];
-      partials = newData[3];
-      holders = newData[4];
-      arity = newData[9] = newData[9] === undefined
-        ? (isBindKey ? 0 : func.length)
-        : nativeMax(newData[9] - length, 0);
-
-      if (!arity && bitmask & (WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG)) {
-        bitmask &= ~(WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG);
-      }
-      if (!bitmask || bitmask == WRAP_BIND_FLAG) {
-        var result = createBind(func, bitmask, thisArg);
-      } else if (bitmask == WRAP_CURRY_FLAG || bitmask == WRAP_CURRY_RIGHT_FLAG) {
-        result = createCurry(func, bitmask, arity);
-      } else if ((bitmask == WRAP_PARTIAL_FLAG || bitmask == (WRAP_BIND_FLAG | WRAP_PARTIAL_FLAG)) && !holders.length) {
-        result = createPartial(func, bitmask, thisArg, partials);
-      } else {
-        result = createHybrid.apply(undefined, newData);
-      }
-      var setter = data ? baseSetData : setData;
-      return setWrapToString(setter(result, newData), func, bitmask);
-    }
-
-    /**
-     * Used by `_.defaults` to customize its `_.assignIn` use to assign properties
-     * of source objects to the destination object for all destination properties
-     * that resolve to `undefined`.
-     *
-     * @private
-     * @param {*} objValue The destination value.
-     * @param {*} srcValue The source value.
-     * @param {string} key The key of the property to assign.
-     * @param {Object} object The parent object of `objValue`.
-     * @returns {*} Returns the value to assign.
-     */
-    function customDefaultsAssignIn(objValue, srcValue, key, object) {
-      if (objValue === undefined ||
-          (eq(objValue, objectProto[key]) && !hasOwnProperty.call(object, key))) {
-        return srcValue;
-      }
-      return objValue;
-    }
-
-    /**
-     * Used by `_.defaultsDeep` to customize its `_.merge` use to merge source
-     * objects into destination objects that are passed thru.
-     *
-     * @private
-     * @param {*} objValue The destination value.
-     * @param {*} srcValue The source value.
-     * @param {string} key The key of the property to merge.
-     * @param {Object} object The parent object of `objValue`.
-     * @param {Object} source The parent object of `srcValue`.
-     * @param {Object} [stack] Tracks traversed source values and their merged
-     *  counterparts.
-     * @returns {*} Returns the value to assign.
-     */
-    function customDefaultsMerge(objValue, srcValue, key, object, source, stack) {
-      if (isObject(objValue) && isObject(srcValue)) {
-        // Recursively merge objects and arrays (susceptible to call stack limits).
-        stack.set(srcValue, objValue);
-        baseMerge(objValue, srcValue, undefined, customDefaultsMerge, stack);
-        stack['delete'](srcValue);
-      }
-      return objValue;
-    }
-
-    /**
-     * Used by `_.omit` to customize its `_.cloneDeep` use to only clone plain
-     * objects.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @param {string} key The key of the property to inspect.
-     * @returns {*} Returns the uncloned value or `undefined` to defer cloning to `_.cloneDeep`.
-     */
-    function customOmitClone(value) {
-      return isPlainObject(value) ? undefined : value;
-    }
-
-    /**
-     * A specialized version of `baseIsEqualDeep` for arrays with support for
-     * partial deep comparisons.
-     *
-     * @private
-     * @param {Array} array The array to compare.
-     * @param {Array} other The other array to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} stack Tracks traversed `array` and `other` objects.
-     * @returns {boolean} Returns `true` if the arrays are equivalent, else `false`.
-     */
-    function equalArrays(array, other, bitmask, customizer, equalFunc, stack) {
-      var isPartial = bitmask & COMPARE_PARTIAL_FLAG,
-          arrLength = array.length,
-          othLength = other.length;
-
-      if (arrLength != othLength && !(isPartial && othLength > arrLength)) {
-        return false;
-      }
-      // Assume cyclic values are equal.
-      var stacked = stack.get(array);
-      if (stacked && stack.get(other)) {
-        return stacked == other;
-      }
-      var index = -1,
-          result = true,
-          seen = (bitmask & COMPARE_UNORDERED_FLAG) ? new SetCache : undefined;
-
-      stack.set(array, other);
-      stack.set(other, array);
-
-      // Ignore non-index properties.
-      while (++index < arrLength) {
-        var arrValue = array[index],
-            othValue = other[index];
-
-        if (customizer) {
-          var compared = isPartial
-            ? customizer(othValue, arrValue, index, other, array, stack)
-            : customizer(arrValue, othValue, index, array, other, stack);
-        }
-        if (compared !== undefined) {
-          if (compared) {
-            continue;
-          }
-          result = false;
-          break;
-        }
-        // Recursively compare arrays (susceptible to call stack limits).
-        if (seen) {
-          if (!arraySome(other, function(othValue, othIndex) {
-                if (!cacheHas(seen, othIndex) &&
-                    (arrValue === othValue || equalFunc(arrValue, othValue, bitmask, customizer, stack))) {
-                  return seen.push(othIndex);
-                }
-              })) {
-            result = false;
-            break;
-          }
-        } else if (!(
-              arrValue === othValue ||
-                equalFunc(arrValue, othValue, bitmask, customizer, stack)
-            )) {
-          result = false;
-          break;
-        }
-      }
-      stack['delete'](array);
-      stack['delete'](other);
-      return result;
-    }
-
-    /**
-     * A specialized version of `baseIsEqualDeep` for comparing objects of
-     * the same `toStringTag`.
-     *
-     * **Note:** This function only supports comparing values with tags of
-     * `Boolean`, `Date`, `Error`, `Number`, `RegExp`, or `String`.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {string} tag The `toStringTag` of the objects to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} stack Tracks traversed `object` and `other` objects.
-     * @returns {boolean} Returns `true` if the objects are equivalent, else `false`.
-     */
-    function equalByTag(object, other, tag, bitmask, customizer, equalFunc, stack) {
-      switch (tag) {
-        case dataViewTag:
-          if ((object.byteLength != other.byteLength) ||
-              (object.byteOffset != other.byteOffset)) {
-            return false;
-          }
-          object = object.buffer;
-          other = other.buffer;
-
-        case arrayBufferTag:
-          if ((object.byteLength != other.byteLength) ||
-              !equalFunc(new Uint8Array(object), new Uint8Array(other))) {
-            return false;
-          }
-          return true;
-
-        case boolTag:
-        case dateTag:
-        case numberTag:
-          // Coerce booleans to `1` or `0` and dates to milliseconds.
-          // Invalid dates are coerced to `NaN`.
-          return eq(+object, +other);
-
-        case errorTag:
-          return object.name == other.name && object.message == other.message;
-
-        case regexpTag:
-        case stringTag:
-          // Coerce regexes to strings and treat strings, primitives and objects,
-          // as equal. See http://www.ecma-international.org/ecma-262/7.0/#sec-regexp.prototype.tostring
-          // for more details.
-          return object == (other + '');
-
-        case mapTag:
-          var convert = mapToArray;
-
-        case setTag:
-          var isPartial = bitmask & COMPARE_PARTIAL_FLAG;
-          convert || (convert = setToArray);
-
-          if (object.size != other.size && !isPartial) {
-            return false;
-          }
-          // Assume cyclic values are equal.
-          var stacked = stack.get(object);
-          if (stacked) {
-            return stacked == other;
-          }
-          bitmask |= COMPARE_UNORDERED_FLAG;
-
-          // Recursively compare objects (susceptible to call stack limits).
-          stack.set(object, other);
-          var result = equalArrays(convert(object), convert(other), bitmask, customizer, equalFunc, stack);
-          stack['delete'](object);
-          return result;
-
-        case symbolTag:
-          if (symbolValueOf) {
-            return symbolValueOf.call(object) == symbolValueOf.call(other);
-          }
-      }
-      return false;
-    }
-
-    /**
-     * A specialized version of `baseIsEqualDeep` for objects with support for
-     * partial deep comparisons.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} stack Tracks traversed `object` and `other` objects.
-     * @returns {boolean} Returns `true` if the objects are equivalent, else `false`.
-     */
-    function equalObjects(object, other, bitmask, customizer, equalFunc, stack) {
-      var isPartial = bitmask & COMPARE_PARTIAL_FLAG,
-          objProps = getAllKeys(object),
-          objLength = objProps.length,
-          othProps = getAllKeys(other),
-          othLength = othProps.length;
-
-      if (objLength != othLength && !isPartial) {
-        return false;
-      }
-      var index = objLength;
-      while (index--) {
-        var key = objProps[index];
-        if (!(isPartial ? key in other : hasOwnProperty.call(other, key))) {
-          return false;
-        }
-      }
-      // Assume cyclic values are equal.
-      var stacked = stack.get(object);
-      if (stacked && stack.get(other)) {
-        return stacked == other;
-      }
-      var result = true;
-      stack.set(object, other);
-      stack.set(other, object);
-
-      var skipCtor = isPartial;
-      while (++index < objLength) {
-        key = objProps[index];
-        var objValue = object[key],
-            othValue = other[key];
-
-        if (customizer) {
-          var compared = isPartial
-            ? customizer(othValue, objValue, key, other, object, stack)
-            : customizer(objValue, othValue, key, object, other, stack);
-        }
-        // Recursively compare objects (susceptible to call stack limits).
-        if (!(compared === undefined
-              ? (objValue === othValue || equalFunc(objValue, othValue, bitmask, customizer, stack))
-              : compared
-            )) {
-          result = false;
-          break;
-        }
-        skipCtor || (skipCtor = key == 'constructor');
-      }
-      if (result && !skipCtor) {
-        var objCtor = object.constructor,
-            othCtor = other.constructor;
-
-        // Non `Object` object instances with different constructors are not equal.
-        if (objCtor != othCtor &&
-            ('constructor' in object && 'constructor' in other) &&
-            !(typeof objCtor == 'function' && objCtor instanceof objCtor &&
-              typeof othCtor == 'function' && othCtor instanceof othCtor)) {
-          result = false;
-        }
-      }
-      stack['delete'](object);
-      stack['delete'](other);
-      return result;
-    }
-
-    /**
-     * A specialized version of `baseRest` which flattens the rest array.
-     *
-     * @private
-     * @param {Function} func The function to apply a rest parameter to.
-     * @returns {Function} Returns the new function.
-     */
-    function flatRest(func) {
-      return setToString(overRest(func, undefined, flatten), func + '');
-    }
-
-    /**
-     * Creates an array of own enumerable property names and symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names and symbols.
-     */
-    function getAllKeys(object) {
-      return baseGetAllKeys(object, keys, getSymbols);
-    }
-
-    /**
-     * Creates an array of own and inherited enumerable property names and
-     * symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names and symbols.
-     */
-    function getAllKeysIn(object) {
-      return baseGetAllKeys(object, keysIn, getSymbolsIn);
-    }
-
-    /**
-     * Gets metadata for `func`.
-     *
-     * @private
-     * @param {Function} func The function to query.
-     * @returns {*} Returns the metadata for `func`.
-     */
-    var getData = !metaMap ? noop : function(func) {
-      return metaMap.get(func);
-    };
-
-    /**
-     * Gets the name of `func`.
-     *
-     * @private
-     * @param {Function} func The function to query.
-     * @returns {string} Returns the function name.
-     */
-    function getFuncName(func) {
-      var result = (func.name + ''),
-          array = realNames[result],
-          length = hasOwnProperty.call(realNames, result) ? array.length : 0;
-
-      while (length--) {
-        var data = array[length],
-            otherFunc = data.func;
-        if (otherFunc == null || otherFunc == func) {
-          return data.name;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Gets the argument placeholder value for `func`.
-     *
-     * @private
-     * @param {Function} func The function to inspect.
-     * @returns {*} Returns the placeholder value.
-     */
-    function getHolder(func) {
-      var object = hasOwnProperty.call(lodash, 'placeholder') ? lodash : func;
-      return object.placeholder;
-    }
-
-    /**
-     * Gets the appropriate "iteratee" function. If `_.iteratee` is customized,
-     * this function returns the custom method, otherwise it returns `baseIteratee`.
-     * If arguments are provided, the chosen function is invoked with them and
-     * its result is returned.
-     *
-     * @private
-     * @param {*} [value] The value to convert to an iteratee.
-     * @param {number} [arity] The arity of the created iteratee.
-     * @returns {Function} Returns the chosen function or its result.
-     */
-    function getIteratee() {
-      var result = lodash.iteratee || iteratee;
-      result = result === iteratee ? baseIteratee : result;
-      return arguments.length ? result(arguments[0], arguments[1]) : result;
-    }
-
-    /**
-     * Gets the data for `map`.
-     *
-     * @private
-     * @param {Object} map The map to query.
-     * @param {string} key The reference key.
-     * @returns {*} Returns the map data.
-     */
-    function getMapData(map, key) {
-      var data = map.__data__;
-      return isKeyable(key)
-        ? data[typeof key == 'string' ? 'string' : 'hash']
-        : data.map;
-    }
-
-    /**
-     * Gets the property names, values, and compare flags of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the match data of `object`.
-     */
-    function getMatchData(object) {
-      var result = keys(object),
-          length = result.length;
-
-      while (length--) {
-        var key = result[length],
-            value = object[key];
-
-        result[length] = [key, value, isStrictComparable(value)];
-      }
-      return result;
-    }
-
-    /**
-     * Gets the native function at `key` of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {string} key The key of the method to get.
-     * @returns {*} Returns the function if it's native, else `undefined`.
-     */
-    function getNative(object, key) {
-      var value = getValue(object, key);
-      return baseIsNative(value) ? value : undefined;
-    }
-
-    /**
-     * A specialized version of `baseGetTag` which ignores `Symbol.toStringTag` values.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @returns {string} Returns the raw `toStringTag`.
-     */
-    function getRawTag(value) {
-      var isOwn = hasOwnProperty.call(value, symToStringTag),
-          tag = value[symToStringTag];
-
-      try {
-        value[symToStringTag] = undefined;
-        var unmasked = true;
-      } catch (e) {}
-
-      var result = nativeObjectToString.call(value);
-      if (unmasked) {
-        if (isOwn) {
-          value[symToStringTag] = tag;
-        } else {
-          delete value[symToStringTag];
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Creates an array of the own enumerable symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of symbols.
-     */
-    var getSymbols = !nativeGetSymbols ? stubArray : function(object) {
-      if (object == null) {
-        return [];
-      }
-      object = Object(object);
-      return arrayFilter(nativeGetSymbols(object), function(symbol) {
-        return propertyIsEnumerable.call(object, symbol);
-      });
-    };
-
-    /**
-     * Creates an array of the own and inherited enumerable symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of symbols.
-     */
-    var getSymbolsIn = !nativeGetSymbols ? stubArray : function(object) {
-      var result = [];
-      while (object) {
-        arrayPush(result, getSymbols(object));
-        object = getPrototype(object);
-      }
-      return result;
-    };
-
-    /**
-     * Gets the `toStringTag` of `value`.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @returns {string} Returns the `toStringTag`.
-     */
-    var getTag = baseGetTag;
-
-    // Fallback for data views, maps, sets, and weak maps in IE 11 and promises in Node.js < 6.
-    if ((DataView && getTag(new DataView(new ArrayBuffer(1))) != dataViewTag) ||
-        (Map && getTag(new Map) != mapTag) ||
-        (Promise && getTag(Promise.resolve()) != promiseTag) ||
-        (Set && getTag(new Set) != setTag) ||
-        (WeakMap && getTag(new WeakMap) != weakMapTag)) {
-      getTag = function(value) {
-        var result = baseGetTag(value),
-            Ctor = result == objectTag ? value.constructor : undefined,
-            ctorString = Ctor ? toSource(Ctor) : '';
-
-        if (ctorString) {
-          switch (ctorString) {
-            case dataViewCtorString: return dataViewTag;
-            case mapCtorString: return mapTag;
-            case promiseCtorString: return promiseTag;
-            case setCtorString: return setTag;
-            case weakMapCtorString: return weakMapTag;
-          }
-        }
-        return result;
-      };
-    }
-
-    /**
-     * Gets the view, applying any `transforms` to the `start` and `end` positions.
-     *
-     * @private
-     * @param {number} start The start of the view.
-     * @param {number} end The end of the view.
-     * @param {Array} transforms The transformations to apply to the view.
-     * @returns {Object} Returns an object containing the `start` and `end`
-     *  positions of the view.
-     */
-    function getView(start, end, transforms) {
-      var index = -1,
-          length = transforms.length;
-
-      while (++index < length) {
-        var data = transforms[index],
-            size = data.size;
-
-        switch (data.type) {
-          case 'drop':      start += size; break;
-          case 'dropRight': end -= size; break;
-          case 'take':      end = nativeMin(end, start + size); break;
-          case 'takeRight': start = nativeMax(start, end - size); break;
-        }
-      }
-      return { 'start': start, 'end': end };
-    }
-
-    /**
-     * Extracts wrapper details from the `source` body comment.
-     *
-     * @private
-     * @param {string} source The source to inspect.
-     * @returns {Array} Returns the wrapper details.
-     */
-    function getWrapDetails(source) {
-      var match = source.match(reWrapDetails);
-      return match ? match[1].split(reSplitDetails) : [];
-    }
-
-    /**
-     * Checks if `path` exists on `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path to check.
-     * @param {Function} hasFunc The function to check properties.
-     * @returns {boolean} Returns `true` if `path` exists, else `false`.
-     */
-    function hasPath(object, path, hasFunc) {
-      path = castPath(path, object);
-
-      var index = -1,
-          length = path.length,
-          result = false;
-
-      while (++index < length) {
-        var key = toKey(path[index]);
-        if (!(result = object != null && hasFunc(object, key))) {
-          break;
-        }
-        object = object[key];
-      }
-      if (result || ++index != length) {
-        return result;
-      }
-      length = object == null ? 0 : object.length;
-      return !!length && isLength(length) && isIndex(key, length) &&
-        (isArray(object) || isArguments(object));
-    }
-
-    /**
-     * Initializes an array clone.
-     *
-     * @private
-     * @param {Array} array The array to clone.
-     * @returns {Array} Returns the initialized clone.
-     */
-    function initCloneArray(array) {
-      var length = array.length,
-          result = new array.constructor(length);
-
-      // Add properties assigned by `RegExp#exec`.
-      if (length && typeof array[0] == 'string' && hasOwnProperty.call(array, 'index')) {
-        result.index = array.index;
-        result.input = array.input;
-      }
-      return result;
-    }
-
-    /**
-     * Initializes an object clone.
-     *
-     * @private
-     * @param {Object} object The object to clone.
-     * @returns {Object} Returns the initialized clone.
-     */
-    function initCloneObject(object) {
-      return (typeof object.constructor == 'function' && !isPrototype(object))
-        ? baseCreate(getPrototype(object))
-        : {};
-    }
-
-    /**
-     * Initializes an object clone based on its `toStringTag`.
-     *
-     * **Note:** This function only supports cloning values with tags of
-     * `Boolean`, `Date`, `Error`, `Map`, `Number`, `RegExp`, `Set`, or `String`.
-     *
-     * @private
-     * @param {Object} object The object to clone.
-     * @param {string} tag The `toStringTag` of the object to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Object} Returns the initialized clone.
-     */
-    function initCloneByTag(object, tag, isDeep) {
-      var Ctor = object.constructor;
-      switch (tag) {
-        case arrayBufferTag:
-          return cloneArrayBuffer(object);
-
-        case boolTag:
-        case dateTag:
-          return new Ctor(+object);
-
-        case dataViewTag:
-          return cloneDataView(object, isDeep);
-
-        case float32Tag: case float64Tag:
-        case int8Tag: case int16Tag: case int32Tag:
-        case uint8Tag: case uint8ClampedTag: case uint16Tag: case uint32Tag:
-          return cloneTypedArray(object, isDeep);
-
-        case mapTag:
-          return new Ctor;
-
-        case numberTag:
-        case stringTag:
-          return new Ctor(object);
-
-        case regexpTag:
-          return cloneRegExp(object);
-
-        case setTag:
-          return new Ctor;
-
-        case symbolTag:
-          return cloneSymbol(object);
-      }
-    }
-
-    /**
-     * Inserts wrapper `details` in a comment at the top of the `source` body.
-     *
-     * @private
-     * @param {string} source The source to modify.
-     * @returns {Array} details The details to insert.
-     * @returns {string} Returns the modified source.
-     */
-    function insertWrapDetails(source, details) {
-      var length = details.length;
-      if (!length) {
-        return source;
-      }
-      var lastIndex = length - 1;
-      details[lastIndex] = (length > 1 ? '& ' : '') + details[lastIndex];
-      details = details.join(length > 2 ? ', ' : ' ');
-      return source.replace(reWrapComment, '{\n/* [wrapped with ' + details + '] */\n');
-    }
-
-    /**
-     * Checks if `value` is a flattenable `arguments` object or array.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is flattenable, else `false`.
-     */
-    function isFlattenable(value) {
-      return isArray(value) || isArguments(value) ||
-        !!(spreadableSymbol && value && value[spreadableSymbol]);
-    }
-
-    /**
-     * Checks if `value` is a valid array-like index.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @param {number} [length=MAX_SAFE_INTEGER] The upper bounds of a valid index.
-     * @returns {boolean} Returns `true` if `value` is a valid index, else `false`.
-     */
-    function isIndex(value, length) {
-      var type = typeof value;
-      length = length == null ? MAX_SAFE_INTEGER : length;
-
-      return !!length &&
-        (type == 'number' ||
-          (type != 'symbol' && reIsUint.test(value))) &&
-            (value > -1 && value % 1 == 0 && value < length);
-    }
-
-    /**
-     * Checks if the given arguments are from an iteratee call.
-     *
-     * @private
-     * @param {*} value The potential iteratee value argument.
-     * @param {*} index The potential iteratee index or key argument.
-     * @param {*} object The potential iteratee object argument.
-     * @returns {boolean} Returns `true` if the arguments are from an iteratee call,
-     *  else `false`.
-     */
-    function isIterateeCall(value, index, object) {
-      if (!isObject(object)) {
-        return false;
-      }
-      var type = typeof index;
-      if (type == 'number'
-            ? (isArrayLike(object) && isIndex(index, object.length))
-            : (type == 'string' && index in object)
-          ) {
-        return eq(object[index], value);
-      }
-      return false;
-    }
-
-    /**
-     * Checks if `value` is a property name and not a property path.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @param {Object} [object] The object to query keys on.
-     * @returns {boolean} Returns `true` if `value` is a property name, else `false`.
-     */
-    function isKey(value, object) {
-      if (isArray(value)) {
-        return false;
-      }
-      var type = typeof value;
-      if (type == 'number' || type == 'symbol' || type == 'boolean' ||
-          value == null || isSymbol(value)) {
-        return true;
-      }
-      return reIsPlainProp.test(value) || !reIsDeepProp.test(value) ||
-        (object != null && value in Object(object));
-    }
-
-    /**
-     * Checks if `value` is suitable for use as unique object key.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is suitable, else `false`.
-     */
-    function isKeyable(value) {
-      var type = typeof value;
-      return (type == 'string' || type == 'number' || type == 'symbol' || type == 'boolean')
-        ? (value !== '__proto__')
-        : (value === null);
-    }
-
-    /**
-     * Checks if `func` has a lazy counterpart.
-     *
-     * @private
-     * @param {Function} func The function to check.
-     * @returns {boolean} Returns `true` if `func` has a lazy counterpart,
-     *  else `false`.
-     */
-    function isLaziable(func) {
-      var funcName = getFuncName(func),
-          other = lodash[funcName];
-
-      if (typeof other != 'function' || !(funcName in LazyWrapper.prototype)) {
-        return false;
-      }
-      if (func === other) {
-        return true;
-      }
-      var data = getData(other);
-      return !!data && func === data[0];
-    }
-
-    /**
-     * Checks if `func` has its source masked.
-     *
-     * @private
-     * @param {Function} func The function to check.
-     * @returns {boolean} Returns `true` if `func` is masked, else `false`.
-     */
-    function isMasked(func) {
-      return !!maskSrcKey && (maskSrcKey in func);
-    }
-
-    /**
-     * Checks if `func` is capable of being masked.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `func` is maskable, else `false`.
-     */
-    var isMaskable = coreJsData ? isFunction : stubFalse;
-
-    /**
-     * Checks if `value` is likely a prototype object.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a prototype, else `false`.
-     */
-    function isPrototype(value) {
-      var Ctor = value && value.constructor,
-          proto = (typeof Ctor == 'function' && Ctor.prototype) || objectProto;
-
-      return value === proto;
-    }
-
-    /**
-     * Checks if `value` is suitable for strict equality comparisons, i.e. `===`.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` if suitable for strict
-     *  equality comparisons, else `false`.
-     */
-    function isStrictComparable(value) {
-      return value === value && !isObject(value);
-    }
-
-    /**
-     * A specialized version of `matchesProperty` for source values suitable
-     * for strict equality comparisons, i.e. `===`.
-     *
-     * @private
-     * @param {string} key The key of the property to get.
-     * @param {*} srcValue The value to match.
-     * @returns {Function} Returns the new spec function.
-     */
-    function matchesStrictComparable(key, srcValue) {
-      return function(object) {
-        if (object == null) {
-          return false;
-        }
-        return object[key] === srcValue &&
-          (srcValue !== undefined || (key in Object(object)));
-      };
-    }
-
-    /**
-     * A specialized version of `_.memoize` which clears the memoized function's
-     * cache when it exceeds `MAX_MEMOIZE_SIZE`.
-     *
-     * @private
-     * @param {Function} func The function to have its output memoized.
-     * @returns {Function} Returns the new memoized function.
-     */
-    function memoizeCapped(func) {
-      var result = memoize(func, function(key) {
-        if (cache.size === MAX_MEMOIZE_SIZE) {
-          cache.clear();
-        }
-        return key;
-      });
-
-      var cache = result.cache;
-      return result;
-    }
-
-    /**
-     * Merges the function metadata of `source` into `data`.
-     *
-     * Merging metadata reduces the number of wrappers used to invoke a function.
-     * This is possible because methods like `_.bind`, `_.curry`, and `_.partial`
-     * may be applied regardless of execution order. Methods like `_.ary` and
-     * `_.rearg` modify function arguments, making the order in which they are
-     * executed important, preventing the merging of metadata. However, we make
-     * an exception for a safe combined case where curried functions have `_.ary`
-     * and or `_.rearg` applied.
-     *
-     * @private
-     * @param {Array} data The destination metadata.
-     * @param {Array} source The source metadata.
-     * @returns {Array} Returns `data`.
-     */
-    function mergeData(data, source) {
-      var bitmask = data[1],
-          srcBitmask = source[1],
-          newBitmask = bitmask | srcBitmask,
-          isCommon = newBitmask < (WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG | WRAP_ARY_FLAG);
-
-      var isCombo =
-        ((srcBitmask == WRAP_ARY_FLAG) && (bitmask == WRAP_CURRY_FLAG)) ||
-        ((srcBitmask == WRAP_ARY_FLAG) && (bitmask == WRAP_REARG_FLAG) && (data[7].length <= source[8])) ||
-        ((srcBitmask == (WRAP_ARY_FLAG | WRAP_REARG_FLAG)) && (source[7].length <= source[8]) && (bitmask == WRAP_CURRY_FLAG));
-
-      // Exit early if metadata can't be merged.
-      if (!(isCommon || isCombo)) {
-        return data;
-      }
-      // Use source `thisArg` if available.
-      if (srcBitmask & WRAP_BIND_FLAG) {
-        data[2] = source[2];
-        // Set when currying a bound function.
-        newBitmask |= bitmask & WRAP_BIND_FLAG ? 0 : WRAP_CURRY_BOUND_FLAG;
-      }
-      // Compose partial arguments.
-      var value = source[3];
-      if (value) {
-        var partials = data[3];
-        data[3] = partials ? composeArgs(partials, value, source[4]) : value;
-        data[4] = partials ? replaceHolders(data[3], PLACEHOLDER) : source[4];
-      }
-      // Compose partial right arguments.
-      value = source[5];
-      if (value) {
-        partials = data[5];
-        data[5] = partials ? composeArgsRight(partials, value, source[6]) : value;
-        data[6] = partials ? replaceHolders(data[5], PLACEHOLDER) : source[6];
-      }
-      // Use source `argPos` if available.
-      value = source[7];
-      if (value) {
-        data[7] = value;
-      }
-      // Use source `ary` if it's smaller.
-      if (srcBitmask & WRAP_ARY_FLAG) {
-        data[8] = data[8] == null ? source[8] : nativeMin(data[8], source[8]);
-      }
-      // Use source `arity` if one is not provided.
-      if (data[9] == null) {
-        data[9] = source[9];
-      }
-      // Use source `func` and merge bitmasks.
-      data[0] = source[0];
-      data[1] = newBitmask;
-
-      return data;
-    }
-
-    /**
-     * This function is like
-     * [`Object.keys`](http://ecma-international.org/ecma-262/7.0/#sec-object.keys)
-     * except that it includes inherited enumerable properties.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     */
-    function nativeKeysIn(object) {
-      var result = [];
-      if (object != null) {
-        for (var key in Object(object)) {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Converts `value` to a string using `Object.prototype.toString`.
-     *
-     * @private
-     * @param {*} value The value to convert.
-     * @returns {string} Returns the converted string.
-     */
-    function objectToString(value) {
-      return nativeObjectToString.call(value);
-    }
-
-    /**
-     * A specialized version of `baseRest` which transforms the rest array.
-     *
-     * @private
-     * @param {Function} func The function to apply a rest parameter to.
-     * @param {number} [start=func.length-1] The start position of the rest parameter.
-     * @param {Function} transform The rest array transform.
-     * @returns {Function} Returns the new function.
-     */
-    function overRest(func, start, transform) {
-      start = nativeMax(start === undefined ? (func.length - 1) : start, 0);
-      return function() {
-        var args = arguments,
-            index = -1,
-            length = nativeMax(args.length - start, 0),
-            array = Array(length);
-
-        while (++index < length) {
-          array[index] = args[start + index];
-        }
-        index = -1;
-        var otherArgs = Array(start + 1);
-        while (++index < start) {
-          otherArgs[index] = args[index];
-        }
-        otherArgs[start] = transform(array);
-        return apply(func, this, otherArgs);
-      };
-    }
-
-    /**
-     * Gets the parent value at `path` of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array} path The path to get the parent value of.
-     * @returns {*} Returns the parent value.
-     */
-    function parent(object, path) {
-      return path.length < 2 ? object : baseGet(object, baseSlice(path, 0, -1));
-    }
-
-    /**
-     * Reorder `array` according to the specified indexes where the element at
-     * the first index is assigned as the first element, the element at
-     * the second index is assigned as the second element, and so on.
-     *
-     * @private
-     * @param {Array} array The array to reorder.
-     * @param {Array} indexes The arranged array indexes.
-     * @returns {Array} Returns `array`.
-     */
-    function reorder(array, indexes) {
-      var arrLength = array.length,
-          length = nativeMin(indexes.length, arrLength),
-          oldArray = copyArray(array);
-
-      while (length--) {
-        var index = indexes[length];
-        array[length] = isIndex(index, arrLength) ? oldArray[index] : undefined;
-      }
-      return array;
-    }
-
-    /**
-     * Gets the value at `key`, unless `key` is "__proto__" or "constructor".
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {string} key The key of the property to get.
-     * @returns {*} Returns the property value.
-     */
-    function safeGet(object, key) {
-      if (key === 'constructor' && typeof object[key] === 'function') {
-        return;
-      }
-
-      if (key == '__proto__') {
-        return;
-      }
-
-      return object[key];
-    }
-
-    /**
-     * Sets metadata for `func`.
-     *
-     * **Note:** If this function becomes hot, i.e. is invoked a lot in a short
-     * period of time, it will trip its breaker and transition to an identity
-     * function to avoid garbage collection pauses in V8. See
-     * [V8 issue 2070](https://bugs.chromium.org/p/v8/issues/detail?id=2070)
-     * for more details.
-     *
-     * @private
-     * @param {Function} func The function to associate metadata with.
-     * @param {*} data The metadata.
-     * @returns {Function} Returns `func`.
-     */
-    var setData = shortOut(baseSetData);
-
-    /**
-     * A simple wrapper around the global [`setTimeout`](https://mdn.io/setTimeout).
-     *
-     * @private
-     * @param {Function} func The function to delay.
-     * @param {number} wait The number of milliseconds to delay invocation.
-     * @returns {number|Object} Returns the timer id or timeout object.
-     */
-    var setTimeout = ctxSetTimeout || function(func, wait) {
-      return root.setTimeout(func, wait);
-    };
-
-    /**
-     * Sets the `toString` method of `func` to return `string`.
-     *
-     * @private
-     * @param {Function} func The function to modify.
-     * @param {Function} string The `toString` result.
-     * @returns {Function} Returns `func`.
-     */
-    var setToString = shortOut(baseSetToString);
-
-    /**
-     * Sets the `toString` method of `wrapper` to mimic the source of `reference`
-     * with wrapper details in a comment at the top of the source body.
-     *
-     * @private
-     * @param {Function} wrapper The function to modify.
-     * @param {Function} reference The reference function.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @returns {Function} Returns `wrapper`.
-     */
-    function setWrapToString(wrapper, reference, bitmask) {
-      var source = (reference + '');
-      return setToString(wrapper, insertWrapDetails(source, updateWrapDetails(getWrapDetails(source), bitmask)));
-    }
-
-    /**
-     * Creates a function that'll short out and invoke `identity` instead
-     * of `func` when it's called `HOT_COUNT` or more times in `HOT_SPAN`
-     * milliseconds.
-     *
-     * @private
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new shortable function.
-     */
-    function shortOut(func) {
-      var count = 0,
-          lastCalled = 0;
-
-      return function() {
-        var stamp = nativeNow(),
-            remaining = HOT_SPAN - (stamp - lastCalled);
-
-        lastCalled = stamp;
-        if (remaining > 0) {
-          if (++count >= HOT_COUNT) {
-            return arguments[0];
-          }
-        } else {
-          count = 0;
-        }
-        return func.apply(undefined, arguments);
-      };
-    }
-
-    /**
-     * A specialized version of `_.shuffle` which mutates and sets the size of `array`.
-     *
-     * @private
-     * @param {Array} array The array to shuffle.
-     * @param {number} [size=array.length] The size of `array`.
-     * @returns {Array} Returns `array`.
-     */
-    function shuffleSelf(array, size) {
-      var index = -1,
-          length = array.length,
-          lastIndex = length - 1;
-
-      size = size === undefined ? length : size;
-      while (++index < size) {
-        var rand = baseRandom(index, lastIndex),
-            value = array[rand];
-
-        array[rand] = array[index];
-        array[index] = value;
-      }
-      array.length = size;
-      return array;
-    }
-
-    /**
-     * Converts `string` to a property path array.
-     *
-     * @private
-     * @param {string} string The string to convert.
-     * @returns {Array} Returns the property path array.
-     */
-    var stringToPath = memoizeCapped(function(string) {
-      var result = [];
-      if (string.charCodeAt(0) === 46 /* . */) {
-        result.push('');
-      }
-      string.replace(rePropName, function(match, number, quote, subString) {
-        result.push(quote ? subString.replace(reEscapeChar, '$1') : (number || match));
-      });
-      return result;
-    });
-
-    /**
-     * Converts `value` to a string key if it's not a string or symbol.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @returns {string|symbol} Returns the key.
-     */
-    function toKey(value) {
-      if (typeof value == 'string' || isSymbol(value)) {
-        return value;
-      }
-      var result = (value + '');
-      return (result == '0' && (1 / value) == -INFINITY) ? '-0' : result;
-    }
-
-    /**
-     * Converts `func` to its source code.
-     *
-     * @private
-     * @param {Function} func The function to convert.
-     * @returns {string} Returns the source code.
-     */
-    function toSource(func) {
-      if (func != null) {
-        try {
-          return funcToString.call(func);
-        } catch (e) {}
-        try {
-          return (func + '');
-        } catch (e) {}
-      }
-      return '';
-    }
-
-    /**
-     * Updates wrapper `details` based on `bitmask` flags.
-     *
-     * @private
-     * @returns {Array} details The details to modify.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @returns {Array} Returns `details`.
-     */
-    function updateWrapDetails(details, bitmask) {
-      arrayEach(wrapFlags, function(pair) {
-        var value = '_.' + pair[0];
-        if ((bitmask & pair[1]) && !arrayIncludes(details, value)) {
-          details.push(value);
-        }
-      });
-      return details.sort();
-    }
-
-    /**
-     * Creates a clone of `wrapper`.
-     *
-     * @private
-     * @param {Object} wrapper The wrapper to clone.
-     * @returns {Object} Returns the cloned wrapper.
-     */
-    function wrapperClone(wrapper) {
-      if (wrapper instanceof LazyWrapper) {
-        return wrapper.clone();
-      }
-      var result = new LodashWrapper(wrapper.__wrapped__, wrapper.__chain__);
-      result.__actions__ = copyArray(wrapper.__actions__);
-      result.__index__  = wrapper.__index__;
-      result.__values__ = wrapper.__values__;
-      return result;
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an array of elements split into groups the length of `size`.
-     * If `array` can't be split evenly, the final chunk will be the remaining
-     * elements.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to process.
-     * @param {number} [size=1] The length of each chunk
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the new array of chunks.
-     * @example
-     *
-     * _.chunk(['a', 'b', 'c', 'd'], 2);
-     * // => [['a', 'b'], ['c', 'd']]
-     *
-     * _.chunk(['a', 'b', 'c', 'd'], 3);
-     * // => [['a', 'b', 'c'], ['d']]
-     */
-    function chunk(array, size, guard) {
-      if ((guard ? isIterateeCall(array, size, guard) : size === undefined)) {
-        size = 1;
-      } else {
-        size = nativeMax(toInteger(size), 0);
-      }
-      var length = array == null ? 0 : array.length;
-      if (!length || size < 1) {
-        return [];
-      }
-      var index = 0,
-          resIndex = 0,
-          result = Array(nativeCeil(length / size));
-
-      while (index < length) {
-        result[resIndex++] = baseSlice(array, index, (index += size));
-      }
-      return result;
-    }
-
-    /**
-     * Creates an array with all falsey values removed. The values `false`, `null`,
-     * `0`, `""`, `undefined`, and `NaN` are falsey.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to compact.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * _.compact([0, 1, false, 2, '', 3]);
-     * // => [1, 2, 3]
-     */
-    function compact(array) {
-      var index = -1,
-          length = array == null ? 0 : array.length,
-          resIndex = 0,
-          result = [];
-
-      while (++index < length) {
-        var value = array[index];
-        if (value) {
-          result[resIndex++] = value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Creates a new array concatenating `array` with any additional arrays
-     * and/or values.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to concatenate.
-     * @param {...*} [values] The values to concatenate.
-     * @returns {Array} Returns the new concatenated array.
-     * @example
-     *
-     * var array = [1];
-     * var other = _.concat(array, 2, [3], [[4]]);
-     *
-     * console.log(other);
-     * // => [1, 2, 3, [4]]
-     *
-     * console.log(array);
-     * // => [1]
-     */
-    function concat() {
-      var length = arguments.length;
-      if (!length) {
-        return [];
-      }
-      var args = Array(length - 1),
-          array = arguments[0],
-          index = length;
-
-      while (index--) {
-        args[index - 1] = arguments[index];
-      }
-      return arrayPush(isArray(array) ? copyArray(array) : [array], baseFlatten(args, 1));
-    }
-
-    /**
-     * Creates an array of `array` values not included in the other given arrays
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons. The order and references of result values are
-     * determined by the first array.
-     *
-     * **Note:** Unlike `_.pullAll`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...Array} [values] The values to exclude.
-     * @returns {Array} Returns the new array of filtered values.
-     * @see _.without, _.xor
-     * @example
-     *
-     * _.difference([2, 1], [2, 3]);
-     * // => [1]
-     */
-    var difference = baseRest(function(array, values) {
-      return isArrayLikeObject(array)
-        ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true))
-        : [];
-    });
-
-    /**
-     * This method is like `_.difference` except that it accepts `iteratee` which
-     * is invoked for each element of `array` and `values` to generate the criterion
-     * by which they're compared. The order and references of result values are
-     * determined by the first array. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * **Note:** Unlike `_.pullAllBy`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...Array} [values] The values to exclude.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * _.differenceBy([2.1, 1.2], [2.3, 3.4], Math.floor);
-     * // => [1.2]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.differenceBy([{ 'x': 2 }, { 'x': 1 }], [{ 'x': 1 }], 'x');
-     * // => [{ 'x': 2 }]
-     */
-    var differenceBy = baseRest(function(array, values) {
-      var iteratee = last(values);
-      if (isArrayLikeObject(iteratee)) {
-        iteratee = undefined;
-      }
-      return isArrayLikeObject(array)
-        ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true), getIteratee(iteratee, 2))
-        : [];
-    });
-
-    /**
-     * This method is like `_.difference` except that it accepts `comparator`
-     * which is invoked to compare elements of `array` to `values`. The order and
-     * references of result values are determined by the first array. The comparator
-     * is invoked with two arguments: (arrVal, othVal).
-     *
-     * **Note:** Unlike `_.pullAllWith`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...Array} [values] The values to exclude.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     *
-     * _.differenceWith(objects, [{ 'x': 1, 'y': 2 }], _.isEqual);
-     * // => [{ 'x': 2, 'y': 1 }]
-     */
-    var differenceWith = baseRest(function(array, values) {
-      var comparator = last(values);
-      if (isArrayLikeObject(comparator)) {
-        comparator = undefined;
-      }
-      return isArrayLikeObject(array)
-        ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true), undefined, comparator)
-        : [];
-    });
-
-    /**
-     * Creates a slice of `array` with `n` elements dropped from the beginning.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.5.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to drop.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.drop([1, 2, 3]);
-     * // => [2, 3]
-     *
-     * _.drop([1, 2, 3], 2);
-     * // => [3]
-     *
-     * _.drop([1, 2, 3], 5);
-     * // => []
-     *
-     * _.drop([1, 2, 3], 0);
-     * // => [1, 2, 3]
-     */
-    function drop(array, n, guard) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      return baseSlice(array, n < 0 ? 0 : n, length);
-    }
-
-    /**
-     * Creates a slice of `array` with `n` elements dropped from the end.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to drop.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.dropRight([1, 2, 3]);
-     * // => [1, 2]
-     *
-     * _.dropRight([1, 2, 3], 2);
-     * // => [1]
-     *
-     * _.dropRight([1, 2, 3], 5);
-     * // => []
-     *
-     * _.dropRight([1, 2, 3], 0);
-     * // => [1, 2, 3]
-     */
-    function dropRight(array, n, guard) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      n = length - n;
-      return baseSlice(array, 0, n < 0 ? 0 : n);
-    }
-
-    /**
-     * Creates a slice of `array` excluding elements dropped from the end.
-     * Elements are dropped until `predicate` returns falsey. The predicate is
-     * invoked with three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': true },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': false }
-     * ];
-     *
-     * _.dropRightWhile(users, function(o) { return !o.active; });
-     * // => objects for ['barney']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.dropRightWhile(users, { 'user': 'pebbles', 'active': false });
-     * // => objects for ['barney', 'fred']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.dropRightWhile(users, ['active', false]);
-     * // => objects for ['barney']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.dropRightWhile(users, 'active');
-     * // => objects for ['barney', 'fred', 'pebbles']
-     */
-    function dropRightWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3), true, true)
-        : [];
-    }
-
-    /**
-     * Creates a slice of `array` excluding elements dropped from the beginning.
-     * Elements are dropped until `predicate` returns falsey. The predicate is
-     * invoked with three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': false },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': true }
-     * ];
-     *
-     * _.dropWhile(users, function(o) { return !o.active; });
-     * // => objects for ['pebbles']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.dropWhile(users, { 'user': 'barney', 'active': false });
-     * // => objects for ['fred', 'pebbles']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.dropWhile(users, ['active', false]);
-     * // => objects for ['pebbles']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.dropWhile(users, 'active');
-     * // => objects for ['barney', 'fred', 'pebbles']
-     */
-    function dropWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3), true)
-        : [];
-    }
-
-    /**
-     * Fills elements of `array` with `value` from `start` up to, but not
-     * including, `end`.
-     *
-     * **Note:** This method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.2.0
-     * @category Array
-     * @param {Array} array The array to fill.
-     * @param {*} value The value to fill `array` with.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [1, 2, 3];
-     *
-     * _.fill(array, 'a');
-     * console.log(array);
-     * // => ['a', 'a', 'a']
-     *
-     * _.fill(Array(3), 2);
-     * // => [2, 2, 2]
-     *
-     * _.fill([4, 6, 8, 10], '*', 1, 3);
-     * // => [4, '*', '*', 10]
-     */
-    function fill(array, value, start, end) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      if (start && typeof start != 'number' && isIterateeCall(array, value, start)) {
-        start = 0;
-        end = length;
-      }
-      return baseFill(array, value, start, end);
-    }
-
-    /**
-     * This method is like `_.find` except that it returns the index of the first
-     * element `predicate` returns truthy for instead of the element itself.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @returns {number} Returns the index of the found element, else `-1`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': false },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': true }
-     * ];
-     *
-     * _.findIndex(users, function(o) { return o.user == 'barney'; });
-     * // => 0
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findIndex(users, { 'user': 'fred', 'active': false });
-     * // => 1
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findIndex(users, ['active', false]);
-     * // => 0
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findIndex(users, 'active');
-     * // => 2
-     */
-    function findIndex(array, predicate, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = fromIndex == null ? 0 : toInteger(fromIndex);
-      if (index < 0) {
-        index = nativeMax(length + index, 0);
-      }
-      return baseFindIndex(array, getIteratee(predicate, 3), index);
-    }
-
-    /**
-     * This method is like `_.findIndex` except that it iterates over elements
-     * of `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=array.length-1] The index to search from.
-     * @returns {number} Returns the index of the found element, else `-1`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': true },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': false }
-     * ];
-     *
-     * _.findLastIndex(users, function(o) { return o.user == 'pebbles'; });
-     * // => 2
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findLastIndex(users, { 'user': 'barney', 'active': true });
-     * // => 0
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findLastIndex(users, ['active', false]);
-     * // => 2
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findLastIndex(users, 'active');
-     * // => 0
-     */
-    function findLastIndex(array, predicate, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = length - 1;
-      if (fromIndex !== undefined) {
-        index = toInteger(fromIndex);
-        index = fromIndex < 0
-          ? nativeMax(length + index, 0)
-          : nativeMin(index, length - 1);
-      }
-      return baseFindIndex(array, getIteratee(predicate, 3), index, true);
-    }
-
-    /**
-     * Flattens `array` a single level deep.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to flatten.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * _.flatten([1, [2, [3, [4]], 5]]);
-     * // => [1, 2, [3, [4]], 5]
-     */
-    function flatten(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseFlatten(array, 1) : [];
-    }
-
-    /**
-     * Recursively flattens `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to flatten.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * _.flattenDeep([1, [2, [3, [4]], 5]]);
-     * // => [1, 2, 3, 4, 5]
-     */
-    function flattenDeep(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseFlatten(array, INFINITY) : [];
-    }
-
-    /**
-     * Recursively flatten `array` up to `depth` times.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.4.0
-     * @category Array
-     * @param {Array} array The array to flatten.
-     * @param {number} [depth=1] The maximum recursion depth.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * var array = [1, [2, [3, [4]], 5]];
-     *
-     * _.flattenDepth(array, 1);
-     * // => [1, 2, [3, [4]], 5]
-     *
-     * _.flattenDepth(array, 2);
-     * // => [1, 2, 3, [4], 5]
-     */
-    function flattenDepth(array, depth) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      depth = depth === undefined ? 1 : toInteger(depth);
-      return baseFlatten(array, depth);
-    }
-
-    /**
-     * The inverse of `_.toPairs`; this method returns an object composed
-     * from key-value `pairs`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} pairs The key-value pairs.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * _.fromPairs([['a', 1], ['b', 2]]);
-     * // => { 'a': 1, 'b': 2 }
-     */
-    function fromPairs(pairs) {
-      var index = -1,
-          length = pairs == null ? 0 : pairs.length,
-          result = {};
-
-      while (++index < length) {
-        var pair = pairs[index];
-        result[pair[0]] = pair[1];
-      }
-      return result;
-    }
-
-    /**
-     * Gets the first element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @alias first
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {*} Returns the first element of `array`.
-     * @example
-     *
-     * _.head([1, 2, 3]);
-     * // => 1
-     *
-     * _.head([]);
-     * // => undefined
-     */
-    function head(array) {
-      return (array && array.length) ? array[0] : undefined;
-    }
-
-    /**
-     * Gets the index at which the first occurrence of `value` is found in `array`
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons. If `fromIndex` is negative, it's used as the
-     * offset from the end of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.indexOf([1, 2, 1, 2], 2);
-     * // => 1
-     *
-     * // Search from the `fromIndex`.
-     * _.indexOf([1, 2, 1, 2], 2, 2);
-     * // => 3
-     */
-    function indexOf(array, value, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = fromIndex == null ? 0 : toInteger(fromIndex);
-      if (index < 0) {
-        index = nativeMax(length + index, 0);
-      }
-      return baseIndexOf(array, value, index);
-    }
-
-    /**
-     * Gets all but the last element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.initial([1, 2, 3]);
-     * // => [1, 2]
-     */
-    function initial(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseSlice(array, 0, -1) : [];
-    }
-
-    /**
-     * Creates an array of unique values that are included in all given arrays
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons. The order and references of result values are
-     * determined by the first array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @returns {Array} Returns the new array of intersecting values.
-     * @example
-     *
-     * _.intersection([2, 1], [2, 3]);
-     * // => [2]
-     */
-    var intersection = baseRest(function(arrays) {
-      var mapped = arrayMap(arrays, castArrayLikeObject);
-      return (mapped.length && mapped[0] === arrays[0])
-        ? baseIntersection(mapped)
-        : [];
-    });
-
-    /**
-     * This method is like `_.intersection` except that it accepts `iteratee`
-     * which is invoked for each element of each `arrays` to generate the criterion
-     * by which they're compared. The order and references of result values are
-     * determined by the first array. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of intersecting values.
-     * @example
-     *
-     * _.intersectionBy([2.1, 1.2], [2.3, 3.4], Math.floor);
-     * // => [2.1]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.intersectionBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 1 }]
-     */
-    var intersectionBy = baseRest(function(arrays) {
-      var iteratee = last(arrays),
-          mapped = arrayMap(arrays, castArrayLikeObject);
-
-      if (iteratee === last(mapped)) {
-        iteratee = undefined;
-      } else {
-        mapped.pop();
-      }
-      return (mapped.length && mapped[0] === arrays[0])
-        ? baseIntersection(mapped, getIteratee(iteratee, 2))
-        : [];
-    });
-
-    /**
-     * This method is like `_.intersection` except that it accepts `comparator`
-     * which is invoked to compare elements of `arrays`. The order and references
-     * of result values are determined by the first array. The comparator is
-     * invoked with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of intersecting values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.intersectionWith(objects, others, _.isEqual);
-     * // => [{ 'x': 1, 'y': 2 }]
-     */
-    var intersectionWith = baseRest(function(arrays) {
-      var comparator = last(arrays),
-          mapped = arrayMap(arrays, castArrayLikeObject);
-
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      if (comparator) {
-        mapped.pop();
-      }
-      return (mapped.length && mapped[0] === arrays[0])
-        ? baseIntersection(mapped, undefined, comparator)
-        : [];
-    });
-
-    /**
-     * Converts all elements in `array` into a string separated by `separator`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to convert.
-     * @param {string} [separator=','] The element separator.
-     * @returns {string} Returns the joined string.
-     * @example
-     *
-     * _.join(['a', 'b', 'c'], '~');
-     * // => 'a~b~c'
-     */
-    function join(array, separator) {
-      return array == null ? '' : nativeJoin.call(array, separator);
-    }
-
-    /**
-     * Gets the last element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {*} Returns the last element of `array`.
-     * @example
-     *
-     * _.last([1, 2, 3]);
-     * // => 3
-     */
-    function last(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? array[length - 1] : undefined;
-    }
-
-    /**
-     * This method is like `_.indexOf` except that it iterates over elements of
-     * `array` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @param {number} [fromIndex=array.length-1] The index to search from.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.lastIndexOf([1, 2, 1, 2], 2);
-     * // => 3
-     *
-     * // Search from the `fromIndex`.
-     * _.lastIndexOf([1, 2, 1, 2], 2, 2);
-     * // => 1
-     */
-    function lastIndexOf(array, value, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = length;
-      if (fromIndex !== undefined) {
-        index = toInteger(fromIndex);
-        index = index < 0 ? nativeMax(length + index, 0) : nativeMin(index, length - 1);
-      }
-      return value === value
-        ? strictLastIndexOf(array, value, index)
-        : baseFindIndex(array, baseIsNaN, index, true);
-    }
-
-    /**
-     * Gets the element at index `n` of `array`. If `n` is negative, the nth
-     * element from the end is returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.11.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=0] The index of the element to return.
-     * @returns {*} Returns the nth element of `array`.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'd'];
-     *
-     * _.nth(array, 1);
-     * // => 'b'
-     *
-     * _.nth(array, -2);
-     * // => 'c';
-     */
-    function nth(array, n) {
-      return (array && array.length) ? baseNth(array, toInteger(n)) : undefined;
-    }
-
-    /**
-     * Removes all given values from `array` using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * **Note:** Unlike `_.without`, this method mutates `array`. Use `_.remove`
-     * to remove elements from an array by predicate.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {...*} [values] The values to remove.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'a', 'b', 'c'];
-     *
-     * _.pull(array, 'a', 'c');
-     * console.log(array);
-     * // => ['b', 'b']
-     */
-    var pull = baseRest(pullAll);
-
-    /**
-     * This method is like `_.pull` except that it accepts an array of values to remove.
-     *
-     * **Note:** Unlike `_.difference`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'a', 'b', 'c'];
-     *
-     * _.pullAll(array, ['a', 'c']);
-     * console.log(array);
-     * // => ['b', 'b']
-     */
-    function pullAll(array, values) {
-      return (array && array.length && values && values.length)
-        ? basePullAll(array, values)
-        : array;
-    }
-
-    /**
-     * This method is like `_.pullAll` except that it accepts `iteratee` which is
-     * invoked for each element of `array` and `values` to generate the criterion
-     * by which they're compared. The iteratee is invoked with one argument: (value).
-     *
-     * **Note:** Unlike `_.differenceBy`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [{ 'x': 1 }, { 'x': 2 }, { 'x': 3 }, { 'x': 1 }];
-     *
-     * _.pullAllBy(array, [{ 'x': 1 }, { 'x': 3 }], 'x');
-     * console.log(array);
-     * // => [{ 'x': 2 }]
-     */
-    function pullAllBy(array, values, iteratee) {
-      return (array && array.length && values && values.length)
-        ? basePullAll(array, values, getIteratee(iteratee, 2))
-        : array;
-    }
-
-    /**
-     * This method is like `_.pullAll` except that it accepts `comparator` which
-     * is invoked to compare elements of `array` to `values`. The comparator is
-     * invoked with two arguments: (arrVal, othVal).
-     *
-     * **Note:** Unlike `_.differenceWith`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.6.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [{ 'x': 1, 'y': 2 }, { 'x': 3, 'y': 4 }, { 'x': 5, 'y': 6 }];
-     *
-     * _.pullAllWith(array, [{ 'x': 3, 'y': 4 }], _.isEqual);
-     * console.log(array);
-     * // => [{ 'x': 1, 'y': 2 }, { 'x': 5, 'y': 6 }]
-     */
-    function pullAllWith(array, values, comparator) {
-      return (array && array.length && values && values.length)
-        ? basePullAll(array, values, undefined, comparator)
-        : array;
-    }
-
-    /**
-     * Removes elements from `array` corresponding to `indexes` and returns an
-     * array of removed elements.
-     *
-     * **Note:** Unlike `_.at`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {...(number|number[])} [indexes] The indexes of elements to remove.
-     * @returns {Array} Returns the new array of removed elements.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'd'];
-     * var pulled = _.pullAt(array, [1, 3]);
-     *
-     * console.log(array);
-     * // => ['a', 'c']
-     *
-     * console.log(pulled);
-     * // => ['b', 'd']
-     */
-    var pullAt = flatRest(function(array, indexes) {
-      var length = array == null ? 0 : array.length,
-          result = baseAt(array, indexes);
-
-      basePullAt(array, arrayMap(indexes, function(index) {
-        return isIndex(index, length) ? +index : index;
-      }).sort(compareAscending));
-
-      return result;
-    });
-
-    /**
-     * Removes all elements from `array` that `predicate` returns truthy for
-     * and returns an array of the removed elements. The predicate is invoked
-     * with three arguments: (value, index, array).
-     *
-     * **Note:** Unlike `_.filter`, this method mutates `array`. Use `_.pull`
-     * to pull elements from an array by value.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new array of removed elements.
-     * @example
-     *
-     * var array = [1, 2, 3, 4];
-     * var evens = _.remove(array, function(n) {
-     *   return n % 2 == 0;
-     * });
-     *
-     * console.log(array);
-     * // => [1, 3]
-     *
-     * console.log(evens);
-     * // => [2, 4]
-     */
-    function remove(array, predicate) {
-      var result = [];
-      if (!(array && array.length)) {
-        return result;
-      }
-      var index = -1,
-          indexes = [],
-          length = array.length;
-
-      predicate = getIteratee(predicate, 3);
-      while (++index < length) {
-        var value = array[index];
-        if (predicate(value, index, array)) {
-          result.push(value);
-          indexes.push(index);
-        }
-      }
-      basePullAt(array, indexes);
-      return result;
-    }
-
-    /**
-     * Reverses `array` so that the first element becomes the last, the second
-     * element becomes the second to last, and so on.
-     *
-     * **Note:** This method mutates `array` and is based on
-     * [`Array#reverse`](https://mdn.io/Array/reverse).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [1, 2, 3];
-     *
-     * _.reverse(array);
-     * // => [3, 2, 1]
-     *
-     * console.log(array);
-     * // => [3, 2, 1]
-     */
-    function reverse(array) {
-      return array == null ? array : nativeReverse.call(array);
-    }
-
-    /**
-     * Creates a slice of `array` from `start` up to, but not including, `end`.
-     *
-     * **Note:** This method is used instead of
-     * [`Array#slice`](https://mdn.io/Array/slice) to ensure dense arrays are
-     * returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to slice.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns the slice of `array`.
-     */
-    function slice(array, start, end) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      if (end && typeof end != 'number' && isIterateeCall(array, start, end)) {
-        start = 0;
-        end = length;
-      }
-      else {
-        start = start == null ? 0 : toInteger(start);
-        end = end === undefined ? length : toInteger(end);
-      }
-      return baseSlice(array, start, end);
-    }
-
-    /**
-     * Uses a binary search to determine the lowest index at which `value`
-     * should be inserted into `array` in order to maintain its sort order.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * _.sortedIndex([30, 50], 40);
-     * // => 1
-     */
-    function sortedIndex(array, value) {
-      return baseSortedIndex(array, value);
-    }
-
-    /**
-     * This method is like `_.sortedIndex` except that it accepts `iteratee`
-     * which is invoked for `value` and each element of `array` to compute their
-     * sort ranking. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * var objects = [{ 'x': 4 }, { 'x': 5 }];
-     *
-     * _.sortedIndexBy(objects, { 'x': 4 }, function(o) { return o.x; });
-     * // => 0
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.sortedIndexBy(objects, { 'x': 4 }, 'x');
-     * // => 0
-     */
-    function sortedIndexBy(array, value, iteratee) {
-      return baseSortedIndexBy(array, value, getIteratee(iteratee, 2));
-    }
-
-    /**
-     * This method is like `_.indexOf` except that it performs a binary
-     * search on a sorted `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.sortedIndexOf([4, 5, 5, 5, 6], 5);
-     * // => 1
-     */
-    function sortedIndexOf(array, value) {
-      var length = array == null ? 0 : array.length;
-      if (length) {
-        var index = baseSortedIndex(array, value);
-        if (index < length && eq(array[index], value)) {
-          return index;
-        }
-      }
-      return -1;
-    }
-
-    /**
-     * This method is like `_.sortedIndex` except that it returns the highest
-     * index at which `value` should be inserted into `array` in order to
-     * maintain its sort order.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * _.sortedLastIndex([4, 5, 5, 5, 6], 5);
-     * // => 4
-     */
-    function sortedLastIndex(array, value) {
-      return baseSortedIndex(array, value, true);
-    }
-
-    /**
-     * This method is like `_.sortedLastIndex` except that it accepts `iteratee`
-     * which is invoked for `value` and each element of `array` to compute their
-     * sort ranking. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * var objects = [{ 'x': 4 }, { 'x': 5 }];
-     *
-     * _.sortedLastIndexBy(objects, { 'x': 4 }, function(o) { return o.x; });
-     * // => 1
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.sortedLastIndexBy(objects, { 'x': 4 }, 'x');
-     * // => 1
-     */
-    function sortedLastIndexBy(array, value, iteratee) {
-      return baseSortedIndexBy(array, value, getIteratee(iteratee, 2), true);
-    }
-
-    /**
-     * This method is like `_.lastIndexOf` except that it performs a binary
-     * search on a sorted `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.sortedLastIndexOf([4, 5, 5, 5, 6], 5);
-     * // => 3
-     */
-    function sortedLastIndexOf(array, value) {
-      var length = array == null ? 0 : array.length;
-      if (length) {
-        var index = baseSortedIndex(array, value, true) - 1;
-        if (eq(array[index], value)) {
-          return index;
-        }
-      }
-      return -1;
-    }
-
-    /**
-     * This method is like `_.uniq` except that it's designed and optimized
-     * for sorted arrays.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.sortedUniq([1, 1, 2]);
-     * // => [1, 2]
-     */
-    function sortedUniq(array) {
-      return (array && array.length)
-        ? baseSortedUniq(array)
-        : [];
-    }
-
-    /**
-     * This method is like `_.uniqBy` except that it's designed and optimized
-     * for sorted arrays.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.sortedUniqBy([1.1, 1.2, 2.3, 2.4], Math.floor);
-     * // => [1.1, 2.3]
-     */
-    function sortedUniqBy(array, iteratee) {
-      return (array && array.length)
-        ? baseSortedUniq(array, getIteratee(iteratee, 2))
-        : [];
-    }
-
-    /**
-     * Gets all but the first element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.tail([1, 2, 3]);
-     * // => [2, 3]
-     */
-    function tail(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseSlice(array, 1, length) : [];
-    }
-
-    /**
-     * Creates a slice of `array` with `n` elements taken from the beginning.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to take.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.take([1, 2, 3]);
-     * // => [1]
-     *
-     * _.take([1, 2, 3], 2);
-     * // => [1, 2]
-     *
-     * _.take([1, 2, 3], 5);
-     * // => [1, 2, 3]
-     *
-     * _.take([1, 2, 3], 0);
-     * // => []
-     */
-    function take(array, n, guard) {
-      if (!(array && array.length)) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      return baseSlice(array, 0, n < 0 ? 0 : n);
-    }
-
-    /**
-     * Creates a slice of `array` with `n` elements taken from the end.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to take.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.takeRight([1, 2, 3]);
-     * // => [3]
-     *
-     * _.takeRight([1, 2, 3], 2);
-     * // => [2, 3]
-     *
-     * _.takeRight([1, 2, 3], 5);
-     * // => [1, 2, 3]
-     *
-     * _.takeRight([1, 2, 3], 0);
-     * // => []
-     */
-    function takeRight(array, n, guard) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      n = length - n;
-      return baseSlice(array, n < 0 ? 0 : n, length);
-    }
-
-    /**
-     * Creates a slice of `array` with elements taken from the end. Elements are
-     * taken until `predicate` returns falsey. The predicate is invoked with
-     * three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': true },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': false }
-     * ];
-     *
-     * _.takeRightWhile(users, function(o) { return !o.active; });
-     * // => objects for ['fred', 'pebbles']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.takeRightWhile(users, { 'user': 'pebbles', 'active': false });
-     * // => objects for ['pebbles']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.takeRightWhile(users, ['active', false]);
-     * // => objects for ['fred', 'pebbles']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.takeRightWhile(users, 'active');
-     * // => []
-     */
-    function takeRightWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3), false, true)
-        : [];
-    }
-
-    /**
-     * Creates a slice of `array` with elements taken from the beginning. Elements
-     * are taken until `predicate` returns falsey. The predicate is invoked with
-     * three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': false },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': true }
-     * ];
-     *
-     * _.takeWhile(users, function(o) { return !o.active; });
-     * // => objects for ['barney', 'fred']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.takeWhile(users, { 'user': 'barney', 'active': false });
-     * // => objects for ['barney']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.takeWhile(users, ['active', false]);
-     * // => objects for ['barney', 'fred']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.takeWhile(users, 'active');
-     * // => []
-     */
-    function takeWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3))
-        : [];
-    }
-
-    /**
-     * Creates an array of unique values, in order, from all given arrays using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @returns {Array} Returns the new array of combined values.
-     * @example
-     *
-     * _.union([2], [1, 2]);
-     * // => [2, 1]
-     */
-    var union = baseRest(function(arrays) {
-      return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true));
-    });
-
-    /**
-     * This method is like `_.union` except that it accepts `iteratee` which is
-     * invoked for each element of each `arrays` to generate the criterion by
-     * which uniqueness is computed. Result values are chosen from the first
-     * array in which the value occurs. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of combined values.
-     * @example
-     *
-     * _.unionBy([2.1], [1.2, 2.3], Math.floor);
-     * // => [2.1, 1.2]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.unionBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 1 }, { 'x': 2 }]
-     */
-    var unionBy = baseRest(function(arrays) {
-      var iteratee = last(arrays);
-      if (isArrayLikeObject(iteratee)) {
-        iteratee = undefined;
-      }
-      return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true), getIteratee(iteratee, 2));
-    });
-
-    /**
-     * This method is like `_.union` except that it accepts `comparator` which
-     * is invoked to compare elements of `arrays`. Result values are chosen from
-     * the first array in which the value occurs. The comparator is invoked
-     * with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of combined values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.unionWith(objects, others, _.isEqual);
-     * // => [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }, { 'x': 1, 'y': 1 }]
-     */
-    var unionWith = baseRest(function(arrays) {
-      var comparator = last(arrays);
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true), undefined, comparator);
-    });
-
-    /**
-     * Creates a duplicate-free version of an array, using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons, in which only the first occurrence of each element
-     * is kept. The order of result values is determined by the order they occur
-     * in the array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.uniq([2, 1, 2]);
-     * // => [2, 1]
-     */
-    function uniq(array) {
-      return (array && array.length) ? baseUniq(array) : [];
-    }
-
-    /**
-     * This method is like `_.uniq` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the criterion by which
-     * uniqueness is computed. The order of result values is determined by the
-     * order they occur in the array. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.uniqBy([2.1, 1.2, 2.3], Math.floor);
-     * // => [2.1, 1.2]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.uniqBy([{ 'x': 1 }, { 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 1 }, { 'x': 2 }]
-     */
-    function uniqBy(array, iteratee) {
-      return (array && array.length) ? baseUniq(array, getIteratee(iteratee, 2)) : [];
-    }
-
-    /**
-     * This method is like `_.uniq` except that it accepts `comparator` which
-     * is invoked to compare elements of `array`. The order of result values is
-     * determined by the order they occur in the array.The comparator is invoked
-     * with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.uniqWith(objects, _.isEqual);
-     * // => [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }]
-     */
-    function uniqWith(array, comparator) {
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      return (array && array.length) ? baseUniq(array, undefined, comparator) : [];
-    }
-
-    /**
-     * This method is like `_.zip` except that it accepts an array of grouped
-     * elements and creates an array regrouping the elements to their pre-zip
-     * configuration.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.2.0
-     * @category Array
-     * @param {Array} array The array of grouped elements to process.
-     * @returns {Array} Returns the new array of regrouped elements.
-     * @example
-     *
-     * var zipped = _.zip(['a', 'b'], [1, 2], [true, false]);
-     * // => [['a', 1, true], ['b', 2, false]]
-     *
-     * _.unzip(zipped);
-     * // => [['a', 'b'], [1, 2], [true, false]]
-     */
-    function unzip(array) {
-      if (!(array && array.length)) {
-        return [];
-      }
-      var length = 0;
-      array = arrayFilter(array, function(group) {
-        if (isArrayLikeObject(group)) {
-          length = nativeMax(group.length, length);
-          return true;
-        }
-      });
-      return baseTimes(length, function(index) {
-        return arrayMap(array, baseProperty(index));
-      });
-    }
-
-    /**
-     * This method is like `_.unzip` except that it accepts `iteratee` to specify
-     * how regrouped values should be combined. The iteratee is invoked with the
-     * elements of each group: (...group).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.8.0
-     * @category Array
-     * @param {Array} array The array of grouped elements to process.
-     * @param {Function} [iteratee=_.identity] The function to combine
-     *  regrouped values.
-     * @returns {Array} Returns the new array of regrouped elements.
-     * @example
-     *
-     * var zipped = _.zip([1, 2], [10, 20], [100, 200]);
-     * // => [[1, 10, 100], [2, 20, 200]]
-     *
-     * _.unzipWith(zipped, _.add);
-     * // => [3, 30, 300]
-     */
-    function unzipWith(array, iteratee) {
-      if (!(array && array.length)) {
-        return [];
-      }
-      var result = unzip(array);
-      if (iteratee == null) {
-        return result;
-      }
-      return arrayMap(result, function(group) {
-        return apply(iteratee, undefined, group);
-      });
-    }
-
-    /**
-     * Creates an array excluding all given values using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * **Note:** Unlike `_.pull`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...*} [values] The values to exclude.
-     * @returns {Array} Returns the new array of filtered values.
-     * @see _.difference, _.xor
-     * @example
-     *
-     * _.without([2, 1, 2, 3], 1, 2);
-     * // => [3]
-     */
-    var without = baseRest(function(array, values) {
-      return isArrayLikeObject(array)
-        ? baseDifference(array, values)
-        : [];
-    });
-
-    /**
-     * Creates an array of unique values that is the
-     * [symmetric difference](https://en.wikipedia.org/wiki/Symmetric_difference)
-     * of the given arrays. The order of result values is determined by the order
-     * they occur in the arrays.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @returns {Array} Returns the new array of filtered values.
-     * @see _.difference, _.without
-     * @example
-     *
-     * _.xor([2, 1], [2, 3]);
-     * // => [1, 3]
-     */
-    var xor = baseRest(function(arrays) {
-      return baseXor(arrayFilter(arrays, isArrayLikeObject));
-    });
-
-    /**
-     * This method is like `_.xor` except that it accepts `iteratee` which is
-     * invoked for each element of each `arrays` to generate the criterion by
-     * which by which they're compared. The order of result values is determined
-     * by the order they occur in the arrays. The iteratee is invoked with one
-     * argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * _.xorBy([2.1, 1.2], [2.3, 3.4], Math.floor);
-     * // => [1.2, 3.4]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.xorBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 2 }]
-     */
-    var xorBy = baseRest(function(arrays) {
-      var iteratee = last(arrays);
-      if (isArrayLikeObject(iteratee)) {
-        iteratee = undefined;
-      }
-      return baseXor(arrayFilter(arrays, isArrayLikeObject), getIteratee(iteratee, 2));
-    });
-
-    /**
-     * This method is like `_.xor` except that it accepts `comparator` which is
-     * invoked to compare elements of `arrays`. The order of result values is
-     * determined by the order they occur in the arrays. The comparator is invoked
-     * with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.xorWith(objects, others, _.isEqual);
-     * // => [{ 'x': 2, 'y': 1 }, { 'x': 1, 'y': 1 }]
-     */
-    var xorWith = baseRest(function(arrays) {
-      var comparator = last(arrays);
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      return baseXor(arrayFilter(arrays, isArrayLikeObject), undefined, comparator);
-    });
-
-    /**
-     * Creates an array of grouped elements, the first of which contains the
-     * first elements of the given arrays, the second of which contains the
-     * second elements of the given arrays, and so on.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to process.
-     * @returns {Array} Returns the new array of grouped elements.
-     * @example
-     *
-     * _.zip(['a', 'b'], [1, 2], [true, false]);
-     * // => [['a', 1, true], ['b', 2, false]]
-     */
-    var zip = baseRest(unzip);
-
-    /**
-     * This method is like `_.fromPairs` except that it accepts two arrays,
-     * one of property identifiers and one of corresponding values.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.4.0
-     * @category Array
-     * @param {Array} [props=[]] The property identifiers.
-     * @param {Array} [values=[]] The property values.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * _.zipObject(['a', 'b'], [1, 2]);
-     * // => { 'a': 1, 'b': 2 }
-     */
-    function zipObject(props, values) {
-      return baseZipObject(props || [], values || [], assignValue);
-    }
-
-    /**
-     * This method is like `_.zipObject` except that it supports property paths.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.1.0
-     * @category Array
-     * @param {Array} [props=[]] The property identifiers.
-     * @param {Array} [values=[]] The property values.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * _.zipObjectDeep(['a.b[0].c', 'a.b[1].d'], [1, 2]);
-     * // => { 'a': { 'b': [{ 'c': 1 }, { 'd': 2 }] } }
-     */
-    function zipObjectDeep(props, values) {
-      return baseZipObject(props || [], values || [], baseSet);
-    }
-
-    /**
-     * This method is like `_.zip` except that it accepts `iteratee` to specify
-     * how grouped values should be combined. The iteratee is invoked with the
-     * elements of each group: (...group).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.8.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to process.
-     * @param {Function} [iteratee=_.identity] The function to combine
-     *  grouped values.
-     * @returns {Array} Returns the new array of grouped elements.
-     * @example
-     *
-     * _.zipWith([1, 2], [10, 20], [100, 200], function(a, b, c) {
-     *   return a + b + c;
-     * });
-     * // => [111, 222]
-     */
-    var zipWith = baseRest(function(arrays) {
-      var length = arrays.length,
-          iteratee = length > 1 ? arrays[length - 1] : undefined;
-
-      iteratee = typeof iteratee == 'function' ? (arrays.pop(), iteratee) : undefined;
-      return unzipWith(arrays, iteratee);
-    });
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a `lodash` wrapper instance that wraps `value` with explicit method
-     * chain sequences enabled. The result of such sequences must be unwrapped
-     * with `_#value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.3.0
-     * @category Seq
-     * @param {*} value The value to wrap.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'age': 36 },
-     *   { 'user': 'fred',    'age': 40 },
-     *   { 'user': 'pebbles', 'age': 1 }
-     * ];
-     *
-     * var youngest = _
-     *   .chain(users)
-     *   .sortBy('age')
-     *   .map(function(o) {
-     *     return o.user + ' is ' + o.age;
-     *   })
-     *   .head()
-     *   .value();
-     * // => 'pebbles is 1'
-     */
-    function chain(value) {
-      var result = lodash(value);
-      result.__chain__ = true;
-      return result;
-    }
-
-    /**
-     * This method invokes `interceptor` and returns `value`. The interceptor
-     * is invoked with one argument; (value). The purpose of this method is to
-     * "tap into" a method chain sequence in order to modify intermediate results.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Seq
-     * @param {*} value The value to provide to `interceptor`.
-     * @param {Function} interceptor The function to invoke.
-     * @returns {*} Returns `value`.
-     * @example
-     *
-     * _([1, 2, 3])
-     *  .tap(function(array) {
-     *    // Mutate input array.
-     *    array.pop();
-     *  })
-     *  .reverse()
-     *  .value();
-     * // => [2, 1]
-     */
-    function tap(value, interceptor) {
-      interceptor(value);
-      return value;
-    }
-
-    /**
-     * This method is like `_.tap` except that it returns the result of `interceptor`.
-     * The purpose of this method is to "pass thru" values replacing intermediate
-     * results in a method chain sequence.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Seq
-     * @param {*} value The value to provide to `interceptor`.
-     * @param {Function} interceptor The function to invoke.
-     * @returns {*} Returns the result of `interceptor`.
-     * @example
-     *
-     * _('  abc  ')
-     *  .chain()
-     *  .trim()
-     *  .thru(function(value) {
-     *    return [value];
-     *  })
-     *  .value();
-     * // => ['abc']
-     */
-    function thru(value, interceptor) {
-      return interceptor(value);
-    }
-
-    /**
-     * This method is the wrapper version of `_.at`.
-     *
-     * @name at
-     * @memberOf _
-     * @since 1.0.0
-     * @category Seq
-     * @param {...(string|string[])} [paths] The property paths to pick.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }, 4] };
-     *
-     * _(object).at(['a[0].b.c', 'a[1]']).value();
-     * // => [3, 4]
-     */
-    var wrapperAt = flatRest(function(paths) {
-      var length = paths.length,
-          start = length ? paths[0] : 0,
-          value = this.__wrapped__,
-          interceptor = function(object) { return baseAt(object, paths); };
-
-      if (length > 1 || this.__actions__.length ||
-          !(value instanceof LazyWrapper) || !isIndex(start)) {
-        return this.thru(interceptor);
-      }
-      value = value.slice(start, +start + (length ? 1 : 0));
-      value.__actions__.push({
-        'func': thru,
-        'args': [interceptor],
-        'thisArg': undefined
-      });
-      return new LodashWrapper(value, this.__chain__).thru(function(array) {
-        if (length && !array.length) {
-          array.push(undefined);
-        }
-        return array;
-      });
-    });
-
-    /**
-     * Creates a `lodash` wrapper instance with explicit method chain sequences enabled.
-     *
-     * @name chain
-     * @memberOf _
-     * @since 0.1.0
-     * @category Seq
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36 },
-     *   { 'user': 'fred',   'age': 40 }
-     * ];
-     *
-     * // A sequence without explicit chaining.
-     * _(users).head();
-     * // => { 'user': 'barney', 'age': 36 }
-     *
-     * // A sequence with explicit chaining.
-     * _(users)
-     *   .chain()
-     *   .head()
-     *   .pick('user')
-     *   .value();
-     * // => { 'user': 'barney' }
-     */
-    function wrapperChain() {
-      return chain(this);
-    }
-
-    /**
-     * Executes the chain sequence and returns the wrapped result.
-     *
-     * @name commit
-     * @memberOf _
-     * @since 3.2.0
-     * @category Seq
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var array = [1, 2];
-     * var wrapped = _(array).push(3);
-     *
-     * console.log(array);
-     * // => [1, 2]
-     *
-     * wrapped = wrapped.commit();
-     * console.log(array);
-     * // => [1, 2, 3]
-     *
-     * wrapped.last();
-     * // => 3
-     *
-     * console.log(array);
-     * // => [1, 2, 3]
-     */
-    function wrapperCommit() {
-      return new LodashWrapper(this.value(), this.__chain__);
-    }
-
-    /**
-     * Gets the next value on a wrapped object following the
-     * [iterator protocol](https://mdn.io/iteration_protocols#iterator).
-     *
-     * @name next
-     * @memberOf _
-     * @since 4.0.0
-     * @category Seq
-     * @returns {Object} Returns the next iterator value.
-     * @example
-     *
-     * var wrapped = _([1, 2]);
-     *
-     * wrapped.next();
-     * // => { 'done': false, 'value': 1 }
-     *
-     * wrapped.next();
-     * // => { 'done': false, 'value': 2 }
-     *
-     * wrapped.next();
-     * // => { 'done': true, 'value': undefined }
-     */
-    function wrapperNext() {
-      if (this.__values__ === undefined) {
-        this.__values__ = toArray(this.value());
-      }
-      var done = this.__index__ >= this.__values__.length,
-          value = done ? undefined : this.__values__[this.__index__++];
-
-      return { 'done': done, 'value': value };
-    }
-
-    /**
-     * Enables the wrapper to be iterable.
-     *
-     * @name Symbol.iterator
-     * @memberOf _
-     * @since 4.0.0
-     * @category Seq
-     * @returns {Object} Returns the wrapper object.
-     * @example
-     *
-     * var wrapped = _([1, 2]);
-     *
-     * wrapped[Symbol.iterator]() === wrapped;
-     * // => true
-     *
-     * Array.from(wrapped);
-     * // => [1, 2]
-     */
-    function wrapperToIterator() {
-      return this;
-    }
-
-    /**
-     * Creates a clone of the chain sequence planting `value` as the wrapped value.
-     *
-     * @name plant
-     * @memberOf _
-     * @since 3.2.0
-     * @category Seq
-     * @param {*} value The value to plant.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var wrapped = _([1, 2]).map(square);
-     * var other = wrapped.plant([3, 4]);
-     *
-     * other.value();
-     * // => [9, 16]
-     *
-     * wrapped.value();
-     * // => [1, 4]
-     */
-    function wrapperPlant(value) {
-      var result,
-          parent = this;
-
-      while (parent instanceof baseLodash) {
-        var clone = wrapperClone(parent);
-        clone.__index__ = 0;
-        clone.__values__ = undefined;
-        if (result) {
-          previous.__wrapped__ = clone;
-        } else {
-          result = clone;
-        }
-        var previous = clone;
-        parent = parent.__wrapped__;
-      }
-      previous.__wrapped__ = value;
-      return result;
-    }
-
-    /**
-     * This method is the wrapper version of `_.reverse`.
-     *
-     * **Note:** This method mutates the wrapped array.
-     *
-     * @name reverse
-     * @memberOf _
-     * @since 0.1.0
-     * @category Seq
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var array = [1, 2, 3];
-     *
-     * _(array).reverse().value()
-     * // => [3, 2, 1]
-     *
-     * console.log(array);
-     * // => [3, 2, 1]
-     */
-    function wrapperReverse() {
-      var value = this.__wrapped__;
-      if (value instanceof LazyWrapper) {
-        var wrapped = value;
-        if (this.__actions__.length) {
-          wrapped = new LazyWrapper(this);
-        }
-        wrapped = wrapped.reverse();
-        wrapped.__actions__.push({
-          'func': thru,
-          'args': [reverse],
-          'thisArg': undefined
-        });
-        return new LodashWrapper(wrapped, this.__chain__);
-      }
-      return this.thru(reverse);
-    }
-
-    /**
-     * Executes the chain sequence to resolve the unwrapped value.
-     *
-     * @name value
-     * @memberOf _
-     * @since 0.1.0
-     * @alias toJSON, valueOf
-     * @category Seq
-     * @returns {*} Returns the resolved unwrapped value.
-     * @example
-     *
-     * _([1, 2, 3]).value();
-     * // => [1, 2, 3]
-     */
-    function wrapperValue() {
-      return baseWrapperValue(this.__wrapped__, this.__actions__);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an object composed of keys generated from the results of running
-     * each element of `collection` thru `iteratee`. The corresponding value of
-     * each key is the number of times the key was returned by `iteratee`. The
-     * iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.5.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee to transform keys.
-     * @returns {Object} Returns the composed aggregate object.
-     * @example
-     *
-     * _.countBy([6.1, 4.2, 6.3], Math.floor);
-     * // => { '4': 1, '6': 2 }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.countBy(['one', 'two', 'three'], 'length');
-     * // => { '3': 2, '5': 1 }
-     */
-    var countBy = createAggregator(function(result, value, key) {
-      if (hasOwnProperty.call(result, key)) {
-        ++result[key];
-      } else {
-        baseAssignValue(result, key, 1);
-      }
-    });
-
-    /**
-     * Checks if `predicate` returns truthy for **all** elements of `collection`.
-     * Iteration is stopped once `predicate` returns falsey. The predicate is
-     * invoked with three arguments: (value, index|key, collection).
-     *
-     * **Note:** This method returns `true` for
-     * [empty collections](https://en.wikipedia.org/wiki/Empty_set) because
-     * [everything is true](https://en.wikipedia.org/wiki/Vacuous_truth) of
-     * elements of empty collections.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {boolean} Returns `true` if all elements pass the predicate check,
-     *  else `false`.
-     * @example
-     *
-     * _.every([true, 1, null, 'yes'], Boolean);
-     * // => false
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': false },
-     *   { 'user': 'fred',   'age': 40, 'active': false }
-     * ];
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.every(users, { 'user': 'barney', 'active': false });
-     * // => false
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.every(users, ['active', false]);
-     * // => true
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.every(users, 'active');
-     * // => false
-     */
-    function every(collection, predicate, guard) {
-      var func = isArray(collection) ? arrayEvery : baseEvery;
-      if (guard && isIterateeCall(collection, predicate, guard)) {
-        predicate = undefined;
-      }
-      return func(collection, getIteratee(predicate, 3));
-    }
-
-    /**
-     * Iterates over elements of `collection`, returning an array of all elements
-     * `predicate` returns truthy for. The predicate is invoked with three
-     * arguments: (value, index|key, collection).
-     *
-     * **Note:** Unlike `_.remove`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new filtered array.
-     * @see _.reject
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': true },
-     *   { 'user': 'fred',   'age': 40, 'active': false }
-     * ];
-     *
-     * _.filter(users, function(o) { return !o.active; });
-     * // => objects for ['fred']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.filter(users, { 'age': 36, 'active': true });
-     * // => objects for ['barney']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.filter(users, ['active', false]);
-     * // => objects for ['fred']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.filter(users, 'active');
-     * // => objects for ['barney']
-     */
-    function filter(collection, predicate) {
-      var func = isArray(collection) ? arrayFilter : baseFilter;
-      return func(collection, getIteratee(predicate, 3));
-    }
-
-    /**
-     * Iterates over elements of `collection`, returning the first element
-     * `predicate` returns truthy for. The predicate is invoked with three
-     * arguments: (value, index|key, collection).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @returns {*} Returns the matched element, else `undefined`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'age': 36, 'active': true },
-     *   { 'user': 'fred',    'age': 40, 'active': false },
-     *   { 'user': 'pebbles', 'age': 1,  'active': true }
-     * ];
-     *
-     * _.find(users, function(o) { return o.age < 40; });
-     * // => object for 'barney'
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.find(users, { 'age': 1, 'active': true });
-     * // => object for 'pebbles'
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.find(users, ['active', false]);
-     * // => object for 'fred'
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.find(users, 'active');
-     * // => object for 'barney'
-     */
-    var find = createFind(findIndex);
-
-    /**
-     * This method is like `_.find` except that it iterates over elements of
-     * `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=collection.length-1] The index to search from.
-     * @returns {*} Returns the matched element, else `undefined`.
-     * @example
-     *
-     * _.findLast([1, 2, 3, 4], function(n) {
-     *   return n % 2 == 1;
-     * });
-     * // => 3
-     */
-    var findLast = createFind(findLastIndex);
-
-    /**
-     * Creates a flattened array of values by running each element in `collection`
-     * thru `iteratee` and flattening the mapped results. The iteratee is invoked
-     * with three arguments: (value, index|key, collection).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * function duplicate(n) {
-     *   return [n, n];
-     * }
-     *
-     * _.flatMap([1, 2], duplicate);
-     * // => [1, 1, 2, 2]
-     */
-    function flatMap(collection, iteratee) {
-      return baseFlatten(map(collection, iteratee), 1);
-    }
-
-    /**
-     * This method is like `_.flatMap` except that it recursively flattens the
-     * mapped results.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * function duplicate(n) {
-     *   return [[[n, n]]];
-     * }
-     *
-     * _.flatMapDeep([1, 2], duplicate);
-     * // => [1, 1, 2, 2]
-     */
-    function flatMapDeep(collection, iteratee) {
-      return baseFlatten(map(collection, iteratee), INFINITY);
-    }
-
-    /**
-     * This method is like `_.flatMap` except that it recursively flattens the
-     * mapped results up to `depth` times.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {number} [depth=1] The maximum recursion depth.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * function duplicate(n) {
-     *   return [[[n, n]]];
-     * }
-     *
-     * _.flatMapDepth([1, 2], duplicate, 2);
-     * // => [[1, 1], [2, 2]]
-     */
-    function flatMapDepth(collection, iteratee, depth) {
-      depth = depth === undefined ? 1 : toInteger(depth);
-      return baseFlatten(map(collection, iteratee), depth);
-    }
-
-    /**
-     * Iterates over elements of `collection` and invokes `iteratee` for each element.
-     * The iteratee is invoked with three arguments: (value, index|key, collection).
-     * Iteratee functions may exit iteration early by explicitly returning `false`.
-     *
-     * **Note:** As with other "Collections" methods, objects with a "length"
-     * property are iterated like arrays. To avoid this behavior use `_.forIn`
-     * or `_.forOwn` for object iteration.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @alias each
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     * @see _.forEachRight
-     * @example
-     *
-     * _.forEach([1, 2], function(value) {
-     *   console.log(value);
-     * });
-     * // => Logs `1` then `2`.
-     *
-     * _.forEach({ 'a': 1, 'b': 2 }, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'a' then 'b' (iteration order is not guaranteed).
-     */
-    function forEach(collection, iteratee) {
-      var func = isArray(collection) ? arrayEach : baseEach;
-      return func(collection, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * This method is like `_.forEach` except that it iterates over elements of
-     * `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @alias eachRight
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     * @see _.forEach
-     * @example
-     *
-     * _.forEachRight([1, 2], function(value) {
-     *   console.log(value);
-     * });
-     * // => Logs `2` then `1`.
-     */
-    function forEachRight(collection, iteratee) {
-      var func = isArray(collection) ? arrayEachRight : baseEachRight;
-      return func(collection, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * Creates an object composed of keys generated from the results of running
-     * each element of `collection` thru `iteratee`. The order of grouped values
-     * is determined by the order they occur in `collection`. The corresponding
-     * value of each key is an array of elements responsible for generating the
-     * key. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee to transform keys.
-     * @returns {Object} Returns the composed aggregate object.
-     * @example
-     *
-     * _.groupBy([6.1, 4.2, 6.3], Math.floor);
-     * // => { '4': [4.2], '6': [6.1, 6.3] }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.groupBy(['one', 'two', 'three'], 'length');
-     * // => { '3': ['one', 'two'], '5': ['three'] }
-     */
-    var groupBy = createAggregator(function(result, value, key) {
-      if (hasOwnProperty.call(result, key)) {
-        result[key].push(value);
-      } else {
-        baseAssignValue(result, key, [value]);
-      }
-    });
-
-    /**
-     * Checks if `value` is in `collection`. If `collection` is a string, it's
-     * checked for a substring of `value`, otherwise
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * is used for equality comparisons. If `fromIndex` is negative, it's used as
-     * the offset from the end of `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object|string} collection The collection to inspect.
-     * @param {*} value The value to search for.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.reduce`.
-     * @returns {boolean} Returns `true` if `value` is found, else `false`.
-     * @example
-     *
-     * _.includes([1, 2, 3], 1);
-     * // => true
-     *
-     * _.includes([1, 2, 3], 1, 2);
-     * // => false
-     *
-     * _.includes({ 'a': 1, 'b': 2 }, 1);
-     * // => true
-     *
-     * _.includes('abcd', 'bc');
-     * // => true
-     */
-    function includes(collection, value, fromIndex, guard) {
-      collection = isArrayLike(collection) ? collection : values(collection);
-      fromIndex = (fromIndex && !guard) ? toInteger(fromIndex) : 0;
-
-      var length = collection.length;
-      if (fromIndex < 0) {
-        fromIndex = nativeMax(length + fromIndex, 0);
-      }
-      return isString(collection)
-        ? (fromIndex <= length && collection.indexOf(value, fromIndex) > -1)
-        : (!!length && baseIndexOf(collection, value, fromIndex) > -1);
-    }
-
-    /**
-     * Invokes the method at `path` of each element in `collection`, returning
-     * an array of the results of each invoked method. Any additional arguments
-     * are provided to each invoked method. If `path` is a function, it's invoked
-     * for, and `this` bound to, each element in `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Array|Function|string} path The path of the method to invoke or
-     *  the function invoked per iteration.
-     * @param {...*} [args] The arguments to invoke each method with.
-     * @returns {Array} Returns the array of results.
-     * @example
-     *
-     * _.invokeMap([[5, 1, 7], [3, 2, 1]], 'sort');
-     * // => [[1, 5, 7], [1, 2, 3]]
-     *
-     * _.invokeMap([123, 456], String.prototype.split, '');
-     * // => [['1', '2', '3'], ['4', '5', '6']]
-     */
-    var invokeMap = baseRest(function(collection, path, args) {
-      var index = -1,
-          isFunc = typeof path == 'function',
-          result = isArrayLike(collection) ? Array(collection.length) : [];
-
-      baseEach(collection, function(value) {
-        result[++index] = isFunc ? apply(path, value, args) : baseInvoke(value, path, args);
-      });
-      return result;
-    });
-
-    /**
-     * Creates an object composed of keys generated from the results of running
-     * each element of `collection` thru `iteratee`. The corresponding value of
-     * each key is the last element responsible for generating the key. The
-     * iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee to transform keys.
-     * @returns {Object} Returns the composed aggregate object.
-     * @example
-     *
-     * var array = [
-     *   { 'dir': 'left', 'code': 97 },
-     *   { 'dir': 'right', 'code': 100 }
-     * ];
-     *
-     * _.keyBy(array, function(o) {
-     *   return String.fromCharCode(o.code);
-     * });
-     * // => { 'a': { 'dir': 'left', 'code': 97 }, 'd': { 'dir': 'right', 'code': 100 } }
-     *
-     * _.keyBy(array, 'dir');
-     * // => { 'left': { 'dir': 'left', 'code': 97 }, 'right': { 'dir': 'right', 'code': 100 } }
-     */
-    var keyBy = createAggregator(function(result, value, key) {
-      baseAssignValue(result, key, value);
-    });
-
-    /**
-     * Creates an array of values by running each element in `collection` thru
-     * `iteratee`. The iteratee is invoked with three arguments:
-     * (value, index|key, collection).
-     *
-     * Many lodash methods are guarded to work as iteratees for methods like
-     * `_.every`, `_.filter`, `_.map`, `_.mapValues`, `_.reject`, and `_.some`.
-     *
-     * The guarded methods are:
-     * `ary`, `chunk`, `curry`, `curryRight`, `drop`, `dropRight`, `every`,
-     * `fill`, `invert`, `parseInt`, `random`, `range`, `rangeRight`, `repeat`,
-     * `sampleSize`, `slice`, `some`, `sortBy`, `split`, `take`, `takeRight`,
-     * `template`, `trim`, `trimEnd`, `trimStart`, and `words`
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new mapped array.
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * _.map([4, 8], square);
-     * // => [16, 64]
-     *
-     * _.map({ 'a': 4, 'b': 8 }, square);
-     * // => [16, 64] (iteration order is not guaranteed)
-     *
-     * var users = [
-     *   { 'user': 'barney' },
-     *   { 'user': 'fred' }
-     * ];
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.map(users, 'user');
-     * // => ['barney', 'fred']
-     */
-    function map(collection, iteratee) {
-      var func = isArray(collection) ? arrayMap : baseMap;
-      return func(collection, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * This method is like `_.sortBy` except that it allows specifying the sort
-     * orders of the iteratees to sort by. If `orders` is unspecified, all values
-     * are sorted in ascending order. Otherwise, specify an order of "desc" for
-     * descending or "asc" for ascending sort order of corresponding values.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Array[]|Function[]|Object[]|string[]} [iteratees=[_.identity]]
-     *  The iteratees to sort by.
-     * @param {string[]} [orders] The sort orders of `iteratees`.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.reduce`.
-     * @returns {Array} Returns the new sorted array.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'fred',   'age': 48 },
-     *   { 'user': 'barney', 'age': 34 },
-     *   { 'user': 'fred',   'age': 40 },
-     *   { 'user': 'barney', 'age': 36 }
-     * ];
-     *
-     * // Sort by `user` in ascending order and by `age` in descending order.
-     * _.orderBy(users, ['user', 'age'], ['asc', 'desc']);
-     * // => objects for [['barney', 36], ['barney', 34], ['fred', 48], ['fred', 40]]
-     */
-    function orderBy(collection, iteratees, orders, guard) {
-      if (collection == null) {
-        return [];
-      }
-      if (!isArray(iteratees)) {
-        iteratees = iteratees == null ? [] : [iteratees];
-      }
-      orders = guard ? undefined : orders;
-      if (!isArray(orders)) {
-        orders = orders == null ? [] : [orders];
-      }
-      return baseOrderBy(collection, iteratees, orders);
-    }
-
-    /**
-     * Creates an array of elements split into two groups, the first of which
-     * contains elements `predicate` returns truthy for, the second of which
-     * contains elements `predicate` returns falsey for. The predicate is
-     * invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the array of grouped elements.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'age': 36, 'active': false },
-     *   { 'user': 'fred',    'age': 40, 'active': true },
-     *   { 'user': 'pebbles', 'age': 1,  'active': false }
-     * ];
-     *
-     * _.partition(users, function(o) { return o.active; });
-     * // => objects for [['fred'], ['barney', 'pebbles']]
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.partition(users, { 'age': 1, 'active': false });
-     * // => objects for [['pebbles'], ['barney', 'fred']]
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.partition(users, ['active', false]);
-     * // => objects for [['barney', 'pebbles'], ['fred']]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.partition(users, 'active');
-     * // => objects for [['fred'], ['barney', 'pebbles']]
-     */
-    var partition = createAggregator(function(result, value, key) {
-      result[key ? 0 : 1].push(value);
-    }, function() { return [[], []]; });
-
-    /**
-     * Reduces `collection` to a value which is the accumulated result of running
-     * each element in `collection` thru `iteratee`, where each successive
-     * invocation is supplied the return value of the previous. If `accumulator`
-     * is not given, the first element of `collection` is used as the initial
-     * value. The iteratee is invoked with four arguments:
-     * (accumulator, value, index|key, collection).
-     *
-     * Many lodash methods are guarded to work as iteratees for methods like
-     * `_.reduce`, `_.reduceRight`, and `_.transform`.
-     *
-     * The guarded methods are:
-     * `assign`, `defaults`, `defaultsDeep`, `includes`, `merge`, `orderBy`,
-     * and `sortBy`
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {*} [accumulator] The initial value.
-     * @returns {*} Returns the accumulated value.
-     * @see _.reduceRight
-     * @example
-     *
-     * _.reduce([1, 2], function(sum, n) {
-     *   return sum + n;
-     * }, 0);
-     * // => 3
-     *
-     * _.reduce({ 'a': 1, 'b': 2, 'c': 1 }, function(result, value, key) {
-     *   (result[value] || (result[value] = [])).push(key);
-     *   return result;
-     * }, {});
-     * // => { '1': ['a', 'c'], '2': ['b'] } (iteration order is not guaranteed)
-     */
-    function reduce(collection, iteratee, accumulator) {
-      var func = isArray(collection) ? arrayReduce : baseReduce,
-          initAccum = arguments.length < 3;
-
-      return func(collection, getIteratee(iteratee, 4), accumulator, initAccum, baseEach);
-    }
-
-    /**
-     * This method is like `_.reduce` except that it iterates over elements of
-     * `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {*} [accumulator] The initial value.
-     * @returns {*} Returns the accumulated value.
-     * @see _.reduce
-     * @example
-     *
-     * var array = [[0, 1], [2, 3], [4, 5]];
-     *
-     * _.reduceRight(array, function(flattened, other) {
-     *   return flattened.concat(other);
-     * }, []);
-     * // => [4, 5, 2, 3, 0, 1]
-     */
-    function reduceRight(collection, iteratee, accumulator) {
-      var func = isArray(collection) ? arrayReduceRight : baseReduce,
-          initAccum = arguments.length < 3;
-
-      return func(collection, getIteratee(iteratee, 4), accumulator, initAccum, baseEachRight);
-    }
-
-    /**
-     * The opposite of `_.filter`; this method returns the elements of `collection`
-     * that `predicate` does **not** return truthy for.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new filtered array.
-     * @see _.filter
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': false },
-     *   { 'user': 'fred',   'age': 40, 'active': true }
-     * ];
-     *
-     * _.reject(users, function(o) { return !o.active; });
-     * // => objects for ['fred']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.reject(users, { 'age': 40, 'active': true });
-     * // => objects for ['barney']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.reject(users, ['active', false]);
-     * // => objects for ['fred']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.reject(users, 'active');
-     * // => objects for ['barney']
-     */
-    function reject(collection, predicate) {
-      var func = isArray(collection) ? arrayFilter : baseFilter;
-      return func(collection, negate(getIteratee(predicate, 3)));
-    }
-
-    /**
-     * Gets a random element from `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to sample.
-     * @returns {*} Returns the random element.
-     * @example
-     *
-     * _.sample([1, 2, 3, 4]);
-     * // => 2
-     */
-    function sample(collection) {
-      var func = isArray(collection) ? arraySample : baseSample;
-      return func(collection);
-    }
-
-    /**
-     * Gets `n` random elements at unique keys from `collection` up to the
-     * size of `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to sample.
-     * @param {number} [n=1] The number of elements to sample.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the random elements.
-     * @example
-     *
-     * _.sampleSize([1, 2, 3], 2);
-     * // => [3, 1]
-     *
-     * _.sampleSize([1, 2, 3], 4);
-     * // => [2, 3, 1]
-     */
-    function sampleSize(collection, n, guard) {
-      if ((guard ? isIterateeCall(collection, n, guard) : n === undefined)) {
-        n = 1;
-      } else {
-        n = toInteger(n);
-      }
-      var func = isArray(collection) ? arraySampleSize : baseSampleSize;
-      return func(collection, n);
-    }
-
-    /**
-     * Creates an array of shuffled values, using a version of the
-     * [Fisher-Yates shuffle](https://en.wikipedia.org/wiki/Fisher-Yates_shuffle).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to shuffle.
-     * @returns {Array} Returns the new shuffled array.
-     * @example
-     *
-     * _.shuffle([1, 2, 3, 4]);
-     * // => [4, 1, 3, 2]
-     */
-    function shuffle(collection) {
-      var func = isArray(collection) ? arrayShuffle : baseShuffle;
-      return func(collection);
-    }
-
-    /**
-     * Gets the size of `collection` by returning its length for array-like
-     * values or the number of own enumerable string keyed properties for objects.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object|string} collection The collection to inspect.
-     * @returns {number} Returns the collection size.
-     * @example
-     *
-     * _.size([1, 2, 3]);
-     * // => 3
-     *
-     * _.size({ 'a': 1, 'b': 2 });
-     * // => 2
-     *
-     * _.size('pebbles');
-     * // => 7
-     */
-    function size(collection) {
-      if (collection == null) {
-        return 0;
-      }
-      if (isArrayLike(collection)) {
-        return isString(collection) ? stringSize(collection) : collection.length;
-      }
-      var tag = getTag(collection);
-      if (tag == mapTag || tag == setTag) {
-        return collection.size;
-      }
-      return baseKeys(collection).length;
-    }
-
-    /**
-     * Checks if `predicate` returns truthy for **any** element of `collection`.
-     * Iteration is stopped once `predicate` returns truthy. The predicate is
-     * invoked with three arguments: (value, index|key, collection).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {boolean} Returns `true` if any element passes the predicate check,
-     *  else `false`.
-     * @example
-     *
-     * _.some([null, 0, 'yes', false], Boolean);
-     * // => true
-     *
-     * var users = [
-     *   { 'user': 'barney', 'active': true },
-     *   { 'user': 'fred',   'active': false }
-     * ];
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.some(users, { 'user': 'barney', 'active': false });
-     * // => false
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.some(users, ['active', false]);
-     * // => true
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.some(users, 'active');
-     * // => true
-     */
-    function some(collection, predicate, guard) {
-      var func = isArray(collection) ? arraySome : baseSome;
-      if (guard && isIterateeCall(collection, predicate, guard)) {
-        predicate = undefined;
-      }
-      return func(collection, getIteratee(predicate, 3));
-    }
-
-    /**
-     * Creates an array of elements, sorted in ascending order by the results of
-     * running each element in a collection thru each iteratee. This method
-     * performs a stable sort, that is, it preserves the original sort order of
-     * equal elements. The iteratees are invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {...(Function|Function[])} [iteratees=[_.identity]]
-     *  The iteratees to sort by.
-     * @returns {Array} Returns the new sorted array.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'fred',   'age': 48 },
-     *   { 'user': 'barney', 'age': 36 },
-     *   { 'user': 'fred',   'age': 40 },
-     *   { 'user': 'barney', 'age': 34 }
-     * ];
-     *
-     * _.sortBy(users, [function(o) { return o.user; }]);
-     * // => objects for [['barney', 36], ['barney', 34], ['fred', 48], ['fred', 40]]
-     *
-     * _.sortBy(users, ['user', 'age']);
-     * // => objects for [['barney', 34], ['barney', 36], ['fred', 40], ['fred', 48]]
-     */
-    var sortBy = baseRest(function(collection, iteratees) {
-      if (collection == null) {
-        return [];
-      }
-      var length = iteratees.length;
-      if (length > 1 && isIterateeCall(collection, iteratees[0], iteratees[1])) {
-        iteratees = [];
-      } else if (length > 2 && isIterateeCall(iteratees[0], iteratees[1], iteratees[2])) {
-        iteratees = [iteratees[0]];
-      }
-      return baseOrderBy(collection, baseFlatten(iteratees, 1), []);
-    });
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Gets the timestamp of the number of milliseconds that have elapsed since
-     * the Unix epoch (1 January 1970 00:00:00 UTC).
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Date
-     * @returns {number} Returns the timestamp.
-     * @example
-     *
-     * _.defer(function(stamp) {
-     *   console.log(_.now() - stamp);
-     * }, _.now());
-     * // => Logs the number of milliseconds it took for the deferred invocation.
-     */
-    var now = ctxNow || function() {
-      return root.Date.now();
-    };
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * The opposite of `_.before`; this method creates a function that invokes
-     * `func` once it's called `n` or more times.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {number} n The number of calls before `func` is invoked.
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new restricted function.
-     * @example
-     *
-     * var saves = ['profile', 'settings'];
-     *
-     * var done = _.after(saves.length, function() {
-     *   console.log('done saving!');
-     * });
-     *
-     * _.forEach(saves, function(type) {
-     *   asyncSave({ 'type': type, 'complete': done });
-     * });
-     * // => Logs 'done saving!' after the two async saves have completed.
-     */
-    function after(n, func) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      n = toInteger(n);
-      return function() {
-        if (--n < 1) {
-          return func.apply(this, arguments);
-        }
-      };
-    }
-
-    /**
-     * Creates a function that invokes `func`, with up to `n` arguments,
-     * ignoring any additional arguments.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} func The function to cap arguments for.
-     * @param {number} [n=func.length] The arity cap.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the new capped function.
-     * @example
-     *
-     * _.map(['6', '8', '10'], _.ary(parseInt, 1));
-     * // => [6, 8, 10]
-     */
-    function ary(func, n, guard) {
-      n = guard ? undefined : n;
-      n = (func && n == null) ? func.length : n;
-      return createWrap(func, WRAP_ARY_FLAG, undefined, undefined, undefined, undefined, n);
-    }
-
-    /**
-     * Creates a function that invokes `func`, with the `this` binding and arguments
-     * of the created function, while it's called less than `n` times. Subsequent
-     * calls to the created function return the result of the last `func` invocation.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {number} n The number of calls at which `func` is no longer invoked.
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new restricted function.
-     * @example
-     *
-     * jQuery(element).on('click', _.before(5, addContactToList));
-     * // => Allows adding up to 4 contacts to the list.
-     */
-    function before(n, func) {
-      var result;
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      n = toInteger(n);
-      return function() {
-        if (--n > 0) {
-          result = func.apply(this, arguments);
-        }
-        if (n <= 1) {
-          func = undefined;
-        }
-        return result;
-      };
-    }
-
-    /**
-     * Creates a function that invokes `func` with the `this` binding of `thisArg`
-     * and `partials` prepended to the arguments it receives.
-     *
-     * The `_.bind.placeholder` value, which defaults to `_` in monolithic builds,
-     * may be used as a placeholder for partially applied arguments.
-     *
-     * **Note:** Unlike native `Function#bind`, this method doesn't set the "length"
-     * property of bound functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to bind.
-     * @param {*} thisArg The `this` binding of `func`.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new bound function.
-     * @example
-     *
-     * function greet(greeting, punctuation) {
-     *   return greeting + ' ' + this.user + punctuation;
-     * }
-     *
-     * var object = { 'user': 'fred' };
-     *
-     * var bound = _.bind(greet, object, 'hi');
-     * bound('!');
-     * // => 'hi fred!'
-     *
-     * // Bound with placeholders.
-     * var bound = _.bind(greet, object, _, '!');
-     * bound('hi');
-     * // => 'hi fred!'
-     */
-    var bind = baseRest(function(func, thisArg, partials) {
-      var bitmask = WRAP_BIND_FLAG;
-      if (partials.length) {
-        var holders = replaceHolders(partials, getHolder(bind));
-        bitmask |= WRAP_PARTIAL_FLAG;
-      }
-      return createWrap(func, bitmask, thisArg, partials, holders);
-    });
-
-    /**
-     * Creates a function that invokes the method at `object[key]` with `partials`
-     * prepended to the arguments it receives.
-     *
-     * This method differs from `_.bind` by allowing bound functions to reference
-     * methods that may be redefined or don't yet exist. See
-     * [Peter Michaux's article](http://peter.michaux.ca/articles/lazy-function-definition-pattern)
-     * for more details.
-     *
-     * The `_.bindKey.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for partially applied arguments.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.10.0
-     * @category Function
-     * @param {Object} object The object to invoke the method on.
-     * @param {string} key The key of the method.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new bound function.
-     * @example
-     *
-     * var object = {
-     *   'user': 'fred',
-     *   'greet': function(greeting, punctuation) {
-     *     return greeting + ' ' + this.user + punctuation;
-     *   }
-     * };
-     *
-     * var bound = _.bindKey(object, 'greet', 'hi');
-     * bound('!');
-     * // => 'hi fred!'
-     *
-     * object.greet = function(greeting, punctuation) {
-     *   return greeting + 'ya ' + this.user + punctuation;
-     * };
-     *
-     * bound('!');
-     * // => 'hiya fred!'
-     *
-     * // Bound with placeholders.
-     * var bound = _.bindKey(object, 'greet', _, '!');
-     * bound('hi');
-     * // => 'hiya fred!'
-     */
-    var bindKey = baseRest(function(object, key, partials) {
-      var bitmask = WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG;
-      if (partials.length) {
-        var holders = replaceHolders(partials, getHolder(bindKey));
-        bitmask |= WRAP_PARTIAL_FLAG;
-      }
-      return createWrap(key, bitmask, object, partials, holders);
-    });
-
-    /**
-     * Creates a function that accepts arguments of `func` and either invokes
-     * `func` returning its result, if at least `arity` number of arguments have
-     * been provided, or returns a function that accepts the remaining `func`
-     * arguments, and so on. The arity of `func` may be specified if `func.length`
-     * is not sufficient.
-     *
-     * The `_.curry.placeholder` value, which defaults to `_` in monolithic builds,
-     * may be used as a placeholder for provided arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of curried functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Function
-     * @param {Function} func The function to curry.
-     * @param {number} [arity=func.length] The arity of `func`.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the new curried function.
-     * @example
-     *
-     * var abc = function(a, b, c) {
-     *   return [a, b, c];
-     * };
-     *
-     * var curried = _.curry(abc);
-     *
-     * curried(1)(2)(3);
-     * // => [1, 2, 3]
-     *
-     * curried(1, 2)(3);
-     * // => [1, 2, 3]
-     *
-     * curried(1, 2, 3);
-     * // => [1, 2, 3]
-     *
-     * // Curried with placeholders.
-     * curried(1)(_, 3)(2);
-     * // => [1, 2, 3]
-     */
-    function curry(func, arity, guard) {
-      arity = guard ? undefined : arity;
-      var result = createWrap(func, WRAP_CURRY_FLAG, undefined, undefined, undefined, undefined, undefined, arity);
-      result.placeholder = curry.placeholder;
-      return result;
-    }
-
-    /**
-     * This method is like `_.curry` except that arguments are applied to `func`
-     * in the manner of `_.partialRight` instead of `_.partial`.
-     *
-     * The `_.curryRight.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for provided arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of curried functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} func The function to curry.
-     * @param {number} [arity=func.length] The arity of `func`.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the new curried function.
-     * @example
-     *
-     * var abc = function(a, b, c) {
-     *   return [a, b, c];
-     * };
-     *
-     * var curried = _.curryRight(abc);
-     *
-     * curried(3)(2)(1);
-     * // => [1, 2, 3]
-     *
-     * curried(2, 3)(1);
-     * // => [1, 2, 3]
-     *
-     * curried(1, 2, 3);
-     * // => [1, 2, 3]
-     *
-     * // Curried with placeholders.
-     * curried(3)(1, _)(2);
-     * // => [1, 2, 3]
-     */
-    function curryRight(func, arity, guard) {
-      arity = guard ? undefined : arity;
-      var result = createWrap(func, WRAP_CURRY_RIGHT_FLAG, undefined, undefined, undefined, undefined, undefined, arity);
-      result.placeholder = curryRight.placeholder;
-      return result;
-    }
-
-    /**
-     * Creates a debounced function that delays invoking `func` until after `wait`
-     * milliseconds have elapsed since the last time the debounced function was
-     * invoked. The debounced function comes with a `cancel` method to cancel
-     * delayed `func` invocations and a `flush` method to immediately invoke them.
-     * Provide `options` to indicate whether `func` should be invoked on the
-     * leading and/or trailing edge of the `wait` timeout. The `func` is invoked
-     * with the last arguments provided to the debounced function. Subsequent
-     * calls to the debounced function return the result of the last `func`
-     * invocation.
-     *
-     * **Note:** If `leading` and `trailing` options are `true`, `func` is
-     * invoked on the trailing edge of the timeout only if the debounced function
-     * is invoked more than once during the `wait` timeout.
-     *
-     * If `wait` is `0` and `leading` is `false`, `func` invocation is deferred
-     * until to the next tick, similar to `setTimeout` with a timeout of `0`.
-     *
-     * See [David Corbacho's article](https://css-tricks.com/debouncing-throttling-explained-examples/)
-     * for details over the differences between `_.debounce` and `_.throttle`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to debounce.
-     * @param {number} [wait=0] The number of milliseconds to delay.
-     * @param {Object} [options={}] The options object.
-     * @param {boolean} [options.leading=false]
-     *  Specify invoking on the leading edge of the timeout.
-     * @param {number} [options.maxWait]
-     *  The maximum time `func` is allowed to be delayed before it's invoked.
-     * @param {boolean} [options.trailing=true]
-     *  Specify invoking on the trailing edge of the timeout.
-     * @returns {Function} Returns the new debounced function.
-     * @example
-     *
-     * // Avoid costly calculations while the window size is in flux.
-     * jQuery(window).on('resize', _.debounce(calculateLayout, 150));
-     *
-     * // Invoke `sendMail` when clicked, debouncing subsequent calls.
-     * jQuery(element).on('click', _.debounce(sendMail, 300, {
-     *   'leading': true,
-     *   'trailing': false
-     * }));
-     *
-     * // Ensure `batchLog` is invoked once after 1 second of debounced calls.
-     * var debounced = _.debounce(batchLog, 250, { 'maxWait': 1000 });
-     * var source = new EventSource('/stream');
-     * jQuery(source).on('message', debounced);
-     *
-     * // Cancel the trailing debounced invocation.
-     * jQuery(window).on('popstate', debounced.cancel);
-     */
-    function debounce(func, wait, options) {
-      var lastArgs,
-          lastThis,
-          maxWait,
-          result,
-          timerId,
-          lastCallTime,
-          lastInvokeTime = 0,
-          leading = false,
-          maxing = false,
-          trailing = true;
-
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      wait = toNumber(wait) || 0;
-      if (isObject(options)) {
-        leading = !!options.leading;
-        maxing = 'maxWait' in options;
-        maxWait = maxing ? nativeMax(toNumber(options.maxWait) || 0, wait) : maxWait;
-        trailing = 'trailing' in options ? !!options.trailing : trailing;
-      }
-
-      function invokeFunc(time) {
-        var args = lastArgs,
-            thisArg = lastThis;
-
-        lastArgs = lastThis = undefined;
-        lastInvokeTime = time;
-        result = func.apply(thisArg, args);
-        return result;
-      }
-
-      function leadingEdge(time) {
-        // Reset any `maxWait` timer.
-        lastInvokeTime = time;
-        // Start the timer for the trailing edge.
-        timerId = setTimeout(timerExpired, wait);
-        // Invoke the leading edge.
-        return leading ? invokeFunc(time) : result;
-      }
-
-      function remainingWait(time) {
-        var timeSinceLastCall = time - lastCallTime,
-            timeSinceLastInvoke = time - lastInvokeTime,
-            timeWaiting = wait - timeSinceLastCall;
-
-        return maxing
-          ? nativeMin(timeWaiting, maxWait - timeSinceLastInvoke)
-          : timeWaiting;
-      }
-
-      function shouldInvoke(time) {
-        var timeSinceLastCall = time - lastCallTime,
-            timeSinceLastInvoke = time - lastInvokeTime;
-
-        // Either this is the first call, activity has stopped and we're at the
-        // trailing edge, the system time has gone backwards and we're treating
-        // it as the trailing edge, or we've hit the `maxWait` limit.
-        return (lastCallTime === undefined || (timeSinceLastCall >= wait) ||
-          (timeSinceLastCall < 0) || (maxing && timeSinceLastInvoke >= maxWait));
-      }
-
-      function timerExpired() {
-        var time = now();
-        if (shouldInvoke(time)) {
-          return trailingEdge(time);
-        }
-        // Restart the timer.
-        timerId = setTimeout(timerExpired, remainingWait(time));
-      }
-
-      function trailingEdge(time) {
-        timerId = undefined;
-
-        // Only invoke if we have `lastArgs` which means `func` has been
-        // debounced at least once.
-        if (trailing && lastArgs) {
-          return invokeFunc(time);
-        }
-        lastArgs = lastThis = undefined;
-        return result;
-      }
-
-      function cancel() {
-        if (timerId !== undefined) {
-          clearTimeout(timerId);
-        }
-        lastInvokeTime = 0;
-        lastArgs = lastCallTime = lastThis = timerId = undefined;
-      }
-
-      function flush() {
-        return timerId === undefined ? result : trailingEdge(now());
-      }
-
-      function debounced() {
-        var time = now(),
-            isInvoking = shouldInvoke(time);
-
-        lastArgs = arguments;
-        lastThis = this;
-        lastCallTime = time;
-
-        if (isInvoking) {
-          if (timerId === undefined) {
-            return leadingEdge(lastCallTime);
-          }
-          if (maxing) {
-            // Handle invocations in a tight loop.
-            clearTimeout(timerId);
-            timerId = setTimeout(timerExpired, wait);
-            return invokeFunc(lastCallTime);
-          }
-        }
-        if (timerId === undefined) {
-          timerId = setTimeout(timerExpired, wait);
-        }
-        return result;
-      }
-      debounced.cancel = cancel;
-      debounced.flush = flush;
-      return debounced;
-    }
-
-    /**
-     * Defers invoking the `func` until the current call stack has cleared. Any
-     * additional arguments are provided to `func` when it's invoked.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to defer.
-     * @param {...*} [args] The arguments to invoke `func` with.
-     * @returns {number} Returns the timer id.
-     * @example
-     *
-     * _.defer(function(text) {
-     *   console.log(text);
-     * }, 'deferred');
-     * // => Logs 'deferred' after one millisecond.
-     */
-    var defer = baseRest(function(func, args) {
-      return baseDelay(func, 1, args);
-    });
-
-    /**
-     * Invokes `func` after `wait` milliseconds. Any additional arguments are
-     * provided to `func` when it's invoked.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to delay.
-     * @param {number} wait The number of milliseconds to delay invocation.
-     * @param {...*} [args] The arguments to invoke `func` with.
-     * @returns {number} Returns the timer id.
-     * @example
-     *
-     * _.delay(function(text) {
-     *   console.log(text);
-     * }, 1000, 'later');
-     * // => Logs 'later' after one second.
-     */
-    var delay = baseRest(function(func, wait, args) {
-      return baseDelay(func, toNumber(wait) || 0, args);
-    });
-
-    /**
-     * Creates a function that invokes `func` with arguments reversed.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Function
-     * @param {Function} func The function to flip arguments for.
-     * @returns {Function} Returns the new flipped function.
-     * @example
-     *
-     * var flipped = _.flip(function() {
-     *   return _.toArray(arguments);
-     * });
-     *
-     * flipped('a', 'b', 'c', 'd');
-     * // => ['d', 'c', 'b', 'a']
-     */
-    function flip(func) {
-      return createWrap(func, WRAP_FLIP_FLAG);
-    }
-
-    /**
-     * Creates a function that memoizes the result of `func`. If `resolver` is
-     * provided, it determines the cache key for storing the result based on the
-     * arguments provided to the memoized function. By default, the first argument
-     * provided to the memoized function is used as the map cache key. The `func`
-     * is invoked with the `this` binding of the memoized function.
-     *
-     * **Note:** The cache is exposed as the `cache` property on the memoized
-     * function. Its creation may be customized by replacing the `_.memoize.Cache`
-     * constructor with one whose instances implement the
-     * [`Map`](http://ecma-international.org/ecma-262/7.0/#sec-properties-of-the-map-prototype-object)
-     * method interface of `clear`, `delete`, `get`, `has`, and `set`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to have its output memoized.
-     * @param {Function} [resolver] The function to resolve the cache key.
-     * @returns {Function} Returns the new memoized function.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2 };
-     * var other = { 'c': 3, 'd': 4 };
-     *
-     * var values = _.memoize(_.values);
-     * values(object);
-     * // => [1, 2]
-     *
-     * values(other);
-     * // => [3, 4]
-     *
-     * object.a = 2;
-     * values(object);
-     * // => [1, 2]
-     *
-     * // Modify the result cache.
-     * values.cache.set(object, ['a', 'b']);
-     * values(object);
-     * // => ['a', 'b']
-     *
-     * // Replace `_.memoize.Cache`.
-     * _.memoize.Cache = WeakMap;
-     */
-    function memoize(func, resolver) {
-      if (typeof func != 'function' || (resolver != null && typeof resolver != 'function')) {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      var memoized = function() {
-        var args = arguments,
-            key = resolver ? resolver.apply(this, args) : args[0],
-            cache = memoized.cache;
-
-        if (cache.has(key)) {
-          return cache.get(key);
-        }
-        var result = func.apply(this, args);
-        memoized.cache = cache.set(key, result) || cache;
-        return result;
-      };
-      memoized.cache = new (memoize.Cache || MapCache);
-      return memoized;
-    }
-
-    // Expose `MapCache`.
-    memoize.Cache = MapCache;
-
-    /**
-     * Creates a function that negates the result of the predicate `func`. The
-     * `func` predicate is invoked with the `this` binding and arguments of the
-     * created function.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} predicate The predicate to negate.
-     * @returns {Function} Returns the new negated function.
-     * @example
-     *
-     * function isEven(n) {
-     *   return n % 2 == 0;
-     * }
-     *
-     * _.filter([1, 2, 3, 4, 5, 6], _.negate(isEven));
-     * // => [1, 3, 5]
-     */
-    function negate(predicate) {
-      if (typeof predicate != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      return function() {
-        var args = arguments;
-        switch (args.length) {
-          case 0: return !predicate.call(this);
-          case 1: return !predicate.call(this, args[0]);
-          case 2: return !predicate.call(this, args[0], args[1]);
-          case 3: return !predicate.call(this, args[0], args[1], args[2]);
-        }
-        return !predicate.apply(this, args);
-      };
-    }
-
-    /**
-     * Creates a function that is restricted to invoking `func` once. Repeat calls
-     * to the function return the value of the first invocation. The `func` is
-     * invoked with the `this` binding and arguments of the created function.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new restricted function.
-     * @example
-     *
-     * var initialize = _.once(createApplication);
-     * initialize();
-     * initialize();
-     * // => `createApplication` is invoked once
-     */
-    function once(func) {
-      return before(2, func);
-    }
-
-    /**
-     * Creates a function that invokes `func` with its arguments transformed.
-     *
-     * @static
-     * @since 4.0.0
-     * @memberOf _
-     * @category Function
-     * @param {Function} func The function to wrap.
-     * @param {...(Function|Function[])} [transforms=[_.identity]]
-     *  The argument transforms.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * function doubled(n) {
-     *   return n * 2;
-     * }
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var func = _.overArgs(function(x, y) {
-     *   return [x, y];
-     * }, [square, doubled]);
-     *
-     * func(9, 3);
-     * // => [81, 6]
-     *
-     * func(10, 5);
-     * // => [100, 10]
-     */
-    var overArgs = castRest(function(func, transforms) {
-      transforms = (transforms.length == 1 && isArray(transforms[0]))
-        ? arrayMap(transforms[0], baseUnary(getIteratee()))
-        : arrayMap(baseFlatten(transforms, 1), baseUnary(getIteratee()));
-
-      var funcsLength = transforms.length;
-      return baseRest(function(args) {
-        var index = -1,
-            length = nativeMin(args.length, funcsLength);
-
-        while (++index < length) {
-          args[index] = transforms[index].call(this, args[index]);
-        }
-        return apply(func, this, args);
-      });
-    });
-
-    /**
-     * Creates a function that invokes `func` with `partials` prepended to the
-     * arguments it receives. This method is like `_.bind` except it does **not**
-     * alter the `this` binding.
-     *
-     * The `_.partial.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for partially applied arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of partially
-     * applied functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.2.0
-     * @category Function
-     * @param {Function} func The function to partially apply arguments to.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new partially applied function.
-     * @example
-     *
-     * function greet(greeting, name) {
-     *   return greeting + ' ' + name;
-     * }
-     *
-     * var sayHelloTo = _.partial(greet, 'hello');
-     * sayHelloTo('fred');
-     * // => 'hello fred'
-     *
-     * // Partially applied with placeholders.
-     * var greetFred = _.partial(greet, _, 'fred');
-     * greetFred('hi');
-     * // => 'hi fred'
-     */
-    var partial = baseRest(function(func, partials) {
-      var holders = replaceHolders(partials, getHolder(partial));
-      return createWrap(func, WRAP_PARTIAL_FLAG, undefined, partials, holders);
-    });
-
-    /**
-     * This method is like `_.partial` except that partially applied arguments
-     * are appended to the arguments it receives.
-     *
-     * The `_.partialRight.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for partially applied arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of partially
-     * applied functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.0.0
-     * @category Function
-     * @param {Function} func The function to partially apply arguments to.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new partially applied function.
-     * @example
-     *
-     * function greet(greeting, name) {
-     *   return greeting + ' ' + name;
-     * }
-     *
-     * var greetFred = _.partialRight(greet, 'fred');
-     * greetFred('hi');
-     * // => 'hi fred'
-     *
-     * // Partially applied with placeholders.
-     * var sayHelloTo = _.partialRight(greet, 'hello', _);
-     * sayHelloTo('fred');
-     * // => 'hello fred'
-     */
-    var partialRight = baseRest(function(func, partials) {
-      var holders = replaceHolders(partials, getHolder(partialRight));
-      return createWrap(func, WRAP_PARTIAL_RIGHT_FLAG, undefined, partials, holders);
-    });
-
-    /**
-     * Creates a function that invokes `func` with arguments arranged according
-     * to the specified `indexes` where the argument value at the first index is
-     * provided as the first argument, the argument value at the second index is
-     * provided as the second argument, and so on.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} func The function to rearrange arguments for.
-     * @param {...(number|number[])} indexes The arranged argument indexes.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var rearged = _.rearg(function(a, b, c) {
-     *   return [a, b, c];
-     * }, [2, 0, 1]);
-     *
-     * rearged('b', 'c', 'a')
-     * // => ['a', 'b', 'c']
-     */
-    var rearg = flatRest(function(func, indexes) {
-      return createWrap(func, WRAP_REARG_FLAG, undefined, undefined, undefined, indexes);
-    });
-
-    /**
-     * Creates a function that invokes `func` with the `this` binding of the
-     * created function and arguments from `start` and beyond provided as
-     * an array.
-     *
-     * **Note:** This method is based on the
-     * [rest parameter](https://mdn.io/rest_parameters).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Function
-     * @param {Function} func The function to apply a rest parameter to.
-     * @param {number} [start=func.length-1] The start position of the rest parameter.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var say = _.rest(function(what, names) {
-     *   return what + ' ' + _.initial(names).join(', ') +
-     *     (_.size(names) > 1 ? ', & ' : '') + _.last(names);
-     * });
-     *
-     * say('hello', 'fred', 'barney', 'pebbles');
-     * // => 'hello fred, barney, & pebbles'
-     */
-    function rest(func, start) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      start = start === undefined ? start : toInteger(start);
-      return baseRest(func, start);
-    }
-
-    /**
-     * Creates a function that invokes `func` with the `this` binding of the
-     * create function and an array of arguments much like
-     * [`Function#apply`](http://www.ecma-international.org/ecma-262/7.0/#sec-function.prototype.apply).
-     *
-     * **Note:** This method is based on the
-     * [spread operator](https://mdn.io/spread_operator).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.2.0
-     * @category Function
-     * @param {Function} func The function to spread arguments over.
-     * @param {number} [start=0] The start position of the spread.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var say = _.spread(function(who, what) {
-     *   return who + ' says ' + what;
-     * });
-     *
-     * say(['fred', 'hello']);
-     * // => 'fred says hello'
-     *
-     * var numbers = Promise.all([
-     *   Promise.resolve(40),
-     *   Promise.resolve(36)
-     * ]);
-     *
-     * numbers.then(_.spread(function(x, y) {
-     *   return x + y;
-     * }));
-     * // => a Promise of 76
-     */
-    function spread(func, start) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      start = start == null ? 0 : nativeMax(toInteger(start), 0);
-      return baseRest(function(args) {
-        var array = args[start],
-            otherArgs = castSlice(args, 0, start);
-
-        if (array) {
-          arrayPush(otherArgs, array);
-        }
-        return apply(func, this, otherArgs);
-      });
-    }
-
-    /**
-     * Creates a throttled function that only invokes `func` at most once per
-     * every `wait` milliseconds. The throttled function comes with a `cancel`
-     * method to cancel delayed `func` invocations and a `flush` method to
-     * immediately invoke them. Provide `options` to indicate whether `func`
-     * should be invoked on the leading and/or trailing edge of the `wait`
-     * timeout. The `func` is invoked with the last arguments provided to the
-     * throttled function. Subsequent calls to the throttled function return the
-     * result of the last `func` invocation.
-     *
-     * **Note:** If `leading` and `trailing` options are `true`, `func` is
-     * invoked on the trailing edge of the timeout only if the throttled function
-     * is invoked more than once during the `wait` timeout.
-     *
-     * If `wait` is `0` and `leading` is `false`, `func` invocation is deferred
-     * until to the next tick, similar to `setTimeout` with a timeout of `0`.
-     *
-     * See [David Corbacho's article](https://css-tricks.com/debouncing-throttling-explained-examples/)
-     * for details over the differences between `_.throttle` and `_.debounce`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to throttle.
-     * @param {number} [wait=0] The number of milliseconds to throttle invocations to.
-     * @param {Object} [options={}] The options object.
-     * @param {boolean} [options.leading=true]
-     *  Specify invoking on the leading edge of the timeout.
-     * @param {boolean} [options.trailing=true]
-     *  Specify invoking on the trailing edge of the timeout.
-     * @returns {Function} Returns the new throttled function.
-     * @example
-     *
-     * // Avoid excessively updating the position while scrolling.
-     * jQuery(window).on('scroll', _.throttle(updatePosition, 100));
-     *
-     * // Invoke `renewToken` when the click event is fired, but not more than once every 5 minutes.
-     * var throttled = _.throttle(renewToken, 300000, { 'trailing': false });
-     * jQuery(element).on('click', throttled);
-     *
-     * // Cancel the trailing throttled invocation.
-     * jQuery(window).on('popstate', throttled.cancel);
-     */
-    function throttle(func, wait, options) {
-      var leading = true,
-          trailing = true;
-
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      if (isObject(options)) {
-        leading = 'leading' in options ? !!options.leading : leading;
-        trailing = 'trailing' in options ? !!options.trailing : trailing;
-      }
-      return debounce(func, wait, {
-        'leading': leading,
-        'maxWait': wait,
-        'trailing': trailing
-      });
-    }
-
-    /**
-     * Creates a function that accepts up to one argument, ignoring any
-     * additional arguments.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Function
-     * @param {Function} func The function to cap arguments for.
-     * @returns {Function} Returns the new capped function.
-     * @example
-     *
-     * _.map(['6', '8', '10'], _.unary(parseInt));
-     * // => [6, 8, 10]
-     */
-    function unary(func) {
-      return ary(func, 1);
-    }
-
-    /**
-     * Creates a function that provides `value` to `wrapper` as its first
-     * argument. Any additional arguments provided to the function are appended
-     * to those provided to the `wrapper`. The wrapper is invoked with the `this`
-     * binding of the created function.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {*} value The value to wrap.
-     * @param {Function} [wrapper=identity] The wrapper function.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var p = _.wrap(_.escape, function(func, text) {
-     *   return '<p>' + func(text) + '</p>';
-     * });
-     *
-     * p('fred, barney, & pebbles');
-     * // => '<p>fred, barney, &amp; pebbles</p>'
-     */
-    function wrap(value, wrapper) {
-      return partial(castFunction(wrapper), value);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Casts `value` as an array if it's not one.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.4.0
-     * @category Lang
-     * @param {*} value The value to inspect.
-     * @returns {Array} Returns the cast array.
-     * @example
-     *
-     * _.castArray(1);
-     * // => [1]
-     *
-     * _.castArray({ 'a': 1 });
-     * // => [{ 'a': 1 }]
-     *
-     * _.castArray('abc');
-     * // => ['abc']
-     *
-     * _.castArray(null);
-     * // => [null]
-     *
-     * _.castArray(undefined);
-     * // => [undefined]
-     *
-     * _.castArray();
-     * // => []
-     *
-     * var array = [1, 2, 3];
-     * console.log(_.castArray(array) === array);
-     * // => true
-     */
-    function castArray() {
-      if (!arguments.length) {
-        return [];
-      }
-      var value = arguments[0];
-      return isArray(value) ? value : [value];
-    }
-
-    /**
-     * Creates a shallow clone of `value`.
-     *
-     * **Note:** This method is loosely based on the
-     * [structured clone algorithm](https://mdn.io/Structured_clone_algorithm)
-     * and supports cloning arrays, array buffers, booleans, date objects, maps,
-     * numbers, `Object` objects, regexes, sets, strings, symbols, and typed
-     * arrays. The own enumerable properties of `arguments` objects are cloned
-     * as plain objects. An empty object is returned for uncloneable values such
-     * as error objects, functions, DOM nodes, and WeakMaps.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to clone.
-     * @returns {*} Returns the cloned value.
-     * @see _.cloneDeep
-     * @example
-     *
-     * var objects = [{ 'a': 1 }, { 'b': 2 }];
-     *
-     * var shallow = _.clone(objects);
-     * console.log(shallow[0] === objects[0]);
-     * // => true
-     */
-    function clone(value) {
-      return baseClone(value, CLONE_SYMBOLS_FLAG);
-    }
-
-    /**
-     * This method is like `_.clone` except that it accepts `customizer` which
-     * is invoked to produce the cloned value. If `customizer` returns `undefined`,
-     * cloning is handled by the method instead. The `customizer` is invoked with
-     * up to four arguments; (value [, index|key, object, stack]).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to clone.
-     * @param {Function} [customizer] The function to customize cloning.
-     * @returns {*} Returns the cloned value.
-     * @see _.cloneDeepWith
-     * @example
-     *
-     * function customizer(value) {
-     *   if (_.isElement(value)) {
-     *     return value.cloneNode(false);
-     *   }
-     * }
-     *
-     * var el = _.cloneWith(document.body, customizer);
-     *
-     * console.log(el === document.body);
-     * // => false
-     * console.log(el.nodeName);
-     * // => 'BODY'
-     * console.log(el.childNodes.length);
-     * // => 0
-     */
-    function cloneWith(value, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return baseClone(value, CLONE_SYMBOLS_FLAG, customizer);
-    }
-
-    /**
-     * This method is like `_.clone` except that it recursively clones `value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.0.0
-     * @category Lang
-     * @param {*} value The value to recursively clone.
-     * @returns {*} Returns the deep cloned value.
-     * @see _.clone
-     * @example
-     *
-     * var objects = [{ 'a': 1 }, { 'b': 2 }];
-     *
-     * var deep = _.cloneDeep(objects);
-     * console.log(deep[0] === objects[0]);
-     * // => false
-     */
-    function cloneDeep(value) {
-      return baseClone(value, CLONE_DEEP_FLAG | CLONE_SYMBOLS_FLAG);
-    }
-
-    /**
-     * This method is like `_.cloneWith` except that it recursively clones `value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to recursively clone.
-     * @param {Function} [customizer] The function to customize cloning.
-     * @returns {*} Returns the deep cloned value.
-     * @see _.cloneWith
-     * @example
-     *
-     * function customizer(value) {
-     *   if (_.isElement(value)) {
-     *     return value.cloneNode(true);
-     *   }
-     * }
-     *
-     * var el = _.cloneDeepWith(document.body, customizer);
-     *
-     * console.log(el === document.body);
-     * // => false
-     * console.log(el.nodeName);
-     * // => 'BODY'
-     * console.log(el.childNodes.length);
-     * // => 20
-     */
-    function cloneDeepWith(value, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return baseClone(value, CLONE_DEEP_FLAG | CLONE_SYMBOLS_FLAG, customizer);
-    }
-
-    /**
-     * Checks if `object` conforms to `source` by invoking the predicate
-     * properties of `source` with the corresponding property values of `object`.
-     *
-     * **Note:** This method is equivalent to `_.conforms` when `source` is
-     * partially applied.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.14.0
-     * @category Lang
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {boolean} Returns `true` if `object` conforms, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2 };
-     *
-     * _.conformsTo(object, { 'b': function(n) { return n > 1; } });
-     * // => true
-     *
-     * _.conformsTo(object, { 'b': function(n) { return n > 2; } });
-     * // => false
-     */
-    function conformsTo(object, source) {
-      return source == null || baseConformsTo(object, source, keys(source));
-    }
-
-    /**
-     * Performs a
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * comparison between two values to determine if they are equivalent.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1 };
-     * var other = { 'a': 1 };
-     *
-     * _.eq(object, object);
-     * // => true
-     *
-     * _.eq(object, other);
-     * // => false
-     *
-     * _.eq('a', 'a');
-     * // => true
-     *
-     * _.eq('a', Object('a'));
-     * // => false
-     *
-     * _.eq(NaN, NaN);
-     * // => true
-     */
-    function eq(value, other) {
-      return value === other || (value !== value && other !== other);
-    }
-
-    /**
-     * Checks if `value` is greater than `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is greater than `other`,
-     *  else `false`.
-     * @see _.lt
-     * @example
-     *
-     * _.gt(3, 1);
-     * // => true
-     *
-     * _.gt(3, 3);
-     * // => false
-     *
-     * _.gt(1, 3);
-     * // => false
-     */
-    var gt = createRelationalOperation(baseGt);
-
-    /**
-     * Checks if `value` is greater than or equal to `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is greater than or equal to
-     *  `other`, else `false`.
-     * @see _.lte
-     * @example
-     *
-     * _.gte(3, 1);
-     * // => true
-     *
-     * _.gte(3, 3);
-     * // => true
-     *
-     * _.gte(1, 3);
-     * // => false
-     */
-    var gte = createRelationalOperation(function(value, other) {
-      return value >= other;
-    });
-
-    /**
-     * Checks if `value` is likely an `arguments` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an `arguments` object,
-     *  else `false`.
-     * @example
-     *
-     * _.isArguments(function() { return arguments; }());
-     * // => true
-     *
-     * _.isArguments([1, 2, 3]);
-     * // => false
-     */
-    var isArguments = baseIsArguments(function() { return arguments; }()) ? baseIsArguments : function(value) {
-      return isObjectLike(value) && hasOwnProperty.call(value, 'callee') &&
-        !propertyIsEnumerable.call(value, 'callee');
-    };
-
-    /**
-     * Checks if `value` is classified as an `Array` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array, else `false`.
-     * @example
-     *
-     * _.isArray([1, 2, 3]);
-     * // => true
-     *
-     * _.isArray(document.body.children);
-     * // => false
-     *
-     * _.isArray('abc');
-     * // => false
-     *
-     * _.isArray(_.noop);
-     * // => false
-     */
-    var isArray = Array.isArray;
-
-    /**
-     * Checks if `value` is classified as an `ArrayBuffer` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array buffer, else `false`.
-     * @example
-     *
-     * _.isArrayBuffer(new ArrayBuffer(2));
-     * // => true
-     *
-     * _.isArrayBuffer(new Array(2));
-     * // => false
-     */
-    var isArrayBuffer = nodeIsArrayBuffer ? baseUnary(nodeIsArrayBuffer) : baseIsArrayBuffer;
-
-    /**
-     * Checks if `value` is array-like. A value is considered array-like if it's
-     * not a function and has a `value.length` that's an integer greater than or
-     * equal to `0` and less than or equal to `Number.MAX_SAFE_INTEGER`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is array-like, else `false`.
-     * @example
-     *
-     * _.isArrayLike([1, 2, 3]);
-     * // => true
-     *
-     * _.isArrayLike(document.body.children);
-     * // => true
-     *
-     * _.isArrayLike('abc');
-     * // => true
-     *
-     * _.isArrayLike(_.noop);
-     * // => false
-     */
-    function isArrayLike(value) {
-      return value != null && isLength(value.length) && !isFunction(value);
-    }
-
-    /**
-     * This method is like `_.isArrayLike` except that it also checks if `value`
-     * is an object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array-like object,
-     *  else `false`.
-     * @example
-     *
-     * _.isArrayLikeObject([1, 2, 3]);
-     * // => true
-     *
-     * _.isArrayLikeObject(document.body.children);
-     * // => true
-     *
-     * _.isArrayLikeObject('abc');
-     * // => false
-     *
-     * _.isArrayLikeObject(_.noop);
-     * // => false
-     */
-    function isArrayLikeObject(value) {
-      return isObjectLike(value) && isArrayLike(value);
-    }
-
-    /**
-     * Checks if `value` is classified as a boolean primitive or object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a boolean, else `false`.
-     * @example
-     *
-     * _.isBoolean(false);
-     * // => true
-     *
-     * _.isBoolean(null);
-     * // => false
-     */
-    function isBoolean(value) {
-      return value === true || value === false ||
-        (isObjectLike(value) && baseGetTag(value) == boolTag);
-    }
-
-    /**
-     * Checks if `value` is a buffer.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a buffer, else `false`.
-     * @example
-     *
-     * _.isBuffer(new Buffer(2));
-     * // => true
-     *
-     * _.isBuffer(new Uint8Array(2));
-     * // => false
-     */
-    var isBuffer = nativeIsBuffer || stubFalse;
-
-    /**
-     * Checks if `value` is classified as a `Date` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a date object, else `false`.
-     * @example
-     *
-     * _.isDate(new Date);
-     * // => true
-     *
-     * _.isDate('Mon April 23 2012');
-     * // => false
-     */
-    var isDate = nodeIsDate ? baseUnary(nodeIsDate) : baseIsDate;
-
-    /**
-     * Checks if `value` is likely a DOM element.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a DOM element, else `false`.
-     * @example
-     *
-     * _.isElement(document.body);
-     * // => true
-     *
-     * _.isElement('<body>');
-     * // => false
-     */
-    function isElement(value) {
-      return isObjectLike(value) && value.nodeType === 1 && !isPlainObject(value);
-    }
-
-    /**
-     * Checks if `value` is an empty object, collection, map, or set.
-     *
-     * Objects are considered empty if they have no own enumerable string keyed
-     * properties.
-     *
-     * Array-like values such as `arguments` objects, arrays, buffers, strings, or
-     * jQuery-like collections are considered empty if they have a `length` of `0`.
-     * Similarly, maps and sets are considered empty if they have a `size` of `0`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is empty, else `false`.
-     * @example
-     *
-     * _.isEmpty(null);
-     * // => true
-     *
-     * _.isEmpty(true);
-     * // => true
-     *
-     * _.isEmpty(1);
-     * // => true
-     *
-     * _.isEmpty([1, 2, 3]);
-     * // => false
-     *
-     * _.isEmpty({ 'a': 1 });
-     * // => false
-     */
-    function isEmpty(value) {
-      if (value == null) {
-        return true;
-      }
-      if (isArrayLike(value) &&
-          (isArray(value) || typeof value == 'string' || typeof value.splice == 'function' ||
-            isBuffer(value) || isTypedArray(value) || isArguments(value))) {
-        return !value.length;
-      }
-      var tag = getTag(value);
-      if (tag == mapTag || tag == setTag) {
-        return !value.size;
-      }
-      if (isPrototype(value)) {
-        return !baseKeys(value).length;
-      }
-      for (var key in value) {
-        if (hasOwnProperty.call(value, key)) {
-          return false;
-        }
-      }
-      return true;
-    }
-
-    /**
-     * Performs a deep comparison between two values to determine if they are
-     * equivalent.
-     *
-     * **Note:** This method supports comparing arrays, array buffers, booleans,
-     * date objects, error objects, maps, numbers, `Object` objects, regexes,
-     * sets, strings, symbols, and typed arrays. `Object` objects are compared
-     * by their own, not inherited, enumerable properties. Functions and DOM
-     * nodes are compared by strict equality, i.e. `===`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1 };
-     * var other = { 'a': 1 };
-     *
-     * _.isEqual(object, other);
-     * // => true
-     *
-     * object === other;
-     * // => false
-     */
-    function isEqual(value, other) {
-      return baseIsEqual(value, other);
-    }
-
-    /**
-     * This method is like `_.isEqual` except that it accepts `customizer` which
-     * is invoked to compare values. If `customizer` returns `undefined`, comparisons
-     * are handled by the method instead. The `customizer` is invoked with up to
-     * six arguments: (objValue, othValue [, index|key, object, other, stack]).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     * @example
-     *
-     * function isGreeting(value) {
-     *   return /^h(?:i|ello)$/.test(value);
-     * }
-     *
-     * function customizer(objValue, othValue) {
-     *   if (isGreeting(objValue) && isGreeting(othValue)) {
-     *     return true;
-     *   }
-     * }
-     *
-     * var array = ['hello', 'goodbye'];
-     * var other = ['hi', 'goodbye'];
-     *
-     * _.isEqualWith(array, other, customizer);
-     * // => true
-     */
-    function isEqualWith(value, other, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      var result = customizer ? customizer(value, other) : undefined;
-      return result === undefined ? baseIsEqual(value, other, undefined, customizer) : !!result;
-    }
-
-    /**
-     * Checks if `value` is an `Error`, `EvalError`, `RangeError`, `ReferenceError`,
-     * `SyntaxError`, `TypeError`, or `URIError` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an error object, else `false`.
-     * @example
-     *
-     * _.isError(new Error);
-     * // => true
-     *
-     * _.isError(Error);
-     * // => false
-     */
-    function isError(value) {
-      if (!isObjectLike(value)) {
-        return false;
-      }
-      var tag = baseGetTag(value);
-      return tag == errorTag || tag == domExcTag ||
-        (typeof value.message == 'string' && typeof value.name == 'string' && !isPlainObject(value));
-    }
-
-    /**
-     * Checks if `value` is a finite primitive number.
-     *
-     * **Note:** This method is based on
-     * [`Number.isFinite`](https://mdn.io/Number/isFinite).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a finite number, else `false`.
-     * @example
-     *
-     * _.isFinite(3);
-     * // => true
-     *
-     * _.isFinite(Number.MIN_VALUE);
-     * // => true
-     *
-     * _.isFinite(Infinity);
-     * // => false
-     *
-     * _.isFinite('3');
-     * // => false
-     */
-    function isFinite(value) {
-      return typeof value == 'number' && nativeIsFinite(value);
-    }
-
-    /**
-     * Checks if `value` is classified as a `Function` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a function, else `false`.
-     * @example
-     *
-     * _.isFunction(_);
-     * // => true
-     *
-     * _.isFunction(/abc/);
-     * // => false
-     */
-    function isFunction(value) {
-      if (!isObject(value)) {
-        return false;
-      }
-      // The use of `Object#toString` avoids issues with the `typeof` operator
-      // in Safari 9 which returns 'object' for typed arrays and other constructors.
-      var tag = baseGetTag(value);
-      return tag == funcTag || tag == genTag || tag == asyncTag || tag == proxyTag;
-    }
-
-    /**
-     * Checks if `value` is an integer.
-     *
-     * **Note:** This method is based on
-     * [`Number.isInteger`](https://mdn.io/Number/isInteger).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an integer, else `false`.
-     * @example
-     *
-     * _.isInteger(3);
-     * // => true
-     *
-     * _.isInteger(Number.MIN_VALUE);
-     * // => false
-     *
-     * _.isInteger(Infinity);
-     * // => false
-     *
-     * _.isInteger('3');
-     * // => false
-     */
-    function isInteger(value) {
-      return typeof value == 'number' && value == toInteger(value);
-    }
-
-    /**
-     * Checks if `value` is a valid array-like length.
-     *
-     * **Note:** This method is loosely based on
-     * [`ToLength`](http://ecma-international.org/ecma-262/7.0/#sec-tolength).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a valid length, else `false`.
-     * @example
-     *
-     * _.isLength(3);
-     * // => true
-     *
-     * _.isLength(Number.MIN_VALUE);
-     * // => false
-     *
-     * _.isLength(Infinity);
-     * // => false
-     *
-     * _.isLength('3');
-     * // => false
-     */
-    function isLength(value) {
-      return typeof value == 'number' &&
-        value > -1 && value % 1 == 0 && value <= MAX_SAFE_INTEGER;
-    }
-
-    /**
-     * Checks if `value` is the
-     * [language type](http://www.ecma-international.org/ecma-262/7.0/#sec-ecmascript-language-types)
-     * of `Object`. (e.g. arrays, functions, objects, regexes, `new Number(0)`, and `new String('')`)
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an object, else `false`.
-     * @example
-     *
-     * _.isObject({});
-     * // => true
-     *
-     * _.isObject([1, 2, 3]);
-     * // => true
-     *
-     * _.isObject(_.noop);
-     * // => true
-     *
-     * _.isObject(null);
-     * // => false
-     */
-    function isObject(value) {
-      var type = typeof value;
-      return value != null && (type == 'object' || type == 'function');
-    }
-
-    /**
-     * Checks if `value` is object-like. A value is object-like if it's not `null`
-     * and has a `typeof` result of "object".
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is object-like, else `false`.
-     * @example
-     *
-     * _.isObjectLike({});
-     * // => true
-     *
-     * _.isObjectLike([1, 2, 3]);
-     * // => true
-     *
-     * _.isObjectLike(_.noop);
-     * // => false
-     *
-     * _.isObjectLike(null);
-     * // => false
-     */
-    function isObjectLike(value) {
-      return value != null && typeof value == 'object';
-    }
-
-    /**
-     * Checks if `value` is classified as a `Map` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a map, else `false`.
-     * @example
-     *
-     * _.isMap(new Map);
-     * // => true
-     *
-     * _.isMap(new WeakMap);
-     * // => false
-     */
-    var isMap = nodeIsMap ? baseUnary(nodeIsMap) : baseIsMap;
-
-    /**
-     * Performs a partial deep comparison between `object` and `source` to
-     * determine if `object` contains equivalent property values.
-     *
-     * **Note:** This method is equivalent to `_.matches` when `source` is
-     * partially applied.
-     *
-     * Partial comparisons will match empty array and empty object `source`
-     * values against any array or object value, respectively. See `_.isEqual`
-     * for a list of supported value comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property values to match.
-     * @returns {boolean} Returns `true` if `object` is a match, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2 };
-     *
-     * _.isMatch(object, { 'b': 2 });
-     * // => true
-     *
-     * _.isMatch(object, { 'b': 1 });
-     * // => false
-     */
-    function isMatch(object, source) {
-      return object === source || baseIsMatch(object, source, getMatchData(source));
-    }
-
-    /**
-     * This method is like `_.isMatch` except that it accepts `customizer` which
-     * is invoked to compare values. If `customizer` returns `undefined`, comparisons
-     * are handled by the method instead. The `customizer` is invoked with five
-     * arguments: (objValue, srcValue, index|key, object, source).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property values to match.
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @returns {boolean} Returns `true` if `object` is a match, else `false`.
-     * @example
-     *
-     * function isGreeting(value) {
-     *   return /^h(?:i|ello)$/.test(value);
-     * }
-     *
-     * function customizer(objValue, srcValue) {
-     *   if (isGreeting(objValue) && isGreeting(srcValue)) {
-     *     return true;
-     *   }
-     * }
-     *
-     * var object = { 'greeting': 'hello' };
-     * var source = { 'greeting': 'hi' };
-     *
-     * _.isMatchWith(object, source, customizer);
-     * // => true
-     */
-    function isMatchWith(object, source, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return baseIsMatch(object, source, getMatchData(source), customizer);
-    }
-
-    /**
-     * Checks if `value` is `NaN`.
-     *
-     * **Note:** This method is based on
-     * [`Number.isNaN`](https://mdn.io/Number/isNaN) and is not the same as
-     * global [`isNaN`](https://mdn.io/isNaN) which returns `true` for
-     * `undefined` and other non-number values.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is `NaN`, else `false`.
-     * @example
-     *
-     * _.isNaN(NaN);
-     * // => true
-     *
-     * _.isNaN(new Number(NaN));
-     * // => true
-     *
-     * isNaN(undefined);
-     * // => true
-     *
-     * _.isNaN(undefined);
-     * // => false
-     */
-    function isNaN(value) {
-      // An `NaN` primitive is the only value that is not equal to itself.
-      // Perform the `toStringTag` check first to avoid errors with some
-      // ActiveX objects in IE.
-      return isNumber(value) && value != +value;
-    }
-
-    /**
-     * Checks if `value` is a pristine native function.
-     *
-     * **Note:** This method can't reliably detect native functions in the presence
-     * of the core-js package because core-js circumvents this kind of detection.
-     * Despite multiple requests, the core-js maintainer has made it clear: any
-     * attempt to fix the detection will be obstructed. As a result, we're left
-     * with little choice but to throw an error. Unfortunately, this also affects
-     * packages, like [babel-polyfill](https://www.npmjs.com/package/babel-polyfill),
-     * which rely on core-js.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a native function,
-     *  else `false`.
-     * @example
-     *
-     * _.isNative(Array.prototype.push);
-     * // => true
-     *
-     * _.isNative(_);
-     * // => false
-     */
-    function isNative(value) {
-      if (isMaskable(value)) {
-        throw new Error(CORE_ERROR_TEXT);
-      }
-      return baseIsNative(value);
-    }
-
-    /**
-     * Checks if `value` is `null`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is `null`, else `false`.
-     * @example
-     *
-     * _.isNull(null);
-     * // => true
-     *
-     * _.isNull(void 0);
-     * // => false
-     */
-    function isNull(value) {
-      return value === null;
-    }
-
-    /**
-     * Checks if `value` is `null` or `undefined`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is nullish, else `false`.
-     * @example
-     *
-     * _.isNil(null);
-     * // => true
-     *
-     * _.isNil(void 0);
-     * // => true
-     *
-     * _.isNil(NaN);
-     * // => false
-     */
-    function isNil(value) {
-      return value == null;
-    }
-
-    /**
-     * Checks if `value` is classified as a `Number` primitive or object.
-     *
-     * **Note:** To exclude `Infinity`, `-Infinity`, and `NaN`, which are
-     * classified as numbers, use the `_.isFinite` method.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a number, else `false`.
-     * @example
-     *
-     * _.isNumber(3);
-     * // => true
-     *
-     * _.isNumber(Number.MIN_VALUE);
-     * // => true
-     *
-     * _.isNumber(Infinity);
-     * // => true
-     *
-     * _.isNumber('3');
-     * // => false
-     */
-    function isNumber(value) {
-      return typeof value == 'number' ||
-        (isObjectLike(value) && baseGetTag(value) == numberTag);
-    }
-
-    /**
-     * Checks if `value` is a plain object, that is, an object created by the
-     * `Object` constructor or one with a `[[Prototype]]` of `null`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.8.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a plain object, else `false`.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     * }
-     *
-     * _.isPlainObject(new Foo);
-     * // => false
-     *
-     * _.isPlainObject([1, 2, 3]);
-     * // => false
-     *
-     * _.isPlainObject({ 'x': 0, 'y': 0 });
-     * // => true
-     *
-     * _.isPlainObject(Object.create(null));
-     * // => true
-     */
-    function isPlainObject(value) {
-      if (!isObjectLike(value) || baseGetTag(value) != objectTag) {
-        return false;
-      }
-      var proto = getPrototype(value);
-      if (proto === null) {
-        return true;
-      }
-      var Ctor = hasOwnProperty.call(proto, 'constructor') && proto.constructor;
-      return typeof Ctor == 'function' && Ctor instanceof Ctor &&
-        funcToString.call(Ctor) == objectCtorString;
-    }
-
-    /**
-     * Checks if `value` is classified as a `RegExp` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a regexp, else `false`.
-     * @example
-     *
-     * _.isRegExp(/abc/);
-     * // => true
-     *
-     * _.isRegExp('/abc/');
-     * // => false
-     */
-    var isRegExp = nodeIsRegExp ? baseUnary(nodeIsRegExp) : baseIsRegExp;
-
-    /**
-     * Checks if `value` is a safe integer. An integer is safe if it's an IEEE-754
-     * double precision number which isn't the result of a rounded unsafe integer.
-     *
-     * **Note:** This method is based on
-     * [`Number.isSafeInteger`](https://mdn.io/Number/isSafeInteger).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a safe integer, else `false`.
-     * @example
-     *
-     * _.isSafeInteger(3);
-     * // => true
-     *
-     * _.isSafeInteger(Number.MIN_VALUE);
-     * // => false
-     *
-     * _.isSafeInteger(Infinity);
-     * // => false
-     *
-     * _.isSafeInteger('3');
-     * // => false
-     */
-    function isSafeInteger(value) {
-      return isInteger(value) && value >= -MAX_SAFE_INTEGER && value <= MAX_SAFE_INTEGER;
-    }
-
-    /**
-     * Checks if `value` is classified as a `Set` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a set, else `false`.
-     * @example
-     *
-     * _.isSet(new Set);
-     * // => true
-     *
-     * _.isSet(new WeakSet);
-     * // => false
-     */
-    var isSet = nodeIsSet ? baseUnary(nodeIsSet) : baseIsSet;
-
-    /**
-     * Checks if `value` is classified as a `String` primitive or object.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a string, else `false`.
-     * @example
-     *
-     * _.isString('abc');
-     * // => true
-     *
-     * _.isString(1);
-     * // => false
-     */
-    function isString(value) {
-      return typeof value == 'string' ||
-        (!isArray(value) && isObjectLike(value) && baseGetTag(value) == stringTag);
-    }
-
-    /**
-     * Checks if `value` is classified as a `Symbol` primitive or object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a symbol, else `false`.
-     * @example
-     *
-     * _.isSymbol(Symbol.iterator);
-     * // => true
-     *
-     * _.isSymbol('abc');
-     * // => false
-     */
-    function isSymbol(value) {
-      return typeof value == 'symbol' ||
-        (isObjectLike(value) && baseGetTag(value) == symbolTag);
-    }
-
-    /**
-     * Checks if `value` is classified as a typed array.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a typed array, else `false`.
-     * @example
-     *
-     * _.isTypedArray(new Uint8Array);
-     * // => true
-     *
-     * _.isTypedArray([]);
-     * // => false
-     */
-    var isTypedArray = nodeIsTypedArray ? baseUnary(nodeIsTypedArray) : baseIsTypedArray;
-
-    /**
-     * Checks if `value` is `undefined`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is `undefined`, else `false`.
-     * @example
-     *
-     * _.isUndefined(void 0);
-     * // => true
-     *
-     * _.isUndefined(null);
-     * // => false
-     */
-    function isUndefined(value) {
-      return value === undefined;
-    }
-
-    /**
-     * Checks if `value` is classified as a `WeakMap` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a weak map, else `false`.
-     * @example
-     *
-     * _.isWeakMap(new WeakMap);
-     * // => true
-     *
-     * _.isWeakMap(new Map);
-     * // => false
-     */
-    function isWeakMap(value) {
-      return isObjectLike(value) && getTag(value) == weakMapTag;
-    }
-
-    /**
-     * Checks if `value` is classified as a `WeakSet` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a weak set, else `false`.
-     * @example
-     *
-     * _.isWeakSet(new WeakSet);
-     * // => true
-     *
-     * _.isWeakSet(new Set);
-     * // => false
-     */
-    function isWeakSet(value) {
-      return isObjectLike(value) && baseGetTag(value) == weakSetTag;
-    }
-
-    /**
-     * Checks if `value` is less than `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is less than `other`,
-     *  else `false`.
-     * @see _.gt
-     * @example
-     *
-     * _.lt(1, 3);
-     * // => true
-     *
-     * _.lt(3, 3);
-     * // => false
-     *
-     * _.lt(3, 1);
-     * // => false
-     */
-    var lt = createRelationalOperation(baseLt);
-
-    /**
-     * Checks if `value` is less than or equal to `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is less than or equal to
-     *  `other`, else `false`.
-     * @see _.gte
-     * @example
-     *
-     * _.lte(1, 3);
-     * // => true
-     *
-     * _.lte(3, 3);
-     * // => true
-     *
-     * _.lte(3, 1);
-     * // => false
-     */
-    var lte = createRelationalOperation(function(value, other) {
-      return value <= other;
-    });
-
-    /**
-     * Converts `value` to an array.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {Array} Returns the converted array.
-     * @example
-     *
-     * _.toArray({ 'a': 1, 'b': 2 });
-     * // => [1, 2]
-     *
-     * _.toArray('abc');
-     * // => ['a', 'b', 'c']
-     *
-     * _.toArray(1);
-     * // => []
-     *
-     * _.toArray(null);
-     * // => []
-     */
-    function toArray(value) {
-      if (!value) {
-        return [];
-      }
-      if (isArrayLike(value)) {
-        return isString(value) ? stringToArray(value) : copyArray(value);
-      }
-      if (symIterator && value[symIterator]) {
-        return iteratorToArray(value[symIterator]());
-      }
-      var tag = getTag(value),
-          func = tag == mapTag ? mapToArray : (tag == setTag ? setToArray : values);
-
-      return func(value);
-    }
-
-    /**
-     * Converts `value` to a finite number.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.12.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted number.
-     * @example
-     *
-     * _.toFinite(3.2);
-     * // => 3.2
-     *
-     * _.toFinite(Number.MIN_VALUE);
-     * // => 5e-324
-     *
-     * _.toFinite(Infinity);
-     * // => 1.7976931348623157e+308
-     *
-     * _.toFinite('3.2');
-     * // => 3.2
-     */
-    function toFinite(value) {
-      if (!value) {
-        return value === 0 ? value : 0;
-      }
-      value = toNumber(value);
-      if (value === INFINITY || value === -INFINITY) {
-        var sign = (value < 0 ? -1 : 1);
-        return sign * MAX_INTEGER;
-      }
-      return value === value ? value : 0;
-    }
-
-    /**
-     * Converts `value` to an integer.
-     *
-     * **Note:** This method is loosely based on
-     * [`ToInteger`](http://www.ecma-international.org/ecma-262/7.0/#sec-tointeger).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.toInteger(3.2);
-     * // => 3
-     *
-     * _.toInteger(Number.MIN_VALUE);
-     * // => 0
-     *
-     * _.toInteger(Infinity);
-     * // => 1.7976931348623157e+308
-     *
-     * _.toInteger('3.2');
-     * // => 3
-     */
-    function toInteger(value) {
-      var result = toFinite(value),
-          remainder = result % 1;
-
-      return result === result ? (remainder ? result - remainder : result) : 0;
-    }
-
-    /**
-     * Converts `value` to an integer suitable for use as the length of an
-     * array-like object.
-     *
-     * **Note:** This method is based on
-     * [`ToLength`](http://ecma-international.org/ecma-262/7.0/#sec-tolength).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.toLength(3.2);
-     * // => 3
-     *
-     * _.toLength(Number.MIN_VALUE);
-     * // => 0
-     *
-     * _.toLength(Infinity);
-     * // => 4294967295
-     *
-     * _.toLength('3.2');
-     * // => 3
-     */
-    function toLength(value) {
-      return value ? baseClamp(toInteger(value), 0, MAX_ARRAY_LENGTH) : 0;
-    }
-
-    /**
-     * Converts `value` to a number.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to process.
-     * @returns {number} Returns the number.
-     * @example
-     *
-     * _.toNumber(3.2);
-     * // => 3.2
-     *
-     * _.toNumber(Number.MIN_VALUE);
-     * // => 5e-324
-     *
-     * _.toNumber(Infinity);
-     * // => Infinity
-     *
-     * _.toNumber('3.2');
-     * // => 3.2
-     */
-    function toNumber(value) {
-      if (typeof value == 'number') {
-        return value;
-      }
-      if (isSymbol(value)) {
-        return NAN;
-      }
-      if (isObject(value)) {
-        var other = typeof value.valueOf == 'function' ? value.valueOf() : value;
-        value = isObject(other) ? (other + '') : other;
-      }
-      if (typeof value != 'string') {
-        return value === 0 ? value : +value;
-      }
-      value = value.replace(reTrim, '');
-      var isBinary = reIsBinary.test(value);
-      return (isBinary || reIsOctal.test(value))
-        ? freeParseInt(value.slice(2), isBinary ? 2 : 8)
-        : (reIsBadHex.test(value) ? NAN : +value);
-    }
-
-    /**
-     * Converts `value` to a plain object flattening inherited enumerable string
-     * keyed properties of `value` to own properties of the plain object.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {Object} Returns the converted plain object.
-     * @example
-     *
-     * function Foo() {
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.assign({ 'a': 1 }, new Foo);
-     * // => { 'a': 1, 'b': 2 }
-     *
-     * _.assign({ 'a': 1 }, _.toPlainObject(new Foo));
-     * // => { 'a': 1, 'b': 2, 'c': 3 }
-     */
-    function toPlainObject(value) {
-      return copyObject(value, keysIn(value));
-    }
-
-    /**
-     * Converts `value` to a safe integer. A safe integer can be compared and
-     * represented correctly.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.toSafeInteger(3.2);
-     * // => 3
-     *
-     * _.toSafeInteger(Number.MIN_VALUE);
-     * // => 0
-     *
-     * _.toSafeInteger(Infinity);
-     * // => 9007199254740991
-     *
-     * _.toSafeInteger('3.2');
-     * // => 3
-     */
-    function toSafeInteger(value) {
-      return value
-        ? baseClamp(toInteger(value), -MAX_SAFE_INTEGER, MAX_SAFE_INTEGER)
-        : (value === 0 ? value : 0);
-    }
-
-    /**
-     * Converts `value` to a string. An empty string is returned for `null`
-     * and `undefined` values. The sign of `-0` is preserved.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {string} Returns the converted string.
-     * @example
-     *
-     * _.toString(null);
-     * // => ''
-     *
-     * _.toString(-0);
-     * // => '-0'
-     *
-     * _.toString([1, 2, 3]);
-     * // => '1,2,3'
-     */
-    function toString(value) {
-      return value == null ? '' : baseToString(value);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Assigns own enumerable string keyed properties of source objects to the
-     * destination object. Source objects are applied from left to right.
-     * Subsequent sources overwrite property assignments of previous sources.
-     *
-     * **Note:** This method mutates `object` and is loosely based on
-     * [`Object.assign`](https://mdn.io/Object/assign).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.10.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.assignIn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     * }
-     *
-     * function Bar() {
-     *   this.c = 3;
-     * }
-     *
-     * Foo.prototype.b = 2;
-     * Bar.prototype.d = 4;
-     *
-     * _.assign({ 'a': 0 }, new Foo, new Bar);
-     * // => { 'a': 1, 'c': 3 }
-     */
-    var assign = createAssigner(function(object, source) {
-      if (isPrototype(source) || isArrayLike(source)) {
-        copyObject(source, keys(source), object);
-        return;
-      }
-      for (var key in source) {
-        if (hasOwnProperty.call(source, key)) {
-          assignValue(object, key, source[key]);
-        }
-      }
-    });
-
-    /**
-     * This method is like `_.assign` except that it iterates over own and
-     * inherited source properties.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias extend
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.assign
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     * }
-     *
-     * function Bar() {
-     *   this.c = 3;
-     * }
-     *
-     * Foo.prototype.b = 2;
-     * Bar.prototype.d = 4;
-     *
-     * _.assignIn({ 'a': 0 }, new Foo, new Bar);
-     * // => { 'a': 1, 'b': 2, 'c': 3, 'd': 4 }
-     */
-    var assignIn = createAssigner(function(object, source) {
-      copyObject(source, keysIn(source), object);
-    });
-
-    /**
-     * This method is like `_.assignIn` except that it accepts `customizer`
-     * which is invoked to produce the assigned values. If `customizer` returns
-     * `undefined`, assignment is handled by the method instead. The `customizer`
-     * is invoked with five arguments: (objValue, srcValue, key, object, source).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias extendWith
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} sources The source objects.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @see _.assignWith
-     * @example
-     *
-     * function customizer(objValue, srcValue) {
-     *   return _.isUndefined(objValue) ? srcValue : objValue;
-     * }
-     *
-     * var defaults = _.partialRight(_.assignInWith, customizer);
-     *
-     * defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 });
-     * // => { 'a': 1, 'b': 2 }
-     */
-    var assignInWith = createAssigner(function(object, source, srcIndex, customizer) {
-      copyObject(source, keysIn(source), object, customizer);
-    });
-
-    /**
-     * This method is like `_.assign` except that it accepts `customizer`
-     * which is invoked to produce the assigned values. If `customizer` returns
-     * `undefined`, assignment is handled by the method instead. The `customizer`
-     * is invoked with five arguments: (objValue, srcValue, key, object, source).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} sources The source objects.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @see _.assignInWith
-     * @example
-     *
-     * function customizer(objValue, srcValue) {
-     *   return _.isUndefined(objValue) ? srcValue : objValue;
-     * }
-     *
-     * var defaults = _.partialRight(_.assignWith, customizer);
-     *
-     * defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 });
-     * // => { 'a': 1, 'b': 2 }
-     */
-    var assignWith = createAssigner(function(object, source, srcIndex, customizer) {
-      copyObject(source, keys(source), object, customizer);
-    });
-
-    /**
-     * Creates an array of values corresponding to `paths` of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.0.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {...(string|string[])} [paths] The property paths to pick.
-     * @returns {Array} Returns the picked values.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }, 4] };
-     *
-     * _.at(object, ['a[0].b.c', 'a[1]']);
-     * // => [3, 4]
-     */
-    var at = flatRest(baseAt);
-
-    /**
-     * Creates an object that inherits from the `prototype` object. If a
-     * `properties` object is given, its own enumerable string keyed properties
-     * are assigned to the created object.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.3.0
-     * @category Object
-     * @param {Object} prototype The object to inherit from.
-     * @param {Object} [properties] The properties to assign to the object.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * function Shape() {
-     *   this.x = 0;
-     *   this.y = 0;
-     * }
-     *
-     * function Circle() {
-     *   Shape.call(this);
-     * }
-     *
-     * Circle.prototype = _.create(Shape.prototype, {
-     *   'constructor': Circle
-     * });
-     *
-     * var circle = new Circle;
-     * circle instanceof Circle;
-     * // => true
-     *
-     * circle instanceof Shape;
-     * // => true
-     */
-    function create(prototype, properties) {
-      var result = baseCreate(prototype);
-      return properties == null ? result : baseAssign(result, properties);
-    }
-
-    /**
-     * Assigns own and inherited enumerable string keyed properties of source
-     * objects to the destination object for all destination properties that
-     * resolve to `undefined`. Source objects are applied from left to right.
-     * Once a property is set, additional values of the same property are ignored.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.defaultsDeep
-     * @example
-     *
-     * _.defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 });
-     * // => { 'a': 1, 'b': 2 }
-     */
-    var defaults = baseRest(function(object, sources) {
-      object = Object(object);
-
-      var index = -1;
-      var length = sources.length;
-      var guard = length > 2 ? sources[2] : undefined;
-
-      if (guard && isIterateeCall(sources[0], sources[1], guard)) {
-        length = 1;
-      }
-
-      while (++index < length) {
-        var source = sources[index];
-        var props = keysIn(source);
-        var propsIndex = -1;
-        var propsLength = props.length;
-
-        while (++propsIndex < propsLength) {
-          var key = props[propsIndex];
-          var value = object[key];
-
-          if (value === undefined ||
-              (eq(value, objectProto[key]) && !hasOwnProperty.call(object, key))) {
-            object[key] = source[key];
-          }
-        }
-      }
-
-      return object;
-    });
-
-    /**
-     * This method is like `_.defaults` except that it recursively assigns
-     * default properties.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.defaults
-     * @example
-     *
-     * _.defaultsDeep({ 'a': { 'b': 2 } }, { 'a': { 'b': 1, 'c': 3 } });
-     * // => { 'a': { 'b': 2, 'c': 3 } }
-     */
-    var defaultsDeep = baseRest(function(args) {
-      args.push(undefined, customDefaultsMerge);
-      return apply(mergeWith, undefined, args);
-    });
-
-    /**
-     * This method is like `_.find` except that it returns the key of the first
-     * element `predicate` returns truthy for instead of the element itself.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.1.0
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {string|undefined} Returns the key of the matched element,
-     *  else `undefined`.
-     * @example
-     *
-     * var users = {
-     *   'barney':  { 'age': 36, 'active': true },
-     *   'fred':    { 'age': 40, 'active': false },
-     *   'pebbles': { 'age': 1,  'active': true }
-     * };
-     *
-     * _.findKey(users, function(o) { return o.age < 40; });
-     * // => 'barney' (iteration order is not guaranteed)
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findKey(users, { 'age': 1, 'active': true });
-     * // => 'pebbles'
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findKey(users, ['active', false]);
-     * // => 'fred'
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findKey(users, 'active');
-     * // => 'barney'
-     */
-    function findKey(object, predicate) {
-      return baseFindKey(object, getIteratee(predicate, 3), baseForOwn);
-    }
-
-    /**
-     * This method is like `_.findKey` except that it iterates over elements of
-     * a collection in the opposite order.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {string|undefined} Returns the key of the matched element,
-     *  else `undefined`.
-     * @example
-     *
-     * var users = {
-     *   'barney':  { 'age': 36, 'active': true },
-     *   'fred':    { 'age': 40, 'active': false },
-     *   'pebbles': { 'age': 1,  'active': true }
-     * };
-     *
-     * _.findLastKey(users, function(o) { return o.age < 40; });
-     * // => returns 'pebbles' assuming `_.findKey` returns 'barney'
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findLastKey(users, { 'age': 36, 'active': true });
-     * // => 'barney'
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findLastKey(users, ['active', false]);
-     * // => 'fred'
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findLastKey(users, 'active');
-     * // => 'pebbles'
-     */
-    function findLastKey(object, predicate) {
-      return baseFindKey(object, getIteratee(predicate, 3), baseForOwnRight);
-    }
-
-    /**
-     * Iterates over own and inherited enumerable string keyed properties of an
-     * object and invokes `iteratee` for each property. The iteratee is invoked
-     * with three arguments: (value, key, object). Iteratee functions may exit
-     * iteration early by explicitly returning `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.3.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forInRight
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forIn(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'a', 'b', then 'c' (iteration order is not guaranteed).
-     */
-    function forIn(object, iteratee) {
-      return object == null
-        ? object
-        : baseFor(object, getIteratee(iteratee, 3), keysIn);
-    }
-
-    /**
-     * This method is like `_.forIn` except that it iterates over properties of
-     * `object` in the opposite order.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forIn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forInRight(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'c', 'b', then 'a' assuming `_.forIn` logs 'a', 'b', then 'c'.
-     */
-    function forInRight(object, iteratee) {
-      return object == null
-        ? object
-        : baseForRight(object, getIteratee(iteratee, 3), keysIn);
-    }
-
-    /**
-     * Iterates over own enumerable string keyed properties of an object and
-     * invokes `iteratee` for each property. The iteratee is invoked with three
-     * arguments: (value, key, object). Iteratee functions may exit iteration
-     * early by explicitly returning `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.3.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forOwnRight
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forOwn(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'a' then 'b' (iteration order is not guaranteed).
-     */
-    function forOwn(object, iteratee) {
-      return object && baseForOwn(object, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * This method is like `_.forOwn` except that it iterates over properties of
-     * `object` in the opposite order.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forOwn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forOwnRight(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'b' then 'a' assuming `_.forOwn` logs 'a' then 'b'.
-     */
-    function forOwnRight(object, iteratee) {
-      return object && baseForOwnRight(object, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * Creates an array of function property names from own enumerable properties
-     * of `object`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @returns {Array} Returns the function names.
-     * @see _.functionsIn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = _.constant('a');
-     *   this.b = _.constant('b');
-     * }
-     *
-     * Foo.prototype.c = _.constant('c');
-     *
-     * _.functions(new Foo);
-     * // => ['a', 'b']
-     */
-    function functions(object) {
-      return object == null ? [] : baseFunctions(object, keys(object));
-    }
-
-    /**
-     * Creates an array of function property names from own and inherited
-     * enumerable properties of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @returns {Array} Returns the function names.
-     * @see _.functions
-     * @example
-     *
-     * function Foo() {
-     *   this.a = _.constant('a');
-     *   this.b = _.constant('b');
-     * }
-     *
-     * Foo.prototype.c = _.constant('c');
-     *
-     * _.functionsIn(new Foo);
-     * // => ['a', 'b', 'c']
-     */
-    function functionsIn(object) {
-      return object == null ? [] : baseFunctions(object, keysIn(object));
-    }
-
-    /**
-     * Gets the value at `path` of `object`. If the resolved value is
-     * `undefined`, the `defaultValue` is returned in its place.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the property to get.
-     * @param {*} [defaultValue] The value returned for `undefined` resolved values.
-     * @returns {*} Returns the resolved value.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }] };
-     *
-     * _.get(object, 'a[0].b.c');
-     * // => 3
-     *
-     * _.get(object, ['a', '0', 'b', 'c']);
-     * // => 3
-     *
-     * _.get(object, 'a.b.c', 'default');
-     * // => 'default'
-     */
-    function get(object, path, defaultValue) {
-      var result = object == null ? undefined : baseGet(object, path);
-      return result === undefined ? defaultValue : result;
-    }
-
-    /**
-     * Checks if `path` is a direct property of `object`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path to check.
-     * @returns {boolean} Returns `true` if `path` exists, else `false`.
-     * @example
-     *
-     * var object = { 'a': { 'b': 2 } };
-     * var other = _.create({ 'a': _.create({ 'b': 2 }) });
-     *
-     * _.has(object, 'a');
-     * // => true
-     *
-     * _.has(object, 'a.b');
-     * // => true
-     *
-     * _.has(object, ['a', 'b']);
-     * // => true
-     *
-     * _.has(other, 'a');
-     * // => false
-     */
-    function has(object, path) {
-      return object != null && hasPath(object, path, baseHas);
-    }
-
-    /**
-     * Checks if `path` is a direct or inherited property of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path to check.
-     * @returns {boolean} Returns `true` if `path` exists, else `false`.
-     * @example
-     *
-     * var object = _.create({ 'a': _.create({ 'b': 2 }) });
-     *
-     * _.hasIn(object, 'a');
-     * // => true
-     *
-     * _.hasIn(object, 'a.b');
-     * // => true
-     *
-     * _.hasIn(object, ['a', 'b']);
-     * // => true
-     *
-     * _.hasIn(object, 'b');
-     * // => false
-     */
-    function hasIn(object, path) {
-      return object != null && hasPath(object, path, baseHasIn);
-    }
-
-    /**
-     * Creates an object composed of the inverted keys and values of `object`.
-     * If `object` contains duplicate values, subsequent values overwrite
-     * property assignments of previous values.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.7.0
-     * @category Object
-     * @param {Object} object The object to invert.
-     * @returns {Object} Returns the new inverted object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2, 'c': 1 };
-     *
-     * _.invert(object);
-     * // => { '1': 'c', '2': 'b' }
-     */
-    var invert = createInverter(function(result, value, key) {
-      if (value != null &&
-          typeof value.toString != 'function') {
-        value = nativeObjectToString.call(value);
-      }
-
-      result[value] = key;
-    }, constant(identity));
-
-    /**
-     * This method is like `_.invert` except that the inverted object is generated
-     * from the results of running each element of `object` thru `iteratee`. The
-     * corresponding inverted value of each inverted key is an array of keys
-     * responsible for generating the inverted value. The iteratee is invoked
-     * with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.1.0
-     * @category Object
-     * @param {Object} object The object to invert.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Object} Returns the new inverted object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2, 'c': 1 };
-     *
-     * _.invertBy(object);
-     * // => { '1': ['a', 'c'], '2': ['b'] }
-     *
-     * _.invertBy(object, function(value) {
-     *   return 'group' + value;
-     * });
-     * // => { 'group1': ['a', 'c'], 'group2': ['b'] }
-     */
-    var invertBy = createInverter(function(result, value, key) {
-      if (value != null &&
-          typeof value.toString != 'function') {
-        value = nativeObjectToString.call(value);
-      }
-
-      if (hasOwnProperty.call(result, value)) {
-        result[value].push(key);
-      } else {
-        result[value] = [key];
-      }
-    }, getIteratee);
-
-    /**
-     * Invokes the method at `path` of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the method to invoke.
-     * @param {...*} [args] The arguments to invoke the method with.
-     * @returns {*} Returns the result of the invoked method.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': [1, 2, 3, 4] } }] };
-     *
-     * _.invoke(object, 'a[0].b.c.slice', 1, 3);
-     * // => [2, 3]
-     */
-    var invoke = baseRest(baseInvoke);
-
-    /**
-     * Creates an array of the own enumerable property names of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects. See the
-     * [ES spec](http://ecma-international.org/ecma-262/7.0/#sec-object.keys)
-     * for more details.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.keys(new Foo);
-     * // => ['a', 'b'] (iteration order is not guaranteed)
-     *
-     * _.keys('hi');
-     * // => ['0', '1']
-     */
-    function keys(object) {
-      return isArrayLike(object) ? arrayLikeKeys(object) : baseKeys(object);
-    }
-
-    /**
-     * Creates an array of the own and inherited enumerable property names of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.keysIn(new Foo);
-     * // => ['a', 'b', 'c'] (iteration order is not guaranteed)
-     */
-    function keysIn(object) {
-      return isArrayLike(object) ? arrayLikeKeys(object, true) : baseKeysIn(object);
-    }
-
-    /**
-     * The opposite of `_.mapValues`; this method creates an object with the
-     * same values as `object` and keys generated by running each own enumerable
-     * string keyed property of `object` thru `iteratee`. The iteratee is invoked
-     * with three arguments: (value, key, object).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.8.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns the new mapped object.
-     * @see _.mapValues
-     * @example
-     *
-     * _.mapKeys({ 'a': 1, 'b': 2 }, function(value, key) {
-     *   return key + value;
-     * });
-     * // => { 'a1': 1, 'b2': 2 }
-     */
-    function mapKeys(object, iteratee) {
-      var result = {};
-      iteratee = getIteratee(iteratee, 3);
-
-      baseForOwn(object, function(value, key, object) {
-        baseAssignValue(result, iteratee(value, key, object), value);
-      });
-      return result;
-    }
-
-    /**
-     * Creates an object with the same keys as `object` and values generated
-     * by running each own enumerable string keyed property of `object` thru
-     * `iteratee`. The iteratee is invoked with three arguments:
-     * (value, key, object).
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns the new mapped object.
-     * @see _.mapKeys
-     * @example
-     *
-     * var users = {
-     *   'fred':    { 'user': 'fred',    'age': 40 },
-     *   'pebbles': { 'user': 'pebbles', 'age': 1 }
-     * };
-     *
-     * _.mapValues(users, function(o) { return o.age; });
-     * // => { 'fred': 40, 'pebbles': 1 } (iteration order is not guaranteed)
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.mapValues(users, 'age');
-     * // => { 'fred': 40, 'pebbles': 1 } (iteration order is not guaranteed)
-     */
-    function mapValues(object, iteratee) {
-      var result = {};
-      iteratee = getIteratee(iteratee, 3);
-
-      baseForOwn(object, function(value, key, object) {
-        baseAssignValue(result, key, iteratee(value, key, object));
-      });
-      return result;
-    }
-
-    /**
-     * This method is like `_.assign` except that it recursively merges own and
-     * inherited enumerable string keyed properties of source objects into the
-     * destination object. Source properties that resolve to `undefined` are
-     * skipped if a destination value exists. Array and plain object properties
-     * are merged recursively. Other objects and value types are overridden by
-     * assignment. Source objects are applied from left to right. Subsequent
-     * sources overwrite property assignments of previous sources.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.5.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = {
-     *   'a': [{ 'b': 2 }, { 'd': 4 }]
-     * };
-     *
-     * var other = {
-     *   'a': [{ 'c': 3 }, { 'e': 5 }]
-     * };
-     *
-     * _.merge(object, other);
-     * // => { 'a': [{ 'b': 2, 'c': 3 }, { 'd': 4, 'e': 5 }] }
-     */
-    var merge = createAssigner(function(object, source, srcIndex) {
-      baseMerge(object, source, srcIndex);
-    });
-
-    /**
-     * This method is like `_.merge` except that it accepts `customizer` which
-     * is invoked to produce the merged values of the destination and source
-     * properties. If `customizer` returns `undefined`, merging is handled by the
-     * method instead. The `customizer` is invoked with six arguments:
-     * (objValue, srcValue, key, object, source, stack).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} sources The source objects.
-     * @param {Function} customizer The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * function customizer(objValue, srcValue) {
-     *   if (_.isArray(objValue)) {
-     *     return objValue.concat(srcValue);
-     *   }
-     * }
-     *
-     * var object = { 'a': [1], 'b': [2] };
-     * var other = { 'a': [3], 'b': [4] };
-     *
-     * _.mergeWith(object, other, customizer);
-     * // => { 'a': [1, 3], 'b': [2, 4] }
-     */
-    var mergeWith = createAssigner(function(object, source, srcIndex, customizer) {
-      baseMerge(object, source, srcIndex, customizer);
-    });
-
-    /**
-     * The opposite of `_.pick`; this method creates an object composed of the
-     * own and inherited enumerable property paths of `object` that are not omitted.
-     *
-     * **Note:** This method is considerably slower than `_.pick`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {...(string|string[])} [paths] The property paths to omit.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.omit(object, ['a', 'c']);
-     * // => { 'b': '2' }
-     */
-    var omit = flatRest(function(object, paths) {
-      var result = {};
-      if (object == null) {
-        return result;
-      }
-      var isDeep = false;
-      paths = arrayMap(paths, function(path) {
-        path = castPath(path, object);
-        isDeep || (isDeep = path.length > 1);
-        return path;
-      });
-      copyObject(object, getAllKeysIn(object), result);
-      if (isDeep) {
-        result = baseClone(result, CLONE_DEEP_FLAG | CLONE_FLAT_FLAG | CLONE_SYMBOLS_FLAG, customOmitClone);
-      }
-      var length = paths.length;
-      while (length--) {
-        baseUnset(result, paths[length]);
-      }
-      return result;
-    });
-
-    /**
-     * The opposite of `_.pickBy`; this method creates an object composed of
-     * the own and inherited enumerable string keyed properties of `object` that
-     * `predicate` doesn't return truthy for. The predicate is invoked with two
-     * arguments: (value, key).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {Function} [predicate=_.identity] The function invoked per property.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.omitBy(object, _.isNumber);
-     * // => { 'b': '2' }
-     */
-    function omitBy(object, predicate) {
-      return pickBy(object, negate(getIteratee(predicate)));
-    }
-
-    /**
-     * Creates an object composed of the picked `object` properties.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {...(string|string[])} [paths] The property paths to pick.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.pick(object, ['a', 'c']);
-     * // => { 'a': 1, 'c': 3 }
-     */
-    var pick = flatRest(function(object, paths) {
-      return object == null ? {} : basePick(object, paths);
-    });
-
-    /**
-     * Creates an object composed of the `object` properties `predicate` returns
-     * truthy for. The predicate is invoked with two arguments: (value, key).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {Function} [predicate=_.identity] The function invoked per property.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.pickBy(object, _.isNumber);
-     * // => { 'a': 1, 'c': 3 }
-     */
-    function pickBy(object, predicate) {
-      if (object == null) {
-        return {};
-      }
-      var props = arrayMap(getAllKeysIn(object), function(prop) {
-        return [prop];
-      });
-      predicate = getIteratee(predicate);
-      return basePickBy(object, props, function(value, path) {
-        return predicate(value, path[0]);
-      });
-    }
-
-    /**
-     * This method is like `_.get` except that if the resolved value is a
-     * function it's invoked with the `this` binding of its parent object and
-     * its result is returned.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the property to resolve.
-     * @param {*} [defaultValue] The value returned for `undefined` resolved values.
-     * @returns {*} Returns the resolved value.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c1': 3, 'c2': _.constant(4) } }] };
-     *
-     * _.result(object, 'a[0].b.c1');
-     * // => 3
-     *
-     * _.result(object, 'a[0].b.c2');
-     * // => 4
-     *
-     * _.result(object, 'a[0].b.c3', 'default');
-     * // => 'default'
-     *
-     * _.result(object, 'a[0].b.c3', _.constant('default'));
-     * // => 'default'
-     */
-    function result(object, path, defaultValue) {
-      path = castPath(path, object);
-
-      var index = -1,
-          length = path.length;
-
-      // Ensure the loop is entered when path is empty.
-      if (!length) {
-        length = 1;
-        object = undefined;
-      }
-      while (++index < length) {
-        var value = object == null ? undefined : object[toKey(path[index])];
-        if (value === undefined) {
-          index = length;
-          value = defaultValue;
-        }
-        object = isFunction(value) ? value.call(object) : value;
-      }
-      return object;
-    }
-
-    /**
-     * Sets the value at `path` of `object`. If a portion of `path` doesn't exist,
-     * it's created. Arrays are created for missing index properties while objects
-     * are created for all other missing properties. Use `_.setWith` to customize
-     * `path` creation.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }] };
-     *
-     * _.set(object, 'a[0].b.c', 4);
-     * console.log(object.a[0].b.c);
-     * // => 4
-     *
-     * _.set(object, ['x', '0', 'y', 'z'], 5);
-     * console.log(object.x[0].y.z);
-     * // => 5
-     */
-    function set(object, path, value) {
-      return object == null ? object : baseSet(object, path, value);
-    }
-
-    /**
-     * This method is like `_.set` except that it accepts `customizer` which is
-     * invoked to produce the objects of `path`.  If `customizer` returns `undefined`
-     * path creation is handled by the method instead. The `customizer` is invoked
-     * with three arguments: (nsValue, key, nsObject).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {*} value The value to set.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = {};
-     *
-     * _.setWith(object, '[0][1]', 'a', Object);
-     * // => { '0': { '1': 'a' } }
-     */
-    function setWith(object, path, value, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return object == null ? object : baseSet(object, path, value, customizer);
-    }
-
-    /**
-     * Creates an array of own enumerable string keyed-value pairs for `object`
-     * which can be consumed by `_.fromPairs`. If `object` is a map or set, its
-     * entries are returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias entries
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the key-value pairs.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.toPairs(new Foo);
-     * // => [['a', 1], ['b', 2]] (iteration order is not guaranteed)
-     */
-    var toPairs = createToPairs(keys);
-
-    /**
-     * Creates an array of own and inherited enumerable string keyed-value pairs
-     * for `object` which can be consumed by `_.fromPairs`. If `object` is a map
-     * or set, its entries are returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias entriesIn
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the key-value pairs.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.toPairsIn(new Foo);
-     * // => [['a', 1], ['b', 2], ['c', 3]] (iteration order is not guaranteed)
-     */
-    var toPairsIn = createToPairs(keysIn);
-
-    /**
-     * An alternative to `_.reduce`; this method transforms `object` to a new
-     * `accumulator` object which is the result of running each of its own
-     * enumerable string keyed properties thru `iteratee`, with each invocation
-     * potentially mutating the `accumulator` object. If `accumulator` is not
-     * provided, a new object with the same `[[Prototype]]` will be used. The
-     * iteratee is invoked with four arguments: (accumulator, value, key, object).
-     * Iteratee functions may exit iteration early by explicitly returning `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.3.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {*} [accumulator] The custom accumulator value.
-     * @returns {*} Returns the accumulated value.
-     * @example
-     *
-     * _.transform([2, 3, 4], function(result, n) {
-     *   result.push(n *= n);
-     *   return n % 2 == 0;
-     * }, []);
-     * // => [4, 9]
-     *
-     * _.transform({ 'a': 1, 'b': 2, 'c': 1 }, function(result, value, key) {
-     *   (result[value] || (result[value] = [])).push(key);
-     * }, {});
-     * // => { '1': ['a', 'c'], '2': ['b'] }
-     */
-    function transform(object, iteratee, accumulator) {
-      var isArr = isArray(object),
-          isArrLike = isArr || isBuffer(object) || isTypedArray(object);
-
-      iteratee = getIteratee(iteratee, 4);
-      if (accumulator == null) {
-        var Ctor = object && object.constructor;
-        if (isArrLike) {
-          accumulator = isArr ? new Ctor : [];
-        }
-        else if (isObject(object)) {
-          accumulator = isFunction(Ctor) ? baseCreate(getPrototype(object)) : {};
-        }
-        else {
-          accumulator = {};
-        }
-      }
-      (isArrLike ? arrayEach : baseForOwn)(object, function(value, index, object) {
-        return iteratee(accumulator, value, index, object);
-      });
-      return accumulator;
-    }
-
-    /**
-     * Removes the property at `path` of `object`.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to unset.
-     * @returns {boolean} Returns `true` if the property is deleted, else `false`.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 7 } }] };
-     * _.unset(object, 'a[0].b.c');
-     * // => true
-     *
-     * console.log(object);
-     * // => { 'a': [{ 'b': {} }] };
-     *
-     * _.unset(object, ['a', '0', 'b', 'c']);
-     * // => true
-     *
-     * console.log(object);
-     * // => { 'a': [{ 'b': {} }] };
-     */
-    function unset(object, path) {
-      return object == null ? true : baseUnset(object, path);
-    }
-
-    /**
-     * This method is like `_.set` except that accepts `updater` to produce the
-     * value to set. Use `_.updateWith` to customize `path` creation. The `updater`
-     * is invoked with one argument: (value).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.6.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {Function} updater The function to produce the updated value.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }] };
-     *
-     * _.update(object, 'a[0].b.c', function(n) { return n * n; });
-     * console.log(object.a[0].b.c);
-     * // => 9
-     *
-     * _.update(object, 'x[0].y.z', function(n) { return n ? n + 1 : 0; });
-     * console.log(object.x[0].y.z);
-     * // => 0
-     */
-    function update(object, path, updater) {
-      return object == null ? object : baseUpdate(object, path, castFunction(updater));
-    }
-
-    /**
-     * This method is like `_.update` except that it accepts `customizer` which is
-     * invoked to produce the objects of `path`.  If `customizer` returns `undefined`
-     * path creation is handled by the method instead. The `customizer` is invoked
-     * with three arguments: (nsValue, key, nsObject).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.6.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {Function} updater The function to produce the updated value.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = {};
-     *
-     * _.updateWith(object, '[0][1]', _.constant('a'), Object);
-     * // => { '0': { '1': 'a' } }
-     */
-    function updateWith(object, path, updater, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return object == null ? object : baseUpdate(object, path, castFunction(updater), customizer);
-    }
-
-    /**
-     * Creates an array of the own enumerable string keyed property values of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property values.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.values(new Foo);
-     * // => [1, 2] (iteration order is not guaranteed)
-     *
-     * _.values('hi');
-     * // => ['h', 'i']
-     */
-    function values(object) {
-      return object == null ? [] : baseValues(object, keys(object));
-    }
-
-    /**
-     * Creates an array of the own and inherited enumerable string keyed property
-     * values of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property values.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.valuesIn(new Foo);
-     * // => [1, 2, 3] (iteration order is not guaranteed)
-     */
-    function valuesIn(object) {
-      return object == null ? [] : baseValues(object, keysIn(object));
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Clamps `number` within the inclusive `lower` and `upper` bounds.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Number
-     * @param {number} number The number to clamp.
-     * @param {number} [lower] The lower bound.
-     * @param {number} upper The upper bound.
-     * @returns {number} Returns the clamped number.
-     * @example
-     *
-     * _.clamp(-10, -5, 5);
-     * // => -5
-     *
-     * _.clamp(10, -5, 5);
-     * // => 5
-     */
-    function clamp(number, lower, upper) {
-      if (upper === undefined) {
-        upper = lower;
-        lower = undefined;
-      }
-      if (upper !== undefined) {
-        upper = toNumber(upper);
-        upper = upper === upper ? upper : 0;
-      }
-      if (lower !== undefined) {
-        lower = toNumber(lower);
-        lower = lower === lower ? lower : 0;
-      }
-      return baseClamp(toNumber(number), lower, upper);
-    }
-
-    /**
-     * Checks if `n` is between `start` and up to, but not including, `end`. If
-     * `end` is not specified, it's set to `start` with `start` then set to `0`.
-     * If `start` is greater than `end` the params are swapped to support
-     * negative ranges.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.3.0
-     * @category Number
-     * @param {number} number The number to check.
-     * @param {number} [start=0] The start of the range.
-     * @param {number} end The end of the range.
-     * @returns {boolean} Returns `true` if `number` is in the range, else `false`.
-     * @see _.range, _.rangeRight
-     * @example
-     *
-     * _.inRange(3, 2, 4);
-     * // => true
-     *
-     * _.inRange(4, 8);
-     * // => true
-     *
-     * _.inRange(4, 2);
-     * // => false
-     *
-     * _.inRange(2, 2);
-     * // => false
-     *
-     * _.inRange(1.2, 2);
-     * // => true
-     *
-     * _.inRange(5.2, 4);
-     * // => false
-     *
-     * _.inRange(-3, -2, -6);
-     * // => true
-     */
-    function inRange(number, start, end) {
-      start = toFinite(start);
-      if (end === undefined) {
-        end = start;
-        start = 0;
-      } else {
-        end = toFinite(end);
-      }
-      number = toNumber(number);
-      return baseInRange(number, start, end);
-    }
-
-    /**
-     * Produces a random number between the inclusive `lower` and `upper` bounds.
-     * If only one argument is provided a number between `0` and the given number
-     * is returned. If `floating` is `true`, or either `lower` or `upper` are
-     * floats, a floating-point number is returned instead of an integer.
-     *
-     * **Note:** JavaScript follows the IEEE-754 standard for resolving
-     * floating-point values which can produce unexpected results.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.7.0
-     * @category Number
-     * @param {number} [lower=0] The lower bound.
-     * @param {number} [upper=1] The upper bound.
-     * @param {boolean} [floating] Specify returning a floating-point number.
-     * @returns {number} Returns the random number.
-     * @example
-     *
-     * _.random(0, 5);
-     * // => an integer between 0 and 5
-     *
-     * _.random(5);
-     * // => also an integer between 0 and 5
-     *
-     * _.random(5, true);
-     * // => a floating-point number between 0 and 5
-     *
-     * _.random(1.2, 5.2);
-     * // => a floating-point number between 1.2 and 5.2
-     */
-    function random(lower, upper, floating) {
-      if (floating && typeof floating != 'boolean' && isIterateeCall(lower, upper, floating)) {
-        upper = floating = undefined;
-      }
-      if (floating === undefined) {
-        if (typeof upper == 'boolean') {
-          floating = upper;
-          upper = undefined;
-        }
-        else if (typeof lower == 'boolean') {
-          floating = lower;
-          lower = undefined;
-        }
-      }
-      if (lower === undefined && upper === undefined) {
-        lower = 0;
-        upper = 1;
-      }
-      else {
-        lower = toFinite(lower);
-        if (upper === undefined) {
-          upper = lower;
-          lower = 0;
-        } else {
-          upper = toFinite(upper);
-        }
-      }
-      if (lower > upper) {
-        var temp = lower;
-        lower = upper;
-        upper = temp;
-      }
-      if (floating || lower % 1 || upper % 1) {
-        var rand = nativeRandom();
-        return nativeMin(lower + (rand * (upper - lower + freeParseFloat('1e-' + ((rand + '').length - 1)))), upper);
-      }
-      return baseRandom(lower, upper);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Converts `string` to [camel case](https://en.wikipedia.org/wiki/CamelCase).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the camel cased string.
-     * @example
-     *
-     * _.camelCase('Foo Bar');
-     * // => 'fooBar'
-     *
-     * _.camelCase('--foo-bar--');
-     * // => 'fooBar'
-     *
-     * _.camelCase('__FOO_BAR__');
-     * // => 'fooBar'
-     */
-    var camelCase = createCompounder(function(result, word, index) {
-      word = word.toLowerCase();
-      return result + (index ? capitalize(word) : word);
-    });
-
-    /**
-     * Converts the first character of `string` to upper case and the remaining
-     * to lower case.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to capitalize.
-     * @returns {string} Returns the capitalized string.
-     * @example
-     *
-     * _.capitalize('FRED');
-     * // => 'Fred'
-     */
-    function capitalize(string) {
-      return upperFirst(toString(string).toLowerCase());
-    }
-
-    /**
-     * Deburrs `string` by converting
-     * [Latin-1 Supplement](https://en.wikipedia.org/wiki/Latin-1_Supplement_(Unicode_block)#Character_table)
-     * and [Latin Extended-A](https://en.wikipedia.org/wiki/Latin_Extended-A)
-     * letters to basic Latin letters and removing
-     * [combining diacritical marks](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to deburr.
-     * @returns {string} Returns the deburred string.
-     * @example
-     *
-     * _.deburr('déjà vu');
-     * // => 'deja vu'
-     */
-    function deburr(string) {
-      string = toString(string);
-      return string && string.replace(reLatin, deburrLetter).replace(reComboMark, '');
-    }
-
-    /**
-     * Checks if `string` ends with the given target string.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to inspect.
-     * @param {string} [target] The string to search for.
-     * @param {number} [position=string.length] The position to search up to.
-     * @returns {boolean} Returns `true` if `string` ends with `target`,
-     *  else `false`.
-     * @example
-     *
-     * _.endsWith('abc', 'c');
-     * // => true
-     *
-     * _.endsWith('abc', 'b');
-     * // => false
-     *
-     * _.endsWith('abc', 'b', 2);
-     * // => true
-     */
-    function endsWith(string, target, position) {
-      string = toString(string);
-      target = baseToString(target);
-
-      var length = string.length;
-      position = position === undefined
-        ? length
-        : baseClamp(toInteger(position), 0, length);
-
-      var end = position;
-      position -= target.length;
-      return position >= 0 && string.slice(position, end) == target;
-    }
-
-    /**
-     * Converts the characters "&", "<", ">", '"', and "'" in `string` to their
-     * corresponding HTML entities.
-     *
-     * **Note:** No other characters are escaped. To escape additional
-     * characters use a third-party library like [_he_](https://mths.be/he).
-     *
-     * Though the ">" character is escaped for symmetry, characters like
-     * ">" and "/" don't need escaping in HTML and have no special meaning
-     * unless they're part of a tag or unquoted attribute value. See
-     * [Mathias Bynens's article](https://mathiasbynens.be/notes/ambiguous-ampersands)
-     * (under "semi-related fun fact") for more details.
-     *
-     * When working with HTML you should always
-     * [quote attribute values](http://wonko.com/post/html-escaping) to reduce
-     * XSS vectors.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category String
-     * @param {string} [string=''] The string to escape.
-     * @returns {string} Returns the escaped string.
-     * @example
-     *
-     * _.escape('fred, barney, & pebbles');
-     * // => 'fred, barney, &amp; pebbles'
-     */
-    function escape(string) {
-      string = toString(string);
-      return (string && reHasUnescapedHtml.test(string))
-        ? string.replace(reUnescapedHtml, escapeHtmlChar)
-        : string;
-    }
-
-    /**
-     * Escapes the `RegExp` special characters "^", "$", "\", ".", "*", "+",
-     * "?", "(", ")", "[", "]", "{", "}", and "|" in `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to escape.
-     * @returns {string} Returns the escaped string.
-     * @example
-     *
-     * _.escapeRegExp('[lodash](https://lodash.com/)');
-     * // => '\[lodash\]\(https://lodash\.com/\)'
-     */
-    function escapeRegExp(string) {
-      string = toString(string);
-      return (string && reHasRegExpChar.test(string))
-        ? string.replace(reRegExpChar, '\\$&')
-        : string;
-    }
-
-    /**
-     * Converts `string` to
-     * [kebab case](https://en.wikipedia.org/wiki/Letter_case#Special_case_styles).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the kebab cased string.
-     * @example
-     *
-     * _.kebabCase('Foo Bar');
-     * // => 'foo-bar'
-     *
-     * _.kebabCase('fooBar');
-     * // => 'foo-bar'
-     *
-     * _.kebabCase('__FOO_BAR__');
-     * // => 'foo-bar'
-     */
-    var kebabCase = createCompounder(function(result, word, index) {
-      return result + (index ? '-' : '') + word.toLowerCase();
-    });
-
-    /**
-     * Converts `string`, as space separated words, to lower case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the lower cased string.
-     * @example
-     *
-     * _.lowerCase('--Foo-Bar--');
-     * // => 'foo bar'
-     *
-     * _.lowerCase('fooBar');
-     * // => 'foo bar'
-     *
-     * _.lowerCase('__FOO_BAR__');
-     * // => 'foo bar'
-     */
-    var lowerCase = createCompounder(function(result, word, index) {
-      return result + (index ? ' ' : '') + word.toLowerCase();
-    });
-
-    /**
-     * Converts the first character of `string` to lower case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the converted string.
-     * @example
-     *
-     * _.lowerFirst('Fred');
-     * // => 'fred'
-     *
-     * _.lowerFirst('FRED');
-     * // => 'fRED'
-     */
-    var lowerFirst = createCaseFirst('toLowerCase');
-
-    /**
-     * Pads `string` on the left and right sides if it's shorter than `length`.
-     * Padding characters are truncated if they can't be evenly divided by `length`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to pad.
-     * @param {number} [length=0] The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padded string.
-     * @example
-     *
-     * _.pad('abc', 8);
-     * // => '  abc   '
-     *
-     * _.pad('abc', 8, '_-');
-     * // => '_-abc_-_'
-     *
-     * _.pad('abc', 3);
-     * // => 'abc'
-     */
-    function pad(string, length, chars) {
-      string = toString(string);
-      length = toInteger(length);
-
-      var strLength = length ? stringSize(string) : 0;
-      if (!length || strLength >= length) {
-        return string;
-      }
-      var mid = (length - strLength) / 2;
-      return (
-        createPadding(nativeFloor(mid), chars) +
-        string +
-        createPadding(nativeCeil(mid), chars)
-      );
-    }
-
-    /**
-     * Pads `string` on the right side if it's shorter than `length`. Padding
-     * characters are truncated if they exceed `length`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to pad.
-     * @param {number} [length=0] The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padded string.
-     * @example
-     *
-     * _.padEnd('abc', 6);
-     * // => 'abc   '
-     *
-     * _.padEnd('abc', 6, '_-');
-     * // => 'abc_-_'
-     *
-     * _.padEnd('abc', 3);
-     * // => 'abc'
-     */
-    function padEnd(string, length, chars) {
-      string = toString(string);
-      length = toInteger(length);
-
-      var strLength = length ? stringSize(string) : 0;
-      return (length && strLength < length)
-        ? (string + createPadding(length - strLength, chars))
-        : string;
-    }
-
-    /**
-     * Pads `string` on the left side if it's shorter than `length`. Padding
-     * characters are truncated if they exceed `length`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to pad.
-     * @param {number} [length=0] The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padded string.
-     * @example
-     *
-     * _.padStart('abc', 6);
-     * // => '   abc'
-     *
-     * _.padStart('abc', 6, '_-');
-     * // => '_-_abc'
-     *
-     * _.padStart('abc', 3);
-     * // => 'abc'
-     */
-    function padStart(string, length, chars) {
-      string = toString(string);
-      length = toInteger(length);
-
-      var strLength = length ? stringSize(string) : 0;
-      return (length && strLength < length)
-        ? (createPadding(length - strLength, chars) + string)
-        : string;
-    }
-
-    /**
-     * Converts `string` to an integer of the specified radix. If `radix` is
-     * `undefined` or `0`, a `radix` of `10` is used unless `value` is a
-     * hexadecimal, in which case a `radix` of `16` is used.
-     *
-     * **Note:** This method aligns with the
-     * [ES5 implementation](https://es5.github.io/#x15.1.2.2) of `parseInt`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.1.0
-     * @category String
-     * @param {string} string The string to convert.
-     * @param {number} [radix=10] The radix to interpret `value` by.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.parseInt('08');
-     * // => 8
-     *
-     * _.map(['6', '08', '10'], _.parseInt);
-     * // => [6, 8, 10]
-     */
-    function parseInt(string, radix, guard) {
-      if (guard || radix == null) {
-        radix = 0;
-      } else if (radix) {
-        radix = +radix;
-      }
-      return nativeParseInt(toString(string).replace(reTrimStart, ''), radix || 0);
-    }
-
-    /**
-     * Repeats the given string `n` times.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to repeat.
-     * @param {number} [n=1] The number of times to repeat the string.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the repeated string.
-     * @example
-     *
-     * _.repeat('*', 3);
-     * // => '***'
-     *
-     * _.repeat('abc', 2);
-     * // => 'abcabc'
-     *
-     * _.repeat('abc', 0);
-     * // => ''
-     */
-    function repeat(string, n, guard) {
-      if ((guard ? isIterateeCall(string, n, guard) : n === undefined)) {
-        n = 1;
-      } else {
-        n = toInteger(n);
-      }
-      return baseRepeat(toString(string), n);
-    }
-
-    /**
-     * Replaces matches for `pattern` in `string` with `replacement`.
-     *
-     * **Note:** This method is based on
-     * [`String#replace`](https://mdn.io/String/replace).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to modify.
-     * @param {RegExp|string} pattern The pattern to replace.
-     * @param {Function|string} replacement The match replacement.
-     * @returns {string} Returns the modified string.
-     * @example
-     *
-     * _.replace('Hi Fred', 'Fred', 'Barney');
-     * // => 'Hi Barney'
-     */
-    function replace() {
-      var args = arguments,
-          string = toString(args[0]);
-
-      return args.length < 3 ? string : string.replace(args[1], args[2]);
-    }
-
-    /**
-     * Converts `string` to
-     * [snake case](https://en.wikipedia.org/wiki/Snake_case).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the snake cased string.
-     * @example
-     *
-     * _.snakeCase('Foo Bar');
-     * // => 'foo_bar'
-     *
-     * _.snakeCase('fooBar');
-     * // => 'foo_bar'
-     *
-     * _.snakeCase('--FOO-BAR--');
-     * // => 'foo_bar'
-     */
-    var snakeCase = createCompounder(function(result, word, index) {
-      return result + (index ? '_' : '') + word.toLowerCase();
-    });
-
-    /**
-     * Splits `string` by `separator`.
-     *
-     * **Note:** This method is based on
-     * [`String#split`](https://mdn.io/String/split).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to split.
-     * @param {RegExp|string} separator The separator pattern to split by.
-     * @param {number} [limit] The length to truncate results to.
-     * @returns {Array} Returns the string segments.
-     * @example
-     *
-     * _.split('a-b-c', '-', 2);
-     * // => ['a', 'b']
-     */
-    function split(string, separator, limit) {
-      if (limit && typeof limit != 'number' && isIterateeCall(string, separator, limit)) {
-        separator = limit = undefined;
-      }
-      limit = limit === undefined ? MAX_ARRAY_LENGTH : limit >>> 0;
-      if (!limit) {
-        return [];
-      }
-      string = toString(string);
-      if (string && (
-            typeof separator == 'string' ||
-            (separator != null && !isRegExp(separator))
-          )) {
-        separator = baseToString(separator);
-        if (!separator && hasUnicode(string)) {
-          return castSlice(stringToArray(string), 0, limit);
-        }
-      }
-      return string.split(separator, limit);
-    }
-
-    /**
-     * Converts `string` to
-     * [start case](https://en.wikipedia.org/wiki/Letter_case#Stylistic_or_specialised_usage).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.1.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the start cased string.
-     * @example
-     *
-     * _.startCase('--foo-bar--');
-     * // => 'Foo Bar'
-     *
-     * _.startCase('fooBar');
-     * // => 'Foo Bar'
-     *
-     * _.startCase('__FOO_BAR__');
-     * // => 'FOO BAR'
-     */
-    var startCase = createCompounder(function(result, word, index) {
-      return result + (index ? ' ' : '') + upperFirst(word);
-    });
-
-    /**
-     * Checks if `string` starts with the given target string.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to inspect.
-     * @param {string} [target] The string to search for.
-     * @param {number} [position=0] The position to search from.
-     * @returns {boolean} Returns `true` if `string` starts with `target`,
-     *  else `false`.
-     * @example
-     *
-     * _.startsWith('abc', 'a');
-     * // => true
-     *
-     * _.startsWith('abc', 'b');
-     * // => false
-     *
-     * _.startsWith('abc', 'b', 1);
-     * // => true
-     */
-    function startsWith(string, target, position) {
-      string = toString(string);
-      position = position == null
-        ? 0
-        : baseClamp(toInteger(position), 0, string.length);
-
-      target = baseToString(target);
-      return string.slice(position, position + target.length) == target;
-    }
-
-    /**
-     * Creates a compiled template function that can interpolate data properties
-     * in "interpolate" delimiters, HTML-escape interpolated data properties in
-     * "escape" delimiters, and execute JavaScript in "evaluate" delimiters. Data
-     * properties may be accessed as free variables in the template. If a setting
-     * object is given, it takes precedence over `_.templateSettings` values.
-     *
-     * **Note:** In the development build `_.template` utilizes
-     * [sourceURLs](http://www.html5rocks.com/en/tutorials/developertools/sourcemaps/#toc-sourceurl)
-     * for easier debugging.
-     *
-     * For more information on precompiling templates see
-     * [lodash's custom builds documentation](https://lodash.com/custom-builds).
-     *
-     * For more information on Chrome extension sandboxes see
-     * [Chrome's extensions documentation](https://developer.chrome.com/extensions/sandboxingEval).
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category String
-     * @param {string} [string=''] The template string.
-     * @param {Object} [options={}] The options object.
-     * @param {RegExp} [options.escape=_.templateSettings.escape]
-     *  The HTML "escape" delimiter.
-     * @param {RegExp} [options.evaluate=_.templateSettings.evaluate]
-     *  The "evaluate" delimiter.
-     * @param {Object} [options.imports=_.templateSettings.imports]
-     *  An object to import into the template as free variables.
-     * @param {RegExp} [options.interpolate=_.templateSettings.interpolate]
-     *  The "interpolate" delimiter.
-     * @param {string} [options.sourceURL='lodash.templateSources[n]']
-     *  The sourceURL of the compiled template.
-     * @param {string} [options.variable='obj']
-     *  The data object variable name.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the compiled template function.
-     * @example
-     *
-     * // Use the "interpolate" delimiter to create a compiled template.
-     * var compiled = _.template('hello <%= user %>!');
-     * compiled({ 'user': 'fred' });
-     * // => 'hello fred!'
-     *
-     * // Use the HTML "escape" delimiter to escape data property values.
-     * var compiled = _.template('<b><%- value %></b>');
-     * compiled({ 'value': '<script>' });
-     * // => '<b>&lt;script&gt;</b>'
-     *
-     * // Use the "evaluate" delimiter to execute JavaScript and generate HTML.
-     * var compiled = _.template('<% _.forEach(users, function(user) { %><li><%- user %></li><% }); %>');
-     * compiled({ 'users': ['fred', 'barney'] });
-     * // => '<li>fred</li><li>barney</li>'
-     *
-     * // Use the internal `print` function in "evaluate" delimiters.
-     * var compiled = _.template('<% print("hello " + user); %>!');
-     * compiled({ 'user': 'barney' });
-     * // => 'hello barney!'
-     *
-     * // Use the ES template literal delimiter as an "interpolate" delimiter.
-     * // Disable support by replacing the "interpolate" delimiter.
-     * var compiled = _.template('hello ${ user }!');
-     * compiled({ 'user': 'pebbles' });
-     * // => 'hello pebbles!'
-     *
-     * // Use backslashes to treat delimiters as plain text.
-     * var compiled = _.template('<%= "\\<%- value %\\>" %>');
-     * compiled({ 'value': 'ignored' });
-     * // => '<%- value %>'
-     *
-     * // Use the `imports` option to import `jQuery` as `jq`.
-     * var text = '<% jq.each(users, function(user) { %><li><%- user %></li><% }); %>';
-     * var compiled = _.template(text, { 'imports': { 'jq': jQuery } });
-     * compiled({ 'users': ['fred', 'barney'] });
-     * // => '<li>fred</li><li>barney</li>'
-     *
-     * // Use the `sourceURL` option to specify a custom sourceURL for the template.
-     * var compiled = _.template('hello <%= user %>!', { 'sourceURL': '/basic/greeting.jst' });
-     * compiled(data);
-     * // => Find the source of "greeting.jst" under the Sources tab or Resources panel of the web inspector.
-     *
-     * // Use the `variable` option to ensure a with-statement isn't used in the compiled template.
-     * var compiled = _.template('hi <%= data.user %>!', { 'variable': 'data' });
-     * compiled.source;
-     * // => function(data) {
-     * //   var __t, __p = '';
-     * //   __p += 'hi ' + ((__t = ( data.user )) == null ? '' : __t) + '!';
-     * //   return __p;
-     * // }
-     *
-     * // Use custom template delimiters.
-     * _.templateSettings.interpolate = /{{([\s\S]+?)}}/g;
-     * var compiled = _.template('hello {{ user }}!');
-     * compiled({ 'user': 'mustache' });
-     * // => 'hello mustache!'
-     *
-     * // Use the `source` property to inline compiled templates for meaningful
-     * // line numbers in error messages and stack traces.
-     * fs.writeFileSync(path.join(process.cwd(), 'jst.js'), '\
-     *   var JST = {\
-     *     "main": ' + _.template(mainText).source + '\
-     *   };\
-     * ');
-     */
-    function template(string, options, guard) {
-      // Based on John Resig's `tmpl` implementation
-      // (http://ejohn.org/blog/javascript-micro-templating/)
-      // and Laura Doktorova's doT.js (https://github.com/olado/doT).
-      var settings = lodash.templateSettings;
-
-      if (guard && isIterateeCall(string, options, guard)) {
-        options = undefined;
-      }
-      string = toString(string);
-      options = assignInWith({}, options, settings, customDefaultsAssignIn);
-
-      var imports = assignInWith({}, options.imports, settings.imports, customDefaultsAssignIn),
-          importsKeys = keys(imports),
-          importsValues = baseValues(imports, importsKeys);
-
-      var isEscaping,
-          isEvaluating,
-          index = 0,
-          interpolate = options.interpolate || reNoMatch,
-          source = "__p += '";
-
-      // Compile the regexp to match each delimiter.
-      var reDelimiters = RegExp(
-        (options.escape || reNoMatch).source + '|' +
-        interpolate.source + '|' +
-        (interpolate === reInterpolate ? reEsTemplate : reNoMatch).source + '|' +
-        (options.evaluate || reNoMatch).source + '|$'
-      , 'g');
-
-      // Use a sourceURL for easier debugging.
-      // The sourceURL gets injected into the source that's eval-ed, so be careful
-      // with lookup (in case of e.g. prototype pollution), and strip newlines if any.
-      // A newline wouldn't be a valid sourceURL anyway, and it'd enable code injection.
-      var sourceURL = '//# sourceURL=' +
-        (hasOwnProperty.call(options, 'sourceURL')
-          ? (options.sourceURL + '').replace(/[\r\n]/g, ' ')
-          : ('lodash.templateSources[' + (++templateCounter) + ']')
-        ) + '\n';
-
-      string.replace(reDelimiters, function(match, escapeValue, interpolateValue, esTemplateValue, evaluateValue, offset) {
-        interpolateValue || (interpolateValue = esTemplateValue);
-
-        // Escape characters that can't be included in string literals.
-        source += string.slice(index, offset).replace(reUnescapedString, escapeStringChar);
-
-        // Replace delimiters with snippets.
-        if (escapeValue) {
-          isEscaping = true;
-          source += "' +\n__e(" + escapeValue + ") +\n'";
-        }
-        if (evaluateValue) {
-          isEvaluating = true;
-          source += "';\n" + evaluateValue + ";\n__p += '";
-        }
-        if (interpolateValue) {
-          source += "' +\n((__t = (" + interpolateValue + ")) == null ? '' : __t) +\n'";
-        }
-        index = offset + match.length;
-
-        // The JS engine embedded in Adobe products needs `match` returned in
-        // order to produce the correct `offset` value.
-        return match;
-      });
-
-      source += "';\n";
-
-      // If `variable` is not specified wrap a with-statement around the generated
-      // code to add the data object to the top of the scope chain.
-      // Like with sourceURL, we take care to not check the option's prototype,
-      // as this configuration is a code injection vector.
-      var variable = hasOwnProperty.call(options, 'variable') && options.variable;
-      if (!variable) {
-        source = 'with (obj) {\n' + source + '\n}\n';
-      }
-      // Cleanup code by stripping empty strings.
-      source = (isEvaluating ? source.replace(reEmptyStringLeading, '') : source)
-        .replace(reEmptyStringMiddle, '$1')
-        .replace(reEmptyStringTrailing, '$1;');
-
-      // Frame code as the function body.
-      source = 'function(' + (variable || 'obj') + ') {\n' +
-        (variable
-          ? ''
-          : 'obj || (obj = {});\n'
-        ) +
-        "var __t, __p = ''" +
-        (isEscaping
-           ? ', __e = _.escape'
-           : ''
-        ) +
-        (isEvaluating
-          ? ', __j = Array.prototype.join;\n' +
-            "function print() { __p += __j.call(arguments, '') }\n"
-          : ';\n'
-        ) +
-        source +
-        'return __p\n}';
-
-      var result = attempt(function() {
-        return Function(importsKeys, sourceURL + 'return ' + source)
-          .apply(undefined, importsValues);
-      });
-
-      // Provide the compiled function's source by its `toString` method or
-      // the `source` property as a convenience for inlining compiled templates.
-      result.source = source;
-      if (isError(result)) {
-        throw result;
-      }
-      return result;
-    }
-
-    /**
-     * Converts `string`, as a whole, to lower case just like
-     * [String#toLowerCase](https://mdn.io/toLowerCase).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the lower cased string.
-     * @example
-     *
-     * _.toLower('--Foo-Bar--');
-     * // => '--foo-bar--'
-     *
-     * _.toLower('fooBar');
-     * // => 'foobar'
-     *
-     * _.toLower('__FOO_BAR__');
-     * // => '__foo_bar__'
-     */
-    function toLower(value) {
-      return toString(value).toLowerCase();
-    }
-
-    /**
-     * Converts `string`, as a whole, to upper case just like
-     * [String#toUpperCase](https://mdn.io/toUpperCase).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the upper cased string.
-     * @example
-     *
-     * _.toUpper('--foo-bar--');
-     * // => '--FOO-BAR--'
-     *
-     * _.toUpper('fooBar');
-     * // => 'FOOBAR'
-     *
-     * _.toUpper('__foo_bar__');
-     * // => '__FOO_BAR__'
-     */
-    function toUpper(value) {
-      return toString(value).toUpperCase();
-    }
-
-    /**
-     * Removes leading and trailing whitespace or specified characters from `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to trim.
-     * @param {string} [chars=whitespace] The characters to trim.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the trimmed string.
-     * @example
-     *
-     * _.trim('  abc  ');
-     * // => 'abc'
-     *
-     * _.trim('-_-abc-_-', '_-');
-     * // => 'abc'
-     *
-     * _.map(['  foo  ', '  bar  '], _.trim);
-     * // => ['foo', 'bar']
-     */
-    function trim(string, chars, guard) {
-      string = toString(string);
-      if (string && (guard || chars === undefined)) {
-        return string.replace(reTrim, '');
-      }
-      if (!string || !(chars = baseToString(chars))) {
-        return string;
-      }
-      var strSymbols = stringToArray(string),
-          chrSymbols = stringToArray(chars),
-          start = charsStartIndex(strSymbols, chrSymbols),
-          end = charsEndIndex(strSymbols, chrSymbols) + 1;
-
-      return castSlice(strSymbols, start, end).join('');
-    }
-
-    /**
-     * Removes trailing whitespace or specified characters from `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to trim.
-     * @param {string} [chars=whitespace] The characters to trim.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the trimmed string.
-     * @example
-     *
-     * _.trimEnd('  abc  ');
-     * // => '  abc'
-     *
-     * _.trimEnd('-_-abc-_-', '_-');
-     * // => '-_-abc'
-     */
-    function trimEnd(string, chars, guard) {
-      string = toString(string);
-      if (string && (guard || chars === undefined)) {
-        return string.replace(reTrimEnd, '');
-      }
-      if (!string || !(chars = baseToString(chars))) {
-        return string;
-      }
-      var strSymbols = stringToArray(string),
-          end = charsEndIndex(strSymbols, stringToArray(chars)) + 1;
-
-      return castSlice(strSymbols, 0, end).join('');
-    }
-
-    /**
-     * Removes leading whitespace or specified characters from `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to trim.
-     * @param {string} [chars=whitespace] The characters to trim.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the trimmed string.
-     * @example
-     *
-     * _.trimStart('  abc  ');
-     * // => 'abc  '
-     *
-     * _.trimStart('-_-abc-_-', '_-');
-     * // => 'abc-_-'
-     */
-    function trimStart(string, chars, guard) {
-      string = toString(string);
-      if (string && (guard || chars === undefined)) {
-        return string.replace(reTrimStart, '');
-      }
-      if (!string || !(chars = baseToString(chars))) {
-        return string;
-      }
-      var strSymbols = stringToArray(string),
-          start = charsStartIndex(strSymbols, stringToArray(chars));
-
-      return castSlice(strSymbols, start).join('');
-    }
-
-    /**
-     * Truncates `string` if it's longer than the given maximum string length.
-     * The last characters of the truncated string are replaced with the omission
-     * string which defaults to "...".
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to truncate.
-     * @param {Object} [options={}] The options object.
-     * @param {number} [options.length=30] The maximum string length.
-     * @param {string} [options.omission='...'] The string to indicate text is omitted.
-     * @param {RegExp|string} [options.separator] The separator pattern to truncate to.
-     * @returns {string} Returns the truncated string.
-     * @example
-     *
-     * _.truncate('hi-diddly-ho there, neighborino');
-     * // => 'hi-diddly-ho there, neighbo...'
-     *
-     * _.truncate('hi-diddly-ho there, neighborino', {
-     *   'length': 24,
-     *   'separator': ' '
-     * });
-     * // => 'hi-diddly-ho there,...'
-     *
-     * _.truncate('hi-diddly-ho there, neighborino', {
-     *   'length': 24,
-     *   'separator': /,? +/
-     * });
-     * // => 'hi-diddly-ho there...'
-     *
-     * _.truncate('hi-diddly-ho there, neighborino', {
-     *   'omission': ' [...]'
-     * });
-     * // => 'hi-diddly-ho there, neig [...]'
-     */
-    function truncate(string, options) {
-      var length = DEFAULT_TRUNC_LENGTH,
-          omission = DEFAULT_TRUNC_OMISSION;
-
-      if (isObject(options)) {
-        var separator = 'separator' in options ? options.separator : separator;
-        length = 'length' in options ? toInteger(options.length) : length;
-        omission = 'omission' in options ? baseToString(options.omission) : omission;
-      }
-      string = toString(string);
-
-      var strLength = string.length;
-      if (hasUnicode(string)) {
-        var strSymbols = stringToArray(string);
-        strLength = strSymbols.length;
-      }
-      if (length >= strLength) {
-        return string;
-      }
-      var end = length - stringSize(omission);
-      if (end < 1) {
-        return omission;
-      }
-      var result = strSymbols
-        ? castSlice(strSymbols, 0, end).join('')
-        : string.slice(0, end);
-
-      if (separator === undefined) {
-        return result + omission;
-      }
-      if (strSymbols) {
-        end += (result.length - end);
-      }
-      if (isRegExp(separator)) {
-        if (string.slice(end).search(separator)) {
-          var match,
-              substring = result;
-
-          if (!separator.global) {
-            separator = RegExp(separator.source, toString(reFlags.exec(separator)) + 'g');
-          }
-          separator.lastIndex = 0;
-          while ((match = separator.exec(substring))) {
-            var newEnd = match.index;
-          }
-          result = result.slice(0, newEnd === undefined ? end : newEnd);
-        }
-      } else if (string.indexOf(baseToString(separator), end) != end) {
-        var index = result.lastIndexOf(separator);
-        if (index > -1) {
-          result = result.slice(0, index);
-        }
-      }
-      return result + omission;
-    }
-
-    /**
-     * The inverse of `_.escape`; this method converts the HTML entities
-     * `&amp;`, `&lt;`, `&gt;`, `&quot;`, and `&#39;` in `string` to
-     * their corresponding characters.
-     *
-     * **Note:** No other HTML entities are unescaped. To unescape additional
-     * HTML entities use a third-party library like [_he_](https://mths.be/he).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.6.0
-     * @category String
-     * @param {string} [string=''] The string to unescape.
-     * @returns {string} Returns the unescaped string.
-     * @example
-     *
-     * _.unescape('fred, barney, &amp; pebbles');
-     * // => 'fred, barney, & pebbles'
-     */
-    function unescape(string) {
-      string = toString(string);
-      return (string && reHasEscapedHtml.test(string))
-        ? string.replace(reEscapedHtml, unescapeHtmlChar)
-        : string;
-    }
-
-    /**
-     * Converts `string`, as space separated words, to upper case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the upper cased string.
-     * @example
-     *
-     * _.upperCase('--foo-bar');
-     * // => 'FOO BAR'
-     *
-     * _.upperCase('fooBar');
-     * // => 'FOO BAR'
-     *
-     * _.upperCase('__foo_bar__');
-     * // => 'FOO BAR'
-     */
-    var upperCase = createCompounder(function(result, word, index) {
-      return result + (index ? ' ' : '') + word.toUpperCase();
-    });
-
-    /**
-     * Converts the first character of `string` to upper case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the converted string.
-     * @example
-     *
-     * _.upperFirst('fred');
-     * // => 'Fred'
-     *
-     * _.upperFirst('FRED');
-     * // => 'FRED'
-     */
-    var upperFirst = createCaseFirst('toUpperCase');
-
-    /**
-     * Splits `string` into an array of its words.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to inspect.
-     * @param {RegExp|string} [pattern] The pattern to match words.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the words of `string`.
-     * @example
-     *
-     * _.words('fred, barney, & pebbles');
-     * // => ['fred', 'barney', 'pebbles']
-     *
-     * _.words('fred, barney, & pebbles', /[^, ]+/g);
-     * // => ['fred', 'barney', '&', 'pebbles']
-     */
-    function words(string, pattern, guard) {
-      string = toString(string);
-      pattern = guard ? undefined : pattern;
-
-      if (pattern === undefined) {
-        return hasUnicodeWord(string) ? unicodeWords(string) : asciiWords(string);
-      }
-      return string.match(pattern) || [];
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Attempts to invoke `func`, returning either the result or the caught error
-     * object. Any additional arguments are provided to `func` when it's invoked.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {Function} func The function to attempt.
-     * @param {...*} [args] The arguments to invoke `func` with.
-     * @returns {*} Returns the `func` result or error object.
-     * @example
-     *
-     * // Avoid throwing errors for invalid selectors.
-     * var elements = _.attempt(function(selector) {
-     *   return document.querySelectorAll(selector);
-     * }, '>_>');
-     *
-     * if (_.isError(elements)) {
-     *   elements = [];
-     * }
-     */
-    var attempt = baseRest(function(func, args) {
-      try {
-        return apply(func, undefined, args);
-      } catch (e) {
-        return isError(e) ? e : new Error(e);
-      }
-    });
-
-    /**
-     * Binds methods of an object to the object itself, overwriting the existing
-     * method.
-     *
-     * **Note:** This method doesn't set the "length" property of bound functions.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {Object} object The object to bind and assign the bound methods to.
-     * @param {...(string|string[])} methodNames The object method names to bind.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var view = {
-     *   'label': 'docs',
-     *   'click': function() {
-     *     console.log('clicked ' + this.label);
-     *   }
-     * };
-     *
-     * _.bindAll(view, ['click']);
-     * jQuery(element).on('click', view.click);
-     * // => Logs 'clicked docs' when clicked.
-     */
-    var bindAll = flatRest(function(object, methodNames) {
-      arrayEach(methodNames, function(key) {
-        key = toKey(key);
-        baseAssignValue(object, key, bind(object[key], object));
-      });
-      return object;
-    });
-
-    /**
-     * Creates a function that iterates over `pairs` and invokes the corresponding
-     * function of the first predicate to return truthy. The predicate-function
-     * pairs are invoked with the `this` binding and arguments of the created
-     * function.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {Array} pairs The predicate-function pairs.
-     * @returns {Function} Returns the new composite function.
-     * @example
-     *
-     * var func = _.cond([
-     *   [_.matches({ 'a': 1 }),           _.constant('matches A')],
-     *   [_.conforms({ 'b': _.isNumber }), _.constant('matches B')],
-     *   [_.stubTrue,                      _.constant('no match')]
-     * ]);
-     *
-     * func({ 'a': 1, 'b': 2 });
-     * // => 'matches A'
-     *
-     * func({ 'a': 0, 'b': 1 });
-     * // => 'matches B'
-     *
-     * func({ 'a': '1', 'b': '2' });
-     * // => 'no match'
-     */
-    function cond(pairs) {
-      var length = pairs == null ? 0 : pairs.length,
-          toIteratee = getIteratee();
-
-      pairs = !length ? [] : arrayMap(pairs, function(pair) {
-        if (typeof pair[1] != 'function') {
-          throw new TypeError(FUNC_ERROR_TEXT);
-        }
-        return [toIteratee(pair[0]), pair[1]];
-      });
-
-      return baseRest(function(args) {
-        var index = -1;
-        while (++index < length) {
-          var pair = pairs[index];
-          if (apply(pair[0], this, args)) {
-            return apply(pair[1], this, args);
-          }
-        }
-      });
-    }
-
-    /**
-     * Creates a function that invokes the predicate properties of `source` with
-     * the corresponding property values of a given object, returning `true` if
-     * all predicates return truthy, else `false`.
-     *
-     * **Note:** The created function is equivalent to `_.conformsTo` with
-     * `source` partially applied.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {Function} Returns the new spec function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': 2, 'b': 1 },
-     *   { 'a': 1, 'b': 2 }
-     * ];
-     *
-     * _.filter(objects, _.conforms({ 'b': function(n) { return n > 1; } }));
-     * // => [{ 'a': 1, 'b': 2 }]
-     */
-    function conforms(source) {
-      return baseConforms(baseClone(source, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that returns `value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Util
-     * @param {*} value The value to return from the new function.
-     * @returns {Function} Returns the new constant function.
-     * @example
-     *
-     * var objects = _.times(2, _.constant({ 'a': 1 }));
-     *
-     * console.log(objects);
-     * // => [{ 'a': 1 }, { 'a': 1 }]
-     *
-     * console.log(objects[0] === objects[1]);
-     * // => true
-     */
-    function constant(value) {
-      return function() {
-        return value;
-      };
-    }
-
-    /**
-     * Checks `value` to determine whether a default value should be returned in
-     * its place. The `defaultValue` is returned if `value` is `NaN`, `null`,
-     * or `undefined`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.14.0
-     * @category Util
-     * @param {*} value The value to check.
-     * @param {*} defaultValue The default value.
-     * @returns {*} Returns the resolved value.
-     * @example
-     *
-     * _.defaultTo(1, 10);
-     * // => 1
-     *
-     * _.defaultTo(undefined, 10);
-     * // => 10
-     */
-    function defaultTo(value, defaultValue) {
-      return (value == null || value !== value) ? defaultValue : value;
-    }
-
-    /**
-     * Creates a function that returns the result of invoking the given functions
-     * with the `this` binding of the created function, where each successive
-     * invocation is supplied the return value of the previous.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [funcs] The functions to invoke.
-     * @returns {Function} Returns the new composite function.
-     * @see _.flowRight
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var addSquare = _.flow([_.add, square]);
-     * addSquare(1, 2);
-     * // => 9
-     */
-    var flow = createFlow();
-
-    /**
-     * This method is like `_.flow` except that it creates a function that
-     * invokes the given functions from right to left.
-     *
-     * @static
-     * @since 3.0.0
-     * @memberOf _
-     * @category Util
-     * @param {...(Function|Function[])} [funcs] The functions to invoke.
-     * @returns {Function} Returns the new composite function.
-     * @see _.flow
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var addSquare = _.flowRight([square, _.add]);
-     * addSquare(1, 2);
-     * // => 9
-     */
-    var flowRight = createFlow(true);
-
-    /**
-     * This method returns the first argument it receives.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {*} value Any value.
-     * @returns {*} Returns `value`.
-     * @example
-     *
-     * var object = { 'a': 1 };
-     *
-     * console.log(_.identity(object) === object);
-     * // => true
-     */
-    function identity(value) {
-      return value;
-    }
-
-    /**
-     * Creates a function that invokes `func` with the arguments of the created
-     * function. If `func` is a property name, the created function returns the
-     * property value for a given element. If `func` is an array or object, the
-     * created function returns `true` for elements that contain the equivalent
-     * source properties, otherwise it returns `false`.
-     *
-     * @static
-     * @since 4.0.0
-     * @memberOf _
-     * @category Util
-     * @param {*} [func=_.identity] The value to convert to a callback.
-     * @returns {Function} Returns the callback.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': true },
-     *   { 'user': 'fred',   'age': 40, 'active': false }
-     * ];
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.filter(users, _.iteratee({ 'user': 'barney', 'active': true }));
-     * // => [{ 'user': 'barney', 'age': 36, 'active': true }]
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.filter(users, _.iteratee(['user', 'fred']));
-     * // => [{ 'user': 'fred', 'age': 40 }]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.map(users, _.iteratee('user'));
-     * // => ['barney', 'fred']
-     *
-     * // Create custom iteratee shorthands.
-     * _.iteratee = _.wrap(_.iteratee, function(iteratee, func) {
-     *   return !_.isRegExp(func) ? iteratee(func) : function(string) {
-     *     return func.test(string);
-     *   };
-     * });
-     *
-     * _.filter(['abc', 'def'], /ef/);
-     * // => ['def']
-     */
-    function iteratee(func) {
-      return baseIteratee(typeof func == 'function' ? func : baseClone(func, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that performs a partial deep comparison between a given
-     * object and `source`, returning `true` if the given object has equivalent
-     * property values, else `false`.
-     *
-     * **Note:** The created function is equivalent to `_.isMatch` with `source`
-     * partially applied.
-     *
-     * Partial comparisons will match empty array and empty object `source`
-     * values against any array or object value, respectively. See `_.isEqual`
-     * for a list of supported value comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {Object} source The object of property values to match.
-     * @returns {Function} Returns the new spec function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': 1, 'b': 2, 'c': 3 },
-     *   { 'a': 4, 'b': 5, 'c': 6 }
-     * ];
-     *
-     * _.filter(objects, _.matches({ 'a': 4, 'c': 6 }));
-     * // => [{ 'a': 4, 'b': 5, 'c': 6 }]
-     */
-    function matches(source) {
-      return baseMatches(baseClone(source, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that performs a partial deep comparison between the
-     * value at `path` of a given object to `srcValue`, returning `true` if the
-     * object value is equivalent, else `false`.
-     *
-     * **Note:** Partial comparisons will match empty array and empty object
-     * `srcValue` values against any array or object value, respectively. See
-     * `_.isEqual` for a list of supported value comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.2.0
-     * @category Util
-     * @param {Array|string} path The path of the property to get.
-     * @param {*} srcValue The value to match.
-     * @returns {Function} Returns the new spec function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': 1, 'b': 2, 'c': 3 },
-     *   { 'a': 4, 'b': 5, 'c': 6 }
-     * ];
-     *
-     * _.find(objects, _.matchesProperty('a', 4));
-     * // => { 'a': 4, 'b': 5, 'c': 6 }
-     */
-    function matchesProperty(path, srcValue) {
-      return baseMatchesProperty(path, baseClone(srcValue, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that invokes the method at `path` of a given object.
-     * Any additional arguments are provided to the invoked method.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Util
-     * @param {Array|string} path The path of the method to invoke.
-     * @param {...*} [args] The arguments to invoke the method with.
-     * @returns {Function} Returns the new invoker function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': { 'b': _.constant(2) } },
-     *   { 'a': { 'b': _.constant(1) } }
-     * ];
-     *
-     * _.map(objects, _.method('a.b'));
-     * // => [2, 1]
-     *
-     * _.map(objects, _.method(['a', 'b']));
-     * // => [2, 1]
-     */
-    var method = baseRest(function(path, args) {
-      return function(object) {
-        return baseInvoke(object, path, args);
-      };
-    });
-
-    /**
-     * The opposite of `_.method`; this method creates a function that invokes
-     * the method at a given path of `object`. Any additional arguments are
-     * provided to the invoked method.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Util
-     * @param {Object} object The object to query.
-     * @param {...*} [args] The arguments to invoke the method with.
-     * @returns {Function} Returns the new invoker function.
-     * @example
-     *
-     * var array = _.times(3, _.constant),
-     *     object = { 'a': array, 'b': array, 'c': array };
-     *
-     * _.map(['a[2]', 'c[0]'], _.methodOf(object));
-     * // => [2, 0]
-     *
-     * _.map([['a', '2'], ['c', '0']], _.methodOf(object));
-     * // => [2, 0]
-     */
-    var methodOf = baseRest(function(object, args) {
-      return function(path) {
-        return baseInvoke(object, path, args);
-      };
-    });
-
-    /**
-     * Adds all own enumerable string keyed function properties of a source
-     * object to the destination object. If `object` is a function, then methods
-     * are added to its prototype as well.
-     *
-     * **Note:** Use `_.runInContext` to create a pristine `lodash` function to
-     * avoid conflicts caused by modifying the original.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {Function|Object} [object=lodash] The destination object.
-     * @param {Object} source The object of functions to add.
-     * @param {Object} [options={}] The options object.
-     * @param {boolean} [options.chain=true] Specify whether mixins are chainable.
-     * @returns {Function|Object} Returns `object`.
-     * @example
-     *
-     * function vowels(string) {
-     *   return _.filter(string, function(v) {
-     *     return /[aeiou]/i.test(v);
-     *   });
-     * }
-     *
-     * _.mixin({ 'vowels': vowels });
-     * _.vowels('fred');
-     * // => ['e']
-     *
-     * _('fred').vowels().value();
-     * // => ['e']
-     *
-     * _.mixin({ 'vowels': vowels }, { 'chain': false });
-     * _('fred').vowels();
-     * // => ['e']
-     */
-    function mixin(object, source, options) {
-      var props = keys(source),
-          methodNames = baseFunctions(source, props);
-
-      if (options == null &&
-          !(isObject(source) && (methodNames.length || !props.length))) {
-        options = source;
-        source = object;
-        object = this;
-        methodNames = baseFunctions(source, keys(source));
-      }
-      var chain = !(isObject(options) && 'chain' in options) || !!options.chain,
-          isFunc = isFunction(object);
-
-      arrayEach(methodNames, function(methodName) {
-        var func = source[methodName];
-        object[methodName] = func;
-        if (isFunc) {
-          object.prototype[methodName] = function() {
-            var chainAll = this.__chain__;
-            if (chain || chainAll) {
-              var result = object(this.__wrapped__),
-                  actions = result.__actions__ = copyArray(this.__actions__);
-
-              actions.push({ 'func': func, 'args': arguments, 'thisArg': object });
-              result.__chain__ = chainAll;
-              return result;
-            }
-            return func.apply(object, arrayPush([this.value()], arguments));
-          };
-        }
-      });
-
-      return object;
-    }
-
-    /**
-     * Reverts the `_` variable to its previous value and returns a reference to
-     * the `lodash` function.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @returns {Function} Returns the `lodash` function.
-     * @example
-     *
-     * var lodash = _.noConflict();
-     */
-    function noConflict() {
-      if (root._ === this) {
-        root._ = oldDash;
-      }
-      return this;
-    }
-
-    /**
-     * This method returns `undefined`.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.3.0
-     * @category Util
-     * @example
-     *
-     * _.times(2, _.noop);
-     * // => [undefined, undefined]
-     */
-    function noop() {
-      // No operation performed.
-    }
-
-    /**
-     * Creates a function that gets the argument at index `n`. If `n` is negative,
-     * the nth argument from the end is returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {number} [n=0] The index of the argument to return.
-     * @returns {Function} Returns the new pass-thru function.
-     * @example
-     *
-     * var func = _.nthArg(1);
-     * func('a', 'b', 'c', 'd');
-     * // => 'b'
-     *
-     * var func = _.nthArg(-2);
-     * func('a', 'b', 'c', 'd');
-     * // => 'c'
-     */
-    function nthArg(n) {
-      n = toInteger(n);
-      return baseRest(function(args) {
-        return baseNth(args, n);
-      });
-    }
-
-    /**
-     * Creates a function that invokes `iteratees` with the arguments it receives
-     * and returns their results.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [iteratees=[_.identity]]
-     *  The iteratees to invoke.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var func = _.over([Math.max, Math.min]);
-     *
-     * func(1, 2, 3, 4);
-     * // => [4, 1]
-     */
-    var over = createOver(arrayMap);
-
-    /**
-     * Creates a function that checks if **all** of the `predicates` return
-     * truthy when invoked with the arguments it receives.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [predicates=[_.identity]]
-     *  The predicates to check.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var func = _.overEvery([Boolean, isFinite]);
-     *
-     * func('1');
-     * // => true
-     *
-     * func(null);
-     * // => false
-     *
-     * func(NaN);
-     * // => false
-     */
-    var overEvery = createOver(arrayEvery);
-
-    /**
-     * Creates a function that checks if **any** of the `predicates` return
-     * truthy when invoked with the arguments it receives.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [predicates=[_.identity]]
-     *  The predicates to check.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var func = _.overSome([Boolean, isFinite]);
-     *
-     * func('1');
-     * // => true
-     *
-     * func(null);
-     * // => true
-     *
-     * func(NaN);
-     * // => false
-     */
-    var overSome = createOver(arraySome);
-
-    /**
-     * Creates a function that returns the value at `path` of a given object.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Util
-     * @param {Array|string} path The path of the property to get.
-     * @returns {Function} Returns the new accessor function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': { 'b': 2 } },
-     *   { 'a': { 'b': 1 } }
-     * ];
-     *
-     * _.map(objects, _.property('a.b'));
-     * // => [2, 1]
-     *
-     * _.map(_.sortBy(objects, _.property(['a', 'b'])), 'a.b');
-     * // => [1, 2]
-     */
-    function property(path) {
-      return isKey(path) ? baseProperty(toKey(path)) : basePropertyDeep(path);
-    }
-
-    /**
-     * The opposite of `_.property`; this method creates a function that returns
-     * the value at a given path of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {Object} object The object to query.
-     * @returns {Function} Returns the new accessor function.
-     * @example
-     *
-     * var array = [0, 1, 2],
-     *     object = { 'a': array, 'b': array, 'c': array };
-     *
-     * _.map(['a[2]', 'c[0]'], _.propertyOf(object));
-     * // => [2, 0]
-     *
-     * _.map([['a', '2'], ['c', '0']], _.propertyOf(object));
-     * // => [2, 0]
-     */
-    function propertyOf(object) {
-      return function(path) {
-        return object == null ? undefined : baseGet(object, path);
-      };
-    }
-
-    /**
-     * Creates an array of numbers (positive and/or negative) progressing from
-     * `start` up to, but not including, `end`. A step of `-1` is used if a negative
-     * `start` is specified without an `end` or `step`. If `end` is not specified,
-     * it's set to `start` with `start` then set to `0`.
-     *
-     * **Note:** JavaScript follows the IEEE-754 standard for resolving
-     * floating-point values which can produce unexpected results.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {number} [start=0] The start of the range.
-     * @param {number} end The end of the range.
-     * @param {number} [step=1] The value to increment or decrement by.
-     * @returns {Array} Returns the range of numbers.
-     * @see _.inRange, _.rangeRight
-     * @example
-     *
-     * _.range(4);
-     * // => [0, 1, 2, 3]
-     *
-     * _.range(-4);
-     * // => [0, -1, -2, -3]
-     *
-     * _.range(1, 5);
-     * // => [1, 2, 3, 4]
-     *
-     * _.range(0, 20, 5);
-     * // => [0, 5, 10, 15]
-     *
-     * _.range(0, -4, -1);
-     * // => [0, -1, -2, -3]
-     *
-     * _.range(1, 4, 0);
-     * // => [1, 1, 1]
-     *
-     * _.range(0);
-     * // => []
-     */
-    var range = createRange();
-
-    /**
-     * This method is like `_.range` except that it populates values in
-     * descending order.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {number} [start=0] The start of the range.
-     * @param {number} end The end of the range.
-     * @param {number} [step=1] The value to increment or decrement by.
-     * @returns {Array} Returns the range of numbers.
-     * @see _.inRange, _.range
-     * @example
-     *
-     * _.rangeRight(4);
-     * // => [3, 2, 1, 0]
-     *
-     * _.rangeRight(-4);
-     * // => [-3, -2, -1, 0]
-     *
-     * _.rangeRight(1, 5);
-     * // => [4, 3, 2, 1]
-     *
-     * _.rangeRight(0, 20, 5);
-     * // => [15, 10, 5, 0]
-     *
-     * _.rangeRight(0, -4, -1);
-     * // => [-3, -2, -1, 0]
-     *
-     * _.rangeRight(1, 4, 0);
-     * // => [1, 1, 1]
-     *
-     * _.rangeRight(0);
-     * // => []
-     */
-    var rangeRight = createRange(true);
-
-    /**
-     * This method returns a new empty array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {Array} Returns the new empty array.
-     * @example
-     *
-     * var arrays = _.times(2, _.stubArray);
-     *
-     * console.log(arrays);
-     * // => [[], []]
-     *
-     * console.log(arrays[0] === arrays[1]);
-     * // => false
-     */
-    function stubArray() {
-      return [];
-    }
-
-    /**
-     * This method returns `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {boolean} Returns `false`.
-     * @example
-     *
-     * _.times(2, _.stubFalse);
-     * // => [false, false]
-     */
-    function stubFalse() {
-      return false;
-    }
-
-    /**
-     * This method returns a new empty object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {Object} Returns the new empty object.
-     * @example
-     *
-     * var objects = _.times(2, _.stubObject);
-     *
-     * console.log(objects);
-     * // => [{}, {}]
-     *
-     * console.log(objects[0] === objects[1]);
-     * // => false
-     */
-    function stubObject() {
-      return {};
-    }
-
-    /**
-     * This method returns an empty string.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {string} Returns the empty string.
-     * @example
-     *
-     * _.times(2, _.stubString);
-     * // => ['', '']
-     */
-    function stubString() {
-      return '';
-    }
-
-    /**
-     * This method returns `true`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {boolean} Returns `true`.
-     * @example
-     *
-     * _.times(2, _.stubTrue);
-     * // => [true, true]
-     */
-    function stubTrue() {
-      return true;
-    }
-
-    /**
-     * Invokes the iteratee `n` times, returning an array of the results of
-     * each invocation. The iteratee is invoked with one argument; (index).
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {number} n The number of times to invoke `iteratee`.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the array of results.
-     * @example
-     *
-     * _.times(3, String);
-     * // => ['0', '1', '2']
-     *
-     *  _.times(4, _.constant(0));
-     * // => [0, 0, 0, 0]
-     */
-    function times(n, iteratee) {
-      n = toInteger(n);
-      if (n < 1 || n > MAX_SAFE_INTEGER) {
-        return [];
-      }
-      var index = MAX_ARRAY_LENGTH,
-          length = nativeMin(n, MAX_ARRAY_LENGTH);
-
-      iteratee = getIteratee(iteratee);
-      n -= MAX_ARRAY_LENGTH;
-
-      var result = baseTimes(length, iteratee);
-      while (++index < n) {
-        iteratee(index);
-      }
-      return result;
-    }
-
-    /**
-     * Converts `value` to a property path array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {*} value The value to convert.
-     * @returns {Array} Returns the new property path array.
-     * @example
-     *
-     * _.toPath('a.b.c');
-     * // => ['a', 'b', 'c']
-     *
-     * _.toPath('a[0].b.c');
-     * // => ['a', '0', 'b', 'c']
-     */
-    function toPath(value) {
-      if (isArray(value)) {
-        return arrayMap(value, toKey);
-      }
-      return isSymbol(value) ? [value] : copyArray(stringToPath(toString(value)));
-    }
-
-    /**
-     * Generates a unique ID. If `prefix` is given, the ID is appended to it.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {string} [prefix=''] The value to prefix the ID with.
-     * @returns {string} Returns the unique ID.
-     * @example
-     *
-     * _.uniqueId('contact_');
-     * // => 'contact_104'
-     *
-     * _.uniqueId();
-     * // => '105'
-     */
-    function uniqueId(prefix) {
-      var id = ++idCounter;
-      return toString(prefix) + id;
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Adds two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.4.0
-     * @category Math
-     * @param {number} augend The first number in an addition.
-     * @param {number} addend The second number in an addition.
-     * @returns {number} Returns the total.
-     * @example
-     *
-     * _.add(6, 4);
-     * // => 10
-     */
-    var add = createMathOperation(function(augend, addend) {
-      return augend + addend;
-    }, 0);
-
-    /**
-     * Computes `number` rounded up to `precision`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Math
-     * @param {number} number The number to round up.
-     * @param {number} [precision=0] The precision to round up to.
-     * @returns {number} Returns the rounded up number.
-     * @example
-     *
-     * _.ceil(4.006);
-     * // => 5
-     *
-     * _.ceil(6.004, 2);
-     * // => 6.01
-     *
-     * _.ceil(6040, -2);
-     * // => 6100
-     */
-    var ceil = createRound('ceil');
-
-    /**
-     * Divide two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Math
-     * @param {number} dividend The first number in a division.
-     * @param {number} divisor The second number in a division.
-     * @returns {number} Returns the quotient.
-     * @example
-     *
-     * _.divide(6, 4);
-     * // => 1.5
-     */
-    var divide = createMathOperation(function(dividend, divisor) {
-      return dividend / divisor;
-    }, 1);
-
-    /**
-     * Computes `number` rounded down to `precision`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Math
-     * @param {number} number The number to round down.
-     * @param {number} [precision=0] The precision to round down to.
-     * @returns {number} Returns the rounded down number.
-     * @example
-     *
-     * _.floor(4.006);
-     * // => 4
-     *
-     * _.floor(0.046, 2);
-     * // => 0.04
-     *
-     * _.floor(4060, -2);
-     * // => 4000
-     */
-    var floor = createRound('floor');
-
-    /**
-     * Computes the maximum value of `array`. If `array` is empty or falsey,
-     * `undefined` is returned.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {*} Returns the maximum value.
-     * @example
-     *
-     * _.max([4, 2, 8, 6]);
-     * // => 8
-     *
-     * _.max([]);
-     * // => undefined
-     */
-    function max(array) {
-      return (array && array.length)
-        ? baseExtremum(array, identity, baseGt)
-        : undefined;
-    }
-
-    /**
-     * This method is like `_.max` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the criterion by which
-     * the value is ranked. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {*} Returns the maximum value.
-     * @example
-     *
-     * var objects = [{ 'n': 1 }, { 'n': 2 }];
-     *
-     * _.maxBy(objects, function(o) { return o.n; });
-     * // => { 'n': 2 }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.maxBy(objects, 'n');
-     * // => { 'n': 2 }
-     */
-    function maxBy(array, iteratee) {
-      return (array && array.length)
-        ? baseExtremum(array, getIteratee(iteratee, 2), baseGt)
-        : undefined;
-    }
-
-    /**
-     * Computes the mean of the values in `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {number} Returns the mean.
-     * @example
-     *
-     * _.mean([4, 2, 8, 6]);
-     * // => 5
-     */
-    function mean(array) {
-      return baseMean(array, identity);
-    }
-
-    /**
-     * This method is like `_.mean` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the value to be averaged.
-     * The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the mean.
-     * @example
-     *
-     * var objects = [{ 'n': 4 }, { 'n': 2 }, { 'n': 8 }, { 'n': 6 }];
-     *
-     * _.meanBy(objects, function(o) { return o.n; });
-     * // => 5
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.meanBy(objects, 'n');
-     * // => 5
-     */
-    function meanBy(array, iteratee) {
-      return baseMean(array, getIteratee(iteratee, 2));
-    }
-
-    /**
-     * Computes the minimum value of `array`. If `array` is empty or falsey,
-     * `undefined` is returned.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {*} Returns the minimum value.
-     * @example
-     *
-     * _.min([4, 2, 8, 6]);
-     * // => 2
-     *
-     * _.min([]);
-     * // => undefined
-     */
-    function min(array) {
-      return (array && array.length)
-        ? baseExtremum(array, identity, baseLt)
-        : undefined;
-    }
-
-    /**
-     * This method is like `_.min` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the criterion by which
-     * the value is ranked. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {*} Returns the minimum value.
-     * @example
-     *
-     * var objects = [{ 'n': 1 }, { 'n': 2 }];
-     *
-     * _.minBy(objects, function(o) { return o.n; });
-     * // => { 'n': 1 }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.minBy(objects, 'n');
-     * // => { 'n': 1 }
-     */
-    function minBy(array, iteratee) {
-      return (array && array.length)
-        ? baseExtremum(array, getIteratee(iteratee, 2), baseLt)
-        : undefined;
-    }
-
-    /**
-     * Multiply two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Math
-     * @param {number} multiplier The first number in a multiplication.
-     * @param {number} multiplicand The second number in a multiplication.
-     * @returns {number} Returns the product.
-     * @example
-     *
-     * _.multiply(6, 4);
-     * // => 24
-     */
-    var multiply = createMathOperation(function(multiplier, multiplicand) {
-      return multiplier * multiplicand;
-    }, 1);
-
-    /**
-     * Computes `number` rounded to `precision`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Math
-     * @param {number} number The number to round.
-     * @param {number} [precision=0] The precision to round to.
-     * @returns {number} Returns the rounded number.
-     * @example
-     *
-     * _.round(4.006);
-     * // => 4
-     *
-     * _.round(4.006, 2);
-     * // => 4.01
-     *
-     * _.round(4060, -2);
-     * // => 4100
-     */
-    var round = createRound('round');
-
-    /**
-     * Subtract two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {number} minuend The first number in a subtraction.
-     * @param {number} subtrahend The second number in a subtraction.
-     * @returns {number} Returns the difference.
-     * @example
-     *
-     * _.subtract(6, 4);
-     * // => 2
-     */
-    var subtract = createMathOperation(function(minuend, subtrahend) {
-      return minuend - subtrahend;
-    }, 0);
-
-    /**
-     * Computes the sum of the values in `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.4.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {number} Returns the sum.
-     * @example
-     *
-     * _.sum([4, 2, 8, 6]);
-     * // => 20
-     */
-    function sum(array) {
-      return (array && array.length)
-        ? baseSum(array, identity)
-        : 0;
-    }
-
-    /**
-     * This method is like `_.sum` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the value to be summed.
-     * The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the sum.
-     * @example
-     *
-     * var objects = [{ 'n': 4 }, { 'n': 2 }, { 'n': 8 }, { 'n': 6 }];
-     *
-     * _.sumBy(objects, function(o) { return o.n; });
-     * // => 20
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.sumBy(objects, 'n');
-     * // => 20
-     */
-    function sumBy(array, iteratee) {
-      return (array && array.length)
-        ? baseSum(array, getIteratee(iteratee, 2))
-        : 0;
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    // Add methods that return wrapped values in chain sequences.
-    lodash.after = after;
-    lodash.ary = ary;
-    lodash.assign = assign;
-    lodash.assignIn = assignIn;
-    lodash.assignInWith = assignInWith;
-    lodash.assignWith = assignWith;
-    lodash.at = at;
-    lodash.before = before;
-    lodash.bind = bind;
-    lodash.bindAll = bindAll;
-    lodash.bindKey = bindKey;
-    lodash.castArray = castArray;
-    lodash.chain = chain;
-    lodash.chunk = chunk;
-    lodash.compact = compact;
-    lodash.concat = concat;
-    lodash.cond = cond;
-    lodash.conforms = conforms;
-    lodash.constant = constant;
-    lodash.countBy = countBy;
-    lodash.create = create;
-    lodash.curry = curry;
-    lodash.curryRight = curryRight;
-    lodash.debounce = debounce;
-    lodash.defaults = defaults;
-    lodash.defaultsDeep = defaultsDeep;
-    lodash.defer = defer;
-    lodash.delay = delay;
-    lodash.difference = difference;
-    lodash.differenceBy = differenceBy;
-    lodash.differenceWith = differenceWith;
-    lodash.drop = drop;
-    lodash.dropRight = dropRight;
-    lodash.dropRightWhile = dropRightWhile;
-    lodash.dropWhile = dropWhile;
-    lodash.fill = fill;
-    lodash.filter = filter;
-    lodash.flatMap = flatMap;
-    lodash.flatMapDeep = flatMapDeep;
-    lodash.flatMapDepth = flatMapDepth;
-    lodash.flatten = flatten;
-    lodash.flattenDeep = flattenDeep;
-    lodash.flattenDepth = flattenDepth;
-    lodash.flip = flip;
-    lodash.flow = flow;
-    lodash.flowRight = flowRight;
-    lodash.fromPairs = fromPairs;
-    lodash.functions = functions;
-    lodash.functionsIn = functionsIn;
-    lodash.groupBy = groupBy;
-    lodash.initial = initial;
-    lodash.intersection = intersection;
-    lodash.intersectionBy = intersectionBy;
-    lodash.intersectionWith = intersectionWith;
-    lodash.invert = invert;
-    lodash.invertBy = invertBy;
-    lodash.invokeMap = invokeMap;
-    lodash.iteratee = iteratee;
-    lodash.keyBy = keyBy;
-    lodash.keys = keys;
-    lodash.keysIn = keysIn;
-    lodash.map = map;
-    lodash.mapKeys = mapKeys;
-    lodash.mapValues = mapValues;
-    lodash.matches = matches;
-    lodash.matchesProperty = matchesProperty;
-    lodash.memoize = memoize;
-    lodash.merge = merge;
-    lodash.mergeWith = mergeWith;
-    lodash.method = method;
-    lodash.methodOf = methodOf;
-    lodash.mixin = mixin;
-    lodash.negate = negate;
-    lodash.nthArg = nthArg;
-    lodash.omit = omit;
-    lodash.omitBy = omitBy;
-    lodash.once = once;
-    lodash.orderBy = orderBy;
-    lodash.over = over;
-    lodash.overArgs = overArgs;
-    lodash.overEvery = overEvery;
-    lodash.overSome = overSome;
-    lodash.partial = partial;
-    lodash.partialRight = partialRight;
-    lodash.partition = partition;
-    lodash.pick = pick;
-    lodash.pickBy = pickBy;
-    lodash.property = property;
-    lodash.propertyOf = propertyOf;
-    lodash.pull = pull;
-    lodash.pullAll = pullAll;
-    lodash.pullAllBy = pullAllBy;
-    lodash.pullAllWith = pullAllWith;
-    lodash.pullAt = pullAt;
-    lodash.range = range;
-    lodash.rangeRight = rangeRight;
-    lodash.rearg = rearg;
-    lodash.reject = reject;
-    lodash.remove = remove;
-    lodash.rest = rest;
-    lodash.reverse = reverse;
-    lodash.sampleSize = sampleSize;
-    lodash.set = set;
-    lodash.setWith = setWith;
-    lodash.shuffle = shuffle;
-    lodash.slice = slice;
-    lodash.sortBy = sortBy;
-    lodash.sortedUniq = sortedUniq;
-    lodash.sortedUniqBy = sortedUniqBy;
-    lodash.split = split;
-    lodash.spread = spread;
-    lodash.tail = tail;
-    lodash.take = take;
-    lodash.takeRight = takeRight;
-    lodash.takeRightWhile = takeRightWhile;
-    lodash.takeWhile = takeWhile;
-    lodash.tap = tap;
-    lodash.throttle = throttle;
-    lodash.thru = thru;
-    lodash.toArray = toArray;
-    lodash.toPairs = toPairs;
-    lodash.toPairsIn = toPairsIn;
-    lodash.toPath = toPath;
-    lodash.toPlainObject = toPlainObject;
-    lodash.transform = transform;
-    lodash.unary = unary;
-    lodash.union = union;
-    lodash.unionBy = unionBy;
-    lodash.unionWith = unionWith;
-    lodash.uniq = uniq;
-    lodash.uniqBy = uniqBy;
-    lodash.uniqWith = uniqWith;
-    lodash.unset = unset;
-    lodash.unzip = unzip;
-    lodash.unzipWith = unzipWith;
-    lodash.update = update;
-    lodash.updateWith = updateWith;
-    lodash.values = values;
-    lodash.valuesIn = valuesIn;
-    lodash.without = without;
-    lodash.words = words;
-    lodash.wrap = wrap;
-    lodash.xor = xor;
-    lodash.xorBy = xorBy;
-    lodash.xorWith = xorWith;
-    lodash.zip = zip;
-    lodash.zipObject = zipObject;
-    lodash.zipObjectDeep = zipObjectDeep;
-    lodash.zipWith = zipWith;
-
-    // Add aliases.
-    lodash.entries = toPairs;
-    lodash.entriesIn = toPairsIn;
-    lodash.extend = assignIn;
-    lodash.extendWith = assignInWith;
-
-    // Add methods to `lodash.prototype`.
-    mixin(lodash, lodash);
-
-    /*------------------------------------------------------------------------*/
-
-    // Add methods that return unwrapped values in chain sequences.
-    lodash.add = add;
-    lodash.attempt = attempt;
-    lodash.camelCase = camelCase;
-    lodash.capitalize = capitalize;
-    lodash.ceil = ceil;
-    lodash.clamp = clamp;
-    lodash.clone = clone;
-    lodash.cloneDeep = cloneDeep;
-    lodash.cloneDeepWith = cloneDeepWith;
-    lodash.cloneWith = cloneWith;
-    lodash.conformsTo = conformsTo;
-    lodash.deburr = deburr;
-    lodash.defaultTo = defaultTo;
-    lodash.divide = divide;
-    lodash.endsWith = endsWith;
-    lodash.eq = eq;
-    lodash.escape = escape;
-    lodash.escapeRegExp = escapeRegExp;
-    lodash.every = every;
-    lodash.find = find;
-    lodash.findIndex = findIndex;
-    lodash.findKey = findKey;
-    lodash.findLast = findLast;
-    lodash.findLastIndex = findLastIndex;
-    lodash.findLastKey = findLastKey;
-    lodash.floor = floor;
-    lodash.forEach = forEach;
-    lodash.forEachRight = forEachRight;
-    lodash.forIn = forIn;
-    lodash.forInRight = forInRight;
-    lodash.forOwn = forOwn;
-    lodash.forOwnRight = forOwnRight;
-    lodash.get = get;
-    lodash.gt = gt;
-    lodash.gte = gte;
-    lodash.has = has;
-    lodash.hasIn = hasIn;
-    lodash.head = head;
-    lodash.identity = identity;
-    lodash.includes = includes;
-    lodash.indexOf = indexOf;
-    lodash.inRange = inRange;
-    lodash.invoke = invoke;
-    lodash.isArguments = isArguments;
-    lodash.isArray = isArray;
-    lodash.isArrayBuffer = isArrayBuffer;
-    lodash.isArrayLike = isArrayLike;
-    lodash.isArrayLikeObject = isArrayLikeObject;
-    lodash.isBoolean = isBoolean;
-    lodash.isBuffer = isBuffer;
-    lodash.isDate = isDate;
-    lodash.isElement = isElement;
-    lodash.isEmpty = isEmpty;
-    lodash.isEqual = isEqual;
-    lodash.isEqualWith = isEqualWith;
-    lodash.isError = isError;
-    lodash.isFinite = isFinite;
-    lodash.isFunction = isFunction;
-    lodash.isInteger = isInteger;
-    lodash.isLength = isLength;
-    lodash.isMap = isMap;
-    lodash.isMatch = isMatch;
-    lodash.isMatchWith = isMatchWith;
-    lodash.isNaN = isNaN;
-    lodash.isNative = isNative;
-    lodash.isNil = isNil;
-    lodash.isNull = isNull;
-    lodash.isNumber = isNumber;
-    lodash.isObject = isObject;
-    lodash.isObjectLike = isObjectLike;
-    lodash.isPlainObject = isPlainObject;
-    lodash.isRegExp = isRegExp;
-    lodash.isSafeInteger = isSafeInteger;
-    lodash.isSet = isSet;
-    lodash.isString = isString;
-    lodash.isSymbol = isSymbol;
-    lodash.isTypedArray = isTypedArray;
-    lodash.isUndefined = isUndefined;
-    lodash.isWeakMap = isWeakMap;
-    lodash.isWeakSet = isWeakSet;
-    lodash.join = join;
-    lodash.kebabCase = kebabCase;
-    lodash.last = last;
-    lodash.lastIndexOf = lastIndexOf;
-    lodash.lowerCase = lowerCase;
-    lodash.lowerFirst = lowerFirst;
-    lodash.lt = lt;
-    lodash.lte = lte;
-    lodash.max = max;
-    lodash.maxBy = maxBy;
-    lodash.mean = mean;
-    lodash.meanBy = meanBy;
-    lodash.min = min;
-    lodash.minBy = minBy;
-    lodash.stubArray = stubArray;
-    lodash.stubFalse = stubFalse;
-    lodash.stubObject = stubObject;
-    lodash.stubString = stubString;
-    lodash.stubTrue = stubTrue;
-    lodash.multiply = multiply;
-    lodash.nth = nth;
-    lodash.noConflict = noConflict;
-    lodash.noop = noop;
-    lodash.now = now;
-    lodash.pad = pad;
-    lodash.padEnd = padEnd;
-    lodash.padStart = padStart;
-    lodash.parseInt = parseInt;
-    lodash.random = random;
-    lodash.reduce = reduce;
-    lodash.reduceRight = reduceRight;
-    lodash.repeat = repeat;
-    lodash.replace = replace;
-    lodash.result = result;
-    lodash.round = round;
-    lodash.runInContext = runInContext;
-    lodash.sample = sample;
-    lodash.size = size;
-    lodash.snakeCase = snakeCase;
-    lodash.some = some;
-    lodash.sortedIndex = sortedIndex;
-    lodash.sortedIndexBy = sortedIndexBy;
-    lodash.sortedIndexOf = sortedIndexOf;
-    lodash.sortedLastIndex = sortedLastIndex;
-    lodash.sortedLastIndexBy = sortedLastIndexBy;
-    lodash.sortedLastIndexOf = sortedLastIndexOf;
-    lodash.startCase = startCase;
-    lodash.startsWith = startsWith;
-    lodash.subtract = subtract;
-    lodash.sum = sum;
-    lodash.sumBy = sumBy;
-    lodash.template = template;
-    lodash.times = times;
-    lodash.toFinite = toFinite;
-    lodash.toInteger = toInteger;
-    lodash.toLength = toLength;
-    lodash.toLower = toLower;
-    lodash.toNumber = toNumber;
-    lodash.toSafeInteger = toSafeInteger;
-    lodash.toString = toString;
-    lodash.toUpper = toUpper;
-    lodash.trim = trim;
-    lodash.trimEnd = trimEnd;
-    lodash.trimStart = trimStart;
-    lodash.truncate = truncate;
-    lodash.unescape = unescape;
-    lodash.uniqueId = uniqueId;
-    lodash.upperCase = upperCase;
-    lodash.upperFirst = upperFirst;
-
-    // Add aliases.
-    lodash.each = forEach;
-    lodash.eachRight = forEachRight;
-    lodash.first = head;
-
-    mixin(lodash, (function() {
-      var source = {};
-      baseForOwn(lodash, function(func, methodName) {
-        if (!hasOwnProperty.call(lodash.prototype, methodName)) {
-          source[methodName] = func;
-        }
-      });
-      return source;
-    }()), { 'chain': false });
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * The semantic version number.
-     *
-     * @static
-     * @memberOf _
-     * @type {string}
-     */
-    lodash.VERSION = VERSION;
-
-    // Assign default placeholders.
-    arrayEach(['bind', 'bindKey', 'curry', 'curryRight', 'partial', 'partialRight'], function(methodName) {
-      lodash[methodName].placeholder = lodash;
-    });
-
-    // Add `LazyWrapper` methods for `_.drop` and `_.take` variants.
-    arrayEach(['drop', 'take'], function(methodName, index) {
-      LazyWrapper.prototype[methodName] = function(n) {
-        n = n === undefined ? 1 : nativeMax(toInteger(n), 0);
-
-        var result = (this.__filtered__ && !index)
-          ? new LazyWrapper(this)
-          : this.clone();
-
-        if (result.__filtered__) {
-          result.__takeCount__ = nativeMin(n, result.__takeCount__);
-        } else {
-          result.__views__.push({
-            'size': nativeMin(n, MAX_ARRAY_LENGTH),
-            'type': methodName + (result.__dir__ < 0 ? 'Right' : '')
-          });
-        }
-        return result;
-      };
-
-      LazyWrapper.prototype[methodName + 'Right'] = function(n) {
-        return this.reverse()[methodName](n).reverse();
-      };
-    });
-
-    // Add `LazyWrapper` methods that accept an `iteratee` value.
-    arrayEach(['filter', 'map', 'takeWhile'], function(methodName, index) {
-      var type = index + 1,
-          isFilter = type == LAZY_FILTER_FLAG || type == LAZY_WHILE_FLAG;
-
-      LazyWrapper.prototype[methodName] = function(iteratee) {
-        var result = this.clone();
-        result.__iteratees__.push({
-          'iteratee': getIteratee(iteratee, 3),
-          'type': type
-        });
-        result.__filtered__ = result.__filtered__ || isFilter;
-        return result;
-      };
-    });
-
-    // Add `LazyWrapper` methods for `_.head` and `_.last`.
-    arrayEach(['head', 'last'], function(methodName, index) {
-      var takeName = 'take' + (index ? 'Right' : '');
-
-      LazyWrapper.prototype[methodName] = function() {
-        return this[takeName](1).value()[0];
-      };
-    });
-
-    // Add `LazyWrapper` methods for `_.initial` and `_.tail`.
-    arrayEach(['initial', 'tail'], function(methodName, index) {
-      var dropName = 'drop' + (index ? '' : 'Right');
-
-      LazyWrapper.prototype[methodName] = function() {
-        return this.__filtered__ ? new LazyWrapper(this) : this[dropName](1);
-      };
-    });
-
-    LazyWrapper.prototype.compact = function() {
-      return this.filter(identity);
-    };
-
-    LazyWrapper.prototype.find = function(predicate) {
-      return this.filter(predicate).head();
-    };
-
-    LazyWrapper.prototype.findLast = function(predicate) {
-      return this.reverse().find(predicate);
-    };
-
-    LazyWrapper.prototype.invokeMap = baseRest(function(path, args) {
-      if (typeof path == 'function') {
-        return new LazyWrapper(this);
-      }
-      return this.map(function(value) {
-        return baseInvoke(value, path, args);
-      });
-    });
-
-    LazyWrapper.prototype.reject = function(predicate) {
-      return this.filter(negate(getIteratee(predicate)));
-    };
-
-    LazyWrapper.prototype.slice = function(start, end) {
-      start = toInteger(start);
-
-      var result = this;
-      if (result.__filtered__ && (start > 0 || end < 0)) {
-        return new LazyWrapper(result);
-      }
-      if (start < 0) {
-        result = result.takeRight(-start);
-      } else if (start) {
-        result = result.drop(start);
-      }
-      if (end !== undefined) {
-        end = toInteger(end);
-        result = end < 0 ? result.dropRight(-end) : result.take(end - start);
-      }
-      return result;
-    };
-
-    LazyWrapper.prototype.takeRightWhile = function(predicate) {
-      return this.reverse().takeWhile(predicate).reverse();
-    };
-
-    LazyWrapper.prototype.toArray = function() {
-      return this.take(MAX_ARRAY_LENGTH);
-    };
-
-    // Add `LazyWrapper` methods to `lodash.prototype`.
-    baseForOwn(LazyWrapper.prototype, function(func, methodName) {
-      var checkIteratee = /^(?:filter|find|map|reject)|While$/.test(methodName),
-          isTaker = /^(?:head|last)$/.test(methodName),
-          lodashFunc = lodash[isTaker ? ('take' + (methodName == 'last' ? 'Right' : '')) : methodName],
-          retUnwrapped = isTaker || /^find/.test(methodName);
-
-      if (!lodashFunc) {
-        return;
-      }
-      lodash.prototype[methodName] = function() {
-        var value = this.__wrapped__,
-            args = isTaker ? [1] : arguments,
-            isLazy = value instanceof LazyWrapper,
-            iteratee = args[0],
-            useLazy = isLazy || isArray(value);
-
-        var interceptor = function(value) {
-          var result = lodashFunc.apply(lodash, arrayPush([value], args));
-          return (isTaker && chainAll) ? result[0] : result;
-        };
-
-        if (useLazy && checkIteratee && typeof iteratee == 'function' && iteratee.length != 1) {
-          // Avoid lazy use if the iteratee has a "length" value other than `1`.
-          isLazy = useLazy = false;
-        }
-        var chainAll = this.__chain__,
-            isHybrid = !!this.__actions__.length,
-            isUnwrapped = retUnwrapped && !chainAll,
-            onlyLazy = isLazy && !isHybrid;
-
-        if (!retUnwrapped && useLazy) {
-          value = onlyLazy ? value : new LazyWrapper(this);
-          var result = func.apply(value, args);
-          result.__actions__.push({ 'func': thru, 'args': [interceptor], 'thisArg': undefined });
-          return new LodashWrapper(result, chainAll);
-        }
-        if (isUnwrapped && onlyLazy) {
-          return func.apply(this, args);
-        }
-        result = this.thru(interceptor);
-        return isUnwrapped ? (isTaker ? result.value()[0] : result.value()) : result;
-      };
-    });
-
-    // Add `Array` methods to `lodash.prototype`.
-    arrayEach(['pop', 'push', 'shift', 'sort', 'splice', 'unshift'], function(methodName) {
-      var func = arrayProto[methodName],
-          chainName = /^(?:push|sort|unshift)$/.test(methodName) ? 'tap' : 'thru',
-          retUnwrapped = /^(?:pop|shift)$/.test(methodName);
-
-      lodash.prototype[methodName] = function() {
-        var args = arguments;
-        if (retUnwrapped && !this.__chain__) {
-          var value = this.value();
-          return func.apply(isArray(value) ? value : [], args);
-        }
-        return this[chainName](function(value) {
-          return func.apply(isArray(value) ? value : [], args);
-        });
-      };
-    });
-
-    // Map minified method names to their real names.
-    baseForOwn(LazyWrapper.prototype, function(func, methodName) {
-      var lodashFunc = lodash[methodName];
-      if (lodashFunc) {
-        var key = lodashFunc.name + '';
-        if (!hasOwnProperty.call(realNames, key)) {
-          realNames[key] = [];
-        }
-        realNames[key].push({ 'name': methodName, 'func': lodashFunc });
-      }
-    });
-
-    realNames[createHybrid(undefined, WRAP_BIND_KEY_FLAG).name] = [{
-      'name': 'wrapper',
-      'func': undefined
-    }];
-
-    // Add methods to `LazyWrapper`.
-    LazyWrapper.prototype.clone = lazyClone;
-    LazyWrapper.prototype.reverse = lazyReverse;
-    LazyWrapper.prototype.value = lazyValue;
-
-    // Add chain sequence methods to the `lodash` wrapper.
-    lodash.prototype.at = wrapperAt;
-    lodash.prototype.chain = wrapperChain;
-    lodash.prototype.commit = wrapperCommit;
-    lodash.prototype.next = wrapperNext;
-    lodash.prototype.plant = wrapperPlant;
-    lodash.prototype.reverse = wrapperReverse;
-    lodash.prototype.toJSON = lodash.prototype.valueOf = lodash.prototype.value = wrapperValue;
-
-    // Add lazy aliases.
-    lodash.prototype.first = lodash.prototype.head;
-
-    if (symIterator) {
-      lodash.prototype[symIterator] = wrapperToIterator;
-    }
-    return lodash;
-  });
-
-  /*--------------------------------------------------------------------------*/
-
-  // Export lodash.
-  var _ = runInContext();
-
-  // Some AMD build optimizers, like r.js, check for condition patterns like:
-  if (typeof define == 'function' && typeof define.amd == 'object' && define.amd) {
-    // Expose Lodash on the global object to prevent errors when Lodash is
-    // loaded by a script tag in the presence of an AMD loader.
-    // See http://requirejs.org/docs/errors.html#mismatch for more details.
-    // Use `_.noConflict` to remove Lodash from the global object.
-    root._ = _;
-
-    // Define as an anonymous module so, through path mapping, it can be
-    // referenced as the "underscore" module.
-    define(function() {
-      return _;
-    });
-  }
-  // Check for `exports` after `define` in case a build optimizer adds it.
-  else if (freeModule) {
-    // Export for Node.js.
-    (freeModule.exports = _)._ = _;
-    // Export for CommonJS support.
-    freeExports._ = _;
-  }
-  else {
-    // Export to the global object.
-    root._ = _;
-  }
-}.call(this));
diff --git a/cwl/src/test/resources/cwl/ontology/EDAM.owl b/cwl/src/test/resources/cwl/ontology/EDAM.owl
deleted file mode 100644
index 092fccdac32..00000000000
--- a/cwl/src/test/resources/cwl/ontology/EDAM.owl
+++ /dev/null
@@ -1,51294 +0,0 @@
-<?xml version="1.0"?>
-
-
-<!DOCTYPE rdf:RDF [
-    <!ENTITY foaf "http://xmlns.com/foaf/0.1/" >
-    <!ENTITY doap "http://usefulinc.com/ns/doap#" >
-    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
-    <!ENTITY oboOther "http://purl.obolibrary.org/obo/" >
-    <!ENTITY dc "http://purl.org/dc/elements/1.1/" >
-    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
-    <!ENTITY edam "http://purl.obolibrary.org/obo/edam#" >
-    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
-    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
-    <!ENTITY oboInOwl "http://www.geneontology.org/formats/oboInOwl#" >
-]>
-
-
-<rdf:RDF xmlns="http://edamontology.org/"
-     xml:base="http://edamontology.org/"
-     xmlns:dc="http://purl.org/dc/elements/1.1/"
-     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-     xmlns:foaf="http://xmlns.com/foaf/0.1/"
-     xmlns:owl="http://www.w3.org/2002/07/owl#"
-     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-     xmlns:oboOther="http://purl.obolibrary.org/obo/"
-     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
-     xmlns:doap="http://usefulinc.com/ns/doap#"
-     xmlns:edam="&oboOther;edam#">
-    <owl:Ontology rdf:about="http://edamontology.org">
-        <oboOther:idspace>EDAM_topic http://edamontology.org/topic_ &quot;EDAM topics&quot;</oboOther:idspace>
-        <oboOther:idspace>EDAM_operation http://edamontology.org/operation_ &quot;EDAM operations&quot;</oboOther:idspace>
-        <oboOther:date>09:07:2015</oboOther:date>
-        <next_id>3625</next_id>
-        <oboInOwl:hasSubset>formats &quot;EDAM data formats&quot;</oboInOwl:hasSubset>
-        <oboOther:default-relationship-id-prefix>EDAM</oboOther:default-relationship-id-prefix>
-        <dc:title>An ontology of bioinformatics topics, operations, types of data including identifiers, and data formats</dc:title>
-        <oboInOwl:hasSubset>identifiers &quot;EDAM types of identifiers&quot;</oboInOwl:hasSubset>
-        <oboInOwl:hasSubset>data &quot;EDAM types of data&quot;</oboInOwl:hasSubset>
-        <oboInOwl:hasSubset>relations &quot;EDAM relations&quot;</oboInOwl:hasSubset>
-        <oboInOwl:hasSubset>edam &quot;EDAM&quot;</oboInOwl:hasSubset>
-        <oboOther:remark>EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence.</oboOther:remark>
-        <oboInOwl:hasSubset>operations &quot;EDAM operations&quot;</oboInOwl:hasSubset>
-        <oboOther:idspace>EDAM http://edamontology.org/ &quot;EDAM relations and concept properties&quot;</oboOther:idspace>
-        <dc:format>application/rdf+xml</dc:format>
-        <oboOther:idspace>EDAM_data http://edamontology.org/data_ &quot;EDAM types of data&quot;</oboOther:idspace>
-        <oboInOwl:hasSubset>concept_properties &quot;EDAM concept properties&quot;</oboInOwl:hasSubset>
-        <dc:creator>Jon Ison</dc:creator>
-        <dc:creator>Matúš Kalaš</dc:creator>
-        <oboInOwl:savedBy>Jon Ison, Matus Kalas, Hervé Ménager</oboInOwl:savedBy>
-        <oboOther:idspace>EDAM_format http://edamontology.org/format_ &quot;EDAM data formats&quot;</oboOther:idspace>
-        <oboInOwl:hasSubset>topics &quot;EDAM topics&quot;</oboInOwl:hasSubset>
-        <doap:Version>1.11</doap:Version>
-        <dc:creator>Hervé Ménager</dc:creator>
-        <oboOther:remark>EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources.  EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.</oboOther:remark>
-        <rdfs:isDefinedBy rdf:resource="http://edamontology.org/EDAM.owl"/>
-        <foaf:page rdf:resource="http://edamontology.org/page"/>
-    </owl:Ontology>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Annotation properties
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-
-
-    <!-- http://edamontology.org/created_in -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/created_in">
-        <rdfs:label>Created in</rdfs:label>
-        <oboInOwl:hasDefinition>Version in which a concept was created.</oboInOwl:hasDefinition>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/documentation -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/documentation">
-        <rdfs:label>Documentation</rdfs:label>
-        <oboInOwl:hasRelatedSynonym>Specification</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>&apos;Documentation&apos; trailing modifier (qualifier, &apos;documentation&apos;) of &apos;xref&apos; links of &apos;Format&apos; concepts. When &apos;true&apos;, the link is pointing to a page with explanation, description, documentation, or specification of the given data format.</oboInOwl:hasDefinition>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/example -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/example">
-        <rdfs:label>Example</rdfs:label>
-        <oboInOwl:hasDefinition>&apos;Example&apos; concept property (&apos;example&apos; metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too.</oboInOwl:hasDefinition>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/noClue -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/noClue"/>
-    
-
-
-    <!-- http://edamontology.org/obsolete_since -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/obsolete_since">
-        <rdfs:label>Obsolete since</rdfs:label>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-        <oboInOwl:hasDefinition>Version in which a concept was made obsolete.</oboInOwl:hasDefinition>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/regex -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/regex">
-        <rdfs:label>Regular expression</rdfs:label>
-        <oboInOwl:hasDefinition>&apos;Regular expression&apos; concept property (&apos;regex&apos; metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_anti_symmetric -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_anti_symmetric"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_metadata_tag -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_metadata_tag"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_reflexive -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_reflexive"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_symmetric -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_symmetric"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/namespace -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;namespace"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/transitive_over -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;transitive_over"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#data -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#data">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#edam -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#edam">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#events -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#events">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#formats -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#formats">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#identifiers -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#identifiers">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#obsolete -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#obsolete">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#operations -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#operations">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#topics -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#topics">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#SubsetProperty -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;SubsetProperty"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#consider -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;consider"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasAlternativeId -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasAlternativeId"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasBroadSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasDbXref"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasDefinition -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasDefinition"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasExactSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasNarrowSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasRelatedSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasSubset -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasSubset"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;inSubset"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#isCyclic -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;isCyclic"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#replacedBy -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;replacedBy"/>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Object Properties
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-
-
-    <!-- http://edamontology.org/has_format -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_format">
-        <rdfs:label>has format</rdfs:label>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000298&quot;</rdfs:seeAlso>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) &apos;Data&apos;, or an input, output, input or output argument of an &apos;Operation&apos;. Object B can either be a concept that is a &apos;Format&apos;, or in unexpected cases an entity outside of an ontology that is a &apos;Format&apos; or is in the role of a &apos;Format&apos;. In EDAM, &apos;has_format&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;is_format_of&apos;.</rdfs:comment>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality&quot;</rdfs:seeAlso>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:hasDefinition>&apos;A has_format B&apos; defines for the subject A, that it has the object B as its data format.</oboInOwl:hasDefinition>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:range rdf:resource="http://edamontology.org/format_1915"/>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://edamontology.org/has_function -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_function">
-        <rdfs:label>has function</rdfs:label>
-        <rdfs:seeAlso>http://wsio.org/has_function</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:bearer_of</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, &apos;has_function&apos; serves only for relating annotated entities outside of EDAM with &apos;Operation&apos; concepts.</rdfs:comment>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality&quot;</rdfs:seeAlso>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:hasDefinition>&apos;A has_function B&apos; defines for the subject A, that it has the object B as its function.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000306&quot;</rdfs:seeAlso>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <rdfs:range rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_function"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:bearer_of&apos; is narrower in the sense that it only relates ontological categories (concepts) that are an &apos;independent_continuant&apos; (snap:IndependentContinuant) with ontological categories that are a &apos;specifically_dependent_continuant&apos; (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject.</rdfs:comment>
-        <owl:annotatedTarget>OBO_REL:bearer_of</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_function"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/has_identifier -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_identifier">
-        <rdfs:label>has identifier</rdfs:label>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:hasDefinition>&apos;A has_identifier B&apos; defines for the subject A, that it has the object B as its identifier.</oboInOwl:hasDefinition>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an &apos;Identifier&apos;, or an entity outside of an ontology that is an &apos;Identifier&apos; or is in the role of an &apos;Identifier&apos;. In EDAM, &apos;has_identifier&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;is_identifier_of&apos;.</rdfs:comment>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0842"/>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://edamontology.org/has_input -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_input">
-        <rdfs:label>has input</rdfs:label>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:has_participant</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000293&quot;</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:seeAlso>http://wsio.org/has_input</rdfs:seeAlso>
-        <rdfs:comment>Subject A can either be concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. Object B can be any concept or entity. In EDAM, only &apos;has_input&apos; is explicitly defined between EDAM concepts (&apos;Operation&apos; &apos;has_input&apos; &apos;Data&apos;). The inverse, &apos;is_input_of&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:hasDefinition>&apos;A has_input B&apos; defines for the subject A, that it has the object B as a necessary or actual input or input argument.</oboInOwl:hasDefinition>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:has_participant</owl:annotatedTarget>
-        <rdfs:comment>&apos;OBO_REL:has_participant&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;process&apos; (span:Process) with ontological categories that are a &apos;continuant&apos; (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_input"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_input"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/has_output -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_output">
-        <rdfs:label>has output</rdfs:label>
-        <rdfs:seeAlso>http://wsio.org/has_output</rdfs:seeAlso>
-        <rdfs:comment>Subject A can either be concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. Object B can be any concept or entity. In EDAM, only &apos;has_output&apos; is explicitly defined between EDAM concepts (&apos;Operation&apos; &apos;has_output&apos; &apos;Data&apos;). The inverse, &apos;is_output_of&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000299&quot;</rdfs:seeAlso>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:has_participant</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:hasDefinition>&apos;A has_output B&apos; defines for the subject A, that it has the object B as a necessary or actual output or output argument.</oboInOwl:hasDefinition>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>&apos;OBO_REL:has_participant&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;process&apos; (span:Process) with ontological categories that are a &apos;continuant&apos; (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it.</rdfs:comment>
-        <owl:annotatedTarget>OBO_REL:has_participant</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_output"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_output"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/has_topic -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_topic">
-        <rdfs:label>has topic</rdfs:label>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a &apos;Topic&apos;, or in unexpected cases an entity outside of an ontology that is a &apos;Topic&apos; or is in the role of a &apos;Topic&apos;. In EDAM, only &apos;has_topic&apos; is explicitly defined between EDAM concepts (&apos;Operation&apos; or &apos;Data&apos; &apos;has_topic&apos; &apos;Topic&apos;). The inverse, &apos;is_topic_of&apos;, is not explicitly defined.</rdfs:comment>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:hasDefinition>&apos;A has_topic B&apos; defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <rdfs:seeAlso>http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000136&quot;</rdfs:seeAlso>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000298&quot;</rdfs:seeAlso>
-        <rdfs:range rdf:resource="http://edamontology.org/topic_0003"/>
-        <rdfs:domain>
-            <owl:Class>
-                <owl:unionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://edamontology.org/data_0006"/>
-                    <rdf:Description rdf:about="http://edamontology.org/operation_0004"/>
-                </owl:unionOf>
-            </owl:Class>
-        </rdfs:domain>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_topic"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_format_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_format_of">
-        <rdfs:label>is format of</rdfs:label>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboInOwl:hasDefinition>&apos;A is_format_of B&apos; defines for the subject A, that it is a data format of the object B.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can either be a concept that is a &apos;Format&apos;, or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a &apos;Format&apos; or is in the role of a &apos;Format&apos;. Object B can be any concept or entity outside of an ontology that is (or is in a role of) &apos;Data&apos;, or  an input, output, input or output argument of an &apos;Operation&apos;. In EDAM, only &apos;is_format_of&apos; is explicitly defined between EDAM concepts (&apos;Format&apos; &apos;is_format_of&apos; &apos;Data&apos;). The inverse, &apos;has_format&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:quality_of</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in</rdfs:seeAlso>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_format"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:quality_of</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:quality_of&apos; might be seen narrower in the sense that it only relates subjects that are a &apos;quality&apos; (snap:Quality) with objects that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_format_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_function_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_function_of">
-        <rdfs:label>is function of</rdfs:label>
-        <rdfs:comment>Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, &apos;is_function_of&apos; is not used.</rdfs:comment>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:inheres_in</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:hasDefinition>&apos;A is_function_of B&apos; defines for the subject A, that it is a function of the object B.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>OBO_REL:function_of</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:seeAlso>http://wsio.org/is_function_of</rdfs:seeAlso>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_function"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:inheres_in</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:inheres_in&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;specifically_dependent_continuant&apos; (snap:SpecificallyDependentContinuant) with ontological categories that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_function_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_function_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:function_of</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:function_of&apos; only relates subjects that are a &apos;function&apos; (snap:Function) with objects that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_function_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_identifier_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_identifier_of">
-        <rdfs:label>is identifier of</rdfs:label>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can either be a concept that is an &apos;Identifier&apos;, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an &apos;Identifier&apos; or is in the role of an &apos;Identifier&apos;. Object B can be any concept or entity outside of an ontology. In EDAM, only &apos;is_identifier_of&apos; is explicitly defined between EDAM concepts (only &apos;Identifier&apos; &apos;is_identifier_of&apos; &apos;Data&apos;). The inverse, &apos;has_identifier&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:hasDefinition>&apos;A is_identifier_of B&apos; defines for the subject A, that it is an identifier of the object B.</oboInOwl:hasDefinition>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0842"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_identifier"/>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://edamontology.org/is_input_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_input_of">
-        <rdfs:label>is input of</rdfs:label>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:seeAlso>http://wsio.org/is_input_of</rdfs:seeAlso>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:participates_in</oboInOwl:hasRelatedSynonym>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000295&quot;</rdfs:seeAlso>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. In EDAM, &apos;is_input_of&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;has_input&apos;.</rdfs:comment>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:hasDefinition>&apos;A is_input_of B&apos; defines for the subject A, that it as a necessary or actual input or input argument of the object B.</oboInOwl:hasDefinition>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_input"/>
-        <rdfs:range rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>&apos;OBO_REL:participates_in&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;continuant&apos; (snap:Continuant) with ontological categories that are a &apos;process&apos; (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments.</rdfs:comment>
-        <owl:annotatedTarget>OBO_REL:participates_in</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_input_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_input_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_output_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_output_of">
-        <rdfs:label>is output of</rdfs:label>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. In EDAM, &apos;is_output_of&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;has_output&apos;.</rdfs:comment>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboInOwl:hasDefinition>&apos;A is_output_of B&apos; defines for the subject A, that it as a necessary or actual output or output argument of the object B.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:participates_in</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>http://wsio.org/is_output_of</rdfs:seeAlso>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000312&quot;</rdfs:seeAlso>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_output"/>
-        <rdfs:range rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_output_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:participates_in</owl:annotatedTarget>
-        <rdfs:comment>&apos;OBO_REL:participates_in&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;continuant&apos; (snap:Continuant) with ontological categories that are a &apos;process&apos; (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_output_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_topic_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_topic_of">
-        <rdfs:label>is topic of</rdfs:label>
-        <oboInOwl:hasDefinition>&apos;A is_topic_of B&apos; defines for the subject A, that it is a topic of the object B (a topic A is the scope of B).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:quality_of</oboInOwl:hasRelatedSynonym>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:comment>Subject A can either be a concept that is a &apos;Topic&apos;, or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a &apos;Topic&apos; or is in the role of a &apos;Topic&apos;. Object B can be any concept or entity outside of an ontology. In EDAM, &apos;is_topic_of&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;has_topic&apos;.</rdfs:comment>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in</rdfs:seeAlso>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_topic"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/topic_0003"/>
-        <rdfs:range>
-            <owl:Class>
-                <owl:unionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://edamontology.org/data_0006"/>
-                    <rdf:Description rdf:about="http://edamontology.org/operation_0004"/>
-                </owl:unionOf>
-            </owl:Class>
-        </rdfs:range>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:quality_of</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:quality_of&apos; might be seen narrower in the sense that it only relates subjects that are a &apos;quality&apos; (snap:Quality) with objects that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_topic_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_topic_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Classes
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-    
-
-
-    <!-- http://edamontology.org/data_0005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0005">
-        <rdfs:label>Resource type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A type of computational resource used in bioinformatics.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0006">
-        <rdfs:label>Data</rdfs:label>
-        <owl:disjointWith rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/topic_0003"/>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <oboInOwl:hasDefinition>Information, represented in an information artefact (data record) that is &apos;understandable&apos; by dedicated computational tools that can use the data as input or produce it as output.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000088</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000069</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000030&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000027&quot;</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Data set</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Data record</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://wsio.org/data_002</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#DigitalEntity</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Datum</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedTarget>Data set</owl:annotatedTarget>
-        <rdfs:comment>EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>Datum</owl:annotatedTarget>
-        <rdfs:comment>EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>Data record</owl:annotatedTarget>
-        <rdfs:comment>EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information).</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasExactSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_0007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0007">
-        <rdfs:label>Tool</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A bioinformatics package or tool, e.g. a standalone application or web service.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0581">
-        <rdfs:label>Database</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0582">
-        <rdfs:label>Ontology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontologies</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0583">
-        <rdfs:label>Directory metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A directory on disk from which files are read.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0831 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0831">
-        <rdfs:label>MeSH vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0832 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0832">
-        <rdfs:label>HGNC vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0835 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0835">
-        <rdfs:label>UMLS vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0842 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0842">
-        <rdfs:label>Identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <owl:disjointWith rdf:resource="http://edamontology.org/data_2048"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/data_2527"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000115</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>ID</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>&quot;http://purl.org/dc/elements/1.1/identifier&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>http://wsio.org/data_005</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-        <oboInOwl:hasNarrowSynonym rdf:resource="&dc;identifier"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>Almost exact but limited to identifying resources.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0842"/>
-        <owl:annotatedTarget rdf:resource="&dc;identifier"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_0843 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0843">
-        <rdfs:label>Database entry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An entry (retrievable via URL) from a biological database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0844 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0844">
-        <rdfs:label>Molecular mass</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasDefinition>Mass of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0845 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0845">
-        <rdfs:label>Molecular charge</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasDefinition>Net charge of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:pdbx_formal_charge</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0846 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0846">
-        <rdfs:label>Chemical formula</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasExactSynonym>Chemical structure specification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A specification of a chemical structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0847 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0847">
-        <rdfs:label>QSAR descriptor</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasDefinition>A QSAR quantitative descriptor (name-value pair) of chemical structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0848 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0848">
-        <rdfs:label>Raw sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <rdfs:comment>Non-sequence characters may be used for example for gaps and translation stop.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0849 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0849">
-        <rdfs:label>Sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D058977</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A molecular sequence and associated metadata.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>SO:2000061</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0850 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0850">
-        <rdfs:label>Sequence set</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for arbitrary sequence sets and associated data arising from processing.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasRelatedSynonym>SO:0001260</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0851 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0851">
-        <rdfs:label>Sequence mask character</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A character used to replace (mask) other characters in a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0852 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0852">
-        <rdfs:label>Sequence mask type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of sequence masking to perform.</oboInOwl:hasDefinition>
-        <rdfs:comment>Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0853 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0853">
-        <rdfs:label>DNA sense specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:hasExactSynonym>DNA strand specification</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Strand</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The strand of a DNA sequence (forward or reverse).</oboInOwl:hasDefinition>
-        <rdfs:comment>The forward or &apos;top&apos; strand might specify a sequence is to be used as given, the reverse or &apos;bottom&apos; strand specifying the reverse complement of the sequence is to be used.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0854 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0854">
-        <rdfs:label>Sequence length specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A specification of sequence length(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0855 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0855">
-        <rdfs:label>Sequence metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Basic or general information concerning molecular sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is used for such things as a report including the sequence identifier, type and length.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2955"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0856 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0856">
-        <rdfs:label>Sequence feature source</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <rdfs:comment>This might be the name and version of a software tool, the name of a database, or &apos;curated&apos; to indicate a manual annotation (made by a human).</rdfs:comment>
-        <oboInOwl:hasDefinition>How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0857 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0857">
-        <rdfs:label>Sequence search results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Database hits (sequence)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym></oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence database hits</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence search hits</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence database search results</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0858 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0858">
-        <rdfs:label>Sequence signature matches</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0860"/>
-        <oboInOwl:hasExactSynonym>Sequence motif matches</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary database search results</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence profile matches</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This ncluding reports of hits from a search of a protein secondary or domain database.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Search results (protein secondary database)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0859 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0859">
-        <rdfs:label>Sequence signature model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data files used by motif or profile methods.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0860 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0860">
-        <rdfs:label>Sequence signature data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element.</oboInOwl:hasDefinition>
-        <oboInOwl:hasSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:hasSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0861 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0861">
-        <rdfs:label>Sequence alignment (words)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence word alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Alignment of exact matches between subsequences (words) within two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0862 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0862">
-        <rdfs:label>Dotplot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:hasDefinition>A dotplot of sequence similarities identified from word-matching or character comparison.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0863 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0863">
-        <rdfs:label>Sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Sequence_alignment</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D016415</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_010066</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of multiple molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0864 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0864">
-        <rdfs:label>Sequence alignment parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Some simple value controlling a sequence alignment (or similar &apos;match&apos;) operation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0865 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0865">
-        <rdfs:label>Sequence similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1772"/>
-        <oboInOwl:hasDefinition>A value representing molecular sequence similarity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0866 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0866">
-        <rdfs:label>Sequence alignment metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0867">
-        <rdfs:label>Sequence alignment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:comment>Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score.</rdfs:comment>
-        <oboInOwl:hasDefinition>An informative report of molecular sequence alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0868">
-        <rdfs:label>Sequence profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A profile-profile alignment (each profile typically representing a sequence alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0869">
-        <rdfs:label>Sequence-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment).</oboInOwl:hasDefinition>
-        <rdfs:comment>Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0870 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0870">
-        <rdfs:label>Sequence distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2855"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:phylogenetic_distance_matrix</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic distance matrix</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0871 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0871">
-        <rdfs:label>Phylogenetic character data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasDefinition>Basic character data from which a phylogenetic tree may be generated.</oboInOwl:hasDefinition>
-        <rdfs:comment>As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments</rdfs:comment>
-        <rdfs:seeAlso>http://www.evolutionaryontology.org/cdao.owl#Character</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0872 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0872">
-        <rdfs:label>Phylogenetic tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phylogeny</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Tree</oboInOwl:hasDbXref>
-        <rdfs:seeAlso>http://www.evolutionaryontology.org/cdao.owl#Tree</rdfs:seeAlso>
-        <rdfs:comment>A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also &apos;Phylogenetic tree image&apos;.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D010802</rdfs:seeAlso>
-        <oboInOwl:hasDbXref>Moby:phylogenetic_tree</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:myTree</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0874 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0874">
-        <rdfs:label>Comparison matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats).</rdfs:comment>
-        <oboInOwl:hasDefinition>Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0875 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0875">
-        <rdfs:label>Protein topology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predicted or actual protein topology represented as a string of protein secondary structure elements.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The location and size of the secondary structure elements and intervening loop regions is usually indicated.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0876"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0876 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0876">
-        <rdfs:label>Protein features report (secondary structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Secondary structure (predicted or real) of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0877 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0877">
-        <rdfs:label>Protein features report (super-secondary)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <rdfs:comment>Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Super-secondary structure of protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0878 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0878">
-        <rdfs:label>Secondary structure alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2366"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3154"/>
-        <oboInOwl:hasDefinition>Alignment of the (1D representations of) secondary structure of two or more proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0879 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0879">
-        <rdfs:label>Secondary structure alignment metadata (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on protein secondary structure alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0880 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0880">
-        <rdfs:label>RNA secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1465"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An informative report of secondary structure (predicted or real) of an RNA molecule.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:RNAStructML</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Secondary structure (RNA)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0881 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0881">
-        <rdfs:label>Secondary structure alignment (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2366"/>
-        <oboInOwl:hasDbXref>Moby:RNAStructAlignmentML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Alignment of the (1D representations of) secondary structure of two or more RNA molecules.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0882 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0882">
-        <rdfs:label>Secondary structure alignment metadata (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report of RNA secondary structure alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0883 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0883">
-        <rdfs:label>Structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0081"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Coordinate model</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure data</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The coordinate data may be predicted or real.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015394</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0884 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0884">
-        <rdfs:label>Tertiary structure record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An entry from a molecular tertiary (3D) structure database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0885">
-        <rdfs:label>Structure database search results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Results (hits) from searching a database of tertiary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0886 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0886">
-        <rdfs:label>Structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <rdfs:comment>A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0887 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0887">
-        <rdfs:label>Structure alignment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasDefinition>An informative report of molecular tertiary structure alignment-derived data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0888 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0888">
-        <rdfs:label>Structure similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1772"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0889 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0889">
-        <rdfs:label>Structural profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>3D profile</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Some type of structural (3D) profile or template (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structural (3D) profile</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0890 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0890">
-        <rdfs:label>Structural (3D) profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structural profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A 3D profile-3D profile alignment (each profile representing structures or a structure alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0891 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0891">
-        <rdfs:label>Sequence-3D profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence-structural profile alignment</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>An alignment of a sequence to a 3D profile (representing structures or a structure alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0893"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0892 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0892">
-        <rdfs:label>Protein sequence-structure scoring matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of values used for scoring sequence-structure compatibility.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0893 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0893">
-        <rdfs:label>Sequence-structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0894 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0894">
-        <rdfs:label>Amino acid annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report about a specific amino acid.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0895 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0895">
-        <rdfs:label>Peptide annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report about a specific peptide.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0896 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0896">
-        <rdfs:label>Protein report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasExactSynonym>Gene product annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0897 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0897">
-        <rdfs:label>Protein property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>Protein physicochemical property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein sequence statistics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein properties</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0899 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0899">
-        <rdfs:label>Protein structural motifs and surfaces</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>3D structural motifs in a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein 3D motifs</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0900 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0900">
-        <rdfs:label>Protein domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning the classification of the sequences and/or structures of protein structural domain(s).</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0901 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0901">
-        <rdfs:label>Protein features report (domains)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>structural domains or 3D folds in a protein or polypeptide chain.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0902 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0902">
-        <rdfs:label>Protein architecture report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on architecture (spatial arrangement of secondary structure) of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein property (architecture)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure report (architecture)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0903 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0903">
-        <rdfs:label>Protein folding report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0904 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0904">
-        <rdfs:label>Protein features (mutation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on the effect of (typically point) mutation on protein folding, stability, structure and function.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein property (mutation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure report (mutation)</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein report (mutation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0905 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0905">
-        <rdfs:label>Protein interaction raw data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0906 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0906">
-        <rdfs:label>Protein interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein report (interaction)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein interaction record</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with some other molecule(s), which might be another protein, nucleic acid or some other ligand.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0907 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0907">
-        <rdfs:label>Protein family report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0724"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific protein family or other classification or group of protein sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein family annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Protein classification data</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0909 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0909">
-        <rdfs:label>Vmax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0910 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0910">
-        <rdfs:label>Km</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <oboInOwl:hasDefinition>Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0911 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0911">
-        <rdfs:label>Nucleotide base annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report about a specific nucleotide base.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0912 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0912">
-        <rdfs:label>Nucleic acid property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasDefinition>A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Nucleic acid physicochemical property</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0914 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0914">
-        <rdfs:label>Codon usage data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0916 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0916">
-        <rdfs:label>Gene report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:hasExactSynonym>Gene structure (repot)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene and transcript structure (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene features report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (gene and transcript structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:gene</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes any report on a particular locus or gene.  This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Gene annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:Human_Readable_Description</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Gene function (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:GeneInfo</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0917 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0917">
-        <rdfs:label>Gene classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0918 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0918">
-        <rdfs:label>DNA variation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0919 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0919">
-        <rdfs:label>Chromosome report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0624"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific chromosome.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0920 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0920">
-        <rdfs:label>Genotype/phenotype report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genotype/phenotype annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0922 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0922">
-        <rdfs:label>Nucleic acid features report (primers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PCR primers and hybridization oligos in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0923 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0923">
-        <rdfs:label>PCR experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PCR experiments, e.g. quantitative real-time PCR.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0924 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0924">
-        <rdfs:label>Sequence trace</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <oboInOwl:hasDefinition>Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is the raw data produced by a DNA sequencing machine.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0925 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0925">
-        <rdfs:label>Sequence assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An assembly of fragments of a (typically genomic) DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Sequence_assembly</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>SO:0001248</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>SO:0000353</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedTarget>SO:0001248</owl:annotatedTarget>
-        <rdfs:comment>Perhaps surprisingly, the definition of &apos;SO:assembly&apos; is narrower than the &apos;SO:sequence_assembly&apos;.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0925"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_0926 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0926">
-        <rdfs:label>Radiation Hybrid (RH) scores</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping.</rdfs:comment>
-        <oboInOwl:hasDefinition>Radiation hybrid scores (RH) scores for one or more markers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0927 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0927">
-        <rdfs:label>Genetic linkage report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene annotation (linkage)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Linkage disequilibrium (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>An informative report on the linkage of alleles.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0928 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0928">
-        <rdfs:label>Gene expression profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <oboInOwl:hasDefinition>Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression pattern</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0931 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0931">
-        <rdfs:label>Microarray experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>microarray experiments including conditions, protocol, sample:data relationships etc.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0932 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0932">
-        <rdfs:label>Oligonucleotide probe data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data on oligonucleotide probes (typically for use with DNA microarrays).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2717"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0933 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0933">
-        <rdfs:label>SAGE experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Output from a serial analysis of gene expression (SAGE) experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Serial analysis of gene expression (SAGE) experimental data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2535"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0934 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0934">
-        <rdfs:label>MPSS experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Massively parallel signature sequencing (MPSS) data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Massively parallel signature sequencing (MPSS) experimental data</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2535"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0935 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0935">
-        <rdfs:label>SBS experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequencing by synthesis (SBS) experimental data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Sequencing by synthesis (SBS) data.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2535"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0936 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0936">
-        <rdfs:label>Sequence tag profile (with gene assignment)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2535"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0937 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0937">
-        <rdfs:label>Protein X-ray crystallographic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2537"/>
-        <oboInOwl:hasDefinition>X-ray crystallography data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0938 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0938">
-        <rdfs:label>Protein NMR data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2537"/>
-        <oboInOwl:hasDefinition>Protein nuclear magnetic resonance (NMR) raw data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0939 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0939">
-        <rdfs:label>Protein circular dichroism (CD) spectroscopic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2537"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0940 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0940">
-        <rdfs:label>Electron microscopy volume map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Volume map data from electron microscopy.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EM volume map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0941 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0941">
-        <rdfs:label>Electron microscopy model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation on a structural 3D model (volume map) from electron microscopy.</oboInOwl:hasDefinition>
-        <rdfs:comment>This might include the location in the model of the known features of a particular macromolecule.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0942 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0942">
-        <rdfs:label>2D PAGE image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Two-dimensional gel electrophoresis image</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0943 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0943">
-        <rdfs:label>Mass spectrometry spectra</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2536"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Spectra from mass spectrometry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0944 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0944">
-        <rdfs:label>Peptide mass fingerprint</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2536"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2979"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Peak list</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein fingerprint</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A set of peptide masses (peptide mass fingerprint) from mass spectrometry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0945 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0945">
-        <rdfs:label>Peptide identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2979"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0946 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0946">
-        <rdfs:label>Pathway or network annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0947 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0947">
-        <rdfs:label>Biological pathway map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A map (typically a diagram) of a biological pathway.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2600"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0948 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0948">
-        <rdfs:label>Data resource definition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0949 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0949">
-        <rdfs:label>Workflow metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Basic information, annotation or documentation concerning a workflow (but not the workflow itself).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0950 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0950">
-        <rdfs:label>Mathematical model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3307"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Biological model</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A biological model represented in mathematical terms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0951 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0951">
-        <rdfs:label>Statistical estimate score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1772"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A value representing estimated statistical significance of some observed data; typically sequence database hits.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0952 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0952">
-        <rdfs:label>EMBOSS database resource definition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Resource definition for an EMBOSS database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0953 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0953">
-        <rdfs:label>Version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000129&quot;</rdfs:seeAlso>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records.</rdfs:comment>
-        <rdfs:seeAlso>http://www.ebi.ac.uk/swo/maturity/SWO_9000061</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a version of software or data, for example name, version number and release date.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000653</rdfs:seeAlso>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:seeAlso>http://usefulinc.com/ns/doap#Version</rdfs:seeAlso>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0954 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0954">
-        <rdfs:label>Database cross-mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases.</oboInOwl:hasDefinition>
-        <rdfs:comment>The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0955 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0955">
-        <rdfs:label>Data index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0220"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An index of data of biological relevance.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0956 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0956">
-        <rdfs:label>Data index report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0220"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A report of an analysis of an index of biological data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database index annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0957 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0957">
-        <rdfs:label>Database metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0958 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0958">
-        <rdfs:label>Tool metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0959 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0959">
-        <rdfs:label>Job metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDbXref>Moby:PDGJOB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Textual metadata on a submitted or completed job.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0960 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0960">
-        <rdfs:label>User metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Textual metadata on a software author or end-user, for example a person or other software.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0962 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0962">
-        <rdfs:label>Small molecule report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0154"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Small molecule annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Small molecule report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Chemical structure report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on a specific chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0963 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0963">
-        <rdfs:label>Cell line report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:hasExactSynonym>Organism strain data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Cell line annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0964 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0964">
-        <rdfs:label>Scent annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report about a specific scent.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0966 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0966">
-        <rdfs:label>Ontology term</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0967"/>
-        <oboInOwl:hasExactSynonym>Ontology class name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term (name) from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ontology terms</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0967 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0967">
-        <rdfs:label>Ontology concept data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2353"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology class metadata</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Ontology term metadata</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning or derived from a concept from a biological ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0968 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0968">
-        <rdfs:label>Keyword</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Phrases</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Keyword(s) or phrase(s) used (typically) for text-searching purposes.</oboInOwl:hasDefinition>
-        <rdfs:comment>Boolean operators (AND, OR and NOT) and wildcard characters may be allowed.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:QueryString</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:BooleanQueryString</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Wildcard_Query</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Global_Keyword</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Terms</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Text</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0970 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0970">
-        <rdfs:label>Citation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2526"/>
-        <oboInOwl:hasDefinition>Bibliographic data that uniquely identifies a scientific article, book or other published material.</oboInOwl:hasDefinition>
-        <rdfs:comment>A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:GCP_SimpleCitation</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Reference</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Bibliographic reference</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Publication</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0971 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0971">
-        <rdfs:label>Article</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3068"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A document of scientific text, typically a full text article from a scientific journal.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0972 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0972">
-        <rdfs:label>Text mining report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An abstract of the results of text mining.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Text mining output</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0974 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0974">
-        <rdfs:label>Entity identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a biological entity or phenomenon.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0975 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0975">
-        <rdfs:label>Data resource identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An identifier of a data resource.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0976 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0976">
-        <rdfs:label>Identifier (typed)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This concept exists only to assist EDAM maintenance and navigation in graphical browsers.  It does not add semantic information.  This branch provides an alternative organisation of the concepts nested under &apos;Accession&apos; and &apos;Name&apos;. All concepts under here are already included under &apos;Accession&apos; or &apos;Name&apos;.</rdfs:comment>
-        <oboInOwl:hasDefinition>An identifier that identifies a particular type of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0977 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0977">
-        <rdfs:label>Tool identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a bioinformatics tool, e.g. an application or web service.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0978 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0978">
-        <rdfs:label>Discrete entity identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0979 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0979">
-        <rdfs:label>Entity feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0980 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0980">
-        <rdfs:label>Entity collection identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of a collection of discrete biological entities.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0981 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0981">
-        <rdfs:label>Phenomenon identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of a physical, observable biological occurrence or event.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0982 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0982">
-        <rdfs:label>Molecule identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>Name or other identifier of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0983 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0983">
-        <rdfs:label>Atom ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasExactSynonym>Atom identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier (e.g. character symbol) of a specific atom.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0984 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0984">
-        <rdfs:label>Molecule name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>Name of a specific molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0985 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0985">
-        <rdfs:label>Molecule type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>For example, &apos;Protein&apos;, &apos;DNA&apos;, &apos;RNA&apos; etc.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A label (text token) describing the type a molecule.</oboInOwl:hasDefinition>
-        <example>Protein|DNA|RNA</example>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0986 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0986">
-        <rdfs:label>Chemical identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Unique identifier of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1086"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0987 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0987">
-        <rdfs:label>Chromosome name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0984"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0919"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a chromosome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0988 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0988">
-        <rdfs:label>Peptide identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <oboInOwl:hasDefinition>Identifier of a peptide chain.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0989 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0989">
-        <rdfs:label>Protein identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0990 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0990">
-        <rdfs:label>Compound name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0984"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <oboInOwl:hasExactSynonym>Chemical name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique name of a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0991 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0991">
-        <rdfs:label>Chemical registry number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0992 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0992">
-        <rdfs:label>Ligand identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Code word for a ligand, for example from a PDB file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1086"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0993 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0993">
-        <rdfs:label>Drug identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2851"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a drug.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0994 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0994">
-        <rdfs:label>Amino acid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2016"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an amino acid.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Residue identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0995 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0995">
-        <rdfs:label>Nucleotide identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of a nucleotide.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0996 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0996">
-        <rdfs:label>Monosaccharide identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a monosaccharide.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0997 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0997">
-        <rdfs:label>Chemical name (ChEBI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasExactSynonym>ChEBI chemical name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is the recommended chemical name for use for example in database annotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0998 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0998">
-        <rdfs:label>Chemical name (IUPAC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasDefinition>IUPAC recommended name of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>IUPAC chemical name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0999 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0999">
-        <rdfs:label>Chemical name (INN)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasExactSynonym>INN chemical name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>International Non-proprietary Name (INN or &apos;generic name&apos;) of a chemical compound, assigned by the World Health Organization (WHO).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1000 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1000">
-        <rdfs:label>Chemical name (brand)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasDefinition>Brand name of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Brand chemical name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1001 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1001">
-        <rdfs:label>Chemical name (synonymous)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Synonymous chemical name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Synonymous name of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1002 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1002">
-        <rdfs:label>Chemical registry number (CAS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0991"/>
-        <oboInOwl:hasExactSynonym>CAS chemical registry number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>CAS registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1003">
-        <rdfs:label>Chemical registry number (Beilstein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0991"/>
-        <oboInOwl:hasExactSynonym>Beilstein chemical registry number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Beilstein registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1004">
-        <rdfs:label>Chemical registry number (Gmelin)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0991"/>
-        <oboInOwl:hasExactSynonym>Gmelin chemical registry number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gmelin registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1005">
-        <rdfs:label>HET group name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasDefinition>3-letter code word for a ligand (HET group) from a PDB file, for example ATP.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Short ligand name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Component identifier code</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1006">
-        <rdfs:label>Amino acid name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0994"/>
-        <oboInOwl:hasDefinition>String of one or more ASCII characters representing an amino acid.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1007">
-        <rdfs:label>Nucleotide code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0995"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>String of one or more ASCII characters representing a nucleotide.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1008 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1008">
-        <rdfs:label>Polypeptide chain ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0988"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1467"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: chain</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Chain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a polypeptide chain from a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_strand_id</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Protein chain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PDB strand id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PDB chain identifier</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Polypeptide chain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1009 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1009">
-        <rdfs:label>Protein name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0984"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <oboInOwl:hasDefinition>Name of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1010 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1010">
-        <rdfs:label>Enzyme identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of an enzyme or record from a database of enzymes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1011 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1011">
-        <rdfs:label>EC number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <regex>[0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>EC code</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:EC_Number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An Enzyme Commission (EC) number of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EC</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Annotated_EC_Number</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Enzyme Commission number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1012 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1012">
-        <rdfs:label>Enzyme name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1010"/>
-        <oboInOwl:hasDefinition>Name of an enzyme.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1013 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1013">
-        <rdfs:label>Restriction enzyme name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1012"/>
-        <oboInOwl:hasDefinition>Name of a restriction enzyme.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1014 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1014">
-        <rdfs:label>Sequence position specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A specification (partial or complete) of one or more positions or regions of a molecular sequence or map.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1016"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1015 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1015">
-        <rdfs:label>Sequence feature ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3034"/>
-        <oboInOwl:hasDefinition>A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1016 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1016">
-        <rdfs:label>Sequence position</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:hasDbXref>WHATIF: number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_atom_site</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.id</oboInOwl:hasDbXref>
-        <oboInOwl:hasRelatedSynonym>SO:0000735</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>A position of one or more points (base or residue) in a sequence, or part of such a specification.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1017 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1017">
-        <rdfs:label>Sequence range</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Specification of range(s) of sequence positions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1018 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1018">
-        <rdfs:label>Nucleic acid feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of an nucleic acid feature.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1015"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1019 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1019">
-        <rdfs:label>Protein feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Name or other identifier of a protein feature.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1015"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1020 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1020">
-        <rdfs:label>Sequence feature key</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <oboInOwl:hasExactSynonym>Sequence feature method</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence feature type</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1021 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1021">
-        <rdfs:label>Sequence feature qualifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Typically one of the EMBL or Swiss-Prot feature qualifiers.</oboInOwl:hasDefinition>
-        <rdfs:comment>Feature qualifiers hold information about a feature beyond that provided by the feature key and location.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1022 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1022">
-        <rdfs:label>Sequence feature label</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <oboInOwl:hasExactSynonym>Sequence feature name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Typically an EMBL or Swiss-Prot feature label.</oboInOwl:hasDefinition>
-        <rdfs:comment>A feature label identifies a feature of a sequence database entry. When used with the database name and the entry&apos;s primary accession number, it is a unique identifier of that feature.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1023 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1023">
-        <rdfs:label>EMBOSS Uniform Feature Object</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3034"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UFO</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1024 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1024">
-        <rdfs:label>Codon name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>String of one or more ASCII characters representing a codon.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1025 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1025">
-        <rdfs:label>Gene identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDbXref>Moby:GeneAccessionList</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1026 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1026">
-        <rdfs:label>Gene symbol</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2299"/>
-        <oboInOwl:hasDbXref>Moby_namespace:Global_GeneSymbol</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:Global_GeneCommonName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1027 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1027">
-        <rdfs:label>Gene ID (NCBI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1098"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>NCBI geneid</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene identifier (NCBI)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Entrez gene ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene identifier (Entrez)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:LocusID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An NCBI unique identifier of a gene.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>NCBI gene ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1028 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1028">
-        <rdfs:label>Gene identifier (NCBI RefSeq)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>An NCBI RefSeq unique identifier of a gene.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1027"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1029 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1029">
-        <rdfs:label>Gene identifier (NCBI UniGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>An NCBI UniGene unique identifier of a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1104"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1030 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1030">
-        <rdfs:label>Gene identifier (Entrez)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An Entrez unique identifier of a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>[0-9]+</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1027"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1031 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1031">
-        <rdfs:label>Gene ID (CGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>CGD ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a gene or feature from the CGD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1032 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1032">
-        <rdfs:label>Gene ID (DictyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a gene from DictyBase.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1033 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1033">
-        <rdfs:label>Ensembl gene ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene ID (Ensembl)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a gene (or other feature) from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1034 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1034">
-        <rdfs:label>Gene ID (SGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2632"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the SGD database.</oboInOwl:hasDefinition>
-        <regex>S[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>SGD identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1035 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1035">
-        <rdfs:label>Gene ID (GeneDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>Moby_namespace:GeneDB</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>GeneDB identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9\.-]*</regex>
-        <oboInOwl:hasDefinition>Identifier of a gene from the GeneDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1036 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1036">
-        <rdfs:label>TIGR identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the TIGR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1037 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1037">
-        <rdfs:label>TAIR accession (gene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2387"/>
-        <regex>Gene:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an gene from the TAIR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1038 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1038">
-        <rdfs:label>Protein domain ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1468"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein structural domain.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is typically a character or string concatenated with a PDB identifier and a chain identifier.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1039 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1039">
-        <rdfs:label>SCOP domain identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1038"/>
-        <oboInOwl:hasDefinition>Identifier of a protein domain (or other node) from the SCOP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1040 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1040">
-        <rdfs:label>CATH domain ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2700"/>
-        <example>1nr3A00</example>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CATH domain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a protein domain from CATH.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1041 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1041">
-        <rdfs:label>SCOP concise classification string (sccs)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1039"/>
-        <oboInOwl:hasDefinition>A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1042 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1042">
-        <rdfs:label>SCOP sunid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1039"/>
-        <oboInOwl:hasDefinition>Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>sunid</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>SCOP unique identifier</oboInOwl:hasExactSynonym>
-        <example>33229</example>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1043 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1043">
-        <rdfs:label>CATH node ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2700"/>
-        <example>3.30.1190.10.1.1.1.1.1</example>
-        <oboInOwl:hasExactSynonym>CATH code</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A code number identifying a node from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>CATH node identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1044 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1044">
-        <rdfs:label>Kingdom name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1045 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1045">
-        <rdfs:label>Species name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a species (typically a taxonomic group) of organism.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Organism species</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1046 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1046">
-        <rdfs:label>Strain name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2379"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a strain of an organism variant, typically a plant, virus or bacterium.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1047 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1047">
-        <rdfs:label>URI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:hasDefinition>A string of characters that name or otherwise identify a resource on the Internet.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>URIs</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1048 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1048">
-        <rdfs:label>Database ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a biological or bioinformatics database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1049 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1049">
-        <rdfs:label>Directory name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a directory.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1050 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1050">
-        <rdfs:label>File name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name (or part of a name) of a file (of any type).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1051 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1051">
-        <rdfs:label>Ontology name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2338"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of an ontology of biological or bioinformatics concepts and relations.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1052 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1052">
-        <rdfs:label>URL</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1047"/>
-        <oboInOwl:hasDefinition>A Uniform Resource Locator (URL).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:URL</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Link</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1053 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1053">
-        <rdfs:label>URN</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1047"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A Uniform Resource Name (URN).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1055 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1055">
-        <rdfs:label>LSID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1053"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:&lt;Authority&gt;:&lt;Namespace&gt;:&lt;ObjectID&gt;[:&lt;Version&gt;]</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Life Science Identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A Life Science Identifier (LSID) - a unique identifier of some data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1056 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1056">
-        <rdfs:label>Database name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1048"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a biological or bioinformatics database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1057 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1057">
-        <rdfs:label>Sequence database name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The name of a molecular sequence database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1056"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1058 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1058">
-        <rdfs:label>Enumerated file name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1050"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a file (of any type) with restricted possible values.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1059 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1059">
-        <rdfs:label>File name extension</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1050"/>
-        <oboInOwl:hasDefinition>The extension of a file name.</oboInOwl:hasDefinition>
-        <rdfs:comment>A file extension is the characters appearing after the final &apos;.&apos; in the file name.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1060 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1060">
-        <rdfs:label>File base name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1050"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The base name of a file.</oboInOwl:hasDefinition>
-        <rdfs:comment>A file base name is the file name stripped of its directory specification and extension.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1061 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1061">
-        <rdfs:label>QSAR descriptor name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2110"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0847"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a QSAR descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1062 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1062">
-        <rdfs:label>Database entry identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This concept is required for completeness. It should never have child concepts.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1063 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1063">
-        <rdfs:label>Sequence identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of molecular sequence(s) or entries from a molecular sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1064 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1064">
-        <rdfs:label>Sequence set ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0850"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a set of molecular sequence(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1065 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1065">
-        <rdfs:label>Sequence signature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1114"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1115"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1066 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1066">
-        <rdfs:label>Sequence alignment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a molecular sequence alignment, for example a record from an alignment database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1067 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1067">
-        <rdfs:label>Phylogenetic distance matrix identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a phylogenetic distance matrix.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1068 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1068">
-        <rdfs:label>Phylogenetic tree ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a phylogenetic tree for example from a phylogenetic tree database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1069 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1069">
-        <rdfs:label>Comparison matrix identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0874"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a comparison matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1070 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1070">
-        <rdfs:label>Structure ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3035"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1071 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1071">
-        <rdfs:label>Structural (3D) profile ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structural profile identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1072 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1072">
-        <rdfs:label>Structure alignment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0886"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of tertiary structure alignments.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1073 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1073">
-        <rdfs:label>Amino acid index ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1501"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an index of amino acid physicochemical and biochemical property data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1074 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1074">
-        <rdfs:label>Protein interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasBroadSynonym>Molecular interaction ID</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Identifier of a report of protein interactions from a protein interaction database (typically).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1075 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1075">
-        <rdfs:label>Protein family identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Protein secondary database record identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a protein family.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1076 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1076">
-        <rdfs:label>Codon usage table name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2111"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Unique name of a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1077">
-        <rdfs:label>Transcription factor identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <oboInOwl:hasDefinition>Identifier of a transcription factor (or a TF binding site).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1078">
-        <rdfs:label>Experiment annotation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of microarray data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1079 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1079">
-        <rdfs:label>Electron microscopy model ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0941"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of electron microscopy data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1080">
-        <rdfs:label>Gene expression report ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession of a report of gene expression (e.g. a gene expression profile) from a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression profile identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1081">
-        <rdfs:label>Genotype and phenotype annotation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0920"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1082 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1082">
-        <rdfs:label>Pathway or network identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of biological pathways or networks.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1083">
-        <rdfs:label>Workflow ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological or biomedical workflow, typically from a database of workflows.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1084">
-        <rdfs:label>Data resource definition ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a data type definition from some provider.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Data resource definition identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1085">
-        <rdfs:label>Biological model ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0950"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Biological model identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a mathematical model, typically an entry from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1086 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1086">
-        <rdfs:label>Compound identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0962"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of chemicals.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Small molecule identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1087 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1087">
-        <rdfs:label>Ontology concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3025"/>
-        <oboInOwl:hasDefinition>A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology concept ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1088 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1088">
-        <rdfs:label>Article ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0971"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a scientific article.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Article identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1089 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1089">
-        <rdfs:label>FlyBase ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>Identifier of an object from the FlyBase database.</oboInOwl:hasDefinition>
-        <regex>FB[a-zA-Z_0-9]{2}[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1091 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1091">
-        <rdfs:label>WormBase name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <oboInOwl:hasDefinition>Name of an object from the WormBase database, usually a human-readable name.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1092">
-        <rdfs:label>WormBase class</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Class of an object from the WormBase database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A WormBase class describes the type of object such as &apos;sequence&apos; or &apos;protein&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1093 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1093">
-        <rdfs:label>Sequence accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1063"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A persistent, unique identifier of a molecular sequence database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1094">
-        <rdfs:label>Sequence type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).</rdfs:comment>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of molecular sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1095 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1095">
-        <rdfs:label>EMBOSS Uniform Sequence Address</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1063"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasExactSynonym>EMBOSS USA</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1096 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1096">
-        <rdfs:label>Sequence accession (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1093"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2976"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession number of a protein sequence database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein sequence accession number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1097">
-        <rdfs:label>Sequence accession (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1093"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession number of a nucleotide sequence database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1098 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1098">
-        <rdfs:label>RefSeq accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2362"/>
-        <oboInOwl:hasDefinition>Accession number of a RefSeq database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>RefSeq ID</oboInOwl:hasExactSynonym>
-        <regex>(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1099">
-        <rdfs:label>UniProt accession (extended)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number.</oboInOwl:hasDefinition>
-        <regex>[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <example>Q7M1G0|P43353-2|P01012.107</example>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3021"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1100">
-        <rdfs:label>PIR identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of PIR sequence database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PIR ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PIR accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1101 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1101">
-        <rdfs:label>TREMBL accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a TREMBL sequence database entry.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.2</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_3021"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1102">
-        <rdfs:label>Gramene primary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2915"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gramene primary ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Primary identifier of a Gramene database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1103 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1103">
-        <rdfs:label>EMBL/GenBank/DDBJ ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <oboInOwl:hasDefinition>Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1104 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1104">
-        <rdfs:label>Sequence cluster ID (UniGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasExactSynonym>UniGene identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniGene cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniGene ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniGene cluster ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of an entry (gene cluster) from the NCBI UniGene database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1105 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1105">
-        <rdfs:label>dbEST accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2292"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <oboInOwl:hasExactSynonym>dbEST ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a dbEST database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1106 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1106">
-        <rdfs:label>dbSNP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>dbSNP identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a dbSNP database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1110">
-        <rdfs:label>EMBOSS sequence type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The EMBOSS type of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1111">
-        <rdfs:label>EMBOSS listfile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1112">
-        <rdfs:label>Sequence cluster ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1064"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a cluster of molecular sequence(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1113 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1113">
-        <rdfs:label>Sequence cluster ID (COG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasExactSynonym>COG ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the COG database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1114 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1114">
-        <rdfs:label>Sequence motif identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1353"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a sequence motif, for example an entry from a motif database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1115 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1115">
-        <rdfs:label>Sequence profile ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a sequence profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A sequence profile typically represents a sequence alignment.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1116 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1116">
-        <rdfs:label>ELM ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1114"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the ELMdb database of protein functional sites.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1117 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1117">
-        <rdfs:label>Prosite accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1114"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry from the Prosite database.</oboInOwl:hasDefinition>
-        <regex>PS[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>Prosite ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1118">
-        <rdfs:label>HMMER hidden Markov model ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1115"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1364"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Unique identifier or name of a HMMER hidden Markov model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1119 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1119">
-        <rdfs:label>JASPAR profile ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1115"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier or name of a profile from the JASPAR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1120 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1120">
-        <rdfs:label>Sequence alignment type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1121 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1121">
-        <rdfs:label>BLAST sequence alignment type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The type of a BLAST sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1122">
-        <rdfs:label>Phylogenetic tree type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>For example &apos;nj&apos;, &apos;upgmp&apos; etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <example>nj|upgmp</example>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1123">
-        <rdfs:label>TreeBASE study accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1068"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the TreeBASE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1124 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1124">
-        <rdfs:label>TreeFam accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1068"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry from the TreeFam database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1125 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1125">
-        <rdfs:label>Comparison matrix type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <example>blosum|pam|gonnet|id</example>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a comparison matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix type</oboInOwl:hasExactSynonym>
-        <rdfs:comment>For example &apos;blosum&apos;, &apos;pam&apos;, &apos;gonnet&apos;, &apos;id&apos; etc. Comparison matrix type may be required where a series of matrices of a certain type are used.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1126">
-        <rdfs:label>Comparison matrix name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1069"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0874"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Substitution matrix name</oboInOwl:hasExactSynonym>
-        <rdfs:comment>See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.</rdfs:comment>
-        <oboInOwl:hasDefinition>Unique name or identifier of a comparison matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1127">
-        <rdfs:label>PDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1070"/>
-        <oboInOwl:hasDefinition>An identifier of an entry from the PDB database.</oboInOwl:hasDefinition>
-        <regex>[a-zA-Z_0-9]{4}</regex>
-        <oboInOwl:hasExactSynonym>PDBID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PDB identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1128">
-        <rdfs:label>AAindex ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1073"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the AAindex database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1129 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1129">
-        <rdfs:label>BIND accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the BIND database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1130">
-        <rdfs:label>IntAct accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>EBI\-[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry from the IntAct database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1131 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1131">
-        <rdfs:label>Protein family name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1075"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a protein family.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1132 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1132">
-        <rdfs:label>InterPro entry name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1131"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of an InterPro entry, usually indicating the type of protein matches for that entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1133">
-        <rdfs:label>InterPro accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Primary accession number of an InterPro entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>InterPro primary accession</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Every InterPro entry has a unique accession number to provide a persistent citation of database records.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>InterPro primary accession number</oboInOwl:hasExactSynonym>
-        <example>IPR015590</example>
-        <regex>IPR[0-9]{6}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1134">
-        <rdfs:label>InterPro secondary accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1133"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Secondary accession number of an InterPro entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>InterPro secondary accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1135">
-        <rdfs:label>Gene3D ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the Gene3D database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1136 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1136">
-        <rdfs:label>PIRSF ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <regex>PIRSF[0-9]{6}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the PIRSF database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1137">
-        <rdfs:label>PRINTS code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PR[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>The unique identifier of an entry in the PRINTS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1138 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1138">
-        <rdfs:label>Pfam accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <regex>PF[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Accession number of a Pfam entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1139">
-        <rdfs:label>SMART accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the SMART database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>SM[0-9]{5}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1140">
-        <rdfs:label>Superfamily hidden Markov model number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>Unique identifier (number) of a hidden Markov model from the Superfamily database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1141">
-        <rdfs:label>TIGRFam ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasExactSynonym>TIGRFam accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of an entry (family) from the TIGRFam database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1142 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1142">
-        <rdfs:label>ProDom accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>A ProDom domain family accession number.</oboInOwl:hasDefinition>
-        <regex>PD[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>ProDom is a protein domain family database.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1143">
-        <rdfs:label>TRANSFAC accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2911"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the TRANSFAC database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1144 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1144">
-        <rdfs:label>ArrayExpress accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the ArrayExpress database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[AEP]-[a-zA-Z_0-9]{4}-[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>ArrayExpress experiment ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1145 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1145">
-        <rdfs:label>PRIDE experiment accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PRIDE experiment accession number.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1146 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1146">
-        <rdfs:label>EMDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1079"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the EMDB electron microscopy database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1147">
-        <rdfs:label>GEO accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the GEO database.</oboInOwl:hasDefinition>
-        <regex>o^GDS[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1148 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1148">
-        <rdfs:label>GermOnline ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GermOnline database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1149 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1149">
-        <rdfs:label>EMAGE ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the EMAGE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1150 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1150">
-        <rdfs:label>Disease ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1622"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of disease.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1151 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1151">
-        <rdfs:label>HGVbase ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1081"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the HGVbase database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1152 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1152">
-        <rdfs:label>HIVDB identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the HIVDB database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1153 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1153">
-        <rdfs:label>OMIM ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1081"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[*#+%^]?[0-9]{6}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry from the OMIM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1154">
-        <rdfs:label>KEGG object identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an object from one of the KEGG databases (excluding the GENES division).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1155 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1155">
-        <rdfs:label>Pathway ID (reactome)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Reactome database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Reactome ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <regex>REACT_[0-9]+(\.[0-9]+)?</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1156">
-        <rdfs:label>Pathway ID (aMAZE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>aMAZE ID</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the aMAZE database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1082"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1157">
-        <rdfs:label>Pathway ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasExactSynonym>BioCyc pathway ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an pathway from the BioCyc biological pathways database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1158">
-        <rdfs:label>Pathway ID (INOH)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>INOH identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from the INOH database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1159">
-        <rdfs:label>Pathway ID (PATIKA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the PATIKA database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>PATIKA ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1160">
-        <rdfs:label>Pathway ID (CPDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <rdfs:comment>This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>CPDB ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1161 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1161">
-        <rdfs:label>Pathway ID (Panther)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of a biological pathway from the Panther Pathways database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PTHR[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>Panther Pathways ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1162 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1162">
-        <rdfs:label>MIRIAM identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2902"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Unique identifier of a MIRIAM data resource.</oboInOwl:hasDefinition>
-        <example>MIR:00100005</example>
-        <regex>MIR:[0-9]{8}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is the identifier used internally by MIRIAM for a data type.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1163">
-        <rdfs:label>MIRIAM data type name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2253"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a data type from the MIRIAM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1164">
-        <rdfs:label>MIRIAM URI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1047"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2902"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The URI (URL or URN) of a data entity from the MIRIAM database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>identifiers.org synonym</oboInOwl:hasExactSynonym>
-        <example>urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202</example>
-        <rdfs:comment>A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1165 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1165">
-        <rdfs:label>MIRIAM data type primary name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1163"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The primary name of a MIRIAM data type is taken from a controlled vocabulary.</rdfs:comment>
-        <example>UniProt|Enzyme Nomenclature</example>
-        <oboInOwl:hasDefinition>The primary name of a data type from the MIRIAM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>A protein entity has the MIRIAM data type &apos;UniProt&apos;, and an enzyme has the MIRIAM data type &apos;Enzyme Nomenclature&apos;.</rdfs:comment>
-        <owl:annotatedTarget>UniProt|Enzyme Nomenclature</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_1165"/>
-        <owl:annotatedProperty rdf:resource="http://edamontology.org/example"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_1166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1166">
-        <rdfs:label>MIRIAM data type synonymous name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1163"/>
-        <oboInOwl:hasDefinition>A synonymous name of a data type from the MIRIAM database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A synonymous name for a MIRIAM data type taken from a controlled vocabulary.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1167">
-        <rdfs:label>Taverna workflow ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1083"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a Taverna workflow.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1170 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1170">
-        <rdfs:label>Biological model name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1085"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a biological (mathematical) model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1171 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1171">
-        <rdfs:label>BioModel ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2891"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the BioModel database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>(BIOMD|MODEL)[0-9]{10}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1172">
-        <rdfs:label>PubChem CID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2639"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>PubChem compound accession identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1173">
-        <rdfs:label>ChemSpider ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the ChemSpider database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1174">
-        <rdfs:label>ChEBI ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the ChEBI database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChEBI IDs</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>ChEBI identifier</oboInOwl:hasExactSynonym>
-        <regex>CHEBI:[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1175">
-        <rdfs:label>BioPax concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the BioPax ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1176">
-        <rdfs:label>GO concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasExactSynonym>GO concept identifier</oboInOwl:hasExactSynonym>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from The Gene Ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1177">
-        <rdfs:label>MeSH concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the MeSH vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1178">
-        <rdfs:label>HGNC concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the HGNC controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1179">
-        <rdfs:label>NCBI taxonomy ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <oboInOwl:hasExactSynonym>NCBI taxonomy identifier</oboInOwl:hasExactSynonym>
-        <regex>[1-9][0-9]{0,8}</regex>
-        <oboInOwl:hasExactSynonym>NCBI tax ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database.</oboInOwl:hasDefinition>
-        <example>9662|3483|182682</example>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1180">
-        <rdfs:label>Plant Ontology concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasDefinition>An identifier of a concept from the Plant Ontology (PO).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1181 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1181">
-        <rdfs:label>UMLS concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasDefinition>An identifier of a concept from the UMLS vocabulary.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1182">
-        <rdfs:label>FMA concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasDefinition>An identifier of a concept from Foundational Model of Anatomy.</oboInOwl:hasDefinition>
-        <regex>FMA:[0-9]+</regex>
-        <rdfs:comment>Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1183">
-        <rdfs:label>EMAP concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the EMAP mouse ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1184">
-        <rdfs:label>ChEBI concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the ChEBI ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1185 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1185">
-        <rdfs:label>MGED concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the MGED ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1186 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1186">
-        <rdfs:label>myGrid concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.</rdfs:comment>
-        <oboInOwl:hasDefinition>An identifier of a concept from the myGrid ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1187 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1187">
-        <rdfs:label>PubMed ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1088"/>
-        <oboInOwl:hasExactSynonym>PMID</oboInOwl:hasExactSynonym>
-        <regex>[1-9][0-9]{0,8}</regex>
-        <oboInOwl:hasDefinition>PubMed unique identifier of an article.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <example>4963447</example>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1188 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1188">
-        <rdfs:label>DOI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1088"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>(doi\:)?[0-9]{2}\.[0-9]{4}/.*</regex>
-        <oboInOwl:hasExactSynonym>Digital Object Identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Digital Object Identifier (DOI) of a published article.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1189 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1189">
-        <rdfs:label>Medline UI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Medline UI (unique identifier) of an article.</oboInOwl:hasDefinition>
-        <rdfs:comment>The use of Medline UI has been replaced by the PubMed unique identifier.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Medline unique identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1190 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1190">
-        <rdfs:label>Tool name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0977"/>
-        <oboInOwl:hasDefinition>The name of a computer package, application, method or function.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1191">
-        <rdfs:label>Tool name (signature)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The unique name of a signature (sequence classifier) method.</oboInOwl:hasDefinition>
-        <rdfs:comment>Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1192 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1192">
-        <rdfs:label>Tool name (BLAST)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <rdfs:comment>This include &apos;blastn&apos;, &apos;blastp&apos;, &apos;blastx&apos;, &apos;tblastn&apos; and &apos;tblastx&apos;.</rdfs:comment>
-        <oboInOwl:hasDefinition>The name of a BLAST tool.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>BLAST name</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1193 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1193">
-        <rdfs:label>Tool name (FASTA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a FASTA tool.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes &apos;fasta3&apos;, &apos;fastx3&apos;, &apos;fasty3&apos;, &apos;fastf3&apos;, &apos;fasts3&apos; and &apos;ssearch&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1194">
-        <rdfs:label>Tool name (EMBOSS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <oboInOwl:hasDefinition>The name of an EMBOSS application.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1195">
-        <rdfs:label>Tool name (EMBASSY package)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <oboInOwl:hasDefinition>The name of an EMBASSY package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1201 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1201">
-        <rdfs:label>QSAR descriptor (constitutional)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <oboInOwl:hasDefinition>A QSAR constitutional descriptor.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>QSAR constitutional descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1202">
-        <rdfs:label>QSAR descriptor (electronic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A QSAR electronic descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>QSAR electronic descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1203">
-        <rdfs:label>QSAR descriptor (geometrical)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <oboInOwl:hasExactSynonym>QSAR geometrical descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A QSAR geometrical descriptor.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1204">
-        <rdfs:label>QSAR descriptor (topological)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>QSAR topological descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A QSAR topological descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1205 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1205">
-        <rdfs:label>QSAR descriptor (molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <oboInOwl:hasDefinition>A QSAR molecular descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>QSAR molecular descriptor</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1233">
-        <rdfs:label>Sequence set (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:hasDefinition>Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1234 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1234">
-        <rdfs:label>Sequence set (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0850"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1235">
-        <rdfs:label>Sequence cluster</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0850"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0724"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.</oboInOwl:hasDefinition>
-        <rdfs:comment>The cluster might include sequences identifiers, short descriptions, alignment and summary information.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1236">
-        <rdfs:label>Psiblast checkpoint file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension &apos;.asn&apos;.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1237">
-        <rdfs:label>HMMER synthetic sequences set</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Sequences generated by HMMER package in FASTA-style format.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1238">
-        <rdfs:label>Proteolytic digest</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1239">
-        <rdfs:label>Restriction digest</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <oboInOwl:hasDefinition>Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>SO:0000412</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1240">
-        <rdfs:label>PCR primers</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1241">
-        <rdfs:label>vectorstrip cloning vector definition file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1242">
-        <rdfs:label>Primer3 internal oligo mishybridizing library</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1243">
-        <rdfs:label>Primer3 mispriming library file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1244 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1244">
-        <rdfs:label>primersearch primer pairs sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>File of one or more pairs of primer sequences, as used by EMBOSS primersearch application.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1245">
-        <rdfs:label>Sequence cluster (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1233"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:hasExactSynonym>Protein sequence cluster</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The sequences are typically related, for example a family of sequences.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A cluster of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1246">
-        <rdfs:label>Sequence cluster (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:hasDefinition>A cluster of nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence cluster</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The sequences are typically related, for example a family of sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1249 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1249">
-        <rdfs:label>Sequence length</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1250">
-        <rdfs:label>Word size</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Word size is used for example in word-based sequence database search methods.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Word length</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Size of a sequence word.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1251 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1251">
-        <rdfs:label>Window size</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Size of a sequence window.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1252">
-        <rdfs:label>Sequence length range</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Specification of range(s) of length of sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1253">
-        <rdfs:label>Sequence information report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2043"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1254">
-        <rdfs:label>Sequence property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2955"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence properties report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1255 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1255">
-        <rdfs:label>Sequence features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Sequence features report</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D058977</rdfs:seeAlso>
-        <oboInOwl:hasRelatedSynonym>SO:0000110</oboInOwl:hasRelatedSynonym>
-        <rdfs:comment>This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features.  General feature reports are a source of sequence feature table information although internal conversion would be required.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>General sequence features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Feature record</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1256 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1256">
-        <rdfs:label>Sequence features (comparative)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1257">
-        <rdfs:label>Sequence property (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report of general sequence properties derived from protein sequence data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1258">
-        <rdfs:label>Sequence property (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report of general sequence properties derived from nucleotide sequence data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0912"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1259">
-        <rdfs:label>Sequence complexity report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1254"/>
-        <oboInOwl:hasDefinition>A report on sequence complexity, for example low-complexity or repeat regions in sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence property (complexity)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1260 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1260">
-        <rdfs:label>Sequence ambiguity report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1254"/>
-        <oboInOwl:hasDefinition>A report on ambiguity in molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence property (ambiguity)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1261 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1261">
-        <rdfs:label>Sequence composition report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1254"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report (typically a table) on character or word composition / frequency of a molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence property (composition)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1262 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1262">
-        <rdfs:label>Peptide molecular weight hits</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1233"/>
-        <oboInOwl:hasDefinition>A report on peptide fragments of certain molecular weight(s) in one or more protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1263 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1263">
-        <rdfs:label>Base position variability plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of third base position variability in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1264">
-        <rdfs:label>Sequence composition table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A table of character or word composition / frequency of a molecular sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1265">
-        <rdfs:label>Base frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A table of base frequencies of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1266 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1266">
-        <rdfs:label>Base word frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A table of word composition of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1267 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1267">
-        <rdfs:label>Amino acid frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasExactSynonym>Sequence composition (amino acid frequencies)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A table of amino acid frequencies of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1268 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1268">
-        <rdfs:label>Amino acid word frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A table of amino acid word composition of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence composition (amino acid words)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1269">
-        <rdfs:label>DAS sequence feature annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Annotation of a molecular sequence in DAS format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1978"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1270 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1270">
-        <rdfs:label>Feature table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:hasExactSynonym>Sequence feature table</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation of positional sequence features, organized into a standard feature table.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1274 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1274">
-        <rdfs:label>Map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>DNA map</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A map of (typically one) DNA sequence annotated with positional or non-positional features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1276 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1276">
-        <rdfs:label>Nucleic acid features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:hasDefinition>An informative report on intrinsic positional features of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Genome features</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Genomic features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid feature table</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Feature table (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1277">
-        <rdfs:label>Protein features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:hasDefinition>An informative report on intrinsic positional features of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Feature table (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein feature table</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1278">
-        <rdfs:label>Genetic map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1274"/>
-        <oboInOwl:hasDefinition>A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Linkage map</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:GeneticMap</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1279 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1279">
-        <rdfs:label>Sequence map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1280"/>
-        <rdfs:comment>A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1280">
-        <rdfs:label>Physical map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1274"/>
-        <oboInOwl:hasDefinition>A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them.</oboInOwl:hasDefinition>
-        <rdfs:comment>Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1281 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1281">
-        <rdfs:label>Sequence signature map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Image of a sequence with matches to signatures, motifs or profiles.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1283 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1283">
-        <rdfs:label>Cytogenetic map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1280"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A map showing banding patterns derived from direct observation of a stained chromosome.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Cytologic map</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Chromosome map</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Cytogenic map</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances.  Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1284">
-        <rdfs:label>DNA transduction map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1278"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A gene map showing distances between loci based on relative cotransduction frequencies.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1285">
-        <rdfs:label>Gene map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <oboInOwl:hasDefinition>Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1286 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1286">
-        <rdfs:label>Plasmid map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <oboInOwl:hasDefinition>Sequence map of a plasmid (circular DNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1288">
-        <rdfs:label>Genome map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence map of a whole genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1289">
-        <rdfs:label>Restriction map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2969"/>
-        <oboInOwl:hasDefinition>Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1290 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1290">
-        <rdfs:label>InterPro compact match image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Image showing matches between protein sequence(s) and InterPro Entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1291 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1291">
-        <rdfs:label>InterPro detailed match image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image showing detailed information on matches between protein sequence(s) and InterPro Entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1292">
-        <rdfs:label>InterPro architecture image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein.</rdfs:comment>
-        <oboInOwl:hasDefinition>Image showing the architecture of InterPro domains in a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1293">
-        <rdfs:label>SMART protein schematic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>SMART protein schematic in PNG format.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1294 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1294">
-        <rdfs:label>GlobPlot domain image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1298">
-        <rdfs:label>Sequence motif matches</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1299">
-        <rdfs:label>Sequence features (repeats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Repeat sequence map</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The report might include derived data map such as classification, annotation, organization, periodicity etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3126"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3129"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1300">
-        <rdfs:label>Gene and transcript structure (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1301">
-        <rdfs:label>Mobile genetic elements</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>regions of a nucleic acid sequence containing mobile genetic elements.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1302">
-        <rdfs:label>Nucleic acid features report (PolyA signal or site)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1303">
-        <rdfs:label>Nucleic acid features (quadruplexes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report on quadruplex-forming motifs in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1304">
-        <rdfs:label>Nucleic acid features report (CpG island and isochore)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>CpG rich regions (isochores) in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1305">
-        <rdfs:label>Nucleic acid features report (restriction sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1306">
-        <rdfs:label>Nucleosome exclusion sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Report on nucleosome formation potential or exclusion sequence(s).</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1307">
-        <rdfs:label>Nucleic acid features report (splice sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>splice sites in a nucleotide sequence or alternative RNA splicing events.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1308">
-        <rdfs:label>Nucleic acid features report (matrix/scaffold attachment sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1309">
-        <rdfs:label>Gene features (exonic splicing enhancer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on exonic splicing enhancers (ESE) in an exon.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1310">
-        <rdfs:label>Nucleic acid features (microRNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3137"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1311">
-        <rdfs:label>Gene features report (operon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>operons (operators, promoters and genes) from a bacterial genome.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1312">
-        <rdfs:label>Nucleic acid features report (promoters)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1313">
-        <rdfs:label>Coding region</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1314">
-        <rdfs:label>Gene features (SECIS element)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1315">
-        <rdfs:label>Transcription factor binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>transcription factor binding sites (TFBS) in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1321">
-        <rdfs:label>Protein features (sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1322">
-        <rdfs:label>Protein features report (signal peptides)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>signal peptides or signal peptide cleavage sites in protein sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1323">
-        <rdfs:label>Protein features report (cleavage sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1324 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1324">
-        <rdfs:label>Protein features (post-translation modifications)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>post-translation modifications in a protein sequence, typically describing the specific sites involved.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1325">
-        <rdfs:label>Protein features report (active sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>catalytic residues (active site) of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1326">
-        <rdfs:label>Protein features report (binding sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1327">
-        <rdfs:label>Protein features (epitopes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Epitope mapping is commonly done during vaccine design.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1326"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1328">
-        <rdfs:label>Protein features report (nucleic acid binding sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>RNA and DNA-binding proteins and binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1329">
-        <rdfs:label>MHC Class I epitopes report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on epitopes that bind to MHC class I molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1326"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1330">
-        <rdfs:label>MHC Class II epitopes report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on predicted epitopes that bind to MHC class II molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1326"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1331">
-        <rdfs:label>Protein features (PEST sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report or plot of PEST sites in a protein sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>&apos;PEST&apos; motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1323"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1338">
-        <rdfs:label>Sequence database hits scores list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Scores from a sequence database search (for example a BLAST search).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0857"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1339">
-        <rdfs:label>Sequence database hits alignments list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignments from a sequence database search (for example a BLAST search).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0857"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1340">
-        <rdfs:label>Sequence database hits evaluation data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0857"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1344">
-        <rdfs:label>MEME motif alphabet</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alphabet for the motifs (patterns) that MEME will search for.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1345">
-        <rdfs:label>MEME background frequencies file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>MEME background frequencies file.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1346">
-        <rdfs:label>MEME motifs directive file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>File of directives for ordering and spacing of MEME motifs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1347 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1347">
-        <rdfs:label>Dirichlet distribution</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:hasDefinition>Dirichlet distribution used by hidden Markov model analysis programs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1348">
-        <rdfs:label>HMM emission and transition counts</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3354"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1352">
-        <rdfs:label>Regular expression</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Regular expression pattern.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1353">
-        <rdfs:label>Sequence motif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0860"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1354">
-        <rdfs:label>Sequence profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0860"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Some type of statistical model representing a (typically multiple) sequence alignment.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_010531</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1355">
-        <rdfs:label>Protein signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2762"/>
-        <oboInOwl:hasDefinition>An informative report about a specific or conserved protein sequence pattern.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>InterPro entry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein repeat signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein region signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein site signature</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein family signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein domain signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1358">
-        <rdfs:label>Prosite nucleotide pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A nucleotide regular expression pattern from the Prosite database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1353"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1359">
-        <rdfs:label>Prosite protein pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein regular expression pattern from the Prosite database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1353"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1361 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1361">
-        <rdfs:label>Position frequency matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PFM</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1362 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1362">
-        <rdfs:label>Position weight matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <oboInOwl:hasExactSynonym>PWM</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.</oboInOwl:hasDefinition>
-        <rdfs:comment>Contributions of individual sequences to the matrix might be uneven (weighted).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1363 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1363">
-        <rdfs:label>Information content matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>ICM</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1364 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1364">
-        <rdfs:label>Hidden Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1354"/>
-        <oboInOwl:hasExactSynonym>HMM</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A hidden Markov model representation of a set or alignment of sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1365">
-        <rdfs:label>Fingerprint</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>One or more fingerprints (sequence classifiers) as used in the PRINTS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1368">
-        <rdfs:label>Domainatrix signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein signature of the type used in the EMBASSY Signature package.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1354"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1371">
-        <rdfs:label>HMMER NULL hidden Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>NULL hidden Markov model representation used by the HMMER package.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1364"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1372">
-        <rdfs:label>Protein family signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Protein family signatures cover all domains in the matching proteins and span &gt;80% of the protein length and with no adjacent protein domain signatures or protein region signatures.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A protein family signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1373 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1373">
-        <rdfs:label>Protein domain signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A protein domain signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <rdfs:comment>Protein domain signatures identify structural or functional domains or other units with defined boundaries.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1374 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1374">
-        <rdfs:label>Protein region signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein region signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>A protein region signature defines a region which cannot be described as a protein family or domain signature.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1375 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1375">
-        <rdfs:label>Protein repeat signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein repeat signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1376 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1376">
-        <rdfs:label>Protein site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>A protein site signature is a classifier for a specific site in a protein.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1377 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1377">
-        <rdfs:label>Protein conserved site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification.</rdfs:comment>
-        <oboInOwl:hasDefinition>A protein conserved site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1378">
-        <rdfs:label>Protein active site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein active site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1379">
-        <rdfs:label>Protein binding site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>A protein binding site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1380 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1380">
-        <rdfs:label>Protein post-translational modification signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein post-translational modification signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible.</rdfs:comment>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1381 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1381">
-        <rdfs:label>Sequence alignment (pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_010068</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1382 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1382">
-        <rdfs:label>Sequence alignment (multiple)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of more than two molecular sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1383">
-        <rdfs:label>Sequence alignment (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of multiple nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1384">
-        <rdfs:label>Sequence alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3154"/>
-        <oboInOwl:hasDefinition>Alignment of multiple protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1385">
-        <rdfs:label>Sequence alignment (hybrid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:hasDefinition>Alignment of multiple molecular sequences of different types.</oboInOwl:hasDefinition>
-        <rdfs:comment>Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1386">
-        <rdfs:label>Sequence alignment (nucleic acid pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1381"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1383"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of exactly two nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1387">
-        <rdfs:label>Sequence alignment (protein pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1381"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1384"/>
-        <oboInOwl:hasDefinition>Alignment of exactly two protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1388">
-        <rdfs:label>Hybrid sequence alignment (pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of exactly two molecular sequences of different types.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1385"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1389 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1389">
-        <rdfs:label>Multiple nucleotide sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of more than two nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1390">
-        <rdfs:label>Multiple protein sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of more than two protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1394 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1394">
-        <rdfs:label>Alignment score or penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2527"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for opening or extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1395">
-        <rdfs:label>Score end gaps control</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Whether end gaps are scored or not.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1396">
-        <rdfs:label>Aligned sequence order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Controls the order of sequences in an output sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1397">
-        <rdfs:label>Gap opening penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2137"/>
-        <oboInOwl:hasDefinition>A penalty for opening a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1398">
-        <rdfs:label>Gap extension penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2137"/>
-        <oboInOwl:hasDefinition>A penalty for extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1399">
-        <rdfs:label>Gap separation penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2137"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A penalty for gaps that are close together in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1400">
-        <rdfs:label>Terminal gap penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5&apos;/3&apos; terminal of nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1410"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1411"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1401">
-        <rdfs:label>Match reward score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The score for a &apos;match&apos; used in various sequence database search applications with simple scoring schemes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1402">
-        <rdfs:label>Mismatch penalty score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The score (penalty) for a &apos;mismatch&apos; used in various alignment and sequence database search applications with simple scoring schemes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1403">
-        <rdfs:label>Drop off score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <oboInOwl:hasDefinition>This is the threshold drop in score at which extension of word alignment is halted.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1404">
-        <rdfs:label>Gap opening penalty (integer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for opening a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1405">
-        <rdfs:label>Gap opening penalty (float)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for opening a gap in an alignment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1406">
-        <rdfs:label>Gap extension penalty (integer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1398"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1407">
-        <rdfs:label>Gap extension penalty (float)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1398"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1408">
-        <rdfs:label>Gap separation penalty (integer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for gaps that are close together in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1409">
-        <rdfs:label>Gap separation penalty (float)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for gaps that are close together in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1410">
-        <rdfs:label>Terminal gap opening penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1397"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5&apos;/3&apos; terminal of nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1411">
-        <rdfs:label>Terminal gap extension penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1398"/>
-        <oboInOwl:hasDefinition>A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5&apos;/3&apos; terminal of nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1412">
-        <rdfs:label>Sequence identity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0865"/>
-        <oboInOwl:hasDefinition>Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1413">
-        <rdfs:label>Sequence similarity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0865"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension.</oboInOwl:hasDefinition>
-        <rdfs:comment>Data Type is float probably.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1414">
-        <rdfs:label>Sequence alignment metadata (quality report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Data on molecular sequence alignment quality (estimated accuracy).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1415">
-        <rdfs:label>Sequence alignment report (site conservation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on character conservation in a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2161"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1416">
-        <rdfs:label>Sequence alignment report (site correlation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1417">
-        <rdfs:label>Sequence-profile alignment (Domainatrix signature)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1418 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1418">
-        <rdfs:label>Sequence-profile alignment (HMM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Alignment of molecular sequence(s) to a hidden Markov model(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1420">
-        <rdfs:label>Sequence-profile alignment (fingerprint)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment of molecular sequences to a protein fingerprint from the PRINTS database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1426">
-        <rdfs:label>Phylogenetic continuous quantitative data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0871"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic continuous quantitative characters</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Quantitative traits</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Continuous quantitative data that may be read during phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1427">
-        <rdfs:label>Phylogenetic discrete data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0871"/>
-        <oboInOwl:hasExactSynonym>Discrete characters</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Character data with discrete states that may be read during phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic discrete states</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Discretely coded characters</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1428">
-        <rdfs:label>Phylogenetic character cliques</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasDefinition>One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic report (cliques)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1429">
-        <rdfs:label>Phylogenetic invariants</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Phylogenetic invariants data for testing alternative tree topologies.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic report (invariants)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1438">
-        <rdfs:label>Phylogenetic report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree report</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Phylogenetic report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree-derived report</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used  for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1439">
-        <rdfs:label>DNA substitution model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:hasExactSynonym>Substitution model</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree report (DNA substitution model)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment report (DNA substitution model)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1440">
-        <rdfs:label>Phylogenetic tree report (tree shape)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>Data about the shape of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1441">
-        <rdfs:label>Phylogenetic tree report (tree evaluation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>Data on the confidence of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1442">
-        <rdfs:label>Phylogenetic tree distances</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree report (tree distances)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Distances, such as Branch Score distance, between two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1443">
-        <rdfs:label>Phylogenetic tree report (tree stratigraphic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1444">
-        <rdfs:label>Phylogenetic character contrasts</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic report (character contrasts)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1446">
-        <rdfs:label>Comparison matrix (integers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Substitution matrix (integers)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer numbers for sequence comparison.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0874"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1447">
-        <rdfs:label>Comparison matrix (floats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Matrix of floating point numbers for sequence comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix (floats)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0874"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1448">
-        <rdfs:label>Comparison matrix (nucleotide)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0874"/>
-        <oboInOwl:hasDefinition>Matrix of integer or floating point numbers for nucleotide comparison.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide substitution matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1449 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1449">
-        <rdfs:label>Comparison matrix (amino acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0874"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2016"/>
-        <oboInOwl:hasExactSynonym>Amino acid comparison matrix</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer or floating point numbers for amino acid comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Amino acid substitution matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1450 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1450">
-        <rdfs:label>Nucleotide comparison matrix (integers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Nucleotide substitution matrix (integers)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer numbers for nucleotide comparison.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1448"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1451">
-        <rdfs:label>Nucleotide comparison matrix (floats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Matrix of floating point numbers for nucleotide comparison.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide substitution matrix (floats)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1448"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1452">
-        <rdfs:label>Amino acid comparison matrix (integers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer numbers for amino acid comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Amino acid substitution matrix (integers)</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1449"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1453">
-        <rdfs:label>Amino acid comparison matrix (floats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Amino acid substitution matrix (floats)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Matrix of floating point numbers for amino acid comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1449"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1456">
-        <rdfs:label>Protein features report (membrane regions)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1459">
-        <rdfs:label>Nucleic acid structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a nucleic acid tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1460">
-        <rdfs:label>Protein structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Protein structures</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1461">
-        <rdfs:label>Protein-ligand complex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:hasDefinition>The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides.  For stable inter-polypeptide interactions use &apos;Protein complex&apos; instead.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1462 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1462">
-        <rdfs:label>Carbohydrate structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0153"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0152"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a carbohydrate (3D) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1463">
-        <rdfs:label>Small molecule structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0154"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>CHEBI:23367</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1464">
-        <rdfs:label>DNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1459"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a DNA tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1465">
-        <rdfs:label>RNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1459"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for an RNA tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1466 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1466">
-        <rdfs:label>tRNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1465"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1467">
-        <rdfs:label>Protein chain</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1468">
-        <rdfs:label>Protein domain</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0736"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the tertiary (3D) structure of a protein domain.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1469">
-        <rdfs:label>Protein structure (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein tertiary (3D) structure (all atoms).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1470">
-        <rdfs:label>C-alpha trace</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only).</oboInOwl:hasDefinition>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein structure (C-alpha atoms)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1471">
-        <rdfs:label>Protein chain (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1467"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1472">
-        <rdfs:label>Protein chain (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1467"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1473">
-        <rdfs:label>Protein domain (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1468"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1474">
-        <rdfs:label>Protein domain (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1468"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1479">
-        <rdfs:label>Structure alignment (pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0886"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Pair structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1480">
-        <rdfs:label>Structure alignment (multiple)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of more than two molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0886"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1481">
-        <rdfs:label>Structure alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0886"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3154"/>
-        <oboInOwl:hasExactSynonym>Protein structure alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of protein tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1482">
-        <rdfs:label>Structure alignment (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0886"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of nucleic acid tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1483">
-        <rdfs:label>Structure alignment (protein pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:hasExactSynonym>Protein pair structural alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1484 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1484">
-        <rdfs:label>Multiple protein tertiary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of more than two protein tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1485">
-        <rdfs:label>Structure alignment (protein all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1486">
-        <rdfs:label>Structure alignment (protein C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered).</oboInOwl:hasDefinition>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be considered.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>C-alpha trace</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1487">
-        <rdfs:label>Pairwise protein tertiary structure alignment (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1488">
-        <rdfs:label>Pairwise protein tertiary structure alignment (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1489">
-        <rdfs:label>Multiple protein tertiary structure alignment (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1490">
-        <rdfs:label>Multiple protein tertiary structure alignment (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1491">
-        <rdfs:label>Structure alignment (nucleic acid pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1482"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid pair structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1492">
-        <rdfs:label>Multiple nucleic acid tertiary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1482"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1493 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1493">
-        <rdfs:label>Structure alignment (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1482"/>
-        <oboInOwl:hasExactSynonym>RNA structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of RNA tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1494 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1494">
-        <rdfs:label>Structural transformation matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1495">
-        <rdfs:label>DaliLite hit table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>DaliLite hit table of protein chain tertiary structure alignment data.</oboInOwl:hasDefinition>
-        <rdfs:comment>The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0887"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1496">
-        <rdfs:label>Molecular similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A score reflecting structural similarities of two molecules.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0888"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1497">
-        <rdfs:label>Root-mean-square deviation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0888"/>
-        <oboInOwl:hasExactSynonym>RMSD</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1498">
-        <rdfs:label>Tanimoto similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0888"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A measure of the similarity between two ligand fingerprints.</oboInOwl:hasDefinition>
-        <rdfs:comment>A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1499">
-        <rdfs:label>3D-1D scoring matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0892"/>
-        <oboInOwl:hasDefinition>A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1501">
-        <rdfs:label>Amino acid index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2016"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1502">
-        <rdfs:label>Amino acid index (chemical classes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasExactSynonym>Chemical classes (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1503">
-        <rdfs:label>Amino acid pair-wise contact potentials</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2016"/>
-        <oboInOwl:hasExactSynonym>Contact potentials (amino acid pair-wise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Statistical protein contact potentials.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1505">
-        <rdfs:label>Amino acid index (molecular weight)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasDefinition>Molecular weights of amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Molecular weight (amino acids)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1506">
-        <rdfs:label>Amino acid index (hydropathy)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasDefinition>Hydrophobic, hydrophilic or charge properties of amino acids.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Hydropathy (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1507">
-        <rdfs:label>Amino acid index (White-Wimley data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>White-Wimley data (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Experimental free energy values for the water-interface and water-octanol transitions for the amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1508">
-        <rdfs:label>Amino acid index (van der Waals radii)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasExactSynonym>van der Waals radii (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Van der Waals radii of atoms for different amino acid residues.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1509">
-        <rdfs:label>Enzyme report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein report (enzyme)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Enzyme report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on a specific enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1517 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1517">
-        <rdfs:label>Restriction enzyme report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a specific restriction enzyme such as enzyme reference data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Restriction enzyme pattern data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein report (restriction enzyme)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Restriction enzyme report</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1519">
-        <rdfs:label>Peptide molecular weights</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report might include associated data such as frequency of peptide fragment molecular weights.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1520">
-        <rdfs:label>Peptide hydrophobic moment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on the hydrophobic moment of a polypeptide sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1521">
-        <rdfs:label>Protein aliphatic index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <oboInOwl:hasDefinition>The aliphatic index of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The aliphatic index is the relative protein volume occupied by aliphatic side chains.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1522">
-        <rdfs:label>Protein sequence hydropathy plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <rdfs:comment>Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1523">
-        <rdfs:label>Protein charge plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1524">
-        <rdfs:label>Protein solubility</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The solubility or atomic solvation energy of a protein sequence or structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein solubility data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1525">
-        <rdfs:label>Protein crystallizability</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein crystallizability data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data on the crystallizability of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1526">
-        <rdfs:label>Protein globularity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <oboInOwl:hasExactSynonym>Protein globularity data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on the stability, intrinsic disorder or globularity of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1527">
-        <rdfs:label>Protein titration curve</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <oboInOwl:hasDefinition>The titration curve of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1528">
-        <rdfs:label>Protein isoelectric point</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The isoelectric point of one proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1529">
-        <rdfs:label>Protein pKa value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>The pKa value of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1530">
-        <rdfs:label>Protein hydrogen exchange rate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The hydrogen exchange rate of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1531">
-        <rdfs:label>Protein extinction coefficient</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>The extinction coefficient of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1532 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1532">
-        <rdfs:label>Protein optical density</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>The optical density of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1533">
-        <rdfs:label>Protein subcellular localization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Protein report (subcellular localization)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1534">
-        <rdfs:label>Peptide immunogenicity data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>An report on allergenicity / immunogenicity of peptides and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Peptide immunogenicity report</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide immunogenicity</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1536">
-        <rdfs:label>MHC peptide immunogenicity report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report on the immunogenicity of MHC class I or class II binding peptides.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1534"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1537">
-        <rdfs:label>Protein structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:hasExactSynonym>Protein structural property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure-derived report</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein property (structural)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein report (structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure report (domain)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1539">
-        <rdfs:label>Protein structural quality report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:hasDefinition>Report on the quality of a protein three-dimensional model.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein structure report (quality evaluation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure validation report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein property (structural quality)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein report (structural quality)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1540">
-        <rdfs:label>Protein residue interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Residue interaction data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Atom interaction data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1541 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1541">
-        <rdfs:label>Protein flexibility or motion report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein property (flexibility or motion)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Informative report on flexibility or motion of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein flexibility or motion</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein structure report (flexibility or motion)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1542">
-        <rdfs:label>Protein solvent accessibility</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on the solvent accessible or buried surface area of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1543">
-        <rdfs:label>Protein surface report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein structure report (surface)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1544 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1544">
-        <rdfs:label>Ramachandran plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2991"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phi/psi angle data or a Ramachandran plot of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1545">
-        <rdfs:label>Protein dipole moment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>Data on the net charge distribution (dipole moment) of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1546">
-        <rdfs:label>Protein distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1547">
-        <rdfs:label>Protein contact map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <oboInOwl:hasDefinition>An amino acid residue contact map for a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1548">
-        <rdfs:label>Protein residue 3D cluster</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on clusters of contacting residues in protein structures such as a key structural residue network.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1549">
-        <rdfs:label>Protein hydrogen bonds</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <oboInOwl:hasDefinition>Patterns of hydrogen bonding in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1550">
-        <rdfs:label>Protein non-canonical interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Protein non-canonical interactions report</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Non-canonical atomic interactions in protein structures.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1553">
-        <rdfs:label>CATH node</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information on a node from the CATH database.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>CATH classification node report</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1554">
-        <rdfs:label>SCOP node</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>SCOP classification node</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Information on a node from the SCOP database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1555">
-        <rdfs:label>EMBASSY domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1556">
-        <rdfs:label>CATH class</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a protein &apos;class&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1557">
-        <rdfs:label>CATH architecture</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a protein &apos;architecture&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1558">
-        <rdfs:label>CATH topology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a protein &apos;topology&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1559">
-        <rdfs:label>CATH homologous superfamily</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a protein &apos;homologous superfamily&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1560">
-        <rdfs:label>CATH structurally similar group</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a protein &apos;structurally similar group&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1561">
-        <rdfs:label>CATH functional category</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information on a protein &apos;functional category&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1564">
-        <rdfs:label>Protein fold recognition report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0901"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1565">
-        <rdfs:label>Protein-protein interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>protein-protein interaction(s), including interactions between protein domains.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1566">
-        <rdfs:label>Protein-ligand interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0906"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on protein-ligand (small molecule) interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1567">
-        <rdfs:label>Protein-nucleic acid interactions report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>protein-DNA/RNA interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1583">
-        <rdfs:label>Nucleic acid melting profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid stability profile</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1584 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1584">
-        <rdfs:label>Nucleic acid enthalpy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1585 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1585">
-        <rdfs:label>Nucleic acid entropy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <oboInOwl:hasDefinition>Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1586 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1586">
-        <rdfs:label>Nucleic acid melting temperature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2139"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1587 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1587">
-        <rdfs:label>Nucleic acid stitch profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <rdfs:comment>A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1588 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1588">
-        <rdfs:label>DNA base pair stacking energies data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <oboInOwl:hasDefinition>DNA base pair stacking energies data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1589 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1589">
-        <rdfs:label>DNA base pair twist angle data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA base pair twist angle data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1590 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1590">
-        <rdfs:label>DNA base trimer roll angles data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA base trimer roll angles data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1591 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1591">
-        <rdfs:label>Vienna RNA parameters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>RNA parameters used by the Vienna package.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1592 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1592">
-        <rdfs:label>Vienna RNA structure constraints</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Structure constraints used by the Vienna package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1593">
-        <rdfs:label>Vienna RNA concentration data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>RNA concentration data used by the Vienna package.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1594">
-        <rdfs:label>Vienna RNA calculated energy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>RNA calculated energy data generated by the Vienna package.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1584"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1595">
-        <rdfs:label>Base pairing probability matrix dotplot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Such as generated by the Vienna package.</rdfs:comment>
-        <oboInOwl:hasDefinition>Dotplot of RNA base pairing probability matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1596 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1596">
-        <rdfs:label>Nucleic acid folding report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (folding)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (folding model)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>RNA secondary structure folding probablities</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>RNA secondary structure folding classification</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1597 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1597">
-        <rdfs:label>Codon usage table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Table of codon usage data calculated from one or more nucleic acid sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1598">
-        <rdfs:label>Genetic code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A genetic code for an organism.</oboInOwl:hasDefinition>
-        <rdfs:comment>A genetic code need not include detailed codon usage information.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1599 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1599">
-        <rdfs:label>Codon adaptation index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple measure of synonymous codon usage bias often used to predict gene expression levels.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>CAI</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2865"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1600 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1600">
-        <rdfs:label>Codon usage bias plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:hasExactSynonym>Synonymous codon usage statistic plot</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of the synonymous codon usage calculated for windows over a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1601">
-        <rdfs:label>Nc statistic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The effective number of codons used in a gene sequence.  This reflects how far codon usage of a gene departs from equal usage of synonymous codons.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2865"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1602">
-        <rdfs:label>Codon usage fraction difference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:hasDefinition>The differences in codon usage fractions between two codon usage tables.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1621">
-        <rdfs:label>Pharmacogenomic test report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0920"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on the influence of genotype on drug response.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1622">
-        <rdfs:label>Disease report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0920"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0634"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An informative report on a specific disease.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Disease report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1634 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1634">
-        <rdfs:label>Linkage disequilibrium (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0927"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1636 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1636">
-        <rdfs:label>Heat map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:hasDefinition>A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1642 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1642">
-        <rdfs:label>Affymetrix probe sets library file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Affymetrix library file of information about which probes belong to which probe set.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>CDF file</oboInOwl:hasRelatedSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1643 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1643">
-        <rdfs:label>Affymetrix probe sets information library file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>GIN file</oboInOwl:hasRelatedSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1646 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1646">
-        <rdfs:label>Molecular weights standard fingerprint</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0944"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1656 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1656">
-        <rdfs:label>Metabolic pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of a metabolic pathway.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1657 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1657">
-        <rdfs:label>Genetic information processing pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>genetic information processing pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1658 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1658">
-        <rdfs:label>Environmental information processing pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>environmental information processing pathways.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1659 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1659">
-        <rdfs:label>Signal transduction pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of a signal transduction pathway.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1660 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1660">
-        <rdfs:label>Cellular process pathways report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Topic concernning cellular process pathways.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1661 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1661">
-        <rdfs:label>Disease pathway or network report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>disease pathways, typically of human disease.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1662 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1662">
-        <rdfs:label>Drug structure relationship map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1696"/>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of drug structure relationships.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1663 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1663">
-        <rdfs:label>Protein interaction networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>networks of protein interactions.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2600"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1664 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1664">
-        <rdfs:label>MIRIAM datatype</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types.</rdfs:comment>
-        <oboInOwl:hasDefinition>An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1667 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1667">
-        <rdfs:label>E-value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0951"/>
-        <rdfs:comment>An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple floating point number defining the lower or upper limit of an expectation value (E-value).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Expectation value</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1668 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1668">
-        <rdfs:label>Z-value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0951"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The z-value is the number of standard deviations a data value is above or below a mean value.</oboInOwl:hasDefinition>
-        <rdfs:comment>A z-value might be specified as a threshold for reporting hits from database searches.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1669 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1669">
-        <rdfs:label>P-value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0951"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A z-value might be specified as a threshold for reporting hits from database searches.</rdfs:comment>
-        <oboInOwl:hasDefinition>The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1670 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1670">
-        <rdfs:label>Database version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Ontology version information</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a database (or ontology) version, for example name, version number and release date.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1671 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1671">
-        <rdfs:label>Tool version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on an application version, for example name, version number and release date.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0958"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1672 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1672">
-        <rdfs:label>CATH version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a version of the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1673 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1673">
-        <rdfs:label>Swiss-Prot to PDB mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Cross-mapping of Swiss-Prot codes to PDB identifiers.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0954"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1674 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1674">
-        <rdfs:label>Sequence database cross-references</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Cross-references from a sequence record to other databases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1675 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1675">
-        <rdfs:label>Job status</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Metadata on the status of a submitted job.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Values for EBI services are &apos;DONE&apos; (job has finished and the results can then be retrieved), &apos;ERROR&apos; (the job failed or no results where found), &apos;NOT_FOUND&apos; (the job id is no longer available; job results might be deleted, &apos;PENDING&apos; (the job is in a queue waiting processing), &apos;RUNNING&apos; (the job is currently being processed).</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1676 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1676">
-        <rdfs:label>Job ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:hasDefinition>The (typically numeric) unique identifier of a submitted job.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1677 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1677">
-        <rdfs:label>Job type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of job, for example interactive or non-interactive.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1678 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1678">
-        <rdfs:label>Tool log</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1679 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1679">
-        <rdfs:label>DaliLite log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1680 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1680">
-        <rdfs:label>STRIDE log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>STRIDE log file.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1678"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1681 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1681">
-        <rdfs:label>NACCESS log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>NACCESS log file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1678"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1682 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1682">
-        <rdfs:label>EMBOSS wordfinder log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>EMBOSS wordfinder log file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1683 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1683">
-        <rdfs:label>EMBOSS domainatrix log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>EMBOSS (EMBASSY) domainatrix application log file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1684 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1684">
-        <rdfs:label>EMBOSS sites log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>EMBOSS (EMBASSY) sites application log file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1685 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1685">
-        <rdfs:label>EMBOSS supermatcher error file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>EMBOSS (EMBASSY) supermatcher error file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1686 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1686">
-        <rdfs:label>EMBOSS megamerger log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>EMBOSS megamerger log file.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1687 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1687">
-        <rdfs:label>EMBOSS whichdb log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>EMBOSS megamerger log file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1688 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1688">
-        <rdfs:label>EMBOSS vectorstrip log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>EMBOSS vectorstrip log file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1689 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1689">
-        <rdfs:label>Username</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2101"/>
-        <oboInOwl:hasDefinition>A username on a computer system.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1690 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1690">
-        <rdfs:label>Password</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2101"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A password on a computer system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1691 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1691">
-        <rdfs:label>Email address</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2101"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:Email</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A valid email address of an end-user.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:EmailAddress</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1692 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1692">
-        <rdfs:label>Person name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2118"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a person.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1693 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1693">
-        <rdfs:label>Number of iterations</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Number of iterations of an algorithm.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1694 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1694">
-        <rdfs:label>Number of output entities</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Number of entities (for example database hits, sequences, alignments etc) to write to an output file.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1695 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1695">
-        <rdfs:label>Hit sort order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Controls the order of hits (reported matches) in an output file from a database search.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2134"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1696 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1696">
-        <rdfs:label>Drug report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0962"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0620"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An informative report on a specific drug.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Drug annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1707 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1707">
-        <rdfs:label>Phylogenetic tree image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information.</oboInOwl:hasDefinition>
-        <rdfs:comment>See also &apos;Phylogenetic tree&apos;</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1708 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1708">
-        <rdfs:label>RNA secondary structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of RNA secondary structure, knots, pseudoknots etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1709 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1709">
-        <rdfs:label>Protein secondary structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3153"/>
-        <oboInOwl:hasDefinition>Image of protein secondary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1710 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1710">
-        <rdfs:label>Structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of one or more molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1711 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1711">
-        <rdfs:label>Sequence alignment image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of two or more aligned molecular sequences possibly annotated with alignment features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1712 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1712">
-        <rdfs:label>Chemical structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1710"/>
-        <oboInOwl:hasDefinition>An image of the structure of a small chemical compound.</oboInOwl:hasDefinition>
-        <rdfs:comment>The molecular identifier and formula are typically included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Small molecule structure image</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1713 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1713">
-        <rdfs:label>Fate map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2530"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3065"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition> A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1714 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1714">
-        <rdfs:label>Microarray spots image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image of spots from a microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1715 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1715">
-        <rdfs:label>BioPax term</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A term from the BioPax ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1716 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1716">
-        <rdfs:label>GO</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Gene Ontology term</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Annotated_GO_Term</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Annotated_GO_Term_With_Probability</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term definition from The Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:GO_Term</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GOTerm</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1717 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1717">
-        <rdfs:label>MeSH</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the MeSH vocabulary.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1718 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1718">
-        <rdfs:label>HGNC</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the HGNC controlled vocabulary.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1719 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1719">
-        <rdfs:label>NCBI taxonomy vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the NCBI taxonomy vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1720 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1720">
-        <rdfs:label>Plant ontology term</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from the Plant Ontology (PO).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1721 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1721">
-        <rdfs:label>UMLS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from the UMLS vocabulary.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1722 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1722">
-        <rdfs:label>FMA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from Foundational Model of Anatomy.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1723 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1723">
-        <rdfs:label>EMAP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A term from the EMAP mouse ontology.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1724 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1724">
-        <rdfs:label>ChEBI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from the ChEBI ontology.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1725 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1725">
-        <rdfs:label>MGED</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the MGED ontology.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1726 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1726">
-        <rdfs:label>myGrid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the myGrid ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1727 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1727">
-        <rdfs:label>GO (biological process)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Data Type is an enumerated string.</rdfs:comment>
-        <oboInOwl:hasDefinition>A term definition for a biological process from the Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1728 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1728">
-        <rdfs:label>GO (molecular function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A term definition for a molecular function from the Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Data Type is an enumerated string.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1729 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1729">
-        <rdfs:label>GO (cellular component)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term definition for a cellular component from the Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Data Type is an enumerated string.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1730 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1730">
-        <rdfs:label>Ontology relation type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A relation type defined in an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0967"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1731 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1731">
-        <rdfs:label>Ontology concept definition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0967"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology class definition</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The definition of a concept from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1732 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1732">
-        <rdfs:label>Ontology concept comment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A comment on a concept from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0967"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1733 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1733">
-        <rdfs:label>Ontology concept reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Reference for a concept from an ontology.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1738 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1738">
-        <rdfs:label>doc2loc document information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The doc2loc output includes the url, format, type and availability code of a document for every service provider.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a published article provided by the doc2loc program.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0970"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1742 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1742">
-        <rdfs:label>PDB residue number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <oboInOwl:hasDbXref>WHATIF: pdb_number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:PDB_residue_no</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A residue identifier (a string) from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1743 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1743">
-        <rdfs:label>Atomic coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1917"/>
-        <oboInOwl:hasDefinition>Cartesian coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Cartesian coordinate</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1744 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1744">
-        <rdfs:label>Atomic x coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1743"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_Cartn_x</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Cartesian x coordinate</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.Cartn_x in PDBML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cartesian x coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1745 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1745">
-        <rdfs:label>Atomic y coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1743"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_Cartn_y</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Cartesian y coordinate</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.Cartn_y in PDBML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cartesian y coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1746 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1746">
-        <rdfs:label>Atomic z coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1743"/>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.Cartn_z</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_Cartn_z</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cartesian z coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Cartesian z coordinate</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1748 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1748">
-        <rdfs:label>PDB atom name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1757"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_type_symbol</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_auth_atom_id</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: alternate_atom</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_atom_name</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: atom_type</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier (a string) of a specific atom from a PDB file for a molecular structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1755 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1755">
-        <rdfs:label>Protein atom</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:hasExactSynonym>Atom data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>CHEBI:33250</oboInOwl:hasRelatedSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on a single atom from a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1756 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1756">
-        <rdfs:label>Protein residue</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on a single amino acid residue position in a protein structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Residue</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1757 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1757">
-        <rdfs:label>Atom name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0983"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>Name of an atom.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1758 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1758">
-        <rdfs:label>PDB residue name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2564"/>
-        <oboInOwl:hasDefinition>Three-letter amino acid residue names as used in PDB files.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: type</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1759 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1759">
-        <rdfs:label>PDB model number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3035"/>
-        <oboInOwl:hasDefinition>Identifier of a model structure from a PDB file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_model_num</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Model number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>WHATIF: model_number</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1762 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1762">
-        <rdfs:label>CATH domain report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.</rdfs:comment>
-        <oboInOwl:hasDefinition>Summary of domain classification information for a CATH domain.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1764 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1764">
-        <rdfs:label>CATH representative domain sequences (ATOM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1765 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1765">
-        <rdfs:label>CATH representative domain sequences (COMBS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1766 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1766">
-        <rdfs:label>CATH domain sequences (ATOM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>FASTA sequence database for all CATH domains (based on PDB ATOM records).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1767 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1767">
-        <rdfs:label>CATH domain sequences (COMBS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>FASTA sequence database for all CATH domains (based on COMBS sequence data).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1771 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1771">
-        <rdfs:label>Sequence version</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on an molecular sequence version.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence version information</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1772 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1772">
-        <rdfs:label>Score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>A numerical value, that is some type of scored value arising for example from a prediction method.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1776 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1776">
-        <rdfs:label>Protein report (function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>For properties that can be mapped to a sequence, use &apos;Sequence report&apos; instead.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Report on general functional properties of specific protein(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1783 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1783">
-        <rdfs:label>Gene name (ASPGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of a gene from Aspergillus Genome Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1784 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1784">
-        <rdfs:label>Gene name (CGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Name of a gene from Candida Genome Database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1785 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1785">
-        <rdfs:label>Gene name (dictyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of a gene from dictyBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1786 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1786">
-        <rdfs:label>Gene name (EcoGene primary)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Primary name of a gene from EcoGene Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EcoGene primary gene name</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1787 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1787">
-        <rdfs:label>Gene name (MaizeGDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus</oboInOwl:hasDbXref>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Name of a gene from MaizeGDB (maize genes) database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1788 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1788">
-        <rdfs:label>Gene name (SGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Name of a gene from Saccharomyces Genome Database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1789 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1789">
-        <rdfs:label>Gene name (TGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Name of a gene from Tetrahymena Genome Database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1790 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1790">
-        <rdfs:label>Gene name (CGSC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: CGSC</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Symbol of a gene from E.coli Genetic Stock Center.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1791 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1791">
-        <rdfs:label>Gene name (HGNC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>HUGO symbol</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>HGNC symbol</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Official gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HUGO gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>HGNC gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HUGO gene symbol</oboInOwl:hasExactSynonym>
-        <regex>HGNC:[0-9]{1,5}</regex>
-        <oboInOwl:hasExactSynonym>Gene name (HUGO)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HGNC gene symbol</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Symbol of a gene approved by the HUGO Gene Nomenclature Committee.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1792 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1792">
-        <rdfs:label>Gene name (MGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>MGI:[0-9]+</regex>
-        <oboInOwl:hasDefinition>Symbol of a gene from the Mouse Genome Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: MGD</oboInOwl:hasDbXref>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1793 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1793">
-        <rdfs:label>Gene name (Bacillus subtilis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Symbol of a gene from Bacillus subtilis Genome Sequence Project.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1794 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1794">
-        <rdfs:label>Gene ID (PlasmoDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier of a gene from PlasmoDB Plasmodium Genome Resource.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1795 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1795">
-        <rdfs:label>Gene ID (EcoGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier of a gene from EcoGene Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EcoGene Accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>EcoGene ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1796 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1796">
-        <rdfs:label>Gene ID (FlyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gene identifier from FlyBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: FB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1797 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1797">
-        <rdfs:label>Gene ID (GeneDB Glossina morsitans)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans</oboInOwl:hasDbXref>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Gene identifier from Glossina morsitans GeneDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1798 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1798">
-        <rdfs:label>Gene ID (GeneDB Leishmania major)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Gene identifier from Leishmania major GeneDB database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1799 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1799">
-        <rdfs:label>Gene ID (GeneDB Plasmodium falciparum)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Gene identifier from Plasmodium falciparum GeneDB database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum</oboInOwl:hasDbXref>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1800 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1800">
-        <rdfs:label>Gene ID (GeneDB Schizosaccharomyces pombe)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Gene identifier from Schizosaccharomyces pombe GeneDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1801 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1801">
-        <rdfs:label>Gene ID (GeneDB Trypanosoma brucei)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Gene identifier from Trypanosoma brucei GeneDB database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1802 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1802">
-        <rdfs:label>Gene ID (Gramene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Gene identifier from Gramene database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1803 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1803">
-        <rdfs:label>Gene ID (Virginia microbial)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Gene identifier from Virginia Bioinformatics Institute microbial database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: VMD</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1804 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1804">
-        <rdfs:label>Gene ID (SGN)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SGN</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Gene identifier from Sol Genomics Network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1805 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1805">
-        <rdfs:label>Gene ID (WormBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Gene identifier used by WormBase database.</oboInOwl:hasDefinition>
-        <regex>WBGene[0-9]{8}</regex>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: WB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: WormBase</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1806 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1806">
-        <rdfs:label>Gene synonym</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Gene name synonym</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Any name (other than the recommended one) for a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1807 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1807">
-        <rdfs:label>ORF name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2795"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of an open reading frame attributed by a sequencing project.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1852 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1852">
-        <rdfs:label>Sequence assembly component</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A component of a larger sequence assembly.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0925"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1853 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1853">
-        <rdfs:label>Chromosome annotation (aberration)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on a chromosome aberration such as abnormalities in chromosome structure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0919"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1855 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1855">
-        <rdfs:label>Clone ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2769"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a clone (cloned molecular sequence) from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1856 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1856">
-        <rdfs:label>PDB insertion code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: insertion_code</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_ins_code</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An insertion code (part of the residue number) for an amino acid residue from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1857 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1857">
-        <rdfs:label>Atomic occupancy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1917"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_occupancy</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The fraction of an atom type present at a site in a molecular structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1858 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1858">
-        <rdfs:label>Isotropic B factor</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1917"/>
-        <oboInOwl:hasDefinition>Isotropic B factor (atomic displacement parameter) for an atom from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_B_iso_or_equiv</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1859 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1859">
-        <rdfs:label>Deletion map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1283"/>
-        <rdfs:comment>A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line (&apos;genome deletion panel&apos;). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Deletion-based cytogenetic map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1860 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1860">
-        <rdfs:label>QTL map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1278"/>
-        <oboInOwl:hasDefinition>A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Quantitative trait locus map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1863 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1863">
-        <rdfs:label>Haplotype map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1278"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:Haplotyping_Study_obj</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1864 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1864">
-        <rdfs:label>Map set data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2019"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:GCP_CorrelatedLinkageMapSet</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_CorrelatedMapSet</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1865 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1865">
-        <rdfs:label>Map feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A feature which may mapped (positioned) on a genetic or other type of map.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:MapFeature</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Mappable features may be based on Gramene&apos;s notion of map features; see http://www.gramene.org/db/cmap/feature_type_info.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2019"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1866 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1866">
-        <rdfs:label>Map type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A designation of the type of map (genetic map, physical map, sequence map etc) or map set.</oboInOwl:hasDefinition>
-        <rdfs:comment>Map types may be based on Gramene&apos;s notion of a map type; see http://www.gramene.org/db/cmap/map_type_info.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1867">
-        <rdfs:label>Protein fold name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a protein fold.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1868">
-        <rdfs:label>Taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDbXref>Moby:PotentialTaxon</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Taxonomy rank</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Taxonomic rank</oboInOwl:hasExactSynonym>
-        <rdfs:comment>For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.</rdfs:comment>
-        <oboInOwl:hasDefinition>The name of a group of organisms belonging to the same taxonomic rank.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:BriefTaxonConcept</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1869">
-        <rdfs:label>Organism identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2530"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a (group of) organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1870 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1870">
-        <rdfs:label>Genus name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a genus of organism.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1872 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1872">
-        <rdfs:label>Taxonomic classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDbXref>Moby:TaxonName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_Taxon</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:iANT_organism-xml</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Taxonomic name</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Name components correspond to levels in a taxonomic hierarchy (e.g. &apos;Genus&apos;, &apos;Species&apos;, etc.) Meta information such as a reference where the name was defined and a date might be included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Taxonomic information</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:TaxonScientificName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:TaxonTCS</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1873 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1873">
-        <rdfs:label>iHOP organism ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:iHOPorganism</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A unique identifier for an organism used in the iHOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1874 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1874">
-        <rdfs:label>Genbank common name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDefinition>Common name for an organism as used in the GenBank database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1875 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1875">
-        <rdfs:label>NCBI taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a taxon from the NCBI taxonomy database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1877 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1877">
-        <rdfs:label>Synonym</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Alternative name</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An alternative for a word.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1878 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1878">
-        <rdfs:label>Misspelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A common misspelling of a word.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1879 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1879">
-        <rdfs:label>Acronym</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An abbreviation of a phrase or word.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1880 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1880">
-        <rdfs:label>Misnomer</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A term which is likely to be misleading of its meaning.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1881 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1881">
-        <rdfs:label>Author ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2118"/>
-        <oboInOwl:hasDefinition>Information on the authors of a published work.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:Author</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1882 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1882">
-        <rdfs:label>DragonDB author identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1881"/>
-        <oboInOwl:hasDefinition>An identifier representing an author in the DragonDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1883 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1883">
-        <rdfs:label>Annotated URI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A URI along with annotation describing the data found at the address.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:DescribedLink</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1884 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1884">
-        <rdfs:label>UniProt keywords</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1885">
-        <rdfs:label>Gene ID (GeneFarm)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>Moby_namespace:GENEFARM_GeneID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier of a gene from the GeneFarm database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1886 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1886">
-        <rdfs:label>Blattner number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:Blattner_number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The blattner identifier for a gene.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1887 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1887">
-        <rdfs:label>Gene ID (MIPS Maize)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>MIPS genetic element identifier (Maize)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier for genetic elements in MIPS Maize database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:MIPS_GE_Maize</oboInOwl:hasDbXref>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2285"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1888 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1888">
-        <rdfs:label>Gene ID (MIPS Medicago)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>MIPS genetic element identifier (Medicago)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>Moby_namespace:MIPS_GE_Medicago</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier for genetic elements in MIPS Medicago database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2285"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1889 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1889">
-        <rdfs:label>Gene name (DragonDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of an Antirrhinum Gene from the DragonDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:DragonDB_Gene</oboInOwl:hasDbXref>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1890 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1890">
-        <rdfs:label>Gene name (Arabidopsis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>Moby_namespace:ArabidopsisGeneSymbol</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1891 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1891">
-        <rdfs:label>iHOP symbol</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>A unique identifier of a protein or gene used in the iHOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:iHOPsymbol</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1892 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1892">
-        <rdfs:label>Gene name (GeneFarm)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of a gene from the GeneFarm database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:GENEFARM_GeneName</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>GeneFarm gene ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1893 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1893">
-        <rdfs:label>Locus ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2012"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Locus name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Locus identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1895 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1895">
-        <rdfs:label>Locus ID (AGI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <regex>AT[1-5]G[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>AGI ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Arabidopsis gene loci number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>AGI locus code</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>AGI identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1896 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1896">
-        <rdfs:label>Locus ID (ASPGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier for loci from ASPGD (Aspergillus Genome Database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1897 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1897">
-        <rdfs:label>Locus ID (MGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier for loci from Magnaporthe grisea Database at the Broad Institute.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1898 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1898">
-        <rdfs:label>Locus ID (CGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier for loci from CGD (Candida Genome Database).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: CGDID</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CGDID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>CGD locus identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: CGD</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1899 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1899">
-        <rdfs:label>Locus ID (CMR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1900 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1900">
-        <rdfs:label>NCBI locus tag</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:LocusID</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Locus ID (NCBI)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier for loci from NCBI database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1901 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1901">
-        <rdfs:label>Locus ID (SGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2632"/>
-        <oboInOwl:hasDefinition>Identifier for loci from SGD (Saccharomyces Genome Database).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SGDID</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SGD</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>SGDID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1902 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1902">
-        <rdfs:label>Locus ID (MMP)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of loci from Maize Mapping Project.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:MMP_Locus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1903 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1903">
-        <rdfs:label>Locus ID (DictyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDbXref>Moby_namespace:DDB_gene</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier of locus from DictyBase (Dictyostelium discoideum).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1904 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1904">
-        <rdfs:label>Locus ID (EntrezGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of a locus from EntrezGene database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:EntrezGene_ID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby_namespace:EntrezGene_EntrezGeneID</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1905 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1905">
-        <rdfs:label>Locus ID (MaizeGDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of locus from MaizeGDB (Maize genome database).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:MaizeGDB_Locus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1906 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1906">
-        <rdfs:label>Quantitative trait locus</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>QTL</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A QTL sometimes but does not necessarily correspond to a gene.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:SO_QTL</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2012"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1907 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1907">
-        <rdfs:label>Gene ID (KOME)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier of a gene from the KOME database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:GeneId</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1908 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1908">
-        <rdfs:label>Locus ID (Tropgene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of a locus from the Tropgene database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:Tropgene_locus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1916 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1916">
-        <rdfs:label>Alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>An alignment of molecular sequences, structures or profiles derived from them.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1917 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1917">
-        <rdfs:label>Atomic property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>General atomic property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data for an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2007">
-        <rdfs:label>UniProt keyword</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:SP_KW</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2009 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2009">
-        <rdfs:label>Ordered locus name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2012 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2012">
-        <rdfs:label>Sequence coordinates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1017"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2019"/>
-        <oboInOwl:hasExactSynonym>Map position</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Position</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Locus</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence co-ordinates</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A position in a map (for example a genetic map), either a single position (point) or a region / interval.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:GenePosition</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:HitPosition</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:MapPosition</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Locus</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_MapInterval</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_MapPosition</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_MapPoint</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.id</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2016 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2016">
-        <rdfs:label>Amino acid property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasDefinition>Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Amino acid data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2018 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2018">
-        <rdfs:label>Annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasDefinition>A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2019 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2019">
-        <rdfs:label>Map data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Map attribute</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An attribute of a molecular map (genetic or physical), or data extracted from or derived from the analysis of such a map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2022 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2022">
-        <rdfs:label>Vienna RNA structural data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data used by the Vienna RNA analysis package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2023 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2023">
-        <rdfs:label>Sequence mask parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data used to replace (mask) characters in a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2024 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2024">
-        <rdfs:label>Enzyme kinetics data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2978"/>
-        <oboInOwl:hasDefinition>Data concerning chemical reaction(s) catalysed by enzyme(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2025 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2025">
-        <rdfs:label>Michaelis Menten plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <oboInOwl:hasDefinition>A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2026 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2026">
-        <rdfs:label>Hanes Woolf plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2028 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2028">
-        <rdfs:label>Experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Raw data from or annotation on laboratory experiments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Experimental measurement data</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3108"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2041 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2041">
-        <rdfs:label>Genome version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a genome version.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2711"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2042 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2042">
-        <rdfs:label>Evidence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2043 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2043">
-        <rdfs:label>Sequence record lite</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2044 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2044">
-        <rdfs:label>Sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D008969</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Sequences</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation</rdfs:seeAlso>
-        <rdfs:comment>This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records.  It should not normally be used for derivatives such as sequence alignments, motifs or profiles.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>One or more molecular sequences, possibly with associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2046 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2046">
-        <rdfs:label>Nucleic acid sequence record (lite)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2047 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2047">
-        <rdfs:label>Protein sequence record (lite)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasExactSynonym>Sequence record lite (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2048 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2048">
-        <rdfs:label>Report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <rdfs:comment>You can use this term by default for any textual report, in case you can&apos;t find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing.</rdfs:comment>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000148</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Document</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2050 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2050">
-        <rdfs:label>Molecular property (general)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>General molecular property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>General data for a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2053 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2053">
-        <rdfs:label>Structural data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning molecular structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0883"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2070 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2070">
-        <rdfs:label>Sequence motif (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1353"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid sequence motif</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>DNA sequence motif</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>A nucleotide sequence motif.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>RNA sequence motif</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2071 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2071">
-        <rdfs:label>Sequence motif (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1353"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An amino acid sequence motif.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein sequence motif</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2079 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2079">
-        <rdfs:label>Search parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Some simple value controlling a search operation, typically a search of a database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2080">
-        <rdfs:label>Database search results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report of hits from searching a database of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Search results</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Database hits</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2081">
-        <rdfs:label>Secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The secondary structure assignment (predicted or real) of a nucleic acid or protein.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2082 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2082">
-        <rdfs:label>Matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Array</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasDefinition>An array of numerical values.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2083">
-        <rdfs:label>Alignment data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of molecular alignment of some type.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Alignment report</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1394"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2084">
-        <rdfs:label>Nucleic acid report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative human-readable report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2085">
-        <rdfs:label>Structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report on general information, properties or features of one or more molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure-derived report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2086 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2086">
-        <rdfs:label>Nucleic acid structure data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0912"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid property (structural)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Nucleic acid structural property</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2087 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2087">
-        <rdfs:label>Molecular property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasRelatedSynonym>SO:0000400</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Physicochemical property</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2088 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2088">
-        <rdfs:label>DNA base structural data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2086"/>
-        <oboInOwl:hasDefinition>Structural data for DNA base pairs or runs of bases, such as energy or angle data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2090 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2090">
-        <rdfs:label>Database entry version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2091 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2091">
-        <rdfs:label>Accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000731</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000675</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2092">
-        <rdfs:label>SNP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>single nucleotide polymorphism (SNP) in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2093 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2093">
-        <rdfs:label>Data reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:comment>A list of database accessions or identifiers are usually included.</rdfs:comment>
-        <oboInOwl:hasDefinition>Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2098 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2098">
-        <rdfs:label>Job identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:seeAlso>http://wsio.org/data_009</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>An identifier of a submitted job.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2099">
-        <rdfs:label>Name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000116</rdfs:seeAlso>
-        <rdfs:seeAlso>http://usefulinc.com/ns/doap#name</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://www.w3.org/2000/01/rdf-schema#label</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A name of a thing, which need not necessarily uniquely identify it.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Symbolic name</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-        <oboInOwl:hasBroadSynonym rdf:resource="&rdfs;label"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>Closely related, but focusing on labeling and human readability but not on identification.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_2099"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasBroadSynonym"/>
-        <owl:annotatedTarget rdf:resource="&rdfs;label"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_2100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2100">
-        <rdfs:label>Type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values).</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.org/dc/elements/1.1/type</rdfs:seeAlso>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2101 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2101">
-        <rdfs:label>User ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2118"/>
-        <oboInOwl:hasDefinition>An identifier of a software end-user (typically a person).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2102">
-        <rdfs:label>KEGG organism code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDefinition>A three-letter code used in the KEGG databases to uniquely identify organisms.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2103 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2103">
-        <rdfs:label>Gene name (KEGG GENES)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>KEGG GENES entry name</oboInOwl:hasExactSynonym>
-        <regex>[a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]*</regex>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the KEGG GENES database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:GeneId</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2104 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2104">
-        <rdfs:label>BioCyc ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>Identifier of an object from one of the BioCyc databases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2105 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2105">
-        <rdfs:label>Compound ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasExactSynonym>BioCyc compound identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a compound from the BioCyc chemical compounds database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>BioCyc compound ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2106 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2106">
-        <rdfs:label>Reaction ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0613"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from the BioCyc reactions database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2107 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2107">
-        <rdfs:label>Enzyme ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasExactSynonym>BioCyc enzyme ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an enzyme from the BioCyc enzymes database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2108 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2108">
-        <rdfs:label>Reaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2978"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2109 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2109">
-        <rdfs:label>Identifier (hybrid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:hasDefinition>An identifier that is re-used for data objects of fundamentally different types (typically served from a single database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This branch provides an alternative organisation of the concepts nested under &apos;Accession&apos; and &apos;Name&apos;. All concepts under here are already included under &apos;Accession&apos; or &apos;Name&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2110">
-        <rdfs:label>Molecular property identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2087"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a molecular property.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2111">
-        <rdfs:label>Codon usage table ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a codon usage table, for example a genetic code.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Codon usage table identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2112">
-        <rdfs:label>FlyBase primary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1089"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Primary identifier of an object from the FlyBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2113 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2113">
-        <rdfs:label>WormBase identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an object from the WormBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2114 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2114">
-        <rdfs:label>WormBase wormpep ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Protein identifier used by WormBase database.</oboInOwl:hasDefinition>
-        <regex>CE[0-9]{5}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2116 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2116">
-        <rdfs:label>Nucleic acid features (codon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2117 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2117">
-        <rdfs:label>Map identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a map of a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2118">
-        <rdfs:label>Person identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a software end-user (typically a person).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2119 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2119">
-        <rdfs:label>Nucleic acid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Name or other identifier of a nucleic acid molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2126">
-        <rdfs:label>Translation frame specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2127">
-        <rdfs:label>Genetic code identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a genetic code.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2128">
-        <rdfs:label>Genetic code name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2127"/>
-        <oboInOwl:hasDefinition>Informal name for a genetic code, typically an organism name.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2129 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2129">
-        <rdfs:label>File format name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3358"/>
-        <oboInOwl:hasDefinition>Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2130">
-        <rdfs:label>Sequence profile type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2131 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2131">
-        <rdfs:label>Operating system name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a computer operating system such as Linux, PC or Mac.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2132 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2132">
-        <rdfs:label>Mutation type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A type of point or block mutation, including insertion, deletion, change, duplication and moves.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2133">
-        <rdfs:label>Logical operator</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A logical operator such as OR, AND, XOR, and NOT.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2134">
-        <rdfs:label>Results sort order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A control of the order of data that is output, for example the order of sequences in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2135">
-        <rdfs:label>Toggle</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple parameter that is a toggle (boolean value), typically a control for a modal tool.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2136 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2136">
-        <rdfs:label>Sequence width</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The width of an output sequence or alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2137">
-        <rdfs:label>Gap penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A penalty for introducing or extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2139">
-        <rdfs:label>Nucleic acid melting temperature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Melting temperature</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2140">
-        <rdfs:label>Concentration</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The concentration of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2141">
-        <rdfs:label>Window step size</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Size of the incremental &apos;step&apos; a sequence window is moved over a sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2142 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2142">
-        <rdfs:label>EMBOSS graph</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image of a graph generated by the EMBOSS suite.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2143">
-        <rdfs:label>EMBOSS report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An application report generated by the EMBOSS suite.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2145 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2145">
-        <rdfs:label>Sequence offset</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>An offset for a single-point sequence position.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2146 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2146">
-        <rdfs:label>Threshold</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A value that serves as a threshold for a tool (usually to control scoring or output).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2147">
-        <rdfs:label>Protein report (transcription factor)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites.</rdfs:comment>
-        <oboInOwl:hasDefinition>An informative report on a transcription factor protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Transcription factor binding site data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2149 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2149">
-        <rdfs:label>Database category name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a category of biological or bioinformatics database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2150 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2150">
-        <rdfs:label>Sequence profile name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Name of a sequence profile.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1115"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2151 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2151">
-        <rdfs:label>Color</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Specification of one or more colors.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2152 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2152">
-        <rdfs:label>Rendering parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A parameter that is used to control rendering (drawing) to a device or image.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Graphics parameter</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Graphical parameter</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2154">
-        <rdfs:label>Sequence name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1063"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>Any arbitrary name of a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2156">
-        <rdfs:label>Date</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A temporal date.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2157">
-        <rdfs:label>Word composition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Word composition data for a molecular sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1266"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1268"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2160">
-        <rdfs:label>Fickett testcode plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <oboInOwl:hasDefinition>A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2161 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2161">
-        <rdfs:label>Sequence similarity plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0867"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <rdfs:comment>Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence conservation report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence similarity plot</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A plot of sequence similarities identified from word-matching or character comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2162 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2162">
-        <rdfs:label>Helical wheel</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1709"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2163">
-        <rdfs:label>Helical net</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1709"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Useful for highlighting amphipathicity and other properties.</rdfs:comment>
-        <oboInOwl:hasDefinition>An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2164">
-        <rdfs:label>Protein sequence properties plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of general physicochemical properties of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2165 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2165">
-        <rdfs:label>Protein ionization curve</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of pK versus pH for a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2166">
-        <rdfs:label>Sequence composition plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of character or word composition / frequency of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2167">
-        <rdfs:label>Nucleic acid density plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Density plot (of base composition) for a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2168 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2168">
-        <rdfs:label>Sequence trace image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2969"/>
-        <oboInOwl:hasDefinition>Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2169 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2169">
-        <rdfs:label>Nucleic acid features (siRNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on siRNA duplexes in mRNA.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3137"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2173">
-        <rdfs:label>Sequence set (stream)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time.</rdfs:comment>
-        <oboInOwl:hasDefinition>A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2174">
-        <rdfs:label>FlyBase secondary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1089"/>
-        <oboInOwl:hasDefinition>Secondary identifier of an object from the FlyBase database.</oboInOwl:hasDefinition>
-        <rdfs:comment>Secondary identifier are used to handle entries that were merged with or split from other entries in the database.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2176">
-        <rdfs:label>Cardinality</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The number of a certain thing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2177">
-        <rdfs:label>Exactly 1</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A single thing.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2178">
-        <rdfs:label>1 or more</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>One or more things.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2179">
-        <rdfs:label>Exactly 2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Exactly two things.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2180">
-        <rdfs:label>2 or more</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Two or more things.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2190 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2190">
-        <rdfs:label>Sequence checksum</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:hasDefinition>A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Hash code</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Hash sum</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Hash</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Hash value</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2191">
-        <rdfs:label>Protein features report (chemical modifications)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>chemical modification of a protein.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2192 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2192">
-        <rdfs:label>Error</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on an error generated by computer system or tool.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2193 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2193">
-        <rdfs:label>Database entry metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Basic information on any arbitrary database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2198 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2198">
-        <rdfs:label>Gene cluster</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A cluster of similar genes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1246"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2201 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2201">
-        <rdfs:label>Sequence record full</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2208">
-        <rdfs:label>Plasmid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <oboInOwl:hasDefinition>An identifier of a plasmid in a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2209">
-        <rdfs:label>Mutation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2538"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a specific mutation catalogued in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2212 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2212">
-        <rdfs:label>Mutation annotation (basic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2213">
-        <rdfs:label>Mutation annotation (prevalence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type)..</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2214 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2214">
-        <rdfs:label>Mutation annotation (prognostic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2215">
-        <rdfs:label>Mutation annotation (functional)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2216 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2216">
-        <rdfs:label>Codon number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The number of a codon, for instance, at which a mutation is located.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2217">
-        <rdfs:label>Tumor annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1622"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2218">
-        <rdfs:label>Server metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Basic information about a server on the web, such as an SRS server.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2219">
-        <rdfs:label>Database field name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a field in a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2220 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2220">
-        <rdfs:label>Sequence cluster ID (SYSTERS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasExactSynonym>SYSTERS cluster ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of a sequence cluster from the SYSTERS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2223 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2223">
-        <rdfs:label>Ontology metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning a biological ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2235">
-        <rdfs:label>Raw SCOP domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw SCOP domain classification data files.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>These are the parsable data files provided by SCOP.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2236">
-        <rdfs:label>Raw CATH domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Raw CATH domain classification data files.</oboInOwl:hasDefinition>
-        <rdfs:comment>These are the parsable data files provided by CATH.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2240">
-        <rdfs:label>Heterogen annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on the types of small molecules or &apos;heterogens&apos; (non-protein groups) that are represented in PDB files.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2242">
-        <rdfs:label>Phylogenetic property values</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic property values data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0871"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2245">
-        <rdfs:label>Sequence set (bootstrapped)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Bootstrapping is often performed in phylogenetic analysis.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A collection of sequences output from a bootstrapping (resampling) procedure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2247">
-        <rdfs:label>Phylogenetic consensus tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A consensus phylogenetic tree derived from comparison of multiple trees.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2248">
-        <rdfs:label>Schema</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A data schema for organising or transforming data of some type.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2249 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2249">
-        <rdfs:label>DTD</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A DTD (document type definition).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2250">
-        <rdfs:label>XML Schema</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>XSD</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An XML Schema.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2251 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2251">
-        <rdfs:label>Relax-NG schema</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A relax-NG schema.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2252">
-        <rdfs:label>XSLT stylesheet</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An XSLT stylesheet.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2253">
-        <rdfs:label>Data resource definition name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1084"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a data type.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2254">
-        <rdfs:label>OBO file format name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2129"/>
-        <oboInOwl:hasDefinition>Name of an OBO file format such as OBO-XML, plain and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2285">
-        <rdfs:label>Gene ID (MIPS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier for genetic elements in MIPS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>MIPS genetic element identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2288">
-        <rdfs:label>Sequence identifier (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An identifier of protein sequence(s) or protein sequence database entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1096"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2289">
-        <rdfs:label>Sequence identifier (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An identifier of nucleotide sequence(s) or nucleotide sequence database entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2290 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2290">
-        <rdfs:label>EMBL accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1103"/>
-        <oboInOwl:hasExactSynonym>EMBL ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>EMBL accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>EMBL identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An accession number of an entry from the EMBL sequence database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2291 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2291">
-        <rdfs:label>UniProt ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2154"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>UniProtKB identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An identifier of a polypeptide in the UniProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniProtKB entry name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniProt identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniProt entry name</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2292">
-        <rdfs:label>GenBank accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1103"/>
-        <oboInOwl:hasExactSynonym>GenBank ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>GenBank identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of an entry from the GenBank sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>GenBank accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2293">
-        <rdfs:label>Gramene secondary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2915"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gramene internal identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gramene internal ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Secondary (internal) identifier of a Gramene database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gramene secondary ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2294 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2294">
-        <rdfs:label>Sequence variation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>An identifier of an entry from a database of molecular sequence variation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2295">
-        <rdfs:label>Gene ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1025"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasExactSynonym>Gene accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene code</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2296 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2296">
-        <rdfs:label>Gene name (AceView)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>AceView gene name</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the AceView genes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2297">
-        <rdfs:label>Gene ID (ECK)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1795"/>
-        <oboInOwl:hasExactSynonym>ECK accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>E. coli K-12 gene identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an E. coli K-12 gene from EcoGene Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ECK</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2298">
-        <rdfs:label>Gene ID (HGNC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>HGNC ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier for a gene approved by the HUGO Gene Nomenclature Committee.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2299">
-        <rdfs:label>Gene name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1025"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Allele name</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2300">
-        <rdfs:label>Gene name (NCBI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>NCBI gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the NCBI genes database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2301">
-        <rdfs:label>SMILES string</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0846"/>
-        <oboInOwl:hasDefinition>A specification of a chemical structure in SMILES format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2302">
-        <rdfs:label>STRING ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the STRING database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2307">
-        <rdfs:label>Virus annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a specific virus.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2308">
-        <rdfs:label>Virus annotation (taxonomy)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on the taxonomy of a specific virus.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2309">
-        <rdfs:label>Reaction ID (SABIO-RK)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from the SABIO-RK reactions database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2313">
-        <rdfs:label>Carbohydrate report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:hasDefinition>Annotation on or information derived from one or more specific carbohydrate 3D structure(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2314">
-        <rdfs:label>GI number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2362"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>NCBI GI number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>gi number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.</oboInOwl:hasDefinition>
-        <rdfs:comment>Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2315">
-        <rdfs:label>NCBI version</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2362"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>NCBI accession.version</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number.</rdfs:comment>
-        <oboInOwl:hasDefinition>An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>accession.version</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2316">
-        <rdfs:label>Cell line name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1046"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2317 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2317">
-        <rdfs:label>Cell line name (exact)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2318">
-        <rdfs:label>Cell line name (truncated)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2319 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2319">
-        <rdfs:label>Cell line name (no punctuation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2320">
-        <rdfs:label>Cell line name (assonant)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2321">
-        <rdfs:label>Enzyme ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1010"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique, persistent identifier of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Enzyme accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2325">
-        <rdfs:label>REBASE enzyme number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasDefinition>Identifier of an enzyme from the REBASE enzymes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2326">
-        <rdfs:label>DrugBank ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>DB[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a drug from the DrugBank database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2327">
-        <rdfs:label>GI number (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2314"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>protein gi number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A unique identifier assigned to NCBI protein sequence records.</oboInOwl:hasDefinition>
-        <rdfs:comment>Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>protein gi</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2335">
-        <rdfs:label>Bit score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1413"/>
-        <oboInOwl:hasDefinition>A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system.</oboInOwl:hasDefinition>
-        <rdfs:comment>Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2336">
-        <rdfs:label>Translation phase specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phase</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2337">
-        <rdfs:label>Resource metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Data concerning or describing some core computational resource, as distinct from primary data.  This includes metadata on the origin, source, history, ownership or location of some thing.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Provenance metadata</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2338">
-        <rdfs:label>Ontology identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Any arbitrary identifier of an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2339">
-        <rdfs:label>Ontology concept name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3025"/>
-        <oboInOwl:hasDefinition>The name of a concept in an ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2340">
-        <rdfs:label>Genome build identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2749"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a build of a particular genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2342">
-        <rdfs:label>Pathway or network name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1082"/>
-        <oboInOwl:hasDefinition>The name of a biological pathway or network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2343">
-        <rdfs:label>Pathway ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the KEGG pathway database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]{2,3}[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>KEGG pathway ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2344">
-        <rdfs:label>Pathway ID (NCI-Nature)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the NCI-Nature pathway database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2345">
-        <rdfs:label>Pathway ID (ConsensusPathDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2917"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the ConsensusPathDB pathway database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2346">
-        <rdfs:label>Sequence cluster ID (UniRef)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniRef cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniRef entry accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2347 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2347">
-        <rdfs:label>Sequence cluster ID (UniRef100)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2346"/>
-        <oboInOwl:hasExactSynonym>UniRef100 cluster id</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniRef100 entry accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef100 database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2348">
-        <rdfs:label>Sequence cluster ID (UniRef90)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2346"/>
-        <oboInOwl:hasExactSynonym>UniRef90 entry accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniRef90 cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef90 database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2349">
-        <rdfs:label>Sequence cluster ID (UniRef50)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2346"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniRef50 cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniRef50 entry accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef50 database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2353">
-        <rdfs:label>Ontology data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data concerning or derived from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ontological data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2354">
-        <rdfs:label>RNA family report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3148"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific RNA family or other group of classified RNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA family annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2355">
-        <rdfs:label>RNA family identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an RNA family, typically an entry from a RNA sequence classification database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2356">
-        <rdfs:label>RFAM accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2355"/>
-        <oboInOwl:hasDefinition>Stable accession number of an entry (RNA family) from the RFAM database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2357">
-        <rdfs:label>Protein signature type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2358">
-        <rdfs:label>Domain-nucleic acid interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on protein domain-DNA/RNA interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1567"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2359">
-        <rdfs:label>Domain-domain interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on protein domain-protein domain interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2360">
-        <rdfs:label>Domain-domain interaction (indirect)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on indirect protein domain-protein domain interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2359"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2362 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2362">
-        <rdfs:label>Sequence accession (hybrid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1093"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession number of a nucleotide or protein sequence database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2363 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2363">
-        <rdfs:label>2D PAGE data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning two-dimensional polygel electrophoresis.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0942"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2364"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2364 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2364">
-        <rdfs:label>2D PAGE report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>two-dimensional gel electrophoresis experiments, gels or spots in a gel.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2365">
-        <rdfs:label>Pathway or network accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>A persistent, unique identifier of a biological pathway or network (typically a database entry).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2366">
-        <rdfs:label>Secondary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <oboInOwl:hasDefinition>Alignment of the (1D representations of) secondary structure of two or more molecules.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2367 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2367">
-        <rdfs:label>ASTD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an object from the ASTD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2368">
-        <rdfs:label>ASTD ID (exon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an exon from the ASTD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2369">
-        <rdfs:label>ASTD ID (intron)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an intron from the ASTD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2370">
-        <rdfs:label>ASTD ID (polya)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <oboInOwl:hasDefinition>Identifier of a polyA signal from the ASTD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2371">
-        <rdfs:label>ASTD ID (tss)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <oboInOwl:hasDefinition>Identifier of a transcription start site from the ASTD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2372">
-        <rdfs:label>2D PAGE spot report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>2D PAGE spot annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2373 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2373">
-        <rdfs:label>Spot ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a spot from a two-dimensional (protein) gel.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2374 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2374">
-        <rdfs:label>Spot serial number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2373"/>
-        <oboInOwl:hasDefinition>Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2375 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2375">
-        <rdfs:label>Spot ID (HSC-2DPAGE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2373"/>
-        <oboInOwl:hasDefinition>Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2378">
-        <rdfs:label>Protein-motif interaction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1565"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2379">
-        <rdfs:label>Strain identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <oboInOwl:hasDefinition>Identifier of a strain of an organism variant, typically a plant, virus or bacterium.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2380 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2380">
-        <rdfs:label>CABRI accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>A unique identifier of an item from the CABRI database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2381 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2381">
-        <rdfs:label>Experiment report (genotyping)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2382 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2382">
-        <rdfs:label>Genotype experiment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of genotype experiment metadata.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2383">
-        <rdfs:label>EGA accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2382"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the EGA database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2384">
-        <rdfs:label>IPI protein ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <oboInOwl:hasDefinition>Identifier of a protein entry catalogued in the International Protein Index (IPI) database.</oboInOwl:hasDefinition>
-        <regex>IPI[0-9]{8}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2385">
-        <rdfs:label>RefSeq accession (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1098"/>
-        <oboInOwl:hasExactSynonym>RefSeq protein ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of a protein from the RefSeq database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2386">
-        <rdfs:label>EPD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2727"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (promoter) from the EPD database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EPD identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2387">
-        <rdfs:label>TAIR accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the TAIR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2388">
-        <rdfs:label>TAIR accession (At gene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1037"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an Arabidopsis thaliana gene from the TAIR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2389 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2389">
-        <rdfs:label>UniSTS accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UniSTS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2390">
-        <rdfs:label>UNITE accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UNITE database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2391">
-        <rdfs:label>UTR accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UTR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2392 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2392">
-        <rdfs:label>UniParc accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>UPI[A-F0-9]{10}</regex>
-        <oboInOwl:hasDefinition>Accession number of a UniParc (protein sequence) database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniParc ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UPI</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2393">
-        <rdfs:label>mFLJ/mKIAA number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Rouge or HUGE databases.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2395">
-        <rdfs:label>Fungi annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on a specific fungus.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2396">
-        <rdfs:label>Fungi annotation (anamorph)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific fungus anamorph.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2397">
-        <rdfs:label>Gene features report (exon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>exons in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2398">
-        <rdfs:label>Ensembl protein ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>Ensembl ID (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein ID (Ensembl)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2399">
-        <rdfs:label>Gene transcriptional features report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>transcription of DNA into RNA including the regulation of transcription.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2400">
-        <rdfs:label>Toxin annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific toxin.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2401">
-        <rdfs:label>Protein report (membrane protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on a membrane protein.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1456"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2402">
-        <rdfs:label>Protein-drug interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1537"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1566"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1696"/>
-        <oboInOwl:hasDefinition>An informative report on tentative or known protein-drug interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2522">
-        <rdfs:label>Map data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning a map of molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1274"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2019"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2523">
-        <rdfs:label>Phylogenetic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic data</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2524">
-        <rdfs:label>Protein data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning one or more protein molecules.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2525">
-        <rdfs:label>Nucleic acid data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning one or more nucleic acid molecules.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2526">
-        <rdfs:label>Article data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Article report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0971"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2527">
-        <rdfs:label>Parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000144</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Tool-specific parameter</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Typically a simple numerical or string value that controls the operation of a tool.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Parameters</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Tool parameter</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2528">
-        <rdfs:label>Molecular data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Molecule-specific data</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning a specific type of molecule.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2529">
-        <rdfs:label>Molecule report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a specific molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Molecular report</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2530">
-        <rdfs:label>Organism report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report on a specific organism.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Organism annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2531">
-        <rdfs:label>Experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasExactSynonym>Experiment metadata</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Experiment annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation on a wet lab experiment, such as experimental conditions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2533">
-        <rdfs:label>Nucleic acid features report (mutation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>DNA mutation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2534">
-        <rdfs:label>Sequence attribute</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:hasDefinition>An attribute of a molecular sequence, possibly in reference to some other sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Sequence parameter</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2535 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2535">
-        <rdfs:label>Sequence tag profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0928"/>
-        <rdfs:comment>SAGE, MPSS and SBS experiments are usually performed to study gene expression.  The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequencing-based expression profile</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment.  In all cases this is a list of short sequence tags and the number of times it is observed.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2536">
-        <rdfs:label>Mass spectrometry data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning a mass spectrometry measurement.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2537">
-        <rdfs:label>Protein structure raw data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw data from experimental methods for determining protein structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2538 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2538">
-        <rdfs:label>Mutation identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a mutation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2539">
-        <rdfs:label>Alignment data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  This includes entities derived from sequences and structures such as motifs and profiles.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning an alignment of two or more molecular sequences, structures or derived data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1916"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2540">
-        <rdfs:label>Data index data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning an index of data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Database index</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0955"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2563">
-        <rdfs:label>Amino acid name (single letter)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Single letter amino acid identifier, e.g. G.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2564">
-        <rdfs:label>Amino acid name (three letter)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Three letter amino acid identifier, e.g. GLY.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2565">
-        <rdfs:label>Amino acid name (full name)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Full name of an amino acid, e.g. Glycine.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2576 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2576">
-        <rdfs:label>Toxin identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2852"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a toxin.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2578">
-        <rdfs:label>ArachnoServer ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2897"/>
-        <oboInOwl:hasDefinition>Unique identifier of a toxin from the ArachnoServer database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2579">
-        <rdfs:label>Expressed gene list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Gene annotation (expressed gene list)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A simple summary of expressed genes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2580 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2580">
-        <rdfs:label>BindingDB Monomer ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Unique identifier of a monomer from the BindingDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2581">
-        <rdfs:label>GO concept name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a concept from the GO ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2582">
-        <rdfs:label>GO concept ID (biological process)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1176"/>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a &apos;biological process&apos; concept from the the Gene Ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2583">
-        <rdfs:label>GO concept ID (molecular function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1176"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <oboInOwl:hasDefinition>An identifier of a &apos;molecular function&apos; concept from the the Gene Ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2584 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2584">
-        <rdfs:label>GO concept name (cellular component)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The name of a concept for a cellular component from the GO ontology.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2586 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2586">
-        <rdfs:label>Northern blot image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image arising from a Northern Blot experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2587 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2587">
-        <rdfs:label>Blot ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Unique identifier of a blot from a Northern Blot.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2588 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2588">
-        <rdfs:label>BlotBase blot ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2587"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a blot from a Northern Blot from the BlotBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2589 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2589">
-        <rdfs:label>Hierarchy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Hierarchy annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2590 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2590">
-        <rdfs:label>Hierarchy identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of biological hierarchies.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2891"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2591 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2591">
-        <rdfs:label>Brite hierarchy ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2891"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Brite database of biological hierarchies.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2592 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2592">
-        <rdfs:label>Cancer type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A type (represented as a string) of cancer.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2100"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2593">
-        <rdfs:label>BRENDA organism ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <oboInOwl:hasDefinition>A unique identifier for an organism used in the BRENDA database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2594">
-        <rdfs:label>UniGene taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a taxon using the controlled vocabulary of the UniGene database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniGene organism abbreviation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2595">
-        <rdfs:label>UTRdb taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a taxon using the controlled vocabulary of the UTRdb database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2596 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2596">
-        <rdfs:label>Catalogue ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a catalogue of biological resources.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Catalogue identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2597 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2597">
-        <rdfs:label>CABRI catalogue name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2596"/>
-        <oboInOwl:hasDefinition>The name of a catalogue of biological resources from the CABRI database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2598">
-        <rdfs:label>Secondary structure alignment metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on protein secondary structure alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2599 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2599">
-        <rdfs:label>Molecule interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Molecular interaction report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Molecular interaction data</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0906"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2600 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2600">
-        <rdfs:label>Pathway or network</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Network</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Pathway</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2601">
-        <rdfs:label>Small molecule data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning one or more small molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2602">
-        <rdfs:label>Genotype and phenotype data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning a particular genotype, phenotype or a genotype / phenotype relation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0920"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2603 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2603">
-        <rdfs:label>Gene expression data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image or hybridisation data for a microarray, typically a study of gene expression.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Microarray data</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  See also http://edamontology.org/data_0931</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2605">
-        <rdfs:label>Compound ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>C[0-9]+</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a chemical compound from the KEGG database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>KEGG compound ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>KEGG compound identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2606">
-        <rdfs:label>RFAM name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2355"/>
-        <oboInOwl:hasDefinition>Name (not necessarily stable) an entry (RNA family) from the RFAM database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2608">
-        <rdfs:label>Reaction ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from the KEGG reactions database.</oboInOwl:hasDefinition>
-        <regex>R[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2609 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2609">
-        <rdfs:label>Drug ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a drug from the KEGG Drug database.</oboInOwl:hasDefinition>
-        <regex>D[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2610">
-        <rdfs:label>Ensembl ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENS[A-Z]*[FPTG][0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ensembl IDs</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2611">
-        <rdfs:label>ICD identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1150"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1622"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a disease from the International Classification of Diseases (ICD) database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[A-Z][0-9]+(\.[-[0-9]+])?</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2612">
-        <rdfs:label>Sequence cluster ID (CluSTr)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasDefinition>Unique identifier of a sequence cluster from the CluSTr database.</oboInOwl:hasDefinition>
-        <regex>[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?</regex>
-        <oboInOwl:hasExactSynonym>CluSTr ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CluSTr cluster ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2613">
-        <rdfs:label>KEGG Glycan ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <regex>G[0-9]+</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2614 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2614">
-        <rdfs:label>TCDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>OBO file for regular expression.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>TC number</oboInOwl:hasExactSynonym>
-        <regex>[0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+</regex>
-        <oboInOwl:hasDefinition>A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2615 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2615">
-        <rdfs:label>MINT ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>MINT\-[0-9]{1,5}</regex>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the MINT database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2616">
-        <rdfs:label>DIP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the DIP database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>DIP[\:\-][0-9]{3}[EN]</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2617">
-        <rdfs:label>Signaling Gateway protein ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database.</oboInOwl:hasDefinition>
-        <regex>A[0-9]{6}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2618">
-        <rdfs:label>Protein modification ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein modification catalogued in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2619 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2619">
-        <rdfs:label>RESID ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2618"/>
-        <oboInOwl:hasDefinition>Identifier of a protein modification catalogued in the RESID database.</oboInOwl:hasDefinition>
-        <regex>AA[0-9]{4}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2620">
-        <rdfs:label>RGD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <regex>[0-9]{4,7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the RGD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2621">
-        <rdfs:label>TAIR accession (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2387"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <regex>AASequence:[0-9]{10}</regex>
-        <oboInOwl:hasDefinition>Identifier of a protein sequence from the TAIR database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2622">
-        <rdfs:label>Compound ID (HMDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>HMDB[0-9]{5}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>HMDB ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2625 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2625">
-        <rdfs:label>LIPID MAPS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2905"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>LM ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from the LIPID MAPS database.</oboInOwl:hasDefinition>
-        <regex>LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2626 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2626">
-        <rdfs:label>PeptideAtlas ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2906"/>
-        <oboInOwl:hasDefinition>Identifier of a peptide from the PeptideAtlas peptide databases.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_strand_id</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PAp[0-9]{8}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2627 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2627">
-        <rdfs:label>Molecular interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of a report of molecular interactions from a database (typically).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2628 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2628">
-        <rdfs:label>BioGRID interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of an interaction from the BioGRID database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2629 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2629">
-        <rdfs:label>Enzyme ID (MEROPS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasExactSynonym>MEROPS ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of a peptidase enzyme from the MEROPS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>S[0-9]{2}\.[0-9]{3}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2630 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2630">
-        <rdfs:label>Mobile genetic element ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>An identifier of a mobile genetic element.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2631 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2631">
-        <rdfs:label>ACLAME ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2630"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>mge:[0-9]+</regex>
-        <oboInOwl:hasDefinition>An identifier of a mobile genetic element from the Aclame database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2632 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2632">
-        <rdfs:label>SGD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <regex>PWY[a-zA-Z_0-9]{2}\-[0-9]{3}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Saccharomyces genome database (SGD).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2633 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2633">
-        <rdfs:label>Book ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a book.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2634 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2634">
-        <rdfs:label>ISBN</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2633"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)</regex>
-        <oboInOwl:hasDefinition>The International Standard Book Number (ISBN) is for identifying printed books.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2635 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2635">
-        <rdfs:label>Compound ID (3DMET)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>B[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>3DMET ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a metabolite from the 3DMET database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2636 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2636">
-        <rdfs:label>MatrixDB interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)</regex>
-        <oboInOwl:hasDefinition>A unique identifier of an interaction from the MatrixDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2637 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2637">
-        <rdfs:label>cPath ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <regex>[0-9]+</regex>
-        <rdfs:comment>These identifiers are unique within the cPath database, however, they are not stable between releases.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2638 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2638">
-        <rdfs:label>PubChem bioassay ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2639"/>
-        <oboInOwl:hasDefinition>Identifier of an assay from the PubChem database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2639 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2639">
-        <rdfs:label>PubChem ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasExactSynonym>PubChem identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the PubChem database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2641 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2641">
-        <rdfs:label>Reaction ID (MACie)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>M[0-9]{4}</regex>
-        <oboInOwl:hasExactSynonym>MACie entry number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an enzyme reaction mechanism from the MACie database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2642 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2642">
-        <rdfs:label>Gene ID (miRBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>miRNA name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>miRNA ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier for a gene from the miRBase database.</oboInOwl:hasDefinition>
-        <regex>MI[0-9]{7}</regex>
-        <oboInOwl:hasExactSynonym>miRNA identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2643 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2643">
-        <rdfs:label>Gene ID (ZFIN)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier for a gene from the Zebrafish information network genome (ZFIN) database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ZDB\-GENE\-[0-9]+\-[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2644 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2644">
-        <rdfs:label>Reaction ID (Rhea)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <regex>[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Identifier of an enzyme-catalysed reaction from the Rhea database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2645 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2645">
-        <rdfs:label>Pathway ID (Unipathway)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <regex>UPA[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>upaid</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological pathway from the Unipathway database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2646 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2646">
-        <rdfs:label>Compound ID (ChEMBL)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of a small molecular from the ChEMBL database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChEMBL ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2647 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2647">
-        <rdfs:label>LGICdb identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2648 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2648">
-        <rdfs:label>Reaction kinetics ID (SABIO-RK)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2309"/>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2649 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2649">
-        <rdfs:label>PharmGKB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2650 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2650">
-        <rdfs:label>Pathway ID (PharmGKB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2649"/>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2651 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2651">
-        <rdfs:label>Disease ID (PharmGKB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1150"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2649"/>
-        <oboInOwl:hasDefinition>Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2652 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2652">
-        <rdfs:label>Drug ID (PharmGKB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2649"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2653 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2653">
-        <rdfs:label>Drug ID (TTD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <regex>DAP[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a drug from the Therapeutic Target Database (TTD).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2654 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2654">
-        <rdfs:label>Target ID (TTD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <regex>TTDS[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a target protein from the Therapeutic Target Database (TTD).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2655 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2655">
-        <rdfs:label>Cell type identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Cell type ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A unique identifier of a type or group of cells.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2656 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2656">
-        <rdfs:label>NeuronDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2893"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a neuron from the NeuronDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2657 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2657">
-        <rdfs:label>NeuroMorpho ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a neuron from the NeuroMorpho database.</oboInOwl:hasDefinition>
-        <regex>[a-zA-Z_0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2658 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2658">
-        <rdfs:label>Compound ID (ChemIDplus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of a chemical from the ChemIDplus database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChemIDplus ID</oboInOwl:hasExactSynonym>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2659 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2659">
-        <rdfs:label>Pathway ID (SMPDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the Small Molecule Pathway Database (SMPDB).</oboInOwl:hasDefinition>
-        <regex>SMP[0-9]{5}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2660 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2660">
-        <rdfs:label>BioNumbers ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2662 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2662">
-        <rdfs:label>T3DB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2897"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>T3D[0-9]+</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2663 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2663">
-        <rdfs:label>Carbohydrate identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2313"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1462"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a carbohydrate.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2664 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2664">
-        <rdfs:label>GlycomeDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GlycomeDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2665 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2665">
-        <rdfs:label>LipidBank ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2905"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]+[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry from the LipidBank database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2666 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2666">
-        <rdfs:label>CDD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1038"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>cd[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Identifier of a conserved domain from the Conserved Domain Database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2667 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2667">
-        <rdfs:label>MMDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1070"/>
-        <regex>[0-9]{1,5}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of an entry from the MMDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>MMDB accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2668 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2668">
-        <rdfs:label>iRefIndex ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the iRefIndex database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2669 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2669">
-        <rdfs:label>ModelDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2891"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the ModelDB database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2670 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2670">
-        <rdfs:label>Pathway ID (DQCS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <regex>[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2671 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2671">
-        <rdfs:label>Ensembl ID (Homo sapiens)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENS([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (Homo sapiens division).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2672 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2672">
-        <rdfs:label>Ensembl ID (&apos;Bos taurus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Bos taurus&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSBTA([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2673 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2673">
-        <rdfs:label>Ensembl ID (&apos;Canis familiaris&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Canis familiaris&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSCAF([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2674 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2674">
-        <rdfs:label>Ensembl ID (&apos;Cavia porcellus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSCPO([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Cavia porcellus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2675 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2675">
-        <rdfs:label>Ensembl ID (&apos;Ciona intestinalis&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Ciona intestinalis&apos; division).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSCIN([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2676 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2676">
-        <rdfs:label>Ensembl ID (&apos;Ciona savignyi&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Ciona savignyi&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSCSAV([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2677 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2677">
-        <rdfs:label>Ensembl ID (&apos;Danio rerio&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Danio rerio&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSDAR([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2678 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2678">
-        <rdfs:label>Ensembl ID (&apos;Dasypus novemcinctus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Dasypus novemcinctus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSDNO([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2679 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2679">
-        <rdfs:label>Ensembl ID (&apos;Echinops telfairi&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSETE([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Echinops telfairi&apos; division).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2680 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2680">
-        <rdfs:label>Ensembl ID (&apos;Erinaceus europaeus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSEEU([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Erinaceus europaeus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2681 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2681">
-        <rdfs:label>Ensembl ID (&apos;Felis catus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSFCA([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Felis catus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2682 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2682">
-        <rdfs:label>Ensembl ID (&apos;Gallus gallus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSGAL([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Gallus gallus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2683 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2683">
-        <rdfs:label>Ensembl ID (&apos;Gasterosteus aculeatus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Gasterosteus aculeatus&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSGAC([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2684 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2684">
-        <rdfs:label>Ensembl ID (&apos;Homo sapiens&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSHUM([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Homo sapiens&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2685 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2685">
-        <rdfs:label>Ensembl ID (&apos;Loxodonta africana&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Loxodonta africana&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSLAF([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2686 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2686">
-        <rdfs:label>Ensembl ID (&apos;Macaca mulatta&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Macaca mulatta&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSMMU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2687 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2687">
-        <rdfs:label>Ensembl ID (&apos;Monodelphis domestica&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Monodelphis domestica&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSMOD([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2688 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2688">
-        <rdfs:label>Ensembl ID (&apos;Mus musculus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSMUS([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Mus musculus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2689 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2689">
-        <rdfs:label>Ensembl ID (&apos;Myotis lucifugus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSMLU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Myotis lucifugus&apos; division).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2690 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2690">
-        <rdfs:label>Ensembl ID (&quot;Ornithorhynchus anatinus&quot;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Ornithorhynchus anatinus&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSOAN([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2691 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2691">
-        <rdfs:label>Ensembl ID (&apos;Oryctolagus cuniculus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSOCU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Oryctolagus cuniculus&apos; division).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2692 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2692">
-        <rdfs:label>Ensembl ID (&apos;Oryzias latipes&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSORL([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Oryzias latipes&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2693 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2693">
-        <rdfs:label>Ensembl ID (&apos;Otolemur garnettii&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Otolemur garnettii&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSSAR([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2694 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2694">
-        <rdfs:label>Ensembl ID (&apos;Pan troglodytes&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSPTR([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Pan troglodytes&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2695 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2695">
-        <rdfs:label>Ensembl ID (&apos;Rattus norvegicus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Rattus norvegicus&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSRNO([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2696 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2696">
-        <rdfs:label>Ensembl ID (&apos;Spermophilus tridecemlineatus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSSTO([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Spermophilus tridecemlineatus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2697 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2697">
-        <rdfs:label>Ensembl ID (&apos;Takifugu rubripes&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Takifugu rubripes&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSFRU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2698 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2698">
-        <rdfs:label>Ensembl ID (&apos;Tupaia belangeri&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Tupaia belangeri&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSTBE([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2699 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2699">
-        <rdfs:label>Ensembl ID (&apos;Xenopus tropicalis&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Xenopus tropicalis&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSXET([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2700 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2700">
-        <rdfs:label>CATH identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1038"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein domain (or other node) from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2701 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2701">
-        <rdfs:label>CATH node ID (family)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1043"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A code number identifying a family from the CATH database.</oboInOwl:hasDefinition>
-        <example>2.10.10.10</example>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2702 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2702">
-        <rdfs:label>Enzyme ID (CAZy)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasDefinition>Identifier of an enzyme from the CAZy enzymes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CAZy ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2704 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2704">
-        <rdfs:label>Clone ID (IMAGE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1855"/>
-        <oboInOwl:hasExactSynonym>I.M.A.G.E. cloneID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>IMAGE cloneID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2705 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2705">
-        <rdfs:label>GO concept ID (cellular compartment)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1176"/>
-        <oboInOwl:hasDefinition>An identifier of a &apos;cellular compartment&apos; concept from the Gene Ontology.</oboInOwl:hasDefinition>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>GO concept identifier (cellular compartment)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2706 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2706">
-        <rdfs:label>Chromosome name (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0987"/>
-        <oboInOwl:hasDefinition>Name of a chromosome as used in the BioCyc database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2709 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2709">
-        <rdfs:label>CleanEx entry name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a gene expression profile from the CleanEx database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2710 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2710">
-        <rdfs:label>CleanEx dataset code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2711 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2711">
-        <rdfs:label>Genome report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:hasDefinition>An informative report of general information concerning a genome as a whole.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2713 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2713">
-        <rdfs:label>Protein ID (CORUM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CORUM complex ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a protein complex from the CORUM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2714 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2714">
-        <rdfs:label>CDD PSSM-ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1115"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a position-specific scoring matrix from the CDD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2715 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2715">
-        <rdfs:label>Protein ID (CuticleDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>CuticleDB ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the CuticleDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2716 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2716">
-        <rdfs:label>DBD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2911"/>
-        <oboInOwl:hasDefinition>Identifier of a predicted transcription factor from the DBD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2717 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2717">
-        <rdfs:label>Oligonucleotide probe annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3115"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>General annotation on an oligonucleotide probe.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2718 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2718">
-        <rdfs:label>Oligonucleotide ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasDefinition>Identifier of an oligonucleotide from a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2719 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2719">
-        <rdfs:label>dbProbe ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2718"/>
-        <oboInOwl:hasDefinition>Identifier of an oligonucleotide probe from the dbProbe database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2720 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2720">
-        <rdfs:label>Dinucleotide property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Physicochemical property data for one or more dinucleotides.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2721 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2721">
-        <rdfs:label>DiProDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2718"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an dinucleotide property from the DiProDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2722 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2722">
-        <rdfs:label>Protein features report (disordered structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>disordered structure in a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2723 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2723">
-        <rdfs:label>Protein ID (DisProt)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>DisProt ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the DisProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2724 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2724">
-        <rdfs:label>Embryo report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Annotation on an embryo or concerning embryological development.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Embryo annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1713"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2725 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2725">
-        <rdfs:label>Ensembl transcript ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2769"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Transcript ID (Ensembl)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a gene transcript from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2726 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2726">
-        <rdfs:label>Inhibitor annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on one or more small molecules that are enzyme inhibitors.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2727 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2727">
-        <rdfs:label>Promoter ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a promoter of a gene that is catalogued in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:GeneAccessionList</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2728 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2728">
-        <rdfs:label>EST accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1855"/>
-        <oboInOwl:hasDefinition>Identifier of an EST sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2729 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2729">
-        <rdfs:label>COGEME EST ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an EST sequence from the COGEME database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2730 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2730">
-        <rdfs:label>COGEME unisequence ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <oboInOwl:hasDefinition>Identifier of a unisequence from the COGEME database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A unisequence is a single sequence assembled from ESTs.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2731 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2731">
-        <rdfs:label>Protein family ID (GeneFarm)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasExactSynonym>GeneFarm family ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry (family) from the TIGRFam database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2732 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2732">
-        <rdfs:label>Family name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a family of organism.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2733 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2733">
-        <rdfs:label>Genus name (virus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a genus of viruses.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1870"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2734 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2734">
-        <rdfs:label>Family name (virus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>The name of a family of viruses.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2732"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2735 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2735">
-        <rdfs:label>Database name (SwissRegulon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>The name of a SwissRegulon database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2736 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2736">
-        <rdfs:label>Sequence feature ID (SwissRegulon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1015"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A feature identifier as used in the SwissRegulon database.</oboInOwl:hasDefinition>
-        <rdfs:comment>This can be name of a gene, the ID of a TFBS, or genomic coordinates in form &quot;chr:start..end&quot;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2737 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2737">
-        <rdfs:label>FIG ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:comment>A FIG ID consists of four parts: a prefix, genome id, locus type and id number.</rdfs:comment>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the NMPDR database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2738 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2738">
-        <rdfs:label>Gene ID (Xenbase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the Xenbase database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2739 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2739">
-        <rdfs:label>Gene ID (Genolist)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the Genolist database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2740 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2740">
-        <rdfs:label>Gene name (Genolist)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Genolist gene name</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the Genolist genes database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2741 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2741">
-        <rdfs:label>ABS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2727"/>
-        <oboInOwl:hasExactSynonym>ABS identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (promoter) from the ABS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2742 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2742">
-        <rdfs:label>AraC-XylS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2911"/>
-        <oboInOwl:hasDefinition>Identifier of a transcription factor from the AraC-XylS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2743 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2743">
-        <rdfs:label>Gene name (HUGO)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the HUGO database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1791"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2744 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2744">
-        <rdfs:label>Locus ID (PseudoCAP)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a locus from the PseudoCAP database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2745 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2745">
-        <rdfs:label>Locus ID (UTR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a locus from the UTR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2746 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2746">
-        <rdfs:label>MonosaccharideDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2898"/>
-        <oboInOwl:hasDefinition>Unique identifier of a monosaccharide from the MonosaccharideDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2747 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2747">
-        <rdfs:label>Database name (CMD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a subdivision of the Collagen Mutation Database (CMD) database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2748 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2748">
-        <rdfs:label>Database name (Osteogenesis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>The name of a subdivision of the Osteogenesis database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2749 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2749">
-        <rdfs:label>Genome identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a particular genome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2751 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2751">
-        <rdfs:label>GenomeReviews ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2903"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a particular genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2752 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2752">
-        <rdfs:label>GlycoMap ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GlycosciencesDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2753 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2753">
-        <rdfs:label>Carbohydrate conformational map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3425"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A conformational energy map of the glycosidic linkages in a carbohydrate molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2754 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2754">
-        <rdfs:label>Gene features report (intron)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>introns in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2755 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2755">
-        <rdfs:label>Transcription factor name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1077"/>
-        <oboInOwl:hasDefinition>The name of a transcription factor.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2756 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2756">
-        <rdfs:label>TCID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Identifier of a membrane transport proteins from the transport classification database (TCDB).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2757 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2757">
-        <rdfs:label>Pfam domain name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1131"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a domain from the Pfam database.</oboInOwl:hasDefinition>
-        <regex>PF[0-9]{5}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2758 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2758">
-        <rdfs:label>Pfam clan ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>CL[0-9]{4}</regex>
-        <oboInOwl:hasDefinition>Accession number of a Pfam clan.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2759 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2759">
-        <rdfs:label>Gene ID (VectorBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>VectorBase ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier for a gene from the VectorBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2761 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2761">
-        <rdfs:label>UTRSite ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1114"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2762 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2762">
-        <rdfs:label>Sequence signature report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence motif report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2763 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2763">
-        <rdfs:label>Locus annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Locus report</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a particular locus.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2764 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2764">
-        <rdfs:label>Protein name (UniProt)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <oboInOwl:hasDefinition>Official name of a protein as used in the UniProt database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2765 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2765">
-        <rdfs:label>Term ID list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>One or more terms from one or more controlled vocabularies which are annotations on an entity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2766 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2766">
-        <rdfs:label>HAMAP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>Name of a protein family from the HAMAP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2767 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2767">
-        <rdfs:label>Identifier with metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:hasDefinition>Basic information concerning an identifier of data (typically including the identifier itself).  For example, a gene symbol with information concerning its provenance.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2768 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2768">
-        <rdfs:label>Gene symbol annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation about a gene symbol.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2767"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2769 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2769">
-        <rdfs:label>Transcript ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1276"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a RNA transcript.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2770 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2770">
-        <rdfs:label>HIT ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2769"/>
-        <oboInOwl:hasDefinition>Identifier of an RNA transcript from the H-InvDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2771 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2771">
-        <rdfs:label>HIX ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>A unique identifier of gene cluster in the H-InvDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2772 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2772">
-        <rdfs:label>HPA antibody id</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a antibody from the HPA database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2773 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2773">
-        <rdfs:label>IMGT/HLA ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2774 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2774">
-        <rdfs:label>Gene ID (JCVI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2775 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2775">
-        <rdfs:label>Kinase name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a kinase protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2776 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2776">
-        <rdfs:label>ConsensusPathDB entity ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2917"/>
-        <oboInOwl:hasDefinition>Identifier of a physical entity from the ConsensusPathDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2777 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2777">
-        <rdfs:label>ConsensusPathDB entity name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2917"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a physical entity from the ConsensusPathDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2778 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2778">
-        <rdfs:label>CCAP strain number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2912"/>
-        <oboInOwl:hasDefinition>The number of a strain of algae and protozoa from the CCAP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2779 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2779">
-        <rdfs:label>Stock number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of stock from a catalogue of biological resources.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2780 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2780">
-        <rdfs:label>Stock number (TAIR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2779"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A stock number from The Arabidopsis information resource (TAIR).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2781 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2781">
-        <rdfs:label>REDIdb ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the RNA editing database (REDIdb).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2782 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2782">
-        <rdfs:label>SMART domain name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1131"/>
-        <oboInOwl:hasDefinition>Name of a domain from the SMART database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2783 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2783">
-        <rdfs:label>Protein family ID (PANTHER)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Panther family ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of an entry (family) from the PANTHER database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2784 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2784">
-        <rdfs:label>RNAVirusDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2785"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.</rdfs:comment>
-        <oboInOwl:hasDefinition>A unique identifier for a virus from the RNAVirusDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2785 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2785">
-        <rdfs:label>Virus ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2913"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An accession of annotation on a (group of) viruses (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2786 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2786">
-        <rdfs:label>NCBI Genome Project ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2903"/>
-        <oboInOwl:hasDefinition>An identifier of a genome project assigned by NCBI.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2787 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2787">
-        <rdfs:label>NCBI genome accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2903"/>
-        <oboInOwl:hasDefinition>A unique identifier of a whole genome assigned by the NCBI.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2788 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2788">
-        <rdfs:label>Sequence profile data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it&apos;s construction, the biological role or annotation, and so on.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0860"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2789 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2789">
-        <rdfs:label>Protein ID (TopDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>TopDB ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a membrane protein from the TopDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2790 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2790">
-        <rdfs:label>Gel ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasExactSynonym>Gel identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a two-dimensional (protein) gel.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2791 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2791">
-        <rdfs:label>Reference map name (SWISS-2DPAGE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2790"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a reference map gel from the SWISS-2DPAGE database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2792 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2792">
-        <rdfs:label>Protein ID (PeroxiBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>PeroxiBase ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a peroxidase protein from the PeroxiBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2793 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2793">
-        <rdfs:label>SISYPHUS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1072"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the SISYPHUS database of tertiary structure alignments.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2794 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2794">
-        <rdfs:label>ORF ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2795"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of an open reading frame (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2795 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2795">
-        <rdfs:label>ORF identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of an open reading frame.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2796 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2796">
-        <rdfs:label>Linucs ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GlycosciencesDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2797 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2797">
-        <rdfs:label>Protein ID (LGICdb)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>LGICdb ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a ligand-gated ion channel protein from the LGICdb database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2798 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2798">
-        <rdfs:label>MaizeDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an EST sequence from the MaizeDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2799 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2799">
-        <rdfs:label>Gene ID (MfunGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the MfunGD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2800 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2800">
-        <rdfs:label>Orpha number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1150"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1622"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a disease from the Orpha database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2802 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2802">
-        <rdfs:label>Protein ID (EcID)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the EcID database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2803 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2803">
-        <rdfs:label>Clone ID (RefSeq)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1098"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1855"/>
-        <oboInOwl:hasDefinition>A unique identifier of a cDNA molecule catalogued in the RefSeq database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2804 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2804">
-        <rdfs:label>Protein ID (ConoServer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a cone snail toxin protein from the ConoServer database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2805 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2805">
-        <rdfs:label>GeneSNP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <oboInOwl:hasDefinition>Identifier of a GeneSNP database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2812 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2812">
-        <rdfs:label>Lipid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2850"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2879"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a lipid.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2831 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2831">
-        <rdfs:label>Databank</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A flat-file (textual) data archive.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2832 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2832">
-        <rdfs:label>Web portal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A web site providing data (web pages) on a common theme to a HTTP client.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2835 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2835">
-        <rdfs:label>Gene ID (VBASE2)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier for a gene from the VBASE2 database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>VBASE2 ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2836 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2836">
-        <rdfs:label>DPVweb ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2785"/>
-        <oboInOwl:hasExactSynonym>DPVweb virus ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier for a virus from the DPVweb database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2837 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2837">
-        <rdfs:label>Pathway ID (BioSystems)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the BioSystems pathway database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2838 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2838">
-        <rdfs:label>Experimental data (proteomics)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning a proteomics experiment.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3147"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2849 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2849">
-        <rdfs:label>Abstract</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2526"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An abstract of a scientific article.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2850 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2850">
-        <rdfs:label>Lipid structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a lipid structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2851 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2851">
-        <rdfs:label>Drug structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1463"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the (3D) structure of a drug.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2852 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2852">
-        <rdfs:label>Toxin structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1463"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the (3D) structure of a toxin.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2854 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2854">
-        <rdfs:label>Position-specific scoring matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1354"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PSSM</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2855 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2855">
-        <rdfs:label>Distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2856 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2856">
-        <rdfs:label>Structural distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2855"/>
-        <oboInOwl:hasDefinition>Distances (values representing similarity) between a group of molecular structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2857 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2857">
-        <rdfs:label>Article metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Bibliographic data concerning scientific article(s).</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2526"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2858 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2858">
-        <rdfs:label>Ontology concept</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2353"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes any fields from the concept definition such as concept name, definition, comments and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>A concept from a biological ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2865 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2865">
-        <rdfs:label>Codon usage bias</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:hasDefinition>A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2866 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2866">
-        <rdfs:label>Northern blot report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Northern Blot experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2867">
-        <rdfs:label>Nucleic acid features report (VNTR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>variable number of tandem repeat (VNTR) polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2868">
-        <rdfs:label>Nucleic acid features report (microsatellite)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>microsatellite polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2868"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2869">
-        <rdfs:label>Nucleic acid features report (RFLP)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>restriction fragment length polymorphisms (RFLP) in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2870 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2870">
-        <rdfs:label>Radiation hybrid map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1280"/>
-        <rdfs:comment>The radiation method can break very closely linked markers providing a more detailed map.  Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map.</rdfs:comment>
-        <oboInOwl:hasDefinition>A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>RH map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2872 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2872">
-        <rdfs:label>ID list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:hasDefinition>A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2873 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2873">
-        <rdfs:label>Phylogenetic gene frequencies data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1426"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gene frequencies data that may be read during phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2874 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2874">
-        <rdfs:label>Sequence set (polymorphic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1234"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2875 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2875">
-        <rdfs:label>DRCAT resource</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>An entry (resource) from the DRCAT bioinformatics resource catalogue.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2877 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2877">
-        <rdfs:label>Protein complex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2878 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2878">
-        <rdfs:label>Protein structural motif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2879 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2879">
-        <rdfs:label>Lipid report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation on or information derived from one or more specific lipid 3D structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2880 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2880">
-        <rdfs:label>Secondary structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of one or more molecular secondary structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2992"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2881 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2881">
-        <rdfs:label>Secondary structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Secondary structure-derived report</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on general information, properties or features of one or more molecular secondary structures.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2882 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2882">
-        <rdfs:label>DNA features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>DNA sequence-specific feature annotation (not in a feature table).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2883 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2883">
-        <rdfs:label>RNA features report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Features concerning RNA or regions of DNA that encode an RNA molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (RNA features)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2884 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2884">
-        <rdfs:label>Plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Biological data that has been plotted as a graph of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2885">
-        <rdfs:label>Nucleic acid features report (polymorphism)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>DNA polymorphism.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2886 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2886">
-        <rdfs:label>Protein sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0849"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2976"/>
-        <oboInOwl:hasDefinition>A protein sequence and associated metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein sequence record</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence record (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2887 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2887">
-        <rdfs:label>Nucleic acid sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0849"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasNarrowSynonym>RNA sequence record</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence record</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A nucleic acid sequence and associated metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>DNA sequence record</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequence record (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2888 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2888">
-        <rdfs:label>Protein sequence record (full)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2889 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2889">
-        <rdfs:label>Nucleic acid sequence record (full) </rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2891 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2891">
-        <rdfs:label>Biological model accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1085"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a mathematical model, typically an entry from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2892 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2892">
-        <rdfs:label>Cell type name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2655"/>
-        <oboInOwl:hasDefinition>The name of a type or group of cells.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2893 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2893">
-        <rdfs:label>Cell type accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2655"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a type or group of cells (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2894 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2894">
-        <rdfs:label>Compound accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasExactSynonym>Small molecule accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of chemicals.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2895 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2895">
-        <rdfs:label>Drug accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0993"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Accession of a drug.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2896 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2896">
-        <rdfs:label>Toxin name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2576"/>
-        <oboInOwl:hasDefinition>Name of a toxin.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2897 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2897">
-        <rdfs:label>Toxin accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2576"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a toxin (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2898 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2898">
-        <rdfs:label>Monosaccharide accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0996"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Accession of a monosaccharide (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2899 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2899">
-        <rdfs:label>Drug name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0993"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Common name of a drug.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2900 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2900">
-        <rdfs:label>Carbohydrate accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2663"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of carbohydrates.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2901 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2901">
-        <rdfs:label>Molecule accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Accession of a specific molecule (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2902 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2902">
-        <rdfs:label>Data resource definition accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1084"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a data definition (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2903 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2903">
-        <rdfs:label>Genome accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2749"/>
-        <oboInOwl:hasDefinition>An accession of a particular genome (in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2904 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2904">
-        <rdfs:label>Map accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2117"/>
-        <oboInOwl:hasDefinition>An accession of a map of a molecular sequence (deposited in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2905 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2905">
-        <rdfs:label>Lipid accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2812"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of lipids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2906 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2906">
-        <rdfs:label>Peptide ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0988"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a peptide deposited in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2907 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2907">
-        <rdfs:label>Protein accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasExactSynonym>Protein accessions</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a protein deposited in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2908 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2908">
-        <rdfs:label>Organism accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>An accession of annotation on a (group of) organisms (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2909 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2909">
-        <rdfs:label>Organism name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDbXref>Moby:Organism_Name</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:OrganismsShortName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:OccurrenceRecord</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:BriefOccurrenceRecord</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:FirstEpithet</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:InfraspecificEpithet</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:OrganismsLongName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The name of an organism (or group of organisms).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2910 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2910">
-        <rdfs:label>Protein family accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1075"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a protein family (that is deposited in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2911 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2911">
-        <rdfs:label>Transcription factor accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1077"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of transcription factors or binding sites.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2912 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2912">
-        <rdfs:label>Strain accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2379"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0963"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a strain of an organism variant, typically a plant, virus or bacterium.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2913 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2913">
-        <rdfs:label>Virus identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <oboInOwl:hasDefinition>An accession of annotation on a (group of) viruses (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2914 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2914">
-        <rdfs:label>Sequence features metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2527"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Metadata on sequence features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2915 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2915">
-        <rdfs:label>Gramene identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a Gramene database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2916 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2916">
-        <rdfs:label>DDBJ accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1103"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>DDBJ accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>DDBJ identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>DDBJ ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An identifier of an entry from the DDBJ sequence database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2917 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2917">
-        <rdfs:label>ConsensusPathDB identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of an entity from the ConsensusPathDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2925 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2925">
-        <rdfs:label>Sequence data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of molecular sequence(s). </oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2927 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2927">
-        <rdfs:label>Codon usage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning codon usage.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2954 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2954">
-        <rdfs:label>Article report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Data derived from the analysis of a scientific text such as a full text article from a scientific journal.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2526"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2955 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2955">
-        <rdfs:label>Sequence report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence-derived report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2956 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2956">
-        <rdfs:label>Protein secondary structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:hasDefinition>An informative report about the properties or features of one or more protein secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2957 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2957">
-        <rdfs:label>Hopp and Woods plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1534"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <oboInOwl:hasDefinition>A Hopp and Woods plot of predicted antigenicity of a peptide or protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2958 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2958">
-        <rdfs:label>Nucleic acid melting curve</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <rdfs:comment>Shows the proportion of nucleic acid which are double-stranded versus temperature.</rdfs:comment>
-        <oboInOwl:hasDefinition>A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2959 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2959">
-        <rdfs:label>Nucleic acid probability profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <oboInOwl:hasDefinition>A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2960 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2960">
-        <rdfs:label>Nucleic acid temperature profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <oboInOwl:hasDefinition>A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).</oboInOwl:hasDefinition>
-        <rdfs:comment>Plots melting temperature versus base position.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Melting map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2961 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2961">
-        <rdfs:label>Gene regulatory network report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of a gene regulatory network.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2965 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2965">
-        <rdfs:label>2D PAGE gel report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a two-dimensional (2D PAGE) gel.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>2D PAGE image report</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>2D PAGE gel annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>2D PAGE image annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2966 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2966">
-        <rdfs:label>Oligonucleotide probe sets annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2717"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2967 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2967">
-        <rdfs:label>Microarray image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression image</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2968 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2968">
-        <rdfs:label>Image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000081</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Biological or biomedical data has been rendered into an image, typically for display on screen.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000079</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Image data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2969 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2969">
-        <rdfs:label>Sequence image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2955"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:hasDefinition>Image of a molecular sequence, possibly with sequence features or properties shown.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2970 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2970">
-        <rdfs:label>Protein hydropathy data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasExactSynonym>Protein hydropathy report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report on protein properties concerning hydropathy.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2971 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2971">
-        <rdfs:label>Workflow data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning a computational workflow.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2972 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2972">
-        <rdfs:label>Workflow</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A computational workflow.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2973 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2973">
-        <rdfs:label>Secondary structure data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning molecular secondary structure data.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2974 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2974">
-        <rdfs:label>Protein sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0848"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2976"/>
-        <oboInOwl:hasExactSynonym>Raw protein sequence</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Raw sequence (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A raw protein sequence (string of characters).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2975 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2975">
-        <rdfs:label>Nucleic acid sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0848"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid raw sequence</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence (raw)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Raw sequence (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A raw nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2976 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2976">
-        <rdfs:label>Protein sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <oboInOwl:hasDefinition>One or more protein sequences, possibly with associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein sequences</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2977 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2977">
-        <rdfs:label>Nucleic acid sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <oboInOwl:hasDefinition>One or more nucleic acid sequences, possibly with associated annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>DNA sequence</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleotide sequences</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid sequences</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2978 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2978">
-        <rdfs:label>Reaction data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Enzyme kinetics annotation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Reaction annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2979 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2979">
-        <rdfs:label>Peptide property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning small peptides.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2980 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2980">
-        <rdfs:label>Protein classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein classification data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report concerning the classification of protein sequences or structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2981 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2981">
-        <rdfs:label>Sequence motif data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning specific or conserved pattern in molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0860"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2982 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2982">
-        <rdfs:label>Sequence profile data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning models representing a (typically multiple) sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1354"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2983 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2983">
-        <rdfs:label>Pathway or network data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data concerning a specific biological pathway or network.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2600"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2984 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2984">
-        <rdfs:label>Pathway or network report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2985 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2985">
-        <rdfs:label>Nucleic acid thermodynamic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0912"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid property (thermodynamic or kinetic)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A thermodynamic or kinetic property of a nucleic acid molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid thermodynamic property</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2986 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2986">
-        <rdfs:label>Nucleic acid classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning the classification of nucleic acid sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid classification data</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3148"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2987 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2987">
-        <rdfs:label>Classification report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Classification data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report on a classification of molecular sequences, structures or other entities.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2989 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2989">
-        <rdfs:label>Protein features report (key folding sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>key residues involved in protein folding.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2991 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2991">
-        <rdfs:label>Protein torsion angle data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasExactSynonym>Torsion angle data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Torsion angle data for a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2992 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2992">
-        <rdfs:label>Protein structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1710"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3153"/>
-        <oboInOwl:hasDefinition>An image of protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure image (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2994 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2994">
-        <rdfs:label>Phylogenetic character weights</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasDefinition>Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3002 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3002">
-        <rdfs:label>Annotation track</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Genomic track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome annotation track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome-browser track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence annotation track</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3021 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3021">
-        <rdfs:label>UniProt accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>UniProtKB accession number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <example>P43353|Q7M1G0|Q9C199|A5A6J6</example>
-        <oboInOwl:hasExactSynonym>UniProt entry accession</oboInOwl:hasExactSynonym>
-        <regex>[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}</regex>
-        <oboInOwl:hasNarrowSynonym>Swiss-Prot entry accession</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>TrEMBL entry accession</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Accession number of a UniProt (protein sequence) database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniProtKB accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniProt accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3022 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3022">
-        <rdfs:label>NCBI genetic code ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Identifier of a genetic code in the NCBI list of genetic codes.</oboInOwl:hasDefinition>
-        <regex>[1-9][0-9]?</regex>
-        <example>16</example>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3025 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3025">
-        <rdfs:label>Ontology concept identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a concept in an ontology of biological or bioinformatics concepts and relations.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3026 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3026">
-        <rdfs:label>GO concept name (biological process)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a concept for a biological process from the GO ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3027 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3027">
-        <rdfs:label>GO concept name (molecular function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a concept for a molecular function from the GO ontology.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3028 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3028">
-        <rdfs:label>Taxonomy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning the classification, identification and naming of organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Taxonomic data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3029 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3029">
-        <rdfs:label>Protein ID (EMBL/GenBank/DDBJ)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.</oboInOwl:hasDefinition>
-        <rdfs:comment>This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3031 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3031">
-        <rdfs:label>Core data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Core data entities typically have a format and may be identified by an accession number.</rdfs:comment>
-        <oboInOwl:hasDefinition>A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3034 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3034">
-        <rdfs:label>Sequence feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of molecular sequence feature(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3035 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3035">
-        <rdfs:label>Structure identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>An identifier of a molecular tertiary structure, typically an entry from a structure database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3036 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3036">
-        <rdfs:label>Matrix identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of an array of numerical values, such as a comparison matrix.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3085">
-        <rdfs:label>Protein sequence composition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report (typically a table) on character or word composition / frequency of protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3086 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3086">
-        <rdfs:label>Nucleic acid sequence composition (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3101 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3101">
-        <rdfs:label>Protein domain classification node</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>A node from a classification of protein structural domain(s).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3102">
-        <rdfs:label>CAS number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>CAS registry number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3103 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3103">
-        <rdfs:label>ATC code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <oboInOwl:hasDefinition>Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC).</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3104 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3104">
-        <rdfs:label>UNII</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Unique Ingredient Identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3105 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3105">
-        <rdfs:label>Geotemporal metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Basic information concerning geographical location or time.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3106 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3106">
-        <rdfs:label>System metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Metadata concerning the software, hardware or other aspects of a computer system.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3107 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3107">
-        <rdfs:label>Sequence feature name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3034"/>
-        <oboInOwl:hasDefinition>A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3108 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3108">
-        <rdfs:label>Experimental measurement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Experimental measurement data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Measurement</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Measured data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Experimentally measured data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Measurement metadata</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Measurement data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Raw experimental data</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3110">
-        <rdfs:label>Raw microarray data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3117"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment.</oboInOwl:hasDefinition>
-        <rdfs:comment>Such data as found in Affymetrix CEL or GPR files.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3111">
-        <rdfs:label>Processed microarray data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3117"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data generated from processing and analysis of probe set data from a microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene annotation (expression)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray probe set data</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression report</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3112">
-        <rdfs:label>Gene expression matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:comment>This combines data from all hybridisations.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Normalised microarray data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The final processed (normalised) data for a set of hybridisations in a microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene expression data matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3113 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3113">
-        <rdfs:label>Sample annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Annotation on a biological sample, for example experimental factors and their values.</oboInOwl:hasDefinition>
-        <rdfs:comment>This might include compound and dose in a dose response experiment.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3115 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3115">
-        <rdfs:label>Microarray metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:comment>This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Annotation on the array itself used in a microarray experiment.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3116 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3116">
-        <rdfs:label>Microarray protocol annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This might describe e.g. the normalisation methods used to process the raw data.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Annotation on laboratory and/or data processing protocols used in an microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3117 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3117">
-        <rdfs:label>Microarray hybridisation data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <oboInOwl:hasDefinition>Data concerning the hybridisations measured during a microarray experiment.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3118">
-        <rdfs:label>Protein features report (topological domains)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>topological domains such as cytoplasmic regions in a protein.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3119 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3119">
-        <rdfs:label>Sequence features (compositionally-biased regions)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report of regions in a molecular sequence that are biased to certain characters.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3122">
-        <rdfs:label>Nucleic acid features (difference and change)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>A report on features in a nucleic acid sequence that indicate changes to or differences between sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0918"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3123">
-        <rdfs:label>Nucleic acid features report (expression signal)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>regions within a nucleic acid sequence containing a signal that alters a biological function.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3125 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3125">
-        <rdfs:label>Nucleic acid features report (binding)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>nucleic acids binding to some other molecule.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <rdfs:comment>This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes).</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3126">
-        <rdfs:label>Nucleic acid repeats (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>repetitive elements within a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3127">
-        <rdfs:label>Nucleic acid features report (replication and recombination)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>DNA replication or recombination.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3128">
-        <rdfs:label>Nucleic acid structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:hasDefinition>A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Stem loop (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>d-loop (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Quadruplexes (report)</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3129 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3129">
-        <rdfs:label>Protein features report (repeats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>short repetitive subsequences (repeat sequences) in a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3130">
-        <rdfs:label>Sequence motif matches (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3131 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3131">
-        <rdfs:label>Sequence motif matches (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3132 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3132">
-        <rdfs:label>Nucleic acid features (d-loop)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report on displacement loops in a mitochondrial DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3133">
-        <rdfs:label>Nucleic acid features (stem loop)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on stem loops in a DNA sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3134">
-        <rdfs:label>Gene transcript report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0916"/>
-        <rdfs:comment>This includes 5&apos;untranslated region (5&apos;UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3&apos;untranslated regions (3&apos;UTR).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (mRNA features)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Transcript (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>mRNA features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene transcript annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Clone or EST (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>mRNA (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3135">
-        <rdfs:label>Nucleic acid features report (signal or transit peptide)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>coding sequences for a signal or transit peptide.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3137">
-        <rdfs:label>Non-coding RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>features of non-coding or functional RNA molecules, including tRNA and rRNA.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3138 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3138">
-        <rdfs:label>Transcriptional features (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.</rdfs:comment>
-        <oboInOwl:hasDefinition>Features concerning transcription of DNA into RNA including the regulation of transcription.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3139">
-        <rdfs:label>Nucleic acid features report (STS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>sequence tagged sites (STS) in nucleic acid sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3140">
-        <rdfs:label>Nucleic acid features (immunoglobulin gene structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3141">
-        <rdfs:label>SCOP class</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a &apos;class&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3142 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3142">
-        <rdfs:label>SCOP fold</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Information on a &apos;fold&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3143">
-        <rdfs:label>SCOP superfamily</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Information on a &apos;superfamily&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3144 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3144">
-        <rdfs:label>SCOP family</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a &apos;family&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3145 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3145">
-        <rdfs:label>SCOP protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information on a &apos;protein&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3146 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3146">
-        <rdfs:label>SCOP species</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Information on a &apos;species&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3147">
-        <rdfs:label>Mass spectrometry experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>mass spectrometry experiments.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3148 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3148">
-        <rdfs:label>Gene family report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:hasDefinition>An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene, or any other classification of nucleic acid sequences or structures that reflects gene structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes reports on on gene homologues between species.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Gene annotation (homology information)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Homology information</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene annotation (homology)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Nucleic acid classification</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>Gene family annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene homology (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3153 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3153">
-        <rdfs:label>Protein image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>An image of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3154">
-        <rdfs:label>Protein alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <oboInOwl:hasDefinition>An alignment of protein sequences and/or structures.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3165 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3165">
-        <rdfs:label>NGS experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>sequencing experiment, including samples, sampling, preparation, sequencing, and analysis.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3181 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3181">
-        <rdfs:label>Sequence assembly report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:hasDefinition>An informative report about a DNA sequence assembly.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Assembly report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3210">
-        <rdfs:label>Genome index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0955"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.</rdfs:comment>
-        <oboInOwl:hasDefinition>An index of a genome sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3231 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3231">
-        <rdfs:label>GWAS report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Report concerning genome-wide association study experiments.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Genome-wide association study</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3236">
-        <rdfs:label>Cytoband position</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2012"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>The position of a cytogenetic band in a genome.</oboInOwl:hasDefinition>
-        <rdfs:comment>Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3238">
-        <rdfs:label>Cell type ontology ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2893"/>
-        <oboInOwl:hasExactSynonym>CL ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Cell type ontology concept ID.</oboInOwl:hasDefinition>
-        <regex>CL_[0-9]{7}</regex>
-        <created_in>1.2</created_in>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3241">
-        <rdfs:label>Kinetic model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Mathematical model of a network, that contains biochemical kinetics.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3264">
-        <rdfs:label>COSMIC ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <oboInOwl:hasExactSynonym>COSMIC identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>cosmic ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a COSMIC database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>cosmic identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>cosmic id</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3265">
-        <rdfs:label>HGMD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <oboInOwl:hasDefinition>Identifier of a HGMD database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>hgmd ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>hgmd identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>hgmd id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HGMD identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3266 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3266">
-        <rdfs:label>Sequence assembly ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1064"/>
-        <oboInOwl:hasNarrowSynonym>Sequence assembly version</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of sequence assembly.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3268 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3268">
-        <rdfs:label>Sequence feature type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3269">
-        <rdfs:label>Gene homology (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on gene homologues between species.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3148"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3270 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3270">
-        <rdfs:label>Ensembl gene tree ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <example>ENSGT00390000003602</example>
-        <oboInOwl:hasExactSynonym>Ensembl ID (gene tree)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a gene tree from the Ensembl database.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3271 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3271">
-        <rdfs:label>Gene tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0872"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>A phylogenetic tree that is an estimate of the character&apos;s phylogeny.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3272 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3272">
-        <rdfs:label>Species tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0872"/>
-        <oboInOwl:hasDefinition>A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3273 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3273">
-        <rdfs:label>Sample ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3113"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Sample accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Name or other identifier of an entry from a biosample database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3274 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3274">
-        <rdfs:label>MGI accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>Identifier of an object from the MGI database.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3275 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3275">
-        <rdfs:label>Phenotype name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Name of a phenotype.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phenotypes</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phenotype</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3354">
-        <rdfs:label>Transition matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A HMM transition matrix contains the probabilities of switching from one HMM state to another.</oboInOwl:hasDefinition>
-        <rdfs:comment>Consider for example an HMM with two states (AT-rich and GC-rich).  The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>HMM transition matrix</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3355">
-        <rdfs:label>Emission matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <rdfs:comment>Consider for example an HMM with two states (AT-rich and GC-rich).  The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>HMM emission matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3356">
-        <rdfs:label xml:lang="en">Hidden Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:hasDefinition>A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3358">
-        <rdfs:label>Format identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a data format.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3424">
-        <rdfs:label>Raw image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>1.5</created_in>
-        <oboInOwl:hasExactSynonym>Amino acid data</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000081</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Image data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Raw biological or biomedical image generated by some experimental technique.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3425">
-        <rdfs:label>Carbohydrate property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>Carbohydrate data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates.</oboInOwl:hasDefinition>
-        <created_in>1.5</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3426">
-        <rdfs:label>Proteomics experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Report concerning proteomics experiments.</oboInOwl:hasDefinition>
-        <created_in>1.5</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3427">
-        <rdfs:label>RNAi report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.5</created_in>
-        <oboInOwl:hasDefinition>RNAi experiments.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3428">
-        <rdfs:label>Simulation experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.5</created_in>
-        <oboInOwl:hasDefinition>biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3442">
-        <rdfs:label>MRI image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3384"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>MRT image</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>Magnetic resonance tomography image </oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nuclear magnetic resonance imaging image
-</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Magnetic resonance imaging image
-</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>NMRI image</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3449 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3449">
-        <rdfs:label>Cell migration track image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2229"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>An image from a cell migration track assay.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3451">
-        <rdfs:label>Rate of association</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasExactSynonym>kon</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Rate of association of a protein with another protein or some other molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3479">
-        <rdfs:label>Gene order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <rdfs:comment>Such data are often used for genome rearrangement tools and phylogenetic tree labeling.</rdfs:comment>
-        <oboInOwl:hasDefinition>Multiple gene identifiers in a specific order.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3483">
-        <rdfs:label>Spectrum</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Spectra</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3488">
-        <rdfs:label>NMR spectrum</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3483"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Spectral information for a molecule from a nuclear magnetic resonance experiment.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>NMR spectra</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3490">
-        <rdfs:label>Chemical structure sketch</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1712"/>
-        <rdfs:comment>Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software.</rdfs:comment>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Small molecule sketch</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A sketch of a small molecule made with some specialised drawing package.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3492">
-        <rdfs:label>Nucleic acid signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2762"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>An informative report about a specific or conserved nucleic acid sequence pattern.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3494 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3494">
-        <rdfs:label>DNA sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasExactSynonym>DNA sequences</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>A DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3495">
-        <rdfs:label>RNA sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasDefinition>A DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>DNA sequences</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA sequences</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3496">
-        <rdfs:label>RNA sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3495"/>
-        <oboInOwl:hasExactSynonym>Raw sequence (RNA)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>A raw RNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA raw sequence</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3497">
-        <rdfs:label>DNA sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3494"/>
-        <oboInOwl:hasExactSynonym>Raw sequence (DNA)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A raw DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>DNA raw sequence</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3498">
-        <rdfs:label>Sequence variations</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene sequence variations</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Variations are stored along with a reference genome.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3505">
-        <rdfs:label>Bibliography</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2526"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>A list of publications such as scientic papers or books.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3509">
-        <rdfs:label>Ontology mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:hasDefinition>A mapping of supplied textual terms or phrases to ontology concepts (URIs).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3546">
-        <rdfs:label>Image metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Image-associated data</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This can include basic provenance and technical information about the image, scientific annotation and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Any data concerning a specific biological or biomedical image.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasExactSynonym>Image data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Image-related data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3558">
-        <rdfs:label>Clinical trial report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasExactSynonym>Clinical trial information</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report concerning a clinical trial.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3567">
-        <rdfs:label>Reference sample report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>A report about a biosample.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Biosample report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3568">
-        <rdfs:label>Gene Expression Atlas Experiment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the Gene Expression Atlas.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1196">
-        <rdfs:label>SMILES</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification"/>
-        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"/>
-        <documentation rdf:resource="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1197 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1197">
-        <rdfs:label>InChI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1198 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1198">
-        <rdfs:label>mf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The general MF query format consists of a series of valid atomic symbols, with an optional number or range.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1199 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1199">
-        <rdfs:label>inchikey</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1200">
-        <rdfs:label>smarts</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1196"/>
-        <oboInOwl:hasDefinition>SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1206 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1206">
-        <rdfs:label>unambiguous pure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2096"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1207 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1207">
-        <rdfs:label>nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <rdfs:comment>Non-sequence characters may be used for example for gaps.</rdfs:comment>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1208">
-        <rdfs:label>protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Non-sequence characters may be used for gaps and translation stop.</rdfs:comment>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1209">
-        <rdfs:label>consensus</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2095"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for the consensus of two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1210">
-        <rdfs:label>pure nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1211">
-        <rdfs:label>unambiguous pure nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters .</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1212 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1212">
-        <rdfs:label>dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1213">
-        <rdfs:label>rna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1214 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1214">
-        <rdfs:label>unambiguous pure dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1212"/>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1215">
-        <rdfs:label>pure dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1210"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1212"/>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1216 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1216">
-        <rdfs:label>unambiguous pure rna sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1213"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1217">
-        <rdfs:label>pure rna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1210"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1213"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1218">
-        <rdfs:label>unambiguous pure protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1208"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1219">
-        <rdfs:label>pure protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1208"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1228 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1228">
-        <rdfs:label>UniGene entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from UniGene.</oboInOwl:hasDefinition>
-        <rdfs:comment>A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1247">
-        <rdfs:label>COG sequence cluster format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the COG database of clusters of (related) protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1248">
-        <rdfs:label>EMBL feature location</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2078"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Feature location</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1295">
-        <rdfs:label>quicktandem</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2155"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1296 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1296">
-        <rdfs:label>Sanger inverted repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2155"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1297">
-        <rdfs:label>EMBOSS repeat</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2155"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format for tandem repeats in a sequence (an EMBOSS report format).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1316">
-        <rdfs:label>est2genome format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2031"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a report on exon-intron structure generated by EMBOSS est2genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1318">
-        <rdfs:label>restrict format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2158"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format for restriction enzyme recognition sites used by EMBOSS restrict program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1319 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1319">
-        <rdfs:label>restover format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2158"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report format for restriction enzyme recognition sites used by EMBOSS restover program.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1320">
-        <rdfs:label>REBASE restriction sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2158"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report format for restriction enzyme recognition sites used by REBASE database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1332">
-        <rdfs:label>FASTA search results format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using FASTA.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.)</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1333 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1333">
-        <rdfs:label>BLAST results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using some variant of BLAST.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes score data, alignment data and summary table.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1334">
-        <rdfs:label>mspcrunch</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using some variant of MSPCrunch.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1335">
-        <rdfs:label>Smith-Waterman format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using some variant of Smith Waterman.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1336">
-        <rdfs:label>dhf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1337">
-        <rdfs:label>lhf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information.</oboInOwl:hasDefinition>
-        <rdfs:comment>The hits are putative ligand-binding sequences and are found from a search of a sequence database.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1341">
-        <rdfs:label>InterPro hits format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Results format for searches of the InterPro database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1342">
-        <rdfs:label>InterPro protein view report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1341"/>
-        <oboInOwl:hasDefinition>Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1343">
-        <rdfs:label>InterPro match table format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1341"/>
-        <oboInOwl:hasDefinition>Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1349">
-        <rdfs:label>HMMER Dirichlet prior</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2074"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Dirichlet distribution HMMER format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1350">
-        <rdfs:label>MEME Dirichlet prior</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2074"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Dirichlet distribution MEME format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1351 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1351">
-        <rdfs:label>HMMER emission and transition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2075"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1356">
-        <rdfs:label>prosite-pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of a regular expression pattern from the Prosite database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1357">
-        <rdfs:label>EMBOSS sequence pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of an EMBOSS sequence pattern.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1360">
-        <rdfs:label>meme-motif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>A motif in the format generated by the MEME program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1366">
-        <rdfs:label>prosite-profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2069"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Sequence profile (sequence classifier) format used in the PROSITE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1367 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1367">
-        <rdfs:label>JASPAR format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2069"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A profile (sequence classifier) in the format used in the JASPAR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1369">
-        <rdfs:label>MEME background Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2072"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of the model of random sequences used by MEME.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1370">
-        <rdfs:label>HMMER format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2072"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of a hidden Markov model representation used by the HMMER package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1391">
-        <rdfs:label>HMMER-aln</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>FASTA-style format for multiple sequences aligned by HMMER package to an HMM.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1392 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1392">
-        <rdfs:label>DIALIGN format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Format of multiple sequences aligned by DIALIGN package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1393">
-        <rdfs:label>daf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <rdfs:comment>The format is clustal-like and includes annotation of domain family classification information.</rdfs:comment>
-        <oboInOwl:hasDefinition>EMBASSY &apos;domain alignment file&apos; (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1419">
-        <rdfs:label>Sequence-MEME profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2014"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1421">
-        <rdfs:label>HMMER profile alignment (sequences versus HMMs)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2014"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1422">
-        <rdfs:label>HMMER profile alignment (HMM versus sequences)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2014"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1423">
-        <rdfs:label>Phylip distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2067"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of PHYLIP phylogenetic distance matrix data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1424">
-        <rdfs:label>ClustalW dendrogram</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Dendrogram (tree file) format generated by ClustalW.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1425">
-        <rdfs:label>Phylip tree raw</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasDefinition>Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1430">
-        <rdfs:label>Phylip continuous quantitative characters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2037"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PHYLIP file format for continuous quantitative character data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1431 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1431">
-        <rdfs:label>Phylogenetic property values format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of phylogenetic property data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2036"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1432">
-        <rdfs:label>Phylip character frequencies format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2037"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PHYLIP file format for phylogenetics character frequency data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1433">
-        <rdfs:label>Phylip discrete states format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2038"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of PHYLIP discrete states data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1434">
-        <rdfs:label>Phylip cliques format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2039"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of PHYLIP cliques data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1435">
-        <rdfs:label>Phylip tree format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasDefinition>Phylogenetic tree data format used by the PHYLIP program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1436">
-        <rdfs:label>TreeBASE format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the TreeBASE database of phylogenetic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1437">
-        <rdfs:label>TreeFam format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the TreeFam database of phylogenetic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1445">
-        <rdfs:label>Phylip tree distance format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2049"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1454 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1454">
-        <rdfs:label>dssp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2077"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format.</rdfs:comment>
-        <oboInOwl:hasDefinition>Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1455 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1455">
-        <rdfs:label>hssp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2077"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1457">
-        <rdfs:label>Dot-bracket format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Vienna RNA secondary structure format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Vienna RNA format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1458 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1458">
-        <rdfs:label>Vienna local RNA secondary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1457"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1475">
-        <rdfs:label>PDB database entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2033"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PDB entry format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of an entry (or part of an entry) from the PDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1476">
-        <rdfs:label>PDB</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasExactSynonym>PDB format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of PDB database in PDB format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1477 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1477">
-        <rdfs:label>mmCIF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasExactSynonym>Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Entry format of PDB database in mmCIF format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>mmcif</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1478">
-        <rdfs:label>PDBML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Entry format of PDB database in PDBML (XML) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1500">
-        <rdfs:label>Domainatrix 3D-1D scoring matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1504">
-        <rdfs:label>aaindex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2017"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Amino acid index format used by the AAindex database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1511">
-        <rdfs:label>IntEnz enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from IntEnz (The Integrated Relational Enzyme Database).</oboInOwl:hasDefinition>
-        <rdfs:comment>IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1512">
-        <rdfs:label>BRENDA enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of an entry from the BRENDA enzyme database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1513 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1513">
-        <rdfs:label>KEGG REACTION enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the KEGG REACTION database of biochemical reactions.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1514">
-        <rdfs:label>KEGG ENZYME enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of an entry from the KEGG ENZYME database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1515">
-        <rdfs:label>REBASE proto enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of an entry from the proto section of the REBASE enzyme database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1516">
-        <rdfs:label>REBASE withrefm enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the withrefm section of the REBASE enzyme database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1551">
-        <rdfs:label>Pcons report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2065"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of output of the Pcons Model Quality Assessment Program (MQAP).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1552">
-        <rdfs:label>ProQ report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2065"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features.</rdfs:comment>
-        <oboInOwl:hasDefinition>Format of output of the ProQ protein model quality predictor.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1563">
-        <rdfs:label>SMART domain assignment report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of SMART domain assignment data.</oboInOwl:hasDefinition>
-        <rdfs:comment>The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1568">
-        <rdfs:label>BIND entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the BIND database of protein interaction.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1569">
-        <rdfs:label>IntAct entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the IntAct database of protein interaction.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1570">
-        <rdfs:label>InterPro entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1571">
-        <rdfs:label>InterPro entry abstract format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>References are included and a functional inference is made where possible.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format for the textual abstract of signatures in an InterPro entry and its protein matches.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1572">
-        <rdfs:label>Gene3D entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the Gene3D protein secondary database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1573">
-        <rdfs:label>PIRSF entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the PIRSF protein secondary database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1574">
-        <rdfs:label>PRINTS entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format for the PRINTS protein secondary database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1575">
-        <rdfs:label>Panther Families and HMMs entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the Panther library of protein families and subfamilies.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1576 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1576">
-        <rdfs:label>Pfam entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the Pfam protein secondary database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1577 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1577">
-        <rdfs:label>SMART entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the SMART protein secondary database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1578">
-        <rdfs:label>Superfamily entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the Superfamily protein secondary database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1579">
-        <rdfs:label>TIGRFam entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format for the TIGRFam protein secondary database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1580 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1580">
-        <rdfs:label>ProDom entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the ProDom protein domain classification database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1581">
-        <rdfs:label>FSSP entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the FSSP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1582">
-        <rdfs:label>findkm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2027"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1603 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1603">
-        <rdfs:label>Ensembl gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of Ensembl genome database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1604 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1604">
-        <rdfs:label>DictyBase gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of DictyBase genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1605">
-        <rdfs:label>CGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of Candida Genome database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1606">
-        <rdfs:label>DragonDB gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of DragonDB genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1607">
-        <rdfs:label>EcoCyc gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of EcoCyc genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1608">
-        <rdfs:label>FlyBase gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of FlyBase genome database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1609 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1609">
-        <rdfs:label>Gramene gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of Gramene genome database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1610">
-        <rdfs:label>KEGG GENES gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of KEGG GENES genome database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1611">
-        <rdfs:label>MaizeGDB gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format of the Maize genetics and genomics database (MaizeGDB).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1612">
-        <rdfs:label>MGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of the Mouse Genome Database (MGD).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1613">
-        <rdfs:label>RGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of the Rat Genome Database (RGD).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1614 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1614">
-        <rdfs:label>SGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of the Saccharomyces Genome Database (SGD).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1615 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1615">
-        <rdfs:label>GeneDB gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of the Sanger GeneDB genome database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1616">
-        <rdfs:label>TAIR gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of The Arabidopsis Information Resource (TAIR) genome database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1617">
-        <rdfs:label>WormBase gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of the WormBase genomes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1618">
-        <rdfs:label>ZFIN gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format of the Zebrafish Information Network (ZFIN) genome database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1619 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1619">
-        <rdfs:label>TIGR gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format of the TIGR genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1620">
-        <rdfs:label>dbSNP polymorphism report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the dbSNP database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1623 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1623">
-        <rdfs:label>OMIM entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of an entry from the OMIM database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1624 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1624">
-        <rdfs:label>HGVbase entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of a record from the HGVbase database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1625 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1625">
-        <rdfs:label>HIVDB entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of a record from the HIVDB database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1626 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1626">
-        <rdfs:label>KEGG DISEASE entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the KEGG DISEASE database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1627 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1627">
-        <rdfs:label>Primer3 primer</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2061"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1628 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1628">
-        <rdfs:label>ABI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>A format of raw sequence read data from an Applied Biosystems sequencing machine.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1629 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1629">
-        <rdfs:label>mira</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of MIRA sequence trace information file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1630 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1630">
-        <rdfs:label>CAF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2561"/>
-        <oboInOwl:hasDefinition>Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.sanger.ac.uk/resources/software/caf/"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.sanger.ac.uk/resources/software/caf/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1631 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1631">
-        <rdfs:label>exp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2561"/>
-        <oboInOwl:hasDefinition>Sequence assembly project file EXP format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1632 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1632">
-        <rdfs:label>SCF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://staden.sourceforge.net/manual/formats_unix_2.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://staden.sourceforge.net/manual/formats_unix_2.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1633 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1633">
-        <rdfs:label>PHD</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PHD sequence trace format to store serialised chromatogram data (reads).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.bioperl.org/wiki/PHD_sequence_format"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.bioperl.org/wiki/PHD_sequence_format"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1637 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1637">
-        <rdfs:label>dat</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1714"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of Affymetrix data file of raw image data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Affymetrix image data file format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1638 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1638">
-        <rdfs:label>cel</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3110"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Affymetrix probe raw data format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of Affymetrix data file of information about (raw) expression levels of the individual probes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1639 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1639">
-        <rdfs:label>affymetrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2172"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1640 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1640">
-        <rdfs:label>ArrayExpress entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format for the ArrayExpress microarrays database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1641 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1641">
-        <rdfs:label>affymetrix-exp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2056"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Affymetrix data file format for information about experimental conditions and protocols.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Affymetrix experimental conditions data file format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1644 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1644">
-        <rdfs:label>CHP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Affymetrix probe normalised data format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of Affymetrix data file of information about (normalised) expression levels of the individual probes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1645 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1645">
-        <rdfs:label>EMDB entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the Electron Microscopy DataBase (EMDB).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1647 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1647">
-        <rdfs:label>KEGG PATHWAY entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1648 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1648">
-        <rdfs:label>MetaCyc entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the MetaCyc metabolic pathways database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1649 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1649">
-        <rdfs:label>HumanCyc entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of a report from the HumanCyc metabolic pathways database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1650 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1650">
-        <rdfs:label>INOH entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The format of an entry from the INOH signal transduction pathways database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1651 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1651">
-        <rdfs:label>PATIKA entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the PATIKA biological pathways database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1652 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1652">
-        <rdfs:label>Reactome entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the reactome biological pathways database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1653 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1653">
-        <rdfs:label>aMAZE entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The format of an entry from the aMAZE biological pathways and molecular interactions database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1654 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1654">
-        <rdfs:label>CPDB entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the CPDB database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1655 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1655">
-        <rdfs:label>Panther Pathways entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the Panther Pathways database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1665 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1665">
-        <rdfs:label>Taverna workflow format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2032"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Format of Taverna workflows.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1666 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1666">
-        <rdfs:label>BioModel mathematical model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of mathematical models from the BioModel database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1697 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1697">
-        <rdfs:label>KEGG LIGAND entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG LIGAND chemical database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1698 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1698">
-        <rdfs:label>KEGG COMPOUND entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG COMPOUND database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1699 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1699">
-        <rdfs:label>KEGG PLANT entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG PLANT database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1700 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1700">
-        <rdfs:label>KEGG GLYCAN entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG GLYCAN database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1701 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1701">
-        <rdfs:label>PubChem entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from PubChem.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1702 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1702">
-        <rdfs:label>ChemSpider entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from a database of chemical structures and property predictions.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1703 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1703">
-        <rdfs:label>ChEBI entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from Chemical Entities of Biological Interest (ChEBI).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>ChEBI includes an ontological classification defining relations between entities or classes of entities.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1704 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1704">
-        <rdfs:label>MSDchem ligand dictionary entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the MSDchem ligand dictionary.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1705 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1705">
-        <rdfs:label>HET group dictionary entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2030"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>The format of an entry from the HET group dictionary (HET groups from PDB files).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1706 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1706">
-        <rdfs:label>KEGG DRUG entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG DRUG database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1734 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1734">
-        <rdfs:label>PubMed citation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of bibliographic reference as used by the PubMed database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1735 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1735">
-        <rdfs:label>Medline Display Format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for abstracts of scientific articles from the Medline database.</oboInOwl:hasDefinition>
-        <rdfs:comment>Bibliographic reference information including citation information is included</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1736 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1736">
-        <rdfs:label>CiteXplore-core</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>CiteXplore &apos;core&apos; citation format including title, journal, authors and abstract.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1737 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1737">
-        <rdfs:label>CiteXplore-all</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <oboInOwl:hasDefinition>CiteXplore &apos;all&apos; citation format includes all known details such as Mesh terms and cross-references.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1739 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1739">
-        <rdfs:label>pmc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2020"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Article format of the PubMed Central database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1740 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1740">
-        <rdfs:label>iHOP text mining abstract format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2021"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>iHOP abstract format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1741 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1741">
-        <rdfs:label>Oscar3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2021"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document.</rdfs:comment>
-        <oboInOwl:hasDefinition>Text mining abstract format from the Oscar 3 application.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1747 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1747">
-        <rdfs:label>PDB atom record format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an ATOM record (describing data for an individual atom) from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1476"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1760 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1760">
-        <rdfs:label>CATH chain report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of CATH domain classification information for a polypeptide chain.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1761 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1761">
-        <rdfs:label>CATH PDB report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of CATH domain classification information for a protein PDB file.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1782 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1782">
-        <rdfs:label>NCBI gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry (gene) format of the NCBI database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1808 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1808">
-        <rdfs:label>GeneIlluminator gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:GI_Gene</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1809 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1809">
-        <rdfs:label>BacMap gene card format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDbXref>Moby:BacMapGeneCard</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1810 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1810">
-        <rdfs:label>ColiCard report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDbXref>Moby:ColiCard</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1861 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1861">
-        <rdfs:label>PlasMapper TextMap</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2060"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Map of a plasmid (circular DNA) in PlasMapper TextMap format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1910 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1910">
-        <rdfs:label>newick</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasExactSynonym>nh</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic tree Newick (text) format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1911 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1911">
-        <rdfs:label>TreeCon format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic tree TreeCon (text) format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1912 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1912">
-        <rdfs:label>Nexus format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasDefinition>Phylogenetic tree Nexus (text) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1915 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1915">
-        <rdfs:label>Format</rdfs:label>
-        <owl:disjointWith rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/topic_0003"/>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/File_format</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#MachineLanguage</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>File format</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Data model</oboInOwl:hasBroadSynonym>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Exchange format</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000098&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000612</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000618</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.org/dc/elements/1.1/format&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>http://wsio.org/compression_004</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/List_of_file_formats</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Quality</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Data format</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#Quality</rdfs:seeAlso>
-        <rdfs:comment>The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format &apos;is format of&apos; Data.</rdfs:comment>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to &apos;Data model&apos; would be an &apos;Information model&apos;.)</rdfs:comment>
-        <owl:annotatedTarget>Data model</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasBroadSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages.</rdfs:comment>
-        <owl:annotatedTarget>File format</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/format_1918 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1918">
-        <rdfs:label>Atomic data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data format for an individual atom.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1475"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1919 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1919">
-        <rdfs:label>Sequence record format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1920 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1920">
-        <rdfs:label>Sequence feature annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for molecular sequence feature information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1921 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1921">
-        <rdfs:label>Alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for molecular sequence alignment information.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1923 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1923">
-        <rdfs:label>acedb</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ACEDB sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1924 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1924">
-        <rdfs:label>clustal sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Clustalw output format.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1982"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1925 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1925">
-        <rdfs:label>codata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Codata entry format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1926 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1926">
-        <rdfs:label>dbid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Fasta format variant with database name before ID.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1927 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1927">
-        <rdfs:label>EMBL format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2181"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <oboInOwl:hasDefinition>EMBL entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EMBL sequence format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>EMBL</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1928 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1928">
-        <rdfs:label>Staden experiment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Staden experiment file format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1929 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1929">
-        <rdfs:label>FASTA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>FASTA format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>FASTA sequence format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>FASTA format including NCBI-style IDs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1930 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1930">
-        <rdfs:label>FASTQ</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ short read format ignoring quality scores.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>FASTAQ</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>fq</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1931 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1931">
-        <rdfs:label>FASTQ-illumina</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ Illumina 1.3 short read format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1932 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1932">
-        <rdfs:label>FASTQ-sanger</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ short read format with phred quality.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1933 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1933">
-        <rdfs:label>FASTQ-solexa</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ Solexa/Illumina 1.0 short read format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1934 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1934">
-        <rdfs:label>fitch program</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Fitch program format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1935 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1935">
-        <rdfs:label>GCG</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3486"/>
-        <oboInOwl:hasExactSynonym>GCG SSF</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment> GCG SSF (single sequence file) file format.</rdfs:comment>
-        <oboInOwl:hasDefinition>GCG sequence file format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1936 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1936">
-        <rdfs:label>GenBank format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2205"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Genbank entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1937 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1937">
-        <rdfs:label>genpept</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2205"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Genpept protein entry format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Currently identical to refseqp format</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1938 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1938">
-        <rdfs:label>GFF2-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1974"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>GFF feature file format with sequence in the header.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1939 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1939">
-        <rdfs:label>GFF3-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>GFF3 feature file format with sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1940 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1940">
-        <rdfs:label>giFASTA format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <oboInOwl:hasDefinition>FASTA sequence format including NCBI-style GIs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1941 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1941">
-        <rdfs:label>hennig86</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Hennig86 output sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1942 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1942">
-        <rdfs:label>ig</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Intelligenetics sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1943 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1943">
-        <rdfs:label>igstrict</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Intelligenetics sequence format (strict version).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1944 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1944">
-        <rdfs:label>jackknifer</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Jackknifer interleaved and non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1945 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1945">
-        <rdfs:label>mase format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mase program sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1946 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1946">
-        <rdfs:label>mega-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mega interleaved and non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1947 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1947">
-        <rdfs:label>MSF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3486"/>
-        <oboInOwl:hasExactSynonym>GCG MSF</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>GCG MSF (multiple sequence file) file format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1948 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1948">
-        <rdfs:label>nbrf/pir</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>NBRF/PIR entry sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>nbrf</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>pir</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1949 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1949">
-        <rdfs:label>nexus-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Nexus/paup interleaved sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1950 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1950">
-        <rdfs:label>pdbatom</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:comment>pdb format in EMBOSS.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PDB sequence format (ATOM lines).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1951 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1951">
-        <rdfs:label>pdbatomnuc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>pdbnuc format in EMBOSS.</rdfs:comment>
-        <oboInOwl:hasDefinition>PDB nucleotide sequence format (ATOM lines).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1952 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1952">
-        <rdfs:label>pdbseqresnuc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:comment>pdbnucseq format in EMBOSS.</rdfs:comment>
-        <oboInOwl:hasDefinition>PDB nucleotide sequence format (SEQRES lines).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1953 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1953">
-        <rdfs:label>pdbseqres</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>PDB sequence format (SEQRES lines).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>pdbseq format in EMBOSS.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1954 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1954">
-        <rdfs:label>Pearson format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Plain old FASTA sequence format (unspecified format for IDs).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1955 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1955">
-        <rdfs:label>phylip sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylip interleaved sequence format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1997"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1956 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1956">
-        <rdfs:label>phylipnon sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Phylip non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1998"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1957 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1957">
-        <rdfs:label>raw</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw sequence format with no non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1958 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1958">
-        <rdfs:label>refseqp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Refseq protein entry sequence format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Currently identical to genpept format</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1959 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1959">
-        <rdfs:label>selex sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Selex sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2000"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1960 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1960">
-        <rdfs:label>Staden format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Staden suite sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html"/>
-        <documentation rdf:resource="http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1961 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1961">
-        <rdfs:label>Stockholm format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Stockholm multiple sequence alignment format (used by Pfam and Rfam).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://en.wikipedia.org/wiki/Stockholm_format"/>
-        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/Stockholm_format"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1962 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1962">
-        <rdfs:label>strider format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>DNA strider output sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1963 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1963">
-        <rdfs:label>UniProtKB format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2187"/>
-        <oboInOwl:hasExactSynonym>UniProt format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>SwissProt format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>UniProtKB entry sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1964 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1964">
-        <rdfs:label>plain text format (unformatted)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Plain text sequence format (essentially unformatted).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1965 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1965">
-        <rdfs:label>treecon sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Treecon output sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2005"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1966 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1966">
-        <rdfs:label>ASN.1 sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>NCBI ASN.1-based sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1967 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1967">
-        <rdfs:label>DAS format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2552"/>
-        <oboInOwl:hasExactSynonym>das sequence format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>DAS sequence (XML) format (any type).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1968 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1968">
-        <rdfs:label>dasdna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2552"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DAS sequence (XML) format (nucleotide-only).</oboInOwl:hasDefinition>
-        <rdfs:comment>The use of this format is deprecated.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1969 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1969">
-        <rdfs:label>debug-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>EMBOSS debugging trace sequence format of full internal data content.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1970 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1970">
-        <rdfs:label>jackknifernon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Jackknifer output sequence non-interleaved format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1971 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1971">
-        <rdfs:label>meganon sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mega non-interleaved output sequence format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1992"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1972 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1972">
-        <rdfs:label>NCBI format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <oboInOwl:hasDefinition>NCBI FASTA sequence format with NCBI-style IDs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>There are several variants of this.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1973 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1973">
-        <rdfs:label>nexusnon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Nexus/paup non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1974 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1974">
-        <rdfs:label>GFF2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2305"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>General Feature Format (GFF) of sequence features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.sanger.ac.uk/resources/software/gff/spec.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.sanger.ac.uk/resources/software/gff/spec.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1975 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1975">
-        <rdfs:label>GFF3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2305"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generic Feature Format version 3 (GFF3) of sequence features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1976 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1976">
-        <rdfs:label>pir</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>PIR feature format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1948"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1977 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1977">
-        <rdfs:label>swiss feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Swiss-Prot feature format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1963"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1978 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1978">
-        <rdfs:label>DASGFF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2553"/>
-        <oboInOwl:hasDefinition>DAS GFF (XML) feature format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>das feature</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>DASGFF feature</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1979 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1979">
-        <rdfs:label>debug-feat</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>EMBOSS debugging trace feature format of full internal data content.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1980 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1980">
-        <rdfs:label>EMBL feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>EMBL feature format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1927"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1981 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1981">
-        <rdfs:label>GenBank feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Genbank feature format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1936"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1982 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1982">
-        <rdfs:label>ClustalW format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasExactSynonym>clustal</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ClustalW format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1983 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1983">
-        <rdfs:label>debug</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS alignment format for debugging trace of full internal data content.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1984 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1984">
-        <rdfs:label>FASTA-aln</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Fasta format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1985 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1985">
-        <rdfs:label>markx0</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX0 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1986 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1986">
-        <rdfs:label>markx1</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <oboInOwl:hasDefinition>Pearson MARKX1 alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1987 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1987">
-        <rdfs:label>markx10</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX10 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1988 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1988">
-        <rdfs:label>markx2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX2 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1989 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1989">
-        <rdfs:label>markx3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX3 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1990 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1990">
-        <rdfs:label>match</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Alignment format for start and end of matches between sequence pairs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1991 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1991">
-        <rdfs:label>mega</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2923"/>
-        <oboInOwl:hasDefinition>Mega format for (typically aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1992 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1992">
-        <rdfs:label>meganon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2923"/>
-        <oboInOwl:hasDefinition>Mega non-interleaved format for (typically aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1993 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1993">
-        <rdfs:label>msf alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>MSF format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1947"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1994 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1994">
-        <rdfs:label>nexus alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Nexus/paup format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1995 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1995">
-        <rdfs:label>nexusnon alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Nexus/paup non-interleaved format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1973"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1996 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1996">
-        <rdfs:label>pair</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS simple sequence pair alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1997 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1997">
-        <rdfs:label>PHYLIP format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2924"/>
-        <oboInOwl:hasExactSynonym>phy</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>ph</oboInOwl:hasExactSynonym>
-        <documentation>http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format</documentation>
-        <oboInOwl:hasExactSynonym>PHYLIP interleaved format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Phylip format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1998 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1998">
-        <rdfs:label>phylipnon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2924"/>
-        <documentation>http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format</documentation>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PHYLIP sequential format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Phylip non-interleaved format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1999 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1999">
-        <rdfs:label>scores format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Alignment format for score values for pairs of sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2000 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2000">
-        <rdfs:label>selex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>SELEX format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2001 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2001">
-        <rdfs:label>EMBOSS simple format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS simple multiple alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2002 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2002">
-        <rdfs:label>srs format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simple multiple sequence (alignment) format for SRS.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2003">
-        <rdfs:label>srspair</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simple sequence pair (alignment) format for SRS.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2004">
-        <rdfs:label>T-Coffee format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>T-Coffee program alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2005">
-        <rdfs:label>TreeCon-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Treecon format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2006">
-        <rdfs:label>Phylogenetic tree format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2013 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2013">
-        <rdfs:label>Biological pathway or network format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2014 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2014">
-        <rdfs:label>Sequence-profile alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0869"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a sequence-profile alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2015 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2015">
-        <rdfs:label>Sequence-profile alignment (HMM) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data format for a sequence-HMM profile alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2014"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2017 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2017">
-        <rdfs:label>Amino acid index format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3033"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1501"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for an amino acid index.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2020 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2020">
-        <rdfs:label>Article format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0971"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Literature format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data format for a full-text scientific article.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2021 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2021">
-        <rdfs:label>Text mining report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0972"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for an abstract (report) from text mining.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2027 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2027">
-        <rdfs:label>Enzyme kinetics report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2024"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for reports on enzyme kinetics.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2030 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2030">
-        <rdfs:label>Small molecule report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0962"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound annotation format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of a report on a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2031 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2031">
-        <rdfs:label>Gene annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report on a particular locus, gene, gene system or groups of genes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene features format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2032 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2032">
-        <rdfs:label>Workflow format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a workflow.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2033 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2033">
-        <rdfs:label>Tertiary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular tertiary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2034 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2034">
-        <rdfs:label>Biological model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data format for a biological model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.2</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2013"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2035 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2035">
-        <rdfs:label>Chemical formula format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0846"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Text format of a chemical formula.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2036 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2036">
-        <rdfs:label>Phylogenetic character data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0871"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of raw (unplotted) phylogenetic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2037 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2037">
-        <rdfs:label>Phylogenetic continuous quantitative character format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1426"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of phylogenetic continuous quantitative character data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2038 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2038">
-        <rdfs:label>Phylogenetic discrete states format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1427"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of phylogenetic discrete states data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2039 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2039">
-        <rdfs:label>Phylogenetic tree report (cliques) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1428"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of phylogenetic cliques data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2040 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2040">
-        <rdfs:label>Phylogenetic tree report (invariants) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1429"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of phylogenetic invariants data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2045 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2045">
-        <rdfs:label>Electron microscopy model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Annotation format for electron microscopy models.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2049 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2049">
-        <rdfs:label>Phylogenetic tree report (tree distances) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1442"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format for phylogenetic tree distance data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2051 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2051">
-        <rdfs:label>Polymorphism report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:hasDefinition>Format for sequence polymorphism data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2052 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2052">
-        <rdfs:label>Protein family report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for reports on a protein family.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2054 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2054">
-        <rdfs:label>Protein interaction format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for molecular interaction data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Molecular interaction format</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2055 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2055">
-        <rdfs:label>Sequence assembly format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for sequence assembly data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2056 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2056">
-        <rdfs:label>Microarray experiment data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <oboInOwl:hasDefinition>Format for information about a microarray experimental per se (not the data generated from that experiment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2057 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2057">
-        <rdfs:label>Sequence trace format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0924"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format for sequence trace data (i.e. including base call information).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2058 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2058">
-        <rdfs:label>Gene expression report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2603"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Gene expression data format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of a file of gene expression data, e.g. a gene expression matrix or profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2059 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2059">
-        <rdfs:label>Genotype and phenotype annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of a report on genotype / phenotype information.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2060 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2060">
-        <rdfs:label>Map format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a map of (typically one) molecular sequence annotated with features.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2061 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2061">
-        <rdfs:label>Nucleic acid features (primers) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2062 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2062">
-        <rdfs:label>Protein report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report of general information about a specific protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2063 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2063">
-        <rdfs:label>Protein report (enzyme) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report of general information about a specific enzyme.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2064 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2064">
-        <rdfs:label>3D-1D scoring matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3033"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1499"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a matrix of 3D-1D scores (amino acid environment probabilities).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2065 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2065">
-        <rdfs:label>Protein structure report (quality evaluation) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1539"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report on the quality of a protein three-dimensional model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2066 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2066">
-        <rdfs:label>Database hits (sequence) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0857"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report on sequence hits and associated data from searching a sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2067 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2067">
-        <rdfs:label>Sequence distance matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0870"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a matrix of genetic distances between molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2068 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2068">
-        <rdfs:label>Sequence motif format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1353"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a sequence motif.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2069 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2069">
-        <rdfs:label>Sequence profile format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a sequence profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2072 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2072">
-        <rdfs:label>Hidden Markov model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2069"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1364"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a hidden Markov model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2074 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2074">
-        <rdfs:label>Dirichlet distribution format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1347"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format of a dirichlet distribution.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2075 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2075">
-        <rdfs:label>HMM emission and transition counts format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for the emission and transition counts of a hidden Markov model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2076 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2076">
-        <rdfs:label>RNA secondary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for secondary structure (predicted or real) of an RNA molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2077">
-        <rdfs:label>Protein secondary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Format for secondary structure (predicted or real) of a protein molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2078">
-        <rdfs:label>Sequence range format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1017"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used to specify range(s) of sequence positions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2094">
-        <rdfs:label>pure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for molecular sequence with possible unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2095 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2095">
-        <rdfs:label>unpure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2096 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2096">
-        <rdfs:label>unambiguous sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2097">
-        <rdfs:label>ambiguous</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2155 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2155">
-        <rdfs:label>Sequence features (repeats) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for map of repeats in molecular (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2158">
-        <rdfs:label>Nucleic acid features (restriction sites) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for report on restriction enzyme recognition sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2159">
-        <rdfs:label>Gene features (coding region) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for report on coding regions in nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.10</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_2031"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2170 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2170">
-        <rdfs:label>Sequence cluster format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for clusters of molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2171 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2171">
-        <rdfs:label>Sequence cluster format (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2170"/>
-        <oboInOwl:hasDefinition>Format used for clusters of protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2172">
-        <rdfs:label>Sequence cluster format (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2170"/>
-        <oboInOwl:hasDefinition>Format used for clusters of nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2175">
-        <rdfs:label>Gene cluster format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for clusters of genes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2172"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2181 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2181">
-        <rdfs:label>EMBL-like (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2543"/>
-        <rdfs:comment>This concept may be used for the many non-standard EMBL-like text formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A text format resembling EMBL entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2182">
-        <rdfs:label>FASTQ-like format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2545"/>
-        <oboInOwl:hasDefinition>A text format resembling FASTQ short read format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for non-standard FASTQ short read-like formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2183">
-        <rdfs:label>EMBLXML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2204"/>
-        <oboInOwl:hasDefinition>XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2184">
-        <rdfs:label>cdsxml</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2204"/>
-        <oboInOwl:hasDefinition>XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2185 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2185">
-        <rdfs:label>insdxml</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2204"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2186 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2186">
-        <rdfs:label>geneseq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2181"/>
-        <oboInOwl:hasDefinition>Geneseq sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2187 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2187">
-        <rdfs:label>UniProt-like (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2547"/>
-        <oboInOwl:hasDefinition>A text sequence format resembling uniprotkb entry format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2188 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2188">
-        <rdfs:label>UniProt format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>UniProt entry sequence format.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1963"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2189 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2189">
-        <rdfs:label>ipi</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ipi sequence format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1963"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2194">
-        <rdfs:label>medline</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2020"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Abstract format used by MedLine database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2195">
-        <rdfs:label>Ontology format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format used for ontologies.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2196">
-        <rdfs:label>OBO format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A serialisation format conforming to the Open Biomedical Ontologies (OBO) model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2197 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2197">
-        <rdfs:label>OWL format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>A serialisation format conforming to the Web Ontology Language (OWL) model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2200">
-        <rdfs:label>FASTA-like (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2546"/>
-        <rdfs:comment>This concept may also be used for the many non-standard FASTA-like formats.</rdfs:comment>
-        <rdfs:seeAlso>http://filext.com/file-extension/FASTA</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A text format resembling FASTA format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2202">
-        <rdfs:label>Sequence record full format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2203">
-        <rdfs:label>Sequence record lite format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record &apos;lite&apos;, typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2204">
-        <rdfs:label>EMBL format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2558"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a placeholder for other more specific concepts. It should not normally be used for annotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2205 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2205">
-        <rdfs:label>GenBank-like format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2559"/>
-        <oboInOwl:hasDefinition>A text format resembling GenBank entry (plain text) format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for the non-standard GenBank-like text formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2206 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2206">
-        <rdfs:label>Sequence feature table format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2548"/>
-        <oboInOwl:hasDefinition>Text format for a sequence feature table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2210">
-        <rdfs:label>Strain data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on organism strain data / cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2211">
-        <rdfs:label>CIP strain data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format for a report of strain data as used for CIP database entries.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2243">
-        <rdfs:label>phylip property values</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>PHYLIP file format for phylogenetic property data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2036"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2303">
-        <rdfs:label>STRING entry format (HTML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format (HTML) for the STRING database of protein interaction.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2304">
-        <rdfs:label>STRING entry format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2054"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Entry format (XML) for the STRING database of protein interaction.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2305">
-        <rdfs:label>GFF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>GFF feature format (of indeterminate version).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2306">
-        <rdfs:label>GTF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2305"/>
-        <oboInOwl:hasDefinition>Gene Transfer Format (GTF), a restricted version of GFF.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format4"/>
-        <oboInOwl:hasDbXref rdf:resource="http://mblab.wustl.edu/GTF22.html"/>
-        <documentation rdf:resource="http://mblab.wustl.edu/GTF22.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2310">
-        <rdfs:label>FASTA-HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2546"/>
-        <oboInOwl:hasDefinition>FASTA format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2311">
-        <rdfs:label>EMBL-HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2543"/>
-        <oboInOwl:hasDefinition>EMBL entry format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2322">
-        <rdfs:label>BioCyc enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of an entry from the BioCyc enzyme database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2323">
-        <rdfs:label>ENZYME enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of an entry from the Enzyme nomenclature database (ENZYME).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2328">
-        <rdfs:label>PseudoCAP gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a report on a gene from the PseudoCAP database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2329">
-        <rdfs:label>GeneCards gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on a gene from the GeneCards database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2330">
-        <rdfs:label>Textual format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:seeAlso>http://filext.com/file-extension/TSV</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.iana.org/assignments/media-types/text/plain</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Textual format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>txt</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://filext.com/file-extension/TXT</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Plain text</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://www.iana.org/assignments/media-types/media-types.xhtml#text</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2331">
-        <rdfs:label>HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2048"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>HTML format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://filext.com/file-extension/HTML</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Hypertext Markup Language</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2332">
-        <rdfs:label>XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:comment>Data in XML format can be serialised into text, or binary format.</rdfs:comment>
-        <oboInOwl:hasDefinition>eXtensible Markup Language (XML) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://filext.com/file-extension/XML</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Extensible Markup Language</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2333 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2333">
-        <rdfs:label>Binary format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:comment>Only specific native binary formats are listed under &apos;Binary format&apos; in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Binary format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2334">
-        <rdfs:label>URI format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Typical textual representation of a URI.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1047"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2341">
-        <rdfs:label>NCI-Nature pathway entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The format of an entry from the NCI-Nature pathways database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2350">
-        <rdfs:label>Format (typed)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:comment>This concept exists only to assist EDAM maintenance and navigation in graphical browsers.  It does not add semantic information. The concept branch under &apos;Format (typed)&apos; provides an alternative organisation of the concepts nested under the other top-level branches (&apos;Binary&apos;, &apos;HTML&apos;, &apos;RDF&apos;, &apos;Text&apos; and &apos;XML&apos;. All concepts under here are already included under those branches.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A broad class of format distinguished by the scientific nature of the data that is identified.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2352">
-        <rdfs:label>BioXSD</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2555"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>BioXSD XML format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more).</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://bioxsd.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://bioxsd.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2376 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2376">
-        <rdfs:label>RDF format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A serialisation format conforming to the Resource Description Framework (RDF) model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2532 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2532">
-        <rdfs:label>GenBank-HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2559"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Genbank entry format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2542">
-        <rdfs:label>Protein features (domains) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of a report on protein features (domain composition).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2543">
-        <rdfs:label>EMBL-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A format resembling EMBL entry (plain text) format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for the many non-standard EMBL-like formats.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2545">
-        <rdfs:label>FASTQ-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <oboInOwl:hasDefinition>A format resembling FASTQ short read format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for non-standard FASTQ short read-like formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2546">
-        <rdfs:label>FASTA-like</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:comment>This concept may be used for the many non-standard FASTA-like formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A format resembling FASTA format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2547">
-        <rdfs:label>uniprotkb-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A sequence format resembling uniprotkb entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2548">
-        <rdfs:label>Sequence feature table format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format for a sequence feature table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2549">
-        <rdfs:label>OBO</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2196"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>OBO ontology text format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2550">
-        <rdfs:label>OBO-XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2196"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>OBO ontology XML format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2551">
-        <rdfs:label>Sequence record format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2552">
-        <rdfs:label>Sequence record format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2553">
-        <rdfs:label>Sequence feature table format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2548"/>
-        <oboInOwl:hasDefinition>XML format for a sequence feature table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2554">
-        <rdfs:label>Alignment format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <oboInOwl:hasDefinition>Text format for molecular sequence alignment information.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2555">
-        <rdfs:label>Alignment format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <oboInOwl:hasDefinition>XML format for molecular sequence alignment information.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2556">
-        <rdfs:label>Phylogenetic tree format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Text format for a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2557">
-        <rdfs:label>Phylogenetic tree format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>XML format for a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2558">
-        <rdfs:label>EMBL-like (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2543"/>
-        <oboInOwl:hasDefinition>An XML format resembling EMBL entry format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for the any non-standard EMBL-like XML formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2559">
-        <rdfs:label>GenBank-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:hasDefinition>A format resembling GenBank entry (plain text) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This concept may be used for the non-standard GenBank-like formats.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2560">
-        <rdfs:label>STRING entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the STRING database of protein interaction.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2561">
-        <rdfs:label>Sequence assembly format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2055"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Text format for sequence assembly data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2562 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2562">
-        <rdfs:label>Amino acid identifier format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Text format (representation) of amino acid residues.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0994"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2566">
-        <rdfs:label>completely unambiguous</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence without any unknown positions or ambiguity characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2567">
-        <rdfs:label>completely unambiguous pure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2566"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2568">
-        <rdfs:label>completely unambiguous pure nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters .</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2569">
-        <rdfs:label>completely unambiguous pure dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1212"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2570">
-        <rdfs:label>completely unambiguous pure rna sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1213"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2571">
-        <rdfs:label>Raw sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0848"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a raw molecular sequence (i.e. the alphabet used).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2572">
-        <rdfs:label>BAM</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2573">
-        <rdfs:label>SAM</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <rdfs:comment>The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2585 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2585">
-        <rdfs:label>SBML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://sbml.org"/>
-        <documentation rdf:resource="http://sbml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2607">
-        <rdfs:label>completely unambiguous pure protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1208"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2848 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2848">
-        <rdfs:label>Bibliographic reference format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0970"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a bibliographic reference.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2919 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2919">
-        <rdfs:label>Sequence annotation track format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3002"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a sequence annotation track.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2920 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2920">
-        <rdfs:label>Alignment format (pair only)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1381"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2921 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2921">
-        <rdfs:label>Sequence variation annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3498"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of sequence variation annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2922 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2922">
-        <rdfs:label>markx0 variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Some variant of Pearson MARKX alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2923 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2923">
-        <rdfs:label>mega variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Some variant of Mega format for (typically aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2924 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2924">
-        <rdfs:label>Phylip format variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Some variant of Phylip format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3000 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3000">
-        <rdfs:label>AB1</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>AB1 binary format of raw DNA sequence reads (output of Applied Biosystems&apos; sequencing analysis software). Contains an electropherogram and the DNA base sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3001 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3001">
-        <rdfs:label>ACE</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2055"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt"/>
-        <oboInOwl:hasDbXref rdf:resource="http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3003">
-        <rdfs:label>BED</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track).</rdfs:comment>
-        <oboInOwl:hasDefinition>Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3004">
-        <rdfs:label>bigBed</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>bigBed format for large sequence annotation tracks, similar to textual BED format.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.5"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.5"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3005">
-        <rdfs:label>WIG</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/goldenPath/help/wiggle.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/goldenPath/help/wiggle.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3006">
-        <rdfs:label>bigWig</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format6.1"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format6.1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3007">
-        <rdfs:label>PSL</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <oboInOwl:hasDefinition>PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format2"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format2"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3008 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3008">
-        <rdfs:label>MAF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth.</oboInOwl:hasDefinition>
-        <rdfs:comment>Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format5"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format5"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3009 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3009">
-        <rdfs:label>2bit</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case &apos;masking&apos;.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD"/>
-        <documentation rdf:resource="http://jcomeau.freeshell.org/www/genome/2bitformat.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://jcomeau.freeshell.org/www/genome/2bitformat.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3010 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3010">
-        <rdfs:label>.nib</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>.nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case &apos;masking&apos;.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format8"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format8"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3011 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3011">
-        <rdfs:label>genePred</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>genePred table format for gene prediction tracks.</oboInOwl:hasDefinition>
-        <rdfs:comment>genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format9"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format9"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3012 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3012">
-        <rdfs:label>pgSnp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format10"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format10"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3013 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3013">
-        <rdfs:label>axt</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>axt format of alignments, typically produced from BLASTZ.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/goldenPath/help/axt.html"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/goldenPath/help/axt.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3014 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3014">
-        <rdfs:label>LAV</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>LAV format of alignments generated by BLASTZ and LASTZ.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.bx.psu.edu/miller_lab/dist/lav_format.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.bx.psu.edu/miller_lab/dist/lav_format.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3015 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3015">
-        <rdfs:label>Pileup</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/pileup.shtml"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/pileup.shtml"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3016 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3016">
-        <rdfs:label>VCF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://vcftools.sourceforge.net/specs.html"/>
-        <documentation rdf:resource="http://vcftools.sourceforge.net/specs.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3017 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3017">
-        <rdfs:label>SRF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://srf.sourceforge.net/"/>
-        <oboInOwl:hasDbXref rdf:resource="http://srf.sourceforge.net/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3018 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3018">
-        <rdfs:label>ZTR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>ZTR format for storing chromatogram data from DNA sequencing instruments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://staden.sourceforge.net/manual/formats_unix_12.html"/>
-        <documentation rdf:resource="http://staden.sourceforge.net/manual/formats_unix_12.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3019 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3019">
-        <rdfs:label>GVF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <oboInOwl:hasDefinition>Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://sequenceontology.org/gvf.html"/>
-        <documentation rdf:resource="http://sequenceontology.org/gvf.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3020 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3020">
-        <rdfs:label>BCF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/mpileup.shtml"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3033 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3033">
-        <rdfs:label>Matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a matrix (array) of numerical values.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3097">
-        <rdfs:label>Protein domain classification format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of data concerning the classification of the sequences and/or structures of protein structural domain(s).</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3098 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3098">
-        <rdfs:label>Raw SCOP domain classification format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3097"/>
-        <oboInOwl:hasDefinition>Format of raw SCOP domain classification data files.</oboInOwl:hasDefinition>
-        <rdfs:comment>These are the parsable data files provided by SCOP.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3099">
-        <rdfs:label>Raw CATH domain classification format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3097"/>
-        <rdfs:comment>These are the parsable data files provided by CATH.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Format of raw CATH domain classification data files.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3100 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3100">
-        <rdfs:label>CATH domain report format</rdfs:label>
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-        <oboInOwl:hasDefinition>Format of summary of domain classification information for a CATH domain.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <rdfs:comment>The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3155 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3155">
-        <rdfs:label>SBRML</rdfs:label>
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-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3166"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.comp-sys-bio.org/tiki-index.php?page=SBRML"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.comp-sys-bio.org/tiki-index.php?page=SBRML"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3156">
-        <rdfs:label>BioPAX</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <oboInOwl:hasDefinition>BioPAX is an exchange format for pathway data, with its data model defined in OWL.</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://www.biopax.org"/>
-        <documentation rdf:resource="http://www.biopax.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3157">
-        <rdfs:label>EBI Application Result XML</rdfs:label>
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-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <oboInOwl:hasDefinition>EBI Application Result XML is a format returned by sequence similarity search Web services at EBI.</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.ebi.ac.uk/schema/ApplicationResult.xsd"/>
-        <documentation rdf:resource="http://www.ebi.ac.uk/schema/ApplicationResult.xsd"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3158 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3158">
-        <rdfs:label>PSI MI XML (MIF)</rdfs:label>
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-        <oboInOwl:hasDefinition>XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>MIF</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.psidev.info/mif"/>
-        <documentation rdf:resource="http://www.psidev.info/mif"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3159 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3159">
-        <rdfs:label>phyloXML</rdfs:label>
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-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2557"/>
-        <oboInOwl:hasDefinition>phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data.</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://www.phyloxml.org"/>
-        <documentation rdf:resource="http://www.phyloxml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3160">
-        <rdfs:label>NeXML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2557"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>NeXML is a standardised XML format for rich phyloinformatic data.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://www.nexml.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.nexml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3161 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3161">
-        <rdfs:label>MAGE-ML</rdfs:label>
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-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
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-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.mged.org/Workgroups/MAGE/mage-ml.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.mged.org/Workgroups/MAGE/mage-ml.html"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3162 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3162">
-        <rdfs:label>MAGE-TAB</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
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-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
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-        <oboInOwl:hasDefinition>MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED).</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.mged.org/mage-tab"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.mged.org/mage-tab"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3163 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3163">
-        <rdfs:label>GCDML</rdfs:label>
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-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <oboInOwl:hasDefinition>GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC).</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <documentation rdf:resource="http://gcdml.gensc.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://gcdml.gensc.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3164 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3164">
-        <rdfs:label>GTrack</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG).</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://www.gtrack.no"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.gtrack.no"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3166">
-        <rdfs:label>Biological pathway or network report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
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-        <oboInOwl:hasDefinition>Data format for a report of information derived from a biological pathway or network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3167">
-        <rdfs:label>Experiment annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for annotation on a laboratory experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3235 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3235">
-        <rdfs:label>Cytoband format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2078"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
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-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Cytoband format for chromosome cytobands.</oboInOwl:hasDefinition>
-        <rdfs:comment>Reflects a UCSC Browser DB table.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.broadinstitute.org/software/igv/Cytoband"/>
-        <documentation rdf:resource="http://www.broadinstitute.org/software/igv/Cytoband"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3239">
-        <rdfs:label>CopasiML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3166"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>CopasiML, the native format of COPASI.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.copasi.org/tiki-index.php?page_ref_id=128"/>
-        <documentation rdf:resource="http://www.copasi.org/tiki-index.php?page_ref_id=128"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3240 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3240">
-        <rdfs:label>CellML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>CellML, the format for mathematical models of biological and other networks.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <documentation rdf:resource="http://www.cellml.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.cellml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
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-
-
-    <!-- http://edamontology.org/format_3242 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3242">
-        <rdfs:label>PSI MI TAB (MITAB)</rdfs:label>
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-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README"/>
-        <documentation rdf:resource="ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3243 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3243">
-        <rdfs:label>PSI-PAR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3158"/>
-        <oboInOwl:hasDefinition>Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.psidev.info/psi-par"/>
-        <documentation rdf:resource="http://www.psidev.info/psi-par"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3244 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3244">
-        <rdfs:label>mzML</rdfs:label>
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-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3245"/>
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-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://psidev.info/mzml"/>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/mzml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
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-
-
-    <!-- http://edamontology.org/format_3245 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3245">
-        <rdfs:label>Mass spectrometry data format</rdfs:label>
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-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
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-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Format for mass spectrometry data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
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-
-
-    <!-- http://edamontology.org/format_3246 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3246">
-        <rdfs:label>TraML</rdfs:label>
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-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3245"/>
-        <oboInOwl:hasDefinition>TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <documentation rdf:resource="http://psidev.info/traml"/>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/traml"/>
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-
-
-    <!-- http://edamontology.org/format_3247 -->
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-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/mzidentml"/>
-        <documentation rdf:resource="http://psidev.info/mzidentml"/>
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-
-
-    <!-- http://edamontology.org/format_3248 -->
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-        <oboInOwl:hasDefinition>mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics.</oboInOwl:hasDefinition>
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-        <documentation rdf:resource="http://psidev.info/mzquantml"/>
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-
-    <!-- http://edamontology.org/format_3249 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3249">
-        <rdfs:label>GelML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/gelml"/>
-        <documentation rdf:resource="http://psidev.info/gelml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3250">
-        <rdfs:label>spML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info"/>
-        <documentation rdf:resource="http://psidev.info"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3252">
-        <rdfs:label>OWL Functional Syntax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>A human-readable encoding for the Web Ontology Language (OWL).</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3253">
-        <rdfs:label>Manchester OWL Syntax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>A syntax for writing OWL class expressions.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <rdfs:comment>This format was influenced by the OWL Abstract Syntax and the DL style syntax.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3254">
-        <rdfs:label>KRSS2 Syntax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>This format is used in Protege 4.</rdfs:comment>
-        <oboInOwl:hasDefinition>A superset of the &quot;Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort&quot;.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3255 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3255">
-        <rdfs:label>Turtle</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <rdfs:comment>The SPARQL Query Language incorporates a very similar syntax.</rdfs:comment>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3256 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3256">
-        <rdfs:label>N-Triples</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <rdfs:comment>N-Triples should not be confused with Notation 3 which is a superset of Turtle.</rdfs:comment>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3257">
-        <rdfs:label>Notation3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <oboInOwl:hasExactSynonym>N3</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3261 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3261">
-        <rdfs:label>RDF/XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <oboInOwl:hasNarrowSynonym>RDF</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Resource Description Framework (RDF) XML format.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <rdfs:seeAlso>http://www.ebi.ac.uk/SWO/data/SWO_3000006</rdfs:seeAlso>
-        <rdfs:comment>RDF/XML is a serialization syntax for OWL DL, but not for OWL Full.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3262 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3262">
-        <rdfs:label>OWL/XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>OWL ontology XML serialisation format.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasNarrowSynonym>OWL</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3281 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3281">
-        <rdfs:label>A2M</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://compbio.soe.ucsc.edu/a2m-desc.html"/>
-        <documentation rdf:resource="http://compbio.soe.ucsc.edu/a2m-desc.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3284">
-        <rdfs:label>SFF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasExactSynonym>Standard flowgram format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&amp;f=formats&amp;m=doc&amp;s=format#sff"/>
-        <documentation rdf:resource="http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&amp;f=formats&amp;m=doc&amp;s=format#sff"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3285">
-        <rdfs:label>MAP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3288"/>
-        <oboInOwl:hasDefinition>The MAP file describes SNPs and is used by the Plink package.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Plink MAP</oboInOwl:hasExactSynonym>
-        <documentation rdf:resource="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3286 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3286">
-        <rdfs:label>PED</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3288"/>
-        <oboInOwl:hasExactSynonym>Plink PED</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The PED file describes individuals and genetic data and is used by the Plink package.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3287 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3287">
-        <rdfs:label>Individual genetic data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Data format for a metadata on an individual and their genetic data.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3288">
-        <rdfs:label>PED/MAP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3287"/>
-        <oboInOwl:hasDefinition>The PED/MAP file describes data used by the Plink package.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Plink PED/MAP</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <documentation rdf:resource="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3309">
-        <rdfs:label>CT</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>File format of a CT (Connectivity Table) file from the RNAstructure package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Connect format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Connectivity Table file format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://rna.urmc.rochester.edu/Text/File_Formats.html"/>
-        <documentation rdf:resource="http://www.ibi.vu.nl/programs/k2nwww/static/data_formats.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3310">
-        <rdfs:label>SS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>XRNA old input style format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://rna.ucsc.edu/rnacenter/xrna/xrna_faq.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3311">
-        <rdfs:label>RNAML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>RNA Markup Language.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www-lbit.iro.umontreal.ca/rnaml/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3312">
-        <rdfs:label>GDE</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Format for the Genetic Data Environment (GDE).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://home.cc.umanitoba.ca/~psgendb/birchhomedir/local/pkg/gde/doc/GDE2.2_manual.pdf"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3313">
-        <rdfs:label>BLC</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Block file format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.compbio.dundee.ac.uk/manuals/amps/subsubsection3_18_2_5.html#SECTION00018250000000000000"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3326">
-        <rdfs:label>Data index format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3327">
-        <rdfs:label>BAI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3326"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>BAM indexing format</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/SAMv1.pdf"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3328">
-        <rdfs:label>HMMER2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1370"/>
-        <oboInOwl:hasDefinition>HMMER profile HMM file for HMMER versions 2.x</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <documentation rdf:resource="ftp://selab.janelia.org/pub/software/hmmer/2.4i/Userguide.pdf"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3329">
-        <rdfs:label>HMMER3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1370"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>HMMER profile HMM file for HMMER versions 3.x</oboInOwl:hasDefinition>
-        <documentation rdf:resource="ftp://selab.janelia.org/pub/software/hmmer/CURRENT/Userguide.pdf"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3330">
-        <rdfs:label>PO</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS simple sequence pair alignment format.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://sourceforge.net/projects/poamsa/files/latest/download?source=files"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3331">
-        <rdfs:label>BLAST XML results format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>XML format as produced by the NCBI Blast package</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3462 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3462">
-        <rdfs:label>CRAM</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <oboInOwl:hasDefinition>Reference-based compression of alignment format</oboInOwl:hasDefinition>
-        <documentation>http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf</documentation>
-        <oboInOwl:hasDbXref>http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf</oboInOwl:hasDbXref>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3464">
-        <rdfs:label>JSON</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Javascript Object Notation format; a lightweight, text-based format to represent structured data using key-value pairs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3466 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3466">
-        <rdfs:label>EPS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Encapsulated PostScript format</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3467">
-        <rdfs:label>GIF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Graphics Interchange Format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3468">
-        <rdfs:label>xls</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <oboInOwl:hasDefinition>Microsoft Excel spreadsheet format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microsoft Excel format</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3475">
-        <rdfs:label>TSV</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasExactSynonym>Tabular format</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://filext.com/file-extension/CSV</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.iana.org/assignments/media-types/text/csv</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Tabular data represented as tab-separated values in a text file.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:seeAlso>http://filext.com/file-extension/TSV</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>CSV</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3476">
-        <rdfs:label>Gene expression data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.10</obsolete_since>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Format of a file of gene expression data, e.g. a gene expression matrix or profile.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_2058"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3477 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3477">
-        <rdfs:label>Cytoscape input file format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3484 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3484">
-        <rdfs:label>ebwt</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3326"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3210"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <documentation>https://github.com/BenLangmead/bowtie/blob/master/MANUAL</documentation>
-        <oboInOwl:hasExactSynonym>Bowtie index format</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Bowtie format for indexed reference genome for &quot;small&quot; genomes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3485">
-        <rdfs:label>RSF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3486"/>
-        <documentation>http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf</documentation>
-        <rdfs:comment>RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual).</rdfs:comment>
-        <oboInOwl:hasDefinition>Rich sequence format.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>GCG RSF</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3486">
-        <rdfs:label>GCG format variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Some format based on the GCG format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3487">
-        <rdfs:label>BSML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2552"/>
-        <documentation>http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc</documentation>
-        <oboInOwl:hasDefinition>Bioinformatics Sequence Markup Language format.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3491">
-        <rdfs:label>ebwtl</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3326"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3210"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <documentation>https://github.com/BenLangmead/bowtie/blob/master/MANUAL</documentation>
-        <oboInOwl:hasExactSynonym>Bowtie long index format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Bowtie format for indexed reference genome for &quot;large&quot; genomes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3499">
-        <rdfs:label>Ensembl variation file format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <oboInOwl:hasDefinition>Ensembl standard format for variation data.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.ensembl.org/info/website/upload/var.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3506">
-        <rdfs:label>docx</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Microsoft Word format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>doc</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Microsoft Word format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3507">
-        <rdfs:label>Document format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Portable Document Format</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microsoft Word format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of documents including word processor, spreadsheet and presentation.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>doc</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3508">
-        <rdfs:label>PDF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Portable Document Format</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3547">
-        <rdfs:label>Image format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2968"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format used for images and image metadata.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3548">
-        <rdfs:label>DICOM format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard.
-
-</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://dicom.nema.org/"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3549">
-        <rdfs:label>nii</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>Medical image and metadata format of the Neuroimaging Informatics Technology Initiative.
-
-</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>NIfTI-1 format</oboInOwl:hasExactSynonym>
-        <created_in>1.9</created_in>
-        <documentation rdf:resource="http://nifti.nimh.nih.gov/nifti-1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3550">
-        <rdfs:label>mhd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasExactSynonym>Metalmage format</oboInOwl:hasExactSynonym>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Text-based tagged file format for medical images generated using the MetaImage software package.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.itk.org/Wiki/ITK/MetaIO/Documentation"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3551">
-        <rdfs:label>nrrd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Nearly Raw Rasta Data format designed to support scientific visualization and image processing involving N-dimensional raster data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://teem.sourceforge.net/nrrd/format.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3554">
-        <rdfs:label>R file format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics.
-</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3555">
-        <rdfs:label>SPSS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>File format used for scripts for the Statistical Package for the Social Sciences.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3556">
-        <rdfs:label>MHT</rdfs:label>
-        <rdfs:label>MIME  HTML format for Web pages, which can include external resources, including images, Flash animations and so on. </rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:hasDefinition>EMBL entry format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasExactSynonym>MHTML</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3578">
-        <rdfs:label>IDAT</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3110"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3579">
-        <rdfs:label>JPG</rdfs:label>
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-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Joint Picture Group file format for lossy graphics file.
-</oboInOwl:hasDefinition>
-        <rdfs:comment>Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/jpeg/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3580 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3580">
-        <rdfs:label>rcc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3581">
-        <rdfs:label>arff</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <rdfs:comment>This file format is for machine learning.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.cs.waikato.ac.nz/ml/weka/arff.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.cs.waikato.ac.nz/ml/weka/arff.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3582">
-        <rdfs:label>afg</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2055"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>AFG is a single text-based file assembly format  that holds read and consensus information together</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://seqanswers.com/wiki/AFG"/>
-        <documentation rdf:resource="http://seqanswers.com/wiki/AFG"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3583">
-        <rdfs:label>bedgraph</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <rdfs:comment>Holds a tab-delimited chromosome /start /end / datavalue dataset.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.8"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.8"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3584 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3584">
-        <rdfs:label>bedstrict</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3003"/>
-        <oboInOwl:hasDefinition>Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns.  </oboInOwl:hasDefinition>
-        <rdfs:comment>Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.  </rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3585 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3585">
-        <rdfs:label>bed6</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3584"/>
-        <rdfs:comment>Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6</rdfs:comment>
-        <oboInOwl:hasDefinition>BED file format where each feature is described by chromosome, start, end, name, score, and strand.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3586 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3586">
-        <rdfs:label>bed12</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3584"/>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12</rdfs:comment>
-        <oboInOwl:hasDefinition>A BED file where each feature is described by all twelve columns.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <documentation rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3587 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3587">
-        <rdfs:label>chrominfo</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3003"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Tabular format of chromosome names and sizes used by Galaxy.</oboInOwl:hasDefinition>
-        <rdfs:comment>Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.  </rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables?hgsid=43553_onGgm5PMjz4VDV1NySxolABvN978&amp;hgta_doSchemaDb=mm10&amp;hgta_doSchemaTable=chromInfo"/>
-        <oboInOwl:hasDbXref rdf:resource="http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables?hgsid=43553_onGgm5PMjz4VDV1NySxolABvN978&amp;hgta_doSchemaDb=mm10&amp;hgta_doSchemaTable=chromInfo"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3588 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3588">
-        <rdfs:label>customtrack</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Custom Sequence annotation track format used by Galaxy.</oboInOwl:hasDefinition>
-        <rdfs:comment>Used for tracks/track views within galaxy.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://genome.ucsc.edu/goldenPath/help/customTrack.html"/>
-        <oboInOwl:hasDbXref rdf:resource="https://genome.ucsc.edu/goldenPath/help/customTrack.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3589 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3589">
-        <rdfs:label>csfasta</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Color space FASTA format sequence variant.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <rdfs:comment>FASTA format extended for color space information.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.clcsupport.com/clcassemblycell/420/index.php?manual=Color_space_file_formats.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.clcsupport.com/clcassemblycell/420/index.php?manual=Color_space_file_formats.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3590 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3590">
-        <rdfs:label>hdf5</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:comment>An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. H5py uses straightforward NumPy and Python metaphors, like dictionary and NumPy array syntax.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasExactSynonym>h5</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Binary format used by Galaxy for hierarchical data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="https://www.hdfgroup.org/HDF5/doc/H5.format.html"/>
-        <documentation rdf:resource="https://www.hdfgroup.org/HDF5/doc/H5.format.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3591 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3591">
-        <rdfs:label>tiff</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>The TIFF format is perhaps the most versatile and diverse bitmap format in existence. Its extensible nature and support for numerous data compression schemes allow developers to customize the TIFF format to fit any peculiar data storage needs.
-</rdfs:comment>
-        <oboInOwl:hasDefinition>A versatile bitmap format.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/tiff/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3592 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3592">
-        <rdfs:label>bmp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>Standard bitmap storage format in the Microsoft Windows environment.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Although it is based on Windows internal bitmap data structures, it is supported by many non-Windows and non-PC applications.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/bmp/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3593">
-        <rdfs:label>im</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>IM is a format used by LabEye and other applications based on the IFUNC image processing library.</oboInOwl:hasDefinition>
-        <rdfs:comment>IFUNC library reads and writes most uncompressed interchange versions of this format.
-</rdfs:comment>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://pillow.readthedocs.org/en/latest/handbook/image-file-formats.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3594">
-        <rdfs:label>pcd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>PCD was developed by Kodak. A PCD file contains five different resolution (ranging from low to high) of a slide or film negative. Due to it PCD is often used by many photographers and graphics professionals for high-end printed applications.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Photo CD format, which is the highest resolution format for images on a CD.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://www.coolutils.com/Formats/PCD"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3595">
-        <rdfs:label>pcx</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>PCX is an image file format that uses a simple form of run-length encoding. It is lossless.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://www.coolutils.com/Formats/PCX"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3596 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3596">
-        <rdfs:label>ppm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>The PPM format is a lowest common denominator color image file format.
-</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://netpbm.sourceforge.net/doc/ppm.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3597 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3597">
-        <rdfs:label>psd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>PSD (Photoshop Document) is a proprietary file that allows the user to work with the images’ individual layers even after the file has been saved.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/psd/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3598">
-        <rdfs:label>xbm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>The XBM format was replaced by XPM for X11 in 1989.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI. </oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/xbm/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3599 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3599">
-        <rdfs:label>xpm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.</rdfs:comment>
-        <oboInOwl:hasDefinition>X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/xpm/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3600 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3600">
-        <rdfs:label>rgb</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>RGB file format is the native raster graphics file format for Silicon Graphics workstations.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/jpeg/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3601">
-        <rdfs:label>pbm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters.
-</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://netpbm.sourceforge.net/doc/pbm.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3602">
-        <rdfs:label>pgm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>It is designed to be extremely easy to learn and write programs for.</rdfs:comment>
-        <oboInOwl:hasDefinition>The PGM format is a lowest common denominator grayscale file format.
-</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://netpbm.sourceforge.net/doc/pgm.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3603 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3603">
-        <rdfs:label>png</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>PNG is a file format for image compression.
-</oboInOwl:hasDefinition>
-        <rdfs:comment>It iis expected to replace the Graphics Interchange Format (GIF).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.w3.org/TR/PNG/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3604 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3604">
-        <rdfs:label>svg</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment> The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.</rdfs:comment>
-        <oboInOwl:hasDefinition>Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.w3.org/Graphics/SVG/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3605">
-        <rdfs:label>rast</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <rdfs:comment> The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://en.wikipedia.org/wiki/Sun_Raster"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3606">
-        <rdfs:label>Sequence quality report format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2048"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Textual report format for sequence quality for reports from sequencing machines.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3607">
-        <rdfs:label>qual</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3606"/>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Phred quality scores  are defined as a property which is logarithmically related to the base-calling error probabilities.</rdfs:comment>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3608">
-        <rdfs:label>qualsolexa</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1933"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <rdfs:comment>Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3609 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3609">
-        <rdfs:label>qualillumina</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1931"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <rdfs:comment>Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 &quot;B&quot;, is used also at the end of reads as a Read Segment Quality Control Indicator.</rdfs:comment>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3610">
-        <rdfs:label>qualsolid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <rdfs:comment>For SOLiD data, the sequence is in color space, except the first position. The quality values are those of the Sanger format.</rdfs:comment>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3611">
-        <rdfs:label>qual454</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3612">
-        <rdfs:label>ENCODE peak format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3585"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Human ENCODE peak format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Format that covers both the broad peak format and narrow peak format from ENCODE.</rdfs:comment>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format13"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format13"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3613">
-        <rdfs:label>ENCODE narrow peak format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3612"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Human ENCODE narrow peak format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Format that covers both the broad peak format and narrow peak format from ENCODE.</rdfs:comment>
-        <oboInOwl:hasDbXref rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?"/>
-        <documentation rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3614 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3614">
-        <rdfs:label>ENCODE broad peak format </rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3612"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Human ENCODE broad peak format.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format12"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format12"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3615 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3615">
-        <rdfs:label>bgzip</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>BAM files are compressed using a variant of GZIP (GNU ZIP), into a format called BGZF (Blocked GNU Zip Format).</rdfs:comment>
-        <oboInOwl:hasDefinition>Blocked GNU Zip format.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.htslib.org/doc/tabix.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3616">
-        <rdfs:label>tabix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>TAB-delimited genome position file index format.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.htslib.org/doc/tabix.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.htslib.org/doc/tabix.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3617">
-        <rdfs:label>Graph format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Data format for graph data.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3618">
-        <rdfs:label>xgmml</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3617"/>
-        <oboInOwl:hasDefinition>XML-based format used to store graph descriptions within Galaxy.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?highlight=datatypes%20graph#module-galaxy.datatypes.graph"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3619 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3619">
-        <rdfs:label>sif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?highlight=datatypes%20graph#module-galaxy.datatypes.graph"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3620">
-        <rdfs:label>xlsx</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3621">
-        <rdfs:label>SQLite</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <documentation>https://www.sqlite.org/fileformat2.html</documentation>
-        <oboInOwl:hasDefinition>Data format used by the SQLite database.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3622">
-        <rdfs:label>GeminiSQLite</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <documentation>https://gemini.readthedocs.org/en/latest/content/quick_start.html</documentation>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Data format used by the SQLite database conformant to the Gemini schema.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3623 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3623">
-        <rdfs:label>Index format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a data index of some type.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3624 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3624">
-        <rdfs:label>snpeffdb</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3623"/>
-        <oboInOwl:hasDefinition>An index of a genome database, indexed for use by the snpeff tool.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0004">
-        <rdfs:label>Operation</rdfs:label>
-        <owl:disjointWith rdf:resource="http://edamontology.org/topic_0003"/>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <oboInOwl:hasRelatedSynonym>Computational tool</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Function</oboInOwl:hasBroadSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#Function</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Function</rdfs:seeAlso>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Function_(mathematics)</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Computational method</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000017</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ebi.ac.uk/swo/SWO_0000003</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Mathematical operation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasRelatedSynonym>sumo:Function</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasRelatedSynonym>Process</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasNarrowSynonym>Computational operation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Computational subroutine</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000649</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/span#Process</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Computational procedure</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Mathematical function</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Lambda abstraction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Function (programming)</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Process</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://wsio.org/operation_001</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Function</rdfs:seeAlso>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Function_(computer_science)</rdfs:seeAlso>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Subroutine</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedTarget>Process</owl:annotatedTarget>
-        <rdfs:comment>Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>Computational tool provides one or more operations.</rdfs:comment>
-        <owl:annotatedTarget>Computational tool</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>Function</owl:annotatedTarget>
-        <rdfs:comment>Operation is a function that is computational. It typically has input(s) and output(s), which are always data.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasBroadSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/operation_0224 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0224">
-        <rdfs:label>Query and retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0090"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Query</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Retrieval</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Search or query a data resource and retrieve entries and / or annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0225 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0225">
-        <rdfs:label>Data retrieval (database cross-reference)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search database to retrieve all relevant references to a particular entity or entry.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0226 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0226">
-        <rdfs:label>Annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0227 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0227">
-        <rdfs:label>Indexing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Data indexing</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate an index of (typically a file of) biological data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database indexing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0228 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0228">
-        <rdfs:label>Data index analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Database index analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse an index of biological data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0227"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0229 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0229">
-        <rdfs:label>Annotation retrieval (sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Retrieve basic information about a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_1813"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0230 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0230">
-        <rdfs:label>Sequence generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a molecular sequence by some means.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0231 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0231">
-        <rdfs:label>Sequence editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <oboInOwl:hasDefinition>Edit or change a molecular sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0232 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0232">
-        <rdfs:label>Sequence merging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Merge two or more (typically overlapping) molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence splicing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0233">
-        <rdfs:label>Sequence conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3434"/>
-        <oboInOwl:hasDefinition>Convert a molecular sequence from one type to another.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0234 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0234">
-        <rdfs:label>Sequence complexity calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1259"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate sequence complexity, for example to find low-complexity regions in sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0235">
-        <rdfs:label>Sequence ambiguity calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1260"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0236">
-        <rdfs:label>Sequence composition calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1261"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate character or word composition or frequency of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0237">
-        <rdfs:label>Repeat sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Find and/or analyse repeat sequences in (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0238">
-        <rdfs:label>Sequence motif discovery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Motifs and patterns might be conserved or over-represented (occur with improbable frequency).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Motif discovery</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0239">
-        <rdfs:label>Sequence signature recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Motif search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence motif search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Motif detection</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence motif recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequence signature detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence profile search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Sequence motif detection</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Motif recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0240">
-        <rdfs:label>Sequence motif comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find motifs shared by molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0241">
-        <rdfs:label>Transcription regulatory sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0438"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0242">
-        <rdfs:label>Conserved transcription regulatory sequence identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:comment>For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0243">
-        <rdfs:label>Protein property calculation (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0250"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein structural property calculation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0244 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0244">
-        <rdfs:label>Protein flexibility and motion analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2476"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse flexibility and motion in protein structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0245">
-        <rdfs:label>Protein structural motif recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0166"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or screen for 3D structural motifs in protein structure(s).</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein structural feature identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0246">
-        <rdfs:label>Protein domain recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0736"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify structural domains in a protein structure from first principles (for example calculations on structural compactness).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0247">
-        <rdfs:label>Protein architecture analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0248">
-        <rdfs:label>Residue interaction calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1540"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDbXref>WHATIF: SymShellTenXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ListContactsRelaxed</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: SymShellTwoXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ListSideChainContactsRelaxed</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ListSideChainContactsNormal</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ListContactsNormal</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: SymShellFiveXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: SymShellOneXML</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0249 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0249">
-        <rdfs:label>Torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2991"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate, visualise or analyse phi/psi angles of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0250">
-        <rdfs:label>Protein property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods to render and visualise the properties of a protein sequence.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein property rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0252">
-        <rdfs:label>Peptide immunogenicity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1534"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0253">
-        <rdfs:label>Sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence feature prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence feature recognition</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Motif database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasRelatedSynonym>SO:0000110</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0254">
-        <rdfs:label>Data retrieval (feature table)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Extract a sequence feature table from a sequence database entry.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0255 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0255">
-        <rdfs:label>Feature table query</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query the features (in a feature table) of molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0256 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0256">
-        <rdfs:label>Sequence feature comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1270"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare the feature tables of two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Feature comparison</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Feature table comparison</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0257">
-        <rdfs:label>Data retrieval (sequence alignment)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Display basic information about a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0258">
-        <rdfs:label>Sequence alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0259">
-        <rdfs:label>Sequence alignment comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <oboInOwl:hasDefinition>Compare (typically by aligning) two molecular sequence alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>See also &apos;Sequence profile alignment&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0260 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0260">
-        <rdfs:label>Sequence alignment conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3081"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3434"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0261 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0261">
-        <rdfs:label>Nucleic acid property processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) physicochemical property data of nucleic acids.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0262"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0262 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0262">
-        <rdfs:label>Nucleic acid property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0912"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0264">
-        <rdfs:label>Splice transcript prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2499"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict splicing alternatives or transcript isoforms from analysis of sequence data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0265">
-        <rdfs:label>Frameshift detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3202"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Frameshift error detection</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods include sequence alignment (if related sequences are available) and word-based sequence comparison.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0266 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0266">
-        <rdfs:label>Vector sequence detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0267 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0267">
-        <rdfs:label>Protein secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0172"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict secondary structure of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Secondary structure prediction (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0268 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0268">
-        <rdfs:label>Protein super-secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1277"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict super-secondary structure of protein sequence(s).</oboInOwl:hasDefinition>
-        <rdfs:comment>Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0269">
-        <rdfs:label>Transmembrane protein prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0270"/>
-        <oboInOwl:hasDefinition>Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0270 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0270">
-        <rdfs:label>Transmembrane protein analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0820"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions.</oboInOwl:hasDefinition>
-        <rdfs:comment>Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0271 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0271">
-        <rdfs:label>Structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict tertiary structure of a molecular (biopolymer) sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0272 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0272">
-        <rdfs:label>Residue interaction prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2506"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Methods usually involve multiple sequence alignment analysis.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0273 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0273">
-        <rdfs:label>Protein interaction raw data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2949"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0905"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0274 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0274">
-        <rdfs:label>Protein-protein interaction prediction (from protein sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1777"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2464"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0275 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0275">
-        <rdfs:label>Protein-protein interaction prediction (from protein structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2464"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0276 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0276">
-        <rdfs:label>Protein interaction network analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2497"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2949"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse a network of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0277">
-        <rdfs:label>Protein interaction network comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0276"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1778"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more networks of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0278">
-        <rdfs:label>RNA secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0279"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0279 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0279">
-        <rdfs:label>Nucleic acid folding prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2481"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1596"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid folding modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid folding</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0280">
-        <rdfs:label>Data retrieval (restriction enzyme annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Restriction enzyme information retrieval</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Retrieve information on restriction enzymes or restriction enzyme sites.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0281 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0281">
-        <rdfs:label>Genetic marker identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Identify genetic markers in DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0415"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0282 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0282">
-        <rdfs:label>Genetic mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2520"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1278"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>QTL mapping</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Linkage mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genetic map generation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genetic map construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Functional mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0283 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0283">
-        <rdfs:label>Linkage analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0927"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse genetic linkage.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0284">
-        <rdfs:label>Codon usage table generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2433"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate codon usage statistics and create a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Codon usage table construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0285">
-        <rdfs:label>Codon usage table comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2433"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more codon usage tables.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0286 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0286">
-        <rdfs:label>Codon usage analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0914"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>synon: Codon usage data analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>synon: Codon usage table analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0287 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0287">
-        <rdfs:label>Base position variability plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1263"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify and plot third base position variability in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0288">
-        <rdfs:label>Sequence word comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <oboInOwl:hasDefinition>Find exact character or word matches between molecular sequences without full sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0289">
-        <rdfs:label>Sequence distance matrix generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0870"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence distance matrix construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phylogenetic distance matrix generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0290 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0290">
-        <rdfs:label>Sequence redundancy removal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0291 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0291">
-        <rdfs:label>Sequence clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3432"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>The clusters may be output or used internally for some other purpose.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence cluster construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence cluster generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0292">
-        <rdfs:label>Sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align (identify equivalent sites within) molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment computation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0293">
-        <rdfs:label>Hybrid sequence alignment construction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Hybrid sequence alignment</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Hybrid sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0294 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0294">
-        <rdfs:label>Structure-based sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Structure-based sequence alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (structure-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure-based sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment (structure-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure-based sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align molecular sequences using sequence and structural information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0295">
-        <rdfs:label>Structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0886"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Align (superimpose) molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0296 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0296">
-        <rdfs:label>Sequence profile generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence profile construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0297">
-        <rdfs:label>3D profile generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0886"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structural profile generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate some type of structural (3D) profile or template from a structure or structure alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structural profile construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0298">
-        <rdfs:label>Profile-to-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0868"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>See also &apos;Sequence alignment comparison&apos;.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align sequence profiles (representing sequence alignments).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0299">
-        <rdfs:label>3D profile-to-3D profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0890"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>3D profile alignment (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>3D profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple 3D profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align structural (3D) profiles or templates (representing structures or structure alignments).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0300">
-        <rdfs:label>Sequence-to-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0869"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence-profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence-profile alignment generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align molecular sequence(s) to sequence profile(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence-profile alignment</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0301">
-        <rdfs:label>Sequence-to-3D-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0303"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0893"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence-3D profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence-3D profile alignment generation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence-3D profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0302">
-        <rdfs:label>Protein threading</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0303"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0893"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align molecular sequence to structure in 3D space (threading).</oboInOwl:hasDefinition>
-        <rdfs:comment>Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence-structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0303">
-        <rdfs:label>Protein fold recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0180"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein domain prediction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.</rdfs:comment>
-        <oboInOwl:hasDefinition>Recognize (predict and identify) known protein structural domains or folds in protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein fold prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0304">
-        <rdfs:label>Metadata retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2422"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2337"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Data retrieval (documentation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Data retrieval (metadata)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes documentation, general information and other metadata on entities such as databases, database entries and tools.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0305">
-        <rdfs:label>Literature search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0970"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3068"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Query the biomedical and informatics literature.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0306">
-        <rdfs:label>Text mining</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2048"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0972"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0218"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Text data mining</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process and analyse text (typically the biomedical and informatics literature) to extract information from it.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0307">
-        <rdfs:label>Virtual PCR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform in-silico (virtual) PCR.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0308">
-        <rdfs:label>PCR primer design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2419"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1240"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>PCR primer prediction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set.</rdfs:comment>
-        <oboInOwl:hasDefinition>Design or predict oligonucleotide primers for PCR and DNA amplification etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0309">
-        <rdfs:label>Microarray probe design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2419"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2717"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray probe prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0310">
-        <rdfs:label>Sequence assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3433"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0925"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.</rdfs:comment>
-        <oboInOwl:hasDefinition>Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0311">
-        <rdfs:label>Microarray data standardization and normalization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3435"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3117"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3117"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Standardize or normalize microarray data.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0312">
-        <rdfs:label>Sequencing-based expression profile data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) SAGE, MPSS or SBS experimental data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0313">
-        <rdfs:label>Gene expression profile clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0315"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3432"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0314">
-        <rdfs:label>Gene expression profiling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0928"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Expression profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene expression profile construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Functional profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a gene expression profile or pattern, for example from microarray data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression profile generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0315">
-        <rdfs:label>Gene expression profile comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare gene expression profiles or patterns.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0316">
-        <rdfs:label>Functional profiling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Interpret (in functional terms) and annotate gene expression data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0532"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0317 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0317">
-        <rdfs:label>EST and cDNA sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse EST or cDNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2403"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0318">
-        <rdfs:label>Structural genomics target selection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identify and select targets for protein structural determination.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods will typically navigate a graph of protein families of known structure.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2406"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0319 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0319">
-        <rdfs:label>Protein secondary structure assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign secondary structure from protein coordinate or experimental data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0320">
-        <rdfs:label>Protein structure assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign a protein tertiary structure (3D coordinates) from raw experimental data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0321">
-        <rdfs:label>Protein model validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1539"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0172"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2275"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Evaluate the quality or correctness a protein three-dimensional model.</oboInOwl:hasDefinition>
-        <rdfs:comment>Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF: CorrectedPDBasXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Protein structure validation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>WHATIF: UseFileDB</oboInOwl:hasDbXref>
-        <rdfs:comment>The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0322">
-        <rdfs:label>Molecular model refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2425"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <oboInOwl:hasNarrowSynonym>Protein model refinement</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>WHATIF: CorrectedPDBasXML</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0323">
-        <rdfs:label>Phylogenetic tree generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0324 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0324">
-        <rdfs:label>Phylogenetic tree analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2523"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0325">
-        <rdfs:label>Phylogenetic tree comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0326">
-        <rdfs:label>Phylogenetic tree editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Edit a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0327">
-        <rdfs:label>Phylogenetic footprinting / shadowing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0540"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0194"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>A phylogenetic &apos;shadow&apos; represents the additive differences between individual sequences. By masking or &apos;shadowing&apos; variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0328">
-        <rdfs:label>Protein folding simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2415"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simulate the folding of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0329">
-        <rdfs:label>Protein folding pathway prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <oboInOwl:hasDefinition>Predict the folding pathway(s) or non-native structural intermediates of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0330">
-        <rdfs:label>Protein SNP mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2277"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0331">
-        <rdfs:label>Protein modelling (mutation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Methods might predict silent or pathological mutations.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein mutation modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0332">
-        <rdfs:label>Immunogen design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Design molecules that elicit an immune response (immunogens).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0559"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0333 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0333">
-        <rdfs:label>Zinc finger prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0334">
-        <rdfs:label>Enzyme kinetics calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2024"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0821"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate Km, Vmax and derived data for an enzyme reaction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0335">
-        <rdfs:label>Formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Reformat a file of data (or equivalent entity in memory).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Format conversion</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File formatting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Reformatting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File reformatting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File format conversion</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0336">
-        <rdfs:label>Format validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <oboInOwl:hasDefinition>Test and validate the format and content of a data file.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>File format validation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0337">
-        <rdfs:label>Visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2968"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2968"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0092"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0338">
-        <rdfs:label>Sequence database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0857"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Search a sequence database by sequence comparison and retrieve similar sequences.
-
-sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This excludes direct retrieval methods (e.g. the dbfetch program).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0339">
-        <rdfs:label>Structure database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0081"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0340">
-        <rdfs:label>Protein secondary database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_3087"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0341">
-        <rdfs:label>Motif database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Screen a sequence against a motif or pattern database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0253"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0342">
-        <rdfs:label>Sequence profile database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a database of sequence profiles with a query sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0239"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0343">
-        <rdfs:label>Transmembrane protein database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Search a database of transmembrane proteins, for example for sequence or structural similarities.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2421"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0344">
-        <rdfs:label>Sequence retrieval (by code)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query a database and retrieve sequences with a given entry code or accession number.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0345">
-        <rdfs:label>Sequence retrieval (by keyword)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query a database and retrieve sequences containing a given keyword.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0346">
-        <rdfs:label>Sequence similarity search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <oboInOwl:hasNarrowSynonym>Structure database search (by sequence)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence database search (by sequence)</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences that are similar to a query sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0347 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0347">
-        <rdfs:label>Sequence database search (by motif or pattern)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0239"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0348">
-        <rdfs:label>Sequence database search (by amino acid composition)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences of a given amino acid composition.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0349">
-        <rdfs:label>Sequence database search (by property)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0350">
-        <rdfs:label>Sequence database search (by sequence using word-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (word-based methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0351 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0351">
-        <rdfs:label>Sequence database search (by sequence using profile-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (profile-based methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes tools based on PSI-BLAST.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0352">
-        <rdfs:label>Sequence database search (by sequence using local alignment-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (local alignment-based methods) </oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes tools based on the Smith-Waterman algorithm or FASTA.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0353">
-        <rdfs:label>Sequence database search (by sequence using global alignment-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes tools based on the Needleman and Wunsch algorithm.</rdfs:comment>
-        <oboInOwl:hasDefinition>Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (global alignment-based methods)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0354">
-        <rdfs:label>Sequence database search (by sequence for primer sequences)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <rdfs:comment>STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (primer sequences)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0355">
-        <rdfs:label>Sequence database search (by molecular weight)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein fingerprinting</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide mass fingerprinting</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0356">
-        <rdfs:label>Sequence database search (by isoelectric point)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search sequence(s) or a sequence database for sequences of a given isoelectric point.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0357">
-        <rdfs:label>Structure retrieval (by code)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query a tertiary structure database and retrieve entries with a given entry code or accession number.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0358">
-        <rdfs:label>Structure retrieval (by keyword)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Query a tertiary structure database and retrieve entries containing a given keyword.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0359">
-        <rdfs:label>Structure database search (by sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0360">
-        <rdfs:label>Structural similarity search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0339"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a database of molecular structure and retrieve structures that are similar to a query structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structure database search (by structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure retrieval by structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0361 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0361">
-        <rdfs:label>Sequence annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotate a molecular sequence record with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0362 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0362">
-        <rdfs:label>Genome annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0361"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotate a genome sequence with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0363 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0363">
-        <rdfs:label>Nucleic acid sequence reverse and complement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2513"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate the reverse and / or complement of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0364 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0364">
-        <rdfs:label>Random sequence generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <oboInOwl:hasDefinition>Generate a random sequence, for example, with a specific character composition.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0365">
-        <rdfs:label>Nucleic acid restriction digest</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2513"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1239"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate digest fragments for a nucleotide sequence containing restriction sites.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0366">
-        <rdfs:label>Protein sequence cleavage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2514"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1238"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0367 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0367">
-        <rdfs:label>Sequence mutation and randomization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0368">
-        <rdfs:label>Sequence masking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:hasDefinition>Mask characters in a molecular sequence (replacing those characters with a mask character).</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, SNPs or repeats in a DNA sequence might be masked.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0369">
-        <rdfs:label>Sequence cutting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:hasDefinition>Cut (remove) characters or a region from a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0370">
-        <rdfs:label>Restriction site creation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:hasDefinition>Create (or remove) restriction sites in sequences, for example using silent mutations.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0371">
-        <rdfs:label>DNA translation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0108"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Translate a DNA sequence into protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0372">
-        <rdfs:label>DNA transcription</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Transcribe a nucleotide sequence into mRNA sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0377 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0377">
-        <rdfs:label>Sequence composition calculation (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Calculate base frequency or word composition of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0236"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0378">
-        <rdfs:label>Sequence composition calculation (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Calculate amino acid frequency or word composition of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0236"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0379">
-        <rdfs:label>Repeat sequence detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0237"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0380 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0380">
-        <rdfs:label>Repeat sequence organisation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0237"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse repeat sequence organization such as periodicity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0383">
-        <rdfs:label>Protein hydropathy calculation (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2574"/>
-        <oboInOwl:hasDefinition>Analyse the hydrophobic, hydrophilic or charge properties of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0384">
-        <rdfs:label>Protein solvent accessibility calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1542"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate solvent accessible or buried surface areas in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0385">
-        <rdfs:label>Protein hydropathy cluster calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0383"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0393"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify clusters of hydrophobic or charged residues in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0386">
-        <rdfs:label>Protein dipole moment calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1545"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate whether a protein structure has an unusually large net charge (dipole moment).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0387">
-        <rdfs:label>Protein surface and interior calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0384"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0166"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0388">
-        <rdfs:label>Protein binding site prediction (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0245"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2575"/>
-        <oboInOwl:hasDefinition>Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ligand-binding and active site prediction (from structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Binding site prediction (from structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0389 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0389">
-        <rdfs:label>Protein-nucleic acid binding site analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2949"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse RNA or DNA-binding sites in protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0390">
-        <rdfs:label>Protein peeling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0246"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Decompose a structure into compact or globular fragments (protein peeling).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0391">
-        <rdfs:label>Protein distance matrix calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1546"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0392 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0392">
-        <rdfs:label>Protein contact map calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1547"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0393">
-        <rdfs:label>Protein residue cluster calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1548"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Cluster of contacting residues might be key structural residues.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate clusters of contacting residues in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0394 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0394">
-        <rdfs:label>Hydrogen bond calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1549"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDbXref>WHATIF:ShowHydrogenBonds</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:HasHydrogenBonds</oboInOwl:hasDbXref>
-        <rdfs:comment>The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ShowHydrogenBondsM</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identify potential hydrogen bonds between amino acids and other groups.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0395">
-        <rdfs:label>Residue non-canonical interaction detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate non-canonical atomic interactions in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0396">
-        <rdfs:label>Ramachandran plot calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1544"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate a Ramachandran plot of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0397">
-        <rdfs:label>Ramachandran plot validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1844"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1544"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1539"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Validate a Ramachandran plot of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0398">
-        <rdfs:label>Protein molecular weight calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1519"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate the molecular weight of a protein sequence or fragments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0399">
-        <rdfs:label>Protein extinction coefficient calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict extinction coefficients or optical density of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0400">
-        <rdfs:label>Protein pH-dependent property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate pH-dependent properties from pKa calculations of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0401">
-        <rdfs:label>Protein hydropathy calculation (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2574"/>
-        <oboInOwl:hasDefinition>Hydropathy calculation on a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0402">
-        <rdfs:label>Protein titration curve plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0400"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1527"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Plot a protein titration curve.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0403">
-        <rdfs:label>Protein isoelectric point calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0400"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1528"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate isoelectric point of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0404">
-        <rdfs:label>Protein hydrogen exchange rate calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0400"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1530"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Estimate hydrogen exchange rate of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0405">
-        <rdfs:label>Protein hydrophobic region calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <oboInOwl:hasDefinition>Calculate hydrophobic or hydrophilic / charged regions of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0406">
-        <rdfs:label>Protein aliphatic index calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1521"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0407">
-        <rdfs:label>Protein hydrophobic moment plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1520"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0408">
-        <rdfs:label>Protein globularity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1526"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0409">
-        <rdfs:label>Protein solubility prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1524"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict the solubility or atomic solvation energy of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0410">
-        <rdfs:label>Protein crystallizability prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1525"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict crystallizability of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0411">
-        <rdfs:label>Protein signal peptide detection (eukaryotes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0418"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0412">
-        <rdfs:label>Protein signal peptide detection (bacteria)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0418"/>
-        <oboInOwl:hasDefinition>Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0413">
-        <rdfs:label>MHC peptide immunogenicity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0252"/>
-        <oboInOwl:hasDefinition>Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0414">
-        <rdfs:label>Protein feature prediction (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Methods typically involve scanning for known motifs, patterns and regular expressions.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence feature detection (protein)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_3092"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0415">
-        <rdfs:label>Nucleic acid feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1276"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence feature detection (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods typically involve scanning for known motifs, patterns and regular expressions.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid feature recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid feature prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0416">
-        <rdfs:label>Epitope mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict antigenic determinant sites (epitopes) in protein sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Epitope mapping is commonly done during vaccine design.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0417">
-        <rdfs:label>Protein post-translation modification site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0601"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict post-translation modification sites in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0418 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0418">
-        <rdfs:label>Protein signal peptide detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2489"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0140"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Detect or predict signal peptides and signal peptide cleavage sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0419">
-        <rdfs:label>Protein binding site prediction (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2575"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <oboInOwl:hasExactSynonym>Binding site prediction (from sequence)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict catalytic residues, active sites or other ligand-binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ligand-binding and active site prediction (from sequence)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein binding site detection</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0420">
-        <rdfs:label>Protein-nucleic acid binding prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0419"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict RNA and DNA-binding binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0421">
-        <rdfs:label>Protein folding site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <oboInOwl:hasDefinition>Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0422">
-        <rdfs:label>Protein cleavage site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect or predict cleavage sites (enzymatic or chemical) in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0423">
-        <rdfs:label>Epitope mapping (MHC Class I)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict epitopes that bind to MHC class I molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0416"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0424">
-        <rdfs:label>Epitope mapping (MHC Class II)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Predict epitopes that bind to MHC class II molecules.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0416"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0425">
-        <rdfs:label>Whole gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2454"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0426">
-        <rdfs:label>Gene component prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2454"/>
-        <rdfs:comment>Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0427">
-        <rdfs:label>Transposon prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect or predict transposons, retrotransposons / retrotransposition signatures etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0428">
-        <rdfs:label>PolyA signal detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <oboInOwl:hasDefinition>Detect polyA signals in nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0429">
-        <rdfs:label>Quadruplex formation site detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Quadruplex structure prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Detect quadruplex-forming motifs in nucleotide sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0430">
-        <rdfs:label>CpG island and isochore detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>An isochore is long region (&gt; 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find CpG rich regions in a nucleotide sequence or isochores in genome sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>CpG island and isochores rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>CpG island and isochores detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0431 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0431">
-        <rdfs:label>Restriction site recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0432">
-        <rdfs:label>Nucleosome formation or exclusion sequence prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0433">
-        <rdfs:label>Splice site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify, predict or analyse splice sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods might require a pre-mRNA or genomic DNA sequence.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0434">
-        <rdfs:label>Integrated gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0425"/>
-        <oboInOwl:hasDefinition>Predict whole gene structure using a combination of multiple methods to achieve better predictions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0435">
-        <rdfs:label>Operon prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0425"/>
-        <oboInOwl:hasDefinition>Find operons (operators, promoters and genes) in bacteria genes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0436">
-        <rdfs:label>Coding region prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0426"/>
-        <oboInOwl:hasDefinition>Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ORF prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>ORF finding</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0437">
-        <rdfs:label>Selenocysteine insertion sequence (SECIS) prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict selenocysteine insertion sequence (SECIS) in a DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0438">
-        <rdfs:label>Regulatory element prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0749"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Translational regulatory element prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Transcription regulatory element prediction</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0439">
-        <rdfs:label>Translation initiation site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0436"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0108"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict translation initiation sites, possibly by searching a database of sites.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0440">
-        <rdfs:label>Promoter prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <oboInOwl:hasDefinition>Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods might recognize CG content, CpG islands, splice sites, polyA signals etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0441">
-        <rdfs:label>Transcription regulatory element prediction (DNA-cis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5&apos; promoter region of the gene, in an intron, or in the 3&apos; untranslated region. Cis-elements are often binding sites of one or more trans-acting factors.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0442">
-        <rdfs:label>Transcription regulatory element prediction (RNA-cis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:comment>Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene&apos;s activity.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0443">
-        <rdfs:label>Transcription regulatory element prediction (trans)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Trans-regulatory elements regulate genes distant from the gene from which they were transcribed.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Functional RNA identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0444">
-        <rdfs:label>Matrix/scaffold attachment site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:comment>MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0445">
-        <rdfs:label>Transcription factor binding site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0440"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict transcription factor binding sites in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0446">
-        <rdfs:label>Exonic splicing enhancer prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0440"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify or predict exonic splicing enhancers (ESE) in exons.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0447">
-        <rdfs:label>Sequence alignment validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:comment>Evaluation might be purely sequence-based or use structural information.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence alignment quality evaluation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Evaluate molecular sequence alignment accuracy.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0448">
-        <rdfs:label>Sequence alignment analysis (conservation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Residue conservation analysis</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0449 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0449">
-        <rdfs:label>Sequence alignment analysis (site correlation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3465"/>
-        <oboInOwl:hasDefinition>Analyse correlations between sites in a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0450 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0450">
-        <rdfs:label>Chimeric sequence detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles.</rdfs:comment>
-        <oboInOwl:hasDefinition>Detects chimeric sequences (chimeras) from a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (chimeric sequence detection)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0451">
-        <rdfs:label>Recombination detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (recombination detection)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment.</oboInOwl:hasDefinition>
-        <rdfs:comment>Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0452">
-        <rdfs:label>Indel detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (indel detection)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify insertion, deletion and duplication events from a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0453">
-        <rdfs:label>Nucleosome formation potential prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Predict nucleosome formation potential of DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0432"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0455 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0455">
-        <rdfs:label>Nucleic acid thermodynamic property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2985"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0456">
-        <rdfs:label>Nucleic acid melting profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1583"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA melting profile.</oboInOwl:hasDefinition>
-        <rdfs:comment>A melting profile is used to visualise and analyse partly melted DNA conformations.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0457">
-        <rdfs:label>Nucleic acid stitch profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1587"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA stitch profile.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0458 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0458">
-        <rdfs:label>Nucleic acid melting curve plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2958"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA melting curve.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0459">
-        <rdfs:label>Nucleic acid probability profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2959"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA probability profile.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0460">
-        <rdfs:label>Nucleic acid temperature profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2960"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA temperature profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0461">
-        <rdfs:label>Nucleic acid curvature calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0912"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate curvature and flexibility / stiffness of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes properties such as.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0463">
-        <rdfs:label>microRNA detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0443"/>
-        <oboInOwl:hasDefinition>Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0464">
-        <rdfs:label>tRNA gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0425"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or predict tRNA genes in genomic sequences (tRNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0465">
-        <rdfs:label>siRNA binding specificity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0467">
-        <rdfs:label>Protein secondary structure prediction (integrated)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <oboInOwl:hasDefinition>Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0468">
-        <rdfs:label>Protein secondary structure prediction (helices)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict helical secondary structure of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0469">
-        <rdfs:label>Protein secondary structure prediction (turns)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <oboInOwl:hasDefinition>Predict turn structure (for example beta hairpin turns) of protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0470">
-        <rdfs:label>Protein secondary structure prediction (coils)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0471">
-        <rdfs:label>Protein secondary structure prediction (disulfide bonds)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict cysteine bonding state and disulfide bond partners in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0472">
-        <rdfs:label>GPCR prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0269"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0473"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>G protein-coupled receptor (GPCR) prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict G protein-coupled receptors (GPCR).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0473">
-        <rdfs:label>GPCR analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0270"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0820"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse G-protein coupled receptor proteins (GPCRs).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>G protein-coupled receptor (GPCR) analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0474">
-        <rdfs:label>Protein structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0271"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0172"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict tertiary structure (backbone and side-chain conformation) of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0475">
-        <rdfs:label>Nucleic acid structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0271"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1459"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might identify thermodynamically stable or evolutionarily conserved structures.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict tertiary structure of DNA or RNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0476">
-        <rdfs:label>Ab initio structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0474"/>
-        <oboInOwl:hasDefinition>Predict tertiary structure of protein sequence(s) without homologs of known structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>de novo structure prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0477 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0477">
-        <rdfs:label>Protein modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0474"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2275"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Comparative modelling</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Build a three-dimensional protein model based on known (for example homologs) structures.</oboInOwl:hasDefinition>
-        <rdfs:comment>The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Homology modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Homology structure modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure comparative modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0478">
-        <rdfs:label>Molecular docking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0177"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1461"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2877"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Model the structure of a protein in complex with a small molecule or another macromolecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Docking simulation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein docking</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0479">
-        <rdfs:label>Protein modelling (backbone)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <oboInOwl:hasDefinition>Model protein backbone conformation.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods might require a preliminary C(alpha) trace.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0480">
-        <rdfs:label>Protein modelling (side chains)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might use a residue rotamer library.</rdfs:comment>
-        <oboInOwl:hasDefinition>Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0481">
-        <rdfs:label>Protein modelling (loops)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Model loop conformation in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0482">
-        <rdfs:label>Protein-ligand docking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1461"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Ligand-binding simulation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Virtual ligand screening</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0483">
-        <rdfs:label>Structured RNA prediction and optimisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3095"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1234"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Nucleic acid folding family identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA inverse folding</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0484 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0484">
-        <rdfs:label>SNP detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3202"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <oboInOwl:hasDefinition>Find single nucleotide polymorphisms (SNPs) between sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Single nucleotide polymorphism detection</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0485">
-        <rdfs:label>Radiation Hybrid Mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2870"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0486">
-        <rdfs:label>Functional mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).</rdfs:comment>
-        <oboInOwl:hasDefinition>Map the genetic architecture of dynamic complex traits.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0282"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0487">
-        <rdfs:label>Haplotype mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0282"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0283"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Haplotype map generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Haplotype inference</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual&apos;s haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Haplotype reconstruction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0488">
-        <rdfs:label>Linkage disequilibrium calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0283"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0927"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0489">
-        <rdfs:label>Genetic code prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict genetic code from analysis of codon usage data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0490">
-        <rdfs:label>Dotplot plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0288"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0565"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0862"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Draw a dotplot of sequence similarities identified from word-matching or character comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0491">
-        <rdfs:label>Pairwise sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1381"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasDefinition>Align exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0492">
-        <rdfs:label>Multiple sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0493 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0493">
-        <rdfs:label>Pairwise sequence alignment generation (local)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Local pairwise sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Locally align exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment (local)</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Local alignment methods identify regions of local similarity.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment construction (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0491"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0494 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0494">
-        <rdfs:label>Pairwise sequence alignment generation (global)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Global pairwise sequence alignment construction</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Globally align exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Global alignment methods identify similarity across the entire length of the sequences.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0491"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0496"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0495">
-        <rdfs:label>Local sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Local multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Local alignment methods identify regions of local similarity.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Locally align two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0496">
-        <rdfs:label>Global sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Global multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (global)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Globally align two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (global)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Global alignment methods identify similarity across the entire length of the sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0497">
-        <rdfs:label>Constrained sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences with user-defined constraints.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Constrained multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0498">
-        <rdfs:label>Consensus-based sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Consensus multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment (consensus)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences using multiple methods to achieve higher quality.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0499">
-        <rdfs:label>Tree-based sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is supposed to give a more biologically meaningful alignment than standard alignments.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree-based multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0500">
-        <rdfs:label>Secondary structure alignment generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Align molecular secondary structure (represented as a 1D string).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2928"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0501">
-        <rdfs:label>Protein secondary structure alignment generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2488"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0878"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Protein secondary structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align protein secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein secondary structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0502">
-        <rdfs:label>RNA secondary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0881"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>RNA secondary structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA secondary structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align RNA secondary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA secondary structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment (RNA)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0503">
-        <rdfs:label>Pairwise structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align (superimpose) exactly two molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0504">
-        <rdfs:label>Multiple structure alignment construction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Align (superimpose) two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that use an existing alignment.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0505">
-        <rdfs:label>Structure alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align protein tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0506">
-        <rdfs:label>Structure alignment (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Align RNA tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0507">
-        <rdfs:label>Pairwise structure alignment generation (local)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Locally align (superimpose) exactly two molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment (local)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Local alignment methods identify regions of local similarity, common substructures etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment construction (local)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Local pairwise structure alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0509"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0508">
-        <rdfs:label>Pairwise structure alignment generation (global)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Global pairwise structure alignment construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Global alignment methods identify similarity across the entire structures.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Globally align (superimpose) exactly two molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0510"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0509">
-        <rdfs:label>Local structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:hasExactSynonym>Local multiple structure alignment construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Local alignment methods identify regions of local similarity, common substructures etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Structure alignment construction (local)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Locally align (superimpose) two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment construction (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure alignment generation (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0510 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0510">
-        <rdfs:label>Global structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:hasExactSynonym>Structure alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure alignment generation (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment construction (global)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Global alignment methods identify similarity across the entire structures.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Global multiple structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Globally align (superimpose) two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0511">
-        <rdfs:label>Profile-to-profile alignment (pairwise)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0298"/>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (pairwise profile)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise sequence profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment construction (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment (pairwise)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align exactly two molecular profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment generation (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0512">
-        <rdfs:label>Sequence alignment generation (multiple profile)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Align two or more molecular profiles.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment generation (multiple)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment construction (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0513 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0513">
-        <rdfs:label>3D profile-to-3D profile alignment (pairwise)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0299"/>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise structural (3D) profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural (3D) profile alignment (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align exactly two molecular Structural (3D) profiles.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structural profile alignment generation (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0514">
-        <rdfs:label>Structural profile alignment generation (multiple)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align two or more molecular 3D profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Multiple structural (3D) profile alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structural (3D) profile alignment (multiple)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0299"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0515">
-        <rdfs:label>Data retrieval (tool metadata)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Data retrieval (tool annotation)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Tool information retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0304"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0516">
-        <rdfs:label>Data retrieval (database metadata)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Data retrieval (database annotation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database information retrieval</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0304"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0517 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0517">
-        <rdfs:label>PCR primer design (for large scale sequencing)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict primers for large scale sequencing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0518 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0518">
-        <rdfs:label>PCR primer design (for genotyping polymorphisms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0519">
-        <rdfs:label>PCR primer design (for gene transcription profiling)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict primers for gene transcription profiling.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0520">
-        <rdfs:label>PCR primer design (for conserved primers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <oboInOwl:hasDefinition>Predict primers that are conserved across multiple genomes or species.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0521">
-        <rdfs:label>PCR primer design (based on gene structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict primers based on gene structure, promoters, exon-exon junctions etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0522">
-        <rdfs:label>PCR primer design (for methylation PCRs)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict primers for methylation PCRs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0523">
-        <rdfs:label>Sequence assembly (mapping assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0524">
-        <rdfs:label>Sequence assembly (de-novo assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Sequence assembly by combining fragments without the aid of a reference sequence or genome.</oboInOwl:hasDefinition>
-        <rdfs:comment>De-novo assemblers are much slower and more memory intensive than mapping assemblers.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0525">
-        <rdfs:label>Sequence assembly (genome assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Sequence assembly capable on a very large scale such as assembly of whole genomes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0526">
-        <rdfs:label>Sequence assembly (EST assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence assembly for EST sequences (transcribed mRNA).</oboInOwl:hasDefinition>
-        <rdfs:comment>Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0527">
-        <rdfs:label>Tag mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2520"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0936"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Tag to gene assignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0528">
-        <rdfs:label>SAGE data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Serial analysis of gene expression data processing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) serial analysis of gene expression (SAGE) data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0529">
-        <rdfs:label>MPSS data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) massively parallel signature sequencing (MPSS) data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Massively parallel signature sequencing data processing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0530">
-        <rdfs:label>SBS data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequencing by synthesis data processing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) sequencing by synthesis (SBS) data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0531">
-        <rdfs:label>Heat map generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1636"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Heat map construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a heat map of gene expression from microarray data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0532 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0532">
-        <rdfs:label>Gene expression profile analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Functional profiling</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse one or more gene expression profiles, typically to interpret them in functional terms.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0533">
-        <rdfs:label>Gene expression profile pathway mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2497"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0534">
-        <rdfs:label>Protein secondary structure assignment (from coordinate data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0319"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign secondary structure from protein coordinate data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0535 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0535">
-        <rdfs:label>Protein secondary structure assignment (from CD data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0319"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0939"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Assign secondary structure from circular dichroism (CD) spectroscopic data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0536">
-        <rdfs:label>Protein structure assignment (from X-ray crystallographic data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0320"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0537">
-        <rdfs:label>Protein structure assignment (from NMR data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0320"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0538 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0538">
-        <rdfs:label>Phylogenetic tree generation (data centric)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (data centric)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree from a specific type of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0539">
-        <rdfs:label>Phylogenetic tree generation (method centric)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (method centric)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree using a specific method.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0540">
-        <rdfs:label>Phylogenetic tree generation (from molecular sequences)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (from molecular sequences)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0541 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0541">
-        <rdfs:label>Phylogenetic tree generation (from continuous quantitative characters)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1426"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (from continuous quantitative characters)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from continuous quantitative character data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0542">
-        <rdfs:label>Phylogenetic tree generation (from gene frequencies)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2873"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (from gene frequencies)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from gene frequency data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0543">
-        <rdfs:label>Phylogenetic tree construction (from polymorphism data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree generation (from polymorphism data)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0544 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0544">
-        <rdfs:label>Phylogenetic species tree construction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0540"/>
-        <oboInOwl:hasDefinition>Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic species tree generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0545">
-        <rdfs:label>Phylogenetic tree generation (parsimony methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (parsimony methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes evolutionary parsimony (invariants) methods.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0546">
-        <rdfs:label>Phylogenetic tree generation (minimum distance methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <rdfs:comment>This includes neighbor joining (NJ) clustering method.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (minimum distance methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0547">
-        <rdfs:label>Phylogenetic tree generation (maximum likelihood and Bayesian methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (maximum likelihood and Bayesian methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution.</oboInOwl:hasDefinition>
-        <rdfs:comment>Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0548">
-        <rdfs:label>Phylogenetic tree generation (quartet methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (quartet methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0549">
-        <rdfs:label>Phylogenetic tree generation (AI methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (AI methods)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0550">
-        <rdfs:label>DNA substitution modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1439"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (phylogenetic modelling)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify a plausible model of DNA substitution that explains a DNA sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0551">
-        <rdfs:label>Phylogenetic tree analysis (shape)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree topology analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse the shape (topology) of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0552">
-        <rdfs:label>Phylogenetic tree bootstrapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <oboInOwl:hasDefinition>Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0553">
-        <rdfs:label>Phylogenetic tree analysis (gene family prediction)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0194"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict families of genes and gene function based on their position in a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0554">
-        <rdfs:label>Phylogenetic tree analysis (natural selection)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0555">
-        <rdfs:label>Phylogenetic tree generation (consensus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0325"/>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees to produce a consensus tree.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods typically test for topological similarity between trees using for example a congruence index.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0556">
-        <rdfs:label>Phylogenetic sub/super tree detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0325"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees to detect subtrees or supertrees.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0557">
-        <rdfs:label>Phylogenetic tree distances calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0325"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1442"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees to calculate distances between trees.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0558">
-        <rdfs:label>Phylogenetic tree annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Annotate a phylogenetic tree with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0559">
-        <rdfs:label>Immunogenicity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0252"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide immunogen prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict and optimise peptide ligands that elicit an immunological response.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0560">
-        <rdfs:label>DNA vaccine design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2430"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3095"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict or optimise DNA to elicit (via DNA vaccination) an immunological response.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0561">
-        <rdfs:label>Sequence formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Reformat (a file or other report of) molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence file format conversion</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0562 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0562">
-        <rdfs:label>Sequence alignment formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Reformat (a file or other report of) molecular sequence alignment(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0563">
-        <rdfs:label>Codon usage table formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2433"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Reformat a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0564">
-        <rdfs:label>Sequence visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2969"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render a molecular sequence, possibly with sequence features or properties shown.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0565">
-        <rdfs:label>Sequence alignment visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1711"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise, format or print a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0566">
-        <rdfs:label>Sequence cluster visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence cluster rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render sequence clusters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0567">
-        <rdfs:label>Phylogenetic tree visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Render or visualise a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0568">
-        <rdfs:label>RNA secondary structure visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>RNA secondary structure rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise RNA secondary structure, knots, pseudoknots etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0569">
-        <rdfs:label>Protein secondary structure rendering</rdfs:label>
-        <rdfs:label>Protein secondary structure visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Render and visualise protein secondary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0570">
-        <rdfs:label>Structure visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1710"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structure rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0571">
-        <rdfs:label>Microarray data rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3117"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise microarray data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0572">
-        <rdfs:label>Protein interaction network rendering</rdfs:label>
-        <rdfs:label>Protein interaction network visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3083"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym></oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify and analyse networks of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0573">
-        <rdfs:label>Map drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>DNA map drawing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Map rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Draw or visualise a DNA map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0574">
-        <rdfs:label>Sequence motif rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Render a sequence with motifs.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0575">
-        <rdfs:label>Restriction map drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0431"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0573"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1289"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Draw or visualise restriction maps in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0577 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0577">
-        <rdfs:label>DNA linear map rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Draw a linear maps of DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0573"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0578">
-        <rdfs:label>Plasmid map drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0573"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasBroadSynonym>DNA circular map rendering</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Draw a circular maps of DNA, for example a plasmid map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0579">
-        <rdfs:label>Operon drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0573"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise operon structure etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Operon rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1768 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1768">
-        <rdfs:label>Nucleic acid folding family identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identify folding families of related RNAs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0483"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1769 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1769">
-        <rdfs:label>Nucleic acid folding energy calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0279"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1774 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1774">
-        <rdfs:label>Annotation retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations.</rdfs:comment>
-        <oboInOwl:hasDefinition>Retrieve existing annotation (or documentation), typically annotation on a database entity.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1777 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1777">
-        <rdfs:label>Protein function prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2414"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict general functional properties of a protein.</oboInOwl:hasDefinition>
-        <rdfs:comment>For functional properties that can be mapped to a sequence, use &apos;Sequence feature detection (protein)&apos; instead.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1778 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1778">
-        <rdfs:label>Protein function comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2414"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare the functional properties of two or more proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1780 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1780">
-        <rdfs:label>Sequence submission</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Submit a molecular sequence to a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_3431"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1781 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1781">
-        <rdfs:label>Gene regulatory network analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2497"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2846"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse a known network of gene regulation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_1781"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1812 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1812">
-        <rdfs:label>Loading</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0842"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Data loading</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>WHATIF:UploadPDB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Prepare or load a user-specified data file so that it is available for use.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1813 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1813">
-        <rdfs:label>Sequence retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Data retrieval (sequences)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1814 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1814">
-        <rdfs:label>Structure retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>WHATIF:EchoPDB</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:DownloadPDB</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes direct retrieval methods but not those that perform calculations on the sequence or structure.</rdfs:comment>
-        <oboInOwl:hasDefinition>Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1816 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1816">
-        <rdfs:label>Surface rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0570"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2462"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:GetSurfaceDots</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate the positions of dots that are homogeneously distributed over the surface of a molecule.</oboInOwl:hasDefinition>
-        <rdfs:comment>A dot has three coordinates (x,y,z) and (typically) a color.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1817 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1817">
-        <rdfs:label>Protein atom surface calculation (accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilitySolventPlus</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilitySolvent</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible surface&apos;) for each atom in a structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>Waters are not considered.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1818 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1818">
-        <rdfs:label>Protein atom surface calculation (accessible molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible molecular surface&apos;) for each atom in a structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>Waters are not considered.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilityMolecular</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilityMolecularPlus</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1819 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1819">
-        <rdfs:label>Protein residue surface calculation (accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilitySolvent</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible surface&apos;) for each residue in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1820 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1820">
-        <rdfs:label>Protein residue surface calculation (vacuum accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;vacuum accessible surface&apos;) for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilityVacuum</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1821 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1821">
-        <rdfs:label>Protein residue surface calculation (accessible molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible molecular surface&apos;) for each residue in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilityMolecular</oboInOwl:hasDbXref>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1822 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1822">
-        <rdfs:label>Protein residue surface calculation (vacuum molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;vacuum molecular surface&apos;) for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilityVacuumMolecular</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1823 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1823">
-        <rdfs:label>Protein surface calculation (accessible molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2462"/>
-        <oboInOwl:hasDbXref>WHATIF:TotAccessibilityMolecular</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible molecular surface&apos;) for a structure as a whole.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1824 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1824">
-        <rdfs:label>Protein surface calculation (accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2462"/>
-        <oboInOwl:hasDbXref>WHATIF:TotAccessibilitySolvent</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible surface&apos;) for a structure as a whole.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1825 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1825">
-        <rdfs:label>Backbone torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ResidueTorsionsBB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate for each residue in a protein structure all its backbone torsion angles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1826 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1826">
-        <rdfs:label>Full torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate for each residue in a protein structure all its torsion angles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueTorsions</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1827 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1827">
-        <rdfs:label>Cysteine torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate for each cysteine (bridge) all its torsion angles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:CysteineTorsions</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1828 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1828">
-        <rdfs:label>Tau angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowTauAngle</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Tau is the backbone angle N-Calpha-C (angle over the C-alpha).</rdfs:comment>
-        <oboInOwl:hasDefinition>For each amino acid in a protein structure calculate the backbone angle tau.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1829 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1829">
-        <rdfs:label>Cysteine bridge detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1850"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowCysteineBridge</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Detect cysteine bridges (from coordinate data) in a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1830 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1830">
-        <rdfs:label>Free cysteine detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1850"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal.</rdfs:comment>
-        <oboInOwl:hasDefinition>Detect free cysteines in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ShowCysteineFree</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1831 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1831">
-        <rdfs:label>Metal-bound cysteine detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1850"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ShowCysteineMetal</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Detect cysteines that are bound to metal in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1832 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1832">
-        <rdfs:label>Residue contact calculation (residue-nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0245"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0389"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ShowProteiNucleicContacts</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate protein residue contacts with nucleic acids in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:HasNucleicContacts</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1834 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1834">
-        <rdfs:label>Residue contact calculation (residue-metal)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0388"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <oboInOwl:hasDbXref>WHATIF:HasMetalContacts</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate protein residue contacts with metal in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:HasMetalContactsPlus</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1835 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1835">
-        <rdfs:label>Residue contact calculation (residue-negative ion)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <oboInOwl:hasDefinition>Calculate ion contacts in a structure (all ions for all side chain atoms).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:HasNegativeIonContactsPlus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:HasNegativeIonContacts</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1836 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1836">
-        <rdfs:label>Residue bump detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0395"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowBumps</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect &apos;bumps&apos; between residues in a structure, i.e. those with pairs of atoms whose Van der Waals&apos; radii interpenetrate more than a defined distance.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1837 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1837">
-        <rdfs:label>Residue symmetry contact calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <oboInOwl:hasDefinition>Calculate the number of symmetry contacts made by residues in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:SymmetryContact</oboInOwl:hasDbXref>
-        <rdfs:comment>A symmetry contact is a contact between two atoms in different asymmetric unit.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1838 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1838">
-        <rdfs:label>Residue contact calculation (residue-ligand)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0388"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate contacts between residues and ligands in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ShowDrugContactsShort</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLigandContacts</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowDrugContacts</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1839 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1839">
-        <rdfs:label>Salt bridge calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <rdfs:comment>Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF:HasSaltBridgePlus</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowSaltBridges</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:HasSaltBridge</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowSaltBridgesH</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate (and possibly score) salt bridges in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1841 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1841">
-        <rdfs:label>Rotamer likelihood prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0480"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers500</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers800</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers600</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers900</oboInOwl:hasDbXref>
-        <rdfs:comment>Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers700</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers400</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers300</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers200</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers100</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1842 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1842">
-        <rdfs:label>Proline mutation value calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0331"/>
-        <oboInOwl:hasDefinition>Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ProlineMutationValue</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1843 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1843">
-        <rdfs:label>Residue packing validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0395"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify poorly packed residues in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: PackingQuality</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1844 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1844">
-        <rdfs:label>Dihedral angle validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <oboInOwl:hasDbXref>WHATIF: ImproperQualitySum</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identify for each residue in a protein structure any improper dihedral (phi/psi) angles.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: ImproperQualityMax</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1845 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1845">
-        <rdfs:label>PDB file sequence retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Extract a molecular sequence from a PDB file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDbXref>WHATIF: PDB_sequence</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0344"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1846 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1846">
-        <rdfs:label>HET group detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1838"/>
-        <oboInOwl:hasDefinition>Identify HET groups in PDB files.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: HETGroupNames</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1847 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1847">
-        <rdfs:label>DSSP secondary structure assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Determine for residue the DSSP determined secondary structure in three-state (HSC).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: ResidueDSSP</oboInOwl:hasDbXref>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0534"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1848 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1848">
-        <rdfs:label>Structure formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <oboInOwl:hasDefinition>Reformat (a file or other report of) tertiary structure data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: PDBasXML</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1850 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1850">
-        <rdfs:label>Protein cysteine and disulfide bond assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0534"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Assign cysteine bonding state and disulfide bond partners in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1913 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1913">
-        <rdfs:label>Residue validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <oboInOwl:hasDefinition>Identify poor quality amino acid positions in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: UseResidueDB</oboInOwl:hasDbXref>
-        <rdfs:comment>The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1914 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1914">
-        <rdfs:label>Structure retrieval (water)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDbXref>WHATIF:MovedWaterPDB</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query a tertiary structure database and retrieve water molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2008 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2008">
-        <rdfs:label>siRNA duplex prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict siRNA duplexes in RNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2089 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2089">
-        <rdfs:label>Sequence alignment refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2425"/>
-        <oboInOwl:hasDefinition>Refine an existing sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2120 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2120">
-        <rdfs:label>Listfile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2121 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2121">
-        <rdfs:label>Sequence file editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2122">
-        <rdfs:label>Sequence alignment file processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2123">
-        <rdfs:label>Small molecule data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) physicochemical property data for small molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2222 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2222">
-        <rdfs:label>Data retrieval (ontology annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Ontology information retrieval</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search and retrieve documentation on a bioinformatics ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2224 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2224">
-        <rdfs:label>Data retrieval (ontology concept)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query an ontology and retrieve concepts or relations.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2233">
-        <rdfs:label>Representative sequence identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2234 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2234">
-        <rdfs:label>Structure file processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Perform basic (non-analytical) operations on a file of molecular tertiary structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2237">
-        <rdfs:label>Data retrieval (sequence profile)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query a profile data resource and retrieve one or more profile(s) and / or associated annotation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This includes direct retrieval methods that retrieve a profile by, e.g. the profile name.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2238">
-        <rdfs:label>Statistical calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <oboInOwl:hasExactSynonym>Statistical analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Perform a statistical data operation of some type, e.g. calibration or validation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2239">
-        <rdfs:label>3D-1D scoring matrix generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1499"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>3D-1D scoring matrix construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2241">
-        <rdfs:label>Transmembrane protein visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0270"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0569"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2992"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise transmembrane proteins, typically the transmembrane regions within a sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Transmembrane protein rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2246">
-        <rdfs:label>Demonstration</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An operation performing purely illustrative (pedagogical) purposes.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2264">
-        <rdfs:label>Data retrieval (pathway or network)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query a biological pathways database and retrieve annotation on one or more pathways.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2265">
-        <rdfs:label>Data retrieval (identifier)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Query a database and retrieve one or more data identifiers.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2284">
-        <rdfs:label>Nucleic acid density plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a density plot (of base composition) for a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2403">
-        <rdfs:label>Sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse one or more known molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence analysis (general)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2404">
-        <rdfs:label>Sequence motif processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular sequence motifs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0239"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2405">
-        <rdfs:label>Protein interaction data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) protein interaction data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2406">
-        <rdfs:label>Protein structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structure analysis (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse protein tertiary structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2407">
-        <rdfs:label>Annotation processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2408">
-        <rdfs:label>Sequence feature analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Analyse features in molecular sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0253"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2409">
-        <rdfs:label>Utility operation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0220"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Basic (non-analytical) operations of some data, either a file or equivalent entity in memory.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>File processing</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Report handling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File handling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data file processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2410">
-        <rdfs:label>Gene expression analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse gene expression and regulation data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2411">
-        <rdfs:label>Structural profile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>3D profile processing</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2952"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2412">
-        <rdfs:label>Data index processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Database index processing</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) an index of (typically a file of) biological data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0227"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2413">
-        <rdfs:label>Sequence profile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) some type of sequence profile.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2463"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2414">
-        <rdfs:label>Protein function analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2415">
-        <rdfs:label>Protein folding analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1537"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein folding modelling</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2416">
-        <rdfs:label>Protein secondary structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2956"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse known protein secondary structure data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Secondary structure analysis (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2417">
-        <rdfs:label>Physicochemical property data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) data on the physicochemical property of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2419">
-        <rdfs:label>Primer and probe design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3095"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Primer and probe prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict oligonucleotide primers or probes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2420">
-        <rdfs:label>Operation (typed)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <oboInOwl:hasExactSynonym>Computation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Calculation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) data of a specific type, for example applying analytical methods.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2421">
-        <rdfs:label>Database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0224"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database.</rdfs:comment>
-        <oboInOwl:hasDefinition>Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2422">
-        <rdfs:label>Data retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0224"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0842"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasBroadSynonym>Information retrieval</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2423">
-        <rdfs:label>Prediction and recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise, detect or identify some properties of a biomolecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Detection</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2424">
-        <rdfs:label>Comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more things to identify similarities.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2425">
-        <rdfs:label>Optimisation and refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Refine or optimise some data model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2426">
-        <rdfs:label>Modelling and simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2275"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Model or simulate some biological entity or system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2427">
-        <rdfs:label>Data handling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Perform basic operations on some data or a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2428">
-        <rdfs:label>Validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Validation and standardisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Validate some data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2429">
-        <rdfs:label>Mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <oboInOwl:hasDefinition>Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2430">
-        <rdfs:label>Design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Design a biological entity (typically a molecular sequence or structure) with specific properties.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2432">
-        <rdfs:label>Microarray data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) microarray data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2433">
-        <rdfs:label>Codon usage table processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2434">
-        <rdfs:label>Data retrieval (codon usage table)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve a codon usage table and / or associated annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2435">
-        <rdfs:label>Gene expression profile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) a gene expression profile.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2436">
-        <rdfs:label>Functional enrichment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression profile annotation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The Gene Ontology (GO) is invariably used, the input is a set of Gene IDs and the output of the analysis is typically a ranked list of GO terms, each associated with a p-value.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse a set of genes (genes corresponding to an expression profile, or any other set) with respect to concepts from an ontology of gene functions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>GO term enrichment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2437">
-        <rdfs:label>Gene regulatory network prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2846"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict a network of gene regulation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2438">
-        <rdfs:label>Pathway or network processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Generate, analyse or handle a biological pathway or network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2439">
-        <rdfs:label>RNA secondary structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2481"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) RNA secondary structure data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2440">
-        <rdfs:label>Structure processing (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) RNA tertiary structure data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2519"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2441">
-        <rdfs:label>RNA structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0475"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1465"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict RNA tertiary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2442">
-        <rdfs:label>DNA structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0475"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1464"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict DNA tertiary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2443">
-        <rdfs:label>Phylogenetic tree processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2444">
-        <rdfs:label>Protein secondary structure processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) protein secondary structure data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2416"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2445">
-        <rdfs:label>Protein interaction network processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a network of protein interactions.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2446">
-        <rdfs:label>Sequence processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence processing (general)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) one or more molecular sequences and associated annotation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2403"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2447">
-        <rdfs:label>Sequence processing (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a protein sequence and associated annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2446"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2448">
-        <rdfs:label>Sequence processing (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a nucleotide sequence and associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2446"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2451">
-        <rdfs:label>Sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare two or more molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2452">
-        <rdfs:label>Sequence cluster processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a sequence cluster.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0291"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2453">
-        <rdfs:label>Feature table processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a sequence feature table.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2446"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2454 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2454">
-        <rdfs:label>Gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Gene and gene component prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect, predict and identify genes or components of genes in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene finding</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2456">
-        <rdfs:label>GPCR classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0473"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2995"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>G protein-coupled receptor (GPCR) classification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Classify G-protein coupled receptors (GPCRs) into families and subfamilies.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2457">
-        <rdfs:label>GPCR coupling selectivity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0473"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict G-protein coupled receptor (GPCR) coupling selectivity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2459">
-        <rdfs:label>Structure processing (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a protein tertiary structure.</oboInOwl:hasDefinition>
-        <rdfs:comment rdf:resource="http://edamontology.org/operation_2406"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2460">
-        <rdfs:label>Protein atom surface calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0387"/>
-        <rdfs:comment>Waters are not considered.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility for each atom in a structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2461">
-        <rdfs:label>Protein residue surface calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0387"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility for each residue in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2462 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2462">
-        <rdfs:label>Protein surface calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0387"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility of a structure as a whole.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2463">
-        <rdfs:label>Sequence alignment processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2464">
-        <rdfs:label>Protein-protein interaction prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or predict protein-protein interactions, interfaces, binding sites etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2465">
-        <rdfs:label>Structure processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular tertiary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2480"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2466 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2466">
-        <rdfs:label>Map annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Annotate a DNA map of some type with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0362"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2467">
-        <rdfs:label>Data retrieval (protein annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve information on a protein.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Protein information retrieval</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2468">
-        <rdfs:label>Data retrieval (phylogenetic tree)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Retrieve a phylogenetic tree from a data resource.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2469">
-        <rdfs:label>Data retrieval (protein interaction annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve information on a protein interaction.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2470">
-        <rdfs:label>Data retrieval (protein family annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein family information retrieval</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Retrieve information on a protein family.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2471">
-        <rdfs:label>Data retrieval (RNA family annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Retrieve information on an RNA family.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA family information retrieval</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2472">
-        <rdfs:label>Data retrieval (gene annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene information retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Retrieve information on a specific gene.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2473">
-        <rdfs:label>Data retrieval (genotype and phenotype annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve information on a specific genotype or phenotype.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genotype and phenotype information retrieval</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2474">
-        <rdfs:label>Protein architecture comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0247"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2488"/>
-        <oboInOwl:hasDefinition>Compare the architecture of two or more protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2475">
-        <rdfs:label>Protein architecture recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0247"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2996"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify the architecture of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2476">
-        <rdfs:label>Molecular dynamics simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0176"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2478">
-        <rdfs:label>Nucleic acid sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence analysis (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2479">
-        <rdfs:label>Protein sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2976"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a protein sequence (using methods that are only applicable to protein sequences).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence analysis (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2480">
-        <rdfs:label>Structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0081"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse known molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2481">
-        <rdfs:label>Nucleic acid structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1459"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse nucleic acid tertiary structural data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2482">
-        <rdfs:label>Secondary structure processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular secondary structure.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2465"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2483">
-        <rdfs:label>Structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2485">
-        <rdfs:label>Helical wheel drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0569"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2162"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Helical wheel rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Render a helical wheel representation of protein secondary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2486">
-        <rdfs:label>Topology diagram drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0569"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2992"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Topology diagram rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Render a topology diagram of protein secondary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2487">
-        <rdfs:label>Protein structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure comparison (protein)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might identify structural neighbors, find structural similarities or define a structural core.</rdfs:comment>
-        <oboInOwl:hasDefinition>Compare protein tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2488">
-        <rdfs:label>Protein secondary structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2416"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2931"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <oboInOwl:hasDefinition>Compare protein secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Secondary structure comparison (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein secondary structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2489">
-        <rdfs:label>Protein subcellular localization prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1777"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0140"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict the subcellular localization of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein targeting prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2490">
-        <rdfs:label>Residue contact calculation (residue-residue)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate contacts between residues in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2491">
-        <rdfs:label>Hydrogen bond calculation (inter-residue)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0394"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <oboInOwl:hasDefinition>Identify potential hydrogen bonds between amino acid residues.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2492">
-        <rdfs:label>Protein interaction prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict the interactions of proteins with other molecules.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2493 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2493">
-        <rdfs:label>Codon usage data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) codon usage data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0286"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2495">
-        <rdfs:label>Gene expression data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider>Gene expression profile analysis</oboInOwl:consider>
-        <oboInOwl:hasExactSynonym>Gene expression (microarray) data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene expression data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2496">
-        <rdfs:label>Gene regulatory network processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a network of gene regulation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2497">
-        <rdfs:label>Pathway or network analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a known biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Network analysis</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2498">
-        <rdfs:label>Sequencing-based expression profile data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2499">
-        <rdfs:label>Splicing model analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Splicing analysis</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2500">
-        <rdfs:label>Microarray raw data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Analyse raw microarray data.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2501">
-        <rdfs:label>Nucleic acid analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Process (read and / or write) nucleic acid sequence or structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid data processing</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2502">
-        <rdfs:label>Protein analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0078"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) protein sequence or structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2503">
-        <rdfs:label>Sequence data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular sequence data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2504">
-        <rdfs:label>Structural data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2465"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2505">
-        <rdfs:label>Text processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) text.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0306"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2506">
-        <rdfs:label>Protein sequence alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1384"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a protein sequence alignment, typically to detect features or make predictions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2507">
-        <rdfs:label>Nucleic acid sequence alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2501"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1383"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse a protein sequence alignment, typically to detect features or make predictions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2508">
-        <rdfs:label>Nucleic acid sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <oboInOwl:hasExactSynonym>Sequence comparison (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Compare two or more nucleic acid sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2509">
-        <rdfs:label>Protein sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence comparison (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Compare two or more protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2510 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2510">
-        <rdfs:label>DNA back-translation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0108"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Back-translate a protein sequence into DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2511">
-        <rdfs:label>Sequence editing (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Edit or change a nucleic acid sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2512">
-        <rdfs:label>Sequence editing (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Edit or change a protein sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2513 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2513">
-        <rdfs:label>Sequence generation (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <oboInOwl:hasDefinition>Generate a nucleic acid sequence by some means.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2514">
-        <rdfs:label>Sequence generation (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <oboInOwl:hasDefinition>Generate a protein sequence by some means.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2515">
-        <rdfs:label>Nucleic acid sequence visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Visualise, format or render a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.</rdfs:comment>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2516">
-        <rdfs:label>Protein sequence visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render a protein sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <rdfs:comment>Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2518 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2518">
-        <rdfs:label>Nucleic acid structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2481"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <oboInOwl:hasDefinition>Compare nucleic acid tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure comparison (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2519">
-        <rdfs:label>Structure processing (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) nucleic acid tertiary structure data.</oboInOwl:hasDefinition>
-        <rdfs:comment rdf:resource="http://edamontology.org/operation_2481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2520">
-        <rdfs:label>DNA mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a map of a DNA sequence annotated with positional or non-positional features of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2521">
-        <rdfs:label>Map data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>DNA map data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) a DNA map of some type.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2520"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2574">
-        <rdfs:label>Protein hydropathy calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0250"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2970"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2575">
-        <rdfs:label>Protein binding site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Ligand-binding and active site prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Binding site prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2871 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2871">
-        <rdfs:label>Sequence tagged site (STS) mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1279"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence mapping</oboInOwl:hasExactSynonym>
-        <rdfs:comment>An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2928 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2928">
-        <rdfs:label>Alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Alignment generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2929 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2929">
-        <rdfs:label>Protein fragment weight comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0398"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2930"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2930 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2930">
-        <rdfs:label>Protein property comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare the physicochemical properties of two or more proteins (or reference data).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2931 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2931">
-        <rdfs:label>Secondary structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare two or more molecular secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2932 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2932">
-        <rdfs:label>Hopp and Woods plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0252"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a Hopp and Woods plot of antigenicity of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2934 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2934">
-        <rdfs:label>Microarray cluster textual view generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise gene clusters with gene names.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2935 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2935">
-        <rdfs:label>Microarray wave graph plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasExactSynonym>Microarray wave graph rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray cluster temporal graph rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This view can be rendered as a pie graph.  The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades.</rdfs:comment>
-        <oboInOwl:hasDefinition>Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2936 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2936">
-        <rdfs:label>Microarray dendrograph plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasNarrowSynonym>Microarray dendrograph rendering</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Generate a dendrograph of raw, preprocessed or clustered microarray data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray checks view rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray view rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2937 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2937">
-        <rdfs:label>Microarray proximity map plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray distance map rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a plot of distances (distance matrix) between genes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microarray proximity map rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2938 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2938">
-        <rdfs:label>Microarray tree or dendrogram rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasNarrowSynonym>Microarray 2-way dendrogram rendering</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microarray matrix tree plot rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2939 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2939">
-        <rdfs:label>Microarray principal component plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray principal component rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2940 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2940">
-        <rdfs:label>Microarray scatter plot plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasDefinition>Generate a scatter plot of microarray data, typically after principal component analysis.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray scatter plot rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2941 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2941">
-        <rdfs:label>Whole microarray graph plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasDefinition>Visualise gene expression data where each band (or line graph) corresponds to a sample.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Whole microarray graph rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2942 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2942">
-        <rdfs:label>Microarray tree-map rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise gene expression data after hierarchical clustering for representing hierarchical relationships.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2943 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2943">
-        <rdfs:label>Microarray Box-Whisker plot plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2944 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2944">
-        <rdfs:label>Physical mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2520"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1280"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2945 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2945">
-        <rdfs:label>Analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <oboInOwl:hasDefinition>Apply analytical methods to existing data of a specific type.</oboInOwl:hasDefinition>
-        <rdfs:comment>For non-analytical operations, see the &apos;Processing&apos; branch.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2946 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2946">
-        <rdfs:label>Alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process or analyse an alignment of molecular sequences or structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>1.8</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2928"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2947 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2947">
-        <rdfs:label>Article analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0306"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3068"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2526"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0971"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a body of scientific text (typically a full text article from a scientific journal.)</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Article analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2948 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2948">
-        <rdfs:label>Molecular interaction analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2949 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2949">
-        <rdfs:label>Protein interaction analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2950 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2950">
-        <rdfs:label>Residue contact calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <oboInOwl:hasDefinition>Calculate contacts between residues and some other group in a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2951 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2951">
-        <rdfs:label>Alignment processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2463"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2952"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2952 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2952">
-        <rdfs:label>Structure alignment processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular tertiary (3D) structure alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2962 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2962">
-        <rdfs:label>Codon usage bias calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2865"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate codon usage bias.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2963 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2963">
-        <rdfs:label>Codon usage bias plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2962"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a codon usage bias plot.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2964 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2964">
-        <rdfs:label>Codon usage fraction calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2990 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2990">
-        <rdfs:label>Classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2993 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2993">
-        <rdfs:label>Molecular interaction data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular interaction data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2995 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2995">
-        <rdfs:label>Sequence classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2990"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign molecular sequence(s) to a group or category.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2996 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2996">
-        <rdfs:label>Structure classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2990"/>
-        <oboInOwl:hasDefinition>Assign molecular structure(s) to a group or category.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2997 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2997">
-        <rdfs:label>Protein comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <oboInOwl:hasDefinition>Compare two or more proteins (or some aspect) to identify similarities.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2998 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2998">
-        <rdfs:label>Nucleic acid comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more nucleic acids to identify similarities.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3023 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3023">
-        <rdfs:label>Prediction and recognition (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict, recognise, detect or identify some properties of proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3024 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3024">
-        <rdfs:label>Prediction and recognition (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict, recognise, detect or identify some properties of nucleic acids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3080">
-        <rdfs:label>Structure editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Edit, convert or otherwise change a  molecular tertiary structure, either randomly or specifically.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3081">
-        <rdfs:label>Sequence alignment editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <oboInOwl:hasDefinition>Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3083">
-        <rdfs:label>Pathway or network visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Render (visualise) a biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway or network rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3084">
-        <rdfs:label>Protein function prediction (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Predict general (non-positional) functional properties of a protein from analysing its sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>For functional properties that are positional, use &apos;Protein site detection&apos; instead.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_1777"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3087 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3087">
-        <rdfs:label>Protein sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <oboInOwl:hasNarrowSynonym>Protein site recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein site prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence profile database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein site detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequence feature detection (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3088 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3088">
-        <rdfs:label>Protein property calculation (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0250"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3090 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3090">
-        <rdfs:label>Protein feature prediction (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in proteins from analysing protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_3092"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3092">
-        <rdfs:label>Protein feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1277"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group.
-</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in proteins from analysing protein sequences or structures.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Protein feature recognition</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein feature prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3093 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3093">
-        <rdfs:label>Database search (by sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence screening</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2421"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3094">
-        <rdfs:label>Protein interaction network prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Predict a network of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3095 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3095">
-        <rdfs:label>Nucleic acid design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2430"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Design (or predict) nucleic acid sequences with specific chemical or physical properties.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3096 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3096">
-        <rdfs:label>Editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Edit a data entity, either randomly or specifically.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3180">
-        <rdfs:label>Sequence assembly validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0925"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3181"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Evaluate a DNA sequence assembly, typically for purposes of quality control.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3182">
-        <rdfs:label>Genome alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasDefinition>Align two or more (tpyically huge) molecular sequences that represent genomes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Genome alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3183">
-        <rdfs:label>Localized reassembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Reconstruction of a sequence assembly in a localised area.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3184">
-        <rdfs:label>Sequence assembly visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:hasExactSynonym>Assembly rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence assembly rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Render and visualise a DNA sequence assembly.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Assembly visualisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3185 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3185">
-        <rdfs:label>Base-calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2513"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phred base calling</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Identify base (nucleobase) sequence from a fluorescence &apos;trace&apos; data generated by an automated DNA sequencer.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Base calling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phred base-calling</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3186 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3186">
-        <rdfs:label>Bisulfite mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected.</rdfs:comment>
-        <oboInOwl:hasDefinition>The mapping of methylation sites in a DNA (genome) sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Bisulfite sequence alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Bisulfite sequence mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3187 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3187">
-        <rdfs:label>Sequence contamination filtering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3189 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3189">
-        <rdfs:label>Trim ends</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3192"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Trim sequences (typically from an automated DNA sequencer) to remove misleading ends.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3190 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3190">
-        <rdfs:label>Trim vector</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3192"/>
-        <oboInOwl:hasDefinition>Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3191">
-        <rdfs:label>Trim to reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3192"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3192 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3192">
-        <rdfs:label>Sequence trimming</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0369"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Cut (remove) the end from a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3194">
-        <rdfs:label>Genome feature comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0256"/>
-        <rdfs:comment>Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Compare the features of two genome sequences.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3195">
-        <rdfs:label>Sequencing error detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Short read error correction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Short-read error correction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect errors in DNA sequences generated from sequencing projects).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3196">
-        <rdfs:label>Genotyping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual&apos;s or a reference sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3197 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3197">
-        <rdfs:label>Genetic variation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Sequence variation analysis</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Genetic variation annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3198 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3198">
-        <rdfs:label>Read mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <oboInOwl:hasExactSynonym>Short oligonucleotide alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Oligonucleotide mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Oligonucleotide alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Short read mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Oligonucleotide alignment construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Oligonucleotide alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Read alignment</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Short read alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Short sequence read mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3199 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3199">
-        <rdfs:label>Split read mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3198"/>
-        <oboInOwl:hasDefinition>A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3200">
-        <rdfs:label>DNA barcoding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasDefinition>Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Sample barcoding</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3201 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3201">
-        <rdfs:label>SNP calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0484"/>
-        <oboInOwl:hasDefinition>Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism.</oboInOwl:hasDefinition>
-        <rdfs:comment>Operations usually score confidence in the prediction or some other statistical measure of evidence.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3202">
-        <rdfs:label>Mutation detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasExactSynonym>Polymorphism detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3203">
-        <rdfs:label>Chromatogram visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <oboInOwl:hasDefinition>Visualise, format or render an image of a Chromatogram.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Chromatogram viewing</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3204">
-        <rdfs:label>Methylation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Determine cytosine methylation states in nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3205 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3205">
-        <rdfs:label>Methylation calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3204"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Determine cytosine methylation status of specific positions in a nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3206 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3206">
-        <rdfs:label>Methylation level analysis (global)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3205"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Global methylation analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3207 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3207">
-        <rdfs:label>Methylation level analysis (gene-specific)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3205"/>
-        <oboInOwl:hasExactSynonym>Gene-specific methylation analysis</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Many different techniques are available for this.</rdfs:comment>
-        <oboInOwl:hasDefinition>Measure the level of methyl cytosines in specific genes.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3208">
-        <rdfs:label>Genome visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0564"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Genome visualization</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome visualisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome viewing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome browsing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3209">
-        <rdfs:label>Genome comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <oboInOwl:hasDefinition>Compare the sequence or features of two or more genomes, for example, to find matching regions.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Genomic region matching</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3211">
-        <rdfs:label>Genome indexing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0227"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3210"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate an index of a genome sequence.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3212 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3212">
-        <rdfs:label>Genome indexing (Burrows-Wheeler)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3211"/>
-        <rdfs:comment>The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate an index of a genome sequence using the Burrows-Wheeler algorithm.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3213">
-        <rdfs:label>Genome indexing (suffix arrays)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3211"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Generate an index of a genome sequence using a suffix arrays algorithm.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>suffix arrays</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A suffix array consists of the lexicographically sorted list of suffixes of a genome.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3214 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3214">
-        <rdfs:label>Spectral analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasExactSynonym>Spectral analysis</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Spectrum analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse a spectrum from a mass spectrometry (or other) experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Mass spectrum analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3215">
-        <rdfs:label>Peak detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3214"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0943"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Peak finding</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Peak assignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3216 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3216">
-        <rdfs:label>Scaffolding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Scaffold construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length.  The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Scaffold may be positioned along a chromosome physical map to create a &quot;golden path&quot;.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Scaffold generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3217">
-        <rdfs:label>Scaffold gap completion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3216"/>
-        <oboInOwl:hasDefinition>Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used.  For large (&gt;20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3218">
-        <rdfs:label>Sequencing quality control</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasDefinition>Raw sequence data quality control.</oboInOwl:hasDefinition>
-        <rdfs:comment>Analyse raw sequence data from a sequencing pipeline and identify problems.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequencing QC</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3219">
-        <rdfs:label>Read pre-processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasExactSynonym>Sequence read pre-processing</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.  For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Pre-process sequence reads to ensure (or improve) quality and reliability.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3221 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3221">
-        <rdfs:label>Species frequency estimation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3174"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3222 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3222">
-        <rdfs:label>Peak calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:comment>Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence.  The enriched areas contain the binding sites of DNA-associated proteins.  For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation (&apos;ChIP&apos;) with microarray (&apos;chip&apos;).</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein binding peak detection</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3223 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3223">
-        <rdfs:label>Differential expression analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0315"/>
-        <oboInOwl:hasDefinition>Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Differentially expressed gene identification</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3224 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3224">
-        <rdfs:label>Gene set testing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Gene sets can be defined beforehand by biological function, chromosome locations and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3225 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3225">
-        <rdfs:label>Variant classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2995"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasDefinition>Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.)</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3226 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3226">
-        <rdfs:label>Variant prioritization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <rdfs:comment>Variant prioritization can be used for example to produce a list of variants responsible for &apos;knocking out&apos; genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3227 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3227">
-        <rdfs:label>Variant calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasExactSynonym>Variant mapping</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods often utilise a database of aligned reads.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3228 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3228">
-        <rdfs:label>Structural variation discovery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasDefinition>Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s).</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3229 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3229">
-        <rdfs:label>Exome analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Targeted exome capture</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Exome sequencing is considered a cheap alternative to whole genome sequencing.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Exome sequence analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3230 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3230">
-        <rdfs:label>Read depth analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3232 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3232">
-        <rdfs:label>Gene expression QTL analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>expression quantitative trait loci profiling</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>eQTL profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>expression QTL profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3233">
-        <rdfs:label>Copy number estimation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:comment>Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Transcript copy number estimation</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3237">
-        <rdfs:label>Primer removal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0369"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3258">
-        <rdfs:label>Transcriptome assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0925"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Infer a transcriptome sequence by analysis of short sequence reads.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3259">
-        <rdfs:label>Transcriptome assembly (de novo)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>de novo transcriptome assembly</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0524"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3260 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3260">
-        <rdfs:label>Transcriptome assembly (mapping)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Infer a transcriptome sequence by mapping short reads to a reference genome.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>1.2</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3267 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3267">
-        <rdfs:label>Sequence coordinate conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3434"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2012"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2012"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3278">
-        <rdfs:label>Document similarity calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3437"/>
-        <oboInOwl:hasDefinition>Calculate similarity between 2 or more documents.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3279 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3279">
-        <rdfs:label>Document clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3432"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3437"/>
-        <oboInOwl:hasDefinition>Cluster (group) documents on the basis of their calculated similarity.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3280">
-        <rdfs:label>Named entity recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0306"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <oboInOwl:hasExactSynonym>Entity identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Entity chunking</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Entity extraction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Recognise named entities (text tokens) within documents.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3282 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3282">
-        <rdfs:label>ID mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <oboInOwl:hasExactSynonym>Identifier mapping</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Accession mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3283 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3283">
-        <rdfs:label>Anonymisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:hasDefinition>Process data in such a way that makes it hard to trace to the person which the data concerns.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Data anonymisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3289">
-        <rdfs:label>ID retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0304"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0842"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>id retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data retrieval (accession)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data retrieval (ID)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Identifier retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data retrieval (id)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Accession retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search for and retrieve a data identifier of some kind, e.g. a database entry accession.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3348">
-        <rdfs:label>Sequence checksum generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Generate a checksum of a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3349">
-        <rdfs:label>Bibliography generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3505"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Bibliography construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a bibliography from the scientific literature.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3350">
-        <rdfs:label>Protein quaternary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0474"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Predict the structure of a multi-subunit protein and particularly how the subunits fit together.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3351 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3351">
-        <rdfs:label>Protein surface analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Analyse the surface properties of proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3352">
-        <rdfs:label>Ontology comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Compare two or more ontologies, e.g. identify differences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3353">
-        <rdfs:label>Ontology comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Compare two or more ontologies, e.g. identify differences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.9</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_3352"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3357">
-        <rdfs:label>Format detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3358"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Recognition of which format the given data is in.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Format identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Format recognition</oboInOwl:hasExactSynonym>
-        <rdfs:comment>&apos;Format recognition&apos; is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Format inference</oboInOwl:hasExactSynonym>
-        <noClue rdf:resource="http://edamontology.org/noClue"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>The has_input &quot;Data&quot; (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs.</rdfs:comment>
-        <owl:annotatedProperty rdf:resource="http://edamontology.org/noClue"/>
-        <owl:annotatedTarget rdf:resource="http://edamontology.org/noClue"/>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_3357"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/operation_3359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3359">
-        <rdfs:label>Splitting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:hasExactSynonym>File splitting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Split a file containing multiple data items into many files, each containing one item</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3429">
-        <rdfs:label>Generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasExactSynonym>Construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>For non-analytical operations, see the &apos;Processing&apos; branch.</rdfs:comment>
-        <oboInOwl:hasDefinition>Construct some data entity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3430">
-        <rdfs:label>Nucleic acid sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid site prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid site recognition</oboInOwl:hasExactSynonym>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid site detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3431 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3431">
-        <rdfs:label>Deposition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <oboInOwl:hasDefinition>Deposit some data in a database or some other type of repository or software system.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasExactSynonym>Database submission</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Submission</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data submission</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data deposition</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Database deposition</oboInOwl:hasExactSynonym>
-        <rdfs:comment>For non-analytical operations, see the &apos;Processing&apos; branch.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3432">
-        <rdfs:label>Clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3433">
-        <rdfs:label>Assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Construct some entity (typically a molecule sequence) from component pieces.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3434">
-        <rdfs:label>Conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Non-analytical data conversion.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3435">
-        <rdfs:label>Standardization and normalization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Standardize or normalize data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3436">
-        <rdfs:label>Aggregation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:hasDefinition>Combine multiple files or data items into a single file or object.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3437">
-        <rdfs:label>Article comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <oboInOwl:hasDefinition>Compare two or more scientific articles.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3438">
-        <rdfs:label>Calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasDefinition>Mathemetical determination of the value of something, typically a properly of a  molecule.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3439">
-        <rdfs:label>Pathway or network prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2438"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Predict a molecular pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3440">
-        <rdfs:label>Genome assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3441">
-        <rdfs:label>Plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasDefinition>Generate a graph, or other visual representation, of data, showing the relationship between two or more variables.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3443">
-        <rdfs:label>Image analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3382"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>The analysis of a image (typically a digital image) of some type in order to extract information from it.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Image processing</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3445">
-        <rdfs:label>Diffraction data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Analysis of data from a diffraction experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3446">
-        <rdfs:label>Cell migration analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2229"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3447">
-        <rdfs:label>Diffraction data reduction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3445"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Processing of diffraction data into a corrected, ordered, and simplified form.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3450 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3450">
-        <rdfs:label>Neurite measurement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2229"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3453">
-        <rdfs:label>Diffraction data integration</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3445"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasNarrowSynonym>Diffraction summation integration</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Diffraction profile fitting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3454 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3454">
-        <rdfs:label>Phasing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3445"/>
-        <oboInOwl:hasDefinition>Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3455 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3455">
-        <rdfs:label>Molecular replacement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0322"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form.</oboInOwl:hasDefinition>
-        <rdfs:comment>The technique solves the phase problem, i.e. retrieve information concern phases of the structure.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3456">
-        <rdfs:label>Rigid body refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0322"/>
-        <created_in>1.7</created_in>
-        <rdfs:comment>Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data.</rdfs:comment>
-        <oboInOwl:hasDefinition>A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3457">
-        <rdfs:label>Single particle analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:comment>Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3458 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3458">
-        <rdfs:label>Single particle alignment and classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2990"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3457"/>
-        <oboInOwl:hasDefinition>Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle. </oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:comment>A micrograph can include particles in multiple different orientations and/or conformations.  Particles are compared and organised into sets based on their similarity.  Typically iterations of classification and alignment and are performed to optimise the final image; average images produced by classification are used as a reference image for subsequent alignment of the whole image set.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3459">
-        <rdfs:label>Functional clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0291"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Functional sequence clustering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3460">
-        <rdfs:label>Taxonomic classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2995"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Classifiication of molecular sequences by assignment to some taxonomic hierarchy.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3461">
-        <rdfs:label>Virulence prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3301"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Pathogenicity prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3463">
-        <rdfs:label>Gene expression correlation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0315"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3465"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>Gene co-expression network analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse the correlation patterns among genes across across a variety of experiments, microarray samples etc.
- </oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3465">
-        <rdfs:label>Correlation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3469">
-        <rdfs:label>RNA structure covariance model generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compute the covariance model for (a family of) RNA secondary structures.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3470">
-        <rdfs:label>RNA secondary structure prediction (shape-based)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0278"/>
-        <oboInOwl:hasExactSynonym>RNA shape prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3471">
-        <rdfs:label>Nucleic acid alignment folding prediction (alignment-based)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0279"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Prediction of nucleic-acid folding using sequence alignments as a source of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3472">
-        <rdfs:label>k-mer counting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <oboInOwl:hasDefinition>Count k-mers (substrings of length k) in DNA sequence data.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:comment>k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads. </rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3478">
-        <rdfs:label>Phylogenetic tree reconstruction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Reconstructing the inner node labels of a phylogenetic tree from its leafes.</oboInOwl:hasDefinition>
-        <rdfs:comment>Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one.</rdfs:comment>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3480">
-        <rdfs:label>Probabilistic data generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <oboInOwl:hasDefinition>Generate some data from a choosen probibalistic model, possibly to evaluate algorithms.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3481">
-        <rdfs:label>Probabilistic sequence generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3480"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Generate sequences from some probabilistic model, e.g. a model that simulates evolution.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3482">
-        <rdfs:label>Antimicrobial resistance prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3301"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Identify or predict causes for antibiotic resistance from molecular sequence analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3501">
-        <rdfs:label>Enrichment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>A relevant ontology will be used. The input is typically a set of identifiers or other data, and the output of the analysis is typically a ranked list of ontology terms, each associated with a p-value.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Term enrichment</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Analyse a dataset with respect to concepts from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3502">
-        <rdfs:label>Chemical class enrichment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Analyse a dataset with respect to concepts from an ontology of chemical structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3503">
-        <rdfs:label>Incident curve plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Plot an incident curve such as a survival curve, death curve, mortality curve.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3504">
-        <rdfs:label>Variant pattern analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <rdfs:comment>Methods often utilise a database of aligned reads.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify and map patterns of genomic variations.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3545">
-        <rdfs:label>Mathematical modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <oboInOwl:hasDefinition>Model some biological system using mathematical techniques including  dynamical systems, statistical models, differential equations, and game theoretic models.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3552">
-        <rdfs:label>Microscope image visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3382"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise images resulting from various types of microscopy.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasExactSynonym>Microscopy image visualisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3553">
-        <rdfs:label>Image annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Annotate an image of some sort, typically with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3557">
-        <rdfs:label>Imputation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2238"/>
-        <oboInOwl:hasExactSynonym>Data imputation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Replace missing data with substituted values, usually by using some statistical or other mathematical approach.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3559">
-        <rdfs:label>Ontology visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render data from an ontology, typically a tree of terms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ontology browsing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3560">
-        <rdfs:label>Maximum occurence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <oboInOwl:hasDefinition>A method for making numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data. </oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3561">
-        <rdfs:label>Database comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasNarrowSynonym>Data model comparison</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Compare the models or schemas used by two or more databases, or any other general comparison of databases rather than a detailed comparison of the entries themselves.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Schema comparison</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3562 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3562">
-        <rdfs:label>Network simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2259"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Simulate the bevaviour of a biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway simulation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Network topology simulation</oboInOwl:hasExactSynonym>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3563">
-        <rdfs:label>RNA-seq read count analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasDefinition>Analyze read counts from RNA-seq experiments.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3564">
-        <rdfs:label>Chemical redundancy removal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Identify and remove redudancy from a set of small molecule structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3565">
-        <rdfs:label>RNA-seq time series data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Analyze time series data from an RNA-seq experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3566">
-        <rdfs:label>Simulated gene expression data generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Simulate gene expression data, e.g. for purposes of benchmarking.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0003">
-        <rdfs:label>Topic</rdfs:label>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#Quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Category</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <oboInOwl:hasRelatedSynonym>sumo:FieldOfStudy</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0077">
-        <rdfs:label>Nucleic acids</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <oboInOwl:hasDefinition>The processing and analysis of nucleic acid sequence, structural and other data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid bioinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid informatics</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D017423</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid properties</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid physicochemistry</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D017422</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0078">
-        <rdfs:label>Proteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <oboInOwl:hasExactSynonym>Protein bioinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein databases</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein analysis</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D020539</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Archival, processing and analysis of protein data, typically molecular sequence and structural data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0079 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0079">
-        <rdfs:label>Metabolites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <oboInOwl:hasExactSynonym>Metabolite structures</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This concept excludes macromolecules such as proteins and nucleic acids.</rdfs:comment>
-        <oboInOwl:hasDefinition>The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0080">
-        <rdfs:label>Sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3307"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Sequence databases</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequences</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D017421</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0081">
-        <rdfs:label>Structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3307"/>
-        <oboInOwl:hasNarrowSynonym>Computational structural biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015394</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Structure analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural bioinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Structure databases</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes related concepts such as structural properties, alignments and structural motifs.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Structure data resources</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0082 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0082">
-        <rdfs:label>Structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The prediction of molecular (secondary or tertiary) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0083">
-        <rdfs:label>Alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0183"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0184"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0084">
-        <rdfs:label>Phylogeny</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3299"/>
-        <oboInOwl:hasNarrowSynonym>Phylogeny reconstruction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic stratigraphy</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic dating</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic clocks</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D010802</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The study of evolutionary relationships amongst organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic simulation</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0085">
-        <rdfs:label>Functional genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1775"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0089 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0089">
-        <rdfs:label>Ontology and terminology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasNarrowSynonym>Terminology</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D002965</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Applied ontology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Ontology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Ontologies</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0090 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0090">
-        <rdfs:label>Information retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Data retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes, for example, search, query and retrieval of molecular sequences and associated data.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Data search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.3.3 Information retrieval</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Data query</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0091 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0091">
-        <rdfs:label>Bioinformatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <rdfs:comment>This includes data  processing in general, including basic handling of files and databases, datatypes, workflows and annotation.</rdfs:comment>
-        <oboInOwl:hasDbXref>VT 1.5.6 Bioinformatics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The archival, curation, processing and analysis of complex biological data.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D016247</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0092">
-        <rdfs:label>Data visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasExactSynonym>Data rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.2.5 Computer graphics</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasBroadSynonym>Computer graphics</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0094">
-        <rdfs:label>Nucleic acid thermodynamics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The study of the thermodynamic properties of a nucleic acid.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0097">
-        <rdfs:label>Nucleic acid structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <rdfs:comment>Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>DNA melting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid denaturation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>RNA alignment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>RNA structure alignment</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid thermodynamics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>RNA structure</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0099">
-        <rdfs:label>RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0077"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>RNA sequences and structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0100">
-        <rdfs:label>Nucleic acid restriction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0747"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0102">
-        <rdfs:label>Mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Genetic linkage</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Linkage</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Linkage mapping</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Synteny</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>DNA mapping</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The mapping of complete (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0107 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0107">
-        <rdfs:label>Genetic codes and codon usage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Codon usage analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The study of codon usage in nucleotide sequence(s), genetic codes and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0108 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0108">
-        <rdfs:label>Protein expression</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <oboInOwl:hasNarrowSynonym>Translation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The translation of mRNA into protein and subsequent protein processing in the cell.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0109 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0109">
-        <rdfs:label>Gene finding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:comment>This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Gene discovery</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene prediction</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0110">
-        <rdfs:label>Transcription</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>The transcription of DNA into mRNA.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0111">
-        <rdfs:label>Promoters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins).</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0749"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0112">
-        <rdfs:label>Nucleic acid folding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The folding (in 3D space) of nucleic acid molecules.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0173"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0114 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0114">
-        <rdfs:label>Gene structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3321"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <rdfs:comment>This includes the study of promoters, coding regions etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0121 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0121">
-        <rdfs:label>Proteomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3391"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Protein and peptide identification, especially in the study of whole proteomes of organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein and peptide identification</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Peptide identification</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D040901</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Protein expression</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0122">
-        <rdfs:label>Structural genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The elucidation of the three dimensional structure for all (available) proteins in a given organism.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0123">
-        <rdfs:label>Protein properties</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <oboInOwl:hasDefinition>The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein hydropathy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein physicochemistry</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0128">
-        <rdfs:label>Protein interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein-nucleic acid interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein-RNA interaction</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Protein-protein interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein-ligand interactions</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein-DNA interaction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0130">
-        <rdfs:label>Protein folding, stability and design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:hasNarrowSynonym>Protein folding</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein stability</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Protein stability, folding (in 3D space) and protein sequence-structure-function relationships.  This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein residue interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Rational protein design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0133">
-        <rdfs:label>Two-dimensional gel electrophoresis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Two-dimensional gel electrophoresis image and related data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0121"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0134">
-        <rdfs:label>Mass spectrometry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3520"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0135">
-        <rdfs:label>Protein microarrays</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Protein microarray data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0121"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0137">
-        <rdfs:label>Protein hydropathy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The study of the hydrophobic, hydrophilic and charge properties of a protein.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0123"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0140">
-        <rdfs:label>Protein targeting and localization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0108"/>
-        <oboInOwl:hasNarrowSynonym>Protein targeting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein sorting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein localization</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0141">
-        <rdfs:label>Protein cleavage sites and proteolysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0767"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0143">
-        <rdfs:label>Protein structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The comparison of two or more protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Use this concept for methods that are exclusively for protein structure.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0698"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0144 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0144">
-        <rdfs:label>Protein residue interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein residue interactions</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0130"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0147">
-        <rdfs:label>Protein-protein interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasNarrowSynonym>Protein interaction networks</oboInOwl:hasNarrowSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0148 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0148">
-        <rdfs:label>Protein-ligand interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein-ligand (small molecule) interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0149 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0149">
-        <rdfs:label>Protein-nucleic acid interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein-DNA/RNA interactions.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0150 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0150">
-        <rdfs:label>Protein design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0130"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0151 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0151">
-        <rdfs:label>G protein-coupled receptors (GPCR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>G-protein coupled receptors (GPCRs).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0152 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0152">
-        <rdfs:label>Carbohydrates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Carbohydrates, typically including structural information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0153 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0153">
-        <rdfs:label>Lipids</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Lipids and their structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0154">
-        <rdfs:label>Small molecules</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <oboInOwl:hasDefinition>Small molecules of biological significance, typically archival, curation, processing and analysis of structural information.</oboInOwl:hasDefinition>
-        <rdfs:comment>Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides.  Structural data is usually included.</rdfs:comment>
-        <oboInOwl:hasRelatedSynonym>CHEBI:23367</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0156">
-        <rdfs:label>Sequence editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Edit, convert or otherwise change a molecular sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0091"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0157">
-        <rdfs:label>Sequence composition, complexity and repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Sequence complexity</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Repeat sequences</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Sequence repeats</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Low complexity sequences</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence composition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0158">
-        <rdfs:label>Sequence motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Motifs</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0159">
-        <rdfs:label>Sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <rdfs:comment>The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The comparison of two or more molecular sequences, for example sequence alignment and clustering.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0160">
-        <rdfs:label>Sequence sites, features and motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Sequence features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The archival, detection, prediction and analysis of
-positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Functional sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence motifs</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence profiles</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>HMMs</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0163">
-        <rdfs:label>Sequence database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The query is a sequence-based entity such as another sequence, a motif or profile.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0164">
-        <rdfs:label>Sequence clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes systems that generate, process and analyse sequence clusters.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>The comparison and grouping together of molecular sequences on the basis of their similarities.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence clusters</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0166">
-        <rdfs:label>Protein structural motifs and surfaces</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <rdfs:comment>This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Protein structural features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Structural motifs</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein 3D motifs</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein structural motifs</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein surfaces</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0167">
-        <rdfs:label>Structural (3D) profiles</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Structural profiles</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0172">
-        <rdfs:label>Protein structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0173">
-        <rdfs:label>Nucleic acid structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:hasDefinition>The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>DNA structure prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>RNA structure prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid folding</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0174">
-        <rdfs:label>Ab initio structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>The prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0082"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0175">
-        <rdfs:label>Homology modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>The modelling of the three-dimensional structure of a protein using known sequence and structural data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2275"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0176">
-        <rdfs:label>Molecular dynamics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:comment>This includes resources concerning flexibility and motion in protein and other molecular structures.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Protein dynamics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Molecular flexibility</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Molecular motions</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0177">
-        <rdfs:label>Molecular docking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The modelling the structure of proteins in complex with small molecules or other macromolecules.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0178">
-        <rdfs:label>Protein secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>The prediction of secondary or supersecondary structure of protein sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0172"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0694"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0179">
-        <rdfs:label>Protein tertiary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The prediction of tertiary structure of protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0172"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0698"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0180">
-        <rdfs:label>Protein fold recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:comment>For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).</rdfs:comment>
-        <oboInOwl:hasDefinition>The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0182">
-        <rdfs:label>Sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>The alignment of molecular sequences or sequence profiles (representing sequence alignments).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0183">
-        <rdfs:label>Structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes the generation, storage, analysis, rendering etc. of structure alignments.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0184">
-        <rdfs:label>Threading</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence-structure alignment</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0180"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0188 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0188">
-        <rdfs:label>Sequence profiles and HMMs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Sequence profiles; typically a positional, numerical matrix representing a sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:comment>Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0191">
-        <rdfs:label>Phylogeny reconstruction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Currently too specific for the topic sub-ontology (but might be unobsoleted).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3293"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0194">
-        <rdfs:label>Phylogenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0195">
-        <rdfs:label>Virtual PCR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Polymerase chain reaction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simulated polymerase chain reaction (PCR).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>PCR</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0077"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0196">
-        <rdfs:label>Sequence assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Assembly</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The assembly of fragments of a DNA sequence to reconstruct the original sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0199 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0199">
-        <rdfs:label>Genetic variation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0625"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D014644</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>DNA variation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Mutation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Polymorphism</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0200">
-        <rdfs:label>Microarrays</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D046228</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Microarrays, for example, to process microarray data or design probes and experiments.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasNarrowSynonym>DNA microarrays</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0202">
-        <rdfs:label>Pharmacology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasNarrowSynonym>Computational pharmacology</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Pharmacoinformatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of drugs and their effects or responses in living systems. </oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.7 Pharmacology and pharmacy</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0203">
-        <rdfs:label>Gene expression</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <rdfs:comment>This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Gene expression profiling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Expression profiling</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasAlternativeId>http://edamontology.org/topic_0197</oboInOwl:hasAlternativeId>
-        <rdfs:comment>Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015870</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Gene expression analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>DNA microarrays</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Codon usage</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0204">
-        <rdfs:label>Gene regulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0203"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The regulation of gene expression.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0208">
-        <rdfs:label>Pharmacogenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0202"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0209">
-        <rdfs:label>Medicinal chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3336"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3371"/>
-        <oboInOwl:hasDbXref>VT 3.1.4 Medicinal chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Drug design</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0210">
-        <rdfs:label>Fish</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a specific fish genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0211">
-        <rdfs:label>Flies</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a specific fly genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2819"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0213">
-        <rdfs:label>Mice or rats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2820"/>
-        <oboInOwl:hasDefinition>Information on a specific mouse or rat genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <rdfs:comment>The resource may be specific to a group of mice / rats or all mice / rats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0215">
-        <rdfs:label>Worms</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a specific worm genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2819"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0217">
-        <rdfs:label>Literature analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0218"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0218">
-        <rdfs:label>Data mining</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3068"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Text data mining</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The analysis of the biomedical and informatics literature.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Literature analysis</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Text mining</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Literature mining</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0219">
-        <rdfs:label>Data deposition, annotation and curation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>Deposition and curation of database accessions, including annotation, typically with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database curation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0220 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0220">
-        <rdfs:label>Document, record and content management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasExactSynonym>Document management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File management</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Content management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The management and manipulation of digital documents, including database records, files and reports.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.3.6 Multimedia, hypermedia</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Record management</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0221 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0221">
-        <rdfs:label>Sequence annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Annotation of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0219"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0222 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0222">
-        <rdfs:label>Genome annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Annotation of a genome.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0219"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0593">
-        <rdfs:label>NMR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasNarrowSynonym>ROESY</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>NOESY</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nuclear Overhauser Effect Spectroscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>HOESY</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Heteronuclear Overhauser Effect Spectroscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nuclear magnetic resonance spectroscopy</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Spectroscopy</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>NMR spectroscopy</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Rotational Frame Nuclear Overhauser Effect Spectroscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0594">
-        <rdfs:label>Sequence classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The classification of molecular sequences based on some measure of their similarity.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0595">
-        <rdfs:label>Protein classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0598">
-        <rdfs:label>Sequence motif or profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes comparison, discovery, recognition etc. of sequence motifs.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0158"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0188"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0601">
-        <rdfs:label>Protein modifications</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0108"/>
-        <oboInOwl:hasRelatedSynonym>GO:0006464</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>Protein chemical modifications, e.g. post-translational modifications.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein post-translational modification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>MOD:00000</oboInOwl:hasRelatedSynonym>
-        <rdfs:comment>EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000)</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0602">
-        <rdfs:label>Molecular interactions, pathways and networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasNarrowSynonym>Biological networks</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Network or pathway analysis</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasNarrowSynonym>Molecular interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Biological models</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Molecular interactions, biological pathways, networks and other models.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Biological pathways</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasAlternativeId>http://edamontology.org/topic_3076</oboInOwl:hasAlternativeId>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0605">
-        <rdfs:label>Informatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The study and practice of information processing and use of computer information systems.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.3.99 Other</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Knowledge management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.3.4 Information management</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Information management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.3.5 Knowledge management</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.3.3 Information retrieval</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.3 Information sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Information science</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0606">
-        <rdfs:label>Literature data resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data resources for the biological or biomedical literature, either a primary source of literature or some derivative.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3068"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0607">
-        <rdfs:label>Laboratory information management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasDefinition>Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Laboratory resources</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0608">
-        <rdfs:label>Cell and tissue culture</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasNarrowSynonym>Tissue culture</oboInOwl:hasNarrowSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>General cell culture or data on a specific cell lines.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Cell culture</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2229"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0610">
-        <rdfs:label>Ecology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDefinition>The ecological and environmental sciences and especially the application of information technology (ecoinformatics).</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D004777</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Ecological informatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.15 Ecology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Computational ecology</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Ecoinformatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Environmental science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0611">
-        <rdfs:label>Electron microscopy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasNarrowSynonym>SEM</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Scanning electron microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>TEM</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light.
-</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Transmission electron microscopy</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Electron crystallography</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Electron diffraction experiment</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Single particle electron microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0612">
-        <rdfs:label>Cell cycle</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The cell cycle including key genes and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2229"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0613">
-        <rdfs:label>Peptides and amino acids</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The physicochemical, biochemical or structural properties of amino acids or peptides.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Amino acids</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Peptides</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0616">
-        <rdfs:label>Organelles</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasNarrowSynonym>Cell membrane</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Cytoplasm</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Organelle genes and proteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Smooth endoplasmic reticulum</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Lysosome</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Centriole</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Ribosome</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleus</oboInOwl:hasNarrowSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Mitochondria</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Golgi apparatus</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Rough endoplasmic reticulum</oboInOwl:hasNarrowSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2229"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0617">
-        <rdfs:label>Ribosomes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Ribosomes, typically of ribosome-related genes and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Ribosome genes and proteins</oboInOwl:hasNarrowSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0616"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0618">
-        <rdfs:label>Scents</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A database about scents.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0154"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0620">
-        <rdfs:label>Drugs and target structures</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3336"/>
-        <oboInOwl:hasNarrowSynonym>Drug structures</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The structures of drugs, drug target, their interactions and binding affinities.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Target structures</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0621">
-        <rdfs:label>Model organisms</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:comment>This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A specific organism, or group of organisms, used to study a particular aspect of biology.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Organisms</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0622">
-        <rdfs:label>Genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3391"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D023281</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0623 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0623">
-        <rdfs:label>Gene families</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasDefinition>Particular gene(s), gene family or other gene group or system and their encoded proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene family</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene system</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genes, gene family or system</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene and protein families</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0624 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0624">
-        <rdfs:label>Chromosomes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Study of chromosomes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0625 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0625">
-        <rdfs:label>Genotype and phenotype</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasExactSynonym>Genotype and phenotype resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Genotyping</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Phenotyping</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0629 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0629">
-        <rdfs:label>Gene expression and microarray</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0200"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0632 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0632">
-        <rdfs:label>Sequence design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Probes</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes the design of primers for PCR and DNA amplification or the design of molecular probes.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015335</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Gene design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Probe design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>in silico cloning</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Primer design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Primers</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0634 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0634">
-        <rdfs:label>Pathology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Diseases</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.1.6 Pathology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0635 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0635">
-        <rdfs:label>Specific protein resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>A particular protein, protein family or other group of proteins.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Specific protein</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0637 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0637">
-        <rdfs:label>Taxonomy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3299"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.25 Taxonomy</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Organism classification, identification and naming.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0639 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0639">
-        <rdfs:label>Protein sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0640 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0640">
-        <rdfs:label>Nucleic acid sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0641 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0641">
-        <rdfs:label>Repeat sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The repetitive nature of molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0157"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0642 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0642">
-        <rdfs:label>Low complexity sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The (character) complexity of molecular sequences, particularly regions of low complexity.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0157"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0644 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0644">
-        <rdfs:label>Proteome</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A specific proteome including protein sequences and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0654 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0654">
-        <rdfs:label>DNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0077"/>
-        <oboInOwl:hasExactSynonym>DNA analysis</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA sequences and structure, including processes such as methylation and replication.</oboInOwl:hasDefinition>
-        <rdfs:comment>The DNA sequences might be coding or non-coding sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0655 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0655">
-        <rdfs:label>Coding RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <oboInOwl:hasNarrowSynonym>EST</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>cDNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>mRNA</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes expressed sequence tag (EST) or complementary DNA (cDNA) sequences.</rdfs:comment>
-        <oboInOwl:hasDefinition>Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0659 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0659">
-        <rdfs:label>Functional, regulatory and non-coding RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasNarrowSynonym>ncRNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Non-coding RNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Functional RNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Regulatory RNA</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>Non-coding RNA includes  piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA).  Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0660 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0660">
-        <rdfs:label>rRNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>One or more ribosomal RNA (rRNA) sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0659"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0663 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0663">
-        <rdfs:label>tRNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>One or more transfer RNA (tRNA) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0659"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0694 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0694">
-        <rdfs:label>Protein secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Protein secondary structure or secondary structure alignments.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data.</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0697 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0697">
-        <rdfs:label>RNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>RNA secondary or tertiary structure and alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0698 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0698">
-        <rdfs:label>Protein tertiary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Protein tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0722 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0722">
-        <rdfs:label>Nucleic acid classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Classification of nucleic acid sequences and structures.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0623"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0724 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0724">
-        <rdfs:label>Protein families</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein sequence classification</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary databases</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>A protein families database might include the classifier (e.g. a sequence profile) used to build the classification.</rdfs:comment>
-        <oboInOwl:hasDefinition>Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0736 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0736">
-        <rdfs:label>Protein domains and folds</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein folds</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Protein tertiary structural domains and folds.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein domains</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0740 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0740">
-        <rdfs:label>Nucleic acid sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Nucleotide sequence alignments.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0741 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0741">
-        <rdfs:label>Protein sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein sequence alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A sequence profile typically represents a sequence alignment.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0747 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0747">
-        <rdfs:label>Nucleic acid sites and features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The archival, detection, prediction and analysis of
-positional features such as functional sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0640"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0748 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0748">
-        <rdfs:label>Protein sites and features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The detection, identification and analysis of positional features in proteins, such as functional sites.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0639"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0749 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0749">
-        <rdfs:label>Transcription factors and regulatory sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1312"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3125"/>
-        <rdfs:comment>Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase.  Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators.</rdfs:comment>
-        <oboInOwl:hasDefinition>Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Transcriptional regulatory sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>TFBS</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Transcription factors</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Transcription factor binding sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0751 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0751">
-        <rdfs:label>Phosphorylation sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:hasDefinition>Protein phosphorylation and phosphorylation sites in protein sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0601"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0748"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0753 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0753">
-        <rdfs:label>Metabolic pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Metabolic pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0754 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0754">
-        <rdfs:label>Signaling pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Signaling pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Signal transduction pathways</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0767 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0767">
-        <rdfs:label>Protein and peptide identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0121"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0769 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0769">
-        <rdfs:label>Workflows</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Biological or biomedical analytical workflows or pipelines.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0770 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0770">
-        <rdfs:label>Data types and objects</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Structuring data into basic types and (computational) objects.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.0</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0091"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0771 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0771">
-        <rdfs:label>Theoretical biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3307"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0779 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0779">
-        <rdfs:label>Mitochondria</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Mitochondria, typically of mitochondrial genes and proteins.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0616"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0780 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0780">
-        <rdfs:label>Plants</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <rdfs:comment>The resource may be specific to a plant, a group of plants or all plants.</rdfs:comment>
-        <oboInOwl:hasBroadSynonym>Plant science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Plant biology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Botany</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.22 Plant science</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Plant</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.10 Botany</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0781 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0781">
-        <rdfs:label>Viruses</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:hasBroadSynonym>Virology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.28 Virology</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <rdfs:comment>The resource may be specific to a virus, a group of viruses or all viruses.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0782 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0782">
-        <rdfs:label>Fungi</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <oboInOwl:hasBroadSynonym>Mycology</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The resource may be specific to a fungus, a group of fungi or all fungi.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Yeast</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.21 Mycology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0783 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0783">
-        <rdfs:label>Pathogens</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:hasDefinition>Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The resource may be specific to a pathogen, a group of pathogens or all pathogens.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0786 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0786">
-        <rdfs:label>Arabidopsis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Arabidopsis-specific data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0780"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0787 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0787">
-        <rdfs:label>Rice</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Rice-specific data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0780"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0796 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0796">
-        <rdfs:label>Genetic mapping and linkage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Linkage mapping</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Genetic linkage</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0102"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0797 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0797">
-        <rdfs:label>Comparative genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <oboInOwl:hasDefinition>The study (typically comparison) of the sequence, structure or function of multiple genomes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0798 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0798">
-        <rdfs:label>Mobile genetic elements</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <oboInOwl:hasNarrowSynonym>Transposons</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0803 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0803">
-        <rdfs:label>Human disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Human diseases, typically describing the genes, mutations and proteins implicated in disease.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0804 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0804">
-        <rdfs:label>Immunology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDbXref>VT 3.1.3 Immunology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Immunoinformatics</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D007120</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D007125</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Computational immunology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0820 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0820">
-        <rdfs:label>Membrane and  lipoproteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:hasDefinition>Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Membrane proteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Lipoproteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Transmembrane proteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0821 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0821">
-        <rdfs:label>Enzymes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:hasDefinition>Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Enzymology</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0922 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0922">
-        <rdfs:label>Primers</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <oboInOwl:hasDefinition>PCR primers and hybridization oligos in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (primers)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Primer binding sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_0922"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1302">
-        <rdfs:label>PolyA signal or sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (PolyA signal or site)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PolyA signal</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>PolyA site</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1302"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1304">
-        <rdfs:label>CpG island and isochores</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (CpG island and isochore)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>CpG rich regions (isochores) in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1304"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1305">
-        <rdfs:label>Restriction sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3125"/>
-        <oboInOwl:hasDefinition>Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (restriction sites)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid restriction sites (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1305"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1307">
-        <rdfs:label>Splice sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3320"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (splice sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (RNA splicing)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Splice sites in a nucleotide sequence or alternative RNA splicing events.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (RNA splice model)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1307"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1308">
-        <rdfs:label>Matrix/scaffold attachment sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (matrix/scaffold attachment sites)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1308"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1311">
-        <rdfs:label>Operon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasExactSynonym>Gene features (operon)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (operon)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query.</rdfs:comment>
-        <oboInOwl:hasDefinition>Operons (operators, promoters and genes) from a bacterial genome.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1311"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1312">
-        <rdfs:label>Promoters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <oboInOwl:hasDefinition>Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (promoters)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1312"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1317 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1317">
-        <rdfs:label>Structural biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasNarrowSynonym>Structural assignment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Structure determination</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:consider>This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy.  Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen.</oboInOwl:consider>
-        <oboInOwl:hasDefinition>The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.5.24 Structural biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Structural determination</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1456">
-        <rdfs:label>Protein membrane regions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0736"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3539"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (membrane regions)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Intramembrane regions</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein transmembrane regions</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Transmembrane regions</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1456"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1770 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1770">
-        <rdfs:label>Structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <rdfs:comment>This might involve comparison of secondary or tertiary (3D) structural information.</rdfs:comment>
-        <oboInOwl:hasDefinition>The comparison of two or more molecular structures, for example structure alignment and clustering.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1775 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1775">
-        <rdfs:label>Function analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3307"/>
-        <oboInOwl:hasNarrowSynonym>Protein function prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of gene and protein function including the prediction of functional properties of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein function analysis</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1811 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1811">
-        <rdfs:label>Prokaryotes and archae</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <rdfs:comment>The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes.</rdfs:comment>
-        <oboInOwl:hasDbXref>VT 1.5.2 Bacteriology</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Bacteriology</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2225 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2225">
-        <rdfs:label>Protein databases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein data resources.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein data resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0078"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2226 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2226">
-        <rdfs:label>Structure determination</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1317"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2229 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2229">
-        <rdfs:label>Cell biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.11 Cell biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cells, such as key genes and proteins involved in the cell cycle.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2230 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2230">
-        <rdfs:label>Classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0089"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2232 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2232">
-        <rdfs:label>Lipoproteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Lipoproteins (protein-lipid assemblies).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2257">
-        <rdfs:label>Phylogeny visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Visualise a phylogeny, for example, render a phylogenetic tree.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0084"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2258">
-        <rdfs:label>Cheminformatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasDefinition>The application of information technology to chemistry in biological research environment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Chemical informatics</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemoinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2259">
-        <rdfs:label>Systems biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Systems_biology</rdfs:seeAlso>
-        <rdfs:comment>This includes databases of models and methods to construct or analyse a model.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Biological models</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D049490</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Biological modelling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Biological system modelling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The holistic modelling and analysis of complex biological systems and the interactions therein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2269">
-        <rdfs:label>Statistics and probability</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3315"/>
-        <oboInOwl:hasNarrowSynonym>Biostatistics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The application of statistical methods to biological problems.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Biostatistics</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D056808</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2271 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2271">
-        <rdfs:label>Structure database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2275 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2275">
-        <rdfs:label>Molecular modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <oboInOwl:hasNarrowSynonym>Homology modeling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Comparative modeling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Comparative modelling</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Homology modelling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Molecular modeling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2276 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2276">
-        <rdfs:label>Protein function prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.2</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The prediction of functional properties of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1775"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2277">
-        <rdfs:label>SNP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <oboInOwl:hasDefinition>Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Single nucleotide polymorphism</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2278">
-        <rdfs:label>Transmembrane protein prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Predict transmembrane domains and topology in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0172"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2280">
-        <rdfs:label>Nucleic acid structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Use this concept for methods that are exclusively for nucleic acid structures.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2397">
-        <rdfs:label>Exons</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0655"/>
-        <oboInOwl:hasExactSynonym>Gene features (exon)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Exons in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2399">
-        <rdfs:label>Gene transcription features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasNarrowSynonym>GC signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>CAAT signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>-35 signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Gene transcriptional features</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Enhancers (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Terminators (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Transcription of DNA into RNA including the regulation of transcription.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Ribosome binding sites (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>-10 signals (report)</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>TATA signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Attenuators (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2533">
-        <rdfs:label>DNA mutation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0199"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <oboInOwl:hasExactSynonym>Mutation annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA mutation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (mutation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2640 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2640">
-        <rdfs:label>Oncology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>VT 3.2.16 Oncology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Cancer</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of cancer, for example, genes and proteins implicated in cancer.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Cancer biology</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2661 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2661">
-        <rdfs:label>Toxins and targets</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2840"/>
-        <oboInOwl:hasNarrowSynonym>Toxins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Targets</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Structural and associated data for toxic chemical substances.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2754 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2754">
-        <rdfs:label>Introns</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <oboInOwl:hasExactSynonym>Gene features (intron)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (intron)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Introns in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2754"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2807 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2807">
-        <rdfs:label>Tool topic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2809 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2809">
-        <rdfs:label>Study topic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2811 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2811">
-        <rdfs:label>Nomenclature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Biological nomenclature (naming), symbols and terminology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0089"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2813 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2813">
-        <rdfs:label>Disease genes and proteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The genes, gene variations and proteins involved in one or more specific diseases.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2814 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2814">
-        <rdfs:label>Protein structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <oboInOwl:hasExactSynonym>Protein structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Protein secondary or tertiary structural data and/or associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId>http://edamontology.org/topic_3040</oboInOwl:hasAlternativeId>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2815 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2815">
-        <rdfs:label>Humans</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2820"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2816 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2816">
-        <rdfs:label>Gene resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Gene resource</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Informatics resource (typically a database) primarily focussed on genes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene database</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2817 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2817">
-        <rdfs:label>Yeast</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0782"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2818 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2818">
-        <rdfs:label>Eukaryotes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:hasExactSynonym>Eukaryote</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <rdfs:comment>The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2819 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2819">
-        <rdfs:label>Invertebrates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3500"/>
-        <rdfs:comment>The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2820 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2820">
-        <rdfs:label>Vertebrates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3500"/>
-        <rdfs:comment>The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates.</rdfs:comment>
-        <oboInOwl:hasDefinition>Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2821 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2821">
-        <rdfs:label>Unicellular eukaryotes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <oboInOwl:hasDefinition>Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2826 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2826">
-        <rdfs:label>Protein structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Protein secondary or tertiary structure alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0183"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2828 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2828">
-        <rdfs:label>X-ray diffraction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>X-ray microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Crystallography</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>X-ray crystallography</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2829 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2829">
-        <rdfs:label>Ontologies, nomenclature and classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D002965</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0089"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2830 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2830">
-        <rdfs:label>Immunoproteins, genes and antigens</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0804"/>
-        <oboInOwl:hasNarrowSynonym>Immunopeptides</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Immunity-related genes, proteins and their ligands.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Antigens</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc.&quot;</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Immunoproteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Immunogenes</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2839 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2839">
-        <rdfs:label>Molecules</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasRelatedSynonym>CHEBI:23367</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3047"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2840 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2840">
-        <rdfs:label>Toxicology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3377"/>
-        <oboInOwl:hasDefinition>Toxins and the adverse effects of these chemical substances on living organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.9 Toxicology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Toxicoinformatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Toxicology</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Computational toxicology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2842 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2842">
-        <rdfs:label>High-throughput sequencing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Next-generation sequencing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3168"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2844 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2844">
-        <rdfs:label>Structural clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters.</oboInOwl:hasDefinition>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasExactSynonym>Structure classification</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2846 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2846">
-        <rdfs:label>Gene regulatory networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0204"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Gene regulatory networks.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2847 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2847">
-        <rdfs:label>Disease (specific)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Informatics resources dedicated to one or more specific diseases (not diseases in general).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2867">
-        <rdfs:label>VNTR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (VNTR)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Variable number of tandem repeat polymorphism</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>VNTR annotation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times.</rdfs:comment>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2868">
-        <rdfs:label>Microsatellites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (microsatellite)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Microsatellite annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Microsatellite polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2868"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2869">
-        <rdfs:label>RFLP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <oboInOwl:hasDefinition>Restriction fragment length polymorphisms (RFLP) in a DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>RFLP annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (RFLP)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2885">
-        <rdfs:label>DNA polymorphism</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0199"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (polymorphism)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>DNA polymorphism.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Polymorphism annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2885"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2953 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2953">
-        <rdfs:label>Nucleic acid design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Topic for the design of nucleic acid sequences with specific conformations.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0173"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3032 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3032">
-        <rdfs:label>Primer or probe design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The design of primers for PCR and DNA amplification or the design of molecular probes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0632"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3038 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3038">
-        <rdfs:label>Structure databases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.2</obsolete_since>
-        <oboInOwl:hasExactSynonym>Structure data resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0081"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3039 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3039">
-        <rdfs:label>Nucleic acid structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.2</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3041 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3041">
-        <rdfs:label>Sequence databases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Molecular sequence data resources, including sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Sequence data resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence data resource</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3042 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3042">
-        <rdfs:label>Nucleic acid sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Nucleotide sequences</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0640"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3043 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3043">
-        <rdfs:label>Protein sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0639"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3044 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3044">
-        <rdfs:label>Protein interaction networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0147"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3047 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3047">
-        <rdfs:label>Molecular biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDbXref>VT 1.5.4 Biochemistry and molecular biology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3048 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3048">
-        <rdfs:label>Mammals</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3050 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3050">
-        <rdfs:label>Biodiversity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0610"/>
-        <oboInOwl:hasDefinition>The degree of variation of life forms within a given ecosystem, biome or an entire planet.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.5 Biodiversity conservation</oboInOwl:hasDbXref>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D044822</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3052 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3052">
-        <rdfs:label>Sequence clusters and classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>The comparison, grouping together and classification of macromolecules on the basis of sequence similarity.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence families</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence clusters</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0594"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3053 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3053">
-        <rdfs:label>Genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D005823</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The study of genes, genetic variation and heredity in living organisms.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasNarrowSynonym>Heredity</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3055 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3055">
-        <rdfs:label>Quantitative genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0625"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3056 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3056">
-        <rdfs:label>Population genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasDefinition>The distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3060 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3060">
-        <rdfs:label>Regulatory RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0659"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3061 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3061">
-        <rdfs:label>Documentation and help</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3068"/>
-        <oboInOwl:hasDefinition>The documentation of resources such as tools, services and databases and how to get help.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Help</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasNarrowSynonym>Documentation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3062 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3062">
-        <rdfs:label>Genetic organisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The structural and functional organisation of genes and other genetic elements.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3063 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3063">
-        <rdfs:label>Medical informatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasExactSynonym>Health informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Clinical informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Biomedical informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Translational medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>The application of information technology to health, disease and biomedicine.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Healthcare informatics</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Health and disease</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Molecular medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3064 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3064">
-        <rdfs:label>Developmental biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDbXref>VT 1.5.14 Developmental biology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>How organisms grow and develop.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3065 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3065">
-        <rdfs:label>Embryology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3064"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3067 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3067">
-        <rdfs:label>Anatomy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDbXref>VT 3.1.1 Anatomy and morphology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The form and function of the structures of living organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3068 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3068">
-        <rdfs:label>Literature and reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasNarrowSynonym>Literature search</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The scientific literature, reference information and documentation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Literature sources</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D011642</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3070 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3070">
-        <rdfs:label>Biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDbXref>VT 1.5.8 Biology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDbXref>VT 1.5 Biological sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.23 Reproductive biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Cryobiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Biological rhythms</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>A particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.5.7 Biological rhythm</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Biological science</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Aerobiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.99 Other</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Chronobiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.13 Cryobiology
-</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.1 Aerobiology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.3 Behavioural biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Reproductive biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Behavioural biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3071 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3071">
-        <rdfs:label>Data management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasDefinition>The development and use of architectures, policies, practices and procedures for management of data.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Data handling</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D030541</rdfs:seeAlso>
-        <oboInOwl:hasDbXref>VT 1.3.1 Data management</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3072 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3072">
-        <rdfs:label>Sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The detection of the positional features, such as functional and other key sites, in molecular sequences.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D058977</rdfs:seeAlso>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3073 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3073">
-        <rdfs:label>Nucleic acid feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The detection of positional features such as functional sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition rdf:resource="http://edamontology.org/topic_0747"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3074 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3074">
-        <rdfs:label>Protein feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The detection, identification and analysis of positional protein sequence features, such as functional sites.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3075 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3075">
-        <rdfs:label>Biological system modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.2</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Topic for modelling biological systems in mathematical terms.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2259"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3077">
-        <rdfs:label>Data acquisition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3078">
-        <rdfs:label>Genes and proteins resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Gene family</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Gene and protein families</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0623"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3118">
-        <rdfs:label>Protein topological domains</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0736"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3539"/>
-        <oboInOwl:hasDefinition>Topological domains such as cytoplasmic regions in a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (topological domains)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3118"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3120 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3120">
-        <rdfs:label>Protein variants</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:hasDefinition>protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3120"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3123">
-        <rdfs:label>Expression signals</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0203"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (expression signal)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Regions within a nucleic acid sequence containing a signal that alters a biological function.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3123"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3125 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3125">
-        <rdfs:label>DNA binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <rdfs:comment>This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes).</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (binding)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Nucleic acids binding to some other molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3125"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3126">
-        <rdfs:label>Nucleic acid repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <created_in>beta13</created_in>
-        <rdfs:comment>This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at  both ends of a defined sequence and other types of repeating unit.</rdfs:comment>
-        <oboInOwl:hasDefinition>Repetitive elements within a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3126"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3127">
-        <rdfs:label>DNA replication and recombination</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3125"/>
-        <oboInOwl:hasDefinition>DNA replication or recombination.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Nucleosome exclusion sequences</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (replication and recombination)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3127"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3135">
-        <rdfs:label>Signal or transit peptide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (signal or transit peptide)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle.</rdfs:comment>
-        <oboInOwl:hasDefinition>Coding sequences for a signal or transit peptide.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3135"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3139">
-        <rdfs:label>Sequence tagged sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (STS)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <rdfs:comment>Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs.</rdfs:comment>
-        <oboInOwl:hasDefinition>Sequence tagged sites (STS) in nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3139"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3168 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3168">
-        <rdfs:label>Sequencing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D059014</rdfs:seeAlso>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasNarrowSynonym>NGS</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Next generation sequencing</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Next gen sequencing</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3169 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3169">
-        <rdfs:label>ChIP-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Chip sequencing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Chip seq</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>The analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Chip-sequencing</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3170 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3170">
-        <rdfs:label>RNA-Seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Small RNA-seq</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Whole transcriptome shotgun sequencing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA-seq</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Small RNA-Seq</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>WTSS</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3171 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3171">
-        <rdfs:label>DNA methylation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D019175</rdfs:seeAlso>
-        <created_in>1.1</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3172">
-        <rdfs:label>Metabolomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3391"/>
-        <oboInOwl:hasDefinition>The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D055432</rdfs:seeAlso>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3173">
-        <rdfs:label>Epigenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3295"/>
-        <rdfs:comment>Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D057890</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The study of the epigenetic modifications of a whole cell, tissue, organism etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3174">
-        <rdfs:label>Metagenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0610"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D056186</rdfs:seeAlso>
-        <oboInOwl:hasBroadSynonym>Ecogenomics</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Community genomics</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Environmental genomics</oboInOwl:hasBroadSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>The study of genetic material recovered from environmental samples, and associated environmental data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3175">
-        <rdfs:label>Structural variation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0199"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0624"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genomic structural variation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3176">
-        <rdfs:label>DNA packaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D042003</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3177">
-        <rdfs:label>DNA-Seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>DNA-seq</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3168"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3178">
-        <rdfs:label>RNA-Seq alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>RNA-seq alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The alignment of sequences of (typically millions) of short reads to a reference genome.  This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0196"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3179">
-        <rdfs:label>ChIP-on-chip</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Experimental techniques that combine chromatin immunoprecipitation (&apos;ChIP&apos;) with microarray (&apos;chip&apos;). ChIP-on-chip is used for high-throughput study protein-DNA interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChIP-chip</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3263 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3263">
-        <rdfs:label>Data security</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Data privacy</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The protection of data, such as patient health data, from damage or unwanted access from unauthorized users.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3277">
-        <rdfs:label>Sample collections</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasNarrowSynonym>samples</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>biobanking</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>biosamples</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Biological samples and specimens.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Specimen collections</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3292">
-        <rdfs:label>Biochemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <oboInOwl:hasDbXref>VT 1.5.4 Biochemistry and molecular biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Chemical biology</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Biological chemistry</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Chemical substances and physico-chemical processes and that occur within living organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3293">
-        <rdfs:label>Phylogenetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0084"/>
-        <oboInOwl:hasDefinition>The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences).</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D010802</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3295">
-        <rdfs:label>Epigenetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3321"/>
-        <oboInOwl:hasNarrowSynonym>Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence.</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>DNA methylation</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes sub-topics such as histone modification and DNA methylation.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D019175</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Histone modification</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3297">
-        <rdfs:label>Biotechnology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3298">
-        <rdfs:label>Phenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0625"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3299"/>
-        <oboInOwl:hasDefinition>Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. </oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3299">
-        <rdfs:label>Evolutionary biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDbXref>VT 1.5.16 Evolutionary biology</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3300">
-        <rdfs:label>Physiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The functions of living organisms and their constituent parts.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 3.1.8 Physiology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3301">
-        <rdfs:label>Microbiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDefinition>The biology of microorganisms.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.20 Microbiology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3302">
-        <rdfs:label>Parasitology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The biology of parasites.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3303">
-        <rdfs:label>Medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasNarrowSynonym>General medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Research in support of healing by diagnosis, treatment, and prevention of disease.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 3.1 Basic medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.2.9 General and internal medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Experimental medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Biomedical research</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Clinical medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.2 Clinical medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Internal medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3304">
-        <rdfs:label>Neurobiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasBroadSynonym>Neuroscience</oboInOwl:hasBroadSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The study of the nervous system and brain; its anatomy, physiology and function.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.5 Neuroscience</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3305">
-        <rdfs:label>Public health and epidemiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.3.1 Epidemiology</oboInOwl:hasDbXref>
-        <oboInOwl:hasAlternativeId>Topic concerning the the patterns, cause, and effect of disease within populations.</oboInOwl:hasAlternativeId>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>Public health</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Epidemiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3306">
-        <rdfs:label>Biophysics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3318"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.9 Biophysics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The use of physics to study biological system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3307">
-        <rdfs:label>Computational biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasDbXref>VT 1.5.19 Mathematical biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.12 Computational biology</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology).</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Mathematical biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.26 Theoretical biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Theoretical biology</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Biomathematics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3308">
-        <rdfs:label>Transcriptomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0203"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <oboInOwl:hasDefinition>The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Transcriptome</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3314">
-        <rdfs:label>Chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasBroadSynonym>VT 1.7.10 Polymer science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.7 Mathematical chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.7.3 Colloid chemistry</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>Mathematical chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Physical chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.9 Physical chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Polymer science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Chemical science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Organic chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.6 Inorganic and nuclear chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.7 Chemical sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.7.5 Electrochemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Inorganic chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.2 Chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Nuclear chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.8 Organic chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The composition and properties of matter, reactions, and the use of reactions to create new substances.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3315">
-        <rdfs:label>Mathematics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The study of numbers (quantity) and other topics including structure, space, and change.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT:1.1 Mathematics</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Maths</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.1.99 Other</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3316">
-        <rdfs:label>Computer science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.2 Computer sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.2.99 Other</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The theory and practical use of computer systems.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3318">
-        <rdfs:label>Physics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The study of matter, space and time, and related concepts such as energy and force.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3320">
-        <rdfs:label>RNA splicing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3321"/>
-        <oboInOwl:hasDefinition>RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3321">
-        <rdfs:label>Molecular genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The structure and function of genes at a molecular level.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3322">
-        <rdfs:label>Respiratory medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.25 Respiratory systems</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Pulmonology</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The study of respiratory system.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pulmonary medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Respiratory disease</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>Pulmonary disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3323">
-        <rdfs:label>Metabolic disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The study of metabolic diseases.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>1.3</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3407"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3324 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3324">
-        <rdfs:label>Infectious disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:hasExactSynonym>Transmissable disease</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.3.4 Infectious diseases</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Communicable disease</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions).</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3325">
-        <rdfs:label>Rare diseases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0634"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The study of rare diseases.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3332">
-        <rdfs:label>Computational chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.7.4 Computational chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems.</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3334">
-        <rdfs:label>Neurology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Neurological disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the anatomy, functions and disorders of the nervous system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3335">
-        <rdfs:label>Cardiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Cardiovascular disease</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.4 Cardiac and Cardiovascular systems</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Cardiovascular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Heart disease</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.22 Peripheral vascular disease</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The diseases and abnormalities of the heart and circulatory system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3336">
-        <rdfs:label>Drug discovery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The discovery and design of drugs or potential drug compounds.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3337">
-        <rdfs:label>Biobank</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <oboInOwl:hasExactSynonym>biobanking</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Repositories of biological samples, typically human, for basic biological and clinical research.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Tissue collection</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3338">
-        <rdfs:label>Mouse clinic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3339">
-        <rdfs:label>Microbial collection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <oboInOwl:hasDefinition>Collections of microbial cells including bacteria, yeasts and moulds.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3340">
-        <rdfs:label>Cell culture collection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3341">
-        <rdfs:label>Clone library</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3342">
-        <rdfs:label>Translational medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>&apos;translating&apos; the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3343">
-        <rdfs:label>Compound libraries and screening</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3336"/>
-        <oboInOwl:hasBroadSynonym>Translational medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Chemical library</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Collections of chemicals, typically for use in high-throughput screening experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Compound library</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Chemical screening</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3344">
-        <rdfs:label>Biomedical science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Topic concerning biological science that is (typically) performed in the context of medicine.</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.3 Health sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Health science</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3345">
-        <rdfs:label>Data identity and mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasExactSynonym>Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases.</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3346">
-        <rdfs:label>Sequence search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Sequence database search</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The search and retrieval from a database on the basis of molecular sequence similarity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3360">
-        <rdfs:label>Biomarkers</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasExactSynonym>Diagnostic markers</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Objective indicators of biological state often used to assess health, and determinate treatment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3361 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3361">
-        <rdfs:label>Laboratory techniques</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The procedures used to conduct an experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Lab techniques</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3365">
-        <rdfs:label>Data architecture, analysis and design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>The development of policies, models and standards that cover data acquisitioin, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Data analysis</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data design</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Data architecture</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3366">
-        <rdfs:label>Data integration and warehousing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data.
-
-</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Data integration</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Data warehousing</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3368">
-        <rdfs:label>Biomaterials</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3297"/>
-        <oboInOwl:hasDefinition>Any matter, surface or construct that interacts with a biological system.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Diagnostic markers</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3369">
-        <rdfs:label>Chemical biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3371"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The use of synthetic chemistry to study and manipulate biological systems.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3370">
-        <rdfs:label>Analytical chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The study of the separation, identification, and quantification of the chemical components of natural and artificial materials.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.7.1 Analytical chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3371">
-        <rdfs:label>Synthetic chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <oboInOwl:hasExactSynonym>Synthetic organic chemistry</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The use of chemistry to create new compounds.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3372">
-        <rdfs:label>Software engineering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasDbXref>VT 1.2.1 Algorithms</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym> Programming languages</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.2.7 Data structures</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Software development</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Software engineering</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Computer programming</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>1.2.12 Programming languages</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The process that leads from an original formulation of a computing problem to executable programs.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Data structures</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Algorithms</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.2.14 Software engineering</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3373 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3373">
-        <rdfs:label>Drug development</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Medicine development</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The process of bringing a new drug to market once a lead compounds has been identified through drug discovery.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Drug development science</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Medicines development</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3374 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3374">
-        <rdfs:label>Drug formulation and delivery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Drug delivery</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Drug formulation</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3375 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3375">
-        <rdfs:label>Pharmacokinetics and pharmacodynamics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasNarrowSynonym>Pharmacodynamics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Pharmacokinetics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Drug distribution</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Drug excretion</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of how a drug interacts with the body.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Drug absorption</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>ADME</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Drug metabolism</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Drug metabolism</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3376 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3376">
-        <rdfs:label>Medicines research and development</rdfs:label>
-        <rdfs:label>Medicine research and development</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDefinition>The discovery, development and approval of medicines.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Health care research</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>Drug discovery and development</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasBroadSynonym>Health care science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3377 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3377">
-        <rdfs:label>Safety sciences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Drug safety</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The safety (or lack) of drugs and other medical interventions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3378">
-        <rdfs:label>Pharmacovigilence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3377"/>
-        <created_in>1.4</created_in>
-        <rdfs:comment>Pharmacovigilence concerns safety once a drug has gone to market.</rdfs:comment>
-        <oboInOwl:hasDefinition>The detection, assesment, understanding and prevention of adverse effects of medicines.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3379">
-        <rdfs:label>Preclinical and clinical studies</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Preclinical studies</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Clinical studies</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3382 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3382">
-        <rdfs:label>Imaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <rdfs:comment>This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as  X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Microscopy imaging</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Diffraction experiment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The visual representation of an object.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3383">
-        <rdfs:label>Biological imaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The use of imaging techniques to understand biology.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3384">
-        <rdfs:label>Medical imaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDbXref>VT 3.2.24 Radiology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The use of imaging techniques for clinical purposes for medical research.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Radiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.14 Nuclear medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Nuclear medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.13 Medical imaging</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3385">
-        <rdfs:label>Light microscopy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The use of optical instruments to magnify the image of an object.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3386">
-        <rdfs:label>Laboratory animal science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The use of animals and alternatives in experimental research.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3387">
-        <rdfs:label>Marine biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.18 Marine and Freshwater biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The study of organisms in the ocean or brackish waters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3388">
-        <rdfs:label>Molecular medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3342"/>
-        <oboInOwl:hasDefinition>The identification of molecular and genetic causes of disease and the development of interventions to correct them.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3390">
-        <rdfs:label>Nutritional science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 3.3.7 Nutrition and Dietetics</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Dietetics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals.  It also includes the study of human behaviours related to food choices.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nutrition science</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3391">
-        <rdfs:label>Omics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDefinition>The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3393">
-        <rdfs:label>Quality affairs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The processes that need to be in place to ensure the quality of products for human or animal use.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Good clinical practice</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Good manufacturing practice</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Quality assurance</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Good laboratory practice</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3394 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3394">
-        <rdfs:label>Regulatory affairs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3395">
-        <rdfs:label>Regnerative medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasExactSynonym>Stem cell research</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Biomedical approaches to clinical interventions that involve the use of stem cells.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3396">
-        <rdfs:label>Systems medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3397">
-        <rdfs:label>Veterinary medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasAlternativeId>Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals.</oboInOwl:hasAlternativeId>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3398">
-        <rdfs:label>Bioengineering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3297"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The application of biological concepts and methods to the analytical and synthetic methodologies of engineering.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Diagnostic markers</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3399">
-        <rdfs:label>Geriatric medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.10 Geriatrics and gerontology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Ageing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Aging</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Gerontology</oboInOwl:hasBroadSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Geriatrics</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3400">
-        <rdfs:label>Allergy, clinical immunology and immunotherapeutics.</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.1 Allergy</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Health issues related to the immune system and their prevention, diagnosis and mangement.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Immune disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Clinical immunology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Immunomodulators</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Allergy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Immunotherapeutics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3401">
-        <rdfs:label>Pain medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Ageing</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Algiatry</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3402">
-        <rdfs:label>Anaesthesiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Anaesthetics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Anaesthesia and anaesthetics.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 3.2.2 Anaesthesiology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3403">
-        <rdfs:label>Critical care medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Acute medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Geriatrics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.5 Critical care/Emergency medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Emergency medicine</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The multidisciplinary that cares for patients with acute, life-threatening illness or injury.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3404">
-        <rdfs:label>Dermatology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Dermatological disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 3.2.7 Dermatology and venereal diseases</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3405">
-        <rdfs:label>Dentistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3406">
-        <rdfs:label>Ear, nose and throat medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Otolaryngology</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Otorhinolaryngology</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Head and neck disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.20 Otorhinolaryngology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Audiovestibular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3407">
-        <rdfs:label>Endocrinology and metabolism</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Metabolic disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Metabolism</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Endocrinology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Endocrine disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3408">
-        <rdfs:label>Haematology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.11 Hematology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the blood, blood-forming organs and blood diseases.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Haematological disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Blood disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3409">
-        <rdfs:label>Gastroenterology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Gastrointestinal disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.8 Gastroenterology and hepatology</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3410">
-        <rdfs:label>Gender medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3411">
-        <rdfs:label>Gynaecology and obstetrics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.15 Obstetrics and gynaecology</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Gynaecology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Gynaecological disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Obstetrics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3412">
-        <rdfs:label>Hepatic and biliary medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Hepatobiliary medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Liver disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the liver, gallbladder, bile ducts and bile.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3413">
-        <rdfs:label>Infectious tropical disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3324"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the infectious diseases of the tropics. </oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3414">
-        <rdfs:label>Trauma medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3415">
-        <rdfs:label>Medical toxicology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3416">
-        <rdfs:label>Musculoskeletal medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue.  It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.26 Rheumatology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.2.19 Orthopaedics</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Musculoskeletal disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Orthopaedics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Rheumatology</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3417">
-        <rdfs:label>Opthalmology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Eye disoders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.18 Optometry</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasBroadSynonym>Optometry</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.17 Ophthalmology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Audiovestibular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3418 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3418">
-        <rdfs:label>Paediatrics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the medical care of infants, children and adolescents.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.21 Paediatrics</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Child health</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3419">
-        <rdfs:label>Psychiatry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Psychiatric disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.23 Psychiatry</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Mental health</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3420">
-        <rdfs:label>Reproductive health</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Reproductive disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Audiovestibular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.3 Andrology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Andrology</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Family planning</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The health of the reproductive processes, functions and systems at all stages of life.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Fertility medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3421">
-        <rdfs:label>Surgery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Transplantation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.28 Transplantation</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3422">
-        <rdfs:label>Urology and nephrology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.29 Urology and nephrology</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Urology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Kidney disease</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Urological disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nephrology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3423">
-        <rdfs:label>Complementary medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.12 Integrative and Complementary medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Holistic medicine</oboInOwl:hasBroadSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasBroadSynonym>Alternative medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Integrative medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3444">
-        <rdfs:label>MRI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasExactSynonym>Nuclear magnetic resonance imaging</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>MRT</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Magnetic resonance tomography</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>NMRI</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Magnetic resonance imaging
-</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3448">
-        <rdfs:label>Neutron diffraction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Neutron microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Elastic neutron scattering</oboInOwl:hasNarrowSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>Neutron diffraction experiment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3452">
-        <rdfs:label>Tomography</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasNarrowSynonym>X-ray tomography</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Electron tomography</oboInOwl:hasNarrowSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3473">
-        <rdfs:label>Data mining</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDbXref>VT 1.3.2 Data mining</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>KDD</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Knowledge discovery in databases</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3474">
-        <rdfs:label>Machine learning</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasDefinition>A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Artificial Intelligence</oboInOwl:hasBroadSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDbXref>VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics)</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3489">
-        <rdfs:label>Database management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasNarrowSynonym>Data maintenance</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Databases</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Database administration</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources.
-</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Biological databases</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3500">
-        <rdfs:label>Animals</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasBroadSynonym>Animal biology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Zoology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>Animal</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.29 Zoology</oboInOwl:hasDbXref>
-        <rdfs:comment>The resource may be specific to a plant, a group of plants or all plants.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Metazoa</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3510 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3510">
-        <rdfs:label>Protein sites, features and motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:hasNarrowSynonym>Protein sequence features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein functional sites</oboInOwl:hasNarrowSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3511">
-        <rdfs:label>Nucleic acid sites, features and motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid sequence features</oboInOwl:hasNarrowSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid functional sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3512">
-        <rdfs:label>Gene transcript features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (mRNA features)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>mRNA features</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes 5&apos;untranslated region (5&apos;UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3&apos;untranslated regions (3&apos;UTR).</rdfs:comment>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3514">
-        <rdfs:label>Protein-ligand interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0128"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Protein-ligand (small molecule) interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3515">
-        <rdfs:label>Protein-drug interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3514"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Protein-drug interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3516">
-        <rdfs:label>Genotyping experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3517 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3517">
-        <rdfs:label>GWAS study</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Genome-wide association study experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome-wide association study</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3518 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3518">
-        <rdfs:label>Microarray experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <rdfs:comment>This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates.</rdfs:comment>
-        <oboInOwl:hasDefinition>Microarray experiments including conditions, protocol, sample:data relationships etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3519">
-        <rdfs:label>PCR experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>PCR experiments, e.g. quantitative real-time PCR.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3520">
-        <rdfs:label>Proteomics experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <oboInOwl:hasDefinition>Proteomics experiments.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3521">
-        <rdfs:label>2D PAGE experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3520"/>
-        <oboInOwl:hasDefinition>Two-dimensional gel electrophoresis experiments, gels or spots in a gel.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3522">
-        <rdfs:label>Northern blot experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3520"/>
-        <oboInOwl:hasDefinition>Northern Blot experiments.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3523">
-        <rdfs:label>RNAi experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3168"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>RNAi experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3524">
-        <rdfs:label>Simulation experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3525">
-        <rdfs:label>Protein-nucleic acid interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0128"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Protein-DNA/RNA interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3526">
-        <rdfs:label>Protein-protein interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:hasNarrowSynonym>Domain-domain interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Protein-protein interaction(s), including interactions between protein domains.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein interaction networks</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3527">
-        <rdfs:label>Cellular process pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Cellular process pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3528">
-        <rdfs:label>Disease pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Disease pathways, typically of human disease.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway or network (disease)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3529">
-        <rdfs:label>Environmental information processing pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Environmental information processing pathways.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Pathway or network (environmental information processing)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3530">
-        <rdfs:label>Genetic information processing pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasExactSynonym>Pathway or network (genetic information processing)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Genetic information processing pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3531">
-        <rdfs:label>Protein super-secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasDefinition>Super-secondary structure of protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (super-secondary)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <rdfs:comment>Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3533">
-        <rdfs:label>Protein active sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasExactSynonym>Enzyme active site</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (active sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Catalytic residues (active site) of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3534">
-        <rdfs:label>Protein binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasDefinition>Ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (binding sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3535 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3535">
-        <rdfs:label>Protein-nucleic acid binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasDefinition>RNA and DNA-binding proteins and binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (nucleic acid binding sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3536">
-        <rdfs:label>Protein cleavage sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasDefinition>Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (cleavage sites)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3537">
-        <rdfs:label>Protein chemical modifications</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasDefinition>Chemical modification of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (chemical modifications)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>MOD:00000</oboInOwl:hasRelatedSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasRelatedSynonym>GO:0006464</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3538 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3538">
-        <rdfs:label>Protein disordered structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasDefinition>Disordered structure in a protein.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (disordered structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3539">
-        <rdfs:label>Protein domains</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0736"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <rdfs:comment>The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Structural domains or 3D folds in a protein or polypeptide chain.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein structural domains</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein features (domains)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3540">
-        <rdfs:label>Protein key folding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0130"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasExactSynonym>Protein features (key folding sites)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Key residues involved in protein folding.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3541 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3541">
-        <rdfs:label>Protein post-translational modifications</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasExactSynonym>Protein features (post-translation modifications)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Post-translation modifications</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Post-translation modifications in a protein sequence, typically describing the specific sites involved.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3542">
-        <rdfs:label>Protein secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <rdfs:comment>The location and size of the secondary structure elements and intervening loop regions is typically given.  The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks).</rdfs:comment>
-        <oboInOwl:hasDefinition>Secondary structure (predicted or real) of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (secondary structure)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3543">
-        <rdfs:label>Protein sequence repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (repeats)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Short repetitive subsequences (repeat sequences) in a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein repeats</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3544 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3544">
-        <rdfs:label>Protein signal peptides</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasExactSynonym>Protein features (signal peptides)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Signal peptides or signal peptide cleavage sites in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3569">
-        <rdfs:label>Applied mathematics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3315"/>
-        <oboInOwl:hasDbXref>VT 1.1.1 Applied mathematics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3570">
-        <rdfs:label>Pure mathematics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3315"/>
-        <oboInOwl:hasDbXref>VT 1.1.1 Pure mathematics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The study of abstract mathematical concepts.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3571">
-        <rdfs:label>Data governance</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasExactSynonym>Data handling</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D030541</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasNarrowSynonym>Data stewardship</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3572">
-        <rdfs:label>Data quality management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D030541</rdfs:seeAlso>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasNarrowSynonym>Data quality</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data integrity</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data clean-up</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data enrichment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The quality, integrity, cleaning up and enrichment of data. </oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3573">
-        <rdfs:label>Freshwater biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.18 Marine and Freshwater biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The study of organisms in freshwater ecosystems.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3574">
-        <rdfs:label>Human genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasDefinition>The study of inheritatnce in human beings.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.2 Human genetics</oboInOwl:hasDbXref>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3575">
-        <rdfs:label>Tropical medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Health problems that are prevalent in tropical and subtropical regions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.3.14 Tropical medicine</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3576 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3576">
-        <rdfs:label>Medical biotechnology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3297"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDbXref>VT 3.4.1 Biomedical devices</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.4.2 Health-related biotechnology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.4 Medical biotechnology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.3.14 Tropical medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Pharmaceutical biotechnology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Biotechnology applied to the medical sciences and the development of medicines.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3577 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3577">
-        <rdfs:label>Personalized medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Health problems that are prevalent in tropical and subtropical regions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Molecular diagnostics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.4.5 Molecular diagnostics</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#ObsoleteClass -->
-
-    <owl:Class rdf:about="&oboInOwl;ObsoleteClass">
-        <rdfs:label>Obsolete concept (EDAM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:subClassOf rdf:resource="&owl;DeprecatedClass"/>
-        <created_in>1.2</created_in>
-        <rdfs:comment>Needed for conversion to the OBO format.</rdfs:comment>
-        <oboInOwl:hasDefinition>An obsolete concept (redefined in EDAM).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-    </owl:Class>
-    
-
-
-    <!-- http://www.w3.org/2002/07/owl#DeprecatedClass -->
-
-    <owl:Class rdf:about="&owl;DeprecatedClass"/>
-</rdf:RDF>
-
-
-
-<!-- Generated by the OWL API (version 3.4.2) http://owlapi.sourceforge.net -->
-
diff --git a/cwl/src/test/resources/cwl/ontology/gx_edam.ttl b/cwl/src/test/resources/cwl/ontology/gx_edam.ttl
deleted file mode 100644
index 8182f719d21..00000000000
--- a/cwl/src/test/resources/cwl/ontology/gx_edam.ttl
+++ /dev/null
@@ -1,7 +0,0 @@
-@prefix gx: <http://galaxyproject.org/formats/> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix edam: <http://edamontology.org/> .
-
-gx:fasta a owl:Class .
-gx:fasta owl:equivalentClass edam:format_1929 .
diff --git a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/complex_workflow/expected_result.json
deleted file mode 100644
index fd297c8da92..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/expected_result.json
+++ /dev/null
@@ -1,204 +0,0 @@
-{
-  "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2",
-  "class" : "Workflow",
-  "requirements" : [
-    {
-      "class" : "StepInputExpressionRequirement"
-    }
-  ],
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/tool"
-    }
-  ],
-  "outputs" : [
-  ],
-  "steps" : [
-    {
-      "run" : {
-        "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1",
-        "class" : "Workflow",
-        "requirements" : [
-          {
-            "class" : "StepInputExpressionRequirement"
-          }
-        ],
-        "inputs" : [
-          {
-            "type" : "File",
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/tool"
-          }
-        ],
-        "outputs" : [
-        ],
-        "steps" : [
-          {
-            "run" : {
-              "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1",
-              "class" : "Workflow",
-              "requirements" : [
-                {
-                  "class" : "StepInputExpressionRequirement"
-                }
-              ],
-              "inputs" : [
-                {
-                  "type" : "File",
-                  "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool"
-                }
-              ],
-              "outputs" : [
-              ],
-              "steps" : [
-                {
-                  "run" : {
-                    "cwlVersion" : "v1.0",
-                    "class" : "CommandLineTool",
-                    "baseCommand" : [
-                      "echo"
-                    ],
-                    "inputs" : [
-                      {
-                        "type" : "string",
-                        "inputBinding" : {
-                          "position" : 1
-                        },
-                        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-                      }
-                    ],
-                    "outputs" : [
-                      {
-                        "type" : "string",
-                        "valueFrom" : "hello",
-                        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-                      }
-                    ],
-                    "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-                  },
-                  "in" : [
-                    {
-                      "valueFrom" : "$(inputs.tool.nameroot)",
-                      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/in"
-                    },
-                    {
-                      "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool",
-                      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/tool"
-                    }
-                  ],
-                  "out" : [
-                    "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/out"
-                  ],
-                  "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root"
-                }
-              ]
-            },
-            "in" : [
-              {
-                "valueFrom" : "$(inputs.tool.nameroot)",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root/in"
-              },
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/tool",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root/tool"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root/out"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root"
-          }
-        ]
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/tool",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1"
-    },
-    {
-      "run" : {
-        "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1",
-        "class" : "Workflow",
-        "requirements" : [
-          {
-            "class" : "StepInputExpressionRequirement"
-          }
-        ],
-        "inputs" : [
-          {
-            "type" : "File",
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool"
-          }
-        ],
-        "outputs" : [
-        ],
-        "steps" : [
-          {
-            "run" : {
-              "cwlVersion" : "v1.0",
-              "class" : "CommandLineTool",
-              "baseCommand" : [
-                "echo"
-              ],
-              "inputs" : [
-                {
-                  "type" : "string",
-                  "inputBinding" : {
-                    "position" : 1
-                  },
-                  "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-                }
-              ],
-              "outputs" : [
-                {
-                  "type" : "string",
-                  "valueFrom" : "hello",
-                  "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-                }
-              ],
-              "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-            },
-            "in" : [
-              {
-                "valueFrom" : "$(inputs.tool.nameroot)",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/in"
-              },
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/tool"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/out"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root"
-          }
-        ]
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/tool",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2"
-    }
-  ]
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/complex_workflow/root_workflow.cwl
deleted file mode 100644
index 6aa8f741dad..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/root_workflow.cwl
+++ /dev/null
@@ -1,41 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root1:
-      run: "sub/sub_workflow.cwl#sub-echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-    root2:
-      run: "#echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: echo-workflow-1
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: ../echo_tool.cwl
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/sub/sub_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/complex_workflow/sub/sub_workflow.cwl
deleted file mode 100644
index de293ab19ce..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/sub/sub_workflow.cwl
+++ /dev/null
@@ -1,34 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: sub-echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: ../../echo_tool.cwl
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: sub-echo-workflow-1
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "../root_workflow.cwl#echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/expected_result.json
deleted file mode 100644
index 59fea901d3b..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/expected_result.json
+++ /dev/null
@@ -1,132 +0,0 @@
-{
-  "class" : "Workflow",
-  "cwlVersion" : "v1.0",
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#file1"
-    }
-  ],
-  "outputs" : [
-    {
-      "type" : "int",
-      "outputSource" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/count_output",
-      "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#count_output"
-    }
-  ],
-  "requirements" : [
-    {
-      "class" : "SubworkflowFeatureRequirement"
-    }
-  ],
-  "steps" : [
-    {
-      "in" : [
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#file1",
-          "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/file1"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/count_output"
-      ],
-      "run" : {
-        "class" : "Workflow",
-        "inputs" : [
-          {
-            "type" : "File",
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/file1"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "int",
-            "outputSource" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2/output",
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/count_output"
-          }
-        ],
-        "steps" : [
-          {
-            "run" : {
-              "class" : "CommandLineTool",
-              "cwlVersion" : "v1.0",
-              "inputs" : [
-                {
-                  "type" : "File",
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/wc-tool.cwl#file1"
-                }
-              ],
-              "outputs" : [
-                {
-                  "type" : "File",
-                  "outputBinding" : {
-                    "glob" : "output"
-                  },
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/wc-tool.cwl#output"
-                }
-              ],
-              "baseCommand" : [
-                "wc",
-                "-l"
-              ],
-              "stdin" : "$(inputs.file1.path)",
-              "stdout" : "output",
-              "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/wc-tool.cwl"
-            },
-            "in" : [
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/file1",
-                "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1/file1"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1/output"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1"
-          },
-          {
-            "run" : {
-              "class" : "ExpressionTool",
-              "requirements" : [
-                {
-                  "class" : "InlineJavascriptRequirement"
-                }
-              ],
-              "cwlVersion" : "v1.0",
-              "inputs" : [
-                {
-                  "type" : "File",
-                  "inputBinding" : {
-                    "loadContents" : true
-                  },
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/parseInt-tool.cwl#file1"
-                }
-              ],
-              "outputs" : [
-                {
-                  "type" : "int",
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/parseInt-tool.cwl#output"
-                }
-              ],
-              "expression" : "$({'output': parseInt(inputs.file1.contents)})",
-              "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/parseInt-tool.cwl"
-            },
-            "in" : [
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1/output",
-                "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2/file1"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2/output"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2"
-          }
-        ],
-        "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>"
-      },
-      "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0"
-    }
-  ],
-  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl"
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/parseInt-tool.cwl b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/parseInt-tool.cwl
deleted file mode 100644
index 15460db136b..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/parseInt-tool.cwl
+++ /dev/null
@@ -1,14 +0,0 @@
-class: ExpressionTool
-requirements:
-  - class: InlineJavascriptRequirement
-cwlVersion: v1.0
-
-inputs:
-  file1:
-    type: File
-    inputBinding: { loadContents: true }
-
-outputs:
-  output: int
-
-expression: "$({'output': parseInt(inputs.file1.contents)})"
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/root_workflow.cwl
deleted file mode 100644
index 9d3d313c348..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/root_workflow.cwl
+++ /dev/null
@@ -1,21 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-inputs:
-  file1: File
-outputs:
-  count_output: {type: int, outputSource: step0/count_output}
-requirements:
-  SubworkflowFeatureRequirement: {}
-steps:
-  step0:
-    in: {file1: file1}
-    out: [count_output]
-    run:
-      class: Workflow
-      inputs:
-        file1: File
-      outputs:
-        count_output: {type: int, outputSource: step2/output}
-      steps:
-        step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]}
-        step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]}
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/wc-tool.cwl b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/wc-tool.cwl
deleted file mode 100644
index 3eb09378514..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/wc-tool.cwl
+++ /dev/null
@@ -1,15 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-
-inputs:
-  file1: File
-
-outputs:
-  output:
-    type: File
-    outputBinding: { glob: output }
-
-baseCommand: [wc, -l]
-
-stdin: $(inputs.file1.path)
-stdout: output
diff --git a/cwl/src/test/resources/cwl/preprocessor/echo_tool.cwl b/cwl/src/test/resources/cwl/preprocessor/echo_tool.cwl
deleted file mode 100644
index f253c2a435f..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/echo_tool.cwl
+++ /dev/null
@@ -1,13 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: [echo]
-inputs:
-  in:
-    type: string
-    inputBinding:
-      position: 1
-outputs:
-  out:
-    type: string
-    valueFrom: "hello"
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/same_file_cyclic_dependency/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/same_file_cyclic_dependency/root_workflow.cwl
deleted file mode 100644
index fddea7eb644..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/same_file_cyclic_dependency/root_workflow.cwl
+++ /dev/null
@@ -1,34 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "#echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: echo-workflow-1
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "#echo-workflow-2"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/self_reference/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/self_reference/expected_result.json
deleted file mode 100644
index f6c98537192..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/self_reference/expected_result.json
+++ /dev/null
@@ -1,58 +0,0 @@
-{
-  "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2",
-  "class" : "Workflow",
-  "requirements" : [
-    {
-      "class" : "StepInputExpressionRequirement"
-    }
-  ],
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/tool"
-    }
-  ],
-  "outputs" : [
-  ],
-  "steps" : [
-    {
-      "run" : {
-        "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-tool",
-        "class" : "CommandLineTool",
-        "baseCommand" : [
-          "echo"
-        ],
-        "inputs" : [
-          {
-            "type" : "string",
-            "inputBinding" : {
-              "position" : 1
-            },
-            "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-tool/in"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "string",
-            "valueFrom" : "hello",
-            "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-tool/out"
-          }
-        ]
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/tool",
-          "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root"
-    }
-  ]
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/self_reference/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/self_reference/root_workflow.cwl
deleted file mode 100644
index 06a70f19f01..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/self_reference/root_workflow.cwl
+++ /dev/null
@@ -1,31 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "#echo-tool"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: echo-tool
-  class: CommandLineTool
-  baseCommand: [echo]
-  inputs:
-    in:
-      type: string
-      inputBinding:
-        position: 1
-  outputs:
-    out:
-      type: string
-      valueFrom: "hello"
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/simple_workflow/expected_result.json
deleted file mode 100644
index 82176bc4177..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/expected_result.json
+++ /dev/null
@@ -1,100 +0,0 @@
-{
-  "cwlVersion" : "v1.0",
-  "class" : "Workflow",
-  "requirements" : [
-    {
-      "class" : "StepInputExpressionRequirement"
-    }
-  ],
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#tool"
-    }
-  ],
-  "outputs" : [
-  ],
-  "steps" : [
-    {
-      "run" : {
-        "cwlVersion" : "v1.0",
-        "class" : "CommandLineTool",
-        "baseCommand" : [
-          "echo"
-        ],
-        "inputs" : [
-          {
-            "type" : "string",
-            "inputBinding" : {
-              "position" : 1
-            },
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "string",
-            "valueFrom" : "hello",
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-          }
-        ],
-        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#tool",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1"
-    },
-    {
-      "run" : {
-        "cwlVersion" : "v1.0",
-        "class" : "CommandLineTool",
-        "baseCommand" : [
-          "echo"
-        ],
-        "inputs" : [
-          {
-            "type" : "string",
-            "inputBinding" : {
-              "position" : 1
-            },
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "string",
-            "valueFrom" : "hello",
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-          }
-        ],
-        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#tool",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2"
-    }
-  ],
-  "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl"
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/simple_workflow/root_workflow.cwl
deleted file mode 100644
index 86ba8b08658..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/root_workflow.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-   tool: File
-outputs: []
-steps:
-  step1:
-    run: ../echo_tool.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-  step2:
-    run: ../echo_tool.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/root_workflow.cwl
deleted file mode 100644
index 8871f99a932..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/root_workflow.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-  tool: File
-outputs: []
-steps:
-  root:
-    run: sub_workflow_1.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_1.cwl b/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_1.cwl
deleted file mode 100644
index 13f85d169b5..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_1.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-  tool: File
-outputs: []
-steps:
-  root:
-    run: sub_workflow_2.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_2.cwl b/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_2.cwl
deleted file mode 100644
index 0d8c5a49691..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_2.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-  tool: File
-outputs: []
-steps:
-  root:
-    run: root_workflow.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/dir_example.cwl b/cwl/src/test/resources/dir_example.cwl
deleted file mode 100644
index 70efc02596a..00000000000
--- a/cwl/src/test/resources/dir_example.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-requirements:
-  - class: ShellCommandRequirement
-inputs:
-  - id: indir
-    type: Directory
-    default:
-      class: Directory
-      location: exampledir
-outputs:
-  outlist:
-    type: File
-    outputBinding:
-      glob: output.txt
-arguments: ["echo", "$(inputs.indir.basename)"]
-stdout: output.txt
diff --git a/cwl/src/test/resources/env.cwl b/cwl/src/test/resources/env.cwl
deleted file mode 100644
index 19a23e77948..00000000000
--- a/cwl/src/test/resources/env.cwl
+++ /dev/null
@@ -1,10 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: env
-requirements:
-  EnvVarRequirement:
-    envDef:
-      HELLO: $(inputs.message)
-inputs:
-  message: string
-outputs: []
diff --git a/cwl/src/test/resources/exampledir/example.txt b/cwl/src/test/resources/exampledir/example.txt
deleted file mode 100644
index 3b18e512dba..00000000000
--- a/cwl/src/test/resources/exampledir/example.txt
+++ /dev/null
@@ -1 +0,0 @@
-hello world
diff --git a/cwl/src/test/resources/file_example.cwl b/cwl/src/test/resources/file_example.cwl
deleted file mode 100644
index 6245d3232be..00000000000
--- a/cwl/src/test/resources/file_example.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-requirements:
-  - class: ShellCommandRequirement
-inputs:
-  - id: infile
-    type: File
-    default:
-      class: File
-      location: exampledir/example.txt
-outputs:
-  outlist:
-    type: File
-    outputBinding:
-      glob: output.txt
-arguments: ["echo", "$(inputs.infile.basename)"]
-stdout: output.txt
diff --git a/cwl/src/test/resources/file_size_example.cwl b/cwl/src/test/resources/file_size_example.cwl
deleted file mode 100644
index 3b24a1f5cdd..00000000000
--- a/cwl/src/test/resources/file_size_example.cwl
+++ /dev/null
@@ -1,18 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-requirements:
-  - class: ShellCommandRequirement
-inputs:
-  - id: infile
-    type: File
-    default:
-      class: File
-      location: exampledir/example.txt
-outputs:
-  outlist:
-    type: File
-    outputBinding:
-      glob: output.txt
-# size is optional according to the spec, however there are real world CWLs using it
-arguments: ["echo", "$(inputs.infile.size)"]
-stdout: output.txt
diff --git a/cwl/src/test/resources/links_dont_parse.cwl b/cwl/src/test/resources/links_dont_parse.cwl
deleted file mode 100644
index 2cab593fce8..00000000000
--- a/cwl/src/test/resources/links_dont_parse.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: File
-  ex: string
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classfile
-
-steps:
-  untar:
-    run: bad.cwl
-    in:
-      tarfile: inp
-      extractfile: ex
-    out: [example_out]
-
-  compile:
-    run: bad2.cwl
-    in:
-      src: untar/example_out
-    out: [classfile]
diff --git a/cwl/src/test/resources/logback-test.xml b/cwl/src/test/resources/logback-test.xml
deleted file mode 100644
index 5ef34ca9aad..00000000000
--- a/cwl/src/test/resources/logback-test.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<configuration>
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-            <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n</pattern>
-        </encoder>
-    </appender>
-
-    <root level="info">
-        <appender-ref ref="STDOUT"/>
-    </root>
-
-    <logger name="org.mockserver" level="WARN"/>
-    <logger name="liquibase" level="WARN"/>
-    <logger name="com.zaxxer.hikari" level="ERROR"/>
-    <logger name="HikariPool" level="ERROR"/>
-    <logger name="com.google.cloud.hadoop.gcsio.GoogleCloudStorageReadChannel" level="ERROR"/>
-</configuration>
diff --git a/cwl/src/test/resources/nestedworkflows.cwl b/cwl/src/test/resources/nestedworkflows.cwl
deleted file mode 100644
index 3963109e630..00000000000
--- a/cwl/src/test/resources/nestedworkflows.cwl
+++ /dev/null
@@ -1,52 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-
-inputs: []
-
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classout
-
-requirements:
-  - class: SubworkflowFeatureRequirement
-
-steps:
-  compile:
-    run: 1st-workflow.cwl
-    in:
-      inp:
-        source: create-tar/tar
-      ex:
-        default: "Hello.java"
-    out: [classout]
-
-  create-tar:
-    requirements:
-      - class: InitialWorkDirRequirement
-        listing:
-          - entryname: Hello.java
-            entry: |
-              public class Hello {
-                public static void main(String[] argv) {
-                    System.out.println("Hello from Java");
-                }
-              }
-    in: []
-    out: [tar]
-    run:
-      class: CommandLineTool
-      requirements:
-        - class: ShellCommandRequirement
-      arguments:
-        - shellQuote: false
-          valueFrom: |
-            date
-            tar cf hello.tar Hello.java
-            date
-      inputs: []
-      outputs:
-        tar:
-          type: File
-          outputBinding:
-            glob: "hello.tar"
diff --git a/cwl/src/test/resources/tar-param.cwl b/cwl/src/test/resources/tar-param.cwl
deleted file mode 100644
index 39e9aa07016..00000000000
--- a/cwl/src/test/resources/tar-param.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-cwlVersion: "v1.0"
-class: "CommandLineTool"
-baseCommand: ["tar", "xf"]
-inputs: 
-  - type: "string"
-    inputBinding: 
-      position: 2
-    id: "extractfile"
-  - type: "File"
-    inputBinding: 
-      position: 1
-    id: "tarfile"
-outputs: 
-  - type: "File"
-    outputBinding: 
-      glob: "$(inputs.extractfile)"
-    id: "example_out"
diff --git a/cwl/src/test/resources/three_step.cwl b/cwl/src/test/resources/three_step.cwl
deleted file mode 100644
index e9cd1267b86..00000000000
--- a/cwl/src/test/resources/three_step.cwl
+++ /dev/null
@@ -1,112 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-id: three_step
-hints:
-# hints can be anything (CwlAny)
-- fee: fi
-  fo: fum
-- eenie: meenie
-  minie: mo
-- 42
-- class: DockerRequirement
-  dockerPull: "ubuntu:latest"
-inputs:
-- id: pattern
-  type: string
-outputs:
-- id: cgrep-count
-  outputSource: "#cgrep/cgrep-count"
-  type: int
-- id: wc-count
-  outputSource: "#wc/wc-count"
-  type: int
-steps:
-- id: ps
-  in: []
-  out:
-  - id: ps-stdOut
-  run:
-    inputs: []
-    outputs:
-    - id: ps-stdOut
-      outputBinding:
-        glob: ps-stdOut.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-    - class: DockerRequirement
-      dockerPull: "debian:wheezy"
-    baseCommand: ps
-    stdout: ps-stdOut.txt
-- id: cgrep
-  in:
-  - id: pattern
-    source: "#pattern"
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: cgrep-count
-  run:
-    inputs:
-    - id: pattern
-      type: string
-    - id: file
-      type: File
-    outputs:
-    - id: cgrep-count
-      outputBinding:
-        glob: cgrep-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: grep
-      shellQuote: false
-    - valueFrom: $(inputs.pattern)
-      shellQuote: false
-    - valueFrom: ${return inputs.file}
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: cgrep-stdOut.txt
-- id: wc
-  in:
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: wc-count
-  run:
-    inputs:
-    - id: file
-      type: File
-    outputs:
-    - id: wc-count
-      outputBinding:
-        glob: wc-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: cat
-      shellQuote: false
-    - valueFrom: $(inputs.file)
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: wc-stdOut.txt
diff --git a/cwl/src/test/scala/cwl/CommandLineToolSpec.scala b/cwl/src/test/scala/cwl/CommandLineToolSpec.scala
deleted file mode 100644
index b466f1f3e90..00000000000
--- a/cwl/src/test/scala/cwl/CommandLineToolSpec.scala
+++ /dev/null
@@ -1,279 +0,0 @@
-package cwl
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.assertion.CromwellTimeoutSpec
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.ParallelTestExecution
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.callable.Callable.RequiredInputDefinition
-import wom.callable.RuntimeEnvironment
-import wom.expression.NoIoFunctionSet
-import wom.types._
-import wom.values.{WomArray, WomBoolean, WomEvaluatedCallInputs, WomInteger, WomObject, WomSingleFile, WomString, WomValue}
-
-class CommandLineToolSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ParallelTestExecution {
-
-  behavior of "CommandLineTool"
-
-  val inputs: WomEvaluatedCallInputs = Map(
-    RequiredInputDefinition("a", WomStringType) -> WomString("helloA"),
-    RequiredInputDefinition("b", WomStringType) -> WomString("helloB"),
-    RequiredInputDefinition("c", WomStringType) -> WomString("helloC"),
-    RequiredInputDefinition("d", WomArrayType(WomStringType)) -> WomArray(WomArrayType(WomStringType), List(WomString("helloD0"), WomString("helloD1"))),
-    RequiredInputDefinition("e", WomCompositeType(Map("fa" -> WomSingleFileType, "fb" -> WomIntegerType)))
-      -> WomObject.withTypeUnsafe(Map("fa" -> WomSingleFile("helloEfa"), "fb" -> WomInteger(0)), WomCompositeType(Map("fa" -> WomSingleFileType, "fb" -> WomIntegerType))),
-    RequiredInputDefinition("f", WomBooleanType) -> WomBoolean.True,
-    RequiredInputDefinition("g", WomBooleanType) -> WomBoolean.False,
-    RequiredInputDefinition("h", WomIntegerType) -> WomInteger(0),
-    RequiredInputDefinition("i", WomSingleFileType) -> WomSingleFile("ifile")
-  )
-  
-  val localNameValues = inputs.map({ case (k, v) => k.localName -> v })
-  
-  val noIoFunctionSet = NoIoFunctionSet
-  
-  val runtimeEnv = RuntimeEnvironment("", "", refineMV[Positive](1), 0D, 0L, 0L)
-  
-  def validate(tool: String, expectation: List[String]) = {
-    val cltFile = better.files.File.newTemporaryFile()().write(tool)
-
-    val clt = CwlDecoder.decodeCwlFile(cltFile, None).value.unsafeRunSync() match {
-      case Left(errors) => fail("Cannot parse command line tool " + errors.toList.mkString(", "))
-      case Right(cwlFile) => cwlFile.select[CommandLineTool].get
-    }
-
-    val template = clt
-      .buildCommandTemplate.run((RequirementsAndHints(List.empty), Vector.empty,inputs))
-      .valueOr(errors => fail(errors.toList.mkString(", ")))
-    template
-      .flatTraverse(_.instantiate(localNameValues, noIoFunctionSet, identity[WomValue], runtimeEnv).map(_.map(_.commandString)))
-      .valueOr(errors => fail(errors.toList.mkString(", "))) shouldBe expectation
-    
-    cltFile.delete(true)
-  }
-  
-  it should "filter input arguments when not bound to command line" in {
-    val tool = """
-      |class: CommandLineTool
-      |cwlVersion: v1.0
-      |inputs:
-      |  - id: a
-      |    type: string
-      |    inputBinding: { position: 2 }
-      |
-      |  - id: b
-      |    type: string
-      |
-      |baseCommand: echo
-      |outputs: []
-    """.stripMargin
-
-    validate(tool, List("'echo'", "'helloA'"))
-  }
-
-  it should "order input arguments that are bound to command line" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  - id: b
-                 |    type: string
-                 |    inputBinding: { position: 2 }
-                 |    
-                 |  - id: c
-                 |    type: string
-                 |    inputBinding: { position: 3 }
-                 |
-                 |  - id: a
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'helloA'", "'helloB'", "'helloC'"))
-  }
-
-  it should "include arguments and sort them" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  - id: b
-                 |    type: string
-                 |    inputBinding: { position: 4 }
-                 |    
-                 |  - id: c
-                 |    type: string
-                 |    inputBinding: { position: 5 }
-                 |
-                 |  - id: a
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |arguments:
-                 |  - arg0
-                 |  - valueFrom: "arg2"
-                 |    position: 3
-                 |  - valueFrom: "arg1"
-                 |    position: 2
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'arg0'", "'helloA'", "'arg1'", "'arg2'", "'helloB'", "'helloC'"))
-  }
-
-  it should "handle array types" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  - id: d
-                 |    type:
-                 |      type: array
-                 |      items: string
-                 |      inputBinding: { prefix: "-YYY" }
-                 |    inputBinding: { position: 3, prefix: "-XXX" }
-                 |    
-                 |  - id: a
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |arguments:
-                 |  - valueFrom: "arg2"
-                 |    position: 2
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'helloA'", "'arg2'", "'-XXX'", "'-YYY'", "'helloD0'", "'-YYY'", "'helloD1'"))
-  }
-
-  it should "handle record schema" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  e:
-                 |    type:
-                 |      name: e
-                 |      type: record
-                 |      fields:
-                 |      - name: fa
-                 |        type: File
-                 |        inputBinding:
-                 |          position: 2
-                 |          prefix: "--prefixFa"
-                 |      - name: fb
-                 |        type: int
-                 |        inputBinding:
-                 |          position: 4
-                 |          prefix: "--prefixFb"
-                 |    inputBinding:      
-                 |      prefix: "--prefixRecord"
-                 |  a:
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |arguments:
-                 |  - valueFrom: "arg2"
-                 |    position: 3
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--prefixRecord'", "'--prefixFa'", "'helloEfa'", "'--prefixFb'", "'0'", "'helloA'", "'arg2'"))
-  }
-
-  it should "handle prefixes properly for primitive types" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  a:
-                 |    type: string
-                 |    inputBinding: { position: 1, prefix: --aprefix }
-                 |  f:
-                 |    type: boolean
-                 |    inputBinding: { position: 2, prefix: --show }
-                 |  g:
-                 |    type: boolean
-                 |    inputBinding: { position: 3, prefix: --noshow }
-                 |  h:
-                 |    type: string
-                 |    inputBinding: { position: 4, prefix: --hprefix }
-                 |  i:
-                 |    type: File
-                 |    inputBinding: { position: 5, prefix: --iprefix }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--aprefix'", "'helloA'", "'--show'", "'--hprefix'", "'0'", "'--iprefix'", "'ifile'"))
-  }
-
-  it should "handle arrays with item separator" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  d:
-                 |    type:
-                 |      type: array
-                 |      items: string
-                 |      inputBinding: { position: 2, prefix: --item }
-                 |    inputBinding: { position: 2, prefix: --array, itemSeparator: ", " }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--array'", "'helloD0, helloD1'"))
-  }
-
-  it should "handle arrays with valueFrom" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  d:
-                 |    type:
-                 |      type: array
-                 |      items: string
-                 |      inputBinding: { position: 2, prefix: --item }
-                 |    inputBinding: { position: 2, prefix: --array, valueFrom: "hello" }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--array'", "'hello'"))
-  }
-
-  it should "handle the separate field" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  a:
-                 |    type: string
-                 |    inputBinding: { position: 0, prefix: --prefix, separate: false }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--prefixhelloA'"))
-  }
-
-  it should "pull expression libs from all requirements" in {
-    val list = List(Coproduct[Requirement](InlineJavascriptRequirement(`class` = "InlineJavascriptRequirement", expressionLib = Some(Array("a")))))
-    Tool.inlineJavascriptRequirements(list).head shouldBe "a"
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CommandOutputExpressionSpec.scala b/cwl/src/test/scala/cwl/CommandOutputExpressionSpec.scala
deleted file mode 100644
index f2cc446e65f..00000000000
--- a/cwl/src/test/scala/cwl/CommandOutputExpressionSpec.scala
+++ /dev/null
@@ -1,57 +0,0 @@
-package cwl
-
-import java.util.concurrent.Executors
-
-import cats.syntax.all._
-import common.assertion.CromwellTimeoutSpec
-import cwl.CommandLineTool.CommandOutputParameter
-import cwl.ExpressionEvaluator._
-import eu.timepit.refined._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.expression.{EmptyIoFunctionSet, FileEvaluation, NoIoFunctionSet}
-import wom.types.WomIntegerType
-import wom.values._
-
-import scala.concurrent.{ExecutionContext, Future}
-
-
-class CommandOutputExpressionSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "CommandOutputExpression"
-
-  def ioFunctionSet(data: String) =
-    new EmptyIoFunctionSet {
-      override implicit def ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(1))
-      override def readFile(path: String, maxBytes: Option[Int] = None, failOnOverflow: Boolean = false) = Future.successful(data)
-      // For this test just "match" the submitted file.
-      override def glob(pattern: String): Future[Seq[String]] = Future.successful(List(pattern))
-    }
-
-  it should "evaluateValue" in {
-    val data = "41.1"
-    val tempFile = better.files.File.newTemporaryFile("glob.", ".txt").write(data)
-    val globExpression = Coproduct[Expression](refineMV[MatchesECMAScriptExpression]("$(inputs.myTempFile)"))
-    val outputEvalExpression = Coproduct[Expression](refineMV[MatchesECMAScriptExpression](
-      "$((parseInt(self[0].contents) + 1).toFixed())"))
-    val glob = Coproduct[Glob](Coproduct[StringOrExpression](globExpression))
-    val outputEval = Coproduct[StringOrExpression](outputEvalExpression)
-    val outputBinding = CommandOutputBinding(Option(glob), Option(true), Option(outputEval))
-    val commandOutputParameter = CommandOutputParameter("id", outputBinding = Option(outputBinding))
-    val commandOutputExpression = OutputParameterExpression(commandOutputParameter, WomIntegerType, Set.empty, Vector.empty, SchemaDefRequirement())
-    val inputValues = Map("myTempFile" -> WomString(tempFile.pathAsString))
-    val result = commandOutputExpression.evaluateValue(inputValues, ioFunctionSet(data))
-    result should be(WomInteger(42).valid)
-  }
-
-  it should "figure out stdout" in {
-    val glob = Coproduct[Glob](Coproduct[StringOrExpression]("stdout"))
-    val outputBinding = CommandOutputBinding(Option(glob))
-    val commandOutputParameter = CommandOutputParameter("id", outputBinding = Option(outputBinding))
-    val commandOutputExpression = OutputParameterExpression(commandOutputParameter, WomIntegerType, Set.empty, Vector.empty, SchemaDefRequirement())
-    val result = commandOutputExpression.evaluateFiles(Map.empty, NoIoFunctionSet, WomIntegerType)
-    // TODO: This should be a glob. See [[cwl.CommandOutputBinding.dependingIfGlobLike]]
-    result shouldBe Set(FileEvaluation.requiredFile(WomSingleFile("stdout"))).valid
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlDecoderSpec.scala b/cwl/src/test/scala/cwl/CwlDecoderSpec.scala
deleted file mode 100644
index c206c116a84..00000000000
--- a/cwl/src/test/scala/cwl/CwlDecoderSpec.scala
+++ /dev/null
@@ -1,48 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class CwlDecoderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "cwl decoder"
-
-  import TestSetup._
-
-  it should "read nested workflow" in {
-      decodeCwlFile(rootPath / "nestedworkflows.cwl").
-        value.
-        unsafeRunSync() match {
-        case Right(cwl) =>
-          val wf = cwl.select[Workflow].get
-          wf.steps.flatMap(_.run.select[String].toList).length shouldBe 0
-        case Left(other) => fail(other.toList.mkString(", "))
-      }
-  }
-
-  it should "fail to parse broken linked cwl" in {
-    val result: Either[NonEmptyList[String], Cwl] = decodeCwlFile(rootPath / "brokenlinks.cwl").
-      value.
-      unsafeRunSync()
-
-    result.isLeft shouldBe true
-    withClue(s"Actual message: ${result.swap.toOption.get.head}") {
-      "Field `run` contains undefined reference to `file://.+/wrong.cwl`".r.findAllIn(result.swap.toOption.get.head).size shouldBe 1
-      "Field `run` contains undefined reference to `file://.+/wrong2.cwl`".r.findAllIn(result.swap.toOption.get.head).size shouldBe 1
-    }
-  }
-
-  it should "fail to parse invalid linked cwl" in {
-      decodeCwlFile(rootPath/"links_dont_parse.cwl").
-        value.
-        unsafeRunSync() match {
-        case Left(errors) =>
-          errors.filter(_.contains("bad.cwl")).size + errors.filter(_.contains("bad2.cwl")).size shouldBe 1
-        case Right(_) => fail("should not have passed!")
-      }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlEcmaScriptDecoderSpec.scala b/cwl/src/test/scala/cwl/CwlEcmaScriptDecoderSpec.scala
deleted file mode 100644
index 6c6918efaaa..00000000000
--- a/cwl/src/test/scala/cwl/CwlEcmaScriptDecoderSpec.scala
+++ /dev/null
@@ -1,77 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.internal.{EcmaScriptEncoder, EcmaScriptUtil}
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.values.{WomFloat, WomMaybePopulatedFile, WomString, WomValue}
-
-
-class CwlEcmaScriptDecoderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-  behavior of "CwlJsDecoder"
-
-  val decodeTests= Table[String, String, Map[String, Map[String, WomValue]], WomValue](
-    (
-      "description",
-      "expr",
-      "values",
-      "expected"
-    ),
-    (
-      "a passed through file",
-      "inputMap",
-      Map("inputMap" -> Map(
-        "class" -> WomString("File"),
-        "location" -> WomString("path/to/file.txt"),
-        "checksum" -> WomString("hash_here"),
-        "size" -> WomFloat(Double.box(123.4)),
-        "format" -> WomString("file_format"),
-        "contents" -> WomString("file_contents")
-      )),
-      WomMaybePopulatedFile(
-        valueOption = Option("path/to/file.txt"),
-        checksumOption = Option("hash_here"),
-        sizeOption = Option(123L),
-        formatOption = Option("file_format"),
-        contentsOption = Option("file_contents"),
-        secondaryFiles = Vector()
-      )
-    ),
-    (
-      "a script generated file",
-      """|var result = {
-         |"class": "File",
-         |"path": "other/dir/img.jpg",
-         |"checksum": "check_sum",
-         |"size": 567.8,
-         |"format": "more_jpeg",
-         |"contents": "lol_cat"
-         |};
-         |result;
-         |""".stripMargin,
-      Map(),
-      WomMaybePopulatedFile(
-        valueOption = Option("other/dir/img.jpg"),
-        checksumOption = Option("check_sum"),
-        sizeOption = Option(567L),
-        formatOption = Option("more_jpeg"),
-        contentsOption = Option("lol_cat"),
-        secondaryFiles = Vector()
-      )
-    )
-  )
-
-  forAll(decodeTests) { (description, expr, values: Map[String, Map[String, WomValue]], expected) =>
-    it should s"decode $description" in {
-      val result = EcmaScriptUtil.evalStructish(
-        expr,
-        "fake" -> WomString("unused"),
-        values,
-        new EcmaScriptEncoder()
-      ).toTry.get
-      result should be(expected)
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlEcmaScriptEncoderSpec.scala b/cwl/src/test/scala/cwl/CwlEcmaScriptEncoderSpec.scala
deleted file mode 100644
index 9119f75c421..00000000000
--- a/cwl/src/test/scala/cwl/CwlEcmaScriptEncoderSpec.scala
+++ /dev/null
@@ -1,35 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.internal.EcmaScriptUtil.{ESArray, ESObject, ESPrimitive}
-import cwl.internal.{EcmaScriptEncoder, EcmaScriptUtil}
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.values.WomMaybePopulatedFile
-
-
-class CwlEcmaScriptEncoderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "EcmaScriptEncoder"
-
-  it should "encode" in {
-    val encoder = new EcmaScriptEncoder()
-    val file = WomMaybePopulatedFile("path/to/file.txt")
-    val expected = Map(
-      "class" -> ESPrimitive("File"),
-      "location" -> ESPrimitive("path/to/file.txt"),
-      "path" -> ESPrimitive("path/to/file.txt"),
-      "dirname" -> ESPrimitive("path/to"),
-      "basename" -> ESPrimitive("file.txt"),
-      "nameroot" -> ESPrimitive("file"),
-      "nameext" -> ESPrimitive(".txt")
-    )
-    val result: EcmaScriptUtil.ECMAScriptVariable = encoder.encode(file)
-    val resultMap = result.asInstanceOf[ESObject].fields
-    resultMap.view.filterKeys(_ != "secondaryFiles").toList should contain theSameElementsAs expected
-    resultMap("secondaryFiles") should be(a[ESArray])
-    resultMap("secondaryFiles").asInstanceOf[ESArray].array should be(empty)
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/CwlExpressionCommandPartSpec.scala b/cwl/src/test/scala/cwl/CwlExpressionCommandPartSpec.scala
deleted file mode 100644
index 0d675397a11..00000000000
--- a/cwl/src/test/scala/cwl/CwlExpressionCommandPartSpec.scala
+++ /dev/null
@@ -1,34 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.ExpressionEvaluator._
-import eu.timepit.refined._
-import eu.timepit.refined.numeric.Positive
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.callable.RuntimeEnvironment
-import wom.expression.NoIoFunctionSet
-import wom.graph.LocalName
-import wom.values.WomString
-
-
-class CwlExpressionCommandPartSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "CwlExpressionCommandPart"
-
-  val emptyEnvironment = RuntimeEnvironment("","",refineMV[Positive](1),1,1,1)
-
-  it should "instantiate" in {
-    // NOTE: toFixed used to remove the fraction part of ECMAScript numbers
-    // https://stackoverflow.com/questions/25989642/why-does-java-8-nashorn-javascript-modulo-returns-0-0-double-instead-of-0-i#answer-25991982
-    // https://community.apigee.com/questions/33936/javascript-parseint-not-converting-to-int-value-ne.html
-    val commandPart = CwlExpressionCommandPart(Coproduct[Expression](refineMV[MatchesECMAScriptExpression](
-      "$(parseInt(inputs.myStringInt).toFixed())"
-    )))(false, Vector.empty)
-    val result = commandPart.instantiate(Map(LocalName("myStringInt") -> WomString("3")), NoIoFunctionSet, identity, emptyEnvironment).toTry.get.head.commandString
-    result should be("'3'")
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/CwlInputValidationSpec.scala b/cwl/src/test/scala/cwl/CwlInputValidationSpec.scala
deleted file mode 100644
index c9d5272b07b..00000000000
--- a/cwl/src/test/scala/cwl/CwlInputValidationSpec.scala
+++ /dev/null
@@ -1,203 +0,0 @@
-package cwl
-
-import better.files.{File => BFile}
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder.decodeCwlFile
-import org.scalatest.BeforeAndAfterAll
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import shapeless.Coproduct
-import wom.expression.NoIoFunctionSet
-import wom.graph.Graph.ResolvedExecutableInput
-import wom.graph.GraphNodePort
-import wom.types.{WomArrayType, WomStringType}
-import wom.values._
-
-
-class CwlInputValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks with BeforeAndAfterAll {
-  behavior of "CWL Wom executable"
-
-  var cwlFile: BFile = _
-  var inputTempFile: BFile = _
-
-  override def beforeAll(): Unit = {
-    inputTempFile = BFile.newTemporaryFile()
-    cwlFile = BFile.newTemporaryFile().write(
-      """
-        |cwlVersion: v1.0
-        |class: Workflow
-        |inputs:
-        | w0:
-        |   type: string
-        |   default: "hi w0 !"
-        | w1: File
-        | w2:
-        |   type: string
-        |   default: "hi w2 !"
-        | w3: int
-        | w4: long
-        | w5: double
-        | w6: float
-        | w7: boolean
-        | w8:
-        |   type:
-        |     type: array
-        |     items:
-        |       type: array
-        |       items: string
-        | # enable this when InputRecordSchemas are enabled
-        | #w9:
-        | #  type:
-        | #    name: w9
-        | #    type: record
-        | #    fields:
-        | #    - name: w9a
-        | #      type: record
-        | #      fields:
-        | #      - name: w9aa
-        | #        type: string
-        | w10: Directory
-        |steps: []
-        |outputs: []
-      """.stripMargin
-    )
-  }
-
-  override def afterAll(): Unit = {
-    cwlFile.delete()
-    inputTempFile.delete()
-    ()
-  }
-
-  lazy val cwlWorkflow = decodeCwlFile(cwlFile).map {
-    _.select[Workflow].get
-  }.value.unsafeRunSync().fold(error => throw new RuntimeException(s"broken parse! msg was $error"), identity)
-
-  lazy val graph = cwlWorkflow.womDefinition(AcceptAllRequirements, Vector.empty) match {
-    case Left(errors) => fail(s"Failed to build wom definition: ${errors.toList.mkString(", ")}")
-    case Right(womDef) => womDef.graph
-  }
-
-  def getOutputPort(n: Int) = graph.inputNodes.find(_.localName == s"w$n").getOrElse(fail(s"Failed to find an input node for w$n")).singleOutputPort
-
-  lazy val w0OutputPort = getOutputPort(0)
-  lazy val w1OutputPort = getOutputPort(1)
-  lazy val w2OutputPort = getOutputPort(2)
-  lazy val w3OutputPort = getOutputPort(3)
-  lazy val w4OutputPort = getOutputPort(4)
-  lazy val w5OutputPort = getOutputPort(5)
-  lazy val w6OutputPort = getOutputPort(6)
-  lazy val w7OutputPort = getOutputPort(7)
-  lazy val w8OutputPort = getOutputPort(8)
-//  lazy val w9OutputPort = getOutputPort(9)
-  lazy val w10OutputPort = getOutputPort(10)
-
-  def validate(inputFile: String): Map[GraphNodePort.OutputPort, ResolvedExecutableInput] = {
-    cwlWorkflow.womExecutable(AcceptAllRequirements, Option(inputFile), LocalIoFunctionSet, strictValidation = false) match {
-      case Left(errors) => fail(s"Failed to build a wom executable: ${errors.toList.mkString(", ")}")
-      case Right(executable) => executable.resolvedExecutableInputs
-    }
-  }
-
-  it should "parse and validate a valid input file" in {
-    val inputFile =
-      s"""
-        w1:
-          class: File
-          path: ${inputTempFile.toString()}
-          secondaryFiles:
-            - class: File
-              path: secondaryFile.txt
-        w2: hello !
-        w3: 3
-        w4: 4
-        w5: 5.1
-        w6: 6.1
-        w7: true
-        w8: [
-          ["a", "b"],
-          ["c", "d"]
-        ]
-        w10:
-          class: Directory
-          location: "directory_location"
-          listing:
-            - class: Directory
-              path: "innerDirectory"
-            - class: File
-              location: "innerFile"
-      """.stripMargin
-    // TODO: With record schema, re-add:
-    //        w9:
-    //          w9a:
-    //            w9aa: "hello"
-
-    val validInputs = validate(inputFile).map {
-      case (port, resolvedInput) => (port.name, resolvedInput)
-    }
-
-    // w0 has no input value in the input file, so it should fallback to the default value
-    validInputs(w0OutputPort.name).select[WomValue].get.valueString shouldBe "hi w0 !"
-    validInputs(w1OutputPort.name) shouldBe
-      Coproduct[ResolvedExecutableInput](WomMaybePopulatedFile(
-        valueOption = Option(inputTempFile.toString()),
-        secondaryFiles = List(WomMaybePopulatedFile("secondaryFile.txt")),
-        sizeOption = Option(0)
-      ): WomValue)
-    validInputs(w2OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomString("hello !"): WomValue)
-    validInputs(w3OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomInteger(3): WomValue)
-    validInputs(w4OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomLong(4): WomValue)
-    validInputs(w5OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomFloat(5.1D): WomValue)
-    validInputs(w6OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomFloat(6.1D): WomValue)
-    validInputs(w7OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomBoolean(true): WomValue)
-    validInputs(w8OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](
-      WomArray(
-        WomArrayType(WomArrayType(WomStringType)),
-        List(
-          WomArray(WomArrayType(WomStringType), List(WomString("a"), WomString("b"))),
-          WomArray(WomArrayType(WomStringType), List(WomString("c"), WomString("d")))
-        )
-      ): WomValue
-    )
-    // Enable this when InputRecordSchema is enabled
-//    validInputs(w9OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](
-//      WomObject(
-//        Map(
-//          "w9a" -> WomObject(Map("w9aa" -> WomString("hello")))
-//        )
-//      ): WomValue
-//    )
-    validInputs(w10OutputPort.name) shouldBe
-      Coproduct[ResolvedExecutableInput](WomMaybeListedDirectory(
-        valueOption = Option("directory_location"),
-        listingOption = Option(
-          List(
-            WomMaybeListedDirectory("innerDirectory"),
-            WomMaybePopulatedFile("innerFile")
-          )
-        )
-      ): WomValue)
-  }
-
-  it should "not validate when required inputs are missing" in {
-    val inputFile =
-      """
-        w2: hello !
-      """.stripMargin
-
-    cwlWorkflow.womExecutable(AcceptAllRequirements, Option(inputFile), NoIoFunctionSet, strictValidation = false) match {
-      case Right(booh) => fail(s"Expected failed validation but got valid input map: $booh")
-      case Left(errors) => errors.toList.toSet shouldBe Set(
-        "Required workflow input 'w1' not specified",
-        "Required workflow input 'w3' not specified",
-        "Required workflow input 'w4' not specified",
-        "Required workflow input 'w5' not specified",
-        "Required workflow input 'w6' not specified",
-        "Required workflow input 'w7' not specified",
-        "Required workflow input 'w8' not specified",
-        "Required workflow input 'w10' not specified"
-      )
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlWorkflowWomSpec.scala b/cwl/src/test/scala/cwl/CwlWorkflowWomSpec.scala
deleted file mode 100644
index 52f511fd9b7..00000000000
--- a/cwl/src/test/scala/cwl/CwlWorkflowWomSpec.scala
+++ /dev/null
@@ -1,216 +0,0 @@
-package cwl
-
-import cats.syntax.either._
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder._
-import cwl.ExpressionEvaluator._
-import cwl.command.ParentName
-import eu.timepit.refined._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import shapeless._
-import wom.WomMatchers._
-import wom.callable.{Callable, CommandTaskDefinition, WorkflowDefinition}
-import wom.graph.GraphNodePort.OutputPort
-import wom.graph._
-import wom.graph.expression.ExpressionNode
-import wom.types.{WomMaybePopulatedFileType, WomStringType, WomType}
-
-
-class CwlWorkflowWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-  import TestSetup._
-
-  implicit val parentName = ParentName.empty
-
-  "A Cwl object for 1st-tool" should "convert to WOM" in {
-    def validateWom(callable: Callable): Unit = callable match {
-      case taskDefinition: CommandTaskDefinition =>
-        val inputDef = taskDefinition.inputs.head
-        inputDef.name shouldBe "message"
-        inputDef.womType shouldBe WomStringType
-        ()
-
-      case _ => fail("not a task definition")
-    }
-
-    import cats.syntax.validated._
-    (for {
-      clt <- decodeCwlFile(rootPath/"1st-tool.cwl").
-              map(_.select[CommandLineTool].get).
-              value.
-              unsafeRunSync()
-      taskDef <- clt.buildTaskDefinition(_.validNel, Vector.empty)
-    } yield validateWom(taskDef)).leftMap(e => throw new RuntimeException(s"error! $e"))
-  }
-
-  "Cwl for 1st workflow" should "convert to WOM" in {
-    (for {
-      wf <- decodeCwlFile(rootPath/"1st-workflow.cwl").
-              value.
-              unsafeRunSync().
-              map(_.select[Workflow].get)
-
-      womDefinition <- wf.womDefinition(AcceptAllRequirements, Vector.empty)
-    } yield validateWom(womDefinition)).leftMap(e => throw new RuntimeException(s"error! ${e.toList.mkString("\n")}"))
-
-    def shouldBeRequiredGraphInputNode(node: GraphNode, localName: String, womType: WomType): Unit = {
-      node.isInstanceOf[RequiredGraphInputNode] shouldBe true
-      val requiredGraphInputNode = node.asInstanceOf[RequiredGraphInputNode]
-      requiredGraphInputNode.localName shouldBe localName
-      requiredGraphInputNode.womType shouldBe womType
-      ()
-    }
-
-    def validateWom(callable: Callable) = {
-      callable match {
-        case wf: WorkflowDefinition =>
-          val nodes = wf.innerGraph.nodes
-
-          nodes collect {
-            case gin: GraphInputNode => gin.localName
-          } should be(Set("ex", "inp"))
-
-          nodes collect {
-            case cn: CallNode => cn.localName
-          } should be(Set("compile", "untar"))
-
-          val untarUpstream = nodes.collectFirst {
-            case tarParam: CallNode if tarParam.localName == s"untar" => tarParam
-          }.get.
-            upstream
-
-          untarUpstream should have size 2
-          untarUpstream.collectFirst({
-            case exprNode: ExpressionNode if exprNode.localName == s"file://$rootPath/1st-workflow.cwl#untar/extractfile.merge" =>
-              shouldBeRequiredGraphInputNode(exprNode.inputPorts.head.upstream.graphNode, "ex", WomStringType)
-          }).getOrElse(fail("Can't find expression node for ex"))
-
-          untarUpstream.collectFirst({
-            case exprNode: ExpressionNode if exprNode.localName == s"file://$rootPath/1st-workflow.cwl#untar/tarfile.merge" =>
-              exprNode.inputPorts.map(_.upstream.graphNode).count {
-                case rgin: RequiredGraphInputNode =>
-                  rgin.identifier.localName == LocalName("inp") &&
-                    rgin.womType == WomMaybePopulatedFileType
-              }  shouldBe 1
-          }).getOrElse(fail("Can't find expression node for inp"))
-
-          val compileUpstreamExpressionPort = nodes.collectFirst {
-            case compile: CallNode if compile.localName == s"compile" => compile
-          }.get.inputPorts.map(_.upstream).head
-
-          compileUpstreamExpressionPort.name shouldBe s"file://$rootPath/1st-workflow.cwl#compile/src.merge"
-          compileUpstreamExpressionPort.graphNode.asInstanceOf[ExpressionNode].inputPorts.map(_.upstream.internalName).count(_ == "example_out") shouldBe 1
-
-          nodes.collect {
-            case c: PortBasedGraphOutputNode => c
-          }.map(_.localName) shouldBe Set("classout")
-        case wth: Any => fail(s"Parsed unexpected Callable: $wth")
-      }
-    }
-  }
-
-  behavior of "A decoded CWL 3step"
-
-  private val stringOrExpressionTests = Table(
-    ("index", "result"),
-    (0, Coproduct[StringOrExpression]("grep")),
-    (1, Coproduct[StringOrExpression](Coproduct[Expression](refineMV[MatchesECMAScriptExpression]("$(inputs.pattern)")))),
-    (2, Coproduct[StringOrExpression](Coproduct[Expression](refineMV[MatchesECMAScriptFunction]("$" + "{return inputs.file}")))),
-    (3, Coproduct[StringOrExpression]("|")),
-    (4, Coproduct[StringOrExpression]("wc")),
-    (5, Coproduct[StringOrExpression]("-l"))
-  )
-
-  private def getTestName(stringOrExpression: StringOrExpression): String = stringOrExpression match {
-    case StringOrExpression.String(s) => s"string $s"
-    // Although these two cases look the same, they're actually calling different 'value' functions. So we
-    // can't collapse this to a single "case StringOrExpression.Expression(e) => e.value":
-    case StringOrExpression.ECMAScriptExpression(e) => e.value
-    case StringOrExpression.ECMAScriptFunction(f) => f.value
-    case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-  }
-
-  private lazy val commandLineTool: CommandLineTool = {
-    val wf = decodeCwlFile(rootPath / "three_step.cwl").map { wf =>
-      wf.select[Workflow].get
-    }.value.unsafeRunSync().fold(error => throw new RuntimeException(s"broken parse! msg was ${error.toList.mkString(", ")}"), identity)
-
-    wf.id should include("three_step")
-
-    // The second step (aka 1) step should be cgrep
-    val run: WorkflowStep.Run = wf.steps.apply(1).run
-    val commandLineTool: CommandLineTool = run.select[CommandLineTool].getOrElse(fail(s"$run wasn't a CommandLineTool"))
-
-    commandLineTool.id should include("cgrep")
-    commandLineTool
-  }
-
-  forAll(stringOrExpressionTests) { (index, expected) =>
-    it should s"correctly identify the ${getTestName(expected)}" in {
-      val argument: CommandLineTool.Argument = commandLineTool.arguments.get.apply(index)
-      val commandLineBinding: ArgumentCommandLineBinding = argument.select[ArgumentCommandLineBinding]
-        .getOrElse(fail(s"$argument wasn't a CommandLineBinding"))
-      val stringOrExpression: StringOrExpression = commandLineBinding.valueFrom
-      stringOrExpression should be(expected)
-    }
-  }
-
-  "A CwlNamespace for 3step" should "provide conversion to WOM" in {
-
-    val wf = decodeCwlFile(rootPath/"three_step.cwl").map {
-      _.select[Workflow].get
-    }.value.unsafeRunSync().fold(error => throw new RuntimeException(s"broken parse: $error"), identity)
-
-    wf.id should include("three_step")
-
-    val wfd = wf.womDefinition(AcceptAllRequirements, Vector.empty) match {
-      case Right(wf: WorkflowDefinition) => wf
-      case Left(o) => fail(s"Workflow definition was not produced correctly: ${o.toList.mkString(", ")}")
-      case Right(callable) => fail(s"produced $callable when a Workflow Definition was expected!")
-    }
-
-    val nodes = wfd.innerGraph.nodes
-
-    val graphInputNodes = nodes collect { case gin: GraphInputNode => gin }
-    graphInputNodes should have size 1
-    val patternInputNode = graphInputNodes.head
-    patternInputNode.localName should be("pattern")
-
-    nodes collect { case gon: GraphOutputNode => gon.localName } should be(Set(
-      "cgrep-count",
-      "wc-count"
-    ))
-
-    nodes collect { case cn: CallNode => cn.localName } should be(Set("ps", "cgrep", "wc"))
-
-    val ps = nodes.collectFirst({ case ps: CallNode if ps.localName == "ps" => ps }).get
-    val cgrep = nodes.collectFirst({ case cgrep: CallNode if cgrep.localName == "cgrep" => cgrep }).get
-    val cgrepFileExpression = nodes.collectFirst({ case cgrepInput: ExpressionNode if s"${FileStepAndId(cgrepInput.localName).stepId}/${FileStepAndId(cgrepInput.localName).id}" == "cgrep/file.merge" => cgrepInput }).get
-    val cgrepPatternExpression = nodes.collectFirst({ case cgrepInput: ExpressionNode if s"${FileStepAndId(cgrepInput.localName).stepId}/${FileStepAndId(cgrepInput.localName).id}" == "cgrep/pattern.merge" => cgrepInput }).get
-    val wc = nodes.collectFirst({ case wc: CallNode if wc.localName == "wc" => wc }).get
-    val wcFileExpression = nodes.collectFirst({ case wcInput: ExpressionNode if s"${FileStepAndId(wcInput.localName).stepId}/${FileStepAndId(wcInput.localName).id}" == "wc/file.merge" => wcInput }).get
-
-    ps.upstream shouldBe empty
-
-    cgrep.upstream should contain theSameElementsAs Set(cgrepFileExpression, cgrepPatternExpression)
-    wc.upstream should contain theSameElementsAs Set(wcFileExpression)
-
-    // Check that expressions input ports point to the right output port
-    cgrepPatternExpression.inputPorts.head.upstream should be theSameInstanceAs patternInputNode.singleOutputPort
-    cgrepFileExpression.inputPorts.map(_.upstream).count(_ eq ps.outputPorts.head) shouldBe 1
-    wcFileExpression.inputPorts.map(_.upstream).count(_ eq ps.outputPorts.head) shouldBe 1
-
-    // Check that the inputDefinitionMappings are correct
-    ps.inputDefinitionMappings shouldBe empty
-    cgrep.inputDefinitionMappings should have size 2
-
-    val cgrepInputs = cgrep.inputDefinitionMappings.toMap
-    val cgrepFileInputDef = cgrep.callable.inputs.find(_.name == "file").get
-    cgrepInputs(cgrepFileInputDef).select[OutputPort].get should be theSameInstanceAs cgrepFileExpression.singleOutputPort
-
-    val cgrepPatternInputDef = cgrep.callable.inputs.find(_.name == "pattern").get
-    cgrepInputs(cgrepPatternInputDef).select[OutputPort].get should be theSameInstanceAs cgrepPatternExpression.singleOutputPort
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/DirectorySpec.scala b/cwl/src/test/scala/cwl/DirectorySpec.scala
deleted file mode 100644
index 1e7db881753..00000000000
--- a/cwl/src/test/scala/cwl/DirectorySpec.scala
+++ /dev/null
@@ -1,41 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.CwlDecoder.decodeCwlFile
-import cwl.TestSetup.rootPath
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.callable.Callable.InputDefinition
-import wom.callable.{CallableTaskDefinition, RuntimeEnvironment}
-import wom.expression.NoIoFunctionSet
-import wom.graph.OptionalGraphInputNodeWithDefault
-import wom.values.WomValue
-
-
-class DirectorySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "Directory"
-
-  it should "dir_example" in {
-    val cwl = decodeCwlFile(rootPath / "dir_example.cwl").value.unsafeRunSync().toOption.get
-    val executable = cwl.womExecutable(AcceptAllRequirements, None, NoIoFunctionSet, strictValidation = false).toOption.get
-    val call = executable.graph.calls.head
-    val runtimeEnvironment = RuntimeEnvironment("output/path", "temp/path",refineMV[Positive](1), 2e10, 100, 100)
-    val defaultCallInputs = executable.graph.nodes.collect({
-      case oginwd: OptionalGraphInputNodeWithDefault =>
-        val key: InputDefinition = call.inputDefinitionMappings.toMap.keys.find(
-          _.localName == oginwd.identifier.localName
-        ).get
-        val value: WomValue = oginwd.default.evaluateValue(Map.empty, NoIoFunctionSet).toTry.get
-        key -> value
-    }).toMap
-    val command = call.callable.asInstanceOf[CallableTaskDefinition].instantiateCommand(
-      defaultCallInputs, NoIoFunctionSet, identity, runtimeEnvironment
-    ).toTry.get
-    command.commandString should be("""   'echo' 'exampledir'   """.trim)
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/ExportCwlSamplesSpec.scala b/cwl/src/test/scala/cwl/ExportCwlSamplesSpec.scala
deleted file mode 100644
index e18c95a9966..00000000000
--- a/cwl/src/test/scala/cwl/ExportCwlSamplesSpec.scala
+++ /dev/null
@@ -1,146 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.CommandLineTool.{BaseCommand, CommandInputParameter}
-import cwl.Workflow.{WorkflowInputParameter, WorkflowOutputParameter}
-import cwl.WorkflowStep.WorkflowStepOutputInnerType
-import cwl.WorkflowStepInput.InputSource
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-
-
-
-  /**
-   * BROKEN
-   *
-   * (DB)Ability to write JSON removed due to conflicting circe-yaml cats dependency.
-   * See issue https://github.com/broadinstitute/wdl4s/issues/216 for more information.
-   */
-class ExportCwlSamplesSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  def assertCorrectJson(cwl: Cwl, expectedYaml: String) = throw new UnsupportedOperationException // shouldBe expectedYaml
-
-  it should "encode sample CWL command line tool" ignore {
-    val tool =
-      CommandLineTool(
-        id = "echo",
-        inputs =  Array(CommandInputParameter(
-          id = "message",
-          inputBinding = Option(InputCommandLineBinding(
-            position = Option(1)
-          ))
-        )),
-        baseCommand = Option(Coproduct[BaseCommand]("echo"))
-      )
-    val expectedToolJsonString =
-"""inputs:
-- id: message
-  inputBinding:
-    position: 1
-outputs: []
-class: CommandLineTool
-cwlVersion: v1.0
-baseCommand: echo
-"""
-    assertCorrectJson(tool.asCwl, expectedToolJsonString)
-  }
-
-  it should "encode sample CWL workflow" ignore {
-    val workflow = Workflow(
-      id = "MyCwlWorkflow",
-      inputs = Array(
-          WorkflowInputParameter(id = "inp", `type` = Option(Coproduct[MyriadInputType](Coproduct[MyriadInputInnerType](CwlType.File)))),
-          WorkflowInputParameter(id = "ex", `type` = Option(Coproduct[MyriadInputType](Coproduct[MyriadInputInnerType](CwlType.String))))
-        ),
-      outputs = Array(
-        WorkflowOutputParameter(
-          id = "classout",
-          `type` = Option(Coproduct[MyriadOutputType](Coproduct[MyriadOutputInnerType](CwlType.File))),
-          outputSource = Option(Coproduct[WorkflowOutputParameter#OutputSource]("compile/classfile"))
-        )
-      ),
-      steps =
-        Array(
-           WorkflowStep(
-            id = "untar",
-            run = Coproduct[WorkflowStep.Run]("tar-param.cwl"),
-            in =
-              Array(
-                WorkflowStepInput(id = "tarfile", source = Option(Coproduct[InputSource]("inp"))),
-                WorkflowStepInput(id = "extractfile", source =  Option(Coproduct[InputSource]("ex")))
-              ),
-            out = Array(Coproduct[WorkflowStepOutputInnerType](WorkflowStepOutput("example_out")))
-          ),
-          WorkflowStep(
-            id = "compile",
-            run = Coproduct[WorkflowStep.Run]("arguments.cwl"),
-            in = Array(
-                 WorkflowStepInput(id = "src", source = Option(Coproduct[InputSource]("untar/example_out")))
-              ),
-            out = Array(Coproduct[WorkflowStepOutputInnerType](WorkflowStepOutput("classfile")))
-          )
-        )
-      )
-    val expectedWorkflowJsonString =
-      """cwlVersion: v1.0
-class: Workflow
-inputs:
-- id: inp
-  type: File
-- id: ex
-  type: string
-outputs:
-- id: classout
-  outputSource: compile/classfile
-  type: File
-steps:
-- id: untar
-  in:
-  - id: tarfile
-    source: inp
-  - id: extractfile
-    source: ex
-  out:
-  - example_out
-  run: tar-param.cwl
-- id: compile
-  in:
-  - id: src
-    source: untar/example_out
-  out:
-  - classfile
-  run: arguments.cwl
-""".stripMargin
-    assertCorrectJson(workflow.asCwl, expectedWorkflowJsonString)
-  }
-
-  it should "encode sample CWL env" ignore {
-    val tool = CommandLineTool(
-      id = "env",
-      baseCommand = Option(Coproduct[BaseCommand]("env")),
-      requirements = Option(Array(Coproduct[Requirement](EnvVarRequirement(
-        envDef = Array(EnvironmentDef("HELLO", Coproduct[StringOrExpression]("$(inputs.message)")))
-      )))),
-      inputs = Array(
-        CommandInputParameter(id =  "message", `type` = Option(Coproduct[MyriadInputType](Coproduct[MyriadInputInnerType](CwlType.String))))
-      )
-    )
-    val expectedToolJsonString =
-"""inputs:
-- id: message
-  type: string
-outputs: []
-class: CommandLineTool
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: HELLO
-    envValue: $(inputs.message)
-cwlVersion: v1.0
-baseCommand: env
-""".stripMargin
-    assertCorrectJson(tool.asCwl, expectedToolJsonString)
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/ExpressionEvaluatorSpec.scala b/cwl/src/test/scala/cwl/ExpressionEvaluatorSpec.scala
deleted file mode 100644
index c723d923901..00000000000
--- a/cwl/src/test/scala/cwl/ExpressionEvaluatorSpec.scala
+++ /dev/null
@@ -1,24 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.expression.DefaultSizeIoFunctionSet
-import wom.values.{WomBoolean, WomString, WomValue}
-
-
-class ExpressionEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "ExpressionEvaluator"
-
-  it should "eval inputs of different types" in {
-    val values: Map[String, WomValue] = Map(
-      "myName" -> WomString("hi"),
-      "someother" -> WomBoolean(false)
-    )
-    val parameterContext = ParameterContext(DefaultSizeIoFunctionSet, Vector.empty, values)
-    ExpressionEvaluator.eval("inputs.myName", parameterContext).toTry.get should be(WomString("hi"))
-    ExpressionEvaluator.eval("inputs.someother", parameterContext).toTry.get should be(WomBoolean(false))
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ExpressionInterpolatorSpec.scala b/cwl/src/test/scala/cwl/ExpressionInterpolatorSpec.scala
deleted file mode 100644
index df27b5736e1..00000000000
--- a/cwl/src/test/scala/cwl/ExpressionInterpolatorSpec.scala
+++ /dev/null
@@ -1,121 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.ExpressionInterpolator.SubstitutionException
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.callable.RuntimeEnvironment
-import wom.expression.DefaultSizeIoFunctionSet
-import wom.values._
-
-
-class ExpressionInterpolatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "ExpressionInterpolator"
-
-  private lazy val expressionLib = Vector(
-    better.files.File(getClass.getResource("lodash.js").getPath).contentAsString,
-    "var t = function(s) { return _.template(s, {variable: 'data'})({'inputs': inputs}); };"
-  )
-
-  private lazy val parameterContext = {
-    val runtime = RuntimeEnvironment("out", "tmp", refineMV[Positive](1), 2.0D, 100L, 200L)
-    val inputs = Map(
-      "cram" -> WomSingleFile("/path/to/my.cram"),
-      "file1" -> WomSingleFile("/path/to/my.file.txt")
-    )
-    ParameterContext(DefaultSizeIoFunctionSet, expressionLib, inputs = inputs, runtimeOption = Option(runtime))
-  }
-
-  private def evaluator(string: String): ErrorOr[WomValue] = {
-    ExpressionEvaluator.eval(string, parameterContext)
-  }
-
-  private val validTests = Table(
-    ("description", "expression", "expected"),
-    ("an empty string", "", WomString("")),
-    ("a space", " ", WomString("")),
-    ("two spaces", "  ", WomString("")),
-    ("whitespace string", " \n \t", WomString("")),
-    ("a regular string", "hello world", WomString("hello world")),
-    ("a dollar sign", "$6.28", WomString("$6.28")),
-    ("two dollar signs", "$$(6.28)", WomString("$$(6.28)")),
-    ("three dollar signs", "$$$(6.28)", WomString("$$6.28")),
-    ("a backslash and a dollar sign", """\$(6.28)""", WomString("$(6.28)")),
-    ("two backslashes and a dollar sign", """\\$(6.28)""", WomString("""\6.28""")),
-    ("a underscore and a dollar sign", "_$(6.28)", WomString("_6.28")),
-    ("nested parens", """$(parseInt("6")).$(parseInt(("2")) + "" + parseInt(((("8")))))""", WomString("6.28")),
-    ("missing open parens", """$(parseInt("6")).$(parseInt(("2")) + "" + parseInt((("8")))))""", WomString("6.28)")),
-    ("quoted open parens", """$("(")""", WomString("(")),
-    ("quoted closing parens", """$(")")""", WomString(")")),
-    ("prefixed/suffixed nested parens",
-      """6.$(parseInt("2"))$(parseInt(("8")) + "" + parseInt(((("3")))))1""",
-      WomString("6.2831")),
-    ("expressions using libs",
-      """$(t("The file is <%= data.inputs.file1.path.split('/').slice(-1)[0] %>\n"))""",
-      WomString("The file is my.file.txt\n")),
-    ("two expressions", """$(runtime.outdir)/$(inputs.cram.basename)""", WomString("out/my.cram")),
-    ("two expressions suffixed", "$(runtime.outdir)/$(inputs.cram.basename).crai", WomString("out/my.cram.crai")),
-    ("two expressions prefixed/suffixed",
-      "/path/to/$(runtime.outdir)/$(inputs.cram.basename).crai",
-      WomString("/path/to/out/my.cram.crai")),
-    ("a replacement that must be escaped", """$("$(hello)")""", WomString("$(hello)")),
-    ("a string containing a start prefix", """$("$(")""", WomString("$(")),
-    ("a replacement returning a json object",
-      "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})",
-      WomObject(Map("output" -> WomInteger(2))))
-  )
-
-  forAll(validTests) { (description, expression, expected) =>
-    it should s"interpolate $description" in {
-      ExpressionInterpolator.interpolate(expression, evaluator).toTry.get should be(expected)
-    }
-  }
-
-  private val substitutionErrorTests = Table(
-    ("description", "expression", "expected"),
-    ("a missing closing paren", "$(", "0: $("),
-    ("a missing quote", """$("))""", """0: $("))"""),
-    ("complex missing closing parens",
-      """$(parseInt("6")).$(parseInt(("2")) + "" + parseInt(((("8"))))""",
-      """1: $(parseInt(("2")) + "" + parseInt(((("8"))))""")
-  )
-
-  forAll(substitutionErrorTests) { (description, expression, expected) =>
-    it should s"throw a substitution error for $description" in {
-      the[SubstitutionException] thrownBy {
-        ExpressionInterpolator.interpolate(expression, evaluator)
-      } should have message s"Substitution error, unfinished block starting at position $expected"
-    }
-  }
-
-  /**
-    * Tests that sorta work but do not generate the same _exact_ responses as cwltool.
-    *
-    * See docs at top of [[ExpressionInterpolator]].
-    *
-    * According to cwltool's expression.py when an interpolated string contains more than just an expression,
-    * `json.dumps` should be used to serialize Arrays and Maps, and Maps should sort their keys.
-    *
-    * We don't even test maps with multiple keys here as WomMap does not guarantee key order.
-    */
-  private val semiSupportedTests = Table(
-    ("description", "expression", "expected"),
-    ("an array", """$(["hello", "world"])""", """["hello", "world"]"""),
-    ("a map", """$({"hello": "world"})""", """object {hello: "world"}"""),
-    ("an array of maps", """$([{"hello": "world"}])""", """[object {hello: "world"}]"""),
-    ("a map of arrays", """$({"hello": ["world"]})""", """object {hello: ["world"]}""")
-  )
-
-  forAll(semiSupportedTests) { (description, expression, expected) =>
-    it should s"semi-interpolate a string plus $description" in {
-      val actual = ExpressionInterpolator.interpolate("_" + expression, evaluator).map(_.valueString).toTry.get
-      actual should be("_" + expected)
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/FileSpec.scala b/cwl/src/test/scala/cwl/FileSpec.scala
deleted file mode 100644
index 814c164bc16..00000000000
--- a/cwl/src/test/scala/cwl/FileSpec.scala
+++ /dev/null
@@ -1,54 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.CwlDecoder.decodeCwlFile
-import cwl.TestSetup.rootPath
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.callable.Callable.InputDefinition
-import wom.callable.{CallableTaskDefinition, RuntimeEnvironment}
-import wom.graph.OptionalGraphInputNodeWithDefault
-import wom.values.WomValue
-
-
-class FileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "File"
-
-  private val fileTests = Table(
-    ("description", "filePath", "ioFunctionSet", "expectedCommand"),
-    ("get the basename of a file", "file_example.cwl", LocalIoFunctionSet, """   'echo' 'example.txt'   """.trim),
-    ("get the size of a file", "file_size_example.cwl", LocalIoFunctionSet, """   'echo' '12'   """.trim)
-  )
-
-  forAll(fileTests) { (description, filePath, ioFunctionSet, expectedCommand) =>
-    it should description in {
-      val cwl = decodeCwlFile(rootPath / filePath).value.unsafeRunSync().toOption.get
-      val executable = cwl.womExecutable(AcceptAllRequirements, None, ioFunctionSet, strictValidation = false).toOption.get
-      val call = executable.graph.calls.head
-      val runtimeEnvironment = RuntimeEnvironment("output/path", "temp/path", refineMV[Positive](1), 2e10, 100, 100)
-      val defaultCallInputs = executable.graph.nodes.collect({
-        case oginwd: OptionalGraphInputNodeWithDefault =>
-          val key: InputDefinition = call.inputDefinitionMappings.toMap.keys.find(
-            _.localName == oginwd.identifier.localName
-          ).get
-          val value: WomValue = key
-            .valueMapper(ioFunctionSet)(oginwd.default.evaluateValue(Map.empty, ioFunctionSet).toTry.get)
-            .value.unsafeRunSync()
-            .toOption.get
-
-          key -> value
-      }).toMap
-      val commandEither = call.callable.asInstanceOf[CallableTaskDefinition].instantiateCommand(
-        defaultCallInputs, ioFunctionSet, identity, runtimeEnvironment
-      ).toEither
-      val command = commandEither.toOption.get.commandString
-      command should be(expectedCommand)
-    }
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/FullyQualifiedNameSpec.scala b/cwl/src/test/scala/cwl/FullyQualifiedNameSpec.scala
deleted file mode 100644
index 9c3babfc634..00000000000
--- a/cwl/src/test/scala/cwl/FullyQualifiedNameSpec.scala
+++ /dev/null
@@ -1,27 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.command.ParentName
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class FullyQualifiedNameSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  implicit val parentName = ParentName.empty
-  
-  "workflow input id " should "get filename and id" in {
-    val wfid = FileAndId("file#id")
-
-    wfid.fileName shouldBe "file"
-    wfid.id shouldBe "id"
-  }
-
-  "workflow step output id " should "get filename, id, and step" in {
-    val wfid = FileStepAndId("file#step/id")
-
-    wfid.fileName shouldBe "file"
-    wfid.id shouldBe "id"
-    wfid.stepId shouldBe "step"
-  }
-}
diff --git a/cwl/src/test/scala/cwl/LocalIoFunctionSet.scala b/cwl/src/test/scala/cwl/LocalIoFunctionSet.scala
deleted file mode 100644
index b3ab33a5809..00000000000
--- a/cwl/src/test/scala/cwl/LocalIoFunctionSet.scala
+++ /dev/null
@@ -1,48 +0,0 @@
-package cwl
-
-import java.nio.file.{Files, Paths}
-import java.util.concurrent.Executors
-
-import wom.expression.EmptyIoFunctionSet
-
-import scala.jdk.CollectionConverters._
-import scala.concurrent.{ExecutionContext, Future}
-import scala.util.Try
-
-/**
-  * Test io functions that can read from local file systems.
-  */
-object LocalIoFunctionSet extends EmptyIoFunctionSet {
-  override implicit def ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(1))
-
-  private def stripLocalPrefix(path: String): String = {
-    path.stripPrefix("file://")
-  }
-
-  private def fileSize(path: String): Long = {
-    Files.size(Paths.get(stripLocalPrefix(path)))
-  }
-
-  private def contentsAsString(path: String): String = {
-    Files.readAllLines(Paths.get(stripLocalPrefix(path))).asScala.mkString("\n")
-  }
-
-  override def readFile(path: String, maxBytesOption: Option[Int] = None,
-                        failOnOverflow: Boolean = false): Future[String] = {
-    Future.fromTry(Try {
-      maxBytesOption match {
-        case Some(maxBytes) if failOnOverflow && fileSize(path) > maxBytes =>
-          throw new RuntimeException(s"overflow while reading $path: ${fileSize(path)} > $maxBytes")
-        case Some(maxBytes) => contentsAsString(path).take(maxBytes)
-        case None => contentsAsString(path)
-      }
-    })
-  }
-
-  override def size(params: String): Future[Long] = {
-    Future.fromTry(Try {
-        fileSize(params)
-    }
-    )
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ParseBigThreeSpec.scala b/cwl/src/test/scala/cwl/ParseBigThreeSpec.scala
deleted file mode 100644
index e5ac02e80f4..00000000000
--- a/cwl/src/test/scala/cwl/ParseBigThreeSpec.scala
+++ /dev/null
@@ -1,34 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder._
-import cwl.TestSetup._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class ParseBigThreeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  val namespace = "cwl"
-
-  it should "parse 1st tool" in {
-
-  decodeCwlFile(rootPath/"1st-tool.cwl").
-    value.
-    unsafeRunSync().
-    isRight shouldBe true
-  }
-
-  it should "parse first workflow" in {
-    decodeCwlFile(rootPath/"1st-workflow.cwl").
-      value.
-      unsafeRunSync().
-      isRight shouldBe true
-  }
-
-  it should "parse env cwl" in {
-    decodeCwlFile(rootPath/"env.cwl").
-      value.
-      unsafeRunSync().
-      isRight shouldBe true
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ParsingSpec.scala b/cwl/src/test/scala/cwl/ParsingSpec.scala
deleted file mode 100644
index 92c454a0964..00000000000
--- a/cwl/src/test/scala/cwl/ParsingSpec.scala
+++ /dev/null
@@ -1,63 +0,0 @@
-package cwl
-
-import CwlDecoder._
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class WorkflowParsingSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "Workflow Json Parser"
-
-  def workflowJson(classValue: String) = s"""{"class":"$classValue", "cwlVersion": "v1.0", "id": "MyCwlWorkflow", "inputs":[], "outputs":[], "steps":[]}"""
-
-  it should "accept the Workflow argument" in {
-     decodeCwlString(workflowJson("Workflow")).value.unsafeRunSync() match {
-       case Right(_) => // great!
-       case Left(e) => fail(s"Workflow rejected because: ${e.toList.mkString(", ")}")
-     }
-  }
-
-  it should "not parse w/something other than Workflow as class" in {
-    decodeCwlString(workflowJson("wrong")).value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(wf) => fail(s"workflow unexpectedly accepted: $wf")
-    }
-  }
-
-  it should "not parse when class argument is missing" in {
-    decodeCwlString("""{"cwlVersion": "v1.0", "inputs":[], "outputs":[], "steps":[]}""").value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(wf) => fail(s"workflow unexpectedly accepted: $wf")
-    }
-  }
-}
-
-class CommandLineToolParsingSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "CommandLineTool Json Parser"
-
-  def commandLineToolJson(classValue: String) = s"""{"class":"$classValue", "cwlVersion":"v1.0", "id": "MyCwlTask", "inputs":[], "outputs":[]}"""
-
-  it should "accept the CommandLineTool argument for class" in {
-    decodeCwlString(commandLineToolJson("CommandLineTool")).value.unsafeRunSync() match {
-      case Right(_) => // great!
-      case Left(e) => fail(s"CommandLineTool rejected because: $e")
-    }
-  }
-
-  it should "not parse w/something other than CommandLineTool" in {
-    decodeCwlString(commandLineToolJson("wrong")).value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(clt) => fail(s"CommandLineTool unexpectedly accepted: $clt")
-    }
-  }
-
-  it should "doesn't parse when class argument is missing" in {
-    decodeCwlString("""{"inputs":[], "outputs":[]}""").value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(clt) => fail(s"CommandLineTool unexpectedly accepted: $clt")
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ScatterLogicSpec.scala b/cwl/src/test/scala/cwl/ScatterLogicSpec.scala
deleted file mode 100644
index 8afd3c9df16..00000000000
--- a/cwl/src/test/scala/cwl/ScatterLogicSpec.scala
+++ /dev/null
@@ -1,140 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.BeforeAndAfterEach
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import spray.json.DefaultJsonProtocol
-import wom.graph.ScatterNode.ScatterVariableAndValue
-import wom.graph.expression.PlainAnonymousExpressionNode
-import wom.graph.{ScatterNode, ScatterVariableNode, WomIdentifier}
-import wom.types.{WomArrayType, WomStringType}
-import wom.values.{WomArray, WomString, WomValue}
-
-class ScatterLogicSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks
-  with DefaultJsonProtocol with BeforeAndAfterEach {
-  private val expressionNode = PlainAnonymousExpressionNode(WomIdentifier("name"), null, WomStringType, Map.empty)
-  private val arrayStringType = WomArrayType(WomStringType)
-
-  private val emptyArray = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List.empty)
-  )
-  private val simpleArray2 = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List(WomString("a"), WomString("b")))
-  )
-  private val simpleArray3 = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List(WomString("a"), WomString("b"), WomString("c")))
-  )
-  private val simpleArray4 = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List(WomString("a"), WomString("b"), WomString("c"), WomString("d")))
-  )
-
-  override def beforeEach(): Unit = {
-    // The index length of the SVN is a mutable value, to avoid tests stepping on each others reset it to the default value
-    // before each test
-    emptyArray.scatterVariableNode.withRelativeIndexLength(1)
-    simpleArray2.scatterVariableNode.withRelativeIndexLength(1)
-    simpleArray3.scatterVariableNode.withRelativeIndexLength(1)
-    simpleArray4.scatterVariableNode.withRelativeIndexLength(1)
-  }
-
-  private val valueA = WomString("a")
-  private val valueB = WomString("b")
-  private val valueC = WomString("c")
-  private val valueD = WomString("d")
-
-  private def validateScatterCombinations(list: List[ScatterNode.ScatterVariableAndValue],
-                                  scatterSize: Int,
-                                  expected: List[List[Int]]) = {
-    // Go through all the variable nodes and feed all the shard numbers to the indexForShard function
-    val combinations = list.map({
-      case ScatterVariableAndValue(node, values) =>
-        (0 until scatterSize).map(node.indexForShard(_, values.size)).toList
-    })
-
-    combinations should contain theSameElementsInOrderAs expected
-  }
-
-  "CrossProduct scattering function" should "generate correct results" in {
-    val nonEmptyVariables = Table(
-      // None for the index length means "don't check because irrelevant"
-      ("variablesAndValues", "scatterSize", "arrayIndexes"),
-      (List(simpleArray2), 2, List(List(0, 1))),
-      (List(simpleArray2, simpleArray3), 6, List(List(0, 0, 0, 1, 1, 1), List(0, 1, 2, 0, 1, 2))),
-      (List(simpleArray2, simpleArray3, simpleArray4), 24, List(
-        List(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
-        List(0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2),
-        List(0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3))
-      )
-    )
-
-    forAll(nonEmptyVariables) { case (list, scatterSize, expected) =>
-      ScatterLogic.CrossProductScatterProcessingFunction(list) shouldBe Right(scatterSize)
-      validateScatterCombinations(list, scatterSize, expected)
-    }
-
-    List(List(emptyArray), List(emptyArray, simpleArray2), List(simpleArray2, emptyArray)) foreach { list =>
-      ScatterLogic.CrossProductScatterProcessingFunction(list) shouldBe Right(0)
-    }
-  }
-
-  "DotProduct scattering function" should "generate correct results" in {
-    import common.validation.Checked._
-    val simpleArray2Duplicate = ScatterVariableAndValue(
-      ScatterVariableNode(null, expressionNode, WomStringType),
-      WomArray(arrayStringType, List(WomString("a"), WomString("b")))
-    )
-    val nonEmptyVariables = Table(
-      // None for the index length means "don't check because irrelevant"
-      ("variablesAndValues", "scatterSize", "arrayIndexes"),
-      (List(simpleArray2, simpleArray2Duplicate), 2.validNelCheck, List(List(0, 1), List(0, 1))),
-      (List(simpleArray2, simpleArray3), "All arrays must have the same number of element when using the dot product scatter method".invalidNelCheck, List.empty)
-    )
-
-    forAll(nonEmptyVariables) { case (list, expectedScatterSize, expected) =>
-      ScatterLogic.DotProductScatterProcessingFunction(list) shouldBe expectedScatterSize
-
-      expectedScatterSize match {
-        case Right(scatterSize) => validateScatterCombinations(list, scatterSize, expected)
-        case _ => // Only verify combinations if the scatter is valid
-      }
-    }
-  }
-
-  "NestedCrossProduct collecting function builder" should "generate correct results" in {
-    import spray.json._
-
-    val arrayString = arrayStringType
-    val nestedArrayString = WomArrayType(arrayString)
-    val nestedArrayString2 = WomArrayType(nestedArrayString)
-
-    val variables = Table(
-      ("arraySizes", "shards", "valueType", "result"),
-      (List(0), List.empty, arrayString, "[]"),
-      (List(0, 2), List.empty, nestedArrayString, "[]"),
-      (List(2, 0), List.empty, nestedArrayString, "[[], []]"),
-      (List(2, 3, 0), List.empty, nestedArrayString2, "[[[], [], []], [[], [], []]]"),
-      (List(2, 0, 3), List.empty, nestedArrayString2, "[[], []]"),
-      // This technically should not happen since to have a cross product we need at least 2 scatter variables but..
-      (List(2), List(valueA, valueB), arrayString, """["a", "b"]"""),
-      (List(2, 2), List(valueA, valueB, valueC, valueD), nestedArrayString, """[["a", "b"], ["c", "d"]]"""),
-      (List(3, 2), List(valueA, valueB, valueC, valueD, valueA, valueB), nestedArrayString, """[["a", "b"], ["c", "d"], ["a", "b"]]"""),
-      (List(2, 3), List(valueA, valueB, valueC, valueC, valueB, valueA), nestedArrayString, """[["a", "b", "c"], ["c", "b", "a"]]"""),
-      (List(2, 3, 2), List(
-        valueA, valueB, valueA, valueB, valueA, valueB,
-        valueC, valueD, valueC, valueD, valueC, valueD
-      ), nestedArrayString2, """[[["a", "b"], ["a", "b"], ["a", "b"]], [["c", "d"], ["c", "d"], ["c", "d"]]]""")
-    )
-
-    forAll(variables) { case (arraySizes, shards, valueType, result) =>
-      val collection = ScatterLogic.NestedCrossProductScatterCollectionFunctionBuilder(arraySizes)(shards, valueType)
-      collection.arrayType shouldBe valueType
-      (collection: WomValue).toJson(WomValueJsonFormatter.WomValueJsonFormat) shouldBe result.parseJson
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/TestSetup.scala b/cwl/src/test/scala/cwl/TestSetup.scala
deleted file mode 100644
index 14e5dbe9b05..00000000000
--- a/cwl/src/test/scala/cwl/TestSetup.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cwl
-
-import better.files.File.currentWorkingDirectory
-
-object TestSetup {
-
-  val rootPath = currentWorkingDirectory/"cwl"/"src"/"test"/"resources"
-
-}
diff --git a/cwl/src/test/scala/cwl/WomTypeConversionSpec.scala b/cwl/src/test/scala/cwl/WomTypeConversionSpec.scala
deleted file mode 100644
index e7b76b153dc..00000000000
--- a/cwl/src/test/scala/cwl/WomTypeConversionSpec.scala
+++ /dev/null
@@ -1,134 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.types._
-import mouse.`try`._
-
-import scala.util.Try
-
-class WomTypeConversionSpec extends AnyFlatSpec with Matchers {
-  behavior of "WomTypeConversion"
-
-  /* ******** Inputs *********** */
-  it should "convert ArrayInputSchema" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val x = InputArraySchema(items = Coproduct[MyriadInputType](y))
-    val z = Coproduct[MyriadInputInnerType](x)
-    Coproduct[MyriadInputType](z).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomArrayType(WomStringType)
-  }
-
-  it should "convert Cwl Input String" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    Coproduct[MyriadInputType](y).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe WomStringType
-  }
-
-  it should "convert Array of a single type is actually one type not in an array" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    Coproduct[MyriadInputType](Array(y)).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomStringType
-  }
-
-  it should "convert Array of more than one type becomes a coproduct" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Boolean)
-    Coproduct[MyriadInputType](Array(y, z)).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType))
-  }
-
-  it should "convert Array of more than one type and a null becomes an optional coproduct" in {
-    val x = Coproduct[MyriadInputInnerType](CwlType.Null)
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Boolean)
-    Coproduct[MyriadInputType](Array(x, y, z)).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomOptionalType(WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType)))
-  }
-
-  it should "convert a 2-element Input Array of a single type accompanied by a null is an optional type" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Null)
-    testInputArray(Array(y,z), WomOptionalType(WomStringType))
-  }
-
-  private def testInputArray(array: Array[MyriadInputInnerType], assertedType: WomType ) = {
-    def f(array: Array[MyriadInputInnerType]) =
-      Try(Coproduct[MyriadInputType](array).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement())).cata(
-        success => withClue("input should evaluate to an optional array of files type")(success shouldBe assertedType),
-        failure => fail(s"expected an optional array of files type but received a failure: $failure")
-      )
-    f(array)
-    f(array.reverse)
-  }
-
-  it should "convert Optional Array of a type is interpreted correctly as input type" in {
-    val miit = Coproduct[MyriadInputInnerType](CwlType.File)
-    val mit = Coproduct[MyriadInputType](miit)
-    val ias =  InputArraySchema(items = mit)
-    val y = Coproduct[MyriadInputInnerType](ias)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Null)
-    testInputArray(Array(y, z), WomOptionalType(WomMaybeEmptyArrayType(WomMaybePopulatedFileType)))
-  }
-
-  /* ******** Outputs *********** */
-  it should "convert ArrayOutputSchema" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val x = OutputArraySchema(items = Coproduct[MyriadOutputType](y))
-    val z = Coproduct[MyriadOutputInnerType](x)
-    Coproduct[MyriadOutputType](z).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomArrayType(WomStringType)
-  }
-
-  it should "convert Cwl Output String" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    Coproduct[MyriadOutputType](y).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe WomStringType
-  }
-
-  it should "convert Array of a single type is the same as one type not in an array" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    Coproduct[MyriadOutputType](Array(y)).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomStringType
-  }
-
-  it should "convert Output Array of more than one type becomes a coproduct" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val z = Coproduct[MyriadOutputInnerType](CwlType.Boolean)
-    Coproduct[MyriadOutputType](Array(y, z)).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType))
-  }
-
-  it should "convert Output Array of more than one types including a null is an optional coproduct" in {
-    val x = Coproduct[MyriadOutputInnerType](CwlType.Null)
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val z = Coproduct[MyriadOutputInnerType](CwlType.Boolean)
-    Coproduct[MyriadOutputType](Array(x, y, z)).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomOptionalType(WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType)))
-  }
-
-  private def testOutputArray(array: Array[MyriadOutputInnerType], assertedType: WomType) = {
-    def f(array: Array[MyriadOutputInnerType]) =
-      Try(Coproduct[MyriadOutputType](array).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement())).cata(
-        success => withClue("input should evaluate to an optional string type")(success shouldBe assertedType),
-        failure => fail(s"expected an optional string type but received a failure: $failure")
-      )
-    f(array)
-    f(array.reverse)
-  }
-
-  it should "convert a 2-element Output Array of a single type accompanied by a null is an optional type" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val z = Coproduct[MyriadOutputInnerType](CwlType.Null)
-    testOutputArray(Array(y,z), WomOptionalType(WomStringType))
-  }
-
-  it should "convert Optional Array of a type is interpreted correctly as output type" in {
-    val moit = Coproduct[MyriadOutputInnerType](CwlType.File)
-    val mot = Coproduct[MyriadOutputType](moit)
-    val oas =  OutputArraySchema(items = mot)
-    val moit2 = Coproduct[MyriadOutputInnerType](oas)
-    val moit3 = Coproduct[MyriadOutputInnerType](CwlType.Null)
-    testOutputArray(Array(moit2,moit3), WomOptionalType(WomMaybeEmptyArrayType(WomMaybePopulatedFileType)))
-  }
-}
diff --git a/cwl/src/test/scala/cwl/WomValueJsonFormatter.scala b/cwl/src/test/scala/cwl/WomValueJsonFormatter.scala
deleted file mode 100644
index 7939a076dc2..00000000000
--- a/cwl/src/test/scala/cwl/WomValueJsonFormatter.scala
+++ /dev/null
@@ -1,27 +0,0 @@
-package cwl
-
-import spray.json.{JsArray, JsBoolean, JsNull, JsNumber, JsObject, JsString, JsValue, RootJsonFormat}
-import wom.values.{WomArray, WomBoolean, WomFile, WomFloat, WomInteger, WomMap, WomObjectLike, WomOptionalValue, WomPair, WomString, WomValue}
-
-// Sometimes it's hard for compiler plugins to find this in ScatterLogicSpec, so here it is again:
-object WomValueJsonFormatter {
-  implicit object WomValueJsonFormat extends RootJsonFormat[WomValue] {
-    def write(value: WomValue): JsValue = value match {
-      case s: WomString => JsString(s.value)
-      case i: WomInteger => JsNumber(i.value)
-      case f: WomFloat => JsNumber(f.value)
-      case b: WomBoolean => JsBoolean(b.value)
-      case f: WomFile => JsString(f.value)
-      case o: WomObjectLike => new JsObject(o.values map {case(k, v) => k -> write(v)})
-      case a: WomArray => new JsArray(a.value.map(write).toVector)
-      case m: WomMap => new JsObject(m.value map {case(k,v) => k.valueString -> write(v)})
-      case q: WomPair => new JsObject(Map("left" -> write(q.left), "right" -> write(q.right)))
-      case WomOptionalValue(_, Some(innerValue)) => write(innerValue)
-      case WomOptionalValue(_, None) => JsNull
-      // handles WdlExpression
-      case v: WomValue => JsString(v.toWomString)
-
-    }
-    def read(value: JsValue): WomValue = throw new UnsupportedOperationException
-  }
-}
diff --git a/cwl/src/test/scala/cwl/WorkflowStepInputExpressionSpec.scala b/cwl/src/test/scala/cwl/WorkflowStepInputExpressionSpec.scala
deleted file mode 100644
index 122156b4f4e..00000000000
--- a/cwl/src/test/scala/cwl/WorkflowStepInputExpressionSpec.scala
+++ /dev/null
@@ -1,59 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.data.Validated._
-import cwl.WorkflowStepInput.InputSource
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.graph.GraphNodePort.GraphNodeOutputPort
-import wom.graph.WomIdentifier
-import wom.types._
-import wom.values.{WomArray, WomInteger, WomString}
-
-class WorkflowStepInputExpressionSpec extends AnyFlatSpec with Matchers {
-  behavior of "WorkflowStepInputExpression"
-
-  it should "assert source arrays are concatenated when merge_flattened LinkMergeMethod is used" in {
-    val inputSource = Coproduct[InputSource](Array("i1", "i2"))
-    val i1OutputPort = GraphNodeOutputPort(WomIdentifier("i1"), WomStringType, null)
-    val i2OutputPort = GraphNodeOutputPort(WomIdentifier("i2"), WomStringType, null)
-    val wsi = WorkflowStepInput("s#h", source = Option(inputSource), linkMerge = Option(LinkMergeMethod.MergeFlattened))
-
-    val mergeTpeEither = wsi.determineMergeType(
-      sources = Map("i1" -> WomArrayType(WomStringType), "i2" -> WomArrayType(WomStringType)),
-      expectedTypeAsWom = Option(WomArrayType(WomStringType)))
-
-    val tpe: WomType = fromEither(mergeTpeEither).getOrElse(throw new RuntimeException("expected a womType but evaluation of determineType failed"))
-
-    val expression = WorkflowStepInputMergeExpression(wsi, tpe, NonEmptyList.of("i1" -> i1OutputPort, "i2" -> i2OutputPort), Vector.empty)
-
-    val r = expression.evaluateValue(Map("i1" -> WomString("1"), "i2" -> WomString("2")), null)
-    r shouldBe Valid(WomArray(Seq(WomString("1"), WomString("2"))))
-  }
-
-  it should "array of one entry for each input link when merge_nested is used" in {
-    val inputSource =  Coproduct[InputSource](Array("i1", "i2"))
-    val i1OutputPort = GraphNodeOutputPort(WomIdentifier("i1"), WomStringType, null)
-    val i2OutputPort = GraphNodeOutputPort(WomIdentifier("i2"), WomStringType, null)
-    val wsi = WorkflowStepInput("s#h", source = Option(inputSource))
-    val expression = WorkflowStepInputMergeExpression(wsi, null, NonEmptyList.of("i1" -> i1OutputPort, "i2" -> i2OutputPort), Vector.empty)
-
-    expression.evaluateValue(Map("i1" -> WomInteger(1), "i2" -> WomInteger(2)), null) shouldBe
-      Valid(WomArray(Seq(
-        WomInteger(1),
-        WomInteger(2)
-      )))
-  }
-
-  it should "list of one entry for when there is only one input link and when merge_nested is used" in {
-    val inputSource =  Coproduct[InputSource]("i1")
-    val wsi = WorkflowStepInput("s#h", source = Option(inputSource))
-    val i1OutputPort = GraphNodeOutputPort(WomIdentifier("i1"), WomStringType, null)
-    val expression = WorkflowStepInputMergeExpression(wsi, null, NonEmptyList.of("i1" -> i1OutputPort), Vector.empty)
-
-    expression.evaluateValue(Map("i1" -> WomInteger(1), "i2" -> WomInteger(2)), null) shouldBe
-      Valid(WomInteger(1))
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/WorkflowStepInputSpec.scala b/cwl/src/test/scala/cwl/WorkflowStepInputSpec.scala
deleted file mode 100644
index 5592e2ffddd..00000000000
--- a/cwl/src/test/scala/cwl/WorkflowStepInputSpec.scala
+++ /dev/null
@@ -1,109 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.types._
-
-class WorkflowStepInputSpec extends AnyFlatSpec with Matchers {
-  behavior of "WorkflowStepInput"
-
-  it should "use single source type if no default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = false
-    ) shouldBe
-      Right(WomStringType)
-  }
-
-  it should "use optional single source type if no default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomOptionalType(WomStringType)),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe
-      Right(WomOptionalType(WomStringType))
-  }
-
-  it should "use single source type if there's a default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = true,
-    ) shouldBe
-      Right(WomStringType)
-  }
-
-  it should "use unpacked single source type if there's a default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomOptionalType(WomStringType)),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = true,
-    ) shouldBe
-      Right(WomStringType)
-  }
-
-  it should "wrap single source type in an array if merge method is nested" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType),
-      linkMerge = Option(LinkMergeMethod.MergeNested),
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe
-      Right(WomArrayType(WomStringType))
-  }
-
-  it should "find the closest common type to all sources if merge method is nested" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType, "s#in2" -> WomIntegerType),
-      linkMerge = Option(LinkMergeMethod.MergeNested),
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe
-      Right(WomMaybeEmptyArrayType(WomStringType))
-  }
-
-  it should "validate array inner type against target type if merge method is flattened" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType, "s#in2" -> WomStringType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = Option(WomArrayType(WomStringType)),
-      hasDefault = false,
-    ) shouldBe Right(WomArrayType(WomStringType))
-  }
-
-  it should "validate type against target type if merge method is flattened" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType, "s#in2" -> WomStringType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = Option(WomStringType),
-      hasDefault = false,
-    ) shouldBe Right(WomArrayType(WomStringType))
-  }
-
-  it should "fail if target type does not conform to source types if merge method is flattened" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomObjectType, "s#in2" -> WomObjectType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = Option(WomStringType),
-      hasDefault = false,
-    ) shouldBe Left(NonEmptyList.one(
-      "could not verify that types Map(s#in -> WomObjectType, s#in2 -> WomObjectType)" +
-        " and the items type of the run's InputArraySchema WomStringType were compatible"
-    ))
-  }
-
-  it should "fall back to the closest common type" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomBooleanType, "s#in2" -> WomIntegerType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe Right(WomStringType)
-  }
-}
diff --git a/cwl/src/test/scala/cwl/internal/EcmaScriptUtilSpec.scala b/cwl/src/test/scala/cwl/internal/EcmaScriptUtilSpec.scala
deleted file mode 100644
index adf482c2e82..00000000000
--- a/cwl/src/test/scala/cwl/internal/EcmaScriptUtilSpec.scala
+++ /dev/null
@@ -1,96 +0,0 @@
-package cwl.internal
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import delight.rhinosandox.exceptions.ScriptDurationException
-import org.mozilla.javascript.{EcmaError, EvaluatorException}
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.types._
-import wom.values._
-
-class EcmaScriptUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "EcmaScriptUtil"
-
-  private lazy val encoder = new EcmaScriptEncoder()
-
-  it should "lookup a map entry with a string key" in {
-    val values =
-      "myName" -> WomMap(
-        WomMapType(WomBooleanType, WomArrayType(WomStringType)),
-        Map(WomBoolean(true) -> WomArray(WomArrayType(WomStringType), Seq(WomString("myValue"))))
-      )
-    val expr = """myName["true"][0] + 'Plus'"""
-    val result: WomValue = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(WomString("myValuePlus"))
-  }
-
-  it should "lookup a map entry with a boolean key" in {
-    val values =
-      "myName" -> WomMap(
-        WomMapType(WomBooleanType, WomArrayType(WomStringType)),
-        Map(WomBoolean(true) -> WomArray(WomArrayType(WomStringType), Seq(WomString("myValue"))))
-      )
-    val expr = "myName[true][0] + 'PlusPlus'"
-    val result = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(WomString("myValuePlusPlus"))
-  }
-
-  it should "JSON.stringify" in {
-    val values =
-      "myName" -> WomMap(
-        WomMapType(WomBooleanType, WomArrayType(WomStringType)),
-        Map(WomBoolean(true) -> WomArray(WomArrayType(WomStringType), Seq(WomString("myValue"))))
-      )
-    val expr = "JSON.stringify(myName)"
-    val result: WomValue = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(WomString("""{"true":["myValue"]}"""))
-  }
-
-  it should "Array.prototype.sort" in {
-    val values = "myName" -> WomArray(List("hello", "world", "alpha", "zulu", "indigo").map(WomString))
-    val expr = "myName.sort()"
-    val expected = WomArray(List("alpha", "hello", "indigo", "world", "zulu").map(WomString))
-    val result = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(expected)
-  }
-
-  it should "run in strict mode" in {
-    the[EvaluatorException] thrownBy {
-      EcmaScriptUtil.evalRaw(
-        """|function sum(a, a, c) { // !!! syntax error
-           |  return a + a + c; // wrong if this code ran
-           |}
-           |""".stripMargin) { (_, _) => () }
-    } should have message
-      """Parameter "a" already declared in this function. (<ecmascript>#1)"""
-  }
-
-  it should "not run java code" in {
-    the[EcmaError] thrownBy {
-      EcmaScriptUtil.evalRaw(
-        """|var path = java.nio.file.Paths.get("/etc/passwd");
-           |java.nio.file.Files.exists(path);
-           |// Or even... java.lang.System.exit(42);
-           |""".stripMargin) { (_, _) => () }
-    } should have message
-      """ReferenceError: "java" is not defined. (<ecmascript>#1)"""
-  }
-
-  it should "not run forever" in {
-    a[ScriptDurationException] should be thrownBy {
-      EcmaScriptUtil.evalRaw(
-        """|function sleep(milliseconds) {
-           |  var start = new Date().getTime();
-           |  while(true) {
-           |    if ((new Date().getTime() - start) > milliseconds){
-           |      break;
-           |    }
-           |  }
-           |}
-           |sleep(120 * 1000);
-           |""".stripMargin) { (_, _) => () }
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/internal/EnhancedRhinoSandboxSpec.scala b/cwl/src/test/scala/cwl/internal/EnhancedRhinoSandboxSpec.scala
deleted file mode 100644
index 01409d3c546..00000000000
--- a/cwl/src/test/scala/cwl/internal/EnhancedRhinoSandboxSpec.scala
+++ /dev/null
@@ -1,141 +0,0 @@
-package cwl.internal
-
-import java.util.concurrent.{CountDownLatch, TimeUnit}
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.internal.EnhancedRhinoSandboxSpec.CachedClassLoader
-import org.apache.commons.io.IOUtils
-import org.mozilla.javascript.ContextFactory
-import org.scalatest.concurrent.ScaledTimeSpans
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-import scala.concurrent.duration._
-
-class EnhancedRhinoSandboxSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScaledTimeSpans {
-
-  behavior of "EnhancedRhinoSandbox"
-
-  it should "synchronize global ContextFactory initialization" in {
-    // Initialize the context factory here to be sure that our loaded runner is actually using a fresh ContextFactory
-    new EnhancedRhinoSandbox(true).assertContextFactory()
-
-    val threadCount = 10
-
-    // A custom loader that will contain our fresh static ContextFactory
-    val cachedClassLoader = new CachedClassLoader
-    // A latch that lets this test know the threads are ready
-    val threadReadyLatch = new CountDownLatch(threadCount)
-    // A latch to ensure that all threads try to run at the same time
-    val threadGoLatch = new CountDownLatch(1)
-
-    class Runner(name: String) extends Thread {
-      var success = false
-
-      override def run(): Unit = {
-        EnhancedRhinoSandboxSpec.runClassLoaded(
-          cachedClassLoader,
-          threadReadyLatch = threadReadyLatch,
-          threadGoLatch = threadGoLatch
-        )
-        success = true
-      }
-    }
-
-    val threads = (0 until threadCount).map(i => new Runner(i.toString))
-    // move all the threads to the starting line...
-    threads.foreach(_.start())
-    // Wait for threads to say they're ready
-    threadReadyLatch.await(scaled(10.seconds).toMillis, TimeUnit.MILLISECONDS)
-    // go!
-    threadGoLatch.countDown()
-    // Maximum time to wait for each runner to finish
-    threads.foreach(_.join(scaled(10.seconds).toMillis))
-
-    withClue("all threads did not complete successfully:") {
-      threads.map(_.success) should contain only true
-    }
-  }
-}
-
-object EnhancedRhinoSandboxSpec extends ScaledTimeSpans {
-  /**
-    * Runs a runner loaded from a custom class loader.
-    */
-  private def runClassLoaded(ecmaScriptUtilClassLoader: CachedClassLoader,
-                             threadReadyLatch: CountDownLatch,
-                             threadGoLatch: CountDownLatch): Unit = {
-    val cls = ecmaScriptUtilClassLoader.loadClass(classOf[LatchedRunner].getName)
-    val obj = cls.getDeclaredConstructor().newInstance()
-    cls
-      .getMethod("run", classOf[CountDownLatch], classOf[CountDownLatch])
-      .invoke(obj, threadReadyLatch, threadGoLatch)
-    ()
-  }
-
-  /**
-    * Waits for a shared latch and then quickly tries to run the EcmaScriptUtil.
-    * Before running, there is a test that ensures that the ContextFactory has _not_ been initialized.
-    *
-    * Inspired by: https://stackoverflow.com/questions/13263079/run-two-thread-at-the-same-time-in-java#13263273
-    */
-  class LatchedRunner {
-    def run(threadReadyLatch: CountDownLatch, threadGoLatch: CountDownLatch): Unit = {
-      require(!ContextFactory.hasExplicitGlobal, "The ContextFactory within this classloader is already initialized")
-      // Notify the test we're at the starting line.
-      threadReadyLatch.countDown()
-      // This await is for the time between all the threads `start()`-ing up, and the `countDownLatch.countDown()`
-      threadGoLatch.await(scaled(5.seconds).toMillis, TimeUnit.MILLISECONDS)
-      new EnhancedRhinoSandbox(true).assertContextFactory()
-      ()
-    }
-  }
-
-  /**
-    * Locates a class but instead of returning the class from the original classloader it instead returns a cached copy.
-    *
-    * This is needed when we want to ensure that a static variable has NOT been initialized on a class instance.
-    *
-    * Parent class loader must be the current thread's class loader since the system class loader is NOT sufficient
-    * under sbt.
-    *
-    * Inspired by: https://stackoverflow.com/questions/14316996/how-to-replace-classes-in-a-running-application-in-java#14317506
-    */
-  class CachedClassLoader extends ClassLoader(Thread.currentThread.getContextClassLoader) {
-
-    override def loadClass(name: String): Class[_] = {
-      loadedClasses synchronized {
-        loadedClasses.getOrElseUpdate(name, internalLoadClass(name))
-      }
-    }
-
-    /** Classes to always load from the parent. */
-    private val parentPackages = List("scala", "java", "sun")
-    /** Synchronized mutable map of our already loaded classes. */
-    private val loadedClasses = scala.collection.mutable.Map.empty[String, Class[_]]
-
-    /**
-      * Locates a class but returns our _own_ copy of it. Classes under "scala", "java", and "sun" will use the parent.
-      * If a class cannot be located for any reason, the parent is also returned.
-      *
-      * @param name Name of the class to load.
-      * @return The loaded class.
-      */
-    private def internalLoadClass(name: String): Class[_] = {
-      if (!parentPackages.exists(pkg => name.startsWith(pkg + "."))) {
-        val inputStream = getParent.getResourceAsStream(name.replace(".", "/").concat(".class"))
-        try {
-          val bytes = IOUtils.toByteArray(inputStream)
-          return defineClass(name, bytes, 0, bytes.length)
-        } catch {
-          case _: Throwable => /* ignore and fall through to loading from the parent */
-        } finally {
-          if (inputStream != null)
-            inputStream.close()
-        }
-      }
-      getParent.loadClass(name)
-    }
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/ontology/SchemaSpec.scala b/cwl/src/test/scala/cwl/ontology/SchemaSpec.scala
deleted file mode 100644
index 06f552797a8..00000000000
--- a/cwl/src/test/scala/cwl/ontology/SchemaSpec.scala
+++ /dev/null
@@ -1,114 +0,0 @@
-package cwl.ontology
-
-import com.typesafe.config.ConfigFactory
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import org.semanticweb.owlapi.apibinding.OWLManager
-
-class SchemaSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "Schema"
-
-  val resolveTests = Table(
-    ("base", "iri", "expected"),
-    ("file:///hello/world", "custom.owl", "file:/hello/custom.owl"),
-    ("file:///hello/world", "file:./custom.owl", "file:./custom.owl"),
-    ("file:///hello/world", "file:///custom.owl", "file:///custom.owl"),
-    ("http://hello/world", "custom.owl", "http://hello/custom.owl"),
-    ("http://hello/world", "file:./custom.owl", "file:./custom.owl"),
-    ("http://hello/world", "file:///custom.owl", "file:///custom.owl"),
-  )
-
-  forAll(resolveTests) { (base, iri, expected) =>
-    it should s"resolve $iri relative to $base to create $expected" in {
-      Schema.getIriPath(base, iri) should be(expected)
-    }
-  }
-
-  val fullIriTests = Table(
-    ("schemaDescription", "schema", "iri", "fullIri"),
-    ("galaxy", galaxySchema, "edam:format_1929", "http://edamontology.org/format_1929"),
-    ("galaxy", galaxySchema, "<edam:format_1929>", "edam:format_1929"),
-    ("galaxy", galaxySchema, "edam:format_2200", "http://edamontology.org/format_2200"),
-    ("galaxy", galaxySchema, "http://galaxyproject.org/formats/fasta", "http://galaxyproject.org/formats/fasta"),
-    ("galaxy", galaxySchema, "gx:fasta", "http://galaxyproject.org/formats/fasta"),
-    ("galaxy", galaxySchema, "not:real", "not:real"),
-    ("galaxy", galaxySchema, "owl:Thing", "http://www.w3.org/2002/07/owl#Thing"),
-    ("galaxy", galaxySchema, "owl:Nothing", "http://www.w3.org/2002/07/owl#Nothing"),
-    ("edam", edamSchema, "edam:format_1929", "http://purl.obolibrary.org/obo/edam#format_1929"),
-    ("edam w/ namespace", edamNamespaceSchema, "edam:format_1929", "http://edamontology.org/format_1929"),
-  )
-
-  forAll(fullIriTests) { (schemaDescription, schema, iri, fullIri) =>
-    it should s"expand $iri to $fullIri using schema $schemaDescription" in {
-      schema.fullIri(iri) should be(fullIri)
-    }
-  }
-
-  val subClassTests = Table(
-    ("isSubClass", "schemaDescription", "schema", "child", "ancestor"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "http://galaxyproject.org/formats/fasta"),
-    (true, "galaxy", galaxySchema, "http://galaxyproject.org/formats/fasta", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "gx:fasta", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "gx:fasta", "edam:format_2330"),
-    (false, "galaxy", galaxySchema, "not:real", "edam:format_1929"),
-    (false, "galaxy", galaxySchema, "edam:format_1929", "not:real"),
-    (false, "galaxy", galaxySchema, "owl:Thing", "owl:Nothing"),
-    (true, "galaxy", galaxySchema, "owl:Nothing", "owl:Thing"),
-    (false, "galaxy", galaxySchema, "owl:Thing", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "owl:Thing"),
-    (false, "galaxy", galaxySchema, "edam:format_1929", "owl:Nothing"),
-    (true, "galaxy", galaxySchema, "owl:Nothing", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "http://edamontology.org/format_2330"),
-    (false, "edam", edamSchema, "edam:format_1929", "http://edamontology.org/format_2330"),
-    (true, "edam w/ namespace", edamNamespaceSchema, "edam:format_1929", "http://edamontology.org/format_2330"),
-  )
-
-  forAll(subClassTests) { (isSubClass, schemaDescription, schema, child, ancestor) =>
-    it should s"return $isSubClass that $child is a sub class of $ancestor when checking schema $schemaDescription" in {
-      schema.isSubClass(child, ancestor) should be(isSubClass)
-    }
-  }
-  
-  it should "cache ontologies" in {
-    val cache = Schema.makeOntologyCache(ConfigFactory.parseString("max-size=5"))
-    val ontologyManager1 = OWLManager.createOWLOntologyManager
-    val ontologyManager2 = OWLManager.createOWLOntologyManager
-    val ontology1 = Schema.loadOntologyFromIri(ontologyManager1, Option(cache))(getClass.getResource("EDAM.owl").toExternalForm)
-    ontology1.isValid shouldBe true
-    val ontology2 = Schema.loadOntologyFromIri(ontologyManager2, Option(cache))(getClass.getResource("EDAM.owl").toExternalForm)
-    ontology2.isValid shouldBe true
-    ontology2.getOrElse(fail()).getOWLOntologyManager shouldBe ontologyManager2
-  }
-
-  private lazy val galaxySchema = {
-    Schema(
-      List(
-        getClass.getResource("EDAM.owl").toExternalForm,
-        getClass.getResource("gx_edam.ttl").toExternalForm
-      ),
-      Map.empty
-    )
-  }
-
-  private lazy val edamSchema = {
-    Schema(
-      List(
-        getClass.getResource("EDAM.owl").toExternalForm
-      ),
-      Map.empty
-    )
-  }
-
-  private lazy val edamNamespaceSchema = {
-    Schema(
-      List(
-        getClass.getResource("EDAM.owl").toExternalForm
-      ),
-      Map("edam" -> "http://edamontology.org/")
-    )
-  }
-}
diff --git a/cwl/src/test/scala/cwl/preprocessor/CwlPreProcessorSpec.scala b/cwl/src/test/scala/cwl/preprocessor/CwlPreProcessorSpec.scala
deleted file mode 100644
index c0aba9c975d..00000000000
--- a/cwl/src/test/scala/cwl/preprocessor/CwlPreProcessorSpec.scala
+++ /dev/null
@@ -1,125 +0,0 @@
-package cwl.preprocessor
-
-import better.files.File
-import cats.data.NonEmptyList
-import common.assertion.CromwellTimeoutSpec
-import common.mock.MockSugar
-import cwl.preprocessor.CwlPreProcessor.SaladFunction
-import io.circe.Printer
-import org.mockito.ArgumentMatchers._
-import org.mockito.Mockito._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-class CwlPreProcessorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with MockSugar {
-  behavior of "CwlPreProcessor"
-
-  private val resourcesRoot = File(getClass.getResource(".").getPath)
-  private val echoFileTool = CwlFileReference(resourcesRoot / "echo_tool.cwl", None)
-
-  it should "flatten a simple file" in {
-    validate(makeTestRoot("simple_workflow"), None) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(echoFileTool)
-    }
-  }
-
-  it should "flatten file with a self reference" in {
-    validate(makeTestRoot("self_reference"), Option("echo-workflow-2")) { _ => }
-  }
-
-  /*
-    * A "valid" cyclic dependency means for example
-    * file_1
-    *   - workflow_1 -> depends on workflow_3
-    *   - workflow_2
-    * file_2
-    *   - workflow_3 -> depends on workflow_2
-    * workflow_1 (in file_1) references a workflow in file_2 that references a workflow in file_1,
-    * but that's ok since the cycle is only over the file, not the workflows themselves.
-   */
-  it should "flatten file with sub workflow, self reference and valid cyclic dependency" in {
-    val testRoot = makeTestRoot("complex_workflow")
-    val subWorkflow =  CwlFileReference(testRoot / "sub" / "sub_workflow.cwl", Option("sub-echo-workflow-1"))
-
-    validate(testRoot, Option("echo-workflow-2")) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(echoFileTool)
-      verify(mockSaladingFunction).apply(subWorkflow)
-    }
-  }
-
-  it should "detect invalid cyclic dependencies in the same file and fail" in {
-    val testRoot = makeTestRoot("same_file_cyclic_dependency")
-
-    validate(testRoot, Option("echo-workflow-2"),
-      expectedFailure = Option(
-        NonEmptyList.one(s"Found a circular dependency on file://$testRoot/root_workflow.cwl#echo-workflow-2")
-      )
-    ) { _ => }
-  }
-
-  it should "detect invalid transitive cyclic dependencies (A => B => C => A) and fail" in {
-    val testRoot = makeTestRoot("transitive_cyclic_dependency")
-
-    val subWorkflow1 = CwlFileReference(testRoot / "sub_workflow_1.cwl", None)
-    val subWorkflow2 =  CwlFileReference(testRoot / "sub_workflow_2.cwl", None)
-
-    validate(testRoot, None,
-      expectedFailure = Option(
-        NonEmptyList.one(s"Found a circular dependency on file://$testRoot/root_workflow.cwl")
-      )
-    ) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(subWorkflow1)
-      verify(mockSaladingFunction).apply(subWorkflow2)
-    }
-  }
-
-  it should "pre-process inlined workflows" in {
-    val testRoot = makeTestRoot("deep_nesting")
-
-    val subWorkflow1 = CwlFileReference(testRoot / "wc-tool.cwl", None)
-    val subWorkflow2 =  CwlFileReference(testRoot / "parseInt-tool.cwl", None)
-
-    validate(testRoot, None, uuidExtractor = Option("step0/([0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12})/")) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(subWorkflow1)
-      verify(mockSaladingFunction).apply(subWorkflow2)
-    }
-  }
-
-  private def makeTestRoot(testDirectoryName: String) = resourcesRoot / testDirectoryName
-
-  def validate[T](testRoot: File,
-                  root: Option[String],
-                  expectedFailure: Option[NonEmptyList[String]] = None,
-                  uuidExtractor: Option[String] = None
-                 )(additionalValidation: SaladFunction => T): Unit = {
-    val rootWorkflowReference = CwlFileReference(testRoot / "root_workflow.cwl", root)
-
-    // Mocking the salad function allows us to validate how many times it is called exactly and with which parameters
-    val mockSaladingFunction = mock[SaladFunction]
-    when(mockSaladingFunction.apply(any[CwlReference])) thenAnswer {
-      invocationOnMock =>
-        CwlPreProcessor.saladCwlFile(invocationOnMock.getArgument[CwlReference](0))
-    }
-    val preProcessor = new CwlPreProcessor(mockSaladingFunction)
-
-    val process = preProcessor.preProcessCwl(rootWorkflowReference).value.unsafeRunSync()
-    // Asserts that dependencies are only saladed once and exactly once
-    verify(mockSaladingFunction).apply(rootWorkflowReference)
-    additionalValidation(mockSaladingFunction)
-
-    (process, expectedFailure) match {
-      case (Left(errors), Some(failures)) => errors shouldBe failures
-      case (Left(errors), None) => fail("Unexpected failure to pre-process workflow: " + errors.toList.mkString(", "))
-      case (Right(result), None) =>
-        val content = (testRoot / "expected_result.json").contentAsString
-        val uuid = uuidExtractor.flatMap(_.r.findFirstMatchIn(result.printWith(Printer.noSpaces)).map(_.group(1)))
-        val expectationContent = content
-          .replaceAll("<<RESOURCES_ROOT>>", resourcesRoot.pathAsString)
-          .replaceAll("<<RANDOM_UUID>>", uuid.getOrElse(""))
-
-        result shouldBe io.circe.parser.parse(expectationContent).getOrElse(fail("Failed to parse expectation. Your test is broken !"))
-      case (Right(_), Some(failures)) => fail("Unexpected success to pre-process workflow, was expecting failures: " + failures.toList.mkString(", "))
-    }
-    ()
-  }
-}
diff --git a/cwl/src/test/scala/cwl/preprocessor/CwlReferenceSpec.scala b/cwl/src/test/scala/cwl/preprocessor/CwlReferenceSpec.scala
deleted file mode 100644
index a2c382c5bc9..00000000000
--- a/cwl/src/test/scala/cwl/preprocessor/CwlReferenceSpec.scala
+++ /dev/null
@@ -1,79 +0,0 @@
-package cwl.preprocessor
-
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-class CwlReferenceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  behavior of "CwlReference.apply"
-
-  it should "identify a pointerless local file reference" in {
-
-    val reference = "file:///blah/di/blah.cwl"
-    val cwlReference = CwlReference.fromString(reference)
-
-    cwlReference match {
-      case Some(ref @ CwlFileReference(file, _)) =>
-        file.pathAsString should be ("/blah/di/blah.cwl")
-        ref.pathAsString should be (reference)
-        ref.pointerWithinFile should be(None)
-        ref.fullReference should be (reference)
-      case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-      case None => fail("Failed to identify reference")
-    }
-  }
-
-  it should "identify a local file reference with a pointer" in {
-
-    val filePath = "/blah/di/blah.cwl"
-    val pointer = "1st-tool"
-    val reference = s"file://$filePath#$pointer"
-    val cwlReference = CwlReference.fromString(reference)
-
-    cwlReference match {
-      case Some(ref @ CwlFileReference(file, _)) =>
-        file.pathAsString should be (filePath)
-        ref.pathAsString should be (s"file://$filePath")
-        ref.pointerWithinFile should be(Some(pointer))
-        ref.fullReference should be (reference)
-      case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-      case None => fail("Failed to identify reference")
-    }
-  }
-
-  List("http://", "https://") foreach { scheme =>
-    it should s"identify a pointerless $scheme reference" in {
-
-      val reference = s"$scheme/blah.com/di/blah.cwl"
-      val cwlReference = CwlReference.fromString(reference)
-
-      cwlReference match {
-        case Some(ref @ CwlHttpReference(pathAsString, _)) =>
-          pathAsString should be (reference)
-          ref.pathAsString should be (reference)
-          ref.pointerWithinFile should be(None)
-          ref.fullReference should be (reference)
-        case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-        case None => fail("Failed to identify reference")
-      }
-    }
-
-    it should s"identify $scheme references with pointers" in {
-
-      val referencePath = s"$scheme/blah.com/di/blah.cwl"
-      val pointer = "1st-tool"
-      val reference = s"$referencePath#$pointer"
-      val cwlReference = CwlReference.fromString(reference)
-
-      cwlReference match {
-        case Some(ref @ CwlHttpReference(pathAsString, _)) =>
-          pathAsString should be (referencePath)
-          ref.pathAsString should be (referencePath)
-          ref.pointerWithinFile should be(Some(pointer))
-          ref.fullReference should be (reference)
-        case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-        case None => fail("Failed to identify reference")
-      }
-    }
-  }
-}
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
index b4d775f7389..e32316f3649 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
@@ -22,7 +22,7 @@ class ServiceInfoSpec extends AsyncFlatSpec with ScalatestRouteTest with Matcher
 
   behavior of "ServiceInfo"
 
-  val expectedResponse = WesStatusInfoResponse(Map("CWL" -> Set("v1.0"), "WDL" -> Set("draft-2", "1.0", "biscayne")),
+  val expectedResponse = WesStatusInfoResponse(Map("WDL" -> Set("draft-2", "1.0", "biscayne")),
     List("1.0"),
     Set("ftp", "s3", "drs", "gcs", "http"),
     Map("Cromwell" -> CromwellApiService.cromwellVersion),
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 3aac8c77c8c..42e6ee7bf79 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -147,7 +147,8 @@ object Dependencies {
     "generic",
     "shapes",
     "refined",
-    "literal"
+    "literal",
+    "optics"
   ).map(m => "io.circe" %% s"circe-$m" % circeV) :+ circeYamlDependency :+
   "io.circe" %% "circe-generic-extras" % circeGenericExtrasV :+
   "io.circe" %% "circe-config" % circeConfigV
@@ -493,52 +494,8 @@ object Dependencies {
     "org.mock-server" % "mockserver-netty" % mockserverNettyV % Test
   )
 
-  /*
-  The distro artifact contains the actual impl, but transitively includes OSGI bundles that conflict with assembly:
-  - https://github.com/owlcs/owlapi/wiki/Documentation/45d8f63d055f820c6ac2ca6c4679a2a7b705449b#howto
-  - https://github.com/owlcs/owlapi/issues/455
-  - https://github.com/owlcs/owlapi/issues/603
-
-  jcl-over-slf4j.jar is a replacement for commons-logging 1.1.1. Meanwhile our extensive transitive use of apache's
-  httpclient has been including commons-logging 1.2 for a while. Now the owl api dependency jcl-over-slf4j is
-  conflicting during assembly. As there have been no reported errors AFAIK with commons-logging leaving it in for now.
-  However as we use slf4j for cromwell log configuration the correct thing might actually be to exclude commons-logging
-  whenever importing httpclient and include jcl-over-slf4j. That way we can control all of our logging in one place.
-
-  - https://www.slf4j.org/legacy.html#jclOverSLF4J
-   */
-  val owlApiDependencies = List(
-    // This whole section (incl. javax->jakarta issues) is probably going to be removed when CWL support is removed
-    // For now, replace javax usage with jakarta.
-    "net.sourceforge.owlapi" % "owlapi-distribution" % owlApiV
-      exclude("javax.inject", "javax.inject")
-      exclude("javax.xml.bind", "jaxb-api")
-      exclude("org.apache.httpcomponents", "httpclient-osgi")
-      exclude("org.apache.httpcomponents", "httpcore-osgi")
-      exclude("org.slf4j", "jcl-over-slf4j"),
-    "org.glassfish.hk2.external" % "jakarta.inject" % jakartaInjectV,
-    "jakarta.xml.bind" % "jakarta.xml.bind-api" % jakartaXmlBindApiV,
-    "org.apache.httpcomponents" % "httpclient-cache" % apacheHttpClientV,
-    "org.apache.httpcomponents" % "httpclient" % apacheHttpClientV
-  )
-
-  val cwlDependencies: List[ModuleID] = List(
-    "com.lihaoyi" %% "ammonite-ops" % ammoniteOpsV,
-    "org.broadinstitute" % "heterodon" % heterodonV classifier "single",
-    "org.scalactic" %% "scalactic" % scalacticV,
-    "io.circe" %% "circe-optics" % circeOpticsV,
-    "org.mozilla" % "rhino" % rhinoV,
-    "org.javadelight" % "delight-rhino-sandbox" % delightRhinoSandboxV,
-    "commons-io" % "commons-io" % commonsIoV % Test
-  ) ++ betterFilesDependencies ++ owlApiDependencies
-
   val womtoolDependencies: List[ModuleID] = catsDependencies ++ slf4jBindingDependencies
 
-  val centaurCwlRunnerDependencies: List[ModuleID] = List(
-    "com.github.scopt" %% "scopt" % scoptV,
-    "io.circe" %% "circe-optics" % circeOpticsV
-  ) ++ slf4jBindingDependencies
-
   val coreDependencies: List[ModuleID] = List(
     "com.google.auth" % "google-auth-library-oauth2-http" % googleOauth2V,
     "com.chuusai" %% "shapeless" % shapelessV,
@@ -661,14 +618,12 @@ object Dependencies {
 
   val allProjectDependencies: List[ModuleID] =
     backendDependencies ++
-      centaurCwlRunnerDependencies ++
       centaurDependencies ++
       cloudSupportDependencies ++
       commonDependencies ++
       coreDependencies ++
       cromiamDependencies ++
       cromwellApiClientDependencies ++
-      cwlDependencies ++
       databaseMigrationDependencies ++
       databaseSqlDependencies ++
       draft2LanguageFactoryDependencies ++
diff --git a/project/plugins.sbt b/project/plugins.sbt
index 34bccb47a0a..bdb54f675bf 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -2,4 +2,5 @@ addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.9.0")
 addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.1")
 addSbtPlugin("com.github.sbt" % "sbt-git" % "2.0.0")
 addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.4")
+addSbtPlugin("com.github.cb372" % "sbt-explicit-dependencies" % "0.2.16")
 addDependencyTreePlugin
diff --git a/server/src/main/scala/cromwell/CommandLineArguments.scala b/server/src/main/scala/cromwell/CommandLineArguments.scala
index 8064c115b78..986a33a4dc2 100644
--- a/server/src/main/scala/cromwell/CommandLineArguments.scala
+++ b/server/src/main/scala/cromwell/CommandLineArguments.scala
@@ -5,21 +5,17 @@ import java.nio.file.InvalidPathException
 
 import better.files.File
 import cats.syntax.apply._
-import cats.syntax.either._
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
-import common.validation.IOChecked._
 import common.validation.Validation._
 import cromwell.CommandLineArguments._
 import cromwell.CromwellApp.Command
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import cromwell.webservice.PartialWorkflowSources
-import cwl.preprocessor.CwlFileReference
-import cwl.preprocessor.CwlPreProcessor
 import org.slf4j.Logger
 
-import scala.util.{Failure, Success, Try}
+import scala.util.{Failure, Success}
 
 object CommandLineArguments {
   val DefaultCromwellHost = new URL("http://localhost:8000")
@@ -46,41 +42,10 @@ case class CommandLineArguments(command: Option[Command] = None,
                                 metadataOutput: Option[Path] = None,
                                 host: URL = CommandLineArguments.DefaultCromwellHost
                                ) {
-  private lazy val cwlPreProcessor = new CwlPreProcessor()
-  private lazy val isCwl = workflowType.exists(_.equalsIgnoreCase("cwl"))
-
-  /*
-    * If the file is a relative local path, resolve it against the path of the input json.
-   */
-  private def inputFilesMapper(inputJsonPath: Path)(file: String) = {
-    DefaultPathBuilder.build(file) match {
-      case Success(path) if !path.isAbsolute => inputJsonPath.sibling(file).pathAsString
-      case _ => file
-    }
-  }
-
-  private def preProcessCwlInputFile(path: Path): ErrorOr[String] = {
-    cwlPreProcessor.preProcessInputFiles(path.contentAsString, inputFilesMapper(path)).toErrorOr
-  }
-
   def validateSubmission(logger: Logger): ErrorOr[ValidSubmission] = {
-    def preProcessCwlWorkflowSource(workflowSourcePath: Path): ErrorOr[String] = {
-      val workflowPath = File(workflowSourcePath.pathAsString)
-
-      logger.info("Pre Processing Workflow...")
-      lazy val preProcessedCwl = cwlPreProcessor.preProcessCwlToString(CwlFileReference(workflowPath, workflowRoot))
-
-      Try(preProcessedCwl.value.unsafeRunSync())
-        .toChecked
-        .flatMap(identity)
-        .toValidated
-    }
 
     def getWorkflowSourceFromPath(workflowPath: Path): ErrorOr[WorkflowSourceOrUrl] = {
-      (isCwl, imports) match {
-        case (true, None) => preProcessCwlWorkflowSource(workflowPath).map(src => WorkflowSourceOrUrl(Option(src), None))
-        case (true, Some(_)) | (false, _) => WorkflowSourceOrUrl(None, Option(workflowPath.pathAsString)).validNel
-      }
+      WorkflowSourceOrUrl(None, Option(workflowPath.pathAsString)).validNel
     }
 
     val workflowSourceAndUrl: ErrorOr[WorkflowSourceOrUrl] = DefaultPathBuilder.build(workflowSource.get) match {
@@ -93,10 +58,7 @@ case class CommandLineArguments(command: Option[Command] = None,
       case Failure(_) => PartialWorkflowSources.validateWorkflowUrl(workflowSource.get).map(validUrl => WorkflowSourceOrUrl(None, Option(validUrl)))
     }
 
-    val inputsJson: ErrorOr[String] = if (isCwl) {
-      logger.info("Pre Processing Inputs...")
-      workflowInputs.map(preProcessCwlInputFile).getOrElse(readOptionContent("Workflow inputs", workflowInputs))
-    } else readOptionContent("Workflow inputs", workflowInputs)
+    val inputsJson: ErrorOr[String] = readOptionContent("Workflow inputs", workflowInputs)
 
     import common.validation.ErrorOr.ShortCircuitingFlatMap
     val optionsJson = readOptionContent("Workflow options", workflowOptions).flatMap { WorkflowOptions.fromJsonString(_).toErrorOr }
diff --git a/server/src/test/resources/cwl_glob_sort.cwl b/server/src/test/resources/cwl_glob_sort.cwl
deleted file mode 100644
index 330c896eea6..00000000000
--- a/server/src/test/resources/cwl_glob_sort.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-requirements:
-  - class: InlineJavascriptRequirement
-hints:
-  DockerRequirement:
-    dockerPull: "debian:stretch-slim"
-inputs: []
-baseCommand: [touch, z, y, x, w, c, b, a]
-outputs:
-  letters:
-    type: string
-    outputBinding:
-      glob: '?'
-      outputEval: |
-        ${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(" ") }
diff --git a/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala b/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
index 58d2154f9b7..41b1edccb36 100644
--- a/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
+++ b/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
@@ -95,32 +95,6 @@ class CromwellCommandLineSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     validation.get.workflowUrl shouldBe Option(url)
   }
 
-  it should "run single when supplying cwl workflow" in {
-    val source = raw"""{"cwlVersion":"v1.0","class":"CommandLineTool","requirements":[{"class":"InlineJavascriptRequirement"}],"hints":[{"dockerPull":"debian:stretch-slim","class":"DockerRequirement"}],"inputs":[],"baseCommand":["touch","z","y","x","w","c","b","a"],"outputs":[{"type":"string","outputBinding":{"glob":"?","outputEval":"$${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(\" \") }\n""""
-    val command = parser.parse(Array("run", "server/src/test/resources/cwl_glob_sort.cwl", "--type", "CWL"), CommandLineArguments()).get
-
-    command.command shouldBe Some(Run)
-    command.workflowSource.get shouldBe "server/src/test/resources/cwl_glob_sort.cwl"
-
-    val validation = Try(CromwellEntryPoint.validateRunArguments(command))
-    validation.isSuccess shouldBe true
-    validation.get.workflowSource.get should include(source)
-    validation.get.workflowUrl shouldBe None
-  }
-
-  it should "run single when supplying cwl workflow using url" in {
-    val url = "https://path_to_url"
-    val command = parser.parse(Array("run", url, "--type", "CWL"), CommandLineArguments()).get
-
-    command.command shouldBe Some(Run)
-    command.workflowSource.get shouldBe url
-
-    val validation = Try(CromwellEntryPoint.validateRunArguments(command))
-    validation.isSuccess shouldBe true
-    validation.get.workflowSource shouldBe None
-    validation.get.workflowUrl shouldBe Option(url)
-  }
-
   it should "run single when supplying wdl and inputs and options" in {
     val optionsLast = parser.parse(Array("run", "3step.wdl", "--inputs", "3step.inputs", "--options", "3step.options"), CommandLineArguments()).get
     optionsLast.command shouldBe Some(Run)
diff --git a/src/ci/bin/testSingleWorkflowRunner.sh b/src/ci/bin/testSingleWorkflowRunner.sh
index ce8e3e4c65e..fcf0f626822 100755
--- a/src/ci/bin/testSingleWorkflowRunner.sh
+++ b/src/ci/bin/testSingleWorkflowRunner.sh
@@ -92,26 +92,3 @@ if [ $retVal -eq 0 ]; then
 else
     grep "Error: Unknown argument" console_output.txt
 fi
-
-# Test 5: application should run cwl with inputs
-STANDARD_TEST_CASES="$PWD/centaur/src/main/resources/standardTestCases/cwl_run"
-pushd "$STANDARD_TEST_CASES" > /dev/null
-
-java -jar ${CROMWELL_BUILD_CROMWELL_JAR} run ./1st-tool.cwl --inputs ./echo-job.yml --metadata-output ./run_mode_metadata.json | tee console_output.txt
-
-cat > expected.json <<FIN
-{
-  "actualWorkflowLanguage": "CWL",
-  "actualWorkflowLanguageVersion": "v1.0",
-  "status": "Succeeded"
-}
-FIN
-
-jq '{
-  actualWorkflowLanguage,
-  actualWorkflowLanguageVersion,
-  status
-}' run_mode_metadata.json > actual.json
-
-cmp <(jq -cS . actual.json) <(jq -cS . expected.json)
-popd > /dev/null
diff --git a/womtool/src/main/scala/womtool/graph/WomGraph.scala b/womtool/src/main/scala/womtool/graph/WomGraph.scala
index d81f36e5538..b1957a1545c 100644
--- a/womtool/src/main/scala/womtool/graph/WomGraph.scala
+++ b/womtool/src/main/scala/womtool/graph/WomGraph.scala
@@ -10,8 +10,6 @@ import common.Checked
 import common.transforms.CheckedAtoB
 import common.validation.Validation._
 import common.collections.EnhancedCollections._
-import cwl.CwlDecoder
-import cwl.preprocessor.CwlPreProcessor
 import spray.json.{JsArray, JsBoolean, JsNull, JsNumber, JsObject, JsString, JsValue}
 import wdl.draft2.model.{WdlNamespace, WdlNamespaceWithWorkflow}
 import wdl.transforms.base.wdlom2wom.FileElementToWomBundleInputs
@@ -21,7 +19,6 @@ import wdl.draft3.transforms.parsing.fileToAst
 import wdl.transforms.draft2.wdlom2wom.WdlDraft2WomBundleMakers._
 import wom.callable.WorkflowDefinition
 import wom.executable.WomBundle
-import wom.expression.NoIoFunctionSet
 import wom.graph._
 import wom.transforms.WomBundleMaker.ops._
 import wom.types._
@@ -161,8 +158,6 @@ class WomGraph(graphName: String, graph: Graph) {
 
 object WomGraph {
 
-  implicit val cwlPreProcessor = CwlPreProcessor.noLogging
-
   final case class WorkflowDigraph(workflowName: String, digraph: NodesAndLinks)
   final case class NodesAndLinks(nodes: Set[String], links: Set[String]) {
     def wrapNodes(f: Set[String] => String) = this.copy(Set(f(nodes)), links)
@@ -174,7 +169,7 @@ object WomGraph {
   }
 
   def fromFiles(mainFile: String) = {
-    val graph = if (mainFile.toLowerCase().endsWith("wdl")) womExecutableFromWdl(mainFile) else womExecutableFromCwl(mainFile)
+    val graph = womExecutableFromWdl(mainFile)
     new WomGraph("workflow", graph)
   }
 
@@ -204,21 +199,6 @@ object WomGraph {
     }
   }
 
-  private def womExecutableFromCwl(filePath: String): Graph = {
-    import cwl.AcceptAllRequirements
-    (for {
-      clt <- CwlDecoder.decodeCwlFile(File(filePath)).
-        value.
-        unsafeRunSync()
-      inputs = clt.requiredInputs
-      fakedInputs = JsObject(inputs map { i => i._1 -> fakeInput(i._2) })
-      wom <- clt.womExecutable(AcceptAllRequirements, Option(fakedInputs.prettyPrint), NoIoFunctionSet, strictValidation = false)
-    } yield wom) match {
-      case Right(womExecutable) => womExecutable.graph
-      case Left(e) => throw new Exception(s"Can't build WOM executable from CWL: ${e.toList.mkString("\n", "\n", "\n")}")
-    }
-  }
-
   def fakeInput(womType: WomType): JsValue = womType match {
     case WomStringType => JsString("hio")
     case WomIntegerType | WomFloatType | WomLongType => JsNumber(25)
diff --git a/womtool/src/main/scala/womtool/input/WomGraphMaker.scala b/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
index 50749640bcc..f0d238392fa 100644
--- a/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
+++ b/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
@@ -8,7 +8,6 @@ import common.validation.Validation._
 import cromwell.core.path.Path
 import cromwell.languages.LanguageFactory
 import cromwell.languages.util.ImportResolver._
-import languages.cwl.CwlV1_0LanguageFactory
 import languages.wdl.biscayne.WdlBiscayneLanguageFactory
 import languages.wdl.draft2.WdlDraft2LanguageFactory
 import languages.wdl.draft3.WdlDraft3LanguageFactory
@@ -32,8 +31,7 @@ object WomGraphMaker {
       val languageFactory =
         List(
           new WdlDraft3LanguageFactory(ConfigFactory.empty()),
-          new WdlBiscayneLanguageFactory(ConfigFactory.empty()),
-          new CwlV1_0LanguageFactory(ConfigFactory.empty()))
+          new WdlBiscayneLanguageFactory(ConfigFactory.empty()))
           .find(_.looksParsable(mainFileContents))
           .getOrElse(new WdlDraft2LanguageFactory(ConfigFactory.empty()))
 

From 46a791817c08f376873722a24840d7b139ca6ef9 Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Thu, 1 Dec 2022 16:23:31 -0500
Subject: [PATCH 113/326] WX-696 Enable getting SAS token from WSM (#6954)

* WX-696 Enable getting SAS token from WSM

* Wire container resource id from config

* Move resource-container-id config path

* First pass at config for WSM

* Remove unused singleton config

* Tests for new config

* Fix config parsing

* Modified b2c token to be provided each time

* Remove singletonConfig arg from factory

* Restore types to factory configs

* Clean up comments and empty token default

* Default to config b2c before searching environment

* Fix token default on api client

* Fix test

* Refactor error handling for when there is no token

* Remove token constructor arg for clientProvider

* Move configs to global singleton config

* Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

* default -> override

* Add override token to test

* Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Parentheses

* Reduce token timeout

* Move AzureCredentials to separate file

* Make AzureCredentials an object

* WSM token cleanup

* Config refactor (#6960)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Initial blob token documentation

* Refine language in BlobSasTokenGenerator

* Update comment and formatting

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 .../cloud/nio/impl/drs/DrsCredentials.scala   |   2 +-
 .../filesystems/blob/AzureCredentials.scala   |  52 +++++++
 .../blob/BlobFileSystemConfig.scala           |  75 ++++++++++
 .../blob/BlobFileSystemManager.scala          | 133 +++++++++++++-----
 .../blob/BlobPathBuilderFactory.scala         |  58 +++++---
 .../WorkspaceManagerApiClientProvider.scala   |  22 ++-
 .../blob/BlobFileSystemConfigSpec.scala       |  75 ++++++++++
 .../blob/BlobPathBuilderFactorySpec.scala     |  39 ++---
 .../blob/BlobPathBuilderSpec.scala            |   6 +-
 src/ci/resources/tes_application.conf         |  24 ++--
 10 files changed, 368 insertions(+), 118 deletions(-)
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
 create mode 100644 filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala

diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
index 9fae8552fa7..2d3e972508a 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
@@ -80,7 +80,7 @@ case object GoogleAppDefaultTokenStrategy extends DrsCredentials {
   */
 case class AzureDrsCredentials(identityClientId: Option[String]) extends DrsCredentials {
 
-  final val tokenAcquisitionTimeout = 30.seconds
+  final val tokenAcquisitionTimeout = 5.seconds
 
   val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
   val tokenScope = "https://management.azure.com/.default"
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
new file mode 100644
index 00000000000..ae84e39adbe
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
@@ -0,0 +1,52 @@
+package cromwell.filesystems.blob
+
+import cats.implicits.catsSyntaxValidatedId
+import com.azure.core.credential.TokenRequestContext
+import com.azure.core.management.AzureEnvironment
+import com.azure.core.management.profile.AzureProfile
+import com.azure.identity.DefaultAzureCredentialBuilder
+import common.validation.ErrorOr.ErrorOr
+
+import scala.concurrent.duration._
+import scala.jdk.DurationConverters._
+
+import scala.util.{Failure, Success, Try}
+
+/**
+  * Strategy for obtaining an access token in an environment with available Azure identity.
+  * If you need to disambiguate among multiple active user-assigned managed identities, pass
+  * in the client id of the identity that should be used.
+  */
+case object AzureCredentials {
+
+  final val tokenAcquisitionTimeout = 5.seconds
+
+  val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
+  val tokenScope = "https://management.azure.com/.default"
+
+  private def tokenRequestContext: TokenRequestContext = {
+    val trc = new TokenRequestContext()
+    trc.addScopes(tokenScope)
+    trc
+  }
+
+  private def defaultCredentialBuilder: DefaultAzureCredentialBuilder =
+    new DefaultAzureCredentialBuilder()
+      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
+
+  def getAccessToken(identityClientId: Option[String]): ErrorOr[String] = {
+    val credentials = identityClientId.foldLeft(defaultCredentialBuilder) {
+      (builder, clientId) => builder.managedIdentityClientId(clientId)
+    }.build()
+
+    Try(
+      credentials
+        .getToken(tokenRequestContext)
+        .block(tokenAcquisitionTimeout.toJava)
+    ) match {
+      case Success(null) => "null token value attempting to obtain access token".invalidNel
+      case Success(token) => token.getToken.validNel
+      case Failure(error) => s"Failed to refresh access token: ${error.getMessage}".invalidNel
+    }
+  }
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
new file mode 100644
index 00000000000..f68bf7f5176
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
@@ -0,0 +1,75 @@
+package cromwell.filesystems.blob
+
+import cats.implicits.catsSyntaxValidatedId
+import cats.syntax.apply._
+import com.typesafe.config.Config
+import common.validation.Validation._
+import net.ceedubs.ficus.Ficus._
+
+import java.util.UUID
+
+// WSM config is needed for accessing WSM-managed blob containers created in Terra workspaces.
+// If the identity executing Cromwell has native access to the blob container, this can be ignored.
+final case class WorkspaceManagerConfig(url: WorkspaceManagerURL,
+                                        workspaceId: WorkspaceId,
+                                        containerResourceId: ContainerResourceId,
+                                        overrideWsmAuthToken: Option[String]) // dev-only
+
+final case class BlobFileSystemConfig(endpointURL: EndpointURL,
+                                      blobContainerName: BlobContainerName,
+                                      subscriptionId: Option[SubscriptionId],
+                                      expiryBufferMinutes: Long,
+                                      workspaceManagerConfig: Option[WorkspaceManagerConfig])
+
+object BlobFileSystemConfig {
+
+  final val defaultExpiryBufferMinutes = 10L
+
+  def apply(config: Config): BlobFileSystemConfig = {
+    val endpointURL = parseString(config, "endpoint").map(EndpointURL)
+    val blobContainer = parseString(config, "container").map(BlobContainerName)
+    val subscriptionId = parseUUIDOpt(config, "subscription").map(_.map(SubscriptionId))
+    val expiryBufferMinutes =
+      parseLongOpt(config, "expiry-buffer-minutes")
+        .map(_.getOrElse(defaultExpiryBufferMinutes))
+
+    val wsmConfig =
+      if (config.hasPath("workspace-manager")) {
+        val wsmConf = config.getConfig("workspace-manager")
+        val wsmURL = parseString(wsmConf, "url").map(WorkspaceManagerURL)
+        val workspaceId = parseUUID(wsmConf, "workspace-id").map(WorkspaceId)
+        val containerResourceId = parseUUID(wsmConf, "container-resource-id").map(ContainerResourceId)
+        val overrideWsmAuthToken = parseStringOpt(wsmConf, "b2cToken")
+
+        (wsmURL, workspaceId, containerResourceId, overrideWsmAuthToken)
+          .mapN(WorkspaceManagerConfig)
+          .map(Option(_))
+      }
+      else None.validNel
+
+    (endpointURL, blobContainer, subscriptionId, expiryBufferMinutes, wsmConfig)
+      .mapN(BlobFileSystemConfig.apply)
+      .unsafe("Couldn't parse blob filesystem config")
+  }
+
+  private def parseString(config: Config, path: String) =
+    validate[String] { config.as[String](path) }
+
+  private def parseStringOpt(config: Config, path: String) =
+    validate[Option[String]] { config.as[Option[String]](path) }
+
+  private def parseUUID(config: Config, path: String) =
+    validate[UUID] { UUID.fromString(config.as[String](path)) }
+
+  private def parseUUIDOpt(config: Config, path: String) =
+    validate[Option[UUID]] { config.as[Option[String]](path).map(UUID.fromString) }
+
+  private def parseLongOpt(config: Config, path: String) =
+    validate[Option[Long]] { config.as[Option[Long]](path) }
+}
+
+// Our filesystem setup magic can't use BlobFileSystemConfig.apply directly, so we need this
+// wrapper class.
+class BlobFileSystemConfigWrapper(val config: BlobFileSystemConfig) {
+  def this(config: Config) = this(BlobFileSystemConfig(config))
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index 877cefdfab5..a184729c38b 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -5,10 +5,13 @@ import com.azure.core.management.AzureEnvironment
 import com.azure.core.management.profile.AzureProfile
 import com.azure.identity.DefaultAzureCredentialBuilder
 import com.azure.resourcemanager.AzureResourceManager
+import com.azure.resourcemanager.storage.models.StorageAccountKey
 import com.azure.storage.blob.nio.AzureFileSystem
 import com.azure.storage.blob.sas.{BlobContainerSasPermission, BlobServiceSasSignatureValues}
 import com.azure.storage.blob.{BlobContainerClient, BlobContainerClientBuilder}
 import com.azure.storage.common.StorageSharedKeyCredential
+import com.typesafe.scalalogging.LazyLogging
+import common.validation.Validation._
 
 import java.net.URI
 import java.nio.file.{FileSystem, FileSystemNotFoundException, FileSystems}
@@ -16,17 +19,18 @@ import java.time.temporal.ChronoUnit
 import java.time.{Duration, Instant, OffsetDateTime}
 import scala.jdk.CollectionConverters._
 import scala.util.{Failure, Success, Try}
-import com.azure.resourcemanager.storage.models.StorageAccountKey
-import com.typesafe.scalalogging.LazyLogging
-
-import java.util.UUID
 
 case class FileSystemAPI() {
   def getFileSystem(uri: URI): Try[FileSystem] = Try(FileSystems.getFileSystem(uri))
   def newFileSystem(uri: URI, config: Map[String, Object]): FileSystem = FileSystems.newFileSystem(uri, config.asJava)
   def closeFileSystem(uri: URI): Option[Unit] = getFileSystem(uri).toOption.map(_.close)
 }
-
+/**
+  * The BlobFileSystemManager is an object that is responsible for managing the open filesystem,
+  * and refreshing the SAS token that is used to access the blob container containing that filesystem.
+  *
+  * See BlobSasTokenGenerator for more information on how a SAS token is generated
+  */
 object BlobFileSystemManager {
   def parseTokenExpiry(token: AzureSasCredential): Option[Instant] = for {
     expiryString <- token.getSignature.split("&").find(_.startsWith("se")).map(_.replaceFirst("se=","")).map(_.replace("%3A", ":"))
@@ -45,7 +49,7 @@ case class BlobFileSystemManager(
     container: BlobContainerName,
     endpoint: EndpointURL,
     expiryBufferMinutes: Long,
-    blobTokenGenerator: BlobTokenGenerator,
+    blobTokenGenerator: BlobSasTokenGenerator,
     fileSystemAPI: FileSystemAPI = FileSystemAPI(),
     private val initialExpiration: Option[Instant] = None) extends LazyLogging {
   private var expiry: Option[Instant] = initialExpiration
@@ -62,13 +66,13 @@ case class BlobFileSystemManager(
           // If no filesystem already exists, this will create a new connection, with the provided configs
           case _: FileSystemNotFoundException =>
             logger.info(s"Creating new blob filesystem for URI $uri")
-            blobTokenGenerator.generateAccessToken.flatMap(generateFilesystem(uri, container, _))
+            blobTokenGenerator.generateBlobSasToken.flatMap(generateFilesystem(uri, container, _))
         }
         // If the token has expired, OR there is no token record, try to close the FS and regenerate
         case true =>
           logger.info(s"Closing & regenerating token for existing blob filesystem at URI $uri")
           fileSystemAPI.closeFileSystem(uri)
-          blobTokenGenerator.generateAccessToken.flatMap(generateFilesystem(uri, container, _))
+          blobTokenGenerator.generateBlobSasToken.flatMap(generateFilesystem(uri, container, _))
       }
     }
   }
@@ -81,44 +85,96 @@ case class BlobFileSystemManager(
 
 }
 
-sealed trait BlobTokenGenerator {def generateAccessToken: Try[AzureSasCredential]}
-object BlobTokenGenerator {
-  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId]): BlobTokenGenerator = {
-    NativeBlobTokenGenerator(container, endpoint, subscription)
+sealed trait BlobSasTokenGenerator { def generateBlobSasToken: Try[AzureSasCredential] }
+object BlobSasTokenGenerator {
+  /**
+    * Native SAS token generator, uses the DefaultAzureCredentialBuilder in the local environment
+    * to produce a SAS token.
+    *
+    * @param container The BlobContainerName of the blob container to be accessed by the generated SAS token
+    * @param endpoint The EndpointURL containing the storage account of the blob container to be accessed by
+    * this SAS token
+    * @param subscription Optional subscription parameter to use for local authorization.
+    * If one is not provided the default subscription is used
+    * @return A NativeBlobTokenGenerator, able to produce a valid SAS token for accessing the provided blob
+    * container and endpoint locally
+    */
+  def createBlobTokenGenerator(container: BlobContainerName,
+                               endpoint: EndpointURL,
+                               subscription: Option[SubscriptionId]): BlobSasTokenGenerator = {
+    NativeBlobSasTokenGenerator(container, endpoint, subscription)
   }
-  def createBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, workspaceId: WorkspaceId, workspaceManagerClient: WorkspaceManagerApiClientProvider): BlobTokenGenerator = {
-    WSMBlobTokenGenerator(container, endpoint, workspaceId, workspaceManagerClient)
+
+  /**
+    * WSM-mediated SAS token generator, uses the DefaultAzureCredentialBuilder in the cloud environment
+    * to request a SAS token from the WSM to access the given blob container. If an overrideWsmAuthToken
+    * is provided this is used instead.
+    *
+    * @param container The BlobContainerName of the blob container to be accessed by the generated SAS token
+    * @param endpoint The EndpointURL containing the storage account of the blob container to be accessed by
+    * this SAS token
+    * @param workspaceId The WorkspaceId of the account to authenticate against
+    * @param containerResourceId The ContainterResourceId of the blob container as WSM knows it
+    * @param workspaceManagerClient The client for making requests against WSM
+    * @param overrideWsmAuthToken An optional WsmAuthToken used for authenticating against the WSM for a valid
+    * SAS token to access the given container and endpoint. This is a dev only option that is only intended
+    * for local testing of the WSM interface
+    * @return A WSMBlobTokenGenerator, able to produce a valid SAS token for accessing the provided blob
+    * container and endpoint that is managed by WSM
+    */
+  def createBlobTokenGenerator(container: BlobContainerName,
+                               endpoint: EndpointURL,
+                               workspaceId: WorkspaceId,
+                               containerResourceId: ContainerResourceId,
+                               workspaceManagerClient: WorkspaceManagerApiClientProvider,
+                               overrideWsmAuthToken: Option[String]): BlobSasTokenGenerator = {
+    WSMBlobSasTokenGenerator(container, endpoint, workspaceId, containerResourceId, workspaceManagerClient, overrideWsmAuthToken)
   }
 
 }
 
-case class WSMBlobTokenGenerator(
-  container: BlobContainerName,
-  endpoint: EndpointURL,
-  workspaceId: WorkspaceId,
-  wsmClient: WorkspaceManagerApiClientProvider) extends BlobTokenGenerator {
-
-  def generateAccessToken: Try[AzureSasCredential] = Try {
-    val token = wsmClient.getControlledAzureResourceApi.createAzureStorageContainerSasToken(
-      UUID.fromString(workspaceId.value),
-      UUID.fromString("00001111-2222-3333-aaaa-bbbbccccdddd"),
-      null,
-      null,
-      null,
-      null
-    ).getToken // TODO `null` items may be required, investigate in WX-696
-
-    new AzureSasCredential(token) // TODO Does `signature` actually mean token? save for WX-696
+case class WSMBlobSasTokenGenerator(container: BlobContainerName,
+                                    endpoint: EndpointURL,
+                                    workspaceId: WorkspaceId,
+                                    containerResourceId: ContainerResourceId,
+                                    wsmClientProvider: WorkspaceManagerApiClientProvider,
+                                    overrideWsmAuthToken: Option[String]) extends BlobSasTokenGenerator {
+
+  /**
+    * Generate a BlobSasToken by using the available authorization information
+    * If an overrideWsmAuthToken is provided, use this in the wsmClient request
+    * Else try to use the environment azure identity to request the SAS token
+    *
+    * @return an AzureSasCredential for accessing a blob container
+    */
+  def generateBlobSasToken: Try[AzureSasCredential] = {
+    val wsmAuthToken: Try[String] = overrideWsmAuthToken match {
+      case Some(t) => Success(t)
+      case None => AzureCredentials.getAccessToken(None).toTry
+    }
+
+    for {
+      wsmAuth <- wsmAuthToken
+      wsmClient = wsmClientProvider.getControlledAzureResourceApi(wsmAuth)
+      sasToken <- Try(  // Java library throws
+        wsmClient.createAzureStorageContainerSasToken(
+          workspaceId.value,
+          containerResourceId.value,
+          null,
+          null,
+          null,
+          null
+        ).getToken)
+    } yield new AzureSasCredential(sasToken)
   }
 }
 
-case class NativeBlobTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId] = None) extends BlobTokenGenerator {
-
+case class NativeBlobSasTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId] = None) extends BlobSasTokenGenerator {
   private val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
   private def azureCredentialBuilder = new DefaultAzureCredentialBuilder()
       .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
       .build
-  private def authenticateWithSubscription(sub: SubscriptionId) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub.value)
+  private def authenticateWithSubscription(sub: SubscriptionId) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub.toString)
   private def authenticateWithDefaultSubscription = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withDefaultSubscription()
   private def azure = subscription.map(authenticateWithSubscription(_)).getOrElse(authenticateWithDefaultSubscription)
 
@@ -137,8 +193,13 @@ case class NativeBlobTokenGenerator(container: BlobContainerName, endpoint: Endp
     .setListPermission(true)
     .setWritePermission(true)
 
-
-  def generateAccessToken: Try[AzureSasCredential] = for {
+  /**
+    * Generate a BlobSasToken by using the local environment azure identity
+    * This will use a default subscription if one is not provided.
+    *
+    * @return an AzureSasCredential for accessing a blob container
+    */
+  def generateBlobSasToken: Try[AzureSasCredential] = for {
     uri <- BlobPathBuilder.parseURI(endpoint.value)
     configuredAccount <- BlobPathBuilder.parseStorageAccount(uri)
     azureAccount <- findAzureStorageAccount(configuredAccount)
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index e0f7c992bb6..6e8f84eb0d4 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -5,37 +5,49 @@ import com.typesafe.config.Config
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.PathBuilderFactory
 import cromwell.core.path.PathBuilderFactory.PriorityBlob
-import net.ceedubs.ficus.Ficus._
 
+import java.util.UUID
 import scala.concurrent.{ExecutionContext, Future}
 
-final case class BlobFileSystemConfig(config: Config)
-
-final case class SubscriptionId(value: String) {override def toString: String = value}
+final case class SubscriptionId(value: UUID) {override def toString: String = value.toString}
 final case class BlobContainerName(value: String) {override def toString: String = value}
 final case class StorageAccountName(value: String) {override def toString: String = value}
 final case class EndpointURL(value: String) {override def toString: String = value}
-final case class WorkspaceId(value: String) {override def toString: String = value}
+final case class WorkspaceId(value: UUID) {override def toString: String = value.toString}
+final case class ContainerResourceId(value: UUID) {override def toString: String = value.toString}
 final case class WorkspaceManagerURL(value: String) {override def toString: String = value}
-final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, singletonConfig: BlobFileSystemConfig) extends PathBuilderFactory {
-  val subscription: Option[SubscriptionId] = instanceConfig.as[Option[String]]("subscription").map(SubscriptionId)
-  val container: BlobContainerName = BlobContainerName(instanceConfig.as[String]("container"))
-  val endpoint: EndpointURL = EndpointURL(instanceConfig.as[String]("endpoint"))
-  val workspaceId: Option[WorkspaceId] = instanceConfig.as[Option[String]]("workspace-id").map(WorkspaceId)
-  val expiryBufferMinutes: Long = instanceConfig.as[Option[Long]]("expiry-buffer-minutes").getOrElse(10)
-  val workspaceManagerURL: Option[WorkspaceManagerURL] = singletonConfig.config.as[Option[String]]("workspace-manager-url").map(WorkspaceManagerURL)
-  val b2cToken: Option[String] = instanceConfig.as[Option[String]]("b2cToken")
-
-  val blobTokenGenerator: BlobTokenGenerator = (workspaceManagerURL, b2cToken, workspaceId) match {
-    case (Some(url), Some(token), Some(workspaceId)) =>
-      val wsmClient: WorkspaceManagerApiClientProvider = new HttpWorkspaceManagerClientProvider(url, token)
-      // parameterizing client instead of URL to make injecting mock client possible
-      BlobTokenGenerator.createBlobTokenGenerator(container, endpoint, workspaceId, wsmClient)
-    case _ =>
-      BlobTokenGenerator.createBlobTokenGenerator(container, endpoint, subscription)
-  }
 
-  val fsm: BlobFileSystemManager = BlobFileSystemManager(container, endpoint, expiryBufferMinutes, blobTokenGenerator)
+final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, singletonConfig: BlobFileSystemConfigWrapper) extends PathBuilderFactory {
+
+  private val config = singletonConfig.config
+  private val container = config.blobContainerName
+  private val endpoint = config.endpointURL
+  private val subscription = config.subscriptionId
+  private val expiryBufferMinutes = config.expiryBufferMinutes
+
+  /**
+   * This generator is responsible for producing a valid SAS token for use in accessing a Azure blob storage container
+   * Two types of generators can be produced here:
+   * > Workspace Manager (WSM) mediated SAS token generator, used to create SAS tokens that allow access for
+   * blob containers mediated by the WSM, and is enabled when a WSM config is provided. This is what is intended for use inside Terra
+   *    OR
+   * > Native SAS token generator, which obtains a valid SAS token from your local environment to reach blob containers
+   * your local azure identity has access to and is the default if a WSM config is not found. This is intended for use outside of Terra
+   *
+   * Both of these generators require an authentication token to authorize the generation of the SAS token.
+   * See BlobSasTokenGenerator for more information on how these generators work.
+   */
+  val blobSasTokenGenerator: BlobSasTokenGenerator = config.workspaceManagerConfig.map { wsmConfig =>
+    val wsmClient: WorkspaceManagerApiClientProvider = new HttpWorkspaceManagerClientProvider(wsmConfig.url)
+    // WSM-mediated mediated SAS token generator
+    // parameterizing client instead of URL to make injecting mock client possible
+    BlobSasTokenGenerator.createBlobTokenGenerator(container, endpoint, wsmConfig.workspaceId, wsmConfig.containerResourceId, wsmClient, wsmConfig.overrideWsmAuthToken)
+  }.getOrElse(
+    // Native SAS token generator
+    BlobSasTokenGenerator.createBlobTokenGenerator(container, endpoint, subscription)
+  )
+
+  val fsm: BlobFileSystemManager = BlobFileSystemManager(container, endpoint, expiryBufferMinutes, blobSasTokenGenerator)
 
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[BlobPathBuilder] = {
     Future {
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
index c083d262151..a9f52d92a91 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
@@ -4,29 +4,27 @@ import bio.terra.workspace.api.ControlledAzureResourceApi
 import bio.terra.workspace.client.ApiClient
 
 /**
-  * Represents a way to get various workspace manager clients
+  * Represents a way to get a client for interacting with workspace manager controlled resources.
+  * Additional WSM clients can be added here if needed.
   *
   * Pared down from `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.WorkspaceManagerApiClientProvider`
   *
   * For testing, create an anonymous subclass as in `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.HttpWorkspaceManagerDAOSpec`
   */
 trait WorkspaceManagerApiClientProvider {
-  def getApiClient: ApiClient
-
-  def getControlledAzureResourceApi: ControlledAzureResourceApi
-
+  def getControlledAzureResourceApi(token: String): ControlledAzureResourceApi
 }
 
-class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManagerURL, token: String) extends WorkspaceManagerApiClientProvider {
-  def getApiClient: ApiClient = {
+class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManagerURL) extends WorkspaceManagerApiClientProvider {
+  private def getApiClient: ApiClient = {
     val client: ApiClient = new ApiClient()
     client.setBasePath(baseWorkspaceManagerUrl.value)
-    client.setAccessToken(token)
-
     client
   }
 
-  def getControlledAzureResourceApi: ControlledAzureResourceApi =
-    new ControlledAzureResourceApi(getApiClient)
-
+  def getControlledAzureResourceApi(token: String): ControlledAzureResourceApi = {
+    val apiClient = getApiClient
+    apiClient.setAccessToken(token)
+    new ControlledAzureResourceApi(apiClient)
+  }
 }
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
new file mode 100644
index 00000000000..607ad5606f7
--- /dev/null
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
@@ -0,0 +1,75 @@
+package cromwell.filesystems.blob
+
+import com.typesafe.config.ConfigFactory
+import common.exception.AggregatedMessageException
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import java.util.UUID
+
+class BlobFileSystemConfigSpec extends AnyFlatSpec with Matchers {
+
+  private val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+  private val container = BlobContainerName("storageContainer")
+  private val workspaceId = WorkspaceId(UUID.fromString("B0BAFE77-0000-0000-0000-000000000000"))
+  private val containerResourceId = ContainerResourceId(UUID.fromString("F00B4911-0000-0000-0000-000000000000"))
+  private val workspaceManagerURL = WorkspaceManagerURL("https://wsm.example.com")
+  private val b2cToken = "b0gus-t0ken"
+
+  it should "parse configs for a minimal functioning factory with native blob access" in {
+    val config = BlobFileSystemConfig(
+      ConfigFactory.parseString(
+      s"""
+         |container = "$container"
+         |endpoint = "$endpoint"
+      """.stripMargin)
+    )
+    config.blobContainerName should equal(container)
+    config.endpointURL should equal(endpoint)
+    config.expiryBufferMinutes should equal(BlobFileSystemConfig.defaultExpiryBufferMinutes)
+  }
+
+  it should "parse configs for a functioning factory with WSM-mediated blob access" in {
+    val config = BlobFileSystemConfig(
+      ConfigFactory.parseString(
+        s"""
+           |container = "$container"
+           |endpoint = "$endpoint"
+           |expiry-buffer-minutes = "20"
+           |workspace-manager {
+           |  url = "$workspaceManagerURL"
+           |  workspace-id = "$workspaceId"
+           |  container-resource-id = "$containerResourceId"
+           |  b2cToken = "$b2cToken"
+           |}
+           |
+        """.stripMargin)
+    )
+    config.blobContainerName should equal(container)
+    config.endpointURL should equal(endpoint)
+    config.expiryBufferMinutes should equal(20L)
+    config.workspaceManagerConfig.isDefined shouldBe true
+    config.workspaceManagerConfig.get.url shouldBe workspaceManagerURL
+    config.workspaceManagerConfig.get.workspaceId shouldBe workspaceId
+    config.workspaceManagerConfig.get.containerResourceId shouldBe containerResourceId
+    config.workspaceManagerConfig.get.overrideWsmAuthToken.contains(b2cToken) shouldBe true
+  }
+
+  it should "fail when partial WSM config is supplied" in {
+    val rawConfig =
+      ConfigFactory.parseString(
+        s"""
+         |container = "$container"
+         |endpoint = "$endpoint"
+         |expiry-buffer-minutes = "10"
+         |workspace-manager {
+         |  url = "$workspaceManagerURL"
+         |  container-resource-id = "$containerResourceId"
+         |}
+         |
+        """.stripMargin)
+
+    val error = intercept[AggregatedMessageException](BlobFileSystemConfig(rawConfig))
+    error.getMessage should include("No configuration setting found for key 'workspace-id'")
+  }
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
index 0cad162c860..6bf00d66915 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
@@ -1,7 +1,6 @@
 package cromwell.filesystems.blob
 
 import com.azure.core.credential.AzureSasCredential
-import com.typesafe.config.ConfigFactory
 import common.mock.MockSugar
 import org.mockito.Mockito._
 import org.scalatest.flatspec.AnyFlatSpec
@@ -24,28 +23,6 @@ object BlobPathBuilderFactorySpec {
 }
 class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSugar {
   def generateTokenExpiration(minutes: Long) = Instant.now.plus(minutes, ChronoUnit.MINUTES)
-  it should "parse configs for a functioning factory" in {
-    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = BlobContainerName("storageContainer")
-    val workspaceId = WorkspaceId("B0BAFE77-0000-0000-0000-000000000000")
-    val workspaceManagerURL = WorkspaceManagerURL("https://wsm.example.com")
-    val instanceConfig = ConfigFactory.parseString(
-      s"""
-      |container = "$container"
-
-      |endpoint = "$endpoint"
-      |expiry-buffer-minutes = "10"
-      |workspace-id = "$workspaceId"
-      """.stripMargin)
-    val singletonConfig = ConfigFactory.parseString(s"""workspace-manager-url = "$workspaceManagerURL" """)
-    val globalConfig = ConfigFactory.parseString("""""")
-    val factory = BlobPathBuilderFactory(globalConfig, instanceConfig, new BlobFileSystemConfig(singletonConfig))
-    factory.container should equal(container)
-    factory.endpoint should equal(endpoint)
-    factory.expiryBufferMinutes should equal(10L)
-    factory.workspaceId should contain(workspaceId)
-    factory.workspaceManagerURL should contain(workspaceManagerURL)
-  }
 
   it should "build an example sas token of the correct format" in {
     val testToken = BlobPathBuilderFactorySpec.buildExampleSasToken(Instant.ofEpochMilli(1603794041000L))
@@ -94,8 +71,8 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val azureUri = BlobFileSystemManager.uri(endpoint)
 
     val fileSystems = mock[FileSystemAPI]
-    val blobTokenGenerator = mock[BlobTokenGenerator]
-    when(blobTokenGenerator.generateAccessToken).thenReturn(Try(sasToken))
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
 
     val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(expiredToken))
     fsm.getExpiry should contain(expiredToken)
@@ -123,8 +100,8 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val fileSystems = mock[FileSystemAPI]
     when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(dummyFileSystem))
 
-    val blobTokenGenerator = mock[BlobTokenGenerator]
-    when(blobTokenGenerator.generateAccessToken).thenReturn(Try(sasToken))
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
 
     val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(initialToken))
     fsm.getExpiry should contain(initialToken)
@@ -148,8 +125,8 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
 
     val fileSystems = mock[FileSystemAPI]
     when(fileSystems.getFileSystem(azureUri)).thenReturn(Failure(new FileSystemNotFoundException))
-    val blobTokenGenerator = mock[BlobTokenGenerator]
-    when(blobTokenGenerator.generateAccessToken).thenReturn(Try(sasToken))
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
 
     val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(refreshedToken))
     fsm.getExpiry.isDefined shouldBe true
@@ -172,8 +149,8 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val azureUri = BlobFileSystemManager.uri(endpoint)
 
     val fileSystems = mock[FileSystemAPI]
-    val blobTokenGenerator = mock[BlobTokenGenerator]
-    when(blobTokenGenerator.generateAccessToken).thenReturn(Try(sasToken))
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
 
     val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems)
     fsm.getExpiry.isDefined shouldBe false
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index 671e7b2d35b..b20e2e2fe96 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -62,7 +62,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val endpointHost = BlobPathBuilder.parseURI(endpoint.value).map(_.getHost).getOrElse(fail("Could not parse URI"))
     val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
-    val blobTokenGenerator = NativeBlobTokenGenerator(store, endpoint)
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
     val fsm: BlobFileSystemManager = BlobFileSystemManager(store, endpoint, 10L, blobTokenGenerator)
     val testString = endpoint.value + "/" + store + evalPath
     val blobPath: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
@@ -80,7 +80,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
     val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
-    val blobTokenGenerator = NativeBlobTokenGenerator(store, endpoint)
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
     val fsm: BlobFileSystemManager = BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
     val testString = endpoint.value + "/" + store + evalPath
     val blobPath1: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
@@ -95,7 +95,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   ignore should "resolve a path without duplicating container name" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
     val store = BlobContainerName("inputs")
-    val blobTokenGenerator = NativeBlobTokenGenerator(store, endpoint)
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
     val fsm: BlobFileSystemManager = BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
 
     val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
diff --git a/src/ci/resources/tes_application.conf b/src/ci/resources/tes_application.conf
index e6595c8e941..9914bd54dff 100644
--- a/src/ci/resources/tes_application.conf
+++ b/src/ci/resources/tes_application.conf
@@ -5,9 +5,19 @@ filesystems {
   blob {
     class = "cromwell.filesystems.blob.BlobPathBuilderFactory"
     global {
-      class = "cromwell.filesystems.blob.BlobFileSystemConfig"
+      class = "cromwell.filesystems.blob.BlobFileSystemConfigWrapper"
       config {
-        workspace-manager-url: "https://workspace.dsde-dev.broadinstitute.org"
+        container: "cromwell"
+        endpoint: "https://<storage-account>.blob.core.windows.net"
+        subscription: "00001111-2222-3333-aaaa-bbbbccccdddd"
+        # WSM config is needed for accessing WSM-managed blob containers
+        # created in Terra workspaces.
+        workspace-manager {
+          url: "https://workspace.dsde-dev.broadinstitute.org"
+          workspace-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
+          container-resource-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
+          b2cToken: "Zardoz"
+        }
       }
     }
   }
@@ -23,11 +33,6 @@ engine {
     }
     blob {
       enabled: false
-      container: "cromwell"
-      endpoint: "https://<storage-account>.blob.core.windows.net"
-      subscription: "00001111-2222-3333-aaaa-bbbbccccdddd"
-      workspace-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
-      b2cToken: "Zardoz"
     }
   }
 }
@@ -49,11 +54,6 @@ backend {
         filesystems {
           blob {
             enabled: false
-            container: "cromwell"
-            endpoint: "https://<storage-account>.blob.core.windows.net"
-            subscription: "00001111-2222-3333-aaaa-bbbbccccdddd"
-            workspace-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
-            b2cToken: "Zardoz"
           }
           local {
             enabled: true

From 6e1c75927ce8bc4509ed49bde477d70d1814c4ea Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 6 Dec 2022 16:09:35 -0500
Subject: [PATCH 114/326] WX-853 Remove CWL language factory, Centaur runner
 (#6961)

---
 .../src/bin/centaur-cwl-runner.bash           |  26 --
 .../src/main/resources/application.conf       |  23 --
 .../src/main/resources/logback.xml            |  48 ---
 .../src/main/resources/reference.conf         |  29 --
 .../src/main/resources/skipped_tests.csv      |   2 -
 .../scala/centaur/cwl/CentaurCwlRunner.scala  | 255 -------------
 .../centaur/cwl/CentaurCwlRunnerConfig.scala  |   7 -
 .../centaur/cwl/CentaurCwlRunnerRunMode.scala |  94 -----
 .../scala/centaur/cwl/CloudPreprocessor.scala | 102 ------
 .../scala/centaur/cwl/OutputManipulator.scala | 237 ------------
 .../src/main/scala/centaur/cwl/Outputs.scala  |  93 -----
 .../src/test/resources/application.conf       |   1 -
 .../test/scala/CloudPreprocessorSpec.scala    | 342 ------------------
 .../cwl/CwlV1_0LanguageFactory.scala          |  75 ----
 project/ContinuousIntegration.scala           |   4 +-
 15 files changed, 1 insertion(+), 1337 deletions(-)
 delete mode 100755 centaurCwlRunner/src/bin/centaur-cwl-runner.bash
 delete mode 100644 centaurCwlRunner/src/main/resources/application.conf
 delete mode 100644 centaurCwlRunner/src/main/resources/logback.xml
 delete mode 100644 centaurCwlRunner/src/main/resources/reference.conf
 delete mode 100644 centaurCwlRunner/src/main/resources/skipped_tests.csv
 delete mode 100644 centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunner.scala
 delete mode 100644 centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerConfig.scala
 delete mode 100644 centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala
 delete mode 100644 centaurCwlRunner/src/main/scala/centaur/cwl/CloudPreprocessor.scala
 delete mode 100644 centaurCwlRunner/src/main/scala/centaur/cwl/OutputManipulator.scala
 delete mode 100644 centaurCwlRunner/src/main/scala/centaur/cwl/Outputs.scala
 delete mode 100644 centaurCwlRunner/src/test/resources/application.conf
 delete mode 100644 centaurCwlRunner/src/test/scala/CloudPreprocessorSpec.scala
 delete mode 100644 languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala

diff --git a/centaurCwlRunner/src/bin/centaur-cwl-runner.bash b/centaurCwlRunner/src/bin/centaur-cwl-runner.bash
deleted file mode 100755
index 8f39c3ec130..00000000000
--- a/centaurCwlRunner/src/bin/centaur-cwl-runner.bash
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env bash
-
-# `sbt assembly` must have already been run.
-build_root="$( dirname "${BASH_SOURCE[0]}" )/../../.."
-centaur_cwl_jar="${CENTAUR_CWL_JAR:-"$( \
-    find "${build_root}/centaurCwlRunner/target/scala-2.13" -name 'centaur-cwl-runner-*.jar' -print0 \
-    | xargs -0 ls -1 -t \
-    | head -n 1 \
-    )"}"
-centaur_cwl_skip_file="${build_root}/centaurCwlRunner/src/main/resources/skipped_tests.csv"
-
-centaur_cwl_java_args=("-Xmx1g")
-if [[ -n "${CENTAUR_CWL_JAVA_ARGS-}" ]]; then
-    # Allow splitting on space to simulate an exported array
-    # https://stackoverflow.com/questions/5564418/exporting-an-array-in-bash-script#answer-5564589
-    # shellcheck disable=SC2206
-    centaur_cwl_java_args+=(${CENTAUR_CWL_JAVA_ARGS})
-fi
-
-# Handle empty arrays in older versions of bash
-# https://stackoverflow.com/questions/7577052/bash-empty-array-expansion-with-set-u#answer-7577209
-java \
-    ${centaur_cwl_java_args[@]+"${centaur_cwl_java_args[@]}"} \
-    -jar "${centaur_cwl_jar}" \
-    --skip-file "${centaur_cwl_skip_file}" \
-    "$@"
diff --git a/centaurCwlRunner/src/main/resources/application.conf b/centaurCwlRunner/src/main/resources/application.conf
deleted file mode 100644
index fcdd3da9c57..00000000000
--- a/centaurCwlRunner/src/main/resources/application.conf
+++ /dev/null
@@ -1,23 +0,0 @@
-akka {
-  loggers = ["akka.event.slf4j.Slf4jLogger"]
-  logging-filter = "akka.event.slf4j.Slf4jLoggingFilter"
-
-  # Silence Akka-Http warning logging of:
-  # [WARN] [01/28/2019 06:50:04.293] [centaur-acting-like-a-system-akka.actor.default-dispatcher-3] [centaur-acting-like-a-system/Pool(shared->http://localhost:8000)] Connection attempt failed. Backing off new connection attempts for at least 100 milliseconds.
-  #
-  # via:
-  # https://github.com/akka/akka/blob/v2.5.19/akka-actor/src/main/resources/reference.conf#L41-L44
-  # https://github.com/akka/akka/blob/v2.5.19/akka-actor/src/main/scala/akka/event/Logging.scala#L377
-  # https://github.com/akka/akka-http/blob/v10.1.7/akka-http-core/src/main/scala/akka/http/impl/engine/client/pool/NewHostConnectionPool.scala#L134
-  stdout-loglevel = "ERROR"
-}
-
-centaur {
-  # When running the tests in parallel on a Travis instance we need a bit more time for a reply to come back.
-  sendReceiveTimeout: 1 minute
-}
-
-cwltool-runner {
-  # When running the tests in parallel it takes a while for each JVM to initialize Heterodon. Instead use the process.
-  class = "cwl.CwltoolProcess"
-}
diff --git a/centaurCwlRunner/src/main/resources/logback.xml b/centaurCwlRunner/src/main/resources/logback.xml
deleted file mode 100644
index d92bac61949..00000000000
--- a/centaurCwlRunner/src/main/resources/logback.xml
+++ /dev/null
@@ -1,48 +0,0 @@
-<configuration>
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-            <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger - %msg%n</pattern>
-        </encoder>
-    </appender>
-
-    <!-- lower logging level, especially to stdout -->
-    <root level="warn">
-        <appender-ref ref="STDOUT"/>
-    </root>
-
-    <!--
-    Silence occasional PoolMasterActor error logging of:
-    04:20:04.785 [centaur-acting-like-a-system-akka.actor.default-dispatcher-5] ERROR akka.http.impl.engine.client.PoolMasterActor - connection pool for PoolGateway(hcps = HostConnectionPoolSetup(localhost,8000,ConnectionPoolSetup(ConnectionPoolSettings(4,0,5,32,1,30 seconds,ClientConnectionSettings(Some(User-Agent: akka-http/10.0.10),10 seconds,1 minute,512,None,<function0>,List(),ParserSettings(2048,16,64,64,8192,64,8388608,256,1048576,Strict,RFC6265,true,Full,Error,Map(If-Range -> 0, If-Modified-Since -> 0, If-Unmodified-Since -> 0, default -> 12, Content-MD5 -> 0, Date -> 0, If-Match -> 0, If-None-Match -> 0, User-Agent -> 32),false,akka.stream.impl.ConstantFun$$$Lambda$286/1579280783@2287c189,akka.stream.impl.ConstantFun$$$Lambda$286/1579280783@2287c189,akka.stream.impl.ConstantFun$$$Lambda$287/1370074462@628a0265),None),TCPTransport),akka.http.scaladsl.HttpConnectionContext$@164c4af,akka.event.MarkerLoggingAdapter@4204728))) has shut down unexpectedly
-
-    via:
-    https://github.com/akka/akka-http/blob/v10.0.10/akka-http-core/src/main/scala/akka/http/impl/engine/client/PoolMasterActor.scala#L117
-    -->
-    <logger name="akka.http.impl.engine.client.PoolMasterActor" level="off" additivity="false"/>
-
-    <!--
-    Silence Injector warning logging of:
-    06:36:48.095 [main] WARN  org.semanticweb.owlapi.utilities.Injector - No files found for META-INF/services/org.semanticweb.owlapi.model.OWLOntologyIRIMapper
-
-    via:
-    https://github.com/owlcs/owlapi/blob/owlapi-parent-5.1.7/api/src/main/java/org/semanticweb/owlapi/utilities/Injector.java#L383
-    -->
-    <logger name="org.semanticweb.owlapi.utilities.Injector" level="error" additivity="false"/>
-
-    <!--
-    Silence Akka warning logging of:
-    10:18:20.629 [centaur-acting-like-a-system-akka.actor.default-dispatcher-8] WARN  akka.io.InetAddressDnsResolver - No caching TTL defined. Using default value Ttl(30 seconds).
-
-    via:
-    https://github.com/akka/akka/blob/v2.5.19/akka-actor/src/main/scala/akka/io/InetAddressDnsResolver.scala#L40
-    -->
-    <logger name="akka.io.InetAddressDnsResolver" level="error" additivity="false"/>
-
-    <!--
-    Silence Akka-Http warning logging of:
-    00:53:57.537 [centaur-acting-like-a-system-akka.actor.default-dispatcher-10] WARN  akka.http.impl.engine.client.PoolGateway - Connection attempt failed. Backing off new connection attempts for at least 100 milliseconds.
-
-    via:
-    https://github.com/akka/akka-http/blob/v10.1.7/akka-http-core/src/main/scala/akka/http/impl/engine/client/pool/NewHostConnectionPool.scala#L134
-    -->
-    <logger name="akka.http.impl.engine.client.PoolGateway" level="error" additivity="false"/>
-</configuration>
diff --git a/centaurCwlRunner/src/main/resources/reference.conf b/centaurCwlRunner/src/main/resources/reference.conf
deleted file mode 100644
index a906e824372..00000000000
--- a/centaurCwlRunner/src/main/resources/reference.conf
+++ /dev/null
@@ -1,29 +0,0 @@
-centaur {
-  cwl-runner {
-    mode = local
-
-    # End of actual references and begin BA-6546 exceptions...
-    # Not sure if this reference conf is used by testers outside of DSP/broad?
-    # If you know for sure then do some combination of:
-    # - update this comment with the location of those tests
-    # - update the external tests to explicitly pass in their own config
-    # - if the external tests are 100% confirmed not to exist state how you know that
-    # Not really reference, but leaving just in case someone is relying on these values.
-    papi.default-input-gcs-prefix = "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/"
-    tesk.default-input-ftp-prefix = "ftp://ftp.hexdump.org/centaur-cwl-conformance/cwl-inputs/"
-    google {
-      application-name = "centaur-cwl-runner"
-      genomics.endpoint-url = "https://lifesciences.googleapis.com/"
-      genomics.location = "us-central1"
-      max-attempts = 3
-      auth = "application-default"
-      auths = [
-        {
-          name = "application-default"
-          scheme = "application_default"
-        }
-      ]
-    }
-    # End BA-6546 exceptions
-  }
-}
diff --git a/centaurCwlRunner/src/main/resources/skipped_tests.csv b/centaurCwlRunner/src/main/resources/skipped_tests.csv
deleted file mode 100644
index 08b6b117906..00000000000
--- a/centaurCwlRunner/src/main/resources/skipped_tests.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-vf-concat.cwl,empty.json
-dir5.cwl,dir-job.yml
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunner.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunner.scala
deleted file mode 100644
index ec5dcad537e..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunner.scala
+++ /dev/null
@@ -1,255 +0,0 @@
-package centaur.cwl
-
-import better.files._
-import cats.effect.IO
-import centaur.api.CentaurCromwellClient
-import centaur.cwl.Outputs._
-import centaur.test.TestOptions
-import centaur.test.standard.{CentaurTestCase, CentaurTestFormat}
-import centaur.test.submit.{SubmitHttpResponse, SubmitWorkflowResponse}
-import centaur.test.workflow.{AllBackendsRequired, SubmittedWorkflowTracker, Workflow, WorkflowData}
-import com.typesafe.scalalogging.StrictLogging
-import common.util.VersionUtil
-import cromwell.api.model.{Aborted, Failed, NonTerminalStatus, Succeeded}
-import cromwell.core.WorkflowOptions
-import cromwell.core.path.PathBuilderFactory
-import cromwell.core.path.BetterFileMethods.Cmds
-import cwl.preprocessor.{CwlFileReference, CwlPreProcessor}
-import spray.json._
-
-import scala.concurrent.Await
-import scala.concurrent.duration.Duration
-
-/**
-  * Runs workflows in a "cwl-runner" friendly way.
-  *
-  * https://github.com/broadinstitute/cromwell/issues/2590
-  * https://github.com/common-workflow-language/common-workflow-language/blob/v1.0.1/CONFORMANCE_TESTS.md
-  * https://github.com/common-workflow-language/common-workflow-language/blob/v1.0.1/draft-3/cwl-runner.cwl#L5-L68
-  * https://github.com/common-workflow-language/common-workflow-language/pull/278/files#diff-ee814a9c027fc9750beb075c283a973cR49
-  */
-object CentaurCwlRunner extends StrictLogging {
-
-  case class SkippedTest(sourceName: String, inputsName: String) {
-    def shouldSkip(args: CommandLineArguments) = {
-      args.workflowSource.exists(_.name.equalsIgnoreCase(sourceName)) &&
-        args.workflowInputs.exists(_.name.equalsIgnoreCase(inputsName))
-    }
-  }
-
-  case class CommandLineArguments(workflowSource: Option[File] = None,
-                                  workflowInputs: Option[File] = None,
-                                  quiet: Boolean = false,
-                                  outdir: Option[File] = None,
-                                  skipFile: Option[File] = None)
-
-  // TODO: This would be cleaner with Enumeratum
-  object ExitCode extends Enumeration {
-
-    protected case class ExitVal(status: Int) extends super.Val
-
-    implicit class ValueToVal(val exitCodeValue: Value) extends AnyVal {
-      def status: Int = exitCodeValue.asInstanceOf[ExitVal].status
-    }
-
-    val Success = ExitVal(0)
-    val Failure = ExitVal(1)
-    val NotImplemented = ExitVal(33)
-  }
-
-  private val cwlPreProcessor = new CwlPreProcessor()
-  private val centaurCwlRunnerRunMode = CentaurCwlRunnerRunMode.fromConfig(CentaurCwlRunnerConfig.conf)
-  private val parser = buildParser()
-  private lazy val centaurCwlRunnerVersion = VersionUtil.getVersion("centaur-cwl-runner")
-  private lazy val versionString = s"$centaurCwlRunnerVersion ${centaurCwlRunnerRunMode.description}"
-
-  private def showUsage(): ExitCode.Value = {
-    System.err.println(parser.usage)
-    ExitCode.Failure
-  }
-
-  private def buildParser(): scopt.OptionParser[CommandLineArguments] = {
-    new scopt.OptionParser[CommandLineArguments]("java -jar /path/to/centaurCwlRunner.jar") {
-      head("centaur-cwl-runner", versionString)
-
-      help("help").text("Centaur CWL Runner - Cromwell integration testing environment")
-
-      version("version").text("Print version and exit")
-
-      arg[String]("workflow-source").text("Workflow source file.").required().
-        action((s, c) => c.copy(workflowSource = Option(File(s))))
-
-      arg[String]("inputs").text("Workflow inputs file.").optional().
-        action((s, c) => c.copy(workflowInputs = Option(File(s))))
-
-      opt[Unit]("quiet").text("Only print warnings and errors.").optional().
-        action((_, c) => c.copy(quiet = true))
-
-      opt[String]("outdir").text("Output directory, default current directory.").optional().
-        action((s, c) =>
-          c.copy(outdir = Option(File(s))))
-
-      opt[String]("skip-file").text("A csv file describing workflows to be skipped based on their name.").optional().
-        action((s, c) =>
-          c.copy(skipFile = Option(File(s))))
-    }
-  }
-
-  private def runCentaur(args: CommandLineArguments): ExitCode.Value = {
-
-    def zipSiblings(file: File): File = {
-      val zipFile = File.newTemporaryFile("cwl_imports.", ".zip")
-      val dir = file.parent
-      if (!args.quiet) {
-        logger.info(s"Zipping files under 1mb in $dir to $zipFile")
-      }
-      // TODO: Only include files under 1mb for now. When cwl runners run in parallel this can use a lot of space.
-      val files = dir
-        .children
-        .filter(_.isRegularFile)
-        .filter(_.size < 1 * 1024 * 1024)
-      Cmds.zip(files.toSeq: _*)(zipFile)
-      zipFile
-    }
-
-    val workflowPath = args.workflowSource.get
-    val (parsedWorkflowPath, workflowRoot) = workflowPath.path.toAbsolutePath.toString.split("#") match {
-      case Array(file) => File(file) -> None
-      case Array(file, root) => File(file) -> Option(root)
-    }
-    val outdirOption = args.outdir.map(_.pathAsString)
-    val testName = workflowPath.name
-    val preProcessedWorkflow = cwlPreProcessor
-      .preProcessCwlToString(CwlFileReference(parsedWorkflowPath, workflowRoot))
-      .value.unsafeRunSync() match {
-      case Left(errors) =>
-        logger.error(s"Failed to pre process cwl workflow: ${errors.toList.mkString(", ")}")
-        return ExitCode.Failure
-      case Right(v) => v
-    }
-
-    val workflowContents = centaurCwlRunnerRunMode.preProcessWorkflow(preProcessedWorkflow)
-    val inputContents = args.workflowInputs
-      .map(centaurCwlRunnerRunMode.preProcessInput)
-      .map(preProcessed => {
-        preProcessed.value.unsafeRunSync() match {
-          case Left(errors) =>
-            logger.error(s"Failed to pre process cwl workflow: ${errors.toList.mkString(", ")}")
-            return ExitCode.Failure
-          case Right(value) => value
-        }
-      })
-
-    val workflowType = Option("cwl")
-    val workflowTypeVersion = None
-    val optionsContents = outdirOption map { outdir =>
-      JsObject("cwl_outdir" -> JsString(outdir)).compactPrint
-    }
-    val labels = List.empty
-    val zippedImports = Option(zipSiblings(workflowPath)) // TODO: Zipping all the things! Be more selective.
-    val backends = AllBackendsRequired(List.empty)
-    val workflowMetadata = None
-    val notInMetadata = List.empty
-    val directoryContentCounts = None
-    val testFormat = CentaurTestFormat.WorkflowSuccessTest
-    val testOptions = TestOptions(List.empty, ignore = false)
-    val submitResponseOption = None
-
-    val submittedWorkflowTracker = new SubmittedWorkflowTracker()
-
-    val workflowData = WorkflowData(
-      Option(workflowContents),
-      None,
-      None,
-      workflowType,
-      workflowTypeVersion,
-      inputContents.map(IO.pure),
-      optionsContents.map(IO.pure),
-      labels,
-      zippedImports
-    )
-    val workflow = Workflow(
-      testName,
-      workflowData,
-      workflowMetadata,
-      notInMetadata,
-      directoryContentCounts,
-      backends,
-      retryTestFailures = false,
-      allowOtherOutputs = true,
-      skipDescribeEndpointValidation = true,
-      submittedWorkflowTracker = submittedWorkflowTracker,
-      maximumAllowedTime = None
-    )
-
-    val testCase = CentaurTestCase(workflow, testFormat, testOptions, submittedWorkflowTracker, submitResponseOption)(cromwellTracker = None)
-
-    if (!args.quiet) {
-      logger.info(s"Starting test for $workflowPath")
-    }
-
-    val pathBuilderFactory: PathBuilderFactory = centaurCwlRunnerRunMode.pathBuilderFactory
-
-    try {
-      import CentaurCromwellClient.{blockingEc, system}
-      lazy val pathBuilder = Await.result(pathBuilderFactory.withOptions(WorkflowOptions.empty), Duration.Inf)
-
-      testCase.testFunction.run.unsafeRunSync() match {
-        case unexpected: SubmitHttpResponse =>
-          logger.error(s"Unexpected response: $unexpected")
-          ExitCode.Failure
-        case SubmitWorkflowResponse(submittedWorkflow) =>
-          val status = CentaurCromwellClient.status(submittedWorkflow).unsafeRunSync()
-          status match {
-            case unexpected: NonTerminalStatus =>
-              logger.error(s"Unexpected status: $unexpected")
-              ExitCode.Failure
-            case Aborted =>
-              logger.error(s"Unexpected abort.")
-              ExitCode.Failure
-            case Failed =>
-              logger.error(s"Unexpected failure.")
-              ExitCode.Failure
-            case Succeeded =>
-              val result = handleOutput(submittedWorkflow, pathBuilder)
-              if (!args.quiet) {
-                logger.info(s"Result: $result")
-              } else {
-                // Print directly to stdout during --quiet
-                println(result)
-              }
-              ExitCode.Success
-          }
-      }
-    } finally {
-      zippedImports map { zipFile =>
-        if (!args.quiet) {
-          logger.info(s"Deleting $zipFile")
-        }
-        zipFile.delete(swallowIOExceptions = true)
-      }
-      Await.result(CentaurCromwellClient.system.terminate(), Duration.Inf)
-      ()
-    }
-  }
-
-  private def skip(args: CommandLineArguments): Boolean =
-    args.skipFile
-      .map(_.lines).getOrElse(List.empty)
-      .map(_.split(','))
-      .map({
-        case Array(source, inputs) => SkippedTest(source, inputs)
-        case invalid => throw new RuntimeException(s"Invalid skipped_tests file: $invalid")
-      })
-      .exists(_.shouldSkip(args))
-
-  def main(args: Array[String]): Unit = {
-    val parsedArgsOption = parser.parse(args, CommandLineArguments())
-    val exitCode = parsedArgsOption match {
-      case Some(parsedArgs) if skip(parsedArgs) => ExitCode.NotImplemented
-      case Some(parsedArgs) => runCentaur(parsedArgs)
-      case None => showUsage()
-    }
-    System.exit(exitCode.status)
-  }
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerConfig.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerConfig.scala
deleted file mode 100644
index 0123efd7b8d..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerConfig.scala
+++ /dev/null
@@ -1,7 +0,0 @@
-package centaur.cwl
-
-import centaur.CentaurConfig
-
-object CentaurCwlRunnerConfig {
-  lazy val conf = CentaurConfig.conf.getConfig("cwl-runner")
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala
deleted file mode 100644
index 83b6626c983..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala
+++ /dev/null
@@ -1,94 +0,0 @@
-package centaur.cwl
-
-import better.files.File
-import cloud.nio.impl.ftp.FtpFileSystems
-import com.typesafe.config.Config
-import common.validation.IOChecked._
-import cromwell.core.path.Obsolete.Paths
-import cromwell.core.path.{DefaultPathBuilderFactory, PathBuilderFactory}
-import cromwell.filesystems.ftp.{CromwellFtpFileSystems, FtpPathBuilderFactory}
-import cromwell.filesystems.gcs.GcsPathBuilderFactory
-import cwl.preprocessor.CwlPreProcessor
-
-sealed trait CentaurCwlRunnerRunMode {
-  /**
-    * Returns a user friendly of this run mode.
-    */
-  def description: String
-
-  /**
-    * Returns a factory that can create a path builder for this run mode.
-    */
-  def pathBuilderFactory: PathBuilderFactory
-
-  /**
-    * Runs any preprocessing as needed on a workflow.
-    *
-    * For example, may prefix relative paths so that absolute URLs are used.
-    */
-  def preProcessWorkflow(workflow: String): String = workflow
-
-  /**
-    * Runs any preprocessing as needed on inputs.
-    *
-    * For example, may prefix relative paths so that absolute URLs are used.
-    */
-  def preProcessInput(path: File): IOChecked[String] = path.contentAsString.validIOChecked
-}
-
-object CentaurCwlRunnerRunMode {
-  def fromConfig(conf: Config): CentaurCwlRunnerRunMode = {
-    conf.getString("mode") match {
-      case "local" => LocalRunMode
-      case "papi_v2alpha1" | "papi_v2beta" => PapiRunMode(conf)
-      case "tesk" => TeskRunMode(conf)
-      case unknown => throw new UnsupportedOperationException(s"mode not recognized: $unknown")
-    }
-  }
-}
-
-case object LocalRunMode extends CentaurCwlRunnerRunMode {
-  val cwlPreProcessor = new CwlPreProcessor()
-  override lazy val description: String = "local"
-  override lazy val pathBuilderFactory: PathBuilderFactory = DefaultPathBuilderFactory
-  /*
-    * If the file is a relative local path, resolve it against the path of the input json.
-   */
-  private def inputFilesMapper(inputJsonPath: File)(file: String) = {
-    if (!Paths.get(file).isAbsolute) inputJsonPath.sibling(file).toString
-    else file
-  }
-
-  override def preProcessInput(input: File): IOChecked[String] = cwlPreProcessor.preProcessInputFiles(input.contentAsString, inputFilesMapper(input))
-}
-
-case class PapiRunMode(conf: Config) extends CentaurCwlRunnerRunMode {
-  private lazy val googleConfig = conf.getConfig("google")
-  private lazy val preprocessor = new CloudPreprocessor(conf, "papi.default-input-gcs-prefix")
-
-  override lazy val description: String = s"papi ${googleConfig.getString("auth")}"
-
-  override lazy val pathBuilderFactory: PathBuilderFactory = {
-    GcsPathBuilderFactory(conf, googleConfig)
-  }
-
-  override def preProcessWorkflow(workflow: String): String = preprocessor.preProcessWorkflow(workflow)
-
-  override def preProcessInput(input: File): IOChecked[String] = preprocessor.preProcessInput(input.contentAsString)
-}
-
-case class TeskRunMode(conf: Config) extends CentaurCwlRunnerRunMode {
-  private lazy val ftpConfig = conf.getConfig("ftp")
-  private lazy val preprocessor = new CloudPreprocessor(conf, "tesk.default-input-ftp-prefix")
-
-  override lazy val description: String = "tesk"
-
-  override lazy val pathBuilderFactory: PathBuilderFactory = {
-    val fileSystemsConfiguration = FtpFileSystems.DefaultConfig.copy(capacity = 2)
-    new FtpPathBuilderFactory(conf, ftpConfig, new CromwellFtpFileSystems(new FtpFileSystems(fileSystemsConfiguration)))
-  }
-
-  override def preProcessWorkflow(workflow: String): String = preprocessor.preProcessWorkflow(workflow)
-
-  override def preProcessInput(input: File): IOChecked[String] = preprocessor.preProcessInput(input.contentAsString)
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CloudPreprocessor.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CloudPreprocessor.scala
deleted file mode 100644
index 68e79b9b701..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CloudPreprocessor.scala
+++ /dev/null
@@ -1,102 +0,0 @@
-package centaur.cwl
-import better.files.File
-import com.typesafe.config.Config
-import common.util.StringUtil._
-import common.validation.IOChecked.IOChecked
-import cwl.preprocessor.CwlPreProcessor
-import io.circe.optics.JsonPath
-import io.circe.optics.JsonPath._
-import io.circe.yaml.Printer.StringStyle
-import io.circe.{Json, yaml}
-import net.ceedubs.ficus.Ficus._
-import wom.util.YamlUtils
-
-/**
-  * Tools to pre-process the CWL workflows and inputs before feeding them to Cromwell so they can be executed on PAPI.
-  */
-class CloudPreprocessor(config: Config, prefixConfigPath: String) {
-  val cwlPreProcessor = new CwlPreProcessor()
-  
-  // Cloud directory where inputs for conformance tests are stored
-  private val cloudPrefix = config.as[String](prefixConfigPath).ensureSlashed
-
-  // Default docker pull image
-  val DefaultDockerPull = "dockerPull" -> Json.fromString("ubuntu:latest")
-  
-  // Default docker image to be injected in a pre-existing requirements array
-  private val DefaultDockerHint: Json = {
-    Json.obj(
-      "class" -> Json.fromString("DockerRequirement"),
-      DefaultDockerPull
-    )
-  }
-
-  // hints array with default docker requirement
-  private val DefaultDockerHintList: Json = {
-    Json.obj(
-      "hints" -> Json.arr(DefaultDockerHint)
-    )
-  }
-
-  // Parse value, apply f to it, and print it back to String using the printer
-  private def process(value: String, f: Json => Json, printer: Json => String) = {
-    YamlUtils.parse(value) match {
-      case Left(error) => throw new Exception(error.getMessage)
-      case Right(json) => printer(f(json))
-    }
-  }
-
-  // Process and print back as YAML
-  private def processYaml(value: String)(f: Json => Json) =
-    process(value, f, yaml.Printer.spaces2.copy(stringStyle = StringStyle.DoubleQuoted).pretty)
-
-  // Prefix the string at "key" with the cloud prefix
-  private def prefixLocation(value: String): String = {
-    cloudPrefix + File(value.stripPrefix("file://")).name
-  }
-
-  // Function to check if the given json has the provided key / value pair
-  private def hasKeyValue(key: String, value: String): Json => Boolean = {
-    root.selectDynamic(key).string.exist(_.equalsIgnoreCase(value))
-  }
-
-  /**
-    * Pre-process input file by prefixing all files and directories with the cloud prefix
-    */
-  def preProcessInput(input: String): IOChecked[String] = cwlPreProcessor.preProcessInputFiles(input, prefixLocation)
-
-  // Check if the given path (as an array or object) has a DockerRequirement element
-  def hasDocker(jsonPath: JsonPath)(json: Json): Boolean = {
-    val hasDockerInArray: Json => Boolean = jsonPath.arr.exist(_.exists(hasKeyValue("class", "DockerRequirement")))
-    val hasDockerInObject: Json => Boolean = jsonPath.obj.exist(_.kleisli("DockerRequirement").nonEmpty)
-
-    hasDockerInArray(json) || hasDockerInObject(json)
-  }
-
-  // Check if the given Json has a docker image in hints or requirements
-  def hasDocker(json: Json): Boolean = hasDocker(root.hints)(json) || hasDocker(root.requirements)(json)
-
-  // Add a default docker hint to the workflow if it doesn't have one
-  private val addDefaultDocker: Json => Json = workflow => if (!hasDocker(workflow)) {
-    /*
-      * deepMerge does not combine objects together but replaces keys which would overwrite existing hints
-      * so first check if there are hints already and if so add our docker one.
-      * Also turns out that the hints section can be either an array or an object.
-      * When it gets saladed the object is transformed to an array but because we deal with unsaladed cwl here
-      * we have to handle both cases.
-     */
-    val hintsAsArray = root.hints.arr.modifyOption(_ :+ DefaultDockerHint)(workflow)
-    val hintsAsObject = root.hints.obj.modifyOption(_.add("DockerRequirement", Json.obj(DefaultDockerPull)))(workflow)
-
-    hintsAsArray
-      .orElse(hintsAsObject)
-      .getOrElse(workflow.deepMerge(DefaultDockerHintList))
-  } else workflow
-  
-  private val prefixDefaultFilesInCwl = CwlPreProcessor.mapFilesAndDirectories(prefixLocation) _
-
-  /**
-    * Pre-process the workflow by adding a default docker hint iff it doesn't have one
-    */
-  def preProcessWorkflow(workflow: String): String = processYaml(workflow)(addDefaultDocker.andThen(prefixDefaultFilesInCwl))
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/OutputManipulator.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/OutputManipulator.scala
deleted file mode 100644
index dcbe3a70ec8..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/OutputManipulator.scala
+++ /dev/null
@@ -1,237 +0,0 @@
-package centaur.cwl
-
-import common.util.StringUtil._
-import cromwell.core.path.{Path, PathBuilder}
-import cwl.CwlCodecs._
-import cwl.command.ParentName
-import cwl.ontology.Schema
-import cwl.{File => CwlFile, _}
-import io.circe.literal._
-import io.circe.syntax._
-import io.circe.{Json, JsonObject}
-import mouse.all._
-import org.apache.commons.codec.digest.DigestUtils
-import shapeless.{Inl, Poly1}
-import spray.json.{JsArray, JsBoolean, JsNull, JsNumber, JsObject, JsString, JsValue}
-
-//Take cromwell's outputs and format them as expected by the spec
-object OutputManipulator extends Poly1 {
-
-  //In an Ideal world I'd return a Coproduct of these types and leave the asJson-ing to the handleOutput
-  def resolveOutput(jsValue: JsValue,
-                    pathBuilder: PathBuilder,
-                    mot: MyriadOutputType,
-                    schemaOption: Option[Schema]): Json  = {
-    mot.fold(this).apply(jsValue, pathBuilder, schemaOption)
-  }
-
-  private def hashFile(path: Path): Option[String] = path.exists.option("sha1$" + path.sha1.toLowerCase)
-  private def sizeFile(path: Path): Option[Long] = path.exists.option(path.size)
-
-  private def stringToFile(pathAsString: String, pathBuilder: PathBuilder): Json = {
-    val path = pathBuilder.build(pathAsString).get
-
-    if (path.exists()) {
-      CwlFile(
-        location = Option(path.name),
-        checksum = hashFile(path),
-        size = sizeFile(path)
-      ).asJson
-    } else {
-      Json.Null
-    }
-  }
-
-  private def populateFileFields(pathBuilder: PathBuilder,
-                                 schemaOption: Option[Schema]
-                                )(obj: JsonObject): JsonObject = {
-    val path = pathBuilder.build(obj.kleisli("location").get.asString.get).get
-    val isFile = obj.kleisli("class").exists(_.asString.contains("File"))
-    val isDirectory = obj.kleisli("class").exists(_.asString.contains("Directory"))
-
-    // Return the default value if the value at key is either absent or null, otherwise return the value
-    def valueOrNull(key: String, default: Json) = obj.kleisli(key) match {
-      case Some(Json.Null) => default
-      case Some(other) => other
-      case None => default
-    }
-
-    def populateInnerFiles(json: Json): Option[Json] = {
-
-      def populateInnerFile(file: Json): Json = {
-        file.asObject
-          .map(populateFileFields(pathBuilder, schemaOption))
-          .map(Json.fromJsonObject)
-          .orElse(file.asString.map(stringToFile(_, pathBuilder)))
-          .getOrElse(file)
-      }
-
-      // Assume the json is an array ("secondaryFiles" and "listing" are both arrays).
-      val innerFiles = json.asArray.get
-      // Remove any files that don't actually exist.
-      val filteredFiles = innerFiles.map(populateInnerFile).filterNot(_.isNull)
-      // The cwl test runner doesn't expect a "secondaryFiles" or "listing" field at all if it's empty.
-      if (filteredFiles.nonEmpty) Option(Json.arr(filteredFiles: _*)) else None
-    }
-
-    def updateFileOrDirectoryWithNestedFiles(obj: JsonObject, fieldName: String) = {
-      // Cromwell metadata has a field for all values even if their content is empty
-      // remove it as the cwl test runner expects nothing instead
-      val withoutField = obj.remove(fieldName)
-
-      // If the field was not empty, add it back with each inner file / directory properly updated as well
-      populateInnerFiles(obj.kleisli(fieldName).get)
-        .map(withoutField.add(fieldName, _))
-        .getOrElse(withoutField)
-    }
-
-    // Get sha1 from the content field
-    // We need this because some task return a "File" object that actually does not exist on disk but has its content provided directly instead
-    def hashContent: Option[String] = obj.kleisli("contents").flatMap(_.asString.map(DigestUtils.sha1Hex).map("sha1$" + _))
-
-    // Get size from the content field
-    // We need this because some task return a "File" object that actually does not exist on disk but has its content provided directly instead
-    def sizeContent: Option[Long] = obj.kleisli("contents").flatMap(_.asString.map(_.length.toLong))
-
-    // "as a special case, cwltest only matches the trailing part of location in the output sections so that it
-    // can do something reasonable regardless of URL scheme or prefix" - Peter Amstutz, 2019-04-16, CWL gitter
-    val updatedLocation = obj.add("location", Json.fromString(path.pathAsString))
-
-    // Get the format
-    def formatOption: Option[String] = for {
-      klesliFormat <- obj.kleisli("format")
-      format <- klesliFormat.asString
-    } yield format
-
-    // Lookup the full format using the namespaces
-    def fullFormatOption: Option[String] = for {
-      format <- formatOption
-      schema <- schemaOption
-    } yield schema.fullIri(format)
-
-    if (isFile) {
-      /*
-        * In order of priority use: 
-        * 1) the checksum value in the metadata
-        * 2) the checksum calculated from the value of the "contents" field of the metadata
-        * 3) the checksum calculated from the file itself
-        */
-      val defaultChecksum = hashContent.orElse(hashFile(path)).map(Json.fromString).getOrElse(Json.Null)
-      val checksum = valueOrNull("checksum", defaultChecksum)
-
-      /*
-        * In order of priority use: 
-        * 1) the size value in the metadata
-        * 2) the size calculated from the value of the "contents" field of the metadata
-        * 3) the size calculated from the file itself
-        */
-      val defaultSize = sizeContent.orElse(sizeFile(path)).map(Json.fromLong).getOrElse(Json.Null)
-      val size = valueOrNull("size", defaultSize)
-
-      val basename: Option[Json] =
-        Option(valueOrNull("basename", path.exists.option(path.name).map(Json.fromString).getOrElse(Json.Null)))
-
-      /*
-      In order of priority use:
-      1) the full format if $namespaces are available
-      2) the original format
-       */
-      val defaultFormatOption: Option[Json] = fullFormatOption.orElse(formatOption).map(Json.fromString)
-
-      val withChecksumAndSize = updatedLocation
-        .add("checksum", checksum)
-        .add("size", size)
-        // conformance test does not expect "contents" in the output
-        .remove("contents")
-
-      val withBasename = basename
-        .map(withChecksumAndSize.add("basename", _))
-        .getOrElse(withChecksumAndSize)
-
-      val withFormat = defaultFormatOption
-        .map(withBasename.add("format", _))
-        .getOrElse(withBasename)
-
-      updateFileOrDirectoryWithNestedFiles(withFormat, "secondaryFiles")
-    } else if (isDirectory) {
-      updateFileOrDirectoryWithNestedFiles(updatedLocation, "listing").
-        add("basename", path.nameWithoutExtension |> Json.fromString)
-    } else throw new RuntimeException(s"${path.pathAsString} is neither a valid file or a directory")
-  }
-
-  private def resolveOutputViaInnerType(moits: Array[MyriadOutputInnerType])
-                                       (jsValue: JsValue,
-                                        pathBuilder: PathBuilder,
-                                        schemaOption: Option[Schema]): Json = {
-    def sprayJsonToCirce(jsValue: JsValue): Json = {
-      import io.circe.parser._
-      val jsonString = jsValue.compactPrint
-      parse(jsonString).getOrElse(
-        sys.error(s"Failed to parse Json output as Json... something is very wrong: '$jsonString'")
-      )
-    }
-
-    (jsValue, moits) match {
-      //CWL expects quite a few enhancements to the File structure, hence...
-      case (JsString(metadata), Array(Inl(CwlType.File))) => stringToFile(metadata, pathBuilder)
-      // If it's a JsObject it means it's already in the right format, we just want to fill in some values that might not
-      // have been populated like "checksum" and "size"
-      case (obj: JsObject, a) if a.contains(Inl(CwlType.File)) || a.contains(Inl(CwlType.Directory)) =>
-        val json: Json = sprayJsonToCirce(obj)
-        val fileExists = (for {
-          o <- json.asObject
-          l <- o.kleisli("location")
-          s <- l.asString
-          c = if (a.contains(Inl(CwlType.Directory))) s.ensureSlashed else s
-          p <- pathBuilder.build(c).toOption
-        } yield p.exists).getOrElse(false)
-        if (fileExists) json.mapObject(populateFileFields(pathBuilder, schemaOption)) else Json.Null
-      case (JsNumber(metadata), Array(Inl(CwlType.Long))) => metadata.longValue.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Float))) => metadata.floatValue.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Double))) => metadata.doubleValue.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Int))) => metadata.intValue.asJson
-      case (JsString(metadata), Array(Inl(CwlType.String))) => metadata.asJson
-
-      //The Anys.  They have to be done for each type so that the asJson can use this type information when going back to Json representation
-      case (JsString(metadata), Array(Inl(CwlType.Any))) => metadata.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Any))) => metadata.asJson
-      case (obj: JsObject, Array(Inl(CwlType.Any))) => sprayJsonToCirce(obj)
-      case (JsBoolean(metadata), Array(Inl(CwlType.Any))) => metadata.asJson
-      case (array: JsArray, Array(Inl(CwlType.Any))) => sprayJsonToCirce(array)
-      case (JsNull, a) if a.contains(Inl(CwlType.Any)) || a.contains(Inl(CwlType.Null)) => Json.Null
-
-      case (JsArray(metadata), Array(tpe)) if tpe.select[OutputArraySchema].isDefined =>
-        (for {
-          schema <- tpe.select[OutputArraySchema]
-          items = schema.items
-          innerType <- items.select[MyriadOutputInnerType]
-          outputJson = metadata.map(m =>
-            resolveOutputViaInnerType(Array(innerType))(m, pathBuilder, schemaOption)).asJson
-        } yield outputJson).getOrElse(throw new RuntimeException(s"We currently do not support output arrays with ${tpe.select[OutputArraySchema].get.items} inner type"))
-      case (JsObject(metadata), Array(tpe)) if tpe.select[OutputRecordSchema].isDefined =>
-        def processField(field: OutputRecordField) = {
-          val parsedName = FullyQualifiedName(field.name)(ParentName.empty).id
-          field.`type`.select[MyriadOutputInnerType] map { parsedName -> _ }
-        }
-
-        (for {
-          schema <- tpe.select[OutputRecordSchema]
-          fields <- schema.fields
-          typeMap = fields.flatMap(processField).toMap
-          outputJson = metadata.map({
-            case (k, v) => k -> resolveOutputViaInnerType(Array(typeMap(k)))(v, pathBuilder, schemaOption)
-          }).asJson
-        } yield outputJson).getOrElse(throw new RuntimeException(s"We currently do not support output record schemas with ${tpe.select[OutputArraySchema].get.items} inner type"))
-      case (json, tpe) => throw new RuntimeException(s"We currently do not support outputs (${json.getClass.getSimpleName}) of $json and type $tpe")
-    }
-  }
-
-  implicit val moit: Case.Aux[MyriadOutputInnerType, (JsValue, PathBuilder, Option[Schema]) => Json] = at { t =>
-    resolveOutputViaInnerType(Array(t))
-  }
-
-  implicit val amoit: Case.Aux[Array[MyriadOutputInnerType], (JsValue, PathBuilder, Option[Schema]) => Json] =
-    at { amoit =>
-      resolveOutputViaInnerType(amoit)
-    }
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/Outputs.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/Outputs.scala
deleted file mode 100644
index c63d95399d7..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/Outputs.scala
+++ /dev/null
@@ -1,93 +0,0 @@
-package centaur.cwl
-
-import centaur.api.CentaurCromwellClient
-import centaur.test.metadata.WorkflowFlatMetadata._
-import common.collections.EnhancedCollections._
-import common.validation.IOChecked._
-import cromwell.api.model.SubmittedWorkflow
-import cromwell.core.path.PathBuilder
-import cwl.ontology.Schema
-import cwl.{Cwl, CwlDecoder, MyriadOutputType}
-import io.circe.Json
-import io.circe.syntax._
-import mouse.map._
-import shapeless.Poly1
-import spray.json.{JsObject, JsString, JsValue}
-
-object Outputs {
-
-  //When the string returned is not valid JSON, it is effectively an exception as CWL runner expects JSON to be returned
-  def handleOutput(submittedWorkflow: SubmittedWorkflow, pathBuilder: PathBuilder): String = {
-    val metadata: Map[String, JsValue] = CentaurCromwellClient.metadata(submittedWorkflow).unsafeRunSync().asFlat.value
-
-    // Wrapper function to provide the right signature for `intersectWith` below.
-    def outputResolver(schemaOption: Option[Schema])(jsValue: JsValue, mot: MyriadOutputType): Json = {
-      OutputManipulator.resolveOutput(jsValue, pathBuilder, mot, schemaOption)
-    }
-
-    //Sorry for all the nesting, but spray json JsValue doesn't have optional access methods like Argonaut/circe,
-    //thus no for comprehensions for us :(
-    metadata.get("submittedFiles.workflow") match {
-      case Some(JsString(workflow)) =>
-
-        val parseCwl: IOChecked[Cwl] = CwlDecoder.decodeCwlString(
-          workflow,
-          submittedWorkflow.workflow.zippedImports,
-          submittedWorkflow.workflow.workflowRoot
-        )
-
-        parseCwl.value.attempt.unsafeRunSync() match {
-          case Right(Right(cwl)) =>
-
-            CentaurCromwellClient.outputs(submittedWorkflow).unsafeRunSync().outputs match {
-              case JsObject(map) =>
-                val typeMap: Map[String, MyriadOutputType] = cwl.fold(CwlOutputsFold)
-                val mungeTypeMap = typeMap.mapKeys(stripTypeMapKey)
-
-                val mungeOutputMap = map.mapKeys(stripOutputKey)
-
-                mungeOutputMap.
-                  //This lets us operate on the values of the output values and types for a particular output key
-                  intersectWith(mungeTypeMap)(outputResolver(cwl.schemaOption)).
-                  //converting the whole response to Json using Circe's auto-encoder derivation
-                  asJson.
-                  //drop null values so that we don't print when Option == None
-                  printWith(io.circe.Printer.spaces2.copy(dropNullValues = true))
-              case other => s"it seems cromwell is not returning outputs as a Jsobject but is instead a $other"
-            }
-          case Right(Left(error)) => s"couldn't parse workflow: $workflow failed with error: $error"
-          case Left(error) => s"Exception when trying to read workflow: $workflow failed with error: $error"
-        }
-      case Some(other) => s"received the value $other when the workflow string was expected"
-      case None => "the workflow is no longer in the metadata payload, it's a problem"
-    }
-  }
-
-  //Ids come out of SALAD pre-processing with a filename prepended. This gets rid of it
-  // Also gets rid of the parent workflow name if present
-  def stripTypeMapKey(key: String): String = key
-    .substring(key.lastIndexOf("#") + 1, key.length)
-    .split("/").last
-
-  //Ids come out of Cromwell with a prefix, separated by a ".". This takes everything to the right,
-  //as CWL wants it
-  def stripOutputKey(key: String): String = key.substring(key.lastIndexOf(".") + 1, key.length)
-
-}
-
-object CwlOutputsFold extends Poly1 {
-  import cwl._
-
-  implicit def wf: Case.Aux[cwl.Workflow, Map[String, MyriadOutputType]] = at[cwl.Workflow] {
-    _.outputs.map(output => output.id -> output.`type`.get).toMap
-  }
-
-  implicit def clt: Case.Aux[cwl.CommandLineTool, Map[String, MyriadOutputType]] = at[cwl.CommandLineTool] {
-    _.outputs.map(output => output.id -> output.`type`.get).toMap
-  }
-
-  implicit def et: Case.Aux[cwl.ExpressionTool, Map[String, MyriadOutputType]] = at[cwl.ExpressionTool] {
-    _.outputs.map(output => output.id -> output.`type`.get).toMap
-  }
-}
-
diff --git a/centaurCwlRunner/src/test/resources/application.conf b/centaurCwlRunner/src/test/resources/application.conf
deleted file mode 100644
index 27c24fa07bf..00000000000
--- a/centaurCwlRunner/src/test/resources/application.conf
+++ /dev/null
@@ -1 +0,0 @@
-papi.default-input-gcs-prefix="gs://centaur-cwl-conformance-1f501e3/cwl-inputs/"
diff --git a/centaurCwlRunner/src/test/scala/CloudPreprocessorSpec.scala b/centaurCwlRunner/src/test/scala/CloudPreprocessorSpec.scala
deleted file mode 100644
index df13e49b666..00000000000
--- a/centaurCwlRunner/src/test/scala/CloudPreprocessorSpec.scala
+++ /dev/null
@@ -1,342 +0,0 @@
-import centaur.cwl.CloudPreprocessor
-import com.typesafe.config.ConfigFactory
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.util.YamlUtils
-
-class CloudPreprocessorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  behavior of "PAPIPreProcessor"
-
-  val pAPIPreprocessor = new CloudPreprocessor(ConfigFactory.load(), "papi.default-input-gcs-prefix")
-
-  def validate(result: String, expectation: String) = {
-    val parsedResult = YamlUtils.parse(result).toOption.get
-    val parsedExpectation = YamlUtils.parse(expectation).toOption.get
-
-    // This is an actual Json comparison from circe
-    parsedResult shouldBe parsedExpectation
-  }
-
-  it should "prefix files and directories in inputs" in {
-    validate(
-      pAPIPreprocessor.preProcessInput(
-        """|{
-           |  "input": {
-           |    "null": null,
-           |    "file": {
-           |      "location": "whale.txt",
-           |      "class": "File",
-           |      "secondaryFiles": [
-           |        {
-           |          "class": File,
-           |          "location": "hello.txt"
-           |        }
-           |      ],
-           |      "default": {
-           |        "location": "default_whale.txt",
-           |        "class": "File",
-           |      }
-           |    },
-           |    "directory": {
-           |      "location": "ref.fasta",
-           |      "class": "Directory",
-           |      "listing": [
-           |        {
-           |          "class": File,
-           |          "location": "hello.txt"
-           |        }
-           |      ]
-           |    }
-           |  }
-           |}
-           |""".stripMargin).value.unsafeRunSync().toOption.get,
-      """|{
-         |  "input": {
-         |    "null": null,
-         |    "file": {
-         |      "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/whale.txt",
-         |      "class": "File",
-         |      "secondaryFiles": [
-         |        {
-         |          "class": File,
-         |          "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/hello.txt"
-         |        }
-         |      ],
-         |      "default": {
-         |        "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/default_whale.txt",
-         |        "class": "File",
-         |      }
-         |    },
-         |    "directory": {
-         |      "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/ref.fasta",
-         |      "class": "Directory",
-         |      "listing": [
-         |        {
-         |          "class": File,
-         |          "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/hello.txt"
-         |        }
-         |      ]
-         |    }
-         |  }
-         |}
-         |""".stripMargin
-    )
-  }
-
-  it should "prefix files and directories in workflow" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |cwlVersion: v1.0
-           |requirements:
-           |  - class: DockerRequirement
-           |    dockerPull: ubuntu:latest
-           |inputs:
-           |  - id: reference
-           |    type: File
-           |    inputBinding: { position: 2 }
-           |    default:
-           |      class: File
-           |      location: args.py
-           |
-           |outputs:
-           |  args: string[]
-           |
-           |baseCommand: python
-           |arguments: ["bwa", "mem"]
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |cwlVersion: v1.0
-         |requirements:
-         |  - class: DockerRequirement
-         |    dockerPull: ubuntu:latest
-         |inputs:
-         |  - id: reference
-         |    type: File
-         |    inputBinding: { position: 2 }
-         |    default:
-         |      class: File
-         |      location: gs://centaur-cwl-conformance-1f501e3/cwl-inputs/args.py
-         |
-         |outputs:
-         |  args: string[]
-         |
-         |baseCommand: python
-         |arguments: ["bwa", "mem"]
-         |""".stripMargin
-    )
-  }
-
-  it should "add default docker image if there's no hint" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |cwlVersion: v1.0
-           |inputs:
-           |  - id: reference
-           |    type: File
-           |    inputBinding: { position: 2 }
-           |
-           |outputs:
-           |  args: string[]
-           |
-           |baseCommand: python
-           |arguments: ["bwa", "mem"]
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |hints:
-         |  - class: DockerRequirement
-         |    dockerPull: ubuntu:latest
-         |cwlVersion: v1.0
-         |inputs:
-         |  - id: reference
-         |    type: File
-         |    inputBinding: { position: 2 }
-         |
-         |outputs:
-         |  args: string[]
-         |
-         |baseCommand: python
-         |arguments: ["bwa", "mem"]
-         |""".stripMargin
-    )
-  }
-
-  it should "append default docker image to existing hint as an array" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |hints:
-           |  - class: EnvVarRequirement
-           |    envDef:
-           |      TEST_ENV: $(inputs.in)
-           |cwlVersion: v1.0
-           |inputs:
-           |  - id: reference
-           |    type: File
-           |    inputBinding: { position: 2 }
-           |
-           |outputs:
-           |  args: string[]
-           |
-           |baseCommand: python
-           |arguments: ["bwa", "mem"]
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |hints:
-         |  - class: EnvVarRequirement
-         |    envDef:
-         |      TEST_ENV: $(inputs.in)
-         |  - class: DockerRequirement
-         |    dockerPull: ubuntu:latest
-         |cwlVersion: v1.0
-         |inputs:
-         |  - id: reference
-         |    type: File
-         |    inputBinding: { position: 2 }
-         |
-         |outputs:
-         |  args: string[]
-         |
-         |baseCommand: python
-         |arguments: ["bwa", "mem"]
-         |""".stripMargin
-    )
-  }
-
-  it should "append default docker image to existing hints as an object" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |cwlVersion: v1.0
-           |inputs:
-           |  in: string
-           |outputs:
-           |  out:
-           |    type: File
-           |    outputBinding:
-           |      glob: out
-           |
-           |hints:
-           |  EnvVarRequirement:
-           |    envDef:
-           |      TEST_ENV: $(inputs.in)
-           |
-           |baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"]
-           |
-           |stdout: out
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |cwlVersion: v1.0
-         |inputs:
-         |  in: string
-         |outputs:
-         |  out:
-         |    type: File
-         |    outputBinding:
-         |      glob: out
-         |
-         |hints:
-         |  EnvVarRequirement:
-         |    envDef:
-         |      TEST_ENV: $(inputs.in)
-         |  DockerRequirement:
-         |    dockerPull: ubuntu:latest
-         |
-         |baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"]
-         |
-         |stdout: out
-         |""".stripMargin
-    )
-  }
-
-  it should "not replace existing docker requirement in an object" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |requirements:
-                      |  DockerRequirement:
-                      |    dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "not replace existing docker hint in an object" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |hints:
-                      |  DockerRequirement:
-                      |    dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "not replace existing docker hint in an array" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |hints:
-                      |- class: DockerRequirement
-                      |  dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "not replace existing docker requirement in an array" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |requirements:
-                      |- class: DockerRequirement
-                      |  dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "throw an exception if yaml / json can't be parse" in {
-    val invalid =
-      """
-        |{ [invalid]: }
-      """.stripMargin
-
-    an[Exception] shouldBe thrownBy(pAPIPreprocessor.preProcessWorkflow(invalid))
-  }
-}
diff --git a/languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala b/languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala
deleted file mode 100644
index e3a6387c739..00000000000
--- a/languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala
+++ /dev/null
@@ -1,75 +0,0 @@
-package languages.cwl
-
-import better.files.File
-import cats.data.EitherT.fromEither
-import cats.effect.IO
-import com.typesafe.config.Config
-import common.Checked
-import common.validation.Checked._
-import common.validation.IOChecked.IOChecked
-import cromwell.core.{WorkflowId, WorkflowOptions, WorkflowSourceFilesCollection}
-import cromwell.languages.util.ImportResolver.ImportResolver
-import cromwell.languages.util.LanguageFactoryUtil
-import cromwell.languages.{LanguageFactory, ValidatedWomNamespace}
-import cwl.preprocessor.CwlReference
-import cwl.{Cwl, CwlDecoder}
-import wom.ResolvedImportRecord
-import wom.core.{WorkflowJson, WorkflowOptionsJson, WorkflowSource}
-import wom.executable.WomBundle
-import wom.expression.IoFunctionSet
-
-class CwlV1_0LanguageFactory(override val config: Config) extends LanguageFactory {
-
-  override val languageName: String = "CWL"
-  override val languageVersionName: String = "v1.0"
-
-  override def validateNamespace(source: WorkflowSourceFilesCollection,
-                                 workflowSource: WorkflowSource,
-                                 workflowOptions: WorkflowOptions,
-                                 importLocalFilesystem: Boolean,
-                                 workflowIdForLogging: WorkflowId,
-                                 ioFunctions: IoFunctionSet,
-                                 importResolvers: List[ImportResolver]): IOChecked[ValidatedWomNamespace] = {
-
-    def parse(): IOChecked[Cwl] = {
-      val decodedCwlReference =
-        for {
-          url <- source.workflowUrl
-          reference <- CwlReference.fromString(url)
-        } yield CwlDecoder.decodeCwlReference(reference.changePointer(source.workflowRoot))
-
-      decodedCwlReference
-        .getOrElse(
-          CwlDecoder.decodeCwlString(
-            workflowSource,
-            source.importsZipFileOption.map(File.newTemporaryFile().appendByteArray(_)),
-            source.workflowRoot,
-            cwlFilename = s"cwl_temp_file_$workflowIdForLogging"
-          ))
-    }
-
-    import cwl.AcceptAllRequirements
-    for {
-      _ <- fromEither[IO](enabledCheck)
-      cwl <- parse()
-      executable <- fromEither[IO](cwl.womExecutable(AcceptAllRequirements, Option(source.inputsJson), ioFunctions, strictValidation))
-      validatedWomNamespace <- fromEither[IO](LanguageFactoryUtil.validateWomNamespace(executable, ioFunctions))
-    } yield validatedWomNamespace
-  }
-
-  override def getWomBundle(workflowSource: WorkflowSource,
-                            workflowSourceOrigin: Option[ResolvedImportRecord],
-                            workflowOptionsJson: WorkflowOptionsJson,
-                            importResolvers: List[ImportResolver],
-                            languageFactories: List[LanguageFactory],
-                            convertNestedScatterToSubworkflow : Boolean = true): Checked[WomBundle] =
-    enabledCheck flatMap { _ => "No getWomBundle method implemented in CWL v1".invalidNelCheck }
-
-  override def createExecutable(womBundle: WomBundle, inputs: WorkflowJson, ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace] =
-    enabledCheck flatMap { _ => "No createExecutable method implemented in CWL v1".invalidNelCheck }
-
-  override def looksParsable(content: String): Boolean = content.linesIterator.exists { l =>
-    val trimmed = l.trim.stripSuffix(",")
-    trimmed == """"cwlVersion": "v1.0"""" || trimmed == "cwlVersion: v1.0"
-  }
-}
diff --git a/project/ContinuousIntegration.scala b/project/ContinuousIntegration.scala
index 321ac0a69ab..e2b61994c22 100644
--- a/project/ContinuousIntegration.scala
+++ b/project/ContinuousIntegration.scala
@@ -67,9 +67,7 @@ object ContinuousIntegration {
   /**
     * For "reasons" these projects are excluded from the root aggregation in build.sbt.
     */
-  private val unaggregatedProjects = Map(
-    "cwlEncoder" -> "not sure what this is"
-  )
+  private val unaggregatedProjects = Map.empty
 
   /**
     * Get the list of projects defined in build.sbt excluding the passed in root project.

From 308714a429fa2076f69fc03a7943b38d1bdad8ac Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Thu, 15 Dec 2022 09:58:14 -0500
Subject: [PATCH 115/326] WX-842 Add Pact Dependency for Cromwell (#6962)

* WX-842 Add Pact Dependency for Cromwell

* Remove incomplete test spec

* Initial Pact Test

* Fix pact so it compiles

* Add breadcrumb comment and clean up
---
 .../blob/BlobFileSystemContractSpec.scala     | 50 +++++++++++++++++++
 project/Dependencies.scala                    |  4 +-
 .../Repo template_ CromIAM.run.xml            |  2 +-
 3 files changed, 54 insertions(+), 2 deletions(-)
 create mode 100644 filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala

diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
new file mode 100644
index 00000000000..611a50f5603
--- /dev/null
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
@@ -0,0 +1,50 @@
+package cromwell.filesystems.blob
+
+import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
+import au.com.dius.pact.core.model.RequestResponsePact
+import io.circe.Json
+import io.circe.syntax._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import pact4s.circe.implicits._
+import pact4s.scalatest.RequestResponsePactForger
+
+class BlobFileSystemContractSpec extends AnyFlatSpec with Matchers with RequestResponsePactForger {
+
+  val resourceId = "";
+  val workspaceId = "";
+  /**
+   * we can define the folder that the pact contracts get written to upon completion of this test suite.
+   */
+  override val pactTestExecutionContext: PactTestExecutionContext = new PactTestExecutionContext(
+    "./filesystems/blob/target/pacts"
+  )
+
+  /**
+   * The following is an outline for what a RequestResponsePact might look like for requesting
+   * from WSM form the blob filesystem. To generate a pact file however tests must be written
+   * against this pact to validate that the agreement is met. These tests get run with other
+   * scala tests on build and if the tests pass when run a pact file will be generated locally
+   */
+  override def pact: RequestResponsePact = ConsumerPactBuilder
+      .consumer("cromwell-blob-filesystem-consumer")
+      .hasPactWith("wsm-provider")
+      .`given`(
+        "resource exists",
+        Map("id" -> resourceId.asJson, "value" -> 123.asJson) // we can use parameters to specify details about the provider state
+      )
+      .`given`(
+        "workspace exists",
+        Map("id" -> workspaceId, "value" -> 123) // we can use parameters to specify details about the provider state
+      )
+      .uponReceiving("Request to fetch SAS Token")
+      .method("POST")
+      .path(s"/api/workspaces/v1/${workspaceId}/resources/controlled/azure/storageContainer/${resourceId}/getSasToken")
+      .headers("Authorization" -> "sampleToken")
+      .willRespondWith()
+      .status(200)
+      .body(
+        Json.obj("id" -> "".asJson, "value" -> 123.asJson)
+      ).toPact()
+
+}
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 42e6ee7bf79..ddc3b002f00 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -595,7 +595,9 @@ object Dependencies {
     "org.scalatest" %% "scalatest" % scalatestV,
     // Use mockito Java DSL directly instead of the numerous and often hard to keep updated Scala DSLs.
     // See also scaladoc in common.mock.MockSugar and that trait's various usages.
-    "org.mockito" % "mockito-core" % mockitoV
+    "org.mockito" % "mockito-core" % mockitoV,
+    "io.github.jbwheatley" %% "pact4s-scalatest"  % "0.7.0",
+    "io.github.jbwheatley" %% "pact4s-circe" %  "0.7.0"
   ) ++ slf4jBindingDependencies // During testing, add an slf4j binding for _all_ libraries.
 
   val kindProjectorPlugin = "org.typelevel" % "kind-projector" % kindProjectorV cross CrossVersion.full
diff --git a/runConfigurations/Repo template_ CromIAM.run.xml b/runConfigurations/Repo template_ CromIAM.run.xml
index 420ee26cae1..7fa2a61acd7 100644
--- a/runConfigurations/Repo template_ CromIAM.run.xml	
+++ b/runConfigurations/Repo template_ CromIAM.run.xml	
@@ -7,4 +7,4 @@
       <option name="Make" enabled="true" />
     </method>
   </configuration>
-</component>
\ No newline at end of file
+</component>

From aa9e876cdc69f52811421925af459ec1de996291 Mon Sep 17 00:00:00 2001
From: Trevyn Langsford <tlangs@broadinstitute.org>
Date: Thu, 15 Dec 2022 13:49:16 -0500
Subject: [PATCH 116/326] ID-125 Add support for drshub, rename all the things
 (#6959)

* Add support for drshub, rename all the things

* fallback to martha if resolver is not in config
---
 .../drs_tests/drs_usa_jdr.inputs              |   2 +-
 .../standardTestCases/drs_usa_jdr.test        |   1 +
 .../drs_usa_jdr_preresolve.test               |   1 +
 .../impl/drs/DrsCloudNioFileProvider.scala    |  30 ++---
 .../drs/DrsCloudNioFileSystemProvider.scala   |   3 +-
 .../DrsCloudNioRegularFileAttributes.scala    |   4 +-
 .../scala/cloud/nio/impl/drs/DrsConfig.scala  |  53 ++++----
 .../cloud/nio/impl/drs/DrsPathResolver.scala  | 115 +++++++++---------
 ...DrsResolverHttpRequestRetryStrategy.scala} |   2 +-
 .../drs/DrsCloudNioFileProviderSpec.scala     |  40 +++---
 .../nio/impl/drs/DrsPathResolverSpec.scala    |  66 +++++-----
 ...esolverHttpRequestRetryStrategySpec.scala} |  14 +--
 .../MockDrsCloudNioFileSystemProvider.scala   |   2 +-
 .../cloud/nio/impl/drs/MockDrsPaths.scala     |   6 +-
 .../impl/drs/MockEngineDrsPathResolver.scala  |  34 +++---
 core/src/main/resources/reference.conf        |   4 +-
 .../drs/localizer/DrsLocalizerMain.scala      |  13 +-
 .../downloaders/GcsUriDownloader.scala        |   8 +-
 .../localizer/downloaders/GetmChecksum.scala  |   2 +-
 .../drs/localizer/DrsLocalizerMainSpec.scala  |  20 +--
 .../downloaders/GcsUriDownloaderSpec.scala    |   8 +-
 docs/filesystems/DataRepositoryService.md     |   4 +-
 docs/filesystems/Filesystems.md               |   4 +-
 .../cromwell/filesystems/drs/DrsPath.scala    |   2 +-
 .../filesystems/drs/DrsPathBuilder.scala      |   2 +-
 .../drs/DrsPathBuilderFactory.scala           |  12 +-
 .../cromwell/filesystems/drs/DrsReader.scala  |  18 +--
 .../filesystems/drs/DrsResolver.scala         |  42 +++----
 .../drs/DrsPathBuilderFactorySpec.scala       |   4 +-
 .../filesystems/drs/DrsPathBuilderSpec.scala  |  10 +-
 .../filesystems/drs/DrsReaderSpec.scala       |  18 +--
 .../filesystems/drs/DrsResolverSpec.scala     |  12 +-
 ...o template_ Cromwell DRS Localizer.run.xml |   2 +-
 .../resources/papi_application.inc.conf.ctmpl |   2 +-
 .../pipelines/v2alpha1/GenomicsFactory.scala  |   2 +-
 .../PipelinesParameterConversions.scala       |   4 +-
 .../v2alpha1/PipelinesConversionsSpec.scala   |   8 +-
 .../v2beta/LifeSciencesFactory.scala          |   2 +-
 .../pipelines/v2beta/api/Localization.scala   |   8 +-
 ...ApiAsyncBackendJobExecutionActorSpec.scala |   8 +-
 40 files changed, 298 insertions(+), 294 deletions(-)
 rename cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/{MarthaHttpRequestRetryStrategy.scala => DrsResolverHttpRequestRetryStrategy.scala} (96%)
 rename cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/{MarthaHttpRequestRetryStrategySpec.scala => DrsResolverHttpRequestRetryStrategySpec.scala} (89%)

diff --git a/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs b/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs
index d5738ac4d17..d1712641dd2 100644
--- a/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs
+++ b/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs
@@ -1,5 +1,5 @@
 {
-    # Martha does not return service accounts for JDR paths. Therefore they shouldn't need to be localized using the
+    # DRSHub does not return service accounts for JDR paths. Therefore they shouldn't need to be localized using the
     # Cromwell custom DOS/DRS localizer.
     #
     # However, the first file1 was generated before JDR stared saving file names at the end of the gsUri.
diff --git a/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test b/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test
index 4025860ed8d..510c9215c1f 100644
--- a/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test
+++ b/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test
@@ -1,6 +1,7 @@
 name: drs_usa_jdr
 testFormat: WorkflowSuccess
 backends: ["papi-v2-usa"]
+tags: [ drs ]
 skipDescribeEndpointValidation: true
 
 files {
diff --git a/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test b/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test
index ab050aea69f..15e41d95529 100644
--- a/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test
+++ b/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test
@@ -1,6 +1,7 @@
 name: drs_usa_jdr_preresolve
 testFormat: WorkflowSuccess
 backends: ["papi-v2-usa"]
+tags: [ drs ]
 skipDescribeEndpointValidation: true
 
 files {
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
index a1156fc33e9..93f4cf77d34 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
@@ -15,7 +15,7 @@ import org.apache.http.HttpStatus
 class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
                               drsReadInterpreter: DrsReadInterpreter) extends CloudNioFileProvider {
 
-  private def checkIfPathExistsThroughMartha(drsPath: String): IO[Boolean] = {
+  private def checkIfPathExistsThroughDrsResolver(drsPath: String): IO[Boolean] = {
     /*
      * Unlike other cloud providers where directories are identified with a trailing slash at the end like `gs://bucket/dir/`,
      * DRS has a concept of bundles for directories (not supported yet). Hence for method `checkDirectoryExists` which appends a trailing '/'
@@ -23,15 +23,15 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
      */
     if (drsPath.endsWith("/")) IO(false)
     else {
-      drsPathResolver.rawMarthaResponse(drsPath, NonEmptyList.one(MarthaField.GsUri)).use { marthaResponse =>
-        val errorMsg = s"Status line was null for martha response $marthaResponse."
-        toIO(Option(marthaResponse.getStatusLine), errorMsg)
+      drsPathResolver.rawDrsResolverResponse(drsPath, NonEmptyList.one(DrsResolverField.GsUri)).use { drsResolverResponse =>
+        val errorMsg = s"Status line was null for DRS Resolver response $drsResolverResponse."
+        toIO(Option(drsResolverResponse.getStatusLine), errorMsg)
       }.map(_.getStatusCode == HttpStatus.SC_OK)
     }
   }
 
   override def existsPath(drsPath: String, unused: String): Boolean =
-    checkIfPathExistsThroughMartha(drsPath).unsafeRunSync()
+    checkIfPathExistsThroughDrsResolver(drsPath).unsafeRunSync()
 
   override def existsPaths(cloudHost: String, cloudPathPrefix: String): Boolean =
     existsPath(cloudHost, cloudPathPrefix)
@@ -47,11 +47,11 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
     throw new UnsupportedOperationException("DRS currently doesn't support delete.")
 
   override def read(drsPath: String, unused: String, offset: Long): ReadableByteChannel = {
-    val fields = NonEmptyList.of(MarthaField.GsUri, MarthaField.GoogleServiceAccount, MarthaField.AccessUrl)
+    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl)
 
     val byteChannelIO = for {
-      marthaResponse <- drsPathResolver.resolveDrsThroughMartha(drsPath, fields)
-      byteChannel <- drsReadInterpreter(drsPathResolver, marthaResponse)
+      drsResolverResponse <- drsPathResolver.resolveDrs(drsPath, fields)
+      byteChannel <- drsReadInterpreter(drsPathResolver, drsResolverResponse)
     } yield byteChannel
 
     byteChannelIO.handleErrorWith {
@@ -63,14 +63,14 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
     throw new UnsupportedOperationException("DRS currently doesn't support write.")
 
   override def fileAttributes(drsPath: String, unused: String): Option[CloudNioRegularFileAttributes] = {
-    val fields = NonEmptyList.of(MarthaField.Size, MarthaField.TimeCreated, MarthaField.TimeUpdated, MarthaField.Hashes)
+    val fields = NonEmptyList.of(DrsResolverField.Size, DrsResolverField.TimeCreated, DrsResolverField.TimeUpdated, DrsResolverField.Hashes)
 
     val fileAttributesIO = for {
-      marthaResponse <- drsPathResolver.resolveDrsThroughMartha(drsPath, fields)
-      sizeOption = marthaResponse.size
-      hashOption = getPreferredHash(marthaResponse.hashes)
-      timeCreatedOption <- convertToFileTime(drsPath, MarthaField.TimeCreated, marthaResponse.timeCreated)
-      timeUpdatedOption <- convertToFileTime(drsPath, MarthaField.TimeUpdated, marthaResponse.timeUpdated)
+      drsResolverResponse <- drsPathResolver.resolveDrs(drsPath, fields)
+      sizeOption = drsResolverResponse.size
+      hashOption = getPreferredHash(drsResolverResponse.hashes)
+      timeCreatedOption <- convertToFileTime(drsPath, DrsResolverField.TimeCreated, drsResolverResponse.timeCreated)
+      timeUpdatedOption <- convertToFileTime(drsPath, DrsResolverField.TimeUpdated, drsResolverResponse.timeUpdated)
     } yield new DrsCloudNioRegularFileAttributes(drsPath, sizeOption, hashOption, timeCreatedOption, timeUpdatedOption)
 
     Option(fileAttributesIO.unsafeRunSync())
@@ -78,5 +78,5 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
 }
 
 object DrsCloudNioFileProvider {
-  type DrsReadInterpreter = (DrsPathResolver, MarthaResponse) => IO[ReadableByteChannel]
+  type DrsReadInterpreter = (DrsPathResolver, DrsResolverResponse) => IO[ReadableByteChannel]
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
index 8721ab9b43e..884072e4a31 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
@@ -11,7 +11,8 @@ class DrsCloudNioFileSystemProvider(rootConfig: Config,
                                     drsReadInterpreter: DrsReadInterpreter,
                                    ) extends CloudNioFileSystemProvider {
 
-  lazy val drsConfig: DrsConfig = DrsConfig.fromConfig(rootConfig.getConfig("martha"))
+  lazy val drsResolverConfig = if (rootConfig.hasPath("resolver")) rootConfig.getConfig("resolver") else rootConfig.getConfig("martha")
+  lazy val drsConfig: DrsConfig = DrsConfig.fromConfig(drsResolverConfig)
 
   lazy val drsPathResolver: EngineDrsPathResolver =
     EngineDrsPathResolver(drsConfig, drsCredentials)
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
index 3c9293f2bd7..778d9b8380e 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
@@ -61,7 +61,7 @@ object DrsCloudNioRegularFileAttributes {
       .map(FileTime.from)
   }
 
-  def convertToFileTime(drsPath: String, key: MarthaField.Value, timeInStringOption: Option[String]): IO[Option[FileTime]] = {
+  def convertToFileTime(drsPath: String, key: DrsResolverField.Value, timeInStringOption: Option[String]): IO[Option[FileTime]] = {
     timeInStringOption match {
       case None => IO.pure(None)
       case Some(timeInString) =>
@@ -71,7 +71,7 @@ object DrsCloudNioRegularFileAttributes {
             throwable =>
               IO.raiseError(
                 new RuntimeException(
-                  s"Error while parsing '$key' value from Martha to FileTime for DRS path $drsPath. " +
+                  s"Error while parsing '$key' value from DRS Resolver to FileTime for DRS path $drsPath. " +
                     s"Reason: ${ExceptionUtils.getMessage(throwable)}.",
                   throwable,
                 )
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
index e9dc760162e..c8333a57a66 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
@@ -6,7 +6,7 @@ import net.ceedubs.ficus.Ficus._
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-final case class DrsConfig(marthaUrl: String,
+final case class DrsConfig(drsResolverUrl: String,
                            numRetries: Int,
                            waitInitial: FiniteDuration,
                            waitMaximum: FiniteDuration,
@@ -22,45 +22,46 @@ object DrsConfig {
   private val DefaultWaitMultiplier = 1.5d
   private val DefaultWaitRandomizationFactor = 0.1
 
-  private val EnvMarthaUrl = "MARTHA_URL"
-  private val EnvMarthaNumRetries = "MARTHA_NUM_RETRIES"
-  private val EnvMarthaWaitInitialSeconds = "MARTHA_WAIT_INITIAL_SECONDS"
-  private val EnvMarthaWaitMaximumSeconds = "MARTHA_WAIT_MAXIMUM_SECONDS"
-  private val EnvMarthaWaitMultiplier = "MARTHA_WAIT_MULTIPLIER"
-  private val EnvMarthaWaitRandomizationFactor = "MARTHA_WAIT_RANDOMIZATION_FACTOR"
+  private val EnvDrsResolverUrl = "DRS_RESOLVER_URL"
+  private val EnvDrsResolverNumRetries = "DRS_RESOLVER_NUM_RETRIES"
+  private val EnvDrsResolverWaitInitialSeconds = "DRS_RESOLVER_WAIT_INITIAL_SECONDS"
+  private val EnvDrsResolverWaitMaximumSeconds = "DRS_RESOLVER_WAIT_MAXIMUM_SECONDS"
+  private val EnvDrsResolverWaitMultiplier = "DRS_RESOLVER_WAIT_MULTIPLIER"
+  private val EnvDrsResolverWaitRandomizationFactor = "DRS_RESOLVER_WAIT_RANDOMIZATION_FACTOR"
 
-  def fromConfig(marthaConfig: Config): DrsConfig = {
+
+  def fromConfig(drsResolverConfig: Config): DrsConfig = {
     DrsConfig(
-      marthaUrl = marthaConfig.getString("url"),
-      numRetries = marthaConfig.getOrElse("num-retries", DefaultNumRetries),
-      waitInitial = marthaConfig.getOrElse("wait-initial", DefaultWaitInitial),
-      waitMaximum = marthaConfig.getOrElse("wait-maximum", DefaultWaitMaximum),
-      waitMultiplier = marthaConfig.getOrElse("wait-multiplier", DefaultWaitMultiplier),
+      drsResolverUrl = drsResolverConfig.getString("url"),
+      numRetries = drsResolverConfig.getOrElse("num-retries", DefaultNumRetries),
+      waitInitial = drsResolverConfig.getOrElse("wait-initial", DefaultWaitInitial),
+      waitMaximum = drsResolverConfig.getOrElse("wait-maximum", DefaultWaitMaximum),
+      waitMultiplier = drsResolverConfig.getOrElse("wait-multiplier", DefaultWaitMultiplier),
       waitRandomizationFactor =
-        marthaConfig.getOrElse("wait-randomization-factor", DefaultWaitRandomizationFactor),
+        drsResolverConfig.getOrElse("wait-randomization-factor", DefaultWaitRandomizationFactor),
     )
   }
 
   def fromEnv(env: Map[String, String]): DrsConfig = {
     DrsConfig(
-      marthaUrl = env(EnvMarthaUrl),
-      numRetries = env.get(EnvMarthaNumRetries).map(_.toInt).getOrElse(DefaultNumRetries),
-      waitInitial = env.get(EnvMarthaWaitInitialSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitInitial),
-      waitMaximum = env.get(EnvMarthaWaitMaximumSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitMaximum),
-      waitMultiplier = env.get(EnvMarthaWaitMultiplier).map(_.toDouble).getOrElse(DefaultWaitMultiplier),
+      drsResolverUrl = env(EnvDrsResolverUrl),
+      numRetries = env.get(EnvDrsResolverNumRetries).map(_.toInt).getOrElse(DefaultNumRetries),
+      waitInitial = env.get(EnvDrsResolverWaitInitialSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitInitial),
+      waitMaximum = env.get(EnvDrsResolverWaitMaximumSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitMaximum),
+      waitMultiplier = env.get(EnvDrsResolverWaitMultiplier).map(_.toDouble).getOrElse(DefaultWaitMultiplier),
       waitRandomizationFactor =
-        env.get(EnvMarthaWaitRandomizationFactor).map(_.toDouble).getOrElse(DefaultWaitRandomizationFactor),
+        env.get(EnvDrsResolverWaitRandomizationFactor).map(_.toDouble).getOrElse(DefaultWaitRandomizationFactor),
     )
   }
 
   def toEnv(drsConfig: DrsConfig): Map[String, String] = {
     Map(
-      EnvMarthaUrl -> drsConfig.marthaUrl,
-      EnvMarthaNumRetries -> s"${drsConfig.numRetries}",
-      EnvMarthaWaitInitialSeconds -> s"${drsConfig.waitInitial.toSeconds}",
-      EnvMarthaWaitMaximumSeconds -> s"${drsConfig.waitMaximum.toSeconds}",
-      EnvMarthaWaitMultiplier -> s"${drsConfig.waitMultiplier}",
-      EnvMarthaWaitRandomizationFactor -> s"${drsConfig.waitRandomizationFactor}",
+      EnvDrsResolverUrl -> drsConfig.drsResolverUrl,
+      EnvDrsResolverNumRetries -> s"${drsConfig.numRetries}",
+      EnvDrsResolverWaitInitialSeconds -> s"${drsConfig.waitInitial.toSeconds}",
+      EnvDrsResolverWaitMaximumSeconds -> s"${drsConfig.waitMaximum.toSeconds}",
+      EnvDrsResolverWaitMultiplier -> s"${drsConfig.waitMultiplier}",
+      EnvDrsResolverWaitRandomizationFactor -> s"${drsConfig.waitRandomizationFactor}",
     )
   }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
index 9e0b45e259e..f9ae5b62e03 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
@@ -5,7 +5,7 @@ import cats.data.Validated.{Invalid, Valid}
 import cats.effect.{IO, Resource}
 import cats.implicits._
 import cloud.nio.impl.drs.DrsPathResolver.{FatalRetryDisposition, RegularRetryDisposition}
-import cloud.nio.impl.drs.MarthaResponseSupport._
+import cloud.nio.impl.drs.DrsResolverResponseSupport._
 import common.exception.{AggregatedMessageException, toIO}
 import common.validation.ErrorOr.ErrorOr
 import io.circe._
@@ -29,7 +29,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
   protected lazy val httpClientBuilder: HttpClientBuilder = {
     val clientBuilder = HttpClientBuilder.create()
     if (retryInternally) {
-      val retryHandler = new MarthaHttpRequestRetryStrategy(drsConfig)
+      val retryHandler = new DrsResolverHttpRequestRetryStrategy(drsConfig)
       clientBuilder
         .setRetryHandler(retryHandler)
         .setServiceUnavailableRetryStrategy(retryHandler)
@@ -39,11 +39,11 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
 
   def getAccessToken: ErrorOr[String]
 
-  private def makeHttpRequestToMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): Resource[IO, HttpPost] = {
+  private def makeHttpRequestToDrsResolver(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): Resource[IO, HttpPost] = {
     val io = getAccessToken match {
       case Valid(token) => IO {
-        val postRequest = new HttpPost(drsConfig.marthaUrl)
-        val requestJson = MarthaRequest(drsPath, fields).asJson.noSpaces
+        val postRequest = new HttpPost(drsConfig.drsResolverUrl)
+        val requestJson = DrsResolverRequest(drsPath, fields).asJson.noSpaces
         postRequest.setEntity(new StringEntity(requestJson, ContentType.APPLICATION_JSON))
         postRequest.setHeader("Authorization", s"Bearer $token")
         postRequest
@@ -54,7 +54,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
     Resource.eval(io)
   }
 
-  private def httpResponseToMarthaResponse(drsPathForDebugging: String)(httpResponse: HttpResponse): IO[MarthaResponse] = {
+  private def httpResponseToDrsResolverResponse(drsPathForDebugging: String)(httpResponse: HttpResponse): IO[DrsResolverResponse] = {
     val responseStatusLine = httpResponse.getStatusLine
     val status = responseStatusLine.getStatusCode
 
@@ -71,39 +71,39 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
       case s if s / 100 == 5 =>
         IO.raiseError(new RuntimeException(retryMessage) with RegularRetryDisposition)
       case _ =>
-        val marthaResponseEntityOption = Option(httpResponse.getEntity).map(EntityUtils.toString)
-        val exceptionMsg = errorMessageFromResponse(drsPathForDebugging, marthaResponseEntityOption, responseStatusLine, drsConfig.marthaUrl)
-        val responseEntityOption = (responseStatusLine.getStatusCode == HttpStatus.SC_OK).valueOrZero(marthaResponseEntityOption)
+        val drsResolverResponseEntityOption = Option(httpResponse.getEntity).map(EntityUtils.toString)
+        val exceptionMsg = errorMessageFromResponse(drsPathForDebugging, drsResolverResponseEntityOption, responseStatusLine, drsConfig.drsResolverUrl)
+        val responseEntityOption = (responseStatusLine.getStatusCode == HttpStatus.SC_OK).valueOrZero(drsResolverResponseEntityOption)
         val responseContentIO = toIO(responseEntityOption, exceptionMsg)
 
         responseContentIO.flatMap { responseContent =>
-          IO.fromEither(decode[MarthaResponse](responseContent))
+          IO.fromEither(decode[DrsResolverResponse](responseContent))
         }.handleErrorWith {
           e => IO.raiseError(new RuntimeException(s"Unexpected response during DRS resolution: ${ExceptionUtils.getMessage(e)}"))
         }
     }
   }
 
-  private def executeMarthaRequest(httpPost: HttpPost): Resource[IO, HttpResponse]= {
+  private def executeDrsResolverRequest(httpPost: HttpPost): Resource[IO, HttpResponse]= {
     for {
       httpClient <- Resource.fromAutoCloseable(IO(httpClientBuilder.build()))
       httpResponse <- Resource.fromAutoCloseable(IO(httpClient.execute(httpPost)))
     } yield httpResponse
   }
 
-  def rawMarthaResponse(drsPath: String, fields: NonEmptyList[MarthaField.Value]): Resource[IO, HttpResponse] = {
+  def rawDrsResolverResponse(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): Resource[IO, HttpResponse] = {
     for {
-      httpPost <- makeHttpRequestToMartha(drsPath, fields)
-      response <- executeMarthaRequest(httpPost)
+      httpPost <- makeHttpRequestToDrsResolver(drsPath, fields)
+      response <- executeDrsResolverRequest(httpPost)
     } yield response
   }
 
   /** *
-    * Resolves the DRS path through Martha url provided in the config.
-    * Please note, this method returns an IO that would make a synchronous HTTP request to Martha when run.
+    * Resolves the DRS path through DRS Resolver url provided in the config.
+    * Please note, this method returns an IO that would make a synchronous HTTP request to DRS Resolver when run.
     */
-  def resolveDrsThroughMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): IO[MarthaResponse] = {
-    rawMarthaResponse(drsPath, fields).use(httpResponseToMarthaResponse(drsPathForDebugging = drsPath))
+  def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
+    rawDrsResolverResponse(drsPath, fields).use(httpResponseToDrsResolverResponse(drsPathForDebugging = drsPath))
   }
 
   def openChannel(accessUrl: AccessUrl): IO[ReadableByteChannel] = {
@@ -144,7 +144,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
 }
 
 object DrsPathResolver {
-  final val ExtractUriErrorMsg = "No access URL nor GCS URI starting with 'gs://' found in Martha response!"
+  final val ExtractUriErrorMsg = "No access URL nor GCS URI starting with 'gs://' found in the DRS Resolver response!"
   sealed trait RetryDisposition
   // Should immediately fail the download attempt.
   trait FatalRetryDisposition extends RetryDisposition
@@ -152,27 +152,27 @@ object DrsPathResolver {
   trait RegularRetryDisposition extends RetryDisposition
 }
 
-object MarthaField extends Enumeration {
-  val GsUri: MarthaField.Value = Value("gsUri")
-  val Size: MarthaField.Value = Value("size")
-  val TimeCreated: MarthaField.Value = Value("timeCreated")
-  val TimeUpdated: MarthaField.Value = Value("timeUpdated")
-  val BondProvider: MarthaField.Value = Value("bondProvider")
-  val GoogleServiceAccount: MarthaField.Value = Value("googleServiceAccount")
-  val Hashes: MarthaField.Value = Value("hashes")
-  val FileName: MarthaField.Value = Value("fileName")
-  val AccessUrl: MarthaField.Value = Value("accessUrl")
-  val LocalizationPath: MarthaField.Value = Value("localizationPath")
+object DrsResolverField extends Enumeration {
+  val GsUri: DrsResolverField.Value = Value("gsUri")
+  val Size: DrsResolverField.Value = Value("size")
+  val TimeCreated: DrsResolverField.Value = Value("timeCreated")
+  val TimeUpdated: DrsResolverField.Value = Value("timeUpdated")
+  val BondProvider: DrsResolverField.Value = Value("bondProvider")
+  val GoogleServiceAccount: DrsResolverField.Value = Value("googleServiceAccount")
+  val Hashes: DrsResolverField.Value = Value("hashes")
+  val FileName: DrsResolverField.Value = Value("fileName")
+  val AccessUrl: DrsResolverField.Value = Value("accessUrl")
+  val LocalizationPath: DrsResolverField.Value = Value("localizationPath")
 }
 
-final case class MarthaRequest(url: String, fields: NonEmptyList[MarthaField.Value])
+final case class DrsResolverRequest(url: String, fields: NonEmptyList[DrsResolverField.Value])
 
 final case class SADataObject(data: Json)
 
 final case class AccessUrl(url: String, headers: Option[Map[String, String]])
 
 /**
-  * A response from `martha_v3`.
+  * A response from `drshub_v4`.
   *
   * @param size Size of the object stored at gsUri
   * @param timeCreated The creation time of the object at gsUri
@@ -187,34 +187,33 @@ final case class AccessUrl(url: String, headers: Option[Map[String, String]])
   *                         DRS metadata, via the `aliases` field. As this is a distinct field from `fileName` in DRS
   *                         metadata it is also made a distinct field in this response object.
   */
-final case class MarthaResponse(size: Option[Long] = None,
-                                timeCreated: Option[String] = None,
-                                timeUpdated: Option[String] = None,
-                                gsUri: Option[String] = None,
-                                bondProvider: Option[String] = None,
-                                googleServiceAccount: Option[SADataObject] = None,
-                                fileName: Option[String] = None,
-                                hashes: Option[Map[String, String]] = None,
-                                accessUrl: Option[AccessUrl] = None,
-                                localizationPath: Option[String] = None
+final case class DrsResolverResponse(size: Option[Long] = None,
+                                     timeCreated: Option[String] = None,
+                                     timeUpdated: Option[String] = None,
+                                     gsUri: Option[String] = None,
+                                     bondProvider: Option[String] = None,
+                                     googleServiceAccount: Option[SADataObject] = None,
+                                     fileName: Option[String] = None,
+                                     hashes: Option[Map[String, String]] = None,
+                                     accessUrl: Option[AccessUrl] = None,
+                                     localizationPath: Option[String] = None
                                )
 
-// Adapted from https://github.com/broadinstitute/martha/blob/f31933a3a11e20d30698ec4b4dc1e0abbb31a8bc/common/helpers.js#L210-L218
-final case class MarthaFailureResponse(response: MarthaFailureResponsePayload)
-final case class MarthaFailureResponsePayload(text: String)
+final case class DrsResolverFailureResponse(response: DrsResolverFailureResponsePayload)
+final case class DrsResolverFailureResponsePayload(text: String)
 
-object MarthaResponseSupport {
+object DrsResolverResponseSupport {
 
-  implicit lazy val marthaFieldEncoder: Encoder[MarthaField.Value] = Encoder.encodeEnumeration(MarthaField)
-  implicit lazy val marthaRequestEncoder: Encoder[MarthaRequest] = deriveEncoder
+  implicit lazy val drsResolverFieldEncoder: Encoder[DrsResolverField.Value] = Encoder.encodeEnumeration(DrsResolverField)
+  implicit lazy val drsResolverRequestEncoder: Encoder[DrsResolverRequest] = deriveEncoder
 
   implicit lazy val saDataObjectDecoder: Decoder[SADataObject] = deriveDecoder
-  implicit lazy val marthaResponseDecoder: Decoder[MarthaResponse] = deriveDecoder
+  implicit lazy val drsResolverResponseDecoder: Decoder[DrsResolverResponse] = deriveDecoder
 
-  implicit lazy val marthaFailureResponseDecoder: Decoder[MarthaFailureResponse] = deriveDecoder
-  implicit lazy val marthaFailureResponsePayloadDecoder: Decoder[MarthaFailureResponsePayload] = deriveDecoder
+  implicit lazy val drsResolverFailureResponseDecoder: Decoder[DrsResolverFailureResponse] = deriveDecoder
+  implicit lazy val drsResolverFailureResponsePayloadDecoder: Decoder[DrsResolverFailureResponsePayload] = deriveDecoder
 
-  implicit lazy val marthaAccessUrlDecoder: Decoder[AccessUrl] = deriveDecoder
+  implicit lazy val drsResolverAccessUrlDecoder: Decoder[AccessUrl] = deriveDecoder
 
   private val GcsScheme = "gs://"
 
@@ -223,18 +222,18 @@ object MarthaResponseSupport {
       (array(0), array(1))
   }
 
-  def errorMessageFromResponse(drsPathForDebugging: String, marthaResponseEntityOption: Option[String], responseStatusLine: StatusLine, marthaUri: String): String = {
-    val baseMessage = s"Could not access object \'$drsPathForDebugging\'. Status: ${responseStatusLine.getStatusCode}, reason: \'${responseStatusLine.getReasonPhrase}\', Martha location: \'$marthaUri\', message: "
+  def errorMessageFromResponse(drsPathForDebugging: String, drsResolverResponseEntityOption: Option[String], responseStatusLine: StatusLine, drsResolverUri: String): String = {
+    val baseMessage = s"Could not access object \'$drsPathForDebugging\'. Status: ${responseStatusLine.getStatusCode}, reason: \'${responseStatusLine.getReasonPhrase}\', DRS Resolver location: \'$drsResolverUri\', message: "
 
-    marthaResponseEntityOption match {
+    drsResolverResponseEntityOption match {
       case Some(entity) =>
-        val maybeErrorResponse: Either[Error, MarthaFailureResponse] = decode[MarthaFailureResponse](entity)
+        val maybeErrorResponse: Either[Error, DrsResolverFailureResponse] = decode[DrsResolverFailureResponse](entity)
         maybeErrorResponse match {
           case Left(_) =>
-            // Not parsable as a `MarthaFailureResponse`
+            // Not parsable as a `DrsResolverFailureResponse`
             baseMessage + s"\'$entity\'"
           case Right(decoded) =>
-            // Is a `MarthaFailureResponse`
+            // Is a `DrsResolverFailureResponse`
             baseMessage + s"\'${decoded.response.text}\'"
         }
       case None =>
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategy.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
similarity index 96%
rename from cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategy.scala
rename to cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
index 2881fc60b05..39020f5a684 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategy.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
@@ -7,7 +7,7 @@ import org.apache.http.HttpResponse
 import org.apache.http.client.{HttpRequestRetryHandler, ServiceUnavailableRetryStrategy}
 import org.apache.http.protocol.HttpContext
 
-class MarthaHttpRequestRetryStrategy(drsConfig: DrsConfig)
+class DrsResolverHttpRequestRetryStrategy(drsConfig: DrsConfig)
   extends ServiceUnavailableRetryStrategy with HttpRequestRetryHandler {
 
   // We can execute a total of one time, plus the number of retries
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
index 405f22b3b20..f61c608bd71 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
@@ -25,13 +25,13 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "parse a config and create a working file system provider" in {
     val config = ConfigFactory.parseString(
-      """martha.url = "https://from.config"
+      """resolver.url = "https://from.config"
         |access-token-acceptable-ttl = 1 minute
         |""".stripMargin
     )
 
     val fileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = config)
-    fileSystemProvider.drsConfig.marthaUrl should be("https://from.config")
+    fileSystemProvider.drsConfig.drsResolverUrl should be("https://from.config")
     fileSystemProvider.drsCredentials match {
       case GoogleOauthDrsCredentials(_, ttl) => ttl should be(1.minute)
       case error => fail(s"Expected GoogleDrsCredentials, found $error")
@@ -79,19 +79,19 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "return a file provider that can read bytes from gcs" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrsThroughMartha(drsPath: String,
-                                           fields: NonEmptyList[MarthaField.Value],
-                                          ): IO[MarthaResponse] = {
-        IO(MarthaResponse(gsUri = Option("gs://bucket/object/path")))
+      override def resolveDrs(drsPath: String,
+                              fields: NonEmptyList[DrsResolverField.Value],
+                                          ): IO[DrsResolverResponse] = {
+        IO(DrsResolverResponse(gsUri = Option("gs://bucket/object/path")))
       }
     }
 
     val readChannel = mock[ReadableByteChannel]
-    val drsReadInterpreter: DrsReadInterpreter = (_, marthaResponse) => {
+    val drsReadInterpreter: DrsReadInterpreter = (_, drsResolverResponse) => {
       IO(
-        (marthaResponse.gsUri, marthaResponse.googleServiceAccount) match {
+        (drsResolverResponse.gsUri, drsResolverResponse.googleServiceAccount) match {
           case (Some("gs://bucket/object/path"), None) => readChannel
-          case _ => fail(s"Unexpected parameters passed: $marthaResponse")
+          case _ => fail(s"Unexpected parameters passed: $drsResolverResponse")
         }
       )
     }
@@ -105,19 +105,19 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "return a file provider that can read bytes from an access url" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrsThroughMartha(drsPath: String,
-                                           fields: NonEmptyList[MarthaField.Value],
-                                          ): IO[MarthaResponse] = {
-        IO(MarthaResponse(accessUrl = Option(AccessUrl("https://host/object/path", None))))
+      override def resolveDrs(drsPath: String,
+                              fields: NonEmptyList[DrsResolverField.Value],
+                                          ): IO[DrsResolverResponse] = {
+        IO(DrsResolverResponse(accessUrl = Option(AccessUrl("https://host/object/path", None))))
       }
     }
 
     val readChannel = mock[ReadableByteChannel]
-    val drsReadInterpreter: DrsReadInterpreter = (_, marthaResponse) => {
+    val drsReadInterpreter: DrsReadInterpreter = (_, drsResolverResponse) => {
       IO(
-        marthaResponse.accessUrl match {
+        drsResolverResponse.accessUrl match {
           case Some(AccessUrl("https://host/object/path", None)) => readChannel
-          case _ => fail(s"Unexpected parameters passed: $marthaResponse")
+          case _ => fail(s"Unexpected parameters passed: $drsResolverResponse")
         }
       )
     }
@@ -131,13 +131,13 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "return a file provider that can return file attributes" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrsThroughMartha(drsPath: String,
-                                           fields: NonEmptyList[MarthaField.Value],
-                                          ): IO[MarthaResponse] = {
+      override def resolveDrs(drsPath: String,
+                              fields: NonEmptyList[DrsResolverField.Value],
+                                          ): IO[DrsResolverResponse] = {
         val instantCreated = Instant.ofEpochMilli(123L)
         val instantUpdated = Instant.ofEpochMilli(456L)
         IO(
-          MarthaResponse(
+          DrsResolverResponse(
             size = Option(789L),
             timeCreated = Option(OffsetDateTime.ofInstant(instantCreated, ZoneOffset.UTC).toString),
             timeUpdated = Option(OffsetDateTime.ofInstant(instantUpdated, ZoneOffset.UTC).toString),
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
index 78585c96ed9..b4e5968e048 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
@@ -17,7 +17,7 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   private val md5HashValue = "336ea55913bc261b72875bd259753046"
   private val shaHashValue = "f76877f8e86ec3932fd2ae04239fbabb8c90199dab0019ae55fa42b31c314c44"
 
-  private val fullMarthaResponse = MarthaResponse(
+  private val fullDrsResolverResponse = DrsResolverResponse(
     size = Option(34905345),
     timeCreated = Option(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toString),
     timeUpdated = Option(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toString),
@@ -27,17 +27,17 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
     hashes = Option(Map("md5" -> md5HashValue, "crc32c" -> crcHashValue))
   )
 
-  private val fullMarthaResponseNoTz =
-    fullMarthaResponse
-      .copy(timeUpdated = fullMarthaResponse.timeUpdated.map(_.stripSuffix("Z")))
+  private val fullDrsResolverResponseNoTz =
+    fullDrsResolverResponse
+      .copy(timeUpdated = fullDrsResolverResponse.timeUpdated.map(_.stripSuffix("Z")))
 
-  private val fullMarthaResponseNoTime =
-    fullMarthaResponse
+  private val fullDrsResolverResponseNoTime =
+    fullDrsResolverResponse
       .copy(timeUpdated = None)
 
-  private val fullMarthaResponseBadTz =
-    fullMarthaResponse
-      .copy(timeUpdated = fullMarthaResponse.timeUpdated.map(_.stripSuffix("Z") + "BADTZ"))
+  private val fullDrsResolverResponseBadTz =
+    fullDrsResolverResponse
+      .copy(timeUpdated = fullDrsResolverResponse.timeUpdated.map(_.stripSuffix("Z") + "BADTZ"))
 
   private val etagHashValue = "something"
   private val completeHashesMap = Option(Map(
@@ -74,19 +74,19 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
 
   behavior of "fileHash()"
 
-  it should "return crc32c hash from `hashes` in Martha response when there is a crc32c" in {
+  it should "return crc32c hash from `hashes` in DRS Resolver response when there is a crc32c" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(completeHashesMap) shouldBe Option(FileHash(HashType.Crc32c, crcHashValue))
   }
 
-  it should "return md5 hash from `hashes` in Martha response when there is no crc32c" in {
+  it should "return md5 hash from `hashes` in DRS Resolver response when there is no crc32c" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(missingCRCHashesMap) shouldBe Option(FileHash(HashType.Md5, md5HashValue))
   }
 
-  it should "return sha256 hash from `hashes` in Martha response when there is only a sha256" in {
+  it should "return sha256 hash from `hashes` in DRS Resolver response when there is only a sha256" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(onlySHAHashesMap) shouldBe Option(FileHash(HashType.Sha256, shaHashValue))
   }
 
-  it should "return etag hash from `hashes` in Martha response when there is only an etag" in {
+  it should "return etag hash from `hashes` in DRS Resolver response when there is only an etag" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(onlyEtagHashesMap) shouldBe Option(FileHash(HashType.S3Etag, etagHashValue))
   }
 
@@ -127,10 +127,10 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
 
   it should "successfully parse a failure" in {
     import io.circe.parser.decode
-    import cloud.nio.impl.drs.MarthaResponseSupport.marthaFailureResponseDecoder
+    import cloud.nio.impl.drs.DrsResolverResponseSupport.drsResolverFailureResponseDecoder
 
-    val maybeDecoded = decode[MarthaFailureResponse](failureResponseJson)
-    maybeDecoded map { decoded: MarthaFailureResponse =>
+    val maybeDecoded = decode[DrsResolverFailureResponse](failureResponseJson)
+    maybeDecoded map { decoded: DrsResolverFailureResponse =>
       decoded.response.text shouldBe "{\"msg\":\"User 'null' does not have required action: read_data\",\"status_code\":500}"
     }
   }
@@ -139,37 +139,37 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
 
   val drsPathForDebugging = "drs://my_awesome_drs"
   val responseStatusLine = new BasicStatusLine(new ProtocolVersion("http", 1, 2) , 345, "test-reason")
-  val testMarthaUri = "www.martha_v3.com"
+  val testDrsResolverUri = "www.drshub_v4.com"
 
   it should "construct an error message from a populated, well-formed failure response" in {
     val failureResponse = Option(failureResponseJson)
 
-    MarthaResponseSupport.errorMessageFromResponse(drsPathForDebugging, failureResponse, responseStatusLine, testMarthaUri) shouldBe {
-      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', Martha location: 'www.martha_v3.com', message: '{\"msg\":\"User 'null' does not have required action: read_data\",\"status_code\":500}'"
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, failureResponse, responseStatusLine, testDrsResolverUri) shouldBe {
+      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: '{\"msg\":\"User 'null' does not have required action: read_data\",\"status_code\":500}'"
     }
   }
 
   it should "construct an error message from an empty failure response" in {
-    MarthaResponseSupport.errorMessageFromResponse(drsPathForDebugging, None, responseStatusLine, testMarthaUri) shouldBe {
-      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', Martha location: 'www.martha_v3.com', message: (empty response)"
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, None, responseStatusLine, testDrsResolverUri) shouldBe {
+      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: (empty response)"
     }
   }
 
-  // Technically we enter this case when preparing the "error message" for a successful response, because naturally `MarthaResponse` does not deserialize to `MarthaFailureResponse`
+  // Technically we enter this case when preparing the "error message" for a successful response, because naturally `DrsResolverResponse` does not deserialize to `DrsResolverFailureResponse`
   // But then there's no error so we throw it away :shrug:
   it should "construct an error message from a malformed failure response" in {
     val unparsableFailureResponse = Option("something went horribly wrong")
 
-    MarthaResponseSupport.errorMessageFromResponse(drsPathForDebugging, unparsableFailureResponse, responseStatusLine, testMarthaUri) shouldBe {
-      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', Martha location: 'www.martha_v3.com', message: 'something went horribly wrong'"
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, unparsableFailureResponse, responseStatusLine, testDrsResolverUri) shouldBe {
+      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: 'something went horribly wrong'"
     }
   }
 
   it should "resolve an ISO-8601 date with timezone" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponse.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponse.timeUpdated,
     )
     lastModifiedTimeIO.unsafeRunSync() should
       be(Option(FileTime.from(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toInstant)))
@@ -178,8 +178,8 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   it should "resolve an ISO-8601 date without timezone" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponseNoTz.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponseNoTz.timeUpdated,
     )
     lastModifiedTimeIO.unsafeRunSync() should
       be(Option(FileTime.from(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toInstant)))
@@ -188,8 +188,8 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   it should "not resolve an date that does not contain a timeUpdated" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponseNoTime.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponseNoTime.timeUpdated,
     )
     lastModifiedTimeIO.unsafeRunSync() should be(None)
   }
@@ -197,11 +197,11 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   it should "not resolve an date that is not ISO-8601" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponseBadTz.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponseBadTz.timeUpdated,
     )
     the[RuntimeException] thrownBy lastModifiedTimeIO.unsafeRunSync() should have message
-      "Error while parsing 'timeUpdated' value from Martha to FileTime for DRS path drs://my_awesome_drs. " +
+      "Error while parsing 'timeUpdated' value from DRS Resolver to FileTime for DRS path drs://my_awesome_drs. " +
         "Reason: DateTimeParseException: Text '2020-04-27T15:56:09.696BADTZ' could not be parsed at index 23."
   }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategySpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
similarity index 89%
rename from cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategySpec.scala
rename to cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
index 8fd1e948607..b221038bedb 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategySpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
@@ -12,13 +12,13 @@ import common.mock.MockSugar
 
 import scala.concurrent.duration._
 
-class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with MockSugar {
+class DrsResolverHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with MockSugar {
 
-  behavior of "MarthaHttpRequestRetryStrategy"
+  behavior of "DrsResolverHttpRequestRetryStrategy"
 
   it should "retry 500 errors a configured number of times" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val http500Response = mock[CloseableHttpResponse]
     http500Response.getStatusLine returns new BasicStatusLine(HttpVersion.HTTP_1_1, 500, "Testing 500")
     val httpContext = mock[HttpContext]
@@ -35,7 +35,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
 
   it should "retry 500 errors even after a number of 408/429 errors" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val http500Response = mock[CloseableHttpResponse]
     http500Response.getStatusLine returns new BasicStatusLine(HttpVersion.HTTP_1_1, 500, "Testing 500")
     val http408Response = mock[CloseableHttpResponse]
@@ -63,7 +63,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
 
   it should "not retry an HTTP 401" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val http400Response = mock[CloseableHttpResponse]
     http400Response.getStatusLine returns new BasicStatusLine(HttpVersion.HTTP_1_1, 401, "Testing 401")
     val httpContext = mock[HttpContext]
@@ -73,7 +73,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
 
   it should "retry IO exceptions a configured number of times" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val exception = mock[IOException]
     val httpContext = mock[HttpContext]
 
@@ -95,7 +95,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
         waitMaximum = 1.minute,
         waitRandomizationFactor = 0d,
       )
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
 
     retryStrategy.getRetryInterval should be(10000L)
     retryStrategy.getRetryInterval should be(20000L)
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
index 08683a6d820..07a02e096dc 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
@@ -31,7 +31,7 @@ class MockDrsCloudNioFileSystemProvider(config: Config = mockConfig,
 
 object MockDrsCloudNioFileSystemProvider {
   private lazy val mockConfig = ConfigFactory.parseString(
-    """martha.url = "https://mock.martha"
+    """resolver.url = "https://mock.drshub"
       |access-token-acceptable-ttl = 1 hour
       |""".stripMargin
   )
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala
index b6825dcbbd2..a24385bc15f 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala
@@ -3,9 +3,9 @@ package cloud.nio.impl.drs
 import scala.concurrent.duration._
 
 object MockDrsPaths {
-  val marthaUrl = "http://mock.martha"
+  val drsResolverUrl = "http://mock.drshub"
 
-  val mockDrsConfig: DrsConfig = DrsConfig(MockDrsPaths.marthaUrl, 1, 1.seconds, 1.seconds, 1d, 0d)
+  val mockDrsConfig: DrsConfig = DrsConfig(MockDrsPaths.drsResolverUrl, 1, 1.seconds, 1.seconds, 1d, 0d)
 
   val mockToken = "mock.token"
 
@@ -35,5 +35,5 @@ object MockDrsPaths {
 
   val drsPathResolvingToNoGcsPath = s"$drsPathPrefix/226686cf-22c9-4472-9f79-7a0b0044f253"
 
-  val drsPathNotExistingInMartha = s"$drsPathPrefix/5e21b8c3-8eda-48d5-9a04-2b32e1571765"
+  val drsPathNotExistingInDrsResolver = s"$drsPathPrefix/5e21b8c3-8eda-48d5-9a04-2b32e1571765"
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
index 8395233ce4d..9e22544c38b 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
@@ -19,7 +19,7 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
   override protected lazy val httpClientBuilder: HttpClientBuilder =
     httpClientBuilderOverride getOrElse MockSugar.mock[HttpClientBuilder]
 
-  private lazy val mockMarthaUri = drsConfig.marthaUrl
+  private lazy val mockDrsResolverUri = drsConfig.drsResolverUrl
 
   private val hashesObj = Map(
     "md5" -> "336ea55913bc261b72875bd259753046",
@@ -27,8 +27,8 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
     "crc32c" -> "8a366443"
   )
 
-  private val marthaObjWithGcsPath =
-    MarthaResponse(
+  private val drsResolverObjWithGcsPath =
+    DrsResolverResponse(
       size = Option(156018255),
       timeCreated = Option("2020-04-27T15:56:09.696Z"),
       timeUpdated = Option("2020-04-27T15:56:09.696Z"),
@@ -36,27 +36,27 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
       hashes = Option(hashesObj)
     )
 
-  private val marthaObjWithFileName = marthaObjWithGcsPath.copy(fileName = Option("file.txt"))
+  private val drsResolverObjWithFileName = drsResolverObjWithGcsPath.copy(fileName = Option("file.txt"))
 
-  private val marthaObjWithLocalizationPath = marthaObjWithGcsPath.copy(localizationPath = Option("/dir/subdir/file.txt"))
+  private val drsResolverObjWithLocalizationPath = drsResolverObjWithGcsPath.copy(localizationPath = Option("/dir/subdir/file.txt"))
 
-  private val marthaObjWithAllThePaths = marthaObjWithLocalizationPath.copy(fileName = marthaObjWithFileName.fileName)
+  private val drsResolverObjWithAllThePaths = drsResolverObjWithLocalizationPath.copy(fileName = drsResolverObjWithFileName.fileName)
 
-  private val marthaObjWithNoGcsPath = marthaObjWithGcsPath.copy(gsUri = None)
+  private val drsResolverObjWithNoGcsPath = drsResolverObjWithGcsPath.copy(gsUri = None)
 
-  override def resolveDrsThroughMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): IO[MarthaResponse] = {
+  override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
     drsPath match {
-      case MockDrsPaths.drsPathResolvingGcsPath => IO(marthaObjWithGcsPath)
-      case MockDrsPaths.drsPathWithNonPathChars => IO(marthaObjWithGcsPath)
-      case MockDrsPaths.drsPathResolvingWithFileName => IO(marthaObjWithFileName)
-      case MockDrsPaths.drsPathResolvingWithLocalizationPath => IO.pure(marthaObjWithLocalizationPath)
-      case MockDrsPaths.drsPathResolvingWithAllThePaths => IO.pure(marthaObjWithAllThePaths)
-      case MockDrsPaths.drsPathResolvingToNoGcsPath => IO(marthaObjWithNoGcsPath)
-      case MockDrsPaths.drsPathNotExistingInMartha =>
+      case MockDrsPaths.drsPathResolvingGcsPath => IO(drsResolverObjWithGcsPath)
+      case MockDrsPaths.drsPathWithNonPathChars => IO(drsResolverObjWithGcsPath)
+      case MockDrsPaths.drsPathResolvingWithFileName => IO(drsResolverObjWithFileName)
+      case MockDrsPaths.drsPathResolvingWithLocalizationPath => IO.pure(drsResolverObjWithLocalizationPath)
+      case MockDrsPaths.drsPathResolvingWithAllThePaths => IO.pure(drsResolverObjWithAllThePaths)
+      case MockDrsPaths.drsPathResolvingToNoGcsPath => IO(drsResolverObjWithNoGcsPath)
+      case MockDrsPaths.`drsPathNotExistingInDrsResolver` =>
         IO.raiseError(
           new RuntimeException(
-            s"Unexpected response resolving ${MockDrsPaths.drsPathNotExistingInMartha} " +
-              s"through Martha url $mockMarthaUri. Error: 404 Not Found."
+            s"Unexpected response resolving ${MockDrsPaths.drsPathNotExistingInDrsResolver} " +
+              s"through DRS Resolver url $mockDrsResolverUri. Error: 404 Not Found."
           )
         )
     }
diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index b5573e0249f..4ecdf1ce233 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -328,8 +328,8 @@ filesystems {
       # Class to instantiate and propagate to all factories. Takes a single typesafe config argument
       class = "cromwell.filesystems.drs.DrsFileSystemConfig"
       config {
-        martha {
-          url = "https://martha-url-here"
+        resolver {
+          url = "https://martha-url-here or https://drshub-url-here"
           # When true (and when possible) any DrsPath will be internally converted to another compatible Path such as a
           # GcsPath. This enables other optimizations such as using batch requests for GCS for hashes, using the
           # existing GCS downloader in Papi, etc.
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
index df184efae92..1858f395024 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
@@ -86,6 +86,7 @@ class DrsLocalizerMain(drsUrl: String,
   def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] = {
     IO {
       val drsConfig = DrsConfig.fromEnv(sys.env)
+      logger.info(s"Using ${drsConfig.drsResolverUrl} to resolve DRS Objects")
       new DrsLocalizerDrsPathResolver(drsConfig, drsCredentials)
     }
   }
@@ -141,17 +142,17 @@ class DrsLocalizerMain(drsUrl: String,
   }
 
   private [localizer] def resolve(downloaderFactory: DownloaderFactory): IO[Downloader] = {
-    val fields = NonEmptyList.of(MarthaField.GsUri, MarthaField.GoogleServiceAccount, MarthaField.AccessUrl, MarthaField.Hashes)
+    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl, DrsResolverField.Hashes)
     for {
       resolver <- getDrsPathResolver
-      marthaResponse <- resolver.resolveDrsThroughMartha(drsUrl, fields)
+      drsResolverResponse <- resolver.resolveDrs(drsUrl, fields)
 
-      // Currently Martha only supports resolving DRS paths to access URLs or GCS paths.
-      downloader <- (marthaResponse.accessUrl, marthaResponse.gsUri) match {
+      // Currently DRS Resolver only supports resolving DRS paths to access URLs or GCS paths.
+      downloader <- (drsResolverResponse.accessUrl, drsResolverResponse.gsUri) match {
         case (Some(accessUrl), _) =>
-          downloaderFactory.buildAccessUrlDownloader(accessUrl, downloadLoc, marthaResponse.hashes)
+          downloaderFactory.buildAccessUrlDownloader(accessUrl, downloadLoc, drsResolverResponse.hashes)
         case (_, Some(gcsPath)) =>
-          val serviceAccountJsonOption = marthaResponse.googleServiceAccount.map(_.data.spaces2)
+          val serviceAccountJsonOption = drsResolverResponse.googleServiceAccount.map(_.data.spaces2)
           downloaderFactory.buildGcsUriDownloader(
             gcsPath = gcsPath,
             serviceAccountJsonOption = serviceAccountJsonOption,
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
index 345a14f63e4..d4c81af6300 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
@@ -19,7 +19,7 @@ case class GcsUriDownloader(gcsUrl: String,
 
     val copyProcess = serviceAccountJson match {
       case Some(sa) =>
-        // if Martha returned a SA, use that SA for gsutil instead of default credentials
+        // if DRS Resolver returned a SA, use that SA for gsutil instead of default credentials
         val tempCredentialDir: Path = Files.createTempDirectory("gcloudTemp_").toAbsolutePath
         val saJsonPath: Path = tempCredentialDir.resolve("sa.json")
         Files.write(saJsonPath, sa.getBytes(StandardCharsets.UTF_8))
@@ -27,7 +27,7 @@ case class GcsUriDownloader(gcsUrl: String,
         val copyCommand = Seq("bash", "-c", generateDownloadScript(gcsUrl, Option(saJsonPath)))
         Process(copyCommand, None, extraEnv.toSeq: _*)
       case None =>
-        // No SA returned from Martha. gsutil will use the application default credentials.
+        // No SA returned from DRS Resolver. gsutil will use the application default credentials.
         val copyCommand = Seq("bash", "-c", generateDownloadScript(gcsUrl, None))
         Process(copyCommand)
     }
@@ -50,11 +50,11 @@ case class GcsUriDownloader(gcsUrl: String,
     def setServiceAccount(): String = {
       saJsonPathOption match {
         case Some(saJsonPath) =>
-          s"""# Set gsutil to use the service account returned from Martha
+          s"""# Set gsutil to use the service account returned from the DRS Resolver
              |gcloud auth activate-service-account --key-file=$saJsonPath > gcloud_output.txt 2>&1
              |RC_GCLOUD=$$?
              |if [ "$$RC_GCLOUD" != "0" ]; then
-             |  echo "Failed to activate service account returned from Martha. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
+             |  echo "Failed to activate service account returned from the DRS Resolver. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
              |  exit "$$RC_GCLOUD"
              |else
              |  echo "Successfully activated service account; Will continue with download. $$(cat gcloud_output.txt)"
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
index 252971c0b5e..551099b8e21 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
@@ -61,7 +61,7 @@ object GetmChecksum {
   def apply(hashes: Hashes, accessUrl: AccessUrl): GetmChecksum = {
     hashes match {
       case Some(hashes) if hashes.nonEmpty =>
-        // `hashes` is keyed by the Martha names for these hash algorithms, which in turn are the forwarded DRS
+        // `hashes` is keyed by the DRS Resolver names for these hash algorithms, which in turn are the forwarded DRS
         // providers' names for the algorithms. `getm` has its own notions of what these algorithms are called.
         // For the specific case of `md5` the algorithm names are the same between DRS providers and `getm`,
         // but all of the other algorithm names currently differ between DRS providers and `getm`.
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
index b306c0a3a94..66799fcc099 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
@@ -4,7 +4,7 @@ import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO}
 import cats.syntax.validated._
 import cloud.nio.impl.drs.DrsPathResolver.FatalRetryDisposition
-import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsCredentials, MarthaField, MarthaResponse}
+import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsCredentials, DrsResolverField, DrsResolverResponse}
 import common.assertion.CromwellTimeoutSpec
 import common.validation.ErrorOr.ErrorOr
 import drs.localizer.MockDrsLocalizerDrsPathResolver.{FakeAccessTokenStrategy, FakeHashes}
@@ -49,12 +49,12 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync() shouldBe expected
   }
 
-  it should "fail and throw error if Martha response does not have gs:// url" in {
+  it should "fail and throw error if the DRS Resolver response does not have gs:// url" in {
     val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithoutAnyResolution, fakeDownloadLocation, None)
 
     the[RuntimeException] thrownBy {
       mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync()
-    } should have message "No access URL nor GCS URI starting with 'gs://' found in Martha response!"
+    } should have message "No access URL nor GCS URI starting with 'gs://' found in the DRS Resolver response!"
   }
 
   it should "resolve to use the correct downloader for an access url" in {
@@ -67,7 +67,7 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync() shouldBe expected
   }
 
-  it should "resolve to use the correct downloader for an access url when the Martha response also contains a gs url" in {
+  it should "resolve to use the correct downloader for an access url when the DRS Resolver response also contains a gs url" in {
     val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithAccessUrlAndGcsResolution, fakeDownloadLocation, None)
     val expected = AccessUrlDownloader(
       accessUrl = AccessUrl(url = "http://abc/def/ghi.bam", headers = None), downloadLoc = fakeDownloadLocation,
@@ -315,23 +315,23 @@ class MockDrsLocalizerMain(drsUrl: String,
 class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig) extends
   DrsLocalizerDrsPathResolver(drsConfig, FakeAccessTokenStrategy) {
 
-  override def resolveDrsThroughMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): IO[MarthaResponse] = {
-    val marthaResponse = MarthaResponse(
+  override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
+    val drsResolverResponse = DrsResolverResponse(
       size = Option(1234),
       hashes = FakeHashes
     )
 
     IO.pure(drsPath) map {
       case MockDrsPaths.fakeDrsUrlWithGcsResolutionOnly =>
-        marthaResponse.copy(
+        drsResolverResponse.copy(
           gsUri = Option("gs://abc/foo-123/abc123"))
       case MockDrsPaths.fakeDrsUrlWithoutAnyResolution =>
-        marthaResponse
+        drsResolverResponse
       case MockDrsPaths.fakeDrsUrlWithAccessUrlResolutionOnly =>
-        marthaResponse.copy(
+        drsResolverResponse.copy(
           accessUrl = Option(AccessUrl(url = "http://abc/def/ghi.bam", headers = None)))
       case MockDrsPaths.fakeDrsUrlWithAccessUrlAndGcsResolution =>
-        marthaResponse.copy(
+        drsResolverResponse.copy(
           accessUrl = Option(AccessUrl(url = "http://abc/def/ghi.bam", headers = None)),
           gsUri = Option("gs://some/uri"))
       case e => throw new RuntimeException(s"Unexpected exception in DRS localization test code: $e")
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala
index 66c4ff6fabd..07eb5ede181 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala
@@ -11,7 +11,7 @@ class GcsUriDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
   val fakeDownloadLocation = "/root/foo/foo-123.bam"
   val fakeRequesterPaysId = "fake-billing-project"
 
-  it should "return correct download script for a drs url without Requester Pays ID and Google SA returned from Martha" in {
+  it should "return correct download script for a drs url without Requester Pays ID and Google SA returned from the DRS Resolver" in {
     val gcsUrl = "gs://foo/bar.bam"
     val downloader = new GcsUriDownloader(
       gcsUrl = gcsUrl,
@@ -44,7 +44,7 @@ class GcsUriDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     downloader.generateDownloadScript(gcsUrl = gcsUrl, saJsonPathOption = None) shouldBe expectedDownloadScript
   }
 
-  it should "inject Requester Pays flag & gcloud auth using SA returned from Martha" in {
+  it should "inject Requester Pays flag & gcloud auth using SA returned from the DRS Resolver" in {
     val gcsUrl = "gs://foo/bar.bam"
     val downloader = new GcsUriDownloader(
       gcsUrl = gcsUrl,
@@ -60,11 +60,11 @@ class GcsUriDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
       s"""set -euo pipefail
          |set +e
          |
-         |# Set gsutil to use the service account returned from Martha
+         |# Set gsutil to use the service account returned from the DRS Resolver
          |gcloud auth activate-service-account --key-file=${fakeSAJsonPath.toString} > gcloud_output.txt 2>&1
          |RC_GCLOUD=$$?
          |if [ "$$RC_GCLOUD" != "0" ]; then
-         |  echo "Failed to activate service account returned from Martha. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
+         |  echo "Failed to activate service account returned from the DRS Resolver. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
          |  exit "$$RC_GCLOUD"
          |else
          |  echo "Successfully activated service account; Will continue with download. $$(cat gcloud_output.txt)"
diff --git a/docs/filesystems/DataRepositoryService.md b/docs/filesystems/DataRepositoryService.md
index 21a33f8a668..770fc65207f 100644
--- a/docs/filesystems/DataRepositoryService.md
+++ b/docs/filesystems/DataRepositoryService.md
@@ -6,12 +6,12 @@ The Cromwell configuration for DRS is as follows:
 
 ```hocon
 drs {
-    # A reference to a potentially different auth required to contact Martha service.
+    # A reference to a potentially different auth required to contact DRS Resolution service.
     auth = "application-default"
 }
 ```
 
-The `auth` field refers to the authentication schema that should be used to authenticate requests to Martha service.
+The `auth` field refers to the authentication schema that should be used to authenticate requests to DRS Resolution service.
 
 The `drs` section needs to be added to
 - `engine.filesystems` block
diff --git a/docs/filesystems/Filesystems.md b/docs/filesystems/Filesystems.md
index 67f663650ca..0630e421c0b 100644
--- a/docs/filesystems/Filesystems.md
+++ b/docs/filesystems/Filesystems.md
@@ -18,8 +18,8 @@ filesystems {
         # Class to instantiate and propagate to all factories. Takes a single typesafe config argument
         class = "cromwell.filesystems.drs.DrsFileSystemConfig"
         config {
-          martha {
-            url = "https://martha-url-here"
+          resolver {
+            url = "https://martha-url-here or https://drshub-url-here"
             # The number of times to retry failures connecting or HTTP 429 or HTTP 5XX responses, default 3.
             num-retries = 3
             # How long to wait between retrying HTTP 429 or HTTP 5XX responses, default 10 seconds.
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
index 4f899c318bb..5856e41f97b 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
@@ -28,7 +28,7 @@ case class DrsPath(drsPath: CloudNioPath, requesterPaysProjectIdOption: Option[S
       case Some(fileAttributes) =>
         fileAttributes.fileHash match {
           case Some(fileHash) => fileHash
-          case None => throw new IOException(s"Error while resolving DRS path $this. The response from Martha doesn't contain the 'md5' hash for the file.")
+          case None => throw new IOException(s"Error while resolving DRS path $this. The response from DRS Resolver doesn't contain the 'md5' hash for the file.")
         }
       case None => throw new IOException(s"Error getting file hash of DRS path $this. Reason: File attributes class DrsCloudNioRegularFileAttributes wasn't defined in DrsCloudNioFileProvider.")
     }
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
index f22023c87fd..b464772eec8 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
@@ -60,7 +60,7 @@ case class DrsPathBuilder(fileSystemProvider: DrsCloudNioFileSystemProvider,
     val gcsPathOption = for {
       // Right now, only pre-resolving GCS. In the future, could pull others like FTP, HTTP, S3, SRA, etc.
       gsUriOption <- logAttempt(
-        "resolve the uri through Martha",
+        "resolve the uri through DRS Resolver",
         DrsResolver.getSimpleGsUri(pathAsString, fileSystemProvider.drsPathResolver).unsafeRunSync()
       )
       gcsUrlWithNoCreds <- gsUriOption
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
index ae49cf0b5e4..873874912a0 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
@@ -28,8 +28,8 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
 
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] = {
     Future {
-      val marthaScopes = List(
-        // Profile and Email scopes are requirements for interacting with Martha
+      val drsResolverScopes = List(
+        // Profile and Email scopes are requirements for interacting with DRS Resolvers
         Oauth2Scopes.USERINFO_EMAIL,
         Oauth2Scopes.USERINFO_PROFILE
       )
@@ -39,7 +39,7 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
         case googleAuthScheme => googleConfiguration.auth(googleAuthScheme) match {
           case Valid(auth) => (
             Option(auth),
-            GoogleOauthDrsCredentials(auth.credentials(options.get(_).get, marthaScopes), singletonConfig.config)
+            GoogleOauthDrsCredentials(auth.credentials(options.get(_).get, drsResolverScopes), singletonConfig.config)
           )
           case Invalid(error) => throw new RuntimeException(s"Error while instantiating DRS path builder factory. Errors: ${error.toString}")
         }
@@ -50,7 +50,7 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
       val requesterPaysProjectIdOption = options.get("google_project").toOption
 
       /*
-      `override_preresolve_for_test` is a workflow option to override the default `martha.preresolve` specified in the
+      `override_preresolve_for_test` is a workflow option to override the default `resolver.preresolve` specified in the
       global config. This is only used for testing purposes.
        */
       val preResolve: Boolean =
@@ -60,7 +60,7 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
           .getOrElse(
             singletonConfig
               .config
-              .getBoolean("martha.preresolve")
+              .getBoolean("resolver.preresolve")
           )
 
       DrsPathBuilder(
@@ -78,4 +78,4 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
 
 case class UrlNotFoundException(scheme: String) extends Exception(s"No $scheme url associated with given DRS path.")
 
-case class MarthaResponseMissingKeyException(missingKey: String) extends Exception(s"The response from Martha doesn't contain the key '$missingKey'.")
+case class DrsResolverResponseMissingKeyException(missingKey: String) extends Exception(s"The response from the DRS Resolver doesn't contain the key '$missingKey'.")
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
index 3cc1cc3530a..3256d6da248 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
@@ -1,8 +1,8 @@
 package cromwell.filesystems.drs
 
 import cats.effect.IO
-import cloud.nio.impl.drs.MarthaResponseSupport.getGcsBucketAndName
-import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, MarthaResponse, SADataObject}
+import cloud.nio.impl.drs.DrsResolverResponseSupport.getGcsBucketAndName
+import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, DrsResolverResponse, SADataObject}
 import com.google.api.services.storage.StorageScopes
 import com.google.auth.oauth2.OAuth2Credentials
 import com.google.cloud.storage.Storage.BlobGetOption
@@ -21,8 +21,8 @@ object DrsReader {
              options: WorkflowOptions,
              requesterPaysProjectIdOption: Option[String],
              drsPathResolver: DrsPathResolver,
-             marthaResponse: MarthaResponse): IO[DrsReader] = {
-    (marthaResponse.accessUrl, marthaResponse.gsUri, googleAuthMode) match {
+             drsResolverResponse: DrsResolverResponse): IO[DrsReader] = {
+    (drsResolverResponse.accessUrl, drsResolverResponse.gsUri, googleAuthMode) match {
       case (Some(accessUrl), _, _) =>
         IO.pure(AccessUrlReader(drsPathResolver, accessUrl))
       case (_, Some(gcsPath), Some(authMode)) =>
@@ -31,10 +31,10 @@ object DrsReader {
           options,
           requesterPaysProjectIdOption,
           gcsPath,
-          marthaResponse.googleServiceAccount,
+          drsResolverResponse.googleServiceAccount,
         ))
       case (_, Some(_), _) =>
-        IO.raiseError(new RuntimeException("GCS URI found in Martha response, but no Google auth found!"))
+        IO.raiseError(new RuntimeException("GCS URI found in the DRS Resolver response, but no Google auth found!"))
       case _ =>
         IO.raiseError(new RuntimeException(DrsPathResolver.ExtractUriErrorMsg))
     }
@@ -44,9 +44,9 @@ object DrsReader {
                       options: WorkflowOptions,
                       requesterPaysProjectIdOption: Option[String])
                      (drsPathResolver: DrsPathResolver,
-                      marthaResponse: MarthaResponse): IO[ReadableByteChannel] = {
+                      drsResolverResponse: DrsResolverResponse): IO[ReadableByteChannel] = {
     for {
-      reader <- reader(googleAuthMode, options, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      reader <- reader(googleAuthMode, options, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
       channel <- reader.read()
     } yield channel
   }
@@ -69,7 +69,7 @@ case class GcsReader(googleAuthMode: GoogleAuthMode,
     val credentialsIo = googleServiceAccount match {
       case Some(googleSA) =>
         IO(
-          UserServiceAccountMode("martha_service_account").credentials(
+          UserServiceAccountMode("drs_resolver_service_account").credentials(
             Map(GoogleAuthMode.UserServiceAccountKey -> googleSA.data.noSpaces),
             readScopes,
           )
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
index 0f24e803480..4aa760f17e1 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
@@ -2,7 +2,7 @@ package cromwell.filesystems.drs
 
 import cats.data.NonEmptyList
 import cats.effect.IO
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, DrsPathResolver, MarthaField}
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, DrsPathResolver, DrsResolverField}
 import common.exception._
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import org.apache.commons.lang3.exception.ExceptionUtils
@@ -34,31 +34,31 @@ object DrsResolver {
     } yield drsFileSystemProvider.drsPathResolver
   }
 
-  case class MarthaLocalizationData(gsUri: Option[String],
-                                    fileName: Option[String],
-                                    bondProvider: Option[String],
-                                    localizationPath: Option[String])
+  case class DrsResolverLocalizationData(gsUri: Option[String],
+                                         fileName: Option[String],
+                                         bondProvider: Option[String],
+                                         localizationPath: Option[String])
 
-  private def getMarthaLocalizationData(pathAsString: String,
-                                        drsPathResolver: DrsPathResolver): IO[MarthaLocalizationData] = {
-    val fields = NonEmptyList.of(MarthaField.GsUri, MarthaField.FileName, MarthaField.BondProvider, MarthaField.LocalizationPath)
+  private def getDrsResolverLocalizationData(pathAsString: String,
+                                        drsPathResolver: DrsPathResolver): IO[DrsResolverLocalizationData] = {
+    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.FileName, DrsResolverField.BondProvider, DrsResolverField.LocalizationPath)
 
-    drsPathResolver.resolveDrsThroughMartha(pathAsString, fields) map { r =>
-      MarthaLocalizationData(r.gsUri, r.fileName, r.bondProvider, r.localizationPath)
+    drsPathResolver.resolveDrs(pathAsString, fields) map { r =>
+      DrsResolverLocalizationData(r.gsUri, r.fileName, r.bondProvider, r.localizationPath)
     }
   }
 
   /** Returns the `gsUri` if it ends in the `fileName` and the `bondProvider` is empty. */
-  private def getSimpleGsUri(localizationData: MarthaLocalizationData): Option[String] = {
+  private def getSimpleGsUri(localizationData: DrsResolverLocalizationData): Option[String] = {
     localizationData match {
       // `gsUri` not defined so no gsUri can be returned.
-      case MarthaLocalizationData(None, _, _, _) => None
+      case DrsResolverLocalizationData(None, _, _, _) => None
       // `bondProvider` defined, cannot "preresolve" to GCS.
-      case MarthaLocalizationData(_, _, Some(_), _) => None
+      case DrsResolverLocalizationData(_, _, Some(_), _) => None
       // Do not return the simple GS URI if the `fileName` from metadata is mismatched to the filename in the `gsUri`.
-      case MarthaLocalizationData(Some(gsUri), Some(fileName), _, _) if !gsUri.endsWith(s"/$fileName") => None
+      case DrsResolverLocalizationData(Some(gsUri), Some(fileName), _, _) if !gsUri.endsWith(s"/$fileName") => None
       // Barring any of the situations above return the `gsUri`.
-      case MarthaLocalizationData(Some(gsUri), _, _, _) => Option(gsUri)
+      case DrsResolverLocalizationData(Some(gsUri), _, _, _) => Option(gsUri)
     }
   }
 
@@ -66,7 +66,7 @@ object DrsResolver {
   def getSimpleGsUri(pathAsString: String,
                      drsPathResolver: DrsPathResolver): IO[Option[String]] = {
 
-    val gsUriIO = getMarthaLocalizationData(pathAsString, drsPathResolver) map getSimpleGsUri
+    val gsUriIO = getDrsResolverLocalizationData(pathAsString, drsPathResolver) map getSimpleGsUri
 
     gsUriIO.handleErrorWith(resolveError(pathAsString))
   }
@@ -82,15 +82,15 @@ object DrsResolver {
   def getContainerRelativePath(drsPath: DrsPath): IO[String] = {
     val pathIO = for {
       drsPathResolver <- getDrsPathResolver(drsPath)
-      localizationData <- getMarthaLocalizationData(drsPath.pathAsString, drsPathResolver)
+      localizationData <- getDrsResolverLocalizationData(drsPath.pathAsString, drsPathResolver)
       containerRelativePath <- buildContainerRelativePath(localizationData, drsPath)
     } yield containerRelativePath.pathAsString
 
     pathIO.handleErrorWith(resolveError(drsPath.pathAsString))
   }
 
-  // Return the container relative path built from the Martha-specified localization path, file name, or gs URI.
-  private def buildContainerRelativePath(localizationData: MarthaLocalizationData, drsPath: Path): IO[Path] = {
+  // Return the container relative path built from the DRS Resolver-specified localization path, file name, or gs URI.
+  private def buildContainerRelativePath(localizationData: DrsResolverLocalizationData, drsPath: Path): IO[Path] = {
     // Return a relative path constructed from the DRS path minus the leading scheme.
     // In the DOS/DRS spec file names are safe for file systems but not necessarily the DRS URIs.
     // Reuse the regex defined for ContentsObject.name, plus add "/" for directory separators.
@@ -99,13 +99,13 @@ object DrsResolver {
       DefaultPathBuilder.get(drsPath.pathWithoutScheme.replaceAll("[^/A-Za-z0-9._-]", "_"))
 
     localizationData match {
-      case MarthaLocalizationData(_, _, _, Some(localizationPath)) =>
+      case DrsResolverLocalizationData(_, _, _, Some(localizationPath)) =>
         // TDR may return an explicit localization path and if so we should not use the `drsPathRelativePath`.
         // We want to end up with something like /cromwell_root/drs_localization_paths/tdr/specified/path/foo.bam.
         // Calling code will add the `/cromwell_root/`, so strip any leading slashes to make this a relative path:
         val relativeLocalizationPath = if (localizationPath.startsWith("/")) localizationPath.tail else localizationPath
         IO.fromTry(DefaultPathBuilder.build(DrsLocalizationPathsContainer).map(_.resolve(relativeLocalizationPath)))
-      case MarthaLocalizationData(_, Some(fileName), _, _) =>
+      case DrsResolverLocalizationData(_, Some(fileName), _, _) =>
         // Paths specified by filename only are made relative to `drsPathRelativePath`.
         IO(drsPathRelativePath.resolve(fileName))
       case _ =>
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
index 1d941b5f6b2..d207bba8d86 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
@@ -18,8 +18,8 @@ class DrsPathBuilderFactorySpec extends AnyFlatSpec with CromwellTimeoutSpec wit
          |    global {
          |      class = "cromwell.filesystems.drs.DrsFileSystemConfig"
          |      config {
-         |        martha {
-         |          url = "http://martha-url"
+         |        resolver {
+         |          url = "http://drshub-url"
          |        }
          |      }
          |    }
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
index bc556c9bdf3..315e51b5d04 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
@@ -313,7 +313,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       isAbsolute = false,
     ),
 
-    // No spec says this is illegal... so pass it to Martha's various GCFs JIC
+    // No spec says this is illegal... so pass it to the DRS Resolver's various GCFs JIC
     GoodPath(
       description = "a bucketless path",
       path = s"drs://",
@@ -377,9 +377,9 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   private val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
     throw new UnsupportedOperationException("Currently DrsPathBuilderSpec doesn't need to use drs read interpreter.")
 
-  private val marthaConfig: Config = ConfigFactory.parseString(
-    """martha {
-      |   url = "http://martha-url"
+  private val drsResolverConfig: Config = ConfigFactory.parseString(
+    """resolver {
+      |   url = "http://drshub-url"
       |}
       |""".stripMargin
   )
@@ -387,7 +387,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   private lazy val fakeCredentials = NoCredentials.getInstance
 
   private lazy val drsPathBuilder = DrsPathBuilder(
-    new DrsCloudNioFileSystemProvider(marthaConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+    new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
     None,
   )
 }
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
index fbcd900f371..b5bee55b301 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
@@ -1,6 +1,6 @@
 package cromwell.filesystems.drs
 
-import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, MarthaResponse, MockEngineDrsPathResolver}
+import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, DrsResolverResponse, MockEngineDrsPathResolver}
 import common.assertion.CromwellTimeoutSpec
 import cromwell.cloudsupport.gcp.auth.MockAuthMode
 import cromwell.core.WorkflowOptions
@@ -29,9 +29,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val drsPathResolver = new MockEngineDrsPathResolver()
     val gsUri = "gs://bucket/object"
     val googleServiceAccount = None
-    val marthaResponse = MarthaResponse(gsUri = Option(gsUri), googleServiceAccount = googleServiceAccount)
+    val drsResolverResponse = DrsResolverResponse(gsUri = Option(gsUri), googleServiceAccount = googleServiceAccount)
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
     readerIo.unsafeRunSync() should be(
       GcsReader(googleAuthMode, workflowOptions, requesterPaysProjectIdOption, gsUri, googleServiceAccount)
     )
@@ -43,9 +43,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val requesterPaysProjectIdOption = None
     val drsPathResolver = new MockEngineDrsPathResolver()
     val accessUrl = AccessUrl("https://host/object/path", Option(Map("hello" -> "world")))
-    val marthaResponse = MarthaResponse(accessUrl = Option(accessUrl))
+    val drsResolverResponse = DrsResolverResponse(accessUrl = Option(accessUrl))
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
     readerIo.unsafeRunSync() should be(
       AccessUrlReader(drsPathResolver, accessUrl)
     )
@@ -56,9 +56,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val workflowOptions = WorkflowOptions.empty
     val requesterPaysProjectIdOption = None
     val drsPathResolver = new MockEngineDrsPathResolver()
-    val marthaResponse = MarthaResponse()
+    val drsResolverResponse = DrsResolverResponse()
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
     the[RuntimeException] thrownBy {
       readerIo.unsafeRunSync()
     } should have message DrsPathResolver.ExtractUriErrorMsg
@@ -78,9 +78,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val drsPathResolver = new MockEngineDrsPathResolver(httpClientBuilderOverride = Option(httpClientBuilder))
 
     val accessUrl = AccessUrl("https://host/object/path", Option(Map("hello" -> "world")))
-    val marthaResponse = MarthaResponse(accessUrl = Option(accessUrl))
+    val drsResolverResponse = DrsResolverResponse(accessUrl = Option(accessUrl))
     val channelIo =
-      DrsReader.readInterpreter(Option(MockAuthMode("unused")), WorkflowOptions.empty, None)(drsPathResolver, marthaResponse)
+      DrsReader.readInterpreter(Option(MockAuthMode("unused")), WorkflowOptions.empty, None)(drsPathResolver, drsResolverResponse)
     val channel = channelIo.unsafeRunSync()
 
     val buffer = ByteBuffer.allocate(exampleBytes.length)
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
index 98d4140029b..23dcb1bcd66 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
@@ -11,14 +11,14 @@ import scala.jdk.CollectionConverters._
 
 class DrsResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
-  private val marthaConfig: Config = ConfigFactory.parseMap(
+  private val drsResolverConfig: Config = ConfigFactory.parseMap(
     Map(
-      "martha.url" -> "https://martha-url/martha_v3",
+      "resolver.url" -> "https://drshub-url/drshub_v4",
       "access-token-acceptable-ttl" -> "1 minute"
     ).asJava
   )
 
-  private val mockFileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = marthaConfig)
+  private val mockFileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = drsResolverConfig)
   private val drsPathBuilder = DrsPathBuilder(mockFileSystemProvider, None)
 
 
@@ -62,14 +62,14 @@ class DrsResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     } should have message s"Error while resolving DRS path: ${drsPath.pathAsString}. Error: UrlNotFoundException: No gs url associated with given DRS path."
   }
 
-  it should "throw Runtime Exception when Martha can't find the given DRS path " in {
-    val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathNotExistingInMartha).get.asInstanceOf[DrsPath]
+  it should "throw Runtime Exception when the DRS Resolver can't find the given DRS path " in {
+    val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathNotExistingInDrsResolver).get.asInstanceOf[DrsPath]
 
     the[RuntimeException] thrownBy {
       DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
     } should have message
       s"Error while resolving DRS path: ${drsPath.pathAsString}. " +
         s"Error: RuntimeException: Unexpected response resolving ${drsPath.pathAsString} " +
-        s"through Martha url https://martha-url/martha_v3. Error: 404 Not Found."
+        s"through DRS Resolver url https://drshub-url/drshub_v4. Error: 404 Not Found."
   }
 }
diff --git a/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml b/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml
index c718d7ff1f1..91b36d9277e 100644
--- a/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml	
+++ b/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml	
@@ -1,7 +1,7 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="Repo template: Cromwell DRS Localizer" type="Application" factoryName="Application">
     <envs>
-      <env name="MARTHA_URL" value="https://us-central1-broad-dsde-dev.cloudfunctions.net/martha_v3" />
+      <env name="DRS_RESOLVER_URL" value="https://drshub.dsde-dev.broadinstitute.org/api/v4/drs/resolve" />
     </envs>
     <option name="MAIN_CLASS_NAME" value="drs.localizer.DrsLocalizerMain" />
     <module name="cromwell-drs-localizer" />
diff --git a/src/ci/resources/papi_application.inc.conf.ctmpl b/src/ci/resources/papi_application.inc.conf.ctmpl
index 9d6a06428dd..04d6690a6ba 100644
--- a/src/ci/resources/papi_application.inc.conf.ctmpl
+++ b/src/ci/resources/papi_application.inc.conf.ctmpl
@@ -63,7 +63,7 @@ services {
   }
 }
 
-filesystems.drs.global.config.martha.url = "https://us-central1-broad-dsde-dev.cloudfunctions.net/martha_v3"
+filesystems.drs.global.config.resolver.url = "https://drshub.dsde-dev.broadinstitute.org/api/v4/drs/resolve"
 
 drs {
   localization {
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
index 09fb0713de0..7710f3de98e 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
@@ -126,7 +126,7 @@ case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, en
             ComputeScopes.COMPUTE,
             StorageScopes.DEVSTORAGE_FULL_CONTROL,
             GoogleCloudScopes.KmsScope,
-            // Profile and Email scopes are requirements for interacting with Martha
+            // Profile and Email scopes are requirements for interacting with DRS Resolver
             Oauth2Scopes.USERINFO_EMAIL,
             Oauth2Scopes.USERINFO_PROFILE,
             // Monitoring scope as POC
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
index b445f4786f8..19774a4cc41 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
@@ -38,12 +38,12 @@ trait PipelinesParameterConversions {
           val drsCommand =
             List(fileInput.cloudPath.pathAsString, fileInput.containerPath.pathAsString) ++
               drsPath.requesterPaysProjectIdOption.toList
-          val marthaEnv = DrsConfig.toEnv(drsFileSystemProvider.drsConfig)
+          val drsResolverEnv = DrsConfig.toEnv(drsFileSystemProvider.drsConfig)
           val localizationAction = ActionBuilder
             .withImage(drsDockerImage)
             .withCommand(drsCommand: _*)
             .withMounts(mounts)
-            .setEnvironment(marthaEnv.asJava)
+            .setEnvironment(drsResolverEnv.asJava)
             .withLabels(labels)
           List(ActionBuilder.describeParameter(fileInput, labels), localizationAction)
         case sraPath: SraPath =>
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
index d9fe26e7c0c..18c84ee66eb 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
@@ -24,9 +24,9 @@ class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   implicit val gcsTransferConfiguration: GcsTransferConfiguration =
     GcsTransferConfiguration(transferAttempts = refineMV(1), parallelCompositeUploadThreshold = "0")
 
-  private val marthaConfig: Config = ConfigFactory.parseString(
-    """martha {
-      |   url = "http://martha-url"
+  private val drsResolverConfig: Config = ConfigFactory.parseString(
+    """resolver {
+      |   url = "http://drshub-url"
       |}
       |""".stripMargin
   )
@@ -39,7 +39,7 @@ class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   it should "create a DRS input parameter" in {
 
     val drsPathBuilder = DrsPathBuilder(
-      new DrsCloudNioFileSystemProvider(marthaConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+      new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
       None,
     )
     val drsPath = drsPathBuilder.build("drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba").get
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
index e4c95dcb1e0..8d8f52d3773 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
@@ -119,7 +119,7 @@ case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode
             ComputeScopes.COMPUTE,
             StorageScopes.DEVSTORAGE_FULL_CONTROL,
             GoogleCloudScopes.KmsScope,
-            // Profile and Email scopes are requirements for interacting with Martha
+            // Profile and Email scopes are requirements for interacting with DRS Resolvers
             Oauth2Scopes.USERINFO_EMAIL,
             Oauth2Scopes.USERINFO_PROFILE,
             // Monitoring scope as POC
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
index 8e8065fe679..3b470b9096b 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
@@ -80,20 +80,20 @@ object Localization {
                 requesterPaysProjectId: Option[String]
                ): Action = {
     val config = ConfigFactory.load
-    val marthaConfig = config.getConfig("filesystems.drs.global.config.martha")
-    val drsConfig = DrsConfig.fromConfig(marthaConfig)
+    val drsResolverConfig = config.getConfig("filesystems.drs.global.config.resolver")
+    val drsConfig = DrsConfig.fromConfig(drsResolverConfig)
     val drsDockerImage = config.getString("drs.localization.docker-image")
 
     val manifestArg = List("-m", manifestPath.pathAsString)
     val requesterPaysArg = requesterPaysProjectId.map(r => List("-r", r)).getOrElse(List.empty)
     val drsCommand = manifestArg ++ requesterPaysArg
 
-    val marthaEnv = DrsConfig.toEnv(drsConfig)
+    val drsResolverEnv = DrsConfig.toEnv(drsConfig)
     ActionBuilder
       .withImage(drsDockerImage)
       .withCommand(drsCommand: _*)
       .withMounts(mounts)
-      .setEnvironment(marthaEnv.asJava)
+      .setEnvironment(drsResolverEnv.asJava)
       .withLabels(labels)
   }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
index 5764bbbc2e4..e7189d453ad 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
@@ -55,9 +55,9 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Cro
 
   it should "generate a CSV manifest for DRS inputs, ignoring non-DRS inputs" in {
     def makeDrsPathBuilder: DrsPathBuilder = {
-      val marthaConfig: Config = ConfigFactory.parseString(
-        """martha {
-          |   url = "http://martha-url"
+      val drsResolverConfig: Config = ConfigFactory.parseString(
+        """resolver {
+          |   url = "http://drshub-url"
           |}
           |""".stripMargin
       )
@@ -68,7 +68,7 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Cro
         throw new UnsupportedOperationException("PipelinesApiAsyncBackendJobExecutionActorSpec doesn't need to use drs read interpreter.")
 
       DrsPathBuilder(
-        new DrsCloudNioFileSystemProvider(marthaConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+        new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
         None,
       )
     }

From 2242b749e248840fa2f8d94535f3cea6171a0f58 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 16 Dec 2022 10:08:45 -0500
Subject: [PATCH 117/326] WX-867 Translate crc32c hashes to b64 for getm
 (#6970)

* Translate crc32c hashes to b64 for getm

* Update tests

* Remove obsolete b64 handling for md5, centralize hex validation

* Restore old test, fix other test
---
 .../localizer/downloaders/GetmChecksum.scala  | 34 ++++++++++---------
 .../downloaders/GetmChecksumSpec.scala        | 22 ++++++++++--
 2 files changed, 37 insertions(+), 19 deletions(-)

diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
index 551099b8e21..2a39a6543a3 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
@@ -4,9 +4,8 @@ import cats.syntax.validated._
 import cloud.nio.impl.drs.AccessUrl
 import common.validation.ErrorOr.ErrorOr
 import drs.localizer.downloaders.AccessUrlDownloader.Hashes
-import mouse.all.anySyntaxMouse
-import org.apache.commons.codec.binary.Base64.{decodeBase64, isBase64}
-import org.apache.commons.codec.binary.Hex.encodeHexString
+import org.apache.commons.codec.binary.Base64.encodeBase64String
+import org.apache.commons.codec.binary.Hex.decodeHex
 import org.apache.commons.text.StringEscapeUtils
 
 
@@ -26,23 +25,18 @@ sealed trait GetmChecksum {
 }
 
 case class Md5(override val rawValue: String) extends GetmChecksum {
-  override def value: ErrorOr[String] = {
-    val trimmed = rawValue.trim
-    if (trimmed.matches("[A-Fa-f0-9]+"))
-      trimmed.validNel
-    // TDR currently returns a base64-encoded MD5 because that's what Azure seems to do. However,
-    // the DRS spec does not specify that any checksums should be base64-encoded, and `getm` also
-    // does not expect base64. This case handles the current behavior in the short term until
-    // https://broadworkbench.atlassian.net/browse/DR-2259 is done.
-    else if (isBase64(trimmed))
-      (trimmed |> decodeBase64 |> encodeHexString).validNel
-    else
-      s"Invalid md5 checksum value is neither hex nor base64: $rawValue".invalidNel
-  }
+  override def value: ErrorOr[String] = GetmChecksum.validateHex(rawValue)
   override def getmAlgorithm: String = "md5"
 }
 
 case class Crc32c(override val rawValue: String) extends GetmChecksum {
+  // The DRS spec says that all hash values should be hex strings,
+  // but getm expects crc32c values to be base64.
+  override def value: ErrorOr[String] =
+    GetmChecksum.validateHex(rawValue)
+      .map(decodeHex)
+      .map(encodeBase64String)
+
   override def getmAlgorithm: String = "gs_crc32c"
 }
 case class AwsEtag(override val rawValue: String) extends GetmChecksum {
@@ -88,4 +82,12 @@ object GetmChecksum {
       case _ => Null // None or an empty hashes map.
     }
   }
+
+  def validateHex(s: String): ErrorOr[String] = {
+    val trimmed = s.trim
+    if (trimmed.matches("[A-Fa-f0-9]+"))
+      trimmed.validNel
+    else
+      s"Invalid checksum value, expected hex but got: $trimmed".invalidNel
+  }
 }
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
index 24ea087cb8f..69c063ff616 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
@@ -31,9 +31,10 @@ class GetmChecksumSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     val results = Table(
       ("description", "algorithm", "expected"),
       ("md5 hex", Md5("abcdef"), "--checksum-algorithm 'md5' --checksum abcdef".validNel),
-      ("md5 base64", Md5("cR84lXY1y17c3q7/7riLEA=="), "--checksum-algorithm 'md5' --checksum 711f38957635cb5edcdeaeffeeb88b10".validNel),
-      ("md5 gibberish", Md5("what is this???"), "Invalid md5 checksum value is neither hex nor base64: what is this???".invalidNel),
-      ("crc32c", Crc32c("012345"), "--checksum-algorithm 'gs_crc32c' --checksum 012345".validNel),
+      ("md5 base64", Md5("cR84lXY1y17c3q7/7riLEA=="), "Invalid checksum value, expected hex but got: cR84lXY1y17c3q7/7riLEA==".invalidNel),
+      ("md5 gibberish", Md5("what is this???"), "Invalid checksum value, expected hex but got: what is this???".invalidNel),
+      ("crc32c", Crc32c("012345"), "--checksum-algorithm 'gs_crc32c' --checksum ASNF".validNel),
+      ("crc32c gibberish", Crc32c("????"), "Invalid checksum value, expected hex but got: ????".invalidNel),
       ("AWS ETag", AwsEtag("012345"), "--checksum-algorithm 's3_etag' --checksum 012345".validNel),
       // Escape checksum values constructed from unvalidated data returned by DRS servers.
       ("Unsupported", Unsupported("Robert'); DROP TABLE Students;\n --\\"), raw"--checksum-algorithm 'null' --checksum Robert\'\)\;\ DROP\ TABLE\ Students\;\ --\\".validNel),
@@ -46,4 +47,19 @@ class GetmChecksumSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
       }
     }
   }
+
+  it should "correctly validate hex strings" in {
+    val results = Table(
+      ("test string", "expected"),
+      ("", "Invalid checksum value, expected hex but got: ".invalidNel),
+      (" ", "Invalid checksum value, expected hex but got: ".invalidNel),
+      ("myfavoritestring", "Invalid checksum value, expected hex but got: myfavoritestring".invalidNel),
+      (" AbC123 ", "AbC123".validNel),
+      ("456", "456".validNel),
+    )
+
+    forAll(results) { (testString, expected) =>
+      GetmChecksum.validateHex(testString) shouldBe expected
+    }
+  }
 }

From dce3fe7d53766559d038fea27ee1201b2a1f305e Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 16 Dec 2022 17:52:41 -0500
Subject: [PATCH 118/326] WX-843 Workflow failure reason should accurately
 indicate issues opening blob filesystem (#6965)

---
 core/src/main/scala/cromwell/core/io/IoCommand.scala        | 6 ++++++
 .../main/scala/cromwell/core/io/IoPromiseProxyActor.scala   | 2 ++
 2 files changed, 8 insertions(+)

diff --git a/core/src/main/scala/cromwell/core/io/IoCommand.scala b/core/src/main/scala/cromwell/core/io/IoCommand.scala
index a21b6f8cebd..7d71f9bd307 100644
--- a/core/src/main/scala/cromwell/core/io/IoCommand.scala
+++ b/core/src/main/scala/cromwell/core/io/IoCommand.scala
@@ -38,6 +38,12 @@ trait IoCommand[+T] {
 
   def commandDescription: String
 
+  /**
+    * IO commands side-effect and/or have exceptions. We don't want that when evaluating identity, e.g. to check presence in cache.
+    * @return Hash code based on the description, which captures file path & action
+    */
+  override def hashCode(): Int = commandDescription.hashCode
+
   def logIOMsgOverLimit(message: => String): Unit = {
     val millis: Long = java.time.Duration.between(creation, OffsetDateTime.now).toMillis
     if (millis > IoCommand.IOCommandWarnLimit.toMillis) {
diff --git a/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala b/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
index 15097a92a99..dd8f44464f3 100644
--- a/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
+++ b/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
@@ -10,6 +10,8 @@ import scala.concurrent.duration.FiniteDuration
 object IoPromiseProxyActor {
   case class IoCommandWithPromise[A](ioCommand: IoCommand[A], timeout: FiniteDuration = defaultTimeout) {
     val promise = Promise[A]()
+
+    override def hashCode(): Int = ioCommand.hashCode()
   }
   def props(ioActor: ActorRef) = Props(new IoPromiseProxyActor(ioActor))
 }

From 60c2c8688c659105c8a121c3a6a034052a549dd8 Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Tue, 3 Jan 2023 09:22:21 -0500
Subject: [PATCH 119/326] WX-859 Accept workflow execution identity in config
 (#6967)

---
 .../backend/impl/tes/TesConfiguration.scala   |  4 +-
 .../cromwell/backend/impl/tes/TesTask.scala   | 45 ++++++++++++++-----
 .../backend/impl/tes/TesTaskSpec.scala        | 38 ++++++++++------
 3 files changed, 61 insertions(+), 26 deletions(-)

diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
index 3d55a9f3a1c..264ba6299bd 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
@@ -11,10 +11,10 @@ class TesConfiguration(val configurationDescriptor: BackendConfigurationDescript
   val useBackendParameters =
     configurationDescriptor
       .backendConfig
-      .as[Option[Boolean]](TesConfiguration.useBackendParamtersKey)
+      .as[Option[Boolean]](TesConfiguration.useBackendParametersKey)
       .getOrElse(false)
 }
 
 object TesConfiguration {
-  final val useBackendParamtersKey = "use_tes_11_preview_backend_parameters"
+  final val useBackendParametersKey = "use_tes_11_preview_backend_parameters"
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index 719ad36942b..5d1a844bb83 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -3,9 +3,14 @@ package cromwell.backend.impl.tes
 import common.collections.EnhancedCollections._
 import common.util.StringUtil._
 import cromwell.backend.impl.tes.OutputMode.OutputMode
-import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendWorkflowDescriptor}
+import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor}
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.{DefaultPathBuilder, Path}
+import net.ceedubs.ficus.Ficus._
+
+import scala.language.postfixOps
+import scala.util.Try
+
 import wdl.draft2.model.FullyQualifiedName
 import wdl4s.parser.MemoryUnit
 import wom.InstantiatedCommand
@@ -13,9 +18,8 @@ import wom.callable.Callable.OutputDefinition
 import wom.expression.NoIoFunctionSet
 import wom.values._
 
-import scala.language.postfixOps
-import scala.util.Try
-
+final case class WorkflowExecutionIdentityConfig(value: String) {override def toString: String = value.toString}
+final case class WorkflowExecutionIdentityOption(value: String) {override def toString: String = value}
 final case class TesTask(jobDescriptor: BackendJobDescriptor,
                          configurationDescriptor: BackendConfigurationDescriptor,
                          jobLogger: JobLogger,
@@ -32,6 +36,16 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
   private val workflowDescriptor = jobDescriptor.workflowDescriptor
   private val workflowName = workflowDescriptor.callable.name
   private val fullyQualifiedTaskName = jobDescriptor.taskCall.fullyQualifiedName
+  private val workflowExecutionIdentityConfig: Option[WorkflowExecutionIdentityConfig] =
+    configurationDescriptor.backendConfig
+      .getAs[String]("workflow-execution-identity")
+      .map(WorkflowExecutionIdentityConfig)
+  private val workflowExecutionIdentityOption: Option[WorkflowExecutionIdentityOption] =
+    workflowDescriptor
+      .workflowOptions
+      .get(TesWorkflowOptionKeys.WorkflowExecutionIdentity)
+      .toOption
+      .map(WorkflowExecutionIdentityOption)
   val name: String = fullyQualifiedTaskName
   val description: String = jobDescriptor.toString
 
@@ -212,7 +226,15 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
     result
   }
 
-  val resources: Resources = TesTask.makeResources(runtimeAttributes, workflowDescriptor)
+  val preferedWorkflowExecutionIdentity = TesTask.getPreferredWorkflowExecutionIdentity(
+      workflowExecutionIdentityConfig,
+      workflowExecutionIdentityOption
+  )
+
+  val resources: Resources = TesTask.makeResources(
+    runtimeAttributes,
+    preferedWorkflowExecutionIdentity
+  )
 
   val executors = Seq(Executor(
     image = dockerImageUsed,
@@ -226,21 +248,22 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
 }
 
 object TesTask {
+  // Helper to determine which source to use for a workflowExecutionIdentity
+  def getPreferredWorkflowExecutionIdentity(configIdentity: Option[WorkflowExecutionIdentityConfig],
+                                           workflowOptionsIdentity: Option[WorkflowExecutionIdentityOption]): Option[String] = {
+    configIdentity.map(_.value).orElse(workflowOptionsIdentity.map(_.value))
+  }
   def makeResources(runtimeAttributes: TesRuntimeAttributes,
-                    workflowDescriptor: BackendWorkflowDescriptor): Resources = {
+                    workflowExecutionId: Option[String]): Resources = {
 
     // This was added in BT-409 to let us pass information to an Azure
     // TES server about which user identity to run tasks as.
     // Note that we validate the type of WorkflowExecutionIdentity
     // in TesInitializationActor.
     val backendParameters = runtimeAttributes.backendParameters ++
-      workflowDescriptor
-        .workflowOptions
-        .get(TesWorkflowOptionKeys.WorkflowExecutionIdentity)
-        .toOption
+      workflowExecutionId
         .map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option(_))
         .toMap
-
     val disk :: ram :: _ = Seq(runtimeAttributes.disk, runtimeAttributes.memory) map {
       case Some(x) =>
         Option(x.to(MemoryUnit.GB).amount)
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index c2ee68e0068..3e5a79b33c9 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -2,15 +2,15 @@ package cromwell.backend.impl.tes
 
 import common.assertion.CromwellTimeoutSpec
 import common.mock.MockSugar
-import cromwell.backend.{BackendSpec, TestConfig}
 import cromwell.backend.validation.ContinueOnReturnCodeSet
+import cromwell.backend.{BackendSpec, TestConfig}
 import cromwell.core.WorkflowOptions
 import cromwell.core.labels.Labels
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.DefaultPathBuilder
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
-import spray.json.{JsObject, JsString, JsValue}
+import spray.json.{JsObject, JsValue}
 import wom.InstantiatedCommand
 
 class TesTaskSpec
@@ -32,32 +32,44 @@ class TesTaskSpec
     Map.empty
   )
 
-  def workflowDescriptorWithIdentity(excIdentity: Option[String]) = {
-    val optionsMap: Map[String, JsValue] = excIdentity.map(i => TesWorkflowOptionKeys.WorkflowExecutionIdentity -> JsString(i)).toMap
-    buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld, None, WorkflowOptions(JsObject(optionsMap)))
-  }
-
   it should "create the correct resources when an identity is passed in WorkflowOptions" in {
-    val wd = workflowDescriptorWithIdentity(Option("abc123"))
-    TesTask.makeResources(runtimeAttributes, wd) shouldEqual
+    val wei = Option("abc123")
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
         Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123")))
     )
   }
 
   it should "create the correct resources when an empty identity is passed in WorkflowOptions" in {
-    val wd = workflowDescriptorWithIdentity(Option(""))
-    TesTask.makeResources(runtimeAttributes, wd) shouldEqual
+    val wei = Option("")
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
         Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("")))
     )
   }
 
   it should "create the correct resources when no identity is passed in WorkflowOptions" in {
-    val wd = workflowDescriptorWithIdentity(None)
-    TesTask.makeResources(runtimeAttributes, wd) shouldEqual
+    val wei = None
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
         Resources(None, None, None, Option(false), None, Option(Map.empty[String, Option[String]])
     )
   }
 
+  it should "create the correct resources when an identity is passed in via backend config" in {
+    val weic = Option(WorkflowExecutionIdentityConfig("abc123"))
+    val weio = Option(WorkflowExecutionIdentityOption("def456"))
+    val wei = TesTask.getPreferredWorkflowExecutionIdentity(weic, weio)
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
+        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123")))
+    )
+  }
+
+  it should "create the correct resources when no identity is passed in via backend config" in {
+    val weic = None
+    val weio = Option(WorkflowExecutionIdentityOption("def456"))
+    val wei = TesTask.getPreferredWorkflowExecutionIdentity(weic, weio)
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
+        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("def456")))
+    )
+  }
 
   it should "copy labels to tags" in {
     val jobLogger = mock[JobLogger]

From 505a3702147bd27d4be73033fcb289f9af620f53 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 17 Jan 2023 16:45:57 -0500
Subject: [PATCH 120/326] WX-892 Trim down `ValueStore` logging to prevent OOMs
 (#6981)

---
 .../workflow/lifecycle/execution/stores/ValueStore.scala     | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
index e913e5c6b3b..a5c1d6fc995 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
@@ -27,12 +27,13 @@ object ValueStore {
 case class ValueStore(store: Table[OutputPort, ExecutionIndex, WomValue]) {
 
   override def toString: String = {
+    import common.util.StringUtil.EnhancedToStringable
     import io.circe.syntax._
     import io.circe.Printer
 
     val values = store.valuesTriplet.map {
-      case (node, None, value) => node.name -> value.valueString
-      case (node, index, value) => s"${node.name}:${index.fromIndex}" -> value.valueString
+      case (node, None, value) => node.name -> value.toPrettyElidedString(limit = 100)
+      case (node, index, value) => s"${node.name}:${index.fromIndex}" -> value.toPrettyElidedString(limit = 100)
     }.toMap
 
     values.asJson.printWith(Printer.spaces2.copy(dropNullValues = true, colonLeft = ""))

From 32f8a90f2aa2ddd1da6df21726c82349f9fd5833 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@users.noreply.github.com>
Date: Wed, 18 Jan 2023 11:45:36 -0500
Subject: [PATCH 121/326] Add Nirvana 3.18.1 reference image test, minor
 cleanup [VS-705] (#6975)

---
 .../reference_disk/reference_disk_test.inputs |    3 +-
 .../reference_disk/reference_disk_test.wdl    |   30 +-
 .../reference_disk_false_options.test         |    3 +-
 .../reference_disk_true_options.test          |    3 +-
 .../reference_disk_unspecified_options.test   |    3 +-
 .../papi_v2_reference_image_manifest.conf     | 4989 +----------------
 6 files changed, 290 insertions(+), 4741 deletions(-)

diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
index 8e28a8ef541..f23615ee7f0 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
@@ -1,3 +1,4 @@
 {
-  "wf_reference_disk_test.check_if_localized_as_symlink.reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.tile_db_header.vcf"
+  "wf_reference_disk_test.broad_reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
+  "wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx"
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
index 43a298f18ab..4d469cbe552 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
@@ -1,11 +1,20 @@
+version 1.0
+
 task check_if_localized_as_symlink {
-  File reference_file_input
+  input {
+    File broad_reference_file_input
+    File nirvana_reference_file_input
+  }
+  String broad_input_symlink = "broad_input_symlink.txt"
+  String nirvana_input_symlink = "nirvana_input_symlink.txt"
   command {
-     # print true if file is a symlink, otherwise print false
-     if test -h ${reference_file_input}; then echo "true"; else echo "false"; fi;
+    # Print true if input is a symlink, otherwise print false.
+    if test -h ~{broad_reference_file_input}; then echo true; else echo false; fi > ~{broad_input_symlink}
+    if test -h ~{nirvana_reference_file_input}; then echo true; else echo false; fi > ~{nirvana_input_symlink}
   }
   output {
-    Boolean is_symlink = read_boolean(stdout())
+    Boolean is_broad_input_symlink = read_boolean("~{broad_input_symlink}")
+    Boolean is_nirvana_input_symlink = read_boolean("~{nirvana_input_symlink}")
   }
   runtime {
     docker: "ubuntu:latest"
@@ -14,8 +23,17 @@ task check_if_localized_as_symlink {
 }
 
 workflow wf_reference_disk_test {
-  call check_if_localized_as_symlink
+  input {
+    File broad_reference_file_input
+    File nirvana_reference_file_input
+  }
+  call check_if_localized_as_symlink {
+    input:
+      broad_reference_file_input = broad_reference_file_input,
+      nirvana_reference_file_input = nirvana_reference_file_input
+  }
   output {
-     Boolean is_input_file_a_symlink = check_if_localized_as_symlink.is_symlink
+    Boolean is_broad_input_file_a_symlink = check_if_localized_as_symlink.is_broad_input_symlink
+    Boolean is_nirvana_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_input_symlink
   }
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
index b75ef58dabc..8b80bea061e 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
@@ -11,5 +11,6 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
index dab9c516164..fd8b508a221 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
@@ -11,5 +11,6 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": true
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": true
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": true
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
index 441db8748f2..04391e4b2ab 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
@@ -11,5 +11,6 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
 }
diff --git a/src/ci/resources/papi_v2_reference_image_manifest.conf b/src/ci/resources/papi_v2_reference_image_manifest.conf
index 8c15fc44636..d31c961e15e 100644
--- a/src/ci/resources/papi_v2_reference_image_manifest.conf
+++ b/src/ci/resources/papi_v2_reference_image_manifest.conf
@@ -1,4819 +1,346 @@
 reference-disk-localization-manifests = [
   {
-    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/broad-references-disk-image",
-    "diskSizeGb" : 500,
+    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/hg38-public-2020-10-26",
+    "diskSizeGb" : 20,
     "files" : [ {
-      "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.nhr",
-      "crc32c" : 407769621
-    }, {
-      "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.sa",
-      "crc32c" : 1902048083
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00129.disc.txt.gz",
-      "crc32c" : 3404974518
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG04118.split.txt.gz.tbi",
-      "crc32c" : 4024172857
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19449.split.txt.gz.tbi",
-      "crc32c" : 1977253058
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02272.disc.txt.gz",
-      "crc32c" : 1166548962
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA21133.disc.txt.gz",
-      "crc32c" : 1427281614
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03864.disc.txt.gz.tbi",
-      "crc32c" : 1529087048
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA20764.disc.txt.gz.tbi",
-      "crc32c" : 1417763527
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA21102.disc.txt.gz.tbi",
-      "crc32c" : 1680978475
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00096.split.txt.gz",
-      "crc32c" : 1667331591
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18638.split.txt.gz.tbi",
-      "crc32c" : 2563684534
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01112.disc.txt.gz",
-      "crc32c" : 3289968657
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.pac",
-      "crc32c" : 299013300
-    }, {
-      "path" : "gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi",
-      "crc32c" : 1373876197
-    }, {
-      "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.delly_exclusionRegions.shard2.tsv",
-      "crc32c" : 422023470
-    }, {
-      "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.delly_exclusionRegions.shard6.tsv",
-      "crc32c" : 2641621150
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_044.wham.HG02002.vcf.gz",
-      "crc32c" : 61945186
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_113.wham.NA18553.vcf.gz",
-      "crc32c" : 2270157672
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_088.wham.HG03709.vcf.gz",
-      "crc32c" : 1143326201
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_116.wham.NA18923.vcf.gz",
-      "crc32c" : 408469998
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_149.wham.NA20802.vcf.gz",
-      "crc32c" : 2170731227
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_014.wham.HG00599.vcf.gz",
-      "crc32c" : 2268306580
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_050.wham.HG02186.vcf.gz",
-      "crc32c" : 2164894354
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_135.wham.NA19684.vcf.gz",
-      "crc32c" : 2251666164
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_007.wham.HG00288.vcf.gz",
-      "crc32c" : 3615266090
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_120.wham.NA18995.vcf.gz",
-      "crc32c" : 851480900
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_024.wham.HG01344.vcf.gz",
-      "crc32c" : 1569598141
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_080.manta.HG03449.vcf.gz",
-      "crc32c" : 3827948923
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_081.manta.HG03472.vcf.gz",
-      "crc32c" : 1026539483
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_006.manta.HG00277.vcf.gz",
-      "crc32c" : 3528734581
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_116.manta.NA18923.vcf.gz",
-      "crc32c" : 1495065630
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_062.manta.HG02586.vcf.gz",
-      "crc32c" : 1681406320
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_135.manta.NA19684.vcf.gz",
-      "crc32c" : 2897751567
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_019.manta.HG01060.vcf.gz",
-      "crc32c" : 610810668
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_020.manta.HG01085.vcf.gz",
-      "crc32c" : 2504924512
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_136.manta.NA19746.vcf.gz",
-      "crc32c" : 3534117012
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_040.manta.HG01880.vcf.gz",
-      "crc32c" : 2294307211
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19377.split.txt.gz.tbi",
-      "crc32c" : 3454882291
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03370.disc.txt.gz",
-      "crc32c" : 3230324326
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18539.disc.txt.gz.tbi",
-      "crc32c" : 42990821
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02002.disc.txt.gz.tbi",
-      "crc32c" : 3745118809
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18945.disc.txt.gz",
-      "crc32c" : 3310721851
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19184.split.txt.gz",
-      "crc32c" : 3448306521
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19449.disc.txt.gz",
-      "crc32c" : 4252958454
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01085.disc.txt.gz",
-      "crc32c" : 2389602066
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA11894.split.txt.gz.tbi",
-      "crc32c" : 3846004317
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02235.disc.txt.gz.tbi",
-      "crc32c" : 365742494
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA12489.disc.txt.gz.tbi",
-      "crc32c" : 2818219097
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03744.split.txt.gz",
-      "crc32c" : 2737584475
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA20802.disc.txt.gz.tbi",
-      "crc32c" : 1912617588
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02588.split.txt.gz.tbi",
-      "crc32c" : 2099872645
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01874.split.txt.gz",
-      "crc32c" : 3854913913
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19035.split.txt.gz.tbi",
-      "crc32c" : 3286945483
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA20845.disc.txt.gz",
-      "crc32c" : 1337716767
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02611.split.txt.gz",
-      "crc32c" : 133841208
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00557.split.txt.gz",
-      "crc32c" : 4255423837
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19062.disc.txt.gz",
-      "crc32c" : 3841480226
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-153.tar.gz",
-      "crc32c" : 3007069952
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-99.tar.gz",
-      "crc32c" : 4195646517
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-266.tar.gz",
-      "crc32c" : 1379685624
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-36.tar.gz",
-      "crc32c" : 3789968460
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-211.tar.gz",
-      "crc32c" : 1973914077
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-207.tar.gz",
-      "crc32c" : 540019804
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-129.tar.gz",
-      "crc32c" : 1607611122
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-278.tar.gz",
-      "crc32c" : 3655125191
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-156.tar.gz",
-      "crc32c" : 844061657
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-106.tar.gz",
-      "crc32c" : 1226511555
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-119.tar.gz",
-      "crc32c" : 582423981
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-113.tar.gz",
-      "crc32c" : 2360388371
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-127.tar.gz",
-      "crc32c" : 701818403
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-274.tar.gz",
-      "crc32c" : 498038628
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-181.tar.gz",
-      "crc32c" : 2512969958
+      "path" : "gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
+      "crc32c" : 930173616
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-6.tar.gz",
-      "crc32c" : 721406268
+      "path" : "gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
+      "crc32c" : 289077232
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-29.tar.gz",
-      "crc32c" : 94522894
+      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
+      "crc32c" : 2366715186
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-173.tar.gz",
-      "crc32c" : 1827993197
+      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
+      "crc32c" : 510227671
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-255.tar.gz",
-      "crc32c" : 2620821232
+      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
+      "crc32c" : 1970999569
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-97.tar.gz",
-      "crc32c" : 74623336
+      "path" : "gcp-public-data--broad-references/hg38/v0/exome_calling_regions.v1.interval_list",
+      "crc32c" : 2361720184
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-150.tar.gz",
-      "crc32c" : 3297915748
+      "path" : "gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.UD",
+      "crc32c" : 1848694786
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-37.tar.gz",
-      "crc32c" : 4120921275
+      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz",
+      "crc32c" : 4148917717
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0004_of_50/scattered.interval_list",
-      "crc32c" : 3093457205
+      "path" : "gcp-public-data--broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
+      "crc32c" : 4231387187
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0041_of_50/scattered.interval_list",
-      "crc32c" : 3846894395
+      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi",
+      "crc32c" : 2674622110
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0034_of_50/scattered.interval_list",
-      "crc32c" : 1997301122
+      "path" : "gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
+      "crc32c" : 728804713
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.contam.bed",
-      "crc32c" : 160303630
+      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
+      "crc32c" : 1637948248
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.targets.interval_list",
-      "crc32c" : 2223466122
+      "path" : "gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
+      "crc32c" : 2003730493
     }, {
       "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac",
       "crc32c" : 299013300
     }, {
-      "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
-      "crc32c" : 159565724
-    }, {
-      "path" : "gcp-public-data--broad-references/hg19/v0/hapmap_3.3.b37.vcf.gz.tbi",
-      "crc32c" : 2429032567
-    }, {
-      "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.64.sa",
-      "crc32c" : 376202099
-    }, {
-      "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.bfa",
-      "crc32c" : 3973369900
-    }, {
-      "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.1kg_pilot_indels.vcf.idx",
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-      "crc32c" : 4214876679
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/References/Homo_sapiens.GRCh38.Nirvana.dat",
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-      "crc32c" : 3830060763
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.sift.ndb",
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03850.split.txt.gz",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20220512.nsi",
+      "crc32c" : 3787486272
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa",
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-      "crc32c" : 3924662460
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsa",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa.idx",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_SV_2.1.nsi",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_disease_validity_curations_20220512.nga",
+      "crc32c" : 4116422668
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/OMIM_20220516.nga",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa",
+      "crc32c" : 710316739
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-      "crc32c" : 373531354
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/GME_20160618.nsa.idx",
+      "crc32c" : 1732177354
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-      "crc32c" : 1320364908
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa.idx",
+      "crc32c" : 245207854
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-      "crc32c" : 462909423
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa",
+      "crc32c" : 4136875677
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-134.tar.gz",
-      "crc32c" : 1188579016
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsi",
+      "crc32c" : 1056818502
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-43.tar.gz",
-      "crc32c" : 2098432647
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/GME_20160618.nsa",
+      "crc32c" : 1210977352
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-47.tar.gz",
-      "crc32c" : 1722109761
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa.idx",
+      "crc32c" : 870728029
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-28.tar.gz",
-      "crc32c" : 3161256248
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_LCR_2.1.lcr",
+      "crc32c" : 3602069872
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-197.tar.gz",
-      "crc32c" : 852592090
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa.idx",
+      "crc32c" : 2835194789
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-140.tar.gz",
-      "crc32c" : 4051126385
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20220512.nga",
+      "crc32c" : 2485206803
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-121.tar.gz",
-      "crc32c" : 623697692
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_SV_20200819.nsi",
+      "crc32c" : 1378887803
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-182.tar.gz",
-      "crc32c" : 2255237725
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa.idx",
+      "crc32c" : 302652747
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-273.tar.gz",
-      "crc32c" : 2368431717
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_20160414.nsi",
+      "crc32c" : 1181611304
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-269.tar.gz",
-      "crc32c" : 3912509849
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa.idx",
+      "crc32c" : 980438557
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-4.tar.gz",
-      "crc32c" : 1832890207
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DECIPHER_201509.nsi",
+      "crc32c" : 2426309371
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-194.tar.gz",
-      "crc32c" : 2371872678
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa",
+      "crc32c" : 3457097933
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-232.tar.gz",
-      "crc32c" : 645276377
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_3.1.2.nsa.idx",
+      "crc32c" : 3582543830
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-81.tar.gz",
-      "crc32c" : 615405862
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/COSMIC_GeneFusions_94.gfj",
+      "crc32c" : 429830169
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-61.tar.gz",
-      "crc32c" : 3254549888
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa.idx",
+      "crc32c" : 37093822
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-256.tar.gz",
-      "crc32c" : 2225664241
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/FusionCatcher_1.33.gfs",
+      "crc32c" : 1420426876
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/genomestrip/Homo_sapiens_assembly38.vdjregions.bed",
-      "crc32c" : 665778154
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi",
+      "crc32c" : 2492681982
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/genomestrip/Homo_sapiens_assembly38.gcprof.zip",
-      "crc32c" : 954030109
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx",
+      "crc32c" : 2375984948
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0008_of_50/scattered.interval_list",
-      "crc32c" : 2145467013
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsa.idx",
+      "crc32c" : 1539516090
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0038_of_50/scattered.interval_list",
-      "crc32c" : 1218417681
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma",
+      "crc32c" : 1696693985
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0019_of_50/scattered.interval_list",
-      "crc32c" : 2638902162
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa.idx",
+      "crc32c" : 3139541733
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0047_of_50/scattered.interval_list",
-      "crc32c" : 1761876709
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa",
+      "crc32c" : 1721491427
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/CrossSpeciesContamination/CrossSpeciesContaminant/pathseq_microbe.fa.img",
-      "crc32c" : 2373170979
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_3.1.2.nsa",
+      "crc32c" : 4247114985
     } ]
   }
 ]

From 3841619bfe413cc79ff2300f56a14d1bba009da0 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 18 Jan 2023 16:06:19 -0500
Subject: [PATCH 122/326] WX-863 Turn off Azure NIO logging (#6982)

* Turn off Azure NIO logging

* Poke Travis
---
 server/src/main/resources/logback.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/server/src/main/resources/logback.xml b/server/src/main/resources/logback.xml
index b4d4ac4a335..006ca3953f4 100644
--- a/server/src/main/resources/logback.xml
+++ b/server/src/main/resources/logback.xml
@@ -106,4 +106,7 @@
     <logger name="HikariPool" level="ERROR"/>
     <logger name="com.google.cloud.hadoop.gcsio.GoogleCloudStorageReadChannel" level="ERROR"/>
     <logger name="org.semanticweb.owlapi.utilities.Injector" level="ERROR"/>
+
+    <!-- Guilty of logging ERROR under non-erroneous conditions -->
+    <logger name="com.azure.storage.blob.nio" level="OFF"/>
 </configuration>

From 276ecb1e3c9488c79ca0e751632ee9199760b08b Mon Sep 17 00:00:00 2001
From: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Date: Thu, 19 Jan 2023 14:45:25 -0500
Subject: [PATCH 123/326] WM-1616: Allow repeating attempts at initialization
 (take 2) (#6985)

---
 .../engine/workflow/WorkflowActor.scala       | 139 +++++++++++-------
 .../engine/workflow/WorkflowActorSpec.scala   | 108 ++++++++++++--
 2 files changed, 188 insertions(+), 59 deletions(-)

diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
index ba82bab3e96..b4ccf3de53b 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
@@ -135,6 +135,12 @@ object WorkflowActor {
 
   case class StateCheckpoint(state: WorkflowActorState, failures: Option[List[Throwable]] = None)
 
+  /**
+    * Message sent from WorkflowActor to itself to trigger the initialization to start. Allows us to idle
+    * in the initializing state without an assigned actor for a few seconds if the first attempt fails.
+    */
+  case object StartInitializing
+
   /**
     * @param currentLifecycleStateActor The current lifecycle stage, represented by an ActorRef.
     */
@@ -145,7 +151,8 @@ object WorkflowActor {
                                effectiveStartableState: StartableState,
                                workflowFinalOutputs: Set[WomValue] = Set.empty,
                                workflowAllOutputs: Set[WomValue] = Set.empty,
-                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty)
+                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty,
+                               failedInitializationAttempts: Int = 0)
   object WorkflowActorData {
     def apply(startableState: StartableState): WorkflowActorData = WorkflowActorData(
       currentLifecycleStateActor = None,
@@ -255,6 +262,9 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
 
   protected val pathBuilderFactories: List[PathBuilderFactory] = EngineFilesystems.configuredPathBuilderFactories
 
+  protected val maxInitializationAttempts: Int = 16
+  protected val initializationRetryInterval: FiniteDuration = 1.minute
+
   startWith(WorkflowUnstartedState, WorkflowActorData(initialStartableState))
 
   pushCurrentStateToMetadataService(workflowId, WorkflowUnstartedState.workflowState)
@@ -299,18 +309,8 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
 
   when(MaterializingWorkflowDescriptorState) {
     case Event(MaterializeWorkflowDescriptorSuccessResponse(workflowDescriptor), data) =>
-      val initializerActor = context.actorOf(
-        WorkflowInitializationActor.props(
-          workflowIdForLogging,
-          rootWorkflowIdForLogging,
-          workflowDescriptor,
-          ioActor,
-          serviceRegistryActor,
-          restarting
-        ),
-        name = s"WorkflowInitializationActor-$workflowId")
-      initializerActor ! StartInitializationCommand
-      goto(InitializingWorkflowState) using data.copy(currentLifecycleStateActor = Option(initializerActor), workflowDescriptor = Option(workflowDescriptor))
+      self ! StartInitializing
+      goto(InitializingWorkflowState) using data.copy(workflowDescriptor = Option(workflowDescriptor))
     case Event(MaterializeWorkflowDescriptorFailureResponse(reason: Throwable), data) =>
       goto(WorkflowFailedState) using data.copy(lastStateReached = StateCheckpoint(MaterializingWorkflowDescriptorState, Option(List(reason))))
     // If the workflow is not being restarted then we can abort it immediately as nothing happened yet
@@ -320,40 +320,45 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   /* ************************** */
   /* ****** Initializing ****** */
   /* ************************** */
-
-  when(InitializingWorkflowState) {
-    case Event(WorkflowInitializationSucceededResponse(initializationData), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
-      val executionActor = context.actorOf(WorkflowExecutionActor.props(
+  protected def createInitializationActor(workflowDescriptor: EngineWorkflowDescriptor, name: String): ActorRef = {
+    context.actorOf(
+      WorkflowInitializationActor.props(
+        workflowIdForLogging,
+        rootWorkflowIdForLogging,
         workflowDescriptor,
-        ioActor = ioActor,
-        serviceRegistryActor = serviceRegistryActor,
-        jobStoreActor = jobStoreActor,
-        subWorkflowStoreActor = subWorkflowStoreActor,
-        callCacheReadActor = callCacheReadActor,
-        callCacheWriteActor = callCacheWriteActor,
-        workflowDockerLookupActor = workflowDockerLookupActor,
-        jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
-        jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
-        backendSingletonCollection,
-        initializationData,
-        startState = data.effectiveStartableState,
-        rootConfig = conf,
-        totalJobsByRootWf = totalJobsByRootWf,
-        fileHashCacheActor = fileHashCacheActorProps map context.system.actorOf,
-        blacklistCache = blacklistCache), name = s"WorkflowExecutionActor-$workflowId")
+        ioActor,
+        serviceRegistryActor,
+        restarting
+      ),
+      name)
+  }
 
+  when(InitializingWorkflowState) {
+    case Event(StartInitializing, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+      val initializerActor = createInitializationActor(workflowDescriptor, s"WorkflowInitializationActor-$workflowId-${data.failedInitializationAttempts + 1}")
+      initializerActor ! StartInitializationCommand
+      goto(InitializingWorkflowState) using data.copy(currentLifecycleStateActor = Option(initializerActor), workflowDescriptor = Option(workflowDescriptor))
+    case Event(WorkflowInitializationSucceededResponse(initializationData), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+      val dataWithInitializationData = data.copy(initializationData = initializationData)
+      val executionActor = createWorkflowExecutionActor(workflowDescriptor, dataWithInitializationData)
       executionActor ! ExecuteWorkflowCommand
-
       val nextState = data.effectiveStartableState match {
         case RestartableAborting => WorkflowAbortingState
         case _ => ExecutingWorkflowState
       }
-      goto(nextState) using data.copy(currentLifecycleStateActor = Option(executionActor), initializationData = initializationData)
-    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
-      finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
+      goto(nextState) using dataWithInitializationData.copy(currentLifecycleStateActor = Option(executionActor))
+    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+      val failedInitializationAttempts = data.failedInitializationAttempts + 1
+      if (failedInitializationAttempts < maxInitializationAttempts) {
+        workflowLogger.info(s"Initialization failed on attempt $failedInitializationAttempts. Will retry up to $maxInitializationAttempts times. Next retry is in $initializationRetryInterval", CromwellAggregatedException(reason, "Initialization Failure"))
+        context.system.scheduler.scheduleOnce(initializationRetryInterval) { self ! StartInitializing}
+        stay() using data.copy(currentLifecycleStateActor = None, failedInitializationAttempts = failedInitializationAttempts)
+      } else {
+        finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
+      }
 
     // If the workflow is not restarting, handle the Abort command normally and send an abort message to the init actor
-    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) if !restarting =>
+    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) if !restarting =>
       handleAbortCommand(data, workflowDescriptor)
   }
 
@@ -361,24 +366,45 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   /* ****** Running ****** */
   /* ********************* */
 
+  def createWorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor, data: WorkflowActorData): ActorRef = {
+    context.actorOf(WorkflowExecutionActor.props(
+      workflowDescriptor,
+      ioActor = ioActor,
+      serviceRegistryActor = serviceRegistryActor,
+      jobStoreActor = jobStoreActor,
+      subWorkflowStoreActor = subWorkflowStoreActor,
+      callCacheReadActor = callCacheReadActor,
+      callCacheWriteActor = callCacheWriteActor,
+      workflowDockerLookupActor = workflowDockerLookupActor,
+      jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
+      jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
+      backendSingletonCollection,
+      data.initializationData,
+      startState = data.effectiveStartableState,
+      rootConfig = conf,
+      totalJobsByRootWf = totalJobsByRootWf,
+      fileHashCacheActor = fileHashCacheActorProps map context.system.actorOf,
+      blacklistCache = blacklistCache), name = s"WorkflowExecutionActor-$workflowId")
+  }
+
   // Handles workflow completion events from the WEA and abort command
   val executionResponseHandler: StateFunction = {
     // Workflow responses
     case Event(WorkflowExecutionSucceededResponse(jobKeys, rootAndSubworklowIds, finalOutputs, allOutputs),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, finalOutputs, None, allOutputs, rootAndSubworklowIds)
     case Event(WorkflowExecutionFailedResponse(jobKeys, failures),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, CallOutputs.empty, Option(List(failures)))
     case Event(WorkflowExecutionAbortedResponse(jobKeys),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, StateCheckpoint(_, failures), _, _, _, _)) =>
+    data @ WorkflowActorData(_, Some(workflowDescriptor), _, StateCheckpoint(_, failures), _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, CallOutputs.empty, failures)
 
     // Whether we're running or aborting, restarting or not, pass along the abort command.
     // Note that aborting a workflow multiple times will result in as many abort commands sent to the execution actor
-    case Event(AbortWorkflowWithExceptionCommand(ex), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(AbortWorkflowWithExceptionCommand(ex), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       handleAbortCommand(data, workflowDescriptor, Option(ex))
-    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       handleAbortCommand(data, workflowDescriptor)
   }
 
@@ -391,12 +417,16 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   // Handles initialization responses we can get if the abort came in when we were initializing the workflow
   val abortHandler: StateFunction = {
     // If the initialization failed, record the failure in the data and finalize the workflow
-    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
 
     // Otherwise (success or abort), finalize the workflow without failures
-    case Event(_: WorkflowInitializationResponse, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(_: WorkflowInitializationResponse, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, failures = None)
+
+    case Event(StartInitializing, _) =>
+      // An initialization trigger we no longer need to action. Ignore:
+      stay()
   }
 
   // In aborting state, we can receive initialization responses or execution responses.
@@ -413,6 +443,9 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
       val failures = data.lastStateReached.failures.getOrElse(List.empty) ++ finalizationFailures
       goto(WorkflowFailedState) using data.copy(lastStateReached = StateCheckpoint(FinalizingWorkflowState, Option(failures)))
     case Event(AbortWorkflowCommand, _) => stay()
+    case Event(StartInitializing, _) =>
+      // An initialization trigger we no longer need to action. Ignore:
+      stay()
   }
 
   when(MetadataIntegrityValidationState) {
@@ -431,13 +464,18 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   }
 
   def handleAbortCommand(data: WorkflowActorData, workflowDescriptor: EngineWorkflowDescriptor, exceptionCausedAbortOpt: Option[Throwable] = None) = {
+    val updatedData = data.copy(lastStateReached = StateCheckpoint(stateName, exceptionCausedAbortOpt.map(List(_))))
     data.currentLifecycleStateActor match {
       case Some(currentActor) =>
         currentActor ! EngineLifecycleActorAbortCommand
-        goto(WorkflowAbortingState) using data.copy(lastStateReached = StateCheckpoint(stateName, exceptionCausedAbortOpt.map(List(_))))
+        goto(WorkflowAbortingState) using updatedData
       case None =>
-        workflowLogger.warn(s"Received an abort command in state $stateName but there's no lifecycle actor associated. This is an abnormal state, finalizing the workflow anyway.")
-        finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, None)
+        if (stateName == InitializingWorkflowState) {
+          workflowLogger.info(s"Received an abort command in state $stateName (while awaiting an initialization retry). Finalizing the workflow.")
+        } else {
+          workflowLogger.warn(s"Received an abort command in state $stateName but there's no lifecycle actor associated. This is an abnormal state, finalizing the workflow anyway.")
+        }
+        finalizeWorkflow(updatedData, workflowDescriptor, Map.empty, CallOutputs.empty, failures = None, lastStateOverride = Option(WorkflowAbortingState))
     }
   }
 
@@ -645,11 +683,12 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
                                workflowFinalOutputs: CallOutputs,
                                failures: Option[List[Throwable]],
                                workflowAllOutputs: Set[WomValue] = Set.empty,
-                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty) = {
+                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty,
+                               lastStateOverride: Option[WorkflowActorState] = None) = {
     val finalizationActor = makeFinalizationActor(workflowDescriptor, jobExecutionMap, workflowFinalOutputs)
     finalizationActor ! StartFinalizationCommand
     goto(FinalizingWorkflowState) using data.copy(
-      lastStateReached = StateCheckpoint (stateName, failures),
+      lastStateReached = StateCheckpoint (lastStateOverride.getOrElse(stateName), failures),
       workflowFinalOutputs = workflowFinalOutputs.outputs.values.toSet,
       workflowAllOutputs = workflowAllOutputs,
       rootAndSubworkflowIds = rootAndSubworkflowIds
diff --git a/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala b/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
index ab47dedeb5c..d9de71b9125 100644
--- a/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
@@ -2,7 +2,6 @@ package cromwell.engine.workflow
 
 import java.time.OffsetDateTime
 import java.util.concurrent.atomic.AtomicInteger
-
 import akka.actor.{Actor, ActorRef, ActorSystem, Kill, Props}
 import akka.testkit.{EventFilter, TestActorRef, TestFSMRef, TestProbe}
 import com.typesafe.config.{Config, ConfigFactory}
@@ -15,10 +14,10 @@ import cromwell.engine.backend.BackendSingletonCollection
 import cromwell.engine.workflow.WorkflowActor._
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowActorWorkComplete
 import cromwell.engine.workflow.lifecycle.EngineLifecycleActorAbortCommand
-import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{WorkflowExecutionAbortedResponse, WorkflowExecutionFailedResponse, WorkflowExecutionSucceededResponse}
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{ExecuteWorkflowCommand, WorkflowExecutionAbortedResponse, WorkflowExecutionFailedResponse, WorkflowExecutionSucceededResponse}
 import cromwell.engine.workflow.lifecycle.finalization.CopyWorkflowLogsActor
 import cromwell.engine.workflow.lifecycle.finalization.WorkflowFinalizationActor.{StartFinalizationCommand, WorkflowFinalizationSucceededResponse}
-import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{WorkflowInitializationAbortedResponse, WorkflowInitializationFailedResponse}
+import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{StartInitializationCommand, WorkflowInitializationAbortedResponse, WorkflowInitializationFailedResponse, WorkflowInitializationSucceededResponse}
 import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.MaterializeWorkflowDescriptorFailureResponse
 import cromwell.engine.workflow.workflowstore.{StartableState, Submitted, WorkflowHeartbeatConfig, WorkflowToStart}
 import cromwell.engine.{EngineFilesystems, EngineWorkflowDescriptor}
@@ -60,6 +59,8 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
     createMaterializedEngineWorkflowDescriptor(WorkflowId.randomId(), workflowSources = workflowSources)
   val supervisorProbe: TestProbe = TestProbe("supervisorProbe")
   val deathwatch: TestProbe = TestProbe("deathwatch")
+  val initializationProbe: TestProbe = TestProbe("initializationProbe")
+  val executionProbe: TestProbe = TestProbe("executionProbe")
   val finalizationProbe: TestProbe = TestProbe("finalizationProbe")
   var copyWorkflowLogsProbe: TestProbe = _
   val AwaitAlmostNothing: FiniteDuration = 100.milliseconds
@@ -78,7 +79,7 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 
   private val workflowHeartbeatConfig = WorkflowHeartbeatConfig(ConfigFactory.load())
 
-  private def createWorkflowActor(state: WorkflowActorState, extraPathBuilderFactory: Option[PathBuilderFactory] = None) = {
+  private def createWorkflowActor(state: WorkflowActorState, extraPathBuilderFactory: Option[PathBuilderFactory] = None, initializationMaxRetries: Int = 3, initializationInterval: FiniteDuration = 10.millis) = {
     val actor = TestFSMRef(
       factory = new WorkflowActorWithTestAddons(
         finalizationProbe = finalizationProbe,
@@ -102,7 +103,11 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
         workflowStoreActor = system.actorOf(Props.empty, s"workflowStoreActor-$currentWorkflowId"),
         workflowHeartbeatConfig = workflowHeartbeatConfig,
         totalJobsByRootWf = initialJobCtByRootWf,
-        extraPathBuilderFactory = extraPathBuilderFactory
+        extraPathBuilderFactory = extraPathBuilderFactory,
+        initializationMaxRetries = initializationMaxRetries,
+        initializationInterval = initializationInterval,
+        workflowInitializationActorProbe = initializationProbe,
+        workflowExecutionActorProbe = executionProbe
       ),
       supervisor = supervisorProbe.ref,
       name = s"workflowActor-$currentWorkflowId",
@@ -124,10 +129,17 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 
   "WorkflowActor" should {
 
-    "run Finalization actor if Initialization fails" in {
-      val actor = createWorkflowActor(InitializingWorkflowState)
+    "run Finalization actor if Initialization repeatedly fails" in {
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationMaxRetries = 3)
       deathwatch watch actor
-      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Materialization Failed")))
+
+      // Expect the WorkflowActor to retry up to three times:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (2)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (3)")))
+
       finalizationProbe.expectMsg(StartFinalizationCommand)
       actor.stateName should be(FinalizingWorkflowState)
       actor ! WorkflowFinalizationSucceededResponse
@@ -136,6 +148,24 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       deathwatch.expectTerminated(actor)
     }
 
+    "begin execution if Initialization eventually succeeds" in {
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationMaxRetries = 3)
+      deathwatch watch actor
+
+      // Expect the WorkflowActor to retry up to three times:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (2)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationSucceededResponse(AllBackendInitializationData(Map.empty))
+
+      executionProbe.expectMsg(ExecuteWorkflowCommand)
+      actor.stateName should be(ExecutingWorkflowState)
+      // Tidy up (and satisfy the deathwatch):
+      system.stop(actor)
+      deathwatch.expectTerminated(actor)
+    }
+
     "run Finalization actor if Initialization is aborted" in {
       val actor = createWorkflowActor(InitializingWorkflowState)
       deathwatch watch actor
@@ -151,6 +181,56 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       deathwatch.expectTerminated(actor)
     }
 
+    "run Finalization actor if Initialization is aborted during a retry" in {
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationInterval = 1.second)
+      deathwatch watch actor
+
+      // Set the stage with a few unfortunate retries:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (2)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+
+      actor ! AbortWorkflowCommand
+      eventually { actor.stateName should be(WorkflowAbortingState) }
+      // Because we failed a few times, the actor test's initial "currentLifecycleActor will have been replaced by this
+      // new initializationProbe:
+      initializationProbe.expectMsgPF(TimeoutDuration) {
+        case EngineLifecycleActorAbortCommand => actor ! WorkflowInitializationAbortedResponse
+      }
+
+      finalizationProbe.expectMsg(StartFinalizationCommand)
+      actor.stateName should be(FinalizingWorkflowState)
+      actor ! WorkflowFinalizationSucceededResponse
+      workflowManagerActorExpectsSingleWorkCompleteNotification(WorkflowAborted)
+      deathwatch.expectTerminated(actor)
+    }
+
+    "run Finalization actor if Initialization is aborted between retries" in {
+      // Set the interval long so that we can guarantee the "between retries" part
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationInterval = 10.seconds)
+      deathwatch watch actor
+
+      // Set the stage with a few unfortunate retries:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      eventually { actor.stateData.currentLifecycleStateActor should be(None) }
+
+      actor ! AbortWorkflowCommand
+      // Because there are no active lifecycle actors, this actor should jump to Finalizing without
+      // needing any further input:
+      eventually { actor.stateName should be(FinalizingWorkflowState) }
+
+      // Expect the mailboxes for the initialization actor to be empty (and check "currentLifecycleActor" for good measure)
+      currentLifecycleActor.expectNoMessage(10.millis)
+      initializationProbe.expectNoMessage(10.millis)
+
+      finalizationProbe.expectMsg(StartFinalizationCommand)
+      actor.stateName should be(FinalizingWorkflowState)
+      actor ! WorkflowFinalizationSucceededResponse
+      workflowManagerActorExpectsSingleWorkCompleteNotification(WorkflowAborted)
+      deathwatch.expectTerminated(actor)
+    }
+
     "run Finalization if Execution fails" in {
       val actor = createWorkflowActor(ExecutingWorkflowState)
       deathwatch watch actor
@@ -283,7 +363,11 @@ class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
                                   workflowStoreActor: ActorRef,
                                   workflowHeartbeatConfig: WorkflowHeartbeatConfig,
                                   totalJobsByRootWf: AtomicInteger,
-                                  extraPathBuilderFactory: Option[PathBuilderFactory]) extends WorkflowActor(
+                                  extraPathBuilderFactory: Option[PathBuilderFactory],
+                                  initializationMaxRetries: Int,
+                                  initializationInterval: FiniteDuration,
+                                  workflowInitializationActorProbe: TestProbe,
+                                  workflowExecutionActorProbe: TestProbe) extends WorkflowActor(
   workflowToStart = WorkflowToStart(id = workflowId,
     submissionTime = OffsetDateTime.now,
     state = startState,
@@ -310,6 +394,12 @@ class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
   fileHashCacheActorProps = None,
   blacklistCache = None) {
 
+  override def createInitializationActor(workflowDescriptor: EngineWorkflowDescriptor, name: String): ActorRef = workflowInitializationActorProbe.ref
+  override def createWorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor, data: WorkflowActorData): ActorRef = workflowExecutionActorProbe.ref
+
+  override val initializationRetryInterval: FiniteDuration = initializationInterval
+  override val maxInitializationAttempts: Int = initializationMaxRetries
+
   override val pathBuilderFactories: List[PathBuilderFactory] = extraPathBuilderFactory match {
     case Some(pbf) => EngineFilesystems.configuredPathBuilderFactories :+ pbf
     case None => EngineFilesystems.configuredPathBuilderFactories

From 098d12baf5ce76e167d57b3eb05780002425ed1b Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Tue, 24 Jan 2023 12:13:42 -0500
Subject: [PATCH 124/326] WX-878 Single shared BlobFileSystemManager (#6986)

* Make BlobFileSystemManager shared across all BlobPathBuilders

* Update TES conf file to reflect new singleton config
---
 .../blob/BlobFileSystemManager.scala          | 69 ++++++++++++++++---
 .../blob/BlobPathBuilderFactory.scala         | 34 +--------
 .../blob/BlobPathBuilderFactorySpec.scala     |  8 +--
 .../blob/BlobPathBuilderSpec.scala            |  6 +-
 src/ci/resources/tes_application.conf         |  3 +-
 5 files changed, 72 insertions(+), 48 deletions(-)

diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index a184729c38b..7b198f09f6f 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -10,6 +10,7 @@ import com.azure.storage.blob.nio.AzureFileSystem
 import com.azure.storage.blob.sas.{BlobContainerSasPermission, BlobServiceSasSignatureValues}
 import com.azure.storage.blob.{BlobContainerClient, BlobContainerClientBuilder}
 import com.azure.storage.common.StorageSharedKeyCredential
+import com.typesafe.config.Config
 import com.typesafe.scalalogging.LazyLogging
 import common.validation.Validation._
 
@@ -20,6 +21,8 @@ import java.time.{Duration, Instant, OffsetDateTime}
 import scala.jdk.CollectionConverters._
 import scala.util.{Failure, Success, Try}
 
+// We encapsulate this functionality here so that we can easily mock it out, to allow for testing without
+// actually connecting to Blob storage.
 case class FileSystemAPI() {
   def getFileSystem(uri: URI): Try[FileSystem] = Try(FileSystems.getFileSystem(uri))
   def newFileSystem(uri: URI, config: Map[String, Object]): FileSystem = FileSystems.newFileSystem(uri, config.asJava)
@@ -45,15 +48,27 @@ object BlobFileSystemManager {
   def hasTokenExpired(tokenExpiry: Instant, buffer: Duration): Boolean = Instant.now.plus(buffer).isAfter(tokenExpiry)
   def uri(endpoint: EndpointURL) = new URI("azb://?endpoint=" + endpoint)
 }
-case class BlobFileSystemManager(
-    container: BlobContainerName,
-    endpoint: EndpointURL,
-    expiryBufferMinutes: Long,
-    blobTokenGenerator: BlobSasTokenGenerator,
-    fileSystemAPI: FileSystemAPI = FileSystemAPI(),
-    private val initialExpiration: Option[Instant] = None) extends LazyLogging {
-  private var expiry: Option[Instant] = initialExpiration
+
+class BlobFileSystemManager(val container: BlobContainerName,
+                            val endpoint: EndpointURL,
+                            val expiryBufferMinutes: Long,
+                            val blobTokenGenerator: BlobSasTokenGenerator,
+                            val fileSystemAPI: FileSystemAPI = FileSystemAPI(),
+                            private val initialExpiration: Option[Instant] = None) extends LazyLogging {
+
+  def this(config: BlobFileSystemConfig) = {
+    this(
+      config.blobContainerName,
+      config.endpointURL,
+      config.expiryBufferMinutes,
+      BlobSasTokenGenerator.createBlobTokenGeneratorFromConfig(config)
+    )
+  }
+
+  def this(rawConfig: Config) = this(BlobFileSystemConfig(rawConfig))
+
   val buffer: Duration = Duration.of(expiryBufferMinutes, ChronoUnit.MINUTES)
+  private var expiry: Option[Instant] = initialExpiration
 
   def getExpiry: Option[Instant] = expiry
   def uri: URI = BlobFileSystemManager.uri(endpoint)
@@ -87,6 +102,44 @@ case class BlobFileSystemManager(
 
 sealed trait BlobSasTokenGenerator { def generateBlobSasToken: Try[AzureSasCredential] }
 object BlobSasTokenGenerator {
+
+  /**
+    * Creates the correct BlobSasTokenGenerator based on config inputs. This generator is responsible for producing
+    * a valid SAS token for use in accessing a Azure blob storage container.
+    * Two types of generators can be produced here:
+    * > Workspace Manager (WSM) mediated SAS token generator, used to create SAS tokens that allow access for
+    * blob containers mediated by the WSM, and is enabled when a WSM config is provided. This is what is intended
+    * for use inside Terra
+    *    OR
+    * > Native SAS token generator, which obtains a valid SAS token from your local environment to reach blob containers
+    * your local azure identity has access to and is the default if a WSM config is not found. This is intended for
+    * use outside of Terra
+    *
+    * Both of these generators require an authentication token to authorize the generation of the SAS token.
+    * See BlobSasTokenGenerator for more information on how these generators work.
+    *
+    * @param config A BlobFileSystemConfig object
+    * @return An appropriate BlobSasTokenGenerator
+    */
+  def createBlobTokenGeneratorFromConfig(config: BlobFileSystemConfig): BlobSasTokenGenerator =
+    config.workspaceManagerConfig.map { wsmConfig =>
+      val wsmClient: WorkspaceManagerApiClientProvider = new HttpWorkspaceManagerClientProvider(wsmConfig.url)
+
+      // WSM-mediated mediated SAS token generator
+      // parameterizing client instead of URL to make injecting mock client possible
+      BlobSasTokenGenerator.createBlobTokenGenerator(
+        config.blobContainerName,
+        config.endpointURL,
+        wsmConfig.workspaceId,
+        wsmConfig.containerResourceId,
+        wsmClient,
+        wsmConfig.overrideWsmAuthToken
+      )
+    }.getOrElse(
+      // Native SAS token generator
+      BlobSasTokenGenerator.createBlobTokenGenerator(config.blobContainerName, config.endpointURL, config.subscriptionId)
+    )
+
   /**
     * Native SAS token generator, uses the DefaultAzureCredentialBuilder in the local environment
     * to produce a SAS token.
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index 6e8f84eb0d4..c263841dc8a 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -17,41 +17,11 @@ final case class WorkspaceId(value: UUID) {override def toString: String = value
 final case class ContainerResourceId(value: UUID) {override def toString: String = value.toString}
 final case class WorkspaceManagerURL(value: String) {override def toString: String = value}
 
-final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, singletonConfig: BlobFileSystemConfigWrapper) extends PathBuilderFactory {
-
-  private val config = singletonConfig.config
-  private val container = config.blobContainerName
-  private val endpoint = config.endpointURL
-  private val subscription = config.subscriptionId
-  private val expiryBufferMinutes = config.expiryBufferMinutes
-
-  /**
-   * This generator is responsible for producing a valid SAS token for use in accessing a Azure blob storage container
-   * Two types of generators can be produced here:
-   * > Workspace Manager (WSM) mediated SAS token generator, used to create SAS tokens that allow access for
-   * blob containers mediated by the WSM, and is enabled when a WSM config is provided. This is what is intended for use inside Terra
-   *    OR
-   * > Native SAS token generator, which obtains a valid SAS token from your local environment to reach blob containers
-   * your local azure identity has access to and is the default if a WSM config is not found. This is intended for use outside of Terra
-   *
-   * Both of these generators require an authentication token to authorize the generation of the SAS token.
-   * See BlobSasTokenGenerator for more information on how these generators work.
-   */
-  val blobSasTokenGenerator: BlobSasTokenGenerator = config.workspaceManagerConfig.map { wsmConfig =>
-    val wsmClient: WorkspaceManagerApiClientProvider = new HttpWorkspaceManagerClientProvider(wsmConfig.url)
-    // WSM-mediated mediated SAS token generator
-    // parameterizing client instead of URL to make injecting mock client possible
-    BlobSasTokenGenerator.createBlobTokenGenerator(container, endpoint, wsmConfig.workspaceId, wsmConfig.containerResourceId, wsmClient, wsmConfig.overrideWsmAuthToken)
-  }.getOrElse(
-    // Native SAS token generator
-    BlobSasTokenGenerator.createBlobTokenGenerator(container, endpoint, subscription)
-  )
-
-  val fsm: BlobFileSystemManager = BlobFileSystemManager(container, endpoint, expiryBufferMinutes, blobSasTokenGenerator)
+final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, fsm: BlobFileSystemManager) extends PathBuilderFactory {
 
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[BlobPathBuilder] = {
     Future {
-      new BlobPathBuilder(container, endpoint)(fsm)
+      new BlobPathBuilder(fsm.container, fsm.endpoint)(fsm)
     }
   }
 
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
index 6bf00d66915..881cd3669a1 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
@@ -74,7 +74,7 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val blobTokenGenerator = mock[BlobSasTokenGenerator]
     when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
 
-    val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(expiredToken))
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(expiredToken))
     fsm.getExpiry should contain(expiredToken)
     fsm.isTokenExpired shouldBe true
     fsm.retrieveFilesystem()
@@ -103,7 +103,7 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val blobTokenGenerator = mock[BlobSasTokenGenerator]
     when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
 
-    val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(initialToken))
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(initialToken))
     fsm.getExpiry should contain(initialToken)
     fsm.isTokenExpired shouldBe false
     fsm.retrieveFilesystem()
@@ -128,7 +128,7 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val blobTokenGenerator = mock[BlobSasTokenGenerator]
     when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
 
-    val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(refreshedToken))
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(refreshedToken))
     fsm.getExpiry.isDefined shouldBe true
     fsm.isTokenExpired shouldBe false
     fsm.retrieveFilesystem()
@@ -152,7 +152,7 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val blobTokenGenerator = mock[BlobSasTokenGenerator]
     when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
 
-    val fsm = BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems)
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems)
     fsm.getExpiry.isDefined shouldBe false
     fsm.isTokenExpired shouldBe false
     fsm.retrieveFilesystem()
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index b20e2e2fe96..2aa9b2b43aa 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -63,7 +63,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
     val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
-    val fsm: BlobFileSystemManager = BlobFileSystemManager(store, endpoint, 10L, blobTokenGenerator)
+    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10L, blobTokenGenerator)
     val testString = endpoint.value + "/" + store + evalPath
     val blobPath: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
 
@@ -81,7 +81,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
     val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
-    val fsm: BlobFileSystemManager = BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
+    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
     val testString = endpoint.value + "/" + store + evalPath
     val blobPath1: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
     blobPath1.nioPath.getFileSystem.close()
@@ -96,7 +96,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
     val store = BlobContainerName("inputs")
     val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
-    val fsm: BlobFileSystemManager = BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
+    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
 
     val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
     val blobRoot: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build rootString getOrElse fail()
diff --git a/src/ci/resources/tes_application.conf b/src/ci/resources/tes_application.conf
index 9914bd54dff..7f4c42a7d58 100644
--- a/src/ci/resources/tes_application.conf
+++ b/src/ci/resources/tes_application.conf
@@ -5,7 +5,8 @@ filesystems {
   blob {
     class = "cromwell.filesystems.blob.BlobPathBuilderFactory"
     global {
-      class = "cromwell.filesystems.blob.BlobFileSystemConfigWrapper"
+      # One BFSM is shared across all BlobPathBuilders
+      class = "cromwell.filesystems.blob.BlobFileSystemManager"
       config {
         container: "cromwell"
         endpoint: "https://<storage-account>.blob.core.windows.net"

From 32d747dd5002b58302f1bc7cc7ca6e7e7ecaf0b6 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@users.noreply.github.com>
Date: Tue, 24 Jan 2023 17:41:58 -0500
Subject: [PATCH 125/326] Shell escape reference image  files [VS-796] [WX-910]
 (#6989)

---
 .../reference_disk/reference_disk_test.inputs         |  3 ++-
 .../reference_disk/reference_disk_test.wdl            | 11 ++++++++++-
 .../PipelinesApiAsyncBackendJobExecutionActor.scala   |  3 ++-
 .../PipelinesApiAsyncBackendJobExecutionActor.scala   |  3 ++-
 4 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
index f23615ee7f0..4caf94c0f77 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
@@ -1,4 +1,5 @@
 {
   "wf_reference_disk_test.broad_reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
-  "wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx"
+  "wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
+  "wf_reference_disk_test.nirvana_reference_file_metachar_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi"
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
index 4d469cbe552..fe01ae34d06 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
@@ -4,17 +4,23 @@ task check_if_localized_as_symlink {
   input {
     File broad_reference_file_input
     File nirvana_reference_file_input
+    File nirvana_reference_file_metachar_input
   }
   String broad_input_symlink = "broad_input_symlink.txt"
   String nirvana_input_symlink = "nirvana_input_symlink.txt"
+  String nirvana_metachar_input_symlink = "nirvana_metachar_input_symlink.txt"
   command {
     # Print true if input is a symlink, otherwise print false.
     if test -h ~{broad_reference_file_input}; then echo true; else echo false; fi > ~{broad_input_symlink}
     if test -h ~{nirvana_reference_file_input}; then echo true; else echo false; fi > ~{nirvana_input_symlink}
+
+    # Quotes added here due to the metachar in the filename.
+    if test -h "~{nirvana_reference_file_metachar_input}"; then echo true; else echo false; fi > ~{nirvana_metachar_input_symlink}
   }
   output {
     Boolean is_broad_input_symlink = read_boolean("~{broad_input_symlink}")
     Boolean is_nirvana_input_symlink = read_boolean("~{nirvana_input_symlink}")
+    Boolean is_nirvana_metachar_input_symlink = read_boolean("~{nirvana_metachar_input_symlink}")
   }
   runtime {
     docker: "ubuntu:latest"
@@ -26,14 +32,17 @@ workflow wf_reference_disk_test {
   input {
     File broad_reference_file_input
     File nirvana_reference_file_input
+    File nirvana_reference_file_metachar_input
   }
   call check_if_localized_as_symlink {
     input:
       broad_reference_file_input = broad_reference_file_input,
-      nirvana_reference_file_input = nirvana_reference_file_input
+      nirvana_reference_file_input = nirvana_reference_file_input,
+      nirvana_reference_file_metachar_input = nirvana_reference_file_metachar_input
   }
   output {
     Boolean is_broad_input_file_a_symlink = check_if_localized_as_symlink.is_broad_input_symlink
     Boolean is_nirvana_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_input_symlink
+    Boolean is_nirvana_metachar_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_metachar_input_symlink
   }
 }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
index 2da04c65e92..481f7d6c5a8 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -179,11 +179,12 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
                                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
+    import cromwell.backend.google.pipelines.common.action.ActionUtils.shellEscaped
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
         referenceInputsToMountedPaths map {
           case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${input.containerPath.parent.pathAsString} && ln -s $absolutePathOnRefDisk ${input.containerPath.pathAsString}"
+            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }
 
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
index fb6c8d425f7..3c0f5ca63f9 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -192,11 +192,12 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
                                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
+    import cromwell.backend.google.pipelines.common.action.ActionUtils.shellEscaped
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
         referenceInputsToMountedPaths map {
           case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${input.containerPath.parent.pathAsString} && ln -s $absolutePathOnRefDisk ${input.containerPath.pathAsString}"
+            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }
 

From c01e3117c178dde09eecbad7c2af29aa563cc9a6 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 31 Jan 2023 10:52:15 -0500
Subject: [PATCH 126/326] WX-769 `disks` compatibility for TES backend (#6991)

---
 CHANGELOG.md                                  |  6 +++
 build.sbt                                     |  2 +
 docs/RuntimeAttributes.md                     | 45 ++++++++++++-----
 docs/backends/TES.md                          | 27 ++++++++---
 .../impl/tes/TesRuntimeAttributes.scala       | 46 +++++++++++++++++-
 .../impl/tes/TesRuntimeAttributesSpec.scala   | 48 +++++++++++++++++++
 6 files changed, 154 insertions(+), 20 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 408660d8953..a43c3b6e22d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -60,6 +60,12 @@ This release removes the `cwl` top-level artifact. Some nonfunctional references
 
 For more information, see the [Cromwell 79 release notes](https://github.com/broadinstitute/cromwell/releases/tag/79). 
 
+### TES backend supports `disks` attribute
+
+Cromwell now attempts to translate `disks` attributes [written for GCP](https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/#disks) into valid `disk` attributes for TES.
+
+For information on supported conversions, refer to the [TES documentation](https://cromwell.readthedocs.io/en/stable/backends/TES/).
+
 ## 84 Release Notes
 
 ### CromIAM enabled user checks
diff --git a/build.sbt b/build.sbt
index e2e0c490767..76f6f27e2c9 100644
--- a/build.sbt
+++ b/build.sbt
@@ -239,6 +239,8 @@ lazy val tesBackend = (project in backendRoot / "tes")
   .dependsOn(ftpFileSystem)
   .dependsOn(drsFileSystem)
   .dependsOn(azureBlobFileSystem)
+  // TES backend provides a compatibility layer to run WDLs with PAPI runtime attributes [WX-769]
+  .dependsOn(googlePipelinesCommon)
   .dependsOn(backend % "test->test")
   .dependsOn(common % "test->test")
 
diff --git a/docs/RuntimeAttributes.md b/docs/RuntimeAttributes.md
index ffac8a705d5..3924c1de3e4 100644
--- a/docs/RuntimeAttributes.md
+++ b/docs/RuntimeAttributes.md
@@ -30,18 +30,29 @@ workflow jes_workflow {
 
 Cromwell recognizes certain runtime attributes and has the ability to format these for some [Backends](/backends/Backends). See the table below for common attributes that apply to _most_ backends.
 
-| Runtime Attribute    | LOCAL |  Google Cloud  | AWS Batch |  HPC  |
-| -------------------- |:-----:|:-----:|:-----:|:------:|
-| [cpu](#cpu)                  |       |   x   |   x   |  `cpu`  |
-| [memory](#memory)                              |       |   x   |   x   |  `memory_mb` / `memory_gb`  |
-| [disks](#disks)                                |       |   x   |       |  *  |
-| [docker](#docker)                              |   x   |   x   |   x   |  `docker` (see below)  |
-| [maxRetries](#maxretries)                      |   x   |   x   |   x   | * |
-| [continueOnReturnCode](#continueonreturncode) |   x   |   x   |   x   | * |
-| [failOnStderr](#failonstderr)                  |   x   |   x   |   x   |  *  |
-
-
-> `*` The HPC [Shared Filesystem backend](/backends/HPC#shared-filesystem) (SFS) is fully configurable and any number of attributes can be exposed. Cromwell recognizes some of these attributes (`cpu`, `memory` and `docker`) and parses them into the attribute listed in the table which can be used within the HPC backend configuration.
+| Runtime Attribute                               | Local | Google Cloud | TES       | AWS Batch |            HPC            |
+|-------------------------------------------------|:-----:|:------------:|-----------|:---------:|:-------------------------:|
+| [`cpu`](#cpu)                                   |       |      ✅       |           |     ✅     |           `cpu`           |
+| [`memory`](#memory)                             |       |      ✅       |           |     ✅     | `memory_mb` / `memory_gb` |
+| [`disks`](#disks)                               |       |      ✅       | ⚠️ Note 1 | ⚠️ Note 2 |         ℹ️ Note 3         |
+| [`disk`](#disk)                                 |       |              | ✅         |           |                           |
+| [`docker`](#docker)                             |   ✅   |      ✅       |           |     ✅     |    `docker` ℹ️ Note 3     |
+| [`maxRetries`](#maxretries)                     |   ✅   |      ✅       |           |     ✅     |         ℹ️ Note 3         |
+| [`continueOnReturnCode`](#continueonreturncode) |   ✅   |      ✅       |           |     ✅     |         ℹ️ Note 3         |
+| [`failOnStderr`](#failonstderr)                 |   ✅   |      ✅       |           |     ✅     |         ℹ️ Note 3         |
+
+
+> **Note 1**
+> 
+> Partial support. See [TES documentation](/backends/TES) for details. 
+ 
+> **Note 2**
+>
+> Partial support. See [`disks`](#disks) for details.
+
+> **Note 3**
+> 
+> The HPC [Shared Filesystem backend](/backends/HPC#shared-filesystem) (SFS) is fully configurable and any number of attributes can be exposed. Cromwell recognizes some of these attributes (`cpu`, `memory` and `docker`) and parses them into the attribute listed in the table which can be used within the HPC backend configuration.
 
 
 ### Google Cloud Specific Attributes
@@ -206,6 +217,16 @@ runtime {
 }
 ```
 
+### `disk`
+
+Specific to the TES backend, sets the `disk_gb` resource.
+
+```
+runtime {
+  disk: "25 GB"
+}
+```
+
 ### `docker`
 
 When specified, Cromwell will run your task within the specified Docker image. 
diff --git a/docs/backends/TES.md b/docs/backends/TES.md
index e19917ec126..b90fa30bc3d 100644
--- a/docs/backends/TES.md
+++ b/docs/backends/TES.md
@@ -1,4 +1,4 @@
-**TES Backend**
+## TES Backend
 
 The TES backend submits jobs to a server that complies with the protocol described by the [GA4GH schema](https://github.com/ga4gh/task-execution-schemas).
 
@@ -19,7 +19,7 @@ echo $? > rc
 
 `<container_call_root>` would be equal to the runtime attribute `dockerWorkingDir`  or `/cromwell-executions/<workflow_uuid>/call-<call_name>/execution` if this attribute is not supplied.
 
-**Configuring**
+### Configuring
 
 Configuring the TES backend is straightforward; one must only provide the TES API endpoint for the service.
 
@@ -40,18 +40,18 @@ backend {
 }
 ```
 
-**Supported File Systems**  
+### Supported File Systems
 
 Currently this backend only works with files on a Local or Shared File System.
 
-**Docker**
+### Docker
 
 This backend supports the following optional [Runtime Attributes](../RuntimeAttributes) and [Workflow Options](../wf_options/Overview/) for working with Docker:
 
 * `docker`: Docker image to use such as "Ubuntu".
 * `dockerWorkingDir`: defines the working directory in the container.
 
-**CPU, Memory and Disk**
+### CPU, Memory and Disk
 
 This backend supports CPU, memory and disk size configuration through the use of the following [Runtime Attributes](../RuntimeAttributes) and [Workflow Options](../wf_options/Overview/):  
 
@@ -61,16 +61,29 @@ This backend supports CPU, memory and disk size configuration through the use of
     * Type: String (ex: "4 GB" or "4096 MB")
 * `disk` defines the amount of disk to use.
     * Type: String (ex: "1 GB" or "1024 MB")
+* `disks` accepts a GCP-style disk declaration and attempts to translate it for use on TES
+    * See table below for supported translations 
 * `preemptible` defines whether or not to use preemptible VMs.
     * Type: Boolean (ex: "true" or "false")
     * Integers are accepted and will be converted to boolean (true if > 0)
 
 If they are not set, the TES backend may use default values.
 
-**Azure**
+#### GCP `disks` to TES `disk` compatibility
+
+| GCP `disks` value                     | Supported | TES translation | Remark                            |
+|---------------------------------------|-----------|-----------------|-----------------------------------|
+| `local-disk 25 HDD`                   | ✅        | 25 GB disk      |                                   |
+| `local-disk 25 SSD`                   | ✅        | 25 GB disk      | Disk type info is dropped         |
+| `/some/mnt 25 SSD`                    | ❌        |                 | Custom mount points not supported | 
+| `local-disk 25 HDD, /some/mnt 50 SSD` | ❌        |                 | Multiple disks are not supported  | 
+            
+> Note: if both `disk` and `disks` attributes are specified, the TES backend will automatically use the value in `disk` and not attempt to translate `disks`.
+
+### Azure
 [Azure](Azure) is an implementation of Cromwell that uses the TES interface for orchestrating the tasks on Azure.
 
-**TESK**
+### TESK
 
 [TESK](https://github.com/EMBL-EBI-TSI/TESK) is an implementation of the TES interface that uses Kubernetes and FTP.
 When running Cromwell with a TESK backend, you will want to customize the way Cromwell process globs, as kubernetes will not work well with hard links in a lot of cases which is the default behavior in Cromwell.
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
index 4212ff4be67..c5b3c4df66d 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
@@ -3,10 +3,13 @@ package cromwell.backend.impl.tes
 import cats.syntax.validated._
 import com.typesafe.config.Config
 import common.validation.ErrorOr.ErrorOr
+import cromwell.backend.google.pipelines.common.DisksValidation
+import cromwell.backend.google.pipelines.common.io.{PipelinesApiAttachedDisk, PipelinesApiEmptyMountedDisk, PipelinesApiWorkingDisk}
 import cromwell.backend.standard.StandardValidatedRuntimeAttributesBuilder
 import cromwell.backend.validation._
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
+import wdl4s.parser.MemoryUnit
 import wom.RuntimeAttributesKeys
 import wom.format.MemorySize
 import wom.types.{WomIntegerType, WomStringType}
@@ -36,6 +39,9 @@ object TesRuntimeAttributes {
 
   private def diskSizeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[MemorySize] = MemoryValidation.optional(DiskSizeKey)
 
+  private def diskSizeCompatValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Seq[PipelinesApiAttachedDisk]] =
+    DisksValidation.optional
+
   private def memoryValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[MemorySize] = MemoryValidation.optional(RuntimeAttributesKeys.MemoryKey)
 
   private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
@@ -45,10 +51,14 @@ object TesRuntimeAttributes {
   private def preemptibleValidation(runtimeConfig: Option[Config]) = PreemptibleValidation.default(runtimeConfig)
 
   def runtimeAttributesBuilder(backendRuntimeConfig: Option[Config]): StandardValidatedRuntimeAttributesBuilder =
+    // !! NOTE !! If new validated attributes are added to TesRuntimeAttributes, be sure to include
+    // their validations here so that they will be handled correctly with backendParameters.
+    // Location 2 of 2
     StandardValidatedRuntimeAttributesBuilder.default(backendRuntimeConfig).withValidation(
       cpuValidation(backendRuntimeConfig),
       memoryValidation(backendRuntimeConfig),
       diskSizeValidation(backendRuntimeConfig),
+      diskSizeCompatValidation(backendRuntimeConfig),
       dockerValidation,
       dockerWorkingDirValidation,
       preemptibleValidation(backendRuntimeConfig),
@@ -71,13 +81,45 @@ object TesRuntimeAttributes {
       Map.empty
   }
 
+  private def detectDiskFormat(backendRuntimeConfig: Option[Config], validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[MemorySize] = {
+
+    def adaptPapiDisks(disks: Seq[PipelinesApiAttachedDisk]): MemorySize = {
+      disks match {
+        case disk :: Nil if disk.isInstanceOf[PipelinesApiWorkingDisk] =>
+            MemorySize(disk.sizeGb.toDouble, MemoryUnit.GB)
+        case _ :: _ =>
+          // When a user specifies only a custom disk, we add the default disk in the background, so we technically have multiple disks.
+          // But we don't want to confuse the user with `multiple disks` message when they only put one.
+          if (disks.exists(_.isInstanceOf[PipelinesApiEmptyMountedDisk]))
+            throw new IllegalArgumentException("Disks with custom mount points are not supported by this backend")
+          else
+            // Multiple `local-disk` is not legal, but possible and should be detected
+            throw new IllegalArgumentException("Expecting exactly one disk definition on this backend, found multiple")
+      }
+    }
+
+    val maybeTesDisk: Option[MemorySize] =
+      RuntimeAttributesValidation.extractOption(diskSizeValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+    val maybePapiDisk: Option[Seq[PipelinesApiAttachedDisk]] =
+      RuntimeAttributesValidation.extractOption(diskSizeCompatValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+
+    (maybeTesDisk, maybePapiDisk) match {
+      case (Some(tesDisk: MemorySize), _) =>
+        Option(tesDisk) // If WDLs are in circulation with both `disk` and `disks`, pick the one intended for this backend
+      case (None, Some(papiDisks: Seq[PipelinesApiAttachedDisk])) =>
+        Option(adaptPapiDisks(papiDisks))
+      case _ =>
+        None
+    }
+  }
+
   def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes, rawRuntimeAttributes: Map[String, WomValue], config: TesConfiguration): TesRuntimeAttributes = {
     val backendRuntimeConfig = config.runtimeConfig
     val docker: String = RuntimeAttributesValidation.extract(dockerValidation, validatedRuntimeAttributes)
     val dockerWorkingDir: Option[String] = RuntimeAttributesValidation.extractOption(dockerWorkingDirValidation.key, validatedRuntimeAttributes)
     val cpu: Option[Int Refined Positive] = RuntimeAttributesValidation.extractOption(cpuValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
     val memory: Option[MemorySize] = RuntimeAttributesValidation.extractOption(memoryValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
-    val disk: Option[MemorySize] = RuntimeAttributesValidation.extractOption(diskSizeValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+    val disk: Option[MemorySize] = detectDiskFormat(backendRuntimeConfig, validatedRuntimeAttributes)
     val failOnStderr: Boolean =
       RuntimeAttributesValidation.extract(failOnStderrValidation(backendRuntimeConfig), validatedRuntimeAttributes)
     val continueOnReturnCode: ContinueOnReturnCode =
@@ -87,12 +129,14 @@ object TesRuntimeAttributes {
 
     // !! NOTE !! If new validated attributes are added to TesRuntimeAttributes, be sure to include
     // their validations here so that they will be handled correctly with backendParameters.
+    // Location 1 of 2
     val validations = Set(
       dockerValidation,
       dockerWorkingDirValidation,
       cpuValidation(backendRuntimeConfig),
       memoryValidation(backendRuntimeConfig),
       diskSizeValidation(backendRuntimeConfig),
+      diskSizeCompatValidation(backendRuntimeConfig),
       failOnStderrValidation(backendRuntimeConfig),
       continueOnReturnCodeValidation(backendRuntimeConfig),
       preemptibleValidation(backendRuntimeConfig)
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
index 1b3b3b7aea8..e1984fb65dc 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
@@ -160,6 +160,54 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
       assertFailure(runtimeAttributes, "Expecting disk runtime attribute to be an Integer or String with format '8 GB'")
     }
 
+    "parse an HDD definition" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 HDD"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(disk = Option(MemorySize.parse("10 GB").get))
+      assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "parse an SSD definition" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 SSD"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(disk = Option(MemorySize.parse("10 GB").get))
+      assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "refuse multiple `local-disk` instances" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 SSD, local-disk 20 SSD"))
+      assertFailure(runtimeAttributes, "Expecting exactly one disk definition on this backend, found multiple")
+    }
+
+    "refuse custom mount points" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("/some/mnt 20 SSD"))
+      assertFailure(runtimeAttributes, "Disks with custom mount points are not supported by this backend")
+    }
+
+    "refuse custom AND multiple mount points" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("/mnt/tmp 10 LOCAL, local-disk 20 HDD"))
+      assertFailure(runtimeAttributes, "Disks with custom mount points are not supported by this backend")
+    }
+
+    "not accept a single comma" ignore {
+      // Surprisingly, the PAPI code we call under the covers validates `,` and give the user a default disk.
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString(","))
+      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: ','")
+    }
+
+    "not accept empty string" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString(""))
+      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: ''")
+    }
+
+    "not accept `banana`" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("banana"))
+      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: 'banana'")
+    }
+
+    "not accept a random number (chosen by fair dice roll)" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomInteger(4))
+      assertFailure(runtimeAttributes, "Expecting disks runtime attribute to be a comma separated String or Array[String]")
+    }
+
     "validate a valid dockerWorkingDir entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "dockerWorkingDir" -> WomString("/tmp"))
       val expectedRuntimeAttributes = expectedDefaults.copy(dockerWorkingDir = Option("/tmp"))

From f2ddab71f63e62bfd40cd648fb23fa291a07c20f Mon Sep 17 00:00:00 2001
From: ekiernan <55763654+ekiernan@users.noreply.github.com>
Date: Wed, 1 Feb 2023 12:36:06 -0500
Subject: [PATCH 127/326] Update FiveMinuteIntro.md (#6994)

---
 docs/tutorials/FiveMinuteIntro.md | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/docs/tutorials/FiveMinuteIntro.md b/docs/tutorials/FiveMinuteIntro.md
index 87a9acd125d..2e203354bee 100644
--- a/docs/tutorials/FiveMinuteIntro.md
+++ b/docs/tutorials/FiveMinuteIntro.md
@@ -3,9 +3,10 @@
 ### Prerequisites:
 
 * A Unix-based operating system (yes, that includes Mac!)
-* A Java 8 runtime environment 
-	* You can see what you have by running `$ java -version` on a terminal. You're looking for a version that's at least `1.8` or higher.
-	* If not, you can download Java [here](http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html).
+* A Java 11 runtime environment 
+	* You can see what you have by running `$ java -version` on a terminal. 
+	* If not, you can download Java [here](https://adoptopenjdk.net/).
+	* You might need to update the `export JAVA_HOME` in your bash profile to point to your JAVA install location.
 * A sense of adventure!
 
 ### Goals
@@ -41,14 +42,17 @@ This bit is easy, you're just going to copy and paste something from the interne
 Open your favorite editor. Paste in the following content and save it as `myWorkflow.wdl` in your new `cromwell` directory:
 
 ```wdl
+# Example workflow
+# Declare WDL version 1.0 if working in Terra
+version 1.0
 workflow myWorkflow {
 	call myTask
 }
 
 task myTask {
-	command {
+	command <<<
 		echo "hello world"
-	}
+	>>>
 	output {
 		String out = read_string(stdout())
 	}

From a5b0f693df3a4e234d5624e889601e5a3ea9a3ef Mon Sep 17 00:00:00 2001
From: Tom Wiseman <tom.h.wiseman@gmail.com>
Date: Wed, 1 Feb 2023 16:01:58 -0500
Subject: [PATCH 128/326] WX-906 Sbt Unit Tests as Github Actions (#6992)

---
 .github/set_up_cromwell_action/action.yml | 47 +++++++++++++++++++++++
 .github/workflows/cromwell_unit_tests.yml | 32 +++++++++++++++
 2 files changed, 79 insertions(+)
 create mode 100644 .github/set_up_cromwell_action/action.yml
 create mode 100644 .github/workflows/cromwell_unit_tests.yml

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
new file mode 100644
index 00000000000..13cb11601db
--- /dev/null
+++ b/.github/set_up_cromwell_action/action.yml
@@ -0,0 +1,47 @@
+#This is a series of steps that will setup Java/sbt/Cromwell on the local runner.
+#These steps are meant to be re-used and invoked by other Github Action Workflows
+name: 'Set Up Cromwell Steps'
+description: Specific steps that will set up git secrets, java, sbt, and Cromwell on the local machine. 
+inputs:
+  cromwell_repo_token: #As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell.
+    required: true
+
+runs:
+  using: "composite" # <-- this allows these steps to be used by other workflows.
+  steps:
+      #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
+      - uses: actions/checkout@v3
+        name: Checkout Coursier Cache
+      - uses: coursier/cache-action@v6  
+        name: Enable Coursier Cache
+
+      #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
+      - name: Git secrets setup 
+        run: |
+          git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
+          cd ~/git-secrets
+          git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
+          sudo make install
+        shell: bash
+
+      - name: Secrets check
+        run: |
+          sudo ln -s "$(which echo)" /usr/local/bin/say
+          ./minnie-kenny.sh --force
+          git secrets --scan-history
+        shell: bash
+
+      #Clone the cromwell repo to this VM.
+      - name: Clone Cromwell
+        uses: actions/checkout@v3
+        with:
+          repository: broadinstitute/cromwell
+          token: ${{ inputs.cromwell_repo_token }}
+
+      #Install Java to this VM. This Java version and distribution is compatible with Cromwell.
+      - name: Setup JDK
+        uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 11
+
diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
new file mode 100644
index 00000000000..d0927f8b954
--- /dev/null
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -0,0 +1,32 @@
+name: 'Cromwell unit tests'
+
+#This github action runs all of Cromwell's unit tests.
+
+#This is what shows up in the github workflows page as the title. 
+run-name: ${{ github.actor }} running Cromwell sbt unit tests.
+
+#What will trigger the workflow to run. 
+on:
+  workflow_dispatch: #Manual trigger from GitHub UI
+  push:
+
+permissions: 
+  contents: read
+
+jobs:
+  build-and-test: 
+    #This action is using a Github free runner, rather than a Broad self-hosted one.
+    #This is because the Broad ones don't have sbt installed by default.
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3 # checkout the cromwell repo
+    - uses: ./.github/set_up_cromwell_action #Exectute this reusable github action. It will set up java/sbt/git-secrets/cromwell.
+      with:
+        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+  
+    #Invoke SBT to run all unit tests for Cromwell. 
+    - name: Run tests
+      run: |
+        set -e
+        sbt "test"

From 790c892d5241f0d820738dbd72a28cdd6ab57fe8 Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Tue, 7 Feb 2023 16:53:05 -0500
Subject: [PATCH 129/326] WX-926 Support falling back to OCI Manifest Format
 (#7003)

* WX-926 Support falling back to OCI Manifest Forma
---
 .../registryv2/DockerRegistryV2Abstract.scala | 42 ++++++++++++-------
 .../DockerRegistryV2AbstractSpec.scala        |  6 +--
 2 files changed, 30 insertions(+), 18 deletions(-)

diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
index b8f78476eac..1a5a02d95bd 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
@@ -5,8 +5,8 @@ import cats.effect.IO
 import cats.syntax.either._
 import common.validation.Validation._
 import cromwell.docker.DockerInfoActor._
+import cromwell.docker._
 import cromwell.docker.registryv2.DockerRegistryV2Abstract._
-import cromwell.docker.{DockerHashResult, DockerImageIdentifier, DockerRegistry, DockerRegistryConfig}
 import io.circe.Decoder
 import io.circe.generic.auto._
 import org.http4s.Uri.{Authority, Scheme}
@@ -27,19 +27,27 @@ object DockerRegistryV2Abstract {
   }
 
   val DigestHeaderName = CaseInsensitiveString("Docker-Content-Digest")
-  val ManifestV2MediaType = "application/vnd.docker.distribution.manifest.v2+json"
-  val ManifestListV2MediaType = "application/vnd.docker.distribution.manifest.list.v2+json"
+  val DockerManifestV2MediaType = "application/vnd.docker.distribution.manifest.v2+json"
+  val DockerManifestListV2MediaType = "application/vnd.docker.distribution.manifest.list.v2+json"
+  // See https://github.com/opencontainers/image-spec/blob/main/image-index.md
+  // This is the media type that current images of Ubuntu use, https://github.com/docker-library/official-images/pull/13950
+  val OCIIndexV1MediaType = "application/vnd.oci.image.index.v1+json"
 
   // If one of those fails it means someone changed one of the strings above to an invalid one.
-  val ManifestV2MediaRange = MediaRange.parse(ManifestV2MediaType)
+  val DockerManifestV2MediaRange = MediaRange.parse(DockerManifestV2MediaType)
     .unsafe("Cannot parse invalid manifest v2 content type. Please report this error.")
-  val ManifestListV2MediaRange = MediaRange.parse(ManifestListV2MediaType)
+  val DockerManifestListV2MediaRange = MediaRange.parse(DockerManifestListV2MediaType)
     .unsafe("Cannot parse invalid manifest list v2 content type. Please report this error.")
-  val AcceptManifestV2Header = Accept.parse(ManifestV2MediaType)
+  val AcceptDockerManifestV2Header = Accept.parse(DockerManifestV2MediaType)
     .unsafe("Cannot parse invalid manifest v2 Accept header. Please report this error.")
 
-  implicit val entityManifestDecoder = jsonEntityDecoder[DockerManifest](ManifestV2MediaRange)
-  implicit val entityManifestListDecoder = jsonEntityDecoder[DockerManifestList](ManifestListV2MediaRange)
+  val OCIIndexV1MediaRange = MediaRange.parse(OCIIndexV1MediaType)
+    .unsafe("Cannot parse invalid OCI index v1 content type. Please report this error.")
+  val AcceptOCIIndexV1Header = Accept.parse(OCIIndexV1MediaType)
+    .unsafe("Cannot parse invalid OCI index v1 Accept header. Please report this error.")
+
+  implicit val entityManifestDecoder = jsonEntityDecoder[DockerManifest](DockerManifestV2MediaRange)
+  implicit val entityManifestListDecoder = jsonEntityDecoder[DockerManifestList](DockerManifestListV2MediaRange)
   implicit val entityTokenDecoder = jsonOf[IO, DockerAccessToken]
 
   /**
@@ -121,8 +129,12 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * @return docker info response
     */
   protected def getDockerResponse(token: Option[String], dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]): IO[DockerInfoSuccessResponse] = {
-    val request = manifestRequest(token, dockerInfoContext.dockerImageID)
-    executeRequest(request, handleManifestResponse(dockerInfoContext, token))
+    val requestDockerManifest = manifestRequest(token, dockerInfoContext.dockerImageID, AcceptDockerManifestV2Header)
+    lazy val requestOCIManifest = manifestRequest(token, dockerInfoContext.dockerImageID, AcceptOCIIndexV1Header)
+    def tryOCIManifest(err: Throwable) = executeRequest(requestOCIManifest, handleManifestResponse(dockerInfoContext, token))
+    // Try to execute a request using the Docker Manifest format, and if that fails, try using the newer OCI manifest format
+    executeRequest(requestDockerManifest, handleManifestResponse(dockerInfoContext, token))
+      .handleErrorWith(tryOCIManifest)
   }
 
   /**
@@ -203,12 +215,12 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
   /**
     * Request to get the manifest, using the auth token if provided
     */
-  private def manifestRequest(token: Option[String], imageId: DockerImageIdentifier): IO[Request[IO]] = {
+  private def manifestRequest(token: Option[String], imageId: DockerImageIdentifier, manifestHeader: Accept): IO[Request[IO]] = {
     val authorizationHeader = token.map(t => Authorization(Credentials.Token(AuthScheme.Bearer, t)))
     val request = Method.GET(
       buildManifestUri(imageId),
       List(
-        Option(AcceptManifestV2Header),
+        Option(manifestHeader),
         authorizationHeader
       ).flatten: _*
     )
@@ -244,9 +256,9 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * If that assumption turns out to be incorrect, a smarter decision may need to be made to choose the manifest to lookup.
     */
   private def parseManifest(dockerImageIdentifier: DockerImageIdentifier, token: Option[String])(response: Response[IO])(implicit client: Client[IO]): IO[Option[DockerManifest]] = response match {
-    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(ManifestV2MediaType)) =>
+    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(DockerManifestV2MediaType)) =>
       r.as[DockerManifest].map(Option.apply)
-    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(ManifestListV2MediaType)) =>
+    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(DockerManifestListV2MediaType)) =>
       r.as[DockerManifestList].flatMap({ dockerManifestList =>
         obtainManifestFromList(dockerManifestList, dockerImageIdentifier, token)
       })
@@ -260,7 +272,7 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
       .map(_.digest)
       .map(dockerImageIdentifier.swapReference) match {
       case Some(identifierWithNewHash) =>
-        val request = manifestRequest(token, identifierWithNewHash)
+        val request = manifestRequest(token, identifierWithNewHash, AcceptDockerManifestV2Header)
         executeRequest(request, parseManifest(dockerImageIdentifier, token))
       case None =>
         logger.error(s"The manifest list for ${dockerImageIdentifier.fullName} was empty. Cannot proceed to obtain the size of image")
diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
index e567aa540cd..e99383ac131 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
@@ -3,10 +3,10 @@ package cromwell.docker.registryv2
 import cats.effect.{IO, Resource}
 import common.assertion.CromwellTimeoutSpec
 import cromwell.docker.DockerInfoActor.{DockerInfoContext, DockerInfoFailedResponse}
-import cromwell.docker.{DockerImageIdentifier, DockerInfoActor, DockerInfoRequest, DockerRegistryConfig}
+import cromwell.docker._
+import org.http4s._
 import org.http4s.client.Client
 import org.http4s.headers.`Content-Type`
-import org.http4s.{Header, Headers, MediaType, Request, Response}
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
@@ -20,7 +20,7 @@ class DockerRegistryV2AbstractSpec extends AnyFlatSpec with CromwellTimeoutSpec
       override protected def buildTokenRequestHeaders(dockerInfoContext: DockerInfoActor.DockerInfoContext) = List.empty
     }
 
-    val mediaType = MediaType.parse(DockerRegistryV2Abstract.ManifestV2MediaType).toOption.get
+    val mediaType = MediaType.parse(DockerRegistryV2Abstract.DockerManifestV2MediaType).toOption.get
     val contentType: Header = `Content-Type`(mediaType)
 
     val mockClient = Client({ _: Request[IO] =>

From d142bd4a9b890605a2e61ee6469f01a442dfb74e Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@users.noreply.github.com>
Date: Wed, 8 Feb 2023 14:48:58 -0500
Subject: [PATCH 130/326] Only mount reference disks if requested [WX-925]
 (#7001)

---
 ...ference_disk_mounted_only_if_requested.wdl | 49 +++++++++++++++++++
 ..._disk_mounted_only_if_requested_false.test | 14 ++++++
 ...e_disk_mounted_only_if_requested_true.test | 14 ++++++
 ...mounted_only_if_requested_unspecified.test | 14 ++++++
 ...inesApiAsyncBackendJobExecutionActor.scala |  4 +-
 5 files changed, 94 insertions(+), 1 deletion(-)
 create mode 100644 centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl
 create mode 100644 centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test
 create mode 100644 centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test
 create mode 100644 centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test

diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl
new file mode 100644
index 00000000000..33153c1157c
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl
@@ -0,0 +1,49 @@
+version 1.0
+
+
+workflow ReferenceDiskMountedOnlyIfRequested {
+    call MentionsNirvanaReference {}
+    output {
+        Boolean disk_mounted = MentionsNirvanaReference.disk_mounted
+    }
+}
+
+
+task MentionsNirvanaReference {
+    input {
+        # Tiny 116 byte reference file, certainly not worth attaching a 55 GiB Nirvana reference disk for this.
+        File mention =
+            "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
+    }
+    command <<<
+        PS4='\D{+%F %T} \w $ '
+        set -o nounset -o xtrace
+
+        # Debug output
+        lsblk
+
+        CANDIDATE_MOUNT_POINT=$(lsblk | sed -E -n 's!.*(/mnt/[a-f0-9]+).*!\1!p')
+
+        if [[ ! -z ${CANDIDATE_MOUNT_POINT} ]]; then
+            echo "Found unexpected mounted disk, investigating further."
+            find ${CANDIDATE_MOUNT_POINT} -print | tee find.out
+
+            if grep -i nirvana find.out; then
+                echo "Found what appears to be a Nirvana reference disk."
+            else
+                echo "Found unknown volume mounted, see 'find.out' for manifest."
+            fi
+            echo true > disk_mounted.out
+        else
+            echo false > disk_mounted.out
+        fi
+    >>>
+    runtime {
+        docker: "ubuntu:latest"
+        backend: "Papiv2-Reference-Disk-Localization"
+    }
+    output {
+        Boolean disk_mounted = read_boolean("disk_mounted.out")
+        File? find_out = "find.out"
+    }
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test
new file mode 100644
index 00000000000..32c6d83e5c3
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test
@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_false
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_false.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": false
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test
new file mode 100644
index 00000000000..165e1c6d1f4
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test
@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_true
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_true.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": true
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test
new file mode 100644
index 00000000000..860159b594e
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test
@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_unspecified
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_unspecified.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": false
+}
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
index c1c68b7dd39..745e11bee35 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -452,7 +452,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
 
         val inputFilePaths = inputOutputParameters.jobInputParameters.map(_.cloudPath.pathAsString).toSet
         val referenceDisksToMount =
-          jesAttributes.referenceFileToDiskImageMappingOpt.map(getReferenceDisksToMount(_, inputFilePaths))
+          if (useReferenceDisks)
+            jesAttributes.referenceFileToDiskImageMappingOpt.map(getReferenceDisksToMount(_, inputFilePaths))
+          else None
 
         val workflowOptions = workflowDescriptor.workflowOptions
 

From 092059f2d68de1ec617c2471d62f834ac2d91543 Mon Sep 17 00:00:00 2001
From: Saloni Shah <salonipshah11@gmail.com>
Date: Wed, 8 Feb 2023 16:24:29 -0500
Subject: [PATCH 131/326] [WM-1646] Add missing fields for
 `WorkflowDescription` for WomTool /describe endpoint to Swagger (#7004)

---
 docs/api/RESTAPI.md                             |  6 +++++-
 engine/src/main/resources/swagger/cromwell.yaml | 12 ++++++++++++
 processes/release_processes/README.MD           |  4 +++-
 3 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/docs/api/RESTAPI.md b/docs/api/RESTAPI.md
index 42eb3969d5d..ffb2af329de 100644
--- a/docs/api/RESTAPI.md
+++ b/docs/api/RESTAPI.md
@@ -1,5 +1,5 @@
 <!--
-This file was generated by `sbt generateRestApiDocs` on Tue, 15 Nov 2022 14:26:23 -0500
+This file was generated by `sbt generateRestApiDocs` on Wed, 8 Feb 2023 09:46:32 -0500
 
 !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
 
@@ -1247,10 +1247,14 @@ Returns the version of Cromwell
 |Name|Description|Schema|
 |---|---|---|
 |**errors**  <br>*required*|The set of validation failure messages  <br>**Example** : `[ "The 'errors' field will be filled if 'valid' is false", "We might also provide warnings to a 'valid' workflow here", "Otherwise, 'errors' will be the empty array" ]`|< string > array|
+|**images**  <br>*optional*||< string > array|
+|**importedDescriptorTypes**  <br>*optional*||< [DescriptorTypeAndVersion](#descriptortypeandversion) > array|
 |**inputs**  <br>*required*|A list of inputs for this tool  <br>**Example** : `[ {<br>  "name" : "my_wf.string_input",<br>  "valueType" : {<br>    "typeName" : "String"<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "String"<br>}, {<br>  "name" : "my_wf.array_input",<br>  "valueType" : {<br>    "typeName" : "Array",<br>    "arrayType" : {<br>      "typeName" : "String"<br>    }<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Array[String]"<br>}, {<br>  "name" : "my_wf.optional_input",<br>  "valueType" : {<br>    "typeName" : "Optional",<br>    "optionalType" : {<br>      "typeName" : "String"<br>    }<br>  },<br>  "optional" : true,<br>  "default" : "hello",<br>  "typeDisplayName" : "String?"<br>}, {<br>  "name" : "my_wf.map_input",<br>  "valueType" : {<br>    "typeName" : "Map",<br>    "mapType" : {<br>      "keyType" : {<br>        "typeName" : "String"<br>      },<br>      "valueType" : {<br>        "typeName" : "Int"<br>      }<br>    }<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Map[String, Int]"<br>}, {<br>  "name" : "my_wf.object_input",<br>  "valueType" : {<br>    "typeName" : "Object",<br>    "objectFieldTypes" : [ {<br>      "fieldName" : "int_field",<br>      "fieldType" : {<br>        "typeName" : "Int"<br>      }<br>    }, {<br>      "fieldName" : "int_array_field",<br>      "fieldType" : {<br>        "typeName" : "Array",<br>        "arrayType" : {<br>          "typeName" : "Int"<br>        }<br>      }<br>    } ]<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Object"<br>}, {<br>  "name" : "my_wf.int_string_pair_input",<br>  "valueType" : {<br>    "typeName" : "Pair",<br>    "pairTypes" : [ {<br>      "leftType" : [ {<br>        "typeName" : "Int"<br>      } ]<br>    }, {<br>      "rightType" : [ {<br>        "typeName" : "String"<br>      } ]<br>    } ]<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Pair[Int, String]"<br>} ]`|< [ToolInputParameter](#toolinputparameter) > array|
 |**isRunnableWorkflow**  <br>*required*|Indicates whether this file can be run on its own (e.g. a WDL workflow)|boolean|
+|**meta**  <br>*optional*||object|
 |**name**  <br>*required*|For a source file with one workflow and zero or more tasks, the name of the workflow. For a single task, the name of the task. For a source file with multiple tasks but no workflows, the empty string.|string|
 |**outputs**  <br>*required*|A list of outputs for this tool  <br>**Example** : `[ {<br>  "name" : "my_wf.string_output",<br>  "valueType" : {<br>    "typeName" : "String"<br>  },<br>  "typeDisplayName" : "String"<br>}, {<br>  "name" : "my_wf.array_output",<br>  "valueType" : {<br>    "typeName" : "Array",<br>    "arrayType" : {<br>      "typeName" : "String"<br>    }<br>  },<br>  "typeDisplayName" : "Array[String]"<br>}, {<br>  "name" : "my_wf.map_output",<br>  "valueType" : {<br>    "typeName" : "Map",<br>    "mapType" : {<br>      "keyType" : {<br>        "typeName" : "String"<br>      },<br>      "valueType" : {<br>        "typeName" : "Int"<br>      }<br>    }<br>  },<br>  "typeDisplayName" : "Map[String, Int]"<br>}, {<br>  "name" : "my_wf.object_output",<br>  "valueType" : {<br>    "typeName" : "Object",<br>    "objectFieldTypes" : [ {<br>      "fieldName" : "int_field",<br>      "fieldType" : {<br>        "typeName" : "Int"<br>      }<br>    }, {<br>      "fieldName" : "int_array_field",<br>      "fieldType" : {<br>        "typeName" : "Array",<br>        "arrayType" : {<br>          "typeName" : "Int"<br>        }<br>      }<br>    } ]<br>  },<br>  "typeDisplayName" : "Object"<br>}, {<br>  "name" : "my_wf.int_string_pair_output",<br>  "valueType" : {<br>    "typeName" : "Pair",<br>    "tupleTypes" : [ {<br>      "typeName" : "Int"<br>    }, {<br>      "typeName" : "String"<br>    } ]<br>  },<br>  "typeDisplayName" : "Pair[Int, String]"<br>} ]`|< [ToolOutputParameter](#tooloutputparameter) > array|
+|**parameterMeta**  <br>*optional*||object|
 |**submittedDescriptorType**  <br>*required*||[DescriptorTypeAndVersion](#descriptortypeandversion)|
 |**valid**  <br>*required*|Indicates that the workflow is valid and that the inputs, if provided, are compatible with the workflow.|boolean|
 |**validWorkflow**  <br>*required*|Indicates whether the workflow file is valid by itself. If inputs are provided, they are not considered when calculating this field; if inputs are not provided, the value is identical to `valid`.|boolean|
diff --git a/engine/src/main/resources/swagger/cromwell.yaml b/engine/src/main/resources/swagger/cromwell.yaml
index f3230b3c171..6e840160d36 100644
--- a/engine/src/main/resources/swagger/cromwell.yaml
+++ b/engine/src/main/resources/swagger/cromwell.yaml
@@ -1251,8 +1251,20 @@ definitions:
                 - typeName: Int
                 - typeName: String
             typeDisplayName: Pair[Int, String]
+      images:
+        type: array
+        items:
+          type: string
       submittedDescriptorType:
         $ref: '#/definitions/DescriptorTypeAndVersion'
+      importedDescriptorTypes:
+        type: array
+        items:
+          $ref: '#/definitions/DescriptorTypeAndVersion'
+      meta:
+        type: object
+      parameterMeta:
+        type: object
       isRunnableWorkflow:
         description: Indicates whether this file can be run on its own (e.g. a WDL workflow)
         type: boolean
diff --git a/processes/release_processes/README.MD b/processes/release_processes/README.MD
index d23d601b747..66e27fd28a7 100644
--- a/processes/release_processes/README.MD
+++ b/processes/release_processes/README.MD
@@ -140,7 +140,7 @@ This generates the client library and runs the generated tests as well.  A succe
 [success] Total time: 4 s, completed Jun 26, 2019 3:01:19 PM
 ```
 
-To publish to artifactory, first obtain the artifactory username and credentials.  Then run
+To publish to artifactory, first obtain the artifactory username and credentials. Credentials are located in Vault at path `secret/dsde/cromwell/common/cromwell-artifactory`. Then run
 
 ```
 export ARTIFACTORY_USERNAME=<the-username>
@@ -148,6 +148,8 @@ export ARTIFACTORY_PASSWORD=<the-password>
 ./scripts/publish-client.sh
 ```
 
+A SNAP version of the client library will be published in jFrog at [this path](https://broadinstitute.jfrog.io/ui/repos/tree/General/libs-release-local/org/broadinstitute/cromwell).
+
 ## Cromwell setup for publishing
 
 One can run a publishing-friendly Cromwell using a containerized MySQL server and config files

From 417adfa0ee7812134c12dcb61046dfb0acba63da Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Thu, 9 Feb 2023 13:49:08 -0500
Subject: [PATCH 132/326] WX-876 Surface TES System Logs to Cromwell when TES
 backend returns task error status (#6980)

* WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status

* Address feedback

* Address feedback (#6997)

* Address additional feedback (#7000)

* Fix copy/paste error (#7005)

* Address additional feedback

* Fix copy/paste error

* Trigger CI

---------

Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .../TesAsyncBackendJobExecutionActor.scala    | 45 +++++++++++++++++--
 1 file changed, 42 insertions(+), 3 deletions(-)

diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 63b43ddbcf5..1e5637fff0e 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -1,5 +1,6 @@
 package cromwell.backend.impl.tes
 
+import common.exception.AggregatedMessageException
 import java.io.FileNotFoundException
 import java.nio.file.FileAlreadyExistsException
 import cats.syntax.apply._
@@ -30,6 +31,7 @@ import scala.util.{Failure, Success}
 
 sealed trait TesRunStatus {
   def isTerminal: Boolean
+  def sysLogs: Seq[String] = Seq.empty[String]
 }
 
 case object Running extends TesRunStatus {
@@ -40,8 +42,14 @@ case object Complete extends TesRunStatus {
   def isTerminal = true
 }
 
-case object FailedOrError extends TesRunStatus {
+case class Error(override val sysLogs: Seq[String] = Seq.empty[String]) extends TesRunStatus {
   def isTerminal = true
+  override def toString = "SYSTEM_ERROR"
+}
+
+case class Failed(override val sysLogs: Seq[String] = Seq.empty[String]) extends TesRunStatus {
+  def isTerminal = true
+  override def toString = "EXECUTOR_ERROR"
 }
 
 case object Cancelled extends TesRunStatus {
@@ -217,6 +225,21 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
   override def requestsAbortAndDiesImmediately: Boolean = false
 
   override def pollStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[TesRunStatus] = {
+    for {
+      status <- queryStatusAsync(handle)
+      errorLog <- status match {
+          case Error(_) | Failed(_) => getErrorLogs(handle)
+          case _ => Future.successful(Seq.empty[String])
+      }
+      statusWithLog = status match {
+        case Error(_) => Error(errorLog)
+        case Failed(_) => Failed(errorLog)
+        case _ => status
+      }
+    } yield statusWithLog
+  }
+
+  private def queryStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[TesRunStatus] = {
     makeRequest[MinimalTaskView](HttpRequest(uri = s"$tesEndpoint/${handle.pendingJob.jobId}?view=MINIMAL")) map {
       response =>
         val state = response.state
@@ -229,24 +252,40 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
             jobLogger.info(s"Job ${handle.pendingJob.jobId} was canceled")
             Cancelled
 
-          case s if s.contains("ERROR") =>
+          case s if s.contains("EXECUTOR_ERROR") =>
+            jobLogger.info(s"TES reported a failure for Job ${handle.pendingJob.jobId}: '$s'")
+            Failed()
+
+          case s if s.contains("SYSTEM_ERROR") =>
             jobLogger.info(s"TES reported an error for Job ${handle.pendingJob.jobId}: '$s'")
-            FailedOrError
+            Error()
 
           case _ => Running
         }
     }
   }
 
+  private def getErrorLogs(handle: StandardAsyncPendingExecutionHandle): Future[Seq[String]] = {
+    makeRequest[Task](HttpRequest(uri = s"$tesEndpoint/${handle.pendingJob.jobId}?view=FULL")) map { response =>
+      response.logs.flatMap(_.lastOption).flatMap(_.system_logs).getOrElse(Seq.empty[String])
+    }
+  }
+
   override def customPollStatusFailure: PartialFunction[(ExecutionHandle, Exception), ExecutionHandle] = {
     case (oldHandle: StandardAsyncPendingExecutionHandle@unchecked, e: Exception) =>
       jobLogger.error(s"$tag TES Job ${oldHandle.pendingJob.jobId} has not been found, failing call")
       FailedNonRetryableExecutionHandle(e, kvPairsToSave = None)
   }
 
+  private def handleExecutionError(status: TesRunStatus, returnCode: Option[Int]): Future[ExecutionHandle] = {
+    val exception = new AggregatedMessageException(s"Task ${jobDescriptor.key.tag} failed for unknown reason: ${status.toString()}", status.sysLogs)
+    Future.successful(FailedNonRetryableExecutionHandle(exception, returnCode, None))
+  }
+
   override def handleExecutionFailure(status: StandardAsyncRunState, returnCode: Option[Int]) = {
     status match {
       case Cancelled => Future.successful(AbortedExecutionHandle)
+      case Error(_) | Failed(_) => handleExecutionError(status, returnCode)
       case _ => super.handleExecutionFailure(status, returnCode)
     }
   }

From 1795391add9f3e570c146d690ac2b740862cba58 Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@users.noreply.github.com>
Date: Thu, 9 Feb 2023 16:28:55 -0500
Subject: [PATCH 133/326] Centaur reference image test should validate symlinks
 [VS-796] (#6996)

---
 .../reference_disk/reference_disk_test.wdl    | 48 ++++++++++++-------
 .../reference_disk_false_options.test         |  5 +-
 .../reference_disk_true_options.test          |  5 +-
 .../reference_disk_unspecified_options.test   |  5 +-
 .../papi_v2_reference_image_manifest.conf     |  2 +-
 5 files changed, 40 insertions(+), 25 deletions(-)

diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
index fe01ae34d06..51fb467598b 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
@@ -1,26 +1,38 @@
 version 1.0
 
-task check_if_localized_as_symlink {
+task check_if_localized_with_valid_symlink {
   input {
     File broad_reference_file_input
     File nirvana_reference_file_input
     File nirvana_reference_file_metachar_input
   }
-  String broad_input_symlink = "broad_input_symlink.txt"
-  String nirvana_input_symlink = "nirvana_input_symlink.txt"
-  String nirvana_metachar_input_symlink = "nirvana_metachar_input_symlink.txt"
-  command {
-    # Print true if input is a symlink, otherwise print false.
-    if test -h ~{broad_reference_file_input}; then echo true; else echo false; fi > ~{broad_input_symlink}
-    if test -h ~{nirvana_reference_file_input}; then echo true; else echo false; fi > ~{nirvana_input_symlink}
+  String broad_input_valid_symlink = "broad_input_valid_symlink.txt"
+  String nirvana_input_valid_symlink = "nirvana_input_valid_symlink.txt"
+  String nirvana_metachar_input_valid_symlink = "nirvana_metachar_input_valid_symlink.txt"
+  command <<<
+      PS4='\D{+%F %T} \w $ '
+      set -o nounset -o pipefail -o xtrace
 
-    # Quotes added here due to the metachar in the filename.
-    if test -h "~{nirvana_reference_file_metachar_input}"; then echo true; else echo false; fi > ~{nirvana_metachar_input_symlink}
-  }
+      # Echo true to stdout if the argument is a symlink pointing to an extant file, otherwise echo false.
+      check_if_valid_symlink() {
+          local reference_input="$1"
+
+          if [[ -h "${reference_input}" && -f $(readlink "${reference_input}") ]]; then
+              echo true
+          else
+              echo false
+          fi
+      }
+
+      check_if_valid_symlink "~{broad_reference_file_input}" > ~{broad_input_valid_symlink}
+      check_if_valid_symlink "~{nirvana_reference_file_input}" > ~{nirvana_input_valid_symlink}
+      check_if_valid_symlink "~{nirvana_reference_file_metachar_input}" > ~{nirvana_metachar_input_valid_symlink}
+
+  >>>
   output {
-    Boolean is_broad_input_symlink = read_boolean("~{broad_input_symlink}")
-    Boolean is_nirvana_input_symlink = read_boolean("~{nirvana_input_symlink}")
-    Boolean is_nirvana_metachar_input_symlink = read_boolean("~{nirvana_metachar_input_symlink}")
+    Boolean is_broad_input_valid_symlink = read_boolean("~{broad_input_valid_symlink}")
+    Boolean is_nirvana_input_valid_symlink = read_boolean("~{nirvana_input_valid_symlink}")
+    Boolean is_nirvana_metachar_input_valid_symlink = read_boolean("~{nirvana_metachar_input_valid_symlink}")
   }
   runtime {
     docker: "ubuntu:latest"
@@ -34,15 +46,15 @@ workflow wf_reference_disk_test {
     File nirvana_reference_file_input
     File nirvana_reference_file_metachar_input
   }
-  call check_if_localized_as_symlink {
+  call check_if_localized_with_valid_symlink {
     input:
       broad_reference_file_input = broad_reference_file_input,
       nirvana_reference_file_input = nirvana_reference_file_input,
       nirvana_reference_file_metachar_input = nirvana_reference_file_metachar_input
   }
   output {
-    Boolean is_broad_input_file_a_symlink = check_if_localized_as_symlink.is_broad_input_symlink
-    Boolean is_nirvana_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_input_symlink
-    Boolean is_nirvana_metachar_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_metachar_input_symlink
+    Boolean is_broad_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_broad_input_valid_symlink
+    Boolean is_nirvana_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_nirvana_input_valid_symlink
+    Boolean is_nirvana_metachar_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_nirvana_metachar_input_valid_symlink
   }
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
index 8b80bea061e..bb8be222691 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
@@ -11,6 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
-  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": false
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
index fd8b508a221..6d957bf55b7 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
@@ -11,6 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": true
-  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": true
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": true
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": true
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": true
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
index 04391e4b2ab..7625bcd7806 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
@@ -11,6 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
-  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": false
 }
diff --git a/src/ci/resources/papi_v2_reference_image_manifest.conf b/src/ci/resources/papi_v2_reference_image_manifest.conf
index d31c961e15e..ef12cef1b66 100644
--- a/src/ci/resources/papi_v2_reference_image_manifest.conf
+++ b/src/ci/resources/papi_v2_reference_image_manifest.conf
@@ -192,7 +192,7 @@ reference-disk-localization-manifests = [
     ]
   },
   {
-    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2023-01-03",
+    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2023-02-01",
     "diskSizeGb" : 55,
     "files" : [ {
       "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd",

From cde42c34246e27ed070cb8e3c5a9eb6c02db405b Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 10 Feb 2023 11:09:56 -0500
Subject: [PATCH 134/326] WX-903 Pre-GHA test suite disablement

---
 .travis.yml | 23 +----------------------
 1 file changed, 1 insertion(+), 22 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index d733b16432c..9ffb48b1147 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -28,24 +28,13 @@ env:
     - >-
       BUILD_TYPE=centaurEngineUpgradeLocal
       BUILD_MYSQL=5.7
+    # Temporarily keeping until `centaurEngineUpgradePapiV2beta` or similar exists
     - >-
       BUILD_TYPE=centaurEngineUpgradePapiV2alpha1
       BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurHoricromtalPapiV2alpha1
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=centaurHoricromtalPapiV2beta
       BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurHoricromtalEngineUpgradePapiV2alpha1
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurPapiUpgradePapiV2alpha1
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurPapiUpgradeNewWorkflowsPapiV2alpha1
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=centaurLocal
       BUILD_MARIADB=10.3
@@ -55,9 +44,6 @@ env:
     - >-
       BUILD_TYPE=centaurLocal
       BUILD_POSTGRESQL=11.3
-    - >-
-      BUILD_TYPE=centaurPapiV2alpha1
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=centaurPapiV2beta
       BUILD_MYSQL=5.7
@@ -67,15 +53,10 @@ env:
     - >-
       BUILD_TYPE=centaurTes
       BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurWdlUpgradeLocal
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=checkPublish
     - >-
       BUILD_TYPE=horicromtalDeadlock
-    - >-
-      BUILD_TYPE=dockerScripts
     - >-
       BUILD_TYPE=sbt
       BUILD_SBT_INCLUDE=engine
@@ -92,8 +73,6 @@ env:
       BUILD_TYPE=dbms
     - >-
       BUILD_TYPE=singleWorkflowRunner
-    - >-
-      BUILD_TYPE=metadataComparisonPython
     - >-
       BUILD_TYPE=referenceDiskManifestBuilderApp
 script:

From e8449151075b569cf4ea694d6f56af6eeb5033a3 Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Mon, 13 Feb 2023 12:33:05 -0500
Subject: [PATCH 135/326] WX-877 Update CHANGELOG for release 85 (#7011)

---
 CHANGELOG.md                          | 278 ++++++++++++++------------
 processes/release_processes/README.MD |  38 ++--
 2 files changed, 159 insertions(+), 157 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a43c3b6e22d..0084c05171b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@
 
 ### Migration of PKs to BIGINT
 
-The PK of below tables will be migrated from INT to BIGINT. Also, since `ROOT_WORKFLOW_ID` in `SUB_WORKFLOW_STORE_ENTRY` is a FK to `WORKFLOW_STORE_ENTRY_ID` in `WORKFLOW_STORE_ENTRY` 
+The PK of below tables will be migrated from INT to BIGINT. Also, since `ROOT_WORKFLOW_ID` in `SUB_WORKFLOW_STORE_ENTRY` is a FK to `WORKFLOW_STORE_ENTRY_ID` in `WORKFLOW_STORE_ENTRY`
 it is also being migrated from INT to BIGINT.
 * DOCKER_HASH_STORE_ENTRY
 * WORKFLOW_STORE_ENTRY
@@ -15,30 +15,29 @@ it is also being migrated from INT to BIGINT.
 Cromwell will now retry a task with more memory after it fails with return code 137, provided all
 the other requirements for retrying with more memory are met.
 
-### Support for invoking `CromwellDRSLocalizer` with manifest file
+### DRS Improvements
 
-`CromwellDRSLocalizer` can now handle multiple file localizations in a single invocation. Users can provide a 
-manifest file containing multiple (DRS id, local container path) pairs in CSV format, and they will be localized in 
+#### Support for invoking `CromwellDRSLocalizer` with manifest file
+
+`CromwellDRSLocalizer` can now handle multiple file localizations in a single invocation. Users can provide a
+manifest file containing multiple (DRS id, local container path) pairs in CSV format, and they will be localized in
 sequence, with the program exiting if any fail.
 ```
 java -jar /path/to/localizer.jar [options] -m /local/path/to/manifest/file.txt
 ```
 
-The previous method of passing in a single DRS file and container destination using positional arguments is still 
+The previous method of passing in a single DRS file and container destination using positional arguments is still
 supported.
 
-### Improvement to DRS localization in GCP papiv2beta backend
+#### Improvement to DRS localization in GCP papiv2beta backend
 
 All DRS inputs to a task are now localized in a single PAPI action, which should improve speed and resolve
 failures observed when attempting to localize a large number of DRS files.
 
-### Security Patching
-
-Updates to dependencies to fix security vulnerabilities.
 
 ### Allow list for HTTP WDL resolution
 
-Administrators can now configure Cromwell with an allow list that limits the domains from which WDLs can be resolved and imported. 
+Administrators can now configure Cromwell with an allow list that limits the domains from which WDLs can be resolved and imported.
 Default behavior is unchanged (Cromwell attempts to resolve WDL files from any URI). Example configuration:
 ```
 languages {
@@ -56,15 +55,28 @@ languages {
 
 ### CWL implementation removed
 
-This release removes the `cwl` top-level artifact. Some nonfunctional references may remain, and will be addressed over time. 
+This release removes the `cwl` top-level artifact. Some nonfunctional references may remain, and will be addressed over time.
+
+For more information, see the [Cromwell 79 release notes](https://github.com/broadinstitute/cromwell/releases/tag/79).
+
+### TES Improvments
+
+* Tes system errors are are now reported in Cromwell execution logs when the TES backend returns a task error.
+
+* Cromwell now attempts to translate `disks` attributes [written for GCP](https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/#disks) into valid `disk` attributes for TES. For information on supported conversions, refer to the [TES documentation](https://cromwell.readthedocs.io/en/stable/backends/TES/).
+
+### Bug Fixes
 
-For more information, see the [Cromwell 79 release notes](https://github.com/broadinstitute/cromwell/releases/tag/79). 
+* Reference disks are only mounted if configured in the workflow options.
 
-### TES backend supports `disks` attribute
+* Recent docker images of Ubuntu use a new manifest format, ensure that these newer image versions can be pulled from Docker Registry without issue.
 
-Cromwell now attempts to translate `disks` attributes [written for GCP](https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/#disks) into valid `disk` attributes for TES.
+* When converting ValueStore objects to strings for logging, we truncate long values to limit memory usage.
 
-For information on supported conversions, refer to the [TES documentation](https://cromwell.readthedocs.io/en/stable/backends/TES/).
+
+### Security Patching
+
+Updates to dependencies to fix security vulnerabilities.
 
 ## 84 Release Notes
 
@@ -74,7 +86,7 @@ For Cromwell instances utilizing the optional CromIAM identity and access manage
 * `/api/workflows/v1/backends`
 * `/api/womtool/v1/describe`
 
-This change makes the above endpoints consistent with the existing behavior of all the other endpoints in the `/api/` path of CromIAM. 
+This change makes the above endpoints consistent with the existing behavior of all the other endpoints in the `/api/` path of CromIAM.
 
 ## 83 Release Notes
 
@@ -107,7 +119,7 @@ The BCS backend and OSS filesystem (both of which support Alibaba Cloud) have be
 Cromwell 80 no longer supports the wes2cromwell project within the Cromwell repository.
 
 In the previous release, 3 Wes2Cromwell endpoints in the Cromwell project were implemented and documented in the Swagger API. Three new endpoints,
-located within the wes2cromwell project, will also be moved, implemented, and documented within Cromwell. As a result of this, we can safely remove 
+located within the wes2cromwell project, will also be moved, implemented, and documented within Cromwell. As a result of this, we can safely remove
 and deprecate the wes2cromwell project from the repo.
 
 Previous endpoints:
@@ -191,11 +203,11 @@ Previously:
 
 ### New 'requestedWorkflowId' API Option
 
-Allows users to choose their own workflow IDs at workflow submission time. 
+Allows users to choose their own workflow IDs at workflow submission time.
 
 If supplied for single workflows, this value must be a JSON string containing a valid, and not already used, UUID. For batch submissions, this value must be a JSON array of valid UUIDs.
 
-If not supplied, the behavior is as today: Cromwell will generate a random workflow ID for every workflow submitted. 
+If not supplied, the behavior is as today: Cromwell will generate a random workflow ID for every workflow submitted.
 
 ### Bug Fixes
 
@@ -308,8 +320,8 @@ AccessURLs](https://ga4gh.github.io/data-repository-service-schemas/preview/rele
 
 ### No labels update for Archived workflows
 
-If **- and ONLY if -** you have metadata archiving turned on, then for a workflow whose metadata has been archived by Cromwell 
-according to the lifecycle policy, Cromwell will no longer add new labels or update existing labels for this workflow 
+If **- and ONLY if -** you have metadata archiving turned on, then for a workflow whose metadata has been archived by Cromwell
+according to the lifecycle policy, Cromwell will no longer add new labels or update existing labels for this workflow
 coming through PATCH `/labels` endpoint.
 
 ## 60 Release Notes
@@ -321,12 +333,12 @@ containerized using [AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/).
 
 ### Hybrid metadata storage ("carboniting") removed
 
-Carboniting functionality has been removed from Cromwell. 
+Carboniting functionality has been removed from Cromwell.
 There will be no effect for customers who store metadata permanently in the relational database (most common),
 and there will also be no effect for customers who use the in-memory database.
 
 Breaking change only for customers who explicitly enabled `carbonite-metadata-service` in their configuration to split
-metadata storage between a relational database and Google Cloud Storage. If you had previously enabled carboniting and 
+metadata storage between a relational database and Google Cloud Storage. If you had previously enabled carboniting and
 deletion, any workflows marked as `ArchivedAndPurged` in your database will no longer be accessible via the Cromwell metadata API.
 
 ## 59 Release Notes
@@ -353,9 +365,9 @@ rather than through a level of indirection to a manifest file stored in GCS. Mor
 ### Retry with More Memory as workflow option
 
 The experimental memory retry feature gains per-workflow customization and includes breaking changes:
-* The per-backend configuration key `<backend>.config.memory-retry.error-keys` has been removed and replaced 
+* The per-backend configuration key `<backend>.config.memory-retry.error-keys` has been removed and replaced
 with global key `system.memory-retry-error-keys`
-* The per-backend configuration key `<backend>.config.memory-retry.multiplier` has been replaced with **workflow option** 
+* The per-backend configuration key `<backend>.config.memory-retry.multiplier` has been replaced with **workflow option**
 `memory_retry_multiplier`
 
 More details can be found [here](https://cromwell.readthedocs.io/en/develop/wf_options/Overview.md#retry-with-more-memory-multiplier).
@@ -364,7 +376,7 @@ More details can be found [here](https://cromwell.readthedocs.io/en/develop/wf_o
 
 * Fixed a bug that caused Cromwell to mark workflows as failed after a single `500`, `503`, or `504` error from Google Cloud Storage.
   * Cromwell will now retry these errors as designed.
-  * The default retry count is `5` and may be customized with `system.io.number-of-attempts`. 
+  * The default retry count is `5` and may be customized with `system.io.number-of-attempts`.
 
 ## 55 Release Notes
 
@@ -374,7 +386,7 @@ Users with access to the new Mac hardware should review [important information p
 
 ### Bug Fixes
 
-* Fixed a bug that prevented `read_json()` from working with arrays and primitives. The function now works as expected for all valid JSON data inputs. 
+* Fixed a bug that prevented `read_json()` from working with arrays and primitives. The function now works as expected for all valid JSON data inputs.
 More information on JSON Type to WDL Type conversion can be found [here](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#mixed-read_jsonstringfile).
 
 * Now retries HTTP 408 responses as well as HTTP 429 responses during DOS/DRS resolution requests.
@@ -402,19 +414,19 @@ to the worker VM on the next attempt if the task is interrupted. More details [h
 ### Bug Fixes
 
 * Fixed a bug that prevented `write_json()` from working with arrays and primitives. The function now works as expected for `Boolean`, `String`, `Integer`, `Float`,
- `Pair[_, _]`, `Object`, `Map[_, _]` and `Array[_]` (including array of objects) type inputs. More information on WDL Type to JSON Type 
+ `Pair[_, _]`, `Object`, `Map[_, _]` and `Array[_]` (including array of objects) type inputs. More information on WDL Type to JSON Type
  conversion can be found [here](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#mixed-read_jsonstringfile).
 
 ### Spark backend support removal
 
-Spark backend was not widely used and it was decided to remove it from the codebase in order to narrow the scope of Cromwell code. 
+Spark backend was not widely used and it was decided to remove it from the codebase in order to narrow the scope of Cromwell code.
 
 ### Improved DRS Localizer logging
 
 Error logging while localizing a DRS URI should now be more clear especially when there is a Requester Pays bucket involved.
 
 ### Per-backend hog factors
-Cromwell now allows overriding system-level log factors on back-end level. First, Cromwell will try to use hog-factor 
+Cromwell now allows overriding system-level log factors on back-end level. First, Cromwell will try to use hog-factor
 defined in the backend config, and if it is not defined, it will default to using system-wide hog factor.
 ```conf
 backend {
@@ -482,16 +494,16 @@ https://cromwell.readthedocs.io/en/stable/tutorials/Containers/#singularity).
 
 ### Google library upgrade [(#5565)](https://github.com/broadinstitute/cromwell/pull/5565)
 
-All previous versions of Cromwell shipped with Google Cloud Storage (GCS) libraries that are now deprecated and will [stop working in August 2020](https://developers.googleblog.com/2018/03/discontinuing-support-for-json-rpc-and.html). This release adopts updated libraries to ensure uninterrupted operation. The only user action required is upgrading Cromwell.   
+All previous versions of Cromwell shipped with Google Cloud Storage (GCS) libraries that are now deprecated and will [stop working in August 2020](https://developers.googleblog.com/2018/03/discontinuing-support-for-json-rpc-and.html). This release adopts updated libraries to ensure uninterrupted operation. The only user action required is upgrading Cromwell.
 
 ### Bug fixes
 
 * Fixed a bug that required Cromwell to be restarted in order to pick up DNS changes.
     * By default, the JVM caches DNS records with a TTL of infinity.
-    * Cromwell now configures its JVM with a 3-minute TTL. This value can be customized by setting `system.dns-cache-ttl`.  
+    * Cromwell now configures its JVM with a 3-minute TTL. This value can be customized by setting `system.dns-cache-ttl`.
 * Clarified an error message that Cromwell emits when the compute backend terminates a job of its own volition (as opposed to termination in response to an abort request from Cromwell)
     * Previously, the error read `The job was aborted from outside Cromwell`
-    * The new error reads `The compute backend terminated the job. If this termination is unexpected, examine likely causes such as preemption, running out of disk or memory on the compute instance, or exceeding the backend's maximum job duration.` 
+    * The new error reads `The compute backend terminated the job. If this termination is unexpected, examine likely causes such as preemption, running out of disk or memory on the compute instance, or exceeding the backend's maximum job duration.`
 
 ## 51 Release Notes
 
@@ -502,8 +514,8 @@ https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching) for details
 
 ### Bug fixes
 
-* Fixed a bug where the `size(...)` function did not work correctly on files 
-  from a shared filesystem if `size(...)` was called in the input section on a 
+* Fixed a bug where the `size(...)` function did not work correctly on files
+  from a shared filesystem if `size(...)` was called in the input section on a
   relative path.
 + Fixed a bug where the `use_relative_output_paths` option would not preserve intermediate folders.
 
@@ -511,17 +523,17 @@ https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching) for details
 
 #### Call caching blacklisting improvements
 
-Cromwell previously supported blacklisting GCS buckets containing cache hits which could not be copied for permissions 
+Cromwell previously supported blacklisting GCS buckets containing cache hits which could not be copied for permissions
 reasons. Cromwell now adds support for blacklisting individual cache hits which could not be copied for any reason,
 as well as grouping blacklist caches according to a workflow option key. More information available in the [
-call caching documentation]( https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching). 
+call caching documentation]( https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching).
 
 #### new xxh64 and fingerprint strategies for call caching
 
-Existing call cache strategies `path` and `path+modtime` don't work when using docker on shared filesystems 
+Existing call cache strategies `path` and `path+modtime` don't work when using docker on shared filesystems
 (SFS backend, i.e. not in cloud storage). The `file` (md5sum) strategy works, but uses a lot of resources.
-Two faster strategies have been added for this use case: `xxh64` and 
-`fingerprint`. `xxh64` is a lightweight hashing algorithm, `fingerprint` is a strategy designed to be very 
+Two faster strategies have been added for this use case: `xxh64` and
+`fingerprint`. `xxh64` is a lightweight hashing algorithm, `fingerprint` is a strategy designed to be very
 lightweight. Read more about it in the [call caching documentation](
 https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching).
 
@@ -555,7 +567,7 @@ SELECT table_rows FROM INFORMATION_SCHEMA.TABLES WHERE TABLE_SCHEMA = 'cromwell'
 
 #### Execution Directory Layout (cache copies)
 
-When an attempt to copy a cache result is made, you'll now see a `cacheCopy` directory in the call root directory. 
+When an attempt to copy a cache result is made, you'll now see a `cacheCopy` directory in the call root directory.
 This prevents them clashing with the files staged to the same directory for attempt 1 if the cache copy fails (see also: Bug Fixes).
 
 The directory layout used to be:
@@ -592,7 +604,7 @@ but is now:
 
 #### Disable call-caching for tasks
 
-It is now possible to indicate in a workflow that a task should not be call-cached. See details 
+It is now possible to indicate in a workflow that a task should not be call-cached. See details
 [here](https://cromwell.readthedocs.io/en/stable/optimizations/VolatileTasks).
 
 #### Delete Intermediate Outputs on PapiV2
@@ -605,13 +617,13 @@ for more information.
 #### Metadata Archival Support
 
 Cromwell 49 now offers the option to archive metadata to GCS and remove the equivalent metadata from relational
-database storage. Please see 
-[the documentation](https://cromwell.readthedocs.io/en/stable/Configuring#hybrid-metadata-storage-classic-carbonite) for more details. 
+database storage. Please see
+[the documentation](https://cromwell.readthedocs.io/en/stable/Configuring#hybrid-metadata-storage-classic-carbonite) for more details.
 
 #### Adding support for Google Cloud Life Sciences v2beta
-Cromwell now supports running workflows using Google Cloud Life Sciences v2beta API in addition to Google Cloud Genomics v2alpha1. 
-More information about migration to the new API from v2alpha1 
-[here](https://cromwell.readthedocs.io/en/stable/backends/Google#migration-from-google-cloud-genomics-v2alpha1-to-google-cloud-life-sciences-v2beta). 
+Cromwell now supports running workflows using Google Cloud Life Sciences v2beta API in addition to Google Cloud Genomics v2alpha1.
+More information about migration to the new API from v2alpha1
+[here](https://cromwell.readthedocs.io/en/stable/backends/Google#migration-from-google-cloud-genomics-v2alpha1-to-google-cloud-life-sciences-v2beta).
 * **Note** Google Cloud Life Sciences is the new name for newer versions of Google Cloud Genomics.
 * **Note** Support for Google Cloud Genomics v2alpha1 will be removed in a future version of Cromwell. Advance notice will be provided.
 
@@ -619,23 +631,23 @@ More information about migration to the new API from v2alpha1
 
 #### Installation methods
 
-Links to the conda package and docker container are now available in 
+Links to the conda package and docker container are now available in
 [the install documentation](https://cromwell.readthedocs.io/en/stable/Getting/).
 
 
 ### Bug Fixes
 
-+ Fix a bug where zip files with directories could not be imported. 
-  For example a zip with `a.wdl` and `b.wdl` could be imported but one with `sub_workflows/a.wdl` 
++ Fix a bug where zip files with directories could not be imported.
+  For example a zip with `a.wdl` and `b.wdl` could be imported but one with `sub_workflows/a.wdl`
   and `imports/b.wdl` could not.
 + Fix a bug which sometimes allowed execution scripts copied by a failed cache-copy to be run instead
-  of the attempt-1 script for a live job execution. 
-  
+  of the attempt-1 script for a live job execution.
+
 ## 48 Release Notes
 
 ### Womtool Graph for WDL 1.0
 
-The `womtool graph` command now supports WDL 1.0 workflows. 
+The `womtool graph` command now supports WDL 1.0 workflows.
 * **Note:** Generated graphs - including in WDL draft 2 - may look slightly different than they did in version 47.
 
 ### Documentation
@@ -647,7 +659,7 @@ The `womtool graph` command now supports WDL 1.0 workflows.
 
 ### Retry with more memory on Papiv2 [(#5180)](https://github.com/broadinstitute/cromwell/pull/5180)
 
-Cromwell now allows user defined retries. With `memory-retry` config you can specify an array of strings which when encountered in the `stderr` 
+Cromwell now allows user defined retries. With `memory-retry` config you can specify an array of strings which when encountered in the `stderr`
 file by Cromwell, allows the task to be retried with multiplier factor mentioned in the config. More information [here](https://cromwell.readthedocs.io/en/stable/backends/Google/).
 
 ### GCS Parallel Composite Upload Support
@@ -681,7 +693,7 @@ PAPI error code 14. Task was preempted for the 2nd time.
 ```
 Cromwell 44 introduced special handling that detects both preemption indicators and re-runs the job consistent with the `preemptible` setting.
 
-Cromwell 46 enhances this handling in response to user reports of possible continued issues.   
+Cromwell 46 enhances this handling in response to user reports of possible continued issues.
 
 ## 45 Release Notes
 
@@ -699,7 +711,7 @@ More info [here](https://cromwell.readthedocs.io/en/stable/WOMtool/)
 ### BCS backend new Features support
 
 #### New docker registry
-Alibaba Cloud Container Registry is now supported for the `docker` runtime attribute, and the previous `dockerTag` 
+Alibaba Cloud Container Registry is now supported for the `docker` runtime attribute, and the previous `dockerTag`
 runtime attribute continues to be available for Alibaba Cloud OSS Registry.
 #### Call caching
 Cromwell now supports Call caching when using the BCS backend.
@@ -727,7 +739,7 @@ Cromwell's PAPI v2 backend will now handle this type of preemption.
 
 ### Virtual Private Cloud with Subnetworks
 
-Cromwell now allows PAPIV2 jobs to run on a specific subnetwork inside a private network by adding the subnetwork key 
+Cromwell now allows PAPIV2 jobs to run on a specific subnetwork inside a private network by adding the subnetwork key
 `subnetwork-label-key` inside `virtual-private-cloud` in backend configuration. More info [here](https://cromwell.readthedocs.io/en/stable/backends/Google/).
 
 ### Call caching database refactoring
@@ -735,7 +747,7 @@ Cromwell now allows PAPIV2 jobs to run on a specific subnetwork inside a private
 Cromwell's `CALL_CACHING_HASH_ENTRY` primary key has been refactored to use a `BIGINT` datatype in place of the previous
 `INT` datatype. Cromwell will not be usable during the time the Liquibase migration for this refactor is running.
 In the Google Cloud SQL with SSD environment this migration runs at a rate of approximately 100,000 `CALL_CACHING_HASH_ENTRY`
-rows per second. In deployments with millions or billions of `CALL_CACHING_HASH_ENTRY` rows the migration may require  
+rows per second. In deployments with millions or billions of `CALL_CACHING_HASH_ENTRY` rows the migration may require
 a significant amount of downtime so please plan accordingly. The following SQL could be used to estimate the number of
 rows in this table:
 
@@ -745,7 +757,7 @@ select max(CALL_CACHING_HASH_ENTRY_ID) from CALL_CACHING_HASH_ENTRY
 
 ### Stackdriver Instrumentation
 
-Cromwell now supports sending metrics to [Google's Stackdriver API](https://cloud.google.com/monitoring/api/v3/). 
+Cromwell now supports sending metrics to [Google's Stackdriver API](https://cloud.google.com/monitoring/api/v3/).
 Learn more on how to configure [here](https://cromwell.readthedocs.io/en/stable/developers/Instrumentation/).
 
 ### BigQuery in PAPI
@@ -762,7 +774,7 @@ which now has been updated to `services.Instrumentation.config`. More info on it
 
 #### cached-copy
 
-A new experimental feature, the `cached-copy` localization strategy is available for the shared filesystem. 
+A new experimental feature, the `cached-copy` localization strategy is available for the shared filesystem.
 More information can be found in the [documentation on localization](https://cromwell.readthedocs.io/en/stable/backends/HPC).
 
 #### Yaml node limits
@@ -796,7 +808,7 @@ Specifically, the new `validWorkflow` key indicates whether the workflow file is
 ### Configuration Changes
 
  *  Virtual private networks can now be configured. See the section below for details.
- 
+
 #### Batch Request Timeouts
 
 The timeout on Cromwell's requests to PAPIv2 can now be configured. See the sample PAPIv2.conf for more documentation:
@@ -805,7 +817,7 @@ The timeout on Cromwell's requests to PAPIv2 can now be configured. See the samp
 backend {
   providers {
     PAPIv2 {
-      config { 
+      config {
         batch-requests {
           timeouts {
             read = 10 seconds
@@ -882,14 +894,14 @@ This field is now accepted within WDL files as well as within the configuration
 
 #### Logging long running jobs
 
-All backends can now emit slow job warnings after a configurable time running. 
+All backends can now emit slow job warnings after a configurable time running.
 NB This example shows how to configure this setting for the PAPIv2 backend:
 ```conf
 # Emit a warning if jobs last longer than this amount of time. This might indicate that something got stuck.
 backend {
   providers {
     PAPIv2 {
-      config { 
+      config {
         slow-job-warning-time: 24 hours
       }
     }
@@ -904,7 +916,7 @@ backend {
 * The `gpuType` attribute is no longer validated against a whitelist at workflow submission time. Instead, validation now happens at runtime. This allows any valid accelerator to be used.
 * The `nvidiaDriverVersion` attribute is now available in WDL `runtime` sections. The default continues to be `390.46` which applies if and only if GPUs are being used.
 * A default `gpuType` ("nvidia-tesla-k80") will now be applied if `gpuCount` is specified but `gpuType` is not.
-* Similarly, a default `gpuCount` (1) will be applied if `gpuType` is specified but `cpuCount` is not. 
+* Similarly, a default `gpuCount` (1) will be applied if `gpuType` is specified but `cpuCount` is not.
 
 ### Bug fixes
 
@@ -945,7 +957,7 @@ services {
         class = "cromwell.services.healthmonitor.impl.standard.StandardHealthMonitorServiceActor"
     }
 }
-``` 
+```
 With this one:
 ```
 services {
@@ -956,7 +968,7 @@ services {
         }
     }
 }
-``` 
+```
 ###### From `WorkbenchHealthMonitorServiceActor`:
 Replace this stanza:
 ```
@@ -973,7 +985,7 @@ services {
         }
     }
 }
-``` 
+```
 With this one:
 ```
 services {
@@ -989,12 +1001,12 @@ services {
     }
   }
 }
-``` 
+```
 ### Workflow options changes
 
-A new workflow option is added. If the `final_workflow_outputs_dir` is set 
-`use_relative_output_paths` can be used. When set to `true` this will copy 
-all the outputs relative to their execution directory. 
+A new workflow option is added. If the `final_workflow_outputs_dir` is set
+`use_relative_output_paths` can be used. When set to `true` this will copy
+all the outputs relative to their execution directory.
 my_final_workflow_outputs_dir/~~MyWorkflow/af76876d8-6e8768fa/call-MyTask/execution/~~output_of_interest.
 More information can be found in [the workflow options documentation](https://cromwell.readthedocs.io/en/stable/wf_options/Overview/#output-copying).
 
@@ -1024,10 +1036,10 @@ shutdown.
 
 ### Bug fixes
 
-#### Format fix for `write_map()` 
+#### Format fix for `write_map()`
 
 Fixed an issue that caused the `write_map()` function in Cromwell's WDL 1.0 implementation to produce output in the wrong format. Specifically, the output's rows and columns were swapped. WDL draft-2 was not affected.
-  
+
 Incorrect `write_map()` output in Cromwell 38 and earlier:
 ```
 key1    key2    key3
@@ -1067,7 +1079,7 @@ available as `StandardHealthMonitorServiceActor`.
 ### Docker
 
 - Adds support for retrieving docker digests of asia.gcr.io images
-- Adds configuration settings for docker digest lookups. See the `docker` section of the `reference.conf` for more information 
+- Adds configuration settings for docker digest lookups. See the `docker` section of the `reference.conf` for more information
 - Attempt to automatically adjust the boot disk size on the Google Cloud Backend (version 2) if the size of the image is greater than the default disk size or the required disk size in the runtime attributes.
 Only works for registries that support the version 2 of the manifest schema (https://docs.docker.com/registry/spec/manifest-v2-2/)
 At this date (12/09/18) this includes GCR and Dockerhub.
@@ -1112,28 +1124,28 @@ Support `InputResourceRequirement` hint
 In cases where its not obvious why jobs are queued in Cromwell, you can enable logging for the Job Execution Token Dispenser, using
 the `system.hog-safety.token-log-interval-seconds` configuration value.
 
-The default, `0`, means that no logging will occur. 
+The default, `0`, means that no logging will occur.
 
 #### HTTP Filesystem
 
-- The HTTP filesystem is now enabled for engine use by default. To continue without an HTTP filesystem, you can add the 
+- The HTTP filesystem is now enabled for engine use by default. To continue without an HTTP filesystem, you can add the
 following content into the appropriate stanza of your configuration file:
 ```
 engine {
   filesystems {
-    http { 
-      enabled: false 
+    http {
+      enabled: false
     }
   }
 }
-``` 
+```
 - When the value `exit-code-timeout-seconds` is set, `check-alive` command is now only called once every timeout interval instead of each poll.
 
 ### Beta preview of new Womtool `/describe` endpoint
 
 This new endpoint brings the functionality of Womtool to the world of web services. Submit workflows for validation and receive a JSON description in response.
 
-The endpoint is still undergoing heavy development and should not be used in production. The final version will ship in a future release of Cromwell; watch this space.   
+The endpoint is still undergoing heavy development and should not be used in production. The final version will ship in a future release of Cromwell; watch this space.
 
 ### Bug fixes
 
@@ -1173,7 +1185,7 @@ Details [here](https://cromwell.readthedocs.io/en/develop/backends/HPC/#exit-cod
 
 Coalesce metadata requests to eliminate expensive and redundant queries and metadata construction.
 
-#### Eliminate redundant SFS logging and metadata 
+#### Eliminate redundant SFS logging and metadata
 
 Eliminate superfluous logging and metadata publishing in the shared filesystem backend on poll intervals where there was not a state change.
 
@@ -1186,7 +1198,7 @@ Previously US-EAST-1 was hardcoded in places.
 ### Submit workflow using URL
 
 Cromwell now allows for a user to submit the URL pointing to workflow file to run a workflow.
-More details on how to use it in: 
+More details on how to use it in:
 - `Server` mode can be found [here](https://cromwell.readthedocs.io/en/develop/api/RESTAPI/).
 - `Run` mode can be found [here](https://cromwell.readthedocs.io/en/develop/CommandLine/#run).
 
@@ -1212,7 +1224,7 @@ Cromwell now offers the ability to cache file hashes on a root workflow level ba
 
 ### Extra configuration options
 
-The value `dockerRoot` can now be set in a backend configuration. 
+The value `dockerRoot` can now be set in a backend configuration.
 This will set the execution folder in the container (default: `/cromwell-executions`).
 
 ### Bug Fixes
@@ -1318,7 +1330,7 @@ Cromwell now supports retrying failed tasks up to a specified count by declaring
 * Cromwell now publishes the labels as soon as the workflow is submitted (whether started or on hold). If the labels are invalid, the workflow will not be submitted and request will fail.
 
 ### Scala 2.11 Removed
-From version 32 onwards we will no longer be publishing build artifacts compatible with Scala 2.11. 
+From version 32 onwards we will no longer be publishing build artifacts compatible with Scala 2.11.
 
 * If you don't import the classes into your own scala project then this should have no impact on you.
 * If you **are** importing the classes into your own scala project, make sure you are using Scala 2.12.
@@ -1410,12 +1422,12 @@ Workflow metadata for jobs run on a Google Pipelines API backend will report the
 
 ## 31 Release Notes
 
-* **Cromwell server**  
-The Cromwell server source code is now located under `server/src`. `sbt assembly` will build the runnable Cromwell JAR in 
+* **Cromwell server**
+The Cromwell server source code is now located under `server/src`. `sbt assembly` will build the runnable Cromwell JAR in
 `server/target/scala-2.12/` with a name like `cromwell-<VERSION>.jar`.
 
 * **Robustness**
-    + The rate at which jobs are being started can now be controlled using the `system.job-rate-control` configuration stanza.  
+    + The rate at which jobs are being started can now be controlled using the `system.job-rate-control` configuration stanza.
     + A load controller service has been added to allow Cromwell to self-monitor and adjust its load accordingly.
 The load controller is currently a simple on/off switch controlling the job start rate. It gathers metrics from different parts of the system
 to inform its decision to stop the creation of jobs.
@@ -1423,7 +1435,7 @@ You can find relevant configuration in the `services.LoadController` section of
 as well as in the `load-control` section in `reference.conf`.
 The load level of the monitored sub-systems are instrumented and can be found under the `cromwell.load` statsD path.
     + The statsD metrics have been re-shuffled a bit. If you had a dashboard you might find that you need to update it.
-Changes include: 
+Changes include:
         + Removed artificially inserted "count" and "timing" the path
         + Added a `load` section
         + Metrics were prefixed twice with `cromwell` (`cromwell.cromwell.my_metric`), now they're only prefixed once
@@ -1432,8 +1444,8 @@ Changes include:
 
 * Added a configuration option under `docker.hash-lookup.enabled` to disable docker hash lookup.
  Disabling it will also disable call caching for jobs with floating docker tags.
- 
-* **API**    
+
+* **API**
     + Updated the `/query` response to include the total number of query results returned. See [here](http://cromwell.readthedocs.io/en/develop/api/RESTAPI/#workflowqueryresponse) for more information.
 
 ## 30.1 Release Notes
@@ -1448,14 +1460,14 @@ Changes include:
 
 ### Other changes
 
-* **New Cromwell documentation**  
+* **New Cromwell documentation**
 Our documentation has moved from our [README](https://github.com/broadinstitute/cromwell/blob/29_hotfix/README.md) to a new website: [Cromwell Documentation](http://cromwell.readthedocs.io/en/develop/). There are new [Tutorials](http://cromwell.readthedocs.io/en/develop/tutorials/FiveMinuteIntro/) and much of the documentation has been re-written. The source files are in the [/docs](https://github.com/broadinstitute/cromwell/tree/develop/docs) directory.
 
-* **API**  
+* **API**
     + Cromwell now supports input files in the yaml format (JSON format is still supported).
     + Added a [GET version for the `labels` endpoint](http://cromwell.readthedocs.io/en/develop/api/RESTAPI/#retrieves-the-current-labels-for-a-workflow) which will return current labels for a workflow.
 
-* **Database**  
+* **Database**
 You have the option of storing the metadata in a separate SQL database than the database containing the internal engine
 data. When switching connection information for an existing database containing historical data, the tables
 should be manually replicated from one database instance to another using the tools appropriate for your specific
@@ -1464,48 +1476,48 @@ and likely to change in the future. See the [Database Documentation](https://cro
 [cromwell.examples.conf](https://www.github.com/broadinstitute/cromwell/tree/develop/cromwell.example.backends/cromwell.examples.conf) for more
 information.
 
-* **StatsD**  
+* **StatsD**
 Added initial support for StatsD instrumentation. See the [Instrumentation Documentation](https://cromwell.readthedocs.io/en/develop/Instrumentation) for details on how to use it.
 
-* **User Service Account auth mode for Google**  
+* **User Service Account auth mode for Google**
 Added a new authentication mode for [Google Cloud Platform](https://cromwell.readthedocs.io/en/develop/backends/Google) which will allow a user to supply the JSON key file in their workflow options to allow for per-workflow authentication via service account. This is analogous to the previously existing refresh token authentication scheme. As with the refresh token scheme it is encouraged that the **user_service_account_json** workflow option field is added to the **encrypted-fields** list in the configuration.
 
-* **Bugfixes**  
+* **Bugfixes**
 Abort of Dockerized tasks on the Local backend should now work as expected. Cromwell uses `docker kill` to kill the Docker container.
 
 ## 29 Release Notes
 
 ### Breaking Changes
 
-* **Command line**  
+* **Command line**
 In preparation for supporting CWL scripts (yes, you read that right!), we have extensively revised the Command Line in Cromwell 29. For more details about the usage changes please see the [README](https://github.com/broadinstitute/cromwell#command-line-usage). And stay tuned to the [WDL/Cromwell blog](https://software.broadinstitute.org/wdl/blog) over the next couple of months for more news about CWL.
 
-* **Request timeouts**   
+* **Request timeouts**
 Cromwell now returns more specific `503 Service Unavailable` error codes on request timeouts, rather than the more generic `500 Internal Server Error`. The response for a request timeout will now be plain text, rather than a JSON format.
 
-* **Metadata endpoint**  
+* **Metadata endpoint**
 The response from the metadata endpoint can be quite large depending on your workflow. You can now opt-in to have Cromwell gzip your metadata file, in order to reduce file size, by sending the `Accept-Encoding: gzip` header. The default behavior now does not gzip encode responses.
 
-* **Engine endpoints**  
+* **Engine endpoints**
 Previously the engine endpoints were available under `/api/engine` but now the endpoints are under `/engine` so they don't require authentication. Workflow endpoints are still available under `/api/workflows`. We also deprecated the setting `api.routeUnwrapped` as a part of this internal consistency effort.
 
-* **Call caching diff**  
+* **Call caching diff**
 We updated the response format of the [callcaching/diff](https://github.com/broadinstitute/cromwell#get-apiworkflowsversioncallcachingdiff) endpoint.
 
 ### Other changes
 
-* **Cromwell server**  
+* **Cromwell server**
 When running in server mode, Cromwell now attempts to gracefully shutdown after receiving a `SIGINT` (`Ctrl-C`) or `SIGTERM` (`kill`) signal. This means that Cromwell waits for all pending database writes before exiting, as long as you include `application.conf` at the top of your config file. You can find detailed information about how to configure this feature in the [Cromwell Wiki](https://github.com/broadinstitute/cromwell/wiki/DevZone#graceful-server-shutdown).
 
-* **Concurrent jobs**  
+* **Concurrent jobs**
 You can now limit the number of concurrent jobs for any backend. Previously this was only possible in some backend implementations. Please see the [README](https://github.com/broadinstitute/cromwell#backend-job-limits) for details.
 
 ### WDL
 
-* **Optional WDL variables**  
+* **Optional WDL variables**
 Empty optional WDL values are now rendered as the `null` JSON value instead of the JSON string `"null"` in the metadata and output endpoints. You do not need to migrate previous workflows. Workflows run on Cromwell 28 and prior will still render empty values as `"null"`.
 
-* **Empty WDL variables**  
+* **Empty WDL variables**
 Cromwell now accepts `null` JSON values in the input file and coerces them as an empty WDL value. WDL variables must be declared optional in order to be supplied with a `null` JSON value.
 
 input.json
@@ -1554,8 +1566,8 @@ task writer {
 #### `ContinueWhilePossible`
 
 A workflow utilizing the WorkflowFailureMode Workflow Option `ContinueWhilePossible` will now successfully reach a terminal state once all runnable jobs have completed.
-#### `FailOnStderr` 
-When `FailOnStderr` is set to false, Cromwell no longer checks for the existence of a stderr file for that task. 
+#### `FailOnStderr`
+When `FailOnStderr` is set to false, Cromwell no longer checks for the existence of a stderr file for that task.
 
 ### WDL Functions
 
@@ -1571,7 +1583,7 @@ task foo {
     command { ... }
     runtime {
       docker: "..."
-      memory: ceil(size(in_file)) * 4 
+      memory: ceil(size(in_file)) * 4
     }
 }
 ```
@@ -1586,7 +1598,7 @@ If the hashes fail to be calculated, the reason is indicated in a `hashFailures`
 
 See the [README](https://github.com/broadinstitute/cromwell#get-apiworkflowsversionidmetadata) for an example metadata response.
 
-* New endpoint returning the hash differential for 2 calls. 
+* New endpoint returning the hash differential for 2 calls.
 
 `GET /api/workflows/:version/callcaching/diff`
 
@@ -1615,7 +1627,7 @@ A second value is allowed, `reference`, that will instead point to the original
 filesystems {
   gcs {
     auth = "application-default"
-    
+
     caching {
       duplication-strategy = "reference"
     }
@@ -1643,7 +1655,7 @@ than the previous default.
  The migration will only be executed on MySQL. Other databases will lose their previous cached jobs.
  In order to run properly on MySQL, **the following flag needs to be adjusted**: https://dev.mysql.com/doc/refman/5.5/en/server-system-variables.html#sysvar_group_concat_max_len
  The following query will give you a minimum to set the group_concat_max_len value to:
- 
+
  ```sql
 SELECT MAX(aggregated) as group_concat_max_len FROM
       (
@@ -1654,15 +1666,15 @@ SELECT MAX(aggregated) as group_concat_max_len FROM
  ```
 
  Here is the SQL command to run to set the group_concat_max_len flag to the proper value:
- 
+
  ```sql
 SET GLOBAL group_concat_max_len = value
  ```
- 
+
  Where `value` is replaced with the value you want to set it to.
- 
+
  Note that the migration will fail if the flag is not set properly.
- 
+
 ### Breaking Changes
 
 * The update to Slick 3.2 requires a database stanza to
@@ -1710,7 +1722,7 @@ run the call:
 
 ### Docker
 
-* The Docker section of the configuration has been slightly reworked 
+* The Docker section of the configuration has been slightly reworked
 An option to specify how a Docker hash should be looked up has been added. Two methods are available.
     "local" will try to look for the image on the machine where cromwell is running. If it can't be found, Cromwell will try to `pull` the image and use the hash from the retrieved image.
     "remote" will try to look up the image hash directly on the remote repository where the image is located (Docker Hub and GCR are supported)
@@ -1774,14 +1786,14 @@ failures: [{
 
 * Added a configuration option under `system.io` to throttle the number of I/O queries that Cromwell makes, as well as configure retry parameters.
  This is mostly useful for the JES backend and should be updated to match the GCS quota available for the project.
- 
+
 ```
 system.io {
   # Global Throttling - This is mostly useful for GCS and can be adjusted to match
   # the quota availble on the GCS API
   number-of-requests = 100000
   per = 100 seconds
-  
+
   # Number of times an I/O operation should be attempted before giving up and failing it.
   number-of-attempts = 5
 }
@@ -1805,7 +1817,7 @@ system.io {
 
 ### Config Changes
 
-* Added a field `insert-batch-size` to the `database` stanza which defines how many values from a batch insert will be processed at a time. This value defaults to 2000. 
+* Added a field `insert-batch-size` to the `database` stanza which defines how many values from a batch insert will be processed at a time. This value defaults to 2000.
 * Moved the config value `services.MetadataService.metadata-summary-refresh-interval` to `services.MetadataService.config.metadata-summary-refresh-interval`
 * Added ability to override the default zone(s) used by JES via the config structure by setting `genomics.default-zones` in the JES configuration
 * The cromwell server TCP binding timeout is now configurable via the config key `webservice.binding-timeout`, defaulted
@@ -1828,15 +1840,15 @@ system.io {
 * In some cases the SFS backend, used for Local, SGE, etc., coerced `WdlFile` to `WdlString` by using `.toUri`. This
 resulted in strings prepended with `file:///path/to/file`. Now absolute file paths will not contain the uri scheme.
 * Launch jobs on servers that support the GA4GH Task Execution Schema using the TES backend.
-* **Call caching: Cromwell will no longer try to use the cache for WDL tasks that contain a floating docker tag.** 
+* **Call caching: Cromwell will no longer try to use the cache for WDL tasks that contain a floating docker tag.**
   Call caching will still behave the same for tasks having a docker image with a specific hash.
-  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details. 
+  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details.
 * Added docker hash lookup. Cromwell will try to lookup the hash for a docker image with a floating tag, and use that hash when executing the job.
   This will be reflected in the metadata where the docker runtime attribute will contains the hash that was used.
   If Cromwell is unable to lookup the docker hash, the job will be run with the original user defined floating tag.
   Cromwell is currently able to lookup public and private docker hashes for images on Docker Hub and Google Container Engine for job running on the JES backend.
   For other backends, cromwell is able to lookup public docker hashes for Docker Hub and Google Container Engine.
-  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details. 
+  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details.
 
 ### Database schema changes
 * Added CUSTOM_LABELS as a field of WORKFLOW_STORE_ENTRY, to store workflow store entries.
@@ -1855,7 +1867,7 @@ resulted in strings prepended with `file:///path/to/file`. Now absolute file pat
 * Timing diagrams and metadata now receive more fine grained workflow states between submission and Running.
 * Support for the Pair WDL type (e.g. `Pair[Int, File] floo = (3, "gs://blar/blaz/qlux.txt")`)
 * Added support for new WDL functions:
-  * `zip: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - align items in the two arrays by index and return them as WDL pairs 
+  * `zip: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - align items in the two arrays by index and return them as WDL pairs
   * `cross: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - create every possible pair from the two input arrays and return them all as WDL pairs
   * `transpose: (Array[Array[X]]) => Array[Array[X]]` compute the matrix transpose for a 2D array. Assumes each inner array has the same length.
 * By default, `system.abort-jobs-on-terminate` is false when running `java -jar cromwell.jar server`, and true when running `java -jar cromwell.jar run <wdl> <inputs>`.
@@ -1871,9 +1883,9 @@ resulted in strings prepended with `file:///path/to/file`. Now absolute file pat
 * Fix bugs related to the behavior of Cromwell in Single Workflow Runner Mode. Cromwell will now exit once a workflow completes in Single Workflow Runner Mode. Additionally, when restarting Cromwell in Single Workflow Runner Mode, Cromwell will no longer restart incomplete workflows from a previous session.
 
 ### Annex A - Workflow outputs
-    
+
 The WDL specification has changed regarding [workflow outputs](https://github.com/openwdl/wdl/blob/master/versions/draft-2/SPEC.md#outputs) to accommodate sub workflows.
-This change is backward compatible in terms of runnable WDLs (WDL files using the deprecated workflow outputs syntax will still run the same). 
+This change is backward compatible in terms of runnable WDLs (WDL files using the deprecated workflow outputs syntax will still run the same).
 The only visible change lies in the metadata (as well as the console output in single workflow mode, when workflow outputs are printed out at the end of a successful workflow).
 
 TL;DR Unless you are parsing or manipulating the "key" by which workflow outputs are referenced in the metadata (and/or the console output for single workflow mode), you can skip the following explanation.
@@ -1926,7 +1938,7 @@ task t {
 
 The new syntax allows for type checking of the outputs as well as expressions. It also allows for explicitly naming to the outputs.
 The old syntax doesn't give the ability to name workflow outputs. For consistency reasons, Cromwell will generate a "new syntax" workflow output for each task output, and name them.
-Their name will be generated using their FQN, which would give 
+Their name will be generated using their FQN, which would give
 
 ```
 output {
@@ -1934,8 +1946,8 @@ output {
    String w.t.out2 = t.out2
 }
 ```
-        
-However as the FQN separator is `.`, the name itself cannot contain any `.`. 
+
+However as the FQN separator is `.`, the name itself cannot contain any `.`.
 For that reason, `.` are replaced with `_` :
 
 *Old syntax expanded to new syntax*
@@ -1946,16 +1958,16 @@ output {
 }
 ```
 
-The consequence is that the workflow outputs section of the metadata for `old_syntax` would previously look like 
- 
+The consequence is that the workflow outputs section of the metadata for `old_syntax` would previously look like
+
  ```
     outputs {
         "w.t.out1": "hello",
         "w.t.out2": "hello"
     }
  ```
- 
-but it will now look like 
+
+but it will now look like
 
 ```
     outputs {
diff --git a/processes/release_processes/README.MD b/processes/release_processes/README.MD
index 66e27fd28a7..5dffe3224a5 100644
--- a/processes/release_processes/README.MD
+++ b/processes/release_processes/README.MD
@@ -2,30 +2,31 @@
 
 ## How to update these processes
 
-Have a better idea about how the deployment processes should work? 
+Have a better idea about how the deployment processes should work?
 See our "updating the process" [process](../README.MD)!
 
 ## Core Process: How to Publish and Release Cromwell
 
-If you're the lucky "Release Rotation Engineer" this time, you should do the following four things:
+Cromwell versions are updated on a weekly cadence automatically. For more information see [here](https://support.terra.bio/hc/en-us/articles/9512163608731-Faster-Cromwell-updates-in-Terra-)
 
-1. Create a Jira ticket for the release (look at previous release tickets if you're not sure how). In the Suggested 
+Manually cutting a numeric release is expected to continue being done on a cadence of every ~6 months. If you're the lucky "Release Rotation Engineer" this time, you should do the following four things:
+
+1. Create a Jira ticket for the release (look at previous release tickets if you're not sure how). In the Suggested
 Release Notes field, add "Terra is now running Cromwell <version>" along with any other release notes relevant to Terra
 users.
-1. Check that all most recent executions of Cromwell's Jenkins tests have succeeded, and that all those executions were 
-against the most recent commit in "develop" branch. There are 2 groups of Jenkins tests which have to be checked (you 
+1. Check that all most recent executions of Cromwell's Jenkins tests have succeeded, and that all those executions were
+against the most recent commit in "develop" branch. There are 2 groups of Jenkins tests which have to be checked (you
 will need to be on the Broad internal network or VPN to open the following links):
     1. Tests for various backends supported by Cromwell. Log into Jenkins [here](https://fc-jenkins.dsp-techops.broadinstitute.org), check the tests [here](https://fc-jenkins.dsp-techops.broadinstitute.org/job/cromwell-cron-parent/).
     1. Tests for Cromwell in Terra environment. Log into Jenkins [here](https://fc-jenkins.dsp-techops.broadinstitute.org), check the tests [here](https://fc-jenkins.dsp-techops.broadinstitute.org/view/Batch/).
-1. [Run the publish script to create a new version of Cromwell](#how-to-publish-a-new-cromwell-version)  
-1. [Run through the "How to Release Cromwell into Firecloud/Terra" process](#how-to-release-cromwell-into-firecloud--terra)  
-1. [Run through the "How to Deploy Cromwell in CaaS prod" process](#how-to-deploy-cromwell-in-caas-staging-and-caas-prod)  
+1. [Run the publish script to create a new version of Cromwell](#how-to-publish-a-new-cromwell-version)
+1. [Run through the "How to Deploy Cromwell in CaaS prod" process](#how-to-deploy-cromwell-in-caas-staging-and-caas-prod)
 
 ### How to publish a new Cromwell version
 
 #### Announce your intentions
 
-Post a message in `#dsp-batch-private` letting people know that a publish is imminent in case there are PRs they want to get
+Post a message in `#dsp-workflows-private` letting people know that a publish is imminent in case there are PRs they want to get
 wrapped up and merged to `develop` to go out in the forthcoming version of Cromwell.
 
 #### Get a Github token
@@ -46,7 +47,7 @@ Make or copy the following files into a temporary `release/` directory outside t
 
 * A copy of the workflow file to run (https://github.com/broadinstitute/cromwell/blob/develop/publish/publish_workflow.wdl)
 * An inputs json like this one.
-  * `publishHomebrew` is `false` due to Homebrew taking on this part themselves. Homebrew remains an active distribution channel. 
+  * `publishHomebrew` is `false` due to Homebrew taking on this part themselves. Homebrew remains an active distribution channel.
 
 ```json
 {
@@ -83,7 +84,7 @@ The workflow outputs its status to the console.
 
 #### Make sure it all went swimmingly
 
-* Check that the workflow succeeded. 
+* Check that the workflow succeeded.
 * Check that there's now a new Cromwell release listed [here](https://github.com/broadinstitute/cromwell/releases).
 * Look [in Travis](https://app.travis-ci.com/github/broadinstitute/cromwell/branches) for the release tag build that will publish Docker images for the new version.
 * Let `#dsp-batch-private` know that it's okay to resume merges to `develop`.
@@ -93,17 +94,6 @@ The workflow outputs its status to the console.
     * See the `cromwell::build::publish_artifacts()` function for details
 * **One business day later,** confirm that [the Homebrew package](https://formulae.brew.sh/formula/cromwell) has the latest version. If it doesn't, start investigation by looking at [Homebrew PR's](https://github.com/Homebrew/homebrew-core/pulls?q=is%3Apr+cromwell).
 
-### How to Release Cromwell into Firecloud / Terra
-
-**Note:** If the Cromwell CHANGELOG indicates that the upgrade might take some time (e.g., because of a database migration), checking in with the release engineer
-and user support/comms to let them know that the upgrade may involve downtime is also required. You may need to help draft an impact statement and co-ordinate timing
-the deploy to make sure user impact in minimized.
-
-**Note:** How to accomplish some of these steps might be non-obvious to you (e.g., generating the release notes).
-If so, refer to the additional details in the [full document](https://docs.google.com/document/d/1EEzwemE8IedCplIwL506fiqXr0262Pz4G0x6Cr6V-5E). 
-
-![firecloud-develop](firecloud-develop.dot.png) 
-
 ### How to Deploy Cromwell in CaaS staging and CaaS prod
 
 CaaS is "Cromwell as a Service". It is used by a couple of Broad teams (Pipelines and Epigenomics), though the long-term plan is for those teams to migrate to using Terra.
@@ -111,7 +101,7 @@ CaaS is "Cromwell as a Service". It is used by a couple of Broad teams (Pipeline
 **Note:** If the Cromwell CHANGELOG indicates that the upgrade might take some time (e.g., because of a database migration), checking in with the CaaS users
 to let them know that the upgrade is about to happen is a good idea.
 
-Deploying to CaaS is detailed in the [Quick CaaS Deployment Guide](https://docs.google.com/document/d/1s0YC-oohJ7o-OGcgnH_-YBtIEKmLIPTRpG36yvWxUpE) 
+Deploying to CaaS is detailed in the [Quick CaaS Deployment Guide](https://docs.google.com/document/d/1s0YC-oohJ7o-OGcgnH_-YBtIEKmLIPTRpG36yvWxUpE)
 
 ### How to be Sure You're Done
 
@@ -153,5 +143,5 @@ A SNAP version of the client library will be published in jFrog at [this path](h
 ## Cromwell setup for publishing
 
 One can run a publishing-friendly Cromwell using a containerized MySQL server and config files
-from Cromwell's CI. See the `start_publish_mysql_docker.sh` and `start_publish_cromwell.sh` 
+from Cromwell's CI. See the `start_publish_mysql_docker.sh` and `start_publish_cromwell.sh`
 scripts under `release_processes/scripts`.

From 931f312cd3f5780104d6a834f4fa9383f5b8bc6d Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Thu, 16 Feb 2023 19:52:47 +0000
Subject: [PATCH 136/326] Update cromwell version from 85 to 86

---
 project/Version.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Version.scala b/project/Version.scala
index ca782b990e2..cfdd3352dc2 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -6,7 +6,7 @@ import com.github.sbt.git.SbtGit
 
 object Version {
   // Upcoming release, or current if we're on a master / hotfix branch
-  val cromwellVersion = "85"
+  val cromwellVersion = "86"
 
   /**
     * Returns true if this project should be considered a snapshot.

From 8aa0dd560dd785b201e6201f592d6f24f8175dfa Mon Sep 17 00:00:00 2001
From: Tom Wiseman <tom.h.wiseman@gmail.com>
Date: Tue, 21 Feb 2023 11:32:25 -0500
Subject: [PATCH 137/326] WX-905 (#7012)

Co-authored-by: Thomas Wiseman <twiseman@wm275-315.lan>
Co-authored-by: Tom Wiseman <twiseman@broadinstitute.org>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .github/workflows/cromwell_unit_tests.yml |  1 +
 .github/workflows/integration_tests.yml   | 83 +++++++++++++++++++++++
 .gitignore                                |  6 ++
 src/ci/bin/test.inc.sh                    | 39 ++++++++++-
 4 files changed, 127 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/integration_tests.yml

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index d0927f8b954..797f38efd96 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -9,6 +9,7 @@ run-name: ${{ github.actor }} running Cromwell sbt unit tests.
 on:
   workflow_dispatch: #Manual trigger from GitHub UI
   push:
+  merge_group:
 
 permissions: 
   contents: read
diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
new file mode 100644
index 00000000000..489e9e731a9
--- /dev/null
+++ b/.github/workflows/integration_tests.yml
@@ -0,0 +1,83 @@
+name: 'Integration Tests'
+
+#This github action runs all of Cromwell's integration tests.
+
+#This is what shows up in the github workflows page as the title. 
+run-name: ${{ github.actor }} Integration Testing.
+
+#What will trigger the workflow to run. 
+on:
+  workflow_dispatch: #Manual trigger from GitHub UI
+  push: #git push
+  merge_group:
+
+permissions: 
+  contents: read
+
+jobs:
+  integration-tests:
+    strategy:
+      fail-fast: false #disabling fail-fast means that even if one test fails, the others will still try to complete.
+      #Each entry below is a single integration test that lives in /src/ci/bin/. 
+      #Each will be launched on its own runner so they can occur in parallel.
+      #Friendly names are displayed on the Github UI and aren't used anywhere else.
+      matrix:
+        include:
+          - build_type: centaurPapiV2beta
+            build_mysql: 5.7
+            friendly_name: Centaur Papi V2 Beta with MySQL 5.7
+          - build_type: dbms
+            friendly_name: DBMS
+          - build_type: centaurTes
+            build_mysql: 5.7
+            friendly_name: Centaur TES with MySQL 5.7
+          - build_type: centaurLocal
+            build_mysql: 5.7
+            friendly_name: Centaur Local with MySQL 5.7
+          - build_type: checkPublish
+            friendly_name: Check Publish
+          - build_type: centaurAws
+            build_mysql: 5.7
+            friendly_name: Centaur AWS with MySQL 5.7
+          - build_type: centaurDummy
+            build_mysql: 5.7
+            friendly_name: Centaur Dummy with MySQL 5.7
+          - build_type: centaurHoricromtalPapiV2beta
+            build_mysql: 5.7
+            friendly_name: Centaur Horicromtal PapiV2 Beta with MySQL 5.7
+          - build_type: horicromtalDeadlock
+            friendly_name: Horicromtal Deadlock
+          - build_type: singleWorkflowRunner
+            friendly_name: Single Workflow Runner
+          - build_type: centaurLocal
+            build_mariadb: 10.3
+            friendly_name: Centaur Local with MariaDB 10.3
+          - build_type: centaurLocal
+            build_postgresql: 11.3
+            friendly_name: Centaur Local with PostgreSQL 11.3
+          - build_type: centaurEngineUpgradeLocal
+            build_mysql: 5.7
+            friendly_name: Centaur Engine Upgrade Local with MySQL 5.7
+    name: ${{ matrix.friendly_name }}
+    env:
+      BUILD_NAME: ${{ matrix.build_type }}
+      BUILD_TYPE: ${{ matrix.build_type }} #intentionally duplicated variable
+      BUILD_MYSQL: ${{ matrix.build_mysql }}
+      BUILD_POSTGRESQL: ${{ matrix.build_postgresql }}
+      BUILD_MARIADB: ${{ matrix.build_mariadb }}
+      VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
+      VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    steps:
+    - uses: actions/checkout@v3 # checkout the cromwell repo
+    - uses: ./.github/set_up_cromwell_action #This github action will set up git-secrets, caching, java, and sbt.
+      with:
+        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+    #This script bascially just looks up another script to run, assuming that the other script's filename is:
+    #src/ci/bin/test${BUILD_TYPE}.sh. The first letter of the BUILD_TYPE is automatically capitalized when looking.
+    - name: Run Integration Test
+      run: |
+        set -e
+        echo Running test.sh
+        ./src/ci/bin/test.sh
diff --git a/.gitignore b/.gitignore
index 571a12c5873..a80b4a21713 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,6 +17,12 @@ tags
 target
 /site
 
+#from running integration tests locally
+actual.json
+console_output.txt
+expected.json
+run_mode_metadata.json
+
 # custom config
 cromwell-executions
 cromwell-test-executions
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 95820513dfe..a5d9d4fe509 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -83,6 +83,7 @@ cromwell::private::create_build_variables() {
     CROMWELL_BUILD_PROVIDER_TRAVIS="travis"
     CROMWELL_BUILD_PROVIDER_JENKINS="jenkins"
     CROMWELL_BUILD_PROVIDER_CIRCLE="circle"
+    CROMWELL_BUILD_PROVIDER_GITHUB="github"
     CROMWELL_BUILD_PROVIDER_UNKNOWN="unknown"
 
     if [[ "${TRAVIS-false}" == "true" ]]; then
@@ -91,6 +92,8 @@ cromwell::private::create_build_variables() {
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_JENKINS}"
     elif [[ "${CIRCLECI-false}" == "true" ]]; then
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_CIRCLE}"
+    elif [[ "${GITHUB_ACTIONS-false}" == "true" ]]; then
+        CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_GITHUB}"
     else
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_UNKNOWN}"
     fi
@@ -300,6 +303,21 @@ cromwell::private::create_build_variables() {
                 CROMWELL_BUILD_RUN_TESTS=true
             fi
             ;;
+        "${CROMWELL_BUILD_PROVIDER_GITHUB}")
+            CROMWELL_BUILD_IS_CI=true
+            CROMWELL_BUILD_IS_SECURE=true
+            CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
+            CROMWELL_BUILD_BRANCH="${GITHUB_REF_NAME}"
+            CROMWELL_BUILD_EVENT="${GITHUB_EVENT_NAME}"
+            CROMWELL_BUILD_TAG=""
+            CROMWELL_BUILD_NUMBER="${GITHUB_RUN_ID}"
+            CROMWELL_BUILD_URL="${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}"
+            CROMWELL_BUILD_GIT_USER_EMAIL=""
+            CROMWELL_BUILD_GIT_USER_NAME="${GITHUB_ACTOR}"
+            CROMWELL_BUILD_HEARTBEAT_PATTERN="…"
+            CROMWELL_BUILD_GENERATE_COVERAGE=true
+            CROMWELL_BUILD_RUN_TESTS=true
+            ;;
         *)
             CROMWELL_BUILD_IS_CI=false
             CROMWELL_BUILD_IS_SECURE=true
@@ -476,7 +494,8 @@ cromwell::private::create_database_variables() {
 
     case "${CROMWELL_BUILD_PROVIDER}" in
         "${CROMWELL_BUILD_PROVIDER_TRAVIS}"|\
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}")
+        "${CROMWELL_BUILD_PROVIDER_CIRCLE}"|\
+        "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             CROMWELL_BUILD_MARIADB_HOSTNAME="localhost"
             CROMWELL_BUILD_MARIADB_PORT="23306"
             CROMWELL_BUILD_MARIADB_DOCKER_TAG="${BUILD_MARIADB-}"
@@ -633,7 +652,8 @@ cromwell::private::create_centaur_variables() {
     # Pick **one** of the databases to run Centaur against
     case "${CROMWELL_BUILD_PROVIDER}" in
         "${CROMWELL_BUILD_PROVIDER_TRAVIS}"|\
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}")
+        "${CROMWELL_BUILD_PROVIDER_CIRCLE}"|\
+        "${CROMWELL_BUILD_PROVIDER_GITHUB}")
 
             if [[ -n "${CROMWELL_BUILD_MYSQL_DOCKER_TAG:+set}" ]]; then
                 CROMWELL_BUILD_CENTAUR_SLICK_PROFILE="slick.jdbc.MySQLProfile$"
@@ -1436,6 +1456,21 @@ cromwell::build::setup_common_environment() {
             cromwell::private::setup_pyenv_python_latest
             cromwell::private::start_docker_databases
             ;;
+        "${CROMWELL_BUILD_PROVIDER_GITHUB}")
+            # Try to login to vault, and if successful then use vault creds to login to docker.
+            # For those committers with vault access this avoids pull rate limits reported in BT-143.
+            cromwell::private::install_vault
+            cromwell::private::login_vault
+            cromwell::private::login_docker
+            #Note: Unlike with other CI providers, we are using Github Actions to install Java and sbt for us.
+            #This is automatically handled in the set_up_cromwell Github Action, which can be found in
+            #[cromwell root]/.github/set_up_cromwell_aciton.
+            cromwell::private::install_docker_compose
+            cromwell::private::delete_boto_config
+            cromwell::private::delete_sbt_boot
+            cromwell::private::upgrade_pip
+            cromwell::private::start_docker_databases
+            ;;
         "${CROMWELL_BUILD_PROVIDER_JENKINS}"|\
         *)
             ;;

From c3344cb4dd997b75dd6648b7f38ec14d572c6b6b Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 21 Feb 2023 16:04:06 -0500
Subject: [PATCH 138/326] WX-719 modernize `cromwell-publish` image (#7013)

---
 publish/Dockerfile      |  5 ++---
 publish/docker-build.sh | 10 ++++++++--
 publish/docker-setup.sh | 26 +++++++++++---------------
 3 files changed, 21 insertions(+), 20 deletions(-)

diff --git a/publish/Dockerfile b/publish/Dockerfile
index 7b276e50490..16dfcff30a7 100644
--- a/publish/Dockerfile
+++ b/publish/Dockerfile
@@ -1,6 +1,5 @@
-# Alternatively instead of `FROM linuxbrew/brew` we could run all of the steps used to install brew in docker-setup.sh
-# https://github.com/Homebrew/brew/blob/0ff2afdfa8c5943a0e55d9bfe3cdb5d11da8342a/Dockerfile
-FROM linuxbrew/brew
+# Latest stable release including non-LTS
+FROM ubuntu:rolling
 
 WORKDIR /cromwell-publish/
 COPY docker-setup.sh git-setup.sh ./
diff --git a/publish/docker-build.sh b/publish/docker-build.sh
index 4630a066dcd..460e62f4430 100755
--- a/publish/docker-build.sh
+++ b/publish/docker-build.sh
@@ -4,6 +4,12 @@
 
 set -euo pipefail
 
+export DOCKER_CLI_EXPERIMENTAL=enabled
+
+docker buildx rm cromwell-multi-arch-builder || true
+docker buildx create --use --name cromwell-multi-arch-builder
+
 build_root="$( dirname "${BASH_SOURCE[0]}" )"
-docker build "${build_root}" -t broadinstitute/cromwell-publish
-docker push broadinstitute/cromwell-publish
+docker buildx build "${build_root}" --platform linux/amd64,linux/arm64 -t broadinstitute/cromwell-publish:latest --push
+
+docker buildx rm cromwell-multi-arch-builder
diff --git a/publish/docker-setup.sh b/publish/docker-setup.sh
index 1ef181bae19..613d251df96 100755
--- a/publish/docker-setup.sh
+++ b/publish/docker-setup.sh
@@ -4,36 +4,32 @@
 
 set -eou pipefail
 
-apt-get update
-apt-get install \
+apt update
+apt install \
     apt-transport-https \
     curl \
     git \
     gnupg \
     wget \
+    ca-certificates \
+    unzip \
+    zip \
     -y --no-install-recommends
 
-# setup install for adoptopenjdk
-# https://adoptopenjdk.net/installation.html#linux-pkg-deb
-wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add -
-echo "deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(
-        grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
-    ) main" |
-    tee /etc/apt/sources.list.d/adoptopenjdk.list
+mkdir -p /etc/apt/keyrings
+wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
+echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
+apt update
+apt install -y temurin-11-jdk
 
 # Install jq 1.6 to ensure --rawfile is supported
 curl -L https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 -o /usr/bin/jq
 chmod +x /usr/bin/jq
 
-apt-get update
-apt-get install \
-    adoptopenjdk-11-hotspot \
-    -y --no-install-recommends
-
 # sbt launcher non-deb package installation instructions adapted from
 # - https://github.com/sbt/sbt/releases/tag/v1.4.9
 # - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-curl --location --fail --silent --show-error "https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz" |
+curl --location --fail --silent --show-error "https://github.com/sbt/sbt/releases/download/v1.8.2/sbt-1.8.2.tgz" |
     tar zxf - -C /usr/share
 update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1
 

From f5a9e054ff510ddb5c6b2482372ba8c0a7c1fcdb Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 21 Feb 2023 16:40:18 -0500
Subject: [PATCH 139/326] WX-930 Add `CODEOWNERS` file (#7015)

---
 CODEOWNERS | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 CODEOWNERS

diff --git a/CODEOWNERS b/CODEOWNERS
new file mode 100644
index 00000000000..34ece8d7792
--- /dev/null
+++ b/CODEOWNERS
@@ -0,0 +1,5 @@
+# These owners will be the default owners for everything in
+# the repo. Unless a later match takes precedence,
+# @broadinstitute/dsp-batch will be requested for
+# review when someone opens a pull request.
+* @broadinstitute/dsp-batch

From cb4d8fac492b7498135cbd7d01581af0e175c86a Mon Sep 17 00:00:00 2001
From: Stephen Fleming <sjfleming@users.noreply.github.com>
Date: Tue, 21 Feb 2023 17:38:05 -0500
Subject: [PATCH 140/326] Update FiveMinuteIntro: Java 11 requirement (#6830)

Co-authored-by: Adam Nichols <aednichols@gmail.com>
---
 docs/Releases.md                  | 5 +++--
 docs/tutorials/FiveMinuteIntro.md | 8 +++++---
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/docs/Releases.md b/docs/Releases.md
index 1a446c90bc2..9699d7d44bc 100644
--- a/docs/Releases.md
+++ b/docs/Releases.md
@@ -6,8 +6,9 @@ You are strongly encouraged to use the latest release of Cromwell whenever possi
 Cromwell is distributed as a conda package on [conda-forge](https://conda-forge.org/).
 These instructions need to be followed for [installing the miniconda distribution](https://docs.conda.io/en/latest/miniconda.html) and 
 [activating the conda-forge channel](https://conda-forge.org/#about). After this Cromwell can be installed in the 
-base environment with `conda install cromwell` or a separate environment for Cromwell can be created with 
-`conda create -n cromwell cromwell`. If you are using Cromwell for bioinformatics workflows, you might like to take
+base environment with `conda install -c conda-forge cromwell` or a separate environment for Cromwell can be created with 
+`conda create -n cromwell cromwell` (be sure to activate the conda-forge channel first). 
+If you are using Cromwell for bioinformatics workflows, you might like to take
 a look at [bioconda](http://bioconda.github.io)  as well. 
 The conda installation of Cromwell comes with a wrapper that locates the jar for you and allows for running Cromwell or Womtool with a 
 `cromwell run`, `womtool validate` or other command. Conda also installs the required Java dependency 
diff --git a/docs/tutorials/FiveMinuteIntro.md b/docs/tutorials/FiveMinuteIntro.md
index 2e203354bee..1c16a56c606 100644
--- a/docs/tutorials/FiveMinuteIntro.md
+++ b/docs/tutorials/FiveMinuteIntro.md
@@ -4,9 +4,11 @@
 
 * A Unix-based operating system (yes, that includes Mac!)
 * A Java 11 runtime environment 
-	* You can see what you have by running `$ java -version` on a terminal. 
-	* If not, you can download Java [here](https://adoptopenjdk.net/).
-	* You might need to update the `export JAVA_HOME` in your bash profile to point to your JAVA install location.
+    * You can see what you have by running `$ java -version` on a terminal.
+    * If not, consider installing via conda or brew [as explained here](../Releases.md).
+    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 11 build of [Temurin](https://adoptium.net/temurin/releases/?version=11)
+      * `sdk install java 11.0.16-tem` as of the time of this writing
+    * You might need to update the `export JAVA_HOME` in your bash profile to point to your JAVA install location.
 * A sense of adventure!
 
 ### Goals

From 0854d6c79886ea6fa2f4add6064eef139e54a94f Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 22 Feb 2023 09:35:16 -0500
Subject: [PATCH 141/326] WX-952 Fix Cromwell version update in Helm chart
 (#7014)

---
 .github/workflows/chart_update_on_merge.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index aa7a2c9c9ad..0eb8facd927 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -76,8 +76,8 @@ jobs:
         cd cromwhelm
         git checkout main
         ls -la
-        sed -i "s/appVersion.*/appVersion: \"$CROMWELL_VERSION\"/" cromwell-helm/Chart.yaml
-        sed -i "s/image: broadinstitute\/cromwell.*/image: broadinstitute\/cromwell:$CROMWELL_VERSION/" cromwell-helm/templates/cromwell.yaml
+        sed -i "s|image: broadinstitute/cromwell:.*|image: broadinstitute/cromwell:$CROMWELL_VERSION|" terra-batch-libchart/values.yaml
+
         git diff
         git config --global user.name "broadbot"
         git config --global user.email "broadbot@broadinstitute.org"

From 65e122368a8d14bc24e7dc4cf5dcd850be7d757f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 28 Feb 2023 11:49:38 -0500
Subject: [PATCH 142/326] Reference Disk Manifest Builder App Test (#7017)

---
 .github/workflows/integration_tests.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 489e9e731a9..aec72777d78 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -58,6 +58,8 @@ jobs:
           - build_type: centaurEngineUpgradeLocal
             build_mysql: 5.7
             friendly_name: Centaur Engine Upgrade Local with MySQL 5.7
+          - build_type: referenceDiskManifestBuilderApp
+            friendly_name: Reference Disk Manifest Builder App
     name: ${{ matrix.friendly_name }}
     env:
       BUILD_NAME: ${{ matrix.build_type }}
@@ -77,7 +79,13 @@ jobs:
     #This script bascially just looks up another script to run, assuming that the other script's filename is:
     #src/ci/bin/test${BUILD_TYPE}.sh. The first letter of the BUILD_TYPE is automatically capitalized when looking.
     - name: Run Integration Test
+      shell: 'script -q -e -c "bash --noprofile --norc -eo pipefail {0}"' #See comment below
       run: |
         set -e
         echo Running test.sh
         ./src/ci/bin/test.sh
+    #The "shell: ..."" line is a way to force the Github Action Runner to use a bash shell that thinks it has a TTY.
+    #The issue and solution are described here: https://github.com/actions/runner/issues/241#issuecomment-842566950
+    #This is only needed for ReferenceDiskManifestBuilderApp test. 
+    #This test uses fancy colors in the output, which likely causes the problem.
+    #See WX-938. 

From 514a5469734587bb096df6b482b94fc031b77607 Mon Sep 17 00:00:00 2001
From: Katrina P <68349264+kpierre13@users.noreply.github.com>
Date: Tue, 28 Feb 2023 16:43:17 -0500
Subject: [PATCH 143/326] [WM-1696] Update Womtool (#7019)

Co-authored-by: Tom Wiseman <twiseman@broadinstitute.org>
---
 docs/api/RESTAPI.md                             | 12 +++++++++++-
 engine/src/main/resources/swagger/cromwell.yaml | 10 ++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/docs/api/RESTAPI.md b/docs/api/RESTAPI.md
index ffb2af329de..7a0585ca08e 100644
--- a/docs/api/RESTAPI.md
+++ b/docs/api/RESTAPI.md
@@ -1,5 +1,5 @@
 <!--
-This file was generated by `sbt generateRestApiDocs` on Wed, 8 Feb 2023 09:46:32 -0500
+This file was generated by `sbt generateRestApiDocs` on Mon, 27 Feb 2023 15:52:59 -0500
 
 !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
 
@@ -1217,8 +1217,10 @@ The type expected for a given value.
 |---|---|---|
 |**arrayType**  <br>*optional*||[ValueType](#valuetype)|
 |**mapType**  <br>*optional*||[MapValueType](#mapvaluetype)|
+|**nonEmpty**  <br>*optional*|Boolean representation of the contents in an array.|boolean|
 |**objectFieldTypes**  <br>*optional*||< [objectFieldTypes](#valuetype-objectfieldtypes) > array|
 |**optionalType**  <br>*optional*||[ValueType](#valuetype)|
+|**pairType**  <br>*optional*||[pairType](#valuetype-pairtype)|
 |**tupleTypes**  <br>*optional*||< [ValueType](#valuetype) > array|
 |**typeName**  <br>*optional*|The type of this value|enum (String, File, Directory, Float, Int, Boolean, Optional, Array, Tuple, Map, Object, Pair)|
 
@@ -1230,6 +1232,14 @@ The type expected for a given value.
 |**fieldName**  <br>*optional*|string|
 |**fieldType**  <br>*optional*|[ValueType](#valuetype)|
 
+<a name="valuetype-pairtype"></a>
+**pairType**
+
+|Name|Schema|
+|---|---|
+|**leftType**  <br>*optional*|[ValueType](#valuetype)|
+|**rightType**  <br>*optional*|[ValueType](#valuetype)|
+
 
 <a name="versionresponse"></a>
 ### VersionResponse
diff --git a/engine/src/main/resources/swagger/cromwell.yaml b/engine/src/main/resources/swagger/cromwell.yaml
index 6e840160d36..bc34cb6476b 100644
--- a/engine/src/main/resources/swagger/cromwell.yaml
+++ b/engine/src/main/resources/swagger/cromwell.yaml
@@ -1353,6 +1353,16 @@ definitions:
               type: string
             fieldType:
               $ref: '#/definitions/ValueType'
+      nonEmpty:
+        type: boolean
+        description: Boolean representation of the contents in an array.
+      pairType:
+        type: object
+        properties:
+          leftType:
+            $ref: '#/definitions/ValueType'
+          rightType:
+            $ref: '#/definitions/ValueType'
   MapValueType:
     type: object
     description: A type representing a map from one type to another.

From b9b1adef95bea3c74db8534736b61625b6c66ebe Mon Sep 17 00:00:00 2001
From: Miguel Covarrubias <mcovarr@users.noreply.github.com>
Date: Wed, 1 Mar 2023 10:43:13 -0500
Subject: [PATCH 144/326] WX-958 write_map() should write its last entry with a
 newline (#7022)

---
 wom/src/main/scala/wom/values/WomMap.scala    |  8 ++++-
 .../test/scala/wom/types/WomMapTypeSpec.scala | 29 +++++++++++++++++++
 2 files changed, 36 insertions(+), 1 deletion(-)

diff --git a/wom/src/main/scala/wom/values/WomMap.scala b/wom/src/main/scala/wom/values/WomMap.scala
index 6c0ada18849..5d42b1d3364 100644
--- a/wom/src/main/scala/wom/values/WomMap.scala
+++ b/wom/src/main/scala/wom/values/WomMap.scala
@@ -69,8 +69,14 @@ final case class WomMap private(womType: WomMapType, value: Map[WomValue, WomVal
 
   def tsvSerialize: Try[String] = {
     (womType.keyType, womType.valueType) match {
+      case (_: WomPrimitiveType, _: WomPrimitiveType) if value.isEmpty =>
+        // WDL 1.1 spec on `write_map()` https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#file-write_mapmapstring-string
+        // Earlier versions of the spec are not as opinionated on `write_map()` behavior.
+        // "If the Map is empty, an empty file is written."
+        Success("")
       case (_: WomPrimitiveType, _: WomPrimitiveType) =>
-        Success(value.map({case (k, v) => s"${k.valueString}\t${v.valueString}"}).mkString("\n"))
+        // "All lines are terminated by the newline (\n) character."
+        Success(value.map({case (k, v) => s"${k.valueString}\t${v.valueString}"}).mkString(start="", sep="\n", end="\n"))
       case _ =>
         Failure(new UnsupportedOperationException("Can only TSV serialize a Map[Primitive, Primitive]"))
     }
diff --git a/wom/src/test/scala/wom/types/WomMapTypeSpec.scala b/wom/src/test/scala/wom/types/WomMapTypeSpec.scala
index 5bd274b830c..214e150f873 100644
--- a/wom/src/test/scala/wom/types/WomMapTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomMapTypeSpec.scala
@@ -109,4 +109,33 @@ class WomMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
       case _: UnsupportedOperationException => // expected
     }
   }
+
+  it should "tsvSerialize non-empty maps correctly and with newlines after every line" in {
+    stringIntMap.tsvSerialize shouldEqual Success("a\t1\nb\t2\nc\t3\n")
+
+    val intIntMap = WomMap(WomMapType(WomIntegerType, WomIntegerType), Map(
+      WomInteger(4) -> WomInteger(1),
+      WomInteger(5) -> WomInteger(2),
+      WomInteger(6) -> WomInteger(3),
+    ))
+    intIntMap.tsvSerialize shouldEqual Success("4\t1\n5\t2\n6\t3\n")
+
+    val stringStringMap = WomMap(WomMapType(WomStringType, WomStringType), Map(
+      WomString("a") -> WomString("x"),
+      WomString("b") -> WomString("y"),
+      WomString("c") -> WomString("z")
+    ))
+    stringStringMap.tsvSerialize shouldEqual Success("a\tx\nb\ty\nc\tz\n")
+  }
+
+  it should "tsvSerialize empty maps to empty Strings" in {
+    val emptyStringIntMap = WomMap(WomMapType(WomStringType, WomIntegerType), Map.empty)
+    emptyStringIntMap.tsvSerialize shouldEqual Success("")
+
+    val emptyIntIntMap = WomMap(WomMapType(WomIntegerType, WomIntegerType), Map.empty)
+    emptyIntIntMap.tsvSerialize shouldEqual Success("")
+
+    val emptyStringStringMap = WomMap(WomMapType(WomStringType, WomStringType), Map.empty)
+    emptyStringStringMap.tsvSerialize shouldEqual Success("")
+  }
 }

From ce68a47f58ac713c54dbf6bee367f2e37a23ac15 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 3 Mar 2023 09:50:34 -0500
Subject: [PATCH 145/326] Centaur slurm (#7083)

---
 .github/workflows/integration_tests.yml |  3 +++
 .travis.yml                             |  3 ---
 src/ci/bin/test_slurm.inc.sh            | 14 ++++++++------
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index aec72777d78..3923d7f37d1 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -60,6 +60,9 @@ jobs:
             friendly_name: Centaur Engine Upgrade Local with MySQL 5.7
           - build_type: referenceDiskManifestBuilderApp
             friendly_name: Reference Disk Manifest Builder App
+          - build_type: centaurSlurm
+            build_mysql: 5.7
+            friendly_name: "Centaur Slurm with MySQL 5.7"
     name: ${{ matrix.friendly_name }}
     env:
       BUILD_NAME: ${{ matrix.build_type }}
diff --git a/.travis.yml b/.travis.yml
index 9ffb48b1147..6e9ad601439 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -47,9 +47,6 @@ env:
     - >-
       BUILD_TYPE=centaurPapiV2beta
       BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurSlurm
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=centaurTes
       BUILD_MYSQL=5.7
diff --git a/src/ci/bin/test_slurm.inc.sh b/src/ci/bin/test_slurm.inc.sh
index 039408271f9..f5c0434a3ce 100644
--- a/src/ci/bin/test_slurm.inc.sh
+++ b/src/ci/bin/test_slurm.inc.sh
@@ -21,21 +21,23 @@ cromwell::build::slurm::setup_slurm_environment() {
     # https://slurm.schedmd.com/
     sudo apt-get update
 
-    # Try the Lawrence Livermore National Laboratory (LLNL) version first
-    sudo apt-get install -y slurm-llnl || sudo apt-get install -y slurm-wlm
+    sudo apt-get install -y slurm-wlm
+    # As an alternative to 'slurm-wlm', you may also try 'slurm-llnl'.
+    # If you use 'slurm-llnl', change the below tee path to '/etc/slurm-llnl/slurm.conf'
+    # For reasons that are unclear, slurm-llnl doesn't work in Github Actions, and slurm-wlm doesn't work in Travis.
+    # We transitioned from slurm-llnl to slurm-wlm when moving from Travis to Github Actions.
+    # See the PR associated with ticket WX-888.  
 
     # Create various directories used by slurm
-    sudo mkdir -p /etc/slurm-llnl
-    sudo mkdir -p /var/run/slurm-llnl
     sudo mkdir -p /var/run/munge
     sudo mkdir -p /var/spool/slurmd
 
-    # A mash of configure-until-it-runs. Feel free to PR suggestions/fixes
+    # A mash of configure-until-it-runs. Feel free to PR suggestions/fixes.
     # https://slurm.schedmd.com/tutorials.html
     # https://slurm.schedmd.com/configurator.html
     # https://slurm.schedmd.com/slurm.conf.html
     # https://slurm.schedmd.com/quickstart_admin.html
-    cat <<SLURM_CONF | sudo tee /etc/slurm-llnl/slurm.conf >/dev/null
+    cat <<SLURM_CONF | sudo tee /etc/slurm/slurm.conf >/dev/null
 ClusterName=localhost
 ControlMachine=localhost
 NodeName=localhost

From bb6065ddf8b44ea63b76f132f0f9458b81fda4e3 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 6 Mar 2023 17:19:51 -0500
Subject: [PATCH 146/326] Remove Deploy Key (#7084)

---
 .gitignore                                    |  1 -
 .travis.yml                                   | 12 ---
 src/ci/bin/test.inc.sh                        | 89 -------------------
 src/ci/bin/testSbt.sh                         | 24 -----
 .../resources/github_private_deploy_key.ctmpl |  3 -
 5 files changed, 129 deletions(-)
 delete mode 100755 src/ci/bin/testSbt.sh
 delete mode 100644 src/ci/resources/github_private_deploy_key.ctmpl

diff --git a/.gitignore b/.gitignore
index a80b4a21713..a5b72f6b263 100644
--- a/.gitignore
+++ b/.gitignore
@@ -44,7 +44,6 @@ cromwell-service-account.json
 cwl_conformance_test.inputs.json
 dockerhub_provider_config_v1.inc.conf
 dockerhub_provider_config_v2.inc.conf
-github_private_deploy_key
 papi_application.inc.conf
 papi_refresh_token.options.json
 papi_v2_gcsa.options.json
diff --git a/.travis.yml b/.travis.yml
index 6e9ad601439..295d133cbaa 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -54,18 +54,6 @@ env:
       BUILD_TYPE=checkPublish
     - >-
       BUILD_TYPE=horicromtalDeadlock
-    - >-
-      BUILD_TYPE=sbt
-      BUILD_SBT_INCLUDE=engine
-    - >-
-      BUILD_TYPE=sbt
-      BUILD_SBT_INCLUDE=server
-    - >-
-      BUILD_TYPE=sbt
-      BUILD_SBT_INCLUDE=services
-    - >-
-      BUILD_TYPE=sbt
-      BUILD_SBT_EXCLUDE='engine|server|services'
     - >-
       BUILD_TYPE=dbms
     - >-
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index a5d9d4fe509..017fbd95b54 100644
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -1228,45 +1228,6 @@ cromwell::private::generate_code_coverage() {
     bash <(curl -s https://codecov.io/bash) > /dev/null || true
 }
 
-cromwell::private::publish_artifacts_only() {
-    sbt 'set ThisBuild / assembly / logLevel := Level.Warn' -Dsbt.supershell=false --warn "$@" publish
-}
-
-cromwell::private::publish_artifacts_and_docker() {
-    sbt 'set ThisBuild / assembly / logLevel := Level.Warn' -Dsbt.supershell=false --warn "$@" publish dockerBuildAndPush
-}
-
-cromwell::private::publish_artifacts_check() {
-    sbt -Dsbt.supershell=false --warn verifyArtifactoryCredentialsExist
-}
-
-# Some CI environments want to know when new docker images are published. They do not currently poll dockerhub but do
-# poll github. To help those environments, signal that a new set of docker images has been published to dockerhub by
-# updating a well known branch in github.
-cromwell::private::push_publish_complete() {
-    local github_private_deploy_key="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/github_private_deploy_key"
-    local git_repo="git@github.com:broadinstitute/cromwell.git"
-    local git_publish_branch="${CROMWELL_BUILD_BRANCH}_publish_complete"
-    local git_publish_remote="publish_complete"
-    local git_publish_message="publish complete [skip ci]"
-
-    # Loosely adapted from https://github.com/broadinstitute/workbench-libs/blob/435a932/scripts/version_update.sh
-    mkdir publish_complete
-    pushd publish_complete > /dev/null
-
-    git init
-    git config core.sshCommand "ssh -i ${github_private_deploy_key} -F /dev/null"
-    git config user.email "${CROMWELL_BUILD_GIT_USER_EMAIL}"
-    git config user.name "${CROMWELL_BUILD_GIT_USER_NAME}"
-
-    git remote add "${git_publish_remote}" "${git_repo}"
-    git checkout -b "${git_publish_branch}"
-    git commit --allow-empty -m "${git_publish_message}"
-    git push -f "${git_publish_remote}" "${git_publish_branch}"
-
-    popd > /dev/null
-}
-
 cromwell::private::start_build_heartbeat() {
     # Sleep one minute between printouts, but don't zombie forever
     for ((i=0; i < "${CROMWELL_BUILD_HEARTBEAT_MINUTES}"; i++)); do
@@ -1639,56 +1600,6 @@ cromwell::build::generate_code_coverage() {
     fi
 }
 
-cromwell::build::check_published_artifacts() {
-    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_TRAVIS}" ]] && \
-        [[ "${CROMWELL_BUILD_TYPE}" == "sbt" ]] && \
-        [[ "${CROMWELL_BUILD_SBT_INCLUDE}" == "" ]] && \
-        [[ "${CROMWELL_BUILD_EVENT}" == "push" ]]; then
-
-        if [[ "${CROMWELL_BUILD_BRANCH}" == "develop" ]] || \
-            [[ "${CROMWELL_BUILD_BRANCH}" =~ ^[0-9\.]+_hotfix$ ]] || \
-            [[ -n "${CROMWELL_BUILD_TAG:+set}" ]]; then
-            # If cromwell::build::publish_artifacts is going to be publishing later check now that it will work
-            sbt \
-                -Dsbt.supershell=false \
-                --error \
-                errorIfAlreadyPublished
-        fi
-
-    fi
-}
-
-cromwell::build::publish_artifacts() {
-    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_TRAVIS}" ]] && \
-        [[ "${CROMWELL_BUILD_TYPE}" == "sbt" ]] && \
-        [[ "${CROMWELL_BUILD_SBT_INCLUDE}" == "" ]] && \
-        [[ "${CROMWELL_BUILD_EVENT}" == "push" ]]; then
-
-        if [[ "${CROMWELL_BUILD_BRANCH}" == "develop" ]]; then
-            # Publish images for both the "cromwell develop branch" and the "cromwell dev environment".
-            CROMWELL_SBT_DOCKER_TAGS=develop,dev \
-                cromwell::private::publish_artifacts_and_docker \
-                -Dproject.isSnapshot=true
-            cromwell::private::push_publish_complete
-
-        elif [[ "${CROMWELL_BUILD_BRANCH}" =~ ^[0-9\.]+_hotfix$ ]]; then
-            # Docker tags float. "30" is the latest hotfix. Those dockers are published here on each hotfix commit.
-            cromwell::private::publish_artifacts_and_docker -Dproject.isSnapshot=false
-
-        elif [[ -n "${CROMWELL_BUILD_TAG:+set}" ]]; then
-            # Artifact tags are static. Once "30" is set that is only "30" forever. Those artifacts are published here.
-            cromwell::private::publish_artifacts_only \
-                -Dproject.version="${CROMWELL_BUILD_TAG}" \
-                -Dproject.isSnapshot=false
-
-        elif [[ "${CROMWELL_BUILD_IS_SECURE}" == "true" ]]; then
-            cromwell::private::publish_artifacts_check
-
-        fi
-
-    fi
-}
-
 cromwell::build::exec_retry_function() {
     local retried_function
     local retry_count
diff --git a/src/ci/bin/testSbt.sh b/src/ci/bin/testSbt.sh
deleted file mode 100755
index 55e38fae9b7..00000000000
--- a/src/ci/bin/testSbt.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test_unit.inc.sh" || source test_unit.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::check_published_artifacts
-
-cromwell::build::unit::setup_scale_factor
-
-cromwell::build::unit::setup_exclude_tags
-
-CROMWELL_SBT_TEST_EXCLUDE_TAGS="${CROMWELL_BUILD_UNIT_EXCLUDE_TAGS}" \
-CROMWELL_SBT_TEST_SPAN_SCALE_FACTOR="${CROMWELL_BUILD_UNIT_SPAN_SCALE_FACTOR}" \
-cromwell:build::run_sbt_test
-
-cromwell::build::generate_code_coverage
-
-cromwell::build::publish_artifacts
diff --git a/src/ci/resources/github_private_deploy_key.ctmpl b/src/ci/resources/github_private_deploy_key.ctmpl
deleted file mode 100644
index dfbdec6a48e..00000000000
--- a/src/ci/resources/github_private_deploy_key.ctmpl
+++ /dev/null
@@ -1,3 +0,0 @@
-{{with $cromwellGithub := secret (printf "secret/dsde/cromwell/common/cromwell-github")}}
-{{$cromwellGithub.Data.private_deploy_key}}
-{{end}}

From 28c780bfa09212e564d0dccb5d4dcc91da25c86d Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 9 Mar 2023 12:05:52 -0500
Subject: [PATCH 147/326] WX-950 Set user agent in Java client (#7087)

---
 scripts/gen_java_client.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scripts/gen_java_client.sh b/scripts/gen_java_client.sh
index 59642098b1d..beeac43ed2f 100755
--- a/scripts/gen_java_client.sh
+++ b/scripts/gen_java_client.sh
@@ -5,6 +5,7 @@ BASE_PACKAGE="cromwell.client"
 ORIGINAL_API_YAML=engine/src/main/resources/swagger/cromwell.yaml
 API_YAML=codegen_java/cromwell.nofile.yaml
 OPENAPI_DOCKER="openapitools/openapi-generator-cli@sha256:ddd1b01cbe8f494c6612c548e91f983938164ab713a4d18d099a1fc4a77c651d"
+CROMWELL_HASH=$(git rev-parse --short=7 HEAD)
 
 # Cromwell doesn't specify the OAuth configuration in its swagger, and
 # without it the client doesn't support authentication.
@@ -42,6 +43,7 @@ docker run --rm -v ${PWD}:/local ${OPENAPI_DOCKER} generate \
   -i /local/$API_YAML \
   -g java \
   -o /local/codegen_java \
+  --http-user-agent "Cromwell-Java-Client/${CROMWELL_HASH}" \
   --skip-validate-spec \
   --api-package ${BASE_PACKAGE}.api \
   --model-package ${BASE_PACKAGE}.model

From 64e386670a2174de84e4823ef98c2440623ac622 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 10 Mar 2023 14:26:38 -0500
Subject: [PATCH 148/326] WX-950 Upgrade Azure libs to probably fix extraneous
 log (#7088)

---
 project/Dependencies.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index ddc3b002f00..43a5e1c80a6 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -205,7 +205,7 @@ object Dependencies {
     "com.azure" % "azure-identity" % azureIdentitySdkV
       exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
       exclude("jakarta.activation", "jakarta.activation-api"),
-    "com.azure" % "azure-core-management" % "1.7.1",
+    "com.azure" % "azure-core-management" % "1.10.2",
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0"
   )
 

From 68a1425b625ee7a90809d8813724662ef633bbba Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 17 Mar 2023 10:03:46 -0400
Subject: [PATCH 149/326] WX-984 Revert "WX-950 Upgrade Azure libs to probably
 fix extraneous log" (#7090)

---
 project/Dependencies.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 43a5e1c80a6..ddc3b002f00 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -205,7 +205,7 @@ object Dependencies {
     "com.azure" % "azure-identity" % azureIdentitySdkV
       exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
       exclude("jakarta.activation", "jakarta.activation-api"),
-    "com.azure" % "azure-core-management" % "1.10.2",
+    "com.azure" % "azure-core-management" % "1.7.1",
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0"
   )
 

From b04d895919c95eb0317966e0d8bceb05ef26c5a7 Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Mon, 20 Mar 2023 09:39:37 -0400
Subject: [PATCH 150/326] Add cron run integrations each day of the week
 (#7089)

---
 .github/workflows/integration_tests.yml       | 41 ++++++++++++++++---
 .../workflows/nightly_integration_tests.yml   | 23 +++++++++++
 2 files changed, 58 insertions(+), 6 deletions(-)
 create mode 100644 .github/workflows/nightly_integration_tests.yml

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 3923d7f37d1..aacd46ffe78 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -2,23 +2,43 @@ name: 'Integration Tests'
 
 #This github action runs all of Cromwell's integration tests.
 
-#This is what shows up in the github workflows page as the title. 
+#This is what shows up in the github workflows page as the title.
 run-name: ${{ github.actor }} Integration Testing.
 
-#What will trigger the workflow to run. 
+#What will trigger the workflow to run.
 on:
+  workflow_call:
+    inputs:
+      target-branch:
+        description: 'The branch to run integration tests against'
+        required: false
+        type: string
+      slack-alert:
+        description: 'A flag to enable slack alerts. True if this should alert via slack'
+        required: true
+        default: false
+        type: boolean
+    secrets:
+      VAULT_ROLE_ID_CI:
+        required: true
+      VAULT_SECRET_ID_CI:
+        required: true
+      BROADBOT_GITHUB_TOKEN:
+        required: true
+      SLACK_WEBHOOK_URL:
+        required: false
   workflow_dispatch: #Manual trigger from GitHub UI
   push: #git push
   merge_group:
 
-permissions: 
+permissions:
   contents: read
 
 jobs:
   integration-tests:
     strategy:
       fail-fast: false #disabling fail-fast means that even if one test fails, the others will still try to complete.
-      #Each entry below is a single integration test that lives in /src/ci/bin/. 
+      #Each entry below is a single integration test that lives in /src/ci/bin/.
       #Each will be launched on its own runner so they can occur in parallel.
       #Friendly names are displayed on the Github UI and aren't used anywhere else.
       matrix:
@@ -76,6 +96,8 @@ jobs:
     timeout-minutes: 120
     steps:
     - uses: actions/checkout@v3 # checkout the cromwell repo
+      with:
+        ref: ${{ inputs.target-branch }}
     - uses: ./.github/set_up_cromwell_action #This github action will set up git-secrets, caching, java, and sbt.
       with:
         cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
@@ -87,8 +109,15 @@ jobs:
         set -e
         echo Running test.sh
         ./src/ci/bin/test.sh
+    - uses: ravsamhq/notify-slack-action@v2
+      if: inputs.slack-alert
+      with:
+        status: ${{ job.status }}
+        notify_when: "failure"
+      env:
+        SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
     #The "shell: ..."" line is a way to force the Github Action Runner to use a bash shell that thinks it has a TTY.
     #The issue and solution are described here: https://github.com/actions/runner/issues/241#issuecomment-842566950
-    #This is only needed for ReferenceDiskManifestBuilderApp test. 
+    #This is only needed for ReferenceDiskManifestBuilderApp test.
     #This test uses fancy colors in the output, which likely causes the problem.
-    #See WX-938. 
+    #See WX-938.
diff --git a/.github/workflows/nightly_integration_tests.yml b/.github/workflows/nightly_integration_tests.yml
new file mode 100644
index 00000000000..024588b4ac5
--- /dev/null
+++ b/.github/workflows/nightly_integration_tests.yml
@@ -0,0 +1,23 @@
+#This github action runs all of Cromwell's integration tests nightly.
+name: 'Nightly Integration Tests'
+
+#This is what shows up in the github workflows page as the title.
+run-name: Nightly ${{ github.actor }} Integration Testing.
+
+#What will trigger the workflow to run.
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 * * 1-5'
+
+permissions:
+  contents: read
+
+# Use if as arg to only send slack notifications on nightly
+jobs:
+  integration-tests:
+    uses: broadinstitute/cromwell/.github/workflows/integration_tests.yml@develop
+    with:
+      target-branch: 'develop'
+      slack-alert: true
+    secrets: inherit

From 53f29d3bed055e9205cc8583c56157c00407fc02 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Mon, 20 Mar 2023 16:25:47 +0100
Subject: [PATCH 151/326] EFS support and Merge conflict resolution (#27)

* fully relocate handleExectionResult to resolve merge conflict

* changes for EFS support

* updated readme for EFS info

* removed a debug statement

* documentation
---
 .../main/scala/cromwell/backend/backend.scala |   2 +
 .../StandardAsyncExecutionActor.scala         | 134 +++++++---------
 ...wsBatchAsyncBackendJobExecutionActor.scala | 135 ++++++++++++++--
 .../backend/impl/aws/AwsBatchAttributes.scala |  46 +++++-
 .../impl/aws/AwsBatchConfiguration.scala      |   3 +
 .../backend/impl/aws/AwsBatchJob.scala        |  86 +++++++++--
 .../impl/aws/AwsBatchJobDefinition.scala      |  20 ++-
 .../impl/aws/AwsBatchRuntimeAttributes.scala  |  80 +++++++++-
 .../scala/cromwell/backend/impl/aws/README.md | 146 ++++++++++++++++++
 9 files changed, 534 insertions(+), 118 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index 18718f0e76f..bf9f67e27a1 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -141,6 +141,8 @@ object CommonBackendConfigurationAttributes {
     "default-runtime-attributes.queueArn",
     "default-runtime-attributes.awsBatchRetryAttempts",
     "default-runtime-attributes.ulimits",
+    "default-runtime-attributes.efsDelocalize",
+    "default-runtime-attributes.efsMakeMD5",
     "default-runtime-attributes.failOnStderr",
     "slow-job-warning-time",
     "dockerhub",
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index d136acd905c..5c415cc3c50 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -1266,59 +1266,97 @@ trait StandardAsyncExecutionActor
   def handleExecutionResult(status: StandardAsyncRunState,
                             oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
     
+    // get the memory retry code.
+    def memoryRetryRC: Future[Boolean] = {
+      // convert int to boolean
+      def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
+        codeAsOption match {
+          case Some(codeAsString) =>
+            Try(codeAsString.trim.toInt) match {
+              case Success(code) => code match {
+                case StderrContainsRetryKeysCode => true
+                case _ => false
+              }
+              case Failure(e) =>
+                log.error(s"'CheckingForMemoryRetry' action exited with code '$codeAsString' which couldn't be " +
+                  s"converted to an Integer. Task will not be retried with more memory. Error: ${ExceptionUtils.getMessage(e)}")
+                false
+            }
+          case None => false
+        }
+      }
+      // read if the file exists
+      def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] = {
+        if (fileExists)
+          asyncIo.contentAsStringAsync(jobPaths.memoryRetryRC, None, failOnOverflow = false).map(Option(_))
+        else
+          Future.successful(None)
+      }
+      //finally : assign the yielded variable
+      for {
+        fileExists <- asyncIo.existsAsync(jobPaths.memoryRetryRC)
+        retryCheckRCAsOption <- readMemoryRetryRCFile(fileExists)
+        retryWithMoreMemory = returnCodeAsBoolean(retryCheckRCAsOption)
+      } yield retryWithMoreMemory
+    }
+
+    // get the exit code of the job.
+    def JobExitCode: Future[String] = {
+      
+      // read if the file exists
+      def readRCFile(fileExists: Boolean): Future[String] = {
+        if (fileExists)
+          asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
+        else {
+          jobLogger.warn("RC file not found. Setting job to failed & waiting 5m before retry.")
+          Thread.sleep(300000)
+          Future("1")
+        }
+      }
+      //finally : assign the yielded variable
+      for {
+        fileExists <- asyncIo.existsAsync(jobPaths.returnCode)
+        jobRC <- readRCFile(fileExists)
+      } yield jobRC
+    }
+
     // get path to sderr
     val stderr = jobPaths.standardPaths.error
     lazy val stderrAsOption: Option[Path] = Option(stderr)
-    // get the three needed variables, using helper functions below, or direct assignment.
+    // get the three needed variables, using functions above or direct assignment.
     val stderrSizeAndReturnCodeAndMemoryRetry = for {
       returnCodeAsString <- JobExitCode
       // Only check stderr size if we need to, otherwise this results in a lot of unnecessary I/O that
       // may fail due to race conditions on quickly-executing jobs.
       stderrSize <- if (failOnStdErr) asyncIo.sizeAsync(stderr) else Future.successful(0L)
-      retryWithMoreMemory <- memoryRetryRC(oldHandle.pendingJob)
+      retryWithMoreMemory <- memoryRetryRC
     } yield (stderrSize, returnCodeAsString, retryWithMoreMemory)
 
     stderrSizeAndReturnCodeAndMemoryRetry flatMap {
       case (stderrSize, returnCodeAsString, retryWithMoreMemory) =>
         val tryReturnCodeAsInt = Try(returnCodeAsString.trim.toInt)
-        jobLogger.debug(s"Handling execution Result with status '${status.toString()}' and returnCode ${returnCodeAsString}")
+
         if (isDone(status)) {
           tryReturnCodeAsInt match {
-            // stderr not empty : retry
             case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
-            // job was aborted (cancelled by user?) 
-            // on AWS OOM kill are code 137 : check retryWithMoreMemory here 
-            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) && !retryWithMoreMemory =>
-              jobLogger.debug(s"Job was aborted, code was : '${returnCodeAsString}'")
+            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
               Future.successful(AbortedExecutionHandle)
-            // if instance killed after RC.txt creation : edge case with status == Failed AND returnCode == [accepted values] => retry.
-            case Success(returnCodeAsInt) if status.toString() == "Failed" && continueOnReturnCode.continueFor(returnCodeAsInt) =>
-                jobLogger.debug(s"Suspected spot kill due to status/RC mismatch")
-                val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(UnExpectedStatus(jobDescriptor.key.tag, returnCodeAsInt, status.toString(), stderrAsOption), Option(returnCodeAsInt), None))
-                retryElseFail(executionHandle)
-            // job considered ok by accepted exit code
             case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
               handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
-            // job failed on out-of-memory : retry
             case Success(returnCodeAsInt) if retryWithMoreMemory  =>
-              jobLogger.info(s"Retrying job due to OOM with exit code : '${returnCodeAsString}' ")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle, retryWithMoreMemory)
-            // unaccepted return code : retry.
             case Success(returnCodeAsInt) =>
-              jobLogger.debug(s"Retrying with wrong exit code : '${returnCodeAsString}'")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
             case Failure(_) =>
-              jobLogger.warn(s"General failure of job with exit code : '${returnCodeAsString}'")
               Future.successful(FailedNonRetryableExecutionHandle(ReturnCodeIsNotAnInt(jobDescriptor.key.tag, returnCodeAsString, stderrAsOption), kvPairsToSave = None))
           }
         } else {
           tryReturnCodeAsInt match {
             case Success(returnCodeAsInt) if retryWithMoreMemory && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
-              jobLogger.debug(s"job not done but retrying already? : ${status.toString()}")
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle, retryWithMoreMemory)
             case _ =>
@@ -1335,61 +1373,7 @@ trait StandardAsyncExecutionActor
         }
     }
   }
-
-  // helper function for handleExecutionResult : get the exit code of the job.
-  def JobExitCode: Future[String] = {
-      
-    // read if the file exists
-    def readRCFile(fileExists: Boolean): Future[String] = {
-      if (fileExists)
-        asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
-      else {
-        jobLogger.debug("RC file not found. Setting job to failed.")
-        Future("1")
-      }
-    }
-    //finally : assign the yielded variable
-    for {
-      fileExists <- asyncIo.existsAsync(jobPaths.returnCode)
-      jobRC <- readRCFile(fileExists)
-    } yield jobRC
-  }
-
-  // helper function for handleExecutionResult : get the memory retry code.
-  def memoryRetryRC(job: StandardAsyncJob): Future[Boolean] = {
-    // job is used in aws override version. use here to prevent compilation error.
-    log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
-    // convert int to boolean
-    def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
-      codeAsOption match {
-        case Some(codeAsString) =>
-          Try(codeAsString.trim.toInt) match {
-            case Success(code) => code match {
-              case StderrContainsRetryKeysCode => true
-              case _ => false
-            }
-            case Failure(e) =>
-              log.error(s"'CheckingForMemoryRetry' action exited with code '$codeAsString' which couldn't be " +
-                s"converted to an Integer. Task will not be retried with more memory. Error: ${ExceptionUtils.getMessage(e)}")
-              false
-          }
-        case None => false
-      }
-    }
-    // read if the file exists
-    def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] = {
-      if (fileExists)
-        asyncIo.contentAsStringAsync(jobPaths.memoryRetryRC, None, failOnOverflow = false).map(Option(_))
-      else
-        Future.successful(None)
-    }
-    //finally : assign the yielded variable
-    for {
-      fileExists <- asyncIo.existsAsync(jobPaths.memoryRetryRC)
-      retryCheckRCAsOption <- readMemoryRetryRCFile(fileExists)
-      retryWithMoreMemory = returnCodeAsBoolean(retryCheckRCAsOption)
-    } yield retryWithMoreMemory
-  }
+  
 
 
   /**
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index af9d95f8b66..8d2464a8ee3 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -55,7 +55,6 @@ import cromwell.backend.io.DirectoryFunctions
 import cromwell.backend.io.JobPaths
 import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
 import cromwell.backend.OutputEvaluator._
-
 import cromwell.core._
 import cromwell.core.path.{DefaultPathBuilder, Path, PathBuilder, PathFactory}
 import cromwell.core.io.{DefaultIoCommandBuilder, IoCommandBuilder}
@@ -80,8 +79,7 @@ import scala.concurrent._
 import scala.concurrent.duration._
 import scala.language.postfixOps
 import scala.util.control.NoStackTrace
-import scala.util.{Success, Try}
-
+import scala.util.{Success, Try, Failure}
 /**
   * The `AwsBatchAsyncBackendJobExecutionActor` creates and manages a job. The job itself is encapsulated by the
   * functionality in `AwsBatchJob`
@@ -194,7 +192,10 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       jobPaths, Seq.empty[AwsBatchParameter],
       configuration.awsConfig.region,
       Option(configuration.awsAuth),
-      configuration.fsxMntPoint)
+      configuration.fsxMntPoint,
+      configuration.efsMntPoint,
+      Option(runtimeAttributes.efsMakeMD5),
+      Option(runtimeAttributes.efsDelocalize))
   }
 
   // setup batch client to query job container info
@@ -307,16 +308,19 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     *
     * @throws Exception if the `path` does not live in one of the supplied `disks`
     */
-  private def relativePathAndVolume(path: String, disks: Seq[AwsBatchVolume]): (Path, AwsBatchVolume) = {
+  private def relativePathAndVolume(path: String, disks: Seq[AwsBatchVolume] ): (Path, AwsBatchVolume) = {
 
     def getAbsolutePath(path: Path) = {
       configuration.fileSystem match {
         case AWSBatchStorageSystems.s3 => AwsBatchWorkingDisk.MountPoint.resolve(path)
         // case _ => DefaultPathBuilder.get(configuration.root).resolve(path)
-        case _ => AwsBatchWorkingDisk.MountPoint.resolve(path)
+        case _ => 
+            Log.info("non-s3 path detected")
+            Log.info(path.toString)
+            AwsBatchWorkingDisk.MountPoint.resolve(path)
       }
     }
-
+    
     val absolutePath = DefaultPathBuilder.get(path) match {
       case p if !p.isAbsolute => getAbsolutePath(p)
       case p => p
@@ -348,7 +352,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     }
 
     val womFileOutputs = jobDescriptor.taskCall.callable.outputs.flatMap(evaluateFiles) map relativeLocalizationPath
-
+    Log.debug("WomFileOutputs:")
+    Log.debug(womFileOutputs.toString())
     val outputs: Seq[AwsBatchFileOutput] = womFileOutputs.distinct flatMap {
       _.flattenFiles flatMap {
         case unlistedDirectory: WomUnlistedDirectory => generateUnlistedDirectoryOutputs(unlistedDirectory)
@@ -533,14 +538,110 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     } yield guaranteedAnswer
   }
 
-  // new OOM detection 
-  override def memoryRetryRC(job: StandardAsyncJob): Future[Boolean] = Future {
+  override def handleExecutionResult(status: StandardAsyncRunState,
+                            oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
+    
+
+    // get path to sderr
+    val stderr = jobPaths.standardPaths.error
+    lazy val stderrAsOption: Option[Path] = Option(stderr)
+    // get the three needed variables, using helper functions below, or direct assignment.
+    val stderrSizeAndReturnCodeAndMemoryRetry = for {
+      returnCodeAsString <- JobExitCode
+      // Only check stderr size if we need to, otherwise this results in a lot of unnecessary I/O that
+      // may fail due to race conditions on quickly-executing jobs.
+      stderrSize <- if (failOnStdErr) asyncIo.sizeAsync(stderr) else Future.successful(0L)
+      retryWithMoreMemory <- memoryRetryRC(oldHandle.pendingJob)
+    } yield (stderrSize, returnCodeAsString, retryWithMoreMemory)
+
+    stderrSizeAndReturnCodeAndMemoryRetry flatMap {
+      case (stderrSize, returnCodeAsString, retryWithMoreMemory) =>
+        val tryReturnCodeAsInt = Try(returnCodeAsString.trim.toInt)
+        jobLogger.debug(s"Handling execution Result with status '${status.toString()}' and returnCode ${returnCodeAsString}")
+        if (isDone(status)) {
+          tryReturnCodeAsInt match {
+            // stderr not empty : retry
+            case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
+              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
+              retryElseFail(executionHandle)
+            // job was aborted (cancelled by user?) 
+            // on AWS OOM kill are code 137 : check retryWithMoreMemory here 
+            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) && !retryWithMoreMemory =>
+              jobLogger.debug(s"Job was aborted, code was : '${returnCodeAsString.stripLineEnd}'")
+              Future.successful(AbortedExecutionHandle)
+            // if instance killed after RC.txt creation : edge case with status == Failed AND returnCode == [accepted values] => retry.
+            case Success(returnCodeAsInt) if status.toString() == "Failed" && continueOnReturnCode.continueFor(returnCodeAsInt) =>
+                jobLogger.debug(s"Suspected spot kill due to status/RC mismatch")
+                val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(UnExpectedStatus(jobDescriptor.key.tag, returnCodeAsInt, status.toString(), stderrAsOption), Option(returnCodeAsInt), None))
+                retryElseFail(executionHandle)
+            // job considered ok by accepted exit code
+            case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
+              handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
+            // job failed on out-of-memory : retry
+            case Success(returnCodeAsInt) if retryWithMoreMemory  =>
+              jobLogger.info(s"Retrying job due to OOM with exit code : '${returnCodeAsString.stripLineEnd}' ")
+              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
+              retryElseFail(executionHandle, retryWithMoreMemory)
+            // unaccepted return code : retry.
+            case Success(returnCodeAsInt) =>
+              jobLogger.debug(s"Retrying with wrong exit code : '${returnCodeAsString.stripLineEnd}'")
+              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption), Option(returnCodeAsInt), None))
+              retryElseFail(executionHandle)
+            case Failure(_) =>
+              jobLogger.warn(s"General failure of job with exit code : '${returnCodeAsString.stripLineEnd}'")
+              Future.successful(FailedNonRetryableExecutionHandle(ReturnCodeIsNotAnInt(jobDescriptor.key.tag, returnCodeAsString, stderrAsOption), kvPairsToSave = None))
+          }
+        } else {
+          tryReturnCodeAsInt match {
+            case Success(returnCodeAsInt) if retryWithMoreMemory && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
+              jobLogger.debug(s"job not done but retrying already? : ${status.toString()}")
+              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
+              retryElseFail(executionHandle, retryWithMoreMemory)
+            case _ =>
+              val failureStatus = handleExecutionFailure(status, tryReturnCodeAsInt.toOption)
+              retryElseFail(failureStatus)
+          }
+        }
+    } recoverWith {
+      case exception =>
+        if (isDone(status)) Future.successful(FailedNonRetryableExecutionHandle(exception, kvPairsToSave = None))
+        else {
+          val failureStatus = handleExecutionFailure(status, None)
+          retryElseFail(failureStatus)
+        }
+    }
+  
+    
+  }
+    
+ 
+   // get the exit code of the job.
+   def JobExitCode: Future[String] = {
+     
+     // read if the file exists
+     def readRCFile(fileExists: Boolean): Future[String] = {
+       if (fileExists)
+         asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
+       else {
+         jobLogger.warn("RC file not found in aws version. Setting job to failed.")
+         //Thread.sleep(300000)
+         Future("1")
+       }
+     }
+     //finally : assign the yielded variable
+     for {
+       fileExists <- asyncIo.existsAsync(jobPaths.returnCode)
+       jobRC <- readRCFile(fileExists)
+     } yield jobRC
+   }
+    
+   // new OOM detection 
+   def memoryRetryRC(job: StandardAsyncJob): Future[Boolean] = Future {
       // STATUS LOGIC:
       //   - success : container exit code is zero
       //   - command failure: container exit code > 0, no statusReason in container
       //   - OOM kill : container exit code > 0, statusReason contains "OutOfMemory"
-      //   - spot kill : no container exit code set. statusReason of ATTEMPT (not container) says "host EC2 (...) terminated"
-
+      //   - spot kill : no container exit code set. statusReason of ATTEMPT (not container) says "host EC2 (...) terminated"     
       Log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
       val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(job.jobId).build)
       val jobDetail = describeJobsResponse.jobs.get(0) //OrElse(throw new RuntimeException(s"Could not get job details for job '${job.jobId}'"))
@@ -555,8 +656,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       if (lastattempt == null ) {
         Log.info(s"No attempts were made for job '${job.jobId}'. no memory-related retry needed.")
         false
-      }
-
+      }     
       var containerRC = 
           try {
               lastattempt.container.exitCode
@@ -594,8 +694,11 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       }
         
         
-    }
- 
+   }
+
+  
+
+
   // Despite being a "runtime" exception, BatchExceptions for 429 (too many requests) are *not* fatal:
   override def isFatal(throwable: Throwable): Boolean = throwable match {
     case be: BatchException => !be.getMessage.contains("Status Code: 429")
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index 8bfa2bcc42c..cc019f51004 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -58,7 +58,11 @@ case class AwsBatchAttributes(fileSystem: String,
                               duplicationStrategy: AwsBatchCacheHitDuplicationStrategy,
                               submitAttempts: Int Refined Positive,
                               createDefinitionAttempts: Int Refined Positive,
-                              fsxMntPoint: Option[List[String]])
+                              fsxMntPoint: Option[List[String]],
+                              efsMntPoint: Option[String],
+                              efsMakeMD5: Option[Boolean],
+                              efsDelocalize: Option[Boolean]
+                              )
 
 object AwsBatchAttributes {
   lazy val Logger = LoggerFactory.getLogger(this.getClass)
@@ -69,17 +73,24 @@ object AwsBatchAttributes {
     "filesystems",
     "filesystems.local.auth",
     "filesystems.local.fsx",
+    "filesystems.local.efs",
     "filesystems.local.localization",
     "filesystems.local.caching.hashing-strategy",
     "filesystems.local.caching.duplication-strategy",
+    "filesystems.local.caching.check-sibling-md5",
     "filesystems.s3.auth",
     "filesystems.s3.caching.duplication-strategy",
     "auth",
     "numCreateDefinitionAttempts",
     "numSubmitAttempts",
     "default-runtime-attributes.scriptBucketName",
+    //"default-runtime-attributes.efsMountPoint",
+    //"default-runtime-attributes.efsMakeMD5",
+    //"default-runtime-attributes.efsDelocalize",
     "awsBatchRetryAttempts",
-    "ulimits"
+    "ulimits",
+    "efsDelocalize",
+    "efsMakeMD5"
   )
 
   private val deprecatedAwsBatchKeys: Map[String, String] = Map(
@@ -105,6 +116,13 @@ object AwsBatchAttributes {
       }
     }
 
+    def parseEFS(config: String): Option[String] = {
+      config.isEmpty match {
+        case true => None
+        case false => Some(config)
+      }
+    }
+
     warnDeprecated(configKeys, deprecatedAwsBatchKeys, context, Logger)
 
     val executionBucket: ErrorOr[String] = validate { backendConfig.as[String]("root") }
@@ -145,6 +163,25 @@ object AwsBatchAttributes {
       }
     }
 
+    // EFS settings:
+    val efsMntPoint:ErrorOr[Option[String]] = validate {backendConfig.hasPath("filesystems.local.efs") match {
+        case true => parseEFS(backendConfig.getString("filesystems.local.efs"))
+        case false => None
+      }
+    }
+    val efsMakeMD5:ErrorOr[Option[Boolean]] = validate {backendConfig.hasPath("default-runtime-attributes.efsMakeMD5") match {
+        case true => Some(backendConfig.getBoolean("default-runtime-attributes.efsMakeMD5"))
+        case false => None
+      }
+    }
+    // if set for job : use that; else from defaults; else None
+    val efsDelocalize:ErrorOr[Option[Boolean]] = validate {
+        backendConfig.hasPath("default-runtime-attributes.efsDelocalize") match {
+            case true => Some(backendConfig.getBoolean("default-runtime-attributes.efsDelocalize"))
+            case false => None
+      }
+    }
+
     (
       fileSysStr,
       filesystemAuthMode,
@@ -152,7 +189,10 @@ object AwsBatchAttributes {
       duplicationStrategy,
       backendConfig.as[ErrorOr[Int Refined Positive]]("numSubmitAttempts"),
       backendConfig.as[ErrorOr[Int Refined Positive]]("numCreateDefinitionAttempts"),
-      fsxMntPoint
+      fsxMntPoint,
+      efsMntPoint,
+      efsMakeMD5,
+      efsDelocalize
     ).tupled.map((AwsBatchAttributes.apply _).tupled) match {
       case Valid(r) => r
       case Invalid(f) =>
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
index 78bbb2d1a51..5f6d9eaf17a 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
@@ -57,6 +57,9 @@ class AwsBatchConfiguration(val configurationDescriptor: BackendConfigurationDes
   val dockerCredentials = BackendDockerConfiguration.build(configurationDescriptor.backendConfig).dockerCredentials
   val dockerToken: Option[String] = dockerCredentials map { _.token }
   val fsxMntPoint = batchAttributes.fsxMntPoint
+  val efsMntPoint = batchAttributes.efsMntPoint
+  val efsMakeMD5 = batchAttributes.efsMakeMD5
+  val efsDelocalize = batchAttributes.efsDelocalize
 }
 
 object AWSBatchStorageSystems {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 90739469e4d..283b97ebd97 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -84,12 +84,14 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                              parameters: Seq[AwsBatchParameter],
                              configRegion: Option[Region],
                              optAwsAuthMode: Option[AwsAuthMode] = None,
-                             fsxMntPoint: Option[List[String]]
+                             fsxMntPoint: Option[List[String]],
+                             efsMntPoint: Option[String],
+                             efsMakeMD5: Option[Boolean],
+                             efsDelocalize: Option[Boolean]
                             ) {
 
 
   val Log: Logger = LoggerFactory.getLogger(AwsBatchJob.getClass)
-
   //this will be the "folder" that scripts will live in (underneath the script bucket)
   val scriptKeyPrefix = "scripts/"
 
@@ -121,7 +123,9 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     //working in a mount will cause collisions in long running workers
     val replaced = commandScript.replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
     val insertionPoint = replaced.indexOf("\n", replaced.indexOf("#!")) +1 //just after the new line after the shebang!
-
+    // load the config
+    val conf : Config = ConfigFactory.load();
+    
     /* generate a series of s3 copy statements to copy any s3 files into the container. */
     val inputCopyCommand = inputs.map {
       case input: AwsBatchFileInput if input.s3key.startsWith("s3://") && input.s3key.endsWith(".tmp") =>
@@ -131,23 +135,32 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
            |sed -i 's#${AwsBatchWorkingDisk.MountPoint.pathAsString}#$workDir#g' $workDir/${input.local}
            |""".stripMargin
 
-
-      case input: AwsBatchFileInput if input.s3key.startsWith("s3://") =>
+      
+      case input: AwsBatchFileInput if input.s3key.startsWith("s3://") => 
+        // regular s3 objects : download to working dir.
         s"_s3_localize_with_retry ${input.s3key} ${input.mount.mountPoint.pathAsString}/${input.local}"
           .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
 
-      case input: AwsBatchFileInput =>
+      
+       
+      case input: AwsBatchFileInput if efsMntPoint.isDefined && input.s3key.startsWith(efsMntPoint.get) =>  
+        // EFS located file : test for presence on provided path.
+        Log.debug("EFS input file detected: "+ input.s3key + " / "+ input.local.pathAsString)
+        s"test -e ${input.s3key} || (echo 'input file: ${input.s3key} does not exist' && exit 1)"
+      
+      case input: AwsBatchFileInput => 
+        // an entry in 'disks' => keep mount as it is.. 
         //here we don't need a copy command but the centaurTests expect us to verify the existence of the file
-        val filePath = s"${input.mount.mountPoint.pathAsString}/${input.local.pathAsString}"
-          .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
-
-        s"test -e $filePath || echo 'input file: $filePath does not exist' && exit 1"
-
+        //val filePath = s"${input.mount.mountPoint.pathAsString}/${input.local.pathAsString}"
+        //  .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
+        val filePath = input.local.pathAsString
+        Log.debug("input entry in disks detected "+ input.s3key + " / "+ input.local.pathAsString)
+        s"test -e $filePath || (echo 'input file: $filePath does not exist' && exit 1)"
+      
       case _ => ""
     }.toList.mkString("\n")
 
     // get multipart threshold from config.
-    val conf : Config = ConfigFactory.load();
     val mp_threshold : Long = if (conf.hasPath("engine.filesystems.s3.MultipartThreshold") ) conf.getMemorySize("engine.filesystems.s3.MultipartThreshold").toBytes() else 5L * 1024L * 1024L * 1024L; 
     Log.debug(s"MultiPart Threshold for delocalizing is $mp_threshold")
 
@@ -304,14 +317,51 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
            |touch ${output.name}
            |_s3_delocalize_with_retry ${output.name} ${output.s3key}
            |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi""".stripMargin
+           
 
-
+      // files on /cromwell/ working dir must be delocalized
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
         //output is on working disk mount
+        Log.info("output Data on working disk mount" + output.local.pathAsString)
         s"""_s3_delocalize_with_retry $workDir/${output.local.pathAsString} ${output.s3key}""".stripMargin
 
+      // file(name (full path), s3key (delocalized path), local (file basename), mount (disk details))
+      // files on EFS mounts are optionally delocalized. 
+      case output: AwsBatchFileOutput if efsMntPoint.isDefined && output.mount.mountPoint.pathAsString == efsMntPoint.get =>  
+        Log.debug("EFS output file detected: "+ output.s3key + s" / ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}")
+        // EFS located file : test existence or delocalize.
+        var test_cmd = ""
+        if (efsDelocalize.isDefined && efsDelocalize.getOrElse(false)) {
+            Log.debug("efs-delocalization enabled")
+            test_cmd = s"_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
+        } else {
+            Log.debug("efs-delocalization disabled")
+            // check file for existence
+            test_cmd = s"test -e ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && exit 1)"
+        }
+        // need to make md5sum? 
+        var md5_cmd = ""
+        if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
+            Log.debug("Add cmd to create MD5 sibling.")
+            md5_cmd = s"""
+                            |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
+                            |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && exit 1 ); 
+                            |fi
+                            |""".stripMargin 
+        } else {
+            Log.debug("MD5 not enabled: "+efsMakeMD5.get.toString())
+            md5_cmd = ""
+        } 
+        // return combined result
+        s"""
+          |${test_cmd}
+          |${md5_cmd}
+          | """.stripMargin
+      
       case output: AwsBatchFileOutput =>
         //output on a different mount
+        Log.debug("output data on other mount")
+        Log.debug(output.toString)
         s"_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
       case _ => ""
     }.mkString("\n") + "\n" +
@@ -423,7 +473,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
   private def findOrCreateS3Script(commandLine :String, scriptS3BucketName: String) :String = {
 
     val bucketName = scriptS3BucketName
-
+    // this is md5 digest of the script contents ( == commandLine)
     val key = MessageDigest.getInstance("MD5")
       .digest(commandLine.getBytes())
       .foldLeft("")(_ + "%02x".format(_))
@@ -437,7 +487,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         .bucket(bucketName)
         .key( scriptKeyPrefix + key )
         .build
-      ).eTag().equals(key)
+      ).eTag().equals(key) // as key is the md5 of script content, and script is small (<8mb) => key should be equal to eTag if the file exists.
 
       // if there's no exception then the script already exists
       Log.debug(s"""Found script $bucketName/$scriptKeyPrefix$key""")
@@ -485,7 +535,11 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         jobPaths = jobPaths,
         inputs = inputs,
         outputs = outputs,
-        fsxMntPoint = fsxMntPoint)
+        fsxMntPoint = fsxMntPoint,
+        efsMntPoint = efsMntPoint,
+        efsMakeMD5 = efsMakeMD5,
+        efsDelocalize = efsDelocalize
+        )
 
       val jobDefinitionBuilder = StandardAwsBatchJobDefinitionBuilder
       val jobDefinition = jobDefinitionBuilder.build(jobDefinitionContext)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index f8442d70c3f..e1e5af42539 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -140,8 +140,8 @@ trait AwsBatchJobDefinitionBuilder {
       ).toList
     }
 
-    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit]): String = {
-      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}"
+    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit], efsDelocalize: Boolean, efsMakeMD5: Boolean): String = {
+      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}"
     }
 
     val environment = List.empty[KeyValuePair]
@@ -153,13 +153,18 @@ trait AwsBatchJobDefinitionBuilder {
     val volumes =  buildVolumes( context.runtimeAttributes.disks, context.fsxMntPoint)
     val mountPoints = buildMountPoints( context.runtimeAttributes.disks, context.fsxMntPoint)
     val ulimits = buildUlimits( context.runtimeAttributes.ulimits)
+    val efsDelocalize = context.runtimeAttributes.efsDelocalize
+    val efsMakeMD5 = context.runtimeAttributes.efsMakeMD5
+
     val containerPropsName = buildName(
       context.runtimeAttributes.dockerImage,
       packedCommand.mkString(","),
       volumes,
       mountPoints,
       environment,
-      ulimits
+      ulimits,
+      efsDelocalize,
+      efsMakeMD5
     )
 
     (ContainerProperties.builder()
@@ -240,7 +245,11 @@ case class AwsBatchJobDefinitionContext(
             jobPaths: JobPaths,
             inputs: Set[AwsBatchInput],
             outputs: Set[AwsBatchFileOutput],
-            fsxMntPoint: Option[List[String]]){
+            fsxMntPoint: Option[List[String]],
+            efsMntPoint: Option[String],
+            efsMakeMD5: Option[Boolean],
+            efsDelocalize: Option[Boolean]
+            ) {
 
   override def toString: String = {
     new ToStringBuilder(this, ToStringStyle.JSON_STYLE)
@@ -254,6 +263,9 @@ case class AwsBatchJobDefinitionContext(
       .append("inputs", inputs)
       .append("outputs", outputs)
       .append("fsxMntPoint", fsxMntPoint)
+      .append("efsMntPoint", efsMntPoint)
+      .append("efsMakeMD5", efsMakeMD5)
+      .append("efsDelocalize", efsDelocalize)
       .build
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index c6dcd6aecfa..ceca53a7c85 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -44,8 +44,10 @@ import wom.RuntimeAttributesKeys
 import wom.format.MemorySize
 import wom.types._
 import wom.values._
+import com.typesafe.config.{ConfigException,ConfigValueFactory}
 
 import scala.util.matching.Regex
+import org.slf4j.{Logger, LoggerFactory}
 
 /**
  * Attributes that are provided to the job at runtime
@@ -62,6 +64,8 @@ import scala.util.matching.Regex
  * @param fileSystem the filesystem type, default is "s3"
  * @param awsBatchRetryAttempts number of attempts that AWS Batch will retry the task if it fails
  * @param ulimits ulimit values to be passed to the container
+ * @param efsDelocalize should we delocalize efs files to s3
+ * @param efsMakeMD5 should we make a sibling md5 file as part of the job 
  */
 case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      zones: Vector[String],
@@ -75,16 +79,21 @@ case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      scriptS3BucketName: String,
                                      awsBatchRetryAttempts: Int,
                                      ulimits: Vector[Map[String, String]],
+                                     efsDelocalize: Boolean,
+                                     efsMakeMD5 : Boolean,
                                      fileSystem: String= "s3")
 
 object AwsBatchRuntimeAttributes {
-
+  val Log: Logger = LoggerFactory.getLogger(this.getClass)
   val QueueArnKey = "queueArn"
 
   val scriptS3BucketKey = "scriptBucketName"
 
   val awsBatchRetryAttemptsKey = "awsBatchRetryAttempts"
 
+  val awsBatchefsDelocalizeKey = "efsDelocalize"
+  val awsBatchefsMakeMD5Key = "efsMakeMD5"
+
   val ZonesKey = "zones"
   private val ZonesDefaultValue = WomString("us-east-1a")
 
@@ -148,11 +157,48 @@ object AwsBatchRuntimeAttributes {
     .configDefaultWomValue(runtimeConfig).getOrElse(WomInteger(0)))
   }
 
+  private def awsBatchefsDelocalizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = {
+    AwsBatchefsDelocalizeValidation(awsBatchefsDelocalizeKey).withDefault(AwsBatchefsDelocalizeValidation(awsBatchefsDelocalizeKey)
+    .configDefaultWomValue(runtimeConfig).getOrElse(WomBoolean(false)))
+  }
+
+  private def awsBatchefsMakeMD5Validation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = {
+    AwsBatchefsMakeMD5Validation(awsBatchefsMakeMD5Key).withDefault(AwsBatchefsMakeMD5Validation(awsBatchefsMakeMD5Key)
+    .configDefaultWomValue(runtimeConfig).getOrElse(WomBoolean(false)))
+  }
+
   private def ulimitsValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[Map[String, String]]] =
    UlimitsValidation.withDefault(UlimitsValidation.configDefaultWomValue(runtimeConfig) getOrElse UlimitsDefaultValue)
 
+
+  // routine that aggregates disks from default-runtime-attributes and efs.
+  def aggregateDisksInRuntimeConfig(configuration: AwsBatchConfiguration): Option[Config] = {
+    // get the runtime attributes out of full config
+    val rtc: Config = configuration.runtimeConfig match {
+        case Some(x) => x
+        case None => 
+            Log.error("aws-batch default runtime attributes not found.")
+            throw new RuntimeException("Default runtime attributes not found in config. This should always be present for AWS ! ")
+    }
+    // efs disk configs is set (can be None) in configuration
+    val efs_disks = configuration.efsMntPoint.getOrElse("")
+    // TODO : fsx ? 
+    // additional disks optionally set as runtime attributes
+    val rtc_disks = try {
+        rtc.getAnyRef(AwsBatchRuntimeAttributes.DisksKey).asInstanceOf[String] // just to prevent complaints about var/val
+    } catch {
+        case _: ConfigException.Missing => 
+           ""
+    }
+    // combine
+    val disks = s"${efs_disks},${rtc_disks}".split(",").toSet.mkString(",")
+    val runtimeConfig = Some(rtc.withValue(AwsBatchRuntimeAttributes.DisksKey, ConfigValueFactory.fromAnyRef(disks)))
+    return runtimeConfig
+  }
+
   def runtimeAttributesBuilder(configuration: AwsBatchConfiguration): StandardValidatedRuntimeAttributesBuilder = {
-    val runtimeConfig = configuration.runtimeConfig
+    val runtimeConfig = aggregateDisksInRuntimeConfig(configuration)
+    
     def validationsS3backend = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
                         cpuValidation(runtimeConfig),
                         cpuMinValidation(runtimeConfig),
@@ -166,6 +212,8 @@ object AwsBatchRuntimeAttributes {
                         scriptS3BucketNameValidation(runtimeConfig),
                         awsBatchRetryAttemptsValidation(runtimeConfig),
                         ulimitsValidation(runtimeConfig),
+                        awsBatchefsDelocalizeValidation(runtimeConfig),
+                        awsBatchefsMakeMD5Validation(runtimeConfig)
                       )
    def validationsLocalBackend  = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
       cpuValidation(runtimeConfig),
@@ -178,7 +226,9 @@ object AwsBatchRuntimeAttributes {
       dockerValidation,
       queueArnValidation(runtimeConfig),
       awsBatchRetryAttemptsValidation(runtimeConfig),
-      ulimitsValidation(runtimeConfig)
+      ulimitsValidation(runtimeConfig),
+      awsBatchefsDelocalizeValidation(runtimeConfig),
+      awsBatchefsMakeMD5Validation(runtimeConfig)
     )
 
     configuration.fileSystem match  {
@@ -204,7 +254,9 @@ object AwsBatchRuntimeAttributes {
     }
     val awsBatchRetryAttempts: Int = RuntimeAttributesValidation.extract(awsBatchRetryAttemptsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val ulimits: Vector[Map[String, String]] = RuntimeAttributesValidation.extract(ulimitsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-
+    val efsDelocalize: Boolean = RuntimeAttributesValidation.extract(awsBatchefsDelocalizeValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
+    val efsMakeMD5: Boolean = RuntimeAttributesValidation.extract(awsBatchefsMakeMD5Validation(runtimeAttrsConfig),validatedRuntimeAttributes)
+    
     new AwsBatchRuntimeAttributes(
       cpu,
       zones,
@@ -218,6 +270,8 @@ object AwsBatchRuntimeAttributes {
       scriptS3BucketName,
       awsBatchRetryAttempts,
       ulimits,
+      efsDelocalize,
+      efsMakeMD5,
       fileSystem
     )
   }
@@ -418,6 +472,24 @@ class AwsBatchRetryAttemptsValidation(key: String) extends IntRuntimeAttributesV
   override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Integer"
 }
 
+object AwsBatchefsDelocalizeValidation {
+  def apply(key: String): AwsBatchefsDelocalizeValidation = new AwsBatchefsDelocalizeValidation(key)
+}
+
+class AwsBatchefsDelocalizeValidation(key: String) extends BooleanRuntimeAttributesValidation(key) {
+  
+  override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Boolean"
+}
+
+object AwsBatchefsMakeMD5Validation {
+  def apply(key: String): AwsBatchefsMakeMD5Validation = new AwsBatchefsMakeMD5Validation(key)
+}
+
+class AwsBatchefsMakeMD5Validation(key: String) extends BooleanRuntimeAttributesValidation(key) {
+  
+  override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Boolean"
+}
+
 
 object UlimitsValidation
     extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 61bb351c7e9..8576dcb6de9 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -252,6 +252,152 @@ services {
 2. Add `events:PutEvents` IAM policy to your Cromwell server IAM role. 
 
 
+#### AWS EFS
+
+Cromwell EC2 instances can be equipped with a shared elastic filesystem, termed EFS. Using this filesystem for intermediate data bypasses the need to pass these files around between the cromwell jobs and S3. 
+
+1.  Setup an EFS filesystem: 
+
+Following the [GenomicsWorkFlows](https://docs.opendata.aws/genomics-workflows/orchestration/cromwell/cromwell-overview.html) deployment stack and selecting "Create EFS", you will end up with an EFS filesystem accessible within the provided subnets. It is mounted by default in EC2 workers under /mnt/efs. This is specified in the launch templates USER_DATA if you want to change this. 
+
+Next, it is recommended to change the EFS setup (in console : select EFS service, then the "SharedDataGenomics" volume, edit). Change performance settings to Enhanced/Elastic, because the bursting throughput is usually insufficient. Optionally set the lifecycle to archive infrequently accessed data and reduce costs. 
+
+2. Set Cromwell Configuration
+
+The following directives need to be added to the cromwell configuration:
+
+```
+backend {
+    providers {
+        AWSBatch {
+            config{
+                default-runtime-attributes {
+                    // keep you other settings as they are (queueArn etc)
+
+                    // DEFAULT EFS CONFIG
+                    // delocalize output files under /mnt/efs to the cromwell tmp bucket
+                    efsDelocalize = false
+                    // make md5 sums of output files under /mnt/efs as part of the job 
+                    efsMakeMD5 = false
+                }
+                filesystems {
+                    s3 {
+                        // your s3 settings should remain as they are
+                    }
+                    // add the local directive
+                    local {
+                        // the mountpoint of the EFS volume within the HOST (specified in EC2 launch template)
+                        efs = "/mnt/efs"
+                    }
+
+                }
+            }
+        }
+    }
+}
+
+```
+
+Now, Cromwell is able to correctly handle output files both located in the cromwell working directory (delocalized to S3), and on the EFS volume (kept, and optionally delocalized).
+
+3. Current limitations:
+
+- To read an task output file in wdl using eg read_tsv(), it must be set to output type 'String' OR 'efsDelocalize' must be enabled for the job.
+- Call caching is not yet possible when using input files located on EFS.  Cromwell does not crash but issues errors and skips callcaching for that task. 
+- There is no unique temp/scratch folder generated per workflow ID. Data collision prevention is left to the user. 
+- Cleanup must be done manually
+
+4. Example Workflow
+
+The following workflow highlights the following features: 
+ 
+ - take input data from an s3 bucket. 
+ - keep intermediate data on efs
+ - delocalize output from efs volume 
+ - read a file on efs in the main wdl cromwell process.
+
+ 
+```
+version 1.0
+workflow TestEFS {
+    input {
+        # input file for WF is located on S3
+        File s3_file = 's3://aws-quickstart/quickstart-aws-vpc/templates/aws-vpc.template.yaml'
+        # set an input parameter holding the working dir on EFS
+        String efs_wd = "/mnt/efs/MyProject"
+    }
+    # task one : create a file on efs.
+    call task_one {input:
+        infile = s3_file,
+        wd = efs_wd    
+    }
+    # read the outfile straight in a wdl structure
+    Array[Array[String]] myOutString_info = read_tsv(task_one.outfile)
+
+    # task two : reuse the file on the wd and delocalize to s3
+    call task_two {input:
+        wd = efs_wd,
+        infile = task_one.outfile
+    }
+    Array[Array[String]] myOutFile_info = read_tsv(task_two.outfile)
+
+    ## outputs
+    output{
+        Array[Array[String]] wf_out_info_returned_as_string = myOutString_info
+        Array[Array[String]] wf_out_info_returned_as_file = myOutFile_info
+        String wf_out_file = task_two.outfile
+    }
+}
+
+task task_one {
+    input {
+	    File infile
+        String wd
+    }
+    command {
+        # mk the wd:
+        mkdir -p ~{wd}
+        # mv the infile to wd
+        mv ~{infile} ~{wd}/
+        # generate an outfile for output Testing
+        ls -alh ~{wd} > ~{wd}/MyOutFile
+    }
+     runtime {
+        docker: "ubuntu:22.04"
+        cpu : "1"
+        memory: "500M" 
+     }
+     output {
+        # to read a file in cromwell/wdl : pass it back as a string or delocalize (see task_two)
+        String outfile = '~{wd}/MyOutFile'
+     }
+}
+
+task task_two {
+    input {
+        String wd
+        File infile
+    }
+    command {
+        # put something new in the file:
+        ls -alh /tmp > ~{infile}
+        
+    }
+     runtime {
+        docker: "ubuntu:22.04"
+        cpu : "1"
+        memory: "500M" 
+        efsDelocalize: true
+     }
+     output {
+        File outfile = "~{infile}"
+     }
+}
+```
+
+
+
+
 AWS Batch
 ---------
 

From 8982e07c0fee9fec63da68b4216166a5ca7904be Mon Sep 17 00:00:00 2001
From: Henrique Ribeiro <henriqueribeiro@users.noreply.github.com>
Date: Mon, 20 Mar 2023 15:33:26 +0000
Subject: [PATCH 152/326] 85 release (#28)

* Update cromwell version from 83 to 84

* BW-1255 Implement POST /runs endpoint (#6779)

* Adding route

* Fixing HTTP method error

* All formFields made optional

* A compliling state

* Saving

* Saving

* All three endpoints functioning as expected; updated RESTAPI.md

* Updated response for submission from 200 to 201 to pass tests

* Test submission response

* Moved updated submission response to askSubmit

* test

* updating RESTAPI.md

* saving

* Adding utility file for submitRequest

* cleanup

* Update awssdkv from 2.17.152 to 2.17.194 (#6814)

* BW-1305 Swagger Update (#6818)

* Properly documenting metadataArchiveStatus in WorkflowQueryResult model

* Update docs

* BT-710 Add configs for BlobPathBuilderFactory (#6817)

BT-710 Add configs for BlobPathBuilderFactory

* BW-1305 Make "name" optional in workflow query response (#6821)

* BT-724 Fix BlobPathBuilder failing on retrieving existing filesystem (#6816)

Modify blobPathBuilder to fallback to creating a filesystem if one is not found

* Logging updates: (#6813)

* [BT-698] first pass on BlobTokenGenerator with E2E test (#6824)

* first pass on BlobTokenGenerator with E2E test

* update BlobPathBuilder constructor args in test

* account -> container level client

* [BT-687] specify correct types (#6829)

* specify correct types

* fix test with new type

* remove type declarations in function call

* remove unnecessary sas-token config

* BW-1206 - Combine all Wes Endpoints & add Tests (#6833)

* Add tests, getting frid of WesRunRoutes.scala

* wesWorkflowId fix, ec implicits errors gone

* Refactoring path for GET /runs

* Indentation fix

* Commit to rollback

* Revert "Indentation fix"

This reverts commit 63fc4842c9d4eff68ec9cb7c3ef19e110696598b.

* PR trigger

* Optimize imports

* Missed import

* BW-1354 - Porting CBAS preliminary step (#6837)

* Getting rid of shared utility file; Adding/Updating WES version of submit.

* Edit spec file

* Adding Wes-like error

* BW-1378 Addl CromIAM user enablement checks (#6826)

* Update cromwell version from 84 to 85

* BW-1393 Release doc updates (#6839)

* BT-732 Checksum validation for blobs read by engine (#6838)

* Draft support for optional FileHash

* Draft getMd5 for BlobPath

* Resolve non-parallel IO to fix tests

* Checksum validation for BlobPath

* Nicer error message

* Test for missing Blob hash

* Break attr acquisition into separate method

* Cleanup, comments

* In-progress tests of blob hash command

* Remove test

* Remove unused import

* BT-711 Refresh SAS token for filesystem on expiry (#6831)

* BT-711 Refresh SAS token for filesystem on expiry

* Rough cut of token refresh using exceptions

* Ignore tests, and minor cleanup

* Remove stray line

* Draft of manager class for handling expiring file systems

* Style fixes

* Refactor of blobfilesystemManager and tests covering its functionality

* Refined tests to validate close filesystem as separate unit

* Ignore connected tests

* Clean up of some things

* Refactor BlobFileSystemManager to separate file, and some other cleanup

* Some additional scala-ifying

* Small cleanup

* Correcting imports

* trigger tests

* trigger tests

* Batch 1 of scala steward updates (#6903)

* Batch 1 of scala steward updates

* Rollback snakeYAML

* Attempt 3, with only the passing dependancies

* Revert google API and Big Query udpates

* Winding back other google deps

* rollback remaining google updates

* trigger tests

* trigger tests

* [BW-1398] Migrate PKs to BIGINT (#6907)

* BT-745  Batch 2 of scala steward updates (#6906)

* Update SBT to 2.0.0

* Fix sbt-git import

* Update mouse to 1.0.11

* Update rhino 1.7.14

* SUP-692 Retry with more memory after RC 137 (#6912)

* Reorder execution result checks so 137 can retry with more memory

* Test for memory retry after 137 RC

* Fix test expectations

* Make memory retry checks consistent

* Revert changes to existing test

* Rename retryWithMoreMemory to outOfMemoryDetected

* Scala steward updates batch 3 (#6913)

* Scala steward updates batch 3

* WX-745 Batch 4 scala steward updates (#6916)

* WX-746 Localize all DRS inputs in a single Action (#6914)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* WX-755 Build all images instead of just Cromwell (#6919)

* WX-755 Add `isRelease` option for Docker builds (#6923)

* WX-755 Cromwell/CromIAM automatically board train (#6924)

* WX-755 Fix environment variable syntax (#6926)

* WX-743 Enable TES task creation with BlobPaths (#6921)

* Give blob SAS tokens write permission

* Case class wrapper for subscription id

* Resolve duplicate container name in absolute BlobPath

* Ignored test demonstrating correct absolute path generation

* Update filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala

Co-authored-by: Brian Reilly <breilly@broadinstitute.org>

* PR feedback

Co-authored-by: Brian Reilly <breilly@broadinstitute.org>

* [WX-765] Update snakeyaml to 1.33 (#6927)

* update snakeyaml to 1.33

* Don't use deprecated no-arg Constructor constructor

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* WM-1414 Refactoring WesRunLog to omit Cromwell's "workflowLog" object (#6925)

* Upgrade Postgres to 42.4.1 (#6932)

* WX-735 Fix incorrect and/or nondeterministic filesystem ordering (#6930)

* WX-772 Update Scala to 2.13.9 (#6928)

* Update Scala to 2.13.9

* Try updating sbt-scoverage

* Does this version exist anywhere we can see?

* This version actually exists

* Update library version to remove conflict

* Codegen version

* Fix fun new 2.13.9 compiler errors

* Resolve warnings

* Newest Scala?

* I guess not

* Does this please Travis?

* force ci

* Back out changes to generated code

Co-authored-by: Adam Nichols <aednichols@gmail.com>

* WX-781 Bump jackson-databind in /CromwellRefdiskManifestCreator (#6935)

Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.13.2.2 to 2.13.4.1.
- [Release notes](https://github.com/FasterXML/jackson/releases)
- [Commits](https://github.com/FasterXML/jackson/commits)

---
updated-dependencies:
- dependency-name: com.fasterxml.jackson.core:jackson-databind
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* WX-808 Host allowlist for HTTP imports (#6938)

* `hostAllowlist` that allows everything

* Refactor

* Stick allow list in HttpResolver

* Better default config

* Allow list tests

* Make it build

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Update commons text to 1.10.0 (#6937)

* WX-751 Token refresh signal for monitoring (#6939)

* Log messages

* `DEBUG` -> `INFO`

* WX-744 Optionally rewrite blob paths to appear as local paths (#6941)

* Modify blob paths for TES

* Make blob transformation configurable

* Update supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Apply PR feedback in second place

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Update changelog for wdl http allow list (#6944)

* WM-1491 Fixing Cromwell-client (#6943)

* More updated client for use in cbas

* Removing excess code

* Fix client build script (#6945)

* WX-837: Remove CWL references from documentation (#6949)

* wx-837 removed cwl references in markdown doc files

* wx-837 removed cwlParsingOverview.md, updated mkdocs.yml

* wx-837 updated cromwell.yaml, generated new RESTAPI file

* WX-728 Add configurable WSM client to Cromwell (#6948)

* Dependencies

* Compiles but no tests

* Formatting

* Moar exclusions

* Update to latest WSM

* Add additional dependency

* We need some UUID here to make the request

* Formatting

* Clarify what is fake

* Formatting

* Use our own version of Jersey and Jackson stuff

* Port-in Khalid's changes (thank you!)

Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>

* Test longevity

Don't break the test if someone decides to add a cert to `ws.org`

* Cleanup

* Cleanup

* Cleanup

* Adjust TES config file for CI

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>

* CROM-6554: Removed PAPIv1 references from doc (#6950)

* crom-6554 removed references to PAPI v1 from doc

* crom-6554 pr feedback, reworded doc to use example conf as a starting point

* WX-833 Real Azure DRS Credentials (#6952)

* Remove B2C reference from name

* Get token for current user rather than getting from KeyVault

* Remove KeyVault config for engine

* Remove KeyVault config for DRSLocalizer

* Remove KeyVault dependency

* Remove KeyVault support from localizer repo template

* Cleaned up and working Azure token acquisition for engine

* Collapse localizer's AccessTokenStrategy into DrsCredentials

* Cleanup

* WX-853 Remove most CWL (#6955)

* WX-696 Enable getting SAS token from WSM (#6954)

* WX-696 Enable getting SAS token from WSM

* Wire container resource id from config

* Move resource-container-id config path

* First pass at config for WSM

* Remove unused singleton config

* Tests for new config

* Fix config parsing

* Modified b2c token to be provided each time

* Remove singletonConfig arg from factory

* Restore types to factory configs

* Clean up comments and empty token default

* Default to config b2c before searching environment

* Fix token default on api client

* Fix test

* Refactor error handling for when there is no token

* Remove token constructor arg for clientProvider

* Move configs to global singleton config

* Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

* default -> override

* Add override token to test

* Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Parentheses

* Reduce token timeout

* Move AzureCredentials to separate file

* Make AzureCredentials an object

* WSM token cleanup

* Config refactor (#6960)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Initial blob token documentation

* Refine language in BlobSasTokenGenerator

* Update comment and formatting

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* WX-853 Remove CWL language factory, Centaur runner (#6961)

* WX-842 Add Pact Dependency for Cromwell (#6962)

* WX-842 Add Pact Dependency for Cromwell

* Remove incomplete test spec

* Initial Pact Test

* Fix pact so it compiles

* Add breadcrumb comment and clean up

* ID-125 Add support for drshub, rename all the things (#6959)

* Add support for drshub, rename all the things

* fallback to martha if resolver is not in config

* WX-867 Translate crc32c hashes to b64 for getm (#6970)

* Translate crc32c hashes to b64 for getm

* Update tests

* Remove obsolete b64 handling for md5, centralize hex validation

* Restore old test, fix other test

* WX-843 Workflow failure reason should accurately indicate issues opening blob filesystem (#6965)

* WX-859 Accept workflow execution identity in config (#6967)

* WX-892 Trim down `ValueStore` logging to prevent OOMs (#6981)

* Add Nirvana 3.18.1 reference image test, minor cleanup [VS-705] (#6975)

* WX-863 Turn off Azure NIO logging (#6982)

* Turn off Azure NIO logging

* Poke Travis

* WM-1616: Allow repeating attempts at initialization (take 2) (#6985)

* WX-878 Single shared BlobFileSystemManager (#6986)

* Make BlobFileSystemManager shared across all BlobPathBuilders

* Update TES conf file to reflect new singleton config

* Shell escape reference image  files [VS-796] [WX-910] (#6989)

* WX-769 `disks` compatibility for TES backend (#6991)

* Update FiveMinuteIntro.md (#6994)

* WX-906 Sbt Unit Tests as Github Actions (#6992)

* WX-926 Support falling back to OCI Manifest Format (#7003)

* WX-926 Support falling back to OCI Manifest Forma

* Only mount reference disks if requested [WX-925] (#7001)

* [WM-1646] Add missing fields for `WorkflowDescription` for WomTool /describe endpoint to Swagger (#7004)

* WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status (#6980)

* WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status

* Address feedback

* Address feedback (#6997)

* Address additional feedback (#7000)

* Fix copy/paste error (#7005)

* Address additional feedback

* Fix copy/paste error

* Trigger CI

---------

Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Centaur reference image test should validate symlinks [VS-796] (#6996)

* WX-903 Pre-GHA test suite disablement

* WX-877 Update CHANGELOG for release 85 (#7011)

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Katrina P <68349264+kpierre13@users.noreply.github.com>
Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Co-authored-by: Christian Freitas <christian.j.freitas@gmail.com>
Co-authored-by: Saloni Shah <salonipshah11@gmail.com>
Co-authored-by: kshakir <kshakir@broadinstitute.org>
Co-authored-by: mspector <michael.l.spector@gmail.com>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
Co-authored-by: Brian Reilly <breilly@broadinstitute.org>
Co-authored-by: Adam Nichols <aednichols@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Justin Variath Thomas <JVThomas@users.noreply.github.com>
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Co-authored-by: Tom Wiseman <tom.h.wiseman@gmail.com>
Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>
---
 .github/set_up_cromwell_action/action.yml     |    47 +
 .github/workflows/chart_update_on_merge.yml   |    26 +-
 .github/workflows/cromwell_unit_tests.yml     |    32 +
 .travis.yml                                   |    23 +-
 CHANGELOG.md                                  |   326 +-
 CromIAM/src/main/resources/application.conf   |     2 +-
 CromIAM/src/main/resources/logback.xml        |    14 +-
 .../CromIamInstrumentation.scala              |     1 +
 .../main/scala/cromiam/sam/SamClient.scala    |    33 +
 .../webservice/CromIamApiService.scala        |    16 +-
 .../cromiam/webservice/QuerySupport.scala     |     2 +-
 .../cromiam/webservice/RequestSupport.scala   |    26 +-
 .../webservice/SubmissionSupport.scala        |     2 +-
 .../webservice/WomtoolRouteSupport.scala      |    10 +-
 .../webservice/CromIamApiServiceSpec.scala    |    38 +-
 .../cromiam/webservice/MockClients.scala      |     9 +
 .../webservice/SwaggerServiceSpec.scala       |     7 +-
 .../webservice/WomtoolRouteSupportSpec.scala  |    54 +-
 CromwellRefdiskManifestCreator/pom.xml        |     2 +-
 .../StandardAsyncExecutionActor.scala         |    26 +-
 .../standard/StandardCachingActorHelper.scala |     2 +-
 .../RootWorkflowFileHashCacheActor.scala      |     2 +-
 build.sbt                                     |    30 +-
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 delete mode 100644 centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala
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 delete mode 100644 centaurCwlRunner/src/test/resources/application.conf
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 rename cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/{MarthaHttpRequestRetryStrategy.scala => DrsResolverHttpRequestRetryStrategy.scala} (96%)
 rename cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/{MarthaHttpRequestRetryStrategySpec.scala => DrsResolverHttpRequestRetryStrategySpec.scala} (89%)
 create mode 100644 core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala
 create mode 100644 core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala
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 create mode 100644 core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala
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 delete mode 100644 cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
 delete mode 100644 cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala
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 create mode 100644 database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml
 create mode 100644 database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml
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 delete mode 100644 engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala
 create mode 100644 engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
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 create mode 100644 filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
 create mode 100644 filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
 create mode 100644 filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
 delete mode 100644 languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala
 create mode 100644 runConfigurations/Repo template_ Cromwell server TES.run.xml
 delete mode 100644 server/src/test/resources/cwl_glob_sort.cwl
 delete mode 100644 supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala
 create mode 100644 supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
new file mode 100644
index 00000000000..13cb11601db
--- /dev/null
+++ b/.github/set_up_cromwell_action/action.yml
@@ -0,0 +1,47 @@
+#This is a series of steps that will setup Java/sbt/Cromwell on the local runner.
+#These steps are meant to be re-used and invoked by other Github Action Workflows
+name: 'Set Up Cromwell Steps'
+description: Specific steps that will set up git secrets, java, sbt, and Cromwell on the local machine. 
+inputs:
+  cromwell_repo_token: #As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell.
+    required: true
+
+runs:
+  using: "composite" # <-- this allows these steps to be used by other workflows.
+  steps:
+      #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
+      - uses: actions/checkout@v3
+        name: Checkout Coursier Cache
+      - uses: coursier/cache-action@v6  
+        name: Enable Coursier Cache
+
+      #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
+      - name: Git secrets setup 
+        run: |
+          git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
+          cd ~/git-secrets
+          git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
+          sudo make install
+        shell: bash
+
+      - name: Secrets check
+        run: |
+          sudo ln -s "$(which echo)" /usr/local/bin/say
+          ./minnie-kenny.sh --force
+          git secrets --scan-history
+        shell: bash
+
+      #Clone the cromwell repo to this VM.
+      - name: Clone Cromwell
+        uses: actions/checkout@v3
+        with:
+          repository: broadinstitute/cromwell
+          token: ${{ inputs.cromwell_repo_token }}
+
+      #Install Java to this VM. This Java version and distribution is compatible with Cromwell.
+      - name: Setup JDK
+        uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 11
+
diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index 9e847bc17eb..aa7a2c9c9ad 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -41,19 +41,33 @@ jobs:
         echo "CROMWELL_NUMBER=$((previous_version + 1))" >> $GITHUB_ENV
     - name: Save complete image ID
       run: |
-        echo "CROMWELL_SNAP_VERSION=`echo "$CROMWELL_NUMBER-$CROMWELL_SHORT_SHA-SNAP"`" >> $GITHUB_ENV
+        echo "CROMWELL_VERSION=`echo "$CROMWELL_NUMBER-$CROMWELL_SHORT_SHA"`" >> $GITHUB_ENV
     # `DSDEJENKINS_PASSWORD` auto syncs from vault with https://github.com/broadinstitute/terraform-ap-deployments/pull/614
     - name: Login to Docker Hub
       uses: docker/login-action@v1
       with:
         username: dsdejenkins
         password: ${{ secrets.DSDEJENKINS_PASSWORD }}
+    # Build & push `cromwell`, `womtool`, `cromiam`, and `cromwell-drs-localizer`
     - name: Build Cromwell Docker
       run: |
         set -e
         cd cromwell
-        sbt server/docker
-        docker push broadinstitute/cromwell:$CROMWELL_SNAP_VERSION
+        sbt -Dproject.isSnapshot=false -Dproject.isRelease=false dockerBuildAndPush
+    - name: Deploy to dev and board release train (Cromwell)
+      uses: broadinstitute/repository-dispatch@master
+      with:
+        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+        repository: broadinstitute/terra-helmfile
+        event-type: update-service
+        client-payload: '{"service": "cromwell", "version": "${{ env.CROMWELL_VERSION }}", "dev_only": false}'
+    - name: Deploy to dev and board release train (CromIAM)
+      uses: broadinstitute/repository-dispatch@master
+      with:
+        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+        repository: broadinstitute/terra-helmfile
+        event-type: update-service
+        client-payload: '{"service": "cromiam", "version": "${{ env.CROMWELL_VERSION }}", "dev_only": false}'
     - name: Edit & push chart
       env:
         BROADBOT_GITHUB_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
@@ -62,10 +76,10 @@ jobs:
         cd cromwhelm
         git checkout main
         ls -la
-        sed -i "s/appVersion.*/appVersion: \"$CROMWELL_SNAP_VERSION\"/" cromwell-helm/Chart.yaml
-        sed -i "s/image: broadinstitute\/cromwell.*/image: broadinstitute\/cromwell:$CROMWELL_SNAP_VERSION/" cromwell-helm/templates/cromwell.yaml
+        sed -i "s/appVersion.*/appVersion: \"$CROMWELL_VERSION\"/" cromwell-helm/Chart.yaml
+        sed -i "s/image: broadinstitute\/cromwell.*/image: broadinstitute\/cromwell:$CROMWELL_VERSION/" cromwell-helm/templates/cromwell.yaml
         git diff
         git config --global user.name "broadbot"
         git config --global user.email "broadbot@broadinstitute.org"
-        git commit -am "Auto update to Cromwell $CROMWELL_SNAP_VERSION"
+        git commit -am "Auto update to Cromwell $CROMWELL_VERSION"
         git push https://broadbot:$BROADBOT_GITHUB_TOKEN@github.com/broadinstitute/cromwhelm.git main
diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
new file mode 100644
index 00000000000..d0927f8b954
--- /dev/null
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -0,0 +1,32 @@
+name: 'Cromwell unit tests'
+
+#This github action runs all of Cromwell's unit tests.
+
+#This is what shows up in the github workflows page as the title. 
+run-name: ${{ github.actor }} running Cromwell sbt unit tests.
+
+#What will trigger the workflow to run. 
+on:
+  workflow_dispatch: #Manual trigger from GitHub UI
+  push:
+
+permissions: 
+  contents: read
+
+jobs:
+  build-and-test: 
+    #This action is using a Github free runner, rather than a Broad self-hosted one.
+    #This is because the Broad ones don't have sbt installed by default.
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3 # checkout the cromwell repo
+    - uses: ./.github/set_up_cromwell_action #Exectute this reusable github action. It will set up java/sbt/git-secrets/cromwell.
+      with:
+        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+  
+    #Invoke SBT to run all unit tests for Cromwell. 
+    - name: Run tests
+      run: |
+        set -e
+        sbt "test"
diff --git a/.travis.yml b/.travis.yml
index d733b16432c..9ffb48b1147 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -28,24 +28,13 @@ env:
     - >-
       BUILD_TYPE=centaurEngineUpgradeLocal
       BUILD_MYSQL=5.7
+    # Temporarily keeping until `centaurEngineUpgradePapiV2beta` or similar exists
     - >-
       BUILD_TYPE=centaurEngineUpgradePapiV2alpha1
       BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurHoricromtalPapiV2alpha1
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=centaurHoricromtalPapiV2beta
       BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurHoricromtalEngineUpgradePapiV2alpha1
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurPapiUpgradePapiV2alpha1
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurPapiUpgradeNewWorkflowsPapiV2alpha1
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=centaurLocal
       BUILD_MARIADB=10.3
@@ -55,9 +44,6 @@ env:
     - >-
       BUILD_TYPE=centaurLocal
       BUILD_POSTGRESQL=11.3
-    - >-
-      BUILD_TYPE=centaurPapiV2alpha1
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=centaurPapiV2beta
       BUILD_MYSQL=5.7
@@ -67,15 +53,10 @@ env:
     - >-
       BUILD_TYPE=centaurTes
       BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurWdlUpgradeLocal
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=checkPublish
     - >-
       BUILD_TYPE=horicromtalDeadlock
-    - >-
-      BUILD_TYPE=dockerScripts
     - >-
       BUILD_TYPE=sbt
       BUILD_SBT_INCLUDE=engine
@@ -92,8 +73,6 @@ env:
       BUILD_TYPE=dbms
     - >-
       BUILD_TYPE=singleWorkflowRunner
-    - >-
-      BUILD_TYPE=metadataComparisonPython
     - >-
       BUILD_TYPE=referenceDiskManifestBuilderApp
 script:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0c40f47b651..0084c05171b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,97 @@
 # Cromwell Change Log
 
+## 85 Release Notes
+
+### Migration of PKs to BIGINT
+
+The PK of below tables will be migrated from INT to BIGINT. Also, since `ROOT_WORKFLOW_ID` in `SUB_WORKFLOW_STORE_ENTRY` is a FK to `WORKFLOW_STORE_ENTRY_ID` in `WORKFLOW_STORE_ENTRY`
+it is also being migrated from INT to BIGINT.
+* DOCKER_HASH_STORE_ENTRY
+* WORKFLOW_STORE_ENTRY
+* SUB_WORKFLOW_STORE_ENTRY
+
+### Improvement to "retry with more memory" behavior
+
+Cromwell will now retry a task with more memory after it fails with return code 137, provided all
+the other requirements for retrying with more memory are met.
+
+### DRS Improvements
+
+#### Support for invoking `CromwellDRSLocalizer` with manifest file
+
+`CromwellDRSLocalizer` can now handle multiple file localizations in a single invocation. Users can provide a
+manifest file containing multiple (DRS id, local container path) pairs in CSV format, and they will be localized in
+sequence, with the program exiting if any fail.
+```
+java -jar /path/to/localizer.jar [options] -m /local/path/to/manifest/file.txt
+```
+
+The previous method of passing in a single DRS file and container destination using positional arguments is still
+supported.
+
+#### Improvement to DRS localization in GCP papiv2beta backend
+
+All DRS inputs to a task are now localized in a single PAPI action, which should improve speed and resolve
+failures observed when attempting to localize a large number of DRS files.
+
+
+### Allow list for HTTP WDL resolution
+
+Administrators can now configure Cromwell with an allow list that limits the domains from which WDLs can be resolved and imported.
+Default behavior is unchanged (Cromwell attempts to resolve WDL files from any URI). Example configuration:
+```
+languages {
+  WDL {
+    http-allow-list {
+      enabled: true
+      allowed-http-hosts: [
+        "my.wdl.repo.org",
+        "raw.githubusercontent.com"
+      ]
+    }
+  }
+}
+```
+
+### CWL implementation removed
+
+This release removes the `cwl` top-level artifact. Some nonfunctional references may remain, and will be addressed over time.
+
+For more information, see the [Cromwell 79 release notes](https://github.com/broadinstitute/cromwell/releases/tag/79).
+
+### TES Improvments
+
+* Tes system errors are are now reported in Cromwell execution logs when the TES backend returns a task error.
+
+* Cromwell now attempts to translate `disks` attributes [written for GCP](https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/#disks) into valid `disk` attributes for TES. For information on supported conversions, refer to the [TES documentation](https://cromwell.readthedocs.io/en/stable/backends/TES/).
+
+### Bug Fixes
+
+* Reference disks are only mounted if configured in the workflow options.
+
+* Recent docker images of Ubuntu use a new manifest format, ensure that these newer image versions can be pulled from Docker Registry without issue.
+
+* When converting ValueStore objects to strings for logging, we truncate long values to limit memory usage.
+
+
+### Security Patching
+
+Updates to dependencies to fix security vulnerabilities.
+
+## 84 Release Notes
+
+### CromIAM enabled user checks
+
+For Cromwell instances utilizing the optional CromIAM identity and access management component, the following endpoints now verify that the calling user is enabled before forwarding the request.
+* `/api/workflows/v1/backends`
+* `/api/womtool/v1/describe`
+
+This change makes the above endpoints consistent with the existing behavior of all the other endpoints in the `/api/` path of CromIAM.
+
+## 83 Release Notes
+
+* Changes the type of several primary key columns in call caching tables from int to bigint. The database migration may be lengthy if your database contains a large amount of call caching data.
+
 ## 82 Release Notes
 
  * Restored missing example configuration file
@@ -27,7 +119,7 @@ The BCS backend and OSS filesystem (both of which support Alibaba Cloud) have be
 Cromwell 80 no longer supports the wes2cromwell project within the Cromwell repository.
 
 In the previous release, 3 Wes2Cromwell endpoints in the Cromwell project were implemented and documented in the Swagger API. Three new endpoints,
-located within the wes2cromwell project, will also be moved, implemented, and documented within Cromwell. As a result of this, we can safely remove 
+located within the wes2cromwell project, will also be moved, implemented, and documented within Cromwell. As a result of this, we can safely remove
 and deprecate the wes2cromwell project from the repo.
 
 Previous endpoints:
@@ -111,11 +203,11 @@ Previously:
 
 ### New 'requestedWorkflowId' API Option
 
-Allows users to choose their own workflow IDs at workflow submission time. 
+Allows users to choose their own workflow IDs at workflow submission time.
 
 If supplied for single workflows, this value must be a JSON string containing a valid, and not already used, UUID. For batch submissions, this value must be a JSON array of valid UUIDs.
 
-If not supplied, the behavior is as today: Cromwell will generate a random workflow ID for every workflow submitted. 
+If not supplied, the behavior is as today: Cromwell will generate a random workflow ID for every workflow submitted.
 
 ### Bug Fixes
 
@@ -228,8 +320,8 @@ AccessURLs](https://ga4gh.github.io/data-repository-service-schemas/preview/rele
 
 ### No labels update for Archived workflows
 
-If **- and ONLY if -** you have metadata archiving turned on, then for a workflow whose metadata has been archived by Cromwell 
-according to the lifecycle policy, Cromwell will no longer add new labels or update existing labels for this workflow 
+If **- and ONLY if -** you have metadata archiving turned on, then for a workflow whose metadata has been archived by Cromwell
+according to the lifecycle policy, Cromwell will no longer add new labels or update existing labels for this workflow
 coming through PATCH `/labels` endpoint.
 
 ## 60 Release Notes
@@ -241,12 +333,12 @@ containerized using [AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/).
 
 ### Hybrid metadata storage ("carboniting") removed
 
-Carboniting functionality has been removed from Cromwell. 
+Carboniting functionality has been removed from Cromwell.
 There will be no effect for customers who store metadata permanently in the relational database (most common),
 and there will also be no effect for customers who use the in-memory database.
 
 Breaking change only for customers who explicitly enabled `carbonite-metadata-service` in their configuration to split
-metadata storage between a relational database and Google Cloud Storage. If you had previously enabled carboniting and 
+metadata storage between a relational database and Google Cloud Storage. If you had previously enabled carboniting and
 deletion, any workflows marked as `ArchivedAndPurged` in your database will no longer be accessible via the Cromwell metadata API.
 
 ## 59 Release Notes
@@ -273,9 +365,9 @@ rather than through a level of indirection to a manifest file stored in GCS. Mor
 ### Retry with More Memory as workflow option
 
 The experimental memory retry feature gains per-workflow customization and includes breaking changes:
-* The per-backend configuration key `<backend>.config.memory-retry.error-keys` has been removed and replaced 
+* The per-backend configuration key `<backend>.config.memory-retry.error-keys` has been removed and replaced
 with global key `system.memory-retry-error-keys`
-* The per-backend configuration key `<backend>.config.memory-retry.multiplier` has been replaced with **workflow option** 
+* The per-backend configuration key `<backend>.config.memory-retry.multiplier` has been replaced with **workflow option**
 `memory_retry_multiplier`
 
 More details can be found [here](https://cromwell.readthedocs.io/en/develop/wf_options/Overview.md#retry-with-more-memory-multiplier).
@@ -284,7 +376,7 @@ More details can be found [here](https://cromwell.readthedocs.io/en/develop/wf_o
 
 * Fixed a bug that caused Cromwell to mark workflows as failed after a single `500`, `503`, or `504` error from Google Cloud Storage.
   * Cromwell will now retry these errors as designed.
-  * The default retry count is `5` and may be customized with `system.io.number-of-attempts`. 
+  * The default retry count is `5` and may be customized with `system.io.number-of-attempts`.
 
 ## 55 Release Notes
 
@@ -294,7 +386,7 @@ Users with access to the new Mac hardware should review [important information p
 
 ### Bug Fixes
 
-* Fixed a bug that prevented `read_json()` from working with arrays and primitives. The function now works as expected for all valid JSON data inputs. 
+* Fixed a bug that prevented `read_json()` from working with arrays and primitives. The function now works as expected for all valid JSON data inputs.
 More information on JSON Type to WDL Type conversion can be found [here](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#mixed-read_jsonstringfile).
 
 * Now retries HTTP 408 responses as well as HTTP 429 responses during DOS/DRS resolution requests.
@@ -322,19 +414,19 @@ to the worker VM on the next attempt if the task is interrupted. More details [h
 ### Bug Fixes
 
 * Fixed a bug that prevented `write_json()` from working with arrays and primitives. The function now works as expected for `Boolean`, `String`, `Integer`, `Float`,
- `Pair[_, _]`, `Object`, `Map[_, _]` and `Array[_]` (including array of objects) type inputs. More information on WDL Type to JSON Type 
+ `Pair[_, _]`, `Object`, `Map[_, _]` and `Array[_]` (including array of objects) type inputs. More information on WDL Type to JSON Type
  conversion can be found [here](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#mixed-read_jsonstringfile).
 
 ### Spark backend support removal
 
-Spark backend was not widely used and it was decided to remove it from the codebase in order to narrow the scope of Cromwell code. 
+Spark backend was not widely used and it was decided to remove it from the codebase in order to narrow the scope of Cromwell code.
 
 ### Improved DRS Localizer logging
 
 Error logging while localizing a DRS URI should now be more clear especially when there is a Requester Pays bucket involved.
 
 ### Per-backend hog factors
-Cromwell now allows overriding system-level log factors on back-end level. First, Cromwell will try to use hog-factor 
+Cromwell now allows overriding system-level log factors on back-end level. First, Cromwell will try to use hog-factor
 defined in the backend config, and if it is not defined, it will default to using system-wide hog factor.
 ```conf
 backend {
@@ -402,16 +494,16 @@ https://cromwell.readthedocs.io/en/stable/tutorials/Containers/#singularity).
 
 ### Google library upgrade [(#5565)](https://github.com/broadinstitute/cromwell/pull/5565)
 
-All previous versions of Cromwell shipped with Google Cloud Storage (GCS) libraries that are now deprecated and will [stop working in August 2020](https://developers.googleblog.com/2018/03/discontinuing-support-for-json-rpc-and.html). This release adopts updated libraries to ensure uninterrupted operation. The only user action required is upgrading Cromwell.   
+All previous versions of Cromwell shipped with Google Cloud Storage (GCS) libraries that are now deprecated and will [stop working in August 2020](https://developers.googleblog.com/2018/03/discontinuing-support-for-json-rpc-and.html). This release adopts updated libraries to ensure uninterrupted operation. The only user action required is upgrading Cromwell.
 
 ### Bug fixes
 
 * Fixed a bug that required Cromwell to be restarted in order to pick up DNS changes.
     * By default, the JVM caches DNS records with a TTL of infinity.
-    * Cromwell now configures its JVM with a 3-minute TTL. This value can be customized by setting `system.dns-cache-ttl`.  
+    * Cromwell now configures its JVM with a 3-minute TTL. This value can be customized by setting `system.dns-cache-ttl`.
 * Clarified an error message that Cromwell emits when the compute backend terminates a job of its own volition (as opposed to termination in response to an abort request from Cromwell)
     * Previously, the error read `The job was aborted from outside Cromwell`
-    * The new error reads `The compute backend terminated the job. If this termination is unexpected, examine likely causes such as preemption, running out of disk or memory on the compute instance, or exceeding the backend's maximum job duration.` 
+    * The new error reads `The compute backend terminated the job. If this termination is unexpected, examine likely causes such as preemption, running out of disk or memory on the compute instance, or exceeding the backend's maximum job duration.`
 
 ## 51 Release Notes
 
@@ -422,8 +514,8 @@ https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching) for details
 
 ### Bug fixes
 
-* Fixed a bug where the `size(...)` function did not work correctly on files 
-  from a shared filesystem if `size(...)` was called in the input section on a 
+* Fixed a bug where the `size(...)` function did not work correctly on files
+  from a shared filesystem if `size(...)` was called in the input section on a
   relative path.
 + Fixed a bug where the `use_relative_output_paths` option would not preserve intermediate folders.
 
@@ -431,17 +523,17 @@ https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching) for details
 
 #### Call caching blacklisting improvements
 
-Cromwell previously supported blacklisting GCS buckets containing cache hits which could not be copied for permissions 
+Cromwell previously supported blacklisting GCS buckets containing cache hits which could not be copied for permissions
 reasons. Cromwell now adds support for blacklisting individual cache hits which could not be copied for any reason,
 as well as grouping blacklist caches according to a workflow option key. More information available in the [
-call caching documentation]( https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching). 
+call caching documentation]( https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching).
 
 #### new xxh64 and fingerprint strategies for call caching
 
-Existing call cache strategies `path` and `path+modtime` don't work when using docker on shared filesystems 
+Existing call cache strategies `path` and `path+modtime` don't work when using docker on shared filesystems
 (SFS backend, i.e. not in cloud storage). The `file` (md5sum) strategy works, but uses a lot of resources.
-Two faster strategies have been added for this use case: `xxh64` and 
-`fingerprint`. `xxh64` is a lightweight hashing algorithm, `fingerprint` is a strategy designed to be very 
+Two faster strategies have been added for this use case: `xxh64` and
+`fingerprint`. `xxh64` is a lightweight hashing algorithm, `fingerprint` is a strategy designed to be very
 lightweight. Read more about it in the [call caching documentation](
 https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching).
 
@@ -475,7 +567,7 @@ SELECT table_rows FROM INFORMATION_SCHEMA.TABLES WHERE TABLE_SCHEMA = 'cromwell'
 
 #### Execution Directory Layout (cache copies)
 
-When an attempt to copy a cache result is made, you'll now see a `cacheCopy` directory in the call root directory. 
+When an attempt to copy a cache result is made, you'll now see a `cacheCopy` directory in the call root directory.
 This prevents them clashing with the files staged to the same directory for attempt 1 if the cache copy fails (see also: Bug Fixes).
 
 The directory layout used to be:
@@ -512,7 +604,7 @@ but is now:
 
 #### Disable call-caching for tasks
 
-It is now possible to indicate in a workflow that a task should not be call-cached. See details 
+It is now possible to indicate in a workflow that a task should not be call-cached. See details
 [here](https://cromwell.readthedocs.io/en/stable/optimizations/VolatileTasks).
 
 #### Delete Intermediate Outputs on PapiV2
@@ -525,13 +617,13 @@ for more information.
 #### Metadata Archival Support
 
 Cromwell 49 now offers the option to archive metadata to GCS and remove the equivalent metadata from relational
-database storage. Please see 
-[the documentation](https://cromwell.readthedocs.io/en/stable/Configuring#hybrid-metadata-storage-classic-carbonite) for more details. 
+database storage. Please see
+[the documentation](https://cromwell.readthedocs.io/en/stable/Configuring#hybrid-metadata-storage-classic-carbonite) for more details.
 
 #### Adding support for Google Cloud Life Sciences v2beta
-Cromwell now supports running workflows using Google Cloud Life Sciences v2beta API in addition to Google Cloud Genomics v2alpha1. 
-More information about migration to the new API from v2alpha1 
-[here](https://cromwell.readthedocs.io/en/stable/backends/Google#migration-from-google-cloud-genomics-v2alpha1-to-google-cloud-life-sciences-v2beta). 
+Cromwell now supports running workflows using Google Cloud Life Sciences v2beta API in addition to Google Cloud Genomics v2alpha1.
+More information about migration to the new API from v2alpha1
+[here](https://cromwell.readthedocs.io/en/stable/backends/Google#migration-from-google-cloud-genomics-v2alpha1-to-google-cloud-life-sciences-v2beta).
 * **Note** Google Cloud Life Sciences is the new name for newer versions of Google Cloud Genomics.
 * **Note** Support for Google Cloud Genomics v2alpha1 will be removed in a future version of Cromwell. Advance notice will be provided.
 
@@ -539,23 +631,23 @@ More information about migration to the new API from v2alpha1
 
 #### Installation methods
 
-Links to the conda package and docker container are now available in 
+Links to the conda package and docker container are now available in
 [the install documentation](https://cromwell.readthedocs.io/en/stable/Getting/).
 
 
 ### Bug Fixes
 
-+ Fix a bug where zip files with directories could not be imported. 
-  For example a zip with `a.wdl` and `b.wdl` could be imported but one with `sub_workflows/a.wdl` 
++ Fix a bug where zip files with directories could not be imported.
+  For example a zip with `a.wdl` and `b.wdl` could be imported but one with `sub_workflows/a.wdl`
   and `imports/b.wdl` could not.
 + Fix a bug which sometimes allowed execution scripts copied by a failed cache-copy to be run instead
-  of the attempt-1 script for a live job execution. 
-  
+  of the attempt-1 script for a live job execution.
+
 ## 48 Release Notes
 
 ### Womtool Graph for WDL 1.0
 
-The `womtool graph` command now supports WDL 1.0 workflows. 
+The `womtool graph` command now supports WDL 1.0 workflows.
 * **Note:** Generated graphs - including in WDL draft 2 - may look slightly different than they did in version 47.
 
 ### Documentation
@@ -567,7 +659,7 @@ The `womtool graph` command now supports WDL 1.0 workflows.
 
 ### Retry with more memory on Papiv2 [(#5180)](https://github.com/broadinstitute/cromwell/pull/5180)
 
-Cromwell now allows user defined retries. With `memory-retry` config you can specify an array of strings which when encountered in the `stderr` 
+Cromwell now allows user defined retries. With `memory-retry` config you can specify an array of strings which when encountered in the `stderr`
 file by Cromwell, allows the task to be retried with multiplier factor mentioned in the config. More information [here](https://cromwell.readthedocs.io/en/stable/backends/Google/).
 
 ### GCS Parallel Composite Upload Support
@@ -601,7 +693,7 @@ PAPI error code 14. Task was preempted for the 2nd time.
 ```
 Cromwell 44 introduced special handling that detects both preemption indicators and re-runs the job consistent with the `preemptible` setting.
 
-Cromwell 46 enhances this handling in response to user reports of possible continued issues.   
+Cromwell 46 enhances this handling in response to user reports of possible continued issues.
 
 ## 45 Release Notes
 
@@ -619,7 +711,7 @@ More info [here](https://cromwell.readthedocs.io/en/stable/WOMtool/)
 ### BCS backend new Features support
 
 #### New docker registry
-Alibaba Cloud Container Registry is now supported for the `docker` runtime attribute, and the previous `dockerTag` 
+Alibaba Cloud Container Registry is now supported for the `docker` runtime attribute, and the previous `dockerTag`
 runtime attribute continues to be available for Alibaba Cloud OSS Registry.
 #### Call caching
 Cromwell now supports Call caching when using the BCS backend.
@@ -647,7 +739,7 @@ Cromwell's PAPI v2 backend will now handle this type of preemption.
 
 ### Virtual Private Cloud with Subnetworks
 
-Cromwell now allows PAPIV2 jobs to run on a specific subnetwork inside a private network by adding the subnetwork key 
+Cromwell now allows PAPIV2 jobs to run on a specific subnetwork inside a private network by adding the subnetwork key
 `subnetwork-label-key` inside `virtual-private-cloud` in backend configuration. More info [here](https://cromwell.readthedocs.io/en/stable/backends/Google/).
 
 ### Call caching database refactoring
@@ -655,7 +747,7 @@ Cromwell now allows PAPIV2 jobs to run on a specific subnetwork inside a private
 Cromwell's `CALL_CACHING_HASH_ENTRY` primary key has been refactored to use a `BIGINT` datatype in place of the previous
 `INT` datatype. Cromwell will not be usable during the time the Liquibase migration for this refactor is running.
 In the Google Cloud SQL with SSD environment this migration runs at a rate of approximately 100,000 `CALL_CACHING_HASH_ENTRY`
-rows per second. In deployments with millions or billions of `CALL_CACHING_HASH_ENTRY` rows the migration may require  
+rows per second. In deployments with millions or billions of `CALL_CACHING_HASH_ENTRY` rows the migration may require
 a significant amount of downtime so please plan accordingly. The following SQL could be used to estimate the number of
 rows in this table:
 
@@ -665,7 +757,7 @@ select max(CALL_CACHING_HASH_ENTRY_ID) from CALL_CACHING_HASH_ENTRY
 
 ### Stackdriver Instrumentation
 
-Cromwell now supports sending metrics to [Google's Stackdriver API](https://cloud.google.com/monitoring/api/v3/). 
+Cromwell now supports sending metrics to [Google's Stackdriver API](https://cloud.google.com/monitoring/api/v3/).
 Learn more on how to configure [here](https://cromwell.readthedocs.io/en/stable/developers/Instrumentation/).
 
 ### BigQuery in PAPI
@@ -682,7 +774,7 @@ which now has been updated to `services.Instrumentation.config`. More info on it
 
 #### cached-copy
 
-A new experimental feature, the `cached-copy` localization strategy is available for the shared filesystem. 
+A new experimental feature, the `cached-copy` localization strategy is available for the shared filesystem.
 More information can be found in the [documentation on localization](https://cromwell.readthedocs.io/en/stable/backends/HPC).
 
 #### Yaml node limits
@@ -716,7 +808,7 @@ Specifically, the new `validWorkflow` key indicates whether the workflow file is
 ### Configuration Changes
 
  *  Virtual private networks can now be configured. See the section below for details.
- 
+
 #### Batch Request Timeouts
 
 The timeout on Cromwell's requests to PAPIv2 can now be configured. See the sample PAPIv2.conf for more documentation:
@@ -725,7 +817,7 @@ The timeout on Cromwell's requests to PAPIv2 can now be configured. See the samp
 backend {
   providers {
     PAPIv2 {
-      config { 
+      config {
         batch-requests {
           timeouts {
             read = 10 seconds
@@ -802,14 +894,14 @@ This field is now accepted within WDL files as well as within the configuration
 
 #### Logging long running jobs
 
-All backends can now emit slow job warnings after a configurable time running. 
+All backends can now emit slow job warnings after a configurable time running.
 NB This example shows how to configure this setting for the PAPIv2 backend:
 ```conf
 # Emit a warning if jobs last longer than this amount of time. This might indicate that something got stuck.
 backend {
   providers {
     PAPIv2 {
-      config { 
+      config {
         slow-job-warning-time: 24 hours
       }
     }
@@ -824,7 +916,7 @@ backend {
 * The `gpuType` attribute is no longer validated against a whitelist at workflow submission time. Instead, validation now happens at runtime. This allows any valid accelerator to be used.
 * The `nvidiaDriverVersion` attribute is now available in WDL `runtime` sections. The default continues to be `390.46` which applies if and only if GPUs are being used.
 * A default `gpuType` ("nvidia-tesla-k80") will now be applied if `gpuCount` is specified but `gpuType` is not.
-* Similarly, a default `gpuCount` (1) will be applied if `gpuType` is specified but `cpuCount` is not. 
+* Similarly, a default `gpuCount` (1) will be applied if `gpuType` is specified but `cpuCount` is not.
 
 ### Bug fixes
 
@@ -865,7 +957,7 @@ services {
         class = "cromwell.services.healthmonitor.impl.standard.StandardHealthMonitorServiceActor"
     }
 }
-``` 
+```
 With this one:
 ```
 services {
@@ -876,7 +968,7 @@ services {
         }
     }
 }
-``` 
+```
 ###### From `WorkbenchHealthMonitorServiceActor`:
 Replace this stanza:
 ```
@@ -893,7 +985,7 @@ services {
         }
     }
 }
-``` 
+```
 With this one:
 ```
 services {
@@ -909,12 +1001,12 @@ services {
     }
   }
 }
-``` 
+```
 ### Workflow options changes
 
-A new workflow option is added. If the `final_workflow_outputs_dir` is set 
-`use_relative_output_paths` can be used. When set to `true` this will copy 
-all the outputs relative to their execution directory. 
+A new workflow option is added. If the `final_workflow_outputs_dir` is set
+`use_relative_output_paths` can be used. When set to `true` this will copy
+all the outputs relative to their execution directory.
 my_final_workflow_outputs_dir/~~MyWorkflow/af76876d8-6e8768fa/call-MyTask/execution/~~output_of_interest.
 More information can be found in [the workflow options documentation](https://cromwell.readthedocs.io/en/stable/wf_options/Overview/#output-copying).
 
@@ -944,10 +1036,10 @@ shutdown.
 
 ### Bug fixes
 
-#### Format fix for `write_map()` 
+#### Format fix for `write_map()`
 
 Fixed an issue that caused the `write_map()` function in Cromwell's WDL 1.0 implementation to produce output in the wrong format. Specifically, the output's rows and columns were swapped. WDL draft-2 was not affected.
-  
+
 Incorrect `write_map()` output in Cromwell 38 and earlier:
 ```
 key1    key2    key3
@@ -987,7 +1079,7 @@ available as `StandardHealthMonitorServiceActor`.
 ### Docker
 
 - Adds support for retrieving docker digests of asia.gcr.io images
-- Adds configuration settings for docker digest lookups. See the `docker` section of the `reference.conf` for more information 
+- Adds configuration settings for docker digest lookups. See the `docker` section of the `reference.conf` for more information
 - Attempt to automatically adjust the boot disk size on the Google Cloud Backend (version 2) if the size of the image is greater than the default disk size or the required disk size in the runtime attributes.
 Only works for registries that support the version 2 of the manifest schema (https://docs.docker.com/registry/spec/manifest-v2-2/)
 At this date (12/09/18) this includes GCR and Dockerhub.
@@ -1032,28 +1124,28 @@ Support `InputResourceRequirement` hint
 In cases where its not obvious why jobs are queued in Cromwell, you can enable logging for the Job Execution Token Dispenser, using
 the `system.hog-safety.token-log-interval-seconds` configuration value.
 
-The default, `0`, means that no logging will occur. 
+The default, `0`, means that no logging will occur.
 
 #### HTTP Filesystem
 
-- The HTTP filesystem is now enabled for engine use by default. To continue without an HTTP filesystem, you can add the 
+- The HTTP filesystem is now enabled for engine use by default. To continue without an HTTP filesystem, you can add the
 following content into the appropriate stanza of your configuration file:
 ```
 engine {
   filesystems {
-    http { 
-      enabled: false 
+    http {
+      enabled: false
     }
   }
 }
-``` 
+```
 - When the value `exit-code-timeout-seconds` is set, `check-alive` command is now only called once every timeout interval instead of each poll.
 
 ### Beta preview of new Womtool `/describe` endpoint
 
 This new endpoint brings the functionality of Womtool to the world of web services. Submit workflows for validation and receive a JSON description in response.
 
-The endpoint is still undergoing heavy development and should not be used in production. The final version will ship in a future release of Cromwell; watch this space.   
+The endpoint is still undergoing heavy development and should not be used in production. The final version will ship in a future release of Cromwell; watch this space.
 
 ### Bug fixes
 
@@ -1093,7 +1185,7 @@ Details [here](https://cromwell.readthedocs.io/en/develop/backends/HPC/#exit-cod
 
 Coalesce metadata requests to eliminate expensive and redundant queries and metadata construction.
 
-#### Eliminate redundant SFS logging and metadata 
+#### Eliminate redundant SFS logging and metadata
 
 Eliminate superfluous logging and metadata publishing in the shared filesystem backend on poll intervals where there was not a state change.
 
@@ -1106,7 +1198,7 @@ Previously US-EAST-1 was hardcoded in places.
 ### Submit workflow using URL
 
 Cromwell now allows for a user to submit the URL pointing to workflow file to run a workflow.
-More details on how to use it in: 
+More details on how to use it in:
 - `Server` mode can be found [here](https://cromwell.readthedocs.io/en/develop/api/RESTAPI/).
 - `Run` mode can be found [here](https://cromwell.readthedocs.io/en/develop/CommandLine/#run).
 
@@ -1132,7 +1224,7 @@ Cromwell now offers the ability to cache file hashes on a root workflow level ba
 
 ### Extra configuration options
 
-The value `dockerRoot` can now be set in a backend configuration. 
+The value `dockerRoot` can now be set in a backend configuration.
 This will set the execution folder in the container (default: `/cromwell-executions`).
 
 ### Bug Fixes
@@ -1238,7 +1330,7 @@ Cromwell now supports retrying failed tasks up to a specified count by declaring
 * Cromwell now publishes the labels as soon as the workflow is submitted (whether started or on hold). If the labels are invalid, the workflow will not be submitted and request will fail.
 
 ### Scala 2.11 Removed
-From version 32 onwards we will no longer be publishing build artifacts compatible with Scala 2.11. 
+From version 32 onwards we will no longer be publishing build artifacts compatible with Scala 2.11.
 
 * If you don't import the classes into your own scala project then this should have no impact on you.
 * If you **are** importing the classes into your own scala project, make sure you are using Scala 2.12.
@@ -1330,12 +1422,12 @@ Workflow metadata for jobs run on a Google Pipelines API backend will report the
 
 ## 31 Release Notes
 
-* **Cromwell server**  
-The Cromwell server source code is now located under `server/src`. `sbt assembly` will build the runnable Cromwell JAR in 
+* **Cromwell server**
+The Cromwell server source code is now located under `server/src`. `sbt assembly` will build the runnable Cromwell JAR in
 `server/target/scala-2.12/` with a name like `cromwell-<VERSION>.jar`.
 
 * **Robustness**
-    + The rate at which jobs are being started can now be controlled using the `system.job-rate-control` configuration stanza.  
+    + The rate at which jobs are being started can now be controlled using the `system.job-rate-control` configuration stanza.
     + A load controller service has been added to allow Cromwell to self-monitor and adjust its load accordingly.
 The load controller is currently a simple on/off switch controlling the job start rate. It gathers metrics from different parts of the system
 to inform its decision to stop the creation of jobs.
@@ -1343,7 +1435,7 @@ You can find relevant configuration in the `services.LoadController` section of
 as well as in the `load-control` section in `reference.conf`.
 The load level of the monitored sub-systems are instrumented and can be found under the `cromwell.load` statsD path.
     + The statsD metrics have been re-shuffled a bit. If you had a dashboard you might find that you need to update it.
-Changes include: 
+Changes include:
         + Removed artificially inserted "count" and "timing" the path
         + Added a `load` section
         + Metrics were prefixed twice with `cromwell` (`cromwell.cromwell.my_metric`), now they're only prefixed once
@@ -1352,8 +1444,8 @@ Changes include:
 
 * Added a configuration option under `docker.hash-lookup.enabled` to disable docker hash lookup.
  Disabling it will also disable call caching for jobs with floating docker tags.
- 
-* **API**    
+
+* **API**
     + Updated the `/query` response to include the total number of query results returned. See [here](http://cromwell.readthedocs.io/en/develop/api/RESTAPI/#workflowqueryresponse) for more information.
 
 ## 30.1 Release Notes
@@ -1368,14 +1460,14 @@ Changes include:
 
 ### Other changes
 
-* **New Cromwell documentation**  
+* **New Cromwell documentation**
 Our documentation has moved from our [README](https://github.com/broadinstitute/cromwell/blob/29_hotfix/README.md) to a new website: [Cromwell Documentation](http://cromwell.readthedocs.io/en/develop/). There are new [Tutorials](http://cromwell.readthedocs.io/en/develop/tutorials/FiveMinuteIntro/) and much of the documentation has been re-written. The source files are in the [/docs](https://github.com/broadinstitute/cromwell/tree/develop/docs) directory.
 
-* **API**  
+* **API**
     + Cromwell now supports input files in the yaml format (JSON format is still supported).
     + Added a [GET version for the `labels` endpoint](http://cromwell.readthedocs.io/en/develop/api/RESTAPI/#retrieves-the-current-labels-for-a-workflow) which will return current labels for a workflow.
 
-* **Database**  
+* **Database**
 You have the option of storing the metadata in a separate SQL database than the database containing the internal engine
 data. When switching connection information for an existing database containing historical data, the tables
 should be manually replicated from one database instance to another using the tools appropriate for your specific
@@ -1384,48 +1476,48 @@ and likely to change in the future. See the [Database Documentation](https://cro
 [cromwell.examples.conf](https://www.github.com/broadinstitute/cromwell/tree/develop/cromwell.example.backends/cromwell.examples.conf) for more
 information.
 
-* **StatsD**  
+* **StatsD**
 Added initial support for StatsD instrumentation. See the [Instrumentation Documentation](https://cromwell.readthedocs.io/en/develop/Instrumentation) for details on how to use it.
 
-* **User Service Account auth mode for Google**  
+* **User Service Account auth mode for Google**
 Added a new authentication mode for [Google Cloud Platform](https://cromwell.readthedocs.io/en/develop/backends/Google) which will allow a user to supply the JSON key file in their workflow options to allow for per-workflow authentication via service account. This is analogous to the previously existing refresh token authentication scheme. As with the refresh token scheme it is encouraged that the **user_service_account_json** workflow option field is added to the **encrypted-fields** list in the configuration.
 
-* **Bugfixes**  
+* **Bugfixes**
 Abort of Dockerized tasks on the Local backend should now work as expected. Cromwell uses `docker kill` to kill the Docker container.
 
 ## 29 Release Notes
 
 ### Breaking Changes
 
-* **Command line**  
+* **Command line**
 In preparation for supporting CWL scripts (yes, you read that right!), we have extensively revised the Command Line in Cromwell 29. For more details about the usage changes please see the [README](https://github.com/broadinstitute/cromwell#command-line-usage). And stay tuned to the [WDL/Cromwell blog](https://software.broadinstitute.org/wdl/blog) over the next couple of months for more news about CWL.
 
-* **Request timeouts**   
+* **Request timeouts**
 Cromwell now returns more specific `503 Service Unavailable` error codes on request timeouts, rather than the more generic `500 Internal Server Error`. The response for a request timeout will now be plain text, rather than a JSON format.
 
-* **Metadata endpoint**  
+* **Metadata endpoint**
 The response from the metadata endpoint can be quite large depending on your workflow. You can now opt-in to have Cromwell gzip your metadata file, in order to reduce file size, by sending the `Accept-Encoding: gzip` header. The default behavior now does not gzip encode responses.
 
-* **Engine endpoints**  
+* **Engine endpoints**
 Previously the engine endpoints were available under `/api/engine` but now the endpoints are under `/engine` so they don't require authentication. Workflow endpoints are still available under `/api/workflows`. We also deprecated the setting `api.routeUnwrapped` as a part of this internal consistency effort.
 
-* **Call caching diff**  
+* **Call caching diff**
 We updated the response format of the [callcaching/diff](https://github.com/broadinstitute/cromwell#get-apiworkflowsversioncallcachingdiff) endpoint.
 
 ### Other changes
 
-* **Cromwell server**  
+* **Cromwell server**
 When running in server mode, Cromwell now attempts to gracefully shutdown after receiving a `SIGINT` (`Ctrl-C`) or `SIGTERM` (`kill`) signal. This means that Cromwell waits for all pending database writes before exiting, as long as you include `application.conf` at the top of your config file. You can find detailed information about how to configure this feature in the [Cromwell Wiki](https://github.com/broadinstitute/cromwell/wiki/DevZone#graceful-server-shutdown).
 
-* **Concurrent jobs**  
+* **Concurrent jobs**
 You can now limit the number of concurrent jobs for any backend. Previously this was only possible in some backend implementations. Please see the [README](https://github.com/broadinstitute/cromwell#backend-job-limits) for details.
 
 ### WDL
 
-* **Optional WDL variables**  
+* **Optional WDL variables**
 Empty optional WDL values are now rendered as the `null` JSON value instead of the JSON string `"null"` in the metadata and output endpoints. You do not need to migrate previous workflows. Workflows run on Cromwell 28 and prior will still render empty values as `"null"`.
 
-* **Empty WDL variables**  
+* **Empty WDL variables**
 Cromwell now accepts `null` JSON values in the input file and coerces them as an empty WDL value. WDL variables must be declared optional in order to be supplied with a `null` JSON value.
 
 input.json
@@ -1474,8 +1566,8 @@ task writer {
 #### `ContinueWhilePossible`
 
 A workflow utilizing the WorkflowFailureMode Workflow Option `ContinueWhilePossible` will now successfully reach a terminal state once all runnable jobs have completed.
-#### `FailOnStderr` 
-When `FailOnStderr` is set to false, Cromwell no longer checks for the existence of a stderr file for that task. 
+#### `FailOnStderr`
+When `FailOnStderr` is set to false, Cromwell no longer checks for the existence of a stderr file for that task.
 
 ### WDL Functions
 
@@ -1491,7 +1583,7 @@ task foo {
     command { ... }
     runtime {
       docker: "..."
-      memory: ceil(size(in_file)) * 4 
+      memory: ceil(size(in_file)) * 4
     }
 }
 ```
@@ -1506,7 +1598,7 @@ If the hashes fail to be calculated, the reason is indicated in a `hashFailures`
 
 See the [README](https://github.com/broadinstitute/cromwell#get-apiworkflowsversionidmetadata) for an example metadata response.
 
-* New endpoint returning the hash differential for 2 calls. 
+* New endpoint returning the hash differential for 2 calls.
 
 `GET /api/workflows/:version/callcaching/diff`
 
@@ -1535,7 +1627,7 @@ A second value is allowed, `reference`, that will instead point to the original
 filesystems {
   gcs {
     auth = "application-default"
-    
+
     caching {
       duplication-strategy = "reference"
     }
@@ -1563,7 +1655,7 @@ than the previous default.
  The migration will only be executed on MySQL. Other databases will lose their previous cached jobs.
  In order to run properly on MySQL, **the following flag needs to be adjusted**: https://dev.mysql.com/doc/refman/5.5/en/server-system-variables.html#sysvar_group_concat_max_len
  The following query will give you a minimum to set the group_concat_max_len value to:
- 
+
  ```sql
 SELECT MAX(aggregated) as group_concat_max_len FROM
       (
@@ -1574,15 +1666,15 @@ SELECT MAX(aggregated) as group_concat_max_len FROM
  ```
 
  Here is the SQL command to run to set the group_concat_max_len flag to the proper value:
- 
+
  ```sql
 SET GLOBAL group_concat_max_len = value
  ```
- 
+
  Where `value` is replaced with the value you want to set it to.
- 
+
  Note that the migration will fail if the flag is not set properly.
- 
+
 ### Breaking Changes
 
 * The update to Slick 3.2 requires a database stanza to
@@ -1630,7 +1722,7 @@ run the call:
 
 ### Docker
 
-* The Docker section of the configuration has been slightly reworked 
+* The Docker section of the configuration has been slightly reworked
 An option to specify how a Docker hash should be looked up has been added. Two methods are available.
     "local" will try to look for the image on the machine where cromwell is running. If it can't be found, Cromwell will try to `pull` the image and use the hash from the retrieved image.
     "remote" will try to look up the image hash directly on the remote repository where the image is located (Docker Hub and GCR are supported)
@@ -1694,14 +1786,14 @@ failures: [{
 
 * Added a configuration option under `system.io` to throttle the number of I/O queries that Cromwell makes, as well as configure retry parameters.
  This is mostly useful for the JES backend and should be updated to match the GCS quota available for the project.
- 
+
 ```
 system.io {
   # Global Throttling - This is mostly useful for GCS and can be adjusted to match
   # the quota availble on the GCS API
   number-of-requests = 100000
   per = 100 seconds
-  
+
   # Number of times an I/O operation should be attempted before giving up and failing it.
   number-of-attempts = 5
 }
@@ -1725,7 +1817,7 @@ system.io {
 
 ### Config Changes
 
-* Added a field `insert-batch-size` to the `database` stanza which defines how many values from a batch insert will be processed at a time. This value defaults to 2000. 
+* Added a field `insert-batch-size` to the `database` stanza which defines how many values from a batch insert will be processed at a time. This value defaults to 2000.
 * Moved the config value `services.MetadataService.metadata-summary-refresh-interval` to `services.MetadataService.config.metadata-summary-refresh-interval`
 * Added ability to override the default zone(s) used by JES via the config structure by setting `genomics.default-zones` in the JES configuration
 * The cromwell server TCP binding timeout is now configurable via the config key `webservice.binding-timeout`, defaulted
@@ -1748,15 +1840,15 @@ system.io {
 * In some cases the SFS backend, used for Local, SGE, etc., coerced `WdlFile` to `WdlString` by using `.toUri`. This
 resulted in strings prepended with `file:///path/to/file`. Now absolute file paths will not contain the uri scheme.
 * Launch jobs on servers that support the GA4GH Task Execution Schema using the TES backend.
-* **Call caching: Cromwell will no longer try to use the cache for WDL tasks that contain a floating docker tag.** 
+* **Call caching: Cromwell will no longer try to use the cache for WDL tasks that contain a floating docker tag.**
   Call caching will still behave the same for tasks having a docker image with a specific hash.
-  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details. 
+  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details.
 * Added docker hash lookup. Cromwell will try to lookup the hash for a docker image with a floating tag, and use that hash when executing the job.
   This will be reflected in the metadata where the docker runtime attribute will contains the hash that was used.
   If Cromwell is unable to lookup the docker hash, the job will be run with the original user defined floating tag.
   Cromwell is currently able to lookup public and private docker hashes for images on Docker Hub and Google Container Engine for job running on the JES backend.
   For other backends, cromwell is able to lookup public docker hashes for Docker Hub and Google Container Engine.
-  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details. 
+  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details.
 
 ### Database schema changes
 * Added CUSTOM_LABELS as a field of WORKFLOW_STORE_ENTRY, to store workflow store entries.
@@ -1775,7 +1867,7 @@ resulted in strings prepended with `file:///path/to/file`. Now absolute file pat
 * Timing diagrams and metadata now receive more fine grained workflow states between submission and Running.
 * Support for the Pair WDL type (e.g. `Pair[Int, File] floo = (3, "gs://blar/blaz/qlux.txt")`)
 * Added support for new WDL functions:
-  * `zip: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - align items in the two arrays by index and return them as WDL pairs 
+  * `zip: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - align items in the two arrays by index and return them as WDL pairs
   * `cross: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - create every possible pair from the two input arrays and return them all as WDL pairs
   * `transpose: (Array[Array[X]]) => Array[Array[X]]` compute the matrix transpose for a 2D array. Assumes each inner array has the same length.
 * By default, `system.abort-jobs-on-terminate` is false when running `java -jar cromwell.jar server`, and true when running `java -jar cromwell.jar run <wdl> <inputs>`.
@@ -1791,9 +1883,9 @@ resulted in strings prepended with `file:///path/to/file`. Now absolute file pat
 * Fix bugs related to the behavior of Cromwell in Single Workflow Runner Mode. Cromwell will now exit once a workflow completes in Single Workflow Runner Mode. Additionally, when restarting Cromwell in Single Workflow Runner Mode, Cromwell will no longer restart incomplete workflows from a previous session.
 
 ### Annex A - Workflow outputs
-    
+
 The WDL specification has changed regarding [workflow outputs](https://github.com/openwdl/wdl/blob/master/versions/draft-2/SPEC.md#outputs) to accommodate sub workflows.
-This change is backward compatible in terms of runnable WDLs (WDL files using the deprecated workflow outputs syntax will still run the same). 
+This change is backward compatible in terms of runnable WDLs (WDL files using the deprecated workflow outputs syntax will still run the same).
 The only visible change lies in the metadata (as well as the console output in single workflow mode, when workflow outputs are printed out at the end of a successful workflow).
 
 TL;DR Unless you are parsing or manipulating the "key" by which workflow outputs are referenced in the metadata (and/or the console output for single workflow mode), you can skip the following explanation.
@@ -1846,7 +1938,7 @@ task t {
 
 The new syntax allows for type checking of the outputs as well as expressions. It also allows for explicitly naming to the outputs.
 The old syntax doesn't give the ability to name workflow outputs. For consistency reasons, Cromwell will generate a "new syntax" workflow output for each task output, and name them.
-Their name will be generated using their FQN, which would give 
+Their name will be generated using their FQN, which would give
 
 ```
 output {
@@ -1854,8 +1946,8 @@ output {
    String w.t.out2 = t.out2
 }
 ```
-        
-However as the FQN separator is `.`, the name itself cannot contain any `.`. 
+
+However as the FQN separator is `.`, the name itself cannot contain any `.`.
 For that reason, `.` are replaced with `_` :
 
 *Old syntax expanded to new syntax*
@@ -1866,16 +1958,16 @@ output {
 }
 ```
 
-The consequence is that the workflow outputs section of the metadata for `old_syntax` would previously look like 
- 
+The consequence is that the workflow outputs section of the metadata for `old_syntax` would previously look like
+
  ```
     outputs {
         "w.t.out1": "hello",
         "w.t.out2": "hello"
     }
  ```
- 
-but it will now look like 
+
+but it will now look like
 
 ```
     outputs {
diff --git a/CromIAM/src/main/resources/application.conf b/CromIAM/src/main/resources/application.conf
index c809d0daafb..ff1006ab91b 100644
--- a/CromIAM/src/main/resources/application.conf
+++ b/CromIAM/src/main/resources/application.conf
@@ -24,7 +24,7 @@ swagger_oauth {
 
 akka {
   log-dead-letters = "off"
-  loggers = ["akka.event.slf4j.Slf4jLogger"]
+  loggers = ["cromwell.core.logging.EnhancedSlf4jLogger"]
 
   http {
     server {
diff --git a/CromIAM/src/main/resources/logback.xml b/CromIAM/src/main/resources/logback.xml
index 030868d3259..e9e2b753466 100644
--- a/CromIAM/src/main/resources/logback.xml
+++ b/CromIAM/src/main/resources/logback.xml
@@ -1,5 +1,15 @@
 <configuration>
 
+    <!-- Enhanced thread and date reporting. -->
+    <conversionRule
+            conversionWord="et"
+            converterClass="cromwell.core.logging.EnhancedThreadConverter"
+    />
+    <conversionRule
+            conversionWord="ed"
+            converterClass="cromwell.core.logging.EnhancedDateConverter"
+    />
+
     <!-- default properties for FILEROLLER need to be set upfront -->
 
     <if condition='property("FILEROLLER_DIR").equals("")'>
@@ -18,7 +28,7 @@
         <then>
             <appender name="STANDARD_APPENDER" class="ch.qos.logback.core.ConsoleAppender">
                 <encoder>
-                    <pattern>%date %X{sourceThread} %-5level - %msg%n</pattern>
+                    <pattern>%ed{yyyy-MM-dd HH:mm:ss,SSS} %et %-5level - %msg%n</pattern>
                 </encoder>
             </appender>
         </then>
@@ -68,7 +78,7 @@
 
                 </rollingPolicy>
                 <encoder>
-                    <pattern>%d{yyyy-MM-dd HH:mm:ss,SSS} [%thread] %-5level %logger{35} - %msg%n</pattern>
+                    <pattern>%ed{yyyy-MM-dd HH:mm:ss,SSS} [%et] %-5level %logger{35} - %msg%n</pattern>
                 </encoder>
             </appender>
         </then>
diff --git a/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala b/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
index 63f48073146..65b164f00f6 100644
--- a/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
+++ b/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
@@ -20,6 +20,7 @@ trait CromIamInstrumentation extends CromwellInstrumentation {
 
   val samPrefix: NonEmptyList[String] = NonEmptyList.one("sam")
   val getWhitelistPrefix = NonEmptyList.one("get-whitelist")
+  val getUserEnabledPrefix = NonEmptyList.one("get-user-enabled")
   val userCollectionPrefix = NonEmptyList.one("user-collection")
   val authCollectionPrefix = NonEmptyList.one("auth-collection")
   val registerCollectionPrefix = NonEmptyList.one("register-collection")
diff --git a/CromIAM/src/main/scala/cromiam/sam/SamClient.scala b/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
index f289251a2fb..d6a315f8241 100644
--- a/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
+++ b/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
@@ -18,6 +18,7 @@ import cromiam.sam.SamResourceJsonSupport._
 import cromiam.server.status.StatusCheckedSubsystem
 import cromwell.api.model._
 import mouse.boolean._
+import spray.json.RootJsonFormat
 
 import scala.concurrent.ExecutionContextExecutor
 
@@ -73,6 +74,33 @@ class SamClient(scheme: String,
     } yield whitelisted
   }
 
+  def isUserEnabledSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+    val request = HttpRequest(
+      method = HttpMethods.GET,
+      uri = samUserStatusUri,
+      headers = List[HttpHeader](user.authorization)
+    )
+
+    for {
+      response <- instrumentRequest(
+        () => Http().singleRequest(request).asFailureResponseOrT,
+        cromIamRequest,
+        instrumentationPrefixForSam(getUserEnabledPrefix)
+      )
+      userEnabled <- response.status match {
+        case StatusCodes.OK =>
+          val unmarshal: IO[UserStatusInfo] = IO.fromFuture(IO(Unmarshal(response.entity).to[UserStatusInfo]))
+          FailureResponseOrT.right[HttpResponse](unmarshal).map { userInfo =>
+            if (!userInfo.enabled) log.info("Access denied for user {}", user.userId)
+            userInfo.enabled
+          }
+        case _ =>
+          log.error("Could not verify access with Sam for user {}, error was {} {}", user.userId, response.status, response.toString().take(100))
+          FailureResponseOrT.pure[IO, HttpResponse](false)
+      }
+    } yield userEnabled
+  }
+
   def collectionsForUser(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[List[Collection]] = {
     val request = HttpRequest(method = HttpMethods.GET, uri = samBaseCollectionUri, headers = List[HttpHeader](user.authorization))
 
@@ -170,6 +198,7 @@ class SamClient(scheme: String,
   private lazy val samBaseResourceUri = s"$samBaseUri/api/resource"
   private lazy val samBaseCollectionUri = s"$samBaseResourceUri/workflow-collection"
   private lazy val samSubmitWhitelistUri = s"$samBaseResourceUri/caas/submit/action/get_whitelist"
+  private lazy val samUserStatusUri = s"$samBaseUri/register/user/v2/self/info"
 
 }
 
@@ -188,4 +217,8 @@ object SamClient {
 
   def SamRegisterCollectionExceptionResp(statusCode: StatusCode) = HttpResponse(status = statusCode, entity = SamRegisterCollectionException(statusCode).getMessage)
 
+  case class UserStatusInfo(adminEnabled: Boolean, enabled: Boolean, userEmail: String, userSubjectId: String)
+
+  implicit val UserStatusInfoFormat: RootJsonFormat[UserStatusInfo] = jsonFormat4(UserStatusInfo)
+
 }
diff --git a/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala b/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
index 63694599476..7a16e5ea797 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
@@ -81,7 +81,7 @@ trait CromIamApiService extends RequestSupport
 
   def abortRoute: Route = path("api" / "workflows" / Segment / Segment / Abort) { (_, workflowId) =>
     post {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserWorkflowAction(user, workflowId, Abort)
         complete {
           authorizeAbortThenForwardToCromwell(user, workflowId, req).asHttpResponse
@@ -93,7 +93,7 @@ trait CromIamApiService extends RequestSupport
   //noinspection MutatorLikeMethodIsParameterless
   def releaseHoldRoute: Route =  path("api" / "workflows" / Segment / Segment / ReleaseHold) { (_, workflowId) =>
     post {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserWorkflowAction(user, workflowId, ReleaseHold)
         complete {
           authorizeUpdateThenForwardToCromwell(user, workflowId, req).asHttpResponse
@@ -112,7 +112,7 @@ trait CromIamApiService extends RequestSupport
   def labelPatchRoute: Route = {
     path("api" / "workflows" / Segment / Segment / Labels) { (_, workflowId) =>
       patch {
-        extractUserAndRequest { (user, req) =>
+        extractUserAndStrictRequest { (user, req) =>
           entity(as[String]) { labels =>
             logUserWorkflowAction(user, workflowId, Labels)
             validateLabels(Option(labels)) { _ => // Not using the labels, just using this to verify they didn't specify labels we don't want them to
@@ -130,7 +130,7 @@ trait CromIamApiService extends RequestSupport
 
   def callCacheDiffRoute: Route = path("api" / "workflows" / Segment / "callcaching" / "diff") { _ =>
     get {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserAction(user, "call caching diff")
         parameterSeq { parameters =>
           val paramMap = parameters.toMap
@@ -150,11 +150,9 @@ trait CromIamApiService extends RequestSupport
     */
   private def workflowGetRoute(urlSuffix: String): Route = path("api" / "workflows" / Segment / urlSuffix) { _ =>
     get {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserAction(user, urlSuffix)
-        complete {
-          cromwellClient.forwardToCromwell(req).asHttpResponse
-        }
+        forwardIfUserEnabled(user, req, cromwellClient, samClient)
       }
     }
   }
@@ -166,7 +164,7 @@ trait CromIamApiService extends RequestSupport
 
   private def workflowRoute(urlSuffix: String, method: Directive0): Route = path("api" / "workflows" / Segment / Segment / urlSuffix) { (_, workflowId) =>
     method {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserWorkflowAction(user, workflowId, urlSuffix)
         complete {
           authorizeReadThenForwardToCromwell(user, List(workflowId), req).asHttpResponse
diff --git a/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala b/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
index cddabe74a57..e9397605c6a 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
@@ -55,7 +55,7 @@ trait QuerySupport extends RequestSupport {
     * directive
     */
   private def preprocessQuery: Directive[(User, List[Collection], HttpRequest)] = {
-    extractUserAndRequest tflatMap { case (user, cromIamRequest) =>
+    extractUserAndStrictRequest tflatMap { case (user, cromIamRequest) =>
       log.info("Received query " + cromIamRequest.method.value + " request for user " + user.userId)
 
       onComplete(samClient.collectionsForUser(user, cromIamRequest).value.unsafeToFuture()) flatMap {
diff --git a/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
index 12b231485f7..c9b6a196368 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
@@ -6,6 +6,13 @@ import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server._
 import cromiam.auth.User
 import org.broadinstitute.dsde.workbench.model.WorkbenchUserId
+import akka.http.scaladsl.model.HttpResponse
+import akka.http.scaladsl.server.Directives.{authorize, complete, onComplete}
+import akka.http.scaladsl.server.Route
+import cromiam.cromwell.CromwellClient
+import cromiam.sam.SamClient
+
+import scala.util.{Failure, Success}
 
 trait RequestSupport {
   def extractStrictRequest: Directive1[HttpRequest] = {
@@ -26,10 +33,27 @@ trait RequestSupport {
     }
   }
 
-  def extractUserAndRequest: Directive[(User, HttpRequest)] = {
+  def extractUserAndStrictRequest: Directive[(User, HttpRequest)] = {
     for {
       user <- extractUser
       request <- extractStrictRequest
     } yield (user, request)
   }
+
+  def forwardIfUserEnabled(user: User, req: HttpRequest, cromwellClient: CromwellClient, samClient: SamClient): Route = {
+    import cromwell.api.model.EnhancedFailureResponseOrHttpResponseT
+
+    onComplete(samClient.isUserEnabledSam(user, req).value.unsafeToFuture()) {
+      case Success(Left(httpResponse: HttpResponse)) => complete(httpResponse)
+      case Success(Right(isEnabled: Boolean)) =>
+        authorize(isEnabled) {
+          complete {
+            cromwellClient.forwardToCromwell(req).asHttpResponse
+          }
+        }
+      case Failure(e) =>
+        val message = s"Unable to look up enablement status for user ${user.userId}: ${e.getMessage}. Please try again later."
+        throw new RuntimeException(message, e)
+    }
+  }
 }
diff --git a/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
index c1f5477475b..52a05d1cdc7 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
@@ -31,7 +31,7 @@ trait SubmissionSupport extends RequestSupport {
   // FIXME - getting pathPrefix to shrink this keeps hosing up, there's gotta be some way to do this
   def submitRoute: Route = (path("api" / "workflows" / Segment) | path("api" / "workflows" / Segment / "batch")) { _ =>
     post {
-      extractUserAndRequest { (user, request) =>
+      extractUserAndStrictRequest { (user, request) =>
         log.info("Received submission request from user " + user.userId)
         onComplete(samClient.isSubmitWhitelisted(user, request).value.unsafeToFuture()) {
           case Success(Left(httpResponse)) => complete(httpResponse)
diff --git a/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala
index 671d4a76543..a6098b1fae0 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala
@@ -2,20 +2,18 @@ package cromiam.webservice
 
 import akka.http.scaladsl.server.Directives._
 import cromiam.cromwell.CromwellClient
-import cromwell.api.model._
+import cromiam.sam.SamClient
 
 trait WomtoolRouteSupport extends RequestSupport {
   // When this trait is mixed into `CromIamApiService` the value of `cromwellClient` is the reader (non-abort) address
   val cromwellClient: CromwellClient
+  val samClient: SamClient
 
   val womtoolRoutes =
     path("api" / "womtool" / Segment / "describe") { _ =>
       post {
-        extractStrictRequest { req =>
-          complete {
-            // This endpoint requires authn which it gets for free from the proxy, does not care about authz
-            cromwellClient.forwardToCromwell(req).asHttpResponse
-          }
+        extractUserAndStrictRequest { (user, req) =>
+          forwardIfUserEnabled(user, req, cromwellClient, samClient)
         }
       }
     }
diff --git a/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
index 5ad6a976204..89945c5bfcb 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
@@ -4,7 +4,8 @@ import akka.event.NoLogging
 import akka.http.scaladsl.model.StatusCodes._
 import akka.http.scaladsl.model.headers.{Authorization, OAuth2BearerToken, RawHeader}
 import akka.http.scaladsl.model.{ContentTypes, HttpEntity, HttpHeader}
-import akka.http.scaladsl.server.MissingHeaderRejection
+import akka.http.scaladsl.server.Route.seal
+import akka.http.scaladsl.server.{AuthorizationFailedRejection, MissingHeaderRejection}
 import akka.http.scaladsl.testkit.ScalatestRouteTest
 import com.typesafe.config.Config
 import common.assertion.CromwellTimeoutSpec
@@ -303,12 +304,45 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-  it should "reject request if it doesn't contain OIDC_CLAIM_user_id in header" in {
+  it should "reject request if it doesn't contain OIDC_CLAIM_user_id or token" in {
     Get(s"/api/workflows/$version/backends") ~> allRoutes ~> check {
       rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
     }
   }
 
+  it should "return 403 when we request with a disabled user" in {
+    Get(
+      s"/api/workflows/$version/backends"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")), RawHeader("OIDC_CLAIM_user_id", "disabled@example.com"))
+    ) ~> allRoutes ~> check {
+      rejection shouldEqual AuthorizationFailedRejection
+    }
+  }
+
+  it should "reject request if it contains a token and no OIDC_CLAIM_user_id in header" in {
+    Get(
+      s"/api/workflows/$version/backends"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")))
+    ) ~> allRoutes ~> check {
+      rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
+    }
+  }
+
+  it should "return 404 when no auth token provided" in {
+    Get(
+      s"/api/workflows/$version/backends"
+    ).withHeaders(
+      List(RawHeader("OIDC_CLAIM_user_id", "enabled@example.com"))
+      // "[An] explicit call on the Route.seal method is needed in test code, but in your application code it is not necessary."
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/testkit.html#testing-sealed-routes
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/routes.html#sealing-a-route
+    ) ~> seal(allRoutes) ~> check {
+      responseAs[String] shouldEqual "The requested resource could not be found."
+      status shouldBe NotFound
+    }
+  }
 
   behavior of "ReleaseHold endpoint"
   it should "return 200 for authorized user who has collection associated with root workflow" in {
diff --git a/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala b/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
index 3fb9689e5cc..59e75347159 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
@@ -141,6 +141,15 @@ class MockSamClient(checkSubmitWhitelist: Boolean = true)
     FailureResponseOrT.pure(!user.userId.value.equalsIgnoreCase(NotWhitelistedUser))
   }
 
+  override def isUserEnabledSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+    if (user.userId.value == "enabled@example.com" || user.userId.value == MockSamClient.AuthorizedUserCollectionStr)
+      FailureResponseOrT.pure(true)
+    else if (user.userId.value == "disabled@example.com")
+      FailureResponseOrT.pure(false)
+    else
+      throw new Exception("Misconfigured test")
+  }
+
   override def requestAuth(authorizationRequest: CollectionAuthorizationRequest,
                            cromIamRequest: HttpRequest): FailureResponseOrT[Unit] = {
     authorizationRequest.user.userId.value match {
diff --git a/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
index c0277fd92c0..838a523f4eb 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
@@ -12,7 +12,7 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 import org.yaml.snakeyaml.constructor.Constructor
 import org.yaml.snakeyaml.error.YAMLException
 import org.yaml.snakeyaml.nodes.MappingNode
-import org.yaml.snakeyaml.{Yaml => SnakeYaml}
+import org.yaml.snakeyaml.{LoaderOptions, Yaml => SnakeYaml}
 
 import scala.jdk.CollectionConverters._
 
@@ -21,6 +21,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
   with TableDrivenPropertyChecks {
   def actorRefFactory = system
   override def oauthConfig: SwaggerOauthConfig = SwaggerOauthConfig("clientId", "realm", "appName")
+  val yamlLoaderOptions = new LoaderOptions
 
   behavior of "SwaggerService"
 
@@ -32,7 +33,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
         contentType should be(ContentTypes.`application/octet-stream`)
 
         val body = responseAs[String]
-        val yaml = new SnakeYaml(new UniqueKeyConstructor()).loadAs(body, classOf[java.util.Map[String, AnyRef]])
+        val yaml = new SnakeYaml(new UniqueKeyConstructor(new LoaderOptions)).loadAs(body, classOf[java.util.Map[String, AnyRef]])
 
         yaml.get("swagger") should be("2.0")
       }
@@ -109,7 +110,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
   * Adapted from:
   * https://bitbucket.org/asomov/snakeyaml/src/e9cd9f5e8d76c61eb983e29b3dc039c1fac9c393/src/test/java/org/yaml/snakeyaml/issues/issue139/UniqueKeyTest.java?fileviewer=file-view-default#UniqueKeyTest.java-43:62
   */
-class UniqueKeyConstructor extends Constructor {
+class UniqueKeyConstructor(val loaderOptions: LoaderOptions) extends Constructor(loaderOptions) {
 
   import java.util.{Map => JMap}
 
diff --git a/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
index 7ba1c495f23..785c887c374 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
@@ -2,6 +2,9 @@ package cromiam.webservice
 
 import akka.http.scaladsl.model.ContentTypes
 import akka.http.scaladsl.model.StatusCodes._
+import akka.http.scaladsl.model.headers.{Authorization, OAuth2BearerToken, RawHeader}
+import akka.http.scaladsl.server.Route.seal
+import akka.http.scaladsl.server.{AuthorizationFailedRejection, MissingHeaderRejection}
 import akka.http.scaladsl.testkit.ScalatestRouteTest
 import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
@@ -11,15 +14,64 @@ import org.scalatest.matchers.should.Matchers
 class WomtoolRouteSupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with WomtoolRouteSupport with ScalatestRouteTest {
 
   override lazy val cromwellClient = new MockCromwellClient()
+  override lazy val samClient = new MockSamClient()
 
   behavior of "Womtool endpoint routes"
 
   it should "return 200 when we request to the right path" in {
-    Post(s"/api/womtool/v1/describe") ~> womtoolRoutes ~> check {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")), RawHeader("OIDC_CLAIM_user_id", "enabled@example.com"))
+    ) ~> womtoolRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Hey there, workflow describer"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
+  it should "return 403 when we request with a disabled user" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")), RawHeader("OIDC_CLAIM_user_id", "disabled@example.com"))
+    ) ~> womtoolRoutes ~> check {
+      rejection shouldEqual AuthorizationFailedRejection
+    }
+  }
+
+  it should "bail out with no user ID" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")))
+    ) ~> womtoolRoutes ~> check {
+      rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
+    }
+  }
+
+  it should "return 404 when no auth token provided" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(RawHeader("OIDC_CLAIM_user_id", "enabled@example.com"))
+      // "[An] explicit call on the Route.seal method is needed in test code, but in your application code it is not necessary."
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/testkit.html#testing-sealed-routes
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/routes.html#sealing-a-route
+    ) ~> seal(womtoolRoutes) ~> check {
+      responseAs[String] shouldEqual "The requested resource could not be found."
+      status shouldBe NotFound
+    }
+  }
+
+  it should "bail out with no headers" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List.empty
+    ) ~> womtoolRoutes ~> check {
+      rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
+    }
+  }
+
 }
diff --git a/CromwellRefdiskManifestCreator/pom.xml b/CromwellRefdiskManifestCreator/pom.xml
index 987aad421be..829f64b5fd3 100644
--- a/CromwellRefdiskManifestCreator/pom.xml
+++ b/CromwellRefdiskManifestCreator/pom.xml
@@ -48,7 +48,7 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>2.13.2.2</version>
+            <version>2.13.4.1</version>
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 5c415cc3c50..02c2a2577a2 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -244,6 +244,8 @@ trait StandardAsyncExecutionActor
     }
   }
 
+  lazy val memoryRetryRequested: Boolean = memoryRetryFactor.nonEmpty
+
   /**
     * Returns the shell scripting for finding all files listed within a directory.
     *
@@ -1265,8 +1267,8 @@ trait StandardAsyncExecutionActor
     */
   def handleExecutionResult(status: StandardAsyncRunState,
                             oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
-    
-    // get the memory retry code.
+
+    // Returns true if the task has written an RC file that indicates OOM, false otherwise
     def memoryRetryRC: Future[Boolean] = {
       // convert int to boolean
       def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
@@ -1329,11 +1331,11 @@ trait StandardAsyncExecutionActor
       // Only check stderr size if we need to, otherwise this results in a lot of unnecessary I/O that
       // may fail due to race conditions on quickly-executing jobs.
       stderrSize <- if (failOnStdErr) asyncIo.sizeAsync(stderr) else Future.successful(0L)
-      retryWithMoreMemory <- memoryRetryRC
-    } yield (stderrSize, returnCodeAsString, retryWithMoreMemory)
+      outOfMemoryDetected <- memoryRetryRC
+    } yield (stderrSize, returnCodeAsString, outOfMemoryDetected)
 
     stderrSizeAndReturnCodeAndMemoryRetry flatMap {
-      case (stderrSize, returnCodeAsString, retryWithMoreMemory) =>
+      case (stderrSize, returnCodeAsString, outOfMemoryDetected) =>
         val tryReturnCodeAsInt = Try(returnCodeAsString.trim.toInt)
 
         if (isDone(status)) {
@@ -1341,13 +1343,15 @@ trait StandardAsyncExecutionActor
             case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
-            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
-              Future.successful(AbortedExecutionHandle)
             case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
               handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
-            case Success(returnCodeAsInt) if retryWithMoreMemory  =>
+            // It's important that we check retryWithMoreMemory case before isAbort. RC could be 137 in either case;
+            // if it was caused by OOM killer, want to handle as OOM and not job abort.
+            case Success(returnCodeAsInt) if outOfMemoryDetected && memoryRetryRequested  =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
-              retryElseFail(executionHandle, retryWithMoreMemory)
+              retryElseFail(executionHandle, outOfMemoryDetected)
+            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
+              Future.successful(AbortedExecutionHandle)
             case Success(returnCodeAsInt) =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
@@ -1356,9 +1360,9 @@ trait StandardAsyncExecutionActor
           }
         } else {
           tryReturnCodeAsInt match {
-            case Success(returnCodeAsInt) if retryWithMoreMemory && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
+            case Success(returnCodeAsInt) if outOfMemoryDetected && memoryRetryRequested && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
-              retryElseFail(executionHandle, retryWithMoreMemory)
+              retryElseFail(executionHandle, outOfMemoryDetected)
             case _ =>
               val failureStatus = handleExecutionFailure(status, tryReturnCodeAsInt.toOption)
               retryElseFail(failureStatus)
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala b/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
index dd4254c8439..a64c6a5439c 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
@@ -78,7 +78,7 @@ trait StandardCachingActorHelper extends JobCachingActorHelper {
 
     val fileMetadata = jobPaths.metadataPaths
 
-    runtimeAttributesMetadata ++ fileMetadata ++ nonStandardMetadata
+    nonStandardMetadata ++ runtimeAttributesMetadata ++ fileMetadata
   }
 
   /**
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
index e33625741b3..c3d1452660e 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
@@ -48,7 +48,7 @@ class RootWorkflowFileHashCacheActor private[callcaching](override val ioActor:
           // hash to become available.
           cache.put(key, FileHashValueRequested(requesters = requester :: requesters))
         case FileHashSuccess(value) =>
-          sender() ! Tuple2(hashCommand.fileHashContext, IoSuccess(requester.ioCommand, value))
+          sender() ! Tuple2[Any, Any](hashCommand.fileHashContext, IoSuccess(requester.ioCommand, value))
         case FileHashFailure(error) =>
           sender() ! Tuple2(hashCommand.fileHashContext, IoFailure(requester.ioCommand, new IOException(error)))
       }
diff --git a/build.sbt b/build.sbt
index 3b255d0e0e5..76f6f27e2c9 100644
--- a/build.sbt
+++ b/build.sbt
@@ -74,12 +74,6 @@ lazy val wdlTransformsBiscayne = (project in wdlTransformsRoot / "biscayne")
   .dependsOn(common % "test->test")
   .dependsOn(wom % "test->test")
 
-lazy val cwl = project
-  .withLibrarySettings("cromwell-cwl", cwlDependencies)
-  .dependsOn(wom)
-  .dependsOn(wom % "test->test")
-  .dependsOn(common % "test->test")
-
 lazy val core = project
   .withLibrarySettings("cromwell-core", coreDependencies)
   .dependsOn(wom)
@@ -183,7 +177,6 @@ lazy val services = project
   .dependsOn(wdlDraft2LanguageFactory % "test->test") // because the WaaS tests init language config with all languages
   .dependsOn(wdlDraft3LanguageFactory % "test->test")
   .dependsOn(wdlBiscayneLanguageFactory % "test->test")
-  .dependsOn(cwlV1_0LanguageFactory % "test->test")
   .dependsOn(core % "test->test")
   .dependsOn(ftpFileSystem % "test->test")
   .dependsOn(common % "test->test")
@@ -245,6 +238,9 @@ lazy val tesBackend = (project in backendRoot / "tes")
   .dependsOn(sfsBackend)
   .dependsOn(ftpFileSystem)
   .dependsOn(drsFileSystem)
+  .dependsOn(azureBlobFileSystem)
+  // TES backend provides a compatibility layer to run WDLs with PAPI runtime attributes [WX-769]
+  .dependsOn(googlePipelinesCommon)
   .dependsOn(backend % "test->test")
   .dependsOn(common % "test->test")
 
@@ -263,7 +259,6 @@ lazy val engine = project
   .dependsOn(azureBlobFileSystem % "test->test")
   .dependsOn(`cloud-nio-spi`)
   .dependsOn(languageFactoryCore)
-  .dependsOn(cwlV1_0LanguageFactory % "test->test")
   .dependsOn(wdlDraft2LanguageFactory % "test->test")
   .dependsOn(wdlDraft3LanguageFactory % "test->test")
   .dependsOn(wdlBiscayneLanguageFactory % "test->test")
@@ -278,20 +273,11 @@ lazy val engine = project
 
 // Executables
 
-lazy val centaurCwlRunner = project
-  .withExecutableSettings("centaur-cwl-runner", centaurCwlRunnerDependencies, buildDocker = false)
-  .dependsOn(cwl)
-  .dependsOn(centaur)
-  .dependsOn(gcsFileSystem)
-  .dependsOn(ftpFileSystem)
-  .dependsOn(common % "test->test")
-
 lazy val womtool = project
   .withExecutableSettings("womtool", womtoolDependencies)
   .dependsOn(wdlDraft2LanguageFactory)
   .dependsOn(wdlDraft3LanguageFactory)
   .dependsOn(wdlBiscayneLanguageFactory)
-  .dependsOn(cwlV1_0LanguageFactory)
   .dependsOn(wom % "test->test")
   .dependsOn(common % "test->test")
 
@@ -337,12 +323,6 @@ lazy val wdlBiscayneLanguageFactory = (project in languageFactoryRoot / "wdl-bis
   .dependsOn(wdlTransformsBiscayne)
   .dependsOn(common % "test->test")
 
-lazy val cwlV1_0LanguageFactory = (project in languageFactoryRoot / "cwl-v1-0")
-  .withLibrarySettings("cwl-v1-0")
-  .dependsOn(languageFactoryCore)
-  .dependsOn(cwl)
-  .dependsOn(common % "test->test")
-
 lazy val `cloud-nio-spi` = (project in cloudNio / "cloud-nio-spi")
   .withLibrarySettings(libraryName = "cloud-nio-spi", dependencies = spiDependencies)
   .dependsOn(common % "test->test")
@@ -385,7 +365,6 @@ lazy val server = project
   .dependsOn(wdlDraft2LanguageFactory)
   .dependsOn(wdlDraft3LanguageFactory)
   .dependsOn(wdlBiscayneLanguageFactory)
-  .dependsOn(cwlV1_0LanguageFactory)
   .dependsOn(engine % "test->test")
   .dependsOn(common % "test->test")
 
@@ -402,14 +381,11 @@ lazy val root = (project in file("."))
   .aggregate(azureBlobFileSystem)
   .aggregate(backend)
   .aggregate(centaur)
-  .aggregate(centaurCwlRunner)
   .aggregate(cloudSupport)
   .aggregate(common)
   .aggregate(core)
   .aggregate(cromiam)
   .aggregate(cromwellApiClient)
-  .aggregate(cwl)
-  .aggregate(cwlV1_0LanguageFactory)
   .aggregate(databaseMigration)
   .aggregate(databaseSql)
   .aggregate(dockerHashing)
diff --git a/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala b/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
index 16463742632..9a88a9ac109 100644
--- a/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
+++ b/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
@@ -189,7 +189,7 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
   }
 
   private def toJobKeyValueRow(jobKeyValueEntry: JobKeyValueEntry): RowToInsert = {
-    RowToInsert of Map(
+    RowToInsert of Map[String, Any](
       "call_fully_qualified_name" -> jobKeyValueEntry.callFullyQualifiedName,
       "job_attempt" -> jobKeyValueEntry.jobAttempt,
       "job_index" -> jobKeyValueEntry.jobIndex,
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_joint_gvcf.test b/centaur/src/main/resources/integrationTestCases/bcbio_joint_gvcf.test
deleted file mode 100644
index ef32cbc7d7c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_joint_gvcf.test
+++ /dev/null
@@ -1,23 +0,0 @@
-name: bcbio_joint_gvcf
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-
-files {
-  workflow: cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl
-  inputs: cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json
-  imports: [
-    cwl/bcbio/gvcf-joint-workflow/steps,
-    cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl,
-    cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl,
-    cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_prealign.test b/centaur/src/main/resources/integrationTestCases/bcbio_prealign.test
deleted file mode 100644
index 2c4a6db3f45..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_prealign.test
+++ /dev/null
@@ -1,20 +0,0 @@
-name: bcbio_prealign
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/prealign-workflow/main-prealign.cwl
-  inputs: cwl/bcbio/prealign-workflow/main-prealign-samples.json
-    imports: [
-      cwl/bcbio/prealign-workflow/steps,
-      cwl/bcbio/prealign-workflow/wf-variantcall.cwl
-    ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_rnaseq.test b/centaur/src/main/resources/integrationTestCases/bcbio_rnaseq.test
deleted file mode 100644
index 64ac876c568..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_rnaseq.test
+++ /dev/null
@@ -1,19 +0,0 @@
-name: bcbio_rnaseq
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl
-  inputs: cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json
-  imports: [
-    cwl/bcbio/rnaseq-workflow/steps
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_somatic.test b/centaur/src/main/resources/integrationTestCases/bcbio_somatic.test
deleted file mode 100644
index 440099f280e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_somatic.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: bcbio_somatic
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/somatic-workflow/main-somatic.cwl
-  inputs: cwl/bcbio/somatic-workflow/main-somatic-samples.json
-  imports: [
-    cwl/bcbio/somatic-workflow/steps,
-    cwl/bcbio/somatic-workflow/wf-alignment.cwl,
-    cwl/bcbio/somatic-workflow/wf-svcall.cwl,
-    cwl/bcbio/somatic-workflow/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_svcall.test b/centaur/src/main/resources/integrationTestCases/bcbio_svcall.test
deleted file mode 100644
index 9116814fe6d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_svcall.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: bcbio_svcall
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/svcall-workflow/main-svcall.cwl
-  inputs: cwl/bcbio/svcall-workflow/main-svcall-samples.json
-  imports: [
-    cwl/bcbio/svcall-workflow/steps,
-    cwl/bcbio/svcall-workflow/wf-alignment.cwl,
-    cwl/bcbio/svcall-workflow/wf-svcall.cwl,
-    cwl/bcbio/svcall-workflow/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_wes-chr21-test-workflow.test b/centaur/src/main/resources/integrationTestCases/bcbio_wes-chr21-test-workflow.test
deleted file mode 100644
index 1969d6bef66..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_wes-chr21-test-workflow.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: wes_chr21_test-workflow
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
-  inputs: cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json
-  imports: [
-    cwl/bcbio/wes_chr21_test-workflow-gcp/steps,
-    cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl,
-    cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl,
-    cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/bcbio.options b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/bcbio.options
deleted file mode 100644
index 1340bda7f1c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/bcbio.options
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-  "default_runtime_attributes": {
-    "bootDiskSizeGb": 20
-  }
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json
deleted file mode 100644
index b7080e81448..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json
+++ /dev/null
@@ -1,615 +0,0 @@
-{
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__adapters": [
-        [
-            "polyx"
-        ],
-        [
-            "polyx"
-        ]
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
-        },
-        null
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants"
-        ],
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "gvcf"
-        ],
-        [
-            "gvcf"
-        ]
-    ],
-    "config__algorithm__trim_reads": [
-        "read_through",
-        "False"
-    ],
-    "config__algorithm__validate": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/7_100326_FC6107FAAXX-grade.vcf"
-        },
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__variantcaller": [
-        [
-            "gatk-haplotype",
-            "strelka2"
-        ],
-        [
-            "gatk-haplotype",
-            "strelka2"
-        ]
-    ],
-    "config__algorithm__vcfanno": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ]
-    ],
-    "description": [
-        "Test1",
-        "Test2"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX.bam"
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        "b1",
-        "b1"
-    ],
-    "metadata__phenotype": [
-        "",
-        ""
-    ],
-    "reference__bwa__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__lb": [
-        null,
-        null
-    ],
-    "rgnames__pl": [
-        "illumina",
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__rg": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__sample": [
-        "Test1",
-        "Test2"
-    ],
-    "vrn_file": [
-        null,
-        null
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl
deleted file mode 100644
index a798100dc12..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl
+++ /dev/null
@@ -1,794 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: config__algorithm__coverage
-    source: config__algorithm__coverage
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: batch_for_jointvc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: jointvc_batch_rec
-  run: steps/batch_for_jointvc.cwl
-- id: jointcall
-  in:
-  - id: jointvc_batch_rec
-    source: batch_for_jointvc/jointvc_batch_rec
-  out:
-  - id: jointvc_rec
-  - id: vrn_file_joint
-  run: wf-jointcall.cwl
-  scatter:
-  - jointvc_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: jointvc_rec
-    source: jointcall/jointvc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/alignment_to_rec.cwl
deleted file mode 100644
index 1379c575535..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-          items: string
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: rgnames__pu
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_jointvc.cwl
deleted file mode 100644
index 523567ed191..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_jointvc.cwl
+++ /dev/null
@@ -1,329 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=jointvc_batch_rec:resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: jointvc_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index ca40e5b30cf..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,401 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 2048
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index d876db22bd2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index 06152084c58..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,337 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index d486086c79e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,196 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl
deleted file mode 100644
index dbb0f54be94..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl
+++ /dev/null
@@ -1,209 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file_joint
-- sentinel_inputs=jointvc_batch_rec:record,region:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: region
-  type:
-    items: string
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/finalize_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/finalize_jointvc.cwl
deleted file mode 100644
index fd1e04762e4..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/finalize_jointvc.cwl
+++ /dev/null
@@ -1,331 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=jointvc_rec:resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions;vrn_file_joint
-- sentinel_inputs=jointvc_batch_rec:record,vrn_file_joint:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- finalize_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: jointvc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      - name: vrn_file_joint
-        type: File
-      name: jointvc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index 18e635c4006..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,171 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 2048
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl
deleted file mode 100644
index fac484f75ca..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl
+++ /dev/null
@@ -1,184 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region
-- sentinel_inputs=jointvc_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-outputs:
-- id: region
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/merge_split_alignments.cwl
deleted file mode 100644
index 66e17dc7aa9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,168 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1035
-  ramMin: 4096
-  tmpdirMin: 6
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 45a90274381..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 2048
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index 75e0c7a35d5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,219 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 4096
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index 09728af2814..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,223 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1033
-  ramMin: 4096
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 813f3fed737..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,233 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;config__algorithm__coverage;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index a300aa5be18..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,195 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file_joint
-- sentinel_inputs=jointvc_batch_rec:record,vrn_file_joint:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: vrn_file_joint_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_align_inputs.cwl
deleted file mode 100644
index 8179e185e8b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,142 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples.cwl
deleted file mode 100644
index 244502016fb..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 830e65f0404..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__coverage;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=config__algorithm__coverage:var,rgnames__sample:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/process_alignment.cwl
deleted file mode 100644
index b12a9946b5c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 4096
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 7
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 53e0a326097..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,295 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;config__algorithm__coverage;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/run_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/run_jointvc.cwl
deleted file mode 100644
index 897c1e02ca8..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/run_jointvc.cwl
+++ /dev/null
@@ -1,203 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region
-- sentinel_inputs=jointvc_batch_rec:record,region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- run_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: gvcfgenotyper
-    specs:
-    - https://anaconda.org/bioconda/gvcfgenotyper
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: region_toolinput
-  type: string
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region
-  type: string
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index 85b8a8f01e0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,225 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=jointvc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: jointvc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        - name: vrn_file_joint
-          type: File
-        name: jointvc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index eb58aa47177..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,266 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 4096
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl
deleted file mode 100644
index 27c76c747c5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl
+++ /dev/null
@@ -1,143 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl
deleted file mode 100644
index 3091d1de370..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl
+++ /dev/null
@@ -1,360 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-outputs:
-- id: jointvc_rec
-  outputSource: finalize_jointvc/jointvc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      - name: vrn_file_joint
-        type: File
-      name: jointvc_rec
-      type: record
-    type: array
-- id: vrn_file_joint
-  outputSource: postprocess_variants/vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  out:
-  - id: region
-  run: steps/get_parallel_regions_jointvc.cwl
-- id: run_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: region_toolinput
-    source: get_parallel_regions_jointvc/region
-  out:
-  - id: vrn_file_region
-  - id: region
-  run: steps/run_jointvc.cwl
-  scatter:
-  - region_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: region
-    source: run_jointvc/region
-  - id: vrn_file_region
-    source: run_jointvc/vrn_file_region
-  out:
-  - id: vrn_file_joint
-  run: steps/concat_batch_variantcalls_jointvc.cwl
-- id: postprocess_variants
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: vrn_file_joint_toolinput
-    source: concat_batch_variantcalls_jointvc/vrn_file_joint
-  out:
-  - id: vrn_file_joint
-  run: steps/postprocess_variants.cwl
-- id: finalize_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: vrn_file_joint
-    source: postprocess_variants/vrn_file_joint
-  out:
-  - id: jointvc_rec
-  run: steps/finalize_jointvc.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl
deleted file mode 100644
index ffabd7e9f1e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,329 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign-samples.json
deleted file mode 100644
index 3e1234addda..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign-samples.json
+++ /dev/null
@@ -1,526 +0,0 @@
-{
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__coverage": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
-        }
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "qualimap",
-            "samtools",
-            "variants"
-        ],
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "qualimap",
-            "samtools",
-            "variants"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "qualimap_full"
-        ],
-        [
-            "qualimap_full"
-        ]
-    ],
-    "config__algorithm__validate": [
-        null,
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        null,
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__variantcaller": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__vcfanno": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ]
-    ],
-    "description": [
-        "Test1",
-        "Test2"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX.bam"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX_2.bam"
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        null,
-        null
-    ],
-    "metadata__phenotype": [
-        "",
-        ""
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__sample": [
-        "Test1",
-        "Test2"
-    ],
-    "vrn_file": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test1-gatk-haplotype.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test1-gatk-haplotype.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test2-gatk-haplotype.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test2-gatk-haplotype.vcf.gz.tbi"
-                }
-            ]
-        }
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign.cwl
deleted file mode 100644
index 535082448ed..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign.cwl
+++ /dev/null
@@ -1,672 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: organize_noalign
-  in:
-  - id: files
-    source: files
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/organize_noalign.cwl
-  scatter:
-  - files
-  - resources
-  - description
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: config__algorithm__coverage
-    source: config__algorithm__coverage
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: organize_noalign/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 1ad9465444b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,407 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type:
-          - boolean
-          - 'null'
-          - string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type: File
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index 2df313f7a8f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,101 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index ab4909659ca..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,315 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index ae12d21651d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,199 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index c4e3997bca4..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,174 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 82ce9f97a43..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/organize_noalign.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/organize_noalign.cwl
deleted file mode 100644
index 370f2ccf982..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/organize_noalign.cwl
+++ /dev/null
@@ -1,59 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=files:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- organize_noalign
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1024
-  ramMin: 3072
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-inputs:
-- id: files
-  type:
-    items: File
-    type: array
-- id: resources
-  type: string
-- id: description
-  type: string
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type: File
-- id: work_bam_plus__disc
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index c0e41e5ba62..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type:
-      - 'null'
-      - string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index 6a261c205af..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1033
-  ramMin: 6144
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type: File
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index e61b71f4d28..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,229 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;config__algorithm__coverage;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type: File
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index dd7e67c7d61..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,183 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1025
-  ramMin: 6144
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples.cwl
deleted file mode 100644
index f473b969345..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,93 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage
-      type: File
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 54f7781bb21..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,81 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__coverage;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=config__algorithm__coverage:var,rgnames__sample:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: config__algorithm__coverage
-  type:
-    items: File
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage
-        type: File
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 3de03a1a1a8..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,299 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;config__algorithm__coverage;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index e9fde20378c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type:
-          - boolean
-          - 'null'
-          - string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index e9192828e62..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,269 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/wf-variantcall.cwl
deleted file mode 100644
index b48a8254984..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,316 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json
deleted file mode 100644
index 3e67d52727e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json
+++ /dev/null
@@ -1,111 +0,0 @@
-{
-    "analysis": [
-        "RNA-seq"
-    ],
-    "config__algorithm__aligner": [
-        "hisat2"
-    ],
-    "config__algorithm__coverage_interval": [
-        null
-    ],
-    "config__algorithm__expression_caller": [
-        [
-            "salmon",
-            "kallisto"
-        ]
-    ],
-    "config__algorithm__fusion_caller": [
-        [
-            "pizzly"
-        ]
-    ],
-    "config__algorithm__qc": [
-        [
-            "fastqc",
-            "qualimap_rnaseq",
-            "samtools"
-        ]
-    ],
-    "config__algorithm__quality_format": [
-        "standard"
-    ],
-    "config__algorithm__tools_off": [
-        []
-    ],
-    "config__algorithm__tools_on": [
-        []
-    ],
-    "description": [
-        "Test1"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbio-cromwell-dev-test/test_bcbio_cwl/testdata/test_fusion/fusion-1_1.fq.gz"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbio-cromwell-dev-test/test_bcbio_cwl/testdata/test_fusion/fusion-1_2.fq.gz"
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19"
-    ],
-    "genome_resources__rnaseq__transcripts": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.gtf",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.gtf.db"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__hisat2__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/hisat2-wf.tar.gz"
-        }
-    ],
-    "resources": [
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test1"
-    ],
-    "rgnames__lb": [
-        null
-    ],
-    "rgnames__pl": [
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test1"
-    ],
-    "rgnames__rg": [
-        "Test1"
-    ],
-    "rgnames__sample": [
-        "Test1"
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl
deleted file mode 100644
index 2dd258ac786..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl
+++ /dev/null
@@ -1,304 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: config__algorithm__expression_caller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: reference__hisat2__indexes
-  type:
-    items: File
-    type: array
-- id: config__algorithm__fusion_caller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__rnaseq__transcripts
-  secondaryFiles:
-  - .db
-  type:
-    items: File
-    type: array
-- id: config__algorithm__quality_format
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: process_alignment/align_bam
-  type:
-    items: File
-    type: array
-- id: quant__tsv
-  outputSource: rnaseq_quantitate/quant__tsv
-  type:
-    items: File
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prepare_sample
-  in:
-  - id: files
-    source: files
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: genome_build
-    source: genome_build
-  - id: genome_resources__rnaseq__transcripts
-    source: genome_resources__rnaseq__transcripts
-  - id: analysis
-    source: analysis
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__hisat2__indexes
-    source: reference__hisat2__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__expression_caller
-    source: config__algorithm__expression_caller
-  - id: config__algorithm__fusion_caller
-    source: config__algorithm__fusion_caller
-  - id: config__algorithm__quality_format
-    source: config__algorithm__quality_format
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_rec
-  run: steps/prepare_sample.cwl
-  scatter:
-  - files
-  - rgnames__sample
-  - reference__fasta__base
-  - genome_build
-  - genome_resources__rnaseq__transcripts
-  - analysis
-  - rgnames__pl
-  - rgnames__pu
-  - rgnames__lane
-  - rgnames__rg
-  - rgnames__lb
-  - reference__hisat2__indexes
-  - config__algorithm__aligner
-  - config__algorithm__expression_caller
-  - config__algorithm__fusion_caller
-  - config__algorithm__quality_format
-  - resources
-  - description
-  scatterMethod: dotproduct
-- id: trim_sample
-  in:
-  - id: prep_rec
-    source: prepare_sample/prep_rec
-  out:
-  - id: trim_rec
-  run: steps/trim_sample.cwl
-  scatter:
-  - prep_rec
-  scatterMethod: dotproduct
-- id: process_alignment
-  in:
-  - id: trim_rec
-    source: trim_sample/trim_rec
-  out:
-  - id: align_bam
-  run: steps/process_alignment.cwl
-  scatter:
-  - trim_rec
-  scatterMethod: dotproduct
-- id: rnaseq_quantitate
-  in:
-  - id: trim_rec
-    source: trim_sample/trim_rec
-  - id: align_bam
-    source: process_alignment/align_bam
-  out:
-  - id: count_file
-  - id: quant__tsv
-  - id: quant__hdf5
-  - id: quant__fusion
-  run: steps/rnaseq_quantitate.cwl
-  scatter:
-  - trim_rec
-  - align_bam
-  scatterMethod: dotproduct
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: process_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: genome_resources__rnaseq__transcripts
-    source: genome_resources__rnaseq__transcripts
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  run: steps/multiqc_summary.cwl
-- id: detect_fusions
-  in:
-  - id: quant__fusion
-    source: rnaseq_quantitate/quant__fusion
-  - id: quant__hdf5
-    source: rnaseq_quantitate/quant__hdf5
-  - id: trim_rec
-    source: trim_sample/trim_rec
-  out:
-  - id: fusion__fasta
-  - id: fusion__json
-  run: steps/detect_fusions.cwl
-  scatter:
-  - quant__fusion
-  - quant__hdf5
-  - trim_rec
-  scatterMethod: dotproduct
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/detect_fusions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/detect_fusions.cwl
deleted file mode 100644
index 8803c214f31..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/detect_fusions.cwl
+++ /dev/null
@@ -1,97 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=fusion__fasta,fusion__json
-- sentinel_inputs=quant__fusion:var,quant__hdf5:var,trim_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_fusions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: pizzly
-    specs:
-    - https://anaconda.org/bioconda/pizzly
-inputs:
-- id: quant__fusion
-  type: File
-- id: quant__hdf5
-  type: File
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-outputs:
-- id: fusion__fasta
-  type: File
-- id: fusion__json
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 604f9291df7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,96 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__rnaseq__transcripts
-        type: File
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type: File
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index 230b84afc66..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,155 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_build;genome_resources__rnaseq__transcripts;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;align_bam
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=4
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=4
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_build
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type: File
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_build
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type: File
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/prepare_sample.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/prepare_sample.cwl
deleted file mode 100644
index e5b8cdf645e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/prepare_sample.cwl
+++ /dev/null
@@ -1,146 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=prep_rec:resources;description;files;reference__fasta__base;config__algorithm__expression_caller;rgnames__lb;rgnames__rg;reference__hisat2__indexes;config__algorithm__fusion_caller;config__algorithm__aligner;rgnames__pl;genome_build;rgnames__pu;genome_resources__rnaseq__transcripts;config__algorithm__quality_format;analysis;rgnames__sample;rgnames__lane
-- sentinel_inputs=files:var,rgnames__sample:var,reference__fasta__base:var,genome_build:var,genome_resources__rnaseq__transcripts:var,analysis:var,rgnames__pl:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__hisat2__indexes:var,config__algorithm__aligner:var,config__algorithm__expression_caller:var,config__algorithm__fusion_caller:var,config__algorithm__quality_format:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prepare_sample
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-inputs:
-- id: files
-  type:
-    items: File
-    type: array
-- id: rgnames__sample
-  type: string
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type: File
-- id: genome_build
-  type: string
-- id: genome_resources__rnaseq__transcripts
-  secondaryFiles:
-  - .db
-  type: File
-- id: analysis
-  type: string
-- id: rgnames__pl
-  type: string
-- id: rgnames__pu
-  type: string
-- id: rgnames__lane
-  type: string
-- id: rgnames__rg
-  type: string
-- id: rgnames__lb
-  type:
-  - 'null'
-  - string
-- id: reference__hisat2__indexes
-  type: File
-- id: config__algorithm__aligner
-  type: string
-- id: config__algorithm__expression_caller
-  type:
-    items: string
-    type: array
-- id: config__algorithm__fusion_caller
-  type:
-    items: string
-    type: array
-- id: config__algorithm__quality_format
-  type: string
-- id: resources
-  type: string
-- id: description
-  type: string
-outputs:
-- id: prep_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: prep_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/process_alignment.cwl
deleted file mode 100644
index 88af1224f95..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,108 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=align_bam
-- sentinel_inputs=trim_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: star
-    specs:
-    - https://anaconda.org/bioconda/star
-  - package: hisat2
-    specs:
-    - https://anaconda.org/bioconda/hisat2
-  - package: tophat
-    specs:
-    - https://anaconda.org/bioconda/tophat
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-inputs:
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 5ff5b2f10e0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,135 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_build;genome_resources__rnaseq__transcripts;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;align_bam
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,genome_resources__rnaseq__transcripts:var,genome_build:var,config__algorithm__coverage_interval:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__qc:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items: File
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: genome_resources__rnaseq__transcripts
-  secondaryFiles:
-  - .db
-  type:
-    items: File
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__rnaseq__transcripts
-        type: File
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type: File
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/rnaseq_quantitate.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/rnaseq_quantitate.cwl
deleted file mode 100644
index 05d2ec813ae..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/rnaseq_quantitate.cwl
+++ /dev/null
@@ -1,123 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=count_file,quant__tsv,quant__hdf5,quant__fusion
-- sentinel_inputs=trim_rec:record,align_bam:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- rnaseq_quantitate
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1025
-  ramMin: 4096
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: sailfish
-    specs:
-    - https://anaconda.org/bioconda/sailfish
-  - package: salmon
-    specs:
-    - https://anaconda.org/bioconda/salmon
-  - package: kallisto>
-    specs:
-    - https://anaconda.org/bioconda/kallisto>
-    version:
-    - 0.43.1
-  - package: subread
-    specs:
-    - https://anaconda.org/bioconda/subread
-  - package: gffread
-    specs:
-    - https://anaconda.org/bioconda/gffread
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-wasabi
-    specs:
-    - https://anaconda.org/bioconda/r-wasabi
-inputs:
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type: File
-outputs:
-- id: count_file
-  type: File
-- id: quant__tsv
-  type: File
-- id: quant__hdf5
-  type: File
-- id: quant__fusion
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/trim_sample.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/trim_sample.cwl
deleted file mode 100644
index 14124636cec..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/trim_sample.cwl
+++ /dev/null
@@ -1,140 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=trim_rec:resources;description;files;reference__fasta__base;config__algorithm__expression_caller;rgnames__lb;rgnames__rg;reference__hisat2__indexes;config__algorithm__fusion_caller;config__algorithm__aligner;rgnames__pl;genome_build;rgnames__pu;genome_resources__rnaseq__transcripts;config__algorithm__quality_format;analysis;rgnames__sample;rgnames__lane
-- sentinel_inputs=prep_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- trim_sample
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-inputs:
-- id: prep_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: prep_rec
-    type: record
-outputs:
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic-samples.json
deleted file mode 100644
index cbafda3641d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic-samples.json
+++ /dev/null
@@ -1,680 +0,0 @@
-{
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__adapters": [
-        [],
-        []
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants",
-            "viral"
-        ],
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants",
-            "viral"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__svcaller": [
-        [
-            "manta"
-        ],
-        [
-            "manta"
-        ]
-    ],
-    "config__algorithm__svprioritize": [
-        null,
-        null
-    ],
-    "config__algorithm__svvalidate": [
-        null,
-        null
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [],
-        []
-    ],
-    "config__algorithm__trim_reads": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__validate": [
-        null,
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/Test1-grade.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/Test1-grade.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "config__algorithm__validate_regions": [
-        null,
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__variant_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__variantcaller": [
-        [
-            "vardict"
-        ],
-        [
-            "vardict"
-        ]
-    ],
-    "config__algorithm__vcfanno": [
-        [],
-        []
-    ],
-    "description": [
-        "Test2",
-        "Test1"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX.bam"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gc_profile": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/gc/GC_profile.1000bp.cnp"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/gc/GC_profile.1000bp.cnp"
-        }
-    ],
-    "genome_resources__variation__germline_het_pon": [
-        null,
-        null
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        "b1",
-        "b1"
-    ],
-    "metadata__phenotype": [
-        "normal",
-        "tumor"
-    ],
-    "reference__bwa__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "reference__viral": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.sa"
-                }
-            ]
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test2",
-        "Test1"
-    ],
-    "rgnames__lb": [
-        null,
-        null
-    ],
-    "rgnames__pl": [
-        "illumina",
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test2",
-        "Test1"
-    ],
-    "rgnames__rg": [
-        "Test2",
-        "Test1"
-    ],
-    "rgnames__sample": [
-        "Test2",
-        "Test1"
-    ],
-    "vrn_file": [
-        null,
-        null
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic.cwl
deleted file mode 100644
index 699d99a4690..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic.cwl
+++ /dev/null
@@ -1,973 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__calls
-  outputSource: summarize_sv/sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  outputSource: summarize_sv/svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: sv__prioritize__tsv
-  outputSource: summarize_sv/sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  outputSource: summarize_sv/sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  outputSource: summarize_sv/sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: calculate_sv_bins
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__seq2c_bed_ready
-    source: postprocess_alignment/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: sv_bin_rec
-  run: steps/calculate_sv_bins.cwl
-- id: calculate_sv_coverage
-  in:
-  - id: sv_bin_rec
-    source: calculate_sv_bins/sv_bin_rec
-  out:
-  - id: sv_rawcoverage_rec
-  run: steps/calculate_sv_coverage.cwl
-  scatter:
-  - sv_bin_rec
-  scatterMethod: dotproduct
-- id: normalize_sv_coverage
-  in:
-  - id: sv_rawcoverage_rec
-    source: calculate_sv_coverage/sv_rawcoverage_rec
-  out:
-  - id: sv_coverage_rec
-  run: steps/normalize_sv_coverage.cwl
-- id: batch_for_sv
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: work_bam_plus__disc
-    source: alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr
-    source: alignment/work_bam_plus__sr
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__svprioritize
-    source: config__algorithm__svprioritize
-  - id: config__algorithm__svvalidate
-    source: config__algorithm__svvalidate
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: genome_resources__variation__gc_profile
-    source: genome_resources__variation__gc_profile
-  - id: genome_resources__variation__germline_het_pon
-    source: genome_resources__variation__germline_het_pon
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: sv_coverage_rec
-    source: normalize_sv_coverage/sv_coverage_rec
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  out:
-  - id: sv_batch_rec
-  run: steps/batch_for_sv.cwl
-- id: svcall
-  in:
-  - id: sv_batch_rec
-    source: batch_for_sv/sv_batch_rec
-  out:
-  - id: sv_rec
-  run: wf-svcall.cwl
-  scatter:
-  - sv_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_sv
-  in:
-  - id: sv_rec
-    source: svcall/sv_rec
-  out:
-  - id: sv__calls
-  - id: sv__supplemental
-  - id: sv__prioritize__tsv
-  - id: sv__prioritize__raw
-  - id: svvalidate__grading_summary
-  - id: svvalidate__grading_plots
-  run: steps/summarize_sv.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: reference__viral
-    source: reference__viral
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/alignment_to_rec.cwl
deleted file mode 100644
index 11cd9fc8d40..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,200 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: rgnames__pu
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_sv.cwl
deleted file mode 100644
index 16b905acacf..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_sv.cwl
+++ /dev/null
@@ -1,375 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=sv_batch_rec:resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;reference__snpeff__hg19;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;work_bam_plus__disc;work_bam_plus__sr;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,work_bam_plus__disc:var,work_bam_plus__sr:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__svprioritize:var,config__algorithm__svvalidate:var,regions__sample_callable:var,genome_resources__variation__gc_profile:var,genome_resources__variation__germline_het_pon:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,sv_coverage_rec:record,variants__samples:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10240
-  ramMin: 6144
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-outputs:
-- id: sv_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: work_bam_plus__disc
-          type:
-          - File
-          - 'null'
-        - name: work_bam_plus__sr
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 60af6c4469e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,407 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;genome_resources__variation__1000g;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10246
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_bins.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_bins.cwl
deleted file mode 100644
index 40bd035478a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_bins.cwl
+++ /dev/null
@@ -1,225 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_bin_rec:regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;resources;description;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=align_bam:var,reference__fasta__base:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__svcaller:var,depth__variant_regions__regions:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__rnaseq__gene_bed:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_bins
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: sv_bin_rec
-  type:
-    items:
-      fields:
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_bin_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_coverage.cwl
deleted file mode 100644
index fc75d2c1b71..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_coverage.cwl
+++ /dev/null
@@ -1,218 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=sv_rawcoverage_rec:depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;resources;description;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_bin_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-inputs:
-- id: sv_bin_rec
-  type:
-    fields:
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_bin_rec
-    type: record
-outputs:
-- id: sv_rawcoverage_rec
-  type:
-    fields:
-    - name: depth__bins__target
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__seq2c
-      type:
-      - File
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_rawcoverage_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index 5a8f8a3c6cb..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index d6b910b7f9e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,311 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index ef31b2ffe4f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/detect_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/detect_sv.cwl
deleted file mode 100644
index 234bcc60d69..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/detect_sv.cwl
+++ /dev/null
@@ -1,414 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=sv_rec:sv__variantcaller;sv__vrn_file;sv__supplemental;svvalidate__summary;resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: delly
-    specs:
-    - https://anaconda.org/bioconda/delly
-  - package: duphold
-    specs:
-    - https://anaconda.org/bioconda/duphold
-  - package: extract-sv-reads
-    specs:
-    - https://anaconda.org/bioconda/extract-sv-reads
-  - package: lumpy-sv
-    specs:
-    - https://anaconda.org/bioconda/lumpy-sv
-  - package: manta
-    specs:
-    - https://anaconda.org/bioconda/manta
-  - package: break-point-inspector
-    specs:
-    - https://anaconda.org/bioconda/break-point-inspector
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: smoove
-    specs:
-    - https://anaconda.org/bioconda/smoove
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-  - package: simple_sv_annotation
-    specs:
-    - https://anaconda.org/bioconda/simple_sv_annotation
-  - package: survivor
-    specs:
-    - https://anaconda.org/bioconda/survivor
-  - package: svtools
-    specs:
-    - https://anaconda.org/bioconda/svtools
-  - package: svtyper
-    specs:
-    - https://anaconda.org/bioconda/svtyper
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: xorg-libxt
-    specs:
-    - https://anaconda.org/bioconda/xorg-libxt
-  - package: vawk
-    specs:
-    - https://anaconda.org/bioconda/vawk
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index 48e5f050eb3..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,173 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10246
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/merge_split_alignments.cwl
deleted file mode 100644
index 029b704bbb2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,169 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10251
-  ramMin: 6144
-  tmpdirMin: 6
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 9d65504ba6b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,96 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10246
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/normalize_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/normalize_sv_coverage.cwl
deleted file mode 100644
index 1bdc8dbc3b8..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/normalize_sv_coverage.cwl
+++ /dev/null
@@ -1,236 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_coverage_rec:depth__bins__normalized;depth__bins__background;resources;description;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_rawcoverage_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- normalize_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_rawcoverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rawcoverage_rec
-      type: record
-    type: array
-outputs:
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index 89f6372949c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,223 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: reference__viral
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index 8585bfb3074..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,224 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10249
-  ramMin: 6144
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 9d93ac8f1db..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,235 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index 6fba055bcd7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,182 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10241
-  ramMin: 6144
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_align_inputs.cwl
deleted file mode 100644
index c40a38fc01a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,143 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples.cwl
deleted file mode 100644
index 4e62820988d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 9268efdafcb..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__svcaller;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=rgnames__sample:var,config__algorithm__svcaller:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/process_alignment.cwl
deleted file mode 100644
index 45b58d1ab98..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,199 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 7
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index eccc8330618..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,310 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;metadata__phenotype;config__algorithm__tools_off;reference__viral;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,reference__viral:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__viral
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_sv.cwl
deleted file mode 100644
index be7b4a8c87f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_sv.cwl
+++ /dev/null
@@ -1,242 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv__calls,sv__supplemental,sv__prioritize__tsv,sv__prioritize__raw,svvalidate__grading_summary,svvalidate__grading_plots
-- sentinel_inputs=sv_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10243
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcbio-prioritize
-    specs:
-    - https://anaconda.org/bioconda/bcbio-prioritize
-inputs:
-- id: sv_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: sv__variantcaller
-          type:
-          - string
-          - 'null'
-        - name: sv__vrn_file
-          type:
-          - File
-          - 'null'
-        - name: sv__supplemental
-          type:
-            items:
-            - File
-            type: array
-        - name: svvalidate__summary
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: svvalidate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index 62c64099b31..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,195 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - File
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index 1dc7a6e7128..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,268 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-alignment.cwl
deleted file mode 100644
index c2ce73cfc61..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-alignment.cwl
+++ /dev/null
@@ -1,144 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-svcall.cwl
deleted file mode 100644
index db9522935a1..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-svcall.cwl
+++ /dev/null
@@ -1,328 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  outputSource: detect_sv/sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: detect_sv
-  in:
-  - id: sv_batch_rec
-    source: sv_batch_rec
-  out:
-  - id: sv_rec
-  run: steps/detect_sv.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-variantcall.cwl
deleted file mode 100644
index da6bab7ac21..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,312 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall-samples.json
deleted file mode 100644
index 28826670c5c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall-samples.json
+++ /dev/null
@@ -1,707 +0,0 @@
-{
-    "analysis": [
-        "variant",
-        "variant"
-    ],
-    "config__algorithm__adapters": [
-        [],
-        []
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "samtools"
-        ],
-        [
-            "samtools"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__sv_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__svcaller": [
-        [
-            "cnvkit",
-            "manta",
-            "lumpy"
-        ],
-        [
-            "cnvkit",
-            "manta",
-            "lumpy"
-        ]
-    ],
-    "config__algorithm__svprioritize": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__svvalidate": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/Test1-grade.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/Test1-grade.vcf.gz.tbi"
-                }
-            ]
-        },
-        null
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "coverage_perbase"
-        ],
-        [
-            "coverage_perbase"
-        ]
-    ],
-    "config__algorithm__trim_reads": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__validate": [
-        null,
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        null,
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        null,
-        null
-    ],
-    "config__algorithm__variantcaller": [
-        [
-            "vardict"
-        ],
-        [
-            "vardict"
-        ]
-    ],
-    "config__algorithm__vcfanno": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/somatic.conf"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ]
-    ],
-    "description": [
-        "Test1",
-        "Test2"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gc_profile": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/gc/GC_profile.1000bp.cnp"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/gc/GC_profile.1000bp.cnp"
-        }
-    ],
-    "genome_resources__variation__germline_het_pon": [
-        null,
-        null
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        "b1",
-        "b1"
-    ],
-    "metadata__phenotype": [
-        "tumor",
-        "normal"
-    ],
-    "reference__bwa__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "reference__viral": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.sa"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.bwt"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.sa"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.bwt"
-                }
-            ]
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__lb": [
-        null,
-        null
-    ],
-    "rgnames__pl": [
-        "illumina",
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__rg": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__sample": [
-        "Test1",
-        "Test2"
-    ],
-    "vrn_file": [
-        null,
-        null
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall.cwl
deleted file mode 100644
index ec310cc54cd..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall.cwl
+++ /dev/null
@@ -1,975 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__sv_regions
-  type:
-    items: File
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__svvalidate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__calls
-  outputSource: summarize_sv/sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  outputSource: summarize_sv/svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: sv__prioritize__tsv
-  outputSource: summarize_sv/sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  outputSource: summarize_sv/sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  outputSource: summarize_sv/sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: calculate_sv_bins
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__sv_regions
-    source: config__algorithm__sv_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: sv_bin_rec
-  run: steps/calculate_sv_bins.cwl
-- id: calculate_sv_coverage
-  in:
-  - id: sv_bin_rec
-    source: calculate_sv_bins/sv_bin_rec
-  out:
-  - id: sv_rawcoverage_rec
-  run: steps/calculate_sv_coverage.cwl
-  scatter:
-  - sv_bin_rec
-  scatterMethod: dotproduct
-- id: normalize_sv_coverage
-  in:
-  - id: sv_rawcoverage_rec
-    source: calculate_sv_coverage/sv_rawcoverage_rec
-  out:
-  - id: sv_coverage_rec
-  run: steps/normalize_sv_coverage.cwl
-- id: batch_for_sv
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: work_bam_plus__disc
-    source: alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr
-    source: alignment/work_bam_plus__sr
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__svprioritize
-    source: config__algorithm__svprioritize
-  - id: config__algorithm__svvalidate
-    source: config__algorithm__svvalidate
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: genome_resources__variation__gc_profile
-    source: genome_resources__variation__gc_profile
-  - id: genome_resources__variation__germline_het_pon
-    source: genome_resources__variation__germline_het_pon
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: sv_coverage_rec
-    source: normalize_sv_coverage/sv_coverage_rec
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  out:
-  - id: sv_batch_rec
-  run: steps/batch_for_sv.cwl
-- id: svcall
-  in:
-  - id: sv_batch_rec
-    source: batch_for_sv/sv_batch_rec
-  out:
-  - id: sv_rec
-  run: wf-svcall.cwl
-  scatter:
-  - sv_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_sv
-  in:
-  - id: sv_rec
-    source: svcall/sv_rec
-  out:
-  - id: sv__calls
-  - id: sv__supplemental
-  - id: sv__prioritize__tsv
-  - id: sv__prioritize__raw
-  - id: svvalidate__grading_summary
-  - id: svvalidate__grading_plots
-  run: steps/summarize_sv.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: reference__viral
-    source: reference__viral
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/alignment_to_rec.cwl
deleted file mode 100644
index 8208a1f1eed..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,206 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: rgnames__pu
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - 'null'
-        - string
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_sv.cwl
deleted file mode 100644
index 5c725369def..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_sv.cwl
+++ /dev/null
@@ -1,359 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=sv_batch_rec:resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;reference__snpeff__hg19;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;work_bam_plus__disc;work_bam_plus__sr;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,work_bam_plus__disc:var,work_bam_plus__sr:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__svprioritize:var,config__algorithm__svvalidate:var,regions__sample_callable:var,genome_resources__variation__gc_profile:var,genome_resources__variation__germline_het_pon:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,sv_coverage_rec:record,variants__samples:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 6144
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items: File
-    type: array
-- id: config__algorithm__svvalidate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-outputs:
-- id: sv_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type: File
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: work_bam_plus__disc
-          type:
-          - File
-          - 'null'
-        - name: work_bam_plus__sr
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__sv_regions
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 1a04f1e6887..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,401 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;genome_resources__variation__1000g;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_bins.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_bins.cwl
deleted file mode 100644
index 34683452f0d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_bins.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_bin_rec:regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;resources;description;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=align_bam:var,reference__fasta__base:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__sv_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__svcaller:var,depth__variant_regions__regions:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__rnaseq__gene_bed:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_bins
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__sv_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: sv_bin_rec
-  type:
-    items:
-      fields:
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_bin_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_coverage.cwl
deleted file mode 100644
index 79ba8e7eaf5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_coverage.cwl
+++ /dev/null
@@ -1,207 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=sv_rawcoverage_rec:depth__bins__target;depth__bins__antitarget;resources;description;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_bin_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_bin_rec
-  type:
-    fields:
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__sv_regions
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_bin_rec
-    type: record
-outputs:
-- id: sv_rawcoverage_rec
-  type:
-    fields:
-    - name: depth__bins__target
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__sv_regions
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_rawcoverage_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index 434161e89da..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index 142a0d44ce9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,307 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index b8cd24d68bc..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,196 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/detect_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/detect_sv.cwl
deleted file mode 100644
index 4aab2c1343b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/detect_sv.cwl
+++ /dev/null
@@ -1,396 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=sv_rec:sv__variantcaller;sv__vrn_file;sv__supplemental;svvalidate__summary;resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: delly
-    specs:
-    - https://anaconda.org/bioconda/delly
-  - package: duphold
-    specs:
-    - https://anaconda.org/bioconda/duphold
-  - package: extract-sv-reads
-    specs:
-    - https://anaconda.org/bioconda/extract-sv-reads
-  - package: lumpy-sv
-    specs:
-    - https://anaconda.org/bioconda/lumpy-sv
-  - package: manta
-    specs:
-    - https://anaconda.org/bioconda/manta
-  - package: break-point-inspector
-    specs:
-    - https://anaconda.org/bioconda/break-point-inspector
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: smoove
-    specs:
-    - https://anaconda.org/bioconda/smoove
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-  - package: simple_sv_annotation
-    specs:
-    - https://anaconda.org/bioconda/simple_sv_annotation
-  - package: survivor
-    specs:
-    - https://anaconda.org/bioconda/survivor
-  - package: svtools
-    specs:
-    - https://anaconda.org/bioconda/svtools
-  - package: svtyper
-    specs:
-    - https://anaconda.org/bioconda/svtyper
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: xorg-libxt
-    specs:
-    - https://anaconda.org/bioconda/xorg-libxt
-  - package: vawk
-    specs:
-    - https://anaconda.org/bioconda/vawk
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index 71ac417a4ce..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,171 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/merge_split_alignments.cwl
deleted file mode 100644
index afe6f73cfc2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,171 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1035
-  ramMin: 6144
-  tmpdirMin: 6
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 82ce9f97a43..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/normalize_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/normalize_sv_coverage.cwl
deleted file mode 100644
index 813a2a21a63..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/normalize_sv_coverage.cwl
+++ /dev/null
@@ -1,224 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_coverage_rec:depth__bins__normalized;depth__bins__background;resources;description;depth__bins__target;depth__bins__antitarget;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_rawcoverage_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- normalize_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_rawcoverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rawcoverage_rec
-      type: record
-    type: array
-outputs:
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index d320e1afb86..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: reference__viral
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index ccdfc8e177e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,223 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1033
-  ramMin: 6144
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 1f033c9d3c7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,233 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index dd40cf1d9a4..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,180 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1025
-  ramMin: 6144
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_align_inputs.cwl
deleted file mode 100644
index cd325c5f774..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,145 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples.cwl
deleted file mode 100644
index 63d24367261..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,93 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index da7b1d7f2b0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,79 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=rgnames__sample:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - 'null'
-        - string
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/process_alignment.cwl
deleted file mode 100644
index af6768e2f88..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,201 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 7
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 4565b513de7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,308 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;metadata__phenotype;config__algorithm__tools_off;reference__viral;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,reference__viral:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__viral
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_sv.cwl
deleted file mode 100644
index 87f503d9117..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_sv.cwl
+++ /dev/null
@@ -1,228 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv__calls,sv__supplemental,sv__prioritize__tsv,sv__prioritize__raw,svvalidate__grading_summary,svvalidate__grading_plots
-- sentinel_inputs=sv_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1027
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: sv_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: sv__variantcaller
-          type:
-          - string
-          - 'null'
-        - name: sv__vrn_file
-          type:
-          - File
-          - 'null'
-        - name: sv__supplemental
-          type:
-            items:
-            - File
-            type: array
-        - name: svvalidate__summary
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type: File
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__sv_regions
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: svvalidate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index c560affeded..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,193 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index 7e8f1574bfc..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,266 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-alignment.cwl
deleted file mode 100644
index 3785183a8df..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-alignment.cwl
+++ /dev/null
@@ -1,146 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-svcall.cwl
deleted file mode 100644
index 01ae7b07f7a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-svcall.cwl
+++ /dev/null
@@ -1,310 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  outputSource: detect_sv/sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: detect_sv
-  in:
-  - id: sv_batch_rec
-    source: sv_batch_rec
-  out:
-  - id: sv_rec
-  run: steps/detect_sv.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-variantcall.cwl
deleted file mode 100644
index f7dd3955627..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,308 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json
deleted file mode 100644
index 1439ccade50..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json
+++ /dev/null
@@ -1,1059 +0,0 @@
-{
-    "expected_validation":
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/grading-summary-combined-expected.csv"
-        },
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__adapters": [
-        [
-            "polyx"
-        ],
-        [
-            "polyx"
-        ]
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__archive": [
-        null,
-        null
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        "{\"numpass\": 2}",
-        "{\"numpass\": 2}"
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
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diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
deleted file mode 100644
index c325ecade0b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
+++ /dev/null
@@ -1,997 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
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-    items:
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-- id: files
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-      items: File
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-- id: config__algorithm__trim_reads
-  type:
-    items: string
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-- id: reference__fasta__base
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-- id: config__algorithm__vcfanno
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-- id: config__algorithm__svprioritize
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-- id: resources
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-- id: config__algorithm__coverage_interval
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-- id: genome_resources__rnaseq__gene_bed
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-- id: genome_resources__variation__esp
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-- id: rgnames__rg
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-- id: rgnames__lane
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-- id: genome_resources__variation__lcr
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-    items: File
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-- id: config__algorithm__min_allele_fraction
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-    items: double
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-- id: config__algorithm__nomap_split_targets
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-- id: config__algorithm__bam_clean
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-- id: config__algorithm__validate
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-- id: variants__gvcf
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-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__archive
-    source: config__algorithm__archive
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__GRCh37_75
-    source: reference__snpeff__GRCh37_75
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: batch_for_ensemble
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: ensemble_prep_rec
-  run: steps/batch_for_ensemble.cwl
-- id: combine_calls
-  in:
-  - id: ensemble_prep_rec
-    source: batch_for_ensemble/ensemble_prep_rec
-  out:
-  - id: ensemble_rec
-  run: steps/combine_calls.cwl
-  scatter:
-  - ensemble_prep_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  - id: ensemble_rec
-    source: combine_calls/ensemble_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: calculate_sv_bins
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__seq2c_bed_ready
-    source: postprocess_alignment/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: sv_bin_rec
-  run: steps/calculate_sv_bins.cwl
-- id: calculate_sv_coverage
-  in:
-  - id: sv_bin_rec
-    source: calculate_sv_bins/sv_bin_rec
-  out:
-  - id: sv_rawcoverage_rec
-  run: steps/calculate_sv_coverage.cwl
-  scatter:
-  - sv_bin_rec
-  scatterMethod: dotproduct
-- id: normalize_sv_coverage
-  in:
-  - id: sv_rawcoverage_rec
-    source: calculate_sv_coverage/sv_rawcoverage_rec
-  out:
-  - id: sv_coverage_rec
-  run: steps/normalize_sv_coverage.cwl
-- id: batch_for_sv
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: work_bam_plus__disc
-    source: alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr
-    source: alignment/work_bam_plus__sr
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__svprioritize
-    source: config__algorithm__svprioritize
-  - id: config__algorithm__svvalidate
-    source: config__algorithm__svvalidate
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: genome_resources__variation__gc_profile
-    source: genome_resources__variation__gc_profile
-  - id: genome_resources__variation__germline_het_pon
-    source: genome_resources__variation__germline_het_pon
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__GRCh37_75
-    source: reference__snpeff__GRCh37_75
-  - id: sv_coverage_rec
-    source: normalize_sv_coverage/sv_coverage_rec
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  out:
-  - id: sv_batch_rec
-  run: steps/batch_for_sv.cwl
-- id: svcall
-  in:
-  - id: sv_batch_rec
-    source: batch_for_sv/sv_batch_rec
-  out:
-  - id: sv_rec
-  run: wf-svcall.cwl
-  scatter:
-  - sv_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_sv
-  in:
-  - id: sv_rec
-    source: svcall/sv_rec
-  out:
-  - id: sv__calls
-  - id: sv__supplemental
-  - id: sv__prioritize__tsv
-  - id: sv__prioritize__raw
-  - id: svvalidate__grading_summary
-  - id: svvalidate__grading_plots
-  run: steps/summarize_sv.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: reference__viral
-    source: reference__viral
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl
deleted file mode 100644
index 506764917f5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,194 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions;rgnames__pu
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items: string
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-          items: string
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      - name: rgnames__pu
-        type: string
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl
deleted file mode 100644
index df553e9e92f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl
+++ /dev/null
@@ -1,273 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=ensemble_prep_rec:batch_id;variants__calls;variants__variantcallers;resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__snpeff__GRCh37_75;reference__genome_context;reference__rtg;config__algorithm__validate;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_ensemble
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10240
-  ramMin: 3072
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__ensemble
-          type: string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: ensemble_prep_rec
-  type:
-    items:
-      fields:
-      - name: batch_id
-        type: string
-      - name: variants__calls
-        type:
-          items: File
-          type: array
-      - name: variants__variantcallers
-        type:
-          items: string
-          type: array
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: ensemble_prep_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl
deleted file mode 100644
index c25d67e007b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl
+++ /dev/null
@@ -1,363 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=sv_batch_rec:resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;reference__snpeff__GRCh37_75;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;work_bam_plus__disc;work_bam_plus__sr;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,work_bam_plus__disc:var,work_bam_plus__sr:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__svprioritize:var,config__algorithm__svvalidate:var,regions__sample_callable:var,genome_resources__variation__gc_profile:var,genome_resources__variation__germline_het_pon:var,genome_resources__aliases__snpeff:var,reference__snpeff__GRCh37_75:var,sv_coverage_rec:record,variants__samples:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10240
-  ramMin: 49152
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 3656
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__GRCh37_75
-  type:
-    items: File
-    type: array
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-outputs:
-- id: sv_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: work_bam_plus__disc
-          type:
-          - File
-          - 'null'
-        - name: work_bam_plus__sr
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type: File
-        - name: genome_resources__variation__encode_blacklist
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 6504ed26811..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,395 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;reference__snpeff__GRCh37_75;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;reference__rtg;config__algorithm__validate;genome_resources__variation__1000g;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__GRCh37_75:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10477
-  ramMin: 3072
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items: string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__GRCh37_75
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type: File
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type: File
-        - name: genome_resources__variation__encode_blacklist
-          type: File
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type: string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl
deleted file mode 100644
index bee219164db..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl
+++ /dev/null
@@ -1,219 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_bin_rec:regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;resources;description;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=align_bam:var,reference__fasta__base:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__svcaller:var,depth__variant_regions__regions:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__rnaseq__gene_bed:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_bins
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: sv_bin_rec
-  type:
-    items:
-      fields:
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_bin_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl
deleted file mode 100644
index 330224b83db..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl
+++ /dev/null
@@ -1,206 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=sv_rawcoverage_rec:depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;resources;description;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_bin_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-inputs:
-- id: sv_bin_rec
-  type:
-    fields:
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type: File
-    - name: genome_resources__variation__encode_blacklist
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_bin_rec
-    type: record
-outputs:
-- id: sv_rawcoverage_rec
-  type:
-    fields:
-    - name: depth__bins__target
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__seq2c
-      type:
-      - File
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type: File
-    - name: genome_resources__variation__encode_blacklist
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_rawcoverage_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl
deleted file mode 100644
index 7730a2a3223..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl
+++ /dev/null
@@ -1,180 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=ensemble_rec:ensemble__vrn_file;ensemble__validate__summary;ensemble__batch_samples;ensemble__batch_id
-- sentinel_inputs=ensemble_prep_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_calls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10240
-  ramMin: 49152
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4687
-- class: SoftwareRequirement
-  packages:
-  - package: bcbio-variation-recall
-    specs:
-    - https://anaconda.org/bioconda/bcbio-variation-recall
-inputs:
-- id: ensemble_prep_rec
-  type:
-    fields:
-    - name: batch_id
-      type: string
-    - name: variants__calls
-      type:
-        items: File
-        type: array
-    - name: variants__variantcallers
-      type:
-        items: string
-        type: array
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: batch_samples
-      type:
-      - 'null'
-      - items: string
-        type: array
-    - name: validate__summary
-      type:
-      - File
-      - 'null'
-    - name: validate__tp
-      type:
-      - File
-      - 'null'
-    - name: validate__fp
-      type:
-      - File
-      - 'null'
-    - name: validate__fn
-      type:
-      - File
-      - 'null'
-    - name: vrn_file
-      type: File
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__vcfanno
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__variantcaller
-      type: string
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: config__algorithm__min_allele_fraction
-      type: double
-    - name: reference__snpeff__GRCh37_75
-      type: File
-    - name: reference__genome_context
-      type:
-        items: File
-        type: array
-    - name: reference__rtg
-      type: File
-    - name: config__algorithm__validate
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__validate_regions
-      type:
-      - File
-      - 'null'
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__aliases__human
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__tools_off
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__ensemble
-      type: string
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__effects
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: genome_resources__aliases__ensembl
-      type: string
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: genome_resources__aliases__snpeff
-      type: string
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: regions__sample_callable
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: ensemble_prep_rec
-    type: record
-outputs:
-- id: ensemble_rec
-  type:
-    fields:
-    - name: ensemble__vrn_file
-      type:
-      - File
-      - 'null'
-    - name: ensemble__validate__summary
-      type:
-      - File
-      - 'null'
-    - name: ensemble__batch_samples
-      type:
-        items: string
-        type: array
-    - name: ensemble__batch_id
-      type: string
-    name: ensemble_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl
deleted file mode 100644
index e59fc89683e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10299
-  ramMin: 3072
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 3008
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl
deleted file mode 100644
index ed7c9b1e0b1..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,299 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__snpeff__GRCh37_75;reference__genome_context;reference__rtg;config__algorithm__validate;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index a5d59d661a0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,190 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl
deleted file mode 100644
index 66d592642d7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl
+++ /dev/null
@@ -1,402 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=sv_rec:sv__variantcaller;sv__vrn_file;sv__supplemental;svvalidate__summary;resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 3656
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: delly
-    specs:
-    - https://anaconda.org/bioconda/delly
-  - package: duphold
-    specs:
-    - https://anaconda.org/bioconda/duphold
-  - package: extract-sv-reads
-    specs:
-    - https://anaconda.org/bioconda/extract-sv-reads
-  - package: lumpy-sv
-    specs:
-    - https://anaconda.org/bioconda/lumpy-sv
-  - package: manta
-    specs:
-    - https://anaconda.org/bioconda/manta
-  - package: break-point-inspector
-    specs:
-    - https://anaconda.org/bioconda/break-point-inspector
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: smoove
-    specs:
-    - https://anaconda.org/bioconda/smoove
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-  - package: simple_sv_annotation
-    specs:
-    - https://anaconda.org/bioconda/simple_sv_annotation
-  - package: survivor
-    specs:
-    - https://anaconda.org/bioconda/survivor
-  - package: svtools
-    specs:
-    - https://anaconda.org/bioconda/svtools
-  - package: svtyper
-    specs:
-    - https://anaconda.org/bioconda/svtyper
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: xorg-libxt
-    specs:
-    - https://anaconda.org/bioconda/xorg-libxt
-  - package: vawk
-    specs:
-    - https://anaconda.org/bioconda/vawk
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl
deleted file mode 100644
index 71c08911610..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,165 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10477
-  ramMin: 3072
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl
deleted file mode 100644
index 4e139a4d748..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,165 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10655
-  ramMin: 49152
-  tmpdirMin: 208
-- class: dx:InputResourceRequirement
-  indirMin: 3127
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl
deleted file mode 100644
index 96036a07fc2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,94 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10477
-  ramMin: 3072
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: reference__versions
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl
deleted file mode 100644
index af33573637d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl
+++ /dev/null
@@ -1,224 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_coverage_rec:depth__bins__normalized;depth__bins__background;resources;description;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_rawcoverage_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- normalize_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_rawcoverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rawcoverage_rec
-      type: record
-    type: array
-outputs:
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl
deleted file mode 100644
index 4ffe2646ec9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,219 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;genome_build;config__algorithm__tools_off;reference__versions;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 3010
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-        items: string
-        type: array
-    - name: reference__versions
-      type: File
-    - name: reference__viral
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-        items: string
-        type: array
-    - name: reference__versions
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl
deleted file mode 100644
index 92f4acb8c7f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10596
-  ramMin: 49152
-  tmpdirMin: 178
-- class: dx:InputResourceRequirement
-  indirMin: 18018
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type: File
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type: File
-    - name: genome_resources__variation__encode_blacklist
-      type: File
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__archive
-      type:
-      - 'null'
-      - string
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 926d37e91df..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,237 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__archive;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__archive:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__archive
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__archive
-        type:
-        - 'null'
-        - string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl
deleted file mode 100644
index 5151f1520c6..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,174 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10299
-  ramMin: 49152
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl
deleted file mode 100644
index 5c392bdb350..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,139 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3127
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl
deleted file mode 100644
index 8e6d9500406..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10299
-  ramMin: 3072
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 3008
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 9ccaa591fde..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__svcaller;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=rgnames__sample:var,config__algorithm__svcaller:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10299
-  ramMin: 3072
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl
deleted file mode 100644
index 718e2cd14e0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl
+++ /dev/null
@@ -1,195 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 3246
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl
deleted file mode 100644
index 0336669ad83..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,307 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;metadata__batch;genome_build;metadata__phenotype;config__algorithm__tools_off;reference__versions;reference__viral;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,reference__viral:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .fai
-  - .ann
-  - .sa
-  - .pac
-  - .amb
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: reference__versions
-        type: File
-      - name: reference__viral
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl
deleted file mode 100644
index c5f8047d69a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl
+++ /dev/null
@@ -1,236 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv__calls,sv__supplemental,sv__prioritize__tsv,sv__prioritize__raw,svvalidate__grading_summary,svvalidate__grading_plots
-- sentinel_inputs=sv_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10358
-  ramMin: 3072
-  tmpdirMin: 59
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: bcbio-prioritize
-    specs:
-    - https://anaconda.org/bioconda/bcbio-prioritize
-inputs:
-- id: sv_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: sv__variantcaller
-          type:
-          - string
-          - 'null'
-        - name: sv__vrn_file
-          type:
-          - File
-          - 'null'
-        - name: sv__supplemental
-          type:
-            items:
-            - File
-            type: array
-        - name: svvalidate__summary
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type: File
-        - name: genome_resources__variation__encode_blacklist
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: svvalidate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl
deleted file mode 100644
index 48ec1cd601a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,212 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record,ensemble_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1000000
-  ramMin: 3072
-  tmpdirMin: 1000000
-- class: dx:InputResourceRequirement
-  indirMin: 1000000
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__ensemble
-          type: string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-- id: ensemble_rec
-  type:
-    items:
-      fields:
-      - name: ensemble__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: ensemble__validate__summary
-        type:
-        - File
-        - 'null'
-      - name: ensemble__batch_samples
-        type:
-          items: string
-          type: array
-      - name: ensemble__batch_id
-        type: string
-      name: ensemble_rec
-      type: record
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl
deleted file mode 100644
index a4fadb20991..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,260 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl
deleted file mode 100644
index 0f1dfd3dd81..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl
+++ /dev/null
@@ -1,140 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl
deleted file mode 100644
index f8724f9b0b9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl
+++ /dev/null
@@ -1,316 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  outputSource: detect_sv/sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: detect_sv
-  in:
-  - id: sv_batch_rec
-    source: sv_batch_rec
-  out:
-  - id: sv_rec
-  run: steps/detect_sv.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl
deleted file mode 100644
index fc5066d386e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl
+++ /dev/null
@@ -1,300 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file.test
deleted file mode 100644
index 98ddd1a832e..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: inline_file
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_inline_file
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/inline_file.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_inline_file.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file_custom_entryname.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file_custom_entryname.test
deleted file mode 100644
index 1164b6fdf2f..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file_custom_entryname.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: inline_file_custom_entryname
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_inline_file
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/inline_file_custom_entryname.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_inline_file.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string.test
deleted file mode 100644
index 4ec70064ffc..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: iwdr_input_string
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_input_string
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/input_string.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_input_string.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string_function.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string_function.test
deleted file mode 100644
index 1c7973b96d6..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string_function.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: iwdr_input_string_function
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_input_string_function
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/input_string_function.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_input_string_function.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/file_array_listing.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/file_array_listing.cwl
deleted file mode 100644
index 86fb7c060a3..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/file_array_listing.cwl
+++ /dev/null
@@ -1,26 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: iwdr_array_listing
-  class: CommandLineTool
-  baseCommand: ['ls']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing: $(inputs.files)
-
-  stdout: file_list
-  inputs:
-      - id: files
-        type:
-          type: array
-          items: File
-        default: [ "/Users/chrisl/Downloads/cwl/allRequirements.txt" ]
-  arguments: [ "*.txt" ]
-  outputs:
-      - id: file_list
-        type: string
-        outputBinding:
-          glob: file_list
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file.cwl
deleted file mode 100644
index 1980beb52d8..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file.cwl
+++ /dev/null
@@ -1,43 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_inline_file
-  class: CommandLineTool
-  baseCommand: ['python3', 'prime_sieve.py', '100']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: 'prime_sieve.py'
-              entry: |
-                  import sys
-                  import math
-
-                  limit = int(sys.argv[1])
-                  sieve = [True for i in range(limit)]
-                  for i in range(2, math.floor(limit / 2)):
-                      if sieve[i]:
-                          for j in range(i * 2, limit, i):
-                              sieve[j] = False
-
-                  result = "["
-                  for i in range(2, limit):
-                      if sieve[i]:
-                          if result != "[":
-                              result += ", "
-                          result += str(i)
-                  result += "]"
-
-                  print(result)
-
-  stdout: "primes"
-  inputs: []
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file_custom_entryname.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file_custom_entryname.cwl
deleted file mode 100644
index bff672a7e8a..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file_custom_entryname.cwl
+++ /dev/null
@@ -1,47 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_inline_file
-  class: CommandLineTool
-  baseCommand: ['python3']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: $(inputs.script_name)
-              entry: |
-                  import sys
-                  import math
-
-                  limit = int(sys.argv[1])
-                  sieve = [True for i in range(limit)]
-                  for i in range(2, math.floor(limit / 2)):
-                      if sieve[i]:
-                          for j in range(i * 2, limit, i):
-                              sieve[j] = False
-
-                  result = "["
-                  for i in range(2, limit):
-                      if sieve[i]:
-                          if result != "[":
-                              result += ", "
-                          result += str(i)
-                  result += "]"
-
-                  print(result)
-
-  stdout: "primes"
-  inputs:
-      - id: script_name
-        type: string
-        default: "astounding.py"
-  arguments: [ $(inputs.script_name), '100' ]
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string.cwl
deleted file mode 100644
index 286f6b7aedc..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string.cwl
+++ /dev/null
@@ -1,50 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_input_string
-  class: CommandLineTool
-  baseCommand: ['python3', 'prime_sieve.py', '100']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: $(inputs.script_name)
-              entry: $(inputs.script)
-
-  stdout: "primes"
-  inputs:
-      - id: script
-        type: string
-        default: |
-          import sys
-          import math
-
-          limit = int(sys.argv[1])
-          sieve = [True for i in range(limit)]
-          for i in range(2, math.floor(limit / 2)):
-              if sieve[i]:
-                  for j in range(i * 2, limit, i):
-                      sieve[j] = False
-
-          result = "["
-          for i in range(2, limit):
-              if sieve[i]:
-                  if result != "[":
-                      result += ", "
-                  result += str(i)
-          result += "]"
-
-          print(result)
-      - id: script_name
-        type: string
-        default: "prime_sieve.py"
-  arguments: [ $(inputs.script_name), '100' ]
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string_function.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string_function.cwl
deleted file mode 100644
index f70cd7bf8b9..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string_function.cwl
+++ /dev/null
@@ -1,49 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_input_string_function
-  class: CommandLineTool
-  baseCommand: ['python3']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: ${var result = inputs.script_name + ".py"; return result;}
-              entry: ${var scr = inputs.script; return scr + "print(result);"}
-
-  stdout: "primes"
-  inputs:
-      - id: script
-        type: string
-        default: |
-          import sys
-          import math
-
-          limit = int(sys.argv[1])
-          sieve = [True for i in range(limit)]
-          for i in range(2, math.floor(limit / 2)):
-              if sieve[i]:
-                  for j in range(i * 2, limit, i):
-                      sieve[j] = False
-
-          result = "["
-          for i in range(2, limit):
-              if sieve[i]:
-                  if result != "[":
-                      result += ", "
-                  result += str(i)
-          result += "]"
-
-      - id: script_name
-        type: string
-        default: "prime_sieve.py"
-  arguments: [ '${var result = inputs.script_name + ".py"; return result;}', '100' ]
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test.aws.test b/centaur/src/main/resources/standardTestCases/ad_hoc_file_test.aws.test
deleted file mode 100644
index 8016f90f665..00000000000
--- a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test.aws.test
+++ /dev/null
@@ -1,14 +0,0 @@
-name: ad_hoc_file_test.aws
-testFormat: workflowsuccess
-backends: [ AWSBATCH ]
-
-files {
-  workflow: ad_hoc_file_test/workflow.cwl
-  imports: [
-    ad_hoc_file_test/cwl-test.cwl
-  ]
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/cwl-test.cwl b/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/cwl-test.cwl
deleted file mode 100644
index 7ac312f6f3a..00000000000
--- a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/cwl-test.cwl
+++ /dev/null
@@ -1,21 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-baseCommand: ["sh", "example.sh"]
-hints:
-  DockerRequirement:
-    dockerPull: ubuntu:latest
-inputs: []
-
-requirements:
-  InitialWorkDirRequirement:
-    listing:
-      - entryname: example.sh
-        entry: |-
-          PREFIX='Message is:'
-          MSG="\${PREFIX} Hello world!"
-          echo \${MSG}
-
-outputs:
-  example_out:
-    type: stdout
-stdout: output.txt
diff --git a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/workflow.cwl b/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/workflow.cwl
deleted file mode 100644
index 678132165b2..00000000000
--- a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/workflow.cwl
+++ /dev/null
@@ -1,10 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs: []
-outputs: []
-
-steps:
-  test:
-    run: cwl-test.cwl
-    in: []
-    out: []
diff --git a/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json
new file mode 100644
index 00000000000..f004c8be647
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json
@@ -0,0 +1,3 @@
+{
+  "fileChecksum.inputFile": "https://<storage-account>.blob.core.windows.net/cromwell/user-inputs/inputFile.txt"
+}
diff --git a/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl
new file mode 100644
index 00000000000..b482f80d6e4
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl
@@ -0,0 +1,20 @@
+task md5 {
+    File inputFile
+    command {
+        echo "`date`: Running checksum on ${inputFile}..."
+        md5sum ${inputFile} > md5sum.txt
+        echo "`date`: Checksum is complete."
+    }
+    output {
+        File result = "md5sum.txt"
+    }
+    runtime {
+        docker: 'ubuntu:18.04'
+        preemptible: true
+    }
+}
+
+workflow fileChecksum {
+    File inputFile
+    call md5 { input: inputFile=inputFile}
+}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows.test b/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows.test
deleted file mode 100644
index e5381017829..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows.test
+++ /dev/null
@@ -1,19 +0,0 @@
-name: cwl_cache_between_workflows
-testFormat: runtwiceexpectingcallcaching
-workflowRoot: cwl-cache-between-workflows
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_cache_between_workflows/cwl_cache_between_workflows.cwl
-  inputs: cwl_cache_between_workflows/cwl_cache_between_workflows.json
-}
-
-metadata {
-  status: Succeeded
-  "calls.cwl-cache-between-workflows.step-average.callCaching.result": "Cache Hit: <<CACHE_HIT_UUID>>:cwl-cache-between-workflows.step-average:-1"
-  "calls.cwl-cache-between-workflows.step-product.callCaching.result": "Cache Hit: <<CACHE_HIT_UUID>>:cwl-cache-between-workflows.step-product:-1"
-  "outputs.cwl-cache-between-workflows.trapezoidalArea": 77.0,
-  "outputs.cwl-cache-between-workflows.baseAverage": 11.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.cwl b/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.cwl
deleted file mode 100644
index d48e74cd935..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.cwl
+++ /dev/null
@@ -1,79 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: average
-  class: CommandLineTool
-
-  inputs:
-    base1:
-      type: int
-      default: 9
-    base2:
-      type: int
-      default: 13
-
-  outputs:
-    baseAverage:
-      type: float
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseFloat(self[0].contents))
-
-  arguments:
-  - valueFrom: "echo $((inputs.base1 + inputs.base2) / 2)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-- id: height-product
-  class: CommandLineTool
-
-  inputs:
-    baseAverage: float
-    height:
-      type: float
-      default: 7.0
-
-  outputs:
-    trapezoidalArea:
-      type: long
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseFloat(self[0].contents))
-
-  arguments:
-  - valueFrom: "echo $(inputs.baseAverage * inputs.height)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-- id: cwl-cache-between-workflows
-  class: Workflow
-
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  - class: ShellCommandRequirement
-
-  inputs: []
-
-  outputs:
-    baseAverage:
-      type: float
-      outputSource: step-average/baseAverage
-    trapezoidalArea:
-      type: long
-      outputSource: step-product/trapezoidalArea
-
-  steps:
-    step-average:
-      run: "#average"
-      in: []
-      out: [baseAverage]
-
-    step-product:
-      run: "#height-product"
-      in:
-        baseAverage: step-average/baseAverage
-      out: [trapezoidalArea]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.json b/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.json
deleted file mode 100644
index 0967ef424bc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.json
+++ /dev/null
@@ -1 +0,0 @@
-{}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow.test b/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow.test
deleted file mode 100644
index 8ef753b494d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow.test
+++ /dev/null
@@ -1,26 +0,0 @@
-name: cwl_cache_within_workflow
-testFormat: workflowsuccess
-workflowRoot: cwl-cache-within-workflow
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_cache_within_workflow/cwl_cache_within_workflow.cwl
-  inputs: cwl_cache_within_workflow/cwl_cache_within_workflow.json
-}
-
-metadata {
-  status: Succeeded
-  "calls.cwl-cache-within-workflow.foo.callCaching.result": "Cache Miss"
-  "calls.cwl-cache-within-workflow.bar.callCaching.result": "Cache Miss"
-  "calls.cwl-cache-within-workflow.re-bar.callCaching.result": "Cache Hit: <<UUID>>:cwl-cache-within-workflow.bar:-1"
-  "calls.cwl-cache-within-workflow.bar.inputs.pi": 3.14159
-  "calls.cwl-cache-within-workflow.bar.inputs.rSquared": 16.23381791021144
-  "calls.cwl-cache-within-workflow.bar.outputs.area": 51
-  "calls.cwl-cache-within-workflow.bar.outputs.rSquaredCopy": 16.23381791021144
-  "calls.cwl-cache-within-workflow.re-bar.inputs.pi": 3.14159
-  "calls.cwl-cache-within-workflow.re-bar.inputs.rSquared": 16.23381791021144
-  "calls.cwl-cache-within-workflow.re-bar.outputs.area": 51
-  "calls.cwl-cache-within-workflow.re-bar.outputs.rSquaredCopy": 16.23381791021144
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.cwl b/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.cwl
deleted file mode 100644
index 15b1fd79a01..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.cwl
+++ /dev/null
@@ -1,129 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: one
-  class: CommandLineTool
-
-  inputs:
-    r:
-      type: float
-
-  outputs:
-    rSquared:
-      type: float
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseFloat(self[0].contents))
-    rCopy:
-      type: float
-      outputBinding:
-        outputEval: $(inputs.r)
-
-  arguments:
-  - valueFrom: "echo $(inputs.r * inputs.r)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-- id: two
-  class: CommandLineTool
-
-  inputs:
-    rSquared: float
-    pi: float
-
-  outputs:
-    area:
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    rSquaredCopy:
-      outputBinding:
-        outputEval: $(inputs.rSquared)
-      type: float
-
-  arguments:
-  - valueFrom: "echo $(inputs.rSquared * inputs.pi)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-# Throwing in some ExpressionTools for fun. Currently these not only don't cache but aren't even listed in the metadata
-# except in the original workflow blob (see #3499). The current thinking is that these should appear in metadata with a
-# call-like presentation but that they don't need to be eligible for caching since ExpressionTools are supposed to be
-# very lightweight and not worth the expense of hashing and potential cache hit copying.
-- id: three
-  class: ExpressionTool
-
-  inputs:
-    rSquared: float
-    pi: float
-
-  outputs:
-    area: int
-    rSquaredCopy: float
-
-  expression: |
-    ${
-    return {"area": parseInt(inputs.pi * inputs.rSquared),
-            "rSquaredCopy": inputs.rSquared };
-    }
-
-
-- id: cwl-cache-within-workflow
-  class: Workflow
-
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  - class: ShellCommandRequirement
-
-  inputs:
-    radius: float
-    pi: float
-
-  outputs:
-    area:
-      type: int
-      outputSource: re-bar/area
-    area-expression:
-      type: int
-      outputSource: re-baz/area
-
-  steps:
-    foo:
-      run: "#one"
-      in:
-        r: radius
-        pi: pi
-      out: [rSquared, rCopy]
-
-    bar:
-      run: "#two"
-      in:
-        rSquared: "foo/rSquared"
-        pi: pi
-      out: [area, rSquaredCopy]
-
-    re-bar:
-      run: "#two"
-      in:
-        rSquared: "bar/rSquaredCopy"
-        pi: pi
-      out: [area, rSquaredCopy]
-
-    baz:
-      run: "#three"
-      in:
-        rSquared: "foo/rSquared"
-        pi: pi
-      out: [area, rSquaredCopy]
-
-    re-baz:
-      run: "#three"
-      in:
-        rSquared: "baz/rSquaredCopy"
-        pi: pi
-      out: [area, rSquaredCopy]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.json b/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.json
deleted file mode 100644
index 563f2413547..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "radius": 4.029121233,
-  "pi": 3.14159
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_disk_resources_papiv2.test b/centaur/src/main/resources/standardTestCases/cwl_disk_resources_papiv2.test
deleted file mode 100644
index 8677bcf711e..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_disk_resources_papiv2.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_disk_resources_papiv2
-testFormat: workflowsuccess
-backends: [Papiv2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_resources/cwl_disk_resources.cwl
-}
-
-metadata {
-  status: Succeeded
-  "outputs.diskSizeTool.disk_size": 30
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: diskSizeTool
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size.test b/centaur/src/main/resources/standardTestCases/cwl_docker_size.test
deleted file mode 100644
index ca700d5cd9d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_docker_files
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_docker_size/cwl_docker_size.cwl
-  inputs: cwl_docker_size/cwl_docker_size.yaml
-  options: cwl_docker_size/cwl_docker_size.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.main.stdout_output": "execute order=66"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.cwl b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.cwl
deleted file mode 100644
index 5383bccb484..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.cwl
+++ /dev/null
@@ -1,40 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: main
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: INPUT
-      type: File[]
-  stdout: stdout
-  outputs:
-    stdout_output:
-      type: string
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: $(self[0].contents.trim())
-  arguments:
-    - valueFrom: |
-        ${
-          if (inputs.INPUT.length == 0) {
-            var cmd = ['echo', "no inputs"];
-            return cmd
-          }
-          else {
-            var cmd = ["echo", "execute"];
-            var use_input = [];
-            for (var i = 0; i < inputs.INPUT.length; i++) {
-              var filesize = inputs.INPUT[i].size;
-              use_input.push("order=".concat(filesize));
-            }
-
-            var run_cmd = cmd.concat(use_input);
-            return run_cmd
-          }
-
-        }
-  out: stdout
-  baseCommand: []
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.options b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.yaml b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.yaml
deleted file mode 100644
index 097e69e8590..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-INPUT:
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt
deleted file mode 100644
index 1a6374205aa..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt
+++ /dev/null
@@ -1 +0,0 @@
-And you people, you're all astronauts, on some kind of star trek.
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir.test b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir.test
deleted file mode 100644
index 57a69084c62..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir.test
+++ /dev/null
@@ -1,20 +0,0 @@
-name: cwl_dynamic_initial_workdir
-testFormat: workflowsuccess
-ignore: false
-workflowRoot: main
-workflowType: CWL
-workflowTypeVersion: v1.0
-backendsMode: "only"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl
-  inputs: cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs
-}
-
-metadata {
-  status: Succeeded
-  "outputs.main.sha": "13cda8661796ae241da3a18668fb552161a72592\n"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl
deleted file mode 100644
index 6012854d0b7..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl
+++ /dev/null
@@ -1,29 +0,0 @@
-cwlVersion: v1.0
-$graph:
-  id: main
-  class: CommandLineTool
-  cwlVersion: v1.0
-  requirements:
-    - class: ShellCommandRequirement
-    - class: InitialWorkDirRequirement
-      listing: $(inputs.indir.listing)
-    - class: DockerRequirement
-      dockerPull: "ubuntu:latest"
-  inputs:
-    indir: Directory
-  outputs:
-    sha:
-      type: string
-      outputBinding:
-        glob: output.txt
-        loadContents: true
-        outputEval: $(self[0].contents)
-  arguments: ["find", "-L", ".", "-name", "?",
-    {shellQuote: false, valueFrom: "|"},
-    "sort",
-    {shellQuote: false, valueFrom: "|"},
-    "sha1sum",
-    {shellQuote: false, valueFrom: "|"},
-    "cut", "-c", "1-40"
-  ]
-  stdout: output.txt
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs
deleted file mode 100644
index f37fed14367..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs
+++ /dev/null
@@ -1,3 +0,0 @@
-indir:
-  class: Directory
-  location: centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/a b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/a
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/b b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/b
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/c/d b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/c/d
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.cwl b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.cwl
deleted file mode 100644
index c2079a82721..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.cwl
+++ /dev/null
@@ -1,25 +0,0 @@
-cwlVersion: v1.0
-$namespaces:
-  edam: http://edamontology.org/
-  gx: http://galaxyproject.org/formats/
-$schemas:
-  - file:./cwl/src/test/resources/cwl/ontology/EDAM.owl
-  - file:./cwl/src/test/resources/cwl/ontology/gx_edam.ttl
-$graph:
-- id: main
-  class: CommandLineTool
-  cwlVersion: v1.0
-  inputs:
-    - id: reference
-      type: File
-      format: gx:fasta
-      inputBinding: { position: 2 }
-  outputs:
-    - id: lineCount
-      type: int
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: "$(parseInt(self[0].contents))"
-  baseCommand: ["wc", "-l"]
-  stdout: stdout
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.options b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_invalid.yaml b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_invalid.yaml
deleted file mode 100644
index 6e75ae34f28..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_invalid.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Try to pass a fastq in as a fasta
-reference:
-  class: File
-  format: edam:format_1930
-  path: "centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_missing.yaml b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_missing.yaml
deleted file mode 100644
index 4e8a35cb2e9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_missing.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Pass a fastq in as a fasta, but without passing the format
-reference:
-  class: File
-  #format: edam:format_1930
-  path: "centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl
deleted file mode 100644
index b85bf8d2434..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl
+++ /dev/null
@@ -1,27 +0,0 @@
-cwlVersion: v1.0
-$namespaces:
-  edam: http://edamontology.org/
-  gx: http://galaxyproject.org/formats/
-$schemas:
-  # Relative path:
-  - ../../../../../../cwl/src/test/resources/cwl/ontology/EDAM.owl
-  # Absolute (remote) path:
-  - https://raw.githubusercontent.com/broadinstitute/cromwell/develop/cwl/src/test/resources/cwl/ontology/gx_edam.ttl
-$graph:
-- id: main
-  class: CommandLineTool
-  cwlVersion: v1.0
-  inputs:
-    - id: reference
-      type: File
-      format: gx:fasta
-      inputBinding: { position: 2 }
-  outputs:
-    - id: lineCount
-      type: int
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: "$(parseInt(self[0].contents))"
-  baseCommand: ["wc", "-l"]
-  stdout: stdout
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_valid.yaml b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_valid.yaml
deleted file mode 100644
index b598f92b7e1..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_valid.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Pass in a valid input file format
-reference:
-  class: File
-  format: edam:format_1929
-  path: "centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta b/centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta
deleted file mode 100644
index e91d1521810..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->sequence #1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq b/centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq
deleted file mode 100644
index 5ecec0ebec8..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq
+++ /dev/null
@@ -1,4 +0,0 @@
-@SEQ_ID
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
-+
-!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_invalid.test b/centaur/src/main/resources/standardTestCases/cwl_format_invalid.test
deleted file mode 100644
index 43962bb5bfc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_invalid.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_invalid
-testFormat: workflowfailure
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_format/cwl_format.cwl
-  inputs: cwl_format/cwl_format_invalid.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "failures.0.message": "Workflow input processing failed"
-  "failures.0.causedBy.0.message": "Failed to evaluate input 'reference' (reason 1 of 1): edam:format_1930 is not compatible with http://galaxyproject.org/formats/fasta"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_missing.test b/centaur/src/main/resources/standardTestCases/cwl_format_missing.test
deleted file mode 100644
index a7b626f69e4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_missing.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_missing
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_format/cwl_format.cwl
-  inputs: cwl_format/cwl_format_missing.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "workflowName": "main"
-  "outputs.main.lineCount": "4"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_valid.test b/centaur/src/main/resources/standardTestCases/cwl_format_valid.test
deleted file mode 100644
index 6a6452deff5..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_valid.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_valid
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_format/cwl_format.cwl
-  inputs: cwl_format/cwl_format_valid.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "workflowName": "main"
-  "outputs.main.lineCount": "2"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_valid_with_workflow_url.test b/centaur/src/main/resources/standardTestCases/cwl_format_valid_with_workflow_url.test
deleted file mode 100644
index e587dbfe6d6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_valid_with_workflow_url.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_valid_with_workflow_url
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflowUrl: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl"
-  inputs: cwl_format/cwl_format_valid.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "workflowName": "main"
-  "outputs.main.lineCount": "2"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_glob_sort.test b/centaur/src/main/resources/standardTestCases/cwl_glob_sort.test
deleted file mode 100644
index 04856ab66b9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_glob_sort.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: cwl_glob_sort
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: globSort
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_glob_sort/cwl_glob_sort.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.globSort.letters": "a b c w x y z"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl b/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl
deleted file mode 100644
index 8d54af1c040..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl
+++ /dev/null
@@ -1,19 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: globSort
-  cwlVersion: v1.0
-  class: CommandLineTool
-  requirements:
-    - class: InlineJavascriptRequirement
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs: []
-  baseCommand: [touch, z, y, x, w, c, b, a]
-  outputs:
-    letters:
-      type: string
-      outputBinding:
-        glob: '?'
-        outputEval: |
-          ${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(" ") }
diff --git a/centaur/src/main/resources/standardTestCases/cwl_glob_sort_with_workflow_url.test b/centaur/src/main/resources/standardTestCases/cwl_glob_sort_with_workflow_url.test
deleted file mode 100644
index 6e7ed2b1dd2..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_glob_sort_with_workflow_url.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: cwl_glob_sort_with_workflow_url
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: globSort
-skipDescribeEndpointValidation: true
-
-files {
-  workflowUrl: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl"
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.globSort.letters": "a b c w x y z"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type.test b/centaur/src/main/resources/standardTestCases/cwl_import_type.test
deleted file mode 100644
index 9e530a95469..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type.test
+++ /dev/null
@@ -1,14 +0,0 @@
-name: cwl_import_type
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_import_type/test_wf.cwl
-  inputs: cwl_import_type/test_wf_inputs.json
-  imports: [
-    cwl_import_type/capture_kit.yml,
-    cwl_import_type/touch.cwl
-  ]
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/capture_kit.yml b/centaur/src/main/resources/standardTestCases/cwl_import_type/capture_kit.yml
deleted file mode 100644
index 4323dd90f6d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/capture_kit.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-- name: capture_kit
-  type: record
-  fields:
-    - name: bait
-      type: string
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf.cwl b/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf.cwl
deleted file mode 100644
index 3658ab127d0..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf.cwl
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
-
-class: Workflow
-
-requirements:
-  - class: SchemaDefRequirement
-    types:
-      - $import: capture_kit.yml
-
-inputs:
-  - id: bam
-    type: string
-  - id: capture_kit
-    type: capture_kit.yml#capture_kit
-
-outputs:
-  - id: output_bam
-    type: File
-    outputSource: touch_bam/output
-
-steps:
-  - id: touch_bam
-    run: touch.cwl
-    in:
-      - id: input
-        source: bam
-    out:
-      - id: output
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf_inputs.json b/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf_inputs.json
deleted file mode 100644
index 55141261811..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf_inputs.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "bam": "a.bam",
-    "capture_kit": {
-        "bait": "abait"
-    }
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/touch.cwl b/centaur/src/main/resources/standardTestCases/cwl_import_type/touch.cwl
deleted file mode 100644
index 8a0be057c42..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/touch.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
-
-requirements:
-  - class: DockerRequirement
-    dockerPull: ubuntu:bionic-20180426
-
-class: CommandLineTool
-
-inputs:
-  - id: input
-    type: string
-    inputBinding:
-      position: 0
-
-outputs:
-  - id: output
-    type: File
-    outputBinding:
-      glob: $(inputs.input)
-      
-baseCommand: [touch]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed.test b/centaur/src/main/resources/standardTestCases/cwl_import_type_packed.test
deleted file mode 100644
index 0a3fd7c20a4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed.test
+++ /dev/null
@@ -1,11 +0,0 @@
-name: cwl_import_type_packed
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_import_type_packed/test_pack.cwl
-  inputs: cwl_import_type_packed/test_wf_inputs.json
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_pack.cwl b/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_pack.cwl
deleted file mode 100644
index 4150b5a5796..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_pack.cwl
+++ /dev/null
@@ -1,91 +0,0 @@
-{
-    "cwlVersion": "v1.0", 
-    "$graph": [
-        {
-            "inputs": [
-                {
-                    "type": "string", 
-                    "id": "#main/bam"
-                }, 
-                {
-                    "type": "#capture_kit.yml/capture_kit", 
-                    "id": "#main/capture_kit"
-                }
-            ], 
-            "requirements": [
-                {
-                    "class": "SchemaDefRequirement", 
-                    "types": [
-                        {
-                            "fields": [
-                                {
-                                    "type": "string", 
-                                    "name": "#capture_kit.yml/capture_kit/bait"
-                                }
-                            ], 
-                            "type": "record", 
-                            "name": "#capture_kit.yml/capture_kit"
-                        }
-                    ]
-                }
-            ], 
-            "outputs": [
-                {
-                    "outputSource": "#main/touch_bam/output", 
-                    "type": "File", 
-                    "id": "#main/output_bam"
-                }
-            ], 
-            "class": "Workflow", 
-            "steps": [
-                {
-                    "out": [
-                        {
-                            "id": "#main/touch_bam/output"
-                        }
-                    ], 
-                    "run": "#touch.cwl", 
-                    "id": "#main/touch_bam", 
-                    "in": [
-                        {
-                            "source": "#main/bam", 
-                            "id": "#main/touch_bam/input"
-                        }
-                    ]
-                }
-            ], 
-            "id": "#main"
-        }, 
-        {
-            "inputs": [
-                {
-                    "inputBinding": {
-                        "position": 0
-                    }, 
-                    "type": "string", 
-                    "id": "#touch.cwl/input"
-                }
-            ], 
-            "requirements": [
-                {
-                    "dockerPull": "ubuntu:bionic-20180426", 
-                    "class": "DockerRequirement"
-                }
-            ], 
-            "outputs": [
-                {
-                    "outputBinding": {
-                        "glob": "$(inputs.input)"
-                    }, 
-                    "type": "File", 
-                    "id": "#touch.cwl/output"
-                }
-            ], 
-            "baseCommand": [
-                "touch"
-            ], 
-            "class": "CommandLineTool", 
-            "id": "#touch.cwl"
-        }
-    ]
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_wf_inputs.json b/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_wf_inputs.json
deleted file mode 100644
index 55141261811..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_wf_inputs.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "bam": "a.bam",
-    "capture_kit": {
-        "bait": "abait"
-    }
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression.test b/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression.test
deleted file mode 100644
index 0e39f78ce78..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_input_binding_expression
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_input_binding_expression
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_input_binding_expression/cwl_input_binding_expression.cwl
-  inputs: cwl_input_binding_expression/cwl_input_binding_expression.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.cwl_input_binding_expression.b": "hello world"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.cwl b/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.cwl
deleted file mode 100644
index f534adfaa36..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.cwl
+++ /dev/null
@@ -1,25 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: cwl_input_binding_expression
-  class: CommandLineTool
-  requirements:
-    - class: InlineJavascriptRequirement
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: hello
-      type: string
-      inputBinding:
-        valueFrom: $(self + " world")
-        position: 1
-  outputs:
-    b:
-      type: string
-      outputBinding:
-        loadContents: true
-        glob: stdout
-        outputEval: $(self[0].contents.trim())
-  stdout: stdout
-  baseCommand: []
-  arguments: [echo]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.json b/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.json
deleted file mode 100644
index 8920ee8d630..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "hello": "hello"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_json.test b/centaur/src/main/resources/standardTestCases/cwl_input_json.test
deleted file mode 100644
index 1dd81ba8260..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_json.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_input_json
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-backendsMode: "only"
-workflowRoot: cwl_input_json
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_input_json/cwl_input_json.yaml
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_json/cwl_input_json.yaml b/centaur/src/main/resources/standardTestCases/cwl_input_json/cwl_input_json.yaml
deleted file mode 100644
index f6e5616c6c4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_json/cwl_input_json.yaml
+++ /dev/null
@@ -1,70 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: cwl_input_json
-  class: Workflow
-  inputs: []
-  outputs:
-    final_output:
-      type: File
-      outputSource: round/output_file
-  steps:
-    make:
-      run: "#makefile"
-      in: []
-      out: [fileoutput]
-    round:
-      run: "#roundtrip"
-      in:
-        input_record: 
-          source: "make/fileoutput"
-      out: [output_file]
-          
-- id: makefile
-  class: CommandLineTool
-  requirements:
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  inputs: []
-  outputs:
-    fileoutput:
-      type:
-        fields:
-        - name: input_file
-          type: File
-        name: input_record
-        type: record
-  arguments:
-    - valueFrom: >
-         echo foo > foo && echo '{ "fileoutput": { "input_file": {"path": "$(runtime.outdir)/foo", "class": "File"} } }' > cwl.output.json
-      shellQuote: false
-
-- id: roundtrip
-  class: CommandLineTool
-  hints:
-  - class: DockerRequirement
-    dockerPull: "stedolan/jq:latest"
-  inputs:
-  - id: input_record
-    type:
-      fields:
-      - name: input_file
-        type: File
-      name: input_record
-      type: record
-  outputs:
-  - id: output_file
-    type: File
-  requirements:
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: InitialWorkDirRequirement
-    listing:
-    - entry: $(JSON.stringify(inputs))
-      entryname: cwl.inputs.json
-  arguments:
-  # Round-trips the file referenced in cwl.input.json to cwl.output.json. Also ls it in the command to make sure it's there.
-    - valueFrom: >
-         INPUT_FILE=\$(cat cwl.inputs.json | jq -r '.. | .path? // empty') && ls $INPUT_FILE && echo "{\"output_file\": {\"path\": \"\$INPUT_FILE\", \"class\": \"File\"} }" > cwl.output.json
-      shellQuote: false
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray.test b/centaur/src/main/resources/standardTestCases/cwl_input_typearray.test
deleted file mode 100644
index a87bcbf9f65..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_typearray.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_input_typearray
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: input_typearray
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_input_typearray/input_typearray.cwl
-  inputs: cwl_input_typearray/input_typearray.yml
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.input_typearray.response_f": "input.txt"
-  "outputs.input_typearray.response_s": "nonexistent_path.txt"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input.txt b/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.cwl b/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.cwl
deleted file mode 100644
index 897b74822e8..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.cwl
+++ /dev/null
@@ -1,42 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: input_typearray
-  cwlVersion: v1.0
-  class: CommandLineTool
-  baseCommand: ['/bin/echo']
-  stdout: "response.txt"
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  - class: InlineJavascriptRequirement
-  arguments:
-      - position: 3
-        valueFrom: "sentinel"
-  inputs:
-    value_f:
-      type:
-        - string
-        - File
-      inputBinding:
-        position: 1
-      doc: "an input to test with a File value"
-    value_s:
-      type:
-        - string
-        - File
-      inputBinding:
-        position: 2
-      doc: "an input to test with a string value"
-  outputs:
-    response_f:
-      type: string
-      outputBinding:
-        glob: response.txt
-        loadContents: true
-        outputEval: $(self[0].contents.split(" ")[0].split("/").slice(-1)[0])
-    response_s:
-      type: string
-      outputBinding:
-        glob: response.txt
-        loadContents: true
-        outputEval: $(self[0].contents.split(" ")[1].split("/").slice(-1)[0])
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.yml b/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.yml
deleted file mode 100644
index 421402d9289..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-value_f:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_input_typearray/input.txt"
-value_s: "centaur/src/main/resources/standardTestCases/cwl_input_typearray/nonexistent_path.txt"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_inputdir_zero_doesnt_localize_papiv2.test b/centaur/src/main/resources/standardTestCases/cwl_inputdir_zero_doesnt_localize_papiv2.test
deleted file mode 100644
index 564633779a7..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_inputdir_zero_doesnt_localize_papiv2.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_inputdir_zero_doesnt_localize_papiv2
-testFormat: workflowsuccess
-backends: [Papiv2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl
-}
-
-metadata {
-  status: Succeeded
-  "outputs.inputdir_zero_doesnt_localize.errors": ""
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: inputdir_zero_doesnt_localize
diff --git a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings.test b/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings.test
deleted file mode 100644
index 89399e2e8fc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_interpolated_strings
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: interpolatedStrings
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_interpolated_strings/cwl_interpolated_strings.cwl
-  inputs: cwl_interpolated_strings/cwl_interpolated_strings.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.interpolatedStrings.rfc3092": "foo bar baz qux quux"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.cwl b/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.cwl
deleted file mode 100644
index e650061a5cc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.cwl
+++ /dev/null
@@ -1,25 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: interpolatedStrings
-  class: CommandLineTool
-  cwlVersion: v1.0
-  requirements:
-    - class: ShellCommandRequirement
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-
-  inputs:
-    - id: bar
-      type: string
-    - id: qux
-      type: string
-
-  outputs:
-    - id: rfc3092
-      type: string
-
-  arguments:
-     - valueFrom: >
-         echo '{ "rfc3092": "foo $(inputs.bar) baz $(inputs.qux) quux" }' > cwl.output.json
-       shellQuote: false
diff --git a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.json b/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.json
deleted file mode 100644
index 3f1bcedd11f..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.json
+++ /dev/null
@@ -1 +0,0 @@
-{"bar": "bar", "qux": "qux"}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_optionals.test b/centaur/src/main/resources/standardTestCases/cwl_optionals.test
deleted file mode 100644
index 2d945f36ee0..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_optionals.test
+++ /dev/null
@@ -1,13 +0,0 @@
-name: cwl_optionals
-testFormat: workflowsuccess
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_optionals/cwl_optionals.cwl
-  inputs: cwl_optionals/cwl_optionals.json
-}
-
-metadata {
-  "actualWorkflowLanguage": CWL
-  "actualWorkflowLanguageVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.cwl b/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.cwl
deleted file mode 100755
index 592227bf025..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.cwl
+++ /dev/null
@@ -1,12 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-hints:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-baseCommand: echo
-inputs:
-  message:
-    type: string[]?
-  unsupplied_optional:
-    type: string[]?
-outputs: []
diff --git a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.json b/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.json
deleted file mode 100644
index c76e98d49c3..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.json
+++ /dev/null
@@ -1 +0,0 @@
-{"message": ["foo","bar"]}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.cwl b/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.cwl
deleted file mode 100644
index 406301e7ecb..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.cwl
+++ /dev/null
@@ -1,34 +0,0 @@
-cwlVersion: v1.0
-$graph:  
-- id: outputJson
-  # slightly modified version of conformance test #2 to remove the default File that doesn't work on PAPI
-  # It is instead being passed as an input through the input json file
-  class: CommandLineTool
-  cwlVersion: v1.0
-  hints:
-    - class: DockerRequirement
-      dockerPull: python:2-slim
-  inputs:
-    - id: reference
-      type: File
-      inputBinding: { position: 2 }
-  
-    - id: reads
-      type:
-        type: array
-        items: File
-        inputBinding: { prefix: "-YYY" }
-      inputBinding: { position: 3, prefix: "-XXX" }
-  
-    - id: "args.py"
-      type: File
-      inputBinding:
-        position: -1
-  
-  outputs:
-    # note the absence of any sort of valueFrom.
-    # The output value is generated from the "cwl.output.json" file created by the python script
-    args: string[]
-  
-  baseCommand: python
-  arguments: ["bwa", "mem"]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.inputs b/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.inputs
deleted file mode 100644
index d83a30872a9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.inputs
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-    "args.py": {
-      "class": "File",
-      "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/args.py"
-    },
-    "reference": {
-        "class": "File",
-        "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/chr20.fa",
-        "size": 123,
-        "checksum": "sha1$hash"
-    },
-    "reads": [
-        {
-            "class": "File",
-            "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/example_human_Illumina.pe_1.fastq"
-        },
-        {
-            "class": "File",
-            "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/example_human_Illumina.pe_2.fastq"
-        }
-    ]
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_output_json_jes.test b/centaur/src/main/resources/standardTestCases/cwl_output_json_jes.test
deleted file mode 100644
index c7ddf584bd4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_output_json_jes.test
+++ /dev/null
@@ -1,25 +0,0 @@
-name: cwl_output_json_jes
-testFormat: workflowsuccess
-backends: [Papi]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_output_json/cwl_output_json.cwl
-  inputs: cwl_output_json/cwl_output_json.inputs
-}
-
-metadata {
-  status: Succeeded
-  "outputs.outputJson.args.0": "bwa"
-  "outputs.outputJson.args.1": "mem"
-  "outputs.outputJson.args.2": "chr20.fa"
-  "outputs.outputJson.args.3": "-XXX"
-  "outputs.outputJson.args.4": "-YYY"
-  "outputs.outputJson.args.5": "example_human_Illumina.pe_1.fastq"
-  "outputs.outputJson.args.6": "-YYY"
-  "outputs.outputJson.args.7": "example_human_Illumina.pe_2.fastq"
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: outputJson
diff --git a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array.test b/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array.test
deleted file mode 100644
index cea66a37026..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_prefix_for_array
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: prefix-for-array
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_prefix_for_array/prefix_for_array.cwl
-  inputs: cwl_prefix_for_array/prefix_for_array.yml
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.prefix-for-array.out": "--bonus first second\n"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.cwl b/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.cwl
deleted file mode 100644
index ca9044e5c61..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: prefix-for-array
-  cwlVersion: v1.0
-  class: CommandLineTool
-  baseCommand: ['/bin/echo']
-  stdout: "hello.txt"
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  inputs:
-      bonus:
-          type: string[]
-          inputBinding:
-              prefix: "--bonus"
-  outputs:
-    out:
-      type: string
-      outputBinding:
-        glob: hello.txt
-        loadContents: true
-        outputEval: $(self[0].contents)
-
diff --git a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.yml b/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.yml
deleted file mode 100644
index 6a3badb824c..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.yml
+++ /dev/null
@@ -1 +0,0 @@
-bonus: ["first", "second"]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories.test b/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories.test
deleted file mode 100644
index 390c1d66409..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_recursive_link_directories
-testFormat: workflowsuccess
-backends: [Local]
-backendsMode: only
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_recursive_link_directories/cwl_recursive_link_directories.cwl
-}
-
-metadata {
-  status: Succeeded
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_recursive_link_directories
diff --git a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories/cwl_recursive_link_directories.cwl b/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories/cwl_recursive_link_directories.cwl
deleted file mode 100644
index a4a19fd6a5d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories/cwl_recursive_link_directories.cwl
+++ /dev/null
@@ -1,19 +0,0 @@
-cwlVersion: v1.0
-$graph:  
-- id: cwl_recursive_link_directories
-  class: CommandLineTool
-  requirements:
-    - class: ShellCommandRequirement
-  cwlVersion: v1.0
-  hints:
-    - class: DockerRequirement
-      dockerPull: ubuntu:latest
-  inputs: []
-  outputs:
-    output_dir:
-        type: Directory
-        outputBinding:
-          glob: work_dir
-  arguments:
-    - shellQuote: false
-      valueFrom: "mkdir work_dir && ln -s .. work_dir/link"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/cwl_glob_sort.cwl b/centaur/src/main/resources/standardTestCases/cwl_relative_imports/cwl_glob_sort.cwl
deleted file mode 100644
index 330c896eea6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/cwl_glob_sort.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-requirements:
-  - class: InlineJavascriptRequirement
-hints:
-  DockerRequirement:
-    dockerPull: "debian:stretch-slim"
-inputs: []
-baseCommand: [touch, z, y, x, w, c, b, a]
-outputs:
-  letters:
-    type: string
-    outputBinding:
-      glob: '?'
-      outputEval: |
-        ${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(" ") }
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl b/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl
deleted file mode 100644
index 0ba8fc7236d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: relative_imports
-  class: Workflow
-
-  inputs: []
-  outputs:
-    letters:
-      type: string
-      outputSource: globSort/letters
-
-  steps:
-    globSort:
-      in: []
-      run: cwl_glob_sort.cwl
-      out: [letters]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_url.test b/centaur/src/main/resources/standardTestCases/cwl_relative_imports_url.test
deleted file mode 100644
index eabd10754f6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_url.test
+++ /dev/null
@@ -1,20 +0,0 @@
-name: cwl_relative_imports_url
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: relative_imports
-skipDescribeEndpointValidation: true
-# This test has experienced sporadic failures, and CWL is not fully supported. Therefore the test is being disabled.
-ignore: true
-
-files {
-  workflowUrl: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl"
-}
-
-metadata {
-  status: Succeeded
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.relative_imports.globSort.outputs.letters": "a b c w x y z"
-  "outputs.relative_imports.letters": "a b c w x y z"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_zip.test b/centaur/src/main/resources/standardTestCases/cwl_relative_imports_zip.test
deleted file mode 100644
index deccb8d73a3..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_zip.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_relative_imports_zip
-testFormat: workflowsuccess
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_relative_imports/workflow.cwl
-  imports: [
-    cwl_relative_imports/cwl_glob_sort.cwl
-  ]
-}
-
-metadata {
-  status: Succeeded
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.relative_imports.globSort.outputs.letters": "a b c w x y z"
-  "outputs.relative_imports.letters": "a b c w x y z"
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: relative_imports
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_disk_resources.cwl b/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_disk_resources.cwl
deleted file mode 100644
index 683dd5b17e6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_disk_resources.cwl
+++ /dev/null
@@ -1,38 +0,0 @@
-cwlVersion: v1.0
-# Asks for 10 GB (~=10240 MB) of output dir, tmp dir and input dir.
-# Unfortunately the internal metadata from the VM, despite having some information about the disks doesn't give their size.
-# To avoid possibly unreliable computations based on free or other tool, instead use the GCE API directly to look up the disk info.
-# To do that we need project name, zone and name of the disk which we all obtain via the internal metadata
-# Of importance is the assumption that <disk name> == <instance name>-1
-# Note the "-1" after the instance name. That is because the disk just named <instance name> is the boot disk. The working disk has a "-1" suffix
-# The test expectation ensures that the output is 30, which means all 3 resources have been taken into account.
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-$graph:  
-- id: diskSizeTool
-  class: CommandLineTool
-  cwlVersion: v1.0
-  doc: "Asks for disk minimums"
-  requirements:
-    ResourceRequirement:
-      outdirMin: 10240
-      tmpdirMin: 10240
-  hints:
-  - class: ShellCommandRequirement
-  - class: DockerRequirement
-    dockerPull: gcr.io/google.com/cloudsdktool/cloud-sdk:slim
-  - class: dx:InputResourceRequirement
-    indirMin: 10240
-  inputs: []
-  outputs:
-    disk_size:
-      type: int
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents.trim()))
-  arguments:
-    - valueFrom: >
-        apt-get install --assume-yes jq > /dev/null && NAME=`curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/name` && ZONE=`basename \`curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/zone\`` && PROJECT=`curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/project/project-id` && curl -s -H "Authorization: Bearer `gcloud auth print-access-token`" "https://www.googleapis.com/compute/v1/projects/${PROJECT}/zones/${ZONE}/disks/${NAME}-1?fields=sizeGb" | jq -r '.sizeGb'
-      shellQuote: false
-  stdout: stdout
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl b/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl
deleted file mode 100644
index d874ee0bffb..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl
+++ /dev/null
@@ -1,129 +0,0 @@
-cwlVersion: v1.0
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-$graph:
-- id: inputdir_zero_doesnt_localize
-  class: Workflow
-  hints:
-  - class: ShellCommandRequirement
-  - class: DockerRequirement
-    dockerPull: gcr.io/google.com/cloudsdktool/cloud-sdk:slim
-  - class: dx:InputResourceRequirement
-    indirMin: 0
-  inputs: []
-  outputs:
-  - id: errors
-    type: File
-    outputSource: findFile/errors
-  steps:
-  - id: echo
-    in: []
-    out:
-    - id: echoOut
-    - id: echoArrayOut
-    - id: echoRecordOut
-    - id: echoMaybeOut
-    run:
-      class: CommandLineTool
-      inputs: []
-      outputs:
-      - id: echoOut
-        outputBinding:
-          glob: lonely_file
-        type: File
-        secondaryFiles: [.also]
-      - id: echoArrayOut
-        outputBinding:
-          glob: '*.txt*'
-          outputEval: $([self[0]])  
-        type:
-          items: File
-          type: array
-      - id: echoRecordOut
-        secondaryFiles: [.also]
-        type:
-          type: record
-          name: foo
-          fields:
-            - name: a
-              type: File
-              outputBinding:
-                glob: file_in_object
-      - id: echoMaybeOut
-        type: 
-        - File
-        - 'null'
-        secondaryFiles: [.also]
-        outputBinding:
-          glob: maybe_file
-      arguments:
-       - valueFrom: |
-           echo "lonely_file" > lonely_file
-           echo "lonely_file.also" > lonely_file.also
-           echo "file_in_array.txt" > file_in_array.txt
-           echo "file_in_array.txt.also" > file_in_array.txt.also
-           echo "file_in_object" > file_in_object
-           echo "file_in_object.also" > file_in_object.also
-           echo "maybe_file" > maybe_file
-           echo "maybe_file.also" > maybe_file.also
-         shellQuote: false
-  - id: findFile
-    in:
-    - id: f
-      source: "#inputdir_zero_doesnt_localize/echo/echoOut"
-    - id: g
-      source: "#inputdir_zero_doesnt_localize/echo/echoArrayOut"
-    - id: h
-      source: "#inputdir_zero_doesnt_localize/echo/echoRecordOut"
-    - id: i
-      source: "#inputdir_zero_doesnt_localize/echo/echoMaybeOut"
-    out:
-    - id: errors
-    run:
-      inputs:
-      - id: f
-        type: File
-        secondaryFiles: [.also]
-      - id: i
-        type: File?
-        secondaryFiles: [.also]
-      - id: g
-        type:
-          type: array
-          items: File
-        secondaryFiles: [.also]
-      - id: h
-        secondaryFiles: [.also]
-        type:
-          type: record
-          name: foo
-          fields:
-            - name: a
-              type: File
-      outputs:
-      - id: errors
-        type: string
-        outputBinding:
-          glob: errors.txt
-          loadContents: true
-          outputEval: $(self[0].contents)
-      class: CommandLineTool
-      requirements:
-      - class: ShellCommandRequirement
-      - class: InlineJavascriptRequirement
-      arguments:
-      # Unfortunately we can't use the same trick as in draft3_nio_file_papi1 because in papi 2 the instance metadata doesn't seem to contain
-      # the PAPI operation ID. So instead simply check that the input files are not there. This is not as neat as the PAPI1 version
-      # but should check the right thing as long as the files are localized (in general, but not here) somewhere in the same directory as where the command
-      # runs. If that changes then the directory where "find" searches should be updated 
-        - valueFrom: |
-            touch errors.txt
-            find . -name lonely_file >> errors.txt
-            find . -name lonely_file.also >> errors.txt
-            find . -name file_in_array >> errors.txt
-            find . -name file_in_array.also >> errors.txt
-            find . -name file_in_object >> errors.txt
-            find . -name file_in_object.also >> errors.txt
-            find . -name maybe_file >> errors.txt
-            find . -name maybe_file.also >> errors.txt
-          shellQuote: false
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_resources.cwl b/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_resources.cwl
deleted file mode 100644
index 295302acc2e..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_resources.cwl
+++ /dev/null
@@ -1,27 +0,0 @@
-cwlVersion: v1.0
-$graph:  
-- id: machineTypeTool
-  class: CommandLineTool
-  cwlVersion: v1.0
-  doc: "Asks for CPU and Memory minimums"
-  requirements:
-    ResourceRequirement:
-      coresMin: 2
-      coresMax: 2
-      ramMin: 7GB
-      ramMax: 7GB
-  hints:
-    DockerRequirement:
-      dockerPull: python:latest
-  inputs: []
-  outputs:
-    machine_type:
-      type: string
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: $(self[0].contents.trim())
-  baseCommand: ['curl', 'http://metadata.google.internal/computeMetadata/v1/instance/machine-type', '-H', 'Metadata-Flavor: Google']
-  stdout: stdout
-
-
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources_papiv2.test b/centaur/src/main/resources/standardTestCases/cwl_resources_papiv2.test
deleted file mode 100644
index ccb4f0ad534..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources_papiv2.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_resources_papiv2
-testFormat: workflowsuccess
-backends: [Papiv2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_resources/cwl_resources.cwl
-}
-
-metadata {
-  status: Succeeded
-  "outputs.machineTypeTool.machine_type": "projects/1005074806481/machineTypes/custom-2-7168"
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: machineTypeTool
diff --git a/centaur/src/main/resources/standardTestCases/cwl_restart/cwl_restart.cwl b/centaur/src/main/resources/standardTestCases/cwl_restart/cwl_restart.cwl
deleted file mode 100644
index 82664f739b1..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_restart/cwl_restart.cwl
+++ /dev/null
@@ -1,117 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-id: cwl_restart
-# Workflow-level DockerRequirement
-requirements:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-inputs: []
-outputs:
-- id: flag
-  outputSource: "#third_step/flag"
-  type: boolean
-steps:
-- id: first_step
-  in: []
-  out:
-  - id: firstfoofile
-  # A dash is not valid in a WDL identifier and would have broken older `IdentifierAndPathPattern` parsing.
-  - id: first-bar-file
-  run:
-    inputs: []
-    outputs:
-    - id: firstfoofile
-      outputBinding:
-        glob: out.txt
-      type: File
-    - id: first-bar-file
-      outputBinding:
-        glob: out.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    arguments:
-    - valueFrom: echo
-    - valueFrom: "I have a bad feeling about this"
-    - valueFrom: ">"
-      shellQuote: false
-    - valueFrom: "out.txt"
-- id: cromwell_killer
-  in:
-  - id: fooinput
-    source: "#first_step/firstfoofile"
-  - id: bar-input
-    source: "#first_step/first-bar-file"
-  out:
-  - id: "footxt"
-  - id: "bar-txt"
-  run:
-    inputs:
-    - id: fooinput
-      type: File
-    - id: bar-input
-      type: File
-    outputs:
-    - id: "footxt"
-      outputBinding:
-        glob: foo.txt
-      type: File
-    - id: "bar-txt"
-      outputBinding:
-        glob: bar.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    arguments:
-    - valueFrom: sleep
-    - valueFrom: "60"
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: foo
-    - valueFrom: ">"
-      shellQuote: false
-    - valueFrom: "foo.txt"
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: bar
-    - valueFrom: ">"
-      shellQuote: false
-    - valueFrom: "bar.txt"
-- id: third_step
-  in:
-  - id: foo
-    source: "#cromwell_killer/footxt"
-  - id: bar
-    source: "#cromwell_killer/bar-txt"
-  out:
-  - id: flag
-  run:
-    inputs:
-    - id: foo
-      type: File
-    - id: bar
-      type: File
-    outputs:
-    - id: flag
-      outputBinding:
-        outputEval: $(true)
-      type: boolean
-    class: CommandLineTool
-    requirements:
-    - class: InlineJavascriptRequirement
-    - class: ShellCommandRequirement
-    arguments:
-    - valueFrom: echo
-    - valueFrom: "Are we alive???"
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: $(inputs.foo)
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: $(inputs.bar)
diff --git a/centaur/src/main/resources/standardTestCases/cwl_restart_local_with_recover.test b/centaur/src/main/resources/standardTestCases/cwl_restart_local_with_recover.test
deleted file mode 100644
index a45e97769cd..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_restart_local_with_recover.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_restart_local_with_recover
-testFormat: CromwellRestartWithRecover
-callMark: cromwell_killer
-backendsMode: "only"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_restart/cwl_restart.cwl
-}
-
-metadata {
-  status: Succeeded
-  "calls.first_step.executionStatus": Done
-  "calls.cromwell_killer.executionStatus": Done
-  "calls.third_step.executionStatus": Done
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
diff --git a/centaur/src/main/resources/standardTestCases/cwl_run/1st-tool.cwl b/centaur/src/main/resources/standardTestCases/cwl_run/1st-tool.cwl
deleted file mode 100644
index af0c4de297d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_run/1st-tool.cwl
+++ /dev/null
@@ -1,9 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-inputs:
-  message:
-    type: string
-    inputBinding:
-      position: 1
-outputs: []
diff --git a/centaur/src/main/resources/standardTestCases/cwl_run/echo-job.yml b/centaur/src/main/resources/standardTestCases/cwl_run/echo-job.yml
deleted file mode 100644
index 913ff438103..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_run/echo-job.yml
+++ /dev/null
@@ -1 +0,0 @@
-message: Hello CWL!
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files.test b/centaur/src/main/resources/standardTestCases/cwl_secondary_files.test
deleted file mode 100644
index 2c8f861e1e9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_secondary_files
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_secondary_files/cwl_secondary_files.cwl
-  inputs: cwl_secondary_files/cwl_secondary_files.yaml
-  options: cwl_secondary_files/cwl_secondary_files.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.main.the_answer": "$(42)"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.cwl b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.cwl
deleted file mode 100644
index 123a7b574a1..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.cwl
+++ /dev/null
@@ -1,44 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: main
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: command
-      type: string
-    - id: f
-      type: File
-      inputBinding:
-        position: 2
-      secondaryFiles: [.also]
-    - id: of
-      type: File?
-      inputBinding:
-        position: 3
-      secondaryFiles: [.also]
-    - id: fs
-      type:
-        type: array
-        items: File
-        inputBinding:
-          position: 4
-      secondaryFiles: [.also]
-    - id: fr
-      secondaryFiles: [.also]
-      type:
-        type: record
-        name: foo
-        fields:
-          - name: a
-            type: File
-            inputBinding:
-              position: 5
-  outputs:
-    the_answer:
-      type: string
-      outputBinding:
-        outputEval: ${ return "$(" + 42 + ")"; }
-  baseCommand: []
-  arguments: ["bash", "-c", $(inputs.command)]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.options b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.yaml b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.yaml
deleted file mode 100644
index 928cfb8cbb3..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.yaml
+++ /dev/null
@@ -1,17 +0,0 @@
-# This command will stat the secondaryFiles and if they're missing bad times
-command: stat $(echo $* | sed 's/.txt/.txt.also/g') > /dev/null
-f:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt"
-of:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt"
-fs:
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt"
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt"
-fr:
-  a:
-    class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt"
\ No newline at end of file
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow.test b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow.test
deleted file mode 100644
index f6dff3fb727..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_secondary_files_workflow
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_secondary_files_workflow
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl
-  inputs: cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml
-  options: cwl_secondary_files_workflow/cwl_secondary_files_workflow.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.cwl_secondary_files_workflow.the_answer": "$(42)"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl
deleted file mode 100644
index d5f9dc3f8c9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl
+++ /dev/null
@@ -1,55 +0,0 @@
-cwlVersion: v1.0
-$graph:
-# The inputs of the workflow specify secondary files but NOT of the tool
-# Verify that they are still propagated through
-- id: cwl_secondary_files_workflow
-  class: Workflow
-  inputs:
-  - id: command
-    type: string
-  - id: wf_file_input
-    type: File
-    secondaryFiles: [.also]
-  - id: wf_file_input_array
-    type:
-      type: array
-      items: File
-    secondaryFiles: [.also]
-  outputs:
-  - id: the_answer
-    type: string
-    outputSource: run_tool/the_answer
-  steps:
-  - id: run_tool
-    run: "#cwl_secondary_files_workflow_tool"
-    in:
-      command: command
-      f: wf_file_input
-      fs: wf_file_input_array
-    out:
-    - id: the_answer
-- id: cwl_secondary_files_workflow_tool
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: command
-      type: string
-    - id: f
-      type: File
-      inputBinding:
-        position: 2
-    - id: fs
-      type:
-        type: array
-        items: File
-        inputBinding:
-          position: 3
-  outputs:
-    the_answer:
-      type: string
-      outputBinding:
-        outputEval: ${ return "$(" + 42 + ")"; }
-  baseCommand: []
-  arguments: ["bash", "-c", $(inputs.command)]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.options b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml
deleted file mode 100644
index e0cf43d4b1a..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-# This command will stat the secondaryFiles and if they're missing bad times
-command: stat $(echo $* | sed 's/.txt/.txt.also/g') > /dev/null
-wf_file_input:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt"
-wf_file_input_array:
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt"
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.cwl b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.cwl
deleted file mode 100644
index b49ec9b1134..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: cwl_stdout_expression
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: foo
-      type: string
-    - id: bar
-      type: string
-  outputs:
-    b: stdout
-  stdout: "stdout-$(inputs.foo)-$(inputs.bar).txt"
-  baseCommand: []
-  arguments: [echo, $(inputs.foo), $(inputs.bar)]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.json b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.json
deleted file mode 100644
index 82e0295d318..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "foo": "baz",
-  "bar": "qux"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_local.test b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_local.test
deleted file mode 100644
index 13bfbb68e24..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_local.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_stdout_expression_local
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_stdout_expression
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_stdout_expression/cwl_stdout_expression.cwl
-  inputs: cwl_stdout_expression/cwl_stdout_expression.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.cwl_stdout_expression.stdout": "<<WORKFLOW_ROOT>>/call-cwl_stdout_expression/execution/stdout-baz-qux.txt"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_papi.test b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_papi.test
deleted file mode 100644
index b48a0effa79..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_papi.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_stdout_expression_papi
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_stdout_expression
-backends: [Papi2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_stdout_expression/cwl_stdout_expression.cwl
-  inputs: cwl_stdout_expression/cwl_stdout_expression.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.cwl_stdout_expression.stdout": "<<WORKFLOW_ROOT>>call-cwl_stdout_expression/stdout-baz-qux.txt"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwls/scatter-job1.json b/centaur/src/main/resources/standardTestCases/cwls/scatter-job1.json
deleted file mode 100644
index b3ab2751243..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwls/scatter-job1.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "inp": ["one", "two", "three", "four"],
-  "inp2": "yeahhh"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwls/scatter-wf1.cwl b/centaur/src/main/resources/standardTestCases/cwls/scatter-wf1.cwl
deleted file mode 100644
index dc46aa7da4a..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwls/scatter-wf1.cwl
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: string[]
-  inp2: string
-outputs:
-  out:
-    type: string[]
-    outputSource: step1/echo_out
-
-requirements:
-  - class: ScatterFeatureRequirement
-  - class: DockerRequirement
-    dockerPull: ubuntu:latest
-
-steps:
-  step1:
-    in:
-      echo_in: inp
-      echo_in2: inp2
-    out: [echo_out]
-    scatter: echo_in
-    run:
-      class: CommandLineTool
-      inputs:
-        echo_in:
-          type: string
-          inputBinding: {}
-        echo_in2:
-          type: string
-          inputBinding: {}
-      outputs:
-        echo_out:
-          type: string
-          outputBinding:
-            glob: "step1_out"
-            loadContents: true
-            outputEval: $(self[0].contents)
-      baseCommand: "echo"
-      arguments:
-        - "-n"
-        - "foo"
-      stdout: "step1_out"
diff --git a/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs b/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs
index d5738ac4d17..d1712641dd2 100644
--- a/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs
+++ b/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs
@@ -1,5 +1,5 @@
 {
-    # Martha does not return service accounts for JDR paths. Therefore they shouldn't need to be localized using the
+    # DRSHub does not return service accounts for JDR paths. Therefore they shouldn't need to be localized using the
     # Cromwell custom DOS/DRS localizer.
     #
     # However, the first file1 was generated before JDR stared saving file names at the end of the gsUri.
diff --git a/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test b/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test
index 4025860ed8d..510c9215c1f 100644
--- a/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test
+++ b/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test
@@ -1,6 +1,7 @@
 name: drs_usa_jdr
 testFormat: WorkflowSuccess
 backends: ["papi-v2-usa"]
+tags: [ drs ]
 skipDescribeEndpointValidation: true
 
 files {
diff --git a/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test b/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test
index ab050aea69f..15e41d95529 100644
--- a/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test
+++ b/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test
@@ -1,6 +1,7 @@
 name: drs_usa_jdr_preresolve
 testFormat: WorkflowSuccess
 backends: ["papi-v2-usa"]
+tags: [ drs ]
 skipDescribeEndpointValidation: true
 
 files {
diff --git a/centaur/src/main/resources/standardTestCases/expressionLib.test b/centaur/src/main/resources/standardTestCases/expressionLib.test
deleted file mode 100644
index 74299af9bc6..00000000000
--- a/centaur/src/main/resources/standardTestCases/expressionLib.test
+++ /dev/null
@@ -1,15 +0,0 @@
-name: expression_lib_cwl
-cwlVersion: 1.0
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: expressionLib/expressionLib.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/expressionLib/expressionLib.cwl b/centaur/src/main/resources/standardTestCases/expressionLib/expressionLib.cwl
deleted file mode 100644
index fe8df12b4b0..00000000000
--- a/centaur/src/main/resources/standardTestCases/expressionLib/expressionLib.cwl
+++ /dev/null
@@ -1,14 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-requirements:
-  InlineJavascriptRequirement:
-    expressionLib:
-      - "function foo() { return 2; }"
-inputs: []
-outputs:
-  out: stdout
-arguments: [echo, $(foo())]
-stdout: whatever.txt
diff --git a/centaur/src/main/resources/standardTestCases/hello_cwl.test b/centaur/src/main/resources/standardTestCases/hello_cwl.test
deleted file mode 100644
index 18712fd5404..00000000000
--- a/centaur/src/main/resources/standardTestCases/hello_cwl.test
+++ /dev/null
@@ -1,12 +0,0 @@
-name: hello_cwl
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: hello
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: hello_cwl/hello.cwl
-  inputs: hello_cwl/hello.inputs
-  "outputs.hello.salutation": "Hello m'Lord!"
-}
diff --git a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.cwl b/centaur/src/main/resources/standardTestCases/hello_cwl/hello.cwl
deleted file mode 100644
index deb1e4d1f4a..00000000000
--- a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.cwl
+++ /dev/null
@@ -1,21 +0,0 @@
-cwlVersion: v1.0
-$graph:
-  id: hello
-  class: CommandLineTool
-  requirements:
-    - class: DockerRequirement
-      dockerPull: ubuntu:latest
-  baseCommand: echo
-  inputs:
-    message:
-      type: string
-      inputBinding:
-        position: 1
-  stdout: hello-stdout.txt
-  outputs:
-    - id: salutation
-      type: string
-      outputBinding:
-        glob: hello-stdout.txt
-        loadContents: true
-        outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.inputs b/centaur/src/main/resources/standardTestCases/hello_cwl/hello.inputs
deleted file mode 100644
index 11888b548ad..00000000000
--- a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.inputs
+++ /dev/null
@@ -1,3 +0,0 @@
-# Seemingly innocuous but this particular message actually tests proper shell quoting of
-# spaces, single quotes, and exclamation points.
-message: Hello m'Lord!
diff --git a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs.cwl b/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs.cwl
deleted file mode 100644
index e476be06d12..00000000000
--- a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs.cwl
+++ /dev/null
@@ -1,49 +0,0 @@
-cwlVersion: v1.0
-$graph:
-  - id: http_inputs
-    class: Workflow
-    inputs:
-    - id: jamie
-      type: File
-    outputs:
-    - id: md5
-      outputSource: "#http_inputs/sum/md5"
-      type: int
-    steps:
-    - id: sum
-      in:
-      - id: jamie
-        source: "#http_inputs/jamie"
-      out:
-      - id: md5
-      # Workflow step-level DockerRequirement
-      requirements:
-        DockerRequirement:
-          dockerPull: "ubuntu:latest"
-      run:
-        inputs:
-        - id: jamie
-          type: File
-        outputs:
-        - id: md5
-          outputBinding:
-            glob: md5-stdOut.txt
-            loadContents: true
-            outputEval: $(self[0].contents)
-          type: string
-        class: CommandLineTool
-        requirements:
-        - class: ShellCommandRequirement
-        - class: InlineJavascriptRequirement
-        arguments:
-        - valueFrom: "/usr/bin/md5sum"
-          shellQuote: false
-        - valueFrom: $(inputs.jamie)
-          shellQuote: true
-        - valueFrom: '|'
-          shellQuote: false
-        - valueFrom: cut
-          shellQuote: false
-        - valueFrom: -c1-32
-          shellQuote: false
-        stdout: md5-stdOut.txt
diff --git a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs_cwl.inputs b/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs_cwl.inputs
deleted file mode 100644
index 9a7137d1bf9..00000000000
--- a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs_cwl.inputs
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "jamie": "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/docs/jamie_the_cromwell_pig.png",
-}
diff --git a/centaur/src/main/resources/standardTestCases/http_inputs_cwl.test b/centaur/src/main/resources/standardTestCases/http_inputs_cwl.test
deleted file mode 100644
index 7ed111e3ec7..00000000000
--- a/centaur/src/main/resources/standardTestCases/http_inputs_cwl.test
+++ /dev/null
@@ -1,15 +0,0 @@
-name: http_inputs_cwl
-backends: [Local, Papiv2]
-testFormat: workflowsuccess
-workflowRoot: http_inputs
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: http_inputs/http_inputs.cwl
-  inputs: http_inputs/http_inputs_cwl.inputs
-}
-
-metadata {
-  status: Succeeded
-  "outputs.http_inputs.md5": "602d0a4c1d54b7302e2d245a66a1b609\n"
-}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl
new file mode 100644
index 00000000000..33153c1157c
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl
@@ -0,0 +1,49 @@
+version 1.0
+
+
+workflow ReferenceDiskMountedOnlyIfRequested {
+    call MentionsNirvanaReference {}
+    output {
+        Boolean disk_mounted = MentionsNirvanaReference.disk_mounted
+    }
+}
+
+
+task MentionsNirvanaReference {
+    input {
+        # Tiny 116 byte reference file, certainly not worth attaching a 55 GiB Nirvana reference disk for this.
+        File mention =
+            "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
+    }
+    command <<<
+        PS4='\D{+%F %T} \w $ '
+        set -o nounset -o xtrace
+
+        # Debug output
+        lsblk
+
+        CANDIDATE_MOUNT_POINT=$(lsblk | sed -E -n 's!.*(/mnt/[a-f0-9]+).*!\1!p')
+
+        if [[ ! -z ${CANDIDATE_MOUNT_POINT} ]]; then
+            echo "Found unexpected mounted disk, investigating further."
+            find ${CANDIDATE_MOUNT_POINT} -print | tee find.out
+
+            if grep -i nirvana find.out; then
+                echo "Found what appears to be a Nirvana reference disk."
+            else
+                echo "Found unknown volume mounted, see 'find.out' for manifest."
+            fi
+            echo true > disk_mounted.out
+        else
+            echo false > disk_mounted.out
+        fi
+    >>>
+    runtime {
+        docker: "ubuntu:latest"
+        backend: "Papiv2-Reference-Disk-Localization"
+    }
+    output {
+        Boolean disk_mounted = read_boolean("disk_mounted.out")
+        File? find_out = "find.out"
+    }
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
index 8e28a8ef541..4caf94c0f77 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
@@ -1,3 +1,5 @@
 {
-  "wf_reference_disk_test.check_if_localized_as_symlink.reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.tile_db_header.vcf"
+  "wf_reference_disk_test.broad_reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
+  "wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
+  "wf_reference_disk_test.nirvana_reference_file_metachar_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi"
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
index 43a298f18ab..51fb467598b 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
@@ -1,11 +1,38 @@
-task check_if_localized_as_symlink {
-  File reference_file_input
-  command {
-     # print true if file is a symlink, otherwise print false
-     if test -h ${reference_file_input}; then echo "true"; else echo "false"; fi;
+version 1.0
+
+task check_if_localized_with_valid_symlink {
+  input {
+    File broad_reference_file_input
+    File nirvana_reference_file_input
+    File nirvana_reference_file_metachar_input
   }
+  String broad_input_valid_symlink = "broad_input_valid_symlink.txt"
+  String nirvana_input_valid_symlink = "nirvana_input_valid_symlink.txt"
+  String nirvana_metachar_input_valid_symlink = "nirvana_metachar_input_valid_symlink.txt"
+  command <<<
+      PS4='\D{+%F %T} \w $ '
+      set -o nounset -o pipefail -o xtrace
+
+      # Echo true to stdout if the argument is a symlink pointing to an extant file, otherwise echo false.
+      check_if_valid_symlink() {
+          local reference_input="$1"
+
+          if [[ -h "${reference_input}" && -f $(readlink "${reference_input}") ]]; then
+              echo true
+          else
+              echo false
+          fi
+      }
+
+      check_if_valid_symlink "~{broad_reference_file_input}" > ~{broad_input_valid_symlink}
+      check_if_valid_symlink "~{nirvana_reference_file_input}" > ~{nirvana_input_valid_symlink}
+      check_if_valid_symlink "~{nirvana_reference_file_metachar_input}" > ~{nirvana_metachar_input_valid_symlink}
+
+  >>>
   output {
-    Boolean is_symlink = read_boolean(stdout())
+    Boolean is_broad_input_valid_symlink = read_boolean("~{broad_input_valid_symlink}")
+    Boolean is_nirvana_input_valid_symlink = read_boolean("~{nirvana_input_valid_symlink}")
+    Boolean is_nirvana_metachar_input_valid_symlink = read_boolean("~{nirvana_metachar_input_valid_symlink}")
   }
   runtime {
     docker: "ubuntu:latest"
@@ -14,8 +41,20 @@ task check_if_localized_as_symlink {
 }
 
 workflow wf_reference_disk_test {
-  call check_if_localized_as_symlink
+  input {
+    File broad_reference_file_input
+    File nirvana_reference_file_input
+    File nirvana_reference_file_metachar_input
+  }
+  call check_if_localized_with_valid_symlink {
+    input:
+      broad_reference_file_input = broad_reference_file_input,
+      nirvana_reference_file_input = nirvana_reference_file_input,
+      nirvana_reference_file_metachar_input = nirvana_reference_file_metachar_input
+  }
   output {
-     Boolean is_input_file_a_symlink = check_if_localized_as_symlink.is_symlink
+    Boolean is_broad_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_broad_input_valid_symlink
+    Boolean is_nirvana_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_nirvana_input_valid_symlink
+    Boolean is_nirvana_metachar_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_nirvana_metachar_input_valid_symlink
   }
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
index b75ef58dabc..bb8be222691 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
@@ -11,5 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": false
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test
new file mode 100644
index 00000000000..32c6d83e5c3
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test
@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_false
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_false.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": false
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test
new file mode 100644
index 00000000000..165e1c6d1f4
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test
@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_true
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_true.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": true
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test
new file mode 100644
index 00000000000..860159b594e
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test
@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_unspecified
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_unspecified.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": false
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
index dab9c516164..6d957bf55b7 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
@@ -11,5 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": true
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": true
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": true
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": true
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
index 441db8748f2..7625bcd7806 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
@@ -11,5 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": false
 }
diff --git a/centaur/src/main/resources/standardTestCases/retry_with_more_memory/retry_with_more_memory_after_137.wdl b/centaur/src/main/resources/standardTestCases/retry_with_more_memory/retry_with_more_memory_after_137.wdl
new file mode 100644
index 00000000000..2fe434475c6
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/retry_with_more_memory/retry_with_more_memory_after_137.wdl
@@ -0,0 +1,22 @@
+version 1.0
+
+task imitate_oom_error {
+  command {
+    printf "Exception in thread "main" java.lang.OutOfMemoryError: testing\n\tat Test.main(Test.java:1)\n" >&2
+    touch foo
+    exit 137
+  }
+  output {
+    File foo = "foo"
+  }
+  runtime {
+    docker: "python:latest"
+    memory: "1 GB"
+    maxRetries: 2
+    backend: "Papiv2"
+  }
+}
+
+workflow retry_with_more_memory_after_137 {
+  call imitate_oom_error
+}
diff --git a/centaur/src/main/resources/standardTestCases/retry_with_more_memory_after_137.test b/centaur/src/main/resources/standardTestCases/retry_with_more_memory_after_137.test
new file mode 100644
index 00000000000..a69290ca511
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/retry_with_more_memory_after_137.test
@@ -0,0 +1,21 @@
+name: retry_with_more_memory_after_137
+testFormat: workflowfailure
+backends: [Papiv2]
+
+files {
+  workflow: retry_with_more_memory/retry_with_more_memory_after_137.wdl
+  options: retry_with_more_memory/retry_with_more_memory.options
+}
+
+metadata {
+  workflowName: retry_with_more_memory_after_137
+  status: Failed
+  "failures.0.message": "Workflow failed"
+  "failures.0.causedBy.0.message": "stderr for job `retry_with_more_memory_after_137.imitate_oom_error:NA:3` contained one of the `memory-retry-error-keys: [OutOfMemory,Killed]` specified in the Cromwell config. Job might have run out of memory."
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.1.executionStatus": "RetryableFailure"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.1.runtimeAttributes.memory": "1 GB"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.2.executionStatus": "RetryableFailure"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.2.runtimeAttributes.memory": "1.1 GB"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.3.executionStatus": "Failed"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.3.runtimeAttributes.memory": "1.2100000000000002 GB"
+}
diff --git a/centaur/src/main/resources/standardTestCases/scatter-wf1.test b/centaur/src/main/resources/standardTestCases/scatter-wf1.test
deleted file mode 100644
index 397b94710a3..00000000000
--- a/centaur/src/main/resources/standardTestCases/scatter-wf1.test
+++ /dev/null
@@ -1,11 +0,0 @@
-name: cwl_scatter_wf1
-testFormat: workflowsuccess
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwls/scatter-wf1.cwl
-  inputs: cwls/scatter-job1.json
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
diff --git a/centaur/src/main/resources/standardTestCases/three_step.test b/centaur/src/main/resources/standardTestCases/three_step.test
deleted file mode 100644
index b24e649ecce..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: three_step_cwl
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: three_step/three_step.cwl
-  inputs: three_step/inputs.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.wc.executionStatus": Done
-  "calls.ps.executionStatus": Done
-  "calls.cgrep.executionStatus": Done
-  "calls.ps.runtimeAttributes.docker": "ubuntu:bionic"
-  "calls.wc.runtimeAttributes.docker": "ubuntu:latest"
-  "calls.cgrep.runtimeAttributes.docker": "debian:jessie"
-}
diff --git a/centaur/src/main/resources/standardTestCases/three_step/inputs.json b/centaur/src/main/resources/standardTestCases/three_step/inputs.json
deleted file mode 100644
index 8dac4768fff..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step/inputs.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "pattern": "java"
-}
diff --git a/centaur/src/main/resources/standardTestCases/three_step/three_step.cwl b/centaur/src/main/resources/standardTestCases/three_step/three_step.cwl
deleted file mode 100644
index e328003eab1..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step/three_step.cwl
+++ /dev/null
@@ -1,114 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-id: three_step
-# Workflow-level DockerRequirement
-hints:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-inputs:
-- id: pattern
-  type: string
-outputs:
-- id: cgrep-count
-  outputSource: "#cgrep/cgrep-count"
-  type: int
-- id: wc-count
-  outputSource: "#wc/wc-count"
-  type: int
-steps:
-- id: ps
-  in: []
-  out:
-  - id: ps-stdOut
-  run:
-    inputs: []
-    outputs:
-    - id: ps-stdOut
-      outputBinding:
-        glob: ps-stdOut.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-      # Command line tool-level DockerRequirement
-      # Check it: this DockerRequirement does not use the `class` formatting but should still parse
-      # thanks to the magic of SALAD.
-      DockerRequirement:
-        dockerPull: "ubuntu:bionic"
-    baseCommand: ps
-    stdout: ps-stdOut.txt
-- id: cgrep
-  in:
-  - id: pattern
-    source: "#pattern"
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: cgrep-count
-  # Workflow step-level DockerRequirement
-  requirements:
-    DockerRequirement:
-      dockerPull: "debian:jessie"
-  run:
-    inputs:
-    - id: pattern
-      type: string
-    - id: file
-      type: File
-    outputs:
-    - id: cgrep-count
-      outputBinding:
-        glob: cgrep-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: grep
-      shellQuote: false
-    - valueFrom: $(inputs.pattern)
-      shellQuote: false
-    - valueFrom: ${return inputs.file}
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: cgrep-stdOut.txt
-- id: wc
-  in:
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: wc-count
-  run:
-    inputs:
-    - id: file
-      type: File
-    outputs:
-    - id: wc-count
-      outputBinding:
-        glob: wc-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: cat
-      shellQuote: false
-    - valueFrom: $(inputs.file)
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: wc-stdOut.txt
diff --git a/centaur/src/main/resources/standardTestCases/three_step/three_step_caller_wf.cwl b/centaur/src/main/resources/standardTestCases/three_step/three_step_caller_wf.cwl
deleted file mode 100644
index ab5d8ddc458..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step/three_step_caller_wf.cwl
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env cwl-runner
-class: Workflow
-cwlVersion: v1.0
-
-inputs:
-- id: pin
-  type: string
-  default: "v"
-
-outputs:
-    count_output:
-      type: int
-      outputSource: threestep/wc-count
-
-requirements:
-  - class: SubworkflowFeatureRequirement
-
-steps:
-  threestep:
-    run: three_step.cwl
-    in:
-    - id: pattern
-      source: pin
-    out: [wc-count]
diff --git a/centaur/src/main/resources/standardTestCases/three_step_subworkflow.test b/centaur/src/main/resources/standardTestCases/three_step_subworkflow.test
deleted file mode 100644
index 6ae478035b7..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step_subworkflow.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: three_step__subwf_cwl
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-
-files {
-  workflow: three_step/three_step_caller_wf.cwl,
-  imports: [
-    three_step/three_step.cwl
-  ]
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/workflow_type_and_version_cwl.test b/centaur/src/main/resources/standardTestCases/workflow_type_and_version_cwl.test
deleted file mode 100644
index 14ba92c588f..00000000000
--- a/centaur/src/main/resources/standardTestCases/workflow_type_and_version_cwl.test
+++ /dev/null
@@ -1,16 +0,0 @@
-ignore: true
-name: workflow_type_and_version_cwl
-testFormat: workflowsuccess
-
-files {
-  workflow: workflow_type_and_version_cwl/workflow_type_and_version_cwl.wdl
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-
-metadata {
-  workflowName: workflow_type_and_version_cwl
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaurCwlRunner/src/bin/centaur-cwl-runner.bash b/centaurCwlRunner/src/bin/centaur-cwl-runner.bash
deleted file mode 100755
index 8f39c3ec130..00000000000
--- a/centaurCwlRunner/src/bin/centaur-cwl-runner.bash
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env bash
-
-# `sbt assembly` must have already been run.
-build_root="$( dirname "${BASH_SOURCE[0]}" )/../../.."
-centaur_cwl_jar="${CENTAUR_CWL_JAR:-"$( \
-    find "${build_root}/centaurCwlRunner/target/scala-2.13" -name 'centaur-cwl-runner-*.jar' -print0 \
-    | xargs -0 ls -1 -t \
-    | head -n 1 \
-    )"}"
-centaur_cwl_skip_file="${build_root}/centaurCwlRunner/src/main/resources/skipped_tests.csv"
-
-centaur_cwl_java_args=("-Xmx1g")
-if [[ -n "${CENTAUR_CWL_JAVA_ARGS-}" ]]; then
-    # Allow splitting on space to simulate an exported array
-    # https://stackoverflow.com/questions/5564418/exporting-an-array-in-bash-script#answer-5564589
-    # shellcheck disable=SC2206
-    centaur_cwl_java_args+=(${CENTAUR_CWL_JAVA_ARGS})
-fi
-
-# Handle empty arrays in older versions of bash
-# https://stackoverflow.com/questions/7577052/bash-empty-array-expansion-with-set-u#answer-7577209
-java \
-    ${centaur_cwl_java_args[@]+"${centaur_cwl_java_args[@]}"} \
-    -jar "${centaur_cwl_jar}" \
-    --skip-file "${centaur_cwl_skip_file}" \
-    "$@"
diff --git a/centaurCwlRunner/src/main/resources/application.conf b/centaurCwlRunner/src/main/resources/application.conf
deleted file mode 100644
index fcdd3da9c57..00000000000
--- a/centaurCwlRunner/src/main/resources/application.conf
+++ /dev/null
@@ -1,23 +0,0 @@
-akka {
-  loggers = ["akka.event.slf4j.Slf4jLogger"]
-  logging-filter = "akka.event.slf4j.Slf4jLoggingFilter"
-
-  # Silence Akka-Http warning logging of:
-  # [WARN] [01/28/2019 06:50:04.293] [centaur-acting-like-a-system-akka.actor.default-dispatcher-3] [centaur-acting-like-a-system/Pool(shared->http://localhost:8000)] Connection attempt failed. Backing off new connection attempts for at least 100 milliseconds.
-  #
-  # via:
-  # https://github.com/akka/akka/blob/v2.5.19/akka-actor/src/main/resources/reference.conf#L41-L44
-  # https://github.com/akka/akka/blob/v2.5.19/akka-actor/src/main/scala/akka/event/Logging.scala#L377
-  # https://github.com/akka/akka-http/blob/v10.1.7/akka-http-core/src/main/scala/akka/http/impl/engine/client/pool/NewHostConnectionPool.scala#L134
-  stdout-loglevel = "ERROR"
-}
-
-centaur {
-  # When running the tests in parallel on a Travis instance we need a bit more time for a reply to come back.
-  sendReceiveTimeout: 1 minute
-}
-
-cwltool-runner {
-  # When running the tests in parallel it takes a while for each JVM to initialize Heterodon. Instead use the process.
-  class = "cwl.CwltoolProcess"
-}
diff --git a/centaurCwlRunner/src/main/resources/logback.xml b/centaurCwlRunner/src/main/resources/logback.xml
deleted file mode 100644
index d92bac61949..00000000000
--- a/centaurCwlRunner/src/main/resources/logback.xml
+++ /dev/null
@@ -1,48 +0,0 @@
-<configuration>
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-            <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger - %msg%n</pattern>
-        </encoder>
-    </appender>
-
-    <!-- lower logging level, especially to stdout -->
-    <root level="warn">
-        <appender-ref ref="STDOUT"/>
-    </root>
-
-    <!--
-    Silence occasional PoolMasterActor error logging of:
-    04:20:04.785 [centaur-acting-like-a-system-akka.actor.default-dispatcher-5] ERROR akka.http.impl.engine.client.PoolMasterActor - connection pool for PoolGateway(hcps = HostConnectionPoolSetup(localhost,8000,ConnectionPoolSetup(ConnectionPoolSettings(4,0,5,32,1,30 seconds,ClientConnectionSettings(Some(User-Agent: akka-http/10.0.10),10 seconds,1 minute,512,None,<function0>,List(),ParserSettings(2048,16,64,64,8192,64,8388608,256,1048576,Strict,RFC6265,true,Full,Error,Map(If-Range -> 0, If-Modified-Since -> 0, If-Unmodified-Since -> 0, default -> 12, Content-MD5 -> 0, Date -> 0, If-Match -> 0, If-None-Match -> 0, User-Agent -> 32),false,akka.stream.impl.ConstantFun$$$Lambda$286/1579280783@2287c189,akka.stream.impl.ConstantFun$$$Lambda$286/1579280783@2287c189,akka.stream.impl.ConstantFun$$$Lambda$287/1370074462@628a0265),None),TCPTransport),akka.http.scaladsl.HttpConnectionContext$@164c4af,akka.event.MarkerLoggingAdapter@4204728))) has shut down unexpectedly
-
-    via:
-    https://github.com/akka/akka-http/blob/v10.0.10/akka-http-core/src/main/scala/akka/http/impl/engine/client/PoolMasterActor.scala#L117
-    -->
-    <logger name="akka.http.impl.engine.client.PoolMasterActor" level="off" additivity="false"/>
-
-    <!--
-    Silence Injector warning logging of:
-    06:36:48.095 [main] WARN  org.semanticweb.owlapi.utilities.Injector - No files found for META-INF/services/org.semanticweb.owlapi.model.OWLOntologyIRIMapper
-
-    via:
-    https://github.com/owlcs/owlapi/blob/owlapi-parent-5.1.7/api/src/main/java/org/semanticweb/owlapi/utilities/Injector.java#L383
-    -->
-    <logger name="org.semanticweb.owlapi.utilities.Injector" level="error" additivity="false"/>
-
-    <!--
-    Silence Akka warning logging of:
-    10:18:20.629 [centaur-acting-like-a-system-akka.actor.default-dispatcher-8] WARN  akka.io.InetAddressDnsResolver - No caching TTL defined. Using default value Ttl(30 seconds).
-
-    via:
-    https://github.com/akka/akka/blob/v2.5.19/akka-actor/src/main/scala/akka/io/InetAddressDnsResolver.scala#L40
-    -->
-    <logger name="akka.io.InetAddressDnsResolver" level="error" additivity="false"/>
-
-    <!--
-    Silence Akka-Http warning logging of:
-    00:53:57.537 [centaur-acting-like-a-system-akka.actor.default-dispatcher-10] WARN  akka.http.impl.engine.client.PoolGateway - Connection attempt failed. Backing off new connection attempts for at least 100 milliseconds.
-
-    via:
-    https://github.com/akka/akka-http/blob/v10.1.7/akka-http-core/src/main/scala/akka/http/impl/engine/client/pool/NewHostConnectionPool.scala#L134
-    -->
-    <logger name="akka.http.impl.engine.client.PoolGateway" level="error" additivity="false"/>
-</configuration>
diff --git a/centaurCwlRunner/src/main/resources/reference.conf b/centaurCwlRunner/src/main/resources/reference.conf
deleted file mode 100644
index a906e824372..00000000000
--- a/centaurCwlRunner/src/main/resources/reference.conf
+++ /dev/null
@@ -1,29 +0,0 @@
-centaur {
-  cwl-runner {
-    mode = local
-
-    # End of actual references and begin BA-6546 exceptions...
-    # Not sure if this reference conf is used by testers outside of DSP/broad?
-    # If you know for sure then do some combination of:
-    # - update this comment with the location of those tests
-    # - update the external tests to explicitly pass in their own config
-    # - if the external tests are 100% confirmed not to exist state how you know that
-    # Not really reference, but leaving just in case someone is relying on these values.
-    papi.default-input-gcs-prefix = "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/"
-    tesk.default-input-ftp-prefix = "ftp://ftp.hexdump.org/centaur-cwl-conformance/cwl-inputs/"
-    google {
-      application-name = "centaur-cwl-runner"
-      genomics.endpoint-url = "https://lifesciences.googleapis.com/"
-      genomics.location = "us-central1"
-      max-attempts = 3
-      auth = "application-default"
-      auths = [
-        {
-          name = "application-default"
-          scheme = "application_default"
-        }
-      ]
-    }
-    # End BA-6546 exceptions
-  }
-}
diff --git a/centaurCwlRunner/src/main/resources/skipped_tests.csv b/centaurCwlRunner/src/main/resources/skipped_tests.csv
deleted file mode 100644
index 08b6b117906..00000000000
--- a/centaurCwlRunner/src/main/resources/skipped_tests.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-vf-concat.cwl,empty.json
-dir5.cwl,dir-job.yml
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunner.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunner.scala
deleted file mode 100644
index ec5dcad537e..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunner.scala
+++ /dev/null
@@ -1,255 +0,0 @@
-package centaur.cwl
-
-import better.files._
-import cats.effect.IO
-import centaur.api.CentaurCromwellClient
-import centaur.cwl.Outputs._
-import centaur.test.TestOptions
-import centaur.test.standard.{CentaurTestCase, CentaurTestFormat}
-import centaur.test.submit.{SubmitHttpResponse, SubmitWorkflowResponse}
-import centaur.test.workflow.{AllBackendsRequired, SubmittedWorkflowTracker, Workflow, WorkflowData}
-import com.typesafe.scalalogging.StrictLogging
-import common.util.VersionUtil
-import cromwell.api.model.{Aborted, Failed, NonTerminalStatus, Succeeded}
-import cromwell.core.WorkflowOptions
-import cromwell.core.path.PathBuilderFactory
-import cromwell.core.path.BetterFileMethods.Cmds
-import cwl.preprocessor.{CwlFileReference, CwlPreProcessor}
-import spray.json._
-
-import scala.concurrent.Await
-import scala.concurrent.duration.Duration
-
-/**
-  * Runs workflows in a "cwl-runner" friendly way.
-  *
-  * https://github.com/broadinstitute/cromwell/issues/2590
-  * https://github.com/common-workflow-language/common-workflow-language/blob/v1.0.1/CONFORMANCE_TESTS.md
-  * https://github.com/common-workflow-language/common-workflow-language/blob/v1.0.1/draft-3/cwl-runner.cwl#L5-L68
-  * https://github.com/common-workflow-language/common-workflow-language/pull/278/files#diff-ee814a9c027fc9750beb075c283a973cR49
-  */
-object CentaurCwlRunner extends StrictLogging {
-
-  case class SkippedTest(sourceName: String, inputsName: String) {
-    def shouldSkip(args: CommandLineArguments) = {
-      args.workflowSource.exists(_.name.equalsIgnoreCase(sourceName)) &&
-        args.workflowInputs.exists(_.name.equalsIgnoreCase(inputsName))
-    }
-  }
-
-  case class CommandLineArguments(workflowSource: Option[File] = None,
-                                  workflowInputs: Option[File] = None,
-                                  quiet: Boolean = false,
-                                  outdir: Option[File] = None,
-                                  skipFile: Option[File] = None)
-
-  // TODO: This would be cleaner with Enumeratum
-  object ExitCode extends Enumeration {
-
-    protected case class ExitVal(status: Int) extends super.Val
-
-    implicit class ValueToVal(val exitCodeValue: Value) extends AnyVal {
-      def status: Int = exitCodeValue.asInstanceOf[ExitVal].status
-    }
-
-    val Success = ExitVal(0)
-    val Failure = ExitVal(1)
-    val NotImplemented = ExitVal(33)
-  }
-
-  private val cwlPreProcessor = new CwlPreProcessor()
-  private val centaurCwlRunnerRunMode = CentaurCwlRunnerRunMode.fromConfig(CentaurCwlRunnerConfig.conf)
-  private val parser = buildParser()
-  private lazy val centaurCwlRunnerVersion = VersionUtil.getVersion("centaur-cwl-runner")
-  private lazy val versionString = s"$centaurCwlRunnerVersion ${centaurCwlRunnerRunMode.description}"
-
-  private def showUsage(): ExitCode.Value = {
-    System.err.println(parser.usage)
-    ExitCode.Failure
-  }
-
-  private def buildParser(): scopt.OptionParser[CommandLineArguments] = {
-    new scopt.OptionParser[CommandLineArguments]("java -jar /path/to/centaurCwlRunner.jar") {
-      head("centaur-cwl-runner", versionString)
-
-      help("help").text("Centaur CWL Runner - Cromwell integration testing environment")
-
-      version("version").text("Print version and exit")
-
-      arg[String]("workflow-source").text("Workflow source file.").required().
-        action((s, c) => c.copy(workflowSource = Option(File(s))))
-
-      arg[String]("inputs").text("Workflow inputs file.").optional().
-        action((s, c) => c.copy(workflowInputs = Option(File(s))))
-
-      opt[Unit]("quiet").text("Only print warnings and errors.").optional().
-        action((_, c) => c.copy(quiet = true))
-
-      opt[String]("outdir").text("Output directory, default current directory.").optional().
-        action((s, c) =>
-          c.copy(outdir = Option(File(s))))
-
-      opt[String]("skip-file").text("A csv file describing workflows to be skipped based on their name.").optional().
-        action((s, c) =>
-          c.copy(skipFile = Option(File(s))))
-    }
-  }
-
-  private def runCentaur(args: CommandLineArguments): ExitCode.Value = {
-
-    def zipSiblings(file: File): File = {
-      val zipFile = File.newTemporaryFile("cwl_imports.", ".zip")
-      val dir = file.parent
-      if (!args.quiet) {
-        logger.info(s"Zipping files under 1mb in $dir to $zipFile")
-      }
-      // TODO: Only include files under 1mb for now. When cwl runners run in parallel this can use a lot of space.
-      val files = dir
-        .children
-        .filter(_.isRegularFile)
-        .filter(_.size < 1 * 1024 * 1024)
-      Cmds.zip(files.toSeq: _*)(zipFile)
-      zipFile
-    }
-
-    val workflowPath = args.workflowSource.get
-    val (parsedWorkflowPath, workflowRoot) = workflowPath.path.toAbsolutePath.toString.split("#") match {
-      case Array(file) => File(file) -> None
-      case Array(file, root) => File(file) -> Option(root)
-    }
-    val outdirOption = args.outdir.map(_.pathAsString)
-    val testName = workflowPath.name
-    val preProcessedWorkflow = cwlPreProcessor
-      .preProcessCwlToString(CwlFileReference(parsedWorkflowPath, workflowRoot))
-      .value.unsafeRunSync() match {
-      case Left(errors) =>
-        logger.error(s"Failed to pre process cwl workflow: ${errors.toList.mkString(", ")}")
-        return ExitCode.Failure
-      case Right(v) => v
-    }
-
-    val workflowContents = centaurCwlRunnerRunMode.preProcessWorkflow(preProcessedWorkflow)
-    val inputContents = args.workflowInputs
-      .map(centaurCwlRunnerRunMode.preProcessInput)
-      .map(preProcessed => {
-        preProcessed.value.unsafeRunSync() match {
-          case Left(errors) =>
-            logger.error(s"Failed to pre process cwl workflow: ${errors.toList.mkString(", ")}")
-            return ExitCode.Failure
-          case Right(value) => value
-        }
-      })
-
-    val workflowType = Option("cwl")
-    val workflowTypeVersion = None
-    val optionsContents = outdirOption map { outdir =>
-      JsObject("cwl_outdir" -> JsString(outdir)).compactPrint
-    }
-    val labels = List.empty
-    val zippedImports = Option(zipSiblings(workflowPath)) // TODO: Zipping all the things! Be more selective.
-    val backends = AllBackendsRequired(List.empty)
-    val workflowMetadata = None
-    val notInMetadata = List.empty
-    val directoryContentCounts = None
-    val testFormat = CentaurTestFormat.WorkflowSuccessTest
-    val testOptions = TestOptions(List.empty, ignore = false)
-    val submitResponseOption = None
-
-    val submittedWorkflowTracker = new SubmittedWorkflowTracker()
-
-    val workflowData = WorkflowData(
-      Option(workflowContents),
-      None,
-      None,
-      workflowType,
-      workflowTypeVersion,
-      inputContents.map(IO.pure),
-      optionsContents.map(IO.pure),
-      labels,
-      zippedImports
-    )
-    val workflow = Workflow(
-      testName,
-      workflowData,
-      workflowMetadata,
-      notInMetadata,
-      directoryContentCounts,
-      backends,
-      retryTestFailures = false,
-      allowOtherOutputs = true,
-      skipDescribeEndpointValidation = true,
-      submittedWorkflowTracker = submittedWorkflowTracker,
-      maximumAllowedTime = None
-    )
-
-    val testCase = CentaurTestCase(workflow, testFormat, testOptions, submittedWorkflowTracker, submitResponseOption)(cromwellTracker = None)
-
-    if (!args.quiet) {
-      logger.info(s"Starting test for $workflowPath")
-    }
-
-    val pathBuilderFactory: PathBuilderFactory = centaurCwlRunnerRunMode.pathBuilderFactory
-
-    try {
-      import CentaurCromwellClient.{blockingEc, system}
-      lazy val pathBuilder = Await.result(pathBuilderFactory.withOptions(WorkflowOptions.empty), Duration.Inf)
-
-      testCase.testFunction.run.unsafeRunSync() match {
-        case unexpected: SubmitHttpResponse =>
-          logger.error(s"Unexpected response: $unexpected")
-          ExitCode.Failure
-        case SubmitWorkflowResponse(submittedWorkflow) =>
-          val status = CentaurCromwellClient.status(submittedWorkflow).unsafeRunSync()
-          status match {
-            case unexpected: NonTerminalStatus =>
-              logger.error(s"Unexpected status: $unexpected")
-              ExitCode.Failure
-            case Aborted =>
-              logger.error(s"Unexpected abort.")
-              ExitCode.Failure
-            case Failed =>
-              logger.error(s"Unexpected failure.")
-              ExitCode.Failure
-            case Succeeded =>
-              val result = handleOutput(submittedWorkflow, pathBuilder)
-              if (!args.quiet) {
-                logger.info(s"Result: $result")
-              } else {
-                // Print directly to stdout during --quiet
-                println(result)
-              }
-              ExitCode.Success
-          }
-      }
-    } finally {
-      zippedImports map { zipFile =>
-        if (!args.quiet) {
-          logger.info(s"Deleting $zipFile")
-        }
-        zipFile.delete(swallowIOExceptions = true)
-      }
-      Await.result(CentaurCromwellClient.system.terminate(), Duration.Inf)
-      ()
-    }
-  }
-
-  private def skip(args: CommandLineArguments): Boolean =
-    args.skipFile
-      .map(_.lines).getOrElse(List.empty)
-      .map(_.split(','))
-      .map({
-        case Array(source, inputs) => SkippedTest(source, inputs)
-        case invalid => throw new RuntimeException(s"Invalid skipped_tests file: $invalid")
-      })
-      .exists(_.shouldSkip(args))
-
-  def main(args: Array[String]): Unit = {
-    val parsedArgsOption = parser.parse(args, CommandLineArguments())
-    val exitCode = parsedArgsOption match {
-      case Some(parsedArgs) if skip(parsedArgs) => ExitCode.NotImplemented
-      case Some(parsedArgs) => runCentaur(parsedArgs)
-      case None => showUsage()
-    }
-    System.exit(exitCode.status)
-  }
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerConfig.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerConfig.scala
deleted file mode 100644
index 0123efd7b8d..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerConfig.scala
+++ /dev/null
@@ -1,7 +0,0 @@
-package centaur.cwl
-
-import centaur.CentaurConfig
-
-object CentaurCwlRunnerConfig {
-  lazy val conf = CentaurConfig.conf.getConfig("cwl-runner")
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala
deleted file mode 100644
index 83b6626c983..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala
+++ /dev/null
@@ -1,94 +0,0 @@
-package centaur.cwl
-
-import better.files.File
-import cloud.nio.impl.ftp.FtpFileSystems
-import com.typesafe.config.Config
-import common.validation.IOChecked._
-import cromwell.core.path.Obsolete.Paths
-import cromwell.core.path.{DefaultPathBuilderFactory, PathBuilderFactory}
-import cromwell.filesystems.ftp.{CromwellFtpFileSystems, FtpPathBuilderFactory}
-import cromwell.filesystems.gcs.GcsPathBuilderFactory
-import cwl.preprocessor.CwlPreProcessor
-
-sealed trait CentaurCwlRunnerRunMode {
-  /**
-    * Returns a user friendly of this run mode.
-    */
-  def description: String
-
-  /**
-    * Returns a factory that can create a path builder for this run mode.
-    */
-  def pathBuilderFactory: PathBuilderFactory
-
-  /**
-    * Runs any preprocessing as needed on a workflow.
-    *
-    * For example, may prefix relative paths so that absolute URLs are used.
-    */
-  def preProcessWorkflow(workflow: String): String = workflow
-
-  /**
-    * Runs any preprocessing as needed on inputs.
-    *
-    * For example, may prefix relative paths so that absolute URLs are used.
-    */
-  def preProcessInput(path: File): IOChecked[String] = path.contentAsString.validIOChecked
-}
-
-object CentaurCwlRunnerRunMode {
-  def fromConfig(conf: Config): CentaurCwlRunnerRunMode = {
-    conf.getString("mode") match {
-      case "local" => LocalRunMode
-      case "papi_v2alpha1" | "papi_v2beta" => PapiRunMode(conf)
-      case "tesk" => TeskRunMode(conf)
-      case unknown => throw new UnsupportedOperationException(s"mode not recognized: $unknown")
-    }
-  }
-}
-
-case object LocalRunMode extends CentaurCwlRunnerRunMode {
-  val cwlPreProcessor = new CwlPreProcessor()
-  override lazy val description: String = "local"
-  override lazy val pathBuilderFactory: PathBuilderFactory = DefaultPathBuilderFactory
-  /*
-    * If the file is a relative local path, resolve it against the path of the input json.
-   */
-  private def inputFilesMapper(inputJsonPath: File)(file: String) = {
-    if (!Paths.get(file).isAbsolute) inputJsonPath.sibling(file).toString
-    else file
-  }
-
-  override def preProcessInput(input: File): IOChecked[String] = cwlPreProcessor.preProcessInputFiles(input.contentAsString, inputFilesMapper(input))
-}
-
-case class PapiRunMode(conf: Config) extends CentaurCwlRunnerRunMode {
-  private lazy val googleConfig = conf.getConfig("google")
-  private lazy val preprocessor = new CloudPreprocessor(conf, "papi.default-input-gcs-prefix")
-
-  override lazy val description: String = s"papi ${googleConfig.getString("auth")}"
-
-  override lazy val pathBuilderFactory: PathBuilderFactory = {
-    GcsPathBuilderFactory(conf, googleConfig)
-  }
-
-  override def preProcessWorkflow(workflow: String): String = preprocessor.preProcessWorkflow(workflow)
-
-  override def preProcessInput(input: File): IOChecked[String] = preprocessor.preProcessInput(input.contentAsString)
-}
-
-case class TeskRunMode(conf: Config) extends CentaurCwlRunnerRunMode {
-  private lazy val ftpConfig = conf.getConfig("ftp")
-  private lazy val preprocessor = new CloudPreprocessor(conf, "tesk.default-input-ftp-prefix")
-
-  override lazy val description: String = "tesk"
-
-  override lazy val pathBuilderFactory: PathBuilderFactory = {
-    val fileSystemsConfiguration = FtpFileSystems.DefaultConfig.copy(capacity = 2)
-    new FtpPathBuilderFactory(conf, ftpConfig, new CromwellFtpFileSystems(new FtpFileSystems(fileSystemsConfiguration)))
-  }
-
-  override def preProcessWorkflow(workflow: String): String = preprocessor.preProcessWorkflow(workflow)
-
-  override def preProcessInput(input: File): IOChecked[String] = preprocessor.preProcessInput(input.contentAsString)
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CloudPreprocessor.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CloudPreprocessor.scala
deleted file mode 100644
index 68e79b9b701..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CloudPreprocessor.scala
+++ /dev/null
@@ -1,102 +0,0 @@
-package centaur.cwl
-import better.files.File
-import com.typesafe.config.Config
-import common.util.StringUtil._
-import common.validation.IOChecked.IOChecked
-import cwl.preprocessor.CwlPreProcessor
-import io.circe.optics.JsonPath
-import io.circe.optics.JsonPath._
-import io.circe.yaml.Printer.StringStyle
-import io.circe.{Json, yaml}
-import net.ceedubs.ficus.Ficus._
-import wom.util.YamlUtils
-
-/**
-  * Tools to pre-process the CWL workflows and inputs before feeding them to Cromwell so they can be executed on PAPI.
-  */
-class CloudPreprocessor(config: Config, prefixConfigPath: String) {
-  val cwlPreProcessor = new CwlPreProcessor()
-  
-  // Cloud directory where inputs for conformance tests are stored
-  private val cloudPrefix = config.as[String](prefixConfigPath).ensureSlashed
-
-  // Default docker pull image
-  val DefaultDockerPull = "dockerPull" -> Json.fromString("ubuntu:latest")
-  
-  // Default docker image to be injected in a pre-existing requirements array
-  private val DefaultDockerHint: Json = {
-    Json.obj(
-      "class" -> Json.fromString("DockerRequirement"),
-      DefaultDockerPull
-    )
-  }
-
-  // hints array with default docker requirement
-  private val DefaultDockerHintList: Json = {
-    Json.obj(
-      "hints" -> Json.arr(DefaultDockerHint)
-    )
-  }
-
-  // Parse value, apply f to it, and print it back to String using the printer
-  private def process(value: String, f: Json => Json, printer: Json => String) = {
-    YamlUtils.parse(value) match {
-      case Left(error) => throw new Exception(error.getMessage)
-      case Right(json) => printer(f(json))
-    }
-  }
-
-  // Process and print back as YAML
-  private def processYaml(value: String)(f: Json => Json) =
-    process(value, f, yaml.Printer.spaces2.copy(stringStyle = StringStyle.DoubleQuoted).pretty)
-
-  // Prefix the string at "key" with the cloud prefix
-  private def prefixLocation(value: String): String = {
-    cloudPrefix + File(value.stripPrefix("file://")).name
-  }
-
-  // Function to check if the given json has the provided key / value pair
-  private def hasKeyValue(key: String, value: String): Json => Boolean = {
-    root.selectDynamic(key).string.exist(_.equalsIgnoreCase(value))
-  }
-
-  /**
-    * Pre-process input file by prefixing all files and directories with the cloud prefix
-    */
-  def preProcessInput(input: String): IOChecked[String] = cwlPreProcessor.preProcessInputFiles(input, prefixLocation)
-
-  // Check if the given path (as an array or object) has a DockerRequirement element
-  def hasDocker(jsonPath: JsonPath)(json: Json): Boolean = {
-    val hasDockerInArray: Json => Boolean = jsonPath.arr.exist(_.exists(hasKeyValue("class", "DockerRequirement")))
-    val hasDockerInObject: Json => Boolean = jsonPath.obj.exist(_.kleisli("DockerRequirement").nonEmpty)
-
-    hasDockerInArray(json) || hasDockerInObject(json)
-  }
-
-  // Check if the given Json has a docker image in hints or requirements
-  def hasDocker(json: Json): Boolean = hasDocker(root.hints)(json) || hasDocker(root.requirements)(json)
-
-  // Add a default docker hint to the workflow if it doesn't have one
-  private val addDefaultDocker: Json => Json = workflow => if (!hasDocker(workflow)) {
-    /*
-      * deepMerge does not combine objects together but replaces keys which would overwrite existing hints
-      * so first check if there are hints already and if so add our docker one.
-      * Also turns out that the hints section can be either an array or an object.
-      * When it gets saladed the object is transformed to an array but because we deal with unsaladed cwl here
-      * we have to handle both cases.
-     */
-    val hintsAsArray = root.hints.arr.modifyOption(_ :+ DefaultDockerHint)(workflow)
-    val hintsAsObject = root.hints.obj.modifyOption(_.add("DockerRequirement", Json.obj(DefaultDockerPull)))(workflow)
-
-    hintsAsArray
-      .orElse(hintsAsObject)
-      .getOrElse(workflow.deepMerge(DefaultDockerHintList))
-  } else workflow
-  
-  private val prefixDefaultFilesInCwl = CwlPreProcessor.mapFilesAndDirectories(prefixLocation) _
-
-  /**
-    * Pre-process the workflow by adding a default docker hint iff it doesn't have one
-    */
-  def preProcessWorkflow(workflow: String): String = processYaml(workflow)(addDefaultDocker.andThen(prefixDefaultFilesInCwl))
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/OutputManipulator.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/OutputManipulator.scala
deleted file mode 100644
index dcbe3a70ec8..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/OutputManipulator.scala
+++ /dev/null
@@ -1,237 +0,0 @@
-package centaur.cwl
-
-import common.util.StringUtil._
-import cromwell.core.path.{Path, PathBuilder}
-import cwl.CwlCodecs._
-import cwl.command.ParentName
-import cwl.ontology.Schema
-import cwl.{File => CwlFile, _}
-import io.circe.literal._
-import io.circe.syntax._
-import io.circe.{Json, JsonObject}
-import mouse.all._
-import org.apache.commons.codec.digest.DigestUtils
-import shapeless.{Inl, Poly1}
-import spray.json.{JsArray, JsBoolean, JsNull, JsNumber, JsObject, JsString, JsValue}
-
-//Take cromwell's outputs and format them as expected by the spec
-object OutputManipulator extends Poly1 {
-
-  //In an Ideal world I'd return a Coproduct of these types and leave the asJson-ing to the handleOutput
-  def resolveOutput(jsValue: JsValue,
-                    pathBuilder: PathBuilder,
-                    mot: MyriadOutputType,
-                    schemaOption: Option[Schema]): Json  = {
-    mot.fold(this).apply(jsValue, pathBuilder, schemaOption)
-  }
-
-  private def hashFile(path: Path): Option[String] = path.exists.option("sha1$" + path.sha1.toLowerCase)
-  private def sizeFile(path: Path): Option[Long] = path.exists.option(path.size)
-
-  private def stringToFile(pathAsString: String, pathBuilder: PathBuilder): Json = {
-    val path = pathBuilder.build(pathAsString).get
-
-    if (path.exists()) {
-      CwlFile(
-        location = Option(path.name),
-        checksum = hashFile(path),
-        size = sizeFile(path)
-      ).asJson
-    } else {
-      Json.Null
-    }
-  }
-
-  private def populateFileFields(pathBuilder: PathBuilder,
-                                 schemaOption: Option[Schema]
-                                )(obj: JsonObject): JsonObject = {
-    val path = pathBuilder.build(obj.kleisli("location").get.asString.get).get
-    val isFile = obj.kleisli("class").exists(_.asString.contains("File"))
-    val isDirectory = obj.kleisli("class").exists(_.asString.contains("Directory"))
-
-    // Return the default value if the value at key is either absent or null, otherwise return the value
-    def valueOrNull(key: String, default: Json) = obj.kleisli(key) match {
-      case Some(Json.Null) => default
-      case Some(other) => other
-      case None => default
-    }
-
-    def populateInnerFiles(json: Json): Option[Json] = {
-
-      def populateInnerFile(file: Json): Json = {
-        file.asObject
-          .map(populateFileFields(pathBuilder, schemaOption))
-          .map(Json.fromJsonObject)
-          .orElse(file.asString.map(stringToFile(_, pathBuilder)))
-          .getOrElse(file)
-      }
-
-      // Assume the json is an array ("secondaryFiles" and "listing" are both arrays).
-      val innerFiles = json.asArray.get
-      // Remove any files that don't actually exist.
-      val filteredFiles = innerFiles.map(populateInnerFile).filterNot(_.isNull)
-      // The cwl test runner doesn't expect a "secondaryFiles" or "listing" field at all if it's empty.
-      if (filteredFiles.nonEmpty) Option(Json.arr(filteredFiles: _*)) else None
-    }
-
-    def updateFileOrDirectoryWithNestedFiles(obj: JsonObject, fieldName: String) = {
-      // Cromwell metadata has a field for all values even if their content is empty
-      // remove it as the cwl test runner expects nothing instead
-      val withoutField = obj.remove(fieldName)
-
-      // If the field was not empty, add it back with each inner file / directory properly updated as well
-      populateInnerFiles(obj.kleisli(fieldName).get)
-        .map(withoutField.add(fieldName, _))
-        .getOrElse(withoutField)
-    }
-
-    // Get sha1 from the content field
-    // We need this because some task return a "File" object that actually does not exist on disk but has its content provided directly instead
-    def hashContent: Option[String] = obj.kleisli("contents").flatMap(_.asString.map(DigestUtils.sha1Hex).map("sha1$" + _))
-
-    // Get size from the content field
-    // We need this because some task return a "File" object that actually does not exist on disk but has its content provided directly instead
-    def sizeContent: Option[Long] = obj.kleisli("contents").flatMap(_.asString.map(_.length.toLong))
-
-    // "as a special case, cwltest only matches the trailing part of location in the output sections so that it
-    // can do something reasonable regardless of URL scheme or prefix" - Peter Amstutz, 2019-04-16, CWL gitter
-    val updatedLocation = obj.add("location", Json.fromString(path.pathAsString))
-
-    // Get the format
-    def formatOption: Option[String] = for {
-      klesliFormat <- obj.kleisli("format")
-      format <- klesliFormat.asString
-    } yield format
-
-    // Lookup the full format using the namespaces
-    def fullFormatOption: Option[String] = for {
-      format <- formatOption
-      schema <- schemaOption
-    } yield schema.fullIri(format)
-
-    if (isFile) {
-      /*
-        * In order of priority use: 
-        * 1) the checksum value in the metadata
-        * 2) the checksum calculated from the value of the "contents" field of the metadata
-        * 3) the checksum calculated from the file itself
-        */
-      val defaultChecksum = hashContent.orElse(hashFile(path)).map(Json.fromString).getOrElse(Json.Null)
-      val checksum = valueOrNull("checksum", defaultChecksum)
-
-      /*
-        * In order of priority use: 
-        * 1) the size value in the metadata
-        * 2) the size calculated from the value of the "contents" field of the metadata
-        * 3) the size calculated from the file itself
-        */
-      val defaultSize = sizeContent.orElse(sizeFile(path)).map(Json.fromLong).getOrElse(Json.Null)
-      val size = valueOrNull("size", defaultSize)
-
-      val basename: Option[Json] =
-        Option(valueOrNull("basename", path.exists.option(path.name).map(Json.fromString).getOrElse(Json.Null)))
-
-      /*
-      In order of priority use:
-      1) the full format if $namespaces are available
-      2) the original format
-       */
-      val defaultFormatOption: Option[Json] = fullFormatOption.orElse(formatOption).map(Json.fromString)
-
-      val withChecksumAndSize = updatedLocation
-        .add("checksum", checksum)
-        .add("size", size)
-        // conformance test does not expect "contents" in the output
-        .remove("contents")
-
-      val withBasename = basename
-        .map(withChecksumAndSize.add("basename", _))
-        .getOrElse(withChecksumAndSize)
-
-      val withFormat = defaultFormatOption
-        .map(withBasename.add("format", _))
-        .getOrElse(withBasename)
-
-      updateFileOrDirectoryWithNestedFiles(withFormat, "secondaryFiles")
-    } else if (isDirectory) {
-      updateFileOrDirectoryWithNestedFiles(updatedLocation, "listing").
-        add("basename", path.nameWithoutExtension |> Json.fromString)
-    } else throw new RuntimeException(s"${path.pathAsString} is neither a valid file or a directory")
-  }
-
-  private def resolveOutputViaInnerType(moits: Array[MyriadOutputInnerType])
-                                       (jsValue: JsValue,
-                                        pathBuilder: PathBuilder,
-                                        schemaOption: Option[Schema]): Json = {
-    def sprayJsonToCirce(jsValue: JsValue): Json = {
-      import io.circe.parser._
-      val jsonString = jsValue.compactPrint
-      parse(jsonString).getOrElse(
-        sys.error(s"Failed to parse Json output as Json... something is very wrong: '$jsonString'")
-      )
-    }
-
-    (jsValue, moits) match {
-      //CWL expects quite a few enhancements to the File structure, hence...
-      case (JsString(metadata), Array(Inl(CwlType.File))) => stringToFile(metadata, pathBuilder)
-      // If it's a JsObject it means it's already in the right format, we just want to fill in some values that might not
-      // have been populated like "checksum" and "size"
-      case (obj: JsObject, a) if a.contains(Inl(CwlType.File)) || a.contains(Inl(CwlType.Directory)) =>
-        val json: Json = sprayJsonToCirce(obj)
-        val fileExists = (for {
-          o <- json.asObject
-          l <- o.kleisli("location")
-          s <- l.asString
-          c = if (a.contains(Inl(CwlType.Directory))) s.ensureSlashed else s
-          p <- pathBuilder.build(c).toOption
-        } yield p.exists).getOrElse(false)
-        if (fileExists) json.mapObject(populateFileFields(pathBuilder, schemaOption)) else Json.Null
-      case (JsNumber(metadata), Array(Inl(CwlType.Long))) => metadata.longValue.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Float))) => metadata.floatValue.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Double))) => metadata.doubleValue.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Int))) => metadata.intValue.asJson
-      case (JsString(metadata), Array(Inl(CwlType.String))) => metadata.asJson
-
-      //The Anys.  They have to be done for each type so that the asJson can use this type information when going back to Json representation
-      case (JsString(metadata), Array(Inl(CwlType.Any))) => metadata.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Any))) => metadata.asJson
-      case (obj: JsObject, Array(Inl(CwlType.Any))) => sprayJsonToCirce(obj)
-      case (JsBoolean(metadata), Array(Inl(CwlType.Any))) => metadata.asJson
-      case (array: JsArray, Array(Inl(CwlType.Any))) => sprayJsonToCirce(array)
-      case (JsNull, a) if a.contains(Inl(CwlType.Any)) || a.contains(Inl(CwlType.Null)) => Json.Null
-
-      case (JsArray(metadata), Array(tpe)) if tpe.select[OutputArraySchema].isDefined =>
-        (for {
-          schema <- tpe.select[OutputArraySchema]
-          items = schema.items
-          innerType <- items.select[MyriadOutputInnerType]
-          outputJson = metadata.map(m =>
-            resolveOutputViaInnerType(Array(innerType))(m, pathBuilder, schemaOption)).asJson
-        } yield outputJson).getOrElse(throw new RuntimeException(s"We currently do not support output arrays with ${tpe.select[OutputArraySchema].get.items} inner type"))
-      case (JsObject(metadata), Array(tpe)) if tpe.select[OutputRecordSchema].isDefined =>
-        def processField(field: OutputRecordField) = {
-          val parsedName = FullyQualifiedName(field.name)(ParentName.empty).id
-          field.`type`.select[MyriadOutputInnerType] map { parsedName -> _ }
-        }
-
-        (for {
-          schema <- tpe.select[OutputRecordSchema]
-          fields <- schema.fields
-          typeMap = fields.flatMap(processField).toMap
-          outputJson = metadata.map({
-            case (k, v) => k -> resolveOutputViaInnerType(Array(typeMap(k)))(v, pathBuilder, schemaOption)
-          }).asJson
-        } yield outputJson).getOrElse(throw new RuntimeException(s"We currently do not support output record schemas with ${tpe.select[OutputArraySchema].get.items} inner type"))
-      case (json, tpe) => throw new RuntimeException(s"We currently do not support outputs (${json.getClass.getSimpleName}) of $json and type $tpe")
-    }
-  }
-
-  implicit val moit: Case.Aux[MyriadOutputInnerType, (JsValue, PathBuilder, Option[Schema]) => Json] = at { t =>
-    resolveOutputViaInnerType(Array(t))
-  }
-
-  implicit val amoit: Case.Aux[Array[MyriadOutputInnerType], (JsValue, PathBuilder, Option[Schema]) => Json] =
-    at { amoit =>
-      resolveOutputViaInnerType(amoit)
-    }
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/Outputs.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/Outputs.scala
deleted file mode 100644
index c63d95399d7..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/Outputs.scala
+++ /dev/null
@@ -1,93 +0,0 @@
-package centaur.cwl
-
-import centaur.api.CentaurCromwellClient
-import centaur.test.metadata.WorkflowFlatMetadata._
-import common.collections.EnhancedCollections._
-import common.validation.IOChecked._
-import cromwell.api.model.SubmittedWorkflow
-import cromwell.core.path.PathBuilder
-import cwl.ontology.Schema
-import cwl.{Cwl, CwlDecoder, MyriadOutputType}
-import io.circe.Json
-import io.circe.syntax._
-import mouse.map._
-import shapeless.Poly1
-import spray.json.{JsObject, JsString, JsValue}
-
-object Outputs {
-
-  //When the string returned is not valid JSON, it is effectively an exception as CWL runner expects JSON to be returned
-  def handleOutput(submittedWorkflow: SubmittedWorkflow, pathBuilder: PathBuilder): String = {
-    val metadata: Map[String, JsValue] = CentaurCromwellClient.metadata(submittedWorkflow).unsafeRunSync().asFlat.value
-
-    // Wrapper function to provide the right signature for `intersectWith` below.
-    def outputResolver(schemaOption: Option[Schema])(jsValue: JsValue, mot: MyriadOutputType): Json = {
-      OutputManipulator.resolveOutput(jsValue, pathBuilder, mot, schemaOption)
-    }
-
-    //Sorry for all the nesting, but spray json JsValue doesn't have optional access methods like Argonaut/circe,
-    //thus no for comprehensions for us :(
-    metadata.get("submittedFiles.workflow") match {
-      case Some(JsString(workflow)) =>
-
-        val parseCwl: IOChecked[Cwl] = CwlDecoder.decodeCwlString(
-          workflow,
-          submittedWorkflow.workflow.zippedImports,
-          submittedWorkflow.workflow.workflowRoot
-        )
-
-        parseCwl.value.attempt.unsafeRunSync() match {
-          case Right(Right(cwl)) =>
-
-            CentaurCromwellClient.outputs(submittedWorkflow).unsafeRunSync().outputs match {
-              case JsObject(map) =>
-                val typeMap: Map[String, MyriadOutputType] = cwl.fold(CwlOutputsFold)
-                val mungeTypeMap = typeMap.mapKeys(stripTypeMapKey)
-
-                val mungeOutputMap = map.mapKeys(stripOutputKey)
-
-                mungeOutputMap.
-                  //This lets us operate on the values of the output values and types for a particular output key
-                  intersectWith(mungeTypeMap)(outputResolver(cwl.schemaOption)).
-                  //converting the whole response to Json using Circe's auto-encoder derivation
-                  asJson.
-                  //drop null values so that we don't print when Option == None
-                  printWith(io.circe.Printer.spaces2.copy(dropNullValues = true))
-              case other => s"it seems cromwell is not returning outputs as a Jsobject but is instead a $other"
-            }
-          case Right(Left(error)) => s"couldn't parse workflow: $workflow failed with error: $error"
-          case Left(error) => s"Exception when trying to read workflow: $workflow failed with error: $error"
-        }
-      case Some(other) => s"received the value $other when the workflow string was expected"
-      case None => "the workflow is no longer in the metadata payload, it's a problem"
-    }
-  }
-
-  //Ids come out of SALAD pre-processing with a filename prepended. This gets rid of it
-  // Also gets rid of the parent workflow name if present
-  def stripTypeMapKey(key: String): String = key
-    .substring(key.lastIndexOf("#") + 1, key.length)
-    .split("/").last
-
-  //Ids come out of Cromwell with a prefix, separated by a ".". This takes everything to the right,
-  //as CWL wants it
-  def stripOutputKey(key: String): String = key.substring(key.lastIndexOf(".") + 1, key.length)
-
-}
-
-object CwlOutputsFold extends Poly1 {
-  import cwl._
-
-  implicit def wf: Case.Aux[cwl.Workflow, Map[String, MyriadOutputType]] = at[cwl.Workflow] {
-    _.outputs.map(output => output.id -> output.`type`.get).toMap
-  }
-
-  implicit def clt: Case.Aux[cwl.CommandLineTool, Map[String, MyriadOutputType]] = at[cwl.CommandLineTool] {
-    _.outputs.map(output => output.id -> output.`type`.get).toMap
-  }
-
-  implicit def et: Case.Aux[cwl.ExpressionTool, Map[String, MyriadOutputType]] = at[cwl.ExpressionTool] {
-    _.outputs.map(output => output.id -> output.`type`.get).toMap
-  }
-}
-
diff --git a/centaurCwlRunner/src/test/resources/application.conf b/centaurCwlRunner/src/test/resources/application.conf
deleted file mode 100644
index 27c24fa07bf..00000000000
--- a/centaurCwlRunner/src/test/resources/application.conf
+++ /dev/null
@@ -1 +0,0 @@
-papi.default-input-gcs-prefix="gs://centaur-cwl-conformance-1f501e3/cwl-inputs/"
diff --git a/centaurCwlRunner/src/test/scala/CloudPreprocessorSpec.scala b/centaurCwlRunner/src/test/scala/CloudPreprocessorSpec.scala
deleted file mode 100644
index df13e49b666..00000000000
--- a/centaurCwlRunner/src/test/scala/CloudPreprocessorSpec.scala
+++ /dev/null
@@ -1,342 +0,0 @@
-import centaur.cwl.CloudPreprocessor
-import com.typesafe.config.ConfigFactory
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.util.YamlUtils
-
-class CloudPreprocessorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  behavior of "PAPIPreProcessor"
-
-  val pAPIPreprocessor = new CloudPreprocessor(ConfigFactory.load(), "papi.default-input-gcs-prefix")
-
-  def validate(result: String, expectation: String) = {
-    val parsedResult = YamlUtils.parse(result).toOption.get
-    val parsedExpectation = YamlUtils.parse(expectation).toOption.get
-
-    // This is an actual Json comparison from circe
-    parsedResult shouldBe parsedExpectation
-  }
-
-  it should "prefix files and directories in inputs" in {
-    validate(
-      pAPIPreprocessor.preProcessInput(
-        """|{
-           |  "input": {
-           |    "null": null,
-           |    "file": {
-           |      "location": "whale.txt",
-           |      "class": "File",
-           |      "secondaryFiles": [
-           |        {
-           |          "class": File,
-           |          "location": "hello.txt"
-           |        }
-           |      ],
-           |      "default": {
-           |        "location": "default_whale.txt",
-           |        "class": "File",
-           |      }
-           |    },
-           |    "directory": {
-           |      "location": "ref.fasta",
-           |      "class": "Directory",
-           |      "listing": [
-           |        {
-           |          "class": File,
-           |          "location": "hello.txt"
-           |        }
-           |      ]
-           |    }
-           |  }
-           |}
-           |""".stripMargin).value.unsafeRunSync().toOption.get,
-      """|{
-         |  "input": {
-         |    "null": null,
-         |    "file": {
-         |      "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/whale.txt",
-         |      "class": "File",
-         |      "secondaryFiles": [
-         |        {
-         |          "class": File,
-         |          "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/hello.txt"
-         |        }
-         |      ],
-         |      "default": {
-         |        "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/default_whale.txt",
-         |        "class": "File",
-         |      }
-         |    },
-         |    "directory": {
-         |      "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/ref.fasta",
-         |      "class": "Directory",
-         |      "listing": [
-         |        {
-         |          "class": File,
-         |          "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/hello.txt"
-         |        }
-         |      ]
-         |    }
-         |  }
-         |}
-         |""".stripMargin
-    )
-  }
-
-  it should "prefix files and directories in workflow" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |cwlVersion: v1.0
-           |requirements:
-           |  - class: DockerRequirement
-           |    dockerPull: ubuntu:latest
-           |inputs:
-           |  - id: reference
-           |    type: File
-           |    inputBinding: { position: 2 }
-           |    default:
-           |      class: File
-           |      location: args.py
-           |
-           |outputs:
-           |  args: string[]
-           |
-           |baseCommand: python
-           |arguments: ["bwa", "mem"]
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |cwlVersion: v1.0
-         |requirements:
-         |  - class: DockerRequirement
-         |    dockerPull: ubuntu:latest
-         |inputs:
-         |  - id: reference
-         |    type: File
-         |    inputBinding: { position: 2 }
-         |    default:
-         |      class: File
-         |      location: gs://centaur-cwl-conformance-1f501e3/cwl-inputs/args.py
-         |
-         |outputs:
-         |  args: string[]
-         |
-         |baseCommand: python
-         |arguments: ["bwa", "mem"]
-         |""".stripMargin
-    )
-  }
-
-  it should "add default docker image if there's no hint" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |cwlVersion: v1.0
-           |inputs:
-           |  - id: reference
-           |    type: File
-           |    inputBinding: { position: 2 }
-           |
-           |outputs:
-           |  args: string[]
-           |
-           |baseCommand: python
-           |arguments: ["bwa", "mem"]
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |hints:
-         |  - class: DockerRequirement
-         |    dockerPull: ubuntu:latest
-         |cwlVersion: v1.0
-         |inputs:
-         |  - id: reference
-         |    type: File
-         |    inputBinding: { position: 2 }
-         |
-         |outputs:
-         |  args: string[]
-         |
-         |baseCommand: python
-         |arguments: ["bwa", "mem"]
-         |""".stripMargin
-    )
-  }
-
-  it should "append default docker image to existing hint as an array" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |hints:
-           |  - class: EnvVarRequirement
-           |    envDef:
-           |      TEST_ENV: $(inputs.in)
-           |cwlVersion: v1.0
-           |inputs:
-           |  - id: reference
-           |    type: File
-           |    inputBinding: { position: 2 }
-           |
-           |outputs:
-           |  args: string[]
-           |
-           |baseCommand: python
-           |arguments: ["bwa", "mem"]
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |hints:
-         |  - class: EnvVarRequirement
-         |    envDef:
-         |      TEST_ENV: $(inputs.in)
-         |  - class: DockerRequirement
-         |    dockerPull: ubuntu:latest
-         |cwlVersion: v1.0
-         |inputs:
-         |  - id: reference
-         |    type: File
-         |    inputBinding: { position: 2 }
-         |
-         |outputs:
-         |  args: string[]
-         |
-         |baseCommand: python
-         |arguments: ["bwa", "mem"]
-         |""".stripMargin
-    )
-  }
-
-  it should "append default docker image to existing hints as an object" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |cwlVersion: v1.0
-           |inputs:
-           |  in: string
-           |outputs:
-           |  out:
-           |    type: File
-           |    outputBinding:
-           |      glob: out
-           |
-           |hints:
-           |  EnvVarRequirement:
-           |    envDef:
-           |      TEST_ENV: $(inputs.in)
-           |
-           |baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"]
-           |
-           |stdout: out
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |cwlVersion: v1.0
-         |inputs:
-         |  in: string
-         |outputs:
-         |  out:
-         |    type: File
-         |    outputBinding:
-         |      glob: out
-         |
-         |hints:
-         |  EnvVarRequirement:
-         |    envDef:
-         |      TEST_ENV: $(inputs.in)
-         |  DockerRequirement:
-         |    dockerPull: ubuntu:latest
-         |
-         |baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"]
-         |
-         |stdout: out
-         |""".stripMargin
-    )
-  }
-
-  it should "not replace existing docker requirement in an object" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |requirements:
-                      |  DockerRequirement:
-                      |    dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "not replace existing docker hint in an object" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |hints:
-                      |  DockerRequirement:
-                      |    dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "not replace existing docker hint in an array" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |hints:
-                      |- class: DockerRequirement
-                      |  dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "not replace existing docker requirement in an array" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |requirements:
-                      |- class: DockerRequirement
-                      |  dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "throw an exception if yaml / json can't be parse" in {
-    val invalid =
-      """
-        |{ [invalid]: }
-      """.stripMargin
-
-    an[Exception] shouldBe thrownBy(pAPIPreprocessor.preProcessWorkflow(invalid))
-  }
-}
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
index a1156fc33e9..93f4cf77d34 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
@@ -15,7 +15,7 @@ import org.apache.http.HttpStatus
 class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
                               drsReadInterpreter: DrsReadInterpreter) extends CloudNioFileProvider {
 
-  private def checkIfPathExistsThroughMartha(drsPath: String): IO[Boolean] = {
+  private def checkIfPathExistsThroughDrsResolver(drsPath: String): IO[Boolean] = {
     /*
      * Unlike other cloud providers where directories are identified with a trailing slash at the end like `gs://bucket/dir/`,
      * DRS has a concept of bundles for directories (not supported yet). Hence for method `checkDirectoryExists` which appends a trailing '/'
@@ -23,15 +23,15 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
      */
     if (drsPath.endsWith("/")) IO(false)
     else {
-      drsPathResolver.rawMarthaResponse(drsPath, NonEmptyList.one(MarthaField.GsUri)).use { marthaResponse =>
-        val errorMsg = s"Status line was null for martha response $marthaResponse."
-        toIO(Option(marthaResponse.getStatusLine), errorMsg)
+      drsPathResolver.rawDrsResolverResponse(drsPath, NonEmptyList.one(DrsResolverField.GsUri)).use { drsResolverResponse =>
+        val errorMsg = s"Status line was null for DRS Resolver response $drsResolverResponse."
+        toIO(Option(drsResolverResponse.getStatusLine), errorMsg)
       }.map(_.getStatusCode == HttpStatus.SC_OK)
     }
   }
 
   override def existsPath(drsPath: String, unused: String): Boolean =
-    checkIfPathExistsThroughMartha(drsPath).unsafeRunSync()
+    checkIfPathExistsThroughDrsResolver(drsPath).unsafeRunSync()
 
   override def existsPaths(cloudHost: String, cloudPathPrefix: String): Boolean =
     existsPath(cloudHost, cloudPathPrefix)
@@ -47,11 +47,11 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
     throw new UnsupportedOperationException("DRS currently doesn't support delete.")
 
   override def read(drsPath: String, unused: String, offset: Long): ReadableByteChannel = {
-    val fields = NonEmptyList.of(MarthaField.GsUri, MarthaField.GoogleServiceAccount, MarthaField.AccessUrl)
+    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl)
 
     val byteChannelIO = for {
-      marthaResponse <- drsPathResolver.resolveDrsThroughMartha(drsPath, fields)
-      byteChannel <- drsReadInterpreter(drsPathResolver, marthaResponse)
+      drsResolverResponse <- drsPathResolver.resolveDrs(drsPath, fields)
+      byteChannel <- drsReadInterpreter(drsPathResolver, drsResolverResponse)
     } yield byteChannel
 
     byteChannelIO.handleErrorWith {
@@ -63,14 +63,14 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
     throw new UnsupportedOperationException("DRS currently doesn't support write.")
 
   override def fileAttributes(drsPath: String, unused: String): Option[CloudNioRegularFileAttributes] = {
-    val fields = NonEmptyList.of(MarthaField.Size, MarthaField.TimeCreated, MarthaField.TimeUpdated, MarthaField.Hashes)
+    val fields = NonEmptyList.of(DrsResolverField.Size, DrsResolverField.TimeCreated, DrsResolverField.TimeUpdated, DrsResolverField.Hashes)
 
     val fileAttributesIO = for {
-      marthaResponse <- drsPathResolver.resolveDrsThroughMartha(drsPath, fields)
-      sizeOption = marthaResponse.size
-      hashOption = getPreferredHash(marthaResponse.hashes)
-      timeCreatedOption <- convertToFileTime(drsPath, MarthaField.TimeCreated, marthaResponse.timeCreated)
-      timeUpdatedOption <- convertToFileTime(drsPath, MarthaField.TimeUpdated, marthaResponse.timeUpdated)
+      drsResolverResponse <- drsPathResolver.resolveDrs(drsPath, fields)
+      sizeOption = drsResolverResponse.size
+      hashOption = getPreferredHash(drsResolverResponse.hashes)
+      timeCreatedOption <- convertToFileTime(drsPath, DrsResolverField.TimeCreated, drsResolverResponse.timeCreated)
+      timeUpdatedOption <- convertToFileTime(drsPath, DrsResolverField.TimeUpdated, drsResolverResponse.timeUpdated)
     } yield new DrsCloudNioRegularFileAttributes(drsPath, sizeOption, hashOption, timeCreatedOption, timeUpdatedOption)
 
     Option(fileAttributesIO.unsafeRunSync())
@@ -78,5 +78,5 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
 }
 
 object DrsCloudNioFileProvider {
-  type DrsReadInterpreter = (DrsPathResolver, MarthaResponse) => IO[ReadableByteChannel]
+  type DrsReadInterpreter = (DrsPathResolver, DrsResolverResponse) => IO[ReadableByteChannel]
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
index 8721ab9b43e..884072e4a31 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
@@ -11,7 +11,8 @@ class DrsCloudNioFileSystemProvider(rootConfig: Config,
                                     drsReadInterpreter: DrsReadInterpreter,
                                    ) extends CloudNioFileSystemProvider {
 
-  lazy val drsConfig: DrsConfig = DrsConfig.fromConfig(rootConfig.getConfig("martha"))
+  lazy val drsResolverConfig = if (rootConfig.hasPath("resolver")) rootConfig.getConfig("resolver") else rootConfig.getConfig("martha")
+  lazy val drsConfig: DrsConfig = DrsConfig.fromConfig(drsResolverConfig)
 
   lazy val drsPathResolver: EngineDrsPathResolver =
     EngineDrsPathResolver(drsConfig, drsCredentials)
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
index 3c9293f2bd7..778d9b8380e 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
@@ -61,7 +61,7 @@ object DrsCloudNioRegularFileAttributes {
       .map(FileTime.from)
   }
 
-  def convertToFileTime(drsPath: String, key: MarthaField.Value, timeInStringOption: Option[String]): IO[Option[FileTime]] = {
+  def convertToFileTime(drsPath: String, key: DrsResolverField.Value, timeInStringOption: Option[String]): IO[Option[FileTime]] = {
     timeInStringOption match {
       case None => IO.pure(None)
       case Some(timeInString) =>
@@ -71,7 +71,7 @@ object DrsCloudNioRegularFileAttributes {
             throwable =>
               IO.raiseError(
                 new RuntimeException(
-                  s"Error while parsing '$key' value from Martha to FileTime for DRS path $drsPath. " +
+                  s"Error while parsing '$key' value from DRS Resolver to FileTime for DRS path $drsPath. " +
                     s"Reason: ${ExceptionUtils.getMessage(throwable)}.",
                   throwable,
                 )
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
index e9dc760162e..c8333a57a66 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
@@ -6,7 +6,7 @@ import net.ceedubs.ficus.Ficus._
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-final case class DrsConfig(marthaUrl: String,
+final case class DrsConfig(drsResolverUrl: String,
                            numRetries: Int,
                            waitInitial: FiniteDuration,
                            waitMaximum: FiniteDuration,
@@ -22,45 +22,46 @@ object DrsConfig {
   private val DefaultWaitMultiplier = 1.5d
   private val DefaultWaitRandomizationFactor = 0.1
 
-  private val EnvMarthaUrl = "MARTHA_URL"
-  private val EnvMarthaNumRetries = "MARTHA_NUM_RETRIES"
-  private val EnvMarthaWaitInitialSeconds = "MARTHA_WAIT_INITIAL_SECONDS"
-  private val EnvMarthaWaitMaximumSeconds = "MARTHA_WAIT_MAXIMUM_SECONDS"
-  private val EnvMarthaWaitMultiplier = "MARTHA_WAIT_MULTIPLIER"
-  private val EnvMarthaWaitRandomizationFactor = "MARTHA_WAIT_RANDOMIZATION_FACTOR"
+  private val EnvDrsResolverUrl = "DRS_RESOLVER_URL"
+  private val EnvDrsResolverNumRetries = "DRS_RESOLVER_NUM_RETRIES"
+  private val EnvDrsResolverWaitInitialSeconds = "DRS_RESOLVER_WAIT_INITIAL_SECONDS"
+  private val EnvDrsResolverWaitMaximumSeconds = "DRS_RESOLVER_WAIT_MAXIMUM_SECONDS"
+  private val EnvDrsResolverWaitMultiplier = "DRS_RESOLVER_WAIT_MULTIPLIER"
+  private val EnvDrsResolverWaitRandomizationFactor = "DRS_RESOLVER_WAIT_RANDOMIZATION_FACTOR"
 
-  def fromConfig(marthaConfig: Config): DrsConfig = {
+
+  def fromConfig(drsResolverConfig: Config): DrsConfig = {
     DrsConfig(
-      marthaUrl = marthaConfig.getString("url"),
-      numRetries = marthaConfig.getOrElse("num-retries", DefaultNumRetries),
-      waitInitial = marthaConfig.getOrElse("wait-initial", DefaultWaitInitial),
-      waitMaximum = marthaConfig.getOrElse("wait-maximum", DefaultWaitMaximum),
-      waitMultiplier = marthaConfig.getOrElse("wait-multiplier", DefaultWaitMultiplier),
+      drsResolverUrl = drsResolverConfig.getString("url"),
+      numRetries = drsResolverConfig.getOrElse("num-retries", DefaultNumRetries),
+      waitInitial = drsResolverConfig.getOrElse("wait-initial", DefaultWaitInitial),
+      waitMaximum = drsResolverConfig.getOrElse("wait-maximum", DefaultWaitMaximum),
+      waitMultiplier = drsResolverConfig.getOrElse("wait-multiplier", DefaultWaitMultiplier),
       waitRandomizationFactor =
-        marthaConfig.getOrElse("wait-randomization-factor", DefaultWaitRandomizationFactor),
+        drsResolverConfig.getOrElse("wait-randomization-factor", DefaultWaitRandomizationFactor),
     )
   }
 
   def fromEnv(env: Map[String, String]): DrsConfig = {
     DrsConfig(
-      marthaUrl = env(EnvMarthaUrl),
-      numRetries = env.get(EnvMarthaNumRetries).map(_.toInt).getOrElse(DefaultNumRetries),
-      waitInitial = env.get(EnvMarthaWaitInitialSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitInitial),
-      waitMaximum = env.get(EnvMarthaWaitMaximumSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitMaximum),
-      waitMultiplier = env.get(EnvMarthaWaitMultiplier).map(_.toDouble).getOrElse(DefaultWaitMultiplier),
+      drsResolverUrl = env(EnvDrsResolverUrl),
+      numRetries = env.get(EnvDrsResolverNumRetries).map(_.toInt).getOrElse(DefaultNumRetries),
+      waitInitial = env.get(EnvDrsResolverWaitInitialSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitInitial),
+      waitMaximum = env.get(EnvDrsResolverWaitMaximumSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitMaximum),
+      waitMultiplier = env.get(EnvDrsResolverWaitMultiplier).map(_.toDouble).getOrElse(DefaultWaitMultiplier),
       waitRandomizationFactor =
-        env.get(EnvMarthaWaitRandomizationFactor).map(_.toDouble).getOrElse(DefaultWaitRandomizationFactor),
+        env.get(EnvDrsResolverWaitRandomizationFactor).map(_.toDouble).getOrElse(DefaultWaitRandomizationFactor),
     )
   }
 
   def toEnv(drsConfig: DrsConfig): Map[String, String] = {
     Map(
-      EnvMarthaUrl -> drsConfig.marthaUrl,
-      EnvMarthaNumRetries -> s"${drsConfig.numRetries}",
-      EnvMarthaWaitInitialSeconds -> s"${drsConfig.waitInitial.toSeconds}",
-      EnvMarthaWaitMaximumSeconds -> s"${drsConfig.waitMaximum.toSeconds}",
-      EnvMarthaWaitMultiplier -> s"${drsConfig.waitMultiplier}",
-      EnvMarthaWaitRandomizationFactor -> s"${drsConfig.waitRandomizationFactor}",
+      EnvDrsResolverUrl -> drsConfig.drsResolverUrl,
+      EnvDrsResolverNumRetries -> s"${drsConfig.numRetries}",
+      EnvDrsResolverWaitInitialSeconds -> s"${drsConfig.waitInitial.toSeconds}",
+      EnvDrsResolverWaitMaximumSeconds -> s"${drsConfig.waitMaximum.toSeconds}",
+      EnvDrsResolverWaitMultiplier -> s"${drsConfig.waitMultiplier}",
+      EnvDrsResolverWaitRandomizationFactor -> s"${drsConfig.waitRandomizationFactor}",
     )
   }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
index 66a89fe4014..2d3e972508a 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
@@ -1,25 +1,32 @@
 package cloud.nio.impl.drs
 
 import cats.syntax.validated._
+import com.azure.core.credential.TokenRequestContext
+import com.azure.core.management.AzureEnvironment
+import com.azure.core.management.profile.AzureProfile
 import com.azure.identity.DefaultAzureCredentialBuilder
-import com.azure.security.keyvault.secrets.{SecretClient, SecretClientBuilder}
-import com.google.auth.oauth2.{AccessToken, OAuth2Credentials}
+import com.google.auth.oauth2.{AccessToken, GoogleCredentials, OAuth2Credentials}
 import com.typesafe.config.Config
-import common.validation.ErrorOr
 import common.validation.ErrorOr.ErrorOr
 import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.duration._
+import scala.jdk.DurationConverters._
+import scala.util.{Failure, Success, Try}
 
 /**
   * This trait allows us to abstract away different token attainment strategies
   * for different cloud environments.
   **/
-sealed trait DrsCredentials {
+trait DrsCredentials {
   def getAccessToken: ErrorOr[String]
 }
 
-case class GoogleDrsCredentials(credentials: OAuth2Credentials, acceptableTTL: Duration) extends DrsCredentials {
+/**
+  * Strategy for obtaining an access token from an existing OAuth credential. This class
+  * is designed for use within the Cromwell engine.
+  */
+case class GoogleOauthDrsCredentials(credentials: OAuth2Credentials, acceptableTTL: Duration) extends DrsCredentials {
   //Based on method from GoogleRegistry
   def getAccessToken: ErrorOr[String] = {
     def accessTokenTTLIsAcceptable(accessToken: AccessToken): Boolean = {
@@ -39,25 +46,68 @@ case class GoogleDrsCredentials(credentials: OAuth2Credentials, acceptableTTL: D
   }
 }
 
-object GoogleDrsCredentials {
-  def apply(credentials: OAuth2Credentials, config: Config): GoogleDrsCredentials =
-    GoogleDrsCredentials(credentials, config.as[FiniteDuration]("access-token-acceptable-ttl"))
+object GoogleOauthDrsCredentials {
+  def apply(credentials: OAuth2Credentials, config: Config): GoogleOauthDrsCredentials =
+    GoogleOauthDrsCredentials(credentials, config.as[FiniteDuration]("access-token-acceptable-ttl"))
+}
+
+
+/**
+  * Strategy for obtaining an access token from Google Application Default credentials that are assumed to already exist
+  * in the environment. This class is designed for use by standalone executables running in environments
+  * that have direct access to a Google identity (ex. CromwellDrsLocalizer).
+  */
+case object GoogleAppDefaultTokenStrategy extends DrsCredentials {
+  private final val UserInfoEmailScope = "https://www.googleapis.com/auth/userinfo.email"
+  private final val UserInfoProfileScope = "https://www.googleapis.com/auth/userinfo.profile"
+
+  def getAccessToken: ErrorOr[String] = {
+    Try {
+      val scopedCredentials = GoogleCredentials.getApplicationDefault().createScoped(UserInfoEmailScope, UserInfoProfileScope)
+      scopedCredentials.refreshAccessToken().getTokenValue
+    } match {
+      case Success(null) => "null token value attempting to refresh access token".invalidNel
+      case Success(value) => value.validNel
+      case Failure(e) => s"Failed to refresh access token: ${e.getMessage}".invalidNel
+    }
+  }
 }
 
-case class AzureDrsCredentials(identityClientId: Option[String], vaultName: String, secretName: String) extends DrsCredentials {
+/**
+  * Strategy for obtaining an access token in an environment with available Azure identity.
+  * If you need to disambiguate among multiple active user-assigned managed identities, pass
+  * in the client id of the identity that should be used.
+  */
+case class AzureDrsCredentials(identityClientId: Option[String]) extends DrsCredentials {
+
+  final val tokenAcquisitionTimeout = 5.seconds
 
-  lazy val secretClient: ErrorOr[SecretClient] = ErrorOr {
-    val defaultCreds = identityClientId.map(identityId =>
-      new DefaultAzureCredentialBuilder().managedIdentityClientId(identityId)
-    ).getOrElse(
-      new DefaultAzureCredentialBuilder()
-    ).build()
+  val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
+  val tokenScope = "https://management.azure.com/.default"
 
-    new SecretClientBuilder()
-      .vaultUrl(s"https://${vaultName}.vault.azure.net")
-      .credential(defaultCreds)
-      .buildClient()
+  def tokenRequestContext: TokenRequestContext = {
+    val trc = new TokenRequestContext()
+    trc.addScopes(tokenScope)
+    trc
   }
 
-  def getAccessToken: ErrorOr[String] = secretClient.map(_.getSecret(secretName).getValue)
+  def defaultCredentialBuilder: DefaultAzureCredentialBuilder =
+    new DefaultAzureCredentialBuilder()
+      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
+
+  def getAccessToken: ErrorOr[String] = {
+    val credentials = identityClientId.foldLeft(defaultCredentialBuilder) {
+      (builder, clientId) => builder.managedIdentityClientId(clientId)
+    }.build()
+
+    Try(
+      credentials
+        .getToken(tokenRequestContext)
+        .block(tokenAcquisitionTimeout.toJava)
+    ) match {
+      case Success(null) => "null token value attempting to obtain access token".invalidNel
+      case Success(token) => token.getToken.validNel
+      case Failure(error) => s"Failed to refresh access token: ${error.getMessage}".invalidNel
+    }
+  }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
index 9e0b45e259e..f9ae5b62e03 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
@@ -5,7 +5,7 @@ import cats.data.Validated.{Invalid, Valid}
 import cats.effect.{IO, Resource}
 import cats.implicits._
 import cloud.nio.impl.drs.DrsPathResolver.{FatalRetryDisposition, RegularRetryDisposition}
-import cloud.nio.impl.drs.MarthaResponseSupport._
+import cloud.nio.impl.drs.DrsResolverResponseSupport._
 import common.exception.{AggregatedMessageException, toIO}
 import common.validation.ErrorOr.ErrorOr
 import io.circe._
@@ -29,7 +29,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
   protected lazy val httpClientBuilder: HttpClientBuilder = {
     val clientBuilder = HttpClientBuilder.create()
     if (retryInternally) {
-      val retryHandler = new MarthaHttpRequestRetryStrategy(drsConfig)
+      val retryHandler = new DrsResolverHttpRequestRetryStrategy(drsConfig)
       clientBuilder
         .setRetryHandler(retryHandler)
         .setServiceUnavailableRetryStrategy(retryHandler)
@@ -39,11 +39,11 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
 
   def getAccessToken: ErrorOr[String]
 
-  private def makeHttpRequestToMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): Resource[IO, HttpPost] = {
+  private def makeHttpRequestToDrsResolver(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): Resource[IO, HttpPost] = {
     val io = getAccessToken match {
       case Valid(token) => IO {
-        val postRequest = new HttpPost(drsConfig.marthaUrl)
-        val requestJson = MarthaRequest(drsPath, fields).asJson.noSpaces
+        val postRequest = new HttpPost(drsConfig.drsResolverUrl)
+        val requestJson = DrsResolverRequest(drsPath, fields).asJson.noSpaces
         postRequest.setEntity(new StringEntity(requestJson, ContentType.APPLICATION_JSON))
         postRequest.setHeader("Authorization", s"Bearer $token")
         postRequest
@@ -54,7 +54,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
     Resource.eval(io)
   }
 
-  private def httpResponseToMarthaResponse(drsPathForDebugging: String)(httpResponse: HttpResponse): IO[MarthaResponse] = {
+  private def httpResponseToDrsResolverResponse(drsPathForDebugging: String)(httpResponse: HttpResponse): IO[DrsResolverResponse] = {
     val responseStatusLine = httpResponse.getStatusLine
     val status = responseStatusLine.getStatusCode
 
@@ -71,39 +71,39 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
       case s if s / 100 == 5 =>
         IO.raiseError(new RuntimeException(retryMessage) with RegularRetryDisposition)
       case _ =>
-        val marthaResponseEntityOption = Option(httpResponse.getEntity).map(EntityUtils.toString)
-        val exceptionMsg = errorMessageFromResponse(drsPathForDebugging, marthaResponseEntityOption, responseStatusLine, drsConfig.marthaUrl)
-        val responseEntityOption = (responseStatusLine.getStatusCode == HttpStatus.SC_OK).valueOrZero(marthaResponseEntityOption)
+        val drsResolverResponseEntityOption = Option(httpResponse.getEntity).map(EntityUtils.toString)
+        val exceptionMsg = errorMessageFromResponse(drsPathForDebugging, drsResolverResponseEntityOption, responseStatusLine, drsConfig.drsResolverUrl)
+        val responseEntityOption = (responseStatusLine.getStatusCode == HttpStatus.SC_OK).valueOrZero(drsResolverResponseEntityOption)
         val responseContentIO = toIO(responseEntityOption, exceptionMsg)
 
         responseContentIO.flatMap { responseContent =>
-          IO.fromEither(decode[MarthaResponse](responseContent))
+          IO.fromEither(decode[DrsResolverResponse](responseContent))
         }.handleErrorWith {
           e => IO.raiseError(new RuntimeException(s"Unexpected response during DRS resolution: ${ExceptionUtils.getMessage(e)}"))
         }
     }
   }
 
-  private def executeMarthaRequest(httpPost: HttpPost): Resource[IO, HttpResponse]= {
+  private def executeDrsResolverRequest(httpPost: HttpPost): Resource[IO, HttpResponse]= {
     for {
       httpClient <- Resource.fromAutoCloseable(IO(httpClientBuilder.build()))
       httpResponse <- Resource.fromAutoCloseable(IO(httpClient.execute(httpPost)))
     } yield httpResponse
   }
 
-  def rawMarthaResponse(drsPath: String, fields: NonEmptyList[MarthaField.Value]): Resource[IO, HttpResponse] = {
+  def rawDrsResolverResponse(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): Resource[IO, HttpResponse] = {
     for {
-      httpPost <- makeHttpRequestToMartha(drsPath, fields)
-      response <- executeMarthaRequest(httpPost)
+      httpPost <- makeHttpRequestToDrsResolver(drsPath, fields)
+      response <- executeDrsResolverRequest(httpPost)
     } yield response
   }
 
   /** *
-    * Resolves the DRS path through Martha url provided in the config.
-    * Please note, this method returns an IO that would make a synchronous HTTP request to Martha when run.
+    * Resolves the DRS path through DRS Resolver url provided in the config.
+    * Please note, this method returns an IO that would make a synchronous HTTP request to DRS Resolver when run.
     */
-  def resolveDrsThroughMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): IO[MarthaResponse] = {
-    rawMarthaResponse(drsPath, fields).use(httpResponseToMarthaResponse(drsPathForDebugging = drsPath))
+  def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
+    rawDrsResolverResponse(drsPath, fields).use(httpResponseToDrsResolverResponse(drsPathForDebugging = drsPath))
   }
 
   def openChannel(accessUrl: AccessUrl): IO[ReadableByteChannel] = {
@@ -144,7 +144,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
 }
 
 object DrsPathResolver {
-  final val ExtractUriErrorMsg = "No access URL nor GCS URI starting with 'gs://' found in Martha response!"
+  final val ExtractUriErrorMsg = "No access URL nor GCS URI starting with 'gs://' found in the DRS Resolver response!"
   sealed trait RetryDisposition
   // Should immediately fail the download attempt.
   trait FatalRetryDisposition extends RetryDisposition
@@ -152,27 +152,27 @@ object DrsPathResolver {
   trait RegularRetryDisposition extends RetryDisposition
 }
 
-object MarthaField extends Enumeration {
-  val GsUri: MarthaField.Value = Value("gsUri")
-  val Size: MarthaField.Value = Value("size")
-  val TimeCreated: MarthaField.Value = Value("timeCreated")
-  val TimeUpdated: MarthaField.Value = Value("timeUpdated")
-  val BondProvider: MarthaField.Value = Value("bondProvider")
-  val GoogleServiceAccount: MarthaField.Value = Value("googleServiceAccount")
-  val Hashes: MarthaField.Value = Value("hashes")
-  val FileName: MarthaField.Value = Value("fileName")
-  val AccessUrl: MarthaField.Value = Value("accessUrl")
-  val LocalizationPath: MarthaField.Value = Value("localizationPath")
+object DrsResolverField extends Enumeration {
+  val GsUri: DrsResolverField.Value = Value("gsUri")
+  val Size: DrsResolverField.Value = Value("size")
+  val TimeCreated: DrsResolverField.Value = Value("timeCreated")
+  val TimeUpdated: DrsResolverField.Value = Value("timeUpdated")
+  val BondProvider: DrsResolverField.Value = Value("bondProvider")
+  val GoogleServiceAccount: DrsResolverField.Value = Value("googleServiceAccount")
+  val Hashes: DrsResolverField.Value = Value("hashes")
+  val FileName: DrsResolverField.Value = Value("fileName")
+  val AccessUrl: DrsResolverField.Value = Value("accessUrl")
+  val LocalizationPath: DrsResolverField.Value = Value("localizationPath")
 }
 
-final case class MarthaRequest(url: String, fields: NonEmptyList[MarthaField.Value])
+final case class DrsResolverRequest(url: String, fields: NonEmptyList[DrsResolverField.Value])
 
 final case class SADataObject(data: Json)
 
 final case class AccessUrl(url: String, headers: Option[Map[String, String]])
 
 /**
-  * A response from `martha_v3`.
+  * A response from `drshub_v4`.
   *
   * @param size Size of the object stored at gsUri
   * @param timeCreated The creation time of the object at gsUri
@@ -187,34 +187,33 @@ final case class AccessUrl(url: String, headers: Option[Map[String, String]])
   *                         DRS metadata, via the `aliases` field. As this is a distinct field from `fileName` in DRS
   *                         metadata it is also made a distinct field in this response object.
   */
-final case class MarthaResponse(size: Option[Long] = None,
-                                timeCreated: Option[String] = None,
-                                timeUpdated: Option[String] = None,
-                                gsUri: Option[String] = None,
-                                bondProvider: Option[String] = None,
-                                googleServiceAccount: Option[SADataObject] = None,
-                                fileName: Option[String] = None,
-                                hashes: Option[Map[String, String]] = None,
-                                accessUrl: Option[AccessUrl] = None,
-                                localizationPath: Option[String] = None
+final case class DrsResolverResponse(size: Option[Long] = None,
+                                     timeCreated: Option[String] = None,
+                                     timeUpdated: Option[String] = None,
+                                     gsUri: Option[String] = None,
+                                     bondProvider: Option[String] = None,
+                                     googleServiceAccount: Option[SADataObject] = None,
+                                     fileName: Option[String] = None,
+                                     hashes: Option[Map[String, String]] = None,
+                                     accessUrl: Option[AccessUrl] = None,
+                                     localizationPath: Option[String] = None
                                )
 
-// Adapted from https://github.com/broadinstitute/martha/blob/f31933a3a11e20d30698ec4b4dc1e0abbb31a8bc/common/helpers.js#L210-L218
-final case class MarthaFailureResponse(response: MarthaFailureResponsePayload)
-final case class MarthaFailureResponsePayload(text: String)
+final case class DrsResolverFailureResponse(response: DrsResolverFailureResponsePayload)
+final case class DrsResolverFailureResponsePayload(text: String)
 
-object MarthaResponseSupport {
+object DrsResolverResponseSupport {
 
-  implicit lazy val marthaFieldEncoder: Encoder[MarthaField.Value] = Encoder.encodeEnumeration(MarthaField)
-  implicit lazy val marthaRequestEncoder: Encoder[MarthaRequest] = deriveEncoder
+  implicit lazy val drsResolverFieldEncoder: Encoder[DrsResolverField.Value] = Encoder.encodeEnumeration(DrsResolverField)
+  implicit lazy val drsResolverRequestEncoder: Encoder[DrsResolverRequest] = deriveEncoder
 
   implicit lazy val saDataObjectDecoder: Decoder[SADataObject] = deriveDecoder
-  implicit lazy val marthaResponseDecoder: Decoder[MarthaResponse] = deriveDecoder
+  implicit lazy val drsResolverResponseDecoder: Decoder[DrsResolverResponse] = deriveDecoder
 
-  implicit lazy val marthaFailureResponseDecoder: Decoder[MarthaFailureResponse] = deriveDecoder
-  implicit lazy val marthaFailureResponsePayloadDecoder: Decoder[MarthaFailureResponsePayload] = deriveDecoder
+  implicit lazy val drsResolverFailureResponseDecoder: Decoder[DrsResolverFailureResponse] = deriveDecoder
+  implicit lazy val drsResolverFailureResponsePayloadDecoder: Decoder[DrsResolverFailureResponsePayload] = deriveDecoder
 
-  implicit lazy val marthaAccessUrlDecoder: Decoder[AccessUrl] = deriveDecoder
+  implicit lazy val drsResolverAccessUrlDecoder: Decoder[AccessUrl] = deriveDecoder
 
   private val GcsScheme = "gs://"
 
@@ -223,18 +222,18 @@ object MarthaResponseSupport {
       (array(0), array(1))
   }
 
-  def errorMessageFromResponse(drsPathForDebugging: String, marthaResponseEntityOption: Option[String], responseStatusLine: StatusLine, marthaUri: String): String = {
-    val baseMessage = s"Could not access object \'$drsPathForDebugging\'. Status: ${responseStatusLine.getStatusCode}, reason: \'${responseStatusLine.getReasonPhrase}\', Martha location: \'$marthaUri\', message: "
+  def errorMessageFromResponse(drsPathForDebugging: String, drsResolverResponseEntityOption: Option[String], responseStatusLine: StatusLine, drsResolverUri: String): String = {
+    val baseMessage = s"Could not access object \'$drsPathForDebugging\'. Status: ${responseStatusLine.getStatusCode}, reason: \'${responseStatusLine.getReasonPhrase}\', DRS Resolver location: \'$drsResolverUri\', message: "
 
-    marthaResponseEntityOption match {
+    drsResolverResponseEntityOption match {
       case Some(entity) =>
-        val maybeErrorResponse: Either[Error, MarthaFailureResponse] = decode[MarthaFailureResponse](entity)
+        val maybeErrorResponse: Either[Error, DrsResolverFailureResponse] = decode[DrsResolverFailureResponse](entity)
         maybeErrorResponse match {
           case Left(_) =>
-            // Not parsable as a `MarthaFailureResponse`
+            // Not parsable as a `DrsResolverFailureResponse`
             baseMessage + s"\'$entity\'"
           case Right(decoded) =>
-            // Is a `MarthaFailureResponse`
+            // Is a `DrsResolverFailureResponse`
             baseMessage + s"\'${decoded.response.text}\'"
         }
       case None =>
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategy.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
similarity index 96%
rename from cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategy.scala
rename to cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
index 2881fc60b05..39020f5a684 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategy.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
@@ -7,7 +7,7 @@ import org.apache.http.HttpResponse
 import org.apache.http.client.{HttpRequestRetryHandler, ServiceUnavailableRetryStrategy}
 import org.apache.http.protocol.HttpContext
 
-class MarthaHttpRequestRetryStrategy(drsConfig: DrsConfig)
+class DrsResolverHttpRequestRetryStrategy(drsConfig: DrsConfig)
   extends ServiceUnavailableRetryStrategy with HttpRequestRetryHandler {
 
   // We can execute a total of one time, plus the number of retries
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
index fd7b71ef4ee..f61c608bd71 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
@@ -25,15 +25,15 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "parse a config and create a working file system provider" in {
     val config = ConfigFactory.parseString(
-      """martha.url = "https://from.config"
+      """resolver.url = "https://from.config"
         |access-token-acceptable-ttl = 1 minute
         |""".stripMargin
     )
 
     val fileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = config)
-    fileSystemProvider.drsConfig.marthaUrl should be("https://from.config")
+    fileSystemProvider.drsConfig.drsResolverUrl should be("https://from.config")
     fileSystemProvider.drsCredentials match {
-      case GoogleDrsCredentials(_, ttl) => ttl should be(1.minute)
+      case GoogleOauthDrsCredentials(_, ttl) => ttl should be(1.minute)
       case error => fail(s"Expected GoogleDrsCredentials, found $error")
     }
     fileSystemProvider.fileProvider should be(a[DrsCloudNioFileProvider])
@@ -79,19 +79,19 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "return a file provider that can read bytes from gcs" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrsThroughMartha(drsPath: String,
-                                           fields: NonEmptyList[MarthaField.Value],
-                                          ): IO[MarthaResponse] = {
-        IO(MarthaResponse(gsUri = Option("gs://bucket/object/path")))
+      override def resolveDrs(drsPath: String,
+                              fields: NonEmptyList[DrsResolverField.Value],
+                                          ): IO[DrsResolverResponse] = {
+        IO(DrsResolverResponse(gsUri = Option("gs://bucket/object/path")))
       }
     }
 
     val readChannel = mock[ReadableByteChannel]
-    val drsReadInterpreter: DrsReadInterpreter = (_, marthaResponse) => {
+    val drsReadInterpreter: DrsReadInterpreter = (_, drsResolverResponse) => {
       IO(
-        (marthaResponse.gsUri, marthaResponse.googleServiceAccount) match {
+        (drsResolverResponse.gsUri, drsResolverResponse.googleServiceAccount) match {
           case (Some("gs://bucket/object/path"), None) => readChannel
-          case _ => fail(s"Unexpected parameters passed: $marthaResponse")
+          case _ => fail(s"Unexpected parameters passed: $drsResolverResponse")
         }
       )
     }
@@ -105,19 +105,19 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "return a file provider that can read bytes from an access url" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrsThroughMartha(drsPath: String,
-                                           fields: NonEmptyList[MarthaField.Value],
-                                          ): IO[MarthaResponse] = {
-        IO(MarthaResponse(accessUrl = Option(AccessUrl("https://host/object/path", None))))
+      override def resolveDrs(drsPath: String,
+                              fields: NonEmptyList[DrsResolverField.Value],
+                                          ): IO[DrsResolverResponse] = {
+        IO(DrsResolverResponse(accessUrl = Option(AccessUrl("https://host/object/path", None))))
       }
     }
 
     val readChannel = mock[ReadableByteChannel]
-    val drsReadInterpreter: DrsReadInterpreter = (_, marthaResponse) => {
+    val drsReadInterpreter: DrsReadInterpreter = (_, drsResolverResponse) => {
       IO(
-        marthaResponse.accessUrl match {
+        drsResolverResponse.accessUrl match {
           case Some(AccessUrl("https://host/object/path", None)) => readChannel
-          case _ => fail(s"Unexpected parameters passed: $marthaResponse")
+          case _ => fail(s"Unexpected parameters passed: $drsResolverResponse")
         }
       )
     }
@@ -131,13 +131,13 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "return a file provider that can return file attributes" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrsThroughMartha(drsPath: String,
-                                           fields: NonEmptyList[MarthaField.Value],
-                                          ): IO[MarthaResponse] = {
+      override def resolveDrs(drsPath: String,
+                              fields: NonEmptyList[DrsResolverField.Value],
+                                          ): IO[DrsResolverResponse] = {
         val instantCreated = Instant.ofEpochMilli(123L)
         val instantUpdated = Instant.ofEpochMilli(456L)
         IO(
-          MarthaResponse(
+          DrsResolverResponse(
             size = Option(789L),
             timeCreated = Option(OffsetDateTime.ofInstant(instantCreated, ZoneOffset.UTC).toString),
             timeUpdated = Option(OffsetDateTime.ofInstant(instantUpdated, ZoneOffset.UTC).toString),
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
index 78585c96ed9..b4e5968e048 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
@@ -17,7 +17,7 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   private val md5HashValue = "336ea55913bc261b72875bd259753046"
   private val shaHashValue = "f76877f8e86ec3932fd2ae04239fbabb8c90199dab0019ae55fa42b31c314c44"
 
-  private val fullMarthaResponse = MarthaResponse(
+  private val fullDrsResolverResponse = DrsResolverResponse(
     size = Option(34905345),
     timeCreated = Option(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toString),
     timeUpdated = Option(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toString),
@@ -27,17 +27,17 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
     hashes = Option(Map("md5" -> md5HashValue, "crc32c" -> crcHashValue))
   )
 
-  private val fullMarthaResponseNoTz =
-    fullMarthaResponse
-      .copy(timeUpdated = fullMarthaResponse.timeUpdated.map(_.stripSuffix("Z")))
+  private val fullDrsResolverResponseNoTz =
+    fullDrsResolverResponse
+      .copy(timeUpdated = fullDrsResolverResponse.timeUpdated.map(_.stripSuffix("Z")))
 
-  private val fullMarthaResponseNoTime =
-    fullMarthaResponse
+  private val fullDrsResolverResponseNoTime =
+    fullDrsResolverResponse
       .copy(timeUpdated = None)
 
-  private val fullMarthaResponseBadTz =
-    fullMarthaResponse
-      .copy(timeUpdated = fullMarthaResponse.timeUpdated.map(_.stripSuffix("Z") + "BADTZ"))
+  private val fullDrsResolverResponseBadTz =
+    fullDrsResolverResponse
+      .copy(timeUpdated = fullDrsResolverResponse.timeUpdated.map(_.stripSuffix("Z") + "BADTZ"))
 
   private val etagHashValue = "something"
   private val completeHashesMap = Option(Map(
@@ -74,19 +74,19 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
 
   behavior of "fileHash()"
 
-  it should "return crc32c hash from `hashes` in Martha response when there is a crc32c" in {
+  it should "return crc32c hash from `hashes` in DRS Resolver response when there is a crc32c" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(completeHashesMap) shouldBe Option(FileHash(HashType.Crc32c, crcHashValue))
   }
 
-  it should "return md5 hash from `hashes` in Martha response when there is no crc32c" in {
+  it should "return md5 hash from `hashes` in DRS Resolver response when there is no crc32c" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(missingCRCHashesMap) shouldBe Option(FileHash(HashType.Md5, md5HashValue))
   }
 
-  it should "return sha256 hash from `hashes` in Martha response when there is only a sha256" in {
+  it should "return sha256 hash from `hashes` in DRS Resolver response when there is only a sha256" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(onlySHAHashesMap) shouldBe Option(FileHash(HashType.Sha256, shaHashValue))
   }
 
-  it should "return etag hash from `hashes` in Martha response when there is only an etag" in {
+  it should "return etag hash from `hashes` in DRS Resolver response when there is only an etag" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(onlyEtagHashesMap) shouldBe Option(FileHash(HashType.S3Etag, etagHashValue))
   }
 
@@ -127,10 +127,10 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
 
   it should "successfully parse a failure" in {
     import io.circe.parser.decode
-    import cloud.nio.impl.drs.MarthaResponseSupport.marthaFailureResponseDecoder
+    import cloud.nio.impl.drs.DrsResolverResponseSupport.drsResolverFailureResponseDecoder
 
-    val maybeDecoded = decode[MarthaFailureResponse](failureResponseJson)
-    maybeDecoded map { decoded: MarthaFailureResponse =>
+    val maybeDecoded = decode[DrsResolverFailureResponse](failureResponseJson)
+    maybeDecoded map { decoded: DrsResolverFailureResponse =>
       decoded.response.text shouldBe "{\"msg\":\"User 'null' does not have required action: read_data\",\"status_code\":500}"
     }
   }
@@ -139,37 +139,37 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
 
   val drsPathForDebugging = "drs://my_awesome_drs"
   val responseStatusLine = new BasicStatusLine(new ProtocolVersion("http", 1, 2) , 345, "test-reason")
-  val testMarthaUri = "www.martha_v3.com"
+  val testDrsResolverUri = "www.drshub_v4.com"
 
   it should "construct an error message from a populated, well-formed failure response" in {
     val failureResponse = Option(failureResponseJson)
 
-    MarthaResponseSupport.errorMessageFromResponse(drsPathForDebugging, failureResponse, responseStatusLine, testMarthaUri) shouldBe {
-      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', Martha location: 'www.martha_v3.com', message: '{\"msg\":\"User 'null' does not have required action: read_data\",\"status_code\":500}'"
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, failureResponse, responseStatusLine, testDrsResolverUri) shouldBe {
+      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: '{\"msg\":\"User 'null' does not have required action: read_data\",\"status_code\":500}'"
     }
   }
 
   it should "construct an error message from an empty failure response" in {
-    MarthaResponseSupport.errorMessageFromResponse(drsPathForDebugging, None, responseStatusLine, testMarthaUri) shouldBe {
-      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', Martha location: 'www.martha_v3.com', message: (empty response)"
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, None, responseStatusLine, testDrsResolverUri) shouldBe {
+      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: (empty response)"
     }
   }
 
-  // Technically we enter this case when preparing the "error message" for a successful response, because naturally `MarthaResponse` does not deserialize to `MarthaFailureResponse`
+  // Technically we enter this case when preparing the "error message" for a successful response, because naturally `DrsResolverResponse` does not deserialize to `DrsResolverFailureResponse`
   // But then there's no error so we throw it away :shrug:
   it should "construct an error message from a malformed failure response" in {
     val unparsableFailureResponse = Option("something went horribly wrong")
 
-    MarthaResponseSupport.errorMessageFromResponse(drsPathForDebugging, unparsableFailureResponse, responseStatusLine, testMarthaUri) shouldBe {
-      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', Martha location: 'www.martha_v3.com', message: 'something went horribly wrong'"
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, unparsableFailureResponse, responseStatusLine, testDrsResolverUri) shouldBe {
+      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: 'something went horribly wrong'"
     }
   }
 
   it should "resolve an ISO-8601 date with timezone" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponse.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponse.timeUpdated,
     )
     lastModifiedTimeIO.unsafeRunSync() should
       be(Option(FileTime.from(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toInstant)))
@@ -178,8 +178,8 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   it should "resolve an ISO-8601 date without timezone" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponseNoTz.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponseNoTz.timeUpdated,
     )
     lastModifiedTimeIO.unsafeRunSync() should
       be(Option(FileTime.from(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toInstant)))
@@ -188,8 +188,8 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   it should "not resolve an date that does not contain a timeUpdated" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponseNoTime.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponseNoTime.timeUpdated,
     )
     lastModifiedTimeIO.unsafeRunSync() should be(None)
   }
@@ -197,11 +197,11 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   it should "not resolve an date that is not ISO-8601" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponseBadTz.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponseBadTz.timeUpdated,
     )
     the[RuntimeException] thrownBy lastModifiedTimeIO.unsafeRunSync() should have message
-      "Error while parsing 'timeUpdated' value from Martha to FileTime for DRS path drs://my_awesome_drs. " +
+      "Error while parsing 'timeUpdated' value from DRS Resolver to FileTime for DRS path drs://my_awesome_drs. " +
         "Reason: DateTimeParseException: Text '2020-04-27T15:56:09.696BADTZ' could not be parsed at index 23."
   }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategySpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
similarity index 89%
rename from cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategySpec.scala
rename to cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
index 8fd1e948607..b221038bedb 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategySpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
@@ -12,13 +12,13 @@ import common.mock.MockSugar
 
 import scala.concurrent.duration._
 
-class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with MockSugar {
+class DrsResolverHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with MockSugar {
 
-  behavior of "MarthaHttpRequestRetryStrategy"
+  behavior of "DrsResolverHttpRequestRetryStrategy"
 
   it should "retry 500 errors a configured number of times" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val http500Response = mock[CloseableHttpResponse]
     http500Response.getStatusLine returns new BasicStatusLine(HttpVersion.HTTP_1_1, 500, "Testing 500")
     val httpContext = mock[HttpContext]
@@ -35,7 +35,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
 
   it should "retry 500 errors even after a number of 408/429 errors" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val http500Response = mock[CloseableHttpResponse]
     http500Response.getStatusLine returns new BasicStatusLine(HttpVersion.HTTP_1_1, 500, "Testing 500")
     val http408Response = mock[CloseableHttpResponse]
@@ -63,7 +63,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
 
   it should "not retry an HTTP 401" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val http400Response = mock[CloseableHttpResponse]
     http400Response.getStatusLine returns new BasicStatusLine(HttpVersion.HTTP_1_1, 401, "Testing 401")
     val httpContext = mock[HttpContext]
@@ -73,7 +73,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
 
   it should "retry IO exceptions a configured number of times" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val exception = mock[IOException]
     val httpContext = mock[HttpContext]
 
@@ -95,7 +95,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
         waitMaximum = 1.minute,
         waitRandomizationFactor = 0d,
       )
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
 
     retryStrategy.getRetryInterval should be(10000L)
     retryStrategy.getRetryInterval should be(20000L)
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
index 025d7c6d543..07a02e096dc 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
@@ -17,7 +17,7 @@ class MockDrsCloudNioFileSystemProvider(config: Config = mockConfig,
                                           ),
                                         mockResolver: Option[EngineDrsPathResolver] = None,
                                        )
-  extends DrsCloudNioFileSystemProvider(config, GoogleDrsCredentials(NoCredentials.getInstance, config), drsReadInterpreter) {
+  extends DrsCloudNioFileSystemProvider(config, GoogleOauthDrsCredentials(NoCredentials.getInstance, config), drsReadInterpreter) {
 
   override lazy val drsPathResolver: EngineDrsPathResolver = {
     mockResolver getOrElse
@@ -31,7 +31,7 @@ class MockDrsCloudNioFileSystemProvider(config: Config = mockConfig,
 
 object MockDrsCloudNioFileSystemProvider {
   private lazy val mockConfig = ConfigFactory.parseString(
-    """martha.url = "https://mock.martha"
+    """resolver.url = "https://mock.drshub"
       |access-token-acceptable-ttl = 1 hour
       |""".stripMargin
   )
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala
index b6825dcbbd2..a24385bc15f 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala
@@ -3,9 +3,9 @@ package cloud.nio.impl.drs
 import scala.concurrent.duration._
 
 object MockDrsPaths {
-  val marthaUrl = "http://mock.martha"
+  val drsResolverUrl = "http://mock.drshub"
 
-  val mockDrsConfig: DrsConfig = DrsConfig(MockDrsPaths.marthaUrl, 1, 1.seconds, 1.seconds, 1d, 0d)
+  val mockDrsConfig: DrsConfig = DrsConfig(MockDrsPaths.drsResolverUrl, 1, 1.seconds, 1.seconds, 1d, 0d)
 
   val mockToken = "mock.token"
 
@@ -35,5 +35,5 @@ object MockDrsPaths {
 
   val drsPathResolvingToNoGcsPath = s"$drsPathPrefix/226686cf-22c9-4472-9f79-7a0b0044f253"
 
-  val drsPathNotExistingInMartha = s"$drsPathPrefix/5e21b8c3-8eda-48d5-9a04-2b32e1571765"
+  val drsPathNotExistingInDrsResolver = s"$drsPathPrefix/5e21b8c3-8eda-48d5-9a04-2b32e1571765"
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
index 116155753f1..9e22544c38b 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
@@ -14,12 +14,12 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
                                 httpClientBuilderOverride: Option[HttpClientBuilder] = None,
                                 accessTokenAcceptableTTL: Duration = Duration.Inf,
                                )
-  extends EngineDrsPathResolver(drsConfig, GoogleDrsCredentials(NoCredentials.getInstance, accessTokenAcceptableTTL)) {
+  extends EngineDrsPathResolver(drsConfig, GoogleOauthDrsCredentials(NoCredentials.getInstance, accessTokenAcceptableTTL)) {
 
   override protected lazy val httpClientBuilder: HttpClientBuilder =
     httpClientBuilderOverride getOrElse MockSugar.mock[HttpClientBuilder]
 
-  private lazy val mockMarthaUri = drsConfig.marthaUrl
+  private lazy val mockDrsResolverUri = drsConfig.drsResolverUrl
 
   private val hashesObj = Map(
     "md5" -> "336ea55913bc261b72875bd259753046",
@@ -27,8 +27,8 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
     "crc32c" -> "8a366443"
   )
 
-  private val marthaObjWithGcsPath =
-    MarthaResponse(
+  private val drsResolverObjWithGcsPath =
+    DrsResolverResponse(
       size = Option(156018255),
       timeCreated = Option("2020-04-27T15:56:09.696Z"),
       timeUpdated = Option("2020-04-27T15:56:09.696Z"),
@@ -36,27 +36,27 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
       hashes = Option(hashesObj)
     )
 
-  private val marthaObjWithFileName = marthaObjWithGcsPath.copy(fileName = Option("file.txt"))
+  private val drsResolverObjWithFileName = drsResolverObjWithGcsPath.copy(fileName = Option("file.txt"))
 
-  private val marthaObjWithLocalizationPath = marthaObjWithGcsPath.copy(localizationPath = Option("/dir/subdir/file.txt"))
+  private val drsResolverObjWithLocalizationPath = drsResolverObjWithGcsPath.copy(localizationPath = Option("/dir/subdir/file.txt"))
 
-  private val marthaObjWithAllThePaths = marthaObjWithLocalizationPath.copy(fileName = marthaObjWithFileName.fileName)
+  private val drsResolverObjWithAllThePaths = drsResolverObjWithLocalizationPath.copy(fileName = drsResolverObjWithFileName.fileName)
 
-  private val marthaObjWithNoGcsPath = marthaObjWithGcsPath.copy(gsUri = None)
+  private val drsResolverObjWithNoGcsPath = drsResolverObjWithGcsPath.copy(gsUri = None)
 
-  override def resolveDrsThroughMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): IO[MarthaResponse] = {
+  override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
     drsPath match {
-      case MockDrsPaths.drsPathResolvingGcsPath => IO(marthaObjWithGcsPath)
-      case MockDrsPaths.drsPathWithNonPathChars => IO(marthaObjWithGcsPath)
-      case MockDrsPaths.drsPathResolvingWithFileName => IO(marthaObjWithFileName)
-      case MockDrsPaths.drsPathResolvingWithLocalizationPath => IO.pure(marthaObjWithLocalizationPath)
-      case MockDrsPaths.drsPathResolvingWithAllThePaths => IO.pure(marthaObjWithAllThePaths)
-      case MockDrsPaths.drsPathResolvingToNoGcsPath => IO(marthaObjWithNoGcsPath)
-      case MockDrsPaths.drsPathNotExistingInMartha =>
+      case MockDrsPaths.drsPathResolvingGcsPath => IO(drsResolverObjWithGcsPath)
+      case MockDrsPaths.drsPathWithNonPathChars => IO(drsResolverObjWithGcsPath)
+      case MockDrsPaths.drsPathResolvingWithFileName => IO(drsResolverObjWithFileName)
+      case MockDrsPaths.drsPathResolvingWithLocalizationPath => IO.pure(drsResolverObjWithLocalizationPath)
+      case MockDrsPaths.drsPathResolvingWithAllThePaths => IO.pure(drsResolverObjWithAllThePaths)
+      case MockDrsPaths.drsPathResolvingToNoGcsPath => IO(drsResolverObjWithNoGcsPath)
+      case MockDrsPaths.`drsPathNotExistingInDrsResolver` =>
         IO.raiseError(
           new RuntimeException(
-            s"Unexpected response resolving ${MockDrsPaths.drsPathNotExistingInMartha} " +
-              s"through Martha url $mockMarthaUri. Error: 404 Not Found."
+            s"Unexpected response resolving ${MockDrsPaths.drsPathNotExistingInDrsResolver} " +
+              s"through DRS Resolver url $mockDrsResolverUri. Error: 404 Not Found."
           )
         )
     }
diff --git a/codegen_java/build.sbt b/codegen_java/build.sbt
index 2ba35a693c3..0ad461a66b8 100644
--- a/codegen_java/build.sbt
+++ b/codegen_java/build.sbt
@@ -6,7 +6,7 @@ lazy val root = (project in file(".")).
     Seq(organization := "org.broadinstitute.cromwell",
     name := "cromwell-client",
     version := createVersion("0.1"),
-    scalaVersion := "2.13.8",
+    scalaVersion := "2.13.9",
     scalacOptions ++= Seq("-feature"),
     compile / javacOptions ++= Seq("-Xlint:deprecation"),
     Compile / packageDoc / publishArtifact := false,
diff --git a/common/src/main/scala/common/util/TerminalUtil.scala b/common/src/main/scala/common/util/TerminalUtil.scala
index dab7fb9ce17..cb7c980aecb 100644
--- a/common/src/main/scala/common/util/TerminalUtil.scala
+++ b/common/src/main/scala/common/util/TerminalUtil.scala
@@ -6,10 +6,10 @@ object TerminalUtil {
     def maxWidth(lengths: Seq[Seq[Int]], column: Int) = lengths.map { length => length(column) }.max
     val widths = (rows :+ header).map { row => row.map { s => s.length } }
     val maxWidths = widths.head.indices.map { column => maxWidth(widths, column) }
-    val tableHeader = header.indices.map { i => header(i).padTo(maxWidths(i), " ").mkString("") }.mkString("|")
+    val tableHeader = header.indices.map { i => header(i).padTo(maxWidths(i), ' ').mkString("") }.mkString("|")
     val tableDivider = header.indices.map { i => "-" * maxWidths(i) }.mkString("|")
     val tableRows = rows.map { row =>
-      val mdRow = row.indices.map { i => row(i).padTo(maxWidths(i), " ").mkString("") }.mkString("|")
+      val mdRow = row.indices.map { i => row(i).padTo(maxWidths(i), ' ').mkString("") }.mkString("|")
       s"|$mdRow|"
     }
     s"|$tableHeader|\n|$tableDivider|\n${tableRows.mkString("\n")}\n"
diff --git a/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala b/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala
index 12dba2e15d9..d2e0a38878c 100644
--- a/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala
+++ b/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala
@@ -11,7 +11,7 @@ class EnhancedCollectionsSpec extends AsyncFlatSpec with Matchers {
   behavior of "EnhancedCollections"
 
   it should "filter a List by type and return a List" in {
-    val objectList = List("hello", 3, None, "world")
+    val objectList = List[Any]("hello", 3, None, "world")
     val stringList = objectList.filterByType[String]
 
     stringList should be(List("hello", "world"))
@@ -28,14 +28,14 @@ class EnhancedCollectionsSpec extends AsyncFlatSpec with Matchers {
   }
 
   it should "filter a Set by type and return a Set" in {
-    val objectSet = Set("hello", 3, None, "world")
+    val objectSet = Set[Any]("hello", 3, None, "world")
     val intSet: Set[Int] = objectSet.filterByType[Int]
 
     intSet should be(Set(3))
   }
 
   it should "find the first Int in a List" in {
-    val objectSet = List("hello", 3, None, 4, "world")
+    val objectSet = List[Any]("hello", 3, None, 4, "world")
     objectSet.firstByType[Int] should be(Some(3))
   }
 
diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index 41d2b2c14bd..dd2f14c06c8 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -328,8 +328,8 @@ filesystems {
       # Class to instantiate and propagate to all factories. Takes a single typesafe config argument
       class = "cromwell.filesystems.drs.DrsFileSystemConfig"
       config {
-        martha {
-          url = "https://martha-url-here"
+        resolver {
+          url = "https://martha-url-here or https://drshub-url-here"
           # When true (and when possible) any DrsPath will be internally converted to another compatible Path such as a
           # GcsPath. This enables other optimizations such as using batch requests for GCS for hashes, using the
           # existing GCS downloader in Papi, etc.
@@ -441,6 +441,10 @@ engine {
 languages {
   default: WDL
   WDL {
+    http-allow-list {
+      enabled: false
+      allowed-http-hosts: []
+    }
     versions {
       default: "draft-2"
       "draft-2" {
@@ -468,29 +472,6 @@ languages {
       }
     }
   }
-  CWL {
-    versions {
-      default: "v1.0"
-      "v1.0" {
-        language-factory = "languages.cwl.CwlV1_0LanguageFactory"
-        config {
-          strict-validation: false
-          enabled: true
-
-          # Optional section to define a command returning paths to output files that
-          # can only be known after the user's command has been run
-          output-runtime-extractor {
-            # Optional docker image on which the command should be run - Must have bash if provided
-            docker-image = "stedolan/jq@sha256:a61ed0bca213081b64be94c5e1b402ea58bc549f457c2682a86704dd55231e09"
-            # Single line command executed after the tool has run.
-            # It should write to stdout the file paths that are referenced in the cwl.output.json (or any other file path
-            # not already defined in the outputs of the tool and therefore unknown when the tool is run)
-            command = "cat cwl.output.json 2>/dev/null | jq -r '.. | .path? // .location? // empty'"
-          }
-        }
-      }
-    }
-  }
 }
 
 ontology {
diff --git a/core/src/main/scala/cromwell/core/io/IoCommand.scala b/core/src/main/scala/cromwell/core/io/IoCommand.scala
index a21b6f8cebd..7d71f9bd307 100644
--- a/core/src/main/scala/cromwell/core/io/IoCommand.scala
+++ b/core/src/main/scala/cromwell/core/io/IoCommand.scala
@@ -38,6 +38,12 @@ trait IoCommand[+T] {
 
   def commandDescription: String
 
+  /**
+    * IO commands side-effect and/or have exceptions. We don't want that when evaluating identity, e.g. to check presence in cache.
+    * @return Hash code based on the description, which captures file path & action
+    */
+  override def hashCode(): Int = commandDescription.hashCode
+
   def logIOMsgOverLimit(message: => String): Unit = {
     val millis: Long = java.time.Duration.between(creation, OffsetDateTime.now).toMillis
     if (millis > IoCommand.IOCommandWarnLimit.toMillis) {
diff --git a/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala b/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
index 15097a92a99..dd8f44464f3 100644
--- a/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
+++ b/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
@@ -10,6 +10,8 @@ import scala.concurrent.duration.FiniteDuration
 object IoPromiseProxyActor {
   case class IoCommandWithPromise[A](ioCommand: IoCommand[A], timeout: FiniteDuration = defaultTimeout) {
     val promise = Promise[A]()
+
+    override def hashCode(): Int = ioCommand.hashCode()
   }
   def props(ioActor: ActorRef) = Props(new IoPromiseProxyActor(ioActor))
 }
diff --git a/core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala b/core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala
new file mode 100644
index 00000000000..dcf62bc0b28
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala
@@ -0,0 +1,70 @@
+package cromwell.core.logging
+
+import ch.qos.logback.classic.pattern.DateConverter
+import ch.qos.logback.classic.spi.ILoggingEvent
+import ch.qos.logback.core.CoreConstants
+import ch.qos.logback.core.util.CachingDateFormatter
+
+import java.util.TimeZone
+import scala.jdk.CollectionConverters._
+
+/**
+  * Log the Akka akkaTimestamp if found in the MDC, otherwise log the original event timestamp.
+  *
+  *   - https://doc.akka.io/docs/akka/current/logging.html#more-accurate-timestamps-for-log-output-in-mdc
+  *   - https://logback.qos.ch/manual/layouts.html#customConversionSpecifier
+  *
+  * NOTE: For proper configuration both this EnhancedDateConverter should be configured into the logback.xml AND the
+  * configuration file should set akka.loggers = ["cromwell.core.logging.EnhancedSlf4jLogger"].
+  */
+class EnhancedDateConverter extends DateConverter {
+  protected var cachingDateFormatterProtected: CachingDateFormatter = _
+
+  /* Duplicated from ch.qos.logback.classic.pattern.DateConverter as cachingDateFormatter is package private. */
+  override def start(): Unit = {
+    cachingDateFormatterProtected = Option(getFirstOption) match {
+      case Some(CoreConstants.ISO8601_STR) | None => new CachingDateFormatter(CoreConstants.ISO8601_PATTERN)
+      case Some(datePattern) =>
+        try {
+          new CachingDateFormatter(datePattern)
+        } catch {
+          case e: IllegalArgumentException =>
+            addWarn("Could not instantiate SimpleDateFormat with pattern " + datePattern, e)
+            // default to the ISO8601 format
+            new CachingDateFormatter(CoreConstants.ISO8601_PATTERN)
+        }
+    }
+    // if the option list contains a TZ option, then set it.
+    Option(getOptionList)
+      .toList
+      .flatMap(_.asScala)
+      .drop(1)
+      .headOption
+      .map(TimeZone.getTimeZone)
+      .foreach(cachingDateFormatterProtected.setTimeZone)
+
+    // Allow the parent class to start/initialize its private members.
+    super.start()
+  }
+
+  /**
+    * Look for the Akka timestamp and use that to format the date.
+    *
+    * Until this (currently 6+ year) issue is resolved, formatting the date as a Long requires using the
+    * [[EnhancedSlf4jLogger]] versus Akka's basic Slf4jLogger.
+    *
+    *   - https://github.com/akka/akka/issues/18079#issuecomment-125175884
+    */
+  override def convert(event: ILoggingEvent): String = {
+    val mdc = event.getMDCPropertyMap
+    if (mdc.containsKey("akkaTimestamp")) {
+      val timestamp = mdc.get("akkaTimestamp")
+      timestamp.toLongOption match {
+        case Some(value) => cachingDateFormatterProtected.format(value)
+        case None => timestamp // Return the original timestamp string.
+      }
+    } else {
+      super.convert(event)
+    }
+  }
+}
diff --git a/core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala b/core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala
new file mode 100644
index 00000000000..0999ec18055
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala
@@ -0,0 +1,16 @@
+package cromwell.core.logging
+
+import akka.event.slf4j.Slf4jLogger
+
+class EnhancedSlf4jLogger extends Slf4jLogger {
+  /**
+    * Format the timestamp as a simple long. Allows the akkaTimestamp to be retrieved later from the MDC by custom
+    * converters.
+    *
+    * NOTE: Should not be necessary once this issue is resolved: 
+    *   - https://github.com/akka/akka/issues/18079#issuecomment-125175884
+    *
+    * @see [[EnhancedDateConverter.convert()]]
+    */
+  override protected def formatTimestamp(timestamp: Long): String = String.valueOf(timestamp)
+}
diff --git a/core/src/main/scala/cromwell/core/logging/EnhancedThreadConverter.scala b/core/src/main/scala/cromwell/core/logging/EnhancedThreadConverter.scala
new file mode 100644
index 00000000000..73f5876597b
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/logging/EnhancedThreadConverter.scala
@@ -0,0 +1,21 @@
+package cromwell.core.logging
+
+import ch.qos.logback.classic.pattern.ThreadConverter
+import ch.qos.logback.classic.spi.ILoggingEvent
+
+/**
+  * Log the Akka sourceThread if found, otherwise log the event thread.
+  * 
+  *   - https://doc.akka.io/docs/akka/current/logging.html#logging-thread-akka-source-and-actor-system-in-mdc
+  *   - https://logback.qos.ch/manual/layouts.html#customConversionSpecifier
+  */
+class EnhancedThreadConverter extends ThreadConverter {
+  override def convert(event: ILoggingEvent): String = {
+    val mdc = event.getMDCPropertyMap
+    if (mdc.containsKey("sourceThread")) {
+      mdc.get("sourceThread")
+    } else {
+      super.convert(event)
+    }
+  }
+}
diff --git a/core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala b/core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala
new file mode 100644
index 00000000000..1dc10fab46d
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala
@@ -0,0 +1,39 @@
+package cromwell.core.logging
+
+import ch.qos.logback.classic.LoggerContext
+import ch.qos.logback.classic.jul.LevelChangePropagator
+import org.slf4j.LoggerFactory
+import org.slf4j.bridge.SLF4JBridgeHandler
+
+import scala.jdk.CollectionConverters._
+
+object JavaLoggingBridge {
+  /**
+    * Replace java.util.logging with SLF4J while ensuring Logback is configured with a LevelChangePropogator.
+    *
+    * One likely won't need to do this but just in case: note that any libraries using JUL running BEFORE this
+    * initialization which require increasing or decreasing verbosity must be configured via JUL not Logback.
+    *
+    * See also:
+    *   - https://www.slf4j.org/api/org/slf4j/bridge/SLF4JBridgeHandler.html
+    *   - https://docs.oracle.com/en/java/javase/11/docs/api/java.logging/java/util/logging/LogManager.html
+    */
+  def init(): Unit = {
+    // Retrieve the Logback context, and as a side effect initialize Logback.
+    val ctx = LoggerFactory.getILoggerFactory.asInstanceOf[LoggerContext]
+
+    // Ensure that Logback has a LevelChangePropagator, either here or via a logback.xml.
+    val listeners = ctx.getCopyOfListenerList.asScala
+    if (!listeners.exists(_.isInstanceOf[LevelChangePropagator])) {
+      val propagator = new LevelChangePropagator()
+      propagator.setContext(ctx)
+      propagator.start()
+    }
+
+    // Remove all the JUL logging handlers.
+    SLF4JBridgeHandler.removeHandlersForRootLogger()
+
+    // Send all JUL logging to SLF4J.
+    SLF4JBridgeHandler.install()
+  }
+}
diff --git a/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala b/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
index 91f05b10ef7..20a2afdd5ce 100644
--- a/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
+++ b/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
@@ -2,6 +2,7 @@ package cromwell.core.path
 
 import akka.actor.ActorSystem
 import cromwell.core.WorkflowOptions
+import cromwell.core.path.PathBuilderFactory.PriorityDefault
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -9,4 +10,6 @@ case object DefaultPathBuilderFactory extends PathBuilderFactory {
   override def withOptions(options: WorkflowOptions)(implicit actorSystem: ActorSystem, ec: ExecutionContext) = Future.successful(DefaultPathBuilder)
   val name = "local"
   val tuple = name -> this
+
+  override def priority: Int = PriorityDefault
 }
diff --git a/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala b/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
index 1f215ba2933..79adaae4d6b 100644
--- a/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
+++ b/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
@@ -5,6 +5,7 @@ import cromwell.core.{Dispatcher, WorkflowOptions}
 import cats.syntax.traverse._
 import cats.instances.list._
 import cats.instances.future._
+import cromwell.core.path.PathBuilderFactory.PriorityStandard
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -12,16 +13,13 @@ object PathBuilderFactory {
   // Given a list of factories, instantiates the corresponding path builders
   def instantiatePathBuilders(factories: List[PathBuilderFactory], workflowOptions: WorkflowOptions)(implicit as: ActorSystem): Future[List[PathBuilder]] = {
     implicit val ec: ExecutionContext = as.dispatchers.lookup(Dispatcher.IoDispatcher)
-    // The DefaultPathBuilderFactory always needs to be last.
-    // The reason is path builders are tried in order, and the default one is very generous in terms of paths it "thinks" it supports
-    // For instance, it will return a Path for a gcs url even though it doesn't really support it
-    val sortedFactories = factories.sortWith({
-      case (_, DefaultPathBuilderFactory) => true
-      case (DefaultPathBuilderFactory, _) => false
-      case (a, b) => factories.indexOf(a) < factories.indexOf(b)
-    })
+    val sortedFactories = factories.sortBy(_.priority)
     sortedFactories.traverse(_.withOptions(workflowOptions))
   }
+
+  val PriorityBlob     = 100   // High priority to evaluate first, because blob files may inadvertently match other filesystems
+  val PriorityStandard = 1000
+  val PriorityDefault  = 10000 // "Default" is a fallback, evaluate last
 }
 
 /**
@@ -29,4 +27,11 @@ object PathBuilderFactory {
   */
 trait PathBuilderFactory {
   def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder]
+
+  /**
+    * Candidate filesystems are considered in a stable order, as some requests may match multiple filesystems.
+    * To customize this order, the priority of a filesystem may be adjusted. Lower number == higher priority.
+    * @return This filesystem's priority
+    */
+  def priority: Int = PriorityStandard
 }
diff --git a/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala b/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
index f77df6fa011..06132ba152b 100644
--- a/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
+++ b/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
@@ -27,7 +27,7 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
     val testActor = TestActorRef(new IoClientHelperTestActor(ioActorProbe.ref, delegateProbe.ref, backoff, noResponseTimeout))
 
     val command = DefaultIoSizeCommand(mock[Path])
-    val response = IoSuccess(command, 5)
+    val response = IoSuccess(command, 5L)
 
     // Send the command
     testActor.underlyingActor.sendMessage(command)
@@ -58,7 +58,7 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
 
     val commandContext = "context"
     val command = DefaultIoSizeCommand(mock[Path])
-    val response = IoSuccess(command, 5)
+    val response = IoSuccess(command, 5L)
 
     // Send the command
     testActor.underlyingActor.sendMessageWithContext(commandContext, command)
diff --git a/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala b/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
index 58fa597dc03..c6a008feb02 100644
--- a/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
+++ b/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
@@ -54,7 +54,7 @@ class BackoffSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   it should "parse config" in {
     val config = ConfigFactory.parseMap(
-      Map(
+      Map[String, Any](
         "min" -> "5 seconds",
         "max" -> "30 seconds",
         "multiplier" -> 6D,
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
index df0f7c2eba6..3b7be2b38bd 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
@@ -14,40 +14,55 @@ class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage)
 
   head("cromwell-drs-localizer", localizerVersion)
 
-  arg[String]("drs-object-id").text("DRS object ID").required().
+  arg[String]("drs-object-id").text("DRS object ID").optional().
     action((s, c) =>
       c.copy(drsObject = Option(s)))
-  arg[String]("container-path").text("Container path").required().
+  arg[String]("container-path").text("Container path").optional().
     action((s, c) =>
       c.copy(containerPath = Option(s)))
-  arg[String]("requester-pays-project").text("Requester pays project").optional().
+  arg[String]("requester-pays-project").text(s"Requester pays project (only valid with '$Google' auth strategy)").optional().
     action((s, c) =>
       c.copy(googleRequesterPaysProject = Option(s)))
+  opt[String]('m', "manifest-path").text("File path of manifest containing multiple files to localize").
+    action((s, c) =>
+      c.copy(manifestPath = Option(s)))
+  opt[String]('r', "requester-pays-project").text(s"Requester pays project (only valid with '$Google' auth strategy)").optional().
+    action((s, c) => {
+      c.copy(
+        googleRequesterPaysProject = Option(s),
+        googleRequesterPaysProjectConflict = c.googleRequesterPaysProject.exists(_ != s)
+      )
+    })
   opt[String]('t', "access-token-strategy").text(s"Access token strategy, must be one of '$Azure' or '$Google' (default '$Google')").
     action((s, c) =>
       c.copy(accessTokenStrategy = Option(s.toLowerCase())))
-  opt[String]('v', "vault-name").text("Azure vault name").
-    action((s, c) =>
-      c.copy(azureVaultName = Option(s)))
-  opt[String]('s', "secret-name").text("Azure secret name").
-    action((s, c) =>
-      c.copy(azureSecretName = Option(s)))
   opt[String]('i', "identity-client-id").text("Azure identity client id").
     action((s, c) =>
       c.copy(azureIdentityClientId = Option(s)))
+  checkConfig(c =>
+    if (c.googleRequesterPaysProjectConflict)
+      failure("Requester pays project differs between positional argument and option flag")
+    else success
+  )
   checkConfig(c =>
     c.accessTokenStrategy match {
       case Some(Azure) if c.googleRequesterPaysProject.nonEmpty =>
         Left(s"Requester pays project is only valid with access token strategy '$Google'")
-      case Some(Azure) if List(c.azureVaultName, c.azureSecretName).exists(_.isEmpty) =>
-        Left(s"Both vault name and secret name must be specified for access token strategy $Azure")
+      case Some(Google) if c.azureIdentityClientId.nonEmpty =>
+        Left(s"Identity client id is only valid with access token strategy '$Azure'")
       case Some(Azure) => Right(())
-      case Some(Google) if List(c.azureSecretName, c.azureVaultName, c.azureIdentityClientId).forall(_.isEmpty) => Right(())
-      case Some(Google) => Left(s"One or more specified options are only valid with access token strategy '$Azure'")
+      case Some(Google) => Right(())
       case Some(huh) => Left(s"Unrecognized access token strategy '$huh'")
       case None => Left("Programmer error, access token strategy should not be None")
     }
   )
+  checkConfig(c =>
+    (c.drsObject, c.containerPath, c.manifestPath) match {
+      case (Some(_), Some(_), None) => Right(())
+      case (None, None, Some(_)) => Right(())
+      case _ => Left("Must provide either DRS path and container path, OR manifest file (-m).")
+    }
+  )
 }
 
 object CommandLineParser {
@@ -64,9 +79,12 @@ object CommandLineParser {
   val Usage =
     s"""
 Usage:
-    java -jar /path/to/localizer.jar [options] drs://provider/object /local/path/to/file.txt [requester pays project]
 
-    Note that the <requester pays project> optional argument is only valid with access token strategy 'Google'.
+    Can be run to localize a single file with DRS id and local container path provided in args:
+    java -jar /path/to/localizer.jar [options] drs://provider/object /local/path/to/file.txt
+
+    Can also be used to localize multiple files in one invocation with manifest file provided in args:
+    java -jar /path/to/localizer.jar [options] -m /local/path/to/manifest/file
     """
 
 }
@@ -75,6 +93,6 @@ case class CommandLineArguments(accessTokenStrategy: Option[String] = Option(Goo
                                 drsObject: Option[String] = None,
                                 containerPath: Option[String] = None,
                                 googleRequesterPaysProject: Option[String] = None,
-                                azureVaultName: Option[String] = None,
-                                azureSecretName: Option[String] = None,
-                                azureIdentityClientId: Option[String] = None)
+                                azureIdentityClientId: Option[String] = None,
+                                manifestPath: Option[String] = None,
+                                googleRequesterPaysProjectConflict: Boolean = false)
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
index ac27367b932..944d418acbb 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
@@ -1,10 +1,9 @@
 package drs.localizer
 
-import cloud.nio.impl.drs.{DrsConfig, DrsPathResolver}
+import cloud.nio.impl.drs.{DrsConfig, DrsCredentials, DrsPathResolver}
 import common.validation.ErrorOr.ErrorOr
-import drs.localizer.accesstokens.AccessTokenStrategy
 
 
-class DrsLocalizerDrsPathResolver(drsConfig: DrsConfig, accessTokenStrategy: AccessTokenStrategy) extends DrsPathResolver(drsConfig) {
-  override def getAccessToken: ErrorOr[String] = accessTokenStrategy.getAccessToken()
+class DrsLocalizerDrsPathResolver(drsConfig: DrsConfig, drsCredentials: DrsCredentials) extends DrsPathResolver(drsConfig) {
+  override def getAccessToken: ErrorOr[String] = drsCredentials.getAccessToken
 }
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
index c7ecdd3f3e4..1858f395024 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
@@ -2,16 +2,20 @@ package drs.localizer
 
 import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO, IOApp}
+import cats.implicits._
 import cloud.nio.impl.drs.DrsPathResolver.{FatalRetryDisposition, RegularRetryDisposition}
-import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsPathResolver, MarthaField}
+import cloud.nio.impl.drs._
 import cloud.nio.spi.{CloudNioBackoff, CloudNioSimpleExponentialBackoff}
 import com.typesafe.scalalogging.StrictLogging
 import drs.localizer.CommandLineParser.AccessTokenStrategy.{Azure, Google}
-import drs.localizer.accesstokens.{AccessTokenStrategy, AzureB2CAccessTokenStrategy, GoogleAccessTokenStrategy}
 import drs.localizer.downloaders.AccessUrlDownloader.Hashes
 import drs.localizer.downloaders._
+import org.apache.commons.csv.{CSVFormat, CSVParser}
 
+import java.io.File
+import java.nio.charset.Charset
 import scala.concurrent.duration._
+import scala.jdk.CollectionConverters._
 import scala.language.postfixOps
 
 object DrsLocalizerMain extends IOApp with StrictLogging {
@@ -24,8 +28,8 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
     val localize: Option[IO[ExitCode]] = for {
       pa <- parsedArgs
       run <- pa.accessTokenStrategy.collect {
-        case Azure => runLocalizer(pa, AzureB2CAccessTokenStrategy(pa))
-        case Google => runLocalizer(pa, GoogleAccessTokenStrategy)
+        case Azure => runLocalizer(pa, AzureDrsCredentials(pa.azureIdentityClientId))
+        case Google => runLocalizer(pa, GoogleAppDefaultTokenStrategy)
       }
     } yield run
 
@@ -50,23 +54,40 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
     IO.pure(ExitCode.Error)
   }
 
-  def runLocalizer(commandLineArguments: CommandLineArguments, accessTokenStrategy: AccessTokenStrategy): IO[ExitCode] = {
-    val drsObject = commandLineArguments.drsObject.get
-    val containerPath = commandLineArguments.containerPath.get
-    new DrsLocalizerMain(drsObject, containerPath, accessTokenStrategy, commandLineArguments.googleRequesterPaysProject).
+  def runLocalizer(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials): IO[ExitCode] = {
+    commandLineArguments.manifestPath match {
+      case Some(manifestPath) =>
+        val manifestFile = new File(manifestPath)
+        val csvParser = CSVParser.parse(manifestFile, Charset.defaultCharset(), CSVFormat.DEFAULT)
+        val exitCodes: IO[List[ExitCode]] = csvParser.asScala.map(record => {
+          val drsObject = record.get(0)
+          val containerPath = record.get(1)
+          localizeFile(commandLineArguments, drsCredentials, drsObject, containerPath)
+        }).toList.sequence
+        exitCodes.map(_.find(_ != ExitCode.Success).getOrElse(ExitCode.Success))
+      case None =>
+        val drsObject = commandLineArguments.drsObject.get
+        val containerPath = commandLineArguments.containerPath.get
+        localizeFile(commandLineArguments, drsCredentials, drsObject, containerPath)
+    }
+  }
+
+  private def localizeFile(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials, drsObject: String, containerPath: String) = {
+    new DrsLocalizerMain(drsObject, containerPath, drsCredentials, commandLineArguments.googleRequesterPaysProject).
       resolveAndDownloadWithRetries(downloadRetries = 3, checksumRetries = 1, defaultDownloaderFactory, Option(defaultBackoff)).map(_.exitCode)
   }
 }
 
 class DrsLocalizerMain(drsUrl: String,
                        downloadLoc: String,
-                       accessTokenStrategy: AccessTokenStrategy,
+                       drsCredentials: DrsCredentials,
                        requesterPaysProjectIdOption: Option[String]) extends StrictLogging {
 
   def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] = {
     IO {
       val drsConfig = DrsConfig.fromEnv(sys.env)
-      new DrsLocalizerDrsPathResolver(drsConfig, accessTokenStrategy)
+      logger.info(s"Using ${drsConfig.drsResolverUrl} to resolve DRS Objects")
+      new DrsLocalizerDrsPathResolver(drsConfig, drsCredentials)
     }
   }
 
@@ -121,17 +142,17 @@ class DrsLocalizerMain(drsUrl: String,
   }
 
   private [localizer] def resolve(downloaderFactory: DownloaderFactory): IO[Downloader] = {
-    val fields = NonEmptyList.of(MarthaField.GsUri, MarthaField.GoogleServiceAccount, MarthaField.AccessUrl, MarthaField.Hashes)
+    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl, DrsResolverField.Hashes)
     for {
       resolver <- getDrsPathResolver
-      marthaResponse <- resolver.resolveDrsThroughMartha(drsUrl, fields)
+      drsResolverResponse <- resolver.resolveDrs(drsUrl, fields)
 
-      // Currently Martha only supports resolving DRS paths to access URLs or GCS paths.
-      downloader <- (marthaResponse.accessUrl, marthaResponse.gsUri) match {
+      // Currently DRS Resolver only supports resolving DRS paths to access URLs or GCS paths.
+      downloader <- (drsResolverResponse.accessUrl, drsResolverResponse.gsUri) match {
         case (Some(accessUrl), _) =>
-          downloaderFactory.buildAccessUrlDownloader(accessUrl, downloadLoc, marthaResponse.hashes)
+          downloaderFactory.buildAccessUrlDownloader(accessUrl, downloadLoc, drsResolverResponse.hashes)
         case (_, Some(gcsPath)) =>
-          val serviceAccountJsonOption = marthaResponse.googleServiceAccount.map(_.data.spaces2)
+          val serviceAccountJsonOption = drsResolverResponse.googleServiceAccount.map(_.data.spaces2)
           downloaderFactory.buildGcsUriDownloader(
             gcsPath = gcsPath,
             serviceAccountJsonOption = serviceAccountJsonOption,
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AccessTokenStrategy.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AccessTokenStrategy.scala
deleted file mode 100644
index 756f5371c0f..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AccessTokenStrategy.scala
+++ /dev/null
@@ -1,7 +0,0 @@
-package drs.localizer.accesstokens
-
-import common.validation.ErrorOr.ErrorOr
-
-trait AccessTokenStrategy {
-  def getAccessToken(): ErrorOr[String]
-}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
deleted file mode 100644
index cf83171adf0..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
+++ /dev/null
@@ -1,40 +0,0 @@
-package drs.localizer.accesstokens
-
-import cats.syntax.validated._
-import com.azure.identity.DefaultAzureCredentialBuilder
-import com.azure.security.keyvault.secrets.{SecretClient, SecretClientBuilder}
-import common.validation.ErrorOr
-import common.validation.ErrorOr.{ErrorOr,ShortCircuitingFlatMap}
-import drs.localizer.CommandLineArguments
-
-case class AzureB2CAccessTokenStrategy(commandLineArguments: CommandLineArguments) extends AccessTokenStrategy {
-  override def getAccessToken(): ErrorOr[String] = {
-    commandLineArguments match {
-      case CommandLineArguments(_, _, _, _, Some(vault), Some(secret), clientId) =>
-        AzureKeyVaultClient(vault, clientId) flatMap { _.getSecret(secret) }
-      case invalid => s"Invalid command line arguments: $invalid".invalidNel
-    }
-  }
-}
-
-// Note: The AzureKeyVaultClient code here is basically a copy/paste of the code temporarily living in the TES backend.
-// All the current KeyVault interaction in Cromwell is temporary, but the code in the TES backend might be even more
-// temporary than this.
-class AzureKeyVaultClient(client: SecretClient) {
-  def getSecret(secretName: String): ErrorOr[String] = ErrorOr(client.getSecret(secretName).getValue)
-}
-
-object AzureKeyVaultClient {
-  def apply(vaultName: String, identityClientId: Option[String]): ErrorOr[AzureKeyVaultClient] = ErrorOr {
-    val credentialBuilder = identityClientId.foldLeft(new DefaultAzureCredentialBuilder()) {
-      (builder, clientId) => builder.managedIdentityClientId(clientId)
-    }
-
-    val client = new SecretClientBuilder()
-      .vaultUrl(s"https://${vaultName}.vault.azure.net")
-      .credential(credentialBuilder.build())
-      .buildClient()
-
-    new AzureKeyVaultClient(client)
-  }
-}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala
deleted file mode 100644
index 5af2b8af441..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala
+++ /dev/null
@@ -1,28 +0,0 @@
-package drs.localizer.accesstokens
-
-import cats.syntax.validated._
-import com.google.auth.oauth2.GoogleCredentials
-import common.validation.ErrorOr.ErrorOr
-
-import scala.jdk.CollectionConverters._
-import scala.util.{Failure, Success, Try}
-
-/**
- * Strategy for obtaining an access token from Google Application Default credentials that are assumed to already exist.
- */
-case object GoogleAccessTokenStrategy extends AccessTokenStrategy {
-  private final val UserInfoEmailScope = "https://www.googleapis.com/auth/userinfo.email"
-  private final val UserInfoProfileScope = "https://www.googleapis.com/auth/userinfo.profile"
-  private final val UserInfoScopes = List(UserInfoEmailScope, UserInfoProfileScope)
-
-  override def getAccessToken(): ErrorOr[String] = {
-    Try {
-      val scopedCredentials = GoogleCredentials.getApplicationDefault().createScoped(UserInfoScopes.asJava)
-      scopedCredentials.refreshAccessToken().getTokenValue
-    } match {
-      case Success(null) => "null token value attempting to refresh access token".invalidNel
-      case Success(value) => value.validNel
-      case Failure(e) => s"Failed to refresh access token: ${e.getMessage}".invalidNel
-    }
-  }
-}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
index 345a14f63e4..d4c81af6300 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
@@ -19,7 +19,7 @@ case class GcsUriDownloader(gcsUrl: String,
 
     val copyProcess = serviceAccountJson match {
       case Some(sa) =>
-        // if Martha returned a SA, use that SA for gsutil instead of default credentials
+        // if DRS Resolver returned a SA, use that SA for gsutil instead of default credentials
         val tempCredentialDir: Path = Files.createTempDirectory("gcloudTemp_").toAbsolutePath
         val saJsonPath: Path = tempCredentialDir.resolve("sa.json")
         Files.write(saJsonPath, sa.getBytes(StandardCharsets.UTF_8))
@@ -27,7 +27,7 @@ case class GcsUriDownloader(gcsUrl: String,
         val copyCommand = Seq("bash", "-c", generateDownloadScript(gcsUrl, Option(saJsonPath)))
         Process(copyCommand, None, extraEnv.toSeq: _*)
       case None =>
-        // No SA returned from Martha. gsutil will use the application default credentials.
+        // No SA returned from DRS Resolver. gsutil will use the application default credentials.
         val copyCommand = Seq("bash", "-c", generateDownloadScript(gcsUrl, None))
         Process(copyCommand)
     }
@@ -50,11 +50,11 @@ case class GcsUriDownloader(gcsUrl: String,
     def setServiceAccount(): String = {
       saJsonPathOption match {
         case Some(saJsonPath) =>
-          s"""# Set gsutil to use the service account returned from Martha
+          s"""# Set gsutil to use the service account returned from the DRS Resolver
              |gcloud auth activate-service-account --key-file=$saJsonPath > gcloud_output.txt 2>&1
              |RC_GCLOUD=$$?
              |if [ "$$RC_GCLOUD" != "0" ]; then
-             |  echo "Failed to activate service account returned from Martha. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
+             |  echo "Failed to activate service account returned from the DRS Resolver. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
              |  exit "$$RC_GCLOUD"
              |else
              |  echo "Successfully activated service account; Will continue with download. $$(cat gcloud_output.txt)"
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
index 252971c0b5e..2a39a6543a3 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
@@ -4,9 +4,8 @@ import cats.syntax.validated._
 import cloud.nio.impl.drs.AccessUrl
 import common.validation.ErrorOr.ErrorOr
 import drs.localizer.downloaders.AccessUrlDownloader.Hashes
-import mouse.all.anySyntaxMouse
-import org.apache.commons.codec.binary.Base64.{decodeBase64, isBase64}
-import org.apache.commons.codec.binary.Hex.encodeHexString
+import org.apache.commons.codec.binary.Base64.encodeBase64String
+import org.apache.commons.codec.binary.Hex.decodeHex
 import org.apache.commons.text.StringEscapeUtils
 
 
@@ -26,23 +25,18 @@ sealed trait GetmChecksum {
 }
 
 case class Md5(override val rawValue: String) extends GetmChecksum {
-  override def value: ErrorOr[String] = {
-    val trimmed = rawValue.trim
-    if (trimmed.matches("[A-Fa-f0-9]+"))
-      trimmed.validNel
-    // TDR currently returns a base64-encoded MD5 because that's what Azure seems to do. However,
-    // the DRS spec does not specify that any checksums should be base64-encoded, and `getm` also
-    // does not expect base64. This case handles the current behavior in the short term until
-    // https://broadworkbench.atlassian.net/browse/DR-2259 is done.
-    else if (isBase64(trimmed))
-      (trimmed |> decodeBase64 |> encodeHexString).validNel
-    else
-      s"Invalid md5 checksum value is neither hex nor base64: $rawValue".invalidNel
-  }
+  override def value: ErrorOr[String] = GetmChecksum.validateHex(rawValue)
   override def getmAlgorithm: String = "md5"
 }
 
 case class Crc32c(override val rawValue: String) extends GetmChecksum {
+  // The DRS spec says that all hash values should be hex strings,
+  // but getm expects crc32c values to be base64.
+  override def value: ErrorOr[String] =
+    GetmChecksum.validateHex(rawValue)
+      .map(decodeHex)
+      .map(encodeBase64String)
+
   override def getmAlgorithm: String = "gs_crc32c"
 }
 case class AwsEtag(override val rawValue: String) extends GetmChecksum {
@@ -61,7 +55,7 @@ object GetmChecksum {
   def apply(hashes: Hashes, accessUrl: AccessUrl): GetmChecksum = {
     hashes match {
       case Some(hashes) if hashes.nonEmpty =>
-        // `hashes` is keyed by the Martha names for these hash algorithms, which in turn are the forwarded DRS
+        // `hashes` is keyed by the DRS Resolver names for these hash algorithms, which in turn are the forwarded DRS
         // providers' names for the algorithms. `getm` has its own notions of what these algorithms are called.
         // For the specific case of `md5` the algorithm names are the same between DRS providers and `getm`,
         // but all of the other algorithm names currently differ between DRS providers and `getm`.
@@ -88,4 +82,12 @@ object GetmChecksum {
       case _ => Null // None or an empty hashes map.
     }
   }
+
+  def validateHex(s: String): ErrorOr[String] = {
+    val trimmed = s.trim
+    if (trimmed.matches("[A-Fa-f0-9]+"))
+      trimmed.validNel
+    else
+      s"Invalid checksum value, expected hex but got: $trimmed".invalidNel
+  }
 }
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
index 3f7b96f5edc..7be30be8ac0 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
@@ -13,9 +13,8 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   private val drsObject = "drs://provider/object"
   private val containerPath = "/cromwell_root/my.bam"
   private val requesterPaysProject = "i_heart_egress"
-  private val azureVaultName = "Kwikset"
-  private val azureSecretName = "shhh"
   private val azureIdentityClientId = "itme@azure.com"
+  private val manifestPath = "/my/manifest.txt"
 
   behavior of "DRS Localizer command line parser"
 
@@ -38,67 +37,89 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject shouldBe empty
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
   it should "successfully parse with three arguments" in {
     val args = parser.parse(Array(drsObject, containerPath, requesterPaysProject), CommandLineArguments()).get
+    args.drsObject.get shouldBe drsObject
+    args.containerPath.get shouldBe containerPath
+    args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
+    args.googleRequesterPaysProject.get shouldBe requesterPaysProject
+    args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
+  }
+
+  it should "successfully parse requester pays project" in {
+    val args = parser.parse(Array(drsObject, containerPath, "-r", requesterPaysProject), CommandLineArguments()).get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject.get shouldBe requesterPaysProject
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
-  it should "successfully parse an explicit Google access token strategy invocation" in {
-    val args = parser.parse(Array("--access-token-strategy", "google", drsObject, containerPath, requesterPaysProject), CommandLineArguments()).get
+  it should "successfully parse with three arguments and requester pays project" in {
+    val args = parser.parse(Array(drsObject, containerPath, requesterPaysProject, "-r", requesterPaysProject), CommandLineArguments()).get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject.get shouldBe requesterPaysProject
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
-  it should "fail to parse an Azure invocation missing vault name and secret name" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      drsObject, containerPath), CommandLineArguments())
+  it should "fail if requester pays argument and flag specify different projects" in {
+    parser.parse(Array(drsObject, containerPath, requesterPaysProject, "-r", "boom!"), CommandLineArguments()) shouldBe None
+  }
 
-    args shouldBe None
+  it should "successfully parse args with a manifest file" in {
+    val args = parser.parse(Array("-m", manifestPath), CommandLineArguments()).get
+
+    args.drsObject shouldBe empty
+    args.containerPath shouldBe empty
+    args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
+    args.googleRequesterPaysProject shouldBe empty
+    args.azureIdentityClientId shouldBe empty
+    args.manifestPath.get shouldBe manifestPath
   }
 
-  it should "fail to parse an Azure invocation missing vault name" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--secret-name", azureSecretName,
-      drsObject, containerPath), CommandLineArguments())
+  it should "fail to parse with a manifest file and one single-file arg" in {
+    val args = parser.parse(Array(drsObject, "--manifest-path", manifestPath), CommandLineArguments())
+    args shouldBe None
+  }
 
+  it should "fail to parse with a manifest file and two single-file args" in {
+    val args = parser.parse(Array(drsObject, containerPath, "--manifest-path", manifestPath), CommandLineArguments())
     args shouldBe None
   }
 
-  it should "fail to parse an Azure invocation missing secret name" in {
+  it should "successfully parse an explicit Google access token strategy invocation" in {
     val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--vault-name", azureVaultName,
-      drsObject, containerPath), CommandLineArguments())
+      "--access-token-strategy", "google",
+      drsObject,
+      containerPath,
+      "--requester-pays-project", requesterPaysProject
+    ), CommandLineArguments()).get
 
-    args shouldBe None
+    args.drsObject.get shouldBe drsObject
+    args.containerPath.get shouldBe containerPath
+    args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
+    args.googleRequesterPaysProject.get shouldBe requesterPaysProject
+    args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
   it should "fail to parse an Azure invocation that specifies requester pays" in {
     val args = parser.parse(Array(
       "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--secret-name", azureSecretName,
-      "--vault-name", azureVaultName,
-      drsObject, containerPath, requesterPaysProject), CommandLineArguments())
+      drsObject,
+      containerPath,
+      "--requester-pays-project", requesterPaysProject), CommandLineArguments())
 
     args shouldBe None
   }
@@ -106,24 +127,19 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   it should "successfully parse an Azure invocation" in {
     val args = parser.parse(Array(
       "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--secret-name", azureSecretName,
-      "--vault-name", azureVaultName,
       drsObject, containerPath), CommandLineArguments()).get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Azure
     args.googleRequesterPaysProject shouldBe empty
-    args.azureVaultName.get shouldBe azureVaultName
-    args.azureSecretName.get shouldBe azureSecretName
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
-  it should "successfully parse an Azure invocation with all the trimmings" in {
+  it should "successfully parse an Azure invocation with identity" in {
     val args = parser.parse(Array(
       "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--vault-name", azureVaultName,
-      "--secret-name", azureSecretName,
       "--identity-client-id", azureIdentityClientId,
       drsObject, containerPath), CommandLineArguments()).get
 
@@ -131,9 +147,8 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Azure
     args.googleRequesterPaysProject shouldBe empty
-    args.azureVaultName.get shouldBe azureVaultName
-    args.azureSecretName.get shouldBe azureSecretName
     args.azureIdentityClientId.get shouldBe azureIdentityClientId
+    args.manifestPath shouldBe empty
   }
 
   it should "fail to parse with an unrecognized access token strategy" in {
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
index 84b407cec41..66799fcc099 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
@@ -4,10 +4,10 @@ import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO}
 import cats.syntax.validated._
 import cloud.nio.impl.drs.DrsPathResolver.FatalRetryDisposition
-import cloud.nio.impl.drs.{AccessUrl, DrsConfig, MarthaField, MarthaResponse}
+import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsCredentials, DrsResolverField, DrsResolverResponse}
 import common.assertion.CromwellTimeoutSpec
+import common.validation.ErrorOr.ErrorOr
 import drs.localizer.MockDrsLocalizerDrsPathResolver.{FakeAccessTokenStrategy, FakeHashes}
-import drs.localizer.accesstokens.AccessTokenStrategy
 import drs.localizer.downloaders.AccessUrlDownloader.Hashes
 import drs.localizer.downloaders._
 import org.scalatest.flatspec.AnyFlatSpec
@@ -49,12 +49,12 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync() shouldBe expected
   }
 
-  it should "fail and throw error if Martha response does not have gs:// url" in {
+  it should "fail and throw error if the DRS Resolver response does not have gs:// url" in {
     val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithoutAnyResolution, fakeDownloadLocation, None)
 
     the[RuntimeException] thrownBy {
       mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync()
-    } should have message "No access URL nor GCS URI starting with 'gs://' found in Martha response!"
+    } should have message "No access URL nor GCS URI starting with 'gs://' found in the DRS Resolver response!"
   }
 
   it should "resolve to use the correct downloader for an access url" in {
@@ -67,7 +67,7 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync() shouldBe expected
   }
 
-  it should "resolve to use the correct downloader for an access url when the Martha response also contains a gs url" in {
+  it should "resolve to use the correct downloader for an access url when the DRS Resolver response also contains a gs url" in {
     val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithAccessUrlAndGcsResolution, fakeDownloadLocation, None)
     val expected = AccessUrlDownloader(
       accessUrl = AccessUrl(url = "http://abc/def/ghi.bam", headers = None), downloadLoc = fakeDownloadLocation,
@@ -315,23 +315,23 @@ class MockDrsLocalizerMain(drsUrl: String,
 class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig) extends
   DrsLocalizerDrsPathResolver(drsConfig, FakeAccessTokenStrategy) {
 
-  override def resolveDrsThroughMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): IO[MarthaResponse] = {
-    val marthaResponse = MarthaResponse(
+  override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
+    val drsResolverResponse = DrsResolverResponse(
       size = Option(1234),
       hashes = FakeHashes
     )
 
     IO.pure(drsPath) map {
       case MockDrsPaths.fakeDrsUrlWithGcsResolutionOnly =>
-        marthaResponse.copy(
+        drsResolverResponse.copy(
           gsUri = Option("gs://abc/foo-123/abc123"))
       case MockDrsPaths.fakeDrsUrlWithoutAnyResolution =>
-        marthaResponse
+        drsResolverResponse
       case MockDrsPaths.fakeDrsUrlWithAccessUrlResolutionOnly =>
-        marthaResponse.copy(
+        drsResolverResponse.copy(
           accessUrl = Option(AccessUrl(url = "http://abc/def/ghi.bam", headers = None)))
       case MockDrsPaths.fakeDrsUrlWithAccessUrlAndGcsResolution =>
-        marthaResponse.copy(
+        drsResolverResponse.copy(
           accessUrl = Option(AccessUrl(url = "http://abc/def/ghi.bam", headers = None)),
           gsUri = Option("gs://some/uri"))
       case e => throw new RuntimeException(s"Unexpected exception in DRS localization test code: $e")
@@ -341,5 +341,7 @@ class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig) extends
 
 object MockDrsLocalizerDrsPathResolver {
   val FakeHashes: Option[Map[String, String]] = Option(Map("md5" -> "abc123", "crc32c" -> "34fd67"))
-  val FakeAccessTokenStrategy: AccessTokenStrategy = () => "testing code: do not call me".invalidNel
+  val FakeAccessTokenStrategy: DrsCredentials = new DrsCredentials {
+    override def getAccessToken: ErrorOr[String] = "testing code: do not call me".invalidNel
+  }
 }
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala
index 66c4ff6fabd..07eb5ede181 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala
@@ -11,7 +11,7 @@ class GcsUriDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
   val fakeDownloadLocation = "/root/foo/foo-123.bam"
   val fakeRequesterPaysId = "fake-billing-project"
 
-  it should "return correct download script for a drs url without Requester Pays ID and Google SA returned from Martha" in {
+  it should "return correct download script for a drs url without Requester Pays ID and Google SA returned from the DRS Resolver" in {
     val gcsUrl = "gs://foo/bar.bam"
     val downloader = new GcsUriDownloader(
       gcsUrl = gcsUrl,
@@ -44,7 +44,7 @@ class GcsUriDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     downloader.generateDownloadScript(gcsUrl = gcsUrl, saJsonPathOption = None) shouldBe expectedDownloadScript
   }
 
-  it should "inject Requester Pays flag & gcloud auth using SA returned from Martha" in {
+  it should "inject Requester Pays flag & gcloud auth using SA returned from the DRS Resolver" in {
     val gcsUrl = "gs://foo/bar.bam"
     val downloader = new GcsUriDownloader(
       gcsUrl = gcsUrl,
@@ -60,11 +60,11 @@ class GcsUriDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
       s"""set -euo pipefail
          |set +e
          |
-         |# Set gsutil to use the service account returned from Martha
+         |# Set gsutil to use the service account returned from the DRS Resolver
          |gcloud auth activate-service-account --key-file=${fakeSAJsonPath.toString} > gcloud_output.txt 2>&1
          |RC_GCLOUD=$$?
          |if [ "$$RC_GCLOUD" != "0" ]; then
-         |  echo "Failed to activate service account returned from Martha. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
+         |  echo "Failed to activate service account returned from the DRS Resolver. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
          |  exit "$$RC_GCLOUD"
          |else
          |  echo "Successfully activated service account; Will continue with download. $$(cat gcloud_output.txt)"
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
index 24ea087cb8f..69c063ff616 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
@@ -31,9 +31,10 @@ class GetmChecksumSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     val results = Table(
       ("description", "algorithm", "expected"),
       ("md5 hex", Md5("abcdef"), "--checksum-algorithm 'md5' --checksum abcdef".validNel),
-      ("md5 base64", Md5("cR84lXY1y17c3q7/7riLEA=="), "--checksum-algorithm 'md5' --checksum 711f38957635cb5edcdeaeffeeb88b10".validNel),
-      ("md5 gibberish", Md5("what is this???"), "Invalid md5 checksum value is neither hex nor base64: what is this???".invalidNel),
-      ("crc32c", Crc32c("012345"), "--checksum-algorithm 'gs_crc32c' --checksum 012345".validNel),
+      ("md5 base64", Md5("cR84lXY1y17c3q7/7riLEA=="), "Invalid checksum value, expected hex but got: cR84lXY1y17c3q7/7riLEA==".invalidNel),
+      ("md5 gibberish", Md5("what is this???"), "Invalid checksum value, expected hex but got: what is this???".invalidNel),
+      ("crc32c", Crc32c("012345"), "--checksum-algorithm 'gs_crc32c' --checksum ASNF".validNel),
+      ("crc32c gibberish", Crc32c("????"), "Invalid checksum value, expected hex but got: ????".invalidNel),
       ("AWS ETag", AwsEtag("012345"), "--checksum-algorithm 's3_etag' --checksum 012345".validNel),
       // Escape checksum values constructed from unvalidated data returned by DRS servers.
       ("Unsupported", Unsupported("Robert'); DROP TABLE Students;\n --\\"), raw"--checksum-algorithm 'null' --checksum Robert\'\)\;\ DROP\ TABLE\ Students\;\ --\\".validNel),
@@ -46,4 +47,19 @@ class GetmChecksumSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
       }
     }
   }
+
+  it should "correctly validate hex strings" in {
+    val results = Table(
+      ("test string", "expected"),
+      ("", "Invalid checksum value, expected hex but got: ".invalidNel),
+      (" ", "Invalid checksum value, expected hex but got: ".invalidNel),
+      ("myfavoritestring", "Invalid checksum value, expected hex but got: myfavoritestring".invalidNel),
+      (" AbC123 ", "AbC123".validNel),
+      ("456", "456".validNel),
+    )
+
+    forAll(results) { (testString, expected) =>
+      GetmChecksum.validateHex(testString) shouldBe expected
+    }
+  }
 }
diff --git a/cromwell.example.backends/cromwell.examples.conf b/cromwell.example.backends/cromwell.examples.conf
index 49b676a2c7c..4ca250d1202 100644
--- a/cromwell.example.backends/cromwell.examples.conf
+++ b/cromwell.example.backends/cromwell.examples.conf
@@ -308,17 +308,6 @@ languages {
       }
     }
   }
-  CWL {
-    versions {
-      "v1.0" {
-        # language-factory = "languages.cwl.CwlV1_0LanguageFactory"
-        # config {
-        #   strict-validation: false
-        #   enabled: true
-        # }
-      }
-    }
-  }
 }
 
 # Here is where you can define the backend providers that Cromwell understands.
diff --git a/cwl/src/main/resources/reference.conf b/cwl/src/main/resources/reference.conf
deleted file mode 100644
index 0d0d8a980f9..00000000000
--- a/cwl/src/main/resources/reference.conf
+++ /dev/null
@@ -1,3 +0,0 @@
-cwltool-runner {
-  class = "cwl.CwltoolHeterodon"
-}
diff --git a/cwl/src/main/scala/cwl/ArgumentToCommandPart.scala b/cwl/src/main/scala/cwl/ArgumentToCommandPart.scala
deleted file mode 100644
index ca67eaa7ab3..00000000000
--- a/cwl/src/main/scala/cwl/ArgumentToCommandPart.scala
+++ /dev/null
@@ -1,26 +0,0 @@
-package cwl
-
-import cwl.command.StringCommandPart
-import shapeless._
-import wom.CommandPart
-
-object ArgumentToCommandPart extends Poly1 {
-  type MakeCommandPart = (Boolean, ExpressionLib) => CommandPart
-  implicit def caseStringOrExpression: Case.Aux[StringOrExpression, MakeCommandPart] = at {
-    _.fold(this)
-  }
-
-  implicit def caseExpression: Case.Aux[Expression, MakeCommandPart] = at {
-    CwlExpressionCommandPart.apply
-  }
-
-  implicit def caseString: Case.Aux[String, MakeCommandPart] = at {
-    string =>
-      (_, _) =>
-        StringCommandPart(string)
-  }
-
-  implicit def caseCommandLineBinding: Case.Aux[ArgumentCommandLineBinding, MakeCommandPart] = at {
-    ArgumentCommandLineBindingCommandPart.apply
-  }
-}
diff --git a/cwl/src/main/scala/cwl/BaseCommandToCommandParts.scala b/cwl/src/main/scala/cwl/BaseCommandToCommandParts.scala
deleted file mode 100644
index 2f597918082..00000000000
--- a/cwl/src/main/scala/cwl/BaseCommandToCommandParts.scala
+++ /dev/null
@@ -1,11 +0,0 @@
-package cwl
-
-import cwl.command.StringCommandPart
-import shapeless.Poly1
-import wom.CommandPart
-
-object BaseCommandToCommandParts extends Poly1 {
-  implicit def one = at[String] { Seq(_).map(StringCommandPart.apply): Seq[CommandPart] }
-
-  implicit def many = at[Array[String]] { _.toSeq.map(StringCommandPart.apply): Seq[CommandPart] }
-}
diff --git a/cwl/src/main/scala/cwl/CommandLineTool.scala b/cwl/src/main/scala/cwl/CommandLineTool.scala
deleted file mode 100644
index 49a2de8c861..00000000000
--- a/cwl/src/main/scala/cwl/CommandLineTool.scala
+++ /dev/null
@@ -1,439 +0,0 @@
-package cwl
-
-import cats.data.{NonEmptyList, OptionT}
-import cats.syntax.apply._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cats.instances.future._
-import common.Checked
-import common.validation.ErrorOr._
-import cwl.CommandLineTool._
-import cwl.CwlVersion._
-import cwl.internal.CommandPartSortingAlgorithm
-import io.circe.Json
-import shapeless.syntax.singleton._
-import shapeless.{:+:, CNil, Coproduct, Poly1, Witness}
-import wom.callable.CommandTaskDefinition.{EvaluatedOutputs, OutputFunctionResponse}
-import wom.callable.{Callable, CallableTaskDefinition, ContainerizedInputExpression}
-import wom.expression.{IoFunctionSet, ValueAsAnExpression, WomExpression}
-import wom.graph.GraphNodePort.OutputPort
-import wom.types.{WomArrayType, WomIntegerType, WomOptionalType}
-import wom.util.YamlUtils
-import wom.values.{WomArray, WomEvaluatedCallInputs, WomGlobFile, WomInteger, WomString, WomValue}
-import wom.{CommandPart, RuntimeAttributes, RuntimeAttributesKeys}
-
-import scala.concurrent.{ExecutionContext, Future}
-import scala.math.Ordering
-
-/**
-  * @param `class` This _should_ always be "CommandLineTool," however the spec does not -er- specify this.
-  */
-case class CommandLineTool private(
-                                    inputs: Array[CommandInputParameter],
-                                    outputs: Array[CommandOutputParameter],
-                                    `class`: Witness.`"CommandLineTool"`.T,
-                                    id: String,
-                                    requirements: Option[Array[Requirement]],
-                                    hints: Option[Array[Hint]],
-                                    label: Option[String],
-                                    doc: Option[String],
-                                    cwlVersion: Option[CwlVersion],
-                                    baseCommand: Option[BaseCommand],
-                                    arguments: Option[Array[CommandLineTool.Argument]],
-                                    stdin: Option[StringOrExpression],
-                                    stderr: Option[StringOrExpression],
-                                    stdout: Option[StringOrExpression],
-                                    successCodes: Option[Array[Int]],
-                                    temporaryFailCodes: Option[Array[Int]],
-                                    permanentFailCodes: Option[Array[Int]],
-                                    `$namespaces`: Option[Map[String, String]],
-                                    `$schemas`: Option[Array[String]]
-                                  ) extends Tool {
-
-  def asCwl: Cwl = Coproduct[Cwl](this)
-
-  lazy val baseCommandPart: List[CommandPart] = baseCommand.toList.flatMap(_.fold(BaseCommandToCommandParts))
-
-  /*
-   * The command template is built following the rules described here: http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-   * - The baseCommand goes first
-   * - Then the arguments are assigned a sorting key and transformed into a CommandPart
-   * - Finally the inputs are folded one by one into a CommandPartsList
-   * - arguments and inputs CommandParts are sorted according to their sort key
-   */
-  private [cwl] def buildCommandTemplate: CommandPartExpression[List[CommandPart]] =
-    (
-      CommandPartSortingAlgorithm.inputBindingsCommandParts(inputs),
-      CommandPartSortingAlgorithm.argumentCommandParts(arguments)
-    ).mapN ( _ ++ _ ).
-      //sort the highest level, then recursively pull in the nested (and sorted) command parts within each SortKeyAndCommandPart
-      map{ _.sorted.flatMap(_.sortedCommandParts) }.
-      map(baseCommandPart ++ _)
-
-  // This seems like it makes sense only for CommandLineTool and hence is not abstracted in Tool. If this assumption is wrong it could be moved up.
-  private def environmentDefs(requirementsAndHints: List[Requirement], expressionLib: ExpressionLib): ErrorOr[Map[String, WomExpression]] = {
-    // For environment variables we need to make sure that we aren't being asked to evaluate expressions from a containing
-    // workflow step or its containing workflow or anything containing the workflow. The current structure of this code
-    // is not prepared to evaluate those expressions. Actually this is true for attributes too and we're totally not
-    // checking for this condition there. Blurgh.
-    // TODO CWL: for runtime attributes, detect unevaluatable expressions in the containment hierarchy.
-
-    // This traverses all `EnvironmentDef`s within all `EnvVarRequirement`s. The spec doesn't appear to say how to handle
-    // duplicate `envName` keys in a single array of `EnvironmentDef`s; this code gives precedence to the last occurrence.
-    val allEnvVarDefs = for {
-      req <- requirementsAndHints
-      envVarReq <- req.select[EnvVarRequirement].toList
-      // Reverse the defs within an env var requirement so that when we fold from the right below the later defs
-      // will take precedence over the earlier defs.
-      envDef <- envVarReq.envDef.toList.reverse
-    } yield envDef
-
-    // Compact the `EnvironmentDef`s. Don't convert to `WomExpression`s yet, the `StringOrExpression`s need to be
-    // compared to the `EnvVarRequirement`s that were defined on this tool.
-    val effectiveEnvironmentDefs = allEnvVarDefs.foldRight(Map.empty[String, StringOrExpression]) {
-      case (envVarReq, envVarMap) => envVarMap + (envVarReq.envName -> envVarReq.envValue)
-    }
-
-    // These are the effective environment defs irrespective of where they were found in the
-    // Run / WorkflowStep / Workflow containment hierarchy.
-    val effectiveExpressionEnvironmentDefs = effectiveEnvironmentDefs filter { case (_, expr) => expr.select[Expression].isDefined }
-
-    // These are only the environment defs defined on this tool.
-    val cltRequirements = requirements.toList.flatten ++ hints.toList.flatten.flatMap(_.select[Requirement])
-    val cltEnvironmentDefExpressions = (for {
-      cltEnvVarRequirement <- cltRequirements flatMap {
-        _.select[EnvVarRequirement]
-      }
-      cltEnvironmentDef <- cltEnvVarRequirement.envDef.toList
-      expr <- cltEnvironmentDef.envValue.select[Expression].toList
-    } yield expr).toSet
-
-    // If there is an expression in an effective environment def that wasn't defined on this tool then error out since
-    // there isn't currently a way of evaluating it.
-    val unevaluatableEnvironmentDefs = for {
-      (name, stringOrExpression) <- effectiveExpressionEnvironmentDefs.toList
-      expression <- stringOrExpression.select[Expression].toList
-      if !cltEnvironmentDefExpressions.contains(expression)
-    } yield name
-
-    unevaluatableEnvironmentDefs match {
-      case Nil =>
-        // No unevaluatable environment defs => keep on truckin'
-        effectiveEnvironmentDefs.foldRight(Map.empty[String, WomExpression]) { case ((envName, envValue), acc) =>
-          acc + (envName -> envValue.fold(StringOrExpressionToWomExpression).apply(inputNames, expressionLib))
-        }.validNel
-      case xs =>
-        s"Could not evaluate environment variable expressions defined in the call hierarchy of tool $id: ${xs.mkString(", ")}.".invalidNel
-    }
-  }
-
-  /*
-    * Custom evaluation of the outputs of the command line tool (custom as in bypasses the engine provided default implementation).
-    * This is needed because the output of a CWL tool might be defined by the presence of a cwl.output.json file in the output directory.
-    * In that case, the content of the file should be used as output. This means that otherwise provided output expressions should not be evaluated.
-    * This method checks for the existence of this file, and optionally return a Map[OutputPort, WomValue] if the file was found.
-    * It ensures all the output ports of the corresponding WomCallNode get a WomValue which is needed for the engine to keep running the workflow properly.
-    * If the json file happens to be missing values for one or more output ports, it's a failure.
-    * If the file is not present, an empty value is returned and the engine will execute its own output evaluation logic.
-    *
-    * TODO: use IO instead of Future ?
-   */
-  final private def outputEvaluationJsonFunction(outputPorts: Set[OutputPort],
-                                                 inputs: Map[String, WomValue],
-                                                 ioFunctionSet: IoFunctionSet,
-                                                 executionContext: ExecutionContext): OutputFunctionResponse = {
-    implicit val ec = executionContext
-    import cats.syntax.either._
-
-    // Convert the parsed json to Wom-usable output values
-    def jsonToOutputs(json: Map[String, Json]): Checked[List[(OutputPort, WomValue)]] = {
-
-      outputPorts.toList.traverse[ErrorOr, (OutputPort, WomValue)]({ outputPort =>
-        // If the type is optional, then we can set the value to none if there's nothing in the json
-        def emptyValue = outputPort.womType match {
-          case optional: WomOptionalType => Option((outputPort -> optional.none).validNel)
-          case _ => None
-        }
-
-        json.get(outputPort.internalName)
-          .map(
-            _.foldWith(CwlJsonToDelayedCoercionFunction).apply(outputPort.womType)
-              .map(outputPort -> _)
-          )
-          .orElse(emptyValue)
-          .getOrElse(s"Cannot find a value for output ${outputPort.internalName} in output json $json".invalidNel)
-      }).toEither
-    }
-
-    // Parse content as json and return output values for each output port
-    def parseContent(content: String): EvaluatedOutputs = {
-      val yaml = YamlUtils.parse(content)
-      for {
-        parsed <- yaml.flatMap(_.as[Map[String, Json]]).leftMap(error => NonEmptyList.one(error.getMessage))
-        jobOutputsMap <- jsonToOutputs(parsed)
-      } yield jobOutputsMap.toMap
-    }
-
-    for {
-      // Glob for "cwl.output.json"
-      outputJsonGlobs <- OptionT.liftF { ioFunctionSet.glob(CwlOutputJson) }
-      // There can only be 0 or 1, so try to take the head of the list
-      outputJsonFile <- OptionT.fromOption[Future] { outputJsonGlobs.headOption }
-      // Read the content using the ioFunctionSet.readFile function
-      content <- OptionT.liftF { ioFunctionSet.readFile(outputJsonFile, None, failOnOverflow = false) }
-      // parse the content and validate it
-      outputs = parseContent(content)
-    } yield outputs
-  }
-
-  override protected def toolAttributes: Map[String, WomExpression] = {
-    val codes: List[Int] = successCodes match {
-      case Some(c) => c.toList // Use the provided list of success codes.
-      case None => List(0) // Default to allowing only 0 for a success code.
-    }
-
-    val arr = WomArray(WomArrayType(WomIntegerType), codes map WomInteger.apply)
-    Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> ValueAsAnExpression(arr))
-  }
-
-  override def buildTaskDefinition(taskName: String,
-                          inputDefinitions: List[_ <: Callable.InputDefinition],
-                          outputDefinitions: List[Callable.OutputDefinition],
-                          runtimeAttributes: RuntimeAttributes,
-                          requirementsAndHints: List[cwl.Requirement],
-                          expressionLib: ExpressionLib): ErrorOr[CallableTaskDefinition] = {
-
-    def redirect(soe: Option[StringOrExpression]): Option[WomExpression] = soe map {
-      _.fold(StringOrExpressionToWomExpression).apply(inputNames, expressionLib)
-    }
-
-    // This seems like it makes sense only for CommandLineTool and hence is not abstracted in Tool. If this assumption is wrong it could be moved up.
-    val adHocFileCreations: Set[ContainerizedInputExpression] = (for {
-      requirements <- requirements.getOrElse(Array.empty[Requirement])
-      initialWorkDirRequirement <- requirements.select[InitialWorkDirRequirement].toArray
-      listing <- initialWorkDirRequirement.listings
-    } yield InitialWorkDirFileGeneratorExpression(listing, expressionLib)).toSet[ContainerizedInputExpression]
-
-    val dockerOutputDirectory = requirementsAndHints
-      .flatMap(_.select[DockerRequirement])
-      .flatMap(_.dockerOutputDirectory)
-      .headOption
-
-    def inputsToCommandParts(inputs: WomEvaluatedCallInputs) : ErrorOr[Seq[CommandPart]] =
-     buildCommandTemplate.run((RequirementsAndHints(requirementsAndHints), expressionLib, inputs))
-
-    environmentDefs(requirementsAndHints, expressionLib) map { environmentExpressions =>
-      CallableTaskDefinition(
-        taskName,
-        inputsToCommandParts,
-        runtimeAttributes,
-        Map.empty,
-        Map.empty,
-        outputDefinitions,
-        inputDefinitions,
-        adHocFileCreation = adHocFileCreations,
-        environmentExpressions = environmentExpressions,
-        // TODO: This doesn't work in all cases and it feels clunky anyway - find a way to sort that out
-        prefixSeparator = "#",
-        commandPartSeparator = " ",
-        stdinRedirection = redirect(stdin),
-        stdoutOverride = redirect(stdout),
-        stderrOverride = redirect(stderr),
-        additionalGlob = Option(WomGlobFile(CwlOutputJson)),
-        customizedOutputEvaluation = outputEvaluationJsonFunction,
-        homeOverride = Option(_.outputPath),
-        dockerOutputDirectory = dockerOutputDirectory,
-        sourceLocation = None
-      )
-    }
-  }
-}
-
-object CommandLineTool {
-  val CwlOutputJson = "cwl.output.json"
-
-  val DefaultPosition = Coproduct[StringOrInt](0)
-
-  // Elements of the sorting key can be either Strings or Ints
-  type StringOrInt = String :+: Int :+: CNil
-  object StringOrInt {
-    object String { def unapply(stringOrInt: StringOrInt): Option[String] = stringOrInt.select[String] }
-    object Int { def unapply(stringOrInt: StringOrInt): Option[Int] = stringOrInt.select[Int] }
-  }
-
-  /*
-   * The algorithm described here http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding to sort the command line parts
-   * uses a sorting key assigned to each binding. This class represents such a key
-   */
-  object CommandBindingSortingKey {
-    def empty = CommandBindingSortingKey(List.empty, List.empty)
-  }
-  case class CommandBindingSortingKey(head: List[StringOrInt],
-                                      tail: List[StringOrInt] = List.empty) {
-    val value = head ++ tail
-
-    def append(binding: Option[CommandLineBinding], name: StringOrInt): CommandBindingSortingKey = binding match {
-      // If there's an input binding, add the position to the key (or 0)
-      case Some(b) =>
-        // The spec is inconsistent about this as it says "If position is not specified, it is not added to the sorting key"
-        // but also that the position defaults to 0. cwltool uses 0 when there's no position so we'll do that too.
-        val position = b.position.map(Coproduct[StringOrInt](_)) getOrElse DefaultPosition
-        copy(head = head :+ position, tail = tail :+ name)
-      // Otherwise do nothing
-      case None => this
-    }
-
-    /**
-      * Creates a new key with head and tail combined into the new head.
-      */
-    def asNewKey = CommandBindingSortingKey(value)
-  }
-
-  // Maps a sorting key to its (sorted) bindings
-  case class SortKeyAndCommandPart(
-    sortingKey: CommandBindingSortingKey,
-    commandPart: CommandPart,
-    nestedCommandParts: List[SortKeyAndCommandPart] = List.empty) {
-      def sortedCommandParts:List[CommandPart] =
-        List(commandPart) ++ nestedCommandParts.sorted.flatMap(_.sortedCommandParts)
-    }
-
-  type CommandPartsList = List[SortKeyAndCommandPart]
-
-  // Ordering for CommandBindingSortingKeyElement
-  implicit val SortingKeyTypeOrdering: Ordering[StringOrInt] = Ordering.fromLessThan[StringOrInt]({
-    // String comparison
-    case (StringOrInt.String(s1), StringOrInt.String(s2)) => s1 < s2
-    // Int comparison
-    case (StringOrInt.Int(i1), StringOrInt.Int(i2)) => i1 < i2
-    // Int < String (from the spec: "Numeric entries sort before strings.")
-    case (StringOrInt.Int(_), StringOrInt.String(_)) => true
-    // String > Int
-    case (StringOrInt.String(_), StringOrInt.Int(_)) => false
-    case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-  })
-
-  // https://github.com/scala/bug/issues/4097#issuecomment-292388627
-  implicit def IterableSubclass[CC[X] <: Iterable[X], T: Ordering] : Ordering[CC[T]] = {
-    new Ordering[CC[T]] {
-      val ord = implicitly[Ordering[T]]
-      def compare(x: CC[T], y: CC[T]): Int = {
-        val xe = x.iterator
-        val ye = y.iterator
-
-        while (xe.hasNext && ye.hasNext) {
-          val res = ord.compare(xe.next(), ye.next())
-          if (res != 0) return res
-        }
-
-        Ordering.Boolean.compare(xe.hasNext, ye.hasNext)
-      }
-    }
-  }
-
-  // Ordering for a CommandBindingSortingKey
-  implicit val SortingKeyOrdering: Ordering[CommandBindingSortingKey] = Ordering.by(_.value)
-
-  // Ordering for a CommandPartSortMapping: order by sorting key
-  implicit val SortKeyAndCommandPartOrdering: Ordering[SortKeyAndCommandPart] = Ordering.by(_.sortingKey)
-
-  def apply(inputs: Array[CommandInputParameter] = Array.empty,
-            outputs: Array[CommandOutputParameter] = Array.empty,
-            id: String,
-            requirements: Option[Array[Requirement]] = None,
-            hints: Option[Array[Hint]] = None,
-            label: Option[String] = None,
-            doc: Option[String] = None,
-            cwlVersion: Option[CwlVersion] = Option(CwlVersion.Version1),
-            baseCommand: Option[BaseCommand] = None,
-            arguments: Option[Array[CommandLineTool.Argument]] = None,
-            stdin: Option[StringOrExpression] = None,
-            stderr: Option[StringOrExpression] = None,
-            stdout: Option[StringOrExpression] = None,
-            successCodes: Option[Array[Int]] = None,
-            temporaryFailCodes: Option[Array[Int]] = None,
-            permanentFailCodes: Option[Array[Int]] = None,
-            namespaces: Option[Map[String, String]] = None,
-            schemas: Option[Array[String]] = None
-           ): CommandLineTool = {
-    CommandLineTool(
-      inputs,
-      outputs,
-      "CommandLineTool".narrow,
-      id,
-      requirements,
-      hints,
-      label,
-      doc,
-      cwlVersion,
-      baseCommand,
-      arguments,
-      stdin,
-      stderr,
-      stdout,
-      successCodes,
-      temporaryFailCodes,
-      permanentFailCodes,
-      namespaces,
-      schemas
-    )
-  }
-
-  type BaseCommand = SingleOrArrayOfStrings
-
-  type Argument = ArgumentCommandLineBinding :+: StringOrExpression :+: CNil
-
-  case class CommandInputParameter(
-                                    id: String,
-                                    label: Option[String] = None,
-                                    secondaryFiles: Option[SecondaryFiles] = None,
-                                    format: Option[InputParameterFormat] = None, //only valid when type: File
-                                    streamable: Option[Boolean] = None, //only valid when type: File
-                                    doc: Option[Doc] = None,
-                                    inputBinding: Option[InputCommandLineBinding] = None,
-                                    default: Option[CwlAny] = None,
-                                    `type`: Option[MyriadInputType] = None) extends InputParameter
-
-  case class CommandOutputParameter(
-                                     id: String,
-                                     label: Option[String] = None,
-                                     secondaryFiles: Option[SecondaryFiles] = None,
-                                     format: Option[OutputParameterFormat] = None, //only valid when type: File
-                                     streamable: Option[Boolean] = None, //only valid when type: File
-                                     doc: Option[Doc] = None,
-                                     outputBinding: Option[CommandOutputBinding] = None,
-                                     `type`: Option[MyriadOutputType] = None) extends OutputParameter {
-
-    /** Overridden to strip off the intentionally uniquified bits and leave only the stuff that we want to look
-      * at for the purposes of determining cache hits.
-      *
-      * before:
-      *
-      * CommandOutputParameter(file:///var/folders/qh/vvrlr2q92mvb9bb45sttxll4y3gg2g/T/e17762d1-9921-46c5-833e-cb47e3c3bdfd.temp.1197611185902619026/e17762d1-9921-46c5-833e-cb47e3c3bdfd.cwl#ps/ea5165fc-8948-43ae-8dec-3c0468b56bcb/ps-stdOut,None,None,None,None,None,Some(CommandOutputBinding(Some(Inl(Inr(Inl(ps-stdOut.txt)))),None,None)),Some(Inl(Inl(File))))
-      *
-      * after:
-      *
-      * CommandOutputParameter(ps-stdOut,None,None,None,None,None,Some(CommandOutputBinding(Some(Inl(Inr(Inl(ps-stdOut.txt)))),None,None)),Some(Inl(Inl(File))))
-      *
-      * This is possibly too strict (i.e. some of these fields may be irrelevant for cache hit determination), but preferable
-      * to having false positives.
-      * Also two coproduct types that can be either single or Arrays have custom stringifying folds for arrays. */
-    override def cacheString: String = {
-      val cacheableId: String = id.substring(id.lastIndexOf('/') + 1)
-      val cacheableSecondaryFiles = secondaryFiles map { _.fold(SecondaryFilesCacheableString)}
-      val cacheableType: Option[String] = `type`.map(_.fold(MyriadOutputTypeCacheableString))
-      s"CommandOutputParameter($cacheableId,$label,$cacheableSecondaryFiles,$format,$streamable,$doc,$outputBinding,$cacheableType)"
-    }
-  }
-}
-
-object StringOrExpressionToWomExpression extends Poly1 {
-  implicit def string: Case.Aux[String, (Set[String], ExpressionLib) => WomExpression] = at[String] { s => (inputNames, expressionLib) =>
-    ValueAsAnExpression(WomString(s))
-  }
-
-  implicit def expression: Case.Aux[Expression, (Set[String], ExpressionLib) => WomExpression] = at[Expression] { e => (inputNames, expressionLib) =>
-    cwl.ECMAScriptWomExpression(e, inputNames, expressionLib)
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CommandOutputBinding.scala b/cwl/src/main/scala/cwl/CommandOutputBinding.scala
deleted file mode 100644
index bab616f2995..00000000000
--- a/cwl/src/main/scala/cwl/CommandOutputBinding.scala
+++ /dev/null
@@ -1,295 +0,0 @@
-package cwl
-
-import cats.effect.IO
-import cats.effect.IO._
-import cats.syntax.functor._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.syntax.parallel._
-import cats.instances.list._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import wom.expression.IoFunctionSet.{IoDirectory, IoFile}
-import wom.expression.{FileEvaluation, IoFunctionSet}
-import wom.types._
-import wom.values._
-
-/** @see <a href="http://www.commonwl.org/v1.0/Workflow.html#CommandOutputBinding">CommandOutputBinding</a> */
-case class CommandOutputBinding(glob: Option[Glob] = None,
-                                loadContents: Option[Boolean] = None,
-                                outputEval: Option[StringOrExpression] = None)
-
-object CommandOutputBinding {
-  /**
-    * TODO: WOM: WOMFILE: Need to support returning globs for primary and secondary.
-    *
-    * Right now, when numerous glob files are created, the backends place each glob result into a different subdirectory.
-    * Later, when the secondary files are being generated each of their globs are in different sub-directories.
-    * Unfortunately, the secondary file resolution assumes that the secondaries are _next to_ the primaries, not in
-    * sibling directories.
-    *
-    * While this is being worked on, instead of looking up globs return regular files until this can be fixed.
-    */
-  def isRegularFile(path: String): Boolean = {
-    path match {
-      case _ if path.contains("*") => false
-      case _ if path.contains("?") => false
-      case _ => true
-    }
-  }
-
-  /**
-    * Returns all the primary and secondary files that _will be_ created by this command output binding.
-    */
-  def getOutputWomFiles(inputValues: Map[String, WomValue],
-                        outputWomType: WomType,
-                        commandOutputBinding: CommandOutputBinding,
-                        secondaryFilesOption: Option[SecondaryFiles],
-                        ioFunctionSet: IoFunctionSet,
-                        expressionLib: ExpressionLib): IOChecked[Set[FileEvaluation]] = {
-    val parameterContext = ParameterContext(ioFunctionSet, expressionLib, inputs = inputValues)
-
-    /*
-    CWL can output two types of "glob" path types:
-    - File will be a glob path
-    - Directory is a path that will be searched for files. It's assumed that it will not be a glob, but the spec is
-      unclear and doesn't specifically say how Directories are listed. If the backend uses a POSIX
-      `find <dir> -type f`, then a globbed path should still work.
-
-    Either way create one of the two types as a return type that the backend should be looking for when the command
-    completes.
-
-    UPDATE:
-    It turns out that secondary files can be directories. TODO: WOM: WOMFILE: Not sure what to do with that yet.
-    https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/search.cwl#L42
-    https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/index.py#L36-L37
-     */
-    def primaryPathsToWomFiles(primaryPaths: List[String]): ErrorOr[List[WomFile]] = {
-      validate {
-        primaryPaths map { primaryPath =>
-          val outputWomFlatType = outputWomType match {
-            case WomMaybeListedDirectoryType => WomUnlistedDirectoryType
-            case WomArrayType(WomMaybeListedDirectoryType) => WomUnlistedDirectoryType
-            case _ if isRegularFile(primaryPath) => WomSingleFileType
-            case _ => WomGlobFileType
-          }
-
-          WomFile(outputWomFlatType, primaryPath)
-        }
-      }
-    }
-
-    def secondaryFilesToWomFiles(primaryWomFiles: List[WomFile], ioFunctionSet: IoFunctionSet): IOChecked[List[WomFile]] = {
-      primaryWomFiles.flatTraverse[IOChecked, WomFile] { primaryWomFile =>
-        FileParameter.secondaryFiles(primaryWomFile,
-          primaryWomFile.womFileType, secondaryFilesOption, parameterContext, expressionLib, ioFunctionSet)
-      }
-    }
-
-    for {
-      primaryPaths <- GlobEvaluator.globs(commandOutputBinding.glob, parameterContext, expressionLib).toIOChecked
-      primaryWomFiles <- primaryPathsToWomFiles(primaryPaths).toIOChecked
-      // This sets optional = false arbitrarily for now as this code doesn't have the context to make that determination,
-      // the caller can change this if necessary.
-      primaryEvaluations = primaryWomFiles map { FileEvaluation(_, optional = false, secondary = false) }
-      secondaryWomFiles <- secondaryFilesToWomFiles(primaryWomFiles, ioFunctionSet)
-      secondaryEvaluations = secondaryWomFiles map { FileEvaluation(_, optional = false, secondary = true) }
-    } yield (primaryEvaluations ++ secondaryEvaluations).toSet
-  }
-
-  /**
-    * Generates an output wom value based on the specification in command output binding.
-    *
-    * Depending on the outputWomType, the following steps will be applied as specified in the CWL spec:
-    * 1. glob: get a list the globbed files as our primary files
-    * 2. loadContents: load the contents of the primary files
-    * 3. outputEval: pass in the primary files to an expression to generate our return value
-    * 4. secondaryFiles: just before returning the value, fill in the secondary files on the return value
-    *
-    * The result type will be coerced to the output type.
-    */
-  def generateOutputWomValue(inputValues: Map[String, WomValue],
-                             ioFunctionSet: IoFunctionSet,
-                             outputWomType: WomType,
-                             commandOutputBinding: CommandOutputBinding,
-                             secondaryFilesCoproduct: Option[SecondaryFiles],
-                             formatCoproduct: Option[StringOrExpression],
-                             expressionLib: ExpressionLib): IOChecked[WomValue] = {
-    import ioFunctionSet.cs
-
-    val parameterContext = ParameterContext(ioFunctionSet, expressionLib, inputs = inputValues)
-
-    // 3. outputEval: pass in the primary files to an expression to generate our return value
-    def evaluateWomValue(womFilesArray: WomArray): ErrorOr[WomValue] = {
-      commandOutputBinding.outputEval match {
-        case Some(StringOrExpression.String(string)) => WomString(string).valid
-        case Some(StringOrExpression.Expression(expression)) =>
-          val outputEvalParameterContext = parameterContext.copy(self = womFilesArray)
-          ExpressionEvaluator.eval(expression, outputEvalParameterContext)
-        case None =>
-          womFilesArray.valid
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-    }
-
-    // Used to retrieve the file format to be injected into a file result.
-    def formatOptionErrorOr = OutputParameter.format(formatCoproduct, parameterContext, expressionLib)
-
-    // 4. secondaryFiles: just before returning the value, fill in the secondary files on the return value
-    def populateSecondaryFiles(evaluatedWomValue: WomValue): IOChecked[WomValue] = {
-      for {
-        formatOption <- formatOptionErrorOr.toIOChecked
-        womValue <- FileParameter.populateSecondaryFiles(
-          evaluatedWomValue,
-          secondaryFilesCoproduct,
-          formatOption,
-          parameterContext,
-          expressionLib,
-          ioFunctionSet
-        )
-      } yield womValue
-    }
-
-    // CWL tells us the type this output is expected to be. Attempt to coerce the actual output into this type.
-    def coerceWomValue(populatedWomValue: WomValue): ErrorOr[WomValue] = {
-      (outputWomType, populatedWomValue) match {
-
-        case (womType: WomArrayType, womValue: WomArray) =>
-          // Array -from- Array then coerce normally
-          // NOTE: this evaluates to the same as the last case, but guards against the next cases accidentally matching
-          womType.coerceRawValue(womValue).toErrorOr
-
-        case (womType: WomArrayType, womValue) =>
-          // Array -from- Single then coerce a single value to an array
-          womType.coerceRawValue(womValue).toErrorOr.map(value => WomArray(womType, List(value)))
-
-        case (womType, womValue: WomArray) if womValue.value.lengthCompare(1) == 0 =>
-          // Single -from- Array then coerce the head (if there's only a head)
-          womType.coerceRawValue(womValue.value.head).toErrorOr
-
-        case (womType, womValue) =>
-          // <other> to <other> then coerce normally
-          womType.coerceRawValue(womValue).toErrorOr
-
-      }
-    }
-
-    for {
-      // 1. glob: get a list the globbed files as our primary files
-      primaryPaths <- GlobEvaluator.globs(commandOutputBinding.glob, parameterContext, expressionLib).toIOChecked
-
-      // 2. loadContents: load the contents of the primary files
-      primaryAsDirectoryOrFiles <- primaryPaths.parTraverse[IOChecked, List[WomFile]] {
-        loadPrimaryWithContents(ioFunctionSet, outputWomType, commandOutputBinding)
-      } map (_.flatten)
-
-      // Make globbed files absolute paths by prefixing them with the output dir if necessary
-      absolutePaths = primaryAsDirectoryOrFiles.map(_.mapFile(ioFunctionSet.pathFunctions.relativeToHostCallRoot))
-
-      // Load file size
-      withFileSizes <- absolutePaths.parTraverse[IOChecked, WomFile](_.withSize(ioFunctionSet).to[IOChecked])
-
-      womFilesArray = WomArray(withFileSizes)
-
-      // 3. outputEval: pass in the primary files to an expression to generate our return value
-      evaluatedWomValue <- evaluateWomValue(womFilesArray).toIOChecked
-
-      // 4. secondaryFiles: just before returning the value, fill in the secondary files on the return value
-      populatedWomValue <- populateSecondaryFiles(evaluatedWomValue)
-
-      // CWL tells us the type this output is expected to be. Attempt to coerce the actual output into this type.
-      coercedWomValue <- coerceWomValue(populatedWomValue).toIOChecked
-    } yield coercedWomValue
-  }
-
-  /**
-    * Given a cwl glob path and an output type, gets the listing using the ioFunctionSet, and optionally loads the
-    * contents of the file(s).
-    */
-  private def loadPrimaryWithContents(ioFunctionSet: IoFunctionSet,
-                                      outputWomType: WomType,
-                                      commandOutputBinding: CommandOutputBinding)
-                                     (cwlPath: String): IOChecked[List[WomFile]] = {
-    import ioFunctionSet.cs
-
-    /*
-    For each file matched in glob, read up to the first 64 KiB of text from the file and place it in the contents field
-    of the file object for manipulation by outputEval.
-     */
-    val womMaybeListedDirectoryOrFileType = outputWomType match {
-      case WomMaybeListedDirectoryType => WomMaybeListedDirectoryType
-      case WomArrayType(WomMaybeListedDirectoryType) => WomMaybeListedDirectoryType
-      case _ => WomMaybePopulatedFileType
-    }
-    womMaybeListedDirectoryOrFileType match {
-      case WomMaybeListedDirectoryType =>
-        // Even if multiple directories are _somehow_ requested, a single flattened directory is returned.
-        loadDirectoryWithListing(ioFunctionSet, commandOutputBinding)(cwlPath).map(List(_))
-      case WomMaybePopulatedFileType if isRegularFile(cwlPath) =>
-        loadFileWithContents(ioFunctionSet, commandOutputBinding)(cwlPath).to[IOChecked].map(List(_))
-      case WomMaybePopulatedFileType =>
-        //TODO: HACK ALERT - DB: I am starting on ticket https://github.com/broadinstitute/cromwell/issues/3092 which will redeem me of this mortal sin.
-        val detritusFiles = List(
-          "docker_cid",
-          "gcs_delocalization.sh",
-          "gcs_localization.sh",
-          "gcs_transfer.sh",
-          "rc.tmp",
-          "script",
-          "script.background",
-          "script.submit",
-          "stderr",
-          "stderr.background",
-          "stdout",
-          "stdout.background",
-        )
-        val globs: IOChecked[Seq[String]] =
-          ioFunctionSet.glob(cwlPath).toIOChecked
-              .map({
-                _
-                .filterNot{ s =>
-                  detritusFiles exists s.endsWith
-                }
-              })
-
-        globs.flatMap({ files =>
-          files.toList.parTraverse[IOChecked, WomFile](v => loadFileWithContents(ioFunctionSet, commandOutputBinding)(v).to[IOChecked])
-        })
-      case other => s"Program error: $other type was not expected".invalidIOChecked
-    }
-  }
-
-  /**
-    * Loads a directory with the files listed, each file with contents populated.
-    */
-  private def loadDirectoryWithListing(ioFunctionSet: IoFunctionSet,
-                                       commandOutputBinding: CommandOutputBinding)(path: String, visited: Vector[String] = Vector.empty): IOChecked[WomMaybeListedDirectory] = {
-    import ioFunctionSet.cs
-
-    for {
-      listing <- IO.fromFuture(IO { ioFunctionSet.listDirectory(path)(visited) }).to[IOChecked]
-      loadedListing <- listing.toList.parTraverse[IOChecked, WomFile]({
-        case IoFile(p) => loadFileWithContents(ioFunctionSet, commandOutputBinding)(p).to[IOChecked]
-        case IoDirectory(p) => loadDirectoryWithListing(ioFunctionSet, commandOutputBinding)(p, visited :+ path).widen
-      })
-    } yield WomMaybeListedDirectory(valueOption = Option(path), listingOption = Option(loadedListing))
-  }
-
-  /**
-    * Loads a file at path reading 64KiB of data into the contents.
-    */
-  private def loadFileWithContents(ioFunctionSet: IoFunctionSet,
-                                   commandOutputBinding: CommandOutputBinding)(path: String): IO[WomFile] = {
-    val contentsOptionErrorOr = {
-      if (commandOutputBinding.loadContents getOrElse false) {
-        FileParameter.load64KiB(path, ioFunctionSet) map Option.apply
-      } else {
-        IO.pure(None)
-      }
-    }
-    contentsOptionErrorOr map { contentsOption =>
-      WomMaybePopulatedFile(valueOption = Option(path), contentsOption = contentsOption)
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlCodecs.scala b/cwl/src/main/scala/cwl/CwlCodecs.scala
deleted file mode 100644
index d7010494bca..00000000000
--- a/cwl/src/main/scala/cwl/CwlCodecs.scala
+++ /dev/null
@@ -1,153 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import cats.syntax.show._
-import common.Checked
-import common.validation.Checked._
-import cwl.CommandLineTool.{CommandInputParameter, CommandOutputParameter}
-import cwl.CwlType.CwlType
-import cwl.CwlVersion.CwlVersion
-import cwl.ExpressionTool.{ExpressionToolInputParameter, ExpressionToolOutputParameter}
-import cwl.InitialWorkDirRequirement.IwdrListingArrayEntry
-import cwl.LinkMergeMethod.LinkMergeMethod
-import cwl.ScatterMethod.ScatterMethod
-import cwl.SchemaDefRequirement.SchemaDefTypes
-import cwl.Workflow.{WorkflowInputParameter, WorkflowOutputParameter}
-import io.circe.DecodingFailure._
-import io.circe.Json._
-import io.circe._
-import io.circe.generic.semiauto._
-import io.circe.literal._
-import io.circe.refined._
-import io.circe.shapes._
-import shapeless.Coproduct
-
-object CwlCodecs {
-  /*
-  Semi-auto codecs for the Cwl types
-  https://circe.github.io/circe/codecs/semiauto-derivation.html
-
-  Some types, such as BaseCommand are not listed, as they are actually one-for-one type aliases. Having two exact
-  implicits for the same type will confuse the compiler, leading to cryptic error messages elsewhere.
-
-  For example, a duplicated decoder such as:
-
-  ```
-  implicit lazy val decodeSingleOrArrayOfStrings: Decoder[SingleOrArrayOfStrings] = decodeCCons
-  implicit lazy val decodeBaseCommand: Decoder[BaseCommand] = decodeCCons
-  ```
-
-  causes cryptic errors such as:
-
-  ```
-  [error] cwl/src/main/scala/cwl/CwlCodecs.scala:123:456: could not find Lazy implicit value of type io.circe.generic.decoding.DerivedDecoder[A]
-  [error]   implicit lazy val decodeCommandInputParameter: Decoder[CommandInputParameter] = deriveDecoder
-
-  (etc. etc. etc.)
-  ```
-   */
-
-  // Semi-Automatically derived codecs
-  implicit lazy val codecArgumentCommandLineBinding: Codec[ArgumentCommandLineBinding] = deriveCodec
-  implicit lazy val codecCommandInputParameter: Codec[CommandInputParameter] = deriveCodec
-  implicit lazy val codecCommandLineTool: Codec[CommandLineTool] = deriveCodec
-  implicit lazy val codecCommandOutputBinding: Codec[CommandOutputBinding] = deriveCodec
-  implicit lazy val codecCommandOutputParameter: Codec[CommandOutputParameter] = deriveCodec
-  implicit lazy val codecCwlType: Codec[CwlType] = Codec.codecForEnumeration(CwlType)
-  implicit lazy val codecCwlVersion: Codec[CwlVersion] = Codec.codecForEnumeration(CwlVersion)
-  implicit lazy val codecDirectory: Codec[Directory] = deriveCodec
-  implicit lazy val codecDockerRequirement: Codec[DockerRequirement] = deriveCodec
-  implicit lazy val codecEnvVarRequirement: Codec[EnvVarRequirement] = deriveCodec
-  implicit lazy val codecEnvironmentDef: Codec[EnvironmentDef] = deriveCodec
-  implicit lazy val codecExpressionDirent: Codec[ExpressionDirent] = deriveCodec
-  implicit lazy val codecExpressionTool: Codec[ExpressionTool] = deriveCodec
-  implicit lazy val codecExpressionToolInputParameter: Codec[ExpressionToolInputParameter] = deriveCodec
-  implicit lazy val codecExpressionToolOutputParameter: Codec[ExpressionToolOutputParameter] = deriveCodec
-  implicit lazy val codecFile: Codec[File] = deriveCodec
-  implicit lazy val codecInitialWorkDirRequirement: Codec[InitialWorkDirRequirement] = deriveCodec
-  implicit lazy val codecInlineJavascriptRequirement: Codec[InlineJavascriptRequirement] = deriveCodec
-  implicit lazy val codecInputArraySchema: Codec[InputArraySchema] = deriveCodec
-  implicit lazy val codecInputBinding: Codec[InputBinding] = deriveCodec
-  implicit lazy val codecInputCommandLineBinding: Codec[InputCommandLineBinding] = deriveCodec
-  implicit lazy val codecInputEnumSchema: Codec[InputEnumSchema] = deriveCodec
-  implicit lazy val codecInputRecordField: Codec[InputRecordField] = deriveCodec
-  implicit lazy val codecInputRecordSchema: Codec[InputRecordSchema] = deriveCodec
-  implicit lazy val codecInputResourceRequirement: Codec[DnaNexusInputResourceRequirement] = deriveCodec
-  implicit lazy val codecLinkMergeMethod: Codec[LinkMergeMethod] = Codec.codecForEnumeration(LinkMergeMethod)
-  implicit lazy val codecMultipleInputFeatureRequirement: Codec[MultipleInputFeatureRequirement] = deriveCodec
-  implicit lazy val codecOutputArraySchema: Codec[OutputArraySchema] = deriveCodec
-  implicit lazy val codecOutputEnumSchema: Codec[OutputEnumSchema] = deriveCodec
-  implicit lazy val codecOutputRecordField: Codec[OutputRecordField] = deriveCodec
-  implicit lazy val codecOutputRecordSchema: Codec[OutputRecordSchema] = deriveCodec
-  implicit lazy val codecResourceRequirement: Codec[ResourceRequirement] = deriveCodec
-  implicit lazy val codecScatterFeatureRequirement: Codec[ScatterFeatureRequirement] = deriveCodec
-  implicit lazy val codecScatterMethod: Codec[ScatterMethod] = Codec.codecForEnumeration(ScatterMethod)
-  implicit lazy val codecSchemaDefRequirement: Codec[SchemaDefRequirement] = deriveCodec
-  implicit lazy val codecShellCommandRequirement: Codec[ShellCommandRequirement] = deriveCodec
-  implicit lazy val codecSoftwarePackage: Codec[SoftwarePackage] = deriveCodec
-  implicit lazy val codecSoftwareRequirement: Codec[SoftwareRequirement] = deriveCodec
-  implicit lazy val codecStepInputExpressionRequirement: Codec[StepInputExpressionRequirement] = deriveCodec
-  implicit lazy val codecStringDirent: Codec[StringDirent] = deriveCodec
-  implicit lazy val codecSubworkflowFeatureRequirement: Codec[SubworkflowFeatureRequirement] = deriveCodec
-  implicit lazy val codecWorkflow: Codec[Workflow] = deriveCodec
-  implicit lazy val codecWorkflowInputParameter: Codec[WorkflowInputParameter] = deriveCodec
-  implicit lazy val codecWorkflowOutputParameter: Codec[WorkflowOutputParameter] = deriveCodec
-  implicit lazy val codecWorkflowStep: Codec[WorkflowStep] = deriveCodec
-  implicit lazy val codecWorkflowStepInput: Codec[WorkflowStepInput] = deriveCodec
-  implicit lazy val codecWorkflowStepOutput: Codec[WorkflowStepOutput] = deriveCodec
-
-  // Encoders and decoders for Coproduct-based types must be explicitly derived
-  implicit lazy val decodeCwlAny: Decoder[CwlAny] = decodeCCons
-  implicit lazy val decodeExpression: Decoder[Expression] = decodeCCons
-  implicit lazy val decodeFileOrDirectory: Decoder[FileOrDirectory] = decodeCCons
-  implicit lazy val decodeGlob: Decoder[Glob] = decodeCCons
-  implicit lazy val decodeHint: Decoder[Hint] = decodeCCons
-  implicit lazy val decodeIwdrListingArrayEntry: Decoder[IwdrListingArrayEntry] = decodeCCons
-  implicit lazy val decodeMyriadInputInnerType: Decoder[MyriadInputInnerType] = decodeCCons
-  implicit lazy val decodeMyriadInputType: Decoder[MyriadInputType] = decodeCCons
-  implicit lazy val decodeMyriadOutputType: Decoder[MyriadOutputType] = decodeCCons
-  implicit lazy val decodeRequirement: Decoder[Requirement] = decodeCCons
-  implicit lazy val decodeResourceRequirementType: Decoder[ResourceRequirementType] = decodeCCons
-  implicit lazy val decodeSchemaDefTypes: Decoder[SchemaDefTypes] = decodeCCons
-  implicit lazy val decodeSecondaryFiles: Decoder[SecondaryFiles] = decodeCCons
-  implicit lazy val decodeSingleOrArrayOfStrings: Decoder[SingleOrArrayOfStrings] = decodeCCons
-  implicit lazy val decodeStringOrExpression: Decoder[StringOrExpression] = decodeCCons
-
-  implicit lazy val encodeCwlAny: Encoder[CwlAny] = encodeCCons
-  implicit lazy val encodeExpression: Encoder[Expression] = encodeCCons
-  implicit lazy val encodeFileOrDirectory: Encoder[FileOrDirectory] = encodeCCons
-  implicit lazy val encodeGlob: Encoder[Glob] = encodeCCons
-  implicit lazy val encodeHint: Encoder[Hint] = encodeCCons
-  implicit lazy val encodeIwdrListingArrayEntry: Encoder[IwdrListingArrayEntry] = encodeCCons
-  implicit lazy val encodeMyriadInputInnerType: Encoder[MyriadInputInnerType] = encodeCCons
-  implicit lazy val encodeMyriadInputType: Encoder[MyriadInputType] = encodeCCons
-  implicit lazy val encodeMyriadOutputType: Encoder[MyriadOutputType] = encodeCCons
-  implicit lazy val encodeRequirement: Encoder[Requirement] = encodeCCons
-  implicit lazy val encodeResourceRequirementType: Encoder[ResourceRequirementType] = encodeCCons
-  implicit lazy val encodeSchemaDefTypes: Encoder[SchemaDefTypes] = encodeCCons
-  implicit lazy val encodeSecondaryFiles: Encoder[SecondaryFiles] = encodeCCons
-  implicit lazy val encodeSingleOrArrayOfStrings: Encoder[SingleOrArrayOfStrings] = encodeCCons
-  implicit lazy val encodeStringOrExpression: Encoder[StringOrExpression] = encodeCCons
-
-  def decodeCwl(json: Json): Checked[Cwl] = {
-    findClass(json) match {
-      case Some("Workflow") => decodeWithErrorStringsJson[Workflow](json).map(Coproduct[Cwl].apply(_))
-      case Some("CommandLineTool") => decodeWithErrorStringsJson[CommandLineTool](json).map(Coproduct[Cwl].apply(_))
-      case Some("ExpressionTool") => decodeWithErrorStringsJson[ExpressionTool](json).map(Coproduct[Cwl].apply(_))
-      case Some(other) => s"Class field was declared incorrectly: $other is not one of Workflow, CommandLineTool, or ExpressionTool! as seen in ${json.show}".invalidNelCheck
-      case None => s"Class field was omitted in ${json.show}".invalidNelCheck
-    }
-  }
-
-  private def decodeWithErrorStringsJson[A](in: Json)(implicit d: Codec[A]): Checked[A] =
-    in.as[A].leftMap(_.show).leftMap(NonEmptyList.one)
-
-  private def findClass(json: Json): Option[String] =
-    for {
-      obj <- json.asObject
-      map = obj.toMap
-      classObj <- map.get("class")
-      classString <- classObj.asString
-    } yield classString
-}
diff --git a/cwl/src/main/scala/cwl/CwlDecoder.scala b/cwl/src/main/scala/cwl/CwlDecoder.scala
deleted file mode 100644
index b7a4125e5a3..00000000000
--- a/cwl/src/main/scala/cwl/CwlDecoder.scala
+++ /dev/null
@@ -1,84 +0,0 @@
-package cwl
-
-import better.files.{File => BFile}
-import cats.data.EitherT._
-import cats.effect.IO
-import cats.syntax.either._
-import cats.{Applicative, Monad}
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.preprocessor.{CwlFileReference, CwlPreProcessor, CwlReference}
-import io.circe.Json
-
-import scala.util.Try
-
-object CwlDecoder {
-
-  implicit val composedApplicative = Applicative[IO] compose Applicative[ErrorOr]
-
-  def saladCwlFile(reference: CwlReference): IOChecked[String] = {
-    val cwlToolResult =
-      Try(CwltoolRunner.instance.salad(reference))
-        .toCheckedWithContext(s"run cwltool on file ${reference.pathAsString}", throwableToStringFunction = t => t.toString)
-
-    fromEither[IO](cwlToolResult)
-  }
-
-  private lazy val cwlPreProcessor = new CwlPreProcessor()
-
-  // TODO: WOM: During conformance testing the saladed-CWLs are referring to files in the temp directory.
-  // Thus we can't delete the temp directory until after the workflow is complete, like the workflow logs.
-  // All callers to this method should be fixed around the same time.
-  // https://github.com/broadinstitute/cromwell/issues/3186
-  def todoDeleteCwlFileParentDirectory(cwlFile: BFile): IOChecked[Unit] = {
-    goIOChecked {
-      //cwlFile.parent.delete(swallowIOExceptions = true)
-    }
-  }
-
-  def parseJson(json: Json, from: String): IOChecked[Cwl] = fromEither[IO](CwlCodecs.decodeCwl(json).contextualizeErrors(s"parse '$from'"))
-
-  /**
-    * Notice it gives you one instance of Cwl.  This has transformed all embedded files into scala object state
-    */
-  def decodeCwlReference(reference: CwlReference)(implicit processor: CwlPreProcessor = cwlPreProcessor): IOChecked[Cwl] = {
-    def makeStandaloneWorkflow(): IOChecked[Json] = processor.preProcessCwl(reference)
-
-    for {
-      standaloneWorkflow <- makeStandaloneWorkflow()
-      parsedCwl <- parseJson(standaloneWorkflow, reference.pathAsString)
-    } yield parsedCwl
-  }
-
-  def decodeCwlFile(file: BFile, workflowRoot: Option[String] = None) = {
-    decodeCwlReference(CwlFileReference(file, workflowRoot))
-  }
-
-  def decodeCwlString(cwl: String,
-                      zipOption: Option[BFile] = None,
-                      rootName: Option[String] = None,
-                      cwlFilename: String = "cwl_temp_file"): IOChecked[Cwl] = {
-    for {
-      parentDir <- goIOChecked(BFile.newTemporaryDirectory("cwl_temp_dir_")) // has a random long appended like `cwl_temp_dir_100000000000`
-      file <- fromEither[IO](parentDir./(cwlFilename + ".cwl").write(cwl).asRight) // serves as the basis for the output directory name; must remain stable across restarts
-      _ <- zipOption match {
-        case Some(zip) => goIOChecked(zip.unzipTo(parentDir))
-        case None => Monad[IOChecked].unit
-      }
-      out <- decodeCwlFile(file, rootName)
-      _ <- todoDeleteCwlFileParentDirectory(file)
-    } yield out
-  }
-
-  //This is used when traversing over Cwl and replacing links w/ embedded data
-  private[cwl] def decodeCwlAsValidated(fileName: String): IOCheckedValidated[(String, Cwl)] = {
-    //The SALAD preprocess step puts "file://" as a prefix to all filenames.  Better files doesn't like this.
-    val bFileName = fileName.stripPrefix("file://")
-
-    decodeCwlReference(CwlFileReference(BFile(bFileName), None)).
-      map(fileName.toString -> _).
-      value.
-      map(_.toValidated)
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlExecutableValidation.scala b/cwl/src/main/scala/cwl/CwlExecutableValidation.scala
deleted file mode 100644
index f6f8237c5ff..00000000000
--- a/cwl/src/main/scala/cwl/CwlExecutableValidation.scala
+++ /dev/null
@@ -1,38 +0,0 @@
-package cwl
-
-import common.Checked
-import common.validation.Checked._
-import io.circe.Json
-import wom.callable.{ExecutableCallable, TaskDefinition}
-import wom.executable.Executable
-import wom.executable.Executable.{InputParsingFunction, ParsedInputMap}
-import wom.expression.IoFunctionSet
-import wom.util.YamlUtils
-
-object CwlExecutableValidation {
-
-  // Decodes the input file, and build the ParsedInputMap
-  private val inputCoercionFunction: InputParsingFunction =
-    inputFile => {
-      val yaml = YamlUtils.parse(inputFile)
-      yaml.flatMap(_.as[Map[String, Json]]) match {
-        case Left(error) => error.getMessage.invalidNelCheck[ParsedInputMap]
-        case Right(inputValue) => inputValue.map({ case (key, value) => key -> value.foldWith(CwlJsonToDelayedCoercionFunction) }).validNelCheck
-      }
-    }
-
-  def buildWomExecutableCallable(callable: Checked[ExecutableCallable], inputFile: Option[String], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    for {
-      womDefinition <- callable
-      executable <- Executable.withInputs(womDefinition, inputCoercionFunction, inputFile, ioFunctions, strictValidation)
-    } yield executable
-  }
-
-  def buildWomExecutable(callableTaskDefinition: Checked[TaskDefinition], inputFile: Option[String], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    for {
-      taskDefinition <- callableTaskDefinition
-      executableTaskDefinition = taskDefinition.toExecutable.toEither
-      executable <- CwlExecutableValidation.buildWomExecutableCallable(executableTaskDefinition, inputFile, ioFunctions, strictValidation)
-    } yield executable
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlExpressionCommandPart.scala b/cwl/src/main/scala/cwl/CwlExpressionCommandPart.scala
deleted file mode 100644
index f323c74dbd2..00000000000
--- a/cwl/src/main/scala/cwl/CwlExpressionCommandPart.scala
+++ /dev/null
@@ -1,146 +0,0 @@
-package cwl
-
-import cats.syntax.either._
-import cats.syntax.validated._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import wom.callable.RuntimeEnvironment
-import wom.expression.IoFunctionSet
-import wom.graph.LocalName
-import wom.values._
-import wom.{CommandPart, InstantiatedCommand}
-
-import scala.language.postfixOps
-
-case class CwlExpressionCommandPart(expr: Expression)(hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib) extends CommandPart {
-  override def instantiate(inputsMap: Map[LocalName, WomValue],
-                           functions: IoFunctionSet,
-                           valueMapper: (WomValue) => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] = {
-    val stringKeyMap = inputsMap map {
-      case (LocalName(localName), value) => localName -> valueMapper(value)
-    }
-    val parameterContext = ParameterContext(
-      functions,
-      expressionLib,
-      inputs = stringKeyMap, runtimeOption = Option(runtimeEnvironment)
-    )
-    ExpressionEvaluator.eval(expr, parameterContext) map { womValue =>
-      List(InstantiatedCommand(valueMapper(womValue).valueString.shellQuote))
-    }
-  }
-}
-
-/**
-  * Generates command parts from a CWL Binding
-  */
-abstract class CommandLineBindingCommandPart(commandLineBinding: CommandLineBinding)(hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib) extends CommandPart {
-
-
-  private lazy val prefixAsString = commandLineBinding.prefix.getOrElse("")
-  private lazy val prefixAsList = commandLineBinding.prefix.toList
-  private lazy val separate = commandLineBinding.effectiveSeparate
-
-  def handlePrefix(value: String) = {
-    if (separate) prefixAsList :+ value else List(s"$prefixAsString$value")
-  }
-
-  /**
-    * Value bound to this command part.
-    * InputCommandLineBindingCommandPart has one
-    * ArgumentCommandLineBindingCommandPart does not
-    */
-  def boundValue: Option[WomValue]
-
-  // If the bound value is defined but contains an empty optional value, we should not evaluate the valueFrom
-  // Conformance test "stage-unprovided-file" tests this behavior
-  private lazy val evaluateValueFrom = boundValue.forall {
-    case WomOptionalValue(_, None) => false
-    case _ => true
-  }
-
-  override def instantiate(inputsMap: Map[LocalName, WomValue],
-                           functions: IoFunctionSet,
-                           valueMapper: (WomValue) => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] = {
-      val stringInputsMap = inputsMap map {
-        case (LocalName(localName), value) => localName -> valueMapper(value)
-      }
-    val parameterContext = ParameterContext(
-      functions,
-      expressionLib,
-      inputs = stringInputsMap,
-      runtimeOption = Option(runtimeEnvironment),
-      self = boundValue.getOrElse(ParameterContext.EmptySelf)
-    )
-
-    val evaluatedValueFrom = commandLineBinding.optionalValueFrom flatMap {
-      case StringOrExpression.Expression(expression) if evaluateValueFrom => Option(ExpressionEvaluator.eval(expression, parameterContext) map valueMapper)
-      case StringOrExpression.String(string) if evaluateValueFrom => Option(WomString(string).validNel)
-      case _ => None
-    }
-
-    val evaluatedWomValue: Checked[WomValue] = evaluatedValueFrom.orElse(boundValue.map(_.validNel)) match {
-      case Some(womValue) => womValue.map(valueMapper).toEither
-      case None => "Command line binding has no valueFrom field and no bound value".invalidNelCheck
-    }
-
-    def applyShellQuote(value: String): String = commandLineBinding.shellQuote match {
-      // Only honor shellQuote = false if ShellCommandRequirement is enabled.
-      // Conformance test "Test that shell directives are not interpreted."
-      case Some(false) if hasShellCommandRequirement => value
-      case _ => value.shellQuote
-    }
-
-    def processValue(womValue: WomValue): List[String] = womValue match {
-      case WomOptionalValue(_, Some(value)) => processValue(valueMapper(value))
-      case WomOptionalValue(_, None) => List.empty
-      case _: WomString | _: WomInteger | _: WomFile | _: WomLong | _: WomFloat => handlePrefix(valueMapper(womValue).valueString)
-      // For boolean values, use the value of the boolean to choose whether to print the prefix or not
-      case WomBoolean(false) => List.empty
-      case WomBoolean(true) => prefixAsList
-      case WomArray(_, values) => commandLineBinding.itemSeparator match {
-        case Some(_) if values.isEmpty => List.empty
-        case Some(itemSeparator) => handlePrefix(values.map(valueMapper(_).valueString).mkString(itemSeparator))
-
-        /*
-        via: http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding
-
-        > If itemSeparator is specified, add prefix and the join the array into a single string with itemSeparator
-        > separating the items. Otherwise first add prefix, then recursively process individual elements.
-
-        Not 100% sure if this is conformant, as we are only recurse the head into `processValue` here... However the
-        conformance test "Test InlineJavascriptRequirement with multiple expressions in the same tool" is happy with the
-        behavior.
-         */
-        // InstantiatedCommand elements are generated here when there exists an optionalValueFrom
-        case None if commandLineBinding.optionalValueFrom.isDefined => values.toList match {
-          case head :: tail => processValue(head) ++ tail.map(valueMapper(_).valueString)
-          case Nil => prefixAsList
-        }
-
-        // When there is no optionalValueFrom the InstantiatedCommand elements for the womValue are appended elsewhere
-        case _ => prefixAsList
-      }
-      case _: WomObjectLike => prefixAsList
-      case WomEnumerationValue(_, value) => handlePrefix(value)
-      case WomCoproductValue(_, value) => processValue(value)
-      case w => throw new RuntimeException(s"Unhandled CwlExpressionCommandPart value '$w' of type ${w.womType.stableName}")
-    }
-
-    evaluatedWomValue map { v => processValue(v) map applyShellQuote map (InstantiatedCommand(_)) } toValidated
-  }
-}
-
-case class InputCommandLineBindingCommandPart(commandLineBinding: InputCommandLineBinding, associatedValue: WomValue)
-                                             (hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib)
-  extends CommandLineBindingCommandPart(commandLineBinding)(hasShellCommandRequirement, expressionLib) {
-  override lazy val boundValue = Option(associatedValue)
-}
-
-case class ArgumentCommandLineBindingCommandPart(commandLineBinding: ArgumentCommandLineBinding)
-                                                (hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib)
-  extends CommandLineBindingCommandPart(commandLineBinding)(hasShellCommandRequirement, expressionLib) {
-  override lazy val boundValue = None
-}
diff --git a/cwl/src/main/scala/cwl/CwlJsonToDelayedCoercionFunction.scala b/cwl/src/main/scala/cwl/CwlJsonToDelayedCoercionFunction.scala
deleted file mode 100644
index 55dc7f9e3ba..00000000000
--- a/cwl/src/main/scala/cwl/CwlJsonToDelayedCoercionFunction.scala
+++ /dev/null
@@ -1,90 +0,0 @@
-package cwl
-
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import cwl.CwlCodecs._
-import io.circe.{Json, JsonNumber, JsonObject}
-import wom.executable.Executable.DelayedCoercionFunction
-import wom.types._
-import wom.values._
-
-// With recursive types we could let circe parse it for us, but until we figure that out just parse it as Json and
-// manually check for File / Directory structures
-private [cwl] object CwlJsonToDelayedCoercionFunction extends Json.Folder[DelayedCoercionFunction] {
-  private def simpleCoercion(value: Any)(womType: WomType): ErrorOr[WomValue] = womType.coerceRawValue(value).toErrorOr
-
-  override def onNull: DelayedCoercionFunction = WomOptionalValue.none(_).validNel
-
-  override def onBoolean(value: Boolean): DelayedCoercionFunction = simpleCoercion(value)
-
-  override def onNumber(value: JsonNumber): DelayedCoercionFunction = {
-    case WomFloatType => WomFloat(value.toDouble).validNel
-    case WomIntegerType => value.toInt.map(WomInteger.apply).toValidNel(s"$value is not a valid Int")
-    case WomLongType => value.toLong.map(WomLong.apply).toValidNel(s"$value is not a valid Long")
-    case other => other.coerceRawValue(value.toString).toErrorOr
-  }
-
-  override def onString(value: String): DelayedCoercionFunction = simpleCoercion(value)
-
-  override def onArray(value: Vector[Json]): DelayedCoercionFunction = {
-    case womArrayType: WomArrayType =>
-      value.toList
-        .traverse(_.foldWith(this).apply(womArrayType.memberType))
-        .map {
-          WomArray(womArrayType, _)
-        }
-
-    case WomOptionalType(otherType) =>
-      onArray(value).apply(otherType)
-    case WomCoproductType(types) =>
-      val attempts: List[ErrorOr[WomValue]] = types.toList.map(onArray(value)(_))
-      attempts.find(_.isValid).getOrElse(attempts.sequence[ErrorOr, WomValue].map(_.head))
-    case WomAnyType =>
-      // Make an array of WomAny
-      value.toList
-        .traverse(_.foldWith(this).apply(WomAnyType))
-        .map {
-          WomArray(WomArrayType(WomAnyType), _)
-        }
-    case other => s"Cannot convert an array input value into a non array type: $other".invalidNel
-  }
-
-  override def onObject(value: JsonObject): DelayedCoercionFunction = {
-    // CWL files are represented as Json objects, so this could be a file 
-    case WomSingleFileType | WomMaybePopulatedFileType if value.toMap.get("class").flatMap(_.asString).contains("File") =>
-      Json.fromJsonObject(value).as[File] match {
-        case Left(errors) => errors.message.invalidNel
-        case Right(file) => file.asWomValue
-      }
-    case WomMaybeListedDirectoryType | WomUnlistedDirectoryType if value.toMap.get("class").flatMap(_.asString).contains("Directory") =>
-      Json.fromJsonObject(value).as[Directory] match {
-        case Left(errors) => errors.message.invalidNel
-        case Right(directory) => directory.asWomValue
-      }
-    case composite: WomCompositeType =>
-      val foldedMap = value.toList.traverse[ErrorOr, (String, WomValue)]({
-        case (k, v) =>
-          composite.typeMap.get(k).map({ valueType =>
-            v.foldWith(this).apply(valueType).map(k -> _)
-          }).getOrElse(s"Input field $k is not defined in the composite input type $composite".invalidNel)
-      }).map(_.toMap[String, WomValue])
-
-      foldedMap.map(WomObject.withTypeUnsafe(_, composite))
-    case WomObjectType =>
-      val foldedMap = value.toList.traverse[ErrorOr, (String, WomValue)]({
-        case (k, v) => v.foldWith(this).apply(WomAnyType).map(k -> _)
-      }).map(_.toMap[String, WomValue])
-
-      foldedMap.map(WomObject.apply)
-    case WomOptionalType(otherType) => onObject(value).apply(otherType)
-    case WomCoproductType(types) =>
-      val attempts: List[ErrorOr[WomValue]] = types.toList.map(onObject(value)(_))
-      //these are all Invalid, just taking head to satisfy required type of WomValue instead of List[WomValue]
-      attempts.find(_.isValid).getOrElse(attempts.sequence[ErrorOr, WomValue].map(_.head))
-    case other => s"Cannot convert an object value $value into a non array type: $other".invalidNel
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlToRun.scala b/cwl/src/main/scala/cwl/CwlToRun.scala
deleted file mode 100644
index 1571958abb5..00000000000
--- a/cwl/src/main/scala/cwl/CwlToRun.scala
+++ /dev/null
@@ -1,11 +0,0 @@
-package cwl
-
-import shapeless._
-
-object CwlToRun extends Poly1 {
-  implicit def commandLineTool = at[CommandLineTool] { Coproduct[WorkflowStep.Run](_) }
-  implicit def workflow = at[Workflow] { Coproduct[WorkflowStep.Run](_) }
-  implicit def expressionTool = at[ExpressionTool] { Coproduct[WorkflowStep.Run](_) }
-}
-
-
diff --git a/cwl/src/main/scala/cwl/CwlType.scala b/cwl/src/main/scala/cwl/CwlType.scala
deleted file mode 100644
index 7ec171d97fb..00000000000
--- a/cwl/src/main/scala/cwl/CwlType.scala
+++ /dev/null
@@ -1,284 +0,0 @@
-package cwl
-
-import cats.instances.list._
-import cats.instances.option._
-import cats.syntax.functor._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import eu.timepit.refined._
-import mouse.all._
-import shapeless.Poly1
-import shapeless.syntax.singleton._
-import wom.expression.IoFunctionSet.{IoDirectory, IoFile}
-import wom.expression.{IoFunctionSet, PathFunctionSet}
-import wom.types.WomFileType
-import wom.values._
-
-import scala.annotation.tailrec
-
-object CwlType extends Enumeration {
-  type CwlType = Value
-
-  val Any = Value("Any")
-  val Null = Value("null")
-  val Boolean = Value("boolean")
-  val Int = Value("int")
-  val Long = Value("long")
-  val Float = Value("float")
-  val Double = Value("double")
-  val String = Value("string")
-  val File = Value("File")
-  val Directory = Value("Directory")
-}
-
-case class File private
-(
-  `class`: W.`"File"`.T,
-  location: Option[String], //TODO refine w/ regex  of IRI
-  path: Option[String],
-  basename: Option[String],
-  checksum: Option[String],
-  size: Option[Long],
-  secondaryFiles: Option[Array[FileOrDirectory]],
-  format: Option[String],
-  contents: Option[String]
-) {
-  lazy val effectivePath = path.orElse(location)
-
-  lazy val errorOrSecondaryFiles: ErrorOr[List[WomFile]] = {
-    val dirsOrFiles: List[FileOrDirectory] = secondaryFiles.getOrElse(Array.empty).toList
-    dirsOrFiles.traverse{
-      _.fold(CwlDirectoryOrFileAsWomSingleDirectoryOrFile)
-    }
-  }
-
-  lazy val asWomValue: ErrorOr[WomMaybePopulatedFile] = {
-    errorOrSecondaryFiles flatMap { secondaryFiles =>
-      val valueOption = location.orElse(path)
-      (valueOption, contents) match {
-        case (None, None) =>
-          "Cannot convert CWL File to WomValue without either a location, a path, or contents".invalidNel
-        case (None, Some(content)) =>
-          val initializeFunction: WomMaybePopulatedFile => IoFunctionSet => IOChecked[WomValue] = { file =>ioFunctionSet =>
-            val name = basename.getOrElse(content.hashCode.toString)
-            ioFunctionSet.writeFile(name, content).toIOChecked(ioFunctionSet.cs) map { writtenFile =>
-              file.copy(valueOption = Option(writtenFile.value))
-            }
-          }
-
-          new WomMaybePopulatedFile(None, checksum, size, format, contents, initializeFunction = initializeFunction).valid
-        case (_, _) =>
-          WomMaybePopulatedFile(valueOption, checksum, size, format, contents, secondaryFiles).valid
-      }
-    }
-  }
-}
-
-object File {
-  def apply(
-             location: Option[String] = None, //TODO refine w/ regex  of IRI
-             path: Option[String] = None,
-             basename: Option[String] = None,
-             checksum: Option[String] = None,
-             size: Option[Long] = None,
-             secondaryFiles: Option[Array[FileOrDirectory]] = None,
-             format: Option[String] = None,
-             contents: Option[String] = None): File = {
-    new cwl.File(
-      "File".narrow,
-      location,
-      path,
-      basename,
-      checksum,
-      size,
-      secondaryFiles,
-      format,
-      contents
-    )
-  }
-
-  def dirname(value: String): String = {
-    val index = value.lastIndexOf('/')
-    if (index >= 0) {
-      value.substring(0, index)
-    } else {
-      ""
-    }
-  }
-
-  def basename(value: String): String = value.substring(value.lastIndexOf('/') + 1)
-
-  def nameroot(value: String): String = basename(value).stripSuffix(nameext(value))
-
-  def nameext(value: String): String = {
-    val base = basename(value)
-    val index = base.lastIndexOf('.')
-    if (index >= 0) {
-      base.substring(index)
-    } else {
-      ""
-    }
-  }
-
-  def recursivelyBuildDirectory(directory: String, ioFunctions: IoFunctionSet)(visited: Vector[String] = Vector.empty): IOChecked[WomMaybeListedDirectory] = {
-    for {
-      listing <- ioFunctions.listDirectory(directory)(visited).toIOChecked(ioFunctions.cs)
-      fileListing <- listing.toList.traverse[IOChecked, WomFile]({
-        case IoDirectory(e) => recursivelyBuildDirectory(e, ioFunctions)(visited :+ directory).widen
-        case IoFile(e) => WomMaybePopulatedFile(e).validIOChecked.widen
-      })
-    } yield WomMaybeListedDirectory(Option(directory), Option(fileListing))
-  }
-
-  private def asAbsoluteSiblingOfPrimary(primary: WomFile, pathFunctions: PathFunctionSet)(path: String) = {
-    pathFunctions.absoluteSibling(primary.value, path)
-  }
-
-  def secondaryStringFile(primaryWomFile: WomFile,
-                          stringWomFileType: WomFileType,
-                          secondaryValue: String,
-                          ioFunctions: IoFunctionSet): IOChecked[WomFile] = {
-    val secondaryRelativeFileName = File.relativeFileName(primaryWomFile.value, secondaryValue)
-
-    // If the primary file is an absolute path, and the secondary is not, make the secondary file an absolute path and a sibling of the primary
-    // http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter
-    val filePath = asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions)(secondaryRelativeFileName)
-
-    // If the secondary file is in fact a directory, look into it and build its listing
-    for {
-      isDirectory <- ioFunctions.isDirectory(filePath).toIOChecked(ioFunctions.cs)
-      file <- if (isDirectory) recursivelyBuildDirectory(filePath, ioFunctions)() else WomFile(stringWomFileType, filePath).validIOChecked
-    } yield file
-  }
-
-  def secondaryExpressionFiles(primaryWomFile: WomFile,
-                               stringWomFileType: WomFileType,
-                               expression: Expression,
-                               parameterContext: ParameterContext,
-                               expressionLib: ExpressionLib,
-                               ioFunctions: IoFunctionSet): ErrorOr[List[WomFile]] = {
-
-    /*
-    If the value is an expression, the value of self in the expression must be the primary input or output File object
-    to which this binding applies.
-     */
-    val secondaryParameterContext = parameterContext.copy(self = primaryWomFile)
-
-    /*
-    The expression must return a filename string relative to the path to the primary File, a File or Directory object
-    with either path or location and basename fields set, or an array consisting of strings or File or Directory
-    objects.
-     */
-    def parseResult(nestedLevel: Int)(womValue: WomValue): ErrorOr[List[WomFile]] = {
-      womValue match {
-        case womString: WomString =>
-          List(WomFile(stringWomFileType, womString.value |> asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions))).valid
-        case womMaybeListedDirectory: WomMaybeListedDirectory =>
-          List(womMaybeListedDirectory.mapFile(asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions))).valid
-        case womMaybePopulatedFile: WomMaybePopulatedFile =>
-          List(womMaybePopulatedFile.mapFile(asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions))).valid
-        case womArray: WomArray if nestedLevel == 0 =>
-          womArray.value.toList flatTraverse parseResult(nestedLevel + 1)
-        case other => s"Not a valid secondary file: $other".invalidNel
-      }
-    }
-
-    val possibleArrayErrorOr: ErrorOr[WomValue] = ExpressionEvaluator.eval(expression, secondaryParameterContext)
-    possibleArrayErrorOr.flatMap(parseResult(nestedLevel = 0))
-  }
-
-  def relativeFileName(primary: String, secondary: String): String = {
-    /*
-    If a value in secondaryFiles is a string that is not an expression, it specifies that the following pattern should
-    be applied to the path of the primary file to yield a filename relative to the primary File:
-
-    1. If string begins with one or more caret ^ characters, for each caret, remove the last file extension from the
-    path (the last period . and all following characters). If there are no file extensions, the path is unchanged.
-
-    2. Append the remainder of the string to the end of the file path.
-     */
-    if (secondary.startsWith("^")) {
-      @tailrec
-      def stripCaret(primaryAcc: String, secondaryAcc: String): (String, String) = {
-        if (secondaryAcc.startsWith("^")) {
-          val idx = primaryAcc.lastIndexOf('.')
-          if (idx < 0) {
-            (primaryAcc, secondaryAcc.dropWhile(_ == '^'))
-          } else {
-            val primaryNext = primaryAcc.substring(0, idx)
-            val secondaryNext = secondaryAcc.drop(1)
-            stripCaret(primaryNext, secondaryNext)
-          }
-        } else {
-          (primaryAcc, secondaryAcc)
-        }
-      }
-
-      val (prefix, suffix) = stripCaret(primary, secondary)
-      prefix + suffix
-    } else {
-      primary + secondary
-    }
-
-  }
-}
-
-case class Directory private
-(
-  `class`: W.`"Directory"`.T,
-  location: Option[String],
-  path: Option[String],
-  basename: Option[String],
-  listing: Option[Array[FileOrDirectory]]
-) {
-  lazy val errorOrListingOption: ErrorOr[Option[List[WomFile]]] = {
-    val maybeErrorOrList: Option[ErrorOr[List[WomFile]]] =
-      listing map {
-        _.toList.traverse {
-          _.fold(CwlDirectoryOrFileAsWomSingleDirectoryOrFile)
-        }
-      }
-    maybeErrorOrList.sequence[ErrorOr, List[WomFile]]
-  }
-
-  lazy val asWomValue: ErrorOr[WomFile] = {
-    errorOrListingOption flatMap { listingOption =>
-      path.orElse(location) map { value =>
-        WomMaybeListedDirectory(Option(value), listingOption, basename).valid
-      } getOrElse {
-        val initializeFunction: WomMaybeListedDirectory => IoFunctionSet => IOChecked[WomValue] = { dir =>ioFunctionSet =>
-          ioFunctionSet.createTemporaryDirectory(basename).toIOChecked(ioFunctionSet.cs) map { tempDir =>
-            dir.copy(valueOption = Option(tempDir))
-          }
-        }
-        new WomMaybeListedDirectory(None, listingOption, basename, initializeFunction = initializeFunction).valid
-      }
-    }
-  }
-}
-
-object Directory {
-  def apply(location: Option[String] = None,
-            path: Option[String] = None,
-            basename: Option[String] = None,
-            listing: Option[Array[FileOrDirectory]] = None
-           ): Directory =
-    new cwl.Directory("Directory".narrow, location, path, basename, listing)
-
-  def basename(value: String): String = {
-    val stripped = value.stripSuffix("/")
-    stripped.substring(stripped.lastIndexOf('/') + 1)
-  }
-}
-
-private[cwl] object CwlDirectoryOrFileAsWomSingleDirectoryOrFile extends Poly1 {
-  implicit def caseFile: Case.Aux[File, ErrorOr[WomFile]] = at {
-    _.asWomValue
-  }
-
-  implicit def caseDirectory: Case.Aux[Directory, ErrorOr[WomFile]] = at {
-    _.asWomValue
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlVersion.scala b/cwl/src/main/scala/cwl/CwlVersion.scala
deleted file mode 100644
index 12336b1cceb..00000000000
--- a/cwl/src/main/scala/cwl/CwlVersion.scala
+++ /dev/null
@@ -1,7 +0,0 @@
-package cwl
-
-object CwlVersion extends Enumeration {
-  type CwlVersion = Value
-
-  val Version1 = Value("v1.0")
-}
diff --git a/cwl/src/main/scala/cwl/CwlWomExpression.scala b/cwl/src/main/scala/cwl/CwlWomExpression.scala
deleted file mode 100644
index 5d77370ba49..00000000000
--- a/cwl/src/main/scala/cwl/CwlWomExpression.scala
+++ /dev/null
@@ -1,260 +0,0 @@
-package cwl
-
-import cats.instances.list._
-import cats.syntax.functor._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import common.validation.ErrorOr.{ErrorOr, ShortCircuitingFlatMap}
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import cwl.InitialWorkDirFileGeneratorExpression._
-import cwl.InitialWorkDirRequirement.IwdrListingArrayEntry
-import shapeless.Poly1
-import wom.callable.{AdHocValue, ContainerizedInputExpression}
-import wom.expression.IoFunctionSet.{IoDirectory, IoFile}
-import wom.expression.{FileEvaluation, IoFunctionSet, WomExpression}
-import wom.types._
-import wom.values._
-
-import scala.concurrent.Await
-import scala.concurrent.duration.Duration
-
-trait CwlWomExpression extends WomExpression {
-
-  def cwlExpressionType: WomType
-
-  override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] = cwlExpressionType.validNel
-
-  def expressionLib: ExpressionLib
-
-  def evaluate(inputs: Map[String, WomValue], parameterContext: ParameterContext, expression: Expression): ErrorOr[WomValue] =
-    expression.
-      fold(EvaluateExpression).
-      apply(parameterContext)
-}
-
-case class ECMAScriptWomExpression(expression: Expression,
-                                   override val inputs: Set[String],
-                                   override val expressionLib: ExpressionLib) extends CwlWomExpression {
-  val cwlExpressionType = WomAnyType
-
-  override def sourceString = expression match {
-    case Expression.ECMAScriptExpression(s) => s.value
-    case Expression.ECMAScriptFunction(s) => s.value
-    case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-  }
-
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet) = {
-    val pc = ParameterContext(ioFunctionSet, expressionLib, inputValues)
-    evaluate(inputValues, pc, expression)
-  }
-
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType) = Set.empty[FileEvaluation].validNel
-}
-
-final case class InitialWorkDirFileGeneratorExpression(entry: IwdrListingArrayEntry, expressionLib: ExpressionLib) extends ContainerizedInputExpression {
-
-  def evaluate(inputValues: Map[String, WomValue], mappedInputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): IOChecked[List[AdHocValue]] = {
-    def recursivelyBuildDirectory(directory: String): IOChecked[WomMaybeListedDirectory] = {
-      import cats.syntax.traverse._
-      for {
-        listing <- ioFunctionSet.listDirectory(directory)().toIOChecked(ioFunctionSet.cs)
-        fileListing <- listing.toList.traverse[IOChecked, WomFile] {
-          case IoDirectory(e) => recursivelyBuildDirectory(e).widen
-          case IoFile(e) => WomSingleFile(e).validIOChecked.widen
-        }
-      } yield WomMaybeListedDirectory(Option(directory), Option(fileListing))
-    }
-
-    inputValues.toList.traverse[IOChecked, (String, WomValue)]({
-      case (k, v: WomMaybeListedDirectory) =>
-        val absolutePathString = ioFunctionSet.pathFunctions.relativeToHostCallRoot(v.value)
-        recursivelyBuildDirectory(absolutePathString).contextualizeErrors(s"Error building directory $absolutePathString") map { k -> _ }
-      case kv => kv.validIOChecked
-    }).map(_.toMap)
-      .flatMap({ updatedValues =>
-        val unmappedParameterContext = ParameterContext(ioFunctionSet, expressionLib, updatedValues)
-        entry.fold(InitialWorkDirFilePoly).apply(unmappedParameterContext, mappedInputValues).toIOChecked
-      })
-  }
-}
-
-object InitialWorkDirFileGeneratorExpression {
-  type InitialWorkDirFileEvaluator = (ParameterContext, Map[String, WomValue]) => ErrorOr[List[AdHocValue]]
-
-  /**
-    * Converts an InitialWorkDir.
-    *
-    * TODO: Review against the spec. Especially for Dirent values. For example:
-    *
-    * "If the value is an expression that evaluates to a Dirent object, this indicates that the File or Directory in
-    * entry should be added to the designated output directory with the name in entryname."
-    *
-    * - http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement
-    * - http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent
-    */
-  object InitialWorkDirFilePoly extends Poly1 {
-    implicit val caseExpressionDirent: Case.Aux[ExpressionDirent, InitialWorkDirFileEvaluator] = {
-      at { expressionDirent =>
-        (unmappedParameterContext, mappedInputValues) => {
-
-          val mutableInputOption = expressionDirent.entry.fold(ExpressionToMutableInputOptionPoly)
-
-          val entryEvaluation =
-            expressionDirent.entry match {
-                //we need to catch this special case to feed in "value-mapped" input values
-              case expr@Expression.ECMAScriptExpression(exprString) if exprString.value.trim() == "$(JSON.stringify(inputs))" =>
-                val specialParameterContext = ParameterContext(
-                  unmappedParameterContext.ioFunctionSet,
-                  unmappedParameterContext.expressionLib,
-                  mappedInputValues
-                )
-                ExpressionEvaluator.eval(expr, specialParameterContext)
-              case _ => ExpressionEvaluator.eval(expressionDirent.entry, unmappedParameterContext)
-            }
-
-          val womValueErrorOr: ErrorOr[AdHocValue] = entryEvaluation flatMap {
-            case womFile: WomFile =>
-              val errorOrEntryName: ErrorOr[Option[String]] = expressionDirent.entryname match {
-                case Some(actualEntryName) => actualEntryName.fold(EntryNamePoly).apply(unmappedParameterContext).map(Option.apply)
-                case None => None.valid
-              }
-              errorOrEntryName map { entryName =>
-                AdHocValue(womFile, entryName, inputName = mutableInputOption)
-              }
-            case other => for {
-              coerced <- WomStringType.coerceRawValue(other).toErrorOr
-              contentString = coerced.asInstanceOf[WomString].value
-              // We force the entryname to be specified, and then evaluate it:
-              entryNameStringOrExpression <- expressionDirent.entryname.toErrorOr(
-                "Invalid dirent: Entry was a string but no file name was supplied")
-              entryName <- entryNameStringOrExpression.fold(EntryNamePoly).apply(unmappedParameterContext)
-              writeFile = unmappedParameterContext.ioFunctionSet.writeFile(entryName, contentString)
-              writtenFile <- validate(Await.result(writeFile, Duration.Inf))
-            } yield AdHocValue(writtenFile, alternativeName = None, inputName = mutableInputOption)
-          }
-
-          womValueErrorOr.map(List(_))
-        }
-      }
-    }
-
-    implicit val caseStringDirent: Case.Aux[StringDirent, InitialWorkDirFileEvaluator] = {
-      at {
-        stringDirent => {
-          (unmappedParameterContext, _) =>
-            val womValueErrorOr = for {
-              entryName <- stringDirent.entryname.fold(EntryNamePoly).apply(unmappedParameterContext)
-              contentString = stringDirent.entry
-              writeFile = unmappedParameterContext.ioFunctionSet.writeFile(entryName, contentString)
-              writtenFile <- validate(Await.result(writeFile, Duration.Inf))
-            } yield writtenFile
-
-            womValueErrorOr.map(AdHocValue(_, alternativeName = None, inputName = None)).map(List(_))
-        }
-      }
-    }
-
-    implicit val caseExpression: Case.Aux[Expression, InitialWorkDirFileEvaluator] = {
-      at { expression =>
-        (unmappedParameterContext, _) => {
-          // A single expression which must evaluate to an array of Files
-          val expressionEvaluation = ExpressionEvaluator.eval(expression, unmappedParameterContext)
-
-          expressionEvaluation flatMap {
-            case array: WomArray if array.value.forall(_.isInstanceOf[WomFile]) =>
-              array.value.toList.map(_.asInstanceOf[WomFile]).map(AdHocValue(_, alternativeName = None, inputName = None)).validNel
-            case file: WomFile =>
-              List(AdHocValue(file, alternativeName = None, inputName = None)).validNel
-            case other =>
-              val error = "InitialWorkDirRequirement listing expression must be File or Array[File] but got %s: %s"
-                .format(other, other.womType.stableName)
-              error.invalidNel
-          }
-        }
-      }
-    }
-
-    implicit val caseString: Case.Aux[String, InitialWorkDirFileEvaluator] = {
-      at { string =>
-        (_, _) => {
-          List(AdHocValue(WomSingleFile(string), alternativeName = None, inputName = None)).valid
-        }
-      }
-    }
-
-    implicit val caseStringOrExpression: Case.Aux[StringOrExpression, InitialWorkDirFileEvaluator] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit val caseFile: Case.Aux[File, InitialWorkDirFileEvaluator] = {
-      at { file =>
-        (_, _) => {
-          file.asWomValue.map(AdHocValue(_, alternativeName = None, inputName = None)).map(List(_))
-        }
-      }
-    }
-
-    implicit val caseDirectory: Case.Aux[Directory, InitialWorkDirFileEvaluator] = {
-      at { directory =>
-        (_, _) => {
-          directory.asWomValue.map(AdHocValue(_, alternativeName = None, inputName = None)).map(List(_))
-        }
-      }
-    }
-
-  }
-
-  type EntryNameEvaluator = ParameterContext => ErrorOr[String]
-
-  object EntryNamePoly extends Poly1 {
-    implicit val caseString: Case.Aux[String, EntryNameEvaluator] = {
-      at {
-        string => {
-          _ =>
-            string.valid
-        }
-      }
-    }
-
-    implicit val caseExpression: Case.Aux[Expression, EntryNameEvaluator] = {
-      at {
-        expression => {
-          parameterContext =>
-            for {
-              entryNameExpressionEvaluated <- ExpressionEvaluator.eval(expression, parameterContext)
-              entryNameValidated <- mustBeString(entryNameExpressionEvaluated)
-            } yield entryNameValidated
-        }
-      }
-    }
-
-    private def mustBeString(womValue: WomValue): ErrorOr[String] = {
-      womValue match {
-        case WomString(s) => s.valid
-        case other => WomStringType.coerceRawValue(other).map(_.asInstanceOf[WomString].value).toErrorOr
-      }
-    }
-  }
-
-  /**
-    * Searches for ECMAScript expressions that mutate input paths.
-    *
-    * @see [[AdHocValue]]
-    */
-  object ExpressionToMutableInputOptionPoly extends Poly1 {
-    private val MutableInputRegex = """(?s)\s*\$\(\s*inputs\.(\w+)\s*\)\s*""".r
-    implicit val caseECMAScriptExpression: Case.Aux[ECMAScriptExpression, Option[String]] = {
-      at { eCMAScriptExpression =>
-        eCMAScriptExpression.value match {
-          case MutableInputRegex(mutableInput) => Option(mutableInput)
-          case _ => None
-        }
-      }
-    }
-    implicit val caseECMAScriptFunction: Case.Aux[ECMAScriptFunction, Option[String]] = at { _ => None }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwltoolRunner.scala b/cwl/src/main/scala/cwl/CwltoolRunner.scala
deleted file mode 100644
index 834c9d80b23..00000000000
--- a/cwl/src/main/scala/cwl/CwltoolRunner.scala
+++ /dev/null
@@ -1,71 +0,0 @@
-package cwl
-
-import ammonite.ops.ImplicitWd._
-import ammonite.ops._
-import com.typesafe.config.ConfigFactory
-import cwl.preprocessor.CwlReference
-import org.broadinstitute.heterodon.ExecAndEval
-
-/**
-  * Interface for running cwltool.
-  */
-sealed trait CwltoolRunner {
-  def salad(reference: CwlReference): String
-}
-
-object CwltoolRunner {
-  private lazy val config = ConfigFactory.load
-
-  lazy val instance: CwltoolRunner = {
-    val runnerClass = config.getString("cwltool-runner.class")
-    Class.forName(runnerClass).getDeclaredConstructor().newInstance().asInstanceOf[CwltoolRunner]
-  }
-}
-
-/**
-  * Runs cwltool as an external process.
-  */
-final class CwltoolProcess extends CwltoolRunner {
-  override def salad(reference: CwlReference): String = {
-    val commandResult: CommandResult = %%("cwltool", "--quiet", "--print-pre", reference.pathAsString)
-    commandResult.exitCode match {
-      case 0 => commandResult.out.string
-      case error =>
-        throw new RuntimeException(
-          s"running CwlTool on file ${reference.pathAsString} resulted in exit code $error and stderr ${commandResult.err.string}")
-    }
-  }
-}
-
-/**
-  * Runs cwltool via heterodon.
-  *
-  * https://github.com/broadinstitute/heterodon
-  */
-final class CwltoolHeterodon extends CwltoolRunner {
-  // Trimmed down version of
-  // https://github.com/common-workflow-language/cwltool/blob/1a839255795882894b4bbfea6d909a74cacb1d6a/cwltool/main.py#L355
-  private val cwltoolSaladExecScript =
-  """|import json
-     |import logging
-     |
-     |from cwltool.load_tool import fetch_document, resolve_tool_uri, validate_document
-     |from cwltool.loghandler import _logger
-     |
-     |
-     |def cwltool_salad(path):
-     |    _logger.setLevel(logging.WARN)
-     |    uri, tool_file_uri = resolve_tool_uri(path)
-     |    document_loader, workflowobj, uri = fetch_document(uri)
-     |    document_loader, avsc_names, processobj, metadata, uri \
-     |        = validate_document(document_loader, workflowobj, uri, preprocess_only=True)
-     |    return json.dumps(processobj, indent=4)
-     |""".stripMargin
-
-  private def cwltoolSaladEvalStatement(reference: CwlReference): String = s"cwltool_salad('${reference.pathAsString}')"
-
-  def salad(reference: CwlReference): String = {
-    val execAndEval = new ExecAndEval()
-    execAndEval.apply(cwltoolSaladExecScript, cwltoolSaladEvalStatement(reference)).asInstanceOf[String]
-  }
-}
diff --git a/cwl/src/main/scala/cwl/EnumSchema.scala b/cwl/src/main/scala/cwl/EnumSchema.scala
deleted file mode 100644
index 83ff1b05813..00000000000
--- a/cwl/src/main/scala/cwl/EnumSchema.scala
+++ /dev/null
@@ -1,35 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import shapeless.Witness
-import wom.types.WomEnumerationType
-
-trait EnumSchema {
-
-  val name: Option[String]
-  val symbols: Array[String]
-  val `type`: Witness.`"enum"`.T
-  val label: Option[String]
-
-  def toWomEnumerationType: WomEnumerationType = {
-    val symbolIds = symbols.toList.map{
-      s => s.substring(s.lastIndexOf("/") + 1)
-    }
-    WomEnumerationType(NonEmptyList.fromListUnsafe(symbolIds))
-  }
-}
-
-case class InputEnumSchema(
-  name: Option[String],
-  symbols: Array[String],
-  `type`: Witness.`"enum"`.T = Witness("enum").value,
-  label: Option[String] = None,
-  inputBinding: Option[InputCommandLineBinding] = None) extends EnumSchema
-
-case class OutputEnumSchema(
-  name: Option[String],
-  symbols: Array[String],
-  `type`: Witness.`"enum"`.T,
-  label: Option[String],
-  outputBinding: Option[CommandOutputBinding]) extends EnumSchema
-
diff --git a/cwl/src/main/scala/cwl/EvaluateExpression.scala b/cwl/src/main/scala/cwl/EvaluateExpression.scala
deleted file mode 100644
index 00036d49de4..00000000000
--- a/cwl/src/main/scala/cwl/EvaluateExpression.scala
+++ /dev/null
@@ -1,20 +0,0 @@
-package cwl
-
-import common.validation.ErrorOr.ErrorOr
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import shapeless.Poly1
-import wom.values.WomValue
-
-object EvaluateExpression extends Poly1 {
-  implicit val script: Case.Aux[ECMAScriptExpression, ParameterContext => ErrorOr[WomValue]] = {
-    at {
-      ExpressionEvaluator.evalExpression
-    }
-  }
-
-  implicit val function: Case.Aux[ECMAScriptFunction, ParameterContext => ErrorOr[WomValue]] = {
-    at {
-      ExpressionEvaluator.evalFunction
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ExpressionEvaluator.scala b/cwl/src/main/scala/cwl/ExpressionEvaluator.scala
deleted file mode 100644
index a3ed2c7a7c4..00000000000
--- a/cwl/src/main/scala/cwl/ExpressionEvaluator.scala
+++ /dev/null
@@ -1,101 +0,0 @@
-package cwl
-
-import cats.syntax.validated._
-import common.validation.ErrorOr._
-import cwl.internal.{CwlEcmaScriptDecoder, EcmaScriptEncoder, EcmaScriptUtil}
-import eu.timepit.refined.api.Refined
-import eu.timepit.refined.string.MatchesRegex
-import shapeless.Witness
-import wom.callable.RuntimeEnvironment
-import wom.values.{WomFloat, WomInteger, WomString, WomValue}
-
-// http://www.commonwl.org/v1.0/CommandLineTool.html#Expressions
-object ExpressionEvaluator {
-  // A code fragment wrapped in the $(...) syntax must be evaluated as a ECMAScript expression.
-  /*
-  There are several places in cwltool where a simple contains check is used:
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/builder.py#L157
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/command_line_tool.py#L669
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/expression.py#L219
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/process.py#L645
-   */
-  val ECMAScriptExpressionWitness = Witness("""(?s).*\$\(.*""")
-  val ECMAScriptExpressionRegex = ECMAScriptExpressionWitness.value.r
-  type MatchesECMAScriptExpression = MatchesRegex[ECMAScriptExpressionWitness.T]
-  type ECMAScriptExpression = String Refined MatchesECMAScriptExpression
-
-  // A code fragment wrapped in the ${...} syntax must be evaluated as a ECMAScript function body for an anonymous,
-  // zero-argument function.
-  val ECMAScriptFunctionWitness = Witness("""(?s)\s*\$\{(.*)\}\s*""")
-  val ECMAScriptFunctionRegex = ECMAScriptFunctionWitness.value.r
-  type MatchesECMAScriptFunction = MatchesRegex[ECMAScriptFunctionWitness.T]
-  type ECMAScriptFunction = String Refined MatchesECMAScriptFunction
-
-  def eval(expr: Expression, parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    expr.fold(EvaluateExpression).apply(parameterContext)
-  }
-
-  def evalExpression(expression: ECMAScriptExpression)(parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    def evaluator(string: String): ErrorOr[WomValue] = {
-      eval(string, parameterContext)
-    }
-
-    ExpressionInterpolator.interpolate(expression.value, evaluator, strip_whitespace = false)
-  }
-
-  def evalFunction(function: ECMAScriptFunction)(parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    function.value match {
-      case ECMAScriptFunctionRegex(script) =>
-
-        val functionExpression =
-          s"""|(function() {
-              |FUNCTION_BODY
-              |})();
-              |""".stripMargin.replace("FUNCTION_BODY", script)
-
-        eval(functionExpression, parameterContext)
-      case unmatched =>
-        s"Expression '$unmatched' was unable to be matched to regex '${ECMAScriptFunctionWitness.value}'".invalidNel
-    }
-  }
-
-  private lazy val cwlJsDecoder = new CwlEcmaScriptDecoder()
-
-  def eval(expr: String, parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    val script = if (parameterContext.expressionLib.isEmpty) {
-      expr
-    } else {
-      parameterContext.expressionLib.mkString("", ";", s";$expr")
-    }
-    val (rawVals, mapVals) = paramValues(parameterContext)
-    EcmaScriptUtil.evalStructish(
-      script,
-      rawVals,
-      mapVals,
-      new EcmaScriptEncoder(),
-      cwlJsDecoder
-    )
-  }
-
-  def paramValues(parameterContext: ParameterContext): ((String, WomValue), Map[String, Map[String, WomValue]]) = {
-    (
-        "self" -> parameterContext.self
-      ,
-      Map(
-        "inputs" -> parameterContext.inputs,
-        "runtime" -> parameterContext.runtimeOption.map(cwlMap).getOrElse(Map.empty)
-      )
-    )
-  }
-
-  def cwlMap(runtime: RuntimeEnvironment): Map[String, WomValue] = {
-    Map(
-      "outdir" -> WomString(runtime.outputPath),
-      "tmpdir" -> WomString(runtime.tempPath),
-      "cores" -> WomInteger(runtime.cores.value),
-      "ram" -> WomFloat(runtime.ram),
-      "outdirSize" -> WomFloat(runtime.outputPathSize.toDouble),
-      "tmpdirSize" -> WomFloat(runtime.tempPathSize.toDouble)
-    )
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ExpressionInterpolator.scala b/cwl/src/main/scala/cwl/ExpressionInterpolator.scala
deleted file mode 100644
index 9a40ee8e06f..00000000000
--- a/cwl/src/main/scala/cwl/ExpressionInterpolator.scala
+++ /dev/null
@@ -1,173 +0,0 @@
-package cwl
-
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.validation.ErrorOr._
-import wom.types.WomNothingType
-import wom.values._
-
-import scala.jdk.CollectionConverters._
-
-/**
-  * Partial copy-port of cwltool's expression.py.
-  *
-  * Minimizes refactor so that as expression.py continues to update the updates may be manually copied here also.
-  *
-  * Current omissions in `def interpolate`:
-  * - `def evaluator`
-  *   - Utility not copy-ported.
-  *   - `def interpolate` instead ignores absence of InlineJavascriptRequirement and instead always uses fullJS=True
-  * - `leaf = json.dumps(e, sort_keys=True)`
-  *   - When the interpolated string is not just-a-single-expression there is undefined behavior of rendering
-  *     non-WomPrimitive values into json.
-  *   - Even if it did, does not sort the keys.
-  *   - Thus we do not currently return character-for-character equality for these expressions with cwltool, however
-  *     these cases are not explicitly defined in the CWL spec as far as I know.
-  *
-  * @see https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/expression.py
-  */
-//noinspection ZeroIndexToHead,RemoveRedundantReturn
-object ExpressionInterpolator {
-
-  class SubstitutionException(message: String) extends RuntimeException(message)
-
-  /**
-    * Copy-port of expression.py's scanner.
-    */
-  private def scanner(scan: String): List[Int] = {
-    val DEFAULT = 0
-    val DOLLAR = 1
-    val PAREN = 2
-    val BRACE = 3
-    val SINGLE_QUOTE = 4
-    val DOUBLE_QUOTE = 5
-    val BACKSLASH = 6
-
-    var i = 0
-    val stack = new java.util.Stack[Int]
-    stack.push(DEFAULT)
-    var start = 0
-    while (i < scan.length) {
-      val state = stack.peek
-      val c = scan(i)
-
-      if (state == DEFAULT) {
-        if (c == '$') {
-          stack.push(DOLLAR)
-        } else if (c == '\\') {
-          stack.push(BACKSLASH)
-        }
-      } else if (state == BACKSLASH) {
-        stack.pop()
-        if (stack.peek == DEFAULT) {
-          return List(i - 1, i + 1)
-        }
-      } else if (state == DOLLAR) {
-        if (c == '(') {
-          start = i - 1
-          stack.push(PAREN)
-        } else if (c == '{') {
-          start = i - 1
-          stack.push(BRACE)
-        } else {
-          stack.pop()
-        }
-      } else if (state == PAREN) {
-        if (c == '(') {
-          stack.push(PAREN)
-        } else if (c == ')') {
-          stack.pop()
-          if (stack.peek == DOLLAR) {
-            return List(start, i + 1)
-          }
-        } else if (c == '\'') {
-          stack.push(SINGLE_QUOTE)
-        } else if (c == '"') {
-          stack.push(DOUBLE_QUOTE)
-        }
-      } else if (state == BRACE) {
-        if (c == '{') {
-          stack.push(BRACE)
-        } else if (c == '}') {
-          stack.pop()
-          if (stack.peek == DOLLAR) {
-            return List(start, i + 1)
-          }
-        } else if (c == '\'') {
-          stack.push(SINGLE_QUOTE)
-        } else if (c == '"') {
-          stack.push(DOUBLE_QUOTE)
-        }
-      } else if (state == SINGLE_QUOTE) {
-        if (c == '\'') {
-          stack.pop()
-        } else if (c == '\\') {
-          stack.push(BACKSLASH)
-        }
-      } else if (state == DOUBLE_QUOTE) {
-        if (c == '"') {
-          stack.pop()
-        } else if (c == '\\') {
-          stack.push(BACKSLASH)
-        }
-      }
-      i += 1
-    }
-    if (stack.size > 1) {
-      throw new SubstitutionException(
-        "Substitution error, unfinished block starting at position %s: %s".format(start, scan.drop(start)))
-    } else {
-      return null
-    }
-  }
-
-  /**
-    * Copy-port of expression.py's interpolate.
-    */
-  def interpolate(scanParam: String,
-                  evaluator: String => ErrorOr[WomValue],
-                  strip_whitespace: Boolean = true): ErrorOr[WomValue] = {
-    var scan = scanParam
-    if (strip_whitespace) {
-      scan = scan.trim
-    }
-    val parts = new java.util.Stack[ErrorOr[WomValue]]
-    var w = scanner(scan)
-    while (w != null) {
-      parts.push(WomString(scan.slice(0, w(0))).valid)
-
-      if (scan(w(0)) == '$') {
-        val e = evaluator(scan.slice(w(0) + 1, w(1)))
-        if (w(0) == 0 && w(1) == scan.length && parts.size <= 1) {
-          return e
-        }
-        /*
-        Original-ish:
-          var leaf = json.dumps(e, sort_keys=True)
-          if (leaf(0) == '"') {
-            leaf = leaf.drop(1).dropRight(1)
-          }
-        Instead, push the raw WomValue. WomString's won't have been quoted as python's json.dumps does.
-        Other WomPrimitive's should be fine. CWL using other structures (Maps, Arrays, etc.) may have problems.
-         */
-        val leaf = e
-        parts.push(leaf)
-      } else if (scan(w(0)) == '\\') {
-        val e = scan(w(1) - 1)
-        parts.push(WomString(e.toString).valid)
-      }
-
-      scan = scan.drop(w(1))
-      w = scanner(scan)
-    }
-    parts.push(WomString(scan).valid)
-    return parts.asScala.toList.sequence[ErrorOr, WomValue] map { list =>
-      WomString(list.map{
-        //we represent nulls as this type because Wom doesn't have a "null" value, but it does have a nothing type
-        case WomOptionalValue(WomNothingType, None) => "null"
-        case other => other.valueString
-      }.mkString(""))
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ExpressionTool.scala b/cwl/src/main/scala/cwl/ExpressionTool.scala
deleted file mode 100644
index 53c8a675a4c..00000000000
--- a/cwl/src/main/scala/cwl/ExpressionTool.scala
+++ /dev/null
@@ -1,136 +0,0 @@
-package cwl
-
-import cats.syntax.either._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import cwl.CwlVersion._
-import cwl.ExpressionTool.{ExpressionToolInputParameter, ExpressionToolOutputParameter}
-import shapeless.{Coproduct, Witness}
-import wom.RuntimeAttributes
-import wom.callable.{Callable, CallableExpressionTaskDefinition}
-import wom.expression.{IoFunctionSet, ValueAsAnExpression}
-import wom.graph.GraphNodePort.OutputPort
-import wom.types.{WomMapType, WomStringType, WomType}
-import wom.values.{WomMap, WomObject, WomString, WomValue}
-
-case class ExpressionTool(
-                           inputs: Array[ExpressionToolInputParameter] = Array.empty,
-                           outputs: Array[ExpressionToolOutputParameter] = Array.empty,
-                           `class`: Witness.`"ExpressionTool"`.T,
-                           expression: StringOrExpression,
-                           id: String,
-                           requirements: Option[Array[Requirement]] = None,
-                           hints: Option[Array[Hint]] = None,
-                           label: Option[String] = None,
-                           doc: Option[String] = None,
-                           cwlVersion: Option[CwlVersion] = None,
-                           `$namespaces`: Option[Map[String, String]] = None,
-                           `$schemas`: Option[Array[String]] = None
-                         ) extends Tool {
-
-  def asCwl: Cwl = Coproduct[Cwl](this)
-
-  def castWomValueAsMap(evaluatedExpression: WomValue): Checked[Map[String, WomValue]] = {
-    evaluatedExpression match {
-      case WomMap(WomMapType(WomStringType, _), map) =>  map.map{
-        case (WomString(key), value) => key -> value
-        case (key, _) => throw new RuntimeException(s"saw a non-string value $key in wom map $evaluatedExpression typed with string keys ")
-      }.asRight
-      case obj: WomObject => obj.values.asRight
-      case _ => s"Could not cast value $evaluatedExpression to a Map[String, WomValue]".invalidNelCheck
-    }
-  }
-
-  def buildTaskDefinition(taskName: String,
-                          inputDefinitions: List[_ <: Callable.InputDefinition],
-                          outputDefinitions: List[Callable.OutputDefinition],
-                          runtimeAttributes: RuntimeAttributes,
-                          requirementsAndHints: List[cwl.Requirement],
-                          expressionLib: ExpressionLib): ErrorOr[CallableExpressionTaskDefinition] = {
-
-    def evaluate(inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, outputPorts: List[OutputPort]): Checked[Map[OutputPort, WomValue]] = {
-      val womExpression = expression match {
-        case StringOrExpression.String(str) => ValueAsAnExpression(WomString(str))
-        case StringOrExpression.Expression(expr) => ECMAScriptWomExpression(expr, inputNames, expressionLib)
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-
-      // If we expect a certain type for
-      def coerce(womValue: WomValue, womType: WomType): Checked[WomValue] = womType.coerceRawValue(womValue).toChecked
-
-      /*
-        * Look in the object (the result of the expression evaluation) for values to match output each port.
-        * Ideally we'd want to find a value for each output port declared by the tool.
-        * However since the spec is not clear on this and cwltool seems to ignore entirely the outputs declaration,
-        * we'll do the same for now, meaning we'll assign a value to the output port iff the result of the expression has one for them,
-        * otherwise we'll remove the port for the final map.
-        * If there are fields in the expression's result that do not have a matching declared output port, they won't be added either,
-        * because we'd have to create an output port for them now which would be useless anyway since nothing could point to it.
-       */
-      def mapPortsToValues(values: Map[String, WomValue]): Checked[Map[OutputPort, WomValue]] = {
-        import cats.syntax.traverse._
-
-        val coercedValues: List[ErrorOr[(OutputPort, WomValue)]] = for {
-          outputPort <- outputPorts
-          value <- values.get(outputPort.internalName)
-          coerced = coerce(value, outputPort.womType).toValidated
-        } yield coerced.map(outputPort -> _)
-
-        coercedValues.sequence[ErrorOr, (OutputPort, WomValue)].map(_.toMap).toEither
-      }
-
-      for {
-        // Evaluate the expression
-        evaluatedExpression <- womExpression.evaluateValue(inputs, ioFunctionSet).toEither
-        /*
-          * We expect the result to be an object of the form:
-          * {
-          *   "outputName": value,
-          *   ...
-          * }
-         */
-        womMap <- castWomValueAsMap(evaluatedExpression)
-
-        mappedValues <- mapPortsToValues(womMap)
-      } yield mappedValues
-    }
-
-    CallableExpressionTaskDefinition(
-      taskName,
-      evaluate,
-      runtimeAttributes,
-      Map.empty,
-      Map.empty,
-      outputDefinitions,
-      inputDefinitions,
-      // TODO: This doesn't work in all cases and it feels clunky anyway - find a way to sort that out
-      prefixSeparator = "#"
-    ).validNel
-  }
-}
-
-object ExpressionTool {
-
-  case class ExpressionToolInputParameter(id: String,
-                                          label: Option[String] = None,
-                                          secondaryFiles: Option[SecondaryFiles] = None,
-                                          format: Option[InputParameterFormat] = None,
-                                          streamable: Option[Boolean] = None,
-                                          doc: Option[Doc] = None,
-                                          inputBinding: Option[InputCommandLineBinding] = None,
-                                          default: Option[CwlAny] = None,
-                                          `type`: Option[MyriadInputType] = None) extends InputParameter
-
-  case class ExpressionToolOutputParameter(id: String,
-                                           label: Option[String] = None,
-                                           secondaryFiles: Option[SecondaryFiles] = None,
-                                           format: Option[OutputParameterFormat] = None,
-                                           streamable: Option[Boolean] = None,
-                                           doc: Option[Doc] = None,
-                                           outputBinding: Option[CommandOutputBinding] = None,
-                                           `type`: Option[MyriadOutputType] = None) extends OutputParameter
-}
diff --git a/cwl/src/main/scala/cwl/FileParameter.scala b/cwl/src/main/scala/cwl/FileParameter.scala
deleted file mode 100644
index 2413d9d7c02..00000000000
--- a/cwl/src/main/scala/cwl/FileParameter.scala
+++ /dev/null
@@ -1,150 +0,0 @@
-package cwl
-
-import cats.effect.IO
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.ontology.Schema
-import shapeless.Poly1
-import wom.expression.IoFunctionSet
-import wom.types.{WomFileType, WomMaybePopulatedFileType}
-import wom.values.{WomArray, WomFile, WomMaybePopulatedFile, WomValue}
-
-object FileParameter {
-  private val ReadLimit = Option(64 * 1024)
-
-  def populateSecondaryFiles(womValue: WomValue,
-                             secondaryFilesCoproduct: Option[SecondaryFiles],
-                             formatOption: Option[String],
-                             parameterContext: ParameterContext,
-                             expressionLib: ExpressionLib,
-                             ioFunctions: IoFunctionSet): IOChecked[WomValue] = {
-
-    womValue match {
-
-      case womMaybePopulatedFile: WomMaybePopulatedFile =>
-        val secondaryFilesErrorOr = FileParameter.secondaryFiles(
-          womMaybePopulatedFile,
-          WomMaybePopulatedFileType,
-          secondaryFilesCoproduct,
-          parameterContext,
-          expressionLib,
-          ioFunctions
-        )
-
-        secondaryFilesErrorOr map { secondaryFiles =>
-          womMaybePopulatedFile.copy(secondaryFiles = secondaryFiles, formatOption = formatOption)
-        }
-
-      case womArray: WomArray =>
-        womArray.value.toList.traverse(
-          populateSecondaryFiles(_, secondaryFilesCoproduct, formatOption, parameterContext, expressionLib, ioFunctions)
-        ).map(WomArray(_))
-
-      case womValue: WomValue => womValue.validIOChecked
-    }
-  }
-
-  /**
-    * Checks if the file is compatible with a format.
-    */
-  def checkFormat(womMaybePopulatedFile: WomMaybePopulatedFile,
-                  formatsOption: Option[List[String]],
-                  schemaOption: Option[Schema]): ErrorOr[Unit] = {
-    validate {
-      for {
-        schema <- schemaOption
-        fileFormat <- womMaybePopulatedFile.formatOption
-        formats <- formatsOption
-      } yield {
-        if (!formats.exists(schema.isSubClass(fileFormat, _)))
-          throw new RuntimeException(s"$fileFormat is not compatible with ${formats.mkString(", ")}")
-      }
-      ()
-    }
-  }
-
-  /**
-    * Populates the contents if they aren't loaded already.
-    */
-  def maybeLoadContents(womMaybePopulatedFile: WomMaybePopulatedFile,
-                        ioFunctionSet: IoFunctionSet,
-                        loadContents: Boolean): IO[Option[String]] = {
-    womMaybePopulatedFile.contentsOption match {
-      case someContents@Some(_) => IO.pure(someContents)
-      case None if !loadContents => IO.pure(None)
-      case _ => FileParameter.load64KiB(womMaybePopulatedFile.value, ioFunctionSet).map(Option(_))
-    }
-  }
-
-  def load64KiB(path: String, ioFunctionSet: IoFunctionSet): IO[String] = {
-    implicit val ec = IO.contextShift(ioFunctionSet.ec)
-    IO.fromFuture(IO { ioFunctionSet.readFile(path, ReadLimit, failOnOverflow = false) })
-  }
-
-  /**
-    * Returns the list of secondary files for the primary file.
-    */
-  def secondaryFiles(primaryWomFile: WomFile,
-                     stringWomFileType: WomFileType,
-                     secondaryFilesOption: Option[SecondaryFiles],
-                     parameterContext: ParameterContext,
-                     expressionLib: ExpressionLib,
-                     ioFunctions: IoFunctionSet): IOChecked[List[WomFile]] = {
-    secondaryFilesOption
-      .map(secondaryFiles(primaryWomFile, stringWomFileType, _, parameterContext, expressionLib, ioFunctions))
-      .getOrElse(List.empty[WomFile].validIOChecked)
-  }
-
-  /**
-    * Returns the list of secondary files for the primary file.
-    */
-  def secondaryFiles(primaryWomFile: WomFile,
-                     stringWomFileType: WomFileType,
-                     secondaryFiles: SecondaryFiles,
-                     parameterContext: ParameterContext,
-                     expressionLib: ExpressionLib,
-                     ioFunctions: IoFunctionSet): IOChecked[List[WomFile]] = {
-    secondaryFiles
-      .fold(SecondaryFilesPoly)
-      .apply(primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions)
-  }
-
-  type SecondaryFilesFunction = (WomFile, WomFileType, ParameterContext, ExpressionLib, IoFunctionSet) => IOChecked[List[WomFile]]
-
-  object SecondaryFilesPoly extends Poly1 {
-    implicit def caseStringOrExpression: Case.Aux[StringOrExpression, SecondaryFilesFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseExpression: Case.Aux[Expression, SecondaryFilesFunction] = {
-      at {
-        expression =>
-          (primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions) =>
-            File.secondaryExpressionFiles(primaryWomFile, stringWomFileType, expression, parameterContext, expressionLib, ioFunctions).toIOChecked
-      }
-    }
-
-    implicit def caseString: Case.Aux[String, SecondaryFilesFunction] = {
-      at {
-        string =>
-          (primaryWomFile, stringWomFileType, _, _, ioFunctions) =>
-            File.secondaryStringFile(primaryWomFile, stringWomFileType, string, ioFunctions).map(List(_))
-      }
-    }
-
-    implicit def caseArray: Case.Aux[Array[StringOrExpression], SecondaryFilesFunction] = {
-      at {
-        array =>
-          (primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions) =>
-            val functions: List[SecondaryFilesFunction] = array.toList.map(_.fold(this))
-            functions.flatTraverse(_ (primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions))
-      }
-    }
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/FullyQualifiedName.scala b/cwl/src/main/scala/cwl/FullyQualifiedName.scala
deleted file mode 100644
index faabfa44fc4..00000000000
--- a/cwl/src/main/scala/cwl/FullyQualifiedName.scala
+++ /dev/null
@@ -1,61 +0,0 @@
-package cwl
-
-import cwl.command.ParentName
-
-/**
-  * All of these classes decompose a "fully qualified" id into its constituent parts.  They have unique types as
-  * they are seen in different parts of a CWL document and they differ in content.
-  *
-  * The fully qualified names are created by the Schema salad preprocessing step.
-  *
-  * @see <a href="http://www.commonwl.org/v1.0/SchemaSalad.html#Identifier_resolution">Schema salad Identifier Resolution</a>
-  */
-trait FullyQualifiedName {
-  def fileName: String
-  def id: String
-  def parent: Option[String]
-}
-
-case class FileAndId private(fileName: String, parent: Option[String], id: String) extends FullyQualifiedName
-
-object FileAndId {
-  def apply(in: String)(implicit parent: ParentName): FileAndId = {
-    val Array(fileName, id) = in.split("#")
-    val cleanID = parent.stripParent(id)
-    FileAndId(fileName, parent.value, cleanID)
-  }
-}
-
-case class FileStepAndId private(fileName: String, parent: Option[String], stepId: String, id: String) extends FullyQualifiedName
-
-object FileStepAndId {
-  def apply(in: String)(implicit parent: ParentName): FileStepAndId = {
-    val Array(fileName, id) = in.split("#")
-    val cleanID = parent.stripParent(id)
-    val Array(stepId, outputId) = cleanID.split("/")
-    FileStepAndId(fileName, parent.value, stepId, outputId)
-  }
-}
-
-case class ArbitrarilyNested(fileName: String, parent: Option[String], id: String) extends FullyQualifiedName
-
-case class FileStepUUID(fileName: String, parent: Option[String], id: String, uuid: String, stepId: String) extends FullyQualifiedName
-
-object FullyQualifiedName {
-  def apply(in: String)(implicit parent: ParentName): FullyQualifiedName = maybeApply(in)(parent).getOrElse(throw new Exception(s"malformed FQN: $in"))
-
-  def maybeApply(in: String)(implicit parent: ParentName): Option[FullyQualifiedName] = {
-
-    in.split("#") match {
-      case Array(file, after) =>
-        val cleanAfter = parent.stripParent(after)
-        cleanAfter.split("/").toList match {
-          case step :: uuid :: id :: Nil => Option(FileStepUUID(file, parent.value, id, uuid, step))
-          case step :: id :: Nil => Option(FileStepAndId(file, parent.value, step, id))
-          case id :: Nil => Option(FileAndId(file, parent.value, id))
-          case many => Option(ArbitrarilyNested(file, parent.value, many.last))
-        }
-      case _ => None
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/GlobEvaluator.scala b/cwl/src/main/scala/cwl/GlobEvaluator.scala
deleted file mode 100644
index d50b154da2c..00000000000
--- a/cwl/src/main/scala/cwl/GlobEvaluator.scala
+++ /dev/null
@@ -1,67 +0,0 @@
-package cwl
-
-import cats.syntax.validated._
-import common.validation.ErrorOr._
-import shapeless._
-import wom.types.{WomArrayType, WomStringType}
-import wom.values._
-
-/*
-CommandOutputBinding.glob:
-Find files relative to the output directory, using POSIX glob(3) pathname matching. If an array is provided, find
-files that match any pattern in the array. If an expression is provided, the expression must return a string or an
-array of strings, which will then be evaluated as one or more glob patterns. Must only match and return files which
-actually exist.
-
-http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding
- */
-object GlobEvaluator {
-
-  type GlobEvaluatorFunction = (ParameterContext, ExpressionLib) => ErrorOr[List[String]]
-
-  def globs(globOption: Option[Glob], parameterContext: ParameterContext, expressionLib: ExpressionLib): ErrorOr[List[String]] = {
-    globOption map {
-      globs(_, parameterContext, expressionLib)
-    } getOrElse {
-      Nil.valid
-    }
-  }
-
-  def globs(glob: Glob, parameterContext: ParameterContext, expressionLib: ExpressionLib): ErrorOr[List[String]] = {
-    glob.fold(GlobEvaluator.GlobEvaluatorPoly).apply(parameterContext, expressionLib)
-  }
-
-  object GlobEvaluatorPoly extends Poly1 {
-    implicit def caseStringOrExpression: Case.Aux[StringOrExpression, GlobEvaluatorFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseExpression: Case.Aux[Expression, GlobEvaluatorFunction] = {
-      at {
-        expression =>
-          (parameterContext, expressionLib) => {
-            ExpressionEvaluator.eval(expression, parameterContext) flatMap {
-              case WomArray(_, values) if values.isEmpty => Nil.valid
-              case WomString(value) => List(value).valid
-              case WomArray(WomArrayType(WomStringType), values) => values.toList.map(_.valueString).valid
-              case womValue =>
-                val message = s"Unexpected expression result: $womValue while evaluating expression '$expression' " +
-                  s"using inputs '$parameterContext'"
-                message.invalidNel
-            }
-          }
-      }
-    }
-
-    implicit def caseArrayString: Case.Aux[Array[String], GlobEvaluatorFunction] = {
-      at { array => (_, _) => array.toList.valid }
-    }
-
-    implicit def caseString: Case.Aux[String, GlobEvaluatorFunction] = {
-      at { string => (_, _) => List(string).valid }
-    }
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/InitialWorkDirRequirement.scala b/cwl/src/main/scala/cwl/InitialWorkDirRequirement.scala
deleted file mode 100644
index 28e49fe71d9..00000000000
--- a/cwl/src/main/scala/cwl/InitialWorkDirRequirement.scala
+++ /dev/null
@@ -1,63 +0,0 @@
-package cwl
-
-import cwl.InitialWorkDirRequirement._
-import eu.timepit.refined.W
-import shapeless.{:+:, CNil, _}
-
-final case class InitialWorkDirRequirement(
-                                            `class`: W.`"InitialWorkDirRequirement"`.T,
-                                            listing: IwdrListing
-                                          ) {
-  val listings: Array[IwdrListingArrayEntry] = listing.fold(IwdrListingArrayPoly)
-
-  override def toString: WorkflowStepInputId =
-    s"""InitialWorkDirRequirement(
-      |  ${listings.mkString(System.lineSeparator + "  ")}
-      |)""".stripMargin
-}
-
-/**
-  *  Short for "Directory Entry"
-  *  @see <a href="http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent">Dirent Specification</a>
-  *
-  *  Split into two cases because entryName is only optional if entry is an Expression
-  */
-trait Dirent {
-  def writable: Option[Boolean]
-  def writableWithDefault = writable.getOrElse(false)
-}
-
-final case class ExpressionDirent(
-                                   entry: Expression,
-                                   entryname: Option[StringOrExpression],
-                                   writable: Option[Boolean]
-                                 ) extends Dirent
-
-final case class StringDirent(
-                               entry: String,
-                               entryname: StringOrExpression,
-                               writable: Option[Boolean]
-                             ) extends Dirent
-
-object InitialWorkDirRequirement {
-
-  // "ExpressionDirent" has to come before StringDirent because expressions are matched by "String" first if we do it the
-  // other way round.
-  final type IwdrListingArrayEntry = File :+: Directory :+: ExpressionDirent :+: StringDirent :+: StringOrExpression :+: CNil
-  final type IwdrListing = Array[IwdrListingArrayEntry] :+: StringOrExpression :+: CNil
-
-  object IwdrListingArrayPoly extends Poly1 {
-    implicit val caseArrayIwdrListingArrayEntry: Case.Aux[Array[IwdrListingArrayEntry], Array[IwdrListingArrayEntry]] = {
-      at {
-        identity
-      }
-    }
-
-    implicit val caseStringOrExpression: Case.Aux[StringOrExpression, Array[IwdrListingArrayEntry]] = {
-      at {
-        stringOrExpression =>
-          Array(Coproduct[IwdrListingArrayEntry](stringOrExpression))
-      }
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/InputParameter.scala b/cwl/src/main/scala/cwl/InputParameter.scala
deleted file mode 100644
index d8b1579dcef..00000000000
--- a/cwl/src/main/scala/cwl/InputParameter.scala
+++ /dev/null
@@ -1,190 +0,0 @@
-package cwl
-
-import cats.syntax.functor._
-import cats.syntax.parallel._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cats.instances.option._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.FileParameter._
-import cwl.ontology.Schema
-import shapeless.Poly1
-import wom.callable.Callable.InputDefinition.InputValueMapper
-import wom.expression.IoFunctionSet
-import wom.types.{WomSingleFileType, WomType}
-import wom.values.{WomArray, WomMaybeListedDirectory, WomMaybePopulatedFile, WomObject, WomObjectLike, WomOptionalValue, WomValue}
-
-trait InputParameter {
-  def id: String
-  def label: Option[String]
-  def secondaryFiles: Option[SecondaryFiles]
-  def format: Option[InputParameterFormat]
-  def streamable: Option[Boolean]
-  def doc: Option[Doc]
-  def inputBinding: Option[InputCommandLineBinding]
-  def default: Option[CwlAny]
-  def `type`: Option[MyriadInputType]
-  def loadContents = inputBinding.flatMap(_.loadContents).getOrElse(false)
-}
-
-object InputParameter {
-  object IdDefaultAndType {
-    def unapply(arg: InputParameter): Option[(String, CwlAny, MyriadInputType)] = (arg.default, arg.`type`) match {
-      case (Some(default), Some(tpe)) => Option((arg.id, default, tpe))
-      case _ => None
-    }
-  }
-
-  object IdAndType {
-    def unapply(arg: InputParameter): Option[(String, MyriadInputType)] = (arg.default, arg.`type`) match {
-      case (None, Some(tpe)) => Option((arg.id, tpe))
-      case _ => None
-    }
-  }
-
-  type DefaultToWomValueFunction = WomType => ErrorOr[WomValue]
-
-  object DefaultToWomValuePoly extends Poly1 {
-    implicit def caseFileOrDirectory: Case.Aux[FileOrDirectory, DefaultToWomValueFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseFileOrDirectoryArray: Case.Aux[Array[FileOrDirectory], DefaultToWomValueFunction] = {
-      at {
-        fileOrDirectoryArray =>
-          womType =>
-            fileOrDirectoryArray
-              .toList
-              .traverse(_.fold(this).apply(womType))
-              .map(WomArray(_))
-      }
-    }
-
-    implicit def caseFile: Case.Aux[File, DefaultToWomValueFunction] = {
-      at {
-        file =>
-          womType =>
-            file.asWomValue.flatMap(womType.coerceRawValue(_).toErrorOr)
-      }
-    }
-
-    implicit def caseDirectory: Case.Aux[Directory, DefaultToWomValueFunction] = {
-      at {
-        directory =>
-          womType =>
-            directory.asWomValue.flatMap(womType.coerceRawValue(_).toErrorOr)
-      }
-    }
-
-    implicit def caseJson: Case.Aux[io.circe.Json, DefaultToWomValueFunction] = {
-      at {
-        circeJson =>
-          womType =>
-            val stringJson = circeJson.noSpaces
-            import spray.json._
-            val sprayJson = stringJson.parseJson
-            womType.coerceRawValue(sprayJson).toErrorOr
-      }
-    }
-  }
-
-  object InputParameterFormatPoly extends Poly1 {
-    implicit val caseExpression: Case.Aux[Expression, ParameterContext => ErrorOr[List[String]]] = {
-      at { expression =>
-        parameterContext =>
-          ExpressionEvaluator.eval(expression, parameterContext) map {
-            case WomArray(_, values) => values.toList.map(_.valueString)
-            case womValue => List(womValue.valueString)
-          }
-      }
-    }
-
-    implicit val caseString: Case.Aux[String, ParameterContext => ErrorOr[List[String]]] = {
-      at { string =>
-        _ =>
-          List(string).valid
-      }
-    }
-
-    implicit val caseArrayString: Case.Aux[Array[String], ParameterContext => ErrorOr[List[String]]] = {
-      at { array =>
-        _ =>
-          array.toList.valid
-      }
-    }
-  }
-
-  /**
-    * Yet another value mapper. This one is needed because in CWL we might need to "augment" inputs which we can only do
-    * once they have been linked to a WomValue. This input value mapper encapsulates logic to be applied once that is
-    * done. For now, if the inputParameter has an input binding with loadContents = true, load the content of the file.
-    *
-    * This is based on the spec in http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-    *
-    * NOTE: There may be _many_ cases not implemented here that need to be fixed.
-    */
-  def inputValueMapper(inputParameter: InputParameter,
-                       inputType: MyriadInputType,
-                       expressionLib: ExpressionLib,
-                       schemaOption: Option[Schema]): InputValueMapper = {
-    ioFunctionSet: IoFunctionSet => {
-      import ioFunctionSet.cs
-
-      def populateFiles(womValue: WomValue): IOChecked[WomValue] = {
-        womValue match {
-          case womMaybePopulatedFile: WomMaybePopulatedFile =>
-            // Don't include the secondary files in the self variables
-            val parameterContext = ParameterContext(ioFunctionSet, expressionLib, self = womMaybePopulatedFile.copy(secondaryFiles = List.empty))
-            val secondaryFilesFromInputParameter = inputParameter.secondaryFiles
-            val secondaryFilesFromType = inputType.fold(MyriadInputTypeToSecondaryFiles)
-            val secondaryFiles = secondaryFilesFromInputParameter orElse secondaryFilesFromType
-            val inputFormatsErrorOr = inputParameter.format
-                .traverse(_.fold(InputParameterFormatPoly).apply(parameterContext))
-
-            for {
-              inputFormatsOption <- inputFormatsErrorOr.toIOChecked
-              _ <- checkFormat(womMaybePopulatedFile, inputFormatsOption, schemaOption).toIOChecked
-              contentsOption <- FileParameter.maybeLoadContents(
-                womMaybePopulatedFile,
-                ioFunctionSet,
-                inputParameter.loadContents
-              ).to[IOChecked]
-              withSize <- womMaybePopulatedFile.withSize(ioFunctionSet).to[IOChecked]
-              loaded = withSize.copy(contentsOption = contentsOption)
-              secondaries <- FileParameter.secondaryFiles(
-                loaded,
-                WomSingleFileType,
-                secondaryFiles,
-                parameterContext,
-                expressionLib,
-                ioFunctionSet
-              )
-              updated = loaded.copy(secondaryFiles = loaded.secondaryFiles ++  secondaries)
-            } yield updated
-          case womMaybeListedDirectory: WomMaybeListedDirectory => womMaybeListedDirectory.withSize(ioFunctionSet).to[IOChecked].widen
-          case WomArray(_, values) => values.toList.parTraverse[IOChecked, WomValue](populateFiles).map(WomArray(_))
-          case WomOptionalValue(_, Some(innerValue)) => populateFiles(innerValue).map(WomOptionalValue(_))
-          case obj: WomObjectLike =>
-            // Map the values
-            val populated: IOChecked[WomObject] = obj.values.toList.parTraverse[IOChecked, (String, WomValue)]({
-              case (key, value) => populateFiles(value).map(key -> _)
-            })
-            .map(_.toMap)
-            // Validate new types are still valid w.r.t the object
-            .flatMap(WomObject.withTypeChecked(_, obj.womObjectTypeLike).toIOChecked)
-            
-            populated.widen[WomValue]
-          case womValue: WomValue =>
-            pure(womValue)
-        }
-      }
-
-      womValue => populateFiles(womValue)
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/LinkMergeMethod.scala b/cwl/src/main/scala/cwl/LinkMergeMethod.scala
deleted file mode 100644
index bd54ca6b56a..00000000000
--- a/cwl/src/main/scala/cwl/LinkMergeMethod.scala
+++ /dev/null
@@ -1,8 +0,0 @@
-package cwl
-
-object LinkMergeMethod extends Enumeration {
-  type LinkMergeMethod = Value
-
-  val MergeNested = Value("merge_nested")
-  val MergeFlattened = Value("merge_flattened")
-}
diff --git a/cwl/src/main/scala/cwl/MyriadInputTypeToSecondaryFiles.scala b/cwl/src/main/scala/cwl/MyriadInputTypeToSecondaryFiles.scala
deleted file mode 100644
index 4ddc09625d3..00000000000
--- a/cwl/src/main/scala/cwl/MyriadInputTypeToSecondaryFiles.scala
+++ /dev/null
@@ -1,25 +0,0 @@
-package cwl
-
-import cwl.CwlType.CwlType
-import shapeless.Poly1
-
-// IAS.secondaryFiles are NOT listed in 1.0 spec, but according to jgentry they will be, maybe
-object MyriadInputTypeToSecondaryFiles extends Poly1 {
-  implicit val caseMyriadInputInnerType: Case.Aux[MyriadInputInnerType, Option[SecondaryFiles]] = at {
-    _.fold(MyriadInputInnerTypeToSecondaryFiles)
-  }
-
-  implicit val caseArrayMyriadInputInnerType: Case.Aux[Array[MyriadInputInnerType], Option[SecondaryFiles]] = at {
-    _.to(LazyList).flatMap(_.fold(MyriadInputInnerTypeToSecondaryFiles)).headOption
-  }
-}
-
-object MyriadInputInnerTypeToSecondaryFiles extends Poly1 {
-  implicit val caseCwlType: Case.Aux[CwlType, Option[SecondaryFiles]] = at { _ => None }
-  implicit val caseInputRecordSchema: Case.Aux[InputRecordSchema, Option[SecondaryFiles]] = at { _ => None }
-  implicit val caseInputEnumSchema: Case.Aux[InputEnumSchema, Option[SecondaryFiles]] = at { _ => None }
-  implicit val caseInputArraySchema: Case.Aux[InputArraySchema, Option[SecondaryFiles]] = at {
-    inputArraySchema => inputArraySchema.secondaryFiles
-  }
-  implicit val caseString: Case.Aux[String, Option[SecondaryFiles]] = at { _ => None }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadInputTypeToSortedCommandParts.scala b/cwl/src/main/scala/cwl/MyriadInputTypeToSortedCommandParts.scala
deleted file mode 100644
index 498e97c016f..00000000000
--- a/cwl/src/main/scala/cwl/MyriadInputTypeToSortedCommandParts.scala
+++ /dev/null
@@ -1,254 +0,0 @@
-package cwl
-
-import cwl.CommandLineTool.{CommandBindingSortingKey, CommandPartsList, SortKeyAndCommandPart, StringOrInt}
-import cwl.CwlType.CwlType
-import cwl.SchemaDefRequirement.SchemaDefTypes
-import cwl.command.ParentName
-import shapeless.{Coproduct, Poly1}
-import wom.values.{WomArray, WomCoproductValue, WomObjectLike, WomOptionalValue, WomValue}
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.instances.list._
-import cats.instances.option._
-
-/**
-  * Poly1 to fold over a MyriadInputType and create a List of SortingKeyAndCommandPart based on the rules described here:
-  * http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-  */
-object MyriadInputTypeToSortedCommandParts extends Poly1 {
-  import Case._
-
-  /**
-    * CommandLineBinding: binding of the element being processed.
-    *   It's possible for an input not to have an "inputBinding", but to have a complex type which itself has inputBindings for its fields or items.
-    *   e.g:
-    *     - id: arrayInput
-    *       type:
-    *         type: array
-    *         items: File
-    *         inputBinding: { prefix: "-YYY" }
-    *
-    * Here the array type has an inputBinding but the input itself (arrayInput) does not.
-    * This would yield on the command line something like "-YYY arrayItem0 -YYY arrayItem1 ..."
-    *
-    * On the other hand:
-    *     - id: arrayInput
-    *       type:
-    *         type: array
-    *         items: File
-    *         inputBinding: { prefix: "-YYY" }
-    *       inputBinding: { prefix: "-XXX" }
-    *
-    * In this case the input itself has a binding as well, which would yield something like "-XXX -YYY arrayItem0 -YYY arrayItem1 ..."
-    *
-    * For arrays specifically, the presence of an "itemSeparator" and / or "valueFrom" in the input binding will change the way the array is processed,
-    * which is why we need to know about it in this Poly1 that folds over the input types.
-    *
-    * WomValue: value bound to the element (in the cases above it would be the WomArray)
-    * CommandBindingSortingKey: The current sorting key. Because we might need to recurse in nested types we need to propagate the key as we do.
-    */
-  type CommandPartBuilder = (Option[InputCommandLineBinding], WomValue, CommandBindingSortingKey, Boolean, ExpressionLib, SchemaDefRequirement) => CommandPartsList
-
-  implicit def m: Aux[MyriadInputInnerType, CommandPartBuilder] = {
-    at {
-      innerType => {
-        (binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-          innerType
-            .fold(MyriadInputInnerTypeToSortedCommandParts)
-            .apply(binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement).fold(
-              throw new RuntimeException(s"inner type to command part failed!  on type $innerType w/ womValue $womValue"))(identity)
-      }
-    }
-  }
-
-  implicit def am: Aux[Array[MyriadInputInnerType], CommandPartBuilder] = {
-    at {
-      types => {
-        (binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-          def lookupTypes(innerTypes: Array[MyriadInputInnerType]) = {
-            innerTypes.toList.map{
-              _.fold(MyriadInputInnerTypeToSortedCommandParts)
-                .apply(binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-            }.reduce(_ orElse _)
-          }
-          val result: Option[CommandPartsList] =
-            types.partition(_.select[CwlType].contains(CwlType.Null)) match {
-              case (Array(_), types) => lookupTypes(types) orElse Some(List.empty[SortKeyAndCommandPart])
-              case (Array(), types) => lookupTypes(types)
-            }
-         result.fold(
-            throw new RuntimeException(s"could not produce command line parts from input $womValue and types $types"))(
-            identity
-          )
-      }
-    }
-  }
-}
-
-object MyriadInputInnerTypeToSortedCommandParts extends Poly1 {
-
-  type CommandPartBuilder = (Option[InputCommandLineBinding], WomValue, CommandBindingSortingKey, Boolean, ExpressionLib, SchemaDefRequirement) => Option[CommandPartsList]
-
-  import Case._
-
-  // Primitive type: we just need to create a command part from the binding if there's one here.
-  implicit def ct: Aux[CwlType, CommandPartBuilder] = {
-    at {
-      cwlType => {
-        case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-        case (inputBinding, womValue, key, hasShellCommandRequirement, expressionLib, _) => {
-          (cwlType, womValue) match {
-            case (CwlType.Null, _) => List.empty.some
-            case (_, WomOptionalValue(_, None)) => List.empty.some
-            case (_,_) => inputBinding.toList.map(_.toCommandPart(key, womValue, hasShellCommandRequirement, expressionLib)).some
-          }
-        }
-      }
-    }
-  }
-
-  implicit def irs: Aux[InputRecordSchema, CommandPartBuilder] = at[InputRecordSchema] { irs => {
-    def go: CommandPartBuilder = {
-
-      //If the value is optional and is supplied, recurse over the value provided
-      case (inputBinding, WomCoproductValue(_, value), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        go(inputBinding, value, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-
-      //If the value is optional and is supplied, recurse over the value provided
-      case (inputBinding, WomOptionalValue(_, Some(value)), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        go(inputBinding, value, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-
-      // If it's optional and there's no value, do nothing
-      case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-
-      // If there's no input binding and no input bindings within the irs, do nothing
-      case (None, _, _, _, _, _) if !irs.fields.exists(_.exists(_.inputBinding.isDefined)) => List.empty.some
-
-      case (inputBinding, objectLike: WomObjectLike, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        // If there's an input binding, make a SortKeyAndCommandPart for it
-        val sortingKeyFromInputBindingFromInputParameter: Option[SortKeyAndCommandPart] =
-          inputBinding.map(_.toCommandPart(sortingKey, objectLike, hasShellCommandRequirement, expressionLib))
-
-        // iterate through the fields and fold over their type
-        val partsFromFields:Option[CommandPartsList] =
-          irs.fields.toList.flatten.
-            flatTraverse{
-              case InputRecordField(name, tpe, _, inputBinding, _) =>
-                // Parse the name to get a clean id
-                val parsedName = FullyQualifiedName(name)(ParentName.empty).id
-
-                // The field name needs to be added to the key after the input binding (as per the spec)
-                // Also start from the key from the input binding if there was one
-                val fieldSortingKey =
-                  sortingKeyFromInputBindingFromInputParameter.
-                    map(_.sortingKey).
-                    getOrElse(sortingKey).
-                    append(inputBinding, Coproduct[StringOrInt](parsedName))
-
-                val innerValueOption: Option[WomValue] = objectLike.values.get(parsedName)
-
-                val folded = innerValueOption.map(tpe.fold(MyriadInputTypeToSortedCommandParts).
-                  apply(inputBinding, _, fieldSortingKey.asNewKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement))
-                folded
-            }
-
-        sortingKeyFromInputBindingFromInputParameter.fold(
-          partsFromFields )(
-          sortingKeyFromInputBindingFromInputParameter =>
-            partsFromFields.map{k => List(sortingKeyFromInputBindingFromInputParameter.copy(nestedCommandParts = k)) }
-        )
-      case (_, other, _, _, _, _) => throw new RuntimeException(s"Value $other cannot be used for an input of type InputRecordSchema")
-    }
-
-    go
-  }}
-
-  implicit def ies: Aux[InputEnumSchema, CommandPartBuilder] = at[InputEnumSchema] { inputEnumSchema =>
-    def go: CommandPartBuilder = {
-      case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-      case (inputBinding, value, sortingKey, hasShellCommandRequirement, expressionLib, _) =>
-        // If there's an input binding, make a SortKeyAndCommandPart for it
-        val fromInputBinding =
-          inputBinding.map(_.toCommandPart(sortingKey, value, hasShellCommandRequirement, expressionLib)).toList
-
-        val fromIes = inputEnumSchema.inputBinding.map(_.toCommandPart(sortingKey, value, hasShellCommandRequirement, expressionLib)).toList
-
-        (fromInputBinding ++ fromIes).some
-    }
-    go
-  }
-
-  implicit def ias: Aux[InputArraySchema, CommandPartBuilder] = at[InputArraySchema] { ias =>
-    def go: CommandPartBuilder = {
-      case (inputBindingFromInputParameterParent, WomOptionalValue(_, Some(value)), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        go(inputBindingFromInputParameterParent, value, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-
-      //If it's optional and there's no value, do nothing
-      case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-
-      // If there's no input binding and no input bindings for the ias, do nothing
-      case (None, _, _, _, _, _) if ias.inputBinding.isEmpty => List.empty.some
-
-      case (inputBinding, WomArray.WomArrayLike(womArray: WomArray), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-
-
-        // If there's an input binding, make a SortKeyAndCommandPart for it
-        val sortKeyFromInputBindingFromInputerParameterParent: Option[SortKeyAndCommandPart] =
-          inputBinding.
-            map(_.toCommandPart(sortingKey, womArray, hasShellCommandRequirement, expressionLib))
-
-        // Now depending on whether we have an itemSeparator and/or valueFrom or not, we're going to recurse over each element of the array (or not).
-        // See http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding
-        if (inputBinding.flatMap(_.itemSeparator).isDefined || inputBinding.flatMap(_.valueFrom).isDefined) {
-          // If there's an item separator or a valueFrom we can stop here.
-          // When the command part is instantiated (see CommandLineBindingCommandPart) it will evaluate the valueFrom (if defined) and join the items together (if there's an itemSeparator).
-          sortKeyFromInputBindingFromInputerParameterParent.toList.some
-        } else {
-          // If neither valueFrom nor itemSeparator were defined, we need to process each item of the array
-          val fromArray: Option[CommandPartsList] = womArray.value.zipWithIndex.toList.flatTraverse({
-            case (item, index) =>
-              // Update the sorting key with the binding position (if any), add the index
-              val itemSortingKey = {
-
-              // The index needs to be added to the key after the input binding (as per the spec)
-              // Also start from the key from the input binding if there was one
-                val sortKey = sortKeyFromInputBindingFromInputerParameterParent.fold(sortingKey)(_.sortingKey)
-
-                sortKey.append(ias.inputBinding, Coproduct[StringOrInt](index))
-              }
-
-              // Even if the item doesn't have an explicit input binding, it should appear in the command so create a default empty one
-              //there is an explicit input binding!
-              val arrayItemInputBinding =
-                ias.
-                  inputBinding.
-                  orElse(Option(InputCommandLineBinding.default))
-
-              // Fold over the item type of each array element
-              Option(ias.items.fold(MyriadInputTypeToSortedCommandParts).apply(arrayItemInputBinding, item, itemSortingKey.asNewKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement))
-          })
-          sortKeyFromInputBindingFromInputerParameterParent.fold(fromArray){
-            sortKeyFromInputBindingFromInputerParameterParent =>
-              fromArray.map{k => List(sortKeyFromInputBindingFromInputerParameterParent.copy(nestedCommandParts = k)) }
-          }
-        }
-
-      case (_, other, _, _, _, _) => throw new RuntimeException(s"Value $other cannot be used for an input of type InputArraySchema")
-    }
-
-    go
-  }
-
-  implicit def s: Aux[String, CommandPartBuilder] = {
-    at {
-      s => {
-        case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-        case (commandLineBindingFromInput, womValue, sortingKey, boolean, expressionLib, schemaDefRequirement) => {
-          val womType: SchemaDefTypes = schemaDefRequirement.lookupCwlType(s).getOrElse(throw new RuntimeException(s"Looked for type $s in custom types $schemaDefRequirement but no match was found!"))
-
-          womType.fold(this).apply(commandLineBindingFromInput, womValue, sortingKey, boolean, expressionLib, schemaDefRequirement)
-        }
-      }
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadInputTypeToWomType.scala b/cwl/src/main/scala/cwl/MyriadInputTypeToWomType.scala
deleted file mode 100644
index d3be698bd33..00000000000
--- a/cwl/src/main/scala/cwl/MyriadInputTypeToWomType.scala
+++ /dev/null
@@ -1,95 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cwl.CwlType.CwlType
-import cwl.MyriadInputTypeToWomType.SchemaLookup
-import cwl.command.ParentName
-import mouse.all._
-import shapeless.Poly1
-import wom.types._
-
-object MyriadInputInnerTypeToString extends Poly1 {
-  implicit def ct = at[CwlType]{ _.toString }
-  implicit def irs = at[InputRecordSchema]{_.toString}
-  implicit def ies = at[InputEnumSchema]{ _.toString }
-  implicit def ias = at[InputArraySchema]{ _.toString}
-  implicit def s = at[String]{identity}
-}
-
-object MyriadInputTypeToWomType extends Poly1 {
-
-  import Case._
-
-  type SchemaLookup = SchemaDefRequirement => WomType
-
-  implicit def m:Aux[MyriadInputInnerType, SchemaLookup]= at[MyriadInputInnerType] {_.fold(MyriadInputInnerTypeToWomType)}
-
-  // An array of type means "this input value can be in any of those types."
-  // Currently we only accept single types or [null, X] to mean Optional[X]
-  implicit def am: Aux[Array[MyriadInputInnerType], SchemaLookup] = at[Array[MyriadInputInnerType]] {
-    types =>
-      schemaLookup =>
-        types.partition(_.select[CwlType].contains(CwlType.Null)) match {
-          // If there's a single non null type, use that
-          case (Array(), Array(singleNonNullType)) =>
-            singleNonNullType.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup)
-          case (Array(), array: Array[MyriadInputInnerType]) if array.length > 1  =>
-            val types = array.map(_.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup))
-            WomCoproductType(NonEmptyList.fromListUnsafe(types.toList))
-          // If there's a null type and a single non null type, it's a WomOptionalType
-          case (Array(_), Array(singleNonNullType)) =>
-            WomOptionalType(singleNonNullType.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup))
-          case (Array(_), array: Array[MyriadInputInnerType]) if array.length > 1  =>
-            val types = array.map(_.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup))
-            WomOptionalType(WomCoproductType(NonEmptyList.fromListUnsafe(types.toList)))
-          case (Array(_), _) =>
-            val readableTypes = types.map(_.fold(MyriadInputInnerTypeToString)).mkString(", ")
-            throw new UnsupportedOperationException(s"Cromwell only supports single types or optionals (as indicated by [null, X]). Instead we saw: $readableTypes")
-    }
-  }
-}
-
-object MyriadInputInnerTypeToWomType extends Poly1 {
-  import Case._
-
-  def ex(component: String) = throw new RuntimeException(s"input type $component not yet suported by WOM!")
-
-  implicit def ct: Aux[CwlType, SchemaLookup] = at[CwlType]{
-    ct =>
-      cwl.cwlTypeToWomType(ct) |> Function.const
-  }
-
-  def inputRecordSchemaToWomType(irs: InputRecordSchema): SchemaLookup = { schemaLookup: SchemaDefRequirement =>
-    irs match {
-      case InputRecordSchema(_,  Some(fields), _, _) =>
-        val typeMap = fields.map({ field =>
-          FullyQualifiedName(field.name)(ParentName.empty).id -> field.`type`.fold(MyriadInputTypeToWomType).apply(schemaLookup)
-        }).toMap
-        WomCompositeType(typeMap)
-      case irs => irs.toString |> ex
-    }
-  }
-
-  implicit def irs: Aux[InputRecordSchema, SchemaLookup] = at[InputRecordSchema]{
-    inputRecordSchemaToWomType
-  }
-
-  implicit def ies: Aux[InputEnumSchema, SchemaLookup] = at[InputEnumSchema]{
-    ies =>
-      ies.toWomEnumerationType |> Function.const
-  }
-
-  implicit def ias: Aux[InputArraySchema, SchemaLookup] = at[InputArraySchema]{
-    ias =>
-      lookup =>
-        val arrayType: WomType = ias.items.fold(MyriadInputTypeToWomType).apply(lookup)
-        WomArrayType(arrayType)
-  }
-
-  implicit def s: Aux[String, SchemaLookup] = at[String]{
-    string =>
-      schemaReq =>
-        schemaReq.lookupType(string).getOrElse(throw new RuntimeException(s"Custom type $string was referred to but not found in schema def ${schemaReq}."))
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomFiles.scala b/cwl/src/main/scala/cwl/MyriadOutputTypeToWomFiles.scala
deleted file mode 100644
index 7c007d07d46..00000000000
--- a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomFiles.scala
+++ /dev/null
@@ -1,66 +0,0 @@
-package cwl
-
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.validation.IOChecked._
-import cwl.CwlType.CwlType
-import cwl.MyriadOutputTypeToWomFiles.EvaluationFunction
-import mouse.all._
-import shapeless.Poly1
-import wom.expression.FileEvaluation
-
-object MyriadOutputTypeToWomFiles extends Poly1 {
-
-  type EvaluationFunction = CommandOutputBinding => IOChecked[Set[FileEvaluation]]
-
-  import Case._
-
-  implicit def cwlType: Aux[MyriadOutputInnerType, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[MyriadOutputInnerType]{
-    _.fold(MyriadOutputInnerTypeToWomFiles)
-  }
-
-  implicit def acwl: Aux[Array[MyriadOutputInnerType], EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[Array[MyriadOutputInnerType]] { types =>
-    evalFunction =>
-      types.toList.traverse(_.fold(MyriadOutputInnerTypeToWomFiles).apply(evalFunction)).map(_.toSet.flatten)
-  }
-}
-
-object MyriadOutputInnerTypeToWomFiles extends Poly1 {
-
-  import Case._
-
-  def ex(component: String) = throw new RuntimeException(s"output type $component cannot yield wom files")
-
-  implicit def cwlType: Aux[CwlType, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[CwlType] { _ =>_ =>
-    Set.empty[FileEvaluation].validIOChecked
-  }
-
-  implicit def ors: Aux[OutputRecordSchema, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[OutputRecordSchema] {
-    case OutputRecordSchema(_, Some(fields), _) =>
-      evalFunction =>
-        fields.toList.traverse[IOChecked, Set[FileEvaluation]]({ field =>
-          field.outputBinding match {
-            case Some(binding) => evalFunction(binding)
-            case None => field.`type`.fold(MyriadOutputTypeToWomFiles).apply(evalFunction)
-          }
-        }).map(_.toSet.flatten)
-    case ors => ors.toString |> ex
-  }
-
-  implicit def oes: Aux[OutputEnumSchema, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[OutputEnumSchema]{ oes =>_ =>
-    oes.toString |> ex
-  }
-
-  implicit def oas: Aux[OutputArraySchema, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[OutputArraySchema]{ oas =>
-    evalFunction =>
-      import cats.syntax.apply._
-      def fromBinding: IOChecked[Set[FileEvaluation]] = oas.outputBinding.map(evalFunction).getOrElse(Set.empty[FileEvaluation].validIOChecked)
-      def fromType: IOChecked[Set[FileEvaluation]] = oas.items.fold(MyriadOutputTypeToWomFiles).apply(evalFunction)
-
-      (fromBinding, fromType) mapN (_ ++ _)
-  }
-
-  implicit def s: Aux[String, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[String]{ _ =>_ =>
-    Set.empty[FileEvaluation].validIOChecked
-  }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomType.scala b/cwl/src/main/scala/cwl/MyriadOutputTypeToWomType.scala
deleted file mode 100644
index 61107143006..00000000000
--- a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomType.scala
+++ /dev/null
@@ -1,105 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cwl.CwlType.CwlType
-import cwl.command.ParentName
-import mouse.all._
-import shapeless.Poly1
-import wom.types._
-
-object MyriadOutputInnerTypeToString extends Poly1 {
-
-  implicit def cwlType = at[CwlType] {
-    _.toString
-  }
-
-  implicit def ors = at[OutputRecordSchema] {
-    _.toString
-  }
-
-  implicit def oes = at[OutputEnumSchema] {
-    _.toString
-  }
-
-  implicit def oas = at[OutputArraySchema] {
-    _.toString
-  }
-
-  implicit def s = at[String] {
-    identity
-  }
-}
-
-object MyriadOutputTypeToWomType extends Poly1{
-
-  import Case._
-
-  type SchemaDefToWomType = SchemaDefRequirement => WomType
-
-  implicit def cwlType: Aux[MyriadOutputInnerType, SchemaDefToWomType] = at[MyriadOutputInnerType]{ moit => schemaDefRequirement =>
-    moit.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement)
-  }
-
-  implicit def acwl: Aux[Array[MyriadOutputInnerType], SchemaDefToWomType] = at[Array[MyriadOutputInnerType]] { types => schemaDefRequirement =>
-    types.partition(_.select[CwlType].contains(CwlType.Null)) match {
-      // If there's a single non null type, use that
-      case (Array(), Array(singleNonNullType)) =>
-        singleNonNullType.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement)
-      case (Array(), array: Array[MyriadOutputInnerType]) if array.size > 1  =>
-        val types = array.map(_.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement))
-        WomCoproductType(NonEmptyList.fromListUnsafe(types.toList))
-      // If there's a null type and a single non null type, it's a WomOptionalType
-      case (Array(_), Array(singleNonNullType)) =>
-        WomOptionalType(singleNonNullType.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement))
-      case (Array(_), array: Array[MyriadOutputInnerType]) if array.size > 1  =>
-        val types = array.map(_.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement))
-        WomOptionalType(WomCoproductType(NonEmptyList.fromListUnsafe(types.toList)))
-      case _ =>
-        val readableTypes = types.map(_.fold(MyriadOutputInnerTypeToString)).mkString(", ")
-        throw new UnsupportedOperationException(s"Cromwell only supports single types or optionals (as indicated by [null, X]). Instead we saw: $readableTypes")
-    }
-  }
-}
-
-object MyriadOutputInnerTypeToWomType extends Poly1 {
-
-  import Case._
-  import MyriadOutputTypeToWomType.SchemaDefToWomType
-
-  implicit def cwlType: Aux[CwlType, SchemaDefToWomType] =
-    at[CwlType]{
-      cwl.cwlTypeToWomType andThen Function.const
-    }
-
-  implicit def ors: Aux[OutputRecordSchema, SchemaDefToWomType] = at[OutputRecordSchema] {
-    ors => schemaDefRequirement =>
-      ors.fields.fold(
-        WomCompositeType(Map.empty))(
-        {fields =>
-          val typeMap = fields.map({ field =>
-            val parsedName = FullyQualifiedName(field.name)(ParentName.empty).id
-            parsedName -> field.`type`.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-          }).toMap
-          WomCompositeType(typeMap)
-        }
-      )
-  }
-
-  implicit def oes: Aux[OutputEnumSchema, MyriadOutputTypeToWomType.SchemaDefToWomType] =
-    at[OutputEnumSchema] {
-      oes => oes.toWomEnumerationType |> Function.const
-    }
-
-  implicit def oas: Aux[OutputArraySchema, MyriadOutputTypeToWomType.SchemaDefToWomType] =
-    at[OutputArraySchema] {
-      oas => schemaDefRequirement =>
-        val arrayType: WomType = oas.items.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-        WomArrayType(arrayType)
-    }
-
-  implicit def s: Aux[String, MyriadOutputTypeToWomType.SchemaDefToWomType] =
-    at[String] {
-      string => schemaReq =>
-        schemaReq.lookupType(string).getOrElse(throw new RuntimeException(s"Custom type $string was referred to but not found in schema def ${schemaReq.types.mkString(", ")}."))
-    }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomValue.scala b/cwl/src/main/scala/cwl/MyriadOutputTypeToWomValue.scala
deleted file mode 100644
index 332e4ab3888..00000000000
--- a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomValue.scala
+++ /dev/null
@@ -1,100 +0,0 @@
-package cwl
-
-import cats.data.Validated.Valid
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.validation.IOChecked.IOChecked
-import common.validation.IOChecked._
-import cwl.CwlType.CwlType
-import cwl.command.ParentName
-import mouse.all._
-import shapeless.Poly1
-import wom.types._
-import wom.values.{WomObject, WomValue}
-
-/**
-  * Folds a MyriadOutputType into a WomValue
-  * This is needed because the type might define the structure of the final output value (for OutputRecordSchemas for example)
-  */
-object MyriadOutputTypeToWomValue extends Poly1 {
-
-  // We pass in a function that can evaluate a CommandOutputBinding and produce a WomValue. This allows us to recurse into the
-  // MyriadOutputTypes and evaluate values as we do.
-  type EvaluationFunction = (CommandOutputBinding, WomType) => IOChecked[WomValue]
-
-  //Our overall return type gives us the evaluator function and custom types; returns WomValues
-  type Output = (EvaluationFunction, SchemaDefRequirement) => IOChecked[WomValue]
-
-  import Case._
-
-  implicit def cwlType: Aux[MyriadOutputInnerType, Output] = at[MyriadOutputInnerType]{
-    moit => (evalFunction, schemaDefRequirement) => moit.fold(MyriadOutputInnerTypeToWomValue).apply(evalFunction, schemaDefRequirement)
-  }
-
-  // TODO: Not sure what the right thing to do is here, for now go over the list of types and use the first evaluation that yields success
-  implicit def acwl: Aux[Array[MyriadOutputInnerType], Output] = at[Array[MyriadOutputInnerType]] { types =>
-    (evalFunction,schemaDefRequirement) =>
-      types.toList.map(_.fold(MyriadOutputInnerTypeToWomValue).apply(evalFunction, schemaDefRequirement)).map(_.toErrorOr).collectFirst({
-        case Valid(validValue) => validValue
-      }).toValidNel(s"Cannot find a suitable type to build a WomValue from in ${types.mkString(", ")}").toIOChecked
-  }
-}
-
-object MyriadOutputInnerTypeToWomValue extends Poly1 {
-
-  import Case._
-  import MyriadOutputTypeToWomValue.Output
-
-  def ex(component: String) = throw new RuntimeException(s"output type $component cannot yield a wom value")
-
-  implicit def cwlType: Aux[CwlType, Output] = at[CwlType] { _ => (_,_) =>
-    "No output binding is defined. Are you expecting the output to be inferred from a cwl.output.json file ? If so please make sure the file was effectively created.".invalidIOChecked
-  }
-
-  implicit def ors: Aux[OutputRecordSchema, Output] = at[OutputRecordSchema] { ors => (evalFunction, schemaDefRequirement) => ors match {
-    case OutputRecordSchema(_, Some(fields), _) =>
-        // Go over each field and evaluate the binding if there's one, otherwise keep folding over field types
-        def evaluateValues = fields.toList.traverse[IOChecked, ((String, WomValue), (String, WomType))]({ field =>
-          val womType = field.`type`.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-          val womValue: IOChecked[WomValue] = field.outputBinding match {
-            case Some(binding) => evalFunction(binding, womType)
-            case None => field.`type`.fold(MyriadOutputTypeToWomValue).apply(evalFunction, schemaDefRequirement)
-          }
-
-          // TODO: ParentName might need to be passed in here ?
-          // return the value and the type with a clean parsedName
-          womValue map { value =>
-            val parsedName = FullyQualifiedName(field.name)(ParentName.empty).id
-            (parsedName -> value) -> (parsedName -> womType)
-          }
-        })
-
-        evaluateValues map { evaluatedValues =>
-          val (valueMap, typeMap) = evaluatedValues.unzip
-          // Create a typed WomObject from the values and the typeMap
-          WomObject.withTypeUnsafe(valueMap.toMap, WomCompositeType(typeMap.toMap))
-        }
-    case ors => ors.toString |> ex
-  }}
-
-  implicit def oes: Aux[OutputEnumSchema, Output] = at[OutputEnumSchema]{
-    //DB: I tried to do a pattern match as the overall function here but the compiler exploded
-    oes => (f, schemaDefRequirement) => oes match {
-      case oes@OutputEnumSchema(_, _, _, _, Some(outputBinding)) => f(outputBinding, oes.toWomEnumerationType)
-      case _ => s"The enumeration type $oes requires an outputbinding to be evaluated.".invalidIOChecked
-    }
-  }
-
-  implicit def oas: Aux[OutputArraySchema, Output] = at[OutputArraySchema]{ oas => (evalFunction, schemaDefRequirement) => oas match {
-    case OutputArraySchema(itemsType, _, _, outputBinding) =>
-      lazy val itemsWomType = itemsType.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-      def fromBinding = outputBinding.map(evalFunction(_, WomArrayType(itemsWomType)))
-      def fromTypes = itemsType.fold(MyriadOutputTypeToWomValue).apply(evalFunction, schemaDefRequirement)
-      fromBinding.getOrElse(fromTypes)
-  }}
-
-  implicit def s: Aux[String, Output] = at[String]{ s => (_, _) =>
-    s.toString |> ex
-  }
-}
diff --git a/cwl/src/main/scala/cwl/OutputParameter.scala b/cwl/src/main/scala/cwl/OutputParameter.scala
deleted file mode 100644
index 274469da7ee..00000000000
--- a/cwl/src/main/scala/cwl/OutputParameter.scala
+++ /dev/null
@@ -1,62 +0,0 @@
-package cwl
-
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.option._
-import common.validation.ErrorOr._
-import shapeless.{:+:, CNil, Poly1}
-import wom.values.{WomString, WomValue}
-
-trait OutputParameter {
-  def id: String
-  def label: Option[String]
-  def secondaryFiles: Option[SecondaryFiles]
-  def format: Option[OutputParameterFormat]
-  def streamable: Option[Boolean]
-  def doc: Option[String :+: Array[String] :+: CNil]
-  def outputBinding: Option[CommandOutputBinding]
-  def `type`: Option[MyriadOutputType]
-  def cacheString: String = toString
-}
-
-object OutputParameter {
-  object IdAndType {
-    def unapply(arg: OutputParameter): Option[(String, MyriadOutputType)] = arg.`type`.map((arg.id, _))
-  }
-
-  def format(formatOption: Option[StringOrExpression],
-             parameterContext: ParameterContext,
-             expressionLib: ExpressionLib): ErrorOr[Option[String]] = {
-    formatOption.traverse{
-      format(_, parameterContext, expressionLib)
-    }
-  }
-
-  def format(format: StringOrExpression, parameterContext: ParameterContext, expressionLib: ExpressionLib): ErrorOr[String] = {
-    format.fold(OutputParameter.FormatPoly).apply(parameterContext, expressionLib)
-  }
-
-  type FormatFunction = (ParameterContext, ExpressionLib) => ErrorOr[String]
-
-  object FormatPoly extends Poly1 {
-    implicit def caseStringOrExpression: Case.Aux[StringOrExpression, FormatFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseExpression: Case.Aux[Expression, FormatFunction] = {
-      at {
-        expression =>
-          (parameterContext, expressionLib) =>
-            val result: ErrorOr[WomValue] = ExpressionEvaluator.eval(expression, parameterContext)
-            result flatMap {
-              case womString: WomString => womString.value.valid
-              case other => s"Not a valid file format: $other".invalidNel
-            }
-      }
-    }
-
-    implicit def caseString: Case.Aux[String, FormatFunction] = at { string => (_,_) => string.valid }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/OutputParameterExpression.scala b/cwl/src/main/scala/cwl/OutputParameterExpression.scala
deleted file mode 100644
index b044bc36077..00000000000
--- a/cwl/src/main/scala/cwl/OutputParameterExpression.scala
+++ /dev/null
@@ -1,115 +0,0 @@
-package cwl
-
-import common.validation.ErrorOr.ErrorOr
-import common.validation.IOChecked.{IOChecked, _}
-import cwl.CwlType.CwlType
-import shapeless.Poly1
-import wom.expression.{EmptyIoFunctionSet, FileEvaluation, IoFunctionSet}
-import wom.types._
-import wom.values.WomValue
-
-import scala.Function.const
-import scala.concurrent.{ExecutionContext, Future}
-
-case class OutputParameterExpression(parameter: OutputParameter,
-                                     override val cwlExpressionType: WomType,
-                                     override val inputs: Set[String],
-                                     override val expressionLib: ExpressionLib,
-                                     schemaDefRequirement: SchemaDefRequirement) extends CwlWomExpression {
-
-  override def sourceString = parameter.toString
-
-  override def cacheString: String = parameter.cacheString
-
-  private def evaluateOutputBinding(inputValues: Map[String, WomValue],
-                                    ioFunctionSet: IoFunctionSet,
-                                    secondaryFilesOption: Option[SecondaryFiles],
-                                    formatOption: Option[StringOrExpression]
-                                   )(outputBinding: CommandOutputBinding,
-                                    cwlExpressionType: WomType): IOChecked[WomValue] = {
-    CommandOutputBinding.generateOutputWomValue(
-      inputValues,
-      ioFunctionSet,
-      cwlExpressionType,
-      outputBinding,
-      secondaryFilesOption,
-      formatOption,
-      expressionLib
-    )
-  }
-
-  private def evaluateOutputBindingFiles(inputValues: Map[String, WomValue],
-                                    ioFunctionSet: IoFunctionSet,
-                                    secondaryFilesOption: Option[SecondaryFiles],
-                                    coerceTo: WomType
-                                   )(outputBinding: CommandOutputBinding): IOChecked[Set[FileEvaluation]] = {
-    CommandOutputBinding.getOutputWomFiles(
-      inputValues,
-      coerceTo,
-      outputBinding,
-      secondaryFilesOption,
-      ioFunctionSet,
-      expressionLib
-    )
-  }
-  
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
-    def fromOutputBinding =
-      parameter.outputBinding.map(evaluateOutputBinding(inputValues, ioFunctionSet, parameter.secondaryFiles, parameter.format)(_, cwlExpressionType))
-
-    def fromType =
-      parameter.`type`.map(_.fold(MyriadOutputTypeToWomValue).apply(
-        evaluateOutputBinding(inputValues, ioFunctionSet, parameter.secondaryFiles, parameter.format),
-        schemaDefRequirement
-      ))
-
-    fromOutputBinding.orElse(fromType).getOrElse(s"Cannot evaluate ${parameter.toString}".invalidIOChecked).toErrorOr
-  }
-
-  /**
-    * Returns the list of files that _will be_ output after the command is run, unless they are optional and if so _may be_.
-    *
-    * In CWL, a list of outputs is specified as glob, say `*.bam`, plus a list of secondary files that may be in the
-    * form of paths or specified using carets such as `^.bai`.
-    *
-    * The coerceTo may be one of four different values:
-    * - WomMaybePopulatedFileType
-    * - WomArrayType(WomMaybePopulatedFileType)
-    * - WomMaybeListedDirectoryType
-    * - WomArrayType(WomMaybeListedDirectoryType) (Possible according to the way the spec is written, but not likely?)
-    */
-  override def evaluateFiles(inputs: Map[String, WomValue], unused: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
-    import cats.syntax.apply._
-
-    // Ignore the supplied ioFunctionSet and use a custom stubbed IoFunctionSet. This is better than a real I/O function set
-    // because in the context of file evaluation we don't care about the results of these operations. The NoIoFunctionSet
-    // that otherwise would be used throws for all of its operations which doesn't fly for the way our CWL evaluation works.
-    val stubbedIoFunctionSet = new EmptyIoFunctionSet {
-      override def size(path: String): Future[Long] = Future.successful(0L)
-      override def isDirectory(path: String): Future[Boolean] = Future.successful(false)
-      override def ec: ExecutionContext = scala.concurrent.ExecutionContext.global
-    }
-    def fromOutputBinding: IOChecked[Set[FileEvaluation]] = parameter
-      .outputBinding
-      .map(evaluateOutputBindingFiles(inputs, stubbedIoFunctionSet, parameter.secondaryFiles, coerceTo))
-      .getOrElse(Set.empty[FileEvaluation].validIOChecked)
-
-    def fromType: IOChecked[Set[FileEvaluation]] = parameter
-      .`type`
-      .map(_.fold(MyriadOutputTypeToWomFiles).apply(evaluateOutputBindingFiles(inputs, stubbedIoFunctionSet, parameter.secondaryFiles, coerceTo)))
-      .getOrElse(Set.empty[FileEvaluation].validIOChecked)
-
-    val optional: Boolean = parameter.`type`.exists(_.fold(OutputTypeIsOptional))
-
-    ((fromOutputBinding, fromType) mapN (_ ++ _) map { _ map { _.copy(optional = optional) } }).toErrorOr
-  }
-}
-
-object OutputTypeIsOptional extends Poly1 {
-  implicit val one: Case.Aux[MyriadOutputInnerType, Boolean] = at[MyriadOutputInnerType] { const(false) }
-
-  implicit val arr: Case.Aux[Array[MyriadOutputInnerType], Boolean] = at[Array[MyriadOutputInnerType]] {
-    // Possibly too broad, would return true for just single 'null'.
-    _.exists(_.select[CwlType].contains(CwlType.Null))
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ParameterContext.scala b/cwl/src/main/scala/cwl/ParameterContext.scala
deleted file mode 100644
index 4bcb4d132d5..00000000000
--- a/cwl/src/main/scala/cwl/ParameterContext.scala
+++ /dev/null
@@ -1,17 +0,0 @@
-package cwl
-
-import wom.callable.RuntimeEnvironment
-import wom.expression.IoFunctionSet
-import wom.types.WomNothingType
-import wom.values.{WomOptionalValue, WomValue}
-
-object ParameterContext {
-  val EmptySelf = WomOptionalValue(WomNothingType, None)
-}
-
-case class ParameterContext(
-                            ioFunctionSet: IoFunctionSet,
-                            expressionLib: ExpressionLib,
-                            inputs: Map[String, WomValue] = Map.empty,
-                            self: WomValue = ParameterContext.EmptySelf,
-                            runtimeOption: Option[RuntimeEnvironment] = None)
diff --git a/cwl/src/main/scala/cwl/RequirementsAndHints.scala b/cwl/src/main/scala/cwl/RequirementsAndHints.scala
deleted file mode 100644
index 46b5c52e410..00000000000
--- a/cwl/src/main/scala/cwl/RequirementsAndHints.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cwl
-
-case class RequirementsAndHints(list: List[Requirement]) {
-
-  lazy val hasShellCommandRequirement: Boolean = list.exists(_.select[ShellCommandRequirement].nonEmpty)
-
-  //Should we add up all the types instead?  This would mean subworkflows can inherit their parent schemas
-  lazy val schemaDefRequirement = list.flatMap(_.select[SchemaDefRequirement]).headOption.getOrElse(SchemaDefRequirement())
-}
diff --git a/cwl/src/main/scala/cwl/RunOutputsToTypeMap.scala b/cwl/src/main/scala/cwl/RunOutputsToTypeMap.scala
deleted file mode 100644
index f327b5b03ea..00000000000
--- a/cwl/src/main/scala/cwl/RunOutputsToTypeMap.scala
+++ /dev/null
@@ -1,45 +0,0 @@
-package cwl
-
-import shapeless.Poly1
-import wom.types.WomType
-
-object RunOutputsToTypeMap extends Poly1 {
-
-  import Case.Aux
-
-  type SchemaDefToTypeMap = SchemaDefRequirement => WomTypeMap
-
-  def handleOutputParameters[A <: OutputParameter](outputs: Array[A], schemaDefRequirement: SchemaDefRequirement): Map[String, WomType] = {
-    outputs.toList.foldLeft(Map.empty[String, WomType]) {
-      (acc, out) =>
-        acc ++
-          out.
-            `type`.
-            map(_.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)).
-            map(out.id -> _).
-            toList.
-            toMap
-    }
-  }
-
-  implicit def commandLineTool : Aux[CommandLineTool, SchemaDefToTypeMap] =
-    at[CommandLineTool] {
-      clt => handleOutputParameters(clt.outputs, _)
-    }
-
-  implicit def string: Aux[String, SchemaDefToTypeMap] = at[String] {
-    _ => _ =>
-      Map.empty[String, WomType] //should never happen because we dereference/embed CWL subworkflows into one object from the original string references
-  }
-
-  implicit def expressionTool: Aux[ExpressionTool, SchemaDefToTypeMap] = at[ExpressionTool] {
-    et =>
-      handleOutputParameters(et.outputs, _)
-  }
-
-  implicit def workflow: Aux[Workflow, SchemaDefToTypeMap] = at[Workflow] {
-    wf =>
-      handleOutputParameters(wf.outputs, _)
-  }
-}
-
diff --git a/cwl/src/main/scala/cwl/RunToEmbeddedCwl.scala b/cwl/src/main/scala/cwl/RunToEmbeddedCwl.scala
deleted file mode 100644
index 2547b6333a4..00000000000
--- a/cwl/src/main/scala/cwl/RunToEmbeddedCwl.scala
+++ /dev/null
@@ -1,36 +0,0 @@
-package cwl
-
-import shapeless._
-import WorkflowStep.Run
-
-object RunToEmbeddedCwl extends Poly1 {
-  implicit def commandLineTool =
-    at[CommandLineTool] {
-      clt =>
-        (_: Map[String, Cwl]) =>
-         Coproduct[Run](clt)
-    }
-
-  implicit def string = at[String] {
-    fileName =>
-      (cwlMap: Map[String, Cwl]) => {
-        val cwl = cwlMap(fileName)
-        cwl.fold(CwlToRun)
-      }
-  }
-
-
-  implicit def expressionTool = at[ExpressionTool] {
-    et =>
-      (_: Map[String, Cwl]) =>
-        Coproduct[Run](et)
-  }
-
-  implicit def workflow = at[Workflow] {
-    wf =>
-      (_: Map[String, Cwl]) =>
-        Coproduct[Run](wf)
-  }
-}
-
-
diff --git a/cwl/src/main/scala/cwl/RunToInputTypeMap.scala b/cwl/src/main/scala/cwl/RunToInputTypeMap.scala
deleted file mode 100644
index 7111e389050..00000000000
--- a/cwl/src/main/scala/cwl/RunToInputTypeMap.scala
+++ /dev/null
@@ -1,37 +0,0 @@
-package cwl
-
-import cwl.command.ParentName
-import shapeless.Poly1
-
-object RunToInputTypeMap extends Poly1 {
-
-  type MyriadInputTypeMap = Map[String, Option[MyriadInputType]]
-
-  type OutputType = ParentName => MyriadInputTypeMap
-
-  import Case.Aux
-
-  implicit def s: Aux[String, OutputType] =
-    at[String] {
-      run =>  _ => throw new RuntimeException(s"Run field $run was not inlined as expected")
-    }
-
-  implicit def clt: Aux[CommandLineTool, OutputType] =
-    at[CommandLineTool]{clt => parentName => clt.inputs.map{
-      input =>
-          FullyQualifiedName(input.id)(parentName).id -> input.`type`
-    }.toMap}
-
-  implicit def et: Aux[ExpressionTool, OutputType] =
-    at[ExpressionTool]{et => parentName => et.inputs.map{
-      input =>
-        FullyQualifiedName(input.id)(parentName).id -> input.`type`
-    }.toMap}
-
-  implicit def wf: Aux[Workflow, OutputType] =
-    at[Workflow]{ wf => parentName => wf.inputs.map{
-      input =>
-        FullyQualifiedName(input.id)(parentName).id -> input.`type`
-    }.toMap}
-
-}
diff --git a/cwl/src/main/scala/cwl/ScatterLogic.scala b/cwl/src/main/scala/cwl/ScatterLogic.scala
deleted file mode 100644
index 97d87daf6df..00000000000
--- a/cwl/src/main/scala/cwl/ScatterLogic.scala
+++ /dev/null
@@ -1,263 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.instances.list._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import cwl.ScatterMethod.ScatterMethod
-import shapeless.Poly1
-import wom.graph.CallNode.CallNodeAndNewNodes
-import wom.graph.GraphNodePort.ScatterGathererPort
-import wom.graph.ScatterNode._
-import wom.graph._
-import wom.graph.expression.ExpressionNode
-import wom.types.{WomArrayType, WomMaybeEmptyArrayType, WomType}
-import wom.values.{WomArray, WomValue}
-
-import scala.annotation.tailrec
-
-/**
-  * Contains methods used to implement the scatter related logic for CWL workflows.
-  * The general idea is as follows:
-  *
-  * See WorkflowStep for an example of WOM graph for scatters.
-  * 
-  * # Scattering over multiple variables
-  *
-  * When several variables are being scattered over, a scatter method is mandatory to specify how the elements must be combined.
-  * Let's use the following 2 arrays as an example:
-  *
-  * a1: ["one", "two"], a2: ["three", "four"]
-  *
-  * * DotProduct:
-  * DotProduct only works if all the arrays have the same length.
-  *
-  * Shard 0: "one" - "three"
-  * Shard 1: "two" - "four"
-  *
-  * * CrossProduct (nested or flat):
-  * Both cross product methods generate the same shards, the difference is in how they are collected at the end
-  *
-  * Shard 0: "one" - "three"
-  * Shard 1: "one" - "four"
-  * Shard 2: "two" - "three"
-  * Shard 3: "two" - "four"
-  *
-  * To support this, each SVN will have a method which given a shard index will return the index at which the value should be looked up in the array.
-  *
-  * For dot product, this function is the same for all SVN and will be the identity[Int] function.
-  * For cross product, this function depends on the number of elements in each array, which is known at runtime.
-  *   When we do have this information we update each SVN with it in the ScatterProcessingFunction and returns the number of shards to be generated.
-  */
-object ScatterLogic {
-  case class ScatterFunctions(processing: ScatterProcessingFunction, collection: ScatterCollectionFunctionBuilder)
-
-  object ScatterVariablesPoly extends Poly1 {
-    implicit def fromString: Case.Aux[String, List[String]] = at[String] { s: String => List(s) }
-    implicit def fromStringList: Case.Aux[Array[String], List[String]] = at[Array[String]] { l: Array[String] => l.toList }
-  }
-
-  // Validate that the scatter expression is an ArrayLike and return the member type
-  private [cwl] def scatterExpressionItemType(expressionNode: ExpressionNode) = {
-    expressionNode.womType match {
-      case WomArrayType(itemType) => itemType.validNelCheck // Covers maps because this is a custom unapply (see WomArrayType)
-      case other => s"Cannot scatter over a non-traversable type ${other.stableName}".invalidNelCheck
-    }
-  }
-
-  def scatterGatherPortTypeFunction(scatterMethod: Option[ScatterMethod], scatterVariables: NonEmptyList[_]): WomType => WomArrayType = scatterMethod match {
-    case Some(ScatterMethod.NestedCrossProduct) =>
-      innerType: WomType =>
-        scatterVariables.tail.foldLeft(WomArrayType(innerType))({ case (t, _) => WomArrayType(t) })
-    case _ => innerType: WomType => WomArrayType(innerType)
-  }
-
-  // Build a map (potentially empty) of scatterered input steps with their corresponding SVN node.
-  def buildScatterVariableNodes(scatter: ScatterVariables, stepInputMappings: Map[WorkflowStepInput, ExpressionNode], stepId: String): Checked[Map[WorkflowStepInput, ScatterVariableNode]] = {
-    import cats.syntax.all._
-
-    def buildScatterVariable(scatterVariableName: String): ErrorOr[(WorkflowStepInput, ScatterVariableNode)] = {
-      // Assume the variable is a step input (is that always true ??). Find the corresponding expression node
-
-      stepInputMappings.find({ case (stepInput, _) => stepInput.id == scatterVariableName }) match {
-        case Some((stepInput, expressionNode)) =>
-          scatterExpressionItemType(expressionNode).toValidated map { itemType =>
-            // create a scatter variable node for other scattered nodes to point to
-            stepInput -> ScatterVariableNode(WomIdentifier(scatterVariableName), expressionNode, itemType)
-          }
-        case None => s"Could not find a variable $scatterVariableName in the workflow step input to scatter over. Please make sure $scatterVariableName is an input of step $stepId".invalidNel
-      }
-    }
-    // Take the scatter field defining the (list of) input(s) to be scattered over
-    scatter
-      // Fold them so we have a List[String] no matter what (a single scattered input becomes a single element list)
-      .map(_.fold(ScatterVariablesPoly))
-      // If there's no scatter make it an empty list
-      .getOrElse(List.empty)
-      // Traverse the list to create ScatterVariableNodes that will be used later on to create the ScatterNode
-      .traverse(buildScatterVariable)
-      .toEither
-      .map(_.toMap)
-  }
-
-  // Prepare the nodes to be returned if this call is being scattered
-  def buildScatterNode(callNodeAndNewNodes: CallNodeAndNewNodes,
-                       scatterVariableNodes: NonEmptyList[ScatterVariableNode],
-                       ogins: Set[OuterGraphInputNode],
-                       stepExpressionNodes: Set[ExpressionNode],
-                       scatterMethod: Option[ScatterMethod]): Checked[ScatterNode] = {
-
-    val scatterProcessingFunctionCheck = (scatterVariableNodes.size, scatterMethod) match {
-      // If we scatter over one variable only, the default processing method can handle it
-      case (1, _) => ScatterFunctions(ScatterNode.DefaultScatterProcessingFunction, ScatterNode.DefaultScatterCollectionFunctionBuilder).validNelCheck
-      case (_, Some(method)) => ScatterFunctions(processingFunction(method), collectingFunctionBuilder(method)).validNelCheck
-      case (_, None) => "When scattering over multiple variables, a scatter method needs to be defined. See http://www.commonwl.org/v1.0/Workflow.html#WorkflowStep".invalidNelCheck
-    }
-
-    val callNode = callNodeAndNewNodes.node
-
-    // We need to generate PBGONs for every output port of the call, so that they can be linked outside the scatter graph
-    val portBasedGraphOutputNodes = callNode.outputPorts.map(op => PortBasedGraphOutputNode(op.identifier, op.womType, op))
-
-    def buildScatterNode(innerGraph: Graph, scatterFunctions: ScatterFunctions) = {
-      val scatterNodeBuilder = new ScatterNodeBuilder
-      val outputPorts: Set[ScatterGathererPort] = innerGraph.nodes.collect { case gon: PortBasedGraphOutputNode =>
-        scatterNodeBuilder.makeOutputPort(scatterGatherPortTypeFunction(scatterMethod, scatterVariableNodes)(gon.womType), gon)
-      }
-
-      scatterNodeBuilder.build(innerGraph, outputPorts, scatterVariableNodes.toList, scatterFunctions.processing, scatterFunctions.collection)
-    }
-    
-    for {
-      scatterProcessingFunctionAndBuilder <- scatterProcessingFunctionCheck
-      graph <- Graph.validateAndConstruct(
-        Set(callNodeAndNewNodes.node) ++
-          ogins ++
-          stepExpressionNodes ++
-          scatterVariableNodes.toList ++
-          portBasedGraphOutputNodes
-      ).toEither
-      scatterNode = buildScatterNode(graph, scatterProcessingFunctionAndBuilder)
-    } yield scatterNode.node
-  }
-
-  /*
-   * Processing function for cross products. Logic is as follows:
-   * We want 1) know how many shards should be created (which this function will return)
-   *         2) update each SVN with their relative index length (see ScatterVariableNode for more detail)
-   *         
-   * We are going to multiply all the array sizes (which will give us 1) at the end)
-   * Along the way we will update the relative index length for each SVN.
-   * To do so, we start at the end of the list and recurse.
-   */
-  private [cwl] val CrossProductScatterProcessingFunction: ScatterProcessingFunction = { nodesAndValues: List[ScatterVariableAndValue] =>
-    @tailrec
-    def updateIndexLengthRec(currentList: List[ScatterVariableAndValue], combinedArraySize: Int): Int = currentList match {
-      case Nil => combinedArraySize
-      case ScatterVariableAndValue(variableNode, arrayValue) :: tail =>
-        variableNode.withRelativeIndexLength(combinedArraySize)
-        updateIndexLengthRec(tail, combinedArraySize * arrayValue.size)
-    }
-
-    // Reverse the list so that we start from the last variable and make our way back to the first one
-    updateIndexLengthRec(nodesAndValues.reverse, 1).validNelCheck
-  }
-
-  private [cwl] val DotProductScatterProcessingFunction: ScatterProcessingFunction = ScatterNode.DefaultScatterProcessingFunction
-
-  // Recursively nest shard results appropriately based on the size of the scatter variable arrays
-  private [cwl] val NestedCrossProductScatterCollectionFunctionBuilder: ScatterCollectionFunctionBuilder = { arraySizes: List[Int] =>
-    (sortedShards: List[WomValue], valueType: WomArrayType) =>
-
-      @tailrec
-      def buildCollectorArrayRec(currentList: List[Int], currentWomValues: List[WomValue], currentWomType: WomType): WomArray = {
-        /*  We stop right before the last element because it will necessarily be the number of elements in currentWomValues (provided the list is non empty).
-          * e.g if currentList is (2, 3, 2), then currentWomValues will have 2 * 3 * 2 = 12 elements (this is a cross product)
-          * As we recurse, we keep grouping currentWomValues by the numbers in currentList:
-          * 
-          * group by 2: [[_, _], [_, _], [_, _], [_, _], [_, _], [_, _]]
-          * group by 3: [
-          *   [[_, _], [_, _], [_, _]],
-          *   [[_, _], [_, _], [_, _]]
-          * ]
-          * This list has necessarily 2 elements already because 12 / 2 / 3 = 2. So we can make the final WomArray out of that
-        */
-        currentList match {
-          case _ :: Nil | Nil =>
-            WomArray(WomMaybeEmptyArrayType(currentWomType), currentWomValues)
-          case head :: tail =>
-            val arrayType = WomMaybeEmptyArrayType(currentWomType)
-            val womArrays = currentWomValues.grouped(head).toList map { WomArray(arrayType, _) }
-            buildCollectorArrayRec(tail, womArrays, arrayType)
-        }
-      }
-
-      def mostInnerType(tpe: WomType): WomType = tpe match {
-        case WomArrayType(t) => mostInnerType(t)
-        case other => other
-      }
-
-      def buildEmptyArrays(arraySizeList: List[Int], womType: WomType, womValues: List[WomValue]): WomArray = arraySizeList match {
-        case Nil => womType match {
-          case arrayType: WomArrayType => WomArray(arrayType, womValues)
-          case _ =>
-            // This would mean arraySizeList was empty to begin with (otherwise we would have wrapped womType in a WomArrayType at least once)
-            // which should be impossible since it would mean there was no scatter variables, so we shouldn't even be here
-            throw new RuntimeException("Programmer error ! We should not be collecting scatter nodes if there was no scatter !")
-        }
-        case 0 :: tail =>
-          buildEmptyArrays(tail, WomArrayType(womType), List.empty)
-        case head :: tail =>
-          val arrayType = womType match {
-            case array: WomArrayType => array
-            case nonArray => WomArrayType(nonArray)
-          }
-          val womArrays = (0 until head).toList map { _ => WomArray(arrayType, womValues) }
-          buildEmptyArrays(tail, WomArrayType(womType), womArrays)
-      }
-
-      /*
-       * There are 2 distinct cases.
-       * If we have no shards, it means that at least one of the scatter expressions evaluated to an empty array.
-       * In that case we want to create an array structure of empty arrays reflecting the scatter array sizes.
-       * e.g:
-       * 
-       * scatter array sizes   |   collected result
-       *        [0]                       []
-       *       [0, 2]                     [] 
-       *       [2, 0]                   [[], []]
-       *      [2, 0, 3]                 [[], []]
-       *      [2, 3, 0]                [[[], [], []], [[], [], []]] 
-       *
-       * Note that as soon as we reach a size 0, we return an empty array.
-       * 
-       * If we have shards, we successively group the shards list to build arrays of the right size.
-       * 
-       * In both cases we reverse the list so that we can left recurse while still building the result starting from the most nested arrays
-       */
-      if (sortedShards.isEmpty) {
-        buildEmptyArrays(arraySizes.reverse, mostInnerType(valueType), List.empty)
-      } else {
-        // 
-        buildCollectorArrayRec(arraySizes.reverse, sortedShards, mostInnerType(valueType))
-      }
-  }
-
-  // select a processing function based on the scatter method
-  private def processingFunction(scatterMethod: ScatterMethod) = scatterMethod match {
-    case ScatterMethod.DotProduct => DotProductScatterProcessingFunction
-    // Both cross product methods use the same processing function, the difference is in how we collect results (see collectingFunctionBuilder)
-    case ScatterMethod.FlatCrossProduct => CrossProductScatterProcessingFunction
-    case ScatterMethod.NestedCrossProduct => CrossProductScatterProcessingFunction
-  }
-
-  // select a collecting function builder based on the scatter method
-  private def collectingFunctionBuilder(scatterMethod: ScatterMethod) = scatterMethod match {
-    // dot product and flat cross product output a flat array, which is the default behavior
-    case ScatterMethod.DotProduct => ScatterNode.DefaultScatterCollectionFunctionBuilder
-    case ScatterMethod.FlatCrossProduct => ScatterNode.DefaultScatterCollectionFunctionBuilder
-    // nested cross product uses a special collecting function to build nested arrays
-    case ScatterMethod.NestedCrossProduct => NestedCrossProductScatterCollectionFunctionBuilder
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ScatterMethod.scala b/cwl/src/main/scala/cwl/ScatterMethod.scala
deleted file mode 100644
index 0a60575e0cb..00000000000
--- a/cwl/src/main/scala/cwl/ScatterMethod.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cwl
-
-object ScatterMethod extends Enumeration {
-  type ScatterMethod = Value
-
-  val DotProduct = Value("dotproduct")
-  val NestedCrossProduct = Value("nested_crossproduct")
-  val FlatCrossProduct = Value("flat_crossproduct")
-}
diff --git a/cwl/src/main/scala/cwl/StringOrStringArrayToStringList.scala b/cwl/src/main/scala/cwl/StringOrStringArrayToStringList.scala
deleted file mode 100644
index 73afab205b7..00000000000
--- a/cwl/src/main/scala/cwl/StringOrStringArrayToStringList.scala
+++ /dev/null
@@ -1,12 +0,0 @@
-package cwl
-
-import shapeless.Poly1
-
-/**
-  * From a logic standpoint it's easier to treat sources as a list of strings.
-  */
-object StringOrStringArrayToStringList extends Poly1{
-  import Case._
-  implicit def string: Aux[String, List[String]] = at[String]{List(_)}
-  implicit def array: Aux[Array[String], List[String]] = at[Array[String]]{_.toList}
-}
diff --git a/cwl/src/main/scala/cwl/Tool.scala b/cwl/src/main/scala/cwl/Tool.scala
deleted file mode 100644
index d31b7368aee..00000000000
--- a/cwl/src/main/scala/cwl/Tool.scala
+++ /dev/null
@@ -1,189 +0,0 @@
-package cwl
-
-import java.nio.file.Paths
-
-import cats.instances.list._
-import common.Checked
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import cwl.CwlVersion.CwlVersion
-import cwl.Tool.inlineJavascriptRequirements
-import cwl.command.ParentName
-import cwl.requirement.RequirementToAttributeMap
-import shapeless.Inl
-import wom.callable.Callable.{OverridableInputDefinitionWithDefault, OptionalInputDefinition, OutputDefinition, RequiredInputDefinition}
-import wom.callable.MetaValueElement.{MetaValueElementBoolean, MetaValueElementObject}
-import wom.callable.{Callable, MetaValueElement, TaskDefinition}
-import wom.executable.Executable
-import wom.expression.{IoFunctionSet, ValueAsAnExpression, WomExpression}
-import wom.types.WomOptionalType
-import wom.values.{WomInteger, WomLong, WomString}
-import wom.{RuntimeAttributes, RuntimeAttributesKeys}
-
-import scala.util.Try
-
-object Tool {
-  def inlineJavascriptRequirements(allRequirementsAndHints: Seq[Requirement]): Vector[String] = {
-    val inlineJavscriptRequirements: Seq[InlineJavascriptRequirement] = allRequirementsAndHints.toList.collect {
-      case Inl(ijr:InlineJavascriptRequirement) => ijr
-    }
-
-    inlineJavscriptRequirements.flatMap(_.expressionLib.toList.flatten).toVector
-  }
-}
-
-/**
-  * Abstraction over a Tool (CommandLineTool or ExpressionTool)
-  * Contains common logic to both, mostly to build the wom task definition.
-  */
-trait Tool {
-  def inputs: Array[_ <: InputParameter]
-  def outputs: Array[_ <: OutputParameter]
-  def `class`: String
-  def id: String
-  def requirements: Option[Array[Requirement]]
-  def hints: Option[Array[Hint]]
-  def label: Option[String]
-  def doc: Option[String]
-  def cwlVersion: Option[CwlVersion]
-
-  def asCwl: Cwl
-
-  /** Builds an `Executable` directly from a `Tool` CWL with no parent workflow. */
-  def womExecutable(validator: RequirementsValidator, inputFile: Option[String] = None, ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    val taskDefinition = buildTaskDefinition(validator, Vector.empty)
-    CwlExecutableValidation.buildWomExecutable(taskDefinition, inputFile, ioFunctions, strictValidation)
-  }
-
-  protected def buildTaskDefinition(taskName: String,
-                                    inputDefinitions: List[_ <: Callable.InputDefinition],
-                                    outputDefinitions: List[Callable.OutputDefinition],
-                                    runtimeAttributes: RuntimeAttributes,
-                                    requirementsAndHints: List[cwl.Requirement],
-                                    expressionLib: ExpressionLib): ErrorOr[TaskDefinition]
-
-  private [cwl] implicit val explicitWorkflowName = ParentName(id)
-  protected val inputNames: Set[String] = this.inputs.map(i => FullyQualifiedName(i.id).id).toSet
-
-  // Circe can't create bidirectional links between workflow steps and runs (including `CommandLineTool`s) so this
-  // ugly var is here to link back to a possible parent workflow step. This is needed to navigate upward for finding
-  // requirements in the containment hierarchy. There isn't always a containing workflow step so this is an `Option`.
-  private[cwl] var parentWorkflowStep: Option[WorkflowStep] = None
-
-
-  private def validateRequirementsAndHints(validator: RequirementsValidator): ErrorOr[List[Requirement]] = {
-    import cats.syntax.traverse._
-
-    val allRequirements = requirements.toList.flatten ++ parentWorkflowStep.toList.flatMap(_.allRequirements.list)
-    // All requirements must validate or this fails.
-    val errorOrValidatedRequirements: ErrorOr[List[Requirement]] = allRequirements traverse validator
-
-    errorOrValidatedRequirements map { validRequirements =>
-      // Only Requirement hints, everything else is thrown out.
-      // TODO CWL don't throw them out but pass them back to the caller to do with as the caller pleases.
-      val hintRequirements = hints.toList.flatten.flatMap { _.select[Requirement] }
-      val parentHintRequirements = parentWorkflowStep.toList.flatMap(_.allHints)
-
-      // Throw out invalid Requirement hints.
-      // TODO CWL pass invalid hints back to the caller to do with as the caller pleases.
-      val validHints = (hintRequirements ++ parentHintRequirements).collect { case req if validator(req).isValid => req }
-      validRequirements ++ validHints
-    }
-  }
-
-  private def processRequirement(requirement: Requirement, expressionLib: ExpressionLib): Map[String, WomExpression] = {
-    requirement.fold(RequirementToAttributeMap).apply(inputNames, expressionLib)
-  }
-
-  protected def toolAttributes: Map[String, WomExpression] = Map.empty
-
-  def buildTaskDefinition(validator: RequirementsValidator, parentExpressionLib: ExpressionLib): Checked[TaskDefinition] = {
-    def build(requirementsAndHints: Seq[cwl.Requirement]) = {
-      val id = this.id
-
-      val expressionLib: ExpressionLib = parentExpressionLib ++ inlineJavascriptRequirements(requirementsAndHints)
-
-      // This is basically doing a `foldMap` but can't actually be a `foldMap` because:
-      // - There is no monoid instance for `WomExpression`s.
-      // - We want to fold from the right so the hints and requirements with the lowest precedence are processed first
-      //   and later overridden if there are duplicate hints or requirements of the same type with higher precedence.
-      val attributesMap: Map[String, WomExpression] = requirementsAndHints.foldRight(Map.empty[String, WomExpression])({
-        case (requirement, acc) => acc ++ processRequirement(requirement, expressionLib)
-      })
-
-      val runtimeAttributes: RuntimeAttributes = RuntimeAttributes(attributesMap ++ toolAttributes)
-
-      val schemaDefRequirement: SchemaDefRequirement = requirementsAndHints.flatMap{
-        _.select[SchemaDefRequirement].toList
-      }.headOption.getOrElse(SchemaDefRequirement())
-
-      lazy val localizationOptionalMetaObject: MetaValueElement = MetaValueElementObject(
-        Map(
-          "localization_optional" -> MetaValueElementBoolean(true)
-        )
-      )
-
-      // If input dir min == 0 that's a signal not to localize the input files
-      // https://github.com/dnanexus/dx-cwl/blob/fca163d825beb62f8a3004f2e0a6742805e6218c/dx-cwl#L426
-      val localizationOptional = runtimeAttributes.attributes.get(RuntimeAttributesKeys.DnaNexusInputDirMinKey) match {
-        case Some(ValueAsAnExpression(WomInteger(0))) => Option(localizationOptionalMetaObject)
-        case Some(ValueAsAnExpression(WomLong(0L))) => Option(localizationOptionalMetaObject)
-        case Some(ValueAsAnExpression(WomString("0"))) => Option(localizationOptionalMetaObject)
-        case _ => None
-      }
-
-      val inputDefinitions: List[_ <: Callable.InputDefinition] =
-        this.inputs.map {
-          case input @ InputParameter.IdDefaultAndType(inputId, default, tpe) =>
-            val inputType = tpe.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement)
-            val inputName = FullyQualifiedName(inputId).id
-            val defaultWomValue = default.fold(InputParameter.DefaultToWomValuePoly).apply(inputType).toTry.get
-            OverridableInputDefinitionWithDefault(
-              inputName,
-              inputType,
-              ValueAsAnExpression(defaultWomValue),
-              InputParameter.inputValueMapper(input, tpe, expressionLib, asCwl.schemaOption),
-              localizationOptional
-            )
-          case input @ InputParameter.IdAndType(inputId, tpe) =>
-            val inputType = tpe.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement)
-            val inputName = FullyQualifiedName(inputId).id
-            inputType match {
-              case optional: WomOptionalType =>
-                OptionalInputDefinition(
-                  inputName,
-                  optional,
-                  InputParameter.inputValueMapper(input, tpe, expressionLib, asCwl.schemaOption),
-                  localizationOptional
-                )
-              case _ =>
-                RequiredInputDefinition(
-                  inputName,
-                  inputType,
-                  InputParameter.inputValueMapper(input, tpe, expressionLib, asCwl.schemaOption),
-                  localizationOptional
-                )
-            }
-          case other => throw new UnsupportedOperationException(s"command input parameters such as $other are not yet supported")
-        }.toList
-
-      val outputDefinitions: List[Callable.OutputDefinition] = this.outputs.map {
-        case p @ OutputParameter.IdAndType(cop_id, tpe) =>
-          val womType = tpe.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-          OutputDefinition(FullyQualifiedName(cop_id).id, womType, OutputParameterExpression(p, womType, inputNames, expressionLib, schemaDefRequirement))
-        case other => throw new UnsupportedOperationException(s"Command output parameters such as $other are not yet supported")
-      }.toList
-
-      // The try will succeed if this is a task within a step. If it's a standalone file, the ID will be the file,
-      // so the filename is the fallback.
-      def taskName = Try(FullyQualifiedName(id).id).getOrElse(Paths.get(id).getFileName.toString)
-
-      buildTaskDefinition(taskName, inputDefinitions, outputDefinitions, runtimeAttributes, requirementsAndHints.toList, expressionLib).toEither
-    }
-
-    validateRequirementsAndHints(validator).toEither match {
-      case Right(requirementsAndHints: Seq[cwl.Requirement]) => build(requirementsAndHints)
-      case Left(errors) => Left(errors)
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/TypeAliases.scala b/cwl/src/main/scala/cwl/TypeAliases.scala
deleted file mode 100644
index abbfc9e81e0..00000000000
--- a/cwl/src/main/scala/cwl/TypeAliases.scala
+++ /dev/null
@@ -1,115 +0,0 @@
-package cwl
-
-import cwl.CwlType.CwlType
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import io.circe.Json
-import shapeless.{:+:, CNil}
-import wom.types.WomType
-
-trait TypeAliases {
-
-  type Expression = ECMAScriptFunction :+: ECMAScriptExpression :+: CNil
-
-  // http://www.commonwl.org/v1.0/Workflow.html#InputParameter
-  // http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter
-  type InputParameterFormat = Expression :+: String :+: Array[String] :+: CNil
-  
-  // http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter
-  // http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter
-  type OutputParameterFormat = StringOrExpression
-  
-  type Doc = String :+: Array[String] :+: CNil
-
-  type StringOrExpression = Expression :+: String :+: CNil
-
-  type CwlAny =
-    FileOrDirectory :+:
-      Array[FileOrDirectory] :+:
-      Json :+:
-      CNil
-
-  type WorkflowStepInputId = String
-
-  type Requirement =
-    InlineJavascriptRequirement :+:
-      SchemaDefRequirement :+:
-      DockerRequirement :+:
-      SoftwareRequirement :+:
-      InitialWorkDirRequirement :+:
-      EnvVarRequirement :+:
-      ShellCommandRequirement :+:
-      ResourceRequirement :+:
-      SubworkflowFeatureRequirement :+:
-      ScatterFeatureRequirement :+:
-      MultipleInputFeatureRequirement :+:
-      StepInputExpressionRequirement :+:
-      DnaNexusInputResourceRequirement :+:
-      CNil
-
-  type Hint =
-    Requirement :+:
-      CwlAny :+:
-      CNil
-
-  type MyriadInputType =
-    MyriadInputInnerType :+:
-      Array[MyriadInputInnerType] :+:
-      CNil
-
-  type MyriadInputInnerType =
-    CwlType :+:
-      InputRecordSchema :+:
-      InputEnumSchema :+:
-      InputArraySchema :+:
-      String :+:
-      CNil
-
-  type MyriadOutputType =
-    MyriadOutputInnerType :+:
-      Array[MyriadOutputInnerType] :+:
-      CNil
-
-  type MyriadOutputInnerType =
-    CwlType :+:
-      OutputRecordSchema :+:
-      OutputEnumSchema :+:
-      OutputArraySchema :+:
-      String :+:
-      CNil
-
-  type ResourceRequirementType = Long :+: Expression :+: String :+: CNil
-
-  type SingleOrArrayOfStrings = String :+: Array[String] :+: CNil
-
-  type ScatterVariables = Option[SingleOrArrayOfStrings]
-
-  type FileOrDirectory = File :+: Directory :+: CNil
-
-  type Glob = StringOrExpression :+: Array[String] :+: CNil
-
-  type SecondaryFiles = StringOrExpression :+: Array[StringOrExpression] :+: CNil
-}
-
-object MyriadInputType {
-
-  object InputArraySchema {
-    def unapply(m: MyriadInputType): Option[InputArraySchema] = m.select[MyriadInputInnerType].flatMap(_.select[InputArraySchema])
-  }
-
-  object InputArray {
-    def unapply(m: MyriadInputType): Option[Array[MyriadInputInnerType]] = m.select[Array[MyriadInputInnerType]]
-  }
-
-  object CwlType {
-    def unapply(m: MyriadInputType): Option[CwlType] = {
-      m.select[MyriadInputInnerType].flatMap(_.select[CwlType])
-    }
-  }
-
-  object WomType {
-    def unapply(m: MyriadInputType): Option[WomType] = m match {
-      case CwlType(c) => Option(cwl.cwlTypeToWomType(c))
-      case _ => None
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/Workflow.scala b/cwl/src/main/scala/cwl/Workflow.scala
deleted file mode 100644
index 22b30019ff1..00000000000
--- a/cwl/src/main/scala/cwl/Workflow.scala
+++ /dev/null
@@ -1,246 +0,0 @@
-package cwl
-
-import java.nio.file.Paths
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.Checked
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.CwlVersion._
-import cwl.LinkMergeMethod.LinkMergeMethod
-import cwl.Workflow.{WorkflowInputParameter, WorkflowOutputParameter}
-import cwl.command.ParentName
-import shapeless._
-import shapeless.syntax.singleton._
-import wom.SourceFileLocation
-import wom.callable.{MetaValueElement, WorkflowDefinition}
-import wom.executable.Executable
-import wom.expression.{IoFunctionSet, ValueAsAnExpression}
-import wom.graph.GraphNodePort.{GraphNodeOutputPort, OutputPort}
-import wom.graph._
-import wom.types.{WomOptionalType, WomType}
-
-case class Workflow private(
-                             cwlVersion: Option[CwlVersion],
-                             `class`: Witness.`"Workflow"`.T,
-                             id: String,
-                             inputs: Array[WorkflowInputParameter],
-                             outputs: Array[WorkflowOutputParameter],
-                             steps: Array[WorkflowStep],
-                             requirements: Option[Array[Requirement]],
-                             hints: Option[Array[Hint]],
-                             `$namespaces`: Option[Map[String, String]],
-                             `$schemas`: Option[Array[String]]
-                           ) {
-
-  steps.foreach { _.parentWorkflow = this }
-
-  /** Builds an `Executable` from a `Workflow` CWL with no parent `Workflow` */
-  def womExecutable(validator: RequirementsValidator, inputFile: Option[String] = None, ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    CwlExecutableValidation.buildWomExecutableCallable(womDefinition(validator, Vector.empty), inputFile, ioFunctions, strictValidation)
-  }
-
-  /* Circe can't create bidirectional links between workflow steps and runs (including `Workflow`s) so this
-   * ugly var is here to link back to a possible parent workflow step. This is needed to navigate upward for finding
-   * requirements in the containment hierarchy. There isn't always a containing workflow step so this is an `Option`.
-   */
-  private[cwl] var parentWorkflowStep: Option[WorkflowStep] = None
-
-  val allRequirements: RequirementsAndHints = RequirementsAndHints(requirements.toList.flatten ++ parentWorkflowStep.toList.flatMap { _.allRequirements.list })
-
-  private [cwl] implicit val explicitWorkflowName = ParentName(id)
-
-  lazy val womFqn: Option[wom.graph.FullyQualifiedName] = {
-    explicitWorkflowName.value map { workflowName =>
-      /* Sometimes the workflow name is of the form "parentWorkflowStepName/UUID"
-       * In that case, we don't want the fqn to look like "parentWorkflowStepName.parentWorkflowStepName/UUID"
-       * To avoid that, strip the parentWorkflowStepName from the workflowName
-       */
-      val cleanWorkflowName = parentWorkflowStep
-        .map(_.womFqn.value + "/")
-        .map(workflowName.stripPrefix)
-        .getOrElse(workflowName)
-
-      parentWorkflowStep.map(_.womFqn.combine(cleanWorkflowName))
-        .getOrElse(wom.graph.FullyQualifiedName(cleanWorkflowName))
-    }
-  }
-
-  lazy val allHints: List[Requirement] = {
-    // Just ignore any hint that isn't a Requirement.
-    val requirementHints = hints.toList.flatten.flatMap { _.select[Requirement] }
-    requirementHints ++ parentWorkflowStep.toList.flatMap { _.allHints }
-  }
-
-  val fileNames: List[String] = steps.toList.flatMap(_.run.select[String].toList)
-
-  def outputsTypeMap: WomTypeMap = steps.foldLeft(Map.empty[String, WomType]) {
-    /* Not implemented as a `foldMap` because there is no semigroup instance for `WomType`s.  `foldMap` doesn't know that
-     * we don't need a semigroup instance since the map keys should be unique and therefore map values would never need
-     * to be combined under the same key.
-     */
-    (acc, s) => acc ++ s.typedOutputs
-  }
-
-  def womGraph(workflowName: String, validator: RequirementsValidator, expressionLib: ExpressionLib): Checked[Graph] = {
-    val workflowNameIdentifier = explicitWorkflowName.value.map(WomIdentifier.apply).getOrElse(WomIdentifier(workflowName))
-
-    def womTypeForInputParameter(input: InputParameter): Option[WomType] = {
-      input.`type`.map(_.fold(MyriadInputTypeToWomType).apply(allRequirements.schemaDefRequirement))
-    }
-
-    val typeMap: WomTypeMap =
-      outputsTypeMap ++
-        /* Note this is only looking at the workflow inputs and not recursing into steps, because our current thinking
-         * is that in CWL graph inputs can only be defined at the workflow level.  It's possible that's not actually
-         * correct, but that's the assumption being made here.
-         */
-        inputs.toList.flatMap { i =>
-          womTypeForInputParameter(i).map(i.id -> _).toList
-        }.toMap
-
-    val externalGraphInputNodes: Set[ExternalGraphInputNode] = inputs.map { wip =>
-      val womType: WomType = womTypeForInputParameter(wip).get
-      val parsedInputId = FileAndId(wip.id).id
-      val womId = WomIdentifier(parsedInputId, wip.id)
-      val valueMapper =
-        InputParameter.inputValueMapper(wip, wip.`type`.get, expressionLib, asCwl.schemaOption)
-
-      def optionalWithDefault(memberType: WomType): OptionalGraphInputNodeWithDefault = {
-        val defaultValue = wip.default.get.fold(InputParameter.DefaultToWomValuePoly).apply(womType).toTry.get
-        OptionalGraphInputNodeWithDefault(womId, memberType, ValueAsAnExpression(defaultValue), parsedInputId, valueMapper)
-      }
-
-      womType match {
-        case WomOptionalType(memberType) if wip.default.isDefined => optionalWithDefault(memberType)
-        case _ if wip.default.isDefined => optionalWithDefault(womType)
-        case optional @ WomOptionalType(_) => OptionalGraphInputNode(womId, optional, parsedInputId, valueMapper)
-        case _ => RequiredGraphInputNode(womId, womType, parsedInputId, valueMapper)
-      }
-    }.toSet
-
-    val workflowInputs: Map[String, GraphNodeOutputPort] =
-      externalGraphInputNodes.map { egin =>
-        egin.localName -> egin.singleOutputPort
-      }.toMap
-
-    val graphFromSteps: Checked[Set[GraphNode]] =
-      steps.
-        toList.
-        foldLeft((Set.empty[GraphNode] ++ externalGraphInputNodes).asRight[NonEmptyList[String]])(
-          (nodes, step) => nodes.flatMap(step.callWithInputs(typeMap, this, _, workflowInputs, validator, expressionLib)))
-
-    val graphFromOutputs: Checked[Set[GraphNode]] =
-      outputs.toList.traverse[ErrorOr, GraphNode] {
-        case WorkflowOutputParameter(id, _, _, _, _, _, _, Some(Inl(outputSource: String)), _, Some(tpe)) =>
-          val womType: WomType = tpe.fold(MyriadOutputTypeToWomType).apply(allRequirements.schemaDefRequirement)
-
-          val parsedWorkflowOutput = FileAndId(id)
-          val parsedOutputSource = cwl.FullyQualifiedName(outputSource)
-
-          // Try to find an output port for this cwl output in the set of available nodes
-          def lookupOutputSource(fqn: cwl.FullyQualifiedName): Checked[OutputPort] = {
-            def isRightOutputPort(op: GraphNodePort.OutputPort) = cwl.FullyQualifiedName.maybeApply(op.name) match {
-              case Some(f) => f.id == fqn.id
-              case None => op.internalName == fqn.id
-            }
-
-            def sourceNode(graph: Set[GraphNode]): Checked[GraphNode] = {
-              val findSource: PartialFunction[GraphNode, GraphNode] = fqn match {
-                // A step output becoming a workflow output.
-                case fsi: FileStepAndId => {
-                  case callNode: CallNode if callNode.localName == fsi.stepId => callNode
-                  case scatterNode: ScatterNode if scatterNode.innerGraph.calls.exists(_.localName == fsi.stepId) => scatterNode
-                }
-                // A workflow input recycled back to be an output.
-                case fi: FileAndId => {
-                  case gin: ExternalGraphInputNode if gin.nameInInputSet == fi.id => gin
-                }
-              }
-              graph collectFirst findSource toRight NonEmptyList.one(s"Call Node by name $fqn was not found in set $graph")
-            }
-
-            for {
-              set <- graphFromSteps
-              node <- sourceNode(set)
-              output <- node.outputPorts.find(isRightOutputPort).toChecked(s"looking for ${fqn.id} in call $node output ports ${node.outputPorts}")
-            } yield output
-          }
-
-          lookupOutputSource(parsedOutputSource).map({ port =>
-            val localName = LocalName(parsedWorkflowOutput.id)
-            val fullyQualifiedName = workflowNameIdentifier.fullyQualifiedName.combine(parsedWorkflowOutput.id)
-            val outputIdentifier = WomIdentifier(localName, fullyQualifiedName)
-            PortBasedGraphOutputNode(outputIdentifier, womType, port)
-          }).toValidated
-        case wop => throw new UnsupportedOperationException(s"Workflow output parameters such as $wop are not supported.")
-      }.map(_.toSet).toEither
-
-    for {
-      outputs <- graphFromOutputs
-      steps <- graphFromSteps
-      ret <- Graph.validateAndConstruct(steps ++ externalGraphInputNodes ++ outputs).toEither
-    } yield ret
-  }
-
-  def womDefinition(validator: RequirementsValidator, expressionLib: ExpressionLib): Checked[WorkflowDefinition] = {
-    val name: String = Paths.get(id).getFileName.toString
-    val meta: Map[String, MetaValueElement.MetaValueElementString] = Map.empty
-    val paramMeta: Map[String, MetaValueElement.MetaValueElementString] = Map.empty
-    val lexInfo : Option[SourceFileLocation] = None
-
-    womGraph(name, validator, expressionLib).map(graph =>
-      WorkflowDefinition(
-        name,
-        graph,
-        meta,
-        paramMeta,
-        lexInfo
-      )
-    )
-  }
-
-  def asCwl = Coproduct[Cwl](this)
-}
-object Workflow {
-
-  case class WorkflowInputParameter(id: String,
-                                    label: Option[String] = None,
-                                    secondaryFiles: Option[SecondaryFiles] = None,
-                                    format: Option[InputParameterFormat] = None,
-                                    streamable: Option[Boolean] = None,
-                                    doc: Option[Doc] = None,
-                                    inputBinding: Option[InputCommandLineBinding] = None,
-                                    default: Option[CwlAny] = None,
-                                    `type`: Option[MyriadInputType] = None) extends InputParameter
-
-  case class WorkflowOutputParameter(
-                                      id: String,
-                                      label: Option[String] = None,
-                                      secondaryFiles: Option[SecondaryFiles] = None,
-                                      format: Option[OutputParameterFormat] = None,
-                                      streamable: Option[Boolean] = None,
-                                      doc: Option[Doc] = None,
-                                      outputBinding: Option[CommandOutputBinding] = None,
-                                      outputSource: Option[WorkflowOutputParameter#OutputSource] = None,
-                                      linkMerge: Option[LinkMergeMethod] = None,
-                                      `type`: Option[MyriadOutputType] = None) extends OutputParameter {
-
-    type OutputSource = String :+: Array[String] :+: CNil
-  }
-
-  def apply(cwlVersion: Option[CwlVersion] = Option(CwlVersion.Version1),
-            id: String,
-            inputs: Array[WorkflowInputParameter] = Array.empty,
-            outputs: Array[WorkflowOutputParameter] = Array.empty,
-            steps: Array[WorkflowStep] = Array.empty,
-            requirements: Option[Array[Requirement]] = None,
-            hints: Option[Array[Hint]] = None,
-            namespaces: Option[Map[String, String]] = None,
-            schemas: Option[Array[String]] = None
-           ): Workflow  =
-    Workflow(cwlVersion, "Workflow".narrow, id, inputs, outputs, steps, requirements, hints, namespaces, schemas)
-}
diff --git a/cwl/src/main/scala/cwl/WorkflowStep.scala b/cwl/src/main/scala/cwl/WorkflowStep.scala
deleted file mode 100644
index cf39f261bae..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStep.scala
+++ /dev/null
@@ -1,537 +0,0 @@
-package cwl
-
-import cats.Monoid
-import cats.data.NonEmptyList
-import cats.data.Validated._
-import cats.syntax.either._
-import cats.syntax.foldable._
-import cats.syntax.monoid._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import cwl.ScatterLogic.ScatterVariablesPoly
-import cwl.ScatterMethod._
-import cwl.WorkflowStep.{WorkflowStepInputFold, _}
-import cwl.WorkflowStepInput._
-import cwl.command.ParentName
-import shapeless.{:+:, CNil, _}
-import wom.callable.Callable
-import wom.callable.Callable._
-import wom.graph.CallNode._
-import wom.graph.GraphNodePort.{GraphNodeOutputPort, OutputPort}
-import wom.graph._
-import wom.graph.expression.ExpressionNode
-import wom.types.WomType
-import wom.values.WomValue
-import wom.graph.{FullyQualifiedName => WomFullyQualifiedName}
-
-/**
-  * An individual job to run.
-  *
-  * @see <a href="http://www.commonwl.org/v1.0/Workflow.html#WorkflowStep">CWL Spec | Workflow Step</a>
-  * @param run Purposefully not defaulted as it's required in the specification and it is unreasonable to not have something to run.
-  */
-case class WorkflowStep(
-                         id: String,
-                         in: Array[WorkflowStepInput] = Array.empty,
-                         out: WorkflowStepOutputType,
-                         run: Run,
-                         requirements: Option[Array[Requirement]] = None,
-                         hints: Option[Array[Hint]] = None,
-                         label: Option[String] = None,
-                         doc: Option[String] = None,
-                         scatter: ScatterVariables = None,
-                         scatterMethod: Option[ScatterMethod] = None) {
-
-  run.select[Workflow].foreach(_.parentWorkflowStep = Option(this))
-  run.select[CommandLineTool].foreach(_.parentWorkflowStep = Option(this))
-  run.select[ExpressionTool].foreach(_.parentWorkflowStep = Option(this))
-
-  // We're scattering if scatter is defined, and if it's a list of variables the list needs to be non empty
-  private val isScattered: Boolean = scatter exists { _.select[Array[String]].forall(_.nonEmpty) }
-
-  // Circe can't create bidirectional links between workflows and workflow steps so this ugly var is here to link
-  // back to the parent workflow. This is needed to navigate upward for finding requirements in the containment
-  // hierarchy. There is always a workflow containing a workflow step so this is not an `Option`.
-  private[cwl] var parentWorkflow: Workflow = _
-
-  lazy val allRequirements = RequirementsAndHints(requirements.toList.flatten ++ parentWorkflow.allRequirements.list)
-
-  lazy val womFqn: WomFullyQualifiedName = {
-    implicit val parentName = parentWorkflow.explicitWorkflowName
-    val localFqn = cwl.FullyQualifiedName.maybeApply(id).map(_.id).getOrElse(id)
-    parentWorkflow.womFqn.map(_.combine(localFqn)).getOrElse(wom.graph.FullyQualifiedName(localFqn))
-  }
-
-  lazy val allHints: List[Requirement] = {
-    // Just ignore any hint that isn't a Requirement.
-    val requirementHints = hints.toList.flatten.flatMap { _.select[Requirement] }
-    requirementHints ++ parentWorkflow.allHints
-  }
-
-  // If the step is being scattered over, apply the necessary transformation to get the final output array type.
-  lazy val scatterTypeFunction: WomType => WomType = scatter.map(_.fold(ScatterVariablesPoly)) match {
-    case Some(Nil) => identity[WomType]
-    case Some(nonEmpty) => ScatterLogic.scatterGatherPortTypeFunction(scatterMethod, NonEmptyList.fromListUnsafe(nonEmpty))
-    case _ =>  identity[WomType]
-  }
-
-  def typedOutputs: WomTypeMap = {
-    implicit val parentName = ParentName(id)
-    // Find the type of the outputs of the run section
-    val runOutputTypes = run.fold(RunOutputsToTypeMap).apply(allRequirements.schemaDefRequirement)
-      .map({
-        case (runOutputId, womType) => cwl.FullyQualifiedName(runOutputId).id -> womType
-      })
-    // Use them to find get the final type of the workflow outputs, and only the workflow outputs
-    out.map({ stepOutput =>
-      val stepOutputValue = stepOutput.select[WorkflowStepOutput].map(_.id).getOrElse(stepOutput.select[String].get)
-      val stepOutputId = cwl.FullyQualifiedName(stepOutputValue)
-      stepOutputValue -> scatterTypeFunction(runOutputTypes(stepOutputId.id))
-    }).toMap
-  }
-
-  def fileName: Option[String] = run.select[String]
-
-  /**
-    * Generates all GraphNodes necessary to represent call nodes and input nodes
-    * Recursive because dependencies are discovered as we iterate through inputs and corresponding
-    * upstream nodes need to be generated on the fly.
-    *
-    * Example:
-    *
-    * CWL:
-    * inputs:
-    *   
-id: workflow_input_A

-    *    type: string[]
-    *   -id: workflow_input_B

-    *    type: string[]
-    *   
-id: workflow_input_C

-    *    type: string


-    * steps:

-    *   -id: echo
-    *    run: echo.cwl
-    *    scatter: input0
-    *    in:
-    *      -id:input0
-    *       source:
-    *         - "#workflow_input_A"
-    *         - "#workflow_input_B"

-    *       valueFrom:"bonjour"
-    *
-    *      -id: input1
-    *   
    source: "#workflow_input_C"
-    *       valueFrom:"$(inputs.input0)"
-    *
-    * WOM Diagram:
-    *
-    *  +------------+   +------------+   +------------+
-    *  | WF Input A |   | WF Input B |   | WF Input C |
-    *  +--------+---+ +-+------------+   +------+-----+
-    *           |     |                         |
-    *           |     |                         |
-    *     +-----v-----v+                 +------v-----+
-    *     | StepInput0 |                 | StepInput1 |
-    *     | MergeLogic |                 | MergeLogic |
-    *     +-----+------+                 +----+-------+
-    *           |                             |
-    *  +----------------------------------------------+
-    *  |        |                             |       |
-    *  | +------v----------+              +---v--+    |
-    *  | | ScatterVariable +------------+ | OGIN |    |
-    *  | +-----+-----------+            | +--+-+-+    |
-    *  |       |                        |    | |      |
-    *  | +-----v----+                   |    | |      |
-    *  | |StepInput0<------------------------+ |      |
-    *  | |Expression|                   |      |      |
-    *  | +----+-----+                +--v------v+     |
-    *  |      |                      |StepInput1|     |
-    *  |      |                      |Expression|     |
-    *  |      |                      +------+---+     |
-    *  |      |    +-----------+            |         |
-    *  |      +----> Call Node <------------+         |
-    *  |           +-----------+                      |
-    *  |                                 Scatter Node |
-    *  +----------------------------------------------+
-    *
-    * MergeNode: If the step input has one or more sources, a merge node will be created and responsible for merging
-    *   those input sources together. It will NOT evaluate the valueFrom field of the input.
-    *
-    * ScatterVariableNode: If the step input is being scattered over, a scatter variable node will be created and will
-    *   act as a proxy inside the scatter graph for the shards of the scatter. It depends on an upstream merge node outputing an array
-    *   and will provide at runtime shard values for other nodes of the scatter graph.
-    *
-    * OGIN: If the step has at least one input being scattered over, there will be a scatter node created.
-    *   For inputs that are NOT being scattered over but still have one or more input sources (and hence a merge node), an OGIN
-    *   will be created to act as a proxy to the merge node outside the scatter graph.
-    *
-    * ExpressionNode: If an input has a valueFrom field, an expression node will be created to evaluate the expression.
-    *   An important fact to note is that the expression needs access to all other input values
-    *   AFTER their source, default value and shard number has been determined but
-    *   BEFORE their (potential) valueFrom is evaluated (see http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)
-    *   This is why on the above diagram, StepInput0Expression depends on the OGIN, and StepInput1Expression depends on the scatter variable.
-    */
-  def callWithInputs(typeMap: WomTypeMap,
-                     workflow: Workflow,
-                     knownNodes: Set[GraphNode],
-                     workflowInputs: Map[String, GraphNodeOutputPort],
-                     validator: RequirementsValidator,
-                     expressionLib: ExpressionLib): Checked[Set[GraphNode]] = {
-
-    implicit val parentName = workflow.explicitWorkflowName
-
-    val scatterLookupSet =
-      scatter.toList.
-        flatMap(_.fold(StringOrStringArrayToStringList)).
-        map(id => cwl.FullyQualifiedName(id).id)
-
-    def isStepScattered(workflowStepInputId: String) = scatterLookupSet.contains(workflowStepInputId)
-
-    val unqualifiedStepId: WomIdentifier = {
-      cwl.FullyQualifiedName.maybeApply(id).map({ fqn =>
-        WomIdentifier(LocalName(fqn.id), womFqn)
-      }).getOrElse(WomIdentifier(id))
-    }
-
-    def typedRunInputs: Map[String, Option[MyriadInputType]] = run.fold(RunToInputTypeMap).apply(parentName)
-
-    def allIdentifiersRecursively(nodes: Set[GraphNode]): Set[WomIdentifier] = nodes.flatMap({
-      case w: WorkflowCallNode=> Set(w.identifier)
-      case c: CommandCallNode => Set(c.identifier)
-      case e: ExpressionCallNode => Set(e.identifier)
-      // When a node a call node is being scattered over, it is wrapped inside a scatter node. We still don't want to
-      // duplicate it though so look inside scatter nodes to see if it's there.
-      case scatter: ScatterNode => allIdentifiersRecursively(scatter.innerGraph.nodes)
-      case _ => Set.empty[WomIdentifier]
-    })
-
-    // To avoid duplicating nodes, return immediately if we've already covered this node
-    val haveWeSeenThisStep: Boolean = allIdentifiersRecursively(knownNodes).contains(unqualifiedStepId)
-
-    if (haveWeSeenThisStep) Right(knownNodes)
-    else {
-      val callable: Checked[Callable] = run match {
-        case Run.CommandLineTool(clt) => clt.buildTaskDefinition(validator, expressionLib)
-        case Run.Workflow(wf) => wf.womDefinition(validator, expressionLib)
-        case Run.ExpressionTool(et) => et.buildTaskDefinition(validator, expressionLib)
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-
-      val callNodeBuilder = new CallNode.CallNodeBuilder()
-
-      /*
-       * Method used to fold over the list of inputs declared by this step.
-       * Note that because we work on saladed CWL, all ids are fully qualified at this point (e.g: file:///path/to/file/three_step.cwl#cgrep/pattern
-       * The goal of this method is two fold (pardon the pun):
-       *   1) link each input of the step to an output port (which at this point can be from a different step or from a workflow input)
-       *   2) accumulate the nodes created along the way to achieve 1)
-       */
-      def foldStepInput(currentFold: Checked[WorkflowStepInputFold], workflowStepInput: WorkflowStepInput): Checked[WorkflowStepInputFold] = currentFold flatMap {
-        fold =>
-          /*
-            * Try to find in the given set an output port named stepOutputId in a call node named stepId
-            * This is useful when we've determined that the input points to an output of a different step and we want
-            * to get the corresponding output port.
-           */
-          def findThisInputInSet(set: Set[GraphNode], stepId: String, stepOutputId: String): Checked[OutputPort] = {
-            for {
-              // We only care for outputPorts of call nodes or scatter nodes
-              call <- set.collectFirst {
-                case callNode: CallNode if callNode.localName == stepId => callNode
-                case scatterNode: ScatterNode if scatterNode.innerGraph.calls.exists(_.localName == stepId) => scatterNode
-              }.
-                toRight(NonEmptyList.one(s"stepId $stepId not found in known Nodes $set"))
-              output <- call.outputPorts.find(_.internalName == stepOutputId).
-                toRight(NonEmptyList.one(s"step output id $stepOutputId not found in ${call.outputPorts}"))
-            } yield output
-          }
-
-          /*
-           * Build a wom node for the given step and return the newly created nodes
-           * This is useful when we've determined that the input belongs to an upstream step that we haven't covered yet
-           */
-          def buildUpstreamNodes(upstreamStepId: String, accumulatedNodes: Set[GraphNode]): Checked[Set[GraphNode]] =
-          // Find the step corresponding to this upstreamStepId in the set of all the steps of this workflow
-            for {
-              step <- workflow.steps.find { step => cwl.FullyQualifiedName(step.id).id == upstreamStepId }.
-                toRight(NonEmptyList.one(s"no step of id $upstreamStepId found in ${workflow.steps.map(_.id).toList}"))
-              call <- step.callWithInputs(typeMap, workflow, accumulatedNodes, workflowInputs, validator, expressionLib)
-            } yield call
-
-          def fromWorkflowInput(inputName: String): Checked[Map[String, OutputPort]] = {
-            // Try to find it in the workflow inputs map, if we can't it's an error
-            workflowInputs.collectFirst {
-              case (inputId, port) if inputName == inputId => Map(inputId -> port).asRight[NonEmptyList[String]]
-            } getOrElse s"Can't find workflow input for $inputName".invalidNelCheck[Map[String, OutputPort]]
-          }
-
-          def fromStepOutput(stepId: String, stepOutputId: String, accumulatedNodes: Set[GraphNode]): Checked[(Map[String, OutputPort], Set[GraphNode])] = {
-            // First check if we've already built the WOM node for this step, and if so return the associated output port
-            findThisInputInSet(accumulatedNodes, stepId, stepOutputId).map(outputPort => (Map(s"$stepId/$stepOutputId" -> outputPort), accumulatedNodes))
-              .orElse {
-                // Otherwise build the upstream nodes and look again in those newly created nodes
-                for {
-                  newNodes <- buildUpstreamNodes(stepId, accumulatedNodes)
-                  sourceMappings <- findThisInputInSet(newNodes, stepId, stepOutputId).map(outputPort => Map(s"$stepId/$stepOutputId" -> outputPort))
-                } yield (sourceMappings, newNodes ++ accumulatedNodes)
-              }
-          }
-
-          lazy val workflowStepInputId = cwl.FullyQualifiedName(workflowStepInput.id).id
-
-          def updateFold(sourceMappings: Map[String, OutputPort], newNodes: Set[GraphNode]): Checked[WorkflowStepInputFold] = {
-            val typeExpectedByRunInput: Option[cwl.MyriadInputType] = typedRunInputs.get(workflowStepInputId).flatten
-
-            val isThisStepScattered = isStepScattered(workflowStepInputId)
-
-            workflowStepInput.toMergeNode(sourceMappings, expressionLib, typeExpectedByRunInput, isThisStepScattered, allRequirements.schemaDefRequirement) match {
-              // If the input needs a merge node, build it and add it to the input fold
-              case Some(mergeNode) =>
-                mergeNode.toEither.map({ node =>
-                  fold |+| WorkflowStepInputFold(
-                    mergeNodes = Map(workflowStepInput -> node),
-                    generatedNodes = newNodes
-                  )
-                })
-              case None => (fold |+| WorkflowStepInputFold(generatedNodes = newNodes)).validNelCheck
-            }
-          }
-
-          /*
-           * We intend to validate that all of these sources point to a WOM Outputport that we know about.
-           *
-           * If we don't know about them, we find upstream nodes and build them (see "buildUpstreamNodes").
-           */
-          val baseCase = (Map.empty[String, OutputPort], fold.generatedNodes).asRight[NonEmptyList[String]]
-          val inputMappingsAndGraphNodes: Checked[(Map[String, OutputPort], Set[GraphNode])] =
-            workflowStepInput.sources.foldLeft(baseCase) {
-              case (Right((sourceMappings, graphNodes)), inputSource) =>
-                /*
-                 * Parse the inputSource (what this input is pointing to)
-                 * 2 cases:
-                 *   - points to a workflow input
-                 *   - points to an upstream step
-                 */
-                cwl.FullyQualifiedName(inputSource) match {
-                  // The source points to a workflow input, which means it should be in the workflowInputs map
-                  case FileAndId(_, _, inputId) => fromWorkflowInput(inputId).map(newMap => (sourceMappings ++ newMap, graphNodes))
-                  // The source points to an output from a different step
-                  case FileStepAndId(_, _, stepId, stepOutputId) => fromStepOutput(stepId, stepOutputId, graphNodes).map({ case (newMap, newNodes) => (sourceMappings ++ newMap, newNodes) })
-                }
-              case (other, _) => other
-            }
-
-          inputMappingsAndGraphNodes.flatMap((updateFold _).tupled)
-      }
-
-      /*
-       * Folds over input definitions and build an InputDefinitionFold
-       */
-      def foldInputDefinition(pointerNode: Map[String, GraphNodeWithSingleOutputPort])
-                             (inputDefinition: InputDefinition): ErrorOr[InputDefinitionFold] = {
-        inputDefinition match {
-          case _ if pointerNode.contains(inputDefinition.name) =>
-            val expressionNode = pointerNode(inputDefinition.name)
-            InputDefinitionFold(
-              mappings = List(inputDefinition -> expressionNode.inputDefinitionPointer),
-              callInputPorts = Set(callNodeBuilder.makeInputPort(inputDefinition, expressionNode.singleOutputPort))
-            ).validNel
-
-          // No expression node mapping, use the default
-          case withDefault @ OverridableInputDefinitionWithDefault(_, _, expression, _, _) =>
-            InputDefinitionFold(
-              mappings = List(withDefault -> Coproduct[InputDefinitionPointer](expression))
-            ).validNel
-
-          // Required input without default value and without mapping, this is a validation error
-          case RequiredInputDefinition(requiredName, _, _, _) =>
-            s"Input ${requiredName.value} is required and is not bound to any value".invalidNel
-
-          // Optional input without mapping, defaults to empty value
-          case optional: OptionalInputDefinition =>
-            InputDefinitionFold(
-              mappings = List(optional -> Coproduct[InputDefinitionPointer](optional.womType.none: WomValue))
-            ).validNel
-          case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-        }
-      }
-
-      /*
-        If the step is being scattered over, then merge nodes can't directly be referenced because they will be outside the scatter graph.
-        For inputs that are being scattered over, a scatter variable has already been created, but for the others we need
-        an OGIN to link the merge node to the inner scatter graph.
-       */
-      def buildOGINs(mergeNodes: Map[WorkflowStepInput, ExpressionNode],
-                     scatterVariables: Map[WorkflowStepInput, ScatterVariableNode]): Map[WorkflowStepInput, OuterGraphInputNode] = if (isScattered) {
-        mergeNodes
-          .collect({
-            case (input, mergeNode) if !scatterVariables.contains(input) =>
-              val ogin = OuterGraphInputNode(
-                WomIdentifier(input.parsedId).combine("OGIN"),
-                mergeNode.singleOutputPort,
-                preserveScatterIndex = false
-              )
-              input -> ogin
-          })
-      } else Map.empty
-
-      /*
-        * For inputs that have a valueFrom field, create an ExpressionNode responsible for evaluating the expression.
-        * Note that this expression might need access to the other input values, so make each expression node depend on all other
-        * inputs.
-       */
-      def buildStepInputValueFromNodes(sharedInputNodes: Map[WorkflowStepInput, GraphNodeWithSingleOutputPort]): Checked[Map[String, ExpressionNode]] = {
-        // Add new information to the typeMap from the shard input nodes.
-        lazy val updatedTypeMap = sharedInputNodes.map({
-          // If the input node is a scatter variable, make sure the type is the item type, not the array type, as the expression node
-          // will operate on shards not on the whole scattered array.
-          case (stepInput, scatter: ScatterVariableNode) => stepInput.parsedId -> scatter.womType
-          case (stepInput, node) => stepInput.parsedId -> node.singleOutputPort.womType
-        }) ++ typeMap
-
-        // Go over each step input and create an expression node for those which have a valueFrom
-        in.toList.collect({
-          case stepInput @ WorkflowStepInput(_, _, _, _, Some(valueFrom)) =>
-            // Transform the shared inputs map into a usable map to create the expression.
-            lazy val sharedInputMap: Map[String, OutputPort] = sharedInputNodes.map({
-              case (siblingStepInput, graphNode) => siblingStepInput.parsedId -> graphNode.singleOutputPort
-            })
-            val typeExpectedByRunInput: Option[cwl.MyriadInputType] = typedRunInputs.get(stepInput.parsedId).flatten
-            val isThisStepScattered = isStepScattered(stepInput.parsedId)
-
-            stepInput.toExpressionNode(valueFrom, typeExpectedByRunInput, isThisStepScattered, sharedInputMap, updatedTypeMap, expressionLib, allRequirements.schemaDefRequirement).map(stepInput.parsedId -> _)
-        })
-          .sequence[ErrorOr, (String, ExpressionNode)]
-          .toEither
-          .map(_.toMap)
-      }
-
-      //inputs base case consist of the nodes we already know about
-      val baseCase = WorkflowStepInputFold(generatedNodes = knownNodes).asRight[NonEmptyList[String]]
-
-      // WorkflowStepInputFold contains the mappings from step input to ExpressionNode as well as all created nodes
-      val stepInputFoldCheck: Checked[WorkflowStepInputFold] = in.foldLeft(baseCase)(foldStepInput)
-
-      /*
-        * This (big) flatMap builds nodes from top to bottom in the diagram above.
-        * If necessary, the scatter node is built last as it wraps some of the other nodes.
-       */
-      for {
-        /* ************************************ */
-        /* ************ Merge Nodes *********** */
-        /* ************************************ */
-        // Build merge nodes and recursively generates other call nodes that we haven't seen so far
-        stepInputFold <- stepInputFoldCheck
-        // Extract the merge nodes from the fold
-        mergeNodes = stepInputFold.mergeNodes
-
-        /* ************************************ */
-        /* ****** Scatter Variable Nodes ****** */
-        /* ************************************ */
-        scatterVariableNodes <- ScatterLogic.buildScatterVariableNodes(scatter, mergeNodes, unqualifiedStepId.localName.value)
-
-        /* ************************************ */
-        /* *************** OGINS ************** */
-        /* ************************************ */
-        ogins = buildOGINs(mergeNodes, scatterVariableNodes)
-
-        /* ************************************ */
-        /* ********* Expression Nodes ********* */
-        /* ************************************ */
-        // Aggregate the generated nodes so far. This map will be used to generate expression nodes, so the order of aggregation matters:
-        // scatter variables and ogins take precedence over merge nodes (see diagram)
-        aggregatedMapForValueFromNodes = mergeNodes ++ scatterVariableNodes ++ ogins
-        // Build expression nodes for inputs that have a valueFrom field
-        stepInputValueFromNodes <- buildStepInputValueFromNodes(aggregatedMapForValueFromNodes)
-
-        /* ************************************ */
-        /* ************* Call Node ************ */
-        /* ************************************ */
-        // Get the callable object for this step
-        checkedCallable <- callable
-        // Aggregate again by adding generated expression nodes. Again order matters here, expression nodes override other nodes.
-        aggregatedMapForInputDefinitions = aggregatedMapForValueFromNodes.asIdentifierMap ++ stepInputValueFromNodes
-        // Assign each of the callable's input definition to an output port from the pointer map
-        inputDefinitionFold <- checkedCallable.inputs.foldMap(foldInputDefinition(aggregatedMapForInputDefinitions)).toEither
-        // Build the call node
-        callAndNodes = callNodeBuilder.build(unqualifiedStepId, checkedCallable, inputDefinitionFold, Set.empty, None)
-        // Depending on whether the step is being scattered, invoke the scatter node builder or not
-
-        /* ************************************ */
-        /* ************ Scatter Node ********** */
-        /* ************************************ */
-        scatterNodeOrExposedNodes <- if (isScattered) {
-          ScatterLogic.buildScatterNode(
-            callAndNodes,
-            NonEmptyList.fromListUnsafe(scatterVariableNodes.values.toList),
-            ogins.values.toSet,
-            stepInputValueFromNodes.values.toSet,
-            scatterMethod).map(Set(_))
-        } else {
-          // If there's no scatter node then we need to return the expression nodes and the call node explicitly
-          // as they won't be contained in the scatter inner graph
-          (stepInputValueFromNodes.values.toSet + callAndNodes.node).validNelCheck
-        }
-
-        /*
-          * Return all the nodes that need to be made available to the workflow graph:
-          * knownNodes: this method is used to fold over steps so we don't want to forget to accumulate known nodes
-          * mergeNodes: they're always outside of the scatter so always return them
-          * generatedNodes: nodes generated recursively to build this node
-          * scatterNodeOrExposedNodes: see explanation above
-         */
-        allNodes = knownNodes ++ mergeNodes.values.toSet ++ stepInputFold.generatedNodes ++ scatterNodeOrExposedNodes
-      } yield allNodes
-    }
-  }
-}
-
-/**
-  * @see <a href="http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepOutput">WorkflowstepOutput</a>
-  */
-case class WorkflowStepOutput(id: String)
-
-object WorkflowStep {
-
-  // A monoid can't be derived automatically for this class because it contains a Map[String, ExpressionNode],
-  // and there's no monoid defined over ExpressionNode
-  implicit val workflowStepInputFoldMonoid: Monoid[WorkflowStepInputFold] = new Monoid[WorkflowStepInputFold] {
-    override def empty: WorkflowStepInputFold = WorkflowStepInputFold()
-    override def combine(x: WorkflowStepInputFold, y: WorkflowStepInputFold): WorkflowStepInputFold = {
-      WorkflowStepInputFold(
-        mergeNodes = x.mergeNodes ++ y.mergeNodes,
-        generatedNodes = x.generatedNodes ++ y.generatedNodes
-      )
-    }
-  }
-
-  private [cwl] case class WorkflowStepInputFold(mergeNodes: Map[WorkflowStepInput, ExpressionNode] = Map.empty,
-                                                 generatedNodes: Set[GraphNode] = Set.empty)
-
-  /**
-    * Maps input variable (to be scattered over) to their scatter variable node
-    */
-  type ScatterMappings = Map[ExpressionNode, ScatterVariableNode]
-
-  val emptyOutputs: WorkflowStepOutputType = Array.empty
-
-  type Run =
-    String :+:
-      CommandLineTool :+:
-      ExpressionTool :+:
-      Workflow :+:
-      CNil
-
-  object Run {
-    object String { def unapply(run: Run): Option[String] = run.select[String] }
-    object Workflow { def unapply(run: Run): Option[Workflow] = run.select[Workflow] }
-    object CommandLineTool { def unapply(run: Run): Option[CommandLineTool] = run.select[CommandLineTool] }
-    object ExpressionTool { def unapply(run: Run): Option[ExpressionTool] = run.select[ExpressionTool] }
-  }
-
-  type WorkflowStepOutputInnerType = String :+: WorkflowStepOutput :+: CNil
-  type WorkflowStepOutputType = Array[WorkflowStepOutputInnerType]
-}
diff --git a/cwl/src/main/scala/cwl/WorkflowStepInput.scala b/cwl/src/main/scala/cwl/WorkflowStepInput.scala
deleted file mode 100644
index a3d028dbdd6..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStepInput.scala
+++ /dev/null
@@ -1,155 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import cwl.InputParameter.DefaultToWomValuePoly
-import cwl.LinkMergeMethod.LinkMergeMethod
-import cwl.WorkflowStepInput.InputSource
-import cwl.command.ParentName
-import shapeless.{:+:, CNil}
-import wom.expression.ValueAsAnExpression
-import wom.graph.GraphNodePort.OutputPort
-import wom.graph.WomIdentifier
-import wom.graph.expression.{AnonymousExpressionNode, ExposedExpressionNode, ExpressionNode, PlainAnonymousExpressionNode}
-import wom.types._
-
-case class WorkflowStepInput(
-                              id: String,
-                              source: Option[InputSource] = None,
-                              linkMerge: Option[LinkMergeMethod] = None,
-                              default: Option[CwlAny] = None,
-                              valueFrom: Option[StringOrExpression] = None) {
-
-  def parsedId(implicit parentName: ParentName) = FullyQualifiedName(id).id
-
-  def toExpressionNode(valueFromExpression: StringOrExpression,
-                       runInputExpectedType: Option[cwl.MyriadInputType],
-                       isScattered: Boolean,
-                       sourceMappings:Map[String, OutputPort],
-                       outputTypeMap: Map[String, WomType],
-                       expressionLib: ExpressionLib,
-                       schemaDefRequirement: SchemaDefRequirement
-                      )(implicit parentName: ParentName): ErrorOr[ExpressionNode] = {
-    val inputs = sourceMappings.keySet
-    val upstreamMergeType = outputTypeMap.get(parsedId)
-
-    (for {
-      // we may have several sources, we make sure to have a type common to all of them.
-      // In the case where there's no input source, we currently wrap the valueFrom value in a WomString (see WorkflowStepInputExpression)
-      inputType <- WorkflowStepInput.determineValueFromType(upstreamMergeType, runInputExpectedType, isScattered, schemaDefRequirement)
-      womExpression = WorkflowStepInputExpression(parsedId, valueFromExpression, inputType, inputs, expressionLib)
-      identifier = WomIdentifier(id).combine("expression")
-      ret <- ExposedExpressionNode.fromInputMapping(identifier, womExpression, inputType, sourceMappings).toEither
-    } yield ret).toValidated
-  }
-
-  /**
-    *
-    * @param sourceMappings The outputports to which this source refers
-    * @param matchingRunInputType This input matches an input declared in the workflowstep's "run".  This is that step's declared type
-    * @return
-    */
-  def toMergeNode(sourceMappings: Map[String, OutputPort],
-                  expressionLib: ExpressionLib,
-                  matchingRunInputType: Option[MyriadInputType],
-                  isScattered: Boolean,
-                  schemaDefRequirement: SchemaDefRequirement
-                 ): Option[ErrorOr[ExpressionNode]] = {
-
-    val identifier = WomIdentifier(id).combine("merge")
-    val mapType = sourceMappings.map({ case (k, v) => k -> v.womType })
-
-    val maybeMatchingRunInputWomType: Option[WomType] = matchingRunInputType.map(_.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement))
-
-    def makeNode(head: (String, OutputPort), tail: List[(String, OutputPort)]) = for {
-      inputType <- determineMergeType(mapType, maybeMatchingRunInputWomType)
-      womExpression = WorkflowStepInputMergeExpression(this, inputType, NonEmptyList.of(head, tail: _*), expressionLib)
-      node <- AnonymousExpressionNode.fromInputMapping(identifier, womExpression, sourceMappings, PlainAnonymousExpressionNode.apply).toEither
-    } yield node
-
-    val matchingRunInputWomType: WomType = maybeMatchingRunInputWomType.getOrElse(WomAnyType)
-    lazy val defaultValue = default.map { _.fold(DefaultToWomValuePoly).apply(matchingRunInputWomType) }
-
-    sourceMappings.toList match {
-      case head :: tail => Option(makeNode(head, tail).toValidated)
-      case Nil =>
-        defaultValue map { _ map { d =>
-            PlainAnonymousExpressionNode(identifier, ValueAsAnExpression(d), matchingRunInputWomType, Map.empty)
-        } }
-    }
-  }
-
-  def determineMergeType(sources: Map[String, WomType], expectedTypeAsWom: Option[WomType]): Checked[WomType] = {
-    WorkflowStepInput.determineMergeType(sources, linkMerge, expectedTypeAsWom, default.isDefined)
-  }
-
-  lazy val sources: List[String] = source.toList.flatMap(_.fold(StringOrStringArrayToStringList))
-
-  lazy val effectiveLinkMerge: LinkMergeMethod = linkMerge.getOrElse(LinkMergeMethod.MergeNested)
-}
-
-object WorkflowStepInput {
-  type InputSource = String :+: Array[String] :+: CNil
-
-  implicit class EnhancedStepInputMap[A](val map: Map[WorkflowStepInput, A]) extends AnyVal {
-    def asIdentifierMap(implicit parentName: ParentName): Map[String, A] = {
-      map.map({ case (stepInput, value) => stepInput.parsedId -> value })
-    }
-  }
-
-  def determineValueFromType(mergedSourcesType: Option[WomType],
-                             expectedType: Option[MyriadInputType],
-                             isScattered: Boolean,
-                             schemaDefRequirement: SchemaDefRequirement): Checked[WomType] = {
-    val expectedTypeAsWom: Option[WomType] = expectedType.map(_.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement))
-
-    expectedTypeAsWom.getOrElse(WomStringType).asRight
-  }
-
-  def determineMergeType(sources: Map[String, WomType],
-                         linkMerge: Option[LinkMergeMethod],
-                         expectedTypeAsWom: Option[WomType],
-                         hasDefault: Boolean): Checked[WomType] = {
-
-    (sources.toList, expectedTypeAsWom, linkMerge) match {
-      // If there is a single source and no explicit merge method, use the type of the source (unpacked if it's optional
-      // and there's a default since the default would be used if there's no supplied value).
-      case (List((_, WomOptionalType(sourceType))), _, None) if hasDefault => sourceType.asRight
-      case (List((_, opt @ WomOptionalType(_))), _, None) => opt.asRight
-      case (List((_, sourceType)), _, None) => sourceType.asRight
-      // If there is a single source and merge nested is specified, wrap it into an array
-      case (List((_, sourceType)), _, Some(LinkMergeMethod.MergeNested)) => WomArrayType(sourceType).asRight
-      // If there are multiple sources and either no merge method or merge nested, find the closest common type.
-      // TODO: This is technically not enough, cwltool supports sources with totally different types, creating an array with multiple types
-      // Maybe WomCoproduct can help
-      case (_, _, Some(LinkMergeMethod.MergeNested) | None) => WomArrayType(WomType.homogeneousTypeFromTypes(sources.values)).asRight
-
-      //If sink parameter is an array and merge_flattened is used, must validate input & output types are equivalent before proceeding
-      case (_, Some(arrayType @ WomArrayType(itemType)), Some(LinkMergeMethod.MergeFlattened)) if typesToItemMatch(sources.values, itemType) => arrayType.asRight
-      // If sink parameter is not an array and merge flattened is used, validate that the sources types matche the sink type
-      case (_, Some(targetType), Some(LinkMergeMethod.MergeFlattened)) if typesToItemMatch(sources.values, targetType) => WomArrayType(targetType).asRight
-      // If the types are not compatible, fail
-      case (_, Some(targetType), Some(LinkMergeMethod.MergeFlattened)) =>
-        s"could not verify that types $sources and the items type of the run's InputArraySchema $targetType were compatible".invalidNelCheck
-
-      //We don't have type information from the run input so we gather up the sources and try to determine a common type amongst them.
-      case _ => WomType.homogeneousTypeFromTypes(sources.values).asRight
-    }
-  }
-
-  def typesToItemMatch(lst: Iterable[WomType], target: WomType): Boolean = {
-    val effectiveInputType = WomType.homogeneousTypeFromTypes(lst)
-
-    typeToItemMatch(effectiveInputType, target)
-  }
-
-  def typeToItemMatch(upstream: WomType, downstream: WomType): Boolean = {
-    upstream match {
-      case WomType.RecursiveType(innerType) => typeToItemMatch(innerType, downstream)
-      case other => other == downstream
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/WorkflowStepInputExpression.scala b/cwl/src/main/scala/cwl/WorkflowStepInputExpression.scala
deleted file mode 100644
index 476d7f44ef5..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStepInputExpression.scala
+++ /dev/null
@@ -1,51 +0,0 @@
-package cwl
-
-import cats.syntax.validated._
-import wom.expression.{FileEvaluation, IoFunctionSet}
-import wom.types._
-import wom.values._
-
-final case class WorkflowStepInputExpression(inputName: String,
-                                             valueFrom: StringOrExpression,
-                                             override val cwlExpressionType: WomType,
-                                             inputs: Set[String],
-                                             override val expressionLib: ExpressionLib) extends CwlWomExpression {
-
-  override def sourceString = inputName
-
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet) = {
-    valueFrom match {
-      // If valueFrom is a constant string value, use this as the value for this input parameter.
-      // TODO: need to handle case where this is a parameter reference, it currently looks like a String to us!
-      case StringOrExpression.String(value) => WomString(value).validNel
-
-      /*
-       * If valueFrom is a parameter reference or expression, it must be evaluated to yield the actual value to be assiged to the input field.
-       *
-       * The self value of in the parameter reference or expression must be the value of the parameter(s) specified in the source field,
-       * or null if there is no source field.
-       *
-       * The value of inputs in the parameter reference or expression must be the input object to the workflow step after
-       * assigning the source values, applying default, and then scattering. The order of evaluating valueFrom among step
-       * input parameters is undefined and the result of evaluating valueFrom on a parameter must not be visible to
-       * evaluation of valueFrom on other parameters.
-       */
-      case StringOrExpression.Expression(expression) =>
-        //used to determine the value of "self" as expected by CWL Spec
-        def selfValue = inputValues.get(inputName) match {
-          case Some(value) => value
-          case None => WomOptionalValue(WomNothingType, None)
-        }
-
-        val parameterContext = ParameterContext(ioFunctionSet, expressionLib, inputValues, selfValue)
-
-        expression.fold(EvaluateExpression).apply(parameterContext)
-      case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-    }
-  }
-
-  //this is input, so not producing any output files
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType) =
-    Set.empty[FileEvaluation].validNel
-}
-
diff --git a/cwl/src/main/scala/cwl/WorkflowStepInputMergeExpression.scala b/cwl/src/main/scala/cwl/WorkflowStepInputMergeExpression.scala
deleted file mode 100644
index bc7d4f43d75..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStepInputMergeExpression.scala
+++ /dev/null
@@ -1,84 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.Checked
-import common.validation.ErrorOr.ErrorOr
-import cwl.InputParameter.DefaultToWomValuePoly
-import wom.expression.{FileEvaluation, IoFunctionSet}
-import wom.graph.GraphNodePort.OutputPort
-import wom.types.WomType
-import wom.values.{WomArray, WomFile, WomOptionalValue, WomValue}
-
-final case class WorkflowStepInputMergeExpression(input: WorkflowStepInput,
-                                                  cwlExpressionType: WomType,
-                                                  stepInputMappingHead: NonEmptyList[(String, OutputPort)],
-                                                  override val expressionLib: ExpressionLib) extends CwlWomExpression {
-
-  private val allStepInputMappings = stepInputMappingHead.toList
-  private val allStepInputSources = allStepInputMappings.map(_._1)
-
-  override def sourceString: String = s"${input.id}-Merge-Expression"
-  override def inputs: Set[String] = allStepInputSources.toSet
-
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
-    def lookupValue(key: String): ErrorOr[WomValue] =
-      inputValues.
-        get(key).
-        toValidNel(s"source value $key not found in input values ${inputValues.mkString("\n")} and no default value provided.  Graph Inputs were ${allStepInputSources.mkString("\n")}")
-
-    def validateSources(sources: List[String]): ErrorOr[List[WomValue]] =
-      sources.
-        traverse(lookupValue)
-
-    def isEmptyOptionalValue(womValue: WomValue): Boolean = womValue match {
-      case WomOptionalValue(_, None) => true
-      case _ => false
-    }
-
-    (allStepInputSources, input.effectiveLinkMerge, input.default) match {
-      // When we have a single source but no value was provided for it and there's a default.
-      case (List(source), LinkMergeMethod.MergeNested, Some(default)) if isEmptyOptionalValue(inputValues(source)) =>
-        default.fold(DefaultToWomValuePoly).apply(cwlExpressionType)
-
-      case (List(source), LinkMergeMethod.MergeNested, _) => lookupValue(source)
-
-      //When we have several sources, validate they are all present and provide them as a nested array
-      case (sources, LinkMergeMethod.MergeNested, _) => validateSources(sources).map(WomArray.apply)
-
-      case (sources, LinkMergeMethod.MergeFlattened, _) =>
-        val validatedSourceValues: Checked[List[WomValue]] =
-          validateSources(sources).toEither
-
-        def flatten: WomValue => List[WomValue] = {
-          case WomArray(_, value) => value.toList
-          case WomOptionalValue(_, Some(value)) => flatten(value)
-          case other => List(other)
-        }
-
-        //This is the meat of "merge_flattened," where we find arrays and concatenate them to form one array
-        val flattenedValidatedSourceValues: Checked[List[WomValue]] = validatedSourceValues.map(_.flatMap(flatten))
-
-        flattenedValidatedSourceValues.map(list => WomArray(list)).toValidated
-
-      case (List(id), _, _) => lookupValue(id)
-      case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-    }
-  }
-
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
-    if (allStepInputMappings.size > 1) {
-      // TODO add MultipleInputFeatureRequirement logic in here
-      "MultipleInputFeatureRequirement not supported yet".invalidNel
-    } else {
-      val (inputName, _) = allStepInputMappings.head
-      inputTypes(inputName).collectAsSeq({
-        case file: WomFile => file
-      }).toSet[WomFile].map(FileEvaluation.requiredFile).validNel
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/command/ParentName.scala b/cwl/src/main/scala/cwl/command/ParentName.scala
deleted file mode 100644
index 6e34096d4f3..00000000000
--- a/cwl/src/main/scala/cwl/command/ParentName.scala
+++ /dev/null
@@ -1,10 +0,0 @@
-package cwl.command
-
-object ParentName {
-  def empty: ParentName = ParentName(None)
-  def apply(id: String): ParentName = ParentName(id.split("#").tail.headOption)
-}
-
-case class ParentName(value: Option[String]) {
-  def stripParent(in: String) = value.map(v => in.stripPrefix(s"$v/")).getOrElse(in)
-}
diff --git a/cwl/src/main/scala/cwl/command/StringCommandPart.scala b/cwl/src/main/scala/cwl/command/StringCommandPart.scala
deleted file mode 100644
index 9ec668231fb..00000000000
--- a/cwl/src/main/scala/cwl/command/StringCommandPart.scala
+++ /dev/null
@@ -1,18 +0,0 @@
-package cwl.command
-
-import cats.syntax.validated._
-import common.validation.ErrorOr.ErrorOr
-import wom._
-import wom.callable.RuntimeEnvironment
-import wom.expression.IoFunctionSet
-import wom.graph.LocalName
-import wom.values._
-
-case class StringCommandPart(literal: String) extends CommandPart {
-  override def instantiate(inputsMap: Map[LocalName, WomValue],
-                           functions: IoFunctionSet,
-                           valueMapper: (WomValue) => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] =
-    // TODO CWL shellquotes by default, but this shellquotes everything. Only shellquote what should be shellquoted.
-    List(InstantiatedCommand(literal.shellQuote)).validNel
-}
diff --git a/cwl/src/main/scala/cwl/internal/CommandPartSortingAlgorithm.scala b/cwl/src/main/scala/cwl/internal/CommandPartSortingAlgorithm.scala
deleted file mode 100644
index eb6ed0410ce..00000000000
--- a/cwl/src/main/scala/cwl/internal/CommandPartSortingAlgorithm.scala
+++ /dev/null
@@ -1,71 +0,0 @@
-package cwl.internal
-
-import cats.data.Kleisli._
-import cats.data.ReaderT
-import cats.data.Validated._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cwl.CommandLineTool._
-import cwl.command.ParentName
-import cwl.{ArgumentCommandLineBinding, ArgumentToCommandPart, CommandLineTool, CommandPartExpression, FullyQualifiedName, InputParameter, MyriadInputTypeToSortedCommandParts, MyriadInputTypeToWomType}
-import shapeless.Coproduct
-import wom.types.WomStringType
-
-object CommandPartSortingAlgorithm {
-  def argumentCommandParts(arguments: Option[Array[CommandLineTool.Argument]]): CommandPartExpression[List[SortKeyAndCommandPart]] =
-      // arguments is an Option[Array[Argument]], the toList.flatten gives a List[Argument]
-    arguments.toList.flatten
-      // zip the index because we need it in the sorting key
-      .zipWithIndex.flatTraverse(argumentToCommandPart.tupled)
-
-  def argumentToCommandPart: (Argument, Int) => CommandPartExpression[List[SortKeyAndCommandPart]] = (argument, index) => ReaderT {
-    case ((requirementsAndHints, expressionLib, _)) =>
-      val part = argument.fold(ArgumentToCommandPart).apply(requirementsAndHints.hasShellCommandRequirement, expressionLib)
-      // Get the position from the binding if there is one
-      val position = argument.select[ArgumentCommandLineBinding].flatMap(_.position)
-        .map(Coproduct[StringOrInt](_)).getOrElse(CommandLineTool.DefaultPosition)
-
-      // The key consists of the position followed by the index
-      val sortingKey = CommandBindingSortingKey(List(position, Coproduct[StringOrInt](index)))
-
-      List(SortKeyAndCommandPart(sortingKey, part)).validNel
-
-  }
-
-  def inputBindingsCommandParts(inputs: Array[CommandInputParameter]): CommandPartExpression[List[SortKeyAndCommandPart]] =
-    inputs.toList.flatTraverse(inputBindingsCommandPart)
-
-  def inputBindingsCommandPart(inputParameter: CommandInputParameter): CommandPartExpression[List[SortKeyAndCommandPart]] =
-    ReaderT{ case ((hintsAndRequirements, expressionLib, inputValues)) =>
-      val parsedName = FullyQualifiedName(inputParameter.id)(ParentName.empty).id
-
-      val womType = inputParameter.`type`.map(_.fold(MyriadInputTypeToWomType).apply(hintsAndRequirements.schemaDefRequirement)).getOrElse(WomStringType)
-
-      val defaultValue = inputParameter.default.map(_.fold(InputParameter.DefaultToWomValuePoly).apply(womType))
-
-      inputValues
-        .collectFirst({ case (inputDefinition, womValue) if inputDefinition.name == parsedName => womValue.validNel })
-        .orElse(defaultValue) match {
-        case Some(Valid(value)) =>
-          // See http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-          lazy val initialKey = CommandBindingSortingKey.empty
-            .append(inputParameter.inputBinding, Coproduct[StringOrInt](parsedName))
-
-          inputParameter.`type`.toList.
-            flatMap{
-              _.fold(MyriadInputTypeToSortedCommandParts).
-                apply(
-                  inputParameter.inputBinding,
-                  value,
-                  initialKey.asNewKey,
-                  hintsAndRequirements.hasShellCommandRequirement,
-                  expressionLib,
-                  hintsAndRequirements.schemaDefRequirement)
-            }.validNel
-        case Some(Invalid(errors)) => Invalid(errors)
-        case None => s"Could not find an input value for input $parsedName in ${inputValues.prettyString}".invalidNel
-      }
-    }
-
-}
diff --git a/cwl/src/main/scala/cwl/internal/CwlEcmaScriptDecoder.scala b/cwl/src/main/scala/cwl/internal/CwlEcmaScriptDecoder.scala
deleted file mode 100644
index f7f54d3db1c..00000000000
--- a/cwl/src/main/scala/cwl/internal/CwlEcmaScriptDecoder.scala
+++ /dev/null
@@ -1,124 +0,0 @@
-package cwl.internal
-
-import cats.syntax.apply._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cats.instances.option._
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.{Directory, File, FileOrDirectory}
-import org.mozilla.javascript.{ConsString, NativeArray, NativeObject}
-import shapeless.Coproduct
-import wom.types.WomNothingType
-import wom.values._
-
-import scala.jdk.CollectionConverters._
-
-class CwlEcmaScriptDecoder {
-
-  def decode(value: AnyRef): ErrorOr[WomValue] =
-    value match {
-      case map: NativeObject if map.get("class") == "File" => decodeFile(map.asScala.toMap).flatMap(_.asWomValue)
-      case map: NativeObject if map.get("class") == "Directory" => decodeDirectory(map.asScala.toMap).flatMap(_.asWomValue)
-
-      case map: NativeObject => decodeMap(map.asScala.toMap)
-      case array: NativeArray =>
-        val anyList = array.asScala.toList
-        val anyRefArray = anyList.asInstanceOf[List[AnyRef]]
-        anyRefArray.traverse(decode).map(WomArray.apply)
-
-      //we represent nulls as this type because Wom doesn't have a "null" value, but it does have a nothing type
-      //If you wish this to be otherwise please tidy up the Expression interpolator as well
-      case null => WomOptionalValue(WomNothingType, None).valid
-
-      case string: String => WomString(string).valid
-      case consString: ConsString => WomString(consString.toString).valid
-      case int: java.lang.Integer => WomInteger(int).valid
-      case long: java.lang.Long => WomLong(long).valid
-      case double: java.lang.Double if double == double.doubleValue.floor && !double.isInfinite =>
-        WomInteger(double.intValue).valid
-      case double: java.lang.Double => WomFloat(double).valid
-      case boolean: java.lang.Boolean => WomBoolean(boolean).valid
-      case unknown => s"While decoding the output $value of the Javascript interpreter, we encountered $unknown and were unable to reify it.".invalidNel
-    }
-
-  def decodeMap(map: Map[Any, Any]): ErrorOr[WomValue] = {
-    val realMap: Map[AnyRef, AnyRef] = map.asInstanceOf[Map[AnyRef, AnyRef]]
-
-    val tupleList = realMap.toList.traverse{
-      case (k,v) => (k.toString.validNel: ErrorOr[String], decode(v)).tupled
-    }
-    val mapWomValues =  tupleList.map(_.toMap)
-    mapWomValues.map(WomObject.apply)
-  }
-
-  /**
-    * Called to decode a cwl File or Directory.
-    */
-  def decodeDirectoryOrFile(value: Any): ErrorOr[FileOrDirectory] = {
-    val invalidValue = s"Not a valid CWL map or directory: $value".invalidNel
-
-    value match {
-      case map: NativeObject if map.get("class") == "File" => decodeFile(map.asScala.toMap).map(Coproduct[FileOrDirectory](_))
-      case map: NativeObject if map.get("class") == "Directory" => decodeDirectory(map.asScala.toMap).map(Coproduct[FileOrDirectory](_))
-      case _ => invalidValue
-    }
-  }
-
-  /**
-    * Called to decode an array of cwl File or Directory instances.
-    */
-  def decodeDirectoryOrFiles(value: Any): ErrorOr[Array[FileOrDirectory]] = {
-    value match {
-      case na: NativeArray => na.asScala.toList.traverse(decodeDirectoryOrFile).map(_.toArray)
-    }
-  }
-
-  /**
-    * Called to decode a map value using a supplied function.
-    */
-  def decodeMapValue[A](map: Map[Any, Any], key: String, f: Any => A): ErrorOr[Option[A]] = {
-    map.get(key).traverse(anyRef => validate(f(anyRef)))
-  }
-
-  /**
-    * Called to decode an array of files or directories from a map value.
-    */
-  def decodeMapDirectoryOrFiles(map: Map[Any, Any],
-                                key: String): ErrorOr[Option[Array[FileOrDirectory]]] = {
-    map.get(key).traverse(decodeDirectoryOrFiles)
-  }
-
-  /**
-    * Called to decode a cwl File.
-    */
-  def decodeFile(map: Map[Any, Any]): ErrorOr[File] = {
-    val location = decodeMapValue(map, "location", _.toString)
-    val path = decodeMapValue(map, "path", _.toString)
-    val basename = decodeMapValue(map, "basename", _.toString)
-    val checksum = decodeMapValue(map, "checksum", _.toString)
-    val size = decodeMapValue(map, "size", _.toString.toDouble.toLong)
-    val secondaryFiles = decodeMapDirectoryOrFiles(map, "secondaryFiles")
-    val format = decodeMapValue(map, "format", _.toString)
-    val contents = decodeMapValue(map, "contents", _.toString)
-
-    (location, path, basename, checksum, size, secondaryFiles, format, contents).mapN(
-      File(_, _, _, _, _, _, _, _)
-    )
-  }
-
-  /**
-    * Called to decode a cwl Directory.
-    */
-  def decodeDirectory(map: Map[Any, Any]): ErrorOr[Directory] = {
-    val location = decodeMapValue(map, "location", _.toString)
-    val path = decodeMapValue(map, "path", _.toString)
-    val basename = decodeMapValue(map, "basename", _.toString)
-    val listing = decodeMapDirectoryOrFiles(map, "listing")
-
-    (location, path, basename, listing).mapN(
-      Directory(_, _, _, _)
-    )
-  }
-}
diff --git a/cwl/src/main/scala/cwl/internal/EcmaScriptEncoder.scala b/cwl/src/main/scala/cwl/internal/EcmaScriptEncoder.scala
deleted file mode 100644
index e4aed51e215..00000000000
--- a/cwl/src/main/scala/cwl/internal/EcmaScriptEncoder.scala
+++ /dev/null
@@ -1,123 +0,0 @@
-package cwl.internal
-
-import cats.data.Validated.Valid
-import common.validation.ErrorOr.ErrorOr
-import cwl.internal.EcmaScriptUtil.{ECMAScriptVariable, ESArray, ESObject, ESPrimitive}
-import cwl.{Directory, File}
-import mouse.all._
-import wom.values._
-
-/**
-  * Converts a WomValue into a javascript compatible value.
-  */
-class EcmaScriptEncoder {
-
-  /**
-    * Base implementation converts any WomPrimitive (except WomFile) into a javascript compatible value.
-    *
-    * Inputs, and returned output must be one of:
-    * - WomString
-    * - WomBoolean
-    * - WomFloat
-    * - WomInteger
-    * - WomMap
-    * - WomArray
-    * - A "WomNull" equal to WomOptionalValue(WomNothingType, None)
-    *
-    * The WomMap keys and values, and WomArray elements must be the one of the above, recursively.
-    *
-    * Instances of WomFile are not permitted, and must be already converted to one of the above types.
-    *
-    * @param value A WOM value.
-    * @return The javascript equivalent.
-    */
-  def encode(value: WomValue): ECMAScriptVariable = {
-    value match {
-      case file: WomFile => encodeFileOrDirectory(file)
-      case WomOptionalValue(_, None) => ESPrimitive(null)
-      case WomOptionalValue(_, Some(innerValue)) => encode(innerValue)
-      case WomString(string) => string |> ESPrimitive
-      case WomInteger(int) => Int.box(int) |> ESPrimitive
-      case WomLong(long) => Long.box(long) |> ESPrimitive
-      case WomFloat(double) => Double.box(double) |> ESPrimitive
-      case WomBoolean(boolean) => Boolean.box(boolean) |> ESPrimitive
-      case WomArray(_, array) => array.toList.map(encode).toArray |> ESArray
-      case WomMap(_, map) => map.map{
-        case (mapKey, mapValue) => (encodeString(mapKey), encode(mapValue))
-      } |> ESObject
-      case objectLike: WomObjectLike => objectLike.values.map{
-        case (key, innerValue) => (key, encode(innerValue))
-      } |> ESObject
-      case WomCoproductValue(_, womValue) => encode(womValue)
-      case WomEnumerationValue(_, womValue) => womValue |> ESPrimitive
-      case _ => throw new RuntimeException(s"$getClass is unable to encode value: $value")
-    }
-  }
-
-  def encodeString(value: WomValue): String = {
-    encode(value) match {
-      case ESPrimitive(string: String) => string
-
-      //In the case of a non-string, we evaluate a small snippet of Ecma script meant to coerce the object to a string
-      // http://2ality.com/2012/03/converting-to-string.html
-      case _ =>
-        val jsString: ErrorOr[WomValue] = EcmaScriptUtil.evalStructish(""""" + other""","other" -> value, encoder = this)
-        jsString match {
-          case Valid(WomString(string)) => string
-          case unexpected => throw new RuntimeException(s"Expected to convert '$value' to a String but ended up with '$unexpected'")
-        }
-    }
-  }
-
-  /**
-    * Encodes a sequence of wom file or directory values.
-    */
-  def encodeFileOrDirectories(values: Seq[WomFile]): ESArray = {
-    ESArray(values.toList.map(encodeFileOrDirectory).toArray)
-  }
-
-  /**
-    * Encodes a wom file or directory value.
-    */
-  def encodeFileOrDirectory(value: WomFile): ECMAScriptVariable = {
-    value match {
-      case directory: WomUnlistedDirectory => encodeDirectory(WomMaybeListedDirectory(directory.value))
-      case file: WomSingleFile => encodeFile(WomMaybePopulatedFile(file.value))
-      case glob: WomGlobFile => encodeFile(WomMaybePopulatedFile(glob.value))
-      case directory: WomMaybeListedDirectory => encodeDirectory(directory)
-      case file: WomMaybePopulatedFile => encodeFile(file)
-    }
-  }
-
-  /**
-    * Encodes a wom file.
-    */
-  def encodeFile(file: WomMaybePopulatedFile): ECMAScriptVariable =
-    List(
-      Option("class" -> ESPrimitive("File")),
-      file.valueOption.map("location" -> ESPrimitive(_)),
-      file.valueOption.map("path" -> ESPrimitive(_)),
-      Option("basename" -> (File.basename(file.value) |> ESPrimitive)),
-      Option("dirname" -> (File.dirname(file.value) |> ESPrimitive)),
-      Option("nameroot" -> (File.nameroot(file.value) |> ESPrimitive)),
-      Option("nameext" -> (File.nameext(file.value) |> ESPrimitive)),
-      file.checksumOption.map("checksum" -> ESPrimitive(_)),
-      file.sizeOption.map(Long.box).map("size" -> ESPrimitive(_)),
-      Option("secondaryFiles" -> encodeFileOrDirectories(file.secondaryFiles)),
-      file.formatOption.map("format" -> ESPrimitive(_)),
-      file.contentsOption.map("contents" -> ESPrimitive(_))
-    ).flatten.toMap |> ESObject
-
-  /**
-    * Encodes a wom directory.
-    */
-  def encodeDirectory(directory: WomMaybeListedDirectory): ESObject = {
-    List(
-      Option("class" -> ESPrimitive("Directory")),
-      directory.valueOption.map("location" -> ESPrimitive(_)),
-      Option(directory.value).map("path" -> ESPrimitive(_)),
-      Option("basename" -> ESPrimitive(Directory.basename(directory.value))),
-      directory.listingOption.map(encodeFileOrDirectories).map("listing" -> _)
-    ).flatten.toMap |> ESObject
-  }
-}
diff --git a/cwl/src/main/scala/cwl/internal/EcmaScriptUtil.scala b/cwl/src/main/scala/cwl/internal/EcmaScriptUtil.scala
deleted file mode 100644
index d2c5def745f..00000000000
--- a/cwl/src/main/scala/cwl/internal/EcmaScriptUtil.scala
+++ /dev/null
@@ -1,128 +0,0 @@
-package cwl.internal
-
-import common.collections.EnhancedCollections._
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import org.mozilla.javascript._
-import wom.values._
-
-import scala.concurrent.duration._
-import scala.util.Try
-
-/**
-  * This implementation depends on Mozilla Rhino.
-  *
-  * Previously we attempted to use Nashorn which is built into the JDK, but we encountered at least 2 situations where
-  * it didn't work and we found no workarounds to satisfy the use cases.  Namely, JSON.stringify of a Map and calling "sort" on an array.
-  */
-//noinspection VariablePatternShadow
-object EcmaScriptUtil {
-  def writeValue(value: ECMAScriptVariable)(context: Context, scope: Scriptable): AnyRef =
-    value match {
-      case ESObject(fields) =>
-        val newObj = context.newObject(scope)
-
-        fields.toList.foreach{
-          case (name, value) =>
-            val newerObj = writeValue(value)(context, scope)
-            ScriptableObject.putProperty(newObj, name, newerObj)
-        }
-        newObj
-
-      case ESArray(array) =>
-        val newObj = context.newArray(scope, array.length)
-
-        array.toList.zipWithIndex.foreach {
-          case (js, index) =>
-
-            val newerObj = writeValue(js)(context, scope)
-            ScriptableObject.putProperty(newObj, index, newerObj)
-
-        }
-        newObj
-
-      case ESPrimitive(obj) => obj
-    }
-
-  /**
-    * Runs ECMAScript as JS1.8 (aka ES5)
-    *
-    * Uses RhinoSandbox to reduce chances injected JS wreaks havoc on the JVM.
-    *
-    * @see https://en.wikipedia.org/wiki/ECMAScript#Version_correspondence
-    */
-  def evalRaw(expr: String)(block: (Context, Scriptable) => Unit): AnyRef = {
-    // TODO: Parameterize and update callers to pass in source name, max duration, max instructions, etc.?
-    // For now, be very liberal with scripts giving 60 seconds of unrestricted CPU usage and unlimited instructions.
-    val sourceName = "<ecmascript>"
-    val maxDuration: Duration = 60.seconds
-    val maxInstructionsOption: Option[Int] = None
-    val strict = true
-    val languageVersionOption = Option(Context.VERSION_1_8)
-
-    val sandbox = new EnhancedRhinoSandbox(strict, languageVersionOption)
-    if (maxDuration.isFinite) {
-      sandbox.setMaxDuration(maxDuration.toMillis.toInt)
-    }
-    maxInstructionsOption foreach sandbox.setInstructionLimit
-    sandbox.setUseSafeStandardObjects(true)
-    sandbox.setUseSealedScope(true)
-
-    sandbox.eval(sourceName, expr)(block)
-  }
-
-  sealed trait ECMAScriptVariable
-
-  case class ESObject(fields: Map[String, ECMAScriptVariable]) extends ECMAScriptVariable
-  case class ESArray(array: Array[ECMAScriptVariable]) extends ECMAScriptVariable {
-    override def toString: String = s"ESArray(${array.toList})"
-  }
-  case class ESPrimitive(anyRef: AnyRef) extends ECMAScriptVariable
-
-  /**
-    * Evaluates a javascript expression using maps of WOM values.
-    *
-    * TODO: Once custom types are supported as WomValue, this custom method won't be required.
-    *
-    * @param expr      The javascript expression.
-    * @param rawValues A map filled with WOM values.
-    * @param mapValues A map of maps filled with WOM values of various types.
-    * @param encoder   Encodes wom values to javascript.
-    * @param decoder   Decodes wom values from javascript.
-    * @return The result of the expression.
-    */
-  def evalStructish(expr: String,
-                    rawValues: (String, WomValue),
-                    mapValues: Map[String, Map[String, WomValue]] = Map.empty,
-                    encoder: EcmaScriptEncoder,
-                    decoder: CwlEcmaScriptDecoder = new CwlEcmaScriptDecoder): ErrorOr[WomValue] = {
-    def evaluate = evalRaw(expr) { (context, scope) =>
-
-      val (key, value) = rawValues
-
-      val jsValue = encoder.encode(value)
-      val field = writeValue(jsValue)(context, scope)
-      ScriptableObject.putProperty(scope, key, field)
-
-      val jsMap = mapValues.safeMapValues{ _.safeMapValues(encoder.encode) }
-
-      jsMap foreach {
-        case (scopeId, nestedMap) =>
-
-          val newObj = context.newObject(scope)
-          nestedMap.toList foreach {
-            case (key, value) =>
-              val newerObj = writeValue(value)(context, scope)
-              ScriptableObject.putProperty(newObj, key, newerObj)
-          }
-          ScriptableObject.putProperty(scope, scopeId, newObj)
-      }
-
-    }
-    
-    for {
-      evaluated <- Try(evaluate).toErrorOr
-      decoded <- decoder.decode(evaluated)
-    } yield decoded
-  }
-}
diff --git a/cwl/src/main/scala/cwl/internal/EnhancedRhinoSandbox.scala b/cwl/src/main/scala/cwl/internal/EnhancedRhinoSandbox.scala
deleted file mode 100644
index 405c04fdaa2..00000000000
--- a/cwl/src/main/scala/cwl/internal/EnhancedRhinoSandbox.scala
+++ /dev/null
@@ -1,167 +0,0 @@
-package cwl.internal
-
-import cwl.internal.EnhancedRhinoSandbox._
-import delight.rhinosandox.internal._
-import org.mozilla.javascript._
-
-import scala.jdk.CollectionConverters._
-import scala.reflect._
-
-/**
-  * Extends the RhinoSandboxImpl with some fixes and enhancements using java reflection.
-  *
-  * @param strict Should evaluation be strict.
-  * @param languageVersionOption The optional language version to set.
-  */
-class EnhancedRhinoSandbox(strict: Boolean = true, languageVersionOption: Option[Int] = None) extends RhinoSandboxImpl {
-
-  // Allows easier reflection access to private fields
-  private lazy val sandboxImpl: RhinoSandboxImpl = this
-
-  /**
-    * Similar to RhinoSandbox.eval but passes back the context and scope for mutating before evaluation.
-    *
-    * With the original RhinoSandbox.eval not sure how to:
-    * - Create (nested) arrays
-    * - Create (nested) maps
-    * - Set JS/ES version
-    *
-    * So this uses a copy-port of the original, using reflection to read some of RhinoSandbox's private variables.
-    *
-    * Instead of hiding the context and scope as in RhinoSandbox.eval, both are passed back through the block.
-    *
-    * TODO: Ask RhinoSandbox if hacks are even needed, and if so contrib back patches so that reflection isn't required.
-    * - Is there a way to pass nested maps/arrays via a `java.util.Map[String, Object]`, or must we use our `block`?
-    * - Additionally: can we skip passing `context` to a block as a thread may just call `Context.getCurrentContext()`?
-    *
-    * @see https://maxrohde.com/2015/08/06/sandboxing-javascript-in-java-app-link-collection/
-    * @see https://github.com/javadelight/delight-rhino-sandbox/blob/9f5a073/src/main/java/delight/rhinosandox/internal/RhinoSandboxImpl.java#L100-L123
-    * @see delight.rhinosandox.internal.RhinoSandboxImpl#assertContextFactory()
-    */
-  def eval(sourceName: String, js: String)(block: (Context, Scriptable) => Unit): AnyRef = {
-    assertContextFactory()
-    val sandboxImpl_contextFactory = PrivateField(sandboxImpl, "contextFactory").as[ContextFactory]
-    // RhinoSandbox diff: eval has enterContext inside the try, but Rhino docs say it belongs outside.
-    // https://www-archive.mozilla.org/rhino/apidocs/org/mozilla/javascript/ContextFactory.html#enterContext%28%29
-    val context = sandboxImpl_contextFactory.enterContext
-    try {
-      // RhinoSandbox diff: allow setting the language version
-      languageVersionOption foreach context.setLanguageVersion
-      assertSafeScope(context)
-      val sandboxImpl_globalScope = PrivateField(sandboxImpl, "globalScope").as[ScriptableObject]
-      val sandboxImpl_sealScope = PrivateField(sandboxImpl, "sealScope").as[Boolean]
-      if (sandboxImpl_sealScope) {
-        sandboxImpl_globalScope.sealObject()
-      }
-      val sandboxImpl_safeScope = PrivateField(sandboxImpl, "safeScope").as[ScriptableObject]
-      val instanceScope = context.newObject(sandboxImpl_safeScope)
-      instanceScope.setPrototype(sandboxImpl_safeScope)
-      instanceScope.setParentScope(null)
-
-      block(context, instanceScope)
-
-      // RhinoSandbox diff: allow strict JS/ES evaluation
-      // See note at top assertContextFactory as to why we have to put 'use strict'; here.
-      // All on one line to avoid off-by-one error for javascript error messages that report line numbers.
-      // Could also pass zero as the line number, but the RhinoSandbox passes hard codes line number one also.
-      val script = if (strict) s"'use strict';$js" else js
-      context.evaluateString(instanceScope, script, sourceName, 1, null)
-    } finally {
-      Context.exit()
-    }
-  }
-
-  /**
-    * Stricter context factory modified from RhinoSandboxImpl.assertContextFactory().
-    *
-    * ContextFactory.initGlobal() is called within a static synchronized block.
-    * The globalScope initialized via initSafeStandardObjects instead of initStandardObjects.
-    *
-    * The default implementation uses a SafeContext that allows non-strict JS/ES. We would ideally set
-    * FEATURE_STRICT_MODE to true but that only produces warnings and doesn't return an error. Unfortunately when
-    * FEATURE_WARNING_AS_ERROR is enabled then non-strict Rhino warnings like "missing ;" throw errors. Instead,
-    * "'use strict';" is injected before scripts.
-    */
-  override def assertContextFactory(): Unit = {
-    if (PrivateField(sandboxImpl, "contextFactory").as[ContextFactory] != null) {
-      return
-    }
-
-    val _safeContext = new SafeContext
-    PrivateField(sandboxImpl, "contextFactory") := _safeContext
-    val _hasExplicitGlobal = ContextFactory.hasExplicitGlobal
-    val _not = !_hasExplicitGlobal
-    // RhinoSandbox diff: the global does not like to be initialized twice. Synchronize initialization.
-    val sandboxImpl_contextFactory = PrivateField(sandboxImpl, "contextFactory").as[SafeContext]
-    if (_not) initGlobalSynchronized(sandboxImpl_contextFactory)
-
-    val sandboxImpl_instructionLimit = PrivateField(sandboxImpl, "instructionLimit").as[Int]
-    PrivateField(sandboxImpl_contextFactory, "maxInstructions") := sandboxImpl_instructionLimit
-    val sandboxImpl_maxDuration = PrivateField(sandboxImpl, "maxDuration").as[Long]
-    PrivateField(sandboxImpl_contextFactory, "maxRuntimeInMs") := sandboxImpl_maxDuration
-    // RhinoSandbox diff: assertContextFactory has enterContext inside the try, but Rhino docs say it belongs outside.
-    // https://www-archive.mozilla.org/rhino/apidocs/org/mozilla/javascript/ContextFactory.html#enterContext%28%29
-    val context = sandboxImpl_contextFactory.enterContext
-    try {
-      // RhinoSandbox diff: Default globalScope is created via initStandardObjects instead of initSafeStandardObjects.
-      // initStandardObjects would add the various java packages into the global scope, including `java.io.File`, etc.
-      PrivateField(sandboxImpl, "globalScope") := context.initSafeStandardObjects(null, false)
-      val sandboxImpl_inScope = PrivateField(sandboxImpl, "inScope").as[java.util.Map[String, AnyRef]]
-      val _entrySet = sandboxImpl_inScope.entrySet
-      val sandboxImpl_globalScope = PrivateField(sandboxImpl, "globalScope").as[ScriptableObject]
-      for (entry <- _entrySet.asScala) {
-        sandboxImpl_globalScope.put(
-          entry.getKey,
-          sandboxImpl_globalScope,
-          Context.toObject(entry.getValue, sandboxImpl_globalScope))
-      }
-      val parameters = Array(classOf[String])
-      val dealMethod = classOf[RhinoEvalDummy].getMethod("eval", parameters: _*)
-      val _rhinoEval = new RhinoEval("eval", dealMethod, sandboxImpl_globalScope)
-      sandboxImpl_globalScope.defineProperty("eval", _rhinoEval, ScriptableObject.DONTENUM)
-    } finally {
-      Context.exit()
-    }
-  }
-
-}
-
-object EnhancedRhinoSandbox {
-
-  /**
-    * Get or sets a private field.
-    *
-    * @param obj  The instance to retrieve the field from.
-    * @param name The name of the field.
-    * @tparam A The class to retrieve the value from. The field MUST exist on this class, and not a superclass.
-    */
-  final case class PrivateField[A: ClassTag](obj: A, name: String) {
-    private[this] def field = {
-      val field = classTag[A].runtimeClass.getDeclaredField(name)
-      field.setAccessible(true)
-      field
-    }
-
-    def as[B]: B = {
-      field.get(obj).asInstanceOf[B]
-    }
-
-    def :=(value: Any): Unit = {
-      field.set(obj, value)
-    }
-  }
-
-  /**
-    * Call ContextFactory.initGlobal in a static synchronized block.
-    *
-    * @see [[cwl.internal.EnhancedRhinoSandbox.assertContextFactory]]
-    */
-  private def initGlobalSynchronized(sandboxImpl_contextFactory: ContextFactory) = {
-    synchronized {
-      val _hasExplicitGlobal = ContextFactory.hasExplicitGlobal
-      val _not = !_hasExplicitGlobal
-      if (_not) ContextFactory.initGlobal(sandboxImpl_contextFactory)
-    }
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/internal/GigabytesToBytes.scala b/cwl/src/main/scala/cwl/internal/GigabytesToBytes.scala
deleted file mode 100644
index 7e45aeec5ba..00000000000
--- a/cwl/src/main/scala/cwl/internal/GigabytesToBytes.scala
+++ /dev/null
@@ -1,26 +0,0 @@
-package cwl.internal
-
-import shapeless.{Coproduct, Poly1}
-
-object GigabytesToBytes extends Poly1 {
-  val toMebibytesMultiplier = Math.pow(2, 20).toLong
-
-  implicit def long = at[Long] {
-    l =>
-      val value = l * toMebibytesMultiplier
-      Coproduct[cwl.ResourceRequirementType](value)
-  }
-
-  implicit def string = at[String] {
-    s =>
-      //TODO: Scale this by multiplier https://github.com/broadinstitute/cromwell/issues/3382
-      Coproduct[cwl.ResourceRequirementType](s)
-  }
-
-  implicit def expression = at[cwl.Expression] {
-    e =>
-      //TODO: Scale this by multiplier https://github.com/broadinstitute/cromwell/issues/3382
-      Coproduct[cwl.ResourceRequirementType](e)
-  }
-}
-
diff --git a/cwl/src/main/scala/cwl/model.scala b/cwl/src/main/scala/cwl/model.scala
deleted file mode 100644
index 838ee66a98c..00000000000
--- a/cwl/src/main/scala/cwl/model.scala
+++ /dev/null
@@ -1,310 +0,0 @@
-package cwl
-
-import cwl.CommandLineTool.{CommandBindingSortingKey, SortKeyAndCommandPart}
-import cwl.SchemaDefRequirement.{AsInputEnumSchema, AsInputRecordSchema, SchemaDefTypes}
-import cwl.CwlType.CwlType
-import cwl.WorkflowStepInput.InputSource
-import cwl.command.ParentName
-import cwl.internal.GigabytesToBytes
-import eu.timepit.refined._
-import eu.timepit.refined.api.Refined
-import eu.timepit.refined.string.MatchesRegex
-import shapeless.syntax.singleton._
-import shapeless.{:+:, CNil, Coproduct, Poly1, Witness}
-import wom.types.WomType
-import wom.values.WomValue
-import mouse.all._
-
-object WorkflowStepInputSource {
-  object String {
-    def unapply(arg: InputSource): Option[String] = arg.select[String]
-  }
-  object StringArray {
-    def unapply(arg: InputSource): Option[Array[String]] = arg.select[Array[String]]
-  }
-}
-
-/**
-  * Describes a bespoke type.
-  *
-  * @param name This field actually does _not_ appear in the v1.0 schema, but it is used anyway in the conformance tests.
-  *             After some consideration it was determined that we should close our eyes and pretend it is in the spec.  It
-  *             makes its formal appearance as a required field in v1.1.
-  */
-case class InputRecordSchema(
-  name: String,
-  fields: Option[Array[InputRecordField]] = None,
-  `type`: W.`"record"`.T = W("record").value,
-  label: Option[String] = None) {
-
-}
-
-case class InputRecordField(
-  name: String,
-  `type`: MyriadInputType,
-  doc: Option[String] = None,
-  inputBinding: Option[InputCommandLineBinding],
-  label: Option[String] = None)
-
-case class InputArraySchema
-(
-  items: MyriadInputType,
-  `type`: W.`"array"`.T = Witness("array").value,
-  label: Option[String] = None,
-  inputBinding: Option[InputCommandLineBinding] = None,
-  // IAS.secondaryFiles are NOT listed in 1.0 spec, but according to jgentry they will be, maybe
-  secondaryFiles: Option[SecondaryFiles] = None
-)
-
-trait CommandLineBinding {
-  def loadContents: Option[Boolean]
-  def position: Option[Int]
-  def prefix: Option[String]
-  def separate: Option[Boolean]
-  def itemSeparator: Option[String]
-  def optionalValueFrom: Option[StringOrExpression]
-  def shellQuote: Option[Boolean]
-  // separate defaults to true
-  def effectiveSeparate = separate.getOrElse(true)
-}
-
-object InputCommandLineBinding {
-  def default = InputCommandLineBinding()
-}
-
-case class InputCommandLineBinding(
-                               loadContents: Option[Boolean] = None,
-                               position: Option[Int] = None,
-                               prefix: Option[String] = None,
-                               separate: Option[Boolean] = None,
-                               itemSeparator: Option[String] = None,
-                               valueFrom: Option[StringOrExpression] = None,
-                               shellQuote: Option[Boolean] = None) extends CommandLineBinding {
-  override val optionalValueFrom = valueFrom
-
-  def toCommandPart(sortingKey: CommandBindingSortingKey, boundValue: WomValue, hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib) = {
-    SortKeyAndCommandPart(sortingKey, InputCommandLineBindingCommandPart(this, boundValue)(hasShellCommandRequirement, expressionLib))
-  }
-}
-
-// valueFrom is required for command line bindings in the argument section: http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding
-case class ArgumentCommandLineBinding(
-                               valueFrom: StringOrExpression,
-                               loadContents: Option[Boolean] = None,
-                               position: Option[Int] = None,
-                               prefix: Option[String] = None,
-                               separate: Option[Boolean] = None,
-                               itemSeparator: Option[String] = None,
-                               shellQuote: Option[Boolean] = None) extends CommandLineBinding {
-  override val optionalValueFrom = Option(valueFrom)
-}
-
-case class InputBinding(position: Int, prefix: String)
-
-object MyriadOutputInnerTypeCacheableString extends Poly1 {
-  import Case._
-
-  private def cacheableOutputRecordFieldString(field: OutputRecordField): String = {
-    val fieldType = field.`type`.fold(MyriadOutputTypeCacheableString)
-    val lqn = field.name.substring(field.name.lastIndexOf('#') + 1)
-    s"OutputRecordField($lqn,$fieldType,${field.doc},${field.outputBinding})"
-  }
-
-  implicit def recordSchema: Aux[OutputRecordSchema, String] = at[OutputRecordSchema] {
-    s =>
-      val t = s.`type`
-      s"OutputRecordSchema($t,${s.fields.map(a => "Array(" + a.map(cacheableOutputRecordFieldString).mkString(",") + ")" )},${s.label})"
-  }
-
-  implicit def arraySchema: Aux[OutputArraySchema, String] = at[OutputArraySchema] {
-    a =>
-      val is: String = a.items.fold(MyriadOutputTypeCacheableString)
-      val t = a.`type`
-      s"OutputArraySchema($is,$t,${a.label},${a.outputBinding})"
-  }
-
-  implicit def enumSchema: Aux[OutputEnumSchema, String] = at[OutputEnumSchema] { _.toString }
-  implicit def cwlType: Aux[CwlType, String] = at[CwlType] { _.toString }
-  implicit def string: Aux[String, String] = at[String] { identity }
-}
-
-
-object MyriadOutputTypeCacheableString extends Poly1 {
-  import Case._
-
-  implicit def one: Aux[MyriadOutputInnerType, String] = at[MyriadOutputInnerType] {
-    _.fold(MyriadOutputInnerTypeCacheableString)
-  }
-
-  implicit def many: Aux[Array[MyriadOutputInnerType], String] = at[Array[MyriadOutputInnerType]] { a =>
-    val strings: Array[String] = a.map(_.fold(MyriadOutputInnerTypeCacheableString))
-    "Array(" + strings.mkString(",") + ")"
-  }
-}
-
-object SecondaryFilesCacheableString extends Poly1 {
-  import Case._
-
-  implicit def one: Aux[StringOrExpression, String] = at[StringOrExpression] {
-    _.toString
-  }
-
-  implicit def array: Aux[Array[StringOrExpression], String] = at[Array[StringOrExpression]] {
-    _.mkString("Array(", ",", ")")
-  }
-
-}
-
-case class OutputRecordSchema(
-  `type`: W.`"record"`.T,
-  fields: Option[Array[OutputRecordField]],
-  label: Option[String])
-
-case class OutputRecordField(
-  name: String,
-  `type`: MyriadOutputType,
-  doc: Option[String],
-  outputBinding: Option[CommandOutputBinding])
-
-case class OutputArraySchema(
-  items: MyriadOutputType,
-  `type`: W.`"array"`.T = Witness("array").value,
-  label: Option[String] = None,
-  outputBinding: Option[CommandOutputBinding] = None)
-
-case class InlineJavascriptRequirement(
-  `class`: W.`"InlineJavascriptRequirement"`.T = "InlineJavascriptRequirement".narrow,
-  expressionLib: Option[Array[String]] = None)
-
-case class SchemaDefRequirement(
-  types: Array[SchemaDefTypes] = Array.empty,
-  `class`: W.`"SchemaDefRequirement"`.T = Witness("SchemaDefRequirement").value) {
-
-  def lookupType(tpe: String): Option[WomType] =
-    lookupCwlType(tpe).flatMap{
-      case AsInputRecordSchema(inputRecordSchema: InputRecordSchema) => MyriadInputInnerTypeToWomType.inputRecordSchemaToWomType(inputRecordSchema).apply(this) |> Option.apply
-      case _ => None
-    }
-
-  //Currently only InputRecordSchema has a name in the spec, so it is the only thing that can be referenced via string
-  def lookupCwlType(tpe: String): Option[SchemaDefTypes] = {
-
-    def matchesType(inputEnumSchema: InputEnumSchema): Boolean = {
-      inputEnumSchema.name.fold(false){name => FileAndId(name)(ParentName.empty).id equalsIgnoreCase FileAndId(tpe)(ParentName.empty).id}
-    }
-
-    types.toList.flatMap {
-      case AsInputRecordSchema(inputRecordSchema: InputRecordSchema) if FileAndId(inputRecordSchema.name)(ParentName.empty).id equalsIgnoreCase FileAndId(tpe)(ParentName.empty).id =>
-        List(Coproduct[SchemaDefTypes](inputRecordSchema))
-      case AsInputEnumSchema(inputEnumSchema: InputEnumSchema) if matchesType(inputEnumSchema) =>
-        List(Coproduct[SchemaDefTypes](inputEnumSchema))
-      case _ =>
-        List()
-    }.headOption
-  }
-}
-
-object SchemaDefRequirement {
-  type SchemaDefTypes = InputRecordSchema :+: InputEnumSchema :+: InputArraySchema :+: CNil
-
-  object AsInputRecordSchema {
-    def unapply(arg: SchemaDefTypes): Option[InputRecordSchema] = arg.select[InputRecordSchema]
-  }
-
-  object AsInputEnumSchema {
-    def unapply(arg: SchemaDefTypes): Option[InputEnumSchema] = arg.select[InputEnumSchema]
-  }
-
-  object AsInputArraySchema {
-    def unapply(arg: SchemaDefTypes): Option[InputArraySchema] = arg.select[InputArraySchema]
-  }
-}
-
-//There is a large potential for regex refinements on these string types
-case class DockerRequirement(
-  `class`: W.`"DockerRequirement"`.T,
-  dockerPull: Option[String], //TODO Refine to match a docker image regex?
-  dockerLoad: Option[String],
-  dockerFile: Option[String],
-  dockerImport: Option[String],
-  dockerImageId: Option[String],
-  dockerOutputDirectory: Option[String]
-  )
-
-case class SoftwareRequirement(
-  `class`: W.`"SoftwareRequirement"`.T,
-  packages: Array[SoftwarePackage] = Array.empty
-  )
-
-case class SoftwarePackage(
-  `package`: String,
-  version: Option[Array[String]],
-  specs: Option[Array[String]] // This could be refined to match a regex for IRI.
-  ) {
-  type Package = String
-  type Specs = Array[String]
-}
-
-case class EnvVarRequirement(
-                              `class`: EnvVarRequirement.ClassType = EnvVarRequirement.`class`,
-                              envDef: Array[EnvironmentDef]
-                            )
-
-object EnvVarRequirement {
-  type ClassType = Witness.`"EnvVarRequirement"`.T
-
-  val `class`: ClassType = "EnvVarRequirement".asInstanceOf[ClassType]
-}
-
-case class EnvironmentDef(envName: String, envValue: StringOrExpression) {
-  type EnvName = String
-  type EnvValue = String
-}
-
-
-case class ShellCommandRequirement(`class`: W.`"ShellCommandRequirement"`.T = "ShellCommandRequirement".narrow)
-
-case class ResourceRequirement(
-                                `class`: W.`"ResourceRequirement"`.T,
-                                coresMin: Option[ResourceRequirementType],
-                                coresMax: Option[ResourceRequirementType],
-                                ramMin: Option[ResourceRequirementType],
-                                ramMax: Option[ResourceRequirementType],
-                                tmpdirMin: Option[ResourceRequirementType],
-                                tmpdirMax: Option[ResourceRequirementType],
-                                outdirMin: Option[ResourceRequirementType],
-                                outdirMax: Option[ResourceRequirementType]) {
-  def effectiveCoreMin = coresMin.orElse(coresMax)
-  def effectiveCoreMax = coresMax.orElse(coresMin)
-
-  def effectiveRamMin = ramMin.orElse(ramMax).map(_.fold(GigabytesToBytes))
-  def effectiveRamMax = ramMax.orElse(ramMin).map(_.fold(GigabytesToBytes))
-
-  def effectiveTmpdirMin = tmpdirMin.orElse(tmpdirMax)
-  def effectiveTmpdirMax = tmpdirMax.orElse(tmpdirMin)
-
-  def effectiveOutdirMin = outdirMin.orElse(outdirMax)
-  def effectiveOutdirMax = outdirMax.orElse(outdirMin)
-}
-
-/**
-  * This promotes DNA Nexus InputResourceRequirement to a first class citizen requirement, which it really isn't.
-  * Since it's the only one for now it's not a big deal but if more of these pop up we might want to treat custom requirements
-  * in a different way
-  */
-case class DnaNexusInputResourceRequirement(
-                                     `class`: String Refined MatchesRegex[W.`".*InputResourceRequirement"`.T],
-                                     indirMin: Option[Long]
-                                   )
-
-case class SubworkflowFeatureRequirement(
-  `class`: W.`"SubworkflowFeatureRequirement"`.T)
-
-case class ScatterFeatureRequirement(
-  `class`: W.`"ScatterFeatureRequirement"`.T)
-
-case class MultipleInputFeatureRequirement(
-  `class`: W.`"MultipleInputFeatureRequirement"`.T)
-
-case class StepInputExpressionRequirement(
-  `class`: W.`"StepInputExpressionRequirement"`.T)
diff --git a/cwl/src/main/scala/cwl/ontology/CacheConfiguration.scala b/cwl/src/main/scala/cwl/ontology/CacheConfiguration.scala
deleted file mode 100644
index cb82d9db591..00000000000
--- a/cwl/src/main/scala/cwl/ontology/CacheConfiguration.scala
+++ /dev/null
@@ -1,15 +0,0 @@
-package cwl.ontology
-
-import com.typesafe.config.Config
-import common.validation.Validation._
-import net.ceedubs.ficus.Ficus._
-
-case class CacheConfiguration(maxSize: Long)
-
-object CacheConfiguration {
-  def apply(config: Config): CacheConfiguration = {
-    validate(config.getAs[Long]("max-size").getOrElse(0L))
-      .map(new CacheConfiguration(_))
-      .unsafe("Ontology cache configuration")
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ontology/OntologyConfiguration.scala b/cwl/src/main/scala/cwl/ontology/OntologyConfiguration.scala
deleted file mode 100644
index 5382ac35b91..00000000000
--- a/cwl/src/main/scala/cwl/ontology/OntologyConfiguration.scala
+++ /dev/null
@@ -1,27 +0,0 @@
-package cwl.ontology
-
-import cats.syntax.apply._
-import com.typesafe.config.Config
-import common.util.Backoff
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import net.ceedubs.ficus.Ficus._
-
-import scala.concurrent.duration.FiniteDuration
-
-case class OntologyConfiguration(retries: Option[Int], backoff: Backoff, poolSize: Int)
-
-object OntologyConfiguration {
-  def apply(config: Config): OntologyConfiguration = {
-    val retries = validate { Option(config.as[Int]("retries")) }
-    val backoff = validate {
-      Backoff.staticBackoff(
-        config.as[FiniteDuration]("backoff-time")
-      )
-    }
-    val poolSize = validate { config.as[Int]("pool-size") }
-
-    val validated: ErrorOr[OntologyConfiguration] = (retries, backoff, poolSize).mapN(OntologyConfiguration.apply)
-    validated.unsafe("Ontology configuration")
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ontology/Schema.scala b/cwl/src/main/scala/cwl/ontology/Schema.scala
deleted file mode 100644
index a2ed13d7bf3..00000000000
--- a/cwl/src/main/scala/cwl/ontology/Schema.scala
+++ /dev/null
@@ -1,180 +0,0 @@
-package cwl.ontology
-
-import java.util.concurrent.Executors
-
-import cats.effect.IO
-import cats.syntax.traverse._
-import cats.instances.list._
-import com.google.common.cache.{Cache, CacheBuilder}
-import com.typesafe.config.{Config, ConfigFactory}
-import com.typesafe.scalalogging.Logger
-import common.util.IORetry
-import common.util.IORetry.StatefulIoError
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.ontology.Schema._
-import mouse.all._
-import net.ceedubs.ficus.Ficus._
-import org.semanticweb.owlapi.apibinding.OWLManager
-import org.semanticweb.owlapi.model._
-import org.semanticweb.owlapi.model.parameters.OntologyCopy
-import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory
-import org.semanticweb.owlapi.reasoner.{OWLReasoner, OWLReasonerFactory}
-import org.semanticweb.owlapi.util.OWLAPIStreamUtils
-import org.slf4j.LoggerFactory
-
-import scala.jdk.CollectionConverters._
-import scala.concurrent.ExecutionContext
-import scala.util.Try
-
-/**
-  * OWL/RDF Schema lookup.
-  *
-  * @param schemaIris IRI paths to OWL/RDF schemas.
-  * @param namespaces Additional/Override namespace prefixes.
-  */
-case class Schema(schemaIris: Seq[String],
-                  namespaces: Map[String, String],
-                  ontologyManager: OWLOntologyManager = OWLManager.createOWLOntologyManager,
-                  reasonerFactory: OWLReasonerFactory = new StructuralReasonerFactory) {
-
-  /**
-    * Returns a full IRI based on a full or abbreviated IRI.
-    *
-    * A full IRI wrapped in < and > will not be checked for abbreviations but will be returned without the wrapper.
-    *
-    * @see https://www.w3.org/TR/owl2-syntax/#IRIs
-    */
-  def fullIri(name: String): String = getIri(name).getIRIString
-
-  /**
-    * Returns true if child is an equivalent of ancestor, and if not then recursively checks if any of the child's
-    * super classes are an equivalent of ancestor.
-    */
-  def isSubClass(child: String, ancestor: String): Boolean = {
-    val childIri: IRI = getIri(child)
-    val ancestorIri: IRI = getIri(ancestor)
-    val childClass: OWLClass = dataFactory.getOWLClass(childIri)
-    val ancestorClass: OWLClass = dataFactory.getOWLClass(ancestorIri)
-    val schemaReasoner: OWLReasoner = reasonerFactory.createReasoner(schemaOntology)
-    try {
-      Schema.isSubClass(schemaReasoner, childClass, ancestorClass)
-    } finally {
-      schemaReasoner.dispose()
-    }
-  }
-
-  private val dataFactory: OWLDataFactory = ontologyManager.getOWLDataFactory
-  private val schemaOntology: OWLOntology = ontologyManager.createOntology()
-  private val schemaPrefixManager: PrefixManager =
-    ontologyManager.getOntologyFormat(schemaOntology).asPrefixOWLDocumentFormat
-
-  {
-    def addToSchema(originalOntology: OWLOntology): Unit = {
-      schemaOntology.addAxioms(originalOntology.axioms())
-      val originalOntologyFormat: OWLDocumentFormat = ontologyManager.getOntologyFormat(originalOntology)
-      if (originalOntologyFormat.isPrefixOWLDocumentFormat)
-        schemaPrefixManager.copyPrefixesFrom(originalOntologyFormat.asPrefixOWLDocumentFormat)
-    }
-
-    val errorOr: ErrorOr[Unit] = for {
-      ontologies <- schemaIris.toList.traverse(loadOntologyFromIri(ontologyManager))
-      _ = ontologies.foreach(addToSchema)
-    } yield ()
-    errorOr.toTry("Error loading schemas").get
-
-    // Add any namespace overrides
-    namespaces foreach {
-      case (prefixName, prefix) => schemaPrefixManager.setPrefix(prefixName, prefix)
-    }
-  }
-
-  /**
-    * Returns the full IRI for the name using the prefixManager.
-    *
-    * TODO: Not 100% sure why you can't ask owl-api for an iri-with-prefix and have it looked up automatically.
-    *
-    * There does seem to be a difference between abbreviated and full IRIs in the official spec, where full IRIs are
-    * wrapped in < >. But this doesn't seem to be the format used by CWL nor owl-api.
-    *
-    * Please update this comment if/when one knows the correct behavior.
-    *
-    * @see https://www.w3.org/TR/owl2-syntax/#IRIs
-    */
-  private def getIri(name: String): IRI = {
-    Try(schemaPrefixManager.getIRI(name)).getOrElse(IRI.create(name))
-  }
-}
-
-object Schema {
-  // Extending StrictLogging creates a circular dependency here for some reason, so making the logger ourselves
-  private val logger: Logger = Logger(LoggerFactory.getLogger(getClass.getName))
-  private [ontology] val ontologyConfig = ConfigFactory.load.as[Config]("ontology")
-  private val ontologyConfiguration = OntologyConfiguration(ontologyConfig)
-  private [ontology] val cacheConfig = ontologyConfig.getAs[Config]("cache")
-
-  // Simple cache to avoid reloading the same ontologies too often
-  private val ontologyCache = cacheConfig.map(makeOntologyCache)
-
-  private implicit val statefulIoError = StatefulIoError.noop[Unit]
-  private implicit val timer = cats.effect.IO.timer(ExecutionContext.fromExecutor(Executors.newFixedThreadPool(ontologyConfiguration.poolSize)))
-
-  private [ontology] def makeOntologyCache(config: Config): Cache[IRI, OWLOntology] = {
-    val cacheConfig = CacheConfiguration(config)
-    logger.info(s"Ontology cache size: ${cacheConfig.maxSize}")
-    CacheBuilder.newBuilder()
-      .maximumSize(cacheConfig.maxSize)
-      .build[IRI, OWLOntology]()
-  }
-
-  /**
-    * Returns the absolute path for a file, possibly relative to parent.
-    */
-  def getIriPath(parent: String, path: String): String = IRI.create(parent).resolve(path).getIRIString
-
-  /**
-    * Load an ontology either from an IRI.
-    */
-  private [ontology] def loadOntologyFromIri(ontologyManager: OWLOntologyManager, cache: Option[Cache[IRI, OWLOntology]] = ontologyCache)(schemaIri: String): ErrorOr[OWLOntology] = {
-    validate {
-      val iri = IRI.create(schemaIri)
-      cache.flatMap(_.getIfPresent(iri) |> Option.apply) match {
-        case Some(ontology) =>
-          ontologyManager.copyOntology(ontology, OntologyCopy.DEEP)
-        case _ =>
-          logger.info(s"Loading ${iri.toURI.toString}")
-          val ontology = loadOntologyFromIri(ontologyManager, iri)
-          cache.foreach(_.put(iri, ontology))
-          ontology
-      }
-    }
-  }
-
-  // Loading the ontology can fail transiently, so put retires around it. See https://github.com/protegeproject/webprotege/issues/298
-  private [ontology] def loadOntologyFromIri(ontologyManager: OWLOntologyManager, iri: IRI): OWLOntology = {
-    val load = IO { ontologyManager.loadOntologyFromOntologyDocument(iri) }
-    IORetry.withRetry[OWLOntology, Unit](load, (), ontologyConfiguration.retries, ontologyConfiguration.backoff).unsafeRunSync()
-  }
-
-  /**
-    * Returns true if child is an equivalent of ancestor, and if not then recursively checks if any of the child's
-    * super classes are an equivalent of ancestor.
-    */
-  private def isSubClass(reasoner: OWLReasoner, childClass: OWLClass, ancestorClass: OWLClass): Boolean = {
-    val equivalent: Set[OWLClass] = reasoner.getEquivalentClasses(childClass).asScala.toSet + childClass
-    if (equivalent.contains(ancestorClass)) {
-      true
-    } else {
-      val parentClasses: Set[OWLClass] = for {
-        equivalentClass <- equivalent
-        parentClass <- OWLAPIStreamUtils
-          .asSet(reasoner.getSuperClasses(equivalentClass).entities)
-          .asScala
-          .toSet[OWLClass]
-      } yield parentClass
-      parentClasses.collect({
-        case superClass: OWLClass if isSubClass(reasoner, superClass, ancestorClass) => superClass
-      }).nonEmpty
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/package.scala b/cwl/src/main/scala/cwl/package.scala
deleted file mode 100644
index 96796712f1e..00000000000
--- a/cwl/src/main/scala/cwl/package.scala
+++ /dev/null
@@ -1,154 +0,0 @@
-
-import cats.data.ReaderT
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr._
-import cwl.CwlType._
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import cwl.command.ParentName
-import cwl.ontology.Schema
-import shapeless._
-import wom.executable.Executable
-import wom.expression.IoFunctionSet
-import wom.types._
-import wom.values.WomEvaluatedCallInputs
-
-import scala.util.{Failure, Success, Try}
-
-/**
- * This package is intended to parse all CWL files.
- *
- * It makes heavy use of Circe YAML/Json auto derivation feature and
- * Circe modules that support the Scala libraries shapeless and Refined.
- *
- * The [[https://oss.sonatype.org/service/local/repositories/releases/archive/com/chuusai/shapeless_2.12/2.3.2/shapeless_2.12-2.3.2-javadoc.jar/!/shapeless/Coproduct.html shapeless.coproduct]] feature allows us to specify a large
- * number of potential types to be parsed.  A.k.a. a "disjunction" or "OR" relationship amongst these types.
- *
- * The [[https://github.com/fthomas/refined/blob/master/modules/core/shared/src/main/scala/eu/timepit/refined/string.scala MatchesRegex]] "refined type" is used
- * to enforce structure upon String values in the CWL Yaml.  Shapeless' Witness type
- * is used to declare a type containing a String literal.
- *
- * @see <a href="http://www.commonwl.org/v1.0/">CWL Specification</a>
- * @see <a href="https://github.com/circe/circe">circe</a>
- * @see <a href="https://github.com/circe/circe-yaml">circe-yaml</a>
- * @see <a href="https://github.com/fthomas/refined">Refined</a>
- * @see <a href="https://github.com/milessabin/shapeless">Shapeless</a>
- */
-package object cwl extends TypeAliases {
-
-  type CwlFile = Array[Cwl] :+: Cwl :+: CNil
-  type Cwl = Workflow :+: CommandLineTool :+: ExpressionTool :+: CNil
-
-  object Cwl {
-    object Workflow { def unapply(cwl: Cwl): Option[Workflow] = cwl.select[Workflow] }
-    object CommandLineTool { def unapply(cwl: Cwl): Option[CommandLineTool] = cwl.select[CommandLineTool] }
-    object ExpressionTool { def unapply(cwl: Cwl): Option[ExpressionTool] = cwl.select[ExpressionTool] }
-  }
-
-  def cwlTypeToWomType : CwlType => WomType = {
-    case CwlType.Any => WomAnyType
-    case Null => WomNothingType
-    case Boolean => WomBooleanType
-    case Int => WomIntegerType
-    case Long => WomLongType
-    case Float => WomFloatType
-    case Double => WomFloatType
-    case String => WomStringType
-    case CwlType.File => WomMaybePopulatedFileType
-    case CwlType.Directory => WomMaybeListedDirectoryType
-  }
-
-  object StringOrExpression {
-    object String {
-      def unapply(soe: StringOrExpression): Option[String] = soe.select[String]
-    }
-    object Expression {
-      def unapply(soe: StringOrExpression): Option[Expression] = soe.select[Expression]
-    }
-    object ECMAScriptExpression {
-      def unapply(soe: StringOrExpression): Option[ECMAScriptExpression] = soe.select[Expression].flatMap(_.select[ECMAScriptExpression])
-    }
-    object ECMAScriptFunction {
-      def unapply(soe: StringOrExpression): Option[ECMAScriptFunction] = soe.select[Expression].flatMap(_.select[ECMAScriptFunction])
-    }
-  }
-
-  object Expression {
-    object ECMAScriptExpression {
-      def unapply(soe: Expression): Option[ECMAScriptExpression] = soe.select[ECMAScriptExpression]
-    }
-    object ECMAScriptFunction {
-      def unapply(soe: Expression): Option[ECMAScriptFunction] = soe.select[ECMAScriptFunction]
-    }
-  }
-
-  type WomTypeMap = Map[String, WomType]
-
-  type RequirementsValidator = Requirement => ErrorOr[Requirement]
-  import cats.syntax.validated._
-  val AcceptAllRequirements: RequirementsValidator = _.validNel
-
-  implicit class CwlHelper(val cwl: Cwl) extends AnyVal {
-    def womExecutable(validator: RequirementsValidator, inputsFile: Option[String], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-      def executable = cwl match {
-        case Cwl.Workflow(w) => w.womExecutable(validator, inputsFile, ioFunctions, strictValidation)
-        case Cwl.CommandLineTool(clt) => clt.womExecutable(validator, inputsFile, ioFunctions, strictValidation)
-        case Cwl.ExpressionTool(et) => et.womExecutable(validator, inputsFile, ioFunctions, strictValidation)
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-      Try(executable) match {
-        case Success(s) => s
-        case Failure(f) => f.getMessage.invalidNelCheck
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-    }
-
-    def requiredInputs: Map[String, WomType] = {
-      implicit val parent = ParentName.empty
-
-      cwl match {
-        case Cwl.Workflow(w) => selectWomTypeInputs(w.inputs collect {
-          case i if i.`type`.isDefined => FullyQualifiedName(i.id).id -> i.`type`.get
-        })
-        case Cwl.CommandLineTool(clt) => selectWomTypeInputs(clt.inputs collect {
-          case i if i.`type`.isDefined => FullyQualifiedName(i.id).id -> i.`type`.get
-        })
-        case Cwl.ExpressionTool(et) => selectWomTypeInputs(et.inputs collect {
-          case i if i.`type`.isDefined => FullyQualifiedName(i.id).id -> i.`type`.get
-        })
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-    }
-
-    def schemaOption: Option[Schema] = cwl.fold(CwlSchemaOptionPoly)
-
-    private def selectWomTypeInputs(myriadInputMap: Array[(String, MyriadInputType)]): Map[String, WomType] = {
-      (myriadInputMap collect {
-        case (key, MyriadInputType.WomType(w)) => key -> w
-      }).toMap
-    }
-  }
-
-  object CwlSchemaOptionPoly extends Poly1 {
-    implicit val caseWorkflow: Case.Aux[Workflow, Option[Schema]] = at {
-      workflow => getSchema(workflow.`$schemas`, workflow.`$namespaces`)
-    }
-    implicit val caseCommandLineTool: Case.Aux[CommandLineTool, Option[Schema]] = at {
-      commandLineTool => getSchema(commandLineTool.`$schemas`, commandLineTool.`$namespaces`)
-    }
-    implicit val caseExpressionTool: Case.Aux[ExpressionTool, Option[Schema]] = at {
-      expressionTool => getSchema(expressionTool.`$schemas`, expressionTool.`$namespaces`)
-    }
-
-    private def getSchema(schemasOption: Option[Array[String]],
-                          namespacesOption: Option[Map[String, String]]): Option[Schema] = {
-      schemasOption.map(a => Schema(a.toIndexedSeq, namespacesOption getOrElse Map.empty))
-    }
-  }
-
-  type ExpressionLib = Vector[String]
-
-  type Inputs = (RequirementsAndHints, ExpressionLib, WomEvaluatedCallInputs)
-
-  type CommandPartExpression[A] = ReaderT[ErrorOr, Inputs, A]
-}
diff --git a/cwl/src/main/scala/cwl/preprocessor/CwlCanonicalizer.scala b/cwl/src/main/scala/cwl/preprocessor/CwlCanonicalizer.scala
deleted file mode 100644
index b369d404c18..00000000000
--- a/cwl/src/main/scala/cwl/preprocessor/CwlCanonicalizer.scala
+++ /dev/null
@@ -1,249 +0,0 @@
-package cwl.preprocessor
-
-import cats.effect.{ContextShift, IO}
-import cats.syntax.parallel._
-import cats.instances.list._
-import common.validation.ErrorOr.ErrorOr
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.preprocessor.CwlReference.EnhancedCwlId
-import cwl.preprocessor.CwlPreProcessor._
-import io.circe.Json
-import io.circe.optics.JsonPath._
-import cwl.preprocessor.CwlCanonicalizer._
-
-/**
-  * The real guts of the CWL pre-processor is taking a CWL reference and producing a single, self-contained JSON from it.
-  */
-private [preprocessor] class CwlCanonicalizer(saladFunction: SaladFunction)(implicit cs: ContextShift[IO]) {
-
-  def getCanonicalCwl(reference: CwlReference,
-                      namespacesJsonOption: Option[Json] = None,
-                      schemasJsonOption: Option[Json] = None): IOChecked[Json] = {
-    flattenCwlReferenceInner(
-      reference,
-      Map.empty,
-      Map.empty,
-      Set.empty,
-      namespacesJsonOption,
-      schemasJsonOption).map(_.processedJson)
-  }
-
-  /**
-    * Flatten the cwl reference given already known processed references.
-    */
-  private def flattenCwlReferenceInner(cwlReference: CwlReference,
-                                       unProcessedReferences: UnProcessedReferences,
-                                       processedReferences: ProcessedReferences,
-                                       breadCrumbs: Set[CwlReference],
-                                       namespacesJsonOption: Option[Json],
-                                       schemasJsonOption: Option[Json]): IOChecked[ProcessedJsonAndDependencies] = {
-    /*
-     * Salad and parse from a CWL reference into a Json object
-     */
-    def saladAndParse(ref: CwlReference): IOChecked[Json] =  for {
-      saladed <- saladFunction(ref)
-      saladedJson <- parseJson(saladed)
-    } yield saladedJson
-
-    for {
-      // parse the file containing the reference
-      parsed <- saladAndParse(cwlReference)
-      // Get a Map[CwlReference, Json] from the parsed file. If the file is a JSON object and only contains one node, the map will only have 1 element
-      newUnProcessedReferences = mapIdToContent(parsed).toMap
-      // The reference json in the file
-      referenceJson <- newUnProcessedReferences
-        .collectFirst({ case (ref, json) if ref.pointerWithinFile == cwlReference.pointerWithinFile => json })
-        .toIOChecked(s"Cannot find a tool or workflow with ID '${cwlReference.pointerWithinFile}' in file ${cwlReference.pathAsString}'s set: [${newUnProcessedReferences.keySet.mkString(", ")}]")
-      // Process the reference json
-      processed <- flattenJson(
-        referenceJson,
-        newUnProcessedReferences ++ unProcessedReferences,
-        processedReferences,
-        breadCrumbs + cwlReference,
-        namespacesJsonOption,
-        schemasJsonOption
-      )
-    } yield processed
-  }
-
-  /**
-    * Given a Json representing a tool or workflow, flattens it and return the other processed references that were generated.
-    *
-    * NB: Flatten here means two things:
-    *  - Find references within the CWL and convert them into 'local' links
-    *  - Create a map of canonical links to JSON CWL content
-    *
-    * @param saladedJson           json to process
-    * @param unProcessedReferences references that have been parsed and saladed (we have the json), but not flattened yet
-    * @param processedReferences   references that are fully flattened
-    * @param breadCrumbs           list of references that brought us here
-    * @param namespacesJsonOption  Namespaces from the original json
-    * @param schemasJsonOption     Schemas from the original json
-    */
-  private def flattenJson(saladedJson: Json,
-                          unProcessedReferences: UnProcessedReferences,
-                          processedReferences: ProcessedReferences,
-                          breadCrumbs: Set[CwlReference],
-                          namespacesJsonOption: Option[Json],
-                          schemasJsonOption: Option[Json]): IOChecked[ProcessedJsonAndDependencies] = {
-    /*
-     * Given a reference from a step's run field, flattens it and return it
-     * @param unProcessedReferences references that have been parsed and saladed (we have the json), but not flattened yet.
-     * @param checkedProcessedReferences references that are fully processed
-     * @param cwlReference reference being processed
-     * @return a new ProcessedReferences Map including this cwlReference processed along with all the dependencies
-     *         that might have been processed recursively.
-     */
-    def processCwlRunReference(checkedProcessedReferences: IOChecked[ProcessedReferences],
-                               cwlReference: CwlReference): IOChecked[ProcessedReferences] = {
-      def processReference(processedReferences: ProcessedReferences) = {
-
-        val result: IOChecked[ProcessedJsonAndDependencies] = unProcessedReferences.get(cwlReference) match {
-          case Some(unProcessedReferenceJson) =>
-            // Found the json in the unprocessed map, no need to reparse the file, just flatten this json
-            flattenJson(
-              unProcessedReferenceJson,
-              unProcessedReferences,
-              processedReferences,
-              breadCrumbs,
-              namespacesJsonOption,
-              schemasJsonOption
-            )
-          case None =>
-            // This is the first time we're seeing this reference, we need to parse its file and flatten it
-            flattenCwlReferenceInner(
-              cwlReference,
-              unProcessedReferences,
-              processedReferences,
-              breadCrumbs,
-              namespacesJsonOption,
-              schemasJsonOption
-            )
-        }
-
-        result map {
-          // Return everything we've got (the previously known "processedReferences" + our new processed reference + everything that was processed to get to it)
-          case ProcessedJsonAndDependencies(processed, newReferences) => processedReferences ++ newReferences + (cwlReference -> processed)
-        }
-      }
-
-      def processIfNeeded(processedReferences: ProcessedReferences): IOChecked[ProcessedReferences] = {
-        // If the reference has already been processed, no need to do anything
-        if (processedReferences.contains(cwlReference)) processedReferences.validIOChecked
-        // If the reference is in the bread crumbs it means we circled back to it: fail the pre-processing
-        else if (breadCrumbs.contains(cwlReference)) s"Found a circular dependency on $cwlReference".invalidIOChecked
-        // Otherwise let's see if we already have the json for it or if we need to process the file
-        else processReference(processedReferences)
-      }
-
-      for {
-        processedReferences <- checkedProcessedReferences
-        newReferences <- processIfNeeded(processedReferences)
-      } yield newReferences
-    }
-
-    def addJsonKeyValue(originalJson: Json, key: String, valueOption: Option[Json]): Json = {
-      valueOption match {
-        case Some(value) => originalJson.mapObject(_.add(key, value))
-        case None => originalJson
-      }
-    }
-
-    val namespacesJson = addJsonKeyValue(saladedJson, JsonKeyNamespaces, namespacesJsonOption)
-    val schemasJson = addJsonKeyValue(namespacesJson, JsonKeySchemas, schemasJsonOption)
-
-    import cats.syntax.apply._
-
-    // Take the processed runs and inject them in the json
-    def inlineProcessedJsons(newKnownReferences: ProcessedReferences, inlinedRunWorkflows: Map[String, ProcessedJsonAndDependencies]) = {
-      // Provide a function to swap the run reference with its json content
-      val lookupFunction: Json => Json = {
-        json: Json => {
-          val fromRunReferenceMap = for {
-            asString <- json.asString
-            reference <- asString.asReference
-            embeddedJson <- newKnownReferences.get(reference)
-          } yield embeddedJson
-
-          val fromInlinedWorkflow = for {
-            asObject <- json.asObject
-            id <- asObject.kleisli("id")
-            idAsString <- id.asString
-            embeddedJson <- inlinedRunWorkflows.get(idAsString)
-          } yield embeddedJson.processedJson
-
-          fromRunReferenceMap.orElse(fromInlinedWorkflow).getOrElse(json)
-        }
-      }
-
-      val flattenedJson = root.steps.each.run.json.modify(lookupFunction)(schemasJson)
-
-      ProcessedJsonAndDependencies(flattenedJson, newKnownReferences ++ inlinedRunWorkflows.values.flatMap(_.processedDependencies))
-    }
-
-    /*
-     * Given a json, collects all "steps.run" values that are JSON Strings, and convert them to CwlReferences.
-     * A saladed JSON is assumed.
-     */
-    def findRunReferences(json: Json): List[CwlReference] = {
-      json.asArray match {
-        case Some(cwls) => cwls.toList.flatMap(findRunReferences)
-        case _ => root.steps.each.run.string.getAll(json).flatMap(_.asReference).distinct
-      }
-    }
-
-    /*
-     * Given a json, collects all "steps.run" values that are JSON Objects representing a workflow.
-     * A saladed JSON is assumed.
-     * @return a Map[String, Json], where the key is the cwl id of the workflow, and the value its content
-     */
-    def findRunInlinedWorkflows(json: Json): ErrorOr[Map[String, Json]] = {
-      import cats.syntax.traverse._
-
-      json.asArray match {
-        case Some(cwls) => cwls.toList
-          .flatTraverse(findRunInlinedWorkflows(_).map(_.toList))
-          .map(_.toMap)
-        case _ =>
-          // Look for all the "run" steps that are json objects
-          root.steps.each.run.obj.getAll(json)
-            .map(Json.fromJsonObject)
-            // Only keep the workflows (CommandLineTools don't have steps so no need to process them)
-            .filter(root.`class`.string.exist(_.equalsIgnoreCase("Workflow")))
-            .traverse[ErrorOr, (String, Json)]( obj =>
-              // Find the id of the workflow
-              root.id.string.getOption(obj)
-                .toErrorOr("Programmer error: Workflow did not contain an id. Make sure the cwl has been saladed")
-                .map(_ -> obj)
-            ).map(_.toMap)
-      }
-    }
-
-    // Recursively process the run references (where run is a string pointing to another Workflow / Tool)
-    // TODO: it would be nice to accumulate failures here somehow (while still folding and be able to re-use
-    // successfully processed references, so I don't know if ErrorOr would work)
-    val processedRunReferences: IOChecked[ProcessedReferences] = findRunReferences(schemasJson).foldLeft(processedReferences.validIOChecked)(processCwlRunReference)
-
-    // Recursively process the inlined run workflows (where run is a Json object representing a workflow)
-    val processedInlineReferences: IOChecked[Map[String, ProcessedJsonAndDependencies]] = (for {
-      inlineWorkflowReferences <- findRunInlinedWorkflows(saladedJson).toIOChecked
-      flattenedWorkflows <- inlineWorkflowReferences.toList.parTraverse[IOChecked, (String, ProcessedJsonAndDependencies)]({
-        case (id, value) => flattenJson(value, unProcessedReferences, processedReferences, breadCrumbs, namespacesJsonOption, schemasJsonOption).map(id -> _)
-      })
-    } yield flattenedWorkflows).map(_.toMap)
-
-    // Replace the unprocessed runs with their processed value
-    (processedRunReferences, processedInlineReferences).tupled.map(Function.tupled(inlineProcessedJsons))
-  }
-}
-
-private object CwlCanonicalizer {
-  /**
-    * A Cwl json that has been processed (saladed and flattened), as well as its processed dependencies.
-    */
-  final case class ProcessedJsonAndDependencies(processedJson: Json, processedDependencies: ProcessedReferences)
-
-  final type UnProcessedReferences = Map[CwlReference, Json]
-  final type ProcessedReferences = Map[CwlReference, Json]
-}
diff --git a/cwl/src/main/scala/cwl/preprocessor/CwlPreProcessor.scala b/cwl/src/main/scala/cwl/preprocessor/CwlPreProcessor.scala
deleted file mode 100644
index 9855ee73953..00000000000
--- a/cwl/src/main/scala/cwl/preprocessor/CwlPreProcessor.scala
+++ /dev/null
@@ -1,236 +0,0 @@
-package cwl.preprocessor
-
-import java.util.concurrent.Executors
-
-import cats.data.NonEmptyList
-import cats.effect.{ContextShift, IO}
-import cats.syntax.either._
-import common.validation.IOChecked._
-import cwl.CwlDecoder
-import cwl.ontology.Schema
-import cwl.preprocessor.CwlPreProcessor._
-import cwl.preprocessor.CwlReference.EnhancedCwlId
-import io.circe.optics.JsonPath._
-import io.circe.{Json, JsonNumber, JsonObject}
-import mouse.all._
-import org.slf4j.LoggerFactory
-import wom.util.YamlUtils
-
-import scala.concurrent.ExecutionContext
-
-/**
-  * Class to create a standalone version of a CWL file.
-  *
-  * NB: Want to use the pre-processor? Use preProcessCwl(ref: CwlReference)
-  *
-  * @param saladFunction function that takes a file and produce a saladed version of the content
-  */
-class CwlPreProcessor(saladFunction: SaladFunction = saladCwlFile) {
-
-  private val ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(5))
-  private implicit val cs = IO.contextShift(ec)
-
-  /**
-    * This is THE main entry point into the CWL pre-processor. Takes a CWL reference and
-    * returns a canonical JSON version with all references resolved.
-    *
-    * @param ref The reference to the CWL to pre-process
-    * @return A canonical JSON representation of the CWL with all internal references expanded in-place
-    */
-  def preProcessCwl(ref: CwlReference): IOChecked[Json] = ref match {
-    case file: CwlFileReference => preProcessCwlFile(file)
-    case other => preProcessRemoteCwl(other)
-  }
-
-  /**
-    * Convenience method to get the processed workflow as a string.
-    */
-  def preProcessCwlToString(cwlReference: CwlReference): IOChecked[String] = preProcessCwl(cwlReference).map(_.printCompact)
-
-  def preProcessInputFiles(inputContent: String, mappingFunction: String => String): IOChecked[String] = for {
-    parsed <- parseYaml(inputContent)
-    mapped = parsed |> mapFilesAndDirectories(mappingFunction) |> mapNumbers
-  } yield mapped.printCompact
-
-  /**
-    * Pre-process a CWL file and create a standalone, runnable (given proper inputs), inlined version of its content.
-    *
-    * The general idea is to work on CwlReferences, starting from the one coming to this function in the form of file and optional root.
-    * The goal is to look at the steps in this workflow that point to other references, and recursively flatten them until we can replace the step with
-    * its flat version.
-    *
-    * There are 3 pieces of information that are carried around during this process:
-    *  1) ProcessedReferences: A Map[CwlReference, Json] of CwlReference for which we have the fully processed (saladed AND flattened) Json value.
-    *
-    *  2) UnProcessedReferences: A Map[CwlReference, Json] of CwlReference for which we have the saladed but NOT flattened Json value.
-    *     This can happen because a file can contain multiple tools / workflows. When we salad / parse this file, we get (CwlReference, Json) pairs
-    *     for all the workflow / tools in the file, but they are not flattened yet.
-    *     We keep this to avoid having to re-salad / re-parse files unnecessarily.
-    *
-    *  3) BreadCrumb: A Set[CwlReference] used to follow the trail of CwlReferences that we are processing as we recurse down.
-    *     This is used to be able to detect circular dependencies (if the cwlReference being processed is in that set, then we have a circular dependency) .
-    *
-    */
-  private def preProcessCwlFile(reference: CwlFileReference): IOChecked[Json] = {
-
-    def absoluteSchemaPaths(json: Json): Json = {
-      json mapArray {
-        _ map absoluteSchemaPaths
-      } mapString {
-        Schema.getIriPath(reference.fullReference, _)
-      }
-    }
-
-    // NB the JSON here is only used to decide whether or not to flatten. If we do decide to flatten we throw away the
-    // json and request a canonical version from the CwlCanonicalizer.
-    def flattenOrByPass(json: Json): IOChecked[Json] = {
-      def flatten(json: Json): IOChecked[Json] = {
-        val cwlReferenceFlattener = new CwlCanonicalizer(saladFunction)
-        val namespacesJsonOption: Option[Json] = json.asObject.flatMap(_.kleisli(JsonKeyNamespaces))
-        val schemasJsonOption: Option[Json] = json.asObject.flatMap(_.kleisli(JsonKeySchemas)).map(absoluteSchemaPaths)
-
-        cwlReferenceFlattener.getCanonicalCwl(
-          reference,
-          namespacesJsonOption,
-          schemasJsonOption
-        )
-      }
-
-      def bypass(alreadyCanonicalJson: Json): IOChecked[Json] = alreadyCanonicalJson.validIOChecked
-
-      val fileContentReference = for {
-        asObject <- json.asObject
-        fileContentId <- asObject.kleisli("id")
-        stringId <- fileContentId.asString
-        fileContentReference <- CwlReference.fromString(stringId)
-      } yield fileContentReference
-
-      fileContentReference match {
-        // This by passes the pre-processing if the file already has an id for which the file part doesn't match the path of the file
-        // passed to this function, as this would indicate that it has already been saladed and pre-processed.
-        case Some(CwlFileReference(file, _)) if !file.equals(reference.file) => bypass(json)
-        case _ => flatten(json)
-      }
-    }
-
-    for {
-      original <- parseYaml(reference.file.contentAsString)
-      flattened <- flattenOrByPass(original)
-    } yield flattened
-  }
-
-  // Like 'File', except that we don't read any contents before passing the path over to cwltool to canonicalize.
-  private def preProcessRemoteCwl(reference: CwlReference)(implicit cs: ContextShift[IO]): IOChecked[Json] = {
-    val cwlCanonicalizer = new CwlCanonicalizer(saladFunction)
-    cwlCanonicalizer.getCanonicalCwl(reference)
-  }
-}
-
-object CwlPreProcessor {
-  private val Log = LoggerFactory.getLogger("CwlPreProcessor")
-
-  private [preprocessor] type SaladFunction = CwlReference => IOChecked[String]
-  private [preprocessor] val JsonKeyNamespaces = s"$$namespaces"
-  private [preprocessor] val JsonKeySchemas = s"$$schemas"
-
-  private def saladSpinner(doLogging: Boolean): SaladFunction = ref => {
-    if (doLogging) {
-      Log.info(s"Pre-Processing ${ref.pathAsString}")
-    }
-
-    CwlDecoder.saladCwlFile(ref)
-  }
-
-  private [preprocessor] val saladCwlFile: SaladFunction = saladSpinner(true)
-  private val saladCwlFileWithoutLogging: SaladFunction = saladSpinner(false)
-
-  implicit class PrintableJson(val json: Json) extends AnyVal {
-    def printCompact = io.circe.Printer.noSpaces.print(json)
-  }
-
-  def noLogging = new CwlPreProcessor(saladCwlFileWithoutLogging)
-
-  // Fold over a json recursively and prefix all files
-  def mapFilesAndDirectories(mappingFunction: String => String)(json: Json): Json = {
-    // Function to check if the given json has the provided key / value pair
-    def hasKeyValue(key: String, value: String): Json => Boolean = {
-      root.selectDynamic(key).string.exist(_.equalsIgnoreCase(value))
-    }
-
-    // Return true if the given json object represents a File
-    def isFile(obj: JsonObject) = hasKeyValue("class", "File")(Json.fromJsonObject(obj))
-
-    // Return true if the given json object represents a Directory
-    def isDirectory(obj: JsonObject) = hasKeyValue("class", "Directory")(Json.fromJsonObject(obj))
-
-    // Modify the string at "key" using the mappingFunction
-    def mapStringValue(key: String, mappingFunction: String => String): Json => Json = root.selectDynamic(key).string.modify(mappingFunction)
-
-    // Map "location" and "default"
-    def prefix(mappingFunction: String => String): Json => Json = mapStringValue("location", mappingFunction).compose(mapStringValue("path", mappingFunction))
-
-    // Prefix the location or path in the json object if it's a file or directory, otherwise recurse over its fields
-    def prefixObject(mappingFunction: String => String)(obj: JsonObject): Json = {
-      // If the object is file or a directory, prefix it with the gcs prefix
-      if (isFile(obj) || isDirectory(obj)) {
-        prefix(mappingFunction)(Json.fromJsonObject(obj))
-          // Even if it's a file it may have secondary files. So keep recursing on its fields
-          .mapObject(_.mapValues(mapFilesAndDirectories(mappingFunction)))
-      }
-      // Otherwise recursively process its fields
-      else Json.fromJsonObject(obj.mapValues(mapFilesAndDirectories(mappingFunction)))
-    }
-
-    json.fold(
-      jsonNull = json,
-      jsonBoolean = _ => json,
-      jsonNumber = _ => json,
-      jsonString = _ => json,
-      jsonObject = prefixObject(mappingFunction),
-      jsonArray = arr => Json.arr(arr.map(mapFilesAndDirectories(mappingFunction)): _*)
-    )
-  }
-
-  private [preprocessor] def mapNumbers(json: Json): Json = {
-    // Circumvent Circe's scientific format for numbers: convert to a JSON String without exponential notation.
-    def nonScientificNumberFormatting(jsonNumber: JsonNumber): Json = {
-      val conversions = LazyList[JsonNumber => Option[Any]](
-        _.toBigInt.map(_.longValue),
-        _.toBigDecimal.map(_.doubleValue),
-        Function.const(Option("null")))
-
-      // The `get` is safe because `Option("null")` guarantees a match even if the other two Stream elements
-      // do not satisfy the predicate.
-      conversions.map(_.apply(jsonNumber)).find(_.isDefined).flatten.get.toString |> Json.fromString
-    }
-
-    json.fold(
-      jsonNull = json,
-      jsonBoolean = _ => json,
-      jsonNumber = nonScientificNumberFormatting,
-      jsonString = _ => json,
-      jsonObject = _.mapValues(mapNumbers) |> Json.fromJsonObject,
-      jsonArray = _.map(mapNumbers) |> Json.fromValues
-    )
-  }
-
-  private [preprocessor] def parseJson(in: String): IOChecked[Json] = {
-    io.circe.parser.parse(in).leftMap(error => NonEmptyList.one(error.message)).toIOChecked
-  }
-
-  private [preprocessor] def parseYaml(in: String): IOChecked[Json] = {
-    val yaml = YamlUtils.parse(in)
-    yaml.leftMap(error => NonEmptyList.one(error.message)).toIOChecked
-  }
-
-  /**
-    * Given a json, collect all tools or workflows and map them with their reference id.
-    * A saladed JSON is assumed.
-    */
-  private [preprocessor] def mapIdToContent(json: Json): List[(CwlReference, Json)] = {
-    json.asArray match {
-      case Some(cwls) => cwls.toList.flatMap(mapIdToContent)
-      case None => root.id.string.getOption(json).flatMap(_.asReference).map(_ -> json).toList
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/preprocessor/CwlReference.scala b/cwl/src/main/scala/cwl/preprocessor/CwlReference.scala
deleted file mode 100644
index badddf028b4..00000000000
--- a/cwl/src/main/scala/cwl/preprocessor/CwlReference.scala
+++ /dev/null
@@ -1,82 +0,0 @@
-package cwl.preprocessor
-
-import better.files.{File => BFile}
-import cwl.preprocessor.CwlReference._
-import cwl.{FileAndId, FullyQualifiedName}
-import cwl.command.ParentName
-
-sealed trait CwlReference {
-  def pathAsString: String
-  def pointerWithinFile: Option[String]
-  def changePointer(to: Option[String]): CwlReference
-
-  private def pointerWithHash: String = pointerWithinFile.map(p => s"#$p").getOrElse("")
-  lazy val fullReference: String = s"$pathAsString$pointerWithHash"
-
-  override def toString: String = fullReference
-}
-
-/**
-  * Saladed CWLs reference other local CWL "node" (workflow or tool) using a URI as follow:
-  * file:///path/to/file/containing/node.cwl[#pointer_to_node]
-  * #pointer_to_node to node is optional, and will specify which workflow or tool is being targeted in the file.
-  *
-  * e.g:
-  *   {
-  *     "class": "Workflow",
-  *     "id": "file:///path/to/workflow/workflow.cwl",
-  *     ...
-  *     "steps": [
-  *       {
-  *         "run": "file:///path/to/workflow/multi_tools.cwl#my_tool",
-  *         ...
-  *       }
-  *     ]
-  *   }
-  *
-  * This snippet contains 2 references, one that is the ID of this workflow, the other one is the run step pointing to "my_tool" in "/path/to/workflow/multi_tools.cwl"
-  *
-  */
-final case class CwlFileReference(file: BFile, pointerWithinFile: Option[String]) extends CwlReference {
-  override val pathAsString: String = s"$LocalScheme${file.toString}"
-  override def changePointer(to: Option[String]): CwlReference = this.copy(pointerWithinFile = to)
-}
-
-final case class CwlHttpReference(pathAsString: String, pointerWithinFile: Option[String]) extends CwlReference {
-  override def changePointer(to: Option[String]): CwlReference = this.copy(pointerWithinFile = to)
-}
-
-object CwlReference {
-  val LocalScheme = "file://"
-  val HttpScheme = "http://"
-  val HttpsScheme = "https://"
-
-  implicit class EnhancedCwlId(val id: String) extends AnyVal {
-    def asReference: Option[CwlReference] = CwlReference.fromString(id)
-    def stripFilePrefix = id.stripPrefix(LocalScheme)
-  }
-
-  val ReferenceRegex = "(.*://)?([^#]*)(#(.*))?".r
-
-  def fromString(in: String): Option[CwlReference] = {
-    in match {
-      case ReferenceRegex(scheme, path, _, pointerWithinFile) =>
-        if (scheme == LocalScheme) {
-          FullyQualifiedName.maybeApply(in)(ParentName.empty) match {
-            case Some(FileAndId(file, _, _)) => Option(CwlFileReference(BFile(file.stripFilePrefix), Option(pointerWithinFile)))
-            case _ => Option(CwlFileReference(BFile(in.stripFilePrefix), Option(pointerWithinFile)))
-          }
-        } else if (scheme == HttpScheme || scheme == HttpsScheme) {
-          Option(CwlHttpReference(s"$scheme$path", Option(pointerWithinFile)))
-        } else {
-          None
-        }
-    }
-  }
-}
-
-object CwlFileReference {
-  def apply(file: BFile, pointer: Option[String]) = {
-    new CwlFileReference(file, pointer)
-  }
-}
diff --git a/cwl/src/main/scala/cwl/requirement/RequirementToAttributeMap.scala b/cwl/src/main/scala/cwl/requirement/RequirementToAttributeMap.scala
deleted file mode 100644
index 1a727837172..00000000000
--- a/cwl/src/main/scala/cwl/requirement/RequirementToAttributeMap.scala
+++ /dev/null
@@ -1,79 +0,0 @@
-package cwl.requirement
-
-import cwl._
-import shapeless.Poly1
-import wom.RuntimeAttributesKeys._
-import wom.expression.{ValueAsAnExpression, WomExpression}
-import wom.values.{WomLong, WomString}
-
-object RequirementToAttributeMap extends Poly1 {
-  type ResourcesToExpressionMap = (Set[String], ExpressionLib) => Map[String, WomExpression]
-  implicit def fromJs: Case.Aux[InlineJavascriptRequirement, ResourcesToExpressionMap] = at[InlineJavascriptRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromSchemaDef: Case.Aux[SchemaDefRequirement, ResourcesToExpressionMap] = at[SchemaDefRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromDocker: Case.Aux[DockerRequirement, ResourcesToExpressionMap] = at[DockerRequirement] {
-    docker => (_,_) => docker.dockerPull.orElse(docker.dockerImageId).map({ pull =>
-      DockerKey -> ValueAsAnExpression(WomString(pull))
-    }).toMap
-  }
-
-  implicit def fromSoftware: Case.Aux[SoftwareRequirement, ResourcesToExpressionMap] = at[SoftwareRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromInitialWorkDir: Case.Aux[InitialWorkDirRequirement, ResourcesToExpressionMap] = at[InitialWorkDirRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromEnvVar: Case.Aux[EnvVarRequirement, ResourcesToExpressionMap] = at[EnvVarRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromShellCommand: Case.Aux[ShellCommandRequirement, ResourcesToExpressionMap] = at[ShellCommandRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromResource: Case.Aux[ResourceRequirement, ResourcesToExpressionMap] = at[ResourceRequirement] {
-    resource => (inputNames, expressionLib) =>
-      def toExpression(resourceRequirement: ResourceRequirementType) =
-        resourceRequirement.fold(ResourceRequirementToWomExpression).apply(inputNames, expressionLib)
-
-      List(
-        // Map cpuMin to both cpuMin and cpu keys
-        resource.effectiveCoreMin.toList.map(toExpression).flatMap(min => List(CpuMinKey -> min, CpuKey -> min)),
-        resource.effectiveCoreMax.toList.map(toExpression).map(CpuMaxKey -> _),
-        // Map ramMin to both memoryMin and memory keys
-        resource.effectiveRamMin.toList.map(toExpression).flatMap(min => List(MemoryMinKey -> min, MemoryKey -> min)),
-        resource.effectiveRamMax.toList.map(toExpression).map(MemoryMaxKey -> _),
-        resource.effectiveTmpdirMin.toList.map(toExpression).map(TmpDirMinKey -> _),
-        resource.effectiveTmpdirMax.toList.map(toExpression).map(TmpDirMaxKey -> _),
-        resource.effectiveOutdirMin.toList.map(toExpression).map(OutDirMinKey -> _),
-        resource.effectiveOutdirMax.toList.map(toExpression).map(OutDirMaxKey -> _)
-      ).flatten.toMap
-  }
-
-  implicit def fromInputResourceRequirement: Case.Aux[DnaNexusInputResourceRequirement, ResourcesToExpressionMap] = at[DnaNexusInputResourceRequirement] {
-    case DnaNexusInputResourceRequirement(_, indirMin) => (_, _) => indirMin.map(value => ValueAsAnExpression(WomLong(value))).map(DnaNexusInputDirMinKey -> _).toMap
-  }
-
-  implicit def fromSubWorkflow: Case.Aux[SubworkflowFeatureRequirement, ResourcesToExpressionMap] = at[SubworkflowFeatureRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromScatter: Case.Aux[ScatterFeatureRequirement, ResourcesToExpressionMap] = at[ScatterFeatureRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromMultipleInput: Case.Aux[MultipleInputFeatureRequirement, ResourcesToExpressionMap] = at[MultipleInputFeatureRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromStepInput: Case.Aux[StepInputExpressionRequirement, ResourcesToExpressionMap] = at[StepInputExpressionRequirement] {
-    _ => (_,_) => Map.empty
-  }
-}
diff --git a/cwl/src/main/scala/cwl/requirement/ResourceRequirementToWomExpression.scala b/cwl/src/main/scala/cwl/requirement/ResourceRequirementToWomExpression.scala
deleted file mode 100644
index 74727947657..00000000000
--- a/cwl/src/main/scala/cwl/requirement/ResourceRequirementToWomExpression.scala
+++ /dev/null
@@ -1,15 +0,0 @@
-package cwl.requirement
-
-import cwl.{Expression, ExpressionLib}
-import shapeless.Poly1
-import wom.expression.{ValueAsAnExpression, WomExpression}
-import wom.values.{WomLong, WomString}
-
-object ResourceRequirementToWomExpression extends Poly1 {
-  type ResourceRequirementStringSetToWomExpression = (Set[String], ExpressionLib) => WomExpression
-  implicit def fromLong: Case.Aux[Long, ResourceRequirementStringSetToWomExpression] = at[Long] { l => (_, _) => ValueAsAnExpression(WomLong(l)) }
-  implicit def fromString: Case.Aux[String, ResourceRequirementStringSetToWomExpression] = at[String] { s =>  (_, _) => ValueAsAnExpression(WomString(s)) }
-  implicit def fromExpression: Case.Aux[Expression, ResourceRequirementStringSetToWomExpression] = at[Expression] { e => (inputs, expressionLib) =>
-    cwl.ECMAScriptWomExpression(e, inputs, expressionLib)
-  }
-}
diff --git a/cwl/src/test/resources/1st-tool.cwl b/cwl/src/test/resources/1st-tool.cwl
deleted file mode 100755
index af0c4de297d..00000000000
--- a/cwl/src/test/resources/1st-tool.cwl
+++ /dev/null
@@ -1,9 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-inputs:
-  message:
-    type: string
-    inputBinding:
-      position: 1
-outputs: []
diff --git a/cwl/src/test/resources/1st-workflow.cwl b/cwl/src/test/resources/1st-workflow.cwl
deleted file mode 100644
index ce4b4b0bd71..00000000000
--- a/cwl/src/test/resources/1st-workflow.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: File
-  ex: string
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classfile
-
-steps:
-  untar:
-    run: tar-param.cwl
-    in:
-      tarfile: inp
-      extractfile: ex
-    out: [example_out]
-
-  compile:
-    run: arguments.cwl
-    in:
-      src: untar/example_out
-    out: [classfile]
diff --git a/cwl/src/test/resources/application.conf b/cwl/src/test/resources/application.conf
deleted file mode 100644
index 8d12b670cd3..00000000000
--- a/cwl/src/test/resources/application.conf
+++ /dev/null
@@ -1,14 +0,0 @@
-akka {
-  log-dead-letters = "off"
-  loggers = ["akka.event.slf4j.Slf4jLogger"]
-}
-
-ontology {
-  # Uncomment to enable caching of ontologies. Improves performance when loading ontologies from remote IRIs.
-  #cache {
-  #  max-size = 20
-  #}
-  retries = 3
-  pool-size = 3
-  backoff-time = 2 seconds
-}
diff --git a/cwl/src/test/resources/arguments.cwl b/cwl/src/test/resources/arguments.cwl
deleted file mode 100644
index 730030e7437..00000000000
--- a/cwl/src/test/resources/arguments.cwl
+++ /dev/null
@@ -1,22 +0,0 @@
-cwlVersion: "v1.0"
-class: "CommandLineTool"
-label: "Example trivial wrapper for Java 7 compiler"
-hints: 
-  - dockerPull: "java:7-jdk"
-    class: "DockerRequirement"
-baseCommand: "javac"
-arguments: 
-  - "-d"
-  - "$(runtime.outdir)"
-inputs: 
-  - type: "File"
-    inputBinding: 
-      position: 1
-    id: "file:///home/dan/wdl4s/arguments.cwl#src"
-outputs: 
-  - type: "File"
-    outputBinding: 
-      glob: "*.class"
-    id: "file:///home/dan/wdl4s/arguments.cwl#classfile"
-id: "file:///home/dan/wdl4s/arguments.cwl"
-name: "file:///home/dan/wdl4s/arguments.cwl"
diff --git a/cwl/src/test/resources/bad.cwl b/cwl/src/test/resources/bad.cwl
deleted file mode 100644
index d38ed298731..00000000000
--- a/cwl/src/test/resources/bad.cwl
+++ /dev/null
@@ -1 +0,0 @@
-gibberish
diff --git a/cwl/src/test/resources/bad2.cwl b/cwl/src/test/resources/bad2.cwl
deleted file mode 100644
index d38ed298731..00000000000
--- a/cwl/src/test/resources/bad2.cwl
+++ /dev/null
@@ -1 +0,0 @@
-gibberish
diff --git a/cwl/src/test/resources/brokenlinks.cwl b/cwl/src/test/resources/brokenlinks.cwl
deleted file mode 100644
index c710358ce61..00000000000
--- a/cwl/src/test/resources/brokenlinks.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: File
-  ex: string
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classfile
-
-steps:
-  untar:
-    run: wrong.cwl
-    in:
-      tarfile: inp
-      extractfile: ex
-    out: [example_out]
-
-  compile:
-    run: wrong2.cwl
-    in:
-      src: untar/example_out
-    out: [classfile]
diff --git a/cwl/src/test/resources/cwl/lodash.js b/cwl/src/test/resources/cwl/lodash.js
deleted file mode 100644
index 9b95dfefe87..00000000000
--- a/cwl/src/test/resources/cwl/lodash.js
+++ /dev/null
@@ -1,17112 +0,0 @@
-/**
- * @license
- * Lodash <https://lodash.com/>
- * Copyright OpenJS Foundation and other contributors <https://openjsf.org/>
- * Released under MIT license <https://lodash.com/license>
- * Based on Underscore.js 1.8.3 <http://underscorejs.org/LICENSE>
- * Copyright Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
- */
-;(function() {
-
-  /** Used as a safe reference for `undefined` in pre-ES5 environments. */
-  var undefined;
-
-  /** Used as the semantic version number. */
-  var VERSION = '4.17.15';
-
-  /** Used as the size to enable large array optimizations. */
-  var LARGE_ARRAY_SIZE = 200;
-
-  /** Error message constants. */
-  var CORE_ERROR_TEXT = 'Unsupported core-js use. Try https://npms.io/search?q=ponyfill.',
-      FUNC_ERROR_TEXT = 'Expected a function';
-
-  /** Used to stand-in for `undefined` hash values. */
-  var HASH_UNDEFINED = '__lodash_hash_undefined__';
-
-  /** Used as the maximum memoize cache size. */
-  var MAX_MEMOIZE_SIZE = 500;
-
-  /** Used as the internal argument placeholder. */
-  var PLACEHOLDER = '__lodash_placeholder__';
-
-  /** Used to compose bitmasks for cloning. */
-  var CLONE_DEEP_FLAG = 1,
-      CLONE_FLAT_FLAG = 2,
-      CLONE_SYMBOLS_FLAG = 4;
-
-  /** Used to compose bitmasks for value comparisons. */
-  var COMPARE_PARTIAL_FLAG = 1,
-      COMPARE_UNORDERED_FLAG = 2;
-
-  /** Used to compose bitmasks for function metadata. */
-  var WRAP_BIND_FLAG = 1,
-      WRAP_BIND_KEY_FLAG = 2,
-      WRAP_CURRY_BOUND_FLAG = 4,
-      WRAP_CURRY_FLAG = 8,
-      WRAP_CURRY_RIGHT_FLAG = 16,
-      WRAP_PARTIAL_FLAG = 32,
-      WRAP_PARTIAL_RIGHT_FLAG = 64,
-      WRAP_ARY_FLAG = 128,
-      WRAP_REARG_FLAG = 256,
-      WRAP_FLIP_FLAG = 512;
-
-  /** Used as default options for `_.truncate`. */
-  var DEFAULT_TRUNC_LENGTH = 30,
-      DEFAULT_TRUNC_OMISSION = '...';
-
-  /** Used to detect hot functions by number of calls within a span of milliseconds. */
-  var HOT_COUNT = 800,
-      HOT_SPAN = 16;
-
-  /** Used to indicate the type of lazy iteratees. */
-  var LAZY_FILTER_FLAG = 1,
-      LAZY_MAP_FLAG = 2,
-      LAZY_WHILE_FLAG = 3;
-
-  /** Used as references for various `Number` constants. */
-  var INFINITY = 1 / 0,
-      MAX_SAFE_INTEGER = 9007199254740991,
-      MAX_INTEGER = 1.7976931348623157e+308,
-      NAN = 0 / 0;
-
-  /** Used as references for the maximum length and index of an array. */
-  var MAX_ARRAY_LENGTH = 4294967295,
-      MAX_ARRAY_INDEX = MAX_ARRAY_LENGTH - 1,
-      HALF_MAX_ARRAY_LENGTH = MAX_ARRAY_LENGTH >>> 1;
-
-  /** Used to associate wrap methods with their bit flags. */
-  var wrapFlags = [
-    ['ary', WRAP_ARY_FLAG],
-    ['bind', WRAP_BIND_FLAG],
-    ['bindKey', WRAP_BIND_KEY_FLAG],
-    ['curry', WRAP_CURRY_FLAG],
-    ['curryRight', WRAP_CURRY_RIGHT_FLAG],
-    ['flip', WRAP_FLIP_FLAG],
-    ['partial', WRAP_PARTIAL_FLAG],
-    ['partialRight', WRAP_PARTIAL_RIGHT_FLAG],
-    ['rearg', WRAP_REARG_FLAG]
-  ];
-
-  /** `Object#toString` result references. */
-  var argsTag = '[object Arguments]',
-      arrayTag = '[object Array]',
-      asyncTag = '[object AsyncFunction]',
-      boolTag = '[object Boolean]',
-      dateTag = '[object Date]',
-      domExcTag = '[object DOMException]',
-      errorTag = '[object Error]',
-      funcTag = '[object Function]',
-      genTag = '[object GeneratorFunction]',
-      mapTag = '[object Map]',
-      numberTag = '[object Number]',
-      nullTag = '[object Null]',
-      objectTag = '[object Object]',
-      promiseTag = '[object Promise]',
-      proxyTag = '[object Proxy]',
-      regexpTag = '[object RegExp]',
-      setTag = '[object Set]',
-      stringTag = '[object String]',
-      symbolTag = '[object Symbol]',
-      undefinedTag = '[object Undefined]',
-      weakMapTag = '[object WeakMap]',
-      weakSetTag = '[object WeakSet]';
-
-  var arrayBufferTag = '[object ArrayBuffer]',
-      dataViewTag = '[object DataView]',
-      float32Tag = '[object Float32Array]',
-      float64Tag = '[object Float64Array]',
-      int8Tag = '[object Int8Array]',
-      int16Tag = '[object Int16Array]',
-      int32Tag = '[object Int32Array]',
-      uint8Tag = '[object Uint8Array]',
-      uint8ClampedTag = '[object Uint8ClampedArray]',
-      uint16Tag = '[object Uint16Array]',
-      uint32Tag = '[object Uint32Array]';
-
-  /** Used to match empty string literals in compiled template source. */
-  var reEmptyStringLeading = /\b__p \+= '';/g,
-      reEmptyStringMiddle = /\b(__p \+=) '' \+/g,
-      reEmptyStringTrailing = /(__e\(.*?\)|\b__t\)) \+\n'';/g;
-
-  /** Used to match HTML entities and HTML characters. */
-  var reEscapedHtml = /&(?:amp|lt|gt|quot|#39);/g,
-      reUnescapedHtml = /[&<>"']/g,
-      reHasEscapedHtml = RegExp(reEscapedHtml.source),
-      reHasUnescapedHtml = RegExp(reUnescapedHtml.source);
-
-  /** Used to match template delimiters. */
-  var reEscape = /<%-([\s\S]+?)%>/g,
-      reEvaluate = /<%([\s\S]+?)%>/g,
-      reInterpolate = /<%=([\s\S]+?)%>/g;
-
-  /** Used to match property names within property paths. */
-  var reIsDeepProp = /\.|\[(?:[^[\]]*|(["'])(?:(?!\1)[^\\]|\\.)*?\1)\]/,
-      reIsPlainProp = /^\w*$/,
-      rePropName = /[^.[\]]+|\[(?:(-?\d+(?:\.\d+)?)|(["'])((?:(?!\2)[^\\]|\\.)*?)\2)\]|(?=(?:\.|\[\])(?:\.|\[\]|$))/g;
-
-  /**
-   * Used to match `RegExp`
-   * [syntax characters](http://ecma-international.org/ecma-262/7.0/#sec-patterns).
-   */
-  var reRegExpChar = /[\\^$.*+?()[\]{}|]/g,
-      reHasRegExpChar = RegExp(reRegExpChar.source);
-
-  /** Used to match leading and trailing whitespace. */
-  var reTrim = /^\s+|\s+$/g,
-      reTrimStart = /^\s+/,
-      reTrimEnd = /\s+$/;
-
-  /** Used to match wrap detail comments. */
-  var reWrapComment = /\{(?:\n\/\* \[wrapped with .+\] \*\/)?\n?/,
-      reWrapDetails = /\{\n\/\* \[wrapped with (.+)\] \*/,
-      reSplitDetails = /,? & /;
-
-  /** Used to match words composed of alphanumeric characters. */
-  var reAsciiWord = /[^\x00-\x2f\x3a-\x40\x5b-\x60\x7b-\x7f]+/g;
-
-  /** Used to match backslashes in property paths. */
-  var reEscapeChar = /\\(\\)?/g;
-
-  /**
-   * Used to match
-   * [ES template delimiters](http://ecma-international.org/ecma-262/7.0/#sec-template-literal-lexical-components).
-   */
-  var reEsTemplate = /\$\{([^\\}]*(?:\\.[^\\}]*)*)\}/g;
-
-  /** Used to match `RegExp` flags from their coerced string values. */
-  var reFlags = /\w*$/;
-
-  /** Used to detect bad signed hexadecimal string values. */
-  var reIsBadHex = /^[-+]0x[0-9a-f]+$/i;
-
-  /** Used to detect binary string values. */
-  var reIsBinary = /^0b[01]+$/i;
-
-  /** Used to detect host constructors (Safari). */
-  var reIsHostCtor = /^\[object .+?Constructor\]$/;
-
-  /** Used to detect octal string values. */
-  var reIsOctal = /^0o[0-7]+$/i;
-
-  /** Used to detect unsigned integer values. */
-  var reIsUint = /^(?:0|[1-9]\d*)$/;
-
-  /** Used to match Latin Unicode letters (excluding mathematical operators). */
-  var reLatin = /[\xc0-\xd6\xd8-\xf6\xf8-\xff\u0100-\u017f]/g;
-
-  /** Used to ensure capturing order of template delimiters. */
-  var reNoMatch = /($^)/;
-
-  /** Used to match unescaped characters in compiled string literals. */
-  var reUnescapedString = /['\n\r\u2028\u2029\\]/g;
-
-  /** Used to compose unicode character classes. */
-  var rsAstralRange = '\\ud800-\\udfff',
-      rsComboMarksRange = '\\u0300-\\u036f',
-      reComboHalfMarksRange = '\\ufe20-\\ufe2f',
-      rsComboSymbolsRange = '\\u20d0-\\u20ff',
-      rsComboRange = rsComboMarksRange + reComboHalfMarksRange + rsComboSymbolsRange,
-      rsDingbatRange = '\\u2700-\\u27bf',
-      rsLowerRange = 'a-z\\xdf-\\xf6\\xf8-\\xff',
-      rsMathOpRange = '\\xac\\xb1\\xd7\\xf7',
-      rsNonCharRange = '\\x00-\\x2f\\x3a-\\x40\\x5b-\\x60\\x7b-\\xbf',
-      rsPunctuationRange = '\\u2000-\\u206f',
-      rsSpaceRange = ' \\t\\x0b\\f\\xa0\\ufeff\\n\\r\\u2028\\u2029\\u1680\\u180e\\u2000\\u2001\\u2002\\u2003\\u2004\\u2005\\u2006\\u2007\\u2008\\u2009\\u200a\\u202f\\u205f\\u3000',
-      rsUpperRange = 'A-Z\\xc0-\\xd6\\xd8-\\xde',
-      rsVarRange = '\\ufe0e\\ufe0f',
-      rsBreakRange = rsMathOpRange + rsNonCharRange + rsPunctuationRange + rsSpaceRange;
-
-  /** Used to compose unicode capture groups. */
-  var rsApos = "['\u2019]",
-      rsAstral = '[' + rsAstralRange + ']',
-      rsBreak = '[' + rsBreakRange + ']',
-      rsCombo = '[' + rsComboRange + ']',
-      rsDigits = '\\d+',
-      rsDingbat = '[' + rsDingbatRange + ']',
-      rsLower = '[' + rsLowerRange + ']',
-      rsMisc = '[^' + rsAstralRange + rsBreakRange + rsDigits + rsDingbatRange + rsLowerRange + rsUpperRange + ']',
-      rsFitz = '\\ud83c[\\udffb-\\udfff]',
-      rsModifier = '(?:' + rsCombo + '|' + rsFitz + ')',
-      rsNonAstral = '[^' + rsAstralRange + ']',
-      rsRegional = '(?:\\ud83c[\\udde6-\\uddff]){2}',
-      rsSurrPair = '[\\ud800-\\udbff][\\udc00-\\udfff]',
-      rsUpper = '[' + rsUpperRange + ']',
-      rsZWJ = '\\u200d';
-
-  /** Used to compose unicode regexes. */
-  var rsMiscLower = '(?:' + rsLower + '|' + rsMisc + ')',
-      rsMiscUpper = '(?:' + rsUpper + '|' + rsMisc + ')',
-      rsOptContrLower = '(?:' + rsApos + '(?:d|ll|m|re|s|t|ve))?',
-      rsOptContrUpper = '(?:' + rsApos + '(?:D|LL|M|RE|S|T|VE))?',
-      reOptMod = rsModifier + '?',
-      rsOptVar = '[' + rsVarRange + ']?',
-      rsOptJoin = '(?:' + rsZWJ + '(?:' + [rsNonAstral, rsRegional, rsSurrPair].join('|') + ')' + rsOptVar + reOptMod + ')*',
-      rsOrdLower = '\\d*(?:1st|2nd|3rd|(?![123])\\dth)(?=\\b|[A-Z_])',
-      rsOrdUpper = '\\d*(?:1ST|2ND|3RD|(?![123])\\dTH)(?=\\b|[a-z_])',
-      rsSeq = rsOptVar + reOptMod + rsOptJoin,
-      rsEmoji = '(?:' + [rsDingbat, rsRegional, rsSurrPair].join('|') + ')' + rsSeq,
-      rsSymbol = '(?:' + [rsNonAstral + rsCombo + '?', rsCombo, rsRegional, rsSurrPair, rsAstral].join('|') + ')';
-
-  /** Used to match apostrophes. */
-  var reApos = RegExp(rsApos, 'g');
-
-  /**
-   * Used to match [combining diacritical marks](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks) and
-   * [combining diacritical marks for symbols](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks_for_Symbols).
-   */
-  var reComboMark = RegExp(rsCombo, 'g');
-
-  /** Used to match [string symbols](https://mathiasbynens.be/notes/javascript-unicode). */
-  var reUnicode = RegExp(rsFitz + '(?=' + rsFitz + ')|' + rsSymbol + rsSeq, 'g');
-
-  /** Used to match complex or compound words. */
-  var reUnicodeWord = RegExp([
-    rsUpper + '?' + rsLower + '+' + rsOptContrLower + '(?=' + [rsBreak, rsUpper, '$'].join('|') + ')',
-    rsMiscUpper + '+' + rsOptContrUpper + '(?=' + [rsBreak, rsUpper + rsMiscLower, '$'].join('|') + ')',
-    rsUpper + '?' + rsMiscLower + '+' + rsOptContrLower,
-    rsUpper + '+' + rsOptContrUpper,
-    rsOrdUpper,
-    rsOrdLower,
-    rsDigits,
-    rsEmoji
-  ].join('|'), 'g');
-
-  /** Used to detect strings with [zero-width joiners or code points from the astral planes](http://eev.ee/blog/2015/09/12/dark-corners-of-unicode/). */
-  var reHasUnicode = RegExp('[' + rsZWJ + rsAstralRange  + rsComboRange + rsVarRange + ']');
-
-  /** Used to detect strings that need a more robust regexp to match words. */
-  var reHasUnicodeWord = /[a-z][A-Z]|[A-Z]{2}[a-z]|[0-9][a-zA-Z]|[a-zA-Z][0-9]|[^a-zA-Z0-9 ]/;
-
-  /** Used to assign default `context` object properties. */
-  var contextProps = [
-    'Array', 'Buffer', 'DataView', 'Date', 'Error', 'Float32Array', 'Float64Array',
-    'Function', 'Int8Array', 'Int16Array', 'Int32Array', 'Map', 'Math', 'Object',
-    'Promise', 'RegExp', 'Set', 'String', 'Symbol', 'TypeError', 'Uint8Array',
-    'Uint8ClampedArray', 'Uint16Array', 'Uint32Array', 'WeakMap',
-    '_', 'clearTimeout', 'isFinite', 'parseInt', 'setTimeout'
-  ];
-
-  /** Used to make template sourceURLs easier to identify. */
-  var templateCounter = -1;
-
-  /** Used to identify `toStringTag` values of typed arrays. */
-  var typedArrayTags = {};
-  typedArrayTags[float32Tag] = typedArrayTags[float64Tag] =
-  typedArrayTags[int8Tag] = typedArrayTags[int16Tag] =
-  typedArrayTags[int32Tag] = typedArrayTags[uint8Tag] =
-  typedArrayTags[uint8ClampedTag] = typedArrayTags[uint16Tag] =
-  typedArrayTags[uint32Tag] = true;
-  typedArrayTags[argsTag] = typedArrayTags[arrayTag] =
-  typedArrayTags[arrayBufferTag] = typedArrayTags[boolTag] =
-  typedArrayTags[dataViewTag] = typedArrayTags[dateTag] =
-  typedArrayTags[errorTag] = typedArrayTags[funcTag] =
-  typedArrayTags[mapTag] = typedArrayTags[numberTag] =
-  typedArrayTags[objectTag] = typedArrayTags[regexpTag] =
-  typedArrayTags[setTag] = typedArrayTags[stringTag] =
-  typedArrayTags[weakMapTag] = false;
-
-  /** Used to identify `toStringTag` values supported by `_.clone`. */
-  var cloneableTags = {};
-  cloneableTags[argsTag] = cloneableTags[arrayTag] =
-  cloneableTags[arrayBufferTag] = cloneableTags[dataViewTag] =
-  cloneableTags[boolTag] = cloneableTags[dateTag] =
-  cloneableTags[float32Tag] = cloneableTags[float64Tag] =
-  cloneableTags[int8Tag] = cloneableTags[int16Tag] =
-  cloneableTags[int32Tag] = cloneableTags[mapTag] =
-  cloneableTags[numberTag] = cloneableTags[objectTag] =
-  cloneableTags[regexpTag] = cloneableTags[setTag] =
-  cloneableTags[stringTag] = cloneableTags[symbolTag] =
-  cloneableTags[uint8Tag] = cloneableTags[uint8ClampedTag] =
-  cloneableTags[uint16Tag] = cloneableTags[uint32Tag] = true;
-  cloneableTags[errorTag] = cloneableTags[funcTag] =
-  cloneableTags[weakMapTag] = false;
-
-  /** Used to map Latin Unicode letters to basic Latin letters. */
-  var deburredLetters = {
-    // Latin-1 Supplement block.
-    '\xc0': 'A',  '\xc1': 'A', '\xc2': 'A', '\xc3': 'A', '\xc4': 'A', '\xc5': 'A',
-    '\xe0': 'a',  '\xe1': 'a', '\xe2': 'a', '\xe3': 'a', '\xe4': 'a', '\xe5': 'a',
-    '\xc7': 'C',  '\xe7': 'c',
-    '\xd0': 'D',  '\xf0': 'd',
-    '\xc8': 'E',  '\xc9': 'E', '\xca': 'E', '\xcb': 'E',
-    '\xe8': 'e',  '\xe9': 'e', '\xea': 'e', '\xeb': 'e',
-    '\xcc': 'I',  '\xcd': 'I', '\xce': 'I', '\xcf': 'I',
-    '\xec': 'i',  '\xed': 'i', '\xee': 'i', '\xef': 'i',
-    '\xd1': 'N',  '\xf1': 'n',
-    '\xd2': 'O',  '\xd3': 'O', '\xd4': 'O', '\xd5': 'O', '\xd6': 'O', '\xd8': 'O',
-    '\xf2': 'o',  '\xf3': 'o', '\xf4': 'o', '\xf5': 'o', '\xf6': 'o', '\xf8': 'o',
-    '\xd9': 'U',  '\xda': 'U', '\xdb': 'U', '\xdc': 'U',
-    '\xf9': 'u',  '\xfa': 'u', '\xfb': 'u', '\xfc': 'u',
-    '\xdd': 'Y',  '\xfd': 'y', '\xff': 'y',
-    '\xc6': 'Ae', '\xe6': 'ae',
-    '\xde': 'Th', '\xfe': 'th',
-    '\xdf': 'ss',
-    // Latin Extended-A block.
-    '\u0100': 'A',  '\u0102': 'A', '\u0104': 'A',
-    '\u0101': 'a',  '\u0103': 'a', '\u0105': 'a',
-    '\u0106': 'C',  '\u0108': 'C', '\u010a': 'C', '\u010c': 'C',
-    '\u0107': 'c',  '\u0109': 'c', '\u010b': 'c', '\u010d': 'c',
-    '\u010e': 'D',  '\u0110': 'D', '\u010f': 'd', '\u0111': 'd',
-    '\u0112': 'E',  '\u0114': 'E', '\u0116': 'E', '\u0118': 'E', '\u011a': 'E',
-    '\u0113': 'e',  '\u0115': 'e', '\u0117': 'e', '\u0119': 'e', '\u011b': 'e',
-    '\u011c': 'G',  '\u011e': 'G', '\u0120': 'G', '\u0122': 'G',
-    '\u011d': 'g',  '\u011f': 'g', '\u0121': 'g', '\u0123': 'g',
-    '\u0124': 'H',  '\u0126': 'H', '\u0125': 'h', '\u0127': 'h',
-    '\u0128': 'I',  '\u012a': 'I', '\u012c': 'I', '\u012e': 'I', '\u0130': 'I',
-    '\u0129': 'i',  '\u012b': 'i', '\u012d': 'i', '\u012f': 'i', '\u0131': 'i',
-    '\u0134': 'J',  '\u0135': 'j',
-    '\u0136': 'K',  '\u0137': 'k', '\u0138': 'k',
-    '\u0139': 'L',  '\u013b': 'L', '\u013d': 'L', '\u013f': 'L', '\u0141': 'L',
-    '\u013a': 'l',  '\u013c': 'l', '\u013e': 'l', '\u0140': 'l', '\u0142': 'l',
-    '\u0143': 'N',  '\u0145': 'N', '\u0147': 'N', '\u014a': 'N',
-    '\u0144': 'n',  '\u0146': 'n', '\u0148': 'n', '\u014b': 'n',
-    '\u014c': 'O',  '\u014e': 'O', '\u0150': 'O',
-    '\u014d': 'o',  '\u014f': 'o', '\u0151': 'o',
-    '\u0154': 'R',  '\u0156': 'R', '\u0158': 'R',
-    '\u0155': 'r',  '\u0157': 'r', '\u0159': 'r',
-    '\u015a': 'S',  '\u015c': 'S', '\u015e': 'S', '\u0160': 'S',
-    '\u015b': 's',  '\u015d': 's', '\u015f': 's', '\u0161': 's',
-    '\u0162': 'T',  '\u0164': 'T', '\u0166': 'T',
-    '\u0163': 't',  '\u0165': 't', '\u0167': 't',
-    '\u0168': 'U',  '\u016a': 'U', '\u016c': 'U', '\u016e': 'U', '\u0170': 'U', '\u0172': 'U',
-    '\u0169': 'u',  '\u016b': 'u', '\u016d': 'u', '\u016f': 'u', '\u0171': 'u', '\u0173': 'u',
-    '\u0174': 'W',  '\u0175': 'w',
-    '\u0176': 'Y',  '\u0177': 'y', '\u0178': 'Y',
-    '\u0179': 'Z',  '\u017b': 'Z', '\u017d': 'Z',
-    '\u017a': 'z',  '\u017c': 'z', '\u017e': 'z',
-    '\u0132': 'IJ', '\u0133': 'ij',
-    '\u0152': 'Oe', '\u0153': 'oe',
-    '\u0149': "'n", '\u017f': 's'
-  };
-
-  /** Used to map characters to HTML entities. */
-  var htmlEscapes = {
-    '&': '&amp;',
-    '<': '&lt;',
-    '>': '&gt;',
-    '"': '&quot;',
-    "'": '&#39;'
-  };
-
-  /** Used to map HTML entities to characters. */
-  var htmlUnescapes = {
-    '&amp;': '&',
-    '&lt;': '<',
-    '&gt;': '>',
-    '&quot;': '"',
-    '&#39;': "'"
-  };
-
-  /** Used to escape characters for inclusion in compiled string literals. */
-  var stringEscapes = {
-    '\\': '\\',
-    "'": "'",
-    '\n': 'n',
-    '\r': 'r',
-    '\u2028': 'u2028',
-    '\u2029': 'u2029'
-  };
-
-  /** Built-in method references without a dependency on `root`. */
-  var freeParseFloat = parseFloat,
-      freeParseInt = parseInt;
-
-  /** Detect free variable `global` from Node.js. */
-  var freeGlobal = typeof global == 'object' && global && global.Object === Object && global;
-
-  /** Detect free variable `self`. */
-  var freeSelf = typeof self == 'object' && self && self.Object === Object && self;
-
-  /** Used as a reference to the global object. */
-  var root = freeGlobal || freeSelf || Function('return this')();
-
-  /** Detect free variable `exports`. */
-  var freeExports = typeof exports == 'object' && exports && !exports.nodeType && exports;
-
-  /** Detect free variable `module`. */
-  var freeModule = freeExports && typeof module == 'object' && module && !module.nodeType && module;
-
-  /** Detect the popular CommonJS extension `module.exports`. */
-  var moduleExports = freeModule && freeModule.exports === freeExports;
-
-  /** Detect free variable `process` from Node.js. */
-  var freeProcess = moduleExports && freeGlobal.process;
-
-  /** Used to access faster Node.js helpers. */
-  var nodeUtil = (function() {
-    try {
-      // Use `util.types` for Node.js 10+.
-      var types = freeModule && freeModule.require && freeModule.require('util').types;
-
-      if (types) {
-        return types;
-      }
-
-      // Legacy `process.binding('util')` for Node.js < 10.
-      return freeProcess && freeProcess.binding && freeProcess.binding('util');
-    } catch (e) {}
-  }());
-
-  /* Node.js helper references. */
-  var nodeIsArrayBuffer = nodeUtil && nodeUtil.isArrayBuffer,
-      nodeIsDate = nodeUtil && nodeUtil.isDate,
-      nodeIsMap = nodeUtil && nodeUtil.isMap,
-      nodeIsRegExp = nodeUtil && nodeUtil.isRegExp,
-      nodeIsSet = nodeUtil && nodeUtil.isSet,
-      nodeIsTypedArray = nodeUtil && nodeUtil.isTypedArray;
-
-  /*--------------------------------------------------------------------------*/
-
-  /**
-   * A faster alternative to `Function#apply`, this function invokes `func`
-   * with the `this` binding of `thisArg` and the arguments of `args`.
-   *
-   * @private
-   * @param {Function} func The function to invoke.
-   * @param {*} thisArg The `this` binding of `func`.
-   * @param {Array} args The arguments to invoke `func` with.
-   * @returns {*} Returns the result of `func`.
-   */
-  function apply(func, thisArg, args) {
-    switch (args.length) {
-      case 0: return func.call(thisArg);
-      case 1: return func.call(thisArg, args[0]);
-      case 2: return func.call(thisArg, args[0], args[1]);
-      case 3: return func.call(thisArg, args[0], args[1], args[2]);
-    }
-    return func.apply(thisArg, args);
-  }
-
-  /**
-   * A specialized version of `baseAggregator` for arrays.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} setter The function to set `accumulator` values.
-   * @param {Function} iteratee The iteratee to transform keys.
-   * @param {Object} accumulator The initial aggregated object.
-   * @returns {Function} Returns `accumulator`.
-   */
-  function arrayAggregator(array, setter, iteratee, accumulator) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      var value = array[index];
-      setter(accumulator, value, iteratee(value), array);
-    }
-    return accumulator;
-  }
-
-  /**
-   * A specialized version of `_.forEach` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns `array`.
-   */
-  function arrayEach(array, iteratee) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (iteratee(array[index], index, array) === false) {
-        break;
-      }
-    }
-    return array;
-  }
-
-  /**
-   * A specialized version of `_.forEachRight` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns `array`.
-   */
-  function arrayEachRight(array, iteratee) {
-    var length = array == null ? 0 : array.length;
-
-    while (length--) {
-      if (iteratee(array[length], length, array) === false) {
-        break;
-      }
-    }
-    return array;
-  }
-
-  /**
-   * A specialized version of `_.every` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} predicate The function invoked per iteration.
-   * @returns {boolean} Returns `true` if all elements pass the predicate check,
-   *  else `false`.
-   */
-  function arrayEvery(array, predicate) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (!predicate(array[index], index, array)) {
-        return false;
-      }
-    }
-    return true;
-  }
-
-  /**
-   * A specialized version of `_.filter` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} predicate The function invoked per iteration.
-   * @returns {Array} Returns the new filtered array.
-   */
-  function arrayFilter(array, predicate) {
-    var index = -1,
-        length = array == null ? 0 : array.length,
-        resIndex = 0,
-        result = [];
-
-    while (++index < length) {
-      var value = array[index];
-      if (predicate(value, index, array)) {
-        result[resIndex++] = value;
-      }
-    }
-    return result;
-  }
-
-  /**
-   * A specialized version of `_.includes` for arrays without support for
-   * specifying an index to search from.
-   *
-   * @private
-   * @param {Array} [array] The array to inspect.
-   * @param {*} target The value to search for.
-   * @returns {boolean} Returns `true` if `target` is found, else `false`.
-   */
-  function arrayIncludes(array, value) {
-    var length = array == null ? 0 : array.length;
-    return !!length && baseIndexOf(array, value, 0) > -1;
-  }
-
-  /**
-   * This function is like `arrayIncludes` except that it accepts a comparator.
-   *
-   * @private
-   * @param {Array} [array] The array to inspect.
-   * @param {*} target The value to search for.
-   * @param {Function} comparator The comparator invoked per element.
-   * @returns {boolean} Returns `true` if `target` is found, else `false`.
-   */
-  function arrayIncludesWith(array, value, comparator) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (comparator(value, array[index])) {
-        return true;
-      }
-    }
-    return false;
-  }
-
-  /**
-   * A specialized version of `_.map` for arrays without support for iteratee
-   * shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns the new mapped array.
-   */
-  function arrayMap(array, iteratee) {
-    var index = -1,
-        length = array == null ? 0 : array.length,
-        result = Array(length);
-
-    while (++index < length) {
-      result[index] = iteratee(array[index], index, array);
-    }
-    return result;
-  }
-
-  /**
-   * Appends the elements of `values` to `array`.
-   *
-   * @private
-   * @param {Array} array The array to modify.
-   * @param {Array} values The values to append.
-   * @returns {Array} Returns `array`.
-   */
-  function arrayPush(array, values) {
-    var index = -1,
-        length = values.length,
-        offset = array.length;
-
-    while (++index < length) {
-      array[offset + index] = values[index];
-    }
-    return array;
-  }
-
-  /**
-   * A specialized version of `_.reduce` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @param {*} [accumulator] The initial value.
-   * @param {boolean} [initAccum] Specify using the first element of `array` as
-   *  the initial value.
-   * @returns {*} Returns the accumulated value.
-   */
-  function arrayReduce(array, iteratee, accumulator, initAccum) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    if (initAccum && length) {
-      accumulator = array[++index];
-    }
-    while (++index < length) {
-      accumulator = iteratee(accumulator, array[index], index, array);
-    }
-    return accumulator;
-  }
-
-  /**
-   * A specialized version of `_.reduceRight` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @param {*} [accumulator] The initial value.
-   * @param {boolean} [initAccum] Specify using the last element of `array` as
-   *  the initial value.
-   * @returns {*} Returns the accumulated value.
-   */
-  function arrayReduceRight(array, iteratee, accumulator, initAccum) {
-    var length = array == null ? 0 : array.length;
-    if (initAccum && length) {
-      accumulator = array[--length];
-    }
-    while (length--) {
-      accumulator = iteratee(accumulator, array[length], length, array);
-    }
-    return accumulator;
-  }
-
-  /**
-   * A specialized version of `_.some` for arrays without support for iteratee
-   * shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} predicate The function invoked per iteration.
-   * @returns {boolean} Returns `true` if any element passes the predicate check,
-   *  else `false`.
-   */
-  function arraySome(array, predicate) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (predicate(array[index], index, array)) {
-        return true;
-      }
-    }
-    return false;
-  }
-
-  /**
-   * Gets the size of an ASCII `string`.
-   *
-   * @private
-   * @param {string} string The string inspect.
-   * @returns {number} Returns the string size.
-   */
-  var asciiSize = baseProperty('length');
-
-  /**
-   * Converts an ASCII `string` to an array.
-   *
-   * @private
-   * @param {string} string The string to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function asciiToArray(string) {
-    return string.split('');
-  }
-
-  /**
-   * Splits an ASCII `string` into an array of its words.
-   *
-   * @private
-   * @param {string} The string to inspect.
-   * @returns {Array} Returns the words of `string`.
-   */
-  function asciiWords(string) {
-    return string.match(reAsciiWord) || [];
-  }
-
-  /**
-   * The base implementation of methods like `_.findKey` and `_.findLastKey`,
-   * without support for iteratee shorthands, which iterates over `collection`
-   * using `eachFunc`.
-   *
-   * @private
-   * @param {Array|Object} collection The collection to inspect.
-   * @param {Function} predicate The function invoked per iteration.
-   * @param {Function} eachFunc The function to iterate over `collection`.
-   * @returns {*} Returns the found element or its key, else `undefined`.
-   */
-  function baseFindKey(collection, predicate, eachFunc) {
-    var result;
-    eachFunc(collection, function(value, key, collection) {
-      if (predicate(value, key, collection)) {
-        result = key;
-        return false;
-      }
-    });
-    return result;
-  }
-
-  /**
-   * The base implementation of `_.findIndex` and `_.findLastIndex` without
-   * support for iteratee shorthands.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {Function} predicate The function invoked per iteration.
-   * @param {number} fromIndex The index to search from.
-   * @param {boolean} [fromRight] Specify iterating from right to left.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function baseFindIndex(array, predicate, fromIndex, fromRight) {
-    var length = array.length,
-        index = fromIndex + (fromRight ? 1 : -1);
-
-    while ((fromRight ? index-- : ++index < length)) {
-      if (predicate(array[index], index, array)) {
-        return index;
-      }
-    }
-    return -1;
-  }
-
-  /**
-   * The base implementation of `_.indexOf` without `fromIndex` bounds checks.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function baseIndexOf(array, value, fromIndex) {
-    return value === value
-      ? strictIndexOf(array, value, fromIndex)
-      : baseFindIndex(array, baseIsNaN, fromIndex);
-  }
-
-  /**
-   * This function is like `baseIndexOf` except that it accepts a comparator.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @param {Function} comparator The comparator invoked per element.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function baseIndexOfWith(array, value, fromIndex, comparator) {
-    var index = fromIndex - 1,
-        length = array.length;
-
-    while (++index < length) {
-      if (comparator(array[index], value)) {
-        return index;
-      }
-    }
-    return -1;
-  }
-
-  /**
-   * The base implementation of `_.isNaN` without support for number objects.
-   *
-   * @private
-   * @param {*} value The value to check.
-   * @returns {boolean} Returns `true` if `value` is `NaN`, else `false`.
-   */
-  function baseIsNaN(value) {
-    return value !== value;
-  }
-
-  /**
-   * The base implementation of `_.mean` and `_.meanBy` without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} array The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {number} Returns the mean.
-   */
-  function baseMean(array, iteratee) {
-    var length = array == null ? 0 : array.length;
-    return length ? (baseSum(array, iteratee) / length) : NAN;
-  }
-
-  /**
-   * The base implementation of `_.property` without support for deep paths.
-   *
-   * @private
-   * @param {string} key The key of the property to get.
-   * @returns {Function} Returns the new accessor function.
-   */
-  function baseProperty(key) {
-    return function(object) {
-      return object == null ? undefined : object[key];
-    };
-  }
-
-  /**
-   * The base implementation of `_.propertyOf` without support for deep paths.
-   *
-   * @private
-   * @param {Object} object The object to query.
-   * @returns {Function} Returns the new accessor function.
-   */
-  function basePropertyOf(object) {
-    return function(key) {
-      return object == null ? undefined : object[key];
-    };
-  }
-
-  /**
-   * The base implementation of `_.reduce` and `_.reduceRight`, without support
-   * for iteratee shorthands, which iterates over `collection` using `eachFunc`.
-   *
-   * @private
-   * @param {Array|Object} collection The collection to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @param {*} accumulator The initial value.
-   * @param {boolean} initAccum Specify using the first or last element of
-   *  `collection` as the initial value.
-   * @param {Function} eachFunc The function to iterate over `collection`.
-   * @returns {*} Returns the accumulated value.
-   */
-  function baseReduce(collection, iteratee, accumulator, initAccum, eachFunc) {
-    eachFunc(collection, function(value, index, collection) {
-      accumulator = initAccum
-        ? (initAccum = false, value)
-        : iteratee(accumulator, value, index, collection);
-    });
-    return accumulator;
-  }
-
-  /**
-   * The base implementation of `_.sortBy` which uses `comparer` to define the
-   * sort order of `array` and replaces criteria objects with their corresponding
-   * values.
-   *
-   * @private
-   * @param {Array} array The array to sort.
-   * @param {Function} comparer The function to define sort order.
-   * @returns {Array} Returns `array`.
-   */
-  function baseSortBy(array, comparer) {
-    var length = array.length;
-
-    array.sort(comparer);
-    while (length--) {
-      array[length] = array[length].value;
-    }
-    return array;
-  }
-
-  /**
-   * The base implementation of `_.sum` and `_.sumBy` without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} array The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {number} Returns the sum.
-   */
-  function baseSum(array, iteratee) {
-    var result,
-        index = -1,
-        length = array.length;
-
-    while (++index < length) {
-      var current = iteratee(array[index]);
-      if (current !== undefined) {
-        result = result === undefined ? current : (result + current);
-      }
-    }
-    return result;
-  }
-
-  /**
-   * The base implementation of `_.times` without support for iteratee shorthands
-   * or max array length checks.
-   *
-   * @private
-   * @param {number} n The number of times to invoke `iteratee`.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns the array of results.
-   */
-  function baseTimes(n, iteratee) {
-    var index = -1,
-        result = Array(n);
-
-    while (++index < n) {
-      result[index] = iteratee(index);
-    }
-    return result;
-  }
-
-  /**
-   * The base implementation of `_.toPairs` and `_.toPairsIn` which creates an array
-   * of key-value pairs for `object` corresponding to the property names of `props`.
-   *
-   * @private
-   * @param {Object} object The object to query.
-   * @param {Array} props The property names to get values for.
-   * @returns {Object} Returns the key-value pairs.
-   */
-  function baseToPairs(object, props) {
-    return arrayMap(props, function(key) {
-      return [key, object[key]];
-    });
-  }
-
-  /**
-   * The base implementation of `_.unary` without support for storing metadata.
-   *
-   * @private
-   * @param {Function} func The function to cap arguments for.
-   * @returns {Function} Returns the new capped function.
-   */
-  function baseUnary(func) {
-    return function(value) {
-      return func(value);
-    };
-  }
-
-  /**
-   * The base implementation of `_.values` and `_.valuesIn` which creates an
-   * array of `object` property values corresponding to the property names
-   * of `props`.
-   *
-   * @private
-   * @param {Object} object The object to query.
-   * @param {Array} props The property names to get values for.
-   * @returns {Object} Returns the array of property values.
-   */
-  function baseValues(object, props) {
-    return arrayMap(props, function(key) {
-      return object[key];
-    });
-  }
-
-  /**
-   * Checks if a `cache` value for `key` exists.
-   *
-   * @private
-   * @param {Object} cache The cache to query.
-   * @param {string} key The key of the entry to check.
-   * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-   */
-  function cacheHas(cache, key) {
-    return cache.has(key);
-  }
-
-  /**
-   * Used by `_.trim` and `_.trimStart` to get the index of the first string symbol
-   * that is not found in the character symbols.
-   *
-   * @private
-   * @param {Array} strSymbols The string symbols to inspect.
-   * @param {Array} chrSymbols The character symbols to find.
-   * @returns {number} Returns the index of the first unmatched string symbol.
-   */
-  function charsStartIndex(strSymbols, chrSymbols) {
-    var index = -1,
-        length = strSymbols.length;
-
-    while (++index < length && baseIndexOf(chrSymbols, strSymbols[index], 0) > -1) {}
-    return index;
-  }
-
-  /**
-   * Used by `_.trim` and `_.trimEnd` to get the index of the last string symbol
-   * that is not found in the character symbols.
-   *
-   * @private
-   * @param {Array} strSymbols The string symbols to inspect.
-   * @param {Array} chrSymbols The character symbols to find.
-   * @returns {number} Returns the index of the last unmatched string symbol.
-   */
-  function charsEndIndex(strSymbols, chrSymbols) {
-    var index = strSymbols.length;
-
-    while (index-- && baseIndexOf(chrSymbols, strSymbols[index], 0) > -1) {}
-    return index;
-  }
-
-  /**
-   * Gets the number of `placeholder` occurrences in `array`.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} placeholder The placeholder to search for.
-   * @returns {number} Returns the placeholder count.
-   */
-  function countHolders(array, placeholder) {
-    var length = array.length,
-        result = 0;
-
-    while (length--) {
-      if (array[length] === placeholder) {
-        ++result;
-      }
-    }
-    return result;
-  }
-
-  /**
-   * Used by `_.deburr` to convert Latin-1 Supplement and Latin Extended-A
-   * letters to basic Latin letters.
-   *
-   * @private
-   * @param {string} letter The matched letter to deburr.
-   * @returns {string} Returns the deburred letter.
-   */
-  var deburrLetter = basePropertyOf(deburredLetters);
-
-  /**
-   * Used by `_.escape` to convert characters to HTML entities.
-   *
-   * @private
-   * @param {string} chr The matched character to escape.
-   * @returns {string} Returns the escaped character.
-   */
-  var escapeHtmlChar = basePropertyOf(htmlEscapes);
-
-  /**
-   * Used by `_.template` to escape characters for inclusion in compiled string literals.
-   *
-   * @private
-   * @param {string} chr The matched character to escape.
-   * @returns {string} Returns the escaped character.
-   */
-  function escapeStringChar(chr) {
-    return '\\' + stringEscapes[chr];
-  }
-
-  /**
-   * Gets the value at `key` of `object`.
-   *
-   * @private
-   * @param {Object} [object] The object to query.
-   * @param {string} key The key of the property to get.
-   * @returns {*} Returns the property value.
-   */
-  function getValue(object, key) {
-    return object == null ? undefined : object[key];
-  }
-
-  /**
-   * Checks if `string` contains Unicode symbols.
-   *
-   * @private
-   * @param {string} string The string to inspect.
-   * @returns {boolean} Returns `true` if a symbol is found, else `false`.
-   */
-  function hasUnicode(string) {
-    return reHasUnicode.test(string);
-  }
-
-  /**
-   * Checks if `string` contains a word composed of Unicode symbols.
-   *
-   * @private
-   * @param {string} string The string to inspect.
-   * @returns {boolean} Returns `true` if a word is found, else `false`.
-   */
-  function hasUnicodeWord(string) {
-    return reHasUnicodeWord.test(string);
-  }
-
-  /**
-   * Converts `iterator` to an array.
-   *
-   * @private
-   * @param {Object} iterator The iterator to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function iteratorToArray(iterator) {
-    var data,
-        result = [];
-
-    while (!(data = iterator.next()).done) {
-      result.push(data.value);
-    }
-    return result;
-  }
-
-  /**
-   * Converts `map` to its key-value pairs.
-   *
-   * @private
-   * @param {Object} map The map to convert.
-   * @returns {Array} Returns the key-value pairs.
-   */
-  function mapToArray(map) {
-    var index = -1,
-        result = Array(map.size);
-
-    map.forEach(function(value, key) {
-      result[++index] = [key, value];
-    });
-    return result;
-  }
-
-  /**
-   * Creates a unary function that invokes `func` with its argument transformed.
-   *
-   * @private
-   * @param {Function} func The function to wrap.
-   * @param {Function} transform The argument transform.
-   * @returns {Function} Returns the new function.
-   */
-  function overArg(func, transform) {
-    return function(arg) {
-      return func(transform(arg));
-    };
-  }
-
-  /**
-   * Replaces all `placeholder` elements in `array` with an internal placeholder
-   * and returns an array of their indexes.
-   *
-   * @private
-   * @param {Array} array The array to modify.
-   * @param {*} placeholder The placeholder to replace.
-   * @returns {Array} Returns the new array of placeholder indexes.
-   */
-  function replaceHolders(array, placeholder) {
-    var index = -1,
-        length = array.length,
-        resIndex = 0,
-        result = [];
-
-    while (++index < length) {
-      var value = array[index];
-      if (value === placeholder || value === PLACEHOLDER) {
-        array[index] = PLACEHOLDER;
-        result[resIndex++] = index;
-      }
-    }
-    return result;
-  }
-
-  /**
-   * Converts `set` to an array of its values.
-   *
-   * @private
-   * @param {Object} set The set to convert.
-   * @returns {Array} Returns the values.
-   */
-  function setToArray(set) {
-    var index = -1,
-        result = Array(set.size);
-
-    set.forEach(function(value) {
-      result[++index] = value;
-    });
-    return result;
-  }
-
-  /**
-   * Converts `set` to its value-value pairs.
-   *
-   * @private
-   * @param {Object} set The set to convert.
-   * @returns {Array} Returns the value-value pairs.
-   */
-  function setToPairs(set) {
-    var index = -1,
-        result = Array(set.size);
-
-    set.forEach(function(value) {
-      result[++index] = [value, value];
-    });
-    return result;
-  }
-
-  /**
-   * A specialized version of `_.indexOf` which performs strict equality
-   * comparisons of values, i.e. `===`.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function strictIndexOf(array, value, fromIndex) {
-    var index = fromIndex - 1,
-        length = array.length;
-
-    while (++index < length) {
-      if (array[index] === value) {
-        return index;
-      }
-    }
-    return -1;
-  }
-
-  /**
-   * A specialized version of `_.lastIndexOf` which performs strict equality
-   * comparisons of values, i.e. `===`.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function strictLastIndexOf(array, value, fromIndex) {
-    var index = fromIndex + 1;
-    while (index--) {
-      if (array[index] === value) {
-        return index;
-      }
-    }
-    return index;
-  }
-
-  /**
-   * Gets the number of symbols in `string`.
-   *
-   * @private
-   * @param {string} string The string to inspect.
-   * @returns {number} Returns the string size.
-   */
-  function stringSize(string) {
-    return hasUnicode(string)
-      ? unicodeSize(string)
-      : asciiSize(string);
-  }
-
-  /**
-   * Converts `string` to an array.
-   *
-   * @private
-   * @param {string} string The string to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function stringToArray(string) {
-    return hasUnicode(string)
-      ? unicodeToArray(string)
-      : asciiToArray(string);
-  }
-
-  /**
-   * Used by `_.unescape` to convert HTML entities to characters.
-   *
-   * @private
-   * @param {string} chr The matched character to unescape.
-   * @returns {string} Returns the unescaped character.
-   */
-  var unescapeHtmlChar = basePropertyOf(htmlUnescapes);
-
-  /**
-   * Gets the size of a Unicode `string`.
-   *
-   * @private
-   * @param {string} string The string inspect.
-   * @returns {number} Returns the string size.
-   */
-  function unicodeSize(string) {
-    var result = reUnicode.lastIndex = 0;
-    while (reUnicode.test(string)) {
-      ++result;
-    }
-    return result;
-  }
-
-  /**
-   * Converts a Unicode `string` to an array.
-   *
-   * @private
-   * @param {string} string The string to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function unicodeToArray(string) {
-    return string.match(reUnicode) || [];
-  }
-
-  /**
-   * Splits a Unicode `string` into an array of its words.
-   *
-   * @private
-   * @param {string} The string to inspect.
-   * @returns {Array} Returns the words of `string`.
-   */
-  function unicodeWords(string) {
-    return string.match(reUnicodeWord) || [];
-  }
-
-  /*--------------------------------------------------------------------------*/
-
-  /**
-   * Create a new pristine `lodash` function using the `context` object.
-   *
-   * @static
-   * @memberOf _
-   * @since 1.1.0
-   * @category Util
-   * @param {Object} [context=root] The context object.
-   * @returns {Function} Returns a new `lodash` function.
-   * @example
-   *
-   * _.mixin({ 'foo': _.constant('foo') });
-   *
-   * var lodash = _.runInContext();
-   * lodash.mixin({ 'bar': lodash.constant('bar') });
-   *
-   * _.isFunction(_.foo);
-   * // => true
-   * _.isFunction(_.bar);
-   * // => false
-   *
-   * lodash.isFunction(lodash.foo);
-   * // => false
-   * lodash.isFunction(lodash.bar);
-   * // => true
-   *
-   * // Create a suped-up `defer` in Node.js.
-   * var defer = _.runInContext({ 'setTimeout': setImmediate }).defer;
-   */
-  var runInContext = (function runInContext(context) {
-    context = context == null ? root : _.defaults(root.Object(), context, _.pick(root, contextProps));
-
-    /** Built-in constructor references. */
-    var Array = context.Array,
-        Date = context.Date,
-        Error = context.Error,
-        Function = context.Function,
-        Math = context.Math,
-        Object = context.Object,
-        RegExp = context.RegExp,
-        String = context.String,
-        TypeError = context.TypeError;
-
-    /** Used for built-in method references. */
-    var arrayProto = Array.prototype,
-        funcProto = Function.prototype,
-        objectProto = Object.prototype;
-
-    /** Used to detect overreaching core-js shims. */
-    var coreJsData = context['__core-js_shared__'];
-
-    /** Used to resolve the decompiled source of functions. */
-    var funcToString = funcProto.toString;
-
-    /** Used to check objects for own properties. */
-    var hasOwnProperty = objectProto.hasOwnProperty;
-
-    /** Used to generate unique IDs. */
-    var idCounter = 0;
-
-    /** Used to detect methods masquerading as native. */
-    var maskSrcKey = (function() {
-      var uid = /[^.]+$/.exec(coreJsData && coreJsData.keys && coreJsData.keys.IE_PROTO || '');
-      return uid ? ('Symbol(src)_1.' + uid) : '';
-    }());
-
-    /**
-     * Used to resolve the
-     * [`toStringTag`](http://ecma-international.org/ecma-262/7.0/#sec-object.prototype.tostring)
-     * of values.
-     */
-    var nativeObjectToString = objectProto.toString;
-
-    /** Used to infer the `Object` constructor. */
-    var objectCtorString = funcToString.call(Object);
-
-    /** Used to restore the original `_` reference in `_.noConflict`. */
-    var oldDash = root._;
-
-    /** Used to detect if a method is native. */
-    var reIsNative = RegExp('^' +
-      funcToString.call(hasOwnProperty).replace(reRegExpChar, '\\$&')
-      .replace(/hasOwnProperty|(function).*?(?=\\\()| for .+?(?=\\\])/g, '$1.*?') + '$'
-    );
-
-    /** Built-in value references. */
-    var Buffer = moduleExports ? context.Buffer : undefined,
-        Symbol = context.Symbol,
-        Uint8Array = context.Uint8Array,
-        allocUnsafe = Buffer ? Buffer.allocUnsafe : undefined,
-        getPrototype = overArg(Object.getPrototypeOf, Object),
-        objectCreate = Object.create,
-        propertyIsEnumerable = objectProto.propertyIsEnumerable,
-        splice = arrayProto.splice,
-        spreadableSymbol = Symbol ? Symbol.isConcatSpreadable : undefined,
-        symIterator = Symbol ? Symbol.iterator : undefined,
-        symToStringTag = Symbol ? Symbol.toStringTag : undefined;
-
-    var defineProperty = (function() {
-      try {
-        var func = getNative(Object, 'defineProperty');
-        func({}, '', {});
-        return func;
-      } catch (e) {}
-    }());
-
-    /** Mocked built-ins. */
-    var ctxClearTimeout = context.clearTimeout !== root.clearTimeout && context.clearTimeout,
-        ctxNow = Date && Date.now !== root.Date.now && Date.now,
-        ctxSetTimeout = context.setTimeout !== root.setTimeout && context.setTimeout;
-
-    /* Built-in method references for those with the same name as other `lodash` methods. */
-    var nativeCeil = Math.ceil,
-        nativeFloor = Math.floor,
-        nativeGetSymbols = Object.getOwnPropertySymbols,
-        nativeIsBuffer = Buffer ? Buffer.isBuffer : undefined,
-        nativeIsFinite = context.isFinite,
-        nativeJoin = arrayProto.join,
-        nativeKeys = overArg(Object.keys, Object),
-        nativeMax = Math.max,
-        nativeMin = Math.min,
-        nativeNow = Date.now,
-        nativeParseInt = context.parseInt,
-        nativeRandom = Math.random,
-        nativeReverse = arrayProto.reverse;
-
-    /* Built-in method references that are verified to be native. */
-    var DataView = getNative(context, 'DataView'),
-        Map = getNative(context, 'Map'),
-        Promise = getNative(context, 'Promise'),
-        Set = getNative(context, 'Set'),
-        WeakMap = getNative(context, 'WeakMap'),
-        nativeCreate = getNative(Object, 'create');
-
-    /** Used to store function metadata. */
-    var metaMap = WeakMap && new WeakMap;
-
-    /** Used to lookup unminified function names. */
-    var realNames = {};
-
-    /** Used to detect maps, sets, and weakmaps. */
-    var dataViewCtorString = toSource(DataView),
-        mapCtorString = toSource(Map),
-        promiseCtorString = toSource(Promise),
-        setCtorString = toSource(Set),
-        weakMapCtorString = toSource(WeakMap);
-
-    /** Used to convert symbols to primitives and strings. */
-    var symbolProto = Symbol ? Symbol.prototype : undefined,
-        symbolValueOf = symbolProto ? symbolProto.valueOf : undefined,
-        symbolToString = symbolProto ? symbolProto.toString : undefined;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a `lodash` object which wraps `value` to enable implicit method
-     * chain sequences. Methods that operate on and return arrays, collections,
-     * and functions can be chained together. Methods that retrieve a single value
-     * or may return a primitive value will automatically end the chain sequence
-     * and return the unwrapped value. Otherwise, the value must be unwrapped
-     * with `_#value`.
-     *
-     * Explicit chain sequences, which must be unwrapped with `_#value`, may be
-     * enabled using `_.chain`.
-     *
-     * The execution of chained methods is lazy, that is, it's deferred until
-     * `_#value` is implicitly or explicitly called.
-     *
-     * Lazy evaluation allows several methods to support shortcut fusion.
-     * Shortcut fusion is an optimization to merge iteratee calls; this avoids
-     * the creation of intermediate arrays and can greatly reduce the number of
-     * iteratee executions. Sections of a chain sequence qualify for shortcut
-     * fusion if the section is applied to an array and iteratees accept only
-     * one argument. The heuristic for whether a section qualifies for shortcut
-     * fusion is subject to change.
-     *
-     * Chaining is supported in custom builds as long as the `_#value` method is
-     * directly or indirectly included in the build.
-     *
-     * In addition to lodash methods, wrappers have `Array` and `String` methods.
-     *
-     * The wrapper `Array` methods are:
-     * `concat`, `join`, `pop`, `push`, `shift`, `sort`, `splice`, and `unshift`
-     *
-     * The wrapper `String` methods are:
-     * `replace` and `split`
-     *
-     * The wrapper methods that support shortcut fusion are:
-     * `at`, `compact`, `drop`, `dropRight`, `dropWhile`, `filter`, `find`,
-     * `findLast`, `head`, `initial`, `last`, `map`, `reject`, `reverse`, `slice`,
-     * `tail`, `take`, `takeRight`, `takeRightWhile`, `takeWhile`, and `toArray`
-     *
-     * The chainable wrapper methods are:
-     * `after`, `ary`, `assign`, `assignIn`, `assignInWith`, `assignWith`, `at`,
-     * `before`, `bind`, `bindAll`, `bindKey`, `castArray`, `chain`, `chunk`,
-     * `commit`, `compact`, `concat`, `conforms`, `constant`, `countBy`, `create`,
-     * `curry`, `debounce`, `defaults`, `defaultsDeep`, `defer`, `delay`,
-     * `difference`, `differenceBy`, `differenceWith`, `drop`, `dropRight`,
-     * `dropRightWhile`, `dropWhile`, `extend`, `extendWith`, `fill`, `filter`,
-     * `flatMap`, `flatMapDeep`, `flatMapDepth`, `flatten`, `flattenDeep`,
-     * `flattenDepth`, `flip`, `flow`, `flowRight`, `fromPairs`, `functions`,
-     * `functionsIn`, `groupBy`, `initial`, `intersection`, `intersectionBy`,
-     * `intersectionWith`, `invert`, `invertBy`, `invokeMap`, `iteratee`, `keyBy`,
-     * `keys`, `keysIn`, `map`, `mapKeys`, `mapValues`, `matches`, `matchesProperty`,
-     * `memoize`, `merge`, `mergeWith`, `method`, `methodOf`, `mixin`, `negate`,
-     * `nthArg`, `omit`, `omitBy`, `once`, `orderBy`, `over`, `overArgs`,
-     * `overEvery`, `overSome`, `partial`, `partialRight`, `partition`, `pick`,
-     * `pickBy`, `plant`, `property`, `propertyOf`, `pull`, `pullAll`, `pullAllBy`,
-     * `pullAllWith`, `pullAt`, `push`, `range`, `rangeRight`, `rearg`, `reject`,
-     * `remove`, `rest`, `reverse`, `sampleSize`, `set`, `setWith`, `shuffle`,
-     * `slice`, `sort`, `sortBy`, `splice`, `spread`, `tail`, `take`, `takeRight`,
-     * `takeRightWhile`, `takeWhile`, `tap`, `throttle`, `thru`, `toArray`,
-     * `toPairs`, `toPairsIn`, `toPath`, `toPlainObject`, `transform`, `unary`,
-     * `union`, `unionBy`, `unionWith`, `uniq`, `uniqBy`, `uniqWith`, `unset`,
-     * `unshift`, `unzip`, `unzipWith`, `update`, `updateWith`, `values`,
-     * `valuesIn`, `without`, `wrap`, `xor`, `xorBy`, `xorWith`, `zip`,
-     * `zipObject`, `zipObjectDeep`, and `zipWith`
-     *
-     * The wrapper methods that are **not** chainable by default are:
-     * `add`, `attempt`, `camelCase`, `capitalize`, `ceil`, `clamp`, `clone`,
-     * `cloneDeep`, `cloneDeepWith`, `cloneWith`, `conformsTo`, `deburr`,
-     * `defaultTo`, `divide`, `each`, `eachRight`, `endsWith`, `eq`, `escape`,
-     * `escapeRegExp`, `every`, `find`, `findIndex`, `findKey`, `findLast`,
-     * `findLastIndex`, `findLastKey`, `first`, `floor`, `forEach`, `forEachRight`,
-     * `forIn`, `forInRight`, `forOwn`, `forOwnRight`, `get`, `gt`, `gte`, `has`,
-     * `hasIn`, `head`, `identity`, `includes`, `indexOf`, `inRange`, `invoke`,
-     * `isArguments`, `isArray`, `isArrayBuffer`, `isArrayLike`, `isArrayLikeObject`,
-     * `isBoolean`, `isBuffer`, `isDate`, `isElement`, `isEmpty`, `isEqual`,
-     * `isEqualWith`, `isError`, `isFinite`, `isFunction`, `isInteger`, `isLength`,
-     * `isMap`, `isMatch`, `isMatchWith`, `isNaN`, `isNative`, `isNil`, `isNull`,
-     * `isNumber`, `isObject`, `isObjectLike`, `isPlainObject`, `isRegExp`,
-     * `isSafeInteger`, `isSet`, `isString`, `isUndefined`, `isTypedArray`,
-     * `isWeakMap`, `isWeakSet`, `join`, `kebabCase`, `last`, `lastIndexOf`,
-     * `lowerCase`, `lowerFirst`, `lt`, `lte`, `max`, `maxBy`, `mean`, `meanBy`,
-     * `min`, `minBy`, `multiply`, `noConflict`, `noop`, `now`, `nth`, `pad`,
-     * `padEnd`, `padStart`, `parseInt`, `pop`, `random`, `reduce`, `reduceRight`,
-     * `repeat`, `result`, `round`, `runInContext`, `sample`, `shift`, `size`,
-     * `snakeCase`, `some`, `sortedIndex`, `sortedIndexBy`, `sortedLastIndex`,
-     * `sortedLastIndexBy`, `startCase`, `startsWith`, `stubArray`, `stubFalse`,
-     * `stubObject`, `stubString`, `stubTrue`, `subtract`, `sum`, `sumBy`,
-     * `template`, `times`, `toFinite`, `toInteger`, `toJSON`, `toLength`,
-     * `toLower`, `toNumber`, `toSafeInteger`, `toString`, `toUpper`, `trim`,
-     * `trimEnd`, `trimStart`, `truncate`, `unescape`, `uniqueId`, `upperCase`,
-     * `upperFirst`, `value`, and `words`
-     *
-     * @name _
-     * @constructor
-     * @category Seq
-     * @param {*} value The value to wrap in a `lodash` instance.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var wrapped = _([1, 2, 3]);
-     *
-     * // Returns an unwrapped value.
-     * wrapped.reduce(_.add);
-     * // => 6
-     *
-     * // Returns a wrapped value.
-     * var squares = wrapped.map(square);
-     *
-     * _.isArray(squares);
-     * // => false
-     *
-     * _.isArray(squares.value());
-     * // => true
-     */
-    function lodash(value) {
-      if (isObjectLike(value) && !isArray(value) && !(value instanceof LazyWrapper)) {
-        if (value instanceof LodashWrapper) {
-          return value;
-        }
-        if (hasOwnProperty.call(value, '__wrapped__')) {
-          return wrapperClone(value);
-        }
-      }
-      return new LodashWrapper(value);
-    }
-
-    /**
-     * The base implementation of `_.create` without support for assigning
-     * properties to the created object.
-     *
-     * @private
-     * @param {Object} proto The object to inherit from.
-     * @returns {Object} Returns the new object.
-     */
-    var baseCreate = (function() {
-      function object() {}
-      return function(proto) {
-        if (!isObject(proto)) {
-          return {};
-        }
-        if (objectCreate) {
-          return objectCreate(proto);
-        }
-        object.prototype = proto;
-        var result = new object;
-        object.prototype = undefined;
-        return result;
-      };
-    }());
-
-    /**
-     * The function whose prototype chain sequence wrappers inherit from.
-     *
-     * @private
-     */
-    function baseLodash() {
-      // No operation performed.
-    }
-
-    /**
-     * The base constructor for creating `lodash` wrapper objects.
-     *
-     * @private
-     * @param {*} value The value to wrap.
-     * @param {boolean} [chainAll] Enable explicit method chain sequences.
-     */
-    function LodashWrapper(value, chainAll) {
-      this.__wrapped__ = value;
-      this.__actions__ = [];
-      this.__chain__ = !!chainAll;
-      this.__index__ = 0;
-      this.__values__ = undefined;
-    }
-
-    /**
-     * By default, the template delimiters used by lodash are like those in
-     * embedded Ruby (ERB) as well as ES2015 template strings. Change the
-     * following template settings to use alternative delimiters.
-     *
-     * @static
-     * @memberOf _
-     * @type {Object}
-     */
-    lodash.templateSettings = {
-
-      /**
-       * Used to detect `data` property values to be HTML-escaped.
-       *
-       * @memberOf _.templateSettings
-       * @type {RegExp}
-       */
-      'escape': reEscape,
-
-      /**
-       * Used to detect code to be evaluated.
-       *
-       * @memberOf _.templateSettings
-       * @type {RegExp}
-       */
-      'evaluate': reEvaluate,
-
-      /**
-       * Used to detect `data` property values to inject.
-       *
-       * @memberOf _.templateSettings
-       * @type {RegExp}
-       */
-      'interpolate': reInterpolate,
-
-      /**
-       * Used to reference the data object in the template text.
-       *
-       * @memberOf _.templateSettings
-       * @type {string}
-       */
-      'variable': '',
-
-      /**
-       * Used to import variables into the compiled template.
-       *
-       * @memberOf _.templateSettings
-       * @type {Object}
-       */
-      'imports': {
-
-        /**
-         * A reference to the `lodash` function.
-         *
-         * @memberOf _.templateSettings.imports
-         * @type {Function}
-         */
-        '_': lodash
-      }
-    };
-
-    // Ensure wrappers are instances of `baseLodash`.
-    lodash.prototype = baseLodash.prototype;
-    lodash.prototype.constructor = lodash;
-
-    LodashWrapper.prototype = baseCreate(baseLodash.prototype);
-    LodashWrapper.prototype.constructor = LodashWrapper;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a lazy wrapper object which wraps `value` to enable lazy evaluation.
-     *
-     * @private
-     * @constructor
-     * @param {*} value The value to wrap.
-     */
-    function LazyWrapper(value) {
-      this.__wrapped__ = value;
-      this.__actions__ = [];
-      this.__dir__ = 1;
-      this.__filtered__ = false;
-      this.__iteratees__ = [];
-      this.__takeCount__ = MAX_ARRAY_LENGTH;
-      this.__views__ = [];
-    }
-
-    /**
-     * Creates a clone of the lazy wrapper object.
-     *
-     * @private
-     * @name clone
-     * @memberOf LazyWrapper
-     * @returns {Object} Returns the cloned `LazyWrapper` object.
-     */
-    function lazyClone() {
-      var result = new LazyWrapper(this.__wrapped__);
-      result.__actions__ = copyArray(this.__actions__);
-      result.__dir__ = this.__dir__;
-      result.__filtered__ = this.__filtered__;
-      result.__iteratees__ = copyArray(this.__iteratees__);
-      result.__takeCount__ = this.__takeCount__;
-      result.__views__ = copyArray(this.__views__);
-      return result;
-    }
-
-    /**
-     * Reverses the direction of lazy iteration.
-     *
-     * @private
-     * @name reverse
-     * @memberOf LazyWrapper
-     * @returns {Object} Returns the new reversed `LazyWrapper` object.
-     */
-    function lazyReverse() {
-      if (this.__filtered__) {
-        var result = new LazyWrapper(this);
-        result.__dir__ = -1;
-        result.__filtered__ = true;
-      } else {
-        result = this.clone();
-        result.__dir__ *= -1;
-      }
-      return result;
-    }
-
-    /**
-     * Extracts the unwrapped value from its lazy wrapper.
-     *
-     * @private
-     * @name value
-     * @memberOf LazyWrapper
-     * @returns {*} Returns the unwrapped value.
-     */
-    function lazyValue() {
-      var array = this.__wrapped__.value(),
-          dir = this.__dir__,
-          isArr = isArray(array),
-          isRight = dir < 0,
-          arrLength = isArr ? array.length : 0,
-          view = getView(0, arrLength, this.__views__),
-          start = view.start,
-          end = view.end,
-          length = end - start,
-          index = isRight ? end : (start - 1),
-          iteratees = this.__iteratees__,
-          iterLength = iteratees.length,
-          resIndex = 0,
-          takeCount = nativeMin(length, this.__takeCount__);
-
-      if (!isArr || (!isRight && arrLength == length && takeCount == length)) {
-        return baseWrapperValue(array, this.__actions__);
-      }
-      var result = [];
-
-      outer:
-      while (length-- && resIndex < takeCount) {
-        index += dir;
-
-        var iterIndex = -1,
-            value = array[index];
-
-        while (++iterIndex < iterLength) {
-          var data = iteratees[iterIndex],
-              iteratee = data.iteratee,
-              type = data.type,
-              computed = iteratee(value);
-
-          if (type == LAZY_MAP_FLAG) {
-            value = computed;
-          } else if (!computed) {
-            if (type == LAZY_FILTER_FLAG) {
-              continue outer;
-            } else {
-              break outer;
-            }
-          }
-        }
-        result[resIndex++] = value;
-      }
-      return result;
-    }
-
-    // Ensure `LazyWrapper` is an instance of `baseLodash`.
-    LazyWrapper.prototype = baseCreate(baseLodash.prototype);
-    LazyWrapper.prototype.constructor = LazyWrapper;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a hash object.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function Hash(entries) {
-      var index = -1,
-          length = entries == null ? 0 : entries.length;
-
-      this.clear();
-      while (++index < length) {
-        var entry = entries[index];
-        this.set(entry[0], entry[1]);
-      }
-    }
-
-    /**
-     * Removes all key-value entries from the hash.
-     *
-     * @private
-     * @name clear
-     * @memberOf Hash
-     */
-    function hashClear() {
-      this.__data__ = nativeCreate ? nativeCreate(null) : {};
-      this.size = 0;
-    }
-
-    /**
-     * Removes `key` and its value from the hash.
-     *
-     * @private
-     * @name delete
-     * @memberOf Hash
-     * @param {Object} hash The hash to modify.
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function hashDelete(key) {
-      var result = this.has(key) && delete this.__data__[key];
-      this.size -= result ? 1 : 0;
-      return result;
-    }
-
-    /**
-     * Gets the hash value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf Hash
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function hashGet(key) {
-      var data = this.__data__;
-      if (nativeCreate) {
-        var result = data[key];
-        return result === HASH_UNDEFINED ? undefined : result;
-      }
-      return hasOwnProperty.call(data, key) ? data[key] : undefined;
-    }
-
-    /**
-     * Checks if a hash value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf Hash
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function hashHas(key) {
-      var data = this.__data__;
-      return nativeCreate ? (data[key] !== undefined) : hasOwnProperty.call(data, key);
-    }
-
-    /**
-     * Sets the hash `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf Hash
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the hash instance.
-     */
-    function hashSet(key, value) {
-      var data = this.__data__;
-      this.size += this.has(key) ? 0 : 1;
-      data[key] = (nativeCreate && value === undefined) ? HASH_UNDEFINED : value;
-      return this;
-    }
-
-    // Add methods to `Hash`.
-    Hash.prototype.clear = hashClear;
-    Hash.prototype['delete'] = hashDelete;
-    Hash.prototype.get = hashGet;
-    Hash.prototype.has = hashHas;
-    Hash.prototype.set = hashSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an list cache object.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function ListCache(entries) {
-      var index = -1,
-          length = entries == null ? 0 : entries.length;
-
-      this.clear();
-      while (++index < length) {
-        var entry = entries[index];
-        this.set(entry[0], entry[1]);
-      }
-    }
-
-    /**
-     * Removes all key-value entries from the list cache.
-     *
-     * @private
-     * @name clear
-     * @memberOf ListCache
-     */
-    function listCacheClear() {
-      this.__data__ = [];
-      this.size = 0;
-    }
-
-    /**
-     * Removes `key` and its value from the list cache.
-     *
-     * @private
-     * @name delete
-     * @memberOf ListCache
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function listCacheDelete(key) {
-      var data = this.__data__,
-          index = assocIndexOf(data, key);
-
-      if (index < 0) {
-        return false;
-      }
-      var lastIndex = data.length - 1;
-      if (index == lastIndex) {
-        data.pop();
-      } else {
-        splice.call(data, index, 1);
-      }
-      --this.size;
-      return true;
-    }
-
-    /**
-     * Gets the list cache value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf ListCache
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function listCacheGet(key) {
-      var data = this.__data__,
-          index = assocIndexOf(data, key);
-
-      return index < 0 ? undefined : data[index][1];
-    }
-
-    /**
-     * Checks if a list cache value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf ListCache
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function listCacheHas(key) {
-      return assocIndexOf(this.__data__, key) > -1;
-    }
-
-    /**
-     * Sets the list cache `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf ListCache
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the list cache instance.
-     */
-    function listCacheSet(key, value) {
-      var data = this.__data__,
-          index = assocIndexOf(data, key);
-
-      if (index < 0) {
-        ++this.size;
-        data.push([key, value]);
-      } else {
-        data[index][1] = value;
-      }
-      return this;
-    }
-
-    // Add methods to `ListCache`.
-    ListCache.prototype.clear = listCacheClear;
-    ListCache.prototype['delete'] = listCacheDelete;
-    ListCache.prototype.get = listCacheGet;
-    ListCache.prototype.has = listCacheHas;
-    ListCache.prototype.set = listCacheSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a map cache object to store key-value pairs.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function MapCache(entries) {
-      var index = -1,
-          length = entries == null ? 0 : entries.length;
-
-      this.clear();
-      while (++index < length) {
-        var entry = entries[index];
-        this.set(entry[0], entry[1]);
-      }
-    }
-
-    /**
-     * Removes all key-value entries from the map.
-     *
-     * @private
-     * @name clear
-     * @memberOf MapCache
-     */
-    function mapCacheClear() {
-      this.size = 0;
-      this.__data__ = {
-        'hash': new Hash,
-        'map': new (Map || ListCache),
-        'string': new Hash
-      };
-    }
-
-    /**
-     * Removes `key` and its value from the map.
-     *
-     * @private
-     * @name delete
-     * @memberOf MapCache
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function mapCacheDelete(key) {
-      var result = getMapData(this, key)['delete'](key);
-      this.size -= result ? 1 : 0;
-      return result;
-    }
-
-    /**
-     * Gets the map value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf MapCache
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function mapCacheGet(key) {
-      return getMapData(this, key).get(key);
-    }
-
-    /**
-     * Checks if a map value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf MapCache
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function mapCacheHas(key) {
-      return getMapData(this, key).has(key);
-    }
-
-    /**
-     * Sets the map `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf MapCache
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the map cache instance.
-     */
-    function mapCacheSet(key, value) {
-      var data = getMapData(this, key),
-          size = data.size;
-
-      data.set(key, value);
-      this.size += data.size == size ? 0 : 1;
-      return this;
-    }
-
-    // Add methods to `MapCache`.
-    MapCache.prototype.clear = mapCacheClear;
-    MapCache.prototype['delete'] = mapCacheDelete;
-    MapCache.prototype.get = mapCacheGet;
-    MapCache.prototype.has = mapCacheHas;
-    MapCache.prototype.set = mapCacheSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     *
-     * Creates an array cache object to store unique values.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [values] The values to cache.
-     */
-    function SetCache(values) {
-      var index = -1,
-          length = values == null ? 0 : values.length;
-
-      this.__data__ = new MapCache;
-      while (++index < length) {
-        this.add(values[index]);
-      }
-    }
-
-    /**
-     * Adds `value` to the array cache.
-     *
-     * @private
-     * @name add
-     * @memberOf SetCache
-     * @alias push
-     * @param {*} value The value to cache.
-     * @returns {Object} Returns the cache instance.
-     */
-    function setCacheAdd(value) {
-      this.__data__.set(value, HASH_UNDEFINED);
-      return this;
-    }
-
-    /**
-     * Checks if `value` is in the array cache.
-     *
-     * @private
-     * @name has
-     * @memberOf SetCache
-     * @param {*} value The value to search for.
-     * @returns {number} Returns `true` if `value` is found, else `false`.
-     */
-    function setCacheHas(value) {
-      return this.__data__.has(value);
-    }
-
-    // Add methods to `SetCache`.
-    SetCache.prototype.add = SetCache.prototype.push = setCacheAdd;
-    SetCache.prototype.has = setCacheHas;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a stack cache object to store key-value pairs.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function Stack(entries) {
-      var data = this.__data__ = new ListCache(entries);
-      this.size = data.size;
-    }
-
-    /**
-     * Removes all key-value entries from the stack.
-     *
-     * @private
-     * @name clear
-     * @memberOf Stack
-     */
-    function stackClear() {
-      this.__data__ = new ListCache;
-      this.size = 0;
-    }
-
-    /**
-     * Removes `key` and its value from the stack.
-     *
-     * @private
-     * @name delete
-     * @memberOf Stack
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function stackDelete(key) {
-      var data = this.__data__,
-          result = data['delete'](key);
-
-      this.size = data.size;
-      return result;
-    }
-
-    /**
-     * Gets the stack value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf Stack
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function stackGet(key) {
-      return this.__data__.get(key);
-    }
-
-    /**
-     * Checks if a stack value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf Stack
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function stackHas(key) {
-      return this.__data__.has(key);
-    }
-
-    /**
-     * Sets the stack `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf Stack
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the stack cache instance.
-     */
-    function stackSet(key, value) {
-      var data = this.__data__;
-      if (data instanceof ListCache) {
-        var pairs = data.__data__;
-        if (!Map || (pairs.length < LARGE_ARRAY_SIZE - 1)) {
-          pairs.push([key, value]);
-          this.size = ++data.size;
-          return this;
-        }
-        data = this.__data__ = new MapCache(pairs);
-      }
-      data.set(key, value);
-      this.size = data.size;
-      return this;
-    }
-
-    // Add methods to `Stack`.
-    Stack.prototype.clear = stackClear;
-    Stack.prototype['delete'] = stackDelete;
-    Stack.prototype.get = stackGet;
-    Stack.prototype.has = stackHas;
-    Stack.prototype.set = stackSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an array of the enumerable property names of the array-like `value`.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @param {boolean} inherited Specify returning inherited property names.
-     * @returns {Array} Returns the array of property names.
-     */
-    function arrayLikeKeys(value, inherited) {
-      var isArr = isArray(value),
-          isArg = !isArr && isArguments(value),
-          isBuff = !isArr && !isArg && isBuffer(value),
-          isType = !isArr && !isArg && !isBuff && isTypedArray(value),
-          skipIndexes = isArr || isArg || isBuff || isType,
-          result = skipIndexes ? baseTimes(value.length, String) : [],
-          length = result.length;
-
-      for (var key in value) {
-        if ((inherited || hasOwnProperty.call(value, key)) &&
-            !(skipIndexes && (
-               // Safari 9 has enumerable `arguments.length` in strict mode.
-               key == 'length' ||
-               // Node.js 0.10 has enumerable non-index properties on buffers.
-               (isBuff && (key == 'offset' || key == 'parent')) ||
-               // PhantomJS 2 has enumerable non-index properties on typed arrays.
-               (isType && (key == 'buffer' || key == 'byteLength' || key == 'byteOffset')) ||
-               // Skip index properties.
-               isIndex(key, length)
-            ))) {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * A specialized version of `_.sample` for arrays.
-     *
-     * @private
-     * @param {Array} array The array to sample.
-     * @returns {*} Returns the random element.
-     */
-    function arraySample(array) {
-      var length = array.length;
-      return length ? array[baseRandom(0, length - 1)] : undefined;
-    }
-
-    /**
-     * A specialized version of `_.sampleSize` for arrays.
-     *
-     * @private
-     * @param {Array} array The array to sample.
-     * @param {number} n The number of elements to sample.
-     * @returns {Array} Returns the random elements.
-     */
-    function arraySampleSize(array, n) {
-      return shuffleSelf(copyArray(array), baseClamp(n, 0, array.length));
-    }
-
-    /**
-     * A specialized version of `_.shuffle` for arrays.
-     *
-     * @private
-     * @param {Array} array The array to shuffle.
-     * @returns {Array} Returns the new shuffled array.
-     */
-    function arrayShuffle(array) {
-      return shuffleSelf(copyArray(array));
-    }
-
-    /**
-     * This function is like `assignValue` except that it doesn't assign
-     * `undefined` values.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {string} key The key of the property to assign.
-     * @param {*} value The value to assign.
-     */
-    function assignMergeValue(object, key, value) {
-      if ((value !== undefined && !eq(object[key], value)) ||
-          (value === undefined && !(key in object))) {
-        baseAssignValue(object, key, value);
-      }
-    }
-
-    /**
-     * Assigns `value` to `key` of `object` if the existing value is not equivalent
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {string} key The key of the property to assign.
-     * @param {*} value The value to assign.
-     */
-    function assignValue(object, key, value) {
-      var objValue = object[key];
-      if (!(hasOwnProperty.call(object, key) && eq(objValue, value)) ||
-          (value === undefined && !(key in object))) {
-        baseAssignValue(object, key, value);
-      }
-    }
-
-    /**
-     * Gets the index at which the `key` is found in `array` of key-value pairs.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {*} key The key to search for.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     */
-    function assocIndexOf(array, key) {
-      var length = array.length;
-      while (length--) {
-        if (eq(array[length][0], key)) {
-          return length;
-        }
-      }
-      return -1;
-    }
-
-    /**
-     * Aggregates elements of `collection` on `accumulator` with keys transformed
-     * by `iteratee` and values set by `setter`.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} setter The function to set `accumulator` values.
-     * @param {Function} iteratee The iteratee to transform keys.
-     * @param {Object} accumulator The initial aggregated object.
-     * @returns {Function} Returns `accumulator`.
-     */
-    function baseAggregator(collection, setter, iteratee, accumulator) {
-      baseEach(collection, function(value, key, collection) {
-        setter(accumulator, value, iteratee(value), collection);
-      });
-      return accumulator;
-    }
-
-    /**
-     * The base implementation of `_.assign` without support for multiple sources
-     * or `customizer` functions.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @returns {Object} Returns `object`.
-     */
-    function baseAssign(object, source) {
-      return object && copyObject(source, keys(source), object);
-    }
-
-    /**
-     * The base implementation of `_.assignIn` without support for multiple sources
-     * or `customizer` functions.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @returns {Object} Returns `object`.
-     */
-    function baseAssignIn(object, source) {
-      return object && copyObject(source, keysIn(source), object);
-    }
-
-    /**
-     * The base implementation of `assignValue` and `assignMergeValue` without
-     * value checks.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {string} key The key of the property to assign.
-     * @param {*} value The value to assign.
-     */
-    function baseAssignValue(object, key, value) {
-      if (key == '__proto__' && defineProperty) {
-        defineProperty(object, key, {
-          'configurable': true,
-          'enumerable': true,
-          'value': value,
-          'writable': true
-        });
-      } else {
-        object[key] = value;
-      }
-    }
-
-    /**
-     * The base implementation of `_.at` without support for individual paths.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {string[]} paths The property paths to pick.
-     * @returns {Array} Returns the picked elements.
-     */
-    function baseAt(object, paths) {
-      var index = -1,
-          length = paths.length,
-          result = Array(length),
-          skip = object == null;
-
-      while (++index < length) {
-        result[index] = skip ? undefined : get(object, paths[index]);
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.clamp` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {number} number The number to clamp.
-     * @param {number} [lower] The lower bound.
-     * @param {number} upper The upper bound.
-     * @returns {number} Returns the clamped number.
-     */
-    function baseClamp(number, lower, upper) {
-      if (number === number) {
-        if (upper !== undefined) {
-          number = number <= upper ? number : upper;
-        }
-        if (lower !== undefined) {
-          number = number >= lower ? number : lower;
-        }
-      }
-      return number;
-    }
-
-    /**
-     * The base implementation of `_.clone` and `_.cloneDeep` which tracks
-     * traversed objects.
-     *
-     * @private
-     * @param {*} value The value to clone.
-     * @param {boolean} bitmask The bitmask flags.
-     *  1 - Deep clone
-     *  2 - Flatten inherited properties
-     *  4 - Clone symbols
-     * @param {Function} [customizer] The function to customize cloning.
-     * @param {string} [key] The key of `value`.
-     * @param {Object} [object] The parent object of `value`.
-     * @param {Object} [stack] Tracks traversed objects and their clone counterparts.
-     * @returns {*} Returns the cloned value.
-     */
-    function baseClone(value, bitmask, customizer, key, object, stack) {
-      var result,
-          isDeep = bitmask & CLONE_DEEP_FLAG,
-          isFlat = bitmask & CLONE_FLAT_FLAG,
-          isFull = bitmask & CLONE_SYMBOLS_FLAG;
-
-      if (customizer) {
-        result = object ? customizer(value, key, object, stack) : customizer(value);
-      }
-      if (result !== undefined) {
-        return result;
-      }
-      if (!isObject(value)) {
-        return value;
-      }
-      var isArr = isArray(value);
-      if (isArr) {
-        result = initCloneArray(value);
-        if (!isDeep) {
-          return copyArray(value, result);
-        }
-      } else {
-        var tag = getTag(value),
-            isFunc = tag == funcTag || tag == genTag;
-
-        if (isBuffer(value)) {
-          return cloneBuffer(value, isDeep);
-        }
-        if (tag == objectTag || tag == argsTag || (isFunc && !object)) {
-          result = (isFlat || isFunc) ? {} : initCloneObject(value);
-          if (!isDeep) {
-            return isFlat
-              ? copySymbolsIn(value, baseAssignIn(result, value))
-              : copySymbols(value, baseAssign(result, value));
-          }
-        } else {
-          if (!cloneableTags[tag]) {
-            return object ? value : {};
-          }
-          result = initCloneByTag(value, tag, isDeep);
-        }
-      }
-      // Check for circular references and return its corresponding clone.
-      stack || (stack = new Stack);
-      var stacked = stack.get(value);
-      if (stacked) {
-        return stacked;
-      }
-      stack.set(value, result);
-
-      if (isSet(value)) {
-        value.forEach(function(subValue) {
-          result.add(baseClone(subValue, bitmask, customizer, subValue, value, stack));
-        });
-      } else if (isMap(value)) {
-        value.forEach(function(subValue, key) {
-          result.set(key, baseClone(subValue, bitmask, customizer, key, value, stack));
-        });
-      }
-
-      var keysFunc = isFull
-        ? (isFlat ? getAllKeysIn : getAllKeys)
-        : (isFlat ? keysIn : keys);
-
-      var props = isArr ? undefined : keysFunc(value);
-      arrayEach(props || value, function(subValue, key) {
-        if (props) {
-          key = subValue;
-          subValue = value[key];
-        }
-        // Recursively populate clone (susceptible to call stack limits).
-        assignValue(result, key, baseClone(subValue, bitmask, customizer, key, value, stack));
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.conforms` which doesn't clone `source`.
-     *
-     * @private
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {Function} Returns the new spec function.
-     */
-    function baseConforms(source) {
-      var props = keys(source);
-      return function(object) {
-        return baseConformsTo(object, source, props);
-      };
-    }
-
-    /**
-     * The base implementation of `_.conformsTo` which accepts `props` to check.
-     *
-     * @private
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {boolean} Returns `true` if `object` conforms, else `false`.
-     */
-    function baseConformsTo(object, source, props) {
-      var length = props.length;
-      if (object == null) {
-        return !length;
-      }
-      object = Object(object);
-      while (length--) {
-        var key = props[length],
-            predicate = source[key],
-            value = object[key];
-
-        if ((value === undefined && !(key in object)) || !predicate(value)) {
-          return false;
-        }
-      }
-      return true;
-    }
-
-    /**
-     * The base implementation of `_.delay` and `_.defer` which accepts `args`
-     * to provide to `func`.
-     *
-     * @private
-     * @param {Function} func The function to delay.
-     * @param {number} wait The number of milliseconds to delay invocation.
-     * @param {Array} args The arguments to provide to `func`.
-     * @returns {number|Object} Returns the timer id or timeout object.
-     */
-    function baseDelay(func, wait, args) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      return setTimeout(function() { func.apply(undefined, args); }, wait);
-    }
-
-    /**
-     * The base implementation of methods like `_.difference` without support
-     * for excluding multiple arrays or iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {Array} values The values to exclude.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     */
-    function baseDifference(array, values, iteratee, comparator) {
-      var index = -1,
-          includes = arrayIncludes,
-          isCommon = true,
-          length = array.length,
-          result = [],
-          valuesLength = values.length;
-
-      if (!length) {
-        return result;
-      }
-      if (iteratee) {
-        values = arrayMap(values, baseUnary(iteratee));
-      }
-      if (comparator) {
-        includes = arrayIncludesWith;
-        isCommon = false;
-      }
-      else if (values.length >= LARGE_ARRAY_SIZE) {
-        includes = cacheHas;
-        isCommon = false;
-        values = new SetCache(values);
-      }
-      outer:
-      while (++index < length) {
-        var value = array[index],
-            computed = iteratee == null ? value : iteratee(value);
-
-        value = (comparator || value !== 0) ? value : 0;
-        if (isCommon && computed === computed) {
-          var valuesIndex = valuesLength;
-          while (valuesIndex--) {
-            if (values[valuesIndex] === computed) {
-              continue outer;
-            }
-          }
-          result.push(value);
-        }
-        else if (!includes(values, computed, comparator)) {
-          result.push(value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.forEach` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     */
-    var baseEach = createBaseEach(baseForOwn);
-
-    /**
-     * The base implementation of `_.forEachRight` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     */
-    var baseEachRight = createBaseEach(baseForOwnRight, true);
-
-    /**
-     * The base implementation of `_.every` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} predicate The function invoked per iteration.
-     * @returns {boolean} Returns `true` if all elements pass the predicate check,
-     *  else `false`
-     */
-    function baseEvery(collection, predicate) {
-      var result = true;
-      baseEach(collection, function(value, index, collection) {
-        result = !!predicate(value, index, collection);
-        return result;
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of methods like `_.max` and `_.min` which accepts a
-     * `comparator` to determine the extremum value.
-     *
-     * @private
-     * @param {Array} array The array to iterate over.
-     * @param {Function} iteratee The iteratee invoked per iteration.
-     * @param {Function} comparator The comparator used to compare values.
-     * @returns {*} Returns the extremum value.
-     */
-    function baseExtremum(array, iteratee, comparator) {
-      var index = -1,
-          length = array.length;
-
-      while (++index < length) {
-        var value = array[index],
-            current = iteratee(value);
-
-        if (current != null && (computed === undefined
-              ? (current === current && !isSymbol(current))
-              : comparator(current, computed)
-            )) {
-          var computed = current,
-              result = value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.fill` without an iteratee call guard.
-     *
-     * @private
-     * @param {Array} array The array to fill.
-     * @param {*} value The value to fill `array` with.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns `array`.
-     */
-    function baseFill(array, value, start, end) {
-      var length = array.length;
-
-      start = toInteger(start);
-      if (start < 0) {
-        start = -start > length ? 0 : (length + start);
-      }
-      end = (end === undefined || end > length) ? length : toInteger(end);
-      if (end < 0) {
-        end += length;
-      }
-      end = start > end ? 0 : toLength(end);
-      while (start < end) {
-        array[start++] = value;
-      }
-      return array;
-    }
-
-    /**
-     * The base implementation of `_.filter` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} predicate The function invoked per iteration.
-     * @returns {Array} Returns the new filtered array.
-     */
-    function baseFilter(collection, predicate) {
-      var result = [];
-      baseEach(collection, function(value, index, collection) {
-        if (predicate(value, index, collection)) {
-          result.push(value);
-        }
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.flatten` with support for restricting flattening.
-     *
-     * @private
-     * @param {Array} array The array to flatten.
-     * @param {number} depth The maximum recursion depth.
-     * @param {boolean} [predicate=isFlattenable] The function invoked per iteration.
-     * @param {boolean} [isStrict] Restrict to values that pass `predicate` checks.
-     * @param {Array} [result=[]] The initial result value.
-     * @returns {Array} Returns the new flattened array.
-     */
-    function baseFlatten(array, depth, predicate, isStrict, result) {
-      var index = -1,
-          length = array.length;
-
-      predicate || (predicate = isFlattenable);
-      result || (result = []);
-
-      while (++index < length) {
-        var value = array[index];
-        if (depth > 0 && predicate(value)) {
-          if (depth > 1) {
-            // Recursively flatten arrays (susceptible to call stack limits).
-            baseFlatten(value, depth - 1, predicate, isStrict, result);
-          } else {
-            arrayPush(result, value);
-          }
-        } else if (!isStrict) {
-          result[result.length] = value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `baseForOwn` which iterates over `object`
-     * properties returned by `keysFunc` and invokes `iteratee` for each property.
-     * Iteratee functions may exit iteration early by explicitly returning `false`.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @param {Function} keysFunc The function to get the keys of `object`.
-     * @returns {Object} Returns `object`.
-     */
-    var baseFor = createBaseFor();
-
-    /**
-     * This function is like `baseFor` except that it iterates over properties
-     * in the opposite order.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @param {Function} keysFunc The function to get the keys of `object`.
-     * @returns {Object} Returns `object`.
-     */
-    var baseForRight = createBaseFor(true);
-
-    /**
-     * The base implementation of `_.forOwn` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     */
-    function baseForOwn(object, iteratee) {
-      return object && baseFor(object, iteratee, keys);
-    }
-
-    /**
-     * The base implementation of `_.forOwnRight` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     */
-    function baseForOwnRight(object, iteratee) {
-      return object && baseForRight(object, iteratee, keys);
-    }
-
-    /**
-     * The base implementation of `_.functions` which creates an array of
-     * `object` function property names filtered from `props`.
-     *
-     * @private
-     * @param {Object} object The object to inspect.
-     * @param {Array} props The property names to filter.
-     * @returns {Array} Returns the function names.
-     */
-    function baseFunctions(object, props) {
-      return arrayFilter(props, function(key) {
-        return isFunction(object[key]);
-      });
-    }
-
-    /**
-     * The base implementation of `_.get` without support for default values.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the property to get.
-     * @returns {*} Returns the resolved value.
-     */
-    function baseGet(object, path) {
-      path = castPath(path, object);
-
-      var index = 0,
-          length = path.length;
-
-      while (object != null && index < length) {
-        object = object[toKey(path[index++])];
-      }
-      return (index && index == length) ? object : undefined;
-    }
-
-    /**
-     * The base implementation of `getAllKeys` and `getAllKeysIn` which uses
-     * `keysFunc` and `symbolsFunc` to get the enumerable property names and
-     * symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Function} keysFunc The function to get the keys of `object`.
-     * @param {Function} symbolsFunc The function to get the symbols of `object`.
-     * @returns {Array} Returns the array of property names and symbols.
-     */
-    function baseGetAllKeys(object, keysFunc, symbolsFunc) {
-      var result = keysFunc(object);
-      return isArray(object) ? result : arrayPush(result, symbolsFunc(object));
-    }
-
-    /**
-     * The base implementation of `getTag` without fallbacks for buggy environments.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @returns {string} Returns the `toStringTag`.
-     */
-    function baseGetTag(value) {
-      if (value == null) {
-        return value === undefined ? undefinedTag : nullTag;
-      }
-      return (symToStringTag && symToStringTag in Object(value))
-        ? getRawTag(value)
-        : objectToString(value);
-    }
-
-    /**
-     * The base implementation of `_.gt` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is greater than `other`,
-     *  else `false`.
-     */
-    function baseGt(value, other) {
-      return value > other;
-    }
-
-    /**
-     * The base implementation of `_.has` without support for deep paths.
-     *
-     * @private
-     * @param {Object} [object] The object to query.
-     * @param {Array|string} key The key to check.
-     * @returns {boolean} Returns `true` if `key` exists, else `false`.
-     */
-    function baseHas(object, key) {
-      return object != null && hasOwnProperty.call(object, key);
-    }
-
-    /**
-     * The base implementation of `_.hasIn` without support for deep paths.
-     *
-     * @private
-     * @param {Object} [object] The object to query.
-     * @param {Array|string} key The key to check.
-     * @returns {boolean} Returns `true` if `key` exists, else `false`.
-     */
-    function baseHasIn(object, key) {
-      return object != null && key in Object(object);
-    }
-
-    /**
-     * The base implementation of `_.inRange` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {number} number The number to check.
-     * @param {number} start The start of the range.
-     * @param {number} end The end of the range.
-     * @returns {boolean} Returns `true` if `number` is in the range, else `false`.
-     */
-    function baseInRange(number, start, end) {
-      return number >= nativeMin(start, end) && number < nativeMax(start, end);
-    }
-
-    /**
-     * The base implementation of methods like `_.intersection`, without support
-     * for iteratee shorthands, that accepts an array of arrays to inspect.
-     *
-     * @private
-     * @param {Array} arrays The arrays to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of shared values.
-     */
-    function baseIntersection(arrays, iteratee, comparator) {
-      var includes = comparator ? arrayIncludesWith : arrayIncludes,
-          length = arrays[0].length,
-          othLength = arrays.length,
-          othIndex = othLength,
-          caches = Array(othLength),
-          maxLength = Infinity,
-          result = [];
-
-      while (othIndex--) {
-        var array = arrays[othIndex];
-        if (othIndex && iteratee) {
-          array = arrayMap(array, baseUnary(iteratee));
-        }
-        maxLength = nativeMin(array.length, maxLength);
-        caches[othIndex] = !comparator && (iteratee || (length >= 120 && array.length >= 120))
-          ? new SetCache(othIndex && array)
-          : undefined;
-      }
-      array = arrays[0];
-
-      var index = -1,
-          seen = caches[0];
-
-      outer:
-      while (++index < length && result.length < maxLength) {
-        var value = array[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        value = (comparator || value !== 0) ? value : 0;
-        if (!(seen
-              ? cacheHas(seen, computed)
-              : includes(result, computed, comparator)
-            )) {
-          othIndex = othLength;
-          while (--othIndex) {
-            var cache = caches[othIndex];
-            if (!(cache
-                  ? cacheHas(cache, computed)
-                  : includes(arrays[othIndex], computed, comparator))
-                ) {
-              continue outer;
-            }
-          }
-          if (seen) {
-            seen.push(computed);
-          }
-          result.push(value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.invert` and `_.invertBy` which inverts
-     * `object` with values transformed by `iteratee` and set by `setter`.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} setter The function to set `accumulator` values.
-     * @param {Function} iteratee The iteratee to transform values.
-     * @param {Object} accumulator The initial inverted object.
-     * @returns {Function} Returns `accumulator`.
-     */
-    function baseInverter(object, setter, iteratee, accumulator) {
-      baseForOwn(object, function(value, key, object) {
-        setter(accumulator, iteratee(value), key, object);
-      });
-      return accumulator;
-    }
-
-    /**
-     * The base implementation of `_.invoke` without support for individual
-     * method arguments.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the method to invoke.
-     * @param {Array} args The arguments to invoke the method with.
-     * @returns {*} Returns the result of the invoked method.
-     */
-    function baseInvoke(object, path, args) {
-      path = castPath(path, object);
-      object = parent(object, path);
-      var func = object == null ? object : object[toKey(last(path))];
-      return func == null ? undefined : apply(func, object, args);
-    }
-
-    /**
-     * The base implementation of `_.isArguments`.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an `arguments` object,
-     */
-    function baseIsArguments(value) {
-      return isObjectLike(value) && baseGetTag(value) == argsTag;
-    }
-
-    /**
-     * The base implementation of `_.isArrayBuffer` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array buffer, else `false`.
-     */
-    function baseIsArrayBuffer(value) {
-      return isObjectLike(value) && baseGetTag(value) == arrayBufferTag;
-    }
-
-    /**
-     * The base implementation of `_.isDate` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a date object, else `false`.
-     */
-    function baseIsDate(value) {
-      return isObjectLike(value) && baseGetTag(value) == dateTag;
-    }
-
-    /**
-     * The base implementation of `_.isEqual` which supports partial comparisons
-     * and tracks traversed objects.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @param {boolean} bitmask The bitmask flags.
-     *  1 - Unordered comparison
-     *  2 - Partial comparison
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @param {Object} [stack] Tracks traversed `value` and `other` objects.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     */
-    function baseIsEqual(value, other, bitmask, customizer, stack) {
-      if (value === other) {
-        return true;
-      }
-      if (value == null || other == null || (!isObjectLike(value) && !isObjectLike(other))) {
-        return value !== value && other !== other;
-      }
-      return baseIsEqualDeep(value, other, bitmask, customizer, baseIsEqual, stack);
-    }
-
-    /**
-     * A specialized version of `baseIsEqual` for arrays and objects which performs
-     * deep comparisons and tracks traversed objects enabling objects with circular
-     * references to be compared.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} [stack] Tracks traversed `object` and `other` objects.
-     * @returns {boolean} Returns `true` if the objects are equivalent, else `false`.
-     */
-    function baseIsEqualDeep(object, other, bitmask, customizer, equalFunc, stack) {
-      var objIsArr = isArray(object),
-          othIsArr = isArray(other),
-          objTag = objIsArr ? arrayTag : getTag(object),
-          othTag = othIsArr ? arrayTag : getTag(other);
-
-      objTag = objTag == argsTag ? objectTag : objTag;
-      othTag = othTag == argsTag ? objectTag : othTag;
-
-      var objIsObj = objTag == objectTag,
-          othIsObj = othTag == objectTag,
-          isSameTag = objTag == othTag;
-
-      if (isSameTag && isBuffer(object)) {
-        if (!isBuffer(other)) {
-          return false;
-        }
-        objIsArr = true;
-        objIsObj = false;
-      }
-      if (isSameTag && !objIsObj) {
-        stack || (stack = new Stack);
-        return (objIsArr || isTypedArray(object))
-          ? equalArrays(object, other, bitmask, customizer, equalFunc, stack)
-          : equalByTag(object, other, objTag, bitmask, customizer, equalFunc, stack);
-      }
-      if (!(bitmask & COMPARE_PARTIAL_FLAG)) {
-        var objIsWrapped = objIsObj && hasOwnProperty.call(object, '__wrapped__'),
-            othIsWrapped = othIsObj && hasOwnProperty.call(other, '__wrapped__');
-
-        if (objIsWrapped || othIsWrapped) {
-          var objUnwrapped = objIsWrapped ? object.value() : object,
-              othUnwrapped = othIsWrapped ? other.value() : other;
-
-          stack || (stack = new Stack);
-          return equalFunc(objUnwrapped, othUnwrapped, bitmask, customizer, stack);
-        }
-      }
-      if (!isSameTag) {
-        return false;
-      }
-      stack || (stack = new Stack);
-      return equalObjects(object, other, bitmask, customizer, equalFunc, stack);
-    }
-
-    /**
-     * The base implementation of `_.isMap` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a map, else `false`.
-     */
-    function baseIsMap(value) {
-      return isObjectLike(value) && getTag(value) == mapTag;
-    }
-
-    /**
-     * The base implementation of `_.isMatch` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property values to match.
-     * @param {Array} matchData The property names, values, and compare flags to match.
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @returns {boolean} Returns `true` if `object` is a match, else `false`.
-     */
-    function baseIsMatch(object, source, matchData, customizer) {
-      var index = matchData.length,
-          length = index,
-          noCustomizer = !customizer;
-
-      if (object == null) {
-        return !length;
-      }
-      object = Object(object);
-      while (index--) {
-        var data = matchData[index];
-        if ((noCustomizer && data[2])
-              ? data[1] !== object[data[0]]
-              : !(data[0] in object)
-            ) {
-          return false;
-        }
-      }
-      while (++index < length) {
-        data = matchData[index];
-        var key = data[0],
-            objValue = object[key],
-            srcValue = data[1];
-
-        if (noCustomizer && data[2]) {
-          if (objValue === undefined && !(key in object)) {
-            return false;
-          }
-        } else {
-          var stack = new Stack;
-          if (customizer) {
-            var result = customizer(objValue, srcValue, key, object, source, stack);
-          }
-          if (!(result === undefined
-                ? baseIsEqual(srcValue, objValue, COMPARE_PARTIAL_FLAG | COMPARE_UNORDERED_FLAG, customizer, stack)
-                : result
-              )) {
-            return false;
-          }
-        }
-      }
-      return true;
-    }
-
-    /**
-     * The base implementation of `_.isNative` without bad shim checks.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a native function,
-     *  else `false`.
-     */
-    function baseIsNative(value) {
-      if (!isObject(value) || isMasked(value)) {
-        return false;
-      }
-      var pattern = isFunction(value) ? reIsNative : reIsHostCtor;
-      return pattern.test(toSource(value));
-    }
-
-    /**
-     * The base implementation of `_.isRegExp` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a regexp, else `false`.
-     */
-    function baseIsRegExp(value) {
-      return isObjectLike(value) && baseGetTag(value) == regexpTag;
-    }
-
-    /**
-     * The base implementation of `_.isSet` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a set, else `false`.
-     */
-    function baseIsSet(value) {
-      return isObjectLike(value) && getTag(value) == setTag;
-    }
-
-    /**
-     * The base implementation of `_.isTypedArray` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a typed array, else `false`.
-     */
-    function baseIsTypedArray(value) {
-      return isObjectLike(value) &&
-        isLength(value.length) && !!typedArrayTags[baseGetTag(value)];
-    }
-
-    /**
-     * The base implementation of `_.iteratee`.
-     *
-     * @private
-     * @param {*} [value=_.identity] The value to convert to an iteratee.
-     * @returns {Function} Returns the iteratee.
-     */
-    function baseIteratee(value) {
-      // Don't store the `typeof` result in a variable to avoid a JIT bug in Safari 9.
-      // See https://bugs.webkit.org/show_bug.cgi?id=156034 for more details.
-      if (typeof value == 'function') {
-        return value;
-      }
-      if (value == null) {
-        return identity;
-      }
-      if (typeof value == 'object') {
-        return isArray(value)
-          ? baseMatchesProperty(value[0], value[1])
-          : baseMatches(value);
-      }
-      return property(value);
-    }
-
-    /**
-     * The base implementation of `_.keys` which doesn't treat sparse arrays as dense.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     */
-    function baseKeys(object) {
-      if (!isPrototype(object)) {
-        return nativeKeys(object);
-      }
-      var result = [];
-      for (var key in Object(object)) {
-        if (hasOwnProperty.call(object, key) && key != 'constructor') {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.keysIn` which doesn't treat sparse arrays as dense.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     */
-    function baseKeysIn(object) {
-      if (!isObject(object)) {
-        return nativeKeysIn(object);
-      }
-      var isProto = isPrototype(object),
-          result = [];
-
-      for (var key in object) {
-        if (!(key == 'constructor' && (isProto || !hasOwnProperty.call(object, key)))) {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.lt` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is less than `other`,
-     *  else `false`.
-     */
-    function baseLt(value, other) {
-      return value < other;
-    }
-
-    /**
-     * The base implementation of `_.map` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Array} Returns the new mapped array.
-     */
-    function baseMap(collection, iteratee) {
-      var index = -1,
-          result = isArrayLike(collection) ? Array(collection.length) : [];
-
-      baseEach(collection, function(value, key, collection) {
-        result[++index] = iteratee(value, key, collection);
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.matches` which doesn't clone `source`.
-     *
-     * @private
-     * @param {Object} source The object of property values to match.
-     * @returns {Function} Returns the new spec function.
-     */
-    function baseMatches(source) {
-      var matchData = getMatchData(source);
-      if (matchData.length == 1 && matchData[0][2]) {
-        return matchesStrictComparable(matchData[0][0], matchData[0][1]);
-      }
-      return function(object) {
-        return object === source || baseIsMatch(object, source, matchData);
-      };
-    }
-
-    /**
-     * The base implementation of `_.matchesProperty` which doesn't clone `srcValue`.
-     *
-     * @private
-     * @param {string} path The path of the property to get.
-     * @param {*} srcValue The value to match.
-     * @returns {Function} Returns the new spec function.
-     */
-    function baseMatchesProperty(path, srcValue) {
-      if (isKey(path) && isStrictComparable(srcValue)) {
-        return matchesStrictComparable(toKey(path), srcValue);
-      }
-      return function(object) {
-        var objValue = get(object, path);
-        return (objValue === undefined && objValue === srcValue)
-          ? hasIn(object, path)
-          : baseIsEqual(srcValue, objValue, COMPARE_PARTIAL_FLAG | COMPARE_UNORDERED_FLAG);
-      };
-    }
-
-    /**
-     * The base implementation of `_.merge` without support for multiple sources.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @param {number} srcIndex The index of `source`.
-     * @param {Function} [customizer] The function to customize merged values.
-     * @param {Object} [stack] Tracks traversed source values and their merged
-     *  counterparts.
-     */
-    function baseMerge(object, source, srcIndex, customizer, stack) {
-      if (object === source) {
-        return;
-      }
-      baseFor(source, function(srcValue, key) {
-        stack || (stack = new Stack);
-        if (isObject(srcValue)) {
-          baseMergeDeep(object, source, key, srcIndex, baseMerge, customizer, stack);
-        }
-        else {
-          var newValue = customizer
-            ? customizer(safeGet(object, key), srcValue, (key + ''), object, source, stack)
-            : undefined;
-
-          if (newValue === undefined) {
-            newValue = srcValue;
-          }
-          assignMergeValue(object, key, newValue);
-        }
-      }, keysIn);
-    }
-
-    /**
-     * A specialized version of `baseMerge` for arrays and objects which performs
-     * deep merges and tracks traversed objects enabling objects with circular
-     * references to be merged.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @param {string} key The key of the value to merge.
-     * @param {number} srcIndex The index of `source`.
-     * @param {Function} mergeFunc The function to merge values.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @param {Object} [stack] Tracks traversed source values and their merged
-     *  counterparts.
-     */
-    function baseMergeDeep(object, source, key, srcIndex, mergeFunc, customizer, stack) {
-      var objValue = safeGet(object, key),
-          srcValue = safeGet(source, key),
-          stacked = stack.get(srcValue);
-
-      if (stacked) {
-        assignMergeValue(object, key, stacked);
-        return;
-      }
-      var newValue = customizer
-        ? customizer(objValue, srcValue, (key + ''), object, source, stack)
-        : undefined;
-
-      var isCommon = newValue === undefined;
-
-      if (isCommon) {
-        var isArr = isArray(srcValue),
-            isBuff = !isArr && isBuffer(srcValue),
-            isTyped = !isArr && !isBuff && isTypedArray(srcValue);
-
-        newValue = srcValue;
-        if (isArr || isBuff || isTyped) {
-          if (isArray(objValue)) {
-            newValue = objValue;
-          }
-          else if (isArrayLikeObject(objValue)) {
-            newValue = copyArray(objValue);
-          }
-          else if (isBuff) {
-            isCommon = false;
-            newValue = cloneBuffer(srcValue, true);
-          }
-          else if (isTyped) {
-            isCommon = false;
-            newValue = cloneTypedArray(srcValue, true);
-          }
-          else {
-            newValue = [];
-          }
-        }
-        else if (isPlainObject(srcValue) || isArguments(srcValue)) {
-          newValue = objValue;
-          if (isArguments(objValue)) {
-            newValue = toPlainObject(objValue);
-          }
-          else if (!isObject(objValue) || isFunction(objValue)) {
-            newValue = initCloneObject(srcValue);
-          }
-        }
-        else {
-          isCommon = false;
-        }
-      }
-      if (isCommon) {
-        // Recursively merge objects and arrays (susceptible to call stack limits).
-        stack.set(srcValue, newValue);
-        mergeFunc(newValue, srcValue, srcIndex, customizer, stack);
-        stack['delete'](srcValue);
-      }
-      assignMergeValue(object, key, newValue);
-    }
-
-    /**
-     * The base implementation of `_.nth` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {Array} array The array to query.
-     * @param {number} n The index of the element to return.
-     * @returns {*} Returns the nth element of `array`.
-     */
-    function baseNth(array, n) {
-      var length = array.length;
-      if (!length) {
-        return;
-      }
-      n += n < 0 ? length : 0;
-      return isIndex(n, length) ? array[n] : undefined;
-    }
-
-    /**
-     * The base implementation of `_.orderBy` without param guards.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function[]|Object[]|string[]} iteratees The iteratees to sort by.
-     * @param {string[]} orders The sort orders of `iteratees`.
-     * @returns {Array} Returns the new sorted array.
-     */
-    function baseOrderBy(collection, iteratees, orders) {
-      var index = -1;
-      iteratees = arrayMap(iteratees.length ? iteratees : [identity], baseUnary(getIteratee()));
-
-      var result = baseMap(collection, function(value, key, collection) {
-        var criteria = arrayMap(iteratees, function(iteratee) {
-          return iteratee(value);
-        });
-        return { 'criteria': criteria, 'index': ++index, 'value': value };
-      });
-
-      return baseSortBy(result, function(object, other) {
-        return compareMultiple(object, other, orders);
-      });
-    }
-
-    /**
-     * The base implementation of `_.pick` without support for individual
-     * property identifiers.
-     *
-     * @private
-     * @param {Object} object The source object.
-     * @param {string[]} paths The property paths to pick.
-     * @returns {Object} Returns the new object.
-     */
-    function basePick(object, paths) {
-      return basePickBy(object, paths, function(value, path) {
-        return hasIn(object, path);
-      });
-    }
-
-    /**
-     * The base implementation of  `_.pickBy` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The source object.
-     * @param {string[]} paths The property paths to pick.
-     * @param {Function} predicate The function invoked per property.
-     * @returns {Object} Returns the new object.
-     */
-    function basePickBy(object, paths, predicate) {
-      var index = -1,
-          length = paths.length,
-          result = {};
-
-      while (++index < length) {
-        var path = paths[index],
-            value = baseGet(object, path);
-
-        if (predicate(value, path)) {
-          baseSet(result, castPath(path, object), value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * A specialized version of `baseProperty` which supports deep paths.
-     *
-     * @private
-     * @param {Array|string} path The path of the property to get.
-     * @returns {Function} Returns the new accessor function.
-     */
-    function basePropertyDeep(path) {
-      return function(object) {
-        return baseGet(object, path);
-      };
-    }
-
-    /**
-     * The base implementation of `_.pullAllBy` without support for iteratee
-     * shorthands.
-     *
-     * @private
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns `array`.
-     */
-    function basePullAll(array, values, iteratee, comparator) {
-      var indexOf = comparator ? baseIndexOfWith : baseIndexOf,
-          index = -1,
-          length = values.length,
-          seen = array;
-
-      if (array === values) {
-        values = copyArray(values);
-      }
-      if (iteratee) {
-        seen = arrayMap(array, baseUnary(iteratee));
-      }
-      while (++index < length) {
-        var fromIndex = 0,
-            value = values[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        while ((fromIndex = indexOf(seen, computed, fromIndex, comparator)) > -1) {
-          if (seen !== array) {
-            splice.call(seen, fromIndex, 1);
-          }
-          splice.call(array, fromIndex, 1);
-        }
-      }
-      return array;
-    }
-
-    /**
-     * The base implementation of `_.pullAt` without support for individual
-     * indexes or capturing the removed elements.
-     *
-     * @private
-     * @param {Array} array The array to modify.
-     * @param {number[]} indexes The indexes of elements to remove.
-     * @returns {Array} Returns `array`.
-     */
-    function basePullAt(array, indexes) {
-      var length = array ? indexes.length : 0,
-          lastIndex = length - 1;
-
-      while (length--) {
-        var index = indexes[length];
-        if (length == lastIndex || index !== previous) {
-          var previous = index;
-          if (isIndex(index)) {
-            splice.call(array, index, 1);
-          } else {
-            baseUnset(array, index);
-          }
-        }
-      }
-      return array;
-    }
-
-    /**
-     * The base implementation of `_.random` without support for returning
-     * floating-point numbers.
-     *
-     * @private
-     * @param {number} lower The lower bound.
-     * @param {number} upper The upper bound.
-     * @returns {number} Returns the random number.
-     */
-    function baseRandom(lower, upper) {
-      return lower + nativeFloor(nativeRandom() * (upper - lower + 1));
-    }
-
-    /**
-     * The base implementation of `_.range` and `_.rangeRight` which doesn't
-     * coerce arguments.
-     *
-     * @private
-     * @param {number} start The start of the range.
-     * @param {number} end The end of the range.
-     * @param {number} step The value to increment or decrement by.
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Array} Returns the range of numbers.
-     */
-    function baseRange(start, end, step, fromRight) {
-      var index = -1,
-          length = nativeMax(nativeCeil((end - start) / (step || 1)), 0),
-          result = Array(length);
-
-      while (length--) {
-        result[fromRight ? length : ++index] = start;
-        start += step;
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.repeat` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {string} string The string to repeat.
-     * @param {number} n The number of times to repeat the string.
-     * @returns {string} Returns the repeated string.
-     */
-    function baseRepeat(string, n) {
-      var result = '';
-      if (!string || n < 1 || n > MAX_SAFE_INTEGER) {
-        return result;
-      }
-      // Leverage the exponentiation by squaring algorithm for a faster repeat.
-      // See https://en.wikipedia.org/wiki/Exponentiation_by_squaring for more details.
-      do {
-        if (n % 2) {
-          result += string;
-        }
-        n = nativeFloor(n / 2);
-        if (n) {
-          string += string;
-        }
-      } while (n);
-
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.rest` which doesn't validate or coerce arguments.
-     *
-     * @private
-     * @param {Function} func The function to apply a rest parameter to.
-     * @param {number} [start=func.length-1] The start position of the rest parameter.
-     * @returns {Function} Returns the new function.
-     */
-    function baseRest(func, start) {
-      return setToString(overRest(func, start, identity), func + '');
-    }
-
-    /**
-     * The base implementation of `_.sample`.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to sample.
-     * @returns {*} Returns the random element.
-     */
-    function baseSample(collection) {
-      return arraySample(values(collection));
-    }
-
-    /**
-     * The base implementation of `_.sampleSize` without param guards.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to sample.
-     * @param {number} n The number of elements to sample.
-     * @returns {Array} Returns the random elements.
-     */
-    function baseSampleSize(collection, n) {
-      var array = values(collection);
-      return shuffleSelf(array, baseClamp(n, 0, array.length));
-    }
-
-    /**
-     * The base implementation of `_.set`.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {*} value The value to set.
-     * @param {Function} [customizer] The function to customize path creation.
-     * @returns {Object} Returns `object`.
-     */
-    function baseSet(object, path, value, customizer) {
-      if (!isObject(object)) {
-        return object;
-      }
-      path = castPath(path, object);
-
-      var index = -1,
-          length = path.length,
-          lastIndex = length - 1,
-          nested = object;
-
-      while (nested != null && ++index < length) {
-        var key = toKey(path[index]),
-            newValue = value;
-
-        if (index != lastIndex) {
-          var objValue = nested[key];
-          newValue = customizer ? customizer(objValue, key, nested) : undefined;
-          if (newValue === undefined) {
-            newValue = isObject(objValue)
-              ? objValue
-              : (isIndex(path[index + 1]) ? [] : {});
-          }
-        }
-        assignValue(nested, key, newValue);
-        nested = nested[key];
-      }
-      return object;
-    }
-
-    /**
-     * The base implementation of `setData` without support for hot loop shorting.
-     *
-     * @private
-     * @param {Function} func The function to associate metadata with.
-     * @param {*} data The metadata.
-     * @returns {Function} Returns `func`.
-     */
-    var baseSetData = !metaMap ? identity : function(func, data) {
-      metaMap.set(func, data);
-      return func;
-    };
-
-    /**
-     * The base implementation of `setToString` without support for hot loop shorting.
-     *
-     * @private
-     * @param {Function} func The function to modify.
-     * @param {Function} string The `toString` result.
-     * @returns {Function} Returns `func`.
-     */
-    var baseSetToString = !defineProperty ? identity : function(func, string) {
-      return defineProperty(func, 'toString', {
-        'configurable': true,
-        'enumerable': false,
-        'value': constant(string),
-        'writable': true
-      });
-    };
-
-    /**
-     * The base implementation of `_.shuffle`.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to shuffle.
-     * @returns {Array} Returns the new shuffled array.
-     */
-    function baseShuffle(collection) {
-      return shuffleSelf(values(collection));
-    }
-
-    /**
-     * The base implementation of `_.slice` without an iteratee call guard.
-     *
-     * @private
-     * @param {Array} array The array to slice.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns the slice of `array`.
-     */
-    function baseSlice(array, start, end) {
-      var index = -1,
-          length = array.length;
-
-      if (start < 0) {
-        start = -start > length ? 0 : (length + start);
-      }
-      end = end > length ? length : end;
-      if (end < 0) {
-        end += length;
-      }
-      length = start > end ? 0 : ((end - start) >>> 0);
-      start >>>= 0;
-
-      var result = Array(length);
-      while (++index < length) {
-        result[index] = array[index + start];
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.some` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} predicate The function invoked per iteration.
-     * @returns {boolean} Returns `true` if any element passes the predicate check,
-     *  else `false`.
-     */
-    function baseSome(collection, predicate) {
-      var result;
-
-      baseEach(collection, function(value, index, collection) {
-        result = predicate(value, index, collection);
-        return !result;
-      });
-      return !!result;
-    }
-
-    /**
-     * The base implementation of `_.sortedIndex` and `_.sortedLastIndex` which
-     * performs a binary search of `array` to determine the index at which `value`
-     * should be inserted into `array` in order to maintain its sort order.
-     *
-     * @private
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {boolean} [retHighest] Specify returning the highest qualified index.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     */
-    function baseSortedIndex(array, value, retHighest) {
-      var low = 0,
-          high = array == null ? low : array.length;
-
-      if (typeof value == 'number' && value === value && high <= HALF_MAX_ARRAY_LENGTH) {
-        while (low < high) {
-          var mid = (low + high) >>> 1,
-              computed = array[mid];
-
-          if (computed !== null && !isSymbol(computed) &&
-              (retHighest ? (computed <= value) : (computed < value))) {
-            low = mid + 1;
-          } else {
-            high = mid;
-          }
-        }
-        return high;
-      }
-      return baseSortedIndexBy(array, value, identity, retHighest);
-    }
-
-    /**
-     * The base implementation of `_.sortedIndexBy` and `_.sortedLastIndexBy`
-     * which invokes `iteratee` for `value` and each element of `array` to compute
-     * their sort ranking. The iteratee is invoked with one argument; (value).
-     *
-     * @private
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {Function} iteratee The iteratee invoked per element.
-     * @param {boolean} [retHighest] Specify returning the highest qualified index.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     */
-    function baseSortedIndexBy(array, value, iteratee, retHighest) {
-      value = iteratee(value);
-
-      var low = 0,
-          high = array == null ? 0 : array.length,
-          valIsNaN = value !== value,
-          valIsNull = value === null,
-          valIsSymbol = isSymbol(value),
-          valIsUndefined = value === undefined;
-
-      while (low < high) {
-        var mid = nativeFloor((low + high) / 2),
-            computed = iteratee(array[mid]),
-            othIsDefined = computed !== undefined,
-            othIsNull = computed === null,
-            othIsReflexive = computed === computed,
-            othIsSymbol = isSymbol(computed);
-
-        if (valIsNaN) {
-          var setLow = retHighest || othIsReflexive;
-        } else if (valIsUndefined) {
-          setLow = othIsReflexive && (retHighest || othIsDefined);
-        } else if (valIsNull) {
-          setLow = othIsReflexive && othIsDefined && (retHighest || !othIsNull);
-        } else if (valIsSymbol) {
-          setLow = othIsReflexive && othIsDefined && !othIsNull && (retHighest || !othIsSymbol);
-        } else if (othIsNull || othIsSymbol) {
-          setLow = false;
-        } else {
-          setLow = retHighest ? (computed <= value) : (computed < value);
-        }
-        if (setLow) {
-          low = mid + 1;
-        } else {
-          high = mid;
-        }
-      }
-      return nativeMin(high, MAX_ARRAY_INDEX);
-    }
-
-    /**
-     * The base implementation of `_.sortedUniq` and `_.sortedUniqBy` without
-     * support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     */
-    function baseSortedUniq(array, iteratee) {
-      var index = -1,
-          length = array.length,
-          resIndex = 0,
-          result = [];
-
-      while (++index < length) {
-        var value = array[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        if (!index || !eq(computed, seen)) {
-          var seen = computed;
-          result[resIndex++] = value === 0 ? 0 : value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.toNumber` which doesn't ensure correct
-     * conversions of binary, hexadecimal, or octal string values.
-     *
-     * @private
-     * @param {*} value The value to process.
-     * @returns {number} Returns the number.
-     */
-    function baseToNumber(value) {
-      if (typeof value == 'number') {
-        return value;
-      }
-      if (isSymbol(value)) {
-        return NAN;
-      }
-      return +value;
-    }
-
-    /**
-     * The base implementation of `_.toString` which doesn't convert nullish
-     * values to empty strings.
-     *
-     * @private
-     * @param {*} value The value to process.
-     * @returns {string} Returns the string.
-     */
-    function baseToString(value) {
-      // Exit early for strings to avoid a performance hit in some environments.
-      if (typeof value == 'string') {
-        return value;
-      }
-      if (isArray(value)) {
-        // Recursively convert values (susceptible to call stack limits).
-        return arrayMap(value, baseToString) + '';
-      }
-      if (isSymbol(value)) {
-        return symbolToString ? symbolToString.call(value) : '';
-      }
-      var result = (value + '');
-      return (result == '0' && (1 / value) == -INFINITY) ? '-0' : result;
-    }
-
-    /**
-     * The base implementation of `_.uniqBy` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     */
-    function baseUniq(array, iteratee, comparator) {
-      var index = -1,
-          includes = arrayIncludes,
-          length = array.length,
-          isCommon = true,
-          result = [],
-          seen = result;
-
-      if (comparator) {
-        isCommon = false;
-        includes = arrayIncludesWith;
-      }
-      else if (length >= LARGE_ARRAY_SIZE) {
-        var set = iteratee ? null : createSet(array);
-        if (set) {
-          return setToArray(set);
-        }
-        isCommon = false;
-        includes = cacheHas;
-        seen = new SetCache;
-      }
-      else {
-        seen = iteratee ? [] : result;
-      }
-      outer:
-      while (++index < length) {
-        var value = array[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        value = (comparator || value !== 0) ? value : 0;
-        if (isCommon && computed === computed) {
-          var seenIndex = seen.length;
-          while (seenIndex--) {
-            if (seen[seenIndex] === computed) {
-              continue outer;
-            }
-          }
-          if (iteratee) {
-            seen.push(computed);
-          }
-          result.push(value);
-        }
-        else if (!includes(seen, computed, comparator)) {
-          if (seen !== result) {
-            seen.push(computed);
-          }
-          result.push(value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.unset`.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The property path to unset.
-     * @returns {boolean} Returns `true` if the property is deleted, else `false`.
-     */
-    function baseUnset(object, path) {
-      path = castPath(path, object);
-      object = parent(object, path);
-      return object == null || delete object[toKey(last(path))];
-    }
-
-    /**
-     * The base implementation of `_.update`.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to update.
-     * @param {Function} updater The function to produce the updated value.
-     * @param {Function} [customizer] The function to customize path creation.
-     * @returns {Object} Returns `object`.
-     */
-    function baseUpdate(object, path, updater, customizer) {
-      return baseSet(object, path, updater(baseGet(object, path)), customizer);
-    }
-
-    /**
-     * The base implementation of methods like `_.dropWhile` and `_.takeWhile`
-     * without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to query.
-     * @param {Function} predicate The function invoked per iteration.
-     * @param {boolean} [isDrop] Specify dropping elements instead of taking them.
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Array} Returns the slice of `array`.
-     */
-    function baseWhile(array, predicate, isDrop, fromRight) {
-      var length = array.length,
-          index = fromRight ? length : -1;
-
-      while ((fromRight ? index-- : ++index < length) &&
-        predicate(array[index], index, array)) {}
-
-      return isDrop
-        ? baseSlice(array, (fromRight ? 0 : index), (fromRight ? index + 1 : length))
-        : baseSlice(array, (fromRight ? index + 1 : 0), (fromRight ? length : index));
-    }
-
-    /**
-     * The base implementation of `wrapperValue` which returns the result of
-     * performing a sequence of actions on the unwrapped `value`, where each
-     * successive action is supplied the return value of the previous.
-     *
-     * @private
-     * @param {*} value The unwrapped value.
-     * @param {Array} actions Actions to perform to resolve the unwrapped value.
-     * @returns {*} Returns the resolved value.
-     */
-    function baseWrapperValue(value, actions) {
-      var result = value;
-      if (result instanceof LazyWrapper) {
-        result = result.value();
-      }
-      return arrayReduce(actions, function(result, action) {
-        return action.func.apply(action.thisArg, arrayPush([result], action.args));
-      }, result);
-    }
-
-    /**
-     * The base implementation of methods like `_.xor`, without support for
-     * iteratee shorthands, that accepts an array of arrays to inspect.
-     *
-     * @private
-     * @param {Array} arrays The arrays to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of values.
-     */
-    function baseXor(arrays, iteratee, comparator) {
-      var length = arrays.length;
-      if (length < 2) {
-        return length ? baseUniq(arrays[0]) : [];
-      }
-      var index = -1,
-          result = Array(length);
-
-      while (++index < length) {
-        var array = arrays[index],
-            othIndex = -1;
-
-        while (++othIndex < length) {
-          if (othIndex != index) {
-            result[index] = baseDifference(result[index] || array, arrays[othIndex], iteratee, comparator);
-          }
-        }
-      }
-      return baseUniq(baseFlatten(result, 1), iteratee, comparator);
-    }
-
-    /**
-     * This base implementation of `_.zipObject` which assigns values using `assignFunc`.
-     *
-     * @private
-     * @param {Array} props The property identifiers.
-     * @param {Array} values The property values.
-     * @param {Function} assignFunc The function to assign values.
-     * @returns {Object} Returns the new object.
-     */
-    function baseZipObject(props, values, assignFunc) {
-      var index = -1,
-          length = props.length,
-          valsLength = values.length,
-          result = {};
-
-      while (++index < length) {
-        var value = index < valsLength ? values[index] : undefined;
-        assignFunc(result, props[index], value);
-      }
-      return result;
-    }
-
-    /**
-     * Casts `value` to an empty array if it's not an array like object.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @returns {Array|Object} Returns the cast array-like object.
-     */
-    function castArrayLikeObject(value) {
-      return isArrayLikeObject(value) ? value : [];
-    }
-
-    /**
-     * Casts `value` to `identity` if it's not a function.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @returns {Function} Returns cast function.
-     */
-    function castFunction(value) {
-      return typeof value == 'function' ? value : identity;
-    }
-
-    /**
-     * Casts `value` to a path array if it's not one.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @param {Object} [object] The object to query keys on.
-     * @returns {Array} Returns the cast property path array.
-     */
-    function castPath(value, object) {
-      if (isArray(value)) {
-        return value;
-      }
-      return isKey(value, object) ? [value] : stringToPath(toString(value));
-    }
-
-    /**
-     * A `baseRest` alias which can be replaced with `identity` by module
-     * replacement plugins.
-     *
-     * @private
-     * @type {Function}
-     * @param {Function} func The function to apply a rest parameter to.
-     * @returns {Function} Returns the new function.
-     */
-    var castRest = baseRest;
-
-    /**
-     * Casts `array` to a slice if it's needed.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {number} start The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns the cast slice.
-     */
-    function castSlice(array, start, end) {
-      var length = array.length;
-      end = end === undefined ? length : end;
-      return (!start && end >= length) ? array : baseSlice(array, start, end);
-    }
-
-    /**
-     * A simple wrapper around the global [`clearTimeout`](https://mdn.io/clearTimeout).
-     *
-     * @private
-     * @param {number|Object} id The timer id or timeout object of the timer to clear.
-     */
-    var clearTimeout = ctxClearTimeout || function(id) {
-      return root.clearTimeout(id);
-    };
-
-    /**
-     * Creates a clone of  `buffer`.
-     *
-     * @private
-     * @param {Buffer} buffer The buffer to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Buffer} Returns the cloned buffer.
-     */
-    function cloneBuffer(buffer, isDeep) {
-      if (isDeep) {
-        return buffer.slice();
-      }
-      var length = buffer.length,
-          result = allocUnsafe ? allocUnsafe(length) : new buffer.constructor(length);
-
-      buffer.copy(result);
-      return result;
-    }
-
-    /**
-     * Creates a clone of `arrayBuffer`.
-     *
-     * @private
-     * @param {ArrayBuffer} arrayBuffer The array buffer to clone.
-     * @returns {ArrayBuffer} Returns the cloned array buffer.
-     */
-    function cloneArrayBuffer(arrayBuffer) {
-      var result = new arrayBuffer.constructor(arrayBuffer.byteLength);
-      new Uint8Array(result).set(new Uint8Array(arrayBuffer));
-      return result;
-    }
-
-    /**
-     * Creates a clone of `dataView`.
-     *
-     * @private
-     * @param {Object} dataView The data view to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Object} Returns the cloned data view.
-     */
-    function cloneDataView(dataView, isDeep) {
-      var buffer = isDeep ? cloneArrayBuffer(dataView.buffer) : dataView.buffer;
-      return new dataView.constructor(buffer, dataView.byteOffset, dataView.byteLength);
-    }
-
-    /**
-     * Creates a clone of `regexp`.
-     *
-     * @private
-     * @param {Object} regexp The regexp to clone.
-     * @returns {Object} Returns the cloned regexp.
-     */
-    function cloneRegExp(regexp) {
-      var result = new regexp.constructor(regexp.source, reFlags.exec(regexp));
-      result.lastIndex = regexp.lastIndex;
-      return result;
-    }
-
-    /**
-     * Creates a clone of the `symbol` object.
-     *
-     * @private
-     * @param {Object} symbol The symbol object to clone.
-     * @returns {Object} Returns the cloned symbol object.
-     */
-    function cloneSymbol(symbol) {
-      return symbolValueOf ? Object(symbolValueOf.call(symbol)) : {};
-    }
-
-    /**
-     * Creates a clone of `typedArray`.
-     *
-     * @private
-     * @param {Object} typedArray The typed array to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Object} Returns the cloned typed array.
-     */
-    function cloneTypedArray(typedArray, isDeep) {
-      var buffer = isDeep ? cloneArrayBuffer(typedArray.buffer) : typedArray.buffer;
-      return new typedArray.constructor(buffer, typedArray.byteOffset, typedArray.length);
-    }
-
-    /**
-     * Compares values to sort them in ascending order.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {number} Returns the sort order indicator for `value`.
-     */
-    function compareAscending(value, other) {
-      if (value !== other) {
-        var valIsDefined = value !== undefined,
-            valIsNull = value === null,
-            valIsReflexive = value === value,
-            valIsSymbol = isSymbol(value);
-
-        var othIsDefined = other !== undefined,
-            othIsNull = other === null,
-            othIsReflexive = other === other,
-            othIsSymbol = isSymbol(other);
-
-        if ((!othIsNull && !othIsSymbol && !valIsSymbol && value > other) ||
-            (valIsSymbol && othIsDefined && othIsReflexive && !othIsNull && !othIsSymbol) ||
-            (valIsNull && othIsDefined && othIsReflexive) ||
-            (!valIsDefined && othIsReflexive) ||
-            !valIsReflexive) {
-          return 1;
-        }
-        if ((!valIsNull && !valIsSymbol && !othIsSymbol && value < other) ||
-            (othIsSymbol && valIsDefined && valIsReflexive && !valIsNull && !valIsSymbol) ||
-            (othIsNull && valIsDefined && valIsReflexive) ||
-            (!othIsDefined && valIsReflexive) ||
-            !othIsReflexive) {
-          return -1;
-        }
-      }
-      return 0;
-    }
-
-    /**
-     * Used by `_.orderBy` to compare multiple properties of a value to another
-     * and stable sort them.
-     *
-     * If `orders` is unspecified, all values are sorted in ascending order. Otherwise,
-     * specify an order of "desc" for descending or "asc" for ascending sort order
-     * of corresponding values.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {boolean[]|string[]} orders The order to sort by for each property.
-     * @returns {number} Returns the sort order indicator for `object`.
-     */
-    function compareMultiple(object, other, orders) {
-      var index = -1,
-          objCriteria = object.criteria,
-          othCriteria = other.criteria,
-          length = objCriteria.length,
-          ordersLength = orders.length;
-
-      while (++index < length) {
-        var result = compareAscending(objCriteria[index], othCriteria[index]);
-        if (result) {
-          if (index >= ordersLength) {
-            return result;
-          }
-          var order = orders[index];
-          return result * (order == 'desc' ? -1 : 1);
-        }
-      }
-      // Fixes an `Array#sort` bug in the JS engine embedded in Adobe applications
-      // that causes it, under certain circumstances, to provide the same value for
-      // `object` and `other`. See https://github.com/jashkenas/underscore/pull/1247
-      // for more details.
-      //
-      // This also ensures a stable sort in V8 and other engines.
-      // See https://bugs.chromium.org/p/v8/issues/detail?id=90 for more details.
-      return object.index - other.index;
-    }
-
-    /**
-     * Creates an array that is the composition of partially applied arguments,
-     * placeholders, and provided arguments into a single array of arguments.
-     *
-     * @private
-     * @param {Array} args The provided arguments.
-     * @param {Array} partials The arguments to prepend to those provided.
-     * @param {Array} holders The `partials` placeholder indexes.
-     * @params {boolean} [isCurried] Specify composing for a curried function.
-     * @returns {Array} Returns the new array of composed arguments.
-     */
-    function composeArgs(args, partials, holders, isCurried) {
-      var argsIndex = -1,
-          argsLength = args.length,
-          holdersLength = holders.length,
-          leftIndex = -1,
-          leftLength = partials.length,
-          rangeLength = nativeMax(argsLength - holdersLength, 0),
-          result = Array(leftLength + rangeLength),
-          isUncurried = !isCurried;
-
-      while (++leftIndex < leftLength) {
-        result[leftIndex] = partials[leftIndex];
-      }
-      while (++argsIndex < holdersLength) {
-        if (isUncurried || argsIndex < argsLength) {
-          result[holders[argsIndex]] = args[argsIndex];
-        }
-      }
-      while (rangeLength--) {
-        result[leftIndex++] = args[argsIndex++];
-      }
-      return result;
-    }
-
-    /**
-     * This function is like `composeArgs` except that the arguments composition
-     * is tailored for `_.partialRight`.
-     *
-     * @private
-     * @param {Array} args The provided arguments.
-     * @param {Array} partials The arguments to append to those provided.
-     * @param {Array} holders The `partials` placeholder indexes.
-     * @params {boolean} [isCurried] Specify composing for a curried function.
-     * @returns {Array} Returns the new array of composed arguments.
-     */
-    function composeArgsRight(args, partials, holders, isCurried) {
-      var argsIndex = -1,
-          argsLength = args.length,
-          holdersIndex = -1,
-          holdersLength = holders.length,
-          rightIndex = -1,
-          rightLength = partials.length,
-          rangeLength = nativeMax(argsLength - holdersLength, 0),
-          result = Array(rangeLength + rightLength),
-          isUncurried = !isCurried;
-
-      while (++argsIndex < rangeLength) {
-        result[argsIndex] = args[argsIndex];
-      }
-      var offset = argsIndex;
-      while (++rightIndex < rightLength) {
-        result[offset + rightIndex] = partials[rightIndex];
-      }
-      while (++holdersIndex < holdersLength) {
-        if (isUncurried || argsIndex < argsLength) {
-          result[offset + holders[holdersIndex]] = args[argsIndex++];
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Copies the values of `source` to `array`.
-     *
-     * @private
-     * @param {Array} source The array to copy values from.
-     * @param {Array} [array=[]] The array to copy values to.
-     * @returns {Array} Returns `array`.
-     */
-    function copyArray(source, array) {
-      var index = -1,
-          length = source.length;
-
-      array || (array = Array(length));
-      while (++index < length) {
-        array[index] = source[index];
-      }
-      return array;
-    }
-
-    /**
-     * Copies properties of `source` to `object`.
-     *
-     * @private
-     * @param {Object} source The object to copy properties from.
-     * @param {Array} props The property identifiers to copy.
-     * @param {Object} [object={}] The object to copy properties to.
-     * @param {Function} [customizer] The function to customize copied values.
-     * @returns {Object} Returns `object`.
-     */
-    function copyObject(source, props, object, customizer) {
-      var isNew = !object;
-      object || (object = {});
-
-      var index = -1,
-          length = props.length;
-
-      while (++index < length) {
-        var key = props[index];
-
-        var newValue = customizer
-          ? customizer(object[key], source[key], key, object, source)
-          : undefined;
-
-        if (newValue === undefined) {
-          newValue = source[key];
-        }
-        if (isNew) {
-          baseAssignValue(object, key, newValue);
-        } else {
-          assignValue(object, key, newValue);
-        }
-      }
-      return object;
-    }
-
-    /**
-     * Copies own symbols of `source` to `object`.
-     *
-     * @private
-     * @param {Object} source The object to copy symbols from.
-     * @param {Object} [object={}] The object to copy symbols to.
-     * @returns {Object} Returns `object`.
-     */
-    function copySymbols(source, object) {
-      return copyObject(source, getSymbols(source), object);
-    }
-
-    /**
-     * Copies own and inherited symbols of `source` to `object`.
-     *
-     * @private
-     * @param {Object} source The object to copy symbols from.
-     * @param {Object} [object={}] The object to copy symbols to.
-     * @returns {Object} Returns `object`.
-     */
-    function copySymbolsIn(source, object) {
-      return copyObject(source, getSymbolsIn(source), object);
-    }
-
-    /**
-     * Creates a function like `_.groupBy`.
-     *
-     * @private
-     * @param {Function} setter The function to set accumulator values.
-     * @param {Function} [initializer] The accumulator object initializer.
-     * @returns {Function} Returns the new aggregator function.
-     */
-    function createAggregator(setter, initializer) {
-      return function(collection, iteratee) {
-        var func = isArray(collection) ? arrayAggregator : baseAggregator,
-            accumulator = initializer ? initializer() : {};
-
-        return func(collection, setter, getIteratee(iteratee, 2), accumulator);
-      };
-    }
-
-    /**
-     * Creates a function like `_.assign`.
-     *
-     * @private
-     * @param {Function} assigner The function to assign values.
-     * @returns {Function} Returns the new assigner function.
-     */
-    function createAssigner(assigner) {
-      return baseRest(function(object, sources) {
-        var index = -1,
-            length = sources.length,
-            customizer = length > 1 ? sources[length - 1] : undefined,
-            guard = length > 2 ? sources[2] : undefined;
-
-        customizer = (assigner.length > 3 && typeof customizer == 'function')
-          ? (length--, customizer)
-          : undefined;
-
-        if (guard && isIterateeCall(sources[0], sources[1], guard)) {
-          customizer = length < 3 ? undefined : customizer;
-          length = 1;
-        }
-        object = Object(object);
-        while (++index < length) {
-          var source = sources[index];
-          if (source) {
-            assigner(object, source, index, customizer);
-          }
-        }
-        return object;
-      });
-    }
-
-    /**
-     * Creates a `baseEach` or `baseEachRight` function.
-     *
-     * @private
-     * @param {Function} eachFunc The function to iterate over a collection.
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new base function.
-     */
-    function createBaseEach(eachFunc, fromRight) {
-      return function(collection, iteratee) {
-        if (collection == null) {
-          return collection;
-        }
-        if (!isArrayLike(collection)) {
-          return eachFunc(collection, iteratee);
-        }
-        var length = collection.length,
-            index = fromRight ? length : -1,
-            iterable = Object(collection);
-
-        while ((fromRight ? index-- : ++index < length)) {
-          if (iteratee(iterable[index], index, iterable) === false) {
-            break;
-          }
-        }
-        return collection;
-      };
-    }
-
-    /**
-     * Creates a base function for methods like `_.forIn` and `_.forOwn`.
-     *
-     * @private
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new base function.
-     */
-    function createBaseFor(fromRight) {
-      return function(object, iteratee, keysFunc) {
-        var index = -1,
-            iterable = Object(object),
-            props = keysFunc(object),
-            length = props.length;
-
-        while (length--) {
-          var key = props[fromRight ? length : ++index];
-          if (iteratee(iterable[key], key, iterable) === false) {
-            break;
-          }
-        }
-        return object;
-      };
-    }
-
-    /**
-     * Creates a function that wraps `func` to invoke it with the optional `this`
-     * binding of `thisArg`.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createBind(func, bitmask, thisArg) {
-      var isBind = bitmask & WRAP_BIND_FLAG,
-          Ctor = createCtor(func);
-
-      function wrapper() {
-        var fn = (this && this !== root && this instanceof wrapper) ? Ctor : func;
-        return fn.apply(isBind ? thisArg : this, arguments);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a function like `_.lowerFirst`.
-     *
-     * @private
-     * @param {string} methodName The name of the `String` case method to use.
-     * @returns {Function} Returns the new case function.
-     */
-    function createCaseFirst(methodName) {
-      return function(string) {
-        string = toString(string);
-
-        var strSymbols = hasUnicode(string)
-          ? stringToArray(string)
-          : undefined;
-
-        var chr = strSymbols
-          ? strSymbols[0]
-          : string.charAt(0);
-
-        var trailing = strSymbols
-          ? castSlice(strSymbols, 1).join('')
-          : string.slice(1);
-
-        return chr[methodName]() + trailing;
-      };
-    }
-
-    /**
-     * Creates a function like `_.camelCase`.
-     *
-     * @private
-     * @param {Function} callback The function to combine each word.
-     * @returns {Function} Returns the new compounder function.
-     */
-    function createCompounder(callback) {
-      return function(string) {
-        return arrayReduce(words(deburr(string).replace(reApos, '')), callback, '');
-      };
-    }
-
-    /**
-     * Creates a function that produces an instance of `Ctor` regardless of
-     * whether it was invoked as part of a `new` expression or by `call` or `apply`.
-     *
-     * @private
-     * @param {Function} Ctor The constructor to wrap.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createCtor(Ctor) {
-      return function() {
-        // Use a `switch` statement to work with class constructors. See
-        // http://ecma-international.org/ecma-262/7.0/#sec-ecmascript-function-objects-call-thisargument-argumentslist
-        // for more details.
-        var args = arguments;
-        switch (args.length) {
-          case 0: return new Ctor;
-          case 1: return new Ctor(args[0]);
-          case 2: return new Ctor(args[0], args[1]);
-          case 3: return new Ctor(args[0], args[1], args[2]);
-          case 4: return new Ctor(args[0], args[1], args[2], args[3]);
-          case 5: return new Ctor(args[0], args[1], args[2], args[3], args[4]);
-          case 6: return new Ctor(args[0], args[1], args[2], args[3], args[4], args[5]);
-          case 7: return new Ctor(args[0], args[1], args[2], args[3], args[4], args[5], args[6]);
-        }
-        var thisBinding = baseCreate(Ctor.prototype),
-            result = Ctor.apply(thisBinding, args);
-
-        // Mimic the constructor's `return` behavior.
-        // See https://es5.github.io/#x13.2.2 for more details.
-        return isObject(result) ? result : thisBinding;
-      };
-    }
-
-    /**
-     * Creates a function that wraps `func` to enable currying.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {number} arity The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createCurry(func, bitmask, arity) {
-      var Ctor = createCtor(func);
-
-      function wrapper() {
-        var length = arguments.length,
-            args = Array(length),
-            index = length,
-            placeholder = getHolder(wrapper);
-
-        while (index--) {
-          args[index] = arguments[index];
-        }
-        var holders = (length < 3 && args[0] !== placeholder && args[length - 1] !== placeholder)
-          ? []
-          : replaceHolders(args, placeholder);
-
-        length -= holders.length;
-        if (length < arity) {
-          return createRecurry(
-            func, bitmask, createHybrid, wrapper.placeholder, undefined,
-            args, holders, undefined, undefined, arity - length);
-        }
-        var fn = (this && this !== root && this instanceof wrapper) ? Ctor : func;
-        return apply(fn, this, args);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a `_.find` or `_.findLast` function.
-     *
-     * @private
-     * @param {Function} findIndexFunc The function to find the collection index.
-     * @returns {Function} Returns the new find function.
-     */
-    function createFind(findIndexFunc) {
-      return function(collection, predicate, fromIndex) {
-        var iterable = Object(collection);
-        if (!isArrayLike(collection)) {
-          var iteratee = getIteratee(predicate, 3);
-          collection = keys(collection);
-          predicate = function(key) { return iteratee(iterable[key], key, iterable); };
-        }
-        var index = findIndexFunc(collection, predicate, fromIndex);
-        return index > -1 ? iterable[iteratee ? collection[index] : index] : undefined;
-      };
-    }
-
-    /**
-     * Creates a `_.flow` or `_.flowRight` function.
-     *
-     * @private
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new flow function.
-     */
-    function createFlow(fromRight) {
-      return flatRest(function(funcs) {
-        var length = funcs.length,
-            index = length,
-            prereq = LodashWrapper.prototype.thru;
-
-        if (fromRight) {
-          funcs.reverse();
-        }
-        while (index--) {
-          var func = funcs[index];
-          if (typeof func != 'function') {
-            throw new TypeError(FUNC_ERROR_TEXT);
-          }
-          if (prereq && !wrapper && getFuncName(func) == 'wrapper') {
-            var wrapper = new LodashWrapper([], true);
-          }
-        }
-        index = wrapper ? index : length;
-        while (++index < length) {
-          func = funcs[index];
-
-          var funcName = getFuncName(func),
-              data = funcName == 'wrapper' ? getData(func) : undefined;
-
-          if (data && isLaziable(data[0]) &&
-                data[1] == (WRAP_ARY_FLAG | WRAP_CURRY_FLAG | WRAP_PARTIAL_FLAG | WRAP_REARG_FLAG) &&
-                !data[4].length && data[9] == 1
-              ) {
-            wrapper = wrapper[getFuncName(data[0])].apply(wrapper, data[3]);
-          } else {
-            wrapper = (func.length == 1 && isLaziable(func))
-              ? wrapper[funcName]()
-              : wrapper.thru(func);
-          }
-        }
-        return function() {
-          var args = arguments,
-              value = args[0];
-
-          if (wrapper && args.length == 1 && isArray(value)) {
-            return wrapper.plant(value).value();
-          }
-          var index = 0,
-              result = length ? funcs[index].apply(this, args) : value;
-
-          while (++index < length) {
-            result = funcs[index].call(this, result);
-          }
-          return result;
-        };
-      });
-    }
-
-    /**
-     * Creates a function that wraps `func` to invoke it with optional `this`
-     * binding of `thisArg`, partial application, and currying.
-     *
-     * @private
-     * @param {Function|string} func The function or method name to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @param {Array} [partials] The arguments to prepend to those provided to
-     *  the new function.
-     * @param {Array} [holders] The `partials` placeholder indexes.
-     * @param {Array} [partialsRight] The arguments to append to those provided
-     *  to the new function.
-     * @param {Array} [holdersRight] The `partialsRight` placeholder indexes.
-     * @param {Array} [argPos] The argument positions of the new function.
-     * @param {number} [ary] The arity cap of `func`.
-     * @param {number} [arity] The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createHybrid(func, bitmask, thisArg, partials, holders, partialsRight, holdersRight, argPos, ary, arity) {
-      var isAry = bitmask & WRAP_ARY_FLAG,
-          isBind = bitmask & WRAP_BIND_FLAG,
-          isBindKey = bitmask & WRAP_BIND_KEY_FLAG,
-          isCurried = bitmask & (WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG),
-          isFlip = bitmask & WRAP_FLIP_FLAG,
-          Ctor = isBindKey ? undefined : createCtor(func);
-
-      function wrapper() {
-        var length = arguments.length,
-            args = Array(length),
-            index = length;
-
-        while (index--) {
-          args[index] = arguments[index];
-        }
-        if (isCurried) {
-          var placeholder = getHolder(wrapper),
-              holdersCount = countHolders(args, placeholder);
-        }
-        if (partials) {
-          args = composeArgs(args, partials, holders, isCurried);
-        }
-        if (partialsRight) {
-          args = composeArgsRight(args, partialsRight, holdersRight, isCurried);
-        }
-        length -= holdersCount;
-        if (isCurried && length < arity) {
-          var newHolders = replaceHolders(args, placeholder);
-          return createRecurry(
-            func, bitmask, createHybrid, wrapper.placeholder, thisArg,
-            args, newHolders, argPos, ary, arity - length
-          );
-        }
-        var thisBinding = isBind ? thisArg : this,
-            fn = isBindKey ? thisBinding[func] : func;
-
-        length = args.length;
-        if (argPos) {
-          args = reorder(args, argPos);
-        } else if (isFlip && length > 1) {
-          args.reverse();
-        }
-        if (isAry && ary < length) {
-          args.length = ary;
-        }
-        if (this && this !== root && this instanceof wrapper) {
-          fn = Ctor || createCtor(fn);
-        }
-        return fn.apply(thisBinding, args);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a function like `_.invertBy`.
-     *
-     * @private
-     * @param {Function} setter The function to set accumulator values.
-     * @param {Function} toIteratee The function to resolve iteratees.
-     * @returns {Function} Returns the new inverter function.
-     */
-    function createInverter(setter, toIteratee) {
-      return function(object, iteratee) {
-        return baseInverter(object, setter, toIteratee(iteratee), {});
-      };
-    }
-
-    /**
-     * Creates a function that performs a mathematical operation on two values.
-     *
-     * @private
-     * @param {Function} operator The function to perform the operation.
-     * @param {number} [defaultValue] The value used for `undefined` arguments.
-     * @returns {Function} Returns the new mathematical operation function.
-     */
-    function createMathOperation(operator, defaultValue) {
-      return function(value, other) {
-        var result;
-        if (value === undefined && other === undefined) {
-          return defaultValue;
-        }
-        if (value !== undefined) {
-          result = value;
-        }
-        if (other !== undefined) {
-          if (result === undefined) {
-            return other;
-          }
-          if (typeof value == 'string' || typeof other == 'string') {
-            value = baseToString(value);
-            other = baseToString(other);
-          } else {
-            value = baseToNumber(value);
-            other = baseToNumber(other);
-          }
-          result = operator(value, other);
-        }
-        return result;
-      };
-    }
-
-    /**
-     * Creates a function like `_.over`.
-     *
-     * @private
-     * @param {Function} arrayFunc The function to iterate over iteratees.
-     * @returns {Function} Returns the new over function.
-     */
-    function createOver(arrayFunc) {
-      return flatRest(function(iteratees) {
-        iteratees = arrayMap(iteratees, baseUnary(getIteratee()));
-        return baseRest(function(args) {
-          var thisArg = this;
-          return arrayFunc(iteratees, function(iteratee) {
-            return apply(iteratee, thisArg, args);
-          });
-        });
-      });
-    }
-
-    /**
-     * Creates the padding for `string` based on `length`. The `chars` string
-     * is truncated if the number of characters exceeds `length`.
-     *
-     * @private
-     * @param {number} length The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padding for `string`.
-     */
-    function createPadding(length, chars) {
-      chars = chars === undefined ? ' ' : baseToString(chars);
-
-      var charsLength = chars.length;
-      if (charsLength < 2) {
-        return charsLength ? baseRepeat(chars, length) : chars;
-      }
-      var result = baseRepeat(chars, nativeCeil(length / stringSize(chars)));
-      return hasUnicode(chars)
-        ? castSlice(stringToArray(result), 0, length).join('')
-        : result.slice(0, length);
-    }
-
-    /**
-     * Creates a function that wraps `func` to invoke it with the `this` binding
-     * of `thisArg` and `partials` prepended to the arguments it receives.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {*} thisArg The `this` binding of `func`.
-     * @param {Array} partials The arguments to prepend to those provided to
-     *  the new function.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createPartial(func, bitmask, thisArg, partials) {
-      var isBind = bitmask & WRAP_BIND_FLAG,
-          Ctor = createCtor(func);
-
-      function wrapper() {
-        var argsIndex = -1,
-            argsLength = arguments.length,
-            leftIndex = -1,
-            leftLength = partials.length,
-            args = Array(leftLength + argsLength),
-            fn = (this && this !== root && this instanceof wrapper) ? Ctor : func;
-
-        while (++leftIndex < leftLength) {
-          args[leftIndex] = partials[leftIndex];
-        }
-        while (argsLength--) {
-          args[leftIndex++] = arguments[++argsIndex];
-        }
-        return apply(fn, isBind ? thisArg : this, args);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a `_.range` or `_.rangeRight` function.
-     *
-     * @private
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new range function.
-     */
-    function createRange(fromRight) {
-      return function(start, end, step) {
-        if (step && typeof step != 'number' && isIterateeCall(start, end, step)) {
-          end = step = undefined;
-        }
-        // Ensure the sign of `-0` is preserved.
-        start = toFinite(start);
-        if (end === undefined) {
-          end = start;
-          start = 0;
-        } else {
-          end = toFinite(end);
-        }
-        step = step === undefined ? (start < end ? 1 : -1) : toFinite(step);
-        return baseRange(start, end, step, fromRight);
-      };
-    }
-
-    /**
-     * Creates a function that performs a relational operation on two values.
-     *
-     * @private
-     * @param {Function} operator The function to perform the operation.
-     * @returns {Function} Returns the new relational operation function.
-     */
-    function createRelationalOperation(operator) {
-      return function(value, other) {
-        if (!(typeof value == 'string' && typeof other == 'string')) {
-          value = toNumber(value);
-          other = toNumber(other);
-        }
-        return operator(value, other);
-      };
-    }
-
-    /**
-     * Creates a function that wraps `func` to continue currying.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {Function} wrapFunc The function to create the `func` wrapper.
-     * @param {*} placeholder The placeholder value.
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @param {Array} [partials] The arguments to prepend to those provided to
-     *  the new function.
-     * @param {Array} [holders] The `partials` placeholder indexes.
-     * @param {Array} [argPos] The argument positions of the new function.
-     * @param {number} [ary] The arity cap of `func`.
-     * @param {number} [arity] The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createRecurry(func, bitmask, wrapFunc, placeholder, thisArg, partials, holders, argPos, ary, arity) {
-      var isCurry = bitmask & WRAP_CURRY_FLAG,
-          newHolders = isCurry ? holders : undefined,
-          newHoldersRight = isCurry ? undefined : holders,
-          newPartials = isCurry ? partials : undefined,
-          newPartialsRight = isCurry ? undefined : partials;
-
-      bitmask |= (isCurry ? WRAP_PARTIAL_FLAG : WRAP_PARTIAL_RIGHT_FLAG);
-      bitmask &= ~(isCurry ? WRAP_PARTIAL_RIGHT_FLAG : WRAP_PARTIAL_FLAG);
-
-      if (!(bitmask & WRAP_CURRY_BOUND_FLAG)) {
-        bitmask &= ~(WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG);
-      }
-      var newData = [
-        func, bitmask, thisArg, newPartials, newHolders, newPartialsRight,
-        newHoldersRight, argPos, ary, arity
-      ];
-
-      var result = wrapFunc.apply(undefined, newData);
-      if (isLaziable(func)) {
-        setData(result, newData);
-      }
-      result.placeholder = placeholder;
-      return setWrapToString(result, func, bitmask);
-    }
-
-    /**
-     * Creates a function like `_.round`.
-     *
-     * @private
-     * @param {string} methodName The name of the `Math` method to use when rounding.
-     * @returns {Function} Returns the new round function.
-     */
-    function createRound(methodName) {
-      var func = Math[methodName];
-      return function(number, precision) {
-        number = toNumber(number);
-        precision = precision == null ? 0 : nativeMin(toInteger(precision), 292);
-        if (precision && nativeIsFinite(number)) {
-          // Shift with exponential notation to avoid floating-point issues.
-          // See [MDN](https://mdn.io/round#Examples) for more details.
-          var pair = (toString(number) + 'e').split('e'),
-              value = func(pair[0] + 'e' + (+pair[1] + precision));
-
-          pair = (toString(value) + 'e').split('e');
-          return +(pair[0] + 'e' + (+pair[1] - precision));
-        }
-        return func(number);
-      };
-    }
-
-    /**
-     * Creates a set object of `values`.
-     *
-     * @private
-     * @param {Array} values The values to add to the set.
-     * @returns {Object} Returns the new set.
-     */
-    var createSet = !(Set && (1 / setToArray(new Set([,-0]))[1]) == INFINITY) ? noop : function(values) {
-      return new Set(values);
-    };
-
-    /**
-     * Creates a `_.toPairs` or `_.toPairsIn` function.
-     *
-     * @private
-     * @param {Function} keysFunc The function to get the keys of a given object.
-     * @returns {Function} Returns the new pairs function.
-     */
-    function createToPairs(keysFunc) {
-      return function(object) {
-        var tag = getTag(object);
-        if (tag == mapTag) {
-          return mapToArray(object);
-        }
-        if (tag == setTag) {
-          return setToPairs(object);
-        }
-        return baseToPairs(object, keysFunc(object));
-      };
-    }
-
-    /**
-     * Creates a function that either curries or invokes `func` with optional
-     * `this` binding and partially applied arguments.
-     *
-     * @private
-     * @param {Function|string} func The function or method name to wrap.
-     * @param {number} bitmask The bitmask flags.
-     *    1 - `_.bind`
-     *    2 - `_.bindKey`
-     *    4 - `_.curry` or `_.curryRight` of a bound function
-     *    8 - `_.curry`
-     *   16 - `_.curryRight`
-     *   32 - `_.partial`
-     *   64 - `_.partialRight`
-     *  128 - `_.rearg`
-     *  256 - `_.ary`
-     *  512 - `_.flip`
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @param {Array} [partials] The arguments to be partially applied.
-     * @param {Array} [holders] The `partials` placeholder indexes.
-     * @param {Array} [argPos] The argument positions of the new function.
-     * @param {number} [ary] The arity cap of `func`.
-     * @param {number} [arity] The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createWrap(func, bitmask, thisArg, partials, holders, argPos, ary, arity) {
-      var isBindKey = bitmask & WRAP_BIND_KEY_FLAG;
-      if (!isBindKey && typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      var length = partials ? partials.length : 0;
-      if (!length) {
-        bitmask &= ~(WRAP_PARTIAL_FLAG | WRAP_PARTIAL_RIGHT_FLAG);
-        partials = holders = undefined;
-      }
-      ary = ary === undefined ? ary : nativeMax(toInteger(ary), 0);
-      arity = arity === undefined ? arity : toInteger(arity);
-      length -= holders ? holders.length : 0;
-
-      if (bitmask & WRAP_PARTIAL_RIGHT_FLAG) {
-        var partialsRight = partials,
-            holdersRight = holders;
-
-        partials = holders = undefined;
-      }
-      var data = isBindKey ? undefined : getData(func);
-
-      var newData = [
-        func, bitmask, thisArg, partials, holders, partialsRight, holdersRight,
-        argPos, ary, arity
-      ];
-
-      if (data) {
-        mergeData(newData, data);
-      }
-      func = newData[0];
-      bitmask = newData[1];
-      thisArg = newData[2];
-      partials = newData[3];
-      holders = newData[4];
-      arity = newData[9] = newData[9] === undefined
-        ? (isBindKey ? 0 : func.length)
-        : nativeMax(newData[9] - length, 0);
-
-      if (!arity && bitmask & (WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG)) {
-        bitmask &= ~(WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG);
-      }
-      if (!bitmask || bitmask == WRAP_BIND_FLAG) {
-        var result = createBind(func, bitmask, thisArg);
-      } else if (bitmask == WRAP_CURRY_FLAG || bitmask == WRAP_CURRY_RIGHT_FLAG) {
-        result = createCurry(func, bitmask, arity);
-      } else if ((bitmask == WRAP_PARTIAL_FLAG || bitmask == (WRAP_BIND_FLAG | WRAP_PARTIAL_FLAG)) && !holders.length) {
-        result = createPartial(func, bitmask, thisArg, partials);
-      } else {
-        result = createHybrid.apply(undefined, newData);
-      }
-      var setter = data ? baseSetData : setData;
-      return setWrapToString(setter(result, newData), func, bitmask);
-    }
-
-    /**
-     * Used by `_.defaults` to customize its `_.assignIn` use to assign properties
-     * of source objects to the destination object for all destination properties
-     * that resolve to `undefined`.
-     *
-     * @private
-     * @param {*} objValue The destination value.
-     * @param {*} srcValue The source value.
-     * @param {string} key The key of the property to assign.
-     * @param {Object} object The parent object of `objValue`.
-     * @returns {*} Returns the value to assign.
-     */
-    function customDefaultsAssignIn(objValue, srcValue, key, object) {
-      if (objValue === undefined ||
-          (eq(objValue, objectProto[key]) && !hasOwnProperty.call(object, key))) {
-        return srcValue;
-      }
-      return objValue;
-    }
-
-    /**
-     * Used by `_.defaultsDeep` to customize its `_.merge` use to merge source
-     * objects into destination objects that are passed thru.
-     *
-     * @private
-     * @param {*} objValue The destination value.
-     * @param {*} srcValue The source value.
-     * @param {string} key The key of the property to merge.
-     * @param {Object} object The parent object of `objValue`.
-     * @param {Object} source The parent object of `srcValue`.
-     * @param {Object} [stack] Tracks traversed source values and their merged
-     *  counterparts.
-     * @returns {*} Returns the value to assign.
-     */
-    function customDefaultsMerge(objValue, srcValue, key, object, source, stack) {
-      if (isObject(objValue) && isObject(srcValue)) {
-        // Recursively merge objects and arrays (susceptible to call stack limits).
-        stack.set(srcValue, objValue);
-        baseMerge(objValue, srcValue, undefined, customDefaultsMerge, stack);
-        stack['delete'](srcValue);
-      }
-      return objValue;
-    }
-
-    /**
-     * Used by `_.omit` to customize its `_.cloneDeep` use to only clone plain
-     * objects.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @param {string} key The key of the property to inspect.
-     * @returns {*} Returns the uncloned value or `undefined` to defer cloning to `_.cloneDeep`.
-     */
-    function customOmitClone(value) {
-      return isPlainObject(value) ? undefined : value;
-    }
-
-    /**
-     * A specialized version of `baseIsEqualDeep` for arrays with support for
-     * partial deep comparisons.
-     *
-     * @private
-     * @param {Array} array The array to compare.
-     * @param {Array} other The other array to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} stack Tracks traversed `array` and `other` objects.
-     * @returns {boolean} Returns `true` if the arrays are equivalent, else `false`.
-     */
-    function equalArrays(array, other, bitmask, customizer, equalFunc, stack) {
-      var isPartial = bitmask & COMPARE_PARTIAL_FLAG,
-          arrLength = array.length,
-          othLength = other.length;
-
-      if (arrLength != othLength && !(isPartial && othLength > arrLength)) {
-        return false;
-      }
-      // Assume cyclic values are equal.
-      var stacked = stack.get(array);
-      if (stacked && stack.get(other)) {
-        return stacked == other;
-      }
-      var index = -1,
-          result = true,
-          seen = (bitmask & COMPARE_UNORDERED_FLAG) ? new SetCache : undefined;
-
-      stack.set(array, other);
-      stack.set(other, array);
-
-      // Ignore non-index properties.
-      while (++index < arrLength) {
-        var arrValue = array[index],
-            othValue = other[index];
-
-        if (customizer) {
-          var compared = isPartial
-            ? customizer(othValue, arrValue, index, other, array, stack)
-            : customizer(arrValue, othValue, index, array, other, stack);
-        }
-        if (compared !== undefined) {
-          if (compared) {
-            continue;
-          }
-          result = false;
-          break;
-        }
-        // Recursively compare arrays (susceptible to call stack limits).
-        if (seen) {
-          if (!arraySome(other, function(othValue, othIndex) {
-                if (!cacheHas(seen, othIndex) &&
-                    (arrValue === othValue || equalFunc(arrValue, othValue, bitmask, customizer, stack))) {
-                  return seen.push(othIndex);
-                }
-              })) {
-            result = false;
-            break;
-          }
-        } else if (!(
-              arrValue === othValue ||
-                equalFunc(arrValue, othValue, bitmask, customizer, stack)
-            )) {
-          result = false;
-          break;
-        }
-      }
-      stack['delete'](array);
-      stack['delete'](other);
-      return result;
-    }
-
-    /**
-     * A specialized version of `baseIsEqualDeep` for comparing objects of
-     * the same `toStringTag`.
-     *
-     * **Note:** This function only supports comparing values with tags of
-     * `Boolean`, `Date`, `Error`, `Number`, `RegExp`, or `String`.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {string} tag The `toStringTag` of the objects to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} stack Tracks traversed `object` and `other` objects.
-     * @returns {boolean} Returns `true` if the objects are equivalent, else `false`.
-     */
-    function equalByTag(object, other, tag, bitmask, customizer, equalFunc, stack) {
-      switch (tag) {
-        case dataViewTag:
-          if ((object.byteLength != other.byteLength) ||
-              (object.byteOffset != other.byteOffset)) {
-            return false;
-          }
-          object = object.buffer;
-          other = other.buffer;
-
-        case arrayBufferTag:
-          if ((object.byteLength != other.byteLength) ||
-              !equalFunc(new Uint8Array(object), new Uint8Array(other))) {
-            return false;
-          }
-          return true;
-
-        case boolTag:
-        case dateTag:
-        case numberTag:
-          // Coerce booleans to `1` or `0` and dates to milliseconds.
-          // Invalid dates are coerced to `NaN`.
-          return eq(+object, +other);
-
-        case errorTag:
-          return object.name == other.name && object.message == other.message;
-
-        case regexpTag:
-        case stringTag:
-          // Coerce regexes to strings and treat strings, primitives and objects,
-          // as equal. See http://www.ecma-international.org/ecma-262/7.0/#sec-regexp.prototype.tostring
-          // for more details.
-          return object == (other + '');
-
-        case mapTag:
-          var convert = mapToArray;
-
-        case setTag:
-          var isPartial = bitmask & COMPARE_PARTIAL_FLAG;
-          convert || (convert = setToArray);
-
-          if (object.size != other.size && !isPartial) {
-            return false;
-          }
-          // Assume cyclic values are equal.
-          var stacked = stack.get(object);
-          if (stacked) {
-            return stacked == other;
-          }
-          bitmask |= COMPARE_UNORDERED_FLAG;
-
-          // Recursively compare objects (susceptible to call stack limits).
-          stack.set(object, other);
-          var result = equalArrays(convert(object), convert(other), bitmask, customizer, equalFunc, stack);
-          stack['delete'](object);
-          return result;
-
-        case symbolTag:
-          if (symbolValueOf) {
-            return symbolValueOf.call(object) == symbolValueOf.call(other);
-          }
-      }
-      return false;
-    }
-
-    /**
-     * A specialized version of `baseIsEqualDeep` for objects with support for
-     * partial deep comparisons.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} stack Tracks traversed `object` and `other` objects.
-     * @returns {boolean} Returns `true` if the objects are equivalent, else `false`.
-     */
-    function equalObjects(object, other, bitmask, customizer, equalFunc, stack) {
-      var isPartial = bitmask & COMPARE_PARTIAL_FLAG,
-          objProps = getAllKeys(object),
-          objLength = objProps.length,
-          othProps = getAllKeys(other),
-          othLength = othProps.length;
-
-      if (objLength != othLength && !isPartial) {
-        return false;
-      }
-      var index = objLength;
-      while (index--) {
-        var key = objProps[index];
-        if (!(isPartial ? key in other : hasOwnProperty.call(other, key))) {
-          return false;
-        }
-      }
-      // Assume cyclic values are equal.
-      var stacked = stack.get(object);
-      if (stacked && stack.get(other)) {
-        return stacked == other;
-      }
-      var result = true;
-      stack.set(object, other);
-      stack.set(other, object);
-
-      var skipCtor = isPartial;
-      while (++index < objLength) {
-        key = objProps[index];
-        var objValue = object[key],
-            othValue = other[key];
-
-        if (customizer) {
-          var compared = isPartial
-            ? customizer(othValue, objValue, key, other, object, stack)
-            : customizer(objValue, othValue, key, object, other, stack);
-        }
-        // Recursively compare objects (susceptible to call stack limits).
-        if (!(compared === undefined
-              ? (objValue === othValue || equalFunc(objValue, othValue, bitmask, customizer, stack))
-              : compared
-            )) {
-          result = false;
-          break;
-        }
-        skipCtor || (skipCtor = key == 'constructor');
-      }
-      if (result && !skipCtor) {
-        var objCtor = object.constructor,
-            othCtor = other.constructor;
-
-        // Non `Object` object instances with different constructors are not equal.
-        if (objCtor != othCtor &&
-            ('constructor' in object && 'constructor' in other) &&
-            !(typeof objCtor == 'function' && objCtor instanceof objCtor &&
-              typeof othCtor == 'function' && othCtor instanceof othCtor)) {
-          result = false;
-        }
-      }
-      stack['delete'](object);
-      stack['delete'](other);
-      return result;
-    }
-
-    /**
-     * A specialized version of `baseRest` which flattens the rest array.
-     *
-     * @private
-     * @param {Function} func The function to apply a rest parameter to.
-     * @returns {Function} Returns the new function.
-     */
-    function flatRest(func) {
-      return setToString(overRest(func, undefined, flatten), func + '');
-    }
-
-    /**
-     * Creates an array of own enumerable property names and symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names and symbols.
-     */
-    function getAllKeys(object) {
-      return baseGetAllKeys(object, keys, getSymbols);
-    }
-
-    /**
-     * Creates an array of own and inherited enumerable property names and
-     * symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names and symbols.
-     */
-    function getAllKeysIn(object) {
-      return baseGetAllKeys(object, keysIn, getSymbolsIn);
-    }
-
-    /**
-     * Gets metadata for `func`.
-     *
-     * @private
-     * @param {Function} func The function to query.
-     * @returns {*} Returns the metadata for `func`.
-     */
-    var getData = !metaMap ? noop : function(func) {
-      return metaMap.get(func);
-    };
-
-    /**
-     * Gets the name of `func`.
-     *
-     * @private
-     * @param {Function} func The function to query.
-     * @returns {string} Returns the function name.
-     */
-    function getFuncName(func) {
-      var result = (func.name + ''),
-          array = realNames[result],
-          length = hasOwnProperty.call(realNames, result) ? array.length : 0;
-
-      while (length--) {
-        var data = array[length],
-            otherFunc = data.func;
-        if (otherFunc == null || otherFunc == func) {
-          return data.name;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Gets the argument placeholder value for `func`.
-     *
-     * @private
-     * @param {Function} func The function to inspect.
-     * @returns {*} Returns the placeholder value.
-     */
-    function getHolder(func) {
-      var object = hasOwnProperty.call(lodash, 'placeholder') ? lodash : func;
-      return object.placeholder;
-    }
-
-    /**
-     * Gets the appropriate "iteratee" function. If `_.iteratee` is customized,
-     * this function returns the custom method, otherwise it returns `baseIteratee`.
-     * If arguments are provided, the chosen function is invoked with them and
-     * its result is returned.
-     *
-     * @private
-     * @param {*} [value] The value to convert to an iteratee.
-     * @param {number} [arity] The arity of the created iteratee.
-     * @returns {Function} Returns the chosen function or its result.
-     */
-    function getIteratee() {
-      var result = lodash.iteratee || iteratee;
-      result = result === iteratee ? baseIteratee : result;
-      return arguments.length ? result(arguments[0], arguments[1]) : result;
-    }
-
-    /**
-     * Gets the data for `map`.
-     *
-     * @private
-     * @param {Object} map The map to query.
-     * @param {string} key The reference key.
-     * @returns {*} Returns the map data.
-     */
-    function getMapData(map, key) {
-      var data = map.__data__;
-      return isKeyable(key)
-        ? data[typeof key == 'string' ? 'string' : 'hash']
-        : data.map;
-    }
-
-    /**
-     * Gets the property names, values, and compare flags of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the match data of `object`.
-     */
-    function getMatchData(object) {
-      var result = keys(object),
-          length = result.length;
-
-      while (length--) {
-        var key = result[length],
-            value = object[key];
-
-        result[length] = [key, value, isStrictComparable(value)];
-      }
-      return result;
-    }
-
-    /**
-     * Gets the native function at `key` of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {string} key The key of the method to get.
-     * @returns {*} Returns the function if it's native, else `undefined`.
-     */
-    function getNative(object, key) {
-      var value = getValue(object, key);
-      return baseIsNative(value) ? value : undefined;
-    }
-
-    /**
-     * A specialized version of `baseGetTag` which ignores `Symbol.toStringTag` values.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @returns {string} Returns the raw `toStringTag`.
-     */
-    function getRawTag(value) {
-      var isOwn = hasOwnProperty.call(value, symToStringTag),
-          tag = value[symToStringTag];
-
-      try {
-        value[symToStringTag] = undefined;
-        var unmasked = true;
-      } catch (e) {}
-
-      var result = nativeObjectToString.call(value);
-      if (unmasked) {
-        if (isOwn) {
-          value[symToStringTag] = tag;
-        } else {
-          delete value[symToStringTag];
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Creates an array of the own enumerable symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of symbols.
-     */
-    var getSymbols = !nativeGetSymbols ? stubArray : function(object) {
-      if (object == null) {
-        return [];
-      }
-      object = Object(object);
-      return arrayFilter(nativeGetSymbols(object), function(symbol) {
-        return propertyIsEnumerable.call(object, symbol);
-      });
-    };
-
-    /**
-     * Creates an array of the own and inherited enumerable symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of symbols.
-     */
-    var getSymbolsIn = !nativeGetSymbols ? stubArray : function(object) {
-      var result = [];
-      while (object) {
-        arrayPush(result, getSymbols(object));
-        object = getPrototype(object);
-      }
-      return result;
-    };
-
-    /**
-     * Gets the `toStringTag` of `value`.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @returns {string} Returns the `toStringTag`.
-     */
-    var getTag = baseGetTag;
-
-    // Fallback for data views, maps, sets, and weak maps in IE 11 and promises in Node.js < 6.
-    if ((DataView && getTag(new DataView(new ArrayBuffer(1))) != dataViewTag) ||
-        (Map && getTag(new Map) != mapTag) ||
-        (Promise && getTag(Promise.resolve()) != promiseTag) ||
-        (Set && getTag(new Set) != setTag) ||
-        (WeakMap && getTag(new WeakMap) != weakMapTag)) {
-      getTag = function(value) {
-        var result = baseGetTag(value),
-            Ctor = result == objectTag ? value.constructor : undefined,
-            ctorString = Ctor ? toSource(Ctor) : '';
-
-        if (ctorString) {
-          switch (ctorString) {
-            case dataViewCtorString: return dataViewTag;
-            case mapCtorString: return mapTag;
-            case promiseCtorString: return promiseTag;
-            case setCtorString: return setTag;
-            case weakMapCtorString: return weakMapTag;
-          }
-        }
-        return result;
-      };
-    }
-
-    /**
-     * Gets the view, applying any `transforms` to the `start` and `end` positions.
-     *
-     * @private
-     * @param {number} start The start of the view.
-     * @param {number} end The end of the view.
-     * @param {Array} transforms The transformations to apply to the view.
-     * @returns {Object} Returns an object containing the `start` and `end`
-     *  positions of the view.
-     */
-    function getView(start, end, transforms) {
-      var index = -1,
-          length = transforms.length;
-
-      while (++index < length) {
-        var data = transforms[index],
-            size = data.size;
-
-        switch (data.type) {
-          case 'drop':      start += size; break;
-          case 'dropRight': end -= size; break;
-          case 'take':      end = nativeMin(end, start + size); break;
-          case 'takeRight': start = nativeMax(start, end - size); break;
-        }
-      }
-      return { 'start': start, 'end': end };
-    }
-
-    /**
-     * Extracts wrapper details from the `source` body comment.
-     *
-     * @private
-     * @param {string} source The source to inspect.
-     * @returns {Array} Returns the wrapper details.
-     */
-    function getWrapDetails(source) {
-      var match = source.match(reWrapDetails);
-      return match ? match[1].split(reSplitDetails) : [];
-    }
-
-    /**
-     * Checks if `path` exists on `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path to check.
-     * @param {Function} hasFunc The function to check properties.
-     * @returns {boolean} Returns `true` if `path` exists, else `false`.
-     */
-    function hasPath(object, path, hasFunc) {
-      path = castPath(path, object);
-
-      var index = -1,
-          length = path.length,
-          result = false;
-
-      while (++index < length) {
-        var key = toKey(path[index]);
-        if (!(result = object != null && hasFunc(object, key))) {
-          break;
-        }
-        object = object[key];
-      }
-      if (result || ++index != length) {
-        return result;
-      }
-      length = object == null ? 0 : object.length;
-      return !!length && isLength(length) && isIndex(key, length) &&
-        (isArray(object) || isArguments(object));
-    }
-
-    /**
-     * Initializes an array clone.
-     *
-     * @private
-     * @param {Array} array The array to clone.
-     * @returns {Array} Returns the initialized clone.
-     */
-    function initCloneArray(array) {
-      var length = array.length,
-          result = new array.constructor(length);
-
-      // Add properties assigned by `RegExp#exec`.
-      if (length && typeof array[0] == 'string' && hasOwnProperty.call(array, 'index')) {
-        result.index = array.index;
-        result.input = array.input;
-      }
-      return result;
-    }
-
-    /**
-     * Initializes an object clone.
-     *
-     * @private
-     * @param {Object} object The object to clone.
-     * @returns {Object} Returns the initialized clone.
-     */
-    function initCloneObject(object) {
-      return (typeof object.constructor == 'function' && !isPrototype(object))
-        ? baseCreate(getPrototype(object))
-        : {};
-    }
-
-    /**
-     * Initializes an object clone based on its `toStringTag`.
-     *
-     * **Note:** This function only supports cloning values with tags of
-     * `Boolean`, `Date`, `Error`, `Map`, `Number`, `RegExp`, `Set`, or `String`.
-     *
-     * @private
-     * @param {Object} object The object to clone.
-     * @param {string} tag The `toStringTag` of the object to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Object} Returns the initialized clone.
-     */
-    function initCloneByTag(object, tag, isDeep) {
-      var Ctor = object.constructor;
-      switch (tag) {
-        case arrayBufferTag:
-          return cloneArrayBuffer(object);
-
-        case boolTag:
-        case dateTag:
-          return new Ctor(+object);
-
-        case dataViewTag:
-          return cloneDataView(object, isDeep);
-
-        case float32Tag: case float64Tag:
-        case int8Tag: case int16Tag: case int32Tag:
-        case uint8Tag: case uint8ClampedTag: case uint16Tag: case uint32Tag:
-          return cloneTypedArray(object, isDeep);
-
-        case mapTag:
-          return new Ctor;
-
-        case numberTag:
-        case stringTag:
-          return new Ctor(object);
-
-        case regexpTag:
-          return cloneRegExp(object);
-
-        case setTag:
-          return new Ctor;
-
-        case symbolTag:
-          return cloneSymbol(object);
-      }
-    }
-
-    /**
-     * Inserts wrapper `details` in a comment at the top of the `source` body.
-     *
-     * @private
-     * @param {string} source The source to modify.
-     * @returns {Array} details The details to insert.
-     * @returns {string} Returns the modified source.
-     */
-    function insertWrapDetails(source, details) {
-      var length = details.length;
-      if (!length) {
-        return source;
-      }
-      var lastIndex = length - 1;
-      details[lastIndex] = (length > 1 ? '& ' : '') + details[lastIndex];
-      details = details.join(length > 2 ? ', ' : ' ');
-      return source.replace(reWrapComment, '{\n/* [wrapped with ' + details + '] */\n');
-    }
-
-    /**
-     * Checks if `value` is a flattenable `arguments` object or array.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is flattenable, else `false`.
-     */
-    function isFlattenable(value) {
-      return isArray(value) || isArguments(value) ||
-        !!(spreadableSymbol && value && value[spreadableSymbol]);
-    }
-
-    /**
-     * Checks if `value` is a valid array-like index.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @param {number} [length=MAX_SAFE_INTEGER] The upper bounds of a valid index.
-     * @returns {boolean} Returns `true` if `value` is a valid index, else `false`.
-     */
-    function isIndex(value, length) {
-      var type = typeof value;
-      length = length == null ? MAX_SAFE_INTEGER : length;
-
-      return !!length &&
-        (type == 'number' ||
-          (type != 'symbol' && reIsUint.test(value))) &&
-            (value > -1 && value % 1 == 0 && value < length);
-    }
-
-    /**
-     * Checks if the given arguments are from an iteratee call.
-     *
-     * @private
-     * @param {*} value The potential iteratee value argument.
-     * @param {*} index The potential iteratee index or key argument.
-     * @param {*} object The potential iteratee object argument.
-     * @returns {boolean} Returns `true` if the arguments are from an iteratee call,
-     *  else `false`.
-     */
-    function isIterateeCall(value, index, object) {
-      if (!isObject(object)) {
-        return false;
-      }
-      var type = typeof index;
-      if (type == 'number'
-            ? (isArrayLike(object) && isIndex(index, object.length))
-            : (type == 'string' && index in object)
-          ) {
-        return eq(object[index], value);
-      }
-      return false;
-    }
-
-    /**
-     * Checks if `value` is a property name and not a property path.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @param {Object} [object] The object to query keys on.
-     * @returns {boolean} Returns `true` if `value` is a property name, else `false`.
-     */
-    function isKey(value, object) {
-      if (isArray(value)) {
-        return false;
-      }
-      var type = typeof value;
-      if (type == 'number' || type == 'symbol' || type == 'boolean' ||
-          value == null || isSymbol(value)) {
-        return true;
-      }
-      return reIsPlainProp.test(value) || !reIsDeepProp.test(value) ||
-        (object != null && value in Object(object));
-    }
-
-    /**
-     * Checks if `value` is suitable for use as unique object key.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is suitable, else `false`.
-     */
-    function isKeyable(value) {
-      var type = typeof value;
-      return (type == 'string' || type == 'number' || type == 'symbol' || type == 'boolean')
-        ? (value !== '__proto__')
-        : (value === null);
-    }
-
-    /**
-     * Checks if `func` has a lazy counterpart.
-     *
-     * @private
-     * @param {Function} func The function to check.
-     * @returns {boolean} Returns `true` if `func` has a lazy counterpart,
-     *  else `false`.
-     */
-    function isLaziable(func) {
-      var funcName = getFuncName(func),
-          other = lodash[funcName];
-
-      if (typeof other != 'function' || !(funcName in LazyWrapper.prototype)) {
-        return false;
-      }
-      if (func === other) {
-        return true;
-      }
-      var data = getData(other);
-      return !!data && func === data[0];
-    }
-
-    /**
-     * Checks if `func` has its source masked.
-     *
-     * @private
-     * @param {Function} func The function to check.
-     * @returns {boolean} Returns `true` if `func` is masked, else `false`.
-     */
-    function isMasked(func) {
-      return !!maskSrcKey && (maskSrcKey in func);
-    }
-
-    /**
-     * Checks if `func` is capable of being masked.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `func` is maskable, else `false`.
-     */
-    var isMaskable = coreJsData ? isFunction : stubFalse;
-
-    /**
-     * Checks if `value` is likely a prototype object.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a prototype, else `false`.
-     */
-    function isPrototype(value) {
-      var Ctor = value && value.constructor,
-          proto = (typeof Ctor == 'function' && Ctor.prototype) || objectProto;
-
-      return value === proto;
-    }
-
-    /**
-     * Checks if `value` is suitable for strict equality comparisons, i.e. `===`.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` if suitable for strict
-     *  equality comparisons, else `false`.
-     */
-    function isStrictComparable(value) {
-      return value === value && !isObject(value);
-    }
-
-    /**
-     * A specialized version of `matchesProperty` for source values suitable
-     * for strict equality comparisons, i.e. `===`.
-     *
-     * @private
-     * @param {string} key The key of the property to get.
-     * @param {*} srcValue The value to match.
-     * @returns {Function} Returns the new spec function.
-     */
-    function matchesStrictComparable(key, srcValue) {
-      return function(object) {
-        if (object == null) {
-          return false;
-        }
-        return object[key] === srcValue &&
-          (srcValue !== undefined || (key in Object(object)));
-      };
-    }
-
-    /**
-     * A specialized version of `_.memoize` which clears the memoized function's
-     * cache when it exceeds `MAX_MEMOIZE_SIZE`.
-     *
-     * @private
-     * @param {Function} func The function to have its output memoized.
-     * @returns {Function} Returns the new memoized function.
-     */
-    function memoizeCapped(func) {
-      var result = memoize(func, function(key) {
-        if (cache.size === MAX_MEMOIZE_SIZE) {
-          cache.clear();
-        }
-        return key;
-      });
-
-      var cache = result.cache;
-      return result;
-    }
-
-    /**
-     * Merges the function metadata of `source` into `data`.
-     *
-     * Merging metadata reduces the number of wrappers used to invoke a function.
-     * This is possible because methods like `_.bind`, `_.curry`, and `_.partial`
-     * may be applied regardless of execution order. Methods like `_.ary` and
-     * `_.rearg` modify function arguments, making the order in which they are
-     * executed important, preventing the merging of metadata. However, we make
-     * an exception for a safe combined case where curried functions have `_.ary`
-     * and or `_.rearg` applied.
-     *
-     * @private
-     * @param {Array} data The destination metadata.
-     * @param {Array} source The source metadata.
-     * @returns {Array} Returns `data`.
-     */
-    function mergeData(data, source) {
-      var bitmask = data[1],
-          srcBitmask = source[1],
-          newBitmask = bitmask | srcBitmask,
-          isCommon = newBitmask < (WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG | WRAP_ARY_FLAG);
-
-      var isCombo =
-        ((srcBitmask == WRAP_ARY_FLAG) && (bitmask == WRAP_CURRY_FLAG)) ||
-        ((srcBitmask == WRAP_ARY_FLAG) && (bitmask == WRAP_REARG_FLAG) && (data[7].length <= source[8])) ||
-        ((srcBitmask == (WRAP_ARY_FLAG | WRAP_REARG_FLAG)) && (source[7].length <= source[8]) && (bitmask == WRAP_CURRY_FLAG));
-
-      // Exit early if metadata can't be merged.
-      if (!(isCommon || isCombo)) {
-        return data;
-      }
-      // Use source `thisArg` if available.
-      if (srcBitmask & WRAP_BIND_FLAG) {
-        data[2] = source[2];
-        // Set when currying a bound function.
-        newBitmask |= bitmask & WRAP_BIND_FLAG ? 0 : WRAP_CURRY_BOUND_FLAG;
-      }
-      // Compose partial arguments.
-      var value = source[3];
-      if (value) {
-        var partials = data[3];
-        data[3] = partials ? composeArgs(partials, value, source[4]) : value;
-        data[4] = partials ? replaceHolders(data[3], PLACEHOLDER) : source[4];
-      }
-      // Compose partial right arguments.
-      value = source[5];
-      if (value) {
-        partials = data[5];
-        data[5] = partials ? composeArgsRight(partials, value, source[6]) : value;
-        data[6] = partials ? replaceHolders(data[5], PLACEHOLDER) : source[6];
-      }
-      // Use source `argPos` if available.
-      value = source[7];
-      if (value) {
-        data[7] = value;
-      }
-      // Use source `ary` if it's smaller.
-      if (srcBitmask & WRAP_ARY_FLAG) {
-        data[8] = data[8] == null ? source[8] : nativeMin(data[8], source[8]);
-      }
-      // Use source `arity` if one is not provided.
-      if (data[9] == null) {
-        data[9] = source[9];
-      }
-      // Use source `func` and merge bitmasks.
-      data[0] = source[0];
-      data[1] = newBitmask;
-
-      return data;
-    }
-
-    /**
-     * This function is like
-     * [`Object.keys`](http://ecma-international.org/ecma-262/7.0/#sec-object.keys)
-     * except that it includes inherited enumerable properties.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     */
-    function nativeKeysIn(object) {
-      var result = [];
-      if (object != null) {
-        for (var key in Object(object)) {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Converts `value` to a string using `Object.prototype.toString`.
-     *
-     * @private
-     * @param {*} value The value to convert.
-     * @returns {string} Returns the converted string.
-     */
-    function objectToString(value) {
-      return nativeObjectToString.call(value);
-    }
-
-    /**
-     * A specialized version of `baseRest` which transforms the rest array.
-     *
-     * @private
-     * @param {Function} func The function to apply a rest parameter to.
-     * @param {number} [start=func.length-1] The start position of the rest parameter.
-     * @param {Function} transform The rest array transform.
-     * @returns {Function} Returns the new function.
-     */
-    function overRest(func, start, transform) {
-      start = nativeMax(start === undefined ? (func.length - 1) : start, 0);
-      return function() {
-        var args = arguments,
-            index = -1,
-            length = nativeMax(args.length - start, 0),
-            array = Array(length);
-
-        while (++index < length) {
-          array[index] = args[start + index];
-        }
-        index = -1;
-        var otherArgs = Array(start + 1);
-        while (++index < start) {
-          otherArgs[index] = args[index];
-        }
-        otherArgs[start] = transform(array);
-        return apply(func, this, otherArgs);
-      };
-    }
-
-    /**
-     * Gets the parent value at `path` of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array} path The path to get the parent value of.
-     * @returns {*} Returns the parent value.
-     */
-    function parent(object, path) {
-      return path.length < 2 ? object : baseGet(object, baseSlice(path, 0, -1));
-    }
-
-    /**
-     * Reorder `array` according to the specified indexes where the element at
-     * the first index is assigned as the first element, the element at
-     * the second index is assigned as the second element, and so on.
-     *
-     * @private
-     * @param {Array} array The array to reorder.
-     * @param {Array} indexes The arranged array indexes.
-     * @returns {Array} Returns `array`.
-     */
-    function reorder(array, indexes) {
-      var arrLength = array.length,
-          length = nativeMin(indexes.length, arrLength),
-          oldArray = copyArray(array);
-
-      while (length--) {
-        var index = indexes[length];
-        array[length] = isIndex(index, arrLength) ? oldArray[index] : undefined;
-      }
-      return array;
-    }
-
-    /**
-     * Gets the value at `key`, unless `key` is "__proto__" or "constructor".
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {string} key The key of the property to get.
-     * @returns {*} Returns the property value.
-     */
-    function safeGet(object, key) {
-      if (key === 'constructor' && typeof object[key] === 'function') {
-        return;
-      }
-
-      if (key == '__proto__') {
-        return;
-      }
-
-      return object[key];
-    }
-
-    /**
-     * Sets metadata for `func`.
-     *
-     * **Note:** If this function becomes hot, i.e. is invoked a lot in a short
-     * period of time, it will trip its breaker and transition to an identity
-     * function to avoid garbage collection pauses in V8. See
-     * [V8 issue 2070](https://bugs.chromium.org/p/v8/issues/detail?id=2070)
-     * for more details.
-     *
-     * @private
-     * @param {Function} func The function to associate metadata with.
-     * @param {*} data The metadata.
-     * @returns {Function} Returns `func`.
-     */
-    var setData = shortOut(baseSetData);
-
-    /**
-     * A simple wrapper around the global [`setTimeout`](https://mdn.io/setTimeout).
-     *
-     * @private
-     * @param {Function} func The function to delay.
-     * @param {number} wait The number of milliseconds to delay invocation.
-     * @returns {number|Object} Returns the timer id or timeout object.
-     */
-    var setTimeout = ctxSetTimeout || function(func, wait) {
-      return root.setTimeout(func, wait);
-    };
-
-    /**
-     * Sets the `toString` method of `func` to return `string`.
-     *
-     * @private
-     * @param {Function} func The function to modify.
-     * @param {Function} string The `toString` result.
-     * @returns {Function} Returns `func`.
-     */
-    var setToString = shortOut(baseSetToString);
-
-    /**
-     * Sets the `toString` method of `wrapper` to mimic the source of `reference`
-     * with wrapper details in a comment at the top of the source body.
-     *
-     * @private
-     * @param {Function} wrapper The function to modify.
-     * @param {Function} reference The reference function.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @returns {Function} Returns `wrapper`.
-     */
-    function setWrapToString(wrapper, reference, bitmask) {
-      var source = (reference + '');
-      return setToString(wrapper, insertWrapDetails(source, updateWrapDetails(getWrapDetails(source), bitmask)));
-    }
-
-    /**
-     * Creates a function that'll short out and invoke `identity` instead
-     * of `func` when it's called `HOT_COUNT` or more times in `HOT_SPAN`
-     * milliseconds.
-     *
-     * @private
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new shortable function.
-     */
-    function shortOut(func) {
-      var count = 0,
-          lastCalled = 0;
-
-      return function() {
-        var stamp = nativeNow(),
-            remaining = HOT_SPAN - (stamp - lastCalled);
-
-        lastCalled = stamp;
-        if (remaining > 0) {
-          if (++count >= HOT_COUNT) {
-            return arguments[0];
-          }
-        } else {
-          count = 0;
-        }
-        return func.apply(undefined, arguments);
-      };
-    }
-
-    /**
-     * A specialized version of `_.shuffle` which mutates and sets the size of `array`.
-     *
-     * @private
-     * @param {Array} array The array to shuffle.
-     * @param {number} [size=array.length] The size of `array`.
-     * @returns {Array} Returns `array`.
-     */
-    function shuffleSelf(array, size) {
-      var index = -1,
-          length = array.length,
-          lastIndex = length - 1;
-
-      size = size === undefined ? length : size;
-      while (++index < size) {
-        var rand = baseRandom(index, lastIndex),
-            value = array[rand];
-
-        array[rand] = array[index];
-        array[index] = value;
-      }
-      array.length = size;
-      return array;
-    }
-
-    /**
-     * Converts `string` to a property path array.
-     *
-     * @private
-     * @param {string} string The string to convert.
-     * @returns {Array} Returns the property path array.
-     */
-    var stringToPath = memoizeCapped(function(string) {
-      var result = [];
-      if (string.charCodeAt(0) === 46 /* . */) {
-        result.push('');
-      }
-      string.replace(rePropName, function(match, number, quote, subString) {
-        result.push(quote ? subString.replace(reEscapeChar, '$1') : (number || match));
-      });
-      return result;
-    });
-
-    /**
-     * Converts `value` to a string key if it's not a string or symbol.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @returns {string|symbol} Returns the key.
-     */
-    function toKey(value) {
-      if (typeof value == 'string' || isSymbol(value)) {
-        return value;
-      }
-      var result = (value + '');
-      return (result == '0' && (1 / value) == -INFINITY) ? '-0' : result;
-    }
-
-    /**
-     * Converts `func` to its source code.
-     *
-     * @private
-     * @param {Function} func The function to convert.
-     * @returns {string} Returns the source code.
-     */
-    function toSource(func) {
-      if (func != null) {
-        try {
-          return funcToString.call(func);
-        } catch (e) {}
-        try {
-          return (func + '');
-        } catch (e) {}
-      }
-      return '';
-    }
-
-    /**
-     * Updates wrapper `details` based on `bitmask` flags.
-     *
-     * @private
-     * @returns {Array} details The details to modify.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @returns {Array} Returns `details`.
-     */
-    function updateWrapDetails(details, bitmask) {
-      arrayEach(wrapFlags, function(pair) {
-        var value = '_.' + pair[0];
-        if ((bitmask & pair[1]) && !arrayIncludes(details, value)) {
-          details.push(value);
-        }
-      });
-      return details.sort();
-    }
-
-    /**
-     * Creates a clone of `wrapper`.
-     *
-     * @private
-     * @param {Object} wrapper The wrapper to clone.
-     * @returns {Object} Returns the cloned wrapper.
-     */
-    function wrapperClone(wrapper) {
-      if (wrapper instanceof LazyWrapper) {
-        return wrapper.clone();
-      }
-      var result = new LodashWrapper(wrapper.__wrapped__, wrapper.__chain__);
-      result.__actions__ = copyArray(wrapper.__actions__);
-      result.__index__  = wrapper.__index__;
-      result.__values__ = wrapper.__values__;
-      return result;
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an array of elements split into groups the length of `size`.
-     * If `array` can't be split evenly, the final chunk will be the remaining
-     * elements.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to process.
-     * @param {number} [size=1] The length of each chunk
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the new array of chunks.
-     * @example
-     *
-     * _.chunk(['a', 'b', 'c', 'd'], 2);
-     * // => [['a', 'b'], ['c', 'd']]
-     *
-     * _.chunk(['a', 'b', 'c', 'd'], 3);
-     * // => [['a', 'b', 'c'], ['d']]
-     */
-    function chunk(array, size, guard) {
-      if ((guard ? isIterateeCall(array, size, guard) : size === undefined)) {
-        size = 1;
-      } else {
-        size = nativeMax(toInteger(size), 0);
-      }
-      var length = array == null ? 0 : array.length;
-      if (!length || size < 1) {
-        return [];
-      }
-      var index = 0,
-          resIndex = 0,
-          result = Array(nativeCeil(length / size));
-
-      while (index < length) {
-        result[resIndex++] = baseSlice(array, index, (index += size));
-      }
-      return result;
-    }
-
-    /**
-     * Creates an array with all falsey values removed. The values `false`, `null`,
-     * `0`, `""`, `undefined`, and `NaN` are falsey.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to compact.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * _.compact([0, 1, false, 2, '', 3]);
-     * // => [1, 2, 3]
-     */
-    function compact(array) {
-      var index = -1,
-          length = array == null ? 0 : array.length,
-          resIndex = 0,
-          result = [];
-
-      while (++index < length) {
-        var value = array[index];
-        if (value) {
-          result[resIndex++] = value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Creates a new array concatenating `array` with any additional arrays
-     * and/or values.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to concatenate.
-     * @param {...*} [values] The values to concatenate.
-     * @returns {Array} Returns the new concatenated array.
-     * @example
-     *
-     * var array = [1];
-     * var other = _.concat(array, 2, [3], [[4]]);
-     *
-     * console.log(other);
-     * // => [1, 2, 3, [4]]
-     *
-     * console.log(array);
-     * // => [1]
-     */
-    function concat() {
-      var length = arguments.length;
-      if (!length) {
-        return [];
-      }
-      var args = Array(length - 1),
-          array = arguments[0],
-          index = length;
-
-      while (index--) {
-        args[index - 1] = arguments[index];
-      }
-      return arrayPush(isArray(array) ? copyArray(array) : [array], baseFlatten(args, 1));
-    }
-
-    /**
-     * Creates an array of `array` values not included in the other given arrays
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons. The order and references of result values are
-     * determined by the first array.
-     *
-     * **Note:** Unlike `_.pullAll`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...Array} [values] The values to exclude.
-     * @returns {Array} Returns the new array of filtered values.
-     * @see _.without, _.xor
-     * @example
-     *
-     * _.difference([2, 1], [2, 3]);
-     * // => [1]
-     */
-    var difference = baseRest(function(array, values) {
-      return isArrayLikeObject(array)
-        ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true))
-        : [];
-    });
-
-    /**
-     * This method is like `_.difference` except that it accepts `iteratee` which
-     * is invoked for each element of `array` and `values` to generate the criterion
-     * by which they're compared. The order and references of result values are
-     * determined by the first array. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * **Note:** Unlike `_.pullAllBy`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...Array} [values] The values to exclude.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * _.differenceBy([2.1, 1.2], [2.3, 3.4], Math.floor);
-     * // => [1.2]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.differenceBy([{ 'x': 2 }, { 'x': 1 }], [{ 'x': 1 }], 'x');
-     * // => [{ 'x': 2 }]
-     */
-    var differenceBy = baseRest(function(array, values) {
-      var iteratee = last(values);
-      if (isArrayLikeObject(iteratee)) {
-        iteratee = undefined;
-      }
-      return isArrayLikeObject(array)
-        ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true), getIteratee(iteratee, 2))
-        : [];
-    });
-
-    /**
-     * This method is like `_.difference` except that it accepts `comparator`
-     * which is invoked to compare elements of `array` to `values`. The order and
-     * references of result values are determined by the first array. The comparator
-     * is invoked with two arguments: (arrVal, othVal).
-     *
-     * **Note:** Unlike `_.pullAllWith`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...Array} [values] The values to exclude.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     *
-     * _.differenceWith(objects, [{ 'x': 1, 'y': 2 }], _.isEqual);
-     * // => [{ 'x': 2, 'y': 1 }]
-     */
-    var differenceWith = baseRest(function(array, values) {
-      var comparator = last(values);
-      if (isArrayLikeObject(comparator)) {
-        comparator = undefined;
-      }
-      return isArrayLikeObject(array)
-        ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true), undefined, comparator)
-        : [];
-    });
-
-    /**
-     * Creates a slice of `array` with `n` elements dropped from the beginning.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.5.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to drop.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.drop([1, 2, 3]);
-     * // => [2, 3]
-     *
-     * _.drop([1, 2, 3], 2);
-     * // => [3]
-     *
-     * _.drop([1, 2, 3], 5);
-     * // => []
-     *
-     * _.drop([1, 2, 3], 0);
-     * // => [1, 2, 3]
-     */
-    function drop(array, n, guard) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      return baseSlice(array, n < 0 ? 0 : n, length);
-    }
-
-    /**
-     * Creates a slice of `array` with `n` elements dropped from the end.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to drop.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.dropRight([1, 2, 3]);
-     * // => [1, 2]
-     *
-     * _.dropRight([1, 2, 3], 2);
-     * // => [1]
-     *
-     * _.dropRight([1, 2, 3], 5);
-     * // => []
-     *
-     * _.dropRight([1, 2, 3], 0);
-     * // => [1, 2, 3]
-     */
-    function dropRight(array, n, guard) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      n = length - n;
-      return baseSlice(array, 0, n < 0 ? 0 : n);
-    }
-
-    /**
-     * Creates a slice of `array` excluding elements dropped from the end.
-     * Elements are dropped until `predicate` returns falsey. The predicate is
-     * invoked with three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': true },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': false }
-     * ];
-     *
-     * _.dropRightWhile(users, function(o) { return !o.active; });
-     * // => objects for ['barney']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.dropRightWhile(users, { 'user': 'pebbles', 'active': false });
-     * // => objects for ['barney', 'fred']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.dropRightWhile(users, ['active', false]);
-     * // => objects for ['barney']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.dropRightWhile(users, 'active');
-     * // => objects for ['barney', 'fred', 'pebbles']
-     */
-    function dropRightWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3), true, true)
-        : [];
-    }
-
-    /**
-     * Creates a slice of `array` excluding elements dropped from the beginning.
-     * Elements are dropped until `predicate` returns falsey. The predicate is
-     * invoked with three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': false },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': true }
-     * ];
-     *
-     * _.dropWhile(users, function(o) { return !o.active; });
-     * // => objects for ['pebbles']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.dropWhile(users, { 'user': 'barney', 'active': false });
-     * // => objects for ['fred', 'pebbles']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.dropWhile(users, ['active', false]);
-     * // => objects for ['pebbles']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.dropWhile(users, 'active');
-     * // => objects for ['barney', 'fred', 'pebbles']
-     */
-    function dropWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3), true)
-        : [];
-    }
-
-    /**
-     * Fills elements of `array` with `value` from `start` up to, but not
-     * including, `end`.
-     *
-     * **Note:** This method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.2.0
-     * @category Array
-     * @param {Array} array The array to fill.
-     * @param {*} value The value to fill `array` with.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [1, 2, 3];
-     *
-     * _.fill(array, 'a');
-     * console.log(array);
-     * // => ['a', 'a', 'a']
-     *
-     * _.fill(Array(3), 2);
-     * // => [2, 2, 2]
-     *
-     * _.fill([4, 6, 8, 10], '*', 1, 3);
-     * // => [4, '*', '*', 10]
-     */
-    function fill(array, value, start, end) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      if (start && typeof start != 'number' && isIterateeCall(array, value, start)) {
-        start = 0;
-        end = length;
-      }
-      return baseFill(array, value, start, end);
-    }
-
-    /**
-     * This method is like `_.find` except that it returns the index of the first
-     * element `predicate` returns truthy for instead of the element itself.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @returns {number} Returns the index of the found element, else `-1`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': false },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': true }
-     * ];
-     *
-     * _.findIndex(users, function(o) { return o.user == 'barney'; });
-     * // => 0
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findIndex(users, { 'user': 'fred', 'active': false });
-     * // => 1
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findIndex(users, ['active', false]);
-     * // => 0
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findIndex(users, 'active');
-     * // => 2
-     */
-    function findIndex(array, predicate, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = fromIndex == null ? 0 : toInteger(fromIndex);
-      if (index < 0) {
-        index = nativeMax(length + index, 0);
-      }
-      return baseFindIndex(array, getIteratee(predicate, 3), index);
-    }
-
-    /**
-     * This method is like `_.findIndex` except that it iterates over elements
-     * of `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=array.length-1] The index to search from.
-     * @returns {number} Returns the index of the found element, else `-1`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': true },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': false }
-     * ];
-     *
-     * _.findLastIndex(users, function(o) { return o.user == 'pebbles'; });
-     * // => 2
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findLastIndex(users, { 'user': 'barney', 'active': true });
-     * // => 0
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findLastIndex(users, ['active', false]);
-     * // => 2
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findLastIndex(users, 'active');
-     * // => 0
-     */
-    function findLastIndex(array, predicate, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = length - 1;
-      if (fromIndex !== undefined) {
-        index = toInteger(fromIndex);
-        index = fromIndex < 0
-          ? nativeMax(length + index, 0)
-          : nativeMin(index, length - 1);
-      }
-      return baseFindIndex(array, getIteratee(predicate, 3), index, true);
-    }
-
-    /**
-     * Flattens `array` a single level deep.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to flatten.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * _.flatten([1, [2, [3, [4]], 5]]);
-     * // => [1, 2, [3, [4]], 5]
-     */
-    function flatten(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseFlatten(array, 1) : [];
-    }
-
-    /**
-     * Recursively flattens `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to flatten.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * _.flattenDeep([1, [2, [3, [4]], 5]]);
-     * // => [1, 2, 3, 4, 5]
-     */
-    function flattenDeep(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseFlatten(array, INFINITY) : [];
-    }
-
-    /**
-     * Recursively flatten `array` up to `depth` times.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.4.0
-     * @category Array
-     * @param {Array} array The array to flatten.
-     * @param {number} [depth=1] The maximum recursion depth.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * var array = [1, [2, [3, [4]], 5]];
-     *
-     * _.flattenDepth(array, 1);
-     * // => [1, 2, [3, [4]], 5]
-     *
-     * _.flattenDepth(array, 2);
-     * // => [1, 2, 3, [4], 5]
-     */
-    function flattenDepth(array, depth) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      depth = depth === undefined ? 1 : toInteger(depth);
-      return baseFlatten(array, depth);
-    }
-
-    /**
-     * The inverse of `_.toPairs`; this method returns an object composed
-     * from key-value `pairs`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} pairs The key-value pairs.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * _.fromPairs([['a', 1], ['b', 2]]);
-     * // => { 'a': 1, 'b': 2 }
-     */
-    function fromPairs(pairs) {
-      var index = -1,
-          length = pairs == null ? 0 : pairs.length,
-          result = {};
-
-      while (++index < length) {
-        var pair = pairs[index];
-        result[pair[0]] = pair[1];
-      }
-      return result;
-    }
-
-    /**
-     * Gets the first element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @alias first
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {*} Returns the first element of `array`.
-     * @example
-     *
-     * _.head([1, 2, 3]);
-     * // => 1
-     *
-     * _.head([]);
-     * // => undefined
-     */
-    function head(array) {
-      return (array && array.length) ? array[0] : undefined;
-    }
-
-    /**
-     * Gets the index at which the first occurrence of `value` is found in `array`
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons. If `fromIndex` is negative, it's used as the
-     * offset from the end of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.indexOf([1, 2, 1, 2], 2);
-     * // => 1
-     *
-     * // Search from the `fromIndex`.
-     * _.indexOf([1, 2, 1, 2], 2, 2);
-     * // => 3
-     */
-    function indexOf(array, value, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = fromIndex == null ? 0 : toInteger(fromIndex);
-      if (index < 0) {
-        index = nativeMax(length + index, 0);
-      }
-      return baseIndexOf(array, value, index);
-    }
-
-    /**
-     * Gets all but the last element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.initial([1, 2, 3]);
-     * // => [1, 2]
-     */
-    function initial(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseSlice(array, 0, -1) : [];
-    }
-
-    /**
-     * Creates an array of unique values that are included in all given arrays
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons. The order and references of result values are
-     * determined by the first array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @returns {Array} Returns the new array of intersecting values.
-     * @example
-     *
-     * _.intersection([2, 1], [2, 3]);
-     * // => [2]
-     */
-    var intersection = baseRest(function(arrays) {
-      var mapped = arrayMap(arrays, castArrayLikeObject);
-      return (mapped.length && mapped[0] === arrays[0])
-        ? baseIntersection(mapped)
-        : [];
-    });
-
-    /**
-     * This method is like `_.intersection` except that it accepts `iteratee`
-     * which is invoked for each element of each `arrays` to generate the criterion
-     * by which they're compared. The order and references of result values are
-     * determined by the first array. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of intersecting values.
-     * @example
-     *
-     * _.intersectionBy([2.1, 1.2], [2.3, 3.4], Math.floor);
-     * // => [2.1]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.intersectionBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 1 }]
-     */
-    var intersectionBy = baseRest(function(arrays) {
-      var iteratee = last(arrays),
-          mapped = arrayMap(arrays, castArrayLikeObject);
-
-      if (iteratee === last(mapped)) {
-        iteratee = undefined;
-      } else {
-        mapped.pop();
-      }
-      return (mapped.length && mapped[0] === arrays[0])
-        ? baseIntersection(mapped, getIteratee(iteratee, 2))
-        : [];
-    });
-
-    /**
-     * This method is like `_.intersection` except that it accepts `comparator`
-     * which is invoked to compare elements of `arrays`. The order and references
-     * of result values are determined by the first array. The comparator is
-     * invoked with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of intersecting values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.intersectionWith(objects, others, _.isEqual);
-     * // => [{ 'x': 1, 'y': 2 }]
-     */
-    var intersectionWith = baseRest(function(arrays) {
-      var comparator = last(arrays),
-          mapped = arrayMap(arrays, castArrayLikeObject);
-
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      if (comparator) {
-        mapped.pop();
-      }
-      return (mapped.length && mapped[0] === arrays[0])
-        ? baseIntersection(mapped, undefined, comparator)
-        : [];
-    });
-
-    /**
-     * Converts all elements in `array` into a string separated by `separator`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to convert.
-     * @param {string} [separator=','] The element separator.
-     * @returns {string} Returns the joined string.
-     * @example
-     *
-     * _.join(['a', 'b', 'c'], '~');
-     * // => 'a~b~c'
-     */
-    function join(array, separator) {
-      return array == null ? '' : nativeJoin.call(array, separator);
-    }
-
-    /**
-     * Gets the last element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {*} Returns the last element of `array`.
-     * @example
-     *
-     * _.last([1, 2, 3]);
-     * // => 3
-     */
-    function last(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? array[length - 1] : undefined;
-    }
-
-    /**
-     * This method is like `_.indexOf` except that it iterates over elements of
-     * `array` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @param {number} [fromIndex=array.length-1] The index to search from.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.lastIndexOf([1, 2, 1, 2], 2);
-     * // => 3
-     *
-     * // Search from the `fromIndex`.
-     * _.lastIndexOf([1, 2, 1, 2], 2, 2);
-     * // => 1
-     */
-    function lastIndexOf(array, value, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = length;
-      if (fromIndex !== undefined) {
-        index = toInteger(fromIndex);
-        index = index < 0 ? nativeMax(length + index, 0) : nativeMin(index, length - 1);
-      }
-      return value === value
-        ? strictLastIndexOf(array, value, index)
-        : baseFindIndex(array, baseIsNaN, index, true);
-    }
-
-    /**
-     * Gets the element at index `n` of `array`. If `n` is negative, the nth
-     * element from the end is returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.11.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=0] The index of the element to return.
-     * @returns {*} Returns the nth element of `array`.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'd'];
-     *
-     * _.nth(array, 1);
-     * // => 'b'
-     *
-     * _.nth(array, -2);
-     * // => 'c';
-     */
-    function nth(array, n) {
-      return (array && array.length) ? baseNth(array, toInteger(n)) : undefined;
-    }
-
-    /**
-     * Removes all given values from `array` using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * **Note:** Unlike `_.without`, this method mutates `array`. Use `_.remove`
-     * to remove elements from an array by predicate.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {...*} [values] The values to remove.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'a', 'b', 'c'];
-     *
-     * _.pull(array, 'a', 'c');
-     * console.log(array);
-     * // => ['b', 'b']
-     */
-    var pull = baseRest(pullAll);
-
-    /**
-     * This method is like `_.pull` except that it accepts an array of values to remove.
-     *
-     * **Note:** Unlike `_.difference`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'a', 'b', 'c'];
-     *
-     * _.pullAll(array, ['a', 'c']);
-     * console.log(array);
-     * // => ['b', 'b']
-     */
-    function pullAll(array, values) {
-      return (array && array.length && values && values.length)
-        ? basePullAll(array, values)
-        : array;
-    }
-
-    /**
-     * This method is like `_.pullAll` except that it accepts `iteratee` which is
-     * invoked for each element of `array` and `values` to generate the criterion
-     * by which they're compared. The iteratee is invoked with one argument: (value).
-     *
-     * **Note:** Unlike `_.differenceBy`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [{ 'x': 1 }, { 'x': 2 }, { 'x': 3 }, { 'x': 1 }];
-     *
-     * _.pullAllBy(array, [{ 'x': 1 }, { 'x': 3 }], 'x');
-     * console.log(array);
-     * // => [{ 'x': 2 }]
-     */
-    function pullAllBy(array, values, iteratee) {
-      return (array && array.length && values && values.length)
-        ? basePullAll(array, values, getIteratee(iteratee, 2))
-        : array;
-    }
-
-    /**
-     * This method is like `_.pullAll` except that it accepts `comparator` which
-     * is invoked to compare elements of `array` to `values`. The comparator is
-     * invoked with two arguments: (arrVal, othVal).
-     *
-     * **Note:** Unlike `_.differenceWith`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.6.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [{ 'x': 1, 'y': 2 }, { 'x': 3, 'y': 4 }, { 'x': 5, 'y': 6 }];
-     *
-     * _.pullAllWith(array, [{ 'x': 3, 'y': 4 }], _.isEqual);
-     * console.log(array);
-     * // => [{ 'x': 1, 'y': 2 }, { 'x': 5, 'y': 6 }]
-     */
-    function pullAllWith(array, values, comparator) {
-      return (array && array.length && values && values.length)
-        ? basePullAll(array, values, undefined, comparator)
-        : array;
-    }
-
-    /**
-     * Removes elements from `array` corresponding to `indexes` and returns an
-     * array of removed elements.
-     *
-     * **Note:** Unlike `_.at`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {...(number|number[])} [indexes] The indexes of elements to remove.
-     * @returns {Array} Returns the new array of removed elements.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'd'];
-     * var pulled = _.pullAt(array, [1, 3]);
-     *
-     * console.log(array);
-     * // => ['a', 'c']
-     *
-     * console.log(pulled);
-     * // => ['b', 'd']
-     */
-    var pullAt = flatRest(function(array, indexes) {
-      var length = array == null ? 0 : array.length,
-          result = baseAt(array, indexes);
-
-      basePullAt(array, arrayMap(indexes, function(index) {
-        return isIndex(index, length) ? +index : index;
-      }).sort(compareAscending));
-
-      return result;
-    });
-
-    /**
-     * Removes all elements from `array` that `predicate` returns truthy for
-     * and returns an array of the removed elements. The predicate is invoked
-     * with three arguments: (value, index, array).
-     *
-     * **Note:** Unlike `_.filter`, this method mutates `array`. Use `_.pull`
-     * to pull elements from an array by value.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new array of removed elements.
-     * @example
-     *
-     * var array = [1, 2, 3, 4];
-     * var evens = _.remove(array, function(n) {
-     *   return n % 2 == 0;
-     * });
-     *
-     * console.log(array);
-     * // => [1, 3]
-     *
-     * console.log(evens);
-     * // => [2, 4]
-     */
-    function remove(array, predicate) {
-      var result = [];
-      if (!(array && array.length)) {
-        return result;
-      }
-      var index = -1,
-          indexes = [],
-          length = array.length;
-
-      predicate = getIteratee(predicate, 3);
-      while (++index < length) {
-        var value = array[index];
-        if (predicate(value, index, array)) {
-          result.push(value);
-          indexes.push(index);
-        }
-      }
-      basePullAt(array, indexes);
-      return result;
-    }
-
-    /**
-     * Reverses `array` so that the first element becomes the last, the second
-     * element becomes the second to last, and so on.
-     *
-     * **Note:** This method mutates `array` and is based on
-     * [`Array#reverse`](https://mdn.io/Array/reverse).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [1, 2, 3];
-     *
-     * _.reverse(array);
-     * // => [3, 2, 1]
-     *
-     * console.log(array);
-     * // => [3, 2, 1]
-     */
-    function reverse(array) {
-      return array == null ? array : nativeReverse.call(array);
-    }
-
-    /**
-     * Creates a slice of `array` from `start` up to, but not including, `end`.
-     *
-     * **Note:** This method is used instead of
-     * [`Array#slice`](https://mdn.io/Array/slice) to ensure dense arrays are
-     * returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to slice.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns the slice of `array`.
-     */
-    function slice(array, start, end) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      if (end && typeof end != 'number' && isIterateeCall(array, start, end)) {
-        start = 0;
-        end = length;
-      }
-      else {
-        start = start == null ? 0 : toInteger(start);
-        end = end === undefined ? length : toInteger(end);
-      }
-      return baseSlice(array, start, end);
-    }
-
-    /**
-     * Uses a binary search to determine the lowest index at which `value`
-     * should be inserted into `array` in order to maintain its sort order.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * _.sortedIndex([30, 50], 40);
-     * // => 1
-     */
-    function sortedIndex(array, value) {
-      return baseSortedIndex(array, value);
-    }
-
-    /**
-     * This method is like `_.sortedIndex` except that it accepts `iteratee`
-     * which is invoked for `value` and each element of `array` to compute their
-     * sort ranking. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * var objects = [{ 'x': 4 }, { 'x': 5 }];
-     *
-     * _.sortedIndexBy(objects, { 'x': 4 }, function(o) { return o.x; });
-     * // => 0
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.sortedIndexBy(objects, { 'x': 4 }, 'x');
-     * // => 0
-     */
-    function sortedIndexBy(array, value, iteratee) {
-      return baseSortedIndexBy(array, value, getIteratee(iteratee, 2));
-    }
-
-    /**
-     * This method is like `_.indexOf` except that it performs a binary
-     * search on a sorted `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.sortedIndexOf([4, 5, 5, 5, 6], 5);
-     * // => 1
-     */
-    function sortedIndexOf(array, value) {
-      var length = array == null ? 0 : array.length;
-      if (length) {
-        var index = baseSortedIndex(array, value);
-        if (index < length && eq(array[index], value)) {
-          return index;
-        }
-      }
-      return -1;
-    }
-
-    /**
-     * This method is like `_.sortedIndex` except that it returns the highest
-     * index at which `value` should be inserted into `array` in order to
-     * maintain its sort order.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * _.sortedLastIndex([4, 5, 5, 5, 6], 5);
-     * // => 4
-     */
-    function sortedLastIndex(array, value) {
-      return baseSortedIndex(array, value, true);
-    }
-
-    /**
-     * This method is like `_.sortedLastIndex` except that it accepts `iteratee`
-     * which is invoked for `value` and each element of `array` to compute their
-     * sort ranking. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * var objects = [{ 'x': 4 }, { 'x': 5 }];
-     *
-     * _.sortedLastIndexBy(objects, { 'x': 4 }, function(o) { return o.x; });
-     * // => 1
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.sortedLastIndexBy(objects, { 'x': 4 }, 'x');
-     * // => 1
-     */
-    function sortedLastIndexBy(array, value, iteratee) {
-      return baseSortedIndexBy(array, value, getIteratee(iteratee, 2), true);
-    }
-
-    /**
-     * This method is like `_.lastIndexOf` except that it performs a binary
-     * search on a sorted `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.sortedLastIndexOf([4, 5, 5, 5, 6], 5);
-     * // => 3
-     */
-    function sortedLastIndexOf(array, value) {
-      var length = array == null ? 0 : array.length;
-      if (length) {
-        var index = baseSortedIndex(array, value, true) - 1;
-        if (eq(array[index], value)) {
-          return index;
-        }
-      }
-      return -1;
-    }
-
-    /**
-     * This method is like `_.uniq` except that it's designed and optimized
-     * for sorted arrays.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.sortedUniq([1, 1, 2]);
-     * // => [1, 2]
-     */
-    function sortedUniq(array) {
-      return (array && array.length)
-        ? baseSortedUniq(array)
-        : [];
-    }
-
-    /**
-     * This method is like `_.uniqBy` except that it's designed and optimized
-     * for sorted arrays.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.sortedUniqBy([1.1, 1.2, 2.3, 2.4], Math.floor);
-     * // => [1.1, 2.3]
-     */
-    function sortedUniqBy(array, iteratee) {
-      return (array && array.length)
-        ? baseSortedUniq(array, getIteratee(iteratee, 2))
-        : [];
-    }
-
-    /**
-     * Gets all but the first element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.tail([1, 2, 3]);
-     * // => [2, 3]
-     */
-    function tail(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseSlice(array, 1, length) : [];
-    }
-
-    /**
-     * Creates a slice of `array` with `n` elements taken from the beginning.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to take.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.take([1, 2, 3]);
-     * // => [1]
-     *
-     * _.take([1, 2, 3], 2);
-     * // => [1, 2]
-     *
-     * _.take([1, 2, 3], 5);
-     * // => [1, 2, 3]
-     *
-     * _.take([1, 2, 3], 0);
-     * // => []
-     */
-    function take(array, n, guard) {
-      if (!(array && array.length)) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      return baseSlice(array, 0, n < 0 ? 0 : n);
-    }
-
-    /**
-     * Creates a slice of `array` with `n` elements taken from the end.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to take.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.takeRight([1, 2, 3]);
-     * // => [3]
-     *
-     * _.takeRight([1, 2, 3], 2);
-     * // => [2, 3]
-     *
-     * _.takeRight([1, 2, 3], 5);
-     * // => [1, 2, 3]
-     *
-     * _.takeRight([1, 2, 3], 0);
-     * // => []
-     */
-    function takeRight(array, n, guard) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      n = length - n;
-      return baseSlice(array, n < 0 ? 0 : n, length);
-    }
-
-    /**
-     * Creates a slice of `array` with elements taken from the end. Elements are
-     * taken until `predicate` returns falsey. The predicate is invoked with
-     * three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': true },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': false }
-     * ];
-     *
-     * _.takeRightWhile(users, function(o) { return !o.active; });
-     * // => objects for ['fred', 'pebbles']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.takeRightWhile(users, { 'user': 'pebbles', 'active': false });
-     * // => objects for ['pebbles']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.takeRightWhile(users, ['active', false]);
-     * // => objects for ['fred', 'pebbles']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.takeRightWhile(users, 'active');
-     * // => []
-     */
-    function takeRightWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3), false, true)
-        : [];
-    }
-
-    /**
-     * Creates a slice of `array` with elements taken from the beginning. Elements
-     * are taken until `predicate` returns falsey. The predicate is invoked with
-     * three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': false },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': true }
-     * ];
-     *
-     * _.takeWhile(users, function(o) { return !o.active; });
-     * // => objects for ['barney', 'fred']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.takeWhile(users, { 'user': 'barney', 'active': false });
-     * // => objects for ['barney']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.takeWhile(users, ['active', false]);
-     * // => objects for ['barney', 'fred']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.takeWhile(users, 'active');
-     * // => []
-     */
-    function takeWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3))
-        : [];
-    }
-
-    /**
-     * Creates an array of unique values, in order, from all given arrays using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @returns {Array} Returns the new array of combined values.
-     * @example
-     *
-     * _.union([2], [1, 2]);
-     * // => [2, 1]
-     */
-    var union = baseRest(function(arrays) {
-      return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true));
-    });
-
-    /**
-     * This method is like `_.union` except that it accepts `iteratee` which is
-     * invoked for each element of each `arrays` to generate the criterion by
-     * which uniqueness is computed. Result values are chosen from the first
-     * array in which the value occurs. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of combined values.
-     * @example
-     *
-     * _.unionBy([2.1], [1.2, 2.3], Math.floor);
-     * // => [2.1, 1.2]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.unionBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 1 }, { 'x': 2 }]
-     */
-    var unionBy = baseRest(function(arrays) {
-      var iteratee = last(arrays);
-      if (isArrayLikeObject(iteratee)) {
-        iteratee = undefined;
-      }
-      return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true), getIteratee(iteratee, 2));
-    });
-
-    /**
-     * This method is like `_.union` except that it accepts `comparator` which
-     * is invoked to compare elements of `arrays`. Result values are chosen from
-     * the first array in which the value occurs. The comparator is invoked
-     * with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of combined values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.unionWith(objects, others, _.isEqual);
-     * // => [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }, { 'x': 1, 'y': 1 }]
-     */
-    var unionWith = baseRest(function(arrays) {
-      var comparator = last(arrays);
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true), undefined, comparator);
-    });
-
-    /**
-     * Creates a duplicate-free version of an array, using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons, in which only the first occurrence of each element
-     * is kept. The order of result values is determined by the order they occur
-     * in the array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.uniq([2, 1, 2]);
-     * // => [2, 1]
-     */
-    function uniq(array) {
-      return (array && array.length) ? baseUniq(array) : [];
-    }
-
-    /**
-     * This method is like `_.uniq` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the criterion by which
-     * uniqueness is computed. The order of result values is determined by the
-     * order they occur in the array. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.uniqBy([2.1, 1.2, 2.3], Math.floor);
-     * // => [2.1, 1.2]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.uniqBy([{ 'x': 1 }, { 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 1 }, { 'x': 2 }]
-     */
-    function uniqBy(array, iteratee) {
-      return (array && array.length) ? baseUniq(array, getIteratee(iteratee, 2)) : [];
-    }
-
-    /**
-     * This method is like `_.uniq` except that it accepts `comparator` which
-     * is invoked to compare elements of `array`. The order of result values is
-     * determined by the order they occur in the array.The comparator is invoked
-     * with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.uniqWith(objects, _.isEqual);
-     * // => [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }]
-     */
-    function uniqWith(array, comparator) {
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      return (array && array.length) ? baseUniq(array, undefined, comparator) : [];
-    }
-
-    /**
-     * This method is like `_.zip` except that it accepts an array of grouped
-     * elements and creates an array regrouping the elements to their pre-zip
-     * configuration.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.2.0
-     * @category Array
-     * @param {Array} array The array of grouped elements to process.
-     * @returns {Array} Returns the new array of regrouped elements.
-     * @example
-     *
-     * var zipped = _.zip(['a', 'b'], [1, 2], [true, false]);
-     * // => [['a', 1, true], ['b', 2, false]]
-     *
-     * _.unzip(zipped);
-     * // => [['a', 'b'], [1, 2], [true, false]]
-     */
-    function unzip(array) {
-      if (!(array && array.length)) {
-        return [];
-      }
-      var length = 0;
-      array = arrayFilter(array, function(group) {
-        if (isArrayLikeObject(group)) {
-          length = nativeMax(group.length, length);
-          return true;
-        }
-      });
-      return baseTimes(length, function(index) {
-        return arrayMap(array, baseProperty(index));
-      });
-    }
-
-    /**
-     * This method is like `_.unzip` except that it accepts `iteratee` to specify
-     * how regrouped values should be combined. The iteratee is invoked with the
-     * elements of each group: (...group).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.8.0
-     * @category Array
-     * @param {Array} array The array of grouped elements to process.
-     * @param {Function} [iteratee=_.identity] The function to combine
-     *  regrouped values.
-     * @returns {Array} Returns the new array of regrouped elements.
-     * @example
-     *
-     * var zipped = _.zip([1, 2], [10, 20], [100, 200]);
-     * // => [[1, 10, 100], [2, 20, 200]]
-     *
-     * _.unzipWith(zipped, _.add);
-     * // => [3, 30, 300]
-     */
-    function unzipWith(array, iteratee) {
-      if (!(array && array.length)) {
-        return [];
-      }
-      var result = unzip(array);
-      if (iteratee == null) {
-        return result;
-      }
-      return arrayMap(result, function(group) {
-        return apply(iteratee, undefined, group);
-      });
-    }
-
-    /**
-     * Creates an array excluding all given values using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * **Note:** Unlike `_.pull`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...*} [values] The values to exclude.
-     * @returns {Array} Returns the new array of filtered values.
-     * @see _.difference, _.xor
-     * @example
-     *
-     * _.without([2, 1, 2, 3], 1, 2);
-     * // => [3]
-     */
-    var without = baseRest(function(array, values) {
-      return isArrayLikeObject(array)
-        ? baseDifference(array, values)
-        : [];
-    });
-
-    /**
-     * Creates an array of unique values that is the
-     * [symmetric difference](https://en.wikipedia.org/wiki/Symmetric_difference)
-     * of the given arrays. The order of result values is determined by the order
-     * they occur in the arrays.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @returns {Array} Returns the new array of filtered values.
-     * @see _.difference, _.without
-     * @example
-     *
-     * _.xor([2, 1], [2, 3]);
-     * // => [1, 3]
-     */
-    var xor = baseRest(function(arrays) {
-      return baseXor(arrayFilter(arrays, isArrayLikeObject));
-    });
-
-    /**
-     * This method is like `_.xor` except that it accepts `iteratee` which is
-     * invoked for each element of each `arrays` to generate the criterion by
-     * which by which they're compared. The order of result values is determined
-     * by the order they occur in the arrays. The iteratee is invoked with one
-     * argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * _.xorBy([2.1, 1.2], [2.3, 3.4], Math.floor);
-     * // => [1.2, 3.4]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.xorBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 2 }]
-     */
-    var xorBy = baseRest(function(arrays) {
-      var iteratee = last(arrays);
-      if (isArrayLikeObject(iteratee)) {
-        iteratee = undefined;
-      }
-      return baseXor(arrayFilter(arrays, isArrayLikeObject), getIteratee(iteratee, 2));
-    });
-
-    /**
-     * This method is like `_.xor` except that it accepts `comparator` which is
-     * invoked to compare elements of `arrays`. The order of result values is
-     * determined by the order they occur in the arrays. The comparator is invoked
-     * with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.xorWith(objects, others, _.isEqual);
-     * // => [{ 'x': 2, 'y': 1 }, { 'x': 1, 'y': 1 }]
-     */
-    var xorWith = baseRest(function(arrays) {
-      var comparator = last(arrays);
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      return baseXor(arrayFilter(arrays, isArrayLikeObject), undefined, comparator);
-    });
-
-    /**
-     * Creates an array of grouped elements, the first of which contains the
-     * first elements of the given arrays, the second of which contains the
-     * second elements of the given arrays, and so on.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to process.
-     * @returns {Array} Returns the new array of grouped elements.
-     * @example
-     *
-     * _.zip(['a', 'b'], [1, 2], [true, false]);
-     * // => [['a', 1, true], ['b', 2, false]]
-     */
-    var zip = baseRest(unzip);
-
-    /**
-     * This method is like `_.fromPairs` except that it accepts two arrays,
-     * one of property identifiers and one of corresponding values.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.4.0
-     * @category Array
-     * @param {Array} [props=[]] The property identifiers.
-     * @param {Array} [values=[]] The property values.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * _.zipObject(['a', 'b'], [1, 2]);
-     * // => { 'a': 1, 'b': 2 }
-     */
-    function zipObject(props, values) {
-      return baseZipObject(props || [], values || [], assignValue);
-    }
-
-    /**
-     * This method is like `_.zipObject` except that it supports property paths.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.1.0
-     * @category Array
-     * @param {Array} [props=[]] The property identifiers.
-     * @param {Array} [values=[]] The property values.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * _.zipObjectDeep(['a.b[0].c', 'a.b[1].d'], [1, 2]);
-     * // => { 'a': { 'b': [{ 'c': 1 }, { 'd': 2 }] } }
-     */
-    function zipObjectDeep(props, values) {
-      return baseZipObject(props || [], values || [], baseSet);
-    }
-
-    /**
-     * This method is like `_.zip` except that it accepts `iteratee` to specify
-     * how grouped values should be combined. The iteratee is invoked with the
-     * elements of each group: (...group).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.8.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to process.
-     * @param {Function} [iteratee=_.identity] The function to combine
-     *  grouped values.
-     * @returns {Array} Returns the new array of grouped elements.
-     * @example
-     *
-     * _.zipWith([1, 2], [10, 20], [100, 200], function(a, b, c) {
-     *   return a + b + c;
-     * });
-     * // => [111, 222]
-     */
-    var zipWith = baseRest(function(arrays) {
-      var length = arrays.length,
-          iteratee = length > 1 ? arrays[length - 1] : undefined;
-
-      iteratee = typeof iteratee == 'function' ? (arrays.pop(), iteratee) : undefined;
-      return unzipWith(arrays, iteratee);
-    });
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a `lodash` wrapper instance that wraps `value` with explicit method
-     * chain sequences enabled. The result of such sequences must be unwrapped
-     * with `_#value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.3.0
-     * @category Seq
-     * @param {*} value The value to wrap.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'age': 36 },
-     *   { 'user': 'fred',    'age': 40 },
-     *   { 'user': 'pebbles', 'age': 1 }
-     * ];
-     *
-     * var youngest = _
-     *   .chain(users)
-     *   .sortBy('age')
-     *   .map(function(o) {
-     *     return o.user + ' is ' + o.age;
-     *   })
-     *   .head()
-     *   .value();
-     * // => 'pebbles is 1'
-     */
-    function chain(value) {
-      var result = lodash(value);
-      result.__chain__ = true;
-      return result;
-    }
-
-    /**
-     * This method invokes `interceptor` and returns `value`. The interceptor
-     * is invoked with one argument; (value). The purpose of this method is to
-     * "tap into" a method chain sequence in order to modify intermediate results.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Seq
-     * @param {*} value The value to provide to `interceptor`.
-     * @param {Function} interceptor The function to invoke.
-     * @returns {*} Returns `value`.
-     * @example
-     *
-     * _([1, 2, 3])
-     *  .tap(function(array) {
-     *    // Mutate input array.
-     *    array.pop();
-     *  })
-     *  .reverse()
-     *  .value();
-     * // => [2, 1]
-     */
-    function tap(value, interceptor) {
-      interceptor(value);
-      return value;
-    }
-
-    /**
-     * This method is like `_.tap` except that it returns the result of `interceptor`.
-     * The purpose of this method is to "pass thru" values replacing intermediate
-     * results in a method chain sequence.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Seq
-     * @param {*} value The value to provide to `interceptor`.
-     * @param {Function} interceptor The function to invoke.
-     * @returns {*} Returns the result of `interceptor`.
-     * @example
-     *
-     * _('  abc  ')
-     *  .chain()
-     *  .trim()
-     *  .thru(function(value) {
-     *    return [value];
-     *  })
-     *  .value();
-     * // => ['abc']
-     */
-    function thru(value, interceptor) {
-      return interceptor(value);
-    }
-
-    /**
-     * This method is the wrapper version of `_.at`.
-     *
-     * @name at
-     * @memberOf _
-     * @since 1.0.0
-     * @category Seq
-     * @param {...(string|string[])} [paths] The property paths to pick.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }, 4] };
-     *
-     * _(object).at(['a[0].b.c', 'a[1]']).value();
-     * // => [3, 4]
-     */
-    var wrapperAt = flatRest(function(paths) {
-      var length = paths.length,
-          start = length ? paths[0] : 0,
-          value = this.__wrapped__,
-          interceptor = function(object) { return baseAt(object, paths); };
-
-      if (length > 1 || this.__actions__.length ||
-          !(value instanceof LazyWrapper) || !isIndex(start)) {
-        return this.thru(interceptor);
-      }
-      value = value.slice(start, +start + (length ? 1 : 0));
-      value.__actions__.push({
-        'func': thru,
-        'args': [interceptor],
-        'thisArg': undefined
-      });
-      return new LodashWrapper(value, this.__chain__).thru(function(array) {
-        if (length && !array.length) {
-          array.push(undefined);
-        }
-        return array;
-      });
-    });
-
-    /**
-     * Creates a `lodash` wrapper instance with explicit method chain sequences enabled.
-     *
-     * @name chain
-     * @memberOf _
-     * @since 0.1.0
-     * @category Seq
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36 },
-     *   { 'user': 'fred',   'age': 40 }
-     * ];
-     *
-     * // A sequence without explicit chaining.
-     * _(users).head();
-     * // => { 'user': 'barney', 'age': 36 }
-     *
-     * // A sequence with explicit chaining.
-     * _(users)
-     *   .chain()
-     *   .head()
-     *   .pick('user')
-     *   .value();
-     * // => { 'user': 'barney' }
-     */
-    function wrapperChain() {
-      return chain(this);
-    }
-
-    /**
-     * Executes the chain sequence and returns the wrapped result.
-     *
-     * @name commit
-     * @memberOf _
-     * @since 3.2.0
-     * @category Seq
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var array = [1, 2];
-     * var wrapped = _(array).push(3);
-     *
-     * console.log(array);
-     * // => [1, 2]
-     *
-     * wrapped = wrapped.commit();
-     * console.log(array);
-     * // => [1, 2, 3]
-     *
-     * wrapped.last();
-     * // => 3
-     *
-     * console.log(array);
-     * // => [1, 2, 3]
-     */
-    function wrapperCommit() {
-      return new LodashWrapper(this.value(), this.__chain__);
-    }
-
-    /**
-     * Gets the next value on a wrapped object following the
-     * [iterator protocol](https://mdn.io/iteration_protocols#iterator).
-     *
-     * @name next
-     * @memberOf _
-     * @since 4.0.0
-     * @category Seq
-     * @returns {Object} Returns the next iterator value.
-     * @example
-     *
-     * var wrapped = _([1, 2]);
-     *
-     * wrapped.next();
-     * // => { 'done': false, 'value': 1 }
-     *
-     * wrapped.next();
-     * // => { 'done': false, 'value': 2 }
-     *
-     * wrapped.next();
-     * // => { 'done': true, 'value': undefined }
-     */
-    function wrapperNext() {
-      if (this.__values__ === undefined) {
-        this.__values__ = toArray(this.value());
-      }
-      var done = this.__index__ >= this.__values__.length,
-          value = done ? undefined : this.__values__[this.__index__++];
-
-      return { 'done': done, 'value': value };
-    }
-
-    /**
-     * Enables the wrapper to be iterable.
-     *
-     * @name Symbol.iterator
-     * @memberOf _
-     * @since 4.0.0
-     * @category Seq
-     * @returns {Object} Returns the wrapper object.
-     * @example
-     *
-     * var wrapped = _([1, 2]);
-     *
-     * wrapped[Symbol.iterator]() === wrapped;
-     * // => true
-     *
-     * Array.from(wrapped);
-     * // => [1, 2]
-     */
-    function wrapperToIterator() {
-      return this;
-    }
-
-    /**
-     * Creates a clone of the chain sequence planting `value` as the wrapped value.
-     *
-     * @name plant
-     * @memberOf _
-     * @since 3.2.0
-     * @category Seq
-     * @param {*} value The value to plant.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var wrapped = _([1, 2]).map(square);
-     * var other = wrapped.plant([3, 4]);
-     *
-     * other.value();
-     * // => [9, 16]
-     *
-     * wrapped.value();
-     * // => [1, 4]
-     */
-    function wrapperPlant(value) {
-      var result,
-          parent = this;
-
-      while (parent instanceof baseLodash) {
-        var clone = wrapperClone(parent);
-        clone.__index__ = 0;
-        clone.__values__ = undefined;
-        if (result) {
-          previous.__wrapped__ = clone;
-        } else {
-          result = clone;
-        }
-        var previous = clone;
-        parent = parent.__wrapped__;
-      }
-      previous.__wrapped__ = value;
-      return result;
-    }
-
-    /**
-     * This method is the wrapper version of `_.reverse`.
-     *
-     * **Note:** This method mutates the wrapped array.
-     *
-     * @name reverse
-     * @memberOf _
-     * @since 0.1.0
-     * @category Seq
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var array = [1, 2, 3];
-     *
-     * _(array).reverse().value()
-     * // => [3, 2, 1]
-     *
-     * console.log(array);
-     * // => [3, 2, 1]
-     */
-    function wrapperReverse() {
-      var value = this.__wrapped__;
-      if (value instanceof LazyWrapper) {
-        var wrapped = value;
-        if (this.__actions__.length) {
-          wrapped = new LazyWrapper(this);
-        }
-        wrapped = wrapped.reverse();
-        wrapped.__actions__.push({
-          'func': thru,
-          'args': [reverse],
-          'thisArg': undefined
-        });
-        return new LodashWrapper(wrapped, this.__chain__);
-      }
-      return this.thru(reverse);
-    }
-
-    /**
-     * Executes the chain sequence to resolve the unwrapped value.
-     *
-     * @name value
-     * @memberOf _
-     * @since 0.1.0
-     * @alias toJSON, valueOf
-     * @category Seq
-     * @returns {*} Returns the resolved unwrapped value.
-     * @example
-     *
-     * _([1, 2, 3]).value();
-     * // => [1, 2, 3]
-     */
-    function wrapperValue() {
-      return baseWrapperValue(this.__wrapped__, this.__actions__);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an object composed of keys generated from the results of running
-     * each element of `collection` thru `iteratee`. The corresponding value of
-     * each key is the number of times the key was returned by `iteratee`. The
-     * iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.5.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee to transform keys.
-     * @returns {Object} Returns the composed aggregate object.
-     * @example
-     *
-     * _.countBy([6.1, 4.2, 6.3], Math.floor);
-     * // => { '4': 1, '6': 2 }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.countBy(['one', 'two', 'three'], 'length');
-     * // => { '3': 2, '5': 1 }
-     */
-    var countBy = createAggregator(function(result, value, key) {
-      if (hasOwnProperty.call(result, key)) {
-        ++result[key];
-      } else {
-        baseAssignValue(result, key, 1);
-      }
-    });
-
-    /**
-     * Checks if `predicate` returns truthy for **all** elements of `collection`.
-     * Iteration is stopped once `predicate` returns falsey. The predicate is
-     * invoked with three arguments: (value, index|key, collection).
-     *
-     * **Note:** This method returns `true` for
-     * [empty collections](https://en.wikipedia.org/wiki/Empty_set) because
-     * [everything is true](https://en.wikipedia.org/wiki/Vacuous_truth) of
-     * elements of empty collections.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {boolean} Returns `true` if all elements pass the predicate check,
-     *  else `false`.
-     * @example
-     *
-     * _.every([true, 1, null, 'yes'], Boolean);
-     * // => false
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': false },
-     *   { 'user': 'fred',   'age': 40, 'active': false }
-     * ];
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.every(users, { 'user': 'barney', 'active': false });
-     * // => false
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.every(users, ['active', false]);
-     * // => true
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.every(users, 'active');
-     * // => false
-     */
-    function every(collection, predicate, guard) {
-      var func = isArray(collection) ? arrayEvery : baseEvery;
-      if (guard && isIterateeCall(collection, predicate, guard)) {
-        predicate = undefined;
-      }
-      return func(collection, getIteratee(predicate, 3));
-    }
-
-    /**
-     * Iterates over elements of `collection`, returning an array of all elements
-     * `predicate` returns truthy for. The predicate is invoked with three
-     * arguments: (value, index|key, collection).
-     *
-     * **Note:** Unlike `_.remove`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new filtered array.
-     * @see _.reject
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': true },
-     *   { 'user': 'fred',   'age': 40, 'active': false }
-     * ];
-     *
-     * _.filter(users, function(o) { return !o.active; });
-     * // => objects for ['fred']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.filter(users, { 'age': 36, 'active': true });
-     * // => objects for ['barney']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.filter(users, ['active', false]);
-     * // => objects for ['fred']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.filter(users, 'active');
-     * // => objects for ['barney']
-     */
-    function filter(collection, predicate) {
-      var func = isArray(collection) ? arrayFilter : baseFilter;
-      return func(collection, getIteratee(predicate, 3));
-    }
-
-    /**
-     * Iterates over elements of `collection`, returning the first element
-     * `predicate` returns truthy for. The predicate is invoked with three
-     * arguments: (value, index|key, collection).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @returns {*} Returns the matched element, else `undefined`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'age': 36, 'active': true },
-     *   { 'user': 'fred',    'age': 40, 'active': false },
-     *   { 'user': 'pebbles', 'age': 1,  'active': true }
-     * ];
-     *
-     * _.find(users, function(o) { return o.age < 40; });
-     * // => object for 'barney'
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.find(users, { 'age': 1, 'active': true });
-     * // => object for 'pebbles'
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.find(users, ['active', false]);
-     * // => object for 'fred'
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.find(users, 'active');
-     * // => object for 'barney'
-     */
-    var find = createFind(findIndex);
-
-    /**
-     * This method is like `_.find` except that it iterates over elements of
-     * `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=collection.length-1] The index to search from.
-     * @returns {*} Returns the matched element, else `undefined`.
-     * @example
-     *
-     * _.findLast([1, 2, 3, 4], function(n) {
-     *   return n % 2 == 1;
-     * });
-     * // => 3
-     */
-    var findLast = createFind(findLastIndex);
-
-    /**
-     * Creates a flattened array of values by running each element in `collection`
-     * thru `iteratee` and flattening the mapped results. The iteratee is invoked
-     * with three arguments: (value, index|key, collection).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * function duplicate(n) {
-     *   return [n, n];
-     * }
-     *
-     * _.flatMap([1, 2], duplicate);
-     * // => [1, 1, 2, 2]
-     */
-    function flatMap(collection, iteratee) {
-      return baseFlatten(map(collection, iteratee), 1);
-    }
-
-    /**
-     * This method is like `_.flatMap` except that it recursively flattens the
-     * mapped results.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * function duplicate(n) {
-     *   return [[[n, n]]];
-     * }
-     *
-     * _.flatMapDeep([1, 2], duplicate);
-     * // => [1, 1, 2, 2]
-     */
-    function flatMapDeep(collection, iteratee) {
-      return baseFlatten(map(collection, iteratee), INFINITY);
-    }
-
-    /**
-     * This method is like `_.flatMap` except that it recursively flattens the
-     * mapped results up to `depth` times.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {number} [depth=1] The maximum recursion depth.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * function duplicate(n) {
-     *   return [[[n, n]]];
-     * }
-     *
-     * _.flatMapDepth([1, 2], duplicate, 2);
-     * // => [[1, 1], [2, 2]]
-     */
-    function flatMapDepth(collection, iteratee, depth) {
-      depth = depth === undefined ? 1 : toInteger(depth);
-      return baseFlatten(map(collection, iteratee), depth);
-    }
-
-    /**
-     * Iterates over elements of `collection` and invokes `iteratee` for each element.
-     * The iteratee is invoked with three arguments: (value, index|key, collection).
-     * Iteratee functions may exit iteration early by explicitly returning `false`.
-     *
-     * **Note:** As with other "Collections" methods, objects with a "length"
-     * property are iterated like arrays. To avoid this behavior use `_.forIn`
-     * or `_.forOwn` for object iteration.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @alias each
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     * @see _.forEachRight
-     * @example
-     *
-     * _.forEach([1, 2], function(value) {
-     *   console.log(value);
-     * });
-     * // => Logs `1` then `2`.
-     *
-     * _.forEach({ 'a': 1, 'b': 2 }, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'a' then 'b' (iteration order is not guaranteed).
-     */
-    function forEach(collection, iteratee) {
-      var func = isArray(collection) ? arrayEach : baseEach;
-      return func(collection, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * This method is like `_.forEach` except that it iterates over elements of
-     * `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @alias eachRight
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     * @see _.forEach
-     * @example
-     *
-     * _.forEachRight([1, 2], function(value) {
-     *   console.log(value);
-     * });
-     * // => Logs `2` then `1`.
-     */
-    function forEachRight(collection, iteratee) {
-      var func = isArray(collection) ? arrayEachRight : baseEachRight;
-      return func(collection, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * Creates an object composed of keys generated from the results of running
-     * each element of `collection` thru `iteratee`. The order of grouped values
-     * is determined by the order they occur in `collection`. The corresponding
-     * value of each key is an array of elements responsible for generating the
-     * key. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee to transform keys.
-     * @returns {Object} Returns the composed aggregate object.
-     * @example
-     *
-     * _.groupBy([6.1, 4.2, 6.3], Math.floor);
-     * // => { '4': [4.2], '6': [6.1, 6.3] }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.groupBy(['one', 'two', 'three'], 'length');
-     * // => { '3': ['one', 'two'], '5': ['three'] }
-     */
-    var groupBy = createAggregator(function(result, value, key) {
-      if (hasOwnProperty.call(result, key)) {
-        result[key].push(value);
-      } else {
-        baseAssignValue(result, key, [value]);
-      }
-    });
-
-    /**
-     * Checks if `value` is in `collection`. If `collection` is a string, it's
-     * checked for a substring of `value`, otherwise
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * is used for equality comparisons. If `fromIndex` is negative, it's used as
-     * the offset from the end of `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object|string} collection The collection to inspect.
-     * @param {*} value The value to search for.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.reduce`.
-     * @returns {boolean} Returns `true` if `value` is found, else `false`.
-     * @example
-     *
-     * _.includes([1, 2, 3], 1);
-     * // => true
-     *
-     * _.includes([1, 2, 3], 1, 2);
-     * // => false
-     *
-     * _.includes({ 'a': 1, 'b': 2 }, 1);
-     * // => true
-     *
-     * _.includes('abcd', 'bc');
-     * // => true
-     */
-    function includes(collection, value, fromIndex, guard) {
-      collection = isArrayLike(collection) ? collection : values(collection);
-      fromIndex = (fromIndex && !guard) ? toInteger(fromIndex) : 0;
-
-      var length = collection.length;
-      if (fromIndex < 0) {
-        fromIndex = nativeMax(length + fromIndex, 0);
-      }
-      return isString(collection)
-        ? (fromIndex <= length && collection.indexOf(value, fromIndex) > -1)
-        : (!!length && baseIndexOf(collection, value, fromIndex) > -1);
-    }
-
-    /**
-     * Invokes the method at `path` of each element in `collection`, returning
-     * an array of the results of each invoked method. Any additional arguments
-     * are provided to each invoked method. If `path` is a function, it's invoked
-     * for, and `this` bound to, each element in `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Array|Function|string} path The path of the method to invoke or
-     *  the function invoked per iteration.
-     * @param {...*} [args] The arguments to invoke each method with.
-     * @returns {Array} Returns the array of results.
-     * @example
-     *
-     * _.invokeMap([[5, 1, 7], [3, 2, 1]], 'sort');
-     * // => [[1, 5, 7], [1, 2, 3]]
-     *
-     * _.invokeMap([123, 456], String.prototype.split, '');
-     * // => [['1', '2', '3'], ['4', '5', '6']]
-     */
-    var invokeMap = baseRest(function(collection, path, args) {
-      var index = -1,
-          isFunc = typeof path == 'function',
-          result = isArrayLike(collection) ? Array(collection.length) : [];
-
-      baseEach(collection, function(value) {
-        result[++index] = isFunc ? apply(path, value, args) : baseInvoke(value, path, args);
-      });
-      return result;
-    });
-
-    /**
-     * Creates an object composed of keys generated from the results of running
-     * each element of `collection` thru `iteratee`. The corresponding value of
-     * each key is the last element responsible for generating the key. The
-     * iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee to transform keys.
-     * @returns {Object} Returns the composed aggregate object.
-     * @example
-     *
-     * var array = [
-     *   { 'dir': 'left', 'code': 97 },
-     *   { 'dir': 'right', 'code': 100 }
-     * ];
-     *
-     * _.keyBy(array, function(o) {
-     *   return String.fromCharCode(o.code);
-     * });
-     * // => { 'a': { 'dir': 'left', 'code': 97 }, 'd': { 'dir': 'right', 'code': 100 } }
-     *
-     * _.keyBy(array, 'dir');
-     * // => { 'left': { 'dir': 'left', 'code': 97 }, 'right': { 'dir': 'right', 'code': 100 } }
-     */
-    var keyBy = createAggregator(function(result, value, key) {
-      baseAssignValue(result, key, value);
-    });
-
-    /**
-     * Creates an array of values by running each element in `collection` thru
-     * `iteratee`. The iteratee is invoked with three arguments:
-     * (value, index|key, collection).
-     *
-     * Many lodash methods are guarded to work as iteratees for methods like
-     * `_.every`, `_.filter`, `_.map`, `_.mapValues`, `_.reject`, and `_.some`.
-     *
-     * The guarded methods are:
-     * `ary`, `chunk`, `curry`, `curryRight`, `drop`, `dropRight`, `every`,
-     * `fill`, `invert`, `parseInt`, `random`, `range`, `rangeRight`, `repeat`,
-     * `sampleSize`, `slice`, `some`, `sortBy`, `split`, `take`, `takeRight`,
-     * `template`, `trim`, `trimEnd`, `trimStart`, and `words`
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new mapped array.
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * _.map([4, 8], square);
-     * // => [16, 64]
-     *
-     * _.map({ 'a': 4, 'b': 8 }, square);
-     * // => [16, 64] (iteration order is not guaranteed)
-     *
-     * var users = [
-     *   { 'user': 'barney' },
-     *   { 'user': 'fred' }
-     * ];
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.map(users, 'user');
-     * // => ['barney', 'fred']
-     */
-    function map(collection, iteratee) {
-      var func = isArray(collection) ? arrayMap : baseMap;
-      return func(collection, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * This method is like `_.sortBy` except that it allows specifying the sort
-     * orders of the iteratees to sort by. If `orders` is unspecified, all values
-     * are sorted in ascending order. Otherwise, specify an order of "desc" for
-     * descending or "asc" for ascending sort order of corresponding values.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Array[]|Function[]|Object[]|string[]} [iteratees=[_.identity]]
-     *  The iteratees to sort by.
-     * @param {string[]} [orders] The sort orders of `iteratees`.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.reduce`.
-     * @returns {Array} Returns the new sorted array.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'fred',   'age': 48 },
-     *   { 'user': 'barney', 'age': 34 },
-     *   { 'user': 'fred',   'age': 40 },
-     *   { 'user': 'barney', 'age': 36 }
-     * ];
-     *
-     * // Sort by `user` in ascending order and by `age` in descending order.
-     * _.orderBy(users, ['user', 'age'], ['asc', 'desc']);
-     * // => objects for [['barney', 36], ['barney', 34], ['fred', 48], ['fred', 40]]
-     */
-    function orderBy(collection, iteratees, orders, guard) {
-      if (collection == null) {
-        return [];
-      }
-      if (!isArray(iteratees)) {
-        iteratees = iteratees == null ? [] : [iteratees];
-      }
-      orders = guard ? undefined : orders;
-      if (!isArray(orders)) {
-        orders = orders == null ? [] : [orders];
-      }
-      return baseOrderBy(collection, iteratees, orders);
-    }
-
-    /**
-     * Creates an array of elements split into two groups, the first of which
-     * contains elements `predicate` returns truthy for, the second of which
-     * contains elements `predicate` returns falsey for. The predicate is
-     * invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the array of grouped elements.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'age': 36, 'active': false },
-     *   { 'user': 'fred',    'age': 40, 'active': true },
-     *   { 'user': 'pebbles', 'age': 1,  'active': false }
-     * ];
-     *
-     * _.partition(users, function(o) { return o.active; });
-     * // => objects for [['fred'], ['barney', 'pebbles']]
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.partition(users, { 'age': 1, 'active': false });
-     * // => objects for [['pebbles'], ['barney', 'fred']]
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.partition(users, ['active', false]);
-     * // => objects for [['barney', 'pebbles'], ['fred']]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.partition(users, 'active');
-     * // => objects for [['fred'], ['barney', 'pebbles']]
-     */
-    var partition = createAggregator(function(result, value, key) {
-      result[key ? 0 : 1].push(value);
-    }, function() { return [[], []]; });
-
-    /**
-     * Reduces `collection` to a value which is the accumulated result of running
-     * each element in `collection` thru `iteratee`, where each successive
-     * invocation is supplied the return value of the previous. If `accumulator`
-     * is not given, the first element of `collection` is used as the initial
-     * value. The iteratee is invoked with four arguments:
-     * (accumulator, value, index|key, collection).
-     *
-     * Many lodash methods are guarded to work as iteratees for methods like
-     * `_.reduce`, `_.reduceRight`, and `_.transform`.
-     *
-     * The guarded methods are:
-     * `assign`, `defaults`, `defaultsDeep`, `includes`, `merge`, `orderBy`,
-     * and `sortBy`
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {*} [accumulator] The initial value.
-     * @returns {*} Returns the accumulated value.
-     * @see _.reduceRight
-     * @example
-     *
-     * _.reduce([1, 2], function(sum, n) {
-     *   return sum + n;
-     * }, 0);
-     * // => 3
-     *
-     * _.reduce({ 'a': 1, 'b': 2, 'c': 1 }, function(result, value, key) {
-     *   (result[value] || (result[value] = [])).push(key);
-     *   return result;
-     * }, {});
-     * // => { '1': ['a', 'c'], '2': ['b'] } (iteration order is not guaranteed)
-     */
-    function reduce(collection, iteratee, accumulator) {
-      var func = isArray(collection) ? arrayReduce : baseReduce,
-          initAccum = arguments.length < 3;
-
-      return func(collection, getIteratee(iteratee, 4), accumulator, initAccum, baseEach);
-    }
-
-    /**
-     * This method is like `_.reduce` except that it iterates over elements of
-     * `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {*} [accumulator] The initial value.
-     * @returns {*} Returns the accumulated value.
-     * @see _.reduce
-     * @example
-     *
-     * var array = [[0, 1], [2, 3], [4, 5]];
-     *
-     * _.reduceRight(array, function(flattened, other) {
-     *   return flattened.concat(other);
-     * }, []);
-     * // => [4, 5, 2, 3, 0, 1]
-     */
-    function reduceRight(collection, iteratee, accumulator) {
-      var func = isArray(collection) ? arrayReduceRight : baseReduce,
-          initAccum = arguments.length < 3;
-
-      return func(collection, getIteratee(iteratee, 4), accumulator, initAccum, baseEachRight);
-    }
-
-    /**
-     * The opposite of `_.filter`; this method returns the elements of `collection`
-     * that `predicate` does **not** return truthy for.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new filtered array.
-     * @see _.filter
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': false },
-     *   { 'user': 'fred',   'age': 40, 'active': true }
-     * ];
-     *
-     * _.reject(users, function(o) { return !o.active; });
-     * // => objects for ['fred']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.reject(users, { 'age': 40, 'active': true });
-     * // => objects for ['barney']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.reject(users, ['active', false]);
-     * // => objects for ['fred']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.reject(users, 'active');
-     * // => objects for ['barney']
-     */
-    function reject(collection, predicate) {
-      var func = isArray(collection) ? arrayFilter : baseFilter;
-      return func(collection, negate(getIteratee(predicate, 3)));
-    }
-
-    /**
-     * Gets a random element from `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to sample.
-     * @returns {*} Returns the random element.
-     * @example
-     *
-     * _.sample([1, 2, 3, 4]);
-     * // => 2
-     */
-    function sample(collection) {
-      var func = isArray(collection) ? arraySample : baseSample;
-      return func(collection);
-    }
-
-    /**
-     * Gets `n` random elements at unique keys from `collection` up to the
-     * size of `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to sample.
-     * @param {number} [n=1] The number of elements to sample.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the random elements.
-     * @example
-     *
-     * _.sampleSize([1, 2, 3], 2);
-     * // => [3, 1]
-     *
-     * _.sampleSize([1, 2, 3], 4);
-     * // => [2, 3, 1]
-     */
-    function sampleSize(collection, n, guard) {
-      if ((guard ? isIterateeCall(collection, n, guard) : n === undefined)) {
-        n = 1;
-      } else {
-        n = toInteger(n);
-      }
-      var func = isArray(collection) ? arraySampleSize : baseSampleSize;
-      return func(collection, n);
-    }
-
-    /**
-     * Creates an array of shuffled values, using a version of the
-     * [Fisher-Yates shuffle](https://en.wikipedia.org/wiki/Fisher-Yates_shuffle).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to shuffle.
-     * @returns {Array} Returns the new shuffled array.
-     * @example
-     *
-     * _.shuffle([1, 2, 3, 4]);
-     * // => [4, 1, 3, 2]
-     */
-    function shuffle(collection) {
-      var func = isArray(collection) ? arrayShuffle : baseShuffle;
-      return func(collection);
-    }
-
-    /**
-     * Gets the size of `collection` by returning its length for array-like
-     * values or the number of own enumerable string keyed properties for objects.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object|string} collection The collection to inspect.
-     * @returns {number} Returns the collection size.
-     * @example
-     *
-     * _.size([1, 2, 3]);
-     * // => 3
-     *
-     * _.size({ 'a': 1, 'b': 2 });
-     * // => 2
-     *
-     * _.size('pebbles');
-     * // => 7
-     */
-    function size(collection) {
-      if (collection == null) {
-        return 0;
-      }
-      if (isArrayLike(collection)) {
-        return isString(collection) ? stringSize(collection) : collection.length;
-      }
-      var tag = getTag(collection);
-      if (tag == mapTag || tag == setTag) {
-        return collection.size;
-      }
-      return baseKeys(collection).length;
-    }
-
-    /**
-     * Checks if `predicate` returns truthy for **any** element of `collection`.
-     * Iteration is stopped once `predicate` returns truthy. The predicate is
-     * invoked with three arguments: (value, index|key, collection).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {boolean} Returns `true` if any element passes the predicate check,
-     *  else `false`.
-     * @example
-     *
-     * _.some([null, 0, 'yes', false], Boolean);
-     * // => true
-     *
-     * var users = [
-     *   { 'user': 'barney', 'active': true },
-     *   { 'user': 'fred',   'active': false }
-     * ];
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.some(users, { 'user': 'barney', 'active': false });
-     * // => false
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.some(users, ['active', false]);
-     * // => true
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.some(users, 'active');
-     * // => true
-     */
-    function some(collection, predicate, guard) {
-      var func = isArray(collection) ? arraySome : baseSome;
-      if (guard && isIterateeCall(collection, predicate, guard)) {
-        predicate = undefined;
-      }
-      return func(collection, getIteratee(predicate, 3));
-    }
-
-    /**
-     * Creates an array of elements, sorted in ascending order by the results of
-     * running each element in a collection thru each iteratee. This method
-     * performs a stable sort, that is, it preserves the original sort order of
-     * equal elements. The iteratees are invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {...(Function|Function[])} [iteratees=[_.identity]]
-     *  The iteratees to sort by.
-     * @returns {Array} Returns the new sorted array.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'fred',   'age': 48 },
-     *   { 'user': 'barney', 'age': 36 },
-     *   { 'user': 'fred',   'age': 40 },
-     *   { 'user': 'barney', 'age': 34 }
-     * ];
-     *
-     * _.sortBy(users, [function(o) { return o.user; }]);
-     * // => objects for [['barney', 36], ['barney', 34], ['fred', 48], ['fred', 40]]
-     *
-     * _.sortBy(users, ['user', 'age']);
-     * // => objects for [['barney', 34], ['barney', 36], ['fred', 40], ['fred', 48]]
-     */
-    var sortBy = baseRest(function(collection, iteratees) {
-      if (collection == null) {
-        return [];
-      }
-      var length = iteratees.length;
-      if (length > 1 && isIterateeCall(collection, iteratees[0], iteratees[1])) {
-        iteratees = [];
-      } else if (length > 2 && isIterateeCall(iteratees[0], iteratees[1], iteratees[2])) {
-        iteratees = [iteratees[0]];
-      }
-      return baseOrderBy(collection, baseFlatten(iteratees, 1), []);
-    });
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Gets the timestamp of the number of milliseconds that have elapsed since
-     * the Unix epoch (1 January 1970 00:00:00 UTC).
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Date
-     * @returns {number} Returns the timestamp.
-     * @example
-     *
-     * _.defer(function(stamp) {
-     *   console.log(_.now() - stamp);
-     * }, _.now());
-     * // => Logs the number of milliseconds it took for the deferred invocation.
-     */
-    var now = ctxNow || function() {
-      return root.Date.now();
-    };
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * The opposite of `_.before`; this method creates a function that invokes
-     * `func` once it's called `n` or more times.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {number} n The number of calls before `func` is invoked.
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new restricted function.
-     * @example
-     *
-     * var saves = ['profile', 'settings'];
-     *
-     * var done = _.after(saves.length, function() {
-     *   console.log('done saving!');
-     * });
-     *
-     * _.forEach(saves, function(type) {
-     *   asyncSave({ 'type': type, 'complete': done });
-     * });
-     * // => Logs 'done saving!' after the two async saves have completed.
-     */
-    function after(n, func) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      n = toInteger(n);
-      return function() {
-        if (--n < 1) {
-          return func.apply(this, arguments);
-        }
-      };
-    }
-
-    /**
-     * Creates a function that invokes `func`, with up to `n` arguments,
-     * ignoring any additional arguments.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} func The function to cap arguments for.
-     * @param {number} [n=func.length] The arity cap.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the new capped function.
-     * @example
-     *
-     * _.map(['6', '8', '10'], _.ary(parseInt, 1));
-     * // => [6, 8, 10]
-     */
-    function ary(func, n, guard) {
-      n = guard ? undefined : n;
-      n = (func && n == null) ? func.length : n;
-      return createWrap(func, WRAP_ARY_FLAG, undefined, undefined, undefined, undefined, n);
-    }
-
-    /**
-     * Creates a function that invokes `func`, with the `this` binding and arguments
-     * of the created function, while it's called less than `n` times. Subsequent
-     * calls to the created function return the result of the last `func` invocation.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {number} n The number of calls at which `func` is no longer invoked.
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new restricted function.
-     * @example
-     *
-     * jQuery(element).on('click', _.before(5, addContactToList));
-     * // => Allows adding up to 4 contacts to the list.
-     */
-    function before(n, func) {
-      var result;
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      n = toInteger(n);
-      return function() {
-        if (--n > 0) {
-          result = func.apply(this, arguments);
-        }
-        if (n <= 1) {
-          func = undefined;
-        }
-        return result;
-      };
-    }
-
-    /**
-     * Creates a function that invokes `func` with the `this` binding of `thisArg`
-     * and `partials` prepended to the arguments it receives.
-     *
-     * The `_.bind.placeholder` value, which defaults to `_` in monolithic builds,
-     * may be used as a placeholder for partially applied arguments.
-     *
-     * **Note:** Unlike native `Function#bind`, this method doesn't set the "length"
-     * property of bound functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to bind.
-     * @param {*} thisArg The `this` binding of `func`.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new bound function.
-     * @example
-     *
-     * function greet(greeting, punctuation) {
-     *   return greeting + ' ' + this.user + punctuation;
-     * }
-     *
-     * var object = { 'user': 'fred' };
-     *
-     * var bound = _.bind(greet, object, 'hi');
-     * bound('!');
-     * // => 'hi fred!'
-     *
-     * // Bound with placeholders.
-     * var bound = _.bind(greet, object, _, '!');
-     * bound('hi');
-     * // => 'hi fred!'
-     */
-    var bind = baseRest(function(func, thisArg, partials) {
-      var bitmask = WRAP_BIND_FLAG;
-      if (partials.length) {
-        var holders = replaceHolders(partials, getHolder(bind));
-        bitmask |= WRAP_PARTIAL_FLAG;
-      }
-      return createWrap(func, bitmask, thisArg, partials, holders);
-    });
-
-    /**
-     * Creates a function that invokes the method at `object[key]` with `partials`
-     * prepended to the arguments it receives.
-     *
-     * This method differs from `_.bind` by allowing bound functions to reference
-     * methods that may be redefined or don't yet exist. See
-     * [Peter Michaux's article](http://peter.michaux.ca/articles/lazy-function-definition-pattern)
-     * for more details.
-     *
-     * The `_.bindKey.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for partially applied arguments.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.10.0
-     * @category Function
-     * @param {Object} object The object to invoke the method on.
-     * @param {string} key The key of the method.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new bound function.
-     * @example
-     *
-     * var object = {
-     *   'user': 'fred',
-     *   'greet': function(greeting, punctuation) {
-     *     return greeting + ' ' + this.user + punctuation;
-     *   }
-     * };
-     *
-     * var bound = _.bindKey(object, 'greet', 'hi');
-     * bound('!');
-     * // => 'hi fred!'
-     *
-     * object.greet = function(greeting, punctuation) {
-     *   return greeting + 'ya ' + this.user + punctuation;
-     * };
-     *
-     * bound('!');
-     * // => 'hiya fred!'
-     *
-     * // Bound with placeholders.
-     * var bound = _.bindKey(object, 'greet', _, '!');
-     * bound('hi');
-     * // => 'hiya fred!'
-     */
-    var bindKey = baseRest(function(object, key, partials) {
-      var bitmask = WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG;
-      if (partials.length) {
-        var holders = replaceHolders(partials, getHolder(bindKey));
-        bitmask |= WRAP_PARTIAL_FLAG;
-      }
-      return createWrap(key, bitmask, object, partials, holders);
-    });
-
-    /**
-     * Creates a function that accepts arguments of `func` and either invokes
-     * `func` returning its result, if at least `arity` number of arguments have
-     * been provided, or returns a function that accepts the remaining `func`
-     * arguments, and so on. The arity of `func` may be specified if `func.length`
-     * is not sufficient.
-     *
-     * The `_.curry.placeholder` value, which defaults to `_` in monolithic builds,
-     * may be used as a placeholder for provided arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of curried functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Function
-     * @param {Function} func The function to curry.
-     * @param {number} [arity=func.length] The arity of `func`.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the new curried function.
-     * @example
-     *
-     * var abc = function(a, b, c) {
-     *   return [a, b, c];
-     * };
-     *
-     * var curried = _.curry(abc);
-     *
-     * curried(1)(2)(3);
-     * // => [1, 2, 3]
-     *
-     * curried(1, 2)(3);
-     * // => [1, 2, 3]
-     *
-     * curried(1, 2, 3);
-     * // => [1, 2, 3]
-     *
-     * // Curried with placeholders.
-     * curried(1)(_, 3)(2);
-     * // => [1, 2, 3]
-     */
-    function curry(func, arity, guard) {
-      arity = guard ? undefined : arity;
-      var result = createWrap(func, WRAP_CURRY_FLAG, undefined, undefined, undefined, undefined, undefined, arity);
-      result.placeholder = curry.placeholder;
-      return result;
-    }
-
-    /**
-     * This method is like `_.curry` except that arguments are applied to `func`
-     * in the manner of `_.partialRight` instead of `_.partial`.
-     *
-     * The `_.curryRight.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for provided arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of curried functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} func The function to curry.
-     * @param {number} [arity=func.length] The arity of `func`.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the new curried function.
-     * @example
-     *
-     * var abc = function(a, b, c) {
-     *   return [a, b, c];
-     * };
-     *
-     * var curried = _.curryRight(abc);
-     *
-     * curried(3)(2)(1);
-     * // => [1, 2, 3]
-     *
-     * curried(2, 3)(1);
-     * // => [1, 2, 3]
-     *
-     * curried(1, 2, 3);
-     * // => [1, 2, 3]
-     *
-     * // Curried with placeholders.
-     * curried(3)(1, _)(2);
-     * // => [1, 2, 3]
-     */
-    function curryRight(func, arity, guard) {
-      arity = guard ? undefined : arity;
-      var result = createWrap(func, WRAP_CURRY_RIGHT_FLAG, undefined, undefined, undefined, undefined, undefined, arity);
-      result.placeholder = curryRight.placeholder;
-      return result;
-    }
-
-    /**
-     * Creates a debounced function that delays invoking `func` until after `wait`
-     * milliseconds have elapsed since the last time the debounced function was
-     * invoked. The debounced function comes with a `cancel` method to cancel
-     * delayed `func` invocations and a `flush` method to immediately invoke them.
-     * Provide `options` to indicate whether `func` should be invoked on the
-     * leading and/or trailing edge of the `wait` timeout. The `func` is invoked
-     * with the last arguments provided to the debounced function. Subsequent
-     * calls to the debounced function return the result of the last `func`
-     * invocation.
-     *
-     * **Note:** If `leading` and `trailing` options are `true`, `func` is
-     * invoked on the trailing edge of the timeout only if the debounced function
-     * is invoked more than once during the `wait` timeout.
-     *
-     * If `wait` is `0` and `leading` is `false`, `func` invocation is deferred
-     * until to the next tick, similar to `setTimeout` with a timeout of `0`.
-     *
-     * See [David Corbacho's article](https://css-tricks.com/debouncing-throttling-explained-examples/)
-     * for details over the differences between `_.debounce` and `_.throttle`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to debounce.
-     * @param {number} [wait=0] The number of milliseconds to delay.
-     * @param {Object} [options={}] The options object.
-     * @param {boolean} [options.leading=false]
-     *  Specify invoking on the leading edge of the timeout.
-     * @param {number} [options.maxWait]
-     *  The maximum time `func` is allowed to be delayed before it's invoked.
-     * @param {boolean} [options.trailing=true]
-     *  Specify invoking on the trailing edge of the timeout.
-     * @returns {Function} Returns the new debounced function.
-     * @example
-     *
-     * // Avoid costly calculations while the window size is in flux.
-     * jQuery(window).on('resize', _.debounce(calculateLayout, 150));
-     *
-     * // Invoke `sendMail` when clicked, debouncing subsequent calls.
-     * jQuery(element).on('click', _.debounce(sendMail, 300, {
-     *   'leading': true,
-     *   'trailing': false
-     * }));
-     *
-     * // Ensure `batchLog` is invoked once after 1 second of debounced calls.
-     * var debounced = _.debounce(batchLog, 250, { 'maxWait': 1000 });
-     * var source = new EventSource('/stream');
-     * jQuery(source).on('message', debounced);
-     *
-     * // Cancel the trailing debounced invocation.
-     * jQuery(window).on('popstate', debounced.cancel);
-     */
-    function debounce(func, wait, options) {
-      var lastArgs,
-          lastThis,
-          maxWait,
-          result,
-          timerId,
-          lastCallTime,
-          lastInvokeTime = 0,
-          leading = false,
-          maxing = false,
-          trailing = true;
-
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      wait = toNumber(wait) || 0;
-      if (isObject(options)) {
-        leading = !!options.leading;
-        maxing = 'maxWait' in options;
-        maxWait = maxing ? nativeMax(toNumber(options.maxWait) || 0, wait) : maxWait;
-        trailing = 'trailing' in options ? !!options.trailing : trailing;
-      }
-
-      function invokeFunc(time) {
-        var args = lastArgs,
-            thisArg = lastThis;
-
-        lastArgs = lastThis = undefined;
-        lastInvokeTime = time;
-        result = func.apply(thisArg, args);
-        return result;
-      }
-
-      function leadingEdge(time) {
-        // Reset any `maxWait` timer.
-        lastInvokeTime = time;
-        // Start the timer for the trailing edge.
-        timerId = setTimeout(timerExpired, wait);
-        // Invoke the leading edge.
-        return leading ? invokeFunc(time) : result;
-      }
-
-      function remainingWait(time) {
-        var timeSinceLastCall = time - lastCallTime,
-            timeSinceLastInvoke = time - lastInvokeTime,
-            timeWaiting = wait - timeSinceLastCall;
-
-        return maxing
-          ? nativeMin(timeWaiting, maxWait - timeSinceLastInvoke)
-          : timeWaiting;
-      }
-
-      function shouldInvoke(time) {
-        var timeSinceLastCall = time - lastCallTime,
-            timeSinceLastInvoke = time - lastInvokeTime;
-
-        // Either this is the first call, activity has stopped and we're at the
-        // trailing edge, the system time has gone backwards and we're treating
-        // it as the trailing edge, or we've hit the `maxWait` limit.
-        return (lastCallTime === undefined || (timeSinceLastCall >= wait) ||
-          (timeSinceLastCall < 0) || (maxing && timeSinceLastInvoke >= maxWait));
-      }
-
-      function timerExpired() {
-        var time = now();
-        if (shouldInvoke(time)) {
-          return trailingEdge(time);
-        }
-        // Restart the timer.
-        timerId = setTimeout(timerExpired, remainingWait(time));
-      }
-
-      function trailingEdge(time) {
-        timerId = undefined;
-
-        // Only invoke if we have `lastArgs` which means `func` has been
-        // debounced at least once.
-        if (trailing && lastArgs) {
-          return invokeFunc(time);
-        }
-        lastArgs = lastThis = undefined;
-        return result;
-      }
-
-      function cancel() {
-        if (timerId !== undefined) {
-          clearTimeout(timerId);
-        }
-        lastInvokeTime = 0;
-        lastArgs = lastCallTime = lastThis = timerId = undefined;
-      }
-
-      function flush() {
-        return timerId === undefined ? result : trailingEdge(now());
-      }
-
-      function debounced() {
-        var time = now(),
-            isInvoking = shouldInvoke(time);
-
-        lastArgs = arguments;
-        lastThis = this;
-        lastCallTime = time;
-
-        if (isInvoking) {
-          if (timerId === undefined) {
-            return leadingEdge(lastCallTime);
-          }
-          if (maxing) {
-            // Handle invocations in a tight loop.
-            clearTimeout(timerId);
-            timerId = setTimeout(timerExpired, wait);
-            return invokeFunc(lastCallTime);
-          }
-        }
-        if (timerId === undefined) {
-          timerId = setTimeout(timerExpired, wait);
-        }
-        return result;
-      }
-      debounced.cancel = cancel;
-      debounced.flush = flush;
-      return debounced;
-    }
-
-    /**
-     * Defers invoking the `func` until the current call stack has cleared. Any
-     * additional arguments are provided to `func` when it's invoked.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to defer.
-     * @param {...*} [args] The arguments to invoke `func` with.
-     * @returns {number} Returns the timer id.
-     * @example
-     *
-     * _.defer(function(text) {
-     *   console.log(text);
-     * }, 'deferred');
-     * // => Logs 'deferred' after one millisecond.
-     */
-    var defer = baseRest(function(func, args) {
-      return baseDelay(func, 1, args);
-    });
-
-    /**
-     * Invokes `func` after `wait` milliseconds. Any additional arguments are
-     * provided to `func` when it's invoked.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to delay.
-     * @param {number} wait The number of milliseconds to delay invocation.
-     * @param {...*} [args] The arguments to invoke `func` with.
-     * @returns {number} Returns the timer id.
-     * @example
-     *
-     * _.delay(function(text) {
-     *   console.log(text);
-     * }, 1000, 'later');
-     * // => Logs 'later' after one second.
-     */
-    var delay = baseRest(function(func, wait, args) {
-      return baseDelay(func, toNumber(wait) || 0, args);
-    });
-
-    /**
-     * Creates a function that invokes `func` with arguments reversed.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Function
-     * @param {Function} func The function to flip arguments for.
-     * @returns {Function} Returns the new flipped function.
-     * @example
-     *
-     * var flipped = _.flip(function() {
-     *   return _.toArray(arguments);
-     * });
-     *
-     * flipped('a', 'b', 'c', 'd');
-     * // => ['d', 'c', 'b', 'a']
-     */
-    function flip(func) {
-      return createWrap(func, WRAP_FLIP_FLAG);
-    }
-
-    /**
-     * Creates a function that memoizes the result of `func`. If `resolver` is
-     * provided, it determines the cache key for storing the result based on the
-     * arguments provided to the memoized function. By default, the first argument
-     * provided to the memoized function is used as the map cache key. The `func`
-     * is invoked with the `this` binding of the memoized function.
-     *
-     * **Note:** The cache is exposed as the `cache` property on the memoized
-     * function. Its creation may be customized by replacing the `_.memoize.Cache`
-     * constructor with one whose instances implement the
-     * [`Map`](http://ecma-international.org/ecma-262/7.0/#sec-properties-of-the-map-prototype-object)
-     * method interface of `clear`, `delete`, `get`, `has`, and `set`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to have its output memoized.
-     * @param {Function} [resolver] The function to resolve the cache key.
-     * @returns {Function} Returns the new memoized function.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2 };
-     * var other = { 'c': 3, 'd': 4 };
-     *
-     * var values = _.memoize(_.values);
-     * values(object);
-     * // => [1, 2]
-     *
-     * values(other);
-     * // => [3, 4]
-     *
-     * object.a = 2;
-     * values(object);
-     * // => [1, 2]
-     *
-     * // Modify the result cache.
-     * values.cache.set(object, ['a', 'b']);
-     * values(object);
-     * // => ['a', 'b']
-     *
-     * // Replace `_.memoize.Cache`.
-     * _.memoize.Cache = WeakMap;
-     */
-    function memoize(func, resolver) {
-      if (typeof func != 'function' || (resolver != null && typeof resolver != 'function')) {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      var memoized = function() {
-        var args = arguments,
-            key = resolver ? resolver.apply(this, args) : args[0],
-            cache = memoized.cache;
-
-        if (cache.has(key)) {
-          return cache.get(key);
-        }
-        var result = func.apply(this, args);
-        memoized.cache = cache.set(key, result) || cache;
-        return result;
-      };
-      memoized.cache = new (memoize.Cache || MapCache);
-      return memoized;
-    }
-
-    // Expose `MapCache`.
-    memoize.Cache = MapCache;
-
-    /**
-     * Creates a function that negates the result of the predicate `func`. The
-     * `func` predicate is invoked with the `this` binding and arguments of the
-     * created function.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} predicate The predicate to negate.
-     * @returns {Function} Returns the new negated function.
-     * @example
-     *
-     * function isEven(n) {
-     *   return n % 2 == 0;
-     * }
-     *
-     * _.filter([1, 2, 3, 4, 5, 6], _.negate(isEven));
-     * // => [1, 3, 5]
-     */
-    function negate(predicate) {
-      if (typeof predicate != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      return function() {
-        var args = arguments;
-        switch (args.length) {
-          case 0: return !predicate.call(this);
-          case 1: return !predicate.call(this, args[0]);
-          case 2: return !predicate.call(this, args[0], args[1]);
-          case 3: return !predicate.call(this, args[0], args[1], args[2]);
-        }
-        return !predicate.apply(this, args);
-      };
-    }
-
-    /**
-     * Creates a function that is restricted to invoking `func` once. Repeat calls
-     * to the function return the value of the first invocation. The `func` is
-     * invoked with the `this` binding and arguments of the created function.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new restricted function.
-     * @example
-     *
-     * var initialize = _.once(createApplication);
-     * initialize();
-     * initialize();
-     * // => `createApplication` is invoked once
-     */
-    function once(func) {
-      return before(2, func);
-    }
-
-    /**
-     * Creates a function that invokes `func` with its arguments transformed.
-     *
-     * @static
-     * @since 4.0.0
-     * @memberOf _
-     * @category Function
-     * @param {Function} func The function to wrap.
-     * @param {...(Function|Function[])} [transforms=[_.identity]]
-     *  The argument transforms.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * function doubled(n) {
-     *   return n * 2;
-     * }
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var func = _.overArgs(function(x, y) {
-     *   return [x, y];
-     * }, [square, doubled]);
-     *
-     * func(9, 3);
-     * // => [81, 6]
-     *
-     * func(10, 5);
-     * // => [100, 10]
-     */
-    var overArgs = castRest(function(func, transforms) {
-      transforms = (transforms.length == 1 && isArray(transforms[0]))
-        ? arrayMap(transforms[0], baseUnary(getIteratee()))
-        : arrayMap(baseFlatten(transforms, 1), baseUnary(getIteratee()));
-
-      var funcsLength = transforms.length;
-      return baseRest(function(args) {
-        var index = -1,
-            length = nativeMin(args.length, funcsLength);
-
-        while (++index < length) {
-          args[index] = transforms[index].call(this, args[index]);
-        }
-        return apply(func, this, args);
-      });
-    });
-
-    /**
-     * Creates a function that invokes `func` with `partials` prepended to the
-     * arguments it receives. This method is like `_.bind` except it does **not**
-     * alter the `this` binding.
-     *
-     * The `_.partial.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for partially applied arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of partially
-     * applied functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.2.0
-     * @category Function
-     * @param {Function} func The function to partially apply arguments to.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new partially applied function.
-     * @example
-     *
-     * function greet(greeting, name) {
-     *   return greeting + ' ' + name;
-     * }
-     *
-     * var sayHelloTo = _.partial(greet, 'hello');
-     * sayHelloTo('fred');
-     * // => 'hello fred'
-     *
-     * // Partially applied with placeholders.
-     * var greetFred = _.partial(greet, _, 'fred');
-     * greetFred('hi');
-     * // => 'hi fred'
-     */
-    var partial = baseRest(function(func, partials) {
-      var holders = replaceHolders(partials, getHolder(partial));
-      return createWrap(func, WRAP_PARTIAL_FLAG, undefined, partials, holders);
-    });
-
-    /**
-     * This method is like `_.partial` except that partially applied arguments
-     * are appended to the arguments it receives.
-     *
-     * The `_.partialRight.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for partially applied arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of partially
-     * applied functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.0.0
-     * @category Function
-     * @param {Function} func The function to partially apply arguments to.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new partially applied function.
-     * @example
-     *
-     * function greet(greeting, name) {
-     *   return greeting + ' ' + name;
-     * }
-     *
-     * var greetFred = _.partialRight(greet, 'fred');
-     * greetFred('hi');
-     * // => 'hi fred'
-     *
-     * // Partially applied with placeholders.
-     * var sayHelloTo = _.partialRight(greet, 'hello', _);
-     * sayHelloTo('fred');
-     * // => 'hello fred'
-     */
-    var partialRight = baseRest(function(func, partials) {
-      var holders = replaceHolders(partials, getHolder(partialRight));
-      return createWrap(func, WRAP_PARTIAL_RIGHT_FLAG, undefined, partials, holders);
-    });
-
-    /**
-     * Creates a function that invokes `func` with arguments arranged according
-     * to the specified `indexes` where the argument value at the first index is
-     * provided as the first argument, the argument value at the second index is
-     * provided as the second argument, and so on.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} func The function to rearrange arguments for.
-     * @param {...(number|number[])} indexes The arranged argument indexes.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var rearged = _.rearg(function(a, b, c) {
-     *   return [a, b, c];
-     * }, [2, 0, 1]);
-     *
-     * rearged('b', 'c', 'a')
-     * // => ['a', 'b', 'c']
-     */
-    var rearg = flatRest(function(func, indexes) {
-      return createWrap(func, WRAP_REARG_FLAG, undefined, undefined, undefined, indexes);
-    });
-
-    /**
-     * Creates a function that invokes `func` with the `this` binding of the
-     * created function and arguments from `start` and beyond provided as
-     * an array.
-     *
-     * **Note:** This method is based on the
-     * [rest parameter](https://mdn.io/rest_parameters).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Function
-     * @param {Function} func The function to apply a rest parameter to.
-     * @param {number} [start=func.length-1] The start position of the rest parameter.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var say = _.rest(function(what, names) {
-     *   return what + ' ' + _.initial(names).join(', ') +
-     *     (_.size(names) > 1 ? ', & ' : '') + _.last(names);
-     * });
-     *
-     * say('hello', 'fred', 'barney', 'pebbles');
-     * // => 'hello fred, barney, & pebbles'
-     */
-    function rest(func, start) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      start = start === undefined ? start : toInteger(start);
-      return baseRest(func, start);
-    }
-
-    /**
-     * Creates a function that invokes `func` with the `this` binding of the
-     * create function and an array of arguments much like
-     * [`Function#apply`](http://www.ecma-international.org/ecma-262/7.0/#sec-function.prototype.apply).
-     *
-     * **Note:** This method is based on the
-     * [spread operator](https://mdn.io/spread_operator).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.2.0
-     * @category Function
-     * @param {Function} func The function to spread arguments over.
-     * @param {number} [start=0] The start position of the spread.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var say = _.spread(function(who, what) {
-     *   return who + ' says ' + what;
-     * });
-     *
-     * say(['fred', 'hello']);
-     * // => 'fred says hello'
-     *
-     * var numbers = Promise.all([
-     *   Promise.resolve(40),
-     *   Promise.resolve(36)
-     * ]);
-     *
-     * numbers.then(_.spread(function(x, y) {
-     *   return x + y;
-     * }));
-     * // => a Promise of 76
-     */
-    function spread(func, start) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      start = start == null ? 0 : nativeMax(toInteger(start), 0);
-      return baseRest(function(args) {
-        var array = args[start],
-            otherArgs = castSlice(args, 0, start);
-
-        if (array) {
-          arrayPush(otherArgs, array);
-        }
-        return apply(func, this, otherArgs);
-      });
-    }
-
-    /**
-     * Creates a throttled function that only invokes `func` at most once per
-     * every `wait` milliseconds. The throttled function comes with a `cancel`
-     * method to cancel delayed `func` invocations and a `flush` method to
-     * immediately invoke them. Provide `options` to indicate whether `func`
-     * should be invoked on the leading and/or trailing edge of the `wait`
-     * timeout. The `func` is invoked with the last arguments provided to the
-     * throttled function. Subsequent calls to the throttled function return the
-     * result of the last `func` invocation.
-     *
-     * **Note:** If `leading` and `trailing` options are `true`, `func` is
-     * invoked on the trailing edge of the timeout only if the throttled function
-     * is invoked more than once during the `wait` timeout.
-     *
-     * If `wait` is `0` and `leading` is `false`, `func` invocation is deferred
-     * until to the next tick, similar to `setTimeout` with a timeout of `0`.
-     *
-     * See [David Corbacho's article](https://css-tricks.com/debouncing-throttling-explained-examples/)
-     * for details over the differences between `_.throttle` and `_.debounce`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to throttle.
-     * @param {number} [wait=0] The number of milliseconds to throttle invocations to.
-     * @param {Object} [options={}] The options object.
-     * @param {boolean} [options.leading=true]
-     *  Specify invoking on the leading edge of the timeout.
-     * @param {boolean} [options.trailing=true]
-     *  Specify invoking on the trailing edge of the timeout.
-     * @returns {Function} Returns the new throttled function.
-     * @example
-     *
-     * // Avoid excessively updating the position while scrolling.
-     * jQuery(window).on('scroll', _.throttle(updatePosition, 100));
-     *
-     * // Invoke `renewToken` when the click event is fired, but not more than once every 5 minutes.
-     * var throttled = _.throttle(renewToken, 300000, { 'trailing': false });
-     * jQuery(element).on('click', throttled);
-     *
-     * // Cancel the trailing throttled invocation.
-     * jQuery(window).on('popstate', throttled.cancel);
-     */
-    function throttle(func, wait, options) {
-      var leading = true,
-          trailing = true;
-
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      if (isObject(options)) {
-        leading = 'leading' in options ? !!options.leading : leading;
-        trailing = 'trailing' in options ? !!options.trailing : trailing;
-      }
-      return debounce(func, wait, {
-        'leading': leading,
-        'maxWait': wait,
-        'trailing': trailing
-      });
-    }
-
-    /**
-     * Creates a function that accepts up to one argument, ignoring any
-     * additional arguments.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Function
-     * @param {Function} func The function to cap arguments for.
-     * @returns {Function} Returns the new capped function.
-     * @example
-     *
-     * _.map(['6', '8', '10'], _.unary(parseInt));
-     * // => [6, 8, 10]
-     */
-    function unary(func) {
-      return ary(func, 1);
-    }
-
-    /**
-     * Creates a function that provides `value` to `wrapper` as its first
-     * argument. Any additional arguments provided to the function are appended
-     * to those provided to the `wrapper`. The wrapper is invoked with the `this`
-     * binding of the created function.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {*} value The value to wrap.
-     * @param {Function} [wrapper=identity] The wrapper function.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var p = _.wrap(_.escape, function(func, text) {
-     *   return '<p>' + func(text) + '</p>';
-     * });
-     *
-     * p('fred, barney, & pebbles');
-     * // => '<p>fred, barney, &amp; pebbles</p>'
-     */
-    function wrap(value, wrapper) {
-      return partial(castFunction(wrapper), value);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Casts `value` as an array if it's not one.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.4.0
-     * @category Lang
-     * @param {*} value The value to inspect.
-     * @returns {Array} Returns the cast array.
-     * @example
-     *
-     * _.castArray(1);
-     * // => [1]
-     *
-     * _.castArray({ 'a': 1 });
-     * // => [{ 'a': 1 }]
-     *
-     * _.castArray('abc');
-     * // => ['abc']
-     *
-     * _.castArray(null);
-     * // => [null]
-     *
-     * _.castArray(undefined);
-     * // => [undefined]
-     *
-     * _.castArray();
-     * // => []
-     *
-     * var array = [1, 2, 3];
-     * console.log(_.castArray(array) === array);
-     * // => true
-     */
-    function castArray() {
-      if (!arguments.length) {
-        return [];
-      }
-      var value = arguments[0];
-      return isArray(value) ? value : [value];
-    }
-
-    /**
-     * Creates a shallow clone of `value`.
-     *
-     * **Note:** This method is loosely based on the
-     * [structured clone algorithm](https://mdn.io/Structured_clone_algorithm)
-     * and supports cloning arrays, array buffers, booleans, date objects, maps,
-     * numbers, `Object` objects, regexes, sets, strings, symbols, and typed
-     * arrays. The own enumerable properties of `arguments` objects are cloned
-     * as plain objects. An empty object is returned for uncloneable values such
-     * as error objects, functions, DOM nodes, and WeakMaps.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to clone.
-     * @returns {*} Returns the cloned value.
-     * @see _.cloneDeep
-     * @example
-     *
-     * var objects = [{ 'a': 1 }, { 'b': 2 }];
-     *
-     * var shallow = _.clone(objects);
-     * console.log(shallow[0] === objects[0]);
-     * // => true
-     */
-    function clone(value) {
-      return baseClone(value, CLONE_SYMBOLS_FLAG);
-    }
-
-    /**
-     * This method is like `_.clone` except that it accepts `customizer` which
-     * is invoked to produce the cloned value. If `customizer` returns `undefined`,
-     * cloning is handled by the method instead. The `customizer` is invoked with
-     * up to four arguments; (value [, index|key, object, stack]).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to clone.
-     * @param {Function} [customizer] The function to customize cloning.
-     * @returns {*} Returns the cloned value.
-     * @see _.cloneDeepWith
-     * @example
-     *
-     * function customizer(value) {
-     *   if (_.isElement(value)) {
-     *     return value.cloneNode(false);
-     *   }
-     * }
-     *
-     * var el = _.cloneWith(document.body, customizer);
-     *
-     * console.log(el === document.body);
-     * // => false
-     * console.log(el.nodeName);
-     * // => 'BODY'
-     * console.log(el.childNodes.length);
-     * // => 0
-     */
-    function cloneWith(value, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return baseClone(value, CLONE_SYMBOLS_FLAG, customizer);
-    }
-
-    /**
-     * This method is like `_.clone` except that it recursively clones `value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.0.0
-     * @category Lang
-     * @param {*} value The value to recursively clone.
-     * @returns {*} Returns the deep cloned value.
-     * @see _.clone
-     * @example
-     *
-     * var objects = [{ 'a': 1 }, { 'b': 2 }];
-     *
-     * var deep = _.cloneDeep(objects);
-     * console.log(deep[0] === objects[0]);
-     * // => false
-     */
-    function cloneDeep(value) {
-      return baseClone(value, CLONE_DEEP_FLAG | CLONE_SYMBOLS_FLAG);
-    }
-
-    /**
-     * This method is like `_.cloneWith` except that it recursively clones `value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to recursively clone.
-     * @param {Function} [customizer] The function to customize cloning.
-     * @returns {*} Returns the deep cloned value.
-     * @see _.cloneWith
-     * @example
-     *
-     * function customizer(value) {
-     *   if (_.isElement(value)) {
-     *     return value.cloneNode(true);
-     *   }
-     * }
-     *
-     * var el = _.cloneDeepWith(document.body, customizer);
-     *
-     * console.log(el === document.body);
-     * // => false
-     * console.log(el.nodeName);
-     * // => 'BODY'
-     * console.log(el.childNodes.length);
-     * // => 20
-     */
-    function cloneDeepWith(value, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return baseClone(value, CLONE_DEEP_FLAG | CLONE_SYMBOLS_FLAG, customizer);
-    }
-
-    /**
-     * Checks if `object` conforms to `source` by invoking the predicate
-     * properties of `source` with the corresponding property values of `object`.
-     *
-     * **Note:** This method is equivalent to `_.conforms` when `source` is
-     * partially applied.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.14.0
-     * @category Lang
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {boolean} Returns `true` if `object` conforms, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2 };
-     *
-     * _.conformsTo(object, { 'b': function(n) { return n > 1; } });
-     * // => true
-     *
-     * _.conformsTo(object, { 'b': function(n) { return n > 2; } });
-     * // => false
-     */
-    function conformsTo(object, source) {
-      return source == null || baseConformsTo(object, source, keys(source));
-    }
-
-    /**
-     * Performs a
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * comparison between two values to determine if they are equivalent.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1 };
-     * var other = { 'a': 1 };
-     *
-     * _.eq(object, object);
-     * // => true
-     *
-     * _.eq(object, other);
-     * // => false
-     *
-     * _.eq('a', 'a');
-     * // => true
-     *
-     * _.eq('a', Object('a'));
-     * // => false
-     *
-     * _.eq(NaN, NaN);
-     * // => true
-     */
-    function eq(value, other) {
-      return value === other || (value !== value && other !== other);
-    }
-
-    /**
-     * Checks if `value` is greater than `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is greater than `other`,
-     *  else `false`.
-     * @see _.lt
-     * @example
-     *
-     * _.gt(3, 1);
-     * // => true
-     *
-     * _.gt(3, 3);
-     * // => false
-     *
-     * _.gt(1, 3);
-     * // => false
-     */
-    var gt = createRelationalOperation(baseGt);
-
-    /**
-     * Checks if `value` is greater than or equal to `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is greater than or equal to
-     *  `other`, else `false`.
-     * @see _.lte
-     * @example
-     *
-     * _.gte(3, 1);
-     * // => true
-     *
-     * _.gte(3, 3);
-     * // => true
-     *
-     * _.gte(1, 3);
-     * // => false
-     */
-    var gte = createRelationalOperation(function(value, other) {
-      return value >= other;
-    });
-
-    /**
-     * Checks if `value` is likely an `arguments` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an `arguments` object,
-     *  else `false`.
-     * @example
-     *
-     * _.isArguments(function() { return arguments; }());
-     * // => true
-     *
-     * _.isArguments([1, 2, 3]);
-     * // => false
-     */
-    var isArguments = baseIsArguments(function() { return arguments; }()) ? baseIsArguments : function(value) {
-      return isObjectLike(value) && hasOwnProperty.call(value, 'callee') &&
-        !propertyIsEnumerable.call(value, 'callee');
-    };
-
-    /**
-     * Checks if `value` is classified as an `Array` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array, else `false`.
-     * @example
-     *
-     * _.isArray([1, 2, 3]);
-     * // => true
-     *
-     * _.isArray(document.body.children);
-     * // => false
-     *
-     * _.isArray('abc');
-     * // => false
-     *
-     * _.isArray(_.noop);
-     * // => false
-     */
-    var isArray = Array.isArray;
-
-    /**
-     * Checks if `value` is classified as an `ArrayBuffer` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array buffer, else `false`.
-     * @example
-     *
-     * _.isArrayBuffer(new ArrayBuffer(2));
-     * // => true
-     *
-     * _.isArrayBuffer(new Array(2));
-     * // => false
-     */
-    var isArrayBuffer = nodeIsArrayBuffer ? baseUnary(nodeIsArrayBuffer) : baseIsArrayBuffer;
-
-    /**
-     * Checks if `value` is array-like. A value is considered array-like if it's
-     * not a function and has a `value.length` that's an integer greater than or
-     * equal to `0` and less than or equal to `Number.MAX_SAFE_INTEGER`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is array-like, else `false`.
-     * @example
-     *
-     * _.isArrayLike([1, 2, 3]);
-     * // => true
-     *
-     * _.isArrayLike(document.body.children);
-     * // => true
-     *
-     * _.isArrayLike('abc');
-     * // => true
-     *
-     * _.isArrayLike(_.noop);
-     * // => false
-     */
-    function isArrayLike(value) {
-      return value != null && isLength(value.length) && !isFunction(value);
-    }
-
-    /**
-     * This method is like `_.isArrayLike` except that it also checks if `value`
-     * is an object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array-like object,
-     *  else `false`.
-     * @example
-     *
-     * _.isArrayLikeObject([1, 2, 3]);
-     * // => true
-     *
-     * _.isArrayLikeObject(document.body.children);
-     * // => true
-     *
-     * _.isArrayLikeObject('abc');
-     * // => false
-     *
-     * _.isArrayLikeObject(_.noop);
-     * // => false
-     */
-    function isArrayLikeObject(value) {
-      return isObjectLike(value) && isArrayLike(value);
-    }
-
-    /**
-     * Checks if `value` is classified as a boolean primitive or object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a boolean, else `false`.
-     * @example
-     *
-     * _.isBoolean(false);
-     * // => true
-     *
-     * _.isBoolean(null);
-     * // => false
-     */
-    function isBoolean(value) {
-      return value === true || value === false ||
-        (isObjectLike(value) && baseGetTag(value) == boolTag);
-    }
-
-    /**
-     * Checks if `value` is a buffer.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a buffer, else `false`.
-     * @example
-     *
-     * _.isBuffer(new Buffer(2));
-     * // => true
-     *
-     * _.isBuffer(new Uint8Array(2));
-     * // => false
-     */
-    var isBuffer = nativeIsBuffer || stubFalse;
-
-    /**
-     * Checks if `value` is classified as a `Date` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a date object, else `false`.
-     * @example
-     *
-     * _.isDate(new Date);
-     * // => true
-     *
-     * _.isDate('Mon April 23 2012');
-     * // => false
-     */
-    var isDate = nodeIsDate ? baseUnary(nodeIsDate) : baseIsDate;
-
-    /**
-     * Checks if `value` is likely a DOM element.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a DOM element, else `false`.
-     * @example
-     *
-     * _.isElement(document.body);
-     * // => true
-     *
-     * _.isElement('<body>');
-     * // => false
-     */
-    function isElement(value) {
-      return isObjectLike(value) && value.nodeType === 1 && !isPlainObject(value);
-    }
-
-    /**
-     * Checks if `value` is an empty object, collection, map, or set.
-     *
-     * Objects are considered empty if they have no own enumerable string keyed
-     * properties.
-     *
-     * Array-like values such as `arguments` objects, arrays, buffers, strings, or
-     * jQuery-like collections are considered empty if they have a `length` of `0`.
-     * Similarly, maps and sets are considered empty if they have a `size` of `0`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is empty, else `false`.
-     * @example
-     *
-     * _.isEmpty(null);
-     * // => true
-     *
-     * _.isEmpty(true);
-     * // => true
-     *
-     * _.isEmpty(1);
-     * // => true
-     *
-     * _.isEmpty([1, 2, 3]);
-     * // => false
-     *
-     * _.isEmpty({ 'a': 1 });
-     * // => false
-     */
-    function isEmpty(value) {
-      if (value == null) {
-        return true;
-      }
-      if (isArrayLike(value) &&
-          (isArray(value) || typeof value == 'string' || typeof value.splice == 'function' ||
-            isBuffer(value) || isTypedArray(value) || isArguments(value))) {
-        return !value.length;
-      }
-      var tag = getTag(value);
-      if (tag == mapTag || tag == setTag) {
-        return !value.size;
-      }
-      if (isPrototype(value)) {
-        return !baseKeys(value).length;
-      }
-      for (var key in value) {
-        if (hasOwnProperty.call(value, key)) {
-          return false;
-        }
-      }
-      return true;
-    }
-
-    /**
-     * Performs a deep comparison between two values to determine if they are
-     * equivalent.
-     *
-     * **Note:** This method supports comparing arrays, array buffers, booleans,
-     * date objects, error objects, maps, numbers, `Object` objects, regexes,
-     * sets, strings, symbols, and typed arrays. `Object` objects are compared
-     * by their own, not inherited, enumerable properties. Functions and DOM
-     * nodes are compared by strict equality, i.e. `===`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1 };
-     * var other = { 'a': 1 };
-     *
-     * _.isEqual(object, other);
-     * // => true
-     *
-     * object === other;
-     * // => false
-     */
-    function isEqual(value, other) {
-      return baseIsEqual(value, other);
-    }
-
-    /**
-     * This method is like `_.isEqual` except that it accepts `customizer` which
-     * is invoked to compare values. If `customizer` returns `undefined`, comparisons
-     * are handled by the method instead. The `customizer` is invoked with up to
-     * six arguments: (objValue, othValue [, index|key, object, other, stack]).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     * @example
-     *
-     * function isGreeting(value) {
-     *   return /^h(?:i|ello)$/.test(value);
-     * }
-     *
-     * function customizer(objValue, othValue) {
-     *   if (isGreeting(objValue) && isGreeting(othValue)) {
-     *     return true;
-     *   }
-     * }
-     *
-     * var array = ['hello', 'goodbye'];
-     * var other = ['hi', 'goodbye'];
-     *
-     * _.isEqualWith(array, other, customizer);
-     * // => true
-     */
-    function isEqualWith(value, other, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      var result = customizer ? customizer(value, other) : undefined;
-      return result === undefined ? baseIsEqual(value, other, undefined, customizer) : !!result;
-    }
-
-    /**
-     * Checks if `value` is an `Error`, `EvalError`, `RangeError`, `ReferenceError`,
-     * `SyntaxError`, `TypeError`, or `URIError` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an error object, else `false`.
-     * @example
-     *
-     * _.isError(new Error);
-     * // => true
-     *
-     * _.isError(Error);
-     * // => false
-     */
-    function isError(value) {
-      if (!isObjectLike(value)) {
-        return false;
-      }
-      var tag = baseGetTag(value);
-      return tag == errorTag || tag == domExcTag ||
-        (typeof value.message == 'string' && typeof value.name == 'string' && !isPlainObject(value));
-    }
-
-    /**
-     * Checks if `value` is a finite primitive number.
-     *
-     * **Note:** This method is based on
-     * [`Number.isFinite`](https://mdn.io/Number/isFinite).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a finite number, else `false`.
-     * @example
-     *
-     * _.isFinite(3);
-     * // => true
-     *
-     * _.isFinite(Number.MIN_VALUE);
-     * // => true
-     *
-     * _.isFinite(Infinity);
-     * // => false
-     *
-     * _.isFinite('3');
-     * // => false
-     */
-    function isFinite(value) {
-      return typeof value == 'number' && nativeIsFinite(value);
-    }
-
-    /**
-     * Checks if `value` is classified as a `Function` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a function, else `false`.
-     * @example
-     *
-     * _.isFunction(_);
-     * // => true
-     *
-     * _.isFunction(/abc/);
-     * // => false
-     */
-    function isFunction(value) {
-      if (!isObject(value)) {
-        return false;
-      }
-      // The use of `Object#toString` avoids issues with the `typeof` operator
-      // in Safari 9 which returns 'object' for typed arrays and other constructors.
-      var tag = baseGetTag(value);
-      return tag == funcTag || tag == genTag || tag == asyncTag || tag == proxyTag;
-    }
-
-    /**
-     * Checks if `value` is an integer.
-     *
-     * **Note:** This method is based on
-     * [`Number.isInteger`](https://mdn.io/Number/isInteger).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an integer, else `false`.
-     * @example
-     *
-     * _.isInteger(3);
-     * // => true
-     *
-     * _.isInteger(Number.MIN_VALUE);
-     * // => false
-     *
-     * _.isInteger(Infinity);
-     * // => false
-     *
-     * _.isInteger('3');
-     * // => false
-     */
-    function isInteger(value) {
-      return typeof value == 'number' && value == toInteger(value);
-    }
-
-    /**
-     * Checks if `value` is a valid array-like length.
-     *
-     * **Note:** This method is loosely based on
-     * [`ToLength`](http://ecma-international.org/ecma-262/7.0/#sec-tolength).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a valid length, else `false`.
-     * @example
-     *
-     * _.isLength(3);
-     * // => true
-     *
-     * _.isLength(Number.MIN_VALUE);
-     * // => false
-     *
-     * _.isLength(Infinity);
-     * // => false
-     *
-     * _.isLength('3');
-     * // => false
-     */
-    function isLength(value) {
-      return typeof value == 'number' &&
-        value > -1 && value % 1 == 0 && value <= MAX_SAFE_INTEGER;
-    }
-
-    /**
-     * Checks if `value` is the
-     * [language type](http://www.ecma-international.org/ecma-262/7.0/#sec-ecmascript-language-types)
-     * of `Object`. (e.g. arrays, functions, objects, regexes, `new Number(0)`, and `new String('')`)
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an object, else `false`.
-     * @example
-     *
-     * _.isObject({});
-     * // => true
-     *
-     * _.isObject([1, 2, 3]);
-     * // => true
-     *
-     * _.isObject(_.noop);
-     * // => true
-     *
-     * _.isObject(null);
-     * // => false
-     */
-    function isObject(value) {
-      var type = typeof value;
-      return value != null && (type == 'object' || type == 'function');
-    }
-
-    /**
-     * Checks if `value` is object-like. A value is object-like if it's not `null`
-     * and has a `typeof` result of "object".
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is object-like, else `false`.
-     * @example
-     *
-     * _.isObjectLike({});
-     * // => true
-     *
-     * _.isObjectLike([1, 2, 3]);
-     * // => true
-     *
-     * _.isObjectLike(_.noop);
-     * // => false
-     *
-     * _.isObjectLike(null);
-     * // => false
-     */
-    function isObjectLike(value) {
-      return value != null && typeof value == 'object';
-    }
-
-    /**
-     * Checks if `value` is classified as a `Map` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a map, else `false`.
-     * @example
-     *
-     * _.isMap(new Map);
-     * // => true
-     *
-     * _.isMap(new WeakMap);
-     * // => false
-     */
-    var isMap = nodeIsMap ? baseUnary(nodeIsMap) : baseIsMap;
-
-    /**
-     * Performs a partial deep comparison between `object` and `source` to
-     * determine if `object` contains equivalent property values.
-     *
-     * **Note:** This method is equivalent to `_.matches` when `source` is
-     * partially applied.
-     *
-     * Partial comparisons will match empty array and empty object `source`
-     * values against any array or object value, respectively. See `_.isEqual`
-     * for a list of supported value comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property values to match.
-     * @returns {boolean} Returns `true` if `object` is a match, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2 };
-     *
-     * _.isMatch(object, { 'b': 2 });
-     * // => true
-     *
-     * _.isMatch(object, { 'b': 1 });
-     * // => false
-     */
-    function isMatch(object, source) {
-      return object === source || baseIsMatch(object, source, getMatchData(source));
-    }
-
-    /**
-     * This method is like `_.isMatch` except that it accepts `customizer` which
-     * is invoked to compare values. If `customizer` returns `undefined`, comparisons
-     * are handled by the method instead. The `customizer` is invoked with five
-     * arguments: (objValue, srcValue, index|key, object, source).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property values to match.
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @returns {boolean} Returns `true` if `object` is a match, else `false`.
-     * @example
-     *
-     * function isGreeting(value) {
-     *   return /^h(?:i|ello)$/.test(value);
-     * }
-     *
-     * function customizer(objValue, srcValue) {
-     *   if (isGreeting(objValue) && isGreeting(srcValue)) {
-     *     return true;
-     *   }
-     * }
-     *
-     * var object = { 'greeting': 'hello' };
-     * var source = { 'greeting': 'hi' };
-     *
-     * _.isMatchWith(object, source, customizer);
-     * // => true
-     */
-    function isMatchWith(object, source, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return baseIsMatch(object, source, getMatchData(source), customizer);
-    }
-
-    /**
-     * Checks if `value` is `NaN`.
-     *
-     * **Note:** This method is based on
-     * [`Number.isNaN`](https://mdn.io/Number/isNaN) and is not the same as
-     * global [`isNaN`](https://mdn.io/isNaN) which returns `true` for
-     * `undefined` and other non-number values.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is `NaN`, else `false`.
-     * @example
-     *
-     * _.isNaN(NaN);
-     * // => true
-     *
-     * _.isNaN(new Number(NaN));
-     * // => true
-     *
-     * isNaN(undefined);
-     * // => true
-     *
-     * _.isNaN(undefined);
-     * // => false
-     */
-    function isNaN(value) {
-      // An `NaN` primitive is the only value that is not equal to itself.
-      // Perform the `toStringTag` check first to avoid errors with some
-      // ActiveX objects in IE.
-      return isNumber(value) && value != +value;
-    }
-
-    /**
-     * Checks if `value` is a pristine native function.
-     *
-     * **Note:** This method can't reliably detect native functions in the presence
-     * of the core-js package because core-js circumvents this kind of detection.
-     * Despite multiple requests, the core-js maintainer has made it clear: any
-     * attempt to fix the detection will be obstructed. As a result, we're left
-     * with little choice but to throw an error. Unfortunately, this also affects
-     * packages, like [babel-polyfill](https://www.npmjs.com/package/babel-polyfill),
-     * which rely on core-js.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a native function,
-     *  else `false`.
-     * @example
-     *
-     * _.isNative(Array.prototype.push);
-     * // => true
-     *
-     * _.isNative(_);
-     * // => false
-     */
-    function isNative(value) {
-      if (isMaskable(value)) {
-        throw new Error(CORE_ERROR_TEXT);
-      }
-      return baseIsNative(value);
-    }
-
-    /**
-     * Checks if `value` is `null`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is `null`, else `false`.
-     * @example
-     *
-     * _.isNull(null);
-     * // => true
-     *
-     * _.isNull(void 0);
-     * // => false
-     */
-    function isNull(value) {
-      return value === null;
-    }
-
-    /**
-     * Checks if `value` is `null` or `undefined`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is nullish, else `false`.
-     * @example
-     *
-     * _.isNil(null);
-     * // => true
-     *
-     * _.isNil(void 0);
-     * // => true
-     *
-     * _.isNil(NaN);
-     * // => false
-     */
-    function isNil(value) {
-      return value == null;
-    }
-
-    /**
-     * Checks if `value` is classified as a `Number` primitive or object.
-     *
-     * **Note:** To exclude `Infinity`, `-Infinity`, and `NaN`, which are
-     * classified as numbers, use the `_.isFinite` method.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a number, else `false`.
-     * @example
-     *
-     * _.isNumber(3);
-     * // => true
-     *
-     * _.isNumber(Number.MIN_VALUE);
-     * // => true
-     *
-     * _.isNumber(Infinity);
-     * // => true
-     *
-     * _.isNumber('3');
-     * // => false
-     */
-    function isNumber(value) {
-      return typeof value == 'number' ||
-        (isObjectLike(value) && baseGetTag(value) == numberTag);
-    }
-
-    /**
-     * Checks if `value` is a plain object, that is, an object created by the
-     * `Object` constructor or one with a `[[Prototype]]` of `null`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.8.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a plain object, else `false`.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     * }
-     *
-     * _.isPlainObject(new Foo);
-     * // => false
-     *
-     * _.isPlainObject([1, 2, 3]);
-     * // => false
-     *
-     * _.isPlainObject({ 'x': 0, 'y': 0 });
-     * // => true
-     *
-     * _.isPlainObject(Object.create(null));
-     * // => true
-     */
-    function isPlainObject(value) {
-      if (!isObjectLike(value) || baseGetTag(value) != objectTag) {
-        return false;
-      }
-      var proto = getPrototype(value);
-      if (proto === null) {
-        return true;
-      }
-      var Ctor = hasOwnProperty.call(proto, 'constructor') && proto.constructor;
-      return typeof Ctor == 'function' && Ctor instanceof Ctor &&
-        funcToString.call(Ctor) == objectCtorString;
-    }
-
-    /**
-     * Checks if `value` is classified as a `RegExp` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a regexp, else `false`.
-     * @example
-     *
-     * _.isRegExp(/abc/);
-     * // => true
-     *
-     * _.isRegExp('/abc/');
-     * // => false
-     */
-    var isRegExp = nodeIsRegExp ? baseUnary(nodeIsRegExp) : baseIsRegExp;
-
-    /**
-     * Checks if `value` is a safe integer. An integer is safe if it's an IEEE-754
-     * double precision number which isn't the result of a rounded unsafe integer.
-     *
-     * **Note:** This method is based on
-     * [`Number.isSafeInteger`](https://mdn.io/Number/isSafeInteger).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a safe integer, else `false`.
-     * @example
-     *
-     * _.isSafeInteger(3);
-     * // => true
-     *
-     * _.isSafeInteger(Number.MIN_VALUE);
-     * // => false
-     *
-     * _.isSafeInteger(Infinity);
-     * // => false
-     *
-     * _.isSafeInteger('3');
-     * // => false
-     */
-    function isSafeInteger(value) {
-      return isInteger(value) && value >= -MAX_SAFE_INTEGER && value <= MAX_SAFE_INTEGER;
-    }
-
-    /**
-     * Checks if `value` is classified as a `Set` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a set, else `false`.
-     * @example
-     *
-     * _.isSet(new Set);
-     * // => true
-     *
-     * _.isSet(new WeakSet);
-     * // => false
-     */
-    var isSet = nodeIsSet ? baseUnary(nodeIsSet) : baseIsSet;
-
-    /**
-     * Checks if `value` is classified as a `String` primitive or object.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a string, else `false`.
-     * @example
-     *
-     * _.isString('abc');
-     * // => true
-     *
-     * _.isString(1);
-     * // => false
-     */
-    function isString(value) {
-      return typeof value == 'string' ||
-        (!isArray(value) && isObjectLike(value) && baseGetTag(value) == stringTag);
-    }
-
-    /**
-     * Checks if `value` is classified as a `Symbol` primitive or object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a symbol, else `false`.
-     * @example
-     *
-     * _.isSymbol(Symbol.iterator);
-     * // => true
-     *
-     * _.isSymbol('abc');
-     * // => false
-     */
-    function isSymbol(value) {
-      return typeof value == 'symbol' ||
-        (isObjectLike(value) && baseGetTag(value) == symbolTag);
-    }
-
-    /**
-     * Checks if `value` is classified as a typed array.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a typed array, else `false`.
-     * @example
-     *
-     * _.isTypedArray(new Uint8Array);
-     * // => true
-     *
-     * _.isTypedArray([]);
-     * // => false
-     */
-    var isTypedArray = nodeIsTypedArray ? baseUnary(nodeIsTypedArray) : baseIsTypedArray;
-
-    /**
-     * Checks if `value` is `undefined`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is `undefined`, else `false`.
-     * @example
-     *
-     * _.isUndefined(void 0);
-     * // => true
-     *
-     * _.isUndefined(null);
-     * // => false
-     */
-    function isUndefined(value) {
-      return value === undefined;
-    }
-
-    /**
-     * Checks if `value` is classified as a `WeakMap` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a weak map, else `false`.
-     * @example
-     *
-     * _.isWeakMap(new WeakMap);
-     * // => true
-     *
-     * _.isWeakMap(new Map);
-     * // => false
-     */
-    function isWeakMap(value) {
-      return isObjectLike(value) && getTag(value) == weakMapTag;
-    }
-
-    /**
-     * Checks if `value` is classified as a `WeakSet` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a weak set, else `false`.
-     * @example
-     *
-     * _.isWeakSet(new WeakSet);
-     * // => true
-     *
-     * _.isWeakSet(new Set);
-     * // => false
-     */
-    function isWeakSet(value) {
-      return isObjectLike(value) && baseGetTag(value) == weakSetTag;
-    }
-
-    /**
-     * Checks if `value` is less than `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is less than `other`,
-     *  else `false`.
-     * @see _.gt
-     * @example
-     *
-     * _.lt(1, 3);
-     * // => true
-     *
-     * _.lt(3, 3);
-     * // => false
-     *
-     * _.lt(3, 1);
-     * // => false
-     */
-    var lt = createRelationalOperation(baseLt);
-
-    /**
-     * Checks if `value` is less than or equal to `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is less than or equal to
-     *  `other`, else `false`.
-     * @see _.gte
-     * @example
-     *
-     * _.lte(1, 3);
-     * // => true
-     *
-     * _.lte(3, 3);
-     * // => true
-     *
-     * _.lte(3, 1);
-     * // => false
-     */
-    var lte = createRelationalOperation(function(value, other) {
-      return value <= other;
-    });
-
-    /**
-     * Converts `value` to an array.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {Array} Returns the converted array.
-     * @example
-     *
-     * _.toArray({ 'a': 1, 'b': 2 });
-     * // => [1, 2]
-     *
-     * _.toArray('abc');
-     * // => ['a', 'b', 'c']
-     *
-     * _.toArray(1);
-     * // => []
-     *
-     * _.toArray(null);
-     * // => []
-     */
-    function toArray(value) {
-      if (!value) {
-        return [];
-      }
-      if (isArrayLike(value)) {
-        return isString(value) ? stringToArray(value) : copyArray(value);
-      }
-      if (symIterator && value[symIterator]) {
-        return iteratorToArray(value[symIterator]());
-      }
-      var tag = getTag(value),
-          func = tag == mapTag ? mapToArray : (tag == setTag ? setToArray : values);
-
-      return func(value);
-    }
-
-    /**
-     * Converts `value` to a finite number.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.12.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted number.
-     * @example
-     *
-     * _.toFinite(3.2);
-     * // => 3.2
-     *
-     * _.toFinite(Number.MIN_VALUE);
-     * // => 5e-324
-     *
-     * _.toFinite(Infinity);
-     * // => 1.7976931348623157e+308
-     *
-     * _.toFinite('3.2');
-     * // => 3.2
-     */
-    function toFinite(value) {
-      if (!value) {
-        return value === 0 ? value : 0;
-      }
-      value = toNumber(value);
-      if (value === INFINITY || value === -INFINITY) {
-        var sign = (value < 0 ? -1 : 1);
-        return sign * MAX_INTEGER;
-      }
-      return value === value ? value : 0;
-    }
-
-    /**
-     * Converts `value` to an integer.
-     *
-     * **Note:** This method is loosely based on
-     * [`ToInteger`](http://www.ecma-international.org/ecma-262/7.0/#sec-tointeger).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.toInteger(3.2);
-     * // => 3
-     *
-     * _.toInteger(Number.MIN_VALUE);
-     * // => 0
-     *
-     * _.toInteger(Infinity);
-     * // => 1.7976931348623157e+308
-     *
-     * _.toInteger('3.2');
-     * // => 3
-     */
-    function toInteger(value) {
-      var result = toFinite(value),
-          remainder = result % 1;
-
-      return result === result ? (remainder ? result - remainder : result) : 0;
-    }
-
-    /**
-     * Converts `value` to an integer suitable for use as the length of an
-     * array-like object.
-     *
-     * **Note:** This method is based on
-     * [`ToLength`](http://ecma-international.org/ecma-262/7.0/#sec-tolength).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.toLength(3.2);
-     * // => 3
-     *
-     * _.toLength(Number.MIN_VALUE);
-     * // => 0
-     *
-     * _.toLength(Infinity);
-     * // => 4294967295
-     *
-     * _.toLength('3.2');
-     * // => 3
-     */
-    function toLength(value) {
-      return value ? baseClamp(toInteger(value), 0, MAX_ARRAY_LENGTH) : 0;
-    }
-
-    /**
-     * Converts `value` to a number.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to process.
-     * @returns {number} Returns the number.
-     * @example
-     *
-     * _.toNumber(3.2);
-     * // => 3.2
-     *
-     * _.toNumber(Number.MIN_VALUE);
-     * // => 5e-324
-     *
-     * _.toNumber(Infinity);
-     * // => Infinity
-     *
-     * _.toNumber('3.2');
-     * // => 3.2
-     */
-    function toNumber(value) {
-      if (typeof value == 'number') {
-        return value;
-      }
-      if (isSymbol(value)) {
-        return NAN;
-      }
-      if (isObject(value)) {
-        var other = typeof value.valueOf == 'function' ? value.valueOf() : value;
-        value = isObject(other) ? (other + '') : other;
-      }
-      if (typeof value != 'string') {
-        return value === 0 ? value : +value;
-      }
-      value = value.replace(reTrim, '');
-      var isBinary = reIsBinary.test(value);
-      return (isBinary || reIsOctal.test(value))
-        ? freeParseInt(value.slice(2), isBinary ? 2 : 8)
-        : (reIsBadHex.test(value) ? NAN : +value);
-    }
-
-    /**
-     * Converts `value` to a plain object flattening inherited enumerable string
-     * keyed properties of `value` to own properties of the plain object.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {Object} Returns the converted plain object.
-     * @example
-     *
-     * function Foo() {
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.assign({ 'a': 1 }, new Foo);
-     * // => { 'a': 1, 'b': 2 }
-     *
-     * _.assign({ 'a': 1 }, _.toPlainObject(new Foo));
-     * // => { 'a': 1, 'b': 2, 'c': 3 }
-     */
-    function toPlainObject(value) {
-      return copyObject(value, keysIn(value));
-    }
-
-    /**
-     * Converts `value` to a safe integer. A safe integer can be compared and
-     * represented correctly.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.toSafeInteger(3.2);
-     * // => 3
-     *
-     * _.toSafeInteger(Number.MIN_VALUE);
-     * // => 0
-     *
-     * _.toSafeInteger(Infinity);
-     * // => 9007199254740991
-     *
-     * _.toSafeInteger('3.2');
-     * // => 3
-     */
-    function toSafeInteger(value) {
-      return value
-        ? baseClamp(toInteger(value), -MAX_SAFE_INTEGER, MAX_SAFE_INTEGER)
-        : (value === 0 ? value : 0);
-    }
-
-    /**
-     * Converts `value` to a string. An empty string is returned for `null`
-     * and `undefined` values. The sign of `-0` is preserved.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {string} Returns the converted string.
-     * @example
-     *
-     * _.toString(null);
-     * // => ''
-     *
-     * _.toString(-0);
-     * // => '-0'
-     *
-     * _.toString([1, 2, 3]);
-     * // => '1,2,3'
-     */
-    function toString(value) {
-      return value == null ? '' : baseToString(value);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Assigns own enumerable string keyed properties of source objects to the
-     * destination object. Source objects are applied from left to right.
-     * Subsequent sources overwrite property assignments of previous sources.
-     *
-     * **Note:** This method mutates `object` and is loosely based on
-     * [`Object.assign`](https://mdn.io/Object/assign).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.10.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.assignIn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     * }
-     *
-     * function Bar() {
-     *   this.c = 3;
-     * }
-     *
-     * Foo.prototype.b = 2;
-     * Bar.prototype.d = 4;
-     *
-     * _.assign({ 'a': 0 }, new Foo, new Bar);
-     * // => { 'a': 1, 'c': 3 }
-     */
-    var assign = createAssigner(function(object, source) {
-      if (isPrototype(source) || isArrayLike(source)) {
-        copyObject(source, keys(source), object);
-        return;
-      }
-      for (var key in source) {
-        if (hasOwnProperty.call(source, key)) {
-          assignValue(object, key, source[key]);
-        }
-      }
-    });
-
-    /**
-     * This method is like `_.assign` except that it iterates over own and
-     * inherited source properties.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias extend
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.assign
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     * }
-     *
-     * function Bar() {
-     *   this.c = 3;
-     * }
-     *
-     * Foo.prototype.b = 2;
-     * Bar.prototype.d = 4;
-     *
-     * _.assignIn({ 'a': 0 }, new Foo, new Bar);
-     * // => { 'a': 1, 'b': 2, 'c': 3, 'd': 4 }
-     */
-    var assignIn = createAssigner(function(object, source) {
-      copyObject(source, keysIn(source), object);
-    });
-
-    /**
-     * This method is like `_.assignIn` except that it accepts `customizer`
-     * which is invoked to produce the assigned values. If `customizer` returns
-     * `undefined`, assignment is handled by the method instead. The `customizer`
-     * is invoked with five arguments: (objValue, srcValue, key, object, source).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias extendWith
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} sources The source objects.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @see _.assignWith
-     * @example
-     *
-     * function customizer(objValue, srcValue) {
-     *   return _.isUndefined(objValue) ? srcValue : objValue;
-     * }
-     *
-     * var defaults = _.partialRight(_.assignInWith, customizer);
-     *
-     * defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 });
-     * // => { 'a': 1, 'b': 2 }
-     */
-    var assignInWith = createAssigner(function(object, source, srcIndex, customizer) {
-      copyObject(source, keysIn(source), object, customizer);
-    });
-
-    /**
-     * This method is like `_.assign` except that it accepts `customizer`
-     * which is invoked to produce the assigned values. If `customizer` returns
-     * `undefined`, assignment is handled by the method instead. The `customizer`
-     * is invoked with five arguments: (objValue, srcValue, key, object, source).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} sources The source objects.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @see _.assignInWith
-     * @example
-     *
-     * function customizer(objValue, srcValue) {
-     *   return _.isUndefined(objValue) ? srcValue : objValue;
-     * }
-     *
-     * var defaults = _.partialRight(_.assignWith, customizer);
-     *
-     * defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 });
-     * // => { 'a': 1, 'b': 2 }
-     */
-    var assignWith = createAssigner(function(object, source, srcIndex, customizer) {
-      copyObject(source, keys(source), object, customizer);
-    });
-
-    /**
-     * Creates an array of values corresponding to `paths` of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.0.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {...(string|string[])} [paths] The property paths to pick.
-     * @returns {Array} Returns the picked values.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }, 4] };
-     *
-     * _.at(object, ['a[0].b.c', 'a[1]']);
-     * // => [3, 4]
-     */
-    var at = flatRest(baseAt);
-
-    /**
-     * Creates an object that inherits from the `prototype` object. If a
-     * `properties` object is given, its own enumerable string keyed properties
-     * are assigned to the created object.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.3.0
-     * @category Object
-     * @param {Object} prototype The object to inherit from.
-     * @param {Object} [properties] The properties to assign to the object.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * function Shape() {
-     *   this.x = 0;
-     *   this.y = 0;
-     * }
-     *
-     * function Circle() {
-     *   Shape.call(this);
-     * }
-     *
-     * Circle.prototype = _.create(Shape.prototype, {
-     *   'constructor': Circle
-     * });
-     *
-     * var circle = new Circle;
-     * circle instanceof Circle;
-     * // => true
-     *
-     * circle instanceof Shape;
-     * // => true
-     */
-    function create(prototype, properties) {
-      var result = baseCreate(prototype);
-      return properties == null ? result : baseAssign(result, properties);
-    }
-
-    /**
-     * Assigns own and inherited enumerable string keyed properties of source
-     * objects to the destination object for all destination properties that
-     * resolve to `undefined`. Source objects are applied from left to right.
-     * Once a property is set, additional values of the same property are ignored.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.defaultsDeep
-     * @example
-     *
-     * _.defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 });
-     * // => { 'a': 1, 'b': 2 }
-     */
-    var defaults = baseRest(function(object, sources) {
-      object = Object(object);
-
-      var index = -1;
-      var length = sources.length;
-      var guard = length > 2 ? sources[2] : undefined;
-
-      if (guard && isIterateeCall(sources[0], sources[1], guard)) {
-        length = 1;
-      }
-
-      while (++index < length) {
-        var source = sources[index];
-        var props = keysIn(source);
-        var propsIndex = -1;
-        var propsLength = props.length;
-
-        while (++propsIndex < propsLength) {
-          var key = props[propsIndex];
-          var value = object[key];
-
-          if (value === undefined ||
-              (eq(value, objectProto[key]) && !hasOwnProperty.call(object, key))) {
-            object[key] = source[key];
-          }
-        }
-      }
-
-      return object;
-    });
-
-    /**
-     * This method is like `_.defaults` except that it recursively assigns
-     * default properties.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.defaults
-     * @example
-     *
-     * _.defaultsDeep({ 'a': { 'b': 2 } }, { 'a': { 'b': 1, 'c': 3 } });
-     * // => { 'a': { 'b': 2, 'c': 3 } }
-     */
-    var defaultsDeep = baseRest(function(args) {
-      args.push(undefined, customDefaultsMerge);
-      return apply(mergeWith, undefined, args);
-    });
-
-    /**
-     * This method is like `_.find` except that it returns the key of the first
-     * element `predicate` returns truthy for instead of the element itself.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.1.0
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {string|undefined} Returns the key of the matched element,
-     *  else `undefined`.
-     * @example
-     *
-     * var users = {
-     *   'barney':  { 'age': 36, 'active': true },
-     *   'fred':    { 'age': 40, 'active': false },
-     *   'pebbles': { 'age': 1,  'active': true }
-     * };
-     *
-     * _.findKey(users, function(o) { return o.age < 40; });
-     * // => 'barney' (iteration order is not guaranteed)
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findKey(users, { 'age': 1, 'active': true });
-     * // => 'pebbles'
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findKey(users, ['active', false]);
-     * // => 'fred'
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findKey(users, 'active');
-     * // => 'barney'
-     */
-    function findKey(object, predicate) {
-      return baseFindKey(object, getIteratee(predicate, 3), baseForOwn);
-    }
-
-    /**
-     * This method is like `_.findKey` except that it iterates over elements of
-     * a collection in the opposite order.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {string|undefined} Returns the key of the matched element,
-     *  else `undefined`.
-     * @example
-     *
-     * var users = {
-     *   'barney':  { 'age': 36, 'active': true },
-     *   'fred':    { 'age': 40, 'active': false },
-     *   'pebbles': { 'age': 1,  'active': true }
-     * };
-     *
-     * _.findLastKey(users, function(o) { return o.age < 40; });
-     * // => returns 'pebbles' assuming `_.findKey` returns 'barney'
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findLastKey(users, { 'age': 36, 'active': true });
-     * // => 'barney'
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findLastKey(users, ['active', false]);
-     * // => 'fred'
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findLastKey(users, 'active');
-     * // => 'pebbles'
-     */
-    function findLastKey(object, predicate) {
-      return baseFindKey(object, getIteratee(predicate, 3), baseForOwnRight);
-    }
-
-    /**
-     * Iterates over own and inherited enumerable string keyed properties of an
-     * object and invokes `iteratee` for each property. The iteratee is invoked
-     * with three arguments: (value, key, object). Iteratee functions may exit
-     * iteration early by explicitly returning `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.3.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forInRight
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forIn(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'a', 'b', then 'c' (iteration order is not guaranteed).
-     */
-    function forIn(object, iteratee) {
-      return object == null
-        ? object
-        : baseFor(object, getIteratee(iteratee, 3), keysIn);
-    }
-
-    /**
-     * This method is like `_.forIn` except that it iterates over properties of
-     * `object` in the opposite order.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forIn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forInRight(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'c', 'b', then 'a' assuming `_.forIn` logs 'a', 'b', then 'c'.
-     */
-    function forInRight(object, iteratee) {
-      return object == null
-        ? object
-        : baseForRight(object, getIteratee(iteratee, 3), keysIn);
-    }
-
-    /**
-     * Iterates over own enumerable string keyed properties of an object and
-     * invokes `iteratee` for each property. The iteratee is invoked with three
-     * arguments: (value, key, object). Iteratee functions may exit iteration
-     * early by explicitly returning `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.3.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forOwnRight
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forOwn(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'a' then 'b' (iteration order is not guaranteed).
-     */
-    function forOwn(object, iteratee) {
-      return object && baseForOwn(object, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * This method is like `_.forOwn` except that it iterates over properties of
-     * `object` in the opposite order.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forOwn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forOwnRight(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'b' then 'a' assuming `_.forOwn` logs 'a' then 'b'.
-     */
-    function forOwnRight(object, iteratee) {
-      return object && baseForOwnRight(object, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * Creates an array of function property names from own enumerable properties
-     * of `object`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @returns {Array} Returns the function names.
-     * @see _.functionsIn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = _.constant('a');
-     *   this.b = _.constant('b');
-     * }
-     *
-     * Foo.prototype.c = _.constant('c');
-     *
-     * _.functions(new Foo);
-     * // => ['a', 'b']
-     */
-    function functions(object) {
-      return object == null ? [] : baseFunctions(object, keys(object));
-    }
-
-    /**
-     * Creates an array of function property names from own and inherited
-     * enumerable properties of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @returns {Array} Returns the function names.
-     * @see _.functions
-     * @example
-     *
-     * function Foo() {
-     *   this.a = _.constant('a');
-     *   this.b = _.constant('b');
-     * }
-     *
-     * Foo.prototype.c = _.constant('c');
-     *
-     * _.functionsIn(new Foo);
-     * // => ['a', 'b', 'c']
-     */
-    function functionsIn(object) {
-      return object == null ? [] : baseFunctions(object, keysIn(object));
-    }
-
-    /**
-     * Gets the value at `path` of `object`. If the resolved value is
-     * `undefined`, the `defaultValue` is returned in its place.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the property to get.
-     * @param {*} [defaultValue] The value returned for `undefined` resolved values.
-     * @returns {*} Returns the resolved value.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }] };
-     *
-     * _.get(object, 'a[0].b.c');
-     * // => 3
-     *
-     * _.get(object, ['a', '0', 'b', 'c']);
-     * // => 3
-     *
-     * _.get(object, 'a.b.c', 'default');
-     * // => 'default'
-     */
-    function get(object, path, defaultValue) {
-      var result = object == null ? undefined : baseGet(object, path);
-      return result === undefined ? defaultValue : result;
-    }
-
-    /**
-     * Checks if `path` is a direct property of `object`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path to check.
-     * @returns {boolean} Returns `true` if `path` exists, else `false`.
-     * @example
-     *
-     * var object = { 'a': { 'b': 2 } };
-     * var other = _.create({ 'a': _.create({ 'b': 2 }) });
-     *
-     * _.has(object, 'a');
-     * // => true
-     *
-     * _.has(object, 'a.b');
-     * // => true
-     *
-     * _.has(object, ['a', 'b']);
-     * // => true
-     *
-     * _.has(other, 'a');
-     * // => false
-     */
-    function has(object, path) {
-      return object != null && hasPath(object, path, baseHas);
-    }
-
-    /**
-     * Checks if `path` is a direct or inherited property of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path to check.
-     * @returns {boolean} Returns `true` if `path` exists, else `false`.
-     * @example
-     *
-     * var object = _.create({ 'a': _.create({ 'b': 2 }) });
-     *
-     * _.hasIn(object, 'a');
-     * // => true
-     *
-     * _.hasIn(object, 'a.b');
-     * // => true
-     *
-     * _.hasIn(object, ['a', 'b']);
-     * // => true
-     *
-     * _.hasIn(object, 'b');
-     * // => false
-     */
-    function hasIn(object, path) {
-      return object != null && hasPath(object, path, baseHasIn);
-    }
-
-    /**
-     * Creates an object composed of the inverted keys and values of `object`.
-     * If `object` contains duplicate values, subsequent values overwrite
-     * property assignments of previous values.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.7.0
-     * @category Object
-     * @param {Object} object The object to invert.
-     * @returns {Object} Returns the new inverted object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2, 'c': 1 };
-     *
-     * _.invert(object);
-     * // => { '1': 'c', '2': 'b' }
-     */
-    var invert = createInverter(function(result, value, key) {
-      if (value != null &&
-          typeof value.toString != 'function') {
-        value = nativeObjectToString.call(value);
-      }
-
-      result[value] = key;
-    }, constant(identity));
-
-    /**
-     * This method is like `_.invert` except that the inverted object is generated
-     * from the results of running each element of `object` thru `iteratee`. The
-     * corresponding inverted value of each inverted key is an array of keys
-     * responsible for generating the inverted value. The iteratee is invoked
-     * with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.1.0
-     * @category Object
-     * @param {Object} object The object to invert.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Object} Returns the new inverted object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2, 'c': 1 };
-     *
-     * _.invertBy(object);
-     * // => { '1': ['a', 'c'], '2': ['b'] }
-     *
-     * _.invertBy(object, function(value) {
-     *   return 'group' + value;
-     * });
-     * // => { 'group1': ['a', 'c'], 'group2': ['b'] }
-     */
-    var invertBy = createInverter(function(result, value, key) {
-      if (value != null &&
-          typeof value.toString != 'function') {
-        value = nativeObjectToString.call(value);
-      }
-
-      if (hasOwnProperty.call(result, value)) {
-        result[value].push(key);
-      } else {
-        result[value] = [key];
-      }
-    }, getIteratee);
-
-    /**
-     * Invokes the method at `path` of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the method to invoke.
-     * @param {...*} [args] The arguments to invoke the method with.
-     * @returns {*} Returns the result of the invoked method.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': [1, 2, 3, 4] } }] };
-     *
-     * _.invoke(object, 'a[0].b.c.slice', 1, 3);
-     * // => [2, 3]
-     */
-    var invoke = baseRest(baseInvoke);
-
-    /**
-     * Creates an array of the own enumerable property names of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects. See the
-     * [ES spec](http://ecma-international.org/ecma-262/7.0/#sec-object.keys)
-     * for more details.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.keys(new Foo);
-     * // => ['a', 'b'] (iteration order is not guaranteed)
-     *
-     * _.keys('hi');
-     * // => ['0', '1']
-     */
-    function keys(object) {
-      return isArrayLike(object) ? arrayLikeKeys(object) : baseKeys(object);
-    }
-
-    /**
-     * Creates an array of the own and inherited enumerable property names of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.keysIn(new Foo);
-     * // => ['a', 'b', 'c'] (iteration order is not guaranteed)
-     */
-    function keysIn(object) {
-      return isArrayLike(object) ? arrayLikeKeys(object, true) : baseKeysIn(object);
-    }
-
-    /**
-     * The opposite of `_.mapValues`; this method creates an object with the
-     * same values as `object` and keys generated by running each own enumerable
-     * string keyed property of `object` thru `iteratee`. The iteratee is invoked
-     * with three arguments: (value, key, object).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.8.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns the new mapped object.
-     * @see _.mapValues
-     * @example
-     *
-     * _.mapKeys({ 'a': 1, 'b': 2 }, function(value, key) {
-     *   return key + value;
-     * });
-     * // => { 'a1': 1, 'b2': 2 }
-     */
-    function mapKeys(object, iteratee) {
-      var result = {};
-      iteratee = getIteratee(iteratee, 3);
-
-      baseForOwn(object, function(value, key, object) {
-        baseAssignValue(result, iteratee(value, key, object), value);
-      });
-      return result;
-    }
-
-    /**
-     * Creates an object with the same keys as `object` and values generated
-     * by running each own enumerable string keyed property of `object` thru
-     * `iteratee`. The iteratee is invoked with three arguments:
-     * (value, key, object).
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns the new mapped object.
-     * @see _.mapKeys
-     * @example
-     *
-     * var users = {
-     *   'fred':    { 'user': 'fred',    'age': 40 },
-     *   'pebbles': { 'user': 'pebbles', 'age': 1 }
-     * };
-     *
-     * _.mapValues(users, function(o) { return o.age; });
-     * // => { 'fred': 40, 'pebbles': 1 } (iteration order is not guaranteed)
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.mapValues(users, 'age');
-     * // => { 'fred': 40, 'pebbles': 1 } (iteration order is not guaranteed)
-     */
-    function mapValues(object, iteratee) {
-      var result = {};
-      iteratee = getIteratee(iteratee, 3);
-
-      baseForOwn(object, function(value, key, object) {
-        baseAssignValue(result, key, iteratee(value, key, object));
-      });
-      return result;
-    }
-
-    /**
-     * This method is like `_.assign` except that it recursively merges own and
-     * inherited enumerable string keyed properties of source objects into the
-     * destination object. Source properties that resolve to `undefined` are
-     * skipped if a destination value exists. Array and plain object properties
-     * are merged recursively. Other objects and value types are overridden by
-     * assignment. Source objects are applied from left to right. Subsequent
-     * sources overwrite property assignments of previous sources.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.5.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = {
-     *   'a': [{ 'b': 2 }, { 'd': 4 }]
-     * };
-     *
-     * var other = {
-     *   'a': [{ 'c': 3 }, { 'e': 5 }]
-     * };
-     *
-     * _.merge(object, other);
-     * // => { 'a': [{ 'b': 2, 'c': 3 }, { 'd': 4, 'e': 5 }] }
-     */
-    var merge = createAssigner(function(object, source, srcIndex) {
-      baseMerge(object, source, srcIndex);
-    });
-
-    /**
-     * This method is like `_.merge` except that it accepts `customizer` which
-     * is invoked to produce the merged values of the destination and source
-     * properties. If `customizer` returns `undefined`, merging is handled by the
-     * method instead. The `customizer` is invoked with six arguments:
-     * (objValue, srcValue, key, object, source, stack).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} sources The source objects.
-     * @param {Function} customizer The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * function customizer(objValue, srcValue) {
-     *   if (_.isArray(objValue)) {
-     *     return objValue.concat(srcValue);
-     *   }
-     * }
-     *
-     * var object = { 'a': [1], 'b': [2] };
-     * var other = { 'a': [3], 'b': [4] };
-     *
-     * _.mergeWith(object, other, customizer);
-     * // => { 'a': [1, 3], 'b': [2, 4] }
-     */
-    var mergeWith = createAssigner(function(object, source, srcIndex, customizer) {
-      baseMerge(object, source, srcIndex, customizer);
-    });
-
-    /**
-     * The opposite of `_.pick`; this method creates an object composed of the
-     * own and inherited enumerable property paths of `object` that are not omitted.
-     *
-     * **Note:** This method is considerably slower than `_.pick`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {...(string|string[])} [paths] The property paths to omit.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.omit(object, ['a', 'c']);
-     * // => { 'b': '2' }
-     */
-    var omit = flatRest(function(object, paths) {
-      var result = {};
-      if (object == null) {
-        return result;
-      }
-      var isDeep = false;
-      paths = arrayMap(paths, function(path) {
-        path = castPath(path, object);
-        isDeep || (isDeep = path.length > 1);
-        return path;
-      });
-      copyObject(object, getAllKeysIn(object), result);
-      if (isDeep) {
-        result = baseClone(result, CLONE_DEEP_FLAG | CLONE_FLAT_FLAG | CLONE_SYMBOLS_FLAG, customOmitClone);
-      }
-      var length = paths.length;
-      while (length--) {
-        baseUnset(result, paths[length]);
-      }
-      return result;
-    });
-
-    /**
-     * The opposite of `_.pickBy`; this method creates an object composed of
-     * the own and inherited enumerable string keyed properties of `object` that
-     * `predicate` doesn't return truthy for. The predicate is invoked with two
-     * arguments: (value, key).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {Function} [predicate=_.identity] The function invoked per property.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.omitBy(object, _.isNumber);
-     * // => { 'b': '2' }
-     */
-    function omitBy(object, predicate) {
-      return pickBy(object, negate(getIteratee(predicate)));
-    }
-
-    /**
-     * Creates an object composed of the picked `object` properties.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {...(string|string[])} [paths] The property paths to pick.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.pick(object, ['a', 'c']);
-     * // => { 'a': 1, 'c': 3 }
-     */
-    var pick = flatRest(function(object, paths) {
-      return object == null ? {} : basePick(object, paths);
-    });
-
-    /**
-     * Creates an object composed of the `object` properties `predicate` returns
-     * truthy for. The predicate is invoked with two arguments: (value, key).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {Function} [predicate=_.identity] The function invoked per property.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.pickBy(object, _.isNumber);
-     * // => { 'a': 1, 'c': 3 }
-     */
-    function pickBy(object, predicate) {
-      if (object == null) {
-        return {};
-      }
-      var props = arrayMap(getAllKeysIn(object), function(prop) {
-        return [prop];
-      });
-      predicate = getIteratee(predicate);
-      return basePickBy(object, props, function(value, path) {
-        return predicate(value, path[0]);
-      });
-    }
-
-    /**
-     * This method is like `_.get` except that if the resolved value is a
-     * function it's invoked with the `this` binding of its parent object and
-     * its result is returned.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the property to resolve.
-     * @param {*} [defaultValue] The value returned for `undefined` resolved values.
-     * @returns {*} Returns the resolved value.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c1': 3, 'c2': _.constant(4) } }] };
-     *
-     * _.result(object, 'a[0].b.c1');
-     * // => 3
-     *
-     * _.result(object, 'a[0].b.c2');
-     * // => 4
-     *
-     * _.result(object, 'a[0].b.c3', 'default');
-     * // => 'default'
-     *
-     * _.result(object, 'a[0].b.c3', _.constant('default'));
-     * // => 'default'
-     */
-    function result(object, path, defaultValue) {
-      path = castPath(path, object);
-
-      var index = -1,
-          length = path.length;
-
-      // Ensure the loop is entered when path is empty.
-      if (!length) {
-        length = 1;
-        object = undefined;
-      }
-      while (++index < length) {
-        var value = object == null ? undefined : object[toKey(path[index])];
-        if (value === undefined) {
-          index = length;
-          value = defaultValue;
-        }
-        object = isFunction(value) ? value.call(object) : value;
-      }
-      return object;
-    }
-
-    /**
-     * Sets the value at `path` of `object`. If a portion of `path` doesn't exist,
-     * it's created. Arrays are created for missing index properties while objects
-     * are created for all other missing properties. Use `_.setWith` to customize
-     * `path` creation.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }] };
-     *
-     * _.set(object, 'a[0].b.c', 4);
-     * console.log(object.a[0].b.c);
-     * // => 4
-     *
-     * _.set(object, ['x', '0', 'y', 'z'], 5);
-     * console.log(object.x[0].y.z);
-     * // => 5
-     */
-    function set(object, path, value) {
-      return object == null ? object : baseSet(object, path, value);
-    }
-
-    /**
-     * This method is like `_.set` except that it accepts `customizer` which is
-     * invoked to produce the objects of `path`.  If `customizer` returns `undefined`
-     * path creation is handled by the method instead. The `customizer` is invoked
-     * with three arguments: (nsValue, key, nsObject).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {*} value The value to set.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = {};
-     *
-     * _.setWith(object, '[0][1]', 'a', Object);
-     * // => { '0': { '1': 'a' } }
-     */
-    function setWith(object, path, value, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return object == null ? object : baseSet(object, path, value, customizer);
-    }
-
-    /**
-     * Creates an array of own enumerable string keyed-value pairs for `object`
-     * which can be consumed by `_.fromPairs`. If `object` is a map or set, its
-     * entries are returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias entries
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the key-value pairs.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.toPairs(new Foo);
-     * // => [['a', 1], ['b', 2]] (iteration order is not guaranteed)
-     */
-    var toPairs = createToPairs(keys);
-
-    /**
-     * Creates an array of own and inherited enumerable string keyed-value pairs
-     * for `object` which can be consumed by `_.fromPairs`. If `object` is a map
-     * or set, its entries are returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias entriesIn
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the key-value pairs.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.toPairsIn(new Foo);
-     * // => [['a', 1], ['b', 2], ['c', 3]] (iteration order is not guaranteed)
-     */
-    var toPairsIn = createToPairs(keysIn);
-
-    /**
-     * An alternative to `_.reduce`; this method transforms `object` to a new
-     * `accumulator` object which is the result of running each of its own
-     * enumerable string keyed properties thru `iteratee`, with each invocation
-     * potentially mutating the `accumulator` object. If `accumulator` is not
-     * provided, a new object with the same `[[Prototype]]` will be used. The
-     * iteratee is invoked with four arguments: (accumulator, value, key, object).
-     * Iteratee functions may exit iteration early by explicitly returning `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.3.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {*} [accumulator] The custom accumulator value.
-     * @returns {*} Returns the accumulated value.
-     * @example
-     *
-     * _.transform([2, 3, 4], function(result, n) {
-     *   result.push(n *= n);
-     *   return n % 2 == 0;
-     * }, []);
-     * // => [4, 9]
-     *
-     * _.transform({ 'a': 1, 'b': 2, 'c': 1 }, function(result, value, key) {
-     *   (result[value] || (result[value] = [])).push(key);
-     * }, {});
-     * // => { '1': ['a', 'c'], '2': ['b'] }
-     */
-    function transform(object, iteratee, accumulator) {
-      var isArr = isArray(object),
-          isArrLike = isArr || isBuffer(object) || isTypedArray(object);
-
-      iteratee = getIteratee(iteratee, 4);
-      if (accumulator == null) {
-        var Ctor = object && object.constructor;
-        if (isArrLike) {
-          accumulator = isArr ? new Ctor : [];
-        }
-        else if (isObject(object)) {
-          accumulator = isFunction(Ctor) ? baseCreate(getPrototype(object)) : {};
-        }
-        else {
-          accumulator = {};
-        }
-      }
-      (isArrLike ? arrayEach : baseForOwn)(object, function(value, index, object) {
-        return iteratee(accumulator, value, index, object);
-      });
-      return accumulator;
-    }
-
-    /**
-     * Removes the property at `path` of `object`.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to unset.
-     * @returns {boolean} Returns `true` if the property is deleted, else `false`.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 7 } }] };
-     * _.unset(object, 'a[0].b.c');
-     * // => true
-     *
-     * console.log(object);
-     * // => { 'a': [{ 'b': {} }] };
-     *
-     * _.unset(object, ['a', '0', 'b', 'c']);
-     * // => true
-     *
-     * console.log(object);
-     * // => { 'a': [{ 'b': {} }] };
-     */
-    function unset(object, path) {
-      return object == null ? true : baseUnset(object, path);
-    }
-
-    /**
-     * This method is like `_.set` except that accepts `updater` to produce the
-     * value to set. Use `_.updateWith` to customize `path` creation. The `updater`
-     * is invoked with one argument: (value).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.6.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {Function} updater The function to produce the updated value.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }] };
-     *
-     * _.update(object, 'a[0].b.c', function(n) { return n * n; });
-     * console.log(object.a[0].b.c);
-     * // => 9
-     *
-     * _.update(object, 'x[0].y.z', function(n) { return n ? n + 1 : 0; });
-     * console.log(object.x[0].y.z);
-     * // => 0
-     */
-    function update(object, path, updater) {
-      return object == null ? object : baseUpdate(object, path, castFunction(updater));
-    }
-
-    /**
-     * This method is like `_.update` except that it accepts `customizer` which is
-     * invoked to produce the objects of `path`.  If `customizer` returns `undefined`
-     * path creation is handled by the method instead. The `customizer` is invoked
-     * with three arguments: (nsValue, key, nsObject).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.6.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {Function} updater The function to produce the updated value.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = {};
-     *
-     * _.updateWith(object, '[0][1]', _.constant('a'), Object);
-     * // => { '0': { '1': 'a' } }
-     */
-    function updateWith(object, path, updater, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return object == null ? object : baseUpdate(object, path, castFunction(updater), customizer);
-    }
-
-    /**
-     * Creates an array of the own enumerable string keyed property values of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property values.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.values(new Foo);
-     * // => [1, 2] (iteration order is not guaranteed)
-     *
-     * _.values('hi');
-     * // => ['h', 'i']
-     */
-    function values(object) {
-      return object == null ? [] : baseValues(object, keys(object));
-    }
-
-    /**
-     * Creates an array of the own and inherited enumerable string keyed property
-     * values of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property values.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.valuesIn(new Foo);
-     * // => [1, 2, 3] (iteration order is not guaranteed)
-     */
-    function valuesIn(object) {
-      return object == null ? [] : baseValues(object, keysIn(object));
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Clamps `number` within the inclusive `lower` and `upper` bounds.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Number
-     * @param {number} number The number to clamp.
-     * @param {number} [lower] The lower bound.
-     * @param {number} upper The upper bound.
-     * @returns {number} Returns the clamped number.
-     * @example
-     *
-     * _.clamp(-10, -5, 5);
-     * // => -5
-     *
-     * _.clamp(10, -5, 5);
-     * // => 5
-     */
-    function clamp(number, lower, upper) {
-      if (upper === undefined) {
-        upper = lower;
-        lower = undefined;
-      }
-      if (upper !== undefined) {
-        upper = toNumber(upper);
-        upper = upper === upper ? upper : 0;
-      }
-      if (lower !== undefined) {
-        lower = toNumber(lower);
-        lower = lower === lower ? lower : 0;
-      }
-      return baseClamp(toNumber(number), lower, upper);
-    }
-
-    /**
-     * Checks if `n` is between `start` and up to, but not including, `end`. If
-     * `end` is not specified, it's set to `start` with `start` then set to `0`.
-     * If `start` is greater than `end` the params are swapped to support
-     * negative ranges.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.3.0
-     * @category Number
-     * @param {number} number The number to check.
-     * @param {number} [start=0] The start of the range.
-     * @param {number} end The end of the range.
-     * @returns {boolean} Returns `true` if `number` is in the range, else `false`.
-     * @see _.range, _.rangeRight
-     * @example
-     *
-     * _.inRange(3, 2, 4);
-     * // => true
-     *
-     * _.inRange(4, 8);
-     * // => true
-     *
-     * _.inRange(4, 2);
-     * // => false
-     *
-     * _.inRange(2, 2);
-     * // => false
-     *
-     * _.inRange(1.2, 2);
-     * // => true
-     *
-     * _.inRange(5.2, 4);
-     * // => false
-     *
-     * _.inRange(-3, -2, -6);
-     * // => true
-     */
-    function inRange(number, start, end) {
-      start = toFinite(start);
-      if (end === undefined) {
-        end = start;
-        start = 0;
-      } else {
-        end = toFinite(end);
-      }
-      number = toNumber(number);
-      return baseInRange(number, start, end);
-    }
-
-    /**
-     * Produces a random number between the inclusive `lower` and `upper` bounds.
-     * If only one argument is provided a number between `0` and the given number
-     * is returned. If `floating` is `true`, or either `lower` or `upper` are
-     * floats, a floating-point number is returned instead of an integer.
-     *
-     * **Note:** JavaScript follows the IEEE-754 standard for resolving
-     * floating-point values which can produce unexpected results.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.7.0
-     * @category Number
-     * @param {number} [lower=0] The lower bound.
-     * @param {number} [upper=1] The upper bound.
-     * @param {boolean} [floating] Specify returning a floating-point number.
-     * @returns {number} Returns the random number.
-     * @example
-     *
-     * _.random(0, 5);
-     * // => an integer between 0 and 5
-     *
-     * _.random(5);
-     * // => also an integer between 0 and 5
-     *
-     * _.random(5, true);
-     * // => a floating-point number between 0 and 5
-     *
-     * _.random(1.2, 5.2);
-     * // => a floating-point number between 1.2 and 5.2
-     */
-    function random(lower, upper, floating) {
-      if (floating && typeof floating != 'boolean' && isIterateeCall(lower, upper, floating)) {
-        upper = floating = undefined;
-      }
-      if (floating === undefined) {
-        if (typeof upper == 'boolean') {
-          floating = upper;
-          upper = undefined;
-        }
-        else if (typeof lower == 'boolean') {
-          floating = lower;
-          lower = undefined;
-        }
-      }
-      if (lower === undefined && upper === undefined) {
-        lower = 0;
-        upper = 1;
-      }
-      else {
-        lower = toFinite(lower);
-        if (upper === undefined) {
-          upper = lower;
-          lower = 0;
-        } else {
-          upper = toFinite(upper);
-        }
-      }
-      if (lower > upper) {
-        var temp = lower;
-        lower = upper;
-        upper = temp;
-      }
-      if (floating || lower % 1 || upper % 1) {
-        var rand = nativeRandom();
-        return nativeMin(lower + (rand * (upper - lower + freeParseFloat('1e-' + ((rand + '').length - 1)))), upper);
-      }
-      return baseRandom(lower, upper);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Converts `string` to [camel case](https://en.wikipedia.org/wiki/CamelCase).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the camel cased string.
-     * @example
-     *
-     * _.camelCase('Foo Bar');
-     * // => 'fooBar'
-     *
-     * _.camelCase('--foo-bar--');
-     * // => 'fooBar'
-     *
-     * _.camelCase('__FOO_BAR__');
-     * // => 'fooBar'
-     */
-    var camelCase = createCompounder(function(result, word, index) {
-      word = word.toLowerCase();
-      return result + (index ? capitalize(word) : word);
-    });
-
-    /**
-     * Converts the first character of `string` to upper case and the remaining
-     * to lower case.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to capitalize.
-     * @returns {string} Returns the capitalized string.
-     * @example
-     *
-     * _.capitalize('FRED');
-     * // => 'Fred'
-     */
-    function capitalize(string) {
-      return upperFirst(toString(string).toLowerCase());
-    }
-
-    /**
-     * Deburrs `string` by converting
-     * [Latin-1 Supplement](https://en.wikipedia.org/wiki/Latin-1_Supplement_(Unicode_block)#Character_table)
-     * and [Latin Extended-A](https://en.wikipedia.org/wiki/Latin_Extended-A)
-     * letters to basic Latin letters and removing
-     * [combining diacritical marks](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to deburr.
-     * @returns {string} Returns the deburred string.
-     * @example
-     *
-     * _.deburr('déjà vu');
-     * // => 'deja vu'
-     */
-    function deburr(string) {
-      string = toString(string);
-      return string && string.replace(reLatin, deburrLetter).replace(reComboMark, '');
-    }
-
-    /**
-     * Checks if `string` ends with the given target string.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to inspect.
-     * @param {string} [target] The string to search for.
-     * @param {number} [position=string.length] The position to search up to.
-     * @returns {boolean} Returns `true` if `string` ends with `target`,
-     *  else `false`.
-     * @example
-     *
-     * _.endsWith('abc', 'c');
-     * // => true
-     *
-     * _.endsWith('abc', 'b');
-     * // => false
-     *
-     * _.endsWith('abc', 'b', 2);
-     * // => true
-     */
-    function endsWith(string, target, position) {
-      string = toString(string);
-      target = baseToString(target);
-
-      var length = string.length;
-      position = position === undefined
-        ? length
-        : baseClamp(toInteger(position), 0, length);
-
-      var end = position;
-      position -= target.length;
-      return position >= 0 && string.slice(position, end) == target;
-    }
-
-    /**
-     * Converts the characters "&", "<", ">", '"', and "'" in `string` to their
-     * corresponding HTML entities.
-     *
-     * **Note:** No other characters are escaped. To escape additional
-     * characters use a third-party library like [_he_](https://mths.be/he).
-     *
-     * Though the ">" character is escaped for symmetry, characters like
-     * ">" and "/" don't need escaping in HTML and have no special meaning
-     * unless they're part of a tag or unquoted attribute value. See
-     * [Mathias Bynens's article](https://mathiasbynens.be/notes/ambiguous-ampersands)
-     * (under "semi-related fun fact") for more details.
-     *
-     * When working with HTML you should always
-     * [quote attribute values](http://wonko.com/post/html-escaping) to reduce
-     * XSS vectors.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category String
-     * @param {string} [string=''] The string to escape.
-     * @returns {string} Returns the escaped string.
-     * @example
-     *
-     * _.escape('fred, barney, & pebbles');
-     * // => 'fred, barney, &amp; pebbles'
-     */
-    function escape(string) {
-      string = toString(string);
-      return (string && reHasUnescapedHtml.test(string))
-        ? string.replace(reUnescapedHtml, escapeHtmlChar)
-        : string;
-    }
-
-    /**
-     * Escapes the `RegExp` special characters "^", "$", "\", ".", "*", "+",
-     * "?", "(", ")", "[", "]", "{", "}", and "|" in `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to escape.
-     * @returns {string} Returns the escaped string.
-     * @example
-     *
-     * _.escapeRegExp('[lodash](https://lodash.com/)');
-     * // => '\[lodash\]\(https://lodash\.com/\)'
-     */
-    function escapeRegExp(string) {
-      string = toString(string);
-      return (string && reHasRegExpChar.test(string))
-        ? string.replace(reRegExpChar, '\\$&')
-        : string;
-    }
-
-    /**
-     * Converts `string` to
-     * [kebab case](https://en.wikipedia.org/wiki/Letter_case#Special_case_styles).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the kebab cased string.
-     * @example
-     *
-     * _.kebabCase('Foo Bar');
-     * // => 'foo-bar'
-     *
-     * _.kebabCase('fooBar');
-     * // => 'foo-bar'
-     *
-     * _.kebabCase('__FOO_BAR__');
-     * // => 'foo-bar'
-     */
-    var kebabCase = createCompounder(function(result, word, index) {
-      return result + (index ? '-' : '') + word.toLowerCase();
-    });
-
-    /**
-     * Converts `string`, as space separated words, to lower case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the lower cased string.
-     * @example
-     *
-     * _.lowerCase('--Foo-Bar--');
-     * // => 'foo bar'
-     *
-     * _.lowerCase('fooBar');
-     * // => 'foo bar'
-     *
-     * _.lowerCase('__FOO_BAR__');
-     * // => 'foo bar'
-     */
-    var lowerCase = createCompounder(function(result, word, index) {
-      return result + (index ? ' ' : '') + word.toLowerCase();
-    });
-
-    /**
-     * Converts the first character of `string` to lower case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the converted string.
-     * @example
-     *
-     * _.lowerFirst('Fred');
-     * // => 'fred'
-     *
-     * _.lowerFirst('FRED');
-     * // => 'fRED'
-     */
-    var lowerFirst = createCaseFirst('toLowerCase');
-
-    /**
-     * Pads `string` on the left and right sides if it's shorter than `length`.
-     * Padding characters are truncated if they can't be evenly divided by `length`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to pad.
-     * @param {number} [length=0] The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padded string.
-     * @example
-     *
-     * _.pad('abc', 8);
-     * // => '  abc   '
-     *
-     * _.pad('abc', 8, '_-');
-     * // => '_-abc_-_'
-     *
-     * _.pad('abc', 3);
-     * // => 'abc'
-     */
-    function pad(string, length, chars) {
-      string = toString(string);
-      length = toInteger(length);
-
-      var strLength = length ? stringSize(string) : 0;
-      if (!length || strLength >= length) {
-        return string;
-      }
-      var mid = (length - strLength) / 2;
-      return (
-        createPadding(nativeFloor(mid), chars) +
-        string +
-        createPadding(nativeCeil(mid), chars)
-      );
-    }
-
-    /**
-     * Pads `string` on the right side if it's shorter than `length`. Padding
-     * characters are truncated if they exceed `length`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to pad.
-     * @param {number} [length=0] The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padded string.
-     * @example
-     *
-     * _.padEnd('abc', 6);
-     * // => 'abc   '
-     *
-     * _.padEnd('abc', 6, '_-');
-     * // => 'abc_-_'
-     *
-     * _.padEnd('abc', 3);
-     * // => 'abc'
-     */
-    function padEnd(string, length, chars) {
-      string = toString(string);
-      length = toInteger(length);
-
-      var strLength = length ? stringSize(string) : 0;
-      return (length && strLength < length)
-        ? (string + createPadding(length - strLength, chars))
-        : string;
-    }
-
-    /**
-     * Pads `string` on the left side if it's shorter than `length`. Padding
-     * characters are truncated if they exceed `length`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to pad.
-     * @param {number} [length=0] The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padded string.
-     * @example
-     *
-     * _.padStart('abc', 6);
-     * // => '   abc'
-     *
-     * _.padStart('abc', 6, '_-');
-     * // => '_-_abc'
-     *
-     * _.padStart('abc', 3);
-     * // => 'abc'
-     */
-    function padStart(string, length, chars) {
-      string = toString(string);
-      length = toInteger(length);
-
-      var strLength = length ? stringSize(string) : 0;
-      return (length && strLength < length)
-        ? (createPadding(length - strLength, chars) + string)
-        : string;
-    }
-
-    /**
-     * Converts `string` to an integer of the specified radix. If `radix` is
-     * `undefined` or `0`, a `radix` of `10` is used unless `value` is a
-     * hexadecimal, in which case a `radix` of `16` is used.
-     *
-     * **Note:** This method aligns with the
-     * [ES5 implementation](https://es5.github.io/#x15.1.2.2) of `parseInt`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.1.0
-     * @category String
-     * @param {string} string The string to convert.
-     * @param {number} [radix=10] The radix to interpret `value` by.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.parseInt('08');
-     * // => 8
-     *
-     * _.map(['6', '08', '10'], _.parseInt);
-     * // => [6, 8, 10]
-     */
-    function parseInt(string, radix, guard) {
-      if (guard || radix == null) {
-        radix = 0;
-      } else if (radix) {
-        radix = +radix;
-      }
-      return nativeParseInt(toString(string).replace(reTrimStart, ''), radix || 0);
-    }
-
-    /**
-     * Repeats the given string `n` times.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to repeat.
-     * @param {number} [n=1] The number of times to repeat the string.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the repeated string.
-     * @example
-     *
-     * _.repeat('*', 3);
-     * // => '***'
-     *
-     * _.repeat('abc', 2);
-     * // => 'abcabc'
-     *
-     * _.repeat('abc', 0);
-     * // => ''
-     */
-    function repeat(string, n, guard) {
-      if ((guard ? isIterateeCall(string, n, guard) : n === undefined)) {
-        n = 1;
-      } else {
-        n = toInteger(n);
-      }
-      return baseRepeat(toString(string), n);
-    }
-
-    /**
-     * Replaces matches for `pattern` in `string` with `replacement`.
-     *
-     * **Note:** This method is based on
-     * [`String#replace`](https://mdn.io/String/replace).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to modify.
-     * @param {RegExp|string} pattern The pattern to replace.
-     * @param {Function|string} replacement The match replacement.
-     * @returns {string} Returns the modified string.
-     * @example
-     *
-     * _.replace('Hi Fred', 'Fred', 'Barney');
-     * // => 'Hi Barney'
-     */
-    function replace() {
-      var args = arguments,
-          string = toString(args[0]);
-
-      return args.length < 3 ? string : string.replace(args[1], args[2]);
-    }
-
-    /**
-     * Converts `string` to
-     * [snake case](https://en.wikipedia.org/wiki/Snake_case).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the snake cased string.
-     * @example
-     *
-     * _.snakeCase('Foo Bar');
-     * // => 'foo_bar'
-     *
-     * _.snakeCase('fooBar');
-     * // => 'foo_bar'
-     *
-     * _.snakeCase('--FOO-BAR--');
-     * // => 'foo_bar'
-     */
-    var snakeCase = createCompounder(function(result, word, index) {
-      return result + (index ? '_' : '') + word.toLowerCase();
-    });
-
-    /**
-     * Splits `string` by `separator`.
-     *
-     * **Note:** This method is based on
-     * [`String#split`](https://mdn.io/String/split).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to split.
-     * @param {RegExp|string} separator The separator pattern to split by.
-     * @param {number} [limit] The length to truncate results to.
-     * @returns {Array} Returns the string segments.
-     * @example
-     *
-     * _.split('a-b-c', '-', 2);
-     * // => ['a', 'b']
-     */
-    function split(string, separator, limit) {
-      if (limit && typeof limit != 'number' && isIterateeCall(string, separator, limit)) {
-        separator = limit = undefined;
-      }
-      limit = limit === undefined ? MAX_ARRAY_LENGTH : limit >>> 0;
-      if (!limit) {
-        return [];
-      }
-      string = toString(string);
-      if (string && (
-            typeof separator == 'string' ||
-            (separator != null && !isRegExp(separator))
-          )) {
-        separator = baseToString(separator);
-        if (!separator && hasUnicode(string)) {
-          return castSlice(stringToArray(string), 0, limit);
-        }
-      }
-      return string.split(separator, limit);
-    }
-
-    /**
-     * Converts `string` to
-     * [start case](https://en.wikipedia.org/wiki/Letter_case#Stylistic_or_specialised_usage).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.1.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the start cased string.
-     * @example
-     *
-     * _.startCase('--foo-bar--');
-     * // => 'Foo Bar'
-     *
-     * _.startCase('fooBar');
-     * // => 'Foo Bar'
-     *
-     * _.startCase('__FOO_BAR__');
-     * // => 'FOO BAR'
-     */
-    var startCase = createCompounder(function(result, word, index) {
-      return result + (index ? ' ' : '') + upperFirst(word);
-    });
-
-    /**
-     * Checks if `string` starts with the given target string.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to inspect.
-     * @param {string} [target] The string to search for.
-     * @param {number} [position=0] The position to search from.
-     * @returns {boolean} Returns `true` if `string` starts with `target`,
-     *  else `false`.
-     * @example
-     *
-     * _.startsWith('abc', 'a');
-     * // => true
-     *
-     * _.startsWith('abc', 'b');
-     * // => false
-     *
-     * _.startsWith('abc', 'b', 1);
-     * // => true
-     */
-    function startsWith(string, target, position) {
-      string = toString(string);
-      position = position == null
-        ? 0
-        : baseClamp(toInteger(position), 0, string.length);
-
-      target = baseToString(target);
-      return string.slice(position, position + target.length) == target;
-    }
-
-    /**
-     * Creates a compiled template function that can interpolate data properties
-     * in "interpolate" delimiters, HTML-escape interpolated data properties in
-     * "escape" delimiters, and execute JavaScript in "evaluate" delimiters. Data
-     * properties may be accessed as free variables in the template. If a setting
-     * object is given, it takes precedence over `_.templateSettings` values.
-     *
-     * **Note:** In the development build `_.template` utilizes
-     * [sourceURLs](http://www.html5rocks.com/en/tutorials/developertools/sourcemaps/#toc-sourceurl)
-     * for easier debugging.
-     *
-     * For more information on precompiling templates see
-     * [lodash's custom builds documentation](https://lodash.com/custom-builds).
-     *
-     * For more information on Chrome extension sandboxes see
-     * [Chrome's extensions documentation](https://developer.chrome.com/extensions/sandboxingEval).
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category String
-     * @param {string} [string=''] The template string.
-     * @param {Object} [options={}] The options object.
-     * @param {RegExp} [options.escape=_.templateSettings.escape]
-     *  The HTML "escape" delimiter.
-     * @param {RegExp} [options.evaluate=_.templateSettings.evaluate]
-     *  The "evaluate" delimiter.
-     * @param {Object} [options.imports=_.templateSettings.imports]
-     *  An object to import into the template as free variables.
-     * @param {RegExp} [options.interpolate=_.templateSettings.interpolate]
-     *  The "interpolate" delimiter.
-     * @param {string} [options.sourceURL='lodash.templateSources[n]']
-     *  The sourceURL of the compiled template.
-     * @param {string} [options.variable='obj']
-     *  The data object variable name.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the compiled template function.
-     * @example
-     *
-     * // Use the "interpolate" delimiter to create a compiled template.
-     * var compiled = _.template('hello <%= user %>!');
-     * compiled({ 'user': 'fred' });
-     * // => 'hello fred!'
-     *
-     * // Use the HTML "escape" delimiter to escape data property values.
-     * var compiled = _.template('<b><%- value %></b>');
-     * compiled({ 'value': '<script>' });
-     * // => '<b>&lt;script&gt;</b>'
-     *
-     * // Use the "evaluate" delimiter to execute JavaScript and generate HTML.
-     * var compiled = _.template('<% _.forEach(users, function(user) { %><li><%- user %></li><% }); %>');
-     * compiled({ 'users': ['fred', 'barney'] });
-     * // => '<li>fred</li><li>barney</li>'
-     *
-     * // Use the internal `print` function in "evaluate" delimiters.
-     * var compiled = _.template('<% print("hello " + user); %>!');
-     * compiled({ 'user': 'barney' });
-     * // => 'hello barney!'
-     *
-     * // Use the ES template literal delimiter as an "interpolate" delimiter.
-     * // Disable support by replacing the "interpolate" delimiter.
-     * var compiled = _.template('hello ${ user }!');
-     * compiled({ 'user': 'pebbles' });
-     * // => 'hello pebbles!'
-     *
-     * // Use backslashes to treat delimiters as plain text.
-     * var compiled = _.template('<%= "\\<%- value %\\>" %>');
-     * compiled({ 'value': 'ignored' });
-     * // => '<%- value %>'
-     *
-     * // Use the `imports` option to import `jQuery` as `jq`.
-     * var text = '<% jq.each(users, function(user) { %><li><%- user %></li><% }); %>';
-     * var compiled = _.template(text, { 'imports': { 'jq': jQuery } });
-     * compiled({ 'users': ['fred', 'barney'] });
-     * // => '<li>fred</li><li>barney</li>'
-     *
-     * // Use the `sourceURL` option to specify a custom sourceURL for the template.
-     * var compiled = _.template('hello <%= user %>!', { 'sourceURL': '/basic/greeting.jst' });
-     * compiled(data);
-     * // => Find the source of "greeting.jst" under the Sources tab or Resources panel of the web inspector.
-     *
-     * // Use the `variable` option to ensure a with-statement isn't used in the compiled template.
-     * var compiled = _.template('hi <%= data.user %>!', { 'variable': 'data' });
-     * compiled.source;
-     * // => function(data) {
-     * //   var __t, __p = '';
-     * //   __p += 'hi ' + ((__t = ( data.user )) == null ? '' : __t) + '!';
-     * //   return __p;
-     * // }
-     *
-     * // Use custom template delimiters.
-     * _.templateSettings.interpolate = /{{([\s\S]+?)}}/g;
-     * var compiled = _.template('hello {{ user }}!');
-     * compiled({ 'user': 'mustache' });
-     * // => 'hello mustache!'
-     *
-     * // Use the `source` property to inline compiled templates for meaningful
-     * // line numbers in error messages and stack traces.
-     * fs.writeFileSync(path.join(process.cwd(), 'jst.js'), '\
-     *   var JST = {\
-     *     "main": ' + _.template(mainText).source + '\
-     *   };\
-     * ');
-     */
-    function template(string, options, guard) {
-      // Based on John Resig's `tmpl` implementation
-      // (http://ejohn.org/blog/javascript-micro-templating/)
-      // and Laura Doktorova's doT.js (https://github.com/olado/doT).
-      var settings = lodash.templateSettings;
-
-      if (guard && isIterateeCall(string, options, guard)) {
-        options = undefined;
-      }
-      string = toString(string);
-      options = assignInWith({}, options, settings, customDefaultsAssignIn);
-
-      var imports = assignInWith({}, options.imports, settings.imports, customDefaultsAssignIn),
-          importsKeys = keys(imports),
-          importsValues = baseValues(imports, importsKeys);
-
-      var isEscaping,
-          isEvaluating,
-          index = 0,
-          interpolate = options.interpolate || reNoMatch,
-          source = "__p += '";
-
-      // Compile the regexp to match each delimiter.
-      var reDelimiters = RegExp(
-        (options.escape || reNoMatch).source + '|' +
-        interpolate.source + '|' +
-        (interpolate === reInterpolate ? reEsTemplate : reNoMatch).source + '|' +
-        (options.evaluate || reNoMatch).source + '|$'
-      , 'g');
-
-      // Use a sourceURL for easier debugging.
-      // The sourceURL gets injected into the source that's eval-ed, so be careful
-      // with lookup (in case of e.g. prototype pollution), and strip newlines if any.
-      // A newline wouldn't be a valid sourceURL anyway, and it'd enable code injection.
-      var sourceURL = '//# sourceURL=' +
-        (hasOwnProperty.call(options, 'sourceURL')
-          ? (options.sourceURL + '').replace(/[\r\n]/g, ' ')
-          : ('lodash.templateSources[' + (++templateCounter) + ']')
-        ) + '\n';
-
-      string.replace(reDelimiters, function(match, escapeValue, interpolateValue, esTemplateValue, evaluateValue, offset) {
-        interpolateValue || (interpolateValue = esTemplateValue);
-
-        // Escape characters that can't be included in string literals.
-        source += string.slice(index, offset).replace(reUnescapedString, escapeStringChar);
-
-        // Replace delimiters with snippets.
-        if (escapeValue) {
-          isEscaping = true;
-          source += "' +\n__e(" + escapeValue + ") +\n'";
-        }
-        if (evaluateValue) {
-          isEvaluating = true;
-          source += "';\n" + evaluateValue + ";\n__p += '";
-        }
-        if (interpolateValue) {
-          source += "' +\n((__t = (" + interpolateValue + ")) == null ? '' : __t) +\n'";
-        }
-        index = offset + match.length;
-
-        // The JS engine embedded in Adobe products needs `match` returned in
-        // order to produce the correct `offset` value.
-        return match;
-      });
-
-      source += "';\n";
-
-      // If `variable` is not specified wrap a with-statement around the generated
-      // code to add the data object to the top of the scope chain.
-      // Like with sourceURL, we take care to not check the option's prototype,
-      // as this configuration is a code injection vector.
-      var variable = hasOwnProperty.call(options, 'variable') && options.variable;
-      if (!variable) {
-        source = 'with (obj) {\n' + source + '\n}\n';
-      }
-      // Cleanup code by stripping empty strings.
-      source = (isEvaluating ? source.replace(reEmptyStringLeading, '') : source)
-        .replace(reEmptyStringMiddle, '$1')
-        .replace(reEmptyStringTrailing, '$1;');
-
-      // Frame code as the function body.
-      source = 'function(' + (variable || 'obj') + ') {\n' +
-        (variable
-          ? ''
-          : 'obj || (obj = {});\n'
-        ) +
-        "var __t, __p = ''" +
-        (isEscaping
-           ? ', __e = _.escape'
-           : ''
-        ) +
-        (isEvaluating
-          ? ', __j = Array.prototype.join;\n' +
-            "function print() { __p += __j.call(arguments, '') }\n"
-          : ';\n'
-        ) +
-        source +
-        'return __p\n}';
-
-      var result = attempt(function() {
-        return Function(importsKeys, sourceURL + 'return ' + source)
-          .apply(undefined, importsValues);
-      });
-
-      // Provide the compiled function's source by its `toString` method or
-      // the `source` property as a convenience for inlining compiled templates.
-      result.source = source;
-      if (isError(result)) {
-        throw result;
-      }
-      return result;
-    }
-
-    /**
-     * Converts `string`, as a whole, to lower case just like
-     * [String#toLowerCase](https://mdn.io/toLowerCase).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the lower cased string.
-     * @example
-     *
-     * _.toLower('--Foo-Bar--');
-     * // => '--foo-bar--'
-     *
-     * _.toLower('fooBar');
-     * // => 'foobar'
-     *
-     * _.toLower('__FOO_BAR__');
-     * // => '__foo_bar__'
-     */
-    function toLower(value) {
-      return toString(value).toLowerCase();
-    }
-
-    /**
-     * Converts `string`, as a whole, to upper case just like
-     * [String#toUpperCase](https://mdn.io/toUpperCase).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the upper cased string.
-     * @example
-     *
-     * _.toUpper('--foo-bar--');
-     * // => '--FOO-BAR--'
-     *
-     * _.toUpper('fooBar');
-     * // => 'FOOBAR'
-     *
-     * _.toUpper('__foo_bar__');
-     * // => '__FOO_BAR__'
-     */
-    function toUpper(value) {
-      return toString(value).toUpperCase();
-    }
-
-    /**
-     * Removes leading and trailing whitespace or specified characters from `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to trim.
-     * @param {string} [chars=whitespace] The characters to trim.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the trimmed string.
-     * @example
-     *
-     * _.trim('  abc  ');
-     * // => 'abc'
-     *
-     * _.trim('-_-abc-_-', '_-');
-     * // => 'abc'
-     *
-     * _.map(['  foo  ', '  bar  '], _.trim);
-     * // => ['foo', 'bar']
-     */
-    function trim(string, chars, guard) {
-      string = toString(string);
-      if (string && (guard || chars === undefined)) {
-        return string.replace(reTrim, '');
-      }
-      if (!string || !(chars = baseToString(chars))) {
-        return string;
-      }
-      var strSymbols = stringToArray(string),
-          chrSymbols = stringToArray(chars),
-          start = charsStartIndex(strSymbols, chrSymbols),
-          end = charsEndIndex(strSymbols, chrSymbols) + 1;
-
-      return castSlice(strSymbols, start, end).join('');
-    }
-
-    /**
-     * Removes trailing whitespace or specified characters from `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to trim.
-     * @param {string} [chars=whitespace] The characters to trim.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the trimmed string.
-     * @example
-     *
-     * _.trimEnd('  abc  ');
-     * // => '  abc'
-     *
-     * _.trimEnd('-_-abc-_-', '_-');
-     * // => '-_-abc'
-     */
-    function trimEnd(string, chars, guard) {
-      string = toString(string);
-      if (string && (guard || chars === undefined)) {
-        return string.replace(reTrimEnd, '');
-      }
-      if (!string || !(chars = baseToString(chars))) {
-        return string;
-      }
-      var strSymbols = stringToArray(string),
-          end = charsEndIndex(strSymbols, stringToArray(chars)) + 1;
-
-      return castSlice(strSymbols, 0, end).join('');
-    }
-
-    /**
-     * Removes leading whitespace or specified characters from `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to trim.
-     * @param {string} [chars=whitespace] The characters to trim.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the trimmed string.
-     * @example
-     *
-     * _.trimStart('  abc  ');
-     * // => 'abc  '
-     *
-     * _.trimStart('-_-abc-_-', '_-');
-     * // => 'abc-_-'
-     */
-    function trimStart(string, chars, guard) {
-      string = toString(string);
-      if (string && (guard || chars === undefined)) {
-        return string.replace(reTrimStart, '');
-      }
-      if (!string || !(chars = baseToString(chars))) {
-        return string;
-      }
-      var strSymbols = stringToArray(string),
-          start = charsStartIndex(strSymbols, stringToArray(chars));
-
-      return castSlice(strSymbols, start).join('');
-    }
-
-    /**
-     * Truncates `string` if it's longer than the given maximum string length.
-     * The last characters of the truncated string are replaced with the omission
-     * string which defaults to "...".
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to truncate.
-     * @param {Object} [options={}] The options object.
-     * @param {number} [options.length=30] The maximum string length.
-     * @param {string} [options.omission='...'] The string to indicate text is omitted.
-     * @param {RegExp|string} [options.separator] The separator pattern to truncate to.
-     * @returns {string} Returns the truncated string.
-     * @example
-     *
-     * _.truncate('hi-diddly-ho there, neighborino');
-     * // => 'hi-diddly-ho there, neighbo...'
-     *
-     * _.truncate('hi-diddly-ho there, neighborino', {
-     *   'length': 24,
-     *   'separator': ' '
-     * });
-     * // => 'hi-diddly-ho there,...'
-     *
-     * _.truncate('hi-diddly-ho there, neighborino', {
-     *   'length': 24,
-     *   'separator': /,? +/
-     * });
-     * // => 'hi-diddly-ho there...'
-     *
-     * _.truncate('hi-diddly-ho there, neighborino', {
-     *   'omission': ' [...]'
-     * });
-     * // => 'hi-diddly-ho there, neig [...]'
-     */
-    function truncate(string, options) {
-      var length = DEFAULT_TRUNC_LENGTH,
-          omission = DEFAULT_TRUNC_OMISSION;
-
-      if (isObject(options)) {
-        var separator = 'separator' in options ? options.separator : separator;
-        length = 'length' in options ? toInteger(options.length) : length;
-        omission = 'omission' in options ? baseToString(options.omission) : omission;
-      }
-      string = toString(string);
-
-      var strLength = string.length;
-      if (hasUnicode(string)) {
-        var strSymbols = stringToArray(string);
-        strLength = strSymbols.length;
-      }
-      if (length >= strLength) {
-        return string;
-      }
-      var end = length - stringSize(omission);
-      if (end < 1) {
-        return omission;
-      }
-      var result = strSymbols
-        ? castSlice(strSymbols, 0, end).join('')
-        : string.slice(0, end);
-
-      if (separator === undefined) {
-        return result + omission;
-      }
-      if (strSymbols) {
-        end += (result.length - end);
-      }
-      if (isRegExp(separator)) {
-        if (string.slice(end).search(separator)) {
-          var match,
-              substring = result;
-
-          if (!separator.global) {
-            separator = RegExp(separator.source, toString(reFlags.exec(separator)) + 'g');
-          }
-          separator.lastIndex = 0;
-          while ((match = separator.exec(substring))) {
-            var newEnd = match.index;
-          }
-          result = result.slice(0, newEnd === undefined ? end : newEnd);
-        }
-      } else if (string.indexOf(baseToString(separator), end) != end) {
-        var index = result.lastIndexOf(separator);
-        if (index > -1) {
-          result = result.slice(0, index);
-        }
-      }
-      return result + omission;
-    }
-
-    /**
-     * The inverse of `_.escape`; this method converts the HTML entities
-     * `&amp;`, `&lt;`, `&gt;`, `&quot;`, and `&#39;` in `string` to
-     * their corresponding characters.
-     *
-     * **Note:** No other HTML entities are unescaped. To unescape additional
-     * HTML entities use a third-party library like [_he_](https://mths.be/he).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.6.0
-     * @category String
-     * @param {string} [string=''] The string to unescape.
-     * @returns {string} Returns the unescaped string.
-     * @example
-     *
-     * _.unescape('fred, barney, &amp; pebbles');
-     * // => 'fred, barney, & pebbles'
-     */
-    function unescape(string) {
-      string = toString(string);
-      return (string && reHasEscapedHtml.test(string))
-        ? string.replace(reEscapedHtml, unescapeHtmlChar)
-        : string;
-    }
-
-    /**
-     * Converts `string`, as space separated words, to upper case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the upper cased string.
-     * @example
-     *
-     * _.upperCase('--foo-bar');
-     * // => 'FOO BAR'
-     *
-     * _.upperCase('fooBar');
-     * // => 'FOO BAR'
-     *
-     * _.upperCase('__foo_bar__');
-     * // => 'FOO BAR'
-     */
-    var upperCase = createCompounder(function(result, word, index) {
-      return result + (index ? ' ' : '') + word.toUpperCase();
-    });
-
-    /**
-     * Converts the first character of `string` to upper case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the converted string.
-     * @example
-     *
-     * _.upperFirst('fred');
-     * // => 'Fred'
-     *
-     * _.upperFirst('FRED');
-     * // => 'FRED'
-     */
-    var upperFirst = createCaseFirst('toUpperCase');
-
-    /**
-     * Splits `string` into an array of its words.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to inspect.
-     * @param {RegExp|string} [pattern] The pattern to match words.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the words of `string`.
-     * @example
-     *
-     * _.words('fred, barney, & pebbles');
-     * // => ['fred', 'barney', 'pebbles']
-     *
-     * _.words('fred, barney, & pebbles', /[^, ]+/g);
-     * // => ['fred', 'barney', '&', 'pebbles']
-     */
-    function words(string, pattern, guard) {
-      string = toString(string);
-      pattern = guard ? undefined : pattern;
-
-      if (pattern === undefined) {
-        return hasUnicodeWord(string) ? unicodeWords(string) : asciiWords(string);
-      }
-      return string.match(pattern) || [];
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Attempts to invoke `func`, returning either the result or the caught error
-     * object. Any additional arguments are provided to `func` when it's invoked.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {Function} func The function to attempt.
-     * @param {...*} [args] The arguments to invoke `func` with.
-     * @returns {*} Returns the `func` result or error object.
-     * @example
-     *
-     * // Avoid throwing errors for invalid selectors.
-     * var elements = _.attempt(function(selector) {
-     *   return document.querySelectorAll(selector);
-     * }, '>_>');
-     *
-     * if (_.isError(elements)) {
-     *   elements = [];
-     * }
-     */
-    var attempt = baseRest(function(func, args) {
-      try {
-        return apply(func, undefined, args);
-      } catch (e) {
-        return isError(e) ? e : new Error(e);
-      }
-    });
-
-    /**
-     * Binds methods of an object to the object itself, overwriting the existing
-     * method.
-     *
-     * **Note:** This method doesn't set the "length" property of bound functions.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {Object} object The object to bind and assign the bound methods to.
-     * @param {...(string|string[])} methodNames The object method names to bind.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var view = {
-     *   'label': 'docs',
-     *   'click': function() {
-     *     console.log('clicked ' + this.label);
-     *   }
-     * };
-     *
-     * _.bindAll(view, ['click']);
-     * jQuery(element).on('click', view.click);
-     * // => Logs 'clicked docs' when clicked.
-     */
-    var bindAll = flatRest(function(object, methodNames) {
-      arrayEach(methodNames, function(key) {
-        key = toKey(key);
-        baseAssignValue(object, key, bind(object[key], object));
-      });
-      return object;
-    });
-
-    /**
-     * Creates a function that iterates over `pairs` and invokes the corresponding
-     * function of the first predicate to return truthy. The predicate-function
-     * pairs are invoked with the `this` binding and arguments of the created
-     * function.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {Array} pairs The predicate-function pairs.
-     * @returns {Function} Returns the new composite function.
-     * @example
-     *
-     * var func = _.cond([
-     *   [_.matches({ 'a': 1 }),           _.constant('matches A')],
-     *   [_.conforms({ 'b': _.isNumber }), _.constant('matches B')],
-     *   [_.stubTrue,                      _.constant('no match')]
-     * ]);
-     *
-     * func({ 'a': 1, 'b': 2 });
-     * // => 'matches A'
-     *
-     * func({ 'a': 0, 'b': 1 });
-     * // => 'matches B'
-     *
-     * func({ 'a': '1', 'b': '2' });
-     * // => 'no match'
-     */
-    function cond(pairs) {
-      var length = pairs == null ? 0 : pairs.length,
-          toIteratee = getIteratee();
-
-      pairs = !length ? [] : arrayMap(pairs, function(pair) {
-        if (typeof pair[1] != 'function') {
-          throw new TypeError(FUNC_ERROR_TEXT);
-        }
-        return [toIteratee(pair[0]), pair[1]];
-      });
-
-      return baseRest(function(args) {
-        var index = -1;
-        while (++index < length) {
-          var pair = pairs[index];
-          if (apply(pair[0], this, args)) {
-            return apply(pair[1], this, args);
-          }
-        }
-      });
-    }
-
-    /**
-     * Creates a function that invokes the predicate properties of `source` with
-     * the corresponding property values of a given object, returning `true` if
-     * all predicates return truthy, else `false`.
-     *
-     * **Note:** The created function is equivalent to `_.conformsTo` with
-     * `source` partially applied.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {Function} Returns the new spec function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': 2, 'b': 1 },
-     *   { 'a': 1, 'b': 2 }
-     * ];
-     *
-     * _.filter(objects, _.conforms({ 'b': function(n) { return n > 1; } }));
-     * // => [{ 'a': 1, 'b': 2 }]
-     */
-    function conforms(source) {
-      return baseConforms(baseClone(source, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that returns `value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Util
-     * @param {*} value The value to return from the new function.
-     * @returns {Function} Returns the new constant function.
-     * @example
-     *
-     * var objects = _.times(2, _.constant({ 'a': 1 }));
-     *
-     * console.log(objects);
-     * // => [{ 'a': 1 }, { 'a': 1 }]
-     *
-     * console.log(objects[0] === objects[1]);
-     * // => true
-     */
-    function constant(value) {
-      return function() {
-        return value;
-      };
-    }
-
-    /**
-     * Checks `value` to determine whether a default value should be returned in
-     * its place. The `defaultValue` is returned if `value` is `NaN`, `null`,
-     * or `undefined`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.14.0
-     * @category Util
-     * @param {*} value The value to check.
-     * @param {*} defaultValue The default value.
-     * @returns {*} Returns the resolved value.
-     * @example
-     *
-     * _.defaultTo(1, 10);
-     * // => 1
-     *
-     * _.defaultTo(undefined, 10);
-     * // => 10
-     */
-    function defaultTo(value, defaultValue) {
-      return (value == null || value !== value) ? defaultValue : value;
-    }
-
-    /**
-     * Creates a function that returns the result of invoking the given functions
-     * with the `this` binding of the created function, where each successive
-     * invocation is supplied the return value of the previous.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [funcs] The functions to invoke.
-     * @returns {Function} Returns the new composite function.
-     * @see _.flowRight
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var addSquare = _.flow([_.add, square]);
-     * addSquare(1, 2);
-     * // => 9
-     */
-    var flow = createFlow();
-
-    /**
-     * This method is like `_.flow` except that it creates a function that
-     * invokes the given functions from right to left.
-     *
-     * @static
-     * @since 3.0.0
-     * @memberOf _
-     * @category Util
-     * @param {...(Function|Function[])} [funcs] The functions to invoke.
-     * @returns {Function} Returns the new composite function.
-     * @see _.flow
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var addSquare = _.flowRight([square, _.add]);
-     * addSquare(1, 2);
-     * // => 9
-     */
-    var flowRight = createFlow(true);
-
-    /**
-     * This method returns the first argument it receives.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {*} value Any value.
-     * @returns {*} Returns `value`.
-     * @example
-     *
-     * var object = { 'a': 1 };
-     *
-     * console.log(_.identity(object) === object);
-     * // => true
-     */
-    function identity(value) {
-      return value;
-    }
-
-    /**
-     * Creates a function that invokes `func` with the arguments of the created
-     * function. If `func` is a property name, the created function returns the
-     * property value for a given element. If `func` is an array or object, the
-     * created function returns `true` for elements that contain the equivalent
-     * source properties, otherwise it returns `false`.
-     *
-     * @static
-     * @since 4.0.0
-     * @memberOf _
-     * @category Util
-     * @param {*} [func=_.identity] The value to convert to a callback.
-     * @returns {Function} Returns the callback.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': true },
-     *   { 'user': 'fred',   'age': 40, 'active': false }
-     * ];
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.filter(users, _.iteratee({ 'user': 'barney', 'active': true }));
-     * // => [{ 'user': 'barney', 'age': 36, 'active': true }]
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.filter(users, _.iteratee(['user', 'fred']));
-     * // => [{ 'user': 'fred', 'age': 40 }]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.map(users, _.iteratee('user'));
-     * // => ['barney', 'fred']
-     *
-     * // Create custom iteratee shorthands.
-     * _.iteratee = _.wrap(_.iteratee, function(iteratee, func) {
-     *   return !_.isRegExp(func) ? iteratee(func) : function(string) {
-     *     return func.test(string);
-     *   };
-     * });
-     *
-     * _.filter(['abc', 'def'], /ef/);
-     * // => ['def']
-     */
-    function iteratee(func) {
-      return baseIteratee(typeof func == 'function' ? func : baseClone(func, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that performs a partial deep comparison between a given
-     * object and `source`, returning `true` if the given object has equivalent
-     * property values, else `false`.
-     *
-     * **Note:** The created function is equivalent to `_.isMatch` with `source`
-     * partially applied.
-     *
-     * Partial comparisons will match empty array and empty object `source`
-     * values against any array or object value, respectively. See `_.isEqual`
-     * for a list of supported value comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {Object} source The object of property values to match.
-     * @returns {Function} Returns the new spec function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': 1, 'b': 2, 'c': 3 },
-     *   { 'a': 4, 'b': 5, 'c': 6 }
-     * ];
-     *
-     * _.filter(objects, _.matches({ 'a': 4, 'c': 6 }));
-     * // => [{ 'a': 4, 'b': 5, 'c': 6 }]
-     */
-    function matches(source) {
-      return baseMatches(baseClone(source, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that performs a partial deep comparison between the
-     * value at `path` of a given object to `srcValue`, returning `true` if the
-     * object value is equivalent, else `false`.
-     *
-     * **Note:** Partial comparisons will match empty array and empty object
-     * `srcValue` values against any array or object value, respectively. See
-     * `_.isEqual` for a list of supported value comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.2.0
-     * @category Util
-     * @param {Array|string} path The path of the property to get.
-     * @param {*} srcValue The value to match.
-     * @returns {Function} Returns the new spec function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': 1, 'b': 2, 'c': 3 },
-     *   { 'a': 4, 'b': 5, 'c': 6 }
-     * ];
-     *
-     * _.find(objects, _.matchesProperty('a', 4));
-     * // => { 'a': 4, 'b': 5, 'c': 6 }
-     */
-    function matchesProperty(path, srcValue) {
-      return baseMatchesProperty(path, baseClone(srcValue, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that invokes the method at `path` of a given object.
-     * Any additional arguments are provided to the invoked method.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Util
-     * @param {Array|string} path The path of the method to invoke.
-     * @param {...*} [args] The arguments to invoke the method with.
-     * @returns {Function} Returns the new invoker function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': { 'b': _.constant(2) } },
-     *   { 'a': { 'b': _.constant(1) } }
-     * ];
-     *
-     * _.map(objects, _.method('a.b'));
-     * // => [2, 1]
-     *
-     * _.map(objects, _.method(['a', 'b']));
-     * // => [2, 1]
-     */
-    var method = baseRest(function(path, args) {
-      return function(object) {
-        return baseInvoke(object, path, args);
-      };
-    });
-
-    /**
-     * The opposite of `_.method`; this method creates a function that invokes
-     * the method at a given path of `object`. Any additional arguments are
-     * provided to the invoked method.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Util
-     * @param {Object} object The object to query.
-     * @param {...*} [args] The arguments to invoke the method with.
-     * @returns {Function} Returns the new invoker function.
-     * @example
-     *
-     * var array = _.times(3, _.constant),
-     *     object = { 'a': array, 'b': array, 'c': array };
-     *
-     * _.map(['a[2]', 'c[0]'], _.methodOf(object));
-     * // => [2, 0]
-     *
-     * _.map([['a', '2'], ['c', '0']], _.methodOf(object));
-     * // => [2, 0]
-     */
-    var methodOf = baseRest(function(object, args) {
-      return function(path) {
-        return baseInvoke(object, path, args);
-      };
-    });
-
-    /**
-     * Adds all own enumerable string keyed function properties of a source
-     * object to the destination object. If `object` is a function, then methods
-     * are added to its prototype as well.
-     *
-     * **Note:** Use `_.runInContext` to create a pristine `lodash` function to
-     * avoid conflicts caused by modifying the original.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {Function|Object} [object=lodash] The destination object.
-     * @param {Object} source The object of functions to add.
-     * @param {Object} [options={}] The options object.
-     * @param {boolean} [options.chain=true] Specify whether mixins are chainable.
-     * @returns {Function|Object} Returns `object`.
-     * @example
-     *
-     * function vowels(string) {
-     *   return _.filter(string, function(v) {
-     *     return /[aeiou]/i.test(v);
-     *   });
-     * }
-     *
-     * _.mixin({ 'vowels': vowels });
-     * _.vowels('fred');
-     * // => ['e']
-     *
-     * _('fred').vowels().value();
-     * // => ['e']
-     *
-     * _.mixin({ 'vowels': vowels }, { 'chain': false });
-     * _('fred').vowels();
-     * // => ['e']
-     */
-    function mixin(object, source, options) {
-      var props = keys(source),
-          methodNames = baseFunctions(source, props);
-
-      if (options == null &&
-          !(isObject(source) && (methodNames.length || !props.length))) {
-        options = source;
-        source = object;
-        object = this;
-        methodNames = baseFunctions(source, keys(source));
-      }
-      var chain = !(isObject(options) && 'chain' in options) || !!options.chain,
-          isFunc = isFunction(object);
-
-      arrayEach(methodNames, function(methodName) {
-        var func = source[methodName];
-        object[methodName] = func;
-        if (isFunc) {
-          object.prototype[methodName] = function() {
-            var chainAll = this.__chain__;
-            if (chain || chainAll) {
-              var result = object(this.__wrapped__),
-                  actions = result.__actions__ = copyArray(this.__actions__);
-
-              actions.push({ 'func': func, 'args': arguments, 'thisArg': object });
-              result.__chain__ = chainAll;
-              return result;
-            }
-            return func.apply(object, arrayPush([this.value()], arguments));
-          };
-        }
-      });
-
-      return object;
-    }
-
-    /**
-     * Reverts the `_` variable to its previous value and returns a reference to
-     * the `lodash` function.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @returns {Function} Returns the `lodash` function.
-     * @example
-     *
-     * var lodash = _.noConflict();
-     */
-    function noConflict() {
-      if (root._ === this) {
-        root._ = oldDash;
-      }
-      return this;
-    }
-
-    /**
-     * This method returns `undefined`.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.3.0
-     * @category Util
-     * @example
-     *
-     * _.times(2, _.noop);
-     * // => [undefined, undefined]
-     */
-    function noop() {
-      // No operation performed.
-    }
-
-    /**
-     * Creates a function that gets the argument at index `n`. If `n` is negative,
-     * the nth argument from the end is returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {number} [n=0] The index of the argument to return.
-     * @returns {Function} Returns the new pass-thru function.
-     * @example
-     *
-     * var func = _.nthArg(1);
-     * func('a', 'b', 'c', 'd');
-     * // => 'b'
-     *
-     * var func = _.nthArg(-2);
-     * func('a', 'b', 'c', 'd');
-     * // => 'c'
-     */
-    function nthArg(n) {
-      n = toInteger(n);
-      return baseRest(function(args) {
-        return baseNth(args, n);
-      });
-    }
-
-    /**
-     * Creates a function that invokes `iteratees` with the arguments it receives
-     * and returns their results.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [iteratees=[_.identity]]
-     *  The iteratees to invoke.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var func = _.over([Math.max, Math.min]);
-     *
-     * func(1, 2, 3, 4);
-     * // => [4, 1]
-     */
-    var over = createOver(arrayMap);
-
-    /**
-     * Creates a function that checks if **all** of the `predicates` return
-     * truthy when invoked with the arguments it receives.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [predicates=[_.identity]]
-     *  The predicates to check.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var func = _.overEvery([Boolean, isFinite]);
-     *
-     * func('1');
-     * // => true
-     *
-     * func(null);
-     * // => false
-     *
-     * func(NaN);
-     * // => false
-     */
-    var overEvery = createOver(arrayEvery);
-
-    /**
-     * Creates a function that checks if **any** of the `predicates` return
-     * truthy when invoked with the arguments it receives.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [predicates=[_.identity]]
-     *  The predicates to check.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var func = _.overSome([Boolean, isFinite]);
-     *
-     * func('1');
-     * // => true
-     *
-     * func(null);
-     * // => true
-     *
-     * func(NaN);
-     * // => false
-     */
-    var overSome = createOver(arraySome);
-
-    /**
-     * Creates a function that returns the value at `path` of a given object.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Util
-     * @param {Array|string} path The path of the property to get.
-     * @returns {Function} Returns the new accessor function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': { 'b': 2 } },
-     *   { 'a': { 'b': 1 } }
-     * ];
-     *
-     * _.map(objects, _.property('a.b'));
-     * // => [2, 1]
-     *
-     * _.map(_.sortBy(objects, _.property(['a', 'b'])), 'a.b');
-     * // => [1, 2]
-     */
-    function property(path) {
-      return isKey(path) ? baseProperty(toKey(path)) : basePropertyDeep(path);
-    }
-
-    /**
-     * The opposite of `_.property`; this method creates a function that returns
-     * the value at a given path of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {Object} object The object to query.
-     * @returns {Function} Returns the new accessor function.
-     * @example
-     *
-     * var array = [0, 1, 2],
-     *     object = { 'a': array, 'b': array, 'c': array };
-     *
-     * _.map(['a[2]', 'c[0]'], _.propertyOf(object));
-     * // => [2, 0]
-     *
-     * _.map([['a', '2'], ['c', '0']], _.propertyOf(object));
-     * // => [2, 0]
-     */
-    function propertyOf(object) {
-      return function(path) {
-        return object == null ? undefined : baseGet(object, path);
-      };
-    }
-
-    /**
-     * Creates an array of numbers (positive and/or negative) progressing from
-     * `start` up to, but not including, `end`. A step of `-1` is used if a negative
-     * `start` is specified without an `end` or `step`. If `end` is not specified,
-     * it's set to `start` with `start` then set to `0`.
-     *
-     * **Note:** JavaScript follows the IEEE-754 standard for resolving
-     * floating-point values which can produce unexpected results.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {number} [start=0] The start of the range.
-     * @param {number} end The end of the range.
-     * @param {number} [step=1] The value to increment or decrement by.
-     * @returns {Array} Returns the range of numbers.
-     * @see _.inRange, _.rangeRight
-     * @example
-     *
-     * _.range(4);
-     * // => [0, 1, 2, 3]
-     *
-     * _.range(-4);
-     * // => [0, -1, -2, -3]
-     *
-     * _.range(1, 5);
-     * // => [1, 2, 3, 4]
-     *
-     * _.range(0, 20, 5);
-     * // => [0, 5, 10, 15]
-     *
-     * _.range(0, -4, -1);
-     * // => [0, -1, -2, -3]
-     *
-     * _.range(1, 4, 0);
-     * // => [1, 1, 1]
-     *
-     * _.range(0);
-     * // => []
-     */
-    var range = createRange();
-
-    /**
-     * This method is like `_.range` except that it populates values in
-     * descending order.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {number} [start=0] The start of the range.
-     * @param {number} end The end of the range.
-     * @param {number} [step=1] The value to increment or decrement by.
-     * @returns {Array} Returns the range of numbers.
-     * @see _.inRange, _.range
-     * @example
-     *
-     * _.rangeRight(4);
-     * // => [3, 2, 1, 0]
-     *
-     * _.rangeRight(-4);
-     * // => [-3, -2, -1, 0]
-     *
-     * _.rangeRight(1, 5);
-     * // => [4, 3, 2, 1]
-     *
-     * _.rangeRight(0, 20, 5);
-     * // => [15, 10, 5, 0]
-     *
-     * _.rangeRight(0, -4, -1);
-     * // => [-3, -2, -1, 0]
-     *
-     * _.rangeRight(1, 4, 0);
-     * // => [1, 1, 1]
-     *
-     * _.rangeRight(0);
-     * // => []
-     */
-    var rangeRight = createRange(true);
-
-    /**
-     * This method returns a new empty array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {Array} Returns the new empty array.
-     * @example
-     *
-     * var arrays = _.times(2, _.stubArray);
-     *
-     * console.log(arrays);
-     * // => [[], []]
-     *
-     * console.log(arrays[0] === arrays[1]);
-     * // => false
-     */
-    function stubArray() {
-      return [];
-    }
-
-    /**
-     * This method returns `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {boolean} Returns `false`.
-     * @example
-     *
-     * _.times(2, _.stubFalse);
-     * // => [false, false]
-     */
-    function stubFalse() {
-      return false;
-    }
-
-    /**
-     * This method returns a new empty object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {Object} Returns the new empty object.
-     * @example
-     *
-     * var objects = _.times(2, _.stubObject);
-     *
-     * console.log(objects);
-     * // => [{}, {}]
-     *
-     * console.log(objects[0] === objects[1]);
-     * // => false
-     */
-    function stubObject() {
-      return {};
-    }
-
-    /**
-     * This method returns an empty string.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {string} Returns the empty string.
-     * @example
-     *
-     * _.times(2, _.stubString);
-     * // => ['', '']
-     */
-    function stubString() {
-      return '';
-    }
-
-    /**
-     * This method returns `true`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {boolean} Returns `true`.
-     * @example
-     *
-     * _.times(2, _.stubTrue);
-     * // => [true, true]
-     */
-    function stubTrue() {
-      return true;
-    }
-
-    /**
-     * Invokes the iteratee `n` times, returning an array of the results of
-     * each invocation. The iteratee is invoked with one argument; (index).
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {number} n The number of times to invoke `iteratee`.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the array of results.
-     * @example
-     *
-     * _.times(3, String);
-     * // => ['0', '1', '2']
-     *
-     *  _.times(4, _.constant(0));
-     * // => [0, 0, 0, 0]
-     */
-    function times(n, iteratee) {
-      n = toInteger(n);
-      if (n < 1 || n > MAX_SAFE_INTEGER) {
-        return [];
-      }
-      var index = MAX_ARRAY_LENGTH,
-          length = nativeMin(n, MAX_ARRAY_LENGTH);
-
-      iteratee = getIteratee(iteratee);
-      n -= MAX_ARRAY_LENGTH;
-
-      var result = baseTimes(length, iteratee);
-      while (++index < n) {
-        iteratee(index);
-      }
-      return result;
-    }
-
-    /**
-     * Converts `value` to a property path array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {*} value The value to convert.
-     * @returns {Array} Returns the new property path array.
-     * @example
-     *
-     * _.toPath('a.b.c');
-     * // => ['a', 'b', 'c']
-     *
-     * _.toPath('a[0].b.c');
-     * // => ['a', '0', 'b', 'c']
-     */
-    function toPath(value) {
-      if (isArray(value)) {
-        return arrayMap(value, toKey);
-      }
-      return isSymbol(value) ? [value] : copyArray(stringToPath(toString(value)));
-    }
-
-    /**
-     * Generates a unique ID. If `prefix` is given, the ID is appended to it.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {string} [prefix=''] The value to prefix the ID with.
-     * @returns {string} Returns the unique ID.
-     * @example
-     *
-     * _.uniqueId('contact_');
-     * // => 'contact_104'
-     *
-     * _.uniqueId();
-     * // => '105'
-     */
-    function uniqueId(prefix) {
-      var id = ++idCounter;
-      return toString(prefix) + id;
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Adds two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.4.0
-     * @category Math
-     * @param {number} augend The first number in an addition.
-     * @param {number} addend The second number in an addition.
-     * @returns {number} Returns the total.
-     * @example
-     *
-     * _.add(6, 4);
-     * // => 10
-     */
-    var add = createMathOperation(function(augend, addend) {
-      return augend + addend;
-    }, 0);
-
-    /**
-     * Computes `number` rounded up to `precision`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Math
-     * @param {number} number The number to round up.
-     * @param {number} [precision=0] The precision to round up to.
-     * @returns {number} Returns the rounded up number.
-     * @example
-     *
-     * _.ceil(4.006);
-     * // => 5
-     *
-     * _.ceil(6.004, 2);
-     * // => 6.01
-     *
-     * _.ceil(6040, -2);
-     * // => 6100
-     */
-    var ceil = createRound('ceil');
-
-    /**
-     * Divide two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Math
-     * @param {number} dividend The first number in a division.
-     * @param {number} divisor The second number in a division.
-     * @returns {number} Returns the quotient.
-     * @example
-     *
-     * _.divide(6, 4);
-     * // => 1.5
-     */
-    var divide = createMathOperation(function(dividend, divisor) {
-      return dividend / divisor;
-    }, 1);
-
-    /**
-     * Computes `number` rounded down to `precision`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Math
-     * @param {number} number The number to round down.
-     * @param {number} [precision=0] The precision to round down to.
-     * @returns {number} Returns the rounded down number.
-     * @example
-     *
-     * _.floor(4.006);
-     * // => 4
-     *
-     * _.floor(0.046, 2);
-     * // => 0.04
-     *
-     * _.floor(4060, -2);
-     * // => 4000
-     */
-    var floor = createRound('floor');
-
-    /**
-     * Computes the maximum value of `array`. If `array` is empty or falsey,
-     * `undefined` is returned.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {*} Returns the maximum value.
-     * @example
-     *
-     * _.max([4, 2, 8, 6]);
-     * // => 8
-     *
-     * _.max([]);
-     * // => undefined
-     */
-    function max(array) {
-      return (array && array.length)
-        ? baseExtremum(array, identity, baseGt)
-        : undefined;
-    }
-
-    /**
-     * This method is like `_.max` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the criterion by which
-     * the value is ranked. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {*} Returns the maximum value.
-     * @example
-     *
-     * var objects = [{ 'n': 1 }, { 'n': 2 }];
-     *
-     * _.maxBy(objects, function(o) { return o.n; });
-     * // => { 'n': 2 }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.maxBy(objects, 'n');
-     * // => { 'n': 2 }
-     */
-    function maxBy(array, iteratee) {
-      return (array && array.length)
-        ? baseExtremum(array, getIteratee(iteratee, 2), baseGt)
-        : undefined;
-    }
-
-    /**
-     * Computes the mean of the values in `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {number} Returns the mean.
-     * @example
-     *
-     * _.mean([4, 2, 8, 6]);
-     * // => 5
-     */
-    function mean(array) {
-      return baseMean(array, identity);
-    }
-
-    /**
-     * This method is like `_.mean` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the value to be averaged.
-     * The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the mean.
-     * @example
-     *
-     * var objects = [{ 'n': 4 }, { 'n': 2 }, { 'n': 8 }, { 'n': 6 }];
-     *
-     * _.meanBy(objects, function(o) { return o.n; });
-     * // => 5
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.meanBy(objects, 'n');
-     * // => 5
-     */
-    function meanBy(array, iteratee) {
-      return baseMean(array, getIteratee(iteratee, 2));
-    }
-
-    /**
-     * Computes the minimum value of `array`. If `array` is empty or falsey,
-     * `undefined` is returned.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {*} Returns the minimum value.
-     * @example
-     *
-     * _.min([4, 2, 8, 6]);
-     * // => 2
-     *
-     * _.min([]);
-     * // => undefined
-     */
-    function min(array) {
-      return (array && array.length)
-        ? baseExtremum(array, identity, baseLt)
-        : undefined;
-    }
-
-    /**
-     * This method is like `_.min` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the criterion by which
-     * the value is ranked. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {*} Returns the minimum value.
-     * @example
-     *
-     * var objects = [{ 'n': 1 }, { 'n': 2 }];
-     *
-     * _.minBy(objects, function(o) { return o.n; });
-     * // => { 'n': 1 }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.minBy(objects, 'n');
-     * // => { 'n': 1 }
-     */
-    function minBy(array, iteratee) {
-      return (array && array.length)
-        ? baseExtremum(array, getIteratee(iteratee, 2), baseLt)
-        : undefined;
-    }
-
-    /**
-     * Multiply two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Math
-     * @param {number} multiplier The first number in a multiplication.
-     * @param {number} multiplicand The second number in a multiplication.
-     * @returns {number} Returns the product.
-     * @example
-     *
-     * _.multiply(6, 4);
-     * // => 24
-     */
-    var multiply = createMathOperation(function(multiplier, multiplicand) {
-      return multiplier * multiplicand;
-    }, 1);
-
-    /**
-     * Computes `number` rounded to `precision`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Math
-     * @param {number} number The number to round.
-     * @param {number} [precision=0] The precision to round to.
-     * @returns {number} Returns the rounded number.
-     * @example
-     *
-     * _.round(4.006);
-     * // => 4
-     *
-     * _.round(4.006, 2);
-     * // => 4.01
-     *
-     * _.round(4060, -2);
-     * // => 4100
-     */
-    var round = createRound('round');
-
-    /**
-     * Subtract two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {number} minuend The first number in a subtraction.
-     * @param {number} subtrahend The second number in a subtraction.
-     * @returns {number} Returns the difference.
-     * @example
-     *
-     * _.subtract(6, 4);
-     * // => 2
-     */
-    var subtract = createMathOperation(function(minuend, subtrahend) {
-      return minuend - subtrahend;
-    }, 0);
-
-    /**
-     * Computes the sum of the values in `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.4.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {number} Returns the sum.
-     * @example
-     *
-     * _.sum([4, 2, 8, 6]);
-     * // => 20
-     */
-    function sum(array) {
-      return (array && array.length)
-        ? baseSum(array, identity)
-        : 0;
-    }
-
-    /**
-     * This method is like `_.sum` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the value to be summed.
-     * The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the sum.
-     * @example
-     *
-     * var objects = [{ 'n': 4 }, { 'n': 2 }, { 'n': 8 }, { 'n': 6 }];
-     *
-     * _.sumBy(objects, function(o) { return o.n; });
-     * // => 20
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.sumBy(objects, 'n');
-     * // => 20
-     */
-    function sumBy(array, iteratee) {
-      return (array && array.length)
-        ? baseSum(array, getIteratee(iteratee, 2))
-        : 0;
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    // Add methods that return wrapped values in chain sequences.
-    lodash.after = after;
-    lodash.ary = ary;
-    lodash.assign = assign;
-    lodash.assignIn = assignIn;
-    lodash.assignInWith = assignInWith;
-    lodash.assignWith = assignWith;
-    lodash.at = at;
-    lodash.before = before;
-    lodash.bind = bind;
-    lodash.bindAll = bindAll;
-    lodash.bindKey = bindKey;
-    lodash.castArray = castArray;
-    lodash.chain = chain;
-    lodash.chunk = chunk;
-    lodash.compact = compact;
-    lodash.concat = concat;
-    lodash.cond = cond;
-    lodash.conforms = conforms;
-    lodash.constant = constant;
-    lodash.countBy = countBy;
-    lodash.create = create;
-    lodash.curry = curry;
-    lodash.curryRight = curryRight;
-    lodash.debounce = debounce;
-    lodash.defaults = defaults;
-    lodash.defaultsDeep = defaultsDeep;
-    lodash.defer = defer;
-    lodash.delay = delay;
-    lodash.difference = difference;
-    lodash.differenceBy = differenceBy;
-    lodash.differenceWith = differenceWith;
-    lodash.drop = drop;
-    lodash.dropRight = dropRight;
-    lodash.dropRightWhile = dropRightWhile;
-    lodash.dropWhile = dropWhile;
-    lodash.fill = fill;
-    lodash.filter = filter;
-    lodash.flatMap = flatMap;
-    lodash.flatMapDeep = flatMapDeep;
-    lodash.flatMapDepth = flatMapDepth;
-    lodash.flatten = flatten;
-    lodash.flattenDeep = flattenDeep;
-    lodash.flattenDepth = flattenDepth;
-    lodash.flip = flip;
-    lodash.flow = flow;
-    lodash.flowRight = flowRight;
-    lodash.fromPairs = fromPairs;
-    lodash.functions = functions;
-    lodash.functionsIn = functionsIn;
-    lodash.groupBy = groupBy;
-    lodash.initial = initial;
-    lodash.intersection = intersection;
-    lodash.intersectionBy = intersectionBy;
-    lodash.intersectionWith = intersectionWith;
-    lodash.invert = invert;
-    lodash.invertBy = invertBy;
-    lodash.invokeMap = invokeMap;
-    lodash.iteratee = iteratee;
-    lodash.keyBy = keyBy;
-    lodash.keys = keys;
-    lodash.keysIn = keysIn;
-    lodash.map = map;
-    lodash.mapKeys = mapKeys;
-    lodash.mapValues = mapValues;
-    lodash.matches = matches;
-    lodash.matchesProperty = matchesProperty;
-    lodash.memoize = memoize;
-    lodash.merge = merge;
-    lodash.mergeWith = mergeWith;
-    lodash.method = method;
-    lodash.methodOf = methodOf;
-    lodash.mixin = mixin;
-    lodash.negate = negate;
-    lodash.nthArg = nthArg;
-    lodash.omit = omit;
-    lodash.omitBy = omitBy;
-    lodash.once = once;
-    lodash.orderBy = orderBy;
-    lodash.over = over;
-    lodash.overArgs = overArgs;
-    lodash.overEvery = overEvery;
-    lodash.overSome = overSome;
-    lodash.partial = partial;
-    lodash.partialRight = partialRight;
-    lodash.partition = partition;
-    lodash.pick = pick;
-    lodash.pickBy = pickBy;
-    lodash.property = property;
-    lodash.propertyOf = propertyOf;
-    lodash.pull = pull;
-    lodash.pullAll = pullAll;
-    lodash.pullAllBy = pullAllBy;
-    lodash.pullAllWith = pullAllWith;
-    lodash.pullAt = pullAt;
-    lodash.range = range;
-    lodash.rangeRight = rangeRight;
-    lodash.rearg = rearg;
-    lodash.reject = reject;
-    lodash.remove = remove;
-    lodash.rest = rest;
-    lodash.reverse = reverse;
-    lodash.sampleSize = sampleSize;
-    lodash.set = set;
-    lodash.setWith = setWith;
-    lodash.shuffle = shuffle;
-    lodash.slice = slice;
-    lodash.sortBy = sortBy;
-    lodash.sortedUniq = sortedUniq;
-    lodash.sortedUniqBy = sortedUniqBy;
-    lodash.split = split;
-    lodash.spread = spread;
-    lodash.tail = tail;
-    lodash.take = take;
-    lodash.takeRight = takeRight;
-    lodash.takeRightWhile = takeRightWhile;
-    lodash.takeWhile = takeWhile;
-    lodash.tap = tap;
-    lodash.throttle = throttle;
-    lodash.thru = thru;
-    lodash.toArray = toArray;
-    lodash.toPairs = toPairs;
-    lodash.toPairsIn = toPairsIn;
-    lodash.toPath = toPath;
-    lodash.toPlainObject = toPlainObject;
-    lodash.transform = transform;
-    lodash.unary = unary;
-    lodash.union = union;
-    lodash.unionBy = unionBy;
-    lodash.unionWith = unionWith;
-    lodash.uniq = uniq;
-    lodash.uniqBy = uniqBy;
-    lodash.uniqWith = uniqWith;
-    lodash.unset = unset;
-    lodash.unzip = unzip;
-    lodash.unzipWith = unzipWith;
-    lodash.update = update;
-    lodash.updateWith = updateWith;
-    lodash.values = values;
-    lodash.valuesIn = valuesIn;
-    lodash.without = without;
-    lodash.words = words;
-    lodash.wrap = wrap;
-    lodash.xor = xor;
-    lodash.xorBy = xorBy;
-    lodash.xorWith = xorWith;
-    lodash.zip = zip;
-    lodash.zipObject = zipObject;
-    lodash.zipObjectDeep = zipObjectDeep;
-    lodash.zipWith = zipWith;
-
-    // Add aliases.
-    lodash.entries = toPairs;
-    lodash.entriesIn = toPairsIn;
-    lodash.extend = assignIn;
-    lodash.extendWith = assignInWith;
-
-    // Add methods to `lodash.prototype`.
-    mixin(lodash, lodash);
-
-    /*------------------------------------------------------------------------*/
-
-    // Add methods that return unwrapped values in chain sequences.
-    lodash.add = add;
-    lodash.attempt = attempt;
-    lodash.camelCase = camelCase;
-    lodash.capitalize = capitalize;
-    lodash.ceil = ceil;
-    lodash.clamp = clamp;
-    lodash.clone = clone;
-    lodash.cloneDeep = cloneDeep;
-    lodash.cloneDeepWith = cloneDeepWith;
-    lodash.cloneWith = cloneWith;
-    lodash.conformsTo = conformsTo;
-    lodash.deburr = deburr;
-    lodash.defaultTo = defaultTo;
-    lodash.divide = divide;
-    lodash.endsWith = endsWith;
-    lodash.eq = eq;
-    lodash.escape = escape;
-    lodash.escapeRegExp = escapeRegExp;
-    lodash.every = every;
-    lodash.find = find;
-    lodash.findIndex = findIndex;
-    lodash.findKey = findKey;
-    lodash.findLast = findLast;
-    lodash.findLastIndex = findLastIndex;
-    lodash.findLastKey = findLastKey;
-    lodash.floor = floor;
-    lodash.forEach = forEach;
-    lodash.forEachRight = forEachRight;
-    lodash.forIn = forIn;
-    lodash.forInRight = forInRight;
-    lodash.forOwn = forOwn;
-    lodash.forOwnRight = forOwnRight;
-    lodash.get = get;
-    lodash.gt = gt;
-    lodash.gte = gte;
-    lodash.has = has;
-    lodash.hasIn = hasIn;
-    lodash.head = head;
-    lodash.identity = identity;
-    lodash.includes = includes;
-    lodash.indexOf = indexOf;
-    lodash.inRange = inRange;
-    lodash.invoke = invoke;
-    lodash.isArguments = isArguments;
-    lodash.isArray = isArray;
-    lodash.isArrayBuffer = isArrayBuffer;
-    lodash.isArrayLike = isArrayLike;
-    lodash.isArrayLikeObject = isArrayLikeObject;
-    lodash.isBoolean = isBoolean;
-    lodash.isBuffer = isBuffer;
-    lodash.isDate = isDate;
-    lodash.isElement = isElement;
-    lodash.isEmpty = isEmpty;
-    lodash.isEqual = isEqual;
-    lodash.isEqualWith = isEqualWith;
-    lodash.isError = isError;
-    lodash.isFinite = isFinite;
-    lodash.isFunction = isFunction;
-    lodash.isInteger = isInteger;
-    lodash.isLength = isLength;
-    lodash.isMap = isMap;
-    lodash.isMatch = isMatch;
-    lodash.isMatchWith = isMatchWith;
-    lodash.isNaN = isNaN;
-    lodash.isNative = isNative;
-    lodash.isNil = isNil;
-    lodash.isNull = isNull;
-    lodash.isNumber = isNumber;
-    lodash.isObject = isObject;
-    lodash.isObjectLike = isObjectLike;
-    lodash.isPlainObject = isPlainObject;
-    lodash.isRegExp = isRegExp;
-    lodash.isSafeInteger = isSafeInteger;
-    lodash.isSet = isSet;
-    lodash.isString = isString;
-    lodash.isSymbol = isSymbol;
-    lodash.isTypedArray = isTypedArray;
-    lodash.isUndefined = isUndefined;
-    lodash.isWeakMap = isWeakMap;
-    lodash.isWeakSet = isWeakSet;
-    lodash.join = join;
-    lodash.kebabCase = kebabCase;
-    lodash.last = last;
-    lodash.lastIndexOf = lastIndexOf;
-    lodash.lowerCase = lowerCase;
-    lodash.lowerFirst = lowerFirst;
-    lodash.lt = lt;
-    lodash.lte = lte;
-    lodash.max = max;
-    lodash.maxBy = maxBy;
-    lodash.mean = mean;
-    lodash.meanBy = meanBy;
-    lodash.min = min;
-    lodash.minBy = minBy;
-    lodash.stubArray = stubArray;
-    lodash.stubFalse = stubFalse;
-    lodash.stubObject = stubObject;
-    lodash.stubString = stubString;
-    lodash.stubTrue = stubTrue;
-    lodash.multiply = multiply;
-    lodash.nth = nth;
-    lodash.noConflict = noConflict;
-    lodash.noop = noop;
-    lodash.now = now;
-    lodash.pad = pad;
-    lodash.padEnd = padEnd;
-    lodash.padStart = padStart;
-    lodash.parseInt = parseInt;
-    lodash.random = random;
-    lodash.reduce = reduce;
-    lodash.reduceRight = reduceRight;
-    lodash.repeat = repeat;
-    lodash.replace = replace;
-    lodash.result = result;
-    lodash.round = round;
-    lodash.runInContext = runInContext;
-    lodash.sample = sample;
-    lodash.size = size;
-    lodash.snakeCase = snakeCase;
-    lodash.some = some;
-    lodash.sortedIndex = sortedIndex;
-    lodash.sortedIndexBy = sortedIndexBy;
-    lodash.sortedIndexOf = sortedIndexOf;
-    lodash.sortedLastIndex = sortedLastIndex;
-    lodash.sortedLastIndexBy = sortedLastIndexBy;
-    lodash.sortedLastIndexOf = sortedLastIndexOf;
-    lodash.startCase = startCase;
-    lodash.startsWith = startsWith;
-    lodash.subtract = subtract;
-    lodash.sum = sum;
-    lodash.sumBy = sumBy;
-    lodash.template = template;
-    lodash.times = times;
-    lodash.toFinite = toFinite;
-    lodash.toInteger = toInteger;
-    lodash.toLength = toLength;
-    lodash.toLower = toLower;
-    lodash.toNumber = toNumber;
-    lodash.toSafeInteger = toSafeInteger;
-    lodash.toString = toString;
-    lodash.toUpper = toUpper;
-    lodash.trim = trim;
-    lodash.trimEnd = trimEnd;
-    lodash.trimStart = trimStart;
-    lodash.truncate = truncate;
-    lodash.unescape = unescape;
-    lodash.uniqueId = uniqueId;
-    lodash.upperCase = upperCase;
-    lodash.upperFirst = upperFirst;
-
-    // Add aliases.
-    lodash.each = forEach;
-    lodash.eachRight = forEachRight;
-    lodash.first = head;
-
-    mixin(lodash, (function() {
-      var source = {};
-      baseForOwn(lodash, function(func, methodName) {
-        if (!hasOwnProperty.call(lodash.prototype, methodName)) {
-          source[methodName] = func;
-        }
-      });
-      return source;
-    }()), { 'chain': false });
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * The semantic version number.
-     *
-     * @static
-     * @memberOf _
-     * @type {string}
-     */
-    lodash.VERSION = VERSION;
-
-    // Assign default placeholders.
-    arrayEach(['bind', 'bindKey', 'curry', 'curryRight', 'partial', 'partialRight'], function(methodName) {
-      lodash[methodName].placeholder = lodash;
-    });
-
-    // Add `LazyWrapper` methods for `_.drop` and `_.take` variants.
-    arrayEach(['drop', 'take'], function(methodName, index) {
-      LazyWrapper.prototype[methodName] = function(n) {
-        n = n === undefined ? 1 : nativeMax(toInteger(n), 0);
-
-        var result = (this.__filtered__ && !index)
-          ? new LazyWrapper(this)
-          : this.clone();
-
-        if (result.__filtered__) {
-          result.__takeCount__ = nativeMin(n, result.__takeCount__);
-        } else {
-          result.__views__.push({
-            'size': nativeMin(n, MAX_ARRAY_LENGTH),
-            'type': methodName + (result.__dir__ < 0 ? 'Right' : '')
-          });
-        }
-        return result;
-      };
-
-      LazyWrapper.prototype[methodName + 'Right'] = function(n) {
-        return this.reverse()[methodName](n).reverse();
-      };
-    });
-
-    // Add `LazyWrapper` methods that accept an `iteratee` value.
-    arrayEach(['filter', 'map', 'takeWhile'], function(methodName, index) {
-      var type = index + 1,
-          isFilter = type == LAZY_FILTER_FLAG || type == LAZY_WHILE_FLAG;
-
-      LazyWrapper.prototype[methodName] = function(iteratee) {
-        var result = this.clone();
-        result.__iteratees__.push({
-          'iteratee': getIteratee(iteratee, 3),
-          'type': type
-        });
-        result.__filtered__ = result.__filtered__ || isFilter;
-        return result;
-      };
-    });
-
-    // Add `LazyWrapper` methods for `_.head` and `_.last`.
-    arrayEach(['head', 'last'], function(methodName, index) {
-      var takeName = 'take' + (index ? 'Right' : '');
-
-      LazyWrapper.prototype[methodName] = function() {
-        return this[takeName](1).value()[0];
-      };
-    });
-
-    // Add `LazyWrapper` methods for `_.initial` and `_.tail`.
-    arrayEach(['initial', 'tail'], function(methodName, index) {
-      var dropName = 'drop' + (index ? '' : 'Right');
-
-      LazyWrapper.prototype[methodName] = function() {
-        return this.__filtered__ ? new LazyWrapper(this) : this[dropName](1);
-      };
-    });
-
-    LazyWrapper.prototype.compact = function() {
-      return this.filter(identity);
-    };
-
-    LazyWrapper.prototype.find = function(predicate) {
-      return this.filter(predicate).head();
-    };
-
-    LazyWrapper.prototype.findLast = function(predicate) {
-      return this.reverse().find(predicate);
-    };
-
-    LazyWrapper.prototype.invokeMap = baseRest(function(path, args) {
-      if (typeof path == 'function') {
-        return new LazyWrapper(this);
-      }
-      return this.map(function(value) {
-        return baseInvoke(value, path, args);
-      });
-    });
-
-    LazyWrapper.prototype.reject = function(predicate) {
-      return this.filter(negate(getIteratee(predicate)));
-    };
-
-    LazyWrapper.prototype.slice = function(start, end) {
-      start = toInteger(start);
-
-      var result = this;
-      if (result.__filtered__ && (start > 0 || end < 0)) {
-        return new LazyWrapper(result);
-      }
-      if (start < 0) {
-        result = result.takeRight(-start);
-      } else if (start) {
-        result = result.drop(start);
-      }
-      if (end !== undefined) {
-        end = toInteger(end);
-        result = end < 0 ? result.dropRight(-end) : result.take(end - start);
-      }
-      return result;
-    };
-
-    LazyWrapper.prototype.takeRightWhile = function(predicate) {
-      return this.reverse().takeWhile(predicate).reverse();
-    };
-
-    LazyWrapper.prototype.toArray = function() {
-      return this.take(MAX_ARRAY_LENGTH);
-    };
-
-    // Add `LazyWrapper` methods to `lodash.prototype`.
-    baseForOwn(LazyWrapper.prototype, function(func, methodName) {
-      var checkIteratee = /^(?:filter|find|map|reject)|While$/.test(methodName),
-          isTaker = /^(?:head|last)$/.test(methodName),
-          lodashFunc = lodash[isTaker ? ('take' + (methodName == 'last' ? 'Right' : '')) : methodName],
-          retUnwrapped = isTaker || /^find/.test(methodName);
-
-      if (!lodashFunc) {
-        return;
-      }
-      lodash.prototype[methodName] = function() {
-        var value = this.__wrapped__,
-            args = isTaker ? [1] : arguments,
-            isLazy = value instanceof LazyWrapper,
-            iteratee = args[0],
-            useLazy = isLazy || isArray(value);
-
-        var interceptor = function(value) {
-          var result = lodashFunc.apply(lodash, arrayPush([value], args));
-          return (isTaker && chainAll) ? result[0] : result;
-        };
-
-        if (useLazy && checkIteratee && typeof iteratee == 'function' && iteratee.length != 1) {
-          // Avoid lazy use if the iteratee has a "length" value other than `1`.
-          isLazy = useLazy = false;
-        }
-        var chainAll = this.__chain__,
-            isHybrid = !!this.__actions__.length,
-            isUnwrapped = retUnwrapped && !chainAll,
-            onlyLazy = isLazy && !isHybrid;
-
-        if (!retUnwrapped && useLazy) {
-          value = onlyLazy ? value : new LazyWrapper(this);
-          var result = func.apply(value, args);
-          result.__actions__.push({ 'func': thru, 'args': [interceptor], 'thisArg': undefined });
-          return new LodashWrapper(result, chainAll);
-        }
-        if (isUnwrapped && onlyLazy) {
-          return func.apply(this, args);
-        }
-        result = this.thru(interceptor);
-        return isUnwrapped ? (isTaker ? result.value()[0] : result.value()) : result;
-      };
-    });
-
-    // Add `Array` methods to `lodash.prototype`.
-    arrayEach(['pop', 'push', 'shift', 'sort', 'splice', 'unshift'], function(methodName) {
-      var func = arrayProto[methodName],
-          chainName = /^(?:push|sort|unshift)$/.test(methodName) ? 'tap' : 'thru',
-          retUnwrapped = /^(?:pop|shift)$/.test(methodName);
-
-      lodash.prototype[methodName] = function() {
-        var args = arguments;
-        if (retUnwrapped && !this.__chain__) {
-          var value = this.value();
-          return func.apply(isArray(value) ? value : [], args);
-        }
-        return this[chainName](function(value) {
-          return func.apply(isArray(value) ? value : [], args);
-        });
-      };
-    });
-
-    // Map minified method names to their real names.
-    baseForOwn(LazyWrapper.prototype, function(func, methodName) {
-      var lodashFunc = lodash[methodName];
-      if (lodashFunc) {
-        var key = lodashFunc.name + '';
-        if (!hasOwnProperty.call(realNames, key)) {
-          realNames[key] = [];
-        }
-        realNames[key].push({ 'name': methodName, 'func': lodashFunc });
-      }
-    });
-
-    realNames[createHybrid(undefined, WRAP_BIND_KEY_FLAG).name] = [{
-      'name': 'wrapper',
-      'func': undefined
-    }];
-
-    // Add methods to `LazyWrapper`.
-    LazyWrapper.prototype.clone = lazyClone;
-    LazyWrapper.prototype.reverse = lazyReverse;
-    LazyWrapper.prototype.value = lazyValue;
-
-    // Add chain sequence methods to the `lodash` wrapper.
-    lodash.prototype.at = wrapperAt;
-    lodash.prototype.chain = wrapperChain;
-    lodash.prototype.commit = wrapperCommit;
-    lodash.prototype.next = wrapperNext;
-    lodash.prototype.plant = wrapperPlant;
-    lodash.prototype.reverse = wrapperReverse;
-    lodash.prototype.toJSON = lodash.prototype.valueOf = lodash.prototype.value = wrapperValue;
-
-    // Add lazy aliases.
-    lodash.prototype.first = lodash.prototype.head;
-
-    if (symIterator) {
-      lodash.prototype[symIterator] = wrapperToIterator;
-    }
-    return lodash;
-  });
-
-  /*--------------------------------------------------------------------------*/
-
-  // Export lodash.
-  var _ = runInContext();
-
-  // Some AMD build optimizers, like r.js, check for condition patterns like:
-  if (typeof define == 'function' && typeof define.amd == 'object' && define.amd) {
-    // Expose Lodash on the global object to prevent errors when Lodash is
-    // loaded by a script tag in the presence of an AMD loader.
-    // See http://requirejs.org/docs/errors.html#mismatch for more details.
-    // Use `_.noConflict` to remove Lodash from the global object.
-    root._ = _;
-
-    // Define as an anonymous module so, through path mapping, it can be
-    // referenced as the "underscore" module.
-    define(function() {
-      return _;
-    });
-  }
-  // Check for `exports` after `define` in case a build optimizer adds it.
-  else if (freeModule) {
-    // Export for Node.js.
-    (freeModule.exports = _)._ = _;
-    // Export for CommonJS support.
-    freeExports._ = _;
-  }
-  else {
-    // Export to the global object.
-    root._ = _;
-  }
-}.call(this));
diff --git a/cwl/src/test/resources/cwl/ontology/EDAM.owl b/cwl/src/test/resources/cwl/ontology/EDAM.owl
deleted file mode 100644
index 092fccdac32..00000000000
--- a/cwl/src/test/resources/cwl/ontology/EDAM.owl
+++ /dev/null
@@ -1,51294 +0,0 @@
-<?xml version="1.0"?>
-
-
-<!DOCTYPE rdf:RDF [
-    <!ENTITY foaf "http://xmlns.com/foaf/0.1/" >
-    <!ENTITY doap "http://usefulinc.com/ns/doap#" >
-    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
-    <!ENTITY oboOther "http://purl.obolibrary.org/obo/" >
-    <!ENTITY dc "http://purl.org/dc/elements/1.1/" >
-    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
-    <!ENTITY edam "http://purl.obolibrary.org/obo/edam#" >
-    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
-    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
-    <!ENTITY oboInOwl "http://www.geneontology.org/formats/oboInOwl#" >
-]>
-
-
-<rdf:RDF xmlns="http://edamontology.org/"
-     xml:base="http://edamontology.org/"
-     xmlns:dc="http://purl.org/dc/elements/1.1/"
-     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-     xmlns:foaf="http://xmlns.com/foaf/0.1/"
-     xmlns:owl="http://www.w3.org/2002/07/owl#"
-     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-     xmlns:oboOther="http://purl.obolibrary.org/obo/"
-     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
-     xmlns:doap="http://usefulinc.com/ns/doap#"
-     xmlns:edam="&oboOther;edam#">
-    <owl:Ontology rdf:about="http://edamontology.org">
-        <oboOther:idspace>EDAM_topic http://edamontology.org/topic_ &quot;EDAM topics&quot;</oboOther:idspace>
-        <oboOther:idspace>EDAM_operation http://edamontology.org/operation_ &quot;EDAM operations&quot;</oboOther:idspace>
-        <oboOther:date>09:07:2015</oboOther:date>
-        <next_id>3625</next_id>
-        <oboInOwl:hasSubset>formats &quot;EDAM data formats&quot;</oboInOwl:hasSubset>
-        <oboOther:default-relationship-id-prefix>EDAM</oboOther:default-relationship-id-prefix>
-        <dc:title>An ontology of bioinformatics topics, operations, types of data including identifiers, and data formats</dc:title>
-        <oboInOwl:hasSubset>identifiers &quot;EDAM types of identifiers&quot;</oboInOwl:hasSubset>
-        <oboInOwl:hasSubset>data &quot;EDAM types of data&quot;</oboInOwl:hasSubset>
-        <oboInOwl:hasSubset>relations &quot;EDAM relations&quot;</oboInOwl:hasSubset>
-        <oboInOwl:hasSubset>edam &quot;EDAM&quot;</oboInOwl:hasSubset>
-        <oboOther:remark>EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence.</oboOther:remark>
-        <oboInOwl:hasSubset>operations &quot;EDAM operations&quot;</oboInOwl:hasSubset>
-        <oboOther:idspace>EDAM http://edamontology.org/ &quot;EDAM relations and concept properties&quot;</oboOther:idspace>
-        <dc:format>application/rdf+xml</dc:format>
-        <oboOther:idspace>EDAM_data http://edamontology.org/data_ &quot;EDAM types of data&quot;</oboOther:idspace>
-        <oboInOwl:hasSubset>concept_properties &quot;EDAM concept properties&quot;</oboInOwl:hasSubset>
-        <dc:creator>Jon Ison</dc:creator>
-        <dc:creator>Matúš Kalaš</dc:creator>
-        <oboInOwl:savedBy>Jon Ison, Matus Kalas, Hervé Ménager</oboInOwl:savedBy>
-        <oboOther:idspace>EDAM_format http://edamontology.org/format_ &quot;EDAM data formats&quot;</oboOther:idspace>
-        <oboInOwl:hasSubset>topics &quot;EDAM topics&quot;</oboInOwl:hasSubset>
-        <doap:Version>1.11</doap:Version>
-        <dc:creator>Hervé Ménager</dc:creator>
-        <oboOther:remark>EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources.  EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.</oboOther:remark>
-        <rdfs:isDefinedBy rdf:resource="http://edamontology.org/EDAM.owl"/>
-        <foaf:page rdf:resource="http://edamontology.org/page"/>
-    </owl:Ontology>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Annotation properties
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-
-
-    <!-- http://edamontology.org/created_in -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/created_in">
-        <rdfs:label>Created in</rdfs:label>
-        <oboInOwl:hasDefinition>Version in which a concept was created.</oboInOwl:hasDefinition>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/documentation -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/documentation">
-        <rdfs:label>Documentation</rdfs:label>
-        <oboInOwl:hasRelatedSynonym>Specification</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>&apos;Documentation&apos; trailing modifier (qualifier, &apos;documentation&apos;) of &apos;xref&apos; links of &apos;Format&apos; concepts. When &apos;true&apos;, the link is pointing to a page with explanation, description, documentation, or specification of the given data format.</oboInOwl:hasDefinition>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/example -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/example">
-        <rdfs:label>Example</rdfs:label>
-        <oboInOwl:hasDefinition>&apos;Example&apos; concept property (&apos;example&apos; metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too.</oboInOwl:hasDefinition>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/noClue -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/noClue"/>
-    
-
-
-    <!-- http://edamontology.org/obsolete_since -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/obsolete_since">
-        <rdfs:label>Obsolete since</rdfs:label>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-        <oboInOwl:hasDefinition>Version in which a concept was made obsolete.</oboInOwl:hasDefinition>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/regex -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/regex">
-        <rdfs:label>Regular expression</rdfs:label>
-        <oboInOwl:hasDefinition>&apos;Regular expression&apos; concept property (&apos;regex&apos; metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_anti_symmetric -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_anti_symmetric"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_metadata_tag -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_metadata_tag"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_reflexive -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_reflexive"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_symmetric -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_symmetric"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/namespace -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;namespace"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/transitive_over -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;transitive_over"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#data -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#data">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#edam -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#edam">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#events -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#events">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#formats -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#formats">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#identifiers -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#identifiers">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#obsolete -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#obsolete">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#operations -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#operations">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#topics -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#topics">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#SubsetProperty -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;SubsetProperty"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#consider -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;consider"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasAlternativeId -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasAlternativeId"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasBroadSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasDbXref"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasDefinition -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasDefinition"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasExactSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasNarrowSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasRelatedSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasSubset -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasSubset"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;inSubset"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#isCyclic -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;isCyclic"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#replacedBy -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;replacedBy"/>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Object Properties
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-
-
-    <!-- http://edamontology.org/has_format -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_format">
-        <rdfs:label>has format</rdfs:label>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000298&quot;</rdfs:seeAlso>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) &apos;Data&apos;, or an input, output, input or output argument of an &apos;Operation&apos;. Object B can either be a concept that is a &apos;Format&apos;, or in unexpected cases an entity outside of an ontology that is a &apos;Format&apos; or is in the role of a &apos;Format&apos;. In EDAM, &apos;has_format&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;is_format_of&apos;.</rdfs:comment>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality&quot;</rdfs:seeAlso>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:hasDefinition>&apos;A has_format B&apos; defines for the subject A, that it has the object B as its data format.</oboInOwl:hasDefinition>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:range rdf:resource="http://edamontology.org/format_1915"/>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://edamontology.org/has_function -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_function">
-        <rdfs:label>has function</rdfs:label>
-        <rdfs:seeAlso>http://wsio.org/has_function</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:bearer_of</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, &apos;has_function&apos; serves only for relating annotated entities outside of EDAM with &apos;Operation&apos; concepts.</rdfs:comment>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality&quot;</rdfs:seeAlso>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:hasDefinition>&apos;A has_function B&apos; defines for the subject A, that it has the object B as its function.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000306&quot;</rdfs:seeAlso>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <rdfs:range rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_function"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:bearer_of&apos; is narrower in the sense that it only relates ontological categories (concepts) that are an &apos;independent_continuant&apos; (snap:IndependentContinuant) with ontological categories that are a &apos;specifically_dependent_continuant&apos; (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject.</rdfs:comment>
-        <owl:annotatedTarget>OBO_REL:bearer_of</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_function"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/has_identifier -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_identifier">
-        <rdfs:label>has identifier</rdfs:label>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:hasDefinition>&apos;A has_identifier B&apos; defines for the subject A, that it has the object B as its identifier.</oboInOwl:hasDefinition>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an &apos;Identifier&apos;, or an entity outside of an ontology that is an &apos;Identifier&apos; or is in the role of an &apos;Identifier&apos;. In EDAM, &apos;has_identifier&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;is_identifier_of&apos;.</rdfs:comment>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0842"/>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://edamontology.org/has_input -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_input">
-        <rdfs:label>has input</rdfs:label>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:has_participant</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000293&quot;</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:seeAlso>http://wsio.org/has_input</rdfs:seeAlso>
-        <rdfs:comment>Subject A can either be concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. Object B can be any concept or entity. In EDAM, only &apos;has_input&apos; is explicitly defined between EDAM concepts (&apos;Operation&apos; &apos;has_input&apos; &apos;Data&apos;). The inverse, &apos;is_input_of&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:hasDefinition>&apos;A has_input B&apos; defines for the subject A, that it has the object B as a necessary or actual input or input argument.</oboInOwl:hasDefinition>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:has_participant</owl:annotatedTarget>
-        <rdfs:comment>&apos;OBO_REL:has_participant&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;process&apos; (span:Process) with ontological categories that are a &apos;continuant&apos; (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_input"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_input"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/has_output -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_output">
-        <rdfs:label>has output</rdfs:label>
-        <rdfs:seeAlso>http://wsio.org/has_output</rdfs:seeAlso>
-        <rdfs:comment>Subject A can either be concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. Object B can be any concept or entity. In EDAM, only &apos;has_output&apos; is explicitly defined between EDAM concepts (&apos;Operation&apos; &apos;has_output&apos; &apos;Data&apos;). The inverse, &apos;is_output_of&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000299&quot;</rdfs:seeAlso>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:has_participant</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:hasDefinition>&apos;A has_output B&apos; defines for the subject A, that it has the object B as a necessary or actual output or output argument.</oboInOwl:hasDefinition>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>&apos;OBO_REL:has_participant&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;process&apos; (span:Process) with ontological categories that are a &apos;continuant&apos; (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it.</rdfs:comment>
-        <owl:annotatedTarget>OBO_REL:has_participant</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_output"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_output"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/has_topic -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_topic">
-        <rdfs:label>has topic</rdfs:label>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a &apos;Topic&apos;, or in unexpected cases an entity outside of an ontology that is a &apos;Topic&apos; or is in the role of a &apos;Topic&apos;. In EDAM, only &apos;has_topic&apos; is explicitly defined between EDAM concepts (&apos;Operation&apos; or &apos;Data&apos; &apos;has_topic&apos; &apos;Topic&apos;). The inverse, &apos;is_topic_of&apos;, is not explicitly defined.</rdfs:comment>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:hasDefinition>&apos;A has_topic B&apos; defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <rdfs:seeAlso>http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000136&quot;</rdfs:seeAlso>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000298&quot;</rdfs:seeAlso>
-        <rdfs:range rdf:resource="http://edamontology.org/topic_0003"/>
-        <rdfs:domain>
-            <owl:Class>
-                <owl:unionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://edamontology.org/data_0006"/>
-                    <rdf:Description rdf:about="http://edamontology.org/operation_0004"/>
-                </owl:unionOf>
-            </owl:Class>
-        </rdfs:domain>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_topic"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_format_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_format_of">
-        <rdfs:label>is format of</rdfs:label>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboInOwl:hasDefinition>&apos;A is_format_of B&apos; defines for the subject A, that it is a data format of the object B.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can either be a concept that is a &apos;Format&apos;, or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a &apos;Format&apos; or is in the role of a &apos;Format&apos;. Object B can be any concept or entity outside of an ontology that is (or is in a role of) &apos;Data&apos;, or  an input, output, input or output argument of an &apos;Operation&apos;. In EDAM, only &apos;is_format_of&apos; is explicitly defined between EDAM concepts (&apos;Format&apos; &apos;is_format_of&apos; &apos;Data&apos;). The inverse, &apos;has_format&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:quality_of</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in</rdfs:seeAlso>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_format"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:quality_of</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:quality_of&apos; might be seen narrower in the sense that it only relates subjects that are a &apos;quality&apos; (snap:Quality) with objects that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_format_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_function_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_function_of">
-        <rdfs:label>is function of</rdfs:label>
-        <rdfs:comment>Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, &apos;is_function_of&apos; is not used.</rdfs:comment>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:inheres_in</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:hasDefinition>&apos;A is_function_of B&apos; defines for the subject A, that it is a function of the object B.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>OBO_REL:function_of</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:seeAlso>http://wsio.org/is_function_of</rdfs:seeAlso>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_function"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:inheres_in</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:inheres_in&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;specifically_dependent_continuant&apos; (snap:SpecificallyDependentContinuant) with ontological categories that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_function_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_function_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:function_of</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:function_of&apos; only relates subjects that are a &apos;function&apos; (snap:Function) with objects that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_function_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_identifier_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_identifier_of">
-        <rdfs:label>is identifier of</rdfs:label>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can either be a concept that is an &apos;Identifier&apos;, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an &apos;Identifier&apos; or is in the role of an &apos;Identifier&apos;. Object B can be any concept or entity outside of an ontology. In EDAM, only &apos;is_identifier_of&apos; is explicitly defined between EDAM concepts (only &apos;Identifier&apos; &apos;is_identifier_of&apos; &apos;Data&apos;). The inverse, &apos;has_identifier&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:hasDefinition>&apos;A is_identifier_of B&apos; defines for the subject A, that it is an identifier of the object B.</oboInOwl:hasDefinition>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0842"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_identifier"/>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://edamontology.org/is_input_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_input_of">
-        <rdfs:label>is input of</rdfs:label>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:seeAlso>http://wsio.org/is_input_of</rdfs:seeAlso>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:participates_in</oboInOwl:hasRelatedSynonym>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000295&quot;</rdfs:seeAlso>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. In EDAM, &apos;is_input_of&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;has_input&apos;.</rdfs:comment>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:hasDefinition>&apos;A is_input_of B&apos; defines for the subject A, that it as a necessary or actual input or input argument of the object B.</oboInOwl:hasDefinition>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_input"/>
-        <rdfs:range rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>&apos;OBO_REL:participates_in&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;continuant&apos; (snap:Continuant) with ontological categories that are a &apos;process&apos; (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments.</rdfs:comment>
-        <owl:annotatedTarget>OBO_REL:participates_in</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_input_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_input_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_output_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_output_of">
-        <rdfs:label>is output of</rdfs:label>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. In EDAM, &apos;is_output_of&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;has_output&apos;.</rdfs:comment>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboInOwl:hasDefinition>&apos;A is_output_of B&apos; defines for the subject A, that it as a necessary or actual output or output argument of the object B.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:participates_in</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>http://wsio.org/is_output_of</rdfs:seeAlso>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000312&quot;</rdfs:seeAlso>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_output"/>
-        <rdfs:range rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_output_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:participates_in</owl:annotatedTarget>
-        <rdfs:comment>&apos;OBO_REL:participates_in&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;continuant&apos; (snap:Continuant) with ontological categories that are a &apos;process&apos; (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_output_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_topic_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_topic_of">
-        <rdfs:label>is topic of</rdfs:label>
-        <oboInOwl:hasDefinition>&apos;A is_topic_of B&apos; defines for the subject A, that it is a topic of the object B (a topic A is the scope of B).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:quality_of</oboInOwl:hasRelatedSynonym>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:comment>Subject A can either be a concept that is a &apos;Topic&apos;, or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a &apos;Topic&apos; or is in the role of a &apos;Topic&apos;. Object B can be any concept or entity outside of an ontology. In EDAM, &apos;is_topic_of&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;has_topic&apos;.</rdfs:comment>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in</rdfs:seeAlso>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_topic"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/topic_0003"/>
-        <rdfs:range>
-            <owl:Class>
-                <owl:unionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://edamontology.org/data_0006"/>
-                    <rdf:Description rdf:about="http://edamontology.org/operation_0004"/>
-                </owl:unionOf>
-            </owl:Class>
-        </rdfs:range>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:quality_of</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:quality_of&apos; might be seen narrower in the sense that it only relates subjects that are a &apos;quality&apos; (snap:Quality) with objects that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_topic_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_topic_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Classes
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-    
-
-
-    <!-- http://edamontology.org/data_0005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0005">
-        <rdfs:label>Resource type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A type of computational resource used in bioinformatics.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0006">
-        <rdfs:label>Data</rdfs:label>
-        <owl:disjointWith rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/topic_0003"/>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <oboInOwl:hasDefinition>Information, represented in an information artefact (data record) that is &apos;understandable&apos; by dedicated computational tools that can use the data as input or produce it as output.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000088</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000069</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000030&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000027&quot;</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Data set</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Data record</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://wsio.org/data_002</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#DigitalEntity</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Datum</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedTarget>Data set</owl:annotatedTarget>
-        <rdfs:comment>EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>Datum</owl:annotatedTarget>
-        <rdfs:comment>EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>Data record</owl:annotatedTarget>
-        <rdfs:comment>EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information).</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasExactSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_0007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0007">
-        <rdfs:label>Tool</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A bioinformatics package or tool, e.g. a standalone application or web service.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0581">
-        <rdfs:label>Database</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0582">
-        <rdfs:label>Ontology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontologies</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0583">
-        <rdfs:label>Directory metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A directory on disk from which files are read.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0831 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0831">
-        <rdfs:label>MeSH vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0832 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0832">
-        <rdfs:label>HGNC vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0835 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0835">
-        <rdfs:label>UMLS vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0842 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0842">
-        <rdfs:label>Identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <owl:disjointWith rdf:resource="http://edamontology.org/data_2048"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/data_2527"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000115</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>ID</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>&quot;http://purl.org/dc/elements/1.1/identifier&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>http://wsio.org/data_005</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-        <oboInOwl:hasNarrowSynonym rdf:resource="&dc;identifier"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>Almost exact but limited to identifying resources.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0842"/>
-        <owl:annotatedTarget rdf:resource="&dc;identifier"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_0843 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0843">
-        <rdfs:label>Database entry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An entry (retrievable via URL) from a biological database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0844 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0844">
-        <rdfs:label>Molecular mass</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasDefinition>Mass of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0845 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0845">
-        <rdfs:label>Molecular charge</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasDefinition>Net charge of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:pdbx_formal_charge</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0846 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0846">
-        <rdfs:label>Chemical formula</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasExactSynonym>Chemical structure specification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A specification of a chemical structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0847 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0847">
-        <rdfs:label>QSAR descriptor</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasDefinition>A QSAR quantitative descriptor (name-value pair) of chemical structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0848 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0848">
-        <rdfs:label>Raw sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <rdfs:comment>Non-sequence characters may be used for example for gaps and translation stop.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0849 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0849">
-        <rdfs:label>Sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D058977</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A molecular sequence and associated metadata.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>SO:2000061</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0850 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0850">
-        <rdfs:label>Sequence set</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for arbitrary sequence sets and associated data arising from processing.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasRelatedSynonym>SO:0001260</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0851 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0851">
-        <rdfs:label>Sequence mask character</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A character used to replace (mask) other characters in a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0852 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0852">
-        <rdfs:label>Sequence mask type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of sequence masking to perform.</oboInOwl:hasDefinition>
-        <rdfs:comment>Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0853 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0853">
-        <rdfs:label>DNA sense specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:hasExactSynonym>DNA strand specification</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Strand</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The strand of a DNA sequence (forward or reverse).</oboInOwl:hasDefinition>
-        <rdfs:comment>The forward or &apos;top&apos; strand might specify a sequence is to be used as given, the reverse or &apos;bottom&apos; strand specifying the reverse complement of the sequence is to be used.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0854 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0854">
-        <rdfs:label>Sequence length specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A specification of sequence length(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0855 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0855">
-        <rdfs:label>Sequence metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Basic or general information concerning molecular sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is used for such things as a report including the sequence identifier, type and length.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2955"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0856 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0856">
-        <rdfs:label>Sequence feature source</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <rdfs:comment>This might be the name and version of a software tool, the name of a database, or &apos;curated&apos; to indicate a manual annotation (made by a human).</rdfs:comment>
-        <oboInOwl:hasDefinition>How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0857 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0857">
-        <rdfs:label>Sequence search results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Database hits (sequence)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym></oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence database hits</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence search hits</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence database search results</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0858 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0858">
-        <rdfs:label>Sequence signature matches</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0860"/>
-        <oboInOwl:hasExactSynonym>Sequence motif matches</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary database search results</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence profile matches</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This ncluding reports of hits from a search of a protein secondary or domain database.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Search results (protein secondary database)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0859 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0859">
-        <rdfs:label>Sequence signature model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data files used by motif or profile methods.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0860 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0860">
-        <rdfs:label>Sequence signature data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element.</oboInOwl:hasDefinition>
-        <oboInOwl:hasSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:hasSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0861 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0861">
-        <rdfs:label>Sequence alignment (words)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence word alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Alignment of exact matches between subsequences (words) within two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0862 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0862">
-        <rdfs:label>Dotplot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:hasDefinition>A dotplot of sequence similarities identified from word-matching or character comparison.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0863 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0863">
-        <rdfs:label>Sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Sequence_alignment</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D016415</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_010066</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of multiple molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0864 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0864">
-        <rdfs:label>Sequence alignment parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Some simple value controlling a sequence alignment (or similar &apos;match&apos;) operation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0865 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0865">
-        <rdfs:label>Sequence similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1772"/>
-        <oboInOwl:hasDefinition>A value representing molecular sequence similarity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0866 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0866">
-        <rdfs:label>Sequence alignment metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0867">
-        <rdfs:label>Sequence alignment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:comment>Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score.</rdfs:comment>
-        <oboInOwl:hasDefinition>An informative report of molecular sequence alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0868">
-        <rdfs:label>Sequence profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A profile-profile alignment (each profile typically representing a sequence alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0869">
-        <rdfs:label>Sequence-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment).</oboInOwl:hasDefinition>
-        <rdfs:comment>Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0870 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0870">
-        <rdfs:label>Sequence distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2855"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:phylogenetic_distance_matrix</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic distance matrix</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0871 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0871">
-        <rdfs:label>Phylogenetic character data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasDefinition>Basic character data from which a phylogenetic tree may be generated.</oboInOwl:hasDefinition>
-        <rdfs:comment>As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments</rdfs:comment>
-        <rdfs:seeAlso>http://www.evolutionaryontology.org/cdao.owl#Character</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0872 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0872">
-        <rdfs:label>Phylogenetic tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phylogeny</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Tree</oboInOwl:hasDbXref>
-        <rdfs:seeAlso>http://www.evolutionaryontology.org/cdao.owl#Tree</rdfs:seeAlso>
-        <rdfs:comment>A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also &apos;Phylogenetic tree image&apos;.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D010802</rdfs:seeAlso>
-        <oboInOwl:hasDbXref>Moby:phylogenetic_tree</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:myTree</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0874 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0874">
-        <rdfs:label>Comparison matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats).</rdfs:comment>
-        <oboInOwl:hasDefinition>Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0875 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0875">
-        <rdfs:label>Protein topology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predicted or actual protein topology represented as a string of protein secondary structure elements.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The location and size of the secondary structure elements and intervening loop regions is usually indicated.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0876"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0876 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0876">
-        <rdfs:label>Protein features report (secondary structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Secondary structure (predicted or real) of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0877 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0877">
-        <rdfs:label>Protein features report (super-secondary)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <rdfs:comment>Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Super-secondary structure of protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0878 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0878">
-        <rdfs:label>Secondary structure alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2366"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3154"/>
-        <oboInOwl:hasDefinition>Alignment of the (1D representations of) secondary structure of two or more proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0879 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0879">
-        <rdfs:label>Secondary structure alignment metadata (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on protein secondary structure alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0880 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0880">
-        <rdfs:label>RNA secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1465"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An informative report of secondary structure (predicted or real) of an RNA molecule.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:RNAStructML</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Secondary structure (RNA)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0881 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0881">
-        <rdfs:label>Secondary structure alignment (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2366"/>
-        <oboInOwl:hasDbXref>Moby:RNAStructAlignmentML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Alignment of the (1D representations of) secondary structure of two or more RNA molecules.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0882 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0882">
-        <rdfs:label>Secondary structure alignment metadata (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report of RNA secondary structure alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0883 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0883">
-        <rdfs:label>Structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0081"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Coordinate model</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure data</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The coordinate data may be predicted or real.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015394</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0884 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0884">
-        <rdfs:label>Tertiary structure record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An entry from a molecular tertiary (3D) structure database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0885">
-        <rdfs:label>Structure database search results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Results (hits) from searching a database of tertiary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0886 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0886">
-        <rdfs:label>Structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <rdfs:comment>A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0887 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0887">
-        <rdfs:label>Structure alignment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasDefinition>An informative report of molecular tertiary structure alignment-derived data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0888 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0888">
-        <rdfs:label>Structure similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1772"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0889 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0889">
-        <rdfs:label>Structural profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>3D profile</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Some type of structural (3D) profile or template (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structural (3D) profile</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0890 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0890">
-        <rdfs:label>Structural (3D) profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structural profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A 3D profile-3D profile alignment (each profile representing structures or a structure alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0891 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0891">
-        <rdfs:label>Sequence-3D profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence-structural profile alignment</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>An alignment of a sequence to a 3D profile (representing structures or a structure alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0893"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0892 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0892">
-        <rdfs:label>Protein sequence-structure scoring matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of values used for scoring sequence-structure compatibility.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0893 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0893">
-        <rdfs:label>Sequence-structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0894 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0894">
-        <rdfs:label>Amino acid annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report about a specific amino acid.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0895 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0895">
-        <rdfs:label>Peptide annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report about a specific peptide.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0896 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0896">
-        <rdfs:label>Protein report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasExactSynonym>Gene product annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0897 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0897">
-        <rdfs:label>Protein property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>Protein physicochemical property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein sequence statistics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein properties</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0899 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0899">
-        <rdfs:label>Protein structural motifs and surfaces</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>3D structural motifs in a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein 3D motifs</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0900 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0900">
-        <rdfs:label>Protein domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning the classification of the sequences and/or structures of protein structural domain(s).</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0901 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0901">
-        <rdfs:label>Protein features report (domains)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>structural domains or 3D folds in a protein or polypeptide chain.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0902 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0902">
-        <rdfs:label>Protein architecture report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on architecture (spatial arrangement of secondary structure) of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein property (architecture)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure report (architecture)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0903 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0903">
-        <rdfs:label>Protein folding report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0904 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0904">
-        <rdfs:label>Protein features (mutation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on the effect of (typically point) mutation on protein folding, stability, structure and function.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein property (mutation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure report (mutation)</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein report (mutation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0905 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0905">
-        <rdfs:label>Protein interaction raw data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0906 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0906">
-        <rdfs:label>Protein interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein report (interaction)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein interaction record</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with some other molecule(s), which might be another protein, nucleic acid or some other ligand.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0907 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0907">
-        <rdfs:label>Protein family report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0724"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific protein family or other classification or group of protein sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein family annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Protein classification data</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0909 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0909">
-        <rdfs:label>Vmax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0910 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0910">
-        <rdfs:label>Km</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <oboInOwl:hasDefinition>Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0911 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0911">
-        <rdfs:label>Nucleotide base annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report about a specific nucleotide base.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0912 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0912">
-        <rdfs:label>Nucleic acid property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasDefinition>A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Nucleic acid physicochemical property</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0914 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0914">
-        <rdfs:label>Codon usage data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0916 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0916">
-        <rdfs:label>Gene report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:hasExactSynonym>Gene structure (repot)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene and transcript structure (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene features report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (gene and transcript structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:gene</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes any report on a particular locus or gene.  This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Gene annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:Human_Readable_Description</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Gene function (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:GeneInfo</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0917 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0917">
-        <rdfs:label>Gene classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0918 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0918">
-        <rdfs:label>DNA variation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0919 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0919">
-        <rdfs:label>Chromosome report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0624"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific chromosome.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0920 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0920">
-        <rdfs:label>Genotype/phenotype report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genotype/phenotype annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0922 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0922">
-        <rdfs:label>Nucleic acid features report (primers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PCR primers and hybridization oligos in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0923 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0923">
-        <rdfs:label>PCR experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PCR experiments, e.g. quantitative real-time PCR.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0924 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0924">
-        <rdfs:label>Sequence trace</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <oboInOwl:hasDefinition>Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is the raw data produced by a DNA sequencing machine.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0925 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0925">
-        <rdfs:label>Sequence assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An assembly of fragments of a (typically genomic) DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Sequence_assembly</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>SO:0001248</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>SO:0000353</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedTarget>SO:0001248</owl:annotatedTarget>
-        <rdfs:comment>Perhaps surprisingly, the definition of &apos;SO:assembly&apos; is narrower than the &apos;SO:sequence_assembly&apos;.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0925"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_0926 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0926">
-        <rdfs:label>Radiation Hybrid (RH) scores</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping.</rdfs:comment>
-        <oboInOwl:hasDefinition>Radiation hybrid scores (RH) scores for one or more markers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0927 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0927">
-        <rdfs:label>Genetic linkage report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene annotation (linkage)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Linkage disequilibrium (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>An informative report on the linkage of alleles.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0928 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0928">
-        <rdfs:label>Gene expression profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <oboInOwl:hasDefinition>Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression pattern</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0931 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0931">
-        <rdfs:label>Microarray experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>microarray experiments including conditions, protocol, sample:data relationships etc.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0932 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0932">
-        <rdfs:label>Oligonucleotide probe data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data on oligonucleotide probes (typically for use with DNA microarrays).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2717"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0933 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0933">
-        <rdfs:label>SAGE experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Output from a serial analysis of gene expression (SAGE) experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Serial analysis of gene expression (SAGE) experimental data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2535"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0934 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0934">
-        <rdfs:label>MPSS experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Massively parallel signature sequencing (MPSS) data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Massively parallel signature sequencing (MPSS) experimental data</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2535"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0935 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0935">
-        <rdfs:label>SBS experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequencing by synthesis (SBS) experimental data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Sequencing by synthesis (SBS) data.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2535"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0936 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0936">
-        <rdfs:label>Sequence tag profile (with gene assignment)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2535"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0937 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0937">
-        <rdfs:label>Protein X-ray crystallographic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2537"/>
-        <oboInOwl:hasDefinition>X-ray crystallography data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0938 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0938">
-        <rdfs:label>Protein NMR data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2537"/>
-        <oboInOwl:hasDefinition>Protein nuclear magnetic resonance (NMR) raw data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0939 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0939">
-        <rdfs:label>Protein circular dichroism (CD) spectroscopic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2537"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0940 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0940">
-        <rdfs:label>Electron microscopy volume map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Volume map data from electron microscopy.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EM volume map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0941 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0941">
-        <rdfs:label>Electron microscopy model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation on a structural 3D model (volume map) from electron microscopy.</oboInOwl:hasDefinition>
-        <rdfs:comment>This might include the location in the model of the known features of a particular macromolecule.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0942 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0942">
-        <rdfs:label>2D PAGE image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Two-dimensional gel electrophoresis image</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0943 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0943">
-        <rdfs:label>Mass spectrometry spectra</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2536"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Spectra from mass spectrometry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0944 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0944">
-        <rdfs:label>Peptide mass fingerprint</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2536"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2979"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Peak list</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein fingerprint</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A set of peptide masses (peptide mass fingerprint) from mass spectrometry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0945 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0945">
-        <rdfs:label>Peptide identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2979"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0946 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0946">
-        <rdfs:label>Pathway or network annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0947 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0947">
-        <rdfs:label>Biological pathway map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A map (typically a diagram) of a biological pathway.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2600"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0948 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0948">
-        <rdfs:label>Data resource definition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0949 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0949">
-        <rdfs:label>Workflow metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Basic information, annotation or documentation concerning a workflow (but not the workflow itself).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0950 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0950">
-        <rdfs:label>Mathematical model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3307"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Biological model</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A biological model represented in mathematical terms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0951 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0951">
-        <rdfs:label>Statistical estimate score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1772"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A value representing estimated statistical significance of some observed data; typically sequence database hits.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0952 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0952">
-        <rdfs:label>EMBOSS database resource definition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Resource definition for an EMBOSS database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0953 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0953">
-        <rdfs:label>Version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000129&quot;</rdfs:seeAlso>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records.</rdfs:comment>
-        <rdfs:seeAlso>http://www.ebi.ac.uk/swo/maturity/SWO_9000061</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a version of software or data, for example name, version number and release date.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000653</rdfs:seeAlso>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:seeAlso>http://usefulinc.com/ns/doap#Version</rdfs:seeAlso>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0954 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0954">
-        <rdfs:label>Database cross-mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases.</oboInOwl:hasDefinition>
-        <rdfs:comment>The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0955 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0955">
-        <rdfs:label>Data index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0220"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An index of data of biological relevance.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0956 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0956">
-        <rdfs:label>Data index report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0220"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A report of an analysis of an index of biological data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database index annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0957 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0957">
-        <rdfs:label>Database metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0958 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0958">
-        <rdfs:label>Tool metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0959 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0959">
-        <rdfs:label>Job metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDbXref>Moby:PDGJOB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Textual metadata on a submitted or completed job.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0960 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0960">
-        <rdfs:label>User metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Textual metadata on a software author or end-user, for example a person or other software.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0962 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0962">
-        <rdfs:label>Small molecule report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0154"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Small molecule annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Small molecule report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Chemical structure report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on a specific chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0963 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0963">
-        <rdfs:label>Cell line report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:hasExactSynonym>Organism strain data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Cell line annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0964 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0964">
-        <rdfs:label>Scent annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report about a specific scent.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0966 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0966">
-        <rdfs:label>Ontology term</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0967"/>
-        <oboInOwl:hasExactSynonym>Ontology class name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term (name) from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ontology terms</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0967 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0967">
-        <rdfs:label>Ontology concept data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2353"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology class metadata</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Ontology term metadata</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning or derived from a concept from a biological ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0968 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0968">
-        <rdfs:label>Keyword</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Phrases</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Keyword(s) or phrase(s) used (typically) for text-searching purposes.</oboInOwl:hasDefinition>
-        <rdfs:comment>Boolean operators (AND, OR and NOT) and wildcard characters may be allowed.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:QueryString</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:BooleanQueryString</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Wildcard_Query</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Global_Keyword</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Terms</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Text</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0970 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0970">
-        <rdfs:label>Citation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2526"/>
-        <oboInOwl:hasDefinition>Bibliographic data that uniquely identifies a scientific article, book or other published material.</oboInOwl:hasDefinition>
-        <rdfs:comment>A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:GCP_SimpleCitation</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Reference</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Bibliographic reference</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Publication</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0971 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0971">
-        <rdfs:label>Article</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3068"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A document of scientific text, typically a full text article from a scientific journal.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0972 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0972">
-        <rdfs:label>Text mining report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An abstract of the results of text mining.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Text mining output</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0974 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0974">
-        <rdfs:label>Entity identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a biological entity or phenomenon.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0975 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0975">
-        <rdfs:label>Data resource identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An identifier of a data resource.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0976 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0976">
-        <rdfs:label>Identifier (typed)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This concept exists only to assist EDAM maintenance and navigation in graphical browsers.  It does not add semantic information.  This branch provides an alternative organisation of the concepts nested under &apos;Accession&apos; and &apos;Name&apos;. All concepts under here are already included under &apos;Accession&apos; or &apos;Name&apos;.</rdfs:comment>
-        <oboInOwl:hasDefinition>An identifier that identifies a particular type of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0977 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0977">
-        <rdfs:label>Tool identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a bioinformatics tool, e.g. an application or web service.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0978 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0978">
-        <rdfs:label>Discrete entity identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0979 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0979">
-        <rdfs:label>Entity feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0980 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0980">
-        <rdfs:label>Entity collection identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of a collection of discrete biological entities.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0981 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0981">
-        <rdfs:label>Phenomenon identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of a physical, observable biological occurrence or event.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0982 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0982">
-        <rdfs:label>Molecule identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>Name or other identifier of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0983 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0983">
-        <rdfs:label>Atom ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasExactSynonym>Atom identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier (e.g. character symbol) of a specific atom.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0984 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0984">
-        <rdfs:label>Molecule name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>Name of a specific molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0985 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0985">
-        <rdfs:label>Molecule type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>For example, &apos;Protein&apos;, &apos;DNA&apos;, &apos;RNA&apos; etc.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A label (text token) describing the type a molecule.</oboInOwl:hasDefinition>
-        <example>Protein|DNA|RNA</example>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0986 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0986">
-        <rdfs:label>Chemical identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Unique identifier of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1086"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0987 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0987">
-        <rdfs:label>Chromosome name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0984"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0919"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a chromosome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0988 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0988">
-        <rdfs:label>Peptide identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <oboInOwl:hasDefinition>Identifier of a peptide chain.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0989 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0989">
-        <rdfs:label>Protein identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0990 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0990">
-        <rdfs:label>Compound name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0984"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <oboInOwl:hasExactSynonym>Chemical name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique name of a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0991 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0991">
-        <rdfs:label>Chemical registry number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0992 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0992">
-        <rdfs:label>Ligand identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Code word for a ligand, for example from a PDB file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1086"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0993 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0993">
-        <rdfs:label>Drug identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2851"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a drug.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0994 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0994">
-        <rdfs:label>Amino acid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2016"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an amino acid.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Residue identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0995 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0995">
-        <rdfs:label>Nucleotide identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of a nucleotide.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0996 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0996">
-        <rdfs:label>Monosaccharide identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a monosaccharide.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0997 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0997">
-        <rdfs:label>Chemical name (ChEBI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasExactSynonym>ChEBI chemical name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is the recommended chemical name for use for example in database annotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0998 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0998">
-        <rdfs:label>Chemical name (IUPAC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasDefinition>IUPAC recommended name of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>IUPAC chemical name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0999 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0999">
-        <rdfs:label>Chemical name (INN)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasExactSynonym>INN chemical name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>International Non-proprietary Name (INN or &apos;generic name&apos;) of a chemical compound, assigned by the World Health Organization (WHO).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1000 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1000">
-        <rdfs:label>Chemical name (brand)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasDefinition>Brand name of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Brand chemical name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1001 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1001">
-        <rdfs:label>Chemical name (synonymous)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Synonymous chemical name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Synonymous name of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1002 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1002">
-        <rdfs:label>Chemical registry number (CAS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0991"/>
-        <oboInOwl:hasExactSynonym>CAS chemical registry number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>CAS registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1003">
-        <rdfs:label>Chemical registry number (Beilstein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0991"/>
-        <oboInOwl:hasExactSynonym>Beilstein chemical registry number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Beilstein registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1004">
-        <rdfs:label>Chemical registry number (Gmelin)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0991"/>
-        <oboInOwl:hasExactSynonym>Gmelin chemical registry number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gmelin registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1005">
-        <rdfs:label>HET group name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasDefinition>3-letter code word for a ligand (HET group) from a PDB file, for example ATP.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Short ligand name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Component identifier code</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1006">
-        <rdfs:label>Amino acid name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0994"/>
-        <oboInOwl:hasDefinition>String of one or more ASCII characters representing an amino acid.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1007">
-        <rdfs:label>Nucleotide code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0995"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>String of one or more ASCII characters representing a nucleotide.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1008 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1008">
-        <rdfs:label>Polypeptide chain ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0988"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1467"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: chain</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Chain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a polypeptide chain from a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_strand_id</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Protein chain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PDB strand id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PDB chain identifier</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Polypeptide chain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1009 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1009">
-        <rdfs:label>Protein name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0984"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <oboInOwl:hasDefinition>Name of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1010 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1010">
-        <rdfs:label>Enzyme identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of an enzyme or record from a database of enzymes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1011 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1011">
-        <rdfs:label>EC number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <regex>[0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>EC code</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:EC_Number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An Enzyme Commission (EC) number of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EC</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Annotated_EC_Number</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Enzyme Commission number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1012 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1012">
-        <rdfs:label>Enzyme name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1010"/>
-        <oboInOwl:hasDefinition>Name of an enzyme.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1013 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1013">
-        <rdfs:label>Restriction enzyme name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1012"/>
-        <oboInOwl:hasDefinition>Name of a restriction enzyme.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1014 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1014">
-        <rdfs:label>Sequence position specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A specification (partial or complete) of one or more positions or regions of a molecular sequence or map.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1016"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1015 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1015">
-        <rdfs:label>Sequence feature ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3034"/>
-        <oboInOwl:hasDefinition>A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1016 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1016">
-        <rdfs:label>Sequence position</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:hasDbXref>WHATIF: number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_atom_site</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.id</oboInOwl:hasDbXref>
-        <oboInOwl:hasRelatedSynonym>SO:0000735</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>A position of one or more points (base or residue) in a sequence, or part of such a specification.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1017 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1017">
-        <rdfs:label>Sequence range</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Specification of range(s) of sequence positions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1018 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1018">
-        <rdfs:label>Nucleic acid feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of an nucleic acid feature.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1015"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1019 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1019">
-        <rdfs:label>Protein feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Name or other identifier of a protein feature.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1015"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1020 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1020">
-        <rdfs:label>Sequence feature key</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <oboInOwl:hasExactSynonym>Sequence feature method</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence feature type</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1021 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1021">
-        <rdfs:label>Sequence feature qualifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Typically one of the EMBL or Swiss-Prot feature qualifiers.</oboInOwl:hasDefinition>
-        <rdfs:comment>Feature qualifiers hold information about a feature beyond that provided by the feature key and location.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1022 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1022">
-        <rdfs:label>Sequence feature label</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <oboInOwl:hasExactSynonym>Sequence feature name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Typically an EMBL or Swiss-Prot feature label.</oboInOwl:hasDefinition>
-        <rdfs:comment>A feature label identifies a feature of a sequence database entry. When used with the database name and the entry&apos;s primary accession number, it is a unique identifier of that feature.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1023 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1023">
-        <rdfs:label>EMBOSS Uniform Feature Object</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3034"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UFO</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1024 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1024">
-        <rdfs:label>Codon name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>String of one or more ASCII characters representing a codon.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1025 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1025">
-        <rdfs:label>Gene identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDbXref>Moby:GeneAccessionList</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1026 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1026">
-        <rdfs:label>Gene symbol</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2299"/>
-        <oboInOwl:hasDbXref>Moby_namespace:Global_GeneSymbol</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:Global_GeneCommonName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1027 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1027">
-        <rdfs:label>Gene ID (NCBI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1098"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>NCBI geneid</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene identifier (NCBI)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Entrez gene ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene identifier (Entrez)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:LocusID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An NCBI unique identifier of a gene.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>NCBI gene ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1028 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1028">
-        <rdfs:label>Gene identifier (NCBI RefSeq)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>An NCBI RefSeq unique identifier of a gene.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1027"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1029 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1029">
-        <rdfs:label>Gene identifier (NCBI UniGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>An NCBI UniGene unique identifier of a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1104"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1030 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1030">
-        <rdfs:label>Gene identifier (Entrez)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An Entrez unique identifier of a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>[0-9]+</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1027"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1031 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1031">
-        <rdfs:label>Gene ID (CGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>CGD ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a gene or feature from the CGD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1032 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1032">
-        <rdfs:label>Gene ID (DictyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a gene from DictyBase.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1033 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1033">
-        <rdfs:label>Ensembl gene ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene ID (Ensembl)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a gene (or other feature) from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1034 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1034">
-        <rdfs:label>Gene ID (SGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2632"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the SGD database.</oboInOwl:hasDefinition>
-        <regex>S[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>SGD identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1035 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1035">
-        <rdfs:label>Gene ID (GeneDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>Moby_namespace:GeneDB</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>GeneDB identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9\.-]*</regex>
-        <oboInOwl:hasDefinition>Identifier of a gene from the GeneDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1036 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1036">
-        <rdfs:label>TIGR identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the TIGR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1037 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1037">
-        <rdfs:label>TAIR accession (gene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2387"/>
-        <regex>Gene:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an gene from the TAIR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1038 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1038">
-        <rdfs:label>Protein domain ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1468"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein structural domain.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is typically a character or string concatenated with a PDB identifier and a chain identifier.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1039 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1039">
-        <rdfs:label>SCOP domain identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1038"/>
-        <oboInOwl:hasDefinition>Identifier of a protein domain (or other node) from the SCOP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1040 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1040">
-        <rdfs:label>CATH domain ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2700"/>
-        <example>1nr3A00</example>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CATH domain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a protein domain from CATH.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1041 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1041">
-        <rdfs:label>SCOP concise classification string (sccs)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1039"/>
-        <oboInOwl:hasDefinition>A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1042 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1042">
-        <rdfs:label>SCOP sunid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1039"/>
-        <oboInOwl:hasDefinition>Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>sunid</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>SCOP unique identifier</oboInOwl:hasExactSynonym>
-        <example>33229</example>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1043 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1043">
-        <rdfs:label>CATH node ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2700"/>
-        <example>3.30.1190.10.1.1.1.1.1</example>
-        <oboInOwl:hasExactSynonym>CATH code</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A code number identifying a node from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>CATH node identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1044 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1044">
-        <rdfs:label>Kingdom name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1045 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1045">
-        <rdfs:label>Species name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a species (typically a taxonomic group) of organism.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Organism species</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1046 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1046">
-        <rdfs:label>Strain name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2379"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a strain of an organism variant, typically a plant, virus or bacterium.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1047 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1047">
-        <rdfs:label>URI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:hasDefinition>A string of characters that name or otherwise identify a resource on the Internet.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>URIs</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1048 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1048">
-        <rdfs:label>Database ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a biological or bioinformatics database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1049 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1049">
-        <rdfs:label>Directory name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a directory.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1050 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1050">
-        <rdfs:label>File name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name (or part of a name) of a file (of any type).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1051 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1051">
-        <rdfs:label>Ontology name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2338"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of an ontology of biological or bioinformatics concepts and relations.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1052 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1052">
-        <rdfs:label>URL</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1047"/>
-        <oboInOwl:hasDefinition>A Uniform Resource Locator (URL).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:URL</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Link</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1053 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1053">
-        <rdfs:label>URN</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1047"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A Uniform Resource Name (URN).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1055 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1055">
-        <rdfs:label>LSID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1053"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:&lt;Authority&gt;:&lt;Namespace&gt;:&lt;ObjectID&gt;[:&lt;Version&gt;]</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Life Science Identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A Life Science Identifier (LSID) - a unique identifier of some data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1056 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1056">
-        <rdfs:label>Database name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1048"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a biological or bioinformatics database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1057 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1057">
-        <rdfs:label>Sequence database name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The name of a molecular sequence database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1056"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1058 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1058">
-        <rdfs:label>Enumerated file name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1050"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a file (of any type) with restricted possible values.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1059 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1059">
-        <rdfs:label>File name extension</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1050"/>
-        <oboInOwl:hasDefinition>The extension of a file name.</oboInOwl:hasDefinition>
-        <rdfs:comment>A file extension is the characters appearing after the final &apos;.&apos; in the file name.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1060 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1060">
-        <rdfs:label>File base name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1050"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The base name of a file.</oboInOwl:hasDefinition>
-        <rdfs:comment>A file base name is the file name stripped of its directory specification and extension.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1061 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1061">
-        <rdfs:label>QSAR descriptor name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2110"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0847"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a QSAR descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1062 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1062">
-        <rdfs:label>Database entry identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This concept is required for completeness. It should never have child concepts.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1063 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1063">
-        <rdfs:label>Sequence identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of molecular sequence(s) or entries from a molecular sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1064 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1064">
-        <rdfs:label>Sequence set ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0850"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a set of molecular sequence(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1065 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1065">
-        <rdfs:label>Sequence signature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1114"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1115"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1066 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1066">
-        <rdfs:label>Sequence alignment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a molecular sequence alignment, for example a record from an alignment database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1067 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1067">
-        <rdfs:label>Phylogenetic distance matrix identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a phylogenetic distance matrix.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1068 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1068">
-        <rdfs:label>Phylogenetic tree ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a phylogenetic tree for example from a phylogenetic tree database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1069 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1069">
-        <rdfs:label>Comparison matrix identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0874"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a comparison matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1070 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1070">
-        <rdfs:label>Structure ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3035"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1071 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1071">
-        <rdfs:label>Structural (3D) profile ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structural profile identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1072 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1072">
-        <rdfs:label>Structure alignment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0886"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of tertiary structure alignments.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1073 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1073">
-        <rdfs:label>Amino acid index ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1501"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an index of amino acid physicochemical and biochemical property data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1074 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1074">
-        <rdfs:label>Protein interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasBroadSynonym>Molecular interaction ID</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Identifier of a report of protein interactions from a protein interaction database (typically).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1075 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1075">
-        <rdfs:label>Protein family identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Protein secondary database record identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a protein family.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1076 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1076">
-        <rdfs:label>Codon usage table name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2111"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Unique name of a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1077">
-        <rdfs:label>Transcription factor identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <oboInOwl:hasDefinition>Identifier of a transcription factor (or a TF binding site).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1078">
-        <rdfs:label>Experiment annotation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of microarray data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1079 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1079">
-        <rdfs:label>Electron microscopy model ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0941"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of electron microscopy data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1080">
-        <rdfs:label>Gene expression report ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession of a report of gene expression (e.g. a gene expression profile) from a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression profile identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1081">
-        <rdfs:label>Genotype and phenotype annotation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0920"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1082 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1082">
-        <rdfs:label>Pathway or network identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of biological pathways or networks.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1083">
-        <rdfs:label>Workflow ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological or biomedical workflow, typically from a database of workflows.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1084">
-        <rdfs:label>Data resource definition ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a data type definition from some provider.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Data resource definition identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1085">
-        <rdfs:label>Biological model ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0950"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Biological model identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a mathematical model, typically an entry from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1086 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1086">
-        <rdfs:label>Compound identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0962"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of chemicals.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Small molecule identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1087 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1087">
-        <rdfs:label>Ontology concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3025"/>
-        <oboInOwl:hasDefinition>A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology concept ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1088 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1088">
-        <rdfs:label>Article ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0971"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a scientific article.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Article identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1089 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1089">
-        <rdfs:label>FlyBase ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>Identifier of an object from the FlyBase database.</oboInOwl:hasDefinition>
-        <regex>FB[a-zA-Z_0-9]{2}[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1091 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1091">
-        <rdfs:label>WormBase name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <oboInOwl:hasDefinition>Name of an object from the WormBase database, usually a human-readable name.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1092">
-        <rdfs:label>WormBase class</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Class of an object from the WormBase database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A WormBase class describes the type of object such as &apos;sequence&apos; or &apos;protein&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1093 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1093">
-        <rdfs:label>Sequence accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1063"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A persistent, unique identifier of a molecular sequence database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1094">
-        <rdfs:label>Sequence type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).</rdfs:comment>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of molecular sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1095 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1095">
-        <rdfs:label>EMBOSS Uniform Sequence Address</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1063"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasExactSynonym>EMBOSS USA</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1096 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1096">
-        <rdfs:label>Sequence accession (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1093"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2976"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession number of a protein sequence database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein sequence accession number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1097">
-        <rdfs:label>Sequence accession (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1093"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession number of a nucleotide sequence database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1098 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1098">
-        <rdfs:label>RefSeq accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2362"/>
-        <oboInOwl:hasDefinition>Accession number of a RefSeq database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>RefSeq ID</oboInOwl:hasExactSynonym>
-        <regex>(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1099">
-        <rdfs:label>UniProt accession (extended)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number.</oboInOwl:hasDefinition>
-        <regex>[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <example>Q7M1G0|P43353-2|P01012.107</example>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3021"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1100">
-        <rdfs:label>PIR identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of PIR sequence database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PIR ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PIR accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1101 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1101">
-        <rdfs:label>TREMBL accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a TREMBL sequence database entry.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.2</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_3021"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1102">
-        <rdfs:label>Gramene primary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2915"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gramene primary ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Primary identifier of a Gramene database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1103 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1103">
-        <rdfs:label>EMBL/GenBank/DDBJ ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <oboInOwl:hasDefinition>Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1104 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1104">
-        <rdfs:label>Sequence cluster ID (UniGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasExactSynonym>UniGene identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniGene cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniGene ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniGene cluster ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of an entry (gene cluster) from the NCBI UniGene database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1105 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1105">
-        <rdfs:label>dbEST accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2292"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <oboInOwl:hasExactSynonym>dbEST ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a dbEST database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1106 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1106">
-        <rdfs:label>dbSNP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>dbSNP identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a dbSNP database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1110">
-        <rdfs:label>EMBOSS sequence type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The EMBOSS type of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1111">
-        <rdfs:label>EMBOSS listfile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1112">
-        <rdfs:label>Sequence cluster ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1064"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a cluster of molecular sequence(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1113 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1113">
-        <rdfs:label>Sequence cluster ID (COG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasExactSynonym>COG ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the COG database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1114 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1114">
-        <rdfs:label>Sequence motif identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1353"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a sequence motif, for example an entry from a motif database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1115 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1115">
-        <rdfs:label>Sequence profile ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a sequence profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A sequence profile typically represents a sequence alignment.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1116 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1116">
-        <rdfs:label>ELM ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1114"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the ELMdb database of protein functional sites.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1117 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1117">
-        <rdfs:label>Prosite accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1114"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry from the Prosite database.</oboInOwl:hasDefinition>
-        <regex>PS[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>Prosite ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1118">
-        <rdfs:label>HMMER hidden Markov model ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1115"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1364"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Unique identifier or name of a HMMER hidden Markov model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1119 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1119">
-        <rdfs:label>JASPAR profile ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1115"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier or name of a profile from the JASPAR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1120 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1120">
-        <rdfs:label>Sequence alignment type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1121 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1121">
-        <rdfs:label>BLAST sequence alignment type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The type of a BLAST sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1122">
-        <rdfs:label>Phylogenetic tree type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>For example &apos;nj&apos;, &apos;upgmp&apos; etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <example>nj|upgmp</example>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1123">
-        <rdfs:label>TreeBASE study accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1068"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the TreeBASE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1124 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1124">
-        <rdfs:label>TreeFam accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1068"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry from the TreeFam database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1125 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1125">
-        <rdfs:label>Comparison matrix type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <example>blosum|pam|gonnet|id</example>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a comparison matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix type</oboInOwl:hasExactSynonym>
-        <rdfs:comment>For example &apos;blosum&apos;, &apos;pam&apos;, &apos;gonnet&apos;, &apos;id&apos; etc. Comparison matrix type may be required where a series of matrices of a certain type are used.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1126">
-        <rdfs:label>Comparison matrix name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1069"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0874"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Substitution matrix name</oboInOwl:hasExactSynonym>
-        <rdfs:comment>See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.</rdfs:comment>
-        <oboInOwl:hasDefinition>Unique name or identifier of a comparison matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1127">
-        <rdfs:label>PDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1070"/>
-        <oboInOwl:hasDefinition>An identifier of an entry from the PDB database.</oboInOwl:hasDefinition>
-        <regex>[a-zA-Z_0-9]{4}</regex>
-        <oboInOwl:hasExactSynonym>PDBID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PDB identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1128">
-        <rdfs:label>AAindex ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1073"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the AAindex database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1129 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1129">
-        <rdfs:label>BIND accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the BIND database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1130">
-        <rdfs:label>IntAct accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>EBI\-[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry from the IntAct database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1131 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1131">
-        <rdfs:label>Protein family name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1075"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a protein family.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1132 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1132">
-        <rdfs:label>InterPro entry name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1131"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of an InterPro entry, usually indicating the type of protein matches for that entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1133">
-        <rdfs:label>InterPro accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Primary accession number of an InterPro entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>InterPro primary accession</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Every InterPro entry has a unique accession number to provide a persistent citation of database records.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>InterPro primary accession number</oboInOwl:hasExactSynonym>
-        <example>IPR015590</example>
-        <regex>IPR[0-9]{6}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1134">
-        <rdfs:label>InterPro secondary accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1133"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Secondary accession number of an InterPro entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>InterPro secondary accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1135">
-        <rdfs:label>Gene3D ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the Gene3D database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1136 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1136">
-        <rdfs:label>PIRSF ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <regex>PIRSF[0-9]{6}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the PIRSF database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1137">
-        <rdfs:label>PRINTS code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PR[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>The unique identifier of an entry in the PRINTS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1138 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1138">
-        <rdfs:label>Pfam accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <regex>PF[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Accession number of a Pfam entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1139">
-        <rdfs:label>SMART accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the SMART database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>SM[0-9]{5}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1140">
-        <rdfs:label>Superfamily hidden Markov model number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>Unique identifier (number) of a hidden Markov model from the Superfamily database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1141">
-        <rdfs:label>TIGRFam ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasExactSynonym>TIGRFam accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of an entry (family) from the TIGRFam database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1142 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1142">
-        <rdfs:label>ProDom accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>A ProDom domain family accession number.</oboInOwl:hasDefinition>
-        <regex>PD[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>ProDom is a protein domain family database.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1143">
-        <rdfs:label>TRANSFAC accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2911"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the TRANSFAC database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1144 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1144">
-        <rdfs:label>ArrayExpress accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the ArrayExpress database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[AEP]-[a-zA-Z_0-9]{4}-[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>ArrayExpress experiment ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1145 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1145">
-        <rdfs:label>PRIDE experiment accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PRIDE experiment accession number.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1146 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1146">
-        <rdfs:label>EMDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1079"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the EMDB electron microscopy database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1147">
-        <rdfs:label>GEO accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the GEO database.</oboInOwl:hasDefinition>
-        <regex>o^GDS[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1148 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1148">
-        <rdfs:label>GermOnline ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GermOnline database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1149 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1149">
-        <rdfs:label>EMAGE ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the EMAGE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1150 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1150">
-        <rdfs:label>Disease ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1622"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of disease.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1151 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1151">
-        <rdfs:label>HGVbase ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1081"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the HGVbase database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1152 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1152">
-        <rdfs:label>HIVDB identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the HIVDB database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1153 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1153">
-        <rdfs:label>OMIM ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1081"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[*#+%^]?[0-9]{6}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry from the OMIM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1154">
-        <rdfs:label>KEGG object identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an object from one of the KEGG databases (excluding the GENES division).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1155 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1155">
-        <rdfs:label>Pathway ID (reactome)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Reactome database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Reactome ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <regex>REACT_[0-9]+(\.[0-9]+)?</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1156">
-        <rdfs:label>Pathway ID (aMAZE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>aMAZE ID</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the aMAZE database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1082"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1157">
-        <rdfs:label>Pathway ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasExactSynonym>BioCyc pathway ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an pathway from the BioCyc biological pathways database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1158">
-        <rdfs:label>Pathway ID (INOH)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>INOH identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from the INOH database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1159">
-        <rdfs:label>Pathway ID (PATIKA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the PATIKA database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>PATIKA ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1160">
-        <rdfs:label>Pathway ID (CPDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <rdfs:comment>This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>CPDB ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1161 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1161">
-        <rdfs:label>Pathway ID (Panther)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of a biological pathway from the Panther Pathways database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PTHR[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>Panther Pathways ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1162 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1162">
-        <rdfs:label>MIRIAM identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2902"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Unique identifier of a MIRIAM data resource.</oboInOwl:hasDefinition>
-        <example>MIR:00100005</example>
-        <regex>MIR:[0-9]{8}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is the identifier used internally by MIRIAM for a data type.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1163">
-        <rdfs:label>MIRIAM data type name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2253"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a data type from the MIRIAM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1164">
-        <rdfs:label>MIRIAM URI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1047"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2902"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The URI (URL or URN) of a data entity from the MIRIAM database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>identifiers.org synonym</oboInOwl:hasExactSynonym>
-        <example>urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202</example>
-        <rdfs:comment>A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1165 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1165">
-        <rdfs:label>MIRIAM data type primary name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1163"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The primary name of a MIRIAM data type is taken from a controlled vocabulary.</rdfs:comment>
-        <example>UniProt|Enzyme Nomenclature</example>
-        <oboInOwl:hasDefinition>The primary name of a data type from the MIRIAM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>A protein entity has the MIRIAM data type &apos;UniProt&apos;, and an enzyme has the MIRIAM data type &apos;Enzyme Nomenclature&apos;.</rdfs:comment>
-        <owl:annotatedTarget>UniProt|Enzyme Nomenclature</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_1165"/>
-        <owl:annotatedProperty rdf:resource="http://edamontology.org/example"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_1166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1166">
-        <rdfs:label>MIRIAM data type synonymous name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1163"/>
-        <oboInOwl:hasDefinition>A synonymous name of a data type from the MIRIAM database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A synonymous name for a MIRIAM data type taken from a controlled vocabulary.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1167">
-        <rdfs:label>Taverna workflow ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1083"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a Taverna workflow.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1170 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1170">
-        <rdfs:label>Biological model name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1085"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a biological (mathematical) model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1171 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1171">
-        <rdfs:label>BioModel ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2891"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the BioModel database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>(BIOMD|MODEL)[0-9]{10}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1172">
-        <rdfs:label>PubChem CID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2639"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>PubChem compound accession identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1173">
-        <rdfs:label>ChemSpider ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the ChemSpider database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1174">
-        <rdfs:label>ChEBI ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the ChEBI database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChEBI IDs</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>ChEBI identifier</oboInOwl:hasExactSynonym>
-        <regex>CHEBI:[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1175">
-        <rdfs:label>BioPax concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the BioPax ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1176">
-        <rdfs:label>GO concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasExactSynonym>GO concept identifier</oboInOwl:hasExactSynonym>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from The Gene Ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1177">
-        <rdfs:label>MeSH concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the MeSH vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1178">
-        <rdfs:label>HGNC concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the HGNC controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1179">
-        <rdfs:label>NCBI taxonomy ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <oboInOwl:hasExactSynonym>NCBI taxonomy identifier</oboInOwl:hasExactSynonym>
-        <regex>[1-9][0-9]{0,8}</regex>
-        <oboInOwl:hasExactSynonym>NCBI tax ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database.</oboInOwl:hasDefinition>
-        <example>9662|3483|182682</example>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1180">
-        <rdfs:label>Plant Ontology concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasDefinition>An identifier of a concept from the Plant Ontology (PO).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1181 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1181">
-        <rdfs:label>UMLS concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasDefinition>An identifier of a concept from the UMLS vocabulary.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1182">
-        <rdfs:label>FMA concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasDefinition>An identifier of a concept from Foundational Model of Anatomy.</oboInOwl:hasDefinition>
-        <regex>FMA:[0-9]+</regex>
-        <rdfs:comment>Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1183">
-        <rdfs:label>EMAP concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the EMAP mouse ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1184">
-        <rdfs:label>ChEBI concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the ChEBI ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1185 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1185">
-        <rdfs:label>MGED concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the MGED ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1186 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1186">
-        <rdfs:label>myGrid concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.</rdfs:comment>
-        <oboInOwl:hasDefinition>An identifier of a concept from the myGrid ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1187 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1187">
-        <rdfs:label>PubMed ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1088"/>
-        <oboInOwl:hasExactSynonym>PMID</oboInOwl:hasExactSynonym>
-        <regex>[1-9][0-9]{0,8}</regex>
-        <oboInOwl:hasDefinition>PubMed unique identifier of an article.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <example>4963447</example>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1188 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1188">
-        <rdfs:label>DOI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1088"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>(doi\:)?[0-9]{2}\.[0-9]{4}/.*</regex>
-        <oboInOwl:hasExactSynonym>Digital Object Identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Digital Object Identifier (DOI) of a published article.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1189 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1189">
-        <rdfs:label>Medline UI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Medline UI (unique identifier) of an article.</oboInOwl:hasDefinition>
-        <rdfs:comment>The use of Medline UI has been replaced by the PubMed unique identifier.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Medline unique identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1190 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1190">
-        <rdfs:label>Tool name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0977"/>
-        <oboInOwl:hasDefinition>The name of a computer package, application, method or function.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1191">
-        <rdfs:label>Tool name (signature)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The unique name of a signature (sequence classifier) method.</oboInOwl:hasDefinition>
-        <rdfs:comment>Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1192 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1192">
-        <rdfs:label>Tool name (BLAST)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <rdfs:comment>This include &apos;blastn&apos;, &apos;blastp&apos;, &apos;blastx&apos;, &apos;tblastn&apos; and &apos;tblastx&apos;.</rdfs:comment>
-        <oboInOwl:hasDefinition>The name of a BLAST tool.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>BLAST name</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1193 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1193">
-        <rdfs:label>Tool name (FASTA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a FASTA tool.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes &apos;fasta3&apos;, &apos;fastx3&apos;, &apos;fasty3&apos;, &apos;fastf3&apos;, &apos;fasts3&apos; and &apos;ssearch&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1194">
-        <rdfs:label>Tool name (EMBOSS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <oboInOwl:hasDefinition>The name of an EMBOSS application.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1195">
-        <rdfs:label>Tool name (EMBASSY package)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <oboInOwl:hasDefinition>The name of an EMBASSY package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1201 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1201">
-        <rdfs:label>QSAR descriptor (constitutional)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <oboInOwl:hasDefinition>A QSAR constitutional descriptor.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>QSAR constitutional descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1202">
-        <rdfs:label>QSAR descriptor (electronic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A QSAR electronic descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>QSAR electronic descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1203">
-        <rdfs:label>QSAR descriptor (geometrical)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <oboInOwl:hasExactSynonym>QSAR geometrical descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A QSAR geometrical descriptor.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1204">
-        <rdfs:label>QSAR descriptor (topological)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>QSAR topological descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A QSAR topological descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1205 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1205">
-        <rdfs:label>QSAR descriptor (molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <oboInOwl:hasDefinition>A QSAR molecular descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>QSAR molecular descriptor</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1233">
-        <rdfs:label>Sequence set (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:hasDefinition>Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1234 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1234">
-        <rdfs:label>Sequence set (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0850"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1235">
-        <rdfs:label>Sequence cluster</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0850"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0724"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.</oboInOwl:hasDefinition>
-        <rdfs:comment>The cluster might include sequences identifiers, short descriptions, alignment and summary information.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1236">
-        <rdfs:label>Psiblast checkpoint file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension &apos;.asn&apos;.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1237">
-        <rdfs:label>HMMER synthetic sequences set</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Sequences generated by HMMER package in FASTA-style format.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1238">
-        <rdfs:label>Proteolytic digest</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1239">
-        <rdfs:label>Restriction digest</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <oboInOwl:hasDefinition>Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>SO:0000412</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1240">
-        <rdfs:label>PCR primers</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1241">
-        <rdfs:label>vectorstrip cloning vector definition file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1242">
-        <rdfs:label>Primer3 internal oligo mishybridizing library</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1243">
-        <rdfs:label>Primer3 mispriming library file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1244 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1244">
-        <rdfs:label>primersearch primer pairs sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>File of one or more pairs of primer sequences, as used by EMBOSS primersearch application.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1245">
-        <rdfs:label>Sequence cluster (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1233"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:hasExactSynonym>Protein sequence cluster</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The sequences are typically related, for example a family of sequences.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A cluster of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1246">
-        <rdfs:label>Sequence cluster (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:hasDefinition>A cluster of nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence cluster</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The sequences are typically related, for example a family of sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1249 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1249">
-        <rdfs:label>Sequence length</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1250">
-        <rdfs:label>Word size</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Word size is used for example in word-based sequence database search methods.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Word length</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Size of a sequence word.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1251 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1251">
-        <rdfs:label>Window size</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Size of a sequence window.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1252">
-        <rdfs:label>Sequence length range</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Specification of range(s) of length of sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1253">
-        <rdfs:label>Sequence information report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2043"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1254">
-        <rdfs:label>Sequence property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2955"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence properties report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1255 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1255">
-        <rdfs:label>Sequence features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Sequence features report</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D058977</rdfs:seeAlso>
-        <oboInOwl:hasRelatedSynonym>SO:0000110</oboInOwl:hasRelatedSynonym>
-        <rdfs:comment>This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features.  General feature reports are a source of sequence feature table information although internal conversion would be required.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>General sequence features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Feature record</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1256 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1256">
-        <rdfs:label>Sequence features (comparative)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1257">
-        <rdfs:label>Sequence property (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report of general sequence properties derived from protein sequence data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1258">
-        <rdfs:label>Sequence property (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report of general sequence properties derived from nucleotide sequence data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0912"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1259">
-        <rdfs:label>Sequence complexity report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1254"/>
-        <oboInOwl:hasDefinition>A report on sequence complexity, for example low-complexity or repeat regions in sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence property (complexity)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1260 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1260">
-        <rdfs:label>Sequence ambiguity report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1254"/>
-        <oboInOwl:hasDefinition>A report on ambiguity in molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence property (ambiguity)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1261 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1261">
-        <rdfs:label>Sequence composition report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1254"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report (typically a table) on character or word composition / frequency of a molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence property (composition)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1262 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1262">
-        <rdfs:label>Peptide molecular weight hits</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1233"/>
-        <oboInOwl:hasDefinition>A report on peptide fragments of certain molecular weight(s) in one or more protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1263 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1263">
-        <rdfs:label>Base position variability plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of third base position variability in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1264">
-        <rdfs:label>Sequence composition table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A table of character or word composition / frequency of a molecular sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1265">
-        <rdfs:label>Base frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A table of base frequencies of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1266 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1266">
-        <rdfs:label>Base word frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A table of word composition of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1267 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1267">
-        <rdfs:label>Amino acid frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasExactSynonym>Sequence composition (amino acid frequencies)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A table of amino acid frequencies of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1268 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1268">
-        <rdfs:label>Amino acid word frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A table of amino acid word composition of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence composition (amino acid words)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1269">
-        <rdfs:label>DAS sequence feature annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Annotation of a molecular sequence in DAS format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1978"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1270 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1270">
-        <rdfs:label>Feature table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:hasExactSynonym>Sequence feature table</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation of positional sequence features, organized into a standard feature table.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1274 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1274">
-        <rdfs:label>Map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>DNA map</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A map of (typically one) DNA sequence annotated with positional or non-positional features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1276 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1276">
-        <rdfs:label>Nucleic acid features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:hasDefinition>An informative report on intrinsic positional features of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Genome features</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Genomic features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid feature table</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Feature table (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1277">
-        <rdfs:label>Protein features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:hasDefinition>An informative report on intrinsic positional features of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Feature table (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein feature table</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1278">
-        <rdfs:label>Genetic map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1274"/>
-        <oboInOwl:hasDefinition>A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Linkage map</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:GeneticMap</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1279 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1279">
-        <rdfs:label>Sequence map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1280"/>
-        <rdfs:comment>A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1280">
-        <rdfs:label>Physical map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1274"/>
-        <oboInOwl:hasDefinition>A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them.</oboInOwl:hasDefinition>
-        <rdfs:comment>Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1281 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1281">
-        <rdfs:label>Sequence signature map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Image of a sequence with matches to signatures, motifs or profiles.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1283 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1283">
-        <rdfs:label>Cytogenetic map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1280"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A map showing banding patterns derived from direct observation of a stained chromosome.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Cytologic map</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Chromosome map</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Cytogenic map</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances.  Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1284">
-        <rdfs:label>DNA transduction map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1278"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A gene map showing distances between loci based on relative cotransduction frequencies.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1285">
-        <rdfs:label>Gene map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <oboInOwl:hasDefinition>Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1286 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1286">
-        <rdfs:label>Plasmid map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <oboInOwl:hasDefinition>Sequence map of a plasmid (circular DNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1288">
-        <rdfs:label>Genome map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence map of a whole genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1289">
-        <rdfs:label>Restriction map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2969"/>
-        <oboInOwl:hasDefinition>Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1290 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1290">
-        <rdfs:label>InterPro compact match image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Image showing matches between protein sequence(s) and InterPro Entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1291 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1291">
-        <rdfs:label>InterPro detailed match image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image showing detailed information on matches between protein sequence(s) and InterPro Entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1292">
-        <rdfs:label>InterPro architecture image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein.</rdfs:comment>
-        <oboInOwl:hasDefinition>Image showing the architecture of InterPro domains in a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1293">
-        <rdfs:label>SMART protein schematic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>SMART protein schematic in PNG format.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1294 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1294">
-        <rdfs:label>GlobPlot domain image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1298">
-        <rdfs:label>Sequence motif matches</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1299">
-        <rdfs:label>Sequence features (repeats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Repeat sequence map</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The report might include derived data map such as classification, annotation, organization, periodicity etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3126"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3129"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1300">
-        <rdfs:label>Gene and transcript structure (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1301">
-        <rdfs:label>Mobile genetic elements</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>regions of a nucleic acid sequence containing mobile genetic elements.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1302">
-        <rdfs:label>Nucleic acid features report (PolyA signal or site)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1303">
-        <rdfs:label>Nucleic acid features (quadruplexes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report on quadruplex-forming motifs in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1304">
-        <rdfs:label>Nucleic acid features report (CpG island and isochore)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>CpG rich regions (isochores) in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1305">
-        <rdfs:label>Nucleic acid features report (restriction sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1306">
-        <rdfs:label>Nucleosome exclusion sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Report on nucleosome formation potential or exclusion sequence(s).</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1307">
-        <rdfs:label>Nucleic acid features report (splice sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>splice sites in a nucleotide sequence or alternative RNA splicing events.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1308">
-        <rdfs:label>Nucleic acid features report (matrix/scaffold attachment sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1309">
-        <rdfs:label>Gene features (exonic splicing enhancer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on exonic splicing enhancers (ESE) in an exon.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1310">
-        <rdfs:label>Nucleic acid features (microRNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3137"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1311">
-        <rdfs:label>Gene features report (operon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>operons (operators, promoters and genes) from a bacterial genome.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1312">
-        <rdfs:label>Nucleic acid features report (promoters)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1313">
-        <rdfs:label>Coding region</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1314">
-        <rdfs:label>Gene features (SECIS element)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1315">
-        <rdfs:label>Transcription factor binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>transcription factor binding sites (TFBS) in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1321">
-        <rdfs:label>Protein features (sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1322">
-        <rdfs:label>Protein features report (signal peptides)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>signal peptides or signal peptide cleavage sites in protein sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1323">
-        <rdfs:label>Protein features report (cleavage sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1324 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1324">
-        <rdfs:label>Protein features (post-translation modifications)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>post-translation modifications in a protein sequence, typically describing the specific sites involved.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1325">
-        <rdfs:label>Protein features report (active sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>catalytic residues (active site) of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1326">
-        <rdfs:label>Protein features report (binding sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1327">
-        <rdfs:label>Protein features (epitopes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Epitope mapping is commonly done during vaccine design.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1326"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1328">
-        <rdfs:label>Protein features report (nucleic acid binding sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>RNA and DNA-binding proteins and binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1329">
-        <rdfs:label>MHC Class I epitopes report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on epitopes that bind to MHC class I molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1326"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1330">
-        <rdfs:label>MHC Class II epitopes report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on predicted epitopes that bind to MHC class II molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1326"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1331">
-        <rdfs:label>Protein features (PEST sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report or plot of PEST sites in a protein sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>&apos;PEST&apos; motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1323"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1338">
-        <rdfs:label>Sequence database hits scores list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Scores from a sequence database search (for example a BLAST search).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0857"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1339">
-        <rdfs:label>Sequence database hits alignments list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignments from a sequence database search (for example a BLAST search).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0857"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1340">
-        <rdfs:label>Sequence database hits evaluation data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0857"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1344">
-        <rdfs:label>MEME motif alphabet</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alphabet for the motifs (patterns) that MEME will search for.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1345">
-        <rdfs:label>MEME background frequencies file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>MEME background frequencies file.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1346">
-        <rdfs:label>MEME motifs directive file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>File of directives for ordering and spacing of MEME motifs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1347 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1347">
-        <rdfs:label>Dirichlet distribution</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:hasDefinition>Dirichlet distribution used by hidden Markov model analysis programs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1348">
-        <rdfs:label>HMM emission and transition counts</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3354"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1352">
-        <rdfs:label>Regular expression</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Regular expression pattern.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1353">
-        <rdfs:label>Sequence motif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0860"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1354">
-        <rdfs:label>Sequence profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0860"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Some type of statistical model representing a (typically multiple) sequence alignment.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_010531</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1355">
-        <rdfs:label>Protein signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2762"/>
-        <oboInOwl:hasDefinition>An informative report about a specific or conserved protein sequence pattern.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>InterPro entry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein repeat signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein region signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein site signature</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein family signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein domain signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1358">
-        <rdfs:label>Prosite nucleotide pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A nucleotide regular expression pattern from the Prosite database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1353"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1359">
-        <rdfs:label>Prosite protein pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein regular expression pattern from the Prosite database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1353"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1361 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1361">
-        <rdfs:label>Position frequency matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PFM</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1362 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1362">
-        <rdfs:label>Position weight matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <oboInOwl:hasExactSynonym>PWM</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.</oboInOwl:hasDefinition>
-        <rdfs:comment>Contributions of individual sequences to the matrix might be uneven (weighted).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1363 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1363">
-        <rdfs:label>Information content matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>ICM</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1364 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1364">
-        <rdfs:label>Hidden Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1354"/>
-        <oboInOwl:hasExactSynonym>HMM</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A hidden Markov model representation of a set or alignment of sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1365">
-        <rdfs:label>Fingerprint</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>One or more fingerprints (sequence classifiers) as used in the PRINTS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1368">
-        <rdfs:label>Domainatrix signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein signature of the type used in the EMBASSY Signature package.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1354"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1371">
-        <rdfs:label>HMMER NULL hidden Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>NULL hidden Markov model representation used by the HMMER package.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1364"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1372">
-        <rdfs:label>Protein family signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Protein family signatures cover all domains in the matching proteins and span &gt;80% of the protein length and with no adjacent protein domain signatures or protein region signatures.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A protein family signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1373 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1373">
-        <rdfs:label>Protein domain signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A protein domain signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <rdfs:comment>Protein domain signatures identify structural or functional domains or other units with defined boundaries.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1374 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1374">
-        <rdfs:label>Protein region signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein region signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>A protein region signature defines a region which cannot be described as a protein family or domain signature.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1375 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1375">
-        <rdfs:label>Protein repeat signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein repeat signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1376 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1376">
-        <rdfs:label>Protein site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>A protein site signature is a classifier for a specific site in a protein.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1377 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1377">
-        <rdfs:label>Protein conserved site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification.</rdfs:comment>
-        <oboInOwl:hasDefinition>A protein conserved site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1378">
-        <rdfs:label>Protein active site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein active site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1379">
-        <rdfs:label>Protein binding site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>A protein binding site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1380 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1380">
-        <rdfs:label>Protein post-translational modification signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein post-translational modification signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible.</rdfs:comment>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1381 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1381">
-        <rdfs:label>Sequence alignment (pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_010068</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1382 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1382">
-        <rdfs:label>Sequence alignment (multiple)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of more than two molecular sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1383">
-        <rdfs:label>Sequence alignment (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of multiple nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1384">
-        <rdfs:label>Sequence alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3154"/>
-        <oboInOwl:hasDefinition>Alignment of multiple protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1385">
-        <rdfs:label>Sequence alignment (hybrid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:hasDefinition>Alignment of multiple molecular sequences of different types.</oboInOwl:hasDefinition>
-        <rdfs:comment>Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1386">
-        <rdfs:label>Sequence alignment (nucleic acid pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1381"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1383"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of exactly two nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1387">
-        <rdfs:label>Sequence alignment (protein pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1381"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1384"/>
-        <oboInOwl:hasDefinition>Alignment of exactly two protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1388">
-        <rdfs:label>Hybrid sequence alignment (pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of exactly two molecular sequences of different types.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1385"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1389 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1389">
-        <rdfs:label>Multiple nucleotide sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of more than two nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1390">
-        <rdfs:label>Multiple protein sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of more than two protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1394 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1394">
-        <rdfs:label>Alignment score or penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2527"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for opening or extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1395">
-        <rdfs:label>Score end gaps control</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Whether end gaps are scored or not.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1396">
-        <rdfs:label>Aligned sequence order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Controls the order of sequences in an output sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1397">
-        <rdfs:label>Gap opening penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2137"/>
-        <oboInOwl:hasDefinition>A penalty for opening a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1398">
-        <rdfs:label>Gap extension penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2137"/>
-        <oboInOwl:hasDefinition>A penalty for extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1399">
-        <rdfs:label>Gap separation penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2137"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A penalty for gaps that are close together in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1400">
-        <rdfs:label>Terminal gap penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5&apos;/3&apos; terminal of nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1410"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1411"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1401">
-        <rdfs:label>Match reward score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The score for a &apos;match&apos; used in various sequence database search applications with simple scoring schemes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1402">
-        <rdfs:label>Mismatch penalty score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The score (penalty) for a &apos;mismatch&apos; used in various alignment and sequence database search applications with simple scoring schemes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1403">
-        <rdfs:label>Drop off score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <oboInOwl:hasDefinition>This is the threshold drop in score at which extension of word alignment is halted.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1404">
-        <rdfs:label>Gap opening penalty (integer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for opening a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1405">
-        <rdfs:label>Gap opening penalty (float)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for opening a gap in an alignment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1406">
-        <rdfs:label>Gap extension penalty (integer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1398"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1407">
-        <rdfs:label>Gap extension penalty (float)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1398"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1408">
-        <rdfs:label>Gap separation penalty (integer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for gaps that are close together in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1409">
-        <rdfs:label>Gap separation penalty (float)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for gaps that are close together in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1410">
-        <rdfs:label>Terminal gap opening penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1397"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5&apos;/3&apos; terminal of nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1411">
-        <rdfs:label>Terminal gap extension penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1398"/>
-        <oboInOwl:hasDefinition>A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5&apos;/3&apos; terminal of nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1412">
-        <rdfs:label>Sequence identity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0865"/>
-        <oboInOwl:hasDefinition>Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1413">
-        <rdfs:label>Sequence similarity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0865"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension.</oboInOwl:hasDefinition>
-        <rdfs:comment>Data Type is float probably.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1414">
-        <rdfs:label>Sequence alignment metadata (quality report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Data on molecular sequence alignment quality (estimated accuracy).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1415">
-        <rdfs:label>Sequence alignment report (site conservation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on character conservation in a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2161"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1416">
-        <rdfs:label>Sequence alignment report (site correlation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1417">
-        <rdfs:label>Sequence-profile alignment (Domainatrix signature)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1418 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1418">
-        <rdfs:label>Sequence-profile alignment (HMM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Alignment of molecular sequence(s) to a hidden Markov model(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1420">
-        <rdfs:label>Sequence-profile alignment (fingerprint)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment of molecular sequences to a protein fingerprint from the PRINTS database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1426">
-        <rdfs:label>Phylogenetic continuous quantitative data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0871"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic continuous quantitative characters</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Quantitative traits</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Continuous quantitative data that may be read during phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1427">
-        <rdfs:label>Phylogenetic discrete data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0871"/>
-        <oboInOwl:hasExactSynonym>Discrete characters</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Character data with discrete states that may be read during phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic discrete states</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Discretely coded characters</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1428">
-        <rdfs:label>Phylogenetic character cliques</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasDefinition>One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic report (cliques)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1429">
-        <rdfs:label>Phylogenetic invariants</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Phylogenetic invariants data for testing alternative tree topologies.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic report (invariants)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1438">
-        <rdfs:label>Phylogenetic report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree report</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Phylogenetic report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree-derived report</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used  for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1439">
-        <rdfs:label>DNA substitution model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:hasExactSynonym>Substitution model</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree report (DNA substitution model)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment report (DNA substitution model)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1440">
-        <rdfs:label>Phylogenetic tree report (tree shape)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>Data about the shape of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1441">
-        <rdfs:label>Phylogenetic tree report (tree evaluation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>Data on the confidence of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1442">
-        <rdfs:label>Phylogenetic tree distances</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree report (tree distances)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Distances, such as Branch Score distance, between two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1443">
-        <rdfs:label>Phylogenetic tree report (tree stratigraphic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1444">
-        <rdfs:label>Phylogenetic character contrasts</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic report (character contrasts)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1446">
-        <rdfs:label>Comparison matrix (integers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Substitution matrix (integers)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer numbers for sequence comparison.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0874"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1447">
-        <rdfs:label>Comparison matrix (floats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Matrix of floating point numbers for sequence comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix (floats)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0874"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1448">
-        <rdfs:label>Comparison matrix (nucleotide)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0874"/>
-        <oboInOwl:hasDefinition>Matrix of integer or floating point numbers for nucleotide comparison.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide substitution matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1449 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1449">
-        <rdfs:label>Comparison matrix (amino acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0874"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2016"/>
-        <oboInOwl:hasExactSynonym>Amino acid comparison matrix</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer or floating point numbers for amino acid comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Amino acid substitution matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1450 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1450">
-        <rdfs:label>Nucleotide comparison matrix (integers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Nucleotide substitution matrix (integers)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer numbers for nucleotide comparison.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1448"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1451">
-        <rdfs:label>Nucleotide comparison matrix (floats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Matrix of floating point numbers for nucleotide comparison.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide substitution matrix (floats)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1448"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1452">
-        <rdfs:label>Amino acid comparison matrix (integers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer numbers for amino acid comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Amino acid substitution matrix (integers)</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1449"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1453">
-        <rdfs:label>Amino acid comparison matrix (floats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Amino acid substitution matrix (floats)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Matrix of floating point numbers for amino acid comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1449"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1456">
-        <rdfs:label>Protein features report (membrane regions)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1459">
-        <rdfs:label>Nucleic acid structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a nucleic acid tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1460">
-        <rdfs:label>Protein structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Protein structures</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1461">
-        <rdfs:label>Protein-ligand complex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:hasDefinition>The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides.  For stable inter-polypeptide interactions use &apos;Protein complex&apos; instead.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1462 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1462">
-        <rdfs:label>Carbohydrate structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0153"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0152"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a carbohydrate (3D) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1463">
-        <rdfs:label>Small molecule structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0154"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>CHEBI:23367</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1464">
-        <rdfs:label>DNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1459"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a DNA tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1465">
-        <rdfs:label>RNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1459"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for an RNA tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1466 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1466">
-        <rdfs:label>tRNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1465"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1467">
-        <rdfs:label>Protein chain</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1468">
-        <rdfs:label>Protein domain</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0736"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the tertiary (3D) structure of a protein domain.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1469">
-        <rdfs:label>Protein structure (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein tertiary (3D) structure (all atoms).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1470">
-        <rdfs:label>C-alpha trace</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only).</oboInOwl:hasDefinition>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein structure (C-alpha atoms)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1471">
-        <rdfs:label>Protein chain (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1467"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1472">
-        <rdfs:label>Protein chain (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1467"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1473">
-        <rdfs:label>Protein domain (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1468"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1474">
-        <rdfs:label>Protein domain (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1468"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1479">
-        <rdfs:label>Structure alignment (pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0886"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Pair structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1480">
-        <rdfs:label>Structure alignment (multiple)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of more than two molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0886"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1481">
-        <rdfs:label>Structure alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0886"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3154"/>
-        <oboInOwl:hasExactSynonym>Protein structure alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of protein tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1482">
-        <rdfs:label>Structure alignment (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0886"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of nucleic acid tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1483">
-        <rdfs:label>Structure alignment (protein pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:hasExactSynonym>Protein pair structural alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1484 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1484">
-        <rdfs:label>Multiple protein tertiary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of more than two protein tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1485">
-        <rdfs:label>Structure alignment (protein all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1486">
-        <rdfs:label>Structure alignment (protein C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered).</oboInOwl:hasDefinition>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be considered.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>C-alpha trace</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1487">
-        <rdfs:label>Pairwise protein tertiary structure alignment (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1488">
-        <rdfs:label>Pairwise protein tertiary structure alignment (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1489">
-        <rdfs:label>Multiple protein tertiary structure alignment (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1490">
-        <rdfs:label>Multiple protein tertiary structure alignment (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1491">
-        <rdfs:label>Structure alignment (nucleic acid pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1482"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid pair structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1492">
-        <rdfs:label>Multiple nucleic acid tertiary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1482"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1493 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1493">
-        <rdfs:label>Structure alignment (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1482"/>
-        <oboInOwl:hasExactSynonym>RNA structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of RNA tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1494 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1494">
-        <rdfs:label>Structural transformation matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1495">
-        <rdfs:label>DaliLite hit table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>DaliLite hit table of protein chain tertiary structure alignment data.</oboInOwl:hasDefinition>
-        <rdfs:comment>The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0887"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1496">
-        <rdfs:label>Molecular similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A score reflecting structural similarities of two molecules.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0888"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1497">
-        <rdfs:label>Root-mean-square deviation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0888"/>
-        <oboInOwl:hasExactSynonym>RMSD</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1498">
-        <rdfs:label>Tanimoto similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0888"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A measure of the similarity between two ligand fingerprints.</oboInOwl:hasDefinition>
-        <rdfs:comment>A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1499">
-        <rdfs:label>3D-1D scoring matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0892"/>
-        <oboInOwl:hasDefinition>A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1501">
-        <rdfs:label>Amino acid index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2016"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1502">
-        <rdfs:label>Amino acid index (chemical classes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasExactSynonym>Chemical classes (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1503">
-        <rdfs:label>Amino acid pair-wise contact potentials</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2016"/>
-        <oboInOwl:hasExactSynonym>Contact potentials (amino acid pair-wise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Statistical protein contact potentials.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1505">
-        <rdfs:label>Amino acid index (molecular weight)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasDefinition>Molecular weights of amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Molecular weight (amino acids)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1506">
-        <rdfs:label>Amino acid index (hydropathy)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasDefinition>Hydrophobic, hydrophilic or charge properties of amino acids.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Hydropathy (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1507">
-        <rdfs:label>Amino acid index (White-Wimley data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>White-Wimley data (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Experimental free energy values for the water-interface and water-octanol transitions for the amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1508">
-        <rdfs:label>Amino acid index (van der Waals radii)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasExactSynonym>van der Waals radii (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Van der Waals radii of atoms for different amino acid residues.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1509">
-        <rdfs:label>Enzyme report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein report (enzyme)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Enzyme report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on a specific enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1517 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1517">
-        <rdfs:label>Restriction enzyme report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a specific restriction enzyme such as enzyme reference data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Restriction enzyme pattern data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein report (restriction enzyme)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Restriction enzyme report</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1519">
-        <rdfs:label>Peptide molecular weights</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report might include associated data such as frequency of peptide fragment molecular weights.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1520">
-        <rdfs:label>Peptide hydrophobic moment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on the hydrophobic moment of a polypeptide sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1521">
-        <rdfs:label>Protein aliphatic index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <oboInOwl:hasDefinition>The aliphatic index of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The aliphatic index is the relative protein volume occupied by aliphatic side chains.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1522">
-        <rdfs:label>Protein sequence hydropathy plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <rdfs:comment>Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1523">
-        <rdfs:label>Protein charge plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1524">
-        <rdfs:label>Protein solubility</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The solubility or atomic solvation energy of a protein sequence or structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein solubility data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1525">
-        <rdfs:label>Protein crystallizability</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein crystallizability data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data on the crystallizability of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1526">
-        <rdfs:label>Protein globularity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <oboInOwl:hasExactSynonym>Protein globularity data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on the stability, intrinsic disorder or globularity of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1527">
-        <rdfs:label>Protein titration curve</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <oboInOwl:hasDefinition>The titration curve of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1528">
-        <rdfs:label>Protein isoelectric point</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The isoelectric point of one proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1529">
-        <rdfs:label>Protein pKa value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>The pKa value of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1530">
-        <rdfs:label>Protein hydrogen exchange rate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The hydrogen exchange rate of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1531">
-        <rdfs:label>Protein extinction coefficient</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>The extinction coefficient of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1532 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1532">
-        <rdfs:label>Protein optical density</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>The optical density of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1533">
-        <rdfs:label>Protein subcellular localization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Protein report (subcellular localization)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1534">
-        <rdfs:label>Peptide immunogenicity data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>An report on allergenicity / immunogenicity of peptides and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Peptide immunogenicity report</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide immunogenicity</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1536">
-        <rdfs:label>MHC peptide immunogenicity report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report on the immunogenicity of MHC class I or class II binding peptides.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1534"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1537">
-        <rdfs:label>Protein structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:hasExactSynonym>Protein structural property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure-derived report</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein property (structural)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein report (structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure report (domain)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1539">
-        <rdfs:label>Protein structural quality report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:hasDefinition>Report on the quality of a protein three-dimensional model.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein structure report (quality evaluation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure validation report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein property (structural quality)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein report (structural quality)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1540">
-        <rdfs:label>Protein residue interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Residue interaction data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Atom interaction data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1541 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1541">
-        <rdfs:label>Protein flexibility or motion report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein property (flexibility or motion)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Informative report on flexibility or motion of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein flexibility or motion</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein structure report (flexibility or motion)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1542">
-        <rdfs:label>Protein solvent accessibility</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on the solvent accessible or buried surface area of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1543">
-        <rdfs:label>Protein surface report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein structure report (surface)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1544 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1544">
-        <rdfs:label>Ramachandran plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2991"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phi/psi angle data or a Ramachandran plot of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1545">
-        <rdfs:label>Protein dipole moment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>Data on the net charge distribution (dipole moment) of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1546">
-        <rdfs:label>Protein distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1547">
-        <rdfs:label>Protein contact map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <oboInOwl:hasDefinition>An amino acid residue contact map for a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1548">
-        <rdfs:label>Protein residue 3D cluster</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on clusters of contacting residues in protein structures such as a key structural residue network.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1549">
-        <rdfs:label>Protein hydrogen bonds</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <oboInOwl:hasDefinition>Patterns of hydrogen bonding in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1550">
-        <rdfs:label>Protein non-canonical interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Protein non-canonical interactions report</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Non-canonical atomic interactions in protein structures.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1553">
-        <rdfs:label>CATH node</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information on a node from the CATH database.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>CATH classification node report</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1554">
-        <rdfs:label>SCOP node</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>SCOP classification node</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Information on a node from the SCOP database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1555">
-        <rdfs:label>EMBASSY domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1556">
-        <rdfs:label>CATH class</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a protein &apos;class&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1557">
-        <rdfs:label>CATH architecture</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a protein &apos;architecture&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1558">
-        <rdfs:label>CATH topology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a protein &apos;topology&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1559">
-        <rdfs:label>CATH homologous superfamily</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a protein &apos;homologous superfamily&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1560">
-        <rdfs:label>CATH structurally similar group</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a protein &apos;structurally similar group&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1561">
-        <rdfs:label>CATH functional category</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information on a protein &apos;functional category&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1564">
-        <rdfs:label>Protein fold recognition report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0901"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1565">
-        <rdfs:label>Protein-protein interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>protein-protein interaction(s), including interactions between protein domains.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1566">
-        <rdfs:label>Protein-ligand interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0906"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on protein-ligand (small molecule) interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1567">
-        <rdfs:label>Protein-nucleic acid interactions report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>protein-DNA/RNA interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1583">
-        <rdfs:label>Nucleic acid melting profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid stability profile</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1584 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1584">
-        <rdfs:label>Nucleic acid enthalpy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1585 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1585">
-        <rdfs:label>Nucleic acid entropy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <oboInOwl:hasDefinition>Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1586 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1586">
-        <rdfs:label>Nucleic acid melting temperature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2139"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1587 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1587">
-        <rdfs:label>Nucleic acid stitch profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <rdfs:comment>A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1588 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1588">
-        <rdfs:label>DNA base pair stacking energies data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <oboInOwl:hasDefinition>DNA base pair stacking energies data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1589 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1589">
-        <rdfs:label>DNA base pair twist angle data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA base pair twist angle data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1590 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1590">
-        <rdfs:label>DNA base trimer roll angles data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA base trimer roll angles data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1591 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1591">
-        <rdfs:label>Vienna RNA parameters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>RNA parameters used by the Vienna package.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1592 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1592">
-        <rdfs:label>Vienna RNA structure constraints</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Structure constraints used by the Vienna package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1593">
-        <rdfs:label>Vienna RNA concentration data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>RNA concentration data used by the Vienna package.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1594">
-        <rdfs:label>Vienna RNA calculated energy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>RNA calculated energy data generated by the Vienna package.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1584"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1595">
-        <rdfs:label>Base pairing probability matrix dotplot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Such as generated by the Vienna package.</rdfs:comment>
-        <oboInOwl:hasDefinition>Dotplot of RNA base pairing probability matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1596 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1596">
-        <rdfs:label>Nucleic acid folding report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (folding)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (folding model)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>RNA secondary structure folding probablities</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>RNA secondary structure folding classification</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1597 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1597">
-        <rdfs:label>Codon usage table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Table of codon usage data calculated from one or more nucleic acid sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1598">
-        <rdfs:label>Genetic code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A genetic code for an organism.</oboInOwl:hasDefinition>
-        <rdfs:comment>A genetic code need not include detailed codon usage information.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1599 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1599">
-        <rdfs:label>Codon adaptation index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple measure of synonymous codon usage bias often used to predict gene expression levels.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>CAI</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2865"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1600 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1600">
-        <rdfs:label>Codon usage bias plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:hasExactSynonym>Synonymous codon usage statistic plot</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of the synonymous codon usage calculated for windows over a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1601">
-        <rdfs:label>Nc statistic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The effective number of codons used in a gene sequence.  This reflects how far codon usage of a gene departs from equal usage of synonymous codons.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2865"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1602">
-        <rdfs:label>Codon usage fraction difference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:hasDefinition>The differences in codon usage fractions between two codon usage tables.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1621">
-        <rdfs:label>Pharmacogenomic test report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0920"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on the influence of genotype on drug response.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1622">
-        <rdfs:label>Disease report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0920"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0634"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An informative report on a specific disease.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Disease report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1634 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1634">
-        <rdfs:label>Linkage disequilibrium (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0927"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1636 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1636">
-        <rdfs:label>Heat map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:hasDefinition>A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1642 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1642">
-        <rdfs:label>Affymetrix probe sets library file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Affymetrix library file of information about which probes belong to which probe set.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>CDF file</oboInOwl:hasRelatedSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1643 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1643">
-        <rdfs:label>Affymetrix probe sets information library file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>GIN file</oboInOwl:hasRelatedSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1646 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1646">
-        <rdfs:label>Molecular weights standard fingerprint</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0944"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1656 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1656">
-        <rdfs:label>Metabolic pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of a metabolic pathway.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1657 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1657">
-        <rdfs:label>Genetic information processing pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>genetic information processing pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1658 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1658">
-        <rdfs:label>Environmental information processing pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>environmental information processing pathways.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1659 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1659">
-        <rdfs:label>Signal transduction pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of a signal transduction pathway.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1660 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1660">
-        <rdfs:label>Cellular process pathways report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Topic concernning cellular process pathways.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1661 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1661">
-        <rdfs:label>Disease pathway or network report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>disease pathways, typically of human disease.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1662 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1662">
-        <rdfs:label>Drug structure relationship map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1696"/>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of drug structure relationships.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1663 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1663">
-        <rdfs:label>Protein interaction networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>networks of protein interactions.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2600"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1664 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1664">
-        <rdfs:label>MIRIAM datatype</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types.</rdfs:comment>
-        <oboInOwl:hasDefinition>An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1667 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1667">
-        <rdfs:label>E-value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0951"/>
-        <rdfs:comment>An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple floating point number defining the lower or upper limit of an expectation value (E-value).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Expectation value</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1668 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1668">
-        <rdfs:label>Z-value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0951"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The z-value is the number of standard deviations a data value is above or below a mean value.</oboInOwl:hasDefinition>
-        <rdfs:comment>A z-value might be specified as a threshold for reporting hits from database searches.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1669 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1669">
-        <rdfs:label>P-value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0951"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A z-value might be specified as a threshold for reporting hits from database searches.</rdfs:comment>
-        <oboInOwl:hasDefinition>The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1670 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1670">
-        <rdfs:label>Database version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Ontology version information</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a database (or ontology) version, for example name, version number and release date.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1671 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1671">
-        <rdfs:label>Tool version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on an application version, for example name, version number and release date.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0958"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1672 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1672">
-        <rdfs:label>CATH version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a version of the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1673 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1673">
-        <rdfs:label>Swiss-Prot to PDB mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Cross-mapping of Swiss-Prot codes to PDB identifiers.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0954"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1674 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1674">
-        <rdfs:label>Sequence database cross-references</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Cross-references from a sequence record to other databases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1675 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1675">
-        <rdfs:label>Job status</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Metadata on the status of a submitted job.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Values for EBI services are &apos;DONE&apos; (job has finished and the results can then be retrieved), &apos;ERROR&apos; (the job failed or no results where found), &apos;NOT_FOUND&apos; (the job id is no longer available; job results might be deleted, &apos;PENDING&apos; (the job is in a queue waiting processing), &apos;RUNNING&apos; (the job is currently being processed).</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1676 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1676">
-        <rdfs:label>Job ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:hasDefinition>The (typically numeric) unique identifier of a submitted job.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1677 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1677">
-        <rdfs:label>Job type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of job, for example interactive or non-interactive.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1678 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1678">
-        <rdfs:label>Tool log</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1679 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1679">
-        <rdfs:label>DaliLite log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1680 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1680">
-        <rdfs:label>STRIDE log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>STRIDE log file.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1678"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1681 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1681">
-        <rdfs:label>NACCESS log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>NACCESS log file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1678"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1682 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1682">
-        <rdfs:label>EMBOSS wordfinder log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>EMBOSS wordfinder log file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1683 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1683">
-        <rdfs:label>EMBOSS domainatrix log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>EMBOSS (EMBASSY) domainatrix application log file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1684 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1684">
-        <rdfs:label>EMBOSS sites log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>EMBOSS (EMBASSY) sites application log file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1685 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1685">
-        <rdfs:label>EMBOSS supermatcher error file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>EMBOSS (EMBASSY) supermatcher error file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1686 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1686">
-        <rdfs:label>EMBOSS megamerger log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>EMBOSS megamerger log file.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1687 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1687">
-        <rdfs:label>EMBOSS whichdb log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>EMBOSS megamerger log file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1688 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1688">
-        <rdfs:label>EMBOSS vectorstrip log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>EMBOSS vectorstrip log file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1689 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1689">
-        <rdfs:label>Username</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2101"/>
-        <oboInOwl:hasDefinition>A username on a computer system.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1690 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1690">
-        <rdfs:label>Password</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2101"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A password on a computer system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1691 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1691">
-        <rdfs:label>Email address</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2101"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:Email</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A valid email address of an end-user.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:EmailAddress</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1692 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1692">
-        <rdfs:label>Person name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2118"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a person.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1693 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1693">
-        <rdfs:label>Number of iterations</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Number of iterations of an algorithm.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1694 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1694">
-        <rdfs:label>Number of output entities</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Number of entities (for example database hits, sequences, alignments etc) to write to an output file.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1695 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1695">
-        <rdfs:label>Hit sort order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Controls the order of hits (reported matches) in an output file from a database search.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2134"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1696 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1696">
-        <rdfs:label>Drug report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0962"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0620"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An informative report on a specific drug.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Drug annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1707 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1707">
-        <rdfs:label>Phylogenetic tree image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information.</oboInOwl:hasDefinition>
-        <rdfs:comment>See also &apos;Phylogenetic tree&apos;</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1708 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1708">
-        <rdfs:label>RNA secondary structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of RNA secondary structure, knots, pseudoknots etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1709 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1709">
-        <rdfs:label>Protein secondary structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3153"/>
-        <oboInOwl:hasDefinition>Image of protein secondary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1710 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1710">
-        <rdfs:label>Structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of one or more molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1711 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1711">
-        <rdfs:label>Sequence alignment image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of two or more aligned molecular sequences possibly annotated with alignment features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1712 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1712">
-        <rdfs:label>Chemical structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1710"/>
-        <oboInOwl:hasDefinition>An image of the structure of a small chemical compound.</oboInOwl:hasDefinition>
-        <rdfs:comment>The molecular identifier and formula are typically included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Small molecule structure image</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1713 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1713">
-        <rdfs:label>Fate map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2530"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3065"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition> A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1714 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1714">
-        <rdfs:label>Microarray spots image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image of spots from a microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1715 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1715">
-        <rdfs:label>BioPax term</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A term from the BioPax ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1716 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1716">
-        <rdfs:label>GO</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Gene Ontology term</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Annotated_GO_Term</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Annotated_GO_Term_With_Probability</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term definition from The Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:GO_Term</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GOTerm</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1717 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1717">
-        <rdfs:label>MeSH</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the MeSH vocabulary.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1718 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1718">
-        <rdfs:label>HGNC</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the HGNC controlled vocabulary.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1719 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1719">
-        <rdfs:label>NCBI taxonomy vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the NCBI taxonomy vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1720 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1720">
-        <rdfs:label>Plant ontology term</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from the Plant Ontology (PO).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1721 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1721">
-        <rdfs:label>UMLS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from the UMLS vocabulary.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1722 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1722">
-        <rdfs:label>FMA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from Foundational Model of Anatomy.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1723 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1723">
-        <rdfs:label>EMAP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A term from the EMAP mouse ontology.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1724 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1724">
-        <rdfs:label>ChEBI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from the ChEBI ontology.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1725 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1725">
-        <rdfs:label>MGED</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the MGED ontology.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1726 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1726">
-        <rdfs:label>myGrid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the myGrid ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1727 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1727">
-        <rdfs:label>GO (biological process)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Data Type is an enumerated string.</rdfs:comment>
-        <oboInOwl:hasDefinition>A term definition for a biological process from the Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1728 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1728">
-        <rdfs:label>GO (molecular function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A term definition for a molecular function from the Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Data Type is an enumerated string.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1729 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1729">
-        <rdfs:label>GO (cellular component)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term definition for a cellular component from the Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Data Type is an enumerated string.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1730 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1730">
-        <rdfs:label>Ontology relation type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A relation type defined in an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0967"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1731 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1731">
-        <rdfs:label>Ontology concept definition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0967"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology class definition</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The definition of a concept from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1732 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1732">
-        <rdfs:label>Ontology concept comment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A comment on a concept from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0967"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1733 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1733">
-        <rdfs:label>Ontology concept reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Reference for a concept from an ontology.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1738 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1738">
-        <rdfs:label>doc2loc document information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The doc2loc output includes the url, format, type and availability code of a document for every service provider.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a published article provided by the doc2loc program.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0970"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1742 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1742">
-        <rdfs:label>PDB residue number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <oboInOwl:hasDbXref>WHATIF: pdb_number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:PDB_residue_no</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A residue identifier (a string) from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1743 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1743">
-        <rdfs:label>Atomic coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1917"/>
-        <oboInOwl:hasDefinition>Cartesian coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Cartesian coordinate</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1744 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1744">
-        <rdfs:label>Atomic x coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1743"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_Cartn_x</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Cartesian x coordinate</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.Cartn_x in PDBML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cartesian x coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1745 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1745">
-        <rdfs:label>Atomic y coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1743"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_Cartn_y</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Cartesian y coordinate</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.Cartn_y in PDBML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cartesian y coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1746 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1746">
-        <rdfs:label>Atomic z coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1743"/>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.Cartn_z</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_Cartn_z</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cartesian z coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Cartesian z coordinate</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1748 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1748">
-        <rdfs:label>PDB atom name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1757"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_type_symbol</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_auth_atom_id</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: alternate_atom</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_atom_name</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: atom_type</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier (a string) of a specific atom from a PDB file for a molecular structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1755 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1755">
-        <rdfs:label>Protein atom</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:hasExactSynonym>Atom data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>CHEBI:33250</oboInOwl:hasRelatedSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on a single atom from a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1756 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1756">
-        <rdfs:label>Protein residue</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on a single amino acid residue position in a protein structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Residue</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1757 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1757">
-        <rdfs:label>Atom name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0983"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>Name of an atom.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1758 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1758">
-        <rdfs:label>PDB residue name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2564"/>
-        <oboInOwl:hasDefinition>Three-letter amino acid residue names as used in PDB files.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: type</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1759 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1759">
-        <rdfs:label>PDB model number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3035"/>
-        <oboInOwl:hasDefinition>Identifier of a model structure from a PDB file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_model_num</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Model number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>WHATIF: model_number</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1762 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1762">
-        <rdfs:label>CATH domain report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.</rdfs:comment>
-        <oboInOwl:hasDefinition>Summary of domain classification information for a CATH domain.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1764 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1764">
-        <rdfs:label>CATH representative domain sequences (ATOM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1765 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1765">
-        <rdfs:label>CATH representative domain sequences (COMBS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1766 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1766">
-        <rdfs:label>CATH domain sequences (ATOM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>FASTA sequence database for all CATH domains (based on PDB ATOM records).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1767 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1767">
-        <rdfs:label>CATH domain sequences (COMBS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>FASTA sequence database for all CATH domains (based on COMBS sequence data).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1771 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1771">
-        <rdfs:label>Sequence version</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on an molecular sequence version.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence version information</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1772 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1772">
-        <rdfs:label>Score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>A numerical value, that is some type of scored value arising for example from a prediction method.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1776 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1776">
-        <rdfs:label>Protein report (function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>For properties that can be mapped to a sequence, use &apos;Sequence report&apos; instead.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Report on general functional properties of specific protein(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1783 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1783">
-        <rdfs:label>Gene name (ASPGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of a gene from Aspergillus Genome Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1784 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1784">
-        <rdfs:label>Gene name (CGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Name of a gene from Candida Genome Database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1785 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1785">
-        <rdfs:label>Gene name (dictyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of a gene from dictyBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1786 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1786">
-        <rdfs:label>Gene name (EcoGene primary)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Primary name of a gene from EcoGene Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EcoGene primary gene name</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1787 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1787">
-        <rdfs:label>Gene name (MaizeGDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus</oboInOwl:hasDbXref>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Name of a gene from MaizeGDB (maize genes) database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1788 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1788">
-        <rdfs:label>Gene name (SGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Name of a gene from Saccharomyces Genome Database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1789 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1789">
-        <rdfs:label>Gene name (TGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Name of a gene from Tetrahymena Genome Database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1790 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1790">
-        <rdfs:label>Gene name (CGSC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: CGSC</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Symbol of a gene from E.coli Genetic Stock Center.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1791 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1791">
-        <rdfs:label>Gene name (HGNC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>HUGO symbol</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>HGNC symbol</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Official gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HUGO gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>HGNC gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HUGO gene symbol</oboInOwl:hasExactSynonym>
-        <regex>HGNC:[0-9]{1,5}</regex>
-        <oboInOwl:hasExactSynonym>Gene name (HUGO)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HGNC gene symbol</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Symbol of a gene approved by the HUGO Gene Nomenclature Committee.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1792 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1792">
-        <rdfs:label>Gene name (MGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>MGI:[0-9]+</regex>
-        <oboInOwl:hasDefinition>Symbol of a gene from the Mouse Genome Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: MGD</oboInOwl:hasDbXref>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1793 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1793">
-        <rdfs:label>Gene name (Bacillus subtilis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Symbol of a gene from Bacillus subtilis Genome Sequence Project.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1794 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1794">
-        <rdfs:label>Gene ID (PlasmoDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier of a gene from PlasmoDB Plasmodium Genome Resource.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1795 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1795">
-        <rdfs:label>Gene ID (EcoGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier of a gene from EcoGene Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EcoGene Accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>EcoGene ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1796 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1796">
-        <rdfs:label>Gene ID (FlyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gene identifier from FlyBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: FB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1797 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1797">
-        <rdfs:label>Gene ID (GeneDB Glossina morsitans)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans</oboInOwl:hasDbXref>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Gene identifier from Glossina morsitans GeneDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1798 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1798">
-        <rdfs:label>Gene ID (GeneDB Leishmania major)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Gene identifier from Leishmania major GeneDB database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1799 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1799">
-        <rdfs:label>Gene ID (GeneDB Plasmodium falciparum)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Gene identifier from Plasmodium falciparum GeneDB database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum</oboInOwl:hasDbXref>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1800 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1800">
-        <rdfs:label>Gene ID (GeneDB Schizosaccharomyces pombe)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Gene identifier from Schizosaccharomyces pombe GeneDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1801 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1801">
-        <rdfs:label>Gene ID (GeneDB Trypanosoma brucei)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Gene identifier from Trypanosoma brucei GeneDB database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1802 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1802">
-        <rdfs:label>Gene ID (Gramene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Gene identifier from Gramene database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1803 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1803">
-        <rdfs:label>Gene ID (Virginia microbial)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Gene identifier from Virginia Bioinformatics Institute microbial database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: VMD</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1804 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1804">
-        <rdfs:label>Gene ID (SGN)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SGN</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Gene identifier from Sol Genomics Network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1805 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1805">
-        <rdfs:label>Gene ID (WormBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Gene identifier used by WormBase database.</oboInOwl:hasDefinition>
-        <regex>WBGene[0-9]{8}</regex>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: WB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: WormBase</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1806 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1806">
-        <rdfs:label>Gene synonym</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Gene name synonym</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Any name (other than the recommended one) for a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1807 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1807">
-        <rdfs:label>ORF name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2795"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of an open reading frame attributed by a sequencing project.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1852 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1852">
-        <rdfs:label>Sequence assembly component</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A component of a larger sequence assembly.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0925"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1853 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1853">
-        <rdfs:label>Chromosome annotation (aberration)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on a chromosome aberration such as abnormalities in chromosome structure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0919"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1855 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1855">
-        <rdfs:label>Clone ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2769"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a clone (cloned molecular sequence) from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1856 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1856">
-        <rdfs:label>PDB insertion code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: insertion_code</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_ins_code</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An insertion code (part of the residue number) for an amino acid residue from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1857 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1857">
-        <rdfs:label>Atomic occupancy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1917"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_occupancy</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The fraction of an atom type present at a site in a molecular structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1858 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1858">
-        <rdfs:label>Isotropic B factor</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1917"/>
-        <oboInOwl:hasDefinition>Isotropic B factor (atomic displacement parameter) for an atom from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_B_iso_or_equiv</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1859 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1859">
-        <rdfs:label>Deletion map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1283"/>
-        <rdfs:comment>A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line (&apos;genome deletion panel&apos;). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Deletion-based cytogenetic map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1860 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1860">
-        <rdfs:label>QTL map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1278"/>
-        <oboInOwl:hasDefinition>A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Quantitative trait locus map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1863 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1863">
-        <rdfs:label>Haplotype map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1278"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:Haplotyping_Study_obj</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1864 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1864">
-        <rdfs:label>Map set data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2019"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:GCP_CorrelatedLinkageMapSet</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_CorrelatedMapSet</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1865 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1865">
-        <rdfs:label>Map feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A feature which may mapped (positioned) on a genetic or other type of map.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:MapFeature</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Mappable features may be based on Gramene&apos;s notion of map features; see http://www.gramene.org/db/cmap/feature_type_info.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2019"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1866 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1866">
-        <rdfs:label>Map type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A designation of the type of map (genetic map, physical map, sequence map etc) or map set.</oboInOwl:hasDefinition>
-        <rdfs:comment>Map types may be based on Gramene&apos;s notion of a map type; see http://www.gramene.org/db/cmap/map_type_info.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1867">
-        <rdfs:label>Protein fold name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a protein fold.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1868">
-        <rdfs:label>Taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDbXref>Moby:PotentialTaxon</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Taxonomy rank</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Taxonomic rank</oboInOwl:hasExactSynonym>
-        <rdfs:comment>For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.</rdfs:comment>
-        <oboInOwl:hasDefinition>The name of a group of organisms belonging to the same taxonomic rank.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:BriefTaxonConcept</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1869">
-        <rdfs:label>Organism identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2530"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a (group of) organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1870 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1870">
-        <rdfs:label>Genus name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a genus of organism.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1872 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1872">
-        <rdfs:label>Taxonomic classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDbXref>Moby:TaxonName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_Taxon</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:iANT_organism-xml</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Taxonomic name</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Name components correspond to levels in a taxonomic hierarchy (e.g. &apos;Genus&apos;, &apos;Species&apos;, etc.) Meta information such as a reference where the name was defined and a date might be included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Taxonomic information</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:TaxonScientificName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:TaxonTCS</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1873 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1873">
-        <rdfs:label>iHOP organism ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:iHOPorganism</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A unique identifier for an organism used in the iHOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1874 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1874">
-        <rdfs:label>Genbank common name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDefinition>Common name for an organism as used in the GenBank database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1875 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1875">
-        <rdfs:label>NCBI taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a taxon from the NCBI taxonomy database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1877 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1877">
-        <rdfs:label>Synonym</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Alternative name</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An alternative for a word.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1878 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1878">
-        <rdfs:label>Misspelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A common misspelling of a word.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1879 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1879">
-        <rdfs:label>Acronym</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An abbreviation of a phrase or word.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1880 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1880">
-        <rdfs:label>Misnomer</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A term which is likely to be misleading of its meaning.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1881 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1881">
-        <rdfs:label>Author ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2118"/>
-        <oboInOwl:hasDefinition>Information on the authors of a published work.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:Author</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1882 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1882">
-        <rdfs:label>DragonDB author identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1881"/>
-        <oboInOwl:hasDefinition>An identifier representing an author in the DragonDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1883 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1883">
-        <rdfs:label>Annotated URI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A URI along with annotation describing the data found at the address.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:DescribedLink</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1884 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1884">
-        <rdfs:label>UniProt keywords</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1885">
-        <rdfs:label>Gene ID (GeneFarm)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>Moby_namespace:GENEFARM_GeneID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier of a gene from the GeneFarm database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1886 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1886">
-        <rdfs:label>Blattner number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:Blattner_number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The blattner identifier for a gene.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1887 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1887">
-        <rdfs:label>Gene ID (MIPS Maize)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>MIPS genetic element identifier (Maize)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier for genetic elements in MIPS Maize database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:MIPS_GE_Maize</oboInOwl:hasDbXref>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2285"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1888 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1888">
-        <rdfs:label>Gene ID (MIPS Medicago)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>MIPS genetic element identifier (Medicago)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>Moby_namespace:MIPS_GE_Medicago</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier for genetic elements in MIPS Medicago database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2285"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1889 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1889">
-        <rdfs:label>Gene name (DragonDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of an Antirrhinum Gene from the DragonDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:DragonDB_Gene</oboInOwl:hasDbXref>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1890 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1890">
-        <rdfs:label>Gene name (Arabidopsis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>Moby_namespace:ArabidopsisGeneSymbol</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1891 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1891">
-        <rdfs:label>iHOP symbol</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>A unique identifier of a protein or gene used in the iHOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:iHOPsymbol</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1892 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1892">
-        <rdfs:label>Gene name (GeneFarm)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of a gene from the GeneFarm database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:GENEFARM_GeneName</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>GeneFarm gene ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1893 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1893">
-        <rdfs:label>Locus ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2012"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Locus name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Locus identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1895 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1895">
-        <rdfs:label>Locus ID (AGI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <regex>AT[1-5]G[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>AGI ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Arabidopsis gene loci number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>AGI locus code</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>AGI identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1896 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1896">
-        <rdfs:label>Locus ID (ASPGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier for loci from ASPGD (Aspergillus Genome Database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1897 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1897">
-        <rdfs:label>Locus ID (MGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier for loci from Magnaporthe grisea Database at the Broad Institute.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1898 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1898">
-        <rdfs:label>Locus ID (CGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier for loci from CGD (Candida Genome Database).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: CGDID</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CGDID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>CGD locus identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: CGD</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1899 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1899">
-        <rdfs:label>Locus ID (CMR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1900 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1900">
-        <rdfs:label>NCBI locus tag</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:LocusID</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Locus ID (NCBI)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier for loci from NCBI database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1901 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1901">
-        <rdfs:label>Locus ID (SGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2632"/>
-        <oboInOwl:hasDefinition>Identifier for loci from SGD (Saccharomyces Genome Database).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SGDID</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SGD</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>SGDID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1902 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1902">
-        <rdfs:label>Locus ID (MMP)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of loci from Maize Mapping Project.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:MMP_Locus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1903 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1903">
-        <rdfs:label>Locus ID (DictyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDbXref>Moby_namespace:DDB_gene</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier of locus from DictyBase (Dictyostelium discoideum).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1904 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1904">
-        <rdfs:label>Locus ID (EntrezGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of a locus from EntrezGene database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:EntrezGene_ID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby_namespace:EntrezGene_EntrezGeneID</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1905 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1905">
-        <rdfs:label>Locus ID (MaizeGDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of locus from MaizeGDB (Maize genome database).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:MaizeGDB_Locus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1906 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1906">
-        <rdfs:label>Quantitative trait locus</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>QTL</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A QTL sometimes but does not necessarily correspond to a gene.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:SO_QTL</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2012"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1907 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1907">
-        <rdfs:label>Gene ID (KOME)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier of a gene from the KOME database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:GeneId</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1908 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1908">
-        <rdfs:label>Locus ID (Tropgene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of a locus from the Tropgene database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:Tropgene_locus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1916 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1916">
-        <rdfs:label>Alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>An alignment of molecular sequences, structures or profiles derived from them.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1917 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1917">
-        <rdfs:label>Atomic property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>General atomic property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data for an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2007">
-        <rdfs:label>UniProt keyword</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:SP_KW</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2009 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2009">
-        <rdfs:label>Ordered locus name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2012 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2012">
-        <rdfs:label>Sequence coordinates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1017"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2019"/>
-        <oboInOwl:hasExactSynonym>Map position</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Position</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Locus</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence co-ordinates</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A position in a map (for example a genetic map), either a single position (point) or a region / interval.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:GenePosition</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:HitPosition</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:MapPosition</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Locus</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_MapInterval</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_MapPosition</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_MapPoint</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.id</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2016 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2016">
-        <rdfs:label>Amino acid property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasDefinition>Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Amino acid data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2018 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2018">
-        <rdfs:label>Annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasDefinition>A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2019 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2019">
-        <rdfs:label>Map data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Map attribute</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An attribute of a molecular map (genetic or physical), or data extracted from or derived from the analysis of such a map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2022 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2022">
-        <rdfs:label>Vienna RNA structural data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data used by the Vienna RNA analysis package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2023 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2023">
-        <rdfs:label>Sequence mask parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data used to replace (mask) characters in a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2024 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2024">
-        <rdfs:label>Enzyme kinetics data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2978"/>
-        <oboInOwl:hasDefinition>Data concerning chemical reaction(s) catalysed by enzyme(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2025 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2025">
-        <rdfs:label>Michaelis Menten plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <oboInOwl:hasDefinition>A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2026 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2026">
-        <rdfs:label>Hanes Woolf plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2028 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2028">
-        <rdfs:label>Experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Raw data from or annotation on laboratory experiments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Experimental measurement data</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3108"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2041 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2041">
-        <rdfs:label>Genome version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a genome version.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2711"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2042 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2042">
-        <rdfs:label>Evidence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2043 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2043">
-        <rdfs:label>Sequence record lite</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2044 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2044">
-        <rdfs:label>Sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D008969</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Sequences</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation</rdfs:seeAlso>
-        <rdfs:comment>This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records.  It should not normally be used for derivatives such as sequence alignments, motifs or profiles.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>One or more molecular sequences, possibly with associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2046 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2046">
-        <rdfs:label>Nucleic acid sequence record (lite)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2047 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2047">
-        <rdfs:label>Protein sequence record (lite)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasExactSynonym>Sequence record lite (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2048 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2048">
-        <rdfs:label>Report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <rdfs:comment>You can use this term by default for any textual report, in case you can&apos;t find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing.</rdfs:comment>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000148</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Document</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2050 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2050">
-        <rdfs:label>Molecular property (general)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>General molecular property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>General data for a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2053 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2053">
-        <rdfs:label>Structural data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning molecular structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0883"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2070 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2070">
-        <rdfs:label>Sequence motif (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1353"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid sequence motif</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>DNA sequence motif</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>A nucleotide sequence motif.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>RNA sequence motif</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2071 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2071">
-        <rdfs:label>Sequence motif (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1353"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An amino acid sequence motif.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein sequence motif</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2079 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2079">
-        <rdfs:label>Search parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Some simple value controlling a search operation, typically a search of a database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2080">
-        <rdfs:label>Database search results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report of hits from searching a database of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Search results</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Database hits</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2081">
-        <rdfs:label>Secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The secondary structure assignment (predicted or real) of a nucleic acid or protein.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2082 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2082">
-        <rdfs:label>Matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Array</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasDefinition>An array of numerical values.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2083">
-        <rdfs:label>Alignment data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of molecular alignment of some type.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Alignment report</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1394"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2084">
-        <rdfs:label>Nucleic acid report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative human-readable report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2085">
-        <rdfs:label>Structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report on general information, properties or features of one or more molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure-derived report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2086 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2086">
-        <rdfs:label>Nucleic acid structure data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0912"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid property (structural)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Nucleic acid structural property</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2087 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2087">
-        <rdfs:label>Molecular property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasRelatedSynonym>SO:0000400</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Physicochemical property</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2088 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2088">
-        <rdfs:label>DNA base structural data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2086"/>
-        <oboInOwl:hasDefinition>Structural data for DNA base pairs or runs of bases, such as energy or angle data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2090 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2090">
-        <rdfs:label>Database entry version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2091 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2091">
-        <rdfs:label>Accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000731</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000675</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2092">
-        <rdfs:label>SNP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>single nucleotide polymorphism (SNP) in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2093 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2093">
-        <rdfs:label>Data reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:comment>A list of database accessions or identifiers are usually included.</rdfs:comment>
-        <oboInOwl:hasDefinition>Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2098 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2098">
-        <rdfs:label>Job identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:seeAlso>http://wsio.org/data_009</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>An identifier of a submitted job.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2099">
-        <rdfs:label>Name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000116</rdfs:seeAlso>
-        <rdfs:seeAlso>http://usefulinc.com/ns/doap#name</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://www.w3.org/2000/01/rdf-schema#label</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A name of a thing, which need not necessarily uniquely identify it.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Symbolic name</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-        <oboInOwl:hasBroadSynonym rdf:resource="&rdfs;label"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>Closely related, but focusing on labeling and human readability but not on identification.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_2099"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasBroadSynonym"/>
-        <owl:annotatedTarget rdf:resource="&rdfs;label"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_2100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2100">
-        <rdfs:label>Type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values).</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.org/dc/elements/1.1/type</rdfs:seeAlso>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2101 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2101">
-        <rdfs:label>User ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2118"/>
-        <oboInOwl:hasDefinition>An identifier of a software end-user (typically a person).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2102">
-        <rdfs:label>KEGG organism code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDefinition>A three-letter code used in the KEGG databases to uniquely identify organisms.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2103 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2103">
-        <rdfs:label>Gene name (KEGG GENES)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>KEGG GENES entry name</oboInOwl:hasExactSynonym>
-        <regex>[a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]*</regex>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the KEGG GENES database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:GeneId</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2104 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2104">
-        <rdfs:label>BioCyc ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>Identifier of an object from one of the BioCyc databases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2105 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2105">
-        <rdfs:label>Compound ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasExactSynonym>BioCyc compound identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a compound from the BioCyc chemical compounds database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>BioCyc compound ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2106 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2106">
-        <rdfs:label>Reaction ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0613"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from the BioCyc reactions database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2107 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2107">
-        <rdfs:label>Enzyme ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasExactSynonym>BioCyc enzyme ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an enzyme from the BioCyc enzymes database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2108 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2108">
-        <rdfs:label>Reaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2978"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2109 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2109">
-        <rdfs:label>Identifier (hybrid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:hasDefinition>An identifier that is re-used for data objects of fundamentally different types (typically served from a single database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This branch provides an alternative organisation of the concepts nested under &apos;Accession&apos; and &apos;Name&apos;. All concepts under here are already included under &apos;Accession&apos; or &apos;Name&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2110">
-        <rdfs:label>Molecular property identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2087"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a molecular property.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2111">
-        <rdfs:label>Codon usage table ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a codon usage table, for example a genetic code.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Codon usage table identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2112">
-        <rdfs:label>FlyBase primary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1089"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Primary identifier of an object from the FlyBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2113 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2113">
-        <rdfs:label>WormBase identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an object from the WormBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2114 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2114">
-        <rdfs:label>WormBase wormpep ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Protein identifier used by WormBase database.</oboInOwl:hasDefinition>
-        <regex>CE[0-9]{5}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2116 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2116">
-        <rdfs:label>Nucleic acid features (codon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2117 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2117">
-        <rdfs:label>Map identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a map of a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2118">
-        <rdfs:label>Person identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a software end-user (typically a person).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2119 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2119">
-        <rdfs:label>Nucleic acid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Name or other identifier of a nucleic acid molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2126">
-        <rdfs:label>Translation frame specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2127">
-        <rdfs:label>Genetic code identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a genetic code.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2128">
-        <rdfs:label>Genetic code name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2127"/>
-        <oboInOwl:hasDefinition>Informal name for a genetic code, typically an organism name.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2129 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2129">
-        <rdfs:label>File format name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3358"/>
-        <oboInOwl:hasDefinition>Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2130">
-        <rdfs:label>Sequence profile type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2131 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2131">
-        <rdfs:label>Operating system name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a computer operating system such as Linux, PC or Mac.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2132 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2132">
-        <rdfs:label>Mutation type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A type of point or block mutation, including insertion, deletion, change, duplication and moves.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2133">
-        <rdfs:label>Logical operator</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A logical operator such as OR, AND, XOR, and NOT.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2134">
-        <rdfs:label>Results sort order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A control of the order of data that is output, for example the order of sequences in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2135">
-        <rdfs:label>Toggle</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple parameter that is a toggle (boolean value), typically a control for a modal tool.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2136 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2136">
-        <rdfs:label>Sequence width</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The width of an output sequence or alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2137">
-        <rdfs:label>Gap penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A penalty for introducing or extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2139">
-        <rdfs:label>Nucleic acid melting temperature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Melting temperature</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2140">
-        <rdfs:label>Concentration</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The concentration of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2141">
-        <rdfs:label>Window step size</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Size of the incremental &apos;step&apos; a sequence window is moved over a sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2142 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2142">
-        <rdfs:label>EMBOSS graph</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image of a graph generated by the EMBOSS suite.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2143">
-        <rdfs:label>EMBOSS report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An application report generated by the EMBOSS suite.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2145 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2145">
-        <rdfs:label>Sequence offset</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>An offset for a single-point sequence position.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2146 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2146">
-        <rdfs:label>Threshold</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A value that serves as a threshold for a tool (usually to control scoring or output).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2147">
-        <rdfs:label>Protein report (transcription factor)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites.</rdfs:comment>
-        <oboInOwl:hasDefinition>An informative report on a transcription factor protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Transcription factor binding site data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2149 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2149">
-        <rdfs:label>Database category name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a category of biological or bioinformatics database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2150 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2150">
-        <rdfs:label>Sequence profile name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Name of a sequence profile.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1115"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2151 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2151">
-        <rdfs:label>Color</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Specification of one or more colors.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2152 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2152">
-        <rdfs:label>Rendering parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A parameter that is used to control rendering (drawing) to a device or image.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Graphics parameter</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Graphical parameter</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2154">
-        <rdfs:label>Sequence name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1063"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>Any arbitrary name of a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2156">
-        <rdfs:label>Date</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A temporal date.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2157">
-        <rdfs:label>Word composition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Word composition data for a molecular sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1266"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1268"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2160">
-        <rdfs:label>Fickett testcode plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <oboInOwl:hasDefinition>A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2161 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2161">
-        <rdfs:label>Sequence similarity plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0867"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <rdfs:comment>Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence conservation report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence similarity plot</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A plot of sequence similarities identified from word-matching or character comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2162 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2162">
-        <rdfs:label>Helical wheel</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1709"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2163">
-        <rdfs:label>Helical net</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1709"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Useful for highlighting amphipathicity and other properties.</rdfs:comment>
-        <oboInOwl:hasDefinition>An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2164">
-        <rdfs:label>Protein sequence properties plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of general physicochemical properties of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2165 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2165">
-        <rdfs:label>Protein ionization curve</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of pK versus pH for a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2166">
-        <rdfs:label>Sequence composition plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of character or word composition / frequency of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2167">
-        <rdfs:label>Nucleic acid density plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Density plot (of base composition) for a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2168 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2168">
-        <rdfs:label>Sequence trace image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2969"/>
-        <oboInOwl:hasDefinition>Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2169 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2169">
-        <rdfs:label>Nucleic acid features (siRNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on siRNA duplexes in mRNA.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3137"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2173">
-        <rdfs:label>Sequence set (stream)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time.</rdfs:comment>
-        <oboInOwl:hasDefinition>A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2174">
-        <rdfs:label>FlyBase secondary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1089"/>
-        <oboInOwl:hasDefinition>Secondary identifier of an object from the FlyBase database.</oboInOwl:hasDefinition>
-        <rdfs:comment>Secondary identifier are used to handle entries that were merged with or split from other entries in the database.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2176">
-        <rdfs:label>Cardinality</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The number of a certain thing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2177">
-        <rdfs:label>Exactly 1</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A single thing.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2178">
-        <rdfs:label>1 or more</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>One or more things.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2179">
-        <rdfs:label>Exactly 2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Exactly two things.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2180">
-        <rdfs:label>2 or more</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Two or more things.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2190 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2190">
-        <rdfs:label>Sequence checksum</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:hasDefinition>A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Hash code</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Hash sum</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Hash</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Hash value</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2191">
-        <rdfs:label>Protein features report (chemical modifications)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>chemical modification of a protein.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2192 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2192">
-        <rdfs:label>Error</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on an error generated by computer system or tool.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2193 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2193">
-        <rdfs:label>Database entry metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Basic information on any arbitrary database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2198 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2198">
-        <rdfs:label>Gene cluster</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A cluster of similar genes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1246"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2201 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2201">
-        <rdfs:label>Sequence record full</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2208">
-        <rdfs:label>Plasmid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <oboInOwl:hasDefinition>An identifier of a plasmid in a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2209">
-        <rdfs:label>Mutation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2538"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a specific mutation catalogued in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2212 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2212">
-        <rdfs:label>Mutation annotation (basic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2213">
-        <rdfs:label>Mutation annotation (prevalence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type)..</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2214 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2214">
-        <rdfs:label>Mutation annotation (prognostic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2215">
-        <rdfs:label>Mutation annotation (functional)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2216 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2216">
-        <rdfs:label>Codon number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The number of a codon, for instance, at which a mutation is located.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2217">
-        <rdfs:label>Tumor annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1622"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2218">
-        <rdfs:label>Server metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Basic information about a server on the web, such as an SRS server.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2219">
-        <rdfs:label>Database field name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a field in a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2220 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2220">
-        <rdfs:label>Sequence cluster ID (SYSTERS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasExactSynonym>SYSTERS cluster ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of a sequence cluster from the SYSTERS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2223 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2223">
-        <rdfs:label>Ontology metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning a biological ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2235">
-        <rdfs:label>Raw SCOP domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw SCOP domain classification data files.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>These are the parsable data files provided by SCOP.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2236">
-        <rdfs:label>Raw CATH domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Raw CATH domain classification data files.</oboInOwl:hasDefinition>
-        <rdfs:comment>These are the parsable data files provided by CATH.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2240">
-        <rdfs:label>Heterogen annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on the types of small molecules or &apos;heterogens&apos; (non-protein groups) that are represented in PDB files.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2242">
-        <rdfs:label>Phylogenetic property values</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic property values data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0871"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2245">
-        <rdfs:label>Sequence set (bootstrapped)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Bootstrapping is often performed in phylogenetic analysis.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A collection of sequences output from a bootstrapping (resampling) procedure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2247">
-        <rdfs:label>Phylogenetic consensus tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A consensus phylogenetic tree derived from comparison of multiple trees.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2248">
-        <rdfs:label>Schema</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A data schema for organising or transforming data of some type.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2249 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2249">
-        <rdfs:label>DTD</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A DTD (document type definition).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2250">
-        <rdfs:label>XML Schema</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>XSD</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An XML Schema.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2251 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2251">
-        <rdfs:label>Relax-NG schema</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A relax-NG schema.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2252">
-        <rdfs:label>XSLT stylesheet</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An XSLT stylesheet.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2253">
-        <rdfs:label>Data resource definition name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1084"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a data type.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2254">
-        <rdfs:label>OBO file format name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2129"/>
-        <oboInOwl:hasDefinition>Name of an OBO file format such as OBO-XML, plain and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2285">
-        <rdfs:label>Gene ID (MIPS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier for genetic elements in MIPS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>MIPS genetic element identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2288">
-        <rdfs:label>Sequence identifier (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An identifier of protein sequence(s) or protein sequence database entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1096"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2289">
-        <rdfs:label>Sequence identifier (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An identifier of nucleotide sequence(s) or nucleotide sequence database entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2290 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2290">
-        <rdfs:label>EMBL accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1103"/>
-        <oboInOwl:hasExactSynonym>EMBL ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>EMBL accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>EMBL identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An accession number of an entry from the EMBL sequence database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2291 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2291">
-        <rdfs:label>UniProt ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2154"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>UniProtKB identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An identifier of a polypeptide in the UniProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniProtKB entry name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniProt identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniProt entry name</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2292">
-        <rdfs:label>GenBank accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1103"/>
-        <oboInOwl:hasExactSynonym>GenBank ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>GenBank identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of an entry from the GenBank sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>GenBank accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2293">
-        <rdfs:label>Gramene secondary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2915"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gramene internal identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gramene internal ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Secondary (internal) identifier of a Gramene database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gramene secondary ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2294 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2294">
-        <rdfs:label>Sequence variation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>An identifier of an entry from a database of molecular sequence variation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2295">
-        <rdfs:label>Gene ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1025"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasExactSynonym>Gene accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene code</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2296 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2296">
-        <rdfs:label>Gene name (AceView)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>AceView gene name</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the AceView genes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2297">
-        <rdfs:label>Gene ID (ECK)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1795"/>
-        <oboInOwl:hasExactSynonym>ECK accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>E. coli K-12 gene identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an E. coli K-12 gene from EcoGene Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ECK</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2298">
-        <rdfs:label>Gene ID (HGNC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>HGNC ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier for a gene approved by the HUGO Gene Nomenclature Committee.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2299">
-        <rdfs:label>Gene name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1025"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Allele name</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2300">
-        <rdfs:label>Gene name (NCBI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>NCBI gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the NCBI genes database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2301">
-        <rdfs:label>SMILES string</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0846"/>
-        <oboInOwl:hasDefinition>A specification of a chemical structure in SMILES format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2302">
-        <rdfs:label>STRING ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the STRING database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2307">
-        <rdfs:label>Virus annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a specific virus.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2308">
-        <rdfs:label>Virus annotation (taxonomy)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on the taxonomy of a specific virus.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2309">
-        <rdfs:label>Reaction ID (SABIO-RK)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from the SABIO-RK reactions database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2313">
-        <rdfs:label>Carbohydrate report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:hasDefinition>Annotation on or information derived from one or more specific carbohydrate 3D structure(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2314">
-        <rdfs:label>GI number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2362"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>NCBI GI number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>gi number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.</oboInOwl:hasDefinition>
-        <rdfs:comment>Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2315">
-        <rdfs:label>NCBI version</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2362"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>NCBI accession.version</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number.</rdfs:comment>
-        <oboInOwl:hasDefinition>An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>accession.version</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2316">
-        <rdfs:label>Cell line name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1046"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2317 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2317">
-        <rdfs:label>Cell line name (exact)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2318">
-        <rdfs:label>Cell line name (truncated)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2319 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2319">
-        <rdfs:label>Cell line name (no punctuation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2320">
-        <rdfs:label>Cell line name (assonant)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2321">
-        <rdfs:label>Enzyme ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1010"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique, persistent identifier of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Enzyme accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2325">
-        <rdfs:label>REBASE enzyme number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasDefinition>Identifier of an enzyme from the REBASE enzymes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2326">
-        <rdfs:label>DrugBank ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>DB[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a drug from the DrugBank database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2327">
-        <rdfs:label>GI number (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2314"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>protein gi number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A unique identifier assigned to NCBI protein sequence records.</oboInOwl:hasDefinition>
-        <rdfs:comment>Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>protein gi</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2335">
-        <rdfs:label>Bit score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1413"/>
-        <oboInOwl:hasDefinition>A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system.</oboInOwl:hasDefinition>
-        <rdfs:comment>Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2336">
-        <rdfs:label>Translation phase specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phase</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2337">
-        <rdfs:label>Resource metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Data concerning or describing some core computational resource, as distinct from primary data.  This includes metadata on the origin, source, history, ownership or location of some thing.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Provenance metadata</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2338">
-        <rdfs:label>Ontology identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Any arbitrary identifier of an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2339">
-        <rdfs:label>Ontology concept name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3025"/>
-        <oboInOwl:hasDefinition>The name of a concept in an ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2340">
-        <rdfs:label>Genome build identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2749"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a build of a particular genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2342">
-        <rdfs:label>Pathway or network name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1082"/>
-        <oboInOwl:hasDefinition>The name of a biological pathway or network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2343">
-        <rdfs:label>Pathway ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the KEGG pathway database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]{2,3}[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>KEGG pathway ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2344">
-        <rdfs:label>Pathway ID (NCI-Nature)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the NCI-Nature pathway database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2345">
-        <rdfs:label>Pathway ID (ConsensusPathDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2917"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the ConsensusPathDB pathway database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2346">
-        <rdfs:label>Sequence cluster ID (UniRef)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniRef cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniRef entry accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2347 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2347">
-        <rdfs:label>Sequence cluster ID (UniRef100)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2346"/>
-        <oboInOwl:hasExactSynonym>UniRef100 cluster id</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniRef100 entry accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef100 database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2348">
-        <rdfs:label>Sequence cluster ID (UniRef90)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2346"/>
-        <oboInOwl:hasExactSynonym>UniRef90 entry accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniRef90 cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef90 database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2349">
-        <rdfs:label>Sequence cluster ID (UniRef50)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2346"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniRef50 cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniRef50 entry accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef50 database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2353">
-        <rdfs:label>Ontology data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data concerning or derived from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ontological data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2354">
-        <rdfs:label>RNA family report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3148"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific RNA family or other group of classified RNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA family annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2355">
-        <rdfs:label>RNA family identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an RNA family, typically an entry from a RNA sequence classification database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2356">
-        <rdfs:label>RFAM accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2355"/>
-        <oboInOwl:hasDefinition>Stable accession number of an entry (RNA family) from the RFAM database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2357">
-        <rdfs:label>Protein signature type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2358">
-        <rdfs:label>Domain-nucleic acid interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on protein domain-DNA/RNA interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1567"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2359">
-        <rdfs:label>Domain-domain interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on protein domain-protein domain interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2360">
-        <rdfs:label>Domain-domain interaction (indirect)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on indirect protein domain-protein domain interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2359"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2362 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2362">
-        <rdfs:label>Sequence accession (hybrid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1093"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession number of a nucleotide or protein sequence database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2363 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2363">
-        <rdfs:label>2D PAGE data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning two-dimensional polygel electrophoresis.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0942"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2364"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2364 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2364">
-        <rdfs:label>2D PAGE report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>two-dimensional gel electrophoresis experiments, gels or spots in a gel.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2365">
-        <rdfs:label>Pathway or network accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>A persistent, unique identifier of a biological pathway or network (typically a database entry).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2366">
-        <rdfs:label>Secondary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <oboInOwl:hasDefinition>Alignment of the (1D representations of) secondary structure of two or more molecules.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2367 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2367">
-        <rdfs:label>ASTD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an object from the ASTD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2368">
-        <rdfs:label>ASTD ID (exon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an exon from the ASTD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2369">
-        <rdfs:label>ASTD ID (intron)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an intron from the ASTD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2370">
-        <rdfs:label>ASTD ID (polya)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <oboInOwl:hasDefinition>Identifier of a polyA signal from the ASTD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2371">
-        <rdfs:label>ASTD ID (tss)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <oboInOwl:hasDefinition>Identifier of a transcription start site from the ASTD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2372">
-        <rdfs:label>2D PAGE spot report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>2D PAGE spot annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2373 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2373">
-        <rdfs:label>Spot ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a spot from a two-dimensional (protein) gel.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2374 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2374">
-        <rdfs:label>Spot serial number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2373"/>
-        <oboInOwl:hasDefinition>Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2375 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2375">
-        <rdfs:label>Spot ID (HSC-2DPAGE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2373"/>
-        <oboInOwl:hasDefinition>Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2378">
-        <rdfs:label>Protein-motif interaction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1565"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2379">
-        <rdfs:label>Strain identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <oboInOwl:hasDefinition>Identifier of a strain of an organism variant, typically a plant, virus or bacterium.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2380 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2380">
-        <rdfs:label>CABRI accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>A unique identifier of an item from the CABRI database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2381 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2381">
-        <rdfs:label>Experiment report (genotyping)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2382 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2382">
-        <rdfs:label>Genotype experiment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of genotype experiment metadata.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2383">
-        <rdfs:label>EGA accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2382"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the EGA database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2384">
-        <rdfs:label>IPI protein ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <oboInOwl:hasDefinition>Identifier of a protein entry catalogued in the International Protein Index (IPI) database.</oboInOwl:hasDefinition>
-        <regex>IPI[0-9]{8}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2385">
-        <rdfs:label>RefSeq accession (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1098"/>
-        <oboInOwl:hasExactSynonym>RefSeq protein ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of a protein from the RefSeq database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2386">
-        <rdfs:label>EPD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2727"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (promoter) from the EPD database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EPD identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2387">
-        <rdfs:label>TAIR accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the TAIR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2388">
-        <rdfs:label>TAIR accession (At gene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1037"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an Arabidopsis thaliana gene from the TAIR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2389 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2389">
-        <rdfs:label>UniSTS accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UniSTS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2390">
-        <rdfs:label>UNITE accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UNITE database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2391">
-        <rdfs:label>UTR accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UTR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2392 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2392">
-        <rdfs:label>UniParc accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>UPI[A-F0-9]{10}</regex>
-        <oboInOwl:hasDefinition>Accession number of a UniParc (protein sequence) database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniParc ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UPI</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2393">
-        <rdfs:label>mFLJ/mKIAA number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Rouge or HUGE databases.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2395">
-        <rdfs:label>Fungi annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on a specific fungus.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2396">
-        <rdfs:label>Fungi annotation (anamorph)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific fungus anamorph.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2397">
-        <rdfs:label>Gene features report (exon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>exons in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2398">
-        <rdfs:label>Ensembl protein ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>Ensembl ID (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein ID (Ensembl)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2399">
-        <rdfs:label>Gene transcriptional features report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>transcription of DNA into RNA including the regulation of transcription.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2400">
-        <rdfs:label>Toxin annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific toxin.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2401">
-        <rdfs:label>Protein report (membrane protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on a membrane protein.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1456"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2402">
-        <rdfs:label>Protein-drug interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1537"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1566"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1696"/>
-        <oboInOwl:hasDefinition>An informative report on tentative or known protein-drug interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2522">
-        <rdfs:label>Map data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning a map of molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1274"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2019"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2523">
-        <rdfs:label>Phylogenetic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic data</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2524">
-        <rdfs:label>Protein data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning one or more protein molecules.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2525">
-        <rdfs:label>Nucleic acid data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning one or more nucleic acid molecules.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2526">
-        <rdfs:label>Article data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Article report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0971"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2527">
-        <rdfs:label>Parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000144</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Tool-specific parameter</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Typically a simple numerical or string value that controls the operation of a tool.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Parameters</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Tool parameter</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2528">
-        <rdfs:label>Molecular data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Molecule-specific data</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning a specific type of molecule.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2529">
-        <rdfs:label>Molecule report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a specific molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Molecular report</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2530">
-        <rdfs:label>Organism report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report on a specific organism.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Organism annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2531">
-        <rdfs:label>Experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasExactSynonym>Experiment metadata</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Experiment annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation on a wet lab experiment, such as experimental conditions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2533">
-        <rdfs:label>Nucleic acid features report (mutation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>DNA mutation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2534">
-        <rdfs:label>Sequence attribute</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:hasDefinition>An attribute of a molecular sequence, possibly in reference to some other sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Sequence parameter</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2535 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2535">
-        <rdfs:label>Sequence tag profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0928"/>
-        <rdfs:comment>SAGE, MPSS and SBS experiments are usually performed to study gene expression.  The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequencing-based expression profile</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment.  In all cases this is a list of short sequence tags and the number of times it is observed.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2536">
-        <rdfs:label>Mass spectrometry data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning a mass spectrometry measurement.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2537">
-        <rdfs:label>Protein structure raw data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw data from experimental methods for determining protein structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2538 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2538">
-        <rdfs:label>Mutation identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a mutation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2539">
-        <rdfs:label>Alignment data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  This includes entities derived from sequences and structures such as motifs and profiles.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning an alignment of two or more molecular sequences, structures or derived data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1916"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2540">
-        <rdfs:label>Data index data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning an index of data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Database index</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0955"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2563">
-        <rdfs:label>Amino acid name (single letter)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Single letter amino acid identifier, e.g. G.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2564">
-        <rdfs:label>Amino acid name (three letter)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Three letter amino acid identifier, e.g. GLY.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2565">
-        <rdfs:label>Amino acid name (full name)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Full name of an amino acid, e.g. Glycine.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2576 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2576">
-        <rdfs:label>Toxin identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2852"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a toxin.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2578">
-        <rdfs:label>ArachnoServer ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2897"/>
-        <oboInOwl:hasDefinition>Unique identifier of a toxin from the ArachnoServer database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2579">
-        <rdfs:label>Expressed gene list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Gene annotation (expressed gene list)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A simple summary of expressed genes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2580 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2580">
-        <rdfs:label>BindingDB Monomer ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Unique identifier of a monomer from the BindingDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2581">
-        <rdfs:label>GO concept name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a concept from the GO ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2582">
-        <rdfs:label>GO concept ID (biological process)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1176"/>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a &apos;biological process&apos; concept from the the Gene Ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2583">
-        <rdfs:label>GO concept ID (molecular function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1176"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <oboInOwl:hasDefinition>An identifier of a &apos;molecular function&apos; concept from the the Gene Ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2584 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2584">
-        <rdfs:label>GO concept name (cellular component)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The name of a concept for a cellular component from the GO ontology.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2586 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2586">
-        <rdfs:label>Northern blot image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image arising from a Northern Blot experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2587 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2587">
-        <rdfs:label>Blot ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Unique identifier of a blot from a Northern Blot.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2588 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2588">
-        <rdfs:label>BlotBase blot ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2587"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a blot from a Northern Blot from the BlotBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2589 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2589">
-        <rdfs:label>Hierarchy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Hierarchy annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2590 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2590">
-        <rdfs:label>Hierarchy identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of biological hierarchies.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2891"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2591 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2591">
-        <rdfs:label>Brite hierarchy ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2891"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Brite database of biological hierarchies.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2592 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2592">
-        <rdfs:label>Cancer type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A type (represented as a string) of cancer.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2100"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2593">
-        <rdfs:label>BRENDA organism ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <oboInOwl:hasDefinition>A unique identifier for an organism used in the BRENDA database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2594">
-        <rdfs:label>UniGene taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a taxon using the controlled vocabulary of the UniGene database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniGene organism abbreviation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2595">
-        <rdfs:label>UTRdb taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a taxon using the controlled vocabulary of the UTRdb database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2596 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2596">
-        <rdfs:label>Catalogue ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a catalogue of biological resources.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Catalogue identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2597 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2597">
-        <rdfs:label>CABRI catalogue name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2596"/>
-        <oboInOwl:hasDefinition>The name of a catalogue of biological resources from the CABRI database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2598">
-        <rdfs:label>Secondary structure alignment metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on protein secondary structure alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2599 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2599">
-        <rdfs:label>Molecule interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Molecular interaction report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Molecular interaction data</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0906"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2600 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2600">
-        <rdfs:label>Pathway or network</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Network</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Pathway</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2601">
-        <rdfs:label>Small molecule data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning one or more small molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2602">
-        <rdfs:label>Genotype and phenotype data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning a particular genotype, phenotype or a genotype / phenotype relation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0920"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2603 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2603">
-        <rdfs:label>Gene expression data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image or hybridisation data for a microarray, typically a study of gene expression.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Microarray data</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  See also http://edamontology.org/data_0931</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2605">
-        <rdfs:label>Compound ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>C[0-9]+</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a chemical compound from the KEGG database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>KEGG compound ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>KEGG compound identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2606">
-        <rdfs:label>RFAM name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2355"/>
-        <oboInOwl:hasDefinition>Name (not necessarily stable) an entry (RNA family) from the RFAM database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2608">
-        <rdfs:label>Reaction ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from the KEGG reactions database.</oboInOwl:hasDefinition>
-        <regex>R[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2609 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2609">
-        <rdfs:label>Drug ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a drug from the KEGG Drug database.</oboInOwl:hasDefinition>
-        <regex>D[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2610">
-        <rdfs:label>Ensembl ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENS[A-Z]*[FPTG][0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ensembl IDs</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2611">
-        <rdfs:label>ICD identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1150"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1622"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a disease from the International Classification of Diseases (ICD) database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[A-Z][0-9]+(\.[-[0-9]+])?</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2612">
-        <rdfs:label>Sequence cluster ID (CluSTr)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasDefinition>Unique identifier of a sequence cluster from the CluSTr database.</oboInOwl:hasDefinition>
-        <regex>[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?</regex>
-        <oboInOwl:hasExactSynonym>CluSTr ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CluSTr cluster ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2613">
-        <rdfs:label>KEGG Glycan ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <regex>G[0-9]+</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2614 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2614">
-        <rdfs:label>TCDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>OBO file for regular expression.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>TC number</oboInOwl:hasExactSynonym>
-        <regex>[0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+</regex>
-        <oboInOwl:hasDefinition>A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2615 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2615">
-        <rdfs:label>MINT ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>MINT\-[0-9]{1,5}</regex>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the MINT database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2616">
-        <rdfs:label>DIP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the DIP database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>DIP[\:\-][0-9]{3}[EN]</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2617">
-        <rdfs:label>Signaling Gateway protein ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database.</oboInOwl:hasDefinition>
-        <regex>A[0-9]{6}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2618">
-        <rdfs:label>Protein modification ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein modification catalogued in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2619 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2619">
-        <rdfs:label>RESID ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2618"/>
-        <oboInOwl:hasDefinition>Identifier of a protein modification catalogued in the RESID database.</oboInOwl:hasDefinition>
-        <regex>AA[0-9]{4}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2620">
-        <rdfs:label>RGD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <regex>[0-9]{4,7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the RGD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2621">
-        <rdfs:label>TAIR accession (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2387"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <regex>AASequence:[0-9]{10}</regex>
-        <oboInOwl:hasDefinition>Identifier of a protein sequence from the TAIR database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2622">
-        <rdfs:label>Compound ID (HMDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>HMDB[0-9]{5}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>HMDB ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2625 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2625">
-        <rdfs:label>LIPID MAPS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2905"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>LM ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from the LIPID MAPS database.</oboInOwl:hasDefinition>
-        <regex>LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2626 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2626">
-        <rdfs:label>PeptideAtlas ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2906"/>
-        <oboInOwl:hasDefinition>Identifier of a peptide from the PeptideAtlas peptide databases.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_strand_id</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PAp[0-9]{8}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2627 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2627">
-        <rdfs:label>Molecular interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of a report of molecular interactions from a database (typically).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2628 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2628">
-        <rdfs:label>BioGRID interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of an interaction from the BioGRID database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2629 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2629">
-        <rdfs:label>Enzyme ID (MEROPS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasExactSynonym>MEROPS ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of a peptidase enzyme from the MEROPS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>S[0-9]{2}\.[0-9]{3}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2630 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2630">
-        <rdfs:label>Mobile genetic element ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>An identifier of a mobile genetic element.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2631 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2631">
-        <rdfs:label>ACLAME ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2630"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>mge:[0-9]+</regex>
-        <oboInOwl:hasDefinition>An identifier of a mobile genetic element from the Aclame database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2632 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2632">
-        <rdfs:label>SGD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <regex>PWY[a-zA-Z_0-9]{2}\-[0-9]{3}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Saccharomyces genome database (SGD).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2633 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2633">
-        <rdfs:label>Book ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a book.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2634 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2634">
-        <rdfs:label>ISBN</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2633"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)</regex>
-        <oboInOwl:hasDefinition>The International Standard Book Number (ISBN) is for identifying printed books.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2635 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2635">
-        <rdfs:label>Compound ID (3DMET)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>B[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>3DMET ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a metabolite from the 3DMET database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2636 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2636">
-        <rdfs:label>MatrixDB interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)</regex>
-        <oboInOwl:hasDefinition>A unique identifier of an interaction from the MatrixDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2637 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2637">
-        <rdfs:label>cPath ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <regex>[0-9]+</regex>
-        <rdfs:comment>These identifiers are unique within the cPath database, however, they are not stable between releases.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2638 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2638">
-        <rdfs:label>PubChem bioassay ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2639"/>
-        <oboInOwl:hasDefinition>Identifier of an assay from the PubChem database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2639 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2639">
-        <rdfs:label>PubChem ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasExactSynonym>PubChem identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the PubChem database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2641 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2641">
-        <rdfs:label>Reaction ID (MACie)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>M[0-9]{4}</regex>
-        <oboInOwl:hasExactSynonym>MACie entry number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an enzyme reaction mechanism from the MACie database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2642 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2642">
-        <rdfs:label>Gene ID (miRBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>miRNA name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>miRNA ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier for a gene from the miRBase database.</oboInOwl:hasDefinition>
-        <regex>MI[0-9]{7}</regex>
-        <oboInOwl:hasExactSynonym>miRNA identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2643 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2643">
-        <rdfs:label>Gene ID (ZFIN)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier for a gene from the Zebrafish information network genome (ZFIN) database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ZDB\-GENE\-[0-9]+\-[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2644 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2644">
-        <rdfs:label>Reaction ID (Rhea)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <regex>[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Identifier of an enzyme-catalysed reaction from the Rhea database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2645 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2645">
-        <rdfs:label>Pathway ID (Unipathway)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <regex>UPA[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>upaid</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological pathway from the Unipathway database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2646 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2646">
-        <rdfs:label>Compound ID (ChEMBL)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of a small molecular from the ChEMBL database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChEMBL ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2647 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2647">
-        <rdfs:label>LGICdb identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2648 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2648">
-        <rdfs:label>Reaction kinetics ID (SABIO-RK)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2309"/>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2649 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2649">
-        <rdfs:label>PharmGKB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2650 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2650">
-        <rdfs:label>Pathway ID (PharmGKB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2649"/>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2651 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2651">
-        <rdfs:label>Disease ID (PharmGKB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1150"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2649"/>
-        <oboInOwl:hasDefinition>Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2652 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2652">
-        <rdfs:label>Drug ID (PharmGKB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2649"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2653 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2653">
-        <rdfs:label>Drug ID (TTD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <regex>DAP[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a drug from the Therapeutic Target Database (TTD).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2654 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2654">
-        <rdfs:label>Target ID (TTD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <regex>TTDS[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a target protein from the Therapeutic Target Database (TTD).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2655 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2655">
-        <rdfs:label>Cell type identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Cell type ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A unique identifier of a type or group of cells.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2656 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2656">
-        <rdfs:label>NeuronDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2893"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a neuron from the NeuronDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2657 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2657">
-        <rdfs:label>NeuroMorpho ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a neuron from the NeuroMorpho database.</oboInOwl:hasDefinition>
-        <regex>[a-zA-Z_0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2658 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2658">
-        <rdfs:label>Compound ID (ChemIDplus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of a chemical from the ChemIDplus database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChemIDplus ID</oboInOwl:hasExactSynonym>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2659 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2659">
-        <rdfs:label>Pathway ID (SMPDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the Small Molecule Pathway Database (SMPDB).</oboInOwl:hasDefinition>
-        <regex>SMP[0-9]{5}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2660 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2660">
-        <rdfs:label>BioNumbers ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2662 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2662">
-        <rdfs:label>T3DB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2897"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>T3D[0-9]+</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2663 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2663">
-        <rdfs:label>Carbohydrate identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2313"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1462"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a carbohydrate.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2664 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2664">
-        <rdfs:label>GlycomeDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GlycomeDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2665 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2665">
-        <rdfs:label>LipidBank ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2905"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]+[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry from the LipidBank database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2666 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2666">
-        <rdfs:label>CDD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1038"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>cd[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Identifier of a conserved domain from the Conserved Domain Database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2667 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2667">
-        <rdfs:label>MMDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1070"/>
-        <regex>[0-9]{1,5}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of an entry from the MMDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>MMDB accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2668 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2668">
-        <rdfs:label>iRefIndex ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the iRefIndex database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2669 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2669">
-        <rdfs:label>ModelDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2891"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the ModelDB database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2670 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2670">
-        <rdfs:label>Pathway ID (DQCS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <regex>[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2671 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2671">
-        <rdfs:label>Ensembl ID (Homo sapiens)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENS([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (Homo sapiens division).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2672 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2672">
-        <rdfs:label>Ensembl ID (&apos;Bos taurus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Bos taurus&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSBTA([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2673 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2673">
-        <rdfs:label>Ensembl ID (&apos;Canis familiaris&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Canis familiaris&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSCAF([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2674 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2674">
-        <rdfs:label>Ensembl ID (&apos;Cavia porcellus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSCPO([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Cavia porcellus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2675 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2675">
-        <rdfs:label>Ensembl ID (&apos;Ciona intestinalis&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Ciona intestinalis&apos; division).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSCIN([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2676 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2676">
-        <rdfs:label>Ensembl ID (&apos;Ciona savignyi&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Ciona savignyi&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSCSAV([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2677 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2677">
-        <rdfs:label>Ensembl ID (&apos;Danio rerio&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Danio rerio&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSDAR([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2678 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2678">
-        <rdfs:label>Ensembl ID (&apos;Dasypus novemcinctus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Dasypus novemcinctus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSDNO([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2679 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2679">
-        <rdfs:label>Ensembl ID (&apos;Echinops telfairi&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSETE([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Echinops telfairi&apos; division).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2680 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2680">
-        <rdfs:label>Ensembl ID (&apos;Erinaceus europaeus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSEEU([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Erinaceus europaeus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2681 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2681">
-        <rdfs:label>Ensembl ID (&apos;Felis catus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSFCA([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Felis catus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2682 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2682">
-        <rdfs:label>Ensembl ID (&apos;Gallus gallus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSGAL([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Gallus gallus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2683 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2683">
-        <rdfs:label>Ensembl ID (&apos;Gasterosteus aculeatus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Gasterosteus aculeatus&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSGAC([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2684 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2684">
-        <rdfs:label>Ensembl ID (&apos;Homo sapiens&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSHUM([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Homo sapiens&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2685 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2685">
-        <rdfs:label>Ensembl ID (&apos;Loxodonta africana&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Loxodonta africana&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSLAF([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2686 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2686">
-        <rdfs:label>Ensembl ID (&apos;Macaca mulatta&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Macaca mulatta&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSMMU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2687 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2687">
-        <rdfs:label>Ensembl ID (&apos;Monodelphis domestica&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Monodelphis domestica&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSMOD([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2688 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2688">
-        <rdfs:label>Ensembl ID (&apos;Mus musculus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSMUS([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Mus musculus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2689 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2689">
-        <rdfs:label>Ensembl ID (&apos;Myotis lucifugus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSMLU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Myotis lucifugus&apos; division).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2690 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2690">
-        <rdfs:label>Ensembl ID (&quot;Ornithorhynchus anatinus&quot;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Ornithorhynchus anatinus&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSOAN([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2691 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2691">
-        <rdfs:label>Ensembl ID (&apos;Oryctolagus cuniculus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSOCU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Oryctolagus cuniculus&apos; division).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2692 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2692">
-        <rdfs:label>Ensembl ID (&apos;Oryzias latipes&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSORL([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Oryzias latipes&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2693 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2693">
-        <rdfs:label>Ensembl ID (&apos;Otolemur garnettii&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Otolemur garnettii&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSSAR([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2694 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2694">
-        <rdfs:label>Ensembl ID (&apos;Pan troglodytes&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSPTR([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Pan troglodytes&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2695 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2695">
-        <rdfs:label>Ensembl ID (&apos;Rattus norvegicus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Rattus norvegicus&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSRNO([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2696 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2696">
-        <rdfs:label>Ensembl ID (&apos;Spermophilus tridecemlineatus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSSTO([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Spermophilus tridecemlineatus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2697 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2697">
-        <rdfs:label>Ensembl ID (&apos;Takifugu rubripes&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Takifugu rubripes&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSFRU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2698 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2698">
-        <rdfs:label>Ensembl ID (&apos;Tupaia belangeri&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Tupaia belangeri&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSTBE([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2699 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2699">
-        <rdfs:label>Ensembl ID (&apos;Xenopus tropicalis&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Xenopus tropicalis&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSXET([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2700 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2700">
-        <rdfs:label>CATH identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1038"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein domain (or other node) from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2701 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2701">
-        <rdfs:label>CATH node ID (family)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1043"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A code number identifying a family from the CATH database.</oboInOwl:hasDefinition>
-        <example>2.10.10.10</example>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2702 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2702">
-        <rdfs:label>Enzyme ID (CAZy)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasDefinition>Identifier of an enzyme from the CAZy enzymes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CAZy ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2704 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2704">
-        <rdfs:label>Clone ID (IMAGE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1855"/>
-        <oboInOwl:hasExactSynonym>I.M.A.G.E. cloneID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>IMAGE cloneID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2705 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2705">
-        <rdfs:label>GO concept ID (cellular compartment)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1176"/>
-        <oboInOwl:hasDefinition>An identifier of a &apos;cellular compartment&apos; concept from the Gene Ontology.</oboInOwl:hasDefinition>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>GO concept identifier (cellular compartment)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2706 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2706">
-        <rdfs:label>Chromosome name (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0987"/>
-        <oboInOwl:hasDefinition>Name of a chromosome as used in the BioCyc database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2709 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2709">
-        <rdfs:label>CleanEx entry name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a gene expression profile from the CleanEx database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2710 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2710">
-        <rdfs:label>CleanEx dataset code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2711 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2711">
-        <rdfs:label>Genome report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:hasDefinition>An informative report of general information concerning a genome as a whole.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2713 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2713">
-        <rdfs:label>Protein ID (CORUM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CORUM complex ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a protein complex from the CORUM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2714 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2714">
-        <rdfs:label>CDD PSSM-ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1115"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a position-specific scoring matrix from the CDD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2715 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2715">
-        <rdfs:label>Protein ID (CuticleDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>CuticleDB ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the CuticleDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2716 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2716">
-        <rdfs:label>DBD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2911"/>
-        <oboInOwl:hasDefinition>Identifier of a predicted transcription factor from the DBD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2717 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2717">
-        <rdfs:label>Oligonucleotide probe annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3115"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>General annotation on an oligonucleotide probe.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2718 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2718">
-        <rdfs:label>Oligonucleotide ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasDefinition>Identifier of an oligonucleotide from a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2719 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2719">
-        <rdfs:label>dbProbe ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2718"/>
-        <oboInOwl:hasDefinition>Identifier of an oligonucleotide probe from the dbProbe database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2720 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2720">
-        <rdfs:label>Dinucleotide property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Physicochemical property data for one or more dinucleotides.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2721 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2721">
-        <rdfs:label>DiProDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2718"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an dinucleotide property from the DiProDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2722 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2722">
-        <rdfs:label>Protein features report (disordered structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>disordered structure in a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2723 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2723">
-        <rdfs:label>Protein ID (DisProt)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>DisProt ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the DisProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2724 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2724">
-        <rdfs:label>Embryo report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Annotation on an embryo or concerning embryological development.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Embryo annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1713"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2725 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2725">
-        <rdfs:label>Ensembl transcript ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2769"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Transcript ID (Ensembl)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a gene transcript from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2726 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2726">
-        <rdfs:label>Inhibitor annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on one or more small molecules that are enzyme inhibitors.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2727 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2727">
-        <rdfs:label>Promoter ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a promoter of a gene that is catalogued in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:GeneAccessionList</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2728 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2728">
-        <rdfs:label>EST accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1855"/>
-        <oboInOwl:hasDefinition>Identifier of an EST sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2729 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2729">
-        <rdfs:label>COGEME EST ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an EST sequence from the COGEME database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2730 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2730">
-        <rdfs:label>COGEME unisequence ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <oboInOwl:hasDefinition>Identifier of a unisequence from the COGEME database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A unisequence is a single sequence assembled from ESTs.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2731 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2731">
-        <rdfs:label>Protein family ID (GeneFarm)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasExactSynonym>GeneFarm family ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry (family) from the TIGRFam database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2732 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2732">
-        <rdfs:label>Family name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a family of organism.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2733 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2733">
-        <rdfs:label>Genus name (virus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a genus of viruses.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1870"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2734 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2734">
-        <rdfs:label>Family name (virus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>The name of a family of viruses.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2732"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2735 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2735">
-        <rdfs:label>Database name (SwissRegulon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>The name of a SwissRegulon database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2736 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2736">
-        <rdfs:label>Sequence feature ID (SwissRegulon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1015"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A feature identifier as used in the SwissRegulon database.</oboInOwl:hasDefinition>
-        <rdfs:comment>This can be name of a gene, the ID of a TFBS, or genomic coordinates in form &quot;chr:start..end&quot;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2737 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2737">
-        <rdfs:label>FIG ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:comment>A FIG ID consists of four parts: a prefix, genome id, locus type and id number.</rdfs:comment>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the NMPDR database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2738 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2738">
-        <rdfs:label>Gene ID (Xenbase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the Xenbase database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2739 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2739">
-        <rdfs:label>Gene ID (Genolist)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the Genolist database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2740 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2740">
-        <rdfs:label>Gene name (Genolist)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Genolist gene name</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the Genolist genes database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2741 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2741">
-        <rdfs:label>ABS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2727"/>
-        <oboInOwl:hasExactSynonym>ABS identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (promoter) from the ABS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2742 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2742">
-        <rdfs:label>AraC-XylS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2911"/>
-        <oboInOwl:hasDefinition>Identifier of a transcription factor from the AraC-XylS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2743 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2743">
-        <rdfs:label>Gene name (HUGO)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the HUGO database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1791"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2744 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2744">
-        <rdfs:label>Locus ID (PseudoCAP)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a locus from the PseudoCAP database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2745 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2745">
-        <rdfs:label>Locus ID (UTR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a locus from the UTR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2746 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2746">
-        <rdfs:label>MonosaccharideDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2898"/>
-        <oboInOwl:hasDefinition>Unique identifier of a monosaccharide from the MonosaccharideDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2747 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2747">
-        <rdfs:label>Database name (CMD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a subdivision of the Collagen Mutation Database (CMD) database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2748 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2748">
-        <rdfs:label>Database name (Osteogenesis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>The name of a subdivision of the Osteogenesis database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2749 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2749">
-        <rdfs:label>Genome identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a particular genome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2751 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2751">
-        <rdfs:label>GenomeReviews ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2903"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a particular genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2752 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2752">
-        <rdfs:label>GlycoMap ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GlycosciencesDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2753 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2753">
-        <rdfs:label>Carbohydrate conformational map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3425"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A conformational energy map of the glycosidic linkages in a carbohydrate molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2754 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2754">
-        <rdfs:label>Gene features report (intron)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>introns in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2755 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2755">
-        <rdfs:label>Transcription factor name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1077"/>
-        <oboInOwl:hasDefinition>The name of a transcription factor.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2756 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2756">
-        <rdfs:label>TCID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Identifier of a membrane transport proteins from the transport classification database (TCDB).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2757 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2757">
-        <rdfs:label>Pfam domain name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1131"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a domain from the Pfam database.</oboInOwl:hasDefinition>
-        <regex>PF[0-9]{5}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2758 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2758">
-        <rdfs:label>Pfam clan ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>CL[0-9]{4}</regex>
-        <oboInOwl:hasDefinition>Accession number of a Pfam clan.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2759 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2759">
-        <rdfs:label>Gene ID (VectorBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>VectorBase ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier for a gene from the VectorBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2761 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2761">
-        <rdfs:label>UTRSite ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1114"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2762 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2762">
-        <rdfs:label>Sequence signature report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence motif report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2763 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2763">
-        <rdfs:label>Locus annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Locus report</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a particular locus.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2764 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2764">
-        <rdfs:label>Protein name (UniProt)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <oboInOwl:hasDefinition>Official name of a protein as used in the UniProt database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2765 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2765">
-        <rdfs:label>Term ID list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>One or more terms from one or more controlled vocabularies which are annotations on an entity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2766 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2766">
-        <rdfs:label>HAMAP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>Name of a protein family from the HAMAP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2767 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2767">
-        <rdfs:label>Identifier with metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:hasDefinition>Basic information concerning an identifier of data (typically including the identifier itself).  For example, a gene symbol with information concerning its provenance.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2768 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2768">
-        <rdfs:label>Gene symbol annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation about a gene symbol.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2767"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2769 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2769">
-        <rdfs:label>Transcript ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1276"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a RNA transcript.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2770 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2770">
-        <rdfs:label>HIT ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2769"/>
-        <oboInOwl:hasDefinition>Identifier of an RNA transcript from the H-InvDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2771 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2771">
-        <rdfs:label>HIX ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>A unique identifier of gene cluster in the H-InvDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2772 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2772">
-        <rdfs:label>HPA antibody id</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a antibody from the HPA database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2773 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2773">
-        <rdfs:label>IMGT/HLA ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2774 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2774">
-        <rdfs:label>Gene ID (JCVI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2775 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2775">
-        <rdfs:label>Kinase name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a kinase protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2776 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2776">
-        <rdfs:label>ConsensusPathDB entity ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2917"/>
-        <oboInOwl:hasDefinition>Identifier of a physical entity from the ConsensusPathDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2777 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2777">
-        <rdfs:label>ConsensusPathDB entity name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2917"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a physical entity from the ConsensusPathDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2778 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2778">
-        <rdfs:label>CCAP strain number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2912"/>
-        <oboInOwl:hasDefinition>The number of a strain of algae and protozoa from the CCAP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2779 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2779">
-        <rdfs:label>Stock number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of stock from a catalogue of biological resources.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2780 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2780">
-        <rdfs:label>Stock number (TAIR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2779"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A stock number from The Arabidopsis information resource (TAIR).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2781 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2781">
-        <rdfs:label>REDIdb ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the RNA editing database (REDIdb).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2782 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2782">
-        <rdfs:label>SMART domain name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1131"/>
-        <oboInOwl:hasDefinition>Name of a domain from the SMART database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2783 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2783">
-        <rdfs:label>Protein family ID (PANTHER)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Panther family ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of an entry (family) from the PANTHER database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2784 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2784">
-        <rdfs:label>RNAVirusDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2785"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.</rdfs:comment>
-        <oboInOwl:hasDefinition>A unique identifier for a virus from the RNAVirusDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2785 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2785">
-        <rdfs:label>Virus ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2913"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An accession of annotation on a (group of) viruses (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2786 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2786">
-        <rdfs:label>NCBI Genome Project ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2903"/>
-        <oboInOwl:hasDefinition>An identifier of a genome project assigned by NCBI.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2787 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2787">
-        <rdfs:label>NCBI genome accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2903"/>
-        <oboInOwl:hasDefinition>A unique identifier of a whole genome assigned by the NCBI.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2788 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2788">
-        <rdfs:label>Sequence profile data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it&apos;s construction, the biological role or annotation, and so on.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0860"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2789 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2789">
-        <rdfs:label>Protein ID (TopDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>TopDB ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a membrane protein from the TopDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2790 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2790">
-        <rdfs:label>Gel ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasExactSynonym>Gel identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a two-dimensional (protein) gel.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2791 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2791">
-        <rdfs:label>Reference map name (SWISS-2DPAGE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2790"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a reference map gel from the SWISS-2DPAGE database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2792 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2792">
-        <rdfs:label>Protein ID (PeroxiBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>PeroxiBase ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a peroxidase protein from the PeroxiBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2793 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2793">
-        <rdfs:label>SISYPHUS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1072"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the SISYPHUS database of tertiary structure alignments.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2794 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2794">
-        <rdfs:label>ORF ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2795"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of an open reading frame (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2795 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2795">
-        <rdfs:label>ORF identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of an open reading frame.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2796 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2796">
-        <rdfs:label>Linucs ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GlycosciencesDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2797 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2797">
-        <rdfs:label>Protein ID (LGICdb)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>LGICdb ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a ligand-gated ion channel protein from the LGICdb database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2798 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2798">
-        <rdfs:label>MaizeDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an EST sequence from the MaizeDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2799 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2799">
-        <rdfs:label>Gene ID (MfunGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the MfunGD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2800 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2800">
-        <rdfs:label>Orpha number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1150"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1622"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a disease from the Orpha database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2802 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2802">
-        <rdfs:label>Protein ID (EcID)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the EcID database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2803 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2803">
-        <rdfs:label>Clone ID (RefSeq)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1098"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1855"/>
-        <oboInOwl:hasDefinition>A unique identifier of a cDNA molecule catalogued in the RefSeq database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2804 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2804">
-        <rdfs:label>Protein ID (ConoServer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a cone snail toxin protein from the ConoServer database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2805 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2805">
-        <rdfs:label>GeneSNP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <oboInOwl:hasDefinition>Identifier of a GeneSNP database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2812 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2812">
-        <rdfs:label>Lipid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2850"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2879"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a lipid.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2831 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2831">
-        <rdfs:label>Databank</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A flat-file (textual) data archive.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2832 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2832">
-        <rdfs:label>Web portal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A web site providing data (web pages) on a common theme to a HTTP client.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2835 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2835">
-        <rdfs:label>Gene ID (VBASE2)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier for a gene from the VBASE2 database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>VBASE2 ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2836 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2836">
-        <rdfs:label>DPVweb ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2785"/>
-        <oboInOwl:hasExactSynonym>DPVweb virus ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier for a virus from the DPVweb database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2837 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2837">
-        <rdfs:label>Pathway ID (BioSystems)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the BioSystems pathway database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2838 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2838">
-        <rdfs:label>Experimental data (proteomics)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning a proteomics experiment.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3147"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2849 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2849">
-        <rdfs:label>Abstract</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2526"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An abstract of a scientific article.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2850 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2850">
-        <rdfs:label>Lipid structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a lipid structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2851 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2851">
-        <rdfs:label>Drug structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1463"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the (3D) structure of a drug.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2852 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2852">
-        <rdfs:label>Toxin structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1463"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the (3D) structure of a toxin.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2854 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2854">
-        <rdfs:label>Position-specific scoring matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1354"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PSSM</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2855 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2855">
-        <rdfs:label>Distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2856 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2856">
-        <rdfs:label>Structural distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2855"/>
-        <oboInOwl:hasDefinition>Distances (values representing similarity) between a group of molecular structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2857 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2857">
-        <rdfs:label>Article metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Bibliographic data concerning scientific article(s).</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2526"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2858 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2858">
-        <rdfs:label>Ontology concept</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2353"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes any fields from the concept definition such as concept name, definition, comments and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>A concept from a biological ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2865 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2865">
-        <rdfs:label>Codon usage bias</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:hasDefinition>A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2866 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2866">
-        <rdfs:label>Northern blot report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Northern Blot experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2867">
-        <rdfs:label>Nucleic acid features report (VNTR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>variable number of tandem repeat (VNTR) polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2868">
-        <rdfs:label>Nucleic acid features report (microsatellite)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>microsatellite polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2868"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2869">
-        <rdfs:label>Nucleic acid features report (RFLP)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>restriction fragment length polymorphisms (RFLP) in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2870 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2870">
-        <rdfs:label>Radiation hybrid map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1280"/>
-        <rdfs:comment>The radiation method can break very closely linked markers providing a more detailed map.  Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map.</rdfs:comment>
-        <oboInOwl:hasDefinition>A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>RH map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2872 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2872">
-        <rdfs:label>ID list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:hasDefinition>A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2873 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2873">
-        <rdfs:label>Phylogenetic gene frequencies data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1426"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gene frequencies data that may be read during phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2874 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2874">
-        <rdfs:label>Sequence set (polymorphic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1234"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2875 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2875">
-        <rdfs:label>DRCAT resource</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>An entry (resource) from the DRCAT bioinformatics resource catalogue.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2877 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2877">
-        <rdfs:label>Protein complex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2878 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2878">
-        <rdfs:label>Protein structural motif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2879 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2879">
-        <rdfs:label>Lipid report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation on or information derived from one or more specific lipid 3D structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2880 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2880">
-        <rdfs:label>Secondary structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of one or more molecular secondary structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2992"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2881 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2881">
-        <rdfs:label>Secondary structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Secondary structure-derived report</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on general information, properties or features of one or more molecular secondary structures.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2882 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2882">
-        <rdfs:label>DNA features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>DNA sequence-specific feature annotation (not in a feature table).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2883 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2883">
-        <rdfs:label>RNA features report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Features concerning RNA or regions of DNA that encode an RNA molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (RNA features)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2884 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2884">
-        <rdfs:label>Plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Biological data that has been plotted as a graph of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2885">
-        <rdfs:label>Nucleic acid features report (polymorphism)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>DNA polymorphism.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2886 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2886">
-        <rdfs:label>Protein sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0849"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2976"/>
-        <oboInOwl:hasDefinition>A protein sequence and associated metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein sequence record</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence record (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2887 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2887">
-        <rdfs:label>Nucleic acid sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0849"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasNarrowSynonym>RNA sequence record</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence record</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A nucleic acid sequence and associated metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>DNA sequence record</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequence record (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2888 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2888">
-        <rdfs:label>Protein sequence record (full)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2889 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2889">
-        <rdfs:label>Nucleic acid sequence record (full) </rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2891 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2891">
-        <rdfs:label>Biological model accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1085"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a mathematical model, typically an entry from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2892 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2892">
-        <rdfs:label>Cell type name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2655"/>
-        <oboInOwl:hasDefinition>The name of a type or group of cells.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2893 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2893">
-        <rdfs:label>Cell type accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2655"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a type or group of cells (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2894 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2894">
-        <rdfs:label>Compound accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasExactSynonym>Small molecule accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of chemicals.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2895 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2895">
-        <rdfs:label>Drug accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0993"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Accession of a drug.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2896 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2896">
-        <rdfs:label>Toxin name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2576"/>
-        <oboInOwl:hasDefinition>Name of a toxin.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2897 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2897">
-        <rdfs:label>Toxin accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2576"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a toxin (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2898 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2898">
-        <rdfs:label>Monosaccharide accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0996"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Accession of a monosaccharide (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2899 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2899">
-        <rdfs:label>Drug name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0993"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Common name of a drug.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2900 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2900">
-        <rdfs:label>Carbohydrate accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2663"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of carbohydrates.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2901 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2901">
-        <rdfs:label>Molecule accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Accession of a specific molecule (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2902 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2902">
-        <rdfs:label>Data resource definition accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1084"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a data definition (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2903 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2903">
-        <rdfs:label>Genome accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2749"/>
-        <oboInOwl:hasDefinition>An accession of a particular genome (in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2904 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2904">
-        <rdfs:label>Map accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2117"/>
-        <oboInOwl:hasDefinition>An accession of a map of a molecular sequence (deposited in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2905 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2905">
-        <rdfs:label>Lipid accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2812"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of lipids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2906 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2906">
-        <rdfs:label>Peptide ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0988"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a peptide deposited in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2907 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2907">
-        <rdfs:label>Protein accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasExactSynonym>Protein accessions</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a protein deposited in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2908 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2908">
-        <rdfs:label>Organism accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>An accession of annotation on a (group of) organisms (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2909 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2909">
-        <rdfs:label>Organism name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDbXref>Moby:Organism_Name</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:OrganismsShortName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:OccurrenceRecord</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:BriefOccurrenceRecord</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:FirstEpithet</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:InfraspecificEpithet</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:OrganismsLongName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The name of an organism (or group of organisms).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2910 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2910">
-        <rdfs:label>Protein family accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1075"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a protein family (that is deposited in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2911 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2911">
-        <rdfs:label>Transcription factor accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1077"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of transcription factors or binding sites.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2912 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2912">
-        <rdfs:label>Strain accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2379"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0963"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a strain of an organism variant, typically a plant, virus or bacterium.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2913 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2913">
-        <rdfs:label>Virus identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <oboInOwl:hasDefinition>An accession of annotation on a (group of) viruses (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2914 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2914">
-        <rdfs:label>Sequence features metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2527"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Metadata on sequence features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2915 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2915">
-        <rdfs:label>Gramene identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a Gramene database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2916 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2916">
-        <rdfs:label>DDBJ accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1103"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>DDBJ accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>DDBJ identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>DDBJ ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An identifier of an entry from the DDBJ sequence database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2917 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2917">
-        <rdfs:label>ConsensusPathDB identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of an entity from the ConsensusPathDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2925 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2925">
-        <rdfs:label>Sequence data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of molecular sequence(s). </oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2927 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2927">
-        <rdfs:label>Codon usage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning codon usage.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2954 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2954">
-        <rdfs:label>Article report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Data derived from the analysis of a scientific text such as a full text article from a scientific journal.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2526"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2955 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2955">
-        <rdfs:label>Sequence report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence-derived report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2956 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2956">
-        <rdfs:label>Protein secondary structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:hasDefinition>An informative report about the properties or features of one or more protein secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2957 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2957">
-        <rdfs:label>Hopp and Woods plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1534"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <oboInOwl:hasDefinition>A Hopp and Woods plot of predicted antigenicity of a peptide or protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2958 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2958">
-        <rdfs:label>Nucleic acid melting curve</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <rdfs:comment>Shows the proportion of nucleic acid which are double-stranded versus temperature.</rdfs:comment>
-        <oboInOwl:hasDefinition>A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2959 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2959">
-        <rdfs:label>Nucleic acid probability profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <oboInOwl:hasDefinition>A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2960 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2960">
-        <rdfs:label>Nucleic acid temperature profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <oboInOwl:hasDefinition>A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).</oboInOwl:hasDefinition>
-        <rdfs:comment>Plots melting temperature versus base position.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Melting map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2961 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2961">
-        <rdfs:label>Gene regulatory network report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of a gene regulatory network.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2965 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2965">
-        <rdfs:label>2D PAGE gel report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a two-dimensional (2D PAGE) gel.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>2D PAGE image report</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>2D PAGE gel annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>2D PAGE image annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2966 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2966">
-        <rdfs:label>Oligonucleotide probe sets annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2717"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2967 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2967">
-        <rdfs:label>Microarray image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression image</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2968 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2968">
-        <rdfs:label>Image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000081</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Biological or biomedical data has been rendered into an image, typically for display on screen.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000079</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Image data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2969 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2969">
-        <rdfs:label>Sequence image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2955"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:hasDefinition>Image of a molecular sequence, possibly with sequence features or properties shown.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2970 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2970">
-        <rdfs:label>Protein hydropathy data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasExactSynonym>Protein hydropathy report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report on protein properties concerning hydropathy.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2971 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2971">
-        <rdfs:label>Workflow data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning a computational workflow.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2972 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2972">
-        <rdfs:label>Workflow</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A computational workflow.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2973 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2973">
-        <rdfs:label>Secondary structure data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning molecular secondary structure data.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2974 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2974">
-        <rdfs:label>Protein sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0848"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2976"/>
-        <oboInOwl:hasExactSynonym>Raw protein sequence</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Raw sequence (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A raw protein sequence (string of characters).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2975 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2975">
-        <rdfs:label>Nucleic acid sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0848"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid raw sequence</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence (raw)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Raw sequence (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A raw nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2976 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2976">
-        <rdfs:label>Protein sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <oboInOwl:hasDefinition>One or more protein sequences, possibly with associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein sequences</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2977 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2977">
-        <rdfs:label>Nucleic acid sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <oboInOwl:hasDefinition>One or more nucleic acid sequences, possibly with associated annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>DNA sequence</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleotide sequences</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid sequences</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2978 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2978">
-        <rdfs:label>Reaction data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Enzyme kinetics annotation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Reaction annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2979 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2979">
-        <rdfs:label>Peptide property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning small peptides.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2980 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2980">
-        <rdfs:label>Protein classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein classification data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report concerning the classification of protein sequences or structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2981 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2981">
-        <rdfs:label>Sequence motif data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning specific or conserved pattern in molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0860"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2982 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2982">
-        <rdfs:label>Sequence profile data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning models representing a (typically multiple) sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1354"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2983 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2983">
-        <rdfs:label>Pathway or network data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data concerning a specific biological pathway or network.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2600"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2984 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2984">
-        <rdfs:label>Pathway or network report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2985 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2985">
-        <rdfs:label>Nucleic acid thermodynamic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0912"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid property (thermodynamic or kinetic)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A thermodynamic or kinetic property of a nucleic acid molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid thermodynamic property</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2986 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2986">
-        <rdfs:label>Nucleic acid classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning the classification of nucleic acid sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid classification data</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3148"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2987 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2987">
-        <rdfs:label>Classification report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Classification data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report on a classification of molecular sequences, structures or other entities.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2989 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2989">
-        <rdfs:label>Protein features report (key folding sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>key residues involved in protein folding.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2991 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2991">
-        <rdfs:label>Protein torsion angle data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasExactSynonym>Torsion angle data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Torsion angle data for a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2992 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2992">
-        <rdfs:label>Protein structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1710"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3153"/>
-        <oboInOwl:hasDefinition>An image of protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure image (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2994 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2994">
-        <rdfs:label>Phylogenetic character weights</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasDefinition>Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3002 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3002">
-        <rdfs:label>Annotation track</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Genomic track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome annotation track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome-browser track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence annotation track</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3021 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3021">
-        <rdfs:label>UniProt accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>UniProtKB accession number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <example>P43353|Q7M1G0|Q9C199|A5A6J6</example>
-        <oboInOwl:hasExactSynonym>UniProt entry accession</oboInOwl:hasExactSynonym>
-        <regex>[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}</regex>
-        <oboInOwl:hasNarrowSynonym>Swiss-Prot entry accession</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>TrEMBL entry accession</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Accession number of a UniProt (protein sequence) database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniProtKB accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniProt accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3022 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3022">
-        <rdfs:label>NCBI genetic code ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Identifier of a genetic code in the NCBI list of genetic codes.</oboInOwl:hasDefinition>
-        <regex>[1-9][0-9]?</regex>
-        <example>16</example>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3025 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3025">
-        <rdfs:label>Ontology concept identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a concept in an ontology of biological or bioinformatics concepts and relations.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3026 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3026">
-        <rdfs:label>GO concept name (biological process)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a concept for a biological process from the GO ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3027 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3027">
-        <rdfs:label>GO concept name (molecular function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a concept for a molecular function from the GO ontology.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3028 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3028">
-        <rdfs:label>Taxonomy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning the classification, identification and naming of organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Taxonomic data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3029 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3029">
-        <rdfs:label>Protein ID (EMBL/GenBank/DDBJ)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.</oboInOwl:hasDefinition>
-        <rdfs:comment>This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3031 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3031">
-        <rdfs:label>Core data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Core data entities typically have a format and may be identified by an accession number.</rdfs:comment>
-        <oboInOwl:hasDefinition>A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3034 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3034">
-        <rdfs:label>Sequence feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of molecular sequence feature(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3035 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3035">
-        <rdfs:label>Structure identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>An identifier of a molecular tertiary structure, typically an entry from a structure database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3036 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3036">
-        <rdfs:label>Matrix identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of an array of numerical values, such as a comparison matrix.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3085">
-        <rdfs:label>Protein sequence composition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report (typically a table) on character or word composition / frequency of protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3086 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3086">
-        <rdfs:label>Nucleic acid sequence composition (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3101 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3101">
-        <rdfs:label>Protein domain classification node</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>A node from a classification of protein structural domain(s).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3102">
-        <rdfs:label>CAS number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>CAS registry number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3103 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3103">
-        <rdfs:label>ATC code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <oboInOwl:hasDefinition>Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC).</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3104 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3104">
-        <rdfs:label>UNII</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Unique Ingredient Identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3105 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3105">
-        <rdfs:label>Geotemporal metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Basic information concerning geographical location or time.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3106 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3106">
-        <rdfs:label>System metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Metadata concerning the software, hardware or other aspects of a computer system.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3107 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3107">
-        <rdfs:label>Sequence feature name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3034"/>
-        <oboInOwl:hasDefinition>A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3108 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3108">
-        <rdfs:label>Experimental measurement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Experimental measurement data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Measurement</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Measured data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Experimentally measured data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Measurement metadata</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Measurement data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Raw experimental data</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3110">
-        <rdfs:label>Raw microarray data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3117"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment.</oboInOwl:hasDefinition>
-        <rdfs:comment>Such data as found in Affymetrix CEL or GPR files.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3111">
-        <rdfs:label>Processed microarray data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3117"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data generated from processing and analysis of probe set data from a microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene annotation (expression)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray probe set data</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression report</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3112">
-        <rdfs:label>Gene expression matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:comment>This combines data from all hybridisations.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Normalised microarray data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The final processed (normalised) data for a set of hybridisations in a microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene expression data matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3113 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3113">
-        <rdfs:label>Sample annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Annotation on a biological sample, for example experimental factors and their values.</oboInOwl:hasDefinition>
-        <rdfs:comment>This might include compound and dose in a dose response experiment.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3115 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3115">
-        <rdfs:label>Microarray metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:comment>This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Annotation on the array itself used in a microarray experiment.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3116 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3116">
-        <rdfs:label>Microarray protocol annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This might describe e.g. the normalisation methods used to process the raw data.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Annotation on laboratory and/or data processing protocols used in an microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3117 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3117">
-        <rdfs:label>Microarray hybridisation data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <oboInOwl:hasDefinition>Data concerning the hybridisations measured during a microarray experiment.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3118">
-        <rdfs:label>Protein features report (topological domains)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>topological domains such as cytoplasmic regions in a protein.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3119 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3119">
-        <rdfs:label>Sequence features (compositionally-biased regions)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report of regions in a molecular sequence that are biased to certain characters.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3122">
-        <rdfs:label>Nucleic acid features (difference and change)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>A report on features in a nucleic acid sequence that indicate changes to or differences between sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0918"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3123">
-        <rdfs:label>Nucleic acid features report (expression signal)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>regions within a nucleic acid sequence containing a signal that alters a biological function.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3125 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3125">
-        <rdfs:label>Nucleic acid features report (binding)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>nucleic acids binding to some other molecule.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <rdfs:comment>This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes).</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3126">
-        <rdfs:label>Nucleic acid repeats (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>repetitive elements within a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3127">
-        <rdfs:label>Nucleic acid features report (replication and recombination)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>DNA replication or recombination.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3128">
-        <rdfs:label>Nucleic acid structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:hasDefinition>A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Stem loop (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>d-loop (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Quadruplexes (report)</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3129 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3129">
-        <rdfs:label>Protein features report (repeats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>short repetitive subsequences (repeat sequences) in a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3130">
-        <rdfs:label>Sequence motif matches (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3131 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3131">
-        <rdfs:label>Sequence motif matches (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3132 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3132">
-        <rdfs:label>Nucleic acid features (d-loop)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report on displacement loops in a mitochondrial DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3133">
-        <rdfs:label>Nucleic acid features (stem loop)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on stem loops in a DNA sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3134">
-        <rdfs:label>Gene transcript report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0916"/>
-        <rdfs:comment>This includes 5&apos;untranslated region (5&apos;UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3&apos;untranslated regions (3&apos;UTR).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (mRNA features)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Transcript (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>mRNA features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene transcript annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Clone or EST (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>mRNA (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3135">
-        <rdfs:label>Nucleic acid features report (signal or transit peptide)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>coding sequences for a signal or transit peptide.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3137">
-        <rdfs:label>Non-coding RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>features of non-coding or functional RNA molecules, including tRNA and rRNA.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3138 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3138">
-        <rdfs:label>Transcriptional features (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.</rdfs:comment>
-        <oboInOwl:hasDefinition>Features concerning transcription of DNA into RNA including the regulation of transcription.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3139">
-        <rdfs:label>Nucleic acid features report (STS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>sequence tagged sites (STS) in nucleic acid sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3140">
-        <rdfs:label>Nucleic acid features (immunoglobulin gene structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3141">
-        <rdfs:label>SCOP class</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a &apos;class&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3142 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3142">
-        <rdfs:label>SCOP fold</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Information on a &apos;fold&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3143">
-        <rdfs:label>SCOP superfamily</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Information on a &apos;superfamily&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3144 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3144">
-        <rdfs:label>SCOP family</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a &apos;family&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3145 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3145">
-        <rdfs:label>SCOP protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information on a &apos;protein&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3146 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3146">
-        <rdfs:label>SCOP species</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Information on a &apos;species&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3147">
-        <rdfs:label>Mass spectrometry experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>mass spectrometry experiments.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3148 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3148">
-        <rdfs:label>Gene family report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:hasDefinition>An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene, or any other classification of nucleic acid sequences or structures that reflects gene structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes reports on on gene homologues between species.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Gene annotation (homology information)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Homology information</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene annotation (homology)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Nucleic acid classification</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>Gene family annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene homology (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3153 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3153">
-        <rdfs:label>Protein image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>An image of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3154">
-        <rdfs:label>Protein alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <oboInOwl:hasDefinition>An alignment of protein sequences and/or structures.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3165 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3165">
-        <rdfs:label>NGS experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>sequencing experiment, including samples, sampling, preparation, sequencing, and analysis.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3181 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3181">
-        <rdfs:label>Sequence assembly report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:hasDefinition>An informative report about a DNA sequence assembly.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Assembly report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3210">
-        <rdfs:label>Genome index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0955"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.</rdfs:comment>
-        <oboInOwl:hasDefinition>An index of a genome sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3231 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3231">
-        <rdfs:label>GWAS report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Report concerning genome-wide association study experiments.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Genome-wide association study</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3236">
-        <rdfs:label>Cytoband position</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2012"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>The position of a cytogenetic band in a genome.</oboInOwl:hasDefinition>
-        <rdfs:comment>Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3238">
-        <rdfs:label>Cell type ontology ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2893"/>
-        <oboInOwl:hasExactSynonym>CL ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Cell type ontology concept ID.</oboInOwl:hasDefinition>
-        <regex>CL_[0-9]{7}</regex>
-        <created_in>1.2</created_in>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3241">
-        <rdfs:label>Kinetic model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Mathematical model of a network, that contains biochemical kinetics.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3264">
-        <rdfs:label>COSMIC ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <oboInOwl:hasExactSynonym>COSMIC identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>cosmic ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a COSMIC database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>cosmic identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>cosmic id</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3265">
-        <rdfs:label>HGMD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <oboInOwl:hasDefinition>Identifier of a HGMD database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>hgmd ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>hgmd identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>hgmd id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HGMD identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3266 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3266">
-        <rdfs:label>Sequence assembly ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1064"/>
-        <oboInOwl:hasNarrowSynonym>Sequence assembly version</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of sequence assembly.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3268 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3268">
-        <rdfs:label>Sequence feature type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3269">
-        <rdfs:label>Gene homology (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on gene homologues between species.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3148"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3270 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3270">
-        <rdfs:label>Ensembl gene tree ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <example>ENSGT00390000003602</example>
-        <oboInOwl:hasExactSynonym>Ensembl ID (gene tree)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a gene tree from the Ensembl database.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3271 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3271">
-        <rdfs:label>Gene tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0872"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>A phylogenetic tree that is an estimate of the character&apos;s phylogeny.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3272 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3272">
-        <rdfs:label>Species tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0872"/>
-        <oboInOwl:hasDefinition>A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3273 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3273">
-        <rdfs:label>Sample ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3113"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Sample accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Name or other identifier of an entry from a biosample database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3274 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3274">
-        <rdfs:label>MGI accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>Identifier of an object from the MGI database.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3275 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3275">
-        <rdfs:label>Phenotype name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Name of a phenotype.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phenotypes</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phenotype</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3354">
-        <rdfs:label>Transition matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A HMM transition matrix contains the probabilities of switching from one HMM state to another.</oboInOwl:hasDefinition>
-        <rdfs:comment>Consider for example an HMM with two states (AT-rich and GC-rich).  The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>HMM transition matrix</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3355">
-        <rdfs:label>Emission matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <rdfs:comment>Consider for example an HMM with two states (AT-rich and GC-rich).  The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>HMM emission matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3356">
-        <rdfs:label xml:lang="en">Hidden Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:hasDefinition>A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3358">
-        <rdfs:label>Format identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a data format.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3424">
-        <rdfs:label>Raw image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>1.5</created_in>
-        <oboInOwl:hasExactSynonym>Amino acid data</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000081</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Image data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Raw biological or biomedical image generated by some experimental technique.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3425">
-        <rdfs:label>Carbohydrate property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>Carbohydrate data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates.</oboInOwl:hasDefinition>
-        <created_in>1.5</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3426">
-        <rdfs:label>Proteomics experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Report concerning proteomics experiments.</oboInOwl:hasDefinition>
-        <created_in>1.5</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3427">
-        <rdfs:label>RNAi report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.5</created_in>
-        <oboInOwl:hasDefinition>RNAi experiments.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3428">
-        <rdfs:label>Simulation experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.5</created_in>
-        <oboInOwl:hasDefinition>biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3442">
-        <rdfs:label>MRI image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3384"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>MRT image</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>Magnetic resonance tomography image </oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nuclear magnetic resonance imaging image
-</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Magnetic resonance imaging image
-</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>NMRI image</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3449 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3449">
-        <rdfs:label>Cell migration track image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2229"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>An image from a cell migration track assay.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3451">
-        <rdfs:label>Rate of association</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasExactSynonym>kon</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Rate of association of a protein with another protein or some other molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3479">
-        <rdfs:label>Gene order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <rdfs:comment>Such data are often used for genome rearrangement tools and phylogenetic tree labeling.</rdfs:comment>
-        <oboInOwl:hasDefinition>Multiple gene identifiers in a specific order.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3483">
-        <rdfs:label>Spectrum</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Spectra</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3488">
-        <rdfs:label>NMR spectrum</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3483"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Spectral information for a molecule from a nuclear magnetic resonance experiment.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>NMR spectra</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3490">
-        <rdfs:label>Chemical structure sketch</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1712"/>
-        <rdfs:comment>Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software.</rdfs:comment>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Small molecule sketch</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A sketch of a small molecule made with some specialised drawing package.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3492">
-        <rdfs:label>Nucleic acid signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2762"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>An informative report about a specific or conserved nucleic acid sequence pattern.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3494 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3494">
-        <rdfs:label>DNA sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasExactSynonym>DNA sequences</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>A DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3495">
-        <rdfs:label>RNA sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasDefinition>A DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>DNA sequences</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA sequences</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3496">
-        <rdfs:label>RNA sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3495"/>
-        <oboInOwl:hasExactSynonym>Raw sequence (RNA)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>A raw RNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA raw sequence</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3497">
-        <rdfs:label>DNA sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3494"/>
-        <oboInOwl:hasExactSynonym>Raw sequence (DNA)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A raw DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>DNA raw sequence</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3498">
-        <rdfs:label>Sequence variations</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene sequence variations</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Variations are stored along with a reference genome.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3505">
-        <rdfs:label>Bibliography</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2526"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>A list of publications such as scientic papers or books.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3509">
-        <rdfs:label>Ontology mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:hasDefinition>A mapping of supplied textual terms or phrases to ontology concepts (URIs).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3546">
-        <rdfs:label>Image metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Image-associated data</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This can include basic provenance and technical information about the image, scientific annotation and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Any data concerning a specific biological or biomedical image.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasExactSynonym>Image data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Image-related data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3558">
-        <rdfs:label>Clinical trial report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasExactSynonym>Clinical trial information</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report concerning a clinical trial.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3567">
-        <rdfs:label>Reference sample report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>A report about a biosample.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Biosample report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3568">
-        <rdfs:label>Gene Expression Atlas Experiment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the Gene Expression Atlas.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1196">
-        <rdfs:label>SMILES</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification"/>
-        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"/>
-        <documentation rdf:resource="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1197 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1197">
-        <rdfs:label>InChI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1198 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1198">
-        <rdfs:label>mf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The general MF query format consists of a series of valid atomic symbols, with an optional number or range.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1199 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1199">
-        <rdfs:label>inchikey</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1200">
-        <rdfs:label>smarts</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1196"/>
-        <oboInOwl:hasDefinition>SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1206 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1206">
-        <rdfs:label>unambiguous pure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2096"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1207 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1207">
-        <rdfs:label>nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <rdfs:comment>Non-sequence characters may be used for example for gaps.</rdfs:comment>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1208">
-        <rdfs:label>protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Non-sequence characters may be used for gaps and translation stop.</rdfs:comment>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1209">
-        <rdfs:label>consensus</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2095"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for the consensus of two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1210">
-        <rdfs:label>pure nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1211">
-        <rdfs:label>unambiguous pure nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters .</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1212 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1212">
-        <rdfs:label>dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1213">
-        <rdfs:label>rna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1214 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1214">
-        <rdfs:label>unambiguous pure dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1212"/>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1215">
-        <rdfs:label>pure dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1210"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1212"/>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1216 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1216">
-        <rdfs:label>unambiguous pure rna sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1213"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1217">
-        <rdfs:label>pure rna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1210"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1213"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1218">
-        <rdfs:label>unambiguous pure protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1208"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1219">
-        <rdfs:label>pure protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1208"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1228 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1228">
-        <rdfs:label>UniGene entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from UniGene.</oboInOwl:hasDefinition>
-        <rdfs:comment>A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1247">
-        <rdfs:label>COG sequence cluster format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the COG database of clusters of (related) protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1248">
-        <rdfs:label>EMBL feature location</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2078"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Feature location</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1295">
-        <rdfs:label>quicktandem</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2155"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1296 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1296">
-        <rdfs:label>Sanger inverted repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2155"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1297">
-        <rdfs:label>EMBOSS repeat</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2155"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format for tandem repeats in a sequence (an EMBOSS report format).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1316">
-        <rdfs:label>est2genome format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2031"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a report on exon-intron structure generated by EMBOSS est2genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1318">
-        <rdfs:label>restrict format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2158"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format for restriction enzyme recognition sites used by EMBOSS restrict program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1319 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1319">
-        <rdfs:label>restover format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2158"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report format for restriction enzyme recognition sites used by EMBOSS restover program.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1320">
-        <rdfs:label>REBASE restriction sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2158"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report format for restriction enzyme recognition sites used by REBASE database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1332">
-        <rdfs:label>FASTA search results format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using FASTA.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.)</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1333 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1333">
-        <rdfs:label>BLAST results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using some variant of BLAST.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes score data, alignment data and summary table.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1334">
-        <rdfs:label>mspcrunch</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using some variant of MSPCrunch.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1335">
-        <rdfs:label>Smith-Waterman format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using some variant of Smith Waterman.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1336">
-        <rdfs:label>dhf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1337">
-        <rdfs:label>lhf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information.</oboInOwl:hasDefinition>
-        <rdfs:comment>The hits are putative ligand-binding sequences and are found from a search of a sequence database.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1341">
-        <rdfs:label>InterPro hits format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Results format for searches of the InterPro database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1342">
-        <rdfs:label>InterPro protein view report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1341"/>
-        <oboInOwl:hasDefinition>Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1343">
-        <rdfs:label>InterPro match table format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1341"/>
-        <oboInOwl:hasDefinition>Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1349">
-        <rdfs:label>HMMER Dirichlet prior</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2074"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Dirichlet distribution HMMER format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1350">
-        <rdfs:label>MEME Dirichlet prior</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2074"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Dirichlet distribution MEME format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1351 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1351">
-        <rdfs:label>HMMER emission and transition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2075"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1356">
-        <rdfs:label>prosite-pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of a regular expression pattern from the Prosite database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1357">
-        <rdfs:label>EMBOSS sequence pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of an EMBOSS sequence pattern.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1360">
-        <rdfs:label>meme-motif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>A motif in the format generated by the MEME program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1366">
-        <rdfs:label>prosite-profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2069"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Sequence profile (sequence classifier) format used in the PROSITE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1367 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1367">
-        <rdfs:label>JASPAR format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2069"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A profile (sequence classifier) in the format used in the JASPAR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1369">
-        <rdfs:label>MEME background Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2072"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of the model of random sequences used by MEME.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1370">
-        <rdfs:label>HMMER format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2072"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of a hidden Markov model representation used by the HMMER package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1391">
-        <rdfs:label>HMMER-aln</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>FASTA-style format for multiple sequences aligned by HMMER package to an HMM.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1392 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1392">
-        <rdfs:label>DIALIGN format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Format of multiple sequences aligned by DIALIGN package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1393">
-        <rdfs:label>daf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <rdfs:comment>The format is clustal-like and includes annotation of domain family classification information.</rdfs:comment>
-        <oboInOwl:hasDefinition>EMBASSY &apos;domain alignment file&apos; (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1419">
-        <rdfs:label>Sequence-MEME profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2014"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1421">
-        <rdfs:label>HMMER profile alignment (sequences versus HMMs)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2014"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1422">
-        <rdfs:label>HMMER profile alignment (HMM versus sequences)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2014"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1423">
-        <rdfs:label>Phylip distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2067"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of PHYLIP phylogenetic distance matrix data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1424">
-        <rdfs:label>ClustalW dendrogram</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Dendrogram (tree file) format generated by ClustalW.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1425">
-        <rdfs:label>Phylip tree raw</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasDefinition>Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1430">
-        <rdfs:label>Phylip continuous quantitative characters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2037"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PHYLIP file format for continuous quantitative character data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1431 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1431">
-        <rdfs:label>Phylogenetic property values format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of phylogenetic property data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2036"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1432">
-        <rdfs:label>Phylip character frequencies format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2037"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PHYLIP file format for phylogenetics character frequency data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1433">
-        <rdfs:label>Phylip discrete states format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2038"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of PHYLIP discrete states data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1434">
-        <rdfs:label>Phylip cliques format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2039"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of PHYLIP cliques data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1435">
-        <rdfs:label>Phylip tree format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasDefinition>Phylogenetic tree data format used by the PHYLIP program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1436">
-        <rdfs:label>TreeBASE format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the TreeBASE database of phylogenetic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1437">
-        <rdfs:label>TreeFam format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the TreeFam database of phylogenetic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1445">
-        <rdfs:label>Phylip tree distance format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2049"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1454 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1454">
-        <rdfs:label>dssp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2077"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format.</rdfs:comment>
-        <oboInOwl:hasDefinition>Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1455 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1455">
-        <rdfs:label>hssp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2077"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1457">
-        <rdfs:label>Dot-bracket format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Vienna RNA secondary structure format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Vienna RNA format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1458 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1458">
-        <rdfs:label>Vienna local RNA secondary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1457"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1475">
-        <rdfs:label>PDB database entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2033"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PDB entry format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of an entry (or part of an entry) from the PDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1476">
-        <rdfs:label>PDB</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasExactSynonym>PDB format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of PDB database in PDB format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1477 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1477">
-        <rdfs:label>mmCIF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasExactSynonym>Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Entry format of PDB database in mmCIF format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>mmcif</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1478">
-        <rdfs:label>PDBML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Entry format of PDB database in PDBML (XML) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1500">
-        <rdfs:label>Domainatrix 3D-1D scoring matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1504">
-        <rdfs:label>aaindex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2017"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Amino acid index format used by the AAindex database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1511">
-        <rdfs:label>IntEnz enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from IntEnz (The Integrated Relational Enzyme Database).</oboInOwl:hasDefinition>
-        <rdfs:comment>IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1512">
-        <rdfs:label>BRENDA enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of an entry from the BRENDA enzyme database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1513 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1513">
-        <rdfs:label>KEGG REACTION enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the KEGG REACTION database of biochemical reactions.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1514">
-        <rdfs:label>KEGG ENZYME enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of an entry from the KEGG ENZYME database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1515">
-        <rdfs:label>REBASE proto enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of an entry from the proto section of the REBASE enzyme database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1516">
-        <rdfs:label>REBASE withrefm enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the withrefm section of the REBASE enzyme database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1551">
-        <rdfs:label>Pcons report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2065"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of output of the Pcons Model Quality Assessment Program (MQAP).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1552">
-        <rdfs:label>ProQ report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2065"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features.</rdfs:comment>
-        <oboInOwl:hasDefinition>Format of output of the ProQ protein model quality predictor.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1563">
-        <rdfs:label>SMART domain assignment report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of SMART domain assignment data.</oboInOwl:hasDefinition>
-        <rdfs:comment>The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1568">
-        <rdfs:label>BIND entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the BIND database of protein interaction.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1569">
-        <rdfs:label>IntAct entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the IntAct database of protein interaction.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1570">
-        <rdfs:label>InterPro entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1571">
-        <rdfs:label>InterPro entry abstract format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>References are included and a functional inference is made where possible.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format for the textual abstract of signatures in an InterPro entry and its protein matches.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1572">
-        <rdfs:label>Gene3D entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the Gene3D protein secondary database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1573">
-        <rdfs:label>PIRSF entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the PIRSF protein secondary database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1574">
-        <rdfs:label>PRINTS entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format for the PRINTS protein secondary database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1575">
-        <rdfs:label>Panther Families and HMMs entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the Panther library of protein families and subfamilies.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1576 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1576">
-        <rdfs:label>Pfam entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the Pfam protein secondary database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1577 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1577">
-        <rdfs:label>SMART entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the SMART protein secondary database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1578">
-        <rdfs:label>Superfamily entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the Superfamily protein secondary database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1579">
-        <rdfs:label>TIGRFam entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format for the TIGRFam protein secondary database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1580 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1580">
-        <rdfs:label>ProDom entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the ProDom protein domain classification database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1581">
-        <rdfs:label>FSSP entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the FSSP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1582">
-        <rdfs:label>findkm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2027"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1603 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1603">
-        <rdfs:label>Ensembl gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of Ensembl genome database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1604 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1604">
-        <rdfs:label>DictyBase gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of DictyBase genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1605">
-        <rdfs:label>CGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of Candida Genome database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1606">
-        <rdfs:label>DragonDB gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of DragonDB genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1607">
-        <rdfs:label>EcoCyc gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of EcoCyc genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1608">
-        <rdfs:label>FlyBase gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of FlyBase genome database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1609 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1609">
-        <rdfs:label>Gramene gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of Gramene genome database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1610">
-        <rdfs:label>KEGG GENES gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of KEGG GENES genome database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1611">
-        <rdfs:label>MaizeGDB gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format of the Maize genetics and genomics database (MaizeGDB).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1612">
-        <rdfs:label>MGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of the Mouse Genome Database (MGD).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1613">
-        <rdfs:label>RGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of the Rat Genome Database (RGD).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1614 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1614">
-        <rdfs:label>SGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of the Saccharomyces Genome Database (SGD).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1615 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1615">
-        <rdfs:label>GeneDB gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of the Sanger GeneDB genome database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1616">
-        <rdfs:label>TAIR gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of The Arabidopsis Information Resource (TAIR) genome database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1617">
-        <rdfs:label>WormBase gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of the WormBase genomes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1618">
-        <rdfs:label>ZFIN gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format of the Zebrafish Information Network (ZFIN) genome database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1619 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1619">
-        <rdfs:label>TIGR gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format of the TIGR genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1620">
-        <rdfs:label>dbSNP polymorphism report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the dbSNP database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1623 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1623">
-        <rdfs:label>OMIM entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of an entry from the OMIM database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1624 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1624">
-        <rdfs:label>HGVbase entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of a record from the HGVbase database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1625 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1625">
-        <rdfs:label>HIVDB entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of a record from the HIVDB database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1626 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1626">
-        <rdfs:label>KEGG DISEASE entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the KEGG DISEASE database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1627 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1627">
-        <rdfs:label>Primer3 primer</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2061"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1628 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1628">
-        <rdfs:label>ABI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>A format of raw sequence read data from an Applied Biosystems sequencing machine.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1629 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1629">
-        <rdfs:label>mira</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of MIRA sequence trace information file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1630 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1630">
-        <rdfs:label>CAF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2561"/>
-        <oboInOwl:hasDefinition>Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.sanger.ac.uk/resources/software/caf/"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.sanger.ac.uk/resources/software/caf/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1631 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1631">
-        <rdfs:label>exp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2561"/>
-        <oboInOwl:hasDefinition>Sequence assembly project file EXP format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1632 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1632">
-        <rdfs:label>SCF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://staden.sourceforge.net/manual/formats_unix_2.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://staden.sourceforge.net/manual/formats_unix_2.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1633 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1633">
-        <rdfs:label>PHD</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PHD sequence trace format to store serialised chromatogram data (reads).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.bioperl.org/wiki/PHD_sequence_format"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.bioperl.org/wiki/PHD_sequence_format"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1637 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1637">
-        <rdfs:label>dat</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1714"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of Affymetrix data file of raw image data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Affymetrix image data file format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1638 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1638">
-        <rdfs:label>cel</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3110"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Affymetrix probe raw data format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of Affymetrix data file of information about (raw) expression levels of the individual probes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1639 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1639">
-        <rdfs:label>affymetrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2172"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1640 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1640">
-        <rdfs:label>ArrayExpress entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format for the ArrayExpress microarrays database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1641 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1641">
-        <rdfs:label>affymetrix-exp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2056"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Affymetrix data file format for information about experimental conditions and protocols.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Affymetrix experimental conditions data file format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1644 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1644">
-        <rdfs:label>CHP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Affymetrix probe normalised data format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of Affymetrix data file of information about (normalised) expression levels of the individual probes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1645 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1645">
-        <rdfs:label>EMDB entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the Electron Microscopy DataBase (EMDB).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1647 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1647">
-        <rdfs:label>KEGG PATHWAY entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1648 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1648">
-        <rdfs:label>MetaCyc entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the MetaCyc metabolic pathways database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1649 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1649">
-        <rdfs:label>HumanCyc entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of a report from the HumanCyc metabolic pathways database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1650 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1650">
-        <rdfs:label>INOH entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The format of an entry from the INOH signal transduction pathways database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1651 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1651">
-        <rdfs:label>PATIKA entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the PATIKA biological pathways database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1652 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1652">
-        <rdfs:label>Reactome entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the reactome biological pathways database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1653 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1653">
-        <rdfs:label>aMAZE entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The format of an entry from the aMAZE biological pathways and molecular interactions database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1654 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1654">
-        <rdfs:label>CPDB entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the CPDB database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1655 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1655">
-        <rdfs:label>Panther Pathways entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the Panther Pathways database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1665 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1665">
-        <rdfs:label>Taverna workflow format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2032"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Format of Taverna workflows.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1666 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1666">
-        <rdfs:label>BioModel mathematical model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of mathematical models from the BioModel database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1697 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1697">
-        <rdfs:label>KEGG LIGAND entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG LIGAND chemical database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1698 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1698">
-        <rdfs:label>KEGG COMPOUND entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG COMPOUND database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1699 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1699">
-        <rdfs:label>KEGG PLANT entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG PLANT database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1700 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1700">
-        <rdfs:label>KEGG GLYCAN entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG GLYCAN database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1701 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1701">
-        <rdfs:label>PubChem entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from PubChem.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1702 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1702">
-        <rdfs:label>ChemSpider entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from a database of chemical structures and property predictions.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1703 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1703">
-        <rdfs:label>ChEBI entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from Chemical Entities of Biological Interest (ChEBI).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>ChEBI includes an ontological classification defining relations between entities or classes of entities.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1704 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1704">
-        <rdfs:label>MSDchem ligand dictionary entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the MSDchem ligand dictionary.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1705 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1705">
-        <rdfs:label>HET group dictionary entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2030"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>The format of an entry from the HET group dictionary (HET groups from PDB files).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1706 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1706">
-        <rdfs:label>KEGG DRUG entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG DRUG database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1734 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1734">
-        <rdfs:label>PubMed citation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of bibliographic reference as used by the PubMed database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1735 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1735">
-        <rdfs:label>Medline Display Format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for abstracts of scientific articles from the Medline database.</oboInOwl:hasDefinition>
-        <rdfs:comment>Bibliographic reference information including citation information is included</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1736 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1736">
-        <rdfs:label>CiteXplore-core</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>CiteXplore &apos;core&apos; citation format including title, journal, authors and abstract.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1737 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1737">
-        <rdfs:label>CiteXplore-all</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <oboInOwl:hasDefinition>CiteXplore &apos;all&apos; citation format includes all known details such as Mesh terms and cross-references.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1739 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1739">
-        <rdfs:label>pmc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2020"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Article format of the PubMed Central database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1740 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1740">
-        <rdfs:label>iHOP text mining abstract format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2021"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>iHOP abstract format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1741 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1741">
-        <rdfs:label>Oscar3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2021"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document.</rdfs:comment>
-        <oboInOwl:hasDefinition>Text mining abstract format from the Oscar 3 application.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1747 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1747">
-        <rdfs:label>PDB atom record format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an ATOM record (describing data for an individual atom) from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1476"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1760 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1760">
-        <rdfs:label>CATH chain report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of CATH domain classification information for a polypeptide chain.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1761 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1761">
-        <rdfs:label>CATH PDB report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of CATH domain classification information for a protein PDB file.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1782 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1782">
-        <rdfs:label>NCBI gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry (gene) format of the NCBI database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1808 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1808">
-        <rdfs:label>GeneIlluminator gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:GI_Gene</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1809 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1809">
-        <rdfs:label>BacMap gene card format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDbXref>Moby:BacMapGeneCard</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1810 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1810">
-        <rdfs:label>ColiCard report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDbXref>Moby:ColiCard</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1861 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1861">
-        <rdfs:label>PlasMapper TextMap</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2060"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Map of a plasmid (circular DNA) in PlasMapper TextMap format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1910 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1910">
-        <rdfs:label>newick</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasExactSynonym>nh</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic tree Newick (text) format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1911 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1911">
-        <rdfs:label>TreeCon format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic tree TreeCon (text) format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1912 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1912">
-        <rdfs:label>Nexus format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasDefinition>Phylogenetic tree Nexus (text) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1915 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1915">
-        <rdfs:label>Format</rdfs:label>
-        <owl:disjointWith rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/topic_0003"/>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/File_format</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#MachineLanguage</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>File format</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Data model</oboInOwl:hasBroadSynonym>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Exchange format</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000098&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000612</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000618</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.org/dc/elements/1.1/format&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>http://wsio.org/compression_004</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/List_of_file_formats</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Quality</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Data format</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#Quality</rdfs:seeAlso>
-        <rdfs:comment>The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format &apos;is format of&apos; Data.</rdfs:comment>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to &apos;Data model&apos; would be an &apos;Information model&apos;.)</rdfs:comment>
-        <owl:annotatedTarget>Data model</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasBroadSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages.</rdfs:comment>
-        <owl:annotatedTarget>File format</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/format_1918 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1918">
-        <rdfs:label>Atomic data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data format for an individual atom.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1475"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1919 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1919">
-        <rdfs:label>Sequence record format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1920 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1920">
-        <rdfs:label>Sequence feature annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for molecular sequence feature information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1921 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1921">
-        <rdfs:label>Alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for molecular sequence alignment information.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1923 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1923">
-        <rdfs:label>acedb</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ACEDB sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1924 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1924">
-        <rdfs:label>clustal sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Clustalw output format.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1982"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1925 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1925">
-        <rdfs:label>codata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Codata entry format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1926 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1926">
-        <rdfs:label>dbid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Fasta format variant with database name before ID.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1927 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1927">
-        <rdfs:label>EMBL format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2181"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <oboInOwl:hasDefinition>EMBL entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EMBL sequence format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>EMBL</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1928 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1928">
-        <rdfs:label>Staden experiment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Staden experiment file format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1929 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1929">
-        <rdfs:label>FASTA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>FASTA format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>FASTA sequence format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>FASTA format including NCBI-style IDs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1930 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1930">
-        <rdfs:label>FASTQ</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ short read format ignoring quality scores.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>FASTAQ</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>fq</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1931 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1931">
-        <rdfs:label>FASTQ-illumina</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ Illumina 1.3 short read format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1932 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1932">
-        <rdfs:label>FASTQ-sanger</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ short read format with phred quality.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1933 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1933">
-        <rdfs:label>FASTQ-solexa</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ Solexa/Illumina 1.0 short read format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1934 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1934">
-        <rdfs:label>fitch program</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Fitch program format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1935 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1935">
-        <rdfs:label>GCG</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3486"/>
-        <oboInOwl:hasExactSynonym>GCG SSF</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment> GCG SSF (single sequence file) file format.</rdfs:comment>
-        <oboInOwl:hasDefinition>GCG sequence file format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1936 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1936">
-        <rdfs:label>GenBank format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2205"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Genbank entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1937 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1937">
-        <rdfs:label>genpept</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2205"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Genpept protein entry format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Currently identical to refseqp format</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1938 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1938">
-        <rdfs:label>GFF2-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1974"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>GFF feature file format with sequence in the header.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1939 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1939">
-        <rdfs:label>GFF3-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>GFF3 feature file format with sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1940 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1940">
-        <rdfs:label>giFASTA format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <oboInOwl:hasDefinition>FASTA sequence format including NCBI-style GIs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1941 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1941">
-        <rdfs:label>hennig86</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Hennig86 output sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1942 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1942">
-        <rdfs:label>ig</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Intelligenetics sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1943 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1943">
-        <rdfs:label>igstrict</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Intelligenetics sequence format (strict version).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1944 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1944">
-        <rdfs:label>jackknifer</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Jackknifer interleaved and non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1945 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1945">
-        <rdfs:label>mase format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mase program sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1946 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1946">
-        <rdfs:label>mega-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mega interleaved and non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1947 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1947">
-        <rdfs:label>MSF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3486"/>
-        <oboInOwl:hasExactSynonym>GCG MSF</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>GCG MSF (multiple sequence file) file format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1948 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1948">
-        <rdfs:label>nbrf/pir</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>NBRF/PIR entry sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>nbrf</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>pir</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1949 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1949">
-        <rdfs:label>nexus-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Nexus/paup interleaved sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1950 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1950">
-        <rdfs:label>pdbatom</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:comment>pdb format in EMBOSS.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PDB sequence format (ATOM lines).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1951 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1951">
-        <rdfs:label>pdbatomnuc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>pdbnuc format in EMBOSS.</rdfs:comment>
-        <oboInOwl:hasDefinition>PDB nucleotide sequence format (ATOM lines).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1952 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1952">
-        <rdfs:label>pdbseqresnuc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:comment>pdbnucseq format in EMBOSS.</rdfs:comment>
-        <oboInOwl:hasDefinition>PDB nucleotide sequence format (SEQRES lines).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1953 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1953">
-        <rdfs:label>pdbseqres</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>PDB sequence format (SEQRES lines).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>pdbseq format in EMBOSS.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1954 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1954">
-        <rdfs:label>Pearson format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Plain old FASTA sequence format (unspecified format for IDs).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1955 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1955">
-        <rdfs:label>phylip sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylip interleaved sequence format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1997"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1956 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1956">
-        <rdfs:label>phylipnon sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Phylip non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1998"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1957 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1957">
-        <rdfs:label>raw</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw sequence format with no non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1958 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1958">
-        <rdfs:label>refseqp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Refseq protein entry sequence format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Currently identical to genpept format</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1959 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1959">
-        <rdfs:label>selex sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Selex sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2000"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1960 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1960">
-        <rdfs:label>Staden format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Staden suite sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html"/>
-        <documentation rdf:resource="http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1961 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1961">
-        <rdfs:label>Stockholm format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Stockholm multiple sequence alignment format (used by Pfam and Rfam).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://en.wikipedia.org/wiki/Stockholm_format"/>
-        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/Stockholm_format"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1962 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1962">
-        <rdfs:label>strider format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>DNA strider output sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1963 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1963">
-        <rdfs:label>UniProtKB format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2187"/>
-        <oboInOwl:hasExactSynonym>UniProt format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>SwissProt format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>UniProtKB entry sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1964 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1964">
-        <rdfs:label>plain text format (unformatted)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Plain text sequence format (essentially unformatted).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1965 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1965">
-        <rdfs:label>treecon sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Treecon output sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2005"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1966 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1966">
-        <rdfs:label>ASN.1 sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>NCBI ASN.1-based sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1967 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1967">
-        <rdfs:label>DAS format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2552"/>
-        <oboInOwl:hasExactSynonym>das sequence format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>DAS sequence (XML) format (any type).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1968 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1968">
-        <rdfs:label>dasdna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2552"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DAS sequence (XML) format (nucleotide-only).</oboInOwl:hasDefinition>
-        <rdfs:comment>The use of this format is deprecated.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1969 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1969">
-        <rdfs:label>debug-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>EMBOSS debugging trace sequence format of full internal data content.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1970 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1970">
-        <rdfs:label>jackknifernon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Jackknifer output sequence non-interleaved format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1971 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1971">
-        <rdfs:label>meganon sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mega non-interleaved output sequence format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1992"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1972 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1972">
-        <rdfs:label>NCBI format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <oboInOwl:hasDefinition>NCBI FASTA sequence format with NCBI-style IDs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>There are several variants of this.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1973 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1973">
-        <rdfs:label>nexusnon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Nexus/paup non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1974 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1974">
-        <rdfs:label>GFF2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2305"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>General Feature Format (GFF) of sequence features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.sanger.ac.uk/resources/software/gff/spec.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.sanger.ac.uk/resources/software/gff/spec.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1975 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1975">
-        <rdfs:label>GFF3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2305"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generic Feature Format version 3 (GFF3) of sequence features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1976 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1976">
-        <rdfs:label>pir</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>PIR feature format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1948"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1977 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1977">
-        <rdfs:label>swiss feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Swiss-Prot feature format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1963"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1978 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1978">
-        <rdfs:label>DASGFF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2553"/>
-        <oboInOwl:hasDefinition>DAS GFF (XML) feature format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>das feature</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>DASGFF feature</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1979 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1979">
-        <rdfs:label>debug-feat</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>EMBOSS debugging trace feature format of full internal data content.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1980 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1980">
-        <rdfs:label>EMBL feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>EMBL feature format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1927"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1981 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1981">
-        <rdfs:label>GenBank feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Genbank feature format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1936"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1982 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1982">
-        <rdfs:label>ClustalW format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasExactSynonym>clustal</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ClustalW format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1983 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1983">
-        <rdfs:label>debug</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS alignment format for debugging trace of full internal data content.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1984 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1984">
-        <rdfs:label>FASTA-aln</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Fasta format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1985 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1985">
-        <rdfs:label>markx0</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX0 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1986 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1986">
-        <rdfs:label>markx1</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <oboInOwl:hasDefinition>Pearson MARKX1 alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1987 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1987">
-        <rdfs:label>markx10</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX10 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1988 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1988">
-        <rdfs:label>markx2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX2 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1989 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1989">
-        <rdfs:label>markx3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX3 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1990 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1990">
-        <rdfs:label>match</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Alignment format for start and end of matches between sequence pairs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1991 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1991">
-        <rdfs:label>mega</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2923"/>
-        <oboInOwl:hasDefinition>Mega format for (typically aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1992 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1992">
-        <rdfs:label>meganon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2923"/>
-        <oboInOwl:hasDefinition>Mega non-interleaved format for (typically aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1993 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1993">
-        <rdfs:label>msf alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>MSF format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1947"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1994 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1994">
-        <rdfs:label>nexus alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Nexus/paup format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1995 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1995">
-        <rdfs:label>nexusnon alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Nexus/paup non-interleaved format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1973"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1996 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1996">
-        <rdfs:label>pair</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS simple sequence pair alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1997 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1997">
-        <rdfs:label>PHYLIP format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2924"/>
-        <oboInOwl:hasExactSynonym>phy</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>ph</oboInOwl:hasExactSynonym>
-        <documentation>http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format</documentation>
-        <oboInOwl:hasExactSynonym>PHYLIP interleaved format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Phylip format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1998 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1998">
-        <rdfs:label>phylipnon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2924"/>
-        <documentation>http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format</documentation>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PHYLIP sequential format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Phylip non-interleaved format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1999 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1999">
-        <rdfs:label>scores format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Alignment format for score values for pairs of sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2000 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2000">
-        <rdfs:label>selex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>SELEX format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2001 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2001">
-        <rdfs:label>EMBOSS simple format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS simple multiple alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2002 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2002">
-        <rdfs:label>srs format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simple multiple sequence (alignment) format for SRS.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2003">
-        <rdfs:label>srspair</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simple sequence pair (alignment) format for SRS.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2004">
-        <rdfs:label>T-Coffee format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>T-Coffee program alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2005">
-        <rdfs:label>TreeCon-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Treecon format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2006">
-        <rdfs:label>Phylogenetic tree format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2013 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2013">
-        <rdfs:label>Biological pathway or network format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2014 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2014">
-        <rdfs:label>Sequence-profile alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0869"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a sequence-profile alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2015 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2015">
-        <rdfs:label>Sequence-profile alignment (HMM) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data format for a sequence-HMM profile alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2014"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2017 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2017">
-        <rdfs:label>Amino acid index format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3033"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1501"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for an amino acid index.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2020 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2020">
-        <rdfs:label>Article format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0971"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Literature format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data format for a full-text scientific article.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2021 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2021">
-        <rdfs:label>Text mining report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0972"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for an abstract (report) from text mining.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2027 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2027">
-        <rdfs:label>Enzyme kinetics report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2024"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for reports on enzyme kinetics.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2030 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2030">
-        <rdfs:label>Small molecule report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0962"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound annotation format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of a report on a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2031 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2031">
-        <rdfs:label>Gene annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report on a particular locus, gene, gene system or groups of genes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene features format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2032 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2032">
-        <rdfs:label>Workflow format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a workflow.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2033 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2033">
-        <rdfs:label>Tertiary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular tertiary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2034 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2034">
-        <rdfs:label>Biological model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data format for a biological model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.2</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2013"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2035 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2035">
-        <rdfs:label>Chemical formula format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0846"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Text format of a chemical formula.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2036 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2036">
-        <rdfs:label>Phylogenetic character data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0871"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of raw (unplotted) phylogenetic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2037 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2037">
-        <rdfs:label>Phylogenetic continuous quantitative character format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1426"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of phylogenetic continuous quantitative character data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2038 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2038">
-        <rdfs:label>Phylogenetic discrete states format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1427"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of phylogenetic discrete states data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2039 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2039">
-        <rdfs:label>Phylogenetic tree report (cliques) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1428"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of phylogenetic cliques data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2040 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2040">
-        <rdfs:label>Phylogenetic tree report (invariants) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1429"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of phylogenetic invariants data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2045 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2045">
-        <rdfs:label>Electron microscopy model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Annotation format for electron microscopy models.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2049 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2049">
-        <rdfs:label>Phylogenetic tree report (tree distances) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1442"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format for phylogenetic tree distance data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2051 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2051">
-        <rdfs:label>Polymorphism report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:hasDefinition>Format for sequence polymorphism data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2052 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2052">
-        <rdfs:label>Protein family report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for reports on a protein family.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2054 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2054">
-        <rdfs:label>Protein interaction format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for molecular interaction data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Molecular interaction format</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2055 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2055">
-        <rdfs:label>Sequence assembly format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for sequence assembly data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2056 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2056">
-        <rdfs:label>Microarray experiment data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <oboInOwl:hasDefinition>Format for information about a microarray experimental per se (not the data generated from that experiment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2057 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2057">
-        <rdfs:label>Sequence trace format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0924"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format for sequence trace data (i.e. including base call information).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2058 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2058">
-        <rdfs:label>Gene expression report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2603"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Gene expression data format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of a file of gene expression data, e.g. a gene expression matrix or profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2059 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2059">
-        <rdfs:label>Genotype and phenotype annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of a report on genotype / phenotype information.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2060 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2060">
-        <rdfs:label>Map format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a map of (typically one) molecular sequence annotated with features.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2061 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2061">
-        <rdfs:label>Nucleic acid features (primers) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2062 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2062">
-        <rdfs:label>Protein report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report of general information about a specific protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2063 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2063">
-        <rdfs:label>Protein report (enzyme) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report of general information about a specific enzyme.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2064 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2064">
-        <rdfs:label>3D-1D scoring matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3033"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1499"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a matrix of 3D-1D scores (amino acid environment probabilities).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2065 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2065">
-        <rdfs:label>Protein structure report (quality evaluation) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1539"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report on the quality of a protein three-dimensional model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2066 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2066">
-        <rdfs:label>Database hits (sequence) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0857"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report on sequence hits and associated data from searching a sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2067 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2067">
-        <rdfs:label>Sequence distance matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0870"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a matrix of genetic distances between molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2068 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2068">
-        <rdfs:label>Sequence motif format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1353"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a sequence motif.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2069 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2069">
-        <rdfs:label>Sequence profile format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a sequence profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2072 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2072">
-        <rdfs:label>Hidden Markov model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2069"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1364"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a hidden Markov model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2074 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2074">
-        <rdfs:label>Dirichlet distribution format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1347"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format of a dirichlet distribution.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2075 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2075">
-        <rdfs:label>HMM emission and transition counts format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for the emission and transition counts of a hidden Markov model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2076 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2076">
-        <rdfs:label>RNA secondary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for secondary structure (predicted or real) of an RNA molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2077">
-        <rdfs:label>Protein secondary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Format for secondary structure (predicted or real) of a protein molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2078">
-        <rdfs:label>Sequence range format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1017"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used to specify range(s) of sequence positions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2094">
-        <rdfs:label>pure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for molecular sequence with possible unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2095 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2095">
-        <rdfs:label>unpure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2096 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2096">
-        <rdfs:label>unambiguous sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2097">
-        <rdfs:label>ambiguous</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2155 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2155">
-        <rdfs:label>Sequence features (repeats) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for map of repeats in molecular (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2158">
-        <rdfs:label>Nucleic acid features (restriction sites) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for report on restriction enzyme recognition sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2159">
-        <rdfs:label>Gene features (coding region) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for report on coding regions in nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.10</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_2031"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2170 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2170">
-        <rdfs:label>Sequence cluster format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for clusters of molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2171 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2171">
-        <rdfs:label>Sequence cluster format (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2170"/>
-        <oboInOwl:hasDefinition>Format used for clusters of protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2172">
-        <rdfs:label>Sequence cluster format (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2170"/>
-        <oboInOwl:hasDefinition>Format used for clusters of nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2175">
-        <rdfs:label>Gene cluster format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for clusters of genes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2172"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2181 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2181">
-        <rdfs:label>EMBL-like (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2543"/>
-        <rdfs:comment>This concept may be used for the many non-standard EMBL-like text formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A text format resembling EMBL entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2182">
-        <rdfs:label>FASTQ-like format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2545"/>
-        <oboInOwl:hasDefinition>A text format resembling FASTQ short read format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for non-standard FASTQ short read-like formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2183">
-        <rdfs:label>EMBLXML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2204"/>
-        <oboInOwl:hasDefinition>XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2184">
-        <rdfs:label>cdsxml</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2204"/>
-        <oboInOwl:hasDefinition>XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2185 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2185">
-        <rdfs:label>insdxml</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2204"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2186 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2186">
-        <rdfs:label>geneseq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2181"/>
-        <oboInOwl:hasDefinition>Geneseq sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2187 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2187">
-        <rdfs:label>UniProt-like (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2547"/>
-        <oboInOwl:hasDefinition>A text sequence format resembling uniprotkb entry format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2188 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2188">
-        <rdfs:label>UniProt format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>UniProt entry sequence format.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1963"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2189 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2189">
-        <rdfs:label>ipi</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ipi sequence format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1963"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2194">
-        <rdfs:label>medline</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2020"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Abstract format used by MedLine database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2195">
-        <rdfs:label>Ontology format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format used for ontologies.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2196">
-        <rdfs:label>OBO format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A serialisation format conforming to the Open Biomedical Ontologies (OBO) model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2197 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2197">
-        <rdfs:label>OWL format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>A serialisation format conforming to the Web Ontology Language (OWL) model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2200">
-        <rdfs:label>FASTA-like (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2546"/>
-        <rdfs:comment>This concept may also be used for the many non-standard FASTA-like formats.</rdfs:comment>
-        <rdfs:seeAlso>http://filext.com/file-extension/FASTA</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A text format resembling FASTA format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2202">
-        <rdfs:label>Sequence record full format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2203">
-        <rdfs:label>Sequence record lite format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record &apos;lite&apos;, typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2204">
-        <rdfs:label>EMBL format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2558"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a placeholder for other more specific concepts. It should not normally be used for annotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2205 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2205">
-        <rdfs:label>GenBank-like format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2559"/>
-        <oboInOwl:hasDefinition>A text format resembling GenBank entry (plain text) format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for the non-standard GenBank-like text formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2206 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2206">
-        <rdfs:label>Sequence feature table format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2548"/>
-        <oboInOwl:hasDefinition>Text format for a sequence feature table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2210">
-        <rdfs:label>Strain data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on organism strain data / cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2211">
-        <rdfs:label>CIP strain data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format for a report of strain data as used for CIP database entries.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2243">
-        <rdfs:label>phylip property values</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>PHYLIP file format for phylogenetic property data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2036"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2303">
-        <rdfs:label>STRING entry format (HTML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format (HTML) for the STRING database of protein interaction.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2304">
-        <rdfs:label>STRING entry format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2054"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Entry format (XML) for the STRING database of protein interaction.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2305">
-        <rdfs:label>GFF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>GFF feature format (of indeterminate version).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2306">
-        <rdfs:label>GTF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2305"/>
-        <oboInOwl:hasDefinition>Gene Transfer Format (GTF), a restricted version of GFF.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format4"/>
-        <oboInOwl:hasDbXref rdf:resource="http://mblab.wustl.edu/GTF22.html"/>
-        <documentation rdf:resource="http://mblab.wustl.edu/GTF22.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2310">
-        <rdfs:label>FASTA-HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2546"/>
-        <oboInOwl:hasDefinition>FASTA format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2311">
-        <rdfs:label>EMBL-HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2543"/>
-        <oboInOwl:hasDefinition>EMBL entry format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2322">
-        <rdfs:label>BioCyc enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of an entry from the BioCyc enzyme database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2323">
-        <rdfs:label>ENZYME enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of an entry from the Enzyme nomenclature database (ENZYME).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2328">
-        <rdfs:label>PseudoCAP gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a report on a gene from the PseudoCAP database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2329">
-        <rdfs:label>GeneCards gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on a gene from the GeneCards database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2330">
-        <rdfs:label>Textual format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:seeAlso>http://filext.com/file-extension/TSV</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.iana.org/assignments/media-types/text/plain</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Textual format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>txt</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://filext.com/file-extension/TXT</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Plain text</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://www.iana.org/assignments/media-types/media-types.xhtml#text</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2331">
-        <rdfs:label>HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2048"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>HTML format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://filext.com/file-extension/HTML</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Hypertext Markup Language</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2332">
-        <rdfs:label>XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:comment>Data in XML format can be serialised into text, or binary format.</rdfs:comment>
-        <oboInOwl:hasDefinition>eXtensible Markup Language (XML) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://filext.com/file-extension/XML</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Extensible Markup Language</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2333 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2333">
-        <rdfs:label>Binary format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:comment>Only specific native binary formats are listed under &apos;Binary format&apos; in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Binary format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2334">
-        <rdfs:label>URI format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Typical textual representation of a URI.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1047"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2341">
-        <rdfs:label>NCI-Nature pathway entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The format of an entry from the NCI-Nature pathways database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2350">
-        <rdfs:label>Format (typed)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:comment>This concept exists only to assist EDAM maintenance and navigation in graphical browsers.  It does not add semantic information. The concept branch under &apos;Format (typed)&apos; provides an alternative organisation of the concepts nested under the other top-level branches (&apos;Binary&apos;, &apos;HTML&apos;, &apos;RDF&apos;, &apos;Text&apos; and &apos;XML&apos;. All concepts under here are already included under those branches.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A broad class of format distinguished by the scientific nature of the data that is identified.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2352">
-        <rdfs:label>BioXSD</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2555"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>BioXSD XML format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more).</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://bioxsd.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://bioxsd.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2376 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2376">
-        <rdfs:label>RDF format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A serialisation format conforming to the Resource Description Framework (RDF) model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2532 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2532">
-        <rdfs:label>GenBank-HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2559"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Genbank entry format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2542">
-        <rdfs:label>Protein features (domains) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of a report on protein features (domain composition).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2543">
-        <rdfs:label>EMBL-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A format resembling EMBL entry (plain text) format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for the many non-standard EMBL-like formats.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2545">
-        <rdfs:label>FASTQ-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <oboInOwl:hasDefinition>A format resembling FASTQ short read format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for non-standard FASTQ short read-like formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2546">
-        <rdfs:label>FASTA-like</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:comment>This concept may be used for the many non-standard FASTA-like formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A format resembling FASTA format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2547">
-        <rdfs:label>uniprotkb-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A sequence format resembling uniprotkb entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2548">
-        <rdfs:label>Sequence feature table format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format for a sequence feature table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2549">
-        <rdfs:label>OBO</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2196"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>OBO ontology text format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2550">
-        <rdfs:label>OBO-XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2196"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>OBO ontology XML format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2551">
-        <rdfs:label>Sequence record format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2552">
-        <rdfs:label>Sequence record format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2553">
-        <rdfs:label>Sequence feature table format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2548"/>
-        <oboInOwl:hasDefinition>XML format for a sequence feature table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2554">
-        <rdfs:label>Alignment format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <oboInOwl:hasDefinition>Text format for molecular sequence alignment information.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2555">
-        <rdfs:label>Alignment format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <oboInOwl:hasDefinition>XML format for molecular sequence alignment information.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2556">
-        <rdfs:label>Phylogenetic tree format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Text format for a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2557">
-        <rdfs:label>Phylogenetic tree format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>XML format for a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2558">
-        <rdfs:label>EMBL-like (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2543"/>
-        <oboInOwl:hasDefinition>An XML format resembling EMBL entry format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for the any non-standard EMBL-like XML formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2559">
-        <rdfs:label>GenBank-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:hasDefinition>A format resembling GenBank entry (plain text) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This concept may be used for the non-standard GenBank-like formats.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2560">
-        <rdfs:label>STRING entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the STRING database of protein interaction.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2561">
-        <rdfs:label>Sequence assembly format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2055"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Text format for sequence assembly data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2562 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2562">
-        <rdfs:label>Amino acid identifier format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Text format (representation) of amino acid residues.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0994"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2566">
-        <rdfs:label>completely unambiguous</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence without any unknown positions or ambiguity characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2567">
-        <rdfs:label>completely unambiguous pure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2566"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2568">
-        <rdfs:label>completely unambiguous pure nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters .</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2569">
-        <rdfs:label>completely unambiguous pure dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1212"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2570">
-        <rdfs:label>completely unambiguous pure rna sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1213"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2571">
-        <rdfs:label>Raw sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0848"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a raw molecular sequence (i.e. the alphabet used).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2572">
-        <rdfs:label>BAM</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2573">
-        <rdfs:label>SAM</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <rdfs:comment>The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2585 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2585">
-        <rdfs:label>SBML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://sbml.org"/>
-        <documentation rdf:resource="http://sbml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2607">
-        <rdfs:label>completely unambiguous pure protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1208"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2848 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2848">
-        <rdfs:label>Bibliographic reference format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0970"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a bibliographic reference.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2919 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2919">
-        <rdfs:label>Sequence annotation track format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3002"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a sequence annotation track.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2920 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2920">
-        <rdfs:label>Alignment format (pair only)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1381"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2921 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2921">
-        <rdfs:label>Sequence variation annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3498"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of sequence variation annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2922 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2922">
-        <rdfs:label>markx0 variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Some variant of Pearson MARKX alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2923 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2923">
-        <rdfs:label>mega variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Some variant of Mega format for (typically aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2924 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2924">
-        <rdfs:label>Phylip format variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Some variant of Phylip format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3000 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3000">
-        <rdfs:label>AB1</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>AB1 binary format of raw DNA sequence reads (output of Applied Biosystems&apos; sequencing analysis software). Contains an electropherogram and the DNA base sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3001 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3001">
-        <rdfs:label>ACE</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2055"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt"/>
-        <oboInOwl:hasDbXref rdf:resource="http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3003">
-        <rdfs:label>BED</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track).</rdfs:comment>
-        <oboInOwl:hasDefinition>Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3004">
-        <rdfs:label>bigBed</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>bigBed format for large sequence annotation tracks, similar to textual BED format.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.5"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.5"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3005">
-        <rdfs:label>WIG</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/goldenPath/help/wiggle.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/goldenPath/help/wiggle.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3006">
-        <rdfs:label>bigWig</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format6.1"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format6.1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3007">
-        <rdfs:label>PSL</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <oboInOwl:hasDefinition>PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format2"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format2"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3008 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3008">
-        <rdfs:label>MAF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth.</oboInOwl:hasDefinition>
-        <rdfs:comment>Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format5"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format5"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3009 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3009">
-        <rdfs:label>2bit</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case &apos;masking&apos;.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD"/>
-        <documentation rdf:resource="http://jcomeau.freeshell.org/www/genome/2bitformat.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://jcomeau.freeshell.org/www/genome/2bitformat.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3010 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3010">
-        <rdfs:label>.nib</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>.nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case &apos;masking&apos;.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format8"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format8"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3011 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3011">
-        <rdfs:label>genePred</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>genePred table format for gene prediction tracks.</oboInOwl:hasDefinition>
-        <rdfs:comment>genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format9"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format9"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3012 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3012">
-        <rdfs:label>pgSnp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format10"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format10"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3013 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3013">
-        <rdfs:label>axt</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>axt format of alignments, typically produced from BLASTZ.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/goldenPath/help/axt.html"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/goldenPath/help/axt.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3014 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3014">
-        <rdfs:label>LAV</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>LAV format of alignments generated by BLASTZ and LASTZ.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.bx.psu.edu/miller_lab/dist/lav_format.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.bx.psu.edu/miller_lab/dist/lav_format.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3015 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3015">
-        <rdfs:label>Pileup</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/pileup.shtml"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/pileup.shtml"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3016 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3016">
-        <rdfs:label>VCF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://vcftools.sourceforge.net/specs.html"/>
-        <documentation rdf:resource="http://vcftools.sourceforge.net/specs.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3017 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3017">
-        <rdfs:label>SRF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://srf.sourceforge.net/"/>
-        <oboInOwl:hasDbXref rdf:resource="http://srf.sourceforge.net/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3018 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3018">
-        <rdfs:label>ZTR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>ZTR format for storing chromatogram data from DNA sequencing instruments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://staden.sourceforge.net/manual/formats_unix_12.html"/>
-        <documentation rdf:resource="http://staden.sourceforge.net/manual/formats_unix_12.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3019 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3019">
-        <rdfs:label>GVF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <oboInOwl:hasDefinition>Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://sequenceontology.org/gvf.html"/>
-        <documentation rdf:resource="http://sequenceontology.org/gvf.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3020 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3020">
-        <rdfs:label>BCF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/mpileup.shtml"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3033 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3033">
-        <rdfs:label>Matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a matrix (array) of numerical values.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3097">
-        <rdfs:label>Protein domain classification format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of data concerning the classification of the sequences and/or structures of protein structural domain(s).</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3098 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3098">
-        <rdfs:label>Raw SCOP domain classification format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3097"/>
-        <oboInOwl:hasDefinition>Format of raw SCOP domain classification data files.</oboInOwl:hasDefinition>
-        <rdfs:comment>These are the parsable data files provided by SCOP.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3099">
-        <rdfs:label>Raw CATH domain classification format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3097"/>
-        <rdfs:comment>These are the parsable data files provided by CATH.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Format of raw CATH domain classification data files.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3100">
-        <rdfs:label>CATH domain report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3097"/>
-        <oboInOwl:hasDefinition>Format of summary of domain classification information for a CATH domain.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <rdfs:comment>The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3155 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3155">
-        <rdfs:label>SBRML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3166"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.comp-sys-bio.org/tiki-index.php?page=SBRML"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.comp-sys-bio.org/tiki-index.php?page=SBRML"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3156">
-        <rdfs:label>BioPAX</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <oboInOwl:hasDefinition>BioPAX is an exchange format for pathway data, with its data model defined in OWL.</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://www.biopax.org"/>
-        <documentation rdf:resource="http://www.biopax.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3157">
-        <rdfs:label>EBI Application Result XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <oboInOwl:hasDefinition>EBI Application Result XML is a format returned by sequence similarity search Web services at EBI.</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.ebi.ac.uk/schema/ApplicationResult.xsd"/>
-        <documentation rdf:resource="http://www.ebi.ac.uk/schema/ApplicationResult.xsd"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3158">
-        <rdfs:label>PSI MI XML (MIF)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2054"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>MIF</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.psidev.info/mif"/>
-        <documentation rdf:resource="http://www.psidev.info/mif"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3159">
-        <rdfs:label>phyloXML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2557"/>
-        <oboInOwl:hasDefinition>phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data.</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://www.phyloxml.org"/>
-        <documentation rdf:resource="http://www.phyloxml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3160">
-        <rdfs:label>NeXML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2557"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>NeXML is a standardised XML format for rich phyloinformatic data.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://www.nexml.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.nexml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3161 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3161">
-        <rdfs:label>MAGE-ML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.mged.org/Workgroups/MAGE/mage-ml.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.mged.org/Workgroups/MAGE/mage-ml.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3162 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3162">
-        <rdfs:label>MAGE-TAB</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED).</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.mged.org/mage-tab"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.mged.org/mage-tab"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3163">
-        <rdfs:label>GCDML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <oboInOwl:hasDefinition>GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC).</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <documentation rdf:resource="http://gcdml.gensc.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://gcdml.gensc.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3164">
-        <rdfs:label>GTrack</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG).</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://www.gtrack.no"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.gtrack.no"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3166">
-        <rdfs:label>Biological pathway or network report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for a report of information derived from a biological pathway or network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3167">
-        <rdfs:label>Experiment annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for annotation on a laboratory experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3235">
-        <rdfs:label>Cytoband format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2078"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3236"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Cytoband format for chromosome cytobands.</oboInOwl:hasDefinition>
-        <rdfs:comment>Reflects a UCSC Browser DB table.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.broadinstitute.org/software/igv/Cytoband"/>
-        <documentation rdf:resource="http://www.broadinstitute.org/software/igv/Cytoband"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3239">
-        <rdfs:label>CopasiML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3166"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>CopasiML, the native format of COPASI.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.copasi.org/tiki-index.php?page_ref_id=128"/>
-        <documentation rdf:resource="http://www.copasi.org/tiki-index.php?page_ref_id=128"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3240">
-        <rdfs:label>CellML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>CellML, the format for mathematical models of biological and other networks.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <documentation rdf:resource="http://www.cellml.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.cellml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3242">
-        <rdfs:label>PSI MI TAB (MITAB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2054"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README"/>
-        <documentation rdf:resource="ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3243">
-        <rdfs:label>PSI-PAR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3158"/>
-        <oboInOwl:hasDefinition>Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.psidev.info/psi-par"/>
-        <documentation rdf:resource="http://www.psidev.info/psi-par"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3244 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3244">
-        <rdfs:label>mzML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3245"/>
-        <rdfs:comment>mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center.</rdfs:comment>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://psidev.info/mzml"/>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/mzml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3245">
-        <rdfs:label>Mass spectrometry data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2536"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Format for mass spectrometry data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3246">
-        <rdfs:label>TraML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3245"/>
-        <oboInOwl:hasDefinition>TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <documentation rdf:resource="http://psidev.info/traml"/>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/traml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3247">
-        <rdfs:label>mzIdentML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3245"/>
-        <oboInOwl:hasDefinition>mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/mzidentml"/>
-        <documentation rdf:resource="http://psidev.info/mzidentml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3248">
-        <rdfs:label>mzQuantML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3245"/>
-        <oboInOwl:hasDefinition>mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <documentation rdf:resource="http://psidev.info/mzquantml"/>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/mzquantml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3249 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3249">
-        <rdfs:label>GelML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/gelml"/>
-        <documentation rdf:resource="http://psidev.info/gelml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
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-    
-
-
-    <!-- http://edamontology.org/format_3250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3250">
-        <rdfs:label>spML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info"/>
-        <documentation rdf:resource="http://psidev.info"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
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-
-
-    <!-- http://edamontology.org/format_3252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3252">
-        <rdfs:label>OWL Functional Syntax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>A human-readable encoding for the Web Ontology Language (OWL).</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3253">
-        <rdfs:label>Manchester OWL Syntax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>A syntax for writing OWL class expressions.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <rdfs:comment>This format was influenced by the OWL Abstract Syntax and the DL style syntax.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3254">
-        <rdfs:label>KRSS2 Syntax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>This format is used in Protege 4.</rdfs:comment>
-        <oboInOwl:hasDefinition>A superset of the &quot;Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort&quot;.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3255 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3255">
-        <rdfs:label>Turtle</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <rdfs:comment>The SPARQL Query Language incorporates a very similar syntax.</rdfs:comment>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3256 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3256">
-        <rdfs:label>N-Triples</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <rdfs:comment>N-Triples should not be confused with Notation 3 which is a superset of Turtle.</rdfs:comment>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3257">
-        <rdfs:label>Notation3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <oboInOwl:hasExactSynonym>N3</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3261 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3261">
-        <rdfs:label>RDF/XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <oboInOwl:hasNarrowSynonym>RDF</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Resource Description Framework (RDF) XML format.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <rdfs:seeAlso>http://www.ebi.ac.uk/SWO/data/SWO_3000006</rdfs:seeAlso>
-        <rdfs:comment>RDF/XML is a serialization syntax for OWL DL, but not for OWL Full.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3262 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3262">
-        <rdfs:label>OWL/XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>OWL ontology XML serialisation format.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasNarrowSynonym>OWL</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3281 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3281">
-        <rdfs:label>A2M</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://compbio.soe.ucsc.edu/a2m-desc.html"/>
-        <documentation rdf:resource="http://compbio.soe.ucsc.edu/a2m-desc.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3284">
-        <rdfs:label>SFF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasExactSynonym>Standard flowgram format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&amp;f=formats&amp;m=doc&amp;s=format#sff"/>
-        <documentation rdf:resource="http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&amp;f=formats&amp;m=doc&amp;s=format#sff"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3285">
-        <rdfs:label>MAP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3288"/>
-        <oboInOwl:hasDefinition>The MAP file describes SNPs and is used by the Plink package.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Plink MAP</oboInOwl:hasExactSynonym>
-        <documentation rdf:resource="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3286 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3286">
-        <rdfs:label>PED</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3288"/>
-        <oboInOwl:hasExactSynonym>Plink PED</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The PED file describes individuals and genetic data and is used by the Plink package.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3287 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3287">
-        <rdfs:label>Individual genetic data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Data format for a metadata on an individual and their genetic data.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3288">
-        <rdfs:label>PED/MAP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3287"/>
-        <oboInOwl:hasDefinition>The PED/MAP file describes data used by the Plink package.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Plink PED/MAP</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <documentation rdf:resource="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3309">
-        <rdfs:label>CT</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>File format of a CT (Connectivity Table) file from the RNAstructure package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Connect format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Connectivity Table file format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://rna.urmc.rochester.edu/Text/File_Formats.html"/>
-        <documentation rdf:resource="http://www.ibi.vu.nl/programs/k2nwww/static/data_formats.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3310">
-        <rdfs:label>SS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>XRNA old input style format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://rna.ucsc.edu/rnacenter/xrna/xrna_faq.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3311">
-        <rdfs:label>RNAML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>RNA Markup Language.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www-lbit.iro.umontreal.ca/rnaml/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3312">
-        <rdfs:label>GDE</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Format for the Genetic Data Environment (GDE).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://home.cc.umanitoba.ca/~psgendb/birchhomedir/local/pkg/gde/doc/GDE2.2_manual.pdf"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3313">
-        <rdfs:label>BLC</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Block file format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.compbio.dundee.ac.uk/manuals/amps/subsubsection3_18_2_5.html#SECTION00018250000000000000"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3326">
-        <rdfs:label>Data index format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3327">
-        <rdfs:label>BAI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3326"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>BAM indexing format</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/SAMv1.pdf"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3328">
-        <rdfs:label>HMMER2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1370"/>
-        <oboInOwl:hasDefinition>HMMER profile HMM file for HMMER versions 2.x</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <documentation rdf:resource="ftp://selab.janelia.org/pub/software/hmmer/2.4i/Userguide.pdf"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3329">
-        <rdfs:label>HMMER3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1370"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>HMMER profile HMM file for HMMER versions 3.x</oboInOwl:hasDefinition>
-        <documentation rdf:resource="ftp://selab.janelia.org/pub/software/hmmer/CURRENT/Userguide.pdf"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3330">
-        <rdfs:label>PO</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS simple sequence pair alignment format.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://sourceforge.net/projects/poamsa/files/latest/download?source=files"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3331">
-        <rdfs:label>BLAST XML results format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>XML format as produced by the NCBI Blast package</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3462 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3462">
-        <rdfs:label>CRAM</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <oboInOwl:hasDefinition>Reference-based compression of alignment format</oboInOwl:hasDefinition>
-        <documentation>http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf</documentation>
-        <oboInOwl:hasDbXref>http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf</oboInOwl:hasDbXref>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3464">
-        <rdfs:label>JSON</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Javascript Object Notation format; a lightweight, text-based format to represent structured data using key-value pairs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3466 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3466">
-        <rdfs:label>EPS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Encapsulated PostScript format</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3467">
-        <rdfs:label>GIF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Graphics Interchange Format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3468">
-        <rdfs:label>xls</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <oboInOwl:hasDefinition>Microsoft Excel spreadsheet format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microsoft Excel format</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3475">
-        <rdfs:label>TSV</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasExactSynonym>Tabular format</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://filext.com/file-extension/CSV</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.iana.org/assignments/media-types/text/csv</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Tabular data represented as tab-separated values in a text file.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:seeAlso>http://filext.com/file-extension/TSV</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>CSV</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3476">
-        <rdfs:label>Gene expression data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.10</obsolete_since>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Format of a file of gene expression data, e.g. a gene expression matrix or profile.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_2058"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3477 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3477">
-        <rdfs:label>Cytoscape input file format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3484 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3484">
-        <rdfs:label>ebwt</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3326"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3210"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <documentation>https://github.com/BenLangmead/bowtie/blob/master/MANUAL</documentation>
-        <oboInOwl:hasExactSynonym>Bowtie index format</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Bowtie format for indexed reference genome for &quot;small&quot; genomes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3485">
-        <rdfs:label>RSF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3486"/>
-        <documentation>http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf</documentation>
-        <rdfs:comment>RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual).</rdfs:comment>
-        <oboInOwl:hasDefinition>Rich sequence format.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>GCG RSF</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3486">
-        <rdfs:label>GCG format variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Some format based on the GCG format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3487">
-        <rdfs:label>BSML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2552"/>
-        <documentation>http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc</documentation>
-        <oboInOwl:hasDefinition>Bioinformatics Sequence Markup Language format.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3491">
-        <rdfs:label>ebwtl</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3326"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3210"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <documentation>https://github.com/BenLangmead/bowtie/blob/master/MANUAL</documentation>
-        <oboInOwl:hasExactSynonym>Bowtie long index format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Bowtie format for indexed reference genome for &quot;large&quot; genomes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3499">
-        <rdfs:label>Ensembl variation file format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <oboInOwl:hasDefinition>Ensembl standard format for variation data.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.ensembl.org/info/website/upload/var.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3506">
-        <rdfs:label>docx</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Microsoft Word format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>doc</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Microsoft Word format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3507">
-        <rdfs:label>Document format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Portable Document Format</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microsoft Word format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of documents including word processor, spreadsheet and presentation.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>doc</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3508">
-        <rdfs:label>PDF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Portable Document Format</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3547">
-        <rdfs:label>Image format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2968"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format used for images and image metadata.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3548">
-        <rdfs:label>DICOM format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard.
-
-</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://dicom.nema.org/"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3549">
-        <rdfs:label>nii</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>Medical image and metadata format of the Neuroimaging Informatics Technology Initiative.
-
-</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>NIfTI-1 format</oboInOwl:hasExactSynonym>
-        <created_in>1.9</created_in>
-        <documentation rdf:resource="http://nifti.nimh.nih.gov/nifti-1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3550">
-        <rdfs:label>mhd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasExactSynonym>Metalmage format</oboInOwl:hasExactSynonym>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Text-based tagged file format for medical images generated using the MetaImage software package.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.itk.org/Wiki/ITK/MetaIO/Documentation"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3551">
-        <rdfs:label>nrrd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Nearly Raw Rasta Data format designed to support scientific visualization and image processing involving N-dimensional raster data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://teem.sourceforge.net/nrrd/format.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3554">
-        <rdfs:label>R file format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics.
-</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3555">
-        <rdfs:label>SPSS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>File format used for scripts for the Statistical Package for the Social Sciences.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3556">
-        <rdfs:label>MHT</rdfs:label>
-        <rdfs:label>MIME  HTML format for Web pages, which can include external resources, including images, Flash animations and so on. </rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:hasDefinition>EMBL entry format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasExactSynonym>MHTML</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3578">
-        <rdfs:label>IDAT</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3110"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3579">
-        <rdfs:label>JPG</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Joint Picture Group file format for lossy graphics file.
-</oboInOwl:hasDefinition>
-        <rdfs:comment>Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/jpeg/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3580 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3580">
-        <rdfs:label>rcc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3581 -->
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-    <owl:Class rdf:about="http://edamontology.org/format_3581">
-        <rdfs:label>arff</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <rdfs:comment>This file format is for machine learning.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.cs.waikato.ac.nz/ml/weka/arff.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.cs.waikato.ac.nz/ml/weka/arff.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3582">
-        <rdfs:label>afg</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2055"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>AFG is a single text-based file assembly format  that holds read and consensus information together</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://seqanswers.com/wiki/AFG"/>
-        <documentation rdf:resource="http://seqanswers.com/wiki/AFG"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3583">
-        <rdfs:label>bedgraph</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <rdfs:comment>Holds a tab-delimited chromosome /start /end / datavalue dataset.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.8"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.8"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3584 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3584">
-        <rdfs:label>bedstrict</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3003"/>
-        <oboInOwl:hasDefinition>Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns.  </oboInOwl:hasDefinition>
-        <rdfs:comment>Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.  </rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3585 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3585">
-        <rdfs:label>bed6</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3584"/>
-        <rdfs:comment>Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6</rdfs:comment>
-        <oboInOwl:hasDefinition>BED file format where each feature is described by chromosome, start, end, name, score, and strand.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3586 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3586">
-        <rdfs:label>bed12</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3584"/>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12</rdfs:comment>
-        <oboInOwl:hasDefinition>A BED file where each feature is described by all twelve columns.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <documentation rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3587 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3587">
-        <rdfs:label>chrominfo</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3003"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Tabular format of chromosome names and sizes used by Galaxy.</oboInOwl:hasDefinition>
-        <rdfs:comment>Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.  </rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables?hgsid=43553_onGgm5PMjz4VDV1NySxolABvN978&amp;hgta_doSchemaDb=mm10&amp;hgta_doSchemaTable=chromInfo"/>
-        <oboInOwl:hasDbXref rdf:resource="http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables?hgsid=43553_onGgm5PMjz4VDV1NySxolABvN978&amp;hgta_doSchemaDb=mm10&amp;hgta_doSchemaTable=chromInfo"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3588 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3588">
-        <rdfs:label>customtrack</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Custom Sequence annotation track format used by Galaxy.</oboInOwl:hasDefinition>
-        <rdfs:comment>Used for tracks/track views within galaxy.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://genome.ucsc.edu/goldenPath/help/customTrack.html"/>
-        <oboInOwl:hasDbXref rdf:resource="https://genome.ucsc.edu/goldenPath/help/customTrack.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3589 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3589">
-        <rdfs:label>csfasta</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Color space FASTA format sequence variant.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <rdfs:comment>FASTA format extended for color space information.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.clcsupport.com/clcassemblycell/420/index.php?manual=Color_space_file_formats.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.clcsupport.com/clcassemblycell/420/index.php?manual=Color_space_file_formats.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3590 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3590">
-        <rdfs:label>hdf5</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:comment>An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. H5py uses straightforward NumPy and Python metaphors, like dictionary and NumPy array syntax.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasExactSynonym>h5</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Binary format used by Galaxy for hierarchical data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="https://www.hdfgroup.org/HDF5/doc/H5.format.html"/>
-        <documentation rdf:resource="https://www.hdfgroup.org/HDF5/doc/H5.format.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3591 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3591">
-        <rdfs:label>tiff</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>The TIFF format is perhaps the most versatile and diverse bitmap format in existence. Its extensible nature and support for numerous data compression schemes allow developers to customize the TIFF format to fit any peculiar data storage needs.
-</rdfs:comment>
-        <oboInOwl:hasDefinition>A versatile bitmap format.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/tiff/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3592 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3592">
-        <rdfs:label>bmp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>Standard bitmap storage format in the Microsoft Windows environment.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Although it is based on Windows internal bitmap data structures, it is supported by many non-Windows and non-PC applications.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/bmp/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3593">
-        <rdfs:label>im</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>IM is a format used by LabEye and other applications based on the IFUNC image processing library.</oboInOwl:hasDefinition>
-        <rdfs:comment>IFUNC library reads and writes most uncompressed interchange versions of this format.
-</rdfs:comment>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://pillow.readthedocs.org/en/latest/handbook/image-file-formats.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3594">
-        <rdfs:label>pcd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>PCD was developed by Kodak. A PCD file contains five different resolution (ranging from low to high) of a slide or film negative. Due to it PCD is often used by many photographers and graphics professionals for high-end printed applications.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Photo CD format, which is the highest resolution format for images on a CD.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://www.coolutils.com/Formats/PCD"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3595">
-        <rdfs:label>pcx</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>PCX is an image file format that uses a simple form of run-length encoding. It is lossless.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://www.coolutils.com/Formats/PCX"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3596 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3596">
-        <rdfs:label>ppm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>The PPM format is a lowest common denominator color image file format.
-</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://netpbm.sourceforge.net/doc/ppm.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3597 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3597">
-        <rdfs:label>psd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>PSD (Photoshop Document) is a proprietary file that allows the user to work with the images’ individual layers even after the file has been saved.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/psd/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3598">
-        <rdfs:label>xbm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>The XBM format was replaced by XPM for X11 in 1989.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI. </oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/xbm/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3599 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3599">
-        <rdfs:label>xpm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.</rdfs:comment>
-        <oboInOwl:hasDefinition>X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/xpm/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3600 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3600">
-        <rdfs:label>rgb</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>RGB file format is the native raster graphics file format for Silicon Graphics workstations.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/jpeg/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3601">
-        <rdfs:label>pbm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters.
-</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://netpbm.sourceforge.net/doc/pbm.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3602">
-        <rdfs:label>pgm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>It is designed to be extremely easy to learn and write programs for.</rdfs:comment>
-        <oboInOwl:hasDefinition>The PGM format is a lowest common denominator grayscale file format.
-</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://netpbm.sourceforge.net/doc/pgm.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3603 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3603">
-        <rdfs:label>png</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>PNG is a file format for image compression.
-</oboInOwl:hasDefinition>
-        <rdfs:comment>It iis expected to replace the Graphics Interchange Format (GIF).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.w3.org/TR/PNG/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3604 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3604">
-        <rdfs:label>svg</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment> The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.</rdfs:comment>
-        <oboInOwl:hasDefinition>Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.w3.org/Graphics/SVG/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3605">
-        <rdfs:label>rast</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <rdfs:comment> The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://en.wikipedia.org/wiki/Sun_Raster"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3606">
-        <rdfs:label>Sequence quality report format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2048"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Textual report format for sequence quality for reports from sequencing machines.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3607">
-        <rdfs:label>qual</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3606"/>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Phred quality scores  are defined as a property which is logarithmically related to the base-calling error probabilities.</rdfs:comment>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3608">
-        <rdfs:label>qualsolexa</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1933"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <rdfs:comment>Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3609 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3609">
-        <rdfs:label>qualillumina</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1931"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <rdfs:comment>Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 &quot;B&quot;, is used also at the end of reads as a Read Segment Quality Control Indicator.</rdfs:comment>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3610">
-        <rdfs:label>qualsolid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <rdfs:comment>For SOLiD data, the sequence is in color space, except the first position. The quality values are those of the Sanger format.</rdfs:comment>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3611">
-        <rdfs:label>qual454</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3612">
-        <rdfs:label>ENCODE peak format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3585"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Human ENCODE peak format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Format that covers both the broad peak format and narrow peak format from ENCODE.</rdfs:comment>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format13"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format13"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3613">
-        <rdfs:label>ENCODE narrow peak format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3612"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Human ENCODE narrow peak format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Format that covers both the broad peak format and narrow peak format from ENCODE.</rdfs:comment>
-        <oboInOwl:hasDbXref rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?"/>
-        <documentation rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3614 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3614">
-        <rdfs:label>ENCODE broad peak format </rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3612"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Human ENCODE broad peak format.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format12"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format12"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3615 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3615">
-        <rdfs:label>bgzip</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>BAM files are compressed using a variant of GZIP (GNU ZIP), into a format called BGZF (Blocked GNU Zip Format).</rdfs:comment>
-        <oboInOwl:hasDefinition>Blocked GNU Zip format.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.htslib.org/doc/tabix.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3616">
-        <rdfs:label>tabix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>TAB-delimited genome position file index format.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.htslib.org/doc/tabix.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.htslib.org/doc/tabix.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3617">
-        <rdfs:label>Graph format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Data format for graph data.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3618">
-        <rdfs:label>xgmml</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3617"/>
-        <oboInOwl:hasDefinition>XML-based format used to store graph descriptions within Galaxy.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?highlight=datatypes%20graph#module-galaxy.datatypes.graph"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3619 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3619">
-        <rdfs:label>sif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?highlight=datatypes%20graph#module-galaxy.datatypes.graph"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3620">
-        <rdfs:label>xlsx</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3621">
-        <rdfs:label>SQLite</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <documentation>https://www.sqlite.org/fileformat2.html</documentation>
-        <oboInOwl:hasDefinition>Data format used by the SQLite database.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3622">
-        <rdfs:label>GeminiSQLite</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <documentation>https://gemini.readthedocs.org/en/latest/content/quick_start.html</documentation>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Data format used by the SQLite database conformant to the Gemini schema.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3623 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3623">
-        <rdfs:label>Index format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a data index of some type.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3624 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3624">
-        <rdfs:label>snpeffdb</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3623"/>
-        <oboInOwl:hasDefinition>An index of a genome database, indexed for use by the snpeff tool.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0004">
-        <rdfs:label>Operation</rdfs:label>
-        <owl:disjointWith rdf:resource="http://edamontology.org/topic_0003"/>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <oboInOwl:hasRelatedSynonym>Computational tool</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Function</oboInOwl:hasBroadSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#Function</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Function</rdfs:seeAlso>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Function_(mathematics)</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Computational method</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000017</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ebi.ac.uk/swo/SWO_0000003</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Mathematical operation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasRelatedSynonym>sumo:Function</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasRelatedSynonym>Process</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasNarrowSynonym>Computational operation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Computational subroutine</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000649</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/span#Process</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Computational procedure</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Mathematical function</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Lambda abstraction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Function (programming)</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Process</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://wsio.org/operation_001</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Function</rdfs:seeAlso>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Function_(computer_science)</rdfs:seeAlso>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Subroutine</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedTarget>Process</owl:annotatedTarget>
-        <rdfs:comment>Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>Computational tool provides one or more operations.</rdfs:comment>
-        <owl:annotatedTarget>Computational tool</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>Function</owl:annotatedTarget>
-        <rdfs:comment>Operation is a function that is computational. It typically has input(s) and output(s), which are always data.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasBroadSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/operation_0224 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0224">
-        <rdfs:label>Query and retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0090"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Query</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Retrieval</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Search or query a data resource and retrieve entries and / or annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0225 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0225">
-        <rdfs:label>Data retrieval (database cross-reference)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search database to retrieve all relevant references to a particular entity or entry.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0226 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0226">
-        <rdfs:label>Annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0227 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0227">
-        <rdfs:label>Indexing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Data indexing</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate an index of (typically a file of) biological data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database indexing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0228 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0228">
-        <rdfs:label>Data index analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Database index analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse an index of biological data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0227"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0229 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0229">
-        <rdfs:label>Annotation retrieval (sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Retrieve basic information about a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_1813"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0230 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0230">
-        <rdfs:label>Sequence generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a molecular sequence by some means.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0231 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0231">
-        <rdfs:label>Sequence editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <oboInOwl:hasDefinition>Edit or change a molecular sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0232 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0232">
-        <rdfs:label>Sequence merging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Merge two or more (typically overlapping) molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence splicing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0233">
-        <rdfs:label>Sequence conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3434"/>
-        <oboInOwl:hasDefinition>Convert a molecular sequence from one type to another.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0234 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0234">
-        <rdfs:label>Sequence complexity calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1259"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate sequence complexity, for example to find low-complexity regions in sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0235">
-        <rdfs:label>Sequence ambiguity calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1260"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0236">
-        <rdfs:label>Sequence composition calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1261"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate character or word composition or frequency of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0237">
-        <rdfs:label>Repeat sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Find and/or analyse repeat sequences in (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0238">
-        <rdfs:label>Sequence motif discovery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Motifs and patterns might be conserved or over-represented (occur with improbable frequency).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Motif discovery</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0239">
-        <rdfs:label>Sequence signature recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Motif search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence motif search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Motif detection</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence motif recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequence signature detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence profile search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Sequence motif detection</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Motif recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0240">
-        <rdfs:label>Sequence motif comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find motifs shared by molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0241">
-        <rdfs:label>Transcription regulatory sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0438"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0242">
-        <rdfs:label>Conserved transcription regulatory sequence identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:comment>For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0243">
-        <rdfs:label>Protein property calculation (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0250"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein structural property calculation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0244 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0244">
-        <rdfs:label>Protein flexibility and motion analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2476"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse flexibility and motion in protein structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0245">
-        <rdfs:label>Protein structural motif recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0166"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or screen for 3D structural motifs in protein structure(s).</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein structural feature identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0246">
-        <rdfs:label>Protein domain recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0736"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify structural domains in a protein structure from first principles (for example calculations on structural compactness).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0247">
-        <rdfs:label>Protein architecture analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0248">
-        <rdfs:label>Residue interaction calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1540"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDbXref>WHATIF: SymShellTenXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ListContactsRelaxed</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: SymShellTwoXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ListSideChainContactsRelaxed</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ListSideChainContactsNormal</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ListContactsNormal</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: SymShellFiveXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: SymShellOneXML</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0249 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0249">
-        <rdfs:label>Torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2991"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate, visualise or analyse phi/psi angles of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0250">
-        <rdfs:label>Protein property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods to render and visualise the properties of a protein sequence.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein property rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0252">
-        <rdfs:label>Peptide immunogenicity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1534"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0253">
-        <rdfs:label>Sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence feature prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence feature recognition</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Motif database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasRelatedSynonym>SO:0000110</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0254">
-        <rdfs:label>Data retrieval (feature table)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Extract a sequence feature table from a sequence database entry.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0255 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0255">
-        <rdfs:label>Feature table query</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query the features (in a feature table) of molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0256 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0256">
-        <rdfs:label>Sequence feature comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1270"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare the feature tables of two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Feature comparison</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Feature table comparison</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0257">
-        <rdfs:label>Data retrieval (sequence alignment)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Display basic information about a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0258">
-        <rdfs:label>Sequence alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0259">
-        <rdfs:label>Sequence alignment comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <oboInOwl:hasDefinition>Compare (typically by aligning) two molecular sequence alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>See also &apos;Sequence profile alignment&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0260 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0260">
-        <rdfs:label>Sequence alignment conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3081"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3434"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0261 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0261">
-        <rdfs:label>Nucleic acid property processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) physicochemical property data of nucleic acids.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0262"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0262 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0262">
-        <rdfs:label>Nucleic acid property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0912"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0264">
-        <rdfs:label>Splice transcript prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2499"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict splicing alternatives or transcript isoforms from analysis of sequence data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0265">
-        <rdfs:label>Frameshift detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3202"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Frameshift error detection</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods include sequence alignment (if related sequences are available) and word-based sequence comparison.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0266 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0266">
-        <rdfs:label>Vector sequence detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0267 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0267">
-        <rdfs:label>Protein secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0172"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict secondary structure of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Secondary structure prediction (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0268 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0268">
-        <rdfs:label>Protein super-secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1277"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict super-secondary structure of protein sequence(s).</oboInOwl:hasDefinition>
-        <rdfs:comment>Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0269">
-        <rdfs:label>Transmembrane protein prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0270"/>
-        <oboInOwl:hasDefinition>Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0270 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0270">
-        <rdfs:label>Transmembrane protein analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0820"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions.</oboInOwl:hasDefinition>
-        <rdfs:comment>Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0271 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0271">
-        <rdfs:label>Structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict tertiary structure of a molecular (biopolymer) sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0272 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0272">
-        <rdfs:label>Residue interaction prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2506"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Methods usually involve multiple sequence alignment analysis.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0273 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0273">
-        <rdfs:label>Protein interaction raw data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2949"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0905"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0274 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0274">
-        <rdfs:label>Protein-protein interaction prediction (from protein sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1777"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2464"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0275 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0275">
-        <rdfs:label>Protein-protein interaction prediction (from protein structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2464"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0276 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0276">
-        <rdfs:label>Protein interaction network analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2497"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2949"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse a network of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0277">
-        <rdfs:label>Protein interaction network comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0276"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1778"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more networks of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0278">
-        <rdfs:label>RNA secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0279"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0279 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0279">
-        <rdfs:label>Nucleic acid folding prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2481"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1596"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid folding modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid folding</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0280">
-        <rdfs:label>Data retrieval (restriction enzyme annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Restriction enzyme information retrieval</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Retrieve information on restriction enzymes or restriction enzyme sites.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0281 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0281">
-        <rdfs:label>Genetic marker identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Identify genetic markers in DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0415"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0282 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0282">
-        <rdfs:label>Genetic mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2520"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1278"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>QTL mapping</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Linkage mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genetic map generation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genetic map construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Functional mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0283 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0283">
-        <rdfs:label>Linkage analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0927"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse genetic linkage.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0284">
-        <rdfs:label>Codon usage table generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2433"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate codon usage statistics and create a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Codon usage table construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0285">
-        <rdfs:label>Codon usage table comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2433"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more codon usage tables.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0286 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0286">
-        <rdfs:label>Codon usage analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0914"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>synon: Codon usage data analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>synon: Codon usage table analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0287 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0287">
-        <rdfs:label>Base position variability plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1263"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify and plot third base position variability in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0288">
-        <rdfs:label>Sequence word comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <oboInOwl:hasDefinition>Find exact character or word matches between molecular sequences without full sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0289">
-        <rdfs:label>Sequence distance matrix generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0870"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence distance matrix construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phylogenetic distance matrix generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0290 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0290">
-        <rdfs:label>Sequence redundancy removal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0291 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0291">
-        <rdfs:label>Sequence clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3432"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>The clusters may be output or used internally for some other purpose.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence cluster construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence cluster generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0292">
-        <rdfs:label>Sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align (identify equivalent sites within) molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment computation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0293">
-        <rdfs:label>Hybrid sequence alignment construction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Hybrid sequence alignment</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Hybrid sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0294 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0294">
-        <rdfs:label>Structure-based sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Structure-based sequence alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (structure-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure-based sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment (structure-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure-based sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align molecular sequences using sequence and structural information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0295">
-        <rdfs:label>Structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0886"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Align (superimpose) molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0296 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0296">
-        <rdfs:label>Sequence profile generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence profile construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0297">
-        <rdfs:label>3D profile generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0886"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structural profile generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate some type of structural (3D) profile or template from a structure or structure alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structural profile construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0298">
-        <rdfs:label>Profile-to-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0868"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>See also &apos;Sequence alignment comparison&apos;.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align sequence profiles (representing sequence alignments).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0299">
-        <rdfs:label>3D profile-to-3D profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0890"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>3D profile alignment (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>3D profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple 3D profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align structural (3D) profiles or templates (representing structures or structure alignments).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0300">
-        <rdfs:label>Sequence-to-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0869"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence-profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence-profile alignment generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align molecular sequence(s) to sequence profile(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence-profile alignment</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0301">
-        <rdfs:label>Sequence-to-3D-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0303"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0893"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence-3D profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence-3D profile alignment generation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence-3D profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0302">
-        <rdfs:label>Protein threading</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0303"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0893"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align molecular sequence to structure in 3D space (threading).</oboInOwl:hasDefinition>
-        <rdfs:comment>Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence-structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0303">
-        <rdfs:label>Protein fold recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0180"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein domain prediction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.</rdfs:comment>
-        <oboInOwl:hasDefinition>Recognize (predict and identify) known protein structural domains or folds in protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein fold prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0304">
-        <rdfs:label>Metadata retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2422"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2337"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Data retrieval (documentation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Data retrieval (metadata)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes documentation, general information and other metadata on entities such as databases, database entries and tools.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0305">
-        <rdfs:label>Literature search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0970"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3068"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Query the biomedical and informatics literature.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
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-    
-
-
-    <!-- http://edamontology.org/operation_0306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0306">
-        <rdfs:label>Text mining</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2048"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0972"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0218"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Text data mining</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process and analyse text (typically the biomedical and informatics literature) to extract information from it.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0307">
-        <rdfs:label>Virtual PCR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform in-silico (virtual) PCR.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0308">
-        <rdfs:label>PCR primer design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2419"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1240"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>PCR primer prediction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set.</rdfs:comment>
-        <oboInOwl:hasDefinition>Design or predict oligonucleotide primers for PCR and DNA amplification etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0309">
-        <rdfs:label>Microarray probe design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2419"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
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-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2717"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray probe prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0310">
-        <rdfs:label>Sequence assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3433"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0925"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.</rdfs:comment>
-        <oboInOwl:hasDefinition>Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0311">
-        <rdfs:label>Microarray data standardization and normalization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3435"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3117"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3117"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Standardize or normalize microarray data.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0312">
-        <rdfs:label>Sequencing-based expression profile data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) SAGE, MPSS or SBS experimental data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0313">
-        <rdfs:label>Gene expression profile clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0315"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3432"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0314">
-        <rdfs:label>Gene expression profiling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0928"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Expression profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene expression profile construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Functional profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a gene expression profile or pattern, for example from microarray data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression profile generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0315">
-        <rdfs:label>Gene expression profile comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare gene expression profiles or patterns.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0316">
-        <rdfs:label>Functional profiling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Interpret (in functional terms) and annotate gene expression data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0532"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0317 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0317">
-        <rdfs:label>EST and cDNA sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse EST or cDNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2403"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0318">
-        <rdfs:label>Structural genomics target selection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identify and select targets for protein structural determination.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods will typically navigate a graph of protein families of known structure.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2406"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0319 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0319">
-        <rdfs:label>Protein secondary structure assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
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-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
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-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign secondary structure from protein coordinate or experimental data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0320">
-        <rdfs:label>Protein structure assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign a protein tertiary structure (3D coordinates) from raw experimental data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0321">
-        <rdfs:label>Protein model validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1539"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0172"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2275"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Evaluate the quality or correctness a protein three-dimensional model.</oboInOwl:hasDefinition>
-        <rdfs:comment>Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF: CorrectedPDBasXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Protein structure validation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>WHATIF: UseFileDB</oboInOwl:hasDbXref>
-        <rdfs:comment>The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0322">
-        <rdfs:label>Molecular model refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2425"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <oboInOwl:hasNarrowSynonym>Protein model refinement</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>WHATIF: CorrectedPDBasXML</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0323">
-        <rdfs:label>Phylogenetic tree generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0324 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0324">
-        <rdfs:label>Phylogenetic tree analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2523"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0325">
-        <rdfs:label>Phylogenetic tree comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0326">
-        <rdfs:label>Phylogenetic tree editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Edit a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0327">
-        <rdfs:label>Phylogenetic footprinting / shadowing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0540"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0194"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>A phylogenetic &apos;shadow&apos; represents the additive differences between individual sequences. By masking or &apos;shadowing&apos; variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0328">
-        <rdfs:label>Protein folding simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2415"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simulate the folding of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0329">
-        <rdfs:label>Protein folding pathway prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <oboInOwl:hasDefinition>Predict the folding pathway(s) or non-native structural intermediates of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0330">
-        <rdfs:label>Protein SNP mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2277"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0331">
-        <rdfs:label>Protein modelling (mutation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Methods might predict silent or pathological mutations.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein mutation modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0332">
-        <rdfs:label>Immunogen design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Design molecules that elicit an immune response (immunogens).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0559"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0333 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0333">
-        <rdfs:label>Zinc finger prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0334">
-        <rdfs:label>Enzyme kinetics calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2024"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0821"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate Km, Vmax and derived data for an enzyme reaction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0335">
-        <rdfs:label>Formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Reformat a file of data (or equivalent entity in memory).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Format conversion</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File formatting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Reformatting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File reformatting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File format conversion</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0336">
-        <rdfs:label>Format validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <oboInOwl:hasDefinition>Test and validate the format and content of a data file.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>File format validation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0337">
-        <rdfs:label>Visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2968"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2968"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0092"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0338">
-        <rdfs:label>Sequence database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0857"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Search a sequence database by sequence comparison and retrieve similar sequences.
-
-sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This excludes direct retrieval methods (e.g. the dbfetch program).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0339">
-        <rdfs:label>Structure database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0081"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0340">
-        <rdfs:label>Protein secondary database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_3087"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0341">
-        <rdfs:label>Motif database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Screen a sequence against a motif or pattern database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0253"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0342">
-        <rdfs:label>Sequence profile database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a database of sequence profiles with a query sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0239"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0343">
-        <rdfs:label>Transmembrane protein database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Search a database of transmembrane proteins, for example for sequence or structural similarities.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2421"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0344">
-        <rdfs:label>Sequence retrieval (by code)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query a database and retrieve sequences with a given entry code or accession number.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0345">
-        <rdfs:label>Sequence retrieval (by keyword)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query a database and retrieve sequences containing a given keyword.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0346">
-        <rdfs:label>Sequence similarity search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <oboInOwl:hasNarrowSynonym>Structure database search (by sequence)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence database search (by sequence)</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences that are similar to a query sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0347 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0347">
-        <rdfs:label>Sequence database search (by motif or pattern)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0239"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0348">
-        <rdfs:label>Sequence database search (by amino acid composition)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences of a given amino acid composition.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0349">
-        <rdfs:label>Sequence database search (by property)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0350">
-        <rdfs:label>Sequence database search (by sequence using word-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (word-based methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0351 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0351">
-        <rdfs:label>Sequence database search (by sequence using profile-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (profile-based methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes tools based on PSI-BLAST.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0352">
-        <rdfs:label>Sequence database search (by sequence using local alignment-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (local alignment-based methods) </oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes tools based on the Smith-Waterman algorithm or FASTA.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0353">
-        <rdfs:label>Sequence database search (by sequence using global alignment-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes tools based on the Needleman and Wunsch algorithm.</rdfs:comment>
-        <oboInOwl:hasDefinition>Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (global alignment-based methods)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0354">
-        <rdfs:label>Sequence database search (by sequence for primer sequences)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <rdfs:comment>STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (primer sequences)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0355">
-        <rdfs:label>Sequence database search (by molecular weight)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein fingerprinting</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide mass fingerprinting</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0356">
-        <rdfs:label>Sequence database search (by isoelectric point)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search sequence(s) or a sequence database for sequences of a given isoelectric point.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0357">
-        <rdfs:label>Structure retrieval (by code)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query a tertiary structure database and retrieve entries with a given entry code or accession number.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0358">
-        <rdfs:label>Structure retrieval (by keyword)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Query a tertiary structure database and retrieve entries containing a given keyword.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0359">
-        <rdfs:label>Structure database search (by sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0360">
-        <rdfs:label>Structural similarity search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0339"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a database of molecular structure and retrieve structures that are similar to a query structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structure database search (by structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure retrieval by structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0361 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0361">
-        <rdfs:label>Sequence annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotate a molecular sequence record with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0362 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0362">
-        <rdfs:label>Genome annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0361"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotate a genome sequence with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0363 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0363">
-        <rdfs:label>Nucleic acid sequence reverse and complement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2513"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate the reverse and / or complement of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0364 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0364">
-        <rdfs:label>Random sequence generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <oboInOwl:hasDefinition>Generate a random sequence, for example, with a specific character composition.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0365">
-        <rdfs:label>Nucleic acid restriction digest</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2513"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1239"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate digest fragments for a nucleotide sequence containing restriction sites.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0366">
-        <rdfs:label>Protein sequence cleavage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2514"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1238"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0367 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0367">
-        <rdfs:label>Sequence mutation and randomization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0368">
-        <rdfs:label>Sequence masking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:hasDefinition>Mask characters in a molecular sequence (replacing those characters with a mask character).</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, SNPs or repeats in a DNA sequence might be masked.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0369">
-        <rdfs:label>Sequence cutting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:hasDefinition>Cut (remove) characters or a region from a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0370">
-        <rdfs:label>Restriction site creation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:hasDefinition>Create (or remove) restriction sites in sequences, for example using silent mutations.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0371">
-        <rdfs:label>DNA translation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0108"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Translate a DNA sequence into protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0372">
-        <rdfs:label>DNA transcription</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Transcribe a nucleotide sequence into mRNA sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0377 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0377">
-        <rdfs:label>Sequence composition calculation (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Calculate base frequency or word composition of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0236"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0378">
-        <rdfs:label>Sequence composition calculation (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Calculate amino acid frequency or word composition of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0236"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0379">
-        <rdfs:label>Repeat sequence detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0237"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0380 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0380">
-        <rdfs:label>Repeat sequence organisation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0237"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse repeat sequence organization such as periodicity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0383">
-        <rdfs:label>Protein hydropathy calculation (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2574"/>
-        <oboInOwl:hasDefinition>Analyse the hydrophobic, hydrophilic or charge properties of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0384">
-        <rdfs:label>Protein solvent accessibility calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1542"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate solvent accessible or buried surface areas in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0385">
-        <rdfs:label>Protein hydropathy cluster calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0383"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0393"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify clusters of hydrophobic or charged residues in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0386">
-        <rdfs:label>Protein dipole moment calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1545"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate whether a protein structure has an unusually large net charge (dipole moment).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0387">
-        <rdfs:label>Protein surface and interior calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0384"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0166"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0388">
-        <rdfs:label>Protein binding site prediction (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0245"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2575"/>
-        <oboInOwl:hasDefinition>Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ligand-binding and active site prediction (from structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Binding site prediction (from structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0389 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0389">
-        <rdfs:label>Protein-nucleic acid binding site analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2949"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse RNA or DNA-binding sites in protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0390">
-        <rdfs:label>Protein peeling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0246"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Decompose a structure into compact or globular fragments (protein peeling).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0391">
-        <rdfs:label>Protein distance matrix calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1546"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0392 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0392">
-        <rdfs:label>Protein contact map calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1547"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0393">
-        <rdfs:label>Protein residue cluster calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1548"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Cluster of contacting residues might be key structural residues.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate clusters of contacting residues in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0394 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0394">
-        <rdfs:label>Hydrogen bond calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1549"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDbXref>WHATIF:ShowHydrogenBonds</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:HasHydrogenBonds</oboInOwl:hasDbXref>
-        <rdfs:comment>The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ShowHydrogenBondsM</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identify potential hydrogen bonds between amino acids and other groups.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0395">
-        <rdfs:label>Residue non-canonical interaction detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate non-canonical atomic interactions in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0396">
-        <rdfs:label>Ramachandran plot calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1544"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate a Ramachandran plot of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0397">
-        <rdfs:label>Ramachandran plot validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1844"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1544"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1539"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Validate a Ramachandran plot of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0398">
-        <rdfs:label>Protein molecular weight calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1519"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate the molecular weight of a protein sequence or fragments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0399">
-        <rdfs:label>Protein extinction coefficient calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict extinction coefficients or optical density of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0400">
-        <rdfs:label>Protein pH-dependent property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate pH-dependent properties from pKa calculations of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0401">
-        <rdfs:label>Protein hydropathy calculation (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2574"/>
-        <oboInOwl:hasDefinition>Hydropathy calculation on a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0402">
-        <rdfs:label>Protein titration curve plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0400"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1527"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Plot a protein titration curve.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0403">
-        <rdfs:label>Protein isoelectric point calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0400"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1528"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate isoelectric point of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0404">
-        <rdfs:label>Protein hydrogen exchange rate calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0400"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1530"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Estimate hydrogen exchange rate of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0405">
-        <rdfs:label>Protein hydrophobic region calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <oboInOwl:hasDefinition>Calculate hydrophobic or hydrophilic / charged regions of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0406">
-        <rdfs:label>Protein aliphatic index calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1521"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0407">
-        <rdfs:label>Protein hydrophobic moment plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1520"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0408">
-        <rdfs:label>Protein globularity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1526"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0409">
-        <rdfs:label>Protein solubility prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1524"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict the solubility or atomic solvation energy of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0410">
-        <rdfs:label>Protein crystallizability prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1525"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict crystallizability of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0411">
-        <rdfs:label>Protein signal peptide detection (eukaryotes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0418"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0412">
-        <rdfs:label>Protein signal peptide detection (bacteria)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0418"/>
-        <oboInOwl:hasDefinition>Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0413">
-        <rdfs:label>MHC peptide immunogenicity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0252"/>
-        <oboInOwl:hasDefinition>Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0414">
-        <rdfs:label>Protein feature prediction (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Methods typically involve scanning for known motifs, patterns and regular expressions.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence feature detection (protein)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_3092"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0415">
-        <rdfs:label>Nucleic acid feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1276"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence feature detection (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods typically involve scanning for known motifs, patterns and regular expressions.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid feature recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid feature prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0416">
-        <rdfs:label>Epitope mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict antigenic determinant sites (epitopes) in protein sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Epitope mapping is commonly done during vaccine design.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0417">
-        <rdfs:label>Protein post-translation modification site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0601"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict post-translation modification sites in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0418 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0418">
-        <rdfs:label>Protein signal peptide detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2489"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0140"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Detect or predict signal peptides and signal peptide cleavage sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0419">
-        <rdfs:label>Protein binding site prediction (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2575"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <oboInOwl:hasExactSynonym>Binding site prediction (from sequence)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict catalytic residues, active sites or other ligand-binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ligand-binding and active site prediction (from sequence)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein binding site detection</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0420">
-        <rdfs:label>Protein-nucleic acid binding prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0419"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict RNA and DNA-binding binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0421">
-        <rdfs:label>Protein folding site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <oboInOwl:hasDefinition>Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0422">
-        <rdfs:label>Protein cleavage site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect or predict cleavage sites (enzymatic or chemical) in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0423">
-        <rdfs:label>Epitope mapping (MHC Class I)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict epitopes that bind to MHC class I molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0416"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0424">
-        <rdfs:label>Epitope mapping (MHC Class II)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Predict epitopes that bind to MHC class II molecules.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0416"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0425">
-        <rdfs:label>Whole gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2454"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0426">
-        <rdfs:label>Gene component prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2454"/>
-        <rdfs:comment>Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0427">
-        <rdfs:label>Transposon prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect or predict transposons, retrotransposons / retrotransposition signatures etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0428">
-        <rdfs:label>PolyA signal detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <oboInOwl:hasDefinition>Detect polyA signals in nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0429">
-        <rdfs:label>Quadruplex formation site detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Quadruplex structure prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Detect quadruplex-forming motifs in nucleotide sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0430">
-        <rdfs:label>CpG island and isochore detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>An isochore is long region (&gt; 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find CpG rich regions in a nucleotide sequence or isochores in genome sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>CpG island and isochores rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>CpG island and isochores detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0431 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0431">
-        <rdfs:label>Restriction site recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0432">
-        <rdfs:label>Nucleosome formation or exclusion sequence prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0433">
-        <rdfs:label>Splice site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify, predict or analyse splice sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods might require a pre-mRNA or genomic DNA sequence.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0434">
-        <rdfs:label>Integrated gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0425"/>
-        <oboInOwl:hasDefinition>Predict whole gene structure using a combination of multiple methods to achieve better predictions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0435">
-        <rdfs:label>Operon prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0425"/>
-        <oboInOwl:hasDefinition>Find operons (operators, promoters and genes) in bacteria genes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0436">
-        <rdfs:label>Coding region prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0426"/>
-        <oboInOwl:hasDefinition>Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ORF prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>ORF finding</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0437">
-        <rdfs:label>Selenocysteine insertion sequence (SECIS) prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict selenocysteine insertion sequence (SECIS) in a DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0438">
-        <rdfs:label>Regulatory element prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0749"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Translational regulatory element prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Transcription regulatory element prediction</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0439">
-        <rdfs:label>Translation initiation site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0436"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0108"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict translation initiation sites, possibly by searching a database of sites.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0440">
-        <rdfs:label>Promoter prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <oboInOwl:hasDefinition>Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods might recognize CG content, CpG islands, splice sites, polyA signals etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0441">
-        <rdfs:label>Transcription regulatory element prediction (DNA-cis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5&apos; promoter region of the gene, in an intron, or in the 3&apos; untranslated region. Cis-elements are often binding sites of one or more trans-acting factors.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0442">
-        <rdfs:label>Transcription regulatory element prediction (RNA-cis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:comment>Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene&apos;s activity.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0443">
-        <rdfs:label>Transcription regulatory element prediction (trans)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Trans-regulatory elements regulate genes distant from the gene from which they were transcribed.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Functional RNA identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0444">
-        <rdfs:label>Matrix/scaffold attachment site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:comment>MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0445">
-        <rdfs:label>Transcription factor binding site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0440"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict transcription factor binding sites in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0446">
-        <rdfs:label>Exonic splicing enhancer prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0440"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify or predict exonic splicing enhancers (ESE) in exons.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0447">
-        <rdfs:label>Sequence alignment validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:comment>Evaluation might be purely sequence-based or use structural information.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence alignment quality evaluation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Evaluate molecular sequence alignment accuracy.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0448">
-        <rdfs:label>Sequence alignment analysis (conservation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Residue conservation analysis</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0449 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0449">
-        <rdfs:label>Sequence alignment analysis (site correlation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3465"/>
-        <oboInOwl:hasDefinition>Analyse correlations between sites in a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0450 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0450">
-        <rdfs:label>Chimeric sequence detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles.</rdfs:comment>
-        <oboInOwl:hasDefinition>Detects chimeric sequences (chimeras) from a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (chimeric sequence detection)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0451">
-        <rdfs:label>Recombination detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (recombination detection)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment.</oboInOwl:hasDefinition>
-        <rdfs:comment>Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0452">
-        <rdfs:label>Indel detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (indel detection)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify insertion, deletion and duplication events from a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0453">
-        <rdfs:label>Nucleosome formation potential prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Predict nucleosome formation potential of DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0432"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0455 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0455">
-        <rdfs:label>Nucleic acid thermodynamic property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2985"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0456">
-        <rdfs:label>Nucleic acid melting profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1583"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA melting profile.</oboInOwl:hasDefinition>
-        <rdfs:comment>A melting profile is used to visualise and analyse partly melted DNA conformations.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0457">
-        <rdfs:label>Nucleic acid stitch profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1587"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA stitch profile.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0458 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0458">
-        <rdfs:label>Nucleic acid melting curve plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2958"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA melting curve.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0459">
-        <rdfs:label>Nucleic acid probability profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2959"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA probability profile.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0460">
-        <rdfs:label>Nucleic acid temperature profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2960"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA temperature profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0461">
-        <rdfs:label>Nucleic acid curvature calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0912"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate curvature and flexibility / stiffness of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes properties such as.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0463">
-        <rdfs:label>microRNA detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0443"/>
-        <oboInOwl:hasDefinition>Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0464">
-        <rdfs:label>tRNA gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0425"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or predict tRNA genes in genomic sequences (tRNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0465">
-        <rdfs:label>siRNA binding specificity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0467">
-        <rdfs:label>Protein secondary structure prediction (integrated)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <oboInOwl:hasDefinition>Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0468">
-        <rdfs:label>Protein secondary structure prediction (helices)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict helical secondary structure of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0469">
-        <rdfs:label>Protein secondary structure prediction (turns)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <oboInOwl:hasDefinition>Predict turn structure (for example beta hairpin turns) of protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0470">
-        <rdfs:label>Protein secondary structure prediction (coils)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0471">
-        <rdfs:label>Protein secondary structure prediction (disulfide bonds)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict cysteine bonding state and disulfide bond partners in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0472">
-        <rdfs:label>GPCR prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0269"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0473"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>G protein-coupled receptor (GPCR) prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict G protein-coupled receptors (GPCR).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0473">
-        <rdfs:label>GPCR analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0270"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0820"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse G-protein coupled receptor proteins (GPCRs).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>G protein-coupled receptor (GPCR) analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0474">
-        <rdfs:label>Protein structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0271"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0172"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict tertiary structure (backbone and side-chain conformation) of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0475">
-        <rdfs:label>Nucleic acid structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0271"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1459"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might identify thermodynamically stable or evolutionarily conserved structures.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict tertiary structure of DNA or RNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0476">
-        <rdfs:label>Ab initio structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0474"/>
-        <oboInOwl:hasDefinition>Predict tertiary structure of protein sequence(s) without homologs of known structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>de novo structure prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0477 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0477">
-        <rdfs:label>Protein modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0474"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2275"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Comparative modelling</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Build a three-dimensional protein model based on known (for example homologs) structures.</oboInOwl:hasDefinition>
-        <rdfs:comment>The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Homology modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Homology structure modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure comparative modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0478">
-        <rdfs:label>Molecular docking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0177"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1461"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2877"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Model the structure of a protein in complex with a small molecule or another macromolecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Docking simulation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein docking</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0479">
-        <rdfs:label>Protein modelling (backbone)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <oboInOwl:hasDefinition>Model protein backbone conformation.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods might require a preliminary C(alpha) trace.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0480">
-        <rdfs:label>Protein modelling (side chains)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might use a residue rotamer library.</rdfs:comment>
-        <oboInOwl:hasDefinition>Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0481">
-        <rdfs:label>Protein modelling (loops)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Model loop conformation in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0482">
-        <rdfs:label>Protein-ligand docking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1461"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Ligand-binding simulation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Virtual ligand screening</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0483">
-        <rdfs:label>Structured RNA prediction and optimisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3095"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1234"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Nucleic acid folding family identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA inverse folding</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0484 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0484">
-        <rdfs:label>SNP detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3202"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <oboInOwl:hasDefinition>Find single nucleotide polymorphisms (SNPs) between sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Single nucleotide polymorphism detection</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0485">
-        <rdfs:label>Radiation Hybrid Mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2870"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0486">
-        <rdfs:label>Functional mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).</rdfs:comment>
-        <oboInOwl:hasDefinition>Map the genetic architecture of dynamic complex traits.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0282"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0487">
-        <rdfs:label>Haplotype mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0282"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0283"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Haplotype map generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Haplotype inference</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual&apos;s haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Haplotype reconstruction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0488">
-        <rdfs:label>Linkage disequilibrium calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0283"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0927"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0489">
-        <rdfs:label>Genetic code prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict genetic code from analysis of codon usage data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0490">
-        <rdfs:label>Dotplot plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0288"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0565"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0862"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Draw a dotplot of sequence similarities identified from word-matching or character comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0491">
-        <rdfs:label>Pairwise sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1381"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasDefinition>Align exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0492">
-        <rdfs:label>Multiple sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0493 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0493">
-        <rdfs:label>Pairwise sequence alignment generation (local)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Local pairwise sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Locally align exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment (local)</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Local alignment methods identify regions of local similarity.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment construction (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0491"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0494 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0494">
-        <rdfs:label>Pairwise sequence alignment generation (global)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Global pairwise sequence alignment construction</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Globally align exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Global alignment methods identify similarity across the entire length of the sequences.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0491"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0496"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0495">
-        <rdfs:label>Local sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Local multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Local alignment methods identify regions of local similarity.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Locally align two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0496">
-        <rdfs:label>Global sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Global multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (global)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Globally align two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (global)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Global alignment methods identify similarity across the entire length of the sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0497">
-        <rdfs:label>Constrained sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences with user-defined constraints.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Constrained multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0498">
-        <rdfs:label>Consensus-based sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Consensus multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment (consensus)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences using multiple methods to achieve higher quality.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0499">
-        <rdfs:label>Tree-based sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is supposed to give a more biologically meaningful alignment than standard alignments.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree-based multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0500">
-        <rdfs:label>Secondary structure alignment generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Align molecular secondary structure (represented as a 1D string).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2928"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0501">
-        <rdfs:label>Protein secondary structure alignment generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2488"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0878"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Protein secondary structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align protein secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein secondary structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0502">
-        <rdfs:label>RNA secondary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0881"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>RNA secondary structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA secondary structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align RNA secondary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA secondary structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment (RNA)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0503">
-        <rdfs:label>Pairwise structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align (superimpose) exactly two molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0504">
-        <rdfs:label>Multiple structure alignment construction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Align (superimpose) two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that use an existing alignment.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0505">
-        <rdfs:label>Structure alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align protein tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0506">
-        <rdfs:label>Structure alignment (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Align RNA tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0507">
-        <rdfs:label>Pairwise structure alignment generation (local)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Locally align (superimpose) exactly two molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment (local)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Local alignment methods identify regions of local similarity, common substructures etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment construction (local)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Local pairwise structure alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0509"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0508">
-        <rdfs:label>Pairwise structure alignment generation (global)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Global pairwise structure alignment construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Global alignment methods identify similarity across the entire structures.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Globally align (superimpose) exactly two molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0510"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0509">
-        <rdfs:label>Local structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:hasExactSynonym>Local multiple structure alignment construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Local alignment methods identify regions of local similarity, common substructures etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Structure alignment construction (local)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Locally align (superimpose) two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment construction (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure alignment generation (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0510 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0510">
-        <rdfs:label>Global structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:hasExactSynonym>Structure alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure alignment generation (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment construction (global)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Global alignment methods identify similarity across the entire structures.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Global multiple structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Globally align (superimpose) two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0511">
-        <rdfs:label>Profile-to-profile alignment (pairwise)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0298"/>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (pairwise profile)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise sequence profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment construction (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment (pairwise)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align exactly two molecular profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment generation (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0512">
-        <rdfs:label>Sequence alignment generation (multiple profile)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Align two or more molecular profiles.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment generation (multiple)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment construction (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0513 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0513">
-        <rdfs:label>3D profile-to-3D profile alignment (pairwise)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0299"/>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise structural (3D) profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural (3D) profile alignment (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align exactly two molecular Structural (3D) profiles.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structural profile alignment generation (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0514">
-        <rdfs:label>Structural profile alignment generation (multiple)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align two or more molecular 3D profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Multiple structural (3D) profile alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structural (3D) profile alignment (multiple)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0299"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0515">
-        <rdfs:label>Data retrieval (tool metadata)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Data retrieval (tool annotation)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Tool information retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0304"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0516">
-        <rdfs:label>Data retrieval (database metadata)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Data retrieval (database annotation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database information retrieval</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0304"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0517 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0517">
-        <rdfs:label>PCR primer design (for large scale sequencing)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict primers for large scale sequencing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0518 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0518">
-        <rdfs:label>PCR primer design (for genotyping polymorphisms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0519">
-        <rdfs:label>PCR primer design (for gene transcription profiling)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict primers for gene transcription profiling.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0520">
-        <rdfs:label>PCR primer design (for conserved primers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <oboInOwl:hasDefinition>Predict primers that are conserved across multiple genomes or species.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0521">
-        <rdfs:label>PCR primer design (based on gene structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict primers based on gene structure, promoters, exon-exon junctions etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0522">
-        <rdfs:label>PCR primer design (for methylation PCRs)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict primers for methylation PCRs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0523">
-        <rdfs:label>Sequence assembly (mapping assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0524">
-        <rdfs:label>Sequence assembly (de-novo assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Sequence assembly by combining fragments without the aid of a reference sequence or genome.</oboInOwl:hasDefinition>
-        <rdfs:comment>De-novo assemblers are much slower and more memory intensive than mapping assemblers.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0525">
-        <rdfs:label>Sequence assembly (genome assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Sequence assembly capable on a very large scale such as assembly of whole genomes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0526">
-        <rdfs:label>Sequence assembly (EST assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence assembly for EST sequences (transcribed mRNA).</oboInOwl:hasDefinition>
-        <rdfs:comment>Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0527">
-        <rdfs:label>Tag mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2520"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0936"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Tag to gene assignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0528">
-        <rdfs:label>SAGE data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Serial analysis of gene expression data processing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) serial analysis of gene expression (SAGE) data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0529">
-        <rdfs:label>MPSS data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) massively parallel signature sequencing (MPSS) data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Massively parallel signature sequencing data processing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0530">
-        <rdfs:label>SBS data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequencing by synthesis data processing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) sequencing by synthesis (SBS) data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0531">
-        <rdfs:label>Heat map generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1636"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Heat map construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a heat map of gene expression from microarray data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0532 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0532">
-        <rdfs:label>Gene expression profile analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Functional profiling</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse one or more gene expression profiles, typically to interpret them in functional terms.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0533">
-        <rdfs:label>Gene expression profile pathway mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2497"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0534">
-        <rdfs:label>Protein secondary structure assignment (from coordinate data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0319"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign secondary structure from protein coordinate data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0535 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0535">
-        <rdfs:label>Protein secondary structure assignment (from CD data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0319"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0939"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Assign secondary structure from circular dichroism (CD) spectroscopic data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0536">
-        <rdfs:label>Protein structure assignment (from X-ray crystallographic data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0320"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0537">
-        <rdfs:label>Protein structure assignment (from NMR data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0320"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0538 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0538">
-        <rdfs:label>Phylogenetic tree generation (data centric)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (data centric)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree from a specific type of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0539">
-        <rdfs:label>Phylogenetic tree generation (method centric)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (method centric)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree using a specific method.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0540">
-        <rdfs:label>Phylogenetic tree generation (from molecular sequences)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (from molecular sequences)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0541 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0541">
-        <rdfs:label>Phylogenetic tree generation (from continuous quantitative characters)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1426"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (from continuous quantitative characters)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from continuous quantitative character data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0542">
-        <rdfs:label>Phylogenetic tree generation (from gene frequencies)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2873"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (from gene frequencies)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from gene frequency data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0543">
-        <rdfs:label>Phylogenetic tree construction (from polymorphism data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree generation (from polymorphism data)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0544 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0544">
-        <rdfs:label>Phylogenetic species tree construction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0540"/>
-        <oboInOwl:hasDefinition>Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic species tree generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0545">
-        <rdfs:label>Phylogenetic tree generation (parsimony methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (parsimony methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes evolutionary parsimony (invariants) methods.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0546">
-        <rdfs:label>Phylogenetic tree generation (minimum distance methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <rdfs:comment>This includes neighbor joining (NJ) clustering method.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (minimum distance methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0547">
-        <rdfs:label>Phylogenetic tree generation (maximum likelihood and Bayesian methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (maximum likelihood and Bayesian methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution.</oboInOwl:hasDefinition>
-        <rdfs:comment>Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0548">
-        <rdfs:label>Phylogenetic tree generation (quartet methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (quartet methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0549">
-        <rdfs:label>Phylogenetic tree generation (AI methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (AI methods)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0550">
-        <rdfs:label>DNA substitution modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1439"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (phylogenetic modelling)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify a plausible model of DNA substitution that explains a DNA sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0551">
-        <rdfs:label>Phylogenetic tree analysis (shape)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree topology analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse the shape (topology) of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0552">
-        <rdfs:label>Phylogenetic tree bootstrapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <oboInOwl:hasDefinition>Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0553">
-        <rdfs:label>Phylogenetic tree analysis (gene family prediction)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0194"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict families of genes and gene function based on their position in a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0554">
-        <rdfs:label>Phylogenetic tree analysis (natural selection)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0555">
-        <rdfs:label>Phylogenetic tree generation (consensus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0325"/>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees to produce a consensus tree.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods typically test for topological similarity between trees using for example a congruence index.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0556">
-        <rdfs:label>Phylogenetic sub/super tree detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0325"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees to detect subtrees or supertrees.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0557">
-        <rdfs:label>Phylogenetic tree distances calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0325"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1442"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees to calculate distances between trees.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0558">
-        <rdfs:label>Phylogenetic tree annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Annotate a phylogenetic tree with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0559">
-        <rdfs:label>Immunogenicity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0252"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide immunogen prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict and optimise peptide ligands that elicit an immunological response.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0560">
-        <rdfs:label>DNA vaccine design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2430"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3095"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict or optimise DNA to elicit (via DNA vaccination) an immunological response.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0561">
-        <rdfs:label>Sequence formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Reformat (a file or other report of) molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence file format conversion</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0562 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0562">
-        <rdfs:label>Sequence alignment formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Reformat (a file or other report of) molecular sequence alignment(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0563">
-        <rdfs:label>Codon usage table formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2433"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Reformat a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0564">
-        <rdfs:label>Sequence visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2969"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render a molecular sequence, possibly with sequence features or properties shown.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0565">
-        <rdfs:label>Sequence alignment visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1711"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise, format or print a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0566">
-        <rdfs:label>Sequence cluster visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence cluster rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render sequence clusters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0567">
-        <rdfs:label>Phylogenetic tree visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Render or visualise a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0568">
-        <rdfs:label>RNA secondary structure visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>RNA secondary structure rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise RNA secondary structure, knots, pseudoknots etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0569">
-        <rdfs:label>Protein secondary structure rendering</rdfs:label>
-        <rdfs:label>Protein secondary structure visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Render and visualise protein secondary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0570">
-        <rdfs:label>Structure visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1710"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structure rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0571">
-        <rdfs:label>Microarray data rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3117"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise microarray data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0572">
-        <rdfs:label>Protein interaction network rendering</rdfs:label>
-        <rdfs:label>Protein interaction network visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3083"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym></oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify and analyse networks of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0573">
-        <rdfs:label>Map drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>DNA map drawing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Map rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Draw or visualise a DNA map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0574">
-        <rdfs:label>Sequence motif rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Render a sequence with motifs.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0575">
-        <rdfs:label>Restriction map drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0431"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0573"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1289"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Draw or visualise restriction maps in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0577 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0577">
-        <rdfs:label>DNA linear map rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Draw a linear maps of DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0573"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0578">
-        <rdfs:label>Plasmid map drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0573"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasBroadSynonym>DNA circular map rendering</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Draw a circular maps of DNA, for example a plasmid map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0579">
-        <rdfs:label>Operon drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0573"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise operon structure etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Operon rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1768 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1768">
-        <rdfs:label>Nucleic acid folding family identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identify folding families of related RNAs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0483"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1769 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1769">
-        <rdfs:label>Nucleic acid folding energy calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0279"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1774 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1774">
-        <rdfs:label>Annotation retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations.</rdfs:comment>
-        <oboInOwl:hasDefinition>Retrieve existing annotation (or documentation), typically annotation on a database entity.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1777 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1777">
-        <rdfs:label>Protein function prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2414"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict general functional properties of a protein.</oboInOwl:hasDefinition>
-        <rdfs:comment>For functional properties that can be mapped to a sequence, use &apos;Sequence feature detection (protein)&apos; instead.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1778 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1778">
-        <rdfs:label>Protein function comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2414"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare the functional properties of two or more proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1780 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1780">
-        <rdfs:label>Sequence submission</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Submit a molecular sequence to a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_3431"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1781 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1781">
-        <rdfs:label>Gene regulatory network analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2497"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2846"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse a known network of gene regulation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_1781"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1812 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1812">
-        <rdfs:label>Loading</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0842"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Data loading</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>WHATIF:UploadPDB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Prepare or load a user-specified data file so that it is available for use.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1813 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1813">
-        <rdfs:label>Sequence retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Data retrieval (sequences)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1814 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1814">
-        <rdfs:label>Structure retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>WHATIF:EchoPDB</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:DownloadPDB</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes direct retrieval methods but not those that perform calculations on the sequence or structure.</rdfs:comment>
-        <oboInOwl:hasDefinition>Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1816 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1816">
-        <rdfs:label>Surface rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0570"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2462"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:GetSurfaceDots</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate the positions of dots that are homogeneously distributed over the surface of a molecule.</oboInOwl:hasDefinition>
-        <rdfs:comment>A dot has three coordinates (x,y,z) and (typically) a color.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1817 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1817">
-        <rdfs:label>Protein atom surface calculation (accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilitySolventPlus</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilitySolvent</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible surface&apos;) for each atom in a structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>Waters are not considered.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1818 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1818">
-        <rdfs:label>Protein atom surface calculation (accessible molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible molecular surface&apos;) for each atom in a structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>Waters are not considered.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilityMolecular</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilityMolecularPlus</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1819 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1819">
-        <rdfs:label>Protein residue surface calculation (accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilitySolvent</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible surface&apos;) for each residue in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1820 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1820">
-        <rdfs:label>Protein residue surface calculation (vacuum accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;vacuum accessible surface&apos;) for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilityVacuum</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1821 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1821">
-        <rdfs:label>Protein residue surface calculation (accessible molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible molecular surface&apos;) for each residue in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilityMolecular</oboInOwl:hasDbXref>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1822 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1822">
-        <rdfs:label>Protein residue surface calculation (vacuum molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;vacuum molecular surface&apos;) for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilityVacuumMolecular</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1823 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1823">
-        <rdfs:label>Protein surface calculation (accessible molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2462"/>
-        <oboInOwl:hasDbXref>WHATIF:TotAccessibilityMolecular</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible molecular surface&apos;) for a structure as a whole.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1824 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1824">
-        <rdfs:label>Protein surface calculation (accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2462"/>
-        <oboInOwl:hasDbXref>WHATIF:TotAccessibilitySolvent</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible surface&apos;) for a structure as a whole.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1825 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1825">
-        <rdfs:label>Backbone torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ResidueTorsionsBB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate for each residue in a protein structure all its backbone torsion angles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1826 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1826">
-        <rdfs:label>Full torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate for each residue in a protein structure all its torsion angles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueTorsions</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1827 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1827">
-        <rdfs:label>Cysteine torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate for each cysteine (bridge) all its torsion angles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:CysteineTorsions</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1828 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1828">
-        <rdfs:label>Tau angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowTauAngle</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Tau is the backbone angle N-Calpha-C (angle over the C-alpha).</rdfs:comment>
-        <oboInOwl:hasDefinition>For each amino acid in a protein structure calculate the backbone angle tau.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1829 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1829">
-        <rdfs:label>Cysteine bridge detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1850"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowCysteineBridge</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Detect cysteine bridges (from coordinate data) in a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1830 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1830">
-        <rdfs:label>Free cysteine detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1850"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal.</rdfs:comment>
-        <oboInOwl:hasDefinition>Detect free cysteines in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ShowCysteineFree</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1831 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1831">
-        <rdfs:label>Metal-bound cysteine detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1850"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ShowCysteineMetal</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Detect cysteines that are bound to metal in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1832 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1832">
-        <rdfs:label>Residue contact calculation (residue-nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0245"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0389"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ShowProteiNucleicContacts</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate protein residue contacts with nucleic acids in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:HasNucleicContacts</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1834 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1834">
-        <rdfs:label>Residue contact calculation (residue-metal)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0388"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <oboInOwl:hasDbXref>WHATIF:HasMetalContacts</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate protein residue contacts with metal in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:HasMetalContactsPlus</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1835 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1835">
-        <rdfs:label>Residue contact calculation (residue-negative ion)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <oboInOwl:hasDefinition>Calculate ion contacts in a structure (all ions for all side chain atoms).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:HasNegativeIonContactsPlus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:HasNegativeIonContacts</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1836 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1836">
-        <rdfs:label>Residue bump detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0395"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowBumps</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect &apos;bumps&apos; between residues in a structure, i.e. those with pairs of atoms whose Van der Waals&apos; radii interpenetrate more than a defined distance.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1837 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1837">
-        <rdfs:label>Residue symmetry contact calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <oboInOwl:hasDefinition>Calculate the number of symmetry contacts made by residues in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:SymmetryContact</oboInOwl:hasDbXref>
-        <rdfs:comment>A symmetry contact is a contact between two atoms in different asymmetric unit.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1838 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1838">
-        <rdfs:label>Residue contact calculation (residue-ligand)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0388"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate contacts between residues and ligands in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ShowDrugContactsShort</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLigandContacts</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowDrugContacts</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1839 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1839">
-        <rdfs:label>Salt bridge calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <rdfs:comment>Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF:HasSaltBridgePlus</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowSaltBridges</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:HasSaltBridge</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowSaltBridgesH</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate (and possibly score) salt bridges in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1841 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1841">
-        <rdfs:label>Rotamer likelihood prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0480"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers500</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers800</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers600</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers900</oboInOwl:hasDbXref>
-        <rdfs:comment>Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers700</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers400</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers300</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers200</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers100</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1842 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1842">
-        <rdfs:label>Proline mutation value calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0331"/>
-        <oboInOwl:hasDefinition>Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ProlineMutationValue</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1843 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1843">
-        <rdfs:label>Residue packing validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0395"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify poorly packed residues in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: PackingQuality</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1844 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1844">
-        <rdfs:label>Dihedral angle validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <oboInOwl:hasDbXref>WHATIF: ImproperQualitySum</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identify for each residue in a protein structure any improper dihedral (phi/psi) angles.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: ImproperQualityMax</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1845 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1845">
-        <rdfs:label>PDB file sequence retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Extract a molecular sequence from a PDB file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDbXref>WHATIF: PDB_sequence</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0344"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1846 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1846">
-        <rdfs:label>HET group detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1838"/>
-        <oboInOwl:hasDefinition>Identify HET groups in PDB files.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: HETGroupNames</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1847 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1847">
-        <rdfs:label>DSSP secondary structure assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Determine for residue the DSSP determined secondary structure in three-state (HSC).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: ResidueDSSP</oboInOwl:hasDbXref>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0534"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1848 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1848">
-        <rdfs:label>Structure formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <oboInOwl:hasDefinition>Reformat (a file or other report of) tertiary structure data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: PDBasXML</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1850 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1850">
-        <rdfs:label>Protein cysteine and disulfide bond assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0534"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Assign cysteine bonding state and disulfide bond partners in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1913 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1913">
-        <rdfs:label>Residue validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <oboInOwl:hasDefinition>Identify poor quality amino acid positions in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: UseResidueDB</oboInOwl:hasDbXref>
-        <rdfs:comment>The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1914 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1914">
-        <rdfs:label>Structure retrieval (water)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDbXref>WHATIF:MovedWaterPDB</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query a tertiary structure database and retrieve water molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2008 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2008">
-        <rdfs:label>siRNA duplex prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict siRNA duplexes in RNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2089 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2089">
-        <rdfs:label>Sequence alignment refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2425"/>
-        <oboInOwl:hasDefinition>Refine an existing sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2120 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2120">
-        <rdfs:label>Listfile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2121 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2121">
-        <rdfs:label>Sequence file editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2122">
-        <rdfs:label>Sequence alignment file processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2123">
-        <rdfs:label>Small molecule data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) physicochemical property data for small molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2222 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2222">
-        <rdfs:label>Data retrieval (ontology annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Ontology information retrieval</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search and retrieve documentation on a bioinformatics ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2224 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2224">
-        <rdfs:label>Data retrieval (ontology concept)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query an ontology and retrieve concepts or relations.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2233">
-        <rdfs:label>Representative sequence identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2234 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2234">
-        <rdfs:label>Structure file processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Perform basic (non-analytical) operations on a file of molecular tertiary structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2237">
-        <rdfs:label>Data retrieval (sequence profile)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query a profile data resource and retrieve one or more profile(s) and / or associated annotation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This includes direct retrieval methods that retrieve a profile by, e.g. the profile name.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2238">
-        <rdfs:label>Statistical calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <oboInOwl:hasExactSynonym>Statistical analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Perform a statistical data operation of some type, e.g. calibration or validation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2239">
-        <rdfs:label>3D-1D scoring matrix generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1499"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>3D-1D scoring matrix construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2241">
-        <rdfs:label>Transmembrane protein visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0270"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0569"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2992"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise transmembrane proteins, typically the transmembrane regions within a sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Transmembrane protein rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2246">
-        <rdfs:label>Demonstration</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An operation performing purely illustrative (pedagogical) purposes.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2264">
-        <rdfs:label>Data retrieval (pathway or network)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query a biological pathways database and retrieve annotation on one or more pathways.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2265">
-        <rdfs:label>Data retrieval (identifier)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Query a database and retrieve one or more data identifiers.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2284">
-        <rdfs:label>Nucleic acid density plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a density plot (of base composition) for a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2403">
-        <rdfs:label>Sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse one or more known molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence analysis (general)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2404">
-        <rdfs:label>Sequence motif processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular sequence motifs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0239"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2405">
-        <rdfs:label>Protein interaction data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) protein interaction data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2406">
-        <rdfs:label>Protein structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structure analysis (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse protein tertiary structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2407">
-        <rdfs:label>Annotation processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2408">
-        <rdfs:label>Sequence feature analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Analyse features in molecular sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0253"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2409">
-        <rdfs:label>Utility operation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0220"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Basic (non-analytical) operations of some data, either a file or equivalent entity in memory.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>File processing</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Report handling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File handling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data file processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2410">
-        <rdfs:label>Gene expression analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse gene expression and regulation data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2411">
-        <rdfs:label>Structural profile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>3D profile processing</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2952"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2412">
-        <rdfs:label>Data index processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Database index processing</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) an index of (typically a file of) biological data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0227"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2413">
-        <rdfs:label>Sequence profile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) some type of sequence profile.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2463"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2414">
-        <rdfs:label>Protein function analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2415">
-        <rdfs:label>Protein folding analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1537"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein folding modelling</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2416">
-        <rdfs:label>Protein secondary structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2956"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse known protein secondary structure data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Secondary structure analysis (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2417">
-        <rdfs:label>Physicochemical property data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) data on the physicochemical property of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2419">
-        <rdfs:label>Primer and probe design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3095"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Primer and probe prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict oligonucleotide primers or probes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2420">
-        <rdfs:label>Operation (typed)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <oboInOwl:hasExactSynonym>Computation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Calculation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) data of a specific type, for example applying analytical methods.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2421">
-        <rdfs:label>Database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0224"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database.</rdfs:comment>
-        <oboInOwl:hasDefinition>Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2422">
-        <rdfs:label>Data retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0224"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0842"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasBroadSynonym>Information retrieval</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2423">
-        <rdfs:label>Prediction and recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise, detect or identify some properties of a biomolecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Detection</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2424">
-        <rdfs:label>Comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more things to identify similarities.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2425">
-        <rdfs:label>Optimisation and refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Refine or optimise some data model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2426">
-        <rdfs:label>Modelling and simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2275"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Model or simulate some biological entity or system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2427">
-        <rdfs:label>Data handling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Perform basic operations on some data or a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2428">
-        <rdfs:label>Validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Validation and standardisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Validate some data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2429">
-        <rdfs:label>Mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <oboInOwl:hasDefinition>Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2430">
-        <rdfs:label>Design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Design a biological entity (typically a molecular sequence or structure) with specific properties.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2432">
-        <rdfs:label>Microarray data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) microarray data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2433">
-        <rdfs:label>Codon usage table processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2434">
-        <rdfs:label>Data retrieval (codon usage table)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve a codon usage table and / or associated annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2435">
-        <rdfs:label>Gene expression profile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) a gene expression profile.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2436">
-        <rdfs:label>Functional enrichment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression profile annotation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The Gene Ontology (GO) is invariably used, the input is a set of Gene IDs and the output of the analysis is typically a ranked list of GO terms, each associated with a p-value.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse a set of genes (genes corresponding to an expression profile, or any other set) with respect to concepts from an ontology of gene functions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>GO term enrichment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2437">
-        <rdfs:label>Gene regulatory network prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2846"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict a network of gene regulation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2438">
-        <rdfs:label>Pathway or network processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Generate, analyse or handle a biological pathway or network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2439">
-        <rdfs:label>RNA secondary structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2481"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) RNA secondary structure data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2440">
-        <rdfs:label>Structure processing (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) RNA tertiary structure data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2519"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2441">
-        <rdfs:label>RNA structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0475"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1465"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict RNA tertiary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2442">
-        <rdfs:label>DNA structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0475"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1464"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict DNA tertiary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2443">
-        <rdfs:label>Phylogenetic tree processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2444">
-        <rdfs:label>Protein secondary structure processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) protein secondary structure data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2416"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2445">
-        <rdfs:label>Protein interaction network processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a network of protein interactions.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2446">
-        <rdfs:label>Sequence processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence processing (general)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) one or more molecular sequences and associated annotation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2403"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2447">
-        <rdfs:label>Sequence processing (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a protein sequence and associated annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2446"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2448">
-        <rdfs:label>Sequence processing (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a nucleotide sequence and associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2446"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2451">
-        <rdfs:label>Sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare two or more molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2452">
-        <rdfs:label>Sequence cluster processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a sequence cluster.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0291"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2453">
-        <rdfs:label>Feature table processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a sequence feature table.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2446"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2454 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2454">
-        <rdfs:label>Gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Gene and gene component prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect, predict and identify genes or components of genes in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene finding</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2456">
-        <rdfs:label>GPCR classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0473"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2995"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>G protein-coupled receptor (GPCR) classification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Classify G-protein coupled receptors (GPCRs) into families and subfamilies.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2457">
-        <rdfs:label>GPCR coupling selectivity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0473"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict G-protein coupled receptor (GPCR) coupling selectivity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2459">
-        <rdfs:label>Structure processing (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a protein tertiary structure.</oboInOwl:hasDefinition>
-        <rdfs:comment rdf:resource="http://edamontology.org/operation_2406"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2460">
-        <rdfs:label>Protein atom surface calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0387"/>
-        <rdfs:comment>Waters are not considered.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility for each atom in a structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2461">
-        <rdfs:label>Protein residue surface calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0387"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility for each residue in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2462 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2462">
-        <rdfs:label>Protein surface calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0387"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility of a structure as a whole.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2463">
-        <rdfs:label>Sequence alignment processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2464">
-        <rdfs:label>Protein-protein interaction prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or predict protein-protein interactions, interfaces, binding sites etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2465">
-        <rdfs:label>Structure processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular tertiary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2480"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2466 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2466">
-        <rdfs:label>Map annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Annotate a DNA map of some type with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0362"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2467">
-        <rdfs:label>Data retrieval (protein annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve information on a protein.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Protein information retrieval</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2468">
-        <rdfs:label>Data retrieval (phylogenetic tree)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Retrieve a phylogenetic tree from a data resource.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2469">
-        <rdfs:label>Data retrieval (protein interaction annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve information on a protein interaction.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2470">
-        <rdfs:label>Data retrieval (protein family annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein family information retrieval</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Retrieve information on a protein family.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2471">
-        <rdfs:label>Data retrieval (RNA family annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Retrieve information on an RNA family.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA family information retrieval</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2472">
-        <rdfs:label>Data retrieval (gene annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene information retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Retrieve information on a specific gene.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2473">
-        <rdfs:label>Data retrieval (genotype and phenotype annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve information on a specific genotype or phenotype.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genotype and phenotype information retrieval</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2474">
-        <rdfs:label>Protein architecture comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0247"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2488"/>
-        <oboInOwl:hasDefinition>Compare the architecture of two or more protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2475">
-        <rdfs:label>Protein architecture recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0247"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2996"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify the architecture of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2476">
-        <rdfs:label>Molecular dynamics simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0176"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2478">
-        <rdfs:label>Nucleic acid sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence analysis (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2479">
-        <rdfs:label>Protein sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2976"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a protein sequence (using methods that are only applicable to protein sequences).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence analysis (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2480">
-        <rdfs:label>Structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0081"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse known molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2481">
-        <rdfs:label>Nucleic acid structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1459"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse nucleic acid tertiary structural data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2482">
-        <rdfs:label>Secondary structure processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular secondary structure.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2465"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2483">
-        <rdfs:label>Structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2485">
-        <rdfs:label>Helical wheel drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0569"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2162"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Helical wheel rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Render a helical wheel representation of protein secondary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2486">
-        <rdfs:label>Topology diagram drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0569"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2992"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Topology diagram rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Render a topology diagram of protein secondary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2487">
-        <rdfs:label>Protein structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure comparison (protein)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might identify structural neighbors, find structural similarities or define a structural core.</rdfs:comment>
-        <oboInOwl:hasDefinition>Compare protein tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2488">
-        <rdfs:label>Protein secondary structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2416"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2931"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <oboInOwl:hasDefinition>Compare protein secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Secondary structure comparison (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein secondary structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2489">
-        <rdfs:label>Protein subcellular localization prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1777"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0140"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict the subcellular localization of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein targeting prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2490">
-        <rdfs:label>Residue contact calculation (residue-residue)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate contacts between residues in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2491">
-        <rdfs:label>Hydrogen bond calculation (inter-residue)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0394"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <oboInOwl:hasDefinition>Identify potential hydrogen bonds between amino acid residues.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2492">
-        <rdfs:label>Protein interaction prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict the interactions of proteins with other molecules.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2493 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2493">
-        <rdfs:label>Codon usage data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) codon usage data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0286"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2495">
-        <rdfs:label>Gene expression data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider>Gene expression profile analysis</oboInOwl:consider>
-        <oboInOwl:hasExactSynonym>Gene expression (microarray) data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene expression data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2496">
-        <rdfs:label>Gene regulatory network processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a network of gene regulation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2497">
-        <rdfs:label>Pathway or network analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a known biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Network analysis</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2498">
-        <rdfs:label>Sequencing-based expression profile data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2499">
-        <rdfs:label>Splicing model analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Splicing analysis</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2500">
-        <rdfs:label>Microarray raw data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Analyse raw microarray data.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2501">
-        <rdfs:label>Nucleic acid analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Process (read and / or write) nucleic acid sequence or structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid data processing</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2502">
-        <rdfs:label>Protein analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0078"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) protein sequence or structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2503">
-        <rdfs:label>Sequence data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular sequence data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2504">
-        <rdfs:label>Structural data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2465"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2505">
-        <rdfs:label>Text processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) text.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0306"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2506">
-        <rdfs:label>Protein sequence alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1384"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a protein sequence alignment, typically to detect features or make predictions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2507">
-        <rdfs:label>Nucleic acid sequence alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2501"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1383"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse a protein sequence alignment, typically to detect features or make predictions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2508">
-        <rdfs:label>Nucleic acid sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <oboInOwl:hasExactSynonym>Sequence comparison (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Compare two or more nucleic acid sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2509">
-        <rdfs:label>Protein sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence comparison (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Compare two or more protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2510 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2510">
-        <rdfs:label>DNA back-translation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0108"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Back-translate a protein sequence into DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2511">
-        <rdfs:label>Sequence editing (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Edit or change a nucleic acid sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2512">
-        <rdfs:label>Sequence editing (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Edit or change a protein sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2513 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2513">
-        <rdfs:label>Sequence generation (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <oboInOwl:hasDefinition>Generate a nucleic acid sequence by some means.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2514">
-        <rdfs:label>Sequence generation (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <oboInOwl:hasDefinition>Generate a protein sequence by some means.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2515">
-        <rdfs:label>Nucleic acid sequence visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Visualise, format or render a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.</rdfs:comment>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2516">
-        <rdfs:label>Protein sequence visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render a protein sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <rdfs:comment>Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2518 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2518">
-        <rdfs:label>Nucleic acid structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2481"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <oboInOwl:hasDefinition>Compare nucleic acid tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure comparison (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2519">
-        <rdfs:label>Structure processing (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) nucleic acid tertiary structure data.</oboInOwl:hasDefinition>
-        <rdfs:comment rdf:resource="http://edamontology.org/operation_2481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2520">
-        <rdfs:label>DNA mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a map of a DNA sequence annotated with positional or non-positional features of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2521">
-        <rdfs:label>Map data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>DNA map data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) a DNA map of some type.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2520"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2574">
-        <rdfs:label>Protein hydropathy calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0250"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2970"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2575">
-        <rdfs:label>Protein binding site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Ligand-binding and active site prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Binding site prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2871 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2871">
-        <rdfs:label>Sequence tagged site (STS) mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1279"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence mapping</oboInOwl:hasExactSynonym>
-        <rdfs:comment>An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2928 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2928">
-        <rdfs:label>Alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Alignment generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2929 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2929">
-        <rdfs:label>Protein fragment weight comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0398"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2930"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2930 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2930">
-        <rdfs:label>Protein property comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare the physicochemical properties of two or more proteins (or reference data).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2931 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2931">
-        <rdfs:label>Secondary structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare two or more molecular secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2932 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2932">
-        <rdfs:label>Hopp and Woods plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0252"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a Hopp and Woods plot of antigenicity of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2934 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2934">
-        <rdfs:label>Microarray cluster textual view generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise gene clusters with gene names.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2935 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2935">
-        <rdfs:label>Microarray wave graph plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasExactSynonym>Microarray wave graph rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray cluster temporal graph rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This view can be rendered as a pie graph.  The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades.</rdfs:comment>
-        <oboInOwl:hasDefinition>Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2936 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2936">
-        <rdfs:label>Microarray dendrograph plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasNarrowSynonym>Microarray dendrograph rendering</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Generate a dendrograph of raw, preprocessed or clustered microarray data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray checks view rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray view rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2937 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2937">
-        <rdfs:label>Microarray proximity map plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray distance map rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a plot of distances (distance matrix) between genes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microarray proximity map rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2938 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2938">
-        <rdfs:label>Microarray tree or dendrogram rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasNarrowSynonym>Microarray 2-way dendrogram rendering</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microarray matrix tree plot rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2939 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2939">
-        <rdfs:label>Microarray principal component plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray principal component rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2940 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2940">
-        <rdfs:label>Microarray scatter plot plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasDefinition>Generate a scatter plot of microarray data, typically after principal component analysis.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray scatter plot rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2941 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2941">
-        <rdfs:label>Whole microarray graph plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasDefinition>Visualise gene expression data where each band (or line graph) corresponds to a sample.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Whole microarray graph rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2942 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2942">
-        <rdfs:label>Microarray tree-map rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise gene expression data after hierarchical clustering for representing hierarchical relationships.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2943 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2943">
-        <rdfs:label>Microarray Box-Whisker plot plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2944 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2944">
-        <rdfs:label>Physical mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2520"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1280"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2945 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2945">
-        <rdfs:label>Analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <oboInOwl:hasDefinition>Apply analytical methods to existing data of a specific type.</oboInOwl:hasDefinition>
-        <rdfs:comment>For non-analytical operations, see the &apos;Processing&apos; branch.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2946 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2946">
-        <rdfs:label>Alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process or analyse an alignment of molecular sequences or structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>1.8</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2928"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2947 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2947">
-        <rdfs:label>Article analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0306"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3068"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2526"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0971"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a body of scientific text (typically a full text article from a scientific journal.)</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Article analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2948 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2948">
-        <rdfs:label>Molecular interaction analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2949 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2949">
-        <rdfs:label>Protein interaction analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2950 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2950">
-        <rdfs:label>Residue contact calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <oboInOwl:hasDefinition>Calculate contacts between residues and some other group in a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2951 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2951">
-        <rdfs:label>Alignment processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2463"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2952"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2952 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2952">
-        <rdfs:label>Structure alignment processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular tertiary (3D) structure alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2962 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2962">
-        <rdfs:label>Codon usage bias calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2865"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate codon usage bias.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2963 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2963">
-        <rdfs:label>Codon usage bias plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2962"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a codon usage bias plot.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2964 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2964">
-        <rdfs:label>Codon usage fraction calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2990 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2990">
-        <rdfs:label>Classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2993 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2993">
-        <rdfs:label>Molecular interaction data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular interaction data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2995 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2995">
-        <rdfs:label>Sequence classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2990"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign molecular sequence(s) to a group or category.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2996 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2996">
-        <rdfs:label>Structure classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2990"/>
-        <oboInOwl:hasDefinition>Assign molecular structure(s) to a group or category.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2997 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2997">
-        <rdfs:label>Protein comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <oboInOwl:hasDefinition>Compare two or more proteins (or some aspect) to identify similarities.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2998 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2998">
-        <rdfs:label>Nucleic acid comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more nucleic acids to identify similarities.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3023 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3023">
-        <rdfs:label>Prediction and recognition (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict, recognise, detect or identify some properties of proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3024 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3024">
-        <rdfs:label>Prediction and recognition (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict, recognise, detect or identify some properties of nucleic acids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3080">
-        <rdfs:label>Structure editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Edit, convert or otherwise change a  molecular tertiary structure, either randomly or specifically.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3081">
-        <rdfs:label>Sequence alignment editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <oboInOwl:hasDefinition>Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3083">
-        <rdfs:label>Pathway or network visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Render (visualise) a biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway or network rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3084">
-        <rdfs:label>Protein function prediction (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Predict general (non-positional) functional properties of a protein from analysing its sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>For functional properties that are positional, use &apos;Protein site detection&apos; instead.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_1777"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3087 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3087">
-        <rdfs:label>Protein sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <oboInOwl:hasNarrowSynonym>Protein site recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein site prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence profile database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein site detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequence feature detection (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3088 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3088">
-        <rdfs:label>Protein property calculation (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0250"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3090 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3090">
-        <rdfs:label>Protein feature prediction (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in proteins from analysing protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_3092"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3092">
-        <rdfs:label>Protein feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1277"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group.
-</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in proteins from analysing protein sequences or structures.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Protein feature recognition</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein feature prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3093 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3093">
-        <rdfs:label>Database search (by sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence screening</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2421"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3094">
-        <rdfs:label>Protein interaction network prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Predict a network of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3095 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3095">
-        <rdfs:label>Nucleic acid design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2430"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Design (or predict) nucleic acid sequences with specific chemical or physical properties.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3096 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3096">
-        <rdfs:label>Editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Edit a data entity, either randomly or specifically.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3180">
-        <rdfs:label>Sequence assembly validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0925"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3181"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Evaluate a DNA sequence assembly, typically for purposes of quality control.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3182">
-        <rdfs:label>Genome alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasDefinition>Align two or more (tpyically huge) molecular sequences that represent genomes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Genome alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3183">
-        <rdfs:label>Localized reassembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Reconstruction of a sequence assembly in a localised area.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3184">
-        <rdfs:label>Sequence assembly visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:hasExactSynonym>Assembly rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence assembly rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Render and visualise a DNA sequence assembly.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Assembly visualisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3185 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3185">
-        <rdfs:label>Base-calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2513"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phred base calling</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Identify base (nucleobase) sequence from a fluorescence &apos;trace&apos; data generated by an automated DNA sequencer.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Base calling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phred base-calling</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3186 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3186">
-        <rdfs:label>Bisulfite mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected.</rdfs:comment>
-        <oboInOwl:hasDefinition>The mapping of methylation sites in a DNA (genome) sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Bisulfite sequence alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Bisulfite sequence mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3187 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3187">
-        <rdfs:label>Sequence contamination filtering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3189 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3189">
-        <rdfs:label>Trim ends</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3192"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Trim sequences (typically from an automated DNA sequencer) to remove misleading ends.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3190 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3190">
-        <rdfs:label>Trim vector</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3192"/>
-        <oboInOwl:hasDefinition>Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3191">
-        <rdfs:label>Trim to reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3192"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3192 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3192">
-        <rdfs:label>Sequence trimming</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0369"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Cut (remove) the end from a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3194">
-        <rdfs:label>Genome feature comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0256"/>
-        <rdfs:comment>Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Compare the features of two genome sequences.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3195">
-        <rdfs:label>Sequencing error detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Short read error correction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Short-read error correction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect errors in DNA sequences generated from sequencing projects).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3196">
-        <rdfs:label>Genotyping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual&apos;s or a reference sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3197 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3197">
-        <rdfs:label>Genetic variation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Sequence variation analysis</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Genetic variation annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3198 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3198">
-        <rdfs:label>Read mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <oboInOwl:hasExactSynonym>Short oligonucleotide alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Oligonucleotide mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Oligonucleotide alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Short read mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Oligonucleotide alignment construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Oligonucleotide alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Read alignment</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Short read alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Short sequence read mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3199 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3199">
-        <rdfs:label>Split read mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3198"/>
-        <oboInOwl:hasDefinition>A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3200">
-        <rdfs:label>DNA barcoding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasDefinition>Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Sample barcoding</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3201 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3201">
-        <rdfs:label>SNP calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0484"/>
-        <oboInOwl:hasDefinition>Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism.</oboInOwl:hasDefinition>
-        <rdfs:comment>Operations usually score confidence in the prediction or some other statistical measure of evidence.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3202">
-        <rdfs:label>Mutation detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasExactSynonym>Polymorphism detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3203">
-        <rdfs:label>Chromatogram visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <oboInOwl:hasDefinition>Visualise, format or render an image of a Chromatogram.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Chromatogram viewing</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3204">
-        <rdfs:label>Methylation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Determine cytosine methylation states in nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3205 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3205">
-        <rdfs:label>Methylation calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3204"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Determine cytosine methylation status of specific positions in a nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3206 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3206">
-        <rdfs:label>Methylation level analysis (global)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3205"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Global methylation analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3207 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3207">
-        <rdfs:label>Methylation level analysis (gene-specific)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3205"/>
-        <oboInOwl:hasExactSynonym>Gene-specific methylation analysis</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Many different techniques are available for this.</rdfs:comment>
-        <oboInOwl:hasDefinition>Measure the level of methyl cytosines in specific genes.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3208">
-        <rdfs:label>Genome visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0564"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Genome visualization</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome visualisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome viewing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome browsing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3209">
-        <rdfs:label>Genome comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <oboInOwl:hasDefinition>Compare the sequence or features of two or more genomes, for example, to find matching regions.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Genomic region matching</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3211">
-        <rdfs:label>Genome indexing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0227"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3210"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate an index of a genome sequence.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3212 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3212">
-        <rdfs:label>Genome indexing (Burrows-Wheeler)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3211"/>
-        <rdfs:comment>The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate an index of a genome sequence using the Burrows-Wheeler algorithm.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3213">
-        <rdfs:label>Genome indexing (suffix arrays)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3211"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Generate an index of a genome sequence using a suffix arrays algorithm.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>suffix arrays</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A suffix array consists of the lexicographically sorted list of suffixes of a genome.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3214 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3214">
-        <rdfs:label>Spectral analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasExactSynonym>Spectral analysis</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Spectrum analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse a spectrum from a mass spectrometry (or other) experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Mass spectrum analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3215">
-        <rdfs:label>Peak detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3214"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0943"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Peak finding</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Peak assignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3216 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3216">
-        <rdfs:label>Scaffolding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Scaffold construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length.  The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Scaffold may be positioned along a chromosome physical map to create a &quot;golden path&quot;.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Scaffold generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3217">
-        <rdfs:label>Scaffold gap completion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3216"/>
-        <oboInOwl:hasDefinition>Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used.  For large (&gt;20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3218">
-        <rdfs:label>Sequencing quality control</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasDefinition>Raw sequence data quality control.</oboInOwl:hasDefinition>
-        <rdfs:comment>Analyse raw sequence data from a sequencing pipeline and identify problems.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequencing QC</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3219">
-        <rdfs:label>Read pre-processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasExactSynonym>Sequence read pre-processing</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.  For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Pre-process sequence reads to ensure (or improve) quality and reliability.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3221 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3221">
-        <rdfs:label>Species frequency estimation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3174"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3222 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3222">
-        <rdfs:label>Peak calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:comment>Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence.  The enriched areas contain the binding sites of DNA-associated proteins.  For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation (&apos;ChIP&apos;) with microarray (&apos;chip&apos;).</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein binding peak detection</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3223 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3223">
-        <rdfs:label>Differential expression analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0315"/>
-        <oboInOwl:hasDefinition>Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Differentially expressed gene identification</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3224 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3224">
-        <rdfs:label>Gene set testing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Gene sets can be defined beforehand by biological function, chromosome locations and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3225 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3225">
-        <rdfs:label>Variant classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2995"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasDefinition>Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.)</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3226 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3226">
-        <rdfs:label>Variant prioritization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <rdfs:comment>Variant prioritization can be used for example to produce a list of variants responsible for &apos;knocking out&apos; genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3227 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3227">
-        <rdfs:label>Variant calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasExactSynonym>Variant mapping</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods often utilise a database of aligned reads.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3228 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3228">
-        <rdfs:label>Structural variation discovery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasDefinition>Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s).</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3229 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3229">
-        <rdfs:label>Exome analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Targeted exome capture</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Exome sequencing is considered a cheap alternative to whole genome sequencing.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Exome sequence analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3230 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3230">
-        <rdfs:label>Read depth analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3232 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3232">
-        <rdfs:label>Gene expression QTL analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>expression quantitative trait loci profiling</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>eQTL profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>expression QTL profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3233">
-        <rdfs:label>Copy number estimation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:comment>Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Transcript copy number estimation</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3237">
-        <rdfs:label>Primer removal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0369"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3258">
-        <rdfs:label>Transcriptome assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0925"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Infer a transcriptome sequence by analysis of short sequence reads.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3259">
-        <rdfs:label>Transcriptome assembly (de novo)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>de novo transcriptome assembly</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0524"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3260 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3260">
-        <rdfs:label>Transcriptome assembly (mapping)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Infer a transcriptome sequence by mapping short reads to a reference genome.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>1.2</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3267 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3267">
-        <rdfs:label>Sequence coordinate conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3434"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2012"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2012"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3278">
-        <rdfs:label>Document similarity calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3437"/>
-        <oboInOwl:hasDefinition>Calculate similarity between 2 or more documents.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3279 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3279">
-        <rdfs:label>Document clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3432"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3437"/>
-        <oboInOwl:hasDefinition>Cluster (group) documents on the basis of their calculated similarity.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3280">
-        <rdfs:label>Named entity recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0306"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <oboInOwl:hasExactSynonym>Entity identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Entity chunking</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Entity extraction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Recognise named entities (text tokens) within documents.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3282 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3282">
-        <rdfs:label>ID mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <oboInOwl:hasExactSynonym>Identifier mapping</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Accession mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3283 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3283">
-        <rdfs:label>Anonymisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:hasDefinition>Process data in such a way that makes it hard to trace to the person which the data concerns.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Data anonymisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3289">
-        <rdfs:label>ID retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0304"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0842"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>id retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data retrieval (accession)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data retrieval (ID)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Identifier retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data retrieval (id)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Accession retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search for and retrieve a data identifier of some kind, e.g. a database entry accession.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3348">
-        <rdfs:label>Sequence checksum generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Generate a checksum of a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3349">
-        <rdfs:label>Bibliography generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3505"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Bibliography construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a bibliography from the scientific literature.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3350">
-        <rdfs:label>Protein quaternary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0474"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Predict the structure of a multi-subunit protein and particularly how the subunits fit together.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3351 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3351">
-        <rdfs:label>Protein surface analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Analyse the surface properties of proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3352">
-        <rdfs:label>Ontology comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Compare two or more ontologies, e.g. identify differences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3353">
-        <rdfs:label>Ontology comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Compare two or more ontologies, e.g. identify differences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.9</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_3352"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3357">
-        <rdfs:label>Format detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3358"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Recognition of which format the given data is in.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Format identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Format recognition</oboInOwl:hasExactSynonym>
-        <rdfs:comment>&apos;Format recognition&apos; is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Format inference</oboInOwl:hasExactSynonym>
-        <noClue rdf:resource="http://edamontology.org/noClue"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>The has_input &quot;Data&quot; (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs.</rdfs:comment>
-        <owl:annotatedProperty rdf:resource="http://edamontology.org/noClue"/>
-        <owl:annotatedTarget rdf:resource="http://edamontology.org/noClue"/>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_3357"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/operation_3359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3359">
-        <rdfs:label>Splitting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:hasExactSynonym>File splitting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Split a file containing multiple data items into many files, each containing one item</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3429">
-        <rdfs:label>Generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasExactSynonym>Construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>For non-analytical operations, see the &apos;Processing&apos; branch.</rdfs:comment>
-        <oboInOwl:hasDefinition>Construct some data entity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3430">
-        <rdfs:label>Nucleic acid sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid site prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid site recognition</oboInOwl:hasExactSynonym>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid site detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3431 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3431">
-        <rdfs:label>Deposition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <oboInOwl:hasDefinition>Deposit some data in a database or some other type of repository or software system.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasExactSynonym>Database submission</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Submission</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data submission</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data deposition</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Database deposition</oboInOwl:hasExactSynonym>
-        <rdfs:comment>For non-analytical operations, see the &apos;Processing&apos; branch.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3432">
-        <rdfs:label>Clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3433">
-        <rdfs:label>Assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Construct some entity (typically a molecule sequence) from component pieces.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3434">
-        <rdfs:label>Conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Non-analytical data conversion.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3435">
-        <rdfs:label>Standardization and normalization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Standardize or normalize data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3436">
-        <rdfs:label>Aggregation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:hasDefinition>Combine multiple files or data items into a single file or object.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3437">
-        <rdfs:label>Article comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <oboInOwl:hasDefinition>Compare two or more scientific articles.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3438">
-        <rdfs:label>Calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasDefinition>Mathemetical determination of the value of something, typically a properly of a  molecule.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3439">
-        <rdfs:label>Pathway or network prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2438"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Predict a molecular pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3440">
-        <rdfs:label>Genome assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3441">
-        <rdfs:label>Plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasDefinition>Generate a graph, or other visual representation, of data, showing the relationship between two or more variables.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3443">
-        <rdfs:label>Image analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3382"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>The analysis of a image (typically a digital image) of some type in order to extract information from it.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Image processing</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3445">
-        <rdfs:label>Diffraction data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Analysis of data from a diffraction experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3446">
-        <rdfs:label>Cell migration analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2229"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3447">
-        <rdfs:label>Diffraction data reduction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3445"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Processing of diffraction data into a corrected, ordered, and simplified form.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3450 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3450">
-        <rdfs:label>Neurite measurement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2229"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3453">
-        <rdfs:label>Diffraction data integration</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3445"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasNarrowSynonym>Diffraction summation integration</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Diffraction profile fitting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3454 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3454">
-        <rdfs:label>Phasing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3445"/>
-        <oboInOwl:hasDefinition>Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3455 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3455">
-        <rdfs:label>Molecular replacement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0322"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form.</oboInOwl:hasDefinition>
-        <rdfs:comment>The technique solves the phase problem, i.e. retrieve information concern phases of the structure.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3456">
-        <rdfs:label>Rigid body refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0322"/>
-        <created_in>1.7</created_in>
-        <rdfs:comment>Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data.</rdfs:comment>
-        <oboInOwl:hasDefinition>A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3457">
-        <rdfs:label>Single particle analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:comment>Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3458 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3458">
-        <rdfs:label>Single particle alignment and classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2990"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3457"/>
-        <oboInOwl:hasDefinition>Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle. </oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:comment>A micrograph can include particles in multiple different orientations and/or conformations.  Particles are compared and organised into sets based on their similarity.  Typically iterations of classification and alignment and are performed to optimise the final image; average images produced by classification are used as a reference image for subsequent alignment of the whole image set.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3459">
-        <rdfs:label>Functional clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0291"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Functional sequence clustering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3460">
-        <rdfs:label>Taxonomic classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2995"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Classifiication of molecular sequences by assignment to some taxonomic hierarchy.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3461">
-        <rdfs:label>Virulence prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3301"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Pathogenicity prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3463">
-        <rdfs:label>Gene expression correlation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0315"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3465"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>Gene co-expression network analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse the correlation patterns among genes across across a variety of experiments, microarray samples etc.
- </oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3465">
-        <rdfs:label>Correlation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3469">
-        <rdfs:label>RNA structure covariance model generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compute the covariance model for (a family of) RNA secondary structures.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3470">
-        <rdfs:label>RNA secondary structure prediction (shape-based)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0278"/>
-        <oboInOwl:hasExactSynonym>RNA shape prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3471">
-        <rdfs:label>Nucleic acid alignment folding prediction (alignment-based)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0279"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Prediction of nucleic-acid folding using sequence alignments as a source of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3472">
-        <rdfs:label>k-mer counting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <oboInOwl:hasDefinition>Count k-mers (substrings of length k) in DNA sequence data.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:comment>k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads. </rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3478">
-        <rdfs:label>Phylogenetic tree reconstruction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Reconstructing the inner node labels of a phylogenetic tree from its leafes.</oboInOwl:hasDefinition>
-        <rdfs:comment>Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one.</rdfs:comment>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3480">
-        <rdfs:label>Probabilistic data generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <oboInOwl:hasDefinition>Generate some data from a choosen probibalistic model, possibly to evaluate algorithms.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3481">
-        <rdfs:label>Probabilistic sequence generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3480"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Generate sequences from some probabilistic model, e.g. a model that simulates evolution.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3482">
-        <rdfs:label>Antimicrobial resistance prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3301"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Identify or predict causes for antibiotic resistance from molecular sequence analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3501">
-        <rdfs:label>Enrichment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>A relevant ontology will be used. The input is typically a set of identifiers or other data, and the output of the analysis is typically a ranked list of ontology terms, each associated with a p-value.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Term enrichment</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Analyse a dataset with respect to concepts from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3502">
-        <rdfs:label>Chemical class enrichment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Analyse a dataset with respect to concepts from an ontology of chemical structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3503">
-        <rdfs:label>Incident curve plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Plot an incident curve such as a survival curve, death curve, mortality curve.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3504">
-        <rdfs:label>Variant pattern analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <rdfs:comment>Methods often utilise a database of aligned reads.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify and map patterns of genomic variations.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3545">
-        <rdfs:label>Mathematical modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <oboInOwl:hasDefinition>Model some biological system using mathematical techniques including  dynamical systems, statistical models, differential equations, and game theoretic models.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3552">
-        <rdfs:label>Microscope image visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3382"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise images resulting from various types of microscopy.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasExactSynonym>Microscopy image visualisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3553">
-        <rdfs:label>Image annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Annotate an image of some sort, typically with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3557">
-        <rdfs:label>Imputation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2238"/>
-        <oboInOwl:hasExactSynonym>Data imputation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Replace missing data with substituted values, usually by using some statistical or other mathematical approach.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3559">
-        <rdfs:label>Ontology visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render data from an ontology, typically a tree of terms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ontology browsing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3560">
-        <rdfs:label>Maximum occurence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <oboInOwl:hasDefinition>A method for making numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data. </oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3561">
-        <rdfs:label>Database comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasNarrowSynonym>Data model comparison</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Compare the models or schemas used by two or more databases, or any other general comparison of databases rather than a detailed comparison of the entries themselves.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Schema comparison</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3562 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3562">
-        <rdfs:label>Network simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2259"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Simulate the bevaviour of a biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway simulation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Network topology simulation</oboInOwl:hasExactSynonym>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3563">
-        <rdfs:label>RNA-seq read count analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasDefinition>Analyze read counts from RNA-seq experiments.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3564">
-        <rdfs:label>Chemical redundancy removal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Identify and remove redudancy from a set of small molecule structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3565">
-        <rdfs:label>RNA-seq time series data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Analyze time series data from an RNA-seq experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3566">
-        <rdfs:label>Simulated gene expression data generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Simulate gene expression data, e.g. for purposes of benchmarking.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0003">
-        <rdfs:label>Topic</rdfs:label>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#Quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Category</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <oboInOwl:hasRelatedSynonym>sumo:FieldOfStudy</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0077">
-        <rdfs:label>Nucleic acids</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <oboInOwl:hasDefinition>The processing and analysis of nucleic acid sequence, structural and other data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid bioinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid informatics</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D017423</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid properties</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid physicochemistry</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D017422</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0078">
-        <rdfs:label>Proteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <oboInOwl:hasExactSynonym>Protein bioinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein databases</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein analysis</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D020539</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Archival, processing and analysis of protein data, typically molecular sequence and structural data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0079 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0079">
-        <rdfs:label>Metabolites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <oboInOwl:hasExactSynonym>Metabolite structures</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This concept excludes macromolecules such as proteins and nucleic acids.</rdfs:comment>
-        <oboInOwl:hasDefinition>The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0080">
-        <rdfs:label>Sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3307"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Sequence databases</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequences</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D017421</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0081">
-        <rdfs:label>Structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3307"/>
-        <oboInOwl:hasNarrowSynonym>Computational structural biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015394</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Structure analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural bioinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Structure databases</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes related concepts such as structural properties, alignments and structural motifs.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Structure data resources</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0082 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0082">
-        <rdfs:label>Structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The prediction of molecular (secondary or tertiary) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0083">
-        <rdfs:label>Alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0183"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0184"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0084">
-        <rdfs:label>Phylogeny</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3299"/>
-        <oboInOwl:hasNarrowSynonym>Phylogeny reconstruction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic stratigraphy</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic dating</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic clocks</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D010802</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The study of evolutionary relationships amongst organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic simulation</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0085">
-        <rdfs:label>Functional genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1775"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0089 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0089">
-        <rdfs:label>Ontology and terminology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasNarrowSynonym>Terminology</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D002965</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Applied ontology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Ontology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Ontologies</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0090 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0090">
-        <rdfs:label>Information retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Data retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes, for example, search, query and retrieval of molecular sequences and associated data.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Data search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.3.3 Information retrieval</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Data query</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0091 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0091">
-        <rdfs:label>Bioinformatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <rdfs:comment>This includes data  processing in general, including basic handling of files and databases, datatypes, workflows and annotation.</rdfs:comment>
-        <oboInOwl:hasDbXref>VT 1.5.6 Bioinformatics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The archival, curation, processing and analysis of complex biological data.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D016247</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0092">
-        <rdfs:label>Data visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasExactSynonym>Data rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.2.5 Computer graphics</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasBroadSynonym>Computer graphics</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0094">
-        <rdfs:label>Nucleic acid thermodynamics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The study of the thermodynamic properties of a nucleic acid.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0097">
-        <rdfs:label>Nucleic acid structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <rdfs:comment>Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>DNA melting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid denaturation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>RNA alignment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>RNA structure alignment</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid thermodynamics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>RNA structure</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0099">
-        <rdfs:label>RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0077"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>RNA sequences and structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0100">
-        <rdfs:label>Nucleic acid restriction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0747"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0102">
-        <rdfs:label>Mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Genetic linkage</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Linkage</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Linkage mapping</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Synteny</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>DNA mapping</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The mapping of complete (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0107 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0107">
-        <rdfs:label>Genetic codes and codon usage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Codon usage analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The study of codon usage in nucleotide sequence(s), genetic codes and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0108 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0108">
-        <rdfs:label>Protein expression</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <oboInOwl:hasNarrowSynonym>Translation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The translation of mRNA into protein and subsequent protein processing in the cell.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0109 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0109">
-        <rdfs:label>Gene finding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:comment>This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Gene discovery</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene prediction</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0110">
-        <rdfs:label>Transcription</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>The transcription of DNA into mRNA.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0111">
-        <rdfs:label>Promoters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins).</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0749"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0112">
-        <rdfs:label>Nucleic acid folding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The folding (in 3D space) of nucleic acid molecules.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0173"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0114 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0114">
-        <rdfs:label>Gene structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3321"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <rdfs:comment>This includes the study of promoters, coding regions etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0121 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0121">
-        <rdfs:label>Proteomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3391"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Protein and peptide identification, especially in the study of whole proteomes of organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein and peptide identification</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Peptide identification</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D040901</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Protein expression</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0122">
-        <rdfs:label>Structural genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The elucidation of the three dimensional structure for all (available) proteins in a given organism.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0123">
-        <rdfs:label>Protein properties</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <oboInOwl:hasDefinition>The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein hydropathy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein physicochemistry</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0128">
-        <rdfs:label>Protein interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein-nucleic acid interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein-RNA interaction</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Protein-protein interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein-ligand interactions</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein-DNA interaction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0130">
-        <rdfs:label>Protein folding, stability and design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:hasNarrowSynonym>Protein folding</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein stability</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Protein stability, folding (in 3D space) and protein sequence-structure-function relationships.  This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein residue interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Rational protein design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0133">
-        <rdfs:label>Two-dimensional gel electrophoresis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Two-dimensional gel electrophoresis image and related data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0121"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0134">
-        <rdfs:label>Mass spectrometry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3520"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0135">
-        <rdfs:label>Protein microarrays</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Protein microarray data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0121"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0137">
-        <rdfs:label>Protein hydropathy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The study of the hydrophobic, hydrophilic and charge properties of a protein.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0123"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0140">
-        <rdfs:label>Protein targeting and localization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0108"/>
-        <oboInOwl:hasNarrowSynonym>Protein targeting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein sorting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein localization</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0141">
-        <rdfs:label>Protein cleavage sites and proteolysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0767"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0143">
-        <rdfs:label>Protein structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The comparison of two or more protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Use this concept for methods that are exclusively for protein structure.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0698"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0144 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0144">
-        <rdfs:label>Protein residue interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein residue interactions</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0130"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0147">
-        <rdfs:label>Protein-protein interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasNarrowSynonym>Protein interaction networks</oboInOwl:hasNarrowSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0148 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0148">
-        <rdfs:label>Protein-ligand interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein-ligand (small molecule) interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0149 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0149">
-        <rdfs:label>Protein-nucleic acid interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein-DNA/RNA interactions.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0150 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0150">
-        <rdfs:label>Protein design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0130"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0151 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0151">
-        <rdfs:label>G protein-coupled receptors (GPCR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>G-protein coupled receptors (GPCRs).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0152 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0152">
-        <rdfs:label>Carbohydrates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Carbohydrates, typically including structural information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0153 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0153">
-        <rdfs:label>Lipids</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Lipids and their structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0154">
-        <rdfs:label>Small molecules</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <oboInOwl:hasDefinition>Small molecules of biological significance, typically archival, curation, processing and analysis of structural information.</oboInOwl:hasDefinition>
-        <rdfs:comment>Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides.  Structural data is usually included.</rdfs:comment>
-        <oboInOwl:hasRelatedSynonym>CHEBI:23367</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0156">
-        <rdfs:label>Sequence editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Edit, convert or otherwise change a molecular sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0091"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0157">
-        <rdfs:label>Sequence composition, complexity and repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Sequence complexity</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Repeat sequences</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Sequence repeats</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Low complexity sequences</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence composition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0158">
-        <rdfs:label>Sequence motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Motifs</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0159">
-        <rdfs:label>Sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <rdfs:comment>The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The comparison of two or more molecular sequences, for example sequence alignment and clustering.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0160">
-        <rdfs:label>Sequence sites, features and motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Sequence features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The archival, detection, prediction and analysis of
-positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Functional sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence motifs</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence profiles</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>HMMs</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0163">
-        <rdfs:label>Sequence database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The query is a sequence-based entity such as another sequence, a motif or profile.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0164">
-        <rdfs:label>Sequence clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes systems that generate, process and analyse sequence clusters.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>The comparison and grouping together of molecular sequences on the basis of their similarities.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence clusters</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0166">
-        <rdfs:label>Protein structural motifs and surfaces</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <rdfs:comment>This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Protein structural features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Structural motifs</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein 3D motifs</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein structural motifs</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein surfaces</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0167">
-        <rdfs:label>Structural (3D) profiles</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Structural profiles</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0172">
-        <rdfs:label>Protein structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0173">
-        <rdfs:label>Nucleic acid structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:hasDefinition>The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>DNA structure prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>RNA structure prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid folding</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0174">
-        <rdfs:label>Ab initio structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>The prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0082"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0175">
-        <rdfs:label>Homology modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>The modelling of the three-dimensional structure of a protein using known sequence and structural data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2275"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0176">
-        <rdfs:label>Molecular dynamics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:comment>This includes resources concerning flexibility and motion in protein and other molecular structures.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Protein dynamics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Molecular flexibility</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Molecular motions</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0177">
-        <rdfs:label>Molecular docking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The modelling the structure of proteins in complex with small molecules or other macromolecules.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0178">
-        <rdfs:label>Protein secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>The prediction of secondary or supersecondary structure of protein sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0172"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0694"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0179">
-        <rdfs:label>Protein tertiary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The prediction of tertiary structure of protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0172"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0698"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0180">
-        <rdfs:label>Protein fold recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:comment>For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).</rdfs:comment>
-        <oboInOwl:hasDefinition>The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0182">
-        <rdfs:label>Sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>The alignment of molecular sequences or sequence profiles (representing sequence alignments).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0183">
-        <rdfs:label>Structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes the generation, storage, analysis, rendering etc. of structure alignments.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0184">
-        <rdfs:label>Threading</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence-structure alignment</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0180"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0188 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0188">
-        <rdfs:label>Sequence profiles and HMMs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Sequence profiles; typically a positional, numerical matrix representing a sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:comment>Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0191">
-        <rdfs:label>Phylogeny reconstruction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Currently too specific for the topic sub-ontology (but might be unobsoleted).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3293"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0194">
-        <rdfs:label>Phylogenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0195">
-        <rdfs:label>Virtual PCR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Polymerase chain reaction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simulated polymerase chain reaction (PCR).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>PCR</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0077"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0196">
-        <rdfs:label>Sequence assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Assembly</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The assembly of fragments of a DNA sequence to reconstruct the original sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0199 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0199">
-        <rdfs:label>Genetic variation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0625"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D014644</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>DNA variation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Mutation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Polymorphism</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0200">
-        <rdfs:label>Microarrays</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D046228</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Microarrays, for example, to process microarray data or design probes and experiments.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasNarrowSynonym>DNA microarrays</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0202">
-        <rdfs:label>Pharmacology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasNarrowSynonym>Computational pharmacology</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Pharmacoinformatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of drugs and their effects or responses in living systems. </oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.7 Pharmacology and pharmacy</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0203">
-        <rdfs:label>Gene expression</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <rdfs:comment>This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Gene expression profiling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Expression profiling</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasAlternativeId>http://edamontology.org/topic_0197</oboInOwl:hasAlternativeId>
-        <rdfs:comment>Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015870</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Gene expression analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>DNA microarrays</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Codon usage</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0204">
-        <rdfs:label>Gene regulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0203"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The regulation of gene expression.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0208">
-        <rdfs:label>Pharmacogenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0202"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0209">
-        <rdfs:label>Medicinal chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3336"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3371"/>
-        <oboInOwl:hasDbXref>VT 3.1.4 Medicinal chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Drug design</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0210">
-        <rdfs:label>Fish</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a specific fish genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0211">
-        <rdfs:label>Flies</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a specific fly genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2819"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0213">
-        <rdfs:label>Mice or rats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2820"/>
-        <oboInOwl:hasDefinition>Information on a specific mouse or rat genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <rdfs:comment>The resource may be specific to a group of mice / rats or all mice / rats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0215">
-        <rdfs:label>Worms</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a specific worm genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2819"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0217">
-        <rdfs:label>Literature analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0218"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0218">
-        <rdfs:label>Data mining</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3068"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Text data mining</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The analysis of the biomedical and informatics literature.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Literature analysis</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Text mining</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Literature mining</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0219">
-        <rdfs:label>Data deposition, annotation and curation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>Deposition and curation of database accessions, including annotation, typically with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database curation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0220 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0220">
-        <rdfs:label>Document, record and content management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasExactSynonym>Document management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File management</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Content management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The management and manipulation of digital documents, including database records, files and reports.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.3.6 Multimedia, hypermedia</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Record management</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0221 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0221">
-        <rdfs:label>Sequence annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Annotation of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0219"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0222 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0222">
-        <rdfs:label>Genome annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Annotation of a genome.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0219"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0593">
-        <rdfs:label>NMR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasNarrowSynonym>ROESY</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>NOESY</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nuclear Overhauser Effect Spectroscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>HOESY</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Heteronuclear Overhauser Effect Spectroscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nuclear magnetic resonance spectroscopy</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Spectroscopy</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>NMR spectroscopy</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Rotational Frame Nuclear Overhauser Effect Spectroscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0594">
-        <rdfs:label>Sequence classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The classification of molecular sequences based on some measure of their similarity.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0595">
-        <rdfs:label>Protein classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0598">
-        <rdfs:label>Sequence motif or profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes comparison, discovery, recognition etc. of sequence motifs.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0158"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0188"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0601">
-        <rdfs:label>Protein modifications</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0108"/>
-        <oboInOwl:hasRelatedSynonym>GO:0006464</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>Protein chemical modifications, e.g. post-translational modifications.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein post-translational modification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>MOD:00000</oboInOwl:hasRelatedSynonym>
-        <rdfs:comment>EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000)</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0602">
-        <rdfs:label>Molecular interactions, pathways and networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasNarrowSynonym>Biological networks</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Network or pathway analysis</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasNarrowSynonym>Molecular interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Biological models</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Molecular interactions, biological pathways, networks and other models.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Biological pathways</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasAlternativeId>http://edamontology.org/topic_3076</oboInOwl:hasAlternativeId>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0605">
-        <rdfs:label>Informatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The study and practice of information processing and use of computer information systems.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.3.99 Other</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Knowledge management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.3.4 Information management</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Information management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.3.5 Knowledge management</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.3.3 Information retrieval</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.3 Information sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Information science</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0606">
-        <rdfs:label>Literature data resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data resources for the biological or biomedical literature, either a primary source of literature or some derivative.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3068"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0607">
-        <rdfs:label>Laboratory information management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasDefinition>Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Laboratory resources</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0608">
-        <rdfs:label>Cell and tissue culture</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasNarrowSynonym>Tissue culture</oboInOwl:hasNarrowSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>General cell culture or data on a specific cell lines.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Cell culture</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2229"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0610">
-        <rdfs:label>Ecology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDefinition>The ecological and environmental sciences and especially the application of information technology (ecoinformatics).</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D004777</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Ecological informatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.15 Ecology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Computational ecology</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Ecoinformatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Environmental science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0611">
-        <rdfs:label>Electron microscopy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasNarrowSynonym>SEM</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Scanning electron microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>TEM</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light.
-</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Transmission electron microscopy</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Electron crystallography</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Electron diffraction experiment</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Single particle electron microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0612">
-        <rdfs:label>Cell cycle</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The cell cycle including key genes and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2229"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0613">
-        <rdfs:label>Peptides and amino acids</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The physicochemical, biochemical or structural properties of amino acids or peptides.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Amino acids</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Peptides</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0616">
-        <rdfs:label>Organelles</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasNarrowSynonym>Cell membrane</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Cytoplasm</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Organelle genes and proteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Smooth endoplasmic reticulum</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Lysosome</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Centriole</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Ribosome</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleus</oboInOwl:hasNarrowSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Mitochondria</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Golgi apparatus</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Rough endoplasmic reticulum</oboInOwl:hasNarrowSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2229"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0617">
-        <rdfs:label>Ribosomes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Ribosomes, typically of ribosome-related genes and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Ribosome genes and proteins</oboInOwl:hasNarrowSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0616"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0618">
-        <rdfs:label>Scents</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A database about scents.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0154"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0620">
-        <rdfs:label>Drugs and target structures</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3336"/>
-        <oboInOwl:hasNarrowSynonym>Drug structures</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The structures of drugs, drug target, their interactions and binding affinities.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Target structures</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0621">
-        <rdfs:label>Model organisms</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:comment>This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A specific organism, or group of organisms, used to study a particular aspect of biology.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Organisms</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0622">
-        <rdfs:label>Genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3391"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D023281</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0623 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0623">
-        <rdfs:label>Gene families</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasDefinition>Particular gene(s), gene family or other gene group or system and their encoded proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene family</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene system</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genes, gene family or system</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene and protein families</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0624 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0624">
-        <rdfs:label>Chromosomes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Study of chromosomes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0625 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0625">
-        <rdfs:label>Genotype and phenotype</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasExactSynonym>Genotype and phenotype resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Genotyping</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Phenotyping</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0629 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0629">
-        <rdfs:label>Gene expression and microarray</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0200"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0632 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0632">
-        <rdfs:label>Sequence design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Probes</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes the design of primers for PCR and DNA amplification or the design of molecular probes.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015335</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Gene design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Probe design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>in silico cloning</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Primer design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Primers</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0634 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0634">
-        <rdfs:label>Pathology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Diseases</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.1.6 Pathology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0635 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0635">
-        <rdfs:label>Specific protein resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>A particular protein, protein family or other group of proteins.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Specific protein</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0637 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0637">
-        <rdfs:label>Taxonomy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3299"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.25 Taxonomy</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Organism classification, identification and naming.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0639 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0639">
-        <rdfs:label>Protein sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0640 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0640">
-        <rdfs:label>Nucleic acid sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0641 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0641">
-        <rdfs:label>Repeat sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The repetitive nature of molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0157"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0642 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0642">
-        <rdfs:label>Low complexity sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The (character) complexity of molecular sequences, particularly regions of low complexity.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0157"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0644 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0644">
-        <rdfs:label>Proteome</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A specific proteome including protein sequences and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0654 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0654">
-        <rdfs:label>DNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0077"/>
-        <oboInOwl:hasExactSynonym>DNA analysis</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA sequences and structure, including processes such as methylation and replication.</oboInOwl:hasDefinition>
-        <rdfs:comment>The DNA sequences might be coding or non-coding sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0655 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0655">
-        <rdfs:label>Coding RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <oboInOwl:hasNarrowSynonym>EST</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>cDNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>mRNA</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes expressed sequence tag (EST) or complementary DNA (cDNA) sequences.</rdfs:comment>
-        <oboInOwl:hasDefinition>Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0659 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0659">
-        <rdfs:label>Functional, regulatory and non-coding RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasNarrowSynonym>ncRNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Non-coding RNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Functional RNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Regulatory RNA</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>Non-coding RNA includes  piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA).  Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0660 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0660">
-        <rdfs:label>rRNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>One or more ribosomal RNA (rRNA) sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0659"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0663 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0663">
-        <rdfs:label>tRNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>One or more transfer RNA (tRNA) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0659"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0694 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0694">
-        <rdfs:label>Protein secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Protein secondary structure or secondary structure alignments.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data.</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0697 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0697">
-        <rdfs:label>RNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>RNA secondary or tertiary structure and alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0698 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0698">
-        <rdfs:label>Protein tertiary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Protein tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0722 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0722">
-        <rdfs:label>Nucleic acid classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Classification of nucleic acid sequences and structures.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0623"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0724 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0724">
-        <rdfs:label>Protein families</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein sequence classification</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary databases</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>A protein families database might include the classifier (e.g. a sequence profile) used to build the classification.</rdfs:comment>
-        <oboInOwl:hasDefinition>Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0736 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0736">
-        <rdfs:label>Protein domains and folds</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein folds</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Protein tertiary structural domains and folds.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein domains</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0740 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0740">
-        <rdfs:label>Nucleic acid sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Nucleotide sequence alignments.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0741 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0741">
-        <rdfs:label>Protein sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein sequence alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A sequence profile typically represents a sequence alignment.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0747 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0747">
-        <rdfs:label>Nucleic acid sites and features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The archival, detection, prediction and analysis of
-positional features such as functional sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0640"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0748 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0748">
-        <rdfs:label>Protein sites and features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The detection, identification and analysis of positional features in proteins, such as functional sites.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0639"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0749 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0749">
-        <rdfs:label>Transcription factors and regulatory sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1312"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3125"/>
-        <rdfs:comment>Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase.  Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators.</rdfs:comment>
-        <oboInOwl:hasDefinition>Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Transcriptional regulatory sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>TFBS</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Transcription factors</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Transcription factor binding sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0751 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0751">
-        <rdfs:label>Phosphorylation sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:hasDefinition>Protein phosphorylation and phosphorylation sites in protein sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0601"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0748"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0753 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0753">
-        <rdfs:label>Metabolic pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Metabolic pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0754 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0754">
-        <rdfs:label>Signaling pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Signaling pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Signal transduction pathways</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0767 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0767">
-        <rdfs:label>Protein and peptide identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0121"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0769 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0769">
-        <rdfs:label>Workflows</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Biological or biomedical analytical workflows or pipelines.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0770 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0770">
-        <rdfs:label>Data types and objects</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Structuring data into basic types and (computational) objects.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.0</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0091"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0771 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0771">
-        <rdfs:label>Theoretical biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3307"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0779 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0779">
-        <rdfs:label>Mitochondria</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Mitochondria, typically of mitochondrial genes and proteins.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0616"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0780 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0780">
-        <rdfs:label>Plants</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <rdfs:comment>The resource may be specific to a plant, a group of plants or all plants.</rdfs:comment>
-        <oboInOwl:hasBroadSynonym>Plant science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Plant biology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Botany</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.22 Plant science</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Plant</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.10 Botany</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0781 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0781">
-        <rdfs:label>Viruses</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:hasBroadSynonym>Virology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.28 Virology</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <rdfs:comment>The resource may be specific to a virus, a group of viruses or all viruses.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0782 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0782">
-        <rdfs:label>Fungi</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <oboInOwl:hasBroadSynonym>Mycology</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The resource may be specific to a fungus, a group of fungi or all fungi.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Yeast</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.21 Mycology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0783 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0783">
-        <rdfs:label>Pathogens</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:hasDefinition>Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The resource may be specific to a pathogen, a group of pathogens or all pathogens.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0786 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0786">
-        <rdfs:label>Arabidopsis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Arabidopsis-specific data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0780"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0787 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0787">
-        <rdfs:label>Rice</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Rice-specific data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0780"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0796 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0796">
-        <rdfs:label>Genetic mapping and linkage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Linkage mapping</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Genetic linkage</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0102"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0797 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0797">
-        <rdfs:label>Comparative genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <oboInOwl:hasDefinition>The study (typically comparison) of the sequence, structure or function of multiple genomes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0798 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0798">
-        <rdfs:label>Mobile genetic elements</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <oboInOwl:hasNarrowSynonym>Transposons</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0803 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0803">
-        <rdfs:label>Human disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Human diseases, typically describing the genes, mutations and proteins implicated in disease.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0804 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0804">
-        <rdfs:label>Immunology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDbXref>VT 3.1.3 Immunology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Immunoinformatics</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D007120</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D007125</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Computational immunology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0820 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0820">
-        <rdfs:label>Membrane and  lipoproteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:hasDefinition>Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Membrane proteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Lipoproteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Transmembrane proteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0821 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0821">
-        <rdfs:label>Enzymes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:hasDefinition>Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Enzymology</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0922 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0922">
-        <rdfs:label>Primers</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <oboInOwl:hasDefinition>PCR primers and hybridization oligos in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (primers)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Primer binding sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_0922"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1302">
-        <rdfs:label>PolyA signal or sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (PolyA signal or site)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PolyA signal</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>PolyA site</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1302"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1304">
-        <rdfs:label>CpG island and isochores</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (CpG island and isochore)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>CpG rich regions (isochores) in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1304"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1305">
-        <rdfs:label>Restriction sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3125"/>
-        <oboInOwl:hasDefinition>Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (restriction sites)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid restriction sites (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1305"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1307">
-        <rdfs:label>Splice sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3320"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (splice sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (RNA splicing)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Splice sites in a nucleotide sequence or alternative RNA splicing events.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (RNA splice model)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1307"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1308">
-        <rdfs:label>Matrix/scaffold attachment sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (matrix/scaffold attachment sites)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1308"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1311">
-        <rdfs:label>Operon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasExactSynonym>Gene features (operon)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (operon)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query.</rdfs:comment>
-        <oboInOwl:hasDefinition>Operons (operators, promoters and genes) from a bacterial genome.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1311"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1312">
-        <rdfs:label>Promoters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <oboInOwl:hasDefinition>Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (promoters)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1312"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1317 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1317">
-        <rdfs:label>Structural biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasNarrowSynonym>Structural assignment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Structure determination</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:consider>This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy.  Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen.</oboInOwl:consider>
-        <oboInOwl:hasDefinition>The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.5.24 Structural biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Structural determination</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1456">
-        <rdfs:label>Protein membrane regions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0736"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3539"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (membrane regions)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Intramembrane regions</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein transmembrane regions</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Transmembrane regions</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1456"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1770 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1770">
-        <rdfs:label>Structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <rdfs:comment>This might involve comparison of secondary or tertiary (3D) structural information.</rdfs:comment>
-        <oboInOwl:hasDefinition>The comparison of two or more molecular structures, for example structure alignment and clustering.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1775 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1775">
-        <rdfs:label>Function analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3307"/>
-        <oboInOwl:hasNarrowSynonym>Protein function prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of gene and protein function including the prediction of functional properties of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein function analysis</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1811 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1811">
-        <rdfs:label>Prokaryotes and archae</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <rdfs:comment>The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes.</rdfs:comment>
-        <oboInOwl:hasDbXref>VT 1.5.2 Bacteriology</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Bacteriology</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2225 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2225">
-        <rdfs:label>Protein databases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein data resources.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein data resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0078"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2226 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2226">
-        <rdfs:label>Structure determination</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1317"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2229 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2229">
-        <rdfs:label>Cell biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.11 Cell biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cells, such as key genes and proteins involved in the cell cycle.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2230 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2230">
-        <rdfs:label>Classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0089"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2232 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2232">
-        <rdfs:label>Lipoproteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Lipoproteins (protein-lipid assemblies).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2257">
-        <rdfs:label>Phylogeny visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Visualise a phylogeny, for example, render a phylogenetic tree.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0084"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2258">
-        <rdfs:label>Cheminformatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasDefinition>The application of information technology to chemistry in biological research environment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Chemical informatics</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemoinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2259">
-        <rdfs:label>Systems biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Systems_biology</rdfs:seeAlso>
-        <rdfs:comment>This includes databases of models and methods to construct or analyse a model.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Biological models</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D049490</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Biological modelling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Biological system modelling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The holistic modelling and analysis of complex biological systems and the interactions therein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2269">
-        <rdfs:label>Statistics and probability</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3315"/>
-        <oboInOwl:hasNarrowSynonym>Biostatistics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The application of statistical methods to biological problems.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Biostatistics</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D056808</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2271 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2271">
-        <rdfs:label>Structure database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2275 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2275">
-        <rdfs:label>Molecular modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <oboInOwl:hasNarrowSynonym>Homology modeling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Comparative modeling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Comparative modelling</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Homology modelling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Molecular modeling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2276 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2276">
-        <rdfs:label>Protein function prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.2</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The prediction of functional properties of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1775"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2277">
-        <rdfs:label>SNP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <oboInOwl:hasDefinition>Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Single nucleotide polymorphism</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2278">
-        <rdfs:label>Transmembrane protein prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Predict transmembrane domains and topology in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0172"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2280">
-        <rdfs:label>Nucleic acid structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Use this concept for methods that are exclusively for nucleic acid structures.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2397">
-        <rdfs:label>Exons</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0655"/>
-        <oboInOwl:hasExactSynonym>Gene features (exon)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Exons in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2399">
-        <rdfs:label>Gene transcription features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasNarrowSynonym>GC signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>CAAT signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>-35 signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Gene transcriptional features</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Enhancers (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Terminators (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Transcription of DNA into RNA including the regulation of transcription.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Ribosome binding sites (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>-10 signals (report)</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>TATA signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Attenuators (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2533">
-        <rdfs:label>DNA mutation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0199"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <oboInOwl:hasExactSynonym>Mutation annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA mutation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (mutation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2640 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2640">
-        <rdfs:label>Oncology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>VT 3.2.16 Oncology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Cancer</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of cancer, for example, genes and proteins implicated in cancer.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Cancer biology</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2661 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2661">
-        <rdfs:label>Toxins and targets</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2840"/>
-        <oboInOwl:hasNarrowSynonym>Toxins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Targets</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Structural and associated data for toxic chemical substances.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2754 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2754">
-        <rdfs:label>Introns</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <oboInOwl:hasExactSynonym>Gene features (intron)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (intron)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Introns in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2754"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2807 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2807">
-        <rdfs:label>Tool topic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2809 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2809">
-        <rdfs:label>Study topic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2811 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2811">
-        <rdfs:label>Nomenclature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Biological nomenclature (naming), symbols and terminology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0089"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2813 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2813">
-        <rdfs:label>Disease genes and proteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The genes, gene variations and proteins involved in one or more specific diseases.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2814 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2814">
-        <rdfs:label>Protein structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <oboInOwl:hasExactSynonym>Protein structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Protein secondary or tertiary structural data and/or associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId>http://edamontology.org/topic_3040</oboInOwl:hasAlternativeId>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2815 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2815">
-        <rdfs:label>Humans</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2820"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2816 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2816">
-        <rdfs:label>Gene resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Gene resource</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Informatics resource (typically a database) primarily focussed on genes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene database</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2817 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2817">
-        <rdfs:label>Yeast</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0782"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2818 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2818">
-        <rdfs:label>Eukaryotes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:hasExactSynonym>Eukaryote</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <rdfs:comment>The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2819 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2819">
-        <rdfs:label>Invertebrates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3500"/>
-        <rdfs:comment>The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2820 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2820">
-        <rdfs:label>Vertebrates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3500"/>
-        <rdfs:comment>The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates.</rdfs:comment>
-        <oboInOwl:hasDefinition>Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2821 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2821">
-        <rdfs:label>Unicellular eukaryotes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <oboInOwl:hasDefinition>Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2826 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2826">
-        <rdfs:label>Protein structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Protein secondary or tertiary structure alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0183"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2828 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2828">
-        <rdfs:label>X-ray diffraction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>X-ray microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Crystallography</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>X-ray crystallography</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2829 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2829">
-        <rdfs:label>Ontologies, nomenclature and classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D002965</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0089"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2830 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2830">
-        <rdfs:label>Immunoproteins, genes and antigens</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0804"/>
-        <oboInOwl:hasNarrowSynonym>Immunopeptides</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Immunity-related genes, proteins and their ligands.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Antigens</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc.&quot;</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Immunoproteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Immunogenes</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2839 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2839">
-        <rdfs:label>Molecules</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasRelatedSynonym>CHEBI:23367</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3047"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2840 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2840">
-        <rdfs:label>Toxicology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3377"/>
-        <oboInOwl:hasDefinition>Toxins and the adverse effects of these chemical substances on living organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.9 Toxicology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Toxicoinformatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Toxicology</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Computational toxicology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2842 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2842">
-        <rdfs:label>High-throughput sequencing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Next-generation sequencing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3168"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2844 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2844">
-        <rdfs:label>Structural clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters.</oboInOwl:hasDefinition>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasExactSynonym>Structure classification</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2846 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2846">
-        <rdfs:label>Gene regulatory networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0204"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Gene regulatory networks.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2847 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2847">
-        <rdfs:label>Disease (specific)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Informatics resources dedicated to one or more specific diseases (not diseases in general).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2867">
-        <rdfs:label>VNTR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (VNTR)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Variable number of tandem repeat polymorphism</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>VNTR annotation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times.</rdfs:comment>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2868">
-        <rdfs:label>Microsatellites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (microsatellite)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Microsatellite annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Microsatellite polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2868"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2869">
-        <rdfs:label>RFLP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <oboInOwl:hasDefinition>Restriction fragment length polymorphisms (RFLP) in a DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>RFLP annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (RFLP)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2885">
-        <rdfs:label>DNA polymorphism</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0199"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (polymorphism)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>DNA polymorphism.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Polymorphism annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2885"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2953 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2953">
-        <rdfs:label>Nucleic acid design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Topic for the design of nucleic acid sequences with specific conformations.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0173"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3032 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3032">
-        <rdfs:label>Primer or probe design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The design of primers for PCR and DNA amplification or the design of molecular probes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0632"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3038 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3038">
-        <rdfs:label>Structure databases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.2</obsolete_since>
-        <oboInOwl:hasExactSynonym>Structure data resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0081"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3039 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3039">
-        <rdfs:label>Nucleic acid structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.2</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3041 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3041">
-        <rdfs:label>Sequence databases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Molecular sequence data resources, including sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Sequence data resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence data resource</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3042 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3042">
-        <rdfs:label>Nucleic acid sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Nucleotide sequences</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0640"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3043 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3043">
-        <rdfs:label>Protein sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0639"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3044 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3044">
-        <rdfs:label>Protein interaction networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0147"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3047 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3047">
-        <rdfs:label>Molecular biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDbXref>VT 1.5.4 Biochemistry and molecular biology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3048 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3048">
-        <rdfs:label>Mammals</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3050 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3050">
-        <rdfs:label>Biodiversity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0610"/>
-        <oboInOwl:hasDefinition>The degree of variation of life forms within a given ecosystem, biome or an entire planet.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.5 Biodiversity conservation</oboInOwl:hasDbXref>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D044822</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3052 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3052">
-        <rdfs:label>Sequence clusters and classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>The comparison, grouping together and classification of macromolecules on the basis of sequence similarity.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence families</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence clusters</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0594"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3053 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3053">
-        <rdfs:label>Genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D005823</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The study of genes, genetic variation and heredity in living organisms.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasNarrowSynonym>Heredity</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3055 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3055">
-        <rdfs:label>Quantitative genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0625"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3056 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3056">
-        <rdfs:label>Population genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasDefinition>The distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3060 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3060">
-        <rdfs:label>Regulatory RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0659"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3061 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3061">
-        <rdfs:label>Documentation and help</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3068"/>
-        <oboInOwl:hasDefinition>The documentation of resources such as tools, services and databases and how to get help.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Help</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasNarrowSynonym>Documentation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3062 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3062">
-        <rdfs:label>Genetic organisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The structural and functional organisation of genes and other genetic elements.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3063 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3063">
-        <rdfs:label>Medical informatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasExactSynonym>Health informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Clinical informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Biomedical informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Translational medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>The application of information technology to health, disease and biomedicine.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Healthcare informatics</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Health and disease</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Molecular medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3064 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3064">
-        <rdfs:label>Developmental biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDbXref>VT 1.5.14 Developmental biology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>How organisms grow and develop.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3065 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3065">
-        <rdfs:label>Embryology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3064"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3067 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3067">
-        <rdfs:label>Anatomy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDbXref>VT 3.1.1 Anatomy and morphology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The form and function of the structures of living organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3068 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3068">
-        <rdfs:label>Literature and reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasNarrowSynonym>Literature search</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The scientific literature, reference information and documentation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Literature sources</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D011642</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3070 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3070">
-        <rdfs:label>Biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDbXref>VT 1.5.8 Biology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDbXref>VT 1.5 Biological sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.23 Reproductive biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Cryobiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Biological rhythms</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>A particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.5.7 Biological rhythm</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Biological science</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Aerobiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.99 Other</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Chronobiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.13 Cryobiology
-</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.1 Aerobiology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.3 Behavioural biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Reproductive biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Behavioural biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3071 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3071">
-        <rdfs:label>Data management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasDefinition>The development and use of architectures, policies, practices and procedures for management of data.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Data handling</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D030541</rdfs:seeAlso>
-        <oboInOwl:hasDbXref>VT 1.3.1 Data management</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3072 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3072">
-        <rdfs:label>Sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The detection of the positional features, such as functional and other key sites, in molecular sequences.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D058977</rdfs:seeAlso>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3073 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3073">
-        <rdfs:label>Nucleic acid feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The detection of positional features such as functional sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition rdf:resource="http://edamontology.org/topic_0747"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3074 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3074">
-        <rdfs:label>Protein feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The detection, identification and analysis of positional protein sequence features, such as functional sites.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3075 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3075">
-        <rdfs:label>Biological system modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.2</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Topic for modelling biological systems in mathematical terms.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2259"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3077">
-        <rdfs:label>Data acquisition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3078">
-        <rdfs:label>Genes and proteins resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Gene family</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Gene and protein families</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0623"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3118">
-        <rdfs:label>Protein topological domains</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0736"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3539"/>
-        <oboInOwl:hasDefinition>Topological domains such as cytoplasmic regions in a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (topological domains)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3118"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3120 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3120">
-        <rdfs:label>Protein variants</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:hasDefinition>protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3120"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3123">
-        <rdfs:label>Expression signals</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0203"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (expression signal)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Regions within a nucleic acid sequence containing a signal that alters a biological function.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3123"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3125 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3125">
-        <rdfs:label>DNA binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <rdfs:comment>This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes).</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (binding)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Nucleic acids binding to some other molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3125"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3126">
-        <rdfs:label>Nucleic acid repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <created_in>beta13</created_in>
-        <rdfs:comment>This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at  both ends of a defined sequence and other types of repeating unit.</rdfs:comment>
-        <oboInOwl:hasDefinition>Repetitive elements within a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3126"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3127">
-        <rdfs:label>DNA replication and recombination</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3125"/>
-        <oboInOwl:hasDefinition>DNA replication or recombination.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Nucleosome exclusion sequences</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (replication and recombination)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3127"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3135">
-        <rdfs:label>Signal or transit peptide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (signal or transit peptide)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle.</rdfs:comment>
-        <oboInOwl:hasDefinition>Coding sequences for a signal or transit peptide.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3135"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3139">
-        <rdfs:label>Sequence tagged sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (STS)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <rdfs:comment>Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs.</rdfs:comment>
-        <oboInOwl:hasDefinition>Sequence tagged sites (STS) in nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3139"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3168 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3168">
-        <rdfs:label>Sequencing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D059014</rdfs:seeAlso>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasNarrowSynonym>NGS</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Next generation sequencing</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Next gen sequencing</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3169 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3169">
-        <rdfs:label>ChIP-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Chip sequencing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Chip seq</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>The analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Chip-sequencing</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3170 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3170">
-        <rdfs:label>RNA-Seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Small RNA-seq</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Whole transcriptome shotgun sequencing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA-seq</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Small RNA-Seq</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>WTSS</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3171 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3171">
-        <rdfs:label>DNA methylation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D019175</rdfs:seeAlso>
-        <created_in>1.1</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3172">
-        <rdfs:label>Metabolomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3391"/>
-        <oboInOwl:hasDefinition>The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D055432</rdfs:seeAlso>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3173">
-        <rdfs:label>Epigenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3295"/>
-        <rdfs:comment>Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D057890</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The study of the epigenetic modifications of a whole cell, tissue, organism etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3174">
-        <rdfs:label>Metagenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0610"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D056186</rdfs:seeAlso>
-        <oboInOwl:hasBroadSynonym>Ecogenomics</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Community genomics</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Environmental genomics</oboInOwl:hasBroadSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>The study of genetic material recovered from environmental samples, and associated environmental data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3175">
-        <rdfs:label>Structural variation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0199"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0624"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genomic structural variation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3176">
-        <rdfs:label>DNA packaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D042003</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3177">
-        <rdfs:label>DNA-Seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>DNA-seq</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3168"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3178">
-        <rdfs:label>RNA-Seq alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>RNA-seq alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The alignment of sequences of (typically millions) of short reads to a reference genome.  This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0196"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3179">
-        <rdfs:label>ChIP-on-chip</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Experimental techniques that combine chromatin immunoprecipitation (&apos;ChIP&apos;) with microarray (&apos;chip&apos;). ChIP-on-chip is used for high-throughput study protein-DNA interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChIP-chip</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3263 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3263">
-        <rdfs:label>Data security</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Data privacy</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The protection of data, such as patient health data, from damage or unwanted access from unauthorized users.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3277">
-        <rdfs:label>Sample collections</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasNarrowSynonym>samples</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>biobanking</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>biosamples</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Biological samples and specimens.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Specimen collections</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3292">
-        <rdfs:label>Biochemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <oboInOwl:hasDbXref>VT 1.5.4 Biochemistry and molecular biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Chemical biology</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Biological chemistry</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Chemical substances and physico-chemical processes and that occur within living organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3293">
-        <rdfs:label>Phylogenetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0084"/>
-        <oboInOwl:hasDefinition>The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences).</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D010802</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3295">
-        <rdfs:label>Epigenetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3321"/>
-        <oboInOwl:hasNarrowSynonym>Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence.</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>DNA methylation</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes sub-topics such as histone modification and DNA methylation.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D019175</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Histone modification</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3297">
-        <rdfs:label>Biotechnology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3298">
-        <rdfs:label>Phenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0625"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3299"/>
-        <oboInOwl:hasDefinition>Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. </oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3299">
-        <rdfs:label>Evolutionary biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDbXref>VT 1.5.16 Evolutionary biology</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3300">
-        <rdfs:label>Physiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The functions of living organisms and their constituent parts.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 3.1.8 Physiology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3301">
-        <rdfs:label>Microbiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDefinition>The biology of microorganisms.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.20 Microbiology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3302">
-        <rdfs:label>Parasitology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The biology of parasites.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3303">
-        <rdfs:label>Medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasNarrowSynonym>General medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Research in support of healing by diagnosis, treatment, and prevention of disease.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 3.1 Basic medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.2.9 General and internal medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Experimental medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Biomedical research</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Clinical medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.2 Clinical medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Internal medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3304">
-        <rdfs:label>Neurobiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasBroadSynonym>Neuroscience</oboInOwl:hasBroadSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The study of the nervous system and brain; its anatomy, physiology and function.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.5 Neuroscience</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3305">
-        <rdfs:label>Public health and epidemiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.3.1 Epidemiology</oboInOwl:hasDbXref>
-        <oboInOwl:hasAlternativeId>Topic concerning the the patterns, cause, and effect of disease within populations.</oboInOwl:hasAlternativeId>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>Public health</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Epidemiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3306">
-        <rdfs:label>Biophysics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3318"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.9 Biophysics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The use of physics to study biological system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3307">
-        <rdfs:label>Computational biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasDbXref>VT 1.5.19 Mathematical biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.12 Computational biology</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology).</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Mathematical biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.26 Theoretical biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Theoretical biology</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Biomathematics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3308">
-        <rdfs:label>Transcriptomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0203"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <oboInOwl:hasDefinition>The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Transcriptome</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3314">
-        <rdfs:label>Chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasBroadSynonym>VT 1.7.10 Polymer science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.7 Mathematical chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.7.3 Colloid chemistry</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>Mathematical chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Physical chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.9 Physical chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Polymer science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Chemical science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Organic chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.6 Inorganic and nuclear chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.7 Chemical sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.7.5 Electrochemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Inorganic chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.2 Chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Nuclear chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.8 Organic chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The composition and properties of matter, reactions, and the use of reactions to create new substances.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3315">
-        <rdfs:label>Mathematics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The study of numbers (quantity) and other topics including structure, space, and change.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT:1.1 Mathematics</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Maths</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.1.99 Other</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3316">
-        <rdfs:label>Computer science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.2 Computer sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.2.99 Other</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The theory and practical use of computer systems.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3318">
-        <rdfs:label>Physics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The study of matter, space and time, and related concepts such as energy and force.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3320">
-        <rdfs:label>RNA splicing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3321"/>
-        <oboInOwl:hasDefinition>RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3321">
-        <rdfs:label>Molecular genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The structure and function of genes at a molecular level.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3322">
-        <rdfs:label>Respiratory medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.25 Respiratory systems</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Pulmonology</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The study of respiratory system.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pulmonary medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Respiratory disease</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>Pulmonary disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3323">
-        <rdfs:label>Metabolic disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The study of metabolic diseases.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>1.3</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3407"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3324 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3324">
-        <rdfs:label>Infectious disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:hasExactSynonym>Transmissable disease</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.3.4 Infectious diseases</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Communicable disease</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions).</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3325">
-        <rdfs:label>Rare diseases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0634"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The study of rare diseases.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3332">
-        <rdfs:label>Computational chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.7.4 Computational chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems.</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3334">
-        <rdfs:label>Neurology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Neurological disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the anatomy, functions and disorders of the nervous system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3335">
-        <rdfs:label>Cardiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Cardiovascular disease</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.4 Cardiac and Cardiovascular systems</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Cardiovascular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Heart disease</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.22 Peripheral vascular disease</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The diseases and abnormalities of the heart and circulatory system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3336">
-        <rdfs:label>Drug discovery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The discovery and design of drugs or potential drug compounds.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3337">
-        <rdfs:label>Biobank</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <oboInOwl:hasExactSynonym>biobanking</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Repositories of biological samples, typically human, for basic biological and clinical research.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Tissue collection</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3338">
-        <rdfs:label>Mouse clinic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3339">
-        <rdfs:label>Microbial collection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <oboInOwl:hasDefinition>Collections of microbial cells including bacteria, yeasts and moulds.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3340">
-        <rdfs:label>Cell culture collection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3341">
-        <rdfs:label>Clone library</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3342">
-        <rdfs:label>Translational medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>&apos;translating&apos; the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3343">
-        <rdfs:label>Compound libraries and screening</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3336"/>
-        <oboInOwl:hasBroadSynonym>Translational medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Chemical library</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Collections of chemicals, typically for use in high-throughput screening experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Compound library</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Chemical screening</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3344">
-        <rdfs:label>Biomedical science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Topic concerning biological science that is (typically) performed in the context of medicine.</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.3 Health sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Health science</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3345">
-        <rdfs:label>Data identity and mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasExactSynonym>Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases.</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3346">
-        <rdfs:label>Sequence search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Sequence database search</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The search and retrieval from a database on the basis of molecular sequence similarity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3360">
-        <rdfs:label>Biomarkers</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasExactSynonym>Diagnostic markers</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Objective indicators of biological state often used to assess health, and determinate treatment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3361 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3361">
-        <rdfs:label>Laboratory techniques</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The procedures used to conduct an experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Lab techniques</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3365">
-        <rdfs:label>Data architecture, analysis and design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>The development of policies, models and standards that cover data acquisitioin, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Data analysis</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data design</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Data architecture</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3366">
-        <rdfs:label>Data integration and warehousing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data.
-
-</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Data integration</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Data warehousing</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3368">
-        <rdfs:label>Biomaterials</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3297"/>
-        <oboInOwl:hasDefinition>Any matter, surface or construct that interacts with a biological system.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Diagnostic markers</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3369">
-        <rdfs:label>Chemical biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3371"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The use of synthetic chemistry to study and manipulate biological systems.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3370">
-        <rdfs:label>Analytical chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The study of the separation, identification, and quantification of the chemical components of natural and artificial materials.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.7.1 Analytical chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3371">
-        <rdfs:label>Synthetic chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <oboInOwl:hasExactSynonym>Synthetic organic chemistry</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The use of chemistry to create new compounds.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3372">
-        <rdfs:label>Software engineering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasDbXref>VT 1.2.1 Algorithms</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym> Programming languages</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.2.7 Data structures</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Software development</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Software engineering</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Computer programming</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>1.2.12 Programming languages</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The process that leads from an original formulation of a computing problem to executable programs.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Data structures</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Algorithms</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.2.14 Software engineering</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3373 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3373">
-        <rdfs:label>Drug development</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Medicine development</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The process of bringing a new drug to market once a lead compounds has been identified through drug discovery.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Drug development science</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Medicines development</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3374 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3374">
-        <rdfs:label>Drug formulation and delivery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Drug delivery</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Drug formulation</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3375 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3375">
-        <rdfs:label>Pharmacokinetics and pharmacodynamics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasNarrowSynonym>Pharmacodynamics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Pharmacokinetics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Drug distribution</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Drug excretion</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of how a drug interacts with the body.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Drug absorption</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>ADME</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Drug metabolism</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Drug metabolism</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3376 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3376">
-        <rdfs:label>Medicines research and development</rdfs:label>
-        <rdfs:label>Medicine research and development</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDefinition>The discovery, development and approval of medicines.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Health care research</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>Drug discovery and development</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasBroadSynonym>Health care science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3377 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3377">
-        <rdfs:label>Safety sciences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Drug safety</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The safety (or lack) of drugs and other medical interventions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3378">
-        <rdfs:label>Pharmacovigilence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3377"/>
-        <created_in>1.4</created_in>
-        <rdfs:comment>Pharmacovigilence concerns safety once a drug has gone to market.</rdfs:comment>
-        <oboInOwl:hasDefinition>The detection, assesment, understanding and prevention of adverse effects of medicines.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3379">
-        <rdfs:label>Preclinical and clinical studies</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Preclinical studies</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Clinical studies</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3382 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3382">
-        <rdfs:label>Imaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <rdfs:comment>This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as  X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Microscopy imaging</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Diffraction experiment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The visual representation of an object.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3383">
-        <rdfs:label>Biological imaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The use of imaging techniques to understand biology.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3384">
-        <rdfs:label>Medical imaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDbXref>VT 3.2.24 Radiology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The use of imaging techniques for clinical purposes for medical research.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Radiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.14 Nuclear medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Nuclear medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.13 Medical imaging</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3385">
-        <rdfs:label>Light microscopy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The use of optical instruments to magnify the image of an object.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3386">
-        <rdfs:label>Laboratory animal science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The use of animals and alternatives in experimental research.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3387">
-        <rdfs:label>Marine biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.18 Marine and Freshwater biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The study of organisms in the ocean or brackish waters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3388">
-        <rdfs:label>Molecular medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3342"/>
-        <oboInOwl:hasDefinition>The identification of molecular and genetic causes of disease and the development of interventions to correct them.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3390">
-        <rdfs:label>Nutritional science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 3.3.7 Nutrition and Dietetics</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Dietetics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals.  It also includes the study of human behaviours related to food choices.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nutrition science</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3391">
-        <rdfs:label>Omics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDefinition>The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3393">
-        <rdfs:label>Quality affairs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The processes that need to be in place to ensure the quality of products for human or animal use.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Good clinical practice</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Good manufacturing practice</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Quality assurance</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Good laboratory practice</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3394 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3394">
-        <rdfs:label>Regulatory affairs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3395">
-        <rdfs:label>Regnerative medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasExactSynonym>Stem cell research</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Biomedical approaches to clinical interventions that involve the use of stem cells.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3396">
-        <rdfs:label>Systems medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3397">
-        <rdfs:label>Veterinary medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasAlternativeId>Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals.</oboInOwl:hasAlternativeId>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3398">
-        <rdfs:label>Bioengineering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3297"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The application of biological concepts and methods to the analytical and synthetic methodologies of engineering.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Diagnostic markers</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3399">
-        <rdfs:label>Geriatric medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.10 Geriatrics and gerontology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Ageing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Aging</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Gerontology</oboInOwl:hasBroadSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Geriatrics</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3400">
-        <rdfs:label>Allergy, clinical immunology and immunotherapeutics.</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.1 Allergy</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Health issues related to the immune system and their prevention, diagnosis and mangement.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Immune disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Clinical immunology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Immunomodulators</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Allergy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Immunotherapeutics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3401">
-        <rdfs:label>Pain medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Ageing</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Algiatry</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3402">
-        <rdfs:label>Anaesthesiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Anaesthetics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Anaesthesia and anaesthetics.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 3.2.2 Anaesthesiology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3403">
-        <rdfs:label>Critical care medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Acute medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Geriatrics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.5 Critical care/Emergency medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Emergency medicine</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The multidisciplinary that cares for patients with acute, life-threatening illness or injury.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3404">
-        <rdfs:label>Dermatology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Dermatological disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 3.2.7 Dermatology and venereal diseases</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3405">
-        <rdfs:label>Dentistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3406">
-        <rdfs:label>Ear, nose and throat medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Otolaryngology</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Otorhinolaryngology</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Head and neck disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.20 Otorhinolaryngology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Audiovestibular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3407">
-        <rdfs:label>Endocrinology and metabolism</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Metabolic disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Metabolism</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Endocrinology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Endocrine disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3408">
-        <rdfs:label>Haematology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.11 Hematology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the blood, blood-forming organs and blood diseases.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Haematological disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Blood disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3409">
-        <rdfs:label>Gastroenterology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Gastrointestinal disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.8 Gastroenterology and hepatology</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3410">
-        <rdfs:label>Gender medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3411">
-        <rdfs:label>Gynaecology and obstetrics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.15 Obstetrics and gynaecology</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Gynaecology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Gynaecological disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Obstetrics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3412">
-        <rdfs:label>Hepatic and biliary medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Hepatobiliary medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Liver disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the liver, gallbladder, bile ducts and bile.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3413">
-        <rdfs:label>Infectious tropical disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3324"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the infectious diseases of the tropics. </oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3414">
-        <rdfs:label>Trauma medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3415">
-        <rdfs:label>Medical toxicology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3416">
-        <rdfs:label>Musculoskeletal medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue.  It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.26 Rheumatology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.2.19 Orthopaedics</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Musculoskeletal disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Orthopaedics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Rheumatology</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3417">
-        <rdfs:label>Opthalmology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Eye disoders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.18 Optometry</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasBroadSynonym>Optometry</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.17 Ophthalmology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Audiovestibular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3418 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3418">
-        <rdfs:label>Paediatrics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the medical care of infants, children and adolescents.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.21 Paediatrics</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Child health</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3419">
-        <rdfs:label>Psychiatry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Psychiatric disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.23 Psychiatry</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Mental health</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3420">
-        <rdfs:label>Reproductive health</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Reproductive disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Audiovestibular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.3 Andrology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Andrology</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Family planning</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The health of the reproductive processes, functions and systems at all stages of life.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Fertility medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3421">
-        <rdfs:label>Surgery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Transplantation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.28 Transplantation</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3422">
-        <rdfs:label>Urology and nephrology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.29 Urology and nephrology</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Urology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Kidney disease</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Urological disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nephrology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3423">
-        <rdfs:label>Complementary medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.12 Integrative and Complementary medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Holistic medicine</oboInOwl:hasBroadSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasBroadSynonym>Alternative medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Integrative medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3444">
-        <rdfs:label>MRI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasExactSynonym>Nuclear magnetic resonance imaging</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>MRT</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Magnetic resonance tomography</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>NMRI</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Magnetic resonance imaging
-</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3448">
-        <rdfs:label>Neutron diffraction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Neutron microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Elastic neutron scattering</oboInOwl:hasNarrowSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>Neutron diffraction experiment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3452">
-        <rdfs:label>Tomography</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasNarrowSynonym>X-ray tomography</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Electron tomography</oboInOwl:hasNarrowSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3473">
-        <rdfs:label>Data mining</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDbXref>VT 1.3.2 Data mining</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>KDD</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Knowledge discovery in databases</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3474">
-        <rdfs:label>Machine learning</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasDefinition>A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Artificial Intelligence</oboInOwl:hasBroadSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDbXref>VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics)</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3489">
-        <rdfs:label>Database management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasNarrowSynonym>Data maintenance</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Databases</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Database administration</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources.
-</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Biological databases</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3500">
-        <rdfs:label>Animals</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasBroadSynonym>Animal biology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Zoology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>Animal</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.29 Zoology</oboInOwl:hasDbXref>
-        <rdfs:comment>The resource may be specific to a plant, a group of plants or all plants.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Metazoa</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3510 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3510">
-        <rdfs:label>Protein sites, features and motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:hasNarrowSynonym>Protein sequence features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein functional sites</oboInOwl:hasNarrowSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3511">
-        <rdfs:label>Nucleic acid sites, features and motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid sequence features</oboInOwl:hasNarrowSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid functional sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3512">
-        <rdfs:label>Gene transcript features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (mRNA features)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>mRNA features</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes 5&apos;untranslated region (5&apos;UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3&apos;untranslated regions (3&apos;UTR).</rdfs:comment>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3514">
-        <rdfs:label>Protein-ligand interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0128"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Protein-ligand (small molecule) interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3515">
-        <rdfs:label>Protein-drug interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3514"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Protein-drug interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3516">
-        <rdfs:label>Genotyping experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3517 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3517">
-        <rdfs:label>GWAS study</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Genome-wide association study experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome-wide association study</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3518 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3518">
-        <rdfs:label>Microarray experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <rdfs:comment>This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates.</rdfs:comment>
-        <oboInOwl:hasDefinition>Microarray experiments including conditions, protocol, sample:data relationships etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3519">
-        <rdfs:label>PCR experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>PCR experiments, e.g. quantitative real-time PCR.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3520">
-        <rdfs:label>Proteomics experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <oboInOwl:hasDefinition>Proteomics experiments.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3521">
-        <rdfs:label>2D PAGE experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3520"/>
-        <oboInOwl:hasDefinition>Two-dimensional gel electrophoresis experiments, gels or spots in a gel.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3522">
-        <rdfs:label>Northern blot experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3520"/>
-        <oboInOwl:hasDefinition>Northern Blot experiments.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3523">
-        <rdfs:label>RNAi experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3168"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>RNAi experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3524">
-        <rdfs:label>Simulation experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3525">
-        <rdfs:label>Protein-nucleic acid interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0128"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Protein-DNA/RNA interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3526">
-        <rdfs:label>Protein-protein interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:hasNarrowSynonym>Domain-domain interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Protein-protein interaction(s), including interactions between protein domains.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein interaction networks</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3527">
-        <rdfs:label>Cellular process pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Cellular process pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3528">
-        <rdfs:label>Disease pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Disease pathways, typically of human disease.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway or network (disease)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3529">
-        <rdfs:label>Environmental information processing pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Environmental information processing pathways.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Pathway or network (environmental information processing)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3530">
-        <rdfs:label>Genetic information processing pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasExactSynonym>Pathway or network (genetic information processing)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Genetic information processing pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3531">
-        <rdfs:label>Protein super-secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasDefinition>Super-secondary structure of protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (super-secondary)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <rdfs:comment>Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3533">
-        <rdfs:label>Protein active sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasExactSynonym>Enzyme active site</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (active sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Catalytic residues (active site) of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3534">
-        <rdfs:label>Protein binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasDefinition>Ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (binding sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3535 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3535">
-        <rdfs:label>Protein-nucleic acid binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasDefinition>RNA and DNA-binding proteins and binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (nucleic acid binding sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3536">
-        <rdfs:label>Protein cleavage sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasDefinition>Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (cleavage sites)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3537">
-        <rdfs:label>Protein chemical modifications</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasDefinition>Chemical modification of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (chemical modifications)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>MOD:00000</oboInOwl:hasRelatedSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasRelatedSynonym>GO:0006464</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3538 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3538">
-        <rdfs:label>Protein disordered structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasDefinition>Disordered structure in a protein.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (disordered structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3539">
-        <rdfs:label>Protein domains</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0736"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <rdfs:comment>The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Structural domains or 3D folds in a protein or polypeptide chain.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein structural domains</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein features (domains)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3540">
-        <rdfs:label>Protein key folding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0130"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasExactSynonym>Protein features (key folding sites)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Key residues involved in protein folding.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3541 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3541">
-        <rdfs:label>Protein post-translational modifications</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasExactSynonym>Protein features (post-translation modifications)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Post-translation modifications</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Post-translation modifications in a protein sequence, typically describing the specific sites involved.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3542">
-        <rdfs:label>Protein secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <rdfs:comment>The location and size of the secondary structure elements and intervening loop regions is typically given.  The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks).</rdfs:comment>
-        <oboInOwl:hasDefinition>Secondary structure (predicted or real) of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (secondary structure)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3543">
-        <rdfs:label>Protein sequence repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (repeats)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Short repetitive subsequences (repeat sequences) in a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein repeats</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3544 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3544">
-        <rdfs:label>Protein signal peptides</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasExactSynonym>Protein features (signal peptides)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Signal peptides or signal peptide cleavage sites in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3569">
-        <rdfs:label>Applied mathematics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3315"/>
-        <oboInOwl:hasDbXref>VT 1.1.1 Applied mathematics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3570">
-        <rdfs:label>Pure mathematics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3315"/>
-        <oboInOwl:hasDbXref>VT 1.1.1 Pure mathematics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The study of abstract mathematical concepts.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3571">
-        <rdfs:label>Data governance</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasExactSynonym>Data handling</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D030541</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasNarrowSynonym>Data stewardship</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3572">
-        <rdfs:label>Data quality management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D030541</rdfs:seeAlso>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasNarrowSynonym>Data quality</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data integrity</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data clean-up</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data enrichment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The quality, integrity, cleaning up and enrichment of data. </oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3573">
-        <rdfs:label>Freshwater biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.18 Marine and Freshwater biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The study of organisms in freshwater ecosystems.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3574">
-        <rdfs:label>Human genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasDefinition>The study of inheritatnce in human beings.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.2 Human genetics</oboInOwl:hasDbXref>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3575">
-        <rdfs:label>Tropical medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Health problems that are prevalent in tropical and subtropical regions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.3.14 Tropical medicine</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3576 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3576">
-        <rdfs:label>Medical biotechnology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3297"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDbXref>VT 3.4.1 Biomedical devices</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.4.2 Health-related biotechnology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.4 Medical biotechnology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.3.14 Tropical medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Pharmaceutical biotechnology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Biotechnology applied to the medical sciences and the development of medicines.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3577 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3577">
-        <rdfs:label>Personalized medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Health problems that are prevalent in tropical and subtropical regions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Molecular diagnostics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.4.5 Molecular diagnostics</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#ObsoleteClass -->
-
-    <owl:Class rdf:about="&oboInOwl;ObsoleteClass">
-        <rdfs:label>Obsolete concept (EDAM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:subClassOf rdf:resource="&owl;DeprecatedClass"/>
-        <created_in>1.2</created_in>
-        <rdfs:comment>Needed for conversion to the OBO format.</rdfs:comment>
-        <oboInOwl:hasDefinition>An obsolete concept (redefined in EDAM).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-    </owl:Class>
-    
-
-
-    <!-- http://www.w3.org/2002/07/owl#DeprecatedClass -->
-
-    <owl:Class rdf:about="&owl;DeprecatedClass"/>
-</rdf:RDF>
-
-
-
-<!-- Generated by the OWL API (version 3.4.2) http://owlapi.sourceforge.net -->
-
diff --git a/cwl/src/test/resources/cwl/ontology/gx_edam.ttl b/cwl/src/test/resources/cwl/ontology/gx_edam.ttl
deleted file mode 100644
index 8182f719d21..00000000000
--- a/cwl/src/test/resources/cwl/ontology/gx_edam.ttl
+++ /dev/null
@@ -1,7 +0,0 @@
-@prefix gx: <http://galaxyproject.org/formats/> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix edam: <http://edamontology.org/> .
-
-gx:fasta a owl:Class .
-gx:fasta owl:equivalentClass edam:format_1929 .
diff --git a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/complex_workflow/expected_result.json
deleted file mode 100644
index fd297c8da92..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/expected_result.json
+++ /dev/null
@@ -1,204 +0,0 @@
-{
-  "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2",
-  "class" : "Workflow",
-  "requirements" : [
-    {
-      "class" : "StepInputExpressionRequirement"
-    }
-  ],
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/tool"
-    }
-  ],
-  "outputs" : [
-  ],
-  "steps" : [
-    {
-      "run" : {
-        "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1",
-        "class" : "Workflow",
-        "requirements" : [
-          {
-            "class" : "StepInputExpressionRequirement"
-          }
-        ],
-        "inputs" : [
-          {
-            "type" : "File",
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/tool"
-          }
-        ],
-        "outputs" : [
-        ],
-        "steps" : [
-          {
-            "run" : {
-              "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1",
-              "class" : "Workflow",
-              "requirements" : [
-                {
-                  "class" : "StepInputExpressionRequirement"
-                }
-              ],
-              "inputs" : [
-                {
-                  "type" : "File",
-                  "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool"
-                }
-              ],
-              "outputs" : [
-              ],
-              "steps" : [
-                {
-                  "run" : {
-                    "cwlVersion" : "v1.0",
-                    "class" : "CommandLineTool",
-                    "baseCommand" : [
-                      "echo"
-                    ],
-                    "inputs" : [
-                      {
-                        "type" : "string",
-                        "inputBinding" : {
-                          "position" : 1
-                        },
-                        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-                      }
-                    ],
-                    "outputs" : [
-                      {
-                        "type" : "string",
-                        "valueFrom" : "hello",
-                        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-                      }
-                    ],
-                    "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-                  },
-                  "in" : [
-                    {
-                      "valueFrom" : "$(inputs.tool.nameroot)",
-                      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/in"
-                    },
-                    {
-                      "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool",
-                      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/tool"
-                    }
-                  ],
-                  "out" : [
-                    "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/out"
-                  ],
-                  "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root"
-                }
-              ]
-            },
-            "in" : [
-              {
-                "valueFrom" : "$(inputs.tool.nameroot)",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root/in"
-              },
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/tool",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root/tool"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root/out"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root"
-          }
-        ]
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/tool",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1"
-    },
-    {
-      "run" : {
-        "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1",
-        "class" : "Workflow",
-        "requirements" : [
-          {
-            "class" : "StepInputExpressionRequirement"
-          }
-        ],
-        "inputs" : [
-          {
-            "type" : "File",
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool"
-          }
-        ],
-        "outputs" : [
-        ],
-        "steps" : [
-          {
-            "run" : {
-              "cwlVersion" : "v1.0",
-              "class" : "CommandLineTool",
-              "baseCommand" : [
-                "echo"
-              ],
-              "inputs" : [
-                {
-                  "type" : "string",
-                  "inputBinding" : {
-                    "position" : 1
-                  },
-                  "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-                }
-              ],
-              "outputs" : [
-                {
-                  "type" : "string",
-                  "valueFrom" : "hello",
-                  "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-                }
-              ],
-              "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-            },
-            "in" : [
-              {
-                "valueFrom" : "$(inputs.tool.nameroot)",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/in"
-              },
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/tool"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/out"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root"
-          }
-        ]
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/tool",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2"
-    }
-  ]
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/complex_workflow/root_workflow.cwl
deleted file mode 100644
index 6aa8f741dad..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/root_workflow.cwl
+++ /dev/null
@@ -1,41 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root1:
-      run: "sub/sub_workflow.cwl#sub-echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-    root2:
-      run: "#echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: echo-workflow-1
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: ../echo_tool.cwl
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/sub/sub_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/complex_workflow/sub/sub_workflow.cwl
deleted file mode 100644
index de293ab19ce..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/sub/sub_workflow.cwl
+++ /dev/null
@@ -1,34 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: sub-echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: ../../echo_tool.cwl
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: sub-echo-workflow-1
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "../root_workflow.cwl#echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/expected_result.json
deleted file mode 100644
index 59fea901d3b..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/expected_result.json
+++ /dev/null
@@ -1,132 +0,0 @@
-{
-  "class" : "Workflow",
-  "cwlVersion" : "v1.0",
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#file1"
-    }
-  ],
-  "outputs" : [
-    {
-      "type" : "int",
-      "outputSource" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/count_output",
-      "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#count_output"
-    }
-  ],
-  "requirements" : [
-    {
-      "class" : "SubworkflowFeatureRequirement"
-    }
-  ],
-  "steps" : [
-    {
-      "in" : [
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#file1",
-          "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/file1"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/count_output"
-      ],
-      "run" : {
-        "class" : "Workflow",
-        "inputs" : [
-          {
-            "type" : "File",
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/file1"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "int",
-            "outputSource" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2/output",
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/count_output"
-          }
-        ],
-        "steps" : [
-          {
-            "run" : {
-              "class" : "CommandLineTool",
-              "cwlVersion" : "v1.0",
-              "inputs" : [
-                {
-                  "type" : "File",
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/wc-tool.cwl#file1"
-                }
-              ],
-              "outputs" : [
-                {
-                  "type" : "File",
-                  "outputBinding" : {
-                    "glob" : "output"
-                  },
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/wc-tool.cwl#output"
-                }
-              ],
-              "baseCommand" : [
-                "wc",
-                "-l"
-              ],
-              "stdin" : "$(inputs.file1.path)",
-              "stdout" : "output",
-              "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/wc-tool.cwl"
-            },
-            "in" : [
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/file1",
-                "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1/file1"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1/output"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1"
-          },
-          {
-            "run" : {
-              "class" : "ExpressionTool",
-              "requirements" : [
-                {
-                  "class" : "InlineJavascriptRequirement"
-                }
-              ],
-              "cwlVersion" : "v1.0",
-              "inputs" : [
-                {
-                  "type" : "File",
-                  "inputBinding" : {
-                    "loadContents" : true
-                  },
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/parseInt-tool.cwl#file1"
-                }
-              ],
-              "outputs" : [
-                {
-                  "type" : "int",
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/parseInt-tool.cwl#output"
-                }
-              ],
-              "expression" : "$({'output': parseInt(inputs.file1.contents)})",
-              "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/parseInt-tool.cwl"
-            },
-            "in" : [
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1/output",
-                "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2/file1"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2/output"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2"
-          }
-        ],
-        "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>"
-      },
-      "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0"
-    }
-  ],
-  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl"
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/parseInt-tool.cwl b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/parseInt-tool.cwl
deleted file mode 100644
index 15460db136b..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/parseInt-tool.cwl
+++ /dev/null
@@ -1,14 +0,0 @@
-class: ExpressionTool
-requirements:
-  - class: InlineJavascriptRequirement
-cwlVersion: v1.0
-
-inputs:
-  file1:
-    type: File
-    inputBinding: { loadContents: true }
-
-outputs:
-  output: int
-
-expression: "$({'output': parseInt(inputs.file1.contents)})"
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/root_workflow.cwl
deleted file mode 100644
index 9d3d313c348..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/root_workflow.cwl
+++ /dev/null
@@ -1,21 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-inputs:
-  file1: File
-outputs:
-  count_output: {type: int, outputSource: step0/count_output}
-requirements:
-  SubworkflowFeatureRequirement: {}
-steps:
-  step0:
-    in: {file1: file1}
-    out: [count_output]
-    run:
-      class: Workflow
-      inputs:
-        file1: File
-      outputs:
-        count_output: {type: int, outputSource: step2/output}
-      steps:
-        step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]}
-        step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]}
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/wc-tool.cwl b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/wc-tool.cwl
deleted file mode 100644
index 3eb09378514..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/wc-tool.cwl
+++ /dev/null
@@ -1,15 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-
-inputs:
-  file1: File
-
-outputs:
-  output:
-    type: File
-    outputBinding: { glob: output }
-
-baseCommand: [wc, -l]
-
-stdin: $(inputs.file1.path)
-stdout: output
diff --git a/cwl/src/test/resources/cwl/preprocessor/echo_tool.cwl b/cwl/src/test/resources/cwl/preprocessor/echo_tool.cwl
deleted file mode 100644
index f253c2a435f..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/echo_tool.cwl
+++ /dev/null
@@ -1,13 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: [echo]
-inputs:
-  in:
-    type: string
-    inputBinding:
-      position: 1
-outputs:
-  out:
-    type: string
-    valueFrom: "hello"
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/same_file_cyclic_dependency/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/same_file_cyclic_dependency/root_workflow.cwl
deleted file mode 100644
index fddea7eb644..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/same_file_cyclic_dependency/root_workflow.cwl
+++ /dev/null
@@ -1,34 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "#echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: echo-workflow-1
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "#echo-workflow-2"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/self_reference/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/self_reference/expected_result.json
deleted file mode 100644
index f6c98537192..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/self_reference/expected_result.json
+++ /dev/null
@@ -1,58 +0,0 @@
-{
-  "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2",
-  "class" : "Workflow",
-  "requirements" : [
-    {
-      "class" : "StepInputExpressionRequirement"
-    }
-  ],
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/tool"
-    }
-  ],
-  "outputs" : [
-  ],
-  "steps" : [
-    {
-      "run" : {
-        "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-tool",
-        "class" : "CommandLineTool",
-        "baseCommand" : [
-          "echo"
-        ],
-        "inputs" : [
-          {
-            "type" : "string",
-            "inputBinding" : {
-              "position" : 1
-            },
-            "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-tool/in"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "string",
-            "valueFrom" : "hello",
-            "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-tool/out"
-          }
-        ]
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/tool",
-          "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root"
-    }
-  ]
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/self_reference/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/self_reference/root_workflow.cwl
deleted file mode 100644
index 06a70f19f01..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/self_reference/root_workflow.cwl
+++ /dev/null
@@ -1,31 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "#echo-tool"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: echo-tool
-  class: CommandLineTool
-  baseCommand: [echo]
-  inputs:
-    in:
-      type: string
-      inputBinding:
-        position: 1
-  outputs:
-    out:
-      type: string
-      valueFrom: "hello"
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/simple_workflow/expected_result.json
deleted file mode 100644
index 82176bc4177..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/expected_result.json
+++ /dev/null
@@ -1,100 +0,0 @@
-{
-  "cwlVersion" : "v1.0",
-  "class" : "Workflow",
-  "requirements" : [
-    {
-      "class" : "StepInputExpressionRequirement"
-    }
-  ],
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#tool"
-    }
-  ],
-  "outputs" : [
-  ],
-  "steps" : [
-    {
-      "run" : {
-        "cwlVersion" : "v1.0",
-        "class" : "CommandLineTool",
-        "baseCommand" : [
-          "echo"
-        ],
-        "inputs" : [
-          {
-            "type" : "string",
-            "inputBinding" : {
-              "position" : 1
-            },
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "string",
-            "valueFrom" : "hello",
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-          }
-        ],
-        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#tool",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1"
-    },
-    {
-      "run" : {
-        "cwlVersion" : "v1.0",
-        "class" : "CommandLineTool",
-        "baseCommand" : [
-          "echo"
-        ],
-        "inputs" : [
-          {
-            "type" : "string",
-            "inputBinding" : {
-              "position" : 1
-            },
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "string",
-            "valueFrom" : "hello",
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-          }
-        ],
-        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#tool",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2"
-    }
-  ],
-  "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl"
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/simple_workflow/root_workflow.cwl
deleted file mode 100644
index 86ba8b08658..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/root_workflow.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-   tool: File
-outputs: []
-steps:
-  step1:
-    run: ../echo_tool.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-  step2:
-    run: ../echo_tool.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/root_workflow.cwl
deleted file mode 100644
index 8871f99a932..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/root_workflow.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-  tool: File
-outputs: []
-steps:
-  root:
-    run: sub_workflow_1.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_1.cwl b/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_1.cwl
deleted file mode 100644
index 13f85d169b5..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_1.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-  tool: File
-outputs: []
-steps:
-  root:
-    run: sub_workflow_2.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_2.cwl b/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_2.cwl
deleted file mode 100644
index 0d8c5a49691..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_2.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-  tool: File
-outputs: []
-steps:
-  root:
-    run: root_workflow.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/dir_example.cwl b/cwl/src/test/resources/dir_example.cwl
deleted file mode 100644
index 70efc02596a..00000000000
--- a/cwl/src/test/resources/dir_example.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-requirements:
-  - class: ShellCommandRequirement
-inputs:
-  - id: indir
-    type: Directory
-    default:
-      class: Directory
-      location: exampledir
-outputs:
-  outlist:
-    type: File
-    outputBinding:
-      glob: output.txt
-arguments: ["echo", "$(inputs.indir.basename)"]
-stdout: output.txt
diff --git a/cwl/src/test/resources/env.cwl b/cwl/src/test/resources/env.cwl
deleted file mode 100644
index 19a23e77948..00000000000
--- a/cwl/src/test/resources/env.cwl
+++ /dev/null
@@ -1,10 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: env
-requirements:
-  EnvVarRequirement:
-    envDef:
-      HELLO: $(inputs.message)
-inputs:
-  message: string
-outputs: []
diff --git a/cwl/src/test/resources/exampledir/example.txt b/cwl/src/test/resources/exampledir/example.txt
deleted file mode 100644
index 3b18e512dba..00000000000
--- a/cwl/src/test/resources/exampledir/example.txt
+++ /dev/null
@@ -1 +0,0 @@
-hello world
diff --git a/cwl/src/test/resources/file_example.cwl b/cwl/src/test/resources/file_example.cwl
deleted file mode 100644
index 6245d3232be..00000000000
--- a/cwl/src/test/resources/file_example.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-requirements:
-  - class: ShellCommandRequirement
-inputs:
-  - id: infile
-    type: File
-    default:
-      class: File
-      location: exampledir/example.txt
-outputs:
-  outlist:
-    type: File
-    outputBinding:
-      glob: output.txt
-arguments: ["echo", "$(inputs.infile.basename)"]
-stdout: output.txt
diff --git a/cwl/src/test/resources/file_size_example.cwl b/cwl/src/test/resources/file_size_example.cwl
deleted file mode 100644
index 3b24a1f5cdd..00000000000
--- a/cwl/src/test/resources/file_size_example.cwl
+++ /dev/null
@@ -1,18 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-requirements:
-  - class: ShellCommandRequirement
-inputs:
-  - id: infile
-    type: File
-    default:
-      class: File
-      location: exampledir/example.txt
-outputs:
-  outlist:
-    type: File
-    outputBinding:
-      glob: output.txt
-# size is optional according to the spec, however there are real world CWLs using it
-arguments: ["echo", "$(inputs.infile.size)"]
-stdout: output.txt
diff --git a/cwl/src/test/resources/links_dont_parse.cwl b/cwl/src/test/resources/links_dont_parse.cwl
deleted file mode 100644
index 2cab593fce8..00000000000
--- a/cwl/src/test/resources/links_dont_parse.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: File
-  ex: string
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classfile
-
-steps:
-  untar:
-    run: bad.cwl
-    in:
-      tarfile: inp
-      extractfile: ex
-    out: [example_out]
-
-  compile:
-    run: bad2.cwl
-    in:
-      src: untar/example_out
-    out: [classfile]
diff --git a/cwl/src/test/resources/logback-test.xml b/cwl/src/test/resources/logback-test.xml
deleted file mode 100644
index 5ef34ca9aad..00000000000
--- a/cwl/src/test/resources/logback-test.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<configuration>
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-            <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n</pattern>
-        </encoder>
-    </appender>
-
-    <root level="info">
-        <appender-ref ref="STDOUT"/>
-    </root>
-
-    <logger name="org.mockserver" level="WARN"/>
-    <logger name="liquibase" level="WARN"/>
-    <logger name="com.zaxxer.hikari" level="ERROR"/>
-    <logger name="HikariPool" level="ERROR"/>
-    <logger name="com.google.cloud.hadoop.gcsio.GoogleCloudStorageReadChannel" level="ERROR"/>
-</configuration>
diff --git a/cwl/src/test/resources/nestedworkflows.cwl b/cwl/src/test/resources/nestedworkflows.cwl
deleted file mode 100644
index 3963109e630..00000000000
--- a/cwl/src/test/resources/nestedworkflows.cwl
+++ /dev/null
@@ -1,52 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-
-inputs: []
-
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classout
-
-requirements:
-  - class: SubworkflowFeatureRequirement
-
-steps:
-  compile:
-    run: 1st-workflow.cwl
-    in:
-      inp:
-        source: create-tar/tar
-      ex:
-        default: "Hello.java"
-    out: [classout]
-
-  create-tar:
-    requirements:
-      - class: InitialWorkDirRequirement
-        listing:
-          - entryname: Hello.java
-            entry: |
-              public class Hello {
-                public static void main(String[] argv) {
-                    System.out.println("Hello from Java");
-                }
-              }
-    in: []
-    out: [tar]
-    run:
-      class: CommandLineTool
-      requirements:
-        - class: ShellCommandRequirement
-      arguments:
-        - shellQuote: false
-          valueFrom: |
-            date
-            tar cf hello.tar Hello.java
-            date
-      inputs: []
-      outputs:
-        tar:
-          type: File
-          outputBinding:
-            glob: "hello.tar"
diff --git a/cwl/src/test/resources/tar-param.cwl b/cwl/src/test/resources/tar-param.cwl
deleted file mode 100644
index 39e9aa07016..00000000000
--- a/cwl/src/test/resources/tar-param.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-cwlVersion: "v1.0"
-class: "CommandLineTool"
-baseCommand: ["tar", "xf"]
-inputs: 
-  - type: "string"
-    inputBinding: 
-      position: 2
-    id: "extractfile"
-  - type: "File"
-    inputBinding: 
-      position: 1
-    id: "tarfile"
-outputs: 
-  - type: "File"
-    outputBinding: 
-      glob: "$(inputs.extractfile)"
-    id: "example_out"
diff --git a/cwl/src/test/resources/three_step.cwl b/cwl/src/test/resources/three_step.cwl
deleted file mode 100644
index e9cd1267b86..00000000000
--- a/cwl/src/test/resources/three_step.cwl
+++ /dev/null
@@ -1,112 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-id: three_step
-hints:
-# hints can be anything (CwlAny)
-- fee: fi
-  fo: fum
-- eenie: meenie
-  minie: mo
-- 42
-- class: DockerRequirement
-  dockerPull: "ubuntu:latest"
-inputs:
-- id: pattern
-  type: string
-outputs:
-- id: cgrep-count
-  outputSource: "#cgrep/cgrep-count"
-  type: int
-- id: wc-count
-  outputSource: "#wc/wc-count"
-  type: int
-steps:
-- id: ps
-  in: []
-  out:
-  - id: ps-stdOut
-  run:
-    inputs: []
-    outputs:
-    - id: ps-stdOut
-      outputBinding:
-        glob: ps-stdOut.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-    - class: DockerRequirement
-      dockerPull: "debian:wheezy"
-    baseCommand: ps
-    stdout: ps-stdOut.txt
-- id: cgrep
-  in:
-  - id: pattern
-    source: "#pattern"
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: cgrep-count
-  run:
-    inputs:
-    - id: pattern
-      type: string
-    - id: file
-      type: File
-    outputs:
-    - id: cgrep-count
-      outputBinding:
-        glob: cgrep-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: grep
-      shellQuote: false
-    - valueFrom: $(inputs.pattern)
-      shellQuote: false
-    - valueFrom: ${return inputs.file}
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: cgrep-stdOut.txt
-- id: wc
-  in:
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: wc-count
-  run:
-    inputs:
-    - id: file
-      type: File
-    outputs:
-    - id: wc-count
-      outputBinding:
-        glob: wc-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: cat
-      shellQuote: false
-    - valueFrom: $(inputs.file)
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: wc-stdOut.txt
diff --git a/cwl/src/test/scala/cwl/CommandLineToolSpec.scala b/cwl/src/test/scala/cwl/CommandLineToolSpec.scala
deleted file mode 100644
index b466f1f3e90..00000000000
--- a/cwl/src/test/scala/cwl/CommandLineToolSpec.scala
+++ /dev/null
@@ -1,279 +0,0 @@
-package cwl
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.assertion.CromwellTimeoutSpec
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.ParallelTestExecution
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.callable.Callable.RequiredInputDefinition
-import wom.callable.RuntimeEnvironment
-import wom.expression.NoIoFunctionSet
-import wom.types._
-import wom.values.{WomArray, WomBoolean, WomEvaluatedCallInputs, WomInteger, WomObject, WomSingleFile, WomString, WomValue}
-
-class CommandLineToolSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ParallelTestExecution {
-
-  behavior of "CommandLineTool"
-
-  val inputs: WomEvaluatedCallInputs = Map(
-    RequiredInputDefinition("a", WomStringType) -> WomString("helloA"),
-    RequiredInputDefinition("b", WomStringType) -> WomString("helloB"),
-    RequiredInputDefinition("c", WomStringType) -> WomString("helloC"),
-    RequiredInputDefinition("d", WomArrayType(WomStringType)) -> WomArray(WomArrayType(WomStringType), List(WomString("helloD0"), WomString("helloD1"))),
-    RequiredInputDefinition("e", WomCompositeType(Map("fa" -> WomSingleFileType, "fb" -> WomIntegerType)))
-      -> WomObject.withTypeUnsafe(Map("fa" -> WomSingleFile("helloEfa"), "fb" -> WomInteger(0)), WomCompositeType(Map("fa" -> WomSingleFileType, "fb" -> WomIntegerType))),
-    RequiredInputDefinition("f", WomBooleanType) -> WomBoolean.True,
-    RequiredInputDefinition("g", WomBooleanType) -> WomBoolean.False,
-    RequiredInputDefinition("h", WomIntegerType) -> WomInteger(0),
-    RequiredInputDefinition("i", WomSingleFileType) -> WomSingleFile("ifile")
-  )
-  
-  val localNameValues = inputs.map({ case (k, v) => k.localName -> v })
-  
-  val noIoFunctionSet = NoIoFunctionSet
-  
-  val runtimeEnv = RuntimeEnvironment("", "", refineMV[Positive](1), 0D, 0L, 0L)
-  
-  def validate(tool: String, expectation: List[String]) = {
-    val cltFile = better.files.File.newTemporaryFile()().write(tool)
-
-    val clt = CwlDecoder.decodeCwlFile(cltFile, None).value.unsafeRunSync() match {
-      case Left(errors) => fail("Cannot parse command line tool " + errors.toList.mkString(", "))
-      case Right(cwlFile) => cwlFile.select[CommandLineTool].get
-    }
-
-    val template = clt
-      .buildCommandTemplate.run((RequirementsAndHints(List.empty), Vector.empty,inputs))
-      .valueOr(errors => fail(errors.toList.mkString(", ")))
-    template
-      .flatTraverse(_.instantiate(localNameValues, noIoFunctionSet, identity[WomValue], runtimeEnv).map(_.map(_.commandString)))
-      .valueOr(errors => fail(errors.toList.mkString(", "))) shouldBe expectation
-    
-    cltFile.delete(true)
-  }
-  
-  it should "filter input arguments when not bound to command line" in {
-    val tool = """
-      |class: CommandLineTool
-      |cwlVersion: v1.0
-      |inputs:
-      |  - id: a
-      |    type: string
-      |    inputBinding: { position: 2 }
-      |
-      |  - id: b
-      |    type: string
-      |
-      |baseCommand: echo
-      |outputs: []
-    """.stripMargin
-
-    validate(tool, List("'echo'", "'helloA'"))
-  }
-
-  it should "order input arguments that are bound to command line" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  - id: b
-                 |    type: string
-                 |    inputBinding: { position: 2 }
-                 |    
-                 |  - id: c
-                 |    type: string
-                 |    inputBinding: { position: 3 }
-                 |
-                 |  - id: a
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'helloA'", "'helloB'", "'helloC'"))
-  }
-
-  it should "include arguments and sort them" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  - id: b
-                 |    type: string
-                 |    inputBinding: { position: 4 }
-                 |    
-                 |  - id: c
-                 |    type: string
-                 |    inputBinding: { position: 5 }
-                 |
-                 |  - id: a
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |arguments:
-                 |  - arg0
-                 |  - valueFrom: "arg2"
-                 |    position: 3
-                 |  - valueFrom: "arg1"
-                 |    position: 2
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'arg0'", "'helloA'", "'arg1'", "'arg2'", "'helloB'", "'helloC'"))
-  }
-
-  it should "handle array types" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  - id: d
-                 |    type:
-                 |      type: array
-                 |      items: string
-                 |      inputBinding: { prefix: "-YYY" }
-                 |    inputBinding: { position: 3, prefix: "-XXX" }
-                 |    
-                 |  - id: a
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |arguments:
-                 |  - valueFrom: "arg2"
-                 |    position: 2
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'helloA'", "'arg2'", "'-XXX'", "'-YYY'", "'helloD0'", "'-YYY'", "'helloD1'"))
-  }
-
-  it should "handle record schema" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  e:
-                 |    type:
-                 |      name: e
-                 |      type: record
-                 |      fields:
-                 |      - name: fa
-                 |        type: File
-                 |        inputBinding:
-                 |          position: 2
-                 |          prefix: "--prefixFa"
-                 |      - name: fb
-                 |        type: int
-                 |        inputBinding:
-                 |          position: 4
-                 |          prefix: "--prefixFb"
-                 |    inputBinding:      
-                 |      prefix: "--prefixRecord"
-                 |  a:
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |arguments:
-                 |  - valueFrom: "arg2"
-                 |    position: 3
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--prefixRecord'", "'--prefixFa'", "'helloEfa'", "'--prefixFb'", "'0'", "'helloA'", "'arg2'"))
-  }
-
-  it should "handle prefixes properly for primitive types" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  a:
-                 |    type: string
-                 |    inputBinding: { position: 1, prefix: --aprefix }
-                 |  f:
-                 |    type: boolean
-                 |    inputBinding: { position: 2, prefix: --show }
-                 |  g:
-                 |    type: boolean
-                 |    inputBinding: { position: 3, prefix: --noshow }
-                 |  h:
-                 |    type: string
-                 |    inputBinding: { position: 4, prefix: --hprefix }
-                 |  i:
-                 |    type: File
-                 |    inputBinding: { position: 5, prefix: --iprefix }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--aprefix'", "'helloA'", "'--show'", "'--hprefix'", "'0'", "'--iprefix'", "'ifile'"))
-  }
-
-  it should "handle arrays with item separator" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  d:
-                 |    type:
-                 |      type: array
-                 |      items: string
-                 |      inputBinding: { position: 2, prefix: --item }
-                 |    inputBinding: { position: 2, prefix: --array, itemSeparator: ", " }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--array'", "'helloD0, helloD1'"))
-  }
-
-  it should "handle arrays with valueFrom" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  d:
-                 |    type:
-                 |      type: array
-                 |      items: string
-                 |      inputBinding: { position: 2, prefix: --item }
-                 |    inputBinding: { position: 2, prefix: --array, valueFrom: "hello" }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--array'", "'hello'"))
-  }
-
-  it should "handle the separate field" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  a:
-                 |    type: string
-                 |    inputBinding: { position: 0, prefix: --prefix, separate: false }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--prefixhelloA'"))
-  }
-
-  it should "pull expression libs from all requirements" in {
-    val list = List(Coproduct[Requirement](InlineJavascriptRequirement(`class` = "InlineJavascriptRequirement", expressionLib = Some(Array("a")))))
-    Tool.inlineJavascriptRequirements(list).head shouldBe "a"
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CommandOutputExpressionSpec.scala b/cwl/src/test/scala/cwl/CommandOutputExpressionSpec.scala
deleted file mode 100644
index f2cc446e65f..00000000000
--- a/cwl/src/test/scala/cwl/CommandOutputExpressionSpec.scala
+++ /dev/null
@@ -1,57 +0,0 @@
-package cwl
-
-import java.util.concurrent.Executors
-
-import cats.syntax.all._
-import common.assertion.CromwellTimeoutSpec
-import cwl.CommandLineTool.CommandOutputParameter
-import cwl.ExpressionEvaluator._
-import eu.timepit.refined._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.expression.{EmptyIoFunctionSet, FileEvaluation, NoIoFunctionSet}
-import wom.types.WomIntegerType
-import wom.values._
-
-import scala.concurrent.{ExecutionContext, Future}
-
-
-class CommandOutputExpressionSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "CommandOutputExpression"
-
-  def ioFunctionSet(data: String) =
-    new EmptyIoFunctionSet {
-      override implicit def ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(1))
-      override def readFile(path: String, maxBytes: Option[Int] = None, failOnOverflow: Boolean = false) = Future.successful(data)
-      // For this test just "match" the submitted file.
-      override def glob(pattern: String): Future[Seq[String]] = Future.successful(List(pattern))
-    }
-
-  it should "evaluateValue" in {
-    val data = "41.1"
-    val tempFile = better.files.File.newTemporaryFile("glob.", ".txt").write(data)
-    val globExpression = Coproduct[Expression](refineMV[MatchesECMAScriptExpression]("$(inputs.myTempFile)"))
-    val outputEvalExpression = Coproduct[Expression](refineMV[MatchesECMAScriptExpression](
-      "$((parseInt(self[0].contents) + 1).toFixed())"))
-    val glob = Coproduct[Glob](Coproduct[StringOrExpression](globExpression))
-    val outputEval = Coproduct[StringOrExpression](outputEvalExpression)
-    val outputBinding = CommandOutputBinding(Option(glob), Option(true), Option(outputEval))
-    val commandOutputParameter = CommandOutputParameter("id", outputBinding = Option(outputBinding))
-    val commandOutputExpression = OutputParameterExpression(commandOutputParameter, WomIntegerType, Set.empty, Vector.empty, SchemaDefRequirement())
-    val inputValues = Map("myTempFile" -> WomString(tempFile.pathAsString))
-    val result = commandOutputExpression.evaluateValue(inputValues, ioFunctionSet(data))
-    result should be(WomInteger(42).valid)
-  }
-
-  it should "figure out stdout" in {
-    val glob = Coproduct[Glob](Coproduct[StringOrExpression]("stdout"))
-    val outputBinding = CommandOutputBinding(Option(glob))
-    val commandOutputParameter = CommandOutputParameter("id", outputBinding = Option(outputBinding))
-    val commandOutputExpression = OutputParameterExpression(commandOutputParameter, WomIntegerType, Set.empty, Vector.empty, SchemaDefRequirement())
-    val result = commandOutputExpression.evaluateFiles(Map.empty, NoIoFunctionSet, WomIntegerType)
-    // TODO: This should be a glob. See [[cwl.CommandOutputBinding.dependingIfGlobLike]]
-    result shouldBe Set(FileEvaluation.requiredFile(WomSingleFile("stdout"))).valid
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlDecoderSpec.scala b/cwl/src/test/scala/cwl/CwlDecoderSpec.scala
deleted file mode 100644
index c206c116a84..00000000000
--- a/cwl/src/test/scala/cwl/CwlDecoderSpec.scala
+++ /dev/null
@@ -1,48 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class CwlDecoderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "cwl decoder"
-
-  import TestSetup._
-
-  it should "read nested workflow" in {
-      decodeCwlFile(rootPath / "nestedworkflows.cwl").
-        value.
-        unsafeRunSync() match {
-        case Right(cwl) =>
-          val wf = cwl.select[Workflow].get
-          wf.steps.flatMap(_.run.select[String].toList).length shouldBe 0
-        case Left(other) => fail(other.toList.mkString(", "))
-      }
-  }
-
-  it should "fail to parse broken linked cwl" in {
-    val result: Either[NonEmptyList[String], Cwl] = decodeCwlFile(rootPath / "brokenlinks.cwl").
-      value.
-      unsafeRunSync()
-
-    result.isLeft shouldBe true
-    withClue(s"Actual message: ${result.swap.toOption.get.head}") {
-      "Field `run` contains undefined reference to `file://.+/wrong.cwl`".r.findAllIn(result.swap.toOption.get.head).size shouldBe 1
-      "Field `run` contains undefined reference to `file://.+/wrong2.cwl`".r.findAllIn(result.swap.toOption.get.head).size shouldBe 1
-    }
-  }
-
-  it should "fail to parse invalid linked cwl" in {
-      decodeCwlFile(rootPath/"links_dont_parse.cwl").
-        value.
-        unsafeRunSync() match {
-        case Left(errors) =>
-          errors.filter(_.contains("bad.cwl")).size + errors.filter(_.contains("bad2.cwl")).size shouldBe 1
-        case Right(_) => fail("should not have passed!")
-      }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlEcmaScriptDecoderSpec.scala b/cwl/src/test/scala/cwl/CwlEcmaScriptDecoderSpec.scala
deleted file mode 100644
index 6c6918efaaa..00000000000
--- a/cwl/src/test/scala/cwl/CwlEcmaScriptDecoderSpec.scala
+++ /dev/null
@@ -1,77 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.internal.{EcmaScriptEncoder, EcmaScriptUtil}
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.values.{WomFloat, WomMaybePopulatedFile, WomString, WomValue}
-
-
-class CwlEcmaScriptDecoderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-  behavior of "CwlJsDecoder"
-
-  val decodeTests= Table[String, String, Map[String, Map[String, WomValue]], WomValue](
-    (
-      "description",
-      "expr",
-      "values",
-      "expected"
-    ),
-    (
-      "a passed through file",
-      "inputMap",
-      Map("inputMap" -> Map(
-        "class" -> WomString("File"),
-        "location" -> WomString("path/to/file.txt"),
-        "checksum" -> WomString("hash_here"),
-        "size" -> WomFloat(Double.box(123.4)),
-        "format" -> WomString("file_format"),
-        "contents" -> WomString("file_contents")
-      )),
-      WomMaybePopulatedFile(
-        valueOption = Option("path/to/file.txt"),
-        checksumOption = Option("hash_here"),
-        sizeOption = Option(123L),
-        formatOption = Option("file_format"),
-        contentsOption = Option("file_contents"),
-        secondaryFiles = Vector()
-      )
-    ),
-    (
-      "a script generated file",
-      """|var result = {
-         |"class": "File",
-         |"path": "other/dir/img.jpg",
-         |"checksum": "check_sum",
-         |"size": 567.8,
-         |"format": "more_jpeg",
-         |"contents": "lol_cat"
-         |};
-         |result;
-         |""".stripMargin,
-      Map(),
-      WomMaybePopulatedFile(
-        valueOption = Option("other/dir/img.jpg"),
-        checksumOption = Option("check_sum"),
-        sizeOption = Option(567L),
-        formatOption = Option("more_jpeg"),
-        contentsOption = Option("lol_cat"),
-        secondaryFiles = Vector()
-      )
-    )
-  )
-
-  forAll(decodeTests) { (description, expr, values: Map[String, Map[String, WomValue]], expected) =>
-    it should s"decode $description" in {
-      val result = EcmaScriptUtil.evalStructish(
-        expr,
-        "fake" -> WomString("unused"),
-        values,
-        new EcmaScriptEncoder()
-      ).toTry.get
-      result should be(expected)
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlEcmaScriptEncoderSpec.scala b/cwl/src/test/scala/cwl/CwlEcmaScriptEncoderSpec.scala
deleted file mode 100644
index 9119f75c421..00000000000
--- a/cwl/src/test/scala/cwl/CwlEcmaScriptEncoderSpec.scala
+++ /dev/null
@@ -1,35 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.internal.EcmaScriptUtil.{ESArray, ESObject, ESPrimitive}
-import cwl.internal.{EcmaScriptEncoder, EcmaScriptUtil}
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.values.WomMaybePopulatedFile
-
-
-class CwlEcmaScriptEncoderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "EcmaScriptEncoder"
-
-  it should "encode" in {
-    val encoder = new EcmaScriptEncoder()
-    val file = WomMaybePopulatedFile("path/to/file.txt")
-    val expected = Map(
-      "class" -> ESPrimitive("File"),
-      "location" -> ESPrimitive("path/to/file.txt"),
-      "path" -> ESPrimitive("path/to/file.txt"),
-      "dirname" -> ESPrimitive("path/to"),
-      "basename" -> ESPrimitive("file.txt"),
-      "nameroot" -> ESPrimitive("file"),
-      "nameext" -> ESPrimitive(".txt")
-    )
-    val result: EcmaScriptUtil.ECMAScriptVariable = encoder.encode(file)
-    val resultMap = result.asInstanceOf[ESObject].fields
-    resultMap.view.filterKeys(_ != "secondaryFiles").toList should contain theSameElementsAs expected
-    resultMap("secondaryFiles") should be(a[ESArray])
-    resultMap("secondaryFiles").asInstanceOf[ESArray].array should be(empty)
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/CwlExpressionCommandPartSpec.scala b/cwl/src/test/scala/cwl/CwlExpressionCommandPartSpec.scala
deleted file mode 100644
index 0d675397a11..00000000000
--- a/cwl/src/test/scala/cwl/CwlExpressionCommandPartSpec.scala
+++ /dev/null
@@ -1,34 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.ExpressionEvaluator._
-import eu.timepit.refined._
-import eu.timepit.refined.numeric.Positive
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.callable.RuntimeEnvironment
-import wom.expression.NoIoFunctionSet
-import wom.graph.LocalName
-import wom.values.WomString
-
-
-class CwlExpressionCommandPartSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "CwlExpressionCommandPart"
-
-  val emptyEnvironment = RuntimeEnvironment("","",refineMV[Positive](1),1,1,1)
-
-  it should "instantiate" in {
-    // NOTE: toFixed used to remove the fraction part of ECMAScript numbers
-    // https://stackoverflow.com/questions/25989642/why-does-java-8-nashorn-javascript-modulo-returns-0-0-double-instead-of-0-i#answer-25991982
-    // https://community.apigee.com/questions/33936/javascript-parseint-not-converting-to-int-value-ne.html
-    val commandPart = CwlExpressionCommandPart(Coproduct[Expression](refineMV[MatchesECMAScriptExpression](
-      "$(parseInt(inputs.myStringInt).toFixed())"
-    )))(false, Vector.empty)
-    val result = commandPart.instantiate(Map(LocalName("myStringInt") -> WomString("3")), NoIoFunctionSet, identity, emptyEnvironment).toTry.get.head.commandString
-    result should be("'3'")
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/CwlInputValidationSpec.scala b/cwl/src/test/scala/cwl/CwlInputValidationSpec.scala
deleted file mode 100644
index c9d5272b07b..00000000000
--- a/cwl/src/test/scala/cwl/CwlInputValidationSpec.scala
+++ /dev/null
@@ -1,203 +0,0 @@
-package cwl
-
-import better.files.{File => BFile}
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder.decodeCwlFile
-import org.scalatest.BeforeAndAfterAll
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import shapeless.Coproduct
-import wom.expression.NoIoFunctionSet
-import wom.graph.Graph.ResolvedExecutableInput
-import wom.graph.GraphNodePort
-import wom.types.{WomArrayType, WomStringType}
-import wom.values._
-
-
-class CwlInputValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks with BeforeAndAfterAll {
-  behavior of "CWL Wom executable"
-
-  var cwlFile: BFile = _
-  var inputTempFile: BFile = _
-
-  override def beforeAll(): Unit = {
-    inputTempFile = BFile.newTemporaryFile()
-    cwlFile = BFile.newTemporaryFile().write(
-      """
-        |cwlVersion: v1.0
-        |class: Workflow
-        |inputs:
-        | w0:
-        |   type: string
-        |   default: "hi w0 !"
-        | w1: File
-        | w2:
-        |   type: string
-        |   default: "hi w2 !"
-        | w3: int
-        | w4: long
-        | w5: double
-        | w6: float
-        | w7: boolean
-        | w8:
-        |   type:
-        |     type: array
-        |     items:
-        |       type: array
-        |       items: string
-        | # enable this when InputRecordSchemas are enabled
-        | #w9:
-        | #  type:
-        | #    name: w9
-        | #    type: record
-        | #    fields:
-        | #    - name: w9a
-        | #      type: record
-        | #      fields:
-        | #      - name: w9aa
-        | #        type: string
-        | w10: Directory
-        |steps: []
-        |outputs: []
-      """.stripMargin
-    )
-  }
-
-  override def afterAll(): Unit = {
-    cwlFile.delete()
-    inputTempFile.delete()
-    ()
-  }
-
-  lazy val cwlWorkflow = decodeCwlFile(cwlFile).map {
-    _.select[Workflow].get
-  }.value.unsafeRunSync().fold(error => throw new RuntimeException(s"broken parse! msg was $error"), identity)
-
-  lazy val graph = cwlWorkflow.womDefinition(AcceptAllRequirements, Vector.empty) match {
-    case Left(errors) => fail(s"Failed to build wom definition: ${errors.toList.mkString(", ")}")
-    case Right(womDef) => womDef.graph
-  }
-
-  def getOutputPort(n: Int) = graph.inputNodes.find(_.localName == s"w$n").getOrElse(fail(s"Failed to find an input node for w$n")).singleOutputPort
-
-  lazy val w0OutputPort = getOutputPort(0)
-  lazy val w1OutputPort = getOutputPort(1)
-  lazy val w2OutputPort = getOutputPort(2)
-  lazy val w3OutputPort = getOutputPort(3)
-  lazy val w4OutputPort = getOutputPort(4)
-  lazy val w5OutputPort = getOutputPort(5)
-  lazy val w6OutputPort = getOutputPort(6)
-  lazy val w7OutputPort = getOutputPort(7)
-  lazy val w8OutputPort = getOutputPort(8)
-//  lazy val w9OutputPort = getOutputPort(9)
-  lazy val w10OutputPort = getOutputPort(10)
-
-  def validate(inputFile: String): Map[GraphNodePort.OutputPort, ResolvedExecutableInput] = {
-    cwlWorkflow.womExecutable(AcceptAllRequirements, Option(inputFile), LocalIoFunctionSet, strictValidation = false) match {
-      case Left(errors) => fail(s"Failed to build a wom executable: ${errors.toList.mkString(", ")}")
-      case Right(executable) => executable.resolvedExecutableInputs
-    }
-  }
-
-  it should "parse and validate a valid input file" in {
-    val inputFile =
-      s"""
-        w1:
-          class: File
-          path: ${inputTempFile.toString()}
-          secondaryFiles:
-            - class: File
-              path: secondaryFile.txt
-        w2: hello !
-        w3: 3
-        w4: 4
-        w5: 5.1
-        w6: 6.1
-        w7: true
-        w8: [
-          ["a", "b"],
-          ["c", "d"]
-        ]
-        w10:
-          class: Directory
-          location: "directory_location"
-          listing:
-            - class: Directory
-              path: "innerDirectory"
-            - class: File
-              location: "innerFile"
-      """.stripMargin
-    // TODO: With record schema, re-add:
-    //        w9:
-    //          w9a:
-    //            w9aa: "hello"
-
-    val validInputs = validate(inputFile).map {
-      case (port, resolvedInput) => (port.name, resolvedInput)
-    }
-
-    // w0 has no input value in the input file, so it should fallback to the default value
-    validInputs(w0OutputPort.name).select[WomValue].get.valueString shouldBe "hi w0 !"
-    validInputs(w1OutputPort.name) shouldBe
-      Coproduct[ResolvedExecutableInput](WomMaybePopulatedFile(
-        valueOption = Option(inputTempFile.toString()),
-        secondaryFiles = List(WomMaybePopulatedFile("secondaryFile.txt")),
-        sizeOption = Option(0)
-      ): WomValue)
-    validInputs(w2OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomString("hello !"): WomValue)
-    validInputs(w3OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomInteger(3): WomValue)
-    validInputs(w4OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomLong(4): WomValue)
-    validInputs(w5OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomFloat(5.1D): WomValue)
-    validInputs(w6OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomFloat(6.1D): WomValue)
-    validInputs(w7OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomBoolean(true): WomValue)
-    validInputs(w8OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](
-      WomArray(
-        WomArrayType(WomArrayType(WomStringType)),
-        List(
-          WomArray(WomArrayType(WomStringType), List(WomString("a"), WomString("b"))),
-          WomArray(WomArrayType(WomStringType), List(WomString("c"), WomString("d")))
-        )
-      ): WomValue
-    )
-    // Enable this when InputRecordSchema is enabled
-//    validInputs(w9OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](
-//      WomObject(
-//        Map(
-//          "w9a" -> WomObject(Map("w9aa" -> WomString("hello")))
-//        )
-//      ): WomValue
-//    )
-    validInputs(w10OutputPort.name) shouldBe
-      Coproduct[ResolvedExecutableInput](WomMaybeListedDirectory(
-        valueOption = Option("directory_location"),
-        listingOption = Option(
-          List(
-            WomMaybeListedDirectory("innerDirectory"),
-            WomMaybePopulatedFile("innerFile")
-          )
-        )
-      ): WomValue)
-  }
-
-  it should "not validate when required inputs are missing" in {
-    val inputFile =
-      """
-        w2: hello !
-      """.stripMargin
-
-    cwlWorkflow.womExecutable(AcceptAllRequirements, Option(inputFile), NoIoFunctionSet, strictValidation = false) match {
-      case Right(booh) => fail(s"Expected failed validation but got valid input map: $booh")
-      case Left(errors) => errors.toList.toSet shouldBe Set(
-        "Required workflow input 'w1' not specified",
-        "Required workflow input 'w3' not specified",
-        "Required workflow input 'w4' not specified",
-        "Required workflow input 'w5' not specified",
-        "Required workflow input 'w6' not specified",
-        "Required workflow input 'w7' not specified",
-        "Required workflow input 'w8' not specified",
-        "Required workflow input 'w10' not specified"
-      )
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlWorkflowWomSpec.scala b/cwl/src/test/scala/cwl/CwlWorkflowWomSpec.scala
deleted file mode 100644
index 52f511fd9b7..00000000000
--- a/cwl/src/test/scala/cwl/CwlWorkflowWomSpec.scala
+++ /dev/null
@@ -1,216 +0,0 @@
-package cwl
-
-import cats.syntax.either._
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder._
-import cwl.ExpressionEvaluator._
-import cwl.command.ParentName
-import eu.timepit.refined._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import shapeless._
-import wom.WomMatchers._
-import wom.callable.{Callable, CommandTaskDefinition, WorkflowDefinition}
-import wom.graph.GraphNodePort.OutputPort
-import wom.graph._
-import wom.graph.expression.ExpressionNode
-import wom.types.{WomMaybePopulatedFileType, WomStringType, WomType}
-
-
-class CwlWorkflowWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-  import TestSetup._
-
-  implicit val parentName = ParentName.empty
-
-  "A Cwl object for 1st-tool" should "convert to WOM" in {
-    def validateWom(callable: Callable): Unit = callable match {
-      case taskDefinition: CommandTaskDefinition =>
-        val inputDef = taskDefinition.inputs.head
-        inputDef.name shouldBe "message"
-        inputDef.womType shouldBe WomStringType
-        ()
-
-      case _ => fail("not a task definition")
-    }
-
-    import cats.syntax.validated._
-    (for {
-      clt <- decodeCwlFile(rootPath/"1st-tool.cwl").
-              map(_.select[CommandLineTool].get).
-              value.
-              unsafeRunSync()
-      taskDef <- clt.buildTaskDefinition(_.validNel, Vector.empty)
-    } yield validateWom(taskDef)).leftMap(e => throw new RuntimeException(s"error! $e"))
-  }
-
-  "Cwl for 1st workflow" should "convert to WOM" in {
-    (for {
-      wf <- decodeCwlFile(rootPath/"1st-workflow.cwl").
-              value.
-              unsafeRunSync().
-              map(_.select[Workflow].get)
-
-      womDefinition <- wf.womDefinition(AcceptAllRequirements, Vector.empty)
-    } yield validateWom(womDefinition)).leftMap(e => throw new RuntimeException(s"error! ${e.toList.mkString("\n")}"))
-
-    def shouldBeRequiredGraphInputNode(node: GraphNode, localName: String, womType: WomType): Unit = {
-      node.isInstanceOf[RequiredGraphInputNode] shouldBe true
-      val requiredGraphInputNode = node.asInstanceOf[RequiredGraphInputNode]
-      requiredGraphInputNode.localName shouldBe localName
-      requiredGraphInputNode.womType shouldBe womType
-      ()
-    }
-
-    def validateWom(callable: Callable) = {
-      callable match {
-        case wf: WorkflowDefinition =>
-          val nodes = wf.innerGraph.nodes
-
-          nodes collect {
-            case gin: GraphInputNode => gin.localName
-          } should be(Set("ex", "inp"))
-
-          nodes collect {
-            case cn: CallNode => cn.localName
-          } should be(Set("compile", "untar"))
-
-          val untarUpstream = nodes.collectFirst {
-            case tarParam: CallNode if tarParam.localName == s"untar" => tarParam
-          }.get.
-            upstream
-
-          untarUpstream should have size 2
-          untarUpstream.collectFirst({
-            case exprNode: ExpressionNode if exprNode.localName == s"file://$rootPath/1st-workflow.cwl#untar/extractfile.merge" =>
-              shouldBeRequiredGraphInputNode(exprNode.inputPorts.head.upstream.graphNode, "ex", WomStringType)
-          }).getOrElse(fail("Can't find expression node for ex"))
-
-          untarUpstream.collectFirst({
-            case exprNode: ExpressionNode if exprNode.localName == s"file://$rootPath/1st-workflow.cwl#untar/tarfile.merge" =>
-              exprNode.inputPorts.map(_.upstream.graphNode).count {
-                case rgin: RequiredGraphInputNode =>
-                  rgin.identifier.localName == LocalName("inp") &&
-                    rgin.womType == WomMaybePopulatedFileType
-              }  shouldBe 1
-          }).getOrElse(fail("Can't find expression node for inp"))
-
-          val compileUpstreamExpressionPort = nodes.collectFirst {
-            case compile: CallNode if compile.localName == s"compile" => compile
-          }.get.inputPorts.map(_.upstream).head
-
-          compileUpstreamExpressionPort.name shouldBe s"file://$rootPath/1st-workflow.cwl#compile/src.merge"
-          compileUpstreamExpressionPort.graphNode.asInstanceOf[ExpressionNode].inputPorts.map(_.upstream.internalName).count(_ == "example_out") shouldBe 1
-
-          nodes.collect {
-            case c: PortBasedGraphOutputNode => c
-          }.map(_.localName) shouldBe Set("classout")
-        case wth: Any => fail(s"Parsed unexpected Callable: $wth")
-      }
-    }
-  }
-
-  behavior of "A decoded CWL 3step"
-
-  private val stringOrExpressionTests = Table(
-    ("index", "result"),
-    (0, Coproduct[StringOrExpression]("grep")),
-    (1, Coproduct[StringOrExpression](Coproduct[Expression](refineMV[MatchesECMAScriptExpression]("$(inputs.pattern)")))),
-    (2, Coproduct[StringOrExpression](Coproduct[Expression](refineMV[MatchesECMAScriptFunction]("$" + "{return inputs.file}")))),
-    (3, Coproduct[StringOrExpression]("|")),
-    (4, Coproduct[StringOrExpression]("wc")),
-    (5, Coproduct[StringOrExpression]("-l"))
-  )
-
-  private def getTestName(stringOrExpression: StringOrExpression): String = stringOrExpression match {
-    case StringOrExpression.String(s) => s"string $s"
-    // Although these two cases look the same, they're actually calling different 'value' functions. So we
-    // can't collapse this to a single "case StringOrExpression.Expression(e) => e.value":
-    case StringOrExpression.ECMAScriptExpression(e) => e.value
-    case StringOrExpression.ECMAScriptFunction(f) => f.value
-    case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-  }
-
-  private lazy val commandLineTool: CommandLineTool = {
-    val wf = decodeCwlFile(rootPath / "three_step.cwl").map { wf =>
-      wf.select[Workflow].get
-    }.value.unsafeRunSync().fold(error => throw new RuntimeException(s"broken parse! msg was ${error.toList.mkString(", ")}"), identity)
-
-    wf.id should include("three_step")
-
-    // The second step (aka 1) step should be cgrep
-    val run: WorkflowStep.Run = wf.steps.apply(1).run
-    val commandLineTool: CommandLineTool = run.select[CommandLineTool].getOrElse(fail(s"$run wasn't a CommandLineTool"))
-
-    commandLineTool.id should include("cgrep")
-    commandLineTool
-  }
-
-  forAll(stringOrExpressionTests) { (index, expected) =>
-    it should s"correctly identify the ${getTestName(expected)}" in {
-      val argument: CommandLineTool.Argument = commandLineTool.arguments.get.apply(index)
-      val commandLineBinding: ArgumentCommandLineBinding = argument.select[ArgumentCommandLineBinding]
-        .getOrElse(fail(s"$argument wasn't a CommandLineBinding"))
-      val stringOrExpression: StringOrExpression = commandLineBinding.valueFrom
-      stringOrExpression should be(expected)
-    }
-  }
-
-  "A CwlNamespace for 3step" should "provide conversion to WOM" in {
-
-    val wf = decodeCwlFile(rootPath/"three_step.cwl").map {
-      _.select[Workflow].get
-    }.value.unsafeRunSync().fold(error => throw new RuntimeException(s"broken parse: $error"), identity)
-
-    wf.id should include("three_step")
-
-    val wfd = wf.womDefinition(AcceptAllRequirements, Vector.empty) match {
-      case Right(wf: WorkflowDefinition) => wf
-      case Left(o) => fail(s"Workflow definition was not produced correctly: ${o.toList.mkString(", ")}")
-      case Right(callable) => fail(s"produced $callable when a Workflow Definition was expected!")
-    }
-
-    val nodes = wfd.innerGraph.nodes
-
-    val graphInputNodes = nodes collect { case gin: GraphInputNode => gin }
-    graphInputNodes should have size 1
-    val patternInputNode = graphInputNodes.head
-    patternInputNode.localName should be("pattern")
-
-    nodes collect { case gon: GraphOutputNode => gon.localName } should be(Set(
-      "cgrep-count",
-      "wc-count"
-    ))
-
-    nodes collect { case cn: CallNode => cn.localName } should be(Set("ps", "cgrep", "wc"))
-
-    val ps = nodes.collectFirst({ case ps: CallNode if ps.localName == "ps" => ps }).get
-    val cgrep = nodes.collectFirst({ case cgrep: CallNode if cgrep.localName == "cgrep" => cgrep }).get
-    val cgrepFileExpression = nodes.collectFirst({ case cgrepInput: ExpressionNode if s"${FileStepAndId(cgrepInput.localName).stepId}/${FileStepAndId(cgrepInput.localName).id}" == "cgrep/file.merge" => cgrepInput }).get
-    val cgrepPatternExpression = nodes.collectFirst({ case cgrepInput: ExpressionNode if s"${FileStepAndId(cgrepInput.localName).stepId}/${FileStepAndId(cgrepInput.localName).id}" == "cgrep/pattern.merge" => cgrepInput }).get
-    val wc = nodes.collectFirst({ case wc: CallNode if wc.localName == "wc" => wc }).get
-    val wcFileExpression = nodes.collectFirst({ case wcInput: ExpressionNode if s"${FileStepAndId(wcInput.localName).stepId}/${FileStepAndId(wcInput.localName).id}" == "wc/file.merge" => wcInput }).get
-
-    ps.upstream shouldBe empty
-
-    cgrep.upstream should contain theSameElementsAs Set(cgrepFileExpression, cgrepPatternExpression)
-    wc.upstream should contain theSameElementsAs Set(wcFileExpression)
-
-    // Check that expressions input ports point to the right output port
-    cgrepPatternExpression.inputPorts.head.upstream should be theSameInstanceAs patternInputNode.singleOutputPort
-    cgrepFileExpression.inputPorts.map(_.upstream).count(_ eq ps.outputPorts.head) shouldBe 1
-    wcFileExpression.inputPorts.map(_.upstream).count(_ eq ps.outputPorts.head) shouldBe 1
-
-    // Check that the inputDefinitionMappings are correct
-    ps.inputDefinitionMappings shouldBe empty
-    cgrep.inputDefinitionMappings should have size 2
-
-    val cgrepInputs = cgrep.inputDefinitionMappings.toMap
-    val cgrepFileInputDef = cgrep.callable.inputs.find(_.name == "file").get
-    cgrepInputs(cgrepFileInputDef).select[OutputPort].get should be theSameInstanceAs cgrepFileExpression.singleOutputPort
-
-    val cgrepPatternInputDef = cgrep.callable.inputs.find(_.name == "pattern").get
-    cgrepInputs(cgrepPatternInputDef).select[OutputPort].get should be theSameInstanceAs cgrepPatternExpression.singleOutputPort
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/DirectorySpec.scala b/cwl/src/test/scala/cwl/DirectorySpec.scala
deleted file mode 100644
index 1e7db881753..00000000000
--- a/cwl/src/test/scala/cwl/DirectorySpec.scala
+++ /dev/null
@@ -1,41 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.CwlDecoder.decodeCwlFile
-import cwl.TestSetup.rootPath
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.callable.Callable.InputDefinition
-import wom.callable.{CallableTaskDefinition, RuntimeEnvironment}
-import wom.expression.NoIoFunctionSet
-import wom.graph.OptionalGraphInputNodeWithDefault
-import wom.values.WomValue
-
-
-class DirectorySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "Directory"
-
-  it should "dir_example" in {
-    val cwl = decodeCwlFile(rootPath / "dir_example.cwl").value.unsafeRunSync().toOption.get
-    val executable = cwl.womExecutable(AcceptAllRequirements, None, NoIoFunctionSet, strictValidation = false).toOption.get
-    val call = executable.graph.calls.head
-    val runtimeEnvironment = RuntimeEnvironment("output/path", "temp/path",refineMV[Positive](1), 2e10, 100, 100)
-    val defaultCallInputs = executable.graph.nodes.collect({
-      case oginwd: OptionalGraphInputNodeWithDefault =>
-        val key: InputDefinition = call.inputDefinitionMappings.toMap.keys.find(
-          _.localName == oginwd.identifier.localName
-        ).get
-        val value: WomValue = oginwd.default.evaluateValue(Map.empty, NoIoFunctionSet).toTry.get
-        key -> value
-    }).toMap
-    val command = call.callable.asInstanceOf[CallableTaskDefinition].instantiateCommand(
-      defaultCallInputs, NoIoFunctionSet, identity, runtimeEnvironment
-    ).toTry.get
-    command.commandString should be("""   'echo' 'exampledir'   """.trim)
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/ExportCwlSamplesSpec.scala b/cwl/src/test/scala/cwl/ExportCwlSamplesSpec.scala
deleted file mode 100644
index e18c95a9966..00000000000
--- a/cwl/src/test/scala/cwl/ExportCwlSamplesSpec.scala
+++ /dev/null
@@ -1,146 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.CommandLineTool.{BaseCommand, CommandInputParameter}
-import cwl.Workflow.{WorkflowInputParameter, WorkflowOutputParameter}
-import cwl.WorkflowStep.WorkflowStepOutputInnerType
-import cwl.WorkflowStepInput.InputSource
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-
-
-
-  /**
-   * BROKEN
-   *
-   * (DB)Ability to write JSON removed due to conflicting circe-yaml cats dependency.
-   * See issue https://github.com/broadinstitute/wdl4s/issues/216 for more information.
-   */
-class ExportCwlSamplesSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  def assertCorrectJson(cwl: Cwl, expectedYaml: String) = throw new UnsupportedOperationException // shouldBe expectedYaml
-
-  it should "encode sample CWL command line tool" ignore {
-    val tool =
-      CommandLineTool(
-        id = "echo",
-        inputs =  Array(CommandInputParameter(
-          id = "message",
-          inputBinding = Option(InputCommandLineBinding(
-            position = Option(1)
-          ))
-        )),
-        baseCommand = Option(Coproduct[BaseCommand]("echo"))
-      )
-    val expectedToolJsonString =
-"""inputs:
-- id: message
-  inputBinding:
-    position: 1
-outputs: []
-class: CommandLineTool
-cwlVersion: v1.0
-baseCommand: echo
-"""
-    assertCorrectJson(tool.asCwl, expectedToolJsonString)
-  }
-
-  it should "encode sample CWL workflow" ignore {
-    val workflow = Workflow(
-      id = "MyCwlWorkflow",
-      inputs = Array(
-          WorkflowInputParameter(id = "inp", `type` = Option(Coproduct[MyriadInputType](Coproduct[MyriadInputInnerType](CwlType.File)))),
-          WorkflowInputParameter(id = "ex", `type` = Option(Coproduct[MyriadInputType](Coproduct[MyriadInputInnerType](CwlType.String))))
-        ),
-      outputs = Array(
-        WorkflowOutputParameter(
-          id = "classout",
-          `type` = Option(Coproduct[MyriadOutputType](Coproduct[MyriadOutputInnerType](CwlType.File))),
-          outputSource = Option(Coproduct[WorkflowOutputParameter#OutputSource]("compile/classfile"))
-        )
-      ),
-      steps =
-        Array(
-           WorkflowStep(
-            id = "untar",
-            run = Coproduct[WorkflowStep.Run]("tar-param.cwl"),
-            in =
-              Array(
-                WorkflowStepInput(id = "tarfile", source = Option(Coproduct[InputSource]("inp"))),
-                WorkflowStepInput(id = "extractfile", source =  Option(Coproduct[InputSource]("ex")))
-              ),
-            out = Array(Coproduct[WorkflowStepOutputInnerType](WorkflowStepOutput("example_out")))
-          ),
-          WorkflowStep(
-            id = "compile",
-            run = Coproduct[WorkflowStep.Run]("arguments.cwl"),
-            in = Array(
-                 WorkflowStepInput(id = "src", source = Option(Coproduct[InputSource]("untar/example_out")))
-              ),
-            out = Array(Coproduct[WorkflowStepOutputInnerType](WorkflowStepOutput("classfile")))
-          )
-        )
-      )
-    val expectedWorkflowJsonString =
-      """cwlVersion: v1.0
-class: Workflow
-inputs:
-- id: inp
-  type: File
-- id: ex
-  type: string
-outputs:
-- id: classout
-  outputSource: compile/classfile
-  type: File
-steps:
-- id: untar
-  in:
-  - id: tarfile
-    source: inp
-  - id: extractfile
-    source: ex
-  out:
-  - example_out
-  run: tar-param.cwl
-- id: compile
-  in:
-  - id: src
-    source: untar/example_out
-  out:
-  - classfile
-  run: arguments.cwl
-""".stripMargin
-    assertCorrectJson(workflow.asCwl, expectedWorkflowJsonString)
-  }
-
-  it should "encode sample CWL env" ignore {
-    val tool = CommandLineTool(
-      id = "env",
-      baseCommand = Option(Coproduct[BaseCommand]("env")),
-      requirements = Option(Array(Coproduct[Requirement](EnvVarRequirement(
-        envDef = Array(EnvironmentDef("HELLO", Coproduct[StringOrExpression]("$(inputs.message)")))
-      )))),
-      inputs = Array(
-        CommandInputParameter(id =  "message", `type` = Option(Coproduct[MyriadInputType](Coproduct[MyriadInputInnerType](CwlType.String))))
-      )
-    )
-    val expectedToolJsonString =
-"""inputs:
-- id: message
-  type: string
-outputs: []
-class: CommandLineTool
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: HELLO
-    envValue: $(inputs.message)
-cwlVersion: v1.0
-baseCommand: env
-""".stripMargin
-    assertCorrectJson(tool.asCwl, expectedToolJsonString)
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/ExpressionEvaluatorSpec.scala b/cwl/src/test/scala/cwl/ExpressionEvaluatorSpec.scala
deleted file mode 100644
index c723d923901..00000000000
--- a/cwl/src/test/scala/cwl/ExpressionEvaluatorSpec.scala
+++ /dev/null
@@ -1,24 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.expression.DefaultSizeIoFunctionSet
-import wom.values.{WomBoolean, WomString, WomValue}
-
-
-class ExpressionEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "ExpressionEvaluator"
-
-  it should "eval inputs of different types" in {
-    val values: Map[String, WomValue] = Map(
-      "myName" -> WomString("hi"),
-      "someother" -> WomBoolean(false)
-    )
-    val parameterContext = ParameterContext(DefaultSizeIoFunctionSet, Vector.empty, values)
-    ExpressionEvaluator.eval("inputs.myName", parameterContext).toTry.get should be(WomString("hi"))
-    ExpressionEvaluator.eval("inputs.someother", parameterContext).toTry.get should be(WomBoolean(false))
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ExpressionInterpolatorSpec.scala b/cwl/src/test/scala/cwl/ExpressionInterpolatorSpec.scala
deleted file mode 100644
index df27b5736e1..00000000000
--- a/cwl/src/test/scala/cwl/ExpressionInterpolatorSpec.scala
+++ /dev/null
@@ -1,121 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.ExpressionInterpolator.SubstitutionException
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.callable.RuntimeEnvironment
-import wom.expression.DefaultSizeIoFunctionSet
-import wom.values._
-
-
-class ExpressionInterpolatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "ExpressionInterpolator"
-
-  private lazy val expressionLib = Vector(
-    better.files.File(getClass.getResource("lodash.js").getPath).contentAsString,
-    "var t = function(s) { return _.template(s, {variable: 'data'})({'inputs': inputs}); };"
-  )
-
-  private lazy val parameterContext = {
-    val runtime = RuntimeEnvironment("out", "tmp", refineMV[Positive](1), 2.0D, 100L, 200L)
-    val inputs = Map(
-      "cram" -> WomSingleFile("/path/to/my.cram"),
-      "file1" -> WomSingleFile("/path/to/my.file.txt")
-    )
-    ParameterContext(DefaultSizeIoFunctionSet, expressionLib, inputs = inputs, runtimeOption = Option(runtime))
-  }
-
-  private def evaluator(string: String): ErrorOr[WomValue] = {
-    ExpressionEvaluator.eval(string, parameterContext)
-  }
-
-  private val validTests = Table(
-    ("description", "expression", "expected"),
-    ("an empty string", "", WomString("")),
-    ("a space", " ", WomString("")),
-    ("two spaces", "  ", WomString("")),
-    ("whitespace string", " \n \t", WomString("")),
-    ("a regular string", "hello world", WomString("hello world")),
-    ("a dollar sign", "$6.28", WomString("$6.28")),
-    ("two dollar signs", "$$(6.28)", WomString("$$(6.28)")),
-    ("three dollar signs", "$$$(6.28)", WomString("$$6.28")),
-    ("a backslash and a dollar sign", """\$(6.28)""", WomString("$(6.28)")),
-    ("two backslashes and a dollar sign", """\\$(6.28)""", WomString("""\6.28""")),
-    ("a underscore and a dollar sign", "_$(6.28)", WomString("_6.28")),
-    ("nested parens", """$(parseInt("6")).$(parseInt(("2")) + "" + parseInt(((("8")))))""", WomString("6.28")),
-    ("missing open parens", """$(parseInt("6")).$(parseInt(("2")) + "" + parseInt((("8")))))""", WomString("6.28)")),
-    ("quoted open parens", """$("(")""", WomString("(")),
-    ("quoted closing parens", """$(")")""", WomString(")")),
-    ("prefixed/suffixed nested parens",
-      """6.$(parseInt("2"))$(parseInt(("8")) + "" + parseInt(((("3")))))1""",
-      WomString("6.2831")),
-    ("expressions using libs",
-      """$(t("The file is <%= data.inputs.file1.path.split('/').slice(-1)[0] %>\n"))""",
-      WomString("The file is my.file.txt\n")),
-    ("two expressions", """$(runtime.outdir)/$(inputs.cram.basename)""", WomString("out/my.cram")),
-    ("two expressions suffixed", "$(runtime.outdir)/$(inputs.cram.basename).crai", WomString("out/my.cram.crai")),
-    ("two expressions prefixed/suffixed",
-      "/path/to/$(runtime.outdir)/$(inputs.cram.basename).crai",
-      WomString("/path/to/out/my.cram.crai")),
-    ("a replacement that must be escaped", """$("$(hello)")""", WomString("$(hello)")),
-    ("a string containing a start prefix", """$("$(")""", WomString("$(")),
-    ("a replacement returning a json object",
-      "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})",
-      WomObject(Map("output" -> WomInteger(2))))
-  )
-
-  forAll(validTests) { (description, expression, expected) =>
-    it should s"interpolate $description" in {
-      ExpressionInterpolator.interpolate(expression, evaluator).toTry.get should be(expected)
-    }
-  }
-
-  private val substitutionErrorTests = Table(
-    ("description", "expression", "expected"),
-    ("a missing closing paren", "$(", "0: $("),
-    ("a missing quote", """$("))""", """0: $("))"""),
-    ("complex missing closing parens",
-      """$(parseInt("6")).$(parseInt(("2")) + "" + parseInt(((("8"))))""",
-      """1: $(parseInt(("2")) + "" + parseInt(((("8"))))""")
-  )
-
-  forAll(substitutionErrorTests) { (description, expression, expected) =>
-    it should s"throw a substitution error for $description" in {
-      the[SubstitutionException] thrownBy {
-        ExpressionInterpolator.interpolate(expression, evaluator)
-      } should have message s"Substitution error, unfinished block starting at position $expected"
-    }
-  }
-
-  /**
-    * Tests that sorta work but do not generate the same _exact_ responses as cwltool.
-    *
-    * See docs at top of [[ExpressionInterpolator]].
-    *
-    * According to cwltool's expression.py when an interpolated string contains more than just an expression,
-    * `json.dumps` should be used to serialize Arrays and Maps, and Maps should sort their keys.
-    *
-    * We don't even test maps with multiple keys here as WomMap does not guarantee key order.
-    */
-  private val semiSupportedTests = Table(
-    ("description", "expression", "expected"),
-    ("an array", """$(["hello", "world"])""", """["hello", "world"]"""),
-    ("a map", """$({"hello": "world"})""", """object {hello: "world"}"""),
-    ("an array of maps", """$([{"hello": "world"}])""", """[object {hello: "world"}]"""),
-    ("a map of arrays", """$({"hello": ["world"]})""", """object {hello: ["world"]}""")
-  )
-
-  forAll(semiSupportedTests) { (description, expression, expected) =>
-    it should s"semi-interpolate a string plus $description" in {
-      val actual = ExpressionInterpolator.interpolate("_" + expression, evaluator).map(_.valueString).toTry.get
-      actual should be("_" + expected)
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/FileSpec.scala b/cwl/src/test/scala/cwl/FileSpec.scala
deleted file mode 100644
index 814c164bc16..00000000000
--- a/cwl/src/test/scala/cwl/FileSpec.scala
+++ /dev/null
@@ -1,54 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.CwlDecoder.decodeCwlFile
-import cwl.TestSetup.rootPath
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.callable.Callable.InputDefinition
-import wom.callable.{CallableTaskDefinition, RuntimeEnvironment}
-import wom.graph.OptionalGraphInputNodeWithDefault
-import wom.values.WomValue
-
-
-class FileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "File"
-
-  private val fileTests = Table(
-    ("description", "filePath", "ioFunctionSet", "expectedCommand"),
-    ("get the basename of a file", "file_example.cwl", LocalIoFunctionSet, """   'echo' 'example.txt'   """.trim),
-    ("get the size of a file", "file_size_example.cwl", LocalIoFunctionSet, """   'echo' '12'   """.trim)
-  )
-
-  forAll(fileTests) { (description, filePath, ioFunctionSet, expectedCommand) =>
-    it should description in {
-      val cwl = decodeCwlFile(rootPath / filePath).value.unsafeRunSync().toOption.get
-      val executable = cwl.womExecutable(AcceptAllRequirements, None, ioFunctionSet, strictValidation = false).toOption.get
-      val call = executable.graph.calls.head
-      val runtimeEnvironment = RuntimeEnvironment("output/path", "temp/path", refineMV[Positive](1), 2e10, 100, 100)
-      val defaultCallInputs = executable.graph.nodes.collect({
-        case oginwd: OptionalGraphInputNodeWithDefault =>
-          val key: InputDefinition = call.inputDefinitionMappings.toMap.keys.find(
-            _.localName == oginwd.identifier.localName
-          ).get
-          val value: WomValue = key
-            .valueMapper(ioFunctionSet)(oginwd.default.evaluateValue(Map.empty, ioFunctionSet).toTry.get)
-            .value.unsafeRunSync()
-            .toOption.get
-
-          key -> value
-      }).toMap
-      val commandEither = call.callable.asInstanceOf[CallableTaskDefinition].instantiateCommand(
-        defaultCallInputs, ioFunctionSet, identity, runtimeEnvironment
-      ).toEither
-      val command = commandEither.toOption.get.commandString
-      command should be(expectedCommand)
-    }
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/FullyQualifiedNameSpec.scala b/cwl/src/test/scala/cwl/FullyQualifiedNameSpec.scala
deleted file mode 100644
index 9c3babfc634..00000000000
--- a/cwl/src/test/scala/cwl/FullyQualifiedNameSpec.scala
+++ /dev/null
@@ -1,27 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.command.ParentName
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class FullyQualifiedNameSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  implicit val parentName = ParentName.empty
-  
-  "workflow input id " should "get filename and id" in {
-    val wfid = FileAndId("file#id")
-
-    wfid.fileName shouldBe "file"
-    wfid.id shouldBe "id"
-  }
-
-  "workflow step output id " should "get filename, id, and step" in {
-    val wfid = FileStepAndId("file#step/id")
-
-    wfid.fileName shouldBe "file"
-    wfid.id shouldBe "id"
-    wfid.stepId shouldBe "step"
-  }
-}
diff --git a/cwl/src/test/scala/cwl/LocalIoFunctionSet.scala b/cwl/src/test/scala/cwl/LocalIoFunctionSet.scala
deleted file mode 100644
index b3ab33a5809..00000000000
--- a/cwl/src/test/scala/cwl/LocalIoFunctionSet.scala
+++ /dev/null
@@ -1,48 +0,0 @@
-package cwl
-
-import java.nio.file.{Files, Paths}
-import java.util.concurrent.Executors
-
-import wom.expression.EmptyIoFunctionSet
-
-import scala.jdk.CollectionConverters._
-import scala.concurrent.{ExecutionContext, Future}
-import scala.util.Try
-
-/**
-  * Test io functions that can read from local file systems.
-  */
-object LocalIoFunctionSet extends EmptyIoFunctionSet {
-  override implicit def ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(1))
-
-  private def stripLocalPrefix(path: String): String = {
-    path.stripPrefix("file://")
-  }
-
-  private def fileSize(path: String): Long = {
-    Files.size(Paths.get(stripLocalPrefix(path)))
-  }
-
-  private def contentsAsString(path: String): String = {
-    Files.readAllLines(Paths.get(stripLocalPrefix(path))).asScala.mkString("\n")
-  }
-
-  override def readFile(path: String, maxBytesOption: Option[Int] = None,
-                        failOnOverflow: Boolean = false): Future[String] = {
-    Future.fromTry(Try {
-      maxBytesOption match {
-        case Some(maxBytes) if failOnOverflow && fileSize(path) > maxBytes =>
-          throw new RuntimeException(s"overflow while reading $path: ${fileSize(path)} > $maxBytes")
-        case Some(maxBytes) => contentsAsString(path).take(maxBytes)
-        case None => contentsAsString(path)
-      }
-    })
-  }
-
-  override def size(params: String): Future[Long] = {
-    Future.fromTry(Try {
-        fileSize(params)
-    }
-    )
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ParseBigThreeSpec.scala b/cwl/src/test/scala/cwl/ParseBigThreeSpec.scala
deleted file mode 100644
index e5ac02e80f4..00000000000
--- a/cwl/src/test/scala/cwl/ParseBigThreeSpec.scala
+++ /dev/null
@@ -1,34 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder._
-import cwl.TestSetup._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class ParseBigThreeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  val namespace = "cwl"
-
-  it should "parse 1st tool" in {
-
-  decodeCwlFile(rootPath/"1st-tool.cwl").
-    value.
-    unsafeRunSync().
-    isRight shouldBe true
-  }
-
-  it should "parse first workflow" in {
-    decodeCwlFile(rootPath/"1st-workflow.cwl").
-      value.
-      unsafeRunSync().
-      isRight shouldBe true
-  }
-
-  it should "parse env cwl" in {
-    decodeCwlFile(rootPath/"env.cwl").
-      value.
-      unsafeRunSync().
-      isRight shouldBe true
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ParsingSpec.scala b/cwl/src/test/scala/cwl/ParsingSpec.scala
deleted file mode 100644
index 92c454a0964..00000000000
--- a/cwl/src/test/scala/cwl/ParsingSpec.scala
+++ /dev/null
@@ -1,63 +0,0 @@
-package cwl
-
-import CwlDecoder._
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class WorkflowParsingSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "Workflow Json Parser"
-
-  def workflowJson(classValue: String) = s"""{"class":"$classValue", "cwlVersion": "v1.0", "id": "MyCwlWorkflow", "inputs":[], "outputs":[], "steps":[]}"""
-
-  it should "accept the Workflow argument" in {
-     decodeCwlString(workflowJson("Workflow")).value.unsafeRunSync() match {
-       case Right(_) => // great!
-       case Left(e) => fail(s"Workflow rejected because: ${e.toList.mkString(", ")}")
-     }
-  }
-
-  it should "not parse w/something other than Workflow as class" in {
-    decodeCwlString(workflowJson("wrong")).value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(wf) => fail(s"workflow unexpectedly accepted: $wf")
-    }
-  }
-
-  it should "not parse when class argument is missing" in {
-    decodeCwlString("""{"cwlVersion": "v1.0", "inputs":[], "outputs":[], "steps":[]}""").value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(wf) => fail(s"workflow unexpectedly accepted: $wf")
-    }
-  }
-}
-
-class CommandLineToolParsingSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "CommandLineTool Json Parser"
-
-  def commandLineToolJson(classValue: String) = s"""{"class":"$classValue", "cwlVersion":"v1.0", "id": "MyCwlTask", "inputs":[], "outputs":[]}"""
-
-  it should "accept the CommandLineTool argument for class" in {
-    decodeCwlString(commandLineToolJson("CommandLineTool")).value.unsafeRunSync() match {
-      case Right(_) => // great!
-      case Left(e) => fail(s"CommandLineTool rejected because: $e")
-    }
-  }
-
-  it should "not parse w/something other than CommandLineTool" in {
-    decodeCwlString(commandLineToolJson("wrong")).value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(clt) => fail(s"CommandLineTool unexpectedly accepted: $clt")
-    }
-  }
-
-  it should "doesn't parse when class argument is missing" in {
-    decodeCwlString("""{"inputs":[], "outputs":[]}""").value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(clt) => fail(s"CommandLineTool unexpectedly accepted: $clt")
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ScatterLogicSpec.scala b/cwl/src/test/scala/cwl/ScatterLogicSpec.scala
deleted file mode 100644
index 8afd3c9df16..00000000000
--- a/cwl/src/test/scala/cwl/ScatterLogicSpec.scala
+++ /dev/null
@@ -1,140 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.BeforeAndAfterEach
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import spray.json.DefaultJsonProtocol
-import wom.graph.ScatterNode.ScatterVariableAndValue
-import wom.graph.expression.PlainAnonymousExpressionNode
-import wom.graph.{ScatterNode, ScatterVariableNode, WomIdentifier}
-import wom.types.{WomArrayType, WomStringType}
-import wom.values.{WomArray, WomString, WomValue}
-
-class ScatterLogicSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks
-  with DefaultJsonProtocol with BeforeAndAfterEach {
-  private val expressionNode = PlainAnonymousExpressionNode(WomIdentifier("name"), null, WomStringType, Map.empty)
-  private val arrayStringType = WomArrayType(WomStringType)
-
-  private val emptyArray = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List.empty)
-  )
-  private val simpleArray2 = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List(WomString("a"), WomString("b")))
-  )
-  private val simpleArray3 = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List(WomString("a"), WomString("b"), WomString("c")))
-  )
-  private val simpleArray4 = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List(WomString("a"), WomString("b"), WomString("c"), WomString("d")))
-  )
-
-  override def beforeEach(): Unit = {
-    // The index length of the SVN is a mutable value, to avoid tests stepping on each others reset it to the default value
-    // before each test
-    emptyArray.scatterVariableNode.withRelativeIndexLength(1)
-    simpleArray2.scatterVariableNode.withRelativeIndexLength(1)
-    simpleArray3.scatterVariableNode.withRelativeIndexLength(1)
-    simpleArray4.scatterVariableNode.withRelativeIndexLength(1)
-  }
-
-  private val valueA = WomString("a")
-  private val valueB = WomString("b")
-  private val valueC = WomString("c")
-  private val valueD = WomString("d")
-
-  private def validateScatterCombinations(list: List[ScatterNode.ScatterVariableAndValue],
-                                  scatterSize: Int,
-                                  expected: List[List[Int]]) = {
-    // Go through all the variable nodes and feed all the shard numbers to the indexForShard function
-    val combinations = list.map({
-      case ScatterVariableAndValue(node, values) =>
-        (0 until scatterSize).map(node.indexForShard(_, values.size)).toList
-    })
-
-    combinations should contain theSameElementsInOrderAs expected
-  }
-
-  "CrossProduct scattering function" should "generate correct results" in {
-    val nonEmptyVariables = Table(
-      // None for the index length means "don't check because irrelevant"
-      ("variablesAndValues", "scatterSize", "arrayIndexes"),
-      (List(simpleArray2), 2, List(List(0, 1))),
-      (List(simpleArray2, simpleArray3), 6, List(List(0, 0, 0, 1, 1, 1), List(0, 1, 2, 0, 1, 2))),
-      (List(simpleArray2, simpleArray3, simpleArray4), 24, List(
-        List(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
-        List(0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2),
-        List(0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3))
-      )
-    )
-
-    forAll(nonEmptyVariables) { case (list, scatterSize, expected) =>
-      ScatterLogic.CrossProductScatterProcessingFunction(list) shouldBe Right(scatterSize)
-      validateScatterCombinations(list, scatterSize, expected)
-    }
-
-    List(List(emptyArray), List(emptyArray, simpleArray2), List(simpleArray2, emptyArray)) foreach { list =>
-      ScatterLogic.CrossProductScatterProcessingFunction(list) shouldBe Right(0)
-    }
-  }
-
-  "DotProduct scattering function" should "generate correct results" in {
-    import common.validation.Checked._
-    val simpleArray2Duplicate = ScatterVariableAndValue(
-      ScatterVariableNode(null, expressionNode, WomStringType),
-      WomArray(arrayStringType, List(WomString("a"), WomString("b")))
-    )
-    val nonEmptyVariables = Table(
-      // None for the index length means "don't check because irrelevant"
-      ("variablesAndValues", "scatterSize", "arrayIndexes"),
-      (List(simpleArray2, simpleArray2Duplicate), 2.validNelCheck, List(List(0, 1), List(0, 1))),
-      (List(simpleArray2, simpleArray3), "All arrays must have the same number of element when using the dot product scatter method".invalidNelCheck, List.empty)
-    )
-
-    forAll(nonEmptyVariables) { case (list, expectedScatterSize, expected) =>
-      ScatterLogic.DotProductScatterProcessingFunction(list) shouldBe expectedScatterSize
-
-      expectedScatterSize match {
-        case Right(scatterSize) => validateScatterCombinations(list, scatterSize, expected)
-        case _ => // Only verify combinations if the scatter is valid
-      }
-    }
-  }
-
-  "NestedCrossProduct collecting function builder" should "generate correct results" in {
-    import spray.json._
-
-    val arrayString = arrayStringType
-    val nestedArrayString = WomArrayType(arrayString)
-    val nestedArrayString2 = WomArrayType(nestedArrayString)
-
-    val variables = Table(
-      ("arraySizes", "shards", "valueType", "result"),
-      (List(0), List.empty, arrayString, "[]"),
-      (List(0, 2), List.empty, nestedArrayString, "[]"),
-      (List(2, 0), List.empty, nestedArrayString, "[[], []]"),
-      (List(2, 3, 0), List.empty, nestedArrayString2, "[[[], [], []], [[], [], []]]"),
-      (List(2, 0, 3), List.empty, nestedArrayString2, "[[], []]"),
-      // This technically should not happen since to have a cross product we need at least 2 scatter variables but..
-      (List(2), List(valueA, valueB), arrayString, """["a", "b"]"""),
-      (List(2, 2), List(valueA, valueB, valueC, valueD), nestedArrayString, """[["a", "b"], ["c", "d"]]"""),
-      (List(3, 2), List(valueA, valueB, valueC, valueD, valueA, valueB), nestedArrayString, """[["a", "b"], ["c", "d"], ["a", "b"]]"""),
-      (List(2, 3), List(valueA, valueB, valueC, valueC, valueB, valueA), nestedArrayString, """[["a", "b", "c"], ["c", "b", "a"]]"""),
-      (List(2, 3, 2), List(
-        valueA, valueB, valueA, valueB, valueA, valueB,
-        valueC, valueD, valueC, valueD, valueC, valueD
-      ), nestedArrayString2, """[[["a", "b"], ["a", "b"], ["a", "b"]], [["c", "d"], ["c", "d"], ["c", "d"]]]""")
-    )
-
-    forAll(variables) { case (arraySizes, shards, valueType, result) =>
-      val collection = ScatterLogic.NestedCrossProductScatterCollectionFunctionBuilder(arraySizes)(shards, valueType)
-      collection.arrayType shouldBe valueType
-      (collection: WomValue).toJson(WomValueJsonFormatter.WomValueJsonFormat) shouldBe result.parseJson
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/TestSetup.scala b/cwl/src/test/scala/cwl/TestSetup.scala
deleted file mode 100644
index 14e5dbe9b05..00000000000
--- a/cwl/src/test/scala/cwl/TestSetup.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cwl
-
-import better.files.File.currentWorkingDirectory
-
-object TestSetup {
-
-  val rootPath = currentWorkingDirectory/"cwl"/"src"/"test"/"resources"
-
-}
diff --git a/cwl/src/test/scala/cwl/WomTypeConversionSpec.scala b/cwl/src/test/scala/cwl/WomTypeConversionSpec.scala
deleted file mode 100644
index e7b76b153dc..00000000000
--- a/cwl/src/test/scala/cwl/WomTypeConversionSpec.scala
+++ /dev/null
@@ -1,134 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.types._
-import mouse.`try`._
-
-import scala.util.Try
-
-class WomTypeConversionSpec extends AnyFlatSpec with Matchers {
-  behavior of "WomTypeConversion"
-
-  /* ******** Inputs *********** */
-  it should "convert ArrayInputSchema" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val x = InputArraySchema(items = Coproduct[MyriadInputType](y))
-    val z = Coproduct[MyriadInputInnerType](x)
-    Coproduct[MyriadInputType](z).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomArrayType(WomStringType)
-  }
-
-  it should "convert Cwl Input String" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    Coproduct[MyriadInputType](y).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe WomStringType
-  }
-
-  it should "convert Array of a single type is actually one type not in an array" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    Coproduct[MyriadInputType](Array(y)).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomStringType
-  }
-
-  it should "convert Array of more than one type becomes a coproduct" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Boolean)
-    Coproduct[MyriadInputType](Array(y, z)).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType))
-  }
-
-  it should "convert Array of more than one type and a null becomes an optional coproduct" in {
-    val x = Coproduct[MyriadInputInnerType](CwlType.Null)
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Boolean)
-    Coproduct[MyriadInputType](Array(x, y, z)).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomOptionalType(WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType)))
-  }
-
-  it should "convert a 2-element Input Array of a single type accompanied by a null is an optional type" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Null)
-    testInputArray(Array(y,z), WomOptionalType(WomStringType))
-  }
-
-  private def testInputArray(array: Array[MyriadInputInnerType], assertedType: WomType ) = {
-    def f(array: Array[MyriadInputInnerType]) =
-      Try(Coproduct[MyriadInputType](array).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement())).cata(
-        success => withClue("input should evaluate to an optional array of files type")(success shouldBe assertedType),
-        failure => fail(s"expected an optional array of files type but received a failure: $failure")
-      )
-    f(array)
-    f(array.reverse)
-  }
-
-  it should "convert Optional Array of a type is interpreted correctly as input type" in {
-    val miit = Coproduct[MyriadInputInnerType](CwlType.File)
-    val mit = Coproduct[MyriadInputType](miit)
-    val ias =  InputArraySchema(items = mit)
-    val y = Coproduct[MyriadInputInnerType](ias)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Null)
-    testInputArray(Array(y, z), WomOptionalType(WomMaybeEmptyArrayType(WomMaybePopulatedFileType)))
-  }
-
-  /* ******** Outputs *********** */
-  it should "convert ArrayOutputSchema" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val x = OutputArraySchema(items = Coproduct[MyriadOutputType](y))
-    val z = Coproduct[MyriadOutputInnerType](x)
-    Coproduct[MyriadOutputType](z).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomArrayType(WomStringType)
-  }
-
-  it should "convert Cwl Output String" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    Coproduct[MyriadOutputType](y).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe WomStringType
-  }
-
-  it should "convert Array of a single type is the same as one type not in an array" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    Coproduct[MyriadOutputType](Array(y)).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomStringType
-  }
-
-  it should "convert Output Array of more than one type becomes a coproduct" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val z = Coproduct[MyriadOutputInnerType](CwlType.Boolean)
-    Coproduct[MyriadOutputType](Array(y, z)).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType))
-  }
-
-  it should "convert Output Array of more than one types including a null is an optional coproduct" in {
-    val x = Coproduct[MyriadOutputInnerType](CwlType.Null)
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val z = Coproduct[MyriadOutputInnerType](CwlType.Boolean)
-    Coproduct[MyriadOutputType](Array(x, y, z)).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomOptionalType(WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType)))
-  }
-
-  private def testOutputArray(array: Array[MyriadOutputInnerType], assertedType: WomType) = {
-    def f(array: Array[MyriadOutputInnerType]) =
-      Try(Coproduct[MyriadOutputType](array).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement())).cata(
-        success => withClue("input should evaluate to an optional string type")(success shouldBe assertedType),
-        failure => fail(s"expected an optional string type but received a failure: $failure")
-      )
-    f(array)
-    f(array.reverse)
-  }
-
-  it should "convert a 2-element Output Array of a single type accompanied by a null is an optional type" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val z = Coproduct[MyriadOutputInnerType](CwlType.Null)
-    testOutputArray(Array(y,z), WomOptionalType(WomStringType))
-  }
-
-  it should "convert Optional Array of a type is interpreted correctly as output type" in {
-    val moit = Coproduct[MyriadOutputInnerType](CwlType.File)
-    val mot = Coproduct[MyriadOutputType](moit)
-    val oas =  OutputArraySchema(items = mot)
-    val moit2 = Coproduct[MyriadOutputInnerType](oas)
-    val moit3 = Coproduct[MyriadOutputInnerType](CwlType.Null)
-    testOutputArray(Array(moit2,moit3), WomOptionalType(WomMaybeEmptyArrayType(WomMaybePopulatedFileType)))
-  }
-}
diff --git a/cwl/src/test/scala/cwl/WomValueJsonFormatter.scala b/cwl/src/test/scala/cwl/WomValueJsonFormatter.scala
deleted file mode 100644
index 7939a076dc2..00000000000
--- a/cwl/src/test/scala/cwl/WomValueJsonFormatter.scala
+++ /dev/null
@@ -1,27 +0,0 @@
-package cwl
-
-import spray.json.{JsArray, JsBoolean, JsNull, JsNumber, JsObject, JsString, JsValue, RootJsonFormat}
-import wom.values.{WomArray, WomBoolean, WomFile, WomFloat, WomInteger, WomMap, WomObjectLike, WomOptionalValue, WomPair, WomString, WomValue}
-
-// Sometimes it's hard for compiler plugins to find this in ScatterLogicSpec, so here it is again:
-object WomValueJsonFormatter {
-  implicit object WomValueJsonFormat extends RootJsonFormat[WomValue] {
-    def write(value: WomValue): JsValue = value match {
-      case s: WomString => JsString(s.value)
-      case i: WomInteger => JsNumber(i.value)
-      case f: WomFloat => JsNumber(f.value)
-      case b: WomBoolean => JsBoolean(b.value)
-      case f: WomFile => JsString(f.value)
-      case o: WomObjectLike => new JsObject(o.values map {case(k, v) => k -> write(v)})
-      case a: WomArray => new JsArray(a.value.map(write).toVector)
-      case m: WomMap => new JsObject(m.value map {case(k,v) => k.valueString -> write(v)})
-      case q: WomPair => new JsObject(Map("left" -> write(q.left), "right" -> write(q.right)))
-      case WomOptionalValue(_, Some(innerValue)) => write(innerValue)
-      case WomOptionalValue(_, None) => JsNull
-      // handles WdlExpression
-      case v: WomValue => JsString(v.toWomString)
-
-    }
-    def read(value: JsValue): WomValue = throw new UnsupportedOperationException
-  }
-}
diff --git a/cwl/src/test/scala/cwl/WorkflowStepInputExpressionSpec.scala b/cwl/src/test/scala/cwl/WorkflowStepInputExpressionSpec.scala
deleted file mode 100644
index 122156b4f4e..00000000000
--- a/cwl/src/test/scala/cwl/WorkflowStepInputExpressionSpec.scala
+++ /dev/null
@@ -1,59 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.data.Validated._
-import cwl.WorkflowStepInput.InputSource
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.graph.GraphNodePort.GraphNodeOutputPort
-import wom.graph.WomIdentifier
-import wom.types._
-import wom.values.{WomArray, WomInteger, WomString}
-
-class WorkflowStepInputExpressionSpec extends AnyFlatSpec with Matchers {
-  behavior of "WorkflowStepInputExpression"
-
-  it should "assert source arrays are concatenated when merge_flattened LinkMergeMethod is used" in {
-    val inputSource = Coproduct[InputSource](Array("i1", "i2"))
-    val i1OutputPort = GraphNodeOutputPort(WomIdentifier("i1"), WomStringType, null)
-    val i2OutputPort = GraphNodeOutputPort(WomIdentifier("i2"), WomStringType, null)
-    val wsi = WorkflowStepInput("s#h", source = Option(inputSource), linkMerge = Option(LinkMergeMethod.MergeFlattened))
-
-    val mergeTpeEither = wsi.determineMergeType(
-      sources = Map("i1" -> WomArrayType(WomStringType), "i2" -> WomArrayType(WomStringType)),
-      expectedTypeAsWom = Option(WomArrayType(WomStringType)))
-
-    val tpe: WomType = fromEither(mergeTpeEither).getOrElse(throw new RuntimeException("expected a womType but evaluation of determineType failed"))
-
-    val expression = WorkflowStepInputMergeExpression(wsi, tpe, NonEmptyList.of("i1" -> i1OutputPort, "i2" -> i2OutputPort), Vector.empty)
-
-    val r = expression.evaluateValue(Map("i1" -> WomString("1"), "i2" -> WomString("2")), null)
-    r shouldBe Valid(WomArray(Seq(WomString("1"), WomString("2"))))
-  }
-
-  it should "array of one entry for each input link when merge_nested is used" in {
-    val inputSource =  Coproduct[InputSource](Array("i1", "i2"))
-    val i1OutputPort = GraphNodeOutputPort(WomIdentifier("i1"), WomStringType, null)
-    val i2OutputPort = GraphNodeOutputPort(WomIdentifier("i2"), WomStringType, null)
-    val wsi = WorkflowStepInput("s#h", source = Option(inputSource))
-    val expression = WorkflowStepInputMergeExpression(wsi, null, NonEmptyList.of("i1" -> i1OutputPort, "i2" -> i2OutputPort), Vector.empty)
-
-    expression.evaluateValue(Map("i1" -> WomInteger(1), "i2" -> WomInteger(2)), null) shouldBe
-      Valid(WomArray(Seq(
-        WomInteger(1),
-        WomInteger(2)
-      )))
-  }
-
-  it should "list of one entry for when there is only one input link and when merge_nested is used" in {
-    val inputSource =  Coproduct[InputSource]("i1")
-    val wsi = WorkflowStepInput("s#h", source = Option(inputSource))
-    val i1OutputPort = GraphNodeOutputPort(WomIdentifier("i1"), WomStringType, null)
-    val expression = WorkflowStepInputMergeExpression(wsi, null, NonEmptyList.of("i1" -> i1OutputPort), Vector.empty)
-
-    expression.evaluateValue(Map("i1" -> WomInteger(1), "i2" -> WomInteger(2)), null) shouldBe
-      Valid(WomInteger(1))
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/WorkflowStepInputSpec.scala b/cwl/src/test/scala/cwl/WorkflowStepInputSpec.scala
deleted file mode 100644
index 5592e2ffddd..00000000000
--- a/cwl/src/test/scala/cwl/WorkflowStepInputSpec.scala
+++ /dev/null
@@ -1,109 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.types._
-
-class WorkflowStepInputSpec extends AnyFlatSpec with Matchers {
-  behavior of "WorkflowStepInput"
-
-  it should "use single source type if no default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = false
-    ) shouldBe
-      Right(WomStringType)
-  }
-
-  it should "use optional single source type if no default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomOptionalType(WomStringType)),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe
-      Right(WomOptionalType(WomStringType))
-  }
-
-  it should "use single source type if there's a default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = true,
-    ) shouldBe
-      Right(WomStringType)
-  }
-
-  it should "use unpacked single source type if there's a default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomOptionalType(WomStringType)),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = true,
-    ) shouldBe
-      Right(WomStringType)
-  }
-
-  it should "wrap single source type in an array if merge method is nested" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType),
-      linkMerge = Option(LinkMergeMethod.MergeNested),
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe
-      Right(WomArrayType(WomStringType))
-  }
-
-  it should "find the closest common type to all sources if merge method is nested" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType, "s#in2" -> WomIntegerType),
-      linkMerge = Option(LinkMergeMethod.MergeNested),
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe
-      Right(WomMaybeEmptyArrayType(WomStringType))
-  }
-
-  it should "validate array inner type against target type if merge method is flattened" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType, "s#in2" -> WomStringType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = Option(WomArrayType(WomStringType)),
-      hasDefault = false,
-    ) shouldBe Right(WomArrayType(WomStringType))
-  }
-
-  it should "validate type against target type if merge method is flattened" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType, "s#in2" -> WomStringType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = Option(WomStringType),
-      hasDefault = false,
-    ) shouldBe Right(WomArrayType(WomStringType))
-  }
-
-  it should "fail if target type does not conform to source types if merge method is flattened" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomObjectType, "s#in2" -> WomObjectType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = Option(WomStringType),
-      hasDefault = false,
-    ) shouldBe Left(NonEmptyList.one(
-      "could not verify that types Map(s#in -> WomObjectType, s#in2 -> WomObjectType)" +
-        " and the items type of the run's InputArraySchema WomStringType were compatible"
-    ))
-  }
-
-  it should "fall back to the closest common type" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomBooleanType, "s#in2" -> WomIntegerType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe Right(WomStringType)
-  }
-}
diff --git a/cwl/src/test/scala/cwl/internal/EcmaScriptUtilSpec.scala b/cwl/src/test/scala/cwl/internal/EcmaScriptUtilSpec.scala
deleted file mode 100644
index adf482c2e82..00000000000
--- a/cwl/src/test/scala/cwl/internal/EcmaScriptUtilSpec.scala
+++ /dev/null
@@ -1,96 +0,0 @@
-package cwl.internal
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import delight.rhinosandox.exceptions.ScriptDurationException
-import org.mozilla.javascript.{EcmaError, EvaluatorException}
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.types._
-import wom.values._
-
-class EcmaScriptUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "EcmaScriptUtil"
-
-  private lazy val encoder = new EcmaScriptEncoder()
-
-  it should "lookup a map entry with a string key" in {
-    val values =
-      "myName" -> WomMap(
-        WomMapType(WomBooleanType, WomArrayType(WomStringType)),
-        Map(WomBoolean(true) -> WomArray(WomArrayType(WomStringType), Seq(WomString("myValue"))))
-      )
-    val expr = """myName["true"][0] + 'Plus'"""
-    val result: WomValue = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(WomString("myValuePlus"))
-  }
-
-  it should "lookup a map entry with a boolean key" in {
-    val values =
-      "myName" -> WomMap(
-        WomMapType(WomBooleanType, WomArrayType(WomStringType)),
-        Map(WomBoolean(true) -> WomArray(WomArrayType(WomStringType), Seq(WomString("myValue"))))
-      )
-    val expr = "myName[true][0] + 'PlusPlus'"
-    val result = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(WomString("myValuePlusPlus"))
-  }
-
-  it should "JSON.stringify" in {
-    val values =
-      "myName" -> WomMap(
-        WomMapType(WomBooleanType, WomArrayType(WomStringType)),
-        Map(WomBoolean(true) -> WomArray(WomArrayType(WomStringType), Seq(WomString("myValue"))))
-      )
-    val expr = "JSON.stringify(myName)"
-    val result: WomValue = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(WomString("""{"true":["myValue"]}"""))
-  }
-
-  it should "Array.prototype.sort" in {
-    val values = "myName" -> WomArray(List("hello", "world", "alpha", "zulu", "indigo").map(WomString))
-    val expr = "myName.sort()"
-    val expected = WomArray(List("alpha", "hello", "indigo", "world", "zulu").map(WomString))
-    val result = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(expected)
-  }
-
-  it should "run in strict mode" in {
-    the[EvaluatorException] thrownBy {
-      EcmaScriptUtil.evalRaw(
-        """|function sum(a, a, c) { // !!! syntax error
-           |  return a + a + c; // wrong if this code ran
-           |}
-           |""".stripMargin) { (_, _) => () }
-    } should have message
-      """Parameter "a" already declared in this function. (<ecmascript>#1)"""
-  }
-
-  it should "not run java code" in {
-    the[EcmaError] thrownBy {
-      EcmaScriptUtil.evalRaw(
-        """|var path = java.nio.file.Paths.get("/etc/passwd");
-           |java.nio.file.Files.exists(path);
-           |// Or even... java.lang.System.exit(42);
-           |""".stripMargin) { (_, _) => () }
-    } should have message
-      """ReferenceError: "java" is not defined. (<ecmascript>#1)"""
-  }
-
-  it should "not run forever" in {
-    a[ScriptDurationException] should be thrownBy {
-      EcmaScriptUtil.evalRaw(
-        """|function sleep(milliseconds) {
-           |  var start = new Date().getTime();
-           |  while(true) {
-           |    if ((new Date().getTime() - start) > milliseconds){
-           |      break;
-           |    }
-           |  }
-           |}
-           |sleep(120 * 1000);
-           |""".stripMargin) { (_, _) => () }
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/internal/EnhancedRhinoSandboxSpec.scala b/cwl/src/test/scala/cwl/internal/EnhancedRhinoSandboxSpec.scala
deleted file mode 100644
index 01409d3c546..00000000000
--- a/cwl/src/test/scala/cwl/internal/EnhancedRhinoSandboxSpec.scala
+++ /dev/null
@@ -1,141 +0,0 @@
-package cwl.internal
-
-import java.util.concurrent.{CountDownLatch, TimeUnit}
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.internal.EnhancedRhinoSandboxSpec.CachedClassLoader
-import org.apache.commons.io.IOUtils
-import org.mozilla.javascript.ContextFactory
-import org.scalatest.concurrent.ScaledTimeSpans
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-import scala.concurrent.duration._
-
-class EnhancedRhinoSandboxSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScaledTimeSpans {
-
-  behavior of "EnhancedRhinoSandbox"
-
-  it should "synchronize global ContextFactory initialization" in {
-    // Initialize the context factory here to be sure that our loaded runner is actually using a fresh ContextFactory
-    new EnhancedRhinoSandbox(true).assertContextFactory()
-
-    val threadCount = 10
-
-    // A custom loader that will contain our fresh static ContextFactory
-    val cachedClassLoader = new CachedClassLoader
-    // A latch that lets this test know the threads are ready
-    val threadReadyLatch = new CountDownLatch(threadCount)
-    // A latch to ensure that all threads try to run at the same time
-    val threadGoLatch = new CountDownLatch(1)
-
-    class Runner(name: String) extends Thread {
-      var success = false
-
-      override def run(): Unit = {
-        EnhancedRhinoSandboxSpec.runClassLoaded(
-          cachedClassLoader,
-          threadReadyLatch = threadReadyLatch,
-          threadGoLatch = threadGoLatch
-        )
-        success = true
-      }
-    }
-
-    val threads = (0 until threadCount).map(i => new Runner(i.toString))
-    // move all the threads to the starting line...
-    threads.foreach(_.start())
-    // Wait for threads to say they're ready
-    threadReadyLatch.await(scaled(10.seconds).toMillis, TimeUnit.MILLISECONDS)
-    // go!
-    threadGoLatch.countDown()
-    // Maximum time to wait for each runner to finish
-    threads.foreach(_.join(scaled(10.seconds).toMillis))
-
-    withClue("all threads did not complete successfully:") {
-      threads.map(_.success) should contain only true
-    }
-  }
-}
-
-object EnhancedRhinoSandboxSpec extends ScaledTimeSpans {
-  /**
-    * Runs a runner loaded from a custom class loader.
-    */
-  private def runClassLoaded(ecmaScriptUtilClassLoader: CachedClassLoader,
-                             threadReadyLatch: CountDownLatch,
-                             threadGoLatch: CountDownLatch): Unit = {
-    val cls = ecmaScriptUtilClassLoader.loadClass(classOf[LatchedRunner].getName)
-    val obj = cls.getDeclaredConstructor().newInstance()
-    cls
-      .getMethod("run", classOf[CountDownLatch], classOf[CountDownLatch])
-      .invoke(obj, threadReadyLatch, threadGoLatch)
-    ()
-  }
-
-  /**
-    * Waits for a shared latch and then quickly tries to run the EcmaScriptUtil.
-    * Before running, there is a test that ensures that the ContextFactory has _not_ been initialized.
-    *
-    * Inspired by: https://stackoverflow.com/questions/13263079/run-two-thread-at-the-same-time-in-java#13263273
-    */
-  class LatchedRunner {
-    def run(threadReadyLatch: CountDownLatch, threadGoLatch: CountDownLatch): Unit = {
-      require(!ContextFactory.hasExplicitGlobal, "The ContextFactory within this classloader is already initialized")
-      // Notify the test we're at the starting line.
-      threadReadyLatch.countDown()
-      // This await is for the time between all the threads `start()`-ing up, and the `countDownLatch.countDown()`
-      threadGoLatch.await(scaled(5.seconds).toMillis, TimeUnit.MILLISECONDS)
-      new EnhancedRhinoSandbox(true).assertContextFactory()
-      ()
-    }
-  }
-
-  /**
-    * Locates a class but instead of returning the class from the original classloader it instead returns a cached copy.
-    *
-    * This is needed when we want to ensure that a static variable has NOT been initialized on a class instance.
-    *
-    * Parent class loader must be the current thread's class loader since the system class loader is NOT sufficient
-    * under sbt.
-    *
-    * Inspired by: https://stackoverflow.com/questions/14316996/how-to-replace-classes-in-a-running-application-in-java#14317506
-    */
-  class CachedClassLoader extends ClassLoader(Thread.currentThread.getContextClassLoader) {
-
-    override def loadClass(name: String): Class[_] = {
-      loadedClasses synchronized {
-        loadedClasses.getOrElseUpdate(name, internalLoadClass(name))
-      }
-    }
-
-    /** Classes to always load from the parent. */
-    private val parentPackages = List("scala", "java", "sun")
-    /** Synchronized mutable map of our already loaded classes. */
-    private val loadedClasses = scala.collection.mutable.Map.empty[String, Class[_]]
-
-    /**
-      * Locates a class but returns our _own_ copy of it. Classes under "scala", "java", and "sun" will use the parent.
-      * If a class cannot be located for any reason, the parent is also returned.
-      *
-      * @param name Name of the class to load.
-      * @return The loaded class.
-      */
-    private def internalLoadClass(name: String): Class[_] = {
-      if (!parentPackages.exists(pkg => name.startsWith(pkg + "."))) {
-        val inputStream = getParent.getResourceAsStream(name.replace(".", "/").concat(".class"))
-        try {
-          val bytes = IOUtils.toByteArray(inputStream)
-          return defineClass(name, bytes, 0, bytes.length)
-        } catch {
-          case _: Throwable => /* ignore and fall through to loading from the parent */
-        } finally {
-          if (inputStream != null)
-            inputStream.close()
-        }
-      }
-      getParent.loadClass(name)
-    }
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/ontology/SchemaSpec.scala b/cwl/src/test/scala/cwl/ontology/SchemaSpec.scala
deleted file mode 100644
index 06f552797a8..00000000000
--- a/cwl/src/test/scala/cwl/ontology/SchemaSpec.scala
+++ /dev/null
@@ -1,114 +0,0 @@
-package cwl.ontology
-
-import com.typesafe.config.ConfigFactory
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import org.semanticweb.owlapi.apibinding.OWLManager
-
-class SchemaSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "Schema"
-
-  val resolveTests = Table(
-    ("base", "iri", "expected"),
-    ("file:///hello/world", "custom.owl", "file:/hello/custom.owl"),
-    ("file:///hello/world", "file:./custom.owl", "file:./custom.owl"),
-    ("file:///hello/world", "file:///custom.owl", "file:///custom.owl"),
-    ("http://hello/world", "custom.owl", "http://hello/custom.owl"),
-    ("http://hello/world", "file:./custom.owl", "file:./custom.owl"),
-    ("http://hello/world", "file:///custom.owl", "file:///custom.owl"),
-  )
-
-  forAll(resolveTests) { (base, iri, expected) =>
-    it should s"resolve $iri relative to $base to create $expected" in {
-      Schema.getIriPath(base, iri) should be(expected)
-    }
-  }
-
-  val fullIriTests = Table(
-    ("schemaDescription", "schema", "iri", "fullIri"),
-    ("galaxy", galaxySchema, "edam:format_1929", "http://edamontology.org/format_1929"),
-    ("galaxy", galaxySchema, "<edam:format_1929>", "edam:format_1929"),
-    ("galaxy", galaxySchema, "edam:format_2200", "http://edamontology.org/format_2200"),
-    ("galaxy", galaxySchema, "http://galaxyproject.org/formats/fasta", "http://galaxyproject.org/formats/fasta"),
-    ("galaxy", galaxySchema, "gx:fasta", "http://galaxyproject.org/formats/fasta"),
-    ("galaxy", galaxySchema, "not:real", "not:real"),
-    ("galaxy", galaxySchema, "owl:Thing", "http://www.w3.org/2002/07/owl#Thing"),
-    ("galaxy", galaxySchema, "owl:Nothing", "http://www.w3.org/2002/07/owl#Nothing"),
-    ("edam", edamSchema, "edam:format_1929", "http://purl.obolibrary.org/obo/edam#format_1929"),
-    ("edam w/ namespace", edamNamespaceSchema, "edam:format_1929", "http://edamontology.org/format_1929"),
-  )
-
-  forAll(fullIriTests) { (schemaDescription, schema, iri, fullIri) =>
-    it should s"expand $iri to $fullIri using schema $schemaDescription" in {
-      schema.fullIri(iri) should be(fullIri)
-    }
-  }
-
-  val subClassTests = Table(
-    ("isSubClass", "schemaDescription", "schema", "child", "ancestor"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "http://galaxyproject.org/formats/fasta"),
-    (true, "galaxy", galaxySchema, "http://galaxyproject.org/formats/fasta", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "gx:fasta", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "gx:fasta", "edam:format_2330"),
-    (false, "galaxy", galaxySchema, "not:real", "edam:format_1929"),
-    (false, "galaxy", galaxySchema, "edam:format_1929", "not:real"),
-    (false, "galaxy", galaxySchema, "owl:Thing", "owl:Nothing"),
-    (true, "galaxy", galaxySchema, "owl:Nothing", "owl:Thing"),
-    (false, "galaxy", galaxySchema, "owl:Thing", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "owl:Thing"),
-    (false, "galaxy", galaxySchema, "edam:format_1929", "owl:Nothing"),
-    (true, "galaxy", galaxySchema, "owl:Nothing", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "http://edamontology.org/format_2330"),
-    (false, "edam", edamSchema, "edam:format_1929", "http://edamontology.org/format_2330"),
-    (true, "edam w/ namespace", edamNamespaceSchema, "edam:format_1929", "http://edamontology.org/format_2330"),
-  )
-
-  forAll(subClassTests) { (isSubClass, schemaDescription, schema, child, ancestor) =>
-    it should s"return $isSubClass that $child is a sub class of $ancestor when checking schema $schemaDescription" in {
-      schema.isSubClass(child, ancestor) should be(isSubClass)
-    }
-  }
-  
-  it should "cache ontologies" in {
-    val cache = Schema.makeOntologyCache(ConfigFactory.parseString("max-size=5"))
-    val ontologyManager1 = OWLManager.createOWLOntologyManager
-    val ontologyManager2 = OWLManager.createOWLOntologyManager
-    val ontology1 = Schema.loadOntologyFromIri(ontologyManager1, Option(cache))(getClass.getResource("EDAM.owl").toExternalForm)
-    ontology1.isValid shouldBe true
-    val ontology2 = Schema.loadOntologyFromIri(ontologyManager2, Option(cache))(getClass.getResource("EDAM.owl").toExternalForm)
-    ontology2.isValid shouldBe true
-    ontology2.getOrElse(fail()).getOWLOntologyManager shouldBe ontologyManager2
-  }
-
-  private lazy val galaxySchema = {
-    Schema(
-      List(
-        getClass.getResource("EDAM.owl").toExternalForm,
-        getClass.getResource("gx_edam.ttl").toExternalForm
-      ),
-      Map.empty
-    )
-  }
-
-  private lazy val edamSchema = {
-    Schema(
-      List(
-        getClass.getResource("EDAM.owl").toExternalForm
-      ),
-      Map.empty
-    )
-  }
-
-  private lazy val edamNamespaceSchema = {
-    Schema(
-      List(
-        getClass.getResource("EDAM.owl").toExternalForm
-      ),
-      Map("edam" -> "http://edamontology.org/")
-    )
-  }
-}
diff --git a/cwl/src/test/scala/cwl/preprocessor/CwlPreProcessorSpec.scala b/cwl/src/test/scala/cwl/preprocessor/CwlPreProcessorSpec.scala
deleted file mode 100644
index c0aba9c975d..00000000000
--- a/cwl/src/test/scala/cwl/preprocessor/CwlPreProcessorSpec.scala
+++ /dev/null
@@ -1,125 +0,0 @@
-package cwl.preprocessor
-
-import better.files.File
-import cats.data.NonEmptyList
-import common.assertion.CromwellTimeoutSpec
-import common.mock.MockSugar
-import cwl.preprocessor.CwlPreProcessor.SaladFunction
-import io.circe.Printer
-import org.mockito.ArgumentMatchers._
-import org.mockito.Mockito._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-class CwlPreProcessorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with MockSugar {
-  behavior of "CwlPreProcessor"
-
-  private val resourcesRoot = File(getClass.getResource(".").getPath)
-  private val echoFileTool = CwlFileReference(resourcesRoot / "echo_tool.cwl", None)
-
-  it should "flatten a simple file" in {
-    validate(makeTestRoot("simple_workflow"), None) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(echoFileTool)
-    }
-  }
-
-  it should "flatten file with a self reference" in {
-    validate(makeTestRoot("self_reference"), Option("echo-workflow-2")) { _ => }
-  }
-
-  /*
-    * A "valid" cyclic dependency means for example
-    * file_1
-    *   - workflow_1 -> depends on workflow_3
-    *   - workflow_2
-    * file_2
-    *   - workflow_3 -> depends on workflow_2
-    * workflow_1 (in file_1) references a workflow in file_2 that references a workflow in file_1,
-    * but that's ok since the cycle is only over the file, not the workflows themselves.
-   */
-  it should "flatten file with sub workflow, self reference and valid cyclic dependency" in {
-    val testRoot = makeTestRoot("complex_workflow")
-    val subWorkflow =  CwlFileReference(testRoot / "sub" / "sub_workflow.cwl", Option("sub-echo-workflow-1"))
-
-    validate(testRoot, Option("echo-workflow-2")) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(echoFileTool)
-      verify(mockSaladingFunction).apply(subWorkflow)
-    }
-  }
-
-  it should "detect invalid cyclic dependencies in the same file and fail" in {
-    val testRoot = makeTestRoot("same_file_cyclic_dependency")
-
-    validate(testRoot, Option("echo-workflow-2"),
-      expectedFailure = Option(
-        NonEmptyList.one(s"Found a circular dependency on file://$testRoot/root_workflow.cwl#echo-workflow-2")
-      )
-    ) { _ => }
-  }
-
-  it should "detect invalid transitive cyclic dependencies (A => B => C => A) and fail" in {
-    val testRoot = makeTestRoot("transitive_cyclic_dependency")
-
-    val subWorkflow1 = CwlFileReference(testRoot / "sub_workflow_1.cwl", None)
-    val subWorkflow2 =  CwlFileReference(testRoot / "sub_workflow_2.cwl", None)
-
-    validate(testRoot, None,
-      expectedFailure = Option(
-        NonEmptyList.one(s"Found a circular dependency on file://$testRoot/root_workflow.cwl")
-      )
-    ) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(subWorkflow1)
-      verify(mockSaladingFunction).apply(subWorkflow2)
-    }
-  }
-
-  it should "pre-process inlined workflows" in {
-    val testRoot = makeTestRoot("deep_nesting")
-
-    val subWorkflow1 = CwlFileReference(testRoot / "wc-tool.cwl", None)
-    val subWorkflow2 =  CwlFileReference(testRoot / "parseInt-tool.cwl", None)
-
-    validate(testRoot, None, uuidExtractor = Option("step0/([0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12})/")) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(subWorkflow1)
-      verify(mockSaladingFunction).apply(subWorkflow2)
-    }
-  }
-
-  private def makeTestRoot(testDirectoryName: String) = resourcesRoot / testDirectoryName
-
-  def validate[T](testRoot: File,
-                  root: Option[String],
-                  expectedFailure: Option[NonEmptyList[String]] = None,
-                  uuidExtractor: Option[String] = None
-                 )(additionalValidation: SaladFunction => T): Unit = {
-    val rootWorkflowReference = CwlFileReference(testRoot / "root_workflow.cwl", root)
-
-    // Mocking the salad function allows us to validate how many times it is called exactly and with which parameters
-    val mockSaladingFunction = mock[SaladFunction]
-    when(mockSaladingFunction.apply(any[CwlReference])) thenAnswer {
-      invocationOnMock =>
-        CwlPreProcessor.saladCwlFile(invocationOnMock.getArgument[CwlReference](0))
-    }
-    val preProcessor = new CwlPreProcessor(mockSaladingFunction)
-
-    val process = preProcessor.preProcessCwl(rootWorkflowReference).value.unsafeRunSync()
-    // Asserts that dependencies are only saladed once and exactly once
-    verify(mockSaladingFunction).apply(rootWorkflowReference)
-    additionalValidation(mockSaladingFunction)
-
-    (process, expectedFailure) match {
-      case (Left(errors), Some(failures)) => errors shouldBe failures
-      case (Left(errors), None) => fail("Unexpected failure to pre-process workflow: " + errors.toList.mkString(", "))
-      case (Right(result), None) =>
-        val content = (testRoot / "expected_result.json").contentAsString
-        val uuid = uuidExtractor.flatMap(_.r.findFirstMatchIn(result.printWith(Printer.noSpaces)).map(_.group(1)))
-        val expectationContent = content
-          .replaceAll("<<RESOURCES_ROOT>>", resourcesRoot.pathAsString)
-          .replaceAll("<<RANDOM_UUID>>", uuid.getOrElse(""))
-
-        result shouldBe io.circe.parser.parse(expectationContent).getOrElse(fail("Failed to parse expectation. Your test is broken !"))
-      case (Right(_), Some(failures)) => fail("Unexpected success to pre-process workflow, was expecting failures: " + failures.toList.mkString(", "))
-    }
-    ()
-  }
-}
diff --git a/cwl/src/test/scala/cwl/preprocessor/CwlReferenceSpec.scala b/cwl/src/test/scala/cwl/preprocessor/CwlReferenceSpec.scala
deleted file mode 100644
index a2c382c5bc9..00000000000
--- a/cwl/src/test/scala/cwl/preprocessor/CwlReferenceSpec.scala
+++ /dev/null
@@ -1,79 +0,0 @@
-package cwl.preprocessor
-
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-class CwlReferenceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  behavior of "CwlReference.apply"
-
-  it should "identify a pointerless local file reference" in {
-
-    val reference = "file:///blah/di/blah.cwl"
-    val cwlReference = CwlReference.fromString(reference)
-
-    cwlReference match {
-      case Some(ref @ CwlFileReference(file, _)) =>
-        file.pathAsString should be ("/blah/di/blah.cwl")
-        ref.pathAsString should be (reference)
-        ref.pointerWithinFile should be(None)
-        ref.fullReference should be (reference)
-      case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-      case None => fail("Failed to identify reference")
-    }
-  }
-
-  it should "identify a local file reference with a pointer" in {
-
-    val filePath = "/blah/di/blah.cwl"
-    val pointer = "1st-tool"
-    val reference = s"file://$filePath#$pointer"
-    val cwlReference = CwlReference.fromString(reference)
-
-    cwlReference match {
-      case Some(ref @ CwlFileReference(file, _)) =>
-        file.pathAsString should be (filePath)
-        ref.pathAsString should be (s"file://$filePath")
-        ref.pointerWithinFile should be(Some(pointer))
-        ref.fullReference should be (reference)
-      case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-      case None => fail("Failed to identify reference")
-    }
-  }
-
-  List("http://", "https://") foreach { scheme =>
-    it should s"identify a pointerless $scheme reference" in {
-
-      val reference = s"$scheme/blah.com/di/blah.cwl"
-      val cwlReference = CwlReference.fromString(reference)
-
-      cwlReference match {
-        case Some(ref @ CwlHttpReference(pathAsString, _)) =>
-          pathAsString should be (reference)
-          ref.pathAsString should be (reference)
-          ref.pointerWithinFile should be(None)
-          ref.fullReference should be (reference)
-        case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-        case None => fail("Failed to identify reference")
-      }
-    }
-
-    it should s"identify $scheme references with pointers" in {
-
-      val referencePath = s"$scheme/blah.com/di/blah.cwl"
-      val pointer = "1st-tool"
-      val reference = s"$referencePath#$pointer"
-      val cwlReference = CwlReference.fromString(reference)
-
-      cwlReference match {
-        case Some(ref @ CwlHttpReference(pathAsString, _)) =>
-          pathAsString should be (referencePath)
-          ref.pathAsString should be (referencePath)
-          ref.pointerWithinFile should be(Some(pointer))
-          ref.fullReference should be (reference)
-        case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-        case None => fail("Failed to identify reference")
-      }
-    }
-  }
-}
diff --git a/database/migration/src/main/resources/changelog.xml b/database/migration/src/main/resources/changelog.xml
index 5d711061c31..49d568766b3 100644
--- a/database/migration/src/main/resources/changelog.xml
+++ b/database/migration/src/main/resources/changelog.xml
@@ -87,6 +87,9 @@
     <include file="changesets/enlarge_call_caching_detritus_entry_id.xml" relativeToChangelogFile="true" />
     <include file="changesets/enlarge_call_caching_simpleton_entry_id.xml" relativeToChangelogFile="true" />
     <include file="changesets/reset_call_caching_hash_entry_id_autoincrement.xml" relativeToChangelogFile="true" />
+    <include file="changesets/enlarge_docker_hash_store_entry_id.xml" relativeToChangelogFile="true" />
+    <include file="changesets/enlarge_workflow_store_entry_id.xml" relativeToChangelogFile="true" />
+    <include file="changesets/enlarge_sub_workflow_store_entry_id.xml" relativeToChangelogFile="true" />
     <!-- REMINDER!
       Before appending here, did you remember to include the 'objectQuotingStrategy="QUOTE_ALL_OBJECTS"' line in your changeset/xyz.xml...?
     -->
diff --git a/database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml b/database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml
new file mode 100644
index 00000000000..fc7992268e6
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- BEGIN DOCKER_HASH_STORE_ENTRY_ID PK widening -->
+    <!-- For Postgresql there are 2 changesets: one for modifying the table column type, and another one for altering the autoincrementing sequence.
+         The other DBs can be refactored similarly with a single addAutoIncrement changeset. -->
+    <changeSet author="sshah" id="enlarge_docker_hash_store_entry_id" dbms="mysql,hsqldb,mariadb">
+        <addAutoIncrement
+                columnName="DOCKER_HASH_STORE_ENTRY_ID"
+                columnDataType="BIGINT"
+                incrementBy="1"
+                tableName="DOCKER_HASH_STORE_ENTRY"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_docker_hash_store_entry_id" dbms="postgresql">
+        <modifyDataType
+                columnName="DOCKER_HASH_STORE_ENTRY_ID"
+                tableName="DOCKER_HASH_STORE_ENTRY"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_docker_hash_store_entry_id_seq" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- idempotency check (noop if the sequence is present and already consistent what the alter would do) -->
+            <sqlCheck expectedResult="0">
+                SELECT count(*)
+                FROM information_schema.sequences
+                WHERE sequence_name = 'DOCKER_HASH_STORE_ENTRY_DOCKER_HASH_STORE_ENTRY_ID_seq'
+                AND data_type = 'bigint';
+            </sqlCheck>
+        </preConditions>
+        <sql>alter sequence "DOCKER_HASH_STORE_ENTRY_DOCKER_HASH_STORE_ENTRY_ID_seq" as bigint;</sql>
+    </changeSet>
+    <!-- END DOCKER_HASH_STORE_ENTRY_ID PK widening -->
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml b/database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml
new file mode 100644
index 00000000000..57894db824b
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- BEGIN SUB_WORKFLOW_STORE_ENTRY_ID PK widening -->
+    <!-- For Postgresql there are 2 changesets: one for modifying the table column type, and another one for altering the autoincrementing sequence.
+         The other DBs can be refactored similarly with a single addAutoIncrement changeset. -->
+    <changeSet author="sshah" id="enlarge_sub_workflow_store_entry_id" dbms="mysql,hsqldb,mariadb">
+        <addAutoIncrement
+                columnName="SUB_WORKFLOW_STORE_ENTRY_ID"
+                columnDataType="BIGINT"
+                incrementBy="1"
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_sub_workflow_store_entry_id" dbms="postgresql">
+        <modifyDataType
+                columnName="SUB_WORKFLOW_STORE_ENTRY_ID"
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_sub_workflow_store_entry_id_seq" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- idempotency check (noop if the sequence is present and already consistent what the alter would do) -->
+            <sqlCheck expectedResult="0">
+                SELECT count(*)
+                FROM information_schema.sequences
+                WHERE sequence_name = 'SUB_WORKFLOW_STORE_ENTRY_SUB_WORKFLOW_STORE_ENTRY_ID_seq'
+                AND data_type = 'bigint';
+            </sqlCheck>
+        </preConditions>
+        <sql>alter sequence "SUB_WORKFLOW_STORE_ENTRY_SUB_WORKFLOW_STORE_ENTRY_ID_seq" as bigint;</sql>
+    </changeSet>
+    <!-- END SUB_WORKFLOW_STORE_ENTRY_ID PK widening -->
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml b/database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml
new file mode 100644
index 00000000000..ea2b498fd51
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml
@@ -0,0 +1,82 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- Drop the foreign key constraint from SUB_WORKFLOW_STORE_ENTRY to WORKFLOW_STORE_ENTRY to allow for the latter's PK to be widened. -->
+    <changeSet author="sshah" id="drop_sub_workflow_store_entry_root_workflow_id_fk" dbms="mysql,hsqldb,postgresql,mariadb">
+        <dropForeignKeyConstraint
+                baseTableName="SUB_WORKFLOW_STORE_ENTRY"
+                constraintName="FK_SUB_WORKFLOW_STORE_ENTRY_ROOT_WORKFLOW_ID"
+        />
+    </changeSet>
+
+    <!-- BEGIN WORKFLOW_STORE_ENTRY_ID PK widening -->
+    <!-- For Postgresql there are 2 changesets: one for modifying the table column type, and another one for altering the autoincrementing sequence.
+         The other DBs can be refactored similarly with a single addAutoIncrement changeset. -->
+    <changeSet author="sshah" id="enlarge_workflow_store_entry_id" dbms="mysql,hsqldb,mariadb">
+        <addAutoIncrement
+                columnName="WORKFLOW_STORE_ENTRY_ID"
+                columnDataType="BIGINT"
+                incrementBy="1"
+                tableName="WORKFLOW_STORE_ENTRY"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_workflow_store_entry_id" dbms="postgresql">
+        <modifyDataType
+                columnName="WORKFLOW_STORE_ENTRY_ID"
+                tableName="WORKFLOW_STORE_ENTRY"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_workflow_store_entry_id_seq" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- idempotency check (noop if the sequence is present and already consistent what the alter would do) -->
+            <sqlCheck expectedResult="0">
+                SELECT count(*)
+                FROM information_schema.sequences
+                WHERE sequence_name = 'WORKFLOW_STORE_ENTRY_WORKFLOW_STORE_ENTRY_ID_seq'
+                AND data_type = 'bigint';
+            </sqlCheck>
+        </preConditions>
+        <sql>alter sequence "WORKFLOW_STORE_ENTRY_WORKFLOW_STORE_ENTRY_ID_seq" as bigint;</sql>
+    </changeSet>
+    <!-- END WORKFLOW_STORE_ENTRY_ID PK widening -->
+
+    <!-- BEGIN widening FK to match PK -->
+    <changeSet author="sshah" id="enlarge_sub_workflow_store_entry_fk" dbms="mysql,hsqldb,postgresql,mariadb">
+        <modifyDataType
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+                columnName="ROOT_WORKFLOW_ID"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+    <!-- END widening FK to match PK -->
+
+    <!-- MariaDB's FK NotNull constraint does not survive the widening above and must be recreated explicitly. -->
+    <!-- BEGIN Restoring FK NotNull constraint -->
+    <changeSet author="sshah" id="mariadb_not_null_constraint_sub_workflow_store_entry_fk" dbms="mariadb,mysql">
+        <addNotNullConstraint
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+                columnName="ROOT_WORKFLOW_ID"
+                columnDataType="BIGINT"
+        />
+    </changeSet>
+    <!-- END Restoring FK NotNull constraint -->
+
+    <!-- Restoring the FK -->
+    <changeSet author="sshah" id="recreate_sub_workflow_store_entry_root_workflow_id_fk" dbms="mysql,hsqldb,postgresql,mariadb">
+        <addForeignKeyConstraint
+                constraintName="FK_SUB_WORKFLOW_STORE_ENTRY_ROOT_WORKFLOW_ID"
+                baseColumnNames="ROOT_WORKFLOW_ID"
+                baseTableName="SUB_WORKFLOW_STORE_ENTRY"
+                referencedTableName="WORKFLOW_STORE_ENTRY"
+                referencedColumnNames="WORKFLOW_STORE_ENTRY_ID"
+                onDelete="CASCADE"
+        />
+    </changeSet>
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala b/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala
index 20a77f58c02..e4823b8b0ac 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala
@@ -1,7 +1,5 @@
 package cromwell.database.migration.liquibase
 
-import java.sql.Connection
-
 import liquibase.changelog.{ChangeLogParameters, ChangeSet, DatabaseChangeLog}
 import liquibase.database.jvm.{HsqlConnection, JdbcConnection}
 import liquibase.database.{Database, DatabaseConnection, DatabaseFactory, ObjectQuotingStrategy}
@@ -10,12 +8,21 @@ import liquibase.diff.{DiffGeneratorFactory, DiffResult}
 import liquibase.parser.ChangeLogParserFactory
 import liquibase.resource.ClassLoaderResourceAccessor
 import liquibase.snapshot.{DatabaseSnapshot, SnapshotControl, SnapshotGeneratorFactory}
-import liquibase.{Contexts, LabelExpression, Liquibase}
+import liquibase.ui.LoggerUIService
+import liquibase.{Contexts, LabelExpression, Liquibase, Scope}
 import org.hsqldb.persist.HsqlDatabaseProperties
 
+import java.sql.Connection
 import scala.jdk.CollectionConverters._
 
 object LiquibaseUtils {
+
+  /*
+  Move liquibase calls to System.out.println to a logger.
+  Workaround for issue: https://github.com/liquibase/liquibase/issues/1741#issuecomment-853742652
+   */
+  Scope.enter(Map(Scope.Attr.ui.name -> new LoggerUIService().asInstanceOf[AnyRef]).asJava)
+
   // Paranoia: Create our own mutex. https://stackoverflow.com/questions/442564/avoid-synchronizedthis-in-java
   private val mutex = new Object
   private val DefaultContexts = new Contexts()
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
index e258b40f3b7..5929b2e5a6a 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
@@ -9,7 +9,7 @@ trait DockerHashStoreEntryComponent {
   import driver.api._
 
   class DockerHashStoreEntries(tag: Tag) extends Table[DockerHashStoreEntry](tag, "DOCKER_HASH_STORE_ENTRY") {
-    def dockerHashStoreEntryId = column[Int]("DOCKER_HASH_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
+    def dockerHashStoreEntryId = column[Long]("DOCKER_HASH_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def workflowExecutionUuid = column[String]("WORKFLOW_EXECUTION_UUID", O.Length(255))
 
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
index 2ea7b36782c..11fa2191cb2 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
@@ -10,9 +10,9 @@ trait SubWorkflowStoreEntryComponent {
   import driver.api._
 
   class SubWorkflowStoreEntries(tag: Tag) extends Table[SubWorkflowStoreEntry](tag, "SUB_WORKFLOW_STORE_ENTRY") {
-    def subWorkflowStoreEntryId = column[Int]("SUB_WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
+    def subWorkflowStoreEntryId = column[Long]("SUB_WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
-    def rootWorkflowId = column[Int]("ROOT_WORKFLOW_ID")
+    def rootWorkflowId = column[Long]("ROOT_WORKFLOW_ID")
     
     def parentWorkflowExecutionUuid = column[String]("PARENT_WORKFLOW_EXECUTION_UUID", O.Length(255))
 
@@ -40,7 +40,7 @@ trait SubWorkflowStoreEntryComponent {
   val subWorkflowStoreEntryIdsAutoInc = subWorkflowStoreEntries returning subWorkflowStoreEntries.map(_.subWorkflowStoreEntryId)
 
   val subWorkflowStoreEntriesForRootWorkflowId = Compiled(
-    (rootWorkflowId: Rep[Int]) => for {
+    (rootWorkflowId: Rep[Long]) => for {
       subWorkflowStoreEntry <- subWorkflowStoreEntries
       if subWorkflowStoreEntry.rootWorkflowId === rootWorkflowId
     } yield subWorkflowStoreEntry
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
index 0e29cee651f..847fa862405 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
@@ -11,7 +11,7 @@ trait WorkflowStoreEntryComponent {
   import driver.api._
 
   class WorkflowStoreEntries(tag: Tag) extends Table[WorkflowStoreEntry](tag, "WORKFLOW_STORE_ENTRY") {
-    def workflowStoreEntryId = column[Int]("WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
+    def workflowStoreEntryId = column[Long]("WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def workflowExecutionUuid = column[String]("WORKFLOW_EXECUTION_UUID", O.Length(255))
 
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
index a4a5b1247ee..542558324f5 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
@@ -6,5 +6,5 @@ case class DockerHashStoreEntry
   dockerTag: String,
   dockerHash: String,
   dockerSize: Option[Long],
-  dockerHashStoreEntryId: Option[Int] = None
+  dockerHashStoreEntryId: Option[Long] = None
 )
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
index 96ac39aa672..4cf89381ad0 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
@@ -2,11 +2,11 @@ package cromwell.database.sql.tables
 
 case class SubWorkflowStoreEntry
 (
-  rootWorkflowId: Option[Int],
+  rootWorkflowId: Option[Long],
   parentWorkflowExecutionUuid: String,
   callFullyQualifiedName: String,
   callIndex: Int,
   callAttempt: Int,
   subWorkflowExecutionUuid: String,
-  subWorkflowStoreEntryId: Option[Int] = None
+  subWorkflowStoreEntryId: Option[Long] = None
 )
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
index 6c03db87014..efb594444d4 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
@@ -21,5 +21,5 @@ case class WorkflowStoreEntry
   cromwellId: Option[String],
   heartbeatTimestamp: Option[Timestamp],
   hogGroup: Option[String],
-  workflowStoreEntryId: Option[Int] = None
+  workflowStoreEntryId: Option[Long] = None
 )
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
index 67e1d2fcd28..384f9f09e72 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
@@ -5,8 +5,8 @@ import cats.effect.IO
 import cats.syntax.either._
 import common.validation.Validation._
 import cromwell.docker.DockerInfoActor._
+import cromwell.docker._
 import cromwell.docker.registryv2.DockerRegistryV2Abstract._
-import cromwell.docker.{DockerHashResult, DockerImageIdentifier, DockerRegistry, DockerRegistryConfig}
 import io.circe.Decoder
 import io.circe.generic.auto._
 import org.http4s.Uri.{Authority, Scheme}
@@ -27,19 +27,27 @@ object DockerRegistryV2Abstract {
   }
 
   val DigestHeaderName = CaseInsensitiveString("Docker-Content-Digest")
-  val ManifestV2MediaType = "application/vnd.docker.distribution.manifest.v2+json"
-  val ManifestListV2MediaType = "application/vnd.docker.distribution.manifest.list.v2+json"
+  val DockerManifestV2MediaType = "application/vnd.docker.distribution.manifest.v2+json"
+  val DockerManifestListV2MediaType = "application/vnd.docker.distribution.manifest.list.v2+json"
+  // See https://github.com/opencontainers/image-spec/blob/main/image-index.md
+  // This is the media type that current images of Ubuntu use, https://github.com/docker-library/official-images/pull/13950
+  val OCIIndexV1MediaType = "application/vnd.oci.image.index.v1+json"
 
   // If one of those fails it means someone changed one of the strings above to an invalid one.
-  val ManifestV2MediaRange = MediaRange.parse(ManifestV2MediaType)
+  val DockerManifestV2MediaRange = MediaRange.parse(DockerManifestV2MediaType)
     .unsafe("Cannot parse invalid manifest v2 content type. Please report this error.")
-  val ManifestListV2MediaRange = MediaRange.parse(ManifestListV2MediaType)
+  val DockerManifestListV2MediaRange = MediaRange.parse(DockerManifestListV2MediaType)
     .unsafe("Cannot parse invalid manifest list v2 content type. Please report this error.")
-  val AcceptManifestV2Header = Accept.parse(ManifestV2MediaType)
+  val AcceptDockerManifestV2Header = Accept.parse(DockerManifestV2MediaType)
     .unsafe("Cannot parse invalid manifest v2 Accept header. Please report this error.")
 
-  implicit val entityManifestDecoder = jsonEntityDecoder[DockerManifest](ManifestV2MediaRange)
-  implicit val entityManifestListDecoder = jsonEntityDecoder[DockerManifestList](ManifestListV2MediaRange)
+  val OCIIndexV1MediaRange = MediaRange.parse(OCIIndexV1MediaType)
+    .unsafe("Cannot parse invalid OCI index v1 content type. Please report this error.")
+  val AcceptOCIIndexV1Header = Accept.parse(OCIIndexV1MediaType)
+    .unsafe("Cannot parse invalid OCI index v1 Accept header. Please report this error.")
+
+  implicit val entityManifestDecoder = jsonEntityDecoder[DockerManifest](DockerManifestV2MediaRange)
+  implicit val entityManifestListDecoder = jsonEntityDecoder[DockerManifestList](DockerManifestListV2MediaRange)
   implicit val entityTokenDecoder = jsonOf[IO, DockerAccessToken]
 
   /**
@@ -123,8 +131,12 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * @return docker info response
     */
   protected def getDockerResponse(token: Option[String], dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]): IO[DockerInfoSuccessResponse] = {
-    val request = manifestRequest(token, dockerInfoContext.dockerImageID)
-    executeRequest(request, handleManifestResponse(dockerInfoContext, token))
+    val requestDockerManifest = manifestRequest(token, dockerInfoContext.dockerImageID, AcceptDockerManifestV2Header)
+    lazy val requestOCIManifest = manifestRequest(token, dockerInfoContext.dockerImageID, AcceptOCIIndexV1Header)
+    def tryOCIManifest(err: Throwable) = executeRequest(requestOCIManifest, handleManifestResponse(dockerInfoContext, token))
+    // Try to execute a request using the Docker Manifest format, and if that fails, try using the newer OCI manifest format
+    executeRequest(requestDockerManifest, handleManifestResponse(dockerInfoContext, token))
+      .handleErrorWith(tryOCIManifest)
   }
 
   /**
@@ -205,12 +217,12 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
   /**
     * Request to get the manifest, using the auth token if provided
     */
-  private def manifestRequest(token: Option[String], imageId: DockerImageIdentifier): IO[Request[IO]] = {
-    val authorizationHeader = token.map(t => Authorization(Credentials.Token(authorizationScheme, t)))
+  private def manifestRequest(token: Option[String], imageId: DockerImageIdentifier, manifestHeader: Accept): IO[Request[IO]] = {
+    val authorizationHeader = token.map(t => Authorization(Credentials.Token(AuthScheme.Bearer, t)))
     val request = Method.GET(
       buildManifestUri(imageId),
       List(
-        Option(AcceptManifestV2Header),
+        Option(manifestHeader),
         authorizationHeader
       ).flatten: _*
     )
@@ -246,9 +258,9 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * If that assumption turns out to be incorrect, a smarter decision may need to be made to choose the manifest to lookup.
     */
   private def parseManifest(dockerImageIdentifier: DockerImageIdentifier, token: Option[String])(response: Response[IO])(implicit client: Client[IO]): IO[Option[DockerManifest]] = response match {
-    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(ManifestV2MediaType)) =>
+    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(DockerManifestV2MediaType)) =>
       r.as[DockerManifest].map(Option.apply)
-    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(ManifestListV2MediaType)) =>
+    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(DockerManifestListV2MediaType)) =>
       r.as[DockerManifestList].flatMap({ dockerManifestList =>
         obtainManifestFromList(dockerManifestList, dockerImageIdentifier, token)
       })
@@ -262,7 +274,7 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
       .map(_.digest)
       .map(dockerImageIdentifier.swapReference) match {
       case Some(identifierWithNewHash) =>
-        val request = manifestRequest(token, identifierWithNewHash)
+        val request = manifestRequest(token, identifierWithNewHash, AcceptDockerManifestV2Header)
         executeRequest(request, parseManifest(dockerImageIdentifier, token))
       case None =>
         logger.error(s"The manifest list for ${dockerImageIdentifier.fullName} was empty. Cannot proceed to obtain the size of image")
diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
index e567aa540cd..e99383ac131 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
@@ -3,10 +3,10 @@ package cromwell.docker.registryv2
 import cats.effect.{IO, Resource}
 import common.assertion.CromwellTimeoutSpec
 import cromwell.docker.DockerInfoActor.{DockerInfoContext, DockerInfoFailedResponse}
-import cromwell.docker.{DockerImageIdentifier, DockerInfoActor, DockerInfoRequest, DockerRegistryConfig}
+import cromwell.docker._
+import org.http4s._
 import org.http4s.client.Client
 import org.http4s.headers.`Content-Type`
-import org.http4s.{Header, Headers, MediaType, Request, Response}
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
@@ -20,7 +20,7 @@ class DockerRegistryV2AbstractSpec extends AnyFlatSpec with CromwellTimeoutSpec
       override protected def buildTokenRequestHeaders(dockerInfoContext: DockerInfoActor.DockerInfoContext) = List.empty
     }
 
-    val mediaType = MediaType.parse(DockerRegistryV2Abstract.ManifestV2MediaType).toOption.get
+    val mediaType = MediaType.parse(DockerRegistryV2Abstract.DockerManifestV2MediaType).toOption.get
     val contentType: Header = `Content-Type`(mediaType)
 
     val mockClient = Client({ _: Request[IO] =>
diff --git a/docs/LanguageSupport.md b/docs/LanguageSupport.md
index d14d6751a42..ff7a64164f9 100644
--- a/docs/LanguageSupport.md
+++ b/docs/LanguageSupport.md
@@ -22,13 +22,6 @@ Cromwell also supports WDL version 1.0.
 
 As well as the changes to the WDL spec between draft-2 and 1.0, Cromwell also supports nested scatters and the [localization_optional](optimizations/FileLocalization.md) optimization in WDL 1.0.  
 
-
-### CWL 1.0
-
-Cromwell provides support for Common Workflow Language (CWL), beginning with the core spec, and most heavily used requirements.
-If you spot a CWL feature that Cromwell doesn't support, please notify us using an issue on our [Jira page](https://broadworkbench.atlassian.net/secure/RapidBoard.jspa?rapidView=39&view=planning.nodetail&issueLimit=100)!
-
-
 ## Future Language Support
 
 ### WDL 'development'
diff --git a/docs/RuntimeAttributes.md b/docs/RuntimeAttributes.md
index 1f16e125eff..8b318b617a2 100644
--- a/docs/RuntimeAttributes.md
+++ b/docs/RuntimeAttributes.md
@@ -30,18 +30,29 @@ workflow jes_workflow {
 
 Cromwell recognizes certain runtime attributes and has the ability to format these for some [Backends](/backends/Backends). See the table below for common attributes that apply to _most_ backends.
 
-| Runtime Attribute    | LOCAL |  Google Cloud  | AWS Batch |  HPC  |
-| -------------------- |:-----:|:-----:|:-----:|:------:|
-| [cpu](#cpu)                  |       |   x   |   x   |  `cpu`  |
-| [memory](#memory)                              |       |   x   |   x   |  `memory_mb` / `memory_gb`  |
-| [disks](#disks)                                |       |   x   |       |  *  |
-| [docker](#docker)                              |   x   |   x   |   x   |  `docker` (see below)  |
-| [maxRetries](#maxretries)                      |   x   |   x   |   x   | * |
-| [continueOnReturnCode](#continueonreturncode) |   x   |   x   |   x   | * |
-| [failOnStderr](#failonstderr)                  |   x   |   x   |   x   |  *  |
-
-
-> `*` The HPC [Shared Filesystem backend](/backends/HPC#shared-filesystem) (SFS) is fully configurable and any number of attributes can be exposed. Cromwell recognizes some of these attributes (`cpu`, `memory` and `docker`) and parses them into the attribute listed in the table which can be used within the HPC backend configuration.
+| Runtime Attribute                               | Local | Google Cloud | TES       | AWS Batch |            HPC            |
+|-------------------------------------------------|:-----:|:------------:|-----------|:---------:|:-------------------------:|
+| [`cpu`](#cpu)                                   |       |      ✅       |           |     ✅     |           `cpu`           |
+| [`memory`](#memory)                             |       |      ✅       |           |     ✅     | `memory_mb` / `memory_gb` |
+| [`disks`](#disks)                               |       |      ✅       | ⚠️ Note 1 | ⚠️ Note 2 |         ℹ️ Note 3         |
+| [`disk`](#disk)                                 |       |              | ✅         |           |                           |
+| [`docker`](#docker)                             |   ✅   |      ✅       |           |     ✅     |    `docker` ℹ️ Note 3     |
+| [`maxRetries`](#maxretries)                     |   ✅   |      ✅       |           |     ✅     |         ℹ️ Note 3         |
+| [`continueOnReturnCode`](#continueonreturncode) |   ✅   |      ✅       |           |     ✅     |         ℹ️ Note 3         |
+| [`failOnStderr`](#failonstderr)                 |   ✅   |      ✅       |           |     ✅     |         ℹ️ Note 3         |
+
+
+> **Note 1**
+> 
+> Partial support. See [TES documentation](/backends/TES) for details. 
+ 
+> **Note 2**
+>
+> Partial support. See [`disks`](#disks) for details.
+
+> **Note 3**
+> 
+> The HPC [Shared Filesystem backend](/backends/HPC#shared-filesystem) (SFS) is fully configurable and any number of attributes can be exposed. Cromwell recognizes some of these attributes (`cpu`, `memory` and `docker`) and parses them into the attribute listed in the table which can be used within the HPC backend configuration.
 
 
 ### Google Cloud Specific Attributes
@@ -156,15 +167,6 @@ runtime {
 }
 ```
 
-
-#### CWL
-
-CWL splits the `cpu` requirement into `cpuMin` and `cpuMax`. If one of them is provided, `cpu` will inherit this value. If both of them are provided, `cpu` will take the value of `cpuMin`.
-If none is provided, `cpu` will default to its default value.
-
-Note: If provided, `cpuMin` and/or `cpuMax` will be available to the [HPC runtime attribute configuration](/tutorials/HPCIntro.md#specifying-the-runtime-attributes-for-your-hpc-tasks).
-
-
 ### `memory`
 *Default: "2G"*
 
@@ -183,12 +185,6 @@ runtime {
 
 Within the SFS backend, you can additionally specify `memory_mb` or `memory_gb` as runtime attributes within the configuration. More information can be found [here](https://cromwell.readthedocs.io/en/stable/tutorials/HPCIntro/#specifying-the-runtime-attributes-for-your-hpc-tasks).
 
-#### CWL
-
-CWL splits the `memory` requirement into `ramMin` and `ramMax`. If one of them is provided, `memory` will inherit this value. If both of them are provided, `memory` will take the value of `ramMin`. If none is provided, `memory` will default to its default value.
-
-Note: If provided, `ramMin` and/or `ramMax` will be available to the [HPC runtime attribute configuration](/tutorials/HPCIntro.md#specifying-the-runtime-attributes-for-your-hpc-tasks).
-
 
 ### `disks`
 
@@ -224,6 +220,16 @@ runtime {
 }
 ```
 
+### `disk`
+
+Specific to the TES backend, sets the `disk_gb` resource.
+
+```
+runtime {
+  disk: "25 GB"
+}
+```
+
 ### `docker`
 
 When specified, Cromwell will run your task within the specified Docker image. 
diff --git a/docs/WOMtool.md b/docs/WOMtool.md
index fc8c16c7897..5b88e5a21a6 100644
--- a/docs/WOMtool.md
+++ b/docs/WOMtool.md
@@ -59,9 +59,9 @@ graph <WDL file>
   otherwise. Note that graph currently DOES NOT WORK on
   version 1.0 workflows.
 
-womgraph <WDL or CWL file> [ancillary files]
+womgraph <WDL file> [ancillary files]
 
-  Reads a WDL or CWL file from the first argument and
+  Reads a WDL file from the first argument and
   converts it to a WOM representation then prints out a graph
   of the WOM produced.
   Any imported files can be supplied as subsequent arguments.
diff --git a/docs/api/RESTAPI.md b/docs/api/RESTAPI.md
index b15072f6407..ffb2af329de 100644
--- a/docs/api/RESTAPI.md
+++ b/docs/api/RESTAPI.md
@@ -1,5 +1,5 @@
 <!--
-This file was generated by `sbt generateRestApiDocs` on Thu, 9 Jun 2022 13:29:46 -0400
+This file was generated by `sbt generateRestApiDocs` on Wed, 8 Feb 2023 09:46:32 -0500
 
 !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
 
@@ -32,6 +32,63 @@ Describes the REST API provided by a Cromwell server
 
 
 
+<a name="runworkflow"></a>
+## Run workflow
+```
+POST /api/ga4gh/wes/v1/runs
+```
+
+
+#### Description
+This endpoint creates a new workflow run and returns a `RunId` to monitor its progress.
+
+The `workflow_attachment` array may be used to upload files that are required to execute the workflow, including the primary workflow, tools imported by the workflow, other files referenced by the workflow, or files which are part of the input.  The implementation should stage these files to a temporary directory and execute the workflow from there. These parts must have a Content-Disposition header with a "filename" provided for each part.  Filenames may include subdirectories, but must not include references to parent directories with '..' -- implementations should guard against maliciously constructed filenames.
+
+The `workflow_url` is either an absolute URL to a workflow file that is accessible by the WES endpoint, or a relative URL corresponding to one of the files attached using `workflow_attachment`.
+
+The `workflow_params` JSON object specifies input parameters, such as input files.  The exact format of the JSON object depends on the conventions of the workflow language being used.  Input files should either be absolute URLs, or relative URLs corresponding to files uploaded using `workflow_attachment`.  The WES endpoint must understand and be able to access URLs supplied in the input.  This is implementation specific.
+
+The `workflow_type` is the type of workflow language and must be "WDL" currently (or another alternative supported by this WES instance).
+
+The `workflow_type_version` is the version of the workflow language submitted and must be one supported by this WES instance.
+
+See the `RunRequest` documentation for details about other fields.
+
+
+#### Parameters
+
+|Type|Name|Schema|
+|---|---|---|
+|**FormData**|**tags**  <br>*optional*|string|
+|**FormData**|**workflow_attachment**  <br>*optional*|< file (binary) > array|
+|**FormData**|**workflow_engine_parameters**  <br>*optional*|string|
+|**FormData**|**workflow_params**  <br>*optional*|string|
+|**FormData**|**workflow_type**  <br>*optional*|string|
+|**FormData**|**workflow_type_version**  <br>*optional*|string|
+|**FormData**|**workflow_url**  <br>*optional*|string|
+
+
+#### Responses
+
+|HTTP Code|Description|Schema|
+|---|---|---|
+|**201**|Successful Request|[RunId](#runid)|
+|**400**|Malformed Workflow ID|No Content|
+|**401**|Invalid submission request|No Content|
+|**403**|Workflow in terminal status|No Content|
+|**500**|Internal Error|No Content|
+
+
+#### Consumes
+
+* `multipart/form-data`
+
+
+#### Tags
+
+* GA4GH Workflow Execution Service (WES) - Alpha preview
+
+
 <a name="listruns"></a>
 ## List runs
 ```
@@ -207,8 +264,8 @@ POST /api/womtool/{version}/describe
 |**Path**|**version**  <br>*required*|Cromwell API Version|string|`"v1"`|
 |**FormData**|**workflowInputs**  <br>*optional*|JSON or YAML file containing the inputs as an object.|file||
 |**FormData**|**workflowSource**  <br>*optional*|The workflow source file to submit for execution. Either workflow source or workflow url is required.|file||
-|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.|enum (WDL, CWL)||
-|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.|enum (draft-2, 1.0, v1.0)||
+|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL.|enum (WDL)||
+|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.|enum (draft-2, 1.0)||
 |**FormData**|**workflowUrl**  <br>*optional*|URL which points to the workflow. Either workflow source or workflow url is required.|string||
 
 
@@ -255,10 +312,9 @@ Submits a workflow to Cromwell. Note that this endpoint can accept an unlimited
 |**FormData**|**workflowInputs_5**  <br>*optional*|A fifth JSON or YAML file containing inputs.|file||
 |**FormData**|**workflowOnHold**  <br>*optional*|Put workflow on hold upon submission. By default, it is taken as false.|boolean||
 |**FormData**|**workflowOptions**  <br>*optional*|JSON file containing configuration options for the execution of this workflow.|file||
-|**FormData**|**workflowRoot**  <br>*optional*|The root object to be run. Only necessary for CWL submissions containing multiple objects (in an array).|string||
 |**FormData**|**workflowSource**  <br>*optional*|The workflow source file to submit for execution. Either workflow source or workflow url is required.|file||
-|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.|enum (WDL, CWL)||
-|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.|enum (draft-2, 1.0, v1.0)||
+|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL.|enum (WDL)||
+|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.|enum (draft-2, 1.0)||
 |**FormData**|**workflowUrl**  <br>*optional*|URL which points to the workflow. Either workflow source or workflow url is required.|string||
 
 
@@ -334,8 +390,8 @@ In instances where you want to run the same workflow multiple times with varying
 |**FormData**|**workflowOnHold**  <br>*optional*|Put workflow on hold upon submission. By default, it is taken as false.|boolean||
 |**FormData**|**workflowOptions**  <br>*optional*|JSON file containing configuration options for the execution of this workflow.|file||
 |**FormData**|**workflowSource**  <br>*optional*|The workflow source file to submit for execution. Either workflow source or workflow url is required.|file||
-|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.|enum (WDL, CWL)||
-|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.|enum (draft-2, 1.0, v1.0)||
+|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL.|enum (WDL)||
+|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.|enum (draft-2, 1.0)||
 |**FormData**|**workflowUrl**  <br>*optional*|URL which points to the workflow. Either workflow source or workflow url is required.|string||
 
 
@@ -852,9 +908,9 @@ Call level metadata
 |**backendLogs**  <br>*optional*|Paths to backend specific logs for this call|object|
 |**backendStatus**  <br>*optional*|Status in backend-specific terms.  Currently this will only be defined for the JES backend.|string|
 |**end**  <br>*optional*|End datetime of the call execution in ISO8601 format with milliseconds|string (date-time)|
-|**executionStatus**  <br>*required*|Status in Cromwell execution terms.|string|
-|**failures**  <br>*optional*||[FailureMessage](#failuremessage)|
-|**inputs**  <br>*required*|Mapping of input fully qualified names to stringified values|object|
+|**executionStatus**  <br>*optional*|Status in Cromwell execution terms.|string|
+|**failures**  <br>*optional*||< [FailureMessage](#failuremessage) > array|
+|**inputs**  <br>*optional*|Mapping of input fully qualified names to stringified values|object|
 |**jobId**  <br>*optional*|Backend-specific job ID|string|
 |**returnCode**  <br>*optional*|Call execution return code|integer|
 |**start**  <br>*optional*|Start datetime of the call execution in ISO8601 format with milliseconds|string (date-time)|
@@ -876,9 +932,9 @@ A message that allows one to describe default parameters for a workflow engine.
 
 <a name="descriptortype"></a>
 ### DescriptorType
-One from a list of descriptor type strings (e.g. CWL, WDL). Note that these files can also include associated Docker/container files and test parameters that further describe a version of a tool
+One from a list of descriptor type strings (e.g. WDL). Note that these files can also include associated Docker/container files and test parameters that further describe a version of a tool
 
-*Type* : enum (CWL, WDL)
+*Type* : enum (WDL)
 
 
 <a name="descriptortypeandversion"></a>
@@ -899,8 +955,8 @@ Failure messages
 
 |Name|Description|Schema|
 |---|---|---|
-|**failure**  <br>*required*|The failure message|string|
-|**timestamp**  <br>*required*|The time at which this failure occurred|string (date-time)|
+|**causedBy**  <br>*optional*||< [FailureMessage](#failuremessage) > array|
+|**message**  <br>*optional*|The failure message|string|
 
 
 <a name="labelsresponse"></a>
@@ -981,9 +1037,9 @@ To execute a workflow, send a run request including all the details needed to be
 |**tags**  <br>*optional*||< string, string > map|
 |**workflow_engine_parameters**  <br>*optional*||< string, string > map|
 |**workflow_params**  <br>*optional*|REQUIRED The workflow run parameterizations (JSON encoded), including input and output file locations|object|
-|**workflow_type**  <br>*optional*|REQUIRED The workflow descriptor type, must be "CWL" or "WDL" currently (or another alternative supported by this WES instance)|string|
+|**workflow_type**  <br>*optional*|REQUIRED The workflow descriptor type, must be "WDL" currently (or another alternative supported by this WES instance)|string|
 |**workflow_type_version**  <br>*optional*|REQUIRED The workflow descriptor type version, must be one supported by this WES instance|string|
-|**workflow_url**  <br>*optional*|REQUIRED The workflow CWL or WDL document. When `workflow_attachments` is used to attach files, the `workflow_url` may be a relative path to one of the attachments.|string|
+|**workflow_url**  <br>*optional*|REQUIRED The workflow WDL document. When `workflow_attachments` is used to attach files, the `workflow_url` may be a relative path to one of the attachments.|string|
 
 
 <a name="runstatus"></a>
@@ -1191,10 +1247,14 @@ Returns the version of Cromwell
 |Name|Description|Schema|
 |---|---|---|
 |**errors**  <br>*required*|The set of validation failure messages  <br>**Example** : `[ "The 'errors' field will be filled if 'valid' is false", "We might also provide warnings to a 'valid' workflow here", "Otherwise, 'errors' will be the empty array" ]`|< string > array|
+|**images**  <br>*optional*||< string > array|
+|**importedDescriptorTypes**  <br>*optional*||< [DescriptorTypeAndVersion](#descriptortypeandversion) > array|
 |**inputs**  <br>*required*|A list of inputs for this tool  <br>**Example** : `[ {<br>  "name" : "my_wf.string_input",<br>  "valueType" : {<br>    "typeName" : "String"<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "String"<br>}, {<br>  "name" : "my_wf.array_input",<br>  "valueType" : {<br>    "typeName" : "Array",<br>    "arrayType" : {<br>      "typeName" : "String"<br>    }<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Array[String]"<br>}, {<br>  "name" : "my_wf.optional_input",<br>  "valueType" : {<br>    "typeName" : "Optional",<br>    "optionalType" : {<br>      "typeName" : "String"<br>    }<br>  },<br>  "optional" : true,<br>  "default" : "hello",<br>  "typeDisplayName" : "String?"<br>}, {<br>  "name" : "my_wf.map_input",<br>  "valueType" : {<br>    "typeName" : "Map",<br>    "mapType" : {<br>      "keyType" : {<br>        "typeName" : "String"<br>      },<br>      "valueType" : {<br>        "typeName" : "Int"<br>      }<br>    }<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Map[String, Int]"<br>}, {<br>  "name" : "my_wf.object_input",<br>  "valueType" : {<br>    "typeName" : "Object",<br>    "objectFieldTypes" : [ {<br>      "fieldName" : "int_field",<br>      "fieldType" : {<br>        "typeName" : "Int"<br>      }<br>    }, {<br>      "fieldName" : "int_array_field",<br>      "fieldType" : {<br>        "typeName" : "Array",<br>        "arrayType" : {<br>          "typeName" : "Int"<br>        }<br>      }<br>    } ]<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Object"<br>}, {<br>  "name" : "my_wf.int_string_pair_input",<br>  "valueType" : {<br>    "typeName" : "Pair",<br>    "pairTypes" : [ {<br>      "leftType" : [ {<br>        "typeName" : "Int"<br>      } ]<br>    }, {<br>      "rightType" : [ {<br>        "typeName" : "String"<br>      } ]<br>    } ]<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Pair[Int, String]"<br>} ]`|< [ToolInputParameter](#toolinputparameter) > array|
 |**isRunnableWorkflow**  <br>*required*|Indicates whether this file can be run on its own (e.g. a WDL workflow)|boolean|
+|**meta**  <br>*optional*||object|
 |**name**  <br>*required*|For a source file with one workflow and zero or more tasks, the name of the workflow. For a single task, the name of the task. For a source file with multiple tasks but no workflows, the empty string.|string|
 |**outputs**  <br>*required*|A list of outputs for this tool  <br>**Example** : `[ {<br>  "name" : "my_wf.string_output",<br>  "valueType" : {<br>    "typeName" : "String"<br>  },<br>  "typeDisplayName" : "String"<br>}, {<br>  "name" : "my_wf.array_output",<br>  "valueType" : {<br>    "typeName" : "Array",<br>    "arrayType" : {<br>      "typeName" : "String"<br>    }<br>  },<br>  "typeDisplayName" : "Array[String]"<br>}, {<br>  "name" : "my_wf.map_output",<br>  "valueType" : {<br>    "typeName" : "Map",<br>    "mapType" : {<br>      "keyType" : {<br>        "typeName" : "String"<br>      },<br>      "valueType" : {<br>        "typeName" : "Int"<br>      }<br>    }<br>  },<br>  "typeDisplayName" : "Map[String, Int]"<br>}, {<br>  "name" : "my_wf.object_output",<br>  "valueType" : {<br>    "typeName" : "Object",<br>    "objectFieldTypes" : [ {<br>      "fieldName" : "int_field",<br>      "fieldType" : {<br>        "typeName" : "Int"<br>      }<br>    }, {<br>      "fieldName" : "int_array_field",<br>      "fieldType" : {<br>        "typeName" : "Array",<br>        "arrayType" : {<br>          "typeName" : "Int"<br>        }<br>      }<br>    } ]<br>  },<br>  "typeDisplayName" : "Object"<br>}, {<br>  "name" : "my_wf.int_string_pair_output",<br>  "valueType" : {<br>    "typeName" : "Pair",<br>    "tupleTypes" : [ {<br>      "typeName" : "Int"<br>    }, {<br>      "typeName" : "String"<br>    } ]<br>  },<br>  "typeDisplayName" : "Pair[Int, String]"<br>} ]`|< [ToolOutputParameter](#tooloutputparameter) > array|
+|**parameterMeta**  <br>*optional*||object|
 |**submittedDescriptorType**  <br>*required*||[DescriptorTypeAndVersion](#descriptortypeandversion)|
 |**valid**  <br>*required*|Indicates that the workflow is valid and that the inputs, if provided, are compatible with the workflow.|boolean|
 |**validWorkflow**  <br>*required*|Indicates whether the workflow file is valid by itself. If inputs are provided, they are not considered when calculating this field; if inputs are not provided, the value is identical to `valid`.|boolean|
@@ -1218,13 +1278,13 @@ Workflow and call level metadata
 |---|---|---|
 |**calls**  <br>*optional*||[CallMetadata](#callmetadata)|
 |**end**  <br>*optional*|End datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
-|**failures**  <br>*optional*||[FailureMessage](#failuremessage)|
-|**id**  <br>*required*|The identifier of the workflow|string|
+|**failures**  <br>*optional*||< [FailureMessage](#failuremessage) > array|
+|**id**  <br>*optional*|The identifier of the workflow|string|
 |**inputs**  <br>*optional*|Map of input keys to input values|object|
 |**outputs**  <br>*optional*|Map of output keys to output values|object|
 |**start**  <br>*optional*|Start datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
-|**status**  <br>*required*|The status of the workflow|string|
-|**submission**  <br>*required*|Submission datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
+|**status**  <br>*optional*|The status of the workflow|string|
+|**submission**  <br>*optional*|Submission datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
 
 
 <a name="workflowqueryparameter"></a>
@@ -1267,7 +1327,8 @@ Result for an individual workflow returned by a workflow query
 |---|---|---|
 |**end**  <br>*optional*|Workflow end datetime|string (date-time)|
 |**id**  <br>*required*|Workflow ID|string|
-|**name**  <br>*required*|Workflow name|string|
+|**metadataArchiveStatus**  <br>*optional*|Status in metadata archives|string|
+|**name**  <br>*optional*|Workflow name|string|
 |**start**  <br>*optional*|Workflow start datetime|string (date-time)|
 |**status**  <br>*required*|Workflow status|string|
 |**submission**  <br>*optional*|Workflow submission datetime|string (date-time)|
diff --git a/docs/backends/TES.md b/docs/backends/TES.md
index e19917ec126..b90fa30bc3d 100644
--- a/docs/backends/TES.md
+++ b/docs/backends/TES.md
@@ -1,4 +1,4 @@
-**TES Backend**
+## TES Backend
 
 The TES backend submits jobs to a server that complies with the protocol described by the [GA4GH schema](https://github.com/ga4gh/task-execution-schemas).
 
@@ -19,7 +19,7 @@ echo $? > rc
 
 `<container_call_root>` would be equal to the runtime attribute `dockerWorkingDir`  or `/cromwell-executions/<workflow_uuid>/call-<call_name>/execution` if this attribute is not supplied.
 
-**Configuring**
+### Configuring
 
 Configuring the TES backend is straightforward; one must only provide the TES API endpoint for the service.
 
@@ -40,18 +40,18 @@ backend {
 }
 ```
 
-**Supported File Systems**  
+### Supported File Systems
 
 Currently this backend only works with files on a Local or Shared File System.
 
-**Docker**
+### Docker
 
 This backend supports the following optional [Runtime Attributes](../RuntimeAttributes) and [Workflow Options](../wf_options/Overview/) for working with Docker:
 
 * `docker`: Docker image to use such as "Ubuntu".
 * `dockerWorkingDir`: defines the working directory in the container.
 
-**CPU, Memory and Disk**
+### CPU, Memory and Disk
 
 This backend supports CPU, memory and disk size configuration through the use of the following [Runtime Attributes](../RuntimeAttributes) and [Workflow Options](../wf_options/Overview/):  
 
@@ -61,16 +61,29 @@ This backend supports CPU, memory and disk size configuration through the use of
     * Type: String (ex: "4 GB" or "4096 MB")
 * `disk` defines the amount of disk to use.
     * Type: String (ex: "1 GB" or "1024 MB")
+* `disks` accepts a GCP-style disk declaration and attempts to translate it for use on TES
+    * See table below for supported translations 
 * `preemptible` defines whether or not to use preemptible VMs.
     * Type: Boolean (ex: "true" or "false")
     * Integers are accepted and will be converted to boolean (true if > 0)
 
 If they are not set, the TES backend may use default values.
 
-**Azure**
+#### GCP `disks` to TES `disk` compatibility
+
+| GCP `disks` value                     | Supported | TES translation | Remark                            |
+|---------------------------------------|-----------|-----------------|-----------------------------------|
+| `local-disk 25 HDD`                   | ✅        | 25 GB disk      |                                   |
+| `local-disk 25 SSD`                   | ✅        | 25 GB disk      | Disk type info is dropped         |
+| `/some/mnt 25 SSD`                    | ❌        |                 | Custom mount points not supported | 
+| `local-disk 25 HDD, /some/mnt 50 SSD` | ❌        |                 | Multiple disks are not supported  | 
+            
+> Note: if both `disk` and `disks` attributes are specified, the TES backend will automatically use the value in `disk` and not attempt to translate `disks`.
+
+### Azure
 [Azure](Azure) is an implementation of Cromwell that uses the TES interface for orchestrating the tasks on Azure.
 
-**TESK**
+### TESK
 
 [TESK](https://github.com/EMBL-EBI-TSI/TESK) is an implementation of the TES interface that uses Kubernetes and FTP.
 When running Cromwell with a TESK backend, you will want to customize the way Cromwell process globs, as kubernetes will not work well with hard links in a lot of cases which is the default behavior in Cromwell.
diff --git a/docs/cromwell_features/HogFactors.md b/docs/cromwell_features/HogFactors.md
index c2d5f1b968f..aed82d5ebc9 100644
--- a/docs/cromwell_features/HogFactors.md
+++ b/docs/cromwell_features/HogFactors.md
@@ -2,7 +2,7 @@
 
 ## Introduction
 
-Cromwell has only a finite amount of resources at its disposal. WDL and CWL workflows allow scattered tasks to be
+Cromwell has only a finite amount of resources at its disposal. WDL workflows allow scattered tasks to be
 run a huge number of times with very simple syntax.
 This makes it easy for a very small number of workflows to hog all of the resources of Cromwell, forcing all other 
 workflows (even a simple 'hello_world') to wait in line behind them. 
diff --git a/docs/developers/CwlParsing.md b/docs/developers/CwlParsing.md
deleted file mode 100644
index c3982f784e5..00000000000
--- a/docs/developers/CwlParsing.md
+++ /dev/null
@@ -1,66 +0,0 @@
-# How CWL is Parsed
-
-The ultimate entry point to parsing CWL is in `CwlV1_0LanguageFactory.validateNamespace`. 
-
-Within that method, the process of parsing CWL can be thought of as performing these 4 steps:
-
-1. Produce a canonical one-file representation of the CWL as a JSON object in memory
-    - For the entrypoint into this process, see `CwlPreprocessor.preProcessCwl`
-2. Use Circe to turn that representation into scala case classes
-3. Convert the case classes into an appropriate WOM representations
-4. Mix in inputs to produce a WOM Executable.
-
-## Getting a canonical flat file
-
-### From a source file and dependencies zip:
-
-Note that the recursive implementation of `SALAD and flatten` in code can be found in: `CwlPreprocessor.preProcessCwl`.
-
-The process looks like:
-
-1. Write the workflow source file to disk
-2. Make sure the dependencies are unzipped next to it
-3. `SALAD and flatten` (see `CwlCanonicalizer.getCanonicalCwl`):
-    - Run `cwltool --print-pre` against the source file to get a canonicalize JSON representation (aka `SALAD`) it.
-        - NB: `cwltool --print-pre` must be able to resolve dependencies but it does not flatten them into the file.
-    - Recursively `SALAD and flatten` any references into their own JSON representations of the contents.
-    - Replace every reference in-place with the expanded JSON content.
-4. At the end of this process we will have:
-    - A single flat JSON 
-    - Every imported step expanded to contain an in-line description
-    - No more external references - everything required is provided in-line
-
-### From a workflow URL:
-
-The process looks similar to "source file and dependencies" except we never write anything locally:
-
-1. `SALAD and flatten`:
-    - Run `cwltool --print-pre` against the URL to get a canonicalize JSON representation (aka `SALAD`) it.
-        - NB: `cwltool --print-pre` must be able to resolve dependencies but it does not flatten them into the file.
-    - Recursively `SALAD and flatten` any references into their own JSON representations of the contents.
-    - Replace every reference in-place with the expanded JSON content.
-2. At the end of this process we will have:
-    - A single flat JSON 
-    - Every imported step expanded to contain an in-line description
-    - No more external references - everything required is provided in-line
-
-
-## Using Circe to get case classes
-
-This process is more or less automatic - the case classes define the fields which they anticipate existing in the JSON.
-and Circe does the rest.
-    - Optional fields in case classes are allowed to not exist in the JSON
-    - All fields in the JSON must be represented by fields in the appropriate case classes
-    - In cases where the JSON may be structured in one of several ways, we use Shapeless coproducts to specify "one of" many options.
-
-If a file is failing to parse the first stop should always be to double-check that the case classes accurately represent
-the range of possible CWL JSON.
-
-## Convert the case classes into WOM representations
-
-- This is a recursive process of examining the CWL case classes and creating WOM values instead.
-- Note that the CWL Language Factory (at least as of November 2018) does not implement the provision of WOM Bundles for 
-imports. Instead, CWL Language Factory implements only the all-in-one method of converting CWL source and inputs files 
-together into a WOM Executable.
-    - Pragmatically, this just means that using the CWL language factory to process an import statement in a WDL file 
-    is currently impossible (ie we cannot import CWL from WDL... yet).
diff --git a/docs/developers/bitesize/workflowParsing/cwlParsingOverview.md b/docs/developers/bitesize/workflowParsing/cwlParsingOverview.md
deleted file mode 100644
index 3ba5b13c494..00000000000
--- a/docs/developers/bitesize/workflowParsing/cwlParsingOverview.md
+++ /dev/null
@@ -1 +0,0 @@
-Coming soon.
diff --git a/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md b/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md
index 178ec2f3e8f..666e331334d 100644
--- a/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md
+++ b/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md
@@ -31,7 +31,7 @@ You can think of WDL parsing in Cromwell in terms of the following major steps:
         * Including custom type references, variable references, task calls, subworkflow calls 
 * **WOM Bundle**:
     * A set of tasks, workflows and custom types, and the fully qualified names by which they can be referenced.
-    * In Cromwell's WOM format (the WOM format is the ultimate destination for _all_ languages, including WDL and CWL)
+    * In Cromwell's WOM format (the WOM format is the ultimate destination for _all_ languages, including WDL)
 * **Validated WOM Namespace**:
     * The conjunction of a WOM bundle with an input set.
-    * The entry point workflow (or sometimes task, in CWL) is known.
+    * The entry point workflow is known.
diff --git a/docs/filesystems/DataRepositoryService.md b/docs/filesystems/DataRepositoryService.md
index 21a33f8a668..770fc65207f 100644
--- a/docs/filesystems/DataRepositoryService.md
+++ b/docs/filesystems/DataRepositoryService.md
@@ -6,12 +6,12 @@ The Cromwell configuration for DRS is as follows:
 
 ```hocon
 drs {
-    # A reference to a potentially different auth required to contact Martha service.
+    # A reference to a potentially different auth required to contact DRS Resolution service.
     auth = "application-default"
 }
 ```
 
-The `auth` field refers to the authentication schema that should be used to authenticate requests to Martha service.
+The `auth` field refers to the authentication schema that should be used to authenticate requests to DRS Resolution service.
 
 The `drs` section needs to be added to
 - `engine.filesystems` block
diff --git a/docs/filesystems/Filesystems.md b/docs/filesystems/Filesystems.md
index d5a66de7eba..0630e421c0b 100644
--- a/docs/filesystems/Filesystems.md
+++ b/docs/filesystems/Filesystems.md
@@ -18,8 +18,8 @@ filesystems {
         # Class to instantiate and propagate to all factories. Takes a single typesafe config argument
         class = "cromwell.filesystems.drs.DrsFileSystemConfig"
         config {
-          martha {
-            url = "https://martha-url-here"
+          resolver {
+            url = "https://martha-url-here or https://drshub-url-here"
             # The number of times to retry failures connecting or HTTP 429 or HTTP 5XX responses, default 3.
             num-retries = 3
             # How long to wait between retrying HTTP 429 or HTTP 5XX responses, default 10 seconds.
@@ -150,11 +150,6 @@ engine {
 }
 ```
 
-#### Engine filesystems and CWL
-
-Note that CWL *always* needs to access file attributes from within the engine, so if you are using CWL, please make sure
-that **every filesystem you might use** is added to the `engine.filesystems` stanza.
-
 ### Backend Filesystems
 
 Similarly to the engine, you can also configure backend filesystems individually. Some backends might require the use of a specific filesystem.
diff --git a/docs/tutorials/Containers.md b/docs/tutorials/Containers.md
index 3934f7a4579..595f8305acc 100644
--- a/docs/tutorials/Containers.md
+++ b/docs/tutorials/Containers.md
@@ -2,7 +2,7 @@
 
 Containers are encapsulated environments that include an operating system, libraries, and software. For example, if you have a host machine running Centos, you can run an isolated container with Ubuntu 18.04. At a high level, it's useful to think of a container as a program or binary.
  
-To promote reproducibility and portability, it's considered best practice to define containers for a WDL and CWL task to run in - this ensures that running the same task on a different system will run the exact same software. 
+To promote reproducibility and portability, it's considered best practice to define containers for a WDL task to run in - this ensures that running the same task on a different system will run the exact same software. 
 
 Docker images are the most common container format, but it is not advisable for certain systems to run Docker itself, and for this reason Cromwell can be configured to support a number of alternatives.
 
@@ -71,26 +71,6 @@ workflow hello {
 }
 ```
 
-Similarly in CWL, you can specify a [`DockerRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#DockerRequirement) inside the requirements section:
-
-```cwl
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-inputs:
-    name:
-        type: string
-        default: "World"
-        inputBinding:
-          prefix: "Hello, "
-outputs:
-    out: stdout
-
-requirements:
-    DockerRequirement:
-        dockerPull: "ubuntu:latest"
-``` 
-___
 ### Docker
 
 [Docker](https://www.docker.com) is a popular container technology that is natively supported by Cromwell and WDL.
diff --git a/docs/tutorials/FiveMinuteIntro.md b/docs/tutorials/FiveMinuteIntro.md
index 87a9acd125d..2e203354bee 100644
--- a/docs/tutorials/FiveMinuteIntro.md
+++ b/docs/tutorials/FiveMinuteIntro.md
@@ -3,9 +3,10 @@
 ### Prerequisites:
 
 * A Unix-based operating system (yes, that includes Mac!)
-* A Java 8 runtime environment 
-	* You can see what you have by running `$ java -version` on a terminal. You're looking for a version that's at least `1.8` or higher.
-	* If not, you can download Java [here](http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html).
+* A Java 11 runtime environment 
+	* You can see what you have by running `$ java -version` on a terminal. 
+	* If not, you can download Java [here](https://adoptopenjdk.net/).
+	* You might need to update the `export JAVA_HOME` in your bash profile to point to your JAVA install location.
 * A sense of adventure!
 
 ### Goals
@@ -41,14 +42,17 @@ This bit is easy, you're just going to copy and paste something from the interne
 Open your favorite editor. Paste in the following content and save it as `myWorkflow.wdl` in your new `cromwell` directory:
 
 ```wdl
+# Example workflow
+# Declare WDL version 1.0 if working in Terra
+version 1.0
 workflow myWorkflow {
 	call myTask
 }
 
 task myTask {
-	command {
+	command <<<
 		echo "hello world"
-	}
+	>>>
 	output {
 		String out = read_string(stdout())
 	}
diff --git a/docs/tutorials/PipelinesApi101.md b/docs/tutorials/PipelinesApi101.md
index 6cc7bf72db4..ef94d111d04 100644
--- a/docs/tutorials/PipelinesApi101.md
+++ b/docs/tutorials/PipelinesApi101.md
@@ -2,22 +2,11 @@
 
 ## Pipelines API v2
 
-### Basic Information
-
-Initial support for Google [Pipelines API version 2](https://cloud.google.com/genomics/reference/rest/) was added in Cromwell 32.
-Expect feature parity with v1 except:
-
-* PAPI v2 private Docker support is equivalent to that in PAPI v1 but the configuration differs, please see [Docker configuration](http://cromwell.readthedocs.io/en/develop/filesystems/Google#Docker) for more details.
-* The "refresh token" authentication mode is **NOT** supported on PAPI V2.
-
-In addition, the following changes are to be expected:
-
-* Error messages for failed jobs might differ from V1
-* The Pipelines API log file content might differ from V1
-
 ### Setting up PAPIv2
 
-For now the easiest way to try PAPIv2 is to migrate an existing set up from PAPIv1 (see below). After that, copy the PAPIv2 sample configuration in [cromwell.examples.conf](https://github.com/broadinstitute/cromwell/blob/develop/cromwell.example.backends/PAPIv2.conf) in place of the PAPIv1 backend.
+For now the easiest way to try PAPIv2 is to start with the sample configuration in
+[cromwell.examples.conf](https://github.com/broadinstitute/cromwell/blob/develop/cromwell.example.backends/PAPIv2.conf)
+and adjust it to fit your needs.
 
 #### Permissions:
 
@@ -49,12 +38,6 @@ gsutil acl ch -u "$EMAIL":W gs://"$RANDOM_BUCKET_NAME"
 gcloud iam service-accounts keys create sa.json --iam-account "$EMAIL"
 ```
 
-## Pipelines API v1
-
-### Deprecation warning
-
-Please note that Google intends to deprecate PAPIv1 in the near future (circa mid 2019 or perhaps earlier). 
-
 ### Prerequisites
 
 This tutorial page relies on completing the previous tutorial:
diff --git a/docs/wf_options/Overview.md b/docs/wf_options/Overview.md
index 17ef2dd9f5f..9fcd7317eea 100644
--- a/docs/wf_options/Overview.md
+++ b/docs/wf_options/Overview.md
@@ -11,7 +11,7 @@ You provide workflow options to Cromwell in a JSON format. This can be supplied
 }
 ```
 
-Unless otherwise specified you can expect workflow options to override any hard-coded defaults in Cromwell or defaults provided in the [configuration file](../Configuring.md), but to be overridden by any values provided in the workflow definition file itself (WDL or CWL).
+Unless otherwise specified you can expect workflow options to override any hard-coded defaults in Cromwell or defaults provided in the [configuration file](../Configuring.md), but to be overridden by any values provided in the workflow definition file itself (WDL).
 
 Some workflow options apply only to tasks running on the [Google Pipelines API backend](Google).
 
@@ -27,7 +27,7 @@ Some options allow you to override or set defaults for runtime attributes.
 
 You can supply a default for any [Runtime Attributes](../RuntimeAttributes.md) by adding a `default_runtime_attributes` map to your workflow options file. Use the key to provide the attribute name and the value to supply the default. 
 
-These defaults replace any defaults in the Cromwell configuration file but are themselves replaced by any values explicitly provided by the task in the WDL or CWL file.
+These defaults replace any defaults in the Cromwell configuration file but are themselves replaced by any values explicitly provided by the task in the WDL file.
 
 Example `options.json`:
 ```json
diff --git a/engine/src/main/resources/swagger/cromwell.yaml b/engine/src/main/resources/swagger/cromwell.yaml
index 69fe3df4a71..6e840160d36 100644
--- a/engine/src/main/resources/swagger/cromwell.yaml
+++ b/engine/src/main/resources/swagger/cromwell.yaml
@@ -71,11 +71,6 @@ paths:
           type: file
           in: formData
         - $ref: '#/parameters/workflowTypeParam'
-        - name: workflowRoot
-          description: The root object to be run. Only necessary for CWL submissions containing multiple objects (in an array).
-          required: false
-          type: string
-          in: formData
         - $ref: '#/parameters/workflowTypeVersionParam'
         - name: labels
           description: JSON object of labels to apply to this workflow.
@@ -607,7 +602,7 @@ paths:
         '400':
           $ref: '#/responses/BadRequest'
         '404':
-           description: No matching cache entry. Cromwell versions prior to 28 will not have recorded information necessary for this endpoint and thus will also appear to not exist.
+          description: No matching cache entry. Cromwell versions prior to 28 will not have recorded information necessary for this endpoint and thus will also appear to not exist.
         '500':
           $ref: '#/responses/ServerError'
   '/api/workflows/{version}/backends':
@@ -753,6 +748,109 @@ paths:
         '500':
           description: An unexpected error occurred.
           $ref: '#/responses/ServerError'
+    post:
+      tags:
+        - GA4GH Workflow Execution Service (WES) - Alpha preview
+      summary: Run workflow
+      description: >-
+        This endpoint creates a new workflow run and returns a `RunId` to
+        monitor its progress.
+        
+        
+        The `workflow_attachment` array may be used to upload files that are
+        required to execute the workflow, including the primary workflow, tools
+        imported by the workflow, other files referenced by the workflow, or
+        files which are part of the input.  The implementation should stage
+        these files to a temporary directory and execute the workflow from
+        there. These parts must have a Content-Disposition header with a
+        "filename" provided for each part.  Filenames may include
+        subdirectories, but must not include references to parent directories
+        with '..' -- implementations should guard against maliciously
+        constructed filenames.
+        
+        
+        The `workflow_url` is either an absolute URL to a workflow file that is
+        accessible by the WES endpoint, or a relative URL corresponding to one
+        of the files attached using `workflow_attachment`.
+        
+        
+        The `workflow_params` JSON object specifies input parameters, such as
+        input files.  The exact format of the JSON object depends on the
+        conventions of the workflow language being used.  Input files should
+        either be absolute URLs, or relative URLs corresponding to files
+        uploaded using `workflow_attachment`.  The WES endpoint must understand
+        and be able to access URLs supplied in the input.  This is
+        implementation specific.
+        
+        
+        The `workflow_type` is the type of workflow language and must be "WDL"
+        currently (or another alternative supported by this WES instance).
+        
+        
+        The `workflow_type_version` is the version of the workflow language
+        submitted and must be one supported by this WES instance.
+        
+        
+        See the `RunRequest` documentation for details about other fields.
+      operationId: RunWorkflow
+      consumes:
+        - multipart/form-data
+      parameters:
+        - name: workflow_params
+          description: ""
+          required: false
+          type: string
+          in: formData
+        - name: workflow_type
+          description: ""
+          required: false
+          type: string
+          in: formData
+        - name: workflow_type_version
+          description: ""
+          required: false
+          type: string
+          in: formData
+        - name: tags
+          description: ''
+          required: false
+          type: string
+          in: formData
+        - name: workflow_engine_parameters
+          description: ''
+          required: false
+          type: string
+          in: formData
+        - name: workflow_url
+          description: ''
+          required: false
+          type: string
+          in: formData
+        - name: workflow_attachment
+          description: ''
+          required: false
+          type: array
+          items:
+            type: file
+            format: binary
+          in: formData
+      responses:
+        '201':
+          description: Successful Request
+          schema:
+            $ref: '#/definitions/RunId'
+        '400':
+          description: The request is malformed.
+          $ref: '#/responses/BadRequest'
+        '401':
+          description: The request is unauthorized.
+          $ref: '#/responses/InvalidSubmission'
+        '403':
+          description: The requester is not authorized to perform this action.
+          $ref: '#/responses/Forbidden'
+        '500':
+          description: An unexpected error occurred.
+          $ref: '#/responses/ServerError'
   '/api/ga4gh/wes/v1/runs/{run_id}':
     get:
       tags:
@@ -884,16 +982,16 @@ parameters:
   workflowTypeParam:
     name: workflowType
     type: string
-    description: The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.
-    enum: [WDL, CWL]
+    description: The workflow language for the file you submitted. Cromwell currently supports WDL.
+    enum: [WDL]
     required: false
     in: formData
   workflowTypeVersionParam:
     name: workflowTypeVersion
-    description: The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.
+    description: The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.
     required: false
     type: string
-    enum: ["draft-2", "1.0", "v1.0"]
+    enum: ["draft-2", "1.0"]
     in: formData
   versionParam:
     name: version
@@ -931,10 +1029,6 @@ definitions:
         example: Submitted
   WorkflowMetadataResponse:
     description: Workflow and call level metadata
-    required:
-      - id
-      - status
-      - submission
     properties:
       id:
         type: string
@@ -963,12 +1057,11 @@ definitions:
       calls:
         $ref: '#/definitions/CallMetadata'
       failures:
-        $ref: '#/definitions/FailureMessage'
+        type: array
+        items:
+          $ref: '#/definitions/FailureMessage'
   CallMetadata:
     description: Call level metadata
-    required:
-      - inputs
-      - executionStatus
     properties:
       inputs:
         type: object
@@ -994,7 +1087,9 @@ definitions:
         type: string
         description: Backend-specific job ID
       failures:
-        $ref: '#/definitions/FailureMessage'
+        type: array
+        items:
+          $ref: '#/definitions/FailureMessage'
       returnCode:
         type: integer
         description: Call execution return code
@@ -1009,17 +1104,14 @@ definitions:
         description: Paths to backend specific logs for this call
   FailureMessage:
     description: Failure messages
-    required:
-      - failure
-      - timestamp
     properties:
-      failure:
+      message:
         type: string
         description: The failure message
-      timestamp:
-        type: string
-        format: date-time
-        description: The time at which this failure occurred
+      causedBy:
+        type: array
+        items:
+          $ref: '#/definitions/FailureMessage'
   WorkflowDescription:
     required:
       - valid
@@ -1108,9 +1200,9 @@ definitions:
               typeName: Pair
               pairTypes:
                 - leftType:
-                  -  typeName: Int
+                    -  typeName: Int
                 - rightType:
-                  -  typeName: String
+                    -  typeName: String
             optional: false
             default: null
             typeDisplayName: Pair[Int, String]
@@ -1159,8 +1251,20 @@ definitions:
                 - typeName: Int
                 - typeName: String
             typeDisplayName: Pair[Int, String]
+      images:
+        type: array
+        items:
+          type: string
       submittedDescriptorType:
         $ref: '#/definitions/DescriptorTypeAndVersion'
+      importedDescriptorTypes:
+        type: array
+        items:
+          $ref: '#/definitions/DescriptorTypeAndVersion'
+      meta:
+        type: object
+      parameterMeta:
+        type: object
       isRunnableWorkflow:
         description: Indicates whether this file can be run on its own (e.g. a WDL workflow)
         type: boolean
@@ -1276,12 +1380,11 @@ definitions:
   DescriptorType:
     type: string
     description: >-
-      One from a list of descriptor type strings (e.g. CWL, WDL).
+      One from a list of descriptor type strings (e.g. WDL).
       Note that these files can also include associated Docker/container files
       and test parameters that further describe a version of a tool
     example: "WDL"
     enum:
-      - CWL
       - WDL
   WorkflowQueryParameter:
     description: Workflow query parameters
@@ -1374,7 +1477,6 @@ definitions:
     description: Result for an individual workflow returned by a workflow query
     required:
       - id
-      - name
       - status
     properties:
       id:
@@ -1390,6 +1492,9 @@ definitions:
         type: string
         format: date-time
         description: Workflow submission datetime
+      metadataArchiveStatus:
+        type: string
+        description: Status in metadata archives
       start:
         type: string
         format: date-time
@@ -1678,7 +1783,7 @@ definitions:
         type: string
         description: >-
           REQUIRED
-          The workflow descriptor type, must be "CWL" or "WDL" currently (or
+          The workflow descriptor type, must be "WDL" currently (or
           another alternative supported by this WES instance)
       workflow_type_version:
         type: string
@@ -1698,7 +1803,7 @@ definitions:
         type: string
         description: >-
           REQUIRED
-          The workflow CWL or WDL document. When `workflow_attachments` is
+          The workflow WDL document. When `workflow_attachments` is
           used to attach files, the `workflow_url` may be a relative path to
           one of the attachments.
     description: >-
@@ -1853,4 +1958,3 @@ definitions:
           are also allowed. The version should be changed whenever the service
           is updated.
         example: 1.0.0
-
diff --git a/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala b/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
index 296d227d39f..c648261a7f4 100644
--- a/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
+++ b/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
@@ -8,19 +8,23 @@ import cromwell.core.filesystem.CromwellFileSystems
 import cromwell.core.path.{DefaultPathBuilderFactory, PathBuilder, PathBuilderFactory}
 import net.ceedubs.ficus.Ficus._
 
+import scala.collection.immutable.SortedMap
 import scala.concurrent.Future
 
 object EngineFilesystems {
   private val config: Config = ConfigFactory.load
 
-  private val defaultFileSystemFactory: Map[String, PathBuilderFactory] =
+  private val defaultFileSystemFactory: SortedMap[String, PathBuilderFactory] =
     Option(DefaultPathBuilderFactory.tuple)
       .filter(_ => config.as[Boolean]("engine.filesystems.local.enabled"))
-      .toMap
+      .to(collection.immutable.SortedMap)
 
-  private val pathBuilderFactories: Map[String, PathBuilderFactory] = {
-    CromwellFileSystems.instance.factoriesFromConfig(config.as[Config]("engine"))
-      .unsafe("Failed to instantiate engine filesystem") ++ defaultFileSystemFactory
+  private val pathBuilderFactories: SortedMap[String, PathBuilderFactory] = {
+    // Unordered maps are a classical source of randomness injection into a system
+    (
+      CromwellFileSystems.instance.factoriesFromConfig(config.as[Config]("engine"))
+        .unsafe("Failed to instantiate engine filesystem") ++ defaultFileSystemFactory
+    ).to(collection.immutable.SortedMap)
   }
 
   def configuredPathBuilderFactories: List[PathBuilderFactory] = pathBuilderFactories.values.toList
diff --git a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
index 0598e154f2d..012e771b5a0 100644
--- a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
+++ b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
@@ -12,6 +12,7 @@ import cromwell.core.path.Path
 import cromwell.engine.io.IoActor._
 import cromwell.engine.io.RetryableRequestSupport.{isInfinitelyRetryable, isRetryable}
 import cromwell.engine.io.{IoAttempts, IoCommandContext, IoCommandStalenessBackpressuring}
+import cromwell.filesystems.blob.BlobPath
 import cromwell.filesystems.drs.DrsPath
 import cromwell.filesystems.gcs.GcsPath
 import cromwell.filesystems.s3.S3Path
@@ -128,21 +129,33 @@ class NioFlow(parallelism: Int,
 
     def readFileAndChecksum: IO[String] = {
       for {
-        fileHash <- getHash(command.file)
+        fileHash <- getStoredHash(command.file)
         uncheckedValue <- readFile
-        checksumResult <- checkHash(uncheckedValue, fileHash)
+        checksumResult <- fileHash match {
+          case Some(hash) => checkHash(uncheckedValue, hash)
+          // If there is no stored checksum, don't attempt to validate.
+          // If the missing checksum is itself an error condition, that
+          // should be detected by the code that gets the FileHash.
+          case None => IO.pure(ChecksumSkipped())
+        }
         verifiedValue <- checksumResult match {
           case _: ChecksumSkipped => IO.pure(uncheckedValue)
           case _: ChecksumSuccess => IO.pure(uncheckedValue)
           case failure: ChecksumFailure => IO.raiseError(
             ChecksumFailedException(
-              s"Failed checksum for '${command.file}'. Expected '${fileHash.hashType}' hash of '${fileHash.hash}'. Calculated hash '${failure.calculatedHash}'"))
+              fileHash match {
+                case Some(hash) => s"Failed checksum for '${command.file}'. Expected '${hash.hashType}' hash of '${hash.hash}'. Calculated hash '${failure.calculatedHash}'"
+                case None => s"Failed checksum for '${command.file}'. Couldn't find stored file hash." // This should never happen
+              }
+            )
+          )
         }
       } yield verifiedValue
     }
 
     val fileContentIo = command.file match {
-      case _: DrsPath => readFileAndChecksum
+      case _: DrsPath  => readFileAndChecksum
+      case _: BlobPath => readFileAndChecksum
       case _ => readFile
     }
     fileContentIo.map(_.replaceAll("\\r\\n", "\\\n"))
@@ -153,19 +166,27 @@ class NioFlow(parallelism: Int,
   }
 
   private def hash(hash: IoHashCommand): IO[String] = {
-    getHash(hash.file).map(_.hash)
+    // If there is no hash accessible from the file storage system,
+    // we'll read the file and generate the hash ourselves.
+    getStoredHash(hash.file).flatMap {
+      case Some(storedHash) => IO.pure(storedHash)
+      case None => generateMd5FileHashForPath(hash.file)
+    }.map(_.hash)
   }
 
-  private def getHash(file: Path): IO[FileHash] = {
+  private def getStoredHash(file: Path): IO[Option[FileHash]] = {
     file match {
-      case gcsPath: GcsPath => getFileHashForGcsPath(gcsPath)
+      case gcsPath: GcsPath => getFileHashForGcsPath(gcsPath).map(Option(_))
+      case blobPath: BlobPath => getFileHashForBlobPath(blobPath)
       case drsPath: DrsPath => IO {
+        // We assume all DRS files have a stored hash; this will throw
+        // if the file does not.
         drsPath.getFileHash
-      }
+      }.map(Option(_))
       case s3Path: S3Path => IO {
-        FileHash(HashType.S3Etag, s3Path.eTag)
+        Option(FileHash(HashType.S3Etag, s3Path.eTag))
       }
-      case path => getMd5FileHashForPath(path)
+      case _ => IO.pure(None)
     }
   }
 
@@ -201,7 +222,11 @@ class NioFlow(parallelism: Int,
     gcsPath.objectBlobId.map(id => FileHash(HashType.GcsCrc32c, gcsPath.cloudStorage.get(id).getCrc32c))
   }
 
-  private def getMd5FileHashForPath(path: Path): IO[FileHash] = delayedIoFromTry {
+  private def getFileHashForBlobPath(blobPath: BlobPath): IO[Option[FileHash]] = delayedIoFromTry {
+    blobPath.md5HexString.map(md5 => md5.map(FileHash(HashType.Md5, _)))
+  }
+
+  private def generateMd5FileHashForPath(path: Path): IO[FileHash] = delayedIoFromTry {
     tryWithResource(() => path.newInputStream) { inputStream =>
       FileHash(HashType.Md5, org.apache.commons.codec.digest.DigestUtils.md5Hex(inputStream))
     }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
index ba82bab3e96..b4ccf3de53b 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
@@ -135,6 +135,12 @@ object WorkflowActor {
 
   case class StateCheckpoint(state: WorkflowActorState, failures: Option[List[Throwable]] = None)
 
+  /**
+    * Message sent from WorkflowActor to itself to trigger the initialization to start. Allows us to idle
+    * in the initializing state without an assigned actor for a few seconds if the first attempt fails.
+    */
+  case object StartInitializing
+
   /**
     * @param currentLifecycleStateActor The current lifecycle stage, represented by an ActorRef.
     */
@@ -145,7 +151,8 @@ object WorkflowActor {
                                effectiveStartableState: StartableState,
                                workflowFinalOutputs: Set[WomValue] = Set.empty,
                                workflowAllOutputs: Set[WomValue] = Set.empty,
-                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty)
+                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty,
+                               failedInitializationAttempts: Int = 0)
   object WorkflowActorData {
     def apply(startableState: StartableState): WorkflowActorData = WorkflowActorData(
       currentLifecycleStateActor = None,
@@ -255,6 +262,9 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
 
   protected val pathBuilderFactories: List[PathBuilderFactory] = EngineFilesystems.configuredPathBuilderFactories
 
+  protected val maxInitializationAttempts: Int = 16
+  protected val initializationRetryInterval: FiniteDuration = 1.minute
+
   startWith(WorkflowUnstartedState, WorkflowActorData(initialStartableState))
 
   pushCurrentStateToMetadataService(workflowId, WorkflowUnstartedState.workflowState)
@@ -299,18 +309,8 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
 
   when(MaterializingWorkflowDescriptorState) {
     case Event(MaterializeWorkflowDescriptorSuccessResponse(workflowDescriptor), data) =>
-      val initializerActor = context.actorOf(
-        WorkflowInitializationActor.props(
-          workflowIdForLogging,
-          rootWorkflowIdForLogging,
-          workflowDescriptor,
-          ioActor,
-          serviceRegistryActor,
-          restarting
-        ),
-        name = s"WorkflowInitializationActor-$workflowId")
-      initializerActor ! StartInitializationCommand
-      goto(InitializingWorkflowState) using data.copy(currentLifecycleStateActor = Option(initializerActor), workflowDescriptor = Option(workflowDescriptor))
+      self ! StartInitializing
+      goto(InitializingWorkflowState) using data.copy(workflowDescriptor = Option(workflowDescriptor))
     case Event(MaterializeWorkflowDescriptorFailureResponse(reason: Throwable), data) =>
       goto(WorkflowFailedState) using data.copy(lastStateReached = StateCheckpoint(MaterializingWorkflowDescriptorState, Option(List(reason))))
     // If the workflow is not being restarted then we can abort it immediately as nothing happened yet
@@ -320,40 +320,45 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   /* ************************** */
   /* ****** Initializing ****** */
   /* ************************** */
-
-  when(InitializingWorkflowState) {
-    case Event(WorkflowInitializationSucceededResponse(initializationData), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
-      val executionActor = context.actorOf(WorkflowExecutionActor.props(
+  protected def createInitializationActor(workflowDescriptor: EngineWorkflowDescriptor, name: String): ActorRef = {
+    context.actorOf(
+      WorkflowInitializationActor.props(
+        workflowIdForLogging,
+        rootWorkflowIdForLogging,
         workflowDescriptor,
-        ioActor = ioActor,
-        serviceRegistryActor = serviceRegistryActor,
-        jobStoreActor = jobStoreActor,
-        subWorkflowStoreActor = subWorkflowStoreActor,
-        callCacheReadActor = callCacheReadActor,
-        callCacheWriteActor = callCacheWriteActor,
-        workflowDockerLookupActor = workflowDockerLookupActor,
-        jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
-        jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
-        backendSingletonCollection,
-        initializationData,
-        startState = data.effectiveStartableState,
-        rootConfig = conf,
-        totalJobsByRootWf = totalJobsByRootWf,
-        fileHashCacheActor = fileHashCacheActorProps map context.system.actorOf,
-        blacklistCache = blacklistCache), name = s"WorkflowExecutionActor-$workflowId")
+        ioActor,
+        serviceRegistryActor,
+        restarting
+      ),
+      name)
+  }
 
+  when(InitializingWorkflowState) {
+    case Event(StartInitializing, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+      val initializerActor = createInitializationActor(workflowDescriptor, s"WorkflowInitializationActor-$workflowId-${data.failedInitializationAttempts + 1}")
+      initializerActor ! StartInitializationCommand
+      goto(InitializingWorkflowState) using data.copy(currentLifecycleStateActor = Option(initializerActor), workflowDescriptor = Option(workflowDescriptor))
+    case Event(WorkflowInitializationSucceededResponse(initializationData), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+      val dataWithInitializationData = data.copy(initializationData = initializationData)
+      val executionActor = createWorkflowExecutionActor(workflowDescriptor, dataWithInitializationData)
       executionActor ! ExecuteWorkflowCommand
-
       val nextState = data.effectiveStartableState match {
         case RestartableAborting => WorkflowAbortingState
         case _ => ExecutingWorkflowState
       }
-      goto(nextState) using data.copy(currentLifecycleStateActor = Option(executionActor), initializationData = initializationData)
-    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
-      finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
+      goto(nextState) using dataWithInitializationData.copy(currentLifecycleStateActor = Option(executionActor))
+    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+      val failedInitializationAttempts = data.failedInitializationAttempts + 1
+      if (failedInitializationAttempts < maxInitializationAttempts) {
+        workflowLogger.info(s"Initialization failed on attempt $failedInitializationAttempts. Will retry up to $maxInitializationAttempts times. Next retry is in $initializationRetryInterval", CromwellAggregatedException(reason, "Initialization Failure"))
+        context.system.scheduler.scheduleOnce(initializationRetryInterval) { self ! StartInitializing}
+        stay() using data.copy(currentLifecycleStateActor = None, failedInitializationAttempts = failedInitializationAttempts)
+      } else {
+        finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
+      }
 
     // If the workflow is not restarting, handle the Abort command normally and send an abort message to the init actor
-    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) if !restarting =>
+    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) if !restarting =>
       handleAbortCommand(data, workflowDescriptor)
   }
 
@@ -361,24 +366,45 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   /* ****** Running ****** */
   /* ********************* */
 
+  def createWorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor, data: WorkflowActorData): ActorRef = {
+    context.actorOf(WorkflowExecutionActor.props(
+      workflowDescriptor,
+      ioActor = ioActor,
+      serviceRegistryActor = serviceRegistryActor,
+      jobStoreActor = jobStoreActor,
+      subWorkflowStoreActor = subWorkflowStoreActor,
+      callCacheReadActor = callCacheReadActor,
+      callCacheWriteActor = callCacheWriteActor,
+      workflowDockerLookupActor = workflowDockerLookupActor,
+      jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
+      jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
+      backendSingletonCollection,
+      data.initializationData,
+      startState = data.effectiveStartableState,
+      rootConfig = conf,
+      totalJobsByRootWf = totalJobsByRootWf,
+      fileHashCacheActor = fileHashCacheActorProps map context.system.actorOf,
+      blacklistCache = blacklistCache), name = s"WorkflowExecutionActor-$workflowId")
+  }
+
   // Handles workflow completion events from the WEA and abort command
   val executionResponseHandler: StateFunction = {
     // Workflow responses
     case Event(WorkflowExecutionSucceededResponse(jobKeys, rootAndSubworklowIds, finalOutputs, allOutputs),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, finalOutputs, None, allOutputs, rootAndSubworklowIds)
     case Event(WorkflowExecutionFailedResponse(jobKeys, failures),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, CallOutputs.empty, Option(List(failures)))
     case Event(WorkflowExecutionAbortedResponse(jobKeys),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, StateCheckpoint(_, failures), _, _, _, _)) =>
+    data @ WorkflowActorData(_, Some(workflowDescriptor), _, StateCheckpoint(_, failures), _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, CallOutputs.empty, failures)
 
     // Whether we're running or aborting, restarting or not, pass along the abort command.
     // Note that aborting a workflow multiple times will result in as many abort commands sent to the execution actor
-    case Event(AbortWorkflowWithExceptionCommand(ex), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(AbortWorkflowWithExceptionCommand(ex), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       handleAbortCommand(data, workflowDescriptor, Option(ex))
-    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       handleAbortCommand(data, workflowDescriptor)
   }
 
@@ -391,12 +417,16 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   // Handles initialization responses we can get if the abort came in when we were initializing the workflow
   val abortHandler: StateFunction = {
     // If the initialization failed, record the failure in the data and finalize the workflow
-    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
 
     // Otherwise (success or abort), finalize the workflow without failures
-    case Event(_: WorkflowInitializationResponse, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(_: WorkflowInitializationResponse, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, failures = None)
+
+    case Event(StartInitializing, _) =>
+      // An initialization trigger we no longer need to action. Ignore:
+      stay()
   }
 
   // In aborting state, we can receive initialization responses or execution responses.
@@ -413,6 +443,9 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
       val failures = data.lastStateReached.failures.getOrElse(List.empty) ++ finalizationFailures
       goto(WorkflowFailedState) using data.copy(lastStateReached = StateCheckpoint(FinalizingWorkflowState, Option(failures)))
     case Event(AbortWorkflowCommand, _) => stay()
+    case Event(StartInitializing, _) =>
+      // An initialization trigger we no longer need to action. Ignore:
+      stay()
   }
 
   when(MetadataIntegrityValidationState) {
@@ -431,13 +464,18 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   }
 
   def handleAbortCommand(data: WorkflowActorData, workflowDescriptor: EngineWorkflowDescriptor, exceptionCausedAbortOpt: Option[Throwable] = None) = {
+    val updatedData = data.copy(lastStateReached = StateCheckpoint(stateName, exceptionCausedAbortOpt.map(List(_))))
     data.currentLifecycleStateActor match {
       case Some(currentActor) =>
         currentActor ! EngineLifecycleActorAbortCommand
-        goto(WorkflowAbortingState) using data.copy(lastStateReached = StateCheckpoint(stateName, exceptionCausedAbortOpt.map(List(_))))
+        goto(WorkflowAbortingState) using updatedData
       case None =>
-        workflowLogger.warn(s"Received an abort command in state $stateName but there's no lifecycle actor associated. This is an abnormal state, finalizing the workflow anyway.")
-        finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, None)
+        if (stateName == InitializingWorkflowState) {
+          workflowLogger.info(s"Received an abort command in state $stateName (while awaiting an initialization retry). Finalizing the workflow.")
+        } else {
+          workflowLogger.warn(s"Received an abort command in state $stateName but there's no lifecycle actor associated. This is an abnormal state, finalizing the workflow anyway.")
+        }
+        finalizeWorkflow(updatedData, workflowDescriptor, Map.empty, CallOutputs.empty, failures = None, lastStateOverride = Option(WorkflowAbortingState))
     }
   }
 
@@ -645,11 +683,12 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
                                workflowFinalOutputs: CallOutputs,
                                failures: Option[List[Throwable]],
                                workflowAllOutputs: Set[WomValue] = Set.empty,
-                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty) = {
+                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty,
+                               lastStateOverride: Option[WorkflowActorState] = None) = {
     val finalizationActor = makeFinalizationActor(workflowDescriptor, jobExecutionMap, workflowFinalOutputs)
     finalizationActor ! StartFinalizationCommand
     goto(FinalizingWorkflowState) using data.copy(
-      lastStateReached = StateCheckpoint (stateName, failures),
+      lastStateReached = StateCheckpoint (lastStateOverride.getOrElse(stateName), failures),
       workflowFinalOutputs = workflowFinalOutputs.outputs.values.toSet,
       workflowAllOutputs = workflowAllOutputs,
       rootAndSubworkflowIds = rootAndSubworkflowIds
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
index 0eef565caf2..89745e6523d 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
@@ -37,7 +37,7 @@ class FetchCachedResultsActor(cacheResultId: CallCachingEntryId, replyTo: ActorR
 
         val sourceCacheDetails = Seq(result.callCachingEntry.workflowExecutionUuid,
           result.callCachingEntry.callFullyQualifiedName,
-          result.callCachingEntry.jobIndex).mkString(":")
+          result.callCachingEntry.jobIndex.toString).mkString(":")
 
         CachedOutputLookupSucceeded(simpletons, jobDetritusFiles.toMap,
           result.callCachingEntry.returnCode,
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
index 0f9eec73ef4..57da64de3ce 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
@@ -753,7 +753,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
   private def logCacheHitSuccessAndNotifyMetadata(data: ResponsePendingData): Unit = {
 
-    val metadataMap = Map(callCachingHitResultMetadataKey -> true) ++ data.ejeaCacheHit.flatMap(_.details).map(details => callCachingReadResultMetadataKey -> s"Cache Hit: $details").toMap
+    val metadataMap = Map[String, Any](callCachingHitResultMetadataKey -> true) ++ data.ejeaCacheHit.flatMap(_.details).map(details => callCachingReadResultMetadataKey -> s"Cache Hit: $details").toMap
 
     writeToMetadata(metadataMap)
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
index e913e5c6b3b..a5c1d6fc995 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
@@ -27,12 +27,13 @@ object ValueStore {
 case class ValueStore(store: Table[OutputPort, ExecutionIndex, WomValue]) {
 
   override def toString: String = {
+    import common.util.StringUtil.EnhancedToStringable
     import io.circe.syntax._
     import io.circe.Printer
 
     val values = store.valuesTriplet.map {
-      case (node, None, value) => node.name -> value.valueString
-      case (node, index, value) => s"${node.name}:${index.fromIndex}" -> value.valueString
+      case (node, None, value) => node.name -> value.toPrettyElidedString(limit = 100)
+      case (node, index, value) => s"${node.name}:${index.fromIndex}" -> value.toPrettyElidedString(limit = 100)
     }.toMap
 
     values.asJson.printWith(Printer.spaces2.copy(dropNullValues = true, colonLeft = ""))
diff --git a/engine/src/main/scala/cromwell/server/CromwellServer.scala b/engine/src/main/scala/cromwell/server/CromwellServer.scala
index b5705b91dae..76f784875fc 100644
--- a/engine/src/main/scala/cromwell/server/CromwellServer.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellServer.scala
@@ -11,7 +11,6 @@ import cromwell.services.instrumentation.CromwellInstrumentationActor
 import cromwell.webservice.SwaggerService
 import cromwell.webservice.routes.CromwellApiService
 import cromwell.webservice.routes.wes.WesRouteSupport
-import cromwell.webservice.routes.wes.WesRunRoutes
 
 import scala.concurrent.Future
 import scala.util.{Failure, Success}
@@ -37,7 +36,6 @@ class CromwellServerActor(cromwellSystem: CromwellSystem, gracefulShutdown: Bool
     with CromwellApiService
     with CromwellInstrumentationActor
     with WesRouteSupport
-    with WesRunRoutes
     with SwaggerService
     with ActorLogging {
   implicit val actorSystem = context.system
@@ -53,7 +51,7 @@ class CromwellServerActor(cromwellSystem: CromwellSystem, gracefulShutdown: Bool
     * cromwell.yaml is broken unless the swagger index.html is patched. Copy/paste the code from rawls or cromiam if
     * actual cromwell+swagger+oauth+/api support is needed.
     */
-  val apiRoutes: Route = pathPrefix("api")(concat(workflowRoutes, womtoolRoutes, wesRoutes, runRoutes))
+  val apiRoutes: Route = pathPrefix("api")(concat(workflowRoutes, womtoolRoutes, wesRoutes))
   val nonApiRoutes: Route = concat(engineRoutes, swaggerUiResourceRoute)
   val allRoutes: Route = concat(apiRoutes, nonApiRoutes)
 
diff --git a/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala b/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
index 9b23ec62311..a1c4f023135 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
@@ -81,81 +81,81 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
     path("workflows" / Segment / "backends") { _ =>
       get { instrumentRequest { complete(ToResponseMarshallable(backendResponse)) } }
     } ~
-    path("workflows" / Segment / "callcaching" / "diff") { _ =>
-      parameterSeq { parameters =>
-        get {
-          instrumentRequest {
-            CallCacheDiffQueryParameter.fromParameters(parameters) match {
-              case Valid(queryParameter) =>
-                val diffActor = actorRefFactory.actorOf(CallCacheDiffActor.props(serviceRegistryActor), "CallCacheDiffActor-" + UUID.randomUUID())
-                onComplete(diffActor.ask(queryParameter).mapTo[CallCacheDiffActorResponse]) {
-                  case Success(r: SuccessfulCallCacheDiffResponse) => complete(r)
-                  case Success(r: FailedCallCacheDiffResponse) => r.reason.errorRequest(StatusCodes.InternalServerError)
-                  case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
-                  case Failure(e: CachedCallNotFoundException) => e.errorRequest(StatusCodes.NotFound)
-                  case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
-                  case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
-                }
-              case Invalid(errors) =>
-                val e = AggregatedMessageException("Wrong parameters for call cache diff query", errors.toList)
-                e.errorRequest(StatusCodes.BadRequest)
+      path("workflows" / Segment / "callcaching" / "diff") { _ =>
+        parameterSeq { parameters =>
+          get {
+            instrumentRequest {
+              CallCacheDiffQueryParameter.fromParameters(parameters) match {
+                case Valid(queryParameter) =>
+                  val diffActor = actorRefFactory.actorOf(CallCacheDiffActor.props(serviceRegistryActor), "CallCacheDiffActor-" + UUID.randomUUID())
+                  onComplete(diffActor.ask(queryParameter).mapTo[CallCacheDiffActorResponse]) {
+                    case Success(r: SuccessfulCallCacheDiffResponse) => complete(r)
+                    case Success(r: FailedCallCacheDiffResponse) => r.reason.errorRequest(StatusCodes.InternalServerError)
+                    case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
+                    case Failure(e: CachedCallNotFoundException) => e.errorRequest(StatusCodes.NotFound)
+                    case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
+                    case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
+                  }
+                case Invalid(errors) =>
+                  val e = AggregatedMessageException("Wrong parameters for call cache diff query", errors.toList)
+                  e.errorRequest(StatusCodes.BadRequest)
+              }
             }
           }
         }
-      }
-    } ~
-    path("workflows" / Segment / Segment / "timing") { (_, possibleWorkflowId) =>
-      instrumentRequest {
-        onComplete(validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor)) {
-          case Success(workflowId) => completeTimingRouteResponse(metadataLookupForTimingRoute(workflowId))
-          case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
-          case Failure(e: InvalidWorkflowException) => e.failRequest(StatusCodes.BadRequest)
-          case Failure(e) => e.failRequest(StatusCodes.InternalServerError)
-        }
-      }
-    } ~
-    path("workflows" / Segment / Segment / "abort") { (_, possibleWorkflowId) =>
-      post {
+      } ~
+      path("workflows" / Segment / Segment / "timing") { (_, possibleWorkflowId) =>
         instrumentRequest {
-          abortWorkflow(possibleWorkflowId, workflowStoreActor, workflowManagerActor)
+          onComplete(validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor)) {
+            case Success(workflowId) => completeTimingRouteResponse(metadataLookupForTimingRoute(workflowId))
+            case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
+            case Failure(e: InvalidWorkflowException) => e.failRequest(StatusCodes.BadRequest)
+            case Failure(e) => e.failRequest(StatusCodes.InternalServerError)
+          }
         }
-      }
-    } ~
-  path("workflows" / Segment) { _ =>
-      post {
-        instrumentRequest {
-          entity(as[Multipart.FormData]) { formData =>
-            submitRequest(formData, isSingleSubmission = true)
+      } ~
+      path("workflows" / Segment / Segment / "abort") { (_, possibleWorkflowId) =>
+        post {
+          instrumentRequest {
+            abortWorkflow(possibleWorkflowId, workflowStoreActor, workflowManagerActor)
           }
         }
-      }
-    } ~
-  path("workflows" / Segment / "batch") { _ =>
-    post {
-      instrumentRequest {
-        entity(as[Multipart.FormData]) { formData =>
-          submitRequest(formData, isSingleSubmission = false)
+      } ~
+      path("workflows" / Segment) { _ =>
+        post {
+          instrumentRequest {
+            entity(as[Multipart.FormData]) { formData =>
+              submitRequest(formData, isSingleSubmission = true)
+            }
+          }
         }
-      }
-    }
-  } ~
-  path("workflows" / Segment / Segment / "releaseHold") { (_, possibleWorkflowId) =>
-    post {
-      instrumentRequest {
-        val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor) flatMap { workflowId =>
-          workflowStoreActor.ask(WorkflowStoreActor.WorkflowOnHoldToSubmittedCommand(workflowId)).mapTo[WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedResponse]
+      } ~
+      path("workflows" / Segment / "batch") { _ =>
+        post {
+          instrumentRequest {
+            entity(as[Multipart.FormData]) { formData =>
+              submitRequest(formData, isSingleSubmission = false)
+            }
+          }
         }
-        onComplete(response){
-          case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e: NotInOnHoldStateException)) => e.errorRequest(StatusCodes.Forbidden)
-          case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e)) => e.errorRequest(StatusCodes.InternalServerError)
-          case Success(r: WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedSuccess) => completeResponse(StatusCodes.OK, toResponse(r.workflowId, WorkflowSubmitted), Seq.empty)
-          case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
-          case Failure(e: InvalidWorkflowException) => e.failRequest(StatusCodes.BadRequest)
-          case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
+      } ~
+      path("workflows" / Segment / Segment / "releaseHold") { (_, possibleWorkflowId) =>
+        post {
+          instrumentRequest {
+            val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor) flatMap { workflowId =>
+              workflowStoreActor.ask(WorkflowStoreActor.WorkflowOnHoldToSubmittedCommand(workflowId)).mapTo[WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedResponse]
+            }
+            onComplete(response){
+              case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e: NotInOnHoldStateException)) => e.errorRequest(StatusCodes.Forbidden)
+              case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e)) => e.errorRequest(StatusCodes.InternalServerError)
+              case Success(r: WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedSuccess) => completeResponse(StatusCodes.OK, toResponse(r.workflowId, WorkflowSubmitted), Seq.empty)
+              case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
+              case Failure(e: InvalidWorkflowException) => e.failRequest(StatusCodes.BadRequest)
+              case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
+            }
+          }
         }
-      }
-    }
-  } ~ metadataRoutes
+      } ~ metadataRoutes
 
 
   private def metadataLookupForTimingRoute(workflowId: WorkflowId): Future[MetadataJsonResponse] = {
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
index 32e221272e0..58313cb5946 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
@@ -2,8 +2,7 @@ package cromwell.webservice.routes.wes
 
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport
 import cromwell.webservice.routes.wes.WesState.WesState
-import spray.json.{DefaultJsonProtocol, RootJsonFormat}
-import cromwell.webservice.routes.wes.WesRunLog
+import spray.json.{DefaultJsonProtocol, JsObject, RootJsonFormat}
 
 sealed trait WesResponse extends Product with Serializable
 final case class WesErrorResponse(msg: String, status_code: Int) extends WesResponse
@@ -12,6 +11,18 @@ final case class WesRunStatus(run_id: String, state: WesState) extends WesRespon
 final case class WesResponseRunList(runs: List[WesRunStatus]) extends WesResponse
 final case class WesResponseWorkflowMetadata(workflowLog: WesRunLog) extends WesResponse
 
+final case class WesRunLog(run_id: String,
+                           request: WesRunRequest,
+                           state: WesState,
+                           run_log: Option[WesLog],
+                           task_logs: Option[List[WesLog]],
+                           outputs: Option[JsObject]
+                          ) extends WesResponse
+
+object WesRunLog {
+  def fromJson(json: String): WesRunLog = CromwellMetadata.fromJson(json).wesRunLog
+}
+
 
 final case class WesStatusInfoResponse(workflow_type_version: Map[String, Iterable[String]],
                                     supported_wes_versions: Iterable[String],
@@ -48,6 +59,7 @@ object WesResponseJsonSupport extends SprayJsonSupport with DefaultJsonProtocol
         case i: WesStatusInfoResponse => i.toJson
         case l: WesResponseRunList => l.toJson
         case m: WesResponseWorkflowMetadata => m.toJson
+        case w: WesRunLog => w.toJson
       }
     }
 
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
index e4969702460..41973bb8981 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
@@ -1,34 +1,47 @@
 package cromwell.webservice.routes.wes
 
 import akka.actor.ActorRef
+import akka.http.scaladsl.model.{Multipart, StatusCode, StatusCodes}
 import akka.http.scaladsl.server.Directives._
-import akka.http.scaladsl.server.Route
+import akka.http.scaladsl.server.directives.RouteDirectives.complete
+import akka.http.scaladsl.server.{Directive1, Route}
 import akka.pattern.{AskTimeoutException, ask}
+import akka.stream.ActorMaterializer
 import akka.util.Timeout
-import cromwell.engine.instrumentation.HttpInstrumentation
-import cromwell.services.metadata.MetadataService.{GetStatus, MetadataServiceResponse, StatusLookupFailed}
-import cromwell.webservice.routes.CromwellApiService.{UnrecognizedWorkflowException, validateWorkflowIdInMetadata}
-import cromwell.webservice.WebServiceUtils.EnhancedThrowable
-
-import scala.concurrent.ExecutionContext
-import scala.util.{Failure, Success}
-import WesResponseJsonSupport._
-import akka.http.scaladsl.model.{StatusCode, StatusCodes}
-import akka.http.scaladsl.server.directives.RouteDirectives.complete
-import WesRouteSupport._
+import cats.data.NonEmptyList
+import com.typesafe.config.ConfigFactory
 import cromwell.core.abort.SuccessfulAbortResponse
+import cromwell.core.{WorkflowId, WorkflowOnHold, WorkflowState, WorkflowSubmitted}
+import cromwell.engine.instrumentation.HttpInstrumentation
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
+import cromwell.engine.workflow.workflowstore.{WorkflowStoreActor, WorkflowStoreSubmitActor}
 import cromwell.server.CromwellShutdown
-import cromwell.services.SuccessfulMetadataJsonResponse
+import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, GetSingleWorkflowMetadataAction, GetStatus, MetadataServiceResponse, StatusLookupFailed}
+import cromwell.services.{FailedMetadataJsonResponse, SuccessfulMetadataJsonResponse}
+import cromwell.webservice.PartialWorkflowSources
+import cromwell.webservice.WebServiceUtils.{EnhancedThrowable, completeResponse, materializeFormData}
 import cromwell.webservice.routes.CromwellApiService
+import cromwell.webservice.routes.CromwellApiService.{UnrecognizedWorkflowException, validateWorkflowIdInMetadata}
+import cromwell.webservice.routes.MetadataRouteSupport.{metadataBuilderActorRequest, metadataQueryRequest}
+import cromwell.webservice.routes.wes.WesResponseJsonSupport._
+import cromwell.webservice.routes.wes.WesRouteSupport.{respondWithWesError, _}
+import net.ceedubs.ficus.Ficus._
+
+import scala.concurrent.duration.FiniteDuration
+import scala.concurrent.{ExecutionContext, Future, TimeoutException}
+import scala.util.{Failure, Success}
+
+
 
 trait WesRouteSupport extends HttpInstrumentation {
+
   val serviceRegistryActor: ActorRef
   val workflowManagerActor: ActorRef
   val workflowStoreActor: ActorRef
 
   implicit val ec: ExecutionContext
   implicit val timeout: Timeout
+  implicit val materializer: ActorMaterializer
 
   /*
     Defines routes intended to sit alongside the primary Cromwell REST endpoints. For instance, we'll now have:
@@ -49,44 +62,125 @@ trait WesRouteSupport extends HttpInstrumentation {
         pathPrefix("ga4gh" / "wes" / "v1") {
           concat(
             path("service-info") {
-              complete(ServiceInfo.toWesResponse(workflowStoreActor))
+              get {
+                complete(ServiceInfo.toWesResponse(workflowStoreActor))
+              }
             },
-            pathPrefix("runs") {
-              concat(
-                path(Segment / "status") { possibleWorkflowId =>
-                  val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor).flatMap(w => serviceRegistryActor.ask(GetStatus(w)).mapTo[MetadataServiceResponse])
-                  // WES can also return a 401 or a 403 but that requires user auth knowledge which Cromwell doesn't currently have
-                  onComplete(response) {
-                    case Success(SuccessfulMetadataJsonResponse(_, jsObject)) =>
-                      val wesState = WesState.fromCromwellStatusJson(jsObject)
-                      complete(WesRunStatus(possibleWorkflowId, wesState))
-                    case Success(r: StatusLookupFailed) => r.reason.errorRequest(StatusCodes.InternalServerError)
-                    case Success(m: MetadataServiceResponse) =>
-                      // This should never happen, but ....
-                      val error = new IllegalStateException("Unexpected response from Metadata service: " + m)
-                      error.errorRequest(StatusCodes.InternalServerError)
-                    case Failure(_: UnrecognizedWorkflowException) => complete(NotFoundError)
-                    case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
-                  }
-                },
-                path(Segment / "cancel") { possibleWorkflowId =>
-                  post {
-                    CromwellApiService.abortWorkflow(possibleWorkflowId,
-                      workflowStoreActor,
-                      workflowManagerActor,
-                      successHandler = WesAbortSuccessHandler,
-                      errorHandler = WesAbortErrorHandler)
+            path("runs") {
+              get {
+                parameters(("page_size".as[Int].?, "page_token".?)) { (pageSize, pageToken) =>
+                  completeCromwellResponse(listRuns(pageSize, pageToken, serviceRegistryActor))
+                }
+              } ~
+                post {
+                  extractSubmission() { submission =>
+                    wesSubmitRequest(submission.entity,
+                      isSingleSubmission = true)
                   }
                 }
-              )
+            },
+            path("runs" / Segment) { workflowId =>
+              get {
+                // this is what it was like in code found in the project… it perhaps isn’t ideal but doesn’t seem to hurt, so leaving it like this for now.
+                completeCromwellResponse(runLog(workflowId, (w: WorkflowId) => GetSingleWorkflowMetadataAction(w, None, None, expandSubWorkflows = false), serviceRegistryActor))
+              }
+            },
+            path("runs" / Segment / "status") { possibleWorkflowId =>
+              val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor).flatMap(w => serviceRegistryActor.ask(GetStatus(w)).mapTo[MetadataServiceResponse])
+              // WES can also return a 401 or a 403 but that requires user auth knowledge which Cromwell doesn't currently have
+              onComplete(response) {
+                case Success(SuccessfulMetadataJsonResponse(_, jsObject)) =>
+                  val wesState = WesState.fromCromwellStatusJson(jsObject)
+                  complete(WesRunStatus(possibleWorkflowId, wesState))
+                case Success(r: StatusLookupFailed) => r.reason.errorRequest(StatusCodes.InternalServerError)
+                case Success(m: MetadataServiceResponse) =>
+                  // This should never happen, but ....
+                  val error = new IllegalStateException("Unexpected response from Metadata service: " + m)
+                  error.errorRequest(StatusCodes.InternalServerError)
+                case Failure(_: UnrecognizedWorkflowException) => complete(NotFoundError)
+                case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
+              }
+            },
+            path("runs" / Segment / "cancel") { possibleWorkflowId =>
+              post {
+                CromwellApiService.abortWorkflow(possibleWorkflowId,
+                  workflowStoreActor,
+                  workflowManagerActor,
+                  successHandler = WesAbortSuccessHandler,
+                  errorHandler = WesAbortErrorHandler)
+              }
             }
           )
         }
       )
     }
+
+  def toWesResponse(workflowId: WorkflowId, workflowState: WorkflowState):  WesRunStatus = {
+    WesRunStatus(workflowId.toString, WesState.fromCromwellStatus(workflowState))
+  }
+
+  def toWesResponseId(workflowId: WorkflowId): WesRunId ={
+    WesRunId(workflowId.toString)
+  }
+
+  def wesSubmitRequest(formData: Multipart.FormData, isSingleSubmission: Boolean): Route = {
+    def getWorkflowState(workflowOnHold: Boolean): WorkflowState = {
+      if (workflowOnHold)
+        WorkflowOnHold
+      else WorkflowSubmitted
+    }
+
+    def sendToWorkflowStore(command: WorkflowStoreActor.WorkflowStoreActorSubmitCommand, warnings: Seq[String], workflowState: WorkflowState): Route = {
+      // NOTE: Do not blindly copy the akka-http -to- ask-actor pattern below without knowing the pros and cons.
+      onComplete(workflowStoreActor.ask(command).mapTo[WorkflowStoreSubmitActor.WorkflowStoreSubmitActorResponse]) {
+        case Success(w) =>
+          w match {
+            case WorkflowStoreSubmitActor.WorkflowSubmittedToStore(workflowId, _) =>
+              completeResponse(StatusCodes.Created, toWesResponseId(workflowId), warnings)
+            case WorkflowStoreSubmitActor.WorkflowsBatchSubmittedToStore(workflowIds, _) =>
+              completeResponse(StatusCodes.Created, workflowIds.toList.map(toWesResponse(_, workflowState)), warnings)
+            case WorkflowStoreSubmitActor.WorkflowSubmitFailed(throwable) =>
+              respondWithWesError(throwable.getLocalizedMessage, StatusCodes.BadRequest)
+          }
+        case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => respondWithWesError("Cromwell service is shutting down", StatusCodes.InternalServerError)
+        case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
+        case Failure(e) => e.failRequest(StatusCodes.InternalServerError, warnings)
+      }
+    }
+
+    onComplete(materializeFormData(formData)) {
+      case Success(data) =>
+        PartialWorkflowSources.fromSubmitRoute(data, allowNoInputs = isSingleSubmission) match {
+          case Success(workflowSourceFiles) if isSingleSubmission && workflowSourceFiles.size == 1 =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            sendToWorkflowStore(WorkflowStoreActor.SubmitWorkflow(workflowSourceFiles.head), warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+          // Catches the case where someone has gone through the single submission endpoint w/ more than one workflow
+          case Success(workflowSourceFiles) if isSingleSubmission =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            val e = new IllegalArgumentException("To submit more than one workflow at a time, use the batch endpoint.")
+            e.failRequest(StatusCodes.BadRequest, warnings)
+          case Success(workflowSourceFiles) =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            sendToWorkflowStore(
+              WorkflowStoreActor.BatchSubmitWorkflows(NonEmptyList.fromListUnsafe(workflowSourceFiles.toList)),
+              warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+          case Failure(t) => t.failRequest(StatusCodes.BadRequest)
+        }
+      case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
+      case Failure(e) => respondWithWesError(e.getLocalizedMessage, StatusCodes.InternalServerError)
+    }
+  }
 }
 
+
+
 object WesRouteSupport {
+  import WesResponseJsonSupport._
+
+  implicit lazy val duration: FiniteDuration = ConfigFactory.load().as[FiniteDuration]("akka.http.server.request-timeout")
+  implicit lazy val timeout: Timeout = duration
+  import scala.concurrent.ExecutionContext.Implicits.global
+
   val NotFoundError = WesErrorResponse("The requested workflow run wasn't found", StatusCodes.NotFound.intValue)
 
   def WesAbortSuccessHandler: PartialFunction[SuccessfulAbortResponse, Route] = {
@@ -104,4 +198,38 @@ object WesRouteSupport {
   private def respondWithWesError(errorMsg: String, status: StatusCode): Route = {
     complete((status, WesErrorResponse(errorMsg, status.intValue)))
   }
-}
+
+  def extractSubmission(): Directive1[WesSubmission] = {
+    formFields((
+      "workflow_params".?,
+      "workflow_type".?,
+      "workflow_type_version".?,
+      "tags".?,
+      "workflow_engine_parameters".?,
+      "workflow_url".?,
+      "workflow_attachment".as[String].*
+    )).as(WesSubmission)
+  }
+
+  def completeCromwellResponse(future: => Future[WesResponse]): Route = {
+    onComplete(future) {
+      case Success(response: WesResponse) => complete(response)
+      case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
+    }
+  }
+
+  def listRuns(pageSize: Option[Int], pageToken: Option[String], serviceRegistryActor: ActorRef): Future[WesResponse] = {
+    // FIXME: to handle - page_size, page_token
+    // FIXME: How to handle next_page_token in response?
+    metadataQueryRequest(Seq.empty[(String, String)], serviceRegistryActor).map(RunListResponse.fromMetadataQueryResponse)
+  }
+
+  def runLog(workflowId: String, request: WorkflowId => BuildMetadataJsonAction, serviceRegistryActor: ActorRef): Future[WesResponse] = {
+    val metadataJsonResponse = metadataBuilderActorRequest(workflowId, request, serviceRegistryActor)
+
+    metadataJsonResponse.map {
+      case SuccessfulMetadataJsonResponse(_, responseJson) => WesRunLog.fromJson(responseJson.toString())
+      case FailedMetadataJsonResponse(_, reason) => WesErrorResponse(reason.getMessage, StatusCodes.InternalServerError.intValue)
+    }
+  }
+}
\ No newline at end of file
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
index 344498e51ab..c882ebf4f8b 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
@@ -1,6 +1,5 @@
 package cromwell.webservice.routes.wes
 
-import cromwell.webservice.routes.wes.WesState.WesState
 import spray.json.JsObject
 
 
@@ -20,15 +19,3 @@ final case class WesRunRequest(workflow_params: Option[JsObject],
                                workflow_engine_parameters: Option[JsObject],
                                workflow_url: Option[String]
                               )
-
-final case class WesRunLog(run_id: String,
-                           request: WesRunRequest,
-                           state: WesState,
-                           run_log: Option[WesLog],
-                           task_logs: Option[List[WesLog]],
-                           outputs: Option[JsObject]
-                          )
-
-object WesRunLog {
-  def fromJson(json: String): WesRunLog = CromwellMetadata.fromJson(json).wesRunLog
-}
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala
deleted file mode 100644
index ce4d60fe78e..00000000000
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala
+++ /dev/null
@@ -1,74 +0,0 @@
-package cromwell.webservice.routes.wes
-
-import akka.actor.ActorRef
-import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
-import akka.http.scaladsl.model.StatusCodes
-import akka.http.scaladsl.server.Directives._
-import akka.http.scaladsl.server.Route
-import akka.http.scaladsl.server.directives.RouteDirectives.complete
-import akka.util.Timeout
-import com.typesafe.config.ConfigFactory
-import cromwell.core.WorkflowId
-import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, GetSingleWorkflowMetadataAction}
-import cromwell.services.{FailedMetadataJsonResponse, SuccessfulMetadataJsonResponse}
-import cromwell.webservice.routes.MetadataRouteSupport.{metadataBuilderActorRequest, metadataQueryRequest}
-import cromwell.webservice.routes.wes.WesResponseJsonSupport.{WesResponseErrorFormat, WesResponseFormat}
-import cromwell.webservice.routes.wes.WesRunRoutes.{completeCromwellResponse, runLog}
-import net.ceedubs.ficus.Ficus._
-
-import scala.concurrent.ExecutionContext.Implicits.global
-import scala.concurrent.Future
-import scala.concurrent.duration.FiniteDuration
-import scala.util.{Failure, Success}
-
-trait WesRunRoutes {
-
-  val serviceRegistryActor: ActorRef
-
-  lazy val runRoutes: Route =
-    pathPrefix("ga4gh" / "wes" / "v1") {
-      concat(
-        pathPrefix("runs") {
-          get {
-            parameters(("page_size".as[Int].?, "page_token".?)) { (pageSize, pageToken) =>
-              WesRunRoutes.completeCromwellResponse(WesRunRoutes.listRuns(pageSize, pageToken, serviceRegistryActor))
-            }
-          }
-          path(Segment) { workflowId =>
-            get {
-              // this is what it was like in code found in the project… it perhaps isn’t ideal but doesn’t seem to hurt, so leaving it like this for now.
-              completeCromwellResponse(runLog(workflowId, (w: WorkflowId) => GetSingleWorkflowMetadataAction(w, None, None, expandSubWorkflows = false), serviceRegistryActor))
-            }
-          }
-        }
-      )
-    }
-}
-
-object WesRunRoutes {
-
-  implicit lazy val duration: FiniteDuration = ConfigFactory.load().as[FiniteDuration]("akka.http.server.request-timeout")
-  implicit lazy val timeout: Timeout = duration
-
-  def completeCromwellResponse(future: => Future[WesResponse]): Route = {
-    onComplete(future) {
-      case Success(response: WesResponse) => complete(response)
-      case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
-    }
-  }
-
-  def listRuns(pageSize: Option[Int], pageToken: Option[String], serviceRegistryActor: ActorRef): Future[WesResponse] = {
-    // FIXME: to handle - page_size, page_token
-    // FIXME: How to handle next_page_token in response?
-    metadataQueryRequest(Seq.empty[(String, String)], serviceRegistryActor).map(RunListResponse.fromMetadataQueryResponse)
-  }
-
-  def runLog(workflowId: String, request: WorkflowId => BuildMetadataJsonAction, serviceRegistryActor: ActorRef): Future[WesResponse] = {
-    val metadataJsonResponse = metadataBuilderActorRequest(workflowId, request, serviceRegistryActor)
-
-    metadataJsonResponse.map {
-      case SuccessfulMetadataJsonResponse(_, responseJson) => WesResponseWorkflowMetadata(WesRunLog.fromJson(responseJson.toString()))
-      case FailedMetadataJsonResponse(_, reason) => WesErrorResponse(reason.getMessage, StatusCodes.InternalServerError.intValue)
-    }
-  }
-}
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala
new file mode 100644
index 00000000000..1db2cd801b8
--- /dev/null
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala
@@ -0,0 +1,44 @@
+package cromwell.webservice.routes.wes
+
+import akka.http.scaladsl.model.{HttpEntity, MediaTypes, Multipart}
+import cromwell.webservice.PartialWorkflowSources._
+
+final case class WesSubmission(workflowParams: Option[String],
+                               workflowType: Option[String],
+                               workflowTypeVersion: Option[String],
+                               tags: Option[String],
+                               workflowEngineParameters: Option[String],
+                               workflowUrl: Option[String],
+                               workflowAttachment: Iterable[String]
+                              ) {
+  val entity: Multipart.FormData = {
+    /*
+      FIXME:
+
+      Super oversimplification going on here as Cromwell's API is expected to normalize w/ WES a bit over the course
+      of the quarter and it's not worth doing it here and throwing it out later (there's close to a 0% chance this will
+      be used between now and then)
+
+      At the moment, just taking the head of workflowAttachment (if it exists) and dropping that into the workflow source,
+      and we're ignoring the possible existence of a zip bundle. Eventually the way this will work is that there'll be
+      an Iterable of workflow files and workflowUrl will point to which one is the source and the rest goes into the bundle.
+
+      NB: I think we've already lost too much information for the above to happen as there's an optional use of
+      Content-Disposition headers on each of these files which can be used to describe directory structure and such
+      for relative import resolution
+     */
+    val sourcePart = workflowAttachment.headOption map { a => Multipart.FormData.BodyPart(WorkflowSourceKey, HttpEntity(MediaTypes.`application/json`, a)) }
+
+    val urlPart = workflowUrl map { u => Multipart.FormData.BodyPart(WorkflowUrlKey, HttpEntity(MediaTypes.`application/json`, u)) }
+
+    val typePart = workflowType map { w => Multipart.FormData.BodyPart(WorkflowTypeKey, HttpEntity(MediaTypes.`application/json`, w)) }
+    val typeVersionPart = workflowTypeVersion map { v => Multipart.FormData.BodyPart(WorkflowTypeVersionKey, HttpEntity(MediaTypes.`application/json`, v)) }
+    val inputsPart = workflowParams map { p => Multipart.FormData.BodyPart(WorkflowInputsKey, HttpEntity(MediaTypes.`application/json`, p)) }
+    val optionsPart = workflowEngineParameters map { o => Multipart.FormData.BodyPart(WorkflowOptionsKey, HttpEntity(MediaTypes.`application/json`, o)) }
+    val labelsPart = tags map { t => Multipart.FormData.BodyPart(labelsKey, HttpEntity(MediaTypes.`application/json`, t)) }
+
+    val parts = List(sourcePart, urlPart, typePart, typeVersionPart, inputsPart, optionsPart, labelsPart).flatten
+
+    Multipart.FormData(parts: _*)
+  }
+}
diff --git a/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala b/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
index 4b3461ae7d3..b01d52eece0 100644
--- a/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
@@ -20,13 +20,14 @@ import org.mockito.Mockito.{times, verify, when}
 import org.scalatest.flatspec.AsyncFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import common.mock.MockSugar
+import cromwell.filesystems.blob.BlobPath
 
 import java.nio.file.NoSuchFileException
 import java.util.UUID
 import scala.concurrent.ExecutionContext
 import scala.concurrent.duration._
 import scala.language.postfixOps
-import scala.util.Failure
+import scala.util.{Failure, Success, Try}
 import scala.util.control.NoStackTrace
 
 class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with MockSugar {
@@ -127,6 +128,23 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     }
   }
 
+  it should "get hash from a BlobPath when stored hash exists" in {
+    val testPath = mock[BlobPath]
+    val hashString = "2d01d5d9c24034d54fe4fba0ede5182d" // echo "hello there" | md5sum
+    testPath.md5HexString returns Try(Option(hashString))
+
+    val context = DefaultCommandContext(hashCommand(testPath).get, replyTo)
+    val testSource = Source.single(context)
+
+    val stream = testSource.via(flow).toMat(readSink)(Keep.right)
+
+    stream.run() map {
+      case (success: IoSuccess[_], _) => assert(success.result.asInstanceOf[String] == hashString)
+      case (ack, _) =>
+        fail(s"read returned an unexpected message:\n$ack\n\n")
+    }
+  }
+
   it should "fail if DrsPath hash doesn't match checksum" in {
     val testPath = mock[DrsPath]
     when(testPath.limitFileContent(any[Option[Int]], any[Boolean])(any[ExecutionContext])).thenReturn("hello".getBytes)
@@ -171,6 +189,25 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     }
   }
 
+  it should "succeed if a BlobPath is missing a stored hash" in {
+    val testPath = mock[BlobPath]
+    when(testPath.limitFileContent(any[Option[Int]], any[Boolean])(any[ExecutionContext]))
+      .thenReturn("hello there".getBytes)
+    when(testPath.md5HexString)
+      .thenReturn(Success(None))
+
+    val context = DefaultCommandContext(contentAsStringCommand(testPath, Option(100), failOnOverflow = true).get, replyTo)
+    val testSource = Source.single(context)
+
+    val stream = testSource.via(flow).toMat(readSink)(Keep.right)
+
+    stream.run() map {
+      case (success: IoSuccess[_], _) => assert(success.result.asInstanceOf[String] == "hello there")
+      case (ack, _) =>
+        fail(s"read returned an unexpected message:\n$ack\n\n")
+    }
+  }
+
   it should "copy Nio paths" in {
     val testPath = DefaultPathBuilder.createTempFile()
     val testCopyPath = testPath.sibling(UUID.randomUUID().toString)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
index 40b628a700d..095721569e7 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
@@ -11,7 +11,7 @@ import scala.util.{Failure, Success, Try}
 class ValidatingCachingConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
 
     it should "run config tests" in {
-      val cases = Table(
+      val cases = Table[String, Any](
         ("config"                 , "exceptionMessage"                                                              ),
         ("enabled = not-a-boolean", "String: 1: enabled has type STRING rather than BOOLEAN"                        ),
         ("enabled = true"         , true                                                                            ),
diff --git a/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
index ed4e588cfd1..24cce8ae932 100644
--- a/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
@@ -11,7 +11,7 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 import org.yaml.snakeyaml.constructor.Constructor
 import org.yaml.snakeyaml.error.YAMLException
 import org.yaml.snakeyaml.nodes.MappingNode
-import org.yaml.snakeyaml.{Yaml => SnakeYaml}
+import org.yaml.snakeyaml.{LoaderOptions, Yaml => SnakeYaml}
 
 import scala.jdk.CollectionConverters._
 
@@ -28,7 +28,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
         status should be(StatusCodes.OK)
 
         val body = responseAs[String]
-        val yaml = new SnakeYaml(new UniqueKeyConstructor()).loadAs(body, classOf[java.util.Map[String, AnyRef]])
+        val yaml = new SnakeYaml(new UniqueKeyConstructor(new LoaderOptions)).loadAs(body, classOf[java.util.Map[String, AnyRef]])
 
         yaml.get("swagger") should be("2.0")
       }
@@ -100,7 +100,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
   * Adapted from:
   * https://bitbucket.org/asomov/snakeyaml/src/e9cd9f5e8d76c61eb983e29b3dc039c1fac9c393/src/test/java/org/yaml/snakeyaml/issues/issue139/UniqueKeyTest.java?fileviewer=file-view-default#UniqueKeyTest.java-43:62
   */
-class UniqueKeyConstructor extends Constructor {
+class UniqueKeyConstructor(val loaderOptions: LoaderOptions) extends Constructor(loaderOptions) {
 
   import java.util.{Map => JMap}
 
diff --git a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
index 2a3b11a41c5..c40c84397f7 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
@@ -1,7 +1,5 @@
 package cromwell.webservice.routes
 
-import java.time.OffsetDateTime
-
 import akka.actor.{Actor, ActorLogging, ActorSystem, Props}
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
 import akka.http.scaladsl.model.ContentTypes._
@@ -17,13 +15,13 @@ import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor._
 import cromwell.engine.workflow.workflowstore.WorkflowStoreEngineActor.{WorkflowOnHoldToSubmittedFailure, WorkflowOnHoldToSubmittedSuccess}
 import cromwell.engine.workflow.workflowstore.WorkflowStoreSubmitActor.{WorkflowSubmittedToStore, WorkflowsBatchSubmittedToStore}
+import cromwell.services._
 import cromwell.services.healthmonitor.ProtoHealthMonitorServiceActor.{GetCurrentStatus, StatusCheckResponse, SubsystemStatus}
 import cromwell.services.instrumentation.InstrumentationService.InstrumentationServiceMessage
 import cromwell.services.metadata.MetadataArchiveStatus._
 import cromwell.services.metadata.MetadataService._
 import cromwell.services.metadata._
 import cromwell.services.metadata.impl.builder.MetadataBuilderActor
-import cromwell.services._
 import cromwell.services.womtool.WomtoolServiceMessages.{DescribeFailure, DescribeRequest, DescribeSuccess}
 import cromwell.services.womtool.models.WorkflowDescription
 import cromwell.util.SampleWdl.HelloWorld
@@ -34,6 +32,7 @@ import org.scalatest.flatspec.AsyncFlatSpec
 import org.scalatest.matchers.should.Matchers
 import spray.json._
 
+import java.time.OffsetDateTime
 import scala.concurrent.duration._
 
 class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with Matchers {
@@ -529,6 +528,7 @@ object CromwellApiServiceSpec {
   val WorkflowIdExistingOnlyInSummaryTable = WorkflowId.fromString("f0000000-0000-0000-0000-000000000011")
   val ArchivedWorkflowId = WorkflowId.fromString("c4c6339c-2145-47fb-acc5-b5cb8d2809f5")
   val ArchivedAndDeletedWorkflowId = WorkflowId.fromString("abc1234d-2145-47fb-acc5-b5cb8d2809f5")
+  val wesWorkflowId = WorkflowId.randomId()
   val SummarizedWorkflowIds = Set(
     SummarizedWorkflowId,
     WorkflowIdExistingOnlyInSummaryTable,
@@ -545,7 +545,8 @@ object CromwellApiServiceSpec {
     FailedWorkflowId,
     SummarizedWorkflowId,
     ArchivedWorkflowId,
-    ArchivedAndDeletedWorkflowId
+    ArchivedAndDeletedWorkflowId,
+    wesWorkflowId
   )
 
   class MockApiService()(implicit val system: ActorSystem) extends CromwellApiService {
@@ -564,13 +565,21 @@ object CromwellApiServiceSpec {
       List(
         MetadataEvent(MetadataKey(workflowId, None, "testKey1a"), MetadataValue("myValue1a", MetadataString)),
         MetadataEvent(MetadataKey(workflowId, None, "testKey1b"), MetadataValue("myValue1b", MetadataString)),
-        MetadataEvent(MetadataKey(workflowId, None, "testKey2a"), MetadataValue("myValue2a", MetadataString))
+        MetadataEvent(MetadataKey(workflowId, None, "testKey2a"), MetadataValue("myValue2a", MetadataString)),
+      )
+    }
+    private def wesFullMetadataResponse(workflowId: WorkflowId) = {
+      List(
+        MetadataEvent(MetadataKey(workflowId, None, "status"), MetadataValue("Running", MetadataString)),
+        MetadataEvent(MetadataKey(workflowId, None, "submittedFiles:workflow"), MetadataValue("myValue2a", MetadataString)),
+
       )
     }
 
     def responseMetadataValues(workflowId: WorkflowId, withKeys: List[String], withoutKeys: List[String]): JsObject = {
       def keyFilter(keys: List[String])(m: MetadataEvent) = keys.exists(k => m.key.key.startsWith(k))
-      val events = fullMetadataResponse(workflowId)
+      val metadataEvents = if (workflowId == wesWorkflowId) wesFullMetadataResponse(workflowId) else fullMetadataResponse(workflowId)
+      val events = metadataEvents
         .filter(m => withKeys.isEmpty || keyFilter(withKeys)(m))
         .filter(m => withoutKeys.isEmpty || !keyFilter(withoutKeys)(m))
 
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
index b4d775f7389..e32316f3649 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
@@ -22,7 +22,7 @@ class ServiceInfoSpec extends AsyncFlatSpec with ScalatestRouteTest with Matcher
 
   behavior of "ServiceInfo"
 
-  val expectedResponse = WesStatusInfoResponse(Map("CWL" -> Set("v1.0"), "WDL" -> Set("draft-2", "1.0", "biscayne")),
+  val expectedResponse = WesStatusInfoResponse(Map("WDL" -> Set("draft-2", "1.0", "biscayne")),
     List("1.0"),
     Set("ftp", "s3", "drs", "gcs", "http"),
     Map("Cromwell" -> CromwellApiService.cromwellVersion),
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
index 0c0fe1c8054..00a361a3174 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
@@ -1,22 +1,27 @@
 package cromwell.webservice.routes.wes
 
 import akka.actor.Props
-import akka.http.scaladsl.model.StatusCodes
 import akka.http.scaladsl.model.HttpMethods.POST
-import akka.http.scaladsl.testkit.ScalatestRouteTest
+import akka.http.scaladsl.model._
+import akka.http.scaladsl.server.MethodRejection
+import akka.http.scaladsl.testkit.{RouteTestTimeout, ScalatestRouteTest}
+import cromwell.util.SampleWdl.HelloWorld
 import cromwell.webservice.routes.CromwellApiServiceSpec
-
-import scala.concurrent.duration._
 import cromwell.webservice.routes.CromwellApiServiceSpec.{MockServiceRegistryActor, MockWorkflowManagerActor, MockWorkflowStoreActor}
+import cromwell.webservice.routes.wes.WesResponseJsonSupport._
 import org.scalatest.flatspec.AsyncFlatSpec
 import org.scalatest.matchers.should.Matchers
-import WesResponseJsonSupport._
-import akka.http.scaladsl.server.MethodRejection
+import spray.json._
+
+import scala.concurrent.duration._
 
 class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Matchers with WesRouteSupport {
+
   val actorRefFactory = system
   override implicit val ec = system.dispatcher
-  override implicit val timeout = 5.seconds
+  override val timeout = routeTestTimeout.duration
+  implicit def routeTestTimeout = RouteTestTimeout(5.seconds)
+
 
   override val workflowStoreActor = actorRefFactory.actorOf(Props(new MockWorkflowStoreActor()))
   override val serviceRegistryActor = actorRefFactory.actorOf(Props(new MockServiceRegistryActor()))
@@ -149,4 +154,52 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
         rejection shouldEqual MethodRejection(POST)
       }
   }
-}
+
+  behavior of "WES API /runs POST endpoint"
+  it should "return 201 for a successful workflow submission" in {
+    val workflowSource = Multipart.FormData.BodyPart("workflow_url", HttpEntity(MediaTypes.`application/json`, "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"))
+    val workflowInputs = Multipart.FormData.BodyPart("workflow_params", HttpEntity(MediaTypes.`application/json`, HelloWorld.rawInputs.toJson.toString()))
+    val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
+    Post(s"/ga4gh/wes/$version/runs", formData) ~>
+      wesRoutes ~>
+      check {
+        assertResult(
+          s"""{
+             |  "run_id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}"
+             |}""".stripMargin) {
+          responseAs[String].parseJson.prettyPrint
+        }
+        assertResult(StatusCodes.Created) {
+          status
+        }
+        headers should be(Seq.empty)
+      }
+  }
+
+
+  behavior of "WES API /runs GET endpoint"
+  it should "return results for a good query" in {
+    Get(s"/ga4gh/wes/v1/runs") ~>
+      wesRoutes ~>
+      check {
+        status should be(StatusCodes.OK)
+        contentType should be(ContentTypes.`application/json`)
+        val results = responseAs[JsObject].fields("runs").convertTo[Seq[JsObject]]
+        results.head.fields("run_id") should be(JsString(CromwellApiServiceSpec.ExistingWorkflowId.toString))
+        results.head.fields("state") should be(JsString("COMPLETE"))
+      }
+  }
+
+  behavior of "WES API /runs/{run_id} endpoint"
+  it should "return valid metadata when supplied a run_id" in {
+    Get(s"/ga4gh/wes/v1/runs/${CromwellApiServiceSpec.wesWorkflowId}") ~>
+      wesRoutes ~>
+      check {
+        status should be(StatusCodes.OK)
+        val result = responseAs[JsObject]
+        result.fields.keys should contain allOf("request", "run_id", "state")
+        result.fields("state") should be(JsString("RUNNING"))
+        result.fields("run_id") should be(JsString(CromwellApiServiceSpec.wesWorkflowId.toString))
+      }
+  }
+}
\ No newline at end of file
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
new file mode 100644
index 00000000000..ae84e39adbe
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
@@ -0,0 +1,52 @@
+package cromwell.filesystems.blob
+
+import cats.implicits.catsSyntaxValidatedId
+import com.azure.core.credential.TokenRequestContext
+import com.azure.core.management.AzureEnvironment
+import com.azure.core.management.profile.AzureProfile
+import com.azure.identity.DefaultAzureCredentialBuilder
+import common.validation.ErrorOr.ErrorOr
+
+import scala.concurrent.duration._
+import scala.jdk.DurationConverters._
+
+import scala.util.{Failure, Success, Try}
+
+/**
+  * Strategy for obtaining an access token in an environment with available Azure identity.
+  * If you need to disambiguate among multiple active user-assigned managed identities, pass
+  * in the client id of the identity that should be used.
+  */
+case object AzureCredentials {
+
+  final val tokenAcquisitionTimeout = 5.seconds
+
+  val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
+  val tokenScope = "https://management.azure.com/.default"
+
+  private def tokenRequestContext: TokenRequestContext = {
+    val trc = new TokenRequestContext()
+    trc.addScopes(tokenScope)
+    trc
+  }
+
+  private def defaultCredentialBuilder: DefaultAzureCredentialBuilder =
+    new DefaultAzureCredentialBuilder()
+      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
+
+  def getAccessToken(identityClientId: Option[String]): ErrorOr[String] = {
+    val credentials = identityClientId.foldLeft(defaultCredentialBuilder) {
+      (builder, clientId) => builder.managedIdentityClientId(clientId)
+    }.build()
+
+    Try(
+      credentials
+        .getToken(tokenRequestContext)
+        .block(tokenAcquisitionTimeout.toJava)
+    ) match {
+      case Success(null) => "null token value attempting to obtain access token".invalidNel
+      case Success(token) => token.getToken.validNel
+      case Failure(error) => s"Failed to refresh access token: ${error.getMessage}".invalidNel
+    }
+  }
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
new file mode 100644
index 00000000000..f68bf7f5176
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
@@ -0,0 +1,75 @@
+package cromwell.filesystems.blob
+
+import cats.implicits.catsSyntaxValidatedId
+import cats.syntax.apply._
+import com.typesafe.config.Config
+import common.validation.Validation._
+import net.ceedubs.ficus.Ficus._
+
+import java.util.UUID
+
+// WSM config is needed for accessing WSM-managed blob containers created in Terra workspaces.
+// If the identity executing Cromwell has native access to the blob container, this can be ignored.
+final case class WorkspaceManagerConfig(url: WorkspaceManagerURL,
+                                        workspaceId: WorkspaceId,
+                                        containerResourceId: ContainerResourceId,
+                                        overrideWsmAuthToken: Option[String]) // dev-only
+
+final case class BlobFileSystemConfig(endpointURL: EndpointURL,
+                                      blobContainerName: BlobContainerName,
+                                      subscriptionId: Option[SubscriptionId],
+                                      expiryBufferMinutes: Long,
+                                      workspaceManagerConfig: Option[WorkspaceManagerConfig])
+
+object BlobFileSystemConfig {
+
+  final val defaultExpiryBufferMinutes = 10L
+
+  def apply(config: Config): BlobFileSystemConfig = {
+    val endpointURL = parseString(config, "endpoint").map(EndpointURL)
+    val blobContainer = parseString(config, "container").map(BlobContainerName)
+    val subscriptionId = parseUUIDOpt(config, "subscription").map(_.map(SubscriptionId))
+    val expiryBufferMinutes =
+      parseLongOpt(config, "expiry-buffer-minutes")
+        .map(_.getOrElse(defaultExpiryBufferMinutes))
+
+    val wsmConfig =
+      if (config.hasPath("workspace-manager")) {
+        val wsmConf = config.getConfig("workspace-manager")
+        val wsmURL = parseString(wsmConf, "url").map(WorkspaceManagerURL)
+        val workspaceId = parseUUID(wsmConf, "workspace-id").map(WorkspaceId)
+        val containerResourceId = parseUUID(wsmConf, "container-resource-id").map(ContainerResourceId)
+        val overrideWsmAuthToken = parseStringOpt(wsmConf, "b2cToken")
+
+        (wsmURL, workspaceId, containerResourceId, overrideWsmAuthToken)
+          .mapN(WorkspaceManagerConfig)
+          .map(Option(_))
+      }
+      else None.validNel
+
+    (endpointURL, blobContainer, subscriptionId, expiryBufferMinutes, wsmConfig)
+      .mapN(BlobFileSystemConfig.apply)
+      .unsafe("Couldn't parse blob filesystem config")
+  }
+
+  private def parseString(config: Config, path: String) =
+    validate[String] { config.as[String](path) }
+
+  private def parseStringOpt(config: Config, path: String) =
+    validate[Option[String]] { config.as[Option[String]](path) }
+
+  private def parseUUID(config: Config, path: String) =
+    validate[UUID] { UUID.fromString(config.as[String](path)) }
+
+  private def parseUUIDOpt(config: Config, path: String) =
+    validate[Option[UUID]] { config.as[Option[String]](path).map(UUID.fromString) }
+
+  private def parseLongOpt(config: Config, path: String) =
+    validate[Option[Long]] { config.as[Option[Long]](path) }
+}
+
+// Our filesystem setup magic can't use BlobFileSystemConfig.apply directly, so we need this
+// wrapper class.
+class BlobFileSystemConfigWrapper(val config: BlobFileSystemConfig) {
+  def this(config: Config) = this(BlobFileSystemConfig(config))
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
new file mode 100644
index 00000000000..7b198f09f6f
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -0,0 +1,267 @@
+package cromwell.filesystems.blob
+
+import com.azure.core.credential.AzureSasCredential
+import com.azure.core.management.AzureEnvironment
+import com.azure.core.management.profile.AzureProfile
+import com.azure.identity.DefaultAzureCredentialBuilder
+import com.azure.resourcemanager.AzureResourceManager
+import com.azure.resourcemanager.storage.models.StorageAccountKey
+import com.azure.storage.blob.nio.AzureFileSystem
+import com.azure.storage.blob.sas.{BlobContainerSasPermission, BlobServiceSasSignatureValues}
+import com.azure.storage.blob.{BlobContainerClient, BlobContainerClientBuilder}
+import com.azure.storage.common.StorageSharedKeyCredential
+import com.typesafe.config.Config
+import com.typesafe.scalalogging.LazyLogging
+import common.validation.Validation._
+
+import java.net.URI
+import java.nio.file.{FileSystem, FileSystemNotFoundException, FileSystems}
+import java.time.temporal.ChronoUnit
+import java.time.{Duration, Instant, OffsetDateTime}
+import scala.jdk.CollectionConverters._
+import scala.util.{Failure, Success, Try}
+
+// We encapsulate this functionality here so that we can easily mock it out, to allow for testing without
+// actually connecting to Blob storage.
+case class FileSystemAPI() {
+  def getFileSystem(uri: URI): Try[FileSystem] = Try(FileSystems.getFileSystem(uri))
+  def newFileSystem(uri: URI, config: Map[String, Object]): FileSystem = FileSystems.newFileSystem(uri, config.asJava)
+  def closeFileSystem(uri: URI): Option[Unit] = getFileSystem(uri).toOption.map(_.close)
+}
+/**
+  * The BlobFileSystemManager is an object that is responsible for managing the open filesystem,
+  * and refreshing the SAS token that is used to access the blob container containing that filesystem.
+  *
+  * See BlobSasTokenGenerator for more information on how a SAS token is generated
+  */
+object BlobFileSystemManager {
+  def parseTokenExpiry(token: AzureSasCredential): Option[Instant] = for {
+    expiryString <- token.getSignature.split("&").find(_.startsWith("se")).map(_.replaceFirst("se=","")).map(_.replace("%3A", ":"))
+    instant = Instant.parse(expiryString)
+  } yield instant
+
+  def buildConfigMap(credential: AzureSasCredential, container: BlobContainerName): Map[String, Object] = {
+    Map((AzureFileSystem.AZURE_STORAGE_SAS_TOKEN_CREDENTIAL, credential),
+      (AzureFileSystem.AZURE_STORAGE_FILE_STORES, container.value),
+      (AzureFileSystem.AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK, java.lang.Boolean.TRUE))
+  }
+  def hasTokenExpired(tokenExpiry: Instant, buffer: Duration): Boolean = Instant.now.plus(buffer).isAfter(tokenExpiry)
+  def uri(endpoint: EndpointURL) = new URI("azb://?endpoint=" + endpoint)
+}
+
+class BlobFileSystemManager(val container: BlobContainerName,
+                            val endpoint: EndpointURL,
+                            val expiryBufferMinutes: Long,
+                            val blobTokenGenerator: BlobSasTokenGenerator,
+                            val fileSystemAPI: FileSystemAPI = FileSystemAPI(),
+                            private val initialExpiration: Option[Instant] = None) extends LazyLogging {
+
+  def this(config: BlobFileSystemConfig) = {
+    this(
+      config.blobContainerName,
+      config.endpointURL,
+      config.expiryBufferMinutes,
+      BlobSasTokenGenerator.createBlobTokenGeneratorFromConfig(config)
+    )
+  }
+
+  def this(rawConfig: Config) = this(BlobFileSystemConfig(rawConfig))
+
+  val buffer: Duration = Duration.of(expiryBufferMinutes, ChronoUnit.MINUTES)
+  private var expiry: Option[Instant] = initialExpiration
+
+  def getExpiry: Option[Instant] = expiry
+  def uri: URI = BlobFileSystemManager.uri(endpoint)
+  def isTokenExpired: Boolean = expiry.exists(BlobFileSystemManager.hasTokenExpired(_, buffer))
+  def shouldReopenFilesystem: Boolean = isTokenExpired || expiry.isEmpty
+  def retrieveFilesystem(): Try[FileSystem] = {
+    synchronized {
+      shouldReopenFilesystem match {
+        case false => fileSystemAPI.getFileSystem(uri).recoverWith {
+          // If no filesystem already exists, this will create a new connection, with the provided configs
+          case _: FileSystemNotFoundException =>
+            logger.info(s"Creating new blob filesystem for URI $uri")
+            blobTokenGenerator.generateBlobSasToken.flatMap(generateFilesystem(uri, container, _))
+        }
+        // If the token has expired, OR there is no token record, try to close the FS and regenerate
+        case true =>
+          logger.info(s"Closing & regenerating token for existing blob filesystem at URI $uri")
+          fileSystemAPI.closeFileSystem(uri)
+          blobTokenGenerator.generateBlobSasToken.flatMap(generateFilesystem(uri, container, _))
+      }
+    }
+  }
+
+  private def generateFilesystem(uri: URI, container: BlobContainerName, token: AzureSasCredential): Try[FileSystem] = {
+    expiry = BlobFileSystemManager.parseTokenExpiry(token)
+    if (expiry.isEmpty) return Failure(new Exception("Could not reopen filesystem, no expiration found"))
+    Try(fileSystemAPI.newFileSystem(uri, BlobFileSystemManager.buildConfigMap(token, container)))
+  }
+
+}
+
+sealed trait BlobSasTokenGenerator { def generateBlobSasToken: Try[AzureSasCredential] }
+object BlobSasTokenGenerator {
+
+  /**
+    * Creates the correct BlobSasTokenGenerator based on config inputs. This generator is responsible for producing
+    * a valid SAS token for use in accessing a Azure blob storage container.
+    * Two types of generators can be produced here:
+    * > Workspace Manager (WSM) mediated SAS token generator, used to create SAS tokens that allow access for
+    * blob containers mediated by the WSM, and is enabled when a WSM config is provided. This is what is intended
+    * for use inside Terra
+    *    OR
+    * > Native SAS token generator, which obtains a valid SAS token from your local environment to reach blob containers
+    * your local azure identity has access to and is the default if a WSM config is not found. This is intended for
+    * use outside of Terra
+    *
+    * Both of these generators require an authentication token to authorize the generation of the SAS token.
+    * See BlobSasTokenGenerator for more information on how these generators work.
+    *
+    * @param config A BlobFileSystemConfig object
+    * @return An appropriate BlobSasTokenGenerator
+    */
+  def createBlobTokenGeneratorFromConfig(config: BlobFileSystemConfig): BlobSasTokenGenerator =
+    config.workspaceManagerConfig.map { wsmConfig =>
+      val wsmClient: WorkspaceManagerApiClientProvider = new HttpWorkspaceManagerClientProvider(wsmConfig.url)
+
+      // WSM-mediated mediated SAS token generator
+      // parameterizing client instead of URL to make injecting mock client possible
+      BlobSasTokenGenerator.createBlobTokenGenerator(
+        config.blobContainerName,
+        config.endpointURL,
+        wsmConfig.workspaceId,
+        wsmConfig.containerResourceId,
+        wsmClient,
+        wsmConfig.overrideWsmAuthToken
+      )
+    }.getOrElse(
+      // Native SAS token generator
+      BlobSasTokenGenerator.createBlobTokenGenerator(config.blobContainerName, config.endpointURL, config.subscriptionId)
+    )
+
+  /**
+    * Native SAS token generator, uses the DefaultAzureCredentialBuilder in the local environment
+    * to produce a SAS token.
+    *
+    * @param container The BlobContainerName of the blob container to be accessed by the generated SAS token
+    * @param endpoint The EndpointURL containing the storage account of the blob container to be accessed by
+    * this SAS token
+    * @param subscription Optional subscription parameter to use for local authorization.
+    * If one is not provided the default subscription is used
+    * @return A NativeBlobTokenGenerator, able to produce a valid SAS token for accessing the provided blob
+    * container and endpoint locally
+    */
+  def createBlobTokenGenerator(container: BlobContainerName,
+                               endpoint: EndpointURL,
+                               subscription: Option[SubscriptionId]): BlobSasTokenGenerator = {
+    NativeBlobSasTokenGenerator(container, endpoint, subscription)
+  }
+
+  /**
+    * WSM-mediated SAS token generator, uses the DefaultAzureCredentialBuilder in the cloud environment
+    * to request a SAS token from the WSM to access the given blob container. If an overrideWsmAuthToken
+    * is provided this is used instead.
+    *
+    * @param container The BlobContainerName of the blob container to be accessed by the generated SAS token
+    * @param endpoint The EndpointURL containing the storage account of the blob container to be accessed by
+    * this SAS token
+    * @param workspaceId The WorkspaceId of the account to authenticate against
+    * @param containerResourceId The ContainterResourceId of the blob container as WSM knows it
+    * @param workspaceManagerClient The client for making requests against WSM
+    * @param overrideWsmAuthToken An optional WsmAuthToken used for authenticating against the WSM for a valid
+    * SAS token to access the given container and endpoint. This is a dev only option that is only intended
+    * for local testing of the WSM interface
+    * @return A WSMBlobTokenGenerator, able to produce a valid SAS token for accessing the provided blob
+    * container and endpoint that is managed by WSM
+    */
+  def createBlobTokenGenerator(container: BlobContainerName,
+                               endpoint: EndpointURL,
+                               workspaceId: WorkspaceId,
+                               containerResourceId: ContainerResourceId,
+                               workspaceManagerClient: WorkspaceManagerApiClientProvider,
+                               overrideWsmAuthToken: Option[String]): BlobSasTokenGenerator = {
+    WSMBlobSasTokenGenerator(container, endpoint, workspaceId, containerResourceId, workspaceManagerClient, overrideWsmAuthToken)
+  }
+
+}
+
+case class WSMBlobSasTokenGenerator(container: BlobContainerName,
+                                    endpoint: EndpointURL,
+                                    workspaceId: WorkspaceId,
+                                    containerResourceId: ContainerResourceId,
+                                    wsmClientProvider: WorkspaceManagerApiClientProvider,
+                                    overrideWsmAuthToken: Option[String]) extends BlobSasTokenGenerator {
+
+  /**
+    * Generate a BlobSasToken by using the available authorization information
+    * If an overrideWsmAuthToken is provided, use this in the wsmClient request
+    * Else try to use the environment azure identity to request the SAS token
+    *
+    * @return an AzureSasCredential for accessing a blob container
+    */
+  def generateBlobSasToken: Try[AzureSasCredential] = {
+    val wsmAuthToken: Try[String] = overrideWsmAuthToken match {
+      case Some(t) => Success(t)
+      case None => AzureCredentials.getAccessToken(None).toTry
+    }
+
+    for {
+      wsmAuth <- wsmAuthToken
+      wsmClient = wsmClientProvider.getControlledAzureResourceApi(wsmAuth)
+      sasToken <- Try(  // Java library throws
+        wsmClient.createAzureStorageContainerSasToken(
+          workspaceId.value,
+          containerResourceId.value,
+          null,
+          null,
+          null,
+          null
+        ).getToken)
+    } yield new AzureSasCredential(sasToken)
+  }
+}
+
+case class NativeBlobSasTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId] = None) extends BlobSasTokenGenerator {
+  private val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
+  private def azureCredentialBuilder = new DefaultAzureCredentialBuilder()
+      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
+      .build
+  private def authenticateWithSubscription(sub: SubscriptionId) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub.toString)
+  private def authenticateWithDefaultSubscription = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withDefaultSubscription()
+  private def azure = subscription.map(authenticateWithSubscription(_)).getOrElse(authenticateWithDefaultSubscription)
+
+  private def findAzureStorageAccount(name: StorageAccountName) = azure.storageAccounts.list.asScala.find(_.name.equals(name.value))
+      .map(Success(_)).getOrElse(Failure(new Exception("Azure Storage Account not found")))
+  private def buildBlobContainerClient(credential: StorageSharedKeyCredential, endpoint: EndpointURL, container: BlobContainerName): BlobContainerClient = {
+    new BlobContainerClientBuilder()
+        .credential(credential)
+        .endpoint(endpoint.value)
+        .containerName(container.value)
+        .buildClient()
+  }
+  private val bcsp = new BlobContainerSasPermission()
+    .setReadPermission(true)
+    .setCreatePermission(true)
+    .setListPermission(true)
+    .setWritePermission(true)
+
+  /**
+    * Generate a BlobSasToken by using the local environment azure identity
+    * This will use a default subscription if one is not provided.
+    *
+    * @return an AzureSasCredential for accessing a blob container
+    */
+  def generateBlobSasToken: Try[AzureSasCredential] = for {
+    uri <- BlobPathBuilder.parseURI(endpoint.value)
+    configuredAccount <- BlobPathBuilder.parseStorageAccount(uri)
+    azureAccount <- findAzureStorageAccount(configuredAccount)
+    keys = azureAccount.getKeys.asScala
+    key <- keys.headOption.fold[Try[StorageAccountKey]](Failure(new Exception("Storage account has no keys")))(Success(_))
+    first = key.value
+    sskc = new StorageSharedKeyCredential(configuredAccount.value, first)
+    bcc = buildBlobContainerClient(sskc, endpoint, container)
+    bsssv = new BlobServiceSasSignatureValues(OffsetDateTime.now.plusDays(1), bcsp)
+    asc = new AzureSasCredential(bcc.generateSas(bsssv))
+  } yield asc
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 038936ec46e..1be6bb8e13b 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -1,20 +1,14 @@
 package cromwell.filesystems.blob
 
-import com.azure.core.credential.AzureSasCredential
-import com.azure.storage.blob.nio.AzureFileSystem
+import com.azure.storage.blob.nio.{AzureBlobFileAttributes}
 import com.google.common.net.UrlEscapers
-import cromwell.core.path.NioPath
-import cromwell.core.path.Path
-import cromwell.core.path.PathBuilder
+import cromwell.core.path.{NioPath, Path, PathBuilder}
 import cromwell.filesystems.blob.BlobPathBuilder._
 
-import java.net.MalformedURLException
-import java.net.URI
-import java.nio.file.FileSystems
-import scala.jdk.CollectionConverters._
+import java.net.{MalformedURLException, URI}
 import scala.language.postfixOps
-import scala.util.Failure
-import scala.util.Try
+import scala.util.{Failure, Success, Try}
+import java.nio.file.Files
 
 object BlobPathBuilder {
 
@@ -22,9 +16,10 @@ object BlobPathBuilder {
   case class ValidBlobPath(path: String) extends BlobPathValidation
   case class UnparsableBlobPath(errorMessage: Throwable) extends BlobPathValidation
 
-  def invalidBlobPathMessage(container: String, endpoint: String) = s"Malformed Blob URL for this builder. Expecting a URL for a container $container and endpoint $endpoint"
-  def parseURI(string: String) = URI.create(UrlEscapers.urlFragmentEscaper().escape(string))
-  def parseStorageAccount(uri: URI) = uri.getHost().split("\\.").filter(!_.isEmpty()).headOption
+  def invalidBlobPathMessage(container: BlobContainerName, endpoint: EndpointURL) = s"Malformed Blob URL for this builder. Expecting a URL for a container $container and endpoint $endpoint"
+  def parseURI(string: String): Try[URI] = Try(URI.create(UrlEscapers.urlFragmentEscaper().escape(string)))
+  def parseStorageAccount(uri: URI): Try[StorageAccountName] = uri.getHost.split("\\.").find(_.nonEmpty).map(StorageAccountName(_))
+      .map(Success(_)).getOrElse(Failure(new Exception("Could not parse storage account")))
 
   /**
     * Validates a that a path from a string is a valid BlobPath of the format:
@@ -44,46 +39,84 @@ object BlobPathBuilder {
     *
     * If the configured container and storage account do not match, the string is considered unparsable
     */
-  def validateBlobPath(string: String, container: String, endpoint: String): BlobPathValidation = {
-    Try {
-      val uri = parseURI(string)
-      val storageAccount = parseStorageAccount(parseURI(endpoint))
-      val hasContainer = uri.getPath().split("/").filter(!_.isEmpty()).headOption.contains(container)
-      def hasEndpoint = parseStorageAccount(uri).contains(storageAccount.get)
-      if (hasContainer && !storageAccount.isEmpty && hasEndpoint) {
-        ValidBlobPath(uri.getPath.replaceFirst("/" + container, ""))
-      } else {
-        UnparsableBlobPath(new MalformedURLException(invalidBlobPathMessage(container, endpoint)))
+  def validateBlobPath(string: String, container: BlobContainerName, endpoint: EndpointURL): BlobPathValidation = {
+    val blobValidation = for {
+      testUri <- parseURI(string)
+      endpointUri <- parseURI(endpoint.value)
+      testStorageAccount <- parseStorageAccount(testUri)
+      endpointStorageAccount <- parseStorageAccount(endpointUri)
+      hasContainer = testUri.getPath.split("/").find(_.nonEmpty).contains(container.value)
+      hasEndpoint = testStorageAccount.equals(endpointStorageAccount)
+      blobPathValidation = (hasContainer && hasEndpoint) match {
+        case true => ValidBlobPath(testUri.getPath.replaceFirst("/" + container, ""))
+        case false => UnparsableBlobPath(new MalformedURLException(invalidBlobPathMessage(container, endpoint)))
       }
-    } recover { case t => UnparsableBlobPath(t) } get
+    } yield blobPathValidation
+    blobValidation recover { case t => UnparsableBlobPath(t) } get
   }
 }
 
-class BlobPathBuilder(credential: AzureSasCredential, container: String, endpoint: String) extends PathBuilder {
-
-  val fileSystemConfig: Map[String, Object] = Map((AzureFileSystem.AZURE_STORAGE_SAS_TOKEN_CREDENTIAL, credential),
-                                                  (AzureFileSystem.AZURE_STORAGE_FILE_STORES, container))
+class BlobPathBuilder(container: BlobContainerName, endpoint: EndpointURL)(private val fsm: BlobFileSystemManager) extends PathBuilder {
 
   def build(string: String): Try[BlobPath] = {
     validateBlobPath(string, container, endpoint) match {
-      case ValidBlobPath(path) =>
-        Try {
-          val fileSystem = FileSystems.newFileSystem(new URI("azb://?endpoint=" + endpoint), fileSystemConfig.asJava)
-          val blobStoragePath = fileSystem.getPath(path)
-          BlobPath(blobStoragePath, endpoint, container)
-        }
+      case ValidBlobPath(path) => Try(BlobPath(path, endpoint, container)(fsm))
       case UnparsableBlobPath(errorMessage: Throwable) => Failure(errorMessage)
     }
   }
-
   override def name: String = "Azure Blob Storage"
 }
 
-// Add args for container, storage account name
-case class BlobPath private[blob](nioPath: NioPath, endpoint: String, container: String) extends Path {
-  override protected def newPath(nioPath: NioPath): Path = BlobPath(nioPath, endpoint, container)
+object BlobPath {
+  // The Azure NIO library uses `{containerName}:` as the root of the path.
+  // This doesn't work well for our need to easily transfer back and forth
+  // to and from the blob URL format. This method removes anything up to and including
+  // the first colon, to create a path string useful for working with BlobPath.
+  // This is safe because the NIO library enforces no colons except to mark
+  // the root container name.
+  private def nioPathString(nioPath: NioPath): String = {
+    val pathStr = nioPath.toString
+    pathStr.substring(pathStr.indexOf(":")+1)
+  }
+
+  def apply(nioPath: NioPath,
+            endpoint: EndpointURL,
+            container: BlobContainerName,
+            fsm: BlobFileSystemManager): BlobPath = {
+    BlobPath(nioPathString(nioPath), endpoint, container)(fsm)
+  }
+}
+
+case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, container: BlobContainerName)(private val fsm: BlobFileSystemManager) extends Path {
+  override def nioPath: NioPath = findNioPath(pathString)
 
-  override def pathAsString: String = List(endpoint, container, nioPath.toString()).mkString("/")
+  override protected def newPath(nioPath: NioPath): Path = BlobPath(nioPath, endpoint, container, fsm)
 
-  override def pathWithoutScheme: String = parseURI(endpoint).getHost + "/" + container + "/" + nioPath.toString()
+  override def pathAsString: String = List(endpoint, container, pathString.stripPrefix("/")).mkString("/")
+
+  //This is purposefully an unprotected get because if the endpoint cannot be parsed this should fail loudly rather than quietly
+  override def pathWithoutScheme: String = parseURI(endpoint.value).map(u => List(u.getHost, container, pathString).mkString("/")).get
+
+  private def findNioPath(path: String): NioPath = (for {
+    fileSystem <- fsm.retrieveFilesystem()
+    // The Azure NIO library uses `{container}:` to represent the root of the path
+    nioPath = fileSystem.getPath(s"${container.value}:", path)
+  // This is purposefully an unprotected get because the NIO API needing an unwrapped path object.
+  // If an error occurs the api expects a thrown exception
+  } yield nioPath).get
+
+  def blobFileAttributes: Try[AzureBlobFileAttributes] =
+    Try(Files.readAttributes(nioPath, classOf[AzureBlobFileAttributes]))
+
+  def md5HexString: Try[Option[String]] = {
+    blobFileAttributes.map(h =>
+      Option(h.blobHttpHeaders().getContentMd5) match {
+        case None => None
+        case Some(arr) if arr.isEmpty => None
+        // Convert the bytes to a hex-encoded string. Note that this value
+        // is rendered in base64 in the Azure web portal.
+        case Some(bytes) => Option(bytes.map("%02x".format(_)).mkString)
+      }
+    )
+  }
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index ca5e24fe3d7..c263841dc8a 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -1,22 +1,29 @@
 package cromwell.filesystems.blob
 
 import akka.actor.ActorSystem
-import com.azure.core.credential.AzureSasCredential
 import com.typesafe.config.Config
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.PathBuilderFactory
-import cromwell.filesystems.blob.BlobPathBuilder
+import cromwell.core.path.PathBuilderFactory.PriorityBlob
 
-import scala.concurrent.ExecutionContext
-import scala.concurrent.Future
+import java.util.UUID
+import scala.concurrent.{ExecutionContext, Future}
+
+final case class SubscriptionId(value: UUID) {override def toString: String = value.toString}
+final case class BlobContainerName(value: String) {override def toString: String = value}
+final case class StorageAccountName(value: String) {override def toString: String = value}
+final case class EndpointURL(value: String) {override def toString: String = value}
+final case class WorkspaceId(value: UUID) {override def toString: String = value.toString}
+final case class ContainerResourceId(value: UUID) {override def toString: String = value.toString}
+final case class WorkspaceManagerURL(value: String) {override def toString: String = value}
+
+final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, fsm: BlobFileSystemManager) extends PathBuilderFactory {
 
-final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config) extends PathBuilderFactory {
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[BlobPathBuilder] = {
-    val sasToken: String = instanceConfig.getString("sasToken")
-    val container: String = instanceConfig.getString("store")
-    val endpoint: String = instanceConfig.getString("endpoint")
     Future {
-      new BlobPathBuilder(new AzureSasCredential(sasToken), container, endpoint)
+      new BlobPathBuilder(fsm.container, fsm.endpoint)(fsm)
     }
   }
+
+  override def priority: Int = PriorityBlob
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
new file mode 100644
index 00000000000..a9f52d92a91
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
@@ -0,0 +1,30 @@
+package cromwell.filesystems.blob
+
+import bio.terra.workspace.api.ControlledAzureResourceApi
+import bio.terra.workspace.client.ApiClient
+
+/**
+  * Represents a way to get a client for interacting with workspace manager controlled resources.
+  * Additional WSM clients can be added here if needed.
+  *
+  * Pared down from `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.WorkspaceManagerApiClientProvider`
+  *
+  * For testing, create an anonymous subclass as in `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.HttpWorkspaceManagerDAOSpec`
+  */
+trait WorkspaceManagerApiClientProvider {
+  def getControlledAzureResourceApi(token: String): ControlledAzureResourceApi
+}
+
+class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManagerURL) extends WorkspaceManagerApiClientProvider {
+  private def getApiClient: ApiClient = {
+    val client: ApiClient = new ApiClient()
+    client.setBasePath(baseWorkspaceManagerUrl.value)
+    client
+  }
+
+  def getControlledAzureResourceApi(token: String): ControlledAzureResourceApi = {
+    val apiClient = getApiClient
+    apiClient.setAccessToken(token)
+    new ControlledAzureResourceApi(apiClient)
+  }
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
new file mode 100644
index 00000000000..607ad5606f7
--- /dev/null
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
@@ -0,0 +1,75 @@
+package cromwell.filesystems.blob
+
+import com.typesafe.config.ConfigFactory
+import common.exception.AggregatedMessageException
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import java.util.UUID
+
+class BlobFileSystemConfigSpec extends AnyFlatSpec with Matchers {
+
+  private val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+  private val container = BlobContainerName("storageContainer")
+  private val workspaceId = WorkspaceId(UUID.fromString("B0BAFE77-0000-0000-0000-000000000000"))
+  private val containerResourceId = ContainerResourceId(UUID.fromString("F00B4911-0000-0000-0000-000000000000"))
+  private val workspaceManagerURL = WorkspaceManagerURL("https://wsm.example.com")
+  private val b2cToken = "b0gus-t0ken"
+
+  it should "parse configs for a minimal functioning factory with native blob access" in {
+    val config = BlobFileSystemConfig(
+      ConfigFactory.parseString(
+      s"""
+         |container = "$container"
+         |endpoint = "$endpoint"
+      """.stripMargin)
+    )
+    config.blobContainerName should equal(container)
+    config.endpointURL should equal(endpoint)
+    config.expiryBufferMinutes should equal(BlobFileSystemConfig.defaultExpiryBufferMinutes)
+  }
+
+  it should "parse configs for a functioning factory with WSM-mediated blob access" in {
+    val config = BlobFileSystemConfig(
+      ConfigFactory.parseString(
+        s"""
+           |container = "$container"
+           |endpoint = "$endpoint"
+           |expiry-buffer-minutes = "20"
+           |workspace-manager {
+           |  url = "$workspaceManagerURL"
+           |  workspace-id = "$workspaceId"
+           |  container-resource-id = "$containerResourceId"
+           |  b2cToken = "$b2cToken"
+           |}
+           |
+        """.stripMargin)
+    )
+    config.blobContainerName should equal(container)
+    config.endpointURL should equal(endpoint)
+    config.expiryBufferMinutes should equal(20L)
+    config.workspaceManagerConfig.isDefined shouldBe true
+    config.workspaceManagerConfig.get.url shouldBe workspaceManagerURL
+    config.workspaceManagerConfig.get.workspaceId shouldBe workspaceId
+    config.workspaceManagerConfig.get.containerResourceId shouldBe containerResourceId
+    config.workspaceManagerConfig.get.overrideWsmAuthToken.contains(b2cToken) shouldBe true
+  }
+
+  it should "fail when partial WSM config is supplied" in {
+    val rawConfig =
+      ConfigFactory.parseString(
+        s"""
+         |container = "$container"
+         |endpoint = "$endpoint"
+         |expiry-buffer-minutes = "10"
+         |workspace-manager {
+         |  url = "$workspaceManagerURL"
+         |  container-resource-id = "$containerResourceId"
+         |}
+         |
+        """.stripMargin)
+
+    val error = intercept[AggregatedMessageException](BlobFileSystemConfig(rawConfig))
+    error.getMessage should include("No configuration setting found for key 'workspace-id'")
+  }
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
new file mode 100644
index 00000000000..611a50f5603
--- /dev/null
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
@@ -0,0 +1,50 @@
+package cromwell.filesystems.blob
+
+import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
+import au.com.dius.pact.core.model.RequestResponsePact
+import io.circe.Json
+import io.circe.syntax._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import pact4s.circe.implicits._
+import pact4s.scalatest.RequestResponsePactForger
+
+class BlobFileSystemContractSpec extends AnyFlatSpec with Matchers with RequestResponsePactForger {
+
+  val resourceId = "";
+  val workspaceId = "";
+  /**
+   * we can define the folder that the pact contracts get written to upon completion of this test suite.
+   */
+  override val pactTestExecutionContext: PactTestExecutionContext = new PactTestExecutionContext(
+    "./filesystems/blob/target/pacts"
+  )
+
+  /**
+   * The following is an outline for what a RequestResponsePact might look like for requesting
+   * from WSM form the blob filesystem. To generate a pact file however tests must be written
+   * against this pact to validate that the agreement is met. These tests get run with other
+   * scala tests on build and if the tests pass when run a pact file will be generated locally
+   */
+  override def pact: RequestResponsePact = ConsumerPactBuilder
+      .consumer("cromwell-blob-filesystem-consumer")
+      .hasPactWith("wsm-provider")
+      .`given`(
+        "resource exists",
+        Map("id" -> resourceId.asJson, "value" -> 123.asJson) // we can use parameters to specify details about the provider state
+      )
+      .`given`(
+        "workspace exists",
+        Map("id" -> workspaceId, "value" -> 123) // we can use parameters to specify details about the provider state
+      )
+      .uponReceiving("Request to fetch SAS Token")
+      .method("POST")
+      .path(s"/api/workspaces/v1/${workspaceId}/resources/controlled/azure/storageContainer/${resourceId}/getSasToken")
+      .headers("Authorization" -> "sampleToken")
+      .willRespondWith()
+      .status(200)
+      .body(
+        Json.obj("id" -> "".asJson, "value" -> 123.asJson)
+      ).toPact()
+
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
new file mode 100644
index 00000000000..881cd3669a1
--- /dev/null
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
@@ -0,0 +1,166 @@
+package cromwell.filesystems.blob
+
+import com.azure.core.credential.AzureSasCredential
+import common.mock.MockSugar
+import org.mockito.Mockito._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import java.nio.file.{FileSystem, FileSystemNotFoundException}
+import java.time.format.DateTimeFormatter
+import java.time.temporal.ChronoUnit
+import java.time.{Duration, Instant, ZoneId}
+import scala.util.{Failure, Try}
+
+
+object BlobPathBuilderFactorySpec {
+  def buildExampleSasToken(expiry: Instant): AzureSasCredential = {
+    val formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd").withZone(ZoneId.systemDefault())
+    val sv = formatter.format(expiry)
+    val se = expiry.toString().replace(":","%3A")
+    new AzureSasCredential(s"sv=$sv&se=$se&sr=c&sp=rcl")
+  }
+}
+class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSugar {
+  def generateTokenExpiration(minutes: Long) = Instant.now.plus(minutes, ChronoUnit.MINUTES)
+
+  it should "build an example sas token of the correct format" in {
+    val testToken = BlobPathBuilderFactorySpec.buildExampleSasToken(Instant.ofEpochMilli(1603794041000L))
+    val sourceToken = "sv=2020-10-27&se=2020-10-27T10%3A20%3A41Z&sr=c&sp=rcl"
+    testToken.getSignature should equal(sourceToken)
+  }
+
+  it should "parse an expiration time from a sas token" in {
+    val expiryTime = generateTokenExpiration(20L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(expiryTime)
+    val expiry = BlobFileSystemManager.parseTokenExpiry(sasToken)
+    expiry should contain(expiryTime)
+  }
+
+  it should "verify an unexpired token will be processed as unexpired" in {
+    val expiryTime = generateTokenExpiration(11L)
+    val expired = BlobFileSystemManager.hasTokenExpired(expiryTime, Duration.ofMinutes(10L))
+    expired shouldBe false
+  }
+
+  it should "test an expired token will be processed as expired" in {
+    val expiryTime = generateTokenExpiration(9L)
+    val expired = BlobFileSystemManager.hasTokenExpired(expiryTime, Duration.ofMinutes(10L))
+    expired shouldBe true
+  }
+
+  it should "test that a filesystem gets closed correctly" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+    val fileSystems = mock[FileSystemAPI]
+    val fileSystem = mock[FileSystem]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(fileSystem))
+    when(fileSystems.closeFileSystem(azureUri)).thenCallRealMethod()
+
+    fileSystems.closeFileSystem(azureUri)
+    verify(fileSystem, times(1)).close()
+  }
+
+  it should "test retrieveFileSystem with expired filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val expiredToken = generateTokenExpiration(9L)
+    val refreshedToken = generateTokenExpiration(69L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+
+    val fileSystems = mock[FileSystemAPI]
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(expiredToken))
+    fsm.getExpiry should contain(expiredToken)
+    fsm.isTokenExpired shouldBe true
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(refreshedToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, never()).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
+    verify(fileSystems, times(1)).closeFileSystem(azureUri)
+  }
+
+  it should "test retrieveFileSystem with an unexpired fileSystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val initialToken = generateTokenExpiration(11L)
+    val refreshedToken = generateTokenExpiration(71L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+    // Need a fake filesystem to supply the getFileSystem simulated try
+    val dummyFileSystem = mock[FileSystem]
+
+    val fileSystems = mock[FileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(dummyFileSystem))
+
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(initialToken))
+    fsm.getExpiry should contain(initialToken)
+    fsm.isTokenExpired shouldBe false
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(initialToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, times(1)).getFileSystem(azureUri)
+    verify(fileSystems, never()).newFileSystem(azureUri, configMap)
+    verify(fileSystems, never()).closeFileSystem(azureUri)
+  }
+
+  it should "test retrieveFileSystem with an uninitialized filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val refreshedToken = generateTokenExpiration(71L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+
+    val fileSystems = mock[FileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Failure(new FileSystemNotFoundException))
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(refreshedToken))
+    fsm.getExpiry.isDefined shouldBe true
+    fsm.isTokenExpired shouldBe false
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(refreshedToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, times(1)).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
+    verify(fileSystems, never()).closeFileSystem(azureUri)
+  }
+
+  it should "test retrieveFileSystem with an unknown filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val refreshedToken = generateTokenExpiration(71L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+
+    val fileSystems = mock[FileSystemAPI]
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems)
+    fsm.getExpiry.isDefined shouldBe false
+    fsm.isTokenExpired shouldBe false
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(refreshedToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, never()).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
+    verify(fileSystems, times(1)).closeFileSystem(azureUri)
+  }
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index 454b8f5adaf..2aa9b2b43aa 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -1,23 +1,22 @@
 package cromwell.filesystems.blob
-
-import com.azure.core.credential.AzureSasCredential
-import cromwell.filesystems.blob.BlobPathBuilder
+import common.mock.MockSugar
+import org.mockito.Mockito.when
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-import java.nio.file.Files
+import scala.util.{Failure, Try}
 
 object BlobPathBuilderSpec {
-  def buildEndpoint(storageAccount: String) = s"https://$storageAccount.blob.core.windows.net"
+  def buildEndpoint(storageAccount: String) = EndpointURL(s"https://$storageAccount.blob.core.windows.net")
 }
 
-class BlobPathBuilderSpec extends AnyFlatSpec with Matchers{
-
+class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
+  // ValidateBlobPath
   it should "parse a URI into a path" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = "container"
+    val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
-    val testString = endpoint + "/" + container + evalPath
+    val testString = endpoint.value + "/" + container + evalPath
     BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
       case BlobPathBuilder.ValidBlobPath(path) => path should equal(evalPath)
       case BlobPathBuilder.UnparsableBlobPath(errorMessage) => fail(errorMessage)
@@ -26,40 +25,83 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers{
 
   it should "bad storage account fails causes URI to fail parse into a path" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = "container"
+    val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
-    val testString = BlobPathBuilderSpec.buildEndpoint("badStorageAccount") + container + evalPath
+    val testString = BlobPathBuilderSpec.buildEndpoint("badStorageAccount").value + container.value + evalPath
     BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
       case BlobPathBuilder.ValidBlobPath(path) => fail(s"Valid path: $path found when verifying mismatched storage account")
-      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage() should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
+      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
     }
   }
 
   it should "bad container fails causes URI to fail parse into a path" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = "container"
+    val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
-    val testString = endpoint + "badContainer" + evalPath
+    val testString = endpoint.value + "badContainer" + evalPath
     BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
       case BlobPathBuilder.ValidBlobPath(path) => fail(s"Valid path: $path found when verifying mismatched container")
-      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage() should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
+      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
     }
   }
 
+  it should "provide a readable error when getting an illegal nioPath" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val container = BlobContainerName("container")
+    val evalPath = "/path/to/file"
+    val exception = new Exception("Failed to do the thing")
+    val fsm = mock[BlobFileSystemManager]
+    when(fsm.retrieveFilesystem()).thenReturn(Failure(exception))
+    val path = BlobPath(evalPath, endpoint, container)(fsm)
+    val testException = Try(path.nioPath).failed.toOption
+    testException should contain(exception)
+  }
+
   ignore should "build a blob path from a test string and read a file" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
-    val endpointHost = BlobPathBuilder.parseURI(endpoint).getHost
-    val store = "inputs"
+    val endpointHost = BlobPathBuilder.parseURI(endpoint.value).map(_.getHost).getOrElse(fail("Could not parse URI"))
+    val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
-    val sas = "{SAS TOKEN HERE}"
-    val testString = endpoint + "/" + store + evalPath
-    val blobPath: BlobPath = new BlobPathBuilder(new AzureSasCredential(sas), store, endpoint) build testString getOrElse fail()
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
+    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10L, blobTokenGenerator)
+    val testString = endpoint.value + "/" + store + evalPath
+    val blobPath: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
+
     blobPath.container should equal(store)
     blobPath.endpoint should equal(endpoint)
     blobPath.pathAsString should equal(testString)
     blobPath.pathWithoutScheme should equal(endpointHost + "/" + store + evalPath)
-    val is = Files.newInputStream(blobPath.nioPath)
+    val is = blobPath.newInputStream()
     val fileText = (is.readAllBytes.map(_.toChar)).mkString
     fileText should include ("This is my test file!!!! Did it work?")
   }
+
+  ignore should "build duplicate blob paths in the same filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
+    val store = BlobContainerName("inputs")
+    val evalPath = "/test/inputFile.txt"
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
+    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
+    val testString = endpoint.value + "/" + store + evalPath
+    val blobPath1: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
+    blobPath1.nioPath.getFileSystem.close()
+    val blobPath2: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
+    blobPath1 should equal(blobPath2)
+    val is = blobPath1.newInputStream()
+    val fileText = (is.readAllBytes.map(_.toChar)).mkString
+    fileText should include ("This is my test file!!!! Did it work?")
+  }
+
+  ignore should "resolve a path without duplicating container name" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
+    val store = BlobContainerName("inputs")
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
+    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
+
+    val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
+    val blobRoot: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build rootString getOrElse fail()
+    blobRoot.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution")
+    val otherFile = blobRoot.resolve("test/inputFile.txt")
+    otherFile.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
+  }
 }
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
index 4f899c318bb..5856e41f97b 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
@@ -28,7 +28,7 @@ case class DrsPath(drsPath: CloudNioPath, requesterPaysProjectIdOption: Option[S
       case Some(fileAttributes) =>
         fileAttributes.fileHash match {
           case Some(fileHash) => fileHash
-          case None => throw new IOException(s"Error while resolving DRS path $this. The response from Martha doesn't contain the 'md5' hash for the file.")
+          case None => throw new IOException(s"Error while resolving DRS path $this. The response from DRS Resolver doesn't contain the 'md5' hash for the file.")
         }
       case None => throw new IOException(s"Error getting file hash of DRS path $this. Reason: File attributes class DrsCloudNioRegularFileAttributes wasn't defined in DrsCloudNioFileProvider.")
     }
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
index f22023c87fd..b464772eec8 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
@@ -60,7 +60,7 @@ case class DrsPathBuilder(fileSystemProvider: DrsCloudNioFileSystemProvider,
     val gcsPathOption = for {
       // Right now, only pre-resolving GCS. In the future, could pull others like FTP, HTTP, S3, SRA, etc.
       gsUriOption <- logAttempt(
-        "resolve the uri through Martha",
+        "resolve the uri through DRS Resolver",
         DrsResolver.getSimpleGsUri(pathAsString, fileSystemProvider.drsPathResolver).unsafeRunSync()
       )
       gcsUrlWithNoCreds <- gsUriOption
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
index bc7fb598a81..873874912a0 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
@@ -2,13 +2,12 @@ package cromwell.filesystems.drs
 
 import akka.actor.ActorSystem
 import cats.data.Validated.{Invalid, Valid}
-import cloud.nio.impl.drs.{AzureDrsCredentials, DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import cloud.nio.impl.drs.{AzureDrsCredentials, DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.api.services.oauth2.Oauth2Scopes
 import com.typesafe.config.Config
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.{PathBuilder, PathBuilderFactory}
-import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -24,26 +23,23 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
   private lazy val googleConfiguration: GoogleConfiguration = GoogleConfiguration(globalConfig)
   private lazy val scheme = instanceConfig.getString("auth")
 
-  // For Azure support
+  // For Azure support - this should be the UAMI client id
   private val dataAccessIdentityKey = "data_access_identity"
-  private lazy val azureKeyVault = instanceConfig.as[Option[String]]("azure-keyvault-name")
-  private lazy val azureSecretName = instanceConfig.as[Option[String]]("azure-token-secret")
 
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] = {
     Future {
-      val marthaScopes = List(
-        // Profile and Email scopes are requirements for interacting with Martha
+      val drsResolverScopes = List(
+        // Profile and Email scopes are requirements for interacting with DRS Resolvers
         Oauth2Scopes.USERINFO_EMAIL,
         Oauth2Scopes.USERINFO_PROFILE
       )
 
-      val (googleAuthMode, drsCredentials) = (scheme, azureKeyVault, azureSecretName) match {
-        case ("azure", Some(vaultName), Some(secretName)) => (None, AzureDrsCredentials(options.get(dataAccessIdentityKey).toOption, vaultName, secretName))
-        case ("azure", _, _) => throw new RuntimeException(s"Error while instantiating DRS path builder factory. Couldn't find azure-keyvault-name and azure-token-secret in config.")
-        case (googleAuthScheme, _, _) => googleConfiguration.auth(googleAuthScheme) match {
+      val (googleAuthMode, drsCredentials) = scheme match {
+        case "azure" => (None, AzureDrsCredentials(options.get(dataAccessIdentityKey).toOption))
+        case googleAuthScheme => googleConfiguration.auth(googleAuthScheme) match {
           case Valid(auth) => (
             Option(auth),
-            GoogleDrsCredentials(auth.credentials(options.get(_).get, marthaScopes), singletonConfig.config)
+            GoogleOauthDrsCredentials(auth.credentials(options.get(_).get, drsResolverScopes), singletonConfig.config)
           )
           case Invalid(error) => throw new RuntimeException(s"Error while instantiating DRS path builder factory. Errors: ${error.toString}")
         }
@@ -54,7 +50,7 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
       val requesterPaysProjectIdOption = options.get("google_project").toOption
 
       /*
-      `override_preresolve_for_test` is a workflow option to override the default `martha.preresolve` specified in the
+      `override_preresolve_for_test` is a workflow option to override the default `resolver.preresolve` specified in the
       global config. This is only used for testing purposes.
        */
       val preResolve: Boolean =
@@ -64,7 +60,7 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
           .getOrElse(
             singletonConfig
               .config
-              .getBoolean("martha.preresolve")
+              .getBoolean("resolver.preresolve")
           )
 
       DrsPathBuilder(
@@ -82,4 +78,4 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
 
 case class UrlNotFoundException(scheme: String) extends Exception(s"No $scheme url associated with given DRS path.")
 
-case class MarthaResponseMissingKeyException(missingKey: String) extends Exception(s"The response from Martha doesn't contain the key '$missingKey'.")
+case class DrsResolverResponseMissingKeyException(missingKey: String) extends Exception(s"The response from the DRS Resolver doesn't contain the key '$missingKey'.")
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
index 3cc1cc3530a..3256d6da248 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
@@ -1,8 +1,8 @@
 package cromwell.filesystems.drs
 
 import cats.effect.IO
-import cloud.nio.impl.drs.MarthaResponseSupport.getGcsBucketAndName
-import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, MarthaResponse, SADataObject}
+import cloud.nio.impl.drs.DrsResolverResponseSupport.getGcsBucketAndName
+import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, DrsResolverResponse, SADataObject}
 import com.google.api.services.storage.StorageScopes
 import com.google.auth.oauth2.OAuth2Credentials
 import com.google.cloud.storage.Storage.BlobGetOption
@@ -21,8 +21,8 @@ object DrsReader {
              options: WorkflowOptions,
              requesterPaysProjectIdOption: Option[String],
              drsPathResolver: DrsPathResolver,
-             marthaResponse: MarthaResponse): IO[DrsReader] = {
-    (marthaResponse.accessUrl, marthaResponse.gsUri, googleAuthMode) match {
+             drsResolverResponse: DrsResolverResponse): IO[DrsReader] = {
+    (drsResolverResponse.accessUrl, drsResolverResponse.gsUri, googleAuthMode) match {
       case (Some(accessUrl), _, _) =>
         IO.pure(AccessUrlReader(drsPathResolver, accessUrl))
       case (_, Some(gcsPath), Some(authMode)) =>
@@ -31,10 +31,10 @@ object DrsReader {
           options,
           requesterPaysProjectIdOption,
           gcsPath,
-          marthaResponse.googleServiceAccount,
+          drsResolverResponse.googleServiceAccount,
         ))
       case (_, Some(_), _) =>
-        IO.raiseError(new RuntimeException("GCS URI found in Martha response, but no Google auth found!"))
+        IO.raiseError(new RuntimeException("GCS URI found in the DRS Resolver response, but no Google auth found!"))
       case _ =>
         IO.raiseError(new RuntimeException(DrsPathResolver.ExtractUriErrorMsg))
     }
@@ -44,9 +44,9 @@ object DrsReader {
                       options: WorkflowOptions,
                       requesterPaysProjectIdOption: Option[String])
                      (drsPathResolver: DrsPathResolver,
-                      marthaResponse: MarthaResponse): IO[ReadableByteChannel] = {
+                      drsResolverResponse: DrsResolverResponse): IO[ReadableByteChannel] = {
     for {
-      reader <- reader(googleAuthMode, options, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      reader <- reader(googleAuthMode, options, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
       channel <- reader.read()
     } yield channel
   }
@@ -69,7 +69,7 @@ case class GcsReader(googleAuthMode: GoogleAuthMode,
     val credentialsIo = googleServiceAccount match {
       case Some(googleSA) =>
         IO(
-          UserServiceAccountMode("martha_service_account").credentials(
+          UserServiceAccountMode("drs_resolver_service_account").credentials(
             Map(GoogleAuthMode.UserServiceAccountKey -> googleSA.data.noSpaces),
             readScopes,
           )
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
index 0f24e803480..4aa760f17e1 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
@@ -2,7 +2,7 @@ package cromwell.filesystems.drs
 
 import cats.data.NonEmptyList
 import cats.effect.IO
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, DrsPathResolver, MarthaField}
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, DrsPathResolver, DrsResolverField}
 import common.exception._
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import org.apache.commons.lang3.exception.ExceptionUtils
@@ -34,31 +34,31 @@ object DrsResolver {
     } yield drsFileSystemProvider.drsPathResolver
   }
 
-  case class MarthaLocalizationData(gsUri: Option[String],
-                                    fileName: Option[String],
-                                    bondProvider: Option[String],
-                                    localizationPath: Option[String])
+  case class DrsResolverLocalizationData(gsUri: Option[String],
+                                         fileName: Option[String],
+                                         bondProvider: Option[String],
+                                         localizationPath: Option[String])
 
-  private def getMarthaLocalizationData(pathAsString: String,
-                                        drsPathResolver: DrsPathResolver): IO[MarthaLocalizationData] = {
-    val fields = NonEmptyList.of(MarthaField.GsUri, MarthaField.FileName, MarthaField.BondProvider, MarthaField.LocalizationPath)
+  private def getDrsResolverLocalizationData(pathAsString: String,
+                                        drsPathResolver: DrsPathResolver): IO[DrsResolverLocalizationData] = {
+    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.FileName, DrsResolverField.BondProvider, DrsResolverField.LocalizationPath)
 
-    drsPathResolver.resolveDrsThroughMartha(pathAsString, fields) map { r =>
-      MarthaLocalizationData(r.gsUri, r.fileName, r.bondProvider, r.localizationPath)
+    drsPathResolver.resolveDrs(pathAsString, fields) map { r =>
+      DrsResolverLocalizationData(r.gsUri, r.fileName, r.bondProvider, r.localizationPath)
     }
   }
 
   /** Returns the `gsUri` if it ends in the `fileName` and the `bondProvider` is empty. */
-  private def getSimpleGsUri(localizationData: MarthaLocalizationData): Option[String] = {
+  private def getSimpleGsUri(localizationData: DrsResolverLocalizationData): Option[String] = {
     localizationData match {
       // `gsUri` not defined so no gsUri can be returned.
-      case MarthaLocalizationData(None, _, _, _) => None
+      case DrsResolverLocalizationData(None, _, _, _) => None
       // `bondProvider` defined, cannot "preresolve" to GCS.
-      case MarthaLocalizationData(_, _, Some(_), _) => None
+      case DrsResolverLocalizationData(_, _, Some(_), _) => None
       // Do not return the simple GS URI if the `fileName` from metadata is mismatched to the filename in the `gsUri`.
-      case MarthaLocalizationData(Some(gsUri), Some(fileName), _, _) if !gsUri.endsWith(s"/$fileName") => None
+      case DrsResolverLocalizationData(Some(gsUri), Some(fileName), _, _) if !gsUri.endsWith(s"/$fileName") => None
       // Barring any of the situations above return the `gsUri`.
-      case MarthaLocalizationData(Some(gsUri), _, _, _) => Option(gsUri)
+      case DrsResolverLocalizationData(Some(gsUri), _, _, _) => Option(gsUri)
     }
   }
 
@@ -66,7 +66,7 @@ object DrsResolver {
   def getSimpleGsUri(pathAsString: String,
                      drsPathResolver: DrsPathResolver): IO[Option[String]] = {
 
-    val gsUriIO = getMarthaLocalizationData(pathAsString, drsPathResolver) map getSimpleGsUri
+    val gsUriIO = getDrsResolverLocalizationData(pathAsString, drsPathResolver) map getSimpleGsUri
 
     gsUriIO.handleErrorWith(resolveError(pathAsString))
   }
@@ -82,15 +82,15 @@ object DrsResolver {
   def getContainerRelativePath(drsPath: DrsPath): IO[String] = {
     val pathIO = for {
       drsPathResolver <- getDrsPathResolver(drsPath)
-      localizationData <- getMarthaLocalizationData(drsPath.pathAsString, drsPathResolver)
+      localizationData <- getDrsResolverLocalizationData(drsPath.pathAsString, drsPathResolver)
       containerRelativePath <- buildContainerRelativePath(localizationData, drsPath)
     } yield containerRelativePath.pathAsString
 
     pathIO.handleErrorWith(resolveError(drsPath.pathAsString))
   }
 
-  // Return the container relative path built from the Martha-specified localization path, file name, or gs URI.
-  private def buildContainerRelativePath(localizationData: MarthaLocalizationData, drsPath: Path): IO[Path] = {
+  // Return the container relative path built from the DRS Resolver-specified localization path, file name, or gs URI.
+  private def buildContainerRelativePath(localizationData: DrsResolverLocalizationData, drsPath: Path): IO[Path] = {
     // Return a relative path constructed from the DRS path minus the leading scheme.
     // In the DOS/DRS spec file names are safe for file systems but not necessarily the DRS URIs.
     // Reuse the regex defined for ContentsObject.name, plus add "/" for directory separators.
@@ -99,13 +99,13 @@ object DrsResolver {
       DefaultPathBuilder.get(drsPath.pathWithoutScheme.replaceAll("[^/A-Za-z0-9._-]", "_"))
 
     localizationData match {
-      case MarthaLocalizationData(_, _, _, Some(localizationPath)) =>
+      case DrsResolverLocalizationData(_, _, _, Some(localizationPath)) =>
         // TDR may return an explicit localization path and if so we should not use the `drsPathRelativePath`.
         // We want to end up with something like /cromwell_root/drs_localization_paths/tdr/specified/path/foo.bam.
         // Calling code will add the `/cromwell_root/`, so strip any leading slashes to make this a relative path:
         val relativeLocalizationPath = if (localizationPath.startsWith("/")) localizationPath.tail else localizationPath
         IO.fromTry(DefaultPathBuilder.build(DrsLocalizationPathsContainer).map(_.resolve(relativeLocalizationPath)))
-      case MarthaLocalizationData(_, Some(fileName), _, _) =>
+      case DrsResolverLocalizationData(_, Some(fileName), _, _) =>
         // Paths specified by filename only are made relative to `drsPathRelativePath`.
         IO(drsPathRelativePath.resolve(fileName))
       case _ =>
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
index 1d941b5f6b2..d207bba8d86 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
@@ -18,8 +18,8 @@ class DrsPathBuilderFactorySpec extends AnyFlatSpec with CromwellTimeoutSpec wit
          |    global {
          |      class = "cromwell.filesystems.drs.DrsFileSystemConfig"
          |      config {
-         |        martha {
-         |          url = "http://martha-url"
+         |        resolver {
+         |          url = "http://drshub-url"
          |        }
          |      }
          |    }
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
index 242b662d5ea..315e51b5d04 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
@@ -1,7 +1,7 @@
 package cromwell.filesystems.drs
 
 import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.cloud.NoCredentials
 import com.typesafe.config.{Config, ConfigFactory}
 import cromwell.core.TestKitSuite
@@ -313,7 +313,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       isAbsolute = false,
     ),
 
-    // No spec says this is illegal... so pass it to Martha's various GCFs JIC
+    // No spec says this is illegal... so pass it to the DRS Resolver's various GCFs JIC
     GoodPath(
       description = "a bucketless path",
       path = s"drs://",
@@ -377,9 +377,9 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   private val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
     throw new UnsupportedOperationException("Currently DrsPathBuilderSpec doesn't need to use drs read interpreter.")
 
-  private val marthaConfig: Config = ConfigFactory.parseString(
-    """martha {
-      |   url = "http://martha-url"
+  private val drsResolverConfig: Config = ConfigFactory.parseString(
+    """resolver {
+      |   url = "http://drshub-url"
       |}
       |""".stripMargin
   )
@@ -387,7 +387,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   private lazy val fakeCredentials = NoCredentials.getInstance
 
   private lazy val drsPathBuilder = DrsPathBuilder(
-    new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+    new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
     None,
   )
 }
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
index fbcd900f371..b5bee55b301 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
@@ -1,6 +1,6 @@
 package cromwell.filesystems.drs
 
-import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, MarthaResponse, MockEngineDrsPathResolver}
+import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, DrsResolverResponse, MockEngineDrsPathResolver}
 import common.assertion.CromwellTimeoutSpec
 import cromwell.cloudsupport.gcp.auth.MockAuthMode
 import cromwell.core.WorkflowOptions
@@ -29,9 +29,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val drsPathResolver = new MockEngineDrsPathResolver()
     val gsUri = "gs://bucket/object"
     val googleServiceAccount = None
-    val marthaResponse = MarthaResponse(gsUri = Option(gsUri), googleServiceAccount = googleServiceAccount)
+    val drsResolverResponse = DrsResolverResponse(gsUri = Option(gsUri), googleServiceAccount = googleServiceAccount)
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
     readerIo.unsafeRunSync() should be(
       GcsReader(googleAuthMode, workflowOptions, requesterPaysProjectIdOption, gsUri, googleServiceAccount)
     )
@@ -43,9 +43,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val requesterPaysProjectIdOption = None
     val drsPathResolver = new MockEngineDrsPathResolver()
     val accessUrl = AccessUrl("https://host/object/path", Option(Map("hello" -> "world")))
-    val marthaResponse = MarthaResponse(accessUrl = Option(accessUrl))
+    val drsResolverResponse = DrsResolverResponse(accessUrl = Option(accessUrl))
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
     readerIo.unsafeRunSync() should be(
       AccessUrlReader(drsPathResolver, accessUrl)
     )
@@ -56,9 +56,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val workflowOptions = WorkflowOptions.empty
     val requesterPaysProjectIdOption = None
     val drsPathResolver = new MockEngineDrsPathResolver()
-    val marthaResponse = MarthaResponse()
+    val drsResolverResponse = DrsResolverResponse()
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
     the[RuntimeException] thrownBy {
       readerIo.unsafeRunSync()
     } should have message DrsPathResolver.ExtractUriErrorMsg
@@ -78,9 +78,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val drsPathResolver = new MockEngineDrsPathResolver(httpClientBuilderOverride = Option(httpClientBuilder))
 
     val accessUrl = AccessUrl("https://host/object/path", Option(Map("hello" -> "world")))
-    val marthaResponse = MarthaResponse(accessUrl = Option(accessUrl))
+    val drsResolverResponse = DrsResolverResponse(accessUrl = Option(accessUrl))
     val channelIo =
-      DrsReader.readInterpreter(Option(MockAuthMode("unused")), WorkflowOptions.empty, None)(drsPathResolver, marthaResponse)
+      DrsReader.readInterpreter(Option(MockAuthMode("unused")), WorkflowOptions.empty, None)(drsPathResolver, drsResolverResponse)
     val channel = channelIo.unsafeRunSync()
 
     val buffer = ByteBuffer.allocate(exampleBytes.length)
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
index 98d4140029b..23dcb1bcd66 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
@@ -11,14 +11,14 @@ import scala.jdk.CollectionConverters._
 
 class DrsResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
-  private val marthaConfig: Config = ConfigFactory.parseMap(
+  private val drsResolverConfig: Config = ConfigFactory.parseMap(
     Map(
-      "martha.url" -> "https://martha-url/martha_v3",
+      "resolver.url" -> "https://drshub-url/drshub_v4",
       "access-token-acceptable-ttl" -> "1 minute"
     ).asJava
   )
 
-  private val mockFileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = marthaConfig)
+  private val mockFileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = drsResolverConfig)
   private val drsPathBuilder = DrsPathBuilder(mockFileSystemProvider, None)
 
 
@@ -62,14 +62,14 @@ class DrsResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     } should have message s"Error while resolving DRS path: ${drsPath.pathAsString}. Error: UrlNotFoundException: No gs url associated with given DRS path."
   }
 
-  it should "throw Runtime Exception when Martha can't find the given DRS path " in {
-    val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathNotExistingInMartha).get.asInstanceOf[DrsPath]
+  it should "throw Runtime Exception when the DRS Resolver can't find the given DRS path " in {
+    val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathNotExistingInDrsResolver).get.asInstanceOf[DrsPath]
 
     the[RuntimeException] thrownBy {
       DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
     } should have message
       s"Error while resolving DRS path: ${drsPath.pathAsString}. " +
         s"Error: RuntimeException: Unexpected response resolving ${drsPath.pathAsString} " +
-        s"through Martha url https://martha-url/martha_v3. Error: 404 Not Found."
+        s"through DRS Resolver url https://drshub-url/drshub_v4. Error: 404 Not Found."
   }
 }
diff --git a/languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala b/languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala
deleted file mode 100644
index e3a6387c739..00000000000
--- a/languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala
+++ /dev/null
@@ -1,75 +0,0 @@
-package languages.cwl
-
-import better.files.File
-import cats.data.EitherT.fromEither
-import cats.effect.IO
-import com.typesafe.config.Config
-import common.Checked
-import common.validation.Checked._
-import common.validation.IOChecked.IOChecked
-import cromwell.core.{WorkflowId, WorkflowOptions, WorkflowSourceFilesCollection}
-import cromwell.languages.util.ImportResolver.ImportResolver
-import cromwell.languages.util.LanguageFactoryUtil
-import cromwell.languages.{LanguageFactory, ValidatedWomNamespace}
-import cwl.preprocessor.CwlReference
-import cwl.{Cwl, CwlDecoder}
-import wom.ResolvedImportRecord
-import wom.core.{WorkflowJson, WorkflowOptionsJson, WorkflowSource}
-import wom.executable.WomBundle
-import wom.expression.IoFunctionSet
-
-class CwlV1_0LanguageFactory(override val config: Config) extends LanguageFactory {
-
-  override val languageName: String = "CWL"
-  override val languageVersionName: String = "v1.0"
-
-  override def validateNamespace(source: WorkflowSourceFilesCollection,
-                                 workflowSource: WorkflowSource,
-                                 workflowOptions: WorkflowOptions,
-                                 importLocalFilesystem: Boolean,
-                                 workflowIdForLogging: WorkflowId,
-                                 ioFunctions: IoFunctionSet,
-                                 importResolvers: List[ImportResolver]): IOChecked[ValidatedWomNamespace] = {
-
-    def parse(): IOChecked[Cwl] = {
-      val decodedCwlReference =
-        for {
-          url <- source.workflowUrl
-          reference <- CwlReference.fromString(url)
-        } yield CwlDecoder.decodeCwlReference(reference.changePointer(source.workflowRoot))
-
-      decodedCwlReference
-        .getOrElse(
-          CwlDecoder.decodeCwlString(
-            workflowSource,
-            source.importsZipFileOption.map(File.newTemporaryFile().appendByteArray(_)),
-            source.workflowRoot,
-            cwlFilename = s"cwl_temp_file_$workflowIdForLogging"
-          ))
-    }
-
-    import cwl.AcceptAllRequirements
-    for {
-      _ <- fromEither[IO](enabledCheck)
-      cwl <- parse()
-      executable <- fromEither[IO](cwl.womExecutable(AcceptAllRequirements, Option(source.inputsJson), ioFunctions, strictValidation))
-      validatedWomNamespace <- fromEither[IO](LanguageFactoryUtil.validateWomNamespace(executable, ioFunctions))
-    } yield validatedWomNamespace
-  }
-
-  override def getWomBundle(workflowSource: WorkflowSource,
-                            workflowSourceOrigin: Option[ResolvedImportRecord],
-                            workflowOptionsJson: WorkflowOptionsJson,
-                            importResolvers: List[ImportResolver],
-                            languageFactories: List[LanguageFactory],
-                            convertNestedScatterToSubworkflow : Boolean = true): Checked[WomBundle] =
-    enabledCheck flatMap { _ => "No getWomBundle method implemented in CWL v1".invalidNelCheck }
-
-  override def createExecutable(womBundle: WomBundle, inputs: WorkflowJson, ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace] =
-    enabledCheck flatMap { _ => "No createExecutable method implemented in CWL v1".invalidNelCheck }
-
-  override def looksParsable(content: String): Boolean = content.linesIterator.exists { l =>
-    val trimmed = l.trim.stripSuffix(",")
-    trimmed == """"cwlVersion": "v1.0"""" || trimmed == "cwlVersion: v1.0"
-  }
-}
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
index 01c5db23084..f7fd70cfc56 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
@@ -9,12 +9,14 @@ import cats.syntax.either._
 import cats.syntax.validated._
 import com.softwaremill.sttp._
 import com.softwaremill.sttp.asynchttpclient.cats.AsyncHttpClientCatsBackend
+import com.typesafe.config.ConfigFactory
 import common.Checked
 import common.transforms.CheckedAtoB
 import common.validation.ErrorOr._
 import common.validation.Checked._
 import common.validation.Validation._
 import cromwell.core.path.{DefaultPathBuilder, Path}
+import net.ceedubs.ficus.Ficus._
 
 import java.nio.file.{Path => NioPath}
 import java.security.MessageDigest
@@ -157,7 +159,9 @@ object ImportResolver {
     }
   }
 
-  case class HttpResolver(relativeTo: Option[String] = None, headers: Map[String, String] = Map.empty) extends ImportResolver {
+  case class HttpResolver(relativeTo: Option[String],
+                          headers: Map[String, String],
+                          hostAllowlist: Option[List[String]]) extends ImportResolver {
     import HttpResolver._
 
     override def name: String = relativeTo match {
@@ -169,7 +173,7 @@ object ImportResolver {
     def newResolverList(newRoot: String): List[ImportResolver] = {
       val rootWithoutFilename = newRoot.split('/').init.mkString("", "/", "/")
       List(
-        HttpResolver(relativeTo = Some(canonicalize(rootWithoutFilename)), headers)
+        HttpResolver(relativeTo = Some(canonicalize(rootWithoutFilename)), headers, hostAllowlist)
       )
     }
 
@@ -183,18 +187,20 @@ object ImportResolver {
         else "Relative path".invalidNelCheck
     }
 
+    def isAllowed(uri: Uri): Boolean = hostAllowlist match {
+      case Some(hosts) => hosts.contains(uri.host)
+      case None => true
+    }
+
     override def innerResolver(str: String, currentResolvers: List[ImportResolver]): Checked[ResolvedImportBundle] = {
-      pathToLookup(str) flatMap { toLookup =>
+      pathToLookup(str) flatMap { toLookup: WorkflowSource =>
         (Try {
-          implicit val sttpBackend = HttpResolver.sttpBackend()
-          val responseIO: IO[Response[String]] = sttp.get(uri"$toLookup").headers(headers).send()
-
-          // temporary situation to get functionality working before
-          // starting in on async-ifying the entire WdlNamespace flow
-          val result: Checked[String] = Await.result(responseIO.unsafeToFuture(), 15.seconds).body.leftMap { e => NonEmptyList(e.toString.trim, List.empty) }
+          val uri: Uri = uri"$toLookup"
 
-          result map {
-            ResolvedImportBundle(_, newResolverList(toLookup), ResolvedImportRecord(toLookup))
+          if (isAllowed(uri)) {
+            getUri(toLookup)
+          } else {
+            s"Disallowed domain in URI. ${uri.toString()}".invalidNelCheck
           }
         } match {
           case Success(result) => result
@@ -203,6 +209,19 @@ object ImportResolver {
       }
     }
 
+    private def getUri(toLookup: WorkflowSource): Either[NonEmptyList[WorkflowSource], ResolvedImportBundle] = {
+      implicit val sttpBackend = HttpResolver.sttpBackend()
+      val responseIO: IO[Response[WorkflowSource]] = sttp.get(uri"$toLookup").headers(headers).send()
+
+      // temporary situation to get functionality working before
+      // starting in on async-ifying the entire WdlNamespace flow
+      val result: Checked[WorkflowSource] = Await.result(responseIO.unsafeToFuture(), 15.seconds).body.leftMap { e => NonEmptyList(e.toString.trim, List.empty) }
+
+      result map {
+        ResolvedImportBundle(_, newResolverList(toLookup), ResolvedImportRecord(toLookup))
+      }
+    }
+
     override def cleanupIfNecessary(): ErrorOr[Unit] = ().validNel
 
     override def hashKey: ErrorOr[String] = relativeTo.toString.md5Sum.validNel
@@ -213,6 +232,18 @@ object ImportResolver {
     import common.util.IntrospectableLazy
     import common.util.IntrospectableLazy._
 
+    def apply(relativeTo: Option[String] = None,
+              headers: Map[String, String] = Map.empty): HttpResolver = {
+      val config = ConfigFactory.load().getConfig("languages.WDL.http-allow-list")
+      val allowListEnabled = config.as[Option[Boolean]]("enabled").getOrElse(false)
+      val allowList: Option[List[String]] =
+        if (allowListEnabled)
+          config.as[Option[List[String]]]("allowed-http-hosts")
+        else None
+
+      new HttpResolver(relativeTo, headers, allowList)
+    }
+
     val sttpBackend: IntrospectableLazy[SttpBackend[IO, Nothing]] = lazily {
       // 2.13 Beginning with sttp 1.6.x a `ContextShift` parameter is now required to construct an
       // `AsyncHttpClientCatsBackend`. There may be a more appropriate choice for backing this than the global
diff --git a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
index 26249b02da1..813a688a573 100644
--- a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
+++ b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
@@ -1,7 +1,8 @@
 package cromwell.languages.util
 
-import java.nio.file.{Files, Paths}
+import com.softwaremill.sttp._
 
+import java.nio.file.{Files, Paths}
 import common.assertion.CromwellTimeoutSpec
 import common.assertion.ErrorOrAssertions._
 import cromwell.core.WorkflowId
@@ -41,13 +42,13 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   it should "resolve a path from no initial root" in {
-    val resolver = HttpResolver()
+    val resolver = HttpResolver(None, Map.empty, None)
     val toResolve = resolver.pathToLookup("http://abc.com:8000/blah1/blah2.wdl")
     toResolve shouldBeValid "http://abc.com:8000/blah1/blah2.wdl"
   }
 
   it should "resolve a path and store the import in ResolvedImportRecord" in {
-    val resolver = HttpResolver()
+    val resolver = HttpResolver(None, Map.empty, None)
     val importUri = "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.wdl"
     val resolvedBundle = resolver.innerResolver(importUri, List(resolver))
 
@@ -57,10 +58,42 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     }
   }
 
+  behavior of "HttpResolver with allowList"
+
+  val allowList = Option(List("my.favorite.wdls.com", "anotherwdlsite.org"))
+  val pathEnd = "bob/loblaw/blah/blah.wdl"
+
+  it should "allow any import when there is no allow list" in {
+    val resolver = HttpResolver(None, Map.empty, None)
+    resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"http://some-garbage.whatever.eu/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"localhost:8080/my/secrets") shouldBe true
+  }
+
+  it should "allow any import that's on the allow list" in {
+    val resolver = HttpResolver(None, Map.empty, allowList)
+    resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"http://anotherwdlsite.org/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"https://yetanotherwdlsite.org/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://FOO.my.favorite.wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"localhost:8080/my/secrets") shouldBe false
+  }
+
+  it should "allow nothing with an empty allow list" in {
+    val resolver = HttpResolver(None, Map.empty, Option(List.empty))
+    resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"http://anotherwdlsite.org/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://yetanotherwdlsite.org/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://FOO.my.favorite.wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"localhost:8080/my/secrets") shouldBe false
+  }
+
   behavior of "HttpResolver with a 'relativeTo' value"
 
-  val relativeHttpResolver = HttpResolver(relativeTo = Some("http://abc.com:8000/blah1/blah2/"))
-  val relativeToGithubHttpResolver = HttpResolver(relativeTo = Some(relativeToGithubRoot))
+  val relativeHttpResolver = HttpResolver(relativeTo = Some("http://abc.com:8000/blah1/blah2/"), Map.empty, None)
+  val relativeToGithubHttpResolver = HttpResolver(relativeTo = Some(relativeToGithubRoot), Map.empty, None)
 
   it should "resolve an absolute path from a different initial root" in {
     val pathToLookup = relativeHttpResolver.pathToLookup("http://def.org:8080/blah3.wdl")
diff --git a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
index df87f2fa644..b96cfa5c2f6 100644
--- a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
+++ b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
@@ -61,7 +61,7 @@ class NamespaceCacheSpec extends AnyFlatSpec with CromwellTimeoutSpec with Befor
     )
 
     var lookupCount = 0
-    val countingResolver = new HttpResolver() {
+    val countingResolver = new HttpResolver(None, Map.empty, None) {
       override def pathToLookup(str: String): Checked[String] = {
         lookupCount = lookupCount + 1
         super.pathToLookup(str)
diff --git a/mkdocs.yml b/mkdocs.yml
index 68e73560774..7aea4302d34 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -79,7 +79,6 @@ nav:
     - Integration tests: developers/Centaur.md
     - Security: developers/Security.md
     - Contribute to docs: developers/Contribute.md
-    - CWL Parsing: developers/CwlParsing.md
     - Bitesize Design Docs:
         - Workflow Parsing & Graph Construction:
             - What is WOM?: developers/bitesize/workflowParsing/whatIsWom.md
@@ -87,7 +86,6 @@ nav:
                 - Overview: developers/bitesize/workflowParsing/wdlParsingOverview.md
                 - From WDL to WDLOM: developers/bitesize/workflowParsing/wdlToWdlom.md
                 - Adding new WDL Engine Functions: developers/bitesize/workflowParsing/engineFunctionAddition.md
-            - From CWL Source to WOM: developers/bitesize/workflowParsing/cwlParsingOverview.md
         - Cromwell Actor System:
             - High level view: developers/bitesize/majorActorSystem/5000FtActorSystem.md
             - Workflow Execution:
diff --git a/processes/release_processes/README.MD b/processes/release_processes/README.MD
index d16f97fddef..5dffe3224a5 100644
--- a/processes/release_processes/README.MD
+++ b/processes/release_processes/README.MD
@@ -2,30 +2,31 @@
 
 ## How to update these processes
 
-Have a better idea about how the deployment processes should work? 
+Have a better idea about how the deployment processes should work?
 See our "updating the process" [process](../README.MD)!
 
 ## Core Process: How to Publish and Release Cromwell
 
-If you're the lucky "Release Rotation Engineer" this time, you should do the following four things:
+Cromwell versions are updated on a weekly cadence automatically. For more information see [here](https://support.terra.bio/hc/en-us/articles/9512163608731-Faster-Cromwell-updates-in-Terra-)
 
-1. Create a Jira ticket for the release (look at previous release tickets if you're not sure how). In the Suggested 
+Manually cutting a numeric release is expected to continue being done on a cadence of every ~6 months. If you're the lucky "Release Rotation Engineer" this time, you should do the following four things:
+
+1. Create a Jira ticket for the release (look at previous release tickets if you're not sure how). In the Suggested
 Release Notes field, add "Terra is now running Cromwell <version>" along with any other release notes relevant to Terra
 users.
-1. Check that all most recent executions of Cromwell's Jenkins tests have succeeded, and that all those executions were 
-against the most recent commit in "develop" branch. There are 2 groups of Jenkins tests which have to be checked (you 
+1. Check that all most recent executions of Cromwell's Jenkins tests have succeeded, and that all those executions were
+against the most recent commit in "develop" branch. There are 2 groups of Jenkins tests which have to be checked (you
 will need to be on the Broad internal network or VPN to open the following links):
     1. Tests for various backends supported by Cromwell. Log into Jenkins [here](https://fc-jenkins.dsp-techops.broadinstitute.org), check the tests [here](https://fc-jenkins.dsp-techops.broadinstitute.org/job/cromwell-cron-parent/).
     1. Tests for Cromwell in Terra environment. Log into Jenkins [here](https://fc-jenkins.dsp-techops.broadinstitute.org), check the tests [here](https://fc-jenkins.dsp-techops.broadinstitute.org/view/Batch/).
-1. [Run the publish script to create a new version of Cromwell](#how-to-publish-a-new-cromwell-version)  
-1. [Run through the "How to Release Cromwell into Firecloud/Terra" process](#how-to-release-cromwell-into-firecloud--terra)  
-1. [Run through the "How to Deploy Cromwell in CaaS prod" process](#how-to-deploy-cromwell-in-caas-staging-and-caas-prod)  
+1. [Run the publish script to create a new version of Cromwell](#how-to-publish-a-new-cromwell-version)
+1. [Run through the "How to Deploy Cromwell in CaaS prod" process](#how-to-deploy-cromwell-in-caas-staging-and-caas-prod)
 
 ### How to publish a new Cromwell version
 
 #### Announce your intentions
 
-Post a message in `#dsp-batch-private` letting people know that a publish is imminent in case there are PRs they want to get
+Post a message in `#dsp-workflows-private` letting people know that a publish is imminent in case there are PRs they want to get
 wrapped up and merged to `develop` to go out in the forthcoming version of Cromwell.
 
 #### Get a Github token
@@ -45,7 +46,8 @@ The release WDL uses a github token to perform actions on your behalf.
 Make or copy the following files into a temporary `release/` directory outside the Cromwell repository. This removes any chance of committing your token.
 
 * A copy of the workflow file to run (https://github.com/broadinstitute/cromwell/blob/develop/publish/publish_workflow.wdl)
-* An inputs json like this:
+* An inputs json like this one.
+  * `publishHomebrew` is `false` due to Homebrew taking on this part themselves. Homebrew remains an active distribution channel.
 
 ```json
 {
@@ -82,7 +84,7 @@ The workflow outputs its status to the console.
 
 #### Make sure it all went swimmingly
 
-* Check that the workflow succeeded. 
+* Check that the workflow succeeded.
 * Check that there's now a new Cromwell release listed [here](https://github.com/broadinstitute/cromwell/releases).
 * Look [in Travis](https://app.travis-ci.com/github/broadinstitute/cromwell/branches) for the release tag build that will publish Docker images for the new version.
 * Let `#dsp-batch-private` know that it's okay to resume merges to `develop`.
@@ -92,17 +94,6 @@ The workflow outputs its status to the console.
     * See the `cromwell::build::publish_artifacts()` function for details
 * **One business day later,** confirm that [the Homebrew package](https://formulae.brew.sh/formula/cromwell) has the latest version. If it doesn't, start investigation by looking at [Homebrew PR's](https://github.com/Homebrew/homebrew-core/pulls?q=is%3Apr+cromwell).
 
-### How to Release Cromwell into Firecloud / Terra
-
-**Note:** If the Cromwell CHANGELOG indicates that the upgrade might take some time (e.g., because of a database migration), checking in with the release engineer
-and user support/comms to let them know that the upgrade may involve downtime is also required. You may need to help draft an impact statement and co-ordinate timing
-the deploy to make sure user impact in minimized.
-
-**Note:** How to accomplish some of these steps might be non-obvious to you (e.g., generating the release notes).
-If so, refer to the additional details in the [full document](https://docs.google.com/document/d/1EEzwemE8IedCplIwL506fiqXr0262Pz4G0x6Cr6V-5E). 
-
-![firecloud-develop](firecloud-develop.dot.png) 
-
 ### How to Deploy Cromwell in CaaS staging and CaaS prod
 
 CaaS is "Cromwell as a Service". It is used by a couple of Broad teams (Pipelines and Epigenomics), though the long-term plan is for those teams to migrate to using Terra.
@@ -110,7 +101,7 @@ CaaS is "Cromwell as a Service". It is used by a couple of Broad teams (Pipeline
 **Note:** If the Cromwell CHANGELOG indicates that the upgrade might take some time (e.g., because of a database migration), checking in with the CaaS users
 to let them know that the upgrade is about to happen is a good idea.
 
-Deploying to CaaS is detailed in the [Quick CaaS Deployment Guide](https://docs.google.com/document/d/1s0YC-oohJ7o-OGcgnH_-YBtIEKmLIPTRpG36yvWxUpE) 
+Deploying to CaaS is detailed in the [Quick CaaS Deployment Guide](https://docs.google.com/document/d/1s0YC-oohJ7o-OGcgnH_-YBtIEKmLIPTRpG36yvWxUpE)
 
 ### How to be Sure You're Done
 
@@ -139,7 +130,7 @@ This generates the client library and runs the generated tests as well.  A succe
 [success] Total time: 4 s, completed Jun 26, 2019 3:01:19 PM
 ```
 
-To publish to artifactory, first obtain the artifactory username and credentials.  Then run
+To publish to artifactory, first obtain the artifactory username and credentials. Credentials are located in Vault at path `secret/dsde/cromwell/common/cromwell-artifactory`. Then run
 
 ```
 export ARTIFACTORY_USERNAME=<the-username>
@@ -147,8 +138,10 @@ export ARTIFACTORY_PASSWORD=<the-password>
 ./scripts/publish-client.sh
 ```
 
+A SNAP version of the client library will be published in jFrog at [this path](https://broadinstitute.jfrog.io/ui/repos/tree/General/libs-release-local/org/broadinstitute/cromwell).
+
 ## Cromwell setup for publishing
 
 One can run a publishing-friendly Cromwell using a containerized MySQL server and config files
-from Cromwell's CI. See the `start_publish_mysql_docker.sh` and `start_publish_cromwell.sh` 
+from Cromwell's CI. See the `start_publish_mysql_docker.sh` and `start_publish_cromwell.sh`
 scripts under `release_processes/scripts`.
diff --git a/project/ContinuousIntegration.scala b/project/ContinuousIntegration.scala
index 321ac0a69ab..e2b61994c22 100644
--- a/project/ContinuousIntegration.scala
+++ b/project/ContinuousIntegration.scala
@@ -67,9 +67,7 @@ object ContinuousIntegration {
   /**
     * For "reasons" these projects are excluded from the root aggregation in build.sbt.
     */
-  private val unaggregatedProjects = Map(
-    "cwlEncoder" -> "not sure what this is"
-  )
+  private val unaggregatedProjects = Map.empty
 
   /**
     * Get the list of projects defined in build.sbt excluding the passed in root project.
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 519c13d4c37..5be942f6d38 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -6,13 +6,12 @@ object Dependencies {
   private val akkaV = "2.5.32" // scala-steward:off (CROM-6637)
   private val ammoniteOpsV = "2.4.1"
   private val apacheHttpClientV = "4.5.13"
-  private val awsSdkV = "2.17.152"
+  private val awsSdkV = "2.17.265"
   // We would like to use the BOM to manage Azure SDK versions, but SBT doesn't support it.
   // https://github.com/Azure/azure-sdk-for-java/tree/main/sdk/boms/azure-sdk-bom
   // https://github.com/sbt/sbt/issues/4531
-  private val azureStorageBlobNioV = "12.0.0-beta.18"
-  private val azureIdentitySdkV = "1.4.2"
-  private val azureKeyVaultSdkV = "4.3.7"
+  private val azureStorageBlobNioV = "12.0.0-beta.19"
+  private val azureIdentitySdkV = "1.4.6"
   private val betterFilesV = "3.9.1"
   /*
   cats-effect, fs2, http4s, and sttp (also to v3) should all be upgraded at the same time to use cats-effect 3.x.
@@ -30,11 +29,11 @@ object Dependencies {
   private val commonsLang3V = "3.12.0"
   private val commonsMathV = "3.6.1"
   private val commonNetV = "3.8.0" // via: https://commons.apache.org/proper/commons-net/
-  private val commonsTextV = "1.9"
+  private val commonsTextV = "1.10.0"
   private val configsV = "0.6.1"
   private val delightRhinoSandboxV = "0.0.15"
   private val diffsonSprayJsonV = "4.1.1"
-  private val ficusV = "1.5.1"
+  private val ficusV = "1.5.2"
   private val fs2V = "2.5.9" // scala-steward:off (CROM-6564)
   private val googleApiClientV = "1.33.2"
   private val googleCloudBigQueryV = "2.10.0"
@@ -43,7 +42,7 @@ object Dependencies {
   private val googleCloudMonitoringV = "3.2.5"
   private val googleCloudNioV = "0.124.8"
   private val googleCloudStorageV = "2.9.2"
-  private val googleGaxGrpcV = "2.12.2"
+  private val googleGaxGrpcV = "2.19.0"
   // latest date via: https://mvnrepository.com/artifact/com.google.apis/google-api-services-genomics
   private val googleGenomicsServicesV2Alpha1ApiV = "v2alpha1-rev20210811-1.32.1"
   private val googleHttpClientApacheV = "2.1.2"
@@ -53,19 +52,24 @@ object Dependencies {
   private val googleOauth2V = "1.5.3"
   private val googleOauthClientV = "1.33.1"
   private val googleCloudResourceManagerV = "1.2.5"
-  private val grpcV = "1.45.0"
+  private val grpcV = "1.45.1"
   private val guavaV = "31.0.1-jre"
   private val heterodonV = "1.0.0-beta3"
   private val hsqldbV = "2.6.1"
   private val http4sV = "0.21.31" // this release is EOL. We need to upgrade further for cats3. https://http4s.org/versions/
   private val jacksonV = "2.13.3"
-  private val janinoV = "3.1.6"
+  private val jakartaActivationV = "1.2.1"
+  private val jakartaAnnotationV = "1.3.5"
+  private val jakartaInjectV = "2.6.1"
+  private val jakartaXmlBindApiV = "2.3.2"
+  private val janinoV = "3.1.7"
+  private val jerseyV = "2.32" // Use a jersey compatible with WSM. See notes in wsmDependencies below.
   private val jsr305V = "3.0.2"
   private val junitV = "4.13.2"
   private val kindProjectorV = "0.13.2"
   private val kittensV = "2.3.2"
   private val liquibaseV = "4.8.0"
-  private val logbackV = "1.2.10"
+  private val logbackV = "1.2.11"
   private val lz4JavaV = "1.8.0"
   private val mariadbV = "2.7.4"
   /*
@@ -75,9 +79,10 @@ object Dependencies {
   private val metrics4ScalaV = "4.2.8"
   private val metrics3StatsdV = "4.2.0"
   private val mockFtpServerV = "3.0.0"
-  private val mockitoV = "3.11.2"
-  private val mockserverNettyV = "5.11.2"
-  private val mouseV = "1.0.10"
+  private val mockitoV = "3.12.4"
+  private val mockserverNettyV = "5.14.0"
+  private val mouseV = "1.0.11"
+
   /*
   Newer version 8.0.29 fails `Control characters should work with metadata` Centaur tests, has charset changes mentioned in release notes
   https://dev.mysql.com/doc/relnotes/mysql/8.0/en/news-8-0-29.html#mysqld-8-0-29-charset
@@ -85,22 +90,23 @@ object Dependencies {
   private val mysqlV = "8.0.28"
   private val nettyV = "4.1.72.Final"
   private val owlApiV = "5.1.19"
-  private val postgresV = "42.3.3"
-  private val pprintV = "0.7.1"
+  private val postgresV = "42.4.1"
+  private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
-  private val refinedV = "0.9.28"
-  private val rhinoV = "1.7.13"
+  private val refinedV = "0.10.1"
+  private val rhinoV = "1.7.14"
+
   private val scalaCollectionCompatV = "2.5.0"
   private val scalaGraphV = "1.13.1"
-  private val scalaLoggingV = "3.9.4"
+  private val scalaLoggingV = "3.9.5"
   private val scalaPoolV = "0.4.3"
-  private val scalacticV = "3.2.10"
-  private val scalameterV = "0.19"
+  private val scalacticV = "3.2.13"
+  private val scalameterV = "0.21"
   private val scalatestV = "3.2.10"
   private val scalatestScalacheckV = scalatestV + ".0"
-  private val scoptV = "4.0.1"
-  private val sentryLogbackV = "5.2.4"
-  private val shapelessV = "2.3.7"
+  private val scoptV = "4.1.0"
+  private val sentryLogbackV = "5.7.4"
+  private val shapelessV = "2.3.9"
   private val simulacrumV = "1.0.1"
   private val slf4jV = "1.7.32"
   private val slickCatsV = "0.10.4"
@@ -116,14 +122,14 @@ object Dependencies {
     * https://github.com/slick/slick/pull/2201
   */
   private val slickV = "3.4.0-M1"
-  private val snakeyamlV = "1.30"
+  private val snakeyamlV = "1.33"
   private val sprayJsonV = "1.3.6"
   private val sttpV = "1.7.2"
   private val swaggerParserV = "1.0.56"
-  private val swaggerUiV = "4.5.0"
-  private val testContainersScalaV = "0.40.2"
+  private val swaggerUiV = "4.5.2"
+  private val testContainersScalaV = "0.40.10"
   private val tikaV = "2.3.0"
-  private val typesafeConfigV = "1.4.1"
+  private val typesafeConfigV = "1.4.2"
   private val workbenchGoogleV = "0.21-5c9c4f6" // via: https://github.com/broadinstitute/workbench-libs/blob/develop/google/CHANGELOG.md
   private val workbenchModelV = "0.15-f9f0d4c" // via: https://github.com/broadinstitute/workbench-libs/blob/develop/model/CHANGELOG.md
   private val workbenchUtilV = "0.6-65bba14" // via: https://github.com/broadinstitute/workbench-libs/blob/develop/util/CHANGELOG.md
@@ -141,7 +147,8 @@ object Dependencies {
     "generic",
     "shapes",
     "refined",
-    "literal"
+    "literal",
+    "optics"
   ).map(m => "io.circe" %% s"circe-$m" % circeV) :+ circeYamlDependency :+
   "io.circe" %% "circe-generic-extras" % circeGenericExtrasV :+
   "io.circe" %% "circe-config" % circeConfigV
@@ -170,6 +177,16 @@ object Dependencies {
     "com.google.api-client" % "google-api-client-jackson2" % googleApiClientV
       exclude("com.google.guava", "guava-jdk5"),
     "com.google.cloud" % "google-cloud-resourcemanager" % googleCloudResourceManagerV,
+    /*
+    The google-cloud-java dependencies have similar issues with using an older javax.* vs. jakarta.* as guice.
+    google-cloud-java is still using javax.annotation and guice is sticking with javax.inject:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/google-cloud-java/blob/v0.201.0/google-cloud-jar-parent/pom.xml#L131-L136
+
+     Globally use of jakarta instead of javax until Google does themselves.
+     The javax.annotation exclusion is below in cromwellExcludeDependencies.
+     */
+    "jakarta.annotation" % "jakarta.annotation-api" % jakartaAnnotationV,
   )
 
   val spiDependencies: List[ModuleID] = List(
@@ -188,9 +205,38 @@ object Dependencies {
     "com.azure" % "azure-identity" % azureIdentitySdkV
       exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
       exclude("jakarta.activation", "jakarta.activation-api"),
-    "com.azure" % "azure-security-keyvault-secrets" % azureKeyVaultSdkV
-      exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
-      exclude("jakarta.activation", "jakarta.activation-api")
+    "com.azure" % "azure-core-management" % "1.7.1",
+    "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0"
+  )
+
+  val wsmDependencies: List[ModuleID] = List(
+    "bio.terra" % "workspace-manager-client" % "0.254.452-SNAPSHOT"
+      exclude("com.sun.activation", "jakarta.activation"),
+    /*
+    1. WSM is looking for the rs-api under javax.*.
+
+    Jersey 3.x switched to jakarta.ws.rs-api 3.x. If one uses jakarta's rs-api, 3.x will automatically evict 2.x.
+
+    However, jakarta's rs-api 2.x provides packages javax.* while 3.x provides jakarta.* instead.
+     - https://javadoc.io/doc/jakarta.ws.rs/jakarta.ws.rs-api/2.1.6/javax/ws/rs/package-summary.html
+     - https://javadoc.io/doc/jakarta.ws.rs/jakarta.ws.rs-api/3.1.0/jakarta.ws.rs/module-summary.html
+
+    TODO: Perhaps coordinate with the WSM team to use the jakarta 3.x rs-api and jakarta.* instead of javax.*.
+
+    2. Use the exact version of jersey that WSM is using.
+
+    Jersey libraries cannot be mixed and matched as the various modules cannot be mixed and matched.
+    For example jersey-client 2.32 is not compatible with jersey-common 2.37.
+
+    If needed one may also explicitly enumerate the list of jersey artifacts and explicitly set the versions similar to
+    catsDepeendencies, akkaHttpDependencies, etc.
+     - https://broadinstitute.jfrog.io/ui/repos/tree/PomView/libs-snapshot-local/bio/terra/workspace-manager-client/0.254.452-SNAPSHOT/workspace-manager-client-0.254.452-20221114.190249-1.pom
+     - https://github.com/eclipse-ee4j/jersey/blob/2.32/core-client/src/main/java/org/glassfish/jersey/client/ClientExecutorProvidersConfigurator.java#L139
+     - https://github.com/eclipse-ee4j/jersey/blob/2.37/core-client/src/main/java/org/glassfish/jersey/client/ClientExecutorProvidersConfigurator.java#L136-L137
+     */
+    "org.glassfish.jersey.inject" % "jersey-hk2" % jerseyV
+      exclude("com.sun.activation", "jakarta.activation"),
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
   )
 
   val implFtpDependencies = List(
@@ -236,7 +282,13 @@ object Dependencies {
     "org.codehaus.janino" % "janino" % janinoV,
     // Replace all log4j usage with slf4j
     // https://www.slf4j.org/legacy.html#log4j-over-slf4j
-    "org.slf4j" % "log4j-over-slf4j" % slf4jV
+    "org.slf4j" % "log4j-over-slf4j" % slf4jV,
+    // Replace all commons-logging usage with slf4j
+    // https://www.slf4j.org/legacy.html#jcl-over-slf4j
+    "org.slf4j" % "jcl-over-slf4j" % slf4jV,
+    // Enable runtime replacing of java.util.logging usage with slf4j
+    // https://www.slf4j.org/legacy.html#jul-to-slf4j
+    "org.slf4j" % "jul-to-slf4j" % slf4jV,
   ) ++ slf4jFacadeDependencies
 
   private val slickDependencies = List(
@@ -246,7 +298,11 @@ object Dependencies {
   )
 
   private val liquibaseDependencies = List(
+    // The XML bind API replacement below may be removed when this ticket is addressed:
+    // https://github.com/liquibase/liquibase/issues/2991
     "org.liquibase" % "liquibase-core" % liquibaseV
+      exclude("javax.xml.bind", "jaxb-api"),
+    "jakarta.xml.bind" % "jakarta.xml.bind-api" % jakartaXmlBindApiV,
   )
 
   private val akkaDependencies = List(
@@ -319,15 +375,24 @@ object Dependencies {
   private val googleCloudDependencies = List(
     "io.grpc" % "grpc-core" % grpcV,
     "com.google.guava" % "guava" % guavaV,
+    /*
+    The google-cloud-nio has the same problems with an ancient inject as guice:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/java-storage-nio/blob/v0.124.20/google-cloud-nio/pom.xml#L49-L53
+
+     Force use of jakarta instead of javax until Google does themselves.
+     */
     "com.google.cloud" % "google-cloud-nio" % googleCloudNioV
       exclude("com.google.api.grpc", "grpc-google-common-protos")
       exclude("com.google.cloud.datastore", "datastore-v1-protos")
+      exclude("javax.inject", "javax.inject")
       exclude("org.apache.httpcomponents", "httpclient"),
     "org.broadinstitute.dsde.workbench" %% "workbench-google" % workbenchGoogleV
       exclude("com.google.apis", "google-api-services-genomics"),
     "org.apache.httpcomponents" % "httpclient" % apacheHttpClientV,
     "com.google.apis" % "google-api-services-cloudkms" % googleCloudKmsV
-      exclude("com.google.guava", "guava-jdk5")
+      exclude("com.google.guava", "guava-jdk5"),
+    "org.glassfish.hk2.external" % "jakarta.inject" % jakartaInjectV,
   ) ++ googleGenomicsV2Alpha1Dependency ++ googleLifeSciencesV2BetaDependency
 
   private val dbmsDependencies = List(
@@ -403,7 +468,7 @@ object Dependencies {
     List("scalatest", "mysql", "mariadb", "postgresql")
       .map(name => "com.dimafeng" %% s"testcontainers-scala-$name" % testContainersScalaV % Test)
 
-  val blobFileSystemDependencies: List[ModuleID] = azureDependencies
+  val blobFileSystemDependencies: List[ModuleID] = azureDependencies ++ wsmDependencies
 
   val s3FileSystemDependencies: List[ModuleID] = junitDependencies
 
@@ -427,56 +492,23 @@ object Dependencies {
   val languageFactoryDependencies = List(
     "com.softwaremill.sttp" %% "core" % sttpV,
     "com.softwaremill.sttp" %% "async-http-client-backend-cats" % sttpV
+      exclude("com.sun.activation", "javax.activation"),
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
   )
 
   val draft2LanguageFactoryDependencies = List(
     "org.mock-server" % "mockserver-netty" % mockserverNettyV % Test
   )
 
-  /*
-  The distro artifact contains the actual impl, but transitively includes OSGI bundles that conflict with assembly:
-  - https://github.com/owlcs/owlapi/wiki/Documentation/45d8f63d055f820c6ac2ca6c4679a2a7b705449b#howto
-  - https://github.com/owlcs/owlapi/issues/455
-  - https://github.com/owlcs/owlapi/issues/603
-
-  jcl-over-slf4j.jar is a replacement for commons-logging 1.1.1. Meanwhile our extensive transitive use of apache's
-  httpclient has been including commons-logging 1.2 for a while. Now the owl api dependency jcl-over-slf4j is
-  conflicting during assembly. As there have been no reported errors AFAIK with commons-logging leaving it in for now.
-  However as we use slf4j for cromwell log configuration the correct thing might actually be to exclude commons-logging
-  whenever importing httpclient and include jcl-over-slf4j. That way we can control all of our logging in one place.
-
-  - https://www.slf4j.org/legacy.html#jclOverSLF4J
-   */
-  val owlApiDependencies = List(
-    "net.sourceforge.owlapi" % "owlapi-distribution" % owlApiV
-      exclude("org.apache.httpcomponents", "httpclient-osgi")
-      exclude("org.apache.httpcomponents", "httpcore-osgi")
-      exclude("org.slf4j", "jcl-over-slf4j"),
-    "org.apache.httpcomponents" % "httpclient-cache" % apacheHttpClientV,
-    "org.apache.httpcomponents" % "httpclient" % apacheHttpClientV
-  )
-
-  val cwlDependencies: List[ModuleID] = List(
-    "com.lihaoyi" %% "ammonite-ops" % ammoniteOpsV,
-    "org.broadinstitute" % "heterodon" % heterodonV classifier "single",
-    "org.scalactic" %% "scalactic" % scalacticV,
-    "io.circe" %% "circe-optics" % circeOpticsV,
-    "org.mozilla" % "rhino" % rhinoV,
-    "org.javadelight" % "delight-rhino-sandbox" % delightRhinoSandboxV,
-    "commons-io" % "commons-io" % commonsIoV % Test
-  ) ++ betterFilesDependencies ++ owlApiDependencies
-
   val womtoolDependencies: List[ModuleID] = catsDependencies ++ slf4jBindingDependencies
 
-  val centaurCwlRunnerDependencies: List[ModuleID] = List(
-    "com.github.scopt" %% "scopt" % scoptV,
-    "io.circe" %% "circe-optics" % circeOpticsV
-  ) ++ slf4jBindingDependencies
-
   val coreDependencies: List[ModuleID] = List(
     "com.google.auth" % "google-auth-library-oauth2-http" % googleOauth2V,
     "com.chuusai" %% "shapeless" % shapelessV,
-    "com.storm-enroute" %% "scalameter" % scalameterV % Test,
+    // NOTE: See scalameter comment under engineDependencies
+    "com.storm-enroute" %% "scalameter" % scalameterV % Test
+      exclude("com.fasterxml.jackson.module", "jackson-module-scala_2.13")
+      exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.github.scopt" %% "scopt" % scoptV,
   ) ++ akkaStreamDependencies ++ configDependencies ++ catsDependencies ++ circeDependencies ++
     googleApiClientDependencies ++ statsDDependencies ++ betterFilesDependencies ++
@@ -502,10 +534,24 @@ object Dependencies {
   val engineDependencies: List[ModuleID] = List(
     "commons-codec" % "commons-codec" % commonsCodecV,
     "commons-io" % "commons-io" % commonsIoV,
+    /*
+    Maybe ScalaMeter should be used, but is anyone?
+
+    For now keep its dependencies from breaking jackson for other libraries. If someone wants to use it they can
+    re-fight with dependency-hell at that point.
+
+    Avoid:
+    "com.fasterxml.jackson.databind.JsonMappingException: Scala module 2.11.3 requires Jackson Databind
+    version >= 2.11.0 and < 2.12.0":
+     - https://scalameter.github.io/home/gettingstarted/0.7/sbt/index.html
+     - https://github.com/FasterXML/jackson-module-scala/blob/jackson-module-scala-2.11.3/src/main/scala/com/fasterxml/jackson/module/scala/JacksonModule.scala#L53-L62
+     */
     "com.storm-enroute" %% "scalameter" % scalameterV
       exclude("com.fasterxml.jackson.core", "jackson-databind")
       exclude("com.fasterxml.jackson.module", "jackson-module-scala")
-      exclude("org.scala-tools.testing", "test-interface"),
+      exclude("com.fasterxml.jackson.module", "jackson-module-scala_2.13")
+      exclude("org.scala-tools.testing", "test-interface")
+      exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.fasterxml.jackson.core" % "jackson-databind" % jacksonV,
     "io.github.andrebeat" %% "scala-pool" % scalaPoolV
   ) ++ swaggerUiDependencies ++ akkaHttpDependencies ++ akkaHttpCirceIntegrationDependency ++ circeDependencies ++
@@ -519,11 +565,24 @@ object Dependencies {
   val serverDependencies: List[ModuleID] = slf4jBindingDependencies
 
   val cromiamDependencies: List[ModuleID] = List(
+    /*
+    sttp 1.x was last released in 2019
+    See above comment regarding "cats-effect, fs2, http4s, and sttp" all needing to update together.
+    For now, replace sttp 1.x's com.sun.activation usage with the jakarta version.
+
+    NOTE when upgrading: sttp 3.x no longer requires an async-http-client-backend-future so jakarta.activation can
+    probably be removed from the dependencies:
+     - https://sttp.softwaremill.com/en/v3/backends/future.html#using-async-http-client
+     - https://sttp.softwaremill.com/en/v2/backends/future.html#using-async-http-client
+     - https://sttp.softwaremill.com/en/v1/backends/asynchttpclient.html
+     */
     "com.softwaremill.sttp" %% "core" % sttpV,
-    "com.softwaremill.sttp" %% "async-http-client-backend-future" % sttpV,
+    "com.softwaremill.sttp" %% "async-http-client-backend-future" % sttpV
+      exclude("com.sun.activation", "javax.activation"),
     "com.typesafe.scala-logging" %% "scala-logging" % scalaLoggingV,
     "org.broadinstitute.dsde.workbench" %% "workbench-model" % workbenchModelV,
-    "org.broadinstitute.dsde.workbench" %% "workbench-util" % workbenchUtilV
+    "org.broadinstitute.dsde.workbench" %% "workbench-util" % workbenchUtilV,
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
   ) ++ akkaHttpDependencies ++ swaggerUiDependencies ++ slf4jBindingDependencies
 
   val wes2cromwellDependencies: List[ModuleID] = coreDependencies ++ akkaHttpDependencies
@@ -542,7 +601,9 @@ object Dependencies {
     "org.scalatest" %% "scalatest" % scalatestV,
     // Use mockito Java DSL directly instead of the numerous and often hard to keep updated Scala DSLs.
     // See also scaladoc in common.mock.MockSugar and that trait's various usages.
-    "org.mockito" % "mockito-core" % mockitoV
+    "org.mockito" % "mockito-core" % mockitoV,
+    "io.github.jbwheatley" %% "pact4s-scalatest"  % "0.7.0",
+    "io.github.jbwheatley" %% "pact4s-circe" %  "0.7.0"
   ) ++ slf4jBindingDependencies // During testing, add an slf4j binding for _all_ libraries.
 
   val kindProjectorPlugin = "org.typelevel" % "kind-projector" % kindProjectorV cross CrossVersion.full
@@ -560,18 +621,17 @@ object Dependencies {
     "com.iheart" %% "ficus" % ficusV,
     "com.softwaremill.sttp" %% "circe" % sttpV,
     "com.github.scopt" %% "scopt" % scoptV,
+    "org.apache.commons" % "commons-csv" % commonsCsvV,
   ) ++ circeDependencies ++ catsDependencies ++ slf4jBindingDependencies ++ languageFactoryDependencies ++ azureDependencies
 
   val allProjectDependencies: List[ModuleID] =
     backendDependencies ++
-      centaurCwlRunnerDependencies ++
       centaurDependencies ++
       cloudSupportDependencies ++
       commonDependencies ++
       coreDependencies ++
       cromiamDependencies ++
       cromwellApiClientDependencies ++
-      cwlDependencies ++
       databaseMigrationDependencies ++
       databaseSqlDependencies ++
       draft2LanguageFactoryDependencies ++
@@ -722,4 +782,22 @@ object Dependencies {
       nimbusdsOverrides ++
       bouncyCastleOverrides ++
       protobufJavaOverrides
+
+  /*
+  Libraries that should be globally excluded.
+   */
+  val cromwellExcludeDependencies: List[ExclusionRule] = List(
+    // Replaced with jcl-over-slf4j
+    ExclusionRule("commons-logging", "commons-logging"),
+    /*
+    The google-cloud-java dependencies have similar issues with using an older javax.* vs. jakarta.* as guice.
+    google-cloud-java is still using javax.annotation and guice is sticking with javax.inject:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/google-cloud-java/blob/v0.201.0/google-cloud-jar-parent/pom.xml#L131-L136
+
+     Globally use of jakarta instead of javax until Google does themselves.
+     The jakarta.annotation inclusion is above in googleApiClientDependencies.
+     */
+    ExclusionRule("javax.annotation", "javax.annotation-api"),
+  )
 }
diff --git a/project/GenerateRestApiDocs.scala b/project/GenerateRestApiDocs.scala
index afb1168fa5c..9173a25c3c5 100644
--- a/project/GenerateRestApiDocs.scala
+++ b/project/GenerateRestApiDocs.scala
@@ -1,13 +1,12 @@
-import java.time.OffsetDateTime
-import java.time.format.DateTimeFormatter
-
-import io.github.swagger2markup.Swagger2MarkupConverter
 import io.github.swagger2markup.builder.Swagger2MarkupConfigBuilder
-import io.github.swagger2markup.markup.builder.MarkupLanguage
+import io.github.swagger2markup.{MarkupLanguage, Swagger2MarkupConverter}
 import org.apache.commons.lang3.{ClassUtils, StringUtils}
 import sbt.Keys._
 import sbt._
 
+import java.time.OffsetDateTime
+import java.time.format.DateTimeFormatter
+
 /**
   * Provides a task to generate the REST API markdown from the Swagger YAML.
   *
diff --git a/project/Publishing.scala b/project/Publishing.scala
index 150c30ca293..1d4143fc13e 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -36,7 +36,20 @@ object Publishing {
       ArrayBuffer(broadinstitute/cromwell:dev, broadinstitute/cromwell:develop)
     */
     dockerTags := {
-      val versionsCsv = if (Version.isSnapshot) version.value else s"$cromwellVersion,${version.value}"
+      val versionsCsv = if (Version.isSnapshot) {
+        // Tag looks like `85-443a6fc-SNAP`
+        version.value
+      } else {
+        if (Version.isRelease) {
+          // Tags look like `85`, `85-443a6fc`
+          s"$cromwellVersion,${version.value}"
+        } else {
+          // Tag looks like `85-443a6fc`
+          version.value
+        }
+      }
+
+      // Travis applies (as of 10/22) the `dev` and `develop` tags on merge to `develop`
       sys.env.getOrElse("CROMWELL_SBT_DOCKER_TAGS", versionsCsv).split(",")
     },
     docker / imageNames := dockerTags.value map { tag =>
@@ -137,6 +150,10 @@ object Publishing {
     "Broad Artifactory" at
       "https://broadinstitute.jfrog.io/broadinstitute/libs-release/"
 
+  private val broadArtifactoryResolverSnap: Resolver =
+    "Broad Artifactory Snapshots" at
+      "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot-local/"
+
   // https://stackoverflow.com/questions/9819965/artifactory-snapshot-filename-handling
   private val buildTimestamp = System.currentTimeMillis() / 1000
 
@@ -146,6 +163,7 @@ object Publishing {
 
   val additionalResolvers = List(
     broadArtifactoryResolver,
+    broadArtifactoryResolverSnap,
     Resolver.sonatypeRepo("releases")
   )
 
diff --git a/project/Settings.scala b/project/Settings.scala
index 79242733583..797d7917dd9 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -70,7 +70,7 @@ object Settings {
     assembly / assemblyMergeStrategy := customMergeStrategy.value,
   )
 
-  val Scala2_13Version = "2.13.8"
+  val Scala2_13Version = "2.13.9"
   private val ScalaVersion: String = Scala2_13Version
   private val sharedSettings: Seq[Setting[_]] =
     cromwellVersionWithGit ++ publishingSettings ++ List(
@@ -86,6 +86,7 @@ object Settings {
       Tags.limit(Tags.Test, 1)
     ),
     dependencyOverrides ++= cromwellDependencyOverrides,
+    excludeDependencies ++= cromwellExcludeDependencies,
     scalacOptions ++= baseSettings ++ warningSettings ++ consoleHostileSettings,
     // http://stackoverflow.com/questions/31488335/scaladoc-2-11-6-fails-on-throws-tag-with-unable-to-find-any-member-to-link#31497874
     Compile / doc / scalacOptions ++= baseSettings ++ List("-no-link-warnings"),
diff --git a/project/Version.scala b/project/Version.scala
index 80f74d66d3f..ca782b990e2 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -1,19 +1,31 @@
 import Dependencies._
-import com.typesafe.sbt.SbtGit._
+import com.github.sbt.git.SbtGit._
 import sbt.Keys._
 import sbt._
+import com.github.sbt.git.SbtGit
 
 object Version {
   // Upcoming release, or current if we're on a master / hotfix branch
-  val cromwellVersion = "83"
+  val cromwellVersion = "85"
 
   /**
     * Returns true if this project should be considered a snapshot.
     *
     * The value is read in directly from the system property `project.isSnapshot` as there were confusing issues with
     * the multi-project and sbt.Keys#isSnapshot().
+    *
+    * Default `true`.
+    */
+  val isSnapshot: Boolean = sys.props.get("project.isSnapshot").forall(_.toBoolean)
+
+  /**
+    * Returns `true` if this project should tag a release like `85` in addition to a hash like `85-443a6fc`.
+    *
+    * Has no effect when `isSnapshot` is `true`.
+    *
+    * Default `true`.
     */
-  val isSnapshot = sys.props.get("project.isSnapshot").forall(_.toBoolean)
+  val isRelease: Boolean = sys.props.get("project.isRelease").forall(_.toBoolean)
 
   // Adapted from SbtGit.versionWithGit
   def cromwellVersionWithGit: Seq[Setting[_]] =
diff --git a/project/plugins.sbt b/project/plugins.sbt
index 51289a45e53..bdb54f675bf 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1,5 +1,6 @@
 addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.9.0")
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.0")
-addSbtPlugin("com.typesafe.sbt" % "sbt-git" % "1.0.2")
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.9.3")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.1")
+addSbtPlugin("com.github.sbt" % "sbt-git" % "2.0.0")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.4")
+addSbtPlugin("com.github.cb372" % "sbt-explicit-dependencies" % "0.2.16")
 addDependencyTreePlugin
diff --git a/project/swagger2markup.sbt b/project/swagger2markup.sbt
index 96f836bcc72..1fa882328f1 100644
--- a/project/swagger2markup.sbt
+++ b/project/swagger2markup.sbt
@@ -14,7 +14,7 @@ val jacksonV = "2.8.4"
 val javaslangV = "2.0.5"
 val plexusUtilsV = "3.0.22"
 val slf4jV = "1.7.21"
-val swagger2markupV = "1.3.3"
+val swagger2markupV = "1.3.4"
 
 resolvers ++= List(
   "JCenter" at "https://jcenter.bintray.com"
diff --git a/publish/publish_inputs.json b/publish/publish_inputs.json
index e9c54b9f3d6..ea877b9c34e 100644
--- a/publish/publish_inputs.json
+++ b/publish/publish_inputs.json
@@ -1,7 +1,7 @@
 {
-  "publish_workflow.githubToken": "<<REQUIRED: GithubAPIToken (value, not path)>>",
-  "publish_workflow.organization": "<<REQUIRED: broadinstitute for a real release, your github username if testing>>",
-  "publish_workflow.publishDocker": <<OPTIONAL: the docker image to use for publishing, default broadinstitute/cromwell-publish:latest>>,
-  "publish_workflow.majorRelease": <<OPTIONAL: true for a major release, false for a minor release, default true>>,
-  "publish_workflow.publishHomebrew": <<OPTIONAL: true to publish release to homebrew, false to skip, default true>>
+  "publish_workflow.githubToken": "<<GITHUB TOKEN VALUE>>",
+  "publish_workflow.majorRelease": true,
+  "publish_workflow.publishHomebrew": false,
+  "publish_workflow.publishDocker": "broadinstitute/cromwell-publish:latest",
+  "publish_workflow.organization": "broadinstitute"
 }
diff --git a/runConfigurations/Repo template_ CromIAM.run.xml b/runConfigurations/Repo template_ CromIAM.run.xml
index 420ee26cae1..7fa2a61acd7 100644
--- a/runConfigurations/Repo template_ CromIAM.run.xml	
+++ b/runConfigurations/Repo template_ CromIAM.run.xml	
@@ -7,4 +7,4 @@
       <option name="Make" enabled="true" />
     </method>
   </configuration>
-</component>
\ No newline at end of file
+</component>
diff --git a/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml b/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml
index 1ca941fbfa9..91b36d9277e 100644
--- a/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml	
+++ b/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml	
@@ -1,11 +1,11 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="Repo template: Cromwell DRS Localizer" type="Application" factoryName="Application">
     <envs>
-      <env name="MARTHA_URL" value="https://us-central1-broad-dsde-dev.cloudfunctions.net/martha_v3" />
+      <env name="DRS_RESOLVER_URL" value="https://drshub.dsde-dev.broadinstitute.org/api/v4/drs/resolve" />
     </envs>
     <option name="MAIN_CLASS_NAME" value="drs.localizer.DrsLocalizerMain" />
     <module name="cromwell-drs-localizer" />
-    <option name="PROGRAM_PARAMETERS" value="--access-token-strategy azure drs://jade.datarepo-dev.broadinstitute.org/v1_f3c32ddd-20eb-4033-9716-46866521a3a4_8d651e95-38ce-4bc8-a8a4-8a4cd9513db1 $USER_HOME$/Downloads/NA12878_PLUMBING_wgs.g.vcf.gz.tbi --vault-name vault --secret-name secret --identity-client-id identity" />
+    <option name="PROGRAM_PARAMETERS" value="--access-token-strategy azure drs://jade.datarepo-dev.broadinstitute.org/v1_f3c32ddd-20eb-4033-9716-46866521a3a4_8d651e95-38ce-4bc8-a8a4-8a4cd9513db1 $USER_HOME$/Downloads/NA12878_PLUMBING_wgs.g.vcf.gz.tbi --identity-client-id identity" />
     <method v="2">
       <option name="Make" enabled="true" />
     </method>
diff --git a/runConfigurations/Repo template_ Cromwell server TES.run.xml b/runConfigurations/Repo template_ Cromwell server TES.run.xml
new file mode 100644
index 00000000000..9cb1818a004
--- /dev/null
+++ b/runConfigurations/Repo template_ Cromwell server TES.run.xml	
@@ -0,0 +1,21 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="Repo template: Cromwell server TES" type="Application" factoryName="Application">
+    <option name="ALTERNATIVE_JRE_PATH" value="$USER_HOME$/.sdkman/candidates/java/current" />
+    <envs>
+      <env name="CROMWELL_BUILD_CENTAUR_SLICK_PROFILE" value="slick.jdbc.MySQLProfile$" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_DRIVER" value="com.mysql.cj.jdbc.Driver" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_URL" value="jdbc:mysql://localhost:3306/cromwell_test?allowPublicKeyRetrieval=true&amp;useSSL=false&amp;rewriteBatchedStatements=true&amp;serverTimezone=UTC&amp;useInformationSchema=true" />
+      <env name="CROMWELL_BUILD_RESOURCES_DIRECTORY" value="target/ci/resources" />
+      <env name="CROMWELL_BUILD_PAPI_JSON_FILE" value="target/ci/resources/cromwell-centaur-service-account.json" />
+      <env name="CROMWELL_BUILD_CENTAUR_READ_LINES_LIMIT" value="128000" />
+      <env name="CROMWELL_BUILD_CENTAUR_256_BITS_KEY" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA=" />
+    </envs>
+    <option name="MAIN_CLASS_NAME" value="cromwell.CromwellApp" />
+    <module name="cromwell" />
+    <option name="PROGRAM_PARAMETERS" value="server" />
+    <option name="VM_PARAMETERS" value="-Dconfig.file=target/ci/resources/tes_application.conf" />
+    <method v="2">
+      <option name="Make" enabled="true" />
+    </method>
+  </configuration>
+</component>
\ No newline at end of file
diff --git a/scripts/gen_java_client.sh b/scripts/gen_java_client.sh
index 409af51a83f..59642098b1d 100755
--- a/scripts/gen_java_client.sh
+++ b/scripts/gen_java_client.sh
@@ -4,6 +4,7 @@ BASE_PACKAGE="cromwell.client"
 
 ORIGINAL_API_YAML=engine/src/main/resources/swagger/cromwell.yaml
 API_YAML=codegen_java/cromwell.nofile.yaml
+OPENAPI_DOCKER="openapitools/openapi-generator-cli@sha256:ddd1b01cbe8f494c6612c548e91f983938164ab713a4d18d099a1fc4a77c651d"
 
 # Cromwell doesn't specify the OAuth configuration in its swagger, and
 # without it the client doesn't support authentication.
@@ -37,7 +38,7 @@ cat $ORIGINAL_API_YAML | sed s/type:\ file/type:\ string/g >> $API_YAML
 # generator's build.sbt with ours.
 # 1. Hide our build.sbt
 mv codegen_java/build.sbt codegen_java/build.sbt.bak
-docker run --rm -v ${PWD}:/local openapitools/openapi-generator-cli generate \
+docker run --rm -v ${PWD}:/local ${OPENAPI_DOCKER} generate \
   -i /local/$API_YAML \
   -g java \
   -o /local/codegen_java \
diff --git a/server/src/main/resources/application.conf b/server/src/main/resources/application.conf
index e0769277a6b..e80cd716b4e 100644
--- a/server/src/main/resources/application.conf
+++ b/server/src/main/resources/application.conf
@@ -1,6 +1,6 @@
 akka {
   log-dead-letters = "off"
-  loggers = ["akka.event.slf4j.Slf4jLogger"]
+  loggers = ["cromwell.core.logging.EnhancedSlf4jLogger"]
   logging-filter = "cromwell.server.CromwellAkkaLogFilter"
   actor.guardian-supervisor-strategy = "cromwell.core.CromwellUserGuardianStrategy"
 
diff --git a/server/src/main/resources/logback.xml b/server/src/main/resources/logback.xml
index 4868962f994..006ca3953f4 100644
--- a/server/src/main/resources/logback.xml
+++ b/server/src/main/resources/logback.xml
@@ -1,5 +1,15 @@
 <configuration>
 
+    <!-- Enhanced thread and date reporting. -->
+    <conversionRule
+            conversionWord="et"
+            converterClass="cromwell.core.logging.EnhancedThreadConverter"
+    />
+    <conversionRule
+            conversionWord="ed"
+            converterClass="cromwell.core.logging.EnhancedDateConverter"
+    />
+
     <!-- default properties for FILEROLLER need to be set upfront -->
 
     <if condition='property("FILEROLLER_DIR").equals("")'>
@@ -18,7 +28,7 @@
         <then>
             <appender name="STANDARD_APPENDER" class="ch.qos.logback.core.ConsoleAppender">
                 <encoder>
-                    <pattern>%date %X{sourceThread} %-5level - %msg%n</pattern>
+                    <pattern>%ed{yyyy-MM-dd HH:mm:ss,SSS} %et %-5level - %msg%n</pattern>
                 </encoder>
             </appender>
         </then>
@@ -68,7 +78,7 @@
 
                 </rollingPolicy>
                 <encoder>
-                    <pattern>%d{yyyy-MM-dd HH:mm:ss,SSS} [%thread] %-5level %logger{35} - %msg%n</pattern>
+                    <pattern>%ed{yyyy-MM-dd HH:mm:ss,SSS} [%et] %-5level %logger{35} - %msg%n</pattern>
                 </encoder>
             </appender>
         </then>
@@ -96,4 +106,7 @@
     <logger name="HikariPool" level="ERROR"/>
     <logger name="com.google.cloud.hadoop.gcsio.GoogleCloudStorageReadChannel" level="ERROR"/>
     <logger name="org.semanticweb.owlapi.utilities.Injector" level="ERROR"/>
+
+    <!-- Guilty of logging ERROR under non-erroneous conditions -->
+    <logger name="com.azure.storage.blob.nio" level="OFF"/>
 </configuration>
diff --git a/server/src/main/scala/cromwell/CommandLineArguments.scala b/server/src/main/scala/cromwell/CommandLineArguments.scala
index 8064c115b78..986a33a4dc2 100644
--- a/server/src/main/scala/cromwell/CommandLineArguments.scala
+++ b/server/src/main/scala/cromwell/CommandLineArguments.scala
@@ -5,21 +5,17 @@ import java.nio.file.InvalidPathException
 
 import better.files.File
 import cats.syntax.apply._
-import cats.syntax.either._
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
-import common.validation.IOChecked._
 import common.validation.Validation._
 import cromwell.CommandLineArguments._
 import cromwell.CromwellApp.Command
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import cromwell.webservice.PartialWorkflowSources
-import cwl.preprocessor.CwlFileReference
-import cwl.preprocessor.CwlPreProcessor
 import org.slf4j.Logger
 
-import scala.util.{Failure, Success, Try}
+import scala.util.{Failure, Success}
 
 object CommandLineArguments {
   val DefaultCromwellHost = new URL("http://localhost:8000")
@@ -46,41 +42,10 @@ case class CommandLineArguments(command: Option[Command] = None,
                                 metadataOutput: Option[Path] = None,
                                 host: URL = CommandLineArguments.DefaultCromwellHost
                                ) {
-  private lazy val cwlPreProcessor = new CwlPreProcessor()
-  private lazy val isCwl = workflowType.exists(_.equalsIgnoreCase("cwl"))
-
-  /*
-    * If the file is a relative local path, resolve it against the path of the input json.
-   */
-  private def inputFilesMapper(inputJsonPath: Path)(file: String) = {
-    DefaultPathBuilder.build(file) match {
-      case Success(path) if !path.isAbsolute => inputJsonPath.sibling(file).pathAsString
-      case _ => file
-    }
-  }
-
-  private def preProcessCwlInputFile(path: Path): ErrorOr[String] = {
-    cwlPreProcessor.preProcessInputFiles(path.contentAsString, inputFilesMapper(path)).toErrorOr
-  }
-
   def validateSubmission(logger: Logger): ErrorOr[ValidSubmission] = {
-    def preProcessCwlWorkflowSource(workflowSourcePath: Path): ErrorOr[String] = {
-      val workflowPath = File(workflowSourcePath.pathAsString)
-
-      logger.info("Pre Processing Workflow...")
-      lazy val preProcessedCwl = cwlPreProcessor.preProcessCwlToString(CwlFileReference(workflowPath, workflowRoot))
-
-      Try(preProcessedCwl.value.unsafeRunSync())
-        .toChecked
-        .flatMap(identity)
-        .toValidated
-    }
 
     def getWorkflowSourceFromPath(workflowPath: Path): ErrorOr[WorkflowSourceOrUrl] = {
-      (isCwl, imports) match {
-        case (true, None) => preProcessCwlWorkflowSource(workflowPath).map(src => WorkflowSourceOrUrl(Option(src), None))
-        case (true, Some(_)) | (false, _) => WorkflowSourceOrUrl(None, Option(workflowPath.pathAsString)).validNel
-      }
+      WorkflowSourceOrUrl(None, Option(workflowPath.pathAsString)).validNel
     }
 
     val workflowSourceAndUrl: ErrorOr[WorkflowSourceOrUrl] = DefaultPathBuilder.build(workflowSource.get) match {
@@ -93,10 +58,7 @@ case class CommandLineArguments(command: Option[Command] = None,
       case Failure(_) => PartialWorkflowSources.validateWorkflowUrl(workflowSource.get).map(validUrl => WorkflowSourceOrUrl(None, Option(validUrl)))
     }
 
-    val inputsJson: ErrorOr[String] = if (isCwl) {
-      logger.info("Pre Processing Inputs...")
-      workflowInputs.map(preProcessCwlInputFile).getOrElse(readOptionContent("Workflow inputs", workflowInputs))
-    } else readOptionContent("Workflow inputs", workflowInputs)
+    val inputsJson: ErrorOr[String] = readOptionContent("Workflow inputs", workflowInputs)
 
     import common.validation.ErrorOr.ShortCircuitingFlatMap
     val optionsJson = readOptionContent("Workflow options", workflowOptions).flatMap { WorkflowOptions.fromJsonString(_).toErrorOr }
diff --git a/server/src/main/scala/cromwell/CromwellEntryPoint.scala b/server/src/main/scala/cromwell/CromwellEntryPoint.scala
index 5acddd75ce9..a1707db6488 100644
--- a/server/src/main/scala/cromwell/CromwellEntryPoint.scala
+++ b/server/src/main/scala/cromwell/CromwellEntryPoint.scala
@@ -16,6 +16,7 @@ import cromwell.CommandLineArguments.{ValidSubmission, WorkflowSourceOrUrl}
 import cromwell.CromwellApp._
 import cromwell.api.CromwellClient
 import cromwell.api.model.{Label, LabelsJsonFormatter, WorkflowSingleSubmission}
+import cromwell.core.logging.JavaLoggingBridge
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import cromwell.core.{WorkflowSourceFilesCollection, WorkflowSourceFilesWithDependenciesZip, WorkflowSourceFilesWithoutImports}
 import cromwell.engine.workflow.SingleWorkflowRunnerActor
@@ -166,6 +167,13 @@ object CromwellEntryPoint extends GracefulStopSupport {
     Make sure that the next time one uses the ConfigFactory that our updated system properties are loaded.
      */
     ConfigFactory.invalidateCaches()
+
+    /*
+    Replace java.util.logging with SLF4J.
+    https://www.slf4j.org/api/org/slf4j/bridge/SLF4JBridgeHandler.html
+     */
+    JavaLoggingBridge.init()
+
     ()
   }
 
diff --git a/server/src/test/resources/cwl_glob_sort.cwl b/server/src/test/resources/cwl_glob_sort.cwl
deleted file mode 100644
index 330c896eea6..00000000000
--- a/server/src/test/resources/cwl_glob_sort.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-requirements:
-  - class: InlineJavascriptRequirement
-hints:
-  DockerRequirement:
-    dockerPull: "debian:stretch-slim"
-inputs: []
-baseCommand: [touch, z, y, x, w, c, b, a]
-outputs:
-  letters:
-    type: string
-    outputBinding:
-      glob: '?'
-      outputEval: |
-        ${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(" ") }
diff --git a/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala b/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
index 58d2154f9b7..41b1edccb36 100644
--- a/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
+++ b/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
@@ -95,32 +95,6 @@ class CromwellCommandLineSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     validation.get.workflowUrl shouldBe Option(url)
   }
 
-  it should "run single when supplying cwl workflow" in {
-    val source = raw"""{"cwlVersion":"v1.0","class":"CommandLineTool","requirements":[{"class":"InlineJavascriptRequirement"}],"hints":[{"dockerPull":"debian:stretch-slim","class":"DockerRequirement"}],"inputs":[],"baseCommand":["touch","z","y","x","w","c","b","a"],"outputs":[{"type":"string","outputBinding":{"glob":"?","outputEval":"$${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(\" \") }\n""""
-    val command = parser.parse(Array("run", "server/src/test/resources/cwl_glob_sort.cwl", "--type", "CWL"), CommandLineArguments()).get
-
-    command.command shouldBe Some(Run)
-    command.workflowSource.get shouldBe "server/src/test/resources/cwl_glob_sort.cwl"
-
-    val validation = Try(CromwellEntryPoint.validateRunArguments(command))
-    validation.isSuccess shouldBe true
-    validation.get.workflowSource.get should include(source)
-    validation.get.workflowUrl shouldBe None
-  }
-
-  it should "run single when supplying cwl workflow using url" in {
-    val url = "https://path_to_url"
-    val command = parser.parse(Array("run", url, "--type", "CWL"), CommandLineArguments()).get
-
-    command.command shouldBe Some(Run)
-    command.workflowSource.get shouldBe url
-
-    val validation = Try(CromwellEntryPoint.validateRunArguments(command))
-    validation.isSuccess shouldBe true
-    validation.get.workflowSource shouldBe None
-    validation.get.workflowUrl shouldBe Option(url)
-  }
-
   it should "run single when supplying wdl and inputs and options" in {
     val optionsLast = parser.parse(Array("run", "3step.wdl", "--inputs", "3step.inputs", "--options", "3step.options"), CommandLineArguments()).get
     optionsLast.command shouldBe Some(Run)
diff --git a/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala b/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
index ab47dedeb5c..d9de71b9125 100644
--- a/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
@@ -2,7 +2,6 @@ package cromwell.engine.workflow
 
 import java.time.OffsetDateTime
 import java.util.concurrent.atomic.AtomicInteger
-
 import akka.actor.{Actor, ActorRef, ActorSystem, Kill, Props}
 import akka.testkit.{EventFilter, TestActorRef, TestFSMRef, TestProbe}
 import com.typesafe.config.{Config, ConfigFactory}
@@ -15,10 +14,10 @@ import cromwell.engine.backend.BackendSingletonCollection
 import cromwell.engine.workflow.WorkflowActor._
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowActorWorkComplete
 import cromwell.engine.workflow.lifecycle.EngineLifecycleActorAbortCommand
-import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{WorkflowExecutionAbortedResponse, WorkflowExecutionFailedResponse, WorkflowExecutionSucceededResponse}
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{ExecuteWorkflowCommand, WorkflowExecutionAbortedResponse, WorkflowExecutionFailedResponse, WorkflowExecutionSucceededResponse}
 import cromwell.engine.workflow.lifecycle.finalization.CopyWorkflowLogsActor
 import cromwell.engine.workflow.lifecycle.finalization.WorkflowFinalizationActor.{StartFinalizationCommand, WorkflowFinalizationSucceededResponse}
-import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{WorkflowInitializationAbortedResponse, WorkflowInitializationFailedResponse}
+import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{StartInitializationCommand, WorkflowInitializationAbortedResponse, WorkflowInitializationFailedResponse, WorkflowInitializationSucceededResponse}
 import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.MaterializeWorkflowDescriptorFailureResponse
 import cromwell.engine.workflow.workflowstore.{StartableState, Submitted, WorkflowHeartbeatConfig, WorkflowToStart}
 import cromwell.engine.{EngineFilesystems, EngineWorkflowDescriptor}
@@ -60,6 +59,8 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
     createMaterializedEngineWorkflowDescriptor(WorkflowId.randomId(), workflowSources = workflowSources)
   val supervisorProbe: TestProbe = TestProbe("supervisorProbe")
   val deathwatch: TestProbe = TestProbe("deathwatch")
+  val initializationProbe: TestProbe = TestProbe("initializationProbe")
+  val executionProbe: TestProbe = TestProbe("executionProbe")
   val finalizationProbe: TestProbe = TestProbe("finalizationProbe")
   var copyWorkflowLogsProbe: TestProbe = _
   val AwaitAlmostNothing: FiniteDuration = 100.milliseconds
@@ -78,7 +79,7 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 
   private val workflowHeartbeatConfig = WorkflowHeartbeatConfig(ConfigFactory.load())
 
-  private def createWorkflowActor(state: WorkflowActorState, extraPathBuilderFactory: Option[PathBuilderFactory] = None) = {
+  private def createWorkflowActor(state: WorkflowActorState, extraPathBuilderFactory: Option[PathBuilderFactory] = None, initializationMaxRetries: Int = 3, initializationInterval: FiniteDuration = 10.millis) = {
     val actor = TestFSMRef(
       factory = new WorkflowActorWithTestAddons(
         finalizationProbe = finalizationProbe,
@@ -102,7 +103,11 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
         workflowStoreActor = system.actorOf(Props.empty, s"workflowStoreActor-$currentWorkflowId"),
         workflowHeartbeatConfig = workflowHeartbeatConfig,
         totalJobsByRootWf = initialJobCtByRootWf,
-        extraPathBuilderFactory = extraPathBuilderFactory
+        extraPathBuilderFactory = extraPathBuilderFactory,
+        initializationMaxRetries = initializationMaxRetries,
+        initializationInterval = initializationInterval,
+        workflowInitializationActorProbe = initializationProbe,
+        workflowExecutionActorProbe = executionProbe
       ),
       supervisor = supervisorProbe.ref,
       name = s"workflowActor-$currentWorkflowId",
@@ -124,10 +129,17 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 
   "WorkflowActor" should {
 
-    "run Finalization actor if Initialization fails" in {
-      val actor = createWorkflowActor(InitializingWorkflowState)
+    "run Finalization actor if Initialization repeatedly fails" in {
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationMaxRetries = 3)
       deathwatch watch actor
-      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Materialization Failed")))
+
+      // Expect the WorkflowActor to retry up to three times:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (2)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (3)")))
+
       finalizationProbe.expectMsg(StartFinalizationCommand)
       actor.stateName should be(FinalizingWorkflowState)
       actor ! WorkflowFinalizationSucceededResponse
@@ -136,6 +148,24 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       deathwatch.expectTerminated(actor)
     }
 
+    "begin execution if Initialization eventually succeeds" in {
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationMaxRetries = 3)
+      deathwatch watch actor
+
+      // Expect the WorkflowActor to retry up to three times:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (2)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationSucceededResponse(AllBackendInitializationData(Map.empty))
+
+      executionProbe.expectMsg(ExecuteWorkflowCommand)
+      actor.stateName should be(ExecutingWorkflowState)
+      // Tidy up (and satisfy the deathwatch):
+      system.stop(actor)
+      deathwatch.expectTerminated(actor)
+    }
+
     "run Finalization actor if Initialization is aborted" in {
       val actor = createWorkflowActor(InitializingWorkflowState)
       deathwatch watch actor
@@ -151,6 +181,56 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       deathwatch.expectTerminated(actor)
     }
 
+    "run Finalization actor if Initialization is aborted during a retry" in {
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationInterval = 1.second)
+      deathwatch watch actor
+
+      // Set the stage with a few unfortunate retries:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (2)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+
+      actor ! AbortWorkflowCommand
+      eventually { actor.stateName should be(WorkflowAbortingState) }
+      // Because we failed a few times, the actor test's initial "currentLifecycleActor will have been replaced by this
+      // new initializationProbe:
+      initializationProbe.expectMsgPF(TimeoutDuration) {
+        case EngineLifecycleActorAbortCommand => actor ! WorkflowInitializationAbortedResponse
+      }
+
+      finalizationProbe.expectMsg(StartFinalizationCommand)
+      actor.stateName should be(FinalizingWorkflowState)
+      actor ! WorkflowFinalizationSucceededResponse
+      workflowManagerActorExpectsSingleWorkCompleteNotification(WorkflowAborted)
+      deathwatch.expectTerminated(actor)
+    }
+
+    "run Finalization actor if Initialization is aborted between retries" in {
+      // Set the interval long so that we can guarantee the "between retries" part
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationInterval = 10.seconds)
+      deathwatch watch actor
+
+      // Set the stage with a few unfortunate retries:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      eventually { actor.stateData.currentLifecycleStateActor should be(None) }
+
+      actor ! AbortWorkflowCommand
+      // Because there are no active lifecycle actors, this actor should jump to Finalizing without
+      // needing any further input:
+      eventually { actor.stateName should be(FinalizingWorkflowState) }
+
+      // Expect the mailboxes for the initialization actor to be empty (and check "currentLifecycleActor" for good measure)
+      currentLifecycleActor.expectNoMessage(10.millis)
+      initializationProbe.expectNoMessage(10.millis)
+
+      finalizationProbe.expectMsg(StartFinalizationCommand)
+      actor.stateName should be(FinalizingWorkflowState)
+      actor ! WorkflowFinalizationSucceededResponse
+      workflowManagerActorExpectsSingleWorkCompleteNotification(WorkflowAborted)
+      deathwatch.expectTerminated(actor)
+    }
+
     "run Finalization if Execution fails" in {
       val actor = createWorkflowActor(ExecutingWorkflowState)
       deathwatch watch actor
@@ -283,7 +363,11 @@ class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
                                   workflowStoreActor: ActorRef,
                                   workflowHeartbeatConfig: WorkflowHeartbeatConfig,
                                   totalJobsByRootWf: AtomicInteger,
-                                  extraPathBuilderFactory: Option[PathBuilderFactory]) extends WorkflowActor(
+                                  extraPathBuilderFactory: Option[PathBuilderFactory],
+                                  initializationMaxRetries: Int,
+                                  initializationInterval: FiniteDuration,
+                                  workflowInitializationActorProbe: TestProbe,
+                                  workflowExecutionActorProbe: TestProbe) extends WorkflowActor(
   workflowToStart = WorkflowToStart(id = workflowId,
     submissionTime = OffsetDateTime.now,
     state = startState,
@@ -310,6 +394,12 @@ class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
   fileHashCacheActorProps = None,
   blacklistCache = None) {
 
+  override def createInitializationActor(workflowDescriptor: EngineWorkflowDescriptor, name: String): ActorRef = workflowInitializationActorProbe.ref
+  override def createWorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor, data: WorkflowActorData): ActorRef = workflowExecutionActorProbe.ref
+
+  override val initializationRetryInterval: FiniteDuration = initializationInterval
+  override val maxInitializationAttempts: Int = initializationMaxRetries
+
   override val pathBuilderFactories: List[PathBuilderFactory] = extraPathBuilderFactory match {
     case Some(pbf) => EngineFilesystems.configuredPathBuilderFactories :+ pbf
     case None => EngineFilesystems.configuredPathBuilderFactories
diff --git a/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala b/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
index fd1864d45f0..4df3f966db6 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
@@ -143,7 +143,7 @@ object SelectiveTsvInstrumentationServiceActor {
 
       val header = (List("timestamp") ++ interestingFields).mkString("\t")
       val rows = stateHistory.map { case (timestamp, fieldMap) =>
-        (Vector(timestamp.toString) ++ interestingFields.map(f => fieldMap.getOrElse(f, 0))).mkString("\t")
+        (Vector(timestamp.toString) ++ interestingFields.map(f => fieldMap.getOrElse(f, 0).toString)).mkString("\t")
       }
       Vector(header) ++ rows
     }
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
index 8e6029140e9..2a812419775 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
@@ -287,7 +287,7 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         }
         // Filter by workflow id within random Ids
         _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          (randomIds :+ workflow1Id).map(id => WorkflowQueryKey.Id.name -> id.toString))) map { case (response, _) =>
+          (randomIds :+ workflow1Id.toString).map(id => WorkflowQueryKey.Id.name -> id))) map { case (response, _) =>
           val resultsById = response.results groupBy {
             _.name
           }
diff --git a/src/ci/bin/testSingleWorkflowRunner.sh b/src/ci/bin/testSingleWorkflowRunner.sh
index ce8e3e4c65e..fcf0f626822 100755
--- a/src/ci/bin/testSingleWorkflowRunner.sh
+++ b/src/ci/bin/testSingleWorkflowRunner.sh
@@ -92,26 +92,3 @@ if [ $retVal -eq 0 ]; then
 else
     grep "Error: Unknown argument" console_output.txt
 fi
-
-# Test 5: application should run cwl with inputs
-STANDARD_TEST_CASES="$PWD/centaur/src/main/resources/standardTestCases/cwl_run"
-pushd "$STANDARD_TEST_CASES" > /dev/null
-
-java -jar ${CROMWELL_BUILD_CROMWELL_JAR} run ./1st-tool.cwl --inputs ./echo-job.yml --metadata-output ./run_mode_metadata.json | tee console_output.txt
-
-cat > expected.json <<FIN
-{
-  "actualWorkflowLanguage": "CWL",
-  "actualWorkflowLanguageVersion": "v1.0",
-  "status": "Succeeded"
-}
-FIN
-
-jq '{
-  actualWorkflowLanguage,
-  actualWorkflowLanguageVersion,
-  status
-}' run_mode_metadata.json > actual.json
-
-cmp <(jq -cS . actual.json) <(jq -cS . expected.json)
-popd > /dev/null
diff --git a/src/ci/resources/papi_application.inc.conf.ctmpl b/src/ci/resources/papi_application.inc.conf.ctmpl
index 9d6a06428dd..04d6690a6ba 100644
--- a/src/ci/resources/papi_application.inc.conf.ctmpl
+++ b/src/ci/resources/papi_application.inc.conf.ctmpl
@@ -63,7 +63,7 @@ services {
   }
 }
 
-filesystems.drs.global.config.martha.url = "https://us-central1-broad-dsde-dev.cloudfunctions.net/martha_v3"
+filesystems.drs.global.config.resolver.url = "https://drshub.dsde-dev.broadinstitute.org/api/v4/drs/resolve"
 
 drs {
   localization {
diff --git a/src/ci/resources/papi_v2_reference_image_manifest.conf b/src/ci/resources/papi_v2_reference_image_manifest.conf
index 8c15fc44636..ef12cef1b66 100644
--- a/src/ci/resources/papi_v2_reference_image_manifest.conf
+++ b/src/ci/resources/papi_v2_reference_image_manifest.conf
@@ -1,4819 +1,346 @@
 reference-disk-localization-manifests = [
   {
-    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/broad-references-disk-image",
-    "diskSizeGb" : 500,
+    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/hg38-public-2020-10-26",
+    "diskSizeGb" : 20,
     "files" : [ {
-      "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.nhr",
-      "crc32c" : 407769621
-    }, {
-      "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.sa",
-      "crc32c" : 1902048083
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00129.disc.txt.gz",
-      "crc32c" : 3404974518
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG04118.split.txt.gz.tbi",
-      "crc32c" : 4024172857
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19449.split.txt.gz.tbi",
-      "crc32c" : 1977253058
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02272.disc.txt.gz",
-      "crc32c" : 1166548962
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA21133.disc.txt.gz",
-      "crc32c" : 1427281614
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03864.disc.txt.gz.tbi",
-      "crc32c" : 1529087048
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA20764.disc.txt.gz.tbi",
-      "crc32c" : 1417763527
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA21102.disc.txt.gz.tbi",
-      "crc32c" : 1680978475
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00096.split.txt.gz",
-      "crc32c" : 1667331591
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18638.split.txt.gz.tbi",
-      "crc32c" : 2563684534
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01112.disc.txt.gz",
-      "crc32c" : 3289968657
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.pac",
-      "crc32c" : 299013300
-    }, {
-      "path" : "gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi",
-      "crc32c" : 1373876197
-    }, {
-      "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.delly_exclusionRegions.shard2.tsv",
-      "crc32c" : 422023470
-    }, {
-      "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.delly_exclusionRegions.shard6.tsv",
-      "crc32c" : 2641621150
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_044.wham.HG02002.vcf.gz",
-      "crc32c" : 61945186
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_113.wham.NA18553.vcf.gz",
-      "crc32c" : 2270157672
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_088.wham.HG03709.vcf.gz",
-      "crc32c" : 1143326201
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_116.wham.NA18923.vcf.gz",
-      "crc32c" : 408469998
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_149.wham.NA20802.vcf.gz",
-      "crc32c" : 2170731227
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_014.wham.HG00599.vcf.gz",
-      "crc32c" : 2268306580
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_050.wham.HG02186.vcf.gz",
-      "crc32c" : 2164894354
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_135.wham.NA19684.vcf.gz",
-      "crc32c" : 2251666164
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_007.wham.HG00288.vcf.gz",
-      "crc32c" : 3615266090
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_120.wham.NA18995.vcf.gz",
-      "crc32c" : 851480900
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/wham/std_024.wham.HG01344.vcf.gz",
-      "crc32c" : 1569598141
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_080.manta.HG03449.vcf.gz",
-      "crc32c" : 3827948923
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_081.manta.HG03472.vcf.gz",
-      "crc32c" : 1026539483
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_006.manta.HG00277.vcf.gz",
-      "crc32c" : 3528734581
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_116.manta.NA18923.vcf.gz",
-      "crc32c" : 1495065630
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_062.manta.HG02586.vcf.gz",
-      "crc32c" : 1681406320
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_135.manta.NA19684.vcf.gz",
-      "crc32c" : 2897751567
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_019.manta.HG01060.vcf.gz",
-      "crc32c" : 610810668
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_020.manta.HG01085.vcf.gz",
-      "crc32c" : 2504924512
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_136.manta.NA19746.vcf.gz",
-      "crc32c" : 3534117012
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/v1/manta/std_040.manta.HG01880.vcf.gz",
-      "crc32c" : 2294307211
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19377.split.txt.gz.tbi",
-      "crc32c" : 3454882291
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03370.disc.txt.gz",
-      "crc32c" : 3230324326
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18539.disc.txt.gz.tbi",
-      "crc32c" : 42990821
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02002.disc.txt.gz.tbi",
-      "crc32c" : 3745118809
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18945.disc.txt.gz",
-      "crc32c" : 3310721851
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19184.split.txt.gz",
-      "crc32c" : 3448306521
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19449.disc.txt.gz",
-      "crc32c" : 4252958454
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01085.disc.txt.gz",
-      "crc32c" : 2389602066
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA11894.split.txt.gz.tbi",
-      "crc32c" : 3846004317
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02235.disc.txt.gz.tbi",
-      "crc32c" : 365742494
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA12489.disc.txt.gz.tbi",
-      "crc32c" : 2818219097
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03744.split.txt.gz",
-      "crc32c" : 2737584475
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA20802.disc.txt.gz.tbi",
-      "crc32c" : 1912617588
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02588.split.txt.gz.tbi",
-      "crc32c" : 2099872645
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01874.split.txt.gz",
-      "crc32c" : 3854913913
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19035.split.txt.gz.tbi",
-      "crc32c" : 3286945483
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA20845.disc.txt.gz",
-      "crc32c" : 1337716767
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02611.split.txt.gz",
-      "crc32c" : 133841208
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00557.split.txt.gz",
-      "crc32c" : 4255423837
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19062.disc.txt.gz",
-      "crc32c" : 3841480226
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-153.tar.gz",
-      "crc32c" : 3007069952
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-99.tar.gz",
-      "crc32c" : 4195646517
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-266.tar.gz",
-      "crc32c" : 1379685624
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-36.tar.gz",
-      "crc32c" : 3789968460
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-211.tar.gz",
-      "crc32c" : 1973914077
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-207.tar.gz",
-      "crc32c" : 540019804
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-129.tar.gz",
-      "crc32c" : 1607611122
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-278.tar.gz",
-      "crc32c" : 3655125191
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-156.tar.gz",
-      "crc32c" : 844061657
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-106.tar.gz",
-      "crc32c" : 1226511555
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-119.tar.gz",
-      "crc32c" : 582423981
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-113.tar.gz",
-      "crc32c" : 2360388371
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-127.tar.gz",
-      "crc32c" : 701818403
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-274.tar.gz",
-      "crc32c" : 498038628
-    }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-181.tar.gz",
-      "crc32c" : 2512969958
+      "path" : "gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
+      "crc32c" : 930173616
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-6.tar.gz",
-      "crc32c" : 721406268
+      "path" : "gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
+      "crc32c" : 289077232
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-29.tar.gz",
-      "crc32c" : 94522894
+      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
+      "crc32c" : 2366715186
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-173.tar.gz",
-      "crc32c" : 1827993197
+      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
+      "crc32c" : 510227671
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-255.tar.gz",
-      "crc32c" : 2620821232
+      "path" : "gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
+      "crc32c" : 1970999569
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-97.tar.gz",
-      "crc32c" : 74623336
+      "path" : "gcp-public-data--broad-references/hg38/v0/exome_calling_regions.v1.interval_list",
+      "crc32c" : 2361720184
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-150.tar.gz",
-      "crc32c" : 3297915748
+      "path" : "gcp-public-data--broad-references/hg38/v0/contamination-resources/1000g/1000g.phase3.100k.b38.vcf.gz.dat.UD",
+      "crc32c" : 1848694786
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+  {
+    imageIdentifier: "projects/broad-dsde-cromwell-dev/global/images/mm10-sc-vm23-public-2021-06-29"
+    diskSizeGb: 30
+    files: [
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+        crc32c: 2788602819
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+    ]
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+    diskSizeGb: 35
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+        crc32c: 1597701262
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+      {
+        path: "gcp-public-data--broad-references/mm10/v0/single_nucleus/star/modified_star_2.7.9a_primary_gencode_mouse_vM23.tar"
+        crc32c: 3489248673
+      }
+    ]
+  },
+  {
+    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2023-02-01",
+    "diskSizeGb" : 55,
+    "files" : [ {
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01344.split.txt.gz",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
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-      "crc32c" : 3019198771
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/References/Homo_sapiens.GRCh38.Nirvana.dat",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20220512.nsi",
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01607.disc.txt.gz.tbi",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa",
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18507.split.txt.gz",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa",
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03694.disc.txt.gz",
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.transcripts.ndb",
+      "crc32c" : 2114520493
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+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MultiZ100Way_20171006.pcs",
+      "crc32c" : 1251171842
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00129.disc.txt.gz.tbi",
-      "crc32c" : 3192168410
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_155.nsa.idx",
+      "crc32c" : 2183408606
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18995.split.txt.gz",
-      "crc32c" : 4228428215
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsa",
+      "crc32c" : 482110804
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19443.disc.txt.gz",
-      "crc32c" : 2064476647
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_155.nsa",
+      "crc32c" : 1654978963
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02010.split.txt.gz",
-      "crc32c" : 2709469910
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.polyphen.ndb",
+      "crc32c" : 3178180885
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-159.tar.gz",
-      "crc32c" : 1399388866
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa.idx",
+      "crc32c" : 3807477399
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-137.tar.gz",
-      "crc32c" : 2834363733
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_SV_2.1.nsi",
+      "crc32c" : 2600275374
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-144.tar.gz",
-      "crc32c" : 3432942434
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_disease_validity_curations_20220512.nga",
+      "crc32c" : 4116422668
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-32.tar.gz",
-      "crc32c" : 688658120
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/OMIM_20220516.nga",
+      "crc32c" : 1767833806
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-84.tar.gz",
-      "crc32c" : 2362020576
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa",
+      "crc32c" : 710316739
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-66.tar.gz",
-      "crc32c" : 373531354
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/GME_20160618.nsa.idx",
+      "crc32c" : 1732177354
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-241.tar.gz",
-      "crc32c" : 1320364908
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa.idx",
+      "crc32c" : 245207854
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-107.tar.gz",
-      "crc32c" : 462909423
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa",
+      "crc32c" : 4136875677
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-134.tar.gz",
-      "crc32c" : 1188579016
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsi",
+      "crc32c" : 1056818502
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-43.tar.gz",
-      "crc32c" : 2098432647
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/GME_20160618.nsa",
+      "crc32c" : 1210977352
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-47.tar.gz",
-      "crc32c" : 1722109761
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa.idx",
+      "crc32c" : 870728029
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-28.tar.gz",
-      "crc32c" : 3161256248
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_LCR_2.1.lcr",
+      "crc32c" : 3602069872
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-197.tar.gz",
-      "crc32c" : 852592090
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa.idx",
+      "crc32c" : 2835194789
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-140.tar.gz",
-      "crc32c" : 4051126385
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20220512.nga",
+      "crc32c" : 2485206803
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-121.tar.gz",
-      "crc32c" : 623697692
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_SV_20200819.nsi",
+      "crc32c" : 1378887803
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-182.tar.gz",
-      "crc32c" : 2255237725
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa.idx",
+      "crc32c" : 302652747
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-273.tar.gz",
-      "crc32c" : 2368431717
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_20160414.nsi",
+      "crc32c" : 1181611304
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-269.tar.gz",
-      "crc32c" : 3912509849
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa.idx",
+      "crc32c" : 980438557
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-4.tar.gz",
-      "crc32c" : 1832890207
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DECIPHER_201509.nsi",
+      "crc32c" : 2426309371
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-194.tar.gz",
-      "crc32c" : 2371872678
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa",
+      "crc32c" : 3457097933
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-232.tar.gz",
-      "crc32c" : 645276377
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_3.1.2.nsa.idx",
+      "crc32c" : 3582543830
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-81.tar.gz",
-      "crc32c" : 615405862
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/COSMIC_GeneFusions_94.gfj",
+      "crc32c" : 429830169
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-61.tar.gz",
-      "crc32c" : 3254549888
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa.idx",
+      "crc32c" : 37093822
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-256.tar.gz",
-      "crc32c" : 2225664241
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/FusionCatcher_1.33.gfs",
+      "crc32c" : 1420426876
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/genomestrip/Homo_sapiens_assembly38.vdjregions.bed",
-      "crc32c" : 665778154
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi",
+      "crc32c" : 2492681982
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/genomestrip/Homo_sapiens_assembly38.gcprof.zip",
-      "crc32c" : 954030109
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx",
+      "crc32c" : 2375984948
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0008_of_50/scattered.interval_list",
-      "crc32c" : 2145467013
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsa.idx",
+      "crc32c" : 1539516090
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0038_of_50/scattered.interval_list",
-      "crc32c" : 1218417681
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma",
+      "crc32c" : 1696693985
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0019_of_50/scattered.interval_list",
-      "crc32c" : 2638902162
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa.idx",
+      "crc32c" : 3139541733
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0047_of_50/scattered.interval_list",
-      "crc32c" : 1761876709
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa",
+      "crc32c" : 1721491427
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/CrossSpeciesContamination/CrossSpeciesContaminant/pathseq_microbe.fa.img",
-      "crc32c" : 2373170979
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_3.1.2.nsa",
+      "crc32c" : 4247114985
     } ]
   }
 ]
diff --git a/src/ci/resources/tes_application.conf b/src/ci/resources/tes_application.conf
index 018c13829d8..7f4c42a7d58 100644
--- a/src/ci/resources/tes_application.conf
+++ b/src/ci/resources/tes_application.conf
@@ -1,16 +1,68 @@
 include required(classpath("application.conf"))
 include "build_application.inc.conf"
 
+filesystems {
+  blob {
+    class = "cromwell.filesystems.blob.BlobPathBuilderFactory"
+    global {
+      # One BFSM is shared across all BlobPathBuilders
+      class = "cromwell.filesystems.blob.BlobFileSystemManager"
+      config {
+        container: "cromwell"
+        endpoint: "https://<storage-account>.blob.core.windows.net"
+        subscription: "00001111-2222-3333-aaaa-bbbbccccdddd"
+        # WSM config is needed for accessing WSM-managed blob containers
+        # created in Terra workspaces.
+        workspace-manager {
+          url: "https://workspace.dsde-dev.broadinstitute.org"
+          workspace-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
+          container-resource-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
+          b2cToken: "Zardoz"
+        }
+      }
+    }
+  }
+}
+
+engine {
+  filesystems {
+    local {
+      enabled: true
+    }
+    http {
+      enabled: true
+    }
+    blob {
+      enabled: false
+    }
+  }
+}
+
+
 backend {
   default = "TES"
   providers {
     TES {
       actor-factory = "cromwell.backend.impl.tes.TesBackendLifecycleActorFactory"
       config {
+        # Use for running on blob storage
+        #root = "https://<storage-account>.blob.core.windows.net/cromwell/cromwell-executions"
         root = "cromwell-executions"
         dockerRoot = "/cromwell-executions"
         endpoint = "http://127.0.0.1:9000/v1/tasks"
         concurrent-job-limit = 1000
+        transform-blob-to-local-path = false
+        filesystems {
+          blob {
+            enabled: false
+          }
+          local {
+            enabled: true
+          }
+          http {
+            enabled: true
+          }
+        }
       }
 
       # Have the engine (maybe) authenticate to docker.io. See BT-141 for more info.
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
index e79ef867a54..745e11bee35 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -452,7 +452,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
 
         val inputFilePaths = inputOutputParameters.jobInputParameters.map(_.cloudPath.pathAsString).toSet
         val referenceDisksToMount =
-          jesAttributes.referenceFileToDiskImageMappingOpt.map(getReferenceDisksToMount(_, inputFilePaths))
+          if (useReferenceDisks)
+            jesAttributes.referenceFileToDiskImageMappingOpt.map(getReferenceDisksToMount(_, inputFilePaths))
+          else None
 
         val workflowOptions = workflowDescriptor.workflowOptions
 
@@ -542,6 +544,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     Future.successful(PendingExecutionHandle(jobDescriptor, jobForResumption, Option(Run(jobForResumption)), previousState = None))
   }
 
+  protected def uploadDrsLocalizationManifest(createPipelineParameters: CreatePipelineParameters, cloudPath: Path): Future[Unit] = Future.successful(())
+
   protected def uploadGcsTransferLibrary(createPipelineParameters: CreatePipelineParameters, cloudPath: Path, gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = Future.successful(())
 
   protected def uploadGcsLocalizationScript(createPipelineParameters: CreatePipelineParameters,
@@ -639,6 +643,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
       customLabels <- Future.fromTry(GoogleLabels.fromWorkflowOptions(workflowDescriptor.workflowOptions))
       jesParameters <- generateInputOutputParameters
       createParameters = createPipelineParameters(jesParameters, customLabels)
+      drsLocalizationManifestCloudPath = jobPaths.callExecutionRoot / PipelinesApiJobPaths.DrsLocalizationManifestName
+      _ <- uploadDrsLocalizationManifest(createParameters, drsLocalizationManifestCloudPath)
       gcsTransferConfiguration = initializationData.papiConfiguration.papiAttributes.gcsTransferConfiguration
       gcsTransferLibraryCloudPath = jobPaths.callExecutionRoot / PipelinesApiJobPaths.GcsTransferLibraryName
       transferLibraryContainerPath = createParameters.commandScriptContainerPath.sibling(GcsTransferLibraryName)
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
index 2e6682c2e69..353e33a5019 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
@@ -75,7 +75,7 @@ trait PipelinesApiJobCachingActorHelper extends StandardCachingActorHelper {
       .get(WorkflowOptionKeys.GoogleProject)
       .getOrElse(jesAttributes.project)
 
-    Map(
+    Map[String, Any](
       PipelinesApiMetadataKeys.GoogleProject -> googleProject,
       PipelinesApiMetadataKeys.ExecutionBucket -> initializationData.workflowPaths.executionRootString,
       PipelinesApiMetadataKeys.EndpointUrl -> jesAttributes.endpointUrl,
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
index 0fc9a8ff49d..ae047187825 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
@@ -13,6 +13,7 @@ object PipelinesApiJobPaths {
   val GcsTransferLibraryName = "gcs_transfer.sh"
   val GcsLocalizationScriptName = "gcs_localization.sh"
   val GcsDelocalizationScriptName = "gcs_delocalization.sh"
+  val DrsLocalizationManifestName = "drs_manifest"
 }
 
 // Non-`final` as this is mocked for testing since using a real instance proved too difficult.
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
index 09fb0713de0..7710f3de98e 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
@@ -126,7 +126,7 @@ case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, en
             ComputeScopes.COMPUTE,
             StorageScopes.DEVSTORAGE_FULL_CONTROL,
             GoogleCloudScopes.KmsScope,
-            // Profile and Email scopes are requirements for interacting with Martha
+            // Profile and Email scopes are requirements for interacting with DRS Resolver
             Oauth2Scopes.USERINFO_EMAIL,
             Oauth2Scopes.USERINFO_PROFILE,
             // Monitoring scope as POC
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
index a0f899a26ff..481f7d6c5a8 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -141,9 +141,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       }
 
       val optional = Option(output) collectFirst { case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
-      val contentType = output.contentType.getOrElse("")
+      val contentType = output.contentType.map(_.toString).getOrElse("")
 
-      List(kind, output.cloudPath, output.containerPath, optional, contentType)
+      List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
     } mkString("\"", "\"\n|  \"", "\"")
 
     val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(
@@ -179,11 +179,12 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
                                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
+    import cromwell.backend.google.pipelines.common.action.ActionUtils.shellEscaped
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
         referenceInputsToMountedPaths map {
           case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${input.containerPath.parent.pathAsString} && ln -s $absolutePathOnRefDisk ${input.containerPath.pathAsString}"
+            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }
 
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
index b445f4786f8..19774a4cc41 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
@@ -38,12 +38,12 @@ trait PipelinesParameterConversions {
           val drsCommand =
             List(fileInput.cloudPath.pathAsString, fileInput.containerPath.pathAsString) ++
               drsPath.requesterPaysProjectIdOption.toList
-          val marthaEnv = DrsConfig.toEnv(drsFileSystemProvider.drsConfig)
+          val drsResolverEnv = DrsConfig.toEnv(drsFileSystemProvider.drsConfig)
           val localizationAction = ActionBuilder
             .withImage(drsDockerImage)
             .withCommand(drsCommand: _*)
             .withMounts(mounts)
-            .setEnvironment(marthaEnv.asJava)
+            .setEnvironment(drsResolverEnv.asJava)
             .withLabels(labels)
           List(ActionBuilder.describeParameter(fileInput, labels), localizationAction)
         case sraPath: SraPath =>
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
index 3535f1db8d8..18c84ee66eb 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
@@ -1,7 +1,7 @@
 package cromwell.backend.google.pipelines.v2alpha1
 
 import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.cloud.NoCredentials
 import com.typesafe.config.{Config, ConfigFactory}
 import common.assertion.CromwellTimeoutSpec
@@ -24,9 +24,9 @@ class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   implicit val gcsTransferConfiguration: GcsTransferConfiguration =
     GcsTransferConfiguration(transferAttempts = refineMV(1), parallelCompositeUploadThreshold = "0")
 
-  private val marthaConfig: Config = ConfigFactory.parseString(
-    """martha {
-      |   url = "http://martha-url"
+  private val drsResolverConfig: Config = ConfigFactory.parseString(
+    """resolver {
+      |   url = "http://drshub-url"
       |}
       |""".stripMargin
   )
@@ -39,7 +39,7 @@ class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   it should "create a DRS input parameter" in {
 
     val drsPathBuilder = DrsPathBuilder(
-      new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+      new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
       None,
     )
     val drsPath = drsPathBuilder.build("drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba").get
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
index 1c936e76317..7f10580b700 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
@@ -82,9 +82,9 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
-          "virtualMachine" -> Map(
+          "virtualMachine" -> Map[String, Any](
             "machineType" -> "custom-1-1024",
             "preemptible" -> false
           ).asJava
@@ -117,7 +117,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
           "virtualMachine" -> Map(
             "machineType" -> "custom-1-1024",
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
index e4c95dcb1e0..8d8f52d3773 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
@@ -119,7 +119,7 @@ case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode
             ComputeScopes.COMPUTE,
             StorageScopes.DEVSTORAGE_FULL_CONTROL,
             GoogleCloudScopes.KmsScope,
-            // Profile and Email scopes are requirements for interacting with Martha
+            // Profile and Email scopes are requirements for interacting with DRS Resolvers
             Oauth2Scopes.USERINFO_EMAIL,
             Oauth2Scopes.USERINFO_PROFILE,
             // Monitoring scope as POC
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
index 77370cabc92..3c0f5ca63f9 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -12,14 +12,19 @@ import cromwell.backend.google.pipelines.common.io.PipelinesApiWorkingDisk
 import cromwell.backend.google.pipelines.v2beta.PipelinesApiAsyncBackendJobExecutionActor._
 import cromwell.backend.standard.StandardAsyncExecutionActorParams
 import cromwell.core.path.{DefaultPathBuilder, Path}
+import cromwell.filesystems.drs.DrsPath
 import cromwell.filesystems.gcs.GcsPathBuilder.ValidFullGcsPath
 import cromwell.filesystems.gcs.{GcsPath, GcsPathBuilder}
 import org.apache.commons.codec.digest.DigestUtils
+import org.apache.commons.csv.{CSVFormat, CSVPrinter}
+import org.apache.commons.io.output.ByteArrayOutputStream
 import wom.core.FullyQualifiedName
 import wom.expression.FileEvaluation
 import wom.values.{GlobFunctions, WomFile, WomGlobFile, WomMaybeListedDirectory, WomMaybePopulatedFile, WomSingleFile, WomUnlistedDirectory}
 
-import java.io.FileNotFoundException
+import java.nio.charset.Charset
+
+import java.io.{FileNotFoundException, OutputStreamWriter}
 import scala.concurrent.Future
 import scala.io.Source
 import scala.language.postfixOps
@@ -141,9 +146,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       }
 
       val optional = Option(output) collectFirst { case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
-      val contentType = output.contentType.getOrElse("")
+      val contentType = output.contentType.map(_.toString).getOrElse("")
 
-      List(kind, output.cloudPath, output.containerPath, optional, contentType)
+      List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
     } mkString("\"", "\"\n|  \"", "\"")
 
     val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(
@@ -174,16 +179,25 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
 
   import mouse.all._
 
+  override def uploadDrsLocalizationManifest(createPipelineParameters: CreatePipelineParameters, cloudPath: Path): Future[Unit] = {
+    val content = generateDrsLocalizerManifest(createPipelineParameters.inputOutputParameters.fileInputParameters)
+    if (content.nonEmpty)
+      asyncIo.writeAsync(cloudPath, content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+    else
+      Future.unit
+  }
+
   private def generateGcsLocalizationScript(inputs: List[PipelinesApiInput],
                                             referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]])
                                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
+    import cromwell.backend.google.pipelines.common.action.ActionUtils.shellEscaped
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
         referenceInputsToMountedPaths map {
           case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${input.containerPath.parent.pathAsString} && ln -s $absolutePathOnRefDisk ${input.containerPath.pathAsString}"
+            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }
 
@@ -396,4 +410,17 @@ object PipelinesApiAsyncBackendJobExecutionActor {
       }
     } combineAll
   }
+
+  private [v2beta] def generateDrsLocalizerManifest(inputs: List[PipelinesApiInput]): String = {
+    val outputStream = new ByteArrayOutputStream()
+    val csvPrinter = new CSVPrinter(new OutputStreamWriter(outputStream), CSVFormat.DEFAULT)
+    val drsFileInputs = inputs collect {
+      case drsInput@PipelinesApiFileInput(_, drsPath: DrsPath, _, _) => (drsInput, drsPath)
+    }
+    drsFileInputs foreach { case (drsInput, drsPath) =>
+      csvPrinter.printRecord(drsPath.pathAsString, drsInput.containerPath.pathAsString)
+    }
+    csvPrinter.close(true)
+    outputStream.toString(Charset.defaultCharset())
+  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
index 505c23edb9c..64365fe404f 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
@@ -1,6 +1,5 @@
 package cromwell.backend.google.pipelines.v2beta
 
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, DrsConfig}
 import com.google.api.services.lifesciences.v2beta.model.{Action, Mount}
 import com.typesafe.config.ConfigFactory
 import cromwell.backend.google.pipelines.common.action.ActionCommands._
@@ -27,25 +26,6 @@ trait PipelinesParameterConversions {
 
       val labels = ActionBuilder.parameterLabels(fileInput)
       fileInput.cloudPath match {
-        case drsPath: DrsPath =>
-
-          import scala.jdk.CollectionConverters._
-
-          val drsFileSystemProvider = drsPath.drsPath.getFileSystem.provider.asInstanceOf[DrsCloudNioFileSystemProvider]
-
-          val drsDockerImage = config.getString("drs.localization.docker-image")
-          // Note: Don't ShellPath.escape the paths as we are directly invoking the localizer and NOT launching a shell.
-          val drsCommand =
-            List(fileInput.cloudPath.pathAsString, fileInput.containerPath.pathAsString) ++
-              drsPath.requesterPaysProjectIdOption.toList
-          val marthaEnv = DrsConfig.toEnv(drsFileSystemProvider.drsConfig)
-          val localizationAction = ActionBuilder
-            .withImage(drsDockerImage)
-            .withCommand(drsCommand: _*)
-            .withMounts(mounts)
-            .setEnvironment(marthaEnv.asJava)
-            .withLabels(labels)
-          List(ActionBuilder.describeParameter(fileInput, labels), localizationAction)
         case sraPath: SraPath =>
           val sraConfig = config.getConfig("filesystems.sra")
 
@@ -78,6 +58,9 @@ trait PipelinesParameterConversions {
         case _: GcsPath =>
           // GCS paths will be localized with a separate localization script.
           Nil
+        case _: DrsPath =>
+          // DRS paths will be localized with a single call to cromwell-drs-localizer with a manifest
+          Nil
       }
     }
   }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
index 4aa52f89801..3b470b9096b 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
@@ -1,14 +1,21 @@
 package cromwell.backend.google.pipelines.v2beta.api
 
+import cloud.nio.impl.drs.DrsConfig
 import com.google.api.services.lifesciences.v2beta.model.{Action, Mount}
+import com.typesafe.config.ConfigFactory
 import cromwell.backend.google.pipelines.common.action.ActionCommands.localizeFile
 import cromwell.backend.google.pipelines.common.action.ActionLabels._
 import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.pipelines.common.PipelinesApiFileInput
 import cromwell.backend.google.pipelines.common.PipelinesApiJobPaths._
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.CreatePipelineParameters
 import cromwell.backend.google.pipelines.v2beta.PipelinesConversions._
 import cromwell.backend.google.pipelines.v2beta.ToParameter.ops._
-import cromwell.backend.google.pipelines.v2beta.api.ActionBuilder.cloudSdkShellAction
+import cromwell.backend.google.pipelines.v2beta.api.ActionBuilder.{EnhancedAction, cloudSdkShellAction}
+import cromwell.core.path.Path
+import cromwell.filesystems.drs.DrsPath
+
+import scala.jdk.CollectionConverters._
 
 
 trait Localization {
@@ -34,15 +41,59 @@ trait Localization {
     val runGcsLocalizationScript = cloudSdkShellAction(
       s"/bin/bash $gcsLocalizationContainerPath")(mounts = mounts, labels = localizationLabel)
 
+    val drsInputs: List[DrsPath] = createPipelineParameters.inputOutputParameters.fileInputParameters.collect {
+      case PipelinesApiFileInput(_, drsPath: DrsPath, _, _) => drsPath
+    }
+
+    val drsLocalizationActions = if (drsInputs.nonEmpty) {
+      val drsLocalizationManifestContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(DrsLocalizationManifestName)
+      val localizeDrsLocalizationManifest = cloudSdkShellAction(localizeFile(
+        cloudPath = createPipelineParameters.cloudCallRoot / DrsLocalizationManifestName,
+        containerPath = drsLocalizationManifestContainerPath))(mounts = mounts, labels = localizationLabel)
+
+      // Requester pays project id is stored on each DrsPath, but will be the same for all DRS inputs to a
+      // particular workflow because it's determined by the Google project set in workflow options.
+      val requesterPaysProjectId: Option[String] = drsInputs.flatMap(_.requesterPaysProjectIdOption).headOption
+      val runDrsLocalization = Localization.drsAction(drsLocalizationManifestContainerPath, mounts, localizationLabel, requesterPaysProjectId)
+      List(localizeDrsLocalizationManifest, runDrsLocalization)
+    } else List[Action]()
+
     // Any "classic" PAPI v2 one-at-a-time localizations for non-GCS inputs.
     val singletonLocalizations = createPipelineParameters.inputOutputParameters.fileInputParameters.flatMap(_.toActions(mounts).toList)
 
     val localizations =
       localizeGcsTransferLibrary ::
         localizeGcsLocalizationScript :: runGcsLocalizationScript ::
+        drsLocalizationActions :::
         localizeGcsDelocalizationScript ::
         singletonLocalizations
 
     ActionBuilder.annotateTimestampedActions("localization", Value.Localization)(localizations)
   }
 }
+
+object Localization {
+
+  def drsAction(manifestPath: Path,
+                mounts: List[Mount],
+                labels: Map[String, String],
+                requesterPaysProjectId: Option[String]
+               ): Action = {
+    val config = ConfigFactory.load
+    val drsResolverConfig = config.getConfig("filesystems.drs.global.config.resolver")
+    val drsConfig = DrsConfig.fromConfig(drsResolverConfig)
+    val drsDockerImage = config.getString("drs.localization.docker-image")
+
+    val manifestArg = List("-m", manifestPath.pathAsString)
+    val requesterPaysArg = requesterPaysProjectId.map(r => List("-r", r)).getOrElse(List.empty)
+    val drsCommand = manifestArg ++ requesterPaysArg
+
+    val drsResolverEnv = DrsConfig.toEnv(drsConfig)
+    ActionBuilder
+      .withImage(drsDockerImage)
+      .withCommand(drsCommand: _*)
+      .withMounts(mounts)
+      .setEnvironment(drsResolverEnv.asJava)
+      .withLabels(labels)
+  }
+}
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
index 9b93a976e22..e7189d453ad 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
@@ -2,14 +2,22 @@ package cromwell.backend.google.pipelines.v2beta
 
 import java.nio.file.Paths
 import cats.data.NonEmptyList
+import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
+import com.google.cloud.NoCredentials
+import com.typesafe.config.{Config, ConfigFactory}
 import common.assertion.CromwellTimeoutSpec
 import common.mock.MockSugar
 import cromwell.backend.google.pipelines.common.PipelinesApiFileInput
+import cromwell.backend.google.pipelines.common.io.{DiskType, PipelinesApiWorkingDisk}
 import cromwell.core.path.DefaultPathBuilder
+import cromwell.filesystems.drs.DrsPathBuilder
 import org.mockito.Mockito._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
+import scala.concurrent.duration.DurationInt
+
 class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   with MockSugar {
   behavior of "PipelinesParameterConversions"
@@ -44,4 +52,45 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Cro
 
     PipelinesApiAsyncBackendJobExecutionActor.groupParametersByGcsBucket(inputs) shouldEqual expected
   }
+
+  it should "generate a CSV manifest for DRS inputs, ignoring non-DRS inputs" in {
+    def makeDrsPathBuilder: DrsPathBuilder = {
+      val drsResolverConfig: Config = ConfigFactory.parseString(
+        """resolver {
+          |   url = "http://drshub-url"
+          |}
+          |""".stripMargin
+      )
+
+      val fakeCredentials = NoCredentials.getInstance
+
+      val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
+        throw new UnsupportedOperationException("PipelinesApiAsyncBackendJobExecutionActorSpec doesn't need to use drs read interpreter.")
+
+      DrsPathBuilder(
+        new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+        None,
+      )
+    }
+
+    val mount = PipelinesApiWorkingDisk(DiskType.LOCAL, 1)
+
+    def makeDrsInput(name: String, drsUri: String, containerPath: String): PipelinesApiFileInput = {
+      val drsPath = makeDrsPathBuilder.build(drsUri).get
+      val containerRelativePath = DefaultPathBuilder.get(containerPath)
+      PipelinesApiFileInput(name, drsPath, containerRelativePath, mount)
+    }
+
+    val nonDrsInput: PipelinesApiFileInput = PipelinesApiFileInput("nnn",
+      DefaultPathBuilder.get("/local/nnn.bai"), DefaultPathBuilder.get("/path/to/nnn.bai"), mount)
+
+    val inputs = List(
+      makeDrsInput("aaa", "drs://drs.example.org/aaa", "path/to/aaa.bai"),
+      nonDrsInput,
+      makeDrsInput("bbb", "drs://drs.example.org/bbb", "path/to/bbb.bai")
+    )
+
+    PipelinesApiAsyncBackendJobExecutionActor.generateDrsLocalizerManifest(inputs) shouldEqual
+      "drs://drs.example.org/aaa,/cromwell_root/path/to/aaa.bai\r\ndrs://drs.example.org/bbb,/cromwell_root/path/to/bbb.bai\r\n"
+  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala
deleted file mode 100644
index c3ed9d27b02..00000000000
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala
+++ /dev/null
@@ -1,96 +0,0 @@
-package cromwell.backend.google.pipelines.v2beta
-
-import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
-import com.google.cloud.NoCredentials
-import com.typesafe.config.{Config, ConfigFactory}
-import common.assertion.CromwellTimeoutSpec
-import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.GcsTransferConfiguration
-import cromwell.backend.google.pipelines.common.PipelinesApiFileInput
-import cromwell.backend.google.pipelines.common.action.ActionUtils
-import cromwell.backend.google.pipelines.common.io.{DiskType, PipelinesApiWorkingDisk}
-import cromwell.core.path.DefaultPathBuilder
-import cromwell.filesystems.drs.DrsPathBuilder
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-import scala.jdk.CollectionConverters._
-import scala.concurrent.duration.DurationInt
-
-class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "PipelinesConversions"
-  implicit val gcsTransferConfiguration: GcsTransferConfiguration =
-    GcsTransferConfiguration(transferAttempts = refineMV(1), parallelCompositeUploadThreshold = "0")
-
-  private val marthaConfig: Config = ConfigFactory.parseString(
-    """martha {
-      |   url = "http://martha-url"
-      |}
-      |""".stripMargin
-  )
-
-  private lazy val fakeCredentials = NoCredentials.getInstance
-
-  private val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
-    throw new UnsupportedOperationException("Currently PipelinesConversionsSpec doesn't need to use drs read interpreter.")
-
-  it should "create a DRS input parameter" in {
-
-    val drsPathBuilder = DrsPathBuilder(
-      new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
-      None,
-    )
-    val drsPath = drsPathBuilder.build("drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba").get
-    val containerRelativePath = DefaultPathBuilder.get("path/to/file.bai")
-    val mount = PipelinesApiWorkingDisk(DiskType.LOCAL, 1)
-    val input = PipelinesApiFileInput("example", drsPath, containerRelativePath, mount)
-    val actions = PipelinesConversions.inputToParameter.toActions(input, Nil)
-    actions.size should be(2)
-
-    val logging = actions.head
-
-    logging.keySet.asScala should contain theSameElementsAs
-      Set("entrypoint", "commands", "imageUri", "labels", "mounts", "timeout")
-
-    logging.get("commands") should be(a[java.util.List[_]])
-    logging.get("commands").asInstanceOf[java.util.List[_]] should contain(
-      """printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" """ +
-        """Localizing\ input\ drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba\ """ +
-        """-\>\ /cromwell_root/path/to/file.bai"""
-    )
-
-    logging.get("mounts") should be(a[java.util.List[_]])
-    logging.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
-
-    logging.get("imageUri") should be(ActionUtils.CloudSdkImage)
-
-    val loggingLabels = logging.get("labels").asInstanceOf[java.util.Map[_, _]]
-    loggingLabels.keySet.asScala should contain theSameElementsAs List("logging", "inputName")
-    loggingLabels.get("logging") should be("Localization")
-    loggingLabels.get("inputName") should be("example")
-
-    val action = actions.tail.head
-
-    action.keySet.asScala should contain theSameElementsAs
-      Set("commands", "environment", "imageUri", "labels", "mounts")
-
-    action.get("commands") should be(a[java.util.List[_]])
-    action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
-      "drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba",
-      "/cromwell_root/path/to/file.bai"
-    )
-
-    action.get("mounts") should be(a[java.util.List[_]])
-    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
-
-    action.get("imageUri") should be("somerepo/drs-downloader:tagged")
-
-    val actionLabels = action.get("labels").asInstanceOf[java.util.Map[_, _]]
-    actionLabels.keySet.asScala should contain theSameElementsAs List("tag", "inputName")
-    actionLabels.get("tag") should be("Localization")
-    actionLabels.get("inputName") should be("example")
-  }
-
-}
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
index 37020b0b0d6..6afd75adbd6 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
@@ -81,9 +81,9 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
-          "virtualMachine" -> Map(
+          "virtualMachine" -> Map[String, Any](
             "machineType" -> "custom-1-1024",
             "preemptible" -> false
           ).asJava
@@ -115,7 +115,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
           "virtualMachine" -> Map(
             "machineType" -> "custom-1-1024",
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala
new file mode 100644
index 00000000000..f815ceebd14
--- /dev/null
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala
@@ -0,0 +1,67 @@
+package cromwell.backend.google.pipelines.v2beta.api
+
+import common.assertion.CromwellTimeoutSpec
+import cromwell.backend.google.pipelines.common.PipelinesApiJobPaths.DrsLocalizationManifestName
+import cromwell.core.path.DefaultPathBuilder
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import scala.jdk.CollectionConverters._
+
+class LocalizationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  behavior of "Localization"
+
+  it should "create the right action to localize DRS files using a manifest" in {
+
+    val manifestPathString = s"path/to/${DrsLocalizationManifestName}"
+    val manifestPath = DefaultPathBuilder.get(manifestPathString)
+    val tagKey = "tag"
+    val tagLabel = "myLabel"
+
+    val action = Localization.drsAction(manifestPath, Nil, Map(tagKey -> tagLabel), None)
+    action.keySet.asScala should contain theSameElementsAs
+      Set("commands", "environment", "imageUri", "labels", "mounts")
+
+    action.get("commands") should be(a[java.util.List[_]])
+    action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
+      "-m", manifestPathString
+    )
+
+    action.get("mounts") should be(a[java.util.List[_]])
+    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+
+    action.get("imageUri") should be("somerepo/drs-downloader:tagged")
+
+    val actionLabels = action.get("labels").asInstanceOf[java.util.Map[_, _]]
+    actionLabels.keySet.asScala should contain theSameElementsAs List("tag")
+    actionLabels.get(tagKey) should be(tagLabel)
+  }
+
+  it should "create the right action to localize DRS files using a manifest with requester pays" in {
+
+    val manifestPathString = s"path/to/${DrsLocalizationManifestName}"
+    val manifestPath = DefaultPathBuilder.get(manifestPathString)
+    val tagKey = "tag"
+    val tagLabel = "myLabel"
+    val requesterPaysProjectId = "123"
+
+    val action = Localization.drsAction(manifestPath, Nil, Map(tagKey -> tagLabel), Option(requesterPaysProjectId))
+    action.keySet.asScala should contain theSameElementsAs
+      Set("commands", "environment", "imageUri", "labels", "mounts")
+
+    action.get("commands") should be(a[java.util.List[_]])
+    action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
+      "-m", manifestPathString, "-r", requesterPaysProjectId
+    )
+
+    action.get("mounts") should be(a[java.util.List[_]])
+    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+
+    action.get("imageUri") should be("somerepo/drs-downloader:tagged")
+
+    val actionLabels = action.get("labels").asInstanceOf[java.util.Map[_, _]]
+    actionLabels.keySet.asScala should contain theSameElementsAs List("tag")
+    actionLabels.get(tagKey) should be(tagLabel)
+  }
+}
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 1fe5b743465..1e5637fff0e 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -1,5 +1,6 @@
 package cromwell.backend.impl.tes
 
+import common.exception.AggregatedMessageException
 import java.io.FileNotFoundException
 import java.nio.file.FileAlreadyExistsException
 import cats.syntax.apply._
@@ -30,6 +31,7 @@ import scala.util.{Failure, Success}
 
 sealed trait TesRunStatus {
   def isTerminal: Boolean
+  def sysLogs: Seq[String] = Seq.empty[String]
 }
 
 case object Running extends TesRunStatus {
@@ -40,8 +42,14 @@ case object Complete extends TesRunStatus {
   def isTerminal = true
 }
 
-case object FailedOrError extends TesRunStatus {
+case class Error(override val sysLogs: Seq[String] = Seq.empty[String]) extends TesRunStatus {
   def isTerminal = true
+  override def toString = "SYSTEM_ERROR"
+}
+
+case class Failed(override val sysLogs: Seq[String] = Seq.empty[String]) extends TesRunStatus {
+  def isTerminal = true
+  override def toString = "EXECUTOR_ERROR"
 }
 
 case object Cancelled extends TesRunStatus {
@@ -80,6 +88,14 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
 
   private val tesEndpoint = workflowDescriptor.workflowOptions.getOrElse("endpoint", tesConfiguration.endpointURL)
 
+  // Temporary support for configuring the format we use to send BlobPaths to TES.
+  // Added 10/2022 as a workaround for the CromwellOnAzure TES server expecting
+  // blob containers to be mounted via blobfuse rather than addressed natively.
+  private val transformBlobToLocalPaths: Boolean =
+    configurationDescriptor.backendConfig
+      .getAs[Boolean]("transform-blob-to-local-path")
+      .getOrElse(false)
+
   override lazy val jobTag: String = jobDescriptor.key.tag
 
   private val outputMode = validate {
@@ -148,7 +164,7 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
         mode)
     })
 
-    tesTask.map(TesTask.makeTask)
+    tesTask.map(TesTask.makeTask(_, transformBlobToLocalPaths))
   }
 
   def writeScriptFile(): Future[Unit] = {
@@ -209,6 +225,21 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
   override def requestsAbortAndDiesImmediately: Boolean = false
 
   override def pollStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[TesRunStatus] = {
+    for {
+      status <- queryStatusAsync(handle)
+      errorLog <- status match {
+          case Error(_) | Failed(_) => getErrorLogs(handle)
+          case _ => Future.successful(Seq.empty[String])
+      }
+      statusWithLog = status match {
+        case Error(_) => Error(errorLog)
+        case Failed(_) => Failed(errorLog)
+        case _ => status
+      }
+    } yield statusWithLog
+  }
+
+  private def queryStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[TesRunStatus] = {
     makeRequest[MinimalTaskView](HttpRequest(uri = s"$tesEndpoint/${handle.pendingJob.jobId}?view=MINIMAL")) map {
       response =>
         val state = response.state
@@ -221,24 +252,40 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
             jobLogger.info(s"Job ${handle.pendingJob.jobId} was canceled")
             Cancelled
 
-          case s if s.contains("ERROR") =>
+          case s if s.contains("EXECUTOR_ERROR") =>
+            jobLogger.info(s"TES reported a failure for Job ${handle.pendingJob.jobId}: '$s'")
+            Failed()
+
+          case s if s.contains("SYSTEM_ERROR") =>
             jobLogger.info(s"TES reported an error for Job ${handle.pendingJob.jobId}: '$s'")
-            FailedOrError
+            Error()
 
           case _ => Running
         }
     }
   }
 
+  private def getErrorLogs(handle: StandardAsyncPendingExecutionHandle): Future[Seq[String]] = {
+    makeRequest[Task](HttpRequest(uri = s"$tesEndpoint/${handle.pendingJob.jobId}?view=FULL")) map { response =>
+      response.logs.flatMap(_.lastOption).flatMap(_.system_logs).getOrElse(Seq.empty[String])
+    }
+  }
+
   override def customPollStatusFailure: PartialFunction[(ExecutionHandle, Exception), ExecutionHandle] = {
     case (oldHandle: StandardAsyncPendingExecutionHandle@unchecked, e: Exception) =>
       jobLogger.error(s"$tag TES Job ${oldHandle.pendingJob.jobId} has not been found, failing call")
       FailedNonRetryableExecutionHandle(e, kvPairsToSave = None)
   }
 
+  private def handleExecutionError(status: TesRunStatus, returnCode: Option[Int]): Future[ExecutionHandle] = {
+    val exception = new AggregatedMessageException(s"Task ${jobDescriptor.key.tag} failed for unknown reason: ${status.toString()}", status.sysLogs)
+    Future.successful(FailedNonRetryableExecutionHandle(exception, returnCode, None))
+  }
+
   override def handleExecutionFailure(status: StandardAsyncRunState, returnCode: Option[Int]) = {
     status match {
       case Cancelled => Future.successful(AbortedExecutionHandle)
+      case Error(_) | Failed(_) => handleExecutionError(status, returnCode)
       case _ => super.handleExecutionFailure(status, returnCode)
     }
   }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
index 3d55a9f3a1c..264ba6299bd 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
@@ -11,10 +11,10 @@ class TesConfiguration(val configurationDescriptor: BackendConfigurationDescript
   val useBackendParameters =
     configurationDescriptor
       .backendConfig
-      .as[Option[Boolean]](TesConfiguration.useBackendParamtersKey)
+      .as[Option[Boolean]](TesConfiguration.useBackendParametersKey)
       .getOrElse(false)
 }
 
 object TesConfiguration {
-  final val useBackendParamtersKey = "use_tes_11_preview_backend_parameters"
+  final val useBackendParametersKey = "use_tes_11_preview_backend_parameters"
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
index 4212ff4be67..c5b3c4df66d 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
@@ -3,10 +3,13 @@ package cromwell.backend.impl.tes
 import cats.syntax.validated._
 import com.typesafe.config.Config
 import common.validation.ErrorOr.ErrorOr
+import cromwell.backend.google.pipelines.common.DisksValidation
+import cromwell.backend.google.pipelines.common.io.{PipelinesApiAttachedDisk, PipelinesApiEmptyMountedDisk, PipelinesApiWorkingDisk}
 import cromwell.backend.standard.StandardValidatedRuntimeAttributesBuilder
 import cromwell.backend.validation._
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
+import wdl4s.parser.MemoryUnit
 import wom.RuntimeAttributesKeys
 import wom.format.MemorySize
 import wom.types.{WomIntegerType, WomStringType}
@@ -36,6 +39,9 @@ object TesRuntimeAttributes {
 
   private def diskSizeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[MemorySize] = MemoryValidation.optional(DiskSizeKey)
 
+  private def diskSizeCompatValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Seq[PipelinesApiAttachedDisk]] =
+    DisksValidation.optional
+
   private def memoryValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[MemorySize] = MemoryValidation.optional(RuntimeAttributesKeys.MemoryKey)
 
   private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
@@ -45,10 +51,14 @@ object TesRuntimeAttributes {
   private def preemptibleValidation(runtimeConfig: Option[Config]) = PreemptibleValidation.default(runtimeConfig)
 
   def runtimeAttributesBuilder(backendRuntimeConfig: Option[Config]): StandardValidatedRuntimeAttributesBuilder =
+    // !! NOTE !! If new validated attributes are added to TesRuntimeAttributes, be sure to include
+    // their validations here so that they will be handled correctly with backendParameters.
+    // Location 2 of 2
     StandardValidatedRuntimeAttributesBuilder.default(backendRuntimeConfig).withValidation(
       cpuValidation(backendRuntimeConfig),
       memoryValidation(backendRuntimeConfig),
       diskSizeValidation(backendRuntimeConfig),
+      diskSizeCompatValidation(backendRuntimeConfig),
       dockerValidation,
       dockerWorkingDirValidation,
       preemptibleValidation(backendRuntimeConfig),
@@ -71,13 +81,45 @@ object TesRuntimeAttributes {
       Map.empty
   }
 
+  private def detectDiskFormat(backendRuntimeConfig: Option[Config], validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[MemorySize] = {
+
+    def adaptPapiDisks(disks: Seq[PipelinesApiAttachedDisk]): MemorySize = {
+      disks match {
+        case disk :: Nil if disk.isInstanceOf[PipelinesApiWorkingDisk] =>
+            MemorySize(disk.sizeGb.toDouble, MemoryUnit.GB)
+        case _ :: _ =>
+          // When a user specifies only a custom disk, we add the default disk in the background, so we technically have multiple disks.
+          // But we don't want to confuse the user with `multiple disks` message when they only put one.
+          if (disks.exists(_.isInstanceOf[PipelinesApiEmptyMountedDisk]))
+            throw new IllegalArgumentException("Disks with custom mount points are not supported by this backend")
+          else
+            // Multiple `local-disk` is not legal, but possible and should be detected
+            throw new IllegalArgumentException("Expecting exactly one disk definition on this backend, found multiple")
+      }
+    }
+
+    val maybeTesDisk: Option[MemorySize] =
+      RuntimeAttributesValidation.extractOption(diskSizeValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+    val maybePapiDisk: Option[Seq[PipelinesApiAttachedDisk]] =
+      RuntimeAttributesValidation.extractOption(diskSizeCompatValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+
+    (maybeTesDisk, maybePapiDisk) match {
+      case (Some(tesDisk: MemorySize), _) =>
+        Option(tesDisk) // If WDLs are in circulation with both `disk` and `disks`, pick the one intended for this backend
+      case (None, Some(papiDisks: Seq[PipelinesApiAttachedDisk])) =>
+        Option(adaptPapiDisks(papiDisks))
+      case _ =>
+        None
+    }
+  }
+
   def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes, rawRuntimeAttributes: Map[String, WomValue], config: TesConfiguration): TesRuntimeAttributes = {
     val backendRuntimeConfig = config.runtimeConfig
     val docker: String = RuntimeAttributesValidation.extract(dockerValidation, validatedRuntimeAttributes)
     val dockerWorkingDir: Option[String] = RuntimeAttributesValidation.extractOption(dockerWorkingDirValidation.key, validatedRuntimeAttributes)
     val cpu: Option[Int Refined Positive] = RuntimeAttributesValidation.extractOption(cpuValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
     val memory: Option[MemorySize] = RuntimeAttributesValidation.extractOption(memoryValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
-    val disk: Option[MemorySize] = RuntimeAttributesValidation.extractOption(diskSizeValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+    val disk: Option[MemorySize] = detectDiskFormat(backendRuntimeConfig, validatedRuntimeAttributes)
     val failOnStderr: Boolean =
       RuntimeAttributesValidation.extract(failOnStderrValidation(backendRuntimeConfig), validatedRuntimeAttributes)
     val continueOnReturnCode: ContinueOnReturnCode =
@@ -87,12 +129,14 @@ object TesRuntimeAttributes {
 
     // !! NOTE !! If new validated attributes are added to TesRuntimeAttributes, be sure to include
     // their validations here so that they will be handled correctly with backendParameters.
+    // Location 1 of 2
     val validations = Set(
       dockerValidation,
       dockerWorkingDirValidation,
       cpuValidation(backendRuntimeConfig),
       memoryValidation(backendRuntimeConfig),
       diskSizeValidation(backendRuntimeConfig),
+      diskSizeCompatValidation(backendRuntimeConfig),
       failOnStderrValidation(backendRuntimeConfig),
       continueOnReturnCodeValidation(backendRuntimeConfig),
       preemptibleValidation(backendRuntimeConfig)
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index 52fdd7c3fce..5d1a844bb83 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -3,9 +3,14 @@ package cromwell.backend.impl.tes
 import common.collections.EnhancedCollections._
 import common.util.StringUtil._
 import cromwell.backend.impl.tes.OutputMode.OutputMode
-import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendWorkflowDescriptor}
+import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor}
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.{DefaultPathBuilder, Path}
+import net.ceedubs.ficus.Ficus._
+
+import scala.language.postfixOps
+import scala.util.Try
+
 import wdl.draft2.model.FullyQualifiedName
 import wdl4s.parser.MemoryUnit
 import wom.InstantiatedCommand
@@ -13,9 +18,8 @@ import wom.callable.Callable.OutputDefinition
 import wom.expression.NoIoFunctionSet
 import wom.values._
 
-import scala.language.postfixOps
-import scala.util.Try
-
+final case class WorkflowExecutionIdentityConfig(value: String) {override def toString: String = value.toString}
+final case class WorkflowExecutionIdentityOption(value: String) {override def toString: String = value}
 final case class TesTask(jobDescriptor: BackendJobDescriptor,
                          configurationDescriptor: BackendConfigurationDescriptor,
                          jobLogger: JobLogger,
@@ -32,6 +36,16 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
   private val workflowDescriptor = jobDescriptor.workflowDescriptor
   private val workflowName = workflowDescriptor.callable.name
   private val fullyQualifiedTaskName = jobDescriptor.taskCall.fullyQualifiedName
+  private val workflowExecutionIdentityConfig: Option[WorkflowExecutionIdentityConfig] =
+    configurationDescriptor.backendConfig
+      .getAs[String]("workflow-execution-identity")
+      .map(WorkflowExecutionIdentityConfig)
+  private val workflowExecutionIdentityOption: Option[WorkflowExecutionIdentityOption] =
+    workflowDescriptor
+      .workflowOptions
+      .get(TesWorkflowOptionKeys.WorkflowExecutionIdentity)
+      .toOption
+      .map(WorkflowExecutionIdentityOption)
   val name: String = fullyQualifiedTaskName
   val description: String = jobDescriptor.toString
 
@@ -212,7 +226,15 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
     result
   }
 
-  val resources: Resources = TesTask.makeResources(runtimeAttributes, workflowDescriptor)
+  val preferedWorkflowExecutionIdentity = TesTask.getPreferredWorkflowExecutionIdentity(
+      workflowExecutionIdentityConfig,
+      workflowExecutionIdentityOption
+  )
+
+  val resources: Resources = TesTask.makeResources(
+    runtimeAttributes,
+    preferedWorkflowExecutionIdentity
+  )
 
   val executors = Seq(Executor(
     image = dockerImageUsed,
@@ -226,21 +248,22 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
 }
 
 object TesTask {
+  // Helper to determine which source to use for a workflowExecutionIdentity
+  def getPreferredWorkflowExecutionIdentity(configIdentity: Option[WorkflowExecutionIdentityConfig],
+                                           workflowOptionsIdentity: Option[WorkflowExecutionIdentityOption]): Option[String] = {
+    configIdentity.map(_.value).orElse(workflowOptionsIdentity.map(_.value))
+  }
   def makeResources(runtimeAttributes: TesRuntimeAttributes,
-                    workflowDescriptor: BackendWorkflowDescriptor): Resources = {
+                    workflowExecutionId: Option[String]): Resources = {
 
     // This was added in BT-409 to let us pass information to an Azure
     // TES server about which user identity to run tasks as.
     // Note that we validate the type of WorkflowExecutionIdentity
     // in TesInitializationActor.
     val backendParameters = runtimeAttributes.backendParameters ++
-      workflowDescriptor
-        .workflowOptions
-        .get(TesWorkflowOptionKeys.WorkflowExecutionIdentity)
-        .toOption
+      workflowExecutionId
         .map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option(_))
         .toMap
-
     val disk :: ram :: _ = Seq(runtimeAttributes.disk, runtimeAttributes.memory) map {
       case Some(x) =>
         Option(x.to(MemoryUnit.GB).amount)
@@ -258,14 +281,16 @@ object TesTask {
     )
   }
 
-  def makeTask(tesTask: TesTask): Task = {
+  def makeTask(tesTask: TesTask, transformBlobToLocalPath: Boolean = false): Task = {
+    val inputs = if (transformBlobToLocalPath) transformInputs(tesTask.inputs) else tesTask.inputs
+    val outputs = if (transformBlobToLocalPath) transformOutputs(tesTask.outputs) else tesTask.outputs
     Task(
       id = None,
       state = None,
       name = Option(tesTask.name),
       description = Option(tesTask.description),
-      inputs = Option(tesTask.inputs),
-      outputs = Option(tesTask.outputs),
+      inputs = Option(inputs),
+      outputs = Option(outputs),
       resources = Option(tesTask.resources),
       executors = tesTask.executors,
       volumes = None,
@@ -273,6 +298,20 @@ object TesTask {
       logs = None
     )
   }
+
+  def transformInputs(inputs: Seq[Input]): Seq[Input] = inputs.map(i =>
+    i.copy(url=i.url.map(transformBlobString))
+  )
+
+  def transformOutputs(outputs: Seq[Output]): Seq[Output] = outputs.map(i =>
+    i.copy(url=i.url.map(transformBlobString))
+  )
+
+  val blobSegment = ".blob.core.windows.net"
+  def transformBlobString(s: String): String = if (s.contains(blobSegment)) {
+    s.replaceFirst("https:/", "").replaceFirst(blobSegment, "")
+  } else s
+
 }
 
 // Field requirements in classes below based off GA4GH schema
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
index 1b3b3b7aea8..e1984fb65dc 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
@@ -160,6 +160,54 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
       assertFailure(runtimeAttributes, "Expecting disk runtime attribute to be an Integer or String with format '8 GB'")
     }
 
+    "parse an HDD definition" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 HDD"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(disk = Option(MemorySize.parse("10 GB").get))
+      assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "parse an SSD definition" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 SSD"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(disk = Option(MemorySize.parse("10 GB").get))
+      assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "refuse multiple `local-disk` instances" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 SSD, local-disk 20 SSD"))
+      assertFailure(runtimeAttributes, "Expecting exactly one disk definition on this backend, found multiple")
+    }
+
+    "refuse custom mount points" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("/some/mnt 20 SSD"))
+      assertFailure(runtimeAttributes, "Disks with custom mount points are not supported by this backend")
+    }
+
+    "refuse custom AND multiple mount points" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("/mnt/tmp 10 LOCAL, local-disk 20 HDD"))
+      assertFailure(runtimeAttributes, "Disks with custom mount points are not supported by this backend")
+    }
+
+    "not accept a single comma" ignore {
+      // Surprisingly, the PAPI code we call under the covers validates `,` and give the user a default disk.
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString(","))
+      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: ','")
+    }
+
+    "not accept empty string" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString(""))
+      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: ''")
+    }
+
+    "not accept `banana`" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("banana"))
+      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: 'banana'")
+    }
+
+    "not accept a random number (chosen by fair dice roll)" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomInteger(4))
+      assertFailure(runtimeAttributes, "Expecting disks runtime attribute to be a comma separated String or Array[String]")
+    }
+
     "validate a valid dockerWorkingDir entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "dockerWorkingDir" -> WomString("/tmp"))
       val expectedRuntimeAttributes = expectedDefaults.copy(dockerWorkingDir = Option("/tmp"))
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index 0e8440f2a1d..3e5a79b33c9 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -2,15 +2,15 @@ package cromwell.backend.impl.tes
 
 import common.assertion.CromwellTimeoutSpec
 import common.mock.MockSugar
-import cromwell.backend.{BackendSpec, TestConfig}
 import cromwell.backend.validation.ContinueOnReturnCodeSet
+import cromwell.backend.{BackendSpec, TestConfig}
 import cromwell.core.WorkflowOptions
 import cromwell.core.labels.Labels
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.DefaultPathBuilder
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
-import spray.json.{JsObject, JsString, JsValue}
+import spray.json.{JsObject, JsValue}
 import wom.InstantiatedCommand
 
 class TesTaskSpec
@@ -32,32 +32,44 @@ class TesTaskSpec
     Map.empty
   )
 
-  def workflowDescriptorWithIdentity(excIdentity: Option[String]) = {
-    val optionsMap: Map[String, JsValue] = excIdentity.map(i => TesWorkflowOptionKeys.WorkflowExecutionIdentity -> JsString(i)).toMap
-    buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld, None, WorkflowOptions(JsObject(optionsMap)))
-  }
-
   it should "create the correct resources when an identity is passed in WorkflowOptions" in {
-    val wd = workflowDescriptorWithIdentity(Option("abc123"))
-    TesTask.makeResources(runtimeAttributes, wd) shouldEqual
+    val wei = Option("abc123")
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
         Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123")))
     )
   }
 
   it should "create the correct resources when an empty identity is passed in WorkflowOptions" in {
-    val wd = workflowDescriptorWithIdentity(Option(""))
-    TesTask.makeResources(runtimeAttributes, wd) shouldEqual
+    val wei = Option("")
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
         Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("")))
     )
   }
 
   it should "create the correct resources when no identity is passed in WorkflowOptions" in {
-    val wd = workflowDescriptorWithIdentity(None)
-    TesTask.makeResources(runtimeAttributes, wd) shouldEqual
+    val wei = None
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
         Resources(None, None, None, Option(false), None, Option(Map.empty[String, Option[String]])
     )
   }
 
+  it should "create the correct resources when an identity is passed in via backend config" in {
+    val weic = Option(WorkflowExecutionIdentityConfig("abc123"))
+    val weio = Option(WorkflowExecutionIdentityOption("def456"))
+    val wei = TesTask.getPreferredWorkflowExecutionIdentity(weic, weio)
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
+        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123")))
+    )
+  }
+
+  it should "create the correct resources when no identity is passed in via backend config" in {
+    val weic = None
+    val weio = Option(WorkflowExecutionIdentityOption("def456"))
+    val wei = TesTask.getPreferredWorkflowExecutionIdentity(weic, weio)
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
+        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("def456")))
+    )
+  }
 
   it should "copy labels to tags" in {
     val jobLogger = mock[JobLogger]
@@ -88,4 +100,28 @@ class TesTaskSpec
 
     task.tags shouldBe Option(Map("foo" -> "bar"))
   }
+
+  it should "apply the correct transformation to a blob path" in {
+    val orig = "https://coaexternalstorage.blob.core.windows.net/cromwell/mydir/myfile.txt"
+    TesTask.transformBlobString(orig) shouldBe "/coaexternalstorage/cromwell/mydir/myfile.txt"
+  }
+
+  it should "not transform a non-blob path" in {
+    val orig = "https://some-bogus-url.test/cromwell/mydir/myfile.txt"
+    TesTask.transformBlobString(orig) shouldBe orig
+  }
+
+  it should "transform inputs" in {
+    val baseInput = Input(
+      Option("name"),
+      Option("descr"),
+      Option("https://coaexternalstorage.blob.core.windows.net/cromwell/mydir/myfile.txt"),
+      "path",
+      Option("type"),
+      Option("content"),
+    )
+    val inputs = Option(Seq(baseInput))
+    val outcome = inputs.map(TesTask.transformInputs)
+    outcome.get.head.url.get shouldBe "/coaexternalstorage/cromwell/mydir/myfile.txt"
+  }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
index c1f3c18242b..24194807f17 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
@@ -196,7 +196,7 @@ object AstTools {
           val pairType = womType.asInstanceOf[WomPairType]
           WomPair(subElements.head.womValue(pairType.leftType, wdlSyntaxErrorFormatter), subElements(1).womValue(pairType.rightType, wdlSyntaxErrorFormatter))
         } else {
-          throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).getOrElse("No AST").toString})")
+          throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})")
         }
       }
 
@@ -224,7 +224,7 @@ object AstTools {
         case a: Ast if a.getName == "TupleLiteral" => astTupleToValue(a)
         case a: Ast if a.getName == "MapLiteral" && womType.isInstanceOf[WomMapType] => astToMap(a)
         case a: Ast if a.getName == "ObjectLiteral" && womType == WomObjectType => astToObject(a)
-        case _ => throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).getOrElse("No AST").toString})")
+        case _ => throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})")
       }
     }
   }
diff --git a/wom/src/main/scala/wom/util/YamlUtils.scala b/wom/src/main/scala/wom/util/YamlUtils.scala
index b4e0f063c9b..50dffc0457d 100644
--- a/wom/src/main/scala/wom/util/YamlUtils.scala
+++ b/wom/src/main/scala/wom/util/YamlUtils.scala
@@ -38,7 +38,7 @@ object YamlUtils {
             maxDepth: Int Refined NonNegative = defaultMaxDepth
            ): Either[ParsingFailure, Json] = {
     try {
-      val yamlConstructor = new SafeConstructor()
+      val yamlConstructor = new SafeConstructor(loaderOptions)
       val yamlComposer = new MaxDepthComposer(yaml, maxDepth)
       yamlConstructor.setComposer(yamlComposer)
       val parsed = yamlConstructor.getSingleData(classOf[AnyRef])
@@ -76,12 +76,14 @@ object YamlUtils {
   // org.yaml.snakeyaml.error.YAMLException: Number of aliases for non-scalar nodes exceeds the specified max=50
   // that comes from the SnakeYAML library.
   private val loaderOptions = new LoaderOptions()
+  loaderOptions.setAllowRecursiveKeys(true)
+  loaderOptions.setNestingDepthLimit(1000)
   loaderOptions.setMaxAliasesForCollections(Integer.MAX_VALUE)
 
   /** Extends SnakeYaml's Composer checking for a maximum depth before a StackOverflowError occurs. */
   private class MaxDepthComposer(yaml: String, maxDepth: Int Refined NonNegative)
     extends Composer(
-      new ParserImpl(new StreamReader(new StringReader(yaml))),
+      new ParserImpl(new StreamReader(new StringReader(yaml)), loaderOptions),
       new Resolver(),
       loaderOptions
     ) {
diff --git a/wom/src/test/scala/wom/types/WomFileTypeSpec.scala b/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
index 217c15964cc..c4a90fadb07 100644
--- a/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
@@ -65,7 +65,7 @@ class WomFileTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     }
   }
 
-  lazy val failedCoercionTests = Table(
+  lazy val failedCoercionTests = Table[String, WomType, Any, String](
     ("description", "womFileType", "value", "expected"),
 
     ("a double to a dir", WomUnlistedDirectoryType, 6.28318,
diff --git a/wom/src/test/scala/wom/types/WomTypeSpec.scala b/wom/src/test/scala/wom/types/WomTypeSpec.scala
index 01c5030806d..4d3c7befeb5 100644
--- a/wom/src/test/scala/wom/types/WomTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomTypeSpec.scala
@@ -10,6 +10,7 @@ import wom.values._
 
 import scala.runtime.ScalaRunTime
 import scala.util.Random
+import scala.util.matching.Regex
 
 
 class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
@@ -32,7 +33,7 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     WomSingleFileType.stableName shouldEqual "File"
   }
 
-  val rawValuesCoercedToType = Table(
+  val rawValuesCoercedToType = Table[Any, WomType, Any, Regex](
     (
       "Raw Value",
       "WomType",
@@ -43,33 +44,33 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       WomString("hello"),
       WomIntegerType,
       classOf[NumberFormatException],
-      "For input string: \"hello\""
+      "For input string: \"hello\"".r
     ),
     (
       WomInteger(0),
       WomBooleanType,
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '0' of type 'Int' to 'Boolean'."""
+      """No coercion defined from wom value\(s\) '0' of type 'Int' to 'Boolean'.""".r
     ),
     (
       0,
       WomBooleanType,
       classOf[IllegalArgumentException],
-      "No coercion defined from '0' of type 'java.lang.Integer' to 'Boolean'."
+      "No coercion defined from '0' of type 'java.lang.Integer' to 'Boolean'.".r
     ),
     (
       Array(0, 1, 2, 3, 4),
       WomBooleanType,
       classOf[IllegalArgumentException],
-      """No coercion defined from 'Array\(0, 1, 2\)' of type 'int\[\]' to 'Boolean'."""
+      """No coercion defined from 'Array\(0, 1, 2\)' of type 'int\[\]' to 'Boolean'.""".r
     ),
     (
       new AnyRef {},
       WomBooleanType,
       classOf[IllegalArgumentException],
-      "No coercion defined from" +
+      ("No coercion defined from" +
         """ 'wom.types.WomTypeSpec\$\$anon\$(.*)@.*' of type""" +
-        """ 'wom.types.WomTypeSpec\$\$anon\$\1' to 'Boolean'."""
+        """ 'wom.types.WomTypeSpec\$\$anon\$\1' to 'Boolean'.""").r
     ),
     (
       WomArray(WomArrayType(WomOptionalType(WomIntegerType)), Seq(
@@ -81,19 +82,19 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       ),
       WomOptionalType(WomMaybeEmptyArrayType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '\[0, 1, 2\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'."""
+      """No coercion defined from wom value\(s\) '\[0, 1, 2\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'.""".r
     ),
     (
       WomArray(WomArrayType(WomOptionalType(WomIntegerType)), Seq(WomOptionalValue.none(WomIntegerType))),
       WomOptionalType(WomMaybeEmptyArrayType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '\[null\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'."""
+      """No coercion defined from wom value\(s\) '\[null\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'.""".r
     ),
     (
       WomOptionalValue.none(WomArrayType(WomIntegerType)),
       WomMaybeEmptyArrayType(WomOptionalType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) 'null' of type 'Array\[Int\]\?' to 'Array\[Int\?\]'."""
+      """No coercion defined from wom value\(s\) 'null' of type 'Array\[Int\]\?' to 'Array\[Int\?\]'.""".r
     )
   )
 
diff --git a/womtool/src/main/scala/womtool/graph/WomGraph.scala b/womtool/src/main/scala/womtool/graph/WomGraph.scala
index d81f36e5538..b1957a1545c 100644
--- a/womtool/src/main/scala/womtool/graph/WomGraph.scala
+++ b/womtool/src/main/scala/womtool/graph/WomGraph.scala
@@ -10,8 +10,6 @@ import common.Checked
 import common.transforms.CheckedAtoB
 import common.validation.Validation._
 import common.collections.EnhancedCollections._
-import cwl.CwlDecoder
-import cwl.preprocessor.CwlPreProcessor
 import spray.json.{JsArray, JsBoolean, JsNull, JsNumber, JsObject, JsString, JsValue}
 import wdl.draft2.model.{WdlNamespace, WdlNamespaceWithWorkflow}
 import wdl.transforms.base.wdlom2wom.FileElementToWomBundleInputs
@@ -21,7 +19,6 @@ import wdl.draft3.transforms.parsing.fileToAst
 import wdl.transforms.draft2.wdlom2wom.WdlDraft2WomBundleMakers._
 import wom.callable.WorkflowDefinition
 import wom.executable.WomBundle
-import wom.expression.NoIoFunctionSet
 import wom.graph._
 import wom.transforms.WomBundleMaker.ops._
 import wom.types._
@@ -161,8 +158,6 @@ class WomGraph(graphName: String, graph: Graph) {
 
 object WomGraph {
 
-  implicit val cwlPreProcessor = CwlPreProcessor.noLogging
-
   final case class WorkflowDigraph(workflowName: String, digraph: NodesAndLinks)
   final case class NodesAndLinks(nodes: Set[String], links: Set[String]) {
     def wrapNodes(f: Set[String] => String) = this.copy(Set(f(nodes)), links)
@@ -174,7 +169,7 @@ object WomGraph {
   }
 
   def fromFiles(mainFile: String) = {
-    val graph = if (mainFile.toLowerCase().endsWith("wdl")) womExecutableFromWdl(mainFile) else womExecutableFromCwl(mainFile)
+    val graph = womExecutableFromWdl(mainFile)
     new WomGraph("workflow", graph)
   }
 
@@ -204,21 +199,6 @@ object WomGraph {
     }
   }
 
-  private def womExecutableFromCwl(filePath: String): Graph = {
-    import cwl.AcceptAllRequirements
-    (for {
-      clt <- CwlDecoder.decodeCwlFile(File(filePath)).
-        value.
-        unsafeRunSync()
-      inputs = clt.requiredInputs
-      fakedInputs = JsObject(inputs map { i => i._1 -> fakeInput(i._2) })
-      wom <- clt.womExecutable(AcceptAllRequirements, Option(fakedInputs.prettyPrint), NoIoFunctionSet, strictValidation = false)
-    } yield wom) match {
-      case Right(womExecutable) => womExecutable.graph
-      case Left(e) => throw new Exception(s"Can't build WOM executable from CWL: ${e.toList.mkString("\n", "\n", "\n")}")
-    }
-  }
-
   def fakeInput(womType: WomType): JsValue = womType match {
     case WomStringType => JsString("hio")
     case WomIntegerType | WomFloatType | WomLongType => JsNumber(25)
diff --git a/womtool/src/main/scala/womtool/input/WomGraphMaker.scala b/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
index 50749640bcc..f0d238392fa 100644
--- a/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
+++ b/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
@@ -8,7 +8,6 @@ import common.validation.Validation._
 import cromwell.core.path.Path
 import cromwell.languages.LanguageFactory
 import cromwell.languages.util.ImportResolver._
-import languages.cwl.CwlV1_0LanguageFactory
 import languages.wdl.biscayne.WdlBiscayneLanguageFactory
 import languages.wdl.draft2.WdlDraft2LanguageFactory
 import languages.wdl.draft3.WdlDraft3LanguageFactory
@@ -32,8 +31,7 @@ object WomGraphMaker {
       val languageFactory =
         List(
           new WdlDraft3LanguageFactory(ConfigFactory.empty()),
-          new WdlBiscayneLanguageFactory(ConfigFactory.empty()),
-          new CwlV1_0LanguageFactory(ConfigFactory.empty()))
+          new WdlBiscayneLanguageFactory(ConfigFactory.empty()))
           .find(_.looksParsable(mainFileContents))
           .getOrElse(new WdlDraft2LanguageFactory(ConfigFactory.empty()))
 

From 85ab73afcf42c37e791531583f5e4cae39876492 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 23 Mar 2023 13:03:04 -0400
Subject: [PATCH 153/326] Remove Yaml (#7098)

---
 .circleci/config.yml | 174 -------------------------------------------
 .travis.yml          |  73 ------------------
 2 files changed, 247 deletions(-)
 delete mode 100644 .circleci/config.yml
 delete mode 100644 .travis.yml

diff --git a/.circleci/config.yml b/.circleci/config.yml
deleted file mode 100644
index 29a597bc13e..00000000000
--- a/.circleci/config.yml
+++ /dev/null
@@ -1,174 +0,0 @@
-version: 2.1
-
-orbs:
-  slack: circleci/slack@4.2.1
-  build-tools: circleci/build-tools@2.9.0
-
-jobs:
-  test:
-    parameters:
-      machine-size:
-        type: string
-        default: large
-      build-type:
-        type: string
-      build-mysql:
-        type: string
-        default: ""
-      build-mariadb:
-        type: string
-        default: ""
-      build-postgresql:
-        type: string
-        default: ""
-    machine:
-      image: ubuntu-2004:202010-01
-    resource_class: << parameters.machine-size >>
-    steps:
-      - run:
-          name: Halt builds except SBT test suite if there is no PR associated with the commit
-          command: |
-            if [[ -z "${CI_PULL_REQUEST}" ]] && [[ "${BUILD_TYPE}" != "sbt" ]] ; then
-              circleci-agent step halt
-            fi
-      - checkout
-      - run:
-          name: Custom step - configure GIT identity
-          command: |
-            git config user.email "circleci@example.com"
-            git config user.name "CircleCI"
-      - build-tools/merge-with-parent:
-          parent: develop
-      - restore_cache:
-          key: sbt-cache
-      - run:
-          command: src/ci/bin/test.sh
-          no_output_timeout: 1h
-      - run:
-          name: Do tricks to avoid unnecessary cache updates
-          command: |
-            find ~/.ivy2/cache -name "ivydata-*.properties" -print -delete
-            find ~/.sbt -name "*.lock" -print -delete
-      - store_test_results:
-          path: target/test-reports
-      - save_cache:
-          key: sbt-cache
-          paths:
-            - "~/.ivy2/cache"
-            - "~/.sbt"
-    environment:
-      CIRCLE_COMMIT_RANGE: << pipeline.git.base_revision >>...<< pipeline.git.revision >>
-      BUILD_TYPE: << parameters.build-type >>
-      BUILD_MYSQL: << parameters.build-mysql >>
-      BUILD_MARIADB: << parameters.build-mariadb >>
-      BUILD_POSTGRESQL: << parameters.build-postgresql >>
-
-workflows:
-  all-tests:
-    jobs:
-      - test:
-          name: testSbt
-          build-type: "sbt"
-      - test:
-          name: testSingleWorkflowRunner
-          build-type: "singleWorkflowRunner"
-      - test:
-          name: testDbms
-          build-type: "dbms"
-      - test:
-          name: testHoricromtalDeadlock
-          build-type: "horicromtalDeadlock"
-      - test:
-          name: testDockerScripts
-          build-type: "dockerScripts"
-      - test:
-          name: testReferenceDiskManifestBuilderApp
-          build-type: "referenceDiskManifestBuilderApp"
-      - test:
-          name: testCentaurAws
-          build-type: "centaurAws"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurDummy
-          build-type: "centaurDummy"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurEngineUpgradeLocal
-          build-type: "centaurEngineUpgradeLocal"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurEngineUpgradePapiV2alpha1
-          build-type: "centaurEngineUpgradePapiV2alpha1"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurHoricromtalPapiV2alpha1
-          build-type: "centaurHoricromtalPapiV2alpha1"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurHoricromtalPapiV2beta-MySQL
-          build-type: "centaurHoricromtalPapiV2beta"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurHoricromtalPapiV2beta-MariaDB
-          build-type: "centaurHoricromtalPapiV2beta"
-          build-mariadb: "10.3"
-      - test:
-          name: testCentaurHoricromtalEngineUpgradePapiV2alpha1-MySQL
-          build-type: "centaurHoricromtalEngineUpgradePapiV2alpha1"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurHoricromtalEngineUpgradePapiV2alpha1-MariaDB
-          build-type: "centaurHoricromtalEngineUpgradePapiV2alpha1"
-          build-mariadb: "10.3"
-      - test:
-          name: testCentaurPapiUpgradePapiV2alpha1
-          build-type: "centaurPapiUpgradePapiV2alpha1"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurPapiUpgradeNewWorkflowsPapiV2alpha1
-          build-type: "centaurPapiUpgradeNewWorkflowsPapiV2alpha1"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurLocal-MySQL
-          build-type: "centaurLocal"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurLocal-Postgresql
-          build-type: "centaurLocal"
-          build-postgresql: "11.3"
-      - test:
-          name: testCentaurPapiV2alpha1
-          build-type: "centaurPapiV2alpha1"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurPapiV2beta
-          build-type: "centaurPapiV2beta"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurSlurm
-          build-type: "centaurSlurm"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurTes
-          build-type: "centaurTes"
-          build-mysql: "5.7"
-      - test:
-          name: testCentaurWdlUpgradeLocal
-          build-type: "centaurWdlUpgradeLocal"
-          build-mysql: "5.7"
-      - test:
-          name: testCheckPublish
-          build-type: "checkPublish"
-          build-mysql: "5.7"
-      - test:
-          name: testConformanceLocal
-          build-type: "conformanceLocal"
-          build-mysql: "5.7"
-      - test:
-          name: testConformancePapiV2beta
-          build-type: "conformancePapiV2beta"
-          build-mysql: "5.7"
-      - test:
-          name: testConformanceTesk
-          build-type: "conformanceTesk"
-          build-mysql: "5.7"
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 295d133cbaa..00000000000
--- a/.travis.yml
+++ /dev/null
@@ -1,73 +0,0 @@
-os: linux
-dist: focal
-services:
-  - docker
-language: minimal
-git:
-  depth: false
-cache:
-  directories:
-    - $HOME/.ivy2/cache
-    - $HOME/.coursier/cache
-    # see cromwell::private::delete_sbt_boot for more info
-    #- $HOME/.sbt/boot/
-before_cache:
-  # Tricks to avoid unnecessary cache updates
-  - find $HOME/.ivy2/cache -name "ivydata-*.properties" -print -delete
-  - find $HOME/.coursier/cache -name "ivydata-*.properties" -print -delete
-  - find $HOME/.sbt -name "*.lock" -print -delete
-env:
-  jobs:
-    # Setting this variable twice will cause the 'script' section to run twice with the respective env var invoked
-    - >-
-      BUILD_TYPE=centaurAws
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurDummy
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurEngineUpgradeLocal
-      BUILD_MYSQL=5.7
-    # Temporarily keeping until `centaurEngineUpgradePapiV2beta` or similar exists
-    - >-
-      BUILD_TYPE=centaurEngineUpgradePapiV2alpha1
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurHoricromtalPapiV2beta
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurLocal
-      BUILD_MARIADB=10.3
-    - >-
-      BUILD_TYPE=centaurLocal
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurLocal
-      BUILD_POSTGRESQL=11.3
-    - >-
-      BUILD_TYPE=centaurPapiV2beta
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurTes
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=checkPublish
-    - >-
-      BUILD_TYPE=horicromtalDeadlock
-    - >-
-      BUILD_TYPE=dbms
-    - >-
-      BUILD_TYPE=singleWorkflowRunner
-    - >-
-      BUILD_TYPE=referenceDiskManifestBuilderApp
-script:
-  - src/ci/bin/test.sh
-notifications:
-  slack:
-    rooms:
-      - secure: B5KYcnhk/ujAUWlHsjzP7ROLm6MtYhaGikdYf6JYINovhMbVKnZCTlZEy7rqT3L2T5uJ25iefD500VQGk1Gn7puQ1sNq50wqjzQaj20PWEiBwoWalcV/nKBcQx1TyFT13LJv8fbFnVPxFCkC3YXoHedx8qAhDs8GH/tT5J8XOC8=
-    template:
-      - "Build <%{build_url}|#%{build_number}> (<%{compare_url}|%{commit}>) of %{repository}@%{branch} by %{author} %{result} in %{duration}"
-    on_success: change
-    on_failure: change
-    on_pull_requests: false

From 8b7f702b47f133c109bee2adbcea961cc16fd357 Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Fri, 24 Mar 2023 09:44:58 -0400
Subject: [PATCH 154/326] Azure blob read/write integration test (#7024)

Co-authored-by: Tom Wiseman <twiseman@broadinstitute.org>
---
 .github/workflows/integration_tests.yml       |  6 ++
 .../azure_blob_storage_read.test              | 16 +++++
 .../azure_blob_storage_read.inputs            |  3 +
 .../azure_blob_storage_read.options           |  3 +
 .../azure_blob_storage_read.wdl               | 12 ++++
 .../blob/BlobFileSystemManager.scala          |  1 -
 src/ci/bin/test.inc.sh                        |  7 ++
 src/ci/bin/testCentaurBlob.sh                 | 18 +++++
 src/ci/resources/centaur_blob_test.conf       | 66 +++++++++++++++++++
 9 files changed, 131 insertions(+), 1 deletion(-)
 create mode 100644 centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read.test
 create mode 100644 centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.inputs
 create mode 100644 centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.options
 create mode 100644 centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.wdl
 mode change 100644 => 100755 src/ci/bin/test.inc.sh
 create mode 100755 src/ci/bin/testCentaurBlob.sh
 create mode 100644 src/ci/resources/centaur_blob_test.conf

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index aacd46ffe78..94d3a6611a3 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -83,6 +83,9 @@ jobs:
           - build_type: centaurSlurm
             build_mysql: 5.7
             friendly_name: "Centaur Slurm with MySQL 5.7"
+          - build_type: centaurBlob
+            build_mysql: 5.7
+            friendly_name: Centaur Blob
     name: ${{ matrix.friendly_name }}
     env:
       BUILD_NAME: ${{ matrix.build_type }}
@@ -92,6 +95,9 @@ jobs:
       BUILD_MARIADB: ${{ matrix.build_mariadb }}
       VAULT_ROLE_ID: ${{ secrets.VAULT_ROLE_ID_CI }}
       VAULT_SECRET_ID: ${{ secrets.VAULT_SECRET_ID_CI }}
+      AZURE_CLIENT_ID: ${{ secrets.VAULT_AZURE_CENTAUR_CLIENT_ID }}
+      AZURE_CLIENT_SECRET: ${{ secrets.VAULT_AZURE_CENTAUR_CLIENT_SECRET }}
+      AZURE_TENANT_ID: ${{ secrets.VAULT_AZURE_CENTAUR_TENANT_ID }}
     runs-on: ubuntu-latest
     timeout-minutes: 120
     steps:
diff --git a/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read.test b/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read.test
new file mode 100644
index 00000000000..123a2745e6d
--- /dev/null
+++ b/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read.test
@@ -0,0 +1,16 @@
+name: azure_blob_storage_read
+testFormat: workflowsuccess
+backends: [Local]
+tags: ["blob", "azure"]
+retryTestFailures: false
+
+files {
+  workflow: azure_blob_storage_read/azure_blob_storage_read.wdl
+  inputs: azure_blob_storage_read/azure_blob_storage_read.inputs
+  options: azure_blob_storage_read/azure_blob_storage_read.options
+}
+
+metadata {
+  status: Succeeded
+  "outputs.azure_blob_storage_read.s1": "This is my test file! Did it work??"
+}
diff --git a/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.inputs b/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.inputs
new file mode 100644
index 00000000000..c81e166493f
--- /dev/null
+++ b/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.inputs
@@ -0,0 +1,3 @@
+{
+  "azure_blob_storage_read.file1": "https://centaurtesting.blob.core.windows.net/test-blob/testRead.txt"
+}
diff --git a/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.options b/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.options
new file mode 100644
index 00000000000..8d68fcdd6bf
--- /dev/null
+++ b/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.options
@@ -0,0 +1,3 @@
+{
+  "final_workflow_log_dir": "https://centaurtesting.blob.core.windows.net/test-blob/test-cromwell-workflow-logs"
+}
diff --git a/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.wdl b/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.wdl
new file mode 100644
index 00000000000..d19d417cdd5
--- /dev/null
+++ b/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read/azure_blob_storage_read.wdl
@@ -0,0 +1,12 @@
+version 1.0
+
+workflow azure_blob_storage_read {
+
+  input {
+    File file1
+  }
+
+  output {
+    String s1 = read_string(file1)
+  }
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index 7b198f09f6f..1672bd5bd88 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -230,7 +230,6 @@ case class NativeBlobSasTokenGenerator(container: BlobContainerName, endpoint: E
   private def authenticateWithSubscription(sub: SubscriptionId) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub.toString)
   private def authenticateWithDefaultSubscription = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withDefaultSubscription()
   private def azure = subscription.map(authenticateWithSubscription(_)).getOrElse(authenticateWithDefaultSubscription)
-
   private def findAzureStorageAccount(name: StorageAccountName) = azure.storageAccounts.list.asScala.find(_.name.equals(name.value))
       .map(Success(_)).getOrElse(Failure(new Exception("Azure Storage Account not found")))
   private def buildBlobContainerClient(credential: StorageSharedKeyCredential, endpoint: EndpointURL, container: BlobContainerName): BlobContainerClient = {
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
old mode 100644
new mode 100755
index 017fbd95b54..eef3a9fab6b
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -390,6 +390,9 @@ cromwell::private::create_build_variables() {
         centaurHoricromtalEngineUpgrade*)
             CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2alpha1_horicromtal_application.conf"
             ;;
+        centaurBlob*)
+            CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/centaur_blob_test.conf"
+            ;;
         *)
             CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/${CROMWELL_BUILD_BACKEND_TYPE}_application.conf"
             ;;
@@ -595,6 +598,7 @@ cromwell::private::create_centaur_variables() {
     CROMWELL_BUILD_CENTAUR_TYPE_PAPI_UPGRADE_NEW_WORKFLOWS="papiUpgradeNewWorkflows"
     CROMWELL_BUILD_CENTAUR_TYPE_HORICROMTAL_ENGINE_UPGRADE="horicromtalEngineUpgrade"
     CROMWELL_BUILD_CENTAUR_TYPE_HORICROMTAL="horicromtal"
+    CROMWELL_BUILD_CENTAUR_TYPE_AZURE_BLOB="azureBlob"
 
     case "${CROMWELL_BUILD_TYPE}" in
         centaurEngineUpgrade*)
@@ -612,6 +616,9 @@ cromwell::private::create_centaur_variables() {
         centaurHoricromtal*)
             CROMWELL_BUILD_CENTAUR_TYPE="${CROMWELL_BUILD_CENTAUR_TYPE_HORICROMTAL}"
             ;;
+        centaurBlob*)
+            CROMWELL_BUILD_CENTAUR_TYPE="${CROMWELL_BUILD_CENTAUR_TYPE_AZURE_BLOB}"
+            ;;
         *)
             # Only set the type if Jenkins, etc. has not already set the centaur type
             if [[ -z "${CROMWELL_BUILD_CENTAUR_TYPE-}" ]]; then
diff --git a/src/ci/bin/testCentaurBlob.sh b/src/ci/bin/testCentaurBlob.sh
new file mode 100755
index 00000000000..a0075441b44
--- /dev/null
+++ b/src/ci/bin/testCentaurBlob.sh
@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+set -o errexit -o nounset -o pipefail
+# import in shellcheck / CI / IntelliJ compatible ways
+# shellcheck source=/dev/null
+source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
+
+#NB: This function ensures that the correct .conf file is being used by cromwell (among other things).
+#Blob storage requires a configuration file tailored for Azure.
+cromwell::build::setup_common_environment
+
+cromwell::build::setup_centaur_environment
+
+cromwell::build::assemble_jars
+
+cromwell::build::run_centaur
+
+cromwell::build::generate_code_coverage
diff --git a/src/ci/resources/centaur_blob_test.conf b/src/ci/resources/centaur_blob_test.conf
new file mode 100644
index 00000000000..b97940b856d
--- /dev/null
+++ b/src/ci/resources/centaur_blob_test.conf
@@ -0,0 +1,66 @@
+include required(classpath("application.conf"))
+include "build_application.inc.conf"
+
+filesystems {
+  blob {
+    class = "cromwell.filesystems.blob.BlobPathBuilderFactory"
+    global {
+      # One BFSM is shared across all BlobPathBuilders
+      class = "cromwell.filesystems.blob.BlobFileSystemManager"
+      config {
+        container: "test-blob"
+        endpoint: "https://centaurtesting.blob.core.windows.net"
+        subscription: "62b22893-6bc1-46d9-8a90-806bb3cce3c9"
+      }
+    }
+  }
+}
+
+engine {
+  filesystems {
+    local {
+      enabled: false
+    }
+    http {
+      enabled: false
+    }
+    blob {
+      enabled: true
+    }
+  }
+}
+
+
+backend {
+  # Note that the backend is not selected purposefully here, 
+  # the existing tests at the time of writing do not submit tasks to a backend.
+  default = "TES"
+  providers {
+    TES {
+      actor-factory = "cromwell.backend.impl.tes.TesBackendLifecycleActorFactory"
+      config {
+        # Use for running on blob storage
+        #root = "https://<storage-account>.blob.core.windows.net/cromwell/cromwell-executions"
+        root = "cromwell-executions"
+        dockerRoot = "/cromwell-executions"
+        endpoint = "http://127.0.0.1:9000/v1/tasks"
+        concurrent-job-limit = 1000
+        transform-blob-to-local-path = false
+        filesystems {
+          blob {
+            enabled: true
+          }
+          local {
+            enabled: true
+          }
+          http {
+            enabled: true
+          }
+        }
+      }
+
+      # Have the engine (maybe) authenticate to docker.io. See BT-141 for more info.
+      include "dockerhub_provider_config_v1.inc.conf"
+    }
+  }
+}

From 209f67d738fd0f6bb0c583e3e10896826fbd77b0 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 24 Mar 2023 13:20:23 -0400
Subject: [PATCH 155/326] Goodbye Travis (#7100)

---
 README.md                                     |  1 -
 docs/developers/Centaur.md                    | 74 +++++++++++++++++-
 docs/developers/Contribute.md                 |  7 --
 docs/developers/bitesize/ci/CICD.md           | 29 -------
 docs/developers/bitesize/ci/CaaS_DEV_CD.svg   |  1 -
 .../ci/Cromwell_Deployment_Strategies.svg     |  1 -
 docs/developers/bitesize/ci/travis_centaur.md | 75 -------------------
 mkdocs.yml                                    |  4 +-
 processes/external-contributions/README.MD    | 18 +----
 processes/release_processes/README.MD         | 10 +--
 10 files changed, 78 insertions(+), 142 deletions(-)
 delete mode 100644 docs/developers/bitesize/ci/CICD.md
 delete mode 100644 docs/developers/bitesize/ci/CaaS_DEV_CD.svg
 delete mode 100644 docs/developers/bitesize/ci/Cromwell_Deployment_Strategies.svg
 delete mode 100644 docs/developers/bitesize/ci/travis_centaur.md

diff --git a/README.md b/README.md
index fac1541cf8e..f6e3f8e742e 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,3 @@
-[![Build Status](https://travis-ci.com/broadinstitute/cromwell.svg?branch=develop)](https://travis-ci.com/broadinstitute/cromwell?branch=develop)
 [![codecov](https://codecov.io/gh/broadinstitute/cromwell/branch/develop/graph/badge.svg)](https://codecov.io/gh/broadinstitute/cromwell)
 
 ## Welcome to Cromwell
diff --git a/docs/developers/Centaur.md b/docs/developers/Centaur.md
index cf168a3026c..35d2e350e7d 100644
--- a/docs/developers/Centaur.md
+++ b/docs/developers/Centaur.md
@@ -14,9 +14,11 @@ You can now run the tests from another terminal.
 
 There are two ways to invoke the integration tests:
 
-* `sbt "centaur / IntegrationTest / test"` - compiles and run via sbt directly, simple but also has the problem of running 2x cores tests in parallel which can overwhelm your Cromwell server if running in a development environment
+* `sbt "centaur / IntegrationTest / test"` - compiles Centaur and runs all tests via sbt directly. Tests are expected to be in the `centaur/src/main/standardTestCases` directory. This can be changed by modifying `reference.conf`.
 
-* `src/ci/bin/testCentaurLocal.sh` - runs the same tests using the continuous integration pipeline configuration
+* `src/ci/bin/testCentaurLocal.sh` - runs the same tests using the continuous integration pipeline configuration.
+
+* Tests that require different Cromwell and Centaur configurations can be invoked by calling the various scripts in `src/ci/bin`.
 
 ### Tags
 
@@ -104,3 +106,71 @@ In case the absolute path the cromwell root is used (for example: `/home/my_user
 
 In case testing of the caching is required `<<CACHE_HIT_UUID>>` can be used. 
 The testFormat should be `runtwiceexpectingcallcaching`.
+
+
+## Centaur Test Types
+Both Cromwell and Centaur require configuration files in order to correctly build and test various parts of the system. Because of this, we divide
+our tests into groups depending on which configuration files they require. Below is the current matrix of configuration files and test source directories.
+
+## Upgrade / Horicromtal / etc.
+
+| CI Test Type                  | Cromwell Config                                                  | Centaur Config                                         |
+|-------------------------------|------------------------------------------------------------------|--------------------------------------------------------|
+| Engine Upgrade                | `(backend)_application.conf`                                     | `centaur_application.conf`*                            |
+| Horicromtal                   | `papi_[v2beta or v2alpha1]_horicromtal_application.conf`**       | `centaur_application_`<br>`horicromtal.conf`           |
+| Horicromtal<br>Engine Upgrade | `papi_v2beta_application.conf`**                                 | `centaur_application_`<br>`horicromtal_no_assert.conf` |
+| PAPI Upgrade                  | `papi_v1_v2alpha1_upgrade_application.conf`**                    | `centaur_application.conf`*                            |
+| Papi Upgrade<br>New Workflows | `(backend)_application.conf`                                     | `centaur_application.conf`*                            |
+| Azure Blob                    | `centaur_blob_test.conf`**                                       | `centaur_application.conf`*                            |
+| WDL Upgrade                   | `(backend)_application.conf`                                     | `centaur_application.conf`*                            |
+| (other)                       | `(backend)_application.conf`                                     | `centaur_application.conf`*                            |
+
+| CI Test Type                  | ScalaTest Spec              | Test Directory                      |
+|-------------------------------|-----------------------------|-------------------------------------|
+| Engine Upgrade                | `EngineUpgradeTestCaseSpec` | `engineUpgradeTestCases`            |
+| Horicromtal                   | `CentaurTestSuite`          | `standardTestCases`***              |
+| Horicromtal<br>Engine Upgrade | `EngineUpgradeTestCaseSpec` | `engineUpgradeTestCases`***         |
+| PAPI Upgrade                  | `PapiUpgradeTestCaseSpec`   | `papiUpgradeTestCases`              |
+| PAPI Upgrade<br>New Workflows | `CentaurTestSuite`          | `papiUpgradeNewWorkflowsTestCases`  |
+| Azure Blob                    | `CentaurTestSuite      `    | `azureBlobTestCases`                |
+| WDL Upgrade                   | `WdlUpgradeTestCaseSpec`    | `standardTestCases`****             |
+| (other)                       | `CentaurTestSuite`          | `standardTestCases`                 |
+
+<small>
+\* Centaur Config always uses `centaur_application.conf` except when overridden with `papi_v2alpha1_centaur_application.conf`
+or `papi_v2beta_centaur_application.conf`
+  ([48 preview link](https://github.com/broadinstitute/cromwell/blob/a7d0601/src/ci/bin/test.inc.sh#L455-L457))  
+\*\* Cromwell Config overrides
+  ([47 link](https://github.com/broadinstitute/cromwell/blob/47/src/ci/bin/test.inc.sh#L213-L221))  
+\*\*\* Test Directory overrides
+  ([47 link](https://github.com/broadinstitute/cromwell/blob/47/src/ci/bin/test.inc.sh#L440-L449))  
+\*\*\*\* Test Directory only tests tagged with `wdl_upgrade`
+  ([47 link](https://github.com/broadinstitute/cromwell/blob/47/centaur/src/main/resources/standardTestCases/write_lines.test#L3))  
+</small>
+
+- Engine Upgrade: Retrieves the [Cromwell Version](https://github.com/broadinstitute/cromwell/blob/47/project/Version.scala#L8) then retrieves the previous jar/docker-image from DockerHub. Centaur starts with the prior version, then restarts with the compiled source code.
+- Horicromtal: Runs a [docker-compose](https://github.com/broadinstitute/cromwell/blob/47/src/ci/docker-compose/docker-compose-horicromtal.yml) with:
+    1. db-mstr: started first
+    2. sum-back: runs summarizer
+    3. front-back: exposes HTTP
+- Horicromtal Engine Upgrade: Combination of Horicromtal and Engine Upgrade
+- PAPI Upgrade: Tests run with an older version of Papi and upon restart use a newer version of Papi
+- PAPI Upgrade New Workflows: Test definition [does not run any tests](https://travis-ci.org/broadinstitute/cromwell/jobs/475378412)
+- WDL Upgrade: Upgrades WDL from draft-2 to 1.0 before testing
+- (other): Runs `*.test` files listing the configured backend names
+
+## RDBMS
+
+| Backend | MySQL  | PostgreSQL  | MariaDB  |
+|---------|:------:|:-----------:|:--------:|
+| AWS     |   ✅   |             |          |
+| Local   |   ✅   |      ✅     |          |
+| PAPI V2 |   ✅   |             |    ⭕    |
+| SLURM   |   ✅   |             |          |
+| TES     |   ✅   |             |          |
+
+<small>
+⭕ Tests Horicromtal Engine Upgrade versus standard Centaur suite
+</small>
+
+All backends run against MySQL. The Local backend also test PostgreSQL, allowing contributors ensure WDLs work with PostgreSQL. MariaDB is tested on a specialized upgrade, where the MySQL connector client is used first, and the MariaDB client is used after restart.
diff --git a/docs/developers/Contribute.md b/docs/developers/Contribute.md
index 1f513bd264e..9f40fb982ee 100644
--- a/docs/developers/Contribute.md
+++ b/docs/developers/Contribute.md
@@ -8,13 +8,6 @@ First off, here are useful links:
 * Source on Github: [github.com/broadinstitute/cromwell](https://github.com/broadinstitute/cromwell/tree/develop/docs)
 * Builds on ReadTheDocs: [readthedocs.org/projects/cromwell](https://readthedocs.org/projects/cromwell/builds/)
 * How to build and view the documentation locally: [mkdocs.readthedocs.io](https://mkdocs.readthedocs.io/en/stable/#installation)
-* Public Google Docs - Table of Contents:  [drive.google.com/open?id=1myTVzWx5HG720nPBUAF9vE8XTacrzCW70RpgsjMnchM](https://drive.google.com/open?id=1myTVzWx5HG720nPBUAF9vE8XTacrzCW70RpgsjMnchM)
-
-### "needs docs"
-
-There are plenty of areas of the Cromwell documentation that need to be updated, improved, or added. Within the Cromwell repo on Github there are many issues labeled as ["needs docs"](https://github.com/broadinstitute/cromwell/issues?q=is%3Aopen+is%3Aissue+label%3A%22needs+docs%22), so feel free to start there. 
-
-If you would like to request additional documentation, you can create a [Github issue in the Cromwell repo](https://github.com/broadinstitute/cromwell/issues/new).
 
 ### Writing Tips
 
diff --git a/docs/developers/bitesize/ci/CICD.md b/docs/developers/bitesize/ci/CICD.md
deleted file mode 100644
index 1353deb8f91..00000000000
--- a/docs/developers/bitesize/ci/CICD.md
+++ /dev/null
@@ -1,29 +0,0 @@
-Cromwell uses [Continuous Integration](https://en.wikipedia.org/wiki/Continuous_integration) (CI) testing, along with [Continuous Delivery](https://en.wikipedia.org/wiki/Continuous_delivery) (CD) to the Cromwell-as-a-Service (CaaS) `DEV` environment. [Continuous Deployment](https://en.wikipedia.org/wiki/Continuous_deployment) is not implemented.
-
-## CI testing in Travis and Jenkins
-
-Any suite of tests running under 2.5 hours, using 2 cpus, and 6gb of memory executes on [Travis](https://travis-ci.com/broadinstitute/cromwell/). Travis tests every pull request by a trusted contributor. Larger test suites run on [Jenkins instances](https://github.com/broadinstitute/dsp-jenkins#readme). Examples include the DSP Workbench CI testing ([swatomation](https://fc-jenkins.dsp-techops.broadinstitute.org/job/swatomation-pipeline/)), a nightly test of `develop` on (a snapshot of) the [$5 Genome WDL](https://fc-jenkins.dsp-techops.broadinstitute.org/job/cromwell-cron-aws/), and the [Cromwell-Perf tests](https://fc-jenkins.dsp-techops.broadinstitute.org/job/cromwell-perf-cron/) that call-cache thousands of jobs.
-
-## CD to CaaS DEV
-
-<a href="../CaaS_DEV_CD.svg" title="Cromwell automatically deploys to CaaS DEV using a series of hooks on GitHub, Travis, Jenkins, and Slack" target="_blank">![CaaS DEV CD](CaaS_DEV_CD.svg)</a>
-
-One instance utilizing continuous delivery is the `develop` branch to CaaS `DEV`. While manual testing could occur on `DEV`, users primarily test on `PROD`.
-
-## Manual Deployments
-
-<a href="../Cromwell_Deployment_Strategies.svg" title="Each hosting platform deploys Cromwell differently" target="_blank">![Cromwell Deployment Strategies](Cromwell_Deployment_Strategies.svg)</a>
- 
-The Cromwell developers stage Terra and CaaS `PROD` deployments. All other deployments are performed by respective groups, who decide when and how to redeploy. Some upgrade Cromwell, while others deploy completely new instances, including a new database schema.
-
-## Code Coverage
-
-Only Travis Pull Requests generate [maximal code coverage reports](https://codecov.io/gh/broadinstitute/cromwell/pulls). All other CI either doesn't report coverage, or under-reports due to skipped tests.
-
-## Vulnerability Scanning
-
-In collaboration with the DSP Information Security team, scans include but are not limited to:
-
-- Committed Git secrets
-- Vulnerable Java dependencies
-- Penetration testing
diff --git a/docs/developers/bitesize/ci/CaaS_DEV_CD.svg b/docs/developers/bitesize/ci/CaaS_DEV_CD.svg
deleted file mode 100644
index 9b91e73f87a..00000000000
--- a/docs/developers/bitesize/ci/CaaS_DEV_CD.svg
+++ /dev/null
@@ -1 +0,0 @@
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" 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" 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" 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" 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" 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" 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" 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\ No newline at end of file
diff --git a/docs/developers/bitesize/ci/travis_centaur.md b/docs/developers/bitesize/ci/travis_centaur.md
deleted file mode 100644
index b56ec16c8af..00000000000
--- a/docs/developers/bitesize/ci/travis_centaur.md
+++ /dev/null
@@ -1,75 +0,0 @@
-## Travis builds by user access
-
-For infrastructures that require secured credentials, cloud backend tests only run for developers with write access to the broadinstitute/cromwell GitHub. Secure tests are skipped for all other users.
-
-Other backends run tests for any user.
-
-| Backend       | Read-only users | Write/Admin users |
-|---------------|:---------------:|:-----------------:|
-| AWS           |                 |        ✅         |
-| Local         |       ✅        |        ✅         |
-| PAPI V2alpha1 |                 |        ✅         |
-| PAPI V2beta   |                 |        ✅         |
-| SLURM         |       ✅        |        ✅         |
-| TES           |       ✅        |        ✅         |
-
-## Upgrade / Horicromtal / etc.
-
-| CI Test Type                  | Cromwell Config                                                  | Centaur Config                                         |
-|-------------------------------|------------------------------------------------------------------|--------------------------------------------------------|
-| Engine Upgrade                | `(backend)_application.conf`                                     | `centaur_application.conf`*                            |
-| Horicromtal                   | `papi_[v2beta or v2alpha1]_horicromtal_application.conf`**       | `centaur_application_`<br>`horicromtal.conf`           |
-| Horicromtal<br>Engine Upgrade | `papi_v2beta_application.conf`**                                 | `centaur_application_`<br>`horicromtal_no_assert.conf` |
-| Papi Upgrade                  | `papi_v1_v2alpha1_upgrade_application.conf`**                    | `centaur_application.conf`*                            |
-| Papi Upgrade<br>New Workflows | `(backend)_application.conf`                                     | `centaur_application.conf`*                            |
-| WDL Upgrade                   | `(backend)_application.conf`                                     | `centaur_application.conf`*                            |
-| (other)                       | `(backend)_application.conf`                                     | `centaur_application.conf`*                            |
-
-| CI Test Type                  | ScalaTest Spec              | Test Directory                      |
-|-------------------------------|-----------------------------|-------------------------------------|
-| Engine Upgrade                | `EngineUpgradeTestCaseSpec` | `engineUpgradeTestCases`            |
-| Horicromtal                   | `CentaurTestSuite`          | `standardTestCases`***              |
-| Horicromtal<br>Engine Upgrade | `EngineUpgradeTestCaseSpec` | `engineUpgradeTestCases`***         |
-| PAPI Upgrade                  | `PapiUpgradeTestCaseSpec`   | `papiUpgradeTestCases`              |
-| PAPI Upgrade<br>New Workflows | `CentaurTestSuite`          | `papiUpgradeNewWorkflowsTestCases`  |
-| WDL Upgrade                   | `WdlUpgradeTestCaseSpec`    | `standardTestCases`****             |
-| (other)                       | `CentaurTestSuite`          | `standardTestCases`                 |
-
-<small>
-\* Centaur Config always uses `centaur_application.conf` except when overridden with `papi_v2alpha1_centaur_application.conf`
-or `papi_v2beta_centaur_application.conf`
-  ([48 preview link](https://github.com/broadinstitute/cromwell/blob/a7d0601/src/ci/bin/test.inc.sh#L455-L457))  
-\*\* Cromwell Config overrides
-  ([47 link](https://github.com/broadinstitute/cromwell/blob/47/src/ci/bin/test.inc.sh#L213-L221))  
-\*\*\* Test Directory overrides
-  ([47 link](https://github.com/broadinstitute/cromwell/blob/47/src/ci/bin/test.inc.sh#L440-L449))  
-\*\*\*\* Test Directory only tests tagged with `wdl_upgrade`
-  ([47 link](https://github.com/broadinstitute/cromwell/blob/47/centaur/src/main/resources/standardTestCases/write_lines.test#L3))  
-</small>
-
-- Engine Upgrade: Retrieves the [Cromwell Version](https://github.com/broadinstitute/cromwell/blob/47/project/Version.scala#L8) then retrieves the previous jar/docker-image from DockerHub. Centaur starts with the prior version, then restarts with the compiled source code.
-- Horicromtal: Runs a [docker-compose](https://github.com/broadinstitute/cromwell/blob/47/src/ci/docker-compose/docker-compose-horicromtal.yml) with:
-    1. db-mstr: started first
-    2. sum-back: runs summarizer
-    3. front-back: exposes HTTP
-- Horicromtal Engine Upgrade: Combination of Horicromtal and Engine Upgrade
-- PAPI Upgrade: Tests run with an older version of Papi and upon restart use a newer version of Papi
-- PAPI Upgrade New Workflows: Test definition [does not run any tests](https://travis-ci.org/broadinstitute/cromwell/jobs/475378412)
-- WDL Upgrade: Upgrades WDL from draft-2 to 1.0 before testing
-- (other): Runs `*.test` files listing the configured backend names
-
-## RDBMS
-
-| Backend | MySQL  | PostgreSQL  | MariaDB  |
-|---------|:------:|:-----------:|:--------:|
-| AWS     |   ✅   |             |          |
-| Local   |   ✅   |      ✅     |          |
-| PAPI V2 |   ✅   |             |    ⭕    |
-| SLURM   |   ✅   |             |          |
-| TES     |   ✅   |             |          |
-
-<small>
-⭕ Tests Horicromtal Engine Upgrade versus standard Centaur suite
-</small>
-
-All backends run against MySQL. The Local backend also test PostgreSQL, allowing contributors ensure WDLs work with PostgreSQL. MariaDB is tested on a specialized upgrade, where the MySQL connector client is used first, and the MariaDB client is used after restart.
diff --git a/mkdocs.yml b/mkdocs.yml
index 7aea4302d34..4ea08cf6fa8 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -102,8 +102,6 @@ nav:
         - Horizontal Cromwell ("Horicromtal"): developers/bitesize/horicromtal.md
         - General Topics:
             - Simpletons: developers/bitesize/general/simpletons.md
-        - Continuous Integration (CI) / Continuous Delivery (CD): developers/bitesize/ci/CICD.md
-        - Travis Centaur: developers/bitesize/ci/travis_centaur.md
 
 theme: readthedocs
 
@@ -112,5 +110,5 @@ extra_css:
 extra_javascript:
     - js/extra.js
 
-copyright: Copyright &copy; 2019 <a href="https://broadinstitute.org">Broad Institute</a>
+copyright: Copyright &copy; 2023 <a href="https://broadinstitute.org">Broad Institute</a>
 # google_analytics: ['identifierID', 'URL.org']
diff --git a/processes/external-contributions/README.MD b/processes/external-contributions/README.MD
index 3369c2ca443..677ecd52235 100644
--- a/processes/external-contributions/README.MD
+++ b/processes/external-contributions/README.MD
@@ -38,28 +38,14 @@ Ask the questions:
   
 ### Run CI against the PR
 
-Note: inspired by the community answer [here](https://github.community/t5/How-to-use-Git-and-GitHub/Checkout-a-branch-from-a-fork/td-p/77).
-
-- Problem: our CI will only run against branches of the `broadinstitute/cromwell` repo submitted by team members.
-- To turn a community contribution into a PR that travis will run against:
-  - Run the `scripts/make_pr_clone_branch.sh` script, providing the github PR number of the external PR as the command line argument
-    - Eg: `scripts/make_pr_clone_branch.sh 5333` to make a PR clone branch for PR #5333.  
-  - Push the branch to github
-    - Note: The final `git push` command may not work as-is, depending on your ~/.gitconfig value of `push.default`. If it doesn't work then one of the following solutions may work:
-      - Setting `git`'s `push.default` config value to be '`current`'.
-      - Using `git push --set-upstream origin 5070_pr_clone` instead
-      - Using `git push origin HEAD` instead
-  - Create a new PR for the clone branch. Indicate that it only exists to test a community contribution. 
-    - Example title: `[PR 5333 Clone] PR for CI only`
-- If you need to re-sync the clone PR against changes on the remote branch, the same script will *update* your local reference allowing you to force-push changes to the same github branch!  
+- Opening a PR triggers CI to run automatically. However, if the PR was not opened by a trusted contributor, it will wait in a Github Actions queue until a trusted contributor explicitly allows CI tests run.
 
 ### Cycle through Review and CI
 
 - If the community contributor makes changes following your reviews or the CI results:
   - Glance at the changes to make sure they still seem reasonable.
   - Make any additional comments
-  - Re-fetch the remote reference: `git fetch -f origin refs/pull/860/head:938_pr_clone`
-  - Push the changes back up to github to re-trigger the CI on your clone PR.
+  - Rerun CI.
   
 ### Merge the PR
 
diff --git a/processes/release_processes/README.MD b/processes/release_processes/README.MD
index 5dffe3224a5..146c2479620 100644
--- a/processes/release_processes/README.MD
+++ b/processes/release_processes/README.MD
@@ -66,7 +66,7 @@ Ensure you have at least 8GB; 4GB is not sufficient.
 
 #### Let people know the publish is underway
 
-Post another message in `#dsp-batch-private` that the release is underway, asking everyone to hold off merges to `develop` until
+Post another message in `#dsp-workflows-private` that the release is underway, asking everyone to hold off merges to `develop` until
 the release is published.
 
 #### Run the `publish_workflow.wdl` Workflow
@@ -86,12 +86,8 @@ The workflow outputs its status to the console.
 
 * Check that the workflow succeeded.
 * Check that there's now a new Cromwell release listed [here](https://github.com/broadinstitute/cromwell/releases).
-* Look [in Travis](https://app.travis-ci.com/github/broadinstitute/cromwell/branches) for the release tag build that will publish Docker images for the new version.
-* Let `#dsp-batch-private` know that it's okay to resume merges to `develop`.
-* Announce release in `#dsp-batch`, set expectations about when the new version will be available in Terra.
-* It will take about an additional hour for the Docker image to build in Travis before its tag appears on the [Cromwell Docker Hub page](https://hub.docker.com/r/broadinstitute/cromwell/tags).
-    * The relevant build is the one named `XX_hotfix` in [this list](https://app.travis-ci.com/github/broadinstitute/cromwell/builds).
-    * See the `cromwell::build::publish_artifacts()` function for details
+* Let `#dsp-workflows-private` know that it's okay to resume merges to `develop`.
+* Announce release in `#dsp-workflows`, set expectations about when the new version will be available in Terra.
 * **One business day later,** confirm that [the Homebrew package](https://formulae.brew.sh/formula/cromwell) has the latest version. If it doesn't, start investigation by looking at [Homebrew PR's](https://github.com/Homebrew/homebrew-core/pulls?q=is%3Apr+cromwell).
 
 ### How to Deploy Cromwell in CaaS staging and CaaS prod

From 6cd248b75db27e853fb239fdda80e77a7eaa4fea Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 29 Mar 2023 08:36:08 -0400
Subject: [PATCH 156/326] Single workflow runner (#7106)

---
 src/ci/bin/testSingleWorkflowRunner.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/ci/bin/testSingleWorkflowRunner.sh b/src/ci/bin/testSingleWorkflowRunner.sh
index fcf0f626822..8fad0591238 100755
--- a/src/ci/bin/testSingleWorkflowRunner.sh
+++ b/src/ci/bin/testSingleWorkflowRunner.sh
@@ -68,8 +68,12 @@ cmp <(jq -cS . actual.json) <(jq -cS . expected.json)
 popd > /dev/null
 
 # Test 3: program should exit with error in case if validation of command line arguments failed
+# Redirect stderr for the expected cromwell crash so we don't agitate CI.
+exec 3>&2
+exec 2> /dev/null
 java -jar "${CROMWELL_BUILD_CROMWELL_JAR}" run nonexistent.wdl &
 pid=$!
+exec 2>&3
 sleep 10
 if kill -0 $pid > /dev/null 2>&1; then
   echo "ERROR: Process still exists"

From 2768ccaf8bf870992a93d2d4b692d32b51f73dfd Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 3 Apr 2023 14:47:14 -0400
Subject: [PATCH 157/326] WX-975 Revert special TES path munging (#7103)

---
 build.sbt                                     |  1 -
 .../TesAsyncBackendJobExecutionActor.scala    | 10 +-------
 .../cromwell/backend/impl/tes/TesTask.scala   | 22 +++--------------
 .../backend/impl/tes/TesTaskSpec.scala        | 24 -------------------
 4 files changed, 4 insertions(+), 53 deletions(-)

diff --git a/build.sbt b/build.sbt
index 76f6f27e2c9..e539e5f132b 100644
--- a/build.sbt
+++ b/build.sbt
@@ -238,7 +238,6 @@ lazy val tesBackend = (project in backendRoot / "tes")
   .dependsOn(sfsBackend)
   .dependsOn(ftpFileSystem)
   .dependsOn(drsFileSystem)
-  .dependsOn(azureBlobFileSystem)
   // TES backend provides a compatibility layer to run WDLs with PAPI runtime attributes [WX-769]
   .dependsOn(googlePipelinesCommon)
   .dependsOn(backend % "test->test")
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 1e5637fff0e..27969736b66 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -88,14 +88,6 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
 
   private val tesEndpoint = workflowDescriptor.workflowOptions.getOrElse("endpoint", tesConfiguration.endpointURL)
 
-  // Temporary support for configuring the format we use to send BlobPaths to TES.
-  // Added 10/2022 as a workaround for the CromwellOnAzure TES server expecting
-  // blob containers to be mounted via blobfuse rather than addressed natively.
-  private val transformBlobToLocalPaths: Boolean =
-    configurationDescriptor.backendConfig
-      .getAs[Boolean]("transform-blob-to-local-path")
-      .getOrElse(false)
-
   override lazy val jobTag: String = jobDescriptor.key.tag
 
   private val outputMode = validate {
@@ -164,7 +156,7 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
         mode)
     })
 
-    tesTask.map(TesTask.makeTask(_, transformBlobToLocalPaths))
+    tesTask.map(TesTask.makeTask)
   }
 
   def writeScriptFile(): Future[Unit] = {
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index 5d1a844bb83..f7674c377e7 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -281,16 +281,14 @@ object TesTask {
     )
   }
 
-  def makeTask(tesTask: TesTask, transformBlobToLocalPath: Boolean = false): Task = {
-    val inputs = if (transformBlobToLocalPath) transformInputs(tesTask.inputs) else tesTask.inputs
-    val outputs = if (transformBlobToLocalPath) transformOutputs(tesTask.outputs) else tesTask.outputs
+  def makeTask(tesTask: TesTask): Task = {
     Task(
       id = None,
       state = None,
       name = Option(tesTask.name),
       description = Option(tesTask.description),
-      inputs = Option(inputs),
-      outputs = Option(outputs),
+      inputs = Option(tesTask.inputs),
+      outputs = Option(tesTask.outputs),
       resources = Option(tesTask.resources),
       executors = tesTask.executors,
       volumes = None,
@@ -298,20 +296,6 @@ object TesTask {
       logs = None
     )
   }
-
-  def transformInputs(inputs: Seq[Input]): Seq[Input] = inputs.map(i =>
-    i.copy(url=i.url.map(transformBlobString))
-  )
-
-  def transformOutputs(outputs: Seq[Output]): Seq[Output] = outputs.map(i =>
-    i.copy(url=i.url.map(transformBlobString))
-  )
-
-  val blobSegment = ".blob.core.windows.net"
-  def transformBlobString(s: String): String = if (s.contains(blobSegment)) {
-    s.replaceFirst("https:/", "").replaceFirst(blobSegment, "")
-  } else s
-
 }
 
 // Field requirements in classes below based off GA4GH schema
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index 3e5a79b33c9..e2c743bb718 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -100,28 +100,4 @@ class TesTaskSpec
 
     task.tags shouldBe Option(Map("foo" -> "bar"))
   }
-
-  it should "apply the correct transformation to a blob path" in {
-    val orig = "https://coaexternalstorage.blob.core.windows.net/cromwell/mydir/myfile.txt"
-    TesTask.transformBlobString(orig) shouldBe "/coaexternalstorage/cromwell/mydir/myfile.txt"
-  }
-
-  it should "not transform a non-blob path" in {
-    val orig = "https://some-bogus-url.test/cromwell/mydir/myfile.txt"
-    TesTask.transformBlobString(orig) shouldBe orig
-  }
-
-  it should "transform inputs" in {
-    val baseInput = Input(
-      Option("name"),
-      Option("descr"),
-      Option("https://coaexternalstorage.blob.core.windows.net/cromwell/mydir/myfile.txt"),
-      "path",
-      Option("type"),
-      Option("content"),
-    )
-    val inputs = Option(Seq(baseInput))
-    val outcome = inputs.map(TesTask.transformInputs)
-    outcome.get.head.url.get shouldBe "/coaexternalstorage/cromwell/mydir/myfile.txt"
-  }
 }

From f01cc4be812f94a12f09dada3debaf44f75e1ad4 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 4 Apr 2023 12:29:33 -0400
Subject: [PATCH 158/326] Centaur blob filesystem (#7104)

---
 build.sbt                                     |  1 +
 .../azure_blob_storage_read.test              |  8 +++
 centaur/src/main/resources/reference.conf     |  6 ++
 .../scala/centaur/test/FilesChecker.scala     | 11 ++++
 .../scala/centaur/test/ObjectCounter.scala    | 20 ++++++
 .../src/main/scala/centaur/test/Test.scala    |  9 +++
 .../workflow/DirectoryContentCountCheck.scala |  7 +-
 .../cloudsupport/azure/AzureUtils.scala       | 65 +++++++++++++++++++
 .../blob/BlobFileSystemManager.scala          | 33 +---------
 project/Dependencies.scala                    |  3 +-
 10 files changed, 128 insertions(+), 35 deletions(-)
 create mode 100644 cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureUtils.scala

diff --git a/build.sbt b/build.sbt
index e539e5f132b..a12a94b3b82 100644
--- a/build.sbt
+++ b/build.sbt
@@ -90,6 +90,7 @@ lazy val azureBlobFileSystem = (project in file("filesystems/blob"))
   .dependsOn(core)
   .dependsOn(core % "test->test")
   .dependsOn(common % "test->test")
+  .dependsOn(cloudSupport)
 
 lazy val awsS3FileSystem = (project in file("filesystems/s3"))
   .withLibrarySettings("cromwell-aws-s3filesystem", s3FileSystemDependencies)
diff --git a/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read.test b/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read.test
index 123a2745e6d..b7270ccfb11 100644
--- a/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read.test
+++ b/centaur/src/main/resources/azureBlobTestCases/azure_blob_storage_read.test
@@ -14,3 +14,11 @@ metadata {
   status: Succeeded
   "outputs.azure_blob_storage_read.s1": "This is my test file! Did it work??"
 }
+
+# az:// is the root of the container specified in reference.conf.
+# Here, we verify that exactly one log was written.
+
+fileSystemCheck: "blob"
+outputExpectations: {
+   "az://test-cromwell-workflow-logs/workflow.<<UUID>>.log" : 1
+}
diff --git a/centaur/src/main/resources/reference.conf b/centaur/src/main/resources/reference.conf
index a0428e01235..d570b5beef3 100644
--- a/centaur/src/main/resources/reference.conf
+++ b/centaur/src/main/resources/reference.conf
@@ -86,5 +86,11 @@ centaur {
     include "centaur_aws_credentials.conf"
   }
 
+  azure {
+    container: "test-blob"
+    endpoint: "https://centaurtesting.blob.core.windows.net"
+    subscription: "62b22893-6bc1-46d9-8a90-806bb3cce3c9"
+  }
+
   log-request-failures = false
 }
diff --git a/centaur/src/main/scala/centaur/test/FilesChecker.scala b/centaur/src/main/scala/centaur/test/FilesChecker.scala
index 240552bb755..5f3f1d9e170 100644
--- a/centaur/src/main/scala/centaur/test/FilesChecker.scala
+++ b/centaur/src/main/scala/centaur/test/FilesChecker.scala
@@ -41,3 +41,14 @@ object AWSFilesChecker extends FilesChecker {
 
   override def countObjectsAtPath: String => Int = s3Client.countObjects(s3PrefixRegex)
 }
+
+object BlobFilesChecker extends FilesChecker {
+  import ObjectCounterInstances.blobObjectCounter
+  import ObjectCounterSyntax._
+
+  private lazy val containerClient = Operations.blobContainerClient
+
+  // The root of the endpoint + container specified in reference.conf will be substituted for az://
+  private val azurePrefixRange = "^az:\\/\\/.*"
+  override def countObjectsAtPath: String => Int = ObjectCounterSyntax(containerClient).countObjects(azurePrefixRange)
+}
diff --git a/centaur/src/main/scala/centaur/test/ObjectCounter.scala b/centaur/src/main/scala/centaur/test/ObjectCounter.scala
index 46affc7d552..124f78e1dc8 100644
--- a/centaur/src/main/scala/centaur/test/ObjectCounter.scala
+++ b/centaur/src/main/scala/centaur/test/ObjectCounter.scala
@@ -1,5 +1,6 @@
 package centaur.test
 
+import com.azure.storage.blob.BlobContainerClient
 import com.google.cloud.storage.Storage.BlobListOption
 import com.google.cloud.storage.{Blob, Storage}
 import software.amazon.awssdk.services.s3.S3Client
@@ -38,6 +39,25 @@ object ObjectCounterInstances {
       storage.list(g.bucket, BlobListOption.prefix(g.directory)).iterateAll.asScala
     listObjectsAtPath(_).size
   }
+
+  implicit val blobObjectCounter: ObjectCounter[BlobContainerClient] = (containerClient : BlobContainerClient) => {
+    val pathToInt: Path => Int = providedPath => {
+      //Our path parsing is somewhat GCP centric. Convert to a blob path starting from the container root.
+      def pathToBlobPath(parsedPath : Path) : String = {
+        (Option(parsedPath.bucket), Option(parsedPath.directory)) match {
+          case (None, _) => ""
+          case (Some(_), None) => parsedPath.bucket
+          case (Some(_), Some(_)) => parsedPath.bucket + "/" + parsedPath.directory
+        }
+      }
+
+      val fullPath = pathToBlobPath(providedPath)
+      val blobsInFolder =  containerClient.listBlobsByHierarchy(fullPath)
+      //if something "isPrefix", it's a directory. Otherwise, its a file. We just want to count files.
+      blobsInFolder.asScala.count(!_.isPrefix)
+    }
+    pathToInt(_)
+  }
 }
 
 object ObjectCounterSyntax {
diff --git a/centaur/src/main/scala/centaur/test/Test.scala b/centaur/src/main/scala/centaur/test/Test.scala
index 470de959381..d0a56a2cbf5 100644
--- a/centaur/src/main/scala/centaur/test/Test.scala
+++ b/centaur/src/main/scala/centaur/test/Test.scala
@@ -10,6 +10,7 @@ import centaur.test.metadata.WorkflowFlatMetadata
 import centaur.test.metadata.WorkflowFlatMetadata._
 import centaur.test.submit.SubmitHttpResponse
 import centaur.test.workflow.Workflow
+import com.azure.storage.blob.BlobContainerClient
 import com.google.api.services.genomics.v2alpha1.{Genomics, GenomicsScopes}
 import com.google.api.services.storage.StorageScopes
 import com.google.auth.Credentials
@@ -23,6 +24,7 @@ import configs.syntax._
 import cromwell.api.CromwellClient.UnsuccessfulRequestException
 import cromwell.api.model.{CallCacheDiff, Failed, HashDifference, SubmittedWorkflow, Succeeded, TerminalStatus, WaasDescription, WorkflowId, WorkflowMetadata, WorkflowStatus}
 import cromwell.cloudsupport.aws.AwsConfiguration
+import cromwell.cloudsupport.azure.{AzureUtils}
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
 import io.circe.parser._
@@ -150,6 +152,13 @@ object Operations extends StrictLogging {
       .build()
   }
 
+  lazy val azureConfig: Config = CentaurConfig.conf.getConfig("azure")
+  val azureSubscription = azureConfig.getString("subscription")
+  val blobContainer = azureConfig.getString("container")
+  val azureEndpoint = azureConfig.getString("endpoint")
+  //NB: Centaur will throw an exception if it isn't able to authenticate with Azure blob storage via the local environment.
+  lazy val blobContainerClient: BlobContainerClient = AzureUtils.buildContainerClientFromLocalEnvironment(blobContainer, azureEndpoint, Option(azureSubscription)).get
+
   def submitWorkflow(workflow: Workflow): Test[SubmittedWorkflow] = {
     new Test[SubmittedWorkflow] {
       override def run: IO[SubmittedWorkflow] = for {
diff --git a/centaur/src/main/scala/centaur/test/workflow/DirectoryContentCountCheck.scala b/centaur/src/main/scala/centaur/test/workflow/DirectoryContentCountCheck.scala
index c5813165aea..2bf90619dab 100644
--- a/centaur/src/main/scala/centaur/test/workflow/DirectoryContentCountCheck.scala
+++ b/centaur/src/main/scala/centaur/test/workflow/DirectoryContentCountCheck.scala
@@ -2,7 +2,7 @@ package centaur.test.workflow
 
 import cats.data.Validated._
 import cats.syntax.all._
-import centaur.test.{AWSFilesChecker, FilesChecker, LocalFilesChecker, PipelinesFilesChecker}
+import centaur.test.{AWSFilesChecker, FilesChecker, LocalFilesChecker, PipelinesFilesChecker, BlobFilesChecker}
 import com.typesafe.config.Config
 import common.validation.ErrorOr.ErrorOr
 import configs.Result
@@ -25,8 +25,9 @@ object DirectoryContentCountCheck {
         case Result.Success("gcs") => valid(PipelinesFilesChecker)
         case Result.Success("local") => valid(LocalFilesChecker)
         case Result.Success("aws") => valid(AWSFilesChecker)
-        case Result.Success(_) => invalidNel(s"Test '$name': Invalid 'fileSystemCheck' value (must be either 'local', 'gcs' or 'aws'")
-        case Result.Failure(_) => invalidNel(s"Test '$name': Must specify a 'fileSystemCheck' value (must be either 'local', 'gcs' or 'aws'")
+        case Result.Success("blob") => valid(BlobFilesChecker)
+        case Result.Success(_) => invalidNel(s"Test '$name': Invalid 'fileSystemCheck' value (must be either 'local', 'gcs', 'blob', or 'aws'")
+        case Result.Failure(_) => invalidNel(s"Test '$name': Must specify a 'fileSystemCheck' value (must be either 'local', 'gcs', 'blob', or 'aws'")
       }
 
       (directoryContentCountsValidation, fileSystemChecker) mapN { (d, f) => Option(DirectoryContentCountCheck(d, f)) }
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureUtils.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureUtils.scala
new file mode 100644
index 00000000000..09cf5f3869d
--- /dev/null
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureUtils.scala
@@ -0,0 +1,65 @@
+package cromwell.cloudsupport.azure
+
+import com.azure.core.management.AzureEnvironment
+import com.azure.core.management.profile.AzureProfile
+import com.azure.identity.DefaultAzureCredentialBuilder
+import com.azure.resourcemanager.AzureResourceManager
+import com.azure.resourcemanager.storage.models.StorageAccountKey
+import com.azure.storage.blob.{BlobContainerClient, BlobContainerClientBuilder}
+import com.azure.storage.common.StorageSharedKeyCredential
+import com.google.common.net.UrlEscapers
+
+import java.net.URI
+import scala.jdk.CollectionConverters.IterableHasAsScala
+import scala.util.{Failure, Success, Try}
+
+object AzureUtils {
+  /**
+    * Generates a BlobContainerClient that can interact with the specified container. Authenticates using the local azure client running on the same machine.
+    * @param blobContainer     Name of the blob container. Looks something like "my-blob-container".
+    * @param azureEndpoint     Azure endpoint of the container. Looks something like https://somedomain.blob.core.windows.net.
+    * @param subscription      Azure subscription. A globally unique identifier. If not provided, a default subscription will be used.
+    * @return A blob container client capable of interacting with the specified container.
+    */
+  def buildContainerClientFromLocalEnvironment(blobContainer: String, azureEndpoint: String, subscription : Option[String]): Try[BlobContainerClient] = {
+    def parseURI(string: String): Try[URI] = Try(URI.create(UrlEscapers.urlFragmentEscaper().escape(string)))
+    def parseStorageAccount(uri: URI): Try[String] = uri.getHost.split("\\.").find(_.nonEmpty)
+      .map(Success(_)).getOrElse(Failure(new Exception("Could not parse storage account")))
+
+    val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
+
+    def azureCredentialBuilder = new DefaultAzureCredentialBuilder()
+      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
+      .build
+
+    def authenticateWithSubscription(sub: String) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub)
+
+    def authenticateWithDefaultSubscription = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withDefaultSubscription()
+
+    def azure = subscription.map(authenticateWithSubscription(_)).getOrElse(authenticateWithDefaultSubscription)
+
+    def findAzureStorageAccount(storageAccountName: String) = azure.storageAccounts.list.asScala.find(_.name.equals(storageAccountName))
+      .map(Success(_)).getOrElse(Failure(new Exception("Azure Storage Account not found.")))
+
+    def buildBlobContainerClient(credential: StorageSharedKeyCredential, endpointURL: String, blobContainerName: String): BlobContainerClient = {
+      new BlobContainerClientBuilder()
+        .credential(credential)
+        .endpoint(endpointURL)
+        .containerName(blobContainerName)
+        .buildClient()
+    }
+
+    def generateBlobContainerClient: Try[BlobContainerClient] = for {
+      uri <- parseURI(azureEndpoint)
+      configuredAccount <- parseStorageAccount(uri)
+      azureAccount <- findAzureStorageAccount(configuredAccount)
+      keys = azureAccount.getKeys.asScala
+      key <- keys.headOption.fold[Try[StorageAccountKey]](Failure(new Exception("Storage account has no keys")))(Success(_))
+      first = key.value
+      sskc = new StorageSharedKeyCredential(configuredAccount, first)
+      bcc = buildBlobContainerClient(sskc, azureEndpoint, blobContainer)
+    } yield bcc
+
+    generateBlobContainerClient
+  }
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index 1672bd5bd88..e50446ea294 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -1,18 +1,12 @@
 package cromwell.filesystems.blob
 
 import com.azure.core.credential.AzureSasCredential
-import com.azure.core.management.AzureEnvironment
-import com.azure.core.management.profile.AzureProfile
-import com.azure.identity.DefaultAzureCredentialBuilder
-import com.azure.resourcemanager.AzureResourceManager
-import com.azure.resourcemanager.storage.models.StorageAccountKey
 import com.azure.storage.blob.nio.AzureFileSystem
 import com.azure.storage.blob.sas.{BlobContainerSasPermission, BlobServiceSasSignatureValues}
-import com.azure.storage.blob.{BlobContainerClient, BlobContainerClientBuilder}
-import com.azure.storage.common.StorageSharedKeyCredential
 import com.typesafe.config.Config
 import com.typesafe.scalalogging.LazyLogging
 import common.validation.Validation._
+import cromwell.cloudsupport.azure.AzureUtils
 
 import java.net.URI
 import java.nio.file.{FileSystem, FileSystemNotFoundException, FileSystems}
@@ -223,22 +217,6 @@ case class WSMBlobSasTokenGenerator(container: BlobContainerName,
 }
 
 case class NativeBlobSasTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId] = None) extends BlobSasTokenGenerator {
-  private val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
-  private def azureCredentialBuilder = new DefaultAzureCredentialBuilder()
-      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
-      .build
-  private def authenticateWithSubscription(sub: SubscriptionId) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub.toString)
-  private def authenticateWithDefaultSubscription = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withDefaultSubscription()
-  private def azure = subscription.map(authenticateWithSubscription(_)).getOrElse(authenticateWithDefaultSubscription)
-  private def findAzureStorageAccount(name: StorageAccountName) = azure.storageAccounts.list.asScala.find(_.name.equals(name.value))
-      .map(Success(_)).getOrElse(Failure(new Exception("Azure Storage Account not found")))
-  private def buildBlobContainerClient(credential: StorageSharedKeyCredential, endpoint: EndpointURL, container: BlobContainerName): BlobContainerClient = {
-    new BlobContainerClientBuilder()
-        .credential(credential)
-        .endpoint(endpoint.value)
-        .containerName(container.value)
-        .buildClient()
-  }
   private val bcsp = new BlobContainerSasPermission()
     .setReadPermission(true)
     .setCreatePermission(true)
@@ -252,14 +230,7 @@ case class NativeBlobSasTokenGenerator(container: BlobContainerName, endpoint: E
     * @return an AzureSasCredential for accessing a blob container
     */
   def generateBlobSasToken: Try[AzureSasCredential] = for {
-    uri <- BlobPathBuilder.parseURI(endpoint.value)
-    configuredAccount <- BlobPathBuilder.parseStorageAccount(uri)
-    azureAccount <- findAzureStorageAccount(configuredAccount)
-    keys = azureAccount.getKeys.asScala
-    key <- keys.headOption.fold[Try[StorageAccountKey]](Failure(new Exception("Storage account has no keys")))(Success(_))
-    first = key.value
-    sskc = new StorageSharedKeyCredential(configuredAccount.value, first)
-    bcc = buildBlobContainerClient(sskc, endpoint, container)
+    bcc <- AzureUtils.buildContainerClientFromLocalEnvironment(container.toString, endpoint.toString, subscription.map(_.toString))
     bsssv = new BlobServiceSasSignatureValues(OffsetDateTime.now.plusDays(1), bcsp)
     asc = new AzureSasCredential(bcc.generateSas(bsssv))
   } yield asc
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index ddc3b002f00..c98eba6d346 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -206,6 +206,7 @@ object Dependencies {
       exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
       exclude("jakarta.activation", "jakarta.activation-api"),
     "com.azure" % "azure-core-management" % "1.7.1",
+    "com.fasterxml.jackson.dataformat" % "jackson-dataformat-xml" % jacksonV,
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0"
   )
 
@@ -409,7 +410,7 @@ object Dependencies {
     "com.lihaoyi" %% "pprint" % pprintV,
   ) ++ catsDependencies ++ configDependencies ++ slf4jFacadeDependencies ++ refinedTypeDependenciesList
 
-  val cloudSupportDependencies: List[ModuleID] = googleApiClientDependencies ++ googleCloudDependencies ++ betterFilesDependencies ++ awsCloudDependencies
+  val cloudSupportDependencies: List[ModuleID] = googleApiClientDependencies ++ googleCloudDependencies ++ betterFilesDependencies ++ awsCloudDependencies ++ azureDependencies
 
   val databaseSqlDependencies: List[ModuleID] = List(
     "commons-io" % "commons-io" % commonsIoV,

From 528bb6f3d50a4cbed8eff07f573f41ff033494e9 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 6 Apr 2023 17:35:36 -0400
Subject: [PATCH 159/326] WX-1010 Update Github Actions set output syntax
 (#7111)

---
 .github/workflows/make_publish_prs.yml | 2 +-
 .github/workflows/trivy.yml            | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/make_publish_prs.yml b/.github/workflows/make_publish_prs.yml
index ced80154c80..4a25210dd6e 100644
--- a/.github/workflows/make_publish_prs.yml
+++ b/.github/workflows/make_publish_prs.yml
@@ -50,7 +50,7 @@ jobs:
           git config --global user.email "broadbot@broadinstitute.org"
           git commit -m "Updating Cromwell version to ${NEW_CROMWELL_V}"
           git push https://broadbot:$BROADBOT_GITHUB_TOKEN@github.com/broadinstitute/firecloud-develop.git ${NEW_BRANCH_NAME}
-          echo ::set-output name=NEW_BRANCH_NAME::${NEW_BRANCH_NAME}
+          echo "NEW_BRANCH_NAME=${NEW_BRANCH_NAME}" >> $GITHUB_OUTPUT
       - name: Create firecloud-develop PR
         uses: actions/github-script@v6
         with:
diff --git a/.github/workflows/trivy.yml b/.github/workflows/trivy.yml
index 0590d48ef53..b005da65041 100644
--- a/.github/workflows/trivy.yml
+++ b/.github/workflows/trivy.yml
@@ -46,7 +46,7 @@ jobs:
 
           # export image name from the log
           image=$(grep 'Tagging image' build.log | awk '{print $NF}')
-          echo "::set-output name=image::${image}"
+          echo "image=${image}" >> $GITHUB_OUTPUT
 
       # scan the image
       - uses: broadinstitute/dsp-appsec-trivy-action@v1

From 037f1d0c9c98ec295b0bb0960af8a95a2355c1c2 Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Fri, 14 Apr 2023 09:28:00 -0400
Subject: [PATCH 160/326] WX-1001 Upgrade JSON Small and Fast Parser (#7116)

---
 project/Dependencies.scala | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index c98eba6d346..405ecd2d3c4 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -11,8 +11,9 @@ object Dependencies {
   // https://github.com/Azure/azure-sdk-for-java/tree/main/sdk/boms/azure-sdk-bom
   // https://github.com/sbt/sbt/issues/4531
   private val azureStorageBlobNioV = "12.0.0-beta.19"
-  private val azureIdentitySdkV = "1.4.6"
+  private val azureIdentitySdkV = "1.9.0-beta.2"
   private val betterFilesV = "3.9.1"
+  private val jsonSmartV = "2.4.10"
   /*
   cats-effect, fs2, http4s, and sttp (also to v3) should all be upgraded at the same time to use cats-effect 3.x.
    */
@@ -204,10 +205,12 @@ object Dependencies {
       exclude("jakarta.activation", "jakarta.activation-api"),
     "com.azure" % "azure-identity" % azureIdentitySdkV
       exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
-      exclude("jakarta.activation", "jakarta.activation-api"),
+      exclude("jakarta.activation", "jakarta.activation-api")
+      exclude("net.minidev", "json-smart"),
     "com.azure" % "azure-core-management" % "1.7.1",
     "com.fasterxml.jackson.dataformat" % "jackson-dataformat-xml" % jacksonV,
-    "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0"
+    "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0",
+    "net.minidev" % "json-smart" % jsonSmartV
   )
 
   val wsmDependencies: List[ModuleID] = List(

From b568fac18d6268adb1450bc0384709691df0a27a Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Tue, 18 Apr 2023 13:36:06 -0400
Subject: [PATCH 161/326] WX-1015 Override glob behavior for TES to use
 absolute path (#7120)

---
 .../main/scala/cromwell/backend/io/GlobFunctions.scala    | 2 +-
 .../main/scala/cromwell/core/path/NioPathMethods.scala    | 8 +++++++-
 .../scala/cromwell/filesystems/blob/BlobPathBuilder.scala | 6 ++++--
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala b/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala
index 6f0ae823bd8..680c073bf45 100644
--- a/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala
+++ b/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala
@@ -38,7 +38,7 @@ trait GlobFunctions extends IoFunctionSet with AsyncIoFunctions {
     import GlobFunctions._
     val globPatternName = globName(pattern)
     val listFilePath = callContext.root.resolve(s"${globName(pattern)}.list")
-    asyncIo.readLinesAsync(listFilePath.toRealPath()) map { lines =>
+    asyncIo.readLinesAsync(listFilePath.getSymlinkSafePath()) map { lines =>
       lines.toList map { fileName =>
         (callContext.root /  globPatternName  / fileName).pathAsString
       }
diff --git a/core/src/main/scala/cromwell/core/path/NioPathMethods.scala b/core/src/main/scala/cromwell/core/path/NioPathMethods.scala
index f5791e50c5a..42c17ca3222 100644
--- a/core/src/main/scala/cromwell/core/path/NioPathMethods.scala
+++ b/core/src/main/scala/cromwell/core/path/NioPathMethods.scala
@@ -2,7 +2,6 @@ package cromwell.core.path
 
 import java.nio.file.WatchEvent.{Kind, Modifier}
 import java.nio.file.{LinkOption, WatchKey, WatchService}
-
 import scala.jdk.CollectionConverters._
 
 /**
@@ -68,4 +67,11 @@ trait NioPathMethods {
   final def startsWith(other: String): Boolean = nioPathPrivate.startsWith(other)
 
   final def toRealPath(options: LinkOption*): Path = newPath(nioPathPrivate.toRealPath(options: _*))
+
+  /**
+    * Get a valid path object that resolves symlinks if supported
+    * Default implementation assumes symlinks are supported, and that toRealPath may return a valid path.
+    * This implementation may be overridden for NIO implementations that do not support symbolic links (For example the Azure NIO library)
+    */
+  def getSymlinkSafePath(options: LinkOption*): Path  = toRealPath(options: _*)
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 1be6bb8e13b..1906cc2f911 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -1,14 +1,14 @@
 package cromwell.filesystems.blob
 
-import com.azure.storage.blob.nio.{AzureBlobFileAttributes}
+import com.azure.storage.blob.nio.AzureBlobFileAttributes
 import com.google.common.net.UrlEscapers
 import cromwell.core.path.{NioPath, Path, PathBuilder}
 import cromwell.filesystems.blob.BlobPathBuilder._
 
 import java.net.{MalformedURLException, URI}
+import java.nio.file.{Files, LinkOption}
 import scala.language.postfixOps
 import scala.util.{Failure, Success, Try}
-import java.nio.file.Files
 
 object BlobPathBuilder {
 
@@ -119,4 +119,6 @@ case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, con
       }
     )
   }
+
+  override def getSymlinkSafePath(options: LinkOption*): Path  = toAbsolutePath
 }

From 1a3a68e75cc1fab28fdd1f7ca455171f4ed4ac94 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 24 Apr 2023 10:52:03 -0400
Subject: [PATCH 162/326] WX-990 Make TES request backoff behavior configurable
 (#7122)

---
 cromwell.example.backends/TES.conf            | 16 +++++
 docs/backends/TES.md                          | 14 ++++
 .../TesAsyncBackendJobExecutionActor.scala    | 15 +----
 .../backend/impl/tes/TesConfiguration.scala   | 33 +++++++++-
 .../impl/tes/TesConfigurationSpec.scala       | 47 ++++++++++++++
 .../backend/impl/tes/TesTestConfig.scala      | 65 +++++++++++++++++++
 6 files changed, 176 insertions(+), 14 deletions(-)
 create mode 100644 supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesConfigurationSpec.scala

diff --git a/cromwell.example.backends/TES.conf b/cromwell.example.backends/TES.conf
index a0bfb7cb141..509cd0d5d90 100644
--- a/cromwell.example.backends/TES.conf
+++ b/cromwell.example.backends/TES.conf
@@ -28,6 +28,22 @@ backend {
           disk: "2 GB"
           preemptible: false
         }
+
+        # Backoff behavior for task status polling and execution retries are configurable, with defaults
+        # shown below. All four fields must be set for each backoff if overriding.
+        #
+        # poll-backoff {
+        #   min: "10 seconds"
+        #   max: "5 minutes"
+        #   multiplier: 1.1
+        #   randomization-factor: 0.5
+        # }
+        # execute-or-recover-backoff {
+        #   min: "3 seconds"
+        #   max: "30 seconds"
+        #   multiplier: 1.1
+        #   randomization-factor: 0.5
+        # }
       }
     }
   }
diff --git a/docs/backends/TES.md b/docs/backends/TES.md
index b90fa30bc3d..9ee28e2e140 100644
--- a/docs/backends/TES.md
+++ b/docs/backends/TES.md
@@ -40,6 +40,20 @@ backend {
 }
 ```
 
+Cromwell uses an exponential backoff strategy to control the rate of requests sent to the TES server. 
+Users can override the default settings for this behavior in config, see `cromwell.example.backends/TES.conf` 
+for full expected format.
+
+For example, to force a constant polling rate rather than exponential backoff:
+```hocon
+backend.providers.TES.config.poll-backoff {
+  min: "1 minute"
+  max: "1 minute"
+  multiplier: 1
+  randomization-factor: 0
+}
+```
+
 ### Supported File Systems
 
 Currently this backend only works with files on a Local or Shared File System.
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 27969736b66..f4259de90d8 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -25,8 +25,6 @@ import wom.values.WomFile
 import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.Future
-import scala.concurrent.duration._
-import scala.language.postfixOps
 import scala.util.{Failure, Success}
 
 sealed trait TesRunStatus {
@@ -71,17 +69,8 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
 
   def statusEquivalentTo(thiz: StandardAsyncRunState)(that: StandardAsyncRunState): Boolean = thiz == that
 
-  override lazy val pollBackOff = SimpleExponentialBackoff(
-    initialInterval = 1 seconds,
-    maxInterval = 5 minutes,
-    multiplier = 1.1
-  )
-
-  override lazy val executeOrRecoverBackOff = SimpleExponentialBackoff(
-    initialInterval = 3 seconds,
-    maxInterval = 30 seconds,
-    multiplier = 1.1
-  )
+  override lazy val pollBackOff: SimpleExponentialBackoff = tesConfiguration.pollBackoff
+  override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff = tesConfiguration.executeOrRecoverBackoff
 
   private lazy val realDockerImageUsed: String = jobDescriptor.maybeCallCachingEligible.dockerHash.getOrElse(runtimeAttributes.dockerImage)
   override lazy val dockerImageUsed: Option[String] = Option(realDockerImageUsed)
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
index 264ba6299bd..7c7809d127f 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
@@ -1,9 +1,13 @@
 package cromwell.backend.impl.tes
 
+import com.typesafe.config.Config
 import cromwell.backend.BackendConfigurationDescriptor
-
+import cromwell.core.retry.SimpleExponentialBackoff
 import net.ceedubs.ficus.Ficus._
 
+import scala.concurrent.duration._
+import scala.language.postfixOps
+
 class TesConfiguration(val configurationDescriptor: BackendConfigurationDescriptor) {
 
   val endpointURL = configurationDescriptor.backendConfig.getString("endpoint")
@@ -13,8 +17,35 @@ class TesConfiguration(val configurationDescriptor: BackendConfigurationDescript
       .backendConfig
       .as[Option[Boolean]](TesConfiguration.useBackendParametersKey)
       .getOrElse(false)
+
+  val pollBackoff =
+    configurationDescriptor
+      .backendConfig
+      .as[Option[Config]]("poll-backoff")
+      .map(SimpleExponentialBackoff(_))
+      .getOrElse(TesConfiguration.defaultPollBackoff)
+
+  val executeOrRecoverBackoff =
+    configurationDescriptor
+      .backendConfig
+      .as[Option[Config]]("execute-or-recover-backoff")
+      .map(SimpleExponentialBackoff(_))
+      .getOrElse(TesConfiguration.defaultExecOrRecoverBackoff)
+
 }
 
 object TesConfiguration {
   final val useBackendParametersKey = "use_tes_11_preview_backend_parameters"
+
+  final val defaultPollBackoff = SimpleExponentialBackoff(
+    initialInterval = 10 seconds,
+    maxInterval = 5 minutes,
+    multiplier = 1.1
+  )
+
+  final val defaultExecOrRecoverBackoff = SimpleExponentialBackoff(
+    initialInterval = 3 seconds,
+    maxInterval = 30 seconds,
+    multiplier = 1.1
+  )
 }
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesConfigurationSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesConfigurationSpec.scala
new file mode 100644
index 00000000000..a695e5d6e33
--- /dev/null
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesConfigurationSpec.scala
@@ -0,0 +1,47 @@
+package cromwell.backend.impl.tes
+
+import com.typesafe.config.{Config, ConfigException, ConfigFactory}
+import cromwell.backend.BackendConfigurationDescriptor
+import cromwell.core.retry.SimpleExponentialBackoff
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import scala.concurrent.duration._
+import scala.language.postfixOps
+
+class TesConfigurationSpec extends AnyFlatSpec with Matchers {
+
+  behavior of "TesConfiguration"
+
+  def makeTesConfig(backendConfig: Config) = new TesConfiguration(
+    BackendConfigurationDescriptor(
+      backendConfig,
+      ConfigFactory.empty()
+    )
+  )
+
+  def backoffsAreEquivalent(expectedBackoff: SimpleExponentialBackoff, actualBackoff: SimpleExponentialBackoff): Boolean = {
+    val b1 = expectedBackoff.googleBackoff
+    val b2 = actualBackoff.googleBackoff
+    b1.getInitialIntervalMillis == b2.getInitialIntervalMillis &&
+      b1.getMaxIntervalMillis == b2.getMaxIntervalMillis &&
+      b1.getMultiplier == b2.getMultiplier &&
+      b1.getRandomizationFactor == b2.getRandomizationFactor
+  }
+
+  it should "use default backoffs when no custom config provided" in {
+    val tesConfig = makeTesConfig(TesTestConfig.backendConfig)
+    backoffsAreEquivalent(TesConfiguration.defaultPollBackoff, tesConfig.pollBackoff) shouldBe true
+    backoffsAreEquivalent(TesConfiguration.defaultExecOrRecoverBackoff, tesConfig.executeOrRecoverBackoff) shouldBe true
+  }
+
+  it should "use configured backoffs if they exist" in {
+    val tesConfig = makeTesConfig(TesTestConfig.backendConfigWithBackoffs)
+    backoffsAreEquivalent(SimpleExponentialBackoff(5 seconds, 1 minute, 2.5, .7), tesConfig.pollBackoff) shouldBe true
+    backoffsAreEquivalent(SimpleExponentialBackoff(3 minutes, 1 hours, 5, .1), tesConfig.executeOrRecoverBackoff) shouldBe true
+  }
+
+  it should "fail if user defines an invalid backoff" in {
+    assertThrows[ConfigException.Missing](makeTesConfig(TesTestConfig.backendConfigWithInvalidBackoffs))
+  }
+}
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTestConfig.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTestConfig.scala
index 142b23f07c4..7cbfd7e5348 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTestConfig.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTestConfig.scala
@@ -46,5 +46,70 @@ object TesTestConfig {
       |""".stripMargin
 
   val backendConfigWithBackendParams = ConfigFactory.parseString(backendConfigStringWithBackendParams)
+
+  private val backendConfigStringWithBackoffs =
+    """
+      |root = "local-cromwell-executions"
+      |dockerRoot = "/cromwell-executions"
+      |endpoint = "http://127.0.0.1:9000/v1/jobs"
+      |
+      |default-runtime-attributes {
+      |  cpu: 1
+      |  failOnStderr: false
+      |  continueOnReturnCode: 0
+      |  memory: "2 GB"
+      |  disk: "2 GB"
+      |  preemptible: false
+      |  # The keys below have been commented out as they are optional runtime attributes.
+      |  # dockerWorkingDir
+      |  # docker
+      |}
+      |
+      |poll-backoff {
+      |  min: "5 seconds"
+      |  max: "1 minute"
+      |  multiplier: 2.5
+      |  randomization-factor: .7
+      |}
+      |
+      |execute-or-recover-backoff {
+      |  min: "3 minutes"
+      |  max: "1 hours"
+      |  multiplier: 5
+      |  randomization-factor: .1
+      |}
+      |
+      |""".stripMargin
+
+  val backendConfigWithBackoffs = ConfigFactory.parseString(backendConfigStringWithBackoffs)
+
+  private val backendConfigStringWithInvalidBackoffs =
+    """
+      |root = "local-cromwell-executions"
+      |dockerRoot = "/cromwell-executions"
+      |endpoint = "http://127.0.0.1:9000/v1/jobs"
+      |
+      |default-runtime-attributes {
+      |  cpu: 1
+      |  failOnStderr: false
+      |  continueOnReturnCode: 0
+      |  memory: "2 GB"
+      |  disk: "2 GB"
+      |  preemptible: false
+      |  # The keys below have been commented out as they are optional runtime attributes.
+      |  # dockerWorkingDir
+      |  # docker
+      |}
+      |
+      |poll-backoff {
+      |  min: "5 seconds"
+      |  max: "1 minute"
+      |  multiplier: 2.5
+      |  # missing randomization-factor
+      |}
+      |
+      |""".stripMargin
+
+  val backendConfigWithInvalidBackoffs = ConfigFactory.parseString(backendConfigStringWithInvalidBackoffs)
 }
 

From b1ec16ae70d0e8e67a67e1c956b1d52fc5cfb759 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 3 May 2023 09:47:38 -0400
Subject: [PATCH 163/326] WX-1103 Revert CI to old TES polling behavior (#7126)

---
 src/ci/resources/tes_application.conf | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/ci/resources/tes_application.conf b/src/ci/resources/tes_application.conf
index 7f4c42a7d58..5eb812a52d4 100644
--- a/src/ci/resources/tes_application.conf
+++ b/src/ci/resources/tes_application.conf
@@ -51,7 +51,15 @@ backend {
         dockerRoot = "/cromwell-executions"
         endpoint = "http://127.0.0.1:9000/v1/tasks"
         concurrent-job-limit = 1000
-        transform-blob-to-local-path = false
+
+        # Override default polling to make it faster for speedy tests
+        poll-backoff {
+          min: "1 seconds"
+          max: "5 minutes"
+          multiplier: 1.1
+          randomization-factor: 0.5
+        }
+        
         filesystems {
           blob {
             enabled: false

From a45a32331e0554642223e81680ce0b3189f75765 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Tue, 9 May 2023 10:51:14 +0200
Subject: [PATCH 164/326] Develop aws (#29)

* stuck on globbing

* efs works, no callcaching

* update readme

* extended EFS support

* fix for globbing in nested scatters

* updated config for globbing, to prevent issues with empty folders
---
 .gitignore                                    |   3 +
 .../StandardCacheHitCopyingActor.scala        |   5 +
 .../s3/batch/S3BatchCommandBuilder.scala      |   8 +-
 ...wsBatchAsyncBackendJobExecutionActor.scala | 159 ++++++++++++++----
 .../backend/impl/aws/AwsBatchAttributes.scala |  33 +++-
 .../AwsBatchBackendInitializationData.scala   |   1 +
 ...AwsBatchBackendLifecycleActorFactory.scala |   9 +-
 .../impl/aws/AwsBatchConfiguration.scala      |   2 +
 .../aws/AwsBatchExpressionFunctions.scala     |   8 +-
 .../aws/AwsBatchInitializationActor.scala     |   1 +
 .../backend/impl/aws/AwsBatchJob.scala        |  58 ++++++-
 .../aws/AwsBatchJobCachingActorHelper.scala   |   2 +-
 .../backend/impl/aws/AwsBatchJobPaths.scala   |  20 ++-
 .../impl/aws/AwsBatchWorkflowPaths.scala      |  14 +-
 .../scala/cromwell/backend/impl/aws/README.md | 112 +++++++++---
 .../AwsBatchBackendCacheHitCopyingActor.scala |  12 +-
 .../AwsBatchBackendFileHashingActor.scala     |  26 +++
 .../impl/aws/io/AwsBatchGlobFunctions.scala   |  96 +++++++++++
 18 files changed, 479 insertions(+), 90 deletions(-)
 create mode 100644 supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala

diff --git a/.gitignore b/.gitignore
index 571a12c5873..c7d6e562544 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
 # common scala config
 *~
+.metals/
 .DS_Store
 .artifactory
 .bsp
@@ -50,3 +51,5 @@ tesk_application.conf
 **/venv/
 exome_germline_single_sample_v1.3/
 **/*.pyc
+.scalafmt.conf
+.vscode/
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
index f1662db858b..e23ecd277af 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
@@ -228,6 +228,8 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
           data.commandsToWaitFor.flatten.headOption match {
             case Some(command: IoCopyCommand) =>
               logCacheHitCopyCommand(command)
+            case Some(command: IoTouchCommand) =>
+              logCacheHitTouchCommand(command)
             case huh =>
               log.warning(s"BT-322 {} unexpected commandsToWaitFor: {}", jobTag, huh)
           }
@@ -307,6 +309,9 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
       case _ =>
     }
 
+  private def logCacheHitTouchCommand(command: IoTouchCommand): Unit =
+    log.info(s"BT-322 {} cache hit for file : {}", jobTag, command.toString)
+                                
   def succeedAndStop(returnCode: Option[Int], copiedJobOutputs: CallOutputs, detritusMap: DetritusMap): State = {
     import cromwell.services.metadata.MetadataService.implicits.MetadataAutoPutter
     serviceRegistryActor.putMetadata(jobDescriptor.workflowDescriptor.id, Option(jobDescriptor.key), startMetadataKeyValues)
diff --git a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
index 645600d1613..306f39337dd 100644
--- a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
+++ b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
@@ -30,11 +30,12 @@
  */
 package cromwell.filesystems.s3.batch
 
-import cromwell.core.io.{IoCommandBuilder, IoContentAsStringCommand, IoIsDirectoryCommand, IoReadLinesCommand, IoWriteCommand, PartialIoCommandBuilder}
+import cromwell.core.io.{IoCommandBuilder, IoHashCommand, IoContentAsStringCommand, IoIsDirectoryCommand, IoReadLinesCommand, IoWriteCommand, PartialIoCommandBuilder}
 import cromwell.core.path.BetterFileMethods.OpenOptions
 import cromwell.core.path.Path
 import cromwell.filesystems.s3.S3Path
 import org.slf4j.{Logger, LoggerFactory}
+import cromwell.core.io.DefaultIoCommand.DefaultIoHashCommand
 
 import scala.util.Try
 
@@ -77,8 +78,9 @@ private case object PartialS3BatchCommandBuilder extends PartialIoCommandBuilder
     case (src: S3Path, dest: S3Path) => Try(S3BatchCopyCommand(src, dest))
   }
 
-  override def hashCommand: PartialFunction[Path, Try[S3BatchEtagCommand]] = {
-    case path: S3Path => Try(S3BatchEtagCommand(path))
+  override def hashCommand: PartialFunction[Path, Try[IoHashCommand]] = {
+    case s3_path: S3Path => Try(S3BatchEtagCommand(s3_path).asInstanceOf[IoHashCommand])
+    case local_path: Path => Try(DefaultIoHashCommand(local_path))
   }
 
   override def touchCommand: PartialFunction[Path, Try[S3BatchTouchCommand]] = {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 8d2464a8ee3..87ef19e80cb 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -33,6 +33,7 @@ package cromwell.backend.impl.aws
 
 import java.net.SocketTimeoutException
 import java.io.FileNotFoundException
+import java.nio.file.Paths
 
 import akka.actor.ActorRef
 import akka.pattern.AskSupport
@@ -46,11 +47,12 @@ import common.util.StringUtil._
 import common.validation.Validation._
 
 import cromwell.backend._
-import cromwell.backend.async._ //{ExecutionHandle, PendingExecutionHandle}
+import cromwell.backend.async._ 
 import cromwell.backend.impl.aws.IntervalLimitedAwsJobSubmitActor.SubmitAwsJobRequest
 import cromwell.backend.impl.aws.OccasionalStatusPollingActor.{NotifyOfStatus, WhatsMyStatus}
 import cromwell.backend.impl.aws.RunStatus.{Initializing, TerminalRunStatus}
 import cromwell.backend.impl.aws.io._
+
 import cromwell.backend.io.DirectoryFunctions
 import cromwell.backend.io.JobPaths
 import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
@@ -80,6 +82,7 @@ import scala.concurrent.duration._
 import scala.language.postfixOps
 import scala.util.control.NoStackTrace
 import scala.util.{Success, Try, Failure}
+
 /**
   * The `AwsBatchAsyncBackendJobExecutionActor` creates and manages a job. The job itself is encapsulated by the
   * functionality in `AwsBatchJob`
@@ -175,6 +178,10 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
    * commandScriptContents here
    */
 
+   /* part of the full commandScriptContents is overriden here, in the context of mixed S3/EFS support with globbing. 
+      we'll see how much we need...
+    */ 
+
   lazy val cmdScript = configuration.fileSystem match {
      case AWSBatchStorageSystems.s3 => commandScriptContents.toEither.toOption.get
      case _ => execScript
@@ -239,6 +246,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         }
         Seq(AwsBatchFileInput(s"$namePrefix-$index", remotePath.valueString, DefaultPathBuilder.get(localPathString), workingDisk))
     }
+    
   }
 
   /**
@@ -250,12 +258,17 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   override protected def relativeLocalizationPath(file: WomFile): WomFile = {
     file.mapFile(value =>
       getPath(value) match {
-        case Success(path) =>
+        // for s3 paths :
+        case Success(path: S3Path) =>
           configuration.fileSystem match  {
-            case AWSBatchStorageSystems.s3 => path.pathWithoutScheme
-            case _ =>  path.toString
+            case AWSBatchStorageSystems.s3 => 
+                path.pathWithoutScheme
+            case _ =>  
+                path.toString
           }
-        case _ => value
+        // non-s3 paths
+        case _ => 
+            value
       }
     )
   }
@@ -287,11 +300,11 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
           case womFile: WomFile => womFile
         }
     }
-
+    
     val callInputInputs = callInputFiles flatMap {
       case (name, files) => inputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor, true)
     }
-
+    // this is a list : AwsBatchInput(name_in_wf, origin_such_as_s3, target_in_docker_relative, target_in_docker_disk[name mount] )
     val scriptInput: AwsBatchInput = AwsBatchFileInput(
       "script",
       jobPaths.script.pathAsString,
@@ -313,11 +326,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     def getAbsolutePath(path: Path) = {
       configuration.fileSystem match {
         case AWSBatchStorageSystems.s3 => AwsBatchWorkingDisk.MountPoint.resolve(path)
-        // case _ => DefaultPathBuilder.get(configuration.root).resolve(path)
-        case _ => 
-            Log.info("non-s3 path detected")
-            Log.info(path.toString)
-            AwsBatchWorkingDisk.MountPoint.resolve(path)
+        case _ => AwsBatchWorkingDisk.MountPoint.resolve(path)
       }
     }
     
@@ -325,7 +334,6 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       case p if !p.isAbsolute => getAbsolutePath(p)
       case p => p
     }
-
     disks.find(d => absolutePath.startsWith(d.mountPoint)) match {
       case Some(disk) => (disk.mountPoint.relativize(absolutePath), disk)
       case None =>
@@ -350,10 +358,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       ).getOrElse(List.empty[WomFile].validNel)
        .getOrElse(List.empty)
     }
-
     val womFileOutputs = jobDescriptor.taskCall.callable.outputs.flatMap(evaluateFiles) map relativeLocalizationPath
-    Log.debug("WomFileOutputs:")
-    Log.debug(womFileOutputs.toString())
     val outputs: Seq[AwsBatchFileOutput] = womFileOutputs.distinct flatMap {
       _.flattenFiles flatMap {
         case unlistedDirectory: WomUnlistedDirectory => generateUnlistedDirectoryOutputs(unlistedDirectory)
@@ -363,17 +368,17 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     }
 
     val additionalGlobOutput = jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateAwsBatchGlobFileOutputs).toSet
-
+    
     outputs.toSet ++ additionalGlobOutput
   }
 
+
   // used by generateAwsBatchOutputs, could potentially move this def within that function
   private def generateUnlistedDirectoryOutputs(womFile: WomUnlistedDirectory): List[AwsBatchFileOutput] = {
     val directoryPath = womFile.value.ensureSlashed
     val directoryListFile = womFile.value.ensureUnslashed + ".list"
     val dirDestinationPath = callRootPath.resolve(directoryPath).pathAsString
     val listDestinationPath = callRootPath.resolve(directoryListFile).pathAsString
-
     val (_, directoryDisk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
 
     // We need both the collection directory and the collection list:
@@ -397,6 +402,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
   // used by generateAwsBatchOutputs, could potentially move this def within that function
   private def generateAwsBatchSingleFileOutputs(womFile: WomSingleFile): List[AwsBatchFileOutput] = {
+    // rewrite this to create more flexibility
+    // 
     val destination = configuration.fileSystem match {
       case  AWSBatchStorageSystems.s3 =>  callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
       case _ => DefaultPathBuilder.get(womFile.valueString) match {
@@ -406,26 +413,65 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
     }
     val (relpath, disk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
-    val output = AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), destination, relpath, disk)
+    
+    val output = if (configuration.efsMntPoint.isDefined && 
+                     configuration.efsMntPoint.getOrElse("").equals(disk.toString.split(" ")(1)) &&
+                     ! runtimeAttributes.efsDelocalize) {
+            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), makeSafeAwsBatchReferenceName(womFile.value), relpath, disk)
+        } else {
+            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), destination, relpath, disk)
+        }
     List(output)
   }
+  
+  // get a unique glob name locations & paths.
+  //  1. globName :md5 hash of local PATH and WF_ID
+  //  2. globbedDir : local path of the directory being globbed.
+  //  3. volume on which the globbed data is located (eg root, efs, ...)
+  //  4. target path for delocalization for globDir
+  //  5. target path for delocalization for globList
+  private def generateGlobPaths(womFile: WomGlobFile): (String, String, AwsBatchVolume,String, String) = {
+    // add workflow id to hash for better conflict prevention
+    val wfid = standardParams.jobDescriptor.toString.split(":")(0)
+    val globName = GlobFunctions.globName(s"${womFile.value}-${wfid}")
+    val globbedDir = Paths.get(womFile.value).getParent.toString
+    // generalize folder and list file
+    val globDirectory = DefaultPathBuilder.get(globbedDir + "/." + globName + "/")
+    val globListFile = DefaultPathBuilder.get(globbedDir + "/." + globName + ".list")
+
+    // locate the disk where the globbed data resides
+    val (_, globDirectoryDisk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
 
+    
+    val (globDirectoryDestinationPath, globListFileDestinationPath) = if (configuration.efsMntPoint.isDefined && 
+                     configuration.efsMntPoint.getOrElse("").equals(globDirectoryDisk.toString.split(" ")(1)) &&
+                     ! runtimeAttributes.efsDelocalize) {
+                        (globDirectory, globListFile)
+                     } else {
+                        (callRootPath.resolve(globDirectory).pathAsString, callRootPath.resolve(globListFile).pathAsString)
+                     }
+    // return results
+    return (
+        globName,
+        globbedDir,
+        globDirectoryDisk,
+        globDirectoryDestinationPath.toString,
+        globListFileDestinationPath.toString
+    )
+    
+  }
   // used by generateAwsBatchOutputs, could potentially move this def within that function
   private def generateAwsBatchGlobFileOutputs(womFile: WomGlobFile): List[AwsBatchFileOutput] = {
-    val globName = GlobFunctions.globName(womFile.value)
-    val globDirectory = globName + "/"
-    val globListFile = globName + ".list"
-    val globDirectoryDestinationPath = callRootPath.resolve(globDirectory).pathAsString
-    val globListFileDestinationPath = callRootPath.resolve(globListFile).pathAsString
-
-    val (_, globDirectoryDisk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
-
+    
+    val (globName, globbedDir, globDirectoryDisk, globDirectoryDestinationPath, globListFileDestinationPath) = generateGlobPaths(womFile)
+    val (relpathDir,_) = relativePathAndVolume(DefaultPathBuilder.get(globbedDir + "/." + globName + "/" + "*").toString,runtimeAttributes.disks)
+    val (relpathList,_) = relativePathAndVolume(DefaultPathBuilder.get(globbedDir + "/." + globName + ".list").toString,runtimeAttributes.disks)
     // We need both the glob directory and the glob list:
     List(
-      // The glob directory:
-      AwsBatchFileOutput(makeSafeAwsBatchReferenceName(globDirectory), globDirectoryDestinationPath, DefaultPathBuilder.get(globDirectory + "*"), globDirectoryDisk),
+      // The glob directory:.
+      AwsBatchFileOutput(DefaultPathBuilder.get(globbedDir.toString + "/." + globName + "/" + "*").toString,globDirectoryDestinationPath, relpathDir, globDirectoryDisk),
       // The glob list file:
-      AwsBatchFileOutput(makeSafeAwsBatchReferenceName(globListFile), globListFileDestinationPath, DefaultPathBuilder.get(globListFile), globDirectoryDisk)
+      AwsBatchFileOutput(DefaultPathBuilder.get(globbedDir.toString + "/." + globName + ".list").toString, globListFileDestinationPath, relpathList, globDirectoryDisk)
     )
   }
 
@@ -805,4 +851,57 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     }
   }
 
+
+
+  // overrides for globbing
+  /**
+    * Returns the shell scripting for linking a glob results file.
+    *
+    * @param globFile The glob.
+    * @return The shell scripting.
+    */
+  override def globScript(globFile: WomGlobFile): String = {
+    
+    val (globName, globbedDir, _, _, _) = generateGlobPaths(globFile) 
+    val controlFileName = "cromwell_glob_control_file"
+    val absoluteGlobValue = commandDirectory.resolve(globFile.value).pathAsString
+    val globDirectory = globbedDir + "/." + globName + "/"
+    val globList = globbedDir + "/." + globName + ".list"
+    val globLinkCommand: String = (if (configuration.globLinkCommand.isDefined) {
+       "( " + configuration.globLinkCommand.getOrElse("").toString + " )"
+
+    } else {
+        "( ln -L GLOB_PATTERN GLOB_DIRECTORY 2> /dev/null ) || ( ln GLOB_PATTERN GLOB_DIRECTORY )"
+    }).toString
+      .replaceAll("GLOB_PATTERN", absoluteGlobValue)
+      .replaceAll("GLOB_DIRECTORY", globDirectory)
+    // if on EFS : remove the globbing dir first, to remove leftover links from previous globs. 
+    val mkDirCmd : String = if (configuration.efsMntPoint.isDefined && globDirectory.startsWith(configuration.efsMntPoint.getOrElse(""))) {
+        jobLogger.warn("Globbing on EFS has risks.")
+        jobLogger.warn(s"The globbing target (${globbedDir}/.${globName}/) will be overwritten when existing!")
+        jobLogger.warn("Consider keeping globbed outputs in the cromwell-root folder")
+        s"rm -Rf $globDirectory $globList && mkdir"
+    } else {
+        "mkdir"
+    }
+ 
+    val controlFileContent =
+      """This file is used by Cromwell to allow for globs that would not match any file.
+        |By its presence it works around the limitation of some backends that do not allow empty globs.
+        |Regardless of the outcome of the glob, this file will not be part of the final list of globbed files.
+      """.stripMargin
+    
+    s"""|# make the directory which will keep the matching files
+        |$mkDirCmd $globDirectory
+        |
+        |# create the glob control file that will allow for the globbing to succeed even if there is 0 match
+        |echo "${controlFileContent.trim}" > $globDirectory/$controlFileName
+        |
+        |# hardlink or symlink all the files into the glob directory
+        |$globLinkCommand
+        |
+        |# list all the files (except the control file) that match the glob into a file called glob-[md5 of glob].list
+        |ls -1 $globDirectory | grep -v $controlFileName > $globList
+        |""".stripMargin
+  }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index cc019f51004..ecb6c87a457 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -61,7 +61,9 @@ case class AwsBatchAttributes(fileSystem: String,
                               fsxMntPoint: Option[List[String]],
                               efsMntPoint: Option[String],
                               efsMakeMD5: Option[Boolean],
-                              efsDelocalize: Option[Boolean]
+                              efsDelocalize: Option[Boolean],
+                              globLinkCommand: Option[String],
+                              checkSiblingMd5: Option[Boolean]
                               )
 
 object AwsBatchAttributes {
@@ -84,13 +86,11 @@ object AwsBatchAttributes {
     "numCreateDefinitionAttempts",
     "numSubmitAttempts",
     "default-runtime-attributes.scriptBucketName",
-    //"default-runtime-attributes.efsMountPoint",
-    //"default-runtime-attributes.efsMakeMD5",
-    //"default-runtime-attributes.efsDelocalize",
     "awsBatchRetryAttempts",
     "ulimits",
     "efsDelocalize",
-    "efsMakeMD5"
+    "efsMakeMD5",
+    "glob-link-command"
   )
 
   private val deprecatedAwsBatchKeys: Map[String, String] = Map(
@@ -108,7 +108,6 @@ object AwsBatchAttributes {
       val deprecatedKeys = keys.intersect(deprecated.keySet)
       deprecatedKeys foreach { key => logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}") }
     }
-
     def parseFSx(config: List[String]): Option[List[String]] = {
       config.isEmpty match {
         case true => None
@@ -116,7 +115,7 @@ object AwsBatchAttributes {
       }
     }
 
-    def parseEFS(config: String): Option[String] = {
+    def parseConfigString(config: String): Option[String] = {
       config.isEmpty match {
         case true => None
         case false => Some(config)
@@ -165,7 +164,7 @@ object AwsBatchAttributes {
 
     // EFS settings:
     val efsMntPoint:ErrorOr[Option[String]] = validate {backendConfig.hasPath("filesystems.local.efs") match {
-        case true => parseEFS(backendConfig.getString("filesystems.local.efs"))
+        case true => parseConfigString(backendConfig.getString("filesystems.local.efs"))
         case false => None
       }
     }
@@ -181,6 +180,20 @@ object AwsBatchAttributes {
             case false => None
       }
     }
+    // from config if set.
+    val globLinkCommand:ErrorOr[Option[String]] = validate {
+        backendConfig.hasPath("glob-link-command") match {
+            case true => Some(backendConfig.getString("glob-link-command"))
+            case false => None
+      }
+    }
+    // from config if set:
+    val checkSiblingMd5:ErrorOr[Option[Boolean]] = validate {
+        backendConfig.hasPath("filesystems.local.caching.check-sibling-md5") match {
+            case true => Some(backendConfig.getBoolean("filesystems.local.caching.check-sibling-md5"))
+            case false => None
+      }
+    }
 
     (
       fileSysStr,
@@ -192,7 +205,9 @@ object AwsBatchAttributes {
       fsxMntPoint,
       efsMntPoint,
       efsMakeMD5,
-      efsDelocalize
+      efsDelocalize,
+      globLinkCommand,
+      checkSiblingMd5
     ).tupled.map((AwsBatchAttributes.apply _).tupled) match {
       case Valid(r) => r
       case Invalid(f) =>
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala
index edfbd560362..bff8848e037 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala
@@ -33,6 +33,7 @@ package cromwell.backend.impl.aws
 
 import cromwell.backend.standard.{StandardInitializationData, StandardValidatedRuntimeAttributesBuilder}
 import software.amazon.awssdk.auth.credentials.AwsCredentialsProvider
+import cromwell.backend.impl.aws.io.AwsBatchWorkflowPaths
 
 case class AwsBatchBackendInitializationData
 (
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
index c0ae9210852..acb066d7332 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
@@ -36,7 +36,8 @@ import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationDa
 import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardFinalizationActor, StandardFinalizationActorParams, StandardInitializationActor, StandardInitializationActorParams, StandardLifecycleActorFactory}
 import cromwell.core.CallOutputs
 import wom.graph.CommandCallNode
-
+import cromwell.backend.impl.aws.callcaching.{AwsBatchBackendCacheHitCopyingActor, AwsBatchBackendFileHashingActor}
+import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardFileHashingActor}
 /**
   * Factory to create `Actor` objects to manage the lifecycle of a backend job on AWS Batch. This factory provides an
   * object from the `AwsBatchAsyncBackendJobExecutionActor` class to create and manage the job.
@@ -89,6 +90,12 @@ case class AwsBatchBackendLifecycleActorFactory(
     AwsBatchFinalizationActorParams(workflowDescriptor, ioActor, calls, configuration, jobExecutionMap, workflowOutputs, initializationDataOption)
   }
 
+  override lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] = {
+    Option(classOf[AwsBatchBackendCacheHitCopyingActor])
+  }
+
+  override lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(classOf[AwsBatchBackendFileHashingActor])
+
   override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] = {
     Option(AwsBatchSingletonActor.props(configuration.awsConfig.region, Option(configuration.awsAuth)))
   }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
index 5f6d9eaf17a..8a019110509 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
@@ -60,6 +60,8 @@ class AwsBatchConfiguration(val configurationDescriptor: BackendConfigurationDes
   val efsMntPoint = batchAttributes.efsMntPoint
   val efsMakeMD5 = batchAttributes.efsMakeMD5
   val efsDelocalize = batchAttributes.efsDelocalize
+  val globLinkCommand = batchAttributes.globLinkCommand
+  val checkSiblingMd5 = batchAttributes.checkSiblingMd5
 }
 
 object AWSBatchStorageSystems {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala
index b75d4d6b00f..248ee90e8e3 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala
@@ -37,9 +37,13 @@ import cromwell.filesystems.s3.S3PathBuilder
 import cromwell.filesystems.s3.S3PathBuilder.{InvalidS3Path, PossiblyValidRelativeS3Path, ValidFullS3Path}
 import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
 import cromwell.core.path.{DefaultPath, Path}
+import cromwell.backend.impl.aws.io._
 
-class AwsBatchExpressionFunctions(standardParams: StandardExpressionFunctionsParams)
-  extends StandardExpressionFunctions(standardParams) {
+
+
+class AwsBatchExpressionFunctions(override val standardParams: StandardExpressionFunctionsParams)
+  extends StandardExpressionFunctions(standardParams) with AwsBatchGlobFunctions {
+  
   override lazy val ioCommandBuilder: IoCommandBuilder = S3BatchCommandBuilder
 
   override def preMapping(str: String) = {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
index 16241dbb8ce..5078b5b87f8 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
@@ -47,6 +47,7 @@ import wom.graph.CommandCallNode
 import org.apache.commons.codec.binary.Base64
 import spray.json.{JsObject, JsString}
 import org.slf4j.{Logger, LoggerFactory}
+import cromwell.backend.impl.aws.io.AwsBatchWorkflowPaths
 
 import scala.concurrent.Future
 import scala.jdk.CollectionConverters._
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 283b97ebd97..48f286dc436 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -305,7 +305,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     val outputCopyCommand = outputs.map {
       case output: AwsBatchFileOutput if output.local.pathAsString.contains("*") => "" //filter out globs
       case output: AwsBatchFileOutput if output.name.endsWith(".list") && output.name.contains("glob-") =>
-
+        Log.debug("Globbing : check for EFS settings.")
         val s3GlobOutDirectory = output.s3key.replace(".list", "")
         val globDirectory = output.name.replace(".list", "")
         /*
@@ -313,16 +313,60 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          * if it doesn't exist then 'touch' it so that it can be copied otherwise later steps will get upset
          * about the missing file
          */
-        s"""
-           |touch ${output.name}
-           |_s3_delocalize_with_retry ${output.name} ${output.s3key}
-           |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi""".stripMargin
-           
+        if ( efsMntPoint.isDefined && output.mount.mountPoint.pathAsString == efsMntPoint.get ) {
+           Log.debug("EFS glob output file detected: "+ output.s3key + s" / ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}")
+           val test_cmd = if (efsDelocalize.isDefined && efsDelocalize.getOrElse(false)) {
+                    Log.debug("delocalization on EFS is enabled")
+                    s"""
+                        |touch ${output.name}
+                        |_s3_delocalize_with_retry ${output.name} ${output.s3key}
+                        |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi
+                        |""".stripMargin
+                } else {
+                    
+                    // check file for existence
+                    s"""
+                        |# test the glob list
+                        |test -e ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && exit 1)
+                        |# test individual files.
+                        |for F in $$(cat ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}); do
+                        |   test -e "${globDirectory}/$$F" || (echo 'globbed file: "${globDirectory}/$$F" does not exist' && exit 1)
+                        |done
+                        |"""
+                }
+           // need to make md5sum? 
+           val md5_cmd = if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
+                    Log.debug("Add cmd to create MD5 sibling.")
+                    // this does NOT regenerate the md5 in case the file is overwritten ! 
+                    s"""
+                        |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
+                        |   # the glob list
+                        |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && exit 1 ); 
+                        |   # globbed files, using specified number of cpus for parallel processing.
+                        |   cat ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} | xargs -I% -P${runtimeAttributes.cpu.##.toString} bash -c "md5sum ${globDirectory}/% > ${globDirectory}/%.md5"
+                        |fi
+                        |""".stripMargin 
+                } else {
+                    Log.debug("MD5 not enabled: "+efsMakeMD5.get.toString())
+                    ""
+                }
+           // return combined result
+           s"""
+          |${test_cmd}
+          |${md5_cmd}
+          | """.stripMargin
+        } else {
+          // default delocalization command.
+          s"""
+             |touch ${output.name}
+             |_s3_delocalize_with_retry ${output.name} ${output.s3key}
+             |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi""".stripMargin
+        }
 
       // files on /cromwell/ working dir must be delocalized
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
         //output is on working disk mount
-        Log.info("output Data on working disk mount" + output.local.pathAsString)
+        Log.debug("output Data on working disk mount" + output.local.pathAsString)
         s"""_s3_delocalize_with_retry $workDir/${output.local.pathAsString} ${output.s3key}""".stripMargin
 
       // file(name (full path), s3key (delocalized path), local (file basename), mount (disk details))
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
index a3c693855be..35ca4d0c17c 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
@@ -32,7 +32,7 @@
 package cromwell.backend.impl.aws
 
 import akka.actor.Actor
-import cromwell.backend.impl.aws.io.{AwsBatchVolume, AwsBatchWorkingDisk}
+import cromwell.backend.impl.aws.io.{AwsBatchVolume, AwsBatchWorkingDisk,AwsBatchJobPaths}
 import cromwell.backend.standard.StandardCachingActorHelper
 import cromwell.core.logging.JobLogging
 import cromwell.core.path.Path
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala
index e8d93570dbc..219b264cc93 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala
@@ -29,10 +29,13 @@
  *  POSSIBILITY OF SUCH DAMAGE.
  */
 
-package cromwell.backend.impl.aws
+package cromwell.backend.impl.aws.io
 
 import cromwell.backend.BackendJobDescriptorKey
 import cromwell.backend.io.JobPaths
+import cromwell.core.path.Path
+import cromwell.core.JobKey
+
 
 object AwsBatchJobPaths {
   val AwsBatchLogPathKey = "cromwellLog"
@@ -60,4 +63,19 @@ final case class AwsBatchJobPaths(override val workflowPaths: AwsBatchWorkflowPa
   override def defaultStderrFilename: String = s"$logBasename-stderr.log"
 
   override def forCallCacheCopyAttempts: JobPaths = this.copy(isCallCacheCopyAttempt = true)
+  override lazy val callRoot = callPathBuilder(workflowPaths.workflowRoot, jobKey, isCallCacheCopyAttempt)
+
+  def callPathBuilder(root: Path, jobKey: JobKey, isCallCacheCopyAttempt: Boolean) = {
+    val callName = jobKey.node.localName
+    val call = s"${JobPaths.CallPrefix}-${callName}"
+    val shard = jobKey.index map { s => s"${JobPaths.ShardPrefix}-$s" } getOrElse ""
+
+    val retryOrCallCache =
+      if (isCallCacheCopyAttempt) JobPaths.CacheCopyPrefix
+      else if (jobKey.attempt > 1) s"${JobPaths.AttemptPrefix}-${jobKey.attempt}"
+      else ""
+
+    List(call, shard, retryOrCallCache).foldLeft(root)((path, dir) => path.resolve(dir))
+    
+  }  
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala
index 45d3eafe75d..fb2f3675951 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala
@@ -29,7 +29,7 @@
  *  POSSIBILITY OF SUCH DAMAGE.
  */
 
-package cromwell.backend.impl.aws
+package cromwell.backend.impl.aws.io
 
 import akka.actor.ActorSystem
 import com.typesafe.config.Config
@@ -39,6 +39,7 @@ import cromwell.core.WorkflowOptions
 import cromwell.core.path.PathBuilder
 import cromwell.filesystems.s3.S3PathBuilderFactory
 import software.amazon.awssdk.auth.credentials.AwsCredentialsProvider
+import cromwell.backend.impl.aws.{AwsBatchConfiguration,AWSBatchStorageSystems}
 
 object AwsBatchWorkflowPaths {
   private val RootOptionKey = "aws_s3_root"
@@ -70,8 +71,15 @@ case class AwsBatchWorkflowPaths(workflowDescriptor: BackendWorkflowDescriptor,
   override def config: Config = configuration.configurationDescriptor.backendConfig
   override def pathBuilders: List[PathBuilder] = {
     if (configuration.fileSystem == "s3") {
-      List(configuration.pathBuilderFactory.asInstanceOf[S3PathBuilderFactory].fromProvider(workflowOptions, provider))
+      // if efs is activated : add the default (local) pathbuilders.
+      if (configuration.batchAttributes.efsMntPoint.isDefined) {
+        List(configuration.pathBuilderFactory.asInstanceOf[S3PathBuilderFactory].fromProvider(workflowOptions, provider) ) ++ WorkflowPaths.DefaultPathBuilders
+      }
+      else {
+        List(configuration.pathBuilderFactory.asInstanceOf[S3PathBuilderFactory].fromProvider(workflowOptions, provider) )
+      }
     } else {
-      WorkflowPaths.DefaultPathBuilders}
+      WorkflowPaths.DefaultPathBuilders
+    }
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 8576dcb6de9..a1cdce0ba1b 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -258,7 +258,7 @@ Cromwell EC2 instances can be equipped with a shared elastic filesystem, termed
 
 1.  Setup an EFS filesystem: 
 
-Following the [GenomicsWorkFlows](https://docs.opendata.aws/genomics-workflows/orchestration/cromwell/cromwell-overview.html) deployment stack and selecting "Create EFS", you will end up with an EFS filesystem accessible within the provided subnets. It is mounted by default in EC2 workers under /mnt/efs. This is specified in the launch templates USER_DATA if you want to change this. 
+Following the [GenomicsWorkFlows](https://docs.opendata.aws/genomics-workflows/orchestration/cromwell/cromwell-overview.html) deployment stack and selecting "Create EFS", you will end up with an EFS filesystem accessible within the provided subnets. It is mounted by default in EC2 workers under /mnt/efs. This is specified in the launch templates USER_DATA if you want to change this. *BEWARE* : For globbing to work on EFS, the mountpoint must be left as "/mnt/efs" ! 
 
 Next, it is recommended to change the EFS setup (in console : select EFS service, then the "SharedDataGenomics" volume, edit). Change performance settings to Enhanced/Elastic, because the bursting throughput is usually insufficient. Optionally set the lifecycle to archive infrequently accessed data and reduce costs. 
 
@@ -271,13 +271,18 @@ backend {
     providers {
         AWSBatch {
             config{
+                // ALTER THE GLOBBING COMMAND: 
+                // use symlinks instad of hardlinks (not allowed on EFS)
+                //  "shopt -s nullglob" prevents issues with empty globbed folders.  
+                glob-link-command = " shopt -s nullglob; ln -fs GLOB_PATTERN GLOB_DIRECTORY "
+
                 default-runtime-attributes {
                     // keep you other settings as they are (queueArn etc)
 
                     // DEFAULT EFS CONFIG
                     // delocalize output files under /mnt/efs to the cromwell tmp bucket
                     efsDelocalize = false
-                    // make md5 sums of output files under /mnt/efs as part of the job 
+                    // make sibling-md5 files of output files under /mnt/efs as part of the job. see local.caching!
                     efsMakeMD5 = false
                 }
                 filesystems {
@@ -288,6 +293,11 @@ backend {
                     local {
                         // the mountpoint of the EFS volume within the HOST (specified in EC2 launch template)
                         efs = "/mnt/efs"
+                        caching {
+                            // sibling-md5 files reduce traffic on the EFS share. By default, files are streamed & hashed in cromwell itself
+                            // NOTE: beware on overwriting files. the md5-siblings are not automatically cleaned up or updated !! 
+                            check-sibling-md5 : true
+                        }
                     }
 
                 }
@@ -298,22 +308,31 @@ backend {
 
 ```
 
-Now, Cromwell is able to correctly handle output files both located in the cromwell working directory (delocalized to S3), and on the EFS volume (kept, and optionally delocalized).
+Now, Cromwell is able to : 
+
+- take input from localized files in temp-bucket (default) 
+- take input from files stored on EFS (no localization performed) 
+- generate output files located in the cromwell working directory : delocalized to S3 tmp bucket
+- generate output files located on the EFS volume : checked for presence, kept, and optionally delocalized
+- generate sibling md5 files for default output files and globbed output files
+- detect valid cached job outputs from previous runs, both on S3/tmp-bucket and EFS, for single files and globbed files. 
+
+Note: generating sibling md5 files for globbed output utilized the amount of vCPUs specified for the job.
 
 3. Current limitations:
 
-- To read an task output file in wdl using eg read_tsv(), it must be set to output type 'String' OR 'efsDelocalize' must be enabled for the job.
-- Call caching is not yet possible when using input files located on EFS.  Cromwell does not crash but issues errors and skips callcaching for that task. 
 - There is no unique temp/scratch folder generated per workflow ID. Data collision prevention is left to the user. 
 - Cleanup must be done manually
+- Globbing only works if efs is mounted under "/mnt/efs" (see config above)
 
 4. Example Workflow
 
 The following workflow highlights the following features: 
  
  - take input data from an s3 bucket. 
- - keep intermediate data on efs
- - delocalize output from efs volume 
+ - generate & keep intermediate data on efs
+ - glob files on s3
+ - delocalize output from efs volume to s3
  - read a file on efs in the main wdl cromwell process.
 
  
@@ -324,28 +343,40 @@ workflow TestEFS {
         # input file for WF is located on S3
         File s3_file = 's3://aws-quickstart/quickstart-aws-vpc/templates/aws-vpc.template.yaml'
         # set an input parameter holding the working dir on EFS
-        String efs_wd = "/mnt/efs/MyProject"
+        String efs_wd = "/mnt/efs/MyTestProject"
     }
-    # task one : create a file on efs.
+    # task one : create a file and a glob on efs. do not delocalize
     call task_one {input:
         infile = s3_file,
         wd = efs_wd    
     }
-    # read the outfile straight in a wdl structure
-    Array[Array[String]] myOutString_info = read_tsv(task_one.outfile)
+    # read the outfile on EFS straight in a wdl structure
+    Array[Array[String]] step1_info = read_tsv(task_one.efs_file)
 
-    # task two : reuse the file on the wd and delocalize to s3
+    # task two : reuse the file on the wd and delocalize to s3 (via runtime setting)
     call task_two {input:
         wd = efs_wd,
-        infile = task_one.outfile
+        infile = task_one.efs_file
+    }
+    Array[Array[String]] step2_info = read_tsv(task_two.outfile)
+
+    # run a task on the various files (get md5).
+    call task_three {input:
+        wd = efs_wd,
+        infiles = task_one.file_list,
+        f = task_two.outfile
     }
-    Array[Array[String]] myOutFile_info = read_tsv(task_two.outfile)
+    Array[String] step3_md5s = task_three.md5
 
     ## outputs
     output{
-        Array[Array[String]] wf_out_info_returned_as_string = myOutString_info
-        Array[Array[String]] wf_out_info_returned_as_file = myOutFile_info
-        String wf_out_file = task_two.outfile
+        Array[Array[String]] wf_out_info_step1 = step1_info
+        File wf_out_efs_file = task_one.efs_file
+        File wf_out_s3_file = task_one.s3_file
+        Array[File] wf_out_globList_out = task_one.file_list
+
+        File wf_out_file_step2 = task_two.outfile
+        Array[String] wf_out_step3 = step3_md5s    
     }
 }
 
@@ -356,21 +387,28 @@ task task_one {
     }
     command {
         # mk the wd:
-        mkdir -p ~{wd}
+        mkdir -p ~{wd}/StuffToGlob
+        # create files
+        for i in A B C D E F G H I F K L M N O P Q R; do 
+            echo $i > ~{wd}/StuffToGlob/$i.txt
+        done
         # mv the infile to wd
         mv ~{infile} ~{wd}/
-        # generate an outfile for output Testing
+        # generate an outfile for output Testing on EFS
         ls -alh ~{wd} > ~{wd}/MyOutFile
+        # and on the temp bucket.
+        ls -alh ~{wd} > MyRegularS3File.txt
     }
      runtime {
         docker: "ubuntu:22.04"
         cpu : "1"
-        memory: "500M" 
+        memory: "500M"         
      }
      output {
-        # to read a file in cromwell/wdl : pass it back as a string or delocalize (see task_two)
-        String outfile = '~{wd}/MyOutFile'
-     }
+        File efs_file = '~{wd}/MyOutFile'
+        File s3_file = "MyRegularS3File.txt"
+        Array[File] file_list = glob("~{wd}/StuffToGlob/*.txt")
+     }   
 }
 
 task task_two {
@@ -379,18 +417,38 @@ task task_two {
         File infile
     }
     command {
-        # put something new in the file:
-        ls -alh /tmp > ~{infile}
-        
+        # another derived file:
+        ls -alh /tmp > ~{infile}.step2
     }
      runtime {
         docker: "ubuntu:22.04"
         cpu : "1"
         memory: "500M" 
         efsDelocalize: true
+        
+     }
+     output {
+        File outfile = "~{infile}.step2"
+     }   
+}
+
+task task_three {
+    input {
+        String wd
+        Array[File] infiles
+        File f
+    }
+    command {    
+        #get checksums for globbed + extra infile
+        md5sum ~{sep=' ' infiles} ~{f}
+    }
+    runtime {
+        docker: "ubuntu:22.04"
+        cpu : "1"
+        memory: "500M"         
      }
      output {
-        File outfile = "~{infile}"
+        Array[String] md5 = read_lines(stdout())
      }
 }
 ```
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
index 86bfd46e754..1495e480358 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
@@ -30,10 +30,9 @@
  */
 package cromwell.backend.impl.aws.callcaching
 
-import com.google.cloud.storage.contrib.nio.CloudStorageOptions
 import common.util.TryUtil
 import cromwell.backend.BackendInitializationData
-import cromwell.backend.impl.aws.{AWSBatchStorageSystems, AwsBatchBackendInitializationData}
+import cromwell.backend.impl.aws.{AWSBatchStorageSystems, AwsBatchBackendInitializationData,AwsBatchJobCachingActorHelper}
 import cromwell.backend.io.JobPaths
 import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardCacheHitCopyingActorParams}
 import cromwell.core.CallOutputs
@@ -46,7 +45,7 @@ import wom.values.WomFile
 import scala.language.postfixOps
 import scala.util.Try
 
-class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams) extends StandardCacheHitCopyingActor(standardParams) {
+class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams) extends StandardCacheHitCopyingActor(standardParams) with AwsBatchJobCachingActorHelper{
   private val batchAttributes = BackendInitializationData
     .as[AwsBatchBackendInitializationData](standardParams.backendInitializationDataOption)
     .configuration.batchAttributes
@@ -74,8 +73,9 @@ class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyin
     }
   }
 
+  // detritus files : job script, stdout, stderr and RC files.
   override def processDetritus(sourceJobDetritusFiles: Map[String, String]
-                              ): Try[(Map[String, Path], Set[IoCommand[_]])] =
+                              ): Try[(Map[String, Path], Set[IoCommand[_]])] = {
     (batchAttributes.fileSystem, cachingStrategy) match {
       case (AWSBatchStorageSystems.s3, UseOriginalCachedOutputs) =>
         // apply getPath on each detritus string file
@@ -93,7 +93,7 @@ class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyin
         }
       case (_, _) => super.processDetritus(sourceJobDetritusFiles)
    }
-
+  }
   override protected def additionalIoCommands(sourceCallRootPath: Path,
                                               originalSimpletons: Seq[WomValueSimpleton],
                                               newOutputs: CallOutputs,
@@ -113,7 +113,7 @@ class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyin
           S3BatchCommandBuilder.writeCommand(
             path = jobPaths.forCallCacheCopyAttempts.callExecutionRoot / "call_caching_placeholder.txt",
             content = content,
-            options = Seq(CloudStorageOptions.withMimeType("text/plain")),
+            options = Seq(),
           ).get
         ))
        case (AWSBatchStorageSystems.s3, CopyCachedOutputs) => List.empty
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
index f731fb1b44a..41cb1dae97f 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
@@ -36,6 +36,9 @@ import cromwell.backend.BackendInitializationData
 import cromwell.backend.impl.aws.AwsBatchBackendInitializationData
 import cromwell.backend.impl.aws.AWSBatchStorageSystems
 import cromwell.core.io.DefaultIoCommandBuilder
+import scala.util.Try
+import cromwell.backend.standard.callcaching.StandardFileHashingActor.SingleFileHashRequest
+import cromwell.core.path.DefaultPathBuilder
 
 class AwsBatchBackendFileHashingActor(standardParams: StandardFileHashingActorParams) extends StandardFileHashingActor(standardParams) {
 
@@ -44,4 +47,27 @@ class AwsBatchBackendFileHashingActor(standardParams: StandardFileHashingActorPa
        case AWSBatchStorageSystems.s3  => S3BatchCommandBuilder
        case _ =>  DefaultIoCommandBuilder
   }
+  // get backend config.
+  val aws_config = BackendInitializationData.as[AwsBatchBackendInitializationData](standardParams.backendInitializationDataOption).configuration
+  
+  // custom strategy to handle efs (local) files, in case sibling-md5 file is present. 
+  override def customHashStrategy(fileRequest: SingleFileHashRequest): Option[Try[String]] = {
+    val file = DefaultPathBuilder.get(fileRequest.file.valueString)
+    if (aws_config.efsMntPoint.isDefined && file.toString.startsWith(aws_config.efsMntPoint.getOrElse("--")) && aws_config.checkSiblingMd5.getOrElse(false)) {
+            // check existence of the sibling file
+            val md5 = file.sibling(s"${file.toString}.md5")
+            if (md5.exists) {
+                // read the file.
+                val md5_value: Option[String] = Some(md5.contentAsString.split("\\s+")(0))
+                md5_value.map(str => Try(str))
+            } else {
+                // No sibling found, fall back to default.
+                None
+            }
+            
+    } else {
+        // Detected non-EFS file: return None
+        None  
+    }
+  }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
new file mode 100644
index 00000000000..18505f6d866
--- /dev/null
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
@@ -0,0 +1,96 @@
+/*
+ * Copyright 2018 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+package cromwell.backend.impl.aws.io
+
+
+//import cats.implicits._
+//import common.validation.ErrorOr.ErrorOr
+//import cromwell.backend.BackendJobDescriptor
+//import cromwell.core.CallContext
+//import cromwell.core.io.AsyncIoFunctions
+//import wom.expression.{IoFunctionSet, IoFunctionSetAdapter}
+//import wom.graph.CommandCallNode
+import wom.values._
+import cromwell.backend.io._
+import cromwell.backend.standard._
+import scala.concurrent.Future
+import java.nio.file.Paths
+import cromwell.core.path.DefaultPathBuilder
+
+//import cromwell.backend.impl.aws.AwsBatchAttributes
+//import cromwell.backend.impl.aws._
+
+trait AwsBatchGlobFunctions extends GlobFunctions {
+    
+  def standardParams: StandardExpressionFunctionsParams
+
+  
+
+  /**
+    * Returns a list of path from the glob.
+    *
+    * The paths are read from a list file based on the pattern.
+    *
+    * @param pattern The pattern of the glob. This is the same "glob" passed to globPath().
+    * @return The paths that match the pattern.
+    */
+  override def glob(pattern: String): Future[Seq[String]] = {
+    // get access to globName()
+    import GlobFunctions._
+    
+    // GOAL : 
+    //  - get config (backend / runtime / ...) here to evaluate if efsMntPoint is set & if efs delocalization is set. 
+    //  - according to those values : write the pattern as s3:// or as local path. 
+    //  - get the wf id from the config settings.
+
+    // for now : hard coded as local at mount point /mnt/efs.
+    val wfid_regex = ".{8}-.{4}-.{4}-.{4}-.{12}".r
+    val wfid = callContext.root.toString.split("/").toList.filter(element => wfid_regex.pattern.matcher(element).matches()).lastOption.getOrElse("")
+    val globPatternName = globName(s"${pattern}-${wfid}")
+    val globbedDir = Paths.get(pattern).getParent.toString
+    val listFilePath = if (pattern.startsWith("/mnt/efs/")) {
+        DefaultPathBuilder.get(globbedDir + "/." + globPatternName + ".list")
+    } else {
+        callContext.root.resolve(s"${globPatternName}.list")
+    }
+    asyncIo.readLinesAsync(listFilePath.toRealPath()) map { lines =>
+      lines.toList map { fileName =>
+        // again : this should be config based...
+        if (pattern.startsWith("/mnt/efs/")) {
+            s"${globbedDir}/.${globPatternName}/${fileName}"
+        } else {
+            s"${callContext.root}/${globPatternName}/${fileName}"
+        }
+      }
+    }
+  }
+  
+}
\ No newline at end of file

From 7043c10e2a3d1272fd2a57eca3f08b5337a315e4 Mon Sep 17 00:00:00 2001
From: Henrique Ribeiro <henriqueribeiro@users.noreply.github.com>
Date: Tue, 9 May 2023 10:08:37 +0100
Subject: [PATCH 165/326] Version 85 (#30)

* 85 release (#28)

* Update cromwell version from 83 to 84

* BW-1255 Implement POST /runs endpoint (#6779)

* Adding route

* Fixing HTTP method error

* All formFields made optional

* A compliling state

* Saving

* Saving

* All three endpoints functioning as expected; updated RESTAPI.md

* Updated response for submission from 200 to 201 to pass tests

* Test submission response

* Moved updated submission response to askSubmit

* test

* updating RESTAPI.md

* saving

* Adding utility file for submitRequest

* cleanup

* Update awssdkv from 2.17.152 to 2.17.194 (#6814)

* BW-1305 Swagger Update (#6818)

* Properly documenting metadataArchiveStatus in WorkflowQueryResult model

* Update docs

* BT-710 Add configs for BlobPathBuilderFactory (#6817)

BT-710 Add configs for BlobPathBuilderFactory

* BW-1305 Make "name" optional in workflow query response (#6821)

* BT-724 Fix BlobPathBuilder failing on retrieving existing filesystem (#6816)

Modify blobPathBuilder to fallback to creating a filesystem if one is not found

* Logging updates: (#6813)

* [BT-698] first pass on BlobTokenGenerator with E2E test (#6824)

* first pass on BlobTokenGenerator with E2E test

* update BlobPathBuilder constructor args in test

* account -> container level client

* [BT-687] specify correct types (#6829)

* specify correct types

* fix test with new type

* remove type declarations in function call

* remove unnecessary sas-token config

* BW-1206 - Combine all Wes Endpoints & add Tests (#6833)

* Add tests, getting frid of WesRunRoutes.scala

* wesWorkflowId fix, ec implicits errors gone

* Refactoring path for GET /runs

* Indentation fix

* Commit to rollback

* Revert "Indentation fix"

This reverts commit 63fc4842c9d4eff68ec9cb7c3ef19e110696598b.

* PR trigger

* Optimize imports

* Missed import

* BW-1354 - Porting CBAS preliminary step (#6837)

* Getting rid of shared utility file; Adding/Updating WES version of submit.

* Edit spec file

* Adding Wes-like error

* BW-1378 Addl CromIAM user enablement checks (#6826)

* Update cromwell version from 84 to 85

* BW-1393 Release doc updates (#6839)

* BT-732 Checksum validation for blobs read by engine (#6838)

* Draft support for optional FileHash

* Draft getMd5 for BlobPath

* Resolve non-parallel IO to fix tests

* Checksum validation for BlobPath

* Nicer error message

* Test for missing Blob hash

* Break attr acquisition into separate method

* Cleanup, comments

* In-progress tests of blob hash command

* Remove test

* Remove unused import

* BT-711 Refresh SAS token for filesystem on expiry (#6831)

* BT-711 Refresh SAS token for filesystem on expiry

* Rough cut of token refresh using exceptions

* Ignore tests, and minor cleanup

* Remove stray line

* Draft of manager class for handling expiring file systems

* Style fixes

* Refactor of blobfilesystemManager and tests covering its functionality

* Refined tests to validate close filesystem as separate unit

* Ignore connected tests

* Clean up of some things

* Refactor BlobFileSystemManager to separate file, and some other cleanup

* Some additional scala-ifying

* Small cleanup

* Correcting imports

* trigger tests

* trigger tests

* Batch 1 of scala steward updates (#6903)

* Batch 1 of scala steward updates

* Rollback snakeYAML

* Attempt 3, with only the passing dependancies

* Revert google API and Big Query udpates

* Winding back other google deps

* rollback remaining google updates

* trigger tests

* trigger tests

* [BW-1398] Migrate PKs to BIGINT (#6907)

* BT-745  Batch 2 of scala steward updates (#6906)

* Update SBT to 2.0.0

* Fix sbt-git import

* Update mouse to 1.0.11

* Update rhino 1.7.14

* SUP-692 Retry with more memory after RC 137 (#6912)

* Reorder execution result checks so 137 can retry with more memory

* Test for memory retry after 137 RC

* Fix test expectations

* Make memory retry checks consistent

* Revert changes to existing test

* Rename retryWithMoreMemory to outOfMemoryDetected

* Scala steward updates batch 3 (#6913)

* Scala steward updates batch 3

* WX-745 Batch 4 scala steward updates (#6916)

* WX-746 Localize all DRS inputs in a single Action (#6914)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* WX-755 Build all images instead of just Cromwell (#6919)

* WX-755 Add `isRelease` option for Docker builds (#6923)

* WX-755 Cromwell/CromIAM automatically board train (#6924)

* WX-755 Fix environment variable syntax (#6926)

* WX-743 Enable TES task creation with BlobPaths (#6921)

* Give blob SAS tokens write permission

* Case class wrapper for subscription id

* Resolve duplicate container name in absolute BlobPath

* Ignored test demonstrating correct absolute path generation

* Update filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala

Co-authored-by: Brian Reilly <breilly@broadinstitute.org>

* PR feedback

Co-authored-by: Brian Reilly <breilly@broadinstitute.org>

* [WX-765] Update snakeyaml to 1.33 (#6927)

* update snakeyaml to 1.33

* Don't use deprecated no-arg Constructor constructor

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* WM-1414 Refactoring WesRunLog to omit Cromwell's "workflowLog" object (#6925)

* Upgrade Postgres to 42.4.1 (#6932)

* WX-735 Fix incorrect and/or nondeterministic filesystem ordering (#6930)

* WX-772 Update Scala to 2.13.9 (#6928)

* Update Scala to 2.13.9

* Try updating sbt-scoverage

* Does this version exist anywhere we can see?

* This version actually exists

* Update library version to remove conflict

* Codegen version

* Fix fun new 2.13.9 compiler errors

* Resolve warnings

* Newest Scala?

* I guess not

* Does this please Travis?

* force ci

* Back out changes to generated code

Co-authored-by: Adam Nichols <aednichols@gmail.com>

* WX-781 Bump jackson-databind in /CromwellRefdiskManifestCreator (#6935)

Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.13.2.2 to 2.13.4.1.
- [Release notes](https://github.com/FasterXML/jackson/releases)
- [Commits](https://github.com/FasterXML/jackson/commits)

---
updated-dependencies:
- dependency-name: com.fasterxml.jackson.core:jackson-databind
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* WX-808 Host allowlist for HTTP imports (#6938)

* `hostAllowlist` that allows everything

* Refactor

* Stick allow list in HttpResolver

* Better default config

* Allow list tests

* Make it build

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Update commons text to 1.10.0 (#6937)

* WX-751 Token refresh signal for monitoring (#6939)

* Log messages

* `DEBUG` -> `INFO`

* WX-744 Optionally rewrite blob paths to appear as local paths (#6941)

* Modify blob paths for TES

* Make blob transformation configurable

* Update supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Apply PR feedback in second place

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Update changelog for wdl http allow list (#6944)

* WM-1491 Fixing Cromwell-client (#6943)

* More updated client for use in cbas

* Removing excess code

* Fix client build script (#6945)

* WX-837: Remove CWL references from documentation (#6949)

* wx-837 removed cwl references in markdown doc files

* wx-837 removed cwlParsingOverview.md, updated mkdocs.yml

* wx-837 updated cromwell.yaml, generated new RESTAPI file

* WX-728 Add configurable WSM client to Cromwell (#6948)

* Dependencies

* Compiles but no tests

* Formatting

* Moar exclusions

* Update to latest WSM

* Add additional dependency

* We need some UUID here to make the request

* Formatting

* Clarify what is fake

* Formatting

* Use our own version of Jersey and Jackson stuff

* Port-in Khalid's changes (thank you!)

Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>

* Test longevity

Don't break the test if someone decides to add a cert to `ws.org`

* Cleanup

* Cleanup

* Cleanup

* Adjust TES config file for CI

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>

* CROM-6554: Removed PAPIv1 references from doc (#6950)

* crom-6554 removed references to PAPI v1 from doc

* crom-6554 pr feedback, reworded doc to use example conf as a starting point

* WX-833 Real Azure DRS Credentials (#6952)

* Remove B2C reference from name

* Get token for current user rather than getting from KeyVault

* Remove KeyVault config for engine

* Remove KeyVault config for DRSLocalizer

* Remove KeyVault dependency

* Remove KeyVault support from localizer repo template

* Cleaned up and working Azure token acquisition for engine

* Collapse localizer's AccessTokenStrategy into DrsCredentials

* Cleanup

* WX-853 Remove most CWL (#6955)

* WX-696 Enable getting SAS token from WSM (#6954)

* WX-696 Enable getting SAS token from WSM

* Wire container resource id from config

* Move resource-container-id config path

* First pass at config for WSM

* Remove unused singleton config

* Tests for new config

* Fix config parsing

* Modified b2c token to be provided each time

* Remove singletonConfig arg from factory

* Restore types to factory configs

* Clean up comments and empty token default

* Default to config b2c before searching environment

* Fix token default on api client

* Fix test

* Refactor error handling for when there is no token

* Remove token constructor arg for clientProvider

* Move configs to global singleton config

* Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

* default -> override

* Add override token to test

* Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Parentheses

* Reduce token timeout

* Move AzureCredentials to separate file

* Make AzureCredentials an object

* WSM token cleanup

* Config refactor (#6960)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Initial blob token documentation

* Refine language in BlobSasTokenGenerator

* Update comment and formatting

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* WX-853 Remove CWL language factory, Centaur runner (#6961)

* WX-842 Add Pact Dependency for Cromwell (#6962)

* WX-842 Add Pact Dependency for Cromwell

* Remove incomplete test spec

* Initial Pact Test

* Fix pact so it compiles

* Add breadcrumb comment and clean up

* ID-125 Add support for drshub, rename all the things (#6959)

* Add support for drshub, rename all the things

* fallback to martha if resolver is not in config

* WX-867 Translate crc32c hashes to b64 for getm (#6970)

* Translate crc32c hashes to b64 for getm

* Update tests

* Remove obsolete b64 handling for md5, centralize hex validation

* Restore old test, fix other test

* WX-843 Workflow failure reason should accurately indicate issues opening blob filesystem (#6965)

* WX-859 Accept workflow execution identity in config (#6967)

* WX-892 Trim down `ValueStore` logging to prevent OOMs (#6981)

* Add Nirvana 3.18.1 reference image test, minor cleanup [VS-705] (#6975)

* WX-863 Turn off Azure NIO logging (#6982)

* Turn off Azure NIO logging

* Poke Travis

* WM-1616: Allow repeating attempts at initialization (take 2) (#6985)

* WX-878 Single shared BlobFileSystemManager (#6986)

* Make BlobFileSystemManager shared across all BlobPathBuilders

* Update TES conf file to reflect new singleton config

* Shell escape reference image  files [VS-796] [WX-910] (#6989)

* WX-769 `disks` compatibility for TES backend (#6991)

* Update FiveMinuteIntro.md (#6994)

* WX-906 Sbt Unit Tests as Github Actions (#6992)

* WX-926 Support falling back to OCI Manifest Format (#7003)

* WX-926 Support falling back to OCI Manifest Forma

* Only mount reference disks if requested [WX-925] (#7001)

* [WM-1646] Add missing fields for `WorkflowDescription` for WomTool /describe endpoint to Swagger (#7004)

* WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status (#6980)

* WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status

* Address feedback

* Address feedback (#6997)

* Address additional feedback (#7000)

* Fix copy/paste error (#7005)

* Address additional feedback

* Fix copy/paste error

* Trigger CI

---------

Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Centaur reference image test should validate symlinks [VS-796] (#6996)

* WX-903 Pre-GHA test suite disablement

* WX-877 Update CHANGELOG for release 85 (#7011)

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Katrina P <68349264+kpierre13@users.noreply.github.com>
Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Co-authored-by: Christian Freitas <christian.j.freitas@gmail.com>
Co-authored-by: Saloni Shah <salonipshah11@gmail.com>
Co-authored-by: kshakir <kshakir@broadinstitute.org>
Co-authored-by: mspector <michael.l.spector@gmail.com>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
Co-authored-by: Brian Reilly <breilly@broadinstitute.org>
Co-authored-by: Adam Nichols <aednichols@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Co-authored-by: Christian Freitas <cfreitas@broadinstitute.org>
Co-authored-by: Trevyn Langsford <tlangs@broadinstitute.org>
Co-authored-by: Miguel Covarrubias <mcovarr@users.noreply.github.com>
Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com>
Co-authored-by: Tom Wiseman <tom.h.wiseman@gmail.com>
Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>

* Develop aws (#29)

* stuck on globbing

* efs works, no callcaching

* update readme

* extended EFS support

* fix for globbing in nested scatters

* updated config for globbing, to prevent issues with empty folders

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Katrina P <68349264+kpierre13@users.noreply.github.com>
Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Co-authored-by: Christian Freitas <christian.j.freitas@gmail.com>
Co-authored-by: Saloni Shah <salonipshah11@gmail.com>
Co-authored-by: kshakir <kshakir@broadinstitute.org>
Co-authored-by: mspector <michael.l.spector@gmail.com>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
Co-authored-by: Brian Reilly <breilly@broadinstitute.org>
Co-authored-by: Adam Nichols <aednichols@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Co-authored-by: Christian Freitas <cfreitas@broadinstitute.org>
Co-authored-by: Trevyn Langsford <tlangs@broadinstitute.org>
Co-authored-by: Miguel Covarrubias <mcovarr@users.noreply.github.com>
Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com>
Co-authored-by: Tom Wiseman <tom.h.wiseman@gmail.com>
Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>
Co-authored-by: geertvandeweyer <geertvandeweyer@gmail.com>
---
 .github/set_up_cromwell_action/action.yml     |    47 +
 .github/workflows/chart_update_on_merge.yml   |    26 +-
 .github/workflows/cromwell_unit_tests.yml     |    32 +
 .gitignore                                    |     3 +
 .travis.yml                                   |    23 +-
 CHANGELOG.md                                  |   326 +-
 CromIAM/src/main/resources/application.conf   |     2 +-
 CromIAM/src/main/resources/logback.xml        |    14 +-
 .../CromIamInstrumentation.scala              |     1 +
 .../main/scala/cromiam/sam/SamClient.scala    |    33 +
 .../webservice/CromIamApiService.scala        |    16 +-
 .../cromiam/webservice/QuerySupport.scala     |     2 +-
 .../cromiam/webservice/RequestSupport.scala   |    26 +-
 .../webservice/SubmissionSupport.scala        |     2 +-
 .../webservice/WomtoolRouteSupport.scala      |    10 +-
 .../webservice/CromIamApiServiceSpec.scala    |    38 +-
 .../cromiam/webservice/MockClients.scala      |     9 +
 .../webservice/SwaggerServiceSpec.scala       |     7 +-
 .../webservice/WomtoolRouteSupportSpec.scala  |    54 +-
 CromwellRefdiskManifestCreator/pom.xml        |     2 +-
 .../StandardAsyncExecutionActor.scala         |    26 +-
 .../standard/StandardCachingActorHelper.scala |     2 +-
 .../RootWorkflowFileHashCacheActor.scala      |     2 +-
 .../StandardCacheHitCopyingActor.scala        |     5 +
 build.sbt                                     |    30 +-
 .../centaur/reporting/BigQueryReporter.scala  |     2 +-
 .../bcbio_joint_gvcf.test                     |    23 -
 .../integrationTestCases/bcbio_prealign.test  |    20 -
 .../integrationTestCases/bcbio_rnaseq.test    |    19 -
 .../integrationTestCases/bcbio_somatic.test   |    22 -
 .../integrationTestCases/bcbio_svcall.test    |    22 -
 .../bcbio_wes-chr21-test-workflow.test        |    22 -
 .../cwl/bcbio/bcbio.options                   |     5 -
 .../main-gvcf-joint-samples.json              |   615 -
 .../gvcf-joint-workflow/main-gvcf-joint.cwl   |   794 -
 .../steps/alignment_to_rec.cwl                |   198 -
 .../steps/batch_for_jointvc.cwl               |   329 -
 .../steps/batch_for_variantcall.cwl           |   401 -
 .../steps/combine_sample_regions.cwl          |    99 -
 .../steps/compare_to_rm.cwl                   |   337 -
 .../steps/concat_batch_variantcalls.cwl       |   196 -
 .../concat_batch_variantcalls_jointvc.cwl     |   209 -
 .../steps/finalize_jointvc.cwl                |   331 -
 .../steps/get_parallel_regions.cwl            |   171 -
 .../steps/get_parallel_regions_jointvc.cwl    |   184 -
 .../steps/merge_split_alignments.cwl          |   168 -
 .../steps/multiqc_summary.cwl                 |    95 -
 .../steps/pipeline_summary.cwl                |   219 -
 .../steps/postprocess_alignment.cwl           |   223 -
 .../steps/postprocess_alignment_to_rec.cwl    |   233 -
 .../steps/postprocess_variants.cwl            |   195 -
 .../steps/prep_align_inputs.cwl               |   142 -
 .../steps/prep_samples.cwl                    |    95 -
 .../steps/prep_samples_to_rec.cwl             |    85 -
 .../steps/process_alignment.cwl               |   198 -
 .../gvcf-joint-workflow/steps/qc_to_rec.cwl   |   295 -
 .../gvcf-joint-workflow/steps/run_jointvc.cwl |   203 -
 .../steps/summarize_vc.cwl                    |   225 -
 .../steps/variantcall_batch_region.cwl        |   266 -
 .../gvcf-joint-workflow/wf-alignment.cwl      |   143 -
 .../gvcf-joint-workflow/wf-jointcall.cwl      |   360 -
 .../gvcf-joint-workflow/wf-variantcall.cwl    |   329 -
 .../main-prealign-samples.json                |   526 -
 .../bcbio/prealign-workflow/main-prealign.cwl |   672 -
 .../steps/batch_for_variantcall.cwl           |   407 -
 .../steps/combine_sample_regions.cwl          |   101 -
 .../prealign-workflow/steps/compare_to_rm.cwl |   315 -
 .../steps/concat_batch_variantcalls.cwl       |   199 -
 .../steps/get_parallel_regions.cwl            |   174 -
 .../steps/multiqc_summary.cwl                 |    95 -
 .../steps/organize_noalign.cwl                |    59 -
 .../steps/pipeline_summary.cwl                |   221 -
 .../steps/postprocess_alignment.cwl           |   221 -
 .../steps/postprocess_alignment_to_rec.cwl    |   229 -
 .../steps/postprocess_variants.cwl            |   183 -
 .../prealign-workflow/steps/prep_samples.cwl  |    93 -
 .../steps/prep_samples_to_rec.cwl             |    81 -
 .../prealign-workflow/steps/qc_to_rec.cwl     |   299 -
 .../prealign-workflow/steps/summarize_vc.cwl  |   198 -
 .../steps/variantcall_batch_region.cwl        |   269 -
 .../prealign-workflow/wf-variantcall.cwl      |   316 -
 .../rnaseq-workflow/main-rnaseq-samples.json  |   111 -
 .../cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl |   304 -
 .../rnaseq-workflow/steps/detect_fusions.cwl  |    97 -
 .../rnaseq-workflow/steps/multiqc_summary.cwl |    96 -
 .../steps/pipeline_summary.cwl                |   155 -
 .../rnaseq-workflow/steps/prepare_sample.cwl  |   146 -
 .../steps/process_alignment.cwl               |   108 -
 .../bcbio/rnaseq-workflow/steps/qc_to_rec.cwl |   135 -
 .../steps/rnaseq_quantitate.cwl               |   123 -
 .../rnaseq-workflow/steps/trim_sample.cwl     |   140 -
 .../main-somatic-samples.json                 |   680 -
 .../bcbio/somatic-workflow/main-somatic.cwl   |   973 -
 .../steps/alignment_to_rec.cwl                |   200 -
 .../somatic-workflow/steps/batch_for_sv.cwl   |   375 -
 .../steps/batch_for_variantcall.cwl           |   407 -
 .../steps/calculate_sv_bins.cwl               |   225 -
 .../steps/calculate_sv_coverage.cwl           |   218 -
 .../steps/combine_sample_regions.cwl          |    99 -
 .../somatic-workflow/steps/compare_to_rm.cwl  |   311 -
 .../steps/concat_batch_variantcalls.cwl       |   198 -
 .../somatic-workflow/steps/detect_sv.cwl      |   414 -
 .../steps/get_parallel_regions.cwl            |   173 -
 .../steps/merge_split_alignments.cwl          |   169 -
 .../steps/multiqc_summary.cwl                 |    96 -
 .../steps/normalize_sv_coverage.cwl           |   236 -
 .../steps/pipeline_summary.cwl                |   223 -
 .../steps/postprocess_alignment.cwl           |   224 -
 .../steps/postprocess_alignment_to_rec.cwl    |   235 -
 .../steps/postprocess_variants.cwl            |   182 -
 .../steps/prep_align_inputs.cwl               |   143 -
 .../somatic-workflow/steps/prep_samples.cwl   |    95 -
 .../steps/prep_samples_to_rec.cwl             |    85 -
 .../steps/process_alignment.cwl               |   199 -
 .../somatic-workflow/steps/qc_to_rec.cwl      |   310 -
 .../somatic-workflow/steps/summarize_sv.cwl   |   242 -
 .../somatic-workflow/steps/summarize_vc.cwl   |   195 -
 .../steps/variantcall_batch_region.cwl        |   268 -
 .../bcbio/somatic-workflow/wf-alignment.cwl   |   144 -
 .../cwl/bcbio/somatic-workflow/wf-svcall.cwl  |   328 -
 .../bcbio/somatic-workflow/wf-variantcall.cwl |   312 -
 .../svcall-workflow/main-svcall-samples.json  |   707 -
 .../cwl/bcbio/svcall-workflow/main-svcall.cwl |   975 -
 .../steps/alignment_to_rec.cwl                |   206 -
 .../svcall-workflow/steps/batch_for_sv.cwl    |   359 -
 .../steps/batch_for_variantcall.cwl           |   401 -
 .../steps/calculate_sv_bins.cwl               |   221 -
 .../steps/calculate_sv_coverage.cwl           |   207 -
 .../steps/combine_sample_regions.cwl          |    99 -
 .../svcall-workflow/steps/compare_to_rm.cwl   |   307 -
 .../steps/concat_batch_variantcalls.cwl       |   196 -
 .../bcbio/svcall-workflow/steps/detect_sv.cwl |   396 -
 .../steps/get_parallel_regions.cwl            |   171 -
 .../steps/merge_split_alignments.cwl          |   171 -
 .../svcall-workflow/steps/multiqc_summary.cwl |    95 -
 .../steps/normalize_sv_coverage.cwl           |   224 -
 .../steps/pipeline_summary.cwl                |   221 -
 .../steps/postprocess_alignment.cwl           |   223 -
 .../steps/postprocess_alignment_to_rec.cwl    |   233 -
 .../steps/postprocess_variants.cwl            |   180 -
 .../steps/prep_align_inputs.cwl               |   145 -
 .../svcall-workflow/steps/prep_samples.cwl    |    93 -
 .../steps/prep_samples_to_rec.cwl             |    79 -
 .../steps/process_alignment.cwl               |   201 -
 .../bcbio/svcall-workflow/steps/qc_to_rec.cwl |   308 -
 .../svcall-workflow/steps/summarize_sv.cwl    |   228 -
 .../svcall-workflow/steps/summarize_vc.cwl    |   193 -
 .../steps/variantcall_batch_region.cwl        |   266 -
 .../bcbio/svcall-workflow/wf-alignment.cwl    |   146 -
 .../cwl/bcbio/svcall-workflow/wf-svcall.cwl   |   310 -
 .../bcbio/svcall-workflow/wf-variantcall.cwl  |   308 -
 .../main-wes_chr21_test-samples.json          |  1059 -
 .../main-wes_chr21_test.cwl                   |   997 -
 .../steps/alignment_to_rec.cwl                |   194 -
 .../steps/batch_for_ensemble.cwl              |   273 -
 .../steps/batch_for_sv.cwl                    |   363 -
 .../steps/batch_for_variantcall.cwl           |   395 -
 .../steps/calculate_sv_bins.cwl               |   219 -
 .../steps/calculate_sv_coverage.cwl           |   206 -
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 delete mode 100644 cwl/src/test/resources/bad.cwl
 delete mode 100644 cwl/src/test/resources/bad2.cwl
 delete mode 100644 cwl/src/test/resources/brokenlinks.cwl
 delete mode 100644 cwl/src/test/resources/cwl/lodash.js
 delete mode 100644 cwl/src/test/resources/cwl/ontology/EDAM.owl
 delete mode 100644 cwl/src/test/resources/cwl/ontology/gx_edam.ttl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/complex_workflow/expected_result.json
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/complex_workflow/root_workflow.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/complex_workflow/sub/sub_workflow.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/deep_nesting/expected_result.json
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/deep_nesting/parseInt-tool.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/deep_nesting/root_workflow.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/deep_nesting/wc-tool.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/echo_tool.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/same_file_cyclic_dependency/root_workflow.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/self_reference/expected_result.json
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/self_reference/root_workflow.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/simple_workflow/expected_result.json
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/simple_workflow/root_workflow.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/root_workflow.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_1.cwl
 delete mode 100644 cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_2.cwl
 delete mode 100644 cwl/src/test/resources/dir_example.cwl
 delete mode 100644 cwl/src/test/resources/env.cwl
 delete mode 100644 cwl/src/test/resources/exampledir/example.txt
 delete mode 100644 cwl/src/test/resources/file_example.cwl
 delete mode 100644 cwl/src/test/resources/file_size_example.cwl
 delete mode 100644 cwl/src/test/resources/links_dont_parse.cwl
 delete mode 100644 cwl/src/test/resources/logback-test.xml
 delete mode 100644 cwl/src/test/resources/nestedworkflows.cwl
 delete mode 100644 cwl/src/test/resources/tar-param.cwl
 delete mode 100644 cwl/src/test/resources/three_step.cwl
 delete mode 100644 cwl/src/test/scala/cwl/CommandLineToolSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/CommandOutputExpressionSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/CwlDecoderSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/CwlEcmaScriptDecoderSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/CwlEcmaScriptEncoderSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/CwlExpressionCommandPartSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/CwlInputValidationSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/CwlWorkflowWomSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/DirectorySpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/ExportCwlSamplesSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/ExpressionEvaluatorSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/ExpressionInterpolatorSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/FileSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/FullyQualifiedNameSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/LocalIoFunctionSet.scala
 delete mode 100644 cwl/src/test/scala/cwl/ParseBigThreeSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/ParsingSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/ScatterLogicSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/TestSetup.scala
 delete mode 100644 cwl/src/test/scala/cwl/WomTypeConversionSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/WomValueJsonFormatter.scala
 delete mode 100644 cwl/src/test/scala/cwl/WorkflowStepInputExpressionSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/WorkflowStepInputSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/internal/EcmaScriptUtilSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/internal/EnhancedRhinoSandboxSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/ontology/SchemaSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/preprocessor/CwlPreProcessorSpec.scala
 delete mode 100644 cwl/src/test/scala/cwl/preprocessor/CwlReferenceSpec.scala
 create mode 100644 database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml
 create mode 100644 database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml
 create mode 100644 database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml
 delete mode 100644 docs/developers/CwlParsing.md
 delete mode 100644 docs/developers/bitesize/workflowParsing/cwlParsingOverview.md
 delete mode 100644 engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala
 create mode 100644 engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
 create mode 100644 filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
 create mode 100644 filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
 create mode 100644 filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
 create mode 100644 filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
 delete mode 100644 languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala
 create mode 100644 runConfigurations/Repo template_ Cromwell server TES.run.xml
 delete mode 100644 server/src/test/resources/cwl_glob_sort.cwl
 create mode 100644 supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
 delete mode 100644 supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala
 create mode 100644 supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
new file mode 100644
index 00000000000..13cb11601db
--- /dev/null
+++ b/.github/set_up_cromwell_action/action.yml
@@ -0,0 +1,47 @@
+#This is a series of steps that will setup Java/sbt/Cromwell on the local runner.
+#These steps are meant to be re-used and invoked by other Github Action Workflows
+name: 'Set Up Cromwell Steps'
+description: Specific steps that will set up git secrets, java, sbt, and Cromwell on the local machine. 
+inputs:
+  cromwell_repo_token: #As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell.
+    required: true
+
+runs:
+  using: "composite" # <-- this allows these steps to be used by other workflows.
+  steps:
+      #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
+      - uses: actions/checkout@v3
+        name: Checkout Coursier Cache
+      - uses: coursier/cache-action@v6  
+        name: Enable Coursier Cache
+
+      #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
+      - name: Git secrets setup 
+        run: |
+          git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
+          cd ~/git-secrets
+          git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
+          sudo make install
+        shell: bash
+
+      - name: Secrets check
+        run: |
+          sudo ln -s "$(which echo)" /usr/local/bin/say
+          ./minnie-kenny.sh --force
+          git secrets --scan-history
+        shell: bash
+
+      #Clone the cromwell repo to this VM.
+      - name: Clone Cromwell
+        uses: actions/checkout@v3
+        with:
+          repository: broadinstitute/cromwell
+          token: ${{ inputs.cromwell_repo_token }}
+
+      #Install Java to this VM. This Java version and distribution is compatible with Cromwell.
+      - name: Setup JDK
+        uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 11
+
diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index 9e847bc17eb..aa7a2c9c9ad 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -41,19 +41,33 @@ jobs:
         echo "CROMWELL_NUMBER=$((previous_version + 1))" >> $GITHUB_ENV
     - name: Save complete image ID
       run: |
-        echo "CROMWELL_SNAP_VERSION=`echo "$CROMWELL_NUMBER-$CROMWELL_SHORT_SHA-SNAP"`" >> $GITHUB_ENV
+        echo "CROMWELL_VERSION=`echo "$CROMWELL_NUMBER-$CROMWELL_SHORT_SHA"`" >> $GITHUB_ENV
     # `DSDEJENKINS_PASSWORD` auto syncs from vault with https://github.com/broadinstitute/terraform-ap-deployments/pull/614
     - name: Login to Docker Hub
       uses: docker/login-action@v1
       with:
         username: dsdejenkins
         password: ${{ secrets.DSDEJENKINS_PASSWORD }}
+    # Build & push `cromwell`, `womtool`, `cromiam`, and `cromwell-drs-localizer`
     - name: Build Cromwell Docker
       run: |
         set -e
         cd cromwell
-        sbt server/docker
-        docker push broadinstitute/cromwell:$CROMWELL_SNAP_VERSION
+        sbt -Dproject.isSnapshot=false -Dproject.isRelease=false dockerBuildAndPush
+    - name: Deploy to dev and board release train (Cromwell)
+      uses: broadinstitute/repository-dispatch@master
+      with:
+        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+        repository: broadinstitute/terra-helmfile
+        event-type: update-service
+        client-payload: '{"service": "cromwell", "version": "${{ env.CROMWELL_VERSION }}", "dev_only": false}'
+    - name: Deploy to dev and board release train (CromIAM)
+      uses: broadinstitute/repository-dispatch@master
+      with:
+        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+        repository: broadinstitute/terra-helmfile
+        event-type: update-service
+        client-payload: '{"service": "cromiam", "version": "${{ env.CROMWELL_VERSION }}", "dev_only": false}'
     - name: Edit & push chart
       env:
         BROADBOT_GITHUB_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
@@ -62,10 +76,10 @@ jobs:
         cd cromwhelm
         git checkout main
         ls -la
-        sed -i "s/appVersion.*/appVersion: \"$CROMWELL_SNAP_VERSION\"/" cromwell-helm/Chart.yaml
-        sed -i "s/image: broadinstitute\/cromwell.*/image: broadinstitute\/cromwell:$CROMWELL_SNAP_VERSION/" cromwell-helm/templates/cromwell.yaml
+        sed -i "s/appVersion.*/appVersion: \"$CROMWELL_VERSION\"/" cromwell-helm/Chart.yaml
+        sed -i "s/image: broadinstitute\/cromwell.*/image: broadinstitute\/cromwell:$CROMWELL_VERSION/" cromwell-helm/templates/cromwell.yaml
         git diff
         git config --global user.name "broadbot"
         git config --global user.email "broadbot@broadinstitute.org"
-        git commit -am "Auto update to Cromwell $CROMWELL_SNAP_VERSION"
+        git commit -am "Auto update to Cromwell $CROMWELL_VERSION"
         git push https://broadbot:$BROADBOT_GITHUB_TOKEN@github.com/broadinstitute/cromwhelm.git main
diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
new file mode 100644
index 00000000000..d0927f8b954
--- /dev/null
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -0,0 +1,32 @@
+name: 'Cromwell unit tests'
+
+#This github action runs all of Cromwell's unit tests.
+
+#This is what shows up in the github workflows page as the title. 
+run-name: ${{ github.actor }} running Cromwell sbt unit tests.
+
+#What will trigger the workflow to run. 
+on:
+  workflow_dispatch: #Manual trigger from GitHub UI
+  push:
+
+permissions: 
+  contents: read
+
+jobs:
+  build-and-test: 
+    #This action is using a Github free runner, rather than a Broad self-hosted one.
+    #This is because the Broad ones don't have sbt installed by default.
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3 # checkout the cromwell repo
+    - uses: ./.github/set_up_cromwell_action #Exectute this reusable github action. It will set up java/sbt/git-secrets/cromwell.
+      with:
+        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+  
+    #Invoke SBT to run all unit tests for Cromwell. 
+    - name: Run tests
+      run: |
+        set -e
+        sbt "test"
diff --git a/.gitignore b/.gitignore
index 571a12c5873..c7d6e562544 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
 # common scala config
 *~
+.metals/
 .DS_Store
 .artifactory
 .bsp
@@ -50,3 +51,5 @@ tesk_application.conf
 **/venv/
 exome_germline_single_sample_v1.3/
 **/*.pyc
+.scalafmt.conf
+.vscode/
diff --git a/.travis.yml b/.travis.yml
index d733b16432c..9ffb48b1147 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -28,24 +28,13 @@ env:
     - >-
       BUILD_TYPE=centaurEngineUpgradeLocal
       BUILD_MYSQL=5.7
+    # Temporarily keeping until `centaurEngineUpgradePapiV2beta` or similar exists
     - >-
       BUILD_TYPE=centaurEngineUpgradePapiV2alpha1
       BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurHoricromtalPapiV2alpha1
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=centaurHoricromtalPapiV2beta
       BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurHoricromtalEngineUpgradePapiV2alpha1
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurPapiUpgradePapiV2alpha1
-      BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurPapiUpgradeNewWorkflowsPapiV2alpha1
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=centaurLocal
       BUILD_MARIADB=10.3
@@ -55,9 +44,6 @@ env:
     - >-
       BUILD_TYPE=centaurLocal
       BUILD_POSTGRESQL=11.3
-    - >-
-      BUILD_TYPE=centaurPapiV2alpha1
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=centaurPapiV2beta
       BUILD_MYSQL=5.7
@@ -67,15 +53,10 @@ env:
     - >-
       BUILD_TYPE=centaurTes
       BUILD_MYSQL=5.7
-    - >-
-      BUILD_TYPE=centaurWdlUpgradeLocal
-      BUILD_MYSQL=5.7
     - >-
       BUILD_TYPE=checkPublish
     - >-
       BUILD_TYPE=horicromtalDeadlock
-    - >-
-      BUILD_TYPE=dockerScripts
     - >-
       BUILD_TYPE=sbt
       BUILD_SBT_INCLUDE=engine
@@ -92,8 +73,6 @@ env:
       BUILD_TYPE=dbms
     - >-
       BUILD_TYPE=singleWorkflowRunner
-    - >-
-      BUILD_TYPE=metadataComparisonPython
     - >-
       BUILD_TYPE=referenceDiskManifestBuilderApp
 script:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0c40f47b651..0084c05171b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,97 @@
 # Cromwell Change Log
 
+## 85 Release Notes
+
+### Migration of PKs to BIGINT
+
+The PK of below tables will be migrated from INT to BIGINT. Also, since `ROOT_WORKFLOW_ID` in `SUB_WORKFLOW_STORE_ENTRY` is a FK to `WORKFLOW_STORE_ENTRY_ID` in `WORKFLOW_STORE_ENTRY`
+it is also being migrated from INT to BIGINT.
+* DOCKER_HASH_STORE_ENTRY
+* WORKFLOW_STORE_ENTRY
+* SUB_WORKFLOW_STORE_ENTRY
+
+### Improvement to "retry with more memory" behavior
+
+Cromwell will now retry a task with more memory after it fails with return code 137, provided all
+the other requirements for retrying with more memory are met.
+
+### DRS Improvements
+
+#### Support for invoking `CromwellDRSLocalizer` with manifest file
+
+`CromwellDRSLocalizer` can now handle multiple file localizations in a single invocation. Users can provide a
+manifest file containing multiple (DRS id, local container path) pairs in CSV format, and they will be localized in
+sequence, with the program exiting if any fail.
+```
+java -jar /path/to/localizer.jar [options] -m /local/path/to/manifest/file.txt
+```
+
+The previous method of passing in a single DRS file and container destination using positional arguments is still
+supported.
+
+#### Improvement to DRS localization in GCP papiv2beta backend
+
+All DRS inputs to a task are now localized in a single PAPI action, which should improve speed and resolve
+failures observed when attempting to localize a large number of DRS files.
+
+
+### Allow list for HTTP WDL resolution
+
+Administrators can now configure Cromwell with an allow list that limits the domains from which WDLs can be resolved and imported.
+Default behavior is unchanged (Cromwell attempts to resolve WDL files from any URI). Example configuration:
+```
+languages {
+  WDL {
+    http-allow-list {
+      enabled: true
+      allowed-http-hosts: [
+        "my.wdl.repo.org",
+        "raw.githubusercontent.com"
+      ]
+    }
+  }
+}
+```
+
+### CWL implementation removed
+
+This release removes the `cwl` top-level artifact. Some nonfunctional references may remain, and will be addressed over time.
+
+For more information, see the [Cromwell 79 release notes](https://github.com/broadinstitute/cromwell/releases/tag/79).
+
+### TES Improvments
+
+* Tes system errors are are now reported in Cromwell execution logs when the TES backend returns a task error.
+
+* Cromwell now attempts to translate `disks` attributes [written for GCP](https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/#disks) into valid `disk` attributes for TES. For information on supported conversions, refer to the [TES documentation](https://cromwell.readthedocs.io/en/stable/backends/TES/).
+
+### Bug Fixes
+
+* Reference disks are only mounted if configured in the workflow options.
+
+* Recent docker images of Ubuntu use a new manifest format, ensure that these newer image versions can be pulled from Docker Registry without issue.
+
+* When converting ValueStore objects to strings for logging, we truncate long values to limit memory usage.
+
+
+### Security Patching
+
+Updates to dependencies to fix security vulnerabilities.
+
+## 84 Release Notes
+
+### CromIAM enabled user checks
+
+For Cromwell instances utilizing the optional CromIAM identity and access management component, the following endpoints now verify that the calling user is enabled before forwarding the request.
+* `/api/workflows/v1/backends`
+* `/api/womtool/v1/describe`
+
+This change makes the above endpoints consistent with the existing behavior of all the other endpoints in the `/api/` path of CromIAM.
+
+## 83 Release Notes
+
+* Changes the type of several primary key columns in call caching tables from int to bigint. The database migration may be lengthy if your database contains a large amount of call caching data.
+
 ## 82 Release Notes
 
  * Restored missing example configuration file
@@ -27,7 +119,7 @@ The BCS backend and OSS filesystem (both of which support Alibaba Cloud) have be
 Cromwell 80 no longer supports the wes2cromwell project within the Cromwell repository.
 
 In the previous release, 3 Wes2Cromwell endpoints in the Cromwell project were implemented and documented in the Swagger API. Three new endpoints,
-located within the wes2cromwell project, will also be moved, implemented, and documented within Cromwell. As a result of this, we can safely remove 
+located within the wes2cromwell project, will also be moved, implemented, and documented within Cromwell. As a result of this, we can safely remove
 and deprecate the wes2cromwell project from the repo.
 
 Previous endpoints:
@@ -111,11 +203,11 @@ Previously:
 
 ### New 'requestedWorkflowId' API Option
 
-Allows users to choose their own workflow IDs at workflow submission time. 
+Allows users to choose their own workflow IDs at workflow submission time.
 
 If supplied for single workflows, this value must be a JSON string containing a valid, and not already used, UUID. For batch submissions, this value must be a JSON array of valid UUIDs.
 
-If not supplied, the behavior is as today: Cromwell will generate a random workflow ID for every workflow submitted. 
+If not supplied, the behavior is as today: Cromwell will generate a random workflow ID for every workflow submitted.
 
 ### Bug Fixes
 
@@ -228,8 +320,8 @@ AccessURLs](https://ga4gh.github.io/data-repository-service-schemas/preview/rele
 
 ### No labels update for Archived workflows
 
-If **- and ONLY if -** you have metadata archiving turned on, then for a workflow whose metadata has been archived by Cromwell 
-according to the lifecycle policy, Cromwell will no longer add new labels or update existing labels for this workflow 
+If **- and ONLY if -** you have metadata archiving turned on, then for a workflow whose metadata has been archived by Cromwell
+according to the lifecycle policy, Cromwell will no longer add new labels or update existing labels for this workflow
 coming through PATCH `/labels` endpoint.
 
 ## 60 Release Notes
@@ -241,12 +333,12 @@ containerized using [AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/).
 
 ### Hybrid metadata storage ("carboniting") removed
 
-Carboniting functionality has been removed from Cromwell. 
+Carboniting functionality has been removed from Cromwell.
 There will be no effect for customers who store metadata permanently in the relational database (most common),
 and there will also be no effect for customers who use the in-memory database.
 
 Breaking change only for customers who explicitly enabled `carbonite-metadata-service` in their configuration to split
-metadata storage between a relational database and Google Cloud Storage. If you had previously enabled carboniting and 
+metadata storage between a relational database and Google Cloud Storage. If you had previously enabled carboniting and
 deletion, any workflows marked as `ArchivedAndPurged` in your database will no longer be accessible via the Cromwell metadata API.
 
 ## 59 Release Notes
@@ -273,9 +365,9 @@ rather than through a level of indirection to a manifest file stored in GCS. Mor
 ### Retry with More Memory as workflow option
 
 The experimental memory retry feature gains per-workflow customization and includes breaking changes:
-* The per-backend configuration key `<backend>.config.memory-retry.error-keys` has been removed and replaced 
+* The per-backend configuration key `<backend>.config.memory-retry.error-keys` has been removed and replaced
 with global key `system.memory-retry-error-keys`
-* The per-backend configuration key `<backend>.config.memory-retry.multiplier` has been replaced with **workflow option** 
+* The per-backend configuration key `<backend>.config.memory-retry.multiplier` has been replaced with **workflow option**
 `memory_retry_multiplier`
 
 More details can be found [here](https://cromwell.readthedocs.io/en/develop/wf_options/Overview.md#retry-with-more-memory-multiplier).
@@ -284,7 +376,7 @@ More details can be found [here](https://cromwell.readthedocs.io/en/develop/wf_o
 
 * Fixed a bug that caused Cromwell to mark workflows as failed after a single `500`, `503`, or `504` error from Google Cloud Storage.
   * Cromwell will now retry these errors as designed.
-  * The default retry count is `5` and may be customized with `system.io.number-of-attempts`. 
+  * The default retry count is `5` and may be customized with `system.io.number-of-attempts`.
 
 ## 55 Release Notes
 
@@ -294,7 +386,7 @@ Users with access to the new Mac hardware should review [important information p
 
 ### Bug Fixes
 
-* Fixed a bug that prevented `read_json()` from working with arrays and primitives. The function now works as expected for all valid JSON data inputs. 
+* Fixed a bug that prevented `read_json()` from working with arrays and primitives. The function now works as expected for all valid JSON data inputs.
 More information on JSON Type to WDL Type conversion can be found [here](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#mixed-read_jsonstringfile).
 
 * Now retries HTTP 408 responses as well as HTTP 429 responses during DOS/DRS resolution requests.
@@ -322,19 +414,19 @@ to the worker VM on the next attempt if the task is interrupted. More details [h
 ### Bug Fixes
 
 * Fixed a bug that prevented `write_json()` from working with arrays and primitives. The function now works as expected for `Boolean`, `String`, `Integer`, `Float`,
- `Pair[_, _]`, `Object`, `Map[_, _]` and `Array[_]` (including array of objects) type inputs. More information on WDL Type to JSON Type 
+ `Pair[_, _]`, `Object`, `Map[_, _]` and `Array[_]` (including array of objects) type inputs. More information on WDL Type to JSON Type
  conversion can be found [here](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#mixed-read_jsonstringfile).
 
 ### Spark backend support removal
 
-Spark backend was not widely used and it was decided to remove it from the codebase in order to narrow the scope of Cromwell code. 
+Spark backend was not widely used and it was decided to remove it from the codebase in order to narrow the scope of Cromwell code.
 
 ### Improved DRS Localizer logging
 
 Error logging while localizing a DRS URI should now be more clear especially when there is a Requester Pays bucket involved.
 
 ### Per-backend hog factors
-Cromwell now allows overriding system-level log factors on back-end level. First, Cromwell will try to use hog-factor 
+Cromwell now allows overriding system-level log factors on back-end level. First, Cromwell will try to use hog-factor
 defined in the backend config, and if it is not defined, it will default to using system-wide hog factor.
 ```conf
 backend {
@@ -402,16 +494,16 @@ https://cromwell.readthedocs.io/en/stable/tutorials/Containers/#singularity).
 
 ### Google library upgrade [(#5565)](https://github.com/broadinstitute/cromwell/pull/5565)
 
-All previous versions of Cromwell shipped with Google Cloud Storage (GCS) libraries that are now deprecated and will [stop working in August 2020](https://developers.googleblog.com/2018/03/discontinuing-support-for-json-rpc-and.html). This release adopts updated libraries to ensure uninterrupted operation. The only user action required is upgrading Cromwell.   
+All previous versions of Cromwell shipped with Google Cloud Storage (GCS) libraries that are now deprecated and will [stop working in August 2020](https://developers.googleblog.com/2018/03/discontinuing-support-for-json-rpc-and.html). This release adopts updated libraries to ensure uninterrupted operation. The only user action required is upgrading Cromwell.
 
 ### Bug fixes
 
 * Fixed a bug that required Cromwell to be restarted in order to pick up DNS changes.
     * By default, the JVM caches DNS records with a TTL of infinity.
-    * Cromwell now configures its JVM with a 3-minute TTL. This value can be customized by setting `system.dns-cache-ttl`.  
+    * Cromwell now configures its JVM with a 3-minute TTL. This value can be customized by setting `system.dns-cache-ttl`.
 * Clarified an error message that Cromwell emits when the compute backend terminates a job of its own volition (as opposed to termination in response to an abort request from Cromwell)
     * Previously, the error read `The job was aborted from outside Cromwell`
-    * The new error reads `The compute backend terminated the job. If this termination is unexpected, examine likely causes such as preemption, running out of disk or memory on the compute instance, or exceeding the backend's maximum job duration.` 
+    * The new error reads `The compute backend terminated the job. If this termination is unexpected, examine likely causes such as preemption, running out of disk or memory on the compute instance, or exceeding the backend's maximum job duration.`
 
 ## 51 Release Notes
 
@@ -422,8 +514,8 @@ https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching) for details
 
 ### Bug fixes
 
-* Fixed a bug where the `size(...)` function did not work correctly on files 
-  from a shared filesystem if `size(...)` was called in the input section on a 
+* Fixed a bug where the `size(...)` function did not work correctly on files
+  from a shared filesystem if `size(...)` was called in the input section on a
   relative path.
 + Fixed a bug where the `use_relative_output_paths` option would not preserve intermediate folders.
 
@@ -431,17 +523,17 @@ https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching) for details
 
 #### Call caching blacklisting improvements
 
-Cromwell previously supported blacklisting GCS buckets containing cache hits which could not be copied for permissions 
+Cromwell previously supported blacklisting GCS buckets containing cache hits which could not be copied for permissions
 reasons. Cromwell now adds support for blacklisting individual cache hits which could not be copied for any reason,
 as well as grouping blacklist caches according to a workflow option key. More information available in the [
-call caching documentation]( https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching). 
+call caching documentation]( https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching).
 
 #### new xxh64 and fingerprint strategies for call caching
 
-Existing call cache strategies `path` and `path+modtime` don't work when using docker on shared filesystems 
+Existing call cache strategies `path` and `path+modtime` don't work when using docker on shared filesystems
 (SFS backend, i.e. not in cloud storage). The `file` (md5sum) strategy works, but uses a lot of resources.
-Two faster strategies have been added for this use case: `xxh64` and 
-`fingerprint`. `xxh64` is a lightweight hashing algorithm, `fingerprint` is a strategy designed to be very 
+Two faster strategies have been added for this use case: `xxh64` and
+`fingerprint`. `xxh64` is a lightweight hashing algorithm, `fingerprint` is a strategy designed to be very
 lightweight. Read more about it in the [call caching documentation](
 https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching).
 
@@ -475,7 +567,7 @@ SELECT table_rows FROM INFORMATION_SCHEMA.TABLES WHERE TABLE_SCHEMA = 'cromwell'
 
 #### Execution Directory Layout (cache copies)
 
-When an attempt to copy a cache result is made, you'll now see a `cacheCopy` directory in the call root directory. 
+When an attempt to copy a cache result is made, you'll now see a `cacheCopy` directory in the call root directory.
 This prevents them clashing with the files staged to the same directory for attempt 1 if the cache copy fails (see also: Bug Fixes).
 
 The directory layout used to be:
@@ -512,7 +604,7 @@ but is now:
 
 #### Disable call-caching for tasks
 
-It is now possible to indicate in a workflow that a task should not be call-cached. See details 
+It is now possible to indicate in a workflow that a task should not be call-cached. See details
 [here](https://cromwell.readthedocs.io/en/stable/optimizations/VolatileTasks).
 
 #### Delete Intermediate Outputs on PapiV2
@@ -525,13 +617,13 @@ for more information.
 #### Metadata Archival Support
 
 Cromwell 49 now offers the option to archive metadata to GCS and remove the equivalent metadata from relational
-database storage. Please see 
-[the documentation](https://cromwell.readthedocs.io/en/stable/Configuring#hybrid-metadata-storage-classic-carbonite) for more details. 
+database storage. Please see
+[the documentation](https://cromwell.readthedocs.io/en/stable/Configuring#hybrid-metadata-storage-classic-carbonite) for more details.
 
 #### Adding support for Google Cloud Life Sciences v2beta
-Cromwell now supports running workflows using Google Cloud Life Sciences v2beta API in addition to Google Cloud Genomics v2alpha1. 
-More information about migration to the new API from v2alpha1 
-[here](https://cromwell.readthedocs.io/en/stable/backends/Google#migration-from-google-cloud-genomics-v2alpha1-to-google-cloud-life-sciences-v2beta). 
+Cromwell now supports running workflows using Google Cloud Life Sciences v2beta API in addition to Google Cloud Genomics v2alpha1.
+More information about migration to the new API from v2alpha1
+[here](https://cromwell.readthedocs.io/en/stable/backends/Google#migration-from-google-cloud-genomics-v2alpha1-to-google-cloud-life-sciences-v2beta).
 * **Note** Google Cloud Life Sciences is the new name for newer versions of Google Cloud Genomics.
 * **Note** Support for Google Cloud Genomics v2alpha1 will be removed in a future version of Cromwell. Advance notice will be provided.
 
@@ -539,23 +631,23 @@ More information about migration to the new API from v2alpha1
 
 #### Installation methods
 
-Links to the conda package and docker container are now available in 
+Links to the conda package and docker container are now available in
 [the install documentation](https://cromwell.readthedocs.io/en/stable/Getting/).
 
 
 ### Bug Fixes
 
-+ Fix a bug where zip files with directories could not be imported. 
-  For example a zip with `a.wdl` and `b.wdl` could be imported but one with `sub_workflows/a.wdl` 
++ Fix a bug where zip files with directories could not be imported.
+  For example a zip with `a.wdl` and `b.wdl` could be imported but one with `sub_workflows/a.wdl`
   and `imports/b.wdl` could not.
 + Fix a bug which sometimes allowed execution scripts copied by a failed cache-copy to be run instead
-  of the attempt-1 script for a live job execution. 
-  
+  of the attempt-1 script for a live job execution.
+
 ## 48 Release Notes
 
 ### Womtool Graph for WDL 1.0
 
-The `womtool graph` command now supports WDL 1.0 workflows. 
+The `womtool graph` command now supports WDL 1.0 workflows.
 * **Note:** Generated graphs - including in WDL draft 2 - may look slightly different than they did in version 47.
 
 ### Documentation
@@ -567,7 +659,7 @@ The `womtool graph` command now supports WDL 1.0 workflows.
 
 ### Retry with more memory on Papiv2 [(#5180)](https://github.com/broadinstitute/cromwell/pull/5180)
 
-Cromwell now allows user defined retries. With `memory-retry` config you can specify an array of strings which when encountered in the `stderr` 
+Cromwell now allows user defined retries. With `memory-retry` config you can specify an array of strings which when encountered in the `stderr`
 file by Cromwell, allows the task to be retried with multiplier factor mentioned in the config. More information [here](https://cromwell.readthedocs.io/en/stable/backends/Google/).
 
 ### GCS Parallel Composite Upload Support
@@ -601,7 +693,7 @@ PAPI error code 14. Task was preempted for the 2nd time.
 ```
 Cromwell 44 introduced special handling that detects both preemption indicators and re-runs the job consistent with the `preemptible` setting.
 
-Cromwell 46 enhances this handling in response to user reports of possible continued issues.   
+Cromwell 46 enhances this handling in response to user reports of possible continued issues.
 
 ## 45 Release Notes
 
@@ -619,7 +711,7 @@ More info [here](https://cromwell.readthedocs.io/en/stable/WOMtool/)
 ### BCS backend new Features support
 
 #### New docker registry
-Alibaba Cloud Container Registry is now supported for the `docker` runtime attribute, and the previous `dockerTag` 
+Alibaba Cloud Container Registry is now supported for the `docker` runtime attribute, and the previous `dockerTag`
 runtime attribute continues to be available for Alibaba Cloud OSS Registry.
 #### Call caching
 Cromwell now supports Call caching when using the BCS backend.
@@ -647,7 +739,7 @@ Cromwell's PAPI v2 backend will now handle this type of preemption.
 
 ### Virtual Private Cloud with Subnetworks
 
-Cromwell now allows PAPIV2 jobs to run on a specific subnetwork inside a private network by adding the subnetwork key 
+Cromwell now allows PAPIV2 jobs to run on a specific subnetwork inside a private network by adding the subnetwork key
 `subnetwork-label-key` inside `virtual-private-cloud` in backend configuration. More info [here](https://cromwell.readthedocs.io/en/stable/backends/Google/).
 
 ### Call caching database refactoring
@@ -655,7 +747,7 @@ Cromwell now allows PAPIV2 jobs to run on a specific subnetwork inside a private
 Cromwell's `CALL_CACHING_HASH_ENTRY` primary key has been refactored to use a `BIGINT` datatype in place of the previous
 `INT` datatype. Cromwell will not be usable during the time the Liquibase migration for this refactor is running.
 In the Google Cloud SQL with SSD environment this migration runs at a rate of approximately 100,000 `CALL_CACHING_HASH_ENTRY`
-rows per second. In deployments with millions or billions of `CALL_CACHING_HASH_ENTRY` rows the migration may require  
+rows per second. In deployments with millions or billions of `CALL_CACHING_HASH_ENTRY` rows the migration may require
 a significant amount of downtime so please plan accordingly. The following SQL could be used to estimate the number of
 rows in this table:
 
@@ -665,7 +757,7 @@ select max(CALL_CACHING_HASH_ENTRY_ID) from CALL_CACHING_HASH_ENTRY
 
 ### Stackdriver Instrumentation
 
-Cromwell now supports sending metrics to [Google's Stackdriver API](https://cloud.google.com/monitoring/api/v3/). 
+Cromwell now supports sending metrics to [Google's Stackdriver API](https://cloud.google.com/monitoring/api/v3/).
 Learn more on how to configure [here](https://cromwell.readthedocs.io/en/stable/developers/Instrumentation/).
 
 ### BigQuery in PAPI
@@ -682,7 +774,7 @@ which now has been updated to `services.Instrumentation.config`. More info on it
 
 #### cached-copy
 
-A new experimental feature, the `cached-copy` localization strategy is available for the shared filesystem. 
+A new experimental feature, the `cached-copy` localization strategy is available for the shared filesystem.
 More information can be found in the [documentation on localization](https://cromwell.readthedocs.io/en/stable/backends/HPC).
 
 #### Yaml node limits
@@ -716,7 +808,7 @@ Specifically, the new `validWorkflow` key indicates whether the workflow file is
 ### Configuration Changes
 
  *  Virtual private networks can now be configured. See the section below for details.
- 
+
 #### Batch Request Timeouts
 
 The timeout on Cromwell's requests to PAPIv2 can now be configured. See the sample PAPIv2.conf for more documentation:
@@ -725,7 +817,7 @@ The timeout on Cromwell's requests to PAPIv2 can now be configured. See the samp
 backend {
   providers {
     PAPIv2 {
-      config { 
+      config {
         batch-requests {
           timeouts {
             read = 10 seconds
@@ -802,14 +894,14 @@ This field is now accepted within WDL files as well as within the configuration
 
 #### Logging long running jobs
 
-All backends can now emit slow job warnings after a configurable time running. 
+All backends can now emit slow job warnings after a configurable time running.
 NB This example shows how to configure this setting for the PAPIv2 backend:
 ```conf
 # Emit a warning if jobs last longer than this amount of time. This might indicate that something got stuck.
 backend {
   providers {
     PAPIv2 {
-      config { 
+      config {
         slow-job-warning-time: 24 hours
       }
     }
@@ -824,7 +916,7 @@ backend {
 * The `gpuType` attribute is no longer validated against a whitelist at workflow submission time. Instead, validation now happens at runtime. This allows any valid accelerator to be used.
 * The `nvidiaDriverVersion` attribute is now available in WDL `runtime` sections. The default continues to be `390.46` which applies if and only if GPUs are being used.
 * A default `gpuType` ("nvidia-tesla-k80") will now be applied if `gpuCount` is specified but `gpuType` is not.
-* Similarly, a default `gpuCount` (1) will be applied if `gpuType` is specified but `cpuCount` is not. 
+* Similarly, a default `gpuCount` (1) will be applied if `gpuType` is specified but `cpuCount` is not.
 
 ### Bug fixes
 
@@ -865,7 +957,7 @@ services {
         class = "cromwell.services.healthmonitor.impl.standard.StandardHealthMonitorServiceActor"
     }
 }
-``` 
+```
 With this one:
 ```
 services {
@@ -876,7 +968,7 @@ services {
         }
     }
 }
-``` 
+```
 ###### From `WorkbenchHealthMonitorServiceActor`:
 Replace this stanza:
 ```
@@ -893,7 +985,7 @@ services {
         }
     }
 }
-``` 
+```
 With this one:
 ```
 services {
@@ -909,12 +1001,12 @@ services {
     }
   }
 }
-``` 
+```
 ### Workflow options changes
 
-A new workflow option is added. If the `final_workflow_outputs_dir` is set 
-`use_relative_output_paths` can be used. When set to `true` this will copy 
-all the outputs relative to their execution directory. 
+A new workflow option is added. If the `final_workflow_outputs_dir` is set
+`use_relative_output_paths` can be used. When set to `true` this will copy
+all the outputs relative to their execution directory.
 my_final_workflow_outputs_dir/~~MyWorkflow/af76876d8-6e8768fa/call-MyTask/execution/~~output_of_interest.
 More information can be found in [the workflow options documentation](https://cromwell.readthedocs.io/en/stable/wf_options/Overview/#output-copying).
 
@@ -944,10 +1036,10 @@ shutdown.
 
 ### Bug fixes
 
-#### Format fix for `write_map()` 
+#### Format fix for `write_map()`
 
 Fixed an issue that caused the `write_map()` function in Cromwell's WDL 1.0 implementation to produce output in the wrong format. Specifically, the output's rows and columns were swapped. WDL draft-2 was not affected.
-  
+
 Incorrect `write_map()` output in Cromwell 38 and earlier:
 ```
 key1    key2    key3
@@ -987,7 +1079,7 @@ available as `StandardHealthMonitorServiceActor`.
 ### Docker
 
 - Adds support for retrieving docker digests of asia.gcr.io images
-- Adds configuration settings for docker digest lookups. See the `docker` section of the `reference.conf` for more information 
+- Adds configuration settings for docker digest lookups. See the `docker` section of the `reference.conf` for more information
 - Attempt to automatically adjust the boot disk size on the Google Cloud Backend (version 2) if the size of the image is greater than the default disk size or the required disk size in the runtime attributes.
 Only works for registries that support the version 2 of the manifest schema (https://docs.docker.com/registry/spec/manifest-v2-2/)
 At this date (12/09/18) this includes GCR and Dockerhub.
@@ -1032,28 +1124,28 @@ Support `InputResourceRequirement` hint
 In cases where its not obvious why jobs are queued in Cromwell, you can enable logging for the Job Execution Token Dispenser, using
 the `system.hog-safety.token-log-interval-seconds` configuration value.
 
-The default, `0`, means that no logging will occur. 
+The default, `0`, means that no logging will occur.
 
 #### HTTP Filesystem
 
-- The HTTP filesystem is now enabled for engine use by default. To continue without an HTTP filesystem, you can add the 
+- The HTTP filesystem is now enabled for engine use by default. To continue without an HTTP filesystem, you can add the
 following content into the appropriate stanza of your configuration file:
 ```
 engine {
   filesystems {
-    http { 
-      enabled: false 
+    http {
+      enabled: false
     }
   }
 }
-``` 
+```
 - When the value `exit-code-timeout-seconds` is set, `check-alive` command is now only called once every timeout interval instead of each poll.
 
 ### Beta preview of new Womtool `/describe` endpoint
 
 This new endpoint brings the functionality of Womtool to the world of web services. Submit workflows for validation and receive a JSON description in response.
 
-The endpoint is still undergoing heavy development and should not be used in production. The final version will ship in a future release of Cromwell; watch this space.   
+The endpoint is still undergoing heavy development and should not be used in production. The final version will ship in a future release of Cromwell; watch this space.
 
 ### Bug fixes
 
@@ -1093,7 +1185,7 @@ Details [here](https://cromwell.readthedocs.io/en/develop/backends/HPC/#exit-cod
 
 Coalesce metadata requests to eliminate expensive and redundant queries and metadata construction.
 
-#### Eliminate redundant SFS logging and metadata 
+#### Eliminate redundant SFS logging and metadata
 
 Eliminate superfluous logging and metadata publishing in the shared filesystem backend on poll intervals where there was not a state change.
 
@@ -1106,7 +1198,7 @@ Previously US-EAST-1 was hardcoded in places.
 ### Submit workflow using URL
 
 Cromwell now allows for a user to submit the URL pointing to workflow file to run a workflow.
-More details on how to use it in: 
+More details on how to use it in:
 - `Server` mode can be found [here](https://cromwell.readthedocs.io/en/develop/api/RESTAPI/).
 - `Run` mode can be found [here](https://cromwell.readthedocs.io/en/develop/CommandLine/#run).
 
@@ -1132,7 +1224,7 @@ Cromwell now offers the ability to cache file hashes on a root workflow level ba
 
 ### Extra configuration options
 
-The value `dockerRoot` can now be set in a backend configuration. 
+The value `dockerRoot` can now be set in a backend configuration.
 This will set the execution folder in the container (default: `/cromwell-executions`).
 
 ### Bug Fixes
@@ -1238,7 +1330,7 @@ Cromwell now supports retrying failed tasks up to a specified count by declaring
 * Cromwell now publishes the labels as soon as the workflow is submitted (whether started or on hold). If the labels are invalid, the workflow will not be submitted and request will fail.
 
 ### Scala 2.11 Removed
-From version 32 onwards we will no longer be publishing build artifacts compatible with Scala 2.11. 
+From version 32 onwards we will no longer be publishing build artifacts compatible with Scala 2.11.
 
 * If you don't import the classes into your own scala project then this should have no impact on you.
 * If you **are** importing the classes into your own scala project, make sure you are using Scala 2.12.
@@ -1330,12 +1422,12 @@ Workflow metadata for jobs run on a Google Pipelines API backend will report the
 
 ## 31 Release Notes
 
-* **Cromwell server**  
-The Cromwell server source code is now located under `server/src`. `sbt assembly` will build the runnable Cromwell JAR in 
+* **Cromwell server**
+The Cromwell server source code is now located under `server/src`. `sbt assembly` will build the runnable Cromwell JAR in
 `server/target/scala-2.12/` with a name like `cromwell-<VERSION>.jar`.
 
 * **Robustness**
-    + The rate at which jobs are being started can now be controlled using the `system.job-rate-control` configuration stanza.  
+    + The rate at which jobs are being started can now be controlled using the `system.job-rate-control` configuration stanza.
     + A load controller service has been added to allow Cromwell to self-monitor and adjust its load accordingly.
 The load controller is currently a simple on/off switch controlling the job start rate. It gathers metrics from different parts of the system
 to inform its decision to stop the creation of jobs.
@@ -1343,7 +1435,7 @@ You can find relevant configuration in the `services.LoadController` section of
 as well as in the `load-control` section in `reference.conf`.
 The load level of the monitored sub-systems are instrumented and can be found under the `cromwell.load` statsD path.
     + The statsD metrics have been re-shuffled a bit. If you had a dashboard you might find that you need to update it.
-Changes include: 
+Changes include:
         + Removed artificially inserted "count" and "timing" the path
         + Added a `load` section
         + Metrics were prefixed twice with `cromwell` (`cromwell.cromwell.my_metric`), now they're only prefixed once
@@ -1352,8 +1444,8 @@ Changes include:
 
 * Added a configuration option under `docker.hash-lookup.enabled` to disable docker hash lookup.
  Disabling it will also disable call caching for jobs with floating docker tags.
- 
-* **API**    
+
+* **API**
     + Updated the `/query` response to include the total number of query results returned. See [here](http://cromwell.readthedocs.io/en/develop/api/RESTAPI/#workflowqueryresponse) for more information.
 
 ## 30.1 Release Notes
@@ -1368,14 +1460,14 @@ Changes include:
 
 ### Other changes
 
-* **New Cromwell documentation**  
+* **New Cromwell documentation**
 Our documentation has moved from our [README](https://github.com/broadinstitute/cromwell/blob/29_hotfix/README.md) to a new website: [Cromwell Documentation](http://cromwell.readthedocs.io/en/develop/). There are new [Tutorials](http://cromwell.readthedocs.io/en/develop/tutorials/FiveMinuteIntro/) and much of the documentation has been re-written. The source files are in the [/docs](https://github.com/broadinstitute/cromwell/tree/develop/docs) directory.
 
-* **API**  
+* **API**
     + Cromwell now supports input files in the yaml format (JSON format is still supported).
     + Added a [GET version for the `labels` endpoint](http://cromwell.readthedocs.io/en/develop/api/RESTAPI/#retrieves-the-current-labels-for-a-workflow) which will return current labels for a workflow.
 
-* **Database**  
+* **Database**
 You have the option of storing the metadata in a separate SQL database than the database containing the internal engine
 data. When switching connection information for an existing database containing historical data, the tables
 should be manually replicated from one database instance to another using the tools appropriate for your specific
@@ -1384,48 +1476,48 @@ and likely to change in the future. See the [Database Documentation](https://cro
 [cromwell.examples.conf](https://www.github.com/broadinstitute/cromwell/tree/develop/cromwell.example.backends/cromwell.examples.conf) for more
 information.
 
-* **StatsD**  
+* **StatsD**
 Added initial support for StatsD instrumentation. See the [Instrumentation Documentation](https://cromwell.readthedocs.io/en/develop/Instrumentation) for details on how to use it.
 
-* **User Service Account auth mode for Google**  
+* **User Service Account auth mode for Google**
 Added a new authentication mode for [Google Cloud Platform](https://cromwell.readthedocs.io/en/develop/backends/Google) which will allow a user to supply the JSON key file in their workflow options to allow for per-workflow authentication via service account. This is analogous to the previously existing refresh token authentication scheme. As with the refresh token scheme it is encouraged that the **user_service_account_json** workflow option field is added to the **encrypted-fields** list in the configuration.
 
-* **Bugfixes**  
+* **Bugfixes**
 Abort of Dockerized tasks on the Local backend should now work as expected. Cromwell uses `docker kill` to kill the Docker container.
 
 ## 29 Release Notes
 
 ### Breaking Changes
 
-* **Command line**  
+* **Command line**
 In preparation for supporting CWL scripts (yes, you read that right!), we have extensively revised the Command Line in Cromwell 29. For more details about the usage changes please see the [README](https://github.com/broadinstitute/cromwell#command-line-usage). And stay tuned to the [WDL/Cromwell blog](https://software.broadinstitute.org/wdl/blog) over the next couple of months for more news about CWL.
 
-* **Request timeouts**   
+* **Request timeouts**
 Cromwell now returns more specific `503 Service Unavailable` error codes on request timeouts, rather than the more generic `500 Internal Server Error`. The response for a request timeout will now be plain text, rather than a JSON format.
 
-* **Metadata endpoint**  
+* **Metadata endpoint**
 The response from the metadata endpoint can be quite large depending on your workflow. You can now opt-in to have Cromwell gzip your metadata file, in order to reduce file size, by sending the `Accept-Encoding: gzip` header. The default behavior now does not gzip encode responses.
 
-* **Engine endpoints**  
+* **Engine endpoints**
 Previously the engine endpoints were available under `/api/engine` but now the endpoints are under `/engine` so they don't require authentication. Workflow endpoints are still available under `/api/workflows`. We also deprecated the setting `api.routeUnwrapped` as a part of this internal consistency effort.
 
-* **Call caching diff**  
+* **Call caching diff**
 We updated the response format of the [callcaching/diff](https://github.com/broadinstitute/cromwell#get-apiworkflowsversioncallcachingdiff) endpoint.
 
 ### Other changes
 
-* **Cromwell server**  
+* **Cromwell server**
 When running in server mode, Cromwell now attempts to gracefully shutdown after receiving a `SIGINT` (`Ctrl-C`) or `SIGTERM` (`kill`) signal. This means that Cromwell waits for all pending database writes before exiting, as long as you include `application.conf` at the top of your config file. You can find detailed information about how to configure this feature in the [Cromwell Wiki](https://github.com/broadinstitute/cromwell/wiki/DevZone#graceful-server-shutdown).
 
-* **Concurrent jobs**  
+* **Concurrent jobs**
 You can now limit the number of concurrent jobs for any backend. Previously this was only possible in some backend implementations. Please see the [README](https://github.com/broadinstitute/cromwell#backend-job-limits) for details.
 
 ### WDL
 
-* **Optional WDL variables**  
+* **Optional WDL variables**
 Empty optional WDL values are now rendered as the `null` JSON value instead of the JSON string `"null"` in the metadata and output endpoints. You do not need to migrate previous workflows. Workflows run on Cromwell 28 and prior will still render empty values as `"null"`.
 
-* **Empty WDL variables**  
+* **Empty WDL variables**
 Cromwell now accepts `null` JSON values in the input file and coerces them as an empty WDL value. WDL variables must be declared optional in order to be supplied with a `null` JSON value.
 
 input.json
@@ -1474,8 +1566,8 @@ task writer {
 #### `ContinueWhilePossible`
 
 A workflow utilizing the WorkflowFailureMode Workflow Option `ContinueWhilePossible` will now successfully reach a terminal state once all runnable jobs have completed.
-#### `FailOnStderr` 
-When `FailOnStderr` is set to false, Cromwell no longer checks for the existence of a stderr file for that task. 
+#### `FailOnStderr`
+When `FailOnStderr` is set to false, Cromwell no longer checks for the existence of a stderr file for that task.
 
 ### WDL Functions
 
@@ -1491,7 +1583,7 @@ task foo {
     command { ... }
     runtime {
       docker: "..."
-      memory: ceil(size(in_file)) * 4 
+      memory: ceil(size(in_file)) * 4
     }
 }
 ```
@@ -1506,7 +1598,7 @@ If the hashes fail to be calculated, the reason is indicated in a `hashFailures`
 
 See the [README](https://github.com/broadinstitute/cromwell#get-apiworkflowsversionidmetadata) for an example metadata response.
 
-* New endpoint returning the hash differential for 2 calls. 
+* New endpoint returning the hash differential for 2 calls.
 
 `GET /api/workflows/:version/callcaching/diff`
 
@@ -1535,7 +1627,7 @@ A second value is allowed, `reference`, that will instead point to the original
 filesystems {
   gcs {
     auth = "application-default"
-    
+
     caching {
       duplication-strategy = "reference"
     }
@@ -1563,7 +1655,7 @@ than the previous default.
  The migration will only be executed on MySQL. Other databases will lose their previous cached jobs.
  In order to run properly on MySQL, **the following flag needs to be adjusted**: https://dev.mysql.com/doc/refman/5.5/en/server-system-variables.html#sysvar_group_concat_max_len
  The following query will give you a minimum to set the group_concat_max_len value to:
- 
+
  ```sql
 SELECT MAX(aggregated) as group_concat_max_len FROM
       (
@@ -1574,15 +1666,15 @@ SELECT MAX(aggregated) as group_concat_max_len FROM
  ```
 
  Here is the SQL command to run to set the group_concat_max_len flag to the proper value:
- 
+
  ```sql
 SET GLOBAL group_concat_max_len = value
  ```
- 
+
  Where `value` is replaced with the value you want to set it to.
- 
+
  Note that the migration will fail if the flag is not set properly.
- 
+
 ### Breaking Changes
 
 * The update to Slick 3.2 requires a database stanza to
@@ -1630,7 +1722,7 @@ run the call:
 
 ### Docker
 
-* The Docker section of the configuration has been slightly reworked 
+* The Docker section of the configuration has been slightly reworked
 An option to specify how a Docker hash should be looked up has been added. Two methods are available.
     "local" will try to look for the image on the machine where cromwell is running. If it can't be found, Cromwell will try to `pull` the image and use the hash from the retrieved image.
     "remote" will try to look up the image hash directly on the remote repository where the image is located (Docker Hub and GCR are supported)
@@ -1694,14 +1786,14 @@ failures: [{
 
 * Added a configuration option under `system.io` to throttle the number of I/O queries that Cromwell makes, as well as configure retry parameters.
  This is mostly useful for the JES backend and should be updated to match the GCS quota available for the project.
- 
+
 ```
 system.io {
   # Global Throttling - This is mostly useful for GCS and can be adjusted to match
   # the quota availble on the GCS API
   number-of-requests = 100000
   per = 100 seconds
-  
+
   # Number of times an I/O operation should be attempted before giving up and failing it.
   number-of-attempts = 5
 }
@@ -1725,7 +1817,7 @@ system.io {
 
 ### Config Changes
 
-* Added a field `insert-batch-size` to the `database` stanza which defines how many values from a batch insert will be processed at a time. This value defaults to 2000. 
+* Added a field `insert-batch-size` to the `database` stanza which defines how many values from a batch insert will be processed at a time. This value defaults to 2000.
 * Moved the config value `services.MetadataService.metadata-summary-refresh-interval` to `services.MetadataService.config.metadata-summary-refresh-interval`
 * Added ability to override the default zone(s) used by JES via the config structure by setting `genomics.default-zones` in the JES configuration
 * The cromwell server TCP binding timeout is now configurable via the config key `webservice.binding-timeout`, defaulted
@@ -1748,15 +1840,15 @@ system.io {
 * In some cases the SFS backend, used for Local, SGE, etc., coerced `WdlFile` to `WdlString` by using `.toUri`. This
 resulted in strings prepended with `file:///path/to/file`. Now absolute file paths will not contain the uri scheme.
 * Launch jobs on servers that support the GA4GH Task Execution Schema using the TES backend.
-* **Call caching: Cromwell will no longer try to use the cache for WDL tasks that contain a floating docker tag.** 
+* **Call caching: Cromwell will no longer try to use the cache for WDL tasks that contain a floating docker tag.**
   Call caching will still behave the same for tasks having a docker image with a specific hash.
-  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details. 
+  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details.
 * Added docker hash lookup. Cromwell will try to lookup the hash for a docker image with a floating tag, and use that hash when executing the job.
   This will be reflected in the metadata where the docker runtime attribute will contains the hash that was used.
   If Cromwell is unable to lookup the docker hash, the job will be run with the original user defined floating tag.
   Cromwell is currently able to lookup public and private docker hashes for images on Docker Hub and Google Container Engine for job running on the JES backend.
   For other backends, cromwell is able to lookup public docker hashes for Docker Hub and Google Container Engine.
-  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details. 
+  See https://github.com/broadinstitute/cromwell#call-caching-docker-tags for more details.
 
 ### Database schema changes
 * Added CUSTOM_LABELS as a field of WORKFLOW_STORE_ENTRY, to store workflow store entries.
@@ -1775,7 +1867,7 @@ resulted in strings prepended with `file:///path/to/file`. Now absolute file pat
 * Timing diagrams and metadata now receive more fine grained workflow states between submission and Running.
 * Support for the Pair WDL type (e.g. `Pair[Int, File] floo = (3, "gs://blar/blaz/qlux.txt")`)
 * Added support for new WDL functions:
-  * `zip: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - align items in the two arrays by index and return them as WDL pairs 
+  * `zip: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - align items in the two arrays by index and return them as WDL pairs
   * `cross: (Array[X], Array[Y]) => Array[Pair[X, Y]]` - create every possible pair from the two input arrays and return them all as WDL pairs
   * `transpose: (Array[Array[X]]) => Array[Array[X]]` compute the matrix transpose for a 2D array. Assumes each inner array has the same length.
 * By default, `system.abort-jobs-on-terminate` is false when running `java -jar cromwell.jar server`, and true when running `java -jar cromwell.jar run <wdl> <inputs>`.
@@ -1791,9 +1883,9 @@ resulted in strings prepended with `file:///path/to/file`. Now absolute file pat
 * Fix bugs related to the behavior of Cromwell in Single Workflow Runner Mode. Cromwell will now exit once a workflow completes in Single Workflow Runner Mode. Additionally, when restarting Cromwell in Single Workflow Runner Mode, Cromwell will no longer restart incomplete workflows from a previous session.
 
 ### Annex A - Workflow outputs
-    
+
 The WDL specification has changed regarding [workflow outputs](https://github.com/openwdl/wdl/blob/master/versions/draft-2/SPEC.md#outputs) to accommodate sub workflows.
-This change is backward compatible in terms of runnable WDLs (WDL files using the deprecated workflow outputs syntax will still run the same). 
+This change is backward compatible in terms of runnable WDLs (WDL files using the deprecated workflow outputs syntax will still run the same).
 The only visible change lies in the metadata (as well as the console output in single workflow mode, when workflow outputs are printed out at the end of a successful workflow).
 
 TL;DR Unless you are parsing or manipulating the "key" by which workflow outputs are referenced in the metadata (and/or the console output for single workflow mode), you can skip the following explanation.
@@ -1846,7 +1938,7 @@ task t {
 
 The new syntax allows for type checking of the outputs as well as expressions. It also allows for explicitly naming to the outputs.
 The old syntax doesn't give the ability to name workflow outputs. For consistency reasons, Cromwell will generate a "new syntax" workflow output for each task output, and name them.
-Their name will be generated using their FQN, which would give 
+Their name will be generated using their FQN, which would give
 
 ```
 output {
@@ -1854,8 +1946,8 @@ output {
    String w.t.out2 = t.out2
 }
 ```
-        
-However as the FQN separator is `.`, the name itself cannot contain any `.`. 
+
+However as the FQN separator is `.`, the name itself cannot contain any `.`.
 For that reason, `.` are replaced with `_` :
 
 *Old syntax expanded to new syntax*
@@ -1866,16 +1958,16 @@ output {
 }
 ```
 
-The consequence is that the workflow outputs section of the metadata for `old_syntax` would previously look like 
- 
+The consequence is that the workflow outputs section of the metadata for `old_syntax` would previously look like
+
  ```
     outputs {
         "w.t.out1": "hello",
         "w.t.out2": "hello"
     }
  ```
- 
-but it will now look like 
+
+but it will now look like
 
 ```
     outputs {
diff --git a/CromIAM/src/main/resources/application.conf b/CromIAM/src/main/resources/application.conf
index c809d0daafb..ff1006ab91b 100644
--- a/CromIAM/src/main/resources/application.conf
+++ b/CromIAM/src/main/resources/application.conf
@@ -24,7 +24,7 @@ swagger_oauth {
 
 akka {
   log-dead-letters = "off"
-  loggers = ["akka.event.slf4j.Slf4jLogger"]
+  loggers = ["cromwell.core.logging.EnhancedSlf4jLogger"]
 
   http {
     server {
diff --git a/CromIAM/src/main/resources/logback.xml b/CromIAM/src/main/resources/logback.xml
index 030868d3259..e9e2b753466 100644
--- a/CromIAM/src/main/resources/logback.xml
+++ b/CromIAM/src/main/resources/logback.xml
@@ -1,5 +1,15 @@
 <configuration>
 
+    <!-- Enhanced thread and date reporting. -->
+    <conversionRule
+            conversionWord="et"
+            converterClass="cromwell.core.logging.EnhancedThreadConverter"
+    />
+    <conversionRule
+            conversionWord="ed"
+            converterClass="cromwell.core.logging.EnhancedDateConverter"
+    />
+
     <!-- default properties for FILEROLLER need to be set upfront -->
 
     <if condition='property("FILEROLLER_DIR").equals("")'>
@@ -18,7 +28,7 @@
         <then>
             <appender name="STANDARD_APPENDER" class="ch.qos.logback.core.ConsoleAppender">
                 <encoder>
-                    <pattern>%date %X{sourceThread} %-5level - %msg%n</pattern>
+                    <pattern>%ed{yyyy-MM-dd HH:mm:ss,SSS} %et %-5level - %msg%n</pattern>
                 </encoder>
             </appender>
         </then>
@@ -68,7 +78,7 @@
 
                 </rollingPolicy>
                 <encoder>
-                    <pattern>%d{yyyy-MM-dd HH:mm:ss,SSS} [%thread] %-5level %logger{35} - %msg%n</pattern>
+                    <pattern>%ed{yyyy-MM-dd HH:mm:ss,SSS} [%et] %-5level %logger{35} - %msg%n</pattern>
                 </encoder>
             </appender>
         </then>
diff --git a/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala b/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
index 63f48073146..65b164f00f6 100644
--- a/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
+++ b/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
@@ -20,6 +20,7 @@ trait CromIamInstrumentation extends CromwellInstrumentation {
 
   val samPrefix: NonEmptyList[String] = NonEmptyList.one("sam")
   val getWhitelistPrefix = NonEmptyList.one("get-whitelist")
+  val getUserEnabledPrefix = NonEmptyList.one("get-user-enabled")
   val userCollectionPrefix = NonEmptyList.one("user-collection")
   val authCollectionPrefix = NonEmptyList.one("auth-collection")
   val registerCollectionPrefix = NonEmptyList.one("register-collection")
diff --git a/CromIAM/src/main/scala/cromiam/sam/SamClient.scala b/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
index f289251a2fb..d6a315f8241 100644
--- a/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
+++ b/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
@@ -18,6 +18,7 @@ import cromiam.sam.SamResourceJsonSupport._
 import cromiam.server.status.StatusCheckedSubsystem
 import cromwell.api.model._
 import mouse.boolean._
+import spray.json.RootJsonFormat
 
 import scala.concurrent.ExecutionContextExecutor
 
@@ -73,6 +74,33 @@ class SamClient(scheme: String,
     } yield whitelisted
   }
 
+  def isUserEnabledSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+    val request = HttpRequest(
+      method = HttpMethods.GET,
+      uri = samUserStatusUri,
+      headers = List[HttpHeader](user.authorization)
+    )
+
+    for {
+      response <- instrumentRequest(
+        () => Http().singleRequest(request).asFailureResponseOrT,
+        cromIamRequest,
+        instrumentationPrefixForSam(getUserEnabledPrefix)
+      )
+      userEnabled <- response.status match {
+        case StatusCodes.OK =>
+          val unmarshal: IO[UserStatusInfo] = IO.fromFuture(IO(Unmarshal(response.entity).to[UserStatusInfo]))
+          FailureResponseOrT.right[HttpResponse](unmarshal).map { userInfo =>
+            if (!userInfo.enabled) log.info("Access denied for user {}", user.userId)
+            userInfo.enabled
+          }
+        case _ =>
+          log.error("Could not verify access with Sam for user {}, error was {} {}", user.userId, response.status, response.toString().take(100))
+          FailureResponseOrT.pure[IO, HttpResponse](false)
+      }
+    } yield userEnabled
+  }
+
   def collectionsForUser(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[List[Collection]] = {
     val request = HttpRequest(method = HttpMethods.GET, uri = samBaseCollectionUri, headers = List[HttpHeader](user.authorization))
 
@@ -170,6 +198,7 @@ class SamClient(scheme: String,
   private lazy val samBaseResourceUri = s"$samBaseUri/api/resource"
   private lazy val samBaseCollectionUri = s"$samBaseResourceUri/workflow-collection"
   private lazy val samSubmitWhitelistUri = s"$samBaseResourceUri/caas/submit/action/get_whitelist"
+  private lazy val samUserStatusUri = s"$samBaseUri/register/user/v2/self/info"
 
 }
 
@@ -188,4 +217,8 @@ object SamClient {
 
   def SamRegisterCollectionExceptionResp(statusCode: StatusCode) = HttpResponse(status = statusCode, entity = SamRegisterCollectionException(statusCode).getMessage)
 
+  case class UserStatusInfo(adminEnabled: Boolean, enabled: Boolean, userEmail: String, userSubjectId: String)
+
+  implicit val UserStatusInfoFormat: RootJsonFormat[UserStatusInfo] = jsonFormat4(UserStatusInfo)
+
 }
diff --git a/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala b/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
index 63694599476..7a16e5ea797 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
@@ -81,7 +81,7 @@ trait CromIamApiService extends RequestSupport
 
   def abortRoute: Route = path("api" / "workflows" / Segment / Segment / Abort) { (_, workflowId) =>
     post {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserWorkflowAction(user, workflowId, Abort)
         complete {
           authorizeAbortThenForwardToCromwell(user, workflowId, req).asHttpResponse
@@ -93,7 +93,7 @@ trait CromIamApiService extends RequestSupport
   //noinspection MutatorLikeMethodIsParameterless
   def releaseHoldRoute: Route =  path("api" / "workflows" / Segment / Segment / ReleaseHold) { (_, workflowId) =>
     post {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserWorkflowAction(user, workflowId, ReleaseHold)
         complete {
           authorizeUpdateThenForwardToCromwell(user, workflowId, req).asHttpResponse
@@ -112,7 +112,7 @@ trait CromIamApiService extends RequestSupport
   def labelPatchRoute: Route = {
     path("api" / "workflows" / Segment / Segment / Labels) { (_, workflowId) =>
       patch {
-        extractUserAndRequest { (user, req) =>
+        extractUserAndStrictRequest { (user, req) =>
           entity(as[String]) { labels =>
             logUserWorkflowAction(user, workflowId, Labels)
             validateLabels(Option(labels)) { _ => // Not using the labels, just using this to verify they didn't specify labels we don't want them to
@@ -130,7 +130,7 @@ trait CromIamApiService extends RequestSupport
 
   def callCacheDiffRoute: Route = path("api" / "workflows" / Segment / "callcaching" / "diff") { _ =>
     get {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserAction(user, "call caching diff")
         parameterSeq { parameters =>
           val paramMap = parameters.toMap
@@ -150,11 +150,9 @@ trait CromIamApiService extends RequestSupport
     */
   private def workflowGetRoute(urlSuffix: String): Route = path("api" / "workflows" / Segment / urlSuffix) { _ =>
     get {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserAction(user, urlSuffix)
-        complete {
-          cromwellClient.forwardToCromwell(req).asHttpResponse
-        }
+        forwardIfUserEnabled(user, req, cromwellClient, samClient)
       }
     }
   }
@@ -166,7 +164,7 @@ trait CromIamApiService extends RequestSupport
 
   private def workflowRoute(urlSuffix: String, method: Directive0): Route = path("api" / "workflows" / Segment / Segment / urlSuffix) { (_, workflowId) =>
     method {
-      extractUserAndRequest { (user, req) =>
+      extractUserAndStrictRequest { (user, req) =>
         logUserWorkflowAction(user, workflowId, urlSuffix)
         complete {
           authorizeReadThenForwardToCromwell(user, List(workflowId), req).asHttpResponse
diff --git a/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala b/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
index cddabe74a57..e9397605c6a 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
@@ -55,7 +55,7 @@ trait QuerySupport extends RequestSupport {
     * directive
     */
   private def preprocessQuery: Directive[(User, List[Collection], HttpRequest)] = {
-    extractUserAndRequest tflatMap { case (user, cromIamRequest) =>
+    extractUserAndStrictRequest tflatMap { case (user, cromIamRequest) =>
       log.info("Received query " + cromIamRequest.method.value + " request for user " + user.userId)
 
       onComplete(samClient.collectionsForUser(user, cromIamRequest).value.unsafeToFuture()) flatMap {
diff --git a/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
index 12b231485f7..c9b6a196368 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
@@ -6,6 +6,13 @@ import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server._
 import cromiam.auth.User
 import org.broadinstitute.dsde.workbench.model.WorkbenchUserId
+import akka.http.scaladsl.model.HttpResponse
+import akka.http.scaladsl.server.Directives.{authorize, complete, onComplete}
+import akka.http.scaladsl.server.Route
+import cromiam.cromwell.CromwellClient
+import cromiam.sam.SamClient
+
+import scala.util.{Failure, Success}
 
 trait RequestSupport {
   def extractStrictRequest: Directive1[HttpRequest] = {
@@ -26,10 +33,27 @@ trait RequestSupport {
     }
   }
 
-  def extractUserAndRequest: Directive[(User, HttpRequest)] = {
+  def extractUserAndStrictRequest: Directive[(User, HttpRequest)] = {
     for {
       user <- extractUser
       request <- extractStrictRequest
     } yield (user, request)
   }
+
+  def forwardIfUserEnabled(user: User, req: HttpRequest, cromwellClient: CromwellClient, samClient: SamClient): Route = {
+    import cromwell.api.model.EnhancedFailureResponseOrHttpResponseT
+
+    onComplete(samClient.isUserEnabledSam(user, req).value.unsafeToFuture()) {
+      case Success(Left(httpResponse: HttpResponse)) => complete(httpResponse)
+      case Success(Right(isEnabled: Boolean)) =>
+        authorize(isEnabled) {
+          complete {
+            cromwellClient.forwardToCromwell(req).asHttpResponse
+          }
+        }
+      case Failure(e) =>
+        val message = s"Unable to look up enablement status for user ${user.userId}: ${e.getMessage}. Please try again later."
+        throw new RuntimeException(message, e)
+    }
+  }
 }
diff --git a/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
index c1f5477475b..52a05d1cdc7 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
@@ -31,7 +31,7 @@ trait SubmissionSupport extends RequestSupport {
   // FIXME - getting pathPrefix to shrink this keeps hosing up, there's gotta be some way to do this
   def submitRoute: Route = (path("api" / "workflows" / Segment) | path("api" / "workflows" / Segment / "batch")) { _ =>
     post {
-      extractUserAndRequest { (user, request) =>
+      extractUserAndStrictRequest { (user, request) =>
         log.info("Received submission request from user " + user.userId)
         onComplete(samClient.isSubmitWhitelisted(user, request).value.unsafeToFuture()) {
           case Success(Left(httpResponse)) => complete(httpResponse)
diff --git a/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala
index 671d4a76543..a6098b1fae0 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/WomtoolRouteSupport.scala
@@ -2,20 +2,18 @@ package cromiam.webservice
 
 import akka.http.scaladsl.server.Directives._
 import cromiam.cromwell.CromwellClient
-import cromwell.api.model._
+import cromiam.sam.SamClient
 
 trait WomtoolRouteSupport extends RequestSupport {
   // When this trait is mixed into `CromIamApiService` the value of `cromwellClient` is the reader (non-abort) address
   val cromwellClient: CromwellClient
+  val samClient: SamClient
 
   val womtoolRoutes =
     path("api" / "womtool" / Segment / "describe") { _ =>
       post {
-        extractStrictRequest { req =>
-          complete {
-            // This endpoint requires authn which it gets for free from the proxy, does not care about authz
-            cromwellClient.forwardToCromwell(req).asHttpResponse
-          }
+        extractUserAndStrictRequest { (user, req) =>
+          forwardIfUserEnabled(user, req, cromwellClient, samClient)
         }
       }
     }
diff --git a/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
index 5ad6a976204..89945c5bfcb 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
@@ -4,7 +4,8 @@ import akka.event.NoLogging
 import akka.http.scaladsl.model.StatusCodes._
 import akka.http.scaladsl.model.headers.{Authorization, OAuth2BearerToken, RawHeader}
 import akka.http.scaladsl.model.{ContentTypes, HttpEntity, HttpHeader}
-import akka.http.scaladsl.server.MissingHeaderRejection
+import akka.http.scaladsl.server.Route.seal
+import akka.http.scaladsl.server.{AuthorizationFailedRejection, MissingHeaderRejection}
 import akka.http.scaladsl.testkit.ScalatestRouteTest
 import com.typesafe.config.Config
 import common.assertion.CromwellTimeoutSpec
@@ -303,12 +304,45 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-  it should "reject request if it doesn't contain OIDC_CLAIM_user_id in header" in {
+  it should "reject request if it doesn't contain OIDC_CLAIM_user_id or token" in {
     Get(s"/api/workflows/$version/backends") ~> allRoutes ~> check {
       rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
     }
   }
 
+  it should "return 403 when we request with a disabled user" in {
+    Get(
+      s"/api/workflows/$version/backends"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")), RawHeader("OIDC_CLAIM_user_id", "disabled@example.com"))
+    ) ~> allRoutes ~> check {
+      rejection shouldEqual AuthorizationFailedRejection
+    }
+  }
+
+  it should "reject request if it contains a token and no OIDC_CLAIM_user_id in header" in {
+    Get(
+      s"/api/workflows/$version/backends"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")))
+    ) ~> allRoutes ~> check {
+      rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
+    }
+  }
+
+  it should "return 404 when no auth token provided" in {
+    Get(
+      s"/api/workflows/$version/backends"
+    ).withHeaders(
+      List(RawHeader("OIDC_CLAIM_user_id", "enabled@example.com"))
+      // "[An] explicit call on the Route.seal method is needed in test code, but in your application code it is not necessary."
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/testkit.html#testing-sealed-routes
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/routes.html#sealing-a-route
+    ) ~> seal(allRoutes) ~> check {
+      responseAs[String] shouldEqual "The requested resource could not be found."
+      status shouldBe NotFound
+    }
+  }
 
   behavior of "ReleaseHold endpoint"
   it should "return 200 for authorized user who has collection associated with root workflow" in {
diff --git a/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala b/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
index 3fb9689e5cc..59e75347159 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
@@ -141,6 +141,15 @@ class MockSamClient(checkSubmitWhitelist: Boolean = true)
     FailureResponseOrT.pure(!user.userId.value.equalsIgnoreCase(NotWhitelistedUser))
   }
 
+  override def isUserEnabledSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+    if (user.userId.value == "enabled@example.com" || user.userId.value == MockSamClient.AuthorizedUserCollectionStr)
+      FailureResponseOrT.pure(true)
+    else if (user.userId.value == "disabled@example.com")
+      FailureResponseOrT.pure(false)
+    else
+      throw new Exception("Misconfigured test")
+  }
+
   override def requestAuth(authorizationRequest: CollectionAuthorizationRequest,
                            cromIamRequest: HttpRequest): FailureResponseOrT[Unit] = {
     authorizationRequest.user.userId.value match {
diff --git a/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
index c0277fd92c0..838a523f4eb 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
@@ -12,7 +12,7 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 import org.yaml.snakeyaml.constructor.Constructor
 import org.yaml.snakeyaml.error.YAMLException
 import org.yaml.snakeyaml.nodes.MappingNode
-import org.yaml.snakeyaml.{Yaml => SnakeYaml}
+import org.yaml.snakeyaml.{LoaderOptions, Yaml => SnakeYaml}
 
 import scala.jdk.CollectionConverters._
 
@@ -21,6 +21,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
   with TableDrivenPropertyChecks {
   def actorRefFactory = system
   override def oauthConfig: SwaggerOauthConfig = SwaggerOauthConfig("clientId", "realm", "appName")
+  val yamlLoaderOptions = new LoaderOptions
 
   behavior of "SwaggerService"
 
@@ -32,7 +33,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
         contentType should be(ContentTypes.`application/octet-stream`)
 
         val body = responseAs[String]
-        val yaml = new SnakeYaml(new UniqueKeyConstructor()).loadAs(body, classOf[java.util.Map[String, AnyRef]])
+        val yaml = new SnakeYaml(new UniqueKeyConstructor(new LoaderOptions)).loadAs(body, classOf[java.util.Map[String, AnyRef]])
 
         yaml.get("swagger") should be("2.0")
       }
@@ -109,7 +110,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
   * Adapted from:
   * https://bitbucket.org/asomov/snakeyaml/src/e9cd9f5e8d76c61eb983e29b3dc039c1fac9c393/src/test/java/org/yaml/snakeyaml/issues/issue139/UniqueKeyTest.java?fileviewer=file-view-default#UniqueKeyTest.java-43:62
   */
-class UniqueKeyConstructor extends Constructor {
+class UniqueKeyConstructor(val loaderOptions: LoaderOptions) extends Constructor(loaderOptions) {
 
   import java.util.{Map => JMap}
 
diff --git a/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
index 7ba1c495f23..785c887c374 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
@@ -2,6 +2,9 @@ package cromiam.webservice
 
 import akka.http.scaladsl.model.ContentTypes
 import akka.http.scaladsl.model.StatusCodes._
+import akka.http.scaladsl.model.headers.{Authorization, OAuth2BearerToken, RawHeader}
+import akka.http.scaladsl.server.Route.seal
+import akka.http.scaladsl.server.{AuthorizationFailedRejection, MissingHeaderRejection}
 import akka.http.scaladsl.testkit.ScalatestRouteTest
 import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
@@ -11,15 +14,64 @@ import org.scalatest.matchers.should.Matchers
 class WomtoolRouteSupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with WomtoolRouteSupport with ScalatestRouteTest {
 
   override lazy val cromwellClient = new MockCromwellClient()
+  override lazy val samClient = new MockSamClient()
 
   behavior of "Womtool endpoint routes"
 
   it should "return 200 when we request to the right path" in {
-    Post(s"/api/womtool/v1/describe") ~> womtoolRoutes ~> check {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")), RawHeader("OIDC_CLAIM_user_id", "enabled@example.com"))
+    ) ~> womtoolRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Hey there, workflow describer"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
+  it should "return 403 when we request with a disabled user" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")), RawHeader("OIDC_CLAIM_user_id", "disabled@example.com"))
+    ) ~> womtoolRoutes ~> check {
+      rejection shouldEqual AuthorizationFailedRejection
+    }
+  }
+
+  it should "bail out with no user ID" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(Authorization(OAuth2BearerToken("my-token")))
+    ) ~> womtoolRoutes ~> check {
+      rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
+    }
+  }
+
+  it should "return 404 when no auth token provided" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List(RawHeader("OIDC_CLAIM_user_id", "enabled@example.com"))
+      // "[An] explicit call on the Route.seal method is needed in test code, but in your application code it is not necessary."
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/testkit.html#testing-sealed-routes
+      // https://doc.akka.io/docs/akka-http/current/routing-dsl/routes.html#sealing-a-route
+    ) ~> seal(womtoolRoutes) ~> check {
+      responseAs[String] shouldEqual "The requested resource could not be found."
+      status shouldBe NotFound
+    }
+  }
+
+  it should "bail out with no headers" in {
+    Post(
+      s"/api/womtool/v1/describe"
+    ).withHeaders(
+      List.empty
+    ) ~> womtoolRoutes ~> check {
+      rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
+    }
+  }
+
 }
diff --git a/CromwellRefdiskManifestCreator/pom.xml b/CromwellRefdiskManifestCreator/pom.xml
index 987aad421be..829f64b5fd3 100644
--- a/CromwellRefdiskManifestCreator/pom.xml
+++ b/CromwellRefdiskManifestCreator/pom.xml
@@ -48,7 +48,7 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>2.13.2.2</version>
+            <version>2.13.4.1</version>
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 5c415cc3c50..02c2a2577a2 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -244,6 +244,8 @@ trait StandardAsyncExecutionActor
     }
   }
 
+  lazy val memoryRetryRequested: Boolean = memoryRetryFactor.nonEmpty
+
   /**
     * Returns the shell scripting for finding all files listed within a directory.
     *
@@ -1265,8 +1267,8 @@ trait StandardAsyncExecutionActor
     */
   def handleExecutionResult(status: StandardAsyncRunState,
                             oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
-    
-    // get the memory retry code.
+
+    // Returns true if the task has written an RC file that indicates OOM, false otherwise
     def memoryRetryRC: Future[Boolean] = {
       // convert int to boolean
       def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
@@ -1329,11 +1331,11 @@ trait StandardAsyncExecutionActor
       // Only check stderr size if we need to, otherwise this results in a lot of unnecessary I/O that
       // may fail due to race conditions on quickly-executing jobs.
       stderrSize <- if (failOnStdErr) asyncIo.sizeAsync(stderr) else Future.successful(0L)
-      retryWithMoreMemory <- memoryRetryRC
-    } yield (stderrSize, returnCodeAsString, retryWithMoreMemory)
+      outOfMemoryDetected <- memoryRetryRC
+    } yield (stderrSize, returnCodeAsString, outOfMemoryDetected)
 
     stderrSizeAndReturnCodeAndMemoryRetry flatMap {
-      case (stderrSize, returnCodeAsString, retryWithMoreMemory) =>
+      case (stderrSize, returnCodeAsString, outOfMemoryDetected) =>
         val tryReturnCodeAsInt = Try(returnCodeAsString.trim.toInt)
 
         if (isDone(status)) {
@@ -1341,13 +1343,15 @@ trait StandardAsyncExecutionActor
             case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
-            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
-              Future.successful(AbortedExecutionHandle)
             case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
               handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
-            case Success(returnCodeAsInt) if retryWithMoreMemory  =>
+            // It's important that we check retryWithMoreMemory case before isAbort. RC could be 137 in either case;
+            // if it was caused by OOM killer, want to handle as OOM and not job abort.
+            case Success(returnCodeAsInt) if outOfMemoryDetected && memoryRetryRequested  =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
-              retryElseFail(executionHandle, retryWithMoreMemory)
+              retryElseFail(executionHandle, outOfMemoryDetected)
+            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
+              Future.successful(AbortedExecutionHandle)
             case Success(returnCodeAsInt) =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
@@ -1356,9 +1360,9 @@ trait StandardAsyncExecutionActor
           }
         } else {
           tryReturnCodeAsInt match {
-            case Success(returnCodeAsInt) if retryWithMoreMemory && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
+            case Success(returnCodeAsInt) if outOfMemoryDetected && memoryRetryRequested && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
-              retryElseFail(executionHandle, retryWithMoreMemory)
+              retryElseFail(executionHandle, outOfMemoryDetected)
             case _ =>
               val failureStatus = handleExecutionFailure(status, tryReturnCodeAsInt.toOption)
               retryElseFail(failureStatus)
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala b/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
index dd4254c8439..a64c6a5439c 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
@@ -78,7 +78,7 @@ trait StandardCachingActorHelper extends JobCachingActorHelper {
 
     val fileMetadata = jobPaths.metadataPaths
 
-    runtimeAttributesMetadata ++ fileMetadata ++ nonStandardMetadata
+    nonStandardMetadata ++ runtimeAttributesMetadata ++ fileMetadata
   }
 
   /**
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
index e33625741b3..c3d1452660e 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
@@ -48,7 +48,7 @@ class RootWorkflowFileHashCacheActor private[callcaching](override val ioActor:
           // hash to become available.
           cache.put(key, FileHashValueRequested(requesters = requester :: requesters))
         case FileHashSuccess(value) =>
-          sender() ! Tuple2(hashCommand.fileHashContext, IoSuccess(requester.ioCommand, value))
+          sender() ! Tuple2[Any, Any](hashCommand.fileHashContext, IoSuccess(requester.ioCommand, value))
         case FileHashFailure(error) =>
           sender() ! Tuple2(hashCommand.fileHashContext, IoFailure(requester.ioCommand, new IOException(error)))
       }
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
index f1662db858b..e23ecd277af 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
@@ -228,6 +228,8 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
           data.commandsToWaitFor.flatten.headOption match {
             case Some(command: IoCopyCommand) =>
               logCacheHitCopyCommand(command)
+            case Some(command: IoTouchCommand) =>
+              logCacheHitTouchCommand(command)
             case huh =>
               log.warning(s"BT-322 {} unexpected commandsToWaitFor: {}", jobTag, huh)
           }
@@ -307,6 +309,9 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
       case _ =>
     }
 
+  private def logCacheHitTouchCommand(command: IoTouchCommand): Unit =
+    log.info(s"BT-322 {} cache hit for file : {}", jobTag, command.toString)
+                                
   def succeedAndStop(returnCode: Option[Int], copiedJobOutputs: CallOutputs, detritusMap: DetritusMap): State = {
     import cromwell.services.metadata.MetadataService.implicits.MetadataAutoPutter
     serviceRegistryActor.putMetadata(jobDescriptor.workflowDescriptor.id, Option(jobDescriptor.key), startMetadataKeyValues)
diff --git a/build.sbt b/build.sbt
index 3b255d0e0e5..76f6f27e2c9 100644
--- a/build.sbt
+++ b/build.sbt
@@ -74,12 +74,6 @@ lazy val wdlTransformsBiscayne = (project in wdlTransformsRoot / "biscayne")
   .dependsOn(common % "test->test")
   .dependsOn(wom % "test->test")
 
-lazy val cwl = project
-  .withLibrarySettings("cromwell-cwl", cwlDependencies)
-  .dependsOn(wom)
-  .dependsOn(wom % "test->test")
-  .dependsOn(common % "test->test")
-
 lazy val core = project
   .withLibrarySettings("cromwell-core", coreDependencies)
   .dependsOn(wom)
@@ -183,7 +177,6 @@ lazy val services = project
   .dependsOn(wdlDraft2LanguageFactory % "test->test") // because the WaaS tests init language config with all languages
   .dependsOn(wdlDraft3LanguageFactory % "test->test")
   .dependsOn(wdlBiscayneLanguageFactory % "test->test")
-  .dependsOn(cwlV1_0LanguageFactory % "test->test")
   .dependsOn(core % "test->test")
   .dependsOn(ftpFileSystem % "test->test")
   .dependsOn(common % "test->test")
@@ -245,6 +238,9 @@ lazy val tesBackend = (project in backendRoot / "tes")
   .dependsOn(sfsBackend)
   .dependsOn(ftpFileSystem)
   .dependsOn(drsFileSystem)
+  .dependsOn(azureBlobFileSystem)
+  // TES backend provides a compatibility layer to run WDLs with PAPI runtime attributes [WX-769]
+  .dependsOn(googlePipelinesCommon)
   .dependsOn(backend % "test->test")
   .dependsOn(common % "test->test")
 
@@ -263,7 +259,6 @@ lazy val engine = project
   .dependsOn(azureBlobFileSystem % "test->test")
   .dependsOn(`cloud-nio-spi`)
   .dependsOn(languageFactoryCore)
-  .dependsOn(cwlV1_0LanguageFactory % "test->test")
   .dependsOn(wdlDraft2LanguageFactory % "test->test")
   .dependsOn(wdlDraft3LanguageFactory % "test->test")
   .dependsOn(wdlBiscayneLanguageFactory % "test->test")
@@ -278,20 +273,11 @@ lazy val engine = project
 
 // Executables
 
-lazy val centaurCwlRunner = project
-  .withExecutableSettings("centaur-cwl-runner", centaurCwlRunnerDependencies, buildDocker = false)
-  .dependsOn(cwl)
-  .dependsOn(centaur)
-  .dependsOn(gcsFileSystem)
-  .dependsOn(ftpFileSystem)
-  .dependsOn(common % "test->test")
-
 lazy val womtool = project
   .withExecutableSettings("womtool", womtoolDependencies)
   .dependsOn(wdlDraft2LanguageFactory)
   .dependsOn(wdlDraft3LanguageFactory)
   .dependsOn(wdlBiscayneLanguageFactory)
-  .dependsOn(cwlV1_0LanguageFactory)
   .dependsOn(wom % "test->test")
   .dependsOn(common % "test->test")
 
@@ -337,12 +323,6 @@ lazy val wdlBiscayneLanguageFactory = (project in languageFactoryRoot / "wdl-bis
   .dependsOn(wdlTransformsBiscayne)
   .dependsOn(common % "test->test")
 
-lazy val cwlV1_0LanguageFactory = (project in languageFactoryRoot / "cwl-v1-0")
-  .withLibrarySettings("cwl-v1-0")
-  .dependsOn(languageFactoryCore)
-  .dependsOn(cwl)
-  .dependsOn(common % "test->test")
-
 lazy val `cloud-nio-spi` = (project in cloudNio / "cloud-nio-spi")
   .withLibrarySettings(libraryName = "cloud-nio-spi", dependencies = spiDependencies)
   .dependsOn(common % "test->test")
@@ -385,7 +365,6 @@ lazy val server = project
   .dependsOn(wdlDraft2LanguageFactory)
   .dependsOn(wdlDraft3LanguageFactory)
   .dependsOn(wdlBiscayneLanguageFactory)
-  .dependsOn(cwlV1_0LanguageFactory)
   .dependsOn(engine % "test->test")
   .dependsOn(common % "test->test")
 
@@ -402,14 +381,11 @@ lazy val root = (project in file("."))
   .aggregate(azureBlobFileSystem)
   .aggregate(backend)
   .aggregate(centaur)
-  .aggregate(centaurCwlRunner)
   .aggregate(cloudSupport)
   .aggregate(common)
   .aggregate(core)
   .aggregate(cromiam)
   .aggregate(cromwellApiClient)
-  .aggregate(cwl)
-  .aggregate(cwlV1_0LanguageFactory)
   .aggregate(databaseMigration)
   .aggregate(databaseSql)
   .aggregate(dockerHashing)
diff --git a/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala b/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
index 16463742632..9a88a9ac109 100644
--- a/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
+++ b/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
@@ -189,7 +189,7 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
   }
 
   private def toJobKeyValueRow(jobKeyValueEntry: JobKeyValueEntry): RowToInsert = {
-    RowToInsert of Map(
+    RowToInsert of Map[String, Any](
       "call_fully_qualified_name" -> jobKeyValueEntry.callFullyQualifiedName,
       "job_attempt" -> jobKeyValueEntry.jobAttempt,
       "job_index" -> jobKeyValueEntry.jobIndex,
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_joint_gvcf.test b/centaur/src/main/resources/integrationTestCases/bcbio_joint_gvcf.test
deleted file mode 100644
index ef32cbc7d7c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_joint_gvcf.test
+++ /dev/null
@@ -1,23 +0,0 @@
-name: bcbio_joint_gvcf
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-
-files {
-  workflow: cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl
-  inputs: cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json
-  imports: [
-    cwl/bcbio/gvcf-joint-workflow/steps,
-    cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl,
-    cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl,
-    cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_prealign.test b/centaur/src/main/resources/integrationTestCases/bcbio_prealign.test
deleted file mode 100644
index 2c4a6db3f45..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_prealign.test
+++ /dev/null
@@ -1,20 +0,0 @@
-name: bcbio_prealign
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/prealign-workflow/main-prealign.cwl
-  inputs: cwl/bcbio/prealign-workflow/main-prealign-samples.json
-    imports: [
-      cwl/bcbio/prealign-workflow/steps,
-      cwl/bcbio/prealign-workflow/wf-variantcall.cwl
-    ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_rnaseq.test b/centaur/src/main/resources/integrationTestCases/bcbio_rnaseq.test
deleted file mode 100644
index 64ac876c568..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_rnaseq.test
+++ /dev/null
@@ -1,19 +0,0 @@
-name: bcbio_rnaseq
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl
-  inputs: cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json
-  imports: [
-    cwl/bcbio/rnaseq-workflow/steps
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_somatic.test b/centaur/src/main/resources/integrationTestCases/bcbio_somatic.test
deleted file mode 100644
index 440099f280e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_somatic.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: bcbio_somatic
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/somatic-workflow/main-somatic.cwl
-  inputs: cwl/bcbio/somatic-workflow/main-somatic-samples.json
-  imports: [
-    cwl/bcbio/somatic-workflow/steps,
-    cwl/bcbio/somatic-workflow/wf-alignment.cwl,
-    cwl/bcbio/somatic-workflow/wf-svcall.cwl,
-    cwl/bcbio/somatic-workflow/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_svcall.test b/centaur/src/main/resources/integrationTestCases/bcbio_svcall.test
deleted file mode 100644
index 9116814fe6d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_svcall.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: bcbio_svcall
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/svcall-workflow/main-svcall.cwl
-  inputs: cwl/bcbio/svcall-workflow/main-svcall-samples.json
-  imports: [
-    cwl/bcbio/svcall-workflow/steps,
-    cwl/bcbio/svcall-workflow/wf-alignment.cwl,
-    cwl/bcbio/svcall-workflow/wf-svcall.cwl,
-    cwl/bcbio/svcall-workflow/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/bcbio_wes-chr21-test-workflow.test b/centaur/src/main/resources/integrationTestCases/bcbio_wes-chr21-test-workflow.test
deleted file mode 100644
index 1969d6bef66..00000000000
--- a/centaur/src/main/resources/integrationTestCases/bcbio_wes-chr21-test-workflow.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: wes_chr21_test-workflow
-testFormat: workflowsuccess
-backends: [Papiv2]
-workflowType: CWL
-workflowTypeVersion: v1.0
-tags: [bcbio]
-
-files {
-  workflow: cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
-  inputs: cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json
-  imports: [
-    cwl/bcbio/wes_chr21_test-workflow-gcp/steps,
-    cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl,
-    cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl,
-    cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl
-  ]
-  options: cwl/bcbio/bcbio.options
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/bcbio.options b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/bcbio.options
deleted file mode 100644
index 1340bda7f1c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/bcbio.options
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-  "default_runtime_attributes": {
-    "bootDiskSizeGb": 20
-  }
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json
deleted file mode 100644
index b7080e81448..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint-samples.json
+++ /dev/null
@@ -1,615 +0,0 @@
-{
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__adapters": [
-        [
-            "polyx"
-        ],
-        [
-            "polyx"
-        ]
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
-        },
-        null
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants"
-        ],
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "gvcf"
-        ],
-        [
-            "gvcf"
-        ]
-    ],
-    "config__algorithm__trim_reads": [
-        "read_through",
-        "False"
-    ],
-    "config__algorithm__validate": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/7_100326_FC6107FAAXX-grade.vcf"
-        },
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__variantcaller": [
-        [
-            "gatk-haplotype",
-            "strelka2"
-        ],
-        [
-            "gatk-haplotype",
-            "strelka2"
-        ]
-    ],
-    "config__algorithm__vcfanno": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ]
-    ],
-    "description": [
-        "Test1",
-        "Test2"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX.bam"
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        "b1",
-        "b1"
-    ],
-    "metadata__phenotype": [
-        "",
-        ""
-    ],
-    "reference__bwa__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__lb": [
-        null,
-        null
-    ],
-    "rgnames__pl": [
-        "illumina",
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__rg": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__sample": [
-        "Test1",
-        "Test2"
-    ],
-    "vrn_file": [
-        null,
-        null
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl
deleted file mode 100644
index a798100dc12..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/main-gvcf-joint.cwl
+++ /dev/null
@@ -1,794 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: config__algorithm__coverage
-    source: config__algorithm__coverage
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: batch_for_jointvc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: jointvc_batch_rec
-  run: steps/batch_for_jointvc.cwl
-- id: jointcall
-  in:
-  - id: jointvc_batch_rec
-    source: batch_for_jointvc/jointvc_batch_rec
-  out:
-  - id: jointvc_rec
-  - id: vrn_file_joint
-  run: wf-jointcall.cwl
-  scatter:
-  - jointvc_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: jointvc_rec
-    source: jointcall/jointvc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/alignment_to_rec.cwl
deleted file mode 100644
index 1379c575535..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-          items: string
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: rgnames__pu
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_jointvc.cwl
deleted file mode 100644
index 523567ed191..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_jointvc.cwl
+++ /dev/null
@@ -1,329 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=jointvc_batch_rec:resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: jointvc_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index ca40e5b30cf..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,401 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 2048
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index d876db22bd2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index 06152084c58..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,337 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index d486086c79e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,196 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl
deleted file mode 100644
index dbb0f54be94..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/concat_batch_variantcalls_jointvc.cwl
+++ /dev/null
@@ -1,209 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file_joint
-- sentinel_inputs=jointvc_batch_rec:record,region:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: region
-  type:
-    items: string
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/finalize_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/finalize_jointvc.cwl
deleted file mode 100644
index fd1e04762e4..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/finalize_jointvc.cwl
+++ /dev/null
@@ -1,331 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=jointvc_rec:resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions;vrn_file_joint
-- sentinel_inputs=jointvc_batch_rec:record,vrn_file_joint:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- finalize_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: jointvc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      - name: vrn_file_joint
-        type: File
-      name: jointvc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index 18e635c4006..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,171 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 2048
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl
deleted file mode 100644
index fac484f75ca..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/get_parallel_regions_jointvc.cwl
+++ /dev/null
@@ -1,184 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region
-- sentinel_inputs=jointvc_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-outputs:
-- id: region
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/merge_split_alignments.cwl
deleted file mode 100644
index 66e17dc7aa9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,168 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1035
-  ramMin: 4096
-  tmpdirMin: 6
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 45a90274381..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 2048
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index 75e0c7a35d5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,219 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 4096
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index 09728af2814..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,223 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1033
-  ramMin: 4096
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 813f3fed737..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,233 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;config__algorithm__coverage;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index a300aa5be18..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,195 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file_joint
-- sentinel_inputs=jointvc_batch_rec:record,vrn_file_joint:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: vrn_file_joint_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_align_inputs.cwl
deleted file mode 100644
index 8179e185e8b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,142 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples.cwl
deleted file mode 100644
index 244502016fb..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 830e65f0404..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__coverage;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=config__algorithm__coverage:var,rgnames__sample:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/process_alignment.cwl
deleted file mode 100644
index b12a9946b5c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 4096
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 7
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 53e0a326097..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,295 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;config__algorithm__coverage;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/run_jointvc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/run_jointvc.cwl
deleted file mode 100644
index 897c1e02ca8..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/run_jointvc.cwl
+++ /dev/null
@@ -1,203 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region
-- sentinel_inputs=jointvc_batch_rec:record,region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- run_jointvc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: gvcfgenotyper
-    specs:
-    - https://anaconda.org/bioconda/gvcfgenotyper
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-- id: region_toolinput
-  type: string
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region
-  type: string
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index 85b8a8f01e0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,225 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=jointvc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 2048
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: jointvc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        - name: vrn_file_joint
-          type: File
-        name: jointvc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index eb58aa47177..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,266 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 4096
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl
deleted file mode 100644
index 27c76c747c5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-alignment.cwl
+++ /dev/null
@@ -1,143 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl
deleted file mode 100644
index 3091d1de370..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-jointcall.cwl
+++ /dev/null
@@ -1,360 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: jointvc_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: jointvc_batch_rec
-      type: record
-    type: array
-outputs:
-- id: jointvc_rec
-  outputSource: finalize_jointvc/jointvc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      - name: vrn_file_joint
-        type: File
-      name: jointvc_rec
-      type: record
-    type: array
-- id: vrn_file_joint
-  outputSource: postprocess_variants/vrn_file_joint
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  out:
-  - id: region
-  run: steps/get_parallel_regions_jointvc.cwl
-- id: run_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: region_toolinput
-    source: get_parallel_regions_jointvc/region
-  out:
-  - id: vrn_file_region
-  - id: region
-  run: steps/run_jointvc.cwl
-  scatter:
-  - region_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: region
-    source: run_jointvc/region
-  - id: vrn_file_region
-    source: run_jointvc/vrn_file_region
-  out:
-  - id: vrn_file_joint
-  run: steps/concat_batch_variantcalls_jointvc.cwl
-- id: postprocess_variants
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: vrn_file_joint_toolinput
-    source: concat_batch_variantcalls_jointvc/vrn_file_joint
-  out:
-  - id: vrn_file_joint
-  run: steps/postprocess_variants.cwl
-- id: finalize_jointvc
-  in:
-  - id: jointvc_batch_rec
-    source: jointvc_batch_rec
-  - id: vrn_file_joint
-    source: postprocess_variants/vrn_file_joint
-  out:
-  - id: jointvc_rec
-  run: steps/finalize_jointvc.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl
deleted file mode 100644
index ffabd7e9f1e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/gvcf-joint-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,329 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign-samples.json
deleted file mode 100644
index 3e1234addda..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign-samples.json
+++ /dev/null
@@ -1,526 +0,0 @@
-{
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__coverage": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
-        }
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "qualimap",
-            "samtools",
-            "variants"
-        ],
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "qualimap",
-            "samtools",
-            "variants"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "qualimap_full"
-        ],
-        [
-            "qualimap_full"
-        ]
-    ],
-    "config__algorithm__validate": [
-        null,
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        null,
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__variantcaller": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__vcfanno": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ]
-    ],
-    "description": [
-        "Test1",
-        "Test2"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX.bam"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX_2.bam"
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        null,
-        null
-    ],
-    "metadata__phenotype": [
-        "",
-        ""
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__sample": [
-        "Test1",
-        "Test2"
-    ],
-    "vrn_file": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test1-gatk-haplotype.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test1-gatk-haplotype.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test2-gatk-haplotype.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/Test2-gatk-haplotype.vcf.gz.tbi"
-                }
-            ]
-        }
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign.cwl
deleted file mode 100644
index 535082448ed..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/main-prealign.cwl
+++ /dev/null
@@ -1,672 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: organize_noalign
-  in:
-  - id: files
-    source: files
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/organize_noalign.cwl
-  scatter:
-  - files
-  - resources
-  - description
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: config__algorithm__coverage
-    source: config__algorithm__coverage
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: organize_noalign/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 1ad9465444b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,407 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;genome_resources__variation__1000g;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type:
-          - boolean
-          - 'null'
-          - string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type: File
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index 2df313f7a8f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,101 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index ab4909659ca..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,315 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;metadata__phenotype;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index ae12d21651d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,199 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index c4e3997bca4..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,174 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 82ce9f97a43..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/organize_noalign.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/organize_noalign.cwl
deleted file mode 100644
index 370f2ccf982..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/organize_noalign.cwl
+++ /dev/null
@@ -1,59 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=files:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- organize_noalign
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1024
-  ramMin: 3072
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-inputs:
-- id: files
-  type:
-    items: File
-    type: array
-- id: resources
-  type: string
-- id: description
-  type: string
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type: File
-- id: work_bam_plus__disc
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index c0e41e5ba62..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type:
-      - 'null'
-      - string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index 6a261c205af..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1033
-  ramMin: 6144
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type: File
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index e61b71f4d28..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,229 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;config__algorithm__coverage;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type: File
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index dd7e67c7d61..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,183 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1025
-  ramMin: 6144
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples.cwl
deleted file mode 100644
index f473b969345..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,93 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage
-      type: File
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 54f7781bb21..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,81 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__coverage;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=config__algorithm__coverage:var,rgnames__sample:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: config__algorithm__coverage
-  type:
-    items: File
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage
-        type: File
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 3de03a1a1a8..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,299 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;metadata__phenotype;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;config__algorithm__coverage;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index e9fde20378c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type:
-          - boolean
-          - 'null'
-          - string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index e9192828e62..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,269 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/wf-variantcall.cwl
deleted file mode 100644
index b48a8254984..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/prealign-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,316 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type: File
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type:
-        - boolean
-        - 'null'
-        - string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json
deleted file mode 100644
index 3e67d52727e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq-samples.json
+++ /dev/null
@@ -1,111 +0,0 @@
-{
-    "analysis": [
-        "RNA-seq"
-    ],
-    "config__algorithm__aligner": [
-        "hisat2"
-    ],
-    "config__algorithm__coverage_interval": [
-        null
-    ],
-    "config__algorithm__expression_caller": [
-        [
-            "salmon",
-            "kallisto"
-        ]
-    ],
-    "config__algorithm__fusion_caller": [
-        [
-            "pizzly"
-        ]
-    ],
-    "config__algorithm__qc": [
-        [
-            "fastqc",
-            "qualimap_rnaseq",
-            "samtools"
-        ]
-    ],
-    "config__algorithm__quality_format": [
-        "standard"
-    ],
-    "config__algorithm__tools_off": [
-        []
-    ],
-    "config__algorithm__tools_on": [
-        []
-    ],
-    "description": [
-        "Test1"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbio-cromwell-dev-test/test_bcbio_cwl/testdata/test_fusion/fusion-1_1.fq.gz"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbio-cromwell-dev-test/test_bcbio_cwl/testdata/test_fusion/fusion-1_2.fq.gz"
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19"
-    ],
-    "genome_resources__rnaseq__transcripts": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.gtf",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.gtf.db"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__hisat2__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/hisat2-wf.tar.gz"
-        }
-    ],
-    "resources": [
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test1"
-    ],
-    "rgnames__lb": [
-        null
-    ],
-    "rgnames__pl": [
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test1"
-    ],
-    "rgnames__rg": [
-        "Test1"
-    ],
-    "rgnames__sample": [
-        "Test1"
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl
deleted file mode 100644
index 2dd258ac786..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/main-rnaseq.cwl
+++ /dev/null
@@ -1,304 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: config__algorithm__expression_caller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: reference__hisat2__indexes
-  type:
-    items: File
-    type: array
-- id: config__algorithm__fusion_caller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__rnaseq__transcripts
-  secondaryFiles:
-  - .db
-  type:
-    items: File
-    type: array
-- id: config__algorithm__quality_format
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: process_alignment/align_bam
-  type:
-    items: File
-    type: array
-- id: quant__tsv
-  outputSource: rnaseq_quantitate/quant__tsv
-  type:
-    items: File
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prepare_sample
-  in:
-  - id: files
-    source: files
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: genome_build
-    source: genome_build
-  - id: genome_resources__rnaseq__transcripts
-    source: genome_resources__rnaseq__transcripts
-  - id: analysis
-    source: analysis
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__hisat2__indexes
-    source: reference__hisat2__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__expression_caller
-    source: config__algorithm__expression_caller
-  - id: config__algorithm__fusion_caller
-    source: config__algorithm__fusion_caller
-  - id: config__algorithm__quality_format
-    source: config__algorithm__quality_format
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_rec
-  run: steps/prepare_sample.cwl
-  scatter:
-  - files
-  - rgnames__sample
-  - reference__fasta__base
-  - genome_build
-  - genome_resources__rnaseq__transcripts
-  - analysis
-  - rgnames__pl
-  - rgnames__pu
-  - rgnames__lane
-  - rgnames__rg
-  - rgnames__lb
-  - reference__hisat2__indexes
-  - config__algorithm__aligner
-  - config__algorithm__expression_caller
-  - config__algorithm__fusion_caller
-  - config__algorithm__quality_format
-  - resources
-  - description
-  scatterMethod: dotproduct
-- id: trim_sample
-  in:
-  - id: prep_rec
-    source: prepare_sample/prep_rec
-  out:
-  - id: trim_rec
-  run: steps/trim_sample.cwl
-  scatter:
-  - prep_rec
-  scatterMethod: dotproduct
-- id: process_alignment
-  in:
-  - id: trim_rec
-    source: trim_sample/trim_rec
-  out:
-  - id: align_bam
-  run: steps/process_alignment.cwl
-  scatter:
-  - trim_rec
-  scatterMethod: dotproduct
-- id: rnaseq_quantitate
-  in:
-  - id: trim_rec
-    source: trim_sample/trim_rec
-  - id: align_bam
-    source: process_alignment/align_bam
-  out:
-  - id: count_file
-  - id: quant__tsv
-  - id: quant__hdf5
-  - id: quant__fusion
-  run: steps/rnaseq_quantitate.cwl
-  scatter:
-  - trim_rec
-  - align_bam
-  scatterMethod: dotproduct
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: process_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: genome_resources__rnaseq__transcripts
-    source: genome_resources__rnaseq__transcripts
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  run: steps/multiqc_summary.cwl
-- id: detect_fusions
-  in:
-  - id: quant__fusion
-    source: rnaseq_quantitate/quant__fusion
-  - id: quant__hdf5
-    source: rnaseq_quantitate/quant__hdf5
-  - id: trim_rec
-    source: trim_sample/trim_rec
-  out:
-  - id: fusion__fasta
-  - id: fusion__json
-  run: steps/detect_fusions.cwl
-  scatter:
-  - quant__fusion
-  - quant__hdf5
-  - trim_rec
-  scatterMethod: dotproduct
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/detect_fusions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/detect_fusions.cwl
deleted file mode 100644
index 8803c214f31..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/detect_fusions.cwl
+++ /dev/null
@@ -1,97 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=fusion__fasta,fusion__json
-- sentinel_inputs=quant__fusion:var,quant__hdf5:var,trim_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_fusions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: pizzly
-    specs:
-    - https://anaconda.org/bioconda/pizzly
-inputs:
-- id: quant__fusion
-  type: File
-- id: quant__hdf5
-  type: File
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-outputs:
-- id: fusion__fasta
-  type: File
-- id: fusion__json
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 604f9291df7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,96 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__rnaseq__transcripts
-        type: File
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type: File
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index 230b84afc66..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,155 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_build;genome_resources__rnaseq__transcripts;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;align_bam
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=4
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=4
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_build
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type: File
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_build
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type: File
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/prepare_sample.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/prepare_sample.cwl
deleted file mode 100644
index e5b8cdf645e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/prepare_sample.cwl
+++ /dev/null
@@ -1,146 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=prep_rec:resources;description;files;reference__fasta__base;config__algorithm__expression_caller;rgnames__lb;rgnames__rg;reference__hisat2__indexes;config__algorithm__fusion_caller;config__algorithm__aligner;rgnames__pl;genome_build;rgnames__pu;genome_resources__rnaseq__transcripts;config__algorithm__quality_format;analysis;rgnames__sample;rgnames__lane
-- sentinel_inputs=files:var,rgnames__sample:var,reference__fasta__base:var,genome_build:var,genome_resources__rnaseq__transcripts:var,analysis:var,rgnames__pl:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__hisat2__indexes:var,config__algorithm__aligner:var,config__algorithm__expression_caller:var,config__algorithm__fusion_caller:var,config__algorithm__quality_format:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prepare_sample
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-inputs:
-- id: files
-  type:
-    items: File
-    type: array
-- id: rgnames__sample
-  type: string
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type: File
-- id: genome_build
-  type: string
-- id: genome_resources__rnaseq__transcripts
-  secondaryFiles:
-  - .db
-  type: File
-- id: analysis
-  type: string
-- id: rgnames__pl
-  type: string
-- id: rgnames__pu
-  type: string
-- id: rgnames__lane
-  type: string
-- id: rgnames__rg
-  type: string
-- id: rgnames__lb
-  type:
-  - 'null'
-  - string
-- id: reference__hisat2__indexes
-  type: File
-- id: config__algorithm__aligner
-  type: string
-- id: config__algorithm__expression_caller
-  type:
-    items: string
-    type: array
-- id: config__algorithm__fusion_caller
-  type:
-    items: string
-    type: array
-- id: config__algorithm__quality_format
-  type: string
-- id: resources
-  type: string
-- id: description
-  type: string
-outputs:
-- id: prep_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: prep_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/process_alignment.cwl
deleted file mode 100644
index 88af1224f95..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,108 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=align_bam
-- sentinel_inputs=trim_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 4096
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: star
-    specs:
-    - https://anaconda.org/bioconda/star
-  - package: hisat2
-    specs:
-    - https://anaconda.org/bioconda/hisat2
-  - package: tophat
-    specs:
-    - https://anaconda.org/bioconda/tophat
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-inputs:
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 5ff5b2f10e0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,135 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_build;genome_resources__rnaseq__transcripts;config__algorithm__tools_off;config__algorithm__qc;analysis;config__algorithm__tools_on;align_bam
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,genome_resources__rnaseq__transcripts:var,genome_build:var,config__algorithm__coverage_interval:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__qc:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 2048
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items: File
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: genome_resources__rnaseq__transcripts
-  secondaryFiles:
-  - .db
-  type:
-    items: File
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__rnaseq__transcripts
-        type: File
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type: File
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/rnaseq_quantitate.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/rnaseq_quantitate.cwl
deleted file mode 100644
index 05d2ec813ae..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/rnaseq_quantitate.cwl
+++ /dev/null
@@ -1,123 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=count_file,quant__tsv,quant__hdf5,quant__fusion
-- sentinel_inputs=trim_rec:record,align_bam:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- rnaseq_quantitate
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1025
-  ramMin: 4096
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: sailfish
-    specs:
-    - https://anaconda.org/bioconda/sailfish
-  - package: salmon
-    specs:
-    - https://anaconda.org/bioconda/salmon
-  - package: kallisto>
-    specs:
-    - https://anaconda.org/bioconda/kallisto>
-    version:
-    - 0.43.1
-  - package: subread
-    specs:
-    - https://anaconda.org/bioconda/subread
-  - package: gffread
-    specs:
-    - https://anaconda.org/bioconda/gffread
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-wasabi
-    specs:
-    - https://anaconda.org/bioconda/r-wasabi
-inputs:
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type: File
-outputs:
-- id: count_file
-  type: File
-- id: quant__tsv
-  type: File
-- id: quant__hdf5
-  type: File
-- id: quant__fusion
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/trim_sample.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/trim_sample.cwl
deleted file mode 100644
index 14124636cec..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/rnaseq-workflow/steps/trim_sample.cwl
+++ /dev/null
@@ -1,140 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=trim_rec:resources;description;files;reference__fasta__base;config__algorithm__expression_caller;rgnames__lb;rgnames__rg;reference__hisat2__indexes;config__algorithm__fusion_caller;config__algorithm__aligner;rgnames__pl;genome_build;rgnames__pu;genome_resources__rnaseq__transcripts;config__algorithm__quality_format;analysis;rgnames__sample;rgnames__lane
-- sentinel_inputs=prep_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- trim_sample
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-rnaseq:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 4096
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-inputs:
-- id: prep_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: prep_rec
-    type: record
-outputs:
-- id: trim_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__expression_caller
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: reference__hisat2__indexes
-      type: File
-    - name: config__algorithm__fusion_caller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: genome_build
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: genome_resources__rnaseq__transcripts
-      type: File
-    - name: config__algorithm__quality_format
-      type: string
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: rgnames__lane
-      type: string
-    name: trim_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic-samples.json
deleted file mode 100644
index cbafda3641d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic-samples.json
+++ /dev/null
@@ -1,680 +0,0 @@
-{
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__adapters": [
-        [],
-        []
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
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diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic.cwl
deleted file mode 100644
index 699d99a4690..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/main-somatic.cwl
+++ /dev/null
@@ -1,973 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__calls
-  outputSource: summarize_sv/sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  outputSource: summarize_sv/svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: sv__prioritize__tsv
-  outputSource: summarize_sv/sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  outputSource: summarize_sv/sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  outputSource: summarize_sv/sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: calculate_sv_bins
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__seq2c_bed_ready
-    source: postprocess_alignment/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: sv_bin_rec
-  run: steps/calculate_sv_bins.cwl
-- id: calculate_sv_coverage
-  in:
-  - id: sv_bin_rec
-    source: calculate_sv_bins/sv_bin_rec
-  out:
-  - id: sv_rawcoverage_rec
-  run: steps/calculate_sv_coverage.cwl
-  scatter:
-  - sv_bin_rec
-  scatterMethod: dotproduct
-- id: normalize_sv_coverage
-  in:
-  - id: sv_rawcoverage_rec
-    source: calculate_sv_coverage/sv_rawcoverage_rec
-  out:
-  - id: sv_coverage_rec
-  run: steps/normalize_sv_coverage.cwl
-- id: batch_for_sv
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: work_bam_plus__disc
-    source: alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr
-    source: alignment/work_bam_plus__sr
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__svprioritize
-    source: config__algorithm__svprioritize
-  - id: config__algorithm__svvalidate
-    source: config__algorithm__svvalidate
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: genome_resources__variation__gc_profile
-    source: genome_resources__variation__gc_profile
-  - id: genome_resources__variation__germline_het_pon
-    source: genome_resources__variation__germline_het_pon
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: sv_coverage_rec
-    source: normalize_sv_coverage/sv_coverage_rec
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  out:
-  - id: sv_batch_rec
-  run: steps/batch_for_sv.cwl
-- id: svcall
-  in:
-  - id: sv_batch_rec
-    source: batch_for_sv/sv_batch_rec
-  out:
-  - id: sv_rec
-  run: wf-svcall.cwl
-  scatter:
-  - sv_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_sv
-  in:
-  - id: sv_rec
-    source: svcall/sv_rec
-  out:
-  - id: sv__calls
-  - id: sv__supplemental
-  - id: sv__prioritize__tsv
-  - id: sv__prioritize__raw
-  - id: svvalidate__grading_summary
-  - id: svvalidate__grading_plots
-  run: steps/summarize_sv.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: reference__viral
-    source: reference__viral
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/alignment_to_rec.cwl
deleted file mode 100644
index 11cd9fc8d40..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,200 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: rgnames__pu
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_sv.cwl
deleted file mode 100644
index 16b905acacf..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_sv.cwl
+++ /dev/null
@@ -1,375 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=sv_batch_rec:resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;reference__snpeff__hg19;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;work_bam_plus__disc;work_bam_plus__sr;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,work_bam_plus__disc:var,work_bam_plus__sr:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__svprioritize:var,config__algorithm__svvalidate:var,regions__sample_callable:var,genome_resources__variation__gc_profile:var,genome_resources__variation__germline_het_pon:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,sv_coverage_rec:record,variants__samples:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10240
-  ramMin: 6144
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-outputs:
-- id: sv_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: work_bam_plus__disc
-          type:
-          - File
-          - 'null'
-        - name: work_bam_plus__sr
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 60af6c4469e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,407 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;genome_resources__variation__1000g;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10246
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_bins.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_bins.cwl
deleted file mode 100644
index 40bd035478a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_bins.cwl
+++ /dev/null
@@ -1,225 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_bin_rec:regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;resources;description;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=align_bam:var,reference__fasta__base:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__svcaller:var,depth__variant_regions__regions:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__rnaseq__gene_bed:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_bins
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: sv_bin_rec
-  type:
-    items:
-      fields:
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_bin_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_coverage.cwl
deleted file mode 100644
index fc75d2c1b71..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/calculate_sv_coverage.cwl
+++ /dev/null
@@ -1,218 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=sv_rawcoverage_rec:depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;resources;description;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_bin_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-inputs:
-- id: sv_bin_rec
-  type:
-    fields:
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_bin_rec
-    type: record
-outputs:
-- id: sv_rawcoverage_rec
-  type:
-    fields:
-    - name: depth__bins__target
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__seq2c
-      type:
-      - File
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_rawcoverage_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index 5a8f8a3c6cb..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index d6b910b7f9e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,311 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index ef31b2ffe4f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,198 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/detect_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/detect_sv.cwl
deleted file mode 100644
index 234bcc60d69..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/detect_sv.cwl
+++ /dev/null
@@ -1,414 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=sv_rec:sv__variantcaller;sv__vrn_file;sv__supplemental;svvalidate__summary;resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: delly
-    specs:
-    - https://anaconda.org/bioconda/delly
-  - package: duphold
-    specs:
-    - https://anaconda.org/bioconda/duphold
-  - package: extract-sv-reads
-    specs:
-    - https://anaconda.org/bioconda/extract-sv-reads
-  - package: lumpy-sv
-    specs:
-    - https://anaconda.org/bioconda/lumpy-sv
-  - package: manta
-    specs:
-    - https://anaconda.org/bioconda/manta
-  - package: break-point-inspector
-    specs:
-    - https://anaconda.org/bioconda/break-point-inspector
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: smoove
-    specs:
-    - https://anaconda.org/bioconda/smoove
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-  - package: simple_sv_annotation
-    specs:
-    - https://anaconda.org/bioconda/simple_sv_annotation
-  - package: survivor
-    specs:
-    - https://anaconda.org/bioconda/survivor
-  - package: svtools
-    specs:
-    - https://anaconda.org/bioconda/svtools
-  - package: svtyper
-    specs:
-    - https://anaconda.org/bioconda/svtyper
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: xorg-libxt
-    specs:
-    - https://anaconda.org/bioconda/xorg-libxt
-  - package: vawk
-    specs:
-    - https://anaconda.org/bioconda/vawk
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index 48e5f050eb3..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,173 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10246
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/merge_split_alignments.cwl
deleted file mode 100644
index 029b704bbb2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,169 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10251
-  ramMin: 6144
-  tmpdirMin: 6
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 9d65504ba6b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,96 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10246
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/normalize_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/normalize_sv_coverage.cwl
deleted file mode 100644
index 1bdc8dbc3b8..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/normalize_sv_coverage.cwl
+++ /dev/null
@@ -1,236 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_coverage_rec:depth__bins__normalized;depth__bins__background;resources;description;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_rawcoverage_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- normalize_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_rawcoverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rawcoverage_rec
-      type: record
-    type: array
-outputs:
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index 89f6372949c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,223 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: reference__viral
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index 8585bfb3074..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,224 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10249
-  ramMin: 6144
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 9d93ac8f1db..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,235 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index 6fba055bcd7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,182 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10241
-  ramMin: 6144
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_align_inputs.cwl
deleted file mode 100644
index c40a38fc01a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,143 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10244
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples.cwl
deleted file mode 100644
index 4e62820988d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 9268efdafcb..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__svcaller;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=rgnames__sample:var,config__algorithm__svcaller:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/process_alignment.cwl
deleted file mode 100644
index 45b58d1ab98..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,199 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 7
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index eccc8330618..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,310 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;metadata__phenotype;config__algorithm__tools_off;reference__viral;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,reference__viral:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10244
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__viral
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_sv.cwl
deleted file mode 100644
index be7b4a8c87f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_sv.cwl
+++ /dev/null
@@ -1,242 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv__calls,sv__supplemental,sv__prioritize__tsv,sv__prioritize__raw,svvalidate__grading_summary,svvalidate__grading_plots
-- sentinel_inputs=sv_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10243
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcbio-prioritize
-    specs:
-    - https://anaconda.org/bioconda/bcbio-prioritize
-inputs:
-- id: sv_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: sv__variantcaller
-          type:
-          - string
-          - 'null'
-        - name: sv__vrn_file
-          type:
-          - File
-          - 'null'
-        - name: sv__supplemental
-          type:
-            items:
-            - File
-            type: array
-        - name: svvalidate__summary
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: svvalidate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index 62c64099b31..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,195 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10241
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - File
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index 1dc7a6e7128..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,268 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 10246
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-alignment.cwl
deleted file mode 100644
index c2ce73cfc61..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-alignment.cwl
+++ /dev/null
@@ -1,144 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-svcall.cwl
deleted file mode 100644
index db9522935a1..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-svcall.cwl
+++ /dev/null
@@ -1,328 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  outputSource: detect_sv/sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: detect_sv
-  in:
-  - id: sv_batch_rec
-    source: sv_batch_rec
-  out:
-  - id: sv_rec
-  run: steps/detect_sv.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-variantcall.cwl
deleted file mode 100644
index da6bab7ac21..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/somatic-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,312 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall-samples.json
deleted file mode 100644
index 28826670c5c..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall-samples.json
+++ /dev/null
@@ -1,707 +0,0 @@
-{
-    "analysis": [
-        "variant",
-        "variant"
-    ],
-    "config__algorithm__adapters": [
-        [],
-        []
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        null,
-        null
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "samtools"
-        ],
-        [
-            "samtools"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__sv_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__svcaller": [
-        [
-            "cnvkit",
-            "manta",
-            "lumpy"
-        ],
-        [
-            "cnvkit",
-            "manta",
-            "lumpy"
-        ]
-    ],
-    "config__algorithm__svprioritize": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
-        }
-    ],
-    "config__algorithm__svvalidate": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/Test1-grade.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/reference_material/Test1-grade.vcf.gz.tbi"
-                }
-            ]
-        },
-        null
-    ],
-    "config__algorithm__tools_off": [
-        [],
-        []
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "coverage_perbase"
-        ],
-        [
-            "coverage_perbase"
-        ]
-    ],
-    "config__algorithm__trim_reads": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__validate": [
-        null,
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        null,
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        null,
-        null
-    ],
-    "config__algorithm__variantcaller": [
-        [
-            "vardict"
-        ],
-        [
-            "vardict"
-        ]
-    ],
-    "config__algorithm__vcfanno": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/somatic.conf"
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
-            }
-        ]
-    ],
-    "description": [
-        "Test1",
-        "Test2"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
-                    }
-                ]
-            }
-        ]
-    ],
-    "genome_build": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_vep_83_GRCh37",
-        "homo_sapiens_vep_83_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "hg19",
-        "hg19"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__clinvar": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__cosmic": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__dbsnp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__encode_blacklist": [
-        null,
-        null
-    ],
-    "genome_resources__variation__esp": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__exac": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__gc_profile": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/gc/GC_profile.1000bp.cnp"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/gc/GC_profile.1000bp.cnp"
-        }
-    ],
-    "genome_resources__variation__germline_het_pon": [
-        null,
-        null
-    ],
-    "genome_resources__variation__gnomad_exome": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__lcr": [
-        null,
-        null
-    ],
-    "genome_resources__variation__polyx": [
-        null,
-        null
-    ],
-    "genome_resources__variation__train_hapmap": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "genome_resources__variation__train_indels": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
-                }
-            ]
-        }
-    ],
-    "metadata__batch": [
-        "b1",
-        "b1"
-    ],
-    "metadata__phenotype": [
-        "tumor",
-        "normal"
-    ],
-    "reference__bwa__indexes": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
-                }
-            ]
-        }
-    ],
-    "reference__fasta__base": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
-                }
-            ]
-        }
-    ],
-    "reference__genome_context": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__hg19": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
-        }
-    ],
-    "reference__viral": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.sa"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.bwt"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.sa"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/test_bcbio_cwl/testdata/genomes/hg19/viral/gdc-viral.fa.bwt"
-                }
-            ]
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__lane": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__lb": [
-        null,
-        null
-    ],
-    "rgnames__pl": [
-        "illumina",
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__rg": [
-        "Test1",
-        "Test2"
-    ],
-    "rgnames__sample": [
-        "Test1",
-        "Test2"
-    ],
-    "vrn_file": [
-        null,
-        null
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall.cwl
deleted file mode 100644
index ec310cc54cd..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/main-svcall.cwl
+++ /dev/null
@@ -1,975 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__sv_regions
-  type:
-    items: File
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__svvalidate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__calls
-  outputSource: summarize_sv/sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  outputSource: summarize_sv/svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: sv__prioritize__tsv
-  outputSource: summarize_sv/sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  outputSource: summarize_sv/sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  outputSource: summarize_sv/sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: calculate_sv_bins
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__sv_regions
-    source: config__algorithm__sv_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: sv_bin_rec
-  run: steps/calculate_sv_bins.cwl
-- id: calculate_sv_coverage
-  in:
-  - id: sv_bin_rec
-    source: calculate_sv_bins/sv_bin_rec
-  out:
-  - id: sv_rawcoverage_rec
-  run: steps/calculate_sv_coverage.cwl
-  scatter:
-  - sv_bin_rec
-  scatterMethod: dotproduct
-- id: normalize_sv_coverage
-  in:
-  - id: sv_rawcoverage_rec
-    source: calculate_sv_coverage/sv_rawcoverage_rec
-  out:
-  - id: sv_coverage_rec
-  run: steps/normalize_sv_coverage.cwl
-- id: batch_for_sv
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: work_bam_plus__disc
-    source: alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr
-    source: alignment/work_bam_plus__sr
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__svprioritize
-    source: config__algorithm__svprioritize
-  - id: config__algorithm__svvalidate
-    source: config__algorithm__svvalidate
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: genome_resources__variation__gc_profile
-    source: genome_resources__variation__gc_profile
-  - id: genome_resources__variation__germline_het_pon
-    source: genome_resources__variation__germline_het_pon
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__hg19
-    source: reference__snpeff__hg19
-  - id: sv_coverage_rec
-    source: normalize_sv_coverage/sv_coverage_rec
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  out:
-  - id: sv_batch_rec
-  run: steps/batch_for_sv.cwl
-- id: svcall
-  in:
-  - id: sv_batch_rec
-    source: batch_for_sv/sv_batch_rec
-  out:
-  - id: sv_rec
-  run: wf-svcall.cwl
-  scatter:
-  - sv_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_sv
-  in:
-  - id: sv_rec
-    source: svcall/sv_rec
-  out:
-  - id: sv__calls
-  - id: sv__supplemental
-  - id: sv__prioritize__tsv
-  - id: sv__prioritize__raw
-  - id: svvalidate__grading_summary
-  - id: svvalidate__grading_plots
-  run: steps/summarize_sv.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: reference__viral
-    source: reference__viral
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/alignment_to_rec.cwl
deleted file mode 100644
index 8208a1f1eed..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,206 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: rgnames__pu
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - 'null'
-        - string
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_sv.cwl
deleted file mode 100644
index 5c725369def..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_sv.cwl
+++ /dev/null
@@ -1,359 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=sv_batch_rec:resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;reference__snpeff__hg19;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;work_bam_plus__disc;work_bam_plus__sr;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,work_bam_plus__disc:var,work_bam_plus__sr:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__svprioritize:var,config__algorithm__svvalidate:var,regions__sample_callable:var,genome_resources__variation__gc_profile:var,genome_resources__variation__germline_het_pon:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,sv_coverage_rec:record,variants__samples:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1024
-  ramMin: 6144
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items: File
-    type: array
-- id: config__algorithm__svvalidate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-outputs:
-- id: sv_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type: File
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: reference__snpeff__hg19
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: work_bam_plus__disc
-          type:
-          - File
-          - 'null'
-        - name: work_bam_plus__sr
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__sv_regions
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 1a04f1e6887..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,401 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;genome_resources__variation__1000g;config__algorithm__min_allele_fraction;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__hg19:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__hg19
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_bins.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_bins.cwl
deleted file mode 100644
index 34683452f0d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_bins.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_bin_rec:regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;resources;description;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=align_bam:var,reference__fasta__base:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__sv_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__svcaller:var,depth__variant_regions__regions:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__rnaseq__gene_bed:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_bins
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__sv_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: sv_bin_rec
-  type:
-    items:
-      fields:
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_bin_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_coverage.cwl
deleted file mode 100644
index 79ba8e7eaf5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/calculate_sv_coverage.cwl
+++ /dev/null
@@ -1,207 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=sv_rawcoverage_rec:depth__bins__target;depth__bins__antitarget;resources;description;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_bin_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_bin_rec
-  type:
-    fields:
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__sv_regions
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_bin_rec
-    type: record
-outputs:
-- id: sv_rawcoverage_rec
-  type:
-    fields:
-    - name: depth__bins__target
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__sv_regions
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_rawcoverage_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/combine_sample_regions.cwl
deleted file mode 100644
index 434161e89da..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/compare_to_rm.cwl
deleted file mode 100644
index 142a0d44ce9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,307 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__genome_context;config__algorithm__validate;reference__snpeff__hg19;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;reference__rtg;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index b8cd24d68bc..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,196 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/detect_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/detect_sv.cwl
deleted file mode 100644
index 4aab2c1343b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/detect_sv.cwl
+++ /dev/null
@@ -1,396 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=sv_rec:sv__variantcaller;sv__vrn_file;sv__supplemental;svvalidate__summary;resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: delly
-    specs:
-    - https://anaconda.org/bioconda/delly
-  - package: duphold
-    specs:
-    - https://anaconda.org/bioconda/duphold
-  - package: extract-sv-reads
-    specs:
-    - https://anaconda.org/bioconda/extract-sv-reads
-  - package: lumpy-sv
-    specs:
-    - https://anaconda.org/bioconda/lumpy-sv
-  - package: manta
-    specs:
-    - https://anaconda.org/bioconda/manta
-  - package: break-point-inspector
-    specs:
-    - https://anaconda.org/bioconda/break-point-inspector
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: smoove
-    specs:
-    - https://anaconda.org/bioconda/smoove
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-  - package: simple_sv_annotation
-    specs:
-    - https://anaconda.org/bioconda/simple_sv_annotation
-  - package: survivor
-    specs:
-    - https://anaconda.org/bioconda/survivor
-  - package: svtools
-    specs:
-    - https://anaconda.org/bioconda/svtools
-  - package: svtyper
-    specs:
-    - https://anaconda.org/bioconda/svtyper
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: xorg-libxt
-    specs:
-    - https://anaconda.org/bioconda/xorg-libxt
-  - package: vawk
-    specs:
-    - https://anaconda.org/bioconda/vawk
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/get_parallel_regions.cwl
deleted file mode 100644
index 71ac417a4ce..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,171 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/merge_split_alignments.cwl
deleted file mode 100644
index afe6f73cfc2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,171 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1035
-  ramMin: 6144
-  tmpdirMin: 6
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/multiqc_summary.cwl
deleted file mode 100644
index 82ce9f97a43..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1030
-  ramMin: 3072
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/normalize_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/normalize_sv_coverage.cwl
deleted file mode 100644
index 813a2a21a63..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/normalize_sv_coverage.cwl
+++ /dev/null
@@ -1,224 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_coverage_rec:depth__bins__normalized;depth__bins__background;resources;description;depth__bins__target;depth__bins__antitarget;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__sv_regions;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_rawcoverage_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- normalize_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_rawcoverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rawcoverage_rec
-      type: record
-    type: array
-outputs:
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/pipeline_summary.cwl
deleted file mode 100644
index d320e1afb86..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;reference__versions;genome_build;config__algorithm__tools_off;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: reference__viral
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: reference__versions
-      type: File
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment.cwl
deleted file mode 100644
index ccdfc8e177e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,223 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1033
-  ramMin: 6144
-  tmpdirMin: 5
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__variation__encode_blacklist
-      type:
-      - 'null'
-      - string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 1f033c9d3c7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,233 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__polyx
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_variants.cwl
deleted file mode 100644
index dd40cf1d9a4..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,180 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1025
-  ramMin: 6144
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_align_inputs.cwl
deleted file mode 100644
index cd325c5f774..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,145 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1028
-  ramMin: 6144
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 4
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples.cwl
deleted file mode 100644
index 63d24367261..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples.cwl
+++ /dev/null
@@ -1,93 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index da7b1d7f2b0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,79 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=rgnames__sample:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - 'null'
-        - string
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/process_alignment.cwl
deleted file mode 100644
index af6768e2f88..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/process_alignment.cwl
+++ /dev/null
@@ -1,201 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 7
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/qc_to_rec.cwl
deleted file mode 100644
index 4565b513de7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,308 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;metadata__batch;reference__versions;genome_build;metadata__phenotype;config__algorithm__tools_off;reference__viral;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,reference__viral:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1028
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - .fai
-  - ^.dict
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .amb
-  - .ann
-  - .sa
-  - .pac
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: reference__versions
-        type: File
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__viral
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_sv.cwl
deleted file mode 100644
index 87f503d9117..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_sv.cwl
+++ /dev/null
@@ -1,228 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv__calls,sv__supplemental,sv__prioritize__tsv,sv__prioritize__raw,svvalidate__grading_summary,svvalidate__grading_plots
-- sentinel_inputs=sv_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1027
-  ramMin: 3072
-  tmpdirMin: 2
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: sv_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: sv__variantcaller
-          type:
-          - string
-          - 'null'
-        - name: sv__vrn_file
-          type:
-          - File
-          - 'null'
-        - name: sv__supplemental
-          type:
-            items:
-            - File
-            type: array
-        - name: svvalidate__summary
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type: File
-        - name: genome_resources__variation__gc_profile
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__encode_blacklist
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__sv_regions
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: svvalidate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_vc.cwl
deleted file mode 100644
index c560affeded..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,193 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1025
-  ramMin: 3072
-  tmpdirMin: 1
-- class: dx:InputResourceRequirement
-  indirMin: 1
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: config__algorithm__validate
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__hg19
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__ensemble
-          type:
-          - 'null'
-          - string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/variantcall_batch_region.cwl
deleted file mode 100644
index 7e8f1574bfc..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,266 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 2
-  outdirMin: 1030
-  ramMin: 6144
-  tmpdirMin: 3
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-alignment.cwl
deleted file mode 100644
index 3785183a8df..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-alignment.cwl
+++ /dev/null
@@ -1,146 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: rgnames__pu
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - 'null'
-      - string
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-svcall.cwl
deleted file mode 100644
index 01ae7b07f7a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-svcall.cwl
+++ /dev/null
@@ -1,310 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: reference__snpeff__hg19
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  outputSource: detect_sv/sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type: File
-      - name: genome_resources__variation__gc_profile
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__sv_regions
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: detect_sv
-  in:
-  - id: sv_batch_rec
-    source: sv_batch_rec
-  out:
-  - id: sv_rec
-  run: steps/detect_sv.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-variantcall.cwl
deleted file mode 100644
index f7dd3955627..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/svcall-workflow/wf-variantcall.cwl
+++ /dev/null
@@ -1,308 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__encode_blacklist
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__validate
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__hg19
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__ensemble
-        type:
-        - 'null'
-        - string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json
deleted file mode 100644
index 1439ccade50..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test-samples.json
+++ /dev/null
@@ -1,1059 +0,0 @@
-{
-    "expected_validation":
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/grading-summary-combined-expected.csv"
-        },
-    "analysis": [
-        "variant2",
-        "variant2"
-    ],
-    "config__algorithm__adapters": [
-        [
-            "polyx"
-        ],
-        [
-            "polyx"
-        ]
-    ],
-    "config__algorithm__align_split_size": [
-        null,
-        null
-    ],
-    "config__algorithm__aligner": [
-        "bwa",
-        "bwa"
-    ],
-    "config__algorithm__archive": [
-        null,
-        null
-    ],
-    "config__algorithm__bam_clean": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__coverage_interval": [
-        null,
-        null
-    ],
-    "config__algorithm__effects": [
-        "snpeff",
-        "snpeff"
-    ],
-    "config__algorithm__ensemble": [
-        "{\"numpass\": 2}",
-        "{\"numpass\": 2}"
-    ],
-    "config__algorithm__exclude_regions": [
-        [],
-        []
-    ],
-    "config__algorithm__mark_duplicates": [
-        "True",
-        "True"
-    ],
-    "config__algorithm__min_allele_fraction": [
-        10.0,
-        10.0
-    ],
-    "config__algorithm__nomap_split_size": [
-        250,
-        250
-    ],
-    "config__algorithm__nomap_split_targets": [
-        20,
-        20
-    ],
-    "config__algorithm__qc": [
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants",
-            "viral"
-        ],
-        [
-            "contamination",
-            "coverage",
-            "fastqc",
-            "peddy",
-            "picard",
-            "qsignature",
-            "samtools",
-            "variants",
-            "viral"
-        ]
-    ],
-    "config__algorithm__recalibrate": [
-        "False",
-        "False"
-    ],
-    "config__algorithm__svcaller": [
-        [
-            "cnvkit"
-        ],
-        [
-            "cnvkit"
-        ]
-    ],
-    "config__algorithm__svprioritize": [
-        null,
-        null
-    ],
-    "config__algorithm__svvalidate": [
-        null,
-        null
-    ],
-    "config__algorithm__tools_off": [
-        [
-            "gemini"
-        ],
-        [
-            "gemini"
-        ]
-    ],
-    "config__algorithm__tools_on": [
-        [
-            "gatk4",
-            "break-point-inspector",
-            "noalt_calling"
-        ],
-        [
-            "gatk4",
-            "break-point-inspector",
-            "noalt_calling"
-        ]
-    ],
-    "config__algorithm__trim_reads": [
-        "atropos",
-        "atropos"
-    ],
-    "config__algorithm__validate": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/wes-ensemble-annotated_exome_chr21_noAnnot_somatic.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/wes_agha_test/wes-ensemble-annotated_exome_chr21_noAnnot_somatic.vcf.gz.tbi"
-                }
-            ]
-        },
-        null
-    ],
-    "config__algorithm__validate_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/Exome-Agilent_V6_chr21.bed"
-        },
-        null
-    ],
-    "config__algorithm__variant_regions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/Exome-Agilent_V6_chr21.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/wes_agha_test/Exome-Agilent_V6_chr21.bed"
-        }
-    ],
-    "config__algorithm__variantcaller": [
-        [
-            "germline:vardict",
-            "germline:strelka2",
-            "germline:gatk-haplotype",
-            "somatic:vardict",
-            "somatic:strelka2",
-            "somatic:mutect2"
-        ],
-        [
-            "germline:vardict",
-            "germline:strelka2",
-            "germline:gatk-haplotype",
-            "somatic:vardict",
-            "somatic:strelka2",
-            "somatic:mutect2"
-        ]
-    ],
-    "config__algorithm__vcfanno": [
-        [],
-        []
-    ],
-    "description": [
-        "NA12878_chr21",
-        "NA24385_chr21"
-    ],
-    "files": [
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/wes_agha_test/NA12878-ready_exome21.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/wes_agha_test/NA12878-ready_exome21.bam.bai"
-                    }
-                ]
-            }
-        ],
-        [
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/wes_agha_test/NA24385-ready_exome21.bam",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/wes_agha_test/NA24385-ready_exome21.bam.bai"
-                    }
-                ]
-            }
-        ]
-    ],
-    "genome_build": [
-        "GRCh37",
-        "GRCh37"
-    ],
-    "genome_resources__aliases__ensembl": [
-        "homo_sapiens_merged_vep_93_GRCh37",
-        "homo_sapiens_merged_vep_93_GRCh37"
-    ],
-    "genome_resources__aliases__human": [
-        "True",
-        "True"
-    ],
-    "genome_resources__aliases__snpeff": [
-        "GRCh37.75",
-        "GRCh37.75"
-    ],
-    "genome_resources__rnaseq__gene_bed": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/rnaseq/ref-transcripts.bed"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/rnaseq/ref-transcripts.bed"
-        }
-    ],
-    "genome_resources__variation__1000g": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/variation/1000g.vcf.gz",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/variation/1000g.vcf.gz.tbi"
-                }
-            ]
-        },
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-                        "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/heng_um75-hs37d5.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/low_complexity_51to200bp.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/low_complexity_51to200bp.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/low_complexity_gt200bp.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/low_complexity_gt200bp.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/repeats/polyx.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/repeats/polyx.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/self_chain.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/GA4GH/self_chain.bed.gz.tbi"
-                    }
-                ]
-            },
-            {
-                "class": "File",
-                "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/ENCODE/wgEncodeDacMapabilityConsensusExcludable.bed.gz",
-                "secondaryFiles": [
-                    {
-                        "class": "File",
-                        "path": "gs://bcbiodata/collections/GRCh37/coverage/problem_regions/ENCODE/wgEncodeDacMapabilityConsensusExcludable.bed.gz.tbi"
-                    }
-                ]
-            }
-        ]
-    ],
-    "reference__rtg": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/rtg--GRCh37.sdf-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/rtg--GRCh37.sdf-wf.tar.gz"
-        }
-    ],
-    "reference__snpeff__GRCh37_75": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/snpeff--GRCh37.75-wf.tar.gz"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/snpeff--GRCh37.75-wf.tar.gz"
-        }
-    ],
-    "reference__versions": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/versions.csv"
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/versions.csv"
-        }
-    ],
-    "reference__viral": [
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.sa"
-                }
-            ]
-        },
-        {
-            "class": "File",
-            "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa",
-            "secondaryFiles": [
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.dict"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.amb"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.ann"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.bwt"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.fai"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.pac"
-                },
-                {
-                    "class": "File",
-                    "path": "gs://bcbiodata/collections/GRCh37/viral/gdc-viral.fa.sa"
-                }
-            ]
-        }
-    ],
-    "resources": [
-        "{}",
-        "{}"
-    ],
-    "rgnames__lane": [
-        "NA12878_chr21",
-        "NA24385_chr21"
-    ],
-    "rgnames__lb": [
-        null,
-        null
-    ],
-    "rgnames__pl": [
-        "illumina",
-        "illumina"
-    ],
-    "rgnames__pu": [
-        "NA12878_chr21",
-        "NA24385_chr21"
-    ],
-    "rgnames__rg": [
-        "NA12878_chr21",
-        "NA24385_chr21"
-    ],
-    "rgnames__sample": [
-        "NA12878_chr21",
-        "NA24385_chr21"
-    ],
-    "vrn_file": [
-        null,
-        null
-    ]
-}
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
deleted file mode 100644
index c325ecade0b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/main-wes_chr21_test.cwl
+++ /dev/null
@@ -1,997 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: reference__snpeff__GRCh37_75
-  type:
-    items: File
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .fai
-  - .ann
-  - .sa
-  - .pac
-  - .amb
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: config__algorithm__archive
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-outputs:
-- id: rgnames__sample_out
-  outputSource: prep_samples/rgnames__sample
-  type:
-    items: string
-    type: array
-- id: align_bam
-  outputSource: postprocess_alignment/align_bam
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__sample_callable
-  outputSource: postprocess_alignment/regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_summary
-  outputSource: summarize_vc/validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__calls
-  outputSource: summarize_vc/variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  outputSource: summarize_vc/variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__calls
-  outputSource: summarize_sv/sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  outputSource: summarize_sv/svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: sv__prioritize__tsv
-  outputSource: summarize_sv/sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  outputSource: summarize_sv/sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  outputSource: summarize_sv/sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: summary__multiqc
-  outputSource: multiqc_summary/summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  outputSource: multiqc_summary/versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  outputSource: multiqc_summary/versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: alignment_to_rec
-  in:
-  - id: files
-    source: files
-  - id: analysis
-    source: analysis
-  - id: config__algorithm__align_split_size
-    source: config__algorithm__align_split_size
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: rgnames__pl
-    source: rgnames__pl
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: rgnames__pu
-    source: rgnames__pu
-  - id: rgnames__lane
-    source: rgnames__lane
-  - id: rgnames__rg
-    source: rgnames__rg
-  - id: rgnames__lb
-    source: rgnames__lb
-  - id: reference__bwa__indexes
-    source: reference__bwa__indexes
-  - id: config__algorithm__aligner
-    source: config__algorithm__aligner
-  - id: config__algorithm__trim_reads
-    source: config__algorithm__trim_reads
-  - id: config__algorithm__adapters
-    source: config__algorithm__adapters
-  - id: config__algorithm__bam_clean
-    source: config__algorithm__bam_clean
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: config__algorithm__mark_duplicates
-    source: config__algorithm__mark_duplicates
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: alignment_rec
-  run: steps/alignment_to_rec.cwl
-- id: alignment
-  in:
-  - id: alignment_rec
-    source: alignment_to_rec/alignment_rec
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: wf-alignment.cwl
-  scatter:
-  - alignment_rec
-  scatterMethod: dotproduct
-- id: prep_samples_to_rec
-  in:
-  - id: rgnames__sample
-    source: rgnames__sample
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: config__algorithm__variant_regions
-    source: config__algorithm__variant_regions
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: prep_samples_rec
-  run: steps/prep_samples_to_rec.cwl
-- id: prep_samples
-  in:
-  - id: prep_samples_rec
-    source: prep_samples_to_rec/prep_samples_rec
-  out:
-  - id: rgnames__sample
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  run: steps/prep_samples.cwl
-  scatter:
-  - prep_samples_rec
-  scatterMethod: dotproduct
-- id: postprocess_alignment_to_rec
-  in:
-  - id: align_bam
-    source: alignment/align_bam
-  - id: config__algorithm__archive
-    source: config__algorithm__archive
-  - id: config__algorithm__coverage_interval
-    source: config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: prep_samples/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: prep_samples/config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-    source: prep_samples/config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-    source: prep_samples/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: prep_samples/config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-    source: prep_samples/config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-    source: prep_samples/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__recalibrate
-    source: config__algorithm__recalibrate
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: postprocess_alignment_rec
-  run: steps/postprocess_alignment_to_rec.cwl
-- id: postprocess_alignment
-  in:
-  - id: postprocess_alignment_rec
-    source: postprocess_alignment_to_rec/postprocess_alignment_rec
-  out:
-  - id: config__algorithm__coverage_interval
-  - id: config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-  - id: config__algorithm__variant_regions_orig
-  - id: config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-  - id: config__algorithm__coverage_orig
-  - id: config__algorithm__seq2c_bed_ready
-  - id: regions__callable
-  - id: regions__sample_callable
-  - id: regions__nblock
-  - id: depth__samtools__stats
-  - id: depth__samtools__idxstats
-  - id: depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-  - id: depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-  - id: depth__coverage__regions
-  - id: depth__coverage__dist
-  - id: depth__coverage__thresholds
-  - id: align_bam
-  run: steps/postprocess_alignment.cwl
-  scatter:
-  - postprocess_alignment_rec
-  scatterMethod: dotproduct
-- id: combine_sample_regions
-  in:
-  - id: regions__callable
-    source: postprocess_alignment/regions__callable
-  - id: regions__nblock
-    source: postprocess_alignment/regions__nblock
-  - id: metadata__batch
-    source: metadata__batch
-  - id: config__algorithm__nomap_split_size
-    source: config__algorithm__nomap_split_size
-  - id: config__algorithm__nomap_split_targets
-    source: config__algorithm__nomap_split_targets
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: config__algorithm__callable_regions
-  - id: config__algorithm__non_callable_regions
-  - id: config__algorithm__callable_count
-  run: steps/combine_sample_regions.cwl
-- id: batch_for_variantcall
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: vrn_file
-    source: vrn_file
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: config__algorithm__variantcaller
-    source: config__algorithm__variantcaller
-  - id: config__algorithm__ensemble
-    source: config__algorithm__ensemble
-  - id: config__algorithm__vcfanno
-    source: config__algorithm__vcfanno
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__effects
-    source: config__algorithm__effects
-  - id: config__algorithm__min_allele_fraction
-    source: config__algorithm__min_allele_fraction
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__validate
-    source: config__algorithm__validate
-  - id: config__algorithm__validate_regions
-    source: config__algorithm__validate_regions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__rtg
-    source: reference__rtg
-  - id: reference__genome_context
-    source: reference__genome_context
-  - id: genome_resources__variation__clinvar
-    source: genome_resources__variation__clinvar
-  - id: genome_resources__variation__cosmic
-    source: genome_resources__variation__cosmic
-  - id: genome_resources__variation__dbsnp
-    source: genome_resources__variation__dbsnp
-  - id: genome_resources__variation__esp
-    source: genome_resources__variation__esp
-  - id: genome_resources__variation__exac
-    source: genome_resources__variation__exac
-  - id: genome_resources__variation__gnomad_exome
-    source: genome_resources__variation__gnomad_exome
-  - id: genome_resources__variation__1000g
-    source: genome_resources__variation__1000g
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__aliases__ensembl
-    source: genome_resources__aliases__ensembl
-  - id: genome_resources__aliases__human
-    source: genome_resources__aliases__human
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__GRCh37_75
-    source: reference__snpeff__GRCh37_75
-  - id: genome_resources__variation__train_hapmap
-    source: genome_resources__variation__train_hapmap
-  - id: genome_resources__variation__train_indels
-    source: genome_resources__variation__train_indels
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: batch_rec
-  run: steps/batch_for_variantcall.cwl
-- id: variantcall
-  in:
-  - id: batch_rec
-    source: batch_for_variantcall/batch_rec
-  out:
-  - id: vc_rec
-  run: wf-variantcall.cwl
-  scatter:
-  - batch_rec
-  scatterMethod: dotproduct
-- id: batch_for_ensemble
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  out:
-  - id: ensemble_prep_rec
-  run: steps/batch_for_ensemble.cwl
-- id: combine_calls
-  in:
-  - id: ensemble_prep_rec
-    source: batch_for_ensemble/ensemble_prep_rec
-  out:
-  - id: ensemble_rec
-  run: steps/combine_calls.cwl
-  scatter:
-  - ensemble_prep_rec
-  scatterMethod: dotproduct
-- id: summarize_vc
-  in:
-  - id: vc_rec
-    source: variantcall/vc_rec
-  - id: ensemble_rec
-    source: combine_calls/ensemble_rec
-  out:
-  - id: variants__calls
-  - id: variants__gvcf
-  - id: variants__samples
-  - id: validate__grading_summary
-  - id: validate__grading_plots
-  run: steps/summarize_vc.cwl
-- id: calculate_sv_bins
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__callable_regions
-    source: combine_sample_regions/config__algorithm__callable_regions
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: config__algorithm__exclude_regions
-    source: config__algorithm__exclude_regions
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__seq2c_bed_ready
-    source: postprocess_alignment/config__algorithm__seq2c_bed_ready
-  - id: config__algorithm__svcaller
-    source: config__algorithm__svcaller
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: genome_resources__variation__lcr
-    source: genome_resources__variation__lcr
-  - id: genome_resources__variation__polyx
-    source: genome_resources__variation__polyx
-  - id: genome_resources__variation__encode_blacklist
-    source: genome_resources__variation__encode_blacklist
-  - id: genome_resources__rnaseq__gene_bed
-    source: genome_resources__rnaseq__gene_bed
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: sv_bin_rec
-  run: steps/calculate_sv_bins.cwl
-- id: calculate_sv_coverage
-  in:
-  - id: sv_bin_rec
-    source: calculate_sv_bins/sv_bin_rec
-  out:
-  - id: sv_rawcoverage_rec
-  run: steps/calculate_sv_coverage.cwl
-  scatter:
-  - sv_bin_rec
-  scatterMethod: dotproduct
-- id: normalize_sv_coverage
-  in:
-  - id: sv_rawcoverage_rec
-    source: calculate_sv_coverage/sv_rawcoverage_rec
-  out:
-  - id: sv_coverage_rec
-  run: steps/normalize_sv_coverage.cwl
-- id: batch_for_sv
-  in:
-  - id: analysis
-    source: analysis
-  - id: genome_build
-    source: genome_build
-  - id: work_bam_plus__disc
-    source: alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr
-    source: alignment/work_bam_plus__sr
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: config__algorithm__svprioritize
-    source: config__algorithm__svprioritize
-  - id: config__algorithm__svvalidate
-    source: config__algorithm__svvalidate
-  - id: regions__sample_callable
-    source: postprocess_alignment/regions__sample_callable
-  - id: genome_resources__variation__gc_profile
-    source: genome_resources__variation__gc_profile
-  - id: genome_resources__variation__germline_het_pon
-    source: genome_resources__variation__germline_het_pon
-  - id: genome_resources__aliases__snpeff
-    source: genome_resources__aliases__snpeff
-  - id: reference__snpeff__GRCh37_75
-    source: reference__snpeff__GRCh37_75
-  - id: sv_coverage_rec
-    source: normalize_sv_coverage/sv_coverage_rec
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  out:
-  - id: sv_batch_rec
-  run: steps/batch_for_sv.cwl
-- id: svcall
-  in:
-  - id: sv_batch_rec
-    source: batch_for_sv/sv_batch_rec
-  out:
-  - id: sv_rec
-  run: wf-svcall.cwl
-  scatter:
-  - sv_batch_rec
-  scatterMethod: dotproduct
-- id: summarize_sv
-  in:
-  - id: sv_rec
-    source: svcall/sv_rec
-  out:
-  - id: sv__calls
-  - id: sv__supplemental
-  - id: sv__prioritize__tsv
-  - id: sv__prioritize__raw
-  - id: svvalidate__grading_summary
-  - id: svvalidate__grading_plots
-  run: steps/summarize_sv.cwl
-- id: qc_to_rec
-  in:
-  - id: align_bam
-    source: postprocess_alignment/align_bam
-  - id: analysis
-    source: analysis
-  - id: reference__fasta__base
-    source: reference__fasta__base
-  - id: reference__versions
-    source: reference__versions
-  - id: config__algorithm__tools_on
-    source: config__algorithm__tools_on
-  - id: config__algorithm__tools_off
-    source: config__algorithm__tools_off
-  - id: genome_build
-    source: genome_build
-  - id: config__algorithm__qc
-    source: config__algorithm__qc
-  - id: metadata__batch
-    source: metadata__batch
-  - id: metadata__phenotype
-    source: metadata__phenotype
-  - id: config__algorithm__coverage_interval
-    source: postprocess_alignment/config__algorithm__coverage_interval
-  - id: depth__variant_regions__regions
-    source: postprocess_alignment/depth__variant_regions__regions
-  - id: depth__variant_regions__dist
-    source: postprocess_alignment/depth__variant_regions__dist
-  - id: depth__samtools__stats
-    source: postprocess_alignment/depth__samtools__stats
-  - id: depth__samtools__idxstats
-    source: postprocess_alignment/depth__samtools__idxstats
-  - id: depth__sv_regions__regions
-    source: postprocess_alignment/depth__sv_regions__regions
-  - id: depth__sv_regions__dist
-    source: postprocess_alignment/depth__sv_regions__dist
-  - id: depth__coverage__regions
-    source: postprocess_alignment/depth__coverage__regions
-  - id: depth__coverage__dist
-    source: postprocess_alignment/depth__coverage__dist
-  - id: depth__coverage__thresholds
-    source: postprocess_alignment/depth__coverage__thresholds
-  - id: config__algorithm__variant_regions
-    source: postprocess_alignment/config__algorithm__variant_regions
-  - id: config__algorithm__variant_regions_merged
-    source: postprocess_alignment/config__algorithm__variant_regions_merged
-  - id: config__algorithm__coverage
-    source: postprocess_alignment/config__algorithm__coverage
-  - id: config__algorithm__coverage_merged
-    source: postprocess_alignment/config__algorithm__coverage_merged
-  - id: variants__samples
-    source: summarize_vc/variants__samples
-  - id: reference__viral
-    source: reference__viral
-  - id: resources
-    source: resources
-  - id: description
-    source: description
-  out:
-  - id: qc_rec
-  run: steps/qc_to_rec.cwl
-- id: pipeline_summary
-  in:
-  - id: qc_rec
-    source: qc_to_rec/qc_rec
-  out:
-  - id: qcout_rec
-  run: steps/pipeline_summary.cwl
-  scatter:
-  - qc_rec
-  scatterMethod: dotproduct
-- id: multiqc_summary
-  in:
-  - id: qcout_rec
-    source: pipeline_summary/qcout_rec
-  out:
-  - id: summary__multiqc
-  - id: versions__tools
-  - id: versions__data
-  run: steps/multiqc_summary.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl
deleted file mode 100644
index 506764917f5..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/alignment_to_rec.cwl
+++ /dev/null
@@ -1,194 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;reference__bwa__indexes;config__algorithm__bam_clean;config__algorithm__aligner;rgnames__pl;config__algorithm__mark_duplicates;analysis;rgnames__sample;config__algorithm__variant_regions;rgnames__pu
-- sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__bwa__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__variant_regions:var,config__algorithm__mark_duplicates:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: files
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: config__algorithm__align_split_size
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: rgnames__pl
-  type:
-    items: string
-    type: array
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: rgnames__pu
-  type:
-    items: string
-    type: array
-- id: rgnames__lane
-  type:
-    items: string
-    type: array
-- id: rgnames__rg
-  type:
-    items: string
-    type: array
-- id: rgnames__lb
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: reference__bwa__indexes
-  secondaryFiles:
-  - ^.ann
-  - ^.pac
-  - ^.sa
-  - ^.bwt
-  type:
-    items: File
-    type: array
-- id: config__algorithm__aligner
-  type:
-    items: string
-    type: array
-- id: config__algorithm__trim_reads
-  type:
-    items: string
-    type: array
-- id: config__algorithm__adapters
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__bam_clean
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__mark_duplicates
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__align_split_size
-        type:
-        - 'null'
-        - string
-      - name: files
-        type:
-          items: File
-          type: array
-      - name: config__algorithm__trim_reads
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__adapters
-        type:
-          items: string
-          type: array
-      - name: rgnames__lb
-        type:
-        - 'null'
-        - string
-      - name: rgnames__rg
-        type: string
-      - name: rgnames__lane
-        type: string
-      - name: reference__bwa__indexes
-        type: File
-      - name: config__algorithm__bam_clean
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__aligner
-        type: string
-      - name: rgnames__pl
-        type: string
-      - name: config__algorithm__mark_duplicates
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: analysis
-        type: string
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      - name: rgnames__pu
-        type: string
-      name: alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl
deleted file mode 100644
index df553e9e92f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_ensemble.cwl
+++ /dev/null
@@ -1,273 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=ensemble_prep_rec:batch_id;variants__calls;variants__variantcallers;resources;description;batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__snpeff__GRCh37_75;reference__genome_context;reference__rtg;config__algorithm__validate;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=vc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_ensemble
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10240
-  ramMin: 3072
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__ensemble
-          type: string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: ensemble_prep_rec
-  type:
-    items:
-      fields:
-      - name: batch_id
-        type: string
-      - name: variants__calls
-        type:
-          items: File
-          type: array
-      - name: variants__variantcallers
-        type:
-          items: string
-          type: array
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: ensemble_prep_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl
deleted file mode 100644
index c25d67e007b..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_sv.cwl
+++ /dev/null
@@ -1,363 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=sv_batch_rec:resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;reference__snpeff__GRCh37_75;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;work_bam_plus__disc;work_bam_plus__sr;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,work_bam_plus__disc:var,work_bam_plus__sr:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,config__algorithm__svprioritize:var,config__algorithm__svvalidate:var,regions__sample_callable:var,genome_resources__variation__gc_profile:var,genome_resources__variation__germline_het_pon:var,genome_resources__aliases__snpeff:var,reference__snpeff__GRCh37_75:var,sv_coverage_rec:record,variants__samples:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10240
-  ramMin: 49152
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 3656
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__svprioritize
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__svvalidate
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__gc_profile
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__germline_het_pon
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__GRCh37_75
-  type:
-    items: File
-    type: array
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-outputs:
-- id: sv_batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type:
-          - 'null'
-          - string
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: work_bam_plus__disc
-          type:
-          - File
-          - 'null'
-        - name: work_bam_plus__sr
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type: File
-        - name: genome_resources__variation__encode_blacklist
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl
deleted file mode 100644
index 6504ed26811..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/batch_for_variantcall.cwl
+++ /dev/null
@@ -1,395 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-batch
-- sentinel_outputs=batch_rec:resources;description;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;genome_resources__variation__clinvar;genome_resources__variation__esp;metadata__batch;genome_resources__variation__lcr;config__algorithm__min_allele_fraction;reference__snpeff__GRCh37_75;vrn_file;genome_resources__variation__train_hapmap;reference__genome_context;reference__rtg;config__algorithm__validate;genome_resources__variation__1000g;config__algorithm__validate_regions;genome_build;genome_resources__variation__exac;genome_resources__variation__gnomad_exome;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;genome_resources__variation__cosmic;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;genome_resources__variation__train_indels;genome_resources__aliases__snpeff;align_bam;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=analysis:var,genome_build:var,align_bam:var,vrn_file:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,regions__sample_callable:var,config__algorithm__variantcaller:var,config__algorithm__ensemble:var,config__algorithm__vcfanno:var,config__algorithm__coverage_interval:var,config__algorithm__effects:var,config__algorithm__min_allele_fraction:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__validate:var,config__algorithm__validate_regions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,reference__fasta__base:var,reference__rtg:var,reference__genome_context:var,genome_resources__variation__clinvar:var,genome_resources__variation__cosmic:var,genome_resources__variation__dbsnp:var,genome_resources__variation__esp:var,genome_resources__variation__exac:var,genome_resources__variation__gnomad_exome:var,genome_resources__variation__1000g:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__aliases__ensembl:var,genome_resources__aliases__human:var,genome_resources__aliases__snpeff:var,reference__snpeff__GRCh37_75:var,genome_resources__variation__train_hapmap:var,genome_resources__variation__train_indels:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- batch_for_variantcall
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10477
-  ramMin: 3072
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: vrn_file
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: regions__sample_callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variantcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__ensemble
-  type:
-    items: string
-    type: array
-- id: config__algorithm__vcfanno
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__effects
-  type:
-    items: string
-    type: array
-- id: config__algorithm__min_allele_fraction
-  type:
-    items: double
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__validate_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: reference__rtg
-  type:
-    items: File
-    type: array
-- id: reference__genome_context
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-      items: File
-      type: array
-    type: array
-- id: genome_resources__variation__clinvar
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__cosmic
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__esp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__exac
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__gnomad_exome
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: genome_resources__variation__1000g
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__aliases__ensembl
-  type:
-    items: string
-    type: array
-- id: genome_resources__aliases__human
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: genome_resources__aliases__snpeff
-  type:
-    items: string
-    type: array
-- id: reference__snpeff__GRCh37_75
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_hapmap
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__train_indels
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: batch_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__variation__clinvar
-          type: File
-        - name: genome_resources__variation__esp
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type: File
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: vrn_file
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__train_hapmap
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__variation__1000g
-          type: File
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__exac
-          type: File
-        - name: genome_resources__variation__gnomad_exome
-          type:
-          - 'null'
-          - string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: genome_resources__variation__dbsnp
-          type: File
-        - name: genome_resources__variation__polyx
-          type: File
-        - name: genome_resources__variation__encode_blacklist
-          type: File
-        - name: genome_resources__variation__cosmic
-          type: File
-        - name: config__algorithm__ensemble
-          type: string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__variation__train_indels
-          type: File
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: align_bam
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: batch_rec
-        type: record
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl
deleted file mode 100644
index bee219164db..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_bins.cwl
+++ /dev/null
@@ -1,219 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_bin_rec:regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;resources;description;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=align_bam:var,reference__fasta__base:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__callable_regions:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__svcaller:var,depth__variant_regions__regions:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,genome_resources__rnaseq__gene_bed:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_bins
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: sv_bin_rec
-  type:
-    items:
-      fields:
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_bin_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl
deleted file mode 100644
index 330224b83db..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/calculate_sv_coverage.cwl
+++ /dev/null
@@ -1,206 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=sv_rawcoverage_rec:depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;resources;description;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_bin_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- calculate_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-inputs:
-- id: sv_bin_rec
-  type:
-    fields:
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type: File
-    - name: genome_resources__variation__encode_blacklist
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_bin_rec
-    type: record
-outputs:
-- id: sv_rawcoverage_rec
-  type:
-    fields:
-    - name: depth__bins__target
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: depth__bins__seq2c
-      type:
-      - File
-      - 'null'
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: regions__bins__target
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__antitarget
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__gcannotated
-      type:
-      - File
-      - 'null'
-    - name: regions__bins__group
-      type:
-      - string
-      - 'null'
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: metadata__batch
-      type: string
-    - name: genome_resources__variation__lcr
-      type: File
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__variation__polyx
-      type: File
-    - name: genome_resources__variation__encode_blacklist
-      type: File
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: sv_rawcoverage_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl
deleted file mode 100644
index 7730a2a3223..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_calls.cwl
+++ /dev/null
@@ -1,180 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=ensemble_rec:ensemble__vrn_file;ensemble__validate__summary;ensemble__batch_samples;ensemble__batch_id
-- sentinel_inputs=ensemble_prep_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_calls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10240
-  ramMin: 49152
-  tmpdirMin: 0
-- class: dx:InputResourceRequirement
-  indirMin: 4687
-- class: SoftwareRequirement
-  packages:
-  - package: bcbio-variation-recall
-    specs:
-    - https://anaconda.org/bioconda/bcbio-variation-recall
-inputs:
-- id: ensemble_prep_rec
-  type:
-    fields:
-    - name: batch_id
-      type: string
-    - name: variants__calls
-      type:
-        items: File
-        type: array
-    - name: variants__variantcallers
-      type:
-        items: string
-        type: array
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: batch_samples
-      type:
-      - 'null'
-      - items: string
-        type: array
-    - name: validate__summary
-      type:
-      - File
-      - 'null'
-    - name: validate__tp
-      type:
-      - File
-      - 'null'
-    - name: validate__fp
-      type:
-      - File
-      - 'null'
-    - name: validate__fn
-      type:
-      - File
-      - 'null'
-    - name: vrn_file
-      type: File
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__vcfanno
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__variantcaller
-      type: string
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: config__algorithm__min_allele_fraction
-      type: double
-    - name: reference__snpeff__GRCh37_75
-      type: File
-    - name: reference__genome_context
-      type:
-        items: File
-        type: array
-    - name: reference__rtg
-      type: File
-    - name: config__algorithm__validate
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__validate_regions
-      type:
-      - File
-      - 'null'
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: genome_resources__aliases__human
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__tools_off
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__ensemble
-      type: string
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__effects
-      type: string
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: genome_resources__aliases__ensembl
-      type: string
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: genome_resources__aliases__snpeff
-      type: string
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: regions__sample_callable
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__callable_regions
-      type: File
-    name: ensemble_prep_rec
-    type: record
-outputs:
-- id: ensemble_rec
-  type:
-    fields:
-    - name: ensemble__vrn_file
-      type:
-      - File
-      - 'null'
-    - name: ensemble__validate__summary
-      type:
-      - File
-      - 'null'
-    - name: ensemble__batch_samples
-      type:
-        items: string
-        type: array
-    - name: ensemble__batch_id
-      type: string
-    name: ensemble_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl
deleted file mode 100644
index e59fc89683e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/combine_sample_regions.cwl
+++ /dev/null
@@ -1,99 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=config__algorithm__callable_regions,config__algorithm__non_callable_regions,config__algorithm__callable_count
-- sentinel_inputs=regions__callable:var,regions__nblock:var,metadata__batch:var,config__algorithm__nomap_split_size:var,config__algorithm__nomap_split_targets:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- combine_sample_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10299
-  ramMin: 3072
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 3008
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: regions__callable
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: regions__nblock
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: config__algorithm__nomap_split_size
-  type:
-    items: long
-    type: array
-- id: config__algorithm__nomap_split_targets
-  type:
-    items: long
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: config__algorithm__callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__non_callable_regions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__callable_count
-  type:
-    items: int
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl
deleted file mode 100644
index ed7c9b1e0b1..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/compare_to_rm.cwl
+++ /dev/null
@@ -1,299 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vc_rec:batch_samples;validate__summary;validate__tp;validate__fp;validate__fn;resources;description;vrn_file;reference__fasta__base;config__algorithm__vcfanno;config__algorithm__variantcaller;config__algorithm__coverage_interval;metadata__batch;config__algorithm__min_allele_fraction;reference__snpeff__GRCh37_75;reference__genome_context;reference__rtg;config__algorithm__validate;config__algorithm__validate_regions;genome_build;metadata__phenotype;genome_resources__aliases__human;config__algorithm__tools_off;config__algorithm__ensemble;analysis;config__algorithm__tools_on;config__algorithm__effects;config__algorithm__variant_regions;genome_resources__aliases__ensembl;config__algorithm__exclude_regions;genome_resources__aliases__snpeff;config__algorithm__variant_regions_merged;regions__sample_callable;config__algorithm__callable_regions
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- compare_to_rm
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: gvcf-regions
-    specs:
-    - https://anaconda.org/bioconda/gvcf-regions
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: rtg-tools
-    specs:
-    - https://anaconda.org/bioconda/rtg-tools
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl
deleted file mode 100644
index a5d59d661a0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/concat_batch_variantcalls.cwl
+++ /dev/null
@@ -1,190 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-merge
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,region_block:var,vrn_file_region:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- concat_batch_variantcalls
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-- class: arv:APIRequirement
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl
deleted file mode 100644
index 66d592642d7..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/detect_sv.cwl
+++ /dev/null
@@ -1,402 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=sv_rec:sv__variantcaller;sv__vrn_file;sv__supplemental;svvalidate__summary;resources;description;config__algorithm__svprioritize;genome_resources__variation__gc_profile;genome_build;genome_resources__variation__germline_het_pon;config__algorithm__tools_off;analysis;config__algorithm__tools_on;config__algorithm__svvalidate;genome_resources__aliases__snpeff;regions__sample_callable;variants__samples;depth__bins__normalized;depth__bins__background;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- detect_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 3656
-- class: SoftwareRequirement
-  packages:
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-  - package: delly
-    specs:
-    - https://anaconda.org/bioconda/delly
-  - package: duphold
-    specs:
-    - https://anaconda.org/bioconda/duphold
-  - package: extract-sv-reads
-    specs:
-    - https://anaconda.org/bioconda/extract-sv-reads
-  - package: lumpy-sv
-    specs:
-    - https://anaconda.org/bioconda/lumpy-sv
-  - package: manta
-    specs:
-    - https://anaconda.org/bioconda/manta
-  - package: break-point-inspector
-    specs:
-    - https://anaconda.org/bioconda/break-point-inspector
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: smoove
-    specs:
-    - https://anaconda.org/bioconda/smoove
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: seq2c
-    specs:
-    - https://anaconda.org/bioconda/seq2c
-  - package: simple_sv_annotation
-    specs:
-    - https://anaconda.org/bioconda/simple_sv_annotation
-  - package: survivor
-    specs:
-    - https://anaconda.org/bioconda/survivor
-  - package: svtools
-    specs:
-    - https://anaconda.org/bioconda/svtools
-  - package: svtyper
-    specs:
-    - https://anaconda.org/bioconda/svtyper
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: xorg-libxt
-    specs:
-    - https://anaconda.org/bioconda/xorg-libxt
-  - package: vawk
-    specs:
-    - https://anaconda.org/bioconda/vawk
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl
deleted file mode 100644
index 71c08911610..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/get_parallel_regions.cwl
+++ /dev/null
@@ -1,165 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-split
-- sentinel_outputs=region_block
-- sentinel_inputs=batch_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- get_parallel_regions
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10477
-  ramMin: 3072
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: region_block
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl
deleted file mode 100644
index 4e139a4d748..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/merge_split_alignments.cwl
+++ /dev/null
@@ -1,165 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-merge
-- sentinel_outputs=align_bam,work_bam_plus__disc,work_bam_plus__sr,hla__fastq
-- sentinel_inputs=alignment_rec:record,work_bam:var,align_bam:var,work_bam_plus__disc:var,work_bam_plus__sr:var,hla__fastq:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- merge_split_alignments
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10655
-  ramMin: 49152
-  tmpdirMin: 208
-- class: dx:InputResourceRequirement
-  indirMin: 3127
-- class: SoftwareRequirement
-  packages:
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: align_bam_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__disc_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: work_bam_plus__sr_toolinput
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: hla__fastq_toolinput
-  type:
-    items:
-    - 'null'
-    - items: File
-      type: array
-    type: array
-outputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl
deleted file mode 100644
index 96036a07fc2..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/multiqc_summary.cwl
+++ /dev/null
@@ -1,94 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=summary__multiqc,versions__tools,versions__data
-- sentinel_inputs=qcout_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- multiqc_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10477
-  ramMin: 3072
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 1
-- class: SoftwareRequirement
-  packages:
-  - package: multiqc
-    specs:
-    - https://anaconda.org/bioconda/multiqc
-  - package: multiqc-bcbio
-    specs:
-    - https://anaconda.org/bioconda/multiqc-bcbio
-inputs:
-- id: qcout_rec
-  type:
-    items:
-      fields:
-      - name: summary__qc
-        type:
-        - File
-        - 'null'
-      - name: summary__metrics
-        type:
-        - string
-        - 'null'
-      - name: description
-        type: string
-      - name: genome_build
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: reference__versions
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      name: qcout_rec
-      type: record
-    type: array
-outputs:
-- id: summary__multiqc
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__tools
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: versions__data
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl
deleted file mode 100644
index af33573637d..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/normalize_sv_coverage.cwl
+++ /dev/null
@@ -1,224 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv_coverage_rec:depth__bins__normalized;depth__bins__background;resources;description;depth__bins__target;depth__bins__antitarget;depth__bins__seq2c;regions__bins__target;regions__bins__antitarget;regions__bins__gcannotated;regions__bins__group;reference__fasta__base;config__algorithm__svcaller;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;metadata__batch;genome_resources__variation__lcr;metadata__phenotype;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__variant_regions;config__algorithm__exclude_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__seq2c_bed_ready;depth__variant_regions__regions;config__algorithm__callable_regions
-- sentinel_inputs=sv_rawcoverage_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- normalize_sv_coverage
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: cnvkit
-    specs:
-    - https://anaconda.org/bioconda/cnvkit
-inputs:
-- id: sv_rawcoverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rawcoverage_rec
-      type: record
-    type: array
-outputs:
-- id: sv_coverage_rec
-  type:
-    items:
-      fields:
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_coverage_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl
deleted file mode 100644
index 4ffe2646ec9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/pipeline_summary.cwl
+++ /dev/null
@@ -1,219 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=qcout_rec:summary__qc;summary__metrics;description;genome_build;config__algorithm__tools_off;reference__versions;config__algorithm__qc;config__algorithm__tools_on
-- sentinel_inputs=qc_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- pipeline_summary
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 3010
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: fastqc=0.11.7=5
-    specs:
-    - https://anaconda.org/bioconda/fastqc=0.11.7=5
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: hts-nim-tools
-    specs:
-    - https://anaconda.org/bioconda/hts-nim-tools
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: qsignature
-    specs:
-    - https://anaconda.org/bioconda/qsignature
-  - package: qualimap
-    specs:
-    - https://anaconda.org/bioconda/qualimap
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: preseq
-    specs:
-    - https://anaconda.org/bioconda/preseq
-  - package: peddy
-    specs:
-    - https://anaconda.org/bioconda/peddy
-  - package: verifybamid2
-    specs:
-    - https://anaconda.org/bioconda/verifybamid2
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: qc_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - string
-      - 'null'
-    - name: metadata__batch
-      type: string
-    - name: genome_build
-      type: string
-    - name: metadata__phenotype
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-        items: string
-        type: array
-    - name: reference__versions
-      type: File
-    - name: reference__viral
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: analysis
-      type: string
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__stats
-      type:
-      - File
-      - 'null'
-    - name: depth__samtools__idxstats
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__variant_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__sv_regions__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__regions
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__dist
-      type:
-      - File
-      - 'null'
-    - name: depth__coverage__thresholds
-      type:
-      - File
-      - 'null'
-    - name: variants__samples
-      type:
-        items:
-          items:
-          - File
-          - 'null'
-          type: array
-        type: array
-    name: qc_rec
-    type: record
-outputs:
-- id: qcout_rec
-  type:
-    fields:
-    - name: summary__qc
-      type:
-      - File
-      - 'null'
-    - name: summary__metrics
-      type:
-      - string
-      - 'null'
-    - name: description
-      type: string
-    - name: genome_build
-      type: string
-    - name: config__algorithm__tools_off
-      type:
-        items: string
-        type: array
-    - name: reference__versions
-      type: File
-    - name: config__algorithm__qc
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    name: qcout_rec
-    type: record
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl
deleted file mode 100644
index 92f4acb8c7f..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment.cwl
+++ /dev/null
@@ -1,221 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=config__algorithm__coverage_interval,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready,regions__callable,regions__sample_callable,regions__nblock,depth__samtools__stats,depth__samtools__idxstats,depth__variant_regions__regions,depth__variant_regions__dist,depth__sv_regions__regions,depth__sv_regions__dist,depth__coverage__regions,depth__coverage__dist,depth__coverage__thresholds,align_bam
-- sentinel_inputs=postprocess_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10596
-  ramMin: 49152
-  tmpdirMin: 178
-- class: dx:InputResourceRequirement
-  indirMin: 18018
-- class: SoftwareRequirement
-  packages:
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: goleft
-    specs:
-    - https://anaconda.org/bioconda/goleft
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: mosdepth
-    specs:
-    - https://anaconda.org/bioconda/mosdepth
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-- class: arv:APIRequirement
-inputs:
-- id: postprocess_alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__coverage_interval
-      type:
-      - 'null'
-      - string
-    - name: genome_resources__rnaseq__gene_bed
-      type: File
-    - name: genome_resources__variation__lcr
-      type: File
-    - name: config__algorithm__recalibrate
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: genome_resources__variation__dbsnp
-      type: File
-    - name: genome_resources__variation__polyx
-      type: File
-    - name: genome_resources__variation__encode_blacklist
-      type: File
-    - name: config__algorithm__tools_on
-      type:
-        items: string
-        type: array
-    - name: config__algorithm__variant_regions
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__exclude_regions
-      type:
-      - 'null'
-      - items: 'null'
-        type: array
-    - name: config__algorithm__archive
-      type:
-      - 'null'
-      - string
-    - name: align_bam
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__variant_regions_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_merged
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__coverage_orig
-      type:
-      - File
-      - 'null'
-    - name: config__algorithm__seq2c_bed_ready
-      type:
-      - File
-      - 'null'
-    name: postprocess_alignment_rec
-    type: record
-outputs:
-- id: config__algorithm__coverage_interval
-  type:
-  - string
-  - 'null'
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-- id: regions__callable
-  type:
-  - File
-  - 'null'
-- id: regions__sample_callable
-  type:
-  - File
-  - 'null'
-- id: regions__nblock
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__stats
-  type:
-  - File
-  - 'null'
-- id: depth__samtools__idxstats
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__variant_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__regions
-  type:
-  - File
-  - 'null'
-- id: depth__sv_regions__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__regions
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__dist
-  type:
-  - File
-  - 'null'
-- id: depth__coverage__thresholds
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl
deleted file mode 100644
index 926d37e91df..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_alignment_to_rec.cwl
+++ /dev/null
@@ -1,237 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=postprocess_alignment_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;genome_resources__rnaseq__gene_bed;genome_resources__variation__lcr;config__algorithm__recalibrate;genome_resources__variation__dbsnp;genome_resources__variation__polyx;genome_resources__variation__encode_blacklist;config__algorithm__tools_on;config__algorithm__variant_regions;config__algorithm__exclude_regions;config__algorithm__archive;align_bam;config__algorithm__variant_regions_merged;config__algorithm__variant_regions_orig;config__algorithm__coverage;config__algorithm__coverage_merged;config__algorithm__coverage_orig;config__algorithm__seq2c_bed_ready
-- sentinel_inputs=align_bam:var,config__algorithm__archive:var,config__algorithm__coverage_interval:var,config__algorithm__exclude_regions:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__variant_regions_orig:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,config__algorithm__coverage_orig:var,config__algorithm__seq2c_bed_ready:var,config__algorithm__recalibrate:var,config__algorithm__tools_on:var,genome_resources__rnaseq__gene_bed:var,genome_resources__variation__dbsnp:var,genome_resources__variation__lcr:var,genome_resources__variation__polyx:var,genome_resources__variation__encode_blacklist:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_alignment_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__archive
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - 'null'
-    - string
-    type: array
-- id: config__algorithm__exclude_regions
-  type:
-    items:
-    - 'null'
-    - items: 'null'
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_orig
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__seq2c_bed_ready
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__recalibrate
-  type:
-    items:
-    - string
-    - 'null'
-    - boolean
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_resources__rnaseq__gene_bed
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__dbsnp
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__lcr
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__polyx
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: genome_resources__variation__encode_blacklist
-  secondaryFiles:
-  - .tbi
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: postprocess_alignment_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__recalibrate
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__archive
-        type:
-        - 'null'
-        - string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_orig
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      name: postprocess_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl
deleted file mode 100644
index 5151f1520c6..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/postprocess_variants.cwl
+++ /dev/null
@@ -1,174 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-single
-- sentinel_outputs=vrn_file
-- sentinel_inputs=batch_rec:record,vrn_file:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- postprocess_variants
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10299
-  ramMin: 49152
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: snpeff
-    specs:
-    - https://anaconda.org/bioconda/snpeff
-    version:
-    - 4.3.1t
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: vrn_file_toolinput
-  secondaryFiles:
-  - .tbi
-  type: File
-outputs:
-- id: vrn_file
-  secondaryFiles:
-  - .tbi
-  type: File
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl
deleted file mode 100644
index 5c392bdb350..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_align_inputs.cwl
+++ /dev/null
@@ -1,139 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-split
-- sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split
-- sentinel_inputs=alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_align_inputs
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10418
-  ramMin: 49152
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 3127
-- class: SoftwareRequirement
-  packages:
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: atropos;env
-    specs:
-    - https://anaconda.org/bioconda/atropos;env
-    version:
-    - python3
-  - package: optitype
-    specs:
-    - https://anaconda.org/bioconda/optitype
-  - package: razers3
-    specs:
-    - https://anaconda.org/bioconda/razers3
-    version:
-    - 3.5.0
-  - package: coincbc
-    specs:
-    - https://anaconda.org/bioconda/coincbc
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-outputs:
-- id: process_alignment_rec
-  type:
-    items:
-      fields:
-      - name: files
-        type:
-        - 'null'
-        - items: File
-          type: array
-      - name: config__algorithm__quality_format
-        type:
-        - string
-        - 'null'
-      - name: align_split
-        type:
-        - string
-        - 'null'
-      name: process_alignment_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl
deleted file mode 100644
index 8e6d9500406..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples.cwl
+++ /dev/null
@@ -1,95 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-parallel
-- sentinel_outputs=rgnames__sample,config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready
-- sentinel_inputs=prep_samples_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10299
-  ramMin: 3072
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 3008
-- class: SoftwareRequirement
-  packages:
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-inputs:
-- id: prep_samples_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__svcaller
-      type:
-        items: string
-        type: array
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    name: prep_samples_rec
-    type: record
-outputs:
-- id: rgnames__sample
-  type: string
-- id: config__algorithm__variant_regions
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__variant_regions_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_merged
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__coverage_orig
-  type:
-  - File
-  - 'null'
-- id: config__algorithm__seq2c_bed_ready
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl
deleted file mode 100644
index 9ccaa591fde..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/prep_samples_to_rec.cwl
+++ /dev/null
@@ -1,85 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__svcaller;rgnames__sample;config__algorithm__variant_regions
-- sentinel_inputs=rgnames__sample:var,config__algorithm__svcaller:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- prep_samples_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10299
-  ramMin: 3072
-  tmpdirMin: 30
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: rgnames__sample
-  type:
-    items: string
-    type: array
-- id: config__algorithm__svcaller
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items: File
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: prep_samples_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type:
-          items: string
-          type: array
-      - name: rgnames__sample
-        type: string
-      - name: config__algorithm__variant_regions
-        type: File
-      name: prep_samples_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl
deleted file mode 100644
index 718e2cd14e0..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/process_alignment.cwl
+++ /dev/null
@@ -1,195 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=single-parallel
-- sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr
-- sentinel_inputs=alignment_rec:record,process_alignment_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- process_alignment
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 3246
-- class: SoftwareRequirement
-  packages:
-  - package: bwa
-    specs:
-    - https://anaconda.org/bioconda/bwa
-  - package: bwakit
-    specs:
-    - https://anaconda.org/bioconda/bwakit
-  - package: grabix
-    specs:
-    - https://anaconda.org/bioconda/grabix
-  - package: minimap2
-    specs:
-    - https://anaconda.org/bioconda/minimap2
-  - package: novoalign
-    specs:
-    - https://anaconda.org/bioconda/novoalign
-  - package: snap-aligner
-    specs:
-    - https://anaconda.org/bioconda/snap-aligner
-    version:
-    - 1.0dev.97
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: sambamba
-    specs:
-    - https://anaconda.org/bioconda/sambamba
-  - package: fgbio
-    specs:
-    - https://anaconda.org/bioconda/fgbio
-  - package: umis
-    specs:
-    - https://anaconda.org/bioconda/umis
-  - package: biobambam
-    specs:
-    - https://anaconda.org/bioconda/biobambam
-  - package: seqtk
-    specs:
-    - https://anaconda.org/bioconda/seqtk
-  - package: samblaster
-    specs:
-    - https://anaconda.org/bioconda/samblaster
-  - package: variantbam
-    specs:
-    - https://anaconda.org/bioconda/variantbam
-- class: arv:APIRequirement
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-- id: process_alignment_rec
-  type:
-    fields:
-    - name: files
-      type:
-      - 'null'
-      - items: File
-        type: array
-    - name: config__algorithm__quality_format
-      type:
-      - string
-      - 'null'
-    - name: align_split
-      type:
-      - string
-      - 'null'
-    name: process_alignment_rec
-    type: record
-outputs:
-- id: work_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-- id: work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl
deleted file mode 100644
index 0336669ad83..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/qc_to_rec.cwl
+++ /dev/null
@@ -1,307 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=qc_rec:resources;description;reference__fasta__base;config__algorithm__coverage_interval;metadata__batch;genome_build;metadata__phenotype;config__algorithm__tools_off;reference__versions;reference__viral;config__algorithm__qc;analysis;config__algorithm__tools_on;config__algorithm__variant_regions;align_bam;config__algorithm__variant_regions_merged;config__algorithm__coverage;config__algorithm__coverage_merged;depth__samtools__stats;depth__samtools__idxstats;depth__variant_regions__regions;depth__variant_regions__dist;depth__sv_regions__regions;depth__sv_regions__dist;depth__coverage__regions;depth__coverage__dist;depth__coverage__thresholds;variants__samples
-- sentinel_inputs=align_bam:var,analysis:var,reference__fasta__base:var,reference__versions:var,config__algorithm__tools_on:var,config__algorithm__tools_off:var,genome_build:var,config__algorithm__qc:var,metadata__batch:var,metadata__phenotype:var,config__algorithm__coverage_interval:var,depth__variant_regions__regions:var,depth__variant_regions__dist:var,depth__samtools__stats:var,depth__samtools__idxstats:var,depth__sv_regions__regions:var,depth__sv_regions__dist:var,depth__coverage__regions:var,depth__coverage__dist:var,depth__coverage__thresholds:var,config__algorithm__variant_regions:var,config__algorithm__variant_regions_merged:var,config__algorithm__coverage:var,config__algorithm__coverage_merged:var,variants__samples:var,reference__viral:var,resources:var,description:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- qc_to_rec
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10418
-  ramMin: 3072
-  tmpdirMin: 89
-- class: dx:InputResourceRequirement
-  indirMin: 0
-inputs:
-- id: align_bam
-  secondaryFiles:
-  - .bai
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: analysis
-  type:
-    items: string
-    type: array
-- id: reference__fasta__base
-  secondaryFiles:
-  - ^.dict
-  - .fai
-  type:
-    items: File
-    type: array
-- id: reference__versions
-  type:
-    items: File
-    type: array
-- id: config__algorithm__tools_on
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: config__algorithm__tools_off
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: genome_build
-  type:
-    items: string
-    type: array
-- id: config__algorithm__qc
-  type:
-    items:
-      items: string
-      type: array
-    type: array
-- id: metadata__batch
-  type:
-    items: string
-    type: array
-- id: metadata__phenotype
-  type:
-    items: string
-    type: array
-- id: config__algorithm__coverage_interval
-  type:
-    items:
-    - string
-    - 'null'
-    type: array
-- id: depth__variant_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__variant_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__stats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__samtools__idxstats
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__sv_regions__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__dist
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: depth__coverage__thresholds
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__variant_regions_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: config__algorithm__coverage_merged
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: reference__viral
-  secondaryFiles:
-  - .fai
-  - .ann
-  - .sa
-  - .pac
-  - .amb
-  - ^.dict
-  - .bwt
-  type:
-    items: File
-    type: array
-- id: resources
-  type:
-    items: string
-    type: array
-- id: description
-  type:
-    items: string
-    type: array
-outputs:
-- id: qc_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: reference__versions
-        type: File
-      - name: reference__viral
-        type: File
-      - name: config__algorithm__qc
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__coverage_merged
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__stats
-        type:
-        - File
-        - 'null'
-      - name: depth__samtools__idxstats
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__sv_regions__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__regions
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__dist
-        type:
-        - File
-        - 'null'
-      - name: depth__coverage__thresholds
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      name: qc_rec
-      type: record
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl
deleted file mode 100644
index c5f8047d69a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_sv.cwl
+++ /dev/null
@@ -1,236 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=sv__calls,sv__supplemental,sv__prioritize__tsv,sv__prioritize__raw,svvalidate__grading_summary,svvalidate__grading_plots
-- sentinel_inputs=sv_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_sv
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 10358
-  ramMin: 3072
-  tmpdirMin: 59
-- class: dx:InputResourceRequirement
-  indirMin: 3024
-- class: SoftwareRequirement
-  packages:
-  - package: bcbio-prioritize
-    specs:
-    - https://anaconda.org/bioconda/bcbio-prioritize
-inputs:
-- id: sv_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: sv__variantcaller
-          type:
-          - string
-          - 'null'
-        - name: sv__vrn_file
-          type:
-          - File
-          - 'null'
-        - name: sv__supplemental
-          type:
-            items:
-            - File
-            type: array
-        - name: svvalidate__summary
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: config__algorithm__svprioritize
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__variation__gc_profile
-          type:
-          - 'null'
-          - string
-        - name: genome_build
-          type: string
-        - name: genome_resources__variation__germline_het_pon
-          type:
-          - 'null'
-          - string
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__svvalidate
-          type:
-          - 'null'
-          - string
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: variants__samples
-          type:
-            items:
-              items:
-              - File
-              - 'null'
-              type: array
-            type: array
-        - name: depth__bins__normalized
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__background
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__target
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: depth__bins__seq2c
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__target
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__antitarget
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__gcannotated
-          type:
-          - File
-          - 'null'
-        - name: regions__bins__group
-          type:
-          - string
-          - 'null'
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__svcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: genome_resources__rnaseq__gene_bed
-          type: File
-        - name: metadata__batch
-          type: string
-        - name: genome_resources__variation__lcr
-          type: File
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__variation__polyx
-          type: File
-        - name: genome_resources__variation__encode_blacklist
-          type: File
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__seq2c_bed_ready
-          type:
-          - File
-          - 'null'
-        - name: depth__variant_regions__regions
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: sv_rec
-        type: record
-      type: array
-    type: array
-outputs:
-- id: sv__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__supplemental
-  type:
-    items:
-      items:
-      - File
-      type: array
-    type: array
-- id: sv__prioritize__tsv
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: sv__prioritize__raw
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: svvalidate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: svvalidate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl
deleted file mode 100644
index 48ec1cd601a..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/summarize_vc.cwl
+++ /dev/null
@@ -1,212 +0,0 @@
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=multi-combined
-- sentinel_outputs=variants__calls,variants__gvcf,variants__samples,validate__grading_summary,validate__grading_plots
-- sentinel_inputs=vc_rec:record,ensemble_rec:record
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- summarize_vc
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 1
-  outdirMin: 1000000
-  ramMin: 3072
-  tmpdirMin: 1000000
-- class: dx:InputResourceRequirement
-  indirMin: 1000000
-inputs:
-- id: vc_rec
-  type:
-    items:
-      items:
-        fields:
-        - name: batch_samples
-          type:
-          - 'null'
-          - items: string
-            type: array
-        - name: validate__summary
-          type:
-          - File
-          - 'null'
-        - name: validate__tp
-          type:
-          - File
-          - 'null'
-        - name: validate__fp
-          type:
-          - File
-          - 'null'
-        - name: validate__fn
-          type:
-          - File
-          - 'null'
-        - name: resources
-          type: string
-        - name: description
-          type: string
-        - name: vrn_file
-          type: File
-        - name: reference__fasta__base
-          type: File
-        - name: config__algorithm__vcfanno
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: config__algorithm__variantcaller
-          type: string
-        - name: config__algorithm__coverage_interval
-          type:
-          - string
-          - 'null'
-        - name: metadata__batch
-          type: string
-        - name: config__algorithm__min_allele_fraction
-          type: double
-        - name: reference__snpeff__GRCh37_75
-          type: File
-        - name: reference__genome_context
-          type:
-            items: File
-            type: array
-        - name: reference__rtg
-          type: File
-        - name: config__algorithm__validate
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__validate_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_build
-          type: string
-        - name: metadata__phenotype
-          type: string
-        - name: genome_resources__aliases__human
-          type:
-          - string
-          - 'null'
-          - boolean
-        - name: config__algorithm__tools_off
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__ensemble
-          type: string
-        - name: analysis
-          type: string
-        - name: config__algorithm__tools_on
-          type:
-            items: string
-            type: array
-        - name: config__algorithm__effects
-          type: string
-        - name: config__algorithm__variant_regions
-          type:
-          - File
-          - 'null'
-        - name: genome_resources__aliases__ensembl
-          type: string
-        - name: config__algorithm__exclude_regions
-          type:
-          - 'null'
-          - items: 'null'
-            type: array
-        - name: genome_resources__aliases__snpeff
-          type: string
-        - name: config__algorithm__variant_regions_merged
-          type:
-          - File
-          - 'null'
-        - name: regions__sample_callable
-          type:
-          - File
-          - 'null'
-        - name: config__algorithm__callable_regions
-          type: File
-        name: vc_rec
-        type: record
-      type: array
-    type: array
-- id: ensemble_rec
-  type:
-    items:
-      fields:
-      - name: ensemble__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: ensemble__validate__summary
-        type:
-        - File
-        - 'null'
-      - name: ensemble__batch_samples
-        type:
-          items: string
-          type: array
-      - name: ensemble__batch_id
-        type: string
-      name: ensemble_rec
-      type: record
-    type: array
-outputs:
-- id: variants__calls
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__gvcf
-  type:
-    items:
-    - 'null'
-    - items:
-      - File
-      - 'null'
-      type: array
-    type: array
-- id: variants__samples
-  type:
-    items:
-      items:
-        items:
-        - File
-        - 'null'
-        type: array
-      type: array
-    type: array
-- id: validate__grading_summary
-  type:
-    items:
-    - File
-    - 'null'
-    type: array
-- id: validate__grading_plots
-  type:
-    items:
-      items:
-      - File
-      - 'null'
-      type: array
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl
deleted file mode 100644
index a4fadb20991..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/steps/variantcall_batch_region.cwl
+++ /dev/null
@@ -1,260 +0,0 @@
-$namespaces:
-  arv: http://arvados.org/cwl#
-  dx: https://www.dnanexus.com/cwl#
-arguments:
-- position: 0
-  valueFrom: sentinel_runtime=cores,$(runtime['cores']),ram,$(runtime['ram'])
-- sentinel_parallel=batch-parallel
-- sentinel_outputs=vrn_file_region,region_block
-- sentinel_inputs=batch_rec:record,region_block:var
-- run_number=0
-baseCommand:
-- bcbio_nextgen.py
-- runfn
-- variantcall_batch_region
-- cwl
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-- class: DockerRequirement
-  dockerImageId: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-  dockerPull: quay.io/bcbio/bcbio-vc:1.1.4a-741877e
-- class: ResourceRequirement
-  coresMin: 16
-  outdirMin: 10477
-  ramMin: 49152
-  tmpdirMin: 119
-- class: dx:InputResourceRequirement
-  indirMin: 24883
-- class: SoftwareRequirement
-  packages:
-  - package: bcftools
-    specs:
-    - https://anaconda.org/bioconda/bcftools
-  - package: bedtools
-    specs:
-    - https://anaconda.org/bioconda/bedtools
-  - package: freebayes
-    specs:
-    - https://anaconda.org/bioconda/freebayes
-    version:
-    - 1.1.0.46
-  - package: gatk4
-    specs:
-    - https://anaconda.org/bioconda/gatk4
-  - package: vqsr_cnn
-    specs:
-    - https://anaconda.org/bioconda/vqsr_cnn
-  - package: deepvariant
-    specs:
-    - https://anaconda.org/bioconda/deepvariant
-  - package: sentieon
-    specs:
-    - https://anaconda.org/bioconda/sentieon
-  - package: htslib
-    specs:
-    - https://anaconda.org/bioconda/htslib
-  - package: octopus
-    specs:
-    - https://anaconda.org/bioconda/octopus
-  - package: picard
-    specs:
-    - https://anaconda.org/bioconda/picard
-  - package: platypus-variant
-    specs:
-    - https://anaconda.org/bioconda/platypus-variant
-  - package: pythonpy
-    specs:
-    - https://anaconda.org/bioconda/pythonpy
-  - package: samtools
-    specs:
-    - https://anaconda.org/bioconda/samtools
-  - package: pysam>
-    specs:
-    - https://anaconda.org/bioconda/pysam>
-    version:
-    - 0.13.0
-  - package: strelka
-    specs:
-    - https://anaconda.org/bioconda/strelka
-  - package: vardict
-    specs:
-    - https://anaconda.org/bioconda/vardict
-  - package: vardict-java
-    specs:
-    - https://anaconda.org/bioconda/vardict-java
-  - package: varscan
-    specs:
-    - https://anaconda.org/bioconda/varscan
-  - package: moreutils
-    specs:
-    - https://anaconda.org/bioconda/moreutils
-  - package: vcfanno
-    specs:
-    - https://anaconda.org/bioconda/vcfanno
-  - package: vcflib
-    specs:
-    - https://anaconda.org/bioconda/vcflib
-  - package: vt
-    specs:
-    - https://anaconda.org/bioconda/vt
-  - package: r
-    specs:
-    - https://anaconda.org/bioconda/r
-    version:
-    - 3.4.1
-  - package: r-base=3.4.1=h4fe35fd_8
-    specs:
-    - https://anaconda.org/bioconda/r-base=3.4.1=h4fe35fd_8
-  - package: perl
-    specs:
-    - https://anaconda.org/bioconda/perl
-- class: arv:APIRequirement
-- class: arv:RuntimeConstraints
-  keep_cache: 4096
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-- id: region_block_toolinput
-  type:
-    items: string
-    type: array
-outputs:
-- id: vrn_file_region
-  secondaryFiles:
-  - .tbi
-  type:
-  - File
-  - 'null'
-- id: region_block
-  type:
-    items: string
-    type: array
-requirements:
-- class: InlineJavascriptRequirement
-- class: InitialWorkDirRequirement
-  listing:
-  - entry: $(JSON.stringify(inputs))
-    entryname: cwl.inputs.json
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl
deleted file mode 100644
index 0f1dfd3dd81..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-alignment.cwl
+++ /dev/null
@@ -1,140 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: alignment_rec
-  type:
-    fields:
-    - name: resources
-      type: string
-    - name: description
-      type: string
-    - name: config__algorithm__align_split_size
-      type:
-      - 'null'
-      - string
-    - name: files
-      type:
-        items: File
-        type: array
-    - name: config__algorithm__trim_reads
-      type: string
-    - name: reference__fasta__base
-      type: File
-    - name: config__algorithm__adapters
-      type:
-        items: string
-        type: array
-    - name: rgnames__lb
-      type:
-      - 'null'
-      - string
-    - name: rgnames__rg
-      type: string
-    - name: rgnames__lane
-      type: string
-    - name: reference__bwa__indexes
-      type: File
-    - name: config__algorithm__bam_clean
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: config__algorithm__aligner
-      type: string
-    - name: rgnames__pl
-      type: string
-    - name: config__algorithm__mark_duplicates
-      type:
-      - string
-      - 'null'
-      - boolean
-    - name: analysis
-      type: string
-    - name: rgnames__sample
-      type: string
-    - name: config__algorithm__variant_regions
-      type: File
-    - name: rgnames__pu
-      type: string
-    name: alignment_rec
-    type: record
-outputs:
-- id: align_bam
-  outputSource: merge_split_alignments/align_bam
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__disc
-  outputSource: merge_split_alignments/work_bam_plus__disc
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: work_bam_plus__sr
-  outputSource: merge_split_alignments/work_bam_plus__sr
-  secondaryFiles:
-  - .bai
-  type:
-  - File
-  - 'null'
-- id: hla__fastq
-  outputSource: merge_split_alignments/hla__fastq
-  type:
-  - 'null'
-  - items: File
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: prep_align_inputs
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  out:
-  - id: process_alignment_rec
-  run: steps/prep_align_inputs.cwl
-- id: process_alignment
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: process_alignment_rec
-    source: prep_align_inputs/process_alignment_rec
-  out:
-  - id: work_bam
-  - id: align_bam
-  - id: hla__fastq
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  run: steps/process_alignment.cwl
-  scatter:
-  - process_alignment_rec
-  scatterMethod: dotproduct
-- id: merge_split_alignments
-  in:
-  - id: alignment_rec
-    source: alignment_rec
-  - id: work_bam
-    source: process_alignment/work_bam
-  - id: align_bam_toolinput
-    source: process_alignment/align_bam
-  - id: work_bam_plus__disc_toolinput
-    source: process_alignment/work_bam_plus__disc
-  - id: work_bam_plus__sr_toolinput
-    source: process_alignment/work_bam_plus__sr
-  - id: hla__fastq_toolinput
-    source: process_alignment/hla__fastq
-  out:
-  - id: align_bam
-  - id: work_bam_plus__disc
-  - id: work_bam_plus__sr
-  - id: hla__fastq
-  run: steps/merge_split_alignments.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl
deleted file mode 100644
index f8724f9b0b9..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-svcall.cwl
+++ /dev/null
@@ -1,316 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: sv_batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: work_bam_plus__disc
-        type:
-        - File
-        - 'null'
-      - name: work_bam_plus__sr
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_batch_rec
-      type: record
-    type: array
-outputs:
-- id: sv_rec
-  outputSource: detect_sv/sv_rec
-  type:
-    items:
-      fields:
-      - name: sv__variantcaller
-        type:
-        - string
-        - 'null'
-      - name: sv__vrn_file
-        type:
-        - File
-        - 'null'
-      - name: sv__supplemental
-        type:
-          items:
-          - File
-          type: array
-      - name: svvalidate__summary
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: config__algorithm__svprioritize
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__gc_profile
-        type:
-        - 'null'
-        - string
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__germline_het_pon
-        type:
-        - 'null'
-        - string
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__svvalidate
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: variants__samples
-        type:
-          items:
-            items:
-            - File
-            - 'null'
-            type: array
-          type: array
-      - name: depth__bins__normalized
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__background
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__target
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: depth__bins__seq2c
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__target
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__antitarget
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__gcannotated
-        type:
-        - File
-        - 'null'
-      - name: regions__bins__group
-        type:
-        - string
-        - 'null'
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__svcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__rnaseq__gene_bed
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__seq2c_bed_ready
-        type:
-        - File
-        - 'null'
-      - name: depth__variant_regions__regions
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: sv_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: detect_sv
-  in:
-  - id: sv_batch_rec
-    source: sv_batch_rec
-  out:
-  - id: sv_rec
-  run: steps/detect_sv.cwl
diff --git a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl b/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl
deleted file mode 100644
index fc5066d386e..00000000000
--- a/centaur/src/main/resources/integrationTestCases/cwl/bcbio/wes_chr21_test-workflow-gcp/wf-variantcall.cwl
+++ /dev/null
@@ -1,300 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-hints: []
-inputs:
-- id: batch_rec
-  type:
-    items:
-      fields:
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: genome_resources__variation__clinvar
-        type: File
-      - name: genome_resources__variation__esp
-        type: File
-      - name: metadata__batch
-        type: string
-      - name: genome_resources__variation__lcr
-        type: File
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: vrn_file
-        type:
-        - 'null'
-        - string
-      - name: genome_resources__variation__train_hapmap
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__variation__1000g
-        type: File
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: genome_resources__variation__exac
-        type: File
-      - name: genome_resources__variation__gnomad_exome
-        type:
-        - 'null'
-        - string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: genome_resources__variation__dbsnp
-        type: File
-      - name: genome_resources__variation__polyx
-        type: File
-      - name: genome_resources__variation__encode_blacklist
-        type: File
-      - name: genome_resources__variation__cosmic
-        type: File
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__variation__train_indels
-        type: File
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: align_bam
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: batch_rec
-      type: record
-    type: array
-outputs:
-- id: vc_rec
-  outputSource: compare_to_rm/vc_rec
-  type:
-    items:
-      fields:
-      - name: batch_samples
-        type:
-        - 'null'
-        - items: string
-          type: array
-      - name: validate__summary
-        type:
-        - File
-        - 'null'
-      - name: validate__tp
-        type:
-        - File
-        - 'null'
-      - name: validate__fp
-        type:
-        - File
-        - 'null'
-      - name: validate__fn
-        type:
-        - File
-        - 'null'
-      - name: resources
-        type: string
-      - name: description
-        type: string
-      - name: vrn_file
-        type: File
-      - name: reference__fasta__base
-        type: File
-      - name: config__algorithm__vcfanno
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: config__algorithm__variantcaller
-        type: string
-      - name: config__algorithm__coverage_interval
-        type:
-        - string
-        - 'null'
-      - name: metadata__batch
-        type: string
-      - name: config__algorithm__min_allele_fraction
-        type: double
-      - name: reference__snpeff__GRCh37_75
-        type: File
-      - name: reference__genome_context
-        type:
-          items: File
-          type: array
-      - name: reference__rtg
-        type: File
-      - name: config__algorithm__validate
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__validate_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_build
-        type: string
-      - name: metadata__phenotype
-        type: string
-      - name: genome_resources__aliases__human
-        type:
-        - string
-        - 'null'
-        - boolean
-      - name: config__algorithm__tools_off
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__ensemble
-        type: string
-      - name: analysis
-        type: string
-      - name: config__algorithm__tools_on
-        type:
-          items: string
-          type: array
-      - name: config__algorithm__effects
-        type: string
-      - name: config__algorithm__variant_regions
-        type:
-        - File
-        - 'null'
-      - name: genome_resources__aliases__ensembl
-        type: string
-      - name: config__algorithm__exclude_regions
-        type:
-        - 'null'
-        - items: 'null'
-          type: array
-      - name: genome_resources__aliases__snpeff
-        type: string
-      - name: config__algorithm__variant_regions_merged
-        type:
-        - File
-        - 'null'
-      - name: regions__sample_callable
-        type:
-        - File
-        - 'null'
-      - name: config__algorithm__callable_regions
-        type: File
-      name: vc_rec
-      type: record
-    type: array
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: MPLCONFIGDIR
-    envValue: .
-- class: ScatterFeatureRequirement
-- class: SubworkflowFeatureRequirement
-steps:
-- id: get_parallel_regions
-  in:
-  - id: batch_rec
-    source: batch_rec
-  out:
-  - id: region_block
-  run: steps/get_parallel_regions.cwl
-- id: variantcall_batch_region
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block_toolinput
-    source: get_parallel_regions/region_block
-  out:
-  - id: vrn_file_region
-  - id: region_block
-  run: steps/variantcall_batch_region.cwl
-  scatter:
-  - region_block_toolinput
-  scatterMethod: dotproduct
-- id: concat_batch_variantcalls
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: region_block
-    source: variantcall_batch_region/region_block
-  - id: vrn_file_region
-    source: variantcall_batch_region/vrn_file_region
-  out:
-  - id: vrn_file
-  run: steps/concat_batch_variantcalls.cwl
-- id: postprocess_variants
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file_toolinput
-    source: concat_batch_variantcalls/vrn_file
-  out:
-  - id: vrn_file
-  run: steps/postprocess_variants.cwl
-- id: compare_to_rm
-  in:
-  - id: batch_rec
-    source: batch_rec
-  - id: vrn_file
-    source: postprocess_variants/vrn_file
-  out:
-  - id: vc_rec
-  run: steps/compare_to_rm.cwl
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file.test
deleted file mode 100644
index 98ddd1a832e..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: inline_file
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_inline_file
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/inline_file.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_inline_file.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file_custom_entryname.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file_custom_entryname.test
deleted file mode 100644
index 1164b6fdf2f..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.inline_file_custom_entryname.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: inline_file_custom_entryname
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_inline_file
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/inline_file_custom_entryname.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_inline_file.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string.test
deleted file mode 100644
index 4ec70064ffc..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: iwdr_input_string
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_input_string
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/input_string.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_input_string.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string_function.test b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string_function.test
deleted file mode 100644
index 1c7973b96d6..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement.input_string_function.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: iwdr_input_string_function
-testFormat: workflowsuccess
-workflowType: CWL
-workflowRoot: iwdr_input_string_function
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: InitialWorkDirRequirement/input_string_function.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.iwdr_input_string_function.prime_list": "[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97]"
-}
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/file_array_listing.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/file_array_listing.cwl
deleted file mode 100644
index 86fb7c060a3..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/file_array_listing.cwl
+++ /dev/null
@@ -1,26 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: iwdr_array_listing
-  class: CommandLineTool
-  baseCommand: ['ls']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing: $(inputs.files)
-
-  stdout: file_list
-  inputs:
-      - id: files
-        type:
-          type: array
-          items: File
-        default: [ "/Users/chrisl/Downloads/cwl/allRequirements.txt" ]
-  arguments: [ "*.txt" ]
-  outputs:
-      - id: file_list
-        type: string
-        outputBinding:
-          glob: file_list
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file.cwl
deleted file mode 100644
index 1980beb52d8..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file.cwl
+++ /dev/null
@@ -1,43 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_inline_file
-  class: CommandLineTool
-  baseCommand: ['python3', 'prime_sieve.py', '100']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: 'prime_sieve.py'
-              entry: |
-                  import sys
-                  import math
-
-                  limit = int(sys.argv[1])
-                  sieve = [True for i in range(limit)]
-                  for i in range(2, math.floor(limit / 2)):
-                      if sieve[i]:
-                          for j in range(i * 2, limit, i):
-                              sieve[j] = False
-
-                  result = "["
-                  for i in range(2, limit):
-                      if sieve[i]:
-                          if result != "[":
-                              result += ", "
-                          result += str(i)
-                  result += "]"
-
-                  print(result)
-
-  stdout: "primes"
-  inputs: []
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file_custom_entryname.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file_custom_entryname.cwl
deleted file mode 100644
index bff672a7e8a..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/inline_file_custom_entryname.cwl
+++ /dev/null
@@ -1,47 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_inline_file
-  class: CommandLineTool
-  baseCommand: ['python3']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: $(inputs.script_name)
-              entry: |
-                  import sys
-                  import math
-
-                  limit = int(sys.argv[1])
-                  sieve = [True for i in range(limit)]
-                  for i in range(2, math.floor(limit / 2)):
-                      if sieve[i]:
-                          for j in range(i * 2, limit, i):
-                              sieve[j] = False
-
-                  result = "["
-                  for i in range(2, limit):
-                      if sieve[i]:
-                          if result != "[":
-                              result += ", "
-                          result += str(i)
-                  result += "]"
-
-                  print(result)
-
-  stdout: "primes"
-  inputs:
-      - id: script_name
-        type: string
-        default: "astounding.py"
-  arguments: [ $(inputs.script_name), '100' ]
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string.cwl
deleted file mode 100644
index 286f6b7aedc..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string.cwl
+++ /dev/null
@@ -1,50 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_input_string
-  class: CommandLineTool
-  baseCommand: ['python3', 'prime_sieve.py', '100']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: $(inputs.script_name)
-              entry: $(inputs.script)
-
-  stdout: "primes"
-  inputs:
-      - id: script
-        type: string
-        default: |
-          import sys
-          import math
-
-          limit = int(sys.argv[1])
-          sieve = [True for i in range(limit)]
-          for i in range(2, math.floor(limit / 2)):
-              if sieve[i]:
-                  for j in range(i * 2, limit, i):
-                      sieve[j] = False
-
-          result = "["
-          for i in range(2, limit):
-              if sieve[i]:
-                  if result != "[":
-                      result += ", "
-                  result += str(i)
-          result += "]"
-
-          print(result)
-      - id: script_name
-        type: string
-        default: "prime_sieve.py"
-  arguments: [ $(inputs.script_name), '100' ]
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string_function.cwl b/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string_function.cwl
deleted file mode 100644
index f70cd7bf8b9..00000000000
--- a/centaur/src/main/resources/standardTestCases/InitialWorkDirRequirement/input_string_function.cwl
+++ /dev/null
@@ -1,49 +0,0 @@
-# Little tool that uses a prime sieve to generate primes up to 100
-
-cwlVersion: v1.0
-$graph:
-- id: iwdr_input_string_function
-  class: CommandLineTool
-  baseCommand: ['python3']
-  requirements:
-      - class: DockerRequirement
-        dockerPull: "python:3.5.0"
-      - class: InitialWorkDirRequirement
-        listing:
-            - entryname: ${var result = inputs.script_name + ".py"; return result;}
-              entry: ${var scr = inputs.script; return scr + "print(result);"}
-
-  stdout: "primes"
-  inputs:
-      - id: script
-        type: string
-        default: |
-          import sys
-          import math
-
-          limit = int(sys.argv[1])
-          sieve = [True for i in range(limit)]
-          for i in range(2, math.floor(limit / 2)):
-              if sieve[i]:
-                  for j in range(i * 2, limit, i):
-                      sieve[j] = False
-
-          result = "["
-          for i in range(2, limit):
-              if sieve[i]:
-                  if result != "[":
-                      result += ", "
-                  result += str(i)
-          result += "]"
-
-      - id: script_name
-        type: string
-        default: "prime_sieve.py"
-  arguments: [ '${var result = inputs.script_name + ".py"; return result;}', '100' ]
-  outputs:
-      - id: prime_list
-        type: string
-        outputBinding:
-          glob: primes
-          loadContents: true
-          outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test.aws.test b/centaur/src/main/resources/standardTestCases/ad_hoc_file_test.aws.test
deleted file mode 100644
index 8016f90f665..00000000000
--- a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test.aws.test
+++ /dev/null
@@ -1,14 +0,0 @@
-name: ad_hoc_file_test.aws
-testFormat: workflowsuccess
-backends: [ AWSBATCH ]
-
-files {
-  workflow: ad_hoc_file_test/workflow.cwl
-  imports: [
-    ad_hoc_file_test/cwl-test.cwl
-  ]
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/cwl-test.cwl b/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/cwl-test.cwl
deleted file mode 100644
index 7ac312f6f3a..00000000000
--- a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/cwl-test.cwl
+++ /dev/null
@@ -1,21 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-baseCommand: ["sh", "example.sh"]
-hints:
-  DockerRequirement:
-    dockerPull: ubuntu:latest
-inputs: []
-
-requirements:
-  InitialWorkDirRequirement:
-    listing:
-      - entryname: example.sh
-        entry: |-
-          PREFIX='Message is:'
-          MSG="\${PREFIX} Hello world!"
-          echo \${MSG}
-
-outputs:
-  example_out:
-    type: stdout
-stdout: output.txt
diff --git a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/workflow.cwl b/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/workflow.cwl
deleted file mode 100644
index 678132165b2..00000000000
--- a/centaur/src/main/resources/standardTestCases/ad_hoc_file_test/workflow.cwl
+++ /dev/null
@@ -1,10 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs: []
-outputs: []
-
-steps:
-  test:
-    run: cwl-test.cwl
-    in: []
-    out: []
diff --git a/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json
new file mode 100644
index 00000000000..f004c8be647
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.inputs.json
@@ -0,0 +1,3 @@
+{
+  "fileChecksum.inputFile": "https://<storage-account>.blob.core.windows.net/cromwell/user-inputs/inputFile.txt"
+}
diff --git a/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl
new file mode 100644
index 00000000000..b482f80d6e4
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/blob_md5/blob_md5.wdl
@@ -0,0 +1,20 @@
+task md5 {
+    File inputFile
+    command {
+        echo "`date`: Running checksum on ${inputFile}..."
+        md5sum ${inputFile} > md5sum.txt
+        echo "`date`: Checksum is complete."
+    }
+    output {
+        File result = "md5sum.txt"
+    }
+    runtime {
+        docker: 'ubuntu:18.04'
+        preemptible: true
+    }
+}
+
+workflow fileChecksum {
+    File inputFile
+    call md5 { input: inputFile=inputFile}
+}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows.test b/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows.test
deleted file mode 100644
index e5381017829..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows.test
+++ /dev/null
@@ -1,19 +0,0 @@
-name: cwl_cache_between_workflows
-testFormat: runtwiceexpectingcallcaching
-workflowRoot: cwl-cache-between-workflows
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_cache_between_workflows/cwl_cache_between_workflows.cwl
-  inputs: cwl_cache_between_workflows/cwl_cache_between_workflows.json
-}
-
-metadata {
-  status: Succeeded
-  "calls.cwl-cache-between-workflows.step-average.callCaching.result": "Cache Hit: <<CACHE_HIT_UUID>>:cwl-cache-between-workflows.step-average:-1"
-  "calls.cwl-cache-between-workflows.step-product.callCaching.result": "Cache Hit: <<CACHE_HIT_UUID>>:cwl-cache-between-workflows.step-product:-1"
-  "outputs.cwl-cache-between-workflows.trapezoidalArea": 77.0,
-  "outputs.cwl-cache-between-workflows.baseAverage": 11.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.cwl b/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.cwl
deleted file mode 100644
index d48e74cd935..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.cwl
+++ /dev/null
@@ -1,79 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: average
-  class: CommandLineTool
-
-  inputs:
-    base1:
-      type: int
-      default: 9
-    base2:
-      type: int
-      default: 13
-
-  outputs:
-    baseAverage:
-      type: float
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseFloat(self[0].contents))
-
-  arguments:
-  - valueFrom: "echo $((inputs.base1 + inputs.base2) / 2)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-- id: height-product
-  class: CommandLineTool
-
-  inputs:
-    baseAverage: float
-    height:
-      type: float
-      default: 7.0
-
-  outputs:
-    trapezoidalArea:
-      type: long
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseFloat(self[0].contents))
-
-  arguments:
-  - valueFrom: "echo $(inputs.baseAverage * inputs.height)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-- id: cwl-cache-between-workflows
-  class: Workflow
-
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  - class: ShellCommandRequirement
-
-  inputs: []
-
-  outputs:
-    baseAverage:
-      type: float
-      outputSource: step-average/baseAverage
-    trapezoidalArea:
-      type: long
-      outputSource: step-product/trapezoidalArea
-
-  steps:
-    step-average:
-      run: "#average"
-      in: []
-      out: [baseAverage]
-
-    step-product:
-      run: "#height-product"
-      in:
-        baseAverage: step-average/baseAverage
-      out: [trapezoidalArea]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.json b/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.json
deleted file mode 100644
index 0967ef424bc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_between_workflows/cwl_cache_between_workflows.json
+++ /dev/null
@@ -1 +0,0 @@
-{}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow.test b/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow.test
deleted file mode 100644
index 8ef753b494d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow.test
+++ /dev/null
@@ -1,26 +0,0 @@
-name: cwl_cache_within_workflow
-testFormat: workflowsuccess
-workflowRoot: cwl-cache-within-workflow
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_cache_within_workflow/cwl_cache_within_workflow.cwl
-  inputs: cwl_cache_within_workflow/cwl_cache_within_workflow.json
-}
-
-metadata {
-  status: Succeeded
-  "calls.cwl-cache-within-workflow.foo.callCaching.result": "Cache Miss"
-  "calls.cwl-cache-within-workflow.bar.callCaching.result": "Cache Miss"
-  "calls.cwl-cache-within-workflow.re-bar.callCaching.result": "Cache Hit: <<UUID>>:cwl-cache-within-workflow.bar:-1"
-  "calls.cwl-cache-within-workflow.bar.inputs.pi": 3.14159
-  "calls.cwl-cache-within-workflow.bar.inputs.rSquared": 16.23381791021144
-  "calls.cwl-cache-within-workflow.bar.outputs.area": 51
-  "calls.cwl-cache-within-workflow.bar.outputs.rSquaredCopy": 16.23381791021144
-  "calls.cwl-cache-within-workflow.re-bar.inputs.pi": 3.14159
-  "calls.cwl-cache-within-workflow.re-bar.inputs.rSquared": 16.23381791021144
-  "calls.cwl-cache-within-workflow.re-bar.outputs.area": 51
-  "calls.cwl-cache-within-workflow.re-bar.outputs.rSquaredCopy": 16.23381791021144
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.cwl b/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.cwl
deleted file mode 100644
index 15b1fd79a01..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.cwl
+++ /dev/null
@@ -1,129 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: one
-  class: CommandLineTool
-
-  inputs:
-    r:
-      type: float
-
-  outputs:
-    rSquared:
-      type: float
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseFloat(self[0].contents))
-    rCopy:
-      type: float
-      outputBinding:
-        outputEval: $(inputs.r)
-
-  arguments:
-  - valueFrom: "echo $(inputs.r * inputs.r)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-- id: two
-  class: CommandLineTool
-
-  inputs:
-    rSquared: float
-    pi: float
-
-  outputs:
-    area:
-      outputBinding:
-        glob: stdout.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    rSquaredCopy:
-      outputBinding:
-        outputEval: $(inputs.rSquared)
-      type: float
-
-  arguments:
-  - valueFrom: "echo $(inputs.rSquared * inputs.pi)"
-    shellQuote: false
-
-  stdout: stdout.txt
-
-# Throwing in some ExpressionTools for fun. Currently these not only don't cache but aren't even listed in the metadata
-# except in the original workflow blob (see #3499). The current thinking is that these should appear in metadata with a
-# call-like presentation but that they don't need to be eligible for caching since ExpressionTools are supposed to be
-# very lightweight and not worth the expense of hashing and potential cache hit copying.
-- id: three
-  class: ExpressionTool
-
-  inputs:
-    rSquared: float
-    pi: float
-
-  outputs:
-    area: int
-    rSquaredCopy: float
-
-  expression: |
-    ${
-    return {"area": parseInt(inputs.pi * inputs.rSquared),
-            "rSquaredCopy": inputs.rSquared };
-    }
-
-
-- id: cwl-cache-within-workflow
-  class: Workflow
-
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  - class: ShellCommandRequirement
-
-  inputs:
-    radius: float
-    pi: float
-
-  outputs:
-    area:
-      type: int
-      outputSource: re-bar/area
-    area-expression:
-      type: int
-      outputSource: re-baz/area
-
-  steps:
-    foo:
-      run: "#one"
-      in:
-        r: radius
-        pi: pi
-      out: [rSquared, rCopy]
-
-    bar:
-      run: "#two"
-      in:
-        rSquared: "foo/rSquared"
-        pi: pi
-      out: [area, rSquaredCopy]
-
-    re-bar:
-      run: "#two"
-      in:
-        rSquared: "bar/rSquaredCopy"
-        pi: pi
-      out: [area, rSquaredCopy]
-
-    baz:
-      run: "#three"
-      in:
-        rSquared: "foo/rSquared"
-        pi: pi
-      out: [area, rSquaredCopy]
-
-    re-baz:
-      run: "#three"
-      in:
-        rSquared: "baz/rSquaredCopy"
-        pi: pi
-      out: [area, rSquaredCopy]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.json b/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.json
deleted file mode 100644
index 563f2413547..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_cache_within_workflow/cwl_cache_within_workflow.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "radius": 4.029121233,
-  "pi": 3.14159
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_disk_resources_papiv2.test b/centaur/src/main/resources/standardTestCases/cwl_disk_resources_papiv2.test
deleted file mode 100644
index 8677bcf711e..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_disk_resources_papiv2.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_disk_resources_papiv2
-testFormat: workflowsuccess
-backends: [Papiv2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_resources/cwl_disk_resources.cwl
-}
-
-metadata {
-  status: Succeeded
-  "outputs.diskSizeTool.disk_size": 30
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: diskSizeTool
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size.test b/centaur/src/main/resources/standardTestCases/cwl_docker_size.test
deleted file mode 100644
index ca700d5cd9d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_docker_files
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_docker_size/cwl_docker_size.cwl
-  inputs: cwl_docker_size/cwl_docker_size.yaml
-  options: cwl_docker_size/cwl_docker_size.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.main.stdout_output": "execute order=66"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.cwl b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.cwl
deleted file mode 100644
index 5383bccb484..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.cwl
+++ /dev/null
@@ -1,40 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: main
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: INPUT
-      type: File[]
-  stdout: stdout
-  outputs:
-    stdout_output:
-      type: string
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: $(self[0].contents.trim())
-  arguments:
-    - valueFrom: |
-        ${
-          if (inputs.INPUT.length == 0) {
-            var cmd = ['echo', "no inputs"];
-            return cmd
-          }
-          else {
-            var cmd = ["echo", "execute"];
-            var use_input = [];
-            for (var i = 0; i < inputs.INPUT.length; i++) {
-              var filesize = inputs.INPUT[i].size;
-              use_input.push("order=".concat(filesize));
-            }
-
-            var run_cmd = cmd.concat(use_input);
-            return run_cmd
-          }
-
-        }
-  out: stdout
-  baseCommand: []
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.options b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.yaml b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.yaml
deleted file mode 100644
index 097e69e8590..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-INPUT:
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt b/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt
deleted file mode 100644
index 1a6374205aa..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_docker_size/cwl_docker_size_input.txt
+++ /dev/null
@@ -1 +0,0 @@
-And you people, you're all astronauts, on some kind of star trek.
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir.test b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir.test
deleted file mode 100644
index 57a69084c62..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir.test
+++ /dev/null
@@ -1,20 +0,0 @@
-name: cwl_dynamic_initial_workdir
-testFormat: workflowsuccess
-ignore: false
-workflowRoot: main
-workflowType: CWL
-workflowTypeVersion: v1.0
-backendsMode: "only"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl
-  inputs: cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs
-}
-
-metadata {
-  status: Succeeded
-  "outputs.main.sha": "13cda8661796ae241da3a18668fb552161a72592\n"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl
deleted file mode 100644
index 6012854d0b7..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.cwl
+++ /dev/null
@@ -1,29 +0,0 @@
-cwlVersion: v1.0
-$graph:
-  id: main
-  class: CommandLineTool
-  cwlVersion: v1.0
-  requirements:
-    - class: ShellCommandRequirement
-    - class: InitialWorkDirRequirement
-      listing: $(inputs.indir.listing)
-    - class: DockerRequirement
-      dockerPull: "ubuntu:latest"
-  inputs:
-    indir: Directory
-  outputs:
-    sha:
-      type: string
-      outputBinding:
-        glob: output.txt
-        loadContents: true
-        outputEval: $(self[0].contents)
-  arguments: ["find", "-L", ".", "-name", "?",
-    {shellQuote: false, valueFrom: "|"},
-    "sort",
-    {shellQuote: false, valueFrom: "|"},
-    "sha1sum",
-    {shellQuote: false, valueFrom: "|"},
-    "cut", "-c", "1-40"
-  ]
-  stdout: output.txt
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs
deleted file mode 100644
index f37fed14367..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir.inputs
+++ /dev/null
@@ -1,3 +0,0 @@
-indir:
-  class: Directory
-  location: centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/a b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/a
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/b b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/b
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/c/d b/centaur/src/main/resources/standardTestCases/cwl_dynamic_initial_workdir/testdir/c/d
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.cwl b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.cwl
deleted file mode 100644
index c2079a82721..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.cwl
+++ /dev/null
@@ -1,25 +0,0 @@
-cwlVersion: v1.0
-$namespaces:
-  edam: http://edamontology.org/
-  gx: http://galaxyproject.org/formats/
-$schemas:
-  - file:./cwl/src/test/resources/cwl/ontology/EDAM.owl
-  - file:./cwl/src/test/resources/cwl/ontology/gx_edam.ttl
-$graph:
-- id: main
-  class: CommandLineTool
-  cwlVersion: v1.0
-  inputs:
-    - id: reference
-      type: File
-      format: gx:fasta
-      inputBinding: { position: 2 }
-  outputs:
-    - id: lineCount
-      type: int
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: "$(parseInt(self[0].contents))"
-  baseCommand: ["wc", "-l"]
-  stdout: stdout
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.options b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_invalid.yaml b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_invalid.yaml
deleted file mode 100644
index 6e75ae34f28..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_invalid.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Try to pass a fastq in as a fasta
-reference:
-  class: File
-  format: edam:format_1930
-  path: "centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_missing.yaml b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_missing.yaml
deleted file mode 100644
index 4e8a35cb2e9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_missing.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Pass a fastq in as a fasta, but without passing the format
-reference:
-  class: File
-  #format: edam:format_1930
-  path: "centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl
deleted file mode 100644
index b85bf8d2434..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl
+++ /dev/null
@@ -1,27 +0,0 @@
-cwlVersion: v1.0
-$namespaces:
-  edam: http://edamontology.org/
-  gx: http://galaxyproject.org/formats/
-$schemas:
-  # Relative path:
-  - ../../../../../../cwl/src/test/resources/cwl/ontology/EDAM.owl
-  # Absolute (remote) path:
-  - https://raw.githubusercontent.com/broadinstitute/cromwell/develop/cwl/src/test/resources/cwl/ontology/gx_edam.ttl
-$graph:
-- id: main
-  class: CommandLineTool
-  cwlVersion: v1.0
-  inputs:
-    - id: reference
-      type: File
-      format: gx:fasta
-      inputBinding: { position: 2 }
-  outputs:
-    - id: lineCount
-      type: int
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: "$(parseInt(self[0].contents))"
-  baseCommand: ["wc", "-l"]
-  stdout: stdout
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_valid.yaml b/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_valid.yaml
deleted file mode 100644
index b598f92b7e1..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_valid.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-# Pass in a valid input file format
-reference:
-  class: File
-  format: edam:format_1929
-  path: "centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta b/centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta
deleted file mode 100644
index e91d1521810..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->sequence #1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq b/centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq
deleted file mode 100644
index 5ecec0ebec8..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format/foo.fastq
+++ /dev/null
@@ -1,4 +0,0 @@
-@SEQ_ID
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
-+
-!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_invalid.test b/centaur/src/main/resources/standardTestCases/cwl_format_invalid.test
deleted file mode 100644
index 43962bb5bfc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_invalid.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_invalid
-testFormat: workflowfailure
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_format/cwl_format.cwl
-  inputs: cwl_format/cwl_format_invalid.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "failures.0.message": "Workflow input processing failed"
-  "failures.0.causedBy.0.message": "Failed to evaluate input 'reference' (reason 1 of 1): edam:format_1930 is not compatible with http://galaxyproject.org/formats/fasta"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_missing.test b/centaur/src/main/resources/standardTestCases/cwl_format_missing.test
deleted file mode 100644
index a7b626f69e4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_missing.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_missing
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_format/cwl_format.cwl
-  inputs: cwl_format/cwl_format_missing.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "workflowName": "main"
-  "outputs.main.lineCount": "4"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_valid.test b/centaur/src/main/resources/standardTestCases/cwl_format_valid.test
deleted file mode 100644
index 6a6452deff5..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_valid.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_valid
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_format/cwl_format.cwl
-  inputs: cwl_format/cwl_format_valid.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "workflowName": "main"
-  "outputs.main.lineCount": "2"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_format_valid_with_workflow_url.test b/centaur/src/main/resources/standardTestCases/cwl_format_valid_with_workflow_url.test
deleted file mode 100644
index e587dbfe6d6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_format_valid_with_workflow_url.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_format_valid_with_workflow_url
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflowUrl: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/cwl_format/cwl_format_url.cwl"
-  inputs: cwl_format/cwl_format_valid.yaml
-  options: cwl_format/cwl_format.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "workflowName": "main"
-  "outputs.main.lineCount": "2"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_glob_sort.test b/centaur/src/main/resources/standardTestCases/cwl_glob_sort.test
deleted file mode 100644
index 04856ab66b9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_glob_sort.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: cwl_glob_sort
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: globSort
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_glob_sort/cwl_glob_sort.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.globSort.letters": "a b c w x y z"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl b/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl
deleted file mode 100644
index 8d54af1c040..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl
+++ /dev/null
@@ -1,19 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: globSort
-  cwlVersion: v1.0
-  class: CommandLineTool
-  requirements:
-    - class: InlineJavascriptRequirement
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs: []
-  baseCommand: [touch, z, y, x, w, c, b, a]
-  outputs:
-    letters:
-      type: string
-      outputBinding:
-        glob: '?'
-        outputEval: |
-          ${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(" ") }
diff --git a/centaur/src/main/resources/standardTestCases/cwl_glob_sort_with_workflow_url.test b/centaur/src/main/resources/standardTestCases/cwl_glob_sort_with_workflow_url.test
deleted file mode 100644
index 6e7ed2b1dd2..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_glob_sort_with_workflow_url.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: cwl_glob_sort_with_workflow_url
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: globSort
-skipDescribeEndpointValidation: true
-
-files {
-  workflowUrl: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/cwl_glob_sort/cwl_glob_sort.cwl"
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.globSort.letters": "a b c w x y z"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type.test b/centaur/src/main/resources/standardTestCases/cwl_import_type.test
deleted file mode 100644
index 9e530a95469..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type.test
+++ /dev/null
@@ -1,14 +0,0 @@
-name: cwl_import_type
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_import_type/test_wf.cwl
-  inputs: cwl_import_type/test_wf_inputs.json
-  imports: [
-    cwl_import_type/capture_kit.yml,
-    cwl_import_type/touch.cwl
-  ]
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/capture_kit.yml b/centaur/src/main/resources/standardTestCases/cwl_import_type/capture_kit.yml
deleted file mode 100644
index 4323dd90f6d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/capture_kit.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-- name: capture_kit
-  type: record
-  fields:
-    - name: bait
-      type: string
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf.cwl b/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf.cwl
deleted file mode 100644
index 3658ab127d0..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf.cwl
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
-
-class: Workflow
-
-requirements:
-  - class: SchemaDefRequirement
-    types:
-      - $import: capture_kit.yml
-
-inputs:
-  - id: bam
-    type: string
-  - id: capture_kit
-    type: capture_kit.yml#capture_kit
-
-outputs:
-  - id: output_bam
-    type: File
-    outputSource: touch_bam/output
-
-steps:
-  - id: touch_bam
-    run: touch.cwl
-    in:
-      - id: input
-        source: bam
-    out:
-      - id: output
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf_inputs.json b/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf_inputs.json
deleted file mode 100644
index 55141261811..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/test_wf_inputs.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "bam": "a.bam",
-    "capture_kit": {
-        "bait": "abait"
-    }
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type/touch.cwl b/centaur/src/main/resources/standardTestCases/cwl_import_type/touch.cwl
deleted file mode 100644
index 8a0be057c42..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type/touch.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
-
-requirements:
-  - class: DockerRequirement
-    dockerPull: ubuntu:bionic-20180426
-
-class: CommandLineTool
-
-inputs:
-  - id: input
-    type: string
-    inputBinding:
-      position: 0
-
-outputs:
-  - id: output
-    type: File
-    outputBinding:
-      glob: $(inputs.input)
-      
-baseCommand: [touch]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed.test b/centaur/src/main/resources/standardTestCases/cwl_import_type_packed.test
deleted file mode 100644
index 0a3fd7c20a4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed.test
+++ /dev/null
@@ -1,11 +0,0 @@
-name: cwl_import_type_packed
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_import_type_packed/test_pack.cwl
-  inputs: cwl_import_type_packed/test_wf_inputs.json
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_pack.cwl b/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_pack.cwl
deleted file mode 100644
index 4150b5a5796..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_pack.cwl
+++ /dev/null
@@ -1,91 +0,0 @@
-{
-    "cwlVersion": "v1.0", 
-    "$graph": [
-        {
-            "inputs": [
-                {
-                    "type": "string", 
-                    "id": "#main/bam"
-                }, 
-                {
-                    "type": "#capture_kit.yml/capture_kit", 
-                    "id": "#main/capture_kit"
-                }
-            ], 
-            "requirements": [
-                {
-                    "class": "SchemaDefRequirement", 
-                    "types": [
-                        {
-                            "fields": [
-                                {
-                                    "type": "string", 
-                                    "name": "#capture_kit.yml/capture_kit/bait"
-                                }
-                            ], 
-                            "type": "record", 
-                            "name": "#capture_kit.yml/capture_kit"
-                        }
-                    ]
-                }
-            ], 
-            "outputs": [
-                {
-                    "outputSource": "#main/touch_bam/output", 
-                    "type": "File", 
-                    "id": "#main/output_bam"
-                }
-            ], 
-            "class": "Workflow", 
-            "steps": [
-                {
-                    "out": [
-                        {
-                            "id": "#main/touch_bam/output"
-                        }
-                    ], 
-                    "run": "#touch.cwl", 
-                    "id": "#main/touch_bam", 
-                    "in": [
-                        {
-                            "source": "#main/bam", 
-                            "id": "#main/touch_bam/input"
-                        }
-                    ]
-                }
-            ], 
-            "id": "#main"
-        }, 
-        {
-            "inputs": [
-                {
-                    "inputBinding": {
-                        "position": 0
-                    }, 
-                    "type": "string", 
-                    "id": "#touch.cwl/input"
-                }
-            ], 
-            "requirements": [
-                {
-                    "dockerPull": "ubuntu:bionic-20180426", 
-                    "class": "DockerRequirement"
-                }
-            ], 
-            "outputs": [
-                {
-                    "outputBinding": {
-                        "glob": "$(inputs.input)"
-                    }, 
-                    "type": "File", 
-                    "id": "#touch.cwl/output"
-                }
-            ], 
-            "baseCommand": [
-                "touch"
-            ], 
-            "class": "CommandLineTool", 
-            "id": "#touch.cwl"
-        }
-    ]
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_wf_inputs.json b/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_wf_inputs.json
deleted file mode 100644
index 55141261811..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_import_type_packed/test_wf_inputs.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "bam": "a.bam",
-    "capture_kit": {
-        "bait": "abait"
-    }
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression.test b/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression.test
deleted file mode 100644
index 0e39f78ce78..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_input_binding_expression
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_input_binding_expression
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_input_binding_expression/cwl_input_binding_expression.cwl
-  inputs: cwl_input_binding_expression/cwl_input_binding_expression.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.cwl_input_binding_expression.b": "hello world"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.cwl b/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.cwl
deleted file mode 100644
index f534adfaa36..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.cwl
+++ /dev/null
@@ -1,25 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: cwl_input_binding_expression
-  class: CommandLineTool
-  requirements:
-    - class: InlineJavascriptRequirement
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: hello
-      type: string
-      inputBinding:
-        valueFrom: $(self + " world")
-        position: 1
-  outputs:
-    b:
-      type: string
-      outputBinding:
-        loadContents: true
-        glob: stdout
-        outputEval: $(self[0].contents.trim())
-  stdout: stdout
-  baseCommand: []
-  arguments: [echo]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.json b/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.json
deleted file mode 100644
index 8920ee8d630..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_binding_expression/cwl_input_binding_expression.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "hello": "hello"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_json.test b/centaur/src/main/resources/standardTestCases/cwl_input_json.test
deleted file mode 100644
index 1dd81ba8260..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_json.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_input_json
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-backendsMode: "only"
-workflowRoot: cwl_input_json
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_input_json/cwl_input_json.yaml
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_json/cwl_input_json.yaml b/centaur/src/main/resources/standardTestCases/cwl_input_json/cwl_input_json.yaml
deleted file mode 100644
index f6e5616c6c4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_json/cwl_input_json.yaml
+++ /dev/null
@@ -1,70 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: cwl_input_json
-  class: Workflow
-  inputs: []
-  outputs:
-    final_output:
-      type: File
-      outputSource: round/output_file
-  steps:
-    make:
-      run: "#makefile"
-      in: []
-      out: [fileoutput]
-    round:
-      run: "#roundtrip"
-      in:
-        input_record: 
-          source: "make/fileoutput"
-      out: [output_file]
-          
-- id: makefile
-  class: CommandLineTool
-  requirements:
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  inputs: []
-  outputs:
-    fileoutput:
-      type:
-        fields:
-        - name: input_file
-          type: File
-        name: input_record
-        type: record
-  arguments:
-    - valueFrom: >
-         echo foo > foo && echo '{ "fileoutput": { "input_file": {"path": "$(runtime.outdir)/foo", "class": "File"} } }' > cwl.output.json
-      shellQuote: false
-
-- id: roundtrip
-  class: CommandLineTool
-  hints:
-  - class: DockerRequirement
-    dockerPull: "stedolan/jq:latest"
-  inputs:
-  - id: input_record
-    type:
-      fields:
-      - name: input_file
-        type: File
-      name: input_record
-      type: record
-  outputs:
-  - id: output_file
-    type: File
-  requirements:
-  - class: ShellCommandRequirement
-  - class: InlineJavascriptRequirement
-  - class: InitialWorkDirRequirement
-    listing:
-    - entry: $(JSON.stringify(inputs))
-      entryname: cwl.inputs.json
-  arguments:
-  # Round-trips the file referenced in cwl.input.json to cwl.output.json. Also ls it in the command to make sure it's there.
-    - valueFrom: >
-         INPUT_FILE=\$(cat cwl.inputs.json | jq -r '.. | .path? // empty') && ls $INPUT_FILE && echo "{\"output_file\": {\"path\": \"\$INPUT_FILE\", \"class\": \"File\"} }" > cwl.output.json
-      shellQuote: false
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray.test b/centaur/src/main/resources/standardTestCases/cwl_input_typearray.test
deleted file mode 100644
index a87bcbf9f65..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_typearray.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_input_typearray
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: input_typearray
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_input_typearray/input_typearray.cwl
-  inputs: cwl_input_typearray/input_typearray.yml
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.input_typearray.response_f": "input.txt"
-  "outputs.input_typearray.response_s": "nonexistent_path.txt"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input.txt b/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.cwl b/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.cwl
deleted file mode 100644
index 897b74822e8..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.cwl
+++ /dev/null
@@ -1,42 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: input_typearray
-  cwlVersion: v1.0
-  class: CommandLineTool
-  baseCommand: ['/bin/echo']
-  stdout: "response.txt"
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  - class: InlineJavascriptRequirement
-  arguments:
-      - position: 3
-        valueFrom: "sentinel"
-  inputs:
-    value_f:
-      type:
-        - string
-        - File
-      inputBinding:
-        position: 1
-      doc: "an input to test with a File value"
-    value_s:
-      type:
-        - string
-        - File
-      inputBinding:
-        position: 2
-      doc: "an input to test with a string value"
-  outputs:
-    response_f:
-      type: string
-      outputBinding:
-        glob: response.txt
-        loadContents: true
-        outputEval: $(self[0].contents.split(" ")[0].split("/").slice(-1)[0])
-    response_s:
-      type: string
-      outputBinding:
-        glob: response.txt
-        loadContents: true
-        outputEval: $(self[0].contents.split(" ")[1].split("/").slice(-1)[0])
diff --git a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.yml b/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.yml
deleted file mode 100644
index 421402d9289..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_input_typearray/input_typearray.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-value_f:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_input_typearray/input.txt"
-value_s: "centaur/src/main/resources/standardTestCases/cwl_input_typearray/nonexistent_path.txt"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_inputdir_zero_doesnt_localize_papiv2.test b/centaur/src/main/resources/standardTestCases/cwl_inputdir_zero_doesnt_localize_papiv2.test
deleted file mode 100644
index 564633779a7..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_inputdir_zero_doesnt_localize_papiv2.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_inputdir_zero_doesnt_localize_papiv2
-testFormat: workflowsuccess
-backends: [Papiv2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl
-}
-
-metadata {
-  status: Succeeded
-  "outputs.inputdir_zero_doesnt_localize.errors": ""
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: inputdir_zero_doesnt_localize
diff --git a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings.test b/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings.test
deleted file mode 100644
index 89399e2e8fc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_interpolated_strings
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: interpolatedStrings
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_interpolated_strings/cwl_interpolated_strings.cwl
-  inputs: cwl_interpolated_strings/cwl_interpolated_strings.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.interpolatedStrings.rfc3092": "foo bar baz qux quux"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.cwl b/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.cwl
deleted file mode 100644
index e650061a5cc..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.cwl
+++ /dev/null
@@ -1,25 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: interpolatedStrings
-  class: CommandLineTool
-  cwlVersion: v1.0
-  requirements:
-    - class: ShellCommandRequirement
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-
-  inputs:
-    - id: bar
-      type: string
-    - id: qux
-      type: string
-
-  outputs:
-    - id: rfc3092
-      type: string
-
-  arguments:
-     - valueFrom: >
-         echo '{ "rfc3092": "foo $(inputs.bar) baz $(inputs.qux) quux" }' > cwl.output.json
-       shellQuote: false
diff --git a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.json b/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.json
deleted file mode 100644
index 3f1bcedd11f..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_interpolated_strings/cwl_interpolated_strings.json
+++ /dev/null
@@ -1 +0,0 @@
-{"bar": "bar", "qux": "qux"}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_optionals.test b/centaur/src/main/resources/standardTestCases/cwl_optionals.test
deleted file mode 100644
index 2d945f36ee0..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_optionals.test
+++ /dev/null
@@ -1,13 +0,0 @@
-name: cwl_optionals
-testFormat: workflowsuccess
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_optionals/cwl_optionals.cwl
-  inputs: cwl_optionals/cwl_optionals.json
-}
-
-metadata {
-  "actualWorkflowLanguage": CWL
-  "actualWorkflowLanguageVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.cwl b/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.cwl
deleted file mode 100755
index 592227bf025..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.cwl
+++ /dev/null
@@ -1,12 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-hints:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-baseCommand: echo
-inputs:
-  message:
-    type: string[]?
-  unsupplied_optional:
-    type: string[]?
-outputs: []
diff --git a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.json b/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.json
deleted file mode 100644
index c76e98d49c3..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_optionals/cwl_optionals.json
+++ /dev/null
@@ -1 +0,0 @@
-{"message": ["foo","bar"]}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.cwl b/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.cwl
deleted file mode 100644
index 406301e7ecb..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.cwl
+++ /dev/null
@@ -1,34 +0,0 @@
-cwlVersion: v1.0
-$graph:  
-- id: outputJson
-  # slightly modified version of conformance test #2 to remove the default File that doesn't work on PAPI
-  # It is instead being passed as an input through the input json file
-  class: CommandLineTool
-  cwlVersion: v1.0
-  hints:
-    - class: DockerRequirement
-      dockerPull: python:2-slim
-  inputs:
-    - id: reference
-      type: File
-      inputBinding: { position: 2 }
-  
-    - id: reads
-      type:
-        type: array
-        items: File
-        inputBinding: { prefix: "-YYY" }
-      inputBinding: { position: 3, prefix: "-XXX" }
-  
-    - id: "args.py"
-      type: File
-      inputBinding:
-        position: -1
-  
-  outputs:
-    # note the absence of any sort of valueFrom.
-    # The output value is generated from the "cwl.output.json" file created by the python script
-    args: string[]
-  
-  baseCommand: python
-  arguments: ["bwa", "mem"]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.inputs b/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.inputs
deleted file mode 100644
index d83a30872a9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_output_json/cwl_output_json.inputs
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-    "args.py": {
-      "class": "File",
-      "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/args.py"
-    },
-    "reference": {
-        "class": "File",
-        "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/chr20.fa",
-        "size": 123,
-        "checksum": "sha1$hash"
-    },
-    "reads": [
-        {
-            "class": "File",
-            "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/example_human_Illumina.pe_1.fastq"
-        },
-        {
-            "class": "File",
-            "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/example_human_Illumina.pe_2.fastq"
-        }
-    ]
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_output_json_jes.test b/centaur/src/main/resources/standardTestCases/cwl_output_json_jes.test
deleted file mode 100644
index c7ddf584bd4..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_output_json_jes.test
+++ /dev/null
@@ -1,25 +0,0 @@
-name: cwl_output_json_jes
-testFormat: workflowsuccess
-backends: [Papi]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_output_json/cwl_output_json.cwl
-  inputs: cwl_output_json/cwl_output_json.inputs
-}
-
-metadata {
-  status: Succeeded
-  "outputs.outputJson.args.0": "bwa"
-  "outputs.outputJson.args.1": "mem"
-  "outputs.outputJson.args.2": "chr20.fa"
-  "outputs.outputJson.args.3": "-XXX"
-  "outputs.outputJson.args.4": "-YYY"
-  "outputs.outputJson.args.5": "example_human_Illumina.pe_1.fastq"
-  "outputs.outputJson.args.6": "-YYY"
-  "outputs.outputJson.args.7": "example_human_Illumina.pe_2.fastq"
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: outputJson
diff --git a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array.test b/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array.test
deleted file mode 100644
index cea66a37026..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_prefix_for_array
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: prefix-for-array
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_prefix_for_array/prefix_for_array.cwl
-  inputs: cwl_prefix_for_array/prefix_for_array.yml
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.prefix-for-array.out": "--bonus first second\n"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.cwl b/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.cwl
deleted file mode 100644
index ca9044e5c61..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: prefix-for-array
-  cwlVersion: v1.0
-  class: CommandLineTool
-  baseCommand: ['/bin/echo']
-  stdout: "hello.txt"
-  requirements:
-  - class: DockerRequirement
-    dockerPull: "ubuntu:latest"
-  inputs:
-      bonus:
-          type: string[]
-          inputBinding:
-              prefix: "--bonus"
-  outputs:
-    out:
-      type: string
-      outputBinding:
-        glob: hello.txt
-        loadContents: true
-        outputEval: $(self[0].contents)
-
diff --git a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.yml b/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.yml
deleted file mode 100644
index 6a3badb824c..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_prefix_for_array/prefix_for_array.yml
+++ /dev/null
@@ -1 +0,0 @@
-bonus: ["first", "second"]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories.test b/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories.test
deleted file mode 100644
index 390c1d66409..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_recursive_link_directories
-testFormat: workflowsuccess
-backends: [Local]
-backendsMode: only
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_recursive_link_directories/cwl_recursive_link_directories.cwl
-}
-
-metadata {
-  status: Succeeded
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_recursive_link_directories
diff --git a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories/cwl_recursive_link_directories.cwl b/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories/cwl_recursive_link_directories.cwl
deleted file mode 100644
index a4a19fd6a5d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_recursive_link_directories/cwl_recursive_link_directories.cwl
+++ /dev/null
@@ -1,19 +0,0 @@
-cwlVersion: v1.0
-$graph:  
-- id: cwl_recursive_link_directories
-  class: CommandLineTool
-  requirements:
-    - class: ShellCommandRequirement
-  cwlVersion: v1.0
-  hints:
-    - class: DockerRequirement
-      dockerPull: ubuntu:latest
-  inputs: []
-  outputs:
-    output_dir:
-        type: Directory
-        outputBinding:
-          glob: work_dir
-  arguments:
-    - shellQuote: false
-      valueFrom: "mkdir work_dir && ln -s .. work_dir/link"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/cwl_glob_sort.cwl b/centaur/src/main/resources/standardTestCases/cwl_relative_imports/cwl_glob_sort.cwl
deleted file mode 100644
index 330c896eea6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/cwl_glob_sort.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-requirements:
-  - class: InlineJavascriptRequirement
-hints:
-  DockerRequirement:
-    dockerPull: "debian:stretch-slim"
-inputs: []
-baseCommand: [touch, z, y, x, w, c, b, a]
-outputs:
-  letters:
-    type: string
-    outputBinding:
-      glob: '?'
-      outputEval: |
-        ${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(" ") }
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl b/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl
deleted file mode 100644
index 0ba8fc7236d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: relative_imports
-  class: Workflow
-
-  inputs: []
-  outputs:
-    letters:
-      type: string
-      outputSource: globSort/letters
-
-  steps:
-    globSort:
-      in: []
-      run: cwl_glob_sort.cwl
-      out: [letters]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_url.test b/centaur/src/main/resources/standardTestCases/cwl_relative_imports_url.test
deleted file mode 100644
index eabd10754f6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_url.test
+++ /dev/null
@@ -1,20 +0,0 @@
-name: cwl_relative_imports_url
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: relative_imports
-skipDescribeEndpointValidation: true
-# This test has experienced sporadic failures, and CWL is not fully supported. Therefore the test is being disabled.
-ignore: true
-
-files {
-  workflowUrl: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/cwl_relative_imports/workflow.cwl"
-}
-
-metadata {
-  status: Succeeded
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.relative_imports.globSort.outputs.letters": "a b c w x y z"
-  "outputs.relative_imports.letters": "a b c w x y z"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_zip.test b/centaur/src/main/resources/standardTestCases/cwl_relative_imports_zip.test
deleted file mode 100644
index deccb8d73a3..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_relative_imports_zip.test
+++ /dev/null
@@ -1,22 +0,0 @@
-name: cwl_relative_imports_zip
-testFormat: workflowsuccess
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_relative_imports/workflow.cwl
-  imports: [
-    cwl_relative_imports/cwl_glob_sort.cwl
-  ]
-}
-
-metadata {
-  status: Succeeded
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.relative_imports.globSort.outputs.letters": "a b c w x y z"
-  "outputs.relative_imports.letters": "a b c w x y z"
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: relative_imports
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_disk_resources.cwl b/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_disk_resources.cwl
deleted file mode 100644
index 683dd5b17e6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_disk_resources.cwl
+++ /dev/null
@@ -1,38 +0,0 @@
-cwlVersion: v1.0
-# Asks for 10 GB (~=10240 MB) of output dir, tmp dir and input dir.
-# Unfortunately the internal metadata from the VM, despite having some information about the disks doesn't give their size.
-# To avoid possibly unreliable computations based on free or other tool, instead use the GCE API directly to look up the disk info.
-# To do that we need project name, zone and name of the disk which we all obtain via the internal metadata
-# Of importance is the assumption that <disk name> == <instance name>-1
-# Note the "-1" after the instance name. That is because the disk just named <instance name> is the boot disk. The working disk has a "-1" suffix
-# The test expectation ensures that the output is 30, which means all 3 resources have been taken into account.
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-$graph:  
-- id: diskSizeTool
-  class: CommandLineTool
-  cwlVersion: v1.0
-  doc: "Asks for disk minimums"
-  requirements:
-    ResourceRequirement:
-      outdirMin: 10240
-      tmpdirMin: 10240
-  hints:
-  - class: ShellCommandRequirement
-  - class: DockerRequirement
-    dockerPull: gcr.io/google.com/cloudsdktool/cloud-sdk:slim
-  - class: dx:InputResourceRequirement
-    indirMin: 10240
-  inputs: []
-  outputs:
-    disk_size:
-      type: int
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents.trim()))
-  arguments:
-    - valueFrom: >
-        apt-get install --assume-yes jq > /dev/null && NAME=`curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/name` && ZONE=`basename \`curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/zone\`` && PROJECT=`curl -s -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/project/project-id` && curl -s -H "Authorization: Bearer `gcloud auth print-access-token`" "https://www.googleapis.com/compute/v1/projects/${PROJECT}/zones/${ZONE}/disks/${NAME}-1?fields=sizeGb" | jq -r '.sizeGb'
-      shellQuote: false
-  stdout: stdout
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl b/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl
deleted file mode 100644
index d874ee0bffb..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_inputdir_zero_doesnt_localize.cwl
+++ /dev/null
@@ -1,129 +0,0 @@
-cwlVersion: v1.0
-$namespaces:
-  dx: https://www.dnanexus.com/cwl#
-$graph:
-- id: inputdir_zero_doesnt_localize
-  class: Workflow
-  hints:
-  - class: ShellCommandRequirement
-  - class: DockerRequirement
-    dockerPull: gcr.io/google.com/cloudsdktool/cloud-sdk:slim
-  - class: dx:InputResourceRequirement
-    indirMin: 0
-  inputs: []
-  outputs:
-  - id: errors
-    type: File
-    outputSource: findFile/errors
-  steps:
-  - id: echo
-    in: []
-    out:
-    - id: echoOut
-    - id: echoArrayOut
-    - id: echoRecordOut
-    - id: echoMaybeOut
-    run:
-      class: CommandLineTool
-      inputs: []
-      outputs:
-      - id: echoOut
-        outputBinding:
-          glob: lonely_file
-        type: File
-        secondaryFiles: [.also]
-      - id: echoArrayOut
-        outputBinding:
-          glob: '*.txt*'
-          outputEval: $([self[0]])  
-        type:
-          items: File
-          type: array
-      - id: echoRecordOut
-        secondaryFiles: [.also]
-        type:
-          type: record
-          name: foo
-          fields:
-            - name: a
-              type: File
-              outputBinding:
-                glob: file_in_object
-      - id: echoMaybeOut
-        type: 
-        - File
-        - 'null'
-        secondaryFiles: [.also]
-        outputBinding:
-          glob: maybe_file
-      arguments:
-       - valueFrom: |
-           echo "lonely_file" > lonely_file
-           echo "lonely_file.also" > lonely_file.also
-           echo "file_in_array.txt" > file_in_array.txt
-           echo "file_in_array.txt.also" > file_in_array.txt.also
-           echo "file_in_object" > file_in_object
-           echo "file_in_object.also" > file_in_object.also
-           echo "maybe_file" > maybe_file
-           echo "maybe_file.also" > maybe_file.also
-         shellQuote: false
-  - id: findFile
-    in:
-    - id: f
-      source: "#inputdir_zero_doesnt_localize/echo/echoOut"
-    - id: g
-      source: "#inputdir_zero_doesnt_localize/echo/echoArrayOut"
-    - id: h
-      source: "#inputdir_zero_doesnt_localize/echo/echoRecordOut"
-    - id: i
-      source: "#inputdir_zero_doesnt_localize/echo/echoMaybeOut"
-    out:
-    - id: errors
-    run:
-      inputs:
-      - id: f
-        type: File
-        secondaryFiles: [.also]
-      - id: i
-        type: File?
-        secondaryFiles: [.also]
-      - id: g
-        type:
-          type: array
-          items: File
-        secondaryFiles: [.also]
-      - id: h
-        secondaryFiles: [.also]
-        type:
-          type: record
-          name: foo
-          fields:
-            - name: a
-              type: File
-      outputs:
-      - id: errors
-        type: string
-        outputBinding:
-          glob: errors.txt
-          loadContents: true
-          outputEval: $(self[0].contents)
-      class: CommandLineTool
-      requirements:
-      - class: ShellCommandRequirement
-      - class: InlineJavascriptRequirement
-      arguments:
-      # Unfortunately we can't use the same trick as in draft3_nio_file_papi1 because in papi 2 the instance metadata doesn't seem to contain
-      # the PAPI operation ID. So instead simply check that the input files are not there. This is not as neat as the PAPI1 version
-      # but should check the right thing as long as the files are localized (in general, but not here) somewhere in the same directory as where the command
-      # runs. If that changes then the directory where "find" searches should be updated 
-        - valueFrom: |
-            touch errors.txt
-            find . -name lonely_file >> errors.txt
-            find . -name lonely_file.also >> errors.txt
-            find . -name file_in_array >> errors.txt
-            find . -name file_in_array.also >> errors.txt
-            find . -name file_in_object >> errors.txt
-            find . -name file_in_object.also >> errors.txt
-            find . -name maybe_file >> errors.txt
-            find . -name maybe_file.also >> errors.txt
-          shellQuote: false
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_resources.cwl b/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_resources.cwl
deleted file mode 100644
index 295302acc2e..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources/cwl_resources.cwl
+++ /dev/null
@@ -1,27 +0,0 @@
-cwlVersion: v1.0
-$graph:  
-- id: machineTypeTool
-  class: CommandLineTool
-  cwlVersion: v1.0
-  doc: "Asks for CPU and Memory minimums"
-  requirements:
-    ResourceRequirement:
-      coresMin: 2
-      coresMax: 2
-      ramMin: 7GB
-      ramMax: 7GB
-  hints:
-    DockerRequirement:
-      dockerPull: python:latest
-  inputs: []
-  outputs:
-    machine_type:
-      type: string
-      outputBinding:
-        glob: stdout
-        loadContents: true
-        outputEval: $(self[0].contents.trim())
-  baseCommand: ['curl', 'http://metadata.google.internal/computeMetadata/v1/instance/machine-type', '-H', 'Metadata-Flavor: Google']
-  stdout: stdout
-
-
diff --git a/centaur/src/main/resources/standardTestCases/cwl_resources_papiv2.test b/centaur/src/main/resources/standardTestCases/cwl_resources_papiv2.test
deleted file mode 100644
index ccb4f0ad534..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_resources_papiv2.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: cwl_resources_papiv2
-testFormat: workflowsuccess
-backends: [Papiv2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_resources/cwl_resources.cwl
-}
-
-metadata {
-  status: Succeeded
-  "outputs.machineTypeTool.machine_type": "projects/1005074806481/machineTypes/custom-2-7168"
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: machineTypeTool
diff --git a/centaur/src/main/resources/standardTestCases/cwl_restart/cwl_restart.cwl b/centaur/src/main/resources/standardTestCases/cwl_restart/cwl_restart.cwl
deleted file mode 100644
index 82664f739b1..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_restart/cwl_restart.cwl
+++ /dev/null
@@ -1,117 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-id: cwl_restart
-# Workflow-level DockerRequirement
-requirements:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-inputs: []
-outputs:
-- id: flag
-  outputSource: "#third_step/flag"
-  type: boolean
-steps:
-- id: first_step
-  in: []
-  out:
-  - id: firstfoofile
-  # A dash is not valid in a WDL identifier and would have broken older `IdentifierAndPathPattern` parsing.
-  - id: first-bar-file
-  run:
-    inputs: []
-    outputs:
-    - id: firstfoofile
-      outputBinding:
-        glob: out.txt
-      type: File
-    - id: first-bar-file
-      outputBinding:
-        glob: out.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    arguments:
-    - valueFrom: echo
-    - valueFrom: "I have a bad feeling about this"
-    - valueFrom: ">"
-      shellQuote: false
-    - valueFrom: "out.txt"
-- id: cromwell_killer
-  in:
-  - id: fooinput
-    source: "#first_step/firstfoofile"
-  - id: bar-input
-    source: "#first_step/first-bar-file"
-  out:
-  - id: "footxt"
-  - id: "bar-txt"
-  run:
-    inputs:
-    - id: fooinput
-      type: File
-    - id: bar-input
-      type: File
-    outputs:
-    - id: "footxt"
-      outputBinding:
-        glob: foo.txt
-      type: File
-    - id: "bar-txt"
-      outputBinding:
-        glob: bar.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    arguments:
-    - valueFrom: sleep
-    - valueFrom: "60"
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: foo
-    - valueFrom: ">"
-      shellQuote: false
-    - valueFrom: "foo.txt"
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: bar
-    - valueFrom: ">"
-      shellQuote: false
-    - valueFrom: "bar.txt"
-- id: third_step
-  in:
-  - id: foo
-    source: "#cromwell_killer/footxt"
-  - id: bar
-    source: "#cromwell_killer/bar-txt"
-  out:
-  - id: flag
-  run:
-    inputs:
-    - id: foo
-      type: File
-    - id: bar
-      type: File
-    outputs:
-    - id: flag
-      outputBinding:
-        outputEval: $(true)
-      type: boolean
-    class: CommandLineTool
-    requirements:
-    - class: InlineJavascriptRequirement
-    - class: ShellCommandRequirement
-    arguments:
-    - valueFrom: echo
-    - valueFrom: "Are we alive???"
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: $(inputs.foo)
-    - valueFrom: "&&"
-      shellQuote: false
-    - valueFrom: echo
-    - valueFrom: $(inputs.bar)
diff --git a/centaur/src/main/resources/standardTestCases/cwl_restart_local_with_recover.test b/centaur/src/main/resources/standardTestCases/cwl_restart_local_with_recover.test
deleted file mode 100644
index a45e97769cd..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_restart_local_with_recover.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_restart_local_with_recover
-testFormat: CromwellRestartWithRecover
-callMark: cromwell_killer
-backendsMode: "only"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_restart/cwl_restart.cwl
-}
-
-metadata {
-  status: Succeeded
-  "calls.first_step.executionStatus": Done
-  "calls.cromwell_killer.executionStatus": Done
-  "calls.third_step.executionStatus": Done
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
diff --git a/centaur/src/main/resources/standardTestCases/cwl_run/1st-tool.cwl b/centaur/src/main/resources/standardTestCases/cwl_run/1st-tool.cwl
deleted file mode 100644
index af0c4de297d..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_run/1st-tool.cwl
+++ /dev/null
@@ -1,9 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-inputs:
-  message:
-    type: string
-    inputBinding:
-      position: 1
-outputs: []
diff --git a/centaur/src/main/resources/standardTestCases/cwl_run/echo-job.yml b/centaur/src/main/resources/standardTestCases/cwl_run/echo-job.yml
deleted file mode 100644
index 913ff438103..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_run/echo-job.yml
+++ /dev/null
@@ -1 +0,0 @@
-message: Hello CWL!
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files.test b/centaur/src/main/resources/standardTestCases/cwl_secondary_files.test
deleted file mode 100644
index 2c8f861e1e9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_secondary_files
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: main
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_secondary_files/cwl_secondary_files.cwl
-  inputs: cwl_secondary_files/cwl_secondary_files.yaml
-  options: cwl_secondary_files/cwl_secondary_files.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.main.the_answer": "$(42)"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.cwl b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.cwl
deleted file mode 100644
index 123a7b574a1..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.cwl
+++ /dev/null
@@ -1,44 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: main
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: command
-      type: string
-    - id: f
-      type: File
-      inputBinding:
-        position: 2
-      secondaryFiles: [.also]
-    - id: of
-      type: File?
-      inputBinding:
-        position: 3
-      secondaryFiles: [.also]
-    - id: fs
-      type:
-        type: array
-        items: File
-        inputBinding:
-          position: 4
-      secondaryFiles: [.also]
-    - id: fr
-      secondaryFiles: [.also]
-      type:
-        type: record
-        name: foo
-        fields:
-          - name: a
-            type: File
-            inputBinding:
-              position: 5
-  outputs:
-    the_answer:
-      type: string
-      outputBinding:
-        outputEval: ${ return "$(" + 42 + ")"; }
-  baseCommand: []
-  arguments: ["bash", "-c", $(inputs.command)]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.options b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.yaml b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.yaml
deleted file mode 100644
index 928cfb8cbb3..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/cwl_secondary_files.yaml
+++ /dev/null
@@ -1,17 +0,0 @@
-# This command will stat the secondaryFiles and if they're missing bad times
-command: stat $(echo $* | sed 's/.txt/.txt.also/g') > /dev/null
-f:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt"
-of:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bim.txt"
-fs:
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt"
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt"
-fr:
-  a:
-    class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bam.txt"
\ No newline at end of file
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt.also b/centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt.also
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow.test b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow.test
deleted file mode 100644
index f6dff3fb727..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_secondary_files_workflow
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_secondary_files_workflow
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl
-  inputs: cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml
-  options: cwl_secondary_files_workflow/cwl_secondary_files_workflow.options
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "outputs.cwl_secondary_files_workflow.the_answer": "$(42)"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl
deleted file mode 100644
index d5f9dc3f8c9..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.cwl
+++ /dev/null
@@ -1,55 +0,0 @@
-cwlVersion: v1.0
-$graph:
-# The inputs of the workflow specify secondary files but NOT of the tool
-# Verify that they are still propagated through
-- id: cwl_secondary_files_workflow
-  class: Workflow
-  inputs:
-  - id: command
-    type: string
-  - id: wf_file_input
-    type: File
-    secondaryFiles: [.also]
-  - id: wf_file_input_array
-    type:
-      type: array
-      items: File
-    secondaryFiles: [.also]
-  outputs:
-  - id: the_answer
-    type: string
-    outputSource: run_tool/the_answer
-  steps:
-  - id: run_tool
-    run: "#cwl_secondary_files_workflow_tool"
-    in:
-      command: command
-      f: wf_file_input
-      fs: wf_file_input_array
-    out:
-    - id: the_answer
-- id: cwl_secondary_files_workflow_tool
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: command
-      type: string
-    - id: f
-      type: File
-      inputBinding:
-        position: 2
-    - id: fs
-      type:
-        type: array
-        items: File
-        inputBinding:
-          position: 3
-  outputs:
-    the_answer:
-      type: string
-      outputBinding:
-        outputEval: ${ return "$(" + 42 + ")"; }
-  baseCommand: []
-  arguments: ["bash", "-c", $(inputs.command)]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.options b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.options
deleted file mode 100644
index 71d245d2bf6..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.options
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "backend": "Local"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml b/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml
deleted file mode 100644
index e0cf43d4b1a..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_secondary_files_workflow/cwl_secondary_files_workflow.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-# This command will stat the secondaryFiles and if they're missing bad times
-command: stat $(echo $* | sed 's/.txt/.txt.also/g') > /dev/null
-wf_file_input:
-  class: File
-  path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/foo.txt"
-wf_file_input_array:
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/bar.txt"
-  - class: File
-    path: "centaur/src/main/resources/standardTestCases/cwl_secondary_files/baz.txt"
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.cwl b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.cwl
deleted file mode 100644
index b49ec9b1134..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: cwl_stdout_expression
-  class: CommandLineTool
-  hints:
-    DockerRequirement:
-      dockerPull: "debian:stretch-slim"
-  inputs:
-    - id: foo
-      type: string
-    - id: bar
-      type: string
-  outputs:
-    b: stdout
-  stdout: "stdout-$(inputs.foo)-$(inputs.bar).txt"
-  baseCommand: []
-  arguments: [echo, $(inputs.foo), $(inputs.bar)]
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.json b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.json
deleted file mode 100644
index 82e0295d318..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression/cwl_stdout_expression.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "foo": "baz",
-  "bar": "qux"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_local.test b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_local.test
deleted file mode 100644
index 13bfbb68e24..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_local.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: cwl_stdout_expression_local
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_stdout_expression
-backendsMode: "any"
-backends: [Local, LocalNoDocker]
-tags: [localdockertest]
-
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_stdout_expression/cwl_stdout_expression.cwl
-  inputs: cwl_stdout_expression/cwl_stdout_expression.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.cwl_stdout_expression.stdout": "<<WORKFLOW_ROOT>>/call-cwl_stdout_expression/execution/stdout-baz-qux.txt"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_papi.test b/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_papi.test
deleted file mode 100644
index b48a0effa79..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwl_stdout_expression_papi.test
+++ /dev/null
@@ -1,18 +0,0 @@
-name: cwl_stdout_expression_papi
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: cwl_stdout_expression
-backends: [Papi2]
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwl_stdout_expression/cwl_stdout_expression.cwl
-  inputs: cwl_stdout_expression/cwl_stdout_expression.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.cwl_stdout_expression.stdout": "<<WORKFLOW_ROOT>>call-cwl_stdout_expression/stdout-baz-qux.txt"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwls/scatter-job1.json b/centaur/src/main/resources/standardTestCases/cwls/scatter-job1.json
deleted file mode 100644
index b3ab2751243..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwls/scatter-job1.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "inp": ["one", "two", "three", "four"],
-  "inp2": "yeahhh"
-}
diff --git a/centaur/src/main/resources/standardTestCases/cwls/scatter-wf1.cwl b/centaur/src/main/resources/standardTestCases/cwls/scatter-wf1.cwl
deleted file mode 100644
index dc46aa7da4a..00000000000
--- a/centaur/src/main/resources/standardTestCases/cwls/scatter-wf1.cwl
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: string[]
-  inp2: string
-outputs:
-  out:
-    type: string[]
-    outputSource: step1/echo_out
-
-requirements:
-  - class: ScatterFeatureRequirement
-  - class: DockerRequirement
-    dockerPull: ubuntu:latest
-
-steps:
-  step1:
-    in:
-      echo_in: inp
-      echo_in2: inp2
-    out: [echo_out]
-    scatter: echo_in
-    run:
-      class: CommandLineTool
-      inputs:
-        echo_in:
-          type: string
-          inputBinding: {}
-        echo_in2:
-          type: string
-          inputBinding: {}
-      outputs:
-        echo_out:
-          type: string
-          outputBinding:
-            glob: "step1_out"
-            loadContents: true
-            outputEval: $(self[0].contents)
-      baseCommand: "echo"
-      arguments:
-        - "-n"
-        - "foo"
-      stdout: "step1_out"
diff --git a/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs b/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs
index d5738ac4d17..d1712641dd2 100644
--- a/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs
+++ b/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.inputs
@@ -1,5 +1,5 @@
 {
-    # Martha does not return service accounts for JDR paths. Therefore they shouldn't need to be localized using the
+    # DRSHub does not return service accounts for JDR paths. Therefore they shouldn't need to be localized using the
     # Cromwell custom DOS/DRS localizer.
     #
     # However, the first file1 was generated before JDR stared saving file names at the end of the gsUri.
diff --git a/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test b/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test
index 4025860ed8d..510c9215c1f 100644
--- a/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test
+++ b/centaur/src/main/resources/standardTestCases/drs_usa_jdr.test
@@ -1,6 +1,7 @@
 name: drs_usa_jdr
 testFormat: WorkflowSuccess
 backends: ["papi-v2-usa"]
+tags: [ drs ]
 skipDescribeEndpointValidation: true
 
 files {
diff --git a/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test b/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test
index ab050aea69f..15e41d95529 100644
--- a/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test
+++ b/centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test
@@ -1,6 +1,7 @@
 name: drs_usa_jdr_preresolve
 testFormat: WorkflowSuccess
 backends: ["papi-v2-usa"]
+tags: [ drs ]
 skipDescribeEndpointValidation: true
 
 files {
diff --git a/centaur/src/main/resources/standardTestCases/expressionLib.test b/centaur/src/main/resources/standardTestCases/expressionLib.test
deleted file mode 100644
index 74299af9bc6..00000000000
--- a/centaur/src/main/resources/standardTestCases/expressionLib.test
+++ /dev/null
@@ -1,15 +0,0 @@
-name: expression_lib_cwl
-cwlVersion: 1.0
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: expressionLib/expressionLib.cwl
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/expressionLib/expressionLib.cwl b/centaur/src/main/resources/standardTestCases/expressionLib/expressionLib.cwl
deleted file mode 100644
index fe8df12b4b0..00000000000
--- a/centaur/src/main/resources/standardTestCases/expressionLib/expressionLib.cwl
+++ /dev/null
@@ -1,14 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-hints:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-requirements:
-  InlineJavascriptRequirement:
-    expressionLib:
-      - "function foo() { return 2; }"
-inputs: []
-outputs:
-  out: stdout
-arguments: [echo, $(foo())]
-stdout: whatever.txt
diff --git a/centaur/src/main/resources/standardTestCases/hello_cwl.test b/centaur/src/main/resources/standardTestCases/hello_cwl.test
deleted file mode 100644
index 18712fd5404..00000000000
--- a/centaur/src/main/resources/standardTestCases/hello_cwl.test
+++ /dev/null
@@ -1,12 +0,0 @@
-name: hello_cwl
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-workflowRoot: hello
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: hello_cwl/hello.cwl
-  inputs: hello_cwl/hello.inputs
-  "outputs.hello.salutation": "Hello m'Lord!"
-}
diff --git a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.cwl b/centaur/src/main/resources/standardTestCases/hello_cwl/hello.cwl
deleted file mode 100644
index deb1e4d1f4a..00000000000
--- a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.cwl
+++ /dev/null
@@ -1,21 +0,0 @@
-cwlVersion: v1.0
-$graph:
-  id: hello
-  class: CommandLineTool
-  requirements:
-    - class: DockerRequirement
-      dockerPull: ubuntu:latest
-  baseCommand: echo
-  inputs:
-    message:
-      type: string
-      inputBinding:
-        position: 1
-  stdout: hello-stdout.txt
-  outputs:
-    - id: salutation
-      type: string
-      outputBinding:
-        glob: hello-stdout.txt
-        loadContents: true
-        outputEval: $(self[0].contents.trim())
diff --git a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.inputs b/centaur/src/main/resources/standardTestCases/hello_cwl/hello.inputs
deleted file mode 100644
index 11888b548ad..00000000000
--- a/centaur/src/main/resources/standardTestCases/hello_cwl/hello.inputs
+++ /dev/null
@@ -1,3 +0,0 @@
-# Seemingly innocuous but this particular message actually tests proper shell quoting of
-# spaces, single quotes, and exclamation points.
-message: Hello m'Lord!
diff --git a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs.cwl b/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs.cwl
deleted file mode 100644
index e476be06d12..00000000000
--- a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs.cwl
+++ /dev/null
@@ -1,49 +0,0 @@
-cwlVersion: v1.0
-$graph:
-  - id: http_inputs
-    class: Workflow
-    inputs:
-    - id: jamie
-      type: File
-    outputs:
-    - id: md5
-      outputSource: "#http_inputs/sum/md5"
-      type: int
-    steps:
-    - id: sum
-      in:
-      - id: jamie
-        source: "#http_inputs/jamie"
-      out:
-      - id: md5
-      # Workflow step-level DockerRequirement
-      requirements:
-        DockerRequirement:
-          dockerPull: "ubuntu:latest"
-      run:
-        inputs:
-        - id: jamie
-          type: File
-        outputs:
-        - id: md5
-          outputBinding:
-            glob: md5-stdOut.txt
-            loadContents: true
-            outputEval: $(self[0].contents)
-          type: string
-        class: CommandLineTool
-        requirements:
-        - class: ShellCommandRequirement
-        - class: InlineJavascriptRequirement
-        arguments:
-        - valueFrom: "/usr/bin/md5sum"
-          shellQuote: false
-        - valueFrom: $(inputs.jamie)
-          shellQuote: true
-        - valueFrom: '|'
-          shellQuote: false
-        - valueFrom: cut
-          shellQuote: false
-        - valueFrom: -c1-32
-          shellQuote: false
-        stdout: md5-stdOut.txt
diff --git a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs_cwl.inputs b/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs_cwl.inputs
deleted file mode 100644
index 9a7137d1bf9..00000000000
--- a/centaur/src/main/resources/standardTestCases/http_inputs/http_inputs_cwl.inputs
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "jamie": "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/docs/jamie_the_cromwell_pig.png",
-}
diff --git a/centaur/src/main/resources/standardTestCases/http_inputs_cwl.test b/centaur/src/main/resources/standardTestCases/http_inputs_cwl.test
deleted file mode 100644
index 7ed111e3ec7..00000000000
--- a/centaur/src/main/resources/standardTestCases/http_inputs_cwl.test
+++ /dev/null
@@ -1,15 +0,0 @@
-name: http_inputs_cwl
-backends: [Local, Papiv2]
-testFormat: workflowsuccess
-workflowRoot: http_inputs
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: http_inputs/http_inputs.cwl
-  inputs: http_inputs/http_inputs_cwl.inputs
-}
-
-metadata {
-  status: Succeeded
-  "outputs.http_inputs.md5": "602d0a4c1d54b7302e2d245a66a1b609\n"
-}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl
new file mode 100644
index 00000000000..33153c1157c
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_mounted_only_if_requested.wdl
@@ -0,0 +1,49 @@
+version 1.0
+
+
+workflow ReferenceDiskMountedOnlyIfRequested {
+    call MentionsNirvanaReference {}
+    output {
+        Boolean disk_mounted = MentionsNirvanaReference.disk_mounted
+    }
+}
+
+
+task MentionsNirvanaReference {
+    input {
+        # Tiny 116 byte reference file, certainly not worth attaching a 55 GiB Nirvana reference disk for this.
+        File mention =
+            "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx"
+    }
+    command <<<
+        PS4='\D{+%F %T} \w $ '
+        set -o nounset -o xtrace
+
+        # Debug output
+        lsblk
+
+        CANDIDATE_MOUNT_POINT=$(lsblk | sed -E -n 's!.*(/mnt/[a-f0-9]+).*!\1!p')
+
+        if [[ ! -z ${CANDIDATE_MOUNT_POINT} ]]; then
+            echo "Found unexpected mounted disk, investigating further."
+            find ${CANDIDATE_MOUNT_POINT} -print | tee find.out
+
+            if grep -i nirvana find.out; then
+                echo "Found what appears to be a Nirvana reference disk."
+            else
+                echo "Found unknown volume mounted, see 'find.out' for manifest."
+            fi
+            echo true > disk_mounted.out
+        else
+            echo false > disk_mounted.out
+        fi
+    >>>
+    runtime {
+        docker: "ubuntu:latest"
+        backend: "Papiv2-Reference-Disk-Localization"
+    }
+    output {
+        Boolean disk_mounted = read_boolean("disk_mounted.out")
+        File? find_out = "find.out"
+    }
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
index 8e28a8ef541..4caf94c0f77 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
@@ -1,3 +1,5 @@
 {
-  "wf_reference_disk_test.check_if_localized_as_symlink.reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.tile_db_header.vcf"
+  "wf_reference_disk_test.broad_reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
+  "wf_reference_disk_test.nirvana_reference_file_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd.idx",
+  "wf_reference_disk_test.nirvana_reference_file_metachar_input": "gs://broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi"
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
index 43a298f18ab..51fb467598b 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
+++ b/centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
@@ -1,11 +1,38 @@
-task check_if_localized_as_symlink {
-  File reference_file_input
-  command {
-     # print true if file is a symlink, otherwise print false
-     if test -h ${reference_file_input}; then echo "true"; else echo "false"; fi;
+version 1.0
+
+task check_if_localized_with_valid_symlink {
+  input {
+    File broad_reference_file_input
+    File nirvana_reference_file_input
+    File nirvana_reference_file_metachar_input
   }
+  String broad_input_valid_symlink = "broad_input_valid_symlink.txt"
+  String nirvana_input_valid_symlink = "nirvana_input_valid_symlink.txt"
+  String nirvana_metachar_input_valid_symlink = "nirvana_metachar_input_valid_symlink.txt"
+  command <<<
+      PS4='\D{+%F %T} \w $ '
+      set -o nounset -o pipefail -o xtrace
+
+      # Echo true to stdout if the argument is a symlink pointing to an extant file, otherwise echo false.
+      check_if_valid_symlink() {
+          local reference_input="$1"
+
+          if [[ -h "${reference_input}" && -f $(readlink "${reference_input}") ]]; then
+              echo true
+          else
+              echo false
+          fi
+      }
+
+      check_if_valid_symlink "~{broad_reference_file_input}" > ~{broad_input_valid_symlink}
+      check_if_valid_symlink "~{nirvana_reference_file_input}" > ~{nirvana_input_valid_symlink}
+      check_if_valid_symlink "~{nirvana_reference_file_metachar_input}" > ~{nirvana_metachar_input_valid_symlink}
+
+  >>>
   output {
-    Boolean is_symlink = read_boolean(stdout())
+    Boolean is_broad_input_valid_symlink = read_boolean("~{broad_input_valid_symlink}")
+    Boolean is_nirvana_input_valid_symlink = read_boolean("~{nirvana_input_valid_symlink}")
+    Boolean is_nirvana_metachar_input_valid_symlink = read_boolean("~{nirvana_metachar_input_valid_symlink}")
   }
   runtime {
     docker: "ubuntu:latest"
@@ -14,8 +41,20 @@ task check_if_localized_as_symlink {
 }
 
 workflow wf_reference_disk_test {
-  call check_if_localized_as_symlink
+  input {
+    File broad_reference_file_input
+    File nirvana_reference_file_input
+    File nirvana_reference_file_metachar_input
+  }
+  call check_if_localized_with_valid_symlink {
+    input:
+      broad_reference_file_input = broad_reference_file_input,
+      nirvana_reference_file_input = nirvana_reference_file_input,
+      nirvana_reference_file_metachar_input = nirvana_reference_file_metachar_input
+  }
   output {
-     Boolean is_input_file_a_symlink = check_if_localized_as_symlink.is_symlink
+    Boolean is_broad_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_broad_input_valid_symlink
+    Boolean is_nirvana_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_nirvana_input_valid_symlink
+    Boolean is_nirvana_metachar_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_nirvana_metachar_input_valid_symlink
   }
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
index b75ef58dabc..bb8be222691 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
@@ -11,5 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": false
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test
new file mode 100644
index 00000000000..32c6d83e5c3
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_false.test
@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_false
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_false.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": false
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test
new file mode 100644
index 00000000000..165e1c6d1f4
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_true.test
@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_true
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_true.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": true
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test
new file mode 100644
index 00000000000..860159b594e
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_mounted_only_if_requested_unspecified.test
@@ -0,0 +1,14 @@
+name: reference_disk_mounted_only_if_requested_unspecified
+testFormat: workflowsuccess
+backends: [Papiv2-Reference-Disk-Localization]
+
+files {
+  workflow: reference_disk/reference_disk_mounted_only_if_requested.wdl
+  options: reference_disk/reference_disk_test_unspecified.options.json
+}
+
+metadata {
+  workflowName: ReferenceDiskMountedOnlyIfRequested
+  status: Succeeded
+  "outputs.ReferenceDiskMountedOnlyIfRequested.disk_mounted": false
+}
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
index dab9c516164..6d957bf55b7 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
@@ -11,5 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": true
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": true
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": true
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": true
 }
diff --git a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
index 441db8748f2..7625bcd7806 100644
--- a/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
+++ b/centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
@@ -11,5 +11,7 @@ files {
 metadata {
   workflowName: wf_reference_disk_test
   status: Succeeded
-  "outputs.wf_reference_disk_test.is_input_file_a_symlink": false
+  "outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": false
+  "outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": false
 }
diff --git a/centaur/src/main/resources/standardTestCases/retry_with_more_memory/retry_with_more_memory_after_137.wdl b/centaur/src/main/resources/standardTestCases/retry_with_more_memory/retry_with_more_memory_after_137.wdl
new file mode 100644
index 00000000000..2fe434475c6
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/retry_with_more_memory/retry_with_more_memory_after_137.wdl
@@ -0,0 +1,22 @@
+version 1.0
+
+task imitate_oom_error {
+  command {
+    printf "Exception in thread "main" java.lang.OutOfMemoryError: testing\n\tat Test.main(Test.java:1)\n" >&2
+    touch foo
+    exit 137
+  }
+  output {
+    File foo = "foo"
+  }
+  runtime {
+    docker: "python:latest"
+    memory: "1 GB"
+    maxRetries: 2
+    backend: "Papiv2"
+  }
+}
+
+workflow retry_with_more_memory_after_137 {
+  call imitate_oom_error
+}
diff --git a/centaur/src/main/resources/standardTestCases/retry_with_more_memory_after_137.test b/centaur/src/main/resources/standardTestCases/retry_with_more_memory_after_137.test
new file mode 100644
index 00000000000..a69290ca511
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/retry_with_more_memory_after_137.test
@@ -0,0 +1,21 @@
+name: retry_with_more_memory_after_137
+testFormat: workflowfailure
+backends: [Papiv2]
+
+files {
+  workflow: retry_with_more_memory/retry_with_more_memory_after_137.wdl
+  options: retry_with_more_memory/retry_with_more_memory.options
+}
+
+metadata {
+  workflowName: retry_with_more_memory_after_137
+  status: Failed
+  "failures.0.message": "Workflow failed"
+  "failures.0.causedBy.0.message": "stderr for job `retry_with_more_memory_after_137.imitate_oom_error:NA:3` contained one of the `memory-retry-error-keys: [OutOfMemory,Killed]` specified in the Cromwell config. Job might have run out of memory."
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.1.executionStatus": "RetryableFailure"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.1.runtimeAttributes.memory": "1 GB"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.2.executionStatus": "RetryableFailure"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.2.runtimeAttributes.memory": "1.1 GB"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.3.executionStatus": "Failed"
+  "retry_with_more_memory_after_137.imitate_oom_error.-1.3.runtimeAttributes.memory": "1.2100000000000002 GB"
+}
diff --git a/centaur/src/main/resources/standardTestCases/scatter-wf1.test b/centaur/src/main/resources/standardTestCases/scatter-wf1.test
deleted file mode 100644
index 397b94710a3..00000000000
--- a/centaur/src/main/resources/standardTestCases/scatter-wf1.test
+++ /dev/null
@@ -1,11 +0,0 @@
-name: cwl_scatter_wf1
-testFormat: workflowsuccess
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: cwls/scatter-wf1.cwl
-  inputs: cwls/scatter-job1.json
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
diff --git a/centaur/src/main/resources/standardTestCases/three_step.test b/centaur/src/main/resources/standardTestCases/three_step.test
deleted file mode 100644
index b24e649ecce..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step.test
+++ /dev/null
@@ -1,21 +0,0 @@
-name: three_step_cwl
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-skipDescribeEndpointValidation: true
-
-files {
-  workflow: three_step/three_step.cwl
-  inputs: three_step/inputs.json
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-  "calls.wc.executionStatus": Done
-  "calls.ps.executionStatus": Done
-  "calls.cgrep.executionStatus": Done
-  "calls.ps.runtimeAttributes.docker": "ubuntu:bionic"
-  "calls.wc.runtimeAttributes.docker": "ubuntu:latest"
-  "calls.cgrep.runtimeAttributes.docker": "debian:jessie"
-}
diff --git a/centaur/src/main/resources/standardTestCases/three_step/inputs.json b/centaur/src/main/resources/standardTestCases/three_step/inputs.json
deleted file mode 100644
index 8dac4768fff..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step/inputs.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "pattern": "java"
-}
diff --git a/centaur/src/main/resources/standardTestCases/three_step/three_step.cwl b/centaur/src/main/resources/standardTestCases/three_step/three_step.cwl
deleted file mode 100644
index e328003eab1..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step/three_step.cwl
+++ /dev/null
@@ -1,114 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-id: three_step
-# Workflow-level DockerRequirement
-hints:
-  DockerRequirement:
-    dockerPull: "ubuntu:latest"
-inputs:
-- id: pattern
-  type: string
-outputs:
-- id: cgrep-count
-  outputSource: "#cgrep/cgrep-count"
-  type: int
-- id: wc-count
-  outputSource: "#wc/wc-count"
-  type: int
-steps:
-- id: ps
-  in: []
-  out:
-  - id: ps-stdOut
-  run:
-    inputs: []
-    outputs:
-    - id: ps-stdOut
-      outputBinding:
-        glob: ps-stdOut.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-      # Command line tool-level DockerRequirement
-      # Check it: this DockerRequirement does not use the `class` formatting but should still parse
-      # thanks to the magic of SALAD.
-      DockerRequirement:
-        dockerPull: "ubuntu:bionic"
-    baseCommand: ps
-    stdout: ps-stdOut.txt
-- id: cgrep
-  in:
-  - id: pattern
-    source: "#pattern"
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: cgrep-count
-  # Workflow step-level DockerRequirement
-  requirements:
-    DockerRequirement:
-      dockerPull: "debian:jessie"
-  run:
-    inputs:
-    - id: pattern
-      type: string
-    - id: file
-      type: File
-    outputs:
-    - id: cgrep-count
-      outputBinding:
-        glob: cgrep-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: grep
-      shellQuote: false
-    - valueFrom: $(inputs.pattern)
-      shellQuote: false
-    - valueFrom: ${return inputs.file}
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: cgrep-stdOut.txt
-- id: wc
-  in:
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: wc-count
-  run:
-    inputs:
-    - id: file
-      type: File
-    outputs:
-    - id: wc-count
-      outputBinding:
-        glob: wc-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: cat
-      shellQuote: false
-    - valueFrom: $(inputs.file)
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: wc-stdOut.txt
diff --git a/centaur/src/main/resources/standardTestCases/three_step/three_step_caller_wf.cwl b/centaur/src/main/resources/standardTestCases/three_step/three_step_caller_wf.cwl
deleted file mode 100644
index ab5d8ddc458..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step/three_step_caller_wf.cwl
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env cwl-runner
-class: Workflow
-cwlVersion: v1.0
-
-inputs:
-- id: pin
-  type: string
-  default: "v"
-
-outputs:
-    count_output:
-      type: int
-      outputSource: threestep/wc-count
-
-requirements:
-  - class: SubworkflowFeatureRequirement
-
-steps:
-  threestep:
-    run: three_step.cwl
-    in:
-    - id: pattern
-      source: pin
-    out: [wc-count]
diff --git a/centaur/src/main/resources/standardTestCases/three_step_subworkflow.test b/centaur/src/main/resources/standardTestCases/three_step_subworkflow.test
deleted file mode 100644
index 6ae478035b7..00000000000
--- a/centaur/src/main/resources/standardTestCases/three_step_subworkflow.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: three_step__subwf_cwl
-testFormat: workflowsuccess
-workflowType: CWL
-workflowTypeVersion: v1.0
-
-files {
-  workflow: three_step/three_step_caller_wf.cwl,
-  imports: [
-    three_step/three_step.cwl
-  ]
-}
-
-metadata {
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaur/src/main/resources/standardTestCases/workflow_type_and_version_cwl.test b/centaur/src/main/resources/standardTestCases/workflow_type_and_version_cwl.test
deleted file mode 100644
index 14ba92c588f..00000000000
--- a/centaur/src/main/resources/standardTestCases/workflow_type_and_version_cwl.test
+++ /dev/null
@@ -1,16 +0,0 @@
-ignore: true
-name: workflow_type_and_version_cwl
-testFormat: workflowsuccess
-
-files {
-  workflow: workflow_type_and_version_cwl/workflow_type_and_version_cwl.wdl
-}
-
-workflowType: CWL
-workflowTypeVersion: v1.0
-
-metadata {
-  workflowName: workflow_type_and_version_cwl
-  "submittedFiles.workflowType": CWL
-  "submittedFiles.workflowTypeVersion": v1.0
-}
diff --git a/centaurCwlRunner/src/bin/centaur-cwl-runner.bash b/centaurCwlRunner/src/bin/centaur-cwl-runner.bash
deleted file mode 100755
index 8f39c3ec130..00000000000
--- a/centaurCwlRunner/src/bin/centaur-cwl-runner.bash
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env bash
-
-# `sbt assembly` must have already been run.
-build_root="$( dirname "${BASH_SOURCE[0]}" )/../../.."
-centaur_cwl_jar="${CENTAUR_CWL_JAR:-"$( \
-    find "${build_root}/centaurCwlRunner/target/scala-2.13" -name 'centaur-cwl-runner-*.jar' -print0 \
-    | xargs -0 ls -1 -t \
-    | head -n 1 \
-    )"}"
-centaur_cwl_skip_file="${build_root}/centaurCwlRunner/src/main/resources/skipped_tests.csv"
-
-centaur_cwl_java_args=("-Xmx1g")
-if [[ -n "${CENTAUR_CWL_JAVA_ARGS-}" ]]; then
-    # Allow splitting on space to simulate an exported array
-    # https://stackoverflow.com/questions/5564418/exporting-an-array-in-bash-script#answer-5564589
-    # shellcheck disable=SC2206
-    centaur_cwl_java_args+=(${CENTAUR_CWL_JAVA_ARGS})
-fi
-
-# Handle empty arrays in older versions of bash
-# https://stackoverflow.com/questions/7577052/bash-empty-array-expansion-with-set-u#answer-7577209
-java \
-    ${centaur_cwl_java_args[@]+"${centaur_cwl_java_args[@]}"} \
-    -jar "${centaur_cwl_jar}" \
-    --skip-file "${centaur_cwl_skip_file}" \
-    "$@"
diff --git a/centaurCwlRunner/src/main/resources/application.conf b/centaurCwlRunner/src/main/resources/application.conf
deleted file mode 100644
index fcdd3da9c57..00000000000
--- a/centaurCwlRunner/src/main/resources/application.conf
+++ /dev/null
@@ -1,23 +0,0 @@
-akka {
-  loggers = ["akka.event.slf4j.Slf4jLogger"]
-  logging-filter = "akka.event.slf4j.Slf4jLoggingFilter"
-
-  # Silence Akka-Http warning logging of:
-  # [WARN] [01/28/2019 06:50:04.293] [centaur-acting-like-a-system-akka.actor.default-dispatcher-3] [centaur-acting-like-a-system/Pool(shared->http://localhost:8000)] Connection attempt failed. Backing off new connection attempts for at least 100 milliseconds.
-  #
-  # via:
-  # https://github.com/akka/akka/blob/v2.5.19/akka-actor/src/main/resources/reference.conf#L41-L44
-  # https://github.com/akka/akka/blob/v2.5.19/akka-actor/src/main/scala/akka/event/Logging.scala#L377
-  # https://github.com/akka/akka-http/blob/v10.1.7/akka-http-core/src/main/scala/akka/http/impl/engine/client/pool/NewHostConnectionPool.scala#L134
-  stdout-loglevel = "ERROR"
-}
-
-centaur {
-  # When running the tests in parallel on a Travis instance we need a bit more time for a reply to come back.
-  sendReceiveTimeout: 1 minute
-}
-
-cwltool-runner {
-  # When running the tests in parallel it takes a while for each JVM to initialize Heterodon. Instead use the process.
-  class = "cwl.CwltoolProcess"
-}
diff --git a/centaurCwlRunner/src/main/resources/logback.xml b/centaurCwlRunner/src/main/resources/logback.xml
deleted file mode 100644
index d92bac61949..00000000000
--- a/centaurCwlRunner/src/main/resources/logback.xml
+++ /dev/null
@@ -1,48 +0,0 @@
-<configuration>
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-            <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger - %msg%n</pattern>
-        </encoder>
-    </appender>
-
-    <!-- lower logging level, especially to stdout -->
-    <root level="warn">
-        <appender-ref ref="STDOUT"/>
-    </root>
-
-    <!--
-    Silence occasional PoolMasterActor error logging of:
-    04:20:04.785 [centaur-acting-like-a-system-akka.actor.default-dispatcher-5] ERROR akka.http.impl.engine.client.PoolMasterActor - connection pool for PoolGateway(hcps = HostConnectionPoolSetup(localhost,8000,ConnectionPoolSetup(ConnectionPoolSettings(4,0,5,32,1,30 seconds,ClientConnectionSettings(Some(User-Agent: akka-http/10.0.10),10 seconds,1 minute,512,None,<function0>,List(),ParserSettings(2048,16,64,64,8192,64,8388608,256,1048576,Strict,RFC6265,true,Full,Error,Map(If-Range -> 0, If-Modified-Since -> 0, If-Unmodified-Since -> 0, default -> 12, Content-MD5 -> 0, Date -> 0, If-Match -> 0, If-None-Match -> 0, User-Agent -> 32),false,akka.stream.impl.ConstantFun$$$Lambda$286/1579280783@2287c189,akka.stream.impl.ConstantFun$$$Lambda$286/1579280783@2287c189,akka.stream.impl.ConstantFun$$$Lambda$287/1370074462@628a0265),None),TCPTransport),akka.http.scaladsl.HttpConnectionContext$@164c4af,akka.event.MarkerLoggingAdapter@4204728))) has shut down unexpectedly
-
-    via:
-    https://github.com/akka/akka-http/blob/v10.0.10/akka-http-core/src/main/scala/akka/http/impl/engine/client/PoolMasterActor.scala#L117
-    -->
-    <logger name="akka.http.impl.engine.client.PoolMasterActor" level="off" additivity="false"/>
-
-    <!--
-    Silence Injector warning logging of:
-    06:36:48.095 [main] WARN  org.semanticweb.owlapi.utilities.Injector - No files found for META-INF/services/org.semanticweb.owlapi.model.OWLOntologyIRIMapper
-
-    via:
-    https://github.com/owlcs/owlapi/blob/owlapi-parent-5.1.7/api/src/main/java/org/semanticweb/owlapi/utilities/Injector.java#L383
-    -->
-    <logger name="org.semanticweb.owlapi.utilities.Injector" level="error" additivity="false"/>
-
-    <!--
-    Silence Akka warning logging of:
-    10:18:20.629 [centaur-acting-like-a-system-akka.actor.default-dispatcher-8] WARN  akka.io.InetAddressDnsResolver - No caching TTL defined. Using default value Ttl(30 seconds).
-
-    via:
-    https://github.com/akka/akka/blob/v2.5.19/akka-actor/src/main/scala/akka/io/InetAddressDnsResolver.scala#L40
-    -->
-    <logger name="akka.io.InetAddressDnsResolver" level="error" additivity="false"/>
-
-    <!--
-    Silence Akka-Http warning logging of:
-    00:53:57.537 [centaur-acting-like-a-system-akka.actor.default-dispatcher-10] WARN  akka.http.impl.engine.client.PoolGateway - Connection attempt failed. Backing off new connection attempts for at least 100 milliseconds.
-
-    via:
-    https://github.com/akka/akka-http/blob/v10.1.7/akka-http-core/src/main/scala/akka/http/impl/engine/client/pool/NewHostConnectionPool.scala#L134
-    -->
-    <logger name="akka.http.impl.engine.client.PoolGateway" level="error" additivity="false"/>
-</configuration>
diff --git a/centaurCwlRunner/src/main/resources/reference.conf b/centaurCwlRunner/src/main/resources/reference.conf
deleted file mode 100644
index a906e824372..00000000000
--- a/centaurCwlRunner/src/main/resources/reference.conf
+++ /dev/null
@@ -1,29 +0,0 @@
-centaur {
-  cwl-runner {
-    mode = local
-
-    # End of actual references and begin BA-6546 exceptions...
-    # Not sure if this reference conf is used by testers outside of DSP/broad?
-    # If you know for sure then do some combination of:
-    # - update this comment with the location of those tests
-    # - update the external tests to explicitly pass in their own config
-    # - if the external tests are 100% confirmed not to exist state how you know that
-    # Not really reference, but leaving just in case someone is relying on these values.
-    papi.default-input-gcs-prefix = "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/"
-    tesk.default-input-ftp-prefix = "ftp://ftp.hexdump.org/centaur-cwl-conformance/cwl-inputs/"
-    google {
-      application-name = "centaur-cwl-runner"
-      genomics.endpoint-url = "https://lifesciences.googleapis.com/"
-      genomics.location = "us-central1"
-      max-attempts = 3
-      auth = "application-default"
-      auths = [
-        {
-          name = "application-default"
-          scheme = "application_default"
-        }
-      ]
-    }
-    # End BA-6546 exceptions
-  }
-}
diff --git a/centaurCwlRunner/src/main/resources/skipped_tests.csv b/centaurCwlRunner/src/main/resources/skipped_tests.csv
deleted file mode 100644
index 08b6b117906..00000000000
--- a/centaurCwlRunner/src/main/resources/skipped_tests.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-vf-concat.cwl,empty.json
-dir5.cwl,dir-job.yml
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunner.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunner.scala
deleted file mode 100644
index ec5dcad537e..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunner.scala
+++ /dev/null
@@ -1,255 +0,0 @@
-package centaur.cwl
-
-import better.files._
-import cats.effect.IO
-import centaur.api.CentaurCromwellClient
-import centaur.cwl.Outputs._
-import centaur.test.TestOptions
-import centaur.test.standard.{CentaurTestCase, CentaurTestFormat}
-import centaur.test.submit.{SubmitHttpResponse, SubmitWorkflowResponse}
-import centaur.test.workflow.{AllBackendsRequired, SubmittedWorkflowTracker, Workflow, WorkflowData}
-import com.typesafe.scalalogging.StrictLogging
-import common.util.VersionUtil
-import cromwell.api.model.{Aborted, Failed, NonTerminalStatus, Succeeded}
-import cromwell.core.WorkflowOptions
-import cromwell.core.path.PathBuilderFactory
-import cromwell.core.path.BetterFileMethods.Cmds
-import cwl.preprocessor.{CwlFileReference, CwlPreProcessor}
-import spray.json._
-
-import scala.concurrent.Await
-import scala.concurrent.duration.Duration
-
-/**
-  * Runs workflows in a "cwl-runner" friendly way.
-  *
-  * https://github.com/broadinstitute/cromwell/issues/2590
-  * https://github.com/common-workflow-language/common-workflow-language/blob/v1.0.1/CONFORMANCE_TESTS.md
-  * https://github.com/common-workflow-language/common-workflow-language/blob/v1.0.1/draft-3/cwl-runner.cwl#L5-L68
-  * https://github.com/common-workflow-language/common-workflow-language/pull/278/files#diff-ee814a9c027fc9750beb075c283a973cR49
-  */
-object CentaurCwlRunner extends StrictLogging {
-
-  case class SkippedTest(sourceName: String, inputsName: String) {
-    def shouldSkip(args: CommandLineArguments) = {
-      args.workflowSource.exists(_.name.equalsIgnoreCase(sourceName)) &&
-        args.workflowInputs.exists(_.name.equalsIgnoreCase(inputsName))
-    }
-  }
-
-  case class CommandLineArguments(workflowSource: Option[File] = None,
-                                  workflowInputs: Option[File] = None,
-                                  quiet: Boolean = false,
-                                  outdir: Option[File] = None,
-                                  skipFile: Option[File] = None)
-
-  // TODO: This would be cleaner with Enumeratum
-  object ExitCode extends Enumeration {
-
-    protected case class ExitVal(status: Int) extends super.Val
-
-    implicit class ValueToVal(val exitCodeValue: Value) extends AnyVal {
-      def status: Int = exitCodeValue.asInstanceOf[ExitVal].status
-    }
-
-    val Success = ExitVal(0)
-    val Failure = ExitVal(1)
-    val NotImplemented = ExitVal(33)
-  }
-
-  private val cwlPreProcessor = new CwlPreProcessor()
-  private val centaurCwlRunnerRunMode = CentaurCwlRunnerRunMode.fromConfig(CentaurCwlRunnerConfig.conf)
-  private val parser = buildParser()
-  private lazy val centaurCwlRunnerVersion = VersionUtil.getVersion("centaur-cwl-runner")
-  private lazy val versionString = s"$centaurCwlRunnerVersion ${centaurCwlRunnerRunMode.description}"
-
-  private def showUsage(): ExitCode.Value = {
-    System.err.println(parser.usage)
-    ExitCode.Failure
-  }
-
-  private def buildParser(): scopt.OptionParser[CommandLineArguments] = {
-    new scopt.OptionParser[CommandLineArguments]("java -jar /path/to/centaurCwlRunner.jar") {
-      head("centaur-cwl-runner", versionString)
-
-      help("help").text("Centaur CWL Runner - Cromwell integration testing environment")
-
-      version("version").text("Print version and exit")
-
-      arg[String]("workflow-source").text("Workflow source file.").required().
-        action((s, c) => c.copy(workflowSource = Option(File(s))))
-
-      arg[String]("inputs").text("Workflow inputs file.").optional().
-        action((s, c) => c.copy(workflowInputs = Option(File(s))))
-
-      opt[Unit]("quiet").text("Only print warnings and errors.").optional().
-        action((_, c) => c.copy(quiet = true))
-
-      opt[String]("outdir").text("Output directory, default current directory.").optional().
-        action((s, c) =>
-          c.copy(outdir = Option(File(s))))
-
-      opt[String]("skip-file").text("A csv file describing workflows to be skipped based on their name.").optional().
-        action((s, c) =>
-          c.copy(skipFile = Option(File(s))))
-    }
-  }
-
-  private def runCentaur(args: CommandLineArguments): ExitCode.Value = {
-
-    def zipSiblings(file: File): File = {
-      val zipFile = File.newTemporaryFile("cwl_imports.", ".zip")
-      val dir = file.parent
-      if (!args.quiet) {
-        logger.info(s"Zipping files under 1mb in $dir to $zipFile")
-      }
-      // TODO: Only include files under 1mb for now. When cwl runners run in parallel this can use a lot of space.
-      val files = dir
-        .children
-        .filter(_.isRegularFile)
-        .filter(_.size < 1 * 1024 * 1024)
-      Cmds.zip(files.toSeq: _*)(zipFile)
-      zipFile
-    }
-
-    val workflowPath = args.workflowSource.get
-    val (parsedWorkflowPath, workflowRoot) = workflowPath.path.toAbsolutePath.toString.split("#") match {
-      case Array(file) => File(file) -> None
-      case Array(file, root) => File(file) -> Option(root)
-    }
-    val outdirOption = args.outdir.map(_.pathAsString)
-    val testName = workflowPath.name
-    val preProcessedWorkflow = cwlPreProcessor
-      .preProcessCwlToString(CwlFileReference(parsedWorkflowPath, workflowRoot))
-      .value.unsafeRunSync() match {
-      case Left(errors) =>
-        logger.error(s"Failed to pre process cwl workflow: ${errors.toList.mkString(", ")}")
-        return ExitCode.Failure
-      case Right(v) => v
-    }
-
-    val workflowContents = centaurCwlRunnerRunMode.preProcessWorkflow(preProcessedWorkflow)
-    val inputContents = args.workflowInputs
-      .map(centaurCwlRunnerRunMode.preProcessInput)
-      .map(preProcessed => {
-        preProcessed.value.unsafeRunSync() match {
-          case Left(errors) =>
-            logger.error(s"Failed to pre process cwl workflow: ${errors.toList.mkString(", ")}")
-            return ExitCode.Failure
-          case Right(value) => value
-        }
-      })
-
-    val workflowType = Option("cwl")
-    val workflowTypeVersion = None
-    val optionsContents = outdirOption map { outdir =>
-      JsObject("cwl_outdir" -> JsString(outdir)).compactPrint
-    }
-    val labels = List.empty
-    val zippedImports = Option(zipSiblings(workflowPath)) // TODO: Zipping all the things! Be more selective.
-    val backends = AllBackendsRequired(List.empty)
-    val workflowMetadata = None
-    val notInMetadata = List.empty
-    val directoryContentCounts = None
-    val testFormat = CentaurTestFormat.WorkflowSuccessTest
-    val testOptions = TestOptions(List.empty, ignore = false)
-    val submitResponseOption = None
-
-    val submittedWorkflowTracker = new SubmittedWorkflowTracker()
-
-    val workflowData = WorkflowData(
-      Option(workflowContents),
-      None,
-      None,
-      workflowType,
-      workflowTypeVersion,
-      inputContents.map(IO.pure),
-      optionsContents.map(IO.pure),
-      labels,
-      zippedImports
-    )
-    val workflow = Workflow(
-      testName,
-      workflowData,
-      workflowMetadata,
-      notInMetadata,
-      directoryContentCounts,
-      backends,
-      retryTestFailures = false,
-      allowOtherOutputs = true,
-      skipDescribeEndpointValidation = true,
-      submittedWorkflowTracker = submittedWorkflowTracker,
-      maximumAllowedTime = None
-    )
-
-    val testCase = CentaurTestCase(workflow, testFormat, testOptions, submittedWorkflowTracker, submitResponseOption)(cromwellTracker = None)
-
-    if (!args.quiet) {
-      logger.info(s"Starting test for $workflowPath")
-    }
-
-    val pathBuilderFactory: PathBuilderFactory = centaurCwlRunnerRunMode.pathBuilderFactory
-
-    try {
-      import CentaurCromwellClient.{blockingEc, system}
-      lazy val pathBuilder = Await.result(pathBuilderFactory.withOptions(WorkflowOptions.empty), Duration.Inf)
-
-      testCase.testFunction.run.unsafeRunSync() match {
-        case unexpected: SubmitHttpResponse =>
-          logger.error(s"Unexpected response: $unexpected")
-          ExitCode.Failure
-        case SubmitWorkflowResponse(submittedWorkflow) =>
-          val status = CentaurCromwellClient.status(submittedWorkflow).unsafeRunSync()
-          status match {
-            case unexpected: NonTerminalStatus =>
-              logger.error(s"Unexpected status: $unexpected")
-              ExitCode.Failure
-            case Aborted =>
-              logger.error(s"Unexpected abort.")
-              ExitCode.Failure
-            case Failed =>
-              logger.error(s"Unexpected failure.")
-              ExitCode.Failure
-            case Succeeded =>
-              val result = handleOutput(submittedWorkflow, pathBuilder)
-              if (!args.quiet) {
-                logger.info(s"Result: $result")
-              } else {
-                // Print directly to stdout during --quiet
-                println(result)
-              }
-              ExitCode.Success
-          }
-      }
-    } finally {
-      zippedImports map { zipFile =>
-        if (!args.quiet) {
-          logger.info(s"Deleting $zipFile")
-        }
-        zipFile.delete(swallowIOExceptions = true)
-      }
-      Await.result(CentaurCromwellClient.system.terminate(), Duration.Inf)
-      ()
-    }
-  }
-
-  private def skip(args: CommandLineArguments): Boolean =
-    args.skipFile
-      .map(_.lines).getOrElse(List.empty)
-      .map(_.split(','))
-      .map({
-        case Array(source, inputs) => SkippedTest(source, inputs)
-        case invalid => throw new RuntimeException(s"Invalid skipped_tests file: $invalid")
-      })
-      .exists(_.shouldSkip(args))
-
-  def main(args: Array[String]): Unit = {
-    val parsedArgsOption = parser.parse(args, CommandLineArguments())
-    val exitCode = parsedArgsOption match {
-      case Some(parsedArgs) if skip(parsedArgs) => ExitCode.NotImplemented
-      case Some(parsedArgs) => runCentaur(parsedArgs)
-      case None => showUsage()
-    }
-    System.exit(exitCode.status)
-  }
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerConfig.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerConfig.scala
deleted file mode 100644
index 0123efd7b8d..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerConfig.scala
+++ /dev/null
@@ -1,7 +0,0 @@
-package centaur.cwl
-
-import centaur.CentaurConfig
-
-object CentaurCwlRunnerConfig {
-  lazy val conf = CentaurConfig.conf.getConfig("cwl-runner")
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala
deleted file mode 100644
index 83b6626c983..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CentaurCwlRunnerRunMode.scala
+++ /dev/null
@@ -1,94 +0,0 @@
-package centaur.cwl
-
-import better.files.File
-import cloud.nio.impl.ftp.FtpFileSystems
-import com.typesafe.config.Config
-import common.validation.IOChecked._
-import cromwell.core.path.Obsolete.Paths
-import cromwell.core.path.{DefaultPathBuilderFactory, PathBuilderFactory}
-import cromwell.filesystems.ftp.{CromwellFtpFileSystems, FtpPathBuilderFactory}
-import cromwell.filesystems.gcs.GcsPathBuilderFactory
-import cwl.preprocessor.CwlPreProcessor
-
-sealed trait CentaurCwlRunnerRunMode {
-  /**
-    * Returns a user friendly of this run mode.
-    */
-  def description: String
-
-  /**
-    * Returns a factory that can create a path builder for this run mode.
-    */
-  def pathBuilderFactory: PathBuilderFactory
-
-  /**
-    * Runs any preprocessing as needed on a workflow.
-    *
-    * For example, may prefix relative paths so that absolute URLs are used.
-    */
-  def preProcessWorkflow(workflow: String): String = workflow
-
-  /**
-    * Runs any preprocessing as needed on inputs.
-    *
-    * For example, may prefix relative paths so that absolute URLs are used.
-    */
-  def preProcessInput(path: File): IOChecked[String] = path.contentAsString.validIOChecked
-}
-
-object CentaurCwlRunnerRunMode {
-  def fromConfig(conf: Config): CentaurCwlRunnerRunMode = {
-    conf.getString("mode") match {
-      case "local" => LocalRunMode
-      case "papi_v2alpha1" | "papi_v2beta" => PapiRunMode(conf)
-      case "tesk" => TeskRunMode(conf)
-      case unknown => throw new UnsupportedOperationException(s"mode not recognized: $unknown")
-    }
-  }
-}
-
-case object LocalRunMode extends CentaurCwlRunnerRunMode {
-  val cwlPreProcessor = new CwlPreProcessor()
-  override lazy val description: String = "local"
-  override lazy val pathBuilderFactory: PathBuilderFactory = DefaultPathBuilderFactory
-  /*
-    * If the file is a relative local path, resolve it against the path of the input json.
-   */
-  private def inputFilesMapper(inputJsonPath: File)(file: String) = {
-    if (!Paths.get(file).isAbsolute) inputJsonPath.sibling(file).toString
-    else file
-  }
-
-  override def preProcessInput(input: File): IOChecked[String] = cwlPreProcessor.preProcessInputFiles(input.contentAsString, inputFilesMapper(input))
-}
-
-case class PapiRunMode(conf: Config) extends CentaurCwlRunnerRunMode {
-  private lazy val googleConfig = conf.getConfig("google")
-  private lazy val preprocessor = new CloudPreprocessor(conf, "papi.default-input-gcs-prefix")
-
-  override lazy val description: String = s"papi ${googleConfig.getString("auth")}"
-
-  override lazy val pathBuilderFactory: PathBuilderFactory = {
-    GcsPathBuilderFactory(conf, googleConfig)
-  }
-
-  override def preProcessWorkflow(workflow: String): String = preprocessor.preProcessWorkflow(workflow)
-
-  override def preProcessInput(input: File): IOChecked[String] = preprocessor.preProcessInput(input.contentAsString)
-}
-
-case class TeskRunMode(conf: Config) extends CentaurCwlRunnerRunMode {
-  private lazy val ftpConfig = conf.getConfig("ftp")
-  private lazy val preprocessor = new CloudPreprocessor(conf, "tesk.default-input-ftp-prefix")
-
-  override lazy val description: String = "tesk"
-
-  override lazy val pathBuilderFactory: PathBuilderFactory = {
-    val fileSystemsConfiguration = FtpFileSystems.DefaultConfig.copy(capacity = 2)
-    new FtpPathBuilderFactory(conf, ftpConfig, new CromwellFtpFileSystems(new FtpFileSystems(fileSystemsConfiguration)))
-  }
-
-  override def preProcessWorkflow(workflow: String): String = preprocessor.preProcessWorkflow(workflow)
-
-  override def preProcessInput(input: File): IOChecked[String] = preprocessor.preProcessInput(input.contentAsString)
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/CloudPreprocessor.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/CloudPreprocessor.scala
deleted file mode 100644
index 68e79b9b701..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/CloudPreprocessor.scala
+++ /dev/null
@@ -1,102 +0,0 @@
-package centaur.cwl
-import better.files.File
-import com.typesafe.config.Config
-import common.util.StringUtil._
-import common.validation.IOChecked.IOChecked
-import cwl.preprocessor.CwlPreProcessor
-import io.circe.optics.JsonPath
-import io.circe.optics.JsonPath._
-import io.circe.yaml.Printer.StringStyle
-import io.circe.{Json, yaml}
-import net.ceedubs.ficus.Ficus._
-import wom.util.YamlUtils
-
-/**
-  * Tools to pre-process the CWL workflows and inputs before feeding them to Cromwell so they can be executed on PAPI.
-  */
-class CloudPreprocessor(config: Config, prefixConfigPath: String) {
-  val cwlPreProcessor = new CwlPreProcessor()
-  
-  // Cloud directory where inputs for conformance tests are stored
-  private val cloudPrefix = config.as[String](prefixConfigPath).ensureSlashed
-
-  // Default docker pull image
-  val DefaultDockerPull = "dockerPull" -> Json.fromString("ubuntu:latest")
-  
-  // Default docker image to be injected in a pre-existing requirements array
-  private val DefaultDockerHint: Json = {
-    Json.obj(
-      "class" -> Json.fromString("DockerRequirement"),
-      DefaultDockerPull
-    )
-  }
-
-  // hints array with default docker requirement
-  private val DefaultDockerHintList: Json = {
-    Json.obj(
-      "hints" -> Json.arr(DefaultDockerHint)
-    )
-  }
-
-  // Parse value, apply f to it, and print it back to String using the printer
-  private def process(value: String, f: Json => Json, printer: Json => String) = {
-    YamlUtils.parse(value) match {
-      case Left(error) => throw new Exception(error.getMessage)
-      case Right(json) => printer(f(json))
-    }
-  }
-
-  // Process and print back as YAML
-  private def processYaml(value: String)(f: Json => Json) =
-    process(value, f, yaml.Printer.spaces2.copy(stringStyle = StringStyle.DoubleQuoted).pretty)
-
-  // Prefix the string at "key" with the cloud prefix
-  private def prefixLocation(value: String): String = {
-    cloudPrefix + File(value.stripPrefix("file://")).name
-  }
-
-  // Function to check if the given json has the provided key / value pair
-  private def hasKeyValue(key: String, value: String): Json => Boolean = {
-    root.selectDynamic(key).string.exist(_.equalsIgnoreCase(value))
-  }
-
-  /**
-    * Pre-process input file by prefixing all files and directories with the cloud prefix
-    */
-  def preProcessInput(input: String): IOChecked[String] = cwlPreProcessor.preProcessInputFiles(input, prefixLocation)
-
-  // Check if the given path (as an array or object) has a DockerRequirement element
-  def hasDocker(jsonPath: JsonPath)(json: Json): Boolean = {
-    val hasDockerInArray: Json => Boolean = jsonPath.arr.exist(_.exists(hasKeyValue("class", "DockerRequirement")))
-    val hasDockerInObject: Json => Boolean = jsonPath.obj.exist(_.kleisli("DockerRequirement").nonEmpty)
-
-    hasDockerInArray(json) || hasDockerInObject(json)
-  }
-
-  // Check if the given Json has a docker image in hints or requirements
-  def hasDocker(json: Json): Boolean = hasDocker(root.hints)(json) || hasDocker(root.requirements)(json)
-
-  // Add a default docker hint to the workflow if it doesn't have one
-  private val addDefaultDocker: Json => Json = workflow => if (!hasDocker(workflow)) {
-    /*
-      * deepMerge does not combine objects together but replaces keys which would overwrite existing hints
-      * so first check if there are hints already and if so add our docker one.
-      * Also turns out that the hints section can be either an array or an object.
-      * When it gets saladed the object is transformed to an array but because we deal with unsaladed cwl here
-      * we have to handle both cases.
-     */
-    val hintsAsArray = root.hints.arr.modifyOption(_ :+ DefaultDockerHint)(workflow)
-    val hintsAsObject = root.hints.obj.modifyOption(_.add("DockerRequirement", Json.obj(DefaultDockerPull)))(workflow)
-
-    hintsAsArray
-      .orElse(hintsAsObject)
-      .getOrElse(workflow.deepMerge(DefaultDockerHintList))
-  } else workflow
-  
-  private val prefixDefaultFilesInCwl = CwlPreProcessor.mapFilesAndDirectories(prefixLocation) _
-
-  /**
-    * Pre-process the workflow by adding a default docker hint iff it doesn't have one
-    */
-  def preProcessWorkflow(workflow: String): String = processYaml(workflow)(addDefaultDocker.andThen(prefixDefaultFilesInCwl))
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/OutputManipulator.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/OutputManipulator.scala
deleted file mode 100644
index dcbe3a70ec8..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/OutputManipulator.scala
+++ /dev/null
@@ -1,237 +0,0 @@
-package centaur.cwl
-
-import common.util.StringUtil._
-import cromwell.core.path.{Path, PathBuilder}
-import cwl.CwlCodecs._
-import cwl.command.ParentName
-import cwl.ontology.Schema
-import cwl.{File => CwlFile, _}
-import io.circe.literal._
-import io.circe.syntax._
-import io.circe.{Json, JsonObject}
-import mouse.all._
-import org.apache.commons.codec.digest.DigestUtils
-import shapeless.{Inl, Poly1}
-import spray.json.{JsArray, JsBoolean, JsNull, JsNumber, JsObject, JsString, JsValue}
-
-//Take cromwell's outputs and format them as expected by the spec
-object OutputManipulator extends Poly1 {
-
-  //In an Ideal world I'd return a Coproduct of these types and leave the asJson-ing to the handleOutput
-  def resolveOutput(jsValue: JsValue,
-                    pathBuilder: PathBuilder,
-                    mot: MyriadOutputType,
-                    schemaOption: Option[Schema]): Json  = {
-    mot.fold(this).apply(jsValue, pathBuilder, schemaOption)
-  }
-
-  private def hashFile(path: Path): Option[String] = path.exists.option("sha1$" + path.sha1.toLowerCase)
-  private def sizeFile(path: Path): Option[Long] = path.exists.option(path.size)
-
-  private def stringToFile(pathAsString: String, pathBuilder: PathBuilder): Json = {
-    val path = pathBuilder.build(pathAsString).get
-
-    if (path.exists()) {
-      CwlFile(
-        location = Option(path.name),
-        checksum = hashFile(path),
-        size = sizeFile(path)
-      ).asJson
-    } else {
-      Json.Null
-    }
-  }
-
-  private def populateFileFields(pathBuilder: PathBuilder,
-                                 schemaOption: Option[Schema]
-                                )(obj: JsonObject): JsonObject = {
-    val path = pathBuilder.build(obj.kleisli("location").get.asString.get).get
-    val isFile = obj.kleisli("class").exists(_.asString.contains("File"))
-    val isDirectory = obj.kleisli("class").exists(_.asString.contains("Directory"))
-
-    // Return the default value if the value at key is either absent or null, otherwise return the value
-    def valueOrNull(key: String, default: Json) = obj.kleisli(key) match {
-      case Some(Json.Null) => default
-      case Some(other) => other
-      case None => default
-    }
-
-    def populateInnerFiles(json: Json): Option[Json] = {
-
-      def populateInnerFile(file: Json): Json = {
-        file.asObject
-          .map(populateFileFields(pathBuilder, schemaOption))
-          .map(Json.fromJsonObject)
-          .orElse(file.asString.map(stringToFile(_, pathBuilder)))
-          .getOrElse(file)
-      }
-
-      // Assume the json is an array ("secondaryFiles" and "listing" are both arrays).
-      val innerFiles = json.asArray.get
-      // Remove any files that don't actually exist.
-      val filteredFiles = innerFiles.map(populateInnerFile).filterNot(_.isNull)
-      // The cwl test runner doesn't expect a "secondaryFiles" or "listing" field at all if it's empty.
-      if (filteredFiles.nonEmpty) Option(Json.arr(filteredFiles: _*)) else None
-    }
-
-    def updateFileOrDirectoryWithNestedFiles(obj: JsonObject, fieldName: String) = {
-      // Cromwell metadata has a field for all values even if their content is empty
-      // remove it as the cwl test runner expects nothing instead
-      val withoutField = obj.remove(fieldName)
-
-      // If the field was not empty, add it back with each inner file / directory properly updated as well
-      populateInnerFiles(obj.kleisli(fieldName).get)
-        .map(withoutField.add(fieldName, _))
-        .getOrElse(withoutField)
-    }
-
-    // Get sha1 from the content field
-    // We need this because some task return a "File" object that actually does not exist on disk but has its content provided directly instead
-    def hashContent: Option[String] = obj.kleisli("contents").flatMap(_.asString.map(DigestUtils.sha1Hex).map("sha1$" + _))
-
-    // Get size from the content field
-    // We need this because some task return a "File" object that actually does not exist on disk but has its content provided directly instead
-    def sizeContent: Option[Long] = obj.kleisli("contents").flatMap(_.asString.map(_.length.toLong))
-
-    // "as a special case, cwltest only matches the trailing part of location in the output sections so that it
-    // can do something reasonable regardless of URL scheme or prefix" - Peter Amstutz, 2019-04-16, CWL gitter
-    val updatedLocation = obj.add("location", Json.fromString(path.pathAsString))
-
-    // Get the format
-    def formatOption: Option[String] = for {
-      klesliFormat <- obj.kleisli("format")
-      format <- klesliFormat.asString
-    } yield format
-
-    // Lookup the full format using the namespaces
-    def fullFormatOption: Option[String] = for {
-      format <- formatOption
-      schema <- schemaOption
-    } yield schema.fullIri(format)
-
-    if (isFile) {
-      /*
-        * In order of priority use: 
-        * 1) the checksum value in the metadata
-        * 2) the checksum calculated from the value of the "contents" field of the metadata
-        * 3) the checksum calculated from the file itself
-        */
-      val defaultChecksum = hashContent.orElse(hashFile(path)).map(Json.fromString).getOrElse(Json.Null)
-      val checksum = valueOrNull("checksum", defaultChecksum)
-
-      /*
-        * In order of priority use: 
-        * 1) the size value in the metadata
-        * 2) the size calculated from the value of the "contents" field of the metadata
-        * 3) the size calculated from the file itself
-        */
-      val defaultSize = sizeContent.orElse(sizeFile(path)).map(Json.fromLong).getOrElse(Json.Null)
-      val size = valueOrNull("size", defaultSize)
-
-      val basename: Option[Json] =
-        Option(valueOrNull("basename", path.exists.option(path.name).map(Json.fromString).getOrElse(Json.Null)))
-
-      /*
-      In order of priority use:
-      1) the full format if $namespaces are available
-      2) the original format
-       */
-      val defaultFormatOption: Option[Json] = fullFormatOption.orElse(formatOption).map(Json.fromString)
-
-      val withChecksumAndSize = updatedLocation
-        .add("checksum", checksum)
-        .add("size", size)
-        // conformance test does not expect "contents" in the output
-        .remove("contents")
-
-      val withBasename = basename
-        .map(withChecksumAndSize.add("basename", _))
-        .getOrElse(withChecksumAndSize)
-
-      val withFormat = defaultFormatOption
-        .map(withBasename.add("format", _))
-        .getOrElse(withBasename)
-
-      updateFileOrDirectoryWithNestedFiles(withFormat, "secondaryFiles")
-    } else if (isDirectory) {
-      updateFileOrDirectoryWithNestedFiles(updatedLocation, "listing").
-        add("basename", path.nameWithoutExtension |> Json.fromString)
-    } else throw new RuntimeException(s"${path.pathAsString} is neither a valid file or a directory")
-  }
-
-  private def resolveOutputViaInnerType(moits: Array[MyriadOutputInnerType])
-                                       (jsValue: JsValue,
-                                        pathBuilder: PathBuilder,
-                                        schemaOption: Option[Schema]): Json = {
-    def sprayJsonToCirce(jsValue: JsValue): Json = {
-      import io.circe.parser._
-      val jsonString = jsValue.compactPrint
-      parse(jsonString).getOrElse(
-        sys.error(s"Failed to parse Json output as Json... something is very wrong: '$jsonString'")
-      )
-    }
-
-    (jsValue, moits) match {
-      //CWL expects quite a few enhancements to the File structure, hence...
-      case (JsString(metadata), Array(Inl(CwlType.File))) => stringToFile(metadata, pathBuilder)
-      // If it's a JsObject it means it's already in the right format, we just want to fill in some values that might not
-      // have been populated like "checksum" and "size"
-      case (obj: JsObject, a) if a.contains(Inl(CwlType.File)) || a.contains(Inl(CwlType.Directory)) =>
-        val json: Json = sprayJsonToCirce(obj)
-        val fileExists = (for {
-          o <- json.asObject
-          l <- o.kleisli("location")
-          s <- l.asString
-          c = if (a.contains(Inl(CwlType.Directory))) s.ensureSlashed else s
-          p <- pathBuilder.build(c).toOption
-        } yield p.exists).getOrElse(false)
-        if (fileExists) json.mapObject(populateFileFields(pathBuilder, schemaOption)) else Json.Null
-      case (JsNumber(metadata), Array(Inl(CwlType.Long))) => metadata.longValue.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Float))) => metadata.floatValue.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Double))) => metadata.doubleValue.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Int))) => metadata.intValue.asJson
-      case (JsString(metadata), Array(Inl(CwlType.String))) => metadata.asJson
-
-      //The Anys.  They have to be done for each type so that the asJson can use this type information when going back to Json representation
-      case (JsString(metadata), Array(Inl(CwlType.Any))) => metadata.asJson
-      case (JsNumber(metadata), Array(Inl(CwlType.Any))) => metadata.asJson
-      case (obj: JsObject, Array(Inl(CwlType.Any))) => sprayJsonToCirce(obj)
-      case (JsBoolean(metadata), Array(Inl(CwlType.Any))) => metadata.asJson
-      case (array: JsArray, Array(Inl(CwlType.Any))) => sprayJsonToCirce(array)
-      case (JsNull, a) if a.contains(Inl(CwlType.Any)) || a.contains(Inl(CwlType.Null)) => Json.Null
-
-      case (JsArray(metadata), Array(tpe)) if tpe.select[OutputArraySchema].isDefined =>
-        (for {
-          schema <- tpe.select[OutputArraySchema]
-          items = schema.items
-          innerType <- items.select[MyriadOutputInnerType]
-          outputJson = metadata.map(m =>
-            resolveOutputViaInnerType(Array(innerType))(m, pathBuilder, schemaOption)).asJson
-        } yield outputJson).getOrElse(throw new RuntimeException(s"We currently do not support output arrays with ${tpe.select[OutputArraySchema].get.items} inner type"))
-      case (JsObject(metadata), Array(tpe)) if tpe.select[OutputRecordSchema].isDefined =>
-        def processField(field: OutputRecordField) = {
-          val parsedName = FullyQualifiedName(field.name)(ParentName.empty).id
-          field.`type`.select[MyriadOutputInnerType] map { parsedName -> _ }
-        }
-
-        (for {
-          schema <- tpe.select[OutputRecordSchema]
-          fields <- schema.fields
-          typeMap = fields.flatMap(processField).toMap
-          outputJson = metadata.map({
-            case (k, v) => k -> resolveOutputViaInnerType(Array(typeMap(k)))(v, pathBuilder, schemaOption)
-          }).asJson
-        } yield outputJson).getOrElse(throw new RuntimeException(s"We currently do not support output record schemas with ${tpe.select[OutputArraySchema].get.items} inner type"))
-      case (json, tpe) => throw new RuntimeException(s"We currently do not support outputs (${json.getClass.getSimpleName}) of $json and type $tpe")
-    }
-  }
-
-  implicit val moit: Case.Aux[MyriadOutputInnerType, (JsValue, PathBuilder, Option[Schema]) => Json] = at { t =>
-    resolveOutputViaInnerType(Array(t))
-  }
-
-  implicit val amoit: Case.Aux[Array[MyriadOutputInnerType], (JsValue, PathBuilder, Option[Schema]) => Json] =
-    at { amoit =>
-      resolveOutputViaInnerType(amoit)
-    }
-}
diff --git a/centaurCwlRunner/src/main/scala/centaur/cwl/Outputs.scala b/centaurCwlRunner/src/main/scala/centaur/cwl/Outputs.scala
deleted file mode 100644
index c63d95399d7..00000000000
--- a/centaurCwlRunner/src/main/scala/centaur/cwl/Outputs.scala
+++ /dev/null
@@ -1,93 +0,0 @@
-package centaur.cwl
-
-import centaur.api.CentaurCromwellClient
-import centaur.test.metadata.WorkflowFlatMetadata._
-import common.collections.EnhancedCollections._
-import common.validation.IOChecked._
-import cromwell.api.model.SubmittedWorkflow
-import cromwell.core.path.PathBuilder
-import cwl.ontology.Schema
-import cwl.{Cwl, CwlDecoder, MyriadOutputType}
-import io.circe.Json
-import io.circe.syntax._
-import mouse.map._
-import shapeless.Poly1
-import spray.json.{JsObject, JsString, JsValue}
-
-object Outputs {
-
-  //When the string returned is not valid JSON, it is effectively an exception as CWL runner expects JSON to be returned
-  def handleOutput(submittedWorkflow: SubmittedWorkflow, pathBuilder: PathBuilder): String = {
-    val metadata: Map[String, JsValue] = CentaurCromwellClient.metadata(submittedWorkflow).unsafeRunSync().asFlat.value
-
-    // Wrapper function to provide the right signature for `intersectWith` below.
-    def outputResolver(schemaOption: Option[Schema])(jsValue: JsValue, mot: MyriadOutputType): Json = {
-      OutputManipulator.resolveOutput(jsValue, pathBuilder, mot, schemaOption)
-    }
-
-    //Sorry for all the nesting, but spray json JsValue doesn't have optional access methods like Argonaut/circe,
-    //thus no for comprehensions for us :(
-    metadata.get("submittedFiles.workflow") match {
-      case Some(JsString(workflow)) =>
-
-        val parseCwl: IOChecked[Cwl] = CwlDecoder.decodeCwlString(
-          workflow,
-          submittedWorkflow.workflow.zippedImports,
-          submittedWorkflow.workflow.workflowRoot
-        )
-
-        parseCwl.value.attempt.unsafeRunSync() match {
-          case Right(Right(cwl)) =>
-
-            CentaurCromwellClient.outputs(submittedWorkflow).unsafeRunSync().outputs match {
-              case JsObject(map) =>
-                val typeMap: Map[String, MyriadOutputType] = cwl.fold(CwlOutputsFold)
-                val mungeTypeMap = typeMap.mapKeys(stripTypeMapKey)
-
-                val mungeOutputMap = map.mapKeys(stripOutputKey)
-
-                mungeOutputMap.
-                  //This lets us operate on the values of the output values and types for a particular output key
-                  intersectWith(mungeTypeMap)(outputResolver(cwl.schemaOption)).
-                  //converting the whole response to Json using Circe's auto-encoder derivation
-                  asJson.
-                  //drop null values so that we don't print when Option == None
-                  printWith(io.circe.Printer.spaces2.copy(dropNullValues = true))
-              case other => s"it seems cromwell is not returning outputs as a Jsobject but is instead a $other"
-            }
-          case Right(Left(error)) => s"couldn't parse workflow: $workflow failed with error: $error"
-          case Left(error) => s"Exception when trying to read workflow: $workflow failed with error: $error"
-        }
-      case Some(other) => s"received the value $other when the workflow string was expected"
-      case None => "the workflow is no longer in the metadata payload, it's a problem"
-    }
-  }
-
-  //Ids come out of SALAD pre-processing with a filename prepended. This gets rid of it
-  // Also gets rid of the parent workflow name if present
-  def stripTypeMapKey(key: String): String = key
-    .substring(key.lastIndexOf("#") + 1, key.length)
-    .split("/").last
-
-  //Ids come out of Cromwell with a prefix, separated by a ".". This takes everything to the right,
-  //as CWL wants it
-  def stripOutputKey(key: String): String = key.substring(key.lastIndexOf(".") + 1, key.length)
-
-}
-
-object CwlOutputsFold extends Poly1 {
-  import cwl._
-
-  implicit def wf: Case.Aux[cwl.Workflow, Map[String, MyriadOutputType]] = at[cwl.Workflow] {
-    _.outputs.map(output => output.id -> output.`type`.get).toMap
-  }
-
-  implicit def clt: Case.Aux[cwl.CommandLineTool, Map[String, MyriadOutputType]] = at[cwl.CommandLineTool] {
-    _.outputs.map(output => output.id -> output.`type`.get).toMap
-  }
-
-  implicit def et: Case.Aux[cwl.ExpressionTool, Map[String, MyriadOutputType]] = at[cwl.ExpressionTool] {
-    _.outputs.map(output => output.id -> output.`type`.get).toMap
-  }
-}
-
diff --git a/centaurCwlRunner/src/test/resources/application.conf b/centaurCwlRunner/src/test/resources/application.conf
deleted file mode 100644
index 27c24fa07bf..00000000000
--- a/centaurCwlRunner/src/test/resources/application.conf
+++ /dev/null
@@ -1 +0,0 @@
-papi.default-input-gcs-prefix="gs://centaur-cwl-conformance-1f501e3/cwl-inputs/"
diff --git a/centaurCwlRunner/src/test/scala/CloudPreprocessorSpec.scala b/centaurCwlRunner/src/test/scala/CloudPreprocessorSpec.scala
deleted file mode 100644
index df13e49b666..00000000000
--- a/centaurCwlRunner/src/test/scala/CloudPreprocessorSpec.scala
+++ /dev/null
@@ -1,342 +0,0 @@
-import centaur.cwl.CloudPreprocessor
-import com.typesafe.config.ConfigFactory
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.util.YamlUtils
-
-class CloudPreprocessorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  behavior of "PAPIPreProcessor"
-
-  val pAPIPreprocessor = new CloudPreprocessor(ConfigFactory.load(), "papi.default-input-gcs-prefix")
-
-  def validate(result: String, expectation: String) = {
-    val parsedResult = YamlUtils.parse(result).toOption.get
-    val parsedExpectation = YamlUtils.parse(expectation).toOption.get
-
-    // This is an actual Json comparison from circe
-    parsedResult shouldBe parsedExpectation
-  }
-
-  it should "prefix files and directories in inputs" in {
-    validate(
-      pAPIPreprocessor.preProcessInput(
-        """|{
-           |  "input": {
-           |    "null": null,
-           |    "file": {
-           |      "location": "whale.txt",
-           |      "class": "File",
-           |      "secondaryFiles": [
-           |        {
-           |          "class": File,
-           |          "location": "hello.txt"
-           |        }
-           |      ],
-           |      "default": {
-           |        "location": "default_whale.txt",
-           |        "class": "File",
-           |      }
-           |    },
-           |    "directory": {
-           |      "location": "ref.fasta",
-           |      "class": "Directory",
-           |      "listing": [
-           |        {
-           |          "class": File,
-           |          "location": "hello.txt"
-           |        }
-           |      ]
-           |    }
-           |  }
-           |}
-           |""".stripMargin).value.unsafeRunSync().toOption.get,
-      """|{
-         |  "input": {
-         |    "null": null,
-         |    "file": {
-         |      "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/whale.txt",
-         |      "class": "File",
-         |      "secondaryFiles": [
-         |        {
-         |          "class": File,
-         |          "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/hello.txt"
-         |        }
-         |      ],
-         |      "default": {
-         |        "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/default_whale.txt",
-         |        "class": "File",
-         |      }
-         |    },
-         |    "directory": {
-         |      "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/ref.fasta",
-         |      "class": "Directory",
-         |      "listing": [
-         |        {
-         |          "class": File,
-         |          "location": "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/hello.txt"
-         |        }
-         |      ]
-         |    }
-         |  }
-         |}
-         |""".stripMargin
-    )
-  }
-
-  it should "prefix files and directories in workflow" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |cwlVersion: v1.0
-           |requirements:
-           |  - class: DockerRequirement
-           |    dockerPull: ubuntu:latest
-           |inputs:
-           |  - id: reference
-           |    type: File
-           |    inputBinding: { position: 2 }
-           |    default:
-           |      class: File
-           |      location: args.py
-           |
-           |outputs:
-           |  args: string[]
-           |
-           |baseCommand: python
-           |arguments: ["bwa", "mem"]
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |cwlVersion: v1.0
-         |requirements:
-         |  - class: DockerRequirement
-         |    dockerPull: ubuntu:latest
-         |inputs:
-         |  - id: reference
-         |    type: File
-         |    inputBinding: { position: 2 }
-         |    default:
-         |      class: File
-         |      location: gs://centaur-cwl-conformance-1f501e3/cwl-inputs/args.py
-         |
-         |outputs:
-         |  args: string[]
-         |
-         |baseCommand: python
-         |arguments: ["bwa", "mem"]
-         |""".stripMargin
-    )
-  }
-
-  it should "add default docker image if there's no hint" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |cwlVersion: v1.0
-           |inputs:
-           |  - id: reference
-           |    type: File
-           |    inputBinding: { position: 2 }
-           |
-           |outputs:
-           |  args: string[]
-           |
-           |baseCommand: python
-           |arguments: ["bwa", "mem"]
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |hints:
-         |  - class: DockerRequirement
-         |    dockerPull: ubuntu:latest
-         |cwlVersion: v1.0
-         |inputs:
-         |  - id: reference
-         |    type: File
-         |    inputBinding: { position: 2 }
-         |
-         |outputs:
-         |  args: string[]
-         |
-         |baseCommand: python
-         |arguments: ["bwa", "mem"]
-         |""".stripMargin
-    )
-  }
-
-  it should "append default docker image to existing hint as an array" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |hints:
-           |  - class: EnvVarRequirement
-           |    envDef:
-           |      TEST_ENV: $(inputs.in)
-           |cwlVersion: v1.0
-           |inputs:
-           |  - id: reference
-           |    type: File
-           |    inputBinding: { position: 2 }
-           |
-           |outputs:
-           |  args: string[]
-           |
-           |baseCommand: python
-           |arguments: ["bwa", "mem"]
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |hints:
-         |  - class: EnvVarRequirement
-         |    envDef:
-         |      TEST_ENV: $(inputs.in)
-         |  - class: DockerRequirement
-         |    dockerPull: ubuntu:latest
-         |cwlVersion: v1.0
-         |inputs:
-         |  - id: reference
-         |    type: File
-         |    inputBinding: { position: 2 }
-         |
-         |outputs:
-         |  args: string[]
-         |
-         |baseCommand: python
-         |arguments: ["bwa", "mem"]
-         |""".stripMargin
-    )
-  }
-
-  it should "append default docker image to existing hints as an object" in {
-    validate(
-      pAPIPreprocessor.preProcessWorkflow(
-        """|class: CommandLineTool
-           |cwlVersion: v1.0
-           |inputs:
-           |  in: string
-           |outputs:
-           |  out:
-           |    type: File
-           |    outputBinding:
-           |      glob: out
-           |
-           |hints:
-           |  EnvVarRequirement:
-           |    envDef:
-           |      TEST_ENV: $(inputs.in)
-           |
-           |baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"]
-           |
-           |stdout: out
-           |""".stripMargin),
-      """|class: CommandLineTool
-         |cwlVersion: v1.0
-         |inputs:
-         |  in: string
-         |outputs:
-         |  out:
-         |    type: File
-         |    outputBinding:
-         |      glob: out
-         |
-         |hints:
-         |  EnvVarRequirement:
-         |    envDef:
-         |      TEST_ENV: $(inputs.in)
-         |  DockerRequirement:
-         |    dockerPull: ubuntu:latest
-         |
-         |baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"]
-         |
-         |stdout: out
-         |""".stripMargin
-    )
-  }
-
-  it should "not replace existing docker requirement in an object" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |requirements:
-                      |  DockerRequirement:
-                      |    dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "not replace existing docker hint in an object" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |hints:
-                      |  DockerRequirement:
-                      |    dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "not replace existing docker hint in an array" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |hints:
-                      |- class: DockerRequirement
-                      |  dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "not replace existing docker requirement in an array" in {
-    val workflow = """|class: CommandLineTool
-                      |cwlVersion: v1.0
-                      |requirements:
-                      |- class: DockerRequirement
-                      |  dockerPull: python27:slim
-                      |inputs:
-                      |  - id: reference
-                      |    type: File
-                      |    inputBinding: { position: 2 }
-                      |
-                      |outputs:
-                      |  args: string[]
-                      |
-                      |baseCommand: python
-                      |arguments: ["bwa", "mem"]
-                      |""".stripMargin
-    validate(pAPIPreprocessor.preProcessWorkflow(workflow), workflow)
-  }
-
-  it should "throw an exception if yaml / json can't be parse" in {
-    val invalid =
-      """
-        |{ [invalid]: }
-      """.stripMargin
-
-    an[Exception] shouldBe thrownBy(pAPIPreprocessor.preProcessWorkflow(invalid))
-  }
-}
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
index a1156fc33e9..93f4cf77d34 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
@@ -15,7 +15,7 @@ import org.apache.http.HttpStatus
 class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
                               drsReadInterpreter: DrsReadInterpreter) extends CloudNioFileProvider {
 
-  private def checkIfPathExistsThroughMartha(drsPath: String): IO[Boolean] = {
+  private def checkIfPathExistsThroughDrsResolver(drsPath: String): IO[Boolean] = {
     /*
      * Unlike other cloud providers where directories are identified with a trailing slash at the end like `gs://bucket/dir/`,
      * DRS has a concept of bundles for directories (not supported yet). Hence for method `checkDirectoryExists` which appends a trailing '/'
@@ -23,15 +23,15 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
      */
     if (drsPath.endsWith("/")) IO(false)
     else {
-      drsPathResolver.rawMarthaResponse(drsPath, NonEmptyList.one(MarthaField.GsUri)).use { marthaResponse =>
-        val errorMsg = s"Status line was null for martha response $marthaResponse."
-        toIO(Option(marthaResponse.getStatusLine), errorMsg)
+      drsPathResolver.rawDrsResolverResponse(drsPath, NonEmptyList.one(DrsResolverField.GsUri)).use { drsResolverResponse =>
+        val errorMsg = s"Status line was null for DRS Resolver response $drsResolverResponse."
+        toIO(Option(drsResolverResponse.getStatusLine), errorMsg)
       }.map(_.getStatusCode == HttpStatus.SC_OK)
     }
   }
 
   override def existsPath(drsPath: String, unused: String): Boolean =
-    checkIfPathExistsThroughMartha(drsPath).unsafeRunSync()
+    checkIfPathExistsThroughDrsResolver(drsPath).unsafeRunSync()
 
   override def existsPaths(cloudHost: String, cloudPathPrefix: String): Boolean =
     existsPath(cloudHost, cloudPathPrefix)
@@ -47,11 +47,11 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
     throw new UnsupportedOperationException("DRS currently doesn't support delete.")
 
   override def read(drsPath: String, unused: String, offset: Long): ReadableByteChannel = {
-    val fields = NonEmptyList.of(MarthaField.GsUri, MarthaField.GoogleServiceAccount, MarthaField.AccessUrl)
+    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl)
 
     val byteChannelIO = for {
-      marthaResponse <- drsPathResolver.resolveDrsThroughMartha(drsPath, fields)
-      byteChannel <- drsReadInterpreter(drsPathResolver, marthaResponse)
+      drsResolverResponse <- drsPathResolver.resolveDrs(drsPath, fields)
+      byteChannel <- drsReadInterpreter(drsPathResolver, drsResolverResponse)
     } yield byteChannel
 
     byteChannelIO.handleErrorWith {
@@ -63,14 +63,14 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
     throw new UnsupportedOperationException("DRS currently doesn't support write.")
 
   override def fileAttributes(drsPath: String, unused: String): Option[CloudNioRegularFileAttributes] = {
-    val fields = NonEmptyList.of(MarthaField.Size, MarthaField.TimeCreated, MarthaField.TimeUpdated, MarthaField.Hashes)
+    val fields = NonEmptyList.of(DrsResolverField.Size, DrsResolverField.TimeCreated, DrsResolverField.TimeUpdated, DrsResolverField.Hashes)
 
     val fileAttributesIO = for {
-      marthaResponse <- drsPathResolver.resolveDrsThroughMartha(drsPath, fields)
-      sizeOption = marthaResponse.size
-      hashOption = getPreferredHash(marthaResponse.hashes)
-      timeCreatedOption <- convertToFileTime(drsPath, MarthaField.TimeCreated, marthaResponse.timeCreated)
-      timeUpdatedOption <- convertToFileTime(drsPath, MarthaField.TimeUpdated, marthaResponse.timeUpdated)
+      drsResolverResponse <- drsPathResolver.resolveDrs(drsPath, fields)
+      sizeOption = drsResolverResponse.size
+      hashOption = getPreferredHash(drsResolverResponse.hashes)
+      timeCreatedOption <- convertToFileTime(drsPath, DrsResolverField.TimeCreated, drsResolverResponse.timeCreated)
+      timeUpdatedOption <- convertToFileTime(drsPath, DrsResolverField.TimeUpdated, drsResolverResponse.timeUpdated)
     } yield new DrsCloudNioRegularFileAttributes(drsPath, sizeOption, hashOption, timeCreatedOption, timeUpdatedOption)
 
     Option(fileAttributesIO.unsafeRunSync())
@@ -78,5 +78,5 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
 }
 
 object DrsCloudNioFileProvider {
-  type DrsReadInterpreter = (DrsPathResolver, MarthaResponse) => IO[ReadableByteChannel]
+  type DrsReadInterpreter = (DrsPathResolver, DrsResolverResponse) => IO[ReadableByteChannel]
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
index 8721ab9b43e..884072e4a31 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
@@ -11,7 +11,8 @@ class DrsCloudNioFileSystemProvider(rootConfig: Config,
                                     drsReadInterpreter: DrsReadInterpreter,
                                    ) extends CloudNioFileSystemProvider {
 
-  lazy val drsConfig: DrsConfig = DrsConfig.fromConfig(rootConfig.getConfig("martha"))
+  lazy val drsResolverConfig = if (rootConfig.hasPath("resolver")) rootConfig.getConfig("resolver") else rootConfig.getConfig("martha")
+  lazy val drsConfig: DrsConfig = DrsConfig.fromConfig(drsResolverConfig)
 
   lazy val drsPathResolver: EngineDrsPathResolver =
     EngineDrsPathResolver(drsConfig, drsCredentials)
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
index 3c9293f2bd7..778d9b8380e 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
@@ -61,7 +61,7 @@ object DrsCloudNioRegularFileAttributes {
       .map(FileTime.from)
   }
 
-  def convertToFileTime(drsPath: String, key: MarthaField.Value, timeInStringOption: Option[String]): IO[Option[FileTime]] = {
+  def convertToFileTime(drsPath: String, key: DrsResolverField.Value, timeInStringOption: Option[String]): IO[Option[FileTime]] = {
     timeInStringOption match {
       case None => IO.pure(None)
       case Some(timeInString) =>
@@ -71,7 +71,7 @@ object DrsCloudNioRegularFileAttributes {
             throwable =>
               IO.raiseError(
                 new RuntimeException(
-                  s"Error while parsing '$key' value from Martha to FileTime for DRS path $drsPath. " +
+                  s"Error while parsing '$key' value from DRS Resolver to FileTime for DRS path $drsPath. " +
                     s"Reason: ${ExceptionUtils.getMessage(throwable)}.",
                   throwable,
                 )
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
index e9dc760162e..c8333a57a66 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
@@ -6,7 +6,7 @@ import net.ceedubs.ficus.Ficus._
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-final case class DrsConfig(marthaUrl: String,
+final case class DrsConfig(drsResolverUrl: String,
                            numRetries: Int,
                            waitInitial: FiniteDuration,
                            waitMaximum: FiniteDuration,
@@ -22,45 +22,46 @@ object DrsConfig {
   private val DefaultWaitMultiplier = 1.5d
   private val DefaultWaitRandomizationFactor = 0.1
 
-  private val EnvMarthaUrl = "MARTHA_URL"
-  private val EnvMarthaNumRetries = "MARTHA_NUM_RETRIES"
-  private val EnvMarthaWaitInitialSeconds = "MARTHA_WAIT_INITIAL_SECONDS"
-  private val EnvMarthaWaitMaximumSeconds = "MARTHA_WAIT_MAXIMUM_SECONDS"
-  private val EnvMarthaWaitMultiplier = "MARTHA_WAIT_MULTIPLIER"
-  private val EnvMarthaWaitRandomizationFactor = "MARTHA_WAIT_RANDOMIZATION_FACTOR"
+  private val EnvDrsResolverUrl = "DRS_RESOLVER_URL"
+  private val EnvDrsResolverNumRetries = "DRS_RESOLVER_NUM_RETRIES"
+  private val EnvDrsResolverWaitInitialSeconds = "DRS_RESOLVER_WAIT_INITIAL_SECONDS"
+  private val EnvDrsResolverWaitMaximumSeconds = "DRS_RESOLVER_WAIT_MAXIMUM_SECONDS"
+  private val EnvDrsResolverWaitMultiplier = "DRS_RESOLVER_WAIT_MULTIPLIER"
+  private val EnvDrsResolverWaitRandomizationFactor = "DRS_RESOLVER_WAIT_RANDOMIZATION_FACTOR"
 
-  def fromConfig(marthaConfig: Config): DrsConfig = {
+
+  def fromConfig(drsResolverConfig: Config): DrsConfig = {
     DrsConfig(
-      marthaUrl = marthaConfig.getString("url"),
-      numRetries = marthaConfig.getOrElse("num-retries", DefaultNumRetries),
-      waitInitial = marthaConfig.getOrElse("wait-initial", DefaultWaitInitial),
-      waitMaximum = marthaConfig.getOrElse("wait-maximum", DefaultWaitMaximum),
-      waitMultiplier = marthaConfig.getOrElse("wait-multiplier", DefaultWaitMultiplier),
+      drsResolverUrl = drsResolverConfig.getString("url"),
+      numRetries = drsResolverConfig.getOrElse("num-retries", DefaultNumRetries),
+      waitInitial = drsResolverConfig.getOrElse("wait-initial", DefaultWaitInitial),
+      waitMaximum = drsResolverConfig.getOrElse("wait-maximum", DefaultWaitMaximum),
+      waitMultiplier = drsResolverConfig.getOrElse("wait-multiplier", DefaultWaitMultiplier),
       waitRandomizationFactor =
-        marthaConfig.getOrElse("wait-randomization-factor", DefaultWaitRandomizationFactor),
+        drsResolverConfig.getOrElse("wait-randomization-factor", DefaultWaitRandomizationFactor),
     )
   }
 
   def fromEnv(env: Map[String, String]): DrsConfig = {
     DrsConfig(
-      marthaUrl = env(EnvMarthaUrl),
-      numRetries = env.get(EnvMarthaNumRetries).map(_.toInt).getOrElse(DefaultNumRetries),
-      waitInitial = env.get(EnvMarthaWaitInitialSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitInitial),
-      waitMaximum = env.get(EnvMarthaWaitMaximumSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitMaximum),
-      waitMultiplier = env.get(EnvMarthaWaitMultiplier).map(_.toDouble).getOrElse(DefaultWaitMultiplier),
+      drsResolverUrl = env(EnvDrsResolverUrl),
+      numRetries = env.get(EnvDrsResolverNumRetries).map(_.toInt).getOrElse(DefaultNumRetries),
+      waitInitial = env.get(EnvDrsResolverWaitInitialSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitInitial),
+      waitMaximum = env.get(EnvDrsResolverWaitMaximumSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitMaximum),
+      waitMultiplier = env.get(EnvDrsResolverWaitMultiplier).map(_.toDouble).getOrElse(DefaultWaitMultiplier),
       waitRandomizationFactor =
-        env.get(EnvMarthaWaitRandomizationFactor).map(_.toDouble).getOrElse(DefaultWaitRandomizationFactor),
+        env.get(EnvDrsResolverWaitRandomizationFactor).map(_.toDouble).getOrElse(DefaultWaitRandomizationFactor),
     )
   }
 
   def toEnv(drsConfig: DrsConfig): Map[String, String] = {
     Map(
-      EnvMarthaUrl -> drsConfig.marthaUrl,
-      EnvMarthaNumRetries -> s"${drsConfig.numRetries}",
-      EnvMarthaWaitInitialSeconds -> s"${drsConfig.waitInitial.toSeconds}",
-      EnvMarthaWaitMaximumSeconds -> s"${drsConfig.waitMaximum.toSeconds}",
-      EnvMarthaWaitMultiplier -> s"${drsConfig.waitMultiplier}",
-      EnvMarthaWaitRandomizationFactor -> s"${drsConfig.waitRandomizationFactor}",
+      EnvDrsResolverUrl -> drsConfig.drsResolverUrl,
+      EnvDrsResolverNumRetries -> s"${drsConfig.numRetries}",
+      EnvDrsResolverWaitInitialSeconds -> s"${drsConfig.waitInitial.toSeconds}",
+      EnvDrsResolverWaitMaximumSeconds -> s"${drsConfig.waitMaximum.toSeconds}",
+      EnvDrsResolverWaitMultiplier -> s"${drsConfig.waitMultiplier}",
+      EnvDrsResolverWaitRandomizationFactor -> s"${drsConfig.waitRandomizationFactor}",
     )
   }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
index 66a89fe4014..2d3e972508a 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
@@ -1,25 +1,32 @@
 package cloud.nio.impl.drs
 
 import cats.syntax.validated._
+import com.azure.core.credential.TokenRequestContext
+import com.azure.core.management.AzureEnvironment
+import com.azure.core.management.profile.AzureProfile
 import com.azure.identity.DefaultAzureCredentialBuilder
-import com.azure.security.keyvault.secrets.{SecretClient, SecretClientBuilder}
-import com.google.auth.oauth2.{AccessToken, OAuth2Credentials}
+import com.google.auth.oauth2.{AccessToken, GoogleCredentials, OAuth2Credentials}
 import com.typesafe.config.Config
-import common.validation.ErrorOr
 import common.validation.ErrorOr.ErrorOr
 import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.duration._
+import scala.jdk.DurationConverters._
+import scala.util.{Failure, Success, Try}
 
 /**
   * This trait allows us to abstract away different token attainment strategies
   * for different cloud environments.
   **/
-sealed trait DrsCredentials {
+trait DrsCredentials {
   def getAccessToken: ErrorOr[String]
 }
 
-case class GoogleDrsCredentials(credentials: OAuth2Credentials, acceptableTTL: Duration) extends DrsCredentials {
+/**
+  * Strategy for obtaining an access token from an existing OAuth credential. This class
+  * is designed for use within the Cromwell engine.
+  */
+case class GoogleOauthDrsCredentials(credentials: OAuth2Credentials, acceptableTTL: Duration) extends DrsCredentials {
   //Based on method from GoogleRegistry
   def getAccessToken: ErrorOr[String] = {
     def accessTokenTTLIsAcceptable(accessToken: AccessToken): Boolean = {
@@ -39,25 +46,68 @@ case class GoogleDrsCredentials(credentials: OAuth2Credentials, acceptableTTL: D
   }
 }
 
-object GoogleDrsCredentials {
-  def apply(credentials: OAuth2Credentials, config: Config): GoogleDrsCredentials =
-    GoogleDrsCredentials(credentials, config.as[FiniteDuration]("access-token-acceptable-ttl"))
+object GoogleOauthDrsCredentials {
+  def apply(credentials: OAuth2Credentials, config: Config): GoogleOauthDrsCredentials =
+    GoogleOauthDrsCredentials(credentials, config.as[FiniteDuration]("access-token-acceptable-ttl"))
+}
+
+
+/**
+  * Strategy for obtaining an access token from Google Application Default credentials that are assumed to already exist
+  * in the environment. This class is designed for use by standalone executables running in environments
+  * that have direct access to a Google identity (ex. CromwellDrsLocalizer).
+  */
+case object GoogleAppDefaultTokenStrategy extends DrsCredentials {
+  private final val UserInfoEmailScope = "https://www.googleapis.com/auth/userinfo.email"
+  private final val UserInfoProfileScope = "https://www.googleapis.com/auth/userinfo.profile"
+
+  def getAccessToken: ErrorOr[String] = {
+    Try {
+      val scopedCredentials = GoogleCredentials.getApplicationDefault().createScoped(UserInfoEmailScope, UserInfoProfileScope)
+      scopedCredentials.refreshAccessToken().getTokenValue
+    } match {
+      case Success(null) => "null token value attempting to refresh access token".invalidNel
+      case Success(value) => value.validNel
+      case Failure(e) => s"Failed to refresh access token: ${e.getMessage}".invalidNel
+    }
+  }
 }
 
-case class AzureDrsCredentials(identityClientId: Option[String], vaultName: String, secretName: String) extends DrsCredentials {
+/**
+  * Strategy for obtaining an access token in an environment with available Azure identity.
+  * If you need to disambiguate among multiple active user-assigned managed identities, pass
+  * in the client id of the identity that should be used.
+  */
+case class AzureDrsCredentials(identityClientId: Option[String]) extends DrsCredentials {
+
+  final val tokenAcquisitionTimeout = 5.seconds
 
-  lazy val secretClient: ErrorOr[SecretClient] = ErrorOr {
-    val defaultCreds = identityClientId.map(identityId =>
-      new DefaultAzureCredentialBuilder().managedIdentityClientId(identityId)
-    ).getOrElse(
-      new DefaultAzureCredentialBuilder()
-    ).build()
+  val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
+  val tokenScope = "https://management.azure.com/.default"
 
-    new SecretClientBuilder()
-      .vaultUrl(s"https://${vaultName}.vault.azure.net")
-      .credential(defaultCreds)
-      .buildClient()
+  def tokenRequestContext: TokenRequestContext = {
+    val trc = new TokenRequestContext()
+    trc.addScopes(tokenScope)
+    trc
   }
 
-  def getAccessToken: ErrorOr[String] = secretClient.map(_.getSecret(secretName).getValue)
+  def defaultCredentialBuilder: DefaultAzureCredentialBuilder =
+    new DefaultAzureCredentialBuilder()
+      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
+
+  def getAccessToken: ErrorOr[String] = {
+    val credentials = identityClientId.foldLeft(defaultCredentialBuilder) {
+      (builder, clientId) => builder.managedIdentityClientId(clientId)
+    }.build()
+
+    Try(
+      credentials
+        .getToken(tokenRequestContext)
+        .block(tokenAcquisitionTimeout.toJava)
+    ) match {
+      case Success(null) => "null token value attempting to obtain access token".invalidNel
+      case Success(token) => token.getToken.validNel
+      case Failure(error) => s"Failed to refresh access token: ${error.getMessage}".invalidNel
+    }
+  }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
index 9e0b45e259e..f9ae5b62e03 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
@@ -5,7 +5,7 @@ import cats.data.Validated.{Invalid, Valid}
 import cats.effect.{IO, Resource}
 import cats.implicits._
 import cloud.nio.impl.drs.DrsPathResolver.{FatalRetryDisposition, RegularRetryDisposition}
-import cloud.nio.impl.drs.MarthaResponseSupport._
+import cloud.nio.impl.drs.DrsResolverResponseSupport._
 import common.exception.{AggregatedMessageException, toIO}
 import common.validation.ErrorOr.ErrorOr
 import io.circe._
@@ -29,7 +29,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
   protected lazy val httpClientBuilder: HttpClientBuilder = {
     val clientBuilder = HttpClientBuilder.create()
     if (retryInternally) {
-      val retryHandler = new MarthaHttpRequestRetryStrategy(drsConfig)
+      val retryHandler = new DrsResolverHttpRequestRetryStrategy(drsConfig)
       clientBuilder
         .setRetryHandler(retryHandler)
         .setServiceUnavailableRetryStrategy(retryHandler)
@@ -39,11 +39,11 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
 
   def getAccessToken: ErrorOr[String]
 
-  private def makeHttpRequestToMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): Resource[IO, HttpPost] = {
+  private def makeHttpRequestToDrsResolver(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): Resource[IO, HttpPost] = {
     val io = getAccessToken match {
       case Valid(token) => IO {
-        val postRequest = new HttpPost(drsConfig.marthaUrl)
-        val requestJson = MarthaRequest(drsPath, fields).asJson.noSpaces
+        val postRequest = new HttpPost(drsConfig.drsResolverUrl)
+        val requestJson = DrsResolverRequest(drsPath, fields).asJson.noSpaces
         postRequest.setEntity(new StringEntity(requestJson, ContentType.APPLICATION_JSON))
         postRequest.setHeader("Authorization", s"Bearer $token")
         postRequest
@@ -54,7 +54,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
     Resource.eval(io)
   }
 
-  private def httpResponseToMarthaResponse(drsPathForDebugging: String)(httpResponse: HttpResponse): IO[MarthaResponse] = {
+  private def httpResponseToDrsResolverResponse(drsPathForDebugging: String)(httpResponse: HttpResponse): IO[DrsResolverResponse] = {
     val responseStatusLine = httpResponse.getStatusLine
     val status = responseStatusLine.getStatusCode
 
@@ -71,39 +71,39 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
       case s if s / 100 == 5 =>
         IO.raiseError(new RuntimeException(retryMessage) with RegularRetryDisposition)
       case _ =>
-        val marthaResponseEntityOption = Option(httpResponse.getEntity).map(EntityUtils.toString)
-        val exceptionMsg = errorMessageFromResponse(drsPathForDebugging, marthaResponseEntityOption, responseStatusLine, drsConfig.marthaUrl)
-        val responseEntityOption = (responseStatusLine.getStatusCode == HttpStatus.SC_OK).valueOrZero(marthaResponseEntityOption)
+        val drsResolverResponseEntityOption = Option(httpResponse.getEntity).map(EntityUtils.toString)
+        val exceptionMsg = errorMessageFromResponse(drsPathForDebugging, drsResolverResponseEntityOption, responseStatusLine, drsConfig.drsResolverUrl)
+        val responseEntityOption = (responseStatusLine.getStatusCode == HttpStatus.SC_OK).valueOrZero(drsResolverResponseEntityOption)
         val responseContentIO = toIO(responseEntityOption, exceptionMsg)
 
         responseContentIO.flatMap { responseContent =>
-          IO.fromEither(decode[MarthaResponse](responseContent))
+          IO.fromEither(decode[DrsResolverResponse](responseContent))
         }.handleErrorWith {
           e => IO.raiseError(new RuntimeException(s"Unexpected response during DRS resolution: ${ExceptionUtils.getMessage(e)}"))
         }
     }
   }
 
-  private def executeMarthaRequest(httpPost: HttpPost): Resource[IO, HttpResponse]= {
+  private def executeDrsResolverRequest(httpPost: HttpPost): Resource[IO, HttpResponse]= {
     for {
       httpClient <- Resource.fromAutoCloseable(IO(httpClientBuilder.build()))
       httpResponse <- Resource.fromAutoCloseable(IO(httpClient.execute(httpPost)))
     } yield httpResponse
   }
 
-  def rawMarthaResponse(drsPath: String, fields: NonEmptyList[MarthaField.Value]): Resource[IO, HttpResponse] = {
+  def rawDrsResolverResponse(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): Resource[IO, HttpResponse] = {
     for {
-      httpPost <- makeHttpRequestToMartha(drsPath, fields)
-      response <- executeMarthaRequest(httpPost)
+      httpPost <- makeHttpRequestToDrsResolver(drsPath, fields)
+      response <- executeDrsResolverRequest(httpPost)
     } yield response
   }
 
   /** *
-    * Resolves the DRS path through Martha url provided in the config.
-    * Please note, this method returns an IO that would make a synchronous HTTP request to Martha when run.
+    * Resolves the DRS path through DRS Resolver url provided in the config.
+    * Please note, this method returns an IO that would make a synchronous HTTP request to DRS Resolver when run.
     */
-  def resolveDrsThroughMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): IO[MarthaResponse] = {
-    rawMarthaResponse(drsPath, fields).use(httpResponseToMarthaResponse(drsPathForDebugging = drsPath))
+  def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
+    rawDrsResolverResponse(drsPath, fields).use(httpResponseToDrsResolverResponse(drsPathForDebugging = drsPath))
   }
 
   def openChannel(accessUrl: AccessUrl): IO[ReadableByteChannel] = {
@@ -144,7 +144,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean =
 }
 
 object DrsPathResolver {
-  final val ExtractUriErrorMsg = "No access URL nor GCS URI starting with 'gs://' found in Martha response!"
+  final val ExtractUriErrorMsg = "No access URL nor GCS URI starting with 'gs://' found in the DRS Resolver response!"
   sealed trait RetryDisposition
   // Should immediately fail the download attempt.
   trait FatalRetryDisposition extends RetryDisposition
@@ -152,27 +152,27 @@ object DrsPathResolver {
   trait RegularRetryDisposition extends RetryDisposition
 }
 
-object MarthaField extends Enumeration {
-  val GsUri: MarthaField.Value = Value("gsUri")
-  val Size: MarthaField.Value = Value("size")
-  val TimeCreated: MarthaField.Value = Value("timeCreated")
-  val TimeUpdated: MarthaField.Value = Value("timeUpdated")
-  val BondProvider: MarthaField.Value = Value("bondProvider")
-  val GoogleServiceAccount: MarthaField.Value = Value("googleServiceAccount")
-  val Hashes: MarthaField.Value = Value("hashes")
-  val FileName: MarthaField.Value = Value("fileName")
-  val AccessUrl: MarthaField.Value = Value("accessUrl")
-  val LocalizationPath: MarthaField.Value = Value("localizationPath")
+object DrsResolverField extends Enumeration {
+  val GsUri: DrsResolverField.Value = Value("gsUri")
+  val Size: DrsResolverField.Value = Value("size")
+  val TimeCreated: DrsResolverField.Value = Value("timeCreated")
+  val TimeUpdated: DrsResolverField.Value = Value("timeUpdated")
+  val BondProvider: DrsResolverField.Value = Value("bondProvider")
+  val GoogleServiceAccount: DrsResolverField.Value = Value("googleServiceAccount")
+  val Hashes: DrsResolverField.Value = Value("hashes")
+  val FileName: DrsResolverField.Value = Value("fileName")
+  val AccessUrl: DrsResolverField.Value = Value("accessUrl")
+  val LocalizationPath: DrsResolverField.Value = Value("localizationPath")
 }
 
-final case class MarthaRequest(url: String, fields: NonEmptyList[MarthaField.Value])
+final case class DrsResolverRequest(url: String, fields: NonEmptyList[DrsResolverField.Value])
 
 final case class SADataObject(data: Json)
 
 final case class AccessUrl(url: String, headers: Option[Map[String, String]])
 
 /**
-  * A response from `martha_v3`.
+  * A response from `drshub_v4`.
   *
   * @param size Size of the object stored at gsUri
   * @param timeCreated The creation time of the object at gsUri
@@ -187,34 +187,33 @@ final case class AccessUrl(url: String, headers: Option[Map[String, String]])
   *                         DRS metadata, via the `aliases` field. As this is a distinct field from `fileName` in DRS
   *                         metadata it is also made a distinct field in this response object.
   */
-final case class MarthaResponse(size: Option[Long] = None,
-                                timeCreated: Option[String] = None,
-                                timeUpdated: Option[String] = None,
-                                gsUri: Option[String] = None,
-                                bondProvider: Option[String] = None,
-                                googleServiceAccount: Option[SADataObject] = None,
-                                fileName: Option[String] = None,
-                                hashes: Option[Map[String, String]] = None,
-                                accessUrl: Option[AccessUrl] = None,
-                                localizationPath: Option[String] = None
+final case class DrsResolverResponse(size: Option[Long] = None,
+                                     timeCreated: Option[String] = None,
+                                     timeUpdated: Option[String] = None,
+                                     gsUri: Option[String] = None,
+                                     bondProvider: Option[String] = None,
+                                     googleServiceAccount: Option[SADataObject] = None,
+                                     fileName: Option[String] = None,
+                                     hashes: Option[Map[String, String]] = None,
+                                     accessUrl: Option[AccessUrl] = None,
+                                     localizationPath: Option[String] = None
                                )
 
-// Adapted from https://github.com/broadinstitute/martha/blob/f31933a3a11e20d30698ec4b4dc1e0abbb31a8bc/common/helpers.js#L210-L218
-final case class MarthaFailureResponse(response: MarthaFailureResponsePayload)
-final case class MarthaFailureResponsePayload(text: String)
+final case class DrsResolverFailureResponse(response: DrsResolverFailureResponsePayload)
+final case class DrsResolverFailureResponsePayload(text: String)
 
-object MarthaResponseSupport {
+object DrsResolverResponseSupport {
 
-  implicit lazy val marthaFieldEncoder: Encoder[MarthaField.Value] = Encoder.encodeEnumeration(MarthaField)
-  implicit lazy val marthaRequestEncoder: Encoder[MarthaRequest] = deriveEncoder
+  implicit lazy val drsResolverFieldEncoder: Encoder[DrsResolverField.Value] = Encoder.encodeEnumeration(DrsResolverField)
+  implicit lazy val drsResolverRequestEncoder: Encoder[DrsResolverRequest] = deriveEncoder
 
   implicit lazy val saDataObjectDecoder: Decoder[SADataObject] = deriveDecoder
-  implicit lazy val marthaResponseDecoder: Decoder[MarthaResponse] = deriveDecoder
+  implicit lazy val drsResolverResponseDecoder: Decoder[DrsResolverResponse] = deriveDecoder
 
-  implicit lazy val marthaFailureResponseDecoder: Decoder[MarthaFailureResponse] = deriveDecoder
-  implicit lazy val marthaFailureResponsePayloadDecoder: Decoder[MarthaFailureResponsePayload] = deriveDecoder
+  implicit lazy val drsResolverFailureResponseDecoder: Decoder[DrsResolverFailureResponse] = deriveDecoder
+  implicit lazy val drsResolverFailureResponsePayloadDecoder: Decoder[DrsResolverFailureResponsePayload] = deriveDecoder
 
-  implicit lazy val marthaAccessUrlDecoder: Decoder[AccessUrl] = deriveDecoder
+  implicit lazy val drsResolverAccessUrlDecoder: Decoder[AccessUrl] = deriveDecoder
 
   private val GcsScheme = "gs://"
 
@@ -223,18 +222,18 @@ object MarthaResponseSupport {
       (array(0), array(1))
   }
 
-  def errorMessageFromResponse(drsPathForDebugging: String, marthaResponseEntityOption: Option[String], responseStatusLine: StatusLine, marthaUri: String): String = {
-    val baseMessage = s"Could not access object \'$drsPathForDebugging\'. Status: ${responseStatusLine.getStatusCode}, reason: \'${responseStatusLine.getReasonPhrase}\', Martha location: \'$marthaUri\', message: "
+  def errorMessageFromResponse(drsPathForDebugging: String, drsResolverResponseEntityOption: Option[String], responseStatusLine: StatusLine, drsResolverUri: String): String = {
+    val baseMessage = s"Could not access object \'$drsPathForDebugging\'. Status: ${responseStatusLine.getStatusCode}, reason: \'${responseStatusLine.getReasonPhrase}\', DRS Resolver location: \'$drsResolverUri\', message: "
 
-    marthaResponseEntityOption match {
+    drsResolverResponseEntityOption match {
       case Some(entity) =>
-        val maybeErrorResponse: Either[Error, MarthaFailureResponse] = decode[MarthaFailureResponse](entity)
+        val maybeErrorResponse: Either[Error, DrsResolverFailureResponse] = decode[DrsResolverFailureResponse](entity)
         maybeErrorResponse match {
           case Left(_) =>
-            // Not parsable as a `MarthaFailureResponse`
+            // Not parsable as a `DrsResolverFailureResponse`
             baseMessage + s"\'$entity\'"
           case Right(decoded) =>
-            // Is a `MarthaFailureResponse`
+            // Is a `DrsResolverFailureResponse`
             baseMessage + s"\'${decoded.response.text}\'"
         }
       case None =>
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategy.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
similarity index 96%
rename from cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategy.scala
rename to cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
index 2881fc60b05..39020f5a684 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategy.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
@@ -7,7 +7,7 @@ import org.apache.http.HttpResponse
 import org.apache.http.client.{HttpRequestRetryHandler, ServiceUnavailableRetryStrategy}
 import org.apache.http.protocol.HttpContext
 
-class MarthaHttpRequestRetryStrategy(drsConfig: DrsConfig)
+class DrsResolverHttpRequestRetryStrategy(drsConfig: DrsConfig)
   extends ServiceUnavailableRetryStrategy with HttpRequestRetryHandler {
 
   // We can execute a total of one time, plus the number of retries
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
index fd7b71ef4ee..f61c608bd71 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
@@ -25,15 +25,15 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "parse a config and create a working file system provider" in {
     val config = ConfigFactory.parseString(
-      """martha.url = "https://from.config"
+      """resolver.url = "https://from.config"
         |access-token-acceptable-ttl = 1 minute
         |""".stripMargin
     )
 
     val fileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = config)
-    fileSystemProvider.drsConfig.marthaUrl should be("https://from.config")
+    fileSystemProvider.drsConfig.drsResolverUrl should be("https://from.config")
     fileSystemProvider.drsCredentials match {
-      case GoogleDrsCredentials(_, ttl) => ttl should be(1.minute)
+      case GoogleOauthDrsCredentials(_, ttl) => ttl should be(1.minute)
       case error => fail(s"Expected GoogleDrsCredentials, found $error")
     }
     fileSystemProvider.fileProvider should be(a[DrsCloudNioFileProvider])
@@ -79,19 +79,19 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "return a file provider that can read bytes from gcs" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrsThroughMartha(drsPath: String,
-                                           fields: NonEmptyList[MarthaField.Value],
-                                          ): IO[MarthaResponse] = {
-        IO(MarthaResponse(gsUri = Option("gs://bucket/object/path")))
+      override def resolveDrs(drsPath: String,
+                              fields: NonEmptyList[DrsResolverField.Value],
+                                          ): IO[DrsResolverResponse] = {
+        IO(DrsResolverResponse(gsUri = Option("gs://bucket/object/path")))
       }
     }
 
     val readChannel = mock[ReadableByteChannel]
-    val drsReadInterpreter: DrsReadInterpreter = (_, marthaResponse) => {
+    val drsReadInterpreter: DrsReadInterpreter = (_, drsResolverResponse) => {
       IO(
-        (marthaResponse.gsUri, marthaResponse.googleServiceAccount) match {
+        (drsResolverResponse.gsUri, drsResolverResponse.googleServiceAccount) match {
           case (Some("gs://bucket/object/path"), None) => readChannel
-          case _ => fail(s"Unexpected parameters passed: $marthaResponse")
+          case _ => fail(s"Unexpected parameters passed: $drsResolverResponse")
         }
       )
     }
@@ -105,19 +105,19 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "return a file provider that can read bytes from an access url" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrsThroughMartha(drsPath: String,
-                                           fields: NonEmptyList[MarthaField.Value],
-                                          ): IO[MarthaResponse] = {
-        IO(MarthaResponse(accessUrl = Option(AccessUrl("https://host/object/path", None))))
+      override def resolveDrs(drsPath: String,
+                              fields: NonEmptyList[DrsResolverField.Value],
+                                          ): IO[DrsResolverResponse] = {
+        IO(DrsResolverResponse(accessUrl = Option(AccessUrl("https://host/object/path", None))))
       }
     }
 
     val readChannel = mock[ReadableByteChannel]
-    val drsReadInterpreter: DrsReadInterpreter = (_, marthaResponse) => {
+    val drsReadInterpreter: DrsReadInterpreter = (_, drsResolverResponse) => {
       IO(
-        marthaResponse.accessUrl match {
+        drsResolverResponse.accessUrl match {
           case Some(AccessUrl("https://host/object/path", None)) => readChannel
-          case _ => fail(s"Unexpected parameters passed: $marthaResponse")
+          case _ => fail(s"Unexpected parameters passed: $drsResolverResponse")
         }
       )
     }
@@ -131,13 +131,13 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "return a file provider that can return file attributes" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrsThroughMartha(drsPath: String,
-                                           fields: NonEmptyList[MarthaField.Value],
-                                          ): IO[MarthaResponse] = {
+      override def resolveDrs(drsPath: String,
+                              fields: NonEmptyList[DrsResolverField.Value],
+                                          ): IO[DrsResolverResponse] = {
         val instantCreated = Instant.ofEpochMilli(123L)
         val instantUpdated = Instant.ofEpochMilli(456L)
         IO(
-          MarthaResponse(
+          DrsResolverResponse(
             size = Option(789L),
             timeCreated = Option(OffsetDateTime.ofInstant(instantCreated, ZoneOffset.UTC).toString),
             timeUpdated = Option(OffsetDateTime.ofInstant(instantUpdated, ZoneOffset.UTC).toString),
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
index 78585c96ed9..b4e5968e048 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
@@ -17,7 +17,7 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   private val md5HashValue = "336ea55913bc261b72875bd259753046"
   private val shaHashValue = "f76877f8e86ec3932fd2ae04239fbabb8c90199dab0019ae55fa42b31c314c44"
 
-  private val fullMarthaResponse = MarthaResponse(
+  private val fullDrsResolverResponse = DrsResolverResponse(
     size = Option(34905345),
     timeCreated = Option(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toString),
     timeUpdated = Option(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toString),
@@ -27,17 +27,17 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
     hashes = Option(Map("md5" -> md5HashValue, "crc32c" -> crcHashValue))
   )
 
-  private val fullMarthaResponseNoTz =
-    fullMarthaResponse
-      .copy(timeUpdated = fullMarthaResponse.timeUpdated.map(_.stripSuffix("Z")))
+  private val fullDrsResolverResponseNoTz =
+    fullDrsResolverResponse
+      .copy(timeUpdated = fullDrsResolverResponse.timeUpdated.map(_.stripSuffix("Z")))
 
-  private val fullMarthaResponseNoTime =
-    fullMarthaResponse
+  private val fullDrsResolverResponseNoTime =
+    fullDrsResolverResponse
       .copy(timeUpdated = None)
 
-  private val fullMarthaResponseBadTz =
-    fullMarthaResponse
-      .copy(timeUpdated = fullMarthaResponse.timeUpdated.map(_.stripSuffix("Z") + "BADTZ"))
+  private val fullDrsResolverResponseBadTz =
+    fullDrsResolverResponse
+      .copy(timeUpdated = fullDrsResolverResponse.timeUpdated.map(_.stripSuffix("Z") + "BADTZ"))
 
   private val etagHashValue = "something"
   private val completeHashesMap = Option(Map(
@@ -74,19 +74,19 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
 
   behavior of "fileHash()"
 
-  it should "return crc32c hash from `hashes` in Martha response when there is a crc32c" in {
+  it should "return crc32c hash from `hashes` in DRS Resolver response when there is a crc32c" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(completeHashesMap) shouldBe Option(FileHash(HashType.Crc32c, crcHashValue))
   }
 
-  it should "return md5 hash from `hashes` in Martha response when there is no crc32c" in {
+  it should "return md5 hash from `hashes` in DRS Resolver response when there is no crc32c" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(missingCRCHashesMap) shouldBe Option(FileHash(HashType.Md5, md5HashValue))
   }
 
-  it should "return sha256 hash from `hashes` in Martha response when there is only a sha256" in {
+  it should "return sha256 hash from `hashes` in DRS Resolver response when there is only a sha256" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(onlySHAHashesMap) shouldBe Option(FileHash(HashType.Sha256, shaHashValue))
   }
 
-  it should "return etag hash from `hashes` in Martha response when there is only an etag" in {
+  it should "return etag hash from `hashes` in DRS Resolver response when there is only an etag" in {
     DrsCloudNioRegularFileAttributes.getPreferredHash(onlyEtagHashesMap) shouldBe Option(FileHash(HashType.S3Etag, etagHashValue))
   }
 
@@ -127,10 +127,10 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
 
   it should "successfully parse a failure" in {
     import io.circe.parser.decode
-    import cloud.nio.impl.drs.MarthaResponseSupport.marthaFailureResponseDecoder
+    import cloud.nio.impl.drs.DrsResolverResponseSupport.drsResolverFailureResponseDecoder
 
-    val maybeDecoded = decode[MarthaFailureResponse](failureResponseJson)
-    maybeDecoded map { decoded: MarthaFailureResponse =>
+    val maybeDecoded = decode[DrsResolverFailureResponse](failureResponseJson)
+    maybeDecoded map { decoded: DrsResolverFailureResponse =>
       decoded.response.text shouldBe "{\"msg\":\"User 'null' does not have required action: read_data\",\"status_code\":500}"
     }
   }
@@ -139,37 +139,37 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
 
   val drsPathForDebugging = "drs://my_awesome_drs"
   val responseStatusLine = new BasicStatusLine(new ProtocolVersion("http", 1, 2) , 345, "test-reason")
-  val testMarthaUri = "www.martha_v3.com"
+  val testDrsResolverUri = "www.drshub_v4.com"
 
   it should "construct an error message from a populated, well-formed failure response" in {
     val failureResponse = Option(failureResponseJson)
 
-    MarthaResponseSupport.errorMessageFromResponse(drsPathForDebugging, failureResponse, responseStatusLine, testMarthaUri) shouldBe {
-      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', Martha location: 'www.martha_v3.com', message: '{\"msg\":\"User 'null' does not have required action: read_data\",\"status_code\":500}'"
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, failureResponse, responseStatusLine, testDrsResolverUri) shouldBe {
+      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: '{\"msg\":\"User 'null' does not have required action: read_data\",\"status_code\":500}'"
     }
   }
 
   it should "construct an error message from an empty failure response" in {
-    MarthaResponseSupport.errorMessageFromResponse(drsPathForDebugging, None, responseStatusLine, testMarthaUri) shouldBe {
-      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', Martha location: 'www.martha_v3.com', message: (empty response)"
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, None, responseStatusLine, testDrsResolverUri) shouldBe {
+      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: (empty response)"
     }
   }
 
-  // Technically we enter this case when preparing the "error message" for a successful response, because naturally `MarthaResponse` does not deserialize to `MarthaFailureResponse`
+  // Technically we enter this case when preparing the "error message" for a successful response, because naturally `DrsResolverResponse` does not deserialize to `DrsResolverFailureResponse`
   // But then there's no error so we throw it away :shrug:
   it should "construct an error message from a malformed failure response" in {
     val unparsableFailureResponse = Option("something went horribly wrong")
 
-    MarthaResponseSupport.errorMessageFromResponse(drsPathForDebugging, unparsableFailureResponse, responseStatusLine, testMarthaUri) shouldBe {
-      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', Martha location: 'www.martha_v3.com', message: 'something went horribly wrong'"
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, unparsableFailureResponse, responseStatusLine, testDrsResolverUri) shouldBe {
+      "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: 'something went horribly wrong'"
     }
   }
 
   it should "resolve an ISO-8601 date with timezone" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponse.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponse.timeUpdated,
     )
     lastModifiedTimeIO.unsafeRunSync() should
       be(Option(FileTime.from(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toInstant)))
@@ -178,8 +178,8 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   it should "resolve an ISO-8601 date without timezone" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponseNoTz.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponseNoTz.timeUpdated,
     )
     lastModifiedTimeIO.unsafeRunSync() should
       be(Option(FileTime.from(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toInstant)))
@@ -188,8 +188,8 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   it should "not resolve an date that does not contain a timeUpdated" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponseNoTime.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponseNoTime.timeUpdated,
     )
     lastModifiedTimeIO.unsafeRunSync() should be(None)
   }
@@ -197,11 +197,11 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   it should "not resolve an date that is not ISO-8601" in {
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
-      MarthaField.TimeUpdated,
-      fullMarthaResponseBadTz.timeUpdated,
+      DrsResolverField.TimeUpdated,
+      fullDrsResolverResponseBadTz.timeUpdated,
     )
     the[RuntimeException] thrownBy lastModifiedTimeIO.unsafeRunSync() should have message
-      "Error while parsing 'timeUpdated' value from Martha to FileTime for DRS path drs://my_awesome_drs. " +
+      "Error while parsing 'timeUpdated' value from DRS Resolver to FileTime for DRS path drs://my_awesome_drs. " +
         "Reason: DateTimeParseException: Text '2020-04-27T15:56:09.696BADTZ' could not be parsed at index 23."
   }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategySpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
similarity index 89%
rename from cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategySpec.scala
rename to cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
index 8fd1e948607..b221038bedb 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MarthaHttpRequestRetryStrategySpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
@@ -12,13 +12,13 @@ import common.mock.MockSugar
 
 import scala.concurrent.duration._
 
-class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with MockSugar {
+class DrsResolverHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with MockSugar {
 
-  behavior of "MarthaHttpRequestRetryStrategy"
+  behavior of "DrsResolverHttpRequestRetryStrategy"
 
   it should "retry 500 errors a configured number of times" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val http500Response = mock[CloseableHttpResponse]
     http500Response.getStatusLine returns new BasicStatusLine(HttpVersion.HTTP_1_1, 500, "Testing 500")
     val httpContext = mock[HttpContext]
@@ -35,7 +35,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
 
   it should "retry 500 errors even after a number of 408/429 errors" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val http500Response = mock[CloseableHttpResponse]
     http500Response.getStatusLine returns new BasicStatusLine(HttpVersion.HTTP_1_1, 500, "Testing 500")
     val http408Response = mock[CloseableHttpResponse]
@@ -63,7 +63,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
 
   it should "not retry an HTTP 401" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val http400Response = mock[CloseableHttpResponse]
     http400Response.getStatusLine returns new BasicStatusLine(HttpVersion.HTTP_1_1, 401, "Testing 401")
     val httpContext = mock[HttpContext]
@@ -73,7 +73,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
 
   it should "retry IO exceptions a configured number of times" in {
     val drsConfig = MockDrsPaths.mockDrsConfig.copy(numRetries = 3)
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
     val exception = mock[IOException]
     val httpContext = mock[HttpContext]
 
@@ -95,7 +95,7 @@ class MarthaHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers with
         waitMaximum = 1.minute,
         waitRandomizationFactor = 0d,
       )
-    val retryStrategy = new MarthaHttpRequestRetryStrategy(drsConfig)
+    val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
 
     retryStrategy.getRetryInterval should be(10000L)
     retryStrategy.getRetryInterval should be(20000L)
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
index 025d7c6d543..07a02e096dc 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
@@ -17,7 +17,7 @@ class MockDrsCloudNioFileSystemProvider(config: Config = mockConfig,
                                           ),
                                         mockResolver: Option[EngineDrsPathResolver] = None,
                                        )
-  extends DrsCloudNioFileSystemProvider(config, GoogleDrsCredentials(NoCredentials.getInstance, config), drsReadInterpreter) {
+  extends DrsCloudNioFileSystemProvider(config, GoogleOauthDrsCredentials(NoCredentials.getInstance, config), drsReadInterpreter) {
 
   override lazy val drsPathResolver: EngineDrsPathResolver = {
     mockResolver getOrElse
@@ -31,7 +31,7 @@ class MockDrsCloudNioFileSystemProvider(config: Config = mockConfig,
 
 object MockDrsCloudNioFileSystemProvider {
   private lazy val mockConfig = ConfigFactory.parseString(
-    """martha.url = "https://mock.martha"
+    """resolver.url = "https://mock.drshub"
       |access-token-acceptable-ttl = 1 hour
       |""".stripMargin
   )
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala
index b6825dcbbd2..a24385bc15f 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPaths.scala
@@ -3,9 +3,9 @@ package cloud.nio.impl.drs
 import scala.concurrent.duration._
 
 object MockDrsPaths {
-  val marthaUrl = "http://mock.martha"
+  val drsResolverUrl = "http://mock.drshub"
 
-  val mockDrsConfig: DrsConfig = DrsConfig(MockDrsPaths.marthaUrl, 1, 1.seconds, 1.seconds, 1d, 0d)
+  val mockDrsConfig: DrsConfig = DrsConfig(MockDrsPaths.drsResolverUrl, 1, 1.seconds, 1.seconds, 1d, 0d)
 
   val mockToken = "mock.token"
 
@@ -35,5 +35,5 @@ object MockDrsPaths {
 
   val drsPathResolvingToNoGcsPath = s"$drsPathPrefix/226686cf-22c9-4472-9f79-7a0b0044f253"
 
-  val drsPathNotExistingInMartha = s"$drsPathPrefix/5e21b8c3-8eda-48d5-9a04-2b32e1571765"
+  val drsPathNotExistingInDrsResolver = s"$drsPathPrefix/5e21b8c3-8eda-48d5-9a04-2b32e1571765"
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
index 116155753f1..9e22544c38b 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
@@ -14,12 +14,12 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
                                 httpClientBuilderOverride: Option[HttpClientBuilder] = None,
                                 accessTokenAcceptableTTL: Duration = Duration.Inf,
                                )
-  extends EngineDrsPathResolver(drsConfig, GoogleDrsCredentials(NoCredentials.getInstance, accessTokenAcceptableTTL)) {
+  extends EngineDrsPathResolver(drsConfig, GoogleOauthDrsCredentials(NoCredentials.getInstance, accessTokenAcceptableTTL)) {
 
   override protected lazy val httpClientBuilder: HttpClientBuilder =
     httpClientBuilderOverride getOrElse MockSugar.mock[HttpClientBuilder]
 
-  private lazy val mockMarthaUri = drsConfig.marthaUrl
+  private lazy val mockDrsResolverUri = drsConfig.drsResolverUrl
 
   private val hashesObj = Map(
     "md5" -> "336ea55913bc261b72875bd259753046",
@@ -27,8 +27,8 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
     "crc32c" -> "8a366443"
   )
 
-  private val marthaObjWithGcsPath =
-    MarthaResponse(
+  private val drsResolverObjWithGcsPath =
+    DrsResolverResponse(
       size = Option(156018255),
       timeCreated = Option("2020-04-27T15:56:09.696Z"),
       timeUpdated = Option("2020-04-27T15:56:09.696Z"),
@@ -36,27 +36,27 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
       hashes = Option(hashesObj)
     )
 
-  private val marthaObjWithFileName = marthaObjWithGcsPath.copy(fileName = Option("file.txt"))
+  private val drsResolverObjWithFileName = drsResolverObjWithGcsPath.copy(fileName = Option("file.txt"))
 
-  private val marthaObjWithLocalizationPath = marthaObjWithGcsPath.copy(localizationPath = Option("/dir/subdir/file.txt"))
+  private val drsResolverObjWithLocalizationPath = drsResolverObjWithGcsPath.copy(localizationPath = Option("/dir/subdir/file.txt"))
 
-  private val marthaObjWithAllThePaths = marthaObjWithLocalizationPath.copy(fileName = marthaObjWithFileName.fileName)
+  private val drsResolverObjWithAllThePaths = drsResolverObjWithLocalizationPath.copy(fileName = drsResolverObjWithFileName.fileName)
 
-  private val marthaObjWithNoGcsPath = marthaObjWithGcsPath.copy(gsUri = None)
+  private val drsResolverObjWithNoGcsPath = drsResolverObjWithGcsPath.copy(gsUri = None)
 
-  override def resolveDrsThroughMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): IO[MarthaResponse] = {
+  override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
     drsPath match {
-      case MockDrsPaths.drsPathResolvingGcsPath => IO(marthaObjWithGcsPath)
-      case MockDrsPaths.drsPathWithNonPathChars => IO(marthaObjWithGcsPath)
-      case MockDrsPaths.drsPathResolvingWithFileName => IO(marthaObjWithFileName)
-      case MockDrsPaths.drsPathResolvingWithLocalizationPath => IO.pure(marthaObjWithLocalizationPath)
-      case MockDrsPaths.drsPathResolvingWithAllThePaths => IO.pure(marthaObjWithAllThePaths)
-      case MockDrsPaths.drsPathResolvingToNoGcsPath => IO(marthaObjWithNoGcsPath)
-      case MockDrsPaths.drsPathNotExistingInMartha =>
+      case MockDrsPaths.drsPathResolvingGcsPath => IO(drsResolverObjWithGcsPath)
+      case MockDrsPaths.drsPathWithNonPathChars => IO(drsResolverObjWithGcsPath)
+      case MockDrsPaths.drsPathResolvingWithFileName => IO(drsResolverObjWithFileName)
+      case MockDrsPaths.drsPathResolvingWithLocalizationPath => IO.pure(drsResolverObjWithLocalizationPath)
+      case MockDrsPaths.drsPathResolvingWithAllThePaths => IO.pure(drsResolverObjWithAllThePaths)
+      case MockDrsPaths.drsPathResolvingToNoGcsPath => IO(drsResolverObjWithNoGcsPath)
+      case MockDrsPaths.`drsPathNotExistingInDrsResolver` =>
         IO.raiseError(
           new RuntimeException(
-            s"Unexpected response resolving ${MockDrsPaths.drsPathNotExistingInMartha} " +
-              s"through Martha url $mockMarthaUri. Error: 404 Not Found."
+            s"Unexpected response resolving ${MockDrsPaths.drsPathNotExistingInDrsResolver} " +
+              s"through DRS Resolver url $mockDrsResolverUri. Error: 404 Not Found."
           )
         )
     }
diff --git a/codegen_java/build.sbt b/codegen_java/build.sbt
index 2ba35a693c3..0ad461a66b8 100644
--- a/codegen_java/build.sbt
+++ b/codegen_java/build.sbt
@@ -6,7 +6,7 @@ lazy val root = (project in file(".")).
     Seq(organization := "org.broadinstitute.cromwell",
     name := "cromwell-client",
     version := createVersion("0.1"),
-    scalaVersion := "2.13.8",
+    scalaVersion := "2.13.9",
     scalacOptions ++= Seq("-feature"),
     compile / javacOptions ++= Seq("-Xlint:deprecation"),
     Compile / packageDoc / publishArtifact := false,
diff --git a/common/src/main/scala/common/util/TerminalUtil.scala b/common/src/main/scala/common/util/TerminalUtil.scala
index dab7fb9ce17..cb7c980aecb 100644
--- a/common/src/main/scala/common/util/TerminalUtil.scala
+++ b/common/src/main/scala/common/util/TerminalUtil.scala
@@ -6,10 +6,10 @@ object TerminalUtil {
     def maxWidth(lengths: Seq[Seq[Int]], column: Int) = lengths.map { length => length(column) }.max
     val widths = (rows :+ header).map { row => row.map { s => s.length } }
     val maxWidths = widths.head.indices.map { column => maxWidth(widths, column) }
-    val tableHeader = header.indices.map { i => header(i).padTo(maxWidths(i), " ").mkString("") }.mkString("|")
+    val tableHeader = header.indices.map { i => header(i).padTo(maxWidths(i), ' ').mkString("") }.mkString("|")
     val tableDivider = header.indices.map { i => "-" * maxWidths(i) }.mkString("|")
     val tableRows = rows.map { row =>
-      val mdRow = row.indices.map { i => row(i).padTo(maxWidths(i), " ").mkString("") }.mkString("|")
+      val mdRow = row.indices.map { i => row(i).padTo(maxWidths(i), ' ').mkString("") }.mkString("|")
       s"|$mdRow|"
     }
     s"|$tableHeader|\n|$tableDivider|\n${tableRows.mkString("\n")}\n"
diff --git a/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala b/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala
index 12dba2e15d9..d2e0a38878c 100644
--- a/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala
+++ b/common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala
@@ -11,7 +11,7 @@ class EnhancedCollectionsSpec extends AsyncFlatSpec with Matchers {
   behavior of "EnhancedCollections"
 
   it should "filter a List by type and return a List" in {
-    val objectList = List("hello", 3, None, "world")
+    val objectList = List[Any]("hello", 3, None, "world")
     val stringList = objectList.filterByType[String]
 
     stringList should be(List("hello", "world"))
@@ -28,14 +28,14 @@ class EnhancedCollectionsSpec extends AsyncFlatSpec with Matchers {
   }
 
   it should "filter a Set by type and return a Set" in {
-    val objectSet = Set("hello", 3, None, "world")
+    val objectSet = Set[Any]("hello", 3, None, "world")
     val intSet: Set[Int] = objectSet.filterByType[Int]
 
     intSet should be(Set(3))
   }
 
   it should "find the first Int in a List" in {
-    val objectSet = List("hello", 3, None, 4, "world")
+    val objectSet = List[Any]("hello", 3, None, 4, "world")
     objectSet.firstByType[Int] should be(Some(3))
   }
 
diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index 41d2b2c14bd..dd2f14c06c8 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -328,8 +328,8 @@ filesystems {
       # Class to instantiate and propagate to all factories. Takes a single typesafe config argument
       class = "cromwell.filesystems.drs.DrsFileSystemConfig"
       config {
-        martha {
-          url = "https://martha-url-here"
+        resolver {
+          url = "https://martha-url-here or https://drshub-url-here"
           # When true (and when possible) any DrsPath will be internally converted to another compatible Path such as a
           # GcsPath. This enables other optimizations such as using batch requests for GCS for hashes, using the
           # existing GCS downloader in Papi, etc.
@@ -441,6 +441,10 @@ engine {
 languages {
   default: WDL
   WDL {
+    http-allow-list {
+      enabled: false
+      allowed-http-hosts: []
+    }
     versions {
       default: "draft-2"
       "draft-2" {
@@ -468,29 +472,6 @@ languages {
       }
     }
   }
-  CWL {
-    versions {
-      default: "v1.0"
-      "v1.0" {
-        language-factory = "languages.cwl.CwlV1_0LanguageFactory"
-        config {
-          strict-validation: false
-          enabled: true
-
-          # Optional section to define a command returning paths to output files that
-          # can only be known after the user's command has been run
-          output-runtime-extractor {
-            # Optional docker image on which the command should be run - Must have bash if provided
-            docker-image = "stedolan/jq@sha256:a61ed0bca213081b64be94c5e1b402ea58bc549f457c2682a86704dd55231e09"
-            # Single line command executed after the tool has run.
-            # It should write to stdout the file paths that are referenced in the cwl.output.json (or any other file path
-            # not already defined in the outputs of the tool and therefore unknown when the tool is run)
-            command = "cat cwl.output.json 2>/dev/null | jq -r '.. | .path? // .location? // empty'"
-          }
-        }
-      }
-    }
-  }
 }
 
 ontology {
diff --git a/core/src/main/scala/cromwell/core/io/IoCommand.scala b/core/src/main/scala/cromwell/core/io/IoCommand.scala
index a21b6f8cebd..7d71f9bd307 100644
--- a/core/src/main/scala/cromwell/core/io/IoCommand.scala
+++ b/core/src/main/scala/cromwell/core/io/IoCommand.scala
@@ -38,6 +38,12 @@ trait IoCommand[+T] {
 
   def commandDescription: String
 
+  /**
+    * IO commands side-effect and/or have exceptions. We don't want that when evaluating identity, e.g. to check presence in cache.
+    * @return Hash code based on the description, which captures file path & action
+    */
+  override def hashCode(): Int = commandDescription.hashCode
+
   def logIOMsgOverLimit(message: => String): Unit = {
     val millis: Long = java.time.Duration.between(creation, OffsetDateTime.now).toMillis
     if (millis > IoCommand.IOCommandWarnLimit.toMillis) {
diff --git a/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala b/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
index 15097a92a99..dd8f44464f3 100644
--- a/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
+++ b/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
@@ -10,6 +10,8 @@ import scala.concurrent.duration.FiniteDuration
 object IoPromiseProxyActor {
   case class IoCommandWithPromise[A](ioCommand: IoCommand[A], timeout: FiniteDuration = defaultTimeout) {
     val promise = Promise[A]()
+
+    override def hashCode(): Int = ioCommand.hashCode()
   }
   def props(ioActor: ActorRef) = Props(new IoPromiseProxyActor(ioActor))
 }
diff --git a/core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala b/core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala
new file mode 100644
index 00000000000..dcf62bc0b28
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala
@@ -0,0 +1,70 @@
+package cromwell.core.logging
+
+import ch.qos.logback.classic.pattern.DateConverter
+import ch.qos.logback.classic.spi.ILoggingEvent
+import ch.qos.logback.core.CoreConstants
+import ch.qos.logback.core.util.CachingDateFormatter
+
+import java.util.TimeZone
+import scala.jdk.CollectionConverters._
+
+/**
+  * Log the Akka akkaTimestamp if found in the MDC, otherwise log the original event timestamp.
+  *
+  *   - https://doc.akka.io/docs/akka/current/logging.html#more-accurate-timestamps-for-log-output-in-mdc
+  *   - https://logback.qos.ch/manual/layouts.html#customConversionSpecifier
+  *
+  * NOTE: For proper configuration both this EnhancedDateConverter should be configured into the logback.xml AND the
+  * configuration file should set akka.loggers = ["cromwell.core.logging.EnhancedSlf4jLogger"].
+  */
+class EnhancedDateConverter extends DateConverter {
+  protected var cachingDateFormatterProtected: CachingDateFormatter = _
+
+  /* Duplicated from ch.qos.logback.classic.pattern.DateConverter as cachingDateFormatter is package private. */
+  override def start(): Unit = {
+    cachingDateFormatterProtected = Option(getFirstOption) match {
+      case Some(CoreConstants.ISO8601_STR) | None => new CachingDateFormatter(CoreConstants.ISO8601_PATTERN)
+      case Some(datePattern) =>
+        try {
+          new CachingDateFormatter(datePattern)
+        } catch {
+          case e: IllegalArgumentException =>
+            addWarn("Could not instantiate SimpleDateFormat with pattern " + datePattern, e)
+            // default to the ISO8601 format
+            new CachingDateFormatter(CoreConstants.ISO8601_PATTERN)
+        }
+    }
+    // if the option list contains a TZ option, then set it.
+    Option(getOptionList)
+      .toList
+      .flatMap(_.asScala)
+      .drop(1)
+      .headOption
+      .map(TimeZone.getTimeZone)
+      .foreach(cachingDateFormatterProtected.setTimeZone)
+
+    // Allow the parent class to start/initialize its private members.
+    super.start()
+  }
+
+  /**
+    * Look for the Akka timestamp and use that to format the date.
+    *
+    * Until this (currently 6+ year) issue is resolved, formatting the date as a Long requires using the
+    * [[EnhancedSlf4jLogger]] versus Akka's basic Slf4jLogger.
+    *
+    *   - https://github.com/akka/akka/issues/18079#issuecomment-125175884
+    */
+  override def convert(event: ILoggingEvent): String = {
+    val mdc = event.getMDCPropertyMap
+    if (mdc.containsKey("akkaTimestamp")) {
+      val timestamp = mdc.get("akkaTimestamp")
+      timestamp.toLongOption match {
+        case Some(value) => cachingDateFormatterProtected.format(value)
+        case None => timestamp // Return the original timestamp string.
+      }
+    } else {
+      super.convert(event)
+    }
+  }
+}
diff --git a/core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala b/core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala
new file mode 100644
index 00000000000..0999ec18055
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala
@@ -0,0 +1,16 @@
+package cromwell.core.logging
+
+import akka.event.slf4j.Slf4jLogger
+
+class EnhancedSlf4jLogger extends Slf4jLogger {
+  /**
+    * Format the timestamp as a simple long. Allows the akkaTimestamp to be retrieved later from the MDC by custom
+    * converters.
+    *
+    * NOTE: Should not be necessary once this issue is resolved: 
+    *   - https://github.com/akka/akka/issues/18079#issuecomment-125175884
+    *
+    * @see [[EnhancedDateConverter.convert()]]
+    */
+  override protected def formatTimestamp(timestamp: Long): String = String.valueOf(timestamp)
+}
diff --git a/core/src/main/scala/cromwell/core/logging/EnhancedThreadConverter.scala b/core/src/main/scala/cromwell/core/logging/EnhancedThreadConverter.scala
new file mode 100644
index 00000000000..73f5876597b
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/logging/EnhancedThreadConverter.scala
@@ -0,0 +1,21 @@
+package cromwell.core.logging
+
+import ch.qos.logback.classic.pattern.ThreadConverter
+import ch.qos.logback.classic.spi.ILoggingEvent
+
+/**
+  * Log the Akka sourceThread if found, otherwise log the event thread.
+  * 
+  *   - https://doc.akka.io/docs/akka/current/logging.html#logging-thread-akka-source-and-actor-system-in-mdc
+  *   - https://logback.qos.ch/manual/layouts.html#customConversionSpecifier
+  */
+class EnhancedThreadConverter extends ThreadConverter {
+  override def convert(event: ILoggingEvent): String = {
+    val mdc = event.getMDCPropertyMap
+    if (mdc.containsKey("sourceThread")) {
+      mdc.get("sourceThread")
+    } else {
+      super.convert(event)
+    }
+  }
+}
diff --git a/core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala b/core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala
new file mode 100644
index 00000000000..1dc10fab46d
--- /dev/null
+++ b/core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala
@@ -0,0 +1,39 @@
+package cromwell.core.logging
+
+import ch.qos.logback.classic.LoggerContext
+import ch.qos.logback.classic.jul.LevelChangePropagator
+import org.slf4j.LoggerFactory
+import org.slf4j.bridge.SLF4JBridgeHandler
+
+import scala.jdk.CollectionConverters._
+
+object JavaLoggingBridge {
+  /**
+    * Replace java.util.logging with SLF4J while ensuring Logback is configured with a LevelChangePropogator.
+    *
+    * One likely won't need to do this but just in case: note that any libraries using JUL running BEFORE this
+    * initialization which require increasing or decreasing verbosity must be configured via JUL not Logback.
+    *
+    * See also:
+    *   - https://www.slf4j.org/api/org/slf4j/bridge/SLF4JBridgeHandler.html
+    *   - https://docs.oracle.com/en/java/javase/11/docs/api/java.logging/java/util/logging/LogManager.html
+    */
+  def init(): Unit = {
+    // Retrieve the Logback context, and as a side effect initialize Logback.
+    val ctx = LoggerFactory.getILoggerFactory.asInstanceOf[LoggerContext]
+
+    // Ensure that Logback has a LevelChangePropagator, either here or via a logback.xml.
+    val listeners = ctx.getCopyOfListenerList.asScala
+    if (!listeners.exists(_.isInstanceOf[LevelChangePropagator])) {
+      val propagator = new LevelChangePropagator()
+      propagator.setContext(ctx)
+      propagator.start()
+    }
+
+    // Remove all the JUL logging handlers.
+    SLF4JBridgeHandler.removeHandlersForRootLogger()
+
+    // Send all JUL logging to SLF4J.
+    SLF4JBridgeHandler.install()
+  }
+}
diff --git a/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala b/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
index 91f05b10ef7..20a2afdd5ce 100644
--- a/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
+++ b/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
@@ -2,6 +2,7 @@ package cromwell.core.path
 
 import akka.actor.ActorSystem
 import cromwell.core.WorkflowOptions
+import cromwell.core.path.PathBuilderFactory.PriorityDefault
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -9,4 +10,6 @@ case object DefaultPathBuilderFactory extends PathBuilderFactory {
   override def withOptions(options: WorkflowOptions)(implicit actorSystem: ActorSystem, ec: ExecutionContext) = Future.successful(DefaultPathBuilder)
   val name = "local"
   val tuple = name -> this
+
+  override def priority: Int = PriorityDefault
 }
diff --git a/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala b/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
index 1f215ba2933..79adaae4d6b 100644
--- a/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
+++ b/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
@@ -5,6 +5,7 @@ import cromwell.core.{Dispatcher, WorkflowOptions}
 import cats.syntax.traverse._
 import cats.instances.list._
 import cats.instances.future._
+import cromwell.core.path.PathBuilderFactory.PriorityStandard
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -12,16 +13,13 @@ object PathBuilderFactory {
   // Given a list of factories, instantiates the corresponding path builders
   def instantiatePathBuilders(factories: List[PathBuilderFactory], workflowOptions: WorkflowOptions)(implicit as: ActorSystem): Future[List[PathBuilder]] = {
     implicit val ec: ExecutionContext = as.dispatchers.lookup(Dispatcher.IoDispatcher)
-    // The DefaultPathBuilderFactory always needs to be last.
-    // The reason is path builders are tried in order, and the default one is very generous in terms of paths it "thinks" it supports
-    // For instance, it will return a Path for a gcs url even though it doesn't really support it
-    val sortedFactories = factories.sortWith({
-      case (_, DefaultPathBuilderFactory) => true
-      case (DefaultPathBuilderFactory, _) => false
-      case (a, b) => factories.indexOf(a) < factories.indexOf(b)
-    })
+    val sortedFactories = factories.sortBy(_.priority)
     sortedFactories.traverse(_.withOptions(workflowOptions))
   }
+
+  val PriorityBlob     = 100   // High priority to evaluate first, because blob files may inadvertently match other filesystems
+  val PriorityStandard = 1000
+  val PriorityDefault  = 10000 // "Default" is a fallback, evaluate last
 }
 
 /**
@@ -29,4 +27,11 @@ object PathBuilderFactory {
   */
 trait PathBuilderFactory {
   def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder]
+
+  /**
+    * Candidate filesystems are considered in a stable order, as some requests may match multiple filesystems.
+    * To customize this order, the priority of a filesystem may be adjusted. Lower number == higher priority.
+    * @return This filesystem's priority
+    */
+  def priority: Int = PriorityStandard
 }
diff --git a/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala b/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
index f77df6fa011..06132ba152b 100644
--- a/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
+++ b/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
@@ -27,7 +27,7 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
     val testActor = TestActorRef(new IoClientHelperTestActor(ioActorProbe.ref, delegateProbe.ref, backoff, noResponseTimeout))
 
     val command = DefaultIoSizeCommand(mock[Path])
-    val response = IoSuccess(command, 5)
+    val response = IoSuccess(command, 5L)
 
     // Send the command
     testActor.underlyingActor.sendMessage(command)
@@ -58,7 +58,7 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
 
     val commandContext = "context"
     val command = DefaultIoSizeCommand(mock[Path])
-    val response = IoSuccess(command, 5)
+    val response = IoSuccess(command, 5L)
 
     // Send the command
     testActor.underlyingActor.sendMessageWithContext(commandContext, command)
diff --git a/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala b/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
index 58fa597dc03..c6a008feb02 100644
--- a/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
+++ b/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
@@ -54,7 +54,7 @@ class BackoffSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   it should "parse config" in {
     val config = ConfigFactory.parseMap(
-      Map(
+      Map[String, Any](
         "min" -> "5 seconds",
         "max" -> "30 seconds",
         "multiplier" -> 6D,
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
index df0f7c2eba6..3b7be2b38bd 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
@@ -14,40 +14,55 @@ class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage)
 
   head("cromwell-drs-localizer", localizerVersion)
 
-  arg[String]("drs-object-id").text("DRS object ID").required().
+  arg[String]("drs-object-id").text("DRS object ID").optional().
     action((s, c) =>
       c.copy(drsObject = Option(s)))
-  arg[String]("container-path").text("Container path").required().
+  arg[String]("container-path").text("Container path").optional().
     action((s, c) =>
       c.copy(containerPath = Option(s)))
-  arg[String]("requester-pays-project").text("Requester pays project").optional().
+  arg[String]("requester-pays-project").text(s"Requester pays project (only valid with '$Google' auth strategy)").optional().
     action((s, c) =>
       c.copy(googleRequesterPaysProject = Option(s)))
+  opt[String]('m', "manifest-path").text("File path of manifest containing multiple files to localize").
+    action((s, c) =>
+      c.copy(manifestPath = Option(s)))
+  opt[String]('r', "requester-pays-project").text(s"Requester pays project (only valid with '$Google' auth strategy)").optional().
+    action((s, c) => {
+      c.copy(
+        googleRequesterPaysProject = Option(s),
+        googleRequesterPaysProjectConflict = c.googleRequesterPaysProject.exists(_ != s)
+      )
+    })
   opt[String]('t', "access-token-strategy").text(s"Access token strategy, must be one of '$Azure' or '$Google' (default '$Google')").
     action((s, c) =>
       c.copy(accessTokenStrategy = Option(s.toLowerCase())))
-  opt[String]('v', "vault-name").text("Azure vault name").
-    action((s, c) =>
-      c.copy(azureVaultName = Option(s)))
-  opt[String]('s', "secret-name").text("Azure secret name").
-    action((s, c) =>
-      c.copy(azureSecretName = Option(s)))
   opt[String]('i', "identity-client-id").text("Azure identity client id").
     action((s, c) =>
       c.copy(azureIdentityClientId = Option(s)))
+  checkConfig(c =>
+    if (c.googleRequesterPaysProjectConflict)
+      failure("Requester pays project differs between positional argument and option flag")
+    else success
+  )
   checkConfig(c =>
     c.accessTokenStrategy match {
       case Some(Azure) if c.googleRequesterPaysProject.nonEmpty =>
         Left(s"Requester pays project is only valid with access token strategy '$Google'")
-      case Some(Azure) if List(c.azureVaultName, c.azureSecretName).exists(_.isEmpty) =>
-        Left(s"Both vault name and secret name must be specified for access token strategy $Azure")
+      case Some(Google) if c.azureIdentityClientId.nonEmpty =>
+        Left(s"Identity client id is only valid with access token strategy '$Azure'")
       case Some(Azure) => Right(())
-      case Some(Google) if List(c.azureSecretName, c.azureVaultName, c.azureIdentityClientId).forall(_.isEmpty) => Right(())
-      case Some(Google) => Left(s"One or more specified options are only valid with access token strategy '$Azure'")
+      case Some(Google) => Right(())
       case Some(huh) => Left(s"Unrecognized access token strategy '$huh'")
       case None => Left("Programmer error, access token strategy should not be None")
     }
   )
+  checkConfig(c =>
+    (c.drsObject, c.containerPath, c.manifestPath) match {
+      case (Some(_), Some(_), None) => Right(())
+      case (None, None, Some(_)) => Right(())
+      case _ => Left("Must provide either DRS path and container path, OR manifest file (-m).")
+    }
+  )
 }
 
 object CommandLineParser {
@@ -64,9 +79,12 @@ object CommandLineParser {
   val Usage =
     s"""
 Usage:
-    java -jar /path/to/localizer.jar [options] drs://provider/object /local/path/to/file.txt [requester pays project]
 
-    Note that the <requester pays project> optional argument is only valid with access token strategy 'Google'.
+    Can be run to localize a single file with DRS id and local container path provided in args:
+    java -jar /path/to/localizer.jar [options] drs://provider/object /local/path/to/file.txt
+
+    Can also be used to localize multiple files in one invocation with manifest file provided in args:
+    java -jar /path/to/localizer.jar [options] -m /local/path/to/manifest/file
     """
 
 }
@@ -75,6 +93,6 @@ case class CommandLineArguments(accessTokenStrategy: Option[String] = Option(Goo
                                 drsObject: Option[String] = None,
                                 containerPath: Option[String] = None,
                                 googleRequesterPaysProject: Option[String] = None,
-                                azureVaultName: Option[String] = None,
-                                azureSecretName: Option[String] = None,
-                                azureIdentityClientId: Option[String] = None)
+                                azureIdentityClientId: Option[String] = None,
+                                manifestPath: Option[String] = None,
+                                googleRequesterPaysProjectConflict: Boolean = false)
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
index ac27367b932..944d418acbb 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
@@ -1,10 +1,9 @@
 package drs.localizer
 
-import cloud.nio.impl.drs.{DrsConfig, DrsPathResolver}
+import cloud.nio.impl.drs.{DrsConfig, DrsCredentials, DrsPathResolver}
 import common.validation.ErrorOr.ErrorOr
-import drs.localizer.accesstokens.AccessTokenStrategy
 
 
-class DrsLocalizerDrsPathResolver(drsConfig: DrsConfig, accessTokenStrategy: AccessTokenStrategy) extends DrsPathResolver(drsConfig) {
-  override def getAccessToken: ErrorOr[String] = accessTokenStrategy.getAccessToken()
+class DrsLocalizerDrsPathResolver(drsConfig: DrsConfig, drsCredentials: DrsCredentials) extends DrsPathResolver(drsConfig) {
+  override def getAccessToken: ErrorOr[String] = drsCredentials.getAccessToken
 }
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
index c7ecdd3f3e4..1858f395024 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
@@ -2,16 +2,20 @@ package drs.localizer
 
 import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO, IOApp}
+import cats.implicits._
 import cloud.nio.impl.drs.DrsPathResolver.{FatalRetryDisposition, RegularRetryDisposition}
-import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsPathResolver, MarthaField}
+import cloud.nio.impl.drs._
 import cloud.nio.spi.{CloudNioBackoff, CloudNioSimpleExponentialBackoff}
 import com.typesafe.scalalogging.StrictLogging
 import drs.localizer.CommandLineParser.AccessTokenStrategy.{Azure, Google}
-import drs.localizer.accesstokens.{AccessTokenStrategy, AzureB2CAccessTokenStrategy, GoogleAccessTokenStrategy}
 import drs.localizer.downloaders.AccessUrlDownloader.Hashes
 import drs.localizer.downloaders._
+import org.apache.commons.csv.{CSVFormat, CSVParser}
 
+import java.io.File
+import java.nio.charset.Charset
 import scala.concurrent.duration._
+import scala.jdk.CollectionConverters._
 import scala.language.postfixOps
 
 object DrsLocalizerMain extends IOApp with StrictLogging {
@@ -24,8 +28,8 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
     val localize: Option[IO[ExitCode]] = for {
       pa <- parsedArgs
       run <- pa.accessTokenStrategy.collect {
-        case Azure => runLocalizer(pa, AzureB2CAccessTokenStrategy(pa))
-        case Google => runLocalizer(pa, GoogleAccessTokenStrategy)
+        case Azure => runLocalizer(pa, AzureDrsCredentials(pa.azureIdentityClientId))
+        case Google => runLocalizer(pa, GoogleAppDefaultTokenStrategy)
       }
     } yield run
 
@@ -50,23 +54,40 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
     IO.pure(ExitCode.Error)
   }
 
-  def runLocalizer(commandLineArguments: CommandLineArguments, accessTokenStrategy: AccessTokenStrategy): IO[ExitCode] = {
-    val drsObject = commandLineArguments.drsObject.get
-    val containerPath = commandLineArguments.containerPath.get
-    new DrsLocalizerMain(drsObject, containerPath, accessTokenStrategy, commandLineArguments.googleRequesterPaysProject).
+  def runLocalizer(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials): IO[ExitCode] = {
+    commandLineArguments.manifestPath match {
+      case Some(manifestPath) =>
+        val manifestFile = new File(manifestPath)
+        val csvParser = CSVParser.parse(manifestFile, Charset.defaultCharset(), CSVFormat.DEFAULT)
+        val exitCodes: IO[List[ExitCode]] = csvParser.asScala.map(record => {
+          val drsObject = record.get(0)
+          val containerPath = record.get(1)
+          localizeFile(commandLineArguments, drsCredentials, drsObject, containerPath)
+        }).toList.sequence
+        exitCodes.map(_.find(_ != ExitCode.Success).getOrElse(ExitCode.Success))
+      case None =>
+        val drsObject = commandLineArguments.drsObject.get
+        val containerPath = commandLineArguments.containerPath.get
+        localizeFile(commandLineArguments, drsCredentials, drsObject, containerPath)
+    }
+  }
+
+  private def localizeFile(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials, drsObject: String, containerPath: String) = {
+    new DrsLocalizerMain(drsObject, containerPath, drsCredentials, commandLineArguments.googleRequesterPaysProject).
       resolveAndDownloadWithRetries(downloadRetries = 3, checksumRetries = 1, defaultDownloaderFactory, Option(defaultBackoff)).map(_.exitCode)
   }
 }
 
 class DrsLocalizerMain(drsUrl: String,
                        downloadLoc: String,
-                       accessTokenStrategy: AccessTokenStrategy,
+                       drsCredentials: DrsCredentials,
                        requesterPaysProjectIdOption: Option[String]) extends StrictLogging {
 
   def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] = {
     IO {
       val drsConfig = DrsConfig.fromEnv(sys.env)
-      new DrsLocalizerDrsPathResolver(drsConfig, accessTokenStrategy)
+      logger.info(s"Using ${drsConfig.drsResolverUrl} to resolve DRS Objects")
+      new DrsLocalizerDrsPathResolver(drsConfig, drsCredentials)
     }
   }
 
@@ -121,17 +142,17 @@ class DrsLocalizerMain(drsUrl: String,
   }
 
   private [localizer] def resolve(downloaderFactory: DownloaderFactory): IO[Downloader] = {
-    val fields = NonEmptyList.of(MarthaField.GsUri, MarthaField.GoogleServiceAccount, MarthaField.AccessUrl, MarthaField.Hashes)
+    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl, DrsResolverField.Hashes)
     for {
       resolver <- getDrsPathResolver
-      marthaResponse <- resolver.resolveDrsThroughMartha(drsUrl, fields)
+      drsResolverResponse <- resolver.resolveDrs(drsUrl, fields)
 
-      // Currently Martha only supports resolving DRS paths to access URLs or GCS paths.
-      downloader <- (marthaResponse.accessUrl, marthaResponse.gsUri) match {
+      // Currently DRS Resolver only supports resolving DRS paths to access URLs or GCS paths.
+      downloader <- (drsResolverResponse.accessUrl, drsResolverResponse.gsUri) match {
         case (Some(accessUrl), _) =>
-          downloaderFactory.buildAccessUrlDownloader(accessUrl, downloadLoc, marthaResponse.hashes)
+          downloaderFactory.buildAccessUrlDownloader(accessUrl, downloadLoc, drsResolverResponse.hashes)
         case (_, Some(gcsPath)) =>
-          val serviceAccountJsonOption = marthaResponse.googleServiceAccount.map(_.data.spaces2)
+          val serviceAccountJsonOption = drsResolverResponse.googleServiceAccount.map(_.data.spaces2)
           downloaderFactory.buildGcsUriDownloader(
             gcsPath = gcsPath,
             serviceAccountJsonOption = serviceAccountJsonOption,
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AccessTokenStrategy.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AccessTokenStrategy.scala
deleted file mode 100644
index 756f5371c0f..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AccessTokenStrategy.scala
+++ /dev/null
@@ -1,7 +0,0 @@
-package drs.localizer.accesstokens
-
-import common.validation.ErrorOr.ErrorOr
-
-trait AccessTokenStrategy {
-  def getAccessToken(): ErrorOr[String]
-}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
deleted file mode 100644
index cf83171adf0..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/AzureB2CAccessTokenStrategy.scala
+++ /dev/null
@@ -1,40 +0,0 @@
-package drs.localizer.accesstokens
-
-import cats.syntax.validated._
-import com.azure.identity.DefaultAzureCredentialBuilder
-import com.azure.security.keyvault.secrets.{SecretClient, SecretClientBuilder}
-import common.validation.ErrorOr
-import common.validation.ErrorOr.{ErrorOr,ShortCircuitingFlatMap}
-import drs.localizer.CommandLineArguments
-
-case class AzureB2CAccessTokenStrategy(commandLineArguments: CommandLineArguments) extends AccessTokenStrategy {
-  override def getAccessToken(): ErrorOr[String] = {
-    commandLineArguments match {
-      case CommandLineArguments(_, _, _, _, Some(vault), Some(secret), clientId) =>
-        AzureKeyVaultClient(vault, clientId) flatMap { _.getSecret(secret) }
-      case invalid => s"Invalid command line arguments: $invalid".invalidNel
-    }
-  }
-}
-
-// Note: The AzureKeyVaultClient code here is basically a copy/paste of the code temporarily living in the TES backend.
-// All the current KeyVault interaction in Cromwell is temporary, but the code in the TES backend might be even more
-// temporary than this.
-class AzureKeyVaultClient(client: SecretClient) {
-  def getSecret(secretName: String): ErrorOr[String] = ErrorOr(client.getSecret(secretName).getValue)
-}
-
-object AzureKeyVaultClient {
-  def apply(vaultName: String, identityClientId: Option[String]): ErrorOr[AzureKeyVaultClient] = ErrorOr {
-    val credentialBuilder = identityClientId.foldLeft(new DefaultAzureCredentialBuilder()) {
-      (builder, clientId) => builder.managedIdentityClientId(clientId)
-    }
-
-    val client = new SecretClientBuilder()
-      .vaultUrl(s"https://${vaultName}.vault.azure.net")
-      .credential(credentialBuilder.build())
-      .buildClient()
-
-    new AzureKeyVaultClient(client)
-  }
-}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala
deleted file mode 100644
index 5af2b8af441..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/accesstokens/GoogleAccessTokenStrategy.scala
+++ /dev/null
@@ -1,28 +0,0 @@
-package drs.localizer.accesstokens
-
-import cats.syntax.validated._
-import com.google.auth.oauth2.GoogleCredentials
-import common.validation.ErrorOr.ErrorOr
-
-import scala.jdk.CollectionConverters._
-import scala.util.{Failure, Success, Try}
-
-/**
- * Strategy for obtaining an access token from Google Application Default credentials that are assumed to already exist.
- */
-case object GoogleAccessTokenStrategy extends AccessTokenStrategy {
-  private final val UserInfoEmailScope = "https://www.googleapis.com/auth/userinfo.email"
-  private final val UserInfoProfileScope = "https://www.googleapis.com/auth/userinfo.profile"
-  private final val UserInfoScopes = List(UserInfoEmailScope, UserInfoProfileScope)
-
-  override def getAccessToken(): ErrorOr[String] = {
-    Try {
-      val scopedCredentials = GoogleCredentials.getApplicationDefault().createScoped(UserInfoScopes.asJava)
-      scopedCredentials.refreshAccessToken().getTokenValue
-    } match {
-      case Success(null) => "null token value attempting to refresh access token".invalidNel
-      case Success(value) => value.validNel
-      case Failure(e) => s"Failed to refresh access token: ${e.getMessage}".invalidNel
-    }
-  }
-}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
index 345a14f63e4..d4c81af6300 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
@@ -19,7 +19,7 @@ case class GcsUriDownloader(gcsUrl: String,
 
     val copyProcess = serviceAccountJson match {
       case Some(sa) =>
-        // if Martha returned a SA, use that SA for gsutil instead of default credentials
+        // if DRS Resolver returned a SA, use that SA for gsutil instead of default credentials
         val tempCredentialDir: Path = Files.createTempDirectory("gcloudTemp_").toAbsolutePath
         val saJsonPath: Path = tempCredentialDir.resolve("sa.json")
         Files.write(saJsonPath, sa.getBytes(StandardCharsets.UTF_8))
@@ -27,7 +27,7 @@ case class GcsUriDownloader(gcsUrl: String,
         val copyCommand = Seq("bash", "-c", generateDownloadScript(gcsUrl, Option(saJsonPath)))
         Process(copyCommand, None, extraEnv.toSeq: _*)
       case None =>
-        // No SA returned from Martha. gsutil will use the application default credentials.
+        // No SA returned from DRS Resolver. gsutil will use the application default credentials.
         val copyCommand = Seq("bash", "-c", generateDownloadScript(gcsUrl, None))
         Process(copyCommand)
     }
@@ -50,11 +50,11 @@ case class GcsUriDownloader(gcsUrl: String,
     def setServiceAccount(): String = {
       saJsonPathOption match {
         case Some(saJsonPath) =>
-          s"""# Set gsutil to use the service account returned from Martha
+          s"""# Set gsutil to use the service account returned from the DRS Resolver
              |gcloud auth activate-service-account --key-file=$saJsonPath > gcloud_output.txt 2>&1
              |RC_GCLOUD=$$?
              |if [ "$$RC_GCLOUD" != "0" ]; then
-             |  echo "Failed to activate service account returned from Martha. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
+             |  echo "Failed to activate service account returned from the DRS Resolver. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
              |  exit "$$RC_GCLOUD"
              |else
              |  echo "Successfully activated service account; Will continue with download. $$(cat gcloud_output.txt)"
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
index 252971c0b5e..2a39a6543a3 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
@@ -4,9 +4,8 @@ import cats.syntax.validated._
 import cloud.nio.impl.drs.AccessUrl
 import common.validation.ErrorOr.ErrorOr
 import drs.localizer.downloaders.AccessUrlDownloader.Hashes
-import mouse.all.anySyntaxMouse
-import org.apache.commons.codec.binary.Base64.{decodeBase64, isBase64}
-import org.apache.commons.codec.binary.Hex.encodeHexString
+import org.apache.commons.codec.binary.Base64.encodeBase64String
+import org.apache.commons.codec.binary.Hex.decodeHex
 import org.apache.commons.text.StringEscapeUtils
 
 
@@ -26,23 +25,18 @@ sealed trait GetmChecksum {
 }
 
 case class Md5(override val rawValue: String) extends GetmChecksum {
-  override def value: ErrorOr[String] = {
-    val trimmed = rawValue.trim
-    if (trimmed.matches("[A-Fa-f0-9]+"))
-      trimmed.validNel
-    // TDR currently returns a base64-encoded MD5 because that's what Azure seems to do. However,
-    // the DRS spec does not specify that any checksums should be base64-encoded, and `getm` also
-    // does not expect base64. This case handles the current behavior in the short term until
-    // https://broadworkbench.atlassian.net/browse/DR-2259 is done.
-    else if (isBase64(trimmed))
-      (trimmed |> decodeBase64 |> encodeHexString).validNel
-    else
-      s"Invalid md5 checksum value is neither hex nor base64: $rawValue".invalidNel
-  }
+  override def value: ErrorOr[String] = GetmChecksum.validateHex(rawValue)
   override def getmAlgorithm: String = "md5"
 }
 
 case class Crc32c(override val rawValue: String) extends GetmChecksum {
+  // The DRS spec says that all hash values should be hex strings,
+  // but getm expects crc32c values to be base64.
+  override def value: ErrorOr[String] =
+    GetmChecksum.validateHex(rawValue)
+      .map(decodeHex)
+      .map(encodeBase64String)
+
   override def getmAlgorithm: String = "gs_crc32c"
 }
 case class AwsEtag(override val rawValue: String) extends GetmChecksum {
@@ -61,7 +55,7 @@ object GetmChecksum {
   def apply(hashes: Hashes, accessUrl: AccessUrl): GetmChecksum = {
     hashes match {
       case Some(hashes) if hashes.nonEmpty =>
-        // `hashes` is keyed by the Martha names for these hash algorithms, which in turn are the forwarded DRS
+        // `hashes` is keyed by the DRS Resolver names for these hash algorithms, which in turn are the forwarded DRS
         // providers' names for the algorithms. `getm` has its own notions of what these algorithms are called.
         // For the specific case of `md5` the algorithm names are the same between DRS providers and `getm`,
         // but all of the other algorithm names currently differ between DRS providers and `getm`.
@@ -88,4 +82,12 @@ object GetmChecksum {
       case _ => Null // None or an empty hashes map.
     }
   }
+
+  def validateHex(s: String): ErrorOr[String] = {
+    val trimmed = s.trim
+    if (trimmed.matches("[A-Fa-f0-9]+"))
+      trimmed.validNel
+    else
+      s"Invalid checksum value, expected hex but got: $trimmed".invalidNel
+  }
 }
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
index 3f7b96f5edc..7be30be8ac0 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
@@ -13,9 +13,8 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   private val drsObject = "drs://provider/object"
   private val containerPath = "/cromwell_root/my.bam"
   private val requesterPaysProject = "i_heart_egress"
-  private val azureVaultName = "Kwikset"
-  private val azureSecretName = "shhh"
   private val azureIdentityClientId = "itme@azure.com"
+  private val manifestPath = "/my/manifest.txt"
 
   behavior of "DRS Localizer command line parser"
 
@@ -38,67 +37,89 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject shouldBe empty
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
   it should "successfully parse with three arguments" in {
     val args = parser.parse(Array(drsObject, containerPath, requesterPaysProject), CommandLineArguments()).get
+    args.drsObject.get shouldBe drsObject
+    args.containerPath.get shouldBe containerPath
+    args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
+    args.googleRequesterPaysProject.get shouldBe requesterPaysProject
+    args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
+  }
+
+  it should "successfully parse requester pays project" in {
+    val args = parser.parse(Array(drsObject, containerPath, "-r", requesterPaysProject), CommandLineArguments()).get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject.get shouldBe requesterPaysProject
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
-  it should "successfully parse an explicit Google access token strategy invocation" in {
-    val args = parser.parse(Array("--access-token-strategy", "google", drsObject, containerPath, requesterPaysProject), CommandLineArguments()).get
+  it should "successfully parse with three arguments and requester pays project" in {
+    val args = parser.parse(Array(drsObject, containerPath, requesterPaysProject, "-r", requesterPaysProject), CommandLineArguments()).get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
     args.googleRequesterPaysProject.get shouldBe requesterPaysProject
-    args.azureVaultName shouldBe empty
-    args.azureSecretName shouldBe empty
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
-  it should "fail to parse an Azure invocation missing vault name and secret name" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      drsObject, containerPath), CommandLineArguments())
+  it should "fail if requester pays argument and flag specify different projects" in {
+    parser.parse(Array(drsObject, containerPath, requesterPaysProject, "-r", "boom!"), CommandLineArguments()) shouldBe None
+  }
 
-    args shouldBe None
+  it should "successfully parse args with a manifest file" in {
+    val args = parser.parse(Array("-m", manifestPath), CommandLineArguments()).get
+
+    args.drsObject shouldBe empty
+    args.containerPath shouldBe empty
+    args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
+    args.googleRequesterPaysProject shouldBe empty
+    args.azureIdentityClientId shouldBe empty
+    args.manifestPath.get shouldBe manifestPath
   }
 
-  it should "fail to parse an Azure invocation missing vault name" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--secret-name", azureSecretName,
-      drsObject, containerPath), CommandLineArguments())
+  it should "fail to parse with a manifest file and one single-file arg" in {
+    val args = parser.parse(Array(drsObject, "--manifest-path", manifestPath), CommandLineArguments())
+    args shouldBe None
+  }
 
+  it should "fail to parse with a manifest file and two single-file args" in {
+    val args = parser.parse(Array(drsObject, containerPath, "--manifest-path", manifestPath), CommandLineArguments())
     args shouldBe None
   }
 
-  it should "fail to parse an Azure invocation missing secret name" in {
+  it should "successfully parse an explicit Google access token strategy invocation" in {
     val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--vault-name", azureVaultName,
-      drsObject, containerPath), CommandLineArguments())
+      "--access-token-strategy", "google",
+      drsObject,
+      containerPath,
+      "--requester-pays-project", requesterPaysProject
+    ), CommandLineArguments()).get
 
-    args shouldBe None
+    args.drsObject.get shouldBe drsObject
+    args.containerPath.get shouldBe containerPath
+    args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Google
+    args.googleRequesterPaysProject.get shouldBe requesterPaysProject
+    args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
   it should "fail to parse an Azure invocation that specifies requester pays" in {
     val args = parser.parse(Array(
       "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--secret-name", azureSecretName,
-      "--vault-name", azureVaultName,
-      drsObject, containerPath, requesterPaysProject), CommandLineArguments())
+      drsObject,
+      containerPath,
+      "--requester-pays-project", requesterPaysProject), CommandLineArguments())
 
     args shouldBe None
   }
@@ -106,24 +127,19 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   it should "successfully parse an Azure invocation" in {
     val args = parser.parse(Array(
       "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--secret-name", azureSecretName,
-      "--vault-name", azureVaultName,
       drsObject, containerPath), CommandLineArguments()).get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Azure
     args.googleRequesterPaysProject shouldBe empty
-    args.azureVaultName.get shouldBe azureVaultName
-    args.azureSecretName.get shouldBe azureSecretName
     args.azureIdentityClientId shouldBe empty
+    args.manifestPath shouldBe empty
   }
 
-  it should "successfully parse an Azure invocation with all the trimmings" in {
+  it should "successfully parse an Azure invocation with identity" in {
     val args = parser.parse(Array(
       "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--vault-name", azureVaultName,
-      "--secret-name", azureSecretName,
       "--identity-client-id", azureIdentityClientId,
       drsObject, containerPath), CommandLineArguments()).get
 
@@ -131,9 +147,8 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     args.containerPath.get shouldBe containerPath
     args.accessTokenStrategy.get shouldBe AccessTokenStrategy.Azure
     args.googleRequesterPaysProject shouldBe empty
-    args.azureVaultName.get shouldBe azureVaultName
-    args.azureSecretName.get shouldBe azureSecretName
     args.azureIdentityClientId.get shouldBe azureIdentityClientId
+    args.manifestPath shouldBe empty
   }
 
   it should "fail to parse with an unrecognized access token strategy" in {
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
index 84b407cec41..66799fcc099 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
@@ -4,10 +4,10 @@ import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO}
 import cats.syntax.validated._
 import cloud.nio.impl.drs.DrsPathResolver.FatalRetryDisposition
-import cloud.nio.impl.drs.{AccessUrl, DrsConfig, MarthaField, MarthaResponse}
+import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsCredentials, DrsResolverField, DrsResolverResponse}
 import common.assertion.CromwellTimeoutSpec
+import common.validation.ErrorOr.ErrorOr
 import drs.localizer.MockDrsLocalizerDrsPathResolver.{FakeAccessTokenStrategy, FakeHashes}
-import drs.localizer.accesstokens.AccessTokenStrategy
 import drs.localizer.downloaders.AccessUrlDownloader.Hashes
 import drs.localizer.downloaders._
 import org.scalatest.flatspec.AnyFlatSpec
@@ -49,12 +49,12 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync() shouldBe expected
   }
 
-  it should "fail and throw error if Martha response does not have gs:// url" in {
+  it should "fail and throw error if the DRS Resolver response does not have gs:// url" in {
     val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithoutAnyResolution, fakeDownloadLocation, None)
 
     the[RuntimeException] thrownBy {
       mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync()
-    } should have message "No access URL nor GCS URI starting with 'gs://' found in Martha response!"
+    } should have message "No access URL nor GCS URI starting with 'gs://' found in the DRS Resolver response!"
   }
 
   it should "resolve to use the correct downloader for an access url" in {
@@ -67,7 +67,7 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync() shouldBe expected
   }
 
-  it should "resolve to use the correct downloader for an access url when the Martha response also contains a gs url" in {
+  it should "resolve to use the correct downloader for an access url when the DRS Resolver response also contains a gs url" in {
     val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithAccessUrlAndGcsResolution, fakeDownloadLocation, None)
     val expected = AccessUrlDownloader(
       accessUrl = AccessUrl(url = "http://abc/def/ghi.bam", headers = None), downloadLoc = fakeDownloadLocation,
@@ -315,23 +315,23 @@ class MockDrsLocalizerMain(drsUrl: String,
 class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig) extends
   DrsLocalizerDrsPathResolver(drsConfig, FakeAccessTokenStrategy) {
 
-  override def resolveDrsThroughMartha(drsPath: String, fields: NonEmptyList[MarthaField.Value]): IO[MarthaResponse] = {
-    val marthaResponse = MarthaResponse(
+  override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
+    val drsResolverResponse = DrsResolverResponse(
       size = Option(1234),
       hashes = FakeHashes
     )
 
     IO.pure(drsPath) map {
       case MockDrsPaths.fakeDrsUrlWithGcsResolutionOnly =>
-        marthaResponse.copy(
+        drsResolverResponse.copy(
           gsUri = Option("gs://abc/foo-123/abc123"))
       case MockDrsPaths.fakeDrsUrlWithoutAnyResolution =>
-        marthaResponse
+        drsResolverResponse
       case MockDrsPaths.fakeDrsUrlWithAccessUrlResolutionOnly =>
-        marthaResponse.copy(
+        drsResolverResponse.copy(
           accessUrl = Option(AccessUrl(url = "http://abc/def/ghi.bam", headers = None)))
       case MockDrsPaths.fakeDrsUrlWithAccessUrlAndGcsResolution =>
-        marthaResponse.copy(
+        drsResolverResponse.copy(
           accessUrl = Option(AccessUrl(url = "http://abc/def/ghi.bam", headers = None)),
           gsUri = Option("gs://some/uri"))
       case e => throw new RuntimeException(s"Unexpected exception in DRS localization test code: $e")
@@ -341,5 +341,7 @@ class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig) extends
 
 object MockDrsLocalizerDrsPathResolver {
   val FakeHashes: Option[Map[String, String]] = Option(Map("md5" -> "abc123", "crc32c" -> "34fd67"))
-  val FakeAccessTokenStrategy: AccessTokenStrategy = () => "testing code: do not call me".invalidNel
+  val FakeAccessTokenStrategy: DrsCredentials = new DrsCredentials {
+    override def getAccessToken: ErrorOr[String] = "testing code: do not call me".invalidNel
+  }
 }
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala
index 66c4ff6fabd..07eb5ede181 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GcsUriDownloaderSpec.scala
@@ -11,7 +11,7 @@ class GcsUriDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
   val fakeDownloadLocation = "/root/foo/foo-123.bam"
   val fakeRequesterPaysId = "fake-billing-project"
 
-  it should "return correct download script for a drs url without Requester Pays ID and Google SA returned from Martha" in {
+  it should "return correct download script for a drs url without Requester Pays ID and Google SA returned from the DRS Resolver" in {
     val gcsUrl = "gs://foo/bar.bam"
     val downloader = new GcsUriDownloader(
       gcsUrl = gcsUrl,
@@ -44,7 +44,7 @@ class GcsUriDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     downloader.generateDownloadScript(gcsUrl = gcsUrl, saJsonPathOption = None) shouldBe expectedDownloadScript
   }
 
-  it should "inject Requester Pays flag & gcloud auth using SA returned from Martha" in {
+  it should "inject Requester Pays flag & gcloud auth using SA returned from the DRS Resolver" in {
     val gcsUrl = "gs://foo/bar.bam"
     val downloader = new GcsUriDownloader(
       gcsUrl = gcsUrl,
@@ -60,11 +60,11 @@ class GcsUriDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
       s"""set -euo pipefail
          |set +e
          |
-         |# Set gsutil to use the service account returned from Martha
+         |# Set gsutil to use the service account returned from the DRS Resolver
          |gcloud auth activate-service-account --key-file=${fakeSAJsonPath.toString} > gcloud_output.txt 2>&1
          |RC_GCLOUD=$$?
          |if [ "$$RC_GCLOUD" != "0" ]; then
-         |  echo "Failed to activate service account returned from Martha. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
+         |  echo "Failed to activate service account returned from the DRS Resolver. File won't be downloaded. Error: $$(cat gcloud_output.txt)" >&2
          |  exit "$$RC_GCLOUD"
          |else
          |  echo "Successfully activated service account; Will continue with download. $$(cat gcloud_output.txt)"
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
index 24ea087cb8f..69c063ff616 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
@@ -31,9 +31,10 @@ class GetmChecksumSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     val results = Table(
       ("description", "algorithm", "expected"),
       ("md5 hex", Md5("abcdef"), "--checksum-algorithm 'md5' --checksum abcdef".validNel),
-      ("md5 base64", Md5("cR84lXY1y17c3q7/7riLEA=="), "--checksum-algorithm 'md5' --checksum 711f38957635cb5edcdeaeffeeb88b10".validNel),
-      ("md5 gibberish", Md5("what is this???"), "Invalid md5 checksum value is neither hex nor base64: what is this???".invalidNel),
-      ("crc32c", Crc32c("012345"), "--checksum-algorithm 'gs_crc32c' --checksum 012345".validNel),
+      ("md5 base64", Md5("cR84lXY1y17c3q7/7riLEA=="), "Invalid checksum value, expected hex but got: cR84lXY1y17c3q7/7riLEA==".invalidNel),
+      ("md5 gibberish", Md5("what is this???"), "Invalid checksum value, expected hex but got: what is this???".invalidNel),
+      ("crc32c", Crc32c("012345"), "--checksum-algorithm 'gs_crc32c' --checksum ASNF".validNel),
+      ("crc32c gibberish", Crc32c("????"), "Invalid checksum value, expected hex but got: ????".invalidNel),
       ("AWS ETag", AwsEtag("012345"), "--checksum-algorithm 's3_etag' --checksum 012345".validNel),
       // Escape checksum values constructed from unvalidated data returned by DRS servers.
       ("Unsupported", Unsupported("Robert'); DROP TABLE Students;\n --\\"), raw"--checksum-algorithm 'null' --checksum Robert\'\)\;\ DROP\ TABLE\ Students\;\ --\\".validNel),
@@ -46,4 +47,19 @@ class GetmChecksumSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
       }
     }
   }
+
+  it should "correctly validate hex strings" in {
+    val results = Table(
+      ("test string", "expected"),
+      ("", "Invalid checksum value, expected hex but got: ".invalidNel),
+      (" ", "Invalid checksum value, expected hex but got: ".invalidNel),
+      ("myfavoritestring", "Invalid checksum value, expected hex but got: myfavoritestring".invalidNel),
+      (" AbC123 ", "AbC123".validNel),
+      ("456", "456".validNel),
+    )
+
+    forAll(results) { (testString, expected) =>
+      GetmChecksum.validateHex(testString) shouldBe expected
+    }
+  }
 }
diff --git a/cromwell.example.backends/cromwell.examples.conf b/cromwell.example.backends/cromwell.examples.conf
index 49b676a2c7c..4ca250d1202 100644
--- a/cromwell.example.backends/cromwell.examples.conf
+++ b/cromwell.example.backends/cromwell.examples.conf
@@ -308,17 +308,6 @@ languages {
       }
     }
   }
-  CWL {
-    versions {
-      "v1.0" {
-        # language-factory = "languages.cwl.CwlV1_0LanguageFactory"
-        # config {
-        #   strict-validation: false
-        #   enabled: true
-        # }
-      }
-    }
-  }
 }
 
 # Here is where you can define the backend providers that Cromwell understands.
diff --git a/cwl/src/main/resources/reference.conf b/cwl/src/main/resources/reference.conf
deleted file mode 100644
index 0d0d8a980f9..00000000000
--- a/cwl/src/main/resources/reference.conf
+++ /dev/null
@@ -1,3 +0,0 @@
-cwltool-runner {
-  class = "cwl.CwltoolHeterodon"
-}
diff --git a/cwl/src/main/scala/cwl/ArgumentToCommandPart.scala b/cwl/src/main/scala/cwl/ArgumentToCommandPart.scala
deleted file mode 100644
index ca67eaa7ab3..00000000000
--- a/cwl/src/main/scala/cwl/ArgumentToCommandPart.scala
+++ /dev/null
@@ -1,26 +0,0 @@
-package cwl
-
-import cwl.command.StringCommandPart
-import shapeless._
-import wom.CommandPart
-
-object ArgumentToCommandPart extends Poly1 {
-  type MakeCommandPart = (Boolean, ExpressionLib) => CommandPart
-  implicit def caseStringOrExpression: Case.Aux[StringOrExpression, MakeCommandPart] = at {
-    _.fold(this)
-  }
-
-  implicit def caseExpression: Case.Aux[Expression, MakeCommandPart] = at {
-    CwlExpressionCommandPart.apply
-  }
-
-  implicit def caseString: Case.Aux[String, MakeCommandPart] = at {
-    string =>
-      (_, _) =>
-        StringCommandPart(string)
-  }
-
-  implicit def caseCommandLineBinding: Case.Aux[ArgumentCommandLineBinding, MakeCommandPart] = at {
-    ArgumentCommandLineBindingCommandPart.apply
-  }
-}
diff --git a/cwl/src/main/scala/cwl/BaseCommandToCommandParts.scala b/cwl/src/main/scala/cwl/BaseCommandToCommandParts.scala
deleted file mode 100644
index 2f597918082..00000000000
--- a/cwl/src/main/scala/cwl/BaseCommandToCommandParts.scala
+++ /dev/null
@@ -1,11 +0,0 @@
-package cwl
-
-import cwl.command.StringCommandPart
-import shapeless.Poly1
-import wom.CommandPart
-
-object BaseCommandToCommandParts extends Poly1 {
-  implicit def one = at[String] { Seq(_).map(StringCommandPart.apply): Seq[CommandPart] }
-
-  implicit def many = at[Array[String]] { _.toSeq.map(StringCommandPart.apply): Seq[CommandPart] }
-}
diff --git a/cwl/src/main/scala/cwl/CommandLineTool.scala b/cwl/src/main/scala/cwl/CommandLineTool.scala
deleted file mode 100644
index 49a2de8c861..00000000000
--- a/cwl/src/main/scala/cwl/CommandLineTool.scala
+++ /dev/null
@@ -1,439 +0,0 @@
-package cwl
-
-import cats.data.{NonEmptyList, OptionT}
-import cats.syntax.apply._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cats.instances.future._
-import common.Checked
-import common.validation.ErrorOr._
-import cwl.CommandLineTool._
-import cwl.CwlVersion._
-import cwl.internal.CommandPartSortingAlgorithm
-import io.circe.Json
-import shapeless.syntax.singleton._
-import shapeless.{:+:, CNil, Coproduct, Poly1, Witness}
-import wom.callable.CommandTaskDefinition.{EvaluatedOutputs, OutputFunctionResponse}
-import wom.callable.{Callable, CallableTaskDefinition, ContainerizedInputExpression}
-import wom.expression.{IoFunctionSet, ValueAsAnExpression, WomExpression}
-import wom.graph.GraphNodePort.OutputPort
-import wom.types.{WomArrayType, WomIntegerType, WomOptionalType}
-import wom.util.YamlUtils
-import wom.values.{WomArray, WomEvaluatedCallInputs, WomGlobFile, WomInteger, WomString, WomValue}
-import wom.{CommandPart, RuntimeAttributes, RuntimeAttributesKeys}
-
-import scala.concurrent.{ExecutionContext, Future}
-import scala.math.Ordering
-
-/**
-  * @param `class` This _should_ always be "CommandLineTool," however the spec does not -er- specify this.
-  */
-case class CommandLineTool private(
-                                    inputs: Array[CommandInputParameter],
-                                    outputs: Array[CommandOutputParameter],
-                                    `class`: Witness.`"CommandLineTool"`.T,
-                                    id: String,
-                                    requirements: Option[Array[Requirement]],
-                                    hints: Option[Array[Hint]],
-                                    label: Option[String],
-                                    doc: Option[String],
-                                    cwlVersion: Option[CwlVersion],
-                                    baseCommand: Option[BaseCommand],
-                                    arguments: Option[Array[CommandLineTool.Argument]],
-                                    stdin: Option[StringOrExpression],
-                                    stderr: Option[StringOrExpression],
-                                    stdout: Option[StringOrExpression],
-                                    successCodes: Option[Array[Int]],
-                                    temporaryFailCodes: Option[Array[Int]],
-                                    permanentFailCodes: Option[Array[Int]],
-                                    `$namespaces`: Option[Map[String, String]],
-                                    `$schemas`: Option[Array[String]]
-                                  ) extends Tool {
-
-  def asCwl: Cwl = Coproduct[Cwl](this)
-
-  lazy val baseCommandPart: List[CommandPart] = baseCommand.toList.flatMap(_.fold(BaseCommandToCommandParts))
-
-  /*
-   * The command template is built following the rules described here: http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-   * - The baseCommand goes first
-   * - Then the arguments are assigned a sorting key and transformed into a CommandPart
-   * - Finally the inputs are folded one by one into a CommandPartsList
-   * - arguments and inputs CommandParts are sorted according to their sort key
-   */
-  private [cwl] def buildCommandTemplate: CommandPartExpression[List[CommandPart]] =
-    (
-      CommandPartSortingAlgorithm.inputBindingsCommandParts(inputs),
-      CommandPartSortingAlgorithm.argumentCommandParts(arguments)
-    ).mapN ( _ ++ _ ).
-      //sort the highest level, then recursively pull in the nested (and sorted) command parts within each SortKeyAndCommandPart
-      map{ _.sorted.flatMap(_.sortedCommandParts) }.
-      map(baseCommandPart ++ _)
-
-  // This seems like it makes sense only for CommandLineTool and hence is not abstracted in Tool. If this assumption is wrong it could be moved up.
-  private def environmentDefs(requirementsAndHints: List[Requirement], expressionLib: ExpressionLib): ErrorOr[Map[String, WomExpression]] = {
-    // For environment variables we need to make sure that we aren't being asked to evaluate expressions from a containing
-    // workflow step or its containing workflow or anything containing the workflow. The current structure of this code
-    // is not prepared to evaluate those expressions. Actually this is true for attributes too and we're totally not
-    // checking for this condition there. Blurgh.
-    // TODO CWL: for runtime attributes, detect unevaluatable expressions in the containment hierarchy.
-
-    // This traverses all `EnvironmentDef`s within all `EnvVarRequirement`s. The spec doesn't appear to say how to handle
-    // duplicate `envName` keys in a single array of `EnvironmentDef`s; this code gives precedence to the last occurrence.
-    val allEnvVarDefs = for {
-      req <- requirementsAndHints
-      envVarReq <- req.select[EnvVarRequirement].toList
-      // Reverse the defs within an env var requirement so that when we fold from the right below the later defs
-      // will take precedence over the earlier defs.
-      envDef <- envVarReq.envDef.toList.reverse
-    } yield envDef
-
-    // Compact the `EnvironmentDef`s. Don't convert to `WomExpression`s yet, the `StringOrExpression`s need to be
-    // compared to the `EnvVarRequirement`s that were defined on this tool.
-    val effectiveEnvironmentDefs = allEnvVarDefs.foldRight(Map.empty[String, StringOrExpression]) {
-      case (envVarReq, envVarMap) => envVarMap + (envVarReq.envName -> envVarReq.envValue)
-    }
-
-    // These are the effective environment defs irrespective of where they were found in the
-    // Run / WorkflowStep / Workflow containment hierarchy.
-    val effectiveExpressionEnvironmentDefs = effectiveEnvironmentDefs filter { case (_, expr) => expr.select[Expression].isDefined }
-
-    // These are only the environment defs defined on this tool.
-    val cltRequirements = requirements.toList.flatten ++ hints.toList.flatten.flatMap(_.select[Requirement])
-    val cltEnvironmentDefExpressions = (for {
-      cltEnvVarRequirement <- cltRequirements flatMap {
-        _.select[EnvVarRequirement]
-      }
-      cltEnvironmentDef <- cltEnvVarRequirement.envDef.toList
-      expr <- cltEnvironmentDef.envValue.select[Expression].toList
-    } yield expr).toSet
-
-    // If there is an expression in an effective environment def that wasn't defined on this tool then error out since
-    // there isn't currently a way of evaluating it.
-    val unevaluatableEnvironmentDefs = for {
-      (name, stringOrExpression) <- effectiveExpressionEnvironmentDefs.toList
-      expression <- stringOrExpression.select[Expression].toList
-      if !cltEnvironmentDefExpressions.contains(expression)
-    } yield name
-
-    unevaluatableEnvironmentDefs match {
-      case Nil =>
-        // No unevaluatable environment defs => keep on truckin'
-        effectiveEnvironmentDefs.foldRight(Map.empty[String, WomExpression]) { case ((envName, envValue), acc) =>
-          acc + (envName -> envValue.fold(StringOrExpressionToWomExpression).apply(inputNames, expressionLib))
-        }.validNel
-      case xs =>
-        s"Could not evaluate environment variable expressions defined in the call hierarchy of tool $id: ${xs.mkString(", ")}.".invalidNel
-    }
-  }
-
-  /*
-    * Custom evaluation of the outputs of the command line tool (custom as in bypasses the engine provided default implementation).
-    * This is needed because the output of a CWL tool might be defined by the presence of a cwl.output.json file in the output directory.
-    * In that case, the content of the file should be used as output. This means that otherwise provided output expressions should not be evaluated.
-    * This method checks for the existence of this file, and optionally return a Map[OutputPort, WomValue] if the file was found.
-    * It ensures all the output ports of the corresponding WomCallNode get a WomValue which is needed for the engine to keep running the workflow properly.
-    * If the json file happens to be missing values for one or more output ports, it's a failure.
-    * If the file is not present, an empty value is returned and the engine will execute its own output evaluation logic.
-    *
-    * TODO: use IO instead of Future ?
-   */
-  final private def outputEvaluationJsonFunction(outputPorts: Set[OutputPort],
-                                                 inputs: Map[String, WomValue],
-                                                 ioFunctionSet: IoFunctionSet,
-                                                 executionContext: ExecutionContext): OutputFunctionResponse = {
-    implicit val ec = executionContext
-    import cats.syntax.either._
-
-    // Convert the parsed json to Wom-usable output values
-    def jsonToOutputs(json: Map[String, Json]): Checked[List[(OutputPort, WomValue)]] = {
-
-      outputPorts.toList.traverse[ErrorOr, (OutputPort, WomValue)]({ outputPort =>
-        // If the type is optional, then we can set the value to none if there's nothing in the json
-        def emptyValue = outputPort.womType match {
-          case optional: WomOptionalType => Option((outputPort -> optional.none).validNel)
-          case _ => None
-        }
-
-        json.get(outputPort.internalName)
-          .map(
-            _.foldWith(CwlJsonToDelayedCoercionFunction).apply(outputPort.womType)
-              .map(outputPort -> _)
-          )
-          .orElse(emptyValue)
-          .getOrElse(s"Cannot find a value for output ${outputPort.internalName} in output json $json".invalidNel)
-      }).toEither
-    }
-
-    // Parse content as json and return output values for each output port
-    def parseContent(content: String): EvaluatedOutputs = {
-      val yaml = YamlUtils.parse(content)
-      for {
-        parsed <- yaml.flatMap(_.as[Map[String, Json]]).leftMap(error => NonEmptyList.one(error.getMessage))
-        jobOutputsMap <- jsonToOutputs(parsed)
-      } yield jobOutputsMap.toMap
-    }
-
-    for {
-      // Glob for "cwl.output.json"
-      outputJsonGlobs <- OptionT.liftF { ioFunctionSet.glob(CwlOutputJson) }
-      // There can only be 0 or 1, so try to take the head of the list
-      outputJsonFile <- OptionT.fromOption[Future] { outputJsonGlobs.headOption }
-      // Read the content using the ioFunctionSet.readFile function
-      content <- OptionT.liftF { ioFunctionSet.readFile(outputJsonFile, None, failOnOverflow = false) }
-      // parse the content and validate it
-      outputs = parseContent(content)
-    } yield outputs
-  }
-
-  override protected def toolAttributes: Map[String, WomExpression] = {
-    val codes: List[Int] = successCodes match {
-      case Some(c) => c.toList // Use the provided list of success codes.
-      case None => List(0) // Default to allowing only 0 for a success code.
-    }
-
-    val arr = WomArray(WomArrayType(WomIntegerType), codes map WomInteger.apply)
-    Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> ValueAsAnExpression(arr))
-  }
-
-  override def buildTaskDefinition(taskName: String,
-                          inputDefinitions: List[_ <: Callable.InputDefinition],
-                          outputDefinitions: List[Callable.OutputDefinition],
-                          runtimeAttributes: RuntimeAttributes,
-                          requirementsAndHints: List[cwl.Requirement],
-                          expressionLib: ExpressionLib): ErrorOr[CallableTaskDefinition] = {
-
-    def redirect(soe: Option[StringOrExpression]): Option[WomExpression] = soe map {
-      _.fold(StringOrExpressionToWomExpression).apply(inputNames, expressionLib)
-    }
-
-    // This seems like it makes sense only for CommandLineTool and hence is not abstracted in Tool. If this assumption is wrong it could be moved up.
-    val adHocFileCreations: Set[ContainerizedInputExpression] = (for {
-      requirements <- requirements.getOrElse(Array.empty[Requirement])
-      initialWorkDirRequirement <- requirements.select[InitialWorkDirRequirement].toArray
-      listing <- initialWorkDirRequirement.listings
-    } yield InitialWorkDirFileGeneratorExpression(listing, expressionLib)).toSet[ContainerizedInputExpression]
-
-    val dockerOutputDirectory = requirementsAndHints
-      .flatMap(_.select[DockerRequirement])
-      .flatMap(_.dockerOutputDirectory)
-      .headOption
-
-    def inputsToCommandParts(inputs: WomEvaluatedCallInputs) : ErrorOr[Seq[CommandPart]] =
-     buildCommandTemplate.run((RequirementsAndHints(requirementsAndHints), expressionLib, inputs))
-
-    environmentDefs(requirementsAndHints, expressionLib) map { environmentExpressions =>
-      CallableTaskDefinition(
-        taskName,
-        inputsToCommandParts,
-        runtimeAttributes,
-        Map.empty,
-        Map.empty,
-        outputDefinitions,
-        inputDefinitions,
-        adHocFileCreation = adHocFileCreations,
-        environmentExpressions = environmentExpressions,
-        // TODO: This doesn't work in all cases and it feels clunky anyway - find a way to sort that out
-        prefixSeparator = "#",
-        commandPartSeparator = " ",
-        stdinRedirection = redirect(stdin),
-        stdoutOverride = redirect(stdout),
-        stderrOverride = redirect(stderr),
-        additionalGlob = Option(WomGlobFile(CwlOutputJson)),
-        customizedOutputEvaluation = outputEvaluationJsonFunction,
-        homeOverride = Option(_.outputPath),
-        dockerOutputDirectory = dockerOutputDirectory,
-        sourceLocation = None
-      )
-    }
-  }
-}
-
-object CommandLineTool {
-  val CwlOutputJson = "cwl.output.json"
-
-  val DefaultPosition = Coproduct[StringOrInt](0)
-
-  // Elements of the sorting key can be either Strings or Ints
-  type StringOrInt = String :+: Int :+: CNil
-  object StringOrInt {
-    object String { def unapply(stringOrInt: StringOrInt): Option[String] = stringOrInt.select[String] }
-    object Int { def unapply(stringOrInt: StringOrInt): Option[Int] = stringOrInt.select[Int] }
-  }
-
-  /*
-   * The algorithm described here http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding to sort the command line parts
-   * uses a sorting key assigned to each binding. This class represents such a key
-   */
-  object CommandBindingSortingKey {
-    def empty = CommandBindingSortingKey(List.empty, List.empty)
-  }
-  case class CommandBindingSortingKey(head: List[StringOrInt],
-                                      tail: List[StringOrInt] = List.empty) {
-    val value = head ++ tail
-
-    def append(binding: Option[CommandLineBinding], name: StringOrInt): CommandBindingSortingKey = binding match {
-      // If there's an input binding, add the position to the key (or 0)
-      case Some(b) =>
-        // The spec is inconsistent about this as it says "If position is not specified, it is not added to the sorting key"
-        // but also that the position defaults to 0. cwltool uses 0 when there's no position so we'll do that too.
-        val position = b.position.map(Coproduct[StringOrInt](_)) getOrElse DefaultPosition
-        copy(head = head :+ position, tail = tail :+ name)
-      // Otherwise do nothing
-      case None => this
-    }
-
-    /**
-      * Creates a new key with head and tail combined into the new head.
-      */
-    def asNewKey = CommandBindingSortingKey(value)
-  }
-
-  // Maps a sorting key to its (sorted) bindings
-  case class SortKeyAndCommandPart(
-    sortingKey: CommandBindingSortingKey,
-    commandPart: CommandPart,
-    nestedCommandParts: List[SortKeyAndCommandPart] = List.empty) {
-      def sortedCommandParts:List[CommandPart] =
-        List(commandPart) ++ nestedCommandParts.sorted.flatMap(_.sortedCommandParts)
-    }
-
-  type CommandPartsList = List[SortKeyAndCommandPart]
-
-  // Ordering for CommandBindingSortingKeyElement
-  implicit val SortingKeyTypeOrdering: Ordering[StringOrInt] = Ordering.fromLessThan[StringOrInt]({
-    // String comparison
-    case (StringOrInt.String(s1), StringOrInt.String(s2)) => s1 < s2
-    // Int comparison
-    case (StringOrInt.Int(i1), StringOrInt.Int(i2)) => i1 < i2
-    // Int < String (from the spec: "Numeric entries sort before strings.")
-    case (StringOrInt.Int(_), StringOrInt.String(_)) => true
-    // String > Int
-    case (StringOrInt.String(_), StringOrInt.Int(_)) => false
-    case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-  })
-
-  // https://github.com/scala/bug/issues/4097#issuecomment-292388627
-  implicit def IterableSubclass[CC[X] <: Iterable[X], T: Ordering] : Ordering[CC[T]] = {
-    new Ordering[CC[T]] {
-      val ord = implicitly[Ordering[T]]
-      def compare(x: CC[T], y: CC[T]): Int = {
-        val xe = x.iterator
-        val ye = y.iterator
-
-        while (xe.hasNext && ye.hasNext) {
-          val res = ord.compare(xe.next(), ye.next())
-          if (res != 0) return res
-        }
-
-        Ordering.Boolean.compare(xe.hasNext, ye.hasNext)
-      }
-    }
-  }
-
-  // Ordering for a CommandBindingSortingKey
-  implicit val SortingKeyOrdering: Ordering[CommandBindingSortingKey] = Ordering.by(_.value)
-
-  // Ordering for a CommandPartSortMapping: order by sorting key
-  implicit val SortKeyAndCommandPartOrdering: Ordering[SortKeyAndCommandPart] = Ordering.by(_.sortingKey)
-
-  def apply(inputs: Array[CommandInputParameter] = Array.empty,
-            outputs: Array[CommandOutputParameter] = Array.empty,
-            id: String,
-            requirements: Option[Array[Requirement]] = None,
-            hints: Option[Array[Hint]] = None,
-            label: Option[String] = None,
-            doc: Option[String] = None,
-            cwlVersion: Option[CwlVersion] = Option(CwlVersion.Version1),
-            baseCommand: Option[BaseCommand] = None,
-            arguments: Option[Array[CommandLineTool.Argument]] = None,
-            stdin: Option[StringOrExpression] = None,
-            stderr: Option[StringOrExpression] = None,
-            stdout: Option[StringOrExpression] = None,
-            successCodes: Option[Array[Int]] = None,
-            temporaryFailCodes: Option[Array[Int]] = None,
-            permanentFailCodes: Option[Array[Int]] = None,
-            namespaces: Option[Map[String, String]] = None,
-            schemas: Option[Array[String]] = None
-           ): CommandLineTool = {
-    CommandLineTool(
-      inputs,
-      outputs,
-      "CommandLineTool".narrow,
-      id,
-      requirements,
-      hints,
-      label,
-      doc,
-      cwlVersion,
-      baseCommand,
-      arguments,
-      stdin,
-      stderr,
-      stdout,
-      successCodes,
-      temporaryFailCodes,
-      permanentFailCodes,
-      namespaces,
-      schemas
-    )
-  }
-
-  type BaseCommand = SingleOrArrayOfStrings
-
-  type Argument = ArgumentCommandLineBinding :+: StringOrExpression :+: CNil
-
-  case class CommandInputParameter(
-                                    id: String,
-                                    label: Option[String] = None,
-                                    secondaryFiles: Option[SecondaryFiles] = None,
-                                    format: Option[InputParameterFormat] = None, //only valid when type: File
-                                    streamable: Option[Boolean] = None, //only valid when type: File
-                                    doc: Option[Doc] = None,
-                                    inputBinding: Option[InputCommandLineBinding] = None,
-                                    default: Option[CwlAny] = None,
-                                    `type`: Option[MyriadInputType] = None) extends InputParameter
-
-  case class CommandOutputParameter(
-                                     id: String,
-                                     label: Option[String] = None,
-                                     secondaryFiles: Option[SecondaryFiles] = None,
-                                     format: Option[OutputParameterFormat] = None, //only valid when type: File
-                                     streamable: Option[Boolean] = None, //only valid when type: File
-                                     doc: Option[Doc] = None,
-                                     outputBinding: Option[CommandOutputBinding] = None,
-                                     `type`: Option[MyriadOutputType] = None) extends OutputParameter {
-
-    /** Overridden to strip off the intentionally uniquified bits and leave only the stuff that we want to look
-      * at for the purposes of determining cache hits.
-      *
-      * before:
-      *
-      * CommandOutputParameter(file:///var/folders/qh/vvrlr2q92mvb9bb45sttxll4y3gg2g/T/e17762d1-9921-46c5-833e-cb47e3c3bdfd.temp.1197611185902619026/e17762d1-9921-46c5-833e-cb47e3c3bdfd.cwl#ps/ea5165fc-8948-43ae-8dec-3c0468b56bcb/ps-stdOut,None,None,None,None,None,Some(CommandOutputBinding(Some(Inl(Inr(Inl(ps-stdOut.txt)))),None,None)),Some(Inl(Inl(File))))
-      *
-      * after:
-      *
-      * CommandOutputParameter(ps-stdOut,None,None,None,None,None,Some(CommandOutputBinding(Some(Inl(Inr(Inl(ps-stdOut.txt)))),None,None)),Some(Inl(Inl(File))))
-      *
-      * This is possibly too strict (i.e. some of these fields may be irrelevant for cache hit determination), but preferable
-      * to having false positives.
-      * Also two coproduct types that can be either single or Arrays have custom stringifying folds for arrays. */
-    override def cacheString: String = {
-      val cacheableId: String = id.substring(id.lastIndexOf('/') + 1)
-      val cacheableSecondaryFiles = secondaryFiles map { _.fold(SecondaryFilesCacheableString)}
-      val cacheableType: Option[String] = `type`.map(_.fold(MyriadOutputTypeCacheableString))
-      s"CommandOutputParameter($cacheableId,$label,$cacheableSecondaryFiles,$format,$streamable,$doc,$outputBinding,$cacheableType)"
-    }
-  }
-}
-
-object StringOrExpressionToWomExpression extends Poly1 {
-  implicit def string: Case.Aux[String, (Set[String], ExpressionLib) => WomExpression] = at[String] { s => (inputNames, expressionLib) =>
-    ValueAsAnExpression(WomString(s))
-  }
-
-  implicit def expression: Case.Aux[Expression, (Set[String], ExpressionLib) => WomExpression] = at[Expression] { e => (inputNames, expressionLib) =>
-    cwl.ECMAScriptWomExpression(e, inputNames, expressionLib)
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CommandOutputBinding.scala b/cwl/src/main/scala/cwl/CommandOutputBinding.scala
deleted file mode 100644
index bab616f2995..00000000000
--- a/cwl/src/main/scala/cwl/CommandOutputBinding.scala
+++ /dev/null
@@ -1,295 +0,0 @@
-package cwl
-
-import cats.effect.IO
-import cats.effect.IO._
-import cats.syntax.functor._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.syntax.parallel._
-import cats.instances.list._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import wom.expression.IoFunctionSet.{IoDirectory, IoFile}
-import wom.expression.{FileEvaluation, IoFunctionSet}
-import wom.types._
-import wom.values._
-
-/** @see <a href="http://www.commonwl.org/v1.0/Workflow.html#CommandOutputBinding">CommandOutputBinding</a> */
-case class CommandOutputBinding(glob: Option[Glob] = None,
-                                loadContents: Option[Boolean] = None,
-                                outputEval: Option[StringOrExpression] = None)
-
-object CommandOutputBinding {
-  /**
-    * TODO: WOM: WOMFILE: Need to support returning globs for primary and secondary.
-    *
-    * Right now, when numerous glob files are created, the backends place each glob result into a different subdirectory.
-    * Later, when the secondary files are being generated each of their globs are in different sub-directories.
-    * Unfortunately, the secondary file resolution assumes that the secondaries are _next to_ the primaries, not in
-    * sibling directories.
-    *
-    * While this is being worked on, instead of looking up globs return regular files until this can be fixed.
-    */
-  def isRegularFile(path: String): Boolean = {
-    path match {
-      case _ if path.contains("*") => false
-      case _ if path.contains("?") => false
-      case _ => true
-    }
-  }
-
-  /**
-    * Returns all the primary and secondary files that _will be_ created by this command output binding.
-    */
-  def getOutputWomFiles(inputValues: Map[String, WomValue],
-                        outputWomType: WomType,
-                        commandOutputBinding: CommandOutputBinding,
-                        secondaryFilesOption: Option[SecondaryFiles],
-                        ioFunctionSet: IoFunctionSet,
-                        expressionLib: ExpressionLib): IOChecked[Set[FileEvaluation]] = {
-    val parameterContext = ParameterContext(ioFunctionSet, expressionLib, inputs = inputValues)
-
-    /*
-    CWL can output two types of "glob" path types:
-    - File will be a glob path
-    - Directory is a path that will be searched for files. It's assumed that it will not be a glob, but the spec is
-      unclear and doesn't specifically say how Directories are listed. If the backend uses a POSIX
-      `find <dir> -type f`, then a globbed path should still work.
-
-    Either way create one of the two types as a return type that the backend should be looking for when the command
-    completes.
-
-    UPDATE:
-    It turns out that secondary files can be directories. TODO: WOM: WOMFILE: Not sure what to do with that yet.
-    https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/search.cwl#L42
-    https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/index.py#L36-L37
-     */
-    def primaryPathsToWomFiles(primaryPaths: List[String]): ErrorOr[List[WomFile]] = {
-      validate {
-        primaryPaths map { primaryPath =>
-          val outputWomFlatType = outputWomType match {
-            case WomMaybeListedDirectoryType => WomUnlistedDirectoryType
-            case WomArrayType(WomMaybeListedDirectoryType) => WomUnlistedDirectoryType
-            case _ if isRegularFile(primaryPath) => WomSingleFileType
-            case _ => WomGlobFileType
-          }
-
-          WomFile(outputWomFlatType, primaryPath)
-        }
-      }
-    }
-
-    def secondaryFilesToWomFiles(primaryWomFiles: List[WomFile], ioFunctionSet: IoFunctionSet): IOChecked[List[WomFile]] = {
-      primaryWomFiles.flatTraverse[IOChecked, WomFile] { primaryWomFile =>
-        FileParameter.secondaryFiles(primaryWomFile,
-          primaryWomFile.womFileType, secondaryFilesOption, parameterContext, expressionLib, ioFunctionSet)
-      }
-    }
-
-    for {
-      primaryPaths <- GlobEvaluator.globs(commandOutputBinding.glob, parameterContext, expressionLib).toIOChecked
-      primaryWomFiles <- primaryPathsToWomFiles(primaryPaths).toIOChecked
-      // This sets optional = false arbitrarily for now as this code doesn't have the context to make that determination,
-      // the caller can change this if necessary.
-      primaryEvaluations = primaryWomFiles map { FileEvaluation(_, optional = false, secondary = false) }
-      secondaryWomFiles <- secondaryFilesToWomFiles(primaryWomFiles, ioFunctionSet)
-      secondaryEvaluations = secondaryWomFiles map { FileEvaluation(_, optional = false, secondary = true) }
-    } yield (primaryEvaluations ++ secondaryEvaluations).toSet
-  }
-
-  /**
-    * Generates an output wom value based on the specification in command output binding.
-    *
-    * Depending on the outputWomType, the following steps will be applied as specified in the CWL spec:
-    * 1. glob: get a list the globbed files as our primary files
-    * 2. loadContents: load the contents of the primary files
-    * 3. outputEval: pass in the primary files to an expression to generate our return value
-    * 4. secondaryFiles: just before returning the value, fill in the secondary files on the return value
-    *
-    * The result type will be coerced to the output type.
-    */
-  def generateOutputWomValue(inputValues: Map[String, WomValue],
-                             ioFunctionSet: IoFunctionSet,
-                             outputWomType: WomType,
-                             commandOutputBinding: CommandOutputBinding,
-                             secondaryFilesCoproduct: Option[SecondaryFiles],
-                             formatCoproduct: Option[StringOrExpression],
-                             expressionLib: ExpressionLib): IOChecked[WomValue] = {
-    import ioFunctionSet.cs
-
-    val parameterContext = ParameterContext(ioFunctionSet, expressionLib, inputs = inputValues)
-
-    // 3. outputEval: pass in the primary files to an expression to generate our return value
-    def evaluateWomValue(womFilesArray: WomArray): ErrorOr[WomValue] = {
-      commandOutputBinding.outputEval match {
-        case Some(StringOrExpression.String(string)) => WomString(string).valid
-        case Some(StringOrExpression.Expression(expression)) =>
-          val outputEvalParameterContext = parameterContext.copy(self = womFilesArray)
-          ExpressionEvaluator.eval(expression, outputEvalParameterContext)
-        case None =>
-          womFilesArray.valid
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-    }
-
-    // Used to retrieve the file format to be injected into a file result.
-    def formatOptionErrorOr = OutputParameter.format(formatCoproduct, parameterContext, expressionLib)
-
-    // 4. secondaryFiles: just before returning the value, fill in the secondary files on the return value
-    def populateSecondaryFiles(evaluatedWomValue: WomValue): IOChecked[WomValue] = {
-      for {
-        formatOption <- formatOptionErrorOr.toIOChecked
-        womValue <- FileParameter.populateSecondaryFiles(
-          evaluatedWomValue,
-          secondaryFilesCoproduct,
-          formatOption,
-          parameterContext,
-          expressionLib,
-          ioFunctionSet
-        )
-      } yield womValue
-    }
-
-    // CWL tells us the type this output is expected to be. Attempt to coerce the actual output into this type.
-    def coerceWomValue(populatedWomValue: WomValue): ErrorOr[WomValue] = {
-      (outputWomType, populatedWomValue) match {
-
-        case (womType: WomArrayType, womValue: WomArray) =>
-          // Array -from- Array then coerce normally
-          // NOTE: this evaluates to the same as the last case, but guards against the next cases accidentally matching
-          womType.coerceRawValue(womValue).toErrorOr
-
-        case (womType: WomArrayType, womValue) =>
-          // Array -from- Single then coerce a single value to an array
-          womType.coerceRawValue(womValue).toErrorOr.map(value => WomArray(womType, List(value)))
-
-        case (womType, womValue: WomArray) if womValue.value.lengthCompare(1) == 0 =>
-          // Single -from- Array then coerce the head (if there's only a head)
-          womType.coerceRawValue(womValue.value.head).toErrorOr
-
-        case (womType, womValue) =>
-          // <other> to <other> then coerce normally
-          womType.coerceRawValue(womValue).toErrorOr
-
-      }
-    }
-
-    for {
-      // 1. glob: get a list the globbed files as our primary files
-      primaryPaths <- GlobEvaluator.globs(commandOutputBinding.glob, parameterContext, expressionLib).toIOChecked
-
-      // 2. loadContents: load the contents of the primary files
-      primaryAsDirectoryOrFiles <- primaryPaths.parTraverse[IOChecked, List[WomFile]] {
-        loadPrimaryWithContents(ioFunctionSet, outputWomType, commandOutputBinding)
-      } map (_.flatten)
-
-      // Make globbed files absolute paths by prefixing them with the output dir if necessary
-      absolutePaths = primaryAsDirectoryOrFiles.map(_.mapFile(ioFunctionSet.pathFunctions.relativeToHostCallRoot))
-
-      // Load file size
-      withFileSizes <- absolutePaths.parTraverse[IOChecked, WomFile](_.withSize(ioFunctionSet).to[IOChecked])
-
-      womFilesArray = WomArray(withFileSizes)
-
-      // 3. outputEval: pass in the primary files to an expression to generate our return value
-      evaluatedWomValue <- evaluateWomValue(womFilesArray).toIOChecked
-
-      // 4. secondaryFiles: just before returning the value, fill in the secondary files on the return value
-      populatedWomValue <- populateSecondaryFiles(evaluatedWomValue)
-
-      // CWL tells us the type this output is expected to be. Attempt to coerce the actual output into this type.
-      coercedWomValue <- coerceWomValue(populatedWomValue).toIOChecked
-    } yield coercedWomValue
-  }
-
-  /**
-    * Given a cwl glob path and an output type, gets the listing using the ioFunctionSet, and optionally loads the
-    * contents of the file(s).
-    */
-  private def loadPrimaryWithContents(ioFunctionSet: IoFunctionSet,
-                                      outputWomType: WomType,
-                                      commandOutputBinding: CommandOutputBinding)
-                                     (cwlPath: String): IOChecked[List[WomFile]] = {
-    import ioFunctionSet.cs
-
-    /*
-    For each file matched in glob, read up to the first 64 KiB of text from the file and place it in the contents field
-    of the file object for manipulation by outputEval.
-     */
-    val womMaybeListedDirectoryOrFileType = outputWomType match {
-      case WomMaybeListedDirectoryType => WomMaybeListedDirectoryType
-      case WomArrayType(WomMaybeListedDirectoryType) => WomMaybeListedDirectoryType
-      case _ => WomMaybePopulatedFileType
-    }
-    womMaybeListedDirectoryOrFileType match {
-      case WomMaybeListedDirectoryType =>
-        // Even if multiple directories are _somehow_ requested, a single flattened directory is returned.
-        loadDirectoryWithListing(ioFunctionSet, commandOutputBinding)(cwlPath).map(List(_))
-      case WomMaybePopulatedFileType if isRegularFile(cwlPath) =>
-        loadFileWithContents(ioFunctionSet, commandOutputBinding)(cwlPath).to[IOChecked].map(List(_))
-      case WomMaybePopulatedFileType =>
-        //TODO: HACK ALERT - DB: I am starting on ticket https://github.com/broadinstitute/cromwell/issues/3092 which will redeem me of this mortal sin.
-        val detritusFiles = List(
-          "docker_cid",
-          "gcs_delocalization.sh",
-          "gcs_localization.sh",
-          "gcs_transfer.sh",
-          "rc.tmp",
-          "script",
-          "script.background",
-          "script.submit",
-          "stderr",
-          "stderr.background",
-          "stdout",
-          "stdout.background",
-        )
-        val globs: IOChecked[Seq[String]] =
-          ioFunctionSet.glob(cwlPath).toIOChecked
-              .map({
-                _
-                .filterNot{ s =>
-                  detritusFiles exists s.endsWith
-                }
-              })
-
-        globs.flatMap({ files =>
-          files.toList.parTraverse[IOChecked, WomFile](v => loadFileWithContents(ioFunctionSet, commandOutputBinding)(v).to[IOChecked])
-        })
-      case other => s"Program error: $other type was not expected".invalidIOChecked
-    }
-  }
-
-  /**
-    * Loads a directory with the files listed, each file with contents populated.
-    */
-  private def loadDirectoryWithListing(ioFunctionSet: IoFunctionSet,
-                                       commandOutputBinding: CommandOutputBinding)(path: String, visited: Vector[String] = Vector.empty): IOChecked[WomMaybeListedDirectory] = {
-    import ioFunctionSet.cs
-
-    for {
-      listing <- IO.fromFuture(IO { ioFunctionSet.listDirectory(path)(visited) }).to[IOChecked]
-      loadedListing <- listing.toList.parTraverse[IOChecked, WomFile]({
-        case IoFile(p) => loadFileWithContents(ioFunctionSet, commandOutputBinding)(p).to[IOChecked]
-        case IoDirectory(p) => loadDirectoryWithListing(ioFunctionSet, commandOutputBinding)(p, visited :+ path).widen
-      })
-    } yield WomMaybeListedDirectory(valueOption = Option(path), listingOption = Option(loadedListing))
-  }
-
-  /**
-    * Loads a file at path reading 64KiB of data into the contents.
-    */
-  private def loadFileWithContents(ioFunctionSet: IoFunctionSet,
-                                   commandOutputBinding: CommandOutputBinding)(path: String): IO[WomFile] = {
-    val contentsOptionErrorOr = {
-      if (commandOutputBinding.loadContents getOrElse false) {
-        FileParameter.load64KiB(path, ioFunctionSet) map Option.apply
-      } else {
-        IO.pure(None)
-      }
-    }
-    contentsOptionErrorOr map { contentsOption =>
-      WomMaybePopulatedFile(valueOption = Option(path), contentsOption = contentsOption)
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlCodecs.scala b/cwl/src/main/scala/cwl/CwlCodecs.scala
deleted file mode 100644
index d7010494bca..00000000000
--- a/cwl/src/main/scala/cwl/CwlCodecs.scala
+++ /dev/null
@@ -1,153 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import cats.syntax.show._
-import common.Checked
-import common.validation.Checked._
-import cwl.CommandLineTool.{CommandInputParameter, CommandOutputParameter}
-import cwl.CwlType.CwlType
-import cwl.CwlVersion.CwlVersion
-import cwl.ExpressionTool.{ExpressionToolInputParameter, ExpressionToolOutputParameter}
-import cwl.InitialWorkDirRequirement.IwdrListingArrayEntry
-import cwl.LinkMergeMethod.LinkMergeMethod
-import cwl.ScatterMethod.ScatterMethod
-import cwl.SchemaDefRequirement.SchemaDefTypes
-import cwl.Workflow.{WorkflowInputParameter, WorkflowOutputParameter}
-import io.circe.DecodingFailure._
-import io.circe.Json._
-import io.circe._
-import io.circe.generic.semiauto._
-import io.circe.literal._
-import io.circe.refined._
-import io.circe.shapes._
-import shapeless.Coproduct
-
-object CwlCodecs {
-  /*
-  Semi-auto codecs for the Cwl types
-  https://circe.github.io/circe/codecs/semiauto-derivation.html
-
-  Some types, such as BaseCommand are not listed, as they are actually one-for-one type aliases. Having two exact
-  implicits for the same type will confuse the compiler, leading to cryptic error messages elsewhere.
-
-  For example, a duplicated decoder such as:
-
-  ```
-  implicit lazy val decodeSingleOrArrayOfStrings: Decoder[SingleOrArrayOfStrings] = decodeCCons
-  implicit lazy val decodeBaseCommand: Decoder[BaseCommand] = decodeCCons
-  ```
-
-  causes cryptic errors such as:
-
-  ```
-  [error] cwl/src/main/scala/cwl/CwlCodecs.scala:123:456: could not find Lazy implicit value of type io.circe.generic.decoding.DerivedDecoder[A]
-  [error]   implicit lazy val decodeCommandInputParameter: Decoder[CommandInputParameter] = deriveDecoder
-
-  (etc. etc. etc.)
-  ```
-   */
-
-  // Semi-Automatically derived codecs
-  implicit lazy val codecArgumentCommandLineBinding: Codec[ArgumentCommandLineBinding] = deriveCodec
-  implicit lazy val codecCommandInputParameter: Codec[CommandInputParameter] = deriveCodec
-  implicit lazy val codecCommandLineTool: Codec[CommandLineTool] = deriveCodec
-  implicit lazy val codecCommandOutputBinding: Codec[CommandOutputBinding] = deriveCodec
-  implicit lazy val codecCommandOutputParameter: Codec[CommandOutputParameter] = deriveCodec
-  implicit lazy val codecCwlType: Codec[CwlType] = Codec.codecForEnumeration(CwlType)
-  implicit lazy val codecCwlVersion: Codec[CwlVersion] = Codec.codecForEnumeration(CwlVersion)
-  implicit lazy val codecDirectory: Codec[Directory] = deriveCodec
-  implicit lazy val codecDockerRequirement: Codec[DockerRequirement] = deriveCodec
-  implicit lazy val codecEnvVarRequirement: Codec[EnvVarRequirement] = deriveCodec
-  implicit lazy val codecEnvironmentDef: Codec[EnvironmentDef] = deriveCodec
-  implicit lazy val codecExpressionDirent: Codec[ExpressionDirent] = deriveCodec
-  implicit lazy val codecExpressionTool: Codec[ExpressionTool] = deriveCodec
-  implicit lazy val codecExpressionToolInputParameter: Codec[ExpressionToolInputParameter] = deriveCodec
-  implicit lazy val codecExpressionToolOutputParameter: Codec[ExpressionToolOutputParameter] = deriveCodec
-  implicit lazy val codecFile: Codec[File] = deriveCodec
-  implicit lazy val codecInitialWorkDirRequirement: Codec[InitialWorkDirRequirement] = deriveCodec
-  implicit lazy val codecInlineJavascriptRequirement: Codec[InlineJavascriptRequirement] = deriveCodec
-  implicit lazy val codecInputArraySchema: Codec[InputArraySchema] = deriveCodec
-  implicit lazy val codecInputBinding: Codec[InputBinding] = deriveCodec
-  implicit lazy val codecInputCommandLineBinding: Codec[InputCommandLineBinding] = deriveCodec
-  implicit lazy val codecInputEnumSchema: Codec[InputEnumSchema] = deriveCodec
-  implicit lazy val codecInputRecordField: Codec[InputRecordField] = deriveCodec
-  implicit lazy val codecInputRecordSchema: Codec[InputRecordSchema] = deriveCodec
-  implicit lazy val codecInputResourceRequirement: Codec[DnaNexusInputResourceRequirement] = deriveCodec
-  implicit lazy val codecLinkMergeMethod: Codec[LinkMergeMethod] = Codec.codecForEnumeration(LinkMergeMethod)
-  implicit lazy val codecMultipleInputFeatureRequirement: Codec[MultipleInputFeatureRequirement] = deriveCodec
-  implicit lazy val codecOutputArraySchema: Codec[OutputArraySchema] = deriveCodec
-  implicit lazy val codecOutputEnumSchema: Codec[OutputEnumSchema] = deriveCodec
-  implicit lazy val codecOutputRecordField: Codec[OutputRecordField] = deriveCodec
-  implicit lazy val codecOutputRecordSchema: Codec[OutputRecordSchema] = deriveCodec
-  implicit lazy val codecResourceRequirement: Codec[ResourceRequirement] = deriveCodec
-  implicit lazy val codecScatterFeatureRequirement: Codec[ScatterFeatureRequirement] = deriveCodec
-  implicit lazy val codecScatterMethod: Codec[ScatterMethod] = Codec.codecForEnumeration(ScatterMethod)
-  implicit lazy val codecSchemaDefRequirement: Codec[SchemaDefRequirement] = deriveCodec
-  implicit lazy val codecShellCommandRequirement: Codec[ShellCommandRequirement] = deriveCodec
-  implicit lazy val codecSoftwarePackage: Codec[SoftwarePackage] = deriveCodec
-  implicit lazy val codecSoftwareRequirement: Codec[SoftwareRequirement] = deriveCodec
-  implicit lazy val codecStepInputExpressionRequirement: Codec[StepInputExpressionRequirement] = deriveCodec
-  implicit lazy val codecStringDirent: Codec[StringDirent] = deriveCodec
-  implicit lazy val codecSubworkflowFeatureRequirement: Codec[SubworkflowFeatureRequirement] = deriveCodec
-  implicit lazy val codecWorkflow: Codec[Workflow] = deriveCodec
-  implicit lazy val codecWorkflowInputParameter: Codec[WorkflowInputParameter] = deriveCodec
-  implicit lazy val codecWorkflowOutputParameter: Codec[WorkflowOutputParameter] = deriveCodec
-  implicit lazy val codecWorkflowStep: Codec[WorkflowStep] = deriveCodec
-  implicit lazy val codecWorkflowStepInput: Codec[WorkflowStepInput] = deriveCodec
-  implicit lazy val codecWorkflowStepOutput: Codec[WorkflowStepOutput] = deriveCodec
-
-  // Encoders and decoders for Coproduct-based types must be explicitly derived
-  implicit lazy val decodeCwlAny: Decoder[CwlAny] = decodeCCons
-  implicit lazy val decodeExpression: Decoder[Expression] = decodeCCons
-  implicit lazy val decodeFileOrDirectory: Decoder[FileOrDirectory] = decodeCCons
-  implicit lazy val decodeGlob: Decoder[Glob] = decodeCCons
-  implicit lazy val decodeHint: Decoder[Hint] = decodeCCons
-  implicit lazy val decodeIwdrListingArrayEntry: Decoder[IwdrListingArrayEntry] = decodeCCons
-  implicit lazy val decodeMyriadInputInnerType: Decoder[MyriadInputInnerType] = decodeCCons
-  implicit lazy val decodeMyriadInputType: Decoder[MyriadInputType] = decodeCCons
-  implicit lazy val decodeMyriadOutputType: Decoder[MyriadOutputType] = decodeCCons
-  implicit lazy val decodeRequirement: Decoder[Requirement] = decodeCCons
-  implicit lazy val decodeResourceRequirementType: Decoder[ResourceRequirementType] = decodeCCons
-  implicit lazy val decodeSchemaDefTypes: Decoder[SchemaDefTypes] = decodeCCons
-  implicit lazy val decodeSecondaryFiles: Decoder[SecondaryFiles] = decodeCCons
-  implicit lazy val decodeSingleOrArrayOfStrings: Decoder[SingleOrArrayOfStrings] = decodeCCons
-  implicit lazy val decodeStringOrExpression: Decoder[StringOrExpression] = decodeCCons
-
-  implicit lazy val encodeCwlAny: Encoder[CwlAny] = encodeCCons
-  implicit lazy val encodeExpression: Encoder[Expression] = encodeCCons
-  implicit lazy val encodeFileOrDirectory: Encoder[FileOrDirectory] = encodeCCons
-  implicit lazy val encodeGlob: Encoder[Glob] = encodeCCons
-  implicit lazy val encodeHint: Encoder[Hint] = encodeCCons
-  implicit lazy val encodeIwdrListingArrayEntry: Encoder[IwdrListingArrayEntry] = encodeCCons
-  implicit lazy val encodeMyriadInputInnerType: Encoder[MyriadInputInnerType] = encodeCCons
-  implicit lazy val encodeMyriadInputType: Encoder[MyriadInputType] = encodeCCons
-  implicit lazy val encodeMyriadOutputType: Encoder[MyriadOutputType] = encodeCCons
-  implicit lazy val encodeRequirement: Encoder[Requirement] = encodeCCons
-  implicit lazy val encodeResourceRequirementType: Encoder[ResourceRequirementType] = encodeCCons
-  implicit lazy val encodeSchemaDefTypes: Encoder[SchemaDefTypes] = encodeCCons
-  implicit lazy val encodeSecondaryFiles: Encoder[SecondaryFiles] = encodeCCons
-  implicit lazy val encodeSingleOrArrayOfStrings: Encoder[SingleOrArrayOfStrings] = encodeCCons
-  implicit lazy val encodeStringOrExpression: Encoder[StringOrExpression] = encodeCCons
-
-  def decodeCwl(json: Json): Checked[Cwl] = {
-    findClass(json) match {
-      case Some("Workflow") => decodeWithErrorStringsJson[Workflow](json).map(Coproduct[Cwl].apply(_))
-      case Some("CommandLineTool") => decodeWithErrorStringsJson[CommandLineTool](json).map(Coproduct[Cwl].apply(_))
-      case Some("ExpressionTool") => decodeWithErrorStringsJson[ExpressionTool](json).map(Coproduct[Cwl].apply(_))
-      case Some(other) => s"Class field was declared incorrectly: $other is not one of Workflow, CommandLineTool, or ExpressionTool! as seen in ${json.show}".invalidNelCheck
-      case None => s"Class field was omitted in ${json.show}".invalidNelCheck
-    }
-  }
-
-  private def decodeWithErrorStringsJson[A](in: Json)(implicit d: Codec[A]): Checked[A] =
-    in.as[A].leftMap(_.show).leftMap(NonEmptyList.one)
-
-  private def findClass(json: Json): Option[String] =
-    for {
-      obj <- json.asObject
-      map = obj.toMap
-      classObj <- map.get("class")
-      classString <- classObj.asString
-    } yield classString
-}
diff --git a/cwl/src/main/scala/cwl/CwlDecoder.scala b/cwl/src/main/scala/cwl/CwlDecoder.scala
deleted file mode 100644
index b7a4125e5a3..00000000000
--- a/cwl/src/main/scala/cwl/CwlDecoder.scala
+++ /dev/null
@@ -1,84 +0,0 @@
-package cwl
-
-import better.files.{File => BFile}
-import cats.data.EitherT._
-import cats.effect.IO
-import cats.syntax.either._
-import cats.{Applicative, Monad}
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.preprocessor.{CwlFileReference, CwlPreProcessor, CwlReference}
-import io.circe.Json
-
-import scala.util.Try
-
-object CwlDecoder {
-
-  implicit val composedApplicative = Applicative[IO] compose Applicative[ErrorOr]
-
-  def saladCwlFile(reference: CwlReference): IOChecked[String] = {
-    val cwlToolResult =
-      Try(CwltoolRunner.instance.salad(reference))
-        .toCheckedWithContext(s"run cwltool on file ${reference.pathAsString}", throwableToStringFunction = t => t.toString)
-
-    fromEither[IO](cwlToolResult)
-  }
-
-  private lazy val cwlPreProcessor = new CwlPreProcessor()
-
-  // TODO: WOM: During conformance testing the saladed-CWLs are referring to files in the temp directory.
-  // Thus we can't delete the temp directory until after the workflow is complete, like the workflow logs.
-  // All callers to this method should be fixed around the same time.
-  // https://github.com/broadinstitute/cromwell/issues/3186
-  def todoDeleteCwlFileParentDirectory(cwlFile: BFile): IOChecked[Unit] = {
-    goIOChecked {
-      //cwlFile.parent.delete(swallowIOExceptions = true)
-    }
-  }
-
-  def parseJson(json: Json, from: String): IOChecked[Cwl] = fromEither[IO](CwlCodecs.decodeCwl(json).contextualizeErrors(s"parse '$from'"))
-
-  /**
-    * Notice it gives you one instance of Cwl.  This has transformed all embedded files into scala object state
-    */
-  def decodeCwlReference(reference: CwlReference)(implicit processor: CwlPreProcessor = cwlPreProcessor): IOChecked[Cwl] = {
-    def makeStandaloneWorkflow(): IOChecked[Json] = processor.preProcessCwl(reference)
-
-    for {
-      standaloneWorkflow <- makeStandaloneWorkflow()
-      parsedCwl <- parseJson(standaloneWorkflow, reference.pathAsString)
-    } yield parsedCwl
-  }
-
-  def decodeCwlFile(file: BFile, workflowRoot: Option[String] = None) = {
-    decodeCwlReference(CwlFileReference(file, workflowRoot))
-  }
-
-  def decodeCwlString(cwl: String,
-                      zipOption: Option[BFile] = None,
-                      rootName: Option[String] = None,
-                      cwlFilename: String = "cwl_temp_file"): IOChecked[Cwl] = {
-    for {
-      parentDir <- goIOChecked(BFile.newTemporaryDirectory("cwl_temp_dir_")) // has a random long appended like `cwl_temp_dir_100000000000`
-      file <- fromEither[IO](parentDir./(cwlFilename + ".cwl").write(cwl).asRight) // serves as the basis for the output directory name; must remain stable across restarts
-      _ <- zipOption match {
-        case Some(zip) => goIOChecked(zip.unzipTo(parentDir))
-        case None => Monad[IOChecked].unit
-      }
-      out <- decodeCwlFile(file, rootName)
-      _ <- todoDeleteCwlFileParentDirectory(file)
-    } yield out
-  }
-
-  //This is used when traversing over Cwl and replacing links w/ embedded data
-  private[cwl] def decodeCwlAsValidated(fileName: String): IOCheckedValidated[(String, Cwl)] = {
-    //The SALAD preprocess step puts "file://" as a prefix to all filenames.  Better files doesn't like this.
-    val bFileName = fileName.stripPrefix("file://")
-
-    decodeCwlReference(CwlFileReference(BFile(bFileName), None)).
-      map(fileName.toString -> _).
-      value.
-      map(_.toValidated)
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlExecutableValidation.scala b/cwl/src/main/scala/cwl/CwlExecutableValidation.scala
deleted file mode 100644
index f6f8237c5ff..00000000000
--- a/cwl/src/main/scala/cwl/CwlExecutableValidation.scala
+++ /dev/null
@@ -1,38 +0,0 @@
-package cwl
-
-import common.Checked
-import common.validation.Checked._
-import io.circe.Json
-import wom.callable.{ExecutableCallable, TaskDefinition}
-import wom.executable.Executable
-import wom.executable.Executable.{InputParsingFunction, ParsedInputMap}
-import wom.expression.IoFunctionSet
-import wom.util.YamlUtils
-
-object CwlExecutableValidation {
-
-  // Decodes the input file, and build the ParsedInputMap
-  private val inputCoercionFunction: InputParsingFunction =
-    inputFile => {
-      val yaml = YamlUtils.parse(inputFile)
-      yaml.flatMap(_.as[Map[String, Json]]) match {
-        case Left(error) => error.getMessage.invalidNelCheck[ParsedInputMap]
-        case Right(inputValue) => inputValue.map({ case (key, value) => key -> value.foldWith(CwlJsonToDelayedCoercionFunction) }).validNelCheck
-      }
-    }
-
-  def buildWomExecutableCallable(callable: Checked[ExecutableCallable], inputFile: Option[String], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    for {
-      womDefinition <- callable
-      executable <- Executable.withInputs(womDefinition, inputCoercionFunction, inputFile, ioFunctions, strictValidation)
-    } yield executable
-  }
-
-  def buildWomExecutable(callableTaskDefinition: Checked[TaskDefinition], inputFile: Option[String], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    for {
-      taskDefinition <- callableTaskDefinition
-      executableTaskDefinition = taskDefinition.toExecutable.toEither
-      executable <- CwlExecutableValidation.buildWomExecutableCallable(executableTaskDefinition, inputFile, ioFunctions, strictValidation)
-    } yield executable
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlExpressionCommandPart.scala b/cwl/src/main/scala/cwl/CwlExpressionCommandPart.scala
deleted file mode 100644
index f323c74dbd2..00000000000
--- a/cwl/src/main/scala/cwl/CwlExpressionCommandPart.scala
+++ /dev/null
@@ -1,146 +0,0 @@
-package cwl
-
-import cats.syntax.either._
-import cats.syntax.validated._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import wom.callable.RuntimeEnvironment
-import wom.expression.IoFunctionSet
-import wom.graph.LocalName
-import wom.values._
-import wom.{CommandPart, InstantiatedCommand}
-
-import scala.language.postfixOps
-
-case class CwlExpressionCommandPart(expr: Expression)(hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib) extends CommandPart {
-  override def instantiate(inputsMap: Map[LocalName, WomValue],
-                           functions: IoFunctionSet,
-                           valueMapper: (WomValue) => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] = {
-    val stringKeyMap = inputsMap map {
-      case (LocalName(localName), value) => localName -> valueMapper(value)
-    }
-    val parameterContext = ParameterContext(
-      functions,
-      expressionLib,
-      inputs = stringKeyMap, runtimeOption = Option(runtimeEnvironment)
-    )
-    ExpressionEvaluator.eval(expr, parameterContext) map { womValue =>
-      List(InstantiatedCommand(valueMapper(womValue).valueString.shellQuote))
-    }
-  }
-}
-
-/**
-  * Generates command parts from a CWL Binding
-  */
-abstract class CommandLineBindingCommandPart(commandLineBinding: CommandLineBinding)(hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib) extends CommandPart {
-
-
-  private lazy val prefixAsString = commandLineBinding.prefix.getOrElse("")
-  private lazy val prefixAsList = commandLineBinding.prefix.toList
-  private lazy val separate = commandLineBinding.effectiveSeparate
-
-  def handlePrefix(value: String) = {
-    if (separate) prefixAsList :+ value else List(s"$prefixAsString$value")
-  }
-
-  /**
-    * Value bound to this command part.
-    * InputCommandLineBindingCommandPart has one
-    * ArgumentCommandLineBindingCommandPart does not
-    */
-  def boundValue: Option[WomValue]
-
-  // If the bound value is defined but contains an empty optional value, we should not evaluate the valueFrom
-  // Conformance test "stage-unprovided-file" tests this behavior
-  private lazy val evaluateValueFrom = boundValue.forall {
-    case WomOptionalValue(_, None) => false
-    case _ => true
-  }
-
-  override def instantiate(inputsMap: Map[LocalName, WomValue],
-                           functions: IoFunctionSet,
-                           valueMapper: (WomValue) => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] = {
-      val stringInputsMap = inputsMap map {
-        case (LocalName(localName), value) => localName -> valueMapper(value)
-      }
-    val parameterContext = ParameterContext(
-      functions,
-      expressionLib,
-      inputs = stringInputsMap,
-      runtimeOption = Option(runtimeEnvironment),
-      self = boundValue.getOrElse(ParameterContext.EmptySelf)
-    )
-
-    val evaluatedValueFrom = commandLineBinding.optionalValueFrom flatMap {
-      case StringOrExpression.Expression(expression) if evaluateValueFrom => Option(ExpressionEvaluator.eval(expression, parameterContext) map valueMapper)
-      case StringOrExpression.String(string) if evaluateValueFrom => Option(WomString(string).validNel)
-      case _ => None
-    }
-
-    val evaluatedWomValue: Checked[WomValue] = evaluatedValueFrom.orElse(boundValue.map(_.validNel)) match {
-      case Some(womValue) => womValue.map(valueMapper).toEither
-      case None => "Command line binding has no valueFrom field and no bound value".invalidNelCheck
-    }
-
-    def applyShellQuote(value: String): String = commandLineBinding.shellQuote match {
-      // Only honor shellQuote = false if ShellCommandRequirement is enabled.
-      // Conformance test "Test that shell directives are not interpreted."
-      case Some(false) if hasShellCommandRequirement => value
-      case _ => value.shellQuote
-    }
-
-    def processValue(womValue: WomValue): List[String] = womValue match {
-      case WomOptionalValue(_, Some(value)) => processValue(valueMapper(value))
-      case WomOptionalValue(_, None) => List.empty
-      case _: WomString | _: WomInteger | _: WomFile | _: WomLong | _: WomFloat => handlePrefix(valueMapper(womValue).valueString)
-      // For boolean values, use the value of the boolean to choose whether to print the prefix or not
-      case WomBoolean(false) => List.empty
-      case WomBoolean(true) => prefixAsList
-      case WomArray(_, values) => commandLineBinding.itemSeparator match {
-        case Some(_) if values.isEmpty => List.empty
-        case Some(itemSeparator) => handlePrefix(values.map(valueMapper(_).valueString).mkString(itemSeparator))
-
-        /*
-        via: http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding
-
-        > If itemSeparator is specified, add prefix and the join the array into a single string with itemSeparator
-        > separating the items. Otherwise first add prefix, then recursively process individual elements.
-
-        Not 100% sure if this is conformant, as we are only recurse the head into `processValue` here... However the
-        conformance test "Test InlineJavascriptRequirement with multiple expressions in the same tool" is happy with the
-        behavior.
-         */
-        // InstantiatedCommand elements are generated here when there exists an optionalValueFrom
-        case None if commandLineBinding.optionalValueFrom.isDefined => values.toList match {
-          case head :: tail => processValue(head) ++ tail.map(valueMapper(_).valueString)
-          case Nil => prefixAsList
-        }
-
-        // When there is no optionalValueFrom the InstantiatedCommand elements for the womValue are appended elsewhere
-        case _ => prefixAsList
-      }
-      case _: WomObjectLike => prefixAsList
-      case WomEnumerationValue(_, value) => handlePrefix(value)
-      case WomCoproductValue(_, value) => processValue(value)
-      case w => throw new RuntimeException(s"Unhandled CwlExpressionCommandPart value '$w' of type ${w.womType.stableName}")
-    }
-
-    evaluatedWomValue map { v => processValue(v) map applyShellQuote map (InstantiatedCommand(_)) } toValidated
-  }
-}
-
-case class InputCommandLineBindingCommandPart(commandLineBinding: InputCommandLineBinding, associatedValue: WomValue)
-                                             (hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib)
-  extends CommandLineBindingCommandPart(commandLineBinding)(hasShellCommandRequirement, expressionLib) {
-  override lazy val boundValue = Option(associatedValue)
-}
-
-case class ArgumentCommandLineBindingCommandPart(commandLineBinding: ArgumentCommandLineBinding)
-                                                (hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib)
-  extends CommandLineBindingCommandPart(commandLineBinding)(hasShellCommandRequirement, expressionLib) {
-  override lazy val boundValue = None
-}
diff --git a/cwl/src/main/scala/cwl/CwlJsonToDelayedCoercionFunction.scala b/cwl/src/main/scala/cwl/CwlJsonToDelayedCoercionFunction.scala
deleted file mode 100644
index 55dc7f9e3ba..00000000000
--- a/cwl/src/main/scala/cwl/CwlJsonToDelayedCoercionFunction.scala
+++ /dev/null
@@ -1,90 +0,0 @@
-package cwl
-
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import cwl.CwlCodecs._
-import io.circe.{Json, JsonNumber, JsonObject}
-import wom.executable.Executable.DelayedCoercionFunction
-import wom.types._
-import wom.values._
-
-// With recursive types we could let circe parse it for us, but until we figure that out just parse it as Json and
-// manually check for File / Directory structures
-private [cwl] object CwlJsonToDelayedCoercionFunction extends Json.Folder[DelayedCoercionFunction] {
-  private def simpleCoercion(value: Any)(womType: WomType): ErrorOr[WomValue] = womType.coerceRawValue(value).toErrorOr
-
-  override def onNull: DelayedCoercionFunction = WomOptionalValue.none(_).validNel
-
-  override def onBoolean(value: Boolean): DelayedCoercionFunction = simpleCoercion(value)
-
-  override def onNumber(value: JsonNumber): DelayedCoercionFunction = {
-    case WomFloatType => WomFloat(value.toDouble).validNel
-    case WomIntegerType => value.toInt.map(WomInteger.apply).toValidNel(s"$value is not a valid Int")
-    case WomLongType => value.toLong.map(WomLong.apply).toValidNel(s"$value is not a valid Long")
-    case other => other.coerceRawValue(value.toString).toErrorOr
-  }
-
-  override def onString(value: String): DelayedCoercionFunction = simpleCoercion(value)
-
-  override def onArray(value: Vector[Json]): DelayedCoercionFunction = {
-    case womArrayType: WomArrayType =>
-      value.toList
-        .traverse(_.foldWith(this).apply(womArrayType.memberType))
-        .map {
-          WomArray(womArrayType, _)
-        }
-
-    case WomOptionalType(otherType) =>
-      onArray(value).apply(otherType)
-    case WomCoproductType(types) =>
-      val attempts: List[ErrorOr[WomValue]] = types.toList.map(onArray(value)(_))
-      attempts.find(_.isValid).getOrElse(attempts.sequence[ErrorOr, WomValue].map(_.head))
-    case WomAnyType =>
-      // Make an array of WomAny
-      value.toList
-        .traverse(_.foldWith(this).apply(WomAnyType))
-        .map {
-          WomArray(WomArrayType(WomAnyType), _)
-        }
-    case other => s"Cannot convert an array input value into a non array type: $other".invalidNel
-  }
-
-  override def onObject(value: JsonObject): DelayedCoercionFunction = {
-    // CWL files are represented as Json objects, so this could be a file 
-    case WomSingleFileType | WomMaybePopulatedFileType if value.toMap.get("class").flatMap(_.asString).contains("File") =>
-      Json.fromJsonObject(value).as[File] match {
-        case Left(errors) => errors.message.invalidNel
-        case Right(file) => file.asWomValue
-      }
-    case WomMaybeListedDirectoryType | WomUnlistedDirectoryType if value.toMap.get("class").flatMap(_.asString).contains("Directory") =>
-      Json.fromJsonObject(value).as[Directory] match {
-        case Left(errors) => errors.message.invalidNel
-        case Right(directory) => directory.asWomValue
-      }
-    case composite: WomCompositeType =>
-      val foldedMap = value.toList.traverse[ErrorOr, (String, WomValue)]({
-        case (k, v) =>
-          composite.typeMap.get(k).map({ valueType =>
-            v.foldWith(this).apply(valueType).map(k -> _)
-          }).getOrElse(s"Input field $k is not defined in the composite input type $composite".invalidNel)
-      }).map(_.toMap[String, WomValue])
-
-      foldedMap.map(WomObject.withTypeUnsafe(_, composite))
-    case WomObjectType =>
-      val foldedMap = value.toList.traverse[ErrorOr, (String, WomValue)]({
-        case (k, v) => v.foldWith(this).apply(WomAnyType).map(k -> _)
-      }).map(_.toMap[String, WomValue])
-
-      foldedMap.map(WomObject.apply)
-    case WomOptionalType(otherType) => onObject(value).apply(otherType)
-    case WomCoproductType(types) =>
-      val attempts: List[ErrorOr[WomValue]] = types.toList.map(onObject(value)(_))
-      //these are all Invalid, just taking head to satisfy required type of WomValue instead of List[WomValue]
-      attempts.find(_.isValid).getOrElse(attempts.sequence[ErrorOr, WomValue].map(_.head))
-    case other => s"Cannot convert an object value $value into a non array type: $other".invalidNel
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlToRun.scala b/cwl/src/main/scala/cwl/CwlToRun.scala
deleted file mode 100644
index 1571958abb5..00000000000
--- a/cwl/src/main/scala/cwl/CwlToRun.scala
+++ /dev/null
@@ -1,11 +0,0 @@
-package cwl
-
-import shapeless._
-
-object CwlToRun extends Poly1 {
-  implicit def commandLineTool = at[CommandLineTool] { Coproduct[WorkflowStep.Run](_) }
-  implicit def workflow = at[Workflow] { Coproduct[WorkflowStep.Run](_) }
-  implicit def expressionTool = at[ExpressionTool] { Coproduct[WorkflowStep.Run](_) }
-}
-
-
diff --git a/cwl/src/main/scala/cwl/CwlType.scala b/cwl/src/main/scala/cwl/CwlType.scala
deleted file mode 100644
index 7ec171d97fb..00000000000
--- a/cwl/src/main/scala/cwl/CwlType.scala
+++ /dev/null
@@ -1,284 +0,0 @@
-package cwl
-
-import cats.instances.list._
-import cats.instances.option._
-import cats.syntax.functor._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import eu.timepit.refined._
-import mouse.all._
-import shapeless.Poly1
-import shapeless.syntax.singleton._
-import wom.expression.IoFunctionSet.{IoDirectory, IoFile}
-import wom.expression.{IoFunctionSet, PathFunctionSet}
-import wom.types.WomFileType
-import wom.values._
-
-import scala.annotation.tailrec
-
-object CwlType extends Enumeration {
-  type CwlType = Value
-
-  val Any = Value("Any")
-  val Null = Value("null")
-  val Boolean = Value("boolean")
-  val Int = Value("int")
-  val Long = Value("long")
-  val Float = Value("float")
-  val Double = Value("double")
-  val String = Value("string")
-  val File = Value("File")
-  val Directory = Value("Directory")
-}
-
-case class File private
-(
-  `class`: W.`"File"`.T,
-  location: Option[String], //TODO refine w/ regex  of IRI
-  path: Option[String],
-  basename: Option[String],
-  checksum: Option[String],
-  size: Option[Long],
-  secondaryFiles: Option[Array[FileOrDirectory]],
-  format: Option[String],
-  contents: Option[String]
-) {
-  lazy val effectivePath = path.orElse(location)
-
-  lazy val errorOrSecondaryFiles: ErrorOr[List[WomFile]] = {
-    val dirsOrFiles: List[FileOrDirectory] = secondaryFiles.getOrElse(Array.empty).toList
-    dirsOrFiles.traverse{
-      _.fold(CwlDirectoryOrFileAsWomSingleDirectoryOrFile)
-    }
-  }
-
-  lazy val asWomValue: ErrorOr[WomMaybePopulatedFile] = {
-    errorOrSecondaryFiles flatMap { secondaryFiles =>
-      val valueOption = location.orElse(path)
-      (valueOption, contents) match {
-        case (None, None) =>
-          "Cannot convert CWL File to WomValue without either a location, a path, or contents".invalidNel
-        case (None, Some(content)) =>
-          val initializeFunction: WomMaybePopulatedFile => IoFunctionSet => IOChecked[WomValue] = { file =>ioFunctionSet =>
-            val name = basename.getOrElse(content.hashCode.toString)
-            ioFunctionSet.writeFile(name, content).toIOChecked(ioFunctionSet.cs) map { writtenFile =>
-              file.copy(valueOption = Option(writtenFile.value))
-            }
-          }
-
-          new WomMaybePopulatedFile(None, checksum, size, format, contents, initializeFunction = initializeFunction).valid
-        case (_, _) =>
-          WomMaybePopulatedFile(valueOption, checksum, size, format, contents, secondaryFiles).valid
-      }
-    }
-  }
-}
-
-object File {
-  def apply(
-             location: Option[String] = None, //TODO refine w/ regex  of IRI
-             path: Option[String] = None,
-             basename: Option[String] = None,
-             checksum: Option[String] = None,
-             size: Option[Long] = None,
-             secondaryFiles: Option[Array[FileOrDirectory]] = None,
-             format: Option[String] = None,
-             contents: Option[String] = None): File = {
-    new cwl.File(
-      "File".narrow,
-      location,
-      path,
-      basename,
-      checksum,
-      size,
-      secondaryFiles,
-      format,
-      contents
-    )
-  }
-
-  def dirname(value: String): String = {
-    val index = value.lastIndexOf('/')
-    if (index >= 0) {
-      value.substring(0, index)
-    } else {
-      ""
-    }
-  }
-
-  def basename(value: String): String = value.substring(value.lastIndexOf('/') + 1)
-
-  def nameroot(value: String): String = basename(value).stripSuffix(nameext(value))
-
-  def nameext(value: String): String = {
-    val base = basename(value)
-    val index = base.lastIndexOf('.')
-    if (index >= 0) {
-      base.substring(index)
-    } else {
-      ""
-    }
-  }
-
-  def recursivelyBuildDirectory(directory: String, ioFunctions: IoFunctionSet)(visited: Vector[String] = Vector.empty): IOChecked[WomMaybeListedDirectory] = {
-    for {
-      listing <- ioFunctions.listDirectory(directory)(visited).toIOChecked(ioFunctions.cs)
-      fileListing <- listing.toList.traverse[IOChecked, WomFile]({
-        case IoDirectory(e) => recursivelyBuildDirectory(e, ioFunctions)(visited :+ directory).widen
-        case IoFile(e) => WomMaybePopulatedFile(e).validIOChecked.widen
-      })
-    } yield WomMaybeListedDirectory(Option(directory), Option(fileListing))
-  }
-
-  private def asAbsoluteSiblingOfPrimary(primary: WomFile, pathFunctions: PathFunctionSet)(path: String) = {
-    pathFunctions.absoluteSibling(primary.value, path)
-  }
-
-  def secondaryStringFile(primaryWomFile: WomFile,
-                          stringWomFileType: WomFileType,
-                          secondaryValue: String,
-                          ioFunctions: IoFunctionSet): IOChecked[WomFile] = {
-    val secondaryRelativeFileName = File.relativeFileName(primaryWomFile.value, secondaryValue)
-
-    // If the primary file is an absolute path, and the secondary is not, make the secondary file an absolute path and a sibling of the primary
-    // http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter
-    val filePath = asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions)(secondaryRelativeFileName)
-
-    // If the secondary file is in fact a directory, look into it and build its listing
-    for {
-      isDirectory <- ioFunctions.isDirectory(filePath).toIOChecked(ioFunctions.cs)
-      file <- if (isDirectory) recursivelyBuildDirectory(filePath, ioFunctions)() else WomFile(stringWomFileType, filePath).validIOChecked
-    } yield file
-  }
-
-  def secondaryExpressionFiles(primaryWomFile: WomFile,
-                               stringWomFileType: WomFileType,
-                               expression: Expression,
-                               parameterContext: ParameterContext,
-                               expressionLib: ExpressionLib,
-                               ioFunctions: IoFunctionSet): ErrorOr[List[WomFile]] = {
-
-    /*
-    If the value is an expression, the value of self in the expression must be the primary input or output File object
-    to which this binding applies.
-     */
-    val secondaryParameterContext = parameterContext.copy(self = primaryWomFile)
-
-    /*
-    The expression must return a filename string relative to the path to the primary File, a File or Directory object
-    with either path or location and basename fields set, or an array consisting of strings or File or Directory
-    objects.
-     */
-    def parseResult(nestedLevel: Int)(womValue: WomValue): ErrorOr[List[WomFile]] = {
-      womValue match {
-        case womString: WomString =>
-          List(WomFile(stringWomFileType, womString.value |> asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions))).valid
-        case womMaybeListedDirectory: WomMaybeListedDirectory =>
-          List(womMaybeListedDirectory.mapFile(asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions))).valid
-        case womMaybePopulatedFile: WomMaybePopulatedFile =>
-          List(womMaybePopulatedFile.mapFile(asAbsoluteSiblingOfPrimary(primaryWomFile, ioFunctions.pathFunctions))).valid
-        case womArray: WomArray if nestedLevel == 0 =>
-          womArray.value.toList flatTraverse parseResult(nestedLevel + 1)
-        case other => s"Not a valid secondary file: $other".invalidNel
-      }
-    }
-
-    val possibleArrayErrorOr: ErrorOr[WomValue] = ExpressionEvaluator.eval(expression, secondaryParameterContext)
-    possibleArrayErrorOr.flatMap(parseResult(nestedLevel = 0))
-  }
-
-  def relativeFileName(primary: String, secondary: String): String = {
-    /*
-    If a value in secondaryFiles is a string that is not an expression, it specifies that the following pattern should
-    be applied to the path of the primary file to yield a filename relative to the primary File:
-
-    1. If string begins with one or more caret ^ characters, for each caret, remove the last file extension from the
-    path (the last period . and all following characters). If there are no file extensions, the path is unchanged.
-
-    2. Append the remainder of the string to the end of the file path.
-     */
-    if (secondary.startsWith("^")) {
-      @tailrec
-      def stripCaret(primaryAcc: String, secondaryAcc: String): (String, String) = {
-        if (secondaryAcc.startsWith("^")) {
-          val idx = primaryAcc.lastIndexOf('.')
-          if (idx < 0) {
-            (primaryAcc, secondaryAcc.dropWhile(_ == '^'))
-          } else {
-            val primaryNext = primaryAcc.substring(0, idx)
-            val secondaryNext = secondaryAcc.drop(1)
-            stripCaret(primaryNext, secondaryNext)
-          }
-        } else {
-          (primaryAcc, secondaryAcc)
-        }
-      }
-
-      val (prefix, suffix) = stripCaret(primary, secondary)
-      prefix + suffix
-    } else {
-      primary + secondary
-    }
-
-  }
-}
-
-case class Directory private
-(
-  `class`: W.`"Directory"`.T,
-  location: Option[String],
-  path: Option[String],
-  basename: Option[String],
-  listing: Option[Array[FileOrDirectory]]
-) {
-  lazy val errorOrListingOption: ErrorOr[Option[List[WomFile]]] = {
-    val maybeErrorOrList: Option[ErrorOr[List[WomFile]]] =
-      listing map {
-        _.toList.traverse {
-          _.fold(CwlDirectoryOrFileAsWomSingleDirectoryOrFile)
-        }
-      }
-    maybeErrorOrList.sequence[ErrorOr, List[WomFile]]
-  }
-
-  lazy val asWomValue: ErrorOr[WomFile] = {
-    errorOrListingOption flatMap { listingOption =>
-      path.orElse(location) map { value =>
-        WomMaybeListedDirectory(Option(value), listingOption, basename).valid
-      } getOrElse {
-        val initializeFunction: WomMaybeListedDirectory => IoFunctionSet => IOChecked[WomValue] = { dir =>ioFunctionSet =>
-          ioFunctionSet.createTemporaryDirectory(basename).toIOChecked(ioFunctionSet.cs) map { tempDir =>
-            dir.copy(valueOption = Option(tempDir))
-          }
-        }
-        new WomMaybeListedDirectory(None, listingOption, basename, initializeFunction = initializeFunction).valid
-      }
-    }
-  }
-}
-
-object Directory {
-  def apply(location: Option[String] = None,
-            path: Option[String] = None,
-            basename: Option[String] = None,
-            listing: Option[Array[FileOrDirectory]] = None
-           ): Directory =
-    new cwl.Directory("Directory".narrow, location, path, basename, listing)
-
-  def basename(value: String): String = {
-    val stripped = value.stripSuffix("/")
-    stripped.substring(stripped.lastIndexOf('/') + 1)
-  }
-}
-
-private[cwl] object CwlDirectoryOrFileAsWomSingleDirectoryOrFile extends Poly1 {
-  implicit def caseFile: Case.Aux[File, ErrorOr[WomFile]] = at {
-    _.asWomValue
-  }
-
-  implicit def caseDirectory: Case.Aux[Directory, ErrorOr[WomFile]] = at {
-    _.asWomValue
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwlVersion.scala b/cwl/src/main/scala/cwl/CwlVersion.scala
deleted file mode 100644
index 12336b1cceb..00000000000
--- a/cwl/src/main/scala/cwl/CwlVersion.scala
+++ /dev/null
@@ -1,7 +0,0 @@
-package cwl
-
-object CwlVersion extends Enumeration {
-  type CwlVersion = Value
-
-  val Version1 = Value("v1.0")
-}
diff --git a/cwl/src/main/scala/cwl/CwlWomExpression.scala b/cwl/src/main/scala/cwl/CwlWomExpression.scala
deleted file mode 100644
index 5d77370ba49..00000000000
--- a/cwl/src/main/scala/cwl/CwlWomExpression.scala
+++ /dev/null
@@ -1,260 +0,0 @@
-package cwl
-
-import cats.instances.list._
-import cats.syntax.functor._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import common.validation.ErrorOr.{ErrorOr, ShortCircuitingFlatMap}
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import cwl.InitialWorkDirFileGeneratorExpression._
-import cwl.InitialWorkDirRequirement.IwdrListingArrayEntry
-import shapeless.Poly1
-import wom.callable.{AdHocValue, ContainerizedInputExpression}
-import wom.expression.IoFunctionSet.{IoDirectory, IoFile}
-import wom.expression.{FileEvaluation, IoFunctionSet, WomExpression}
-import wom.types._
-import wom.values._
-
-import scala.concurrent.Await
-import scala.concurrent.duration.Duration
-
-trait CwlWomExpression extends WomExpression {
-
-  def cwlExpressionType: WomType
-
-  override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] = cwlExpressionType.validNel
-
-  def expressionLib: ExpressionLib
-
-  def evaluate(inputs: Map[String, WomValue], parameterContext: ParameterContext, expression: Expression): ErrorOr[WomValue] =
-    expression.
-      fold(EvaluateExpression).
-      apply(parameterContext)
-}
-
-case class ECMAScriptWomExpression(expression: Expression,
-                                   override val inputs: Set[String],
-                                   override val expressionLib: ExpressionLib) extends CwlWomExpression {
-  val cwlExpressionType = WomAnyType
-
-  override def sourceString = expression match {
-    case Expression.ECMAScriptExpression(s) => s.value
-    case Expression.ECMAScriptFunction(s) => s.value
-    case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-  }
-
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet) = {
-    val pc = ParameterContext(ioFunctionSet, expressionLib, inputValues)
-    evaluate(inputValues, pc, expression)
-  }
-
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType) = Set.empty[FileEvaluation].validNel
-}
-
-final case class InitialWorkDirFileGeneratorExpression(entry: IwdrListingArrayEntry, expressionLib: ExpressionLib) extends ContainerizedInputExpression {
-
-  def evaluate(inputValues: Map[String, WomValue], mappedInputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): IOChecked[List[AdHocValue]] = {
-    def recursivelyBuildDirectory(directory: String): IOChecked[WomMaybeListedDirectory] = {
-      import cats.syntax.traverse._
-      for {
-        listing <- ioFunctionSet.listDirectory(directory)().toIOChecked(ioFunctionSet.cs)
-        fileListing <- listing.toList.traverse[IOChecked, WomFile] {
-          case IoDirectory(e) => recursivelyBuildDirectory(e).widen
-          case IoFile(e) => WomSingleFile(e).validIOChecked.widen
-        }
-      } yield WomMaybeListedDirectory(Option(directory), Option(fileListing))
-    }
-
-    inputValues.toList.traverse[IOChecked, (String, WomValue)]({
-      case (k, v: WomMaybeListedDirectory) =>
-        val absolutePathString = ioFunctionSet.pathFunctions.relativeToHostCallRoot(v.value)
-        recursivelyBuildDirectory(absolutePathString).contextualizeErrors(s"Error building directory $absolutePathString") map { k -> _ }
-      case kv => kv.validIOChecked
-    }).map(_.toMap)
-      .flatMap({ updatedValues =>
-        val unmappedParameterContext = ParameterContext(ioFunctionSet, expressionLib, updatedValues)
-        entry.fold(InitialWorkDirFilePoly).apply(unmappedParameterContext, mappedInputValues).toIOChecked
-      })
-  }
-}
-
-object InitialWorkDirFileGeneratorExpression {
-  type InitialWorkDirFileEvaluator = (ParameterContext, Map[String, WomValue]) => ErrorOr[List[AdHocValue]]
-
-  /**
-    * Converts an InitialWorkDir.
-    *
-    * TODO: Review against the spec. Especially for Dirent values. For example:
-    *
-    * "If the value is an expression that evaluates to a Dirent object, this indicates that the File or Directory in
-    * entry should be added to the designated output directory with the name in entryname."
-    *
-    * - http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement
-    * - http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent
-    */
-  object InitialWorkDirFilePoly extends Poly1 {
-    implicit val caseExpressionDirent: Case.Aux[ExpressionDirent, InitialWorkDirFileEvaluator] = {
-      at { expressionDirent =>
-        (unmappedParameterContext, mappedInputValues) => {
-
-          val mutableInputOption = expressionDirent.entry.fold(ExpressionToMutableInputOptionPoly)
-
-          val entryEvaluation =
-            expressionDirent.entry match {
-                //we need to catch this special case to feed in "value-mapped" input values
-              case expr@Expression.ECMAScriptExpression(exprString) if exprString.value.trim() == "$(JSON.stringify(inputs))" =>
-                val specialParameterContext = ParameterContext(
-                  unmappedParameterContext.ioFunctionSet,
-                  unmappedParameterContext.expressionLib,
-                  mappedInputValues
-                )
-                ExpressionEvaluator.eval(expr, specialParameterContext)
-              case _ => ExpressionEvaluator.eval(expressionDirent.entry, unmappedParameterContext)
-            }
-
-          val womValueErrorOr: ErrorOr[AdHocValue] = entryEvaluation flatMap {
-            case womFile: WomFile =>
-              val errorOrEntryName: ErrorOr[Option[String]] = expressionDirent.entryname match {
-                case Some(actualEntryName) => actualEntryName.fold(EntryNamePoly).apply(unmappedParameterContext).map(Option.apply)
-                case None => None.valid
-              }
-              errorOrEntryName map { entryName =>
-                AdHocValue(womFile, entryName, inputName = mutableInputOption)
-              }
-            case other => for {
-              coerced <- WomStringType.coerceRawValue(other).toErrorOr
-              contentString = coerced.asInstanceOf[WomString].value
-              // We force the entryname to be specified, and then evaluate it:
-              entryNameStringOrExpression <- expressionDirent.entryname.toErrorOr(
-                "Invalid dirent: Entry was a string but no file name was supplied")
-              entryName <- entryNameStringOrExpression.fold(EntryNamePoly).apply(unmappedParameterContext)
-              writeFile = unmappedParameterContext.ioFunctionSet.writeFile(entryName, contentString)
-              writtenFile <- validate(Await.result(writeFile, Duration.Inf))
-            } yield AdHocValue(writtenFile, alternativeName = None, inputName = mutableInputOption)
-          }
-
-          womValueErrorOr.map(List(_))
-        }
-      }
-    }
-
-    implicit val caseStringDirent: Case.Aux[StringDirent, InitialWorkDirFileEvaluator] = {
-      at {
-        stringDirent => {
-          (unmappedParameterContext, _) =>
-            val womValueErrorOr = for {
-              entryName <- stringDirent.entryname.fold(EntryNamePoly).apply(unmappedParameterContext)
-              contentString = stringDirent.entry
-              writeFile = unmappedParameterContext.ioFunctionSet.writeFile(entryName, contentString)
-              writtenFile <- validate(Await.result(writeFile, Duration.Inf))
-            } yield writtenFile
-
-            womValueErrorOr.map(AdHocValue(_, alternativeName = None, inputName = None)).map(List(_))
-        }
-      }
-    }
-
-    implicit val caseExpression: Case.Aux[Expression, InitialWorkDirFileEvaluator] = {
-      at { expression =>
-        (unmappedParameterContext, _) => {
-          // A single expression which must evaluate to an array of Files
-          val expressionEvaluation = ExpressionEvaluator.eval(expression, unmappedParameterContext)
-
-          expressionEvaluation flatMap {
-            case array: WomArray if array.value.forall(_.isInstanceOf[WomFile]) =>
-              array.value.toList.map(_.asInstanceOf[WomFile]).map(AdHocValue(_, alternativeName = None, inputName = None)).validNel
-            case file: WomFile =>
-              List(AdHocValue(file, alternativeName = None, inputName = None)).validNel
-            case other =>
-              val error = "InitialWorkDirRequirement listing expression must be File or Array[File] but got %s: %s"
-                .format(other, other.womType.stableName)
-              error.invalidNel
-          }
-        }
-      }
-    }
-
-    implicit val caseString: Case.Aux[String, InitialWorkDirFileEvaluator] = {
-      at { string =>
-        (_, _) => {
-          List(AdHocValue(WomSingleFile(string), alternativeName = None, inputName = None)).valid
-        }
-      }
-    }
-
-    implicit val caseStringOrExpression: Case.Aux[StringOrExpression, InitialWorkDirFileEvaluator] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit val caseFile: Case.Aux[File, InitialWorkDirFileEvaluator] = {
-      at { file =>
-        (_, _) => {
-          file.asWomValue.map(AdHocValue(_, alternativeName = None, inputName = None)).map(List(_))
-        }
-      }
-    }
-
-    implicit val caseDirectory: Case.Aux[Directory, InitialWorkDirFileEvaluator] = {
-      at { directory =>
-        (_, _) => {
-          directory.asWomValue.map(AdHocValue(_, alternativeName = None, inputName = None)).map(List(_))
-        }
-      }
-    }
-
-  }
-
-  type EntryNameEvaluator = ParameterContext => ErrorOr[String]
-
-  object EntryNamePoly extends Poly1 {
-    implicit val caseString: Case.Aux[String, EntryNameEvaluator] = {
-      at {
-        string => {
-          _ =>
-            string.valid
-        }
-      }
-    }
-
-    implicit val caseExpression: Case.Aux[Expression, EntryNameEvaluator] = {
-      at {
-        expression => {
-          parameterContext =>
-            for {
-              entryNameExpressionEvaluated <- ExpressionEvaluator.eval(expression, parameterContext)
-              entryNameValidated <- mustBeString(entryNameExpressionEvaluated)
-            } yield entryNameValidated
-        }
-      }
-    }
-
-    private def mustBeString(womValue: WomValue): ErrorOr[String] = {
-      womValue match {
-        case WomString(s) => s.valid
-        case other => WomStringType.coerceRawValue(other).map(_.asInstanceOf[WomString].value).toErrorOr
-      }
-    }
-  }
-
-  /**
-    * Searches for ECMAScript expressions that mutate input paths.
-    *
-    * @see [[AdHocValue]]
-    */
-  object ExpressionToMutableInputOptionPoly extends Poly1 {
-    private val MutableInputRegex = """(?s)\s*\$\(\s*inputs\.(\w+)\s*\)\s*""".r
-    implicit val caseECMAScriptExpression: Case.Aux[ECMAScriptExpression, Option[String]] = {
-      at { eCMAScriptExpression =>
-        eCMAScriptExpression.value match {
-          case MutableInputRegex(mutableInput) => Option(mutableInput)
-          case _ => None
-        }
-      }
-    }
-    implicit val caseECMAScriptFunction: Case.Aux[ECMAScriptFunction, Option[String]] = at { _ => None }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/CwltoolRunner.scala b/cwl/src/main/scala/cwl/CwltoolRunner.scala
deleted file mode 100644
index 834c9d80b23..00000000000
--- a/cwl/src/main/scala/cwl/CwltoolRunner.scala
+++ /dev/null
@@ -1,71 +0,0 @@
-package cwl
-
-import ammonite.ops.ImplicitWd._
-import ammonite.ops._
-import com.typesafe.config.ConfigFactory
-import cwl.preprocessor.CwlReference
-import org.broadinstitute.heterodon.ExecAndEval
-
-/**
-  * Interface for running cwltool.
-  */
-sealed trait CwltoolRunner {
-  def salad(reference: CwlReference): String
-}
-
-object CwltoolRunner {
-  private lazy val config = ConfigFactory.load
-
-  lazy val instance: CwltoolRunner = {
-    val runnerClass = config.getString("cwltool-runner.class")
-    Class.forName(runnerClass).getDeclaredConstructor().newInstance().asInstanceOf[CwltoolRunner]
-  }
-}
-
-/**
-  * Runs cwltool as an external process.
-  */
-final class CwltoolProcess extends CwltoolRunner {
-  override def salad(reference: CwlReference): String = {
-    val commandResult: CommandResult = %%("cwltool", "--quiet", "--print-pre", reference.pathAsString)
-    commandResult.exitCode match {
-      case 0 => commandResult.out.string
-      case error =>
-        throw new RuntimeException(
-          s"running CwlTool on file ${reference.pathAsString} resulted in exit code $error and stderr ${commandResult.err.string}")
-    }
-  }
-}
-
-/**
-  * Runs cwltool via heterodon.
-  *
-  * https://github.com/broadinstitute/heterodon
-  */
-final class CwltoolHeterodon extends CwltoolRunner {
-  // Trimmed down version of
-  // https://github.com/common-workflow-language/cwltool/blob/1a839255795882894b4bbfea6d909a74cacb1d6a/cwltool/main.py#L355
-  private val cwltoolSaladExecScript =
-  """|import json
-     |import logging
-     |
-     |from cwltool.load_tool import fetch_document, resolve_tool_uri, validate_document
-     |from cwltool.loghandler import _logger
-     |
-     |
-     |def cwltool_salad(path):
-     |    _logger.setLevel(logging.WARN)
-     |    uri, tool_file_uri = resolve_tool_uri(path)
-     |    document_loader, workflowobj, uri = fetch_document(uri)
-     |    document_loader, avsc_names, processobj, metadata, uri \
-     |        = validate_document(document_loader, workflowobj, uri, preprocess_only=True)
-     |    return json.dumps(processobj, indent=4)
-     |""".stripMargin
-
-  private def cwltoolSaladEvalStatement(reference: CwlReference): String = s"cwltool_salad('${reference.pathAsString}')"
-
-  def salad(reference: CwlReference): String = {
-    val execAndEval = new ExecAndEval()
-    execAndEval.apply(cwltoolSaladExecScript, cwltoolSaladEvalStatement(reference)).asInstanceOf[String]
-  }
-}
diff --git a/cwl/src/main/scala/cwl/EnumSchema.scala b/cwl/src/main/scala/cwl/EnumSchema.scala
deleted file mode 100644
index 83ff1b05813..00000000000
--- a/cwl/src/main/scala/cwl/EnumSchema.scala
+++ /dev/null
@@ -1,35 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import shapeless.Witness
-import wom.types.WomEnumerationType
-
-trait EnumSchema {
-
-  val name: Option[String]
-  val symbols: Array[String]
-  val `type`: Witness.`"enum"`.T
-  val label: Option[String]
-
-  def toWomEnumerationType: WomEnumerationType = {
-    val symbolIds = symbols.toList.map{
-      s => s.substring(s.lastIndexOf("/") + 1)
-    }
-    WomEnumerationType(NonEmptyList.fromListUnsafe(symbolIds))
-  }
-}
-
-case class InputEnumSchema(
-  name: Option[String],
-  symbols: Array[String],
-  `type`: Witness.`"enum"`.T = Witness("enum").value,
-  label: Option[String] = None,
-  inputBinding: Option[InputCommandLineBinding] = None) extends EnumSchema
-
-case class OutputEnumSchema(
-  name: Option[String],
-  symbols: Array[String],
-  `type`: Witness.`"enum"`.T,
-  label: Option[String],
-  outputBinding: Option[CommandOutputBinding]) extends EnumSchema
-
diff --git a/cwl/src/main/scala/cwl/EvaluateExpression.scala b/cwl/src/main/scala/cwl/EvaluateExpression.scala
deleted file mode 100644
index 00036d49de4..00000000000
--- a/cwl/src/main/scala/cwl/EvaluateExpression.scala
+++ /dev/null
@@ -1,20 +0,0 @@
-package cwl
-
-import common.validation.ErrorOr.ErrorOr
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import shapeless.Poly1
-import wom.values.WomValue
-
-object EvaluateExpression extends Poly1 {
-  implicit val script: Case.Aux[ECMAScriptExpression, ParameterContext => ErrorOr[WomValue]] = {
-    at {
-      ExpressionEvaluator.evalExpression
-    }
-  }
-
-  implicit val function: Case.Aux[ECMAScriptFunction, ParameterContext => ErrorOr[WomValue]] = {
-    at {
-      ExpressionEvaluator.evalFunction
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ExpressionEvaluator.scala b/cwl/src/main/scala/cwl/ExpressionEvaluator.scala
deleted file mode 100644
index a3ed2c7a7c4..00000000000
--- a/cwl/src/main/scala/cwl/ExpressionEvaluator.scala
+++ /dev/null
@@ -1,101 +0,0 @@
-package cwl
-
-import cats.syntax.validated._
-import common.validation.ErrorOr._
-import cwl.internal.{CwlEcmaScriptDecoder, EcmaScriptEncoder, EcmaScriptUtil}
-import eu.timepit.refined.api.Refined
-import eu.timepit.refined.string.MatchesRegex
-import shapeless.Witness
-import wom.callable.RuntimeEnvironment
-import wom.values.{WomFloat, WomInteger, WomString, WomValue}
-
-// http://www.commonwl.org/v1.0/CommandLineTool.html#Expressions
-object ExpressionEvaluator {
-  // A code fragment wrapped in the $(...) syntax must be evaluated as a ECMAScript expression.
-  /*
-  There are several places in cwltool where a simple contains check is used:
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/builder.py#L157
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/command_line_tool.py#L669
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/expression.py#L219
-  - https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/process.py#L645
-   */
-  val ECMAScriptExpressionWitness = Witness("""(?s).*\$\(.*""")
-  val ECMAScriptExpressionRegex = ECMAScriptExpressionWitness.value.r
-  type MatchesECMAScriptExpression = MatchesRegex[ECMAScriptExpressionWitness.T]
-  type ECMAScriptExpression = String Refined MatchesECMAScriptExpression
-
-  // A code fragment wrapped in the ${...} syntax must be evaluated as a ECMAScript function body for an anonymous,
-  // zero-argument function.
-  val ECMAScriptFunctionWitness = Witness("""(?s)\s*\$\{(.*)\}\s*""")
-  val ECMAScriptFunctionRegex = ECMAScriptFunctionWitness.value.r
-  type MatchesECMAScriptFunction = MatchesRegex[ECMAScriptFunctionWitness.T]
-  type ECMAScriptFunction = String Refined MatchesECMAScriptFunction
-
-  def eval(expr: Expression, parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    expr.fold(EvaluateExpression).apply(parameterContext)
-  }
-
-  def evalExpression(expression: ECMAScriptExpression)(parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    def evaluator(string: String): ErrorOr[WomValue] = {
-      eval(string, parameterContext)
-    }
-
-    ExpressionInterpolator.interpolate(expression.value, evaluator, strip_whitespace = false)
-  }
-
-  def evalFunction(function: ECMAScriptFunction)(parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    function.value match {
-      case ECMAScriptFunctionRegex(script) =>
-
-        val functionExpression =
-          s"""|(function() {
-              |FUNCTION_BODY
-              |})();
-              |""".stripMargin.replace("FUNCTION_BODY", script)
-
-        eval(functionExpression, parameterContext)
-      case unmatched =>
-        s"Expression '$unmatched' was unable to be matched to regex '${ECMAScriptFunctionWitness.value}'".invalidNel
-    }
-  }
-
-  private lazy val cwlJsDecoder = new CwlEcmaScriptDecoder()
-
-  def eval(expr: String, parameterContext: ParameterContext): ErrorOr[WomValue] = {
-    val script = if (parameterContext.expressionLib.isEmpty) {
-      expr
-    } else {
-      parameterContext.expressionLib.mkString("", ";", s";$expr")
-    }
-    val (rawVals, mapVals) = paramValues(parameterContext)
-    EcmaScriptUtil.evalStructish(
-      script,
-      rawVals,
-      mapVals,
-      new EcmaScriptEncoder(),
-      cwlJsDecoder
-    )
-  }
-
-  def paramValues(parameterContext: ParameterContext): ((String, WomValue), Map[String, Map[String, WomValue]]) = {
-    (
-        "self" -> parameterContext.self
-      ,
-      Map(
-        "inputs" -> parameterContext.inputs,
-        "runtime" -> parameterContext.runtimeOption.map(cwlMap).getOrElse(Map.empty)
-      )
-    )
-  }
-
-  def cwlMap(runtime: RuntimeEnvironment): Map[String, WomValue] = {
-    Map(
-      "outdir" -> WomString(runtime.outputPath),
-      "tmpdir" -> WomString(runtime.tempPath),
-      "cores" -> WomInteger(runtime.cores.value),
-      "ram" -> WomFloat(runtime.ram),
-      "outdirSize" -> WomFloat(runtime.outputPathSize.toDouble),
-      "tmpdirSize" -> WomFloat(runtime.tempPathSize.toDouble)
-    )
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ExpressionInterpolator.scala b/cwl/src/main/scala/cwl/ExpressionInterpolator.scala
deleted file mode 100644
index 9a40ee8e06f..00000000000
--- a/cwl/src/main/scala/cwl/ExpressionInterpolator.scala
+++ /dev/null
@@ -1,173 +0,0 @@
-package cwl
-
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.validation.ErrorOr._
-import wom.types.WomNothingType
-import wom.values._
-
-import scala.jdk.CollectionConverters._
-
-/**
-  * Partial copy-port of cwltool's expression.py.
-  *
-  * Minimizes refactor so that as expression.py continues to update the updates may be manually copied here also.
-  *
-  * Current omissions in `def interpolate`:
-  * - `def evaluator`
-  *   - Utility not copy-ported.
-  *   - `def interpolate` instead ignores absence of InlineJavascriptRequirement and instead always uses fullJS=True
-  * - `leaf = json.dumps(e, sort_keys=True)`
-  *   - When the interpolated string is not just-a-single-expression there is undefined behavior of rendering
-  *     non-WomPrimitive values into json.
-  *   - Even if it did, does not sort the keys.
-  *   - Thus we do not currently return character-for-character equality for these expressions with cwltool, however
-  *     these cases are not explicitly defined in the CWL spec as far as I know.
-  *
-  * @see https://github.com/common-workflow-language/cwltool/blob/353dbed/cwltool/expression.py
-  */
-//noinspection ZeroIndexToHead,RemoveRedundantReturn
-object ExpressionInterpolator {
-
-  class SubstitutionException(message: String) extends RuntimeException(message)
-
-  /**
-    * Copy-port of expression.py's scanner.
-    */
-  private def scanner(scan: String): List[Int] = {
-    val DEFAULT = 0
-    val DOLLAR = 1
-    val PAREN = 2
-    val BRACE = 3
-    val SINGLE_QUOTE = 4
-    val DOUBLE_QUOTE = 5
-    val BACKSLASH = 6
-
-    var i = 0
-    val stack = new java.util.Stack[Int]
-    stack.push(DEFAULT)
-    var start = 0
-    while (i < scan.length) {
-      val state = stack.peek
-      val c = scan(i)
-
-      if (state == DEFAULT) {
-        if (c == '$') {
-          stack.push(DOLLAR)
-        } else if (c == '\\') {
-          stack.push(BACKSLASH)
-        }
-      } else if (state == BACKSLASH) {
-        stack.pop()
-        if (stack.peek == DEFAULT) {
-          return List(i - 1, i + 1)
-        }
-      } else if (state == DOLLAR) {
-        if (c == '(') {
-          start = i - 1
-          stack.push(PAREN)
-        } else if (c == '{') {
-          start = i - 1
-          stack.push(BRACE)
-        } else {
-          stack.pop()
-        }
-      } else if (state == PAREN) {
-        if (c == '(') {
-          stack.push(PAREN)
-        } else if (c == ')') {
-          stack.pop()
-          if (stack.peek == DOLLAR) {
-            return List(start, i + 1)
-          }
-        } else if (c == '\'') {
-          stack.push(SINGLE_QUOTE)
-        } else if (c == '"') {
-          stack.push(DOUBLE_QUOTE)
-        }
-      } else if (state == BRACE) {
-        if (c == '{') {
-          stack.push(BRACE)
-        } else if (c == '}') {
-          stack.pop()
-          if (stack.peek == DOLLAR) {
-            return List(start, i + 1)
-          }
-        } else if (c == '\'') {
-          stack.push(SINGLE_QUOTE)
-        } else if (c == '"') {
-          stack.push(DOUBLE_QUOTE)
-        }
-      } else if (state == SINGLE_QUOTE) {
-        if (c == '\'') {
-          stack.pop()
-        } else if (c == '\\') {
-          stack.push(BACKSLASH)
-        }
-      } else if (state == DOUBLE_QUOTE) {
-        if (c == '"') {
-          stack.pop()
-        } else if (c == '\\') {
-          stack.push(BACKSLASH)
-        }
-      }
-      i += 1
-    }
-    if (stack.size > 1) {
-      throw new SubstitutionException(
-        "Substitution error, unfinished block starting at position %s: %s".format(start, scan.drop(start)))
-    } else {
-      return null
-    }
-  }
-
-  /**
-    * Copy-port of expression.py's interpolate.
-    */
-  def interpolate(scanParam: String,
-                  evaluator: String => ErrorOr[WomValue],
-                  strip_whitespace: Boolean = true): ErrorOr[WomValue] = {
-    var scan = scanParam
-    if (strip_whitespace) {
-      scan = scan.trim
-    }
-    val parts = new java.util.Stack[ErrorOr[WomValue]]
-    var w = scanner(scan)
-    while (w != null) {
-      parts.push(WomString(scan.slice(0, w(0))).valid)
-
-      if (scan(w(0)) == '$') {
-        val e = evaluator(scan.slice(w(0) + 1, w(1)))
-        if (w(0) == 0 && w(1) == scan.length && parts.size <= 1) {
-          return e
-        }
-        /*
-        Original-ish:
-          var leaf = json.dumps(e, sort_keys=True)
-          if (leaf(0) == '"') {
-            leaf = leaf.drop(1).dropRight(1)
-          }
-        Instead, push the raw WomValue. WomString's won't have been quoted as python's json.dumps does.
-        Other WomPrimitive's should be fine. CWL using other structures (Maps, Arrays, etc.) may have problems.
-         */
-        val leaf = e
-        parts.push(leaf)
-      } else if (scan(w(0)) == '\\') {
-        val e = scan(w(1) - 1)
-        parts.push(WomString(e.toString).valid)
-      }
-
-      scan = scan.drop(w(1))
-      w = scanner(scan)
-    }
-    parts.push(WomString(scan).valid)
-    return parts.asScala.toList.sequence[ErrorOr, WomValue] map { list =>
-      WomString(list.map{
-        //we represent nulls as this type because Wom doesn't have a "null" value, but it does have a nothing type
-        case WomOptionalValue(WomNothingType, None) => "null"
-        case other => other.valueString
-      }.mkString(""))
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ExpressionTool.scala b/cwl/src/main/scala/cwl/ExpressionTool.scala
deleted file mode 100644
index 53c8a675a4c..00000000000
--- a/cwl/src/main/scala/cwl/ExpressionTool.scala
+++ /dev/null
@@ -1,136 +0,0 @@
-package cwl
-
-import cats.syntax.either._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import cwl.CwlVersion._
-import cwl.ExpressionTool.{ExpressionToolInputParameter, ExpressionToolOutputParameter}
-import shapeless.{Coproduct, Witness}
-import wom.RuntimeAttributes
-import wom.callable.{Callable, CallableExpressionTaskDefinition}
-import wom.expression.{IoFunctionSet, ValueAsAnExpression}
-import wom.graph.GraphNodePort.OutputPort
-import wom.types.{WomMapType, WomStringType, WomType}
-import wom.values.{WomMap, WomObject, WomString, WomValue}
-
-case class ExpressionTool(
-                           inputs: Array[ExpressionToolInputParameter] = Array.empty,
-                           outputs: Array[ExpressionToolOutputParameter] = Array.empty,
-                           `class`: Witness.`"ExpressionTool"`.T,
-                           expression: StringOrExpression,
-                           id: String,
-                           requirements: Option[Array[Requirement]] = None,
-                           hints: Option[Array[Hint]] = None,
-                           label: Option[String] = None,
-                           doc: Option[String] = None,
-                           cwlVersion: Option[CwlVersion] = None,
-                           `$namespaces`: Option[Map[String, String]] = None,
-                           `$schemas`: Option[Array[String]] = None
-                         ) extends Tool {
-
-  def asCwl: Cwl = Coproduct[Cwl](this)
-
-  def castWomValueAsMap(evaluatedExpression: WomValue): Checked[Map[String, WomValue]] = {
-    evaluatedExpression match {
-      case WomMap(WomMapType(WomStringType, _), map) =>  map.map{
-        case (WomString(key), value) => key -> value
-        case (key, _) => throw new RuntimeException(s"saw a non-string value $key in wom map $evaluatedExpression typed with string keys ")
-      }.asRight
-      case obj: WomObject => obj.values.asRight
-      case _ => s"Could not cast value $evaluatedExpression to a Map[String, WomValue]".invalidNelCheck
-    }
-  }
-
-  def buildTaskDefinition(taskName: String,
-                          inputDefinitions: List[_ <: Callable.InputDefinition],
-                          outputDefinitions: List[Callable.OutputDefinition],
-                          runtimeAttributes: RuntimeAttributes,
-                          requirementsAndHints: List[cwl.Requirement],
-                          expressionLib: ExpressionLib): ErrorOr[CallableExpressionTaskDefinition] = {
-
-    def evaluate(inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, outputPorts: List[OutputPort]): Checked[Map[OutputPort, WomValue]] = {
-      val womExpression = expression match {
-        case StringOrExpression.String(str) => ValueAsAnExpression(WomString(str))
-        case StringOrExpression.Expression(expr) => ECMAScriptWomExpression(expr, inputNames, expressionLib)
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-
-      // If we expect a certain type for
-      def coerce(womValue: WomValue, womType: WomType): Checked[WomValue] = womType.coerceRawValue(womValue).toChecked
-
-      /*
-        * Look in the object (the result of the expression evaluation) for values to match output each port.
-        * Ideally we'd want to find a value for each output port declared by the tool.
-        * However since the spec is not clear on this and cwltool seems to ignore entirely the outputs declaration,
-        * we'll do the same for now, meaning we'll assign a value to the output port iff the result of the expression has one for them,
-        * otherwise we'll remove the port for the final map.
-        * If there are fields in the expression's result that do not have a matching declared output port, they won't be added either,
-        * because we'd have to create an output port for them now which would be useless anyway since nothing could point to it.
-       */
-      def mapPortsToValues(values: Map[String, WomValue]): Checked[Map[OutputPort, WomValue]] = {
-        import cats.syntax.traverse._
-
-        val coercedValues: List[ErrorOr[(OutputPort, WomValue)]] = for {
-          outputPort <- outputPorts
-          value <- values.get(outputPort.internalName)
-          coerced = coerce(value, outputPort.womType).toValidated
-        } yield coerced.map(outputPort -> _)
-
-        coercedValues.sequence[ErrorOr, (OutputPort, WomValue)].map(_.toMap).toEither
-      }
-
-      for {
-        // Evaluate the expression
-        evaluatedExpression <- womExpression.evaluateValue(inputs, ioFunctionSet).toEither
-        /*
-          * We expect the result to be an object of the form:
-          * {
-          *   "outputName": value,
-          *   ...
-          * }
-         */
-        womMap <- castWomValueAsMap(evaluatedExpression)
-
-        mappedValues <- mapPortsToValues(womMap)
-      } yield mappedValues
-    }
-
-    CallableExpressionTaskDefinition(
-      taskName,
-      evaluate,
-      runtimeAttributes,
-      Map.empty,
-      Map.empty,
-      outputDefinitions,
-      inputDefinitions,
-      // TODO: This doesn't work in all cases and it feels clunky anyway - find a way to sort that out
-      prefixSeparator = "#"
-    ).validNel
-  }
-}
-
-object ExpressionTool {
-
-  case class ExpressionToolInputParameter(id: String,
-                                          label: Option[String] = None,
-                                          secondaryFiles: Option[SecondaryFiles] = None,
-                                          format: Option[InputParameterFormat] = None,
-                                          streamable: Option[Boolean] = None,
-                                          doc: Option[Doc] = None,
-                                          inputBinding: Option[InputCommandLineBinding] = None,
-                                          default: Option[CwlAny] = None,
-                                          `type`: Option[MyriadInputType] = None) extends InputParameter
-
-  case class ExpressionToolOutputParameter(id: String,
-                                           label: Option[String] = None,
-                                           secondaryFiles: Option[SecondaryFiles] = None,
-                                           format: Option[OutputParameterFormat] = None,
-                                           streamable: Option[Boolean] = None,
-                                           doc: Option[Doc] = None,
-                                           outputBinding: Option[CommandOutputBinding] = None,
-                                           `type`: Option[MyriadOutputType] = None) extends OutputParameter
-}
diff --git a/cwl/src/main/scala/cwl/FileParameter.scala b/cwl/src/main/scala/cwl/FileParameter.scala
deleted file mode 100644
index 2413d9d7c02..00000000000
--- a/cwl/src/main/scala/cwl/FileParameter.scala
+++ /dev/null
@@ -1,150 +0,0 @@
-package cwl
-
-import cats.effect.IO
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.ontology.Schema
-import shapeless.Poly1
-import wom.expression.IoFunctionSet
-import wom.types.{WomFileType, WomMaybePopulatedFileType}
-import wom.values.{WomArray, WomFile, WomMaybePopulatedFile, WomValue}
-
-object FileParameter {
-  private val ReadLimit = Option(64 * 1024)
-
-  def populateSecondaryFiles(womValue: WomValue,
-                             secondaryFilesCoproduct: Option[SecondaryFiles],
-                             formatOption: Option[String],
-                             parameterContext: ParameterContext,
-                             expressionLib: ExpressionLib,
-                             ioFunctions: IoFunctionSet): IOChecked[WomValue] = {
-
-    womValue match {
-
-      case womMaybePopulatedFile: WomMaybePopulatedFile =>
-        val secondaryFilesErrorOr = FileParameter.secondaryFiles(
-          womMaybePopulatedFile,
-          WomMaybePopulatedFileType,
-          secondaryFilesCoproduct,
-          parameterContext,
-          expressionLib,
-          ioFunctions
-        )
-
-        secondaryFilesErrorOr map { secondaryFiles =>
-          womMaybePopulatedFile.copy(secondaryFiles = secondaryFiles, formatOption = formatOption)
-        }
-
-      case womArray: WomArray =>
-        womArray.value.toList.traverse(
-          populateSecondaryFiles(_, secondaryFilesCoproduct, formatOption, parameterContext, expressionLib, ioFunctions)
-        ).map(WomArray(_))
-
-      case womValue: WomValue => womValue.validIOChecked
-    }
-  }
-
-  /**
-    * Checks if the file is compatible with a format.
-    */
-  def checkFormat(womMaybePopulatedFile: WomMaybePopulatedFile,
-                  formatsOption: Option[List[String]],
-                  schemaOption: Option[Schema]): ErrorOr[Unit] = {
-    validate {
-      for {
-        schema <- schemaOption
-        fileFormat <- womMaybePopulatedFile.formatOption
-        formats <- formatsOption
-      } yield {
-        if (!formats.exists(schema.isSubClass(fileFormat, _)))
-          throw new RuntimeException(s"$fileFormat is not compatible with ${formats.mkString(", ")}")
-      }
-      ()
-    }
-  }
-
-  /**
-    * Populates the contents if they aren't loaded already.
-    */
-  def maybeLoadContents(womMaybePopulatedFile: WomMaybePopulatedFile,
-                        ioFunctionSet: IoFunctionSet,
-                        loadContents: Boolean): IO[Option[String]] = {
-    womMaybePopulatedFile.contentsOption match {
-      case someContents@Some(_) => IO.pure(someContents)
-      case None if !loadContents => IO.pure(None)
-      case _ => FileParameter.load64KiB(womMaybePopulatedFile.value, ioFunctionSet).map(Option(_))
-    }
-  }
-
-  def load64KiB(path: String, ioFunctionSet: IoFunctionSet): IO[String] = {
-    implicit val ec = IO.contextShift(ioFunctionSet.ec)
-    IO.fromFuture(IO { ioFunctionSet.readFile(path, ReadLimit, failOnOverflow = false) })
-  }
-
-  /**
-    * Returns the list of secondary files for the primary file.
-    */
-  def secondaryFiles(primaryWomFile: WomFile,
-                     stringWomFileType: WomFileType,
-                     secondaryFilesOption: Option[SecondaryFiles],
-                     parameterContext: ParameterContext,
-                     expressionLib: ExpressionLib,
-                     ioFunctions: IoFunctionSet): IOChecked[List[WomFile]] = {
-    secondaryFilesOption
-      .map(secondaryFiles(primaryWomFile, stringWomFileType, _, parameterContext, expressionLib, ioFunctions))
-      .getOrElse(List.empty[WomFile].validIOChecked)
-  }
-
-  /**
-    * Returns the list of secondary files for the primary file.
-    */
-  def secondaryFiles(primaryWomFile: WomFile,
-                     stringWomFileType: WomFileType,
-                     secondaryFiles: SecondaryFiles,
-                     parameterContext: ParameterContext,
-                     expressionLib: ExpressionLib,
-                     ioFunctions: IoFunctionSet): IOChecked[List[WomFile]] = {
-    secondaryFiles
-      .fold(SecondaryFilesPoly)
-      .apply(primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions)
-  }
-
-  type SecondaryFilesFunction = (WomFile, WomFileType, ParameterContext, ExpressionLib, IoFunctionSet) => IOChecked[List[WomFile]]
-
-  object SecondaryFilesPoly extends Poly1 {
-    implicit def caseStringOrExpression: Case.Aux[StringOrExpression, SecondaryFilesFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseExpression: Case.Aux[Expression, SecondaryFilesFunction] = {
-      at {
-        expression =>
-          (primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions) =>
-            File.secondaryExpressionFiles(primaryWomFile, stringWomFileType, expression, parameterContext, expressionLib, ioFunctions).toIOChecked
-      }
-    }
-
-    implicit def caseString: Case.Aux[String, SecondaryFilesFunction] = {
-      at {
-        string =>
-          (primaryWomFile, stringWomFileType, _, _, ioFunctions) =>
-            File.secondaryStringFile(primaryWomFile, stringWomFileType, string, ioFunctions).map(List(_))
-      }
-    }
-
-    implicit def caseArray: Case.Aux[Array[StringOrExpression], SecondaryFilesFunction] = {
-      at {
-        array =>
-          (primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions) =>
-            val functions: List[SecondaryFilesFunction] = array.toList.map(_.fold(this))
-            functions.flatTraverse(_ (primaryWomFile, stringWomFileType, parameterContext, expressionLib, ioFunctions))
-      }
-    }
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/FullyQualifiedName.scala b/cwl/src/main/scala/cwl/FullyQualifiedName.scala
deleted file mode 100644
index faabfa44fc4..00000000000
--- a/cwl/src/main/scala/cwl/FullyQualifiedName.scala
+++ /dev/null
@@ -1,61 +0,0 @@
-package cwl
-
-import cwl.command.ParentName
-
-/**
-  * All of these classes decompose a "fully qualified" id into its constituent parts.  They have unique types as
-  * they are seen in different parts of a CWL document and they differ in content.
-  *
-  * The fully qualified names are created by the Schema salad preprocessing step.
-  *
-  * @see <a href="http://www.commonwl.org/v1.0/SchemaSalad.html#Identifier_resolution">Schema salad Identifier Resolution</a>
-  */
-trait FullyQualifiedName {
-  def fileName: String
-  def id: String
-  def parent: Option[String]
-}
-
-case class FileAndId private(fileName: String, parent: Option[String], id: String) extends FullyQualifiedName
-
-object FileAndId {
-  def apply(in: String)(implicit parent: ParentName): FileAndId = {
-    val Array(fileName, id) = in.split("#")
-    val cleanID = parent.stripParent(id)
-    FileAndId(fileName, parent.value, cleanID)
-  }
-}
-
-case class FileStepAndId private(fileName: String, parent: Option[String], stepId: String, id: String) extends FullyQualifiedName
-
-object FileStepAndId {
-  def apply(in: String)(implicit parent: ParentName): FileStepAndId = {
-    val Array(fileName, id) = in.split("#")
-    val cleanID = parent.stripParent(id)
-    val Array(stepId, outputId) = cleanID.split("/")
-    FileStepAndId(fileName, parent.value, stepId, outputId)
-  }
-}
-
-case class ArbitrarilyNested(fileName: String, parent: Option[String], id: String) extends FullyQualifiedName
-
-case class FileStepUUID(fileName: String, parent: Option[String], id: String, uuid: String, stepId: String) extends FullyQualifiedName
-
-object FullyQualifiedName {
-  def apply(in: String)(implicit parent: ParentName): FullyQualifiedName = maybeApply(in)(parent).getOrElse(throw new Exception(s"malformed FQN: $in"))
-
-  def maybeApply(in: String)(implicit parent: ParentName): Option[FullyQualifiedName] = {
-
-    in.split("#") match {
-      case Array(file, after) =>
-        val cleanAfter = parent.stripParent(after)
-        cleanAfter.split("/").toList match {
-          case step :: uuid :: id :: Nil => Option(FileStepUUID(file, parent.value, id, uuid, step))
-          case step :: id :: Nil => Option(FileStepAndId(file, parent.value, step, id))
-          case id :: Nil => Option(FileAndId(file, parent.value, id))
-          case many => Option(ArbitrarilyNested(file, parent.value, many.last))
-        }
-      case _ => None
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/GlobEvaluator.scala b/cwl/src/main/scala/cwl/GlobEvaluator.scala
deleted file mode 100644
index d50b154da2c..00000000000
--- a/cwl/src/main/scala/cwl/GlobEvaluator.scala
+++ /dev/null
@@ -1,67 +0,0 @@
-package cwl
-
-import cats.syntax.validated._
-import common.validation.ErrorOr._
-import shapeless._
-import wom.types.{WomArrayType, WomStringType}
-import wom.values._
-
-/*
-CommandOutputBinding.glob:
-Find files relative to the output directory, using POSIX glob(3) pathname matching. If an array is provided, find
-files that match any pattern in the array. If an expression is provided, the expression must return a string or an
-array of strings, which will then be evaluated as one or more glob patterns. Must only match and return files which
-actually exist.
-
-http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding
- */
-object GlobEvaluator {
-
-  type GlobEvaluatorFunction = (ParameterContext, ExpressionLib) => ErrorOr[List[String]]
-
-  def globs(globOption: Option[Glob], parameterContext: ParameterContext, expressionLib: ExpressionLib): ErrorOr[List[String]] = {
-    globOption map {
-      globs(_, parameterContext, expressionLib)
-    } getOrElse {
-      Nil.valid
-    }
-  }
-
-  def globs(glob: Glob, parameterContext: ParameterContext, expressionLib: ExpressionLib): ErrorOr[List[String]] = {
-    glob.fold(GlobEvaluator.GlobEvaluatorPoly).apply(parameterContext, expressionLib)
-  }
-
-  object GlobEvaluatorPoly extends Poly1 {
-    implicit def caseStringOrExpression: Case.Aux[StringOrExpression, GlobEvaluatorFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseExpression: Case.Aux[Expression, GlobEvaluatorFunction] = {
-      at {
-        expression =>
-          (parameterContext, expressionLib) => {
-            ExpressionEvaluator.eval(expression, parameterContext) flatMap {
-              case WomArray(_, values) if values.isEmpty => Nil.valid
-              case WomString(value) => List(value).valid
-              case WomArray(WomArrayType(WomStringType), values) => values.toList.map(_.valueString).valid
-              case womValue =>
-                val message = s"Unexpected expression result: $womValue while evaluating expression '$expression' " +
-                  s"using inputs '$parameterContext'"
-                message.invalidNel
-            }
-          }
-      }
-    }
-
-    implicit def caseArrayString: Case.Aux[Array[String], GlobEvaluatorFunction] = {
-      at { array => (_, _) => array.toList.valid }
-    }
-
-    implicit def caseString: Case.Aux[String, GlobEvaluatorFunction] = {
-      at { string => (_, _) => List(string).valid }
-    }
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/InitialWorkDirRequirement.scala b/cwl/src/main/scala/cwl/InitialWorkDirRequirement.scala
deleted file mode 100644
index 28e49fe71d9..00000000000
--- a/cwl/src/main/scala/cwl/InitialWorkDirRequirement.scala
+++ /dev/null
@@ -1,63 +0,0 @@
-package cwl
-
-import cwl.InitialWorkDirRequirement._
-import eu.timepit.refined.W
-import shapeless.{:+:, CNil, _}
-
-final case class InitialWorkDirRequirement(
-                                            `class`: W.`"InitialWorkDirRequirement"`.T,
-                                            listing: IwdrListing
-                                          ) {
-  val listings: Array[IwdrListingArrayEntry] = listing.fold(IwdrListingArrayPoly)
-
-  override def toString: WorkflowStepInputId =
-    s"""InitialWorkDirRequirement(
-      |  ${listings.mkString(System.lineSeparator + "  ")}
-      |)""".stripMargin
-}
-
-/**
-  *  Short for "Directory Entry"
-  *  @see <a href="http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent">Dirent Specification</a>
-  *
-  *  Split into two cases because entryName is only optional if entry is an Expression
-  */
-trait Dirent {
-  def writable: Option[Boolean]
-  def writableWithDefault = writable.getOrElse(false)
-}
-
-final case class ExpressionDirent(
-                                   entry: Expression,
-                                   entryname: Option[StringOrExpression],
-                                   writable: Option[Boolean]
-                                 ) extends Dirent
-
-final case class StringDirent(
-                               entry: String,
-                               entryname: StringOrExpression,
-                               writable: Option[Boolean]
-                             ) extends Dirent
-
-object InitialWorkDirRequirement {
-
-  // "ExpressionDirent" has to come before StringDirent because expressions are matched by "String" first if we do it the
-  // other way round.
-  final type IwdrListingArrayEntry = File :+: Directory :+: ExpressionDirent :+: StringDirent :+: StringOrExpression :+: CNil
-  final type IwdrListing = Array[IwdrListingArrayEntry] :+: StringOrExpression :+: CNil
-
-  object IwdrListingArrayPoly extends Poly1 {
-    implicit val caseArrayIwdrListingArrayEntry: Case.Aux[Array[IwdrListingArrayEntry], Array[IwdrListingArrayEntry]] = {
-      at {
-        identity
-      }
-    }
-
-    implicit val caseStringOrExpression: Case.Aux[StringOrExpression, Array[IwdrListingArrayEntry]] = {
-      at {
-        stringOrExpression =>
-          Array(Coproduct[IwdrListingArrayEntry](stringOrExpression))
-      }
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/InputParameter.scala b/cwl/src/main/scala/cwl/InputParameter.scala
deleted file mode 100644
index d8b1579dcef..00000000000
--- a/cwl/src/main/scala/cwl/InputParameter.scala
+++ /dev/null
@@ -1,190 +0,0 @@
-package cwl
-
-import cats.syntax.functor._
-import cats.syntax.parallel._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cats.instances.option._
-import common.validation.ErrorOr._
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.FileParameter._
-import cwl.ontology.Schema
-import shapeless.Poly1
-import wom.callable.Callable.InputDefinition.InputValueMapper
-import wom.expression.IoFunctionSet
-import wom.types.{WomSingleFileType, WomType}
-import wom.values.{WomArray, WomMaybeListedDirectory, WomMaybePopulatedFile, WomObject, WomObjectLike, WomOptionalValue, WomValue}
-
-trait InputParameter {
-  def id: String
-  def label: Option[String]
-  def secondaryFiles: Option[SecondaryFiles]
-  def format: Option[InputParameterFormat]
-  def streamable: Option[Boolean]
-  def doc: Option[Doc]
-  def inputBinding: Option[InputCommandLineBinding]
-  def default: Option[CwlAny]
-  def `type`: Option[MyriadInputType]
-  def loadContents = inputBinding.flatMap(_.loadContents).getOrElse(false)
-}
-
-object InputParameter {
-  object IdDefaultAndType {
-    def unapply(arg: InputParameter): Option[(String, CwlAny, MyriadInputType)] = (arg.default, arg.`type`) match {
-      case (Some(default), Some(tpe)) => Option((arg.id, default, tpe))
-      case _ => None
-    }
-  }
-
-  object IdAndType {
-    def unapply(arg: InputParameter): Option[(String, MyriadInputType)] = (arg.default, arg.`type`) match {
-      case (None, Some(tpe)) => Option((arg.id, tpe))
-      case _ => None
-    }
-  }
-
-  type DefaultToWomValueFunction = WomType => ErrorOr[WomValue]
-
-  object DefaultToWomValuePoly extends Poly1 {
-    implicit def caseFileOrDirectory: Case.Aux[FileOrDirectory, DefaultToWomValueFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseFileOrDirectoryArray: Case.Aux[Array[FileOrDirectory], DefaultToWomValueFunction] = {
-      at {
-        fileOrDirectoryArray =>
-          womType =>
-            fileOrDirectoryArray
-              .toList
-              .traverse(_.fold(this).apply(womType))
-              .map(WomArray(_))
-      }
-    }
-
-    implicit def caseFile: Case.Aux[File, DefaultToWomValueFunction] = {
-      at {
-        file =>
-          womType =>
-            file.asWomValue.flatMap(womType.coerceRawValue(_).toErrorOr)
-      }
-    }
-
-    implicit def caseDirectory: Case.Aux[Directory, DefaultToWomValueFunction] = {
-      at {
-        directory =>
-          womType =>
-            directory.asWomValue.flatMap(womType.coerceRawValue(_).toErrorOr)
-      }
-    }
-
-    implicit def caseJson: Case.Aux[io.circe.Json, DefaultToWomValueFunction] = {
-      at {
-        circeJson =>
-          womType =>
-            val stringJson = circeJson.noSpaces
-            import spray.json._
-            val sprayJson = stringJson.parseJson
-            womType.coerceRawValue(sprayJson).toErrorOr
-      }
-    }
-  }
-
-  object InputParameterFormatPoly extends Poly1 {
-    implicit val caseExpression: Case.Aux[Expression, ParameterContext => ErrorOr[List[String]]] = {
-      at { expression =>
-        parameterContext =>
-          ExpressionEvaluator.eval(expression, parameterContext) map {
-            case WomArray(_, values) => values.toList.map(_.valueString)
-            case womValue => List(womValue.valueString)
-          }
-      }
-    }
-
-    implicit val caseString: Case.Aux[String, ParameterContext => ErrorOr[List[String]]] = {
-      at { string =>
-        _ =>
-          List(string).valid
-      }
-    }
-
-    implicit val caseArrayString: Case.Aux[Array[String], ParameterContext => ErrorOr[List[String]]] = {
-      at { array =>
-        _ =>
-          array.toList.valid
-      }
-    }
-  }
-
-  /**
-    * Yet another value mapper. This one is needed because in CWL we might need to "augment" inputs which we can only do
-    * once they have been linked to a WomValue. This input value mapper encapsulates logic to be applied once that is
-    * done. For now, if the inputParameter has an input binding with loadContents = true, load the content of the file.
-    *
-    * This is based on the spec in http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-    *
-    * NOTE: There may be _many_ cases not implemented here that need to be fixed.
-    */
-  def inputValueMapper(inputParameter: InputParameter,
-                       inputType: MyriadInputType,
-                       expressionLib: ExpressionLib,
-                       schemaOption: Option[Schema]): InputValueMapper = {
-    ioFunctionSet: IoFunctionSet => {
-      import ioFunctionSet.cs
-
-      def populateFiles(womValue: WomValue): IOChecked[WomValue] = {
-        womValue match {
-          case womMaybePopulatedFile: WomMaybePopulatedFile =>
-            // Don't include the secondary files in the self variables
-            val parameterContext = ParameterContext(ioFunctionSet, expressionLib, self = womMaybePopulatedFile.copy(secondaryFiles = List.empty))
-            val secondaryFilesFromInputParameter = inputParameter.secondaryFiles
-            val secondaryFilesFromType = inputType.fold(MyriadInputTypeToSecondaryFiles)
-            val secondaryFiles = secondaryFilesFromInputParameter orElse secondaryFilesFromType
-            val inputFormatsErrorOr = inputParameter.format
-                .traverse(_.fold(InputParameterFormatPoly).apply(parameterContext))
-
-            for {
-              inputFormatsOption <- inputFormatsErrorOr.toIOChecked
-              _ <- checkFormat(womMaybePopulatedFile, inputFormatsOption, schemaOption).toIOChecked
-              contentsOption <- FileParameter.maybeLoadContents(
-                womMaybePopulatedFile,
-                ioFunctionSet,
-                inputParameter.loadContents
-              ).to[IOChecked]
-              withSize <- womMaybePopulatedFile.withSize(ioFunctionSet).to[IOChecked]
-              loaded = withSize.copy(contentsOption = contentsOption)
-              secondaries <- FileParameter.secondaryFiles(
-                loaded,
-                WomSingleFileType,
-                secondaryFiles,
-                parameterContext,
-                expressionLib,
-                ioFunctionSet
-              )
-              updated = loaded.copy(secondaryFiles = loaded.secondaryFiles ++  secondaries)
-            } yield updated
-          case womMaybeListedDirectory: WomMaybeListedDirectory => womMaybeListedDirectory.withSize(ioFunctionSet).to[IOChecked].widen
-          case WomArray(_, values) => values.toList.parTraverse[IOChecked, WomValue](populateFiles).map(WomArray(_))
-          case WomOptionalValue(_, Some(innerValue)) => populateFiles(innerValue).map(WomOptionalValue(_))
-          case obj: WomObjectLike =>
-            // Map the values
-            val populated: IOChecked[WomObject] = obj.values.toList.parTraverse[IOChecked, (String, WomValue)]({
-              case (key, value) => populateFiles(value).map(key -> _)
-            })
-            .map(_.toMap)
-            // Validate new types are still valid w.r.t the object
-            .flatMap(WomObject.withTypeChecked(_, obj.womObjectTypeLike).toIOChecked)
-            
-            populated.widen[WomValue]
-          case womValue: WomValue =>
-            pure(womValue)
-        }
-      }
-
-      womValue => populateFiles(womValue)
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/LinkMergeMethod.scala b/cwl/src/main/scala/cwl/LinkMergeMethod.scala
deleted file mode 100644
index bd54ca6b56a..00000000000
--- a/cwl/src/main/scala/cwl/LinkMergeMethod.scala
+++ /dev/null
@@ -1,8 +0,0 @@
-package cwl
-
-object LinkMergeMethod extends Enumeration {
-  type LinkMergeMethod = Value
-
-  val MergeNested = Value("merge_nested")
-  val MergeFlattened = Value("merge_flattened")
-}
diff --git a/cwl/src/main/scala/cwl/MyriadInputTypeToSecondaryFiles.scala b/cwl/src/main/scala/cwl/MyriadInputTypeToSecondaryFiles.scala
deleted file mode 100644
index 4ddc09625d3..00000000000
--- a/cwl/src/main/scala/cwl/MyriadInputTypeToSecondaryFiles.scala
+++ /dev/null
@@ -1,25 +0,0 @@
-package cwl
-
-import cwl.CwlType.CwlType
-import shapeless.Poly1
-
-// IAS.secondaryFiles are NOT listed in 1.0 spec, but according to jgentry they will be, maybe
-object MyriadInputTypeToSecondaryFiles extends Poly1 {
-  implicit val caseMyriadInputInnerType: Case.Aux[MyriadInputInnerType, Option[SecondaryFiles]] = at {
-    _.fold(MyriadInputInnerTypeToSecondaryFiles)
-  }
-
-  implicit val caseArrayMyriadInputInnerType: Case.Aux[Array[MyriadInputInnerType], Option[SecondaryFiles]] = at {
-    _.to(LazyList).flatMap(_.fold(MyriadInputInnerTypeToSecondaryFiles)).headOption
-  }
-}
-
-object MyriadInputInnerTypeToSecondaryFiles extends Poly1 {
-  implicit val caseCwlType: Case.Aux[CwlType, Option[SecondaryFiles]] = at { _ => None }
-  implicit val caseInputRecordSchema: Case.Aux[InputRecordSchema, Option[SecondaryFiles]] = at { _ => None }
-  implicit val caseInputEnumSchema: Case.Aux[InputEnumSchema, Option[SecondaryFiles]] = at { _ => None }
-  implicit val caseInputArraySchema: Case.Aux[InputArraySchema, Option[SecondaryFiles]] = at {
-    inputArraySchema => inputArraySchema.secondaryFiles
-  }
-  implicit val caseString: Case.Aux[String, Option[SecondaryFiles]] = at { _ => None }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadInputTypeToSortedCommandParts.scala b/cwl/src/main/scala/cwl/MyriadInputTypeToSortedCommandParts.scala
deleted file mode 100644
index 498e97c016f..00000000000
--- a/cwl/src/main/scala/cwl/MyriadInputTypeToSortedCommandParts.scala
+++ /dev/null
@@ -1,254 +0,0 @@
-package cwl
-
-import cwl.CommandLineTool.{CommandBindingSortingKey, CommandPartsList, SortKeyAndCommandPart, StringOrInt}
-import cwl.CwlType.CwlType
-import cwl.SchemaDefRequirement.SchemaDefTypes
-import cwl.command.ParentName
-import shapeless.{Coproduct, Poly1}
-import wom.values.{WomArray, WomCoproductValue, WomObjectLike, WomOptionalValue, WomValue}
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.instances.list._
-import cats.instances.option._
-
-/**
-  * Poly1 to fold over a MyriadInputType and create a List of SortingKeyAndCommandPart based on the rules described here:
-  * http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-  */
-object MyriadInputTypeToSortedCommandParts extends Poly1 {
-  import Case._
-
-  /**
-    * CommandLineBinding: binding of the element being processed.
-    *   It's possible for an input not to have an "inputBinding", but to have a complex type which itself has inputBindings for its fields or items.
-    *   e.g:
-    *     - id: arrayInput
-    *       type:
-    *         type: array
-    *         items: File
-    *         inputBinding: { prefix: "-YYY" }
-    *
-    * Here the array type has an inputBinding but the input itself (arrayInput) does not.
-    * This would yield on the command line something like "-YYY arrayItem0 -YYY arrayItem1 ..."
-    *
-    * On the other hand:
-    *     - id: arrayInput
-    *       type:
-    *         type: array
-    *         items: File
-    *         inputBinding: { prefix: "-YYY" }
-    *       inputBinding: { prefix: "-XXX" }
-    *
-    * In this case the input itself has a binding as well, which would yield something like "-XXX -YYY arrayItem0 -YYY arrayItem1 ..."
-    *
-    * For arrays specifically, the presence of an "itemSeparator" and / or "valueFrom" in the input binding will change the way the array is processed,
-    * which is why we need to know about it in this Poly1 that folds over the input types.
-    *
-    * WomValue: value bound to the element (in the cases above it would be the WomArray)
-    * CommandBindingSortingKey: The current sorting key. Because we might need to recurse in nested types we need to propagate the key as we do.
-    */
-  type CommandPartBuilder = (Option[InputCommandLineBinding], WomValue, CommandBindingSortingKey, Boolean, ExpressionLib, SchemaDefRequirement) => CommandPartsList
-
-  implicit def m: Aux[MyriadInputInnerType, CommandPartBuilder] = {
-    at {
-      innerType => {
-        (binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-          innerType
-            .fold(MyriadInputInnerTypeToSortedCommandParts)
-            .apply(binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement).fold(
-              throw new RuntimeException(s"inner type to command part failed!  on type $innerType w/ womValue $womValue"))(identity)
-      }
-    }
-  }
-
-  implicit def am: Aux[Array[MyriadInputInnerType], CommandPartBuilder] = {
-    at {
-      types => {
-        (binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-          def lookupTypes(innerTypes: Array[MyriadInputInnerType]) = {
-            innerTypes.toList.map{
-              _.fold(MyriadInputInnerTypeToSortedCommandParts)
-                .apply(binding, womValue, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-            }.reduce(_ orElse _)
-          }
-          val result: Option[CommandPartsList] =
-            types.partition(_.select[CwlType].contains(CwlType.Null)) match {
-              case (Array(_), types) => lookupTypes(types) orElse Some(List.empty[SortKeyAndCommandPart])
-              case (Array(), types) => lookupTypes(types)
-            }
-         result.fold(
-            throw new RuntimeException(s"could not produce command line parts from input $womValue and types $types"))(
-            identity
-          )
-      }
-    }
-  }
-}
-
-object MyriadInputInnerTypeToSortedCommandParts extends Poly1 {
-
-  type CommandPartBuilder = (Option[InputCommandLineBinding], WomValue, CommandBindingSortingKey, Boolean, ExpressionLib, SchemaDefRequirement) => Option[CommandPartsList]
-
-  import Case._
-
-  // Primitive type: we just need to create a command part from the binding if there's one here.
-  implicit def ct: Aux[CwlType, CommandPartBuilder] = {
-    at {
-      cwlType => {
-        case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-        case (inputBinding, womValue, key, hasShellCommandRequirement, expressionLib, _) => {
-          (cwlType, womValue) match {
-            case (CwlType.Null, _) => List.empty.some
-            case (_, WomOptionalValue(_, None)) => List.empty.some
-            case (_,_) => inputBinding.toList.map(_.toCommandPart(key, womValue, hasShellCommandRequirement, expressionLib)).some
-          }
-        }
-      }
-    }
-  }
-
-  implicit def irs: Aux[InputRecordSchema, CommandPartBuilder] = at[InputRecordSchema] { irs => {
-    def go: CommandPartBuilder = {
-
-      //If the value is optional and is supplied, recurse over the value provided
-      case (inputBinding, WomCoproductValue(_, value), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        go(inputBinding, value, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-
-      //If the value is optional and is supplied, recurse over the value provided
-      case (inputBinding, WomOptionalValue(_, Some(value)), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        go(inputBinding, value, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-
-      // If it's optional and there's no value, do nothing
-      case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-
-      // If there's no input binding and no input bindings within the irs, do nothing
-      case (None, _, _, _, _, _) if !irs.fields.exists(_.exists(_.inputBinding.isDefined)) => List.empty.some
-
-      case (inputBinding, objectLike: WomObjectLike, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        // If there's an input binding, make a SortKeyAndCommandPart for it
-        val sortingKeyFromInputBindingFromInputParameter: Option[SortKeyAndCommandPart] =
-          inputBinding.map(_.toCommandPart(sortingKey, objectLike, hasShellCommandRequirement, expressionLib))
-
-        // iterate through the fields and fold over their type
-        val partsFromFields:Option[CommandPartsList] =
-          irs.fields.toList.flatten.
-            flatTraverse{
-              case InputRecordField(name, tpe, _, inputBinding, _) =>
-                // Parse the name to get a clean id
-                val parsedName = FullyQualifiedName(name)(ParentName.empty).id
-
-                // The field name needs to be added to the key after the input binding (as per the spec)
-                // Also start from the key from the input binding if there was one
-                val fieldSortingKey =
-                  sortingKeyFromInputBindingFromInputParameter.
-                    map(_.sortingKey).
-                    getOrElse(sortingKey).
-                    append(inputBinding, Coproduct[StringOrInt](parsedName))
-
-                val innerValueOption: Option[WomValue] = objectLike.values.get(parsedName)
-
-                val folded = innerValueOption.map(tpe.fold(MyriadInputTypeToSortedCommandParts).
-                  apply(inputBinding, _, fieldSortingKey.asNewKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement))
-                folded
-            }
-
-        sortingKeyFromInputBindingFromInputParameter.fold(
-          partsFromFields )(
-          sortingKeyFromInputBindingFromInputParameter =>
-            partsFromFields.map{k => List(sortingKeyFromInputBindingFromInputParameter.copy(nestedCommandParts = k)) }
-        )
-      case (_, other, _, _, _, _) => throw new RuntimeException(s"Value $other cannot be used for an input of type InputRecordSchema")
-    }
-
-    go
-  }}
-
-  implicit def ies: Aux[InputEnumSchema, CommandPartBuilder] = at[InputEnumSchema] { inputEnumSchema =>
-    def go: CommandPartBuilder = {
-      case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-      case (inputBinding, value, sortingKey, hasShellCommandRequirement, expressionLib, _) =>
-        // If there's an input binding, make a SortKeyAndCommandPart for it
-        val fromInputBinding =
-          inputBinding.map(_.toCommandPart(sortingKey, value, hasShellCommandRequirement, expressionLib)).toList
-
-        val fromIes = inputEnumSchema.inputBinding.map(_.toCommandPart(sortingKey, value, hasShellCommandRequirement, expressionLib)).toList
-
-        (fromInputBinding ++ fromIes).some
-    }
-    go
-  }
-
-  implicit def ias: Aux[InputArraySchema, CommandPartBuilder] = at[InputArraySchema] { ias =>
-    def go: CommandPartBuilder = {
-      case (inputBindingFromInputParameterParent, WomOptionalValue(_, Some(value)), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-        go(inputBindingFromInputParameterParent, value, sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement)
-
-      //If it's optional and there's no value, do nothing
-      case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-
-      // If there's no input binding and no input bindings for the ias, do nothing
-      case (None, _, _, _, _, _) if ias.inputBinding.isEmpty => List.empty.some
-
-      case (inputBinding, WomArray.WomArrayLike(womArray: WomArray), sortingKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement) =>
-
-
-        // If there's an input binding, make a SortKeyAndCommandPart for it
-        val sortKeyFromInputBindingFromInputerParameterParent: Option[SortKeyAndCommandPart] =
-          inputBinding.
-            map(_.toCommandPart(sortingKey, womArray, hasShellCommandRequirement, expressionLib))
-
-        // Now depending on whether we have an itemSeparator and/or valueFrom or not, we're going to recurse over each element of the array (or not).
-        // See http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding
-        if (inputBinding.flatMap(_.itemSeparator).isDefined || inputBinding.flatMap(_.valueFrom).isDefined) {
-          // If there's an item separator or a valueFrom we can stop here.
-          // When the command part is instantiated (see CommandLineBindingCommandPart) it will evaluate the valueFrom (if defined) and join the items together (if there's an itemSeparator).
-          sortKeyFromInputBindingFromInputerParameterParent.toList.some
-        } else {
-          // If neither valueFrom nor itemSeparator were defined, we need to process each item of the array
-          val fromArray: Option[CommandPartsList] = womArray.value.zipWithIndex.toList.flatTraverse({
-            case (item, index) =>
-              // Update the sorting key with the binding position (if any), add the index
-              val itemSortingKey = {
-
-              // The index needs to be added to the key after the input binding (as per the spec)
-              // Also start from the key from the input binding if there was one
-                val sortKey = sortKeyFromInputBindingFromInputerParameterParent.fold(sortingKey)(_.sortingKey)
-
-                sortKey.append(ias.inputBinding, Coproduct[StringOrInt](index))
-              }
-
-              // Even if the item doesn't have an explicit input binding, it should appear in the command so create a default empty one
-              //there is an explicit input binding!
-              val arrayItemInputBinding =
-                ias.
-                  inputBinding.
-                  orElse(Option(InputCommandLineBinding.default))
-
-              // Fold over the item type of each array element
-              Option(ias.items.fold(MyriadInputTypeToSortedCommandParts).apply(arrayItemInputBinding, item, itemSortingKey.asNewKey, hasShellCommandRequirement, expressionLib, schemaDefRequirement))
-          })
-          sortKeyFromInputBindingFromInputerParameterParent.fold(fromArray){
-            sortKeyFromInputBindingFromInputerParameterParent =>
-              fromArray.map{k => List(sortKeyFromInputBindingFromInputerParameterParent.copy(nestedCommandParts = k)) }
-          }
-        }
-
-      case (_, other, _, _, _, _) => throw new RuntimeException(s"Value $other cannot be used for an input of type InputArraySchema")
-    }
-
-    go
-  }
-
-  implicit def s: Aux[String, CommandPartBuilder] = {
-    at {
-      s => {
-        case (_, WomOptionalValue(_, None), _, _, _, _) => List.empty.some
-        case (commandLineBindingFromInput, womValue, sortingKey, boolean, expressionLib, schemaDefRequirement) => {
-          val womType: SchemaDefTypes = schemaDefRequirement.lookupCwlType(s).getOrElse(throw new RuntimeException(s"Looked for type $s in custom types $schemaDefRequirement but no match was found!"))
-
-          womType.fold(this).apply(commandLineBindingFromInput, womValue, sortingKey, boolean, expressionLib, schemaDefRequirement)
-        }
-      }
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadInputTypeToWomType.scala b/cwl/src/main/scala/cwl/MyriadInputTypeToWomType.scala
deleted file mode 100644
index d3be698bd33..00000000000
--- a/cwl/src/main/scala/cwl/MyriadInputTypeToWomType.scala
+++ /dev/null
@@ -1,95 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cwl.CwlType.CwlType
-import cwl.MyriadInputTypeToWomType.SchemaLookup
-import cwl.command.ParentName
-import mouse.all._
-import shapeless.Poly1
-import wom.types._
-
-object MyriadInputInnerTypeToString extends Poly1 {
-  implicit def ct = at[CwlType]{ _.toString }
-  implicit def irs = at[InputRecordSchema]{_.toString}
-  implicit def ies = at[InputEnumSchema]{ _.toString }
-  implicit def ias = at[InputArraySchema]{ _.toString}
-  implicit def s = at[String]{identity}
-}
-
-object MyriadInputTypeToWomType extends Poly1 {
-
-  import Case._
-
-  type SchemaLookup = SchemaDefRequirement => WomType
-
-  implicit def m:Aux[MyriadInputInnerType, SchemaLookup]= at[MyriadInputInnerType] {_.fold(MyriadInputInnerTypeToWomType)}
-
-  // An array of type means "this input value can be in any of those types."
-  // Currently we only accept single types or [null, X] to mean Optional[X]
-  implicit def am: Aux[Array[MyriadInputInnerType], SchemaLookup] = at[Array[MyriadInputInnerType]] {
-    types =>
-      schemaLookup =>
-        types.partition(_.select[CwlType].contains(CwlType.Null)) match {
-          // If there's a single non null type, use that
-          case (Array(), Array(singleNonNullType)) =>
-            singleNonNullType.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup)
-          case (Array(), array: Array[MyriadInputInnerType]) if array.length > 1  =>
-            val types = array.map(_.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup))
-            WomCoproductType(NonEmptyList.fromListUnsafe(types.toList))
-          // If there's a null type and a single non null type, it's a WomOptionalType
-          case (Array(_), Array(singleNonNullType)) =>
-            WomOptionalType(singleNonNullType.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup))
-          case (Array(_), array: Array[MyriadInputInnerType]) if array.length > 1  =>
-            val types = array.map(_.fold(MyriadInputInnerTypeToWomType).apply(schemaLookup))
-            WomOptionalType(WomCoproductType(NonEmptyList.fromListUnsafe(types.toList)))
-          case (Array(_), _) =>
-            val readableTypes = types.map(_.fold(MyriadInputInnerTypeToString)).mkString(", ")
-            throw new UnsupportedOperationException(s"Cromwell only supports single types or optionals (as indicated by [null, X]). Instead we saw: $readableTypes")
-    }
-  }
-}
-
-object MyriadInputInnerTypeToWomType extends Poly1 {
-  import Case._
-
-  def ex(component: String) = throw new RuntimeException(s"input type $component not yet suported by WOM!")
-
-  implicit def ct: Aux[CwlType, SchemaLookup] = at[CwlType]{
-    ct =>
-      cwl.cwlTypeToWomType(ct) |> Function.const
-  }
-
-  def inputRecordSchemaToWomType(irs: InputRecordSchema): SchemaLookup = { schemaLookup: SchemaDefRequirement =>
-    irs match {
-      case InputRecordSchema(_,  Some(fields), _, _) =>
-        val typeMap = fields.map({ field =>
-          FullyQualifiedName(field.name)(ParentName.empty).id -> field.`type`.fold(MyriadInputTypeToWomType).apply(schemaLookup)
-        }).toMap
-        WomCompositeType(typeMap)
-      case irs => irs.toString |> ex
-    }
-  }
-
-  implicit def irs: Aux[InputRecordSchema, SchemaLookup] = at[InputRecordSchema]{
-    inputRecordSchemaToWomType
-  }
-
-  implicit def ies: Aux[InputEnumSchema, SchemaLookup] = at[InputEnumSchema]{
-    ies =>
-      ies.toWomEnumerationType |> Function.const
-  }
-
-  implicit def ias: Aux[InputArraySchema, SchemaLookup] = at[InputArraySchema]{
-    ias =>
-      lookup =>
-        val arrayType: WomType = ias.items.fold(MyriadInputTypeToWomType).apply(lookup)
-        WomArrayType(arrayType)
-  }
-
-  implicit def s: Aux[String, SchemaLookup] = at[String]{
-    string =>
-      schemaReq =>
-        schemaReq.lookupType(string).getOrElse(throw new RuntimeException(s"Custom type $string was referred to but not found in schema def ${schemaReq}."))
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomFiles.scala b/cwl/src/main/scala/cwl/MyriadOutputTypeToWomFiles.scala
deleted file mode 100644
index 7c007d07d46..00000000000
--- a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomFiles.scala
+++ /dev/null
@@ -1,66 +0,0 @@
-package cwl
-
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.validation.IOChecked._
-import cwl.CwlType.CwlType
-import cwl.MyriadOutputTypeToWomFiles.EvaluationFunction
-import mouse.all._
-import shapeless.Poly1
-import wom.expression.FileEvaluation
-
-object MyriadOutputTypeToWomFiles extends Poly1 {
-
-  type EvaluationFunction = CommandOutputBinding => IOChecked[Set[FileEvaluation]]
-
-  import Case._
-
-  implicit def cwlType: Aux[MyriadOutputInnerType, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[MyriadOutputInnerType]{
-    _.fold(MyriadOutputInnerTypeToWomFiles)
-  }
-
-  implicit def acwl: Aux[Array[MyriadOutputInnerType], EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[Array[MyriadOutputInnerType]] { types =>
-    evalFunction =>
-      types.toList.traverse(_.fold(MyriadOutputInnerTypeToWomFiles).apply(evalFunction)).map(_.toSet.flatten)
-  }
-}
-
-object MyriadOutputInnerTypeToWomFiles extends Poly1 {
-
-  import Case._
-
-  def ex(component: String) = throw new RuntimeException(s"output type $component cannot yield wom files")
-
-  implicit def cwlType: Aux[CwlType, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[CwlType] { _ =>_ =>
-    Set.empty[FileEvaluation].validIOChecked
-  }
-
-  implicit def ors: Aux[OutputRecordSchema, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[OutputRecordSchema] {
-    case OutputRecordSchema(_, Some(fields), _) =>
-      evalFunction =>
-        fields.toList.traverse[IOChecked, Set[FileEvaluation]]({ field =>
-          field.outputBinding match {
-            case Some(binding) => evalFunction(binding)
-            case None => field.`type`.fold(MyriadOutputTypeToWomFiles).apply(evalFunction)
-          }
-        }).map(_.toSet.flatten)
-    case ors => ors.toString |> ex
-  }
-
-  implicit def oes: Aux[OutputEnumSchema, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[OutputEnumSchema]{ oes =>_ =>
-    oes.toString |> ex
-  }
-
-  implicit def oas: Aux[OutputArraySchema, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[OutputArraySchema]{ oas =>
-    evalFunction =>
-      import cats.syntax.apply._
-      def fromBinding: IOChecked[Set[FileEvaluation]] = oas.outputBinding.map(evalFunction).getOrElse(Set.empty[FileEvaluation].validIOChecked)
-      def fromType: IOChecked[Set[FileEvaluation]] = oas.items.fold(MyriadOutputTypeToWomFiles).apply(evalFunction)
-
-      (fromBinding, fromType) mapN (_ ++ _)
-  }
-
-  implicit def s: Aux[String, EvaluationFunction => IOChecked[Set[FileEvaluation]]] = at[String]{ _ =>_ =>
-    Set.empty[FileEvaluation].validIOChecked
-  }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomType.scala b/cwl/src/main/scala/cwl/MyriadOutputTypeToWomType.scala
deleted file mode 100644
index 61107143006..00000000000
--- a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomType.scala
+++ /dev/null
@@ -1,105 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cwl.CwlType.CwlType
-import cwl.command.ParentName
-import mouse.all._
-import shapeless.Poly1
-import wom.types._
-
-object MyriadOutputInnerTypeToString extends Poly1 {
-
-  implicit def cwlType = at[CwlType] {
-    _.toString
-  }
-
-  implicit def ors = at[OutputRecordSchema] {
-    _.toString
-  }
-
-  implicit def oes = at[OutputEnumSchema] {
-    _.toString
-  }
-
-  implicit def oas = at[OutputArraySchema] {
-    _.toString
-  }
-
-  implicit def s = at[String] {
-    identity
-  }
-}
-
-object MyriadOutputTypeToWomType extends Poly1{
-
-  import Case._
-
-  type SchemaDefToWomType = SchemaDefRequirement => WomType
-
-  implicit def cwlType: Aux[MyriadOutputInnerType, SchemaDefToWomType] = at[MyriadOutputInnerType]{ moit => schemaDefRequirement =>
-    moit.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement)
-  }
-
-  implicit def acwl: Aux[Array[MyriadOutputInnerType], SchemaDefToWomType] = at[Array[MyriadOutputInnerType]] { types => schemaDefRequirement =>
-    types.partition(_.select[CwlType].contains(CwlType.Null)) match {
-      // If there's a single non null type, use that
-      case (Array(), Array(singleNonNullType)) =>
-        singleNonNullType.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement)
-      case (Array(), array: Array[MyriadOutputInnerType]) if array.size > 1  =>
-        val types = array.map(_.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement))
-        WomCoproductType(NonEmptyList.fromListUnsafe(types.toList))
-      // If there's a null type and a single non null type, it's a WomOptionalType
-      case (Array(_), Array(singleNonNullType)) =>
-        WomOptionalType(singleNonNullType.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement))
-      case (Array(_), array: Array[MyriadOutputInnerType]) if array.size > 1  =>
-        val types = array.map(_.fold(MyriadOutputInnerTypeToWomType).apply(schemaDefRequirement))
-        WomOptionalType(WomCoproductType(NonEmptyList.fromListUnsafe(types.toList)))
-      case _ =>
-        val readableTypes = types.map(_.fold(MyriadOutputInnerTypeToString)).mkString(", ")
-        throw new UnsupportedOperationException(s"Cromwell only supports single types or optionals (as indicated by [null, X]). Instead we saw: $readableTypes")
-    }
-  }
-}
-
-object MyriadOutputInnerTypeToWomType extends Poly1 {
-
-  import Case._
-  import MyriadOutputTypeToWomType.SchemaDefToWomType
-
-  implicit def cwlType: Aux[CwlType, SchemaDefToWomType] =
-    at[CwlType]{
-      cwl.cwlTypeToWomType andThen Function.const
-    }
-
-  implicit def ors: Aux[OutputRecordSchema, SchemaDefToWomType] = at[OutputRecordSchema] {
-    ors => schemaDefRequirement =>
-      ors.fields.fold(
-        WomCompositeType(Map.empty))(
-        {fields =>
-          val typeMap = fields.map({ field =>
-            val parsedName = FullyQualifiedName(field.name)(ParentName.empty).id
-            parsedName -> field.`type`.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-          }).toMap
-          WomCompositeType(typeMap)
-        }
-      )
-  }
-
-  implicit def oes: Aux[OutputEnumSchema, MyriadOutputTypeToWomType.SchemaDefToWomType] =
-    at[OutputEnumSchema] {
-      oes => oes.toWomEnumerationType |> Function.const
-    }
-
-  implicit def oas: Aux[OutputArraySchema, MyriadOutputTypeToWomType.SchemaDefToWomType] =
-    at[OutputArraySchema] {
-      oas => schemaDefRequirement =>
-        val arrayType: WomType = oas.items.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-        WomArrayType(arrayType)
-    }
-
-  implicit def s: Aux[String, MyriadOutputTypeToWomType.SchemaDefToWomType] =
-    at[String] {
-      string => schemaReq =>
-        schemaReq.lookupType(string).getOrElse(throw new RuntimeException(s"Custom type $string was referred to but not found in schema def ${schemaReq.types.mkString(", ")}."))
-    }
-}
diff --git a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomValue.scala b/cwl/src/main/scala/cwl/MyriadOutputTypeToWomValue.scala
deleted file mode 100644
index 332e4ab3888..00000000000
--- a/cwl/src/main/scala/cwl/MyriadOutputTypeToWomValue.scala
+++ /dev/null
@@ -1,100 +0,0 @@
-package cwl
-
-import cats.data.Validated.Valid
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.validation.IOChecked.IOChecked
-import common.validation.IOChecked._
-import cwl.CwlType.CwlType
-import cwl.command.ParentName
-import mouse.all._
-import shapeless.Poly1
-import wom.types._
-import wom.values.{WomObject, WomValue}
-
-/**
-  * Folds a MyriadOutputType into a WomValue
-  * This is needed because the type might define the structure of the final output value (for OutputRecordSchemas for example)
-  */
-object MyriadOutputTypeToWomValue extends Poly1 {
-
-  // We pass in a function that can evaluate a CommandOutputBinding and produce a WomValue. This allows us to recurse into the
-  // MyriadOutputTypes and evaluate values as we do.
-  type EvaluationFunction = (CommandOutputBinding, WomType) => IOChecked[WomValue]
-
-  //Our overall return type gives us the evaluator function and custom types; returns WomValues
-  type Output = (EvaluationFunction, SchemaDefRequirement) => IOChecked[WomValue]
-
-  import Case._
-
-  implicit def cwlType: Aux[MyriadOutputInnerType, Output] = at[MyriadOutputInnerType]{
-    moit => (evalFunction, schemaDefRequirement) => moit.fold(MyriadOutputInnerTypeToWomValue).apply(evalFunction, schemaDefRequirement)
-  }
-
-  // TODO: Not sure what the right thing to do is here, for now go over the list of types and use the first evaluation that yields success
-  implicit def acwl: Aux[Array[MyriadOutputInnerType], Output] = at[Array[MyriadOutputInnerType]] { types =>
-    (evalFunction,schemaDefRequirement) =>
-      types.toList.map(_.fold(MyriadOutputInnerTypeToWomValue).apply(evalFunction, schemaDefRequirement)).map(_.toErrorOr).collectFirst({
-        case Valid(validValue) => validValue
-      }).toValidNel(s"Cannot find a suitable type to build a WomValue from in ${types.mkString(", ")}").toIOChecked
-  }
-}
-
-object MyriadOutputInnerTypeToWomValue extends Poly1 {
-
-  import Case._
-  import MyriadOutputTypeToWomValue.Output
-
-  def ex(component: String) = throw new RuntimeException(s"output type $component cannot yield a wom value")
-
-  implicit def cwlType: Aux[CwlType, Output] = at[CwlType] { _ => (_,_) =>
-    "No output binding is defined. Are you expecting the output to be inferred from a cwl.output.json file ? If so please make sure the file was effectively created.".invalidIOChecked
-  }
-
-  implicit def ors: Aux[OutputRecordSchema, Output] = at[OutputRecordSchema] { ors => (evalFunction, schemaDefRequirement) => ors match {
-    case OutputRecordSchema(_, Some(fields), _) =>
-        // Go over each field and evaluate the binding if there's one, otherwise keep folding over field types
-        def evaluateValues = fields.toList.traverse[IOChecked, ((String, WomValue), (String, WomType))]({ field =>
-          val womType = field.`type`.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-          val womValue: IOChecked[WomValue] = field.outputBinding match {
-            case Some(binding) => evalFunction(binding, womType)
-            case None => field.`type`.fold(MyriadOutputTypeToWomValue).apply(evalFunction, schemaDefRequirement)
-          }
-
-          // TODO: ParentName might need to be passed in here ?
-          // return the value and the type with a clean parsedName
-          womValue map { value =>
-            val parsedName = FullyQualifiedName(field.name)(ParentName.empty).id
-            (parsedName -> value) -> (parsedName -> womType)
-          }
-        })
-
-        evaluateValues map { evaluatedValues =>
-          val (valueMap, typeMap) = evaluatedValues.unzip
-          // Create a typed WomObject from the values and the typeMap
-          WomObject.withTypeUnsafe(valueMap.toMap, WomCompositeType(typeMap.toMap))
-        }
-    case ors => ors.toString |> ex
-  }}
-
-  implicit def oes: Aux[OutputEnumSchema, Output] = at[OutputEnumSchema]{
-    //DB: I tried to do a pattern match as the overall function here but the compiler exploded
-    oes => (f, schemaDefRequirement) => oes match {
-      case oes@OutputEnumSchema(_, _, _, _, Some(outputBinding)) => f(outputBinding, oes.toWomEnumerationType)
-      case _ => s"The enumeration type $oes requires an outputbinding to be evaluated.".invalidIOChecked
-    }
-  }
-
-  implicit def oas: Aux[OutputArraySchema, Output] = at[OutputArraySchema]{ oas => (evalFunction, schemaDefRequirement) => oas match {
-    case OutputArraySchema(itemsType, _, _, outputBinding) =>
-      lazy val itemsWomType = itemsType.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-      def fromBinding = outputBinding.map(evalFunction(_, WomArrayType(itemsWomType)))
-      def fromTypes = itemsType.fold(MyriadOutputTypeToWomValue).apply(evalFunction, schemaDefRequirement)
-      fromBinding.getOrElse(fromTypes)
-  }}
-
-  implicit def s: Aux[String, Output] = at[String]{ s => (_, _) =>
-    s.toString |> ex
-  }
-}
diff --git a/cwl/src/main/scala/cwl/OutputParameter.scala b/cwl/src/main/scala/cwl/OutputParameter.scala
deleted file mode 100644
index 274469da7ee..00000000000
--- a/cwl/src/main/scala/cwl/OutputParameter.scala
+++ /dev/null
@@ -1,62 +0,0 @@
-package cwl
-
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.option._
-import common.validation.ErrorOr._
-import shapeless.{:+:, CNil, Poly1}
-import wom.values.{WomString, WomValue}
-
-trait OutputParameter {
-  def id: String
-  def label: Option[String]
-  def secondaryFiles: Option[SecondaryFiles]
-  def format: Option[OutputParameterFormat]
-  def streamable: Option[Boolean]
-  def doc: Option[String :+: Array[String] :+: CNil]
-  def outputBinding: Option[CommandOutputBinding]
-  def `type`: Option[MyriadOutputType]
-  def cacheString: String = toString
-}
-
-object OutputParameter {
-  object IdAndType {
-    def unapply(arg: OutputParameter): Option[(String, MyriadOutputType)] = arg.`type`.map((arg.id, _))
-  }
-
-  def format(formatOption: Option[StringOrExpression],
-             parameterContext: ParameterContext,
-             expressionLib: ExpressionLib): ErrorOr[Option[String]] = {
-    formatOption.traverse{
-      format(_, parameterContext, expressionLib)
-    }
-  }
-
-  def format(format: StringOrExpression, parameterContext: ParameterContext, expressionLib: ExpressionLib): ErrorOr[String] = {
-    format.fold(OutputParameter.FormatPoly).apply(parameterContext, expressionLib)
-  }
-
-  type FormatFunction = (ParameterContext, ExpressionLib) => ErrorOr[String]
-
-  object FormatPoly extends Poly1 {
-    implicit def caseStringOrExpression: Case.Aux[StringOrExpression, FormatFunction] = {
-      at {
-        _.fold(this)
-      }
-    }
-
-    implicit def caseExpression: Case.Aux[Expression, FormatFunction] = {
-      at {
-        expression =>
-          (parameterContext, expressionLib) =>
-            val result: ErrorOr[WomValue] = ExpressionEvaluator.eval(expression, parameterContext)
-            result flatMap {
-              case womString: WomString => womString.value.valid
-              case other => s"Not a valid file format: $other".invalidNel
-            }
-      }
-    }
-
-    implicit def caseString: Case.Aux[String, FormatFunction] = at { string => (_,_) => string.valid }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/OutputParameterExpression.scala b/cwl/src/main/scala/cwl/OutputParameterExpression.scala
deleted file mode 100644
index b044bc36077..00000000000
--- a/cwl/src/main/scala/cwl/OutputParameterExpression.scala
+++ /dev/null
@@ -1,115 +0,0 @@
-package cwl
-
-import common.validation.ErrorOr.ErrorOr
-import common.validation.IOChecked.{IOChecked, _}
-import cwl.CwlType.CwlType
-import shapeless.Poly1
-import wom.expression.{EmptyIoFunctionSet, FileEvaluation, IoFunctionSet}
-import wom.types._
-import wom.values.WomValue
-
-import scala.Function.const
-import scala.concurrent.{ExecutionContext, Future}
-
-case class OutputParameterExpression(parameter: OutputParameter,
-                                     override val cwlExpressionType: WomType,
-                                     override val inputs: Set[String],
-                                     override val expressionLib: ExpressionLib,
-                                     schemaDefRequirement: SchemaDefRequirement) extends CwlWomExpression {
-
-  override def sourceString = parameter.toString
-
-  override def cacheString: String = parameter.cacheString
-
-  private def evaluateOutputBinding(inputValues: Map[String, WomValue],
-                                    ioFunctionSet: IoFunctionSet,
-                                    secondaryFilesOption: Option[SecondaryFiles],
-                                    formatOption: Option[StringOrExpression]
-                                   )(outputBinding: CommandOutputBinding,
-                                    cwlExpressionType: WomType): IOChecked[WomValue] = {
-    CommandOutputBinding.generateOutputWomValue(
-      inputValues,
-      ioFunctionSet,
-      cwlExpressionType,
-      outputBinding,
-      secondaryFilesOption,
-      formatOption,
-      expressionLib
-    )
-  }
-
-  private def evaluateOutputBindingFiles(inputValues: Map[String, WomValue],
-                                    ioFunctionSet: IoFunctionSet,
-                                    secondaryFilesOption: Option[SecondaryFiles],
-                                    coerceTo: WomType
-                                   )(outputBinding: CommandOutputBinding): IOChecked[Set[FileEvaluation]] = {
-    CommandOutputBinding.getOutputWomFiles(
-      inputValues,
-      coerceTo,
-      outputBinding,
-      secondaryFilesOption,
-      ioFunctionSet,
-      expressionLib
-    )
-  }
-  
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
-    def fromOutputBinding =
-      parameter.outputBinding.map(evaluateOutputBinding(inputValues, ioFunctionSet, parameter.secondaryFiles, parameter.format)(_, cwlExpressionType))
-
-    def fromType =
-      parameter.`type`.map(_.fold(MyriadOutputTypeToWomValue).apply(
-        evaluateOutputBinding(inputValues, ioFunctionSet, parameter.secondaryFiles, parameter.format),
-        schemaDefRequirement
-      ))
-
-    fromOutputBinding.orElse(fromType).getOrElse(s"Cannot evaluate ${parameter.toString}".invalidIOChecked).toErrorOr
-  }
-
-  /**
-    * Returns the list of files that _will be_ output after the command is run, unless they are optional and if so _may be_.
-    *
-    * In CWL, a list of outputs is specified as glob, say `*.bam`, plus a list of secondary files that may be in the
-    * form of paths or specified using carets such as `^.bai`.
-    *
-    * The coerceTo may be one of four different values:
-    * - WomMaybePopulatedFileType
-    * - WomArrayType(WomMaybePopulatedFileType)
-    * - WomMaybeListedDirectoryType
-    * - WomArrayType(WomMaybeListedDirectoryType) (Possible according to the way the spec is written, but not likely?)
-    */
-  override def evaluateFiles(inputs: Map[String, WomValue], unused: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
-    import cats.syntax.apply._
-
-    // Ignore the supplied ioFunctionSet and use a custom stubbed IoFunctionSet. This is better than a real I/O function set
-    // because in the context of file evaluation we don't care about the results of these operations. The NoIoFunctionSet
-    // that otherwise would be used throws for all of its operations which doesn't fly for the way our CWL evaluation works.
-    val stubbedIoFunctionSet = new EmptyIoFunctionSet {
-      override def size(path: String): Future[Long] = Future.successful(0L)
-      override def isDirectory(path: String): Future[Boolean] = Future.successful(false)
-      override def ec: ExecutionContext = scala.concurrent.ExecutionContext.global
-    }
-    def fromOutputBinding: IOChecked[Set[FileEvaluation]] = parameter
-      .outputBinding
-      .map(evaluateOutputBindingFiles(inputs, stubbedIoFunctionSet, parameter.secondaryFiles, coerceTo))
-      .getOrElse(Set.empty[FileEvaluation].validIOChecked)
-
-    def fromType: IOChecked[Set[FileEvaluation]] = parameter
-      .`type`
-      .map(_.fold(MyriadOutputTypeToWomFiles).apply(evaluateOutputBindingFiles(inputs, stubbedIoFunctionSet, parameter.secondaryFiles, coerceTo)))
-      .getOrElse(Set.empty[FileEvaluation].validIOChecked)
-
-    val optional: Boolean = parameter.`type`.exists(_.fold(OutputTypeIsOptional))
-
-    ((fromOutputBinding, fromType) mapN (_ ++ _) map { _ map { _.copy(optional = optional) } }).toErrorOr
-  }
-}
-
-object OutputTypeIsOptional extends Poly1 {
-  implicit val one: Case.Aux[MyriadOutputInnerType, Boolean] = at[MyriadOutputInnerType] { const(false) }
-
-  implicit val arr: Case.Aux[Array[MyriadOutputInnerType], Boolean] = at[Array[MyriadOutputInnerType]] {
-    // Possibly too broad, would return true for just single 'null'.
-    _.exists(_.select[CwlType].contains(CwlType.Null))
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ParameterContext.scala b/cwl/src/main/scala/cwl/ParameterContext.scala
deleted file mode 100644
index 4bcb4d132d5..00000000000
--- a/cwl/src/main/scala/cwl/ParameterContext.scala
+++ /dev/null
@@ -1,17 +0,0 @@
-package cwl
-
-import wom.callable.RuntimeEnvironment
-import wom.expression.IoFunctionSet
-import wom.types.WomNothingType
-import wom.values.{WomOptionalValue, WomValue}
-
-object ParameterContext {
-  val EmptySelf = WomOptionalValue(WomNothingType, None)
-}
-
-case class ParameterContext(
-                            ioFunctionSet: IoFunctionSet,
-                            expressionLib: ExpressionLib,
-                            inputs: Map[String, WomValue] = Map.empty,
-                            self: WomValue = ParameterContext.EmptySelf,
-                            runtimeOption: Option[RuntimeEnvironment] = None)
diff --git a/cwl/src/main/scala/cwl/RequirementsAndHints.scala b/cwl/src/main/scala/cwl/RequirementsAndHints.scala
deleted file mode 100644
index 46b5c52e410..00000000000
--- a/cwl/src/main/scala/cwl/RequirementsAndHints.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cwl
-
-case class RequirementsAndHints(list: List[Requirement]) {
-
-  lazy val hasShellCommandRequirement: Boolean = list.exists(_.select[ShellCommandRequirement].nonEmpty)
-
-  //Should we add up all the types instead?  This would mean subworkflows can inherit their parent schemas
-  lazy val schemaDefRequirement = list.flatMap(_.select[SchemaDefRequirement]).headOption.getOrElse(SchemaDefRequirement())
-}
diff --git a/cwl/src/main/scala/cwl/RunOutputsToTypeMap.scala b/cwl/src/main/scala/cwl/RunOutputsToTypeMap.scala
deleted file mode 100644
index f327b5b03ea..00000000000
--- a/cwl/src/main/scala/cwl/RunOutputsToTypeMap.scala
+++ /dev/null
@@ -1,45 +0,0 @@
-package cwl
-
-import shapeless.Poly1
-import wom.types.WomType
-
-object RunOutputsToTypeMap extends Poly1 {
-
-  import Case.Aux
-
-  type SchemaDefToTypeMap = SchemaDefRequirement => WomTypeMap
-
-  def handleOutputParameters[A <: OutputParameter](outputs: Array[A], schemaDefRequirement: SchemaDefRequirement): Map[String, WomType] = {
-    outputs.toList.foldLeft(Map.empty[String, WomType]) {
-      (acc, out) =>
-        acc ++
-          out.
-            `type`.
-            map(_.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)).
-            map(out.id -> _).
-            toList.
-            toMap
-    }
-  }
-
-  implicit def commandLineTool : Aux[CommandLineTool, SchemaDefToTypeMap] =
-    at[CommandLineTool] {
-      clt => handleOutputParameters(clt.outputs, _)
-    }
-
-  implicit def string: Aux[String, SchemaDefToTypeMap] = at[String] {
-    _ => _ =>
-      Map.empty[String, WomType] //should never happen because we dereference/embed CWL subworkflows into one object from the original string references
-  }
-
-  implicit def expressionTool: Aux[ExpressionTool, SchemaDefToTypeMap] = at[ExpressionTool] {
-    et =>
-      handleOutputParameters(et.outputs, _)
-  }
-
-  implicit def workflow: Aux[Workflow, SchemaDefToTypeMap] = at[Workflow] {
-    wf =>
-      handleOutputParameters(wf.outputs, _)
-  }
-}
-
diff --git a/cwl/src/main/scala/cwl/RunToEmbeddedCwl.scala b/cwl/src/main/scala/cwl/RunToEmbeddedCwl.scala
deleted file mode 100644
index 2547b6333a4..00000000000
--- a/cwl/src/main/scala/cwl/RunToEmbeddedCwl.scala
+++ /dev/null
@@ -1,36 +0,0 @@
-package cwl
-
-import shapeless._
-import WorkflowStep.Run
-
-object RunToEmbeddedCwl extends Poly1 {
-  implicit def commandLineTool =
-    at[CommandLineTool] {
-      clt =>
-        (_: Map[String, Cwl]) =>
-         Coproduct[Run](clt)
-    }
-
-  implicit def string = at[String] {
-    fileName =>
-      (cwlMap: Map[String, Cwl]) => {
-        val cwl = cwlMap(fileName)
-        cwl.fold(CwlToRun)
-      }
-  }
-
-
-  implicit def expressionTool = at[ExpressionTool] {
-    et =>
-      (_: Map[String, Cwl]) =>
-        Coproduct[Run](et)
-  }
-
-  implicit def workflow = at[Workflow] {
-    wf =>
-      (_: Map[String, Cwl]) =>
-        Coproduct[Run](wf)
-  }
-}
-
-
diff --git a/cwl/src/main/scala/cwl/RunToInputTypeMap.scala b/cwl/src/main/scala/cwl/RunToInputTypeMap.scala
deleted file mode 100644
index 7111e389050..00000000000
--- a/cwl/src/main/scala/cwl/RunToInputTypeMap.scala
+++ /dev/null
@@ -1,37 +0,0 @@
-package cwl
-
-import cwl.command.ParentName
-import shapeless.Poly1
-
-object RunToInputTypeMap extends Poly1 {
-
-  type MyriadInputTypeMap = Map[String, Option[MyriadInputType]]
-
-  type OutputType = ParentName => MyriadInputTypeMap
-
-  import Case.Aux
-
-  implicit def s: Aux[String, OutputType] =
-    at[String] {
-      run =>  _ => throw new RuntimeException(s"Run field $run was not inlined as expected")
-    }
-
-  implicit def clt: Aux[CommandLineTool, OutputType] =
-    at[CommandLineTool]{clt => parentName => clt.inputs.map{
-      input =>
-          FullyQualifiedName(input.id)(parentName).id -> input.`type`
-    }.toMap}
-
-  implicit def et: Aux[ExpressionTool, OutputType] =
-    at[ExpressionTool]{et => parentName => et.inputs.map{
-      input =>
-        FullyQualifiedName(input.id)(parentName).id -> input.`type`
-    }.toMap}
-
-  implicit def wf: Aux[Workflow, OutputType] =
-    at[Workflow]{ wf => parentName => wf.inputs.map{
-      input =>
-        FullyQualifiedName(input.id)(parentName).id -> input.`type`
-    }.toMap}
-
-}
diff --git a/cwl/src/main/scala/cwl/ScatterLogic.scala b/cwl/src/main/scala/cwl/ScatterLogic.scala
deleted file mode 100644
index 97d87daf6df..00000000000
--- a/cwl/src/main/scala/cwl/ScatterLogic.scala
+++ /dev/null
@@ -1,263 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.instances.list._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import cwl.ScatterMethod.ScatterMethod
-import shapeless.Poly1
-import wom.graph.CallNode.CallNodeAndNewNodes
-import wom.graph.GraphNodePort.ScatterGathererPort
-import wom.graph.ScatterNode._
-import wom.graph._
-import wom.graph.expression.ExpressionNode
-import wom.types.{WomArrayType, WomMaybeEmptyArrayType, WomType}
-import wom.values.{WomArray, WomValue}
-
-import scala.annotation.tailrec
-
-/**
-  * Contains methods used to implement the scatter related logic for CWL workflows.
-  * The general idea is as follows:
-  *
-  * See WorkflowStep for an example of WOM graph for scatters.
-  * 
-  * # Scattering over multiple variables
-  *
-  * When several variables are being scattered over, a scatter method is mandatory to specify how the elements must be combined.
-  * Let's use the following 2 arrays as an example:
-  *
-  * a1: ["one", "two"], a2: ["three", "four"]
-  *
-  * * DotProduct:
-  * DotProduct only works if all the arrays have the same length.
-  *
-  * Shard 0: "one" - "three"
-  * Shard 1: "two" - "four"
-  *
-  * * CrossProduct (nested or flat):
-  * Both cross product methods generate the same shards, the difference is in how they are collected at the end
-  *
-  * Shard 0: "one" - "three"
-  * Shard 1: "one" - "four"
-  * Shard 2: "two" - "three"
-  * Shard 3: "two" - "four"
-  *
-  * To support this, each SVN will have a method which given a shard index will return the index at which the value should be looked up in the array.
-  *
-  * For dot product, this function is the same for all SVN and will be the identity[Int] function.
-  * For cross product, this function depends on the number of elements in each array, which is known at runtime.
-  *   When we do have this information we update each SVN with it in the ScatterProcessingFunction and returns the number of shards to be generated.
-  */
-object ScatterLogic {
-  case class ScatterFunctions(processing: ScatterProcessingFunction, collection: ScatterCollectionFunctionBuilder)
-
-  object ScatterVariablesPoly extends Poly1 {
-    implicit def fromString: Case.Aux[String, List[String]] = at[String] { s: String => List(s) }
-    implicit def fromStringList: Case.Aux[Array[String], List[String]] = at[Array[String]] { l: Array[String] => l.toList }
-  }
-
-  // Validate that the scatter expression is an ArrayLike and return the member type
-  private [cwl] def scatterExpressionItemType(expressionNode: ExpressionNode) = {
-    expressionNode.womType match {
-      case WomArrayType(itemType) => itemType.validNelCheck // Covers maps because this is a custom unapply (see WomArrayType)
-      case other => s"Cannot scatter over a non-traversable type ${other.stableName}".invalidNelCheck
-    }
-  }
-
-  def scatterGatherPortTypeFunction(scatterMethod: Option[ScatterMethod], scatterVariables: NonEmptyList[_]): WomType => WomArrayType = scatterMethod match {
-    case Some(ScatterMethod.NestedCrossProduct) =>
-      innerType: WomType =>
-        scatterVariables.tail.foldLeft(WomArrayType(innerType))({ case (t, _) => WomArrayType(t) })
-    case _ => innerType: WomType => WomArrayType(innerType)
-  }
-
-  // Build a map (potentially empty) of scatterered input steps with their corresponding SVN node.
-  def buildScatterVariableNodes(scatter: ScatterVariables, stepInputMappings: Map[WorkflowStepInput, ExpressionNode], stepId: String): Checked[Map[WorkflowStepInput, ScatterVariableNode]] = {
-    import cats.syntax.all._
-
-    def buildScatterVariable(scatterVariableName: String): ErrorOr[(WorkflowStepInput, ScatterVariableNode)] = {
-      // Assume the variable is a step input (is that always true ??). Find the corresponding expression node
-
-      stepInputMappings.find({ case (stepInput, _) => stepInput.id == scatterVariableName }) match {
-        case Some((stepInput, expressionNode)) =>
-          scatterExpressionItemType(expressionNode).toValidated map { itemType =>
-            // create a scatter variable node for other scattered nodes to point to
-            stepInput -> ScatterVariableNode(WomIdentifier(scatterVariableName), expressionNode, itemType)
-          }
-        case None => s"Could not find a variable $scatterVariableName in the workflow step input to scatter over. Please make sure $scatterVariableName is an input of step $stepId".invalidNel
-      }
-    }
-    // Take the scatter field defining the (list of) input(s) to be scattered over
-    scatter
-      // Fold them so we have a List[String] no matter what (a single scattered input becomes a single element list)
-      .map(_.fold(ScatterVariablesPoly))
-      // If there's no scatter make it an empty list
-      .getOrElse(List.empty)
-      // Traverse the list to create ScatterVariableNodes that will be used later on to create the ScatterNode
-      .traverse(buildScatterVariable)
-      .toEither
-      .map(_.toMap)
-  }
-
-  // Prepare the nodes to be returned if this call is being scattered
-  def buildScatterNode(callNodeAndNewNodes: CallNodeAndNewNodes,
-                       scatterVariableNodes: NonEmptyList[ScatterVariableNode],
-                       ogins: Set[OuterGraphInputNode],
-                       stepExpressionNodes: Set[ExpressionNode],
-                       scatterMethod: Option[ScatterMethod]): Checked[ScatterNode] = {
-
-    val scatterProcessingFunctionCheck = (scatterVariableNodes.size, scatterMethod) match {
-      // If we scatter over one variable only, the default processing method can handle it
-      case (1, _) => ScatterFunctions(ScatterNode.DefaultScatterProcessingFunction, ScatterNode.DefaultScatterCollectionFunctionBuilder).validNelCheck
-      case (_, Some(method)) => ScatterFunctions(processingFunction(method), collectingFunctionBuilder(method)).validNelCheck
-      case (_, None) => "When scattering over multiple variables, a scatter method needs to be defined. See http://www.commonwl.org/v1.0/Workflow.html#WorkflowStep".invalidNelCheck
-    }
-
-    val callNode = callNodeAndNewNodes.node
-
-    // We need to generate PBGONs for every output port of the call, so that they can be linked outside the scatter graph
-    val portBasedGraphOutputNodes = callNode.outputPorts.map(op => PortBasedGraphOutputNode(op.identifier, op.womType, op))
-
-    def buildScatterNode(innerGraph: Graph, scatterFunctions: ScatterFunctions) = {
-      val scatterNodeBuilder = new ScatterNodeBuilder
-      val outputPorts: Set[ScatterGathererPort] = innerGraph.nodes.collect { case gon: PortBasedGraphOutputNode =>
-        scatterNodeBuilder.makeOutputPort(scatterGatherPortTypeFunction(scatterMethod, scatterVariableNodes)(gon.womType), gon)
-      }
-
-      scatterNodeBuilder.build(innerGraph, outputPorts, scatterVariableNodes.toList, scatterFunctions.processing, scatterFunctions.collection)
-    }
-    
-    for {
-      scatterProcessingFunctionAndBuilder <- scatterProcessingFunctionCheck
-      graph <- Graph.validateAndConstruct(
-        Set(callNodeAndNewNodes.node) ++
-          ogins ++
-          stepExpressionNodes ++
-          scatterVariableNodes.toList ++
-          portBasedGraphOutputNodes
-      ).toEither
-      scatterNode = buildScatterNode(graph, scatterProcessingFunctionAndBuilder)
-    } yield scatterNode.node
-  }
-
-  /*
-   * Processing function for cross products. Logic is as follows:
-   * We want 1) know how many shards should be created (which this function will return)
-   *         2) update each SVN with their relative index length (see ScatterVariableNode for more detail)
-   *         
-   * We are going to multiply all the array sizes (which will give us 1) at the end)
-   * Along the way we will update the relative index length for each SVN.
-   * To do so, we start at the end of the list and recurse.
-   */
-  private [cwl] val CrossProductScatterProcessingFunction: ScatterProcessingFunction = { nodesAndValues: List[ScatterVariableAndValue] =>
-    @tailrec
-    def updateIndexLengthRec(currentList: List[ScatterVariableAndValue], combinedArraySize: Int): Int = currentList match {
-      case Nil => combinedArraySize
-      case ScatterVariableAndValue(variableNode, arrayValue) :: tail =>
-        variableNode.withRelativeIndexLength(combinedArraySize)
-        updateIndexLengthRec(tail, combinedArraySize * arrayValue.size)
-    }
-
-    // Reverse the list so that we start from the last variable and make our way back to the first one
-    updateIndexLengthRec(nodesAndValues.reverse, 1).validNelCheck
-  }
-
-  private [cwl] val DotProductScatterProcessingFunction: ScatterProcessingFunction = ScatterNode.DefaultScatterProcessingFunction
-
-  // Recursively nest shard results appropriately based on the size of the scatter variable arrays
-  private [cwl] val NestedCrossProductScatterCollectionFunctionBuilder: ScatterCollectionFunctionBuilder = { arraySizes: List[Int] =>
-    (sortedShards: List[WomValue], valueType: WomArrayType) =>
-
-      @tailrec
-      def buildCollectorArrayRec(currentList: List[Int], currentWomValues: List[WomValue], currentWomType: WomType): WomArray = {
-        /*  We stop right before the last element because it will necessarily be the number of elements in currentWomValues (provided the list is non empty).
-          * e.g if currentList is (2, 3, 2), then currentWomValues will have 2 * 3 * 2 = 12 elements (this is a cross product)
-          * As we recurse, we keep grouping currentWomValues by the numbers in currentList:
-          * 
-          * group by 2: [[_, _], [_, _], [_, _], [_, _], [_, _], [_, _]]
-          * group by 3: [
-          *   [[_, _], [_, _], [_, _]],
-          *   [[_, _], [_, _], [_, _]]
-          * ]
-          * This list has necessarily 2 elements already because 12 / 2 / 3 = 2. So we can make the final WomArray out of that
-        */
-        currentList match {
-          case _ :: Nil | Nil =>
-            WomArray(WomMaybeEmptyArrayType(currentWomType), currentWomValues)
-          case head :: tail =>
-            val arrayType = WomMaybeEmptyArrayType(currentWomType)
-            val womArrays = currentWomValues.grouped(head).toList map { WomArray(arrayType, _) }
-            buildCollectorArrayRec(tail, womArrays, arrayType)
-        }
-      }
-
-      def mostInnerType(tpe: WomType): WomType = tpe match {
-        case WomArrayType(t) => mostInnerType(t)
-        case other => other
-      }
-
-      def buildEmptyArrays(arraySizeList: List[Int], womType: WomType, womValues: List[WomValue]): WomArray = arraySizeList match {
-        case Nil => womType match {
-          case arrayType: WomArrayType => WomArray(arrayType, womValues)
-          case _ =>
-            // This would mean arraySizeList was empty to begin with (otherwise we would have wrapped womType in a WomArrayType at least once)
-            // which should be impossible since it would mean there was no scatter variables, so we shouldn't even be here
-            throw new RuntimeException("Programmer error ! We should not be collecting scatter nodes if there was no scatter !")
-        }
-        case 0 :: tail =>
-          buildEmptyArrays(tail, WomArrayType(womType), List.empty)
-        case head :: tail =>
-          val arrayType = womType match {
-            case array: WomArrayType => array
-            case nonArray => WomArrayType(nonArray)
-          }
-          val womArrays = (0 until head).toList map { _ => WomArray(arrayType, womValues) }
-          buildEmptyArrays(tail, WomArrayType(womType), womArrays)
-      }
-
-      /*
-       * There are 2 distinct cases.
-       * If we have no shards, it means that at least one of the scatter expressions evaluated to an empty array.
-       * In that case we want to create an array structure of empty arrays reflecting the scatter array sizes.
-       * e.g:
-       * 
-       * scatter array sizes   |   collected result
-       *        [0]                       []
-       *       [0, 2]                     [] 
-       *       [2, 0]                   [[], []]
-       *      [2, 0, 3]                 [[], []]
-       *      [2, 3, 0]                [[[], [], []], [[], [], []]] 
-       *
-       * Note that as soon as we reach a size 0, we return an empty array.
-       * 
-       * If we have shards, we successively group the shards list to build arrays of the right size.
-       * 
-       * In both cases we reverse the list so that we can left recurse while still building the result starting from the most nested arrays
-       */
-      if (sortedShards.isEmpty) {
-        buildEmptyArrays(arraySizes.reverse, mostInnerType(valueType), List.empty)
-      } else {
-        // 
-        buildCollectorArrayRec(arraySizes.reverse, sortedShards, mostInnerType(valueType))
-      }
-  }
-
-  // select a processing function based on the scatter method
-  private def processingFunction(scatterMethod: ScatterMethod) = scatterMethod match {
-    case ScatterMethod.DotProduct => DotProductScatterProcessingFunction
-    // Both cross product methods use the same processing function, the difference is in how we collect results (see collectingFunctionBuilder)
-    case ScatterMethod.FlatCrossProduct => CrossProductScatterProcessingFunction
-    case ScatterMethod.NestedCrossProduct => CrossProductScatterProcessingFunction
-  }
-
-  // select a collecting function builder based on the scatter method
-  private def collectingFunctionBuilder(scatterMethod: ScatterMethod) = scatterMethod match {
-    // dot product and flat cross product output a flat array, which is the default behavior
-    case ScatterMethod.DotProduct => ScatterNode.DefaultScatterCollectionFunctionBuilder
-    case ScatterMethod.FlatCrossProduct => ScatterNode.DefaultScatterCollectionFunctionBuilder
-    // nested cross product uses a special collecting function to build nested arrays
-    case ScatterMethod.NestedCrossProduct => NestedCrossProductScatterCollectionFunctionBuilder
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ScatterMethod.scala b/cwl/src/main/scala/cwl/ScatterMethod.scala
deleted file mode 100644
index 0a60575e0cb..00000000000
--- a/cwl/src/main/scala/cwl/ScatterMethod.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cwl
-
-object ScatterMethod extends Enumeration {
-  type ScatterMethod = Value
-
-  val DotProduct = Value("dotproduct")
-  val NestedCrossProduct = Value("nested_crossproduct")
-  val FlatCrossProduct = Value("flat_crossproduct")
-}
diff --git a/cwl/src/main/scala/cwl/StringOrStringArrayToStringList.scala b/cwl/src/main/scala/cwl/StringOrStringArrayToStringList.scala
deleted file mode 100644
index 73afab205b7..00000000000
--- a/cwl/src/main/scala/cwl/StringOrStringArrayToStringList.scala
+++ /dev/null
@@ -1,12 +0,0 @@
-package cwl
-
-import shapeless.Poly1
-
-/**
-  * From a logic standpoint it's easier to treat sources as a list of strings.
-  */
-object StringOrStringArrayToStringList extends Poly1{
-  import Case._
-  implicit def string: Aux[String, List[String]] = at[String]{List(_)}
-  implicit def array: Aux[Array[String], List[String]] = at[Array[String]]{_.toList}
-}
diff --git a/cwl/src/main/scala/cwl/Tool.scala b/cwl/src/main/scala/cwl/Tool.scala
deleted file mode 100644
index d31b7368aee..00000000000
--- a/cwl/src/main/scala/cwl/Tool.scala
+++ /dev/null
@@ -1,189 +0,0 @@
-package cwl
-
-import java.nio.file.Paths
-
-import cats.instances.list._
-import common.Checked
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import cwl.CwlVersion.CwlVersion
-import cwl.Tool.inlineJavascriptRequirements
-import cwl.command.ParentName
-import cwl.requirement.RequirementToAttributeMap
-import shapeless.Inl
-import wom.callable.Callable.{OverridableInputDefinitionWithDefault, OptionalInputDefinition, OutputDefinition, RequiredInputDefinition}
-import wom.callable.MetaValueElement.{MetaValueElementBoolean, MetaValueElementObject}
-import wom.callable.{Callable, MetaValueElement, TaskDefinition}
-import wom.executable.Executable
-import wom.expression.{IoFunctionSet, ValueAsAnExpression, WomExpression}
-import wom.types.WomOptionalType
-import wom.values.{WomInteger, WomLong, WomString}
-import wom.{RuntimeAttributes, RuntimeAttributesKeys}
-
-import scala.util.Try
-
-object Tool {
-  def inlineJavascriptRequirements(allRequirementsAndHints: Seq[Requirement]): Vector[String] = {
-    val inlineJavscriptRequirements: Seq[InlineJavascriptRequirement] = allRequirementsAndHints.toList.collect {
-      case Inl(ijr:InlineJavascriptRequirement) => ijr
-    }
-
-    inlineJavscriptRequirements.flatMap(_.expressionLib.toList.flatten).toVector
-  }
-}
-
-/**
-  * Abstraction over a Tool (CommandLineTool or ExpressionTool)
-  * Contains common logic to both, mostly to build the wom task definition.
-  */
-trait Tool {
-  def inputs: Array[_ <: InputParameter]
-  def outputs: Array[_ <: OutputParameter]
-  def `class`: String
-  def id: String
-  def requirements: Option[Array[Requirement]]
-  def hints: Option[Array[Hint]]
-  def label: Option[String]
-  def doc: Option[String]
-  def cwlVersion: Option[CwlVersion]
-
-  def asCwl: Cwl
-
-  /** Builds an `Executable` directly from a `Tool` CWL with no parent workflow. */
-  def womExecutable(validator: RequirementsValidator, inputFile: Option[String] = None, ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    val taskDefinition = buildTaskDefinition(validator, Vector.empty)
-    CwlExecutableValidation.buildWomExecutable(taskDefinition, inputFile, ioFunctions, strictValidation)
-  }
-
-  protected def buildTaskDefinition(taskName: String,
-                                    inputDefinitions: List[_ <: Callable.InputDefinition],
-                                    outputDefinitions: List[Callable.OutputDefinition],
-                                    runtimeAttributes: RuntimeAttributes,
-                                    requirementsAndHints: List[cwl.Requirement],
-                                    expressionLib: ExpressionLib): ErrorOr[TaskDefinition]
-
-  private [cwl] implicit val explicitWorkflowName = ParentName(id)
-  protected val inputNames: Set[String] = this.inputs.map(i => FullyQualifiedName(i.id).id).toSet
-
-  // Circe can't create bidirectional links between workflow steps and runs (including `CommandLineTool`s) so this
-  // ugly var is here to link back to a possible parent workflow step. This is needed to navigate upward for finding
-  // requirements in the containment hierarchy. There isn't always a containing workflow step so this is an `Option`.
-  private[cwl] var parentWorkflowStep: Option[WorkflowStep] = None
-
-
-  private def validateRequirementsAndHints(validator: RequirementsValidator): ErrorOr[List[Requirement]] = {
-    import cats.syntax.traverse._
-
-    val allRequirements = requirements.toList.flatten ++ parentWorkflowStep.toList.flatMap(_.allRequirements.list)
-    // All requirements must validate or this fails.
-    val errorOrValidatedRequirements: ErrorOr[List[Requirement]] = allRequirements traverse validator
-
-    errorOrValidatedRequirements map { validRequirements =>
-      // Only Requirement hints, everything else is thrown out.
-      // TODO CWL don't throw them out but pass them back to the caller to do with as the caller pleases.
-      val hintRequirements = hints.toList.flatten.flatMap { _.select[Requirement] }
-      val parentHintRequirements = parentWorkflowStep.toList.flatMap(_.allHints)
-
-      // Throw out invalid Requirement hints.
-      // TODO CWL pass invalid hints back to the caller to do with as the caller pleases.
-      val validHints = (hintRequirements ++ parentHintRequirements).collect { case req if validator(req).isValid => req }
-      validRequirements ++ validHints
-    }
-  }
-
-  private def processRequirement(requirement: Requirement, expressionLib: ExpressionLib): Map[String, WomExpression] = {
-    requirement.fold(RequirementToAttributeMap).apply(inputNames, expressionLib)
-  }
-
-  protected def toolAttributes: Map[String, WomExpression] = Map.empty
-
-  def buildTaskDefinition(validator: RequirementsValidator, parentExpressionLib: ExpressionLib): Checked[TaskDefinition] = {
-    def build(requirementsAndHints: Seq[cwl.Requirement]) = {
-      val id = this.id
-
-      val expressionLib: ExpressionLib = parentExpressionLib ++ inlineJavascriptRequirements(requirementsAndHints)
-
-      // This is basically doing a `foldMap` but can't actually be a `foldMap` because:
-      // - There is no monoid instance for `WomExpression`s.
-      // - We want to fold from the right so the hints and requirements with the lowest precedence are processed first
-      //   and later overridden if there are duplicate hints or requirements of the same type with higher precedence.
-      val attributesMap: Map[String, WomExpression] = requirementsAndHints.foldRight(Map.empty[String, WomExpression])({
-        case (requirement, acc) => acc ++ processRequirement(requirement, expressionLib)
-      })
-
-      val runtimeAttributes: RuntimeAttributes = RuntimeAttributes(attributesMap ++ toolAttributes)
-
-      val schemaDefRequirement: SchemaDefRequirement = requirementsAndHints.flatMap{
-        _.select[SchemaDefRequirement].toList
-      }.headOption.getOrElse(SchemaDefRequirement())
-
-      lazy val localizationOptionalMetaObject: MetaValueElement = MetaValueElementObject(
-        Map(
-          "localization_optional" -> MetaValueElementBoolean(true)
-        )
-      )
-
-      // If input dir min == 0 that's a signal not to localize the input files
-      // https://github.com/dnanexus/dx-cwl/blob/fca163d825beb62f8a3004f2e0a6742805e6218c/dx-cwl#L426
-      val localizationOptional = runtimeAttributes.attributes.get(RuntimeAttributesKeys.DnaNexusInputDirMinKey) match {
-        case Some(ValueAsAnExpression(WomInteger(0))) => Option(localizationOptionalMetaObject)
-        case Some(ValueAsAnExpression(WomLong(0L))) => Option(localizationOptionalMetaObject)
-        case Some(ValueAsAnExpression(WomString("0"))) => Option(localizationOptionalMetaObject)
-        case _ => None
-      }
-
-      val inputDefinitions: List[_ <: Callable.InputDefinition] =
-        this.inputs.map {
-          case input @ InputParameter.IdDefaultAndType(inputId, default, tpe) =>
-            val inputType = tpe.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement)
-            val inputName = FullyQualifiedName(inputId).id
-            val defaultWomValue = default.fold(InputParameter.DefaultToWomValuePoly).apply(inputType).toTry.get
-            OverridableInputDefinitionWithDefault(
-              inputName,
-              inputType,
-              ValueAsAnExpression(defaultWomValue),
-              InputParameter.inputValueMapper(input, tpe, expressionLib, asCwl.schemaOption),
-              localizationOptional
-            )
-          case input @ InputParameter.IdAndType(inputId, tpe) =>
-            val inputType = tpe.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement)
-            val inputName = FullyQualifiedName(inputId).id
-            inputType match {
-              case optional: WomOptionalType =>
-                OptionalInputDefinition(
-                  inputName,
-                  optional,
-                  InputParameter.inputValueMapper(input, tpe, expressionLib, asCwl.schemaOption),
-                  localizationOptional
-                )
-              case _ =>
-                RequiredInputDefinition(
-                  inputName,
-                  inputType,
-                  InputParameter.inputValueMapper(input, tpe, expressionLib, asCwl.schemaOption),
-                  localizationOptional
-                )
-            }
-          case other => throw new UnsupportedOperationException(s"command input parameters such as $other are not yet supported")
-        }.toList
-
-      val outputDefinitions: List[Callable.OutputDefinition] = this.outputs.map {
-        case p @ OutputParameter.IdAndType(cop_id, tpe) =>
-          val womType = tpe.fold(MyriadOutputTypeToWomType).apply(schemaDefRequirement)
-          OutputDefinition(FullyQualifiedName(cop_id).id, womType, OutputParameterExpression(p, womType, inputNames, expressionLib, schemaDefRequirement))
-        case other => throw new UnsupportedOperationException(s"Command output parameters such as $other are not yet supported")
-      }.toList
-
-      // The try will succeed if this is a task within a step. If it's a standalone file, the ID will be the file,
-      // so the filename is the fallback.
-      def taskName = Try(FullyQualifiedName(id).id).getOrElse(Paths.get(id).getFileName.toString)
-
-      buildTaskDefinition(taskName, inputDefinitions, outputDefinitions, runtimeAttributes, requirementsAndHints.toList, expressionLib).toEither
-    }
-
-    validateRequirementsAndHints(validator).toEither match {
-      case Right(requirementsAndHints: Seq[cwl.Requirement]) => build(requirementsAndHints)
-      case Left(errors) => Left(errors)
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/TypeAliases.scala b/cwl/src/main/scala/cwl/TypeAliases.scala
deleted file mode 100644
index abbfc9e81e0..00000000000
--- a/cwl/src/main/scala/cwl/TypeAliases.scala
+++ /dev/null
@@ -1,115 +0,0 @@
-package cwl
-
-import cwl.CwlType.CwlType
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import io.circe.Json
-import shapeless.{:+:, CNil}
-import wom.types.WomType
-
-trait TypeAliases {
-
-  type Expression = ECMAScriptFunction :+: ECMAScriptExpression :+: CNil
-
-  // http://www.commonwl.org/v1.0/Workflow.html#InputParameter
-  // http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter
-  type InputParameterFormat = Expression :+: String :+: Array[String] :+: CNil
-  
-  // http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter
-  // http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter
-  type OutputParameterFormat = StringOrExpression
-  
-  type Doc = String :+: Array[String] :+: CNil
-
-  type StringOrExpression = Expression :+: String :+: CNil
-
-  type CwlAny =
-    FileOrDirectory :+:
-      Array[FileOrDirectory] :+:
-      Json :+:
-      CNil
-
-  type WorkflowStepInputId = String
-
-  type Requirement =
-    InlineJavascriptRequirement :+:
-      SchemaDefRequirement :+:
-      DockerRequirement :+:
-      SoftwareRequirement :+:
-      InitialWorkDirRequirement :+:
-      EnvVarRequirement :+:
-      ShellCommandRequirement :+:
-      ResourceRequirement :+:
-      SubworkflowFeatureRequirement :+:
-      ScatterFeatureRequirement :+:
-      MultipleInputFeatureRequirement :+:
-      StepInputExpressionRequirement :+:
-      DnaNexusInputResourceRequirement :+:
-      CNil
-
-  type Hint =
-    Requirement :+:
-      CwlAny :+:
-      CNil
-
-  type MyriadInputType =
-    MyriadInputInnerType :+:
-      Array[MyriadInputInnerType] :+:
-      CNil
-
-  type MyriadInputInnerType =
-    CwlType :+:
-      InputRecordSchema :+:
-      InputEnumSchema :+:
-      InputArraySchema :+:
-      String :+:
-      CNil
-
-  type MyriadOutputType =
-    MyriadOutputInnerType :+:
-      Array[MyriadOutputInnerType] :+:
-      CNil
-
-  type MyriadOutputInnerType =
-    CwlType :+:
-      OutputRecordSchema :+:
-      OutputEnumSchema :+:
-      OutputArraySchema :+:
-      String :+:
-      CNil
-
-  type ResourceRequirementType = Long :+: Expression :+: String :+: CNil
-
-  type SingleOrArrayOfStrings = String :+: Array[String] :+: CNil
-
-  type ScatterVariables = Option[SingleOrArrayOfStrings]
-
-  type FileOrDirectory = File :+: Directory :+: CNil
-
-  type Glob = StringOrExpression :+: Array[String] :+: CNil
-
-  type SecondaryFiles = StringOrExpression :+: Array[StringOrExpression] :+: CNil
-}
-
-object MyriadInputType {
-
-  object InputArraySchema {
-    def unapply(m: MyriadInputType): Option[InputArraySchema] = m.select[MyriadInputInnerType].flatMap(_.select[InputArraySchema])
-  }
-
-  object InputArray {
-    def unapply(m: MyriadInputType): Option[Array[MyriadInputInnerType]] = m.select[Array[MyriadInputInnerType]]
-  }
-
-  object CwlType {
-    def unapply(m: MyriadInputType): Option[CwlType] = {
-      m.select[MyriadInputInnerType].flatMap(_.select[CwlType])
-    }
-  }
-
-  object WomType {
-    def unapply(m: MyriadInputType): Option[WomType] = m match {
-      case CwlType(c) => Option(cwl.cwlTypeToWomType(c))
-      case _ => None
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/Workflow.scala b/cwl/src/main/scala/cwl/Workflow.scala
deleted file mode 100644
index 22b30019ff1..00000000000
--- a/cwl/src/main/scala/cwl/Workflow.scala
+++ /dev/null
@@ -1,246 +0,0 @@
-package cwl
-
-import java.nio.file.Paths
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.Checked
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.CwlVersion._
-import cwl.LinkMergeMethod.LinkMergeMethod
-import cwl.Workflow.{WorkflowInputParameter, WorkflowOutputParameter}
-import cwl.command.ParentName
-import shapeless._
-import shapeless.syntax.singleton._
-import wom.SourceFileLocation
-import wom.callable.{MetaValueElement, WorkflowDefinition}
-import wom.executable.Executable
-import wom.expression.{IoFunctionSet, ValueAsAnExpression}
-import wom.graph.GraphNodePort.{GraphNodeOutputPort, OutputPort}
-import wom.graph._
-import wom.types.{WomOptionalType, WomType}
-
-case class Workflow private(
-                             cwlVersion: Option[CwlVersion],
-                             `class`: Witness.`"Workflow"`.T,
-                             id: String,
-                             inputs: Array[WorkflowInputParameter],
-                             outputs: Array[WorkflowOutputParameter],
-                             steps: Array[WorkflowStep],
-                             requirements: Option[Array[Requirement]],
-                             hints: Option[Array[Hint]],
-                             `$namespaces`: Option[Map[String, String]],
-                             `$schemas`: Option[Array[String]]
-                           ) {
-
-  steps.foreach { _.parentWorkflow = this }
-
-  /** Builds an `Executable` from a `Workflow` CWL with no parent `Workflow` */
-  def womExecutable(validator: RequirementsValidator, inputFile: Option[String] = None, ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    CwlExecutableValidation.buildWomExecutableCallable(womDefinition(validator, Vector.empty), inputFile, ioFunctions, strictValidation)
-  }
-
-  /* Circe can't create bidirectional links between workflow steps and runs (including `Workflow`s) so this
-   * ugly var is here to link back to a possible parent workflow step. This is needed to navigate upward for finding
-   * requirements in the containment hierarchy. There isn't always a containing workflow step so this is an `Option`.
-   */
-  private[cwl] var parentWorkflowStep: Option[WorkflowStep] = None
-
-  val allRequirements: RequirementsAndHints = RequirementsAndHints(requirements.toList.flatten ++ parentWorkflowStep.toList.flatMap { _.allRequirements.list })
-
-  private [cwl] implicit val explicitWorkflowName = ParentName(id)
-
-  lazy val womFqn: Option[wom.graph.FullyQualifiedName] = {
-    explicitWorkflowName.value map { workflowName =>
-      /* Sometimes the workflow name is of the form "parentWorkflowStepName/UUID"
-       * In that case, we don't want the fqn to look like "parentWorkflowStepName.parentWorkflowStepName/UUID"
-       * To avoid that, strip the parentWorkflowStepName from the workflowName
-       */
-      val cleanWorkflowName = parentWorkflowStep
-        .map(_.womFqn.value + "/")
-        .map(workflowName.stripPrefix)
-        .getOrElse(workflowName)
-
-      parentWorkflowStep.map(_.womFqn.combine(cleanWorkflowName))
-        .getOrElse(wom.graph.FullyQualifiedName(cleanWorkflowName))
-    }
-  }
-
-  lazy val allHints: List[Requirement] = {
-    // Just ignore any hint that isn't a Requirement.
-    val requirementHints = hints.toList.flatten.flatMap { _.select[Requirement] }
-    requirementHints ++ parentWorkflowStep.toList.flatMap { _.allHints }
-  }
-
-  val fileNames: List[String] = steps.toList.flatMap(_.run.select[String].toList)
-
-  def outputsTypeMap: WomTypeMap = steps.foldLeft(Map.empty[String, WomType]) {
-    /* Not implemented as a `foldMap` because there is no semigroup instance for `WomType`s.  `foldMap` doesn't know that
-     * we don't need a semigroup instance since the map keys should be unique and therefore map values would never need
-     * to be combined under the same key.
-     */
-    (acc, s) => acc ++ s.typedOutputs
-  }
-
-  def womGraph(workflowName: String, validator: RequirementsValidator, expressionLib: ExpressionLib): Checked[Graph] = {
-    val workflowNameIdentifier = explicitWorkflowName.value.map(WomIdentifier.apply).getOrElse(WomIdentifier(workflowName))
-
-    def womTypeForInputParameter(input: InputParameter): Option[WomType] = {
-      input.`type`.map(_.fold(MyriadInputTypeToWomType).apply(allRequirements.schemaDefRequirement))
-    }
-
-    val typeMap: WomTypeMap =
-      outputsTypeMap ++
-        /* Note this is only looking at the workflow inputs and not recursing into steps, because our current thinking
-         * is that in CWL graph inputs can only be defined at the workflow level.  It's possible that's not actually
-         * correct, but that's the assumption being made here.
-         */
-        inputs.toList.flatMap { i =>
-          womTypeForInputParameter(i).map(i.id -> _).toList
-        }.toMap
-
-    val externalGraphInputNodes: Set[ExternalGraphInputNode] = inputs.map { wip =>
-      val womType: WomType = womTypeForInputParameter(wip).get
-      val parsedInputId = FileAndId(wip.id).id
-      val womId = WomIdentifier(parsedInputId, wip.id)
-      val valueMapper =
-        InputParameter.inputValueMapper(wip, wip.`type`.get, expressionLib, asCwl.schemaOption)
-
-      def optionalWithDefault(memberType: WomType): OptionalGraphInputNodeWithDefault = {
-        val defaultValue = wip.default.get.fold(InputParameter.DefaultToWomValuePoly).apply(womType).toTry.get
-        OptionalGraphInputNodeWithDefault(womId, memberType, ValueAsAnExpression(defaultValue), parsedInputId, valueMapper)
-      }
-
-      womType match {
-        case WomOptionalType(memberType) if wip.default.isDefined => optionalWithDefault(memberType)
-        case _ if wip.default.isDefined => optionalWithDefault(womType)
-        case optional @ WomOptionalType(_) => OptionalGraphInputNode(womId, optional, parsedInputId, valueMapper)
-        case _ => RequiredGraphInputNode(womId, womType, parsedInputId, valueMapper)
-      }
-    }.toSet
-
-    val workflowInputs: Map[String, GraphNodeOutputPort] =
-      externalGraphInputNodes.map { egin =>
-        egin.localName -> egin.singleOutputPort
-      }.toMap
-
-    val graphFromSteps: Checked[Set[GraphNode]] =
-      steps.
-        toList.
-        foldLeft((Set.empty[GraphNode] ++ externalGraphInputNodes).asRight[NonEmptyList[String]])(
-          (nodes, step) => nodes.flatMap(step.callWithInputs(typeMap, this, _, workflowInputs, validator, expressionLib)))
-
-    val graphFromOutputs: Checked[Set[GraphNode]] =
-      outputs.toList.traverse[ErrorOr, GraphNode] {
-        case WorkflowOutputParameter(id, _, _, _, _, _, _, Some(Inl(outputSource: String)), _, Some(tpe)) =>
-          val womType: WomType = tpe.fold(MyriadOutputTypeToWomType).apply(allRequirements.schemaDefRequirement)
-
-          val parsedWorkflowOutput = FileAndId(id)
-          val parsedOutputSource = cwl.FullyQualifiedName(outputSource)
-
-          // Try to find an output port for this cwl output in the set of available nodes
-          def lookupOutputSource(fqn: cwl.FullyQualifiedName): Checked[OutputPort] = {
-            def isRightOutputPort(op: GraphNodePort.OutputPort) = cwl.FullyQualifiedName.maybeApply(op.name) match {
-              case Some(f) => f.id == fqn.id
-              case None => op.internalName == fqn.id
-            }
-
-            def sourceNode(graph: Set[GraphNode]): Checked[GraphNode] = {
-              val findSource: PartialFunction[GraphNode, GraphNode] = fqn match {
-                // A step output becoming a workflow output.
-                case fsi: FileStepAndId => {
-                  case callNode: CallNode if callNode.localName == fsi.stepId => callNode
-                  case scatterNode: ScatterNode if scatterNode.innerGraph.calls.exists(_.localName == fsi.stepId) => scatterNode
-                }
-                // A workflow input recycled back to be an output.
-                case fi: FileAndId => {
-                  case gin: ExternalGraphInputNode if gin.nameInInputSet == fi.id => gin
-                }
-              }
-              graph collectFirst findSource toRight NonEmptyList.one(s"Call Node by name $fqn was not found in set $graph")
-            }
-
-            for {
-              set <- graphFromSteps
-              node <- sourceNode(set)
-              output <- node.outputPorts.find(isRightOutputPort).toChecked(s"looking for ${fqn.id} in call $node output ports ${node.outputPorts}")
-            } yield output
-          }
-
-          lookupOutputSource(parsedOutputSource).map({ port =>
-            val localName = LocalName(parsedWorkflowOutput.id)
-            val fullyQualifiedName = workflowNameIdentifier.fullyQualifiedName.combine(parsedWorkflowOutput.id)
-            val outputIdentifier = WomIdentifier(localName, fullyQualifiedName)
-            PortBasedGraphOutputNode(outputIdentifier, womType, port)
-          }).toValidated
-        case wop => throw new UnsupportedOperationException(s"Workflow output parameters such as $wop are not supported.")
-      }.map(_.toSet).toEither
-
-    for {
-      outputs <- graphFromOutputs
-      steps <- graphFromSteps
-      ret <- Graph.validateAndConstruct(steps ++ externalGraphInputNodes ++ outputs).toEither
-    } yield ret
-  }
-
-  def womDefinition(validator: RequirementsValidator, expressionLib: ExpressionLib): Checked[WorkflowDefinition] = {
-    val name: String = Paths.get(id).getFileName.toString
-    val meta: Map[String, MetaValueElement.MetaValueElementString] = Map.empty
-    val paramMeta: Map[String, MetaValueElement.MetaValueElementString] = Map.empty
-    val lexInfo : Option[SourceFileLocation] = None
-
-    womGraph(name, validator, expressionLib).map(graph =>
-      WorkflowDefinition(
-        name,
-        graph,
-        meta,
-        paramMeta,
-        lexInfo
-      )
-    )
-  }
-
-  def asCwl = Coproduct[Cwl](this)
-}
-object Workflow {
-
-  case class WorkflowInputParameter(id: String,
-                                    label: Option[String] = None,
-                                    secondaryFiles: Option[SecondaryFiles] = None,
-                                    format: Option[InputParameterFormat] = None,
-                                    streamable: Option[Boolean] = None,
-                                    doc: Option[Doc] = None,
-                                    inputBinding: Option[InputCommandLineBinding] = None,
-                                    default: Option[CwlAny] = None,
-                                    `type`: Option[MyriadInputType] = None) extends InputParameter
-
-  case class WorkflowOutputParameter(
-                                      id: String,
-                                      label: Option[String] = None,
-                                      secondaryFiles: Option[SecondaryFiles] = None,
-                                      format: Option[OutputParameterFormat] = None,
-                                      streamable: Option[Boolean] = None,
-                                      doc: Option[Doc] = None,
-                                      outputBinding: Option[CommandOutputBinding] = None,
-                                      outputSource: Option[WorkflowOutputParameter#OutputSource] = None,
-                                      linkMerge: Option[LinkMergeMethod] = None,
-                                      `type`: Option[MyriadOutputType] = None) extends OutputParameter {
-
-    type OutputSource = String :+: Array[String] :+: CNil
-  }
-
-  def apply(cwlVersion: Option[CwlVersion] = Option(CwlVersion.Version1),
-            id: String,
-            inputs: Array[WorkflowInputParameter] = Array.empty,
-            outputs: Array[WorkflowOutputParameter] = Array.empty,
-            steps: Array[WorkflowStep] = Array.empty,
-            requirements: Option[Array[Requirement]] = None,
-            hints: Option[Array[Hint]] = None,
-            namespaces: Option[Map[String, String]] = None,
-            schemas: Option[Array[String]] = None
-           ): Workflow  =
-    Workflow(cwlVersion, "Workflow".narrow, id, inputs, outputs, steps, requirements, hints, namespaces, schemas)
-}
diff --git a/cwl/src/main/scala/cwl/WorkflowStep.scala b/cwl/src/main/scala/cwl/WorkflowStep.scala
deleted file mode 100644
index cf39f261bae..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStep.scala
+++ /dev/null
@@ -1,537 +0,0 @@
-package cwl
-
-import cats.Monoid
-import cats.data.NonEmptyList
-import cats.data.Validated._
-import cats.syntax.either._
-import cats.syntax.foldable._
-import cats.syntax.monoid._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import cwl.ScatterLogic.ScatterVariablesPoly
-import cwl.ScatterMethod._
-import cwl.WorkflowStep.{WorkflowStepInputFold, _}
-import cwl.WorkflowStepInput._
-import cwl.command.ParentName
-import shapeless.{:+:, CNil, _}
-import wom.callable.Callable
-import wom.callable.Callable._
-import wom.graph.CallNode._
-import wom.graph.GraphNodePort.{GraphNodeOutputPort, OutputPort}
-import wom.graph._
-import wom.graph.expression.ExpressionNode
-import wom.types.WomType
-import wom.values.WomValue
-import wom.graph.{FullyQualifiedName => WomFullyQualifiedName}
-
-/**
-  * An individual job to run.
-  *
-  * @see <a href="http://www.commonwl.org/v1.0/Workflow.html#WorkflowStep">CWL Spec | Workflow Step</a>
-  * @param run Purposefully not defaulted as it's required in the specification and it is unreasonable to not have something to run.
-  */
-case class WorkflowStep(
-                         id: String,
-                         in: Array[WorkflowStepInput] = Array.empty,
-                         out: WorkflowStepOutputType,
-                         run: Run,
-                         requirements: Option[Array[Requirement]] = None,
-                         hints: Option[Array[Hint]] = None,
-                         label: Option[String] = None,
-                         doc: Option[String] = None,
-                         scatter: ScatterVariables = None,
-                         scatterMethod: Option[ScatterMethod] = None) {
-
-  run.select[Workflow].foreach(_.parentWorkflowStep = Option(this))
-  run.select[CommandLineTool].foreach(_.parentWorkflowStep = Option(this))
-  run.select[ExpressionTool].foreach(_.parentWorkflowStep = Option(this))
-
-  // We're scattering if scatter is defined, and if it's a list of variables the list needs to be non empty
-  private val isScattered: Boolean = scatter exists { _.select[Array[String]].forall(_.nonEmpty) }
-
-  // Circe can't create bidirectional links between workflows and workflow steps so this ugly var is here to link
-  // back to the parent workflow. This is needed to navigate upward for finding requirements in the containment
-  // hierarchy. There is always a workflow containing a workflow step so this is not an `Option`.
-  private[cwl] var parentWorkflow: Workflow = _
-
-  lazy val allRequirements = RequirementsAndHints(requirements.toList.flatten ++ parentWorkflow.allRequirements.list)
-
-  lazy val womFqn: WomFullyQualifiedName = {
-    implicit val parentName = parentWorkflow.explicitWorkflowName
-    val localFqn = cwl.FullyQualifiedName.maybeApply(id).map(_.id).getOrElse(id)
-    parentWorkflow.womFqn.map(_.combine(localFqn)).getOrElse(wom.graph.FullyQualifiedName(localFqn))
-  }
-
-  lazy val allHints: List[Requirement] = {
-    // Just ignore any hint that isn't a Requirement.
-    val requirementHints = hints.toList.flatten.flatMap { _.select[Requirement] }
-    requirementHints ++ parentWorkflow.allHints
-  }
-
-  // If the step is being scattered over, apply the necessary transformation to get the final output array type.
-  lazy val scatterTypeFunction: WomType => WomType = scatter.map(_.fold(ScatterVariablesPoly)) match {
-    case Some(Nil) => identity[WomType]
-    case Some(nonEmpty) => ScatterLogic.scatterGatherPortTypeFunction(scatterMethod, NonEmptyList.fromListUnsafe(nonEmpty))
-    case _ =>  identity[WomType]
-  }
-
-  def typedOutputs: WomTypeMap = {
-    implicit val parentName = ParentName(id)
-    // Find the type of the outputs of the run section
-    val runOutputTypes = run.fold(RunOutputsToTypeMap).apply(allRequirements.schemaDefRequirement)
-      .map({
-        case (runOutputId, womType) => cwl.FullyQualifiedName(runOutputId).id -> womType
-      })
-    // Use them to find get the final type of the workflow outputs, and only the workflow outputs
-    out.map({ stepOutput =>
-      val stepOutputValue = stepOutput.select[WorkflowStepOutput].map(_.id).getOrElse(stepOutput.select[String].get)
-      val stepOutputId = cwl.FullyQualifiedName(stepOutputValue)
-      stepOutputValue -> scatterTypeFunction(runOutputTypes(stepOutputId.id))
-    }).toMap
-  }
-
-  def fileName: Option[String] = run.select[String]
-
-  /**
-    * Generates all GraphNodes necessary to represent call nodes and input nodes
-    * Recursive because dependencies are discovered as we iterate through inputs and corresponding
-    * upstream nodes need to be generated on the fly.
-    *
-    * Example:
-    *
-    * CWL:
-    * inputs:
-    *   
-id: workflow_input_A

-    *    type: string[]
-    *   -id: workflow_input_B

-    *    type: string[]
-    *   
-id: workflow_input_C

-    *    type: string


-    * steps:

-    *   -id: echo
-    *    run: echo.cwl
-    *    scatter: input0
-    *    in:
-    *      -id:input0
-    *       source:
-    *         - "#workflow_input_A"
-    *         - "#workflow_input_B"

-    *       valueFrom:"bonjour"
-    *
-    *      -id: input1
-    *   
    source: "#workflow_input_C"
-    *       valueFrom:"$(inputs.input0)"
-    *
-    * WOM Diagram:
-    *
-    *  +------------+   +------------+   +------------+
-    *  | WF Input A |   | WF Input B |   | WF Input C |
-    *  +--------+---+ +-+------------+   +------+-----+
-    *           |     |                         |
-    *           |     |                         |
-    *     +-----v-----v+                 +------v-----+
-    *     | StepInput0 |                 | StepInput1 |
-    *     | MergeLogic |                 | MergeLogic |
-    *     +-----+------+                 +----+-------+
-    *           |                             |
-    *  +----------------------------------------------+
-    *  |        |                             |       |
-    *  | +------v----------+              +---v--+    |
-    *  | | ScatterVariable +------------+ | OGIN |    |
-    *  | +-----+-----------+            | +--+-+-+    |
-    *  |       |                        |    | |      |
-    *  | +-----v----+                   |    | |      |
-    *  | |StepInput0<------------------------+ |      |
-    *  | |Expression|                   |      |      |
-    *  | +----+-----+                +--v------v+     |
-    *  |      |                      |StepInput1|     |
-    *  |      |                      |Expression|     |
-    *  |      |                      +------+---+     |
-    *  |      |    +-----------+            |         |
-    *  |      +----> Call Node <------------+         |
-    *  |           +-----------+                      |
-    *  |                                 Scatter Node |
-    *  +----------------------------------------------+
-    *
-    * MergeNode: If the step input has one or more sources, a merge node will be created and responsible for merging
-    *   those input sources together. It will NOT evaluate the valueFrom field of the input.
-    *
-    * ScatterVariableNode: If the step input is being scattered over, a scatter variable node will be created and will
-    *   act as a proxy inside the scatter graph for the shards of the scatter. It depends on an upstream merge node outputing an array
-    *   and will provide at runtime shard values for other nodes of the scatter graph.
-    *
-    * OGIN: If the step has at least one input being scattered over, there will be a scatter node created.
-    *   For inputs that are NOT being scattered over but still have one or more input sources (and hence a merge node), an OGIN
-    *   will be created to act as a proxy to the merge node outside the scatter graph.
-    *
-    * ExpressionNode: If an input has a valueFrom field, an expression node will be created to evaluate the expression.
-    *   An important fact to note is that the expression needs access to all other input values
-    *   AFTER their source, default value and shard number has been determined but
-    *   BEFORE their (potential) valueFrom is evaluated (see http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)
-    *   This is why on the above diagram, StepInput0Expression depends on the OGIN, and StepInput1Expression depends on the scatter variable.
-    */
-  def callWithInputs(typeMap: WomTypeMap,
-                     workflow: Workflow,
-                     knownNodes: Set[GraphNode],
-                     workflowInputs: Map[String, GraphNodeOutputPort],
-                     validator: RequirementsValidator,
-                     expressionLib: ExpressionLib): Checked[Set[GraphNode]] = {
-
-    implicit val parentName = workflow.explicitWorkflowName
-
-    val scatterLookupSet =
-      scatter.toList.
-        flatMap(_.fold(StringOrStringArrayToStringList)).
-        map(id => cwl.FullyQualifiedName(id).id)
-
-    def isStepScattered(workflowStepInputId: String) = scatterLookupSet.contains(workflowStepInputId)
-
-    val unqualifiedStepId: WomIdentifier = {
-      cwl.FullyQualifiedName.maybeApply(id).map({ fqn =>
-        WomIdentifier(LocalName(fqn.id), womFqn)
-      }).getOrElse(WomIdentifier(id))
-    }
-
-    def typedRunInputs: Map[String, Option[MyriadInputType]] = run.fold(RunToInputTypeMap).apply(parentName)
-
-    def allIdentifiersRecursively(nodes: Set[GraphNode]): Set[WomIdentifier] = nodes.flatMap({
-      case w: WorkflowCallNode=> Set(w.identifier)
-      case c: CommandCallNode => Set(c.identifier)
-      case e: ExpressionCallNode => Set(e.identifier)
-      // When a node a call node is being scattered over, it is wrapped inside a scatter node. We still don't want to
-      // duplicate it though so look inside scatter nodes to see if it's there.
-      case scatter: ScatterNode => allIdentifiersRecursively(scatter.innerGraph.nodes)
-      case _ => Set.empty[WomIdentifier]
-    })
-
-    // To avoid duplicating nodes, return immediately if we've already covered this node
-    val haveWeSeenThisStep: Boolean = allIdentifiersRecursively(knownNodes).contains(unqualifiedStepId)
-
-    if (haveWeSeenThisStep) Right(knownNodes)
-    else {
-      val callable: Checked[Callable] = run match {
-        case Run.CommandLineTool(clt) => clt.buildTaskDefinition(validator, expressionLib)
-        case Run.Workflow(wf) => wf.womDefinition(validator, expressionLib)
-        case Run.ExpressionTool(et) => et.buildTaskDefinition(validator, expressionLib)
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-
-      val callNodeBuilder = new CallNode.CallNodeBuilder()
-
-      /*
-       * Method used to fold over the list of inputs declared by this step.
-       * Note that because we work on saladed CWL, all ids are fully qualified at this point (e.g: file:///path/to/file/three_step.cwl#cgrep/pattern
-       * The goal of this method is two fold (pardon the pun):
-       *   1) link each input of the step to an output port (which at this point can be from a different step or from a workflow input)
-       *   2) accumulate the nodes created along the way to achieve 1)
-       */
-      def foldStepInput(currentFold: Checked[WorkflowStepInputFold], workflowStepInput: WorkflowStepInput): Checked[WorkflowStepInputFold] = currentFold flatMap {
-        fold =>
-          /*
-            * Try to find in the given set an output port named stepOutputId in a call node named stepId
-            * This is useful when we've determined that the input points to an output of a different step and we want
-            * to get the corresponding output port.
-           */
-          def findThisInputInSet(set: Set[GraphNode], stepId: String, stepOutputId: String): Checked[OutputPort] = {
-            for {
-              // We only care for outputPorts of call nodes or scatter nodes
-              call <- set.collectFirst {
-                case callNode: CallNode if callNode.localName == stepId => callNode
-                case scatterNode: ScatterNode if scatterNode.innerGraph.calls.exists(_.localName == stepId) => scatterNode
-              }.
-                toRight(NonEmptyList.one(s"stepId $stepId not found in known Nodes $set"))
-              output <- call.outputPorts.find(_.internalName == stepOutputId).
-                toRight(NonEmptyList.one(s"step output id $stepOutputId not found in ${call.outputPorts}"))
-            } yield output
-          }
-
-          /*
-           * Build a wom node for the given step and return the newly created nodes
-           * This is useful when we've determined that the input belongs to an upstream step that we haven't covered yet
-           */
-          def buildUpstreamNodes(upstreamStepId: String, accumulatedNodes: Set[GraphNode]): Checked[Set[GraphNode]] =
-          // Find the step corresponding to this upstreamStepId in the set of all the steps of this workflow
-            for {
-              step <- workflow.steps.find { step => cwl.FullyQualifiedName(step.id).id == upstreamStepId }.
-                toRight(NonEmptyList.one(s"no step of id $upstreamStepId found in ${workflow.steps.map(_.id).toList}"))
-              call <- step.callWithInputs(typeMap, workflow, accumulatedNodes, workflowInputs, validator, expressionLib)
-            } yield call
-
-          def fromWorkflowInput(inputName: String): Checked[Map[String, OutputPort]] = {
-            // Try to find it in the workflow inputs map, if we can't it's an error
-            workflowInputs.collectFirst {
-              case (inputId, port) if inputName == inputId => Map(inputId -> port).asRight[NonEmptyList[String]]
-            } getOrElse s"Can't find workflow input for $inputName".invalidNelCheck[Map[String, OutputPort]]
-          }
-
-          def fromStepOutput(stepId: String, stepOutputId: String, accumulatedNodes: Set[GraphNode]): Checked[(Map[String, OutputPort], Set[GraphNode])] = {
-            // First check if we've already built the WOM node for this step, and if so return the associated output port
-            findThisInputInSet(accumulatedNodes, stepId, stepOutputId).map(outputPort => (Map(s"$stepId/$stepOutputId" -> outputPort), accumulatedNodes))
-              .orElse {
-                // Otherwise build the upstream nodes and look again in those newly created nodes
-                for {
-                  newNodes <- buildUpstreamNodes(stepId, accumulatedNodes)
-                  sourceMappings <- findThisInputInSet(newNodes, stepId, stepOutputId).map(outputPort => Map(s"$stepId/$stepOutputId" -> outputPort))
-                } yield (sourceMappings, newNodes ++ accumulatedNodes)
-              }
-          }
-
-          lazy val workflowStepInputId = cwl.FullyQualifiedName(workflowStepInput.id).id
-
-          def updateFold(sourceMappings: Map[String, OutputPort], newNodes: Set[GraphNode]): Checked[WorkflowStepInputFold] = {
-            val typeExpectedByRunInput: Option[cwl.MyriadInputType] = typedRunInputs.get(workflowStepInputId).flatten
-
-            val isThisStepScattered = isStepScattered(workflowStepInputId)
-
-            workflowStepInput.toMergeNode(sourceMappings, expressionLib, typeExpectedByRunInput, isThisStepScattered, allRequirements.schemaDefRequirement) match {
-              // If the input needs a merge node, build it and add it to the input fold
-              case Some(mergeNode) =>
-                mergeNode.toEither.map({ node =>
-                  fold |+| WorkflowStepInputFold(
-                    mergeNodes = Map(workflowStepInput -> node),
-                    generatedNodes = newNodes
-                  )
-                })
-              case None => (fold |+| WorkflowStepInputFold(generatedNodes = newNodes)).validNelCheck
-            }
-          }
-
-          /*
-           * We intend to validate that all of these sources point to a WOM Outputport that we know about.
-           *
-           * If we don't know about them, we find upstream nodes and build them (see "buildUpstreamNodes").
-           */
-          val baseCase = (Map.empty[String, OutputPort], fold.generatedNodes).asRight[NonEmptyList[String]]
-          val inputMappingsAndGraphNodes: Checked[(Map[String, OutputPort], Set[GraphNode])] =
-            workflowStepInput.sources.foldLeft(baseCase) {
-              case (Right((sourceMappings, graphNodes)), inputSource) =>
-                /*
-                 * Parse the inputSource (what this input is pointing to)
-                 * 2 cases:
-                 *   - points to a workflow input
-                 *   - points to an upstream step
-                 */
-                cwl.FullyQualifiedName(inputSource) match {
-                  // The source points to a workflow input, which means it should be in the workflowInputs map
-                  case FileAndId(_, _, inputId) => fromWorkflowInput(inputId).map(newMap => (sourceMappings ++ newMap, graphNodes))
-                  // The source points to an output from a different step
-                  case FileStepAndId(_, _, stepId, stepOutputId) => fromStepOutput(stepId, stepOutputId, graphNodes).map({ case (newMap, newNodes) => (sourceMappings ++ newMap, newNodes) })
-                }
-              case (other, _) => other
-            }
-
-          inputMappingsAndGraphNodes.flatMap((updateFold _).tupled)
-      }
-
-      /*
-       * Folds over input definitions and build an InputDefinitionFold
-       */
-      def foldInputDefinition(pointerNode: Map[String, GraphNodeWithSingleOutputPort])
-                             (inputDefinition: InputDefinition): ErrorOr[InputDefinitionFold] = {
-        inputDefinition match {
-          case _ if pointerNode.contains(inputDefinition.name) =>
-            val expressionNode = pointerNode(inputDefinition.name)
-            InputDefinitionFold(
-              mappings = List(inputDefinition -> expressionNode.inputDefinitionPointer),
-              callInputPorts = Set(callNodeBuilder.makeInputPort(inputDefinition, expressionNode.singleOutputPort))
-            ).validNel
-
-          // No expression node mapping, use the default
-          case withDefault @ OverridableInputDefinitionWithDefault(_, _, expression, _, _) =>
-            InputDefinitionFold(
-              mappings = List(withDefault -> Coproduct[InputDefinitionPointer](expression))
-            ).validNel
-
-          // Required input without default value and without mapping, this is a validation error
-          case RequiredInputDefinition(requiredName, _, _, _) =>
-            s"Input ${requiredName.value} is required and is not bound to any value".invalidNel
-
-          // Optional input without mapping, defaults to empty value
-          case optional: OptionalInputDefinition =>
-            InputDefinitionFold(
-              mappings = List(optional -> Coproduct[InputDefinitionPointer](optional.womType.none: WomValue))
-            ).validNel
-          case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-        }
-      }
-
-      /*
-        If the step is being scattered over, then merge nodes can't directly be referenced because they will be outside the scatter graph.
-        For inputs that are being scattered over, a scatter variable has already been created, but for the others we need
-        an OGIN to link the merge node to the inner scatter graph.
-       */
-      def buildOGINs(mergeNodes: Map[WorkflowStepInput, ExpressionNode],
-                     scatterVariables: Map[WorkflowStepInput, ScatterVariableNode]): Map[WorkflowStepInput, OuterGraphInputNode] = if (isScattered) {
-        mergeNodes
-          .collect({
-            case (input, mergeNode) if !scatterVariables.contains(input) =>
-              val ogin = OuterGraphInputNode(
-                WomIdentifier(input.parsedId).combine("OGIN"),
-                mergeNode.singleOutputPort,
-                preserveScatterIndex = false
-              )
-              input -> ogin
-          })
-      } else Map.empty
-
-      /*
-        * For inputs that have a valueFrom field, create an ExpressionNode responsible for evaluating the expression.
-        * Note that this expression might need access to the other input values, so make each expression node depend on all other
-        * inputs.
-       */
-      def buildStepInputValueFromNodes(sharedInputNodes: Map[WorkflowStepInput, GraphNodeWithSingleOutputPort]): Checked[Map[String, ExpressionNode]] = {
-        // Add new information to the typeMap from the shard input nodes.
-        lazy val updatedTypeMap = sharedInputNodes.map({
-          // If the input node is a scatter variable, make sure the type is the item type, not the array type, as the expression node
-          // will operate on shards not on the whole scattered array.
-          case (stepInput, scatter: ScatterVariableNode) => stepInput.parsedId -> scatter.womType
-          case (stepInput, node) => stepInput.parsedId -> node.singleOutputPort.womType
-        }) ++ typeMap
-
-        // Go over each step input and create an expression node for those which have a valueFrom
-        in.toList.collect({
-          case stepInput @ WorkflowStepInput(_, _, _, _, Some(valueFrom)) =>
-            // Transform the shared inputs map into a usable map to create the expression.
-            lazy val sharedInputMap: Map[String, OutputPort] = sharedInputNodes.map({
-              case (siblingStepInput, graphNode) => siblingStepInput.parsedId -> graphNode.singleOutputPort
-            })
-            val typeExpectedByRunInput: Option[cwl.MyriadInputType] = typedRunInputs.get(stepInput.parsedId).flatten
-            val isThisStepScattered = isStepScattered(stepInput.parsedId)
-
-            stepInput.toExpressionNode(valueFrom, typeExpectedByRunInput, isThisStepScattered, sharedInputMap, updatedTypeMap, expressionLib, allRequirements.schemaDefRequirement).map(stepInput.parsedId -> _)
-        })
-          .sequence[ErrorOr, (String, ExpressionNode)]
-          .toEither
-          .map(_.toMap)
-      }
-
-      //inputs base case consist of the nodes we already know about
-      val baseCase = WorkflowStepInputFold(generatedNodes = knownNodes).asRight[NonEmptyList[String]]
-
-      // WorkflowStepInputFold contains the mappings from step input to ExpressionNode as well as all created nodes
-      val stepInputFoldCheck: Checked[WorkflowStepInputFold] = in.foldLeft(baseCase)(foldStepInput)
-
-      /*
-        * This (big) flatMap builds nodes from top to bottom in the diagram above.
-        * If necessary, the scatter node is built last as it wraps some of the other nodes.
-       */
-      for {
-        /* ************************************ */
-        /* ************ Merge Nodes *********** */
-        /* ************************************ */
-        // Build merge nodes and recursively generates other call nodes that we haven't seen so far
-        stepInputFold <- stepInputFoldCheck
-        // Extract the merge nodes from the fold
-        mergeNodes = stepInputFold.mergeNodes
-
-        /* ************************************ */
-        /* ****** Scatter Variable Nodes ****** */
-        /* ************************************ */
-        scatterVariableNodes <- ScatterLogic.buildScatterVariableNodes(scatter, mergeNodes, unqualifiedStepId.localName.value)
-
-        /* ************************************ */
-        /* *************** OGINS ************** */
-        /* ************************************ */
-        ogins = buildOGINs(mergeNodes, scatterVariableNodes)
-
-        /* ************************************ */
-        /* ********* Expression Nodes ********* */
-        /* ************************************ */
-        // Aggregate the generated nodes so far. This map will be used to generate expression nodes, so the order of aggregation matters:
-        // scatter variables and ogins take precedence over merge nodes (see diagram)
-        aggregatedMapForValueFromNodes = mergeNodes ++ scatterVariableNodes ++ ogins
-        // Build expression nodes for inputs that have a valueFrom field
-        stepInputValueFromNodes <- buildStepInputValueFromNodes(aggregatedMapForValueFromNodes)
-
-        /* ************************************ */
-        /* ************* Call Node ************ */
-        /* ************************************ */
-        // Get the callable object for this step
-        checkedCallable <- callable
-        // Aggregate again by adding generated expression nodes. Again order matters here, expression nodes override other nodes.
-        aggregatedMapForInputDefinitions = aggregatedMapForValueFromNodes.asIdentifierMap ++ stepInputValueFromNodes
-        // Assign each of the callable's input definition to an output port from the pointer map
-        inputDefinitionFold <- checkedCallable.inputs.foldMap(foldInputDefinition(aggregatedMapForInputDefinitions)).toEither
-        // Build the call node
-        callAndNodes = callNodeBuilder.build(unqualifiedStepId, checkedCallable, inputDefinitionFold, Set.empty, None)
-        // Depending on whether the step is being scattered, invoke the scatter node builder or not
-
-        /* ************************************ */
-        /* ************ Scatter Node ********** */
-        /* ************************************ */
-        scatterNodeOrExposedNodes <- if (isScattered) {
-          ScatterLogic.buildScatterNode(
-            callAndNodes,
-            NonEmptyList.fromListUnsafe(scatterVariableNodes.values.toList),
-            ogins.values.toSet,
-            stepInputValueFromNodes.values.toSet,
-            scatterMethod).map(Set(_))
-        } else {
-          // If there's no scatter node then we need to return the expression nodes and the call node explicitly
-          // as they won't be contained in the scatter inner graph
-          (stepInputValueFromNodes.values.toSet + callAndNodes.node).validNelCheck
-        }
-
-        /*
-          * Return all the nodes that need to be made available to the workflow graph:
-          * knownNodes: this method is used to fold over steps so we don't want to forget to accumulate known nodes
-          * mergeNodes: they're always outside of the scatter so always return them
-          * generatedNodes: nodes generated recursively to build this node
-          * scatterNodeOrExposedNodes: see explanation above
-         */
-        allNodes = knownNodes ++ mergeNodes.values.toSet ++ stepInputFold.generatedNodes ++ scatterNodeOrExposedNodes
-      } yield allNodes
-    }
-  }
-}
-
-/**
-  * @see <a href="http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepOutput">WorkflowstepOutput</a>
-  */
-case class WorkflowStepOutput(id: String)
-
-object WorkflowStep {
-
-  // A monoid can't be derived automatically for this class because it contains a Map[String, ExpressionNode],
-  // and there's no monoid defined over ExpressionNode
-  implicit val workflowStepInputFoldMonoid: Monoid[WorkflowStepInputFold] = new Monoid[WorkflowStepInputFold] {
-    override def empty: WorkflowStepInputFold = WorkflowStepInputFold()
-    override def combine(x: WorkflowStepInputFold, y: WorkflowStepInputFold): WorkflowStepInputFold = {
-      WorkflowStepInputFold(
-        mergeNodes = x.mergeNodes ++ y.mergeNodes,
-        generatedNodes = x.generatedNodes ++ y.generatedNodes
-      )
-    }
-  }
-
-  private [cwl] case class WorkflowStepInputFold(mergeNodes: Map[WorkflowStepInput, ExpressionNode] = Map.empty,
-                                                 generatedNodes: Set[GraphNode] = Set.empty)
-
-  /**
-    * Maps input variable (to be scattered over) to their scatter variable node
-    */
-  type ScatterMappings = Map[ExpressionNode, ScatterVariableNode]
-
-  val emptyOutputs: WorkflowStepOutputType = Array.empty
-
-  type Run =
-    String :+:
-      CommandLineTool :+:
-      ExpressionTool :+:
-      Workflow :+:
-      CNil
-
-  object Run {
-    object String { def unapply(run: Run): Option[String] = run.select[String] }
-    object Workflow { def unapply(run: Run): Option[Workflow] = run.select[Workflow] }
-    object CommandLineTool { def unapply(run: Run): Option[CommandLineTool] = run.select[CommandLineTool] }
-    object ExpressionTool { def unapply(run: Run): Option[ExpressionTool] = run.select[ExpressionTool] }
-  }
-
-  type WorkflowStepOutputInnerType = String :+: WorkflowStepOutput :+: CNil
-  type WorkflowStepOutputType = Array[WorkflowStepOutputInnerType]
-}
diff --git a/cwl/src/main/scala/cwl/WorkflowStepInput.scala b/cwl/src/main/scala/cwl/WorkflowStepInput.scala
deleted file mode 100644
index a3d028dbdd6..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStepInput.scala
+++ /dev/null
@@ -1,155 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr.ErrorOr
-import cwl.InputParameter.DefaultToWomValuePoly
-import cwl.LinkMergeMethod.LinkMergeMethod
-import cwl.WorkflowStepInput.InputSource
-import cwl.command.ParentName
-import shapeless.{:+:, CNil}
-import wom.expression.ValueAsAnExpression
-import wom.graph.GraphNodePort.OutputPort
-import wom.graph.WomIdentifier
-import wom.graph.expression.{AnonymousExpressionNode, ExposedExpressionNode, ExpressionNode, PlainAnonymousExpressionNode}
-import wom.types._
-
-case class WorkflowStepInput(
-                              id: String,
-                              source: Option[InputSource] = None,
-                              linkMerge: Option[LinkMergeMethod] = None,
-                              default: Option[CwlAny] = None,
-                              valueFrom: Option[StringOrExpression] = None) {
-
-  def parsedId(implicit parentName: ParentName) = FullyQualifiedName(id).id
-
-  def toExpressionNode(valueFromExpression: StringOrExpression,
-                       runInputExpectedType: Option[cwl.MyriadInputType],
-                       isScattered: Boolean,
-                       sourceMappings:Map[String, OutputPort],
-                       outputTypeMap: Map[String, WomType],
-                       expressionLib: ExpressionLib,
-                       schemaDefRequirement: SchemaDefRequirement
-                      )(implicit parentName: ParentName): ErrorOr[ExpressionNode] = {
-    val inputs = sourceMappings.keySet
-    val upstreamMergeType = outputTypeMap.get(parsedId)
-
-    (for {
-      // we may have several sources, we make sure to have a type common to all of them.
-      // In the case where there's no input source, we currently wrap the valueFrom value in a WomString (see WorkflowStepInputExpression)
-      inputType <- WorkflowStepInput.determineValueFromType(upstreamMergeType, runInputExpectedType, isScattered, schemaDefRequirement)
-      womExpression = WorkflowStepInputExpression(parsedId, valueFromExpression, inputType, inputs, expressionLib)
-      identifier = WomIdentifier(id).combine("expression")
-      ret <- ExposedExpressionNode.fromInputMapping(identifier, womExpression, inputType, sourceMappings).toEither
-    } yield ret).toValidated
-  }
-
-  /**
-    *
-    * @param sourceMappings The outputports to which this source refers
-    * @param matchingRunInputType This input matches an input declared in the workflowstep's "run".  This is that step's declared type
-    * @return
-    */
-  def toMergeNode(sourceMappings: Map[String, OutputPort],
-                  expressionLib: ExpressionLib,
-                  matchingRunInputType: Option[MyriadInputType],
-                  isScattered: Boolean,
-                  schemaDefRequirement: SchemaDefRequirement
-                 ): Option[ErrorOr[ExpressionNode]] = {
-
-    val identifier = WomIdentifier(id).combine("merge")
-    val mapType = sourceMappings.map({ case (k, v) => k -> v.womType })
-
-    val maybeMatchingRunInputWomType: Option[WomType] = matchingRunInputType.map(_.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement))
-
-    def makeNode(head: (String, OutputPort), tail: List[(String, OutputPort)]) = for {
-      inputType <- determineMergeType(mapType, maybeMatchingRunInputWomType)
-      womExpression = WorkflowStepInputMergeExpression(this, inputType, NonEmptyList.of(head, tail: _*), expressionLib)
-      node <- AnonymousExpressionNode.fromInputMapping(identifier, womExpression, sourceMappings, PlainAnonymousExpressionNode.apply).toEither
-    } yield node
-
-    val matchingRunInputWomType: WomType = maybeMatchingRunInputWomType.getOrElse(WomAnyType)
-    lazy val defaultValue = default.map { _.fold(DefaultToWomValuePoly).apply(matchingRunInputWomType) }
-
-    sourceMappings.toList match {
-      case head :: tail => Option(makeNode(head, tail).toValidated)
-      case Nil =>
-        defaultValue map { _ map { d =>
-            PlainAnonymousExpressionNode(identifier, ValueAsAnExpression(d), matchingRunInputWomType, Map.empty)
-        } }
-    }
-  }
-
-  def determineMergeType(sources: Map[String, WomType], expectedTypeAsWom: Option[WomType]): Checked[WomType] = {
-    WorkflowStepInput.determineMergeType(sources, linkMerge, expectedTypeAsWom, default.isDefined)
-  }
-
-  lazy val sources: List[String] = source.toList.flatMap(_.fold(StringOrStringArrayToStringList))
-
-  lazy val effectiveLinkMerge: LinkMergeMethod = linkMerge.getOrElse(LinkMergeMethod.MergeNested)
-}
-
-object WorkflowStepInput {
-  type InputSource = String :+: Array[String] :+: CNil
-
-  implicit class EnhancedStepInputMap[A](val map: Map[WorkflowStepInput, A]) extends AnyVal {
-    def asIdentifierMap(implicit parentName: ParentName): Map[String, A] = {
-      map.map({ case (stepInput, value) => stepInput.parsedId -> value })
-    }
-  }
-
-  def determineValueFromType(mergedSourcesType: Option[WomType],
-                             expectedType: Option[MyriadInputType],
-                             isScattered: Boolean,
-                             schemaDefRequirement: SchemaDefRequirement): Checked[WomType] = {
-    val expectedTypeAsWom: Option[WomType] = expectedType.map(_.fold(MyriadInputTypeToWomType).apply(schemaDefRequirement))
-
-    expectedTypeAsWom.getOrElse(WomStringType).asRight
-  }
-
-  def determineMergeType(sources: Map[String, WomType],
-                         linkMerge: Option[LinkMergeMethod],
-                         expectedTypeAsWom: Option[WomType],
-                         hasDefault: Boolean): Checked[WomType] = {
-
-    (sources.toList, expectedTypeAsWom, linkMerge) match {
-      // If there is a single source and no explicit merge method, use the type of the source (unpacked if it's optional
-      // and there's a default since the default would be used if there's no supplied value).
-      case (List((_, WomOptionalType(sourceType))), _, None) if hasDefault => sourceType.asRight
-      case (List((_, opt @ WomOptionalType(_))), _, None) => opt.asRight
-      case (List((_, sourceType)), _, None) => sourceType.asRight
-      // If there is a single source and merge nested is specified, wrap it into an array
-      case (List((_, sourceType)), _, Some(LinkMergeMethod.MergeNested)) => WomArrayType(sourceType).asRight
-      // If there are multiple sources and either no merge method or merge nested, find the closest common type.
-      // TODO: This is technically not enough, cwltool supports sources with totally different types, creating an array with multiple types
-      // Maybe WomCoproduct can help
-      case (_, _, Some(LinkMergeMethod.MergeNested) | None) => WomArrayType(WomType.homogeneousTypeFromTypes(sources.values)).asRight
-
-      //If sink parameter is an array and merge_flattened is used, must validate input & output types are equivalent before proceeding
-      case (_, Some(arrayType @ WomArrayType(itemType)), Some(LinkMergeMethod.MergeFlattened)) if typesToItemMatch(sources.values, itemType) => arrayType.asRight
-      // If sink parameter is not an array and merge flattened is used, validate that the sources types matche the sink type
-      case (_, Some(targetType), Some(LinkMergeMethod.MergeFlattened)) if typesToItemMatch(sources.values, targetType) => WomArrayType(targetType).asRight
-      // If the types are not compatible, fail
-      case (_, Some(targetType), Some(LinkMergeMethod.MergeFlattened)) =>
-        s"could not verify that types $sources and the items type of the run's InputArraySchema $targetType were compatible".invalidNelCheck
-
-      //We don't have type information from the run input so we gather up the sources and try to determine a common type amongst them.
-      case _ => WomType.homogeneousTypeFromTypes(sources.values).asRight
-    }
-  }
-
-  def typesToItemMatch(lst: Iterable[WomType], target: WomType): Boolean = {
-    val effectiveInputType = WomType.homogeneousTypeFromTypes(lst)
-
-    typeToItemMatch(effectiveInputType, target)
-  }
-
-  def typeToItemMatch(upstream: WomType, downstream: WomType): Boolean = {
-    upstream match {
-      case WomType.RecursiveType(innerType) => typeToItemMatch(innerType, downstream)
-      case other => other == downstream
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/WorkflowStepInputExpression.scala b/cwl/src/main/scala/cwl/WorkflowStepInputExpression.scala
deleted file mode 100644
index 476d7f44ef5..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStepInputExpression.scala
+++ /dev/null
@@ -1,51 +0,0 @@
-package cwl
-
-import cats.syntax.validated._
-import wom.expression.{FileEvaluation, IoFunctionSet}
-import wom.types._
-import wom.values._
-
-final case class WorkflowStepInputExpression(inputName: String,
-                                             valueFrom: StringOrExpression,
-                                             override val cwlExpressionType: WomType,
-                                             inputs: Set[String],
-                                             override val expressionLib: ExpressionLib) extends CwlWomExpression {
-
-  override def sourceString = inputName
-
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet) = {
-    valueFrom match {
-      // If valueFrom is a constant string value, use this as the value for this input parameter.
-      // TODO: need to handle case where this is a parameter reference, it currently looks like a String to us!
-      case StringOrExpression.String(value) => WomString(value).validNel
-
-      /*
-       * If valueFrom is a parameter reference or expression, it must be evaluated to yield the actual value to be assiged to the input field.
-       *
-       * The self value of in the parameter reference or expression must be the value of the parameter(s) specified in the source field,
-       * or null if there is no source field.
-       *
-       * The value of inputs in the parameter reference or expression must be the input object to the workflow step after
-       * assigning the source values, applying default, and then scattering. The order of evaluating valueFrom among step
-       * input parameters is undefined and the result of evaluating valueFrom on a parameter must not be visible to
-       * evaluation of valueFrom on other parameters.
-       */
-      case StringOrExpression.Expression(expression) =>
-        //used to determine the value of "self" as expected by CWL Spec
-        def selfValue = inputValues.get(inputName) match {
-          case Some(value) => value
-          case None => WomOptionalValue(WomNothingType, None)
-        }
-
-        val parameterContext = ParameterContext(ioFunctionSet, expressionLib, inputValues, selfValue)
-
-        expression.fold(EvaluateExpression).apply(parameterContext)
-      case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-    }
-  }
-
-  //this is input, so not producing any output files
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType) =
-    Set.empty[FileEvaluation].validNel
-}
-
diff --git a/cwl/src/main/scala/cwl/WorkflowStepInputMergeExpression.scala b/cwl/src/main/scala/cwl/WorkflowStepInputMergeExpression.scala
deleted file mode 100644
index bc7d4f43d75..00000000000
--- a/cwl/src/main/scala/cwl/WorkflowStepInputMergeExpression.scala
+++ /dev/null
@@ -1,84 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.syntax.either._
-import cats.syntax.option._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import common.Checked
-import common.validation.ErrorOr.ErrorOr
-import cwl.InputParameter.DefaultToWomValuePoly
-import wom.expression.{FileEvaluation, IoFunctionSet}
-import wom.graph.GraphNodePort.OutputPort
-import wom.types.WomType
-import wom.values.{WomArray, WomFile, WomOptionalValue, WomValue}
-
-final case class WorkflowStepInputMergeExpression(input: WorkflowStepInput,
-                                                  cwlExpressionType: WomType,
-                                                  stepInputMappingHead: NonEmptyList[(String, OutputPort)],
-                                                  override val expressionLib: ExpressionLib) extends CwlWomExpression {
-
-  private val allStepInputMappings = stepInputMappingHead.toList
-  private val allStepInputSources = allStepInputMappings.map(_._1)
-
-  override def sourceString: String = s"${input.id}-Merge-Expression"
-  override def inputs: Set[String] = allStepInputSources.toSet
-
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
-    def lookupValue(key: String): ErrorOr[WomValue] =
-      inputValues.
-        get(key).
-        toValidNel(s"source value $key not found in input values ${inputValues.mkString("\n")} and no default value provided.  Graph Inputs were ${allStepInputSources.mkString("\n")}")
-
-    def validateSources(sources: List[String]): ErrorOr[List[WomValue]] =
-      sources.
-        traverse(lookupValue)
-
-    def isEmptyOptionalValue(womValue: WomValue): Boolean = womValue match {
-      case WomOptionalValue(_, None) => true
-      case _ => false
-    }
-
-    (allStepInputSources, input.effectiveLinkMerge, input.default) match {
-      // When we have a single source but no value was provided for it and there's a default.
-      case (List(source), LinkMergeMethod.MergeNested, Some(default)) if isEmptyOptionalValue(inputValues(source)) =>
-        default.fold(DefaultToWomValuePoly).apply(cwlExpressionType)
-
-      case (List(source), LinkMergeMethod.MergeNested, _) => lookupValue(source)
-
-      //When we have several sources, validate they are all present and provide them as a nested array
-      case (sources, LinkMergeMethod.MergeNested, _) => validateSources(sources).map(WomArray.apply)
-
-      case (sources, LinkMergeMethod.MergeFlattened, _) =>
-        val validatedSourceValues: Checked[List[WomValue]] =
-          validateSources(sources).toEither
-
-        def flatten: WomValue => List[WomValue] = {
-          case WomArray(_, value) => value.toList
-          case WomOptionalValue(_, Some(value)) => flatten(value)
-          case other => List(other)
-        }
-
-        //This is the meat of "merge_flattened," where we find arrays and concatenate them to form one array
-        val flattenedValidatedSourceValues: Checked[List[WomValue]] = validatedSourceValues.map(_.flatMap(flatten))
-
-        flattenedValidatedSourceValues.map(list => WomArray(list)).toValidated
-
-      case (List(id), _, _) => lookupValue(id)
-      case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-    }
-  }
-
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
-    if (allStepInputMappings.size > 1) {
-      // TODO add MultipleInputFeatureRequirement logic in here
-      "MultipleInputFeatureRequirement not supported yet".invalidNel
-    } else {
-      val (inputName, _) = allStepInputMappings.head
-      inputTypes(inputName).collectAsSeq({
-        case file: WomFile => file
-      }).toSet[WomFile].map(FileEvaluation.requiredFile).validNel
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/command/ParentName.scala b/cwl/src/main/scala/cwl/command/ParentName.scala
deleted file mode 100644
index 6e34096d4f3..00000000000
--- a/cwl/src/main/scala/cwl/command/ParentName.scala
+++ /dev/null
@@ -1,10 +0,0 @@
-package cwl.command
-
-object ParentName {
-  def empty: ParentName = ParentName(None)
-  def apply(id: String): ParentName = ParentName(id.split("#").tail.headOption)
-}
-
-case class ParentName(value: Option[String]) {
-  def stripParent(in: String) = value.map(v => in.stripPrefix(s"$v/")).getOrElse(in)
-}
diff --git a/cwl/src/main/scala/cwl/command/StringCommandPart.scala b/cwl/src/main/scala/cwl/command/StringCommandPart.scala
deleted file mode 100644
index 9ec668231fb..00000000000
--- a/cwl/src/main/scala/cwl/command/StringCommandPart.scala
+++ /dev/null
@@ -1,18 +0,0 @@
-package cwl.command
-
-import cats.syntax.validated._
-import common.validation.ErrorOr.ErrorOr
-import wom._
-import wom.callable.RuntimeEnvironment
-import wom.expression.IoFunctionSet
-import wom.graph.LocalName
-import wom.values._
-
-case class StringCommandPart(literal: String) extends CommandPart {
-  override def instantiate(inputsMap: Map[LocalName, WomValue],
-                           functions: IoFunctionSet,
-                           valueMapper: (WomValue) => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] =
-    // TODO CWL shellquotes by default, but this shellquotes everything. Only shellquote what should be shellquoted.
-    List(InstantiatedCommand(literal.shellQuote)).validNel
-}
diff --git a/cwl/src/main/scala/cwl/internal/CommandPartSortingAlgorithm.scala b/cwl/src/main/scala/cwl/internal/CommandPartSortingAlgorithm.scala
deleted file mode 100644
index eb6ed0410ce..00000000000
--- a/cwl/src/main/scala/cwl/internal/CommandPartSortingAlgorithm.scala
+++ /dev/null
@@ -1,71 +0,0 @@
-package cwl.internal
-
-import cats.data.Kleisli._
-import cats.data.ReaderT
-import cats.data.Validated._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cwl.CommandLineTool._
-import cwl.command.ParentName
-import cwl.{ArgumentCommandLineBinding, ArgumentToCommandPart, CommandLineTool, CommandPartExpression, FullyQualifiedName, InputParameter, MyriadInputTypeToSortedCommandParts, MyriadInputTypeToWomType}
-import shapeless.Coproduct
-import wom.types.WomStringType
-
-object CommandPartSortingAlgorithm {
-  def argumentCommandParts(arguments: Option[Array[CommandLineTool.Argument]]): CommandPartExpression[List[SortKeyAndCommandPart]] =
-      // arguments is an Option[Array[Argument]], the toList.flatten gives a List[Argument]
-    arguments.toList.flatten
-      // zip the index because we need it in the sorting key
-      .zipWithIndex.flatTraverse(argumentToCommandPart.tupled)
-
-  def argumentToCommandPart: (Argument, Int) => CommandPartExpression[List[SortKeyAndCommandPart]] = (argument, index) => ReaderT {
-    case ((requirementsAndHints, expressionLib, _)) =>
-      val part = argument.fold(ArgumentToCommandPart).apply(requirementsAndHints.hasShellCommandRequirement, expressionLib)
-      // Get the position from the binding if there is one
-      val position = argument.select[ArgumentCommandLineBinding].flatMap(_.position)
-        .map(Coproduct[StringOrInt](_)).getOrElse(CommandLineTool.DefaultPosition)
-
-      // The key consists of the position followed by the index
-      val sortingKey = CommandBindingSortingKey(List(position, Coproduct[StringOrInt](index)))
-
-      List(SortKeyAndCommandPart(sortingKey, part)).validNel
-
-  }
-
-  def inputBindingsCommandParts(inputs: Array[CommandInputParameter]): CommandPartExpression[List[SortKeyAndCommandPart]] =
-    inputs.toList.flatTraverse(inputBindingsCommandPart)
-
-  def inputBindingsCommandPart(inputParameter: CommandInputParameter): CommandPartExpression[List[SortKeyAndCommandPart]] =
-    ReaderT{ case ((hintsAndRequirements, expressionLib, inputValues)) =>
-      val parsedName = FullyQualifiedName(inputParameter.id)(ParentName.empty).id
-
-      val womType = inputParameter.`type`.map(_.fold(MyriadInputTypeToWomType).apply(hintsAndRequirements.schemaDefRequirement)).getOrElse(WomStringType)
-
-      val defaultValue = inputParameter.default.map(_.fold(InputParameter.DefaultToWomValuePoly).apply(womType))
-
-      inputValues
-        .collectFirst({ case (inputDefinition, womValue) if inputDefinition.name == parsedName => womValue.validNel })
-        .orElse(defaultValue) match {
-        case Some(Valid(value)) =>
-          // See http://www.commonwl.org/v1.0/CommandLineTool.html#Input_binding
-          lazy val initialKey = CommandBindingSortingKey.empty
-            .append(inputParameter.inputBinding, Coproduct[StringOrInt](parsedName))
-
-          inputParameter.`type`.toList.
-            flatMap{
-              _.fold(MyriadInputTypeToSortedCommandParts).
-                apply(
-                  inputParameter.inputBinding,
-                  value,
-                  initialKey.asNewKey,
-                  hintsAndRequirements.hasShellCommandRequirement,
-                  expressionLib,
-                  hintsAndRequirements.schemaDefRequirement)
-            }.validNel
-        case Some(Invalid(errors)) => Invalid(errors)
-        case None => s"Could not find an input value for input $parsedName in ${inputValues.prettyString}".invalidNel
-      }
-    }
-
-}
diff --git a/cwl/src/main/scala/cwl/internal/CwlEcmaScriptDecoder.scala b/cwl/src/main/scala/cwl/internal/CwlEcmaScriptDecoder.scala
deleted file mode 100644
index f7f54d3db1c..00000000000
--- a/cwl/src/main/scala/cwl/internal/CwlEcmaScriptDecoder.scala
+++ /dev/null
@@ -1,124 +0,0 @@
-package cwl.internal
-
-import cats.syntax.apply._
-import cats.syntax.traverse._
-import cats.syntax.validated._
-import cats.instances.list._
-import cats.instances.option._
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.{Directory, File, FileOrDirectory}
-import org.mozilla.javascript.{ConsString, NativeArray, NativeObject}
-import shapeless.Coproduct
-import wom.types.WomNothingType
-import wom.values._
-
-import scala.jdk.CollectionConverters._
-
-class CwlEcmaScriptDecoder {
-
-  def decode(value: AnyRef): ErrorOr[WomValue] =
-    value match {
-      case map: NativeObject if map.get("class") == "File" => decodeFile(map.asScala.toMap).flatMap(_.asWomValue)
-      case map: NativeObject if map.get("class") == "Directory" => decodeDirectory(map.asScala.toMap).flatMap(_.asWomValue)
-
-      case map: NativeObject => decodeMap(map.asScala.toMap)
-      case array: NativeArray =>
-        val anyList = array.asScala.toList
-        val anyRefArray = anyList.asInstanceOf[List[AnyRef]]
-        anyRefArray.traverse(decode).map(WomArray.apply)
-
-      //we represent nulls as this type because Wom doesn't have a "null" value, but it does have a nothing type
-      //If you wish this to be otherwise please tidy up the Expression interpolator as well
-      case null => WomOptionalValue(WomNothingType, None).valid
-
-      case string: String => WomString(string).valid
-      case consString: ConsString => WomString(consString.toString).valid
-      case int: java.lang.Integer => WomInteger(int).valid
-      case long: java.lang.Long => WomLong(long).valid
-      case double: java.lang.Double if double == double.doubleValue.floor && !double.isInfinite =>
-        WomInteger(double.intValue).valid
-      case double: java.lang.Double => WomFloat(double).valid
-      case boolean: java.lang.Boolean => WomBoolean(boolean).valid
-      case unknown => s"While decoding the output $value of the Javascript interpreter, we encountered $unknown and were unable to reify it.".invalidNel
-    }
-
-  def decodeMap(map: Map[Any, Any]): ErrorOr[WomValue] = {
-    val realMap: Map[AnyRef, AnyRef] = map.asInstanceOf[Map[AnyRef, AnyRef]]
-
-    val tupleList = realMap.toList.traverse{
-      case (k,v) => (k.toString.validNel: ErrorOr[String], decode(v)).tupled
-    }
-    val mapWomValues =  tupleList.map(_.toMap)
-    mapWomValues.map(WomObject.apply)
-  }
-
-  /**
-    * Called to decode a cwl File or Directory.
-    */
-  def decodeDirectoryOrFile(value: Any): ErrorOr[FileOrDirectory] = {
-    val invalidValue = s"Not a valid CWL map or directory: $value".invalidNel
-
-    value match {
-      case map: NativeObject if map.get("class") == "File" => decodeFile(map.asScala.toMap).map(Coproduct[FileOrDirectory](_))
-      case map: NativeObject if map.get("class") == "Directory" => decodeDirectory(map.asScala.toMap).map(Coproduct[FileOrDirectory](_))
-      case _ => invalidValue
-    }
-  }
-
-  /**
-    * Called to decode an array of cwl File or Directory instances.
-    */
-  def decodeDirectoryOrFiles(value: Any): ErrorOr[Array[FileOrDirectory]] = {
-    value match {
-      case na: NativeArray => na.asScala.toList.traverse(decodeDirectoryOrFile).map(_.toArray)
-    }
-  }
-
-  /**
-    * Called to decode a map value using a supplied function.
-    */
-  def decodeMapValue[A](map: Map[Any, Any], key: String, f: Any => A): ErrorOr[Option[A]] = {
-    map.get(key).traverse(anyRef => validate(f(anyRef)))
-  }
-
-  /**
-    * Called to decode an array of files or directories from a map value.
-    */
-  def decodeMapDirectoryOrFiles(map: Map[Any, Any],
-                                key: String): ErrorOr[Option[Array[FileOrDirectory]]] = {
-    map.get(key).traverse(decodeDirectoryOrFiles)
-  }
-
-  /**
-    * Called to decode a cwl File.
-    */
-  def decodeFile(map: Map[Any, Any]): ErrorOr[File] = {
-    val location = decodeMapValue(map, "location", _.toString)
-    val path = decodeMapValue(map, "path", _.toString)
-    val basename = decodeMapValue(map, "basename", _.toString)
-    val checksum = decodeMapValue(map, "checksum", _.toString)
-    val size = decodeMapValue(map, "size", _.toString.toDouble.toLong)
-    val secondaryFiles = decodeMapDirectoryOrFiles(map, "secondaryFiles")
-    val format = decodeMapValue(map, "format", _.toString)
-    val contents = decodeMapValue(map, "contents", _.toString)
-
-    (location, path, basename, checksum, size, secondaryFiles, format, contents).mapN(
-      File(_, _, _, _, _, _, _, _)
-    )
-  }
-
-  /**
-    * Called to decode a cwl Directory.
-    */
-  def decodeDirectory(map: Map[Any, Any]): ErrorOr[Directory] = {
-    val location = decodeMapValue(map, "location", _.toString)
-    val path = decodeMapValue(map, "path", _.toString)
-    val basename = decodeMapValue(map, "basename", _.toString)
-    val listing = decodeMapDirectoryOrFiles(map, "listing")
-
-    (location, path, basename, listing).mapN(
-      Directory(_, _, _, _)
-    )
-  }
-}
diff --git a/cwl/src/main/scala/cwl/internal/EcmaScriptEncoder.scala b/cwl/src/main/scala/cwl/internal/EcmaScriptEncoder.scala
deleted file mode 100644
index e4aed51e215..00000000000
--- a/cwl/src/main/scala/cwl/internal/EcmaScriptEncoder.scala
+++ /dev/null
@@ -1,123 +0,0 @@
-package cwl.internal
-
-import cats.data.Validated.Valid
-import common.validation.ErrorOr.ErrorOr
-import cwl.internal.EcmaScriptUtil.{ECMAScriptVariable, ESArray, ESObject, ESPrimitive}
-import cwl.{Directory, File}
-import mouse.all._
-import wom.values._
-
-/**
-  * Converts a WomValue into a javascript compatible value.
-  */
-class EcmaScriptEncoder {
-
-  /**
-    * Base implementation converts any WomPrimitive (except WomFile) into a javascript compatible value.
-    *
-    * Inputs, and returned output must be one of:
-    * - WomString
-    * - WomBoolean
-    * - WomFloat
-    * - WomInteger
-    * - WomMap
-    * - WomArray
-    * - A "WomNull" equal to WomOptionalValue(WomNothingType, None)
-    *
-    * The WomMap keys and values, and WomArray elements must be the one of the above, recursively.
-    *
-    * Instances of WomFile are not permitted, and must be already converted to one of the above types.
-    *
-    * @param value A WOM value.
-    * @return The javascript equivalent.
-    */
-  def encode(value: WomValue): ECMAScriptVariable = {
-    value match {
-      case file: WomFile => encodeFileOrDirectory(file)
-      case WomOptionalValue(_, None) => ESPrimitive(null)
-      case WomOptionalValue(_, Some(innerValue)) => encode(innerValue)
-      case WomString(string) => string |> ESPrimitive
-      case WomInteger(int) => Int.box(int) |> ESPrimitive
-      case WomLong(long) => Long.box(long) |> ESPrimitive
-      case WomFloat(double) => Double.box(double) |> ESPrimitive
-      case WomBoolean(boolean) => Boolean.box(boolean) |> ESPrimitive
-      case WomArray(_, array) => array.toList.map(encode).toArray |> ESArray
-      case WomMap(_, map) => map.map{
-        case (mapKey, mapValue) => (encodeString(mapKey), encode(mapValue))
-      } |> ESObject
-      case objectLike: WomObjectLike => objectLike.values.map{
-        case (key, innerValue) => (key, encode(innerValue))
-      } |> ESObject
-      case WomCoproductValue(_, womValue) => encode(womValue)
-      case WomEnumerationValue(_, womValue) => womValue |> ESPrimitive
-      case _ => throw new RuntimeException(s"$getClass is unable to encode value: $value")
-    }
-  }
-
-  def encodeString(value: WomValue): String = {
-    encode(value) match {
-      case ESPrimitive(string: String) => string
-
-      //In the case of a non-string, we evaluate a small snippet of Ecma script meant to coerce the object to a string
-      // http://2ality.com/2012/03/converting-to-string.html
-      case _ =>
-        val jsString: ErrorOr[WomValue] = EcmaScriptUtil.evalStructish(""""" + other""","other" -> value, encoder = this)
-        jsString match {
-          case Valid(WomString(string)) => string
-          case unexpected => throw new RuntimeException(s"Expected to convert '$value' to a String but ended up with '$unexpected'")
-        }
-    }
-  }
-
-  /**
-    * Encodes a sequence of wom file or directory values.
-    */
-  def encodeFileOrDirectories(values: Seq[WomFile]): ESArray = {
-    ESArray(values.toList.map(encodeFileOrDirectory).toArray)
-  }
-
-  /**
-    * Encodes a wom file or directory value.
-    */
-  def encodeFileOrDirectory(value: WomFile): ECMAScriptVariable = {
-    value match {
-      case directory: WomUnlistedDirectory => encodeDirectory(WomMaybeListedDirectory(directory.value))
-      case file: WomSingleFile => encodeFile(WomMaybePopulatedFile(file.value))
-      case glob: WomGlobFile => encodeFile(WomMaybePopulatedFile(glob.value))
-      case directory: WomMaybeListedDirectory => encodeDirectory(directory)
-      case file: WomMaybePopulatedFile => encodeFile(file)
-    }
-  }
-
-  /**
-    * Encodes a wom file.
-    */
-  def encodeFile(file: WomMaybePopulatedFile): ECMAScriptVariable =
-    List(
-      Option("class" -> ESPrimitive("File")),
-      file.valueOption.map("location" -> ESPrimitive(_)),
-      file.valueOption.map("path" -> ESPrimitive(_)),
-      Option("basename" -> (File.basename(file.value) |> ESPrimitive)),
-      Option("dirname" -> (File.dirname(file.value) |> ESPrimitive)),
-      Option("nameroot" -> (File.nameroot(file.value) |> ESPrimitive)),
-      Option("nameext" -> (File.nameext(file.value) |> ESPrimitive)),
-      file.checksumOption.map("checksum" -> ESPrimitive(_)),
-      file.sizeOption.map(Long.box).map("size" -> ESPrimitive(_)),
-      Option("secondaryFiles" -> encodeFileOrDirectories(file.secondaryFiles)),
-      file.formatOption.map("format" -> ESPrimitive(_)),
-      file.contentsOption.map("contents" -> ESPrimitive(_))
-    ).flatten.toMap |> ESObject
-
-  /**
-    * Encodes a wom directory.
-    */
-  def encodeDirectory(directory: WomMaybeListedDirectory): ESObject = {
-    List(
-      Option("class" -> ESPrimitive("Directory")),
-      directory.valueOption.map("location" -> ESPrimitive(_)),
-      Option(directory.value).map("path" -> ESPrimitive(_)),
-      Option("basename" -> ESPrimitive(Directory.basename(directory.value))),
-      directory.listingOption.map(encodeFileOrDirectories).map("listing" -> _)
-    ).flatten.toMap |> ESObject
-  }
-}
diff --git a/cwl/src/main/scala/cwl/internal/EcmaScriptUtil.scala b/cwl/src/main/scala/cwl/internal/EcmaScriptUtil.scala
deleted file mode 100644
index d2c5def745f..00000000000
--- a/cwl/src/main/scala/cwl/internal/EcmaScriptUtil.scala
+++ /dev/null
@@ -1,128 +0,0 @@
-package cwl.internal
-
-import common.collections.EnhancedCollections._
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import org.mozilla.javascript._
-import wom.values._
-
-import scala.concurrent.duration._
-import scala.util.Try
-
-/**
-  * This implementation depends on Mozilla Rhino.
-  *
-  * Previously we attempted to use Nashorn which is built into the JDK, but we encountered at least 2 situations where
-  * it didn't work and we found no workarounds to satisfy the use cases.  Namely, JSON.stringify of a Map and calling "sort" on an array.
-  */
-//noinspection VariablePatternShadow
-object EcmaScriptUtil {
-  def writeValue(value: ECMAScriptVariable)(context: Context, scope: Scriptable): AnyRef =
-    value match {
-      case ESObject(fields) =>
-        val newObj = context.newObject(scope)
-
-        fields.toList.foreach{
-          case (name, value) =>
-            val newerObj = writeValue(value)(context, scope)
-            ScriptableObject.putProperty(newObj, name, newerObj)
-        }
-        newObj
-
-      case ESArray(array) =>
-        val newObj = context.newArray(scope, array.length)
-
-        array.toList.zipWithIndex.foreach {
-          case (js, index) =>
-
-            val newerObj = writeValue(js)(context, scope)
-            ScriptableObject.putProperty(newObj, index, newerObj)
-
-        }
-        newObj
-
-      case ESPrimitive(obj) => obj
-    }
-
-  /**
-    * Runs ECMAScript as JS1.8 (aka ES5)
-    *
-    * Uses RhinoSandbox to reduce chances injected JS wreaks havoc on the JVM.
-    *
-    * @see https://en.wikipedia.org/wiki/ECMAScript#Version_correspondence
-    */
-  def evalRaw(expr: String)(block: (Context, Scriptable) => Unit): AnyRef = {
-    // TODO: Parameterize and update callers to pass in source name, max duration, max instructions, etc.?
-    // For now, be very liberal with scripts giving 60 seconds of unrestricted CPU usage and unlimited instructions.
-    val sourceName = "<ecmascript>"
-    val maxDuration: Duration = 60.seconds
-    val maxInstructionsOption: Option[Int] = None
-    val strict = true
-    val languageVersionOption = Option(Context.VERSION_1_8)
-
-    val sandbox = new EnhancedRhinoSandbox(strict, languageVersionOption)
-    if (maxDuration.isFinite) {
-      sandbox.setMaxDuration(maxDuration.toMillis.toInt)
-    }
-    maxInstructionsOption foreach sandbox.setInstructionLimit
-    sandbox.setUseSafeStandardObjects(true)
-    sandbox.setUseSealedScope(true)
-
-    sandbox.eval(sourceName, expr)(block)
-  }
-
-  sealed trait ECMAScriptVariable
-
-  case class ESObject(fields: Map[String, ECMAScriptVariable]) extends ECMAScriptVariable
-  case class ESArray(array: Array[ECMAScriptVariable]) extends ECMAScriptVariable {
-    override def toString: String = s"ESArray(${array.toList})"
-  }
-  case class ESPrimitive(anyRef: AnyRef) extends ECMAScriptVariable
-
-  /**
-    * Evaluates a javascript expression using maps of WOM values.
-    *
-    * TODO: Once custom types are supported as WomValue, this custom method won't be required.
-    *
-    * @param expr      The javascript expression.
-    * @param rawValues A map filled with WOM values.
-    * @param mapValues A map of maps filled with WOM values of various types.
-    * @param encoder   Encodes wom values to javascript.
-    * @param decoder   Decodes wom values from javascript.
-    * @return The result of the expression.
-    */
-  def evalStructish(expr: String,
-                    rawValues: (String, WomValue),
-                    mapValues: Map[String, Map[String, WomValue]] = Map.empty,
-                    encoder: EcmaScriptEncoder,
-                    decoder: CwlEcmaScriptDecoder = new CwlEcmaScriptDecoder): ErrorOr[WomValue] = {
-    def evaluate = evalRaw(expr) { (context, scope) =>
-
-      val (key, value) = rawValues
-
-      val jsValue = encoder.encode(value)
-      val field = writeValue(jsValue)(context, scope)
-      ScriptableObject.putProperty(scope, key, field)
-
-      val jsMap = mapValues.safeMapValues{ _.safeMapValues(encoder.encode) }
-
-      jsMap foreach {
-        case (scopeId, nestedMap) =>
-
-          val newObj = context.newObject(scope)
-          nestedMap.toList foreach {
-            case (key, value) =>
-              val newerObj = writeValue(value)(context, scope)
-              ScriptableObject.putProperty(newObj, key, newerObj)
-          }
-          ScriptableObject.putProperty(scope, scopeId, newObj)
-      }
-
-    }
-    
-    for {
-      evaluated <- Try(evaluate).toErrorOr
-      decoded <- decoder.decode(evaluated)
-    } yield decoded
-  }
-}
diff --git a/cwl/src/main/scala/cwl/internal/EnhancedRhinoSandbox.scala b/cwl/src/main/scala/cwl/internal/EnhancedRhinoSandbox.scala
deleted file mode 100644
index 405c04fdaa2..00000000000
--- a/cwl/src/main/scala/cwl/internal/EnhancedRhinoSandbox.scala
+++ /dev/null
@@ -1,167 +0,0 @@
-package cwl.internal
-
-import cwl.internal.EnhancedRhinoSandbox._
-import delight.rhinosandox.internal._
-import org.mozilla.javascript._
-
-import scala.jdk.CollectionConverters._
-import scala.reflect._
-
-/**
-  * Extends the RhinoSandboxImpl with some fixes and enhancements using java reflection.
-  *
-  * @param strict Should evaluation be strict.
-  * @param languageVersionOption The optional language version to set.
-  */
-class EnhancedRhinoSandbox(strict: Boolean = true, languageVersionOption: Option[Int] = None) extends RhinoSandboxImpl {
-
-  // Allows easier reflection access to private fields
-  private lazy val sandboxImpl: RhinoSandboxImpl = this
-
-  /**
-    * Similar to RhinoSandbox.eval but passes back the context and scope for mutating before evaluation.
-    *
-    * With the original RhinoSandbox.eval not sure how to:
-    * - Create (nested) arrays
-    * - Create (nested) maps
-    * - Set JS/ES version
-    *
-    * So this uses a copy-port of the original, using reflection to read some of RhinoSandbox's private variables.
-    *
-    * Instead of hiding the context and scope as in RhinoSandbox.eval, both are passed back through the block.
-    *
-    * TODO: Ask RhinoSandbox if hacks are even needed, and if so contrib back patches so that reflection isn't required.
-    * - Is there a way to pass nested maps/arrays via a `java.util.Map[String, Object]`, or must we use our `block`?
-    * - Additionally: can we skip passing `context` to a block as a thread may just call `Context.getCurrentContext()`?
-    *
-    * @see https://maxrohde.com/2015/08/06/sandboxing-javascript-in-java-app-link-collection/
-    * @see https://github.com/javadelight/delight-rhino-sandbox/blob/9f5a073/src/main/java/delight/rhinosandox/internal/RhinoSandboxImpl.java#L100-L123
-    * @see delight.rhinosandox.internal.RhinoSandboxImpl#assertContextFactory()
-    */
-  def eval(sourceName: String, js: String)(block: (Context, Scriptable) => Unit): AnyRef = {
-    assertContextFactory()
-    val sandboxImpl_contextFactory = PrivateField(sandboxImpl, "contextFactory").as[ContextFactory]
-    // RhinoSandbox diff: eval has enterContext inside the try, but Rhino docs say it belongs outside.
-    // https://www-archive.mozilla.org/rhino/apidocs/org/mozilla/javascript/ContextFactory.html#enterContext%28%29
-    val context = sandboxImpl_contextFactory.enterContext
-    try {
-      // RhinoSandbox diff: allow setting the language version
-      languageVersionOption foreach context.setLanguageVersion
-      assertSafeScope(context)
-      val sandboxImpl_globalScope = PrivateField(sandboxImpl, "globalScope").as[ScriptableObject]
-      val sandboxImpl_sealScope = PrivateField(sandboxImpl, "sealScope").as[Boolean]
-      if (sandboxImpl_sealScope) {
-        sandboxImpl_globalScope.sealObject()
-      }
-      val sandboxImpl_safeScope = PrivateField(sandboxImpl, "safeScope").as[ScriptableObject]
-      val instanceScope = context.newObject(sandboxImpl_safeScope)
-      instanceScope.setPrototype(sandboxImpl_safeScope)
-      instanceScope.setParentScope(null)
-
-      block(context, instanceScope)
-
-      // RhinoSandbox diff: allow strict JS/ES evaluation
-      // See note at top assertContextFactory as to why we have to put 'use strict'; here.
-      // All on one line to avoid off-by-one error for javascript error messages that report line numbers.
-      // Could also pass zero as the line number, but the RhinoSandbox passes hard codes line number one also.
-      val script = if (strict) s"'use strict';$js" else js
-      context.evaluateString(instanceScope, script, sourceName, 1, null)
-    } finally {
-      Context.exit()
-    }
-  }
-
-  /**
-    * Stricter context factory modified from RhinoSandboxImpl.assertContextFactory().
-    *
-    * ContextFactory.initGlobal() is called within a static synchronized block.
-    * The globalScope initialized via initSafeStandardObjects instead of initStandardObjects.
-    *
-    * The default implementation uses a SafeContext that allows non-strict JS/ES. We would ideally set
-    * FEATURE_STRICT_MODE to true but that only produces warnings and doesn't return an error. Unfortunately when
-    * FEATURE_WARNING_AS_ERROR is enabled then non-strict Rhino warnings like "missing ;" throw errors. Instead,
-    * "'use strict';" is injected before scripts.
-    */
-  override def assertContextFactory(): Unit = {
-    if (PrivateField(sandboxImpl, "contextFactory").as[ContextFactory] != null) {
-      return
-    }
-
-    val _safeContext = new SafeContext
-    PrivateField(sandboxImpl, "contextFactory") := _safeContext
-    val _hasExplicitGlobal = ContextFactory.hasExplicitGlobal
-    val _not = !_hasExplicitGlobal
-    // RhinoSandbox diff: the global does not like to be initialized twice. Synchronize initialization.
-    val sandboxImpl_contextFactory = PrivateField(sandboxImpl, "contextFactory").as[SafeContext]
-    if (_not) initGlobalSynchronized(sandboxImpl_contextFactory)
-
-    val sandboxImpl_instructionLimit = PrivateField(sandboxImpl, "instructionLimit").as[Int]
-    PrivateField(sandboxImpl_contextFactory, "maxInstructions") := sandboxImpl_instructionLimit
-    val sandboxImpl_maxDuration = PrivateField(sandboxImpl, "maxDuration").as[Long]
-    PrivateField(sandboxImpl_contextFactory, "maxRuntimeInMs") := sandboxImpl_maxDuration
-    // RhinoSandbox diff: assertContextFactory has enterContext inside the try, but Rhino docs say it belongs outside.
-    // https://www-archive.mozilla.org/rhino/apidocs/org/mozilla/javascript/ContextFactory.html#enterContext%28%29
-    val context = sandboxImpl_contextFactory.enterContext
-    try {
-      // RhinoSandbox diff: Default globalScope is created via initStandardObjects instead of initSafeStandardObjects.
-      // initStandardObjects would add the various java packages into the global scope, including `java.io.File`, etc.
-      PrivateField(sandboxImpl, "globalScope") := context.initSafeStandardObjects(null, false)
-      val sandboxImpl_inScope = PrivateField(sandboxImpl, "inScope").as[java.util.Map[String, AnyRef]]
-      val _entrySet = sandboxImpl_inScope.entrySet
-      val sandboxImpl_globalScope = PrivateField(sandboxImpl, "globalScope").as[ScriptableObject]
-      for (entry <- _entrySet.asScala) {
-        sandboxImpl_globalScope.put(
-          entry.getKey,
-          sandboxImpl_globalScope,
-          Context.toObject(entry.getValue, sandboxImpl_globalScope))
-      }
-      val parameters = Array(classOf[String])
-      val dealMethod = classOf[RhinoEvalDummy].getMethod("eval", parameters: _*)
-      val _rhinoEval = new RhinoEval("eval", dealMethod, sandboxImpl_globalScope)
-      sandboxImpl_globalScope.defineProperty("eval", _rhinoEval, ScriptableObject.DONTENUM)
-    } finally {
-      Context.exit()
-    }
-  }
-
-}
-
-object EnhancedRhinoSandbox {
-
-  /**
-    * Get or sets a private field.
-    *
-    * @param obj  The instance to retrieve the field from.
-    * @param name The name of the field.
-    * @tparam A The class to retrieve the value from. The field MUST exist on this class, and not a superclass.
-    */
-  final case class PrivateField[A: ClassTag](obj: A, name: String) {
-    private[this] def field = {
-      val field = classTag[A].runtimeClass.getDeclaredField(name)
-      field.setAccessible(true)
-      field
-    }
-
-    def as[B]: B = {
-      field.get(obj).asInstanceOf[B]
-    }
-
-    def :=(value: Any): Unit = {
-      field.set(obj, value)
-    }
-  }
-
-  /**
-    * Call ContextFactory.initGlobal in a static synchronized block.
-    *
-    * @see [[cwl.internal.EnhancedRhinoSandbox.assertContextFactory]]
-    */
-  private def initGlobalSynchronized(sandboxImpl_contextFactory: ContextFactory) = {
-    synchronized {
-      val _hasExplicitGlobal = ContextFactory.hasExplicitGlobal
-      val _not = !_hasExplicitGlobal
-      if (_not) ContextFactory.initGlobal(sandboxImpl_contextFactory)
-    }
-  }
-
-}
diff --git a/cwl/src/main/scala/cwl/internal/GigabytesToBytes.scala b/cwl/src/main/scala/cwl/internal/GigabytesToBytes.scala
deleted file mode 100644
index 7e45aeec5ba..00000000000
--- a/cwl/src/main/scala/cwl/internal/GigabytesToBytes.scala
+++ /dev/null
@@ -1,26 +0,0 @@
-package cwl.internal
-
-import shapeless.{Coproduct, Poly1}
-
-object GigabytesToBytes extends Poly1 {
-  val toMebibytesMultiplier = Math.pow(2, 20).toLong
-
-  implicit def long = at[Long] {
-    l =>
-      val value = l * toMebibytesMultiplier
-      Coproduct[cwl.ResourceRequirementType](value)
-  }
-
-  implicit def string = at[String] {
-    s =>
-      //TODO: Scale this by multiplier https://github.com/broadinstitute/cromwell/issues/3382
-      Coproduct[cwl.ResourceRequirementType](s)
-  }
-
-  implicit def expression = at[cwl.Expression] {
-    e =>
-      //TODO: Scale this by multiplier https://github.com/broadinstitute/cromwell/issues/3382
-      Coproduct[cwl.ResourceRequirementType](e)
-  }
-}
-
diff --git a/cwl/src/main/scala/cwl/model.scala b/cwl/src/main/scala/cwl/model.scala
deleted file mode 100644
index 838ee66a98c..00000000000
--- a/cwl/src/main/scala/cwl/model.scala
+++ /dev/null
@@ -1,310 +0,0 @@
-package cwl
-
-import cwl.CommandLineTool.{CommandBindingSortingKey, SortKeyAndCommandPart}
-import cwl.SchemaDefRequirement.{AsInputEnumSchema, AsInputRecordSchema, SchemaDefTypes}
-import cwl.CwlType.CwlType
-import cwl.WorkflowStepInput.InputSource
-import cwl.command.ParentName
-import cwl.internal.GigabytesToBytes
-import eu.timepit.refined._
-import eu.timepit.refined.api.Refined
-import eu.timepit.refined.string.MatchesRegex
-import shapeless.syntax.singleton._
-import shapeless.{:+:, CNil, Coproduct, Poly1, Witness}
-import wom.types.WomType
-import wom.values.WomValue
-import mouse.all._
-
-object WorkflowStepInputSource {
-  object String {
-    def unapply(arg: InputSource): Option[String] = arg.select[String]
-  }
-  object StringArray {
-    def unapply(arg: InputSource): Option[Array[String]] = arg.select[Array[String]]
-  }
-}
-
-/**
-  * Describes a bespoke type.
-  *
-  * @param name This field actually does _not_ appear in the v1.0 schema, but it is used anyway in the conformance tests.
-  *             After some consideration it was determined that we should close our eyes and pretend it is in the spec.  It
-  *             makes its formal appearance as a required field in v1.1.
-  */
-case class InputRecordSchema(
-  name: String,
-  fields: Option[Array[InputRecordField]] = None,
-  `type`: W.`"record"`.T = W("record").value,
-  label: Option[String] = None) {
-
-}
-
-case class InputRecordField(
-  name: String,
-  `type`: MyriadInputType,
-  doc: Option[String] = None,
-  inputBinding: Option[InputCommandLineBinding],
-  label: Option[String] = None)
-
-case class InputArraySchema
-(
-  items: MyriadInputType,
-  `type`: W.`"array"`.T = Witness("array").value,
-  label: Option[String] = None,
-  inputBinding: Option[InputCommandLineBinding] = None,
-  // IAS.secondaryFiles are NOT listed in 1.0 spec, but according to jgentry they will be, maybe
-  secondaryFiles: Option[SecondaryFiles] = None
-)
-
-trait CommandLineBinding {
-  def loadContents: Option[Boolean]
-  def position: Option[Int]
-  def prefix: Option[String]
-  def separate: Option[Boolean]
-  def itemSeparator: Option[String]
-  def optionalValueFrom: Option[StringOrExpression]
-  def shellQuote: Option[Boolean]
-  // separate defaults to true
-  def effectiveSeparate = separate.getOrElse(true)
-}
-
-object InputCommandLineBinding {
-  def default = InputCommandLineBinding()
-}
-
-case class InputCommandLineBinding(
-                               loadContents: Option[Boolean] = None,
-                               position: Option[Int] = None,
-                               prefix: Option[String] = None,
-                               separate: Option[Boolean] = None,
-                               itemSeparator: Option[String] = None,
-                               valueFrom: Option[StringOrExpression] = None,
-                               shellQuote: Option[Boolean] = None) extends CommandLineBinding {
-  override val optionalValueFrom = valueFrom
-
-  def toCommandPart(sortingKey: CommandBindingSortingKey, boundValue: WomValue, hasShellCommandRequirement: Boolean, expressionLib: ExpressionLib) = {
-    SortKeyAndCommandPart(sortingKey, InputCommandLineBindingCommandPart(this, boundValue)(hasShellCommandRequirement, expressionLib))
-  }
-}
-
-// valueFrom is required for command line bindings in the argument section: http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding
-case class ArgumentCommandLineBinding(
-                               valueFrom: StringOrExpression,
-                               loadContents: Option[Boolean] = None,
-                               position: Option[Int] = None,
-                               prefix: Option[String] = None,
-                               separate: Option[Boolean] = None,
-                               itemSeparator: Option[String] = None,
-                               shellQuote: Option[Boolean] = None) extends CommandLineBinding {
-  override val optionalValueFrom = Option(valueFrom)
-}
-
-case class InputBinding(position: Int, prefix: String)
-
-object MyriadOutputInnerTypeCacheableString extends Poly1 {
-  import Case._
-
-  private def cacheableOutputRecordFieldString(field: OutputRecordField): String = {
-    val fieldType = field.`type`.fold(MyriadOutputTypeCacheableString)
-    val lqn = field.name.substring(field.name.lastIndexOf('#') + 1)
-    s"OutputRecordField($lqn,$fieldType,${field.doc},${field.outputBinding})"
-  }
-
-  implicit def recordSchema: Aux[OutputRecordSchema, String] = at[OutputRecordSchema] {
-    s =>
-      val t = s.`type`
-      s"OutputRecordSchema($t,${s.fields.map(a => "Array(" + a.map(cacheableOutputRecordFieldString).mkString(",") + ")" )},${s.label})"
-  }
-
-  implicit def arraySchema: Aux[OutputArraySchema, String] = at[OutputArraySchema] {
-    a =>
-      val is: String = a.items.fold(MyriadOutputTypeCacheableString)
-      val t = a.`type`
-      s"OutputArraySchema($is,$t,${a.label},${a.outputBinding})"
-  }
-
-  implicit def enumSchema: Aux[OutputEnumSchema, String] = at[OutputEnumSchema] { _.toString }
-  implicit def cwlType: Aux[CwlType, String] = at[CwlType] { _.toString }
-  implicit def string: Aux[String, String] = at[String] { identity }
-}
-
-
-object MyriadOutputTypeCacheableString extends Poly1 {
-  import Case._
-
-  implicit def one: Aux[MyriadOutputInnerType, String] = at[MyriadOutputInnerType] {
-    _.fold(MyriadOutputInnerTypeCacheableString)
-  }
-
-  implicit def many: Aux[Array[MyriadOutputInnerType], String] = at[Array[MyriadOutputInnerType]] { a =>
-    val strings: Array[String] = a.map(_.fold(MyriadOutputInnerTypeCacheableString))
-    "Array(" + strings.mkString(",") + ")"
-  }
-}
-
-object SecondaryFilesCacheableString extends Poly1 {
-  import Case._
-
-  implicit def one: Aux[StringOrExpression, String] = at[StringOrExpression] {
-    _.toString
-  }
-
-  implicit def array: Aux[Array[StringOrExpression], String] = at[Array[StringOrExpression]] {
-    _.mkString("Array(", ",", ")")
-  }
-
-}
-
-case class OutputRecordSchema(
-  `type`: W.`"record"`.T,
-  fields: Option[Array[OutputRecordField]],
-  label: Option[String])
-
-case class OutputRecordField(
-  name: String,
-  `type`: MyriadOutputType,
-  doc: Option[String],
-  outputBinding: Option[CommandOutputBinding])
-
-case class OutputArraySchema(
-  items: MyriadOutputType,
-  `type`: W.`"array"`.T = Witness("array").value,
-  label: Option[String] = None,
-  outputBinding: Option[CommandOutputBinding] = None)
-
-case class InlineJavascriptRequirement(
-  `class`: W.`"InlineJavascriptRequirement"`.T = "InlineJavascriptRequirement".narrow,
-  expressionLib: Option[Array[String]] = None)
-
-case class SchemaDefRequirement(
-  types: Array[SchemaDefTypes] = Array.empty,
-  `class`: W.`"SchemaDefRequirement"`.T = Witness("SchemaDefRequirement").value) {
-
-  def lookupType(tpe: String): Option[WomType] =
-    lookupCwlType(tpe).flatMap{
-      case AsInputRecordSchema(inputRecordSchema: InputRecordSchema) => MyriadInputInnerTypeToWomType.inputRecordSchemaToWomType(inputRecordSchema).apply(this) |> Option.apply
-      case _ => None
-    }
-
-  //Currently only InputRecordSchema has a name in the spec, so it is the only thing that can be referenced via string
-  def lookupCwlType(tpe: String): Option[SchemaDefTypes] = {
-
-    def matchesType(inputEnumSchema: InputEnumSchema): Boolean = {
-      inputEnumSchema.name.fold(false){name => FileAndId(name)(ParentName.empty).id equalsIgnoreCase FileAndId(tpe)(ParentName.empty).id}
-    }
-
-    types.toList.flatMap {
-      case AsInputRecordSchema(inputRecordSchema: InputRecordSchema) if FileAndId(inputRecordSchema.name)(ParentName.empty).id equalsIgnoreCase FileAndId(tpe)(ParentName.empty).id =>
-        List(Coproduct[SchemaDefTypes](inputRecordSchema))
-      case AsInputEnumSchema(inputEnumSchema: InputEnumSchema) if matchesType(inputEnumSchema) =>
-        List(Coproduct[SchemaDefTypes](inputEnumSchema))
-      case _ =>
-        List()
-    }.headOption
-  }
-}
-
-object SchemaDefRequirement {
-  type SchemaDefTypes = InputRecordSchema :+: InputEnumSchema :+: InputArraySchema :+: CNil
-
-  object AsInputRecordSchema {
-    def unapply(arg: SchemaDefTypes): Option[InputRecordSchema] = arg.select[InputRecordSchema]
-  }
-
-  object AsInputEnumSchema {
-    def unapply(arg: SchemaDefTypes): Option[InputEnumSchema] = arg.select[InputEnumSchema]
-  }
-
-  object AsInputArraySchema {
-    def unapply(arg: SchemaDefTypes): Option[InputArraySchema] = arg.select[InputArraySchema]
-  }
-}
-
-//There is a large potential for regex refinements on these string types
-case class DockerRequirement(
-  `class`: W.`"DockerRequirement"`.T,
-  dockerPull: Option[String], //TODO Refine to match a docker image regex?
-  dockerLoad: Option[String],
-  dockerFile: Option[String],
-  dockerImport: Option[String],
-  dockerImageId: Option[String],
-  dockerOutputDirectory: Option[String]
-  )
-
-case class SoftwareRequirement(
-  `class`: W.`"SoftwareRequirement"`.T,
-  packages: Array[SoftwarePackage] = Array.empty
-  )
-
-case class SoftwarePackage(
-  `package`: String,
-  version: Option[Array[String]],
-  specs: Option[Array[String]] // This could be refined to match a regex for IRI.
-  ) {
-  type Package = String
-  type Specs = Array[String]
-}
-
-case class EnvVarRequirement(
-                              `class`: EnvVarRequirement.ClassType = EnvVarRequirement.`class`,
-                              envDef: Array[EnvironmentDef]
-                            )
-
-object EnvVarRequirement {
-  type ClassType = Witness.`"EnvVarRequirement"`.T
-
-  val `class`: ClassType = "EnvVarRequirement".asInstanceOf[ClassType]
-}
-
-case class EnvironmentDef(envName: String, envValue: StringOrExpression) {
-  type EnvName = String
-  type EnvValue = String
-}
-
-
-case class ShellCommandRequirement(`class`: W.`"ShellCommandRequirement"`.T = "ShellCommandRequirement".narrow)
-
-case class ResourceRequirement(
-                                `class`: W.`"ResourceRequirement"`.T,
-                                coresMin: Option[ResourceRequirementType],
-                                coresMax: Option[ResourceRequirementType],
-                                ramMin: Option[ResourceRequirementType],
-                                ramMax: Option[ResourceRequirementType],
-                                tmpdirMin: Option[ResourceRequirementType],
-                                tmpdirMax: Option[ResourceRequirementType],
-                                outdirMin: Option[ResourceRequirementType],
-                                outdirMax: Option[ResourceRequirementType]) {
-  def effectiveCoreMin = coresMin.orElse(coresMax)
-  def effectiveCoreMax = coresMax.orElse(coresMin)
-
-  def effectiveRamMin = ramMin.orElse(ramMax).map(_.fold(GigabytesToBytes))
-  def effectiveRamMax = ramMax.orElse(ramMin).map(_.fold(GigabytesToBytes))
-
-  def effectiveTmpdirMin = tmpdirMin.orElse(tmpdirMax)
-  def effectiveTmpdirMax = tmpdirMax.orElse(tmpdirMin)
-
-  def effectiveOutdirMin = outdirMin.orElse(outdirMax)
-  def effectiveOutdirMax = outdirMax.orElse(outdirMin)
-}
-
-/**
-  * This promotes DNA Nexus InputResourceRequirement to a first class citizen requirement, which it really isn't.
-  * Since it's the only one for now it's not a big deal but if more of these pop up we might want to treat custom requirements
-  * in a different way
-  */
-case class DnaNexusInputResourceRequirement(
-                                     `class`: String Refined MatchesRegex[W.`".*InputResourceRequirement"`.T],
-                                     indirMin: Option[Long]
-                                   )
-
-case class SubworkflowFeatureRequirement(
-  `class`: W.`"SubworkflowFeatureRequirement"`.T)
-
-case class ScatterFeatureRequirement(
-  `class`: W.`"ScatterFeatureRequirement"`.T)
-
-case class MultipleInputFeatureRequirement(
-  `class`: W.`"MultipleInputFeatureRequirement"`.T)
-
-case class StepInputExpressionRequirement(
-  `class`: W.`"StepInputExpressionRequirement"`.T)
diff --git a/cwl/src/main/scala/cwl/ontology/CacheConfiguration.scala b/cwl/src/main/scala/cwl/ontology/CacheConfiguration.scala
deleted file mode 100644
index cb82d9db591..00000000000
--- a/cwl/src/main/scala/cwl/ontology/CacheConfiguration.scala
+++ /dev/null
@@ -1,15 +0,0 @@
-package cwl.ontology
-
-import com.typesafe.config.Config
-import common.validation.Validation._
-import net.ceedubs.ficus.Ficus._
-
-case class CacheConfiguration(maxSize: Long)
-
-object CacheConfiguration {
-  def apply(config: Config): CacheConfiguration = {
-    validate(config.getAs[Long]("max-size").getOrElse(0L))
-      .map(new CacheConfiguration(_))
-      .unsafe("Ontology cache configuration")
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ontology/OntologyConfiguration.scala b/cwl/src/main/scala/cwl/ontology/OntologyConfiguration.scala
deleted file mode 100644
index 5382ac35b91..00000000000
--- a/cwl/src/main/scala/cwl/ontology/OntologyConfiguration.scala
+++ /dev/null
@@ -1,27 +0,0 @@
-package cwl.ontology
-
-import cats.syntax.apply._
-import com.typesafe.config.Config
-import common.util.Backoff
-import common.validation.ErrorOr.ErrorOr
-import common.validation.Validation._
-import net.ceedubs.ficus.Ficus._
-
-import scala.concurrent.duration.FiniteDuration
-
-case class OntologyConfiguration(retries: Option[Int], backoff: Backoff, poolSize: Int)
-
-object OntologyConfiguration {
-  def apply(config: Config): OntologyConfiguration = {
-    val retries = validate { Option(config.as[Int]("retries")) }
-    val backoff = validate {
-      Backoff.staticBackoff(
-        config.as[FiniteDuration]("backoff-time")
-      )
-    }
-    val poolSize = validate { config.as[Int]("pool-size") }
-
-    val validated: ErrorOr[OntologyConfiguration] = (retries, backoff, poolSize).mapN(OntologyConfiguration.apply)
-    validated.unsafe("Ontology configuration")
-  }
-}
diff --git a/cwl/src/main/scala/cwl/ontology/Schema.scala b/cwl/src/main/scala/cwl/ontology/Schema.scala
deleted file mode 100644
index a2ed13d7bf3..00000000000
--- a/cwl/src/main/scala/cwl/ontology/Schema.scala
+++ /dev/null
@@ -1,180 +0,0 @@
-package cwl.ontology
-
-import java.util.concurrent.Executors
-
-import cats.effect.IO
-import cats.syntax.traverse._
-import cats.instances.list._
-import com.google.common.cache.{Cache, CacheBuilder}
-import com.typesafe.config.{Config, ConfigFactory}
-import com.typesafe.scalalogging.Logger
-import common.util.IORetry
-import common.util.IORetry.StatefulIoError
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.ontology.Schema._
-import mouse.all._
-import net.ceedubs.ficus.Ficus._
-import org.semanticweb.owlapi.apibinding.OWLManager
-import org.semanticweb.owlapi.model._
-import org.semanticweb.owlapi.model.parameters.OntologyCopy
-import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory
-import org.semanticweb.owlapi.reasoner.{OWLReasoner, OWLReasonerFactory}
-import org.semanticweb.owlapi.util.OWLAPIStreamUtils
-import org.slf4j.LoggerFactory
-
-import scala.jdk.CollectionConverters._
-import scala.concurrent.ExecutionContext
-import scala.util.Try
-
-/**
-  * OWL/RDF Schema lookup.
-  *
-  * @param schemaIris IRI paths to OWL/RDF schemas.
-  * @param namespaces Additional/Override namespace prefixes.
-  */
-case class Schema(schemaIris: Seq[String],
-                  namespaces: Map[String, String],
-                  ontologyManager: OWLOntologyManager = OWLManager.createOWLOntologyManager,
-                  reasonerFactory: OWLReasonerFactory = new StructuralReasonerFactory) {
-
-  /**
-    * Returns a full IRI based on a full or abbreviated IRI.
-    *
-    * A full IRI wrapped in < and > will not be checked for abbreviations but will be returned without the wrapper.
-    *
-    * @see https://www.w3.org/TR/owl2-syntax/#IRIs
-    */
-  def fullIri(name: String): String = getIri(name).getIRIString
-
-  /**
-    * Returns true if child is an equivalent of ancestor, and if not then recursively checks if any of the child's
-    * super classes are an equivalent of ancestor.
-    */
-  def isSubClass(child: String, ancestor: String): Boolean = {
-    val childIri: IRI = getIri(child)
-    val ancestorIri: IRI = getIri(ancestor)
-    val childClass: OWLClass = dataFactory.getOWLClass(childIri)
-    val ancestorClass: OWLClass = dataFactory.getOWLClass(ancestorIri)
-    val schemaReasoner: OWLReasoner = reasonerFactory.createReasoner(schemaOntology)
-    try {
-      Schema.isSubClass(schemaReasoner, childClass, ancestorClass)
-    } finally {
-      schemaReasoner.dispose()
-    }
-  }
-
-  private val dataFactory: OWLDataFactory = ontologyManager.getOWLDataFactory
-  private val schemaOntology: OWLOntology = ontologyManager.createOntology()
-  private val schemaPrefixManager: PrefixManager =
-    ontologyManager.getOntologyFormat(schemaOntology).asPrefixOWLDocumentFormat
-
-  {
-    def addToSchema(originalOntology: OWLOntology): Unit = {
-      schemaOntology.addAxioms(originalOntology.axioms())
-      val originalOntologyFormat: OWLDocumentFormat = ontologyManager.getOntologyFormat(originalOntology)
-      if (originalOntologyFormat.isPrefixOWLDocumentFormat)
-        schemaPrefixManager.copyPrefixesFrom(originalOntologyFormat.asPrefixOWLDocumentFormat)
-    }
-
-    val errorOr: ErrorOr[Unit] = for {
-      ontologies <- schemaIris.toList.traverse(loadOntologyFromIri(ontologyManager))
-      _ = ontologies.foreach(addToSchema)
-    } yield ()
-    errorOr.toTry("Error loading schemas").get
-
-    // Add any namespace overrides
-    namespaces foreach {
-      case (prefixName, prefix) => schemaPrefixManager.setPrefix(prefixName, prefix)
-    }
-  }
-
-  /**
-    * Returns the full IRI for the name using the prefixManager.
-    *
-    * TODO: Not 100% sure why you can't ask owl-api for an iri-with-prefix and have it looked up automatically.
-    *
-    * There does seem to be a difference between abbreviated and full IRIs in the official spec, where full IRIs are
-    * wrapped in < >. But this doesn't seem to be the format used by CWL nor owl-api.
-    *
-    * Please update this comment if/when one knows the correct behavior.
-    *
-    * @see https://www.w3.org/TR/owl2-syntax/#IRIs
-    */
-  private def getIri(name: String): IRI = {
-    Try(schemaPrefixManager.getIRI(name)).getOrElse(IRI.create(name))
-  }
-}
-
-object Schema {
-  // Extending StrictLogging creates a circular dependency here for some reason, so making the logger ourselves
-  private val logger: Logger = Logger(LoggerFactory.getLogger(getClass.getName))
-  private [ontology] val ontologyConfig = ConfigFactory.load.as[Config]("ontology")
-  private val ontologyConfiguration = OntologyConfiguration(ontologyConfig)
-  private [ontology] val cacheConfig = ontologyConfig.getAs[Config]("cache")
-
-  // Simple cache to avoid reloading the same ontologies too often
-  private val ontologyCache = cacheConfig.map(makeOntologyCache)
-
-  private implicit val statefulIoError = StatefulIoError.noop[Unit]
-  private implicit val timer = cats.effect.IO.timer(ExecutionContext.fromExecutor(Executors.newFixedThreadPool(ontologyConfiguration.poolSize)))
-
-  private [ontology] def makeOntologyCache(config: Config): Cache[IRI, OWLOntology] = {
-    val cacheConfig = CacheConfiguration(config)
-    logger.info(s"Ontology cache size: ${cacheConfig.maxSize}")
-    CacheBuilder.newBuilder()
-      .maximumSize(cacheConfig.maxSize)
-      .build[IRI, OWLOntology]()
-  }
-
-  /**
-    * Returns the absolute path for a file, possibly relative to parent.
-    */
-  def getIriPath(parent: String, path: String): String = IRI.create(parent).resolve(path).getIRIString
-
-  /**
-    * Load an ontology either from an IRI.
-    */
-  private [ontology] def loadOntologyFromIri(ontologyManager: OWLOntologyManager, cache: Option[Cache[IRI, OWLOntology]] = ontologyCache)(schemaIri: String): ErrorOr[OWLOntology] = {
-    validate {
-      val iri = IRI.create(schemaIri)
-      cache.flatMap(_.getIfPresent(iri) |> Option.apply) match {
-        case Some(ontology) =>
-          ontologyManager.copyOntology(ontology, OntologyCopy.DEEP)
-        case _ =>
-          logger.info(s"Loading ${iri.toURI.toString}")
-          val ontology = loadOntologyFromIri(ontologyManager, iri)
-          cache.foreach(_.put(iri, ontology))
-          ontology
-      }
-    }
-  }
-
-  // Loading the ontology can fail transiently, so put retires around it. See https://github.com/protegeproject/webprotege/issues/298
-  private [ontology] def loadOntologyFromIri(ontologyManager: OWLOntologyManager, iri: IRI): OWLOntology = {
-    val load = IO { ontologyManager.loadOntologyFromOntologyDocument(iri) }
-    IORetry.withRetry[OWLOntology, Unit](load, (), ontologyConfiguration.retries, ontologyConfiguration.backoff).unsafeRunSync()
-  }
-
-  /**
-    * Returns true if child is an equivalent of ancestor, and if not then recursively checks if any of the child's
-    * super classes are an equivalent of ancestor.
-    */
-  private def isSubClass(reasoner: OWLReasoner, childClass: OWLClass, ancestorClass: OWLClass): Boolean = {
-    val equivalent: Set[OWLClass] = reasoner.getEquivalentClasses(childClass).asScala.toSet + childClass
-    if (equivalent.contains(ancestorClass)) {
-      true
-    } else {
-      val parentClasses: Set[OWLClass] = for {
-        equivalentClass <- equivalent
-        parentClass <- OWLAPIStreamUtils
-          .asSet(reasoner.getSuperClasses(equivalentClass).entities)
-          .asScala
-          .toSet[OWLClass]
-      } yield parentClass
-      parentClasses.collect({
-        case superClass: OWLClass if isSubClass(reasoner, superClass, ancestorClass) => superClass
-      }).nonEmpty
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/package.scala b/cwl/src/main/scala/cwl/package.scala
deleted file mode 100644
index 96796712f1e..00000000000
--- a/cwl/src/main/scala/cwl/package.scala
+++ /dev/null
@@ -1,154 +0,0 @@
-
-import cats.data.ReaderT
-import common.Checked
-import common.validation.Checked._
-import common.validation.ErrorOr._
-import cwl.CwlType._
-import cwl.ExpressionEvaluator.{ECMAScriptExpression, ECMAScriptFunction}
-import cwl.command.ParentName
-import cwl.ontology.Schema
-import shapeless._
-import wom.executable.Executable
-import wom.expression.IoFunctionSet
-import wom.types._
-import wom.values.WomEvaluatedCallInputs
-
-import scala.util.{Failure, Success, Try}
-
-/**
- * This package is intended to parse all CWL files.
- *
- * It makes heavy use of Circe YAML/Json auto derivation feature and
- * Circe modules that support the Scala libraries shapeless and Refined.
- *
- * The [[https://oss.sonatype.org/service/local/repositories/releases/archive/com/chuusai/shapeless_2.12/2.3.2/shapeless_2.12-2.3.2-javadoc.jar/!/shapeless/Coproduct.html shapeless.coproduct]] feature allows us to specify a large
- * number of potential types to be parsed.  A.k.a. a "disjunction" or "OR" relationship amongst these types.
- *
- * The [[https://github.com/fthomas/refined/blob/master/modules/core/shared/src/main/scala/eu/timepit/refined/string.scala MatchesRegex]] "refined type" is used
- * to enforce structure upon String values in the CWL Yaml.  Shapeless' Witness type
- * is used to declare a type containing a String literal.
- *
- * @see <a href="http://www.commonwl.org/v1.0/">CWL Specification</a>
- * @see <a href="https://github.com/circe/circe">circe</a>
- * @see <a href="https://github.com/circe/circe-yaml">circe-yaml</a>
- * @see <a href="https://github.com/fthomas/refined">Refined</a>
- * @see <a href="https://github.com/milessabin/shapeless">Shapeless</a>
- */
-package object cwl extends TypeAliases {
-
-  type CwlFile = Array[Cwl] :+: Cwl :+: CNil
-  type Cwl = Workflow :+: CommandLineTool :+: ExpressionTool :+: CNil
-
-  object Cwl {
-    object Workflow { def unapply(cwl: Cwl): Option[Workflow] = cwl.select[Workflow] }
-    object CommandLineTool { def unapply(cwl: Cwl): Option[CommandLineTool] = cwl.select[CommandLineTool] }
-    object ExpressionTool { def unapply(cwl: Cwl): Option[ExpressionTool] = cwl.select[ExpressionTool] }
-  }
-
-  def cwlTypeToWomType : CwlType => WomType = {
-    case CwlType.Any => WomAnyType
-    case Null => WomNothingType
-    case Boolean => WomBooleanType
-    case Int => WomIntegerType
-    case Long => WomLongType
-    case Float => WomFloatType
-    case Double => WomFloatType
-    case String => WomStringType
-    case CwlType.File => WomMaybePopulatedFileType
-    case CwlType.Directory => WomMaybeListedDirectoryType
-  }
-
-  object StringOrExpression {
-    object String {
-      def unapply(soe: StringOrExpression): Option[String] = soe.select[String]
-    }
-    object Expression {
-      def unapply(soe: StringOrExpression): Option[Expression] = soe.select[Expression]
-    }
-    object ECMAScriptExpression {
-      def unapply(soe: StringOrExpression): Option[ECMAScriptExpression] = soe.select[Expression].flatMap(_.select[ECMAScriptExpression])
-    }
-    object ECMAScriptFunction {
-      def unapply(soe: StringOrExpression): Option[ECMAScriptFunction] = soe.select[Expression].flatMap(_.select[ECMAScriptFunction])
-    }
-  }
-
-  object Expression {
-    object ECMAScriptExpression {
-      def unapply(soe: Expression): Option[ECMAScriptExpression] = soe.select[ECMAScriptExpression]
-    }
-    object ECMAScriptFunction {
-      def unapply(soe: Expression): Option[ECMAScriptFunction] = soe.select[ECMAScriptFunction]
-    }
-  }
-
-  type WomTypeMap = Map[String, WomType]
-
-  type RequirementsValidator = Requirement => ErrorOr[Requirement]
-  import cats.syntax.validated._
-  val AcceptAllRequirements: RequirementsValidator = _.validNel
-
-  implicit class CwlHelper(val cwl: Cwl) extends AnyVal {
-    def womExecutable(validator: RequirementsValidator, inputsFile: Option[String], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-      def executable = cwl match {
-        case Cwl.Workflow(w) => w.womExecutable(validator, inputsFile, ioFunctions, strictValidation)
-        case Cwl.CommandLineTool(clt) => clt.womExecutable(validator, inputsFile, ioFunctions, strictValidation)
-        case Cwl.ExpressionTool(et) => et.womExecutable(validator, inputsFile, ioFunctions, strictValidation)
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-      Try(executable) match {
-        case Success(s) => s
-        case Failure(f) => f.getMessage.invalidNelCheck
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-    }
-
-    def requiredInputs: Map[String, WomType] = {
-      implicit val parent = ParentName.empty
-
-      cwl match {
-        case Cwl.Workflow(w) => selectWomTypeInputs(w.inputs collect {
-          case i if i.`type`.isDefined => FullyQualifiedName(i.id).id -> i.`type`.get
-        })
-        case Cwl.CommandLineTool(clt) => selectWomTypeInputs(clt.inputs collect {
-          case i if i.`type`.isDefined => FullyQualifiedName(i.id).id -> i.`type`.get
-        })
-        case Cwl.ExpressionTool(et) => selectWomTypeInputs(et.inputs collect {
-          case i if i.`type`.isDefined => FullyQualifiedName(i.id).id -> i.`type`.get
-        })
-        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-      }
-    }
-
-    def schemaOption: Option[Schema] = cwl.fold(CwlSchemaOptionPoly)
-
-    private def selectWomTypeInputs(myriadInputMap: Array[(String, MyriadInputType)]): Map[String, WomType] = {
-      (myriadInputMap collect {
-        case (key, MyriadInputType.WomType(w)) => key -> w
-      }).toMap
-    }
-  }
-
-  object CwlSchemaOptionPoly extends Poly1 {
-    implicit val caseWorkflow: Case.Aux[Workflow, Option[Schema]] = at {
-      workflow => getSchema(workflow.`$schemas`, workflow.`$namespaces`)
-    }
-    implicit val caseCommandLineTool: Case.Aux[CommandLineTool, Option[Schema]] = at {
-      commandLineTool => getSchema(commandLineTool.`$schemas`, commandLineTool.`$namespaces`)
-    }
-    implicit val caseExpressionTool: Case.Aux[ExpressionTool, Option[Schema]] = at {
-      expressionTool => getSchema(expressionTool.`$schemas`, expressionTool.`$namespaces`)
-    }
-
-    private def getSchema(schemasOption: Option[Array[String]],
-                          namespacesOption: Option[Map[String, String]]): Option[Schema] = {
-      schemasOption.map(a => Schema(a.toIndexedSeq, namespacesOption getOrElse Map.empty))
-    }
-  }
-
-  type ExpressionLib = Vector[String]
-
-  type Inputs = (RequirementsAndHints, ExpressionLib, WomEvaluatedCallInputs)
-
-  type CommandPartExpression[A] = ReaderT[ErrorOr, Inputs, A]
-}
diff --git a/cwl/src/main/scala/cwl/preprocessor/CwlCanonicalizer.scala b/cwl/src/main/scala/cwl/preprocessor/CwlCanonicalizer.scala
deleted file mode 100644
index b369d404c18..00000000000
--- a/cwl/src/main/scala/cwl/preprocessor/CwlCanonicalizer.scala
+++ /dev/null
@@ -1,249 +0,0 @@
-package cwl.preprocessor
-
-import cats.effect.{ContextShift, IO}
-import cats.syntax.parallel._
-import cats.instances.list._
-import common.validation.ErrorOr.ErrorOr
-import common.validation.IOChecked._
-import common.validation.Validation._
-import cwl.preprocessor.CwlReference.EnhancedCwlId
-import cwl.preprocessor.CwlPreProcessor._
-import io.circe.Json
-import io.circe.optics.JsonPath._
-import cwl.preprocessor.CwlCanonicalizer._
-
-/**
-  * The real guts of the CWL pre-processor is taking a CWL reference and producing a single, self-contained JSON from it.
-  */
-private [preprocessor] class CwlCanonicalizer(saladFunction: SaladFunction)(implicit cs: ContextShift[IO]) {
-
-  def getCanonicalCwl(reference: CwlReference,
-                      namespacesJsonOption: Option[Json] = None,
-                      schemasJsonOption: Option[Json] = None): IOChecked[Json] = {
-    flattenCwlReferenceInner(
-      reference,
-      Map.empty,
-      Map.empty,
-      Set.empty,
-      namespacesJsonOption,
-      schemasJsonOption).map(_.processedJson)
-  }
-
-  /**
-    * Flatten the cwl reference given already known processed references.
-    */
-  private def flattenCwlReferenceInner(cwlReference: CwlReference,
-                                       unProcessedReferences: UnProcessedReferences,
-                                       processedReferences: ProcessedReferences,
-                                       breadCrumbs: Set[CwlReference],
-                                       namespacesJsonOption: Option[Json],
-                                       schemasJsonOption: Option[Json]): IOChecked[ProcessedJsonAndDependencies] = {
-    /*
-     * Salad and parse from a CWL reference into a Json object
-     */
-    def saladAndParse(ref: CwlReference): IOChecked[Json] =  for {
-      saladed <- saladFunction(ref)
-      saladedJson <- parseJson(saladed)
-    } yield saladedJson
-
-    for {
-      // parse the file containing the reference
-      parsed <- saladAndParse(cwlReference)
-      // Get a Map[CwlReference, Json] from the parsed file. If the file is a JSON object and only contains one node, the map will only have 1 element
-      newUnProcessedReferences = mapIdToContent(parsed).toMap
-      // The reference json in the file
-      referenceJson <- newUnProcessedReferences
-        .collectFirst({ case (ref, json) if ref.pointerWithinFile == cwlReference.pointerWithinFile => json })
-        .toIOChecked(s"Cannot find a tool or workflow with ID '${cwlReference.pointerWithinFile}' in file ${cwlReference.pathAsString}'s set: [${newUnProcessedReferences.keySet.mkString(", ")}]")
-      // Process the reference json
-      processed <- flattenJson(
-        referenceJson,
-        newUnProcessedReferences ++ unProcessedReferences,
-        processedReferences,
-        breadCrumbs + cwlReference,
-        namespacesJsonOption,
-        schemasJsonOption
-      )
-    } yield processed
-  }
-
-  /**
-    * Given a Json representing a tool or workflow, flattens it and return the other processed references that were generated.
-    *
-    * NB: Flatten here means two things:
-    *  - Find references within the CWL and convert them into 'local' links
-    *  - Create a map of canonical links to JSON CWL content
-    *
-    * @param saladedJson           json to process
-    * @param unProcessedReferences references that have been parsed and saladed (we have the json), but not flattened yet
-    * @param processedReferences   references that are fully flattened
-    * @param breadCrumbs           list of references that brought us here
-    * @param namespacesJsonOption  Namespaces from the original json
-    * @param schemasJsonOption     Schemas from the original json
-    */
-  private def flattenJson(saladedJson: Json,
-                          unProcessedReferences: UnProcessedReferences,
-                          processedReferences: ProcessedReferences,
-                          breadCrumbs: Set[CwlReference],
-                          namespacesJsonOption: Option[Json],
-                          schemasJsonOption: Option[Json]): IOChecked[ProcessedJsonAndDependencies] = {
-    /*
-     * Given a reference from a step's run field, flattens it and return it
-     * @param unProcessedReferences references that have been parsed and saladed (we have the json), but not flattened yet.
-     * @param checkedProcessedReferences references that are fully processed
-     * @param cwlReference reference being processed
-     * @return a new ProcessedReferences Map including this cwlReference processed along with all the dependencies
-     *         that might have been processed recursively.
-     */
-    def processCwlRunReference(checkedProcessedReferences: IOChecked[ProcessedReferences],
-                               cwlReference: CwlReference): IOChecked[ProcessedReferences] = {
-      def processReference(processedReferences: ProcessedReferences) = {
-
-        val result: IOChecked[ProcessedJsonAndDependencies] = unProcessedReferences.get(cwlReference) match {
-          case Some(unProcessedReferenceJson) =>
-            // Found the json in the unprocessed map, no need to reparse the file, just flatten this json
-            flattenJson(
-              unProcessedReferenceJson,
-              unProcessedReferences,
-              processedReferences,
-              breadCrumbs,
-              namespacesJsonOption,
-              schemasJsonOption
-            )
-          case None =>
-            // This is the first time we're seeing this reference, we need to parse its file and flatten it
-            flattenCwlReferenceInner(
-              cwlReference,
-              unProcessedReferences,
-              processedReferences,
-              breadCrumbs,
-              namespacesJsonOption,
-              schemasJsonOption
-            )
-        }
-
-        result map {
-          // Return everything we've got (the previously known "processedReferences" + our new processed reference + everything that was processed to get to it)
-          case ProcessedJsonAndDependencies(processed, newReferences) => processedReferences ++ newReferences + (cwlReference -> processed)
-        }
-      }
-
-      def processIfNeeded(processedReferences: ProcessedReferences): IOChecked[ProcessedReferences] = {
-        // If the reference has already been processed, no need to do anything
-        if (processedReferences.contains(cwlReference)) processedReferences.validIOChecked
-        // If the reference is in the bread crumbs it means we circled back to it: fail the pre-processing
-        else if (breadCrumbs.contains(cwlReference)) s"Found a circular dependency on $cwlReference".invalidIOChecked
-        // Otherwise let's see if we already have the json for it or if we need to process the file
-        else processReference(processedReferences)
-      }
-
-      for {
-        processedReferences <- checkedProcessedReferences
-        newReferences <- processIfNeeded(processedReferences)
-      } yield newReferences
-    }
-
-    def addJsonKeyValue(originalJson: Json, key: String, valueOption: Option[Json]): Json = {
-      valueOption match {
-        case Some(value) => originalJson.mapObject(_.add(key, value))
-        case None => originalJson
-      }
-    }
-
-    val namespacesJson = addJsonKeyValue(saladedJson, JsonKeyNamespaces, namespacesJsonOption)
-    val schemasJson = addJsonKeyValue(namespacesJson, JsonKeySchemas, schemasJsonOption)
-
-    import cats.syntax.apply._
-
-    // Take the processed runs and inject them in the json
-    def inlineProcessedJsons(newKnownReferences: ProcessedReferences, inlinedRunWorkflows: Map[String, ProcessedJsonAndDependencies]) = {
-      // Provide a function to swap the run reference with its json content
-      val lookupFunction: Json => Json = {
-        json: Json => {
-          val fromRunReferenceMap = for {
-            asString <- json.asString
-            reference <- asString.asReference
-            embeddedJson <- newKnownReferences.get(reference)
-          } yield embeddedJson
-
-          val fromInlinedWorkflow = for {
-            asObject <- json.asObject
-            id <- asObject.kleisli("id")
-            idAsString <- id.asString
-            embeddedJson <- inlinedRunWorkflows.get(idAsString)
-          } yield embeddedJson.processedJson
-
-          fromRunReferenceMap.orElse(fromInlinedWorkflow).getOrElse(json)
-        }
-      }
-
-      val flattenedJson = root.steps.each.run.json.modify(lookupFunction)(schemasJson)
-
-      ProcessedJsonAndDependencies(flattenedJson, newKnownReferences ++ inlinedRunWorkflows.values.flatMap(_.processedDependencies))
-    }
-
-    /*
-     * Given a json, collects all "steps.run" values that are JSON Strings, and convert them to CwlReferences.
-     * A saladed JSON is assumed.
-     */
-    def findRunReferences(json: Json): List[CwlReference] = {
-      json.asArray match {
-        case Some(cwls) => cwls.toList.flatMap(findRunReferences)
-        case _ => root.steps.each.run.string.getAll(json).flatMap(_.asReference).distinct
-      }
-    }
-
-    /*
-     * Given a json, collects all "steps.run" values that are JSON Objects representing a workflow.
-     * A saladed JSON is assumed.
-     * @return a Map[String, Json], where the key is the cwl id of the workflow, and the value its content
-     */
-    def findRunInlinedWorkflows(json: Json): ErrorOr[Map[String, Json]] = {
-      import cats.syntax.traverse._
-
-      json.asArray match {
-        case Some(cwls) => cwls.toList
-          .flatTraverse(findRunInlinedWorkflows(_).map(_.toList))
-          .map(_.toMap)
-        case _ =>
-          // Look for all the "run" steps that are json objects
-          root.steps.each.run.obj.getAll(json)
-            .map(Json.fromJsonObject)
-            // Only keep the workflows (CommandLineTools don't have steps so no need to process them)
-            .filter(root.`class`.string.exist(_.equalsIgnoreCase("Workflow")))
-            .traverse[ErrorOr, (String, Json)]( obj =>
-              // Find the id of the workflow
-              root.id.string.getOption(obj)
-                .toErrorOr("Programmer error: Workflow did not contain an id. Make sure the cwl has been saladed")
-                .map(_ -> obj)
-            ).map(_.toMap)
-      }
-    }
-
-    // Recursively process the run references (where run is a string pointing to another Workflow / Tool)
-    // TODO: it would be nice to accumulate failures here somehow (while still folding and be able to re-use
-    // successfully processed references, so I don't know if ErrorOr would work)
-    val processedRunReferences: IOChecked[ProcessedReferences] = findRunReferences(schemasJson).foldLeft(processedReferences.validIOChecked)(processCwlRunReference)
-
-    // Recursively process the inlined run workflows (where run is a Json object representing a workflow)
-    val processedInlineReferences: IOChecked[Map[String, ProcessedJsonAndDependencies]] = (for {
-      inlineWorkflowReferences <- findRunInlinedWorkflows(saladedJson).toIOChecked
-      flattenedWorkflows <- inlineWorkflowReferences.toList.parTraverse[IOChecked, (String, ProcessedJsonAndDependencies)]({
-        case (id, value) => flattenJson(value, unProcessedReferences, processedReferences, breadCrumbs, namespacesJsonOption, schemasJsonOption).map(id -> _)
-      })
-    } yield flattenedWorkflows).map(_.toMap)
-
-    // Replace the unprocessed runs with their processed value
-    (processedRunReferences, processedInlineReferences).tupled.map(Function.tupled(inlineProcessedJsons))
-  }
-}
-
-private object CwlCanonicalizer {
-  /**
-    * A Cwl json that has been processed (saladed and flattened), as well as its processed dependencies.
-    */
-  final case class ProcessedJsonAndDependencies(processedJson: Json, processedDependencies: ProcessedReferences)
-
-  final type UnProcessedReferences = Map[CwlReference, Json]
-  final type ProcessedReferences = Map[CwlReference, Json]
-}
diff --git a/cwl/src/main/scala/cwl/preprocessor/CwlPreProcessor.scala b/cwl/src/main/scala/cwl/preprocessor/CwlPreProcessor.scala
deleted file mode 100644
index 9855ee73953..00000000000
--- a/cwl/src/main/scala/cwl/preprocessor/CwlPreProcessor.scala
+++ /dev/null
@@ -1,236 +0,0 @@
-package cwl.preprocessor
-
-import java.util.concurrent.Executors
-
-import cats.data.NonEmptyList
-import cats.effect.{ContextShift, IO}
-import cats.syntax.either._
-import common.validation.IOChecked._
-import cwl.CwlDecoder
-import cwl.ontology.Schema
-import cwl.preprocessor.CwlPreProcessor._
-import cwl.preprocessor.CwlReference.EnhancedCwlId
-import io.circe.optics.JsonPath._
-import io.circe.{Json, JsonNumber, JsonObject}
-import mouse.all._
-import org.slf4j.LoggerFactory
-import wom.util.YamlUtils
-
-import scala.concurrent.ExecutionContext
-
-/**
-  * Class to create a standalone version of a CWL file.
-  *
-  * NB: Want to use the pre-processor? Use preProcessCwl(ref: CwlReference)
-  *
-  * @param saladFunction function that takes a file and produce a saladed version of the content
-  */
-class CwlPreProcessor(saladFunction: SaladFunction = saladCwlFile) {
-
-  private val ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(5))
-  private implicit val cs = IO.contextShift(ec)
-
-  /**
-    * This is THE main entry point into the CWL pre-processor. Takes a CWL reference and
-    * returns a canonical JSON version with all references resolved.
-    *
-    * @param ref The reference to the CWL to pre-process
-    * @return A canonical JSON representation of the CWL with all internal references expanded in-place
-    */
-  def preProcessCwl(ref: CwlReference): IOChecked[Json] = ref match {
-    case file: CwlFileReference => preProcessCwlFile(file)
-    case other => preProcessRemoteCwl(other)
-  }
-
-  /**
-    * Convenience method to get the processed workflow as a string.
-    */
-  def preProcessCwlToString(cwlReference: CwlReference): IOChecked[String] = preProcessCwl(cwlReference).map(_.printCompact)
-
-  def preProcessInputFiles(inputContent: String, mappingFunction: String => String): IOChecked[String] = for {
-    parsed <- parseYaml(inputContent)
-    mapped = parsed |> mapFilesAndDirectories(mappingFunction) |> mapNumbers
-  } yield mapped.printCompact
-
-  /**
-    * Pre-process a CWL file and create a standalone, runnable (given proper inputs), inlined version of its content.
-    *
-    * The general idea is to work on CwlReferences, starting from the one coming to this function in the form of file and optional root.
-    * The goal is to look at the steps in this workflow that point to other references, and recursively flatten them until we can replace the step with
-    * its flat version.
-    *
-    * There are 3 pieces of information that are carried around during this process:
-    *  1) ProcessedReferences: A Map[CwlReference, Json] of CwlReference for which we have the fully processed (saladed AND flattened) Json value.
-    *
-    *  2) UnProcessedReferences: A Map[CwlReference, Json] of CwlReference for which we have the saladed but NOT flattened Json value.
-    *     This can happen because a file can contain multiple tools / workflows. When we salad / parse this file, we get (CwlReference, Json) pairs
-    *     for all the workflow / tools in the file, but they are not flattened yet.
-    *     We keep this to avoid having to re-salad / re-parse files unnecessarily.
-    *
-    *  3) BreadCrumb: A Set[CwlReference] used to follow the trail of CwlReferences that we are processing as we recurse down.
-    *     This is used to be able to detect circular dependencies (if the cwlReference being processed is in that set, then we have a circular dependency) .
-    *
-    */
-  private def preProcessCwlFile(reference: CwlFileReference): IOChecked[Json] = {
-
-    def absoluteSchemaPaths(json: Json): Json = {
-      json mapArray {
-        _ map absoluteSchemaPaths
-      } mapString {
-        Schema.getIriPath(reference.fullReference, _)
-      }
-    }
-
-    // NB the JSON here is only used to decide whether or not to flatten. If we do decide to flatten we throw away the
-    // json and request a canonical version from the CwlCanonicalizer.
-    def flattenOrByPass(json: Json): IOChecked[Json] = {
-      def flatten(json: Json): IOChecked[Json] = {
-        val cwlReferenceFlattener = new CwlCanonicalizer(saladFunction)
-        val namespacesJsonOption: Option[Json] = json.asObject.flatMap(_.kleisli(JsonKeyNamespaces))
-        val schemasJsonOption: Option[Json] = json.asObject.flatMap(_.kleisli(JsonKeySchemas)).map(absoluteSchemaPaths)
-
-        cwlReferenceFlattener.getCanonicalCwl(
-          reference,
-          namespacesJsonOption,
-          schemasJsonOption
-        )
-      }
-
-      def bypass(alreadyCanonicalJson: Json): IOChecked[Json] = alreadyCanonicalJson.validIOChecked
-
-      val fileContentReference = for {
-        asObject <- json.asObject
-        fileContentId <- asObject.kleisli("id")
-        stringId <- fileContentId.asString
-        fileContentReference <- CwlReference.fromString(stringId)
-      } yield fileContentReference
-
-      fileContentReference match {
-        // This by passes the pre-processing if the file already has an id for which the file part doesn't match the path of the file
-        // passed to this function, as this would indicate that it has already been saladed and pre-processed.
-        case Some(CwlFileReference(file, _)) if !file.equals(reference.file) => bypass(json)
-        case _ => flatten(json)
-      }
-    }
-
-    for {
-      original <- parseYaml(reference.file.contentAsString)
-      flattened <- flattenOrByPass(original)
-    } yield flattened
-  }
-
-  // Like 'File', except that we don't read any contents before passing the path over to cwltool to canonicalize.
-  private def preProcessRemoteCwl(reference: CwlReference)(implicit cs: ContextShift[IO]): IOChecked[Json] = {
-    val cwlCanonicalizer = new CwlCanonicalizer(saladFunction)
-    cwlCanonicalizer.getCanonicalCwl(reference)
-  }
-}
-
-object CwlPreProcessor {
-  private val Log = LoggerFactory.getLogger("CwlPreProcessor")
-
-  private [preprocessor] type SaladFunction = CwlReference => IOChecked[String]
-  private [preprocessor] val JsonKeyNamespaces = s"$$namespaces"
-  private [preprocessor] val JsonKeySchemas = s"$$schemas"
-
-  private def saladSpinner(doLogging: Boolean): SaladFunction = ref => {
-    if (doLogging) {
-      Log.info(s"Pre-Processing ${ref.pathAsString}")
-    }
-
-    CwlDecoder.saladCwlFile(ref)
-  }
-
-  private [preprocessor] val saladCwlFile: SaladFunction = saladSpinner(true)
-  private val saladCwlFileWithoutLogging: SaladFunction = saladSpinner(false)
-
-  implicit class PrintableJson(val json: Json) extends AnyVal {
-    def printCompact = io.circe.Printer.noSpaces.print(json)
-  }
-
-  def noLogging = new CwlPreProcessor(saladCwlFileWithoutLogging)
-
-  // Fold over a json recursively and prefix all files
-  def mapFilesAndDirectories(mappingFunction: String => String)(json: Json): Json = {
-    // Function to check if the given json has the provided key / value pair
-    def hasKeyValue(key: String, value: String): Json => Boolean = {
-      root.selectDynamic(key).string.exist(_.equalsIgnoreCase(value))
-    }
-
-    // Return true if the given json object represents a File
-    def isFile(obj: JsonObject) = hasKeyValue("class", "File")(Json.fromJsonObject(obj))
-
-    // Return true if the given json object represents a Directory
-    def isDirectory(obj: JsonObject) = hasKeyValue("class", "Directory")(Json.fromJsonObject(obj))
-
-    // Modify the string at "key" using the mappingFunction
-    def mapStringValue(key: String, mappingFunction: String => String): Json => Json = root.selectDynamic(key).string.modify(mappingFunction)
-
-    // Map "location" and "default"
-    def prefix(mappingFunction: String => String): Json => Json = mapStringValue("location", mappingFunction).compose(mapStringValue("path", mappingFunction))
-
-    // Prefix the location or path in the json object if it's a file or directory, otherwise recurse over its fields
-    def prefixObject(mappingFunction: String => String)(obj: JsonObject): Json = {
-      // If the object is file or a directory, prefix it with the gcs prefix
-      if (isFile(obj) || isDirectory(obj)) {
-        prefix(mappingFunction)(Json.fromJsonObject(obj))
-          // Even if it's a file it may have secondary files. So keep recursing on its fields
-          .mapObject(_.mapValues(mapFilesAndDirectories(mappingFunction)))
-      }
-      // Otherwise recursively process its fields
-      else Json.fromJsonObject(obj.mapValues(mapFilesAndDirectories(mappingFunction)))
-    }
-
-    json.fold(
-      jsonNull = json,
-      jsonBoolean = _ => json,
-      jsonNumber = _ => json,
-      jsonString = _ => json,
-      jsonObject = prefixObject(mappingFunction),
-      jsonArray = arr => Json.arr(arr.map(mapFilesAndDirectories(mappingFunction)): _*)
-    )
-  }
-
-  private [preprocessor] def mapNumbers(json: Json): Json = {
-    // Circumvent Circe's scientific format for numbers: convert to a JSON String without exponential notation.
-    def nonScientificNumberFormatting(jsonNumber: JsonNumber): Json = {
-      val conversions = LazyList[JsonNumber => Option[Any]](
-        _.toBigInt.map(_.longValue),
-        _.toBigDecimal.map(_.doubleValue),
-        Function.const(Option("null")))
-
-      // The `get` is safe because `Option("null")` guarantees a match even if the other two Stream elements
-      // do not satisfy the predicate.
-      conversions.map(_.apply(jsonNumber)).find(_.isDefined).flatten.get.toString |> Json.fromString
-    }
-
-    json.fold(
-      jsonNull = json,
-      jsonBoolean = _ => json,
-      jsonNumber = nonScientificNumberFormatting,
-      jsonString = _ => json,
-      jsonObject = _.mapValues(mapNumbers) |> Json.fromJsonObject,
-      jsonArray = _.map(mapNumbers) |> Json.fromValues
-    )
-  }
-
-  private [preprocessor] def parseJson(in: String): IOChecked[Json] = {
-    io.circe.parser.parse(in).leftMap(error => NonEmptyList.one(error.message)).toIOChecked
-  }
-
-  private [preprocessor] def parseYaml(in: String): IOChecked[Json] = {
-    val yaml = YamlUtils.parse(in)
-    yaml.leftMap(error => NonEmptyList.one(error.message)).toIOChecked
-  }
-
-  /**
-    * Given a json, collect all tools or workflows and map them with their reference id.
-    * A saladed JSON is assumed.
-    */
-  private [preprocessor] def mapIdToContent(json: Json): List[(CwlReference, Json)] = {
-    json.asArray match {
-      case Some(cwls) => cwls.toList.flatMap(mapIdToContent)
-      case None => root.id.string.getOption(json).flatMap(_.asReference).map(_ -> json).toList
-    }
-  }
-}
diff --git a/cwl/src/main/scala/cwl/preprocessor/CwlReference.scala b/cwl/src/main/scala/cwl/preprocessor/CwlReference.scala
deleted file mode 100644
index badddf028b4..00000000000
--- a/cwl/src/main/scala/cwl/preprocessor/CwlReference.scala
+++ /dev/null
@@ -1,82 +0,0 @@
-package cwl.preprocessor
-
-import better.files.{File => BFile}
-import cwl.preprocessor.CwlReference._
-import cwl.{FileAndId, FullyQualifiedName}
-import cwl.command.ParentName
-
-sealed trait CwlReference {
-  def pathAsString: String
-  def pointerWithinFile: Option[String]
-  def changePointer(to: Option[String]): CwlReference
-
-  private def pointerWithHash: String = pointerWithinFile.map(p => s"#$p").getOrElse("")
-  lazy val fullReference: String = s"$pathAsString$pointerWithHash"
-
-  override def toString: String = fullReference
-}
-
-/**
-  * Saladed CWLs reference other local CWL "node" (workflow or tool) using a URI as follow:
-  * file:///path/to/file/containing/node.cwl[#pointer_to_node]
-  * #pointer_to_node to node is optional, and will specify which workflow or tool is being targeted in the file.
-  *
-  * e.g:
-  *   {
-  *     "class": "Workflow",
-  *     "id": "file:///path/to/workflow/workflow.cwl",
-  *     ...
-  *     "steps": [
-  *       {
-  *         "run": "file:///path/to/workflow/multi_tools.cwl#my_tool",
-  *         ...
-  *       }
-  *     ]
-  *   }
-  *
-  * This snippet contains 2 references, one that is the ID of this workflow, the other one is the run step pointing to "my_tool" in "/path/to/workflow/multi_tools.cwl"
-  *
-  */
-final case class CwlFileReference(file: BFile, pointerWithinFile: Option[String]) extends CwlReference {
-  override val pathAsString: String = s"$LocalScheme${file.toString}"
-  override def changePointer(to: Option[String]): CwlReference = this.copy(pointerWithinFile = to)
-}
-
-final case class CwlHttpReference(pathAsString: String, pointerWithinFile: Option[String]) extends CwlReference {
-  override def changePointer(to: Option[String]): CwlReference = this.copy(pointerWithinFile = to)
-}
-
-object CwlReference {
-  val LocalScheme = "file://"
-  val HttpScheme = "http://"
-  val HttpsScheme = "https://"
-
-  implicit class EnhancedCwlId(val id: String) extends AnyVal {
-    def asReference: Option[CwlReference] = CwlReference.fromString(id)
-    def stripFilePrefix = id.stripPrefix(LocalScheme)
-  }
-
-  val ReferenceRegex = "(.*://)?([^#]*)(#(.*))?".r
-
-  def fromString(in: String): Option[CwlReference] = {
-    in match {
-      case ReferenceRegex(scheme, path, _, pointerWithinFile) =>
-        if (scheme == LocalScheme) {
-          FullyQualifiedName.maybeApply(in)(ParentName.empty) match {
-            case Some(FileAndId(file, _, _)) => Option(CwlFileReference(BFile(file.stripFilePrefix), Option(pointerWithinFile)))
-            case _ => Option(CwlFileReference(BFile(in.stripFilePrefix), Option(pointerWithinFile)))
-          }
-        } else if (scheme == HttpScheme || scheme == HttpsScheme) {
-          Option(CwlHttpReference(s"$scheme$path", Option(pointerWithinFile)))
-        } else {
-          None
-        }
-    }
-  }
-}
-
-object CwlFileReference {
-  def apply(file: BFile, pointer: Option[String]) = {
-    new CwlFileReference(file, pointer)
-  }
-}
diff --git a/cwl/src/main/scala/cwl/requirement/RequirementToAttributeMap.scala b/cwl/src/main/scala/cwl/requirement/RequirementToAttributeMap.scala
deleted file mode 100644
index 1a727837172..00000000000
--- a/cwl/src/main/scala/cwl/requirement/RequirementToAttributeMap.scala
+++ /dev/null
@@ -1,79 +0,0 @@
-package cwl.requirement
-
-import cwl._
-import shapeless.Poly1
-import wom.RuntimeAttributesKeys._
-import wom.expression.{ValueAsAnExpression, WomExpression}
-import wom.values.{WomLong, WomString}
-
-object RequirementToAttributeMap extends Poly1 {
-  type ResourcesToExpressionMap = (Set[String], ExpressionLib) => Map[String, WomExpression]
-  implicit def fromJs: Case.Aux[InlineJavascriptRequirement, ResourcesToExpressionMap] = at[InlineJavascriptRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromSchemaDef: Case.Aux[SchemaDefRequirement, ResourcesToExpressionMap] = at[SchemaDefRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromDocker: Case.Aux[DockerRequirement, ResourcesToExpressionMap] = at[DockerRequirement] {
-    docker => (_,_) => docker.dockerPull.orElse(docker.dockerImageId).map({ pull =>
-      DockerKey -> ValueAsAnExpression(WomString(pull))
-    }).toMap
-  }
-
-  implicit def fromSoftware: Case.Aux[SoftwareRequirement, ResourcesToExpressionMap] = at[SoftwareRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromInitialWorkDir: Case.Aux[InitialWorkDirRequirement, ResourcesToExpressionMap] = at[InitialWorkDirRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromEnvVar: Case.Aux[EnvVarRequirement, ResourcesToExpressionMap] = at[EnvVarRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromShellCommand: Case.Aux[ShellCommandRequirement, ResourcesToExpressionMap] = at[ShellCommandRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromResource: Case.Aux[ResourceRequirement, ResourcesToExpressionMap] = at[ResourceRequirement] {
-    resource => (inputNames, expressionLib) =>
-      def toExpression(resourceRequirement: ResourceRequirementType) =
-        resourceRequirement.fold(ResourceRequirementToWomExpression).apply(inputNames, expressionLib)
-
-      List(
-        // Map cpuMin to both cpuMin and cpu keys
-        resource.effectiveCoreMin.toList.map(toExpression).flatMap(min => List(CpuMinKey -> min, CpuKey -> min)),
-        resource.effectiveCoreMax.toList.map(toExpression).map(CpuMaxKey -> _),
-        // Map ramMin to both memoryMin and memory keys
-        resource.effectiveRamMin.toList.map(toExpression).flatMap(min => List(MemoryMinKey -> min, MemoryKey -> min)),
-        resource.effectiveRamMax.toList.map(toExpression).map(MemoryMaxKey -> _),
-        resource.effectiveTmpdirMin.toList.map(toExpression).map(TmpDirMinKey -> _),
-        resource.effectiveTmpdirMax.toList.map(toExpression).map(TmpDirMaxKey -> _),
-        resource.effectiveOutdirMin.toList.map(toExpression).map(OutDirMinKey -> _),
-        resource.effectiveOutdirMax.toList.map(toExpression).map(OutDirMaxKey -> _)
-      ).flatten.toMap
-  }
-
-  implicit def fromInputResourceRequirement: Case.Aux[DnaNexusInputResourceRequirement, ResourcesToExpressionMap] = at[DnaNexusInputResourceRequirement] {
-    case DnaNexusInputResourceRequirement(_, indirMin) => (_, _) => indirMin.map(value => ValueAsAnExpression(WomLong(value))).map(DnaNexusInputDirMinKey -> _).toMap
-  }
-
-  implicit def fromSubWorkflow: Case.Aux[SubworkflowFeatureRequirement, ResourcesToExpressionMap] = at[SubworkflowFeatureRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromScatter: Case.Aux[ScatterFeatureRequirement, ResourcesToExpressionMap] = at[ScatterFeatureRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromMultipleInput: Case.Aux[MultipleInputFeatureRequirement, ResourcesToExpressionMap] = at[MultipleInputFeatureRequirement] {
-    _ => (_,_) => Map.empty
-  }
-
-  implicit def fromStepInput: Case.Aux[StepInputExpressionRequirement, ResourcesToExpressionMap] = at[StepInputExpressionRequirement] {
-    _ => (_,_) => Map.empty
-  }
-}
diff --git a/cwl/src/main/scala/cwl/requirement/ResourceRequirementToWomExpression.scala b/cwl/src/main/scala/cwl/requirement/ResourceRequirementToWomExpression.scala
deleted file mode 100644
index 74727947657..00000000000
--- a/cwl/src/main/scala/cwl/requirement/ResourceRequirementToWomExpression.scala
+++ /dev/null
@@ -1,15 +0,0 @@
-package cwl.requirement
-
-import cwl.{Expression, ExpressionLib}
-import shapeless.Poly1
-import wom.expression.{ValueAsAnExpression, WomExpression}
-import wom.values.{WomLong, WomString}
-
-object ResourceRequirementToWomExpression extends Poly1 {
-  type ResourceRequirementStringSetToWomExpression = (Set[String], ExpressionLib) => WomExpression
-  implicit def fromLong: Case.Aux[Long, ResourceRequirementStringSetToWomExpression] = at[Long] { l => (_, _) => ValueAsAnExpression(WomLong(l)) }
-  implicit def fromString: Case.Aux[String, ResourceRequirementStringSetToWomExpression] = at[String] { s =>  (_, _) => ValueAsAnExpression(WomString(s)) }
-  implicit def fromExpression: Case.Aux[Expression, ResourceRequirementStringSetToWomExpression] = at[Expression] { e => (inputs, expressionLib) =>
-    cwl.ECMAScriptWomExpression(e, inputs, expressionLib)
-  }
-}
diff --git a/cwl/src/test/resources/1st-tool.cwl b/cwl/src/test/resources/1st-tool.cwl
deleted file mode 100755
index af0c4de297d..00000000000
--- a/cwl/src/test/resources/1st-tool.cwl
+++ /dev/null
@@ -1,9 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-inputs:
-  message:
-    type: string
-    inputBinding:
-      position: 1
-outputs: []
diff --git a/cwl/src/test/resources/1st-workflow.cwl b/cwl/src/test/resources/1st-workflow.cwl
deleted file mode 100644
index ce4b4b0bd71..00000000000
--- a/cwl/src/test/resources/1st-workflow.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: File
-  ex: string
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classfile
-
-steps:
-  untar:
-    run: tar-param.cwl
-    in:
-      tarfile: inp
-      extractfile: ex
-    out: [example_out]
-
-  compile:
-    run: arguments.cwl
-    in:
-      src: untar/example_out
-    out: [classfile]
diff --git a/cwl/src/test/resources/application.conf b/cwl/src/test/resources/application.conf
deleted file mode 100644
index 8d12b670cd3..00000000000
--- a/cwl/src/test/resources/application.conf
+++ /dev/null
@@ -1,14 +0,0 @@
-akka {
-  log-dead-letters = "off"
-  loggers = ["akka.event.slf4j.Slf4jLogger"]
-}
-
-ontology {
-  # Uncomment to enable caching of ontologies. Improves performance when loading ontologies from remote IRIs.
-  #cache {
-  #  max-size = 20
-  #}
-  retries = 3
-  pool-size = 3
-  backoff-time = 2 seconds
-}
diff --git a/cwl/src/test/resources/arguments.cwl b/cwl/src/test/resources/arguments.cwl
deleted file mode 100644
index 730030e7437..00000000000
--- a/cwl/src/test/resources/arguments.cwl
+++ /dev/null
@@ -1,22 +0,0 @@
-cwlVersion: "v1.0"
-class: "CommandLineTool"
-label: "Example trivial wrapper for Java 7 compiler"
-hints: 
-  - dockerPull: "java:7-jdk"
-    class: "DockerRequirement"
-baseCommand: "javac"
-arguments: 
-  - "-d"
-  - "$(runtime.outdir)"
-inputs: 
-  - type: "File"
-    inputBinding: 
-      position: 1
-    id: "file:///home/dan/wdl4s/arguments.cwl#src"
-outputs: 
-  - type: "File"
-    outputBinding: 
-      glob: "*.class"
-    id: "file:///home/dan/wdl4s/arguments.cwl#classfile"
-id: "file:///home/dan/wdl4s/arguments.cwl"
-name: "file:///home/dan/wdl4s/arguments.cwl"
diff --git a/cwl/src/test/resources/bad.cwl b/cwl/src/test/resources/bad.cwl
deleted file mode 100644
index d38ed298731..00000000000
--- a/cwl/src/test/resources/bad.cwl
+++ /dev/null
@@ -1 +0,0 @@
-gibberish
diff --git a/cwl/src/test/resources/bad2.cwl b/cwl/src/test/resources/bad2.cwl
deleted file mode 100644
index d38ed298731..00000000000
--- a/cwl/src/test/resources/bad2.cwl
+++ /dev/null
@@ -1 +0,0 @@
-gibberish
diff --git a/cwl/src/test/resources/brokenlinks.cwl b/cwl/src/test/resources/brokenlinks.cwl
deleted file mode 100644
index c710358ce61..00000000000
--- a/cwl/src/test/resources/brokenlinks.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: File
-  ex: string
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classfile
-
-steps:
-  untar:
-    run: wrong.cwl
-    in:
-      tarfile: inp
-      extractfile: ex
-    out: [example_out]
-
-  compile:
-    run: wrong2.cwl
-    in:
-      src: untar/example_out
-    out: [classfile]
diff --git a/cwl/src/test/resources/cwl/lodash.js b/cwl/src/test/resources/cwl/lodash.js
deleted file mode 100644
index 9b95dfefe87..00000000000
--- a/cwl/src/test/resources/cwl/lodash.js
+++ /dev/null
@@ -1,17112 +0,0 @@
-/**
- * @license
- * Lodash <https://lodash.com/>
- * Copyright OpenJS Foundation and other contributors <https://openjsf.org/>
- * Released under MIT license <https://lodash.com/license>
- * Based on Underscore.js 1.8.3 <http://underscorejs.org/LICENSE>
- * Copyright Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
- */
-;(function() {
-
-  /** Used as a safe reference for `undefined` in pre-ES5 environments. */
-  var undefined;
-
-  /** Used as the semantic version number. */
-  var VERSION = '4.17.15';
-
-  /** Used as the size to enable large array optimizations. */
-  var LARGE_ARRAY_SIZE = 200;
-
-  /** Error message constants. */
-  var CORE_ERROR_TEXT = 'Unsupported core-js use. Try https://npms.io/search?q=ponyfill.',
-      FUNC_ERROR_TEXT = 'Expected a function';
-
-  /** Used to stand-in for `undefined` hash values. */
-  var HASH_UNDEFINED = '__lodash_hash_undefined__';
-
-  /** Used as the maximum memoize cache size. */
-  var MAX_MEMOIZE_SIZE = 500;
-
-  /** Used as the internal argument placeholder. */
-  var PLACEHOLDER = '__lodash_placeholder__';
-
-  /** Used to compose bitmasks for cloning. */
-  var CLONE_DEEP_FLAG = 1,
-      CLONE_FLAT_FLAG = 2,
-      CLONE_SYMBOLS_FLAG = 4;
-
-  /** Used to compose bitmasks for value comparisons. */
-  var COMPARE_PARTIAL_FLAG = 1,
-      COMPARE_UNORDERED_FLAG = 2;
-
-  /** Used to compose bitmasks for function metadata. */
-  var WRAP_BIND_FLAG = 1,
-      WRAP_BIND_KEY_FLAG = 2,
-      WRAP_CURRY_BOUND_FLAG = 4,
-      WRAP_CURRY_FLAG = 8,
-      WRAP_CURRY_RIGHT_FLAG = 16,
-      WRAP_PARTIAL_FLAG = 32,
-      WRAP_PARTIAL_RIGHT_FLAG = 64,
-      WRAP_ARY_FLAG = 128,
-      WRAP_REARG_FLAG = 256,
-      WRAP_FLIP_FLAG = 512;
-
-  /** Used as default options for `_.truncate`. */
-  var DEFAULT_TRUNC_LENGTH = 30,
-      DEFAULT_TRUNC_OMISSION = '...';
-
-  /** Used to detect hot functions by number of calls within a span of milliseconds. */
-  var HOT_COUNT = 800,
-      HOT_SPAN = 16;
-
-  /** Used to indicate the type of lazy iteratees. */
-  var LAZY_FILTER_FLAG = 1,
-      LAZY_MAP_FLAG = 2,
-      LAZY_WHILE_FLAG = 3;
-
-  /** Used as references for various `Number` constants. */
-  var INFINITY = 1 / 0,
-      MAX_SAFE_INTEGER = 9007199254740991,
-      MAX_INTEGER = 1.7976931348623157e+308,
-      NAN = 0 / 0;
-
-  /** Used as references for the maximum length and index of an array. */
-  var MAX_ARRAY_LENGTH = 4294967295,
-      MAX_ARRAY_INDEX = MAX_ARRAY_LENGTH - 1,
-      HALF_MAX_ARRAY_LENGTH = MAX_ARRAY_LENGTH >>> 1;
-
-  /** Used to associate wrap methods with their bit flags. */
-  var wrapFlags = [
-    ['ary', WRAP_ARY_FLAG],
-    ['bind', WRAP_BIND_FLAG],
-    ['bindKey', WRAP_BIND_KEY_FLAG],
-    ['curry', WRAP_CURRY_FLAG],
-    ['curryRight', WRAP_CURRY_RIGHT_FLAG],
-    ['flip', WRAP_FLIP_FLAG],
-    ['partial', WRAP_PARTIAL_FLAG],
-    ['partialRight', WRAP_PARTIAL_RIGHT_FLAG],
-    ['rearg', WRAP_REARG_FLAG]
-  ];
-
-  /** `Object#toString` result references. */
-  var argsTag = '[object Arguments]',
-      arrayTag = '[object Array]',
-      asyncTag = '[object AsyncFunction]',
-      boolTag = '[object Boolean]',
-      dateTag = '[object Date]',
-      domExcTag = '[object DOMException]',
-      errorTag = '[object Error]',
-      funcTag = '[object Function]',
-      genTag = '[object GeneratorFunction]',
-      mapTag = '[object Map]',
-      numberTag = '[object Number]',
-      nullTag = '[object Null]',
-      objectTag = '[object Object]',
-      promiseTag = '[object Promise]',
-      proxyTag = '[object Proxy]',
-      regexpTag = '[object RegExp]',
-      setTag = '[object Set]',
-      stringTag = '[object String]',
-      symbolTag = '[object Symbol]',
-      undefinedTag = '[object Undefined]',
-      weakMapTag = '[object WeakMap]',
-      weakSetTag = '[object WeakSet]';
-
-  var arrayBufferTag = '[object ArrayBuffer]',
-      dataViewTag = '[object DataView]',
-      float32Tag = '[object Float32Array]',
-      float64Tag = '[object Float64Array]',
-      int8Tag = '[object Int8Array]',
-      int16Tag = '[object Int16Array]',
-      int32Tag = '[object Int32Array]',
-      uint8Tag = '[object Uint8Array]',
-      uint8ClampedTag = '[object Uint8ClampedArray]',
-      uint16Tag = '[object Uint16Array]',
-      uint32Tag = '[object Uint32Array]';
-
-  /** Used to match empty string literals in compiled template source. */
-  var reEmptyStringLeading = /\b__p \+= '';/g,
-      reEmptyStringMiddle = /\b(__p \+=) '' \+/g,
-      reEmptyStringTrailing = /(__e\(.*?\)|\b__t\)) \+\n'';/g;
-
-  /** Used to match HTML entities and HTML characters. */
-  var reEscapedHtml = /&(?:amp|lt|gt|quot|#39);/g,
-      reUnescapedHtml = /[&<>"']/g,
-      reHasEscapedHtml = RegExp(reEscapedHtml.source),
-      reHasUnescapedHtml = RegExp(reUnescapedHtml.source);
-
-  /** Used to match template delimiters. */
-  var reEscape = /<%-([\s\S]+?)%>/g,
-      reEvaluate = /<%([\s\S]+?)%>/g,
-      reInterpolate = /<%=([\s\S]+?)%>/g;
-
-  /** Used to match property names within property paths. */
-  var reIsDeepProp = /\.|\[(?:[^[\]]*|(["'])(?:(?!\1)[^\\]|\\.)*?\1)\]/,
-      reIsPlainProp = /^\w*$/,
-      rePropName = /[^.[\]]+|\[(?:(-?\d+(?:\.\d+)?)|(["'])((?:(?!\2)[^\\]|\\.)*?)\2)\]|(?=(?:\.|\[\])(?:\.|\[\]|$))/g;
-
-  /**
-   * Used to match `RegExp`
-   * [syntax characters](http://ecma-international.org/ecma-262/7.0/#sec-patterns).
-   */
-  var reRegExpChar = /[\\^$.*+?()[\]{}|]/g,
-      reHasRegExpChar = RegExp(reRegExpChar.source);
-
-  /** Used to match leading and trailing whitespace. */
-  var reTrim = /^\s+|\s+$/g,
-      reTrimStart = /^\s+/,
-      reTrimEnd = /\s+$/;
-
-  /** Used to match wrap detail comments. */
-  var reWrapComment = /\{(?:\n\/\* \[wrapped with .+\] \*\/)?\n?/,
-      reWrapDetails = /\{\n\/\* \[wrapped with (.+)\] \*/,
-      reSplitDetails = /,? & /;
-
-  /** Used to match words composed of alphanumeric characters. */
-  var reAsciiWord = /[^\x00-\x2f\x3a-\x40\x5b-\x60\x7b-\x7f]+/g;
-
-  /** Used to match backslashes in property paths. */
-  var reEscapeChar = /\\(\\)?/g;
-
-  /**
-   * Used to match
-   * [ES template delimiters](http://ecma-international.org/ecma-262/7.0/#sec-template-literal-lexical-components).
-   */
-  var reEsTemplate = /\$\{([^\\}]*(?:\\.[^\\}]*)*)\}/g;
-
-  /** Used to match `RegExp` flags from their coerced string values. */
-  var reFlags = /\w*$/;
-
-  /** Used to detect bad signed hexadecimal string values. */
-  var reIsBadHex = /^[-+]0x[0-9a-f]+$/i;
-
-  /** Used to detect binary string values. */
-  var reIsBinary = /^0b[01]+$/i;
-
-  /** Used to detect host constructors (Safari). */
-  var reIsHostCtor = /^\[object .+?Constructor\]$/;
-
-  /** Used to detect octal string values. */
-  var reIsOctal = /^0o[0-7]+$/i;
-
-  /** Used to detect unsigned integer values. */
-  var reIsUint = /^(?:0|[1-9]\d*)$/;
-
-  /** Used to match Latin Unicode letters (excluding mathematical operators). */
-  var reLatin = /[\xc0-\xd6\xd8-\xf6\xf8-\xff\u0100-\u017f]/g;
-
-  /** Used to ensure capturing order of template delimiters. */
-  var reNoMatch = /($^)/;
-
-  /** Used to match unescaped characters in compiled string literals. */
-  var reUnescapedString = /['\n\r\u2028\u2029\\]/g;
-
-  /** Used to compose unicode character classes. */
-  var rsAstralRange = '\\ud800-\\udfff',
-      rsComboMarksRange = '\\u0300-\\u036f',
-      reComboHalfMarksRange = '\\ufe20-\\ufe2f',
-      rsComboSymbolsRange = '\\u20d0-\\u20ff',
-      rsComboRange = rsComboMarksRange + reComboHalfMarksRange + rsComboSymbolsRange,
-      rsDingbatRange = '\\u2700-\\u27bf',
-      rsLowerRange = 'a-z\\xdf-\\xf6\\xf8-\\xff',
-      rsMathOpRange = '\\xac\\xb1\\xd7\\xf7',
-      rsNonCharRange = '\\x00-\\x2f\\x3a-\\x40\\x5b-\\x60\\x7b-\\xbf',
-      rsPunctuationRange = '\\u2000-\\u206f',
-      rsSpaceRange = ' \\t\\x0b\\f\\xa0\\ufeff\\n\\r\\u2028\\u2029\\u1680\\u180e\\u2000\\u2001\\u2002\\u2003\\u2004\\u2005\\u2006\\u2007\\u2008\\u2009\\u200a\\u202f\\u205f\\u3000',
-      rsUpperRange = 'A-Z\\xc0-\\xd6\\xd8-\\xde',
-      rsVarRange = '\\ufe0e\\ufe0f',
-      rsBreakRange = rsMathOpRange + rsNonCharRange + rsPunctuationRange + rsSpaceRange;
-
-  /** Used to compose unicode capture groups. */
-  var rsApos = "['\u2019]",
-      rsAstral = '[' + rsAstralRange + ']',
-      rsBreak = '[' + rsBreakRange + ']',
-      rsCombo = '[' + rsComboRange + ']',
-      rsDigits = '\\d+',
-      rsDingbat = '[' + rsDingbatRange + ']',
-      rsLower = '[' + rsLowerRange + ']',
-      rsMisc = '[^' + rsAstralRange + rsBreakRange + rsDigits + rsDingbatRange + rsLowerRange + rsUpperRange + ']',
-      rsFitz = '\\ud83c[\\udffb-\\udfff]',
-      rsModifier = '(?:' + rsCombo + '|' + rsFitz + ')',
-      rsNonAstral = '[^' + rsAstralRange + ']',
-      rsRegional = '(?:\\ud83c[\\udde6-\\uddff]){2}',
-      rsSurrPair = '[\\ud800-\\udbff][\\udc00-\\udfff]',
-      rsUpper = '[' + rsUpperRange + ']',
-      rsZWJ = '\\u200d';
-
-  /** Used to compose unicode regexes. */
-  var rsMiscLower = '(?:' + rsLower + '|' + rsMisc + ')',
-      rsMiscUpper = '(?:' + rsUpper + '|' + rsMisc + ')',
-      rsOptContrLower = '(?:' + rsApos + '(?:d|ll|m|re|s|t|ve))?',
-      rsOptContrUpper = '(?:' + rsApos + '(?:D|LL|M|RE|S|T|VE))?',
-      reOptMod = rsModifier + '?',
-      rsOptVar = '[' + rsVarRange + ']?',
-      rsOptJoin = '(?:' + rsZWJ + '(?:' + [rsNonAstral, rsRegional, rsSurrPair].join('|') + ')' + rsOptVar + reOptMod + ')*',
-      rsOrdLower = '\\d*(?:1st|2nd|3rd|(?![123])\\dth)(?=\\b|[A-Z_])',
-      rsOrdUpper = '\\d*(?:1ST|2ND|3RD|(?![123])\\dTH)(?=\\b|[a-z_])',
-      rsSeq = rsOptVar + reOptMod + rsOptJoin,
-      rsEmoji = '(?:' + [rsDingbat, rsRegional, rsSurrPair].join('|') + ')' + rsSeq,
-      rsSymbol = '(?:' + [rsNonAstral + rsCombo + '?', rsCombo, rsRegional, rsSurrPair, rsAstral].join('|') + ')';
-
-  /** Used to match apostrophes. */
-  var reApos = RegExp(rsApos, 'g');
-
-  /**
-   * Used to match [combining diacritical marks](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks) and
-   * [combining diacritical marks for symbols](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks_for_Symbols).
-   */
-  var reComboMark = RegExp(rsCombo, 'g');
-
-  /** Used to match [string symbols](https://mathiasbynens.be/notes/javascript-unicode). */
-  var reUnicode = RegExp(rsFitz + '(?=' + rsFitz + ')|' + rsSymbol + rsSeq, 'g');
-
-  /** Used to match complex or compound words. */
-  var reUnicodeWord = RegExp([
-    rsUpper + '?' + rsLower + '+' + rsOptContrLower + '(?=' + [rsBreak, rsUpper, '$'].join('|') + ')',
-    rsMiscUpper + '+' + rsOptContrUpper + '(?=' + [rsBreak, rsUpper + rsMiscLower, '$'].join('|') + ')',
-    rsUpper + '?' + rsMiscLower + '+' + rsOptContrLower,
-    rsUpper + '+' + rsOptContrUpper,
-    rsOrdUpper,
-    rsOrdLower,
-    rsDigits,
-    rsEmoji
-  ].join('|'), 'g');
-
-  /** Used to detect strings with [zero-width joiners or code points from the astral planes](http://eev.ee/blog/2015/09/12/dark-corners-of-unicode/). */
-  var reHasUnicode = RegExp('[' + rsZWJ + rsAstralRange  + rsComboRange + rsVarRange + ']');
-
-  /** Used to detect strings that need a more robust regexp to match words. */
-  var reHasUnicodeWord = /[a-z][A-Z]|[A-Z]{2}[a-z]|[0-9][a-zA-Z]|[a-zA-Z][0-9]|[^a-zA-Z0-9 ]/;
-
-  /** Used to assign default `context` object properties. */
-  var contextProps = [
-    'Array', 'Buffer', 'DataView', 'Date', 'Error', 'Float32Array', 'Float64Array',
-    'Function', 'Int8Array', 'Int16Array', 'Int32Array', 'Map', 'Math', 'Object',
-    'Promise', 'RegExp', 'Set', 'String', 'Symbol', 'TypeError', 'Uint8Array',
-    'Uint8ClampedArray', 'Uint16Array', 'Uint32Array', 'WeakMap',
-    '_', 'clearTimeout', 'isFinite', 'parseInt', 'setTimeout'
-  ];
-
-  /** Used to make template sourceURLs easier to identify. */
-  var templateCounter = -1;
-
-  /** Used to identify `toStringTag` values of typed arrays. */
-  var typedArrayTags = {};
-  typedArrayTags[float32Tag] = typedArrayTags[float64Tag] =
-  typedArrayTags[int8Tag] = typedArrayTags[int16Tag] =
-  typedArrayTags[int32Tag] = typedArrayTags[uint8Tag] =
-  typedArrayTags[uint8ClampedTag] = typedArrayTags[uint16Tag] =
-  typedArrayTags[uint32Tag] = true;
-  typedArrayTags[argsTag] = typedArrayTags[arrayTag] =
-  typedArrayTags[arrayBufferTag] = typedArrayTags[boolTag] =
-  typedArrayTags[dataViewTag] = typedArrayTags[dateTag] =
-  typedArrayTags[errorTag] = typedArrayTags[funcTag] =
-  typedArrayTags[mapTag] = typedArrayTags[numberTag] =
-  typedArrayTags[objectTag] = typedArrayTags[regexpTag] =
-  typedArrayTags[setTag] = typedArrayTags[stringTag] =
-  typedArrayTags[weakMapTag] = false;
-
-  /** Used to identify `toStringTag` values supported by `_.clone`. */
-  var cloneableTags = {};
-  cloneableTags[argsTag] = cloneableTags[arrayTag] =
-  cloneableTags[arrayBufferTag] = cloneableTags[dataViewTag] =
-  cloneableTags[boolTag] = cloneableTags[dateTag] =
-  cloneableTags[float32Tag] = cloneableTags[float64Tag] =
-  cloneableTags[int8Tag] = cloneableTags[int16Tag] =
-  cloneableTags[int32Tag] = cloneableTags[mapTag] =
-  cloneableTags[numberTag] = cloneableTags[objectTag] =
-  cloneableTags[regexpTag] = cloneableTags[setTag] =
-  cloneableTags[stringTag] = cloneableTags[symbolTag] =
-  cloneableTags[uint8Tag] = cloneableTags[uint8ClampedTag] =
-  cloneableTags[uint16Tag] = cloneableTags[uint32Tag] = true;
-  cloneableTags[errorTag] = cloneableTags[funcTag] =
-  cloneableTags[weakMapTag] = false;
-
-  /** Used to map Latin Unicode letters to basic Latin letters. */
-  var deburredLetters = {
-    // Latin-1 Supplement block.
-    '\xc0': 'A',  '\xc1': 'A', '\xc2': 'A', '\xc3': 'A', '\xc4': 'A', '\xc5': 'A',
-    '\xe0': 'a',  '\xe1': 'a', '\xe2': 'a', '\xe3': 'a', '\xe4': 'a', '\xe5': 'a',
-    '\xc7': 'C',  '\xe7': 'c',
-    '\xd0': 'D',  '\xf0': 'd',
-    '\xc8': 'E',  '\xc9': 'E', '\xca': 'E', '\xcb': 'E',
-    '\xe8': 'e',  '\xe9': 'e', '\xea': 'e', '\xeb': 'e',
-    '\xcc': 'I',  '\xcd': 'I', '\xce': 'I', '\xcf': 'I',
-    '\xec': 'i',  '\xed': 'i', '\xee': 'i', '\xef': 'i',
-    '\xd1': 'N',  '\xf1': 'n',
-    '\xd2': 'O',  '\xd3': 'O', '\xd4': 'O', '\xd5': 'O', '\xd6': 'O', '\xd8': 'O',
-    '\xf2': 'o',  '\xf3': 'o', '\xf4': 'o', '\xf5': 'o', '\xf6': 'o', '\xf8': 'o',
-    '\xd9': 'U',  '\xda': 'U', '\xdb': 'U', '\xdc': 'U',
-    '\xf9': 'u',  '\xfa': 'u', '\xfb': 'u', '\xfc': 'u',
-    '\xdd': 'Y',  '\xfd': 'y', '\xff': 'y',
-    '\xc6': 'Ae', '\xe6': 'ae',
-    '\xde': 'Th', '\xfe': 'th',
-    '\xdf': 'ss',
-    // Latin Extended-A block.
-    '\u0100': 'A',  '\u0102': 'A', '\u0104': 'A',
-    '\u0101': 'a',  '\u0103': 'a', '\u0105': 'a',
-    '\u0106': 'C',  '\u0108': 'C', '\u010a': 'C', '\u010c': 'C',
-    '\u0107': 'c',  '\u0109': 'c', '\u010b': 'c', '\u010d': 'c',
-    '\u010e': 'D',  '\u0110': 'D', '\u010f': 'd', '\u0111': 'd',
-    '\u0112': 'E',  '\u0114': 'E', '\u0116': 'E', '\u0118': 'E', '\u011a': 'E',
-    '\u0113': 'e',  '\u0115': 'e', '\u0117': 'e', '\u0119': 'e', '\u011b': 'e',
-    '\u011c': 'G',  '\u011e': 'G', '\u0120': 'G', '\u0122': 'G',
-    '\u011d': 'g',  '\u011f': 'g', '\u0121': 'g', '\u0123': 'g',
-    '\u0124': 'H',  '\u0126': 'H', '\u0125': 'h', '\u0127': 'h',
-    '\u0128': 'I',  '\u012a': 'I', '\u012c': 'I', '\u012e': 'I', '\u0130': 'I',
-    '\u0129': 'i',  '\u012b': 'i', '\u012d': 'i', '\u012f': 'i', '\u0131': 'i',
-    '\u0134': 'J',  '\u0135': 'j',
-    '\u0136': 'K',  '\u0137': 'k', '\u0138': 'k',
-    '\u0139': 'L',  '\u013b': 'L', '\u013d': 'L', '\u013f': 'L', '\u0141': 'L',
-    '\u013a': 'l',  '\u013c': 'l', '\u013e': 'l', '\u0140': 'l', '\u0142': 'l',
-    '\u0143': 'N',  '\u0145': 'N', '\u0147': 'N', '\u014a': 'N',
-    '\u0144': 'n',  '\u0146': 'n', '\u0148': 'n', '\u014b': 'n',
-    '\u014c': 'O',  '\u014e': 'O', '\u0150': 'O',
-    '\u014d': 'o',  '\u014f': 'o', '\u0151': 'o',
-    '\u0154': 'R',  '\u0156': 'R', '\u0158': 'R',
-    '\u0155': 'r',  '\u0157': 'r', '\u0159': 'r',
-    '\u015a': 'S',  '\u015c': 'S', '\u015e': 'S', '\u0160': 'S',
-    '\u015b': 's',  '\u015d': 's', '\u015f': 's', '\u0161': 's',
-    '\u0162': 'T',  '\u0164': 'T', '\u0166': 'T',
-    '\u0163': 't',  '\u0165': 't', '\u0167': 't',
-    '\u0168': 'U',  '\u016a': 'U', '\u016c': 'U', '\u016e': 'U', '\u0170': 'U', '\u0172': 'U',
-    '\u0169': 'u',  '\u016b': 'u', '\u016d': 'u', '\u016f': 'u', '\u0171': 'u', '\u0173': 'u',
-    '\u0174': 'W',  '\u0175': 'w',
-    '\u0176': 'Y',  '\u0177': 'y', '\u0178': 'Y',
-    '\u0179': 'Z',  '\u017b': 'Z', '\u017d': 'Z',
-    '\u017a': 'z',  '\u017c': 'z', '\u017e': 'z',
-    '\u0132': 'IJ', '\u0133': 'ij',
-    '\u0152': 'Oe', '\u0153': 'oe',
-    '\u0149': "'n", '\u017f': 's'
-  };
-
-  /** Used to map characters to HTML entities. */
-  var htmlEscapes = {
-    '&': '&amp;',
-    '<': '&lt;',
-    '>': '&gt;',
-    '"': '&quot;',
-    "'": '&#39;'
-  };
-
-  /** Used to map HTML entities to characters. */
-  var htmlUnescapes = {
-    '&amp;': '&',
-    '&lt;': '<',
-    '&gt;': '>',
-    '&quot;': '"',
-    '&#39;': "'"
-  };
-
-  /** Used to escape characters for inclusion in compiled string literals. */
-  var stringEscapes = {
-    '\\': '\\',
-    "'": "'",
-    '\n': 'n',
-    '\r': 'r',
-    '\u2028': 'u2028',
-    '\u2029': 'u2029'
-  };
-
-  /** Built-in method references without a dependency on `root`. */
-  var freeParseFloat = parseFloat,
-      freeParseInt = parseInt;
-
-  /** Detect free variable `global` from Node.js. */
-  var freeGlobal = typeof global == 'object' && global && global.Object === Object && global;
-
-  /** Detect free variable `self`. */
-  var freeSelf = typeof self == 'object' && self && self.Object === Object && self;
-
-  /** Used as a reference to the global object. */
-  var root = freeGlobal || freeSelf || Function('return this')();
-
-  /** Detect free variable `exports`. */
-  var freeExports = typeof exports == 'object' && exports && !exports.nodeType && exports;
-
-  /** Detect free variable `module`. */
-  var freeModule = freeExports && typeof module == 'object' && module && !module.nodeType && module;
-
-  /** Detect the popular CommonJS extension `module.exports`. */
-  var moduleExports = freeModule && freeModule.exports === freeExports;
-
-  /** Detect free variable `process` from Node.js. */
-  var freeProcess = moduleExports && freeGlobal.process;
-
-  /** Used to access faster Node.js helpers. */
-  var nodeUtil = (function() {
-    try {
-      // Use `util.types` for Node.js 10+.
-      var types = freeModule && freeModule.require && freeModule.require('util').types;
-
-      if (types) {
-        return types;
-      }
-
-      // Legacy `process.binding('util')` for Node.js < 10.
-      return freeProcess && freeProcess.binding && freeProcess.binding('util');
-    } catch (e) {}
-  }());
-
-  /* Node.js helper references. */
-  var nodeIsArrayBuffer = nodeUtil && nodeUtil.isArrayBuffer,
-      nodeIsDate = nodeUtil && nodeUtil.isDate,
-      nodeIsMap = nodeUtil && nodeUtil.isMap,
-      nodeIsRegExp = nodeUtil && nodeUtil.isRegExp,
-      nodeIsSet = nodeUtil && nodeUtil.isSet,
-      nodeIsTypedArray = nodeUtil && nodeUtil.isTypedArray;
-
-  /*--------------------------------------------------------------------------*/
-
-  /**
-   * A faster alternative to `Function#apply`, this function invokes `func`
-   * with the `this` binding of `thisArg` and the arguments of `args`.
-   *
-   * @private
-   * @param {Function} func The function to invoke.
-   * @param {*} thisArg The `this` binding of `func`.
-   * @param {Array} args The arguments to invoke `func` with.
-   * @returns {*} Returns the result of `func`.
-   */
-  function apply(func, thisArg, args) {
-    switch (args.length) {
-      case 0: return func.call(thisArg);
-      case 1: return func.call(thisArg, args[0]);
-      case 2: return func.call(thisArg, args[0], args[1]);
-      case 3: return func.call(thisArg, args[0], args[1], args[2]);
-    }
-    return func.apply(thisArg, args);
-  }
-
-  /**
-   * A specialized version of `baseAggregator` for arrays.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} setter The function to set `accumulator` values.
-   * @param {Function} iteratee The iteratee to transform keys.
-   * @param {Object} accumulator The initial aggregated object.
-   * @returns {Function} Returns `accumulator`.
-   */
-  function arrayAggregator(array, setter, iteratee, accumulator) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      var value = array[index];
-      setter(accumulator, value, iteratee(value), array);
-    }
-    return accumulator;
-  }
-
-  /**
-   * A specialized version of `_.forEach` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns `array`.
-   */
-  function arrayEach(array, iteratee) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (iteratee(array[index], index, array) === false) {
-        break;
-      }
-    }
-    return array;
-  }
-
-  /**
-   * A specialized version of `_.forEachRight` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns `array`.
-   */
-  function arrayEachRight(array, iteratee) {
-    var length = array == null ? 0 : array.length;
-
-    while (length--) {
-      if (iteratee(array[length], length, array) === false) {
-        break;
-      }
-    }
-    return array;
-  }
-
-  /**
-   * A specialized version of `_.every` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} predicate The function invoked per iteration.
-   * @returns {boolean} Returns `true` if all elements pass the predicate check,
-   *  else `false`.
-   */
-  function arrayEvery(array, predicate) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (!predicate(array[index], index, array)) {
-        return false;
-      }
-    }
-    return true;
-  }
-
-  /**
-   * A specialized version of `_.filter` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} predicate The function invoked per iteration.
-   * @returns {Array} Returns the new filtered array.
-   */
-  function arrayFilter(array, predicate) {
-    var index = -1,
-        length = array == null ? 0 : array.length,
-        resIndex = 0,
-        result = [];
-
-    while (++index < length) {
-      var value = array[index];
-      if (predicate(value, index, array)) {
-        result[resIndex++] = value;
-      }
-    }
-    return result;
-  }
-
-  /**
-   * A specialized version of `_.includes` for arrays without support for
-   * specifying an index to search from.
-   *
-   * @private
-   * @param {Array} [array] The array to inspect.
-   * @param {*} target The value to search for.
-   * @returns {boolean} Returns `true` if `target` is found, else `false`.
-   */
-  function arrayIncludes(array, value) {
-    var length = array == null ? 0 : array.length;
-    return !!length && baseIndexOf(array, value, 0) > -1;
-  }
-
-  /**
-   * This function is like `arrayIncludes` except that it accepts a comparator.
-   *
-   * @private
-   * @param {Array} [array] The array to inspect.
-   * @param {*} target The value to search for.
-   * @param {Function} comparator The comparator invoked per element.
-   * @returns {boolean} Returns `true` if `target` is found, else `false`.
-   */
-  function arrayIncludesWith(array, value, comparator) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (comparator(value, array[index])) {
-        return true;
-      }
-    }
-    return false;
-  }
-
-  /**
-   * A specialized version of `_.map` for arrays without support for iteratee
-   * shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns the new mapped array.
-   */
-  function arrayMap(array, iteratee) {
-    var index = -1,
-        length = array == null ? 0 : array.length,
-        result = Array(length);
-
-    while (++index < length) {
-      result[index] = iteratee(array[index], index, array);
-    }
-    return result;
-  }
-
-  /**
-   * Appends the elements of `values` to `array`.
-   *
-   * @private
-   * @param {Array} array The array to modify.
-   * @param {Array} values The values to append.
-   * @returns {Array} Returns `array`.
-   */
-  function arrayPush(array, values) {
-    var index = -1,
-        length = values.length,
-        offset = array.length;
-
-    while (++index < length) {
-      array[offset + index] = values[index];
-    }
-    return array;
-  }
-
-  /**
-   * A specialized version of `_.reduce` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @param {*} [accumulator] The initial value.
-   * @param {boolean} [initAccum] Specify using the first element of `array` as
-   *  the initial value.
-   * @returns {*} Returns the accumulated value.
-   */
-  function arrayReduce(array, iteratee, accumulator, initAccum) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    if (initAccum && length) {
-      accumulator = array[++index];
-    }
-    while (++index < length) {
-      accumulator = iteratee(accumulator, array[index], index, array);
-    }
-    return accumulator;
-  }
-
-  /**
-   * A specialized version of `_.reduceRight` for arrays without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @param {*} [accumulator] The initial value.
-   * @param {boolean} [initAccum] Specify using the last element of `array` as
-   *  the initial value.
-   * @returns {*} Returns the accumulated value.
-   */
-  function arrayReduceRight(array, iteratee, accumulator, initAccum) {
-    var length = array == null ? 0 : array.length;
-    if (initAccum && length) {
-      accumulator = array[--length];
-    }
-    while (length--) {
-      accumulator = iteratee(accumulator, array[length], length, array);
-    }
-    return accumulator;
-  }
-
-  /**
-   * A specialized version of `_.some` for arrays without support for iteratee
-   * shorthands.
-   *
-   * @private
-   * @param {Array} [array] The array to iterate over.
-   * @param {Function} predicate The function invoked per iteration.
-   * @returns {boolean} Returns `true` if any element passes the predicate check,
-   *  else `false`.
-   */
-  function arraySome(array, predicate) {
-    var index = -1,
-        length = array == null ? 0 : array.length;
-
-    while (++index < length) {
-      if (predicate(array[index], index, array)) {
-        return true;
-      }
-    }
-    return false;
-  }
-
-  /**
-   * Gets the size of an ASCII `string`.
-   *
-   * @private
-   * @param {string} string The string inspect.
-   * @returns {number} Returns the string size.
-   */
-  var asciiSize = baseProperty('length');
-
-  /**
-   * Converts an ASCII `string` to an array.
-   *
-   * @private
-   * @param {string} string The string to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function asciiToArray(string) {
-    return string.split('');
-  }
-
-  /**
-   * Splits an ASCII `string` into an array of its words.
-   *
-   * @private
-   * @param {string} The string to inspect.
-   * @returns {Array} Returns the words of `string`.
-   */
-  function asciiWords(string) {
-    return string.match(reAsciiWord) || [];
-  }
-
-  /**
-   * The base implementation of methods like `_.findKey` and `_.findLastKey`,
-   * without support for iteratee shorthands, which iterates over `collection`
-   * using `eachFunc`.
-   *
-   * @private
-   * @param {Array|Object} collection The collection to inspect.
-   * @param {Function} predicate The function invoked per iteration.
-   * @param {Function} eachFunc The function to iterate over `collection`.
-   * @returns {*} Returns the found element or its key, else `undefined`.
-   */
-  function baseFindKey(collection, predicate, eachFunc) {
-    var result;
-    eachFunc(collection, function(value, key, collection) {
-      if (predicate(value, key, collection)) {
-        result = key;
-        return false;
-      }
-    });
-    return result;
-  }
-
-  /**
-   * The base implementation of `_.findIndex` and `_.findLastIndex` without
-   * support for iteratee shorthands.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {Function} predicate The function invoked per iteration.
-   * @param {number} fromIndex The index to search from.
-   * @param {boolean} [fromRight] Specify iterating from right to left.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function baseFindIndex(array, predicate, fromIndex, fromRight) {
-    var length = array.length,
-        index = fromIndex + (fromRight ? 1 : -1);
-
-    while ((fromRight ? index-- : ++index < length)) {
-      if (predicate(array[index], index, array)) {
-        return index;
-      }
-    }
-    return -1;
-  }
-
-  /**
-   * The base implementation of `_.indexOf` without `fromIndex` bounds checks.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function baseIndexOf(array, value, fromIndex) {
-    return value === value
-      ? strictIndexOf(array, value, fromIndex)
-      : baseFindIndex(array, baseIsNaN, fromIndex);
-  }
-
-  /**
-   * This function is like `baseIndexOf` except that it accepts a comparator.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @param {Function} comparator The comparator invoked per element.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function baseIndexOfWith(array, value, fromIndex, comparator) {
-    var index = fromIndex - 1,
-        length = array.length;
-
-    while (++index < length) {
-      if (comparator(array[index], value)) {
-        return index;
-      }
-    }
-    return -1;
-  }
-
-  /**
-   * The base implementation of `_.isNaN` without support for number objects.
-   *
-   * @private
-   * @param {*} value The value to check.
-   * @returns {boolean} Returns `true` if `value` is `NaN`, else `false`.
-   */
-  function baseIsNaN(value) {
-    return value !== value;
-  }
-
-  /**
-   * The base implementation of `_.mean` and `_.meanBy` without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} array The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {number} Returns the mean.
-   */
-  function baseMean(array, iteratee) {
-    var length = array == null ? 0 : array.length;
-    return length ? (baseSum(array, iteratee) / length) : NAN;
-  }
-
-  /**
-   * The base implementation of `_.property` without support for deep paths.
-   *
-   * @private
-   * @param {string} key The key of the property to get.
-   * @returns {Function} Returns the new accessor function.
-   */
-  function baseProperty(key) {
-    return function(object) {
-      return object == null ? undefined : object[key];
-    };
-  }
-
-  /**
-   * The base implementation of `_.propertyOf` without support for deep paths.
-   *
-   * @private
-   * @param {Object} object The object to query.
-   * @returns {Function} Returns the new accessor function.
-   */
-  function basePropertyOf(object) {
-    return function(key) {
-      return object == null ? undefined : object[key];
-    };
-  }
-
-  /**
-   * The base implementation of `_.reduce` and `_.reduceRight`, without support
-   * for iteratee shorthands, which iterates over `collection` using `eachFunc`.
-   *
-   * @private
-   * @param {Array|Object} collection The collection to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @param {*} accumulator The initial value.
-   * @param {boolean} initAccum Specify using the first or last element of
-   *  `collection` as the initial value.
-   * @param {Function} eachFunc The function to iterate over `collection`.
-   * @returns {*} Returns the accumulated value.
-   */
-  function baseReduce(collection, iteratee, accumulator, initAccum, eachFunc) {
-    eachFunc(collection, function(value, index, collection) {
-      accumulator = initAccum
-        ? (initAccum = false, value)
-        : iteratee(accumulator, value, index, collection);
-    });
-    return accumulator;
-  }
-
-  /**
-   * The base implementation of `_.sortBy` which uses `comparer` to define the
-   * sort order of `array` and replaces criteria objects with their corresponding
-   * values.
-   *
-   * @private
-   * @param {Array} array The array to sort.
-   * @param {Function} comparer The function to define sort order.
-   * @returns {Array} Returns `array`.
-   */
-  function baseSortBy(array, comparer) {
-    var length = array.length;
-
-    array.sort(comparer);
-    while (length--) {
-      array[length] = array[length].value;
-    }
-    return array;
-  }
-
-  /**
-   * The base implementation of `_.sum` and `_.sumBy` without support for
-   * iteratee shorthands.
-   *
-   * @private
-   * @param {Array} array The array to iterate over.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {number} Returns the sum.
-   */
-  function baseSum(array, iteratee) {
-    var result,
-        index = -1,
-        length = array.length;
-
-    while (++index < length) {
-      var current = iteratee(array[index]);
-      if (current !== undefined) {
-        result = result === undefined ? current : (result + current);
-      }
-    }
-    return result;
-  }
-
-  /**
-   * The base implementation of `_.times` without support for iteratee shorthands
-   * or max array length checks.
-   *
-   * @private
-   * @param {number} n The number of times to invoke `iteratee`.
-   * @param {Function} iteratee The function invoked per iteration.
-   * @returns {Array} Returns the array of results.
-   */
-  function baseTimes(n, iteratee) {
-    var index = -1,
-        result = Array(n);
-
-    while (++index < n) {
-      result[index] = iteratee(index);
-    }
-    return result;
-  }
-
-  /**
-   * The base implementation of `_.toPairs` and `_.toPairsIn` which creates an array
-   * of key-value pairs for `object` corresponding to the property names of `props`.
-   *
-   * @private
-   * @param {Object} object The object to query.
-   * @param {Array} props The property names to get values for.
-   * @returns {Object} Returns the key-value pairs.
-   */
-  function baseToPairs(object, props) {
-    return arrayMap(props, function(key) {
-      return [key, object[key]];
-    });
-  }
-
-  /**
-   * The base implementation of `_.unary` without support for storing metadata.
-   *
-   * @private
-   * @param {Function} func The function to cap arguments for.
-   * @returns {Function} Returns the new capped function.
-   */
-  function baseUnary(func) {
-    return function(value) {
-      return func(value);
-    };
-  }
-
-  /**
-   * The base implementation of `_.values` and `_.valuesIn` which creates an
-   * array of `object` property values corresponding to the property names
-   * of `props`.
-   *
-   * @private
-   * @param {Object} object The object to query.
-   * @param {Array} props The property names to get values for.
-   * @returns {Object} Returns the array of property values.
-   */
-  function baseValues(object, props) {
-    return arrayMap(props, function(key) {
-      return object[key];
-    });
-  }
-
-  /**
-   * Checks if a `cache` value for `key` exists.
-   *
-   * @private
-   * @param {Object} cache The cache to query.
-   * @param {string} key The key of the entry to check.
-   * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-   */
-  function cacheHas(cache, key) {
-    return cache.has(key);
-  }
-
-  /**
-   * Used by `_.trim` and `_.trimStart` to get the index of the first string symbol
-   * that is not found in the character symbols.
-   *
-   * @private
-   * @param {Array} strSymbols The string symbols to inspect.
-   * @param {Array} chrSymbols The character symbols to find.
-   * @returns {number} Returns the index of the first unmatched string symbol.
-   */
-  function charsStartIndex(strSymbols, chrSymbols) {
-    var index = -1,
-        length = strSymbols.length;
-
-    while (++index < length && baseIndexOf(chrSymbols, strSymbols[index], 0) > -1) {}
-    return index;
-  }
-
-  /**
-   * Used by `_.trim` and `_.trimEnd` to get the index of the last string symbol
-   * that is not found in the character symbols.
-   *
-   * @private
-   * @param {Array} strSymbols The string symbols to inspect.
-   * @param {Array} chrSymbols The character symbols to find.
-   * @returns {number} Returns the index of the last unmatched string symbol.
-   */
-  function charsEndIndex(strSymbols, chrSymbols) {
-    var index = strSymbols.length;
-
-    while (index-- && baseIndexOf(chrSymbols, strSymbols[index], 0) > -1) {}
-    return index;
-  }
-
-  /**
-   * Gets the number of `placeholder` occurrences in `array`.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} placeholder The placeholder to search for.
-   * @returns {number} Returns the placeholder count.
-   */
-  function countHolders(array, placeholder) {
-    var length = array.length,
-        result = 0;
-
-    while (length--) {
-      if (array[length] === placeholder) {
-        ++result;
-      }
-    }
-    return result;
-  }
-
-  /**
-   * Used by `_.deburr` to convert Latin-1 Supplement and Latin Extended-A
-   * letters to basic Latin letters.
-   *
-   * @private
-   * @param {string} letter The matched letter to deburr.
-   * @returns {string} Returns the deburred letter.
-   */
-  var deburrLetter = basePropertyOf(deburredLetters);
-
-  /**
-   * Used by `_.escape` to convert characters to HTML entities.
-   *
-   * @private
-   * @param {string} chr The matched character to escape.
-   * @returns {string} Returns the escaped character.
-   */
-  var escapeHtmlChar = basePropertyOf(htmlEscapes);
-
-  /**
-   * Used by `_.template` to escape characters for inclusion in compiled string literals.
-   *
-   * @private
-   * @param {string} chr The matched character to escape.
-   * @returns {string} Returns the escaped character.
-   */
-  function escapeStringChar(chr) {
-    return '\\' + stringEscapes[chr];
-  }
-
-  /**
-   * Gets the value at `key` of `object`.
-   *
-   * @private
-   * @param {Object} [object] The object to query.
-   * @param {string} key The key of the property to get.
-   * @returns {*} Returns the property value.
-   */
-  function getValue(object, key) {
-    return object == null ? undefined : object[key];
-  }
-
-  /**
-   * Checks if `string` contains Unicode symbols.
-   *
-   * @private
-   * @param {string} string The string to inspect.
-   * @returns {boolean} Returns `true` if a symbol is found, else `false`.
-   */
-  function hasUnicode(string) {
-    return reHasUnicode.test(string);
-  }
-
-  /**
-   * Checks if `string` contains a word composed of Unicode symbols.
-   *
-   * @private
-   * @param {string} string The string to inspect.
-   * @returns {boolean} Returns `true` if a word is found, else `false`.
-   */
-  function hasUnicodeWord(string) {
-    return reHasUnicodeWord.test(string);
-  }
-
-  /**
-   * Converts `iterator` to an array.
-   *
-   * @private
-   * @param {Object} iterator The iterator to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function iteratorToArray(iterator) {
-    var data,
-        result = [];
-
-    while (!(data = iterator.next()).done) {
-      result.push(data.value);
-    }
-    return result;
-  }
-
-  /**
-   * Converts `map` to its key-value pairs.
-   *
-   * @private
-   * @param {Object} map The map to convert.
-   * @returns {Array} Returns the key-value pairs.
-   */
-  function mapToArray(map) {
-    var index = -1,
-        result = Array(map.size);
-
-    map.forEach(function(value, key) {
-      result[++index] = [key, value];
-    });
-    return result;
-  }
-
-  /**
-   * Creates a unary function that invokes `func` with its argument transformed.
-   *
-   * @private
-   * @param {Function} func The function to wrap.
-   * @param {Function} transform The argument transform.
-   * @returns {Function} Returns the new function.
-   */
-  function overArg(func, transform) {
-    return function(arg) {
-      return func(transform(arg));
-    };
-  }
-
-  /**
-   * Replaces all `placeholder` elements in `array` with an internal placeholder
-   * and returns an array of their indexes.
-   *
-   * @private
-   * @param {Array} array The array to modify.
-   * @param {*} placeholder The placeholder to replace.
-   * @returns {Array} Returns the new array of placeholder indexes.
-   */
-  function replaceHolders(array, placeholder) {
-    var index = -1,
-        length = array.length,
-        resIndex = 0,
-        result = [];
-
-    while (++index < length) {
-      var value = array[index];
-      if (value === placeholder || value === PLACEHOLDER) {
-        array[index] = PLACEHOLDER;
-        result[resIndex++] = index;
-      }
-    }
-    return result;
-  }
-
-  /**
-   * Converts `set` to an array of its values.
-   *
-   * @private
-   * @param {Object} set The set to convert.
-   * @returns {Array} Returns the values.
-   */
-  function setToArray(set) {
-    var index = -1,
-        result = Array(set.size);
-
-    set.forEach(function(value) {
-      result[++index] = value;
-    });
-    return result;
-  }
-
-  /**
-   * Converts `set` to its value-value pairs.
-   *
-   * @private
-   * @param {Object} set The set to convert.
-   * @returns {Array} Returns the value-value pairs.
-   */
-  function setToPairs(set) {
-    var index = -1,
-        result = Array(set.size);
-
-    set.forEach(function(value) {
-      result[++index] = [value, value];
-    });
-    return result;
-  }
-
-  /**
-   * A specialized version of `_.indexOf` which performs strict equality
-   * comparisons of values, i.e. `===`.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function strictIndexOf(array, value, fromIndex) {
-    var index = fromIndex - 1,
-        length = array.length;
-
-    while (++index < length) {
-      if (array[index] === value) {
-        return index;
-      }
-    }
-    return -1;
-  }
-
-  /**
-   * A specialized version of `_.lastIndexOf` which performs strict equality
-   * comparisons of values, i.e. `===`.
-   *
-   * @private
-   * @param {Array} array The array to inspect.
-   * @param {*} value The value to search for.
-   * @param {number} fromIndex The index to search from.
-   * @returns {number} Returns the index of the matched value, else `-1`.
-   */
-  function strictLastIndexOf(array, value, fromIndex) {
-    var index = fromIndex + 1;
-    while (index--) {
-      if (array[index] === value) {
-        return index;
-      }
-    }
-    return index;
-  }
-
-  /**
-   * Gets the number of symbols in `string`.
-   *
-   * @private
-   * @param {string} string The string to inspect.
-   * @returns {number} Returns the string size.
-   */
-  function stringSize(string) {
-    return hasUnicode(string)
-      ? unicodeSize(string)
-      : asciiSize(string);
-  }
-
-  /**
-   * Converts `string` to an array.
-   *
-   * @private
-   * @param {string} string The string to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function stringToArray(string) {
-    return hasUnicode(string)
-      ? unicodeToArray(string)
-      : asciiToArray(string);
-  }
-
-  /**
-   * Used by `_.unescape` to convert HTML entities to characters.
-   *
-   * @private
-   * @param {string} chr The matched character to unescape.
-   * @returns {string} Returns the unescaped character.
-   */
-  var unescapeHtmlChar = basePropertyOf(htmlUnescapes);
-
-  /**
-   * Gets the size of a Unicode `string`.
-   *
-   * @private
-   * @param {string} string The string inspect.
-   * @returns {number} Returns the string size.
-   */
-  function unicodeSize(string) {
-    var result = reUnicode.lastIndex = 0;
-    while (reUnicode.test(string)) {
-      ++result;
-    }
-    return result;
-  }
-
-  /**
-   * Converts a Unicode `string` to an array.
-   *
-   * @private
-   * @param {string} string The string to convert.
-   * @returns {Array} Returns the converted array.
-   */
-  function unicodeToArray(string) {
-    return string.match(reUnicode) || [];
-  }
-
-  /**
-   * Splits a Unicode `string` into an array of its words.
-   *
-   * @private
-   * @param {string} The string to inspect.
-   * @returns {Array} Returns the words of `string`.
-   */
-  function unicodeWords(string) {
-    return string.match(reUnicodeWord) || [];
-  }
-
-  /*--------------------------------------------------------------------------*/
-
-  /**
-   * Create a new pristine `lodash` function using the `context` object.
-   *
-   * @static
-   * @memberOf _
-   * @since 1.1.0
-   * @category Util
-   * @param {Object} [context=root] The context object.
-   * @returns {Function} Returns a new `lodash` function.
-   * @example
-   *
-   * _.mixin({ 'foo': _.constant('foo') });
-   *
-   * var lodash = _.runInContext();
-   * lodash.mixin({ 'bar': lodash.constant('bar') });
-   *
-   * _.isFunction(_.foo);
-   * // => true
-   * _.isFunction(_.bar);
-   * // => false
-   *
-   * lodash.isFunction(lodash.foo);
-   * // => false
-   * lodash.isFunction(lodash.bar);
-   * // => true
-   *
-   * // Create a suped-up `defer` in Node.js.
-   * var defer = _.runInContext({ 'setTimeout': setImmediate }).defer;
-   */
-  var runInContext = (function runInContext(context) {
-    context = context == null ? root : _.defaults(root.Object(), context, _.pick(root, contextProps));
-
-    /** Built-in constructor references. */
-    var Array = context.Array,
-        Date = context.Date,
-        Error = context.Error,
-        Function = context.Function,
-        Math = context.Math,
-        Object = context.Object,
-        RegExp = context.RegExp,
-        String = context.String,
-        TypeError = context.TypeError;
-
-    /** Used for built-in method references. */
-    var arrayProto = Array.prototype,
-        funcProto = Function.prototype,
-        objectProto = Object.prototype;
-
-    /** Used to detect overreaching core-js shims. */
-    var coreJsData = context['__core-js_shared__'];
-
-    /** Used to resolve the decompiled source of functions. */
-    var funcToString = funcProto.toString;
-
-    /** Used to check objects for own properties. */
-    var hasOwnProperty = objectProto.hasOwnProperty;
-
-    /** Used to generate unique IDs. */
-    var idCounter = 0;
-
-    /** Used to detect methods masquerading as native. */
-    var maskSrcKey = (function() {
-      var uid = /[^.]+$/.exec(coreJsData && coreJsData.keys && coreJsData.keys.IE_PROTO || '');
-      return uid ? ('Symbol(src)_1.' + uid) : '';
-    }());
-
-    /**
-     * Used to resolve the
-     * [`toStringTag`](http://ecma-international.org/ecma-262/7.0/#sec-object.prototype.tostring)
-     * of values.
-     */
-    var nativeObjectToString = objectProto.toString;
-
-    /** Used to infer the `Object` constructor. */
-    var objectCtorString = funcToString.call(Object);
-
-    /** Used to restore the original `_` reference in `_.noConflict`. */
-    var oldDash = root._;
-
-    /** Used to detect if a method is native. */
-    var reIsNative = RegExp('^' +
-      funcToString.call(hasOwnProperty).replace(reRegExpChar, '\\$&')
-      .replace(/hasOwnProperty|(function).*?(?=\\\()| for .+?(?=\\\])/g, '$1.*?') + '$'
-    );
-
-    /** Built-in value references. */
-    var Buffer = moduleExports ? context.Buffer : undefined,
-        Symbol = context.Symbol,
-        Uint8Array = context.Uint8Array,
-        allocUnsafe = Buffer ? Buffer.allocUnsafe : undefined,
-        getPrototype = overArg(Object.getPrototypeOf, Object),
-        objectCreate = Object.create,
-        propertyIsEnumerable = objectProto.propertyIsEnumerable,
-        splice = arrayProto.splice,
-        spreadableSymbol = Symbol ? Symbol.isConcatSpreadable : undefined,
-        symIterator = Symbol ? Symbol.iterator : undefined,
-        symToStringTag = Symbol ? Symbol.toStringTag : undefined;
-
-    var defineProperty = (function() {
-      try {
-        var func = getNative(Object, 'defineProperty');
-        func({}, '', {});
-        return func;
-      } catch (e) {}
-    }());
-
-    /** Mocked built-ins. */
-    var ctxClearTimeout = context.clearTimeout !== root.clearTimeout && context.clearTimeout,
-        ctxNow = Date && Date.now !== root.Date.now && Date.now,
-        ctxSetTimeout = context.setTimeout !== root.setTimeout && context.setTimeout;
-
-    /* Built-in method references for those with the same name as other `lodash` methods. */
-    var nativeCeil = Math.ceil,
-        nativeFloor = Math.floor,
-        nativeGetSymbols = Object.getOwnPropertySymbols,
-        nativeIsBuffer = Buffer ? Buffer.isBuffer : undefined,
-        nativeIsFinite = context.isFinite,
-        nativeJoin = arrayProto.join,
-        nativeKeys = overArg(Object.keys, Object),
-        nativeMax = Math.max,
-        nativeMin = Math.min,
-        nativeNow = Date.now,
-        nativeParseInt = context.parseInt,
-        nativeRandom = Math.random,
-        nativeReverse = arrayProto.reverse;
-
-    /* Built-in method references that are verified to be native. */
-    var DataView = getNative(context, 'DataView'),
-        Map = getNative(context, 'Map'),
-        Promise = getNative(context, 'Promise'),
-        Set = getNative(context, 'Set'),
-        WeakMap = getNative(context, 'WeakMap'),
-        nativeCreate = getNative(Object, 'create');
-
-    /** Used to store function metadata. */
-    var metaMap = WeakMap && new WeakMap;
-
-    /** Used to lookup unminified function names. */
-    var realNames = {};
-
-    /** Used to detect maps, sets, and weakmaps. */
-    var dataViewCtorString = toSource(DataView),
-        mapCtorString = toSource(Map),
-        promiseCtorString = toSource(Promise),
-        setCtorString = toSource(Set),
-        weakMapCtorString = toSource(WeakMap);
-
-    /** Used to convert symbols to primitives and strings. */
-    var symbolProto = Symbol ? Symbol.prototype : undefined,
-        symbolValueOf = symbolProto ? symbolProto.valueOf : undefined,
-        symbolToString = symbolProto ? symbolProto.toString : undefined;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a `lodash` object which wraps `value` to enable implicit method
-     * chain sequences. Methods that operate on and return arrays, collections,
-     * and functions can be chained together. Methods that retrieve a single value
-     * or may return a primitive value will automatically end the chain sequence
-     * and return the unwrapped value. Otherwise, the value must be unwrapped
-     * with `_#value`.
-     *
-     * Explicit chain sequences, which must be unwrapped with `_#value`, may be
-     * enabled using `_.chain`.
-     *
-     * The execution of chained methods is lazy, that is, it's deferred until
-     * `_#value` is implicitly or explicitly called.
-     *
-     * Lazy evaluation allows several methods to support shortcut fusion.
-     * Shortcut fusion is an optimization to merge iteratee calls; this avoids
-     * the creation of intermediate arrays and can greatly reduce the number of
-     * iteratee executions. Sections of a chain sequence qualify for shortcut
-     * fusion if the section is applied to an array and iteratees accept only
-     * one argument. The heuristic for whether a section qualifies for shortcut
-     * fusion is subject to change.
-     *
-     * Chaining is supported in custom builds as long as the `_#value` method is
-     * directly or indirectly included in the build.
-     *
-     * In addition to lodash methods, wrappers have `Array` and `String` methods.
-     *
-     * The wrapper `Array` methods are:
-     * `concat`, `join`, `pop`, `push`, `shift`, `sort`, `splice`, and `unshift`
-     *
-     * The wrapper `String` methods are:
-     * `replace` and `split`
-     *
-     * The wrapper methods that support shortcut fusion are:
-     * `at`, `compact`, `drop`, `dropRight`, `dropWhile`, `filter`, `find`,
-     * `findLast`, `head`, `initial`, `last`, `map`, `reject`, `reverse`, `slice`,
-     * `tail`, `take`, `takeRight`, `takeRightWhile`, `takeWhile`, and `toArray`
-     *
-     * The chainable wrapper methods are:
-     * `after`, `ary`, `assign`, `assignIn`, `assignInWith`, `assignWith`, `at`,
-     * `before`, `bind`, `bindAll`, `bindKey`, `castArray`, `chain`, `chunk`,
-     * `commit`, `compact`, `concat`, `conforms`, `constant`, `countBy`, `create`,
-     * `curry`, `debounce`, `defaults`, `defaultsDeep`, `defer`, `delay`,
-     * `difference`, `differenceBy`, `differenceWith`, `drop`, `dropRight`,
-     * `dropRightWhile`, `dropWhile`, `extend`, `extendWith`, `fill`, `filter`,
-     * `flatMap`, `flatMapDeep`, `flatMapDepth`, `flatten`, `flattenDeep`,
-     * `flattenDepth`, `flip`, `flow`, `flowRight`, `fromPairs`, `functions`,
-     * `functionsIn`, `groupBy`, `initial`, `intersection`, `intersectionBy`,
-     * `intersectionWith`, `invert`, `invertBy`, `invokeMap`, `iteratee`, `keyBy`,
-     * `keys`, `keysIn`, `map`, `mapKeys`, `mapValues`, `matches`, `matchesProperty`,
-     * `memoize`, `merge`, `mergeWith`, `method`, `methodOf`, `mixin`, `negate`,
-     * `nthArg`, `omit`, `omitBy`, `once`, `orderBy`, `over`, `overArgs`,
-     * `overEvery`, `overSome`, `partial`, `partialRight`, `partition`, `pick`,
-     * `pickBy`, `plant`, `property`, `propertyOf`, `pull`, `pullAll`, `pullAllBy`,
-     * `pullAllWith`, `pullAt`, `push`, `range`, `rangeRight`, `rearg`, `reject`,
-     * `remove`, `rest`, `reverse`, `sampleSize`, `set`, `setWith`, `shuffle`,
-     * `slice`, `sort`, `sortBy`, `splice`, `spread`, `tail`, `take`, `takeRight`,
-     * `takeRightWhile`, `takeWhile`, `tap`, `throttle`, `thru`, `toArray`,
-     * `toPairs`, `toPairsIn`, `toPath`, `toPlainObject`, `transform`, `unary`,
-     * `union`, `unionBy`, `unionWith`, `uniq`, `uniqBy`, `uniqWith`, `unset`,
-     * `unshift`, `unzip`, `unzipWith`, `update`, `updateWith`, `values`,
-     * `valuesIn`, `without`, `wrap`, `xor`, `xorBy`, `xorWith`, `zip`,
-     * `zipObject`, `zipObjectDeep`, and `zipWith`
-     *
-     * The wrapper methods that are **not** chainable by default are:
-     * `add`, `attempt`, `camelCase`, `capitalize`, `ceil`, `clamp`, `clone`,
-     * `cloneDeep`, `cloneDeepWith`, `cloneWith`, `conformsTo`, `deburr`,
-     * `defaultTo`, `divide`, `each`, `eachRight`, `endsWith`, `eq`, `escape`,
-     * `escapeRegExp`, `every`, `find`, `findIndex`, `findKey`, `findLast`,
-     * `findLastIndex`, `findLastKey`, `first`, `floor`, `forEach`, `forEachRight`,
-     * `forIn`, `forInRight`, `forOwn`, `forOwnRight`, `get`, `gt`, `gte`, `has`,
-     * `hasIn`, `head`, `identity`, `includes`, `indexOf`, `inRange`, `invoke`,
-     * `isArguments`, `isArray`, `isArrayBuffer`, `isArrayLike`, `isArrayLikeObject`,
-     * `isBoolean`, `isBuffer`, `isDate`, `isElement`, `isEmpty`, `isEqual`,
-     * `isEqualWith`, `isError`, `isFinite`, `isFunction`, `isInteger`, `isLength`,
-     * `isMap`, `isMatch`, `isMatchWith`, `isNaN`, `isNative`, `isNil`, `isNull`,
-     * `isNumber`, `isObject`, `isObjectLike`, `isPlainObject`, `isRegExp`,
-     * `isSafeInteger`, `isSet`, `isString`, `isUndefined`, `isTypedArray`,
-     * `isWeakMap`, `isWeakSet`, `join`, `kebabCase`, `last`, `lastIndexOf`,
-     * `lowerCase`, `lowerFirst`, `lt`, `lte`, `max`, `maxBy`, `mean`, `meanBy`,
-     * `min`, `minBy`, `multiply`, `noConflict`, `noop`, `now`, `nth`, `pad`,
-     * `padEnd`, `padStart`, `parseInt`, `pop`, `random`, `reduce`, `reduceRight`,
-     * `repeat`, `result`, `round`, `runInContext`, `sample`, `shift`, `size`,
-     * `snakeCase`, `some`, `sortedIndex`, `sortedIndexBy`, `sortedLastIndex`,
-     * `sortedLastIndexBy`, `startCase`, `startsWith`, `stubArray`, `stubFalse`,
-     * `stubObject`, `stubString`, `stubTrue`, `subtract`, `sum`, `sumBy`,
-     * `template`, `times`, `toFinite`, `toInteger`, `toJSON`, `toLength`,
-     * `toLower`, `toNumber`, `toSafeInteger`, `toString`, `toUpper`, `trim`,
-     * `trimEnd`, `trimStart`, `truncate`, `unescape`, `uniqueId`, `upperCase`,
-     * `upperFirst`, `value`, and `words`
-     *
-     * @name _
-     * @constructor
-     * @category Seq
-     * @param {*} value The value to wrap in a `lodash` instance.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var wrapped = _([1, 2, 3]);
-     *
-     * // Returns an unwrapped value.
-     * wrapped.reduce(_.add);
-     * // => 6
-     *
-     * // Returns a wrapped value.
-     * var squares = wrapped.map(square);
-     *
-     * _.isArray(squares);
-     * // => false
-     *
-     * _.isArray(squares.value());
-     * // => true
-     */
-    function lodash(value) {
-      if (isObjectLike(value) && !isArray(value) && !(value instanceof LazyWrapper)) {
-        if (value instanceof LodashWrapper) {
-          return value;
-        }
-        if (hasOwnProperty.call(value, '__wrapped__')) {
-          return wrapperClone(value);
-        }
-      }
-      return new LodashWrapper(value);
-    }
-
-    /**
-     * The base implementation of `_.create` without support for assigning
-     * properties to the created object.
-     *
-     * @private
-     * @param {Object} proto The object to inherit from.
-     * @returns {Object} Returns the new object.
-     */
-    var baseCreate = (function() {
-      function object() {}
-      return function(proto) {
-        if (!isObject(proto)) {
-          return {};
-        }
-        if (objectCreate) {
-          return objectCreate(proto);
-        }
-        object.prototype = proto;
-        var result = new object;
-        object.prototype = undefined;
-        return result;
-      };
-    }());
-
-    /**
-     * The function whose prototype chain sequence wrappers inherit from.
-     *
-     * @private
-     */
-    function baseLodash() {
-      // No operation performed.
-    }
-
-    /**
-     * The base constructor for creating `lodash` wrapper objects.
-     *
-     * @private
-     * @param {*} value The value to wrap.
-     * @param {boolean} [chainAll] Enable explicit method chain sequences.
-     */
-    function LodashWrapper(value, chainAll) {
-      this.__wrapped__ = value;
-      this.__actions__ = [];
-      this.__chain__ = !!chainAll;
-      this.__index__ = 0;
-      this.__values__ = undefined;
-    }
-
-    /**
-     * By default, the template delimiters used by lodash are like those in
-     * embedded Ruby (ERB) as well as ES2015 template strings. Change the
-     * following template settings to use alternative delimiters.
-     *
-     * @static
-     * @memberOf _
-     * @type {Object}
-     */
-    lodash.templateSettings = {
-
-      /**
-       * Used to detect `data` property values to be HTML-escaped.
-       *
-       * @memberOf _.templateSettings
-       * @type {RegExp}
-       */
-      'escape': reEscape,
-
-      /**
-       * Used to detect code to be evaluated.
-       *
-       * @memberOf _.templateSettings
-       * @type {RegExp}
-       */
-      'evaluate': reEvaluate,
-
-      /**
-       * Used to detect `data` property values to inject.
-       *
-       * @memberOf _.templateSettings
-       * @type {RegExp}
-       */
-      'interpolate': reInterpolate,
-
-      /**
-       * Used to reference the data object in the template text.
-       *
-       * @memberOf _.templateSettings
-       * @type {string}
-       */
-      'variable': '',
-
-      /**
-       * Used to import variables into the compiled template.
-       *
-       * @memberOf _.templateSettings
-       * @type {Object}
-       */
-      'imports': {
-
-        /**
-         * A reference to the `lodash` function.
-         *
-         * @memberOf _.templateSettings.imports
-         * @type {Function}
-         */
-        '_': lodash
-      }
-    };
-
-    // Ensure wrappers are instances of `baseLodash`.
-    lodash.prototype = baseLodash.prototype;
-    lodash.prototype.constructor = lodash;
-
-    LodashWrapper.prototype = baseCreate(baseLodash.prototype);
-    LodashWrapper.prototype.constructor = LodashWrapper;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a lazy wrapper object which wraps `value` to enable lazy evaluation.
-     *
-     * @private
-     * @constructor
-     * @param {*} value The value to wrap.
-     */
-    function LazyWrapper(value) {
-      this.__wrapped__ = value;
-      this.__actions__ = [];
-      this.__dir__ = 1;
-      this.__filtered__ = false;
-      this.__iteratees__ = [];
-      this.__takeCount__ = MAX_ARRAY_LENGTH;
-      this.__views__ = [];
-    }
-
-    /**
-     * Creates a clone of the lazy wrapper object.
-     *
-     * @private
-     * @name clone
-     * @memberOf LazyWrapper
-     * @returns {Object} Returns the cloned `LazyWrapper` object.
-     */
-    function lazyClone() {
-      var result = new LazyWrapper(this.__wrapped__);
-      result.__actions__ = copyArray(this.__actions__);
-      result.__dir__ = this.__dir__;
-      result.__filtered__ = this.__filtered__;
-      result.__iteratees__ = copyArray(this.__iteratees__);
-      result.__takeCount__ = this.__takeCount__;
-      result.__views__ = copyArray(this.__views__);
-      return result;
-    }
-
-    /**
-     * Reverses the direction of lazy iteration.
-     *
-     * @private
-     * @name reverse
-     * @memberOf LazyWrapper
-     * @returns {Object} Returns the new reversed `LazyWrapper` object.
-     */
-    function lazyReverse() {
-      if (this.__filtered__) {
-        var result = new LazyWrapper(this);
-        result.__dir__ = -1;
-        result.__filtered__ = true;
-      } else {
-        result = this.clone();
-        result.__dir__ *= -1;
-      }
-      return result;
-    }
-
-    /**
-     * Extracts the unwrapped value from its lazy wrapper.
-     *
-     * @private
-     * @name value
-     * @memberOf LazyWrapper
-     * @returns {*} Returns the unwrapped value.
-     */
-    function lazyValue() {
-      var array = this.__wrapped__.value(),
-          dir = this.__dir__,
-          isArr = isArray(array),
-          isRight = dir < 0,
-          arrLength = isArr ? array.length : 0,
-          view = getView(0, arrLength, this.__views__),
-          start = view.start,
-          end = view.end,
-          length = end - start,
-          index = isRight ? end : (start - 1),
-          iteratees = this.__iteratees__,
-          iterLength = iteratees.length,
-          resIndex = 0,
-          takeCount = nativeMin(length, this.__takeCount__);
-
-      if (!isArr || (!isRight && arrLength == length && takeCount == length)) {
-        return baseWrapperValue(array, this.__actions__);
-      }
-      var result = [];
-
-      outer:
-      while (length-- && resIndex < takeCount) {
-        index += dir;
-
-        var iterIndex = -1,
-            value = array[index];
-
-        while (++iterIndex < iterLength) {
-          var data = iteratees[iterIndex],
-              iteratee = data.iteratee,
-              type = data.type,
-              computed = iteratee(value);
-
-          if (type == LAZY_MAP_FLAG) {
-            value = computed;
-          } else if (!computed) {
-            if (type == LAZY_FILTER_FLAG) {
-              continue outer;
-            } else {
-              break outer;
-            }
-          }
-        }
-        result[resIndex++] = value;
-      }
-      return result;
-    }
-
-    // Ensure `LazyWrapper` is an instance of `baseLodash`.
-    LazyWrapper.prototype = baseCreate(baseLodash.prototype);
-    LazyWrapper.prototype.constructor = LazyWrapper;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a hash object.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function Hash(entries) {
-      var index = -1,
-          length = entries == null ? 0 : entries.length;
-
-      this.clear();
-      while (++index < length) {
-        var entry = entries[index];
-        this.set(entry[0], entry[1]);
-      }
-    }
-
-    /**
-     * Removes all key-value entries from the hash.
-     *
-     * @private
-     * @name clear
-     * @memberOf Hash
-     */
-    function hashClear() {
-      this.__data__ = nativeCreate ? nativeCreate(null) : {};
-      this.size = 0;
-    }
-
-    /**
-     * Removes `key` and its value from the hash.
-     *
-     * @private
-     * @name delete
-     * @memberOf Hash
-     * @param {Object} hash The hash to modify.
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function hashDelete(key) {
-      var result = this.has(key) && delete this.__data__[key];
-      this.size -= result ? 1 : 0;
-      return result;
-    }
-
-    /**
-     * Gets the hash value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf Hash
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function hashGet(key) {
-      var data = this.__data__;
-      if (nativeCreate) {
-        var result = data[key];
-        return result === HASH_UNDEFINED ? undefined : result;
-      }
-      return hasOwnProperty.call(data, key) ? data[key] : undefined;
-    }
-
-    /**
-     * Checks if a hash value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf Hash
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function hashHas(key) {
-      var data = this.__data__;
-      return nativeCreate ? (data[key] !== undefined) : hasOwnProperty.call(data, key);
-    }
-
-    /**
-     * Sets the hash `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf Hash
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the hash instance.
-     */
-    function hashSet(key, value) {
-      var data = this.__data__;
-      this.size += this.has(key) ? 0 : 1;
-      data[key] = (nativeCreate && value === undefined) ? HASH_UNDEFINED : value;
-      return this;
-    }
-
-    // Add methods to `Hash`.
-    Hash.prototype.clear = hashClear;
-    Hash.prototype['delete'] = hashDelete;
-    Hash.prototype.get = hashGet;
-    Hash.prototype.has = hashHas;
-    Hash.prototype.set = hashSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an list cache object.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function ListCache(entries) {
-      var index = -1,
-          length = entries == null ? 0 : entries.length;
-
-      this.clear();
-      while (++index < length) {
-        var entry = entries[index];
-        this.set(entry[0], entry[1]);
-      }
-    }
-
-    /**
-     * Removes all key-value entries from the list cache.
-     *
-     * @private
-     * @name clear
-     * @memberOf ListCache
-     */
-    function listCacheClear() {
-      this.__data__ = [];
-      this.size = 0;
-    }
-
-    /**
-     * Removes `key` and its value from the list cache.
-     *
-     * @private
-     * @name delete
-     * @memberOf ListCache
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function listCacheDelete(key) {
-      var data = this.__data__,
-          index = assocIndexOf(data, key);
-
-      if (index < 0) {
-        return false;
-      }
-      var lastIndex = data.length - 1;
-      if (index == lastIndex) {
-        data.pop();
-      } else {
-        splice.call(data, index, 1);
-      }
-      --this.size;
-      return true;
-    }
-
-    /**
-     * Gets the list cache value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf ListCache
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function listCacheGet(key) {
-      var data = this.__data__,
-          index = assocIndexOf(data, key);
-
-      return index < 0 ? undefined : data[index][1];
-    }
-
-    /**
-     * Checks if a list cache value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf ListCache
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function listCacheHas(key) {
-      return assocIndexOf(this.__data__, key) > -1;
-    }
-
-    /**
-     * Sets the list cache `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf ListCache
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the list cache instance.
-     */
-    function listCacheSet(key, value) {
-      var data = this.__data__,
-          index = assocIndexOf(data, key);
-
-      if (index < 0) {
-        ++this.size;
-        data.push([key, value]);
-      } else {
-        data[index][1] = value;
-      }
-      return this;
-    }
-
-    // Add methods to `ListCache`.
-    ListCache.prototype.clear = listCacheClear;
-    ListCache.prototype['delete'] = listCacheDelete;
-    ListCache.prototype.get = listCacheGet;
-    ListCache.prototype.has = listCacheHas;
-    ListCache.prototype.set = listCacheSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a map cache object to store key-value pairs.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function MapCache(entries) {
-      var index = -1,
-          length = entries == null ? 0 : entries.length;
-
-      this.clear();
-      while (++index < length) {
-        var entry = entries[index];
-        this.set(entry[0], entry[1]);
-      }
-    }
-
-    /**
-     * Removes all key-value entries from the map.
-     *
-     * @private
-     * @name clear
-     * @memberOf MapCache
-     */
-    function mapCacheClear() {
-      this.size = 0;
-      this.__data__ = {
-        'hash': new Hash,
-        'map': new (Map || ListCache),
-        'string': new Hash
-      };
-    }
-
-    /**
-     * Removes `key` and its value from the map.
-     *
-     * @private
-     * @name delete
-     * @memberOf MapCache
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function mapCacheDelete(key) {
-      var result = getMapData(this, key)['delete'](key);
-      this.size -= result ? 1 : 0;
-      return result;
-    }
-
-    /**
-     * Gets the map value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf MapCache
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function mapCacheGet(key) {
-      return getMapData(this, key).get(key);
-    }
-
-    /**
-     * Checks if a map value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf MapCache
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function mapCacheHas(key) {
-      return getMapData(this, key).has(key);
-    }
-
-    /**
-     * Sets the map `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf MapCache
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the map cache instance.
-     */
-    function mapCacheSet(key, value) {
-      var data = getMapData(this, key),
-          size = data.size;
-
-      data.set(key, value);
-      this.size += data.size == size ? 0 : 1;
-      return this;
-    }
-
-    // Add methods to `MapCache`.
-    MapCache.prototype.clear = mapCacheClear;
-    MapCache.prototype['delete'] = mapCacheDelete;
-    MapCache.prototype.get = mapCacheGet;
-    MapCache.prototype.has = mapCacheHas;
-    MapCache.prototype.set = mapCacheSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     *
-     * Creates an array cache object to store unique values.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [values] The values to cache.
-     */
-    function SetCache(values) {
-      var index = -1,
-          length = values == null ? 0 : values.length;
-
-      this.__data__ = new MapCache;
-      while (++index < length) {
-        this.add(values[index]);
-      }
-    }
-
-    /**
-     * Adds `value` to the array cache.
-     *
-     * @private
-     * @name add
-     * @memberOf SetCache
-     * @alias push
-     * @param {*} value The value to cache.
-     * @returns {Object} Returns the cache instance.
-     */
-    function setCacheAdd(value) {
-      this.__data__.set(value, HASH_UNDEFINED);
-      return this;
-    }
-
-    /**
-     * Checks if `value` is in the array cache.
-     *
-     * @private
-     * @name has
-     * @memberOf SetCache
-     * @param {*} value The value to search for.
-     * @returns {number} Returns `true` if `value` is found, else `false`.
-     */
-    function setCacheHas(value) {
-      return this.__data__.has(value);
-    }
-
-    // Add methods to `SetCache`.
-    SetCache.prototype.add = SetCache.prototype.push = setCacheAdd;
-    SetCache.prototype.has = setCacheHas;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a stack cache object to store key-value pairs.
-     *
-     * @private
-     * @constructor
-     * @param {Array} [entries] The key-value pairs to cache.
-     */
-    function Stack(entries) {
-      var data = this.__data__ = new ListCache(entries);
-      this.size = data.size;
-    }
-
-    /**
-     * Removes all key-value entries from the stack.
-     *
-     * @private
-     * @name clear
-     * @memberOf Stack
-     */
-    function stackClear() {
-      this.__data__ = new ListCache;
-      this.size = 0;
-    }
-
-    /**
-     * Removes `key` and its value from the stack.
-     *
-     * @private
-     * @name delete
-     * @memberOf Stack
-     * @param {string} key The key of the value to remove.
-     * @returns {boolean} Returns `true` if the entry was removed, else `false`.
-     */
-    function stackDelete(key) {
-      var data = this.__data__,
-          result = data['delete'](key);
-
-      this.size = data.size;
-      return result;
-    }
-
-    /**
-     * Gets the stack value for `key`.
-     *
-     * @private
-     * @name get
-     * @memberOf Stack
-     * @param {string} key The key of the value to get.
-     * @returns {*} Returns the entry value.
-     */
-    function stackGet(key) {
-      return this.__data__.get(key);
-    }
-
-    /**
-     * Checks if a stack value for `key` exists.
-     *
-     * @private
-     * @name has
-     * @memberOf Stack
-     * @param {string} key The key of the entry to check.
-     * @returns {boolean} Returns `true` if an entry for `key` exists, else `false`.
-     */
-    function stackHas(key) {
-      return this.__data__.has(key);
-    }
-
-    /**
-     * Sets the stack `key` to `value`.
-     *
-     * @private
-     * @name set
-     * @memberOf Stack
-     * @param {string} key The key of the value to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns the stack cache instance.
-     */
-    function stackSet(key, value) {
-      var data = this.__data__;
-      if (data instanceof ListCache) {
-        var pairs = data.__data__;
-        if (!Map || (pairs.length < LARGE_ARRAY_SIZE - 1)) {
-          pairs.push([key, value]);
-          this.size = ++data.size;
-          return this;
-        }
-        data = this.__data__ = new MapCache(pairs);
-      }
-      data.set(key, value);
-      this.size = data.size;
-      return this;
-    }
-
-    // Add methods to `Stack`.
-    Stack.prototype.clear = stackClear;
-    Stack.prototype['delete'] = stackDelete;
-    Stack.prototype.get = stackGet;
-    Stack.prototype.has = stackHas;
-    Stack.prototype.set = stackSet;
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an array of the enumerable property names of the array-like `value`.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @param {boolean} inherited Specify returning inherited property names.
-     * @returns {Array} Returns the array of property names.
-     */
-    function arrayLikeKeys(value, inherited) {
-      var isArr = isArray(value),
-          isArg = !isArr && isArguments(value),
-          isBuff = !isArr && !isArg && isBuffer(value),
-          isType = !isArr && !isArg && !isBuff && isTypedArray(value),
-          skipIndexes = isArr || isArg || isBuff || isType,
-          result = skipIndexes ? baseTimes(value.length, String) : [],
-          length = result.length;
-
-      for (var key in value) {
-        if ((inherited || hasOwnProperty.call(value, key)) &&
-            !(skipIndexes && (
-               // Safari 9 has enumerable `arguments.length` in strict mode.
-               key == 'length' ||
-               // Node.js 0.10 has enumerable non-index properties on buffers.
-               (isBuff && (key == 'offset' || key == 'parent')) ||
-               // PhantomJS 2 has enumerable non-index properties on typed arrays.
-               (isType && (key == 'buffer' || key == 'byteLength' || key == 'byteOffset')) ||
-               // Skip index properties.
-               isIndex(key, length)
-            ))) {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * A specialized version of `_.sample` for arrays.
-     *
-     * @private
-     * @param {Array} array The array to sample.
-     * @returns {*} Returns the random element.
-     */
-    function arraySample(array) {
-      var length = array.length;
-      return length ? array[baseRandom(0, length - 1)] : undefined;
-    }
-
-    /**
-     * A specialized version of `_.sampleSize` for arrays.
-     *
-     * @private
-     * @param {Array} array The array to sample.
-     * @param {number} n The number of elements to sample.
-     * @returns {Array} Returns the random elements.
-     */
-    function arraySampleSize(array, n) {
-      return shuffleSelf(copyArray(array), baseClamp(n, 0, array.length));
-    }
-
-    /**
-     * A specialized version of `_.shuffle` for arrays.
-     *
-     * @private
-     * @param {Array} array The array to shuffle.
-     * @returns {Array} Returns the new shuffled array.
-     */
-    function arrayShuffle(array) {
-      return shuffleSelf(copyArray(array));
-    }
-
-    /**
-     * This function is like `assignValue` except that it doesn't assign
-     * `undefined` values.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {string} key The key of the property to assign.
-     * @param {*} value The value to assign.
-     */
-    function assignMergeValue(object, key, value) {
-      if ((value !== undefined && !eq(object[key], value)) ||
-          (value === undefined && !(key in object))) {
-        baseAssignValue(object, key, value);
-      }
-    }
-
-    /**
-     * Assigns `value` to `key` of `object` if the existing value is not equivalent
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {string} key The key of the property to assign.
-     * @param {*} value The value to assign.
-     */
-    function assignValue(object, key, value) {
-      var objValue = object[key];
-      if (!(hasOwnProperty.call(object, key) && eq(objValue, value)) ||
-          (value === undefined && !(key in object))) {
-        baseAssignValue(object, key, value);
-      }
-    }
-
-    /**
-     * Gets the index at which the `key` is found in `array` of key-value pairs.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {*} key The key to search for.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     */
-    function assocIndexOf(array, key) {
-      var length = array.length;
-      while (length--) {
-        if (eq(array[length][0], key)) {
-          return length;
-        }
-      }
-      return -1;
-    }
-
-    /**
-     * Aggregates elements of `collection` on `accumulator` with keys transformed
-     * by `iteratee` and values set by `setter`.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} setter The function to set `accumulator` values.
-     * @param {Function} iteratee The iteratee to transform keys.
-     * @param {Object} accumulator The initial aggregated object.
-     * @returns {Function} Returns `accumulator`.
-     */
-    function baseAggregator(collection, setter, iteratee, accumulator) {
-      baseEach(collection, function(value, key, collection) {
-        setter(accumulator, value, iteratee(value), collection);
-      });
-      return accumulator;
-    }
-
-    /**
-     * The base implementation of `_.assign` without support for multiple sources
-     * or `customizer` functions.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @returns {Object} Returns `object`.
-     */
-    function baseAssign(object, source) {
-      return object && copyObject(source, keys(source), object);
-    }
-
-    /**
-     * The base implementation of `_.assignIn` without support for multiple sources
-     * or `customizer` functions.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @returns {Object} Returns `object`.
-     */
-    function baseAssignIn(object, source) {
-      return object && copyObject(source, keysIn(source), object);
-    }
-
-    /**
-     * The base implementation of `assignValue` and `assignMergeValue` without
-     * value checks.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {string} key The key of the property to assign.
-     * @param {*} value The value to assign.
-     */
-    function baseAssignValue(object, key, value) {
-      if (key == '__proto__' && defineProperty) {
-        defineProperty(object, key, {
-          'configurable': true,
-          'enumerable': true,
-          'value': value,
-          'writable': true
-        });
-      } else {
-        object[key] = value;
-      }
-    }
-
-    /**
-     * The base implementation of `_.at` without support for individual paths.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {string[]} paths The property paths to pick.
-     * @returns {Array} Returns the picked elements.
-     */
-    function baseAt(object, paths) {
-      var index = -1,
-          length = paths.length,
-          result = Array(length),
-          skip = object == null;
-
-      while (++index < length) {
-        result[index] = skip ? undefined : get(object, paths[index]);
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.clamp` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {number} number The number to clamp.
-     * @param {number} [lower] The lower bound.
-     * @param {number} upper The upper bound.
-     * @returns {number} Returns the clamped number.
-     */
-    function baseClamp(number, lower, upper) {
-      if (number === number) {
-        if (upper !== undefined) {
-          number = number <= upper ? number : upper;
-        }
-        if (lower !== undefined) {
-          number = number >= lower ? number : lower;
-        }
-      }
-      return number;
-    }
-
-    /**
-     * The base implementation of `_.clone` and `_.cloneDeep` which tracks
-     * traversed objects.
-     *
-     * @private
-     * @param {*} value The value to clone.
-     * @param {boolean} bitmask The bitmask flags.
-     *  1 - Deep clone
-     *  2 - Flatten inherited properties
-     *  4 - Clone symbols
-     * @param {Function} [customizer] The function to customize cloning.
-     * @param {string} [key] The key of `value`.
-     * @param {Object} [object] The parent object of `value`.
-     * @param {Object} [stack] Tracks traversed objects and their clone counterparts.
-     * @returns {*} Returns the cloned value.
-     */
-    function baseClone(value, bitmask, customizer, key, object, stack) {
-      var result,
-          isDeep = bitmask & CLONE_DEEP_FLAG,
-          isFlat = bitmask & CLONE_FLAT_FLAG,
-          isFull = bitmask & CLONE_SYMBOLS_FLAG;
-
-      if (customizer) {
-        result = object ? customizer(value, key, object, stack) : customizer(value);
-      }
-      if (result !== undefined) {
-        return result;
-      }
-      if (!isObject(value)) {
-        return value;
-      }
-      var isArr = isArray(value);
-      if (isArr) {
-        result = initCloneArray(value);
-        if (!isDeep) {
-          return copyArray(value, result);
-        }
-      } else {
-        var tag = getTag(value),
-            isFunc = tag == funcTag || tag == genTag;
-
-        if (isBuffer(value)) {
-          return cloneBuffer(value, isDeep);
-        }
-        if (tag == objectTag || tag == argsTag || (isFunc && !object)) {
-          result = (isFlat || isFunc) ? {} : initCloneObject(value);
-          if (!isDeep) {
-            return isFlat
-              ? copySymbolsIn(value, baseAssignIn(result, value))
-              : copySymbols(value, baseAssign(result, value));
-          }
-        } else {
-          if (!cloneableTags[tag]) {
-            return object ? value : {};
-          }
-          result = initCloneByTag(value, tag, isDeep);
-        }
-      }
-      // Check for circular references and return its corresponding clone.
-      stack || (stack = new Stack);
-      var stacked = stack.get(value);
-      if (stacked) {
-        return stacked;
-      }
-      stack.set(value, result);
-
-      if (isSet(value)) {
-        value.forEach(function(subValue) {
-          result.add(baseClone(subValue, bitmask, customizer, subValue, value, stack));
-        });
-      } else if (isMap(value)) {
-        value.forEach(function(subValue, key) {
-          result.set(key, baseClone(subValue, bitmask, customizer, key, value, stack));
-        });
-      }
-
-      var keysFunc = isFull
-        ? (isFlat ? getAllKeysIn : getAllKeys)
-        : (isFlat ? keysIn : keys);
-
-      var props = isArr ? undefined : keysFunc(value);
-      arrayEach(props || value, function(subValue, key) {
-        if (props) {
-          key = subValue;
-          subValue = value[key];
-        }
-        // Recursively populate clone (susceptible to call stack limits).
-        assignValue(result, key, baseClone(subValue, bitmask, customizer, key, value, stack));
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.conforms` which doesn't clone `source`.
-     *
-     * @private
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {Function} Returns the new spec function.
-     */
-    function baseConforms(source) {
-      var props = keys(source);
-      return function(object) {
-        return baseConformsTo(object, source, props);
-      };
-    }
-
-    /**
-     * The base implementation of `_.conformsTo` which accepts `props` to check.
-     *
-     * @private
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {boolean} Returns `true` if `object` conforms, else `false`.
-     */
-    function baseConformsTo(object, source, props) {
-      var length = props.length;
-      if (object == null) {
-        return !length;
-      }
-      object = Object(object);
-      while (length--) {
-        var key = props[length],
-            predicate = source[key],
-            value = object[key];
-
-        if ((value === undefined && !(key in object)) || !predicate(value)) {
-          return false;
-        }
-      }
-      return true;
-    }
-
-    /**
-     * The base implementation of `_.delay` and `_.defer` which accepts `args`
-     * to provide to `func`.
-     *
-     * @private
-     * @param {Function} func The function to delay.
-     * @param {number} wait The number of milliseconds to delay invocation.
-     * @param {Array} args The arguments to provide to `func`.
-     * @returns {number|Object} Returns the timer id or timeout object.
-     */
-    function baseDelay(func, wait, args) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      return setTimeout(function() { func.apply(undefined, args); }, wait);
-    }
-
-    /**
-     * The base implementation of methods like `_.difference` without support
-     * for excluding multiple arrays or iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {Array} values The values to exclude.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     */
-    function baseDifference(array, values, iteratee, comparator) {
-      var index = -1,
-          includes = arrayIncludes,
-          isCommon = true,
-          length = array.length,
-          result = [],
-          valuesLength = values.length;
-
-      if (!length) {
-        return result;
-      }
-      if (iteratee) {
-        values = arrayMap(values, baseUnary(iteratee));
-      }
-      if (comparator) {
-        includes = arrayIncludesWith;
-        isCommon = false;
-      }
-      else if (values.length >= LARGE_ARRAY_SIZE) {
-        includes = cacheHas;
-        isCommon = false;
-        values = new SetCache(values);
-      }
-      outer:
-      while (++index < length) {
-        var value = array[index],
-            computed = iteratee == null ? value : iteratee(value);
-
-        value = (comparator || value !== 0) ? value : 0;
-        if (isCommon && computed === computed) {
-          var valuesIndex = valuesLength;
-          while (valuesIndex--) {
-            if (values[valuesIndex] === computed) {
-              continue outer;
-            }
-          }
-          result.push(value);
-        }
-        else if (!includes(values, computed, comparator)) {
-          result.push(value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.forEach` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     */
-    var baseEach = createBaseEach(baseForOwn);
-
-    /**
-     * The base implementation of `_.forEachRight` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     */
-    var baseEachRight = createBaseEach(baseForOwnRight, true);
-
-    /**
-     * The base implementation of `_.every` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} predicate The function invoked per iteration.
-     * @returns {boolean} Returns `true` if all elements pass the predicate check,
-     *  else `false`
-     */
-    function baseEvery(collection, predicate) {
-      var result = true;
-      baseEach(collection, function(value, index, collection) {
-        result = !!predicate(value, index, collection);
-        return result;
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of methods like `_.max` and `_.min` which accepts a
-     * `comparator` to determine the extremum value.
-     *
-     * @private
-     * @param {Array} array The array to iterate over.
-     * @param {Function} iteratee The iteratee invoked per iteration.
-     * @param {Function} comparator The comparator used to compare values.
-     * @returns {*} Returns the extremum value.
-     */
-    function baseExtremum(array, iteratee, comparator) {
-      var index = -1,
-          length = array.length;
-
-      while (++index < length) {
-        var value = array[index],
-            current = iteratee(value);
-
-        if (current != null && (computed === undefined
-              ? (current === current && !isSymbol(current))
-              : comparator(current, computed)
-            )) {
-          var computed = current,
-              result = value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.fill` without an iteratee call guard.
-     *
-     * @private
-     * @param {Array} array The array to fill.
-     * @param {*} value The value to fill `array` with.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns `array`.
-     */
-    function baseFill(array, value, start, end) {
-      var length = array.length;
-
-      start = toInteger(start);
-      if (start < 0) {
-        start = -start > length ? 0 : (length + start);
-      }
-      end = (end === undefined || end > length) ? length : toInteger(end);
-      if (end < 0) {
-        end += length;
-      }
-      end = start > end ? 0 : toLength(end);
-      while (start < end) {
-        array[start++] = value;
-      }
-      return array;
-    }
-
-    /**
-     * The base implementation of `_.filter` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} predicate The function invoked per iteration.
-     * @returns {Array} Returns the new filtered array.
-     */
-    function baseFilter(collection, predicate) {
-      var result = [];
-      baseEach(collection, function(value, index, collection) {
-        if (predicate(value, index, collection)) {
-          result.push(value);
-        }
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.flatten` with support for restricting flattening.
-     *
-     * @private
-     * @param {Array} array The array to flatten.
-     * @param {number} depth The maximum recursion depth.
-     * @param {boolean} [predicate=isFlattenable] The function invoked per iteration.
-     * @param {boolean} [isStrict] Restrict to values that pass `predicate` checks.
-     * @param {Array} [result=[]] The initial result value.
-     * @returns {Array} Returns the new flattened array.
-     */
-    function baseFlatten(array, depth, predicate, isStrict, result) {
-      var index = -1,
-          length = array.length;
-
-      predicate || (predicate = isFlattenable);
-      result || (result = []);
-
-      while (++index < length) {
-        var value = array[index];
-        if (depth > 0 && predicate(value)) {
-          if (depth > 1) {
-            // Recursively flatten arrays (susceptible to call stack limits).
-            baseFlatten(value, depth - 1, predicate, isStrict, result);
-          } else {
-            arrayPush(result, value);
-          }
-        } else if (!isStrict) {
-          result[result.length] = value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `baseForOwn` which iterates over `object`
-     * properties returned by `keysFunc` and invokes `iteratee` for each property.
-     * Iteratee functions may exit iteration early by explicitly returning `false`.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @param {Function} keysFunc The function to get the keys of `object`.
-     * @returns {Object} Returns `object`.
-     */
-    var baseFor = createBaseFor();
-
-    /**
-     * This function is like `baseFor` except that it iterates over properties
-     * in the opposite order.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @param {Function} keysFunc The function to get the keys of `object`.
-     * @returns {Object} Returns `object`.
-     */
-    var baseForRight = createBaseFor(true);
-
-    /**
-     * The base implementation of `_.forOwn` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     */
-    function baseForOwn(object, iteratee) {
-      return object && baseFor(object, iteratee, keys);
-    }
-
-    /**
-     * The base implementation of `_.forOwnRight` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     */
-    function baseForOwnRight(object, iteratee) {
-      return object && baseForRight(object, iteratee, keys);
-    }
-
-    /**
-     * The base implementation of `_.functions` which creates an array of
-     * `object` function property names filtered from `props`.
-     *
-     * @private
-     * @param {Object} object The object to inspect.
-     * @param {Array} props The property names to filter.
-     * @returns {Array} Returns the function names.
-     */
-    function baseFunctions(object, props) {
-      return arrayFilter(props, function(key) {
-        return isFunction(object[key]);
-      });
-    }
-
-    /**
-     * The base implementation of `_.get` without support for default values.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the property to get.
-     * @returns {*} Returns the resolved value.
-     */
-    function baseGet(object, path) {
-      path = castPath(path, object);
-
-      var index = 0,
-          length = path.length;
-
-      while (object != null && index < length) {
-        object = object[toKey(path[index++])];
-      }
-      return (index && index == length) ? object : undefined;
-    }
-
-    /**
-     * The base implementation of `getAllKeys` and `getAllKeysIn` which uses
-     * `keysFunc` and `symbolsFunc` to get the enumerable property names and
-     * symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Function} keysFunc The function to get the keys of `object`.
-     * @param {Function} symbolsFunc The function to get the symbols of `object`.
-     * @returns {Array} Returns the array of property names and symbols.
-     */
-    function baseGetAllKeys(object, keysFunc, symbolsFunc) {
-      var result = keysFunc(object);
-      return isArray(object) ? result : arrayPush(result, symbolsFunc(object));
-    }
-
-    /**
-     * The base implementation of `getTag` without fallbacks for buggy environments.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @returns {string} Returns the `toStringTag`.
-     */
-    function baseGetTag(value) {
-      if (value == null) {
-        return value === undefined ? undefinedTag : nullTag;
-      }
-      return (symToStringTag && symToStringTag in Object(value))
-        ? getRawTag(value)
-        : objectToString(value);
-    }
-
-    /**
-     * The base implementation of `_.gt` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is greater than `other`,
-     *  else `false`.
-     */
-    function baseGt(value, other) {
-      return value > other;
-    }
-
-    /**
-     * The base implementation of `_.has` without support for deep paths.
-     *
-     * @private
-     * @param {Object} [object] The object to query.
-     * @param {Array|string} key The key to check.
-     * @returns {boolean} Returns `true` if `key` exists, else `false`.
-     */
-    function baseHas(object, key) {
-      return object != null && hasOwnProperty.call(object, key);
-    }
-
-    /**
-     * The base implementation of `_.hasIn` without support for deep paths.
-     *
-     * @private
-     * @param {Object} [object] The object to query.
-     * @param {Array|string} key The key to check.
-     * @returns {boolean} Returns `true` if `key` exists, else `false`.
-     */
-    function baseHasIn(object, key) {
-      return object != null && key in Object(object);
-    }
-
-    /**
-     * The base implementation of `_.inRange` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {number} number The number to check.
-     * @param {number} start The start of the range.
-     * @param {number} end The end of the range.
-     * @returns {boolean} Returns `true` if `number` is in the range, else `false`.
-     */
-    function baseInRange(number, start, end) {
-      return number >= nativeMin(start, end) && number < nativeMax(start, end);
-    }
-
-    /**
-     * The base implementation of methods like `_.intersection`, without support
-     * for iteratee shorthands, that accepts an array of arrays to inspect.
-     *
-     * @private
-     * @param {Array} arrays The arrays to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of shared values.
-     */
-    function baseIntersection(arrays, iteratee, comparator) {
-      var includes = comparator ? arrayIncludesWith : arrayIncludes,
-          length = arrays[0].length,
-          othLength = arrays.length,
-          othIndex = othLength,
-          caches = Array(othLength),
-          maxLength = Infinity,
-          result = [];
-
-      while (othIndex--) {
-        var array = arrays[othIndex];
-        if (othIndex && iteratee) {
-          array = arrayMap(array, baseUnary(iteratee));
-        }
-        maxLength = nativeMin(array.length, maxLength);
-        caches[othIndex] = !comparator && (iteratee || (length >= 120 && array.length >= 120))
-          ? new SetCache(othIndex && array)
-          : undefined;
-      }
-      array = arrays[0];
-
-      var index = -1,
-          seen = caches[0];
-
-      outer:
-      while (++index < length && result.length < maxLength) {
-        var value = array[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        value = (comparator || value !== 0) ? value : 0;
-        if (!(seen
-              ? cacheHas(seen, computed)
-              : includes(result, computed, comparator)
-            )) {
-          othIndex = othLength;
-          while (--othIndex) {
-            var cache = caches[othIndex];
-            if (!(cache
-                  ? cacheHas(cache, computed)
-                  : includes(arrays[othIndex], computed, comparator))
-                ) {
-              continue outer;
-            }
-          }
-          if (seen) {
-            seen.push(computed);
-          }
-          result.push(value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.invert` and `_.invertBy` which inverts
-     * `object` with values transformed by `iteratee` and set by `setter`.
-     *
-     * @private
-     * @param {Object} object The object to iterate over.
-     * @param {Function} setter The function to set `accumulator` values.
-     * @param {Function} iteratee The iteratee to transform values.
-     * @param {Object} accumulator The initial inverted object.
-     * @returns {Function} Returns `accumulator`.
-     */
-    function baseInverter(object, setter, iteratee, accumulator) {
-      baseForOwn(object, function(value, key, object) {
-        setter(accumulator, iteratee(value), key, object);
-      });
-      return accumulator;
-    }
-
-    /**
-     * The base implementation of `_.invoke` without support for individual
-     * method arguments.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the method to invoke.
-     * @param {Array} args The arguments to invoke the method with.
-     * @returns {*} Returns the result of the invoked method.
-     */
-    function baseInvoke(object, path, args) {
-      path = castPath(path, object);
-      object = parent(object, path);
-      var func = object == null ? object : object[toKey(last(path))];
-      return func == null ? undefined : apply(func, object, args);
-    }
-
-    /**
-     * The base implementation of `_.isArguments`.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an `arguments` object,
-     */
-    function baseIsArguments(value) {
-      return isObjectLike(value) && baseGetTag(value) == argsTag;
-    }
-
-    /**
-     * The base implementation of `_.isArrayBuffer` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array buffer, else `false`.
-     */
-    function baseIsArrayBuffer(value) {
-      return isObjectLike(value) && baseGetTag(value) == arrayBufferTag;
-    }
-
-    /**
-     * The base implementation of `_.isDate` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a date object, else `false`.
-     */
-    function baseIsDate(value) {
-      return isObjectLike(value) && baseGetTag(value) == dateTag;
-    }
-
-    /**
-     * The base implementation of `_.isEqual` which supports partial comparisons
-     * and tracks traversed objects.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @param {boolean} bitmask The bitmask flags.
-     *  1 - Unordered comparison
-     *  2 - Partial comparison
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @param {Object} [stack] Tracks traversed `value` and `other` objects.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     */
-    function baseIsEqual(value, other, bitmask, customizer, stack) {
-      if (value === other) {
-        return true;
-      }
-      if (value == null || other == null || (!isObjectLike(value) && !isObjectLike(other))) {
-        return value !== value && other !== other;
-      }
-      return baseIsEqualDeep(value, other, bitmask, customizer, baseIsEqual, stack);
-    }
-
-    /**
-     * A specialized version of `baseIsEqual` for arrays and objects which performs
-     * deep comparisons and tracks traversed objects enabling objects with circular
-     * references to be compared.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} [stack] Tracks traversed `object` and `other` objects.
-     * @returns {boolean} Returns `true` if the objects are equivalent, else `false`.
-     */
-    function baseIsEqualDeep(object, other, bitmask, customizer, equalFunc, stack) {
-      var objIsArr = isArray(object),
-          othIsArr = isArray(other),
-          objTag = objIsArr ? arrayTag : getTag(object),
-          othTag = othIsArr ? arrayTag : getTag(other);
-
-      objTag = objTag == argsTag ? objectTag : objTag;
-      othTag = othTag == argsTag ? objectTag : othTag;
-
-      var objIsObj = objTag == objectTag,
-          othIsObj = othTag == objectTag,
-          isSameTag = objTag == othTag;
-
-      if (isSameTag && isBuffer(object)) {
-        if (!isBuffer(other)) {
-          return false;
-        }
-        objIsArr = true;
-        objIsObj = false;
-      }
-      if (isSameTag && !objIsObj) {
-        stack || (stack = new Stack);
-        return (objIsArr || isTypedArray(object))
-          ? equalArrays(object, other, bitmask, customizer, equalFunc, stack)
-          : equalByTag(object, other, objTag, bitmask, customizer, equalFunc, stack);
-      }
-      if (!(bitmask & COMPARE_PARTIAL_FLAG)) {
-        var objIsWrapped = objIsObj && hasOwnProperty.call(object, '__wrapped__'),
-            othIsWrapped = othIsObj && hasOwnProperty.call(other, '__wrapped__');
-
-        if (objIsWrapped || othIsWrapped) {
-          var objUnwrapped = objIsWrapped ? object.value() : object,
-              othUnwrapped = othIsWrapped ? other.value() : other;
-
-          stack || (stack = new Stack);
-          return equalFunc(objUnwrapped, othUnwrapped, bitmask, customizer, stack);
-        }
-      }
-      if (!isSameTag) {
-        return false;
-      }
-      stack || (stack = new Stack);
-      return equalObjects(object, other, bitmask, customizer, equalFunc, stack);
-    }
-
-    /**
-     * The base implementation of `_.isMap` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a map, else `false`.
-     */
-    function baseIsMap(value) {
-      return isObjectLike(value) && getTag(value) == mapTag;
-    }
-
-    /**
-     * The base implementation of `_.isMatch` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property values to match.
-     * @param {Array} matchData The property names, values, and compare flags to match.
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @returns {boolean} Returns `true` if `object` is a match, else `false`.
-     */
-    function baseIsMatch(object, source, matchData, customizer) {
-      var index = matchData.length,
-          length = index,
-          noCustomizer = !customizer;
-
-      if (object == null) {
-        return !length;
-      }
-      object = Object(object);
-      while (index--) {
-        var data = matchData[index];
-        if ((noCustomizer && data[2])
-              ? data[1] !== object[data[0]]
-              : !(data[0] in object)
-            ) {
-          return false;
-        }
-      }
-      while (++index < length) {
-        data = matchData[index];
-        var key = data[0],
-            objValue = object[key],
-            srcValue = data[1];
-
-        if (noCustomizer && data[2]) {
-          if (objValue === undefined && !(key in object)) {
-            return false;
-          }
-        } else {
-          var stack = new Stack;
-          if (customizer) {
-            var result = customizer(objValue, srcValue, key, object, source, stack);
-          }
-          if (!(result === undefined
-                ? baseIsEqual(srcValue, objValue, COMPARE_PARTIAL_FLAG | COMPARE_UNORDERED_FLAG, customizer, stack)
-                : result
-              )) {
-            return false;
-          }
-        }
-      }
-      return true;
-    }
-
-    /**
-     * The base implementation of `_.isNative` without bad shim checks.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a native function,
-     *  else `false`.
-     */
-    function baseIsNative(value) {
-      if (!isObject(value) || isMasked(value)) {
-        return false;
-      }
-      var pattern = isFunction(value) ? reIsNative : reIsHostCtor;
-      return pattern.test(toSource(value));
-    }
-
-    /**
-     * The base implementation of `_.isRegExp` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a regexp, else `false`.
-     */
-    function baseIsRegExp(value) {
-      return isObjectLike(value) && baseGetTag(value) == regexpTag;
-    }
-
-    /**
-     * The base implementation of `_.isSet` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a set, else `false`.
-     */
-    function baseIsSet(value) {
-      return isObjectLike(value) && getTag(value) == setTag;
-    }
-
-    /**
-     * The base implementation of `_.isTypedArray` without Node.js optimizations.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a typed array, else `false`.
-     */
-    function baseIsTypedArray(value) {
-      return isObjectLike(value) &&
-        isLength(value.length) && !!typedArrayTags[baseGetTag(value)];
-    }
-
-    /**
-     * The base implementation of `_.iteratee`.
-     *
-     * @private
-     * @param {*} [value=_.identity] The value to convert to an iteratee.
-     * @returns {Function} Returns the iteratee.
-     */
-    function baseIteratee(value) {
-      // Don't store the `typeof` result in a variable to avoid a JIT bug in Safari 9.
-      // See https://bugs.webkit.org/show_bug.cgi?id=156034 for more details.
-      if (typeof value == 'function') {
-        return value;
-      }
-      if (value == null) {
-        return identity;
-      }
-      if (typeof value == 'object') {
-        return isArray(value)
-          ? baseMatchesProperty(value[0], value[1])
-          : baseMatches(value);
-      }
-      return property(value);
-    }
-
-    /**
-     * The base implementation of `_.keys` which doesn't treat sparse arrays as dense.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     */
-    function baseKeys(object) {
-      if (!isPrototype(object)) {
-        return nativeKeys(object);
-      }
-      var result = [];
-      for (var key in Object(object)) {
-        if (hasOwnProperty.call(object, key) && key != 'constructor') {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.keysIn` which doesn't treat sparse arrays as dense.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     */
-    function baseKeysIn(object) {
-      if (!isObject(object)) {
-        return nativeKeysIn(object);
-      }
-      var isProto = isPrototype(object),
-          result = [];
-
-      for (var key in object) {
-        if (!(key == 'constructor' && (isProto || !hasOwnProperty.call(object, key)))) {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.lt` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is less than `other`,
-     *  else `false`.
-     */
-    function baseLt(value, other) {
-      return value < other;
-    }
-
-    /**
-     * The base implementation of `_.map` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} iteratee The function invoked per iteration.
-     * @returns {Array} Returns the new mapped array.
-     */
-    function baseMap(collection, iteratee) {
-      var index = -1,
-          result = isArrayLike(collection) ? Array(collection.length) : [];
-
-      baseEach(collection, function(value, key, collection) {
-        result[++index] = iteratee(value, key, collection);
-      });
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.matches` which doesn't clone `source`.
-     *
-     * @private
-     * @param {Object} source The object of property values to match.
-     * @returns {Function} Returns the new spec function.
-     */
-    function baseMatches(source) {
-      var matchData = getMatchData(source);
-      if (matchData.length == 1 && matchData[0][2]) {
-        return matchesStrictComparable(matchData[0][0], matchData[0][1]);
-      }
-      return function(object) {
-        return object === source || baseIsMatch(object, source, matchData);
-      };
-    }
-
-    /**
-     * The base implementation of `_.matchesProperty` which doesn't clone `srcValue`.
-     *
-     * @private
-     * @param {string} path The path of the property to get.
-     * @param {*} srcValue The value to match.
-     * @returns {Function} Returns the new spec function.
-     */
-    function baseMatchesProperty(path, srcValue) {
-      if (isKey(path) && isStrictComparable(srcValue)) {
-        return matchesStrictComparable(toKey(path), srcValue);
-      }
-      return function(object) {
-        var objValue = get(object, path);
-        return (objValue === undefined && objValue === srcValue)
-          ? hasIn(object, path)
-          : baseIsEqual(srcValue, objValue, COMPARE_PARTIAL_FLAG | COMPARE_UNORDERED_FLAG);
-      };
-    }
-
-    /**
-     * The base implementation of `_.merge` without support for multiple sources.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @param {number} srcIndex The index of `source`.
-     * @param {Function} [customizer] The function to customize merged values.
-     * @param {Object} [stack] Tracks traversed source values and their merged
-     *  counterparts.
-     */
-    function baseMerge(object, source, srcIndex, customizer, stack) {
-      if (object === source) {
-        return;
-      }
-      baseFor(source, function(srcValue, key) {
-        stack || (stack = new Stack);
-        if (isObject(srcValue)) {
-          baseMergeDeep(object, source, key, srcIndex, baseMerge, customizer, stack);
-        }
-        else {
-          var newValue = customizer
-            ? customizer(safeGet(object, key), srcValue, (key + ''), object, source, stack)
-            : undefined;
-
-          if (newValue === undefined) {
-            newValue = srcValue;
-          }
-          assignMergeValue(object, key, newValue);
-        }
-      }, keysIn);
-    }
-
-    /**
-     * A specialized version of `baseMerge` for arrays and objects which performs
-     * deep merges and tracks traversed objects enabling objects with circular
-     * references to be merged.
-     *
-     * @private
-     * @param {Object} object The destination object.
-     * @param {Object} source The source object.
-     * @param {string} key The key of the value to merge.
-     * @param {number} srcIndex The index of `source`.
-     * @param {Function} mergeFunc The function to merge values.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @param {Object} [stack] Tracks traversed source values and their merged
-     *  counterparts.
-     */
-    function baseMergeDeep(object, source, key, srcIndex, mergeFunc, customizer, stack) {
-      var objValue = safeGet(object, key),
-          srcValue = safeGet(source, key),
-          stacked = stack.get(srcValue);
-
-      if (stacked) {
-        assignMergeValue(object, key, stacked);
-        return;
-      }
-      var newValue = customizer
-        ? customizer(objValue, srcValue, (key + ''), object, source, stack)
-        : undefined;
-
-      var isCommon = newValue === undefined;
-
-      if (isCommon) {
-        var isArr = isArray(srcValue),
-            isBuff = !isArr && isBuffer(srcValue),
-            isTyped = !isArr && !isBuff && isTypedArray(srcValue);
-
-        newValue = srcValue;
-        if (isArr || isBuff || isTyped) {
-          if (isArray(objValue)) {
-            newValue = objValue;
-          }
-          else if (isArrayLikeObject(objValue)) {
-            newValue = copyArray(objValue);
-          }
-          else if (isBuff) {
-            isCommon = false;
-            newValue = cloneBuffer(srcValue, true);
-          }
-          else if (isTyped) {
-            isCommon = false;
-            newValue = cloneTypedArray(srcValue, true);
-          }
-          else {
-            newValue = [];
-          }
-        }
-        else if (isPlainObject(srcValue) || isArguments(srcValue)) {
-          newValue = objValue;
-          if (isArguments(objValue)) {
-            newValue = toPlainObject(objValue);
-          }
-          else if (!isObject(objValue) || isFunction(objValue)) {
-            newValue = initCloneObject(srcValue);
-          }
-        }
-        else {
-          isCommon = false;
-        }
-      }
-      if (isCommon) {
-        // Recursively merge objects and arrays (susceptible to call stack limits).
-        stack.set(srcValue, newValue);
-        mergeFunc(newValue, srcValue, srcIndex, customizer, stack);
-        stack['delete'](srcValue);
-      }
-      assignMergeValue(object, key, newValue);
-    }
-
-    /**
-     * The base implementation of `_.nth` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {Array} array The array to query.
-     * @param {number} n The index of the element to return.
-     * @returns {*} Returns the nth element of `array`.
-     */
-    function baseNth(array, n) {
-      var length = array.length;
-      if (!length) {
-        return;
-      }
-      n += n < 0 ? length : 0;
-      return isIndex(n, length) ? array[n] : undefined;
-    }
-
-    /**
-     * The base implementation of `_.orderBy` without param guards.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function[]|Object[]|string[]} iteratees The iteratees to sort by.
-     * @param {string[]} orders The sort orders of `iteratees`.
-     * @returns {Array} Returns the new sorted array.
-     */
-    function baseOrderBy(collection, iteratees, orders) {
-      var index = -1;
-      iteratees = arrayMap(iteratees.length ? iteratees : [identity], baseUnary(getIteratee()));
-
-      var result = baseMap(collection, function(value, key, collection) {
-        var criteria = arrayMap(iteratees, function(iteratee) {
-          return iteratee(value);
-        });
-        return { 'criteria': criteria, 'index': ++index, 'value': value };
-      });
-
-      return baseSortBy(result, function(object, other) {
-        return compareMultiple(object, other, orders);
-      });
-    }
-
-    /**
-     * The base implementation of `_.pick` without support for individual
-     * property identifiers.
-     *
-     * @private
-     * @param {Object} object The source object.
-     * @param {string[]} paths The property paths to pick.
-     * @returns {Object} Returns the new object.
-     */
-    function basePick(object, paths) {
-      return basePickBy(object, paths, function(value, path) {
-        return hasIn(object, path);
-      });
-    }
-
-    /**
-     * The base implementation of  `_.pickBy` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Object} object The source object.
-     * @param {string[]} paths The property paths to pick.
-     * @param {Function} predicate The function invoked per property.
-     * @returns {Object} Returns the new object.
-     */
-    function basePickBy(object, paths, predicate) {
-      var index = -1,
-          length = paths.length,
-          result = {};
-
-      while (++index < length) {
-        var path = paths[index],
-            value = baseGet(object, path);
-
-        if (predicate(value, path)) {
-          baseSet(result, castPath(path, object), value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * A specialized version of `baseProperty` which supports deep paths.
-     *
-     * @private
-     * @param {Array|string} path The path of the property to get.
-     * @returns {Function} Returns the new accessor function.
-     */
-    function basePropertyDeep(path) {
-      return function(object) {
-        return baseGet(object, path);
-      };
-    }
-
-    /**
-     * The base implementation of `_.pullAllBy` without support for iteratee
-     * shorthands.
-     *
-     * @private
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns `array`.
-     */
-    function basePullAll(array, values, iteratee, comparator) {
-      var indexOf = comparator ? baseIndexOfWith : baseIndexOf,
-          index = -1,
-          length = values.length,
-          seen = array;
-
-      if (array === values) {
-        values = copyArray(values);
-      }
-      if (iteratee) {
-        seen = arrayMap(array, baseUnary(iteratee));
-      }
-      while (++index < length) {
-        var fromIndex = 0,
-            value = values[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        while ((fromIndex = indexOf(seen, computed, fromIndex, comparator)) > -1) {
-          if (seen !== array) {
-            splice.call(seen, fromIndex, 1);
-          }
-          splice.call(array, fromIndex, 1);
-        }
-      }
-      return array;
-    }
-
-    /**
-     * The base implementation of `_.pullAt` without support for individual
-     * indexes or capturing the removed elements.
-     *
-     * @private
-     * @param {Array} array The array to modify.
-     * @param {number[]} indexes The indexes of elements to remove.
-     * @returns {Array} Returns `array`.
-     */
-    function basePullAt(array, indexes) {
-      var length = array ? indexes.length : 0,
-          lastIndex = length - 1;
-
-      while (length--) {
-        var index = indexes[length];
-        if (length == lastIndex || index !== previous) {
-          var previous = index;
-          if (isIndex(index)) {
-            splice.call(array, index, 1);
-          } else {
-            baseUnset(array, index);
-          }
-        }
-      }
-      return array;
-    }
-
-    /**
-     * The base implementation of `_.random` without support for returning
-     * floating-point numbers.
-     *
-     * @private
-     * @param {number} lower The lower bound.
-     * @param {number} upper The upper bound.
-     * @returns {number} Returns the random number.
-     */
-    function baseRandom(lower, upper) {
-      return lower + nativeFloor(nativeRandom() * (upper - lower + 1));
-    }
-
-    /**
-     * The base implementation of `_.range` and `_.rangeRight` which doesn't
-     * coerce arguments.
-     *
-     * @private
-     * @param {number} start The start of the range.
-     * @param {number} end The end of the range.
-     * @param {number} step The value to increment or decrement by.
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Array} Returns the range of numbers.
-     */
-    function baseRange(start, end, step, fromRight) {
-      var index = -1,
-          length = nativeMax(nativeCeil((end - start) / (step || 1)), 0),
-          result = Array(length);
-
-      while (length--) {
-        result[fromRight ? length : ++index] = start;
-        start += step;
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.repeat` which doesn't coerce arguments.
-     *
-     * @private
-     * @param {string} string The string to repeat.
-     * @param {number} n The number of times to repeat the string.
-     * @returns {string} Returns the repeated string.
-     */
-    function baseRepeat(string, n) {
-      var result = '';
-      if (!string || n < 1 || n > MAX_SAFE_INTEGER) {
-        return result;
-      }
-      // Leverage the exponentiation by squaring algorithm for a faster repeat.
-      // See https://en.wikipedia.org/wiki/Exponentiation_by_squaring for more details.
-      do {
-        if (n % 2) {
-          result += string;
-        }
-        n = nativeFloor(n / 2);
-        if (n) {
-          string += string;
-        }
-      } while (n);
-
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.rest` which doesn't validate or coerce arguments.
-     *
-     * @private
-     * @param {Function} func The function to apply a rest parameter to.
-     * @param {number} [start=func.length-1] The start position of the rest parameter.
-     * @returns {Function} Returns the new function.
-     */
-    function baseRest(func, start) {
-      return setToString(overRest(func, start, identity), func + '');
-    }
-
-    /**
-     * The base implementation of `_.sample`.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to sample.
-     * @returns {*} Returns the random element.
-     */
-    function baseSample(collection) {
-      return arraySample(values(collection));
-    }
-
-    /**
-     * The base implementation of `_.sampleSize` without param guards.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to sample.
-     * @param {number} n The number of elements to sample.
-     * @returns {Array} Returns the random elements.
-     */
-    function baseSampleSize(collection, n) {
-      var array = values(collection);
-      return shuffleSelf(array, baseClamp(n, 0, array.length));
-    }
-
-    /**
-     * The base implementation of `_.set`.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {*} value The value to set.
-     * @param {Function} [customizer] The function to customize path creation.
-     * @returns {Object} Returns `object`.
-     */
-    function baseSet(object, path, value, customizer) {
-      if (!isObject(object)) {
-        return object;
-      }
-      path = castPath(path, object);
-
-      var index = -1,
-          length = path.length,
-          lastIndex = length - 1,
-          nested = object;
-
-      while (nested != null && ++index < length) {
-        var key = toKey(path[index]),
-            newValue = value;
-
-        if (index != lastIndex) {
-          var objValue = nested[key];
-          newValue = customizer ? customizer(objValue, key, nested) : undefined;
-          if (newValue === undefined) {
-            newValue = isObject(objValue)
-              ? objValue
-              : (isIndex(path[index + 1]) ? [] : {});
-          }
-        }
-        assignValue(nested, key, newValue);
-        nested = nested[key];
-      }
-      return object;
-    }
-
-    /**
-     * The base implementation of `setData` without support for hot loop shorting.
-     *
-     * @private
-     * @param {Function} func The function to associate metadata with.
-     * @param {*} data The metadata.
-     * @returns {Function} Returns `func`.
-     */
-    var baseSetData = !metaMap ? identity : function(func, data) {
-      metaMap.set(func, data);
-      return func;
-    };
-
-    /**
-     * The base implementation of `setToString` without support for hot loop shorting.
-     *
-     * @private
-     * @param {Function} func The function to modify.
-     * @param {Function} string The `toString` result.
-     * @returns {Function} Returns `func`.
-     */
-    var baseSetToString = !defineProperty ? identity : function(func, string) {
-      return defineProperty(func, 'toString', {
-        'configurable': true,
-        'enumerable': false,
-        'value': constant(string),
-        'writable': true
-      });
-    };
-
-    /**
-     * The base implementation of `_.shuffle`.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to shuffle.
-     * @returns {Array} Returns the new shuffled array.
-     */
-    function baseShuffle(collection) {
-      return shuffleSelf(values(collection));
-    }
-
-    /**
-     * The base implementation of `_.slice` without an iteratee call guard.
-     *
-     * @private
-     * @param {Array} array The array to slice.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns the slice of `array`.
-     */
-    function baseSlice(array, start, end) {
-      var index = -1,
-          length = array.length;
-
-      if (start < 0) {
-        start = -start > length ? 0 : (length + start);
-      }
-      end = end > length ? length : end;
-      if (end < 0) {
-        end += length;
-      }
-      length = start > end ? 0 : ((end - start) >>> 0);
-      start >>>= 0;
-
-      var result = Array(length);
-      while (++index < length) {
-        result[index] = array[index + start];
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.some` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} predicate The function invoked per iteration.
-     * @returns {boolean} Returns `true` if any element passes the predicate check,
-     *  else `false`.
-     */
-    function baseSome(collection, predicate) {
-      var result;
-
-      baseEach(collection, function(value, index, collection) {
-        result = predicate(value, index, collection);
-        return !result;
-      });
-      return !!result;
-    }
-
-    /**
-     * The base implementation of `_.sortedIndex` and `_.sortedLastIndex` which
-     * performs a binary search of `array` to determine the index at which `value`
-     * should be inserted into `array` in order to maintain its sort order.
-     *
-     * @private
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {boolean} [retHighest] Specify returning the highest qualified index.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     */
-    function baseSortedIndex(array, value, retHighest) {
-      var low = 0,
-          high = array == null ? low : array.length;
-
-      if (typeof value == 'number' && value === value && high <= HALF_MAX_ARRAY_LENGTH) {
-        while (low < high) {
-          var mid = (low + high) >>> 1,
-              computed = array[mid];
-
-          if (computed !== null && !isSymbol(computed) &&
-              (retHighest ? (computed <= value) : (computed < value))) {
-            low = mid + 1;
-          } else {
-            high = mid;
-          }
-        }
-        return high;
-      }
-      return baseSortedIndexBy(array, value, identity, retHighest);
-    }
-
-    /**
-     * The base implementation of `_.sortedIndexBy` and `_.sortedLastIndexBy`
-     * which invokes `iteratee` for `value` and each element of `array` to compute
-     * their sort ranking. The iteratee is invoked with one argument; (value).
-     *
-     * @private
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {Function} iteratee The iteratee invoked per element.
-     * @param {boolean} [retHighest] Specify returning the highest qualified index.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     */
-    function baseSortedIndexBy(array, value, iteratee, retHighest) {
-      value = iteratee(value);
-
-      var low = 0,
-          high = array == null ? 0 : array.length,
-          valIsNaN = value !== value,
-          valIsNull = value === null,
-          valIsSymbol = isSymbol(value),
-          valIsUndefined = value === undefined;
-
-      while (low < high) {
-        var mid = nativeFloor((low + high) / 2),
-            computed = iteratee(array[mid]),
-            othIsDefined = computed !== undefined,
-            othIsNull = computed === null,
-            othIsReflexive = computed === computed,
-            othIsSymbol = isSymbol(computed);
-
-        if (valIsNaN) {
-          var setLow = retHighest || othIsReflexive;
-        } else if (valIsUndefined) {
-          setLow = othIsReflexive && (retHighest || othIsDefined);
-        } else if (valIsNull) {
-          setLow = othIsReflexive && othIsDefined && (retHighest || !othIsNull);
-        } else if (valIsSymbol) {
-          setLow = othIsReflexive && othIsDefined && !othIsNull && (retHighest || !othIsSymbol);
-        } else if (othIsNull || othIsSymbol) {
-          setLow = false;
-        } else {
-          setLow = retHighest ? (computed <= value) : (computed < value);
-        }
-        if (setLow) {
-          low = mid + 1;
-        } else {
-          high = mid;
-        }
-      }
-      return nativeMin(high, MAX_ARRAY_INDEX);
-    }
-
-    /**
-     * The base implementation of `_.sortedUniq` and `_.sortedUniqBy` without
-     * support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     */
-    function baseSortedUniq(array, iteratee) {
-      var index = -1,
-          length = array.length,
-          resIndex = 0,
-          result = [];
-
-      while (++index < length) {
-        var value = array[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        if (!index || !eq(computed, seen)) {
-          var seen = computed;
-          result[resIndex++] = value === 0 ? 0 : value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.toNumber` which doesn't ensure correct
-     * conversions of binary, hexadecimal, or octal string values.
-     *
-     * @private
-     * @param {*} value The value to process.
-     * @returns {number} Returns the number.
-     */
-    function baseToNumber(value) {
-      if (typeof value == 'number') {
-        return value;
-      }
-      if (isSymbol(value)) {
-        return NAN;
-      }
-      return +value;
-    }
-
-    /**
-     * The base implementation of `_.toString` which doesn't convert nullish
-     * values to empty strings.
-     *
-     * @private
-     * @param {*} value The value to process.
-     * @returns {string} Returns the string.
-     */
-    function baseToString(value) {
-      // Exit early for strings to avoid a performance hit in some environments.
-      if (typeof value == 'string') {
-        return value;
-      }
-      if (isArray(value)) {
-        // Recursively convert values (susceptible to call stack limits).
-        return arrayMap(value, baseToString) + '';
-      }
-      if (isSymbol(value)) {
-        return symbolToString ? symbolToString.call(value) : '';
-      }
-      var result = (value + '');
-      return (result == '0' && (1 / value) == -INFINITY) ? '-0' : result;
-    }
-
-    /**
-     * The base implementation of `_.uniqBy` without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     */
-    function baseUniq(array, iteratee, comparator) {
-      var index = -1,
-          includes = arrayIncludes,
-          length = array.length,
-          isCommon = true,
-          result = [],
-          seen = result;
-
-      if (comparator) {
-        isCommon = false;
-        includes = arrayIncludesWith;
-      }
-      else if (length >= LARGE_ARRAY_SIZE) {
-        var set = iteratee ? null : createSet(array);
-        if (set) {
-          return setToArray(set);
-        }
-        isCommon = false;
-        includes = cacheHas;
-        seen = new SetCache;
-      }
-      else {
-        seen = iteratee ? [] : result;
-      }
-      outer:
-      while (++index < length) {
-        var value = array[index],
-            computed = iteratee ? iteratee(value) : value;
-
-        value = (comparator || value !== 0) ? value : 0;
-        if (isCommon && computed === computed) {
-          var seenIndex = seen.length;
-          while (seenIndex--) {
-            if (seen[seenIndex] === computed) {
-              continue outer;
-            }
-          }
-          if (iteratee) {
-            seen.push(computed);
-          }
-          result.push(value);
-        }
-        else if (!includes(seen, computed, comparator)) {
-          if (seen !== result) {
-            seen.push(computed);
-          }
-          result.push(value);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * The base implementation of `_.unset`.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The property path to unset.
-     * @returns {boolean} Returns `true` if the property is deleted, else `false`.
-     */
-    function baseUnset(object, path) {
-      path = castPath(path, object);
-      object = parent(object, path);
-      return object == null || delete object[toKey(last(path))];
-    }
-
-    /**
-     * The base implementation of `_.update`.
-     *
-     * @private
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to update.
-     * @param {Function} updater The function to produce the updated value.
-     * @param {Function} [customizer] The function to customize path creation.
-     * @returns {Object} Returns `object`.
-     */
-    function baseUpdate(object, path, updater, customizer) {
-      return baseSet(object, path, updater(baseGet(object, path)), customizer);
-    }
-
-    /**
-     * The base implementation of methods like `_.dropWhile` and `_.takeWhile`
-     * without support for iteratee shorthands.
-     *
-     * @private
-     * @param {Array} array The array to query.
-     * @param {Function} predicate The function invoked per iteration.
-     * @param {boolean} [isDrop] Specify dropping elements instead of taking them.
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Array} Returns the slice of `array`.
-     */
-    function baseWhile(array, predicate, isDrop, fromRight) {
-      var length = array.length,
-          index = fromRight ? length : -1;
-
-      while ((fromRight ? index-- : ++index < length) &&
-        predicate(array[index], index, array)) {}
-
-      return isDrop
-        ? baseSlice(array, (fromRight ? 0 : index), (fromRight ? index + 1 : length))
-        : baseSlice(array, (fromRight ? index + 1 : 0), (fromRight ? length : index));
-    }
-
-    /**
-     * The base implementation of `wrapperValue` which returns the result of
-     * performing a sequence of actions on the unwrapped `value`, where each
-     * successive action is supplied the return value of the previous.
-     *
-     * @private
-     * @param {*} value The unwrapped value.
-     * @param {Array} actions Actions to perform to resolve the unwrapped value.
-     * @returns {*} Returns the resolved value.
-     */
-    function baseWrapperValue(value, actions) {
-      var result = value;
-      if (result instanceof LazyWrapper) {
-        result = result.value();
-      }
-      return arrayReduce(actions, function(result, action) {
-        return action.func.apply(action.thisArg, arrayPush([result], action.args));
-      }, result);
-    }
-
-    /**
-     * The base implementation of methods like `_.xor`, without support for
-     * iteratee shorthands, that accepts an array of arrays to inspect.
-     *
-     * @private
-     * @param {Array} arrays The arrays to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of values.
-     */
-    function baseXor(arrays, iteratee, comparator) {
-      var length = arrays.length;
-      if (length < 2) {
-        return length ? baseUniq(arrays[0]) : [];
-      }
-      var index = -1,
-          result = Array(length);
-
-      while (++index < length) {
-        var array = arrays[index],
-            othIndex = -1;
-
-        while (++othIndex < length) {
-          if (othIndex != index) {
-            result[index] = baseDifference(result[index] || array, arrays[othIndex], iteratee, comparator);
-          }
-        }
-      }
-      return baseUniq(baseFlatten(result, 1), iteratee, comparator);
-    }
-
-    /**
-     * This base implementation of `_.zipObject` which assigns values using `assignFunc`.
-     *
-     * @private
-     * @param {Array} props The property identifiers.
-     * @param {Array} values The property values.
-     * @param {Function} assignFunc The function to assign values.
-     * @returns {Object} Returns the new object.
-     */
-    function baseZipObject(props, values, assignFunc) {
-      var index = -1,
-          length = props.length,
-          valsLength = values.length,
-          result = {};
-
-      while (++index < length) {
-        var value = index < valsLength ? values[index] : undefined;
-        assignFunc(result, props[index], value);
-      }
-      return result;
-    }
-
-    /**
-     * Casts `value` to an empty array if it's not an array like object.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @returns {Array|Object} Returns the cast array-like object.
-     */
-    function castArrayLikeObject(value) {
-      return isArrayLikeObject(value) ? value : [];
-    }
-
-    /**
-     * Casts `value` to `identity` if it's not a function.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @returns {Function} Returns cast function.
-     */
-    function castFunction(value) {
-      return typeof value == 'function' ? value : identity;
-    }
-
-    /**
-     * Casts `value` to a path array if it's not one.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @param {Object} [object] The object to query keys on.
-     * @returns {Array} Returns the cast property path array.
-     */
-    function castPath(value, object) {
-      if (isArray(value)) {
-        return value;
-      }
-      return isKey(value, object) ? [value] : stringToPath(toString(value));
-    }
-
-    /**
-     * A `baseRest` alias which can be replaced with `identity` by module
-     * replacement plugins.
-     *
-     * @private
-     * @type {Function}
-     * @param {Function} func The function to apply a rest parameter to.
-     * @returns {Function} Returns the new function.
-     */
-    var castRest = baseRest;
-
-    /**
-     * Casts `array` to a slice if it's needed.
-     *
-     * @private
-     * @param {Array} array The array to inspect.
-     * @param {number} start The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns the cast slice.
-     */
-    function castSlice(array, start, end) {
-      var length = array.length;
-      end = end === undefined ? length : end;
-      return (!start && end >= length) ? array : baseSlice(array, start, end);
-    }
-
-    /**
-     * A simple wrapper around the global [`clearTimeout`](https://mdn.io/clearTimeout).
-     *
-     * @private
-     * @param {number|Object} id The timer id or timeout object of the timer to clear.
-     */
-    var clearTimeout = ctxClearTimeout || function(id) {
-      return root.clearTimeout(id);
-    };
-
-    /**
-     * Creates a clone of  `buffer`.
-     *
-     * @private
-     * @param {Buffer} buffer The buffer to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Buffer} Returns the cloned buffer.
-     */
-    function cloneBuffer(buffer, isDeep) {
-      if (isDeep) {
-        return buffer.slice();
-      }
-      var length = buffer.length,
-          result = allocUnsafe ? allocUnsafe(length) : new buffer.constructor(length);
-
-      buffer.copy(result);
-      return result;
-    }
-
-    /**
-     * Creates a clone of `arrayBuffer`.
-     *
-     * @private
-     * @param {ArrayBuffer} arrayBuffer The array buffer to clone.
-     * @returns {ArrayBuffer} Returns the cloned array buffer.
-     */
-    function cloneArrayBuffer(arrayBuffer) {
-      var result = new arrayBuffer.constructor(arrayBuffer.byteLength);
-      new Uint8Array(result).set(new Uint8Array(arrayBuffer));
-      return result;
-    }
-
-    /**
-     * Creates a clone of `dataView`.
-     *
-     * @private
-     * @param {Object} dataView The data view to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Object} Returns the cloned data view.
-     */
-    function cloneDataView(dataView, isDeep) {
-      var buffer = isDeep ? cloneArrayBuffer(dataView.buffer) : dataView.buffer;
-      return new dataView.constructor(buffer, dataView.byteOffset, dataView.byteLength);
-    }
-
-    /**
-     * Creates a clone of `regexp`.
-     *
-     * @private
-     * @param {Object} regexp The regexp to clone.
-     * @returns {Object} Returns the cloned regexp.
-     */
-    function cloneRegExp(regexp) {
-      var result = new regexp.constructor(regexp.source, reFlags.exec(regexp));
-      result.lastIndex = regexp.lastIndex;
-      return result;
-    }
-
-    /**
-     * Creates a clone of the `symbol` object.
-     *
-     * @private
-     * @param {Object} symbol The symbol object to clone.
-     * @returns {Object} Returns the cloned symbol object.
-     */
-    function cloneSymbol(symbol) {
-      return symbolValueOf ? Object(symbolValueOf.call(symbol)) : {};
-    }
-
-    /**
-     * Creates a clone of `typedArray`.
-     *
-     * @private
-     * @param {Object} typedArray The typed array to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Object} Returns the cloned typed array.
-     */
-    function cloneTypedArray(typedArray, isDeep) {
-      var buffer = isDeep ? cloneArrayBuffer(typedArray.buffer) : typedArray.buffer;
-      return new typedArray.constructor(buffer, typedArray.byteOffset, typedArray.length);
-    }
-
-    /**
-     * Compares values to sort them in ascending order.
-     *
-     * @private
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {number} Returns the sort order indicator for `value`.
-     */
-    function compareAscending(value, other) {
-      if (value !== other) {
-        var valIsDefined = value !== undefined,
-            valIsNull = value === null,
-            valIsReflexive = value === value,
-            valIsSymbol = isSymbol(value);
-
-        var othIsDefined = other !== undefined,
-            othIsNull = other === null,
-            othIsReflexive = other === other,
-            othIsSymbol = isSymbol(other);
-
-        if ((!othIsNull && !othIsSymbol && !valIsSymbol && value > other) ||
-            (valIsSymbol && othIsDefined && othIsReflexive && !othIsNull && !othIsSymbol) ||
-            (valIsNull && othIsDefined && othIsReflexive) ||
-            (!valIsDefined && othIsReflexive) ||
-            !valIsReflexive) {
-          return 1;
-        }
-        if ((!valIsNull && !valIsSymbol && !othIsSymbol && value < other) ||
-            (othIsSymbol && valIsDefined && valIsReflexive && !valIsNull && !valIsSymbol) ||
-            (othIsNull && valIsDefined && valIsReflexive) ||
-            (!othIsDefined && valIsReflexive) ||
-            !othIsReflexive) {
-          return -1;
-        }
-      }
-      return 0;
-    }
-
-    /**
-     * Used by `_.orderBy` to compare multiple properties of a value to another
-     * and stable sort them.
-     *
-     * If `orders` is unspecified, all values are sorted in ascending order. Otherwise,
-     * specify an order of "desc" for descending or "asc" for ascending sort order
-     * of corresponding values.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {boolean[]|string[]} orders The order to sort by for each property.
-     * @returns {number} Returns the sort order indicator for `object`.
-     */
-    function compareMultiple(object, other, orders) {
-      var index = -1,
-          objCriteria = object.criteria,
-          othCriteria = other.criteria,
-          length = objCriteria.length,
-          ordersLength = orders.length;
-
-      while (++index < length) {
-        var result = compareAscending(objCriteria[index], othCriteria[index]);
-        if (result) {
-          if (index >= ordersLength) {
-            return result;
-          }
-          var order = orders[index];
-          return result * (order == 'desc' ? -1 : 1);
-        }
-      }
-      // Fixes an `Array#sort` bug in the JS engine embedded in Adobe applications
-      // that causes it, under certain circumstances, to provide the same value for
-      // `object` and `other`. See https://github.com/jashkenas/underscore/pull/1247
-      // for more details.
-      //
-      // This also ensures a stable sort in V8 and other engines.
-      // See https://bugs.chromium.org/p/v8/issues/detail?id=90 for more details.
-      return object.index - other.index;
-    }
-
-    /**
-     * Creates an array that is the composition of partially applied arguments,
-     * placeholders, and provided arguments into a single array of arguments.
-     *
-     * @private
-     * @param {Array} args The provided arguments.
-     * @param {Array} partials The arguments to prepend to those provided.
-     * @param {Array} holders The `partials` placeholder indexes.
-     * @params {boolean} [isCurried] Specify composing for a curried function.
-     * @returns {Array} Returns the new array of composed arguments.
-     */
-    function composeArgs(args, partials, holders, isCurried) {
-      var argsIndex = -1,
-          argsLength = args.length,
-          holdersLength = holders.length,
-          leftIndex = -1,
-          leftLength = partials.length,
-          rangeLength = nativeMax(argsLength - holdersLength, 0),
-          result = Array(leftLength + rangeLength),
-          isUncurried = !isCurried;
-
-      while (++leftIndex < leftLength) {
-        result[leftIndex] = partials[leftIndex];
-      }
-      while (++argsIndex < holdersLength) {
-        if (isUncurried || argsIndex < argsLength) {
-          result[holders[argsIndex]] = args[argsIndex];
-        }
-      }
-      while (rangeLength--) {
-        result[leftIndex++] = args[argsIndex++];
-      }
-      return result;
-    }
-
-    /**
-     * This function is like `composeArgs` except that the arguments composition
-     * is tailored for `_.partialRight`.
-     *
-     * @private
-     * @param {Array} args The provided arguments.
-     * @param {Array} partials The arguments to append to those provided.
-     * @param {Array} holders The `partials` placeholder indexes.
-     * @params {boolean} [isCurried] Specify composing for a curried function.
-     * @returns {Array} Returns the new array of composed arguments.
-     */
-    function composeArgsRight(args, partials, holders, isCurried) {
-      var argsIndex = -1,
-          argsLength = args.length,
-          holdersIndex = -1,
-          holdersLength = holders.length,
-          rightIndex = -1,
-          rightLength = partials.length,
-          rangeLength = nativeMax(argsLength - holdersLength, 0),
-          result = Array(rangeLength + rightLength),
-          isUncurried = !isCurried;
-
-      while (++argsIndex < rangeLength) {
-        result[argsIndex] = args[argsIndex];
-      }
-      var offset = argsIndex;
-      while (++rightIndex < rightLength) {
-        result[offset + rightIndex] = partials[rightIndex];
-      }
-      while (++holdersIndex < holdersLength) {
-        if (isUncurried || argsIndex < argsLength) {
-          result[offset + holders[holdersIndex]] = args[argsIndex++];
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Copies the values of `source` to `array`.
-     *
-     * @private
-     * @param {Array} source The array to copy values from.
-     * @param {Array} [array=[]] The array to copy values to.
-     * @returns {Array} Returns `array`.
-     */
-    function copyArray(source, array) {
-      var index = -1,
-          length = source.length;
-
-      array || (array = Array(length));
-      while (++index < length) {
-        array[index] = source[index];
-      }
-      return array;
-    }
-
-    /**
-     * Copies properties of `source` to `object`.
-     *
-     * @private
-     * @param {Object} source The object to copy properties from.
-     * @param {Array} props The property identifiers to copy.
-     * @param {Object} [object={}] The object to copy properties to.
-     * @param {Function} [customizer] The function to customize copied values.
-     * @returns {Object} Returns `object`.
-     */
-    function copyObject(source, props, object, customizer) {
-      var isNew = !object;
-      object || (object = {});
-
-      var index = -1,
-          length = props.length;
-
-      while (++index < length) {
-        var key = props[index];
-
-        var newValue = customizer
-          ? customizer(object[key], source[key], key, object, source)
-          : undefined;
-
-        if (newValue === undefined) {
-          newValue = source[key];
-        }
-        if (isNew) {
-          baseAssignValue(object, key, newValue);
-        } else {
-          assignValue(object, key, newValue);
-        }
-      }
-      return object;
-    }
-
-    /**
-     * Copies own symbols of `source` to `object`.
-     *
-     * @private
-     * @param {Object} source The object to copy symbols from.
-     * @param {Object} [object={}] The object to copy symbols to.
-     * @returns {Object} Returns `object`.
-     */
-    function copySymbols(source, object) {
-      return copyObject(source, getSymbols(source), object);
-    }
-
-    /**
-     * Copies own and inherited symbols of `source` to `object`.
-     *
-     * @private
-     * @param {Object} source The object to copy symbols from.
-     * @param {Object} [object={}] The object to copy symbols to.
-     * @returns {Object} Returns `object`.
-     */
-    function copySymbolsIn(source, object) {
-      return copyObject(source, getSymbolsIn(source), object);
-    }
-
-    /**
-     * Creates a function like `_.groupBy`.
-     *
-     * @private
-     * @param {Function} setter The function to set accumulator values.
-     * @param {Function} [initializer] The accumulator object initializer.
-     * @returns {Function} Returns the new aggregator function.
-     */
-    function createAggregator(setter, initializer) {
-      return function(collection, iteratee) {
-        var func = isArray(collection) ? arrayAggregator : baseAggregator,
-            accumulator = initializer ? initializer() : {};
-
-        return func(collection, setter, getIteratee(iteratee, 2), accumulator);
-      };
-    }
-
-    /**
-     * Creates a function like `_.assign`.
-     *
-     * @private
-     * @param {Function} assigner The function to assign values.
-     * @returns {Function} Returns the new assigner function.
-     */
-    function createAssigner(assigner) {
-      return baseRest(function(object, sources) {
-        var index = -1,
-            length = sources.length,
-            customizer = length > 1 ? sources[length - 1] : undefined,
-            guard = length > 2 ? sources[2] : undefined;
-
-        customizer = (assigner.length > 3 && typeof customizer == 'function')
-          ? (length--, customizer)
-          : undefined;
-
-        if (guard && isIterateeCall(sources[0], sources[1], guard)) {
-          customizer = length < 3 ? undefined : customizer;
-          length = 1;
-        }
-        object = Object(object);
-        while (++index < length) {
-          var source = sources[index];
-          if (source) {
-            assigner(object, source, index, customizer);
-          }
-        }
-        return object;
-      });
-    }
-
-    /**
-     * Creates a `baseEach` or `baseEachRight` function.
-     *
-     * @private
-     * @param {Function} eachFunc The function to iterate over a collection.
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new base function.
-     */
-    function createBaseEach(eachFunc, fromRight) {
-      return function(collection, iteratee) {
-        if (collection == null) {
-          return collection;
-        }
-        if (!isArrayLike(collection)) {
-          return eachFunc(collection, iteratee);
-        }
-        var length = collection.length,
-            index = fromRight ? length : -1,
-            iterable = Object(collection);
-
-        while ((fromRight ? index-- : ++index < length)) {
-          if (iteratee(iterable[index], index, iterable) === false) {
-            break;
-          }
-        }
-        return collection;
-      };
-    }
-
-    /**
-     * Creates a base function for methods like `_.forIn` and `_.forOwn`.
-     *
-     * @private
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new base function.
-     */
-    function createBaseFor(fromRight) {
-      return function(object, iteratee, keysFunc) {
-        var index = -1,
-            iterable = Object(object),
-            props = keysFunc(object),
-            length = props.length;
-
-        while (length--) {
-          var key = props[fromRight ? length : ++index];
-          if (iteratee(iterable[key], key, iterable) === false) {
-            break;
-          }
-        }
-        return object;
-      };
-    }
-
-    /**
-     * Creates a function that wraps `func` to invoke it with the optional `this`
-     * binding of `thisArg`.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createBind(func, bitmask, thisArg) {
-      var isBind = bitmask & WRAP_BIND_FLAG,
-          Ctor = createCtor(func);
-
-      function wrapper() {
-        var fn = (this && this !== root && this instanceof wrapper) ? Ctor : func;
-        return fn.apply(isBind ? thisArg : this, arguments);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a function like `_.lowerFirst`.
-     *
-     * @private
-     * @param {string} methodName The name of the `String` case method to use.
-     * @returns {Function} Returns the new case function.
-     */
-    function createCaseFirst(methodName) {
-      return function(string) {
-        string = toString(string);
-
-        var strSymbols = hasUnicode(string)
-          ? stringToArray(string)
-          : undefined;
-
-        var chr = strSymbols
-          ? strSymbols[0]
-          : string.charAt(0);
-
-        var trailing = strSymbols
-          ? castSlice(strSymbols, 1).join('')
-          : string.slice(1);
-
-        return chr[methodName]() + trailing;
-      };
-    }
-
-    /**
-     * Creates a function like `_.camelCase`.
-     *
-     * @private
-     * @param {Function} callback The function to combine each word.
-     * @returns {Function} Returns the new compounder function.
-     */
-    function createCompounder(callback) {
-      return function(string) {
-        return arrayReduce(words(deburr(string).replace(reApos, '')), callback, '');
-      };
-    }
-
-    /**
-     * Creates a function that produces an instance of `Ctor` regardless of
-     * whether it was invoked as part of a `new` expression or by `call` or `apply`.
-     *
-     * @private
-     * @param {Function} Ctor The constructor to wrap.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createCtor(Ctor) {
-      return function() {
-        // Use a `switch` statement to work with class constructors. See
-        // http://ecma-international.org/ecma-262/7.0/#sec-ecmascript-function-objects-call-thisargument-argumentslist
-        // for more details.
-        var args = arguments;
-        switch (args.length) {
-          case 0: return new Ctor;
-          case 1: return new Ctor(args[0]);
-          case 2: return new Ctor(args[0], args[1]);
-          case 3: return new Ctor(args[0], args[1], args[2]);
-          case 4: return new Ctor(args[0], args[1], args[2], args[3]);
-          case 5: return new Ctor(args[0], args[1], args[2], args[3], args[4]);
-          case 6: return new Ctor(args[0], args[1], args[2], args[3], args[4], args[5]);
-          case 7: return new Ctor(args[0], args[1], args[2], args[3], args[4], args[5], args[6]);
-        }
-        var thisBinding = baseCreate(Ctor.prototype),
-            result = Ctor.apply(thisBinding, args);
-
-        // Mimic the constructor's `return` behavior.
-        // See https://es5.github.io/#x13.2.2 for more details.
-        return isObject(result) ? result : thisBinding;
-      };
-    }
-
-    /**
-     * Creates a function that wraps `func` to enable currying.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {number} arity The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createCurry(func, bitmask, arity) {
-      var Ctor = createCtor(func);
-
-      function wrapper() {
-        var length = arguments.length,
-            args = Array(length),
-            index = length,
-            placeholder = getHolder(wrapper);
-
-        while (index--) {
-          args[index] = arguments[index];
-        }
-        var holders = (length < 3 && args[0] !== placeholder && args[length - 1] !== placeholder)
-          ? []
-          : replaceHolders(args, placeholder);
-
-        length -= holders.length;
-        if (length < arity) {
-          return createRecurry(
-            func, bitmask, createHybrid, wrapper.placeholder, undefined,
-            args, holders, undefined, undefined, arity - length);
-        }
-        var fn = (this && this !== root && this instanceof wrapper) ? Ctor : func;
-        return apply(fn, this, args);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a `_.find` or `_.findLast` function.
-     *
-     * @private
-     * @param {Function} findIndexFunc The function to find the collection index.
-     * @returns {Function} Returns the new find function.
-     */
-    function createFind(findIndexFunc) {
-      return function(collection, predicate, fromIndex) {
-        var iterable = Object(collection);
-        if (!isArrayLike(collection)) {
-          var iteratee = getIteratee(predicate, 3);
-          collection = keys(collection);
-          predicate = function(key) { return iteratee(iterable[key], key, iterable); };
-        }
-        var index = findIndexFunc(collection, predicate, fromIndex);
-        return index > -1 ? iterable[iteratee ? collection[index] : index] : undefined;
-      };
-    }
-
-    /**
-     * Creates a `_.flow` or `_.flowRight` function.
-     *
-     * @private
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new flow function.
-     */
-    function createFlow(fromRight) {
-      return flatRest(function(funcs) {
-        var length = funcs.length,
-            index = length,
-            prereq = LodashWrapper.prototype.thru;
-
-        if (fromRight) {
-          funcs.reverse();
-        }
-        while (index--) {
-          var func = funcs[index];
-          if (typeof func != 'function') {
-            throw new TypeError(FUNC_ERROR_TEXT);
-          }
-          if (prereq && !wrapper && getFuncName(func) == 'wrapper') {
-            var wrapper = new LodashWrapper([], true);
-          }
-        }
-        index = wrapper ? index : length;
-        while (++index < length) {
-          func = funcs[index];
-
-          var funcName = getFuncName(func),
-              data = funcName == 'wrapper' ? getData(func) : undefined;
-
-          if (data && isLaziable(data[0]) &&
-                data[1] == (WRAP_ARY_FLAG | WRAP_CURRY_FLAG | WRAP_PARTIAL_FLAG | WRAP_REARG_FLAG) &&
-                !data[4].length && data[9] == 1
-              ) {
-            wrapper = wrapper[getFuncName(data[0])].apply(wrapper, data[3]);
-          } else {
-            wrapper = (func.length == 1 && isLaziable(func))
-              ? wrapper[funcName]()
-              : wrapper.thru(func);
-          }
-        }
-        return function() {
-          var args = arguments,
-              value = args[0];
-
-          if (wrapper && args.length == 1 && isArray(value)) {
-            return wrapper.plant(value).value();
-          }
-          var index = 0,
-              result = length ? funcs[index].apply(this, args) : value;
-
-          while (++index < length) {
-            result = funcs[index].call(this, result);
-          }
-          return result;
-        };
-      });
-    }
-
-    /**
-     * Creates a function that wraps `func` to invoke it with optional `this`
-     * binding of `thisArg`, partial application, and currying.
-     *
-     * @private
-     * @param {Function|string} func The function or method name to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @param {Array} [partials] The arguments to prepend to those provided to
-     *  the new function.
-     * @param {Array} [holders] The `partials` placeholder indexes.
-     * @param {Array} [partialsRight] The arguments to append to those provided
-     *  to the new function.
-     * @param {Array} [holdersRight] The `partialsRight` placeholder indexes.
-     * @param {Array} [argPos] The argument positions of the new function.
-     * @param {number} [ary] The arity cap of `func`.
-     * @param {number} [arity] The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createHybrid(func, bitmask, thisArg, partials, holders, partialsRight, holdersRight, argPos, ary, arity) {
-      var isAry = bitmask & WRAP_ARY_FLAG,
-          isBind = bitmask & WRAP_BIND_FLAG,
-          isBindKey = bitmask & WRAP_BIND_KEY_FLAG,
-          isCurried = bitmask & (WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG),
-          isFlip = bitmask & WRAP_FLIP_FLAG,
-          Ctor = isBindKey ? undefined : createCtor(func);
-
-      function wrapper() {
-        var length = arguments.length,
-            args = Array(length),
-            index = length;
-
-        while (index--) {
-          args[index] = arguments[index];
-        }
-        if (isCurried) {
-          var placeholder = getHolder(wrapper),
-              holdersCount = countHolders(args, placeholder);
-        }
-        if (partials) {
-          args = composeArgs(args, partials, holders, isCurried);
-        }
-        if (partialsRight) {
-          args = composeArgsRight(args, partialsRight, holdersRight, isCurried);
-        }
-        length -= holdersCount;
-        if (isCurried && length < arity) {
-          var newHolders = replaceHolders(args, placeholder);
-          return createRecurry(
-            func, bitmask, createHybrid, wrapper.placeholder, thisArg,
-            args, newHolders, argPos, ary, arity - length
-          );
-        }
-        var thisBinding = isBind ? thisArg : this,
-            fn = isBindKey ? thisBinding[func] : func;
-
-        length = args.length;
-        if (argPos) {
-          args = reorder(args, argPos);
-        } else if (isFlip && length > 1) {
-          args.reverse();
-        }
-        if (isAry && ary < length) {
-          args.length = ary;
-        }
-        if (this && this !== root && this instanceof wrapper) {
-          fn = Ctor || createCtor(fn);
-        }
-        return fn.apply(thisBinding, args);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a function like `_.invertBy`.
-     *
-     * @private
-     * @param {Function} setter The function to set accumulator values.
-     * @param {Function} toIteratee The function to resolve iteratees.
-     * @returns {Function} Returns the new inverter function.
-     */
-    function createInverter(setter, toIteratee) {
-      return function(object, iteratee) {
-        return baseInverter(object, setter, toIteratee(iteratee), {});
-      };
-    }
-
-    /**
-     * Creates a function that performs a mathematical operation on two values.
-     *
-     * @private
-     * @param {Function} operator The function to perform the operation.
-     * @param {number} [defaultValue] The value used for `undefined` arguments.
-     * @returns {Function} Returns the new mathematical operation function.
-     */
-    function createMathOperation(operator, defaultValue) {
-      return function(value, other) {
-        var result;
-        if (value === undefined && other === undefined) {
-          return defaultValue;
-        }
-        if (value !== undefined) {
-          result = value;
-        }
-        if (other !== undefined) {
-          if (result === undefined) {
-            return other;
-          }
-          if (typeof value == 'string' || typeof other == 'string') {
-            value = baseToString(value);
-            other = baseToString(other);
-          } else {
-            value = baseToNumber(value);
-            other = baseToNumber(other);
-          }
-          result = operator(value, other);
-        }
-        return result;
-      };
-    }
-
-    /**
-     * Creates a function like `_.over`.
-     *
-     * @private
-     * @param {Function} arrayFunc The function to iterate over iteratees.
-     * @returns {Function} Returns the new over function.
-     */
-    function createOver(arrayFunc) {
-      return flatRest(function(iteratees) {
-        iteratees = arrayMap(iteratees, baseUnary(getIteratee()));
-        return baseRest(function(args) {
-          var thisArg = this;
-          return arrayFunc(iteratees, function(iteratee) {
-            return apply(iteratee, thisArg, args);
-          });
-        });
-      });
-    }
-
-    /**
-     * Creates the padding for `string` based on `length`. The `chars` string
-     * is truncated if the number of characters exceeds `length`.
-     *
-     * @private
-     * @param {number} length The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padding for `string`.
-     */
-    function createPadding(length, chars) {
-      chars = chars === undefined ? ' ' : baseToString(chars);
-
-      var charsLength = chars.length;
-      if (charsLength < 2) {
-        return charsLength ? baseRepeat(chars, length) : chars;
-      }
-      var result = baseRepeat(chars, nativeCeil(length / stringSize(chars)));
-      return hasUnicode(chars)
-        ? castSlice(stringToArray(result), 0, length).join('')
-        : result.slice(0, length);
-    }
-
-    /**
-     * Creates a function that wraps `func` to invoke it with the `this` binding
-     * of `thisArg` and `partials` prepended to the arguments it receives.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {*} thisArg The `this` binding of `func`.
-     * @param {Array} partials The arguments to prepend to those provided to
-     *  the new function.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createPartial(func, bitmask, thisArg, partials) {
-      var isBind = bitmask & WRAP_BIND_FLAG,
-          Ctor = createCtor(func);
-
-      function wrapper() {
-        var argsIndex = -1,
-            argsLength = arguments.length,
-            leftIndex = -1,
-            leftLength = partials.length,
-            args = Array(leftLength + argsLength),
-            fn = (this && this !== root && this instanceof wrapper) ? Ctor : func;
-
-        while (++leftIndex < leftLength) {
-          args[leftIndex] = partials[leftIndex];
-        }
-        while (argsLength--) {
-          args[leftIndex++] = arguments[++argsIndex];
-        }
-        return apply(fn, isBind ? thisArg : this, args);
-      }
-      return wrapper;
-    }
-
-    /**
-     * Creates a `_.range` or `_.rangeRight` function.
-     *
-     * @private
-     * @param {boolean} [fromRight] Specify iterating from right to left.
-     * @returns {Function} Returns the new range function.
-     */
-    function createRange(fromRight) {
-      return function(start, end, step) {
-        if (step && typeof step != 'number' && isIterateeCall(start, end, step)) {
-          end = step = undefined;
-        }
-        // Ensure the sign of `-0` is preserved.
-        start = toFinite(start);
-        if (end === undefined) {
-          end = start;
-          start = 0;
-        } else {
-          end = toFinite(end);
-        }
-        step = step === undefined ? (start < end ? 1 : -1) : toFinite(step);
-        return baseRange(start, end, step, fromRight);
-      };
-    }
-
-    /**
-     * Creates a function that performs a relational operation on two values.
-     *
-     * @private
-     * @param {Function} operator The function to perform the operation.
-     * @returns {Function} Returns the new relational operation function.
-     */
-    function createRelationalOperation(operator) {
-      return function(value, other) {
-        if (!(typeof value == 'string' && typeof other == 'string')) {
-          value = toNumber(value);
-          other = toNumber(other);
-        }
-        return operator(value, other);
-      };
-    }
-
-    /**
-     * Creates a function that wraps `func` to continue currying.
-     *
-     * @private
-     * @param {Function} func The function to wrap.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @param {Function} wrapFunc The function to create the `func` wrapper.
-     * @param {*} placeholder The placeholder value.
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @param {Array} [partials] The arguments to prepend to those provided to
-     *  the new function.
-     * @param {Array} [holders] The `partials` placeholder indexes.
-     * @param {Array} [argPos] The argument positions of the new function.
-     * @param {number} [ary] The arity cap of `func`.
-     * @param {number} [arity] The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createRecurry(func, bitmask, wrapFunc, placeholder, thisArg, partials, holders, argPos, ary, arity) {
-      var isCurry = bitmask & WRAP_CURRY_FLAG,
-          newHolders = isCurry ? holders : undefined,
-          newHoldersRight = isCurry ? undefined : holders,
-          newPartials = isCurry ? partials : undefined,
-          newPartialsRight = isCurry ? undefined : partials;
-
-      bitmask |= (isCurry ? WRAP_PARTIAL_FLAG : WRAP_PARTIAL_RIGHT_FLAG);
-      bitmask &= ~(isCurry ? WRAP_PARTIAL_RIGHT_FLAG : WRAP_PARTIAL_FLAG);
-
-      if (!(bitmask & WRAP_CURRY_BOUND_FLAG)) {
-        bitmask &= ~(WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG);
-      }
-      var newData = [
-        func, bitmask, thisArg, newPartials, newHolders, newPartialsRight,
-        newHoldersRight, argPos, ary, arity
-      ];
-
-      var result = wrapFunc.apply(undefined, newData);
-      if (isLaziable(func)) {
-        setData(result, newData);
-      }
-      result.placeholder = placeholder;
-      return setWrapToString(result, func, bitmask);
-    }
-
-    /**
-     * Creates a function like `_.round`.
-     *
-     * @private
-     * @param {string} methodName The name of the `Math` method to use when rounding.
-     * @returns {Function} Returns the new round function.
-     */
-    function createRound(methodName) {
-      var func = Math[methodName];
-      return function(number, precision) {
-        number = toNumber(number);
-        precision = precision == null ? 0 : nativeMin(toInteger(precision), 292);
-        if (precision && nativeIsFinite(number)) {
-          // Shift with exponential notation to avoid floating-point issues.
-          // See [MDN](https://mdn.io/round#Examples) for more details.
-          var pair = (toString(number) + 'e').split('e'),
-              value = func(pair[0] + 'e' + (+pair[1] + precision));
-
-          pair = (toString(value) + 'e').split('e');
-          return +(pair[0] + 'e' + (+pair[1] - precision));
-        }
-        return func(number);
-      };
-    }
-
-    /**
-     * Creates a set object of `values`.
-     *
-     * @private
-     * @param {Array} values The values to add to the set.
-     * @returns {Object} Returns the new set.
-     */
-    var createSet = !(Set && (1 / setToArray(new Set([,-0]))[1]) == INFINITY) ? noop : function(values) {
-      return new Set(values);
-    };
-
-    /**
-     * Creates a `_.toPairs` or `_.toPairsIn` function.
-     *
-     * @private
-     * @param {Function} keysFunc The function to get the keys of a given object.
-     * @returns {Function} Returns the new pairs function.
-     */
-    function createToPairs(keysFunc) {
-      return function(object) {
-        var tag = getTag(object);
-        if (tag == mapTag) {
-          return mapToArray(object);
-        }
-        if (tag == setTag) {
-          return setToPairs(object);
-        }
-        return baseToPairs(object, keysFunc(object));
-      };
-    }
-
-    /**
-     * Creates a function that either curries or invokes `func` with optional
-     * `this` binding and partially applied arguments.
-     *
-     * @private
-     * @param {Function|string} func The function or method name to wrap.
-     * @param {number} bitmask The bitmask flags.
-     *    1 - `_.bind`
-     *    2 - `_.bindKey`
-     *    4 - `_.curry` or `_.curryRight` of a bound function
-     *    8 - `_.curry`
-     *   16 - `_.curryRight`
-     *   32 - `_.partial`
-     *   64 - `_.partialRight`
-     *  128 - `_.rearg`
-     *  256 - `_.ary`
-     *  512 - `_.flip`
-     * @param {*} [thisArg] The `this` binding of `func`.
-     * @param {Array} [partials] The arguments to be partially applied.
-     * @param {Array} [holders] The `partials` placeholder indexes.
-     * @param {Array} [argPos] The argument positions of the new function.
-     * @param {number} [ary] The arity cap of `func`.
-     * @param {number} [arity] The arity of `func`.
-     * @returns {Function} Returns the new wrapped function.
-     */
-    function createWrap(func, bitmask, thisArg, partials, holders, argPos, ary, arity) {
-      var isBindKey = bitmask & WRAP_BIND_KEY_FLAG;
-      if (!isBindKey && typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      var length = partials ? partials.length : 0;
-      if (!length) {
-        bitmask &= ~(WRAP_PARTIAL_FLAG | WRAP_PARTIAL_RIGHT_FLAG);
-        partials = holders = undefined;
-      }
-      ary = ary === undefined ? ary : nativeMax(toInteger(ary), 0);
-      arity = arity === undefined ? arity : toInteger(arity);
-      length -= holders ? holders.length : 0;
-
-      if (bitmask & WRAP_PARTIAL_RIGHT_FLAG) {
-        var partialsRight = partials,
-            holdersRight = holders;
-
-        partials = holders = undefined;
-      }
-      var data = isBindKey ? undefined : getData(func);
-
-      var newData = [
-        func, bitmask, thisArg, partials, holders, partialsRight, holdersRight,
-        argPos, ary, arity
-      ];
-
-      if (data) {
-        mergeData(newData, data);
-      }
-      func = newData[0];
-      bitmask = newData[1];
-      thisArg = newData[2];
-      partials = newData[3];
-      holders = newData[4];
-      arity = newData[9] = newData[9] === undefined
-        ? (isBindKey ? 0 : func.length)
-        : nativeMax(newData[9] - length, 0);
-
-      if (!arity && bitmask & (WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG)) {
-        bitmask &= ~(WRAP_CURRY_FLAG | WRAP_CURRY_RIGHT_FLAG);
-      }
-      if (!bitmask || bitmask == WRAP_BIND_FLAG) {
-        var result = createBind(func, bitmask, thisArg);
-      } else if (bitmask == WRAP_CURRY_FLAG || bitmask == WRAP_CURRY_RIGHT_FLAG) {
-        result = createCurry(func, bitmask, arity);
-      } else if ((bitmask == WRAP_PARTIAL_FLAG || bitmask == (WRAP_BIND_FLAG | WRAP_PARTIAL_FLAG)) && !holders.length) {
-        result = createPartial(func, bitmask, thisArg, partials);
-      } else {
-        result = createHybrid.apply(undefined, newData);
-      }
-      var setter = data ? baseSetData : setData;
-      return setWrapToString(setter(result, newData), func, bitmask);
-    }
-
-    /**
-     * Used by `_.defaults` to customize its `_.assignIn` use to assign properties
-     * of source objects to the destination object for all destination properties
-     * that resolve to `undefined`.
-     *
-     * @private
-     * @param {*} objValue The destination value.
-     * @param {*} srcValue The source value.
-     * @param {string} key The key of the property to assign.
-     * @param {Object} object The parent object of `objValue`.
-     * @returns {*} Returns the value to assign.
-     */
-    function customDefaultsAssignIn(objValue, srcValue, key, object) {
-      if (objValue === undefined ||
-          (eq(objValue, objectProto[key]) && !hasOwnProperty.call(object, key))) {
-        return srcValue;
-      }
-      return objValue;
-    }
-
-    /**
-     * Used by `_.defaultsDeep` to customize its `_.merge` use to merge source
-     * objects into destination objects that are passed thru.
-     *
-     * @private
-     * @param {*} objValue The destination value.
-     * @param {*} srcValue The source value.
-     * @param {string} key The key of the property to merge.
-     * @param {Object} object The parent object of `objValue`.
-     * @param {Object} source The parent object of `srcValue`.
-     * @param {Object} [stack] Tracks traversed source values and their merged
-     *  counterparts.
-     * @returns {*} Returns the value to assign.
-     */
-    function customDefaultsMerge(objValue, srcValue, key, object, source, stack) {
-      if (isObject(objValue) && isObject(srcValue)) {
-        // Recursively merge objects and arrays (susceptible to call stack limits).
-        stack.set(srcValue, objValue);
-        baseMerge(objValue, srcValue, undefined, customDefaultsMerge, stack);
-        stack['delete'](srcValue);
-      }
-      return objValue;
-    }
-
-    /**
-     * Used by `_.omit` to customize its `_.cloneDeep` use to only clone plain
-     * objects.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @param {string} key The key of the property to inspect.
-     * @returns {*} Returns the uncloned value or `undefined` to defer cloning to `_.cloneDeep`.
-     */
-    function customOmitClone(value) {
-      return isPlainObject(value) ? undefined : value;
-    }
-
-    /**
-     * A specialized version of `baseIsEqualDeep` for arrays with support for
-     * partial deep comparisons.
-     *
-     * @private
-     * @param {Array} array The array to compare.
-     * @param {Array} other The other array to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} stack Tracks traversed `array` and `other` objects.
-     * @returns {boolean} Returns `true` if the arrays are equivalent, else `false`.
-     */
-    function equalArrays(array, other, bitmask, customizer, equalFunc, stack) {
-      var isPartial = bitmask & COMPARE_PARTIAL_FLAG,
-          arrLength = array.length,
-          othLength = other.length;
-
-      if (arrLength != othLength && !(isPartial && othLength > arrLength)) {
-        return false;
-      }
-      // Assume cyclic values are equal.
-      var stacked = stack.get(array);
-      if (stacked && stack.get(other)) {
-        return stacked == other;
-      }
-      var index = -1,
-          result = true,
-          seen = (bitmask & COMPARE_UNORDERED_FLAG) ? new SetCache : undefined;
-
-      stack.set(array, other);
-      stack.set(other, array);
-
-      // Ignore non-index properties.
-      while (++index < arrLength) {
-        var arrValue = array[index],
-            othValue = other[index];
-
-        if (customizer) {
-          var compared = isPartial
-            ? customizer(othValue, arrValue, index, other, array, stack)
-            : customizer(arrValue, othValue, index, array, other, stack);
-        }
-        if (compared !== undefined) {
-          if (compared) {
-            continue;
-          }
-          result = false;
-          break;
-        }
-        // Recursively compare arrays (susceptible to call stack limits).
-        if (seen) {
-          if (!arraySome(other, function(othValue, othIndex) {
-                if (!cacheHas(seen, othIndex) &&
-                    (arrValue === othValue || equalFunc(arrValue, othValue, bitmask, customizer, stack))) {
-                  return seen.push(othIndex);
-                }
-              })) {
-            result = false;
-            break;
-          }
-        } else if (!(
-              arrValue === othValue ||
-                equalFunc(arrValue, othValue, bitmask, customizer, stack)
-            )) {
-          result = false;
-          break;
-        }
-      }
-      stack['delete'](array);
-      stack['delete'](other);
-      return result;
-    }
-
-    /**
-     * A specialized version of `baseIsEqualDeep` for comparing objects of
-     * the same `toStringTag`.
-     *
-     * **Note:** This function only supports comparing values with tags of
-     * `Boolean`, `Date`, `Error`, `Number`, `RegExp`, or `String`.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {string} tag The `toStringTag` of the objects to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} stack Tracks traversed `object` and `other` objects.
-     * @returns {boolean} Returns `true` if the objects are equivalent, else `false`.
-     */
-    function equalByTag(object, other, tag, bitmask, customizer, equalFunc, stack) {
-      switch (tag) {
-        case dataViewTag:
-          if ((object.byteLength != other.byteLength) ||
-              (object.byteOffset != other.byteOffset)) {
-            return false;
-          }
-          object = object.buffer;
-          other = other.buffer;
-
-        case arrayBufferTag:
-          if ((object.byteLength != other.byteLength) ||
-              !equalFunc(new Uint8Array(object), new Uint8Array(other))) {
-            return false;
-          }
-          return true;
-
-        case boolTag:
-        case dateTag:
-        case numberTag:
-          // Coerce booleans to `1` or `0` and dates to milliseconds.
-          // Invalid dates are coerced to `NaN`.
-          return eq(+object, +other);
-
-        case errorTag:
-          return object.name == other.name && object.message == other.message;
-
-        case regexpTag:
-        case stringTag:
-          // Coerce regexes to strings and treat strings, primitives and objects,
-          // as equal. See http://www.ecma-international.org/ecma-262/7.0/#sec-regexp.prototype.tostring
-          // for more details.
-          return object == (other + '');
-
-        case mapTag:
-          var convert = mapToArray;
-
-        case setTag:
-          var isPartial = bitmask & COMPARE_PARTIAL_FLAG;
-          convert || (convert = setToArray);
-
-          if (object.size != other.size && !isPartial) {
-            return false;
-          }
-          // Assume cyclic values are equal.
-          var stacked = stack.get(object);
-          if (stacked) {
-            return stacked == other;
-          }
-          bitmask |= COMPARE_UNORDERED_FLAG;
-
-          // Recursively compare objects (susceptible to call stack limits).
-          stack.set(object, other);
-          var result = equalArrays(convert(object), convert(other), bitmask, customizer, equalFunc, stack);
-          stack['delete'](object);
-          return result;
-
-        case symbolTag:
-          if (symbolValueOf) {
-            return symbolValueOf.call(object) == symbolValueOf.call(other);
-          }
-      }
-      return false;
-    }
-
-    /**
-     * A specialized version of `baseIsEqualDeep` for objects with support for
-     * partial deep comparisons.
-     *
-     * @private
-     * @param {Object} object The object to compare.
-     * @param {Object} other The other object to compare.
-     * @param {number} bitmask The bitmask flags. See `baseIsEqual` for more details.
-     * @param {Function} customizer The function to customize comparisons.
-     * @param {Function} equalFunc The function to determine equivalents of values.
-     * @param {Object} stack Tracks traversed `object` and `other` objects.
-     * @returns {boolean} Returns `true` if the objects are equivalent, else `false`.
-     */
-    function equalObjects(object, other, bitmask, customizer, equalFunc, stack) {
-      var isPartial = bitmask & COMPARE_PARTIAL_FLAG,
-          objProps = getAllKeys(object),
-          objLength = objProps.length,
-          othProps = getAllKeys(other),
-          othLength = othProps.length;
-
-      if (objLength != othLength && !isPartial) {
-        return false;
-      }
-      var index = objLength;
-      while (index--) {
-        var key = objProps[index];
-        if (!(isPartial ? key in other : hasOwnProperty.call(other, key))) {
-          return false;
-        }
-      }
-      // Assume cyclic values are equal.
-      var stacked = stack.get(object);
-      if (stacked && stack.get(other)) {
-        return stacked == other;
-      }
-      var result = true;
-      stack.set(object, other);
-      stack.set(other, object);
-
-      var skipCtor = isPartial;
-      while (++index < objLength) {
-        key = objProps[index];
-        var objValue = object[key],
-            othValue = other[key];
-
-        if (customizer) {
-          var compared = isPartial
-            ? customizer(othValue, objValue, key, other, object, stack)
-            : customizer(objValue, othValue, key, object, other, stack);
-        }
-        // Recursively compare objects (susceptible to call stack limits).
-        if (!(compared === undefined
-              ? (objValue === othValue || equalFunc(objValue, othValue, bitmask, customizer, stack))
-              : compared
-            )) {
-          result = false;
-          break;
-        }
-        skipCtor || (skipCtor = key == 'constructor');
-      }
-      if (result && !skipCtor) {
-        var objCtor = object.constructor,
-            othCtor = other.constructor;
-
-        // Non `Object` object instances with different constructors are not equal.
-        if (objCtor != othCtor &&
-            ('constructor' in object && 'constructor' in other) &&
-            !(typeof objCtor == 'function' && objCtor instanceof objCtor &&
-              typeof othCtor == 'function' && othCtor instanceof othCtor)) {
-          result = false;
-        }
-      }
-      stack['delete'](object);
-      stack['delete'](other);
-      return result;
-    }
-
-    /**
-     * A specialized version of `baseRest` which flattens the rest array.
-     *
-     * @private
-     * @param {Function} func The function to apply a rest parameter to.
-     * @returns {Function} Returns the new function.
-     */
-    function flatRest(func) {
-      return setToString(overRest(func, undefined, flatten), func + '');
-    }
-
-    /**
-     * Creates an array of own enumerable property names and symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names and symbols.
-     */
-    function getAllKeys(object) {
-      return baseGetAllKeys(object, keys, getSymbols);
-    }
-
-    /**
-     * Creates an array of own and inherited enumerable property names and
-     * symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names and symbols.
-     */
-    function getAllKeysIn(object) {
-      return baseGetAllKeys(object, keysIn, getSymbolsIn);
-    }
-
-    /**
-     * Gets metadata for `func`.
-     *
-     * @private
-     * @param {Function} func The function to query.
-     * @returns {*} Returns the metadata for `func`.
-     */
-    var getData = !metaMap ? noop : function(func) {
-      return metaMap.get(func);
-    };
-
-    /**
-     * Gets the name of `func`.
-     *
-     * @private
-     * @param {Function} func The function to query.
-     * @returns {string} Returns the function name.
-     */
-    function getFuncName(func) {
-      var result = (func.name + ''),
-          array = realNames[result],
-          length = hasOwnProperty.call(realNames, result) ? array.length : 0;
-
-      while (length--) {
-        var data = array[length],
-            otherFunc = data.func;
-        if (otherFunc == null || otherFunc == func) {
-          return data.name;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Gets the argument placeholder value for `func`.
-     *
-     * @private
-     * @param {Function} func The function to inspect.
-     * @returns {*} Returns the placeholder value.
-     */
-    function getHolder(func) {
-      var object = hasOwnProperty.call(lodash, 'placeholder') ? lodash : func;
-      return object.placeholder;
-    }
-
-    /**
-     * Gets the appropriate "iteratee" function. If `_.iteratee` is customized,
-     * this function returns the custom method, otherwise it returns `baseIteratee`.
-     * If arguments are provided, the chosen function is invoked with them and
-     * its result is returned.
-     *
-     * @private
-     * @param {*} [value] The value to convert to an iteratee.
-     * @param {number} [arity] The arity of the created iteratee.
-     * @returns {Function} Returns the chosen function or its result.
-     */
-    function getIteratee() {
-      var result = lodash.iteratee || iteratee;
-      result = result === iteratee ? baseIteratee : result;
-      return arguments.length ? result(arguments[0], arguments[1]) : result;
-    }
-
-    /**
-     * Gets the data for `map`.
-     *
-     * @private
-     * @param {Object} map The map to query.
-     * @param {string} key The reference key.
-     * @returns {*} Returns the map data.
-     */
-    function getMapData(map, key) {
-      var data = map.__data__;
-      return isKeyable(key)
-        ? data[typeof key == 'string' ? 'string' : 'hash']
-        : data.map;
-    }
-
-    /**
-     * Gets the property names, values, and compare flags of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the match data of `object`.
-     */
-    function getMatchData(object) {
-      var result = keys(object),
-          length = result.length;
-
-      while (length--) {
-        var key = result[length],
-            value = object[key];
-
-        result[length] = [key, value, isStrictComparable(value)];
-      }
-      return result;
-    }
-
-    /**
-     * Gets the native function at `key` of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {string} key The key of the method to get.
-     * @returns {*} Returns the function if it's native, else `undefined`.
-     */
-    function getNative(object, key) {
-      var value = getValue(object, key);
-      return baseIsNative(value) ? value : undefined;
-    }
-
-    /**
-     * A specialized version of `baseGetTag` which ignores `Symbol.toStringTag` values.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @returns {string} Returns the raw `toStringTag`.
-     */
-    function getRawTag(value) {
-      var isOwn = hasOwnProperty.call(value, symToStringTag),
-          tag = value[symToStringTag];
-
-      try {
-        value[symToStringTag] = undefined;
-        var unmasked = true;
-      } catch (e) {}
-
-      var result = nativeObjectToString.call(value);
-      if (unmasked) {
-        if (isOwn) {
-          value[symToStringTag] = tag;
-        } else {
-          delete value[symToStringTag];
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Creates an array of the own enumerable symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of symbols.
-     */
-    var getSymbols = !nativeGetSymbols ? stubArray : function(object) {
-      if (object == null) {
-        return [];
-      }
-      object = Object(object);
-      return arrayFilter(nativeGetSymbols(object), function(symbol) {
-        return propertyIsEnumerable.call(object, symbol);
-      });
-    };
-
-    /**
-     * Creates an array of the own and inherited enumerable symbols of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of symbols.
-     */
-    var getSymbolsIn = !nativeGetSymbols ? stubArray : function(object) {
-      var result = [];
-      while (object) {
-        arrayPush(result, getSymbols(object));
-        object = getPrototype(object);
-      }
-      return result;
-    };
-
-    /**
-     * Gets the `toStringTag` of `value`.
-     *
-     * @private
-     * @param {*} value The value to query.
-     * @returns {string} Returns the `toStringTag`.
-     */
-    var getTag = baseGetTag;
-
-    // Fallback for data views, maps, sets, and weak maps in IE 11 and promises in Node.js < 6.
-    if ((DataView && getTag(new DataView(new ArrayBuffer(1))) != dataViewTag) ||
-        (Map && getTag(new Map) != mapTag) ||
-        (Promise && getTag(Promise.resolve()) != promiseTag) ||
-        (Set && getTag(new Set) != setTag) ||
-        (WeakMap && getTag(new WeakMap) != weakMapTag)) {
-      getTag = function(value) {
-        var result = baseGetTag(value),
-            Ctor = result == objectTag ? value.constructor : undefined,
-            ctorString = Ctor ? toSource(Ctor) : '';
-
-        if (ctorString) {
-          switch (ctorString) {
-            case dataViewCtorString: return dataViewTag;
-            case mapCtorString: return mapTag;
-            case promiseCtorString: return promiseTag;
-            case setCtorString: return setTag;
-            case weakMapCtorString: return weakMapTag;
-          }
-        }
-        return result;
-      };
-    }
-
-    /**
-     * Gets the view, applying any `transforms` to the `start` and `end` positions.
-     *
-     * @private
-     * @param {number} start The start of the view.
-     * @param {number} end The end of the view.
-     * @param {Array} transforms The transformations to apply to the view.
-     * @returns {Object} Returns an object containing the `start` and `end`
-     *  positions of the view.
-     */
-    function getView(start, end, transforms) {
-      var index = -1,
-          length = transforms.length;
-
-      while (++index < length) {
-        var data = transforms[index],
-            size = data.size;
-
-        switch (data.type) {
-          case 'drop':      start += size; break;
-          case 'dropRight': end -= size; break;
-          case 'take':      end = nativeMin(end, start + size); break;
-          case 'takeRight': start = nativeMax(start, end - size); break;
-        }
-      }
-      return { 'start': start, 'end': end };
-    }
-
-    /**
-     * Extracts wrapper details from the `source` body comment.
-     *
-     * @private
-     * @param {string} source The source to inspect.
-     * @returns {Array} Returns the wrapper details.
-     */
-    function getWrapDetails(source) {
-      var match = source.match(reWrapDetails);
-      return match ? match[1].split(reSplitDetails) : [];
-    }
-
-    /**
-     * Checks if `path` exists on `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path to check.
-     * @param {Function} hasFunc The function to check properties.
-     * @returns {boolean} Returns `true` if `path` exists, else `false`.
-     */
-    function hasPath(object, path, hasFunc) {
-      path = castPath(path, object);
-
-      var index = -1,
-          length = path.length,
-          result = false;
-
-      while (++index < length) {
-        var key = toKey(path[index]);
-        if (!(result = object != null && hasFunc(object, key))) {
-          break;
-        }
-        object = object[key];
-      }
-      if (result || ++index != length) {
-        return result;
-      }
-      length = object == null ? 0 : object.length;
-      return !!length && isLength(length) && isIndex(key, length) &&
-        (isArray(object) || isArguments(object));
-    }
-
-    /**
-     * Initializes an array clone.
-     *
-     * @private
-     * @param {Array} array The array to clone.
-     * @returns {Array} Returns the initialized clone.
-     */
-    function initCloneArray(array) {
-      var length = array.length,
-          result = new array.constructor(length);
-
-      // Add properties assigned by `RegExp#exec`.
-      if (length && typeof array[0] == 'string' && hasOwnProperty.call(array, 'index')) {
-        result.index = array.index;
-        result.input = array.input;
-      }
-      return result;
-    }
-
-    /**
-     * Initializes an object clone.
-     *
-     * @private
-     * @param {Object} object The object to clone.
-     * @returns {Object} Returns the initialized clone.
-     */
-    function initCloneObject(object) {
-      return (typeof object.constructor == 'function' && !isPrototype(object))
-        ? baseCreate(getPrototype(object))
-        : {};
-    }
-
-    /**
-     * Initializes an object clone based on its `toStringTag`.
-     *
-     * **Note:** This function only supports cloning values with tags of
-     * `Boolean`, `Date`, `Error`, `Map`, `Number`, `RegExp`, `Set`, or `String`.
-     *
-     * @private
-     * @param {Object} object The object to clone.
-     * @param {string} tag The `toStringTag` of the object to clone.
-     * @param {boolean} [isDeep] Specify a deep clone.
-     * @returns {Object} Returns the initialized clone.
-     */
-    function initCloneByTag(object, tag, isDeep) {
-      var Ctor = object.constructor;
-      switch (tag) {
-        case arrayBufferTag:
-          return cloneArrayBuffer(object);
-
-        case boolTag:
-        case dateTag:
-          return new Ctor(+object);
-
-        case dataViewTag:
-          return cloneDataView(object, isDeep);
-
-        case float32Tag: case float64Tag:
-        case int8Tag: case int16Tag: case int32Tag:
-        case uint8Tag: case uint8ClampedTag: case uint16Tag: case uint32Tag:
-          return cloneTypedArray(object, isDeep);
-
-        case mapTag:
-          return new Ctor;
-
-        case numberTag:
-        case stringTag:
-          return new Ctor(object);
-
-        case regexpTag:
-          return cloneRegExp(object);
-
-        case setTag:
-          return new Ctor;
-
-        case symbolTag:
-          return cloneSymbol(object);
-      }
-    }
-
-    /**
-     * Inserts wrapper `details` in a comment at the top of the `source` body.
-     *
-     * @private
-     * @param {string} source The source to modify.
-     * @returns {Array} details The details to insert.
-     * @returns {string} Returns the modified source.
-     */
-    function insertWrapDetails(source, details) {
-      var length = details.length;
-      if (!length) {
-        return source;
-      }
-      var lastIndex = length - 1;
-      details[lastIndex] = (length > 1 ? '& ' : '') + details[lastIndex];
-      details = details.join(length > 2 ? ', ' : ' ');
-      return source.replace(reWrapComment, '{\n/* [wrapped with ' + details + '] */\n');
-    }
-
-    /**
-     * Checks if `value` is a flattenable `arguments` object or array.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is flattenable, else `false`.
-     */
-    function isFlattenable(value) {
-      return isArray(value) || isArguments(value) ||
-        !!(spreadableSymbol && value && value[spreadableSymbol]);
-    }
-
-    /**
-     * Checks if `value` is a valid array-like index.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @param {number} [length=MAX_SAFE_INTEGER] The upper bounds of a valid index.
-     * @returns {boolean} Returns `true` if `value` is a valid index, else `false`.
-     */
-    function isIndex(value, length) {
-      var type = typeof value;
-      length = length == null ? MAX_SAFE_INTEGER : length;
-
-      return !!length &&
-        (type == 'number' ||
-          (type != 'symbol' && reIsUint.test(value))) &&
-            (value > -1 && value % 1 == 0 && value < length);
-    }
-
-    /**
-     * Checks if the given arguments are from an iteratee call.
-     *
-     * @private
-     * @param {*} value The potential iteratee value argument.
-     * @param {*} index The potential iteratee index or key argument.
-     * @param {*} object The potential iteratee object argument.
-     * @returns {boolean} Returns `true` if the arguments are from an iteratee call,
-     *  else `false`.
-     */
-    function isIterateeCall(value, index, object) {
-      if (!isObject(object)) {
-        return false;
-      }
-      var type = typeof index;
-      if (type == 'number'
-            ? (isArrayLike(object) && isIndex(index, object.length))
-            : (type == 'string' && index in object)
-          ) {
-        return eq(object[index], value);
-      }
-      return false;
-    }
-
-    /**
-     * Checks if `value` is a property name and not a property path.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @param {Object} [object] The object to query keys on.
-     * @returns {boolean} Returns `true` if `value` is a property name, else `false`.
-     */
-    function isKey(value, object) {
-      if (isArray(value)) {
-        return false;
-      }
-      var type = typeof value;
-      if (type == 'number' || type == 'symbol' || type == 'boolean' ||
-          value == null || isSymbol(value)) {
-        return true;
-      }
-      return reIsPlainProp.test(value) || !reIsDeepProp.test(value) ||
-        (object != null && value in Object(object));
-    }
-
-    /**
-     * Checks if `value` is suitable for use as unique object key.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is suitable, else `false`.
-     */
-    function isKeyable(value) {
-      var type = typeof value;
-      return (type == 'string' || type == 'number' || type == 'symbol' || type == 'boolean')
-        ? (value !== '__proto__')
-        : (value === null);
-    }
-
-    /**
-     * Checks if `func` has a lazy counterpart.
-     *
-     * @private
-     * @param {Function} func The function to check.
-     * @returns {boolean} Returns `true` if `func` has a lazy counterpart,
-     *  else `false`.
-     */
-    function isLaziable(func) {
-      var funcName = getFuncName(func),
-          other = lodash[funcName];
-
-      if (typeof other != 'function' || !(funcName in LazyWrapper.prototype)) {
-        return false;
-      }
-      if (func === other) {
-        return true;
-      }
-      var data = getData(other);
-      return !!data && func === data[0];
-    }
-
-    /**
-     * Checks if `func` has its source masked.
-     *
-     * @private
-     * @param {Function} func The function to check.
-     * @returns {boolean} Returns `true` if `func` is masked, else `false`.
-     */
-    function isMasked(func) {
-      return !!maskSrcKey && (maskSrcKey in func);
-    }
-
-    /**
-     * Checks if `func` is capable of being masked.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `func` is maskable, else `false`.
-     */
-    var isMaskable = coreJsData ? isFunction : stubFalse;
-
-    /**
-     * Checks if `value` is likely a prototype object.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a prototype, else `false`.
-     */
-    function isPrototype(value) {
-      var Ctor = value && value.constructor,
-          proto = (typeof Ctor == 'function' && Ctor.prototype) || objectProto;
-
-      return value === proto;
-    }
-
-    /**
-     * Checks if `value` is suitable for strict equality comparisons, i.e. `===`.
-     *
-     * @private
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` if suitable for strict
-     *  equality comparisons, else `false`.
-     */
-    function isStrictComparable(value) {
-      return value === value && !isObject(value);
-    }
-
-    /**
-     * A specialized version of `matchesProperty` for source values suitable
-     * for strict equality comparisons, i.e. `===`.
-     *
-     * @private
-     * @param {string} key The key of the property to get.
-     * @param {*} srcValue The value to match.
-     * @returns {Function} Returns the new spec function.
-     */
-    function matchesStrictComparable(key, srcValue) {
-      return function(object) {
-        if (object == null) {
-          return false;
-        }
-        return object[key] === srcValue &&
-          (srcValue !== undefined || (key in Object(object)));
-      };
-    }
-
-    /**
-     * A specialized version of `_.memoize` which clears the memoized function's
-     * cache when it exceeds `MAX_MEMOIZE_SIZE`.
-     *
-     * @private
-     * @param {Function} func The function to have its output memoized.
-     * @returns {Function} Returns the new memoized function.
-     */
-    function memoizeCapped(func) {
-      var result = memoize(func, function(key) {
-        if (cache.size === MAX_MEMOIZE_SIZE) {
-          cache.clear();
-        }
-        return key;
-      });
-
-      var cache = result.cache;
-      return result;
-    }
-
-    /**
-     * Merges the function metadata of `source` into `data`.
-     *
-     * Merging metadata reduces the number of wrappers used to invoke a function.
-     * This is possible because methods like `_.bind`, `_.curry`, and `_.partial`
-     * may be applied regardless of execution order. Methods like `_.ary` and
-     * `_.rearg` modify function arguments, making the order in which they are
-     * executed important, preventing the merging of metadata. However, we make
-     * an exception for a safe combined case where curried functions have `_.ary`
-     * and or `_.rearg` applied.
-     *
-     * @private
-     * @param {Array} data The destination metadata.
-     * @param {Array} source The source metadata.
-     * @returns {Array} Returns `data`.
-     */
-    function mergeData(data, source) {
-      var bitmask = data[1],
-          srcBitmask = source[1],
-          newBitmask = bitmask | srcBitmask,
-          isCommon = newBitmask < (WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG | WRAP_ARY_FLAG);
-
-      var isCombo =
-        ((srcBitmask == WRAP_ARY_FLAG) && (bitmask == WRAP_CURRY_FLAG)) ||
-        ((srcBitmask == WRAP_ARY_FLAG) && (bitmask == WRAP_REARG_FLAG) && (data[7].length <= source[8])) ||
-        ((srcBitmask == (WRAP_ARY_FLAG | WRAP_REARG_FLAG)) && (source[7].length <= source[8]) && (bitmask == WRAP_CURRY_FLAG));
-
-      // Exit early if metadata can't be merged.
-      if (!(isCommon || isCombo)) {
-        return data;
-      }
-      // Use source `thisArg` if available.
-      if (srcBitmask & WRAP_BIND_FLAG) {
-        data[2] = source[2];
-        // Set when currying a bound function.
-        newBitmask |= bitmask & WRAP_BIND_FLAG ? 0 : WRAP_CURRY_BOUND_FLAG;
-      }
-      // Compose partial arguments.
-      var value = source[3];
-      if (value) {
-        var partials = data[3];
-        data[3] = partials ? composeArgs(partials, value, source[4]) : value;
-        data[4] = partials ? replaceHolders(data[3], PLACEHOLDER) : source[4];
-      }
-      // Compose partial right arguments.
-      value = source[5];
-      if (value) {
-        partials = data[5];
-        data[5] = partials ? composeArgsRight(partials, value, source[6]) : value;
-        data[6] = partials ? replaceHolders(data[5], PLACEHOLDER) : source[6];
-      }
-      // Use source `argPos` if available.
-      value = source[7];
-      if (value) {
-        data[7] = value;
-      }
-      // Use source `ary` if it's smaller.
-      if (srcBitmask & WRAP_ARY_FLAG) {
-        data[8] = data[8] == null ? source[8] : nativeMin(data[8], source[8]);
-      }
-      // Use source `arity` if one is not provided.
-      if (data[9] == null) {
-        data[9] = source[9];
-      }
-      // Use source `func` and merge bitmasks.
-      data[0] = source[0];
-      data[1] = newBitmask;
-
-      return data;
-    }
-
-    /**
-     * This function is like
-     * [`Object.keys`](http://ecma-international.org/ecma-262/7.0/#sec-object.keys)
-     * except that it includes inherited enumerable properties.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     */
-    function nativeKeysIn(object) {
-      var result = [];
-      if (object != null) {
-        for (var key in Object(object)) {
-          result.push(key);
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Converts `value` to a string using `Object.prototype.toString`.
-     *
-     * @private
-     * @param {*} value The value to convert.
-     * @returns {string} Returns the converted string.
-     */
-    function objectToString(value) {
-      return nativeObjectToString.call(value);
-    }
-
-    /**
-     * A specialized version of `baseRest` which transforms the rest array.
-     *
-     * @private
-     * @param {Function} func The function to apply a rest parameter to.
-     * @param {number} [start=func.length-1] The start position of the rest parameter.
-     * @param {Function} transform The rest array transform.
-     * @returns {Function} Returns the new function.
-     */
-    function overRest(func, start, transform) {
-      start = nativeMax(start === undefined ? (func.length - 1) : start, 0);
-      return function() {
-        var args = arguments,
-            index = -1,
-            length = nativeMax(args.length - start, 0),
-            array = Array(length);
-
-        while (++index < length) {
-          array[index] = args[start + index];
-        }
-        index = -1;
-        var otherArgs = Array(start + 1);
-        while (++index < start) {
-          otherArgs[index] = args[index];
-        }
-        otherArgs[start] = transform(array);
-        return apply(func, this, otherArgs);
-      };
-    }
-
-    /**
-     * Gets the parent value at `path` of `object`.
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {Array} path The path to get the parent value of.
-     * @returns {*} Returns the parent value.
-     */
-    function parent(object, path) {
-      return path.length < 2 ? object : baseGet(object, baseSlice(path, 0, -1));
-    }
-
-    /**
-     * Reorder `array` according to the specified indexes where the element at
-     * the first index is assigned as the first element, the element at
-     * the second index is assigned as the second element, and so on.
-     *
-     * @private
-     * @param {Array} array The array to reorder.
-     * @param {Array} indexes The arranged array indexes.
-     * @returns {Array} Returns `array`.
-     */
-    function reorder(array, indexes) {
-      var arrLength = array.length,
-          length = nativeMin(indexes.length, arrLength),
-          oldArray = copyArray(array);
-
-      while (length--) {
-        var index = indexes[length];
-        array[length] = isIndex(index, arrLength) ? oldArray[index] : undefined;
-      }
-      return array;
-    }
-
-    /**
-     * Gets the value at `key`, unless `key` is "__proto__" or "constructor".
-     *
-     * @private
-     * @param {Object} object The object to query.
-     * @param {string} key The key of the property to get.
-     * @returns {*} Returns the property value.
-     */
-    function safeGet(object, key) {
-      if (key === 'constructor' && typeof object[key] === 'function') {
-        return;
-      }
-
-      if (key == '__proto__') {
-        return;
-      }
-
-      return object[key];
-    }
-
-    /**
-     * Sets metadata for `func`.
-     *
-     * **Note:** If this function becomes hot, i.e. is invoked a lot in a short
-     * period of time, it will trip its breaker and transition to an identity
-     * function to avoid garbage collection pauses in V8. See
-     * [V8 issue 2070](https://bugs.chromium.org/p/v8/issues/detail?id=2070)
-     * for more details.
-     *
-     * @private
-     * @param {Function} func The function to associate metadata with.
-     * @param {*} data The metadata.
-     * @returns {Function} Returns `func`.
-     */
-    var setData = shortOut(baseSetData);
-
-    /**
-     * A simple wrapper around the global [`setTimeout`](https://mdn.io/setTimeout).
-     *
-     * @private
-     * @param {Function} func The function to delay.
-     * @param {number} wait The number of milliseconds to delay invocation.
-     * @returns {number|Object} Returns the timer id or timeout object.
-     */
-    var setTimeout = ctxSetTimeout || function(func, wait) {
-      return root.setTimeout(func, wait);
-    };
-
-    /**
-     * Sets the `toString` method of `func` to return `string`.
-     *
-     * @private
-     * @param {Function} func The function to modify.
-     * @param {Function} string The `toString` result.
-     * @returns {Function} Returns `func`.
-     */
-    var setToString = shortOut(baseSetToString);
-
-    /**
-     * Sets the `toString` method of `wrapper` to mimic the source of `reference`
-     * with wrapper details in a comment at the top of the source body.
-     *
-     * @private
-     * @param {Function} wrapper The function to modify.
-     * @param {Function} reference The reference function.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @returns {Function} Returns `wrapper`.
-     */
-    function setWrapToString(wrapper, reference, bitmask) {
-      var source = (reference + '');
-      return setToString(wrapper, insertWrapDetails(source, updateWrapDetails(getWrapDetails(source), bitmask)));
-    }
-
-    /**
-     * Creates a function that'll short out and invoke `identity` instead
-     * of `func` when it's called `HOT_COUNT` or more times in `HOT_SPAN`
-     * milliseconds.
-     *
-     * @private
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new shortable function.
-     */
-    function shortOut(func) {
-      var count = 0,
-          lastCalled = 0;
-
-      return function() {
-        var stamp = nativeNow(),
-            remaining = HOT_SPAN - (stamp - lastCalled);
-
-        lastCalled = stamp;
-        if (remaining > 0) {
-          if (++count >= HOT_COUNT) {
-            return arguments[0];
-          }
-        } else {
-          count = 0;
-        }
-        return func.apply(undefined, arguments);
-      };
-    }
-
-    /**
-     * A specialized version of `_.shuffle` which mutates and sets the size of `array`.
-     *
-     * @private
-     * @param {Array} array The array to shuffle.
-     * @param {number} [size=array.length] The size of `array`.
-     * @returns {Array} Returns `array`.
-     */
-    function shuffleSelf(array, size) {
-      var index = -1,
-          length = array.length,
-          lastIndex = length - 1;
-
-      size = size === undefined ? length : size;
-      while (++index < size) {
-        var rand = baseRandom(index, lastIndex),
-            value = array[rand];
-
-        array[rand] = array[index];
-        array[index] = value;
-      }
-      array.length = size;
-      return array;
-    }
-
-    /**
-     * Converts `string` to a property path array.
-     *
-     * @private
-     * @param {string} string The string to convert.
-     * @returns {Array} Returns the property path array.
-     */
-    var stringToPath = memoizeCapped(function(string) {
-      var result = [];
-      if (string.charCodeAt(0) === 46 /* . */) {
-        result.push('');
-      }
-      string.replace(rePropName, function(match, number, quote, subString) {
-        result.push(quote ? subString.replace(reEscapeChar, '$1') : (number || match));
-      });
-      return result;
-    });
-
-    /**
-     * Converts `value` to a string key if it's not a string or symbol.
-     *
-     * @private
-     * @param {*} value The value to inspect.
-     * @returns {string|symbol} Returns the key.
-     */
-    function toKey(value) {
-      if (typeof value == 'string' || isSymbol(value)) {
-        return value;
-      }
-      var result = (value + '');
-      return (result == '0' && (1 / value) == -INFINITY) ? '-0' : result;
-    }
-
-    /**
-     * Converts `func` to its source code.
-     *
-     * @private
-     * @param {Function} func The function to convert.
-     * @returns {string} Returns the source code.
-     */
-    function toSource(func) {
-      if (func != null) {
-        try {
-          return funcToString.call(func);
-        } catch (e) {}
-        try {
-          return (func + '');
-        } catch (e) {}
-      }
-      return '';
-    }
-
-    /**
-     * Updates wrapper `details` based on `bitmask` flags.
-     *
-     * @private
-     * @returns {Array} details The details to modify.
-     * @param {number} bitmask The bitmask flags. See `createWrap` for more details.
-     * @returns {Array} Returns `details`.
-     */
-    function updateWrapDetails(details, bitmask) {
-      arrayEach(wrapFlags, function(pair) {
-        var value = '_.' + pair[0];
-        if ((bitmask & pair[1]) && !arrayIncludes(details, value)) {
-          details.push(value);
-        }
-      });
-      return details.sort();
-    }
-
-    /**
-     * Creates a clone of `wrapper`.
-     *
-     * @private
-     * @param {Object} wrapper The wrapper to clone.
-     * @returns {Object} Returns the cloned wrapper.
-     */
-    function wrapperClone(wrapper) {
-      if (wrapper instanceof LazyWrapper) {
-        return wrapper.clone();
-      }
-      var result = new LodashWrapper(wrapper.__wrapped__, wrapper.__chain__);
-      result.__actions__ = copyArray(wrapper.__actions__);
-      result.__index__  = wrapper.__index__;
-      result.__values__ = wrapper.__values__;
-      return result;
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an array of elements split into groups the length of `size`.
-     * If `array` can't be split evenly, the final chunk will be the remaining
-     * elements.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to process.
-     * @param {number} [size=1] The length of each chunk
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the new array of chunks.
-     * @example
-     *
-     * _.chunk(['a', 'b', 'c', 'd'], 2);
-     * // => [['a', 'b'], ['c', 'd']]
-     *
-     * _.chunk(['a', 'b', 'c', 'd'], 3);
-     * // => [['a', 'b', 'c'], ['d']]
-     */
-    function chunk(array, size, guard) {
-      if ((guard ? isIterateeCall(array, size, guard) : size === undefined)) {
-        size = 1;
-      } else {
-        size = nativeMax(toInteger(size), 0);
-      }
-      var length = array == null ? 0 : array.length;
-      if (!length || size < 1) {
-        return [];
-      }
-      var index = 0,
-          resIndex = 0,
-          result = Array(nativeCeil(length / size));
-
-      while (index < length) {
-        result[resIndex++] = baseSlice(array, index, (index += size));
-      }
-      return result;
-    }
-
-    /**
-     * Creates an array with all falsey values removed. The values `false`, `null`,
-     * `0`, `""`, `undefined`, and `NaN` are falsey.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to compact.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * _.compact([0, 1, false, 2, '', 3]);
-     * // => [1, 2, 3]
-     */
-    function compact(array) {
-      var index = -1,
-          length = array == null ? 0 : array.length,
-          resIndex = 0,
-          result = [];
-
-      while (++index < length) {
-        var value = array[index];
-        if (value) {
-          result[resIndex++] = value;
-        }
-      }
-      return result;
-    }
-
-    /**
-     * Creates a new array concatenating `array` with any additional arrays
-     * and/or values.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to concatenate.
-     * @param {...*} [values] The values to concatenate.
-     * @returns {Array} Returns the new concatenated array.
-     * @example
-     *
-     * var array = [1];
-     * var other = _.concat(array, 2, [3], [[4]]);
-     *
-     * console.log(other);
-     * // => [1, 2, 3, [4]]
-     *
-     * console.log(array);
-     * // => [1]
-     */
-    function concat() {
-      var length = arguments.length;
-      if (!length) {
-        return [];
-      }
-      var args = Array(length - 1),
-          array = arguments[0],
-          index = length;
-
-      while (index--) {
-        args[index - 1] = arguments[index];
-      }
-      return arrayPush(isArray(array) ? copyArray(array) : [array], baseFlatten(args, 1));
-    }
-
-    /**
-     * Creates an array of `array` values not included in the other given arrays
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons. The order and references of result values are
-     * determined by the first array.
-     *
-     * **Note:** Unlike `_.pullAll`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...Array} [values] The values to exclude.
-     * @returns {Array} Returns the new array of filtered values.
-     * @see _.without, _.xor
-     * @example
-     *
-     * _.difference([2, 1], [2, 3]);
-     * // => [1]
-     */
-    var difference = baseRest(function(array, values) {
-      return isArrayLikeObject(array)
-        ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true))
-        : [];
-    });
-
-    /**
-     * This method is like `_.difference` except that it accepts `iteratee` which
-     * is invoked for each element of `array` and `values` to generate the criterion
-     * by which they're compared. The order and references of result values are
-     * determined by the first array. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * **Note:** Unlike `_.pullAllBy`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...Array} [values] The values to exclude.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * _.differenceBy([2.1, 1.2], [2.3, 3.4], Math.floor);
-     * // => [1.2]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.differenceBy([{ 'x': 2 }, { 'x': 1 }], [{ 'x': 1 }], 'x');
-     * // => [{ 'x': 2 }]
-     */
-    var differenceBy = baseRest(function(array, values) {
-      var iteratee = last(values);
-      if (isArrayLikeObject(iteratee)) {
-        iteratee = undefined;
-      }
-      return isArrayLikeObject(array)
-        ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true), getIteratee(iteratee, 2))
-        : [];
-    });
-
-    /**
-     * This method is like `_.difference` except that it accepts `comparator`
-     * which is invoked to compare elements of `array` to `values`. The order and
-     * references of result values are determined by the first array. The comparator
-     * is invoked with two arguments: (arrVal, othVal).
-     *
-     * **Note:** Unlike `_.pullAllWith`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...Array} [values] The values to exclude.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     *
-     * _.differenceWith(objects, [{ 'x': 1, 'y': 2 }], _.isEqual);
-     * // => [{ 'x': 2, 'y': 1 }]
-     */
-    var differenceWith = baseRest(function(array, values) {
-      var comparator = last(values);
-      if (isArrayLikeObject(comparator)) {
-        comparator = undefined;
-      }
-      return isArrayLikeObject(array)
-        ? baseDifference(array, baseFlatten(values, 1, isArrayLikeObject, true), undefined, comparator)
-        : [];
-    });
-
-    /**
-     * Creates a slice of `array` with `n` elements dropped from the beginning.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.5.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to drop.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.drop([1, 2, 3]);
-     * // => [2, 3]
-     *
-     * _.drop([1, 2, 3], 2);
-     * // => [3]
-     *
-     * _.drop([1, 2, 3], 5);
-     * // => []
-     *
-     * _.drop([1, 2, 3], 0);
-     * // => [1, 2, 3]
-     */
-    function drop(array, n, guard) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      return baseSlice(array, n < 0 ? 0 : n, length);
-    }
-
-    /**
-     * Creates a slice of `array` with `n` elements dropped from the end.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to drop.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.dropRight([1, 2, 3]);
-     * // => [1, 2]
-     *
-     * _.dropRight([1, 2, 3], 2);
-     * // => [1]
-     *
-     * _.dropRight([1, 2, 3], 5);
-     * // => []
-     *
-     * _.dropRight([1, 2, 3], 0);
-     * // => [1, 2, 3]
-     */
-    function dropRight(array, n, guard) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      n = length - n;
-      return baseSlice(array, 0, n < 0 ? 0 : n);
-    }
-
-    /**
-     * Creates a slice of `array` excluding elements dropped from the end.
-     * Elements are dropped until `predicate` returns falsey. The predicate is
-     * invoked with three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': true },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': false }
-     * ];
-     *
-     * _.dropRightWhile(users, function(o) { return !o.active; });
-     * // => objects for ['barney']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.dropRightWhile(users, { 'user': 'pebbles', 'active': false });
-     * // => objects for ['barney', 'fred']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.dropRightWhile(users, ['active', false]);
-     * // => objects for ['barney']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.dropRightWhile(users, 'active');
-     * // => objects for ['barney', 'fred', 'pebbles']
-     */
-    function dropRightWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3), true, true)
-        : [];
-    }
-
-    /**
-     * Creates a slice of `array` excluding elements dropped from the beginning.
-     * Elements are dropped until `predicate` returns falsey. The predicate is
-     * invoked with three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': false },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': true }
-     * ];
-     *
-     * _.dropWhile(users, function(o) { return !o.active; });
-     * // => objects for ['pebbles']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.dropWhile(users, { 'user': 'barney', 'active': false });
-     * // => objects for ['fred', 'pebbles']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.dropWhile(users, ['active', false]);
-     * // => objects for ['pebbles']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.dropWhile(users, 'active');
-     * // => objects for ['barney', 'fred', 'pebbles']
-     */
-    function dropWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3), true)
-        : [];
-    }
-
-    /**
-     * Fills elements of `array` with `value` from `start` up to, but not
-     * including, `end`.
-     *
-     * **Note:** This method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.2.0
-     * @category Array
-     * @param {Array} array The array to fill.
-     * @param {*} value The value to fill `array` with.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [1, 2, 3];
-     *
-     * _.fill(array, 'a');
-     * console.log(array);
-     * // => ['a', 'a', 'a']
-     *
-     * _.fill(Array(3), 2);
-     * // => [2, 2, 2]
-     *
-     * _.fill([4, 6, 8, 10], '*', 1, 3);
-     * // => [4, '*', '*', 10]
-     */
-    function fill(array, value, start, end) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      if (start && typeof start != 'number' && isIterateeCall(array, value, start)) {
-        start = 0;
-        end = length;
-      }
-      return baseFill(array, value, start, end);
-    }
-
-    /**
-     * This method is like `_.find` except that it returns the index of the first
-     * element `predicate` returns truthy for instead of the element itself.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @returns {number} Returns the index of the found element, else `-1`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': false },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': true }
-     * ];
-     *
-     * _.findIndex(users, function(o) { return o.user == 'barney'; });
-     * // => 0
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findIndex(users, { 'user': 'fred', 'active': false });
-     * // => 1
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findIndex(users, ['active', false]);
-     * // => 0
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findIndex(users, 'active');
-     * // => 2
-     */
-    function findIndex(array, predicate, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = fromIndex == null ? 0 : toInteger(fromIndex);
-      if (index < 0) {
-        index = nativeMax(length + index, 0);
-      }
-      return baseFindIndex(array, getIteratee(predicate, 3), index);
-    }
-
-    /**
-     * This method is like `_.findIndex` except that it iterates over elements
-     * of `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=array.length-1] The index to search from.
-     * @returns {number} Returns the index of the found element, else `-1`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': true },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': false }
-     * ];
-     *
-     * _.findLastIndex(users, function(o) { return o.user == 'pebbles'; });
-     * // => 2
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findLastIndex(users, { 'user': 'barney', 'active': true });
-     * // => 0
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findLastIndex(users, ['active', false]);
-     * // => 2
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findLastIndex(users, 'active');
-     * // => 0
-     */
-    function findLastIndex(array, predicate, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = length - 1;
-      if (fromIndex !== undefined) {
-        index = toInteger(fromIndex);
-        index = fromIndex < 0
-          ? nativeMax(length + index, 0)
-          : nativeMin(index, length - 1);
-      }
-      return baseFindIndex(array, getIteratee(predicate, 3), index, true);
-    }
-
-    /**
-     * Flattens `array` a single level deep.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to flatten.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * _.flatten([1, [2, [3, [4]], 5]]);
-     * // => [1, 2, [3, [4]], 5]
-     */
-    function flatten(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseFlatten(array, 1) : [];
-    }
-
-    /**
-     * Recursively flattens `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to flatten.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * _.flattenDeep([1, [2, [3, [4]], 5]]);
-     * // => [1, 2, 3, 4, 5]
-     */
-    function flattenDeep(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseFlatten(array, INFINITY) : [];
-    }
-
-    /**
-     * Recursively flatten `array` up to `depth` times.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.4.0
-     * @category Array
-     * @param {Array} array The array to flatten.
-     * @param {number} [depth=1] The maximum recursion depth.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * var array = [1, [2, [3, [4]], 5]];
-     *
-     * _.flattenDepth(array, 1);
-     * // => [1, 2, [3, [4]], 5]
-     *
-     * _.flattenDepth(array, 2);
-     * // => [1, 2, 3, [4], 5]
-     */
-    function flattenDepth(array, depth) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      depth = depth === undefined ? 1 : toInteger(depth);
-      return baseFlatten(array, depth);
-    }
-
-    /**
-     * The inverse of `_.toPairs`; this method returns an object composed
-     * from key-value `pairs`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} pairs The key-value pairs.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * _.fromPairs([['a', 1], ['b', 2]]);
-     * // => { 'a': 1, 'b': 2 }
-     */
-    function fromPairs(pairs) {
-      var index = -1,
-          length = pairs == null ? 0 : pairs.length,
-          result = {};
-
-      while (++index < length) {
-        var pair = pairs[index];
-        result[pair[0]] = pair[1];
-      }
-      return result;
-    }
-
-    /**
-     * Gets the first element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @alias first
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {*} Returns the first element of `array`.
-     * @example
-     *
-     * _.head([1, 2, 3]);
-     * // => 1
-     *
-     * _.head([]);
-     * // => undefined
-     */
-    function head(array) {
-      return (array && array.length) ? array[0] : undefined;
-    }
-
-    /**
-     * Gets the index at which the first occurrence of `value` is found in `array`
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons. If `fromIndex` is negative, it's used as the
-     * offset from the end of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.indexOf([1, 2, 1, 2], 2);
-     * // => 1
-     *
-     * // Search from the `fromIndex`.
-     * _.indexOf([1, 2, 1, 2], 2, 2);
-     * // => 3
-     */
-    function indexOf(array, value, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = fromIndex == null ? 0 : toInteger(fromIndex);
-      if (index < 0) {
-        index = nativeMax(length + index, 0);
-      }
-      return baseIndexOf(array, value, index);
-    }
-
-    /**
-     * Gets all but the last element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.initial([1, 2, 3]);
-     * // => [1, 2]
-     */
-    function initial(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseSlice(array, 0, -1) : [];
-    }
-
-    /**
-     * Creates an array of unique values that are included in all given arrays
-     * using [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons. The order and references of result values are
-     * determined by the first array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @returns {Array} Returns the new array of intersecting values.
-     * @example
-     *
-     * _.intersection([2, 1], [2, 3]);
-     * // => [2]
-     */
-    var intersection = baseRest(function(arrays) {
-      var mapped = arrayMap(arrays, castArrayLikeObject);
-      return (mapped.length && mapped[0] === arrays[0])
-        ? baseIntersection(mapped)
-        : [];
-    });
-
-    /**
-     * This method is like `_.intersection` except that it accepts `iteratee`
-     * which is invoked for each element of each `arrays` to generate the criterion
-     * by which they're compared. The order and references of result values are
-     * determined by the first array. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of intersecting values.
-     * @example
-     *
-     * _.intersectionBy([2.1, 1.2], [2.3, 3.4], Math.floor);
-     * // => [2.1]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.intersectionBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 1 }]
-     */
-    var intersectionBy = baseRest(function(arrays) {
-      var iteratee = last(arrays),
-          mapped = arrayMap(arrays, castArrayLikeObject);
-
-      if (iteratee === last(mapped)) {
-        iteratee = undefined;
-      } else {
-        mapped.pop();
-      }
-      return (mapped.length && mapped[0] === arrays[0])
-        ? baseIntersection(mapped, getIteratee(iteratee, 2))
-        : [];
-    });
-
-    /**
-     * This method is like `_.intersection` except that it accepts `comparator`
-     * which is invoked to compare elements of `arrays`. The order and references
-     * of result values are determined by the first array. The comparator is
-     * invoked with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of intersecting values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.intersectionWith(objects, others, _.isEqual);
-     * // => [{ 'x': 1, 'y': 2 }]
-     */
-    var intersectionWith = baseRest(function(arrays) {
-      var comparator = last(arrays),
-          mapped = arrayMap(arrays, castArrayLikeObject);
-
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      if (comparator) {
-        mapped.pop();
-      }
-      return (mapped.length && mapped[0] === arrays[0])
-        ? baseIntersection(mapped, undefined, comparator)
-        : [];
-    });
-
-    /**
-     * Converts all elements in `array` into a string separated by `separator`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to convert.
-     * @param {string} [separator=','] The element separator.
-     * @returns {string} Returns the joined string.
-     * @example
-     *
-     * _.join(['a', 'b', 'c'], '~');
-     * // => 'a~b~c'
-     */
-    function join(array, separator) {
-      return array == null ? '' : nativeJoin.call(array, separator);
-    }
-
-    /**
-     * Gets the last element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {*} Returns the last element of `array`.
-     * @example
-     *
-     * _.last([1, 2, 3]);
-     * // => 3
-     */
-    function last(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? array[length - 1] : undefined;
-    }
-
-    /**
-     * This method is like `_.indexOf` except that it iterates over elements of
-     * `array` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @param {number} [fromIndex=array.length-1] The index to search from.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.lastIndexOf([1, 2, 1, 2], 2);
-     * // => 3
-     *
-     * // Search from the `fromIndex`.
-     * _.lastIndexOf([1, 2, 1, 2], 2, 2);
-     * // => 1
-     */
-    function lastIndexOf(array, value, fromIndex) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return -1;
-      }
-      var index = length;
-      if (fromIndex !== undefined) {
-        index = toInteger(fromIndex);
-        index = index < 0 ? nativeMax(length + index, 0) : nativeMin(index, length - 1);
-      }
-      return value === value
-        ? strictLastIndexOf(array, value, index)
-        : baseFindIndex(array, baseIsNaN, index, true);
-    }
-
-    /**
-     * Gets the element at index `n` of `array`. If `n` is negative, the nth
-     * element from the end is returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.11.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=0] The index of the element to return.
-     * @returns {*} Returns the nth element of `array`.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'd'];
-     *
-     * _.nth(array, 1);
-     * // => 'b'
-     *
-     * _.nth(array, -2);
-     * // => 'c';
-     */
-    function nth(array, n) {
-      return (array && array.length) ? baseNth(array, toInteger(n)) : undefined;
-    }
-
-    /**
-     * Removes all given values from `array` using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * **Note:** Unlike `_.without`, this method mutates `array`. Use `_.remove`
-     * to remove elements from an array by predicate.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {...*} [values] The values to remove.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'a', 'b', 'c'];
-     *
-     * _.pull(array, 'a', 'c');
-     * console.log(array);
-     * // => ['b', 'b']
-     */
-    var pull = baseRest(pullAll);
-
-    /**
-     * This method is like `_.pull` except that it accepts an array of values to remove.
-     *
-     * **Note:** Unlike `_.difference`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'a', 'b', 'c'];
-     *
-     * _.pullAll(array, ['a', 'c']);
-     * console.log(array);
-     * // => ['b', 'b']
-     */
-    function pullAll(array, values) {
-      return (array && array.length && values && values.length)
-        ? basePullAll(array, values)
-        : array;
-    }
-
-    /**
-     * This method is like `_.pullAll` except that it accepts `iteratee` which is
-     * invoked for each element of `array` and `values` to generate the criterion
-     * by which they're compared. The iteratee is invoked with one argument: (value).
-     *
-     * **Note:** Unlike `_.differenceBy`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [{ 'x': 1 }, { 'x': 2 }, { 'x': 3 }, { 'x': 1 }];
-     *
-     * _.pullAllBy(array, [{ 'x': 1 }, { 'x': 3 }], 'x');
-     * console.log(array);
-     * // => [{ 'x': 2 }]
-     */
-    function pullAllBy(array, values, iteratee) {
-      return (array && array.length && values && values.length)
-        ? basePullAll(array, values, getIteratee(iteratee, 2))
-        : array;
-    }
-
-    /**
-     * This method is like `_.pullAll` except that it accepts `comparator` which
-     * is invoked to compare elements of `array` to `values`. The comparator is
-     * invoked with two arguments: (arrVal, othVal).
-     *
-     * **Note:** Unlike `_.differenceWith`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.6.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Array} values The values to remove.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [{ 'x': 1, 'y': 2 }, { 'x': 3, 'y': 4 }, { 'x': 5, 'y': 6 }];
-     *
-     * _.pullAllWith(array, [{ 'x': 3, 'y': 4 }], _.isEqual);
-     * console.log(array);
-     * // => [{ 'x': 1, 'y': 2 }, { 'x': 5, 'y': 6 }]
-     */
-    function pullAllWith(array, values, comparator) {
-      return (array && array.length && values && values.length)
-        ? basePullAll(array, values, undefined, comparator)
-        : array;
-    }
-
-    /**
-     * Removes elements from `array` corresponding to `indexes` and returns an
-     * array of removed elements.
-     *
-     * **Note:** Unlike `_.at`, this method mutates `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {...(number|number[])} [indexes] The indexes of elements to remove.
-     * @returns {Array} Returns the new array of removed elements.
-     * @example
-     *
-     * var array = ['a', 'b', 'c', 'd'];
-     * var pulled = _.pullAt(array, [1, 3]);
-     *
-     * console.log(array);
-     * // => ['a', 'c']
-     *
-     * console.log(pulled);
-     * // => ['b', 'd']
-     */
-    var pullAt = flatRest(function(array, indexes) {
-      var length = array == null ? 0 : array.length,
-          result = baseAt(array, indexes);
-
-      basePullAt(array, arrayMap(indexes, function(index) {
-        return isIndex(index, length) ? +index : index;
-      }).sort(compareAscending));
-
-      return result;
-    });
-
-    /**
-     * Removes all elements from `array` that `predicate` returns truthy for
-     * and returns an array of the removed elements. The predicate is invoked
-     * with three arguments: (value, index, array).
-     *
-     * **Note:** Unlike `_.filter`, this method mutates `array`. Use `_.pull`
-     * to pull elements from an array by value.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new array of removed elements.
-     * @example
-     *
-     * var array = [1, 2, 3, 4];
-     * var evens = _.remove(array, function(n) {
-     *   return n % 2 == 0;
-     * });
-     *
-     * console.log(array);
-     * // => [1, 3]
-     *
-     * console.log(evens);
-     * // => [2, 4]
-     */
-    function remove(array, predicate) {
-      var result = [];
-      if (!(array && array.length)) {
-        return result;
-      }
-      var index = -1,
-          indexes = [],
-          length = array.length;
-
-      predicate = getIteratee(predicate, 3);
-      while (++index < length) {
-        var value = array[index];
-        if (predicate(value, index, array)) {
-          result.push(value);
-          indexes.push(index);
-        }
-      }
-      basePullAt(array, indexes);
-      return result;
-    }
-
-    /**
-     * Reverses `array` so that the first element becomes the last, the second
-     * element becomes the second to last, and so on.
-     *
-     * **Note:** This method mutates `array` and is based on
-     * [`Array#reverse`](https://mdn.io/Array/reverse).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to modify.
-     * @returns {Array} Returns `array`.
-     * @example
-     *
-     * var array = [1, 2, 3];
-     *
-     * _.reverse(array);
-     * // => [3, 2, 1]
-     *
-     * console.log(array);
-     * // => [3, 2, 1]
-     */
-    function reverse(array) {
-      return array == null ? array : nativeReverse.call(array);
-    }
-
-    /**
-     * Creates a slice of `array` from `start` up to, but not including, `end`.
-     *
-     * **Note:** This method is used instead of
-     * [`Array#slice`](https://mdn.io/Array/slice) to ensure dense arrays are
-     * returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to slice.
-     * @param {number} [start=0] The start position.
-     * @param {number} [end=array.length] The end position.
-     * @returns {Array} Returns the slice of `array`.
-     */
-    function slice(array, start, end) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      if (end && typeof end != 'number' && isIterateeCall(array, start, end)) {
-        start = 0;
-        end = length;
-      }
-      else {
-        start = start == null ? 0 : toInteger(start);
-        end = end === undefined ? length : toInteger(end);
-      }
-      return baseSlice(array, start, end);
-    }
-
-    /**
-     * Uses a binary search to determine the lowest index at which `value`
-     * should be inserted into `array` in order to maintain its sort order.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * _.sortedIndex([30, 50], 40);
-     * // => 1
-     */
-    function sortedIndex(array, value) {
-      return baseSortedIndex(array, value);
-    }
-
-    /**
-     * This method is like `_.sortedIndex` except that it accepts `iteratee`
-     * which is invoked for `value` and each element of `array` to compute their
-     * sort ranking. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * var objects = [{ 'x': 4 }, { 'x': 5 }];
-     *
-     * _.sortedIndexBy(objects, { 'x': 4 }, function(o) { return o.x; });
-     * // => 0
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.sortedIndexBy(objects, { 'x': 4 }, 'x');
-     * // => 0
-     */
-    function sortedIndexBy(array, value, iteratee) {
-      return baseSortedIndexBy(array, value, getIteratee(iteratee, 2));
-    }
-
-    /**
-     * This method is like `_.indexOf` except that it performs a binary
-     * search on a sorted `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.sortedIndexOf([4, 5, 5, 5, 6], 5);
-     * // => 1
-     */
-    function sortedIndexOf(array, value) {
-      var length = array == null ? 0 : array.length;
-      if (length) {
-        var index = baseSortedIndex(array, value);
-        if (index < length && eq(array[index], value)) {
-          return index;
-        }
-      }
-      return -1;
-    }
-
-    /**
-     * This method is like `_.sortedIndex` except that it returns the highest
-     * index at which `value` should be inserted into `array` in order to
-     * maintain its sort order.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * _.sortedLastIndex([4, 5, 5, 5, 6], 5);
-     * // => 4
-     */
-    function sortedLastIndex(array, value) {
-      return baseSortedIndex(array, value, true);
-    }
-
-    /**
-     * This method is like `_.sortedLastIndex` except that it accepts `iteratee`
-     * which is invoked for `value` and each element of `array` to compute their
-     * sort ranking. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The sorted array to inspect.
-     * @param {*} value The value to evaluate.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the index at which `value` should be inserted
-     *  into `array`.
-     * @example
-     *
-     * var objects = [{ 'x': 4 }, { 'x': 5 }];
-     *
-     * _.sortedLastIndexBy(objects, { 'x': 4 }, function(o) { return o.x; });
-     * // => 1
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.sortedLastIndexBy(objects, { 'x': 4 }, 'x');
-     * // => 1
-     */
-    function sortedLastIndexBy(array, value, iteratee) {
-      return baseSortedIndexBy(array, value, getIteratee(iteratee, 2), true);
-    }
-
-    /**
-     * This method is like `_.lastIndexOf` except that it performs a binary
-     * search on a sorted `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {*} value The value to search for.
-     * @returns {number} Returns the index of the matched value, else `-1`.
-     * @example
-     *
-     * _.sortedLastIndexOf([4, 5, 5, 5, 6], 5);
-     * // => 3
-     */
-    function sortedLastIndexOf(array, value) {
-      var length = array == null ? 0 : array.length;
-      if (length) {
-        var index = baseSortedIndex(array, value, true) - 1;
-        if (eq(array[index], value)) {
-          return index;
-        }
-      }
-      return -1;
-    }
-
-    /**
-     * This method is like `_.uniq` except that it's designed and optimized
-     * for sorted arrays.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.sortedUniq([1, 1, 2]);
-     * // => [1, 2]
-     */
-    function sortedUniq(array) {
-      return (array && array.length)
-        ? baseSortedUniq(array)
-        : [];
-    }
-
-    /**
-     * This method is like `_.uniqBy` except that it's designed and optimized
-     * for sorted arrays.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee] The iteratee invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.sortedUniqBy([1.1, 1.2, 2.3, 2.4], Math.floor);
-     * // => [1.1, 2.3]
-     */
-    function sortedUniqBy(array, iteratee) {
-      return (array && array.length)
-        ? baseSortedUniq(array, getIteratee(iteratee, 2))
-        : [];
-    }
-
-    /**
-     * Gets all but the first element of `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.tail([1, 2, 3]);
-     * // => [2, 3]
-     */
-    function tail(array) {
-      var length = array == null ? 0 : array.length;
-      return length ? baseSlice(array, 1, length) : [];
-    }
-
-    /**
-     * Creates a slice of `array` with `n` elements taken from the beginning.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to take.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.take([1, 2, 3]);
-     * // => [1]
-     *
-     * _.take([1, 2, 3], 2);
-     * // => [1, 2]
-     *
-     * _.take([1, 2, 3], 5);
-     * // => [1, 2, 3]
-     *
-     * _.take([1, 2, 3], 0);
-     * // => []
-     */
-    function take(array, n, guard) {
-      if (!(array && array.length)) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      return baseSlice(array, 0, n < 0 ? 0 : n);
-    }
-
-    /**
-     * Creates a slice of `array` with `n` elements taken from the end.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {number} [n=1] The number of elements to take.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * _.takeRight([1, 2, 3]);
-     * // => [3]
-     *
-     * _.takeRight([1, 2, 3], 2);
-     * // => [2, 3]
-     *
-     * _.takeRight([1, 2, 3], 5);
-     * // => [1, 2, 3]
-     *
-     * _.takeRight([1, 2, 3], 0);
-     * // => []
-     */
-    function takeRight(array, n, guard) {
-      var length = array == null ? 0 : array.length;
-      if (!length) {
-        return [];
-      }
-      n = (guard || n === undefined) ? 1 : toInteger(n);
-      n = length - n;
-      return baseSlice(array, n < 0 ? 0 : n, length);
-    }
-
-    /**
-     * Creates a slice of `array` with elements taken from the end. Elements are
-     * taken until `predicate` returns falsey. The predicate is invoked with
-     * three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': true },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': false }
-     * ];
-     *
-     * _.takeRightWhile(users, function(o) { return !o.active; });
-     * // => objects for ['fred', 'pebbles']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.takeRightWhile(users, { 'user': 'pebbles', 'active': false });
-     * // => objects for ['pebbles']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.takeRightWhile(users, ['active', false]);
-     * // => objects for ['fred', 'pebbles']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.takeRightWhile(users, 'active');
-     * // => []
-     */
-    function takeRightWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3), false, true)
-        : [];
-    }
-
-    /**
-     * Creates a slice of `array` with elements taken from the beginning. Elements
-     * are taken until `predicate` returns falsey. The predicate is invoked with
-     * three arguments: (value, index, array).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Array
-     * @param {Array} array The array to query.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the slice of `array`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'active': false },
-     *   { 'user': 'fred',    'active': false },
-     *   { 'user': 'pebbles', 'active': true }
-     * ];
-     *
-     * _.takeWhile(users, function(o) { return !o.active; });
-     * // => objects for ['barney', 'fred']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.takeWhile(users, { 'user': 'barney', 'active': false });
-     * // => objects for ['barney']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.takeWhile(users, ['active', false]);
-     * // => objects for ['barney', 'fred']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.takeWhile(users, 'active');
-     * // => []
-     */
-    function takeWhile(array, predicate) {
-      return (array && array.length)
-        ? baseWhile(array, getIteratee(predicate, 3))
-        : [];
-    }
-
-    /**
-     * Creates an array of unique values, in order, from all given arrays using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @returns {Array} Returns the new array of combined values.
-     * @example
-     *
-     * _.union([2], [1, 2]);
-     * // => [2, 1]
-     */
-    var union = baseRest(function(arrays) {
-      return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true));
-    });
-
-    /**
-     * This method is like `_.union` except that it accepts `iteratee` which is
-     * invoked for each element of each `arrays` to generate the criterion by
-     * which uniqueness is computed. Result values are chosen from the first
-     * array in which the value occurs. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of combined values.
-     * @example
-     *
-     * _.unionBy([2.1], [1.2, 2.3], Math.floor);
-     * // => [2.1, 1.2]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.unionBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 1 }, { 'x': 2 }]
-     */
-    var unionBy = baseRest(function(arrays) {
-      var iteratee = last(arrays);
-      if (isArrayLikeObject(iteratee)) {
-        iteratee = undefined;
-      }
-      return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true), getIteratee(iteratee, 2));
-    });
-
-    /**
-     * This method is like `_.union` except that it accepts `comparator` which
-     * is invoked to compare elements of `arrays`. Result values are chosen from
-     * the first array in which the value occurs. The comparator is invoked
-     * with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of combined values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.unionWith(objects, others, _.isEqual);
-     * // => [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }, { 'x': 1, 'y': 1 }]
-     */
-    var unionWith = baseRest(function(arrays) {
-      var comparator = last(arrays);
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      return baseUniq(baseFlatten(arrays, 1, isArrayLikeObject, true), undefined, comparator);
-    });
-
-    /**
-     * Creates a duplicate-free version of an array, using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons, in which only the first occurrence of each element
-     * is kept. The order of result values is determined by the order they occur
-     * in the array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.uniq([2, 1, 2]);
-     * // => [2, 1]
-     */
-    function uniq(array) {
-      return (array && array.length) ? baseUniq(array) : [];
-    }
-
-    /**
-     * This method is like `_.uniq` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the criterion by which
-     * uniqueness is computed. The order of result values is determined by the
-     * order they occur in the array. The iteratee is invoked with one argument:
-     * (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * _.uniqBy([2.1, 1.2, 2.3], Math.floor);
-     * // => [2.1, 1.2]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.uniqBy([{ 'x': 1 }, { 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 1 }, { 'x': 2 }]
-     */
-    function uniqBy(array, iteratee) {
-      return (array && array.length) ? baseUniq(array, getIteratee(iteratee, 2)) : [];
-    }
-
-    /**
-     * This method is like `_.uniq` except that it accepts `comparator` which
-     * is invoked to compare elements of `array`. The order of result values is
-     * determined by the order they occur in the array.The comparator is invoked
-     * with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new duplicate free array.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.uniqWith(objects, _.isEqual);
-     * // => [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }]
-     */
-    function uniqWith(array, comparator) {
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      return (array && array.length) ? baseUniq(array, undefined, comparator) : [];
-    }
-
-    /**
-     * This method is like `_.zip` except that it accepts an array of grouped
-     * elements and creates an array regrouping the elements to their pre-zip
-     * configuration.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.2.0
-     * @category Array
-     * @param {Array} array The array of grouped elements to process.
-     * @returns {Array} Returns the new array of regrouped elements.
-     * @example
-     *
-     * var zipped = _.zip(['a', 'b'], [1, 2], [true, false]);
-     * // => [['a', 1, true], ['b', 2, false]]
-     *
-     * _.unzip(zipped);
-     * // => [['a', 'b'], [1, 2], [true, false]]
-     */
-    function unzip(array) {
-      if (!(array && array.length)) {
-        return [];
-      }
-      var length = 0;
-      array = arrayFilter(array, function(group) {
-        if (isArrayLikeObject(group)) {
-          length = nativeMax(group.length, length);
-          return true;
-        }
-      });
-      return baseTimes(length, function(index) {
-        return arrayMap(array, baseProperty(index));
-      });
-    }
-
-    /**
-     * This method is like `_.unzip` except that it accepts `iteratee` to specify
-     * how regrouped values should be combined. The iteratee is invoked with the
-     * elements of each group: (...group).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.8.0
-     * @category Array
-     * @param {Array} array The array of grouped elements to process.
-     * @param {Function} [iteratee=_.identity] The function to combine
-     *  regrouped values.
-     * @returns {Array} Returns the new array of regrouped elements.
-     * @example
-     *
-     * var zipped = _.zip([1, 2], [10, 20], [100, 200]);
-     * // => [[1, 10, 100], [2, 20, 200]]
-     *
-     * _.unzipWith(zipped, _.add);
-     * // => [3, 30, 300]
-     */
-    function unzipWith(array, iteratee) {
-      if (!(array && array.length)) {
-        return [];
-      }
-      var result = unzip(array);
-      if (iteratee == null) {
-        return result;
-      }
-      return arrayMap(result, function(group) {
-        return apply(iteratee, undefined, group);
-      });
-    }
-
-    /**
-     * Creates an array excluding all given values using
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * for equality comparisons.
-     *
-     * **Note:** Unlike `_.pull`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {Array} array The array to inspect.
-     * @param {...*} [values] The values to exclude.
-     * @returns {Array} Returns the new array of filtered values.
-     * @see _.difference, _.xor
-     * @example
-     *
-     * _.without([2, 1, 2, 3], 1, 2);
-     * // => [3]
-     */
-    var without = baseRest(function(array, values) {
-      return isArrayLikeObject(array)
-        ? baseDifference(array, values)
-        : [];
-    });
-
-    /**
-     * Creates an array of unique values that is the
-     * [symmetric difference](https://en.wikipedia.org/wiki/Symmetric_difference)
-     * of the given arrays. The order of result values is determined by the order
-     * they occur in the arrays.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @returns {Array} Returns the new array of filtered values.
-     * @see _.difference, _.without
-     * @example
-     *
-     * _.xor([2, 1], [2, 3]);
-     * // => [1, 3]
-     */
-    var xor = baseRest(function(arrays) {
-      return baseXor(arrayFilter(arrays, isArrayLikeObject));
-    });
-
-    /**
-     * This method is like `_.xor` except that it accepts `iteratee` which is
-     * invoked for each element of each `arrays` to generate the criterion by
-     * which by which they're compared. The order of result values is determined
-     * by the order they occur in the arrays. The iteratee is invoked with one
-     * argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * _.xorBy([2.1, 1.2], [2.3, 3.4], Math.floor);
-     * // => [1.2, 3.4]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.xorBy([{ 'x': 1 }], [{ 'x': 2 }, { 'x': 1 }], 'x');
-     * // => [{ 'x': 2 }]
-     */
-    var xorBy = baseRest(function(arrays) {
-      var iteratee = last(arrays);
-      if (isArrayLikeObject(iteratee)) {
-        iteratee = undefined;
-      }
-      return baseXor(arrayFilter(arrays, isArrayLikeObject), getIteratee(iteratee, 2));
-    });
-
-    /**
-     * This method is like `_.xor` except that it accepts `comparator` which is
-     * invoked to compare elements of `arrays`. The order of result values is
-     * determined by the order they occur in the arrays. The comparator is invoked
-     * with two arguments: (arrVal, othVal).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to inspect.
-     * @param {Function} [comparator] The comparator invoked per element.
-     * @returns {Array} Returns the new array of filtered values.
-     * @example
-     *
-     * var objects = [{ 'x': 1, 'y': 2 }, { 'x': 2, 'y': 1 }];
-     * var others = [{ 'x': 1, 'y': 1 }, { 'x': 1, 'y': 2 }];
-     *
-     * _.xorWith(objects, others, _.isEqual);
-     * // => [{ 'x': 2, 'y': 1 }, { 'x': 1, 'y': 1 }]
-     */
-    var xorWith = baseRest(function(arrays) {
-      var comparator = last(arrays);
-      comparator = typeof comparator == 'function' ? comparator : undefined;
-      return baseXor(arrayFilter(arrays, isArrayLikeObject), undefined, comparator);
-    });
-
-    /**
-     * Creates an array of grouped elements, the first of which contains the
-     * first elements of the given arrays, the second of which contains the
-     * second elements of the given arrays, and so on.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to process.
-     * @returns {Array} Returns the new array of grouped elements.
-     * @example
-     *
-     * _.zip(['a', 'b'], [1, 2], [true, false]);
-     * // => [['a', 1, true], ['b', 2, false]]
-     */
-    var zip = baseRest(unzip);
-
-    /**
-     * This method is like `_.fromPairs` except that it accepts two arrays,
-     * one of property identifiers and one of corresponding values.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.4.0
-     * @category Array
-     * @param {Array} [props=[]] The property identifiers.
-     * @param {Array} [values=[]] The property values.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * _.zipObject(['a', 'b'], [1, 2]);
-     * // => { 'a': 1, 'b': 2 }
-     */
-    function zipObject(props, values) {
-      return baseZipObject(props || [], values || [], assignValue);
-    }
-
-    /**
-     * This method is like `_.zipObject` except that it supports property paths.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.1.0
-     * @category Array
-     * @param {Array} [props=[]] The property identifiers.
-     * @param {Array} [values=[]] The property values.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * _.zipObjectDeep(['a.b[0].c', 'a.b[1].d'], [1, 2]);
-     * // => { 'a': { 'b': [{ 'c': 1 }, { 'd': 2 }] } }
-     */
-    function zipObjectDeep(props, values) {
-      return baseZipObject(props || [], values || [], baseSet);
-    }
-
-    /**
-     * This method is like `_.zip` except that it accepts `iteratee` to specify
-     * how grouped values should be combined. The iteratee is invoked with the
-     * elements of each group: (...group).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.8.0
-     * @category Array
-     * @param {...Array} [arrays] The arrays to process.
-     * @param {Function} [iteratee=_.identity] The function to combine
-     *  grouped values.
-     * @returns {Array} Returns the new array of grouped elements.
-     * @example
-     *
-     * _.zipWith([1, 2], [10, 20], [100, 200], function(a, b, c) {
-     *   return a + b + c;
-     * });
-     * // => [111, 222]
-     */
-    var zipWith = baseRest(function(arrays) {
-      var length = arrays.length,
-          iteratee = length > 1 ? arrays[length - 1] : undefined;
-
-      iteratee = typeof iteratee == 'function' ? (arrays.pop(), iteratee) : undefined;
-      return unzipWith(arrays, iteratee);
-    });
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates a `lodash` wrapper instance that wraps `value` with explicit method
-     * chain sequences enabled. The result of such sequences must be unwrapped
-     * with `_#value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.3.0
-     * @category Seq
-     * @param {*} value The value to wrap.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'age': 36 },
-     *   { 'user': 'fred',    'age': 40 },
-     *   { 'user': 'pebbles', 'age': 1 }
-     * ];
-     *
-     * var youngest = _
-     *   .chain(users)
-     *   .sortBy('age')
-     *   .map(function(o) {
-     *     return o.user + ' is ' + o.age;
-     *   })
-     *   .head()
-     *   .value();
-     * // => 'pebbles is 1'
-     */
-    function chain(value) {
-      var result = lodash(value);
-      result.__chain__ = true;
-      return result;
-    }
-
-    /**
-     * This method invokes `interceptor` and returns `value`. The interceptor
-     * is invoked with one argument; (value). The purpose of this method is to
-     * "tap into" a method chain sequence in order to modify intermediate results.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Seq
-     * @param {*} value The value to provide to `interceptor`.
-     * @param {Function} interceptor The function to invoke.
-     * @returns {*} Returns `value`.
-     * @example
-     *
-     * _([1, 2, 3])
-     *  .tap(function(array) {
-     *    // Mutate input array.
-     *    array.pop();
-     *  })
-     *  .reverse()
-     *  .value();
-     * // => [2, 1]
-     */
-    function tap(value, interceptor) {
-      interceptor(value);
-      return value;
-    }
-
-    /**
-     * This method is like `_.tap` except that it returns the result of `interceptor`.
-     * The purpose of this method is to "pass thru" values replacing intermediate
-     * results in a method chain sequence.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Seq
-     * @param {*} value The value to provide to `interceptor`.
-     * @param {Function} interceptor The function to invoke.
-     * @returns {*} Returns the result of `interceptor`.
-     * @example
-     *
-     * _('  abc  ')
-     *  .chain()
-     *  .trim()
-     *  .thru(function(value) {
-     *    return [value];
-     *  })
-     *  .value();
-     * // => ['abc']
-     */
-    function thru(value, interceptor) {
-      return interceptor(value);
-    }
-
-    /**
-     * This method is the wrapper version of `_.at`.
-     *
-     * @name at
-     * @memberOf _
-     * @since 1.0.0
-     * @category Seq
-     * @param {...(string|string[])} [paths] The property paths to pick.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }, 4] };
-     *
-     * _(object).at(['a[0].b.c', 'a[1]']).value();
-     * // => [3, 4]
-     */
-    var wrapperAt = flatRest(function(paths) {
-      var length = paths.length,
-          start = length ? paths[0] : 0,
-          value = this.__wrapped__,
-          interceptor = function(object) { return baseAt(object, paths); };
-
-      if (length > 1 || this.__actions__.length ||
-          !(value instanceof LazyWrapper) || !isIndex(start)) {
-        return this.thru(interceptor);
-      }
-      value = value.slice(start, +start + (length ? 1 : 0));
-      value.__actions__.push({
-        'func': thru,
-        'args': [interceptor],
-        'thisArg': undefined
-      });
-      return new LodashWrapper(value, this.__chain__).thru(function(array) {
-        if (length && !array.length) {
-          array.push(undefined);
-        }
-        return array;
-      });
-    });
-
-    /**
-     * Creates a `lodash` wrapper instance with explicit method chain sequences enabled.
-     *
-     * @name chain
-     * @memberOf _
-     * @since 0.1.0
-     * @category Seq
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36 },
-     *   { 'user': 'fred',   'age': 40 }
-     * ];
-     *
-     * // A sequence without explicit chaining.
-     * _(users).head();
-     * // => { 'user': 'barney', 'age': 36 }
-     *
-     * // A sequence with explicit chaining.
-     * _(users)
-     *   .chain()
-     *   .head()
-     *   .pick('user')
-     *   .value();
-     * // => { 'user': 'barney' }
-     */
-    function wrapperChain() {
-      return chain(this);
-    }
-
-    /**
-     * Executes the chain sequence and returns the wrapped result.
-     *
-     * @name commit
-     * @memberOf _
-     * @since 3.2.0
-     * @category Seq
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var array = [1, 2];
-     * var wrapped = _(array).push(3);
-     *
-     * console.log(array);
-     * // => [1, 2]
-     *
-     * wrapped = wrapped.commit();
-     * console.log(array);
-     * // => [1, 2, 3]
-     *
-     * wrapped.last();
-     * // => 3
-     *
-     * console.log(array);
-     * // => [1, 2, 3]
-     */
-    function wrapperCommit() {
-      return new LodashWrapper(this.value(), this.__chain__);
-    }
-
-    /**
-     * Gets the next value on a wrapped object following the
-     * [iterator protocol](https://mdn.io/iteration_protocols#iterator).
-     *
-     * @name next
-     * @memberOf _
-     * @since 4.0.0
-     * @category Seq
-     * @returns {Object} Returns the next iterator value.
-     * @example
-     *
-     * var wrapped = _([1, 2]);
-     *
-     * wrapped.next();
-     * // => { 'done': false, 'value': 1 }
-     *
-     * wrapped.next();
-     * // => { 'done': false, 'value': 2 }
-     *
-     * wrapped.next();
-     * // => { 'done': true, 'value': undefined }
-     */
-    function wrapperNext() {
-      if (this.__values__ === undefined) {
-        this.__values__ = toArray(this.value());
-      }
-      var done = this.__index__ >= this.__values__.length,
-          value = done ? undefined : this.__values__[this.__index__++];
-
-      return { 'done': done, 'value': value };
-    }
-
-    /**
-     * Enables the wrapper to be iterable.
-     *
-     * @name Symbol.iterator
-     * @memberOf _
-     * @since 4.0.0
-     * @category Seq
-     * @returns {Object} Returns the wrapper object.
-     * @example
-     *
-     * var wrapped = _([1, 2]);
-     *
-     * wrapped[Symbol.iterator]() === wrapped;
-     * // => true
-     *
-     * Array.from(wrapped);
-     * // => [1, 2]
-     */
-    function wrapperToIterator() {
-      return this;
-    }
-
-    /**
-     * Creates a clone of the chain sequence planting `value` as the wrapped value.
-     *
-     * @name plant
-     * @memberOf _
-     * @since 3.2.0
-     * @category Seq
-     * @param {*} value The value to plant.
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var wrapped = _([1, 2]).map(square);
-     * var other = wrapped.plant([3, 4]);
-     *
-     * other.value();
-     * // => [9, 16]
-     *
-     * wrapped.value();
-     * // => [1, 4]
-     */
-    function wrapperPlant(value) {
-      var result,
-          parent = this;
-
-      while (parent instanceof baseLodash) {
-        var clone = wrapperClone(parent);
-        clone.__index__ = 0;
-        clone.__values__ = undefined;
-        if (result) {
-          previous.__wrapped__ = clone;
-        } else {
-          result = clone;
-        }
-        var previous = clone;
-        parent = parent.__wrapped__;
-      }
-      previous.__wrapped__ = value;
-      return result;
-    }
-
-    /**
-     * This method is the wrapper version of `_.reverse`.
-     *
-     * **Note:** This method mutates the wrapped array.
-     *
-     * @name reverse
-     * @memberOf _
-     * @since 0.1.0
-     * @category Seq
-     * @returns {Object} Returns the new `lodash` wrapper instance.
-     * @example
-     *
-     * var array = [1, 2, 3];
-     *
-     * _(array).reverse().value()
-     * // => [3, 2, 1]
-     *
-     * console.log(array);
-     * // => [3, 2, 1]
-     */
-    function wrapperReverse() {
-      var value = this.__wrapped__;
-      if (value instanceof LazyWrapper) {
-        var wrapped = value;
-        if (this.__actions__.length) {
-          wrapped = new LazyWrapper(this);
-        }
-        wrapped = wrapped.reverse();
-        wrapped.__actions__.push({
-          'func': thru,
-          'args': [reverse],
-          'thisArg': undefined
-        });
-        return new LodashWrapper(wrapped, this.__chain__);
-      }
-      return this.thru(reverse);
-    }
-
-    /**
-     * Executes the chain sequence to resolve the unwrapped value.
-     *
-     * @name value
-     * @memberOf _
-     * @since 0.1.0
-     * @alias toJSON, valueOf
-     * @category Seq
-     * @returns {*} Returns the resolved unwrapped value.
-     * @example
-     *
-     * _([1, 2, 3]).value();
-     * // => [1, 2, 3]
-     */
-    function wrapperValue() {
-      return baseWrapperValue(this.__wrapped__, this.__actions__);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Creates an object composed of keys generated from the results of running
-     * each element of `collection` thru `iteratee`. The corresponding value of
-     * each key is the number of times the key was returned by `iteratee`. The
-     * iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.5.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee to transform keys.
-     * @returns {Object} Returns the composed aggregate object.
-     * @example
-     *
-     * _.countBy([6.1, 4.2, 6.3], Math.floor);
-     * // => { '4': 1, '6': 2 }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.countBy(['one', 'two', 'three'], 'length');
-     * // => { '3': 2, '5': 1 }
-     */
-    var countBy = createAggregator(function(result, value, key) {
-      if (hasOwnProperty.call(result, key)) {
-        ++result[key];
-      } else {
-        baseAssignValue(result, key, 1);
-      }
-    });
-
-    /**
-     * Checks if `predicate` returns truthy for **all** elements of `collection`.
-     * Iteration is stopped once `predicate` returns falsey. The predicate is
-     * invoked with three arguments: (value, index|key, collection).
-     *
-     * **Note:** This method returns `true` for
-     * [empty collections](https://en.wikipedia.org/wiki/Empty_set) because
-     * [everything is true](https://en.wikipedia.org/wiki/Vacuous_truth) of
-     * elements of empty collections.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {boolean} Returns `true` if all elements pass the predicate check,
-     *  else `false`.
-     * @example
-     *
-     * _.every([true, 1, null, 'yes'], Boolean);
-     * // => false
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': false },
-     *   { 'user': 'fred',   'age': 40, 'active': false }
-     * ];
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.every(users, { 'user': 'barney', 'active': false });
-     * // => false
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.every(users, ['active', false]);
-     * // => true
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.every(users, 'active');
-     * // => false
-     */
-    function every(collection, predicate, guard) {
-      var func = isArray(collection) ? arrayEvery : baseEvery;
-      if (guard && isIterateeCall(collection, predicate, guard)) {
-        predicate = undefined;
-      }
-      return func(collection, getIteratee(predicate, 3));
-    }
-
-    /**
-     * Iterates over elements of `collection`, returning an array of all elements
-     * `predicate` returns truthy for. The predicate is invoked with three
-     * arguments: (value, index|key, collection).
-     *
-     * **Note:** Unlike `_.remove`, this method returns a new array.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new filtered array.
-     * @see _.reject
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': true },
-     *   { 'user': 'fred',   'age': 40, 'active': false }
-     * ];
-     *
-     * _.filter(users, function(o) { return !o.active; });
-     * // => objects for ['fred']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.filter(users, { 'age': 36, 'active': true });
-     * // => objects for ['barney']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.filter(users, ['active', false]);
-     * // => objects for ['fred']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.filter(users, 'active');
-     * // => objects for ['barney']
-     */
-    function filter(collection, predicate) {
-      var func = isArray(collection) ? arrayFilter : baseFilter;
-      return func(collection, getIteratee(predicate, 3));
-    }
-
-    /**
-     * Iterates over elements of `collection`, returning the first element
-     * `predicate` returns truthy for. The predicate is invoked with three
-     * arguments: (value, index|key, collection).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @returns {*} Returns the matched element, else `undefined`.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'age': 36, 'active': true },
-     *   { 'user': 'fred',    'age': 40, 'active': false },
-     *   { 'user': 'pebbles', 'age': 1,  'active': true }
-     * ];
-     *
-     * _.find(users, function(o) { return o.age < 40; });
-     * // => object for 'barney'
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.find(users, { 'age': 1, 'active': true });
-     * // => object for 'pebbles'
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.find(users, ['active', false]);
-     * // => object for 'fred'
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.find(users, 'active');
-     * // => object for 'barney'
-     */
-    var find = createFind(findIndex);
-
-    /**
-     * This method is like `_.find` except that it iterates over elements of
-     * `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param {number} [fromIndex=collection.length-1] The index to search from.
-     * @returns {*} Returns the matched element, else `undefined`.
-     * @example
-     *
-     * _.findLast([1, 2, 3, 4], function(n) {
-     *   return n % 2 == 1;
-     * });
-     * // => 3
-     */
-    var findLast = createFind(findLastIndex);
-
-    /**
-     * Creates a flattened array of values by running each element in `collection`
-     * thru `iteratee` and flattening the mapped results. The iteratee is invoked
-     * with three arguments: (value, index|key, collection).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * function duplicate(n) {
-     *   return [n, n];
-     * }
-     *
-     * _.flatMap([1, 2], duplicate);
-     * // => [1, 1, 2, 2]
-     */
-    function flatMap(collection, iteratee) {
-      return baseFlatten(map(collection, iteratee), 1);
-    }
-
-    /**
-     * This method is like `_.flatMap` except that it recursively flattens the
-     * mapped results.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * function duplicate(n) {
-     *   return [[[n, n]]];
-     * }
-     *
-     * _.flatMapDeep([1, 2], duplicate);
-     * // => [1, 1, 2, 2]
-     */
-    function flatMapDeep(collection, iteratee) {
-      return baseFlatten(map(collection, iteratee), INFINITY);
-    }
-
-    /**
-     * This method is like `_.flatMap` except that it recursively flattens the
-     * mapped results up to `depth` times.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {number} [depth=1] The maximum recursion depth.
-     * @returns {Array} Returns the new flattened array.
-     * @example
-     *
-     * function duplicate(n) {
-     *   return [[[n, n]]];
-     * }
-     *
-     * _.flatMapDepth([1, 2], duplicate, 2);
-     * // => [[1, 1], [2, 2]]
-     */
-    function flatMapDepth(collection, iteratee, depth) {
-      depth = depth === undefined ? 1 : toInteger(depth);
-      return baseFlatten(map(collection, iteratee), depth);
-    }
-
-    /**
-     * Iterates over elements of `collection` and invokes `iteratee` for each element.
-     * The iteratee is invoked with three arguments: (value, index|key, collection).
-     * Iteratee functions may exit iteration early by explicitly returning `false`.
-     *
-     * **Note:** As with other "Collections" methods, objects with a "length"
-     * property are iterated like arrays. To avoid this behavior use `_.forIn`
-     * or `_.forOwn` for object iteration.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @alias each
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     * @see _.forEachRight
-     * @example
-     *
-     * _.forEach([1, 2], function(value) {
-     *   console.log(value);
-     * });
-     * // => Logs `1` then `2`.
-     *
-     * _.forEach({ 'a': 1, 'b': 2 }, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'a' then 'b' (iteration order is not guaranteed).
-     */
-    function forEach(collection, iteratee) {
-      var func = isArray(collection) ? arrayEach : baseEach;
-      return func(collection, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * This method is like `_.forEach` except that it iterates over elements of
-     * `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @alias eachRight
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array|Object} Returns `collection`.
-     * @see _.forEach
-     * @example
-     *
-     * _.forEachRight([1, 2], function(value) {
-     *   console.log(value);
-     * });
-     * // => Logs `2` then `1`.
-     */
-    function forEachRight(collection, iteratee) {
-      var func = isArray(collection) ? arrayEachRight : baseEachRight;
-      return func(collection, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * Creates an object composed of keys generated from the results of running
-     * each element of `collection` thru `iteratee`. The order of grouped values
-     * is determined by the order they occur in `collection`. The corresponding
-     * value of each key is an array of elements responsible for generating the
-     * key. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee to transform keys.
-     * @returns {Object} Returns the composed aggregate object.
-     * @example
-     *
-     * _.groupBy([6.1, 4.2, 6.3], Math.floor);
-     * // => { '4': [4.2], '6': [6.1, 6.3] }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.groupBy(['one', 'two', 'three'], 'length');
-     * // => { '3': ['one', 'two'], '5': ['three'] }
-     */
-    var groupBy = createAggregator(function(result, value, key) {
-      if (hasOwnProperty.call(result, key)) {
-        result[key].push(value);
-      } else {
-        baseAssignValue(result, key, [value]);
-      }
-    });
-
-    /**
-     * Checks if `value` is in `collection`. If `collection` is a string, it's
-     * checked for a substring of `value`, otherwise
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * is used for equality comparisons. If `fromIndex` is negative, it's used as
-     * the offset from the end of `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object|string} collection The collection to inspect.
-     * @param {*} value The value to search for.
-     * @param {number} [fromIndex=0] The index to search from.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.reduce`.
-     * @returns {boolean} Returns `true` if `value` is found, else `false`.
-     * @example
-     *
-     * _.includes([1, 2, 3], 1);
-     * // => true
-     *
-     * _.includes([1, 2, 3], 1, 2);
-     * // => false
-     *
-     * _.includes({ 'a': 1, 'b': 2 }, 1);
-     * // => true
-     *
-     * _.includes('abcd', 'bc');
-     * // => true
-     */
-    function includes(collection, value, fromIndex, guard) {
-      collection = isArrayLike(collection) ? collection : values(collection);
-      fromIndex = (fromIndex && !guard) ? toInteger(fromIndex) : 0;
-
-      var length = collection.length;
-      if (fromIndex < 0) {
-        fromIndex = nativeMax(length + fromIndex, 0);
-      }
-      return isString(collection)
-        ? (fromIndex <= length && collection.indexOf(value, fromIndex) > -1)
-        : (!!length && baseIndexOf(collection, value, fromIndex) > -1);
-    }
-
-    /**
-     * Invokes the method at `path` of each element in `collection`, returning
-     * an array of the results of each invoked method. Any additional arguments
-     * are provided to each invoked method. If `path` is a function, it's invoked
-     * for, and `this` bound to, each element in `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Array|Function|string} path The path of the method to invoke or
-     *  the function invoked per iteration.
-     * @param {...*} [args] The arguments to invoke each method with.
-     * @returns {Array} Returns the array of results.
-     * @example
-     *
-     * _.invokeMap([[5, 1, 7], [3, 2, 1]], 'sort');
-     * // => [[1, 5, 7], [1, 2, 3]]
-     *
-     * _.invokeMap([123, 456], String.prototype.split, '');
-     * // => [['1', '2', '3'], ['4', '5', '6']]
-     */
-    var invokeMap = baseRest(function(collection, path, args) {
-      var index = -1,
-          isFunc = typeof path == 'function',
-          result = isArrayLike(collection) ? Array(collection.length) : [];
-
-      baseEach(collection, function(value) {
-        result[++index] = isFunc ? apply(path, value, args) : baseInvoke(value, path, args);
-      });
-      return result;
-    });
-
-    /**
-     * Creates an object composed of keys generated from the results of running
-     * each element of `collection` thru `iteratee`. The corresponding value of
-     * each key is the last element responsible for generating the key. The
-     * iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee to transform keys.
-     * @returns {Object} Returns the composed aggregate object.
-     * @example
-     *
-     * var array = [
-     *   { 'dir': 'left', 'code': 97 },
-     *   { 'dir': 'right', 'code': 100 }
-     * ];
-     *
-     * _.keyBy(array, function(o) {
-     *   return String.fromCharCode(o.code);
-     * });
-     * // => { 'a': { 'dir': 'left', 'code': 97 }, 'd': { 'dir': 'right', 'code': 100 } }
-     *
-     * _.keyBy(array, 'dir');
-     * // => { 'left': { 'dir': 'left', 'code': 97 }, 'right': { 'dir': 'right', 'code': 100 } }
-     */
-    var keyBy = createAggregator(function(result, value, key) {
-      baseAssignValue(result, key, value);
-    });
-
-    /**
-     * Creates an array of values by running each element in `collection` thru
-     * `iteratee`. The iteratee is invoked with three arguments:
-     * (value, index|key, collection).
-     *
-     * Many lodash methods are guarded to work as iteratees for methods like
-     * `_.every`, `_.filter`, `_.map`, `_.mapValues`, `_.reject`, and `_.some`.
-     *
-     * The guarded methods are:
-     * `ary`, `chunk`, `curry`, `curryRight`, `drop`, `dropRight`, `every`,
-     * `fill`, `invert`, `parseInt`, `random`, `range`, `rangeRight`, `repeat`,
-     * `sampleSize`, `slice`, `some`, `sortBy`, `split`, `take`, `takeRight`,
-     * `template`, `trim`, `trimEnd`, `trimStart`, and `words`
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new mapped array.
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * _.map([4, 8], square);
-     * // => [16, 64]
-     *
-     * _.map({ 'a': 4, 'b': 8 }, square);
-     * // => [16, 64] (iteration order is not guaranteed)
-     *
-     * var users = [
-     *   { 'user': 'barney' },
-     *   { 'user': 'fred' }
-     * ];
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.map(users, 'user');
-     * // => ['barney', 'fred']
-     */
-    function map(collection, iteratee) {
-      var func = isArray(collection) ? arrayMap : baseMap;
-      return func(collection, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * This method is like `_.sortBy` except that it allows specifying the sort
-     * orders of the iteratees to sort by. If `orders` is unspecified, all values
-     * are sorted in ascending order. Otherwise, specify an order of "desc" for
-     * descending or "asc" for ascending sort order of corresponding values.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Array[]|Function[]|Object[]|string[]} [iteratees=[_.identity]]
-     *  The iteratees to sort by.
-     * @param {string[]} [orders] The sort orders of `iteratees`.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.reduce`.
-     * @returns {Array} Returns the new sorted array.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'fred',   'age': 48 },
-     *   { 'user': 'barney', 'age': 34 },
-     *   { 'user': 'fred',   'age': 40 },
-     *   { 'user': 'barney', 'age': 36 }
-     * ];
-     *
-     * // Sort by `user` in ascending order and by `age` in descending order.
-     * _.orderBy(users, ['user', 'age'], ['asc', 'desc']);
-     * // => objects for [['barney', 36], ['barney', 34], ['fred', 48], ['fred', 40]]
-     */
-    function orderBy(collection, iteratees, orders, guard) {
-      if (collection == null) {
-        return [];
-      }
-      if (!isArray(iteratees)) {
-        iteratees = iteratees == null ? [] : [iteratees];
-      }
-      orders = guard ? undefined : orders;
-      if (!isArray(orders)) {
-        orders = orders == null ? [] : [orders];
-      }
-      return baseOrderBy(collection, iteratees, orders);
-    }
-
-    /**
-     * Creates an array of elements split into two groups, the first of which
-     * contains elements `predicate` returns truthy for, the second of which
-     * contains elements `predicate` returns falsey for. The predicate is
-     * invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the array of grouped elements.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney',  'age': 36, 'active': false },
-     *   { 'user': 'fred',    'age': 40, 'active': true },
-     *   { 'user': 'pebbles', 'age': 1,  'active': false }
-     * ];
-     *
-     * _.partition(users, function(o) { return o.active; });
-     * // => objects for [['fred'], ['barney', 'pebbles']]
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.partition(users, { 'age': 1, 'active': false });
-     * // => objects for [['pebbles'], ['barney', 'fred']]
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.partition(users, ['active', false]);
-     * // => objects for [['barney', 'pebbles'], ['fred']]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.partition(users, 'active');
-     * // => objects for [['fred'], ['barney', 'pebbles']]
-     */
-    var partition = createAggregator(function(result, value, key) {
-      result[key ? 0 : 1].push(value);
-    }, function() { return [[], []]; });
-
-    /**
-     * Reduces `collection` to a value which is the accumulated result of running
-     * each element in `collection` thru `iteratee`, where each successive
-     * invocation is supplied the return value of the previous. If `accumulator`
-     * is not given, the first element of `collection` is used as the initial
-     * value. The iteratee is invoked with four arguments:
-     * (accumulator, value, index|key, collection).
-     *
-     * Many lodash methods are guarded to work as iteratees for methods like
-     * `_.reduce`, `_.reduceRight`, and `_.transform`.
-     *
-     * The guarded methods are:
-     * `assign`, `defaults`, `defaultsDeep`, `includes`, `merge`, `orderBy`,
-     * and `sortBy`
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {*} [accumulator] The initial value.
-     * @returns {*} Returns the accumulated value.
-     * @see _.reduceRight
-     * @example
-     *
-     * _.reduce([1, 2], function(sum, n) {
-     *   return sum + n;
-     * }, 0);
-     * // => 3
-     *
-     * _.reduce({ 'a': 1, 'b': 2, 'c': 1 }, function(result, value, key) {
-     *   (result[value] || (result[value] = [])).push(key);
-     *   return result;
-     * }, {});
-     * // => { '1': ['a', 'c'], '2': ['b'] } (iteration order is not guaranteed)
-     */
-    function reduce(collection, iteratee, accumulator) {
-      var func = isArray(collection) ? arrayReduce : baseReduce,
-          initAccum = arguments.length < 3;
-
-      return func(collection, getIteratee(iteratee, 4), accumulator, initAccum, baseEach);
-    }
-
-    /**
-     * This method is like `_.reduce` except that it iterates over elements of
-     * `collection` from right to left.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {*} [accumulator] The initial value.
-     * @returns {*} Returns the accumulated value.
-     * @see _.reduce
-     * @example
-     *
-     * var array = [[0, 1], [2, 3], [4, 5]];
-     *
-     * _.reduceRight(array, function(flattened, other) {
-     *   return flattened.concat(other);
-     * }, []);
-     * // => [4, 5, 2, 3, 0, 1]
-     */
-    function reduceRight(collection, iteratee, accumulator) {
-      var func = isArray(collection) ? arrayReduceRight : baseReduce,
-          initAccum = arguments.length < 3;
-
-      return func(collection, getIteratee(iteratee, 4), accumulator, initAccum, baseEachRight);
-    }
-
-    /**
-     * The opposite of `_.filter`; this method returns the elements of `collection`
-     * that `predicate` does **not** return truthy for.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the new filtered array.
-     * @see _.filter
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': false },
-     *   { 'user': 'fred',   'age': 40, 'active': true }
-     * ];
-     *
-     * _.reject(users, function(o) { return !o.active; });
-     * // => objects for ['fred']
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.reject(users, { 'age': 40, 'active': true });
-     * // => objects for ['barney']
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.reject(users, ['active', false]);
-     * // => objects for ['fred']
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.reject(users, 'active');
-     * // => objects for ['barney']
-     */
-    function reject(collection, predicate) {
-      var func = isArray(collection) ? arrayFilter : baseFilter;
-      return func(collection, negate(getIteratee(predicate, 3)));
-    }
-
-    /**
-     * Gets a random element from `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to sample.
-     * @returns {*} Returns the random element.
-     * @example
-     *
-     * _.sample([1, 2, 3, 4]);
-     * // => 2
-     */
-    function sample(collection) {
-      var func = isArray(collection) ? arraySample : baseSample;
-      return func(collection);
-    }
-
-    /**
-     * Gets `n` random elements at unique keys from `collection` up to the
-     * size of `collection`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to sample.
-     * @param {number} [n=1] The number of elements to sample.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the random elements.
-     * @example
-     *
-     * _.sampleSize([1, 2, 3], 2);
-     * // => [3, 1]
-     *
-     * _.sampleSize([1, 2, 3], 4);
-     * // => [2, 3, 1]
-     */
-    function sampleSize(collection, n, guard) {
-      if ((guard ? isIterateeCall(collection, n, guard) : n === undefined)) {
-        n = 1;
-      } else {
-        n = toInteger(n);
-      }
-      var func = isArray(collection) ? arraySampleSize : baseSampleSize;
-      return func(collection, n);
-    }
-
-    /**
-     * Creates an array of shuffled values, using a version of the
-     * [Fisher-Yates shuffle](https://en.wikipedia.org/wiki/Fisher-Yates_shuffle).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to shuffle.
-     * @returns {Array} Returns the new shuffled array.
-     * @example
-     *
-     * _.shuffle([1, 2, 3, 4]);
-     * // => [4, 1, 3, 2]
-     */
-    function shuffle(collection) {
-      var func = isArray(collection) ? arrayShuffle : baseShuffle;
-      return func(collection);
-    }
-
-    /**
-     * Gets the size of `collection` by returning its length for array-like
-     * values or the number of own enumerable string keyed properties for objects.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object|string} collection The collection to inspect.
-     * @returns {number} Returns the collection size.
-     * @example
-     *
-     * _.size([1, 2, 3]);
-     * // => 3
-     *
-     * _.size({ 'a': 1, 'b': 2 });
-     * // => 2
-     *
-     * _.size('pebbles');
-     * // => 7
-     */
-    function size(collection) {
-      if (collection == null) {
-        return 0;
-      }
-      if (isArrayLike(collection)) {
-        return isString(collection) ? stringSize(collection) : collection.length;
-      }
-      var tag = getTag(collection);
-      if (tag == mapTag || tag == setTag) {
-        return collection.size;
-      }
-      return baseKeys(collection).length;
-    }
-
-    /**
-     * Checks if `predicate` returns truthy for **any** element of `collection`.
-     * Iteration is stopped once `predicate` returns truthy. The predicate is
-     * invoked with three arguments: (value, index|key, collection).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {boolean} Returns `true` if any element passes the predicate check,
-     *  else `false`.
-     * @example
-     *
-     * _.some([null, 0, 'yes', false], Boolean);
-     * // => true
-     *
-     * var users = [
-     *   { 'user': 'barney', 'active': true },
-     *   { 'user': 'fred',   'active': false }
-     * ];
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.some(users, { 'user': 'barney', 'active': false });
-     * // => false
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.some(users, ['active', false]);
-     * // => true
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.some(users, 'active');
-     * // => true
-     */
-    function some(collection, predicate, guard) {
-      var func = isArray(collection) ? arraySome : baseSome;
-      if (guard && isIterateeCall(collection, predicate, guard)) {
-        predicate = undefined;
-      }
-      return func(collection, getIteratee(predicate, 3));
-    }
-
-    /**
-     * Creates an array of elements, sorted in ascending order by the results of
-     * running each element in a collection thru each iteratee. This method
-     * performs a stable sort, that is, it preserves the original sort order of
-     * equal elements. The iteratees are invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Collection
-     * @param {Array|Object} collection The collection to iterate over.
-     * @param {...(Function|Function[])} [iteratees=[_.identity]]
-     *  The iteratees to sort by.
-     * @returns {Array} Returns the new sorted array.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'fred',   'age': 48 },
-     *   { 'user': 'barney', 'age': 36 },
-     *   { 'user': 'fred',   'age': 40 },
-     *   { 'user': 'barney', 'age': 34 }
-     * ];
-     *
-     * _.sortBy(users, [function(o) { return o.user; }]);
-     * // => objects for [['barney', 36], ['barney', 34], ['fred', 48], ['fred', 40]]
-     *
-     * _.sortBy(users, ['user', 'age']);
-     * // => objects for [['barney', 34], ['barney', 36], ['fred', 40], ['fred', 48]]
-     */
-    var sortBy = baseRest(function(collection, iteratees) {
-      if (collection == null) {
-        return [];
-      }
-      var length = iteratees.length;
-      if (length > 1 && isIterateeCall(collection, iteratees[0], iteratees[1])) {
-        iteratees = [];
-      } else if (length > 2 && isIterateeCall(iteratees[0], iteratees[1], iteratees[2])) {
-        iteratees = [iteratees[0]];
-      }
-      return baseOrderBy(collection, baseFlatten(iteratees, 1), []);
-    });
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Gets the timestamp of the number of milliseconds that have elapsed since
-     * the Unix epoch (1 January 1970 00:00:00 UTC).
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Date
-     * @returns {number} Returns the timestamp.
-     * @example
-     *
-     * _.defer(function(stamp) {
-     *   console.log(_.now() - stamp);
-     * }, _.now());
-     * // => Logs the number of milliseconds it took for the deferred invocation.
-     */
-    var now = ctxNow || function() {
-      return root.Date.now();
-    };
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * The opposite of `_.before`; this method creates a function that invokes
-     * `func` once it's called `n` or more times.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {number} n The number of calls before `func` is invoked.
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new restricted function.
-     * @example
-     *
-     * var saves = ['profile', 'settings'];
-     *
-     * var done = _.after(saves.length, function() {
-     *   console.log('done saving!');
-     * });
-     *
-     * _.forEach(saves, function(type) {
-     *   asyncSave({ 'type': type, 'complete': done });
-     * });
-     * // => Logs 'done saving!' after the two async saves have completed.
-     */
-    function after(n, func) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      n = toInteger(n);
-      return function() {
-        if (--n < 1) {
-          return func.apply(this, arguments);
-        }
-      };
-    }
-
-    /**
-     * Creates a function that invokes `func`, with up to `n` arguments,
-     * ignoring any additional arguments.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} func The function to cap arguments for.
-     * @param {number} [n=func.length] The arity cap.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the new capped function.
-     * @example
-     *
-     * _.map(['6', '8', '10'], _.ary(parseInt, 1));
-     * // => [6, 8, 10]
-     */
-    function ary(func, n, guard) {
-      n = guard ? undefined : n;
-      n = (func && n == null) ? func.length : n;
-      return createWrap(func, WRAP_ARY_FLAG, undefined, undefined, undefined, undefined, n);
-    }
-
-    /**
-     * Creates a function that invokes `func`, with the `this` binding and arguments
-     * of the created function, while it's called less than `n` times. Subsequent
-     * calls to the created function return the result of the last `func` invocation.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {number} n The number of calls at which `func` is no longer invoked.
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new restricted function.
-     * @example
-     *
-     * jQuery(element).on('click', _.before(5, addContactToList));
-     * // => Allows adding up to 4 contacts to the list.
-     */
-    function before(n, func) {
-      var result;
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      n = toInteger(n);
-      return function() {
-        if (--n > 0) {
-          result = func.apply(this, arguments);
-        }
-        if (n <= 1) {
-          func = undefined;
-        }
-        return result;
-      };
-    }
-
-    /**
-     * Creates a function that invokes `func` with the `this` binding of `thisArg`
-     * and `partials` prepended to the arguments it receives.
-     *
-     * The `_.bind.placeholder` value, which defaults to `_` in monolithic builds,
-     * may be used as a placeholder for partially applied arguments.
-     *
-     * **Note:** Unlike native `Function#bind`, this method doesn't set the "length"
-     * property of bound functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to bind.
-     * @param {*} thisArg The `this` binding of `func`.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new bound function.
-     * @example
-     *
-     * function greet(greeting, punctuation) {
-     *   return greeting + ' ' + this.user + punctuation;
-     * }
-     *
-     * var object = { 'user': 'fred' };
-     *
-     * var bound = _.bind(greet, object, 'hi');
-     * bound('!');
-     * // => 'hi fred!'
-     *
-     * // Bound with placeholders.
-     * var bound = _.bind(greet, object, _, '!');
-     * bound('hi');
-     * // => 'hi fred!'
-     */
-    var bind = baseRest(function(func, thisArg, partials) {
-      var bitmask = WRAP_BIND_FLAG;
-      if (partials.length) {
-        var holders = replaceHolders(partials, getHolder(bind));
-        bitmask |= WRAP_PARTIAL_FLAG;
-      }
-      return createWrap(func, bitmask, thisArg, partials, holders);
-    });
-
-    /**
-     * Creates a function that invokes the method at `object[key]` with `partials`
-     * prepended to the arguments it receives.
-     *
-     * This method differs from `_.bind` by allowing bound functions to reference
-     * methods that may be redefined or don't yet exist. See
-     * [Peter Michaux's article](http://peter.michaux.ca/articles/lazy-function-definition-pattern)
-     * for more details.
-     *
-     * The `_.bindKey.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for partially applied arguments.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.10.0
-     * @category Function
-     * @param {Object} object The object to invoke the method on.
-     * @param {string} key The key of the method.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new bound function.
-     * @example
-     *
-     * var object = {
-     *   'user': 'fred',
-     *   'greet': function(greeting, punctuation) {
-     *     return greeting + ' ' + this.user + punctuation;
-     *   }
-     * };
-     *
-     * var bound = _.bindKey(object, 'greet', 'hi');
-     * bound('!');
-     * // => 'hi fred!'
-     *
-     * object.greet = function(greeting, punctuation) {
-     *   return greeting + 'ya ' + this.user + punctuation;
-     * };
-     *
-     * bound('!');
-     * // => 'hiya fred!'
-     *
-     * // Bound with placeholders.
-     * var bound = _.bindKey(object, 'greet', _, '!');
-     * bound('hi');
-     * // => 'hiya fred!'
-     */
-    var bindKey = baseRest(function(object, key, partials) {
-      var bitmask = WRAP_BIND_FLAG | WRAP_BIND_KEY_FLAG;
-      if (partials.length) {
-        var holders = replaceHolders(partials, getHolder(bindKey));
-        bitmask |= WRAP_PARTIAL_FLAG;
-      }
-      return createWrap(key, bitmask, object, partials, holders);
-    });
-
-    /**
-     * Creates a function that accepts arguments of `func` and either invokes
-     * `func` returning its result, if at least `arity` number of arguments have
-     * been provided, or returns a function that accepts the remaining `func`
-     * arguments, and so on. The arity of `func` may be specified if `func.length`
-     * is not sufficient.
-     *
-     * The `_.curry.placeholder` value, which defaults to `_` in monolithic builds,
-     * may be used as a placeholder for provided arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of curried functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Function
-     * @param {Function} func The function to curry.
-     * @param {number} [arity=func.length] The arity of `func`.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the new curried function.
-     * @example
-     *
-     * var abc = function(a, b, c) {
-     *   return [a, b, c];
-     * };
-     *
-     * var curried = _.curry(abc);
-     *
-     * curried(1)(2)(3);
-     * // => [1, 2, 3]
-     *
-     * curried(1, 2)(3);
-     * // => [1, 2, 3]
-     *
-     * curried(1, 2, 3);
-     * // => [1, 2, 3]
-     *
-     * // Curried with placeholders.
-     * curried(1)(_, 3)(2);
-     * // => [1, 2, 3]
-     */
-    function curry(func, arity, guard) {
-      arity = guard ? undefined : arity;
-      var result = createWrap(func, WRAP_CURRY_FLAG, undefined, undefined, undefined, undefined, undefined, arity);
-      result.placeholder = curry.placeholder;
-      return result;
-    }
-
-    /**
-     * This method is like `_.curry` except that arguments are applied to `func`
-     * in the manner of `_.partialRight` instead of `_.partial`.
-     *
-     * The `_.curryRight.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for provided arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of curried functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} func The function to curry.
-     * @param {number} [arity=func.length] The arity of `func`.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the new curried function.
-     * @example
-     *
-     * var abc = function(a, b, c) {
-     *   return [a, b, c];
-     * };
-     *
-     * var curried = _.curryRight(abc);
-     *
-     * curried(3)(2)(1);
-     * // => [1, 2, 3]
-     *
-     * curried(2, 3)(1);
-     * // => [1, 2, 3]
-     *
-     * curried(1, 2, 3);
-     * // => [1, 2, 3]
-     *
-     * // Curried with placeholders.
-     * curried(3)(1, _)(2);
-     * // => [1, 2, 3]
-     */
-    function curryRight(func, arity, guard) {
-      arity = guard ? undefined : arity;
-      var result = createWrap(func, WRAP_CURRY_RIGHT_FLAG, undefined, undefined, undefined, undefined, undefined, arity);
-      result.placeholder = curryRight.placeholder;
-      return result;
-    }
-
-    /**
-     * Creates a debounced function that delays invoking `func` until after `wait`
-     * milliseconds have elapsed since the last time the debounced function was
-     * invoked. The debounced function comes with a `cancel` method to cancel
-     * delayed `func` invocations and a `flush` method to immediately invoke them.
-     * Provide `options` to indicate whether `func` should be invoked on the
-     * leading and/or trailing edge of the `wait` timeout. The `func` is invoked
-     * with the last arguments provided to the debounced function. Subsequent
-     * calls to the debounced function return the result of the last `func`
-     * invocation.
-     *
-     * **Note:** If `leading` and `trailing` options are `true`, `func` is
-     * invoked on the trailing edge of the timeout only if the debounced function
-     * is invoked more than once during the `wait` timeout.
-     *
-     * If `wait` is `0` and `leading` is `false`, `func` invocation is deferred
-     * until to the next tick, similar to `setTimeout` with a timeout of `0`.
-     *
-     * See [David Corbacho's article](https://css-tricks.com/debouncing-throttling-explained-examples/)
-     * for details over the differences between `_.debounce` and `_.throttle`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to debounce.
-     * @param {number} [wait=0] The number of milliseconds to delay.
-     * @param {Object} [options={}] The options object.
-     * @param {boolean} [options.leading=false]
-     *  Specify invoking on the leading edge of the timeout.
-     * @param {number} [options.maxWait]
-     *  The maximum time `func` is allowed to be delayed before it's invoked.
-     * @param {boolean} [options.trailing=true]
-     *  Specify invoking on the trailing edge of the timeout.
-     * @returns {Function} Returns the new debounced function.
-     * @example
-     *
-     * // Avoid costly calculations while the window size is in flux.
-     * jQuery(window).on('resize', _.debounce(calculateLayout, 150));
-     *
-     * // Invoke `sendMail` when clicked, debouncing subsequent calls.
-     * jQuery(element).on('click', _.debounce(sendMail, 300, {
-     *   'leading': true,
-     *   'trailing': false
-     * }));
-     *
-     * // Ensure `batchLog` is invoked once after 1 second of debounced calls.
-     * var debounced = _.debounce(batchLog, 250, { 'maxWait': 1000 });
-     * var source = new EventSource('/stream');
-     * jQuery(source).on('message', debounced);
-     *
-     * // Cancel the trailing debounced invocation.
-     * jQuery(window).on('popstate', debounced.cancel);
-     */
-    function debounce(func, wait, options) {
-      var lastArgs,
-          lastThis,
-          maxWait,
-          result,
-          timerId,
-          lastCallTime,
-          lastInvokeTime = 0,
-          leading = false,
-          maxing = false,
-          trailing = true;
-
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      wait = toNumber(wait) || 0;
-      if (isObject(options)) {
-        leading = !!options.leading;
-        maxing = 'maxWait' in options;
-        maxWait = maxing ? nativeMax(toNumber(options.maxWait) || 0, wait) : maxWait;
-        trailing = 'trailing' in options ? !!options.trailing : trailing;
-      }
-
-      function invokeFunc(time) {
-        var args = lastArgs,
-            thisArg = lastThis;
-
-        lastArgs = lastThis = undefined;
-        lastInvokeTime = time;
-        result = func.apply(thisArg, args);
-        return result;
-      }
-
-      function leadingEdge(time) {
-        // Reset any `maxWait` timer.
-        lastInvokeTime = time;
-        // Start the timer for the trailing edge.
-        timerId = setTimeout(timerExpired, wait);
-        // Invoke the leading edge.
-        return leading ? invokeFunc(time) : result;
-      }
-
-      function remainingWait(time) {
-        var timeSinceLastCall = time - lastCallTime,
-            timeSinceLastInvoke = time - lastInvokeTime,
-            timeWaiting = wait - timeSinceLastCall;
-
-        return maxing
-          ? nativeMin(timeWaiting, maxWait - timeSinceLastInvoke)
-          : timeWaiting;
-      }
-
-      function shouldInvoke(time) {
-        var timeSinceLastCall = time - lastCallTime,
-            timeSinceLastInvoke = time - lastInvokeTime;
-
-        // Either this is the first call, activity has stopped and we're at the
-        // trailing edge, the system time has gone backwards and we're treating
-        // it as the trailing edge, or we've hit the `maxWait` limit.
-        return (lastCallTime === undefined || (timeSinceLastCall >= wait) ||
-          (timeSinceLastCall < 0) || (maxing && timeSinceLastInvoke >= maxWait));
-      }
-
-      function timerExpired() {
-        var time = now();
-        if (shouldInvoke(time)) {
-          return trailingEdge(time);
-        }
-        // Restart the timer.
-        timerId = setTimeout(timerExpired, remainingWait(time));
-      }
-
-      function trailingEdge(time) {
-        timerId = undefined;
-
-        // Only invoke if we have `lastArgs` which means `func` has been
-        // debounced at least once.
-        if (trailing && lastArgs) {
-          return invokeFunc(time);
-        }
-        lastArgs = lastThis = undefined;
-        return result;
-      }
-
-      function cancel() {
-        if (timerId !== undefined) {
-          clearTimeout(timerId);
-        }
-        lastInvokeTime = 0;
-        lastArgs = lastCallTime = lastThis = timerId = undefined;
-      }
-
-      function flush() {
-        return timerId === undefined ? result : trailingEdge(now());
-      }
-
-      function debounced() {
-        var time = now(),
-            isInvoking = shouldInvoke(time);
-
-        lastArgs = arguments;
-        lastThis = this;
-        lastCallTime = time;
-
-        if (isInvoking) {
-          if (timerId === undefined) {
-            return leadingEdge(lastCallTime);
-          }
-          if (maxing) {
-            // Handle invocations in a tight loop.
-            clearTimeout(timerId);
-            timerId = setTimeout(timerExpired, wait);
-            return invokeFunc(lastCallTime);
-          }
-        }
-        if (timerId === undefined) {
-          timerId = setTimeout(timerExpired, wait);
-        }
-        return result;
-      }
-      debounced.cancel = cancel;
-      debounced.flush = flush;
-      return debounced;
-    }
-
-    /**
-     * Defers invoking the `func` until the current call stack has cleared. Any
-     * additional arguments are provided to `func` when it's invoked.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to defer.
-     * @param {...*} [args] The arguments to invoke `func` with.
-     * @returns {number} Returns the timer id.
-     * @example
-     *
-     * _.defer(function(text) {
-     *   console.log(text);
-     * }, 'deferred');
-     * // => Logs 'deferred' after one millisecond.
-     */
-    var defer = baseRest(function(func, args) {
-      return baseDelay(func, 1, args);
-    });
-
-    /**
-     * Invokes `func` after `wait` milliseconds. Any additional arguments are
-     * provided to `func` when it's invoked.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to delay.
-     * @param {number} wait The number of milliseconds to delay invocation.
-     * @param {...*} [args] The arguments to invoke `func` with.
-     * @returns {number} Returns the timer id.
-     * @example
-     *
-     * _.delay(function(text) {
-     *   console.log(text);
-     * }, 1000, 'later');
-     * // => Logs 'later' after one second.
-     */
-    var delay = baseRest(function(func, wait, args) {
-      return baseDelay(func, toNumber(wait) || 0, args);
-    });
-
-    /**
-     * Creates a function that invokes `func` with arguments reversed.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Function
-     * @param {Function} func The function to flip arguments for.
-     * @returns {Function} Returns the new flipped function.
-     * @example
-     *
-     * var flipped = _.flip(function() {
-     *   return _.toArray(arguments);
-     * });
-     *
-     * flipped('a', 'b', 'c', 'd');
-     * // => ['d', 'c', 'b', 'a']
-     */
-    function flip(func) {
-      return createWrap(func, WRAP_FLIP_FLAG);
-    }
-
-    /**
-     * Creates a function that memoizes the result of `func`. If `resolver` is
-     * provided, it determines the cache key for storing the result based on the
-     * arguments provided to the memoized function. By default, the first argument
-     * provided to the memoized function is used as the map cache key. The `func`
-     * is invoked with the `this` binding of the memoized function.
-     *
-     * **Note:** The cache is exposed as the `cache` property on the memoized
-     * function. Its creation may be customized by replacing the `_.memoize.Cache`
-     * constructor with one whose instances implement the
-     * [`Map`](http://ecma-international.org/ecma-262/7.0/#sec-properties-of-the-map-prototype-object)
-     * method interface of `clear`, `delete`, `get`, `has`, and `set`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to have its output memoized.
-     * @param {Function} [resolver] The function to resolve the cache key.
-     * @returns {Function} Returns the new memoized function.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2 };
-     * var other = { 'c': 3, 'd': 4 };
-     *
-     * var values = _.memoize(_.values);
-     * values(object);
-     * // => [1, 2]
-     *
-     * values(other);
-     * // => [3, 4]
-     *
-     * object.a = 2;
-     * values(object);
-     * // => [1, 2]
-     *
-     * // Modify the result cache.
-     * values.cache.set(object, ['a', 'b']);
-     * values(object);
-     * // => ['a', 'b']
-     *
-     * // Replace `_.memoize.Cache`.
-     * _.memoize.Cache = WeakMap;
-     */
-    function memoize(func, resolver) {
-      if (typeof func != 'function' || (resolver != null && typeof resolver != 'function')) {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      var memoized = function() {
-        var args = arguments,
-            key = resolver ? resolver.apply(this, args) : args[0],
-            cache = memoized.cache;
-
-        if (cache.has(key)) {
-          return cache.get(key);
-        }
-        var result = func.apply(this, args);
-        memoized.cache = cache.set(key, result) || cache;
-        return result;
-      };
-      memoized.cache = new (memoize.Cache || MapCache);
-      return memoized;
-    }
-
-    // Expose `MapCache`.
-    memoize.Cache = MapCache;
-
-    /**
-     * Creates a function that negates the result of the predicate `func`. The
-     * `func` predicate is invoked with the `this` binding and arguments of the
-     * created function.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} predicate The predicate to negate.
-     * @returns {Function} Returns the new negated function.
-     * @example
-     *
-     * function isEven(n) {
-     *   return n % 2 == 0;
-     * }
-     *
-     * _.filter([1, 2, 3, 4, 5, 6], _.negate(isEven));
-     * // => [1, 3, 5]
-     */
-    function negate(predicate) {
-      if (typeof predicate != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      return function() {
-        var args = arguments;
-        switch (args.length) {
-          case 0: return !predicate.call(this);
-          case 1: return !predicate.call(this, args[0]);
-          case 2: return !predicate.call(this, args[0], args[1]);
-          case 3: return !predicate.call(this, args[0], args[1], args[2]);
-        }
-        return !predicate.apply(this, args);
-      };
-    }
-
-    /**
-     * Creates a function that is restricted to invoking `func` once. Repeat calls
-     * to the function return the value of the first invocation. The `func` is
-     * invoked with the `this` binding and arguments of the created function.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to restrict.
-     * @returns {Function} Returns the new restricted function.
-     * @example
-     *
-     * var initialize = _.once(createApplication);
-     * initialize();
-     * initialize();
-     * // => `createApplication` is invoked once
-     */
-    function once(func) {
-      return before(2, func);
-    }
-
-    /**
-     * Creates a function that invokes `func` with its arguments transformed.
-     *
-     * @static
-     * @since 4.0.0
-     * @memberOf _
-     * @category Function
-     * @param {Function} func The function to wrap.
-     * @param {...(Function|Function[])} [transforms=[_.identity]]
-     *  The argument transforms.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * function doubled(n) {
-     *   return n * 2;
-     * }
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var func = _.overArgs(function(x, y) {
-     *   return [x, y];
-     * }, [square, doubled]);
-     *
-     * func(9, 3);
-     * // => [81, 6]
-     *
-     * func(10, 5);
-     * // => [100, 10]
-     */
-    var overArgs = castRest(function(func, transforms) {
-      transforms = (transforms.length == 1 && isArray(transforms[0]))
-        ? arrayMap(transforms[0], baseUnary(getIteratee()))
-        : arrayMap(baseFlatten(transforms, 1), baseUnary(getIteratee()));
-
-      var funcsLength = transforms.length;
-      return baseRest(function(args) {
-        var index = -1,
-            length = nativeMin(args.length, funcsLength);
-
-        while (++index < length) {
-          args[index] = transforms[index].call(this, args[index]);
-        }
-        return apply(func, this, args);
-      });
-    });
-
-    /**
-     * Creates a function that invokes `func` with `partials` prepended to the
-     * arguments it receives. This method is like `_.bind` except it does **not**
-     * alter the `this` binding.
-     *
-     * The `_.partial.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for partially applied arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of partially
-     * applied functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.2.0
-     * @category Function
-     * @param {Function} func The function to partially apply arguments to.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new partially applied function.
-     * @example
-     *
-     * function greet(greeting, name) {
-     *   return greeting + ' ' + name;
-     * }
-     *
-     * var sayHelloTo = _.partial(greet, 'hello');
-     * sayHelloTo('fred');
-     * // => 'hello fred'
-     *
-     * // Partially applied with placeholders.
-     * var greetFred = _.partial(greet, _, 'fred');
-     * greetFred('hi');
-     * // => 'hi fred'
-     */
-    var partial = baseRest(function(func, partials) {
-      var holders = replaceHolders(partials, getHolder(partial));
-      return createWrap(func, WRAP_PARTIAL_FLAG, undefined, partials, holders);
-    });
-
-    /**
-     * This method is like `_.partial` except that partially applied arguments
-     * are appended to the arguments it receives.
-     *
-     * The `_.partialRight.placeholder` value, which defaults to `_` in monolithic
-     * builds, may be used as a placeholder for partially applied arguments.
-     *
-     * **Note:** This method doesn't set the "length" property of partially
-     * applied functions.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.0.0
-     * @category Function
-     * @param {Function} func The function to partially apply arguments to.
-     * @param {...*} [partials] The arguments to be partially applied.
-     * @returns {Function} Returns the new partially applied function.
-     * @example
-     *
-     * function greet(greeting, name) {
-     *   return greeting + ' ' + name;
-     * }
-     *
-     * var greetFred = _.partialRight(greet, 'fred');
-     * greetFred('hi');
-     * // => 'hi fred'
-     *
-     * // Partially applied with placeholders.
-     * var sayHelloTo = _.partialRight(greet, 'hello', _);
-     * sayHelloTo('fred');
-     * // => 'hello fred'
-     */
-    var partialRight = baseRest(function(func, partials) {
-      var holders = replaceHolders(partials, getHolder(partialRight));
-      return createWrap(func, WRAP_PARTIAL_RIGHT_FLAG, undefined, partials, holders);
-    });
-
-    /**
-     * Creates a function that invokes `func` with arguments arranged according
-     * to the specified `indexes` where the argument value at the first index is
-     * provided as the first argument, the argument value at the second index is
-     * provided as the second argument, and so on.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Function
-     * @param {Function} func The function to rearrange arguments for.
-     * @param {...(number|number[])} indexes The arranged argument indexes.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var rearged = _.rearg(function(a, b, c) {
-     *   return [a, b, c];
-     * }, [2, 0, 1]);
-     *
-     * rearged('b', 'c', 'a')
-     * // => ['a', 'b', 'c']
-     */
-    var rearg = flatRest(function(func, indexes) {
-      return createWrap(func, WRAP_REARG_FLAG, undefined, undefined, undefined, indexes);
-    });
-
-    /**
-     * Creates a function that invokes `func` with the `this` binding of the
-     * created function and arguments from `start` and beyond provided as
-     * an array.
-     *
-     * **Note:** This method is based on the
-     * [rest parameter](https://mdn.io/rest_parameters).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Function
-     * @param {Function} func The function to apply a rest parameter to.
-     * @param {number} [start=func.length-1] The start position of the rest parameter.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var say = _.rest(function(what, names) {
-     *   return what + ' ' + _.initial(names).join(', ') +
-     *     (_.size(names) > 1 ? ', & ' : '') + _.last(names);
-     * });
-     *
-     * say('hello', 'fred', 'barney', 'pebbles');
-     * // => 'hello fred, barney, & pebbles'
-     */
-    function rest(func, start) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      start = start === undefined ? start : toInteger(start);
-      return baseRest(func, start);
-    }
-
-    /**
-     * Creates a function that invokes `func` with the `this` binding of the
-     * create function and an array of arguments much like
-     * [`Function#apply`](http://www.ecma-international.org/ecma-262/7.0/#sec-function.prototype.apply).
-     *
-     * **Note:** This method is based on the
-     * [spread operator](https://mdn.io/spread_operator).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.2.0
-     * @category Function
-     * @param {Function} func The function to spread arguments over.
-     * @param {number} [start=0] The start position of the spread.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var say = _.spread(function(who, what) {
-     *   return who + ' says ' + what;
-     * });
-     *
-     * say(['fred', 'hello']);
-     * // => 'fred says hello'
-     *
-     * var numbers = Promise.all([
-     *   Promise.resolve(40),
-     *   Promise.resolve(36)
-     * ]);
-     *
-     * numbers.then(_.spread(function(x, y) {
-     *   return x + y;
-     * }));
-     * // => a Promise of 76
-     */
-    function spread(func, start) {
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      start = start == null ? 0 : nativeMax(toInteger(start), 0);
-      return baseRest(function(args) {
-        var array = args[start],
-            otherArgs = castSlice(args, 0, start);
-
-        if (array) {
-          arrayPush(otherArgs, array);
-        }
-        return apply(func, this, otherArgs);
-      });
-    }
-
-    /**
-     * Creates a throttled function that only invokes `func` at most once per
-     * every `wait` milliseconds. The throttled function comes with a `cancel`
-     * method to cancel delayed `func` invocations and a `flush` method to
-     * immediately invoke them. Provide `options` to indicate whether `func`
-     * should be invoked on the leading and/or trailing edge of the `wait`
-     * timeout. The `func` is invoked with the last arguments provided to the
-     * throttled function. Subsequent calls to the throttled function return the
-     * result of the last `func` invocation.
-     *
-     * **Note:** If `leading` and `trailing` options are `true`, `func` is
-     * invoked on the trailing edge of the timeout only if the throttled function
-     * is invoked more than once during the `wait` timeout.
-     *
-     * If `wait` is `0` and `leading` is `false`, `func` invocation is deferred
-     * until to the next tick, similar to `setTimeout` with a timeout of `0`.
-     *
-     * See [David Corbacho's article](https://css-tricks.com/debouncing-throttling-explained-examples/)
-     * for details over the differences between `_.throttle` and `_.debounce`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {Function} func The function to throttle.
-     * @param {number} [wait=0] The number of milliseconds to throttle invocations to.
-     * @param {Object} [options={}] The options object.
-     * @param {boolean} [options.leading=true]
-     *  Specify invoking on the leading edge of the timeout.
-     * @param {boolean} [options.trailing=true]
-     *  Specify invoking on the trailing edge of the timeout.
-     * @returns {Function} Returns the new throttled function.
-     * @example
-     *
-     * // Avoid excessively updating the position while scrolling.
-     * jQuery(window).on('scroll', _.throttle(updatePosition, 100));
-     *
-     * // Invoke `renewToken` when the click event is fired, but not more than once every 5 minutes.
-     * var throttled = _.throttle(renewToken, 300000, { 'trailing': false });
-     * jQuery(element).on('click', throttled);
-     *
-     * // Cancel the trailing throttled invocation.
-     * jQuery(window).on('popstate', throttled.cancel);
-     */
-    function throttle(func, wait, options) {
-      var leading = true,
-          trailing = true;
-
-      if (typeof func != 'function') {
-        throw new TypeError(FUNC_ERROR_TEXT);
-      }
-      if (isObject(options)) {
-        leading = 'leading' in options ? !!options.leading : leading;
-        trailing = 'trailing' in options ? !!options.trailing : trailing;
-      }
-      return debounce(func, wait, {
-        'leading': leading,
-        'maxWait': wait,
-        'trailing': trailing
-      });
-    }
-
-    /**
-     * Creates a function that accepts up to one argument, ignoring any
-     * additional arguments.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Function
-     * @param {Function} func The function to cap arguments for.
-     * @returns {Function} Returns the new capped function.
-     * @example
-     *
-     * _.map(['6', '8', '10'], _.unary(parseInt));
-     * // => [6, 8, 10]
-     */
-    function unary(func) {
-      return ary(func, 1);
-    }
-
-    /**
-     * Creates a function that provides `value` to `wrapper` as its first
-     * argument. Any additional arguments provided to the function are appended
-     * to those provided to the `wrapper`. The wrapper is invoked with the `this`
-     * binding of the created function.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Function
-     * @param {*} value The value to wrap.
-     * @param {Function} [wrapper=identity] The wrapper function.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var p = _.wrap(_.escape, function(func, text) {
-     *   return '<p>' + func(text) + '</p>';
-     * });
-     *
-     * p('fred, barney, & pebbles');
-     * // => '<p>fred, barney, &amp; pebbles</p>'
-     */
-    function wrap(value, wrapper) {
-      return partial(castFunction(wrapper), value);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Casts `value` as an array if it's not one.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.4.0
-     * @category Lang
-     * @param {*} value The value to inspect.
-     * @returns {Array} Returns the cast array.
-     * @example
-     *
-     * _.castArray(1);
-     * // => [1]
-     *
-     * _.castArray({ 'a': 1 });
-     * // => [{ 'a': 1 }]
-     *
-     * _.castArray('abc');
-     * // => ['abc']
-     *
-     * _.castArray(null);
-     * // => [null]
-     *
-     * _.castArray(undefined);
-     * // => [undefined]
-     *
-     * _.castArray();
-     * // => []
-     *
-     * var array = [1, 2, 3];
-     * console.log(_.castArray(array) === array);
-     * // => true
-     */
-    function castArray() {
-      if (!arguments.length) {
-        return [];
-      }
-      var value = arguments[0];
-      return isArray(value) ? value : [value];
-    }
-
-    /**
-     * Creates a shallow clone of `value`.
-     *
-     * **Note:** This method is loosely based on the
-     * [structured clone algorithm](https://mdn.io/Structured_clone_algorithm)
-     * and supports cloning arrays, array buffers, booleans, date objects, maps,
-     * numbers, `Object` objects, regexes, sets, strings, symbols, and typed
-     * arrays. The own enumerable properties of `arguments` objects are cloned
-     * as plain objects. An empty object is returned for uncloneable values such
-     * as error objects, functions, DOM nodes, and WeakMaps.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to clone.
-     * @returns {*} Returns the cloned value.
-     * @see _.cloneDeep
-     * @example
-     *
-     * var objects = [{ 'a': 1 }, { 'b': 2 }];
-     *
-     * var shallow = _.clone(objects);
-     * console.log(shallow[0] === objects[0]);
-     * // => true
-     */
-    function clone(value) {
-      return baseClone(value, CLONE_SYMBOLS_FLAG);
-    }
-
-    /**
-     * This method is like `_.clone` except that it accepts `customizer` which
-     * is invoked to produce the cloned value. If `customizer` returns `undefined`,
-     * cloning is handled by the method instead. The `customizer` is invoked with
-     * up to four arguments; (value [, index|key, object, stack]).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to clone.
-     * @param {Function} [customizer] The function to customize cloning.
-     * @returns {*} Returns the cloned value.
-     * @see _.cloneDeepWith
-     * @example
-     *
-     * function customizer(value) {
-     *   if (_.isElement(value)) {
-     *     return value.cloneNode(false);
-     *   }
-     * }
-     *
-     * var el = _.cloneWith(document.body, customizer);
-     *
-     * console.log(el === document.body);
-     * // => false
-     * console.log(el.nodeName);
-     * // => 'BODY'
-     * console.log(el.childNodes.length);
-     * // => 0
-     */
-    function cloneWith(value, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return baseClone(value, CLONE_SYMBOLS_FLAG, customizer);
-    }
-
-    /**
-     * This method is like `_.clone` except that it recursively clones `value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.0.0
-     * @category Lang
-     * @param {*} value The value to recursively clone.
-     * @returns {*} Returns the deep cloned value.
-     * @see _.clone
-     * @example
-     *
-     * var objects = [{ 'a': 1 }, { 'b': 2 }];
-     *
-     * var deep = _.cloneDeep(objects);
-     * console.log(deep[0] === objects[0]);
-     * // => false
-     */
-    function cloneDeep(value) {
-      return baseClone(value, CLONE_DEEP_FLAG | CLONE_SYMBOLS_FLAG);
-    }
-
-    /**
-     * This method is like `_.cloneWith` except that it recursively clones `value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to recursively clone.
-     * @param {Function} [customizer] The function to customize cloning.
-     * @returns {*} Returns the deep cloned value.
-     * @see _.cloneWith
-     * @example
-     *
-     * function customizer(value) {
-     *   if (_.isElement(value)) {
-     *     return value.cloneNode(true);
-     *   }
-     * }
-     *
-     * var el = _.cloneDeepWith(document.body, customizer);
-     *
-     * console.log(el === document.body);
-     * // => false
-     * console.log(el.nodeName);
-     * // => 'BODY'
-     * console.log(el.childNodes.length);
-     * // => 20
-     */
-    function cloneDeepWith(value, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return baseClone(value, CLONE_DEEP_FLAG | CLONE_SYMBOLS_FLAG, customizer);
-    }
-
-    /**
-     * Checks if `object` conforms to `source` by invoking the predicate
-     * properties of `source` with the corresponding property values of `object`.
-     *
-     * **Note:** This method is equivalent to `_.conforms` when `source` is
-     * partially applied.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.14.0
-     * @category Lang
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {boolean} Returns `true` if `object` conforms, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2 };
-     *
-     * _.conformsTo(object, { 'b': function(n) { return n > 1; } });
-     * // => true
-     *
-     * _.conformsTo(object, { 'b': function(n) { return n > 2; } });
-     * // => false
-     */
-    function conformsTo(object, source) {
-      return source == null || baseConformsTo(object, source, keys(source));
-    }
-
-    /**
-     * Performs a
-     * [`SameValueZero`](http://ecma-international.org/ecma-262/7.0/#sec-samevaluezero)
-     * comparison between two values to determine if they are equivalent.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1 };
-     * var other = { 'a': 1 };
-     *
-     * _.eq(object, object);
-     * // => true
-     *
-     * _.eq(object, other);
-     * // => false
-     *
-     * _.eq('a', 'a');
-     * // => true
-     *
-     * _.eq('a', Object('a'));
-     * // => false
-     *
-     * _.eq(NaN, NaN);
-     * // => true
-     */
-    function eq(value, other) {
-      return value === other || (value !== value && other !== other);
-    }
-
-    /**
-     * Checks if `value` is greater than `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is greater than `other`,
-     *  else `false`.
-     * @see _.lt
-     * @example
-     *
-     * _.gt(3, 1);
-     * // => true
-     *
-     * _.gt(3, 3);
-     * // => false
-     *
-     * _.gt(1, 3);
-     * // => false
-     */
-    var gt = createRelationalOperation(baseGt);
-
-    /**
-     * Checks if `value` is greater than or equal to `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is greater than or equal to
-     *  `other`, else `false`.
-     * @see _.lte
-     * @example
-     *
-     * _.gte(3, 1);
-     * // => true
-     *
-     * _.gte(3, 3);
-     * // => true
-     *
-     * _.gte(1, 3);
-     * // => false
-     */
-    var gte = createRelationalOperation(function(value, other) {
-      return value >= other;
-    });
-
-    /**
-     * Checks if `value` is likely an `arguments` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an `arguments` object,
-     *  else `false`.
-     * @example
-     *
-     * _.isArguments(function() { return arguments; }());
-     * // => true
-     *
-     * _.isArguments([1, 2, 3]);
-     * // => false
-     */
-    var isArguments = baseIsArguments(function() { return arguments; }()) ? baseIsArguments : function(value) {
-      return isObjectLike(value) && hasOwnProperty.call(value, 'callee') &&
-        !propertyIsEnumerable.call(value, 'callee');
-    };
-
-    /**
-     * Checks if `value` is classified as an `Array` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array, else `false`.
-     * @example
-     *
-     * _.isArray([1, 2, 3]);
-     * // => true
-     *
-     * _.isArray(document.body.children);
-     * // => false
-     *
-     * _.isArray('abc');
-     * // => false
-     *
-     * _.isArray(_.noop);
-     * // => false
-     */
-    var isArray = Array.isArray;
-
-    /**
-     * Checks if `value` is classified as an `ArrayBuffer` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array buffer, else `false`.
-     * @example
-     *
-     * _.isArrayBuffer(new ArrayBuffer(2));
-     * // => true
-     *
-     * _.isArrayBuffer(new Array(2));
-     * // => false
-     */
-    var isArrayBuffer = nodeIsArrayBuffer ? baseUnary(nodeIsArrayBuffer) : baseIsArrayBuffer;
-
-    /**
-     * Checks if `value` is array-like. A value is considered array-like if it's
-     * not a function and has a `value.length` that's an integer greater than or
-     * equal to `0` and less than or equal to `Number.MAX_SAFE_INTEGER`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is array-like, else `false`.
-     * @example
-     *
-     * _.isArrayLike([1, 2, 3]);
-     * // => true
-     *
-     * _.isArrayLike(document.body.children);
-     * // => true
-     *
-     * _.isArrayLike('abc');
-     * // => true
-     *
-     * _.isArrayLike(_.noop);
-     * // => false
-     */
-    function isArrayLike(value) {
-      return value != null && isLength(value.length) && !isFunction(value);
-    }
-
-    /**
-     * This method is like `_.isArrayLike` except that it also checks if `value`
-     * is an object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an array-like object,
-     *  else `false`.
-     * @example
-     *
-     * _.isArrayLikeObject([1, 2, 3]);
-     * // => true
-     *
-     * _.isArrayLikeObject(document.body.children);
-     * // => true
-     *
-     * _.isArrayLikeObject('abc');
-     * // => false
-     *
-     * _.isArrayLikeObject(_.noop);
-     * // => false
-     */
-    function isArrayLikeObject(value) {
-      return isObjectLike(value) && isArrayLike(value);
-    }
-
-    /**
-     * Checks if `value` is classified as a boolean primitive or object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a boolean, else `false`.
-     * @example
-     *
-     * _.isBoolean(false);
-     * // => true
-     *
-     * _.isBoolean(null);
-     * // => false
-     */
-    function isBoolean(value) {
-      return value === true || value === false ||
-        (isObjectLike(value) && baseGetTag(value) == boolTag);
-    }
-
-    /**
-     * Checks if `value` is a buffer.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a buffer, else `false`.
-     * @example
-     *
-     * _.isBuffer(new Buffer(2));
-     * // => true
-     *
-     * _.isBuffer(new Uint8Array(2));
-     * // => false
-     */
-    var isBuffer = nativeIsBuffer || stubFalse;
-
-    /**
-     * Checks if `value` is classified as a `Date` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a date object, else `false`.
-     * @example
-     *
-     * _.isDate(new Date);
-     * // => true
-     *
-     * _.isDate('Mon April 23 2012');
-     * // => false
-     */
-    var isDate = nodeIsDate ? baseUnary(nodeIsDate) : baseIsDate;
-
-    /**
-     * Checks if `value` is likely a DOM element.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a DOM element, else `false`.
-     * @example
-     *
-     * _.isElement(document.body);
-     * // => true
-     *
-     * _.isElement('<body>');
-     * // => false
-     */
-    function isElement(value) {
-      return isObjectLike(value) && value.nodeType === 1 && !isPlainObject(value);
-    }
-
-    /**
-     * Checks if `value` is an empty object, collection, map, or set.
-     *
-     * Objects are considered empty if they have no own enumerable string keyed
-     * properties.
-     *
-     * Array-like values such as `arguments` objects, arrays, buffers, strings, or
-     * jQuery-like collections are considered empty if they have a `length` of `0`.
-     * Similarly, maps and sets are considered empty if they have a `size` of `0`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is empty, else `false`.
-     * @example
-     *
-     * _.isEmpty(null);
-     * // => true
-     *
-     * _.isEmpty(true);
-     * // => true
-     *
-     * _.isEmpty(1);
-     * // => true
-     *
-     * _.isEmpty([1, 2, 3]);
-     * // => false
-     *
-     * _.isEmpty({ 'a': 1 });
-     * // => false
-     */
-    function isEmpty(value) {
-      if (value == null) {
-        return true;
-      }
-      if (isArrayLike(value) &&
-          (isArray(value) || typeof value == 'string' || typeof value.splice == 'function' ||
-            isBuffer(value) || isTypedArray(value) || isArguments(value))) {
-        return !value.length;
-      }
-      var tag = getTag(value);
-      if (tag == mapTag || tag == setTag) {
-        return !value.size;
-      }
-      if (isPrototype(value)) {
-        return !baseKeys(value).length;
-      }
-      for (var key in value) {
-        if (hasOwnProperty.call(value, key)) {
-          return false;
-        }
-      }
-      return true;
-    }
-
-    /**
-     * Performs a deep comparison between two values to determine if they are
-     * equivalent.
-     *
-     * **Note:** This method supports comparing arrays, array buffers, booleans,
-     * date objects, error objects, maps, numbers, `Object` objects, regexes,
-     * sets, strings, symbols, and typed arrays. `Object` objects are compared
-     * by their own, not inherited, enumerable properties. Functions and DOM
-     * nodes are compared by strict equality, i.e. `===`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1 };
-     * var other = { 'a': 1 };
-     *
-     * _.isEqual(object, other);
-     * // => true
-     *
-     * object === other;
-     * // => false
-     */
-    function isEqual(value, other) {
-      return baseIsEqual(value, other);
-    }
-
-    /**
-     * This method is like `_.isEqual` except that it accepts `customizer` which
-     * is invoked to compare values. If `customizer` returns `undefined`, comparisons
-     * are handled by the method instead. The `customizer` is invoked with up to
-     * six arguments: (objValue, othValue [, index|key, object, other, stack]).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @returns {boolean} Returns `true` if the values are equivalent, else `false`.
-     * @example
-     *
-     * function isGreeting(value) {
-     *   return /^h(?:i|ello)$/.test(value);
-     * }
-     *
-     * function customizer(objValue, othValue) {
-     *   if (isGreeting(objValue) && isGreeting(othValue)) {
-     *     return true;
-     *   }
-     * }
-     *
-     * var array = ['hello', 'goodbye'];
-     * var other = ['hi', 'goodbye'];
-     *
-     * _.isEqualWith(array, other, customizer);
-     * // => true
-     */
-    function isEqualWith(value, other, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      var result = customizer ? customizer(value, other) : undefined;
-      return result === undefined ? baseIsEqual(value, other, undefined, customizer) : !!result;
-    }
-
-    /**
-     * Checks if `value` is an `Error`, `EvalError`, `RangeError`, `ReferenceError`,
-     * `SyntaxError`, `TypeError`, or `URIError` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an error object, else `false`.
-     * @example
-     *
-     * _.isError(new Error);
-     * // => true
-     *
-     * _.isError(Error);
-     * // => false
-     */
-    function isError(value) {
-      if (!isObjectLike(value)) {
-        return false;
-      }
-      var tag = baseGetTag(value);
-      return tag == errorTag || tag == domExcTag ||
-        (typeof value.message == 'string' && typeof value.name == 'string' && !isPlainObject(value));
-    }
-
-    /**
-     * Checks if `value` is a finite primitive number.
-     *
-     * **Note:** This method is based on
-     * [`Number.isFinite`](https://mdn.io/Number/isFinite).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a finite number, else `false`.
-     * @example
-     *
-     * _.isFinite(3);
-     * // => true
-     *
-     * _.isFinite(Number.MIN_VALUE);
-     * // => true
-     *
-     * _.isFinite(Infinity);
-     * // => false
-     *
-     * _.isFinite('3');
-     * // => false
-     */
-    function isFinite(value) {
-      return typeof value == 'number' && nativeIsFinite(value);
-    }
-
-    /**
-     * Checks if `value` is classified as a `Function` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a function, else `false`.
-     * @example
-     *
-     * _.isFunction(_);
-     * // => true
-     *
-     * _.isFunction(/abc/);
-     * // => false
-     */
-    function isFunction(value) {
-      if (!isObject(value)) {
-        return false;
-      }
-      // The use of `Object#toString` avoids issues with the `typeof` operator
-      // in Safari 9 which returns 'object' for typed arrays and other constructors.
-      var tag = baseGetTag(value);
-      return tag == funcTag || tag == genTag || tag == asyncTag || tag == proxyTag;
-    }
-
-    /**
-     * Checks if `value` is an integer.
-     *
-     * **Note:** This method is based on
-     * [`Number.isInteger`](https://mdn.io/Number/isInteger).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an integer, else `false`.
-     * @example
-     *
-     * _.isInteger(3);
-     * // => true
-     *
-     * _.isInteger(Number.MIN_VALUE);
-     * // => false
-     *
-     * _.isInteger(Infinity);
-     * // => false
-     *
-     * _.isInteger('3');
-     * // => false
-     */
-    function isInteger(value) {
-      return typeof value == 'number' && value == toInteger(value);
-    }
-
-    /**
-     * Checks if `value` is a valid array-like length.
-     *
-     * **Note:** This method is loosely based on
-     * [`ToLength`](http://ecma-international.org/ecma-262/7.0/#sec-tolength).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a valid length, else `false`.
-     * @example
-     *
-     * _.isLength(3);
-     * // => true
-     *
-     * _.isLength(Number.MIN_VALUE);
-     * // => false
-     *
-     * _.isLength(Infinity);
-     * // => false
-     *
-     * _.isLength('3');
-     * // => false
-     */
-    function isLength(value) {
-      return typeof value == 'number' &&
-        value > -1 && value % 1 == 0 && value <= MAX_SAFE_INTEGER;
-    }
-
-    /**
-     * Checks if `value` is the
-     * [language type](http://www.ecma-international.org/ecma-262/7.0/#sec-ecmascript-language-types)
-     * of `Object`. (e.g. arrays, functions, objects, regexes, `new Number(0)`, and `new String('')`)
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is an object, else `false`.
-     * @example
-     *
-     * _.isObject({});
-     * // => true
-     *
-     * _.isObject([1, 2, 3]);
-     * // => true
-     *
-     * _.isObject(_.noop);
-     * // => true
-     *
-     * _.isObject(null);
-     * // => false
-     */
-    function isObject(value) {
-      var type = typeof value;
-      return value != null && (type == 'object' || type == 'function');
-    }
-
-    /**
-     * Checks if `value` is object-like. A value is object-like if it's not `null`
-     * and has a `typeof` result of "object".
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is object-like, else `false`.
-     * @example
-     *
-     * _.isObjectLike({});
-     * // => true
-     *
-     * _.isObjectLike([1, 2, 3]);
-     * // => true
-     *
-     * _.isObjectLike(_.noop);
-     * // => false
-     *
-     * _.isObjectLike(null);
-     * // => false
-     */
-    function isObjectLike(value) {
-      return value != null && typeof value == 'object';
-    }
-
-    /**
-     * Checks if `value` is classified as a `Map` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a map, else `false`.
-     * @example
-     *
-     * _.isMap(new Map);
-     * // => true
-     *
-     * _.isMap(new WeakMap);
-     * // => false
-     */
-    var isMap = nodeIsMap ? baseUnary(nodeIsMap) : baseIsMap;
-
-    /**
-     * Performs a partial deep comparison between `object` and `source` to
-     * determine if `object` contains equivalent property values.
-     *
-     * **Note:** This method is equivalent to `_.matches` when `source` is
-     * partially applied.
-     *
-     * Partial comparisons will match empty array and empty object `source`
-     * values against any array or object value, respectively. See `_.isEqual`
-     * for a list of supported value comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property values to match.
-     * @returns {boolean} Returns `true` if `object` is a match, else `false`.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2 };
-     *
-     * _.isMatch(object, { 'b': 2 });
-     * // => true
-     *
-     * _.isMatch(object, { 'b': 1 });
-     * // => false
-     */
-    function isMatch(object, source) {
-      return object === source || baseIsMatch(object, source, getMatchData(source));
-    }
-
-    /**
-     * This method is like `_.isMatch` except that it accepts `customizer` which
-     * is invoked to compare values. If `customizer` returns `undefined`, comparisons
-     * are handled by the method instead. The `customizer` is invoked with five
-     * arguments: (objValue, srcValue, index|key, object, source).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {Object} object The object to inspect.
-     * @param {Object} source The object of property values to match.
-     * @param {Function} [customizer] The function to customize comparisons.
-     * @returns {boolean} Returns `true` if `object` is a match, else `false`.
-     * @example
-     *
-     * function isGreeting(value) {
-     *   return /^h(?:i|ello)$/.test(value);
-     * }
-     *
-     * function customizer(objValue, srcValue) {
-     *   if (isGreeting(objValue) && isGreeting(srcValue)) {
-     *     return true;
-     *   }
-     * }
-     *
-     * var object = { 'greeting': 'hello' };
-     * var source = { 'greeting': 'hi' };
-     *
-     * _.isMatchWith(object, source, customizer);
-     * // => true
-     */
-    function isMatchWith(object, source, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return baseIsMatch(object, source, getMatchData(source), customizer);
-    }
-
-    /**
-     * Checks if `value` is `NaN`.
-     *
-     * **Note:** This method is based on
-     * [`Number.isNaN`](https://mdn.io/Number/isNaN) and is not the same as
-     * global [`isNaN`](https://mdn.io/isNaN) which returns `true` for
-     * `undefined` and other non-number values.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is `NaN`, else `false`.
-     * @example
-     *
-     * _.isNaN(NaN);
-     * // => true
-     *
-     * _.isNaN(new Number(NaN));
-     * // => true
-     *
-     * isNaN(undefined);
-     * // => true
-     *
-     * _.isNaN(undefined);
-     * // => false
-     */
-    function isNaN(value) {
-      // An `NaN` primitive is the only value that is not equal to itself.
-      // Perform the `toStringTag` check first to avoid errors with some
-      // ActiveX objects in IE.
-      return isNumber(value) && value != +value;
-    }
-
-    /**
-     * Checks if `value` is a pristine native function.
-     *
-     * **Note:** This method can't reliably detect native functions in the presence
-     * of the core-js package because core-js circumvents this kind of detection.
-     * Despite multiple requests, the core-js maintainer has made it clear: any
-     * attempt to fix the detection will be obstructed. As a result, we're left
-     * with little choice but to throw an error. Unfortunately, this also affects
-     * packages, like [babel-polyfill](https://www.npmjs.com/package/babel-polyfill),
-     * which rely on core-js.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a native function,
-     *  else `false`.
-     * @example
-     *
-     * _.isNative(Array.prototype.push);
-     * // => true
-     *
-     * _.isNative(_);
-     * // => false
-     */
-    function isNative(value) {
-      if (isMaskable(value)) {
-        throw new Error(CORE_ERROR_TEXT);
-      }
-      return baseIsNative(value);
-    }
-
-    /**
-     * Checks if `value` is `null`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is `null`, else `false`.
-     * @example
-     *
-     * _.isNull(null);
-     * // => true
-     *
-     * _.isNull(void 0);
-     * // => false
-     */
-    function isNull(value) {
-      return value === null;
-    }
-
-    /**
-     * Checks if `value` is `null` or `undefined`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is nullish, else `false`.
-     * @example
-     *
-     * _.isNil(null);
-     * // => true
-     *
-     * _.isNil(void 0);
-     * // => true
-     *
-     * _.isNil(NaN);
-     * // => false
-     */
-    function isNil(value) {
-      return value == null;
-    }
-
-    /**
-     * Checks if `value` is classified as a `Number` primitive or object.
-     *
-     * **Note:** To exclude `Infinity`, `-Infinity`, and `NaN`, which are
-     * classified as numbers, use the `_.isFinite` method.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a number, else `false`.
-     * @example
-     *
-     * _.isNumber(3);
-     * // => true
-     *
-     * _.isNumber(Number.MIN_VALUE);
-     * // => true
-     *
-     * _.isNumber(Infinity);
-     * // => true
-     *
-     * _.isNumber('3');
-     * // => false
-     */
-    function isNumber(value) {
-      return typeof value == 'number' ||
-        (isObjectLike(value) && baseGetTag(value) == numberTag);
-    }
-
-    /**
-     * Checks if `value` is a plain object, that is, an object created by the
-     * `Object` constructor or one with a `[[Prototype]]` of `null`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.8.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a plain object, else `false`.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     * }
-     *
-     * _.isPlainObject(new Foo);
-     * // => false
-     *
-     * _.isPlainObject([1, 2, 3]);
-     * // => false
-     *
-     * _.isPlainObject({ 'x': 0, 'y': 0 });
-     * // => true
-     *
-     * _.isPlainObject(Object.create(null));
-     * // => true
-     */
-    function isPlainObject(value) {
-      if (!isObjectLike(value) || baseGetTag(value) != objectTag) {
-        return false;
-      }
-      var proto = getPrototype(value);
-      if (proto === null) {
-        return true;
-      }
-      var Ctor = hasOwnProperty.call(proto, 'constructor') && proto.constructor;
-      return typeof Ctor == 'function' && Ctor instanceof Ctor &&
-        funcToString.call(Ctor) == objectCtorString;
-    }
-
-    /**
-     * Checks if `value` is classified as a `RegExp` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.1.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a regexp, else `false`.
-     * @example
-     *
-     * _.isRegExp(/abc/);
-     * // => true
-     *
-     * _.isRegExp('/abc/');
-     * // => false
-     */
-    var isRegExp = nodeIsRegExp ? baseUnary(nodeIsRegExp) : baseIsRegExp;
-
-    /**
-     * Checks if `value` is a safe integer. An integer is safe if it's an IEEE-754
-     * double precision number which isn't the result of a rounded unsafe integer.
-     *
-     * **Note:** This method is based on
-     * [`Number.isSafeInteger`](https://mdn.io/Number/isSafeInteger).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a safe integer, else `false`.
-     * @example
-     *
-     * _.isSafeInteger(3);
-     * // => true
-     *
-     * _.isSafeInteger(Number.MIN_VALUE);
-     * // => false
-     *
-     * _.isSafeInteger(Infinity);
-     * // => false
-     *
-     * _.isSafeInteger('3');
-     * // => false
-     */
-    function isSafeInteger(value) {
-      return isInteger(value) && value >= -MAX_SAFE_INTEGER && value <= MAX_SAFE_INTEGER;
-    }
-
-    /**
-     * Checks if `value` is classified as a `Set` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a set, else `false`.
-     * @example
-     *
-     * _.isSet(new Set);
-     * // => true
-     *
-     * _.isSet(new WeakSet);
-     * // => false
-     */
-    var isSet = nodeIsSet ? baseUnary(nodeIsSet) : baseIsSet;
-
-    /**
-     * Checks if `value` is classified as a `String` primitive or object.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a string, else `false`.
-     * @example
-     *
-     * _.isString('abc');
-     * // => true
-     *
-     * _.isString(1);
-     * // => false
-     */
-    function isString(value) {
-      return typeof value == 'string' ||
-        (!isArray(value) && isObjectLike(value) && baseGetTag(value) == stringTag);
-    }
-
-    /**
-     * Checks if `value` is classified as a `Symbol` primitive or object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a symbol, else `false`.
-     * @example
-     *
-     * _.isSymbol(Symbol.iterator);
-     * // => true
-     *
-     * _.isSymbol('abc');
-     * // => false
-     */
-    function isSymbol(value) {
-      return typeof value == 'symbol' ||
-        (isObjectLike(value) && baseGetTag(value) == symbolTag);
-    }
-
-    /**
-     * Checks if `value` is classified as a typed array.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a typed array, else `false`.
-     * @example
-     *
-     * _.isTypedArray(new Uint8Array);
-     * // => true
-     *
-     * _.isTypedArray([]);
-     * // => false
-     */
-    var isTypedArray = nodeIsTypedArray ? baseUnary(nodeIsTypedArray) : baseIsTypedArray;
-
-    /**
-     * Checks if `value` is `undefined`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is `undefined`, else `false`.
-     * @example
-     *
-     * _.isUndefined(void 0);
-     * // => true
-     *
-     * _.isUndefined(null);
-     * // => false
-     */
-    function isUndefined(value) {
-      return value === undefined;
-    }
-
-    /**
-     * Checks if `value` is classified as a `WeakMap` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a weak map, else `false`.
-     * @example
-     *
-     * _.isWeakMap(new WeakMap);
-     * // => true
-     *
-     * _.isWeakMap(new Map);
-     * // => false
-     */
-    function isWeakMap(value) {
-      return isObjectLike(value) && getTag(value) == weakMapTag;
-    }
-
-    /**
-     * Checks if `value` is classified as a `WeakSet` object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.3.0
-     * @category Lang
-     * @param {*} value The value to check.
-     * @returns {boolean} Returns `true` if `value` is a weak set, else `false`.
-     * @example
-     *
-     * _.isWeakSet(new WeakSet);
-     * // => true
-     *
-     * _.isWeakSet(new Set);
-     * // => false
-     */
-    function isWeakSet(value) {
-      return isObjectLike(value) && baseGetTag(value) == weakSetTag;
-    }
-
-    /**
-     * Checks if `value` is less than `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is less than `other`,
-     *  else `false`.
-     * @see _.gt
-     * @example
-     *
-     * _.lt(1, 3);
-     * // => true
-     *
-     * _.lt(3, 3);
-     * // => false
-     *
-     * _.lt(3, 1);
-     * // => false
-     */
-    var lt = createRelationalOperation(baseLt);
-
-    /**
-     * Checks if `value` is less than or equal to `other`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.9.0
-     * @category Lang
-     * @param {*} value The value to compare.
-     * @param {*} other The other value to compare.
-     * @returns {boolean} Returns `true` if `value` is less than or equal to
-     *  `other`, else `false`.
-     * @see _.gte
-     * @example
-     *
-     * _.lte(1, 3);
-     * // => true
-     *
-     * _.lte(3, 3);
-     * // => true
-     *
-     * _.lte(3, 1);
-     * // => false
-     */
-    var lte = createRelationalOperation(function(value, other) {
-      return value <= other;
-    });
-
-    /**
-     * Converts `value` to an array.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {Array} Returns the converted array.
-     * @example
-     *
-     * _.toArray({ 'a': 1, 'b': 2 });
-     * // => [1, 2]
-     *
-     * _.toArray('abc');
-     * // => ['a', 'b', 'c']
-     *
-     * _.toArray(1);
-     * // => []
-     *
-     * _.toArray(null);
-     * // => []
-     */
-    function toArray(value) {
-      if (!value) {
-        return [];
-      }
-      if (isArrayLike(value)) {
-        return isString(value) ? stringToArray(value) : copyArray(value);
-      }
-      if (symIterator && value[symIterator]) {
-        return iteratorToArray(value[symIterator]());
-      }
-      var tag = getTag(value),
-          func = tag == mapTag ? mapToArray : (tag == setTag ? setToArray : values);
-
-      return func(value);
-    }
-
-    /**
-     * Converts `value` to a finite number.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.12.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted number.
-     * @example
-     *
-     * _.toFinite(3.2);
-     * // => 3.2
-     *
-     * _.toFinite(Number.MIN_VALUE);
-     * // => 5e-324
-     *
-     * _.toFinite(Infinity);
-     * // => 1.7976931348623157e+308
-     *
-     * _.toFinite('3.2');
-     * // => 3.2
-     */
-    function toFinite(value) {
-      if (!value) {
-        return value === 0 ? value : 0;
-      }
-      value = toNumber(value);
-      if (value === INFINITY || value === -INFINITY) {
-        var sign = (value < 0 ? -1 : 1);
-        return sign * MAX_INTEGER;
-      }
-      return value === value ? value : 0;
-    }
-
-    /**
-     * Converts `value` to an integer.
-     *
-     * **Note:** This method is loosely based on
-     * [`ToInteger`](http://www.ecma-international.org/ecma-262/7.0/#sec-tointeger).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.toInteger(3.2);
-     * // => 3
-     *
-     * _.toInteger(Number.MIN_VALUE);
-     * // => 0
-     *
-     * _.toInteger(Infinity);
-     * // => 1.7976931348623157e+308
-     *
-     * _.toInteger('3.2');
-     * // => 3
-     */
-    function toInteger(value) {
-      var result = toFinite(value),
-          remainder = result % 1;
-
-      return result === result ? (remainder ? result - remainder : result) : 0;
-    }
-
-    /**
-     * Converts `value` to an integer suitable for use as the length of an
-     * array-like object.
-     *
-     * **Note:** This method is based on
-     * [`ToLength`](http://ecma-international.org/ecma-262/7.0/#sec-tolength).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.toLength(3.2);
-     * // => 3
-     *
-     * _.toLength(Number.MIN_VALUE);
-     * // => 0
-     *
-     * _.toLength(Infinity);
-     * // => 4294967295
-     *
-     * _.toLength('3.2');
-     * // => 3
-     */
-    function toLength(value) {
-      return value ? baseClamp(toInteger(value), 0, MAX_ARRAY_LENGTH) : 0;
-    }
-
-    /**
-     * Converts `value` to a number.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to process.
-     * @returns {number} Returns the number.
-     * @example
-     *
-     * _.toNumber(3.2);
-     * // => 3.2
-     *
-     * _.toNumber(Number.MIN_VALUE);
-     * // => 5e-324
-     *
-     * _.toNumber(Infinity);
-     * // => Infinity
-     *
-     * _.toNumber('3.2');
-     * // => 3.2
-     */
-    function toNumber(value) {
-      if (typeof value == 'number') {
-        return value;
-      }
-      if (isSymbol(value)) {
-        return NAN;
-      }
-      if (isObject(value)) {
-        var other = typeof value.valueOf == 'function' ? value.valueOf() : value;
-        value = isObject(other) ? (other + '') : other;
-      }
-      if (typeof value != 'string') {
-        return value === 0 ? value : +value;
-      }
-      value = value.replace(reTrim, '');
-      var isBinary = reIsBinary.test(value);
-      return (isBinary || reIsOctal.test(value))
-        ? freeParseInt(value.slice(2), isBinary ? 2 : 8)
-        : (reIsBadHex.test(value) ? NAN : +value);
-    }
-
-    /**
-     * Converts `value` to a plain object flattening inherited enumerable string
-     * keyed properties of `value` to own properties of the plain object.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {Object} Returns the converted plain object.
-     * @example
-     *
-     * function Foo() {
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.assign({ 'a': 1 }, new Foo);
-     * // => { 'a': 1, 'b': 2 }
-     *
-     * _.assign({ 'a': 1 }, _.toPlainObject(new Foo));
-     * // => { 'a': 1, 'b': 2, 'c': 3 }
-     */
-    function toPlainObject(value) {
-      return copyObject(value, keysIn(value));
-    }
-
-    /**
-     * Converts `value` to a safe integer. A safe integer can be compared and
-     * represented correctly.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.toSafeInteger(3.2);
-     * // => 3
-     *
-     * _.toSafeInteger(Number.MIN_VALUE);
-     * // => 0
-     *
-     * _.toSafeInteger(Infinity);
-     * // => 9007199254740991
-     *
-     * _.toSafeInteger('3.2');
-     * // => 3
-     */
-    function toSafeInteger(value) {
-      return value
-        ? baseClamp(toInteger(value), -MAX_SAFE_INTEGER, MAX_SAFE_INTEGER)
-        : (value === 0 ? value : 0);
-    }
-
-    /**
-     * Converts `value` to a string. An empty string is returned for `null`
-     * and `undefined` values. The sign of `-0` is preserved.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Lang
-     * @param {*} value The value to convert.
-     * @returns {string} Returns the converted string.
-     * @example
-     *
-     * _.toString(null);
-     * // => ''
-     *
-     * _.toString(-0);
-     * // => '-0'
-     *
-     * _.toString([1, 2, 3]);
-     * // => '1,2,3'
-     */
-    function toString(value) {
-      return value == null ? '' : baseToString(value);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Assigns own enumerable string keyed properties of source objects to the
-     * destination object. Source objects are applied from left to right.
-     * Subsequent sources overwrite property assignments of previous sources.
-     *
-     * **Note:** This method mutates `object` and is loosely based on
-     * [`Object.assign`](https://mdn.io/Object/assign).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.10.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.assignIn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     * }
-     *
-     * function Bar() {
-     *   this.c = 3;
-     * }
-     *
-     * Foo.prototype.b = 2;
-     * Bar.prototype.d = 4;
-     *
-     * _.assign({ 'a': 0 }, new Foo, new Bar);
-     * // => { 'a': 1, 'c': 3 }
-     */
-    var assign = createAssigner(function(object, source) {
-      if (isPrototype(source) || isArrayLike(source)) {
-        copyObject(source, keys(source), object);
-        return;
-      }
-      for (var key in source) {
-        if (hasOwnProperty.call(source, key)) {
-          assignValue(object, key, source[key]);
-        }
-      }
-    });
-
-    /**
-     * This method is like `_.assign` except that it iterates over own and
-     * inherited source properties.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias extend
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.assign
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     * }
-     *
-     * function Bar() {
-     *   this.c = 3;
-     * }
-     *
-     * Foo.prototype.b = 2;
-     * Bar.prototype.d = 4;
-     *
-     * _.assignIn({ 'a': 0 }, new Foo, new Bar);
-     * // => { 'a': 1, 'b': 2, 'c': 3, 'd': 4 }
-     */
-    var assignIn = createAssigner(function(object, source) {
-      copyObject(source, keysIn(source), object);
-    });
-
-    /**
-     * This method is like `_.assignIn` except that it accepts `customizer`
-     * which is invoked to produce the assigned values. If `customizer` returns
-     * `undefined`, assignment is handled by the method instead. The `customizer`
-     * is invoked with five arguments: (objValue, srcValue, key, object, source).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias extendWith
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} sources The source objects.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @see _.assignWith
-     * @example
-     *
-     * function customizer(objValue, srcValue) {
-     *   return _.isUndefined(objValue) ? srcValue : objValue;
-     * }
-     *
-     * var defaults = _.partialRight(_.assignInWith, customizer);
-     *
-     * defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 });
-     * // => { 'a': 1, 'b': 2 }
-     */
-    var assignInWith = createAssigner(function(object, source, srcIndex, customizer) {
-      copyObject(source, keysIn(source), object, customizer);
-    });
-
-    /**
-     * This method is like `_.assign` except that it accepts `customizer`
-     * which is invoked to produce the assigned values. If `customizer` returns
-     * `undefined`, assignment is handled by the method instead. The `customizer`
-     * is invoked with five arguments: (objValue, srcValue, key, object, source).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} sources The source objects.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @see _.assignInWith
-     * @example
-     *
-     * function customizer(objValue, srcValue) {
-     *   return _.isUndefined(objValue) ? srcValue : objValue;
-     * }
-     *
-     * var defaults = _.partialRight(_.assignWith, customizer);
-     *
-     * defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 });
-     * // => { 'a': 1, 'b': 2 }
-     */
-    var assignWith = createAssigner(function(object, source, srcIndex, customizer) {
-      copyObject(source, keys(source), object, customizer);
-    });
-
-    /**
-     * Creates an array of values corresponding to `paths` of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.0.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {...(string|string[])} [paths] The property paths to pick.
-     * @returns {Array} Returns the picked values.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }, 4] };
-     *
-     * _.at(object, ['a[0].b.c', 'a[1]']);
-     * // => [3, 4]
-     */
-    var at = flatRest(baseAt);
-
-    /**
-     * Creates an object that inherits from the `prototype` object. If a
-     * `properties` object is given, its own enumerable string keyed properties
-     * are assigned to the created object.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.3.0
-     * @category Object
-     * @param {Object} prototype The object to inherit from.
-     * @param {Object} [properties] The properties to assign to the object.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * function Shape() {
-     *   this.x = 0;
-     *   this.y = 0;
-     * }
-     *
-     * function Circle() {
-     *   Shape.call(this);
-     * }
-     *
-     * Circle.prototype = _.create(Shape.prototype, {
-     *   'constructor': Circle
-     * });
-     *
-     * var circle = new Circle;
-     * circle instanceof Circle;
-     * // => true
-     *
-     * circle instanceof Shape;
-     * // => true
-     */
-    function create(prototype, properties) {
-      var result = baseCreate(prototype);
-      return properties == null ? result : baseAssign(result, properties);
-    }
-
-    /**
-     * Assigns own and inherited enumerable string keyed properties of source
-     * objects to the destination object for all destination properties that
-     * resolve to `undefined`. Source objects are applied from left to right.
-     * Once a property is set, additional values of the same property are ignored.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.defaultsDeep
-     * @example
-     *
-     * _.defaults({ 'a': 1 }, { 'b': 2 }, { 'a': 3 });
-     * // => { 'a': 1, 'b': 2 }
-     */
-    var defaults = baseRest(function(object, sources) {
-      object = Object(object);
-
-      var index = -1;
-      var length = sources.length;
-      var guard = length > 2 ? sources[2] : undefined;
-
-      if (guard && isIterateeCall(sources[0], sources[1], guard)) {
-        length = 1;
-      }
-
-      while (++index < length) {
-        var source = sources[index];
-        var props = keysIn(source);
-        var propsIndex = -1;
-        var propsLength = props.length;
-
-        while (++propsIndex < propsLength) {
-          var key = props[propsIndex];
-          var value = object[key];
-
-          if (value === undefined ||
-              (eq(value, objectProto[key]) && !hasOwnProperty.call(object, key))) {
-            object[key] = source[key];
-          }
-        }
-      }
-
-      return object;
-    });
-
-    /**
-     * This method is like `_.defaults` except that it recursively assigns
-     * default properties.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @see _.defaults
-     * @example
-     *
-     * _.defaultsDeep({ 'a': { 'b': 2 } }, { 'a': { 'b': 1, 'c': 3 } });
-     * // => { 'a': { 'b': 2, 'c': 3 } }
-     */
-    var defaultsDeep = baseRest(function(args) {
-      args.push(undefined, customDefaultsMerge);
-      return apply(mergeWith, undefined, args);
-    });
-
-    /**
-     * This method is like `_.find` except that it returns the key of the first
-     * element `predicate` returns truthy for instead of the element itself.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.1.0
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {string|undefined} Returns the key of the matched element,
-     *  else `undefined`.
-     * @example
-     *
-     * var users = {
-     *   'barney':  { 'age': 36, 'active': true },
-     *   'fred':    { 'age': 40, 'active': false },
-     *   'pebbles': { 'age': 1,  'active': true }
-     * };
-     *
-     * _.findKey(users, function(o) { return o.age < 40; });
-     * // => 'barney' (iteration order is not guaranteed)
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findKey(users, { 'age': 1, 'active': true });
-     * // => 'pebbles'
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findKey(users, ['active', false]);
-     * // => 'fred'
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findKey(users, 'active');
-     * // => 'barney'
-     */
-    function findKey(object, predicate) {
-      return baseFindKey(object, getIteratee(predicate, 3), baseForOwn);
-    }
-
-    /**
-     * This method is like `_.findKey` except that it iterates over elements of
-     * a collection in the opposite order.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @param {Function} [predicate=_.identity] The function invoked per iteration.
-     * @returns {string|undefined} Returns the key of the matched element,
-     *  else `undefined`.
-     * @example
-     *
-     * var users = {
-     *   'barney':  { 'age': 36, 'active': true },
-     *   'fred':    { 'age': 40, 'active': false },
-     *   'pebbles': { 'age': 1,  'active': true }
-     * };
-     *
-     * _.findLastKey(users, function(o) { return o.age < 40; });
-     * // => returns 'pebbles' assuming `_.findKey` returns 'barney'
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.findLastKey(users, { 'age': 36, 'active': true });
-     * // => 'barney'
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.findLastKey(users, ['active', false]);
-     * // => 'fred'
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.findLastKey(users, 'active');
-     * // => 'pebbles'
-     */
-    function findLastKey(object, predicate) {
-      return baseFindKey(object, getIteratee(predicate, 3), baseForOwnRight);
-    }
-
-    /**
-     * Iterates over own and inherited enumerable string keyed properties of an
-     * object and invokes `iteratee` for each property. The iteratee is invoked
-     * with three arguments: (value, key, object). Iteratee functions may exit
-     * iteration early by explicitly returning `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.3.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forInRight
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forIn(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'a', 'b', then 'c' (iteration order is not guaranteed).
-     */
-    function forIn(object, iteratee) {
-      return object == null
-        ? object
-        : baseFor(object, getIteratee(iteratee, 3), keysIn);
-    }
-
-    /**
-     * This method is like `_.forIn` except that it iterates over properties of
-     * `object` in the opposite order.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forIn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forInRight(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'c', 'b', then 'a' assuming `_.forIn` logs 'a', 'b', then 'c'.
-     */
-    function forInRight(object, iteratee) {
-      return object == null
-        ? object
-        : baseForRight(object, getIteratee(iteratee, 3), keysIn);
-    }
-
-    /**
-     * Iterates over own enumerable string keyed properties of an object and
-     * invokes `iteratee` for each property. The iteratee is invoked with three
-     * arguments: (value, key, object). Iteratee functions may exit iteration
-     * early by explicitly returning `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.3.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forOwnRight
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forOwn(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'a' then 'b' (iteration order is not guaranteed).
-     */
-    function forOwn(object, iteratee) {
-      return object && baseForOwn(object, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * This method is like `_.forOwn` except that it iterates over properties of
-     * `object` in the opposite order.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.0.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns `object`.
-     * @see _.forOwn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.forOwnRight(new Foo, function(value, key) {
-     *   console.log(key);
-     * });
-     * // => Logs 'b' then 'a' assuming `_.forOwn` logs 'a' then 'b'.
-     */
-    function forOwnRight(object, iteratee) {
-      return object && baseForOwnRight(object, getIteratee(iteratee, 3));
-    }
-
-    /**
-     * Creates an array of function property names from own enumerable properties
-     * of `object`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @returns {Array} Returns the function names.
-     * @see _.functionsIn
-     * @example
-     *
-     * function Foo() {
-     *   this.a = _.constant('a');
-     *   this.b = _.constant('b');
-     * }
-     *
-     * Foo.prototype.c = _.constant('c');
-     *
-     * _.functions(new Foo);
-     * // => ['a', 'b']
-     */
-    function functions(object) {
-      return object == null ? [] : baseFunctions(object, keys(object));
-    }
-
-    /**
-     * Creates an array of function property names from own and inherited
-     * enumerable properties of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to inspect.
-     * @returns {Array} Returns the function names.
-     * @see _.functions
-     * @example
-     *
-     * function Foo() {
-     *   this.a = _.constant('a');
-     *   this.b = _.constant('b');
-     * }
-     *
-     * Foo.prototype.c = _.constant('c');
-     *
-     * _.functionsIn(new Foo);
-     * // => ['a', 'b', 'c']
-     */
-    function functionsIn(object) {
-      return object == null ? [] : baseFunctions(object, keysIn(object));
-    }
-
-    /**
-     * Gets the value at `path` of `object`. If the resolved value is
-     * `undefined`, the `defaultValue` is returned in its place.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the property to get.
-     * @param {*} [defaultValue] The value returned for `undefined` resolved values.
-     * @returns {*} Returns the resolved value.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }] };
-     *
-     * _.get(object, 'a[0].b.c');
-     * // => 3
-     *
-     * _.get(object, ['a', '0', 'b', 'c']);
-     * // => 3
-     *
-     * _.get(object, 'a.b.c', 'default');
-     * // => 'default'
-     */
-    function get(object, path, defaultValue) {
-      var result = object == null ? undefined : baseGet(object, path);
-      return result === undefined ? defaultValue : result;
-    }
-
-    /**
-     * Checks if `path` is a direct property of `object`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path to check.
-     * @returns {boolean} Returns `true` if `path` exists, else `false`.
-     * @example
-     *
-     * var object = { 'a': { 'b': 2 } };
-     * var other = _.create({ 'a': _.create({ 'b': 2 }) });
-     *
-     * _.has(object, 'a');
-     * // => true
-     *
-     * _.has(object, 'a.b');
-     * // => true
-     *
-     * _.has(object, ['a', 'b']);
-     * // => true
-     *
-     * _.has(other, 'a');
-     * // => false
-     */
-    function has(object, path) {
-      return object != null && hasPath(object, path, baseHas);
-    }
-
-    /**
-     * Checks if `path` is a direct or inherited property of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path to check.
-     * @returns {boolean} Returns `true` if `path` exists, else `false`.
-     * @example
-     *
-     * var object = _.create({ 'a': _.create({ 'b': 2 }) });
-     *
-     * _.hasIn(object, 'a');
-     * // => true
-     *
-     * _.hasIn(object, 'a.b');
-     * // => true
-     *
-     * _.hasIn(object, ['a', 'b']);
-     * // => true
-     *
-     * _.hasIn(object, 'b');
-     * // => false
-     */
-    function hasIn(object, path) {
-      return object != null && hasPath(object, path, baseHasIn);
-    }
-
-    /**
-     * Creates an object composed of the inverted keys and values of `object`.
-     * If `object` contains duplicate values, subsequent values overwrite
-     * property assignments of previous values.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.7.0
-     * @category Object
-     * @param {Object} object The object to invert.
-     * @returns {Object} Returns the new inverted object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2, 'c': 1 };
-     *
-     * _.invert(object);
-     * // => { '1': 'c', '2': 'b' }
-     */
-    var invert = createInverter(function(result, value, key) {
-      if (value != null &&
-          typeof value.toString != 'function') {
-        value = nativeObjectToString.call(value);
-      }
-
-      result[value] = key;
-    }, constant(identity));
-
-    /**
-     * This method is like `_.invert` except that the inverted object is generated
-     * from the results of running each element of `object` thru `iteratee`. The
-     * corresponding inverted value of each inverted key is an array of keys
-     * responsible for generating the inverted value. The iteratee is invoked
-     * with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.1.0
-     * @category Object
-     * @param {Object} object The object to invert.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {Object} Returns the new inverted object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': 2, 'c': 1 };
-     *
-     * _.invertBy(object);
-     * // => { '1': ['a', 'c'], '2': ['b'] }
-     *
-     * _.invertBy(object, function(value) {
-     *   return 'group' + value;
-     * });
-     * // => { 'group1': ['a', 'c'], 'group2': ['b'] }
-     */
-    var invertBy = createInverter(function(result, value, key) {
-      if (value != null &&
-          typeof value.toString != 'function') {
-        value = nativeObjectToString.call(value);
-      }
-
-      if (hasOwnProperty.call(result, value)) {
-        result[value].push(key);
-      } else {
-        result[value] = [key];
-      }
-    }, getIteratee);
-
-    /**
-     * Invokes the method at `path` of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the method to invoke.
-     * @param {...*} [args] The arguments to invoke the method with.
-     * @returns {*} Returns the result of the invoked method.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': [1, 2, 3, 4] } }] };
-     *
-     * _.invoke(object, 'a[0].b.c.slice', 1, 3);
-     * // => [2, 3]
-     */
-    var invoke = baseRest(baseInvoke);
-
-    /**
-     * Creates an array of the own enumerable property names of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects. See the
-     * [ES spec](http://ecma-international.org/ecma-262/7.0/#sec-object.keys)
-     * for more details.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.keys(new Foo);
-     * // => ['a', 'b'] (iteration order is not guaranteed)
-     *
-     * _.keys('hi');
-     * // => ['0', '1']
-     */
-    function keys(object) {
-      return isArrayLike(object) ? arrayLikeKeys(object) : baseKeys(object);
-    }
-
-    /**
-     * Creates an array of the own and inherited enumerable property names of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property names.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.keysIn(new Foo);
-     * // => ['a', 'b', 'c'] (iteration order is not guaranteed)
-     */
-    function keysIn(object) {
-      return isArrayLike(object) ? arrayLikeKeys(object, true) : baseKeysIn(object);
-    }
-
-    /**
-     * The opposite of `_.mapValues`; this method creates an object with the
-     * same values as `object` and keys generated by running each own enumerable
-     * string keyed property of `object` thru `iteratee`. The iteratee is invoked
-     * with three arguments: (value, key, object).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.8.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns the new mapped object.
-     * @see _.mapValues
-     * @example
-     *
-     * _.mapKeys({ 'a': 1, 'b': 2 }, function(value, key) {
-     *   return key + value;
-     * });
-     * // => { 'a1': 1, 'b2': 2 }
-     */
-    function mapKeys(object, iteratee) {
-      var result = {};
-      iteratee = getIteratee(iteratee, 3);
-
-      baseForOwn(object, function(value, key, object) {
-        baseAssignValue(result, iteratee(value, key, object), value);
-      });
-      return result;
-    }
-
-    /**
-     * Creates an object with the same keys as `object` and values generated
-     * by running each own enumerable string keyed property of `object` thru
-     * `iteratee`. The iteratee is invoked with three arguments:
-     * (value, key, object).
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Object} Returns the new mapped object.
-     * @see _.mapKeys
-     * @example
-     *
-     * var users = {
-     *   'fred':    { 'user': 'fred',    'age': 40 },
-     *   'pebbles': { 'user': 'pebbles', 'age': 1 }
-     * };
-     *
-     * _.mapValues(users, function(o) { return o.age; });
-     * // => { 'fred': 40, 'pebbles': 1 } (iteration order is not guaranteed)
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.mapValues(users, 'age');
-     * // => { 'fred': 40, 'pebbles': 1 } (iteration order is not guaranteed)
-     */
-    function mapValues(object, iteratee) {
-      var result = {};
-      iteratee = getIteratee(iteratee, 3);
-
-      baseForOwn(object, function(value, key, object) {
-        baseAssignValue(result, key, iteratee(value, key, object));
-      });
-      return result;
-    }
-
-    /**
-     * This method is like `_.assign` except that it recursively merges own and
-     * inherited enumerable string keyed properties of source objects into the
-     * destination object. Source properties that resolve to `undefined` are
-     * skipped if a destination value exists. Array and plain object properties
-     * are merged recursively. Other objects and value types are overridden by
-     * assignment. Source objects are applied from left to right. Subsequent
-     * sources overwrite property assignments of previous sources.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.5.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} [sources] The source objects.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = {
-     *   'a': [{ 'b': 2 }, { 'd': 4 }]
-     * };
-     *
-     * var other = {
-     *   'a': [{ 'c': 3 }, { 'e': 5 }]
-     * };
-     *
-     * _.merge(object, other);
-     * // => { 'a': [{ 'b': 2, 'c': 3 }, { 'd': 4, 'e': 5 }] }
-     */
-    var merge = createAssigner(function(object, source, srcIndex) {
-      baseMerge(object, source, srcIndex);
-    });
-
-    /**
-     * This method is like `_.merge` except that it accepts `customizer` which
-     * is invoked to produce the merged values of the destination and source
-     * properties. If `customizer` returns `undefined`, merging is handled by the
-     * method instead. The `customizer` is invoked with six arguments:
-     * (objValue, srcValue, key, object, source, stack).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The destination object.
-     * @param {...Object} sources The source objects.
-     * @param {Function} customizer The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * function customizer(objValue, srcValue) {
-     *   if (_.isArray(objValue)) {
-     *     return objValue.concat(srcValue);
-     *   }
-     * }
-     *
-     * var object = { 'a': [1], 'b': [2] };
-     * var other = { 'a': [3], 'b': [4] };
-     *
-     * _.mergeWith(object, other, customizer);
-     * // => { 'a': [1, 3], 'b': [2, 4] }
-     */
-    var mergeWith = createAssigner(function(object, source, srcIndex, customizer) {
-      baseMerge(object, source, srcIndex, customizer);
-    });
-
-    /**
-     * The opposite of `_.pick`; this method creates an object composed of the
-     * own and inherited enumerable property paths of `object` that are not omitted.
-     *
-     * **Note:** This method is considerably slower than `_.pick`.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {...(string|string[])} [paths] The property paths to omit.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.omit(object, ['a', 'c']);
-     * // => { 'b': '2' }
-     */
-    var omit = flatRest(function(object, paths) {
-      var result = {};
-      if (object == null) {
-        return result;
-      }
-      var isDeep = false;
-      paths = arrayMap(paths, function(path) {
-        path = castPath(path, object);
-        isDeep || (isDeep = path.length > 1);
-        return path;
-      });
-      copyObject(object, getAllKeysIn(object), result);
-      if (isDeep) {
-        result = baseClone(result, CLONE_DEEP_FLAG | CLONE_FLAT_FLAG | CLONE_SYMBOLS_FLAG, customOmitClone);
-      }
-      var length = paths.length;
-      while (length--) {
-        baseUnset(result, paths[length]);
-      }
-      return result;
-    });
-
-    /**
-     * The opposite of `_.pickBy`; this method creates an object composed of
-     * the own and inherited enumerable string keyed properties of `object` that
-     * `predicate` doesn't return truthy for. The predicate is invoked with two
-     * arguments: (value, key).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {Function} [predicate=_.identity] The function invoked per property.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.omitBy(object, _.isNumber);
-     * // => { 'b': '2' }
-     */
-    function omitBy(object, predicate) {
-      return pickBy(object, negate(getIteratee(predicate)));
-    }
-
-    /**
-     * Creates an object composed of the picked `object` properties.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {...(string|string[])} [paths] The property paths to pick.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.pick(object, ['a', 'c']);
-     * // => { 'a': 1, 'c': 3 }
-     */
-    var pick = flatRest(function(object, paths) {
-      return object == null ? {} : basePick(object, paths);
-    });
-
-    /**
-     * Creates an object composed of the `object` properties `predicate` returns
-     * truthy for. The predicate is invoked with two arguments: (value, key).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The source object.
-     * @param {Function} [predicate=_.identity] The function invoked per property.
-     * @returns {Object} Returns the new object.
-     * @example
-     *
-     * var object = { 'a': 1, 'b': '2', 'c': 3 };
-     *
-     * _.pickBy(object, _.isNumber);
-     * // => { 'a': 1, 'c': 3 }
-     */
-    function pickBy(object, predicate) {
-      if (object == null) {
-        return {};
-      }
-      var props = arrayMap(getAllKeysIn(object), function(prop) {
-        return [prop];
-      });
-      predicate = getIteratee(predicate);
-      return basePickBy(object, props, function(value, path) {
-        return predicate(value, path[0]);
-      });
-    }
-
-    /**
-     * This method is like `_.get` except that if the resolved value is a
-     * function it's invoked with the `this` binding of its parent object and
-     * its result is returned.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @param {Array|string} path The path of the property to resolve.
-     * @param {*} [defaultValue] The value returned for `undefined` resolved values.
-     * @returns {*} Returns the resolved value.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c1': 3, 'c2': _.constant(4) } }] };
-     *
-     * _.result(object, 'a[0].b.c1');
-     * // => 3
-     *
-     * _.result(object, 'a[0].b.c2');
-     * // => 4
-     *
-     * _.result(object, 'a[0].b.c3', 'default');
-     * // => 'default'
-     *
-     * _.result(object, 'a[0].b.c3', _.constant('default'));
-     * // => 'default'
-     */
-    function result(object, path, defaultValue) {
-      path = castPath(path, object);
-
-      var index = -1,
-          length = path.length;
-
-      // Ensure the loop is entered when path is empty.
-      if (!length) {
-        length = 1;
-        object = undefined;
-      }
-      while (++index < length) {
-        var value = object == null ? undefined : object[toKey(path[index])];
-        if (value === undefined) {
-          index = length;
-          value = defaultValue;
-        }
-        object = isFunction(value) ? value.call(object) : value;
-      }
-      return object;
-    }
-
-    /**
-     * Sets the value at `path` of `object`. If a portion of `path` doesn't exist,
-     * it's created. Arrays are created for missing index properties while objects
-     * are created for all other missing properties. Use `_.setWith` to customize
-     * `path` creation.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {*} value The value to set.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }] };
-     *
-     * _.set(object, 'a[0].b.c', 4);
-     * console.log(object.a[0].b.c);
-     * // => 4
-     *
-     * _.set(object, ['x', '0', 'y', 'z'], 5);
-     * console.log(object.x[0].y.z);
-     * // => 5
-     */
-    function set(object, path, value) {
-      return object == null ? object : baseSet(object, path, value);
-    }
-
-    /**
-     * This method is like `_.set` except that it accepts `customizer` which is
-     * invoked to produce the objects of `path`.  If `customizer` returns `undefined`
-     * path creation is handled by the method instead. The `customizer` is invoked
-     * with three arguments: (nsValue, key, nsObject).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {*} value The value to set.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = {};
-     *
-     * _.setWith(object, '[0][1]', 'a', Object);
-     * // => { '0': { '1': 'a' } }
-     */
-    function setWith(object, path, value, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return object == null ? object : baseSet(object, path, value, customizer);
-    }
-
-    /**
-     * Creates an array of own enumerable string keyed-value pairs for `object`
-     * which can be consumed by `_.fromPairs`. If `object` is a map or set, its
-     * entries are returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias entries
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the key-value pairs.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.toPairs(new Foo);
-     * // => [['a', 1], ['b', 2]] (iteration order is not guaranteed)
-     */
-    var toPairs = createToPairs(keys);
-
-    /**
-     * Creates an array of own and inherited enumerable string keyed-value pairs
-     * for `object` which can be consumed by `_.fromPairs`. If `object` is a map
-     * or set, its entries are returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @alias entriesIn
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the key-value pairs.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.toPairsIn(new Foo);
-     * // => [['a', 1], ['b', 2], ['c', 3]] (iteration order is not guaranteed)
-     */
-    var toPairsIn = createToPairs(keysIn);
-
-    /**
-     * An alternative to `_.reduce`; this method transforms `object` to a new
-     * `accumulator` object which is the result of running each of its own
-     * enumerable string keyed properties thru `iteratee`, with each invocation
-     * potentially mutating the `accumulator` object. If `accumulator` is not
-     * provided, a new object with the same `[[Prototype]]` will be used. The
-     * iteratee is invoked with four arguments: (accumulator, value, key, object).
-     * Iteratee functions may exit iteration early by explicitly returning `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.3.0
-     * @category Object
-     * @param {Object} object The object to iterate over.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @param {*} [accumulator] The custom accumulator value.
-     * @returns {*} Returns the accumulated value.
-     * @example
-     *
-     * _.transform([2, 3, 4], function(result, n) {
-     *   result.push(n *= n);
-     *   return n % 2 == 0;
-     * }, []);
-     * // => [4, 9]
-     *
-     * _.transform({ 'a': 1, 'b': 2, 'c': 1 }, function(result, value, key) {
-     *   (result[value] || (result[value] = [])).push(key);
-     * }, {});
-     * // => { '1': ['a', 'c'], '2': ['b'] }
-     */
-    function transform(object, iteratee, accumulator) {
-      var isArr = isArray(object),
-          isArrLike = isArr || isBuffer(object) || isTypedArray(object);
-
-      iteratee = getIteratee(iteratee, 4);
-      if (accumulator == null) {
-        var Ctor = object && object.constructor;
-        if (isArrLike) {
-          accumulator = isArr ? new Ctor : [];
-        }
-        else if (isObject(object)) {
-          accumulator = isFunction(Ctor) ? baseCreate(getPrototype(object)) : {};
-        }
-        else {
-          accumulator = {};
-        }
-      }
-      (isArrLike ? arrayEach : baseForOwn)(object, function(value, index, object) {
-        return iteratee(accumulator, value, index, object);
-      });
-      return accumulator;
-    }
-
-    /**
-     * Removes the property at `path` of `object`.
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to unset.
-     * @returns {boolean} Returns `true` if the property is deleted, else `false`.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 7 } }] };
-     * _.unset(object, 'a[0].b.c');
-     * // => true
-     *
-     * console.log(object);
-     * // => { 'a': [{ 'b': {} }] };
-     *
-     * _.unset(object, ['a', '0', 'b', 'c']);
-     * // => true
-     *
-     * console.log(object);
-     * // => { 'a': [{ 'b': {} }] };
-     */
-    function unset(object, path) {
-      return object == null ? true : baseUnset(object, path);
-    }
-
-    /**
-     * This method is like `_.set` except that accepts `updater` to produce the
-     * value to set. Use `_.updateWith` to customize `path` creation. The `updater`
-     * is invoked with one argument: (value).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.6.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {Function} updater The function to produce the updated value.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = { 'a': [{ 'b': { 'c': 3 } }] };
-     *
-     * _.update(object, 'a[0].b.c', function(n) { return n * n; });
-     * console.log(object.a[0].b.c);
-     * // => 9
-     *
-     * _.update(object, 'x[0].y.z', function(n) { return n ? n + 1 : 0; });
-     * console.log(object.x[0].y.z);
-     * // => 0
-     */
-    function update(object, path, updater) {
-      return object == null ? object : baseUpdate(object, path, castFunction(updater));
-    }
-
-    /**
-     * This method is like `_.update` except that it accepts `customizer` which is
-     * invoked to produce the objects of `path`.  If `customizer` returns `undefined`
-     * path creation is handled by the method instead. The `customizer` is invoked
-     * with three arguments: (nsValue, key, nsObject).
-     *
-     * **Note:** This method mutates `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.6.0
-     * @category Object
-     * @param {Object} object The object to modify.
-     * @param {Array|string} path The path of the property to set.
-     * @param {Function} updater The function to produce the updated value.
-     * @param {Function} [customizer] The function to customize assigned values.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var object = {};
-     *
-     * _.updateWith(object, '[0][1]', _.constant('a'), Object);
-     * // => { '0': { '1': 'a' } }
-     */
-    function updateWith(object, path, updater, customizer) {
-      customizer = typeof customizer == 'function' ? customizer : undefined;
-      return object == null ? object : baseUpdate(object, path, castFunction(updater), customizer);
-    }
-
-    /**
-     * Creates an array of the own enumerable string keyed property values of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property values.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.values(new Foo);
-     * // => [1, 2] (iteration order is not guaranteed)
-     *
-     * _.values('hi');
-     * // => ['h', 'i']
-     */
-    function values(object) {
-      return object == null ? [] : baseValues(object, keys(object));
-    }
-
-    /**
-     * Creates an array of the own and inherited enumerable string keyed property
-     * values of `object`.
-     *
-     * **Note:** Non-object values are coerced to objects.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Object
-     * @param {Object} object The object to query.
-     * @returns {Array} Returns the array of property values.
-     * @example
-     *
-     * function Foo() {
-     *   this.a = 1;
-     *   this.b = 2;
-     * }
-     *
-     * Foo.prototype.c = 3;
-     *
-     * _.valuesIn(new Foo);
-     * // => [1, 2, 3] (iteration order is not guaranteed)
-     */
-    function valuesIn(object) {
-      return object == null ? [] : baseValues(object, keysIn(object));
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Clamps `number` within the inclusive `lower` and `upper` bounds.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Number
-     * @param {number} number The number to clamp.
-     * @param {number} [lower] The lower bound.
-     * @param {number} upper The upper bound.
-     * @returns {number} Returns the clamped number.
-     * @example
-     *
-     * _.clamp(-10, -5, 5);
-     * // => -5
-     *
-     * _.clamp(10, -5, 5);
-     * // => 5
-     */
-    function clamp(number, lower, upper) {
-      if (upper === undefined) {
-        upper = lower;
-        lower = undefined;
-      }
-      if (upper !== undefined) {
-        upper = toNumber(upper);
-        upper = upper === upper ? upper : 0;
-      }
-      if (lower !== undefined) {
-        lower = toNumber(lower);
-        lower = lower === lower ? lower : 0;
-      }
-      return baseClamp(toNumber(number), lower, upper);
-    }
-
-    /**
-     * Checks if `n` is between `start` and up to, but not including, `end`. If
-     * `end` is not specified, it's set to `start` with `start` then set to `0`.
-     * If `start` is greater than `end` the params are swapped to support
-     * negative ranges.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.3.0
-     * @category Number
-     * @param {number} number The number to check.
-     * @param {number} [start=0] The start of the range.
-     * @param {number} end The end of the range.
-     * @returns {boolean} Returns `true` if `number` is in the range, else `false`.
-     * @see _.range, _.rangeRight
-     * @example
-     *
-     * _.inRange(3, 2, 4);
-     * // => true
-     *
-     * _.inRange(4, 8);
-     * // => true
-     *
-     * _.inRange(4, 2);
-     * // => false
-     *
-     * _.inRange(2, 2);
-     * // => false
-     *
-     * _.inRange(1.2, 2);
-     * // => true
-     *
-     * _.inRange(5.2, 4);
-     * // => false
-     *
-     * _.inRange(-3, -2, -6);
-     * // => true
-     */
-    function inRange(number, start, end) {
-      start = toFinite(start);
-      if (end === undefined) {
-        end = start;
-        start = 0;
-      } else {
-        end = toFinite(end);
-      }
-      number = toNumber(number);
-      return baseInRange(number, start, end);
-    }
-
-    /**
-     * Produces a random number between the inclusive `lower` and `upper` bounds.
-     * If only one argument is provided a number between `0` and the given number
-     * is returned. If `floating` is `true`, or either `lower` or `upper` are
-     * floats, a floating-point number is returned instead of an integer.
-     *
-     * **Note:** JavaScript follows the IEEE-754 standard for resolving
-     * floating-point values which can produce unexpected results.
-     *
-     * @static
-     * @memberOf _
-     * @since 0.7.0
-     * @category Number
-     * @param {number} [lower=0] The lower bound.
-     * @param {number} [upper=1] The upper bound.
-     * @param {boolean} [floating] Specify returning a floating-point number.
-     * @returns {number} Returns the random number.
-     * @example
-     *
-     * _.random(0, 5);
-     * // => an integer between 0 and 5
-     *
-     * _.random(5);
-     * // => also an integer between 0 and 5
-     *
-     * _.random(5, true);
-     * // => a floating-point number between 0 and 5
-     *
-     * _.random(1.2, 5.2);
-     * // => a floating-point number between 1.2 and 5.2
-     */
-    function random(lower, upper, floating) {
-      if (floating && typeof floating != 'boolean' && isIterateeCall(lower, upper, floating)) {
-        upper = floating = undefined;
-      }
-      if (floating === undefined) {
-        if (typeof upper == 'boolean') {
-          floating = upper;
-          upper = undefined;
-        }
-        else if (typeof lower == 'boolean') {
-          floating = lower;
-          lower = undefined;
-        }
-      }
-      if (lower === undefined && upper === undefined) {
-        lower = 0;
-        upper = 1;
-      }
-      else {
-        lower = toFinite(lower);
-        if (upper === undefined) {
-          upper = lower;
-          lower = 0;
-        } else {
-          upper = toFinite(upper);
-        }
-      }
-      if (lower > upper) {
-        var temp = lower;
-        lower = upper;
-        upper = temp;
-      }
-      if (floating || lower % 1 || upper % 1) {
-        var rand = nativeRandom();
-        return nativeMin(lower + (rand * (upper - lower + freeParseFloat('1e-' + ((rand + '').length - 1)))), upper);
-      }
-      return baseRandom(lower, upper);
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Converts `string` to [camel case](https://en.wikipedia.org/wiki/CamelCase).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the camel cased string.
-     * @example
-     *
-     * _.camelCase('Foo Bar');
-     * // => 'fooBar'
-     *
-     * _.camelCase('--foo-bar--');
-     * // => 'fooBar'
-     *
-     * _.camelCase('__FOO_BAR__');
-     * // => 'fooBar'
-     */
-    var camelCase = createCompounder(function(result, word, index) {
-      word = word.toLowerCase();
-      return result + (index ? capitalize(word) : word);
-    });
-
-    /**
-     * Converts the first character of `string` to upper case and the remaining
-     * to lower case.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to capitalize.
-     * @returns {string} Returns the capitalized string.
-     * @example
-     *
-     * _.capitalize('FRED');
-     * // => 'Fred'
-     */
-    function capitalize(string) {
-      return upperFirst(toString(string).toLowerCase());
-    }
-
-    /**
-     * Deburrs `string` by converting
-     * [Latin-1 Supplement](https://en.wikipedia.org/wiki/Latin-1_Supplement_(Unicode_block)#Character_table)
-     * and [Latin Extended-A](https://en.wikipedia.org/wiki/Latin_Extended-A)
-     * letters to basic Latin letters and removing
-     * [combining diacritical marks](https://en.wikipedia.org/wiki/Combining_Diacritical_Marks).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to deburr.
-     * @returns {string} Returns the deburred string.
-     * @example
-     *
-     * _.deburr('déjà vu');
-     * // => 'deja vu'
-     */
-    function deburr(string) {
-      string = toString(string);
-      return string && string.replace(reLatin, deburrLetter).replace(reComboMark, '');
-    }
-
-    /**
-     * Checks if `string` ends with the given target string.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to inspect.
-     * @param {string} [target] The string to search for.
-     * @param {number} [position=string.length] The position to search up to.
-     * @returns {boolean} Returns `true` if `string` ends with `target`,
-     *  else `false`.
-     * @example
-     *
-     * _.endsWith('abc', 'c');
-     * // => true
-     *
-     * _.endsWith('abc', 'b');
-     * // => false
-     *
-     * _.endsWith('abc', 'b', 2);
-     * // => true
-     */
-    function endsWith(string, target, position) {
-      string = toString(string);
-      target = baseToString(target);
-
-      var length = string.length;
-      position = position === undefined
-        ? length
-        : baseClamp(toInteger(position), 0, length);
-
-      var end = position;
-      position -= target.length;
-      return position >= 0 && string.slice(position, end) == target;
-    }
-
-    /**
-     * Converts the characters "&", "<", ">", '"', and "'" in `string` to their
-     * corresponding HTML entities.
-     *
-     * **Note:** No other characters are escaped. To escape additional
-     * characters use a third-party library like [_he_](https://mths.be/he).
-     *
-     * Though the ">" character is escaped for symmetry, characters like
-     * ">" and "/" don't need escaping in HTML and have no special meaning
-     * unless they're part of a tag or unquoted attribute value. See
-     * [Mathias Bynens's article](https://mathiasbynens.be/notes/ambiguous-ampersands)
-     * (under "semi-related fun fact") for more details.
-     *
-     * When working with HTML you should always
-     * [quote attribute values](http://wonko.com/post/html-escaping) to reduce
-     * XSS vectors.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category String
-     * @param {string} [string=''] The string to escape.
-     * @returns {string} Returns the escaped string.
-     * @example
-     *
-     * _.escape('fred, barney, & pebbles');
-     * // => 'fred, barney, &amp; pebbles'
-     */
-    function escape(string) {
-      string = toString(string);
-      return (string && reHasUnescapedHtml.test(string))
-        ? string.replace(reUnescapedHtml, escapeHtmlChar)
-        : string;
-    }
-
-    /**
-     * Escapes the `RegExp` special characters "^", "$", "\", ".", "*", "+",
-     * "?", "(", ")", "[", "]", "{", "}", and "|" in `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to escape.
-     * @returns {string} Returns the escaped string.
-     * @example
-     *
-     * _.escapeRegExp('[lodash](https://lodash.com/)');
-     * // => '\[lodash\]\(https://lodash\.com/\)'
-     */
-    function escapeRegExp(string) {
-      string = toString(string);
-      return (string && reHasRegExpChar.test(string))
-        ? string.replace(reRegExpChar, '\\$&')
-        : string;
-    }
-
-    /**
-     * Converts `string` to
-     * [kebab case](https://en.wikipedia.org/wiki/Letter_case#Special_case_styles).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the kebab cased string.
-     * @example
-     *
-     * _.kebabCase('Foo Bar');
-     * // => 'foo-bar'
-     *
-     * _.kebabCase('fooBar');
-     * // => 'foo-bar'
-     *
-     * _.kebabCase('__FOO_BAR__');
-     * // => 'foo-bar'
-     */
-    var kebabCase = createCompounder(function(result, word, index) {
-      return result + (index ? '-' : '') + word.toLowerCase();
-    });
-
-    /**
-     * Converts `string`, as space separated words, to lower case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the lower cased string.
-     * @example
-     *
-     * _.lowerCase('--Foo-Bar--');
-     * // => 'foo bar'
-     *
-     * _.lowerCase('fooBar');
-     * // => 'foo bar'
-     *
-     * _.lowerCase('__FOO_BAR__');
-     * // => 'foo bar'
-     */
-    var lowerCase = createCompounder(function(result, word, index) {
-      return result + (index ? ' ' : '') + word.toLowerCase();
-    });
-
-    /**
-     * Converts the first character of `string` to lower case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the converted string.
-     * @example
-     *
-     * _.lowerFirst('Fred');
-     * // => 'fred'
-     *
-     * _.lowerFirst('FRED');
-     * // => 'fRED'
-     */
-    var lowerFirst = createCaseFirst('toLowerCase');
-
-    /**
-     * Pads `string` on the left and right sides if it's shorter than `length`.
-     * Padding characters are truncated if they can't be evenly divided by `length`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to pad.
-     * @param {number} [length=0] The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padded string.
-     * @example
-     *
-     * _.pad('abc', 8);
-     * // => '  abc   '
-     *
-     * _.pad('abc', 8, '_-');
-     * // => '_-abc_-_'
-     *
-     * _.pad('abc', 3);
-     * // => 'abc'
-     */
-    function pad(string, length, chars) {
-      string = toString(string);
-      length = toInteger(length);
-
-      var strLength = length ? stringSize(string) : 0;
-      if (!length || strLength >= length) {
-        return string;
-      }
-      var mid = (length - strLength) / 2;
-      return (
-        createPadding(nativeFloor(mid), chars) +
-        string +
-        createPadding(nativeCeil(mid), chars)
-      );
-    }
-
-    /**
-     * Pads `string` on the right side if it's shorter than `length`. Padding
-     * characters are truncated if they exceed `length`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to pad.
-     * @param {number} [length=0] The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padded string.
-     * @example
-     *
-     * _.padEnd('abc', 6);
-     * // => 'abc   '
-     *
-     * _.padEnd('abc', 6, '_-');
-     * // => 'abc_-_'
-     *
-     * _.padEnd('abc', 3);
-     * // => 'abc'
-     */
-    function padEnd(string, length, chars) {
-      string = toString(string);
-      length = toInteger(length);
-
-      var strLength = length ? stringSize(string) : 0;
-      return (length && strLength < length)
-        ? (string + createPadding(length - strLength, chars))
-        : string;
-    }
-
-    /**
-     * Pads `string` on the left side if it's shorter than `length`. Padding
-     * characters are truncated if they exceed `length`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to pad.
-     * @param {number} [length=0] The padding length.
-     * @param {string} [chars=' '] The string used as padding.
-     * @returns {string} Returns the padded string.
-     * @example
-     *
-     * _.padStart('abc', 6);
-     * // => '   abc'
-     *
-     * _.padStart('abc', 6, '_-');
-     * // => '_-_abc'
-     *
-     * _.padStart('abc', 3);
-     * // => 'abc'
-     */
-    function padStart(string, length, chars) {
-      string = toString(string);
-      length = toInteger(length);
-
-      var strLength = length ? stringSize(string) : 0;
-      return (length && strLength < length)
-        ? (createPadding(length - strLength, chars) + string)
-        : string;
-    }
-
-    /**
-     * Converts `string` to an integer of the specified radix. If `radix` is
-     * `undefined` or `0`, a `radix` of `10` is used unless `value` is a
-     * hexadecimal, in which case a `radix` of `16` is used.
-     *
-     * **Note:** This method aligns with the
-     * [ES5 implementation](https://es5.github.io/#x15.1.2.2) of `parseInt`.
-     *
-     * @static
-     * @memberOf _
-     * @since 1.1.0
-     * @category String
-     * @param {string} string The string to convert.
-     * @param {number} [radix=10] The radix to interpret `value` by.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {number} Returns the converted integer.
-     * @example
-     *
-     * _.parseInt('08');
-     * // => 8
-     *
-     * _.map(['6', '08', '10'], _.parseInt);
-     * // => [6, 8, 10]
-     */
-    function parseInt(string, radix, guard) {
-      if (guard || radix == null) {
-        radix = 0;
-      } else if (radix) {
-        radix = +radix;
-      }
-      return nativeParseInt(toString(string).replace(reTrimStart, ''), radix || 0);
-    }
-
-    /**
-     * Repeats the given string `n` times.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to repeat.
-     * @param {number} [n=1] The number of times to repeat the string.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the repeated string.
-     * @example
-     *
-     * _.repeat('*', 3);
-     * // => '***'
-     *
-     * _.repeat('abc', 2);
-     * // => 'abcabc'
-     *
-     * _.repeat('abc', 0);
-     * // => ''
-     */
-    function repeat(string, n, guard) {
-      if ((guard ? isIterateeCall(string, n, guard) : n === undefined)) {
-        n = 1;
-      } else {
-        n = toInteger(n);
-      }
-      return baseRepeat(toString(string), n);
-    }
-
-    /**
-     * Replaces matches for `pattern` in `string` with `replacement`.
-     *
-     * **Note:** This method is based on
-     * [`String#replace`](https://mdn.io/String/replace).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to modify.
-     * @param {RegExp|string} pattern The pattern to replace.
-     * @param {Function|string} replacement The match replacement.
-     * @returns {string} Returns the modified string.
-     * @example
-     *
-     * _.replace('Hi Fred', 'Fred', 'Barney');
-     * // => 'Hi Barney'
-     */
-    function replace() {
-      var args = arguments,
-          string = toString(args[0]);
-
-      return args.length < 3 ? string : string.replace(args[1], args[2]);
-    }
-
-    /**
-     * Converts `string` to
-     * [snake case](https://en.wikipedia.org/wiki/Snake_case).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the snake cased string.
-     * @example
-     *
-     * _.snakeCase('Foo Bar');
-     * // => 'foo_bar'
-     *
-     * _.snakeCase('fooBar');
-     * // => 'foo_bar'
-     *
-     * _.snakeCase('--FOO-BAR--');
-     * // => 'foo_bar'
-     */
-    var snakeCase = createCompounder(function(result, word, index) {
-      return result + (index ? '_' : '') + word.toLowerCase();
-    });
-
-    /**
-     * Splits `string` by `separator`.
-     *
-     * **Note:** This method is based on
-     * [`String#split`](https://mdn.io/String/split).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to split.
-     * @param {RegExp|string} separator The separator pattern to split by.
-     * @param {number} [limit] The length to truncate results to.
-     * @returns {Array} Returns the string segments.
-     * @example
-     *
-     * _.split('a-b-c', '-', 2);
-     * // => ['a', 'b']
-     */
-    function split(string, separator, limit) {
-      if (limit && typeof limit != 'number' && isIterateeCall(string, separator, limit)) {
-        separator = limit = undefined;
-      }
-      limit = limit === undefined ? MAX_ARRAY_LENGTH : limit >>> 0;
-      if (!limit) {
-        return [];
-      }
-      string = toString(string);
-      if (string && (
-            typeof separator == 'string' ||
-            (separator != null && !isRegExp(separator))
-          )) {
-        separator = baseToString(separator);
-        if (!separator && hasUnicode(string)) {
-          return castSlice(stringToArray(string), 0, limit);
-        }
-      }
-      return string.split(separator, limit);
-    }
-
-    /**
-     * Converts `string` to
-     * [start case](https://en.wikipedia.org/wiki/Letter_case#Stylistic_or_specialised_usage).
-     *
-     * @static
-     * @memberOf _
-     * @since 3.1.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the start cased string.
-     * @example
-     *
-     * _.startCase('--foo-bar--');
-     * // => 'Foo Bar'
-     *
-     * _.startCase('fooBar');
-     * // => 'Foo Bar'
-     *
-     * _.startCase('__FOO_BAR__');
-     * // => 'FOO BAR'
-     */
-    var startCase = createCompounder(function(result, word, index) {
-      return result + (index ? ' ' : '') + upperFirst(word);
-    });
-
-    /**
-     * Checks if `string` starts with the given target string.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to inspect.
-     * @param {string} [target] The string to search for.
-     * @param {number} [position=0] The position to search from.
-     * @returns {boolean} Returns `true` if `string` starts with `target`,
-     *  else `false`.
-     * @example
-     *
-     * _.startsWith('abc', 'a');
-     * // => true
-     *
-     * _.startsWith('abc', 'b');
-     * // => false
-     *
-     * _.startsWith('abc', 'b', 1);
-     * // => true
-     */
-    function startsWith(string, target, position) {
-      string = toString(string);
-      position = position == null
-        ? 0
-        : baseClamp(toInteger(position), 0, string.length);
-
-      target = baseToString(target);
-      return string.slice(position, position + target.length) == target;
-    }
-
-    /**
-     * Creates a compiled template function that can interpolate data properties
-     * in "interpolate" delimiters, HTML-escape interpolated data properties in
-     * "escape" delimiters, and execute JavaScript in "evaluate" delimiters. Data
-     * properties may be accessed as free variables in the template. If a setting
-     * object is given, it takes precedence over `_.templateSettings` values.
-     *
-     * **Note:** In the development build `_.template` utilizes
-     * [sourceURLs](http://www.html5rocks.com/en/tutorials/developertools/sourcemaps/#toc-sourceurl)
-     * for easier debugging.
-     *
-     * For more information on precompiling templates see
-     * [lodash's custom builds documentation](https://lodash.com/custom-builds).
-     *
-     * For more information on Chrome extension sandboxes see
-     * [Chrome's extensions documentation](https://developer.chrome.com/extensions/sandboxingEval).
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category String
-     * @param {string} [string=''] The template string.
-     * @param {Object} [options={}] The options object.
-     * @param {RegExp} [options.escape=_.templateSettings.escape]
-     *  The HTML "escape" delimiter.
-     * @param {RegExp} [options.evaluate=_.templateSettings.evaluate]
-     *  The "evaluate" delimiter.
-     * @param {Object} [options.imports=_.templateSettings.imports]
-     *  An object to import into the template as free variables.
-     * @param {RegExp} [options.interpolate=_.templateSettings.interpolate]
-     *  The "interpolate" delimiter.
-     * @param {string} [options.sourceURL='lodash.templateSources[n]']
-     *  The sourceURL of the compiled template.
-     * @param {string} [options.variable='obj']
-     *  The data object variable name.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Function} Returns the compiled template function.
-     * @example
-     *
-     * // Use the "interpolate" delimiter to create a compiled template.
-     * var compiled = _.template('hello <%= user %>!');
-     * compiled({ 'user': 'fred' });
-     * // => 'hello fred!'
-     *
-     * // Use the HTML "escape" delimiter to escape data property values.
-     * var compiled = _.template('<b><%- value %></b>');
-     * compiled({ 'value': '<script>' });
-     * // => '<b>&lt;script&gt;</b>'
-     *
-     * // Use the "evaluate" delimiter to execute JavaScript and generate HTML.
-     * var compiled = _.template('<% _.forEach(users, function(user) { %><li><%- user %></li><% }); %>');
-     * compiled({ 'users': ['fred', 'barney'] });
-     * // => '<li>fred</li><li>barney</li>'
-     *
-     * // Use the internal `print` function in "evaluate" delimiters.
-     * var compiled = _.template('<% print("hello " + user); %>!');
-     * compiled({ 'user': 'barney' });
-     * // => 'hello barney!'
-     *
-     * // Use the ES template literal delimiter as an "interpolate" delimiter.
-     * // Disable support by replacing the "interpolate" delimiter.
-     * var compiled = _.template('hello ${ user }!');
-     * compiled({ 'user': 'pebbles' });
-     * // => 'hello pebbles!'
-     *
-     * // Use backslashes to treat delimiters as plain text.
-     * var compiled = _.template('<%= "\\<%- value %\\>" %>');
-     * compiled({ 'value': 'ignored' });
-     * // => '<%- value %>'
-     *
-     * // Use the `imports` option to import `jQuery` as `jq`.
-     * var text = '<% jq.each(users, function(user) { %><li><%- user %></li><% }); %>';
-     * var compiled = _.template(text, { 'imports': { 'jq': jQuery } });
-     * compiled({ 'users': ['fred', 'barney'] });
-     * // => '<li>fred</li><li>barney</li>'
-     *
-     * // Use the `sourceURL` option to specify a custom sourceURL for the template.
-     * var compiled = _.template('hello <%= user %>!', { 'sourceURL': '/basic/greeting.jst' });
-     * compiled(data);
-     * // => Find the source of "greeting.jst" under the Sources tab or Resources panel of the web inspector.
-     *
-     * // Use the `variable` option to ensure a with-statement isn't used in the compiled template.
-     * var compiled = _.template('hi <%= data.user %>!', { 'variable': 'data' });
-     * compiled.source;
-     * // => function(data) {
-     * //   var __t, __p = '';
-     * //   __p += 'hi ' + ((__t = ( data.user )) == null ? '' : __t) + '!';
-     * //   return __p;
-     * // }
-     *
-     * // Use custom template delimiters.
-     * _.templateSettings.interpolate = /{{([\s\S]+?)}}/g;
-     * var compiled = _.template('hello {{ user }}!');
-     * compiled({ 'user': 'mustache' });
-     * // => 'hello mustache!'
-     *
-     * // Use the `source` property to inline compiled templates for meaningful
-     * // line numbers in error messages and stack traces.
-     * fs.writeFileSync(path.join(process.cwd(), 'jst.js'), '\
-     *   var JST = {\
-     *     "main": ' + _.template(mainText).source + '\
-     *   };\
-     * ');
-     */
-    function template(string, options, guard) {
-      // Based on John Resig's `tmpl` implementation
-      // (http://ejohn.org/blog/javascript-micro-templating/)
-      // and Laura Doktorova's doT.js (https://github.com/olado/doT).
-      var settings = lodash.templateSettings;
-
-      if (guard && isIterateeCall(string, options, guard)) {
-        options = undefined;
-      }
-      string = toString(string);
-      options = assignInWith({}, options, settings, customDefaultsAssignIn);
-
-      var imports = assignInWith({}, options.imports, settings.imports, customDefaultsAssignIn),
-          importsKeys = keys(imports),
-          importsValues = baseValues(imports, importsKeys);
-
-      var isEscaping,
-          isEvaluating,
-          index = 0,
-          interpolate = options.interpolate || reNoMatch,
-          source = "__p += '";
-
-      // Compile the regexp to match each delimiter.
-      var reDelimiters = RegExp(
-        (options.escape || reNoMatch).source + '|' +
-        interpolate.source + '|' +
-        (interpolate === reInterpolate ? reEsTemplate : reNoMatch).source + '|' +
-        (options.evaluate || reNoMatch).source + '|$'
-      , 'g');
-
-      // Use a sourceURL for easier debugging.
-      // The sourceURL gets injected into the source that's eval-ed, so be careful
-      // with lookup (in case of e.g. prototype pollution), and strip newlines if any.
-      // A newline wouldn't be a valid sourceURL anyway, and it'd enable code injection.
-      var sourceURL = '//# sourceURL=' +
-        (hasOwnProperty.call(options, 'sourceURL')
-          ? (options.sourceURL + '').replace(/[\r\n]/g, ' ')
-          : ('lodash.templateSources[' + (++templateCounter) + ']')
-        ) + '\n';
-
-      string.replace(reDelimiters, function(match, escapeValue, interpolateValue, esTemplateValue, evaluateValue, offset) {
-        interpolateValue || (interpolateValue = esTemplateValue);
-
-        // Escape characters that can't be included in string literals.
-        source += string.slice(index, offset).replace(reUnescapedString, escapeStringChar);
-
-        // Replace delimiters with snippets.
-        if (escapeValue) {
-          isEscaping = true;
-          source += "' +\n__e(" + escapeValue + ") +\n'";
-        }
-        if (evaluateValue) {
-          isEvaluating = true;
-          source += "';\n" + evaluateValue + ";\n__p += '";
-        }
-        if (interpolateValue) {
-          source += "' +\n((__t = (" + interpolateValue + ")) == null ? '' : __t) +\n'";
-        }
-        index = offset + match.length;
-
-        // The JS engine embedded in Adobe products needs `match` returned in
-        // order to produce the correct `offset` value.
-        return match;
-      });
-
-      source += "';\n";
-
-      // If `variable` is not specified wrap a with-statement around the generated
-      // code to add the data object to the top of the scope chain.
-      // Like with sourceURL, we take care to not check the option's prototype,
-      // as this configuration is a code injection vector.
-      var variable = hasOwnProperty.call(options, 'variable') && options.variable;
-      if (!variable) {
-        source = 'with (obj) {\n' + source + '\n}\n';
-      }
-      // Cleanup code by stripping empty strings.
-      source = (isEvaluating ? source.replace(reEmptyStringLeading, '') : source)
-        .replace(reEmptyStringMiddle, '$1')
-        .replace(reEmptyStringTrailing, '$1;');
-
-      // Frame code as the function body.
-      source = 'function(' + (variable || 'obj') + ') {\n' +
-        (variable
-          ? ''
-          : 'obj || (obj = {});\n'
-        ) +
-        "var __t, __p = ''" +
-        (isEscaping
-           ? ', __e = _.escape'
-           : ''
-        ) +
-        (isEvaluating
-          ? ', __j = Array.prototype.join;\n' +
-            "function print() { __p += __j.call(arguments, '') }\n"
-          : ';\n'
-        ) +
-        source +
-        'return __p\n}';
-
-      var result = attempt(function() {
-        return Function(importsKeys, sourceURL + 'return ' + source)
-          .apply(undefined, importsValues);
-      });
-
-      // Provide the compiled function's source by its `toString` method or
-      // the `source` property as a convenience for inlining compiled templates.
-      result.source = source;
-      if (isError(result)) {
-        throw result;
-      }
-      return result;
-    }
-
-    /**
-     * Converts `string`, as a whole, to lower case just like
-     * [String#toLowerCase](https://mdn.io/toLowerCase).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the lower cased string.
-     * @example
-     *
-     * _.toLower('--Foo-Bar--');
-     * // => '--foo-bar--'
-     *
-     * _.toLower('fooBar');
-     * // => 'foobar'
-     *
-     * _.toLower('__FOO_BAR__');
-     * // => '__foo_bar__'
-     */
-    function toLower(value) {
-      return toString(value).toLowerCase();
-    }
-
-    /**
-     * Converts `string`, as a whole, to upper case just like
-     * [String#toUpperCase](https://mdn.io/toUpperCase).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the upper cased string.
-     * @example
-     *
-     * _.toUpper('--foo-bar--');
-     * // => '--FOO-BAR--'
-     *
-     * _.toUpper('fooBar');
-     * // => 'FOOBAR'
-     *
-     * _.toUpper('__foo_bar__');
-     * // => '__FOO_BAR__'
-     */
-    function toUpper(value) {
-      return toString(value).toUpperCase();
-    }
-
-    /**
-     * Removes leading and trailing whitespace or specified characters from `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to trim.
-     * @param {string} [chars=whitespace] The characters to trim.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the trimmed string.
-     * @example
-     *
-     * _.trim('  abc  ');
-     * // => 'abc'
-     *
-     * _.trim('-_-abc-_-', '_-');
-     * // => 'abc'
-     *
-     * _.map(['  foo  ', '  bar  '], _.trim);
-     * // => ['foo', 'bar']
-     */
-    function trim(string, chars, guard) {
-      string = toString(string);
-      if (string && (guard || chars === undefined)) {
-        return string.replace(reTrim, '');
-      }
-      if (!string || !(chars = baseToString(chars))) {
-        return string;
-      }
-      var strSymbols = stringToArray(string),
-          chrSymbols = stringToArray(chars),
-          start = charsStartIndex(strSymbols, chrSymbols),
-          end = charsEndIndex(strSymbols, chrSymbols) + 1;
-
-      return castSlice(strSymbols, start, end).join('');
-    }
-
-    /**
-     * Removes trailing whitespace or specified characters from `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to trim.
-     * @param {string} [chars=whitespace] The characters to trim.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the trimmed string.
-     * @example
-     *
-     * _.trimEnd('  abc  ');
-     * // => '  abc'
-     *
-     * _.trimEnd('-_-abc-_-', '_-');
-     * // => '-_-abc'
-     */
-    function trimEnd(string, chars, guard) {
-      string = toString(string);
-      if (string && (guard || chars === undefined)) {
-        return string.replace(reTrimEnd, '');
-      }
-      if (!string || !(chars = baseToString(chars))) {
-        return string;
-      }
-      var strSymbols = stringToArray(string),
-          end = charsEndIndex(strSymbols, stringToArray(chars)) + 1;
-
-      return castSlice(strSymbols, 0, end).join('');
-    }
-
-    /**
-     * Removes leading whitespace or specified characters from `string`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to trim.
-     * @param {string} [chars=whitespace] The characters to trim.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {string} Returns the trimmed string.
-     * @example
-     *
-     * _.trimStart('  abc  ');
-     * // => 'abc  '
-     *
-     * _.trimStart('-_-abc-_-', '_-');
-     * // => 'abc-_-'
-     */
-    function trimStart(string, chars, guard) {
-      string = toString(string);
-      if (string && (guard || chars === undefined)) {
-        return string.replace(reTrimStart, '');
-      }
-      if (!string || !(chars = baseToString(chars))) {
-        return string;
-      }
-      var strSymbols = stringToArray(string),
-          start = charsStartIndex(strSymbols, stringToArray(chars));
-
-      return castSlice(strSymbols, start).join('');
-    }
-
-    /**
-     * Truncates `string` if it's longer than the given maximum string length.
-     * The last characters of the truncated string are replaced with the omission
-     * string which defaults to "...".
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to truncate.
-     * @param {Object} [options={}] The options object.
-     * @param {number} [options.length=30] The maximum string length.
-     * @param {string} [options.omission='...'] The string to indicate text is omitted.
-     * @param {RegExp|string} [options.separator] The separator pattern to truncate to.
-     * @returns {string} Returns the truncated string.
-     * @example
-     *
-     * _.truncate('hi-diddly-ho there, neighborino');
-     * // => 'hi-diddly-ho there, neighbo...'
-     *
-     * _.truncate('hi-diddly-ho there, neighborino', {
-     *   'length': 24,
-     *   'separator': ' '
-     * });
-     * // => 'hi-diddly-ho there,...'
-     *
-     * _.truncate('hi-diddly-ho there, neighborino', {
-     *   'length': 24,
-     *   'separator': /,? +/
-     * });
-     * // => 'hi-diddly-ho there...'
-     *
-     * _.truncate('hi-diddly-ho there, neighborino', {
-     *   'omission': ' [...]'
-     * });
-     * // => 'hi-diddly-ho there, neig [...]'
-     */
-    function truncate(string, options) {
-      var length = DEFAULT_TRUNC_LENGTH,
-          omission = DEFAULT_TRUNC_OMISSION;
-
-      if (isObject(options)) {
-        var separator = 'separator' in options ? options.separator : separator;
-        length = 'length' in options ? toInteger(options.length) : length;
-        omission = 'omission' in options ? baseToString(options.omission) : omission;
-      }
-      string = toString(string);
-
-      var strLength = string.length;
-      if (hasUnicode(string)) {
-        var strSymbols = stringToArray(string);
-        strLength = strSymbols.length;
-      }
-      if (length >= strLength) {
-        return string;
-      }
-      var end = length - stringSize(omission);
-      if (end < 1) {
-        return omission;
-      }
-      var result = strSymbols
-        ? castSlice(strSymbols, 0, end).join('')
-        : string.slice(0, end);
-
-      if (separator === undefined) {
-        return result + omission;
-      }
-      if (strSymbols) {
-        end += (result.length - end);
-      }
-      if (isRegExp(separator)) {
-        if (string.slice(end).search(separator)) {
-          var match,
-              substring = result;
-
-          if (!separator.global) {
-            separator = RegExp(separator.source, toString(reFlags.exec(separator)) + 'g');
-          }
-          separator.lastIndex = 0;
-          while ((match = separator.exec(substring))) {
-            var newEnd = match.index;
-          }
-          result = result.slice(0, newEnd === undefined ? end : newEnd);
-        }
-      } else if (string.indexOf(baseToString(separator), end) != end) {
-        var index = result.lastIndexOf(separator);
-        if (index > -1) {
-          result = result.slice(0, index);
-        }
-      }
-      return result + omission;
-    }
-
-    /**
-     * The inverse of `_.escape`; this method converts the HTML entities
-     * `&amp;`, `&lt;`, `&gt;`, `&quot;`, and `&#39;` in `string` to
-     * their corresponding characters.
-     *
-     * **Note:** No other HTML entities are unescaped. To unescape additional
-     * HTML entities use a third-party library like [_he_](https://mths.be/he).
-     *
-     * @static
-     * @memberOf _
-     * @since 0.6.0
-     * @category String
-     * @param {string} [string=''] The string to unescape.
-     * @returns {string} Returns the unescaped string.
-     * @example
-     *
-     * _.unescape('fred, barney, &amp; pebbles');
-     * // => 'fred, barney, & pebbles'
-     */
-    function unescape(string) {
-      string = toString(string);
-      return (string && reHasEscapedHtml.test(string))
-        ? string.replace(reEscapedHtml, unescapeHtmlChar)
-        : string;
-    }
-
-    /**
-     * Converts `string`, as space separated words, to upper case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the upper cased string.
-     * @example
-     *
-     * _.upperCase('--foo-bar');
-     * // => 'FOO BAR'
-     *
-     * _.upperCase('fooBar');
-     * // => 'FOO BAR'
-     *
-     * _.upperCase('__foo_bar__');
-     * // => 'FOO BAR'
-     */
-    var upperCase = createCompounder(function(result, word, index) {
-      return result + (index ? ' ' : '') + word.toUpperCase();
-    });
-
-    /**
-     * Converts the first character of `string` to upper case.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category String
-     * @param {string} [string=''] The string to convert.
-     * @returns {string} Returns the converted string.
-     * @example
-     *
-     * _.upperFirst('fred');
-     * // => 'Fred'
-     *
-     * _.upperFirst('FRED');
-     * // => 'FRED'
-     */
-    var upperFirst = createCaseFirst('toUpperCase');
-
-    /**
-     * Splits `string` into an array of its words.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category String
-     * @param {string} [string=''] The string to inspect.
-     * @param {RegExp|string} [pattern] The pattern to match words.
-     * @param- {Object} [guard] Enables use as an iteratee for methods like `_.map`.
-     * @returns {Array} Returns the words of `string`.
-     * @example
-     *
-     * _.words('fred, barney, & pebbles');
-     * // => ['fred', 'barney', 'pebbles']
-     *
-     * _.words('fred, barney, & pebbles', /[^, ]+/g);
-     * // => ['fred', 'barney', '&', 'pebbles']
-     */
-    function words(string, pattern, guard) {
-      string = toString(string);
-      pattern = guard ? undefined : pattern;
-
-      if (pattern === undefined) {
-        return hasUnicodeWord(string) ? unicodeWords(string) : asciiWords(string);
-      }
-      return string.match(pattern) || [];
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Attempts to invoke `func`, returning either the result or the caught error
-     * object. Any additional arguments are provided to `func` when it's invoked.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {Function} func The function to attempt.
-     * @param {...*} [args] The arguments to invoke `func` with.
-     * @returns {*} Returns the `func` result or error object.
-     * @example
-     *
-     * // Avoid throwing errors for invalid selectors.
-     * var elements = _.attempt(function(selector) {
-     *   return document.querySelectorAll(selector);
-     * }, '>_>');
-     *
-     * if (_.isError(elements)) {
-     *   elements = [];
-     * }
-     */
-    var attempt = baseRest(function(func, args) {
-      try {
-        return apply(func, undefined, args);
-      } catch (e) {
-        return isError(e) ? e : new Error(e);
-      }
-    });
-
-    /**
-     * Binds methods of an object to the object itself, overwriting the existing
-     * method.
-     *
-     * **Note:** This method doesn't set the "length" property of bound functions.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {Object} object The object to bind and assign the bound methods to.
-     * @param {...(string|string[])} methodNames The object method names to bind.
-     * @returns {Object} Returns `object`.
-     * @example
-     *
-     * var view = {
-     *   'label': 'docs',
-     *   'click': function() {
-     *     console.log('clicked ' + this.label);
-     *   }
-     * };
-     *
-     * _.bindAll(view, ['click']);
-     * jQuery(element).on('click', view.click);
-     * // => Logs 'clicked docs' when clicked.
-     */
-    var bindAll = flatRest(function(object, methodNames) {
-      arrayEach(methodNames, function(key) {
-        key = toKey(key);
-        baseAssignValue(object, key, bind(object[key], object));
-      });
-      return object;
-    });
-
-    /**
-     * Creates a function that iterates over `pairs` and invokes the corresponding
-     * function of the first predicate to return truthy. The predicate-function
-     * pairs are invoked with the `this` binding and arguments of the created
-     * function.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {Array} pairs The predicate-function pairs.
-     * @returns {Function} Returns the new composite function.
-     * @example
-     *
-     * var func = _.cond([
-     *   [_.matches({ 'a': 1 }),           _.constant('matches A')],
-     *   [_.conforms({ 'b': _.isNumber }), _.constant('matches B')],
-     *   [_.stubTrue,                      _.constant('no match')]
-     * ]);
-     *
-     * func({ 'a': 1, 'b': 2 });
-     * // => 'matches A'
-     *
-     * func({ 'a': 0, 'b': 1 });
-     * // => 'matches B'
-     *
-     * func({ 'a': '1', 'b': '2' });
-     * // => 'no match'
-     */
-    function cond(pairs) {
-      var length = pairs == null ? 0 : pairs.length,
-          toIteratee = getIteratee();
-
-      pairs = !length ? [] : arrayMap(pairs, function(pair) {
-        if (typeof pair[1] != 'function') {
-          throw new TypeError(FUNC_ERROR_TEXT);
-        }
-        return [toIteratee(pair[0]), pair[1]];
-      });
-
-      return baseRest(function(args) {
-        var index = -1;
-        while (++index < length) {
-          var pair = pairs[index];
-          if (apply(pair[0], this, args)) {
-            return apply(pair[1], this, args);
-          }
-        }
-      });
-    }
-
-    /**
-     * Creates a function that invokes the predicate properties of `source` with
-     * the corresponding property values of a given object, returning `true` if
-     * all predicates return truthy, else `false`.
-     *
-     * **Note:** The created function is equivalent to `_.conformsTo` with
-     * `source` partially applied.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {Object} source The object of property predicates to conform to.
-     * @returns {Function} Returns the new spec function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': 2, 'b': 1 },
-     *   { 'a': 1, 'b': 2 }
-     * ];
-     *
-     * _.filter(objects, _.conforms({ 'b': function(n) { return n > 1; } }));
-     * // => [{ 'a': 1, 'b': 2 }]
-     */
-    function conforms(source) {
-      return baseConforms(baseClone(source, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that returns `value`.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Util
-     * @param {*} value The value to return from the new function.
-     * @returns {Function} Returns the new constant function.
-     * @example
-     *
-     * var objects = _.times(2, _.constant({ 'a': 1 }));
-     *
-     * console.log(objects);
-     * // => [{ 'a': 1 }, { 'a': 1 }]
-     *
-     * console.log(objects[0] === objects[1]);
-     * // => true
-     */
-    function constant(value) {
-      return function() {
-        return value;
-      };
-    }
-
-    /**
-     * Checks `value` to determine whether a default value should be returned in
-     * its place. The `defaultValue` is returned if `value` is `NaN`, `null`,
-     * or `undefined`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.14.0
-     * @category Util
-     * @param {*} value The value to check.
-     * @param {*} defaultValue The default value.
-     * @returns {*} Returns the resolved value.
-     * @example
-     *
-     * _.defaultTo(1, 10);
-     * // => 1
-     *
-     * _.defaultTo(undefined, 10);
-     * // => 10
-     */
-    function defaultTo(value, defaultValue) {
-      return (value == null || value !== value) ? defaultValue : value;
-    }
-
-    /**
-     * Creates a function that returns the result of invoking the given functions
-     * with the `this` binding of the created function, where each successive
-     * invocation is supplied the return value of the previous.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [funcs] The functions to invoke.
-     * @returns {Function} Returns the new composite function.
-     * @see _.flowRight
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var addSquare = _.flow([_.add, square]);
-     * addSquare(1, 2);
-     * // => 9
-     */
-    var flow = createFlow();
-
-    /**
-     * This method is like `_.flow` except that it creates a function that
-     * invokes the given functions from right to left.
-     *
-     * @static
-     * @since 3.0.0
-     * @memberOf _
-     * @category Util
-     * @param {...(Function|Function[])} [funcs] The functions to invoke.
-     * @returns {Function} Returns the new composite function.
-     * @see _.flow
-     * @example
-     *
-     * function square(n) {
-     *   return n * n;
-     * }
-     *
-     * var addSquare = _.flowRight([square, _.add]);
-     * addSquare(1, 2);
-     * // => 9
-     */
-    var flowRight = createFlow(true);
-
-    /**
-     * This method returns the first argument it receives.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {*} value Any value.
-     * @returns {*} Returns `value`.
-     * @example
-     *
-     * var object = { 'a': 1 };
-     *
-     * console.log(_.identity(object) === object);
-     * // => true
-     */
-    function identity(value) {
-      return value;
-    }
-
-    /**
-     * Creates a function that invokes `func` with the arguments of the created
-     * function. If `func` is a property name, the created function returns the
-     * property value for a given element. If `func` is an array or object, the
-     * created function returns `true` for elements that contain the equivalent
-     * source properties, otherwise it returns `false`.
-     *
-     * @static
-     * @since 4.0.0
-     * @memberOf _
-     * @category Util
-     * @param {*} [func=_.identity] The value to convert to a callback.
-     * @returns {Function} Returns the callback.
-     * @example
-     *
-     * var users = [
-     *   { 'user': 'barney', 'age': 36, 'active': true },
-     *   { 'user': 'fred',   'age': 40, 'active': false }
-     * ];
-     *
-     * // The `_.matches` iteratee shorthand.
-     * _.filter(users, _.iteratee({ 'user': 'barney', 'active': true }));
-     * // => [{ 'user': 'barney', 'age': 36, 'active': true }]
-     *
-     * // The `_.matchesProperty` iteratee shorthand.
-     * _.filter(users, _.iteratee(['user', 'fred']));
-     * // => [{ 'user': 'fred', 'age': 40 }]
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.map(users, _.iteratee('user'));
-     * // => ['barney', 'fred']
-     *
-     * // Create custom iteratee shorthands.
-     * _.iteratee = _.wrap(_.iteratee, function(iteratee, func) {
-     *   return !_.isRegExp(func) ? iteratee(func) : function(string) {
-     *     return func.test(string);
-     *   };
-     * });
-     *
-     * _.filter(['abc', 'def'], /ef/);
-     * // => ['def']
-     */
-    function iteratee(func) {
-      return baseIteratee(typeof func == 'function' ? func : baseClone(func, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that performs a partial deep comparison between a given
-     * object and `source`, returning `true` if the given object has equivalent
-     * property values, else `false`.
-     *
-     * **Note:** The created function is equivalent to `_.isMatch` with `source`
-     * partially applied.
-     *
-     * Partial comparisons will match empty array and empty object `source`
-     * values against any array or object value, respectively. See `_.isEqual`
-     * for a list of supported value comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {Object} source The object of property values to match.
-     * @returns {Function} Returns the new spec function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': 1, 'b': 2, 'c': 3 },
-     *   { 'a': 4, 'b': 5, 'c': 6 }
-     * ];
-     *
-     * _.filter(objects, _.matches({ 'a': 4, 'c': 6 }));
-     * // => [{ 'a': 4, 'b': 5, 'c': 6 }]
-     */
-    function matches(source) {
-      return baseMatches(baseClone(source, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that performs a partial deep comparison between the
-     * value at `path` of a given object to `srcValue`, returning `true` if the
-     * object value is equivalent, else `false`.
-     *
-     * **Note:** Partial comparisons will match empty array and empty object
-     * `srcValue` values against any array or object value, respectively. See
-     * `_.isEqual` for a list of supported value comparisons.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.2.0
-     * @category Util
-     * @param {Array|string} path The path of the property to get.
-     * @param {*} srcValue The value to match.
-     * @returns {Function} Returns the new spec function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': 1, 'b': 2, 'c': 3 },
-     *   { 'a': 4, 'b': 5, 'c': 6 }
-     * ];
-     *
-     * _.find(objects, _.matchesProperty('a', 4));
-     * // => { 'a': 4, 'b': 5, 'c': 6 }
-     */
-    function matchesProperty(path, srcValue) {
-      return baseMatchesProperty(path, baseClone(srcValue, CLONE_DEEP_FLAG));
-    }
-
-    /**
-     * Creates a function that invokes the method at `path` of a given object.
-     * Any additional arguments are provided to the invoked method.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Util
-     * @param {Array|string} path The path of the method to invoke.
-     * @param {...*} [args] The arguments to invoke the method with.
-     * @returns {Function} Returns the new invoker function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': { 'b': _.constant(2) } },
-     *   { 'a': { 'b': _.constant(1) } }
-     * ];
-     *
-     * _.map(objects, _.method('a.b'));
-     * // => [2, 1]
-     *
-     * _.map(objects, _.method(['a', 'b']));
-     * // => [2, 1]
-     */
-    var method = baseRest(function(path, args) {
-      return function(object) {
-        return baseInvoke(object, path, args);
-      };
-    });
-
-    /**
-     * The opposite of `_.method`; this method creates a function that invokes
-     * the method at a given path of `object`. Any additional arguments are
-     * provided to the invoked method.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.7.0
-     * @category Util
-     * @param {Object} object The object to query.
-     * @param {...*} [args] The arguments to invoke the method with.
-     * @returns {Function} Returns the new invoker function.
-     * @example
-     *
-     * var array = _.times(3, _.constant),
-     *     object = { 'a': array, 'b': array, 'c': array };
-     *
-     * _.map(['a[2]', 'c[0]'], _.methodOf(object));
-     * // => [2, 0]
-     *
-     * _.map([['a', '2'], ['c', '0']], _.methodOf(object));
-     * // => [2, 0]
-     */
-    var methodOf = baseRest(function(object, args) {
-      return function(path) {
-        return baseInvoke(object, path, args);
-      };
-    });
-
-    /**
-     * Adds all own enumerable string keyed function properties of a source
-     * object to the destination object. If `object` is a function, then methods
-     * are added to its prototype as well.
-     *
-     * **Note:** Use `_.runInContext` to create a pristine `lodash` function to
-     * avoid conflicts caused by modifying the original.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {Function|Object} [object=lodash] The destination object.
-     * @param {Object} source The object of functions to add.
-     * @param {Object} [options={}] The options object.
-     * @param {boolean} [options.chain=true] Specify whether mixins are chainable.
-     * @returns {Function|Object} Returns `object`.
-     * @example
-     *
-     * function vowels(string) {
-     *   return _.filter(string, function(v) {
-     *     return /[aeiou]/i.test(v);
-     *   });
-     * }
-     *
-     * _.mixin({ 'vowels': vowels });
-     * _.vowels('fred');
-     * // => ['e']
-     *
-     * _('fred').vowels().value();
-     * // => ['e']
-     *
-     * _.mixin({ 'vowels': vowels }, { 'chain': false });
-     * _('fred').vowels();
-     * // => ['e']
-     */
-    function mixin(object, source, options) {
-      var props = keys(source),
-          methodNames = baseFunctions(source, props);
-
-      if (options == null &&
-          !(isObject(source) && (methodNames.length || !props.length))) {
-        options = source;
-        source = object;
-        object = this;
-        methodNames = baseFunctions(source, keys(source));
-      }
-      var chain = !(isObject(options) && 'chain' in options) || !!options.chain,
-          isFunc = isFunction(object);
-
-      arrayEach(methodNames, function(methodName) {
-        var func = source[methodName];
-        object[methodName] = func;
-        if (isFunc) {
-          object.prototype[methodName] = function() {
-            var chainAll = this.__chain__;
-            if (chain || chainAll) {
-              var result = object(this.__wrapped__),
-                  actions = result.__actions__ = copyArray(this.__actions__);
-
-              actions.push({ 'func': func, 'args': arguments, 'thisArg': object });
-              result.__chain__ = chainAll;
-              return result;
-            }
-            return func.apply(object, arrayPush([this.value()], arguments));
-          };
-        }
-      });
-
-      return object;
-    }
-
-    /**
-     * Reverts the `_` variable to its previous value and returns a reference to
-     * the `lodash` function.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @returns {Function} Returns the `lodash` function.
-     * @example
-     *
-     * var lodash = _.noConflict();
-     */
-    function noConflict() {
-      if (root._ === this) {
-        root._ = oldDash;
-      }
-      return this;
-    }
-
-    /**
-     * This method returns `undefined`.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.3.0
-     * @category Util
-     * @example
-     *
-     * _.times(2, _.noop);
-     * // => [undefined, undefined]
-     */
-    function noop() {
-      // No operation performed.
-    }
-
-    /**
-     * Creates a function that gets the argument at index `n`. If `n` is negative,
-     * the nth argument from the end is returned.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {number} [n=0] The index of the argument to return.
-     * @returns {Function} Returns the new pass-thru function.
-     * @example
-     *
-     * var func = _.nthArg(1);
-     * func('a', 'b', 'c', 'd');
-     * // => 'b'
-     *
-     * var func = _.nthArg(-2);
-     * func('a', 'b', 'c', 'd');
-     * // => 'c'
-     */
-    function nthArg(n) {
-      n = toInteger(n);
-      return baseRest(function(args) {
-        return baseNth(args, n);
-      });
-    }
-
-    /**
-     * Creates a function that invokes `iteratees` with the arguments it receives
-     * and returns their results.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [iteratees=[_.identity]]
-     *  The iteratees to invoke.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var func = _.over([Math.max, Math.min]);
-     *
-     * func(1, 2, 3, 4);
-     * // => [4, 1]
-     */
-    var over = createOver(arrayMap);
-
-    /**
-     * Creates a function that checks if **all** of the `predicates` return
-     * truthy when invoked with the arguments it receives.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [predicates=[_.identity]]
-     *  The predicates to check.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var func = _.overEvery([Boolean, isFinite]);
-     *
-     * func('1');
-     * // => true
-     *
-     * func(null);
-     * // => false
-     *
-     * func(NaN);
-     * // => false
-     */
-    var overEvery = createOver(arrayEvery);
-
-    /**
-     * Creates a function that checks if **any** of the `predicates` return
-     * truthy when invoked with the arguments it receives.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {...(Function|Function[])} [predicates=[_.identity]]
-     *  The predicates to check.
-     * @returns {Function} Returns the new function.
-     * @example
-     *
-     * var func = _.overSome([Boolean, isFinite]);
-     *
-     * func('1');
-     * // => true
-     *
-     * func(null);
-     * // => true
-     *
-     * func(NaN);
-     * // => false
-     */
-    var overSome = createOver(arraySome);
-
-    /**
-     * Creates a function that returns the value at `path` of a given object.
-     *
-     * @static
-     * @memberOf _
-     * @since 2.4.0
-     * @category Util
-     * @param {Array|string} path The path of the property to get.
-     * @returns {Function} Returns the new accessor function.
-     * @example
-     *
-     * var objects = [
-     *   { 'a': { 'b': 2 } },
-     *   { 'a': { 'b': 1 } }
-     * ];
-     *
-     * _.map(objects, _.property('a.b'));
-     * // => [2, 1]
-     *
-     * _.map(_.sortBy(objects, _.property(['a', 'b'])), 'a.b');
-     * // => [1, 2]
-     */
-    function property(path) {
-      return isKey(path) ? baseProperty(toKey(path)) : basePropertyDeep(path);
-    }
-
-    /**
-     * The opposite of `_.property`; this method creates a function that returns
-     * the value at a given path of `object`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.0.0
-     * @category Util
-     * @param {Object} object The object to query.
-     * @returns {Function} Returns the new accessor function.
-     * @example
-     *
-     * var array = [0, 1, 2],
-     *     object = { 'a': array, 'b': array, 'c': array };
-     *
-     * _.map(['a[2]', 'c[0]'], _.propertyOf(object));
-     * // => [2, 0]
-     *
-     * _.map([['a', '2'], ['c', '0']], _.propertyOf(object));
-     * // => [2, 0]
-     */
-    function propertyOf(object) {
-      return function(path) {
-        return object == null ? undefined : baseGet(object, path);
-      };
-    }
-
-    /**
-     * Creates an array of numbers (positive and/or negative) progressing from
-     * `start` up to, but not including, `end`. A step of `-1` is used if a negative
-     * `start` is specified without an `end` or `step`. If `end` is not specified,
-     * it's set to `start` with `start` then set to `0`.
-     *
-     * **Note:** JavaScript follows the IEEE-754 standard for resolving
-     * floating-point values which can produce unexpected results.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {number} [start=0] The start of the range.
-     * @param {number} end The end of the range.
-     * @param {number} [step=1] The value to increment or decrement by.
-     * @returns {Array} Returns the range of numbers.
-     * @see _.inRange, _.rangeRight
-     * @example
-     *
-     * _.range(4);
-     * // => [0, 1, 2, 3]
-     *
-     * _.range(-4);
-     * // => [0, -1, -2, -3]
-     *
-     * _.range(1, 5);
-     * // => [1, 2, 3, 4]
-     *
-     * _.range(0, 20, 5);
-     * // => [0, 5, 10, 15]
-     *
-     * _.range(0, -4, -1);
-     * // => [0, -1, -2, -3]
-     *
-     * _.range(1, 4, 0);
-     * // => [1, 1, 1]
-     *
-     * _.range(0);
-     * // => []
-     */
-    var range = createRange();
-
-    /**
-     * This method is like `_.range` except that it populates values in
-     * descending order.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {number} [start=0] The start of the range.
-     * @param {number} end The end of the range.
-     * @param {number} [step=1] The value to increment or decrement by.
-     * @returns {Array} Returns the range of numbers.
-     * @see _.inRange, _.range
-     * @example
-     *
-     * _.rangeRight(4);
-     * // => [3, 2, 1, 0]
-     *
-     * _.rangeRight(-4);
-     * // => [-3, -2, -1, 0]
-     *
-     * _.rangeRight(1, 5);
-     * // => [4, 3, 2, 1]
-     *
-     * _.rangeRight(0, 20, 5);
-     * // => [15, 10, 5, 0]
-     *
-     * _.rangeRight(0, -4, -1);
-     * // => [-3, -2, -1, 0]
-     *
-     * _.rangeRight(1, 4, 0);
-     * // => [1, 1, 1]
-     *
-     * _.rangeRight(0);
-     * // => []
-     */
-    var rangeRight = createRange(true);
-
-    /**
-     * This method returns a new empty array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {Array} Returns the new empty array.
-     * @example
-     *
-     * var arrays = _.times(2, _.stubArray);
-     *
-     * console.log(arrays);
-     * // => [[], []]
-     *
-     * console.log(arrays[0] === arrays[1]);
-     * // => false
-     */
-    function stubArray() {
-      return [];
-    }
-
-    /**
-     * This method returns `false`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {boolean} Returns `false`.
-     * @example
-     *
-     * _.times(2, _.stubFalse);
-     * // => [false, false]
-     */
-    function stubFalse() {
-      return false;
-    }
-
-    /**
-     * This method returns a new empty object.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {Object} Returns the new empty object.
-     * @example
-     *
-     * var objects = _.times(2, _.stubObject);
-     *
-     * console.log(objects);
-     * // => [{}, {}]
-     *
-     * console.log(objects[0] === objects[1]);
-     * // => false
-     */
-    function stubObject() {
-      return {};
-    }
-
-    /**
-     * This method returns an empty string.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {string} Returns the empty string.
-     * @example
-     *
-     * _.times(2, _.stubString);
-     * // => ['', '']
-     */
-    function stubString() {
-      return '';
-    }
-
-    /**
-     * This method returns `true`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.13.0
-     * @category Util
-     * @returns {boolean} Returns `true`.
-     * @example
-     *
-     * _.times(2, _.stubTrue);
-     * // => [true, true]
-     */
-    function stubTrue() {
-      return true;
-    }
-
-    /**
-     * Invokes the iteratee `n` times, returning an array of the results of
-     * each invocation. The iteratee is invoked with one argument; (index).
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {number} n The number of times to invoke `iteratee`.
-     * @param {Function} [iteratee=_.identity] The function invoked per iteration.
-     * @returns {Array} Returns the array of results.
-     * @example
-     *
-     * _.times(3, String);
-     * // => ['0', '1', '2']
-     *
-     *  _.times(4, _.constant(0));
-     * // => [0, 0, 0, 0]
-     */
-    function times(n, iteratee) {
-      n = toInteger(n);
-      if (n < 1 || n > MAX_SAFE_INTEGER) {
-        return [];
-      }
-      var index = MAX_ARRAY_LENGTH,
-          length = nativeMin(n, MAX_ARRAY_LENGTH);
-
-      iteratee = getIteratee(iteratee);
-      n -= MAX_ARRAY_LENGTH;
-
-      var result = baseTimes(length, iteratee);
-      while (++index < n) {
-        iteratee(index);
-      }
-      return result;
-    }
-
-    /**
-     * Converts `value` to a property path array.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Util
-     * @param {*} value The value to convert.
-     * @returns {Array} Returns the new property path array.
-     * @example
-     *
-     * _.toPath('a.b.c');
-     * // => ['a', 'b', 'c']
-     *
-     * _.toPath('a[0].b.c');
-     * // => ['a', '0', 'b', 'c']
-     */
-    function toPath(value) {
-      if (isArray(value)) {
-        return arrayMap(value, toKey);
-      }
-      return isSymbol(value) ? [value] : copyArray(stringToPath(toString(value)));
-    }
-
-    /**
-     * Generates a unique ID. If `prefix` is given, the ID is appended to it.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Util
-     * @param {string} [prefix=''] The value to prefix the ID with.
-     * @returns {string} Returns the unique ID.
-     * @example
-     *
-     * _.uniqueId('contact_');
-     * // => 'contact_104'
-     *
-     * _.uniqueId();
-     * // => '105'
-     */
-    function uniqueId(prefix) {
-      var id = ++idCounter;
-      return toString(prefix) + id;
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * Adds two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.4.0
-     * @category Math
-     * @param {number} augend The first number in an addition.
-     * @param {number} addend The second number in an addition.
-     * @returns {number} Returns the total.
-     * @example
-     *
-     * _.add(6, 4);
-     * // => 10
-     */
-    var add = createMathOperation(function(augend, addend) {
-      return augend + addend;
-    }, 0);
-
-    /**
-     * Computes `number` rounded up to `precision`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Math
-     * @param {number} number The number to round up.
-     * @param {number} [precision=0] The precision to round up to.
-     * @returns {number} Returns the rounded up number.
-     * @example
-     *
-     * _.ceil(4.006);
-     * // => 5
-     *
-     * _.ceil(6.004, 2);
-     * // => 6.01
-     *
-     * _.ceil(6040, -2);
-     * // => 6100
-     */
-    var ceil = createRound('ceil');
-
-    /**
-     * Divide two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Math
-     * @param {number} dividend The first number in a division.
-     * @param {number} divisor The second number in a division.
-     * @returns {number} Returns the quotient.
-     * @example
-     *
-     * _.divide(6, 4);
-     * // => 1.5
-     */
-    var divide = createMathOperation(function(dividend, divisor) {
-      return dividend / divisor;
-    }, 1);
-
-    /**
-     * Computes `number` rounded down to `precision`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Math
-     * @param {number} number The number to round down.
-     * @param {number} [precision=0] The precision to round down to.
-     * @returns {number} Returns the rounded down number.
-     * @example
-     *
-     * _.floor(4.006);
-     * // => 4
-     *
-     * _.floor(0.046, 2);
-     * // => 0.04
-     *
-     * _.floor(4060, -2);
-     * // => 4000
-     */
-    var floor = createRound('floor');
-
-    /**
-     * Computes the maximum value of `array`. If `array` is empty or falsey,
-     * `undefined` is returned.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {*} Returns the maximum value.
-     * @example
-     *
-     * _.max([4, 2, 8, 6]);
-     * // => 8
-     *
-     * _.max([]);
-     * // => undefined
-     */
-    function max(array) {
-      return (array && array.length)
-        ? baseExtremum(array, identity, baseGt)
-        : undefined;
-    }
-
-    /**
-     * This method is like `_.max` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the criterion by which
-     * the value is ranked. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {*} Returns the maximum value.
-     * @example
-     *
-     * var objects = [{ 'n': 1 }, { 'n': 2 }];
-     *
-     * _.maxBy(objects, function(o) { return o.n; });
-     * // => { 'n': 2 }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.maxBy(objects, 'n');
-     * // => { 'n': 2 }
-     */
-    function maxBy(array, iteratee) {
-      return (array && array.length)
-        ? baseExtremum(array, getIteratee(iteratee, 2), baseGt)
-        : undefined;
-    }
-
-    /**
-     * Computes the mean of the values in `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {number} Returns the mean.
-     * @example
-     *
-     * _.mean([4, 2, 8, 6]);
-     * // => 5
-     */
-    function mean(array) {
-      return baseMean(array, identity);
-    }
-
-    /**
-     * This method is like `_.mean` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the value to be averaged.
-     * The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the mean.
-     * @example
-     *
-     * var objects = [{ 'n': 4 }, { 'n': 2 }, { 'n': 8 }, { 'n': 6 }];
-     *
-     * _.meanBy(objects, function(o) { return o.n; });
-     * // => 5
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.meanBy(objects, 'n');
-     * // => 5
-     */
-    function meanBy(array, iteratee) {
-      return baseMean(array, getIteratee(iteratee, 2));
-    }
-
-    /**
-     * Computes the minimum value of `array`. If `array` is empty or falsey,
-     * `undefined` is returned.
-     *
-     * @static
-     * @since 0.1.0
-     * @memberOf _
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {*} Returns the minimum value.
-     * @example
-     *
-     * _.min([4, 2, 8, 6]);
-     * // => 2
-     *
-     * _.min([]);
-     * // => undefined
-     */
-    function min(array) {
-      return (array && array.length)
-        ? baseExtremum(array, identity, baseLt)
-        : undefined;
-    }
-
-    /**
-     * This method is like `_.min` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the criterion by which
-     * the value is ranked. The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {*} Returns the minimum value.
-     * @example
-     *
-     * var objects = [{ 'n': 1 }, { 'n': 2 }];
-     *
-     * _.minBy(objects, function(o) { return o.n; });
-     * // => { 'n': 1 }
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.minBy(objects, 'n');
-     * // => { 'n': 1 }
-     */
-    function minBy(array, iteratee) {
-      return (array && array.length)
-        ? baseExtremum(array, getIteratee(iteratee, 2), baseLt)
-        : undefined;
-    }
-
-    /**
-     * Multiply two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.7.0
-     * @category Math
-     * @param {number} multiplier The first number in a multiplication.
-     * @param {number} multiplicand The second number in a multiplication.
-     * @returns {number} Returns the product.
-     * @example
-     *
-     * _.multiply(6, 4);
-     * // => 24
-     */
-    var multiply = createMathOperation(function(multiplier, multiplicand) {
-      return multiplier * multiplicand;
-    }, 1);
-
-    /**
-     * Computes `number` rounded to `precision`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.10.0
-     * @category Math
-     * @param {number} number The number to round.
-     * @param {number} [precision=0] The precision to round to.
-     * @returns {number} Returns the rounded number.
-     * @example
-     *
-     * _.round(4.006);
-     * // => 4
-     *
-     * _.round(4.006, 2);
-     * // => 4.01
-     *
-     * _.round(4060, -2);
-     * // => 4100
-     */
-    var round = createRound('round');
-
-    /**
-     * Subtract two numbers.
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {number} minuend The first number in a subtraction.
-     * @param {number} subtrahend The second number in a subtraction.
-     * @returns {number} Returns the difference.
-     * @example
-     *
-     * _.subtract(6, 4);
-     * // => 2
-     */
-    var subtract = createMathOperation(function(minuend, subtrahend) {
-      return minuend - subtrahend;
-    }, 0);
-
-    /**
-     * Computes the sum of the values in `array`.
-     *
-     * @static
-     * @memberOf _
-     * @since 3.4.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @returns {number} Returns the sum.
-     * @example
-     *
-     * _.sum([4, 2, 8, 6]);
-     * // => 20
-     */
-    function sum(array) {
-      return (array && array.length)
-        ? baseSum(array, identity)
-        : 0;
-    }
-
-    /**
-     * This method is like `_.sum` except that it accepts `iteratee` which is
-     * invoked for each element in `array` to generate the value to be summed.
-     * The iteratee is invoked with one argument: (value).
-     *
-     * @static
-     * @memberOf _
-     * @since 4.0.0
-     * @category Math
-     * @param {Array} array The array to iterate over.
-     * @param {Function} [iteratee=_.identity] The iteratee invoked per element.
-     * @returns {number} Returns the sum.
-     * @example
-     *
-     * var objects = [{ 'n': 4 }, { 'n': 2 }, { 'n': 8 }, { 'n': 6 }];
-     *
-     * _.sumBy(objects, function(o) { return o.n; });
-     * // => 20
-     *
-     * // The `_.property` iteratee shorthand.
-     * _.sumBy(objects, 'n');
-     * // => 20
-     */
-    function sumBy(array, iteratee) {
-      return (array && array.length)
-        ? baseSum(array, getIteratee(iteratee, 2))
-        : 0;
-    }
-
-    /*------------------------------------------------------------------------*/
-
-    // Add methods that return wrapped values in chain sequences.
-    lodash.after = after;
-    lodash.ary = ary;
-    lodash.assign = assign;
-    lodash.assignIn = assignIn;
-    lodash.assignInWith = assignInWith;
-    lodash.assignWith = assignWith;
-    lodash.at = at;
-    lodash.before = before;
-    lodash.bind = bind;
-    lodash.bindAll = bindAll;
-    lodash.bindKey = bindKey;
-    lodash.castArray = castArray;
-    lodash.chain = chain;
-    lodash.chunk = chunk;
-    lodash.compact = compact;
-    lodash.concat = concat;
-    lodash.cond = cond;
-    lodash.conforms = conforms;
-    lodash.constant = constant;
-    lodash.countBy = countBy;
-    lodash.create = create;
-    lodash.curry = curry;
-    lodash.curryRight = curryRight;
-    lodash.debounce = debounce;
-    lodash.defaults = defaults;
-    lodash.defaultsDeep = defaultsDeep;
-    lodash.defer = defer;
-    lodash.delay = delay;
-    lodash.difference = difference;
-    lodash.differenceBy = differenceBy;
-    lodash.differenceWith = differenceWith;
-    lodash.drop = drop;
-    lodash.dropRight = dropRight;
-    lodash.dropRightWhile = dropRightWhile;
-    lodash.dropWhile = dropWhile;
-    lodash.fill = fill;
-    lodash.filter = filter;
-    lodash.flatMap = flatMap;
-    lodash.flatMapDeep = flatMapDeep;
-    lodash.flatMapDepth = flatMapDepth;
-    lodash.flatten = flatten;
-    lodash.flattenDeep = flattenDeep;
-    lodash.flattenDepth = flattenDepth;
-    lodash.flip = flip;
-    lodash.flow = flow;
-    lodash.flowRight = flowRight;
-    lodash.fromPairs = fromPairs;
-    lodash.functions = functions;
-    lodash.functionsIn = functionsIn;
-    lodash.groupBy = groupBy;
-    lodash.initial = initial;
-    lodash.intersection = intersection;
-    lodash.intersectionBy = intersectionBy;
-    lodash.intersectionWith = intersectionWith;
-    lodash.invert = invert;
-    lodash.invertBy = invertBy;
-    lodash.invokeMap = invokeMap;
-    lodash.iteratee = iteratee;
-    lodash.keyBy = keyBy;
-    lodash.keys = keys;
-    lodash.keysIn = keysIn;
-    lodash.map = map;
-    lodash.mapKeys = mapKeys;
-    lodash.mapValues = mapValues;
-    lodash.matches = matches;
-    lodash.matchesProperty = matchesProperty;
-    lodash.memoize = memoize;
-    lodash.merge = merge;
-    lodash.mergeWith = mergeWith;
-    lodash.method = method;
-    lodash.methodOf = methodOf;
-    lodash.mixin = mixin;
-    lodash.negate = negate;
-    lodash.nthArg = nthArg;
-    lodash.omit = omit;
-    lodash.omitBy = omitBy;
-    lodash.once = once;
-    lodash.orderBy = orderBy;
-    lodash.over = over;
-    lodash.overArgs = overArgs;
-    lodash.overEvery = overEvery;
-    lodash.overSome = overSome;
-    lodash.partial = partial;
-    lodash.partialRight = partialRight;
-    lodash.partition = partition;
-    lodash.pick = pick;
-    lodash.pickBy = pickBy;
-    lodash.property = property;
-    lodash.propertyOf = propertyOf;
-    lodash.pull = pull;
-    lodash.pullAll = pullAll;
-    lodash.pullAllBy = pullAllBy;
-    lodash.pullAllWith = pullAllWith;
-    lodash.pullAt = pullAt;
-    lodash.range = range;
-    lodash.rangeRight = rangeRight;
-    lodash.rearg = rearg;
-    lodash.reject = reject;
-    lodash.remove = remove;
-    lodash.rest = rest;
-    lodash.reverse = reverse;
-    lodash.sampleSize = sampleSize;
-    lodash.set = set;
-    lodash.setWith = setWith;
-    lodash.shuffle = shuffle;
-    lodash.slice = slice;
-    lodash.sortBy = sortBy;
-    lodash.sortedUniq = sortedUniq;
-    lodash.sortedUniqBy = sortedUniqBy;
-    lodash.split = split;
-    lodash.spread = spread;
-    lodash.tail = tail;
-    lodash.take = take;
-    lodash.takeRight = takeRight;
-    lodash.takeRightWhile = takeRightWhile;
-    lodash.takeWhile = takeWhile;
-    lodash.tap = tap;
-    lodash.throttle = throttle;
-    lodash.thru = thru;
-    lodash.toArray = toArray;
-    lodash.toPairs = toPairs;
-    lodash.toPairsIn = toPairsIn;
-    lodash.toPath = toPath;
-    lodash.toPlainObject = toPlainObject;
-    lodash.transform = transform;
-    lodash.unary = unary;
-    lodash.union = union;
-    lodash.unionBy = unionBy;
-    lodash.unionWith = unionWith;
-    lodash.uniq = uniq;
-    lodash.uniqBy = uniqBy;
-    lodash.uniqWith = uniqWith;
-    lodash.unset = unset;
-    lodash.unzip = unzip;
-    lodash.unzipWith = unzipWith;
-    lodash.update = update;
-    lodash.updateWith = updateWith;
-    lodash.values = values;
-    lodash.valuesIn = valuesIn;
-    lodash.without = without;
-    lodash.words = words;
-    lodash.wrap = wrap;
-    lodash.xor = xor;
-    lodash.xorBy = xorBy;
-    lodash.xorWith = xorWith;
-    lodash.zip = zip;
-    lodash.zipObject = zipObject;
-    lodash.zipObjectDeep = zipObjectDeep;
-    lodash.zipWith = zipWith;
-
-    // Add aliases.
-    lodash.entries = toPairs;
-    lodash.entriesIn = toPairsIn;
-    lodash.extend = assignIn;
-    lodash.extendWith = assignInWith;
-
-    // Add methods to `lodash.prototype`.
-    mixin(lodash, lodash);
-
-    /*------------------------------------------------------------------------*/
-
-    // Add methods that return unwrapped values in chain sequences.
-    lodash.add = add;
-    lodash.attempt = attempt;
-    lodash.camelCase = camelCase;
-    lodash.capitalize = capitalize;
-    lodash.ceil = ceil;
-    lodash.clamp = clamp;
-    lodash.clone = clone;
-    lodash.cloneDeep = cloneDeep;
-    lodash.cloneDeepWith = cloneDeepWith;
-    lodash.cloneWith = cloneWith;
-    lodash.conformsTo = conformsTo;
-    lodash.deburr = deburr;
-    lodash.defaultTo = defaultTo;
-    lodash.divide = divide;
-    lodash.endsWith = endsWith;
-    lodash.eq = eq;
-    lodash.escape = escape;
-    lodash.escapeRegExp = escapeRegExp;
-    lodash.every = every;
-    lodash.find = find;
-    lodash.findIndex = findIndex;
-    lodash.findKey = findKey;
-    lodash.findLast = findLast;
-    lodash.findLastIndex = findLastIndex;
-    lodash.findLastKey = findLastKey;
-    lodash.floor = floor;
-    lodash.forEach = forEach;
-    lodash.forEachRight = forEachRight;
-    lodash.forIn = forIn;
-    lodash.forInRight = forInRight;
-    lodash.forOwn = forOwn;
-    lodash.forOwnRight = forOwnRight;
-    lodash.get = get;
-    lodash.gt = gt;
-    lodash.gte = gte;
-    lodash.has = has;
-    lodash.hasIn = hasIn;
-    lodash.head = head;
-    lodash.identity = identity;
-    lodash.includes = includes;
-    lodash.indexOf = indexOf;
-    lodash.inRange = inRange;
-    lodash.invoke = invoke;
-    lodash.isArguments = isArguments;
-    lodash.isArray = isArray;
-    lodash.isArrayBuffer = isArrayBuffer;
-    lodash.isArrayLike = isArrayLike;
-    lodash.isArrayLikeObject = isArrayLikeObject;
-    lodash.isBoolean = isBoolean;
-    lodash.isBuffer = isBuffer;
-    lodash.isDate = isDate;
-    lodash.isElement = isElement;
-    lodash.isEmpty = isEmpty;
-    lodash.isEqual = isEqual;
-    lodash.isEqualWith = isEqualWith;
-    lodash.isError = isError;
-    lodash.isFinite = isFinite;
-    lodash.isFunction = isFunction;
-    lodash.isInteger = isInteger;
-    lodash.isLength = isLength;
-    lodash.isMap = isMap;
-    lodash.isMatch = isMatch;
-    lodash.isMatchWith = isMatchWith;
-    lodash.isNaN = isNaN;
-    lodash.isNative = isNative;
-    lodash.isNil = isNil;
-    lodash.isNull = isNull;
-    lodash.isNumber = isNumber;
-    lodash.isObject = isObject;
-    lodash.isObjectLike = isObjectLike;
-    lodash.isPlainObject = isPlainObject;
-    lodash.isRegExp = isRegExp;
-    lodash.isSafeInteger = isSafeInteger;
-    lodash.isSet = isSet;
-    lodash.isString = isString;
-    lodash.isSymbol = isSymbol;
-    lodash.isTypedArray = isTypedArray;
-    lodash.isUndefined = isUndefined;
-    lodash.isWeakMap = isWeakMap;
-    lodash.isWeakSet = isWeakSet;
-    lodash.join = join;
-    lodash.kebabCase = kebabCase;
-    lodash.last = last;
-    lodash.lastIndexOf = lastIndexOf;
-    lodash.lowerCase = lowerCase;
-    lodash.lowerFirst = lowerFirst;
-    lodash.lt = lt;
-    lodash.lte = lte;
-    lodash.max = max;
-    lodash.maxBy = maxBy;
-    lodash.mean = mean;
-    lodash.meanBy = meanBy;
-    lodash.min = min;
-    lodash.minBy = minBy;
-    lodash.stubArray = stubArray;
-    lodash.stubFalse = stubFalse;
-    lodash.stubObject = stubObject;
-    lodash.stubString = stubString;
-    lodash.stubTrue = stubTrue;
-    lodash.multiply = multiply;
-    lodash.nth = nth;
-    lodash.noConflict = noConflict;
-    lodash.noop = noop;
-    lodash.now = now;
-    lodash.pad = pad;
-    lodash.padEnd = padEnd;
-    lodash.padStart = padStart;
-    lodash.parseInt = parseInt;
-    lodash.random = random;
-    lodash.reduce = reduce;
-    lodash.reduceRight = reduceRight;
-    lodash.repeat = repeat;
-    lodash.replace = replace;
-    lodash.result = result;
-    lodash.round = round;
-    lodash.runInContext = runInContext;
-    lodash.sample = sample;
-    lodash.size = size;
-    lodash.snakeCase = snakeCase;
-    lodash.some = some;
-    lodash.sortedIndex = sortedIndex;
-    lodash.sortedIndexBy = sortedIndexBy;
-    lodash.sortedIndexOf = sortedIndexOf;
-    lodash.sortedLastIndex = sortedLastIndex;
-    lodash.sortedLastIndexBy = sortedLastIndexBy;
-    lodash.sortedLastIndexOf = sortedLastIndexOf;
-    lodash.startCase = startCase;
-    lodash.startsWith = startsWith;
-    lodash.subtract = subtract;
-    lodash.sum = sum;
-    lodash.sumBy = sumBy;
-    lodash.template = template;
-    lodash.times = times;
-    lodash.toFinite = toFinite;
-    lodash.toInteger = toInteger;
-    lodash.toLength = toLength;
-    lodash.toLower = toLower;
-    lodash.toNumber = toNumber;
-    lodash.toSafeInteger = toSafeInteger;
-    lodash.toString = toString;
-    lodash.toUpper = toUpper;
-    lodash.trim = trim;
-    lodash.trimEnd = trimEnd;
-    lodash.trimStart = trimStart;
-    lodash.truncate = truncate;
-    lodash.unescape = unescape;
-    lodash.uniqueId = uniqueId;
-    lodash.upperCase = upperCase;
-    lodash.upperFirst = upperFirst;
-
-    // Add aliases.
-    lodash.each = forEach;
-    lodash.eachRight = forEachRight;
-    lodash.first = head;
-
-    mixin(lodash, (function() {
-      var source = {};
-      baseForOwn(lodash, function(func, methodName) {
-        if (!hasOwnProperty.call(lodash.prototype, methodName)) {
-          source[methodName] = func;
-        }
-      });
-      return source;
-    }()), { 'chain': false });
-
-    /*------------------------------------------------------------------------*/
-
-    /**
-     * The semantic version number.
-     *
-     * @static
-     * @memberOf _
-     * @type {string}
-     */
-    lodash.VERSION = VERSION;
-
-    // Assign default placeholders.
-    arrayEach(['bind', 'bindKey', 'curry', 'curryRight', 'partial', 'partialRight'], function(methodName) {
-      lodash[methodName].placeholder = lodash;
-    });
-
-    // Add `LazyWrapper` methods for `_.drop` and `_.take` variants.
-    arrayEach(['drop', 'take'], function(methodName, index) {
-      LazyWrapper.prototype[methodName] = function(n) {
-        n = n === undefined ? 1 : nativeMax(toInteger(n), 0);
-
-        var result = (this.__filtered__ && !index)
-          ? new LazyWrapper(this)
-          : this.clone();
-
-        if (result.__filtered__) {
-          result.__takeCount__ = nativeMin(n, result.__takeCount__);
-        } else {
-          result.__views__.push({
-            'size': nativeMin(n, MAX_ARRAY_LENGTH),
-            'type': methodName + (result.__dir__ < 0 ? 'Right' : '')
-          });
-        }
-        return result;
-      };
-
-      LazyWrapper.prototype[methodName + 'Right'] = function(n) {
-        return this.reverse()[methodName](n).reverse();
-      };
-    });
-
-    // Add `LazyWrapper` methods that accept an `iteratee` value.
-    arrayEach(['filter', 'map', 'takeWhile'], function(methodName, index) {
-      var type = index + 1,
-          isFilter = type == LAZY_FILTER_FLAG || type == LAZY_WHILE_FLAG;
-
-      LazyWrapper.prototype[methodName] = function(iteratee) {
-        var result = this.clone();
-        result.__iteratees__.push({
-          'iteratee': getIteratee(iteratee, 3),
-          'type': type
-        });
-        result.__filtered__ = result.__filtered__ || isFilter;
-        return result;
-      };
-    });
-
-    // Add `LazyWrapper` methods for `_.head` and `_.last`.
-    arrayEach(['head', 'last'], function(methodName, index) {
-      var takeName = 'take' + (index ? 'Right' : '');
-
-      LazyWrapper.prototype[methodName] = function() {
-        return this[takeName](1).value()[0];
-      };
-    });
-
-    // Add `LazyWrapper` methods for `_.initial` and `_.tail`.
-    arrayEach(['initial', 'tail'], function(methodName, index) {
-      var dropName = 'drop' + (index ? '' : 'Right');
-
-      LazyWrapper.prototype[methodName] = function() {
-        return this.__filtered__ ? new LazyWrapper(this) : this[dropName](1);
-      };
-    });
-
-    LazyWrapper.prototype.compact = function() {
-      return this.filter(identity);
-    };
-
-    LazyWrapper.prototype.find = function(predicate) {
-      return this.filter(predicate).head();
-    };
-
-    LazyWrapper.prototype.findLast = function(predicate) {
-      return this.reverse().find(predicate);
-    };
-
-    LazyWrapper.prototype.invokeMap = baseRest(function(path, args) {
-      if (typeof path == 'function') {
-        return new LazyWrapper(this);
-      }
-      return this.map(function(value) {
-        return baseInvoke(value, path, args);
-      });
-    });
-
-    LazyWrapper.prototype.reject = function(predicate) {
-      return this.filter(negate(getIteratee(predicate)));
-    };
-
-    LazyWrapper.prototype.slice = function(start, end) {
-      start = toInteger(start);
-
-      var result = this;
-      if (result.__filtered__ && (start > 0 || end < 0)) {
-        return new LazyWrapper(result);
-      }
-      if (start < 0) {
-        result = result.takeRight(-start);
-      } else if (start) {
-        result = result.drop(start);
-      }
-      if (end !== undefined) {
-        end = toInteger(end);
-        result = end < 0 ? result.dropRight(-end) : result.take(end - start);
-      }
-      return result;
-    };
-
-    LazyWrapper.prototype.takeRightWhile = function(predicate) {
-      return this.reverse().takeWhile(predicate).reverse();
-    };
-
-    LazyWrapper.prototype.toArray = function() {
-      return this.take(MAX_ARRAY_LENGTH);
-    };
-
-    // Add `LazyWrapper` methods to `lodash.prototype`.
-    baseForOwn(LazyWrapper.prototype, function(func, methodName) {
-      var checkIteratee = /^(?:filter|find|map|reject)|While$/.test(methodName),
-          isTaker = /^(?:head|last)$/.test(methodName),
-          lodashFunc = lodash[isTaker ? ('take' + (methodName == 'last' ? 'Right' : '')) : methodName],
-          retUnwrapped = isTaker || /^find/.test(methodName);
-
-      if (!lodashFunc) {
-        return;
-      }
-      lodash.prototype[methodName] = function() {
-        var value = this.__wrapped__,
-            args = isTaker ? [1] : arguments,
-            isLazy = value instanceof LazyWrapper,
-            iteratee = args[0],
-            useLazy = isLazy || isArray(value);
-
-        var interceptor = function(value) {
-          var result = lodashFunc.apply(lodash, arrayPush([value], args));
-          return (isTaker && chainAll) ? result[0] : result;
-        };
-
-        if (useLazy && checkIteratee && typeof iteratee == 'function' && iteratee.length != 1) {
-          // Avoid lazy use if the iteratee has a "length" value other than `1`.
-          isLazy = useLazy = false;
-        }
-        var chainAll = this.__chain__,
-            isHybrid = !!this.__actions__.length,
-            isUnwrapped = retUnwrapped && !chainAll,
-            onlyLazy = isLazy && !isHybrid;
-
-        if (!retUnwrapped && useLazy) {
-          value = onlyLazy ? value : new LazyWrapper(this);
-          var result = func.apply(value, args);
-          result.__actions__.push({ 'func': thru, 'args': [interceptor], 'thisArg': undefined });
-          return new LodashWrapper(result, chainAll);
-        }
-        if (isUnwrapped && onlyLazy) {
-          return func.apply(this, args);
-        }
-        result = this.thru(interceptor);
-        return isUnwrapped ? (isTaker ? result.value()[0] : result.value()) : result;
-      };
-    });
-
-    // Add `Array` methods to `lodash.prototype`.
-    arrayEach(['pop', 'push', 'shift', 'sort', 'splice', 'unshift'], function(methodName) {
-      var func = arrayProto[methodName],
-          chainName = /^(?:push|sort|unshift)$/.test(methodName) ? 'tap' : 'thru',
-          retUnwrapped = /^(?:pop|shift)$/.test(methodName);
-
-      lodash.prototype[methodName] = function() {
-        var args = arguments;
-        if (retUnwrapped && !this.__chain__) {
-          var value = this.value();
-          return func.apply(isArray(value) ? value : [], args);
-        }
-        return this[chainName](function(value) {
-          return func.apply(isArray(value) ? value : [], args);
-        });
-      };
-    });
-
-    // Map minified method names to their real names.
-    baseForOwn(LazyWrapper.prototype, function(func, methodName) {
-      var lodashFunc = lodash[methodName];
-      if (lodashFunc) {
-        var key = lodashFunc.name + '';
-        if (!hasOwnProperty.call(realNames, key)) {
-          realNames[key] = [];
-        }
-        realNames[key].push({ 'name': methodName, 'func': lodashFunc });
-      }
-    });
-
-    realNames[createHybrid(undefined, WRAP_BIND_KEY_FLAG).name] = [{
-      'name': 'wrapper',
-      'func': undefined
-    }];
-
-    // Add methods to `LazyWrapper`.
-    LazyWrapper.prototype.clone = lazyClone;
-    LazyWrapper.prototype.reverse = lazyReverse;
-    LazyWrapper.prototype.value = lazyValue;
-
-    // Add chain sequence methods to the `lodash` wrapper.
-    lodash.prototype.at = wrapperAt;
-    lodash.prototype.chain = wrapperChain;
-    lodash.prototype.commit = wrapperCommit;
-    lodash.prototype.next = wrapperNext;
-    lodash.prototype.plant = wrapperPlant;
-    lodash.prototype.reverse = wrapperReverse;
-    lodash.prototype.toJSON = lodash.prototype.valueOf = lodash.prototype.value = wrapperValue;
-
-    // Add lazy aliases.
-    lodash.prototype.first = lodash.prototype.head;
-
-    if (symIterator) {
-      lodash.prototype[symIterator] = wrapperToIterator;
-    }
-    return lodash;
-  });
-
-  /*--------------------------------------------------------------------------*/
-
-  // Export lodash.
-  var _ = runInContext();
-
-  // Some AMD build optimizers, like r.js, check for condition patterns like:
-  if (typeof define == 'function' && typeof define.amd == 'object' && define.amd) {
-    // Expose Lodash on the global object to prevent errors when Lodash is
-    // loaded by a script tag in the presence of an AMD loader.
-    // See http://requirejs.org/docs/errors.html#mismatch for more details.
-    // Use `_.noConflict` to remove Lodash from the global object.
-    root._ = _;
-
-    // Define as an anonymous module so, through path mapping, it can be
-    // referenced as the "underscore" module.
-    define(function() {
-      return _;
-    });
-  }
-  // Check for `exports` after `define` in case a build optimizer adds it.
-  else if (freeModule) {
-    // Export for Node.js.
-    (freeModule.exports = _)._ = _;
-    // Export for CommonJS support.
-    freeExports._ = _;
-  }
-  else {
-    // Export to the global object.
-    root._ = _;
-  }
-}.call(this));
diff --git a/cwl/src/test/resources/cwl/ontology/EDAM.owl b/cwl/src/test/resources/cwl/ontology/EDAM.owl
deleted file mode 100644
index 092fccdac32..00000000000
--- a/cwl/src/test/resources/cwl/ontology/EDAM.owl
+++ /dev/null
@@ -1,51294 +0,0 @@
-<?xml version="1.0"?>
-
-
-<!DOCTYPE rdf:RDF [
-    <!ENTITY foaf "http://xmlns.com/foaf/0.1/" >
-    <!ENTITY doap "http://usefulinc.com/ns/doap#" >
-    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
-    <!ENTITY oboOther "http://purl.obolibrary.org/obo/" >
-    <!ENTITY dc "http://purl.org/dc/elements/1.1/" >
-    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
-    <!ENTITY edam "http://purl.obolibrary.org/obo/edam#" >
-    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
-    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
-    <!ENTITY oboInOwl "http://www.geneontology.org/formats/oboInOwl#" >
-]>
-
-
-<rdf:RDF xmlns="http://edamontology.org/"
-     xml:base="http://edamontology.org/"
-     xmlns:dc="http://purl.org/dc/elements/1.1/"
-     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-     xmlns:foaf="http://xmlns.com/foaf/0.1/"
-     xmlns:owl="http://www.w3.org/2002/07/owl#"
-     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-     xmlns:oboOther="http://purl.obolibrary.org/obo/"
-     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
-     xmlns:doap="http://usefulinc.com/ns/doap#"
-     xmlns:edam="&oboOther;edam#">
-    <owl:Ontology rdf:about="http://edamontology.org">
-        <oboOther:idspace>EDAM_topic http://edamontology.org/topic_ &quot;EDAM topics&quot;</oboOther:idspace>
-        <oboOther:idspace>EDAM_operation http://edamontology.org/operation_ &quot;EDAM operations&quot;</oboOther:idspace>
-        <oboOther:date>09:07:2015</oboOther:date>
-        <next_id>3625</next_id>
-        <oboInOwl:hasSubset>formats &quot;EDAM data formats&quot;</oboInOwl:hasSubset>
-        <oboOther:default-relationship-id-prefix>EDAM</oboOther:default-relationship-id-prefix>
-        <dc:title>An ontology of bioinformatics topics, operations, types of data including identifiers, and data formats</dc:title>
-        <oboInOwl:hasSubset>identifiers &quot;EDAM types of identifiers&quot;</oboInOwl:hasSubset>
-        <oboInOwl:hasSubset>data &quot;EDAM types of data&quot;</oboInOwl:hasSubset>
-        <oboInOwl:hasSubset>relations &quot;EDAM relations&quot;</oboInOwl:hasSubset>
-        <oboInOwl:hasSubset>edam &quot;EDAM&quot;</oboInOwl:hasSubset>
-        <oboOther:remark>EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence.</oboOther:remark>
-        <oboInOwl:hasSubset>operations &quot;EDAM operations&quot;</oboInOwl:hasSubset>
-        <oboOther:idspace>EDAM http://edamontology.org/ &quot;EDAM relations and concept properties&quot;</oboOther:idspace>
-        <dc:format>application/rdf+xml</dc:format>
-        <oboOther:idspace>EDAM_data http://edamontology.org/data_ &quot;EDAM types of data&quot;</oboOther:idspace>
-        <oboInOwl:hasSubset>concept_properties &quot;EDAM concept properties&quot;</oboInOwl:hasSubset>
-        <dc:creator>Jon Ison</dc:creator>
-        <dc:creator>Matúš Kalaš</dc:creator>
-        <oboInOwl:savedBy>Jon Ison, Matus Kalas, Hervé Ménager</oboInOwl:savedBy>
-        <oboOther:idspace>EDAM_format http://edamontology.org/format_ &quot;EDAM data formats&quot;</oboOther:idspace>
-        <oboInOwl:hasSubset>topics &quot;EDAM topics&quot;</oboInOwl:hasSubset>
-        <doap:Version>1.11</doap:Version>
-        <dc:creator>Hervé Ménager</dc:creator>
-        <oboOther:remark>EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources.  EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.</oboOther:remark>
-        <rdfs:isDefinedBy rdf:resource="http://edamontology.org/EDAM.owl"/>
-        <foaf:page rdf:resource="http://edamontology.org/page"/>
-    </owl:Ontology>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Annotation properties
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-
-
-    <!-- http://edamontology.org/created_in -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/created_in">
-        <rdfs:label>Created in</rdfs:label>
-        <oboInOwl:hasDefinition>Version in which a concept was created.</oboInOwl:hasDefinition>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/documentation -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/documentation">
-        <rdfs:label>Documentation</rdfs:label>
-        <oboInOwl:hasRelatedSynonym>Specification</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>&apos;Documentation&apos; trailing modifier (qualifier, &apos;documentation&apos;) of &apos;xref&apos; links of &apos;Format&apos; concepts. When &apos;true&apos;, the link is pointing to a page with explanation, description, documentation, or specification of the given data format.</oboInOwl:hasDefinition>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/example -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/example">
-        <rdfs:label>Example</rdfs:label>
-        <oboInOwl:hasDefinition>&apos;Example&apos; concept property (&apos;example&apos; metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too.</oboInOwl:hasDefinition>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/noClue -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/noClue"/>
-    
-
-
-    <!-- http://edamontology.org/obsolete_since -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/obsolete_since">
-        <rdfs:label>Obsolete since</rdfs:label>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-        <oboInOwl:hasDefinition>Version in which a concept was made obsolete.</oboInOwl:hasDefinition>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://edamontology.org/regex -->
-
-    <owl:AnnotationProperty rdf:about="http://edamontology.org/regex">
-        <rdfs:label>Regular expression</rdfs:label>
-        <oboInOwl:hasDefinition>&apos;Regular expression&apos; concept property (&apos;regex&apos; metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
-        <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_anti_symmetric -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_anti_symmetric"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_metadata_tag -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_metadata_tag"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_reflexive -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_reflexive"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/is_symmetric -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;is_symmetric"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/namespace -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;namespace"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/transitive_over -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;transitive_over"/>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#data -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#data">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#edam -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#edam">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#events -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#events">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#formats -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#formats">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#identifiers -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#identifiers">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#obsolete -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#obsolete">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#operations -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#operations">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://purl.obolibrary.org/obo/edam#topics -->
-
-    <owl:AnnotationProperty rdf:about="&oboOther;edam#topics">
-        <rdfs:subPropertyOf rdf:resource="&oboInOwl;SubsetProperty"/>
-    </owl:AnnotationProperty>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#SubsetProperty -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;SubsetProperty"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#consider -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;consider"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasAlternativeId -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasAlternativeId"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasBroadSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasDbXref"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasDefinition -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasDefinition"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasExactSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasNarrowSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasRelatedSynonym"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasSubset -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;hasSubset"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;inSubset"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#isCyclic -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;isCyclic"/>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#replacedBy -->
-
-    <owl:AnnotationProperty rdf:about="&oboInOwl;replacedBy"/>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Object Properties
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-
-
-    <!-- http://edamontology.org/has_format -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_format">
-        <rdfs:label>has format</rdfs:label>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000298&quot;</rdfs:seeAlso>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) &apos;Data&apos;, or an input, output, input or output argument of an &apos;Operation&apos;. Object B can either be a concept that is a &apos;Format&apos;, or in unexpected cases an entity outside of an ontology that is a &apos;Format&apos; or is in the role of a &apos;Format&apos;. In EDAM, &apos;has_format&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;is_format_of&apos;.</rdfs:comment>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality&quot;</rdfs:seeAlso>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:hasDefinition>&apos;A has_format B&apos; defines for the subject A, that it has the object B as its data format.</oboInOwl:hasDefinition>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:range rdf:resource="http://edamontology.org/format_1915"/>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://edamontology.org/has_function -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_function">
-        <rdfs:label>has function</rdfs:label>
-        <rdfs:seeAlso>http://wsio.org/has_function</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:bearer_of</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, &apos;has_function&apos; serves only for relating annotated entities outside of EDAM with &apos;Operation&apos; concepts.</rdfs:comment>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality&quot;</rdfs:seeAlso>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:hasDefinition>&apos;A has_function B&apos; defines for the subject A, that it has the object B as its function.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000306&quot;</rdfs:seeAlso>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <rdfs:range rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_function"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:bearer_of&apos; is narrower in the sense that it only relates ontological categories (concepts) that are an &apos;independent_continuant&apos; (snap:IndependentContinuant) with ontological categories that are a &apos;specifically_dependent_continuant&apos; (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject.</rdfs:comment>
-        <owl:annotatedTarget>OBO_REL:bearer_of</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_function"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/has_identifier -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_identifier">
-        <rdfs:label>has identifier</rdfs:label>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:hasDefinition>&apos;A has_identifier B&apos; defines for the subject A, that it has the object B as its identifier.</oboInOwl:hasDefinition>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an &apos;Identifier&apos;, or an entity outside of an ontology that is an &apos;Identifier&apos; or is in the role of an &apos;Identifier&apos;. In EDAM, &apos;has_identifier&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;is_identifier_of&apos;.</rdfs:comment>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0842"/>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://edamontology.org/has_input -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_input">
-        <rdfs:label>has input</rdfs:label>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:has_participant</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000293&quot;</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:seeAlso>http://wsio.org/has_input</rdfs:seeAlso>
-        <rdfs:comment>Subject A can either be concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. Object B can be any concept or entity. In EDAM, only &apos;has_input&apos; is explicitly defined between EDAM concepts (&apos;Operation&apos; &apos;has_input&apos; &apos;Data&apos;). The inverse, &apos;is_input_of&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:hasDefinition>&apos;A has_input B&apos; defines for the subject A, that it has the object B as a necessary or actual input or input argument.</oboInOwl:hasDefinition>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:has_participant</owl:annotatedTarget>
-        <rdfs:comment>&apos;OBO_REL:has_participant&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;process&apos; (span:Process) with ontological categories that are a &apos;continuant&apos; (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_input"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_input"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/has_output -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_output">
-        <rdfs:label>has output</rdfs:label>
-        <rdfs:seeAlso>http://wsio.org/has_output</rdfs:seeAlso>
-        <rdfs:comment>Subject A can either be concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. Object B can be any concept or entity. In EDAM, only &apos;has_output&apos; is explicitly defined between EDAM concepts (&apos;Operation&apos; &apos;has_output&apos; &apos;Data&apos;). The inverse, &apos;is_output_of&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000299&quot;</rdfs:seeAlso>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:has_participant</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:hasDefinition>&apos;A has_output B&apos; defines for the subject A, that it has the object B as a necessary or actual output or output argument.</oboInOwl:hasDefinition>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>&apos;OBO_REL:has_participant&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;process&apos; (span:Process) with ontological categories that are a &apos;continuant&apos; (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it.</rdfs:comment>
-        <owl:annotatedTarget>OBO_REL:has_participant</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_output"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_output"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/has_topic -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/has_topic">
-        <rdfs:label>has topic</rdfs:label>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a &apos;Topic&apos;, or in unexpected cases an entity outside of an ontology that is a &apos;Topic&apos; or is in the role of a &apos;Topic&apos;. In EDAM, only &apos;has_topic&apos; is explicitly defined between EDAM concepts (&apos;Operation&apos; or &apos;Data&apos; &apos;has_topic&apos; &apos;Topic&apos;). The inverse, &apos;is_topic_of&apos;, is not explicitly defined.</rdfs:comment>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:hasDefinition>&apos;A has_topic B&apos; defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <rdfs:seeAlso>http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000136&quot;</rdfs:seeAlso>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000298&quot;</rdfs:seeAlso>
-        <rdfs:range rdf:resource="http://edamontology.org/topic_0003"/>
-        <rdfs:domain>
-            <owl:Class>
-                <owl:unionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://edamontology.org/data_0006"/>
-                    <rdf:Description rdf:about="http://edamontology.org/operation_0004"/>
-                </owl:unionOf>
-            </owl:Class>
-        </rdfs:domain>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/has_topic"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_format_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_format_of">
-        <rdfs:label>is format of</rdfs:label>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboInOwl:hasDefinition>&apos;A is_format_of B&apos; defines for the subject A, that it is a data format of the object B.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can either be a concept that is a &apos;Format&apos;, or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a &apos;Format&apos; or is in the role of a &apos;Format&apos;. Object B can be any concept or entity outside of an ontology that is (or is in a role of) &apos;Data&apos;, or  an input, output, input or output argument of an &apos;Operation&apos;. In EDAM, only &apos;is_format_of&apos; is explicitly defined between EDAM concepts (&apos;Format&apos; &apos;is_format_of&apos; &apos;Data&apos;). The inverse, &apos;has_format&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:quality_of</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in</rdfs:seeAlso>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_format"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:quality_of</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:quality_of&apos; might be seen narrower in the sense that it only relates subjects that are a &apos;quality&apos; (snap:Quality) with objects that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_format_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_function_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_function_of">
-        <rdfs:label>is function of</rdfs:label>
-        <rdfs:comment>Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, &apos;is_function_of&apos; is not used.</rdfs:comment>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:inheres_in</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:hasDefinition>&apos;A is_function_of B&apos; defines for the subject A, that it is a function of the object B.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>OBO_REL:function_of</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:seeAlso>http://wsio.org/is_function_of</rdfs:seeAlso>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in</rdfs:seeAlso>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_function"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:inheres_in</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:inheres_in&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;specifically_dependent_continuant&apos; (snap:SpecificallyDependentContinuant) with ontological categories that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_function_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_function_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:function_of</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:function_of&apos; only relates subjects that are a &apos;function&apos; (snap:Function) with objects that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_function_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_identifier_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_identifier_of">
-        <rdfs:label>is identifier of</rdfs:label>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboInOwl:isCyclic>false</oboInOwl:isCyclic>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can either be a concept that is an &apos;Identifier&apos;, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an &apos;Identifier&apos; or is in the role of an &apos;Identifier&apos;. Object B can be any concept or entity outside of an ontology. In EDAM, only &apos;is_identifier_of&apos; is explicitly defined between EDAM concepts (only &apos;Identifier&apos; &apos;is_identifier_of&apos; &apos;Data&apos;). The inverse, &apos;has_identifier&apos;, is not explicitly defined.</rdfs:comment>
-        <oboInOwl:hasDefinition>&apos;A is_identifier_of B&apos; defines for the subject A, that it is an identifier of the object B.</oboInOwl:hasDefinition>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:range rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0842"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_identifier"/>
-    </owl:ObjectProperty>
-    
-
-
-    <!-- http://edamontology.org/is_input_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_input_of">
-        <rdfs:label>is input of</rdfs:label>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:seeAlso>http://wsio.org/is_input_of</rdfs:seeAlso>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:participates_in</oboInOwl:hasRelatedSynonym>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000295&quot;</rdfs:seeAlso>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. In EDAM, &apos;is_input_of&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;has_input&apos;.</rdfs:comment>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboInOwl:hasDefinition>&apos;A is_input_of B&apos; defines for the subject A, that it as a necessary or actual input or input argument of the object B.</oboInOwl:hasDefinition>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_input"/>
-        <rdfs:range rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>&apos;OBO_REL:participates_in&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;continuant&apos; (snap:Continuant) with ontological categories that are a &apos;process&apos; (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments.</rdfs:comment>
-        <owl:annotatedTarget>OBO_REL:participates_in</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_input_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_input_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_output_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_output_of">
-        <rdfs:label>is output of</rdfs:label>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <rdfs:comment>Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an &apos;Operation&apos; function, or an entity outside of an ontology that has an &apos;Operation&apos; function or is an &apos;Operation&apos;. In EDAM, &apos;is_output_of&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;has_output&apos;.</rdfs:comment>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <oboInOwl:hasDefinition>&apos;A is_output_of B&apos; defines for the subject A, that it as a necessary or actual output or output argument of the object B.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:participates_in</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>http://wsio.org/is_output_of</rdfs:seeAlso>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/OBI_0000312&quot;</rdfs:seeAlso>
-        <rdfs:domain rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_output"/>
-        <rdfs:range rdf:resource="http://edamontology.org/operation_0004"/>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_output_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:participates_in</owl:annotatedTarget>
-        <rdfs:comment>&apos;OBO_REL:participates_in&apos; is narrower in the sense that it only relates ontological categories (concepts) that are a &apos;continuant&apos; (snap:Continuant) with ontological categories that are a &apos;process&apos; (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_output_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/is_topic_of -->
-
-    <owl:ObjectProperty rdf:about="http://edamontology.org/is_topic_of">
-        <rdfs:label>is topic of</rdfs:label>
-        <oboInOwl:hasDefinition>&apos;A is_topic_of B&apos; defines for the subject A, that it is a topic of the object B (a topic A is the scope of B).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset>relations</oboInOwl:inSubset>
-        <oboInOwl:hasRelatedSynonym>OBO_REL:quality_of</oboInOwl:hasRelatedSynonym>
-        <oboOther:is_reflexive>false</oboOther:is_reflexive>
-        <oboInOwl:isCyclic>true</oboInOwl:isCyclic>
-        <oboOther:is_anti_symmetric>false</oboOther:is_anti_symmetric>
-        <rdfs:comment>Subject A can either be a concept that is a &apos;Topic&apos;, or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a &apos;Topic&apos; or is in the role of a &apos;Topic&apos;. Object B can be any concept or entity outside of an ontology. In EDAM, &apos;is_topic_of&apos; is not explicitly defined between EDAM concepts, only the inverse &apos;has_topic&apos;.</rdfs:comment>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in</rdfs:seeAlso>
-        <oboOther:is_symmetric>false</oboOther:is_symmetric>
-        <oboOther:transitive_over>OBO_REL:is_a</oboOther:transitive_over>
-        <oboInOwl:inSubset>edam</oboInOwl:inSubset>
-        <owl:inverseOf rdf:resource="http://edamontology.org/has_topic"/>
-        <rdfs:domain rdf:resource="http://edamontology.org/topic_0003"/>
-        <rdfs:range>
-            <owl:Class>
-                <owl:unionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://edamontology.org/data_0006"/>
-                    <rdf:Description rdf:about="http://edamontology.org/operation_0004"/>
-                </owl:unionOf>
-            </owl:Class>
-        </rdfs:range>
-    </owl:ObjectProperty>
-    <owl:Axiom>
-        <owl:annotatedTarget>OBO_REL:quality_of</owl:annotatedTarget>
-        <rdfs:comment>Is defined anywhere? Not in the &apos;unknown&apos; version of RO. &apos;OBO_REL:quality_of&apos; might be seen narrower in the sense that it only relates subjects that are a &apos;quality&apos; (snap:Quality) with objects that are an &apos;independent_continuant&apos; (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_topic_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>In very unusual cases.</rdfs:comment>
-        <owl:annotatedTarget>true</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/is_topic_of"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;isCyclic"/>
-    </owl:Axiom>
-    
-
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Classes
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-    
-    
-
-
-    <!-- http://edamontology.org/data_0005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0005">
-        <rdfs:label>Resource type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A type of computational resource used in bioinformatics.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0006">
-        <rdfs:label>Data</rdfs:label>
-        <owl:disjointWith rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/topic_0003"/>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <oboInOwl:hasDefinition>Information, represented in an information artefact (data record) that is &apos;understandable&apos; by dedicated computational tools that can use the data as input or produce it as output.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000088</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000069</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000030&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000027&quot;</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Data set</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Data record</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://wsio.org/data_002</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#DigitalEntity</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Datum</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedTarget>Data set</owl:annotatedTarget>
-        <rdfs:comment>EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>Datum</owl:annotatedTarget>
-        <rdfs:comment>EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>Data record</owl:annotatedTarget>
-        <rdfs:comment>EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information).</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0006"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasExactSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_0007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0007">
-        <rdfs:label>Tool</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A bioinformatics package or tool, e.g. a standalone application or web service.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0581">
-        <rdfs:label>Database</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0582">
-        <rdfs:label>Ontology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontologies</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0583">
-        <rdfs:label>Directory metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A directory on disk from which files are read.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0831 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0831">
-        <rdfs:label>MeSH vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0832 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0832">
-        <rdfs:label>HGNC vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0835 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0835">
-        <rdfs:label>UMLS vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0842 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0842">
-        <rdfs:label>Identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <owl:disjointWith rdf:resource="http://edamontology.org/data_2048"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/data_2527"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000115</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>ID</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>&quot;http://purl.org/dc/elements/1.1/identifier&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>http://wsio.org/data_005</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-        <oboInOwl:hasNarrowSynonym rdf:resource="&dc;identifier"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>Almost exact but limited to identifying resources.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0842"/>
-        <owl:annotatedTarget rdf:resource="&dc;identifier"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_0843 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0843">
-        <rdfs:label>Database entry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An entry (retrievable via URL) from a biological database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0844 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0844">
-        <rdfs:label>Molecular mass</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasDefinition>Mass of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0845 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0845">
-        <rdfs:label>Molecular charge</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasDefinition>Net charge of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:pdbx_formal_charge</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0846 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0846">
-        <rdfs:label>Chemical formula</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasExactSynonym>Chemical structure specification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A specification of a chemical structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0847 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0847">
-        <rdfs:label>QSAR descriptor</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <oboInOwl:hasDefinition>A QSAR quantitative descriptor (name-value pair) of chemical structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0848 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0848">
-        <rdfs:label>Raw sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <rdfs:comment>Non-sequence characters may be used for example for gaps and translation stop.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0849 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0849">
-        <rdfs:label>Sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D058977</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A molecular sequence and associated metadata.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>SO:2000061</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0850 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0850">
-        <rdfs:label>Sequence set</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for arbitrary sequence sets and associated data arising from processing.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasRelatedSynonym>SO:0001260</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0851 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0851">
-        <rdfs:label>Sequence mask character</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A character used to replace (mask) other characters in a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0852 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0852">
-        <rdfs:label>Sequence mask type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of sequence masking to perform.</oboInOwl:hasDefinition>
-        <rdfs:comment>Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0853 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0853">
-        <rdfs:label>DNA sense specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:hasExactSynonym>DNA strand specification</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Strand</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The strand of a DNA sequence (forward or reverse).</oboInOwl:hasDefinition>
-        <rdfs:comment>The forward or &apos;top&apos; strand might specify a sequence is to be used as given, the reverse or &apos;bottom&apos; strand specifying the reverse complement of the sequence is to be used.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0854 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0854">
-        <rdfs:label>Sequence length specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A specification of sequence length(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0855 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0855">
-        <rdfs:label>Sequence metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Basic or general information concerning molecular sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is used for such things as a report including the sequence identifier, type and length.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2955"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0856 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0856">
-        <rdfs:label>Sequence feature source</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <rdfs:comment>This might be the name and version of a software tool, the name of a database, or &apos;curated&apos; to indicate a manual annotation (made by a human).</rdfs:comment>
-        <oboInOwl:hasDefinition>How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0857 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0857">
-        <rdfs:label>Sequence search results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Database hits (sequence)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym></oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence database hits</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence search hits</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence database search results</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0858 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0858">
-        <rdfs:label>Sequence signature matches</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0860"/>
-        <oboInOwl:hasExactSynonym>Sequence motif matches</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary database search results</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence profile matches</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This ncluding reports of hits from a search of a protein secondary or domain database.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Search results (protein secondary database)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0859 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0859">
-        <rdfs:label>Sequence signature model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data files used by motif or profile methods.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0860 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0860">
-        <rdfs:label>Sequence signature data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element.</oboInOwl:hasDefinition>
-        <oboInOwl:hasSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:hasSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0861 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0861">
-        <rdfs:label>Sequence alignment (words)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence word alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Alignment of exact matches between subsequences (words) within two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0862 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0862">
-        <rdfs:label>Dotplot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:hasDefinition>A dotplot of sequence similarities identified from word-matching or character comparison.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0863 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0863">
-        <rdfs:label>Sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Sequence_alignment</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D016415</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_010066</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of multiple molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0864 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0864">
-        <rdfs:label>Sequence alignment parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Some simple value controlling a sequence alignment (or similar &apos;match&apos;) operation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0865 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0865">
-        <rdfs:label>Sequence similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1772"/>
-        <oboInOwl:hasDefinition>A value representing molecular sequence similarity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0866 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0866">
-        <rdfs:label>Sequence alignment metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0867">
-        <rdfs:label>Sequence alignment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:comment>Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score.</rdfs:comment>
-        <oboInOwl:hasDefinition>An informative report of molecular sequence alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0868">
-        <rdfs:label>Sequence profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A profile-profile alignment (each profile typically representing a sequence alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0869">
-        <rdfs:label>Sequence-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment).</oboInOwl:hasDefinition>
-        <rdfs:comment>Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0870 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0870">
-        <rdfs:label>Sequence distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2855"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:phylogenetic_distance_matrix</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic distance matrix</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0871 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0871">
-        <rdfs:label>Phylogenetic character data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasDefinition>Basic character data from which a phylogenetic tree may be generated.</oboInOwl:hasDefinition>
-        <rdfs:comment>As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments</rdfs:comment>
-        <rdfs:seeAlso>http://www.evolutionaryontology.org/cdao.owl#Character</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0872 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0872">
-        <rdfs:label>Phylogenetic tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phylogeny</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Tree</oboInOwl:hasDbXref>
-        <rdfs:seeAlso>http://www.evolutionaryontology.org/cdao.owl#Tree</rdfs:seeAlso>
-        <rdfs:comment>A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also &apos;Phylogenetic tree image&apos;.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D010802</rdfs:seeAlso>
-        <oboInOwl:hasDbXref>Moby:phylogenetic_tree</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:myTree</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0874 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0874">
-        <rdfs:label>Comparison matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats).</rdfs:comment>
-        <oboInOwl:hasDefinition>Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0875 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0875">
-        <rdfs:label>Protein topology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predicted or actual protein topology represented as a string of protein secondary structure elements.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The location and size of the secondary structure elements and intervening loop regions is usually indicated.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0876"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0876 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0876">
-        <rdfs:label>Protein features report (secondary structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Secondary structure (predicted or real) of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0877 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0877">
-        <rdfs:label>Protein features report (super-secondary)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <rdfs:comment>Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Super-secondary structure of protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0878 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0878">
-        <rdfs:label>Secondary structure alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2366"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3154"/>
-        <oboInOwl:hasDefinition>Alignment of the (1D representations of) secondary structure of two or more proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0879 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0879">
-        <rdfs:label>Secondary structure alignment metadata (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on protein secondary structure alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0880 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0880">
-        <rdfs:label>RNA secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1465"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An informative report of secondary structure (predicted or real) of an RNA molecule.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:RNAStructML</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Secondary structure (RNA)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0881 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0881">
-        <rdfs:label>Secondary structure alignment (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2366"/>
-        <oboInOwl:hasDbXref>Moby:RNAStructAlignmentML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Alignment of the (1D representations of) secondary structure of two or more RNA molecules.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0882 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0882">
-        <rdfs:label>Secondary structure alignment metadata (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report of RNA secondary structure alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0883 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0883">
-        <rdfs:label>Structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0081"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Coordinate model</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure data</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The coordinate data may be predicted or real.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015394</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0884 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0884">
-        <rdfs:label>Tertiary structure record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An entry from a molecular tertiary (3D) structure database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0885">
-        <rdfs:label>Structure database search results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Results (hits) from searching a database of tertiary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0886 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0886">
-        <rdfs:label>Structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <rdfs:comment>A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0887 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0887">
-        <rdfs:label>Structure alignment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasDefinition>An informative report of molecular tertiary structure alignment-derived data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0888 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0888">
-        <rdfs:label>Structure similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1772"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0889 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0889">
-        <rdfs:label>Structural profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>3D profile</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Some type of structural (3D) profile or template (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structural (3D) profile</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0890 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0890">
-        <rdfs:label>Structural (3D) profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structural profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A 3D profile-3D profile alignment (each profile representing structures or a structure alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0891 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0891">
-        <rdfs:label>Sequence-3D profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence-structural profile alignment</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>An alignment of a sequence to a 3D profile (representing structures or a structure alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0893"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0892 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0892">
-        <rdfs:label>Protein sequence-structure scoring matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of values used for scoring sequence-structure compatibility.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0893 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0893">
-        <rdfs:label>Sequence-structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0894 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0894">
-        <rdfs:label>Amino acid annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report about a specific amino acid.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0895 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0895">
-        <rdfs:label>Peptide annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report about a specific peptide.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0896 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0896">
-        <rdfs:label>Protein report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasExactSynonym>Gene product annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0897 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0897">
-        <rdfs:label>Protein property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>Protein physicochemical property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein sequence statistics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein properties</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0899 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0899">
-        <rdfs:label>Protein structural motifs and surfaces</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>3D structural motifs in a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein 3D motifs</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0900 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0900">
-        <rdfs:label>Protein domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning the classification of the sequences and/or structures of protein structural domain(s).</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0901 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0901">
-        <rdfs:label>Protein features report (domains)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>structural domains or 3D folds in a protein or polypeptide chain.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0902 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0902">
-        <rdfs:label>Protein architecture report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on architecture (spatial arrangement of secondary structure) of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein property (architecture)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure report (architecture)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0903 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0903">
-        <rdfs:label>Protein folding report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0904 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0904">
-        <rdfs:label>Protein features (mutation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on the effect of (typically point) mutation on protein folding, stability, structure and function.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein property (mutation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure report (mutation)</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein report (mutation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0905 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0905">
-        <rdfs:label>Protein interaction raw data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0906 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0906">
-        <rdfs:label>Protein interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein report (interaction)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein interaction record</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with some other molecule(s), which might be another protein, nucleic acid or some other ligand.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0907 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0907">
-        <rdfs:label>Protein family report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0724"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific protein family or other classification or group of protein sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein family annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Protein classification data</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0909 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0909">
-        <rdfs:label>Vmax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0910 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0910">
-        <rdfs:label>Km</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <oboInOwl:hasDefinition>Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0911 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0911">
-        <rdfs:label>Nucleotide base annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report about a specific nucleotide base.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0912 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0912">
-        <rdfs:label>Nucleic acid property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasDefinition>A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Nucleic acid physicochemical property</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0914 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0914">
-        <rdfs:label>Codon usage data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0916 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0916">
-        <rdfs:label>Gene report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:hasExactSynonym>Gene structure (repot)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene and transcript structure (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene features report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (gene and transcript structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:gene</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes any report on a particular locus or gene.  This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Gene annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:Human_Readable_Description</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Gene function (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:GeneInfo</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0917 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0917">
-        <rdfs:label>Gene classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0918 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0918">
-        <rdfs:label>DNA variation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0919 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0919">
-        <rdfs:label>Chromosome report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0624"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific chromosome.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0920 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0920">
-        <rdfs:label>Genotype/phenotype report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genotype/phenotype annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0922 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0922">
-        <rdfs:label>Nucleic acid features report (primers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PCR primers and hybridization oligos in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0923 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0923">
-        <rdfs:label>PCR experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PCR experiments, e.g. quantitative real-time PCR.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0924 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0924">
-        <rdfs:label>Sequence trace</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <oboInOwl:hasDefinition>Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is the raw data produced by a DNA sequencing machine.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0925 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0925">
-        <rdfs:label>Sequence assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An assembly of fragments of a (typically genomic) DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Sequence_assembly</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>SO:0001248</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>SO:0000353</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedTarget>SO:0001248</owl:annotatedTarget>
-        <rdfs:comment>Perhaps surprisingly, the definition of &apos;SO:assembly&apos; is narrower than the &apos;SO:sequence_assembly&apos;.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_0925"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_0926 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0926">
-        <rdfs:label>Radiation Hybrid (RH) scores</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping.</rdfs:comment>
-        <oboInOwl:hasDefinition>Radiation hybrid scores (RH) scores for one or more markers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0927 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0927">
-        <rdfs:label>Genetic linkage report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene annotation (linkage)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Linkage disequilibrium (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>An informative report on the linkage of alleles.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0928 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0928">
-        <rdfs:label>Gene expression profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <oboInOwl:hasDefinition>Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression pattern</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0931 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0931">
-        <rdfs:label>Microarray experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>microarray experiments including conditions, protocol, sample:data relationships etc.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0932 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0932">
-        <rdfs:label>Oligonucleotide probe data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data on oligonucleotide probes (typically for use with DNA microarrays).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2717"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0933 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0933">
-        <rdfs:label>SAGE experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Output from a serial analysis of gene expression (SAGE) experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Serial analysis of gene expression (SAGE) experimental data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2535"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0934 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0934">
-        <rdfs:label>MPSS experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Massively parallel signature sequencing (MPSS) data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Massively parallel signature sequencing (MPSS) experimental data</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2535"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0935 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0935">
-        <rdfs:label>SBS experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequencing by synthesis (SBS) experimental data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Sequencing by synthesis (SBS) data.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2535"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0936 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0936">
-        <rdfs:label>Sequence tag profile (with gene assignment)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2535"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0937 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0937">
-        <rdfs:label>Protein X-ray crystallographic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2537"/>
-        <oboInOwl:hasDefinition>X-ray crystallography data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0938 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0938">
-        <rdfs:label>Protein NMR data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2537"/>
-        <oboInOwl:hasDefinition>Protein nuclear magnetic resonance (NMR) raw data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0939 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0939">
-        <rdfs:label>Protein circular dichroism (CD) spectroscopic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2537"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0940 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0940">
-        <rdfs:label>Electron microscopy volume map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Volume map data from electron microscopy.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EM volume map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0941 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0941">
-        <rdfs:label>Electron microscopy model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation on a structural 3D model (volume map) from electron microscopy.</oboInOwl:hasDefinition>
-        <rdfs:comment>This might include the location in the model of the known features of a particular macromolecule.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0942 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0942">
-        <rdfs:label>2D PAGE image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Two-dimensional gel electrophoresis image</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0943 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0943">
-        <rdfs:label>Mass spectrometry spectra</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2536"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Spectra from mass spectrometry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0944 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0944">
-        <rdfs:label>Peptide mass fingerprint</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2536"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2979"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Peak list</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein fingerprint</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A set of peptide masses (peptide mass fingerprint) from mass spectrometry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0945 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0945">
-        <rdfs:label>Peptide identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2979"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0946 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0946">
-        <rdfs:label>Pathway or network annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0947 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0947">
-        <rdfs:label>Biological pathway map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A map (typically a diagram) of a biological pathway.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2600"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0948 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0948">
-        <rdfs:label>Data resource definition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0949 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0949">
-        <rdfs:label>Workflow metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Basic information, annotation or documentation concerning a workflow (but not the workflow itself).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0950 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0950">
-        <rdfs:label>Mathematical model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3307"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Biological model</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A biological model represented in mathematical terms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0951 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0951">
-        <rdfs:label>Statistical estimate score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1772"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A value representing estimated statistical significance of some observed data; typically sequence database hits.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0952 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0952">
-        <rdfs:label>EMBOSS database resource definition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Resource definition for an EMBOSS database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0953 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0953">
-        <rdfs:label>Version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000129&quot;</rdfs:seeAlso>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records.</rdfs:comment>
-        <rdfs:seeAlso>http://www.ebi.ac.uk/swo/maturity/SWO_9000061</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a version of software or data, for example name, version number and release date.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000653</rdfs:seeAlso>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:seeAlso>http://usefulinc.com/ns/doap#Version</rdfs:seeAlso>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0954 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0954">
-        <rdfs:label>Database cross-mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases.</oboInOwl:hasDefinition>
-        <rdfs:comment>The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0955 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0955">
-        <rdfs:label>Data index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0220"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An index of data of biological relevance.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0956 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0956">
-        <rdfs:label>Data index report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0220"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A report of an analysis of an index of biological data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database index annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0957 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0957">
-        <rdfs:label>Database metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0958 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0958">
-        <rdfs:label>Tool metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0959 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0959">
-        <rdfs:label>Job metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDbXref>Moby:PDGJOB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Textual metadata on a submitted or completed job.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0960 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0960">
-        <rdfs:label>User metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Textual metadata on a software author or end-user, for example a person or other software.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0962 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0962">
-        <rdfs:label>Small molecule report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0154"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Small molecule annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Small molecule report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Chemical structure report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on a specific chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0963 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0963">
-        <rdfs:label>Cell line report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:hasExactSynonym>Organism strain data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Cell line annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0964 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0964">
-        <rdfs:label>Scent annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report about a specific scent.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0966 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0966">
-        <rdfs:label>Ontology term</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0967"/>
-        <oboInOwl:hasExactSynonym>Ontology class name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term (name) from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ontology terms</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0967 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0967">
-        <rdfs:label>Ontology concept data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2353"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology class metadata</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Ontology term metadata</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning or derived from a concept from a biological ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0968 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0968">
-        <rdfs:label>Keyword</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Phrases</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Keyword(s) or phrase(s) used (typically) for text-searching purposes.</oboInOwl:hasDefinition>
-        <rdfs:comment>Boolean operators (AND, OR and NOT) and wildcard characters may be allowed.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:QueryString</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:BooleanQueryString</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Wildcard_Query</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Global_Keyword</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Terms</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Text</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0970 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0970">
-        <rdfs:label>Citation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2526"/>
-        <oboInOwl:hasDefinition>Bibliographic data that uniquely identifies a scientific article, book or other published material.</oboInOwl:hasDefinition>
-        <rdfs:comment>A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:GCP_SimpleCitation</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Reference</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Bibliographic reference</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Publication</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0971 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0971">
-        <rdfs:label>Article</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3068"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A document of scientific text, typically a full text article from a scientific journal.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0972 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0972">
-        <rdfs:label>Text mining report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An abstract of the results of text mining.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Text mining output</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0974 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0974">
-        <rdfs:label>Entity identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a biological entity or phenomenon.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0975 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0975">
-        <rdfs:label>Data resource identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An identifier of a data resource.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0976 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0976">
-        <rdfs:label>Identifier (typed)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This concept exists only to assist EDAM maintenance and navigation in graphical browsers.  It does not add semantic information.  This branch provides an alternative organisation of the concepts nested under &apos;Accession&apos; and &apos;Name&apos;. All concepts under here are already included under &apos;Accession&apos; or &apos;Name&apos;.</rdfs:comment>
-        <oboInOwl:hasDefinition>An identifier that identifies a particular type of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0977 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0977">
-        <rdfs:label>Tool identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a bioinformatics tool, e.g. an application or web service.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0978 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0978">
-        <rdfs:label>Discrete entity identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0979 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0979">
-        <rdfs:label>Entity feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0980 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0980">
-        <rdfs:label>Entity collection identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of a collection of discrete biological entities.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0981 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0981">
-        <rdfs:label>Phenomenon identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of a physical, observable biological occurrence or event.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0982 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0982">
-        <rdfs:label>Molecule identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>Name or other identifier of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0983 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0983">
-        <rdfs:label>Atom ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasExactSynonym>Atom identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier (e.g. character symbol) of a specific atom.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0984 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0984">
-        <rdfs:label>Molecule name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>Name of a specific molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0985 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0985">
-        <rdfs:label>Molecule type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>For example, &apos;Protein&apos;, &apos;DNA&apos;, &apos;RNA&apos; etc.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A label (text token) describing the type a molecule.</oboInOwl:hasDefinition>
-        <example>Protein|DNA|RNA</example>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0986 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0986">
-        <rdfs:label>Chemical identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Unique identifier of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1086"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0987 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0987">
-        <rdfs:label>Chromosome name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0984"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0919"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a chromosome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0988 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0988">
-        <rdfs:label>Peptide identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <oboInOwl:hasDefinition>Identifier of a peptide chain.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0989 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0989">
-        <rdfs:label>Protein identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0990 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0990">
-        <rdfs:label>Compound name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0984"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <oboInOwl:hasExactSynonym>Chemical name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique name of a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0991 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0991">
-        <rdfs:label>Chemical registry number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0992 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0992">
-        <rdfs:label>Ligand identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Code word for a ligand, for example from a PDB file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1086"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0993 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0993">
-        <rdfs:label>Drug identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2851"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a drug.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0994 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0994">
-        <rdfs:label>Amino acid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2016"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an amino acid.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Residue identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0995 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0995">
-        <rdfs:label>Nucleotide identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of a nucleotide.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0996 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0996">
-        <rdfs:label>Monosaccharide identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a monosaccharide.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0997 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0997">
-        <rdfs:label>Chemical name (ChEBI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasExactSynonym>ChEBI chemical name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is the recommended chemical name for use for example in database annotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0998 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0998">
-        <rdfs:label>Chemical name (IUPAC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasDefinition>IUPAC recommended name of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>IUPAC chemical name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_0999 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_0999">
-        <rdfs:label>Chemical name (INN)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasExactSynonym>INN chemical name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>International Non-proprietary Name (INN or &apos;generic name&apos;) of a chemical compound, assigned by the World Health Organization (WHO).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1000 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1000">
-        <rdfs:label>Chemical name (brand)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasDefinition>Brand name of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Brand chemical name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1001 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1001">
-        <rdfs:label>Chemical name (synonymous)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Synonymous chemical name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Synonymous name of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1002 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1002">
-        <rdfs:label>Chemical registry number (CAS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0991"/>
-        <oboInOwl:hasExactSynonym>CAS chemical registry number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>CAS registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1003">
-        <rdfs:label>Chemical registry number (Beilstein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0991"/>
-        <oboInOwl:hasExactSynonym>Beilstein chemical registry number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Beilstein registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1004">
-        <rdfs:label>Chemical registry number (Gmelin)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0991"/>
-        <oboInOwl:hasExactSynonym>Gmelin chemical registry number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gmelin registry number of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1005">
-        <rdfs:label>HET group name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <oboInOwl:hasDefinition>3-letter code word for a ligand (HET group) from a PDB file, for example ATP.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Short ligand name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Component identifier code</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1006">
-        <rdfs:label>Amino acid name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0994"/>
-        <oboInOwl:hasDefinition>String of one or more ASCII characters representing an amino acid.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1007">
-        <rdfs:label>Nucleotide code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0995"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>String of one or more ASCII characters representing a nucleotide.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1008 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1008">
-        <rdfs:label>Polypeptide chain ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0988"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1467"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: chain</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Chain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a polypeptide chain from a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_strand_id</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Protein chain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PDB strand id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PDB chain identifier</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Polypeptide chain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1009 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1009">
-        <rdfs:label>Protein name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0984"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <oboInOwl:hasDefinition>Name of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1010 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1010">
-        <rdfs:label>Enzyme identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of an enzyme or record from a database of enzymes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1011 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1011">
-        <rdfs:label>EC number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <regex>[0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>EC code</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:EC_Number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An Enzyme Commission (EC) number of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EC</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Annotated_EC_Number</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Enzyme Commission number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1012 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1012">
-        <rdfs:label>Enzyme name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1010"/>
-        <oboInOwl:hasDefinition>Name of an enzyme.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1013 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1013">
-        <rdfs:label>Restriction enzyme name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1012"/>
-        <oboInOwl:hasDefinition>Name of a restriction enzyme.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1014 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1014">
-        <rdfs:label>Sequence position specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A specification (partial or complete) of one or more positions or regions of a molecular sequence or map.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1016"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1015 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1015">
-        <rdfs:label>Sequence feature ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3034"/>
-        <oboInOwl:hasDefinition>A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1016 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1016">
-        <rdfs:label>Sequence position</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:hasDbXref>WHATIF: number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_atom_site</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.id</oboInOwl:hasDbXref>
-        <oboInOwl:hasRelatedSynonym>SO:0000735</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>A position of one or more points (base or residue) in a sequence, or part of such a specification.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1017 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1017">
-        <rdfs:label>Sequence range</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Specification of range(s) of sequence positions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1018 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1018">
-        <rdfs:label>Nucleic acid feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of an nucleic acid feature.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1015"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1019 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1019">
-        <rdfs:label>Protein feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Name or other identifier of a protein feature.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1015"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1020 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1020">
-        <rdfs:label>Sequence feature key</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <oboInOwl:hasExactSynonym>Sequence feature method</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence feature type</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1021 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1021">
-        <rdfs:label>Sequence feature qualifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Typically one of the EMBL or Swiss-Prot feature qualifiers.</oboInOwl:hasDefinition>
-        <rdfs:comment>Feature qualifiers hold information about a feature beyond that provided by the feature key and location.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1022 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1022">
-        <rdfs:label>Sequence feature label</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2914"/>
-        <oboInOwl:hasExactSynonym>Sequence feature name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Typically an EMBL or Swiss-Prot feature label.</oboInOwl:hasDefinition>
-        <rdfs:comment>A feature label identifies a feature of a sequence database entry. When used with the database name and the entry&apos;s primary accession number, it is a unique identifier of that feature.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1023 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1023">
-        <rdfs:label>EMBOSS Uniform Feature Object</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3034"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UFO</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1024 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1024">
-        <rdfs:label>Codon name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>String of one or more ASCII characters representing a codon.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1025 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1025">
-        <rdfs:label>Gene identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDbXref>Moby:GeneAccessionList</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1026 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1026">
-        <rdfs:label>Gene symbol</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2299"/>
-        <oboInOwl:hasDbXref>Moby_namespace:Global_GeneSymbol</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:Global_GeneCommonName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1027 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1027">
-        <rdfs:label>Gene ID (NCBI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1098"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>NCBI geneid</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene identifier (NCBI)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Entrez gene ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene identifier (Entrez)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:LocusID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An NCBI unique identifier of a gene.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>NCBI gene ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1028 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1028">
-        <rdfs:label>Gene identifier (NCBI RefSeq)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>An NCBI RefSeq unique identifier of a gene.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1027"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1029 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1029">
-        <rdfs:label>Gene identifier (NCBI UniGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>An NCBI UniGene unique identifier of a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1104"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1030 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1030">
-        <rdfs:label>Gene identifier (Entrez)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An Entrez unique identifier of a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>[0-9]+</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1027"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1031 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1031">
-        <rdfs:label>Gene ID (CGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>CGD ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a gene or feature from the CGD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1032 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1032">
-        <rdfs:label>Gene ID (DictyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a gene from DictyBase.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1033 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1033">
-        <rdfs:label>Ensembl gene ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene ID (Ensembl)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a gene (or other feature) from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1034 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1034">
-        <rdfs:label>Gene ID (SGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2632"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the SGD database.</oboInOwl:hasDefinition>
-        <regex>S[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>SGD identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1035 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1035">
-        <rdfs:label>Gene ID (GeneDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>Moby_namespace:GeneDB</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>GeneDB identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9\.-]*</regex>
-        <oboInOwl:hasDefinition>Identifier of a gene from the GeneDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1036 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1036">
-        <rdfs:label>TIGR identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the TIGR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1037 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1037">
-        <rdfs:label>TAIR accession (gene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2387"/>
-        <regex>Gene:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an gene from the TAIR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1038 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1038">
-        <rdfs:label>Protein domain ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1468"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein structural domain.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is typically a character or string concatenated with a PDB identifier and a chain identifier.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1039 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1039">
-        <rdfs:label>SCOP domain identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1038"/>
-        <oboInOwl:hasDefinition>Identifier of a protein domain (or other node) from the SCOP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1040 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1040">
-        <rdfs:label>CATH domain ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2700"/>
-        <example>1nr3A00</example>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CATH domain identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a protein domain from CATH.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1041 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1041">
-        <rdfs:label>SCOP concise classification string (sccs)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1039"/>
-        <oboInOwl:hasDefinition>A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1042 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1042">
-        <rdfs:label>SCOP sunid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1039"/>
-        <oboInOwl:hasDefinition>Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>sunid</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>SCOP unique identifier</oboInOwl:hasExactSynonym>
-        <example>33229</example>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1043 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1043">
-        <rdfs:label>CATH node ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2700"/>
-        <example>3.30.1190.10.1.1.1.1.1</example>
-        <oboInOwl:hasExactSynonym>CATH code</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A code number identifying a node from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>CATH node identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1044 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1044">
-        <rdfs:label>Kingdom name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1045 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1045">
-        <rdfs:label>Species name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a species (typically a taxonomic group) of organism.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Organism species</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1046 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1046">
-        <rdfs:label>Strain name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2379"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a strain of an organism variant, typically a plant, virus or bacterium.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1047 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1047">
-        <rdfs:label>URI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:hasDefinition>A string of characters that name or otherwise identify a resource on the Internet.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>URIs</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1048 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1048">
-        <rdfs:label>Database ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a biological or bioinformatics database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1049 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1049">
-        <rdfs:label>Directory name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a directory.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1050 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1050">
-        <rdfs:label>File name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name (or part of a name) of a file (of any type).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1051 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1051">
-        <rdfs:label>Ontology name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2338"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of an ontology of biological or bioinformatics concepts and relations.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1052 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1052">
-        <rdfs:label>URL</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1047"/>
-        <oboInOwl:hasDefinition>A Uniform Resource Locator (URL).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:URL</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Link</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1053 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1053">
-        <rdfs:label>URN</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1047"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A Uniform Resource Name (URN).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1055 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1055">
-        <rdfs:label>LSID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1053"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:&lt;Authority&gt;:&lt;Namespace&gt;:&lt;ObjectID&gt;[:&lt;Version&gt;]</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Life Science Identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A Life Science Identifier (LSID) - a unique identifier of some data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1056 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1056">
-        <rdfs:label>Database name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1048"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a biological or bioinformatics database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1057 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1057">
-        <rdfs:label>Sequence database name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The name of a molecular sequence database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1056"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1058 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1058">
-        <rdfs:label>Enumerated file name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1050"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a file (of any type) with restricted possible values.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1059 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1059">
-        <rdfs:label>File name extension</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1050"/>
-        <oboInOwl:hasDefinition>The extension of a file name.</oboInOwl:hasDefinition>
-        <rdfs:comment>A file extension is the characters appearing after the final &apos;.&apos; in the file name.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1060 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1060">
-        <rdfs:label>File base name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1050"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The base name of a file.</oboInOwl:hasDefinition>
-        <rdfs:comment>A file base name is the file name stripped of its directory specification and extension.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1061 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1061">
-        <rdfs:label>QSAR descriptor name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2110"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0847"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a QSAR descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1062 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1062">
-        <rdfs:label>Database entry identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This concept is required for completeness. It should never have child concepts.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1063 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1063">
-        <rdfs:label>Sequence identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of molecular sequence(s) or entries from a molecular sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1064 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1064">
-        <rdfs:label>Sequence set ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0850"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a set of molecular sequence(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1065 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1065">
-        <rdfs:label>Sequence signature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1114"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1115"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1066 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1066">
-        <rdfs:label>Sequence alignment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a molecular sequence alignment, for example a record from an alignment database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1067 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1067">
-        <rdfs:label>Phylogenetic distance matrix identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a phylogenetic distance matrix.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1068 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1068">
-        <rdfs:label>Phylogenetic tree ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a phylogenetic tree for example from a phylogenetic tree database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1069 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1069">
-        <rdfs:label>Comparison matrix identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0874"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a comparison matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1070 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1070">
-        <rdfs:label>Structure ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3035"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1071 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1071">
-        <rdfs:label>Structural (3D) profile ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structural profile identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1072 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1072">
-        <rdfs:label>Structure alignment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0886"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of tertiary structure alignments.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1073 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1073">
-        <rdfs:label>Amino acid index ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1501"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an index of amino acid physicochemical and biochemical property data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1074 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1074">
-        <rdfs:label>Protein interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasBroadSynonym>Molecular interaction ID</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Identifier of a report of protein interactions from a protein interaction database (typically).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1075 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1075">
-        <rdfs:label>Protein family identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Protein secondary database record identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a protein family.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1076 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1076">
-        <rdfs:label>Codon usage table name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2111"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Unique name of a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1077">
-        <rdfs:label>Transcription factor identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <oboInOwl:hasDefinition>Identifier of a transcription factor (or a TF binding site).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1078">
-        <rdfs:label>Experiment annotation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of microarray data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1079 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1079">
-        <rdfs:label>Electron microscopy model ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0941"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of electron microscopy data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1080">
-        <rdfs:label>Gene expression report ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession of a report of gene expression (e.g. a gene expression profile) from a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression profile identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1081">
-        <rdfs:label>Genotype and phenotype annotation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0920"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1082 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1082">
-        <rdfs:label>Pathway or network identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of biological pathways or networks.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1083">
-        <rdfs:label>Workflow ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological or biomedical workflow, typically from a database of workflows.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1084">
-        <rdfs:label>Data resource definition ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a data type definition from some provider.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Data resource definition identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1085">
-        <rdfs:label>Biological model ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0950"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Biological model identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a mathematical model, typically an entry from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1086 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1086">
-        <rdfs:label>Compound identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0962"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of chemicals.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Small molecule identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1087 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1087">
-        <rdfs:label>Ontology concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3025"/>
-        <oboInOwl:hasDefinition>A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology concept ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1088 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1088">
-        <rdfs:label>Article ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0971"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a scientific article.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Article identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1089 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1089">
-        <rdfs:label>FlyBase ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>Identifier of an object from the FlyBase database.</oboInOwl:hasDefinition>
-        <regex>FB[a-zA-Z_0-9]{2}[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1091 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1091">
-        <rdfs:label>WormBase name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <oboInOwl:hasDefinition>Name of an object from the WormBase database, usually a human-readable name.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1092">
-        <rdfs:label>WormBase class</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Class of an object from the WormBase database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A WormBase class describes the type of object such as &apos;sequence&apos; or &apos;protein&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1093 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1093">
-        <rdfs:label>Sequence accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1063"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A persistent, unique identifier of a molecular sequence database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1094">
-        <rdfs:label>Sequence type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).</rdfs:comment>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of molecular sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1095 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1095">
-        <rdfs:label>EMBOSS Uniform Sequence Address</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1063"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasExactSynonym>EMBOSS USA</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1096 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1096">
-        <rdfs:label>Sequence accession (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1093"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2976"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession number of a protein sequence database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein sequence accession number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1097">
-        <rdfs:label>Sequence accession (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1093"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession number of a nucleotide sequence database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1098 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1098">
-        <rdfs:label>RefSeq accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2362"/>
-        <oboInOwl:hasDefinition>Accession number of a RefSeq database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>RefSeq ID</oboInOwl:hasExactSynonym>
-        <regex>(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1099">
-        <rdfs:label>UniProt accession (extended)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number.</oboInOwl:hasDefinition>
-        <regex>[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <example>Q7M1G0|P43353-2|P01012.107</example>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3021"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1100">
-        <rdfs:label>PIR identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of PIR sequence database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PIR ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PIR accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1101 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1101">
-        <rdfs:label>TREMBL accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a TREMBL sequence database entry.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.2</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_3021"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1102">
-        <rdfs:label>Gramene primary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2915"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gramene primary ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Primary identifier of a Gramene database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1103 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1103">
-        <rdfs:label>EMBL/GenBank/DDBJ ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <oboInOwl:hasDefinition>Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1104 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1104">
-        <rdfs:label>Sequence cluster ID (UniGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasExactSynonym>UniGene identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniGene cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniGene ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniGene cluster ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of an entry (gene cluster) from the NCBI UniGene database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1105 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1105">
-        <rdfs:label>dbEST accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2292"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <oboInOwl:hasExactSynonym>dbEST ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a dbEST database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1106 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1106">
-        <rdfs:label>dbSNP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>dbSNP identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a dbSNP database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1110">
-        <rdfs:label>EMBOSS sequence type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The EMBOSS type of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1111">
-        <rdfs:label>EMBOSS listfile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1112">
-        <rdfs:label>Sequence cluster ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1064"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a cluster of molecular sequence(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1113 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1113">
-        <rdfs:label>Sequence cluster ID (COG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasExactSynonym>COG ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the COG database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1114 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1114">
-        <rdfs:label>Sequence motif identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1353"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a sequence motif, for example an entry from a motif database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1115 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1115">
-        <rdfs:label>Sequence profile ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a sequence profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A sequence profile typically represents a sequence alignment.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1116 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1116">
-        <rdfs:label>ELM ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1114"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the ELMdb database of protein functional sites.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1117 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1117">
-        <rdfs:label>Prosite accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1114"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry from the Prosite database.</oboInOwl:hasDefinition>
-        <regex>PS[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>Prosite ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1118">
-        <rdfs:label>HMMER hidden Markov model ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1115"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1364"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Unique identifier or name of a HMMER hidden Markov model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1119 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1119">
-        <rdfs:label>JASPAR profile ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1115"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier or name of a profile from the JASPAR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1120 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1120">
-        <rdfs:label>Sequence alignment type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1121 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1121">
-        <rdfs:label>BLAST sequence alignment type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The type of a BLAST sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1122">
-        <rdfs:label>Phylogenetic tree type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>For example &apos;nj&apos;, &apos;upgmp&apos; etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <example>nj|upgmp</example>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1123">
-        <rdfs:label>TreeBASE study accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1068"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the TreeBASE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1124 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1124">
-        <rdfs:label>TreeFam accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1068"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry from the TreeFam database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1125 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1125">
-        <rdfs:label>Comparison matrix type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <example>blosum|pam|gonnet|id</example>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a comparison matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix type</oboInOwl:hasExactSynonym>
-        <rdfs:comment>For example &apos;blosum&apos;, &apos;pam&apos;, &apos;gonnet&apos;, &apos;id&apos; etc. Comparison matrix type may be required where a series of matrices of a certain type are used.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1126">
-        <rdfs:label>Comparison matrix name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1069"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0874"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Substitution matrix name</oboInOwl:hasExactSynonym>
-        <rdfs:comment>See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.</rdfs:comment>
-        <oboInOwl:hasDefinition>Unique name or identifier of a comparison matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1127">
-        <rdfs:label>PDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1070"/>
-        <oboInOwl:hasDefinition>An identifier of an entry from the PDB database.</oboInOwl:hasDefinition>
-        <regex>[a-zA-Z_0-9]{4}</regex>
-        <oboInOwl:hasExactSynonym>PDBID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PDB identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1128">
-        <rdfs:label>AAindex ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1073"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the AAindex database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1129 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1129">
-        <rdfs:label>BIND accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the BIND database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1130">
-        <rdfs:label>IntAct accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>EBI\-[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry from the IntAct database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1131 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1131">
-        <rdfs:label>Protein family name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1075"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a protein family.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1132 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1132">
-        <rdfs:label>InterPro entry name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1131"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of an InterPro entry, usually indicating the type of protein matches for that entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1133">
-        <rdfs:label>InterPro accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Primary accession number of an InterPro entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>InterPro primary accession</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Every InterPro entry has a unique accession number to provide a persistent citation of database records.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>InterPro primary accession number</oboInOwl:hasExactSynonym>
-        <example>IPR015590</example>
-        <regex>IPR[0-9]{6}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1134">
-        <rdfs:label>InterPro secondary accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1133"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Secondary accession number of an InterPro entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>InterPro secondary accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1135">
-        <rdfs:label>Gene3D ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the Gene3D database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1136 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1136">
-        <rdfs:label>PIRSF ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <regex>PIRSF[0-9]{6}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the PIRSF database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1137">
-        <rdfs:label>PRINTS code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PR[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>The unique identifier of an entry in the PRINTS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1138 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1138">
-        <rdfs:label>Pfam accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <regex>PF[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Accession number of a Pfam entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1139">
-        <rdfs:label>SMART accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the SMART database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>SM[0-9]{5}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1140">
-        <rdfs:label>Superfamily hidden Markov model number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>Unique identifier (number) of a hidden Markov model from the Superfamily database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1141">
-        <rdfs:label>TIGRFam ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasExactSynonym>TIGRFam accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of an entry (family) from the TIGRFam database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1142 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1142">
-        <rdfs:label>ProDom accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>A ProDom domain family accession number.</oboInOwl:hasDefinition>
-        <regex>PD[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>ProDom is a protein domain family database.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1143">
-        <rdfs:label>TRANSFAC accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2911"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the TRANSFAC database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1144 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1144">
-        <rdfs:label>ArrayExpress accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the ArrayExpress database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[AEP]-[a-zA-Z_0-9]{4}-[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>ArrayExpress experiment ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1145 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1145">
-        <rdfs:label>PRIDE experiment accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PRIDE experiment accession number.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1146 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1146">
-        <rdfs:label>EMDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1079"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the EMDB electron microscopy database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1147">
-        <rdfs:label>GEO accession number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the GEO database.</oboInOwl:hasDefinition>
-        <regex>o^GDS[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1148 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1148">
-        <rdfs:label>GermOnline ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GermOnline database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1149 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1149">
-        <rdfs:label>EMAGE ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the EMAGE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1150 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1150">
-        <rdfs:label>Disease ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1622"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of disease.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1151 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1151">
-        <rdfs:label>HGVbase ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1081"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the HGVbase database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1152 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1152">
-        <rdfs:label>HIVDB identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the HIVDB database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1153 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1153">
-        <rdfs:label>OMIM ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1081"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[*#+%^]?[0-9]{6}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry from the OMIM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1154">
-        <rdfs:label>KEGG object identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of an object from one of the KEGG databases (excluding the GENES division).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1155 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1155">
-        <rdfs:label>Pathway ID (reactome)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Reactome database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Reactome ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <regex>REACT_[0-9]+(\.[0-9]+)?</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1156">
-        <rdfs:label>Pathway ID (aMAZE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>aMAZE ID</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the aMAZE database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1082"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1157">
-        <rdfs:label>Pathway ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasExactSynonym>BioCyc pathway ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an pathway from the BioCyc biological pathways database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1158">
-        <rdfs:label>Pathway ID (INOH)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>INOH identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from the INOH database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1159">
-        <rdfs:label>Pathway ID (PATIKA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the PATIKA database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>PATIKA ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1160">
-        <rdfs:label>Pathway ID (CPDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <rdfs:comment>This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>CPDB ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1161 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1161">
-        <rdfs:label>Pathway ID (Panther)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of a biological pathway from the Panther Pathways database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PTHR[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>Panther Pathways ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1162 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1162">
-        <rdfs:label>MIRIAM identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2902"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Unique identifier of a MIRIAM data resource.</oboInOwl:hasDefinition>
-        <example>MIR:00100005</example>
-        <regex>MIR:[0-9]{8}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is the identifier used internally by MIRIAM for a data type.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1163">
-        <rdfs:label>MIRIAM data type name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2253"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a data type from the MIRIAM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1164">
-        <rdfs:label>MIRIAM URI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1047"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2902"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0957"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The URI (URL or URN) of a data entity from the MIRIAM database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>identifiers.org synonym</oboInOwl:hasExactSynonym>
-        <example>urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202</example>
-        <rdfs:comment>A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1165 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1165">
-        <rdfs:label>MIRIAM data type primary name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1163"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The primary name of a MIRIAM data type is taken from a controlled vocabulary.</rdfs:comment>
-        <example>UniProt|Enzyme Nomenclature</example>
-        <oboInOwl:hasDefinition>The primary name of a data type from the MIRIAM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>A protein entity has the MIRIAM data type &apos;UniProt&apos;, and an enzyme has the MIRIAM data type &apos;Enzyme Nomenclature&apos;.</rdfs:comment>
-        <owl:annotatedTarget>UniProt|Enzyme Nomenclature</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_1165"/>
-        <owl:annotatedProperty rdf:resource="http://edamontology.org/example"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_1166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1166">
-        <rdfs:label>MIRIAM data type synonymous name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1163"/>
-        <oboInOwl:hasDefinition>A synonymous name of a data type from the MIRIAM database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A synonymous name for a MIRIAM data type taken from a controlled vocabulary.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1167">
-        <rdfs:label>Taverna workflow ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1083"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a Taverna workflow.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1170 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1170">
-        <rdfs:label>Biological model name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1085"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a biological (mathematical) model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1171 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1171">
-        <rdfs:label>BioModel ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2891"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the BioModel database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>(BIOMD|MODEL)[0-9]{10}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1172">
-        <rdfs:label>PubChem CID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2639"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>[0-9]+</regex>
-        <oboInOwl:hasExactSynonym>PubChem compound accession identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1173">
-        <rdfs:label>ChemSpider ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the ChemSpider database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1174">
-        <rdfs:label>ChEBI ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the ChEBI database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChEBI IDs</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>ChEBI identifier</oboInOwl:hasExactSynonym>
-        <regex>CHEBI:[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1175">
-        <rdfs:label>BioPax concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the BioPax ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1176">
-        <rdfs:label>GO concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasExactSynonym>GO concept identifier</oboInOwl:hasExactSynonym>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from The Gene Ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1177">
-        <rdfs:label>MeSH concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the MeSH vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1178">
-        <rdfs:label>HGNC concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the HGNC controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1179">
-        <rdfs:label>NCBI taxonomy ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <oboInOwl:hasExactSynonym>NCBI taxonomy identifier</oboInOwl:hasExactSynonym>
-        <regex>[1-9][0-9]{0,8}</regex>
-        <oboInOwl:hasExactSynonym>NCBI tax ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database.</oboInOwl:hasDefinition>
-        <example>9662|3483|182682</example>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1180">
-        <rdfs:label>Plant Ontology concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasDefinition>An identifier of a concept from the Plant Ontology (PO).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1181 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1181">
-        <rdfs:label>UMLS concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasDefinition>An identifier of a concept from the UMLS vocabulary.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1182">
-        <rdfs:label>FMA concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <oboInOwl:hasDefinition>An identifier of a concept from Foundational Model of Anatomy.</oboInOwl:hasDefinition>
-        <regex>FMA:[0-9]+</regex>
-        <rdfs:comment>Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1183">
-        <rdfs:label>EMAP concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the EMAP mouse ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1184">
-        <rdfs:label>ChEBI concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the ChEBI ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1185 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1185">
-        <rdfs:label>MGED concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a concept from the MGED ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1186 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1186">
-        <rdfs:label>myGrid concept ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.</rdfs:comment>
-        <oboInOwl:hasDefinition>An identifier of a concept from the myGrid ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1187 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1187">
-        <rdfs:label>PubMed ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1088"/>
-        <oboInOwl:hasExactSynonym>PMID</oboInOwl:hasExactSynonym>
-        <regex>[1-9][0-9]{0,8}</regex>
-        <oboInOwl:hasDefinition>PubMed unique identifier of an article.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <example>4963447</example>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1188 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1188">
-        <rdfs:label>DOI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1088"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>(doi\:)?[0-9]{2}\.[0-9]{4}/.*</regex>
-        <oboInOwl:hasExactSynonym>Digital Object Identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Digital Object Identifier (DOI) of a published article.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1189 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1189">
-        <rdfs:label>Medline UI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Medline UI (unique identifier) of an article.</oboInOwl:hasDefinition>
-        <rdfs:comment>The use of Medline UI has been replaced by the PubMed unique identifier.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Medline unique identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1190 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1190">
-        <rdfs:label>Tool name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0977"/>
-        <oboInOwl:hasDefinition>The name of a computer package, application, method or function.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1191">
-        <rdfs:label>Tool name (signature)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The unique name of a signature (sequence classifier) method.</oboInOwl:hasDefinition>
-        <rdfs:comment>Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1192 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1192">
-        <rdfs:label>Tool name (BLAST)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <rdfs:comment>This include &apos;blastn&apos;, &apos;blastp&apos;, &apos;blastx&apos;, &apos;tblastn&apos; and &apos;tblastx&apos;.</rdfs:comment>
-        <oboInOwl:hasDefinition>The name of a BLAST tool.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>BLAST name</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1193 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1193">
-        <rdfs:label>Tool name (FASTA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a FASTA tool.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes &apos;fasta3&apos;, &apos;fastx3&apos;, &apos;fasty3&apos;, &apos;fastf3&apos;, &apos;fasts3&apos; and &apos;ssearch&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1194">
-        <rdfs:label>Tool name (EMBOSS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <oboInOwl:hasDefinition>The name of an EMBOSS application.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1195">
-        <rdfs:label>Tool name (EMBASSY package)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1190"/>
-        <oboInOwl:hasDefinition>The name of an EMBASSY package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1201 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1201">
-        <rdfs:label>QSAR descriptor (constitutional)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <oboInOwl:hasDefinition>A QSAR constitutional descriptor.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>QSAR constitutional descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1202">
-        <rdfs:label>QSAR descriptor (electronic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A QSAR electronic descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>QSAR electronic descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1203">
-        <rdfs:label>QSAR descriptor (geometrical)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <oboInOwl:hasExactSynonym>QSAR geometrical descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A QSAR geometrical descriptor.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1204">
-        <rdfs:label>QSAR descriptor (topological)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>QSAR topological descriptor</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A QSAR topological descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1205 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1205">
-        <rdfs:label>QSAR descriptor (molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0847"/>
-        <oboInOwl:hasDefinition>A QSAR molecular descriptor.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>QSAR molecular descriptor</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1233">
-        <rdfs:label>Sequence set (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:hasDefinition>Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1234 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1234">
-        <rdfs:label>Sequence set (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0850"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1235">
-        <rdfs:label>Sequence cluster</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0850"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0724"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.</oboInOwl:hasDefinition>
-        <rdfs:comment>The cluster might include sequences identifiers, short descriptions, alignment and summary information.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1236">
-        <rdfs:label>Psiblast checkpoint file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension &apos;.asn&apos;.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1237">
-        <rdfs:label>HMMER synthetic sequences set</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Sequences generated by HMMER package in FASTA-style format.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1238">
-        <rdfs:label>Proteolytic digest</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1239">
-        <rdfs:label>Restriction digest</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <oboInOwl:hasDefinition>Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>SO:0000412</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1240">
-        <rdfs:label>PCR primers</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1241">
-        <rdfs:label>vectorstrip cloning vector definition file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1242">
-        <rdfs:label>Primer3 internal oligo mishybridizing library</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1243">
-        <rdfs:label>Primer3 mispriming library file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1244 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1244">
-        <rdfs:label>primersearch primer pairs sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>File of one or more pairs of primer sequences, as used by EMBOSS primersearch application.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1245">
-        <rdfs:label>Sequence cluster (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1233"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:hasExactSynonym>Protein sequence cluster</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The sequences are typically related, for example a family of sequences.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A cluster of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1246">
-        <rdfs:label>Sequence cluster (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1234"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:hasDefinition>A cluster of nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence cluster</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The sequences are typically related, for example a family of sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1249 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1249">
-        <rdfs:label>Sequence length</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1250">
-        <rdfs:label>Word size</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Word size is used for example in word-based sequence database search methods.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Word length</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Size of a sequence word.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1251 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1251">
-        <rdfs:label>Window size</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Size of a sequence window.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1252">
-        <rdfs:label>Sequence length range</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Specification of range(s) of length of sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1253">
-        <rdfs:label>Sequence information report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2043"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1254">
-        <rdfs:label>Sequence property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2955"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence properties report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1255 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1255">
-        <rdfs:label>Sequence features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Sequence features report</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D058977</rdfs:seeAlso>
-        <oboInOwl:hasRelatedSynonym>SO:0000110</oboInOwl:hasRelatedSynonym>
-        <rdfs:comment>This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features.  General feature reports are a source of sequence feature table information although internal conversion would be required.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>General sequence features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Feature record</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1256 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1256">
-        <rdfs:label>Sequence features (comparative)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1257">
-        <rdfs:label>Sequence property (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report of general sequence properties derived from protein sequence data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1258">
-        <rdfs:label>Sequence property (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report of general sequence properties derived from nucleotide sequence data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0912"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1259">
-        <rdfs:label>Sequence complexity report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1254"/>
-        <oboInOwl:hasDefinition>A report on sequence complexity, for example low-complexity or repeat regions in sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence property (complexity)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1260 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1260">
-        <rdfs:label>Sequence ambiguity report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1254"/>
-        <oboInOwl:hasDefinition>A report on ambiguity in molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence property (ambiguity)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1261 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1261">
-        <rdfs:label>Sequence composition report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1254"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report (typically a table) on character or word composition / frequency of a molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence property (composition)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1262 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1262">
-        <rdfs:label>Peptide molecular weight hits</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1233"/>
-        <oboInOwl:hasDefinition>A report on peptide fragments of certain molecular weight(s) in one or more protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1263 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1263">
-        <rdfs:label>Base position variability plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of third base position variability in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1264">
-        <rdfs:label>Sequence composition table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A table of character or word composition / frequency of a molecular sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1265">
-        <rdfs:label>Base frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A table of base frequencies of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1266 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1266">
-        <rdfs:label>Base word frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A table of word composition of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1267 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1267">
-        <rdfs:label>Amino acid frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasExactSynonym>Sequence composition (amino acid frequencies)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A table of amino acid frequencies of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1268 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1268">
-        <rdfs:label>Amino acid word frequencies table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A table of amino acid word composition of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence composition (amino acid words)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1269">
-        <rdfs:label>DAS sequence feature annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Annotation of a molecular sequence in DAS format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1978"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1270 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1270">
-        <rdfs:label>Feature table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:hasExactSynonym>Sequence feature table</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation of positional sequence features, organized into a standard feature table.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1274 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1274">
-        <rdfs:label>Map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>DNA map</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A map of (typically one) DNA sequence annotated with positional or non-positional features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1276 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1276">
-        <rdfs:label>Nucleic acid features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:hasDefinition>An informative report on intrinsic positional features of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Genome features</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Genomic features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid feature table</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Feature table (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1277">
-        <rdfs:label>Protein features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:hasDefinition>An informative report on intrinsic positional features of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Feature table (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein feature table</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1278">
-        <rdfs:label>Genetic map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1274"/>
-        <oboInOwl:hasDefinition>A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Linkage map</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:GeneticMap</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1279 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1279">
-        <rdfs:label>Sequence map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1280"/>
-        <rdfs:comment>A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1280">
-        <rdfs:label>Physical map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1274"/>
-        <oboInOwl:hasDefinition>A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them.</oboInOwl:hasDefinition>
-        <rdfs:comment>Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1281 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1281">
-        <rdfs:label>Sequence signature map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Image of a sequence with matches to signatures, motifs or profiles.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1283 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1283">
-        <rdfs:label>Cytogenetic map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1280"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A map showing banding patterns derived from direct observation of a stained chromosome.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Cytologic map</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Chromosome map</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Cytogenic map</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances.  Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1284">
-        <rdfs:label>DNA transduction map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1278"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A gene map showing distances between loci based on relative cotransduction frequencies.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1285">
-        <rdfs:label>Gene map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <oboInOwl:hasDefinition>Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1286 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1286">
-        <rdfs:label>Plasmid map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <oboInOwl:hasDefinition>Sequence map of a plasmid (circular DNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1288">
-        <rdfs:label>Genome map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence map of a whole genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1289">
-        <rdfs:label>Restriction map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1279"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2969"/>
-        <oboInOwl:hasDefinition>Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1290 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1290">
-        <rdfs:label>InterPro compact match image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Image showing matches between protein sequence(s) and InterPro Entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1291 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1291">
-        <rdfs:label>InterPro detailed match image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image showing detailed information on matches between protein sequence(s) and InterPro Entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1292">
-        <rdfs:label>InterPro architecture image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein.</rdfs:comment>
-        <oboInOwl:hasDefinition>Image showing the architecture of InterPro domains in a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1293">
-        <rdfs:label>SMART protein schematic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>SMART protein schematic in PNG format.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1294 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1294">
-        <rdfs:label>GlobPlot domain image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1298">
-        <rdfs:label>Sequence motif matches</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1299">
-        <rdfs:label>Sequence features (repeats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Repeat sequence map</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The report might include derived data map such as classification, annotation, organization, periodicity etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3126"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3129"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1300">
-        <rdfs:label>Gene and transcript structure (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1301">
-        <rdfs:label>Mobile genetic elements</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>regions of a nucleic acid sequence containing mobile genetic elements.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1302">
-        <rdfs:label>Nucleic acid features report (PolyA signal or site)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1303">
-        <rdfs:label>Nucleic acid features (quadruplexes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report on quadruplex-forming motifs in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1304">
-        <rdfs:label>Nucleic acid features report (CpG island and isochore)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>CpG rich regions (isochores) in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1305">
-        <rdfs:label>Nucleic acid features report (restriction sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1306">
-        <rdfs:label>Nucleosome exclusion sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Report on nucleosome formation potential or exclusion sequence(s).</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1307">
-        <rdfs:label>Nucleic acid features report (splice sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>splice sites in a nucleotide sequence or alternative RNA splicing events.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1308">
-        <rdfs:label>Nucleic acid features report (matrix/scaffold attachment sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1309">
-        <rdfs:label>Gene features (exonic splicing enhancer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on exonic splicing enhancers (ESE) in an exon.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1310">
-        <rdfs:label>Nucleic acid features (microRNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3137"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1311">
-        <rdfs:label>Gene features report (operon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>operons (operators, promoters and genes) from a bacterial genome.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1312">
-        <rdfs:label>Nucleic acid features report (promoters)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1313">
-        <rdfs:label>Coding region</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1314">
-        <rdfs:label>Gene features (SECIS element)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1315">
-        <rdfs:label>Transcription factor binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>transcription factor binding sites (TFBS) in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1321">
-        <rdfs:label>Protein features (sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1322">
-        <rdfs:label>Protein features report (signal peptides)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>signal peptides or signal peptide cleavage sites in protein sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1323">
-        <rdfs:label>Protein features report (cleavage sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1324 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1324">
-        <rdfs:label>Protein features (post-translation modifications)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>post-translation modifications in a protein sequence, typically describing the specific sites involved.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1325">
-        <rdfs:label>Protein features report (active sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>catalytic residues (active site) of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1326">
-        <rdfs:label>Protein features report (binding sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1327">
-        <rdfs:label>Protein features (epitopes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Epitope mapping is commonly done during vaccine design.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1326"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1328">
-        <rdfs:label>Protein features report (nucleic acid binding sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>RNA and DNA-binding proteins and binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1329">
-        <rdfs:label>MHC Class I epitopes report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on epitopes that bind to MHC class I molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1326"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1330">
-        <rdfs:label>MHC Class II epitopes report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on predicted epitopes that bind to MHC class II molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1326"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1331">
-        <rdfs:label>Protein features (PEST sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report or plot of PEST sites in a protein sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>&apos;PEST&apos; motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1323"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1338">
-        <rdfs:label>Sequence database hits scores list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Scores from a sequence database search (for example a BLAST search).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0857"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1339">
-        <rdfs:label>Sequence database hits alignments list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignments from a sequence database search (for example a BLAST search).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0857"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1340">
-        <rdfs:label>Sequence database hits evaluation data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0857"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1344">
-        <rdfs:label>MEME motif alphabet</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alphabet for the motifs (patterns) that MEME will search for.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1345">
-        <rdfs:label>MEME background frequencies file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>MEME background frequencies file.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1346">
-        <rdfs:label>MEME motifs directive file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>File of directives for ordering and spacing of MEME motifs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1347 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1347">
-        <rdfs:label>Dirichlet distribution</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:hasDefinition>Dirichlet distribution used by hidden Markov model analysis programs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1348">
-        <rdfs:label>HMM emission and transition counts</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3354"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1352">
-        <rdfs:label>Regular expression</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Regular expression pattern.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1353">
-        <rdfs:label>Sequence motif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0860"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1354">
-        <rdfs:label>Sequence profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0860"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Some type of statistical model representing a (typically multiple) sequence alignment.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_010531</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1355">
-        <rdfs:label>Protein signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2762"/>
-        <oboInOwl:hasDefinition>An informative report about a specific or conserved protein sequence pattern.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>InterPro entry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein repeat signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein region signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein site signature</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein family signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein domain signature</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1358">
-        <rdfs:label>Prosite nucleotide pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A nucleotide regular expression pattern from the Prosite database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1353"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1359">
-        <rdfs:label>Prosite protein pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein regular expression pattern from the Prosite database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1353"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1361 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1361">
-        <rdfs:label>Position frequency matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PFM</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1362 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1362">
-        <rdfs:label>Position weight matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <oboInOwl:hasExactSynonym>PWM</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.</oboInOwl:hasDefinition>
-        <rdfs:comment>Contributions of individual sequences to the matrix might be uneven (weighted).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1363 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1363">
-        <rdfs:label>Information content matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>ICM</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1364 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1364">
-        <rdfs:label>Hidden Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1354"/>
-        <oboInOwl:hasExactSynonym>HMM</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A hidden Markov model representation of a set or alignment of sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1365">
-        <rdfs:label>Fingerprint</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2854"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>One or more fingerprints (sequence classifiers) as used in the PRINTS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1368">
-        <rdfs:label>Domainatrix signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein signature of the type used in the EMBASSY Signature package.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1354"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1371">
-        <rdfs:label>HMMER NULL hidden Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>NULL hidden Markov model representation used by the HMMER package.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1364"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1372">
-        <rdfs:label>Protein family signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Protein family signatures cover all domains in the matching proteins and span &gt;80% of the protein length and with no adjacent protein domain signatures or protein region signatures.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A protein family signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1373 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1373">
-        <rdfs:label>Protein domain signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A protein domain signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <rdfs:comment>Protein domain signatures identify structural or functional domains or other units with defined boundaries.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1374 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1374">
-        <rdfs:label>Protein region signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein region signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>A protein region signature defines a region which cannot be described as a protein family or domain signature.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1375 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1375">
-        <rdfs:label>Protein repeat signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein repeat signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1376 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1376">
-        <rdfs:label>Protein site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>A protein site signature is a classifier for a specific site in a protein.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1355"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1377 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1377">
-        <rdfs:label>Protein conserved site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification.</rdfs:comment>
-        <oboInOwl:hasDefinition>A protein conserved site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1378">
-        <rdfs:label>Protein active site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein active site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1379">
-        <rdfs:label>Protein binding site signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>A protein binding site signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1380 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1380">
-        <rdfs:label>Protein post-translational modification signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein post-translational modification signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible.</rdfs:comment>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1381 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1381">
-        <rdfs:label>Sequence alignment (pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_010068</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1382 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1382">
-        <rdfs:label>Sequence alignment (multiple)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of more than two molecular sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1383">
-        <rdfs:label>Sequence alignment (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of multiple nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1384">
-        <rdfs:label>Sequence alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3154"/>
-        <oboInOwl:hasDefinition>Alignment of multiple protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1385">
-        <rdfs:label>Sequence alignment (hybrid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:hasDefinition>Alignment of multiple molecular sequences of different types.</oboInOwl:hasDefinition>
-        <rdfs:comment>Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1386">
-        <rdfs:label>Sequence alignment (nucleic acid pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1381"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1383"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment of exactly two nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1387">
-        <rdfs:label>Sequence alignment (protein pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1381"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1384"/>
-        <oboInOwl:hasDefinition>Alignment of exactly two protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1388">
-        <rdfs:label>Hybrid sequence alignment (pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of exactly two molecular sequences of different types.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1385"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1389 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1389">
-        <rdfs:label>Multiple nucleotide sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of more than two nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1390">
-        <rdfs:label>Multiple protein sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of more than two protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0863"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1394 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1394">
-        <rdfs:label>Alignment score or penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2527"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for opening or extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1395">
-        <rdfs:label>Score end gaps control</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Whether end gaps are scored or not.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1396">
-        <rdfs:label>Aligned sequence order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Controls the order of sequences in an output sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1397">
-        <rdfs:label>Gap opening penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2137"/>
-        <oboInOwl:hasDefinition>A penalty for opening a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1398">
-        <rdfs:label>Gap extension penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2137"/>
-        <oboInOwl:hasDefinition>A penalty for extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1399">
-        <rdfs:label>Gap separation penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2137"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A penalty for gaps that are close together in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1400">
-        <rdfs:label>Terminal gap penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5&apos;/3&apos; terminal of nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1410"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1411"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1401">
-        <rdfs:label>Match reward score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The score for a &apos;match&apos; used in various sequence database search applications with simple scoring schemes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1402">
-        <rdfs:label>Mismatch penalty score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The score (penalty) for a &apos;mismatch&apos; used in various alignment and sequence database search applications with simple scoring schemes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1403">
-        <rdfs:label>Drop off score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <oboInOwl:hasDefinition>This is the threshold drop in score at which extension of word alignment is halted.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1404">
-        <rdfs:label>Gap opening penalty (integer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for opening a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1405">
-        <rdfs:label>Gap opening penalty (float)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for opening a gap in an alignment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1406">
-        <rdfs:label>Gap extension penalty (integer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1398"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1407">
-        <rdfs:label>Gap extension penalty (float)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1398"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1408">
-        <rdfs:label>Gap separation penalty (integer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for gaps that are close together in an alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1409">
-        <rdfs:label>Gap separation penalty (float)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple floating point number defining the penalty for gaps that are close together in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1410">
-        <rdfs:label>Terminal gap opening penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1397"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5&apos;/3&apos; terminal of nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1411">
-        <rdfs:label>Terminal gap extension penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1398"/>
-        <oboInOwl:hasDefinition>A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5&apos;/3&apos; terminal of nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1412">
-        <rdfs:label>Sequence identity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0865"/>
-        <oboInOwl:hasDefinition>Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1413">
-        <rdfs:label>Sequence similarity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0865"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension.</oboInOwl:hasDefinition>
-        <rdfs:comment>Data Type is float probably.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1414">
-        <rdfs:label>Sequence alignment metadata (quality report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Data on molecular sequence alignment quality (estimated accuracy).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1415">
-        <rdfs:label>Sequence alignment report (site conservation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on character conservation in a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2161"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1416">
-        <rdfs:label>Sequence alignment report (site correlation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1417">
-        <rdfs:label>Sequence-profile alignment (Domainatrix signature)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1418 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1418">
-        <rdfs:label>Sequence-profile alignment (HMM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Alignment of molecular sequence(s) to a hidden Markov model(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1420">
-        <rdfs:label>Sequence-profile alignment (fingerprint)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment of molecular sequences to a protein fingerprint from the PRINTS database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1426">
-        <rdfs:label>Phylogenetic continuous quantitative data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0871"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic continuous quantitative characters</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Quantitative traits</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Continuous quantitative data that may be read during phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1427">
-        <rdfs:label>Phylogenetic discrete data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0871"/>
-        <oboInOwl:hasExactSynonym>Discrete characters</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Character data with discrete states that may be read during phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic discrete states</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Discretely coded characters</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1428">
-        <rdfs:label>Phylogenetic character cliques</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasDefinition>One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic report (cliques)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1429">
-        <rdfs:label>Phylogenetic invariants</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Phylogenetic invariants data for testing alternative tree topologies.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic report (invariants)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1438">
-        <rdfs:label>Phylogenetic report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree report</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Phylogenetic report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree-derived report</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used  for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1439">
-        <rdfs:label>DNA substitution model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:hasExactSynonym>Substitution model</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree report (DNA substitution model)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment report (DNA substitution model)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1440">
-        <rdfs:label>Phylogenetic tree report (tree shape)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>Data about the shape of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1441">
-        <rdfs:label>Phylogenetic tree report (tree evaluation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>Data on the confidence of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1442">
-        <rdfs:label>Phylogenetic tree distances</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree report (tree distances)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Distances, such as Branch Score distance, between two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1443">
-        <rdfs:label>Phylogenetic tree report (tree stratigraphic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1444">
-        <rdfs:label>Phylogenetic character contrasts</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic report (character contrasts)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1446">
-        <rdfs:label>Comparison matrix (integers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Substitution matrix (integers)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer numbers for sequence comparison.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0874"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1447">
-        <rdfs:label>Comparison matrix (floats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Matrix of floating point numbers for sequence comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Substitution matrix (floats)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0874"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1448">
-        <rdfs:label>Comparison matrix (nucleotide)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0874"/>
-        <oboInOwl:hasDefinition>Matrix of integer or floating point numbers for nucleotide comparison.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide substitution matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1449 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1449">
-        <rdfs:label>Comparison matrix (amino acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0874"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2016"/>
-        <oboInOwl:hasExactSynonym>Amino acid comparison matrix</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer or floating point numbers for amino acid comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Amino acid substitution matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1450 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1450">
-        <rdfs:label>Nucleotide comparison matrix (integers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Nucleotide substitution matrix (integers)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer numbers for nucleotide comparison.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1448"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1451">
-        <rdfs:label>Nucleotide comparison matrix (floats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Matrix of floating point numbers for nucleotide comparison.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide substitution matrix (floats)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1448"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1452">
-        <rdfs:label>Amino acid comparison matrix (integers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix of integer numbers for amino acid comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Amino acid substitution matrix (integers)</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1449"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1453">
-        <rdfs:label>Amino acid comparison matrix (floats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Amino acid substitution matrix (floats)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Matrix of floating point numbers for amino acid comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1449"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1456">
-        <rdfs:label>Protein features report (membrane regions)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1459">
-        <rdfs:label>Nucleic acid structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a nucleic acid tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1460">
-        <rdfs:label>Protein structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Protein structures</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1461">
-        <rdfs:label>Protein-ligand complex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:hasDefinition>The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides.  For stable inter-polypeptide interactions use &apos;Protein complex&apos; instead.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1462 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1462">
-        <rdfs:label>Carbohydrate structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0153"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0152"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a carbohydrate (3D) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1463">
-        <rdfs:label>Small molecule structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0154"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>CHEBI:23367</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1464">
-        <rdfs:label>DNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1459"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a DNA tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1465">
-        <rdfs:label>RNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1459"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for an RNA tertiary (3D) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1466 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1466">
-        <rdfs:label>tRNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1465"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1467">
-        <rdfs:label>Protein chain</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1468">
-        <rdfs:label>Protein domain</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0736"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the tertiary (3D) structure of a protein domain.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1469">
-        <rdfs:label>Protein structure (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein tertiary (3D) structure (all atoms).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1470">
-        <rdfs:label>C-alpha trace</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only).</oboInOwl:hasDefinition>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein structure (C-alpha atoms)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1471">
-        <rdfs:label>Protein chain (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1467"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1472">
-        <rdfs:label>Protein chain (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1467"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1473">
-        <rdfs:label>Protein domain (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1468"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1474">
-        <rdfs:label>Protein domain (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1468"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1479">
-        <rdfs:label>Structure alignment (pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0886"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Pair structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1480">
-        <rdfs:label>Structure alignment (multiple)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of more than two molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0886"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1481">
-        <rdfs:label>Structure alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0886"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3154"/>
-        <oboInOwl:hasExactSynonym>Protein structure alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of protein tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1482">
-        <rdfs:label>Structure alignment (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0886"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of nucleic acid tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1483">
-        <rdfs:label>Structure alignment (protein pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:hasExactSynonym>Protein pair structural alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1484 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1484">
-        <rdfs:label>Multiple protein tertiary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of more than two protein tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1485">
-        <rdfs:label>Structure alignment (protein all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1486">
-        <rdfs:label>Structure alignment (protein C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered).</oboInOwl:hasDefinition>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be considered.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>C-alpha trace</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1487">
-        <rdfs:label>Pairwise protein tertiary structure alignment (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1488">
-        <rdfs:label>Pairwise protein tertiary structure alignment (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1489">
-        <rdfs:label>Multiple protein tertiary structure alignment (all atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1490">
-        <rdfs:label>Multiple protein tertiary structure alignment (C-alpha atoms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>C-beta atoms from amino acid side-chains may be included.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1491">
-        <rdfs:label>Structure alignment (nucleic acid pair)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1482"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid pair structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1492">
-        <rdfs:label>Multiple nucleic acid tertiary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1482"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1493 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1493">
-        <rdfs:label>Structure alignment (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1482"/>
-        <oboInOwl:hasExactSynonym>RNA structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Alignment (superimposition) of RNA tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1494 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1494">
-        <rdfs:label>Structural transformation matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1495">
-        <rdfs:label>DaliLite hit table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>DaliLite hit table of protein chain tertiary structure alignment data.</oboInOwl:hasDefinition>
-        <rdfs:comment>The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0887"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1496">
-        <rdfs:label>Molecular similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A score reflecting structural similarities of two molecules.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0888"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1497">
-        <rdfs:label>Root-mean-square deviation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0888"/>
-        <oboInOwl:hasExactSynonym>RMSD</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1498">
-        <rdfs:label>Tanimoto similarity score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0888"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A measure of the similarity between two ligand fingerprints.</oboInOwl:hasDefinition>
-        <rdfs:comment>A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1499">
-        <rdfs:label>3D-1D scoring matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0892"/>
-        <oboInOwl:hasDefinition>A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1501">
-        <rdfs:label>Amino acid index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2016"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1502">
-        <rdfs:label>Amino acid index (chemical classes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasExactSynonym>Chemical classes (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1503">
-        <rdfs:label>Amino acid pair-wise contact potentials</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2016"/>
-        <oboInOwl:hasExactSynonym>Contact potentials (amino acid pair-wise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Statistical protein contact potentials.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1505">
-        <rdfs:label>Amino acid index (molecular weight)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasDefinition>Molecular weights of amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Molecular weight (amino acids)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1506">
-        <rdfs:label>Amino acid index (hydropathy)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasDefinition>Hydrophobic, hydrophilic or charge properties of amino acids.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Hydropathy (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1507">
-        <rdfs:label>Amino acid index (White-Wimley data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>White-Wimley data (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Experimental free energy values for the water-interface and water-octanol transitions for the amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1508">
-        <rdfs:label>Amino acid index (van der Waals radii)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1501"/>
-        <oboInOwl:hasExactSynonym>van der Waals radii (amino acids)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Van der Waals radii of atoms for different amino acid residues.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1509">
-        <rdfs:label>Enzyme report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein report (enzyme)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Enzyme report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on a specific enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1517 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1517">
-        <rdfs:label>Restriction enzyme report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a specific restriction enzyme such as enzyme reference data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Restriction enzyme pattern data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein report (restriction enzyme)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Restriction enzyme report</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1519">
-        <rdfs:label>Peptide molecular weights</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report might include associated data such as frequency of peptide fragment molecular weights.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1520">
-        <rdfs:label>Peptide hydrophobic moment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on the hydrophobic moment of a polypeptide sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1521">
-        <rdfs:label>Protein aliphatic index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <oboInOwl:hasDefinition>The aliphatic index of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The aliphatic index is the relative protein volume occupied by aliphatic side chains.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1522">
-        <rdfs:label>Protein sequence hydropathy plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <rdfs:comment>Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1523">
-        <rdfs:label>Protein charge plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1524">
-        <rdfs:label>Protein solubility</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The solubility or atomic solvation energy of a protein sequence or structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein solubility data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1525">
-        <rdfs:label>Protein crystallizability</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein crystallizability data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data on the crystallizability of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1526">
-        <rdfs:label>Protein globularity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2970"/>
-        <oboInOwl:hasExactSynonym>Protein globularity data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on the stability, intrinsic disorder or globularity of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1527">
-        <rdfs:label>Protein titration curve</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <oboInOwl:hasDefinition>The titration curve of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1528">
-        <rdfs:label>Protein isoelectric point</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The isoelectric point of one proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1529">
-        <rdfs:label>Protein pKa value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>The pKa value of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1530">
-        <rdfs:label>Protein hydrogen exchange rate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The hydrogen exchange rate of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1531">
-        <rdfs:label>Protein extinction coefficient</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>The extinction coefficient of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1532 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1532">
-        <rdfs:label>Protein optical density</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>The optical density of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1533">
-        <rdfs:label>Protein subcellular localization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Protein report (subcellular localization)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1534">
-        <rdfs:label>Peptide immunogenicity data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>An report on allergenicity / immunogenicity of peptides and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Peptide immunogenicity report</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide immunogenicity</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1536">
-        <rdfs:label>MHC peptide immunogenicity report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report on the immunogenicity of MHC class I or class II binding peptides.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1534"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1537">
-        <rdfs:label>Protein structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0896"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:hasExactSynonym>Protein structural property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure-derived report</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein property (structural)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein report (structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure report (domain)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1539">
-        <rdfs:label>Protein structural quality report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:hasDefinition>Report on the quality of a protein three-dimensional model.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein structure report (quality evaluation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure validation report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein property (structural quality)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein report (structural quality)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1540">
-        <rdfs:label>Protein residue interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Residue interaction data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Atom interaction data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1541 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1541">
-        <rdfs:label>Protein flexibility or motion report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein property (flexibility or motion)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Informative report on flexibility or motion of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein flexibility or motion</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein structure report (flexibility or motion)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1542">
-        <rdfs:label>Protein solvent accessibility</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on the solvent accessible or buried surface area of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1543">
-        <rdfs:label>Protein surface report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein structure report (surface)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1544 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1544">
-        <rdfs:label>Ramachandran plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2991"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phi/psi angle data or a Ramachandran plot of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1545">
-        <rdfs:label>Protein dipole moment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasDefinition>Data on the net charge distribution (dipole moment) of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1546">
-        <rdfs:label>Protein distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1547">
-        <rdfs:label>Protein contact map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <oboInOwl:hasDefinition>An amino acid residue contact map for a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1548">
-        <rdfs:label>Protein residue 3D cluster</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report on clusters of contacting residues in protein structures such as a key structural residue network.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1549">
-        <rdfs:label>Protein hydrogen bonds</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1540"/>
-        <oboInOwl:hasDefinition>Patterns of hydrogen bonding in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1550">
-        <rdfs:label>Protein non-canonical interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Protein non-canonical interactions report</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Non-canonical atomic interactions in protein structures.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1553">
-        <rdfs:label>CATH node</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information on a node from the CATH database.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>CATH classification node report</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1554">
-        <rdfs:label>SCOP node</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>SCOP classification node</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Information on a node from the SCOP database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1555">
-        <rdfs:label>EMBASSY domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1556">
-        <rdfs:label>CATH class</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a protein &apos;class&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1557">
-        <rdfs:label>CATH architecture</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a protein &apos;architecture&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1558">
-        <rdfs:label>CATH topology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a protein &apos;topology&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1559">
-        <rdfs:label>CATH homologous superfamily</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a protein &apos;homologous superfamily&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1560">
-        <rdfs:label>CATH structurally similar group</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a protein &apos;structurally similar group&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1561">
-        <rdfs:label>CATH functional category</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information on a protein &apos;functional category&apos; node from the CATH database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1564">
-        <rdfs:label>Protein fold recognition report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0901"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1565">
-        <rdfs:label>Protein-protein interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>protein-protein interaction(s), including interactions between protein domains.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1566">
-        <rdfs:label>Protein-ligand interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0906"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on protein-ligand (small molecule) interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1567">
-        <rdfs:label>Protein-nucleic acid interactions report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>protein-DNA/RNA interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1583">
-        <rdfs:label>Nucleic acid melting profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid stability profile</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1584 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1584">
-        <rdfs:label>Nucleic acid enthalpy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1585 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1585">
-        <rdfs:label>Nucleic acid entropy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <oboInOwl:hasDefinition>Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1586 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1586">
-        <rdfs:label>Nucleic acid melting temperature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2139"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1587 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1587">
-        <rdfs:label>Nucleic acid stitch profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA).</oboInOwl:hasDefinition>
-        <rdfs:comment>A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1588 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1588">
-        <rdfs:label>DNA base pair stacking energies data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <oboInOwl:hasDefinition>DNA base pair stacking energies data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1589 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1589">
-        <rdfs:label>DNA base pair twist angle data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA base pair twist angle data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1590 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1590">
-        <rdfs:label>DNA base trimer roll angles data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA base trimer roll angles data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1591 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1591">
-        <rdfs:label>Vienna RNA parameters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>RNA parameters used by the Vienna package.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1592 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1592">
-        <rdfs:label>Vienna RNA structure constraints</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Structure constraints used by the Vienna package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1593">
-        <rdfs:label>Vienna RNA concentration data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>RNA concentration data used by the Vienna package.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1594">
-        <rdfs:label>Vienna RNA calculated energy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>RNA calculated energy data generated by the Vienna package.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1584"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1595">
-        <rdfs:label>Base pairing probability matrix dotplot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Such as generated by the Vienna package.</rdfs:comment>
-        <oboInOwl:hasDefinition>Dotplot of RNA base pairing probability matrix.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1596 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1596">
-        <rdfs:label>Nucleic acid folding report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (folding)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (folding model)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>RNA secondary structure folding probablities</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>RNA secondary structure folding classification</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1597 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1597">
-        <rdfs:label>Codon usage table</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Table of codon usage data calculated from one or more nucleic acid sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1598">
-        <rdfs:label>Genetic code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A genetic code for an organism.</oboInOwl:hasDefinition>
-        <rdfs:comment>A genetic code need not include detailed codon usage information.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1599 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1599">
-        <rdfs:label>Codon adaptation index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A simple measure of synonymous codon usage bias often used to predict gene expression levels.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>CAI</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2865"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1600 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1600">
-        <rdfs:label>Codon usage bias plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:hasExactSynonym>Synonymous codon usage statistic plot</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of the synonymous codon usage calculated for windows over a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1601">
-        <rdfs:label>Nc statistic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The effective number of codons used in a gene sequence.  This reflects how far codon usage of a gene departs from equal usage of synonymous codons.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2865"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1602">
-        <rdfs:label>Codon usage fraction difference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:hasDefinition>The differences in codon usage fractions between two codon usage tables.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1621">
-        <rdfs:label>Pharmacogenomic test report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0920"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on the influence of genotype on drug response.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1622">
-        <rdfs:label>Disease report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0920"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0634"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An informative report on a specific disease.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Disease report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1634 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1634">
-        <rdfs:label>Linkage disequilibrium (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0927"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1636 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1636">
-        <rdfs:label>Heat map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:hasDefinition>A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1642 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1642">
-        <rdfs:label>Affymetrix probe sets library file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Affymetrix library file of information about which probes belong to which probe set.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>CDF file</oboInOwl:hasRelatedSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1643 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1643">
-        <rdfs:label>Affymetrix probe sets information library file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated.</oboInOwl:hasDefinition>
-        <oboInOwl:hasRelatedSynonym>GIN file</oboInOwl:hasRelatedSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1646 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1646">
-        <rdfs:label>Molecular weights standard fingerprint</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0944"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1656 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1656">
-        <rdfs:label>Metabolic pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of a metabolic pathway.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1657 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1657">
-        <rdfs:label>Genetic information processing pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>genetic information processing pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1658 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1658">
-        <rdfs:label>Environmental information processing pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>environmental information processing pathways.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1659 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1659">
-        <rdfs:label>Signal transduction pathway report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of a signal transduction pathway.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1660 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1660">
-        <rdfs:label>Cellular process pathways report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Topic concernning cellular process pathways.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1661 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1661">
-        <rdfs:label>Disease pathway or network report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>disease pathways, typically of human disease.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1662 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1662">
-        <rdfs:label>Drug structure relationship map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1696"/>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of drug structure relationships.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1663 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1663">
-        <rdfs:label>Protein interaction networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>networks of protein interactions.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2600"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1664 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1664">
-        <rdfs:label>MIRIAM datatype</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types.</rdfs:comment>
-        <oboInOwl:hasDefinition>An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1667 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1667">
-        <rdfs:label>E-value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0951"/>
-        <rdfs:comment>An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple floating point number defining the lower or upper limit of an expectation value (E-value).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Expectation value</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1668 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1668">
-        <rdfs:label>Z-value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0951"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The z-value is the number of standard deviations a data value is above or below a mean value.</oboInOwl:hasDefinition>
-        <rdfs:comment>A z-value might be specified as a threshold for reporting hits from database searches.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1669 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1669">
-        <rdfs:label>P-value</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0951"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A z-value might be specified as a threshold for reporting hits from database searches.</rdfs:comment>
-        <oboInOwl:hasDefinition>The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1670 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1670">
-        <rdfs:label>Database version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Ontology version information</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a database (or ontology) version, for example name, version number and release date.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1671 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1671">
-        <rdfs:label>Tool version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on an application version, for example name, version number and release date.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0958"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1672 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1672">
-        <rdfs:label>CATH version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a version of the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1673 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1673">
-        <rdfs:label>Swiss-Prot to PDB mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Cross-mapping of Swiss-Prot codes to PDB identifiers.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0954"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1674 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1674">
-        <rdfs:label>Sequence database cross-references</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Cross-references from a sequence record to other databases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1675 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1675">
-        <rdfs:label>Job status</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Metadata on the status of a submitted job.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Values for EBI services are &apos;DONE&apos; (job has finished and the results can then be retrieved), &apos;ERROR&apos; (the job failed or no results where found), &apos;NOT_FOUND&apos; (the job id is no longer available; job results might be deleted, &apos;PENDING&apos; (the job is in a queue waiting processing), &apos;RUNNING&apos; (the job is currently being processed).</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1676 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1676">
-        <rdfs:label>Job ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:hasDefinition>The (typically numeric) unique identifier of a submitted job.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1677 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1677">
-        <rdfs:label>Job type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of job, for example interactive or non-interactive.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1678 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1678">
-        <rdfs:label>Tool log</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1679 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1679">
-        <rdfs:label>DaliLite log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1680 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1680">
-        <rdfs:label>STRIDE log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>STRIDE log file.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1678"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1681 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1681">
-        <rdfs:label>NACCESS log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>NACCESS log file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1678"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1682 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1682">
-        <rdfs:label>EMBOSS wordfinder log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>EMBOSS wordfinder log file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1683 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1683">
-        <rdfs:label>EMBOSS domainatrix log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>EMBOSS (EMBASSY) domainatrix application log file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1684 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1684">
-        <rdfs:label>EMBOSS sites log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>EMBOSS (EMBASSY) sites application log file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1685 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1685">
-        <rdfs:label>EMBOSS supermatcher error file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>EMBOSS (EMBASSY) supermatcher error file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1686 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1686">
-        <rdfs:label>EMBOSS megamerger log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>EMBOSS megamerger log file.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1687 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1687">
-        <rdfs:label>EMBOSS whichdb log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>EMBOSS megamerger log file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1688 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1688">
-        <rdfs:label>EMBOSS vectorstrip log file</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>EMBOSS vectorstrip log file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1689 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1689">
-        <rdfs:label>Username</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2101"/>
-        <oboInOwl:hasDefinition>A username on a computer system.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1690 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1690">
-        <rdfs:label>Password</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2101"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A password on a computer system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1691 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1691">
-        <rdfs:label>Email address</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2101"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:Email</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A valid email address of an end-user.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:EmailAddress</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1692 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1692">
-        <rdfs:label>Person name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2118"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a person.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1693 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1693">
-        <rdfs:label>Number of iterations</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Number of iterations of an algorithm.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1694 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1694">
-        <rdfs:label>Number of output entities</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Number of entities (for example database hits, sequences, alignments etc) to write to an output file.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1695 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1695">
-        <rdfs:label>Hit sort order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Controls the order of hits (reported matches) in an output file from a database search.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2134"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1696 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1696">
-        <rdfs:label>Drug report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0962"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0620"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An informative report on a specific drug.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Drug annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1707 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1707">
-        <rdfs:label>Phylogenetic tree image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information.</oboInOwl:hasDefinition>
-        <rdfs:comment>See also &apos;Phylogenetic tree&apos;</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1708 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1708">
-        <rdfs:label>RNA secondary structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of RNA secondary structure, knots, pseudoknots etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1709 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1709">
-        <rdfs:label>Protein secondary structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3153"/>
-        <oboInOwl:hasDefinition>Image of protein secondary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1710 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1710">
-        <rdfs:label>Structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of one or more molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1711 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1711">
-        <rdfs:label>Sequence alignment image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of two or more aligned molecular sequences possibly annotated with alignment features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1712 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1712">
-        <rdfs:label>Chemical structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1710"/>
-        <oboInOwl:hasDefinition>An image of the structure of a small chemical compound.</oboInOwl:hasDefinition>
-        <rdfs:comment>The molecular identifier and formula are typically included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Small molecule structure image</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1713 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1713">
-        <rdfs:label>Fate map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2530"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3065"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition> A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1714 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1714">
-        <rdfs:label>Microarray spots image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image of spots from a microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1715 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1715">
-        <rdfs:label>BioPax term</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A term from the BioPax ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1716 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1716">
-        <rdfs:label>GO</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasExactSynonym>Gene Ontology term</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Annotated_GO_Term</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Annotated_GO_Term_With_Probability</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term definition from The Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:GO_Term</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GOTerm</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1717 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1717">
-        <rdfs:label>MeSH</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the MeSH vocabulary.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1718 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1718">
-        <rdfs:label>HGNC</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the HGNC controlled vocabulary.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1719 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1719">
-        <rdfs:label>NCBI taxonomy vocabulary</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the NCBI taxonomy vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1720 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1720">
-        <rdfs:label>Plant ontology term</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from the Plant Ontology (PO).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1721 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1721">
-        <rdfs:label>UMLS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from the UMLS vocabulary.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1722 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1722">
-        <rdfs:label>FMA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from Foundational Model of Anatomy.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1723 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1723">
-        <rdfs:label>EMAP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A term from the EMAP mouse ontology.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1724 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1724">
-        <rdfs:label>ChEBI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A term from the ChEBI ontology.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1725 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1725">
-        <rdfs:label>MGED</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the MGED ontology.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1726 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1726">
-        <rdfs:label>myGrid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term from the myGrid ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0966"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1727 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1727">
-        <rdfs:label>GO (biological process)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Data Type is an enumerated string.</rdfs:comment>
-        <oboInOwl:hasDefinition>A term definition for a biological process from the Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1728 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1728">
-        <rdfs:label>GO (molecular function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A term definition for a molecular function from the Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Data Type is an enumerated string.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1729 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1729">
-        <rdfs:label>GO (cellular component)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A term definition for a cellular component from the Gene Ontology (GO).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Data Type is an enumerated string.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2858"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1730 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1730">
-        <rdfs:label>Ontology relation type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A relation type defined in an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0967"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1731 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1731">
-        <rdfs:label>Ontology concept definition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0967"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology class definition</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The definition of a concept from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1732 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1732">
-        <rdfs:label>Ontology concept comment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A comment on a concept from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0967"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1733 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1733">
-        <rdfs:label>Ontology concept reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Reference for a concept from an ontology.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1738 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1738">
-        <rdfs:label>doc2loc document information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The doc2loc output includes the url, format, type and availability code of a document for every service provider.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a published article provided by the doc2loc program.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0970"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1742 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1742">
-        <rdfs:label>PDB residue number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <oboInOwl:hasDbXref>WHATIF: pdb_number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:PDB_residue_no</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A residue identifier (a string) from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1743 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1743">
-        <rdfs:label>Atomic coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1917"/>
-        <oboInOwl:hasDefinition>Cartesian coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Cartesian coordinate</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1744 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1744">
-        <rdfs:label>Atomic x coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1743"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_Cartn_x</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Cartesian x coordinate</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.Cartn_x in PDBML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cartesian x coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1745 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1745">
-        <rdfs:label>Atomic y coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1743"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_Cartn_y</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Cartesian y coordinate</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.Cartn_y in PDBML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cartesian y coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1746 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1746">
-        <rdfs:label>Atomic z coordinate</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1743"/>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.Cartn_z</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_Cartn_z</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cartesian z coordinate of an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Cartesian z coordinate</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1748 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1748">
-        <rdfs:label>PDB atom name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1757"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_type_symbol</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_auth_atom_id</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: alternate_atom</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_atom_name</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: atom_type</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier (a string) of a specific atom from a PDB file for a molecular structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1755 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1755">
-        <rdfs:label>Protein atom</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <oboInOwl:hasExactSynonym>Atom data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>CHEBI:33250</oboInOwl:hasRelatedSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Data on a single atom from a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1756 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1756">
-        <rdfs:label>Protein residue</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on a single amino acid residue position in a protein structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Residue</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1757 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1757">
-        <rdfs:label>Atom name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0983"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>Name of an atom.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1758 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1758">
-        <rdfs:label>PDB residue name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2564"/>
-        <oboInOwl:hasDefinition>Three-letter amino acid residue names as used in PDB files.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: type</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1759 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1759">
-        <rdfs:label>PDB model number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3035"/>
-        <oboInOwl:hasDefinition>Identifier of a model structure from a PDB file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_model_num</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Model number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>WHATIF: model_number</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1762 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1762">
-        <rdfs:label>CATH domain report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.</rdfs:comment>
-        <oboInOwl:hasDefinition>Summary of domain classification information for a CATH domain.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1764 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1764">
-        <rdfs:label>CATH representative domain sequences (ATOM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1765 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1765">
-        <rdfs:label>CATH representative domain sequences (COMBS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1235"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1766 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1766">
-        <rdfs:label>CATH domain sequences (ATOM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>FASTA sequence database for all CATH domains (based on PDB ATOM records).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1767 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1767">
-        <rdfs:label>CATH domain sequences (COMBS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>FASTA sequence database for all CATH domains (based on COMBS sequence data).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1771 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1771">
-        <rdfs:label>Sequence version</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on an molecular sequence version.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence version information</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1772 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1772">
-        <rdfs:label>Score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>A numerical value, that is some type of scored value arising for example from a prediction method.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1776 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1776">
-        <rdfs:label>Protein report (function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>For properties that can be mapped to a sequence, use &apos;Sequence report&apos; instead.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Report on general functional properties of specific protein(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1783 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1783">
-        <rdfs:label>Gene name (ASPGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of a gene from Aspergillus Genome Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1784 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1784">
-        <rdfs:label>Gene name (CGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Name of a gene from Candida Genome Database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1785 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1785">
-        <rdfs:label>Gene name (dictyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of a gene from dictyBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1786 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1786">
-        <rdfs:label>Gene name (EcoGene primary)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Primary name of a gene from EcoGene Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EcoGene primary gene name</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1787 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1787">
-        <rdfs:label>Gene name (MaizeGDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus</oboInOwl:hasDbXref>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Name of a gene from MaizeGDB (maize genes) database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1788 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1788">
-        <rdfs:label>Gene name (SGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Name of a gene from Saccharomyces Genome Database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1789 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1789">
-        <rdfs:label>Gene name (TGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Name of a gene from Tetrahymena Genome Database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1790 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1790">
-        <rdfs:label>Gene name (CGSC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: CGSC</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Symbol of a gene from E.coli Genetic Stock Center.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1791 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1791">
-        <rdfs:label>Gene name (HGNC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>HUGO symbol</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>HGNC symbol</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Official gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HUGO gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>HGNC gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HUGO gene symbol</oboInOwl:hasExactSynonym>
-        <regex>HGNC:[0-9]{1,5}</regex>
-        <oboInOwl:hasExactSynonym>Gene name (HUGO)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HGNC gene symbol</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Symbol of a gene approved by the HUGO Gene Nomenclature Committee.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1792 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1792">
-        <rdfs:label>Gene name (MGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>MGI:[0-9]+</regex>
-        <oboInOwl:hasDefinition>Symbol of a gene from the Mouse Genome Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: MGD</oboInOwl:hasDbXref>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1793 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1793">
-        <rdfs:label>Gene name (Bacillus subtilis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Symbol of a gene from Bacillus subtilis Genome Sequence Project.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1794 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1794">
-        <rdfs:label>Gene ID (PlasmoDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier of a gene from PlasmoDB Plasmodium Genome Resource.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1795 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1795">
-        <rdfs:label>Gene ID (EcoGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier of a gene from EcoGene Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EcoGene Accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>EcoGene ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1796 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1796">
-        <rdfs:label>Gene ID (FlyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gene identifier from FlyBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: FB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1797 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1797">
-        <rdfs:label>Gene ID (GeneDB Glossina morsitans)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans</oboInOwl:hasDbXref>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Gene identifier from Glossina morsitans GeneDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1798 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1798">
-        <rdfs:label>Gene ID (GeneDB Leishmania major)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Gene identifier from Leishmania major GeneDB database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1799 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1799">
-        <rdfs:label>Gene ID (GeneDB Plasmodium falciparum)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Gene identifier from Plasmodium falciparum GeneDB database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum</oboInOwl:hasDbXref>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1800 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1800">
-        <rdfs:label>Gene ID (GeneDB Schizosaccharomyces pombe)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Gene identifier from Schizosaccharomyces pombe GeneDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1801 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1801">
-        <rdfs:label>Gene ID (GeneDB Trypanosoma brucei)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Gene identifier from Trypanosoma brucei GeneDB database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1035"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1802 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1802">
-        <rdfs:label>Gene ID (Gramene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Gene identifier from Gramene database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1803 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1803">
-        <rdfs:label>Gene ID (Virginia microbial)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Gene identifier from Virginia Bioinformatics Institute microbial database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: VMD</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1804 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1804">
-        <rdfs:label>Gene ID (SGN)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SGN</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Gene identifier from Sol Genomics Network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1805 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1805">
-        <rdfs:label>Gene ID (WormBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Gene identifier used by WormBase database.</oboInOwl:hasDefinition>
-        <regex>WBGene[0-9]{8}</regex>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: WB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: WormBase</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1806 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1806">
-        <rdfs:label>Gene synonym</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Gene name synonym</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Any name (other than the recommended one) for a gene.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1807 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1807">
-        <rdfs:label>ORF name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2795"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of an open reading frame attributed by a sequencing project.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1852 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1852">
-        <rdfs:label>Sequence assembly component</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A component of a larger sequence assembly.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0925"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1853 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1853">
-        <rdfs:label>Chromosome annotation (aberration)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on a chromosome aberration such as abnormalities in chromosome structure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0919"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1855 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1855">
-        <rdfs:label>Clone ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2769"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a clone (cloned molecular sequence) from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1856 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1856">
-        <rdfs:label>PDB insertion code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: insertion_code</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_ins_code</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>An insertion code (part of the residue number) for an amino acid residue from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1857 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1857">
-        <rdfs:label>Atomic occupancy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1917"/>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_occupancy</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The fraction of an atom type present at a site in a molecular structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1858 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1858">
-        <rdfs:label>Isotropic B factor</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1917"/>
-        <oboInOwl:hasDefinition>Isotropic B factor (atomic displacement parameter) for an atom from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: PDBx_B_iso_or_equiv</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1859 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1859">
-        <rdfs:label>Deletion map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1283"/>
-        <rdfs:comment>A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line (&apos;genome deletion panel&apos;). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Deletion-based cytogenetic map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1860 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1860">
-        <rdfs:label>QTL map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1278"/>
-        <oboInOwl:hasDefinition>A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Quantitative trait locus map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1863 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1863">
-        <rdfs:label>Haplotype map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1278"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:Haplotyping_Study_obj</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1864 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1864">
-        <rdfs:label>Map set data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2019"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:GCP_CorrelatedLinkageMapSet</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_CorrelatedMapSet</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1865 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1865">
-        <rdfs:label>Map feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A feature which may mapped (positioned) on a genetic or other type of map.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:MapFeature</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Mappable features may be based on Gramene&apos;s notion of map features; see http://www.gramene.org/db/cmap/feature_type_info.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1255"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2019"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1866 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1866">
-        <rdfs:label>Map type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A designation of the type of map (genetic map, physical map, sequence map etc) or map set.</oboInOwl:hasDefinition>
-        <rdfs:comment>Map types may be based on Gramene&apos;s notion of a map type; see http://www.gramene.org/db/cmap/map_type_info.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1867">
-        <rdfs:label>Protein fold name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a protein fold.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1868">
-        <rdfs:label>Taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDbXref>Moby:PotentialTaxon</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Taxonomy rank</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Taxonomic rank</oboInOwl:hasExactSynonym>
-        <rdfs:comment>For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.</rdfs:comment>
-        <oboInOwl:hasDefinition>The name of a group of organisms belonging to the same taxonomic rank.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:BriefTaxonConcept</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1869">
-        <rdfs:label>Organism identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2530"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a (group of) organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1870 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1870">
-        <rdfs:label>Genus name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a genus of organism.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1872 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1872">
-        <rdfs:label>Taxonomic classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDbXref>Moby:TaxonName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_Taxon</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:iANT_organism-xml</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Taxonomic name</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Name components correspond to levels in a taxonomic hierarchy (e.g. &apos;Genus&apos;, &apos;Species&apos;, etc.) Meta information such as a reference where the name was defined and a date might be included.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Taxonomic information</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:TaxonScientificName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:TaxonTCS</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1873 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1873">
-        <rdfs:label>iHOP organism ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:iHOPorganism</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>A unique identifier for an organism used in the iHOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1874 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1874">
-        <rdfs:label>Genbank common name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDefinition>Common name for an organism as used in the GenBank database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1875 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1875">
-        <rdfs:label>NCBI taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a taxon from the NCBI taxonomy database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1877 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1877">
-        <rdfs:label>Synonym</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Alternative name</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An alternative for a word.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1878 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1878">
-        <rdfs:label>Misspelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A common misspelling of a word.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1879 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1879">
-        <rdfs:label>Acronym</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An abbreviation of a phrase or word.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1880 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1880">
-        <rdfs:label>Misnomer</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A term which is likely to be misleading of its meaning.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1881 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1881">
-        <rdfs:label>Author ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2118"/>
-        <oboInOwl:hasDefinition>Information on the authors of a published work.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:Author</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1882 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1882">
-        <rdfs:label>DragonDB author identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1881"/>
-        <oboInOwl:hasDefinition>An identifier representing an author in the DragonDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1883 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1883">
-        <rdfs:label>Annotated URI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A URI along with annotation describing the data found at the address.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:DescribedLink</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1884 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1884">
-        <rdfs:label>UniProt keywords</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0582"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1885">
-        <rdfs:label>Gene ID (GeneFarm)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDbXref>Moby_namespace:GENEFARM_GeneID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier of a gene from the GeneFarm database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1886 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1886">
-        <rdfs:label>Blattner number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:Blattner_number</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The blattner identifier for a gene.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1887 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1887">
-        <rdfs:label>Gene ID (MIPS Maize)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>MIPS genetic element identifier (Maize)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier for genetic elements in MIPS Maize database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:MIPS_GE_Maize</oboInOwl:hasDbXref>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2285"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1888 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1888">
-        <rdfs:label>Gene ID (MIPS Medicago)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>MIPS genetic element identifier (Medicago)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>Moby_namespace:MIPS_GE_Medicago</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier for genetic elements in MIPS Medicago database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2285"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1889 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1889">
-        <rdfs:label>Gene name (DragonDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of an Antirrhinum Gene from the DragonDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:DragonDB_Gene</oboInOwl:hasDbXref>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1890 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1890">
-        <rdfs:label>Gene name (Arabidopsis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDbXref>Moby_namespace:ArabidopsisGeneSymbol</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1891 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1891">
-        <rdfs:label>iHOP symbol</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>A unique identifier of a protein or gene used in the iHOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:iHOPsymbol</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1892 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1892">
-        <rdfs:label>Gene name (GeneFarm)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of a gene from the GeneFarm database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:GENEFARM_GeneName</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>GeneFarm gene ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1893 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1893">
-        <rdfs:label>Locus ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2012"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Locus name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Locus identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1895 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1895">
-        <rdfs:label>Locus ID (AGI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <regex>AT[1-5]G[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>AGI ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Arabidopsis gene loci number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>AGI locus code</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>AGI identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1896 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1896">
-        <rdfs:label>Locus ID (ASPGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier for loci from ASPGD (Aspergillus Genome Database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1897 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1897">
-        <rdfs:label>Locus ID (MGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier for loci from Magnaporthe grisea Database at the Broad Institute.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1898 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1898">
-        <rdfs:label>Locus ID (CGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier for loci from CGD (Candida Genome Database).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: CGDID</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CGDID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>CGD locus identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: CGD</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1899 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1899">
-        <rdfs:label>Locus ID (CMR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1900 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1900">
-        <rdfs:label>NCBI locus tag</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:LocusID</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Locus ID (NCBI)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier for loci from NCBI database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1901 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1901">
-        <rdfs:label>Locus ID (SGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2632"/>
-        <oboInOwl:hasDefinition>Identifier for loci from SGD (Saccharomyces Genome Database).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SGDID</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SGD</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>SGDID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1902 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1902">
-        <rdfs:label>Locus ID (MMP)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of loci from Maize Mapping Project.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:MMP_Locus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1903 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1903">
-        <rdfs:label>Locus ID (DictyBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDbXref>Moby_namespace:DDB_gene</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identifier of locus from DictyBase (Dictyostelium discoideum).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1904 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1904">
-        <rdfs:label>Locus ID (EntrezGene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of a locus from EntrezGene database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:EntrezGene_ID</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby_namespace:EntrezGene_EntrezGeneID</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1905 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1905">
-        <rdfs:label>Locus ID (MaizeGDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of locus from MaizeGDB (Maize genome database).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:MaizeGDB_Locus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1906 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1906">
-        <rdfs:label>Quantitative trait locus</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>QTL</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A QTL sometimes but does not necessarily correspond to a gene.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:SO_QTL</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2012"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1907 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1907">
-        <rdfs:label>Gene ID (KOME)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier of a gene from the KOME database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby_namespace:GeneId</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1908 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1908">
-        <rdfs:label>Locus ID (Tropgene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasDefinition>Identifier of a locus from the Tropgene database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:Tropgene_locus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1916 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1916">
-        <rdfs:label>Alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>An alignment of molecular sequences, structures or profiles derived from them.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_1917 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_1917">
-        <rdfs:label>Atomic property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>General atomic property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data for an atom (in a molecular structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2007">
-        <rdfs:label>UniProt keyword</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0968"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:SP_KW</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2009 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2009">
-        <rdfs:label>Ordered locus name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2012 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2012">
-        <rdfs:label>Sequence coordinates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1017"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2019"/>
-        <oboInOwl:hasExactSynonym>Map position</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Moby:Position</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Locus</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence co-ordinates</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A position in a map (for example a genetic map), either a single position (point) or a region / interval.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:GenePosition</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position.</rdfs:comment>
-        <oboInOwl:hasDbXref>Moby:HitPosition</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:MapPosition</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:Locus</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_MapInterval</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_MapPosition</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:GCP_MapPoint</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>PDBML:_atom_site.id</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2016 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2016">
-        <rdfs:label>Amino acid property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasDefinition>Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Amino acid data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2018 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2018">
-        <rdfs:label>Annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasDefinition>A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2019 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2019">
-        <rdfs:label>Map data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Map attribute</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An attribute of a molecular map (genetic or physical), or data extracted from or derived from the analysis of such a map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2022 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2022">
-        <rdfs:label>Vienna RNA structural data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data used by the Vienna RNA analysis package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2023 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2023">
-        <rdfs:label>Sequence mask parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data used to replace (mask) characters in a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2024 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2024">
-        <rdfs:label>Enzyme kinetics data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2978"/>
-        <oboInOwl:hasDefinition>Data concerning chemical reaction(s) catalysed by enzyme(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2025 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2025">
-        <rdfs:label>Michaelis Menten plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <oboInOwl:hasDefinition>A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2026 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2026">
-        <rdfs:label>Hanes Woolf plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2024"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2028 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2028">
-        <rdfs:label>Experimental data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Raw data from or annotation on laboratory experiments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Experimental measurement data</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3108"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2041 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2041">
-        <rdfs:label>Genome version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a genome version.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2711"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2042 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2042">
-        <rdfs:label>Evidence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2043 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2043">
-        <rdfs:label>Sequence record lite</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2044 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2044">
-        <rdfs:label>Sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D008969</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Sequences</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation</rdfs:seeAlso>
-        <rdfs:comment>This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records.  It should not normally be used for derivatives such as sequence alignments, motifs or profiles.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>One or more molecular sequences, possibly with associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2046 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2046">
-        <rdfs:label>Nucleic acid sequence record (lite)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2047 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2047">
-        <rdfs:label>Protein sequence record (lite)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasExactSynonym>Sequence record lite (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2048 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2048">
-        <rdfs:label>Report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <rdfs:comment>You can use this term by default for any textual report, in case you can&apos;t find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing.</rdfs:comment>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000148</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Document</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2050 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2050">
-        <rdfs:label>Molecular property (general)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>General molecular property</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>General data for a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2053 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2053">
-        <rdfs:label>Structural data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning molecular structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0883"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2070 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2070">
-        <rdfs:label>Sequence motif (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1353"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid sequence motif</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>DNA sequence motif</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>A nucleotide sequence motif.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>RNA sequence motif</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2071 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2071">
-        <rdfs:label>Sequence motif (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1353"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An amino acid sequence motif.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein sequence motif</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2079 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2079">
-        <rdfs:label>Search parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Some simple value controlling a search operation, typically a search of a database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2080">
-        <rdfs:label>Database search results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report of hits from searching a database of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Search results</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Database hits</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2081">
-        <rdfs:label>Secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The secondary structure assignment (predicted or real) of a nucleic acid or protein.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2082 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2082">
-        <rdfs:label>Matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Array</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasDefinition>An array of numerical values.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2083">
-        <rdfs:label>Alignment data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of molecular alignment of some type.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Alignment report</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1394"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2084">
-        <rdfs:label>Nucleic acid report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative human-readable report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2085">
-        <rdfs:label>Structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report on general information, properties or features of one or more molecular tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure-derived report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2086 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2086">
-        <rdfs:label>Nucleic acid structure data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0912"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid property (structural)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Nucleic acid structural property</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2087 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2087">
-        <rdfs:label>Molecular property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasRelatedSynonym>SO:0000400</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Physicochemical property</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2088 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2088">
-        <rdfs:label>DNA base structural data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2086"/>
-        <oboInOwl:hasDefinition>Structural data for DNA base pairs or runs of bases, such as energy or angle data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2090 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2090">
-        <rdfs:label>Database entry version information</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2091 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2091">
-        <rdfs:label>Accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000731</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000675</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2092">
-        <rdfs:label>SNP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>single nucleotide polymorphism (SNP) in a DNA sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2093 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2093">
-        <rdfs:label>Data reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:comment>A list of database accessions or identifiers are usually included.</rdfs:comment>
-        <oboInOwl:hasDefinition>Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2098 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2098">
-        <rdfs:label>Job identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:seeAlso>http://wsio.org/data_009</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>An identifier of a submitted job.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2099">
-        <rdfs:label>Name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000116</rdfs:seeAlso>
-        <rdfs:seeAlso>http://usefulinc.com/ns/doap#name</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://www.w3.org/2000/01/rdf-schema#label</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A name of a thing, which need not necessarily uniquely identify it.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Symbolic name</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-        <oboInOwl:hasBroadSynonym rdf:resource="&rdfs;label"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>Closely related, but focusing on labeling and human readability but not on identification.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/data_2099"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasBroadSynonym"/>
-        <owl:annotatedTarget rdf:resource="&rdfs;label"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/data_2100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2100">
-        <rdfs:label>Type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values).</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.org/dc/elements/1.1/type</rdfs:seeAlso>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2101 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2101">
-        <rdfs:label>User ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2118"/>
-        <oboInOwl:hasDefinition>An identifier of a software end-user (typically a person).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2102">
-        <rdfs:label>KEGG organism code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2909"/>
-        <oboInOwl:hasDefinition>A three-letter code used in the KEGG databases to uniquely identify organisms.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2103 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2103">
-        <rdfs:label>Gene name (KEGG GENES)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>KEGG GENES entry name</oboInOwl:hasExactSynonym>
-        <regex>[a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]*</regex>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the KEGG GENES database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby_namespace:GeneId</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2104 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2104">
-        <rdfs:label>BioCyc ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>Identifier of an object from one of the BioCyc databases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2105 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2105">
-        <rdfs:label>Compound ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasExactSynonym>BioCyc compound identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a compound from the BioCyc chemical compounds database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>BioCyc compound ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2106 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2106">
-        <rdfs:label>Reaction ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0613"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from the BioCyc reactions database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2107 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2107">
-        <rdfs:label>Enzyme ID (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2104"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasExactSynonym>BioCyc enzyme ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an enzyme from the BioCyc enzymes database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2108 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2108">
-        <rdfs:label>Reaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2978"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2109 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2109">
-        <rdfs:label>Identifier (hybrid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:hasDefinition>An identifier that is re-used for data objects of fundamentally different types (typically served from a single database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This branch provides an alternative organisation of the concepts nested under &apos;Accession&apos; and &apos;Name&apos;. All concepts under here are already included under &apos;Accession&apos; or &apos;Name&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2110">
-        <rdfs:label>Molecular property identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2087"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a molecular property.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2111">
-        <rdfs:label>Codon usage table ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a codon usage table, for example a genetic code.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Codon usage table identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2112">
-        <rdfs:label>FlyBase primary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1089"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Primary identifier of an object from the FlyBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2113 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2113">
-        <rdfs:label>WormBase identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an object from the WormBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2114 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2114">
-        <rdfs:label>WormBase wormpep ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2113"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Protein identifier used by WormBase database.</oboInOwl:hasDefinition>
-        <regex>CE[0-9]{5}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2116 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2116">
-        <rdfs:label>Nucleic acid features (codon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2117 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2117">
-        <rdfs:label>Map identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a map of a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2118">
-        <rdfs:label>Person identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a software end-user (typically a person).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2119 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2119">
-        <rdfs:label>Nucleic acid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Name or other identifier of a nucleic acid molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2126">
-        <rdfs:label>Translation frame specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2127">
-        <rdfs:label>Genetic code identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a genetic code.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2128">
-        <rdfs:label>Genetic code name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2127"/>
-        <oboInOwl:hasDefinition>Informal name for a genetic code, typically an organism name.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2129 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2129">
-        <rdfs:label>File format name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3358"/>
-        <oboInOwl:hasDefinition>Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2130">
-        <rdfs:label>Sequence profile type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2131 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2131">
-        <rdfs:label>Operating system name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a computer operating system such as Linux, PC or Mac.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2132 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2132">
-        <rdfs:label>Mutation type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A type of point or block mutation, including insertion, deletion, change, duplication and moves.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2133">
-        <rdfs:label>Logical operator</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A logical operator such as OR, AND, XOR, and NOT.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2134">
-        <rdfs:label>Results sort order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A control of the order of data that is output, for example the order of sequences in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2135">
-        <rdfs:label>Toggle</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A simple parameter that is a toggle (boolean value), typically a control for a modal tool.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2136 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2136">
-        <rdfs:label>Sequence width</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The width of an output sequence or alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2137">
-        <rdfs:label>Gap penalty</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1394"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A penalty for introducing or extending a gap in an alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2139">
-        <rdfs:label>Nucleic acid melting temperature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2985"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Melting temperature</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2140">
-        <rdfs:label>Concentration</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2050"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The concentration of a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2141">
-        <rdfs:label>Window step size</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Size of the incremental &apos;step&apos; a sequence window is moved over a sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1249"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2142 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2142">
-        <rdfs:label>EMBOSS graph</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image of a graph generated by the EMBOSS suite.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2143">
-        <rdfs:label>EMBOSS report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An application report generated by the EMBOSS suite.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2145 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2145">
-        <rdfs:label>Sequence offset</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>An offset for a single-point sequence position.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2146 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2146">
-        <rdfs:label>Threshold</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A value that serves as a threshold for a tool (usually to control scoring or output).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2147">
-        <rdfs:label>Protein report (transcription factor)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites.</rdfs:comment>
-        <oboInOwl:hasDefinition>An informative report on a transcription factor protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Transcription factor binding site data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2149 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2149">
-        <rdfs:label>Database category name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a category of biological or bioinformatics database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2150 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2150">
-        <rdfs:label>Sequence profile name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Name of a sequence profile.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1115"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2151 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2151">
-        <rdfs:label>Color</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Specification of one or more colors.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2152 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2152">
-        <rdfs:label>Rendering parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A parameter that is used to control rendering (drawing) to a device or image.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Graphics parameter</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Graphical parameter</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2154">
-        <rdfs:label>Sequence name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1063"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>Any arbitrary name of a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2156">
-        <rdfs:label>Date</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A temporal date.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2157">
-        <rdfs:label>Word composition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Word composition data for a molecular sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1266"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1268"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2160">
-        <rdfs:label>Fickett testcode plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <oboInOwl:hasDefinition>A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2161 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2161">
-        <rdfs:label>Sequence similarity plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0867"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <rdfs:comment>Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence conservation report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence similarity plot</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A plot of sequence similarities identified from word-matching or character comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2162 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2162">
-        <rdfs:label>Helical wheel</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1709"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2163">
-        <rdfs:label>Helical net</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1709"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Useful for highlighting amphipathicity and other properties.</rdfs:comment>
-        <oboInOwl:hasDefinition>An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2164">
-        <rdfs:label>Protein sequence properties plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of general physicochemical properties of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2165 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2165">
-        <rdfs:label>Protein ionization curve</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of pK versus pH for a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2166">
-        <rdfs:label>Sequence composition plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A plot of character or word composition / frequency of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2167">
-        <rdfs:label>Nucleic acid density plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1261"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Density plot (of base composition) for a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2168 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2168">
-        <rdfs:label>Sequence trace image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2969"/>
-        <oboInOwl:hasDefinition>Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2169 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2169">
-        <rdfs:label>Nucleic acid features (siRNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report on siRNA duplexes in mRNA.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3137"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2173">
-        <rdfs:label>Sequence set (stream)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time.</rdfs:comment>
-        <oboInOwl:hasDefinition>A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2174">
-        <rdfs:label>FlyBase secondary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1089"/>
-        <oboInOwl:hasDefinition>Secondary identifier of an object from the FlyBase database.</oboInOwl:hasDefinition>
-        <rdfs:comment>Secondary identifier are used to handle entries that were merged with or split from other entries in the database.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2176">
-        <rdfs:label>Cardinality</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The number of a certain thing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2177">
-        <rdfs:label>Exactly 1</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A single thing.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2178">
-        <rdfs:label>1 or more</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>One or more things.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2179">
-        <rdfs:label>Exactly 2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Exactly two things.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2180">
-        <rdfs:label>2 or more</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Two or more things.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2190 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2190">
-        <rdfs:label>Sequence checksum</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:hasDefinition>A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Hash code</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Hash sum</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Hash</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Hash value</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2191">
-        <rdfs:label>Protein features report (chemical modifications)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>chemical modification of a protein.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2192 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2192">
-        <rdfs:label>Error</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on an error generated by computer system or tool.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2193 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2193">
-        <rdfs:label>Database entry metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Basic information on any arbitrary database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2198 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2198">
-        <rdfs:label>Gene cluster</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A cluster of similar genes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1246"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2201 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2201">
-        <rdfs:label>Sequence record full</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2208">
-        <rdfs:label>Plasmid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <oboInOwl:hasDefinition>An identifier of a plasmid in a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2209">
-        <rdfs:label>Mutation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2538"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a specific mutation catalogued in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2212 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2212">
-        <rdfs:label>Mutation annotation (basic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2213">
-        <rdfs:label>Mutation annotation (prevalence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type)..</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2214 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2214">
-        <rdfs:label>Mutation annotation (prognostic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2215">
-        <rdfs:label>Mutation annotation (functional)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2216 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2216">
-        <rdfs:label>Codon number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1016"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The number of a codon, for instance, at which a mutation is located.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2217">
-        <rdfs:label>Tumor annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1622"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2218">
-        <rdfs:label>Server metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Basic information about a server on the web, such as an SRS server.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3106"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2219">
-        <rdfs:label>Database field name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a field in a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2220 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2220">
-        <rdfs:label>Sequence cluster ID (SYSTERS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasExactSynonym>SYSTERS cluster ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of a sequence cluster from the SYSTERS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2223 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2223">
-        <rdfs:label>Ontology metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning a biological ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2235">
-        <rdfs:label>Raw SCOP domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw SCOP domain classification data files.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <rdfs:comment>These are the parsable data files provided by SCOP.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2236">
-        <rdfs:label>Raw CATH domain classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Raw CATH domain classification data files.</oboInOwl:hasDefinition>
-        <rdfs:comment>These are the parsable data files provided by CATH.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2240">
-        <rdfs:label>Heterogen annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on the types of small molecules or &apos;heterogens&apos; (non-protein groups) that are represented in PDB files.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2242">
-        <rdfs:label>Phylogenetic property values</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic property values data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0871"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2245">
-        <rdfs:label>Sequence set (bootstrapped)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Bootstrapping is often performed in phylogenetic analysis.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A collection of sequences output from a bootstrapping (resampling) procedure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0850"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2247">
-        <rdfs:label>Phylogenetic consensus tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A consensus phylogenetic tree derived from comparison of multiple trees.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2248">
-        <rdfs:label>Schema</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A data schema for organising or transforming data of some type.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2249 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2249">
-        <rdfs:label>DTD</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A DTD (document type definition).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2250">
-        <rdfs:label>XML Schema</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>XSD</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An XML Schema.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2251 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2251">
-        <rdfs:label>Relax-NG schema</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A relax-NG schema.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2252">
-        <rdfs:label>XSLT stylesheet</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An XSLT stylesheet.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2253">
-        <rdfs:label>Data resource definition name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1084"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a data type.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2254">
-        <rdfs:label>OBO file format name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2129"/>
-        <oboInOwl:hasDefinition>Name of an OBO file format such as OBO-XML, plain and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2285">
-        <rdfs:label>Gene ID (MIPS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier for genetic elements in MIPS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>MIPS genetic element identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2288">
-        <rdfs:label>Sequence identifier (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An identifier of protein sequence(s) or protein sequence database entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1096"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2289">
-        <rdfs:label>Sequence identifier (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An identifier of nucleotide sequence(s) or nucleotide sequence database entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2290 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2290">
-        <rdfs:label>EMBL accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1103"/>
-        <oboInOwl:hasExactSynonym>EMBL ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>EMBL accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>EMBL identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An accession number of an entry from the EMBL sequence database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2291 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2291">
-        <rdfs:label>UniProt ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2154"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>UniProtKB identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An identifier of a polypeptide in the UniProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniProtKB entry name</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniProt identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniProt entry name</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2292">
-        <rdfs:label>GenBank accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1103"/>
-        <oboInOwl:hasExactSynonym>GenBank ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>GenBank identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of an entry from the GenBank sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>GenBank accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2293">
-        <rdfs:label>Gramene secondary identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2915"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gramene internal identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gramene internal ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Secondary (internal) identifier of a Gramene database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gramene secondary ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2294 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2294">
-        <rdfs:label>Sequence variation ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>An identifier of an entry from a database of molecular sequence variation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2295">
-        <rdfs:label>Gene ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1025"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <oboInOwl:hasExactSynonym>Gene accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene code</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2296 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2296">
-        <rdfs:label>Gene name (AceView)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>AceView gene name</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the AceView genes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2297">
-        <rdfs:label>Gene ID (ECK)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1795"/>
-        <oboInOwl:hasExactSynonym>ECK accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>E. coli K-12 gene identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an E. coli K-12 gene from EcoGene Database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>http://www.geneontology.org/doc/GO.xrf_abbs: ECK</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2298">
-        <rdfs:label>Gene ID (HGNC)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>HGNC ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier for a gene approved by the HUGO Gene Nomenclature Committee.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2299">
-        <rdfs:label>Gene name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1025"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDefinition>The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Allele name</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2300">
-        <rdfs:label>Gene name (NCBI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>NCBI gene name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the NCBI genes database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2301">
-        <rdfs:label>SMILES string</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0846"/>
-        <oboInOwl:hasDefinition>A specification of a chemical structure in SMILES format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2302">
-        <rdfs:label>STRING ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the STRING database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2307">
-        <rdfs:label>Virus annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a specific virus.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2308">
-        <rdfs:label>Virus annotation (taxonomy)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on the taxonomy of a specific virus.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2309">
-        <rdfs:label>Reaction ID (SABIO-RK)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from the SABIO-RK reactions database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2313">
-        <rdfs:label>Carbohydrate report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:hasDefinition>Annotation on or information derived from one or more specific carbohydrate 3D structure(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2314">
-        <rdfs:label>GI number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2362"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>NCBI GI number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>gi number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.</oboInOwl:hasDefinition>
-        <rdfs:comment>Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2315">
-        <rdfs:label>NCBI version</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2362"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>NCBI accession.version</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number.</rdfs:comment>
-        <oboInOwl:hasDefinition>An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>accession.version</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2316">
-        <rdfs:label>Cell line name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1046"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2317 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2317">
-        <rdfs:label>Cell line name (exact)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2318">
-        <rdfs:label>Cell line name (truncated)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2319 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2319">
-        <rdfs:label>Cell line name (no punctuation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2320">
-        <rdfs:label>Cell line name (assonant)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2316"/>
-        <oboInOwl:hasDefinition>The name of a cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2321">
-        <rdfs:label>Enzyme ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1010"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique, persistent identifier of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Enzyme accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2325">
-        <rdfs:label>REBASE enzyme number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasDefinition>Identifier of an enzyme from the REBASE enzymes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2326">
-        <rdfs:label>DrugBank ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>DB[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a drug from the DrugBank database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2327">
-        <rdfs:label>GI number (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2314"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>protein gi number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A unique identifier assigned to NCBI protein sequence records.</oboInOwl:hasDefinition>
-        <rdfs:comment>Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>protein gi</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2335">
-        <rdfs:label>Bit score</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1413"/>
-        <oboInOwl:hasDefinition>A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system.</oboInOwl:hasDefinition>
-        <rdfs:comment>Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2336">
-        <rdfs:label>Translation phase specification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2534"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phase</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2337">
-        <rdfs:label>Resource metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Data concerning or describing some core computational resource, as distinct from primary data.  This includes metadata on the origin, source, history, ownership or location of some thing.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Provenance metadata</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2338">
-        <rdfs:label>Ontology identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Any arbitrary identifier of an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2339">
-        <rdfs:label>Ontology concept name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3025"/>
-        <oboInOwl:hasDefinition>The name of a concept in an ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2340">
-        <rdfs:label>Genome build identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2749"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a build of a particular genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2342">
-        <rdfs:label>Pathway or network name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1082"/>
-        <oboInOwl:hasDefinition>The name of a biological pathway or network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2343">
-        <rdfs:label>Pathway ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the KEGG pathway database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]{2,3}[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>KEGG pathway ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2344">
-        <rdfs:label>Pathway ID (NCI-Nature)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the NCI-Nature pathway database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2345">
-        <rdfs:label>Pathway ID (ConsensusPathDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2917"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the ConsensusPathDB pathway database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2346">
-        <rdfs:label>Sequence cluster ID (UniRef)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniRef cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniRef entry accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2347 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2347">
-        <rdfs:label>Sequence cluster ID (UniRef100)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2346"/>
-        <oboInOwl:hasExactSynonym>UniRef100 cluster id</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniRef100 entry accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef100 database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2348">
-        <rdfs:label>Sequence cluster ID (UniRef90)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2346"/>
-        <oboInOwl:hasExactSynonym>UniRef90 entry accession</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniRef90 cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef90 database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2349">
-        <rdfs:label>Sequence cluster ID (UniRef50)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2346"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>UniRef50 cluster id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniRef50 entry accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the UniRef50 database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2353">
-        <rdfs:label>Ontology data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data concerning or derived from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ontological data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2354">
-        <rdfs:label>RNA family report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3148"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific RNA family or other group of classified RNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA family annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2355">
-        <rdfs:label>RNA family identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an RNA family, typically an entry from a RNA sequence classification database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2356">
-        <rdfs:label>RFAM accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2355"/>
-        <oboInOwl:hasDefinition>Stable accession number of an entry (RNA family) from the RFAM database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2357">
-        <rdfs:label>Protein signature type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2358">
-        <rdfs:label>Domain-nucleic acid interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on protein domain-DNA/RNA interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1567"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2359">
-        <rdfs:label>Domain-domain interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on protein domain-protein domain interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0906"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2360">
-        <rdfs:label>Domain-domain interaction (indirect)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data on indirect protein domain-protein domain interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2359"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2362 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2362">
-        <rdfs:label>Sequence accession (hybrid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1093"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Accession number of a nucleotide or protein sequence database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2363 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2363">
-        <rdfs:label>2D PAGE data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning two-dimensional polygel electrophoresis.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0942"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2364"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2364 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2364">
-        <rdfs:label>2D PAGE report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>two-dimensional gel electrophoresis experiments, gels or spots in a gel.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2365">
-        <rdfs:label>Pathway or network accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>A persistent, unique identifier of a biological pathway or network (typically a database entry).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2366">
-        <rdfs:label>Secondary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <oboInOwl:hasDefinition>Alignment of the (1D representations of) secondary structure of two or more molecules.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2367 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2367">
-        <rdfs:label>ASTD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an object from the ASTD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2368">
-        <rdfs:label>ASTD ID (exon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an exon from the ASTD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2369">
-        <rdfs:label>ASTD ID (intron)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an intron from the ASTD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2370">
-        <rdfs:label>ASTD ID (polya)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <oboInOwl:hasDefinition>Identifier of a polyA signal from the ASTD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2371">
-        <rdfs:label>ASTD ID (tss)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2367"/>
-        <oboInOwl:hasDefinition>Identifier of a transcription start site from the ASTD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2372">
-        <rdfs:label>2D PAGE spot report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>2D PAGE spot annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2373 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2373">
-        <rdfs:label>Spot ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a spot from a two-dimensional (protein) gel.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2374 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2374">
-        <rdfs:label>Spot serial number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2373"/>
-        <oboInOwl:hasDefinition>Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2375 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2375">
-        <rdfs:label>Spot ID (HSC-2DPAGE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2373"/>
-        <oboInOwl:hasDefinition>Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2378">
-        <rdfs:label>Protein-motif interaction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1565"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2379">
-        <rdfs:label>Strain identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <oboInOwl:hasDefinition>Identifier of a strain of an organism variant, typically a plant, virus or bacterium.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2380 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2380">
-        <rdfs:label>CABRI accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>A unique identifier of an item from the CABRI database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2381 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2381">
-        <rdfs:label>Experiment report (genotyping)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2382 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2382">
-        <rdfs:label>Genotype experiment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of genotype experiment metadata.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2383">
-        <rdfs:label>EGA accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2382"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the EGA database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2384">
-        <rdfs:label>IPI protein ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <oboInOwl:hasDefinition>Identifier of a protein entry catalogued in the International Protein Index (IPI) database.</oboInOwl:hasDefinition>
-        <regex>IPI[0-9]{8}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2385">
-        <rdfs:label>RefSeq accession (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1098"/>
-        <oboInOwl:hasExactSynonym>RefSeq protein ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of a protein from the RefSeq database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2386">
-        <rdfs:label>EPD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2727"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (promoter) from the EPD database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EPD identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2387">
-        <rdfs:label>TAIR accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the TAIR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2388">
-        <rdfs:label>TAIR accession (At gene)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1037"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an Arabidopsis thaliana gene from the TAIR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2389 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2389">
-        <rdfs:label>UniSTS accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UniSTS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2390">
-        <rdfs:label>UNITE accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UNITE database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2391">
-        <rdfs:label>UTR accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UTR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2392 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2392">
-        <rdfs:label>UniParc accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>UPI[A-F0-9]{10}</regex>
-        <oboInOwl:hasDefinition>Accession number of a UniParc (protein sequence) database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniParc ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UPI</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2393">
-        <rdfs:label>mFLJ/mKIAA number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Rouge or HUGE databases.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2395">
-        <rdfs:label>Fungi annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>An informative report on a specific fungus.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2396">
-        <rdfs:label>Fungi annotation (anamorph)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific fungus anamorph.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2397">
-        <rdfs:label>Gene features report (exon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>exons in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2398">
-        <rdfs:label>Ensembl protein ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>Ensembl ID (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein ID (Ensembl)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2399">
-        <rdfs:label>Gene transcriptional features report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>transcription of DNA into RNA including the regulation of transcription.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2400">
-        <rdfs:label>Toxin annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a specific toxin.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2401">
-        <rdfs:label>Protein report (membrane protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on a membrane protein.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1456"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2402">
-        <rdfs:label>Protein-drug interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1537"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1566"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1696"/>
-        <oboInOwl:hasDefinition>An informative report on tentative or known protein-drug interaction(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2522">
-        <rdfs:label>Map data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning a map of molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1274"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2019"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2523">
-        <rdfs:label>Phylogenetic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasDefinition>Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic data</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2524">
-        <rdfs:label>Protein data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning one or more protein molecules.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2525">
-        <rdfs:label>Nucleic acid data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning one or more nucleic acid molecules.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2526">
-        <rdfs:label>Article data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Article report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0971"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2527">
-        <rdfs:label>Parameter</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000144</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Tool-specific parameter</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Typically a simple numerical or string value that controls the operation of a tool.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Parameters</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Tool parameter</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2528">
-        <rdfs:label>Molecular data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Molecule-specific data</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning a specific type of molecule.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2529">
-        <rdfs:label>Molecule report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a specific molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Molecular report</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0896"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2530">
-        <rdfs:label>Organism report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report on a specific organism.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Organism annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2531">
-        <rdfs:label>Experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasExactSynonym>Experiment metadata</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Experiment annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation on a wet lab experiment, such as experimental conditions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2533">
-        <rdfs:label>Nucleic acid features report (mutation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>DNA mutation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2534">
-        <rdfs:label>Sequence attribute</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:hasDefinition>An attribute of a molecular sequence, possibly in reference to some other sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Sequence parameter</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2535 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2535">
-        <rdfs:label>Sequence tag profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0928"/>
-        <rdfs:comment>SAGE, MPSS and SBS experiments are usually performed to study gene expression.  The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequencing-based expression profile</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment.  In all cases this is a list of short sequence tags and the number of times it is observed.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2536">
-        <rdfs:label>Mass spectrometry data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning a mass spectrometry measurement.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2537">
-        <rdfs:label>Protein structure raw data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw data from experimental methods for determining protein structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2538 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2538">
-        <rdfs:label>Mutation identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a mutation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2539">
-        <rdfs:label>Alignment data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  This includes entities derived from sequences and structures such as motifs and profiles.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning an alignment of two or more molecular sequences, structures or derived data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1916"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2540">
-        <rdfs:label>Data index data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning an index of data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Database index</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0955"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2563">
-        <rdfs:label>Amino acid name (single letter)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Single letter amino acid identifier, e.g. G.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2564">
-        <rdfs:label>Amino acid name (three letter)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Three letter amino acid identifier, e.g. GLY.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2565">
-        <rdfs:label>Amino acid name (full name)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Full name of an amino acid, e.g. Glycine.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2576 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2576">
-        <rdfs:label>Toxin identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2852"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a toxin.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2578">
-        <rdfs:label>ArachnoServer ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2897"/>
-        <oboInOwl:hasDefinition>Unique identifier of a toxin from the ArachnoServer database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2579">
-        <rdfs:label>Expressed gene list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasExactSynonym>Gene annotation (expressed gene list)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A simple summary of expressed genes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2580 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2580">
-        <rdfs:label>BindingDB Monomer ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Unique identifier of a monomer from the BindingDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2581">
-        <rdfs:label>GO concept name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a concept from the GO ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2582">
-        <rdfs:label>GO concept ID (biological process)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1176"/>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a &apos;biological process&apos; concept from the the Gene Ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2583">
-        <rdfs:label>GO concept ID (molecular function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1176"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <oboInOwl:hasDefinition>An identifier of a &apos;molecular function&apos; concept from the the Gene Ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2584 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2584">
-        <rdfs:label>GO concept name (cellular component)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The name of a concept for a cellular component from the GO ontology.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2586 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2586">
-        <rdfs:label>Northern blot image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An image arising from a Northern Blot experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2587 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2587">
-        <rdfs:label>Blot ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Unique identifier of a blot from a Northern Blot.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2588 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2588">
-        <rdfs:label>BlotBase blot ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2587"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a blot from a Northern Blot from the BlotBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2589 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2589">
-        <rdfs:label>Hierarchy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Hierarchy annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2590 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2590">
-        <rdfs:label>Hierarchy identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from a database of biological hierarchies.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2891"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2591 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2591">
-        <rdfs:label>Brite hierarchy ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2891"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Brite database of biological hierarchies.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2592 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2592">
-        <rdfs:label>Cancer type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A type (represented as a string) of cancer.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2100"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2593">
-        <rdfs:label>BRENDA organism ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <oboInOwl:hasDefinition>A unique identifier for an organism used in the BRENDA database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2594">
-        <rdfs:label>UniGene taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <oboInOwl:hasDefinition>The name of a taxon using the controlled vocabulary of the UniGene database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniGene organism abbreviation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2595">
-        <rdfs:label>UTRdb taxon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a taxon using the controlled vocabulary of the UTRdb database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2596 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2596">
-        <rdfs:label>Catalogue ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a catalogue of biological resources.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Catalogue identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2597 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2597">
-        <rdfs:label>CABRI catalogue name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2596"/>
-        <oboInOwl:hasDefinition>The name of a catalogue of biological resources from the CABRI database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2598">
-        <rdfs:label>Secondary structure alignment metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on protein secondary structure alignment-derived data or metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2083"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2599 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2599">
-        <rdfs:label>Molecule interaction report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Molecular interaction report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Molecular interaction data</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0906"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2600 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2600">
-        <rdfs:label>Pathway or network</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Network</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Pathway</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2601">
-        <rdfs:label>Small molecule data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning one or more small molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2602">
-        <rdfs:label>Genotype and phenotype data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning a particular genotype, phenotype or a genotype / phenotype relation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0920"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2603 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2603">
-        <rdfs:label>Gene expression data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image or hybridisation data for a microarray, typically a study of gene expression.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Microarray data</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.  See also http://edamontology.org/data_0931</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2605">
-        <rdfs:label>Compound ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>C[0-9]+</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a chemical compound from the KEGG database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>KEGG compound ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>KEGG compound identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2606">
-        <rdfs:label>RFAM name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2355"/>
-        <oboInOwl:hasDefinition>Name (not necessarily stable) an entry (RNA family) from the RFAM database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2608">
-        <rdfs:label>Reaction ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction from the KEGG reactions database.</oboInOwl:hasDefinition>
-        <regex>R[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2609 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2609">
-        <rdfs:label>Drug ID (KEGG)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a drug from the KEGG Drug database.</oboInOwl:hasDefinition>
-        <regex>D[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2610">
-        <rdfs:label>Ensembl ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENS[A-Z]*[FPTG][0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ensembl IDs</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2611">
-        <rdfs:label>ICD identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1150"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1622"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of a disease from the International Classification of Diseases (ICD) database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[A-Z][0-9]+(\.[-[0-9]+])?</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2612">
-        <rdfs:label>Sequence cluster ID (CluSTr)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1112"/>
-        <oboInOwl:hasDefinition>Unique identifier of a sequence cluster from the CluSTr database.</oboInOwl:hasDefinition>
-        <regex>[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?</regex>
-        <oboInOwl:hasExactSynonym>CluSTr ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CluSTr cluster ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2613">
-        <rdfs:label>KEGG Glycan ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <regex>G[0-9]+</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2614 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2614">
-        <rdfs:label>TCDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>OBO file for regular expression.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>TC number</oboInOwl:hasExactSynonym>
-        <regex>[0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+</regex>
-        <oboInOwl:hasDefinition>A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2615 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2615">
-        <rdfs:label>MINT ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>MINT\-[0-9]{1,5}</regex>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the MINT database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2616">
-        <rdfs:label>DIP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the DIP database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>DIP[\:\-][0-9]{3}[EN]</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2617">
-        <rdfs:label>Signaling Gateway protein ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database.</oboInOwl:hasDefinition>
-        <regex>A[0-9]{6}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2618">
-        <rdfs:label>Protein modification ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein modification catalogued in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2619 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2619">
-        <rdfs:label>RESID ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2618"/>
-        <oboInOwl:hasDefinition>Identifier of a protein modification catalogued in the RESID database.</oboInOwl:hasDefinition>
-        <regex>AA[0-9]{4}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2620">
-        <rdfs:label>RGD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <regex>[0-9]{4,7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the RGD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2621">
-        <rdfs:label>TAIR accession (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2387"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <regex>AASequence:[0-9]{10}</regex>
-        <oboInOwl:hasDefinition>Identifier of a protein sequence from the TAIR database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2622">
-        <rdfs:label>Compound ID (HMDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>HMDB[0-9]{5}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>HMDB ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2625 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2625">
-        <rdfs:label>LIPID MAPS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2905"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>LM ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an entry from the LIPID MAPS database.</oboInOwl:hasDefinition>
-        <regex>LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2626 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2626">
-        <rdfs:label>PeptideAtlas ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2906"/>
-        <oboInOwl:hasDefinition>Identifier of a peptide from the PeptideAtlas peptide databases.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>PDBML:pdbx_PDB_strand_id</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PAp[0-9]{8}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2627 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2627">
-        <rdfs:label>Molecular interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of a report of molecular interactions from a database (typically).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2628 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2628">
-        <rdfs:label>BioGRID interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of an interaction from the BioGRID database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2629 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2629">
-        <rdfs:label>Enzyme ID (MEROPS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasExactSynonym>MEROPS ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of a peptidase enzyme from the MEROPS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>S[0-9]{2}\.[0-9]{3}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2630 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2630">
-        <rdfs:label>Mobile genetic element ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>An identifier of a mobile genetic element.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2631 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2631">
-        <rdfs:label>ACLAME ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2630"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>mge:[0-9]+</regex>
-        <oboInOwl:hasDefinition>An identifier of a mobile genetic element from the Aclame database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2632 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2632">
-        <rdfs:label>SGD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <regex>PWY[a-zA-Z_0-9]{2}\-[0-9]{3}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the Saccharomyces genome database (SGD).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2633 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2633">
-        <rdfs:label>Book ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a book.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2634 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2634">
-        <rdfs:label>ISBN</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2633"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)</regex>
-        <oboInOwl:hasDefinition>The International Standard Book Number (ISBN) is for identifying printed books.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2635 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2635">
-        <rdfs:label>Compound ID (3DMET)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <regex>B[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>3DMET ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a metabolite from the 3DMET database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2636 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2636">
-        <rdfs:label>MatrixDB interaction ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <regex>([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)</regex>
-        <oboInOwl:hasDefinition>A unique identifier of an interaction from the MatrixDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2637 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2637">
-        <rdfs:label>cPath ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <regex>[0-9]+</regex>
-        <rdfs:comment>These identifiers are unique within the cPath database, however, they are not stable between releases.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2638 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2638">
-        <rdfs:label>PubChem bioassay ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2639"/>
-        <oboInOwl:hasDefinition>Identifier of an assay from the PubChem database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2639 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2639">
-        <rdfs:label>PubChem ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasExactSynonym>PubChem identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the PubChem database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2641 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2641">
-        <rdfs:label>Reaction ID (MACie)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>M[0-9]{4}</regex>
-        <oboInOwl:hasExactSynonym>MACie entry number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of an enzyme reaction mechanism from the MACie database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2642 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2642">
-        <rdfs:label>Gene ID (miRBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>miRNA name</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>miRNA ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier for a gene from the miRBase database.</oboInOwl:hasDefinition>
-        <regex>MI[0-9]{7}</regex>
-        <oboInOwl:hasExactSynonym>miRNA identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2643 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2643">
-        <rdfs:label>Gene ID (ZFIN)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier for a gene from the Zebrafish information network genome (ZFIN) database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ZDB\-GENE\-[0-9]+\-[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2644 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2644">
-        <rdfs:label>Reaction ID (Rhea)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2108"/>
-        <regex>[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Identifier of an enzyme-catalysed reaction from the Rhea database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2645 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2645">
-        <rdfs:label>Pathway ID (Unipathway)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <regex>UPA[0-9]{5}</regex>
-        <oboInOwl:hasExactSynonym>upaid</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a biological pathway from the Unipathway database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2646 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2646">
-        <rdfs:label>Compound ID (ChEMBL)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of a small molecular from the ChEMBL database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChEMBL ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2647 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2647">
-        <rdfs:label>LGICdb identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2648 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2648">
-        <rdfs:label>Reaction kinetics ID (SABIO-RK)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2309"/>
-        <oboInOwl:hasDefinition>Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2649 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2649">
-        <rdfs:label>PharmGKB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2650 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2650">
-        <rdfs:label>Pathway ID (PharmGKB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2649"/>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2651 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2651">
-        <rdfs:label>Disease ID (PharmGKB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1150"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2649"/>
-        <oboInOwl:hasDefinition>Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2652 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2652">
-        <rdfs:label>Drug ID (PharmGKB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2649"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).</oboInOwl:hasDefinition>
-        <regex>PA[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2653 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2653">
-        <rdfs:label>Drug ID (TTD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <regex>DAP[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a drug from the Therapeutic Target Database (TTD).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2654 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2654">
-        <rdfs:label>Target ID (TTD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <regex>TTDS[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a target protein from the Therapeutic Target Database (TTD).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2655 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2655">
-        <rdfs:label>Cell type identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Cell type ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A unique identifier of a type or group of cells.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2656 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2656">
-        <rdfs:label>NeuronDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2893"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a neuron from the NeuronDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2657 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2657">
-        <rdfs:label>NeuroMorpho ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of a neuron from the NeuroMorpho database.</oboInOwl:hasDefinition>
-        <regex>[a-zA-Z_0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2658 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2658">
-        <rdfs:label>Compound ID (ChemIDplus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2894"/>
-        <oboInOwl:hasDefinition>Identifier of a chemical from the ChemIDplus database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChemIDplus ID</oboInOwl:hasExactSynonym>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2659 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2659">
-        <rdfs:label>Pathway ID (SMPDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the Small Molecule Pathway Database (SMPDB).</oboInOwl:hasDefinition>
-        <regex>SMP[0-9]{5}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2660 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2660">
-        <rdfs:label>BioNumbers ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2662 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2662">
-        <rdfs:label>T3DB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2897"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>T3D[0-9]+</regex>
-        <oboInOwl:hasDefinition>Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2663 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2663">
-        <rdfs:label>Carbohydrate identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2313"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1462"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a carbohydrate.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2664 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2664">
-        <rdfs:label>GlycomeDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GlycomeDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2665 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2665">
-        <rdfs:label>LipidBank ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2905"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[a-zA-Z_0-9]+[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry from the LipidBank database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2666 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2666">
-        <rdfs:label>CDD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1038"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>cd[0-9]{5}</regex>
-        <oboInOwl:hasDefinition>Identifier of a conserved domain from the Conserved Domain Database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2667 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2667">
-        <rdfs:label>MMDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1070"/>
-        <regex>[0-9]{1,5}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of an entry from the MMDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>MMDB accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2668 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2668">
-        <rdfs:label>iRefIndex ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1074"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the iRefIndex database of protein-protein interactions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2669 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2669">
-        <rdfs:label>ModelDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2891"/>
-        <oboInOwl:hasDefinition>Unique identifier of an entry from the ModelDB database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2670 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2670">
-        <rdfs:label>Pathway ID (DQCS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <regex>[0-9]+</regex>
-        <oboInOwl:hasDefinition>Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2671 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2671">
-        <rdfs:label>Ensembl ID (Homo sapiens)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENS([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (Homo sapiens division).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2672 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2672">
-        <rdfs:label>Ensembl ID (&apos;Bos taurus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Bos taurus&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSBTA([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2673 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2673">
-        <rdfs:label>Ensembl ID (&apos;Canis familiaris&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Canis familiaris&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSCAF([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2674 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2674">
-        <rdfs:label>Ensembl ID (&apos;Cavia porcellus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSCPO([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Cavia porcellus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2675 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2675">
-        <rdfs:label>Ensembl ID (&apos;Ciona intestinalis&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Ciona intestinalis&apos; division).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSCIN([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2676 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2676">
-        <rdfs:label>Ensembl ID (&apos;Ciona savignyi&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Ciona savignyi&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSCSAV([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2677 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2677">
-        <rdfs:label>Ensembl ID (&apos;Danio rerio&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Danio rerio&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSDAR([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2678 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2678">
-        <rdfs:label>Ensembl ID (&apos;Dasypus novemcinctus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Dasypus novemcinctus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSDNO([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2679 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2679">
-        <rdfs:label>Ensembl ID (&apos;Echinops telfairi&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSETE([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Echinops telfairi&apos; division).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2680 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2680">
-        <rdfs:label>Ensembl ID (&apos;Erinaceus europaeus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSEEU([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Erinaceus europaeus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2681 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2681">
-        <rdfs:label>Ensembl ID (&apos;Felis catus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSFCA([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Felis catus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2682 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2682">
-        <rdfs:label>Ensembl ID (&apos;Gallus gallus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSGAL([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Gallus gallus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2683 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2683">
-        <rdfs:label>Ensembl ID (&apos;Gasterosteus aculeatus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Gasterosteus aculeatus&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSGAC([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2684 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2684">
-        <rdfs:label>Ensembl ID (&apos;Homo sapiens&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSHUM([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Homo sapiens&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2685 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2685">
-        <rdfs:label>Ensembl ID (&apos;Loxodonta africana&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Loxodonta africana&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSLAF([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2686 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2686">
-        <rdfs:label>Ensembl ID (&apos;Macaca mulatta&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Macaca mulatta&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSMMU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2687 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2687">
-        <rdfs:label>Ensembl ID (&apos;Monodelphis domestica&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Monodelphis domestica&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSMOD([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2688 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2688">
-        <rdfs:label>Ensembl ID (&apos;Mus musculus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSMUS([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Mus musculus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2689 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2689">
-        <rdfs:label>Ensembl ID (&apos;Myotis lucifugus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSMLU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Myotis lucifugus&apos; division).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2690 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2690">
-        <rdfs:label>Ensembl ID (&quot;Ornithorhynchus anatinus&quot;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Ornithorhynchus anatinus&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSOAN([EGTP])[0-9]{11}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2691 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2691">
-        <rdfs:label>Ensembl ID (&apos;Oryctolagus cuniculus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSOCU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Oryctolagus cuniculus&apos; division).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2692 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2692">
-        <rdfs:label>Ensembl ID (&apos;Oryzias latipes&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <regex>ENSORL([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Oryzias latipes&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2693 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2693">
-        <rdfs:label>Ensembl ID (&apos;Otolemur garnettii&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Otolemur garnettii&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <regex>ENSSAR([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2694 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2694">
-        <rdfs:label>Ensembl ID (&apos;Pan troglodytes&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSPTR([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Pan troglodytes&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2695 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2695">
-        <rdfs:label>Ensembl ID (&apos;Rattus norvegicus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Rattus norvegicus&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSRNO([EGTP])[0-9]{11}</regex>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2696 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2696">
-        <rdfs:label>Ensembl ID (&apos;Spermophilus tridecemlineatus&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <regex>ENSSTO([EGTP])[0-9]{11}</regex>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Spermophilus tridecemlineatus&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2697 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2697">
-        <rdfs:label>Ensembl ID (&apos;Takifugu rubripes&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Takifugu rubripes&apos; division).</oboInOwl:hasDefinition>
-        <regex>ENSFRU([EGTP])[0-9]{11}</regex>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2698 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2698">
-        <rdfs:label>Ensembl ID (&apos;Tupaia belangeri&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Tupaia belangeri&apos; division).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSTBE([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2699 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2699">
-        <rdfs:label>Ensembl ID (&apos;Xenopus tropicalis&apos;)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Identifier of an entry (exon, gene, transcript or protein) from the Ensembl &apos;core&apos; database (&apos;Xenopus tropicalis&apos; division).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <regex>ENSXET([EGTP])[0-9]{11}</regex>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2610"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2700 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2700">
-        <rdfs:label>CATH identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1038"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a protein domain (or other node) from the CATH database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2701 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2701">
-        <rdfs:label>CATH node ID (family)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1043"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A code number identifying a family from the CATH database.</oboInOwl:hasDefinition>
-        <example>2.10.10.10</example>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2702 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2702">
-        <rdfs:label>Enzyme ID (CAZy)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2321"/>
-        <oboInOwl:hasDefinition>Identifier of an enzyme from the CAZy enzymes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CAZy ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2704 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2704">
-        <rdfs:label>Clone ID (IMAGE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1855"/>
-        <oboInOwl:hasExactSynonym>I.M.A.G.E. cloneID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>IMAGE cloneID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2705 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2705">
-        <rdfs:label>GO concept ID (cellular compartment)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1176"/>
-        <oboInOwl:hasDefinition>An identifier of a &apos;cellular compartment&apos; concept from the Gene Ontology.</oboInOwl:hasDefinition>
-        <regex>[0-9]{7}|GO:[0-9]{7}</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>GO concept identifier (cellular compartment)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2706 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2706">
-        <rdfs:label>Chromosome name (BioCyc)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0987"/>
-        <oboInOwl:hasDefinition>Name of a chromosome as used in the BioCyc database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2709 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2709">
-        <rdfs:label>CleanEx entry name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a gene expression profile from the CleanEx database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2710 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2710">
-        <rdfs:label>CleanEx dataset code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2711 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2711">
-        <rdfs:label>Genome report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2530"/>
-        <oboInOwl:hasDefinition>An informative report of general information concerning a genome as a whole.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2713 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2713">
-        <rdfs:label>Protein ID (CORUM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>CORUM complex ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a protein complex from the CORUM database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2714 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2714">
-        <rdfs:label>CDD PSSM-ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1115"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier of a position-specific scoring matrix from the CDD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2715 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2715">
-        <rdfs:label>Protein ID (CuticleDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>CuticleDB ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the CuticleDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2716 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2716">
-        <rdfs:label>DBD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2911"/>
-        <oboInOwl:hasDefinition>Identifier of a predicted transcription factor from the DBD database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2717 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2717">
-        <rdfs:label>Oligonucleotide probe annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3115"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>General annotation on an oligonucleotide probe.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2718 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2718">
-        <rdfs:label>Oligonucleotide ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasDefinition>Identifier of an oligonucleotide from a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2719 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2719">
-        <rdfs:label>dbProbe ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2718"/>
-        <oboInOwl:hasDefinition>Identifier of an oligonucleotide probe from the dbProbe database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2720 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2720">
-        <rdfs:label>Dinucleotide property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2088"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Physicochemical property data for one or more dinucleotides.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2721 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2721">
-        <rdfs:label>DiProDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2718"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an dinucleotide property from the DiProDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2722 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2722">
-        <rdfs:label>Protein features report (disordered structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>disordered structure in a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2723 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2723">
-        <rdfs:label>Protein ID (DisProt)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>DisProt ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the DisProt database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2724 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2724">
-        <rdfs:label>Embryo report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Annotation on an embryo or concerning embryological development.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Embryo annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1713"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2725 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2725">
-        <rdfs:label>Ensembl transcript ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2769"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Transcript ID (Ensembl)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a gene transcript from the Ensembl database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2726 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2726">
-        <rdfs:label>Inhibitor annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on one or more small molecules that are enzyme inhibitors.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0962"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2727 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2727">
-        <rdfs:label>Promoter ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a promoter of a gene that is catalogued in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>Moby:GeneAccessionList</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2728 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2728">
-        <rdfs:label>EST accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1855"/>
-        <oboInOwl:hasDefinition>Identifier of an EST sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2729 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2729">
-        <rdfs:label>COGEME EST ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an EST sequence from the COGEME database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2730 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2730">
-        <rdfs:label>COGEME unisequence ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <oboInOwl:hasDefinition>Identifier of a unisequence from the COGEME database.</oboInOwl:hasDefinition>
-        <rdfs:comment>A unisequence is a single sequence assembled from ESTs.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2731 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2731">
-        <rdfs:label>Protein family ID (GeneFarm)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasExactSynonym>GeneFarm family ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession number of an entry (family) from the TIGRFam database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2732 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2732">
-        <rdfs:label>Family name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1868"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a family of organism.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2733 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2733">
-        <rdfs:label>Genus name (virus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a genus of viruses.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1870"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2734 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2734">
-        <rdfs:label>Family name (virus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>The name of a family of viruses.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2732"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2735 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2735">
-        <rdfs:label>Database name (SwissRegulon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>The name of a SwissRegulon database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2736 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2736">
-        <rdfs:label>Sequence feature ID (SwissRegulon)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1015"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A feature identifier as used in the SwissRegulon database.</oboInOwl:hasDefinition>
-        <rdfs:comment>This can be name of a gene, the ID of a TFBS, or genomic coordinates in form &quot;chr:start..end&quot;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2737 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2737">
-        <rdfs:label>FIG ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <rdfs:comment>A FIG ID consists of four parts: a prefix, genome id, locus type and id number.</rdfs:comment>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the NMPDR database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2738 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2738">
-        <rdfs:label>Gene ID (Xenbase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the Xenbase database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2739 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2739">
-        <rdfs:label>Gene ID (Genolist)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the Genolist database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2740 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2740">
-        <rdfs:label>Gene name (Genolist)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Genolist gene name</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the Genolist genes database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1026"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2741 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2741">
-        <rdfs:label>ABS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2727"/>
-        <oboInOwl:hasExactSynonym>ABS identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry (promoter) from the ABS database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2742 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2742">
-        <rdfs:label>AraC-XylS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2911"/>
-        <oboInOwl:hasDefinition>Identifier of a transcription factor from the AraC-XylS database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2743 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2743">
-        <rdfs:label>Gene name (HUGO)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Name of an entry (gene) from the HUGO database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1791"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2744 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2744">
-        <rdfs:label>Locus ID (PseudoCAP)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a locus from the PseudoCAP database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2745 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2745">
-        <rdfs:label>Locus ID (UTR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a locus from the UTR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2746 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2746">
-        <rdfs:label>MonosaccharideDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2898"/>
-        <oboInOwl:hasDefinition>Unique identifier of a monosaccharide from the MonosaccharideDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2747 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2747">
-        <rdfs:label>Database name (CMD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a subdivision of the Collagen Mutation Database (CMD) database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2748 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2748">
-        <rdfs:label>Database name (Osteogenesis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>The name of a subdivision of the Osteogenesis database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0957"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2749 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2749">
-        <rdfs:label>Genome identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a particular genome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2751 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2751">
-        <rdfs:label>GenomeReviews ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2903"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a particular genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2752 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2752">
-        <rdfs:label>GlycoMap ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <regex>[0-9]+</regex>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GlycosciencesDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2753 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2753">
-        <rdfs:label>Carbohydrate conformational map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3425"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A conformational energy map of the glycosidic linkages in a carbohydrate molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2754 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2754">
-        <rdfs:label>Gene features report (intron)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>introns in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2755 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2755">
-        <rdfs:label>Transcription factor name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1077"/>
-        <oboInOwl:hasDefinition>The name of a transcription factor.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2756 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2756">
-        <rdfs:label>TCID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Identifier of a membrane transport proteins from the transport classification database (TCDB).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2757 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2757">
-        <rdfs:label>Pfam domain name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1131"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a domain from the Pfam database.</oboInOwl:hasDefinition>
-        <regex>PF[0-9]{5}</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2758 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2758">
-        <rdfs:label>Pfam clan ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <regex>CL[0-9]{4}</regex>
-        <oboInOwl:hasDefinition>Accession number of a Pfam clan.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2759 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2759">
-        <rdfs:label>Gene ID (VectorBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasExactSynonym>VectorBase ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier for a gene from the VectorBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2761 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2761">
-        <rdfs:label>UTRSite ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1114"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2762 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2762">
-        <rdfs:label>Sequence signature report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence motif report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2763 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2763">
-        <rdfs:label>Locus annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Locus report</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report on a particular locus.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2764 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2764">
-        <rdfs:label>Protein name (UniProt)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <oboInOwl:hasDefinition>Official name of a protein as used in the UniProt database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2765 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2765">
-        <rdfs:label>Term ID list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>One or more terms from one or more controlled vocabularies which are annotations on an entity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included.</rdfs:comment>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2872"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2766 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2766">
-        <rdfs:label>HAMAP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <oboInOwl:hasDefinition>Name of a protein family from the HAMAP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2767 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2767">
-        <rdfs:label>Identifier with metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:hasDefinition>Basic information concerning an identifier of data (typically including the identifier itself).  For example, a gene symbol with information concerning its provenance.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2768 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2768">
-        <rdfs:label>Gene symbol annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation about a gene symbol.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2767"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2769 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2769">
-        <rdfs:label>Transcript ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2119"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1276"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a RNA transcript.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2770 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2770">
-        <rdfs:label>HIT ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2769"/>
-        <oboInOwl:hasDefinition>Identifier of an RNA transcript from the H-InvDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2771 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2771">
-        <rdfs:label>HIX ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>A unique identifier of gene cluster in the H-InvDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2772 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2772">
-        <rdfs:label>HPA antibody id</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a antibody from the HPA database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2773 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2773">
-        <rdfs:label>IMGT/HLA ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasDefinition>Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2774 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2774">
-        <rdfs:label>Gene ID (JCVI)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2775 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2775">
-        <rdfs:label>Kinase name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1009"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a kinase protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2776 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2776">
-        <rdfs:label>ConsensusPathDB entity ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2917"/>
-        <oboInOwl:hasDefinition>Identifier of a physical entity from the ConsensusPathDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2777 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2777">
-        <rdfs:label>ConsensusPathDB entity name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2917"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a physical entity from the ConsensusPathDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2778 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2778">
-        <rdfs:label>CCAP strain number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2912"/>
-        <oboInOwl:hasDefinition>The number of a strain of algae and protozoa from the CCAP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2779 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2779">
-        <rdfs:label>Stock number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of stock from a catalogue of biological resources.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2780 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2780">
-        <rdfs:label>Stock number (TAIR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2779"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A stock number from The Arabidopsis information resource (TAIR).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2781 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2781">
-        <rdfs:label>REDIdb ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the RNA editing database (REDIdb).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2782 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2782">
-        <rdfs:label>SMART domain name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1131"/>
-        <oboInOwl:hasDefinition>Name of a domain from the SMART database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2783 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2783">
-        <rdfs:label>Protein family ID (PANTHER)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2910"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Panther family ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession number of an entry (family) from the PANTHER database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2784 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2784">
-        <rdfs:label>RNAVirusDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2785"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.</rdfs:comment>
-        <oboInOwl:hasDefinition>A unique identifier for a virus from the RNAVirusDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2785 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2785">
-        <rdfs:label>Virus ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2913"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An accession of annotation on a (group of) viruses (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2786 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2786">
-        <rdfs:label>NCBI Genome Project ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2903"/>
-        <oboInOwl:hasDefinition>An identifier of a genome project assigned by NCBI.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2787 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2787">
-        <rdfs:label>NCBI genome accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2903"/>
-        <oboInOwl:hasDefinition>A unique identifier of a whole genome assigned by the NCBI.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2788 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2788">
-        <rdfs:label>Sequence profile data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it&apos;s construction, the biological role or annotation, and so on.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0860"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2789 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2789">
-        <rdfs:label>Protein ID (TopDB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>TopDB ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a membrane protein from the TopDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2790 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2790">
-        <rdfs:label>Gel ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasExactSynonym>Gel identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a two-dimensional (protein) gel.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2791 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2791">
-        <rdfs:label>Reference map name (SWISS-2DPAGE)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2790"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Name of a reference map gel from the SWISS-2DPAGE database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2792 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2792">
-        <rdfs:label>Protein ID (PeroxiBase)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <oboInOwl:hasExactSynonym>PeroxiBase ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a peroxidase protein from the PeroxiBase database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2793 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2793">
-        <rdfs:label>SISYPHUS ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1072"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an entry from the SISYPHUS database of tertiary structure alignments.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2794 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2794">
-        <rdfs:label>ORF ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1893"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2795"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of an open reading frame (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2795 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2795">
-        <rdfs:label>ORF identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of an open reading frame.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2796 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2796">
-        <rdfs:label>Linucs ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2900"/>
-        <oboInOwl:hasDefinition>Identifier of an entry from the GlycosciencesDB database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2797 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2797">
-        <rdfs:label>Protein ID (LGICdb)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>LGICdb ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a ligand-gated ion channel protein from the LGICdb database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2798 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2798">
-        <rdfs:label>MaizeDB ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2728"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of an EST sequence from the MaizeDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2799 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2799">
-        <rdfs:label>Gene ID (MfunGD)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier of gene in the MfunGD database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2800 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2800">
-        <rdfs:label>Orpha number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1150"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1622"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of a disease from the Orpha database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2802 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2802">
-        <rdfs:label>Protein ID (EcID)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a protein from the EcID database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2803 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2803">
-        <rdfs:label>Clone ID (RefSeq)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1098"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1855"/>
-        <oboInOwl:hasDefinition>A unique identifier of a cDNA molecule catalogued in the RefSeq database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2804 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2804">
-        <rdfs:label>Protein ID (ConoServer)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Unique identifier for a cone snail toxin protein from the ConoServer database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2805 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2805">
-        <rdfs:label>GeneSNP ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <oboInOwl:hasDefinition>Identifier of a GeneSNP database entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2812 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2812">
-        <rdfs:label>Lipid identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2850"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2879"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a lipid.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2831 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2831">
-        <rdfs:label>Databank</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A flat-file (textual) data archive.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2832 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2832">
-        <rdfs:label>Web portal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A web site providing data (web pages) on a common theme to a HTTP client.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2835 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2835">
-        <rdfs:label>Gene ID (VBASE2)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2295"/>
-        <oboInOwl:hasDefinition>Identifier for a gene from the VBASE2 database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>VBASE2 ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2836 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2836">
-        <rdfs:label>DPVweb ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2785"/>
-        <oboInOwl:hasExactSynonym>DPVweb virus ID</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A unique identifier for a virus from the DPVweb database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2837 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2837">
-        <rdfs:label>Pathway ID (BioSystems)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2365"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a pathway from the BioSystems pathway database.</oboInOwl:hasDefinition>
-        <regex>[0-9]+</regex>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2838 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2838">
-        <rdfs:label>Experimental data (proteomics)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning a proteomics experiment.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3147"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2849 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2849">
-        <rdfs:label>Abstract</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2526"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An abstract of a scientific article.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2850 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2850">
-        <rdfs:label>Lipid structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0883"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a lipid structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2851 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2851">
-        <rdfs:label>Drug structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1463"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the (3D) structure of a drug.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2852 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2852">
-        <rdfs:label>Toxin structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1463"/>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for the (3D) structure of a toxin.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2854 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2854">
-        <rdfs:label>Position-specific scoring matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1354"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PSSM</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2855 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2855">
-        <rdfs:label>Distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2856 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2856">
-        <rdfs:label>Structural distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2855"/>
-        <oboInOwl:hasDefinition>Distances (values representing similarity) between a group of molecular structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2857 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2857">
-        <rdfs:label>Article metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Bibliographic data concerning scientific article(s).</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2526"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2858 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2858">
-        <rdfs:label>Ontology concept</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2353"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes any fields from the concept definition such as concept name, definition, comments and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>A concept from a biological ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2865 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2865">
-        <rdfs:label>Codon usage bias</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:hasDefinition>A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2866 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2866">
-        <rdfs:label>Northern blot report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Northern Blot experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2867">
-        <rdfs:label>Nucleic acid features report (VNTR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>variable number of tandem repeat (VNTR) polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2868">
-        <rdfs:label>Nucleic acid features report (microsatellite)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>microsatellite polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2868"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2869">
-        <rdfs:label>Nucleic acid features report (RFLP)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>restriction fragment length polymorphisms (RFLP) in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2870 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2870">
-        <rdfs:label>Radiation hybrid map</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1280"/>
-        <rdfs:comment>The radiation method can break very closely linked markers providing a more detailed map.  Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map.</rdfs:comment>
-        <oboInOwl:hasDefinition>A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>RH map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2872 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2872">
-        <rdfs:label>ID list</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:hasDefinition>A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2873 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2873">
-        <rdfs:label>Phylogenetic gene frequencies data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1426"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gene frequencies data that may be read during phylogenetic tree calculation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2874 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2874">
-        <rdfs:label>Sequence set (polymorphic)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1234"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2875 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2875">
-        <rdfs:label>DRCAT resource</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>An entry (resource) from the DRCAT bioinformatics resource catalogue.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1883"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2877 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2877">
-        <rdfs:label>Protein complex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2878 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2878">
-        <rdfs:label>Protein structural motif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2879 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2879">
-        <rdfs:label>Lipid report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotation on or information derived from one or more specific lipid 3D structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2880 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2880">
-        <rdfs:label>Secondary structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Image of one or more molecular secondary structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2992"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2881 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2881">
-        <rdfs:label>Secondary structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Secondary structure-derived report</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on general information, properties or features of one or more molecular secondary structures.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2882 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2882">
-        <rdfs:label>DNA features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>DNA sequence-specific feature annotation (not in a feature table).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2883 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2883">
-        <rdfs:label>RNA features report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Features concerning RNA or regions of DNA that encode an RNA molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (RNA features)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2884 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2884">
-        <rdfs:label>Plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Biological data that has been plotted as a graph of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2885">
-        <rdfs:label>Nucleic acid features report (polymorphism)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>DNA polymorphism.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2886 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2886">
-        <rdfs:label>Protein sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0849"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2976"/>
-        <oboInOwl:hasDefinition>A protein sequence and associated metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein sequence record</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence record (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2887 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2887">
-        <rdfs:label>Nucleic acid sequence record</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0849"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasNarrowSynonym>RNA sequence record</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence record</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A nucleic acid sequence and associated metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>DNA sequence record</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequence record (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2888 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2888">
-        <rdfs:label>Protein sequence record (full)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2889 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2889">
-        <rdfs:label>Nucleic acid sequence record (full) </rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0849"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2891 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2891">
-        <rdfs:label>Biological model accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1085"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a mathematical model, typically an entry from a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2892 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2892">
-        <rdfs:label>Cell type name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2655"/>
-        <oboInOwl:hasDefinition>The name of a type or group of cells.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2893 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2893">
-        <rdfs:label>Cell type accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2655"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a type or group of cells (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2894 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2894">
-        <rdfs:label>Compound accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasExactSynonym>Small molecule accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of chemicals.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2895 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2895">
-        <rdfs:label>Drug accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0993"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Accession of a drug.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2896 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2896">
-        <rdfs:label>Toxin name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2576"/>
-        <oboInOwl:hasDefinition>Name of a toxin.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2897 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2897">
-        <rdfs:label>Toxin accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2576"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a toxin (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2898 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2898">
-        <rdfs:label>Monosaccharide accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0996"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Accession of a monosaccharide (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2899 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2899">
-        <rdfs:label>Drug name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0990"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0993"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Common name of a drug.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2900 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2900">
-        <rdfs:label>Carbohydrate accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2663"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of carbohydrates.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2901 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2901">
-        <rdfs:label>Molecule accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0982"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Accession of a specific molecule (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2902 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2902">
-        <rdfs:label>Data resource definition accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1084"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a data definition (catalogued in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2903 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2903">
-        <rdfs:label>Genome accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2749"/>
-        <oboInOwl:hasDefinition>An accession of a particular genome (in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2904 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2904">
-        <rdfs:label>Map accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2117"/>
-        <oboInOwl:hasDefinition>An accession of a map of a molecular sequence (deposited in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2905 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2905">
-        <rdfs:label>Lipid accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2812"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of lipids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2906 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2906">
-        <rdfs:label>Peptide ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0988"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a peptide deposited in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2907 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2907">
-        <rdfs:label>Protein accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0989"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2901"/>
-        <oboInOwl:hasExactSynonym>Protein accessions</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a protein deposited in a database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2908 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2908">
-        <rdfs:label>Organism accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>An accession of annotation on a (group of) organisms (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2909 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2909">
-        <rdfs:label>Organism name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <oboInOwl:hasDbXref>Moby:Organism_Name</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:OrganismsShortName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:OccurrenceRecord</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:BriefOccurrenceRecord</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:FirstEpithet</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Moby:InfraspecificEpithet</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:OrganismsLongName</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The name of an organism (or group of organisms).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2910 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2910">
-        <rdfs:label>Protein family accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1075"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of a protein family (that is deposited in a database).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2911 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2911">
-        <rdfs:label>Transcription factor accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1077"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Accession of an entry from a database of transcription factors or binding sites.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2912 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2912">
-        <rdfs:label>Strain accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2379"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2908"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0963"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a strain of an organism variant, typically a plant, virus or bacterium.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2913 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2913">
-        <rdfs:label>Virus identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1869"/>
-        <oboInOwl:hasDefinition>An accession of annotation on a (group of) viruses (catalogued in a database).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2914 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2914">
-        <rdfs:label>Sequence features metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2527"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Metadata on sequence features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2915 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2915">
-        <rdfs:label>Gramene identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identifier of a Gramene database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2916 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2916">
-        <rdfs:label>DDBJ accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1103"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>DDBJ accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>DDBJ identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>DDBJ ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An identifier of an entry from the DDBJ sequence database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2917 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2917">
-        <rdfs:label>ConsensusPathDB identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An identifier of an entity from the ConsensusPathDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2925 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2925">
-        <rdfs:label>Sequence data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data concerning, extracted from, or derived from the analysis of molecular sequence(s). </oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2534"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2927 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2927">
-        <rdfs:label>Codon usage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning codon usage.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0914"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2954 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2954">
-        <rdfs:label>Article report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>Data derived from the analysis of a scientific text such as a full text article from a scientific journal.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2526"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2955 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2955">
-        <rdfs:label>Sequence report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasDefinition>An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence-derived report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2956 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2956">
-        <rdfs:label>Protein secondary structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1537"/>
-        <oboInOwl:hasDefinition>An informative report about the properties or features of one or more protein secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2957 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2957">
-        <rdfs:label>Hopp and Woods plot</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1534"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <oboInOwl:hasDefinition>A Hopp and Woods plot of predicted antigenicity of a peptide or protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2958 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2958">
-        <rdfs:label>Nucleic acid melting curve</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2884"/>
-        <rdfs:comment>Shows the proportion of nucleic acid which are double-stranded versus temperature.</rdfs:comment>
-        <oboInOwl:hasDefinition>A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2959 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2959">
-        <rdfs:label>Nucleic acid probability profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <oboInOwl:hasDefinition>A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2960 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2960">
-        <rdfs:label>Nucleic acid temperature profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1583"/>
-        <oboInOwl:hasDefinition>A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).</oboInOwl:hasDefinition>
-        <rdfs:comment>Plots melting temperature versus base position.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Melting map</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2961 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2961">
-        <rdfs:label>Gene regulatory network report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>A report typically including a map (diagram) of a gene regulatory network.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2965 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2965">
-        <rdfs:label>2D PAGE gel report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>An informative report on a two-dimensional (2D PAGE) gel.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>2D PAGE image report</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>2D PAGE gel annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>2D PAGE image annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2966 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2966">
-        <rdfs:label>Oligonucleotide probe sets annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2717"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2967 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2967">
-        <rdfs:label>Microarray image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression image</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2968 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2968">
-        <rdfs:label>Image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000081</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Biological or biomedical data has been rendered into an image, typically for display on screen.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000079</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Image data</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2969 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2969">
-        <rdfs:label>Sequence image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2955"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <oboInOwl:hasDefinition>Image of a molecular sequence, possibly with sequence features or properties shown.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2970 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2970">
-        <rdfs:label>Protein hydropathy data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasExactSynonym>Protein hydropathy report</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report on protein properties concerning hydropathy.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2971 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2971">
-        <rdfs:label>Workflow data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning a computational workflow.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2972 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2972">
-        <rdfs:label>Workflow</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A computational workflow.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2973 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2973">
-        <rdfs:label>Secondary structure data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning molecular secondary structure data.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2974 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2974">
-        <rdfs:label>Protein sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0848"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2976"/>
-        <oboInOwl:hasExactSynonym>Raw protein sequence</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Raw sequence (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A raw protein sequence (string of characters).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2975 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2975">
-        <rdfs:label>Nucleic acid sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0848"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid raw sequence</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence (raw)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Raw sequence (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A raw nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2976 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2976">
-        <rdfs:label>Protein sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <oboInOwl:hasDefinition>One or more protein sequences, possibly with associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein sequences</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2977 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2977">
-        <rdfs:label>Nucleic acid sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2044"/>
-        <oboInOwl:hasDefinition>One or more nucleic acid sequences, possibly with associated annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>DNA sequence</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleotide sequence</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleotide sequences</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid sequences</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2978 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2978">
-        <rdfs:label>Reaction data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Enzyme kinetics annotation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Reaction annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2979 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2979">
-        <rdfs:label>Peptide property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning small peptides.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2980 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2980">
-        <rdfs:label>Protein classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein classification data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report concerning the classification of protein sequences or structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0907"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2981 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2981">
-        <rdfs:label>Sequence motif data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning specific or conserved pattern in molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_0860"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2982 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2982">
-        <rdfs:label>Sequence profile data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data concerning models representing a (typically multiple) sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1354"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2983 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2983">
-        <rdfs:label>Pathway or network data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data concerning a specific biological pathway or network.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2600"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2984"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2984 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2984">
-        <rdfs:label>Pathway or network report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2985 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2985">
-        <rdfs:label>Nucleic acid thermodynamic data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0912"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid property (thermodynamic or kinetic)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A thermodynamic or kinetic property of a nucleic acid molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid thermodynamic property</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2986 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2986">
-        <rdfs:label>Nucleic acid classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning the classification of nucleic acid sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid classification data</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3148"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2987 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2987">
-        <rdfs:label>Classification report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Classification data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report on a classification of molecular sequences, structures or other entities.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2989 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2989">
-        <rdfs:label>Protein features report (key folding sites)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>key residues involved in protein folding.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2991 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2991">
-        <rdfs:label>Protein torsion angle data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasExactSynonym>Torsion angle data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Torsion angle data for a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2992 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2992">
-        <rdfs:label>Protein structure image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1710"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3153"/>
-        <oboInOwl:hasDefinition>An image of protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure image (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_2994 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_2994">
-        <rdfs:label>Phylogenetic character weights</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2523"/>
-        <oboInOwl:hasDefinition>Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3002 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3002">
-        <rdfs:label>Annotation track</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1255"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Genomic track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome annotation track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome-browser track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome track</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence annotation track</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3021 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3021">
-        <rdfs:label>UniProt accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>UniProtKB accession number</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <example>P43353|Q7M1G0|Q9C199|A5A6J6</example>
-        <oboInOwl:hasExactSynonym>UniProt entry accession</oboInOwl:hasExactSynonym>
-        <regex>[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}</regex>
-        <oboInOwl:hasNarrowSynonym>Swiss-Prot entry accession</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>TrEMBL entry accession</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Accession number of a UniProt (protein sequence) database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>UniProtKB accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>UniProt accession number</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3022 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3022">
-        <rdfs:label>NCBI genetic code ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <oboInOwl:hasDefinition>Identifier of a genetic code in the NCBI list of genetic codes.</oboInOwl:hasDefinition>
-        <regex>[1-9][0-9]?</regex>
-        <example>16</example>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3025 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3025">
-        <rdfs:label>Ontology concept identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identifier of a concept in an ontology of biological or bioinformatics concepts and relations.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3026 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3026">
-        <rdfs:label>GO concept name (biological process)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The name of a concept for a biological process from the GO ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3027 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3027">
-        <rdfs:label>GO concept name (molecular function)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The name of a concept for a molecular function from the GO ontology.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2339"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3028 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3028">
-        <rdfs:label>Taxonomy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data concerning the classification, identification and naming of organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Taxonomic data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3029 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3029">
-        <rdfs:label>Protein ID (EMBL/GenBank/DDBJ)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2907"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.</oboInOwl:hasDefinition>
-        <rdfs:comment>This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3031 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3031">
-        <rdfs:label>Core data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Core data entities typically have a format and may be identified by an accession number.</rdfs:comment>
-        <oboInOwl:hasDefinition>A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3034 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3034">
-        <rdfs:label>Sequence feature identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Name or other identifier of molecular sequence feature(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3035 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3035">
-        <rdfs:label>Structure identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>An identifier of a molecular tertiary structure, typically an entry from a structure database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3036 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3036">
-        <rdfs:label>Matrix identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An identifier of an array of numerical values, such as a comparison matrix.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3085">
-        <rdfs:label>Protein sequence composition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report (typically a table) on character or word composition / frequency of protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3086 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3086">
-        <rdfs:label>Nucleic acid sequence composition (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3101 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3101">
-        <rdfs:label>Protein domain classification node</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>A node from a classification of protein structural domain(s).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3102">
-        <rdfs:label>CAS number</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>CAS registry number</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3103 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3103">
-        <rdfs:label>ATC code</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2895"/>
-        <oboInOwl:hasDefinition>Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC).</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3104 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3104">
-        <rdfs:label>UNII</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1086"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Unique Ingredient Identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3105 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3105">
-        <rdfs:label>Geotemporal metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Basic information concerning geographical location or time.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2527"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3106 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3106">
-        <rdfs:label>System metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Metadata concerning the software, hardware or other aspects of a computer system.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3107 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3107">
-        <rdfs:label>Sequence feature name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3034"/>
-        <oboInOwl:hasDefinition>A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3108 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3108">
-        <rdfs:label>Experimental measurement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Experimental measurement data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Measurement</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Measured data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Experimentally measured data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Measurement metadata</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Measurement data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Raw experimental data</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3110">
-        <rdfs:label>Raw microarray data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3108"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3117"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment.</oboInOwl:hasDefinition>
-        <rdfs:comment>Such data as found in Affymetrix CEL or GPR files.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3111">
-        <rdfs:label>Processed microarray data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3117"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data generated from processing and analysis of probe set data from a microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene annotation (expression)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray probe set data</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression report</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3112">
-        <rdfs:label>Gene expression matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:comment>This combines data from all hybridisations.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Normalised microarray data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The final processed (normalised) data for a set of hybridisations in a microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene expression data matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3113 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3113">
-        <rdfs:label>Sample annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2337"/>
-        <oboInOwl:hasDefinition>Annotation on a biological sample, for example experimental factors and their values.</oboInOwl:hasDefinition>
-        <rdfs:comment>This might include compound and dose in a dose response experiment.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3115 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3115">
-        <rdfs:label>Microarray metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <rdfs:comment>This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Annotation on the array itself used in a microarray experiment.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3116 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3116">
-        <rdfs:label>Microarray protocol annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This might describe e.g. the normalisation methods used to process the raw data.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Annotation on laboratory and/or data processing protocols used in an microarray experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3117 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3117">
-        <rdfs:label>Microarray hybridisation data</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2603"/>
-        <oboInOwl:hasDefinition>Data concerning the hybridisations measured during a microarray experiment.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3118">
-        <rdfs:label>Protein features report (topological domains)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>topological domains such as cytoplasmic regions in a protein.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3119 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3119">
-        <rdfs:label>Sequence features (compositionally-biased regions)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report of regions in a molecular sequence that are biased to certain characters.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1261"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3122">
-        <rdfs:label>Nucleic acid features (difference and change)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>A report on features in a nucleic acid sequence that indicate changes to or differences between sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0918"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3123">
-        <rdfs:label>Nucleic acid features report (expression signal)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>regions within a nucleic acid sequence containing a signal that alters a biological function.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3125 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3125">
-        <rdfs:label>Nucleic acid features report (binding)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>nucleic acids binding to some other molecule.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <rdfs:comment>This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes).</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3126">
-        <rdfs:label>Nucleic acid repeats (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>repetitive elements within a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3127">
-        <rdfs:label>Nucleic acid features report (replication and recombination)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>DNA replication or recombination.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3128">
-        <rdfs:label>Nucleic acid structure report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2085"/>
-        <oboInOwl:hasDefinition>A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Stem loop (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>d-loop (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Quadruplexes (report)</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3129 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3129">
-        <rdfs:label>Protein features report (repeats)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>short repetitive subsequences (repeat sequences) in a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1277"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3130">
-        <rdfs:label>Sequence motif matches (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3131 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3131">
-        <rdfs:label>Sequence motif matches (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3132 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3132">
-        <rdfs:label>Nucleic acid features (d-loop)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report on displacement loops in a mitochondrial DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3133">
-        <rdfs:label>Nucleic acid features (stem loop)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A report on stem loops in a DNA sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <rdfs:comment>A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3134">
-        <rdfs:label>Gene transcript report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0916"/>
-        <rdfs:comment>This includes 5&apos;untranslated region (5&apos;UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3&apos;untranslated regions (3&apos;UTR).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (mRNA features)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Transcript (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>mRNA features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene transcript annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Clone or EST (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>mRNA (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3135">
-        <rdfs:label>Nucleic acid features report (signal or transit peptide)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>coding sequences for a signal or transit peptide.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3137">
-        <rdfs:label>Non-coding RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>features of non-coding or functional RNA molecules, including tRNA and rRNA.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3138 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3138">
-        <rdfs:label>Transcriptional features (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.</rdfs:comment>
-        <oboInOwl:hasDefinition>Features concerning transcription of DNA into RNA including the regulation of transcription.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3139">
-        <rdfs:label>Nucleic acid features report (STS)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>sequence tagged sites (STS) in nucleic acid sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_1276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3140">
-        <rdfs:label>Nucleic acid features (immunoglobulin gene structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:hasDefinition>A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0916"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3141">
-        <rdfs:label>SCOP class</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a &apos;class&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3142 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3142">
-        <rdfs:label>SCOP fold</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Information on a &apos;fold&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3143">
-        <rdfs:label>SCOP superfamily</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Information on a &apos;superfamily&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3144 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3144">
-        <rdfs:label>SCOP family</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Information on a &apos;family&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3145 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3145">
-        <rdfs:label>SCOP protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Information on a &apos;protein&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3146 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3146">
-        <rdfs:label>SCOP species</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.5</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Information on a &apos;species&apos; node from the SCOP database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_2980"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3147">
-        <rdfs:label>Mass spectrometry experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>mass spectrometry experiments.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3148 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3148">
-        <rdfs:label>Gene family report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2084"/>
-        <oboInOwl:hasDefinition>An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene, or any other classification of nucleic acid sequences or structures that reflects gene structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes reports on on gene homologues between species.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Gene annotation (homology information)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Homology information</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene annotation (homology)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Nucleic acid classification</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>Gene family annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene homology (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3153 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3153">
-        <rdfs:label>Protein image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>An image of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3154">
-        <rdfs:label>Protein alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1916"/>
-        <oboInOwl:hasDefinition>An alignment of protein sequences and/or structures.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3165 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3165">
-        <rdfs:label>NGS experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>sequencing experiment, including samples, sampling, preparation, sequencing, and analysis.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3181 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3181">
-        <rdfs:label>Sequence assembly report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0867"/>
-        <oboInOwl:hasDefinition>An informative report about a DNA sequence assembly.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Assembly report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3210">
-        <rdfs:label>Genome index</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0955"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.</rdfs:comment>
-        <oboInOwl:hasDefinition>An index of a genome sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3231 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3231">
-        <rdfs:label>GWAS report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Report concerning genome-wide association study experiments.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Genome-wide association study</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3236">
-        <rdfs:label>Cytoband position</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2012"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>The position of a cytogenetic band in a genome.</oboInOwl:hasDefinition>
-        <rdfs:comment>Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3238">
-        <rdfs:label>Cell type ontology ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1087"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2893"/>
-        <oboInOwl:hasExactSynonym>CL ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Cell type ontology concept ID.</oboInOwl:hasDefinition>
-        <regex>CL_[0-9]{7}</regex>
-        <created_in>1.2</created_in>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3241">
-        <rdfs:label>Kinetic model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Mathematical model of a network, that contains biochemical kinetics.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3264">
-        <rdfs:label>COSMIC ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <oboInOwl:hasExactSynonym>COSMIC identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>cosmic ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identifier of a COSMIC database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>cosmic identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>cosmic id</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3265">
-        <rdfs:label>HGMD ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2294"/>
-        <oboInOwl:hasDefinition>Identifier of a HGMD database entry.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>hgmd ID</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>hgmd identifier</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>hgmd id</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>HGMD identifier</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3266 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3266">
-        <rdfs:label>Sequence assembly ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1064"/>
-        <oboInOwl:hasNarrowSynonym>Sequence assembly version</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Unique identifier of sequence assembly.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3268 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3268">
-        <rdfs:label>Sequence feature type</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0842"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3269">
-        <rdfs:label>Gene homology (report)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An informative report on gene homologues between species.</oboInOwl:hasDefinition>
-        <obsolete_since>1.5</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_3148"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3270 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3270">
-        <rdfs:label>Ensembl gene tree ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2610"/>
-        <example>ENSGT00390000003602</example>
-        <oboInOwl:hasExactSynonym>Ensembl ID (gene tree)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Unique identifier for a gene tree from the Ensembl database.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3271 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3271">
-        <rdfs:label>Gene tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0872"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>A phylogenetic tree that is an estimate of the character&apos;s phylogeny.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3272 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3272">
-        <rdfs:label>Species tree</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0872"/>
-        <oboInOwl:hasDefinition>A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3273 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3273">
-        <rdfs:label>Sample ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_identifier_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3113"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Sample accession</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Name or other identifier of an entry from a biosample database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3274 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3274">
-        <rdfs:label>MGI accession</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2091"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2109"/>
-        <oboInOwl:hasDefinition>Identifier of an object from the MGI database.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3275 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3275">
-        <rdfs:label>Phenotype name</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2099"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Name of a phenotype.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phenotypes</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phenotype</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3354">
-        <rdfs:label>Transition matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A HMM transition matrix contains the probabilities of switching from one HMM state to another.</oboInOwl:hasDefinition>
-        <rdfs:comment>Consider for example an HMM with two states (AT-rich and GC-rich).  The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>HMM transition matrix</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3355">
-        <rdfs:label>Emission matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <oboInOwl:hasDefinition>A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <rdfs:comment>Consider for example an HMM with two states (AT-rich and GC-rich).  The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>HMM emission matrix</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3356">
-        <rdfs:label xml:lang="en">Hidden Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0950"/>
-        <oboInOwl:hasDefinition>A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3358">
-        <rdfs:label>Format identifier</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0976"/>
-        <oboInOwl:hasDefinition>An identifier of a data format.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3424">
-        <rdfs:label>Raw image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <created_in>1.5</created_in>
-        <oboInOwl:hasExactSynonym>Amino acid data</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000081</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Image data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Raw biological or biomedical image generated by some experimental technique.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3425">
-        <rdfs:label>Carbohydrate property</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2087"/>
-        <oboInOwl:hasExactSynonym>Carbohydrate data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates.</oboInOwl:hasDefinition>
-        <created_in>1.5</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3426">
-        <rdfs:label>Proteomics experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Report concerning proteomics experiments.</oboInOwl:hasDefinition>
-        <created_in>1.5</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3427">
-        <rdfs:label>RNAi report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.5</created_in>
-        <oboInOwl:hasDefinition>RNAi experiments.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3428">
-        <rdfs:label>Simulation experiment report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.5</created_in>
-        <oboInOwl:hasDefinition>biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/data_2531"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3442">
-        <rdfs:label>MRI image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3384"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>MRT image</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>Magnetic resonance tomography image </oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nuclear magnetic resonance imaging image
-</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Magnetic resonance imaging image
-</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>NMRI image</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3449 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3449">
-        <rdfs:label>Cell migration track image</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2968"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2229"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>An image from a cell migration track assay.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3451">
-        <rdfs:label>Rate of association</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0897"/>
-        <oboInOwl:hasExactSynonym>kon</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Rate of association of a protein with another protein or some other molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3479">
-        <rdfs:label>Gene order</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2082"/>
-        <rdfs:comment>Such data are often used for genome rearrangement tools and phylogenetic tree labeling.</rdfs:comment>
-        <oboInOwl:hasDefinition>Multiple gene identifiers in a specific order.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3483">
-        <rdfs:label>Spectrum</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Spectra</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3488">
-        <rdfs:label>NMR spectrum</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3483"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Spectral information for a molecule from a nuclear magnetic resonance experiment.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>NMR spectra</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3490">
-        <rdfs:label>Chemical structure sketch</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1712"/>
-        <rdfs:comment>Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software.</rdfs:comment>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Small molecule sketch</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A sketch of a small molecule made with some specialised drawing package.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3492">
-        <rdfs:label>Nucleic acid signature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2762"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>An informative report about a specific or conserved nucleic acid sequence pattern.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3494 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3494">
-        <rdfs:label>DNA sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasExactSynonym>DNA sequences</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>A DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3495">
-        <rdfs:label>RNA sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2977"/>
-        <oboInOwl:hasDefinition>A DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>DNA sequences</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA sequences</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3496">
-        <rdfs:label>RNA sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3495"/>
-        <oboInOwl:hasExactSynonym>Raw sequence (RNA)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>A raw RNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA raw sequence</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3497">
-        <rdfs:label>DNA sequence (raw)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_3494"/>
-        <oboInOwl:hasExactSynonym>Raw sequence (DNA)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A raw DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>DNA raw sequence</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3498">
-        <rdfs:label>Sequence variations</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene sequence variations</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Variations are stored along with a reference genome.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3505">
-        <rdfs:label>Bibliography</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2526"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>A list of publications such as scientic papers or books.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3509">
-        <rdfs:label>Ontology mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2093"/>
-        <oboInOwl:hasDefinition>A mapping of supplied textual terms or phrases to ontology concepts (URIs).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3546">
-        <rdfs:label>Image metadata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_0006"/>
-        <oboInOwl:hasExactSynonym>Image-associated data</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This can include basic provenance and technical information about the image, scientific annotation and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Any data concerning a specific biological or biomedical image.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasExactSynonym>Image data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Image-related data</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3558">
-        <rdfs:label>Clinical trial report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <oboInOwl:hasExactSynonym>Clinical trial information</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A report concerning a clinical trial.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3567">
-        <rdfs:label>Reference sample report</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_2048"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>A report about a biosample.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Biosample report</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/data_3568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/data_3568">
-        <rdfs:label>Gene Expression Atlas Experiment ID</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/data_1078"/>
-        <oboInOwl:hasDefinition>Accession number of an entry from the Gene Expression Atlas.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#identifiers"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1196">
-        <rdfs:label>SMILES</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification"/>
-        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"/>
-        <documentation rdf:resource="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1197 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1197">
-        <rdfs:label>InChI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1198 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1198">
-        <rdfs:label>mf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The general MF query format consists of a series of valid atomic symbols, with an optional number or range.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1199 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1199">
-        <rdfs:label>inchikey</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2035"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1200">
-        <rdfs:label>smarts</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1196"/>
-        <oboInOwl:hasDefinition>SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1206 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1206">
-        <rdfs:label>unambiguous pure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2096"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1207 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1207">
-        <rdfs:label>nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <rdfs:comment>Non-sequence characters may be used for example for gaps.</rdfs:comment>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1208">
-        <rdfs:label>protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Non-sequence characters may be used for gaps and translation stop.</rdfs:comment>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1209">
-        <rdfs:label>consensus</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2095"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2097"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for the consensus of two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1210">
-        <rdfs:label>pure nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1211">
-        <rdfs:label>unambiguous pure nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters .</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1212 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1212">
-        <rdfs:label>dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1213">
-        <rdfs:label>rna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1214 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1214">
-        <rdfs:label>unambiguous pure dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1212"/>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1215">
-        <rdfs:label>pure dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1210"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1212"/>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1216 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1216">
-        <rdfs:label>unambiguous pure rna sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1213"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1217">
-        <rdfs:label>pure rna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1210"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1213"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1218">
-        <rdfs:label>unambiguous pure protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1208"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1219">
-        <rdfs:label>pure protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1208"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1228 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1228">
-        <rdfs:label>UniGene entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from UniGene.</oboInOwl:hasDefinition>
-        <rdfs:comment>A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1247">
-        <rdfs:label>COG sequence cluster format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the COG database of clusters of (related) protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1248">
-        <rdfs:label>EMBL feature location</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2078"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Feature location</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1295">
-        <rdfs:label>quicktandem</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2155"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1296 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1296">
-        <rdfs:label>Sanger inverted repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2155"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1297">
-        <rdfs:label>EMBOSS repeat</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2155"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format for tandem repeats in a sequence (an EMBOSS report format).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1316">
-        <rdfs:label>est2genome format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2031"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a report on exon-intron structure generated by EMBOSS est2genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1318">
-        <rdfs:label>restrict format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2158"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format for restriction enzyme recognition sites used by EMBOSS restrict program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1319 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1319">
-        <rdfs:label>restover format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2158"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report format for restriction enzyme recognition sites used by EMBOSS restover program.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1320">
-        <rdfs:label>REBASE restriction sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2158"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Report format for restriction enzyme recognition sites used by REBASE database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1332">
-        <rdfs:label>FASTA search results format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using FASTA.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.)</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1333 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1333">
-        <rdfs:label>BLAST results</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using some variant of BLAST.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes score data, alignment data and summary table.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1334">
-        <rdfs:label>mspcrunch</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using some variant of MSPCrunch.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1335">
-        <rdfs:label>Smith-Waterman format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of results of a sequence database search using some variant of Smith Waterman.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1336">
-        <rdfs:label>dhf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1337">
-        <rdfs:label>lhf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information.</oboInOwl:hasDefinition>
-        <rdfs:comment>The hits are putative ligand-binding sequences and are found from a search of a sequence database.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1341">
-        <rdfs:label>InterPro hits format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Results format for searches of the InterPro database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1342">
-        <rdfs:label>InterPro protein view report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1341"/>
-        <oboInOwl:hasDefinition>Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1343">
-        <rdfs:label>InterPro match table format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1341"/>
-        <oboInOwl:hasDefinition>Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1349">
-        <rdfs:label>HMMER Dirichlet prior</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2074"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Dirichlet distribution HMMER format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1350">
-        <rdfs:label>MEME Dirichlet prior</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2074"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Dirichlet distribution MEME format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1351 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1351">
-        <rdfs:label>HMMER emission and transition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2075"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1356">
-        <rdfs:label>prosite-pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of a regular expression pattern from the Prosite database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1357">
-        <rdfs:label>EMBOSS sequence pattern</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of an EMBOSS sequence pattern.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1360">
-        <rdfs:label>meme-motif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2068"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>A motif in the format generated by the MEME program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1366">
-        <rdfs:label>prosite-profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2069"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Sequence profile (sequence classifier) format used in the PROSITE database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1367 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1367">
-        <rdfs:label>JASPAR format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2069"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A profile (sequence classifier) in the format used in the JASPAR database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1369">
-        <rdfs:label>MEME background Markov model</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2072"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of the model of random sequences used by MEME.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1370">
-        <rdfs:label>HMMER format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2072"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of a hidden Markov model representation used by the HMMER package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1391">
-        <rdfs:label>HMMER-aln</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>FASTA-style format for multiple sequences aligned by HMMER package to an HMM.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1392 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1392">
-        <rdfs:label>DIALIGN format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Format of multiple sequences aligned by DIALIGN package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1393">
-        <rdfs:label>daf</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <rdfs:comment>The format is clustal-like and includes annotation of domain family classification information.</rdfs:comment>
-        <oboInOwl:hasDefinition>EMBASSY &apos;domain alignment file&apos; (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1419">
-        <rdfs:label>Sequence-MEME profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2014"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1421">
-        <rdfs:label>HMMER profile alignment (sequences versus HMMs)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2014"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1422">
-        <rdfs:label>HMMER profile alignment (HMM versus sequences)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2014"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1423">
-        <rdfs:label>Phylip distance matrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2067"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of PHYLIP phylogenetic distance matrix data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1424">
-        <rdfs:label>ClustalW dendrogram</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Dendrogram (tree file) format generated by ClustalW.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1425">
-        <rdfs:label>Phylip tree raw</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasDefinition>Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1430">
-        <rdfs:label>Phylip continuous quantitative characters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2037"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PHYLIP file format for continuous quantitative character data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1431 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1431">
-        <rdfs:label>Phylogenetic property values format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of phylogenetic property data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2036"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1432">
-        <rdfs:label>Phylip character frequencies format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2037"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PHYLIP file format for phylogenetics character frequency data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1433">
-        <rdfs:label>Phylip discrete states format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2038"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of PHYLIP discrete states data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1434">
-        <rdfs:label>Phylip cliques format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2039"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of PHYLIP cliques data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1435">
-        <rdfs:label>Phylip tree format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasDefinition>Phylogenetic tree data format used by the PHYLIP program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1436">
-        <rdfs:label>TreeBASE format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the TreeBASE database of phylogenetic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1437">
-        <rdfs:label>TreeFam format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the TreeFam database of phylogenetic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1445">
-        <rdfs:label>Phylip tree distance format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2049"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1454 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1454">
-        <rdfs:label>dssp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2077"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format.</rdfs:comment>
-        <oboInOwl:hasDefinition>Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1455 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1455">
-        <rdfs:label>hssp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2077"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1457">
-        <rdfs:label>Dot-bracket format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Vienna RNA secondary structure format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Vienna RNA format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1458 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1458">
-        <rdfs:label>Vienna local RNA secondary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1457"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1475">
-        <rdfs:label>PDB database entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2033"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PDB entry format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of an entry (or part of an entry) from the PDB database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1476">
-        <rdfs:label>PDB</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasExactSynonym>PDB format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of PDB database in PDB format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1477 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1477">
-        <rdfs:label>mmCIF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasExactSynonym>Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Entry format of PDB database in mmCIF format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>mmcif</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1478">
-        <rdfs:label>PDBML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Entry format of PDB database in PDBML (XML) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1500">
-        <rdfs:label>Domainatrix 3D-1D scoring matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1504">
-        <rdfs:label>aaindex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2017"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Amino acid index format used by the AAindex database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1511">
-        <rdfs:label>IntEnz enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from IntEnz (The Integrated Relational Enzyme Database).</oboInOwl:hasDefinition>
-        <rdfs:comment>IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1512">
-        <rdfs:label>BRENDA enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of an entry from the BRENDA enzyme database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1513 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1513">
-        <rdfs:label>KEGG REACTION enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the KEGG REACTION database of biochemical reactions.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1514">
-        <rdfs:label>KEGG ENZYME enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of an entry from the KEGG ENZYME database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1515">
-        <rdfs:label>REBASE proto enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of an entry from the proto section of the REBASE enzyme database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1516">
-        <rdfs:label>REBASE withrefm enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the withrefm section of the REBASE enzyme database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1551">
-        <rdfs:label>Pcons report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2065"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of output of the Pcons Model Quality Assessment Program (MQAP).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1552">
-        <rdfs:label>ProQ report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2065"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features.</rdfs:comment>
-        <oboInOwl:hasDefinition>Format of output of the ProQ protein model quality predictor.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1563">
-        <rdfs:label>SMART domain assignment report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of SMART domain assignment data.</oboInOwl:hasDefinition>
-        <rdfs:comment>The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1568">
-        <rdfs:label>BIND entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the BIND database of protein interaction.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1569">
-        <rdfs:label>IntAct entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the IntAct database of protein interaction.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1570">
-        <rdfs:label>InterPro entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1571">
-        <rdfs:label>InterPro entry abstract format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>References are included and a functional inference is made where possible.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format for the textual abstract of signatures in an InterPro entry and its protein matches.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1572">
-        <rdfs:label>Gene3D entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the Gene3D protein secondary database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1573">
-        <rdfs:label>PIRSF entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the PIRSF protein secondary database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1574">
-        <rdfs:label>PRINTS entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format for the PRINTS protein secondary database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1575">
-        <rdfs:label>Panther Families and HMMs entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the Panther library of protein families and subfamilies.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1576 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1576">
-        <rdfs:label>Pfam entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the Pfam protein secondary database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1577 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1577">
-        <rdfs:label>SMART entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the SMART protein secondary database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1578">
-        <rdfs:label>Superfamily entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the Superfamily protein secondary database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1579">
-        <rdfs:label>TIGRFam entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format for the TIGRFam protein secondary database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1580 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1580">
-        <rdfs:label>ProDom entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the ProDom protein domain classification database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1581">
-        <rdfs:label>FSSP entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format for the FSSP database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1582">
-        <rdfs:label>findkm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2027"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1603 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1603">
-        <rdfs:label>Ensembl gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of Ensembl genome database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1604 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1604">
-        <rdfs:label>DictyBase gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of DictyBase genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1605">
-        <rdfs:label>CGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of Candida Genome database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1606">
-        <rdfs:label>DragonDB gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of DragonDB genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1607">
-        <rdfs:label>EcoCyc gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of EcoCyc genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1608">
-        <rdfs:label>FlyBase gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of FlyBase genome database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1609 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1609">
-        <rdfs:label>Gramene gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of Gramene genome database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1610">
-        <rdfs:label>KEGG GENES gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of KEGG GENES genome database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1611">
-        <rdfs:label>MaizeGDB gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format of the Maize genetics and genomics database (MaizeGDB).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1612">
-        <rdfs:label>MGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of the Mouse Genome Database (MGD).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1613">
-        <rdfs:label>RGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of the Rat Genome Database (RGD).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1614 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1614">
-        <rdfs:label>SGD gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format of the Saccharomyces Genome Database (SGD).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1615 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1615">
-        <rdfs:label>GeneDB gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of the Sanger GeneDB genome database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1616">
-        <rdfs:label>TAIR gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Entry format of The Arabidopsis Information Resource (TAIR) genome database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1617">
-        <rdfs:label>WormBase gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Entry format of the WormBase genomes database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1618">
-        <rdfs:label>ZFIN gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format of the Zebrafish Information Network (ZFIN) genome database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1619 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1619">
-        <rdfs:label>TIGR gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format of the TIGR genome database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1620">
-        <rdfs:label>dbSNP polymorphism report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the dbSNP database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1623 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1623">
-        <rdfs:label>OMIM entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of an entry from the OMIM database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1624 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1624">
-        <rdfs:label>HGVbase entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of a record from the HGVbase database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1625 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1625">
-        <rdfs:label>HIVDB entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of a record from the HIVDB database of genotypes and phenotypes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1626 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1626">
-        <rdfs:label>KEGG DISEASE entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the KEGG DISEASE database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1627 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1627">
-        <rdfs:label>Primer3 primer</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2061"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1628 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1628">
-        <rdfs:label>ABI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>A format of raw sequence read data from an Applied Biosystems sequencing machine.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1629 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1629">
-        <rdfs:label>mira</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of MIRA sequence trace information file.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1630 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1630">
-        <rdfs:label>CAF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2561"/>
-        <oboInOwl:hasDefinition>Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.sanger.ac.uk/resources/software/caf/"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.sanger.ac.uk/resources/software/caf/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1631 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1631">
-        <rdfs:label>exp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2561"/>
-        <oboInOwl:hasDefinition>Sequence assembly project file EXP format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1632 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1632">
-        <rdfs:label>SCF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://staden.sourceforge.net/manual/formats_unix_2.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://staden.sourceforge.net/manual/formats_unix_2.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1633 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1633">
-        <rdfs:label>PHD</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PHD sequence trace format to store serialised chromatogram data (reads).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.bioperl.org/wiki/PHD_sequence_format"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.bioperl.org/wiki/PHD_sequence_format"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1637 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1637">
-        <rdfs:label>dat</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1714"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of Affymetrix data file of raw image data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Affymetrix image data file format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1638 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1638">
-        <rdfs:label>cel</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3110"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Affymetrix probe raw data format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of Affymetrix data file of information about (raw) expression levels of the individual probes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1639 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1639">
-        <rdfs:label>affymetrix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2172"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1640 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1640">
-        <rdfs:label>ArrayExpress entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry format for the ArrayExpress microarrays database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1641 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1641">
-        <rdfs:label>affymetrix-exp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2056"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Affymetrix data file format for information about experimental conditions and protocols.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Affymetrix experimental conditions data file format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1644 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1644">
-        <rdfs:label>CHP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Affymetrix probe normalised data format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of Affymetrix data file of information about (normalised) expression levels of the individual probes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1645 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1645">
-        <rdfs:label>EMDB entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an entry from the Electron Microscopy DataBase (EMDB).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1647 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1647">
-        <rdfs:label>KEGG PATHWAY entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1648 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1648">
-        <rdfs:label>MetaCyc entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the MetaCyc metabolic pathways database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1649 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1649">
-        <rdfs:label>HumanCyc entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of a report from the HumanCyc metabolic pathways database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1650 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1650">
-        <rdfs:label>INOH entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The format of an entry from the INOH signal transduction pathways database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1651 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1651">
-        <rdfs:label>PATIKA entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the PATIKA biological pathways database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1652 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1652">
-        <rdfs:label>Reactome entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the reactome biological pathways database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1653 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1653">
-        <rdfs:label>aMAZE entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The format of an entry from the aMAZE biological pathways and molecular interactions database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1654 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1654">
-        <rdfs:label>CPDB entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the CPDB database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1655 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1655">
-        <rdfs:label>Panther Pathways entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the Panther Pathways database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1665 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1665">
-        <rdfs:label>Taverna workflow format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2032"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Format of Taverna workflows.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1666 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1666">
-        <rdfs:label>BioModel mathematical model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of mathematical models from the BioModel database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1697 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1697">
-        <rdfs:label>KEGG LIGAND entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG LIGAND chemical database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1698 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1698">
-        <rdfs:label>KEGG COMPOUND entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG COMPOUND database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1699 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1699">
-        <rdfs:label>KEGG PLANT entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG PLANT database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1700 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1700">
-        <rdfs:label>KEGG GLYCAN entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG GLYCAN database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1701 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1701">
-        <rdfs:label>PubChem entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from PubChem.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1702 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1702">
-        <rdfs:label>ChemSpider entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The format of an entry from a database of chemical structures and property predictions.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1703 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1703">
-        <rdfs:label>ChEBI entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The format of an entry from Chemical Entities of Biological Interest (ChEBI).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>ChEBI includes an ontological classification defining relations between entities or classes of entities.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1704 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1704">
-        <rdfs:label>MSDchem ligand dictionary entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the MSDchem ligand dictionary.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1705 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1705">
-        <rdfs:label>HET group dictionary entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2030"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>The format of an entry from the HET group dictionary (HET groups from PDB files).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1706 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1706">
-        <rdfs:label>KEGG DRUG entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The format of an entry from the KEGG DRUG database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1734 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1734">
-        <rdfs:label>PubMed citation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of bibliographic reference as used by the PubMed database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1735 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1735">
-        <rdfs:label>Medline Display Format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for abstracts of scientific articles from the Medline database.</oboInOwl:hasDefinition>
-        <rdfs:comment>Bibliographic reference information including citation information is included</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1736 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1736">
-        <rdfs:label>CiteXplore-core</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>CiteXplore &apos;core&apos; citation format including title, journal, authors and abstract.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1737 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1737">
-        <rdfs:label>CiteXplore-all</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2848"/>
-        <oboInOwl:hasDefinition>CiteXplore &apos;all&apos; citation format includes all known details such as Mesh terms and cross-references.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1739 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1739">
-        <rdfs:label>pmc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2020"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Article format of the PubMed Central database.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1740 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1740">
-        <rdfs:label>iHOP text mining abstract format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2021"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>iHOP abstract format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1741 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1741">
-        <rdfs:label>Oscar3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2021"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document.</rdfs:comment>
-        <oboInOwl:hasDefinition>Text mining abstract format from the Oscar 3 application.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1747 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1747">
-        <rdfs:label>PDB atom record format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of an ATOM record (describing data for an individual atom) from a PDB file.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1476"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1760 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1760">
-        <rdfs:label>CATH chain report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of CATH domain classification information for a polypeptide chain.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1761 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1761">
-        <rdfs:label>CATH PDB report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of CATH domain classification information for a protein PDB file.</oboInOwl:hasDefinition>
-        <rdfs:comment>The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1782 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1782">
-        <rdfs:label>NCBI gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Entry (gene) format of the NCBI database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1808 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1808">
-        <rdfs:label>GeneIlluminator gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>Moby:GI_Gene</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1809 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1809">
-        <rdfs:label>BacMap gene card format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDbXref>Moby:BacMapGeneCard</oboInOwl:hasDbXref>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1810 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1810">
-        <rdfs:label>ColiCard report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDbXref>Moby:ColiCard</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1861 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1861">
-        <rdfs:label>PlasMapper TextMap</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2060"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Map of a plasmid (circular DNA) in PlasMapper TextMap format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1910 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1910">
-        <rdfs:label>newick</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasExactSynonym>nh</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic tree Newick (text) format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1911 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1911">
-        <rdfs:label>TreeCon format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic tree TreeCon (text) format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1912 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1912">
-        <rdfs:label>Nexus format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2556"/>
-        <oboInOwl:hasDefinition>Phylogenetic tree Nexus (text) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1915 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1915">
-        <rdfs:label>Format</rdfs:label>
-        <owl:disjointWith rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:disjointWith rdf:resource="http://edamontology.org/topic_0003"/>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/File_format</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#MachineLanguage</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>File format</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Data model</oboInOwl:hasBroadSynonym>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Exchange format</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>&quot;http://purl.obolibrary.org/obo/IAO_0000098&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000612</rdfs:seeAlso>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000618</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality</rdfs:seeAlso>
-        <rdfs:seeAlso>&quot;http://purl.org/dc/elements/1.1/format&quot;</rdfs:seeAlso>
-        <rdfs:seeAlso>http://wsio.org/compression_004</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/List_of_file_formats</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Quality</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Data format</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#Quality</rdfs:seeAlso>
-        <rdfs:comment>The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format &apos;is format of&apos; Data.</rdfs:comment>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to &apos;Data model&apos; would be an &apos;Information model&apos;.)</rdfs:comment>
-        <owl:annotatedTarget>Data model</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasBroadSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages.</rdfs:comment>
-        <owl:annotatedTarget>File format</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/format_1915"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasNarrowSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/format_1918 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1918">
-        <rdfs:label>Atomic data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Data format for an individual atom.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1475"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1919 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1919">
-        <rdfs:label>Sequence record format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1920 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1920">
-        <rdfs:label>Sequence feature annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for molecular sequence feature information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1921 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1921">
-        <rdfs:label>Alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for molecular sequence alignment information.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1923 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1923">
-        <rdfs:label>acedb</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ACEDB sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1924 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1924">
-        <rdfs:label>clustal sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Clustalw output format.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1982"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1925 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1925">
-        <rdfs:label>codata</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Codata entry format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1926 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1926">
-        <rdfs:label>dbid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Fasta format variant with database name before ID.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1927 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1927">
-        <rdfs:label>EMBL format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2181"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <oboInOwl:hasDefinition>EMBL entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>EMBL sequence format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>EMBL</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1928 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1928">
-        <rdfs:label>Staden experiment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Staden experiment file format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1929 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1929">
-        <rdfs:label>FASTA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>FASTA format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>FASTA sequence format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>FASTA format including NCBI-style IDs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1930 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1930">
-        <rdfs:label>FASTQ</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ short read format ignoring quality scores.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>FASTAQ</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>fq</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1931 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1931">
-        <rdfs:label>FASTQ-illumina</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ Illumina 1.3 short read format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1932 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1932">
-        <rdfs:label>FASTQ-sanger</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ short read format with phred quality.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1933 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1933">
-        <rdfs:label>FASTQ-solexa</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <oboInOwl:hasDefinition>FASTQ Solexa/Illumina 1.0 short read format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1934 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1934">
-        <rdfs:label>fitch program</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Fitch program format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1935 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1935">
-        <rdfs:label>GCG</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3486"/>
-        <oboInOwl:hasExactSynonym>GCG SSF</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment> GCG SSF (single sequence file) file format.</rdfs:comment>
-        <oboInOwl:hasDefinition>GCG sequence file format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1936 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1936">
-        <rdfs:label>GenBank format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2205"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Genbank entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1937 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1937">
-        <rdfs:label>genpept</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2205"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Genpept protein entry format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Currently identical to refseqp format</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1938 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1938">
-        <rdfs:label>GFF2-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1974"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>GFF feature file format with sequence in the header.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1939 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1939">
-        <rdfs:label>GFF3-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>GFF3 feature file format with sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1940 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1940">
-        <rdfs:label>giFASTA format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <oboInOwl:hasDefinition>FASTA sequence format including NCBI-style GIs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1941 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1941">
-        <rdfs:label>hennig86</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Hennig86 output sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1942 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1942">
-        <rdfs:label>ig</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Intelligenetics sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1943 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1943">
-        <rdfs:label>igstrict</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Intelligenetics sequence format (strict version).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1944 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1944">
-        <rdfs:label>jackknifer</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Jackknifer interleaved and non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1945 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1945">
-        <rdfs:label>mase format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mase program sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1946 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1946">
-        <rdfs:label>mega-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mega interleaved and non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1947 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1947">
-        <rdfs:label>MSF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3486"/>
-        <oboInOwl:hasExactSynonym>GCG MSF</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>GCG MSF (multiple sequence file) file format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1948 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1948">
-        <rdfs:label>nbrf/pir</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>NBRF/PIR entry sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>nbrf</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>pir</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1949 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1949">
-        <rdfs:label>nexus-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Nexus/paup interleaved sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1950 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1950">
-        <rdfs:label>pdbatom</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:comment>pdb format in EMBOSS.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>PDB sequence format (ATOM lines).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1951 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1951">
-        <rdfs:label>pdbatomnuc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>pdbnuc format in EMBOSS.</rdfs:comment>
-        <oboInOwl:hasDefinition>PDB nucleotide sequence format (ATOM lines).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1952 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1952">
-        <rdfs:label>pdbseqresnuc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:comment>pdbnucseq format in EMBOSS.</rdfs:comment>
-        <oboInOwl:hasDefinition>PDB nucleotide sequence format (SEQRES lines).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1953 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1953">
-        <rdfs:label>pdbseqres</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1475"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>PDB sequence format (SEQRES lines).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>pdbseq format in EMBOSS.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1954 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1954">
-        <rdfs:label>Pearson format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Plain old FASTA sequence format (unspecified format for IDs).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1955 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1955">
-        <rdfs:label>phylip sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylip interleaved sequence format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1997"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1956 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1956">
-        <rdfs:label>phylipnon sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Phylip non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1998"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1957 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1957">
-        <rdfs:label>raw</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Raw sequence format with no non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1958 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1958">
-        <rdfs:label>refseqp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Refseq protein entry sequence format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Currently identical to genpept format</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1959 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1959">
-        <rdfs:label>selex sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Selex sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2000"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1960 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1960">
-        <rdfs:label>Staden format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Staden suite sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html"/>
-        <documentation rdf:resource="http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1961 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1961">
-        <rdfs:label>Stockholm format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Stockholm multiple sequence alignment format (used by Pfam and Rfam).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://en.wikipedia.org/wiki/Stockholm_format"/>
-        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/Stockholm_format"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1962 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1962">
-        <rdfs:label>strider format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>DNA strider output sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1963 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1963">
-        <rdfs:label>UniProtKB format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2187"/>
-        <oboInOwl:hasExactSynonym>UniProt format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>SwissProt format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>UniProtKB entry sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1964 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1964">
-        <rdfs:label>plain text format (unformatted)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Plain text sequence format (essentially unformatted).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1965 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1965">
-        <rdfs:label>treecon sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Treecon output sequence format.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2005"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1966 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1966">
-        <rdfs:label>ASN.1 sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>NCBI ASN.1-based sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1967 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1967">
-        <rdfs:label>DAS format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2552"/>
-        <oboInOwl:hasExactSynonym>das sequence format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>DAS sequence (XML) format (any type).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1968 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1968">
-        <rdfs:label>dasdna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2552"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DAS sequence (XML) format (nucleotide-only).</oboInOwl:hasDefinition>
-        <rdfs:comment>The use of this format is deprecated.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1969 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1969">
-        <rdfs:label>debug-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>EMBOSS debugging trace sequence format of full internal data content.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1970 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1970">
-        <rdfs:label>jackknifernon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Jackknifer output sequence non-interleaved format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1971 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1971">
-        <rdfs:label>meganon sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mega non-interleaved output sequence format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1992"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1972 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1972">
-        <rdfs:label>NCBI format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <oboInOwl:hasDefinition>NCBI FASTA sequence format with NCBI-style IDs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>There are several variants of this.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1973 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1973">
-        <rdfs:label>nexusnon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Nexus/paup non-interleaved sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1974 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1974">
-        <rdfs:label>GFF2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2305"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>General Feature Format (GFF) of sequence features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.sanger.ac.uk/resources/software/gff/spec.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.sanger.ac.uk/resources/software/gff/spec.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1975 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1975">
-        <rdfs:label>GFF3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2305"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generic Feature Format version 3 (GFF3) of sequence features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://sequenceontology.org/resources/gff3.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1976 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1976">
-        <rdfs:label>pir</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>PIR feature format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1948"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1977 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1977">
-        <rdfs:label>swiss feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Swiss-Prot feature format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1963"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1978 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1978">
-        <rdfs:label>DASGFF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2553"/>
-        <oboInOwl:hasDefinition>DAS GFF (XML) feature format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>das feature</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>DASGFF feature</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1979 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1979">
-        <rdfs:label>debug-feat</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>EMBOSS debugging trace feature format of full internal data content.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1980 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1980">
-        <rdfs:label>EMBL feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>EMBL feature format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1927"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1981 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1981">
-        <rdfs:label>GenBank feature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Genbank feature format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1936"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1982 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1982">
-        <rdfs:label>ClustalW format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasExactSynonym>clustal</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ClustalW format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1983 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1983">
-        <rdfs:label>debug</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS alignment format for debugging trace of full internal data content.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1984 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1984">
-        <rdfs:label>FASTA-aln</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Fasta format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1985 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1985">
-        <rdfs:label>markx0</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX0 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1986 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1986">
-        <rdfs:label>markx1</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <oboInOwl:hasDefinition>Pearson MARKX1 alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1987 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1987">
-        <rdfs:label>markx10</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX10 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1988 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1988">
-        <rdfs:label>markx2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX2 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1989 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1989">
-        <rdfs:label>markx3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2922"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pearson MARKX3 alignment format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1990 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1990">
-        <rdfs:label>match</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Alignment format for start and end of matches between sequence pairs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1991 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1991">
-        <rdfs:label>mega</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2923"/>
-        <oboInOwl:hasDefinition>Mega format for (typically aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1992 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1992">
-        <rdfs:label>meganon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2923"/>
-        <oboInOwl:hasDefinition>Mega non-interleaved format for (typically aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1993 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1993">
-        <rdfs:label>msf alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>MSF format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1947"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1994 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1994">
-        <rdfs:label>nexus alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Nexus/paup format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1995 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1995">
-        <rdfs:label>nexusnon alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Nexus/paup non-interleaved format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1973"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1996 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1996">
-        <rdfs:label>pair</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS simple sequence pair alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1997 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1997">
-        <rdfs:label>PHYLIP format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2924"/>
-        <oboInOwl:hasExactSynonym>phy</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>ph</oboInOwl:hasExactSynonym>
-        <documentation>http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format</documentation>
-        <oboInOwl:hasExactSynonym>PHYLIP interleaved format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Phylip format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1998 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1998">
-        <rdfs:label>phylipnon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2924"/>
-        <documentation>http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format</documentation>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>PHYLIP sequential format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Phylip non-interleaved format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_1999 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_1999">
-        <rdfs:label>scores format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Alignment format for score values for pairs of sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2000 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2000">
-        <rdfs:label>selex</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>SELEX format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2001 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2001">
-        <rdfs:label>EMBOSS simple format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS simple multiple alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2002 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2002">
-        <rdfs:label>srs format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simple multiple sequence (alignment) format for SRS.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2003">
-        <rdfs:label>srspair</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simple sequence pair (alignment) format for SRS.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2004">
-        <rdfs:label>T-Coffee format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>T-Coffee program alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2005">
-        <rdfs:label>TreeCon-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Treecon format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2006">
-        <rdfs:label>Phylogenetic tree format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2013 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2013">
-        <rdfs:label>Biological pathway or network format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2014 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2014">
-        <rdfs:label>Sequence-profile alignment format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0869"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a sequence-profile alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2015 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2015">
-        <rdfs:label>Sequence-profile alignment (HMM) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Data format for a sequence-HMM profile alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2014"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2017 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2017">
-        <rdfs:label>Amino acid index format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3033"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1501"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for an amino acid index.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2020 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2020">
-        <rdfs:label>Article format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0971"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Literature format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Data format for a full-text scientific article.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2021 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2021">
-        <rdfs:label>Text mining report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0972"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for an abstract (report) from text mining.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2027 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2027">
-        <rdfs:label>Enzyme kinetics report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2024"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for reports on enzyme kinetics.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2030 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2030">
-        <rdfs:label>Small molecule report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0962"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemical compound annotation format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of a report on a chemical compound.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2031 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2031">
-        <rdfs:label>Gene annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report on a particular locus, gene, gene system or groups of genes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene features format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2032 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2032">
-        <rdfs:label>Workflow format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a workflow.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2033 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2033">
-        <rdfs:label>Tertiary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular tertiary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2034 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2034">
-        <rdfs:label>Biological model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data format for a biological model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.2</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2013"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2035 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2035">
-        <rdfs:label>Chemical formula format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0846"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Text format of a chemical formula.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2036 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2036">
-        <rdfs:label>Phylogenetic character data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0871"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of raw (unplotted) phylogenetic data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2037 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2037">
-        <rdfs:label>Phylogenetic continuous quantitative character format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1426"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of phylogenetic continuous quantitative character data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2038 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2038">
-        <rdfs:label>Phylogenetic discrete states format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1427"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of phylogenetic discrete states data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2039 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2039">
-        <rdfs:label>Phylogenetic tree report (cliques) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1428"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of phylogenetic cliques data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2040 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2040">
-        <rdfs:label>Phylogenetic tree report (invariants) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2036"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1429"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of phylogenetic invariants data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2045 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2045">
-        <rdfs:label>Electron microscopy model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Annotation format for electron microscopy models.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2049 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2049">
-        <rdfs:label>Phylogenetic tree report (tree distances) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1442"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format for phylogenetic tree distance data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2051 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2051">
-        <rdfs:label>Polymorphism report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:hasDefinition>Format for sequence polymorphism data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2052 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2052">
-        <rdfs:label>Protein family report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for reports on a protein family.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2054 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2054">
-        <rdfs:label>Protein interaction format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for molecular interaction data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Molecular interaction format</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2055 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2055">
-        <rdfs:label>Sequence assembly format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for sequence assembly data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2056 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2056">
-        <rdfs:label>Microarray experiment data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <oboInOwl:hasDefinition>Format for information about a microarray experimental per se (not the data generated from that experiment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2057 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2057">
-        <rdfs:label>Sequence trace format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0924"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format for sequence trace data (i.e. including base call information).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2058 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2058">
-        <rdfs:label>Gene expression report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2603"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Gene expression data format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of a file of gene expression data, e.g. a gene expression matrix or profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2059 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2059">
-        <rdfs:label>Genotype and phenotype annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Format of a report on genotype / phenotype information.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2060 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2060">
-        <rdfs:label>Map format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a map of (typically one) molecular sequence annotated with features.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2061 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2061">
-        <rdfs:label>Nucleic acid features (primers) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2062 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2062">
-        <rdfs:label>Protein report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report of general information about a specific protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2063 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2063">
-        <rdfs:label>Protein report (enzyme) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report of general information about a specific enzyme.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2064 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2064">
-        <rdfs:label>3D-1D scoring matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3033"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1499"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a matrix of 3D-1D scores (amino acid environment probabilities).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2065 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2065">
-        <rdfs:label>Protein structure report (quality evaluation) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1539"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report on the quality of a protein three-dimensional model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2066 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2066">
-        <rdfs:label>Database hits (sequence) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0857"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a report on sequence hits and associated data from searching a sequence database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2067 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2067">
-        <rdfs:label>Sequence distance matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0870"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a matrix of genetic distances between molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2068 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2068">
-        <rdfs:label>Sequence motif format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1353"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a sequence motif.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2069 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2069">
-        <rdfs:label>Sequence profile format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a sequence profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2072 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2072">
-        <rdfs:label>Hidden Markov model format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2069"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1364"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a hidden Markov model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2074 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2074">
-        <rdfs:label>Dirichlet distribution format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1347"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format of a dirichlet distribution.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2075 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2075">
-        <rdfs:label>HMM emission and transition counts format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3355"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for the emission and transition counts of a hidden Markov model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2076 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2076">
-        <rdfs:label>RNA secondary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format for secondary structure (predicted or real) of an RNA molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2077">
-        <rdfs:label>Protein secondary structure format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Format for secondary structure (predicted or real) of a protein molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2078">
-        <rdfs:label>Sequence range format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1017"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used to specify range(s) of sequence positions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2094">
-        <rdfs:label>pure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for molecular sequence with possible unknown positions but without non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2095 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2095">
-        <rdfs:label>unpure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2096 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2096">
-        <rdfs:label>unambiguous sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2097">
-        <rdfs:label>ambiguous</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2155 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2155">
-        <rdfs:label>Sequence features (repeats) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for map of repeats in molecular (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2158">
-        <rdfs:label>Nucleic acid features (restriction sites) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for report on restriction enzyme recognition sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2159">
-        <rdfs:label>Gene features (coding region) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for report on coding regions in nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.10</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_2031"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2170 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2170">
-        <rdfs:label>Sequence cluster format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for clusters of molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2171 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2171">
-        <rdfs:label>Sequence cluster format (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2170"/>
-        <oboInOwl:hasDefinition>Format used for clusters of protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2172">
-        <rdfs:label>Sequence cluster format (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2170"/>
-        <oboInOwl:hasDefinition>Format used for clusters of nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2175">
-        <rdfs:label>Gene cluster format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format used for clusters of genes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2172"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2181 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2181">
-        <rdfs:label>EMBL-like (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2543"/>
-        <rdfs:comment>This concept may be used for the many non-standard EMBL-like text formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A text format resembling EMBL entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2182">
-        <rdfs:label>FASTQ-like format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2545"/>
-        <oboInOwl:hasDefinition>A text format resembling FASTQ short read format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for non-standard FASTQ short read-like formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2183">
-        <rdfs:label>EMBLXML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2204"/>
-        <oboInOwl:hasDefinition>XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2184">
-        <rdfs:label>cdsxml</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2204"/>
-        <oboInOwl:hasDefinition>XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2185 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2185">
-        <rdfs:label>insdxml</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2204"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2186 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2186">
-        <rdfs:label>geneseq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2181"/>
-        <oboInOwl:hasDefinition>Geneseq sequence format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2187 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2187">
-        <rdfs:label>UniProt-like (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2547"/>
-        <oboInOwl:hasDefinition>A text sequence format resembling uniprotkb entry format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2188 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2188">
-        <rdfs:label>UniProt format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>UniProt entry sequence format.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1963"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2189 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2189">
-        <rdfs:label>ipi</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>ipi sequence format.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_1963"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2194">
-        <rdfs:label>medline</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2020"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Abstract format used by MedLine database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2195">
-        <rdfs:label>Ontology format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format used for ontologies.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2196">
-        <rdfs:label>OBO format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A serialisation format conforming to the Open Biomedical Ontologies (OBO) model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2197 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2197">
-        <rdfs:label>OWL format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>A serialisation format conforming to the Web Ontology Language (OWL) model.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2200">
-        <rdfs:label>FASTA-like (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2546"/>
-        <rdfs:comment>This concept may also be used for the many non-standard FASTA-like formats.</rdfs:comment>
-        <rdfs:seeAlso>http://filext.com/file-extension/FASTA</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A text format resembling FASTA format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2202">
-        <rdfs:label>Sequence record full format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2203">
-        <rdfs:label>Sequence record lite format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record &apos;lite&apos;, typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2204">
-        <rdfs:label>EMBL format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2558"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An XML format for EMBL entries.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is a placeholder for other more specific concepts. It should not normally be used for annotation.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2205 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2205">
-        <rdfs:label>GenBank-like format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2559"/>
-        <oboInOwl:hasDefinition>A text format resembling GenBank entry (plain text) format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for the non-standard GenBank-like text formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2206 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2206">
-        <rdfs:label>Sequence feature table format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2548"/>
-        <oboInOwl:hasDefinition>Text format for a sequence feature table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2210">
-        <rdfs:label>Strain data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on organism strain data / cell line.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2211">
-        <rdfs:label>CIP strain data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format for a report of strain data as used for CIP database entries.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2243">
-        <rdfs:label>phylip property values</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>PHYLIP file format for phylogenetic property data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2036"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2303">
-        <rdfs:label>STRING entry format (HTML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format (HTML) for the STRING database of protein interaction.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2304">
-        <rdfs:label>STRING entry format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2054"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Entry format (XML) for the STRING database of protein interaction.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2305">
-        <rdfs:label>GFF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>GFF feature format (of indeterminate version).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2306">
-        <rdfs:label>GTF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2305"/>
-        <oboInOwl:hasDefinition>Gene Transfer Format (GTF), a restricted version of GFF.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format4"/>
-        <oboInOwl:hasDbXref rdf:resource="http://mblab.wustl.edu/GTF22.html"/>
-        <documentation rdf:resource="http://mblab.wustl.edu/GTF22.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2310">
-        <rdfs:label>FASTA-HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2546"/>
-        <oboInOwl:hasDefinition>FASTA format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2311">
-        <rdfs:label>EMBL-HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2543"/>
-        <oboInOwl:hasDefinition>EMBL entry format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2322">
-        <rdfs:label>BioCyc enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of an entry from the BioCyc enzyme database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2323">
-        <rdfs:label>ENZYME enzyme report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of an entry from the Enzyme nomenclature database (ENZYME).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2328">
-        <rdfs:label>PseudoCAP gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a report on a gene from the PseudoCAP database.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2329">
-        <rdfs:label>GeneCards gene report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Format of a report on a gene from the GeneCards database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2330">
-        <rdfs:label>Textual format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:seeAlso>http://filext.com/file-extension/TSV</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.iana.org/assignments/media-types/text/plain</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Textual format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>txt</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://filext.com/file-extension/TXT</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Plain text</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://www.iana.org/assignments/media-types/media-types.xhtml#text</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2331">
-        <rdfs:label>HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2048"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>HTML format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://filext.com/file-extension/HTML</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Hypertext Markup Language</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2332">
-        <rdfs:label>XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:comment>Data in XML format can be serialised into text, or binary format.</rdfs:comment>
-        <oboInOwl:hasDefinition>eXtensible Markup Language (XML) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://filext.com/file-extension/XML</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Extensible Markup Language</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2333 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2333">
-        <rdfs:label>Binary format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:comment>Only specific native binary formats are listed under &apos;Binary format&apos; in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Binary format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2334">
-        <rdfs:label>URI format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Typical textual representation of a URI.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_1047"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2341">
-        <rdfs:label>NCI-Nature pathway entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The format of an entry from the NCI-Nature pathways database.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2350">
-        <rdfs:label>Format (typed)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1915"/>
-        <rdfs:comment>This concept exists only to assist EDAM maintenance and navigation in graphical browsers.  It does not add semantic information. The concept branch under &apos;Format (typed)&apos; provides an alternative organisation of the concepts nested under the other top-level branches (&apos;Binary&apos;, &apos;HTML&apos;, &apos;RDF&apos;, &apos;Text&apos; and &apos;XML&apos;. All concepts under here are already included under those branches.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A broad class of format distinguished by the scientific nature of the data that is identified.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2352">
-        <rdfs:label>BioXSD</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2555"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>BioXSD XML format</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more).</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://bioxsd.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://bioxsd.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2376 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2376">
-        <rdfs:label>RDF format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A serialisation format conforming to the Resource Description Framework (RDF) model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2532 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2532">
-        <rdfs:label>GenBank-HTML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2559"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Genbank entry format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2542">
-        <rdfs:label>Protein features (domains) format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Format of a report on protein features (domain composition).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2543">
-        <rdfs:label>EMBL-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A format resembling EMBL entry (plain text) format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for the many non-standard EMBL-like formats.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2545">
-        <rdfs:label>FASTQ-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <oboInOwl:hasDefinition>A format resembling FASTQ short read format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for non-standard FASTQ short read-like formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2546">
-        <rdfs:label>FASTA-like</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:comment>This concept may be used for the many non-standard FASTA-like formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A format resembling FASTA format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2547">
-        <rdfs:label>uniprotkb-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2206"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A sequence format resembling uniprotkb entry format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2548">
-        <rdfs:label>Sequence feature table format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format for a sequence feature table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2549">
-        <rdfs:label>OBO</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2196"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>OBO ontology text format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2550">
-        <rdfs:label>OBO-XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2196"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>OBO ontology XML format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2551">
-        <rdfs:label>Sequence record format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2552">
-        <rdfs:label>Sequence record format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for a molecular sequence record.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2553">
-        <rdfs:label>Sequence feature table format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2548"/>
-        <oboInOwl:hasDefinition>XML format for a sequence feature table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2554">
-        <rdfs:label>Alignment format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <oboInOwl:hasDefinition>Text format for molecular sequence alignment information.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2555">
-        <rdfs:label>Alignment format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <oboInOwl:hasDefinition>XML format for molecular sequence alignment information.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2556">
-        <rdfs:label>Phylogenetic tree format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Text format for a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2557">
-        <rdfs:label>Phylogenetic tree format (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2006"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>XML format for a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2558">
-        <rdfs:label>EMBL-like (XML)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2543"/>
-        <oboInOwl:hasDefinition>An XML format resembling EMBL entry format.</oboInOwl:hasDefinition>
-        <rdfs:comment>This concept may be used for the any non-standard EMBL-like XML formats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2559">
-        <rdfs:label>GenBank-like format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1919"/>
-        <oboInOwl:hasDefinition>A format resembling GenBank entry (plain text) format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This concept may be used for the non-standard GenBank-like formats.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2560">
-        <rdfs:label>STRING entry format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Entry format for the STRING database of protein interaction.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2561">
-        <rdfs:label>Sequence assembly format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2055"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Text format for sequence assembly data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2562 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2562">
-        <rdfs:label>Amino acid identifier format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Text format (representation) of amino acid residues.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/data_0994"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2566">
-        <rdfs:label>completely unambiguous</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence without any unknown positions or ambiguity characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2567">
-        <rdfs:label>completely unambiguous pure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2094"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2566"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2568">
-        <rdfs:label>completely unambiguous pure nucleotide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1207"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <oboInOwl:hasDefinition>Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters .</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2569">
-        <rdfs:label>completely unambiguous pure dna</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1212"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2570">
-        <rdfs:label>completely unambiguous pure rna sequence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1213"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <oboInOwl:hasDefinition>Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2571">
-        <rdfs:label>Raw sequence format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0848"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Format of a raw molecular sequence (i.e. the alphabet used).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2572">
-        <rdfs:label>BAM</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2573">
-        <rdfs:label>SAM</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <rdfs:comment>The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/SAM-1.3.pdf"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2585 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2585">
-        <rdfs:label>SBML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://sbml.org"/>
-        <documentation rdf:resource="http://sbml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2607">
-        <rdfs:label>completely unambiguous pure protein</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1208"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2567"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2848 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2848">
-        <rdfs:label>Bibliographic reference format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0970"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a bibliographic reference.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2919 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2919">
-        <rdfs:label>Sequence annotation track format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1920"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3002"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a sequence annotation track.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2920 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2920">
-        <rdfs:label>Alignment format (pair only)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1381"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2921 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2921">
-        <rdfs:label>Sequence variation annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3498"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of sequence variation annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2922 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2922">
-        <rdfs:label>markx0 variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Some variant of Pearson MARKX alignment format.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2923 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2923">
-        <rdfs:label>mega variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Some variant of Mega format for (typically aligned) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_2924 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_2924">
-        <rdfs:label>Phylip format variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Some variant of Phylip format for (aligned) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3000 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3000">
-        <rdfs:label>AB1</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>AB1 binary format of raw DNA sequence reads (output of Applied Biosystems&apos; sequencing analysis software). Contains an electropherogram and the DNA base sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3001 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3001">
-        <rdfs:label>ACE</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2055"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt"/>
-        <oboInOwl:hasDbXref rdf:resource="http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3003">
-        <rdfs:label>BED</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track).</rdfs:comment>
-        <oboInOwl:hasDefinition>Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3004">
-        <rdfs:label>bigBed</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>bigBed format for large sequence annotation tracks, similar to textual BED format.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.5"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.5"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3005 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3005">
-        <rdfs:label>WIG</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/goldenPath/help/wiggle.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/goldenPath/help/wiggle.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3006 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3006">
-        <rdfs:label>bigWig</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format6.1"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format6.1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3007 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3007">
-        <rdfs:label>PSL</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <oboInOwl:hasDefinition>PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format2"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format2"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3008 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3008">
-        <rdfs:label>MAF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth.</oboInOwl:hasDefinition>
-        <rdfs:comment>Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format5"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format5"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3009 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3009">
-        <rdfs:label>2bit</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case &apos;masking&apos;.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD"/>
-        <documentation rdf:resource="http://jcomeau.freeshell.org/www/genome/2bitformat.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://jcomeau.freeshell.org/www/genome/2bitformat.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3010 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3010">
-        <rdfs:label>.nib</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>.nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case &apos;masking&apos;.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format8"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format8"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3011 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3011">
-        <rdfs:label>genePred</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>genePred table format for gene prediction tracks.</oboInOwl:hasDefinition>
-        <rdfs:comment>genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format9"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format9"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3012 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3012">
-        <rdfs:label>pgSnp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <oboInOwl:hasDefinition>Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format10"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format10"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3013 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3013">
-        <rdfs:label>axt</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>axt format of alignments, typically produced from BLASTZ.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/goldenPath/help/axt.html"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/goldenPath/help/axt.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3014 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3014">
-        <rdfs:label>LAV</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>LAV format of alignments generated by BLASTZ and LASTZ.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.bx.psu.edu/miller_lab/dist/lav_format.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.bx.psu.edu/miller_lab/dist/lav_format.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3015 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3015">
-        <rdfs:label>Pileup</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/pileup.shtml"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/pileup.shtml"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3016 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3016">
-        <rdfs:label>VCF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://vcftools.sourceforge.net/specs.html"/>
-        <documentation rdf:resource="http://vcftools.sourceforge.net/specs.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3017 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3017">
-        <rdfs:label>SRF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://srf.sourceforge.net/"/>
-        <oboInOwl:hasDbXref rdf:resource="http://srf.sourceforge.net/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3018 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3018">
-        <rdfs:label>ZTR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasDefinition>ZTR format for storing chromatogram data from DNA sequencing instruments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://staden.sourceforge.net/manual/formats_unix_12.html"/>
-        <documentation rdf:resource="http://staden.sourceforge.net/manual/formats_unix_12.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3019 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3019">
-        <rdfs:label>GVF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1975"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <oboInOwl:hasDefinition>Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://sequenceontology.org/gvf.html"/>
-        <documentation rdf:resource="http://sequenceontology.org/gvf.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3020 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3020">
-        <rdfs:label>BCF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://samtools.sourceforge.net/mpileup.shtml"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3033 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3033">
-        <rdfs:label>Matrix format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a matrix (array) of numerical values.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3097">
-        <rdfs:label>Protein domain classification format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of data concerning the classification of the sequences and/or structures of protein structural domain(s).</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3098 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3098">
-        <rdfs:label>Raw SCOP domain classification format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3097"/>
-        <oboInOwl:hasDefinition>Format of raw SCOP domain classification data files.</oboInOwl:hasDefinition>
-        <rdfs:comment>These are the parsable data files provided by SCOP.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3099">
-        <rdfs:label>Raw CATH domain classification format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3097"/>
-        <rdfs:comment>These are the parsable data files provided by CATH.</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Format of raw CATH domain classification data files.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3100">
-        <rdfs:label>CATH domain report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3097"/>
-        <oboInOwl:hasDefinition>Format of summary of domain classification information for a CATH domain.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <rdfs:comment>The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3155 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3155">
-        <rdfs:label>SBRML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3166"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.comp-sys-bio.org/tiki-index.php?page=SBRML"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.comp-sys-bio.org/tiki-index.php?page=SBRML"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3156">
-        <rdfs:label>BioPAX</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <oboInOwl:hasDefinition>BioPAX is an exchange format for pathway data, with its data model defined in OWL.</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://www.biopax.org"/>
-        <documentation rdf:resource="http://www.biopax.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3157">
-        <rdfs:label>EBI Application Result XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2066"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <oboInOwl:hasDefinition>EBI Application Result XML is a format returned by sequence similarity search Web services at EBI.</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.ebi.ac.uk/schema/ApplicationResult.xsd"/>
-        <documentation rdf:resource="http://www.ebi.ac.uk/schema/ApplicationResult.xsd"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3158">
-        <rdfs:label>PSI MI XML (MIF)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2054"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>MIF</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.psidev.info/mif"/>
-        <documentation rdf:resource="http://www.psidev.info/mif"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3159">
-        <rdfs:label>phyloXML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2557"/>
-        <oboInOwl:hasDefinition>phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data.</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://www.phyloxml.org"/>
-        <documentation rdf:resource="http://www.phyloxml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3160">
-        <rdfs:label>NeXML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2557"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>NeXML is a standardised XML format for rich phyloinformatic data.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://www.nexml.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.nexml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3161 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3161">
-        <rdfs:label>MAGE-ML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.mged.org/Workgroups/MAGE/mage-ml.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.mged.org/Workgroups/MAGE/mage-ml.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3162 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3162">
-        <rdfs:label>MAGE-TAB</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED).</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.mged.org/mage-tab"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.mged.org/mage-tab"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3163">
-        <rdfs:label>GCDML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <oboInOwl:hasDefinition>GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC).</oboInOwl:hasDefinition>
-        <created_in>1.0</created_in>
-        <documentation rdf:resource="http://gcdml.gensc.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://gcdml.gensc.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3164">
-        <rdfs:label>GTrack</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>1.0</created_in>
-        <oboInOwl:hasDefinition>GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG).</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://www.gtrack.no"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.gtrack.no"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3166">
-        <rdfs:label>Biological pathway or network report format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Data format for a report of information derived from a biological pathway or network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3167">
-        <rdfs:label>Experiment annotation format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Data format for annotation on a laboratory experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3235">
-        <rdfs:label>Cytoband format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2078"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3236"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Cytoband format for chromosome cytobands.</oboInOwl:hasDefinition>
-        <rdfs:comment>Reflects a UCSC Browser DB table.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.broadinstitute.org/software/igv/Cytoband"/>
-        <documentation rdf:resource="http://www.broadinstitute.org/software/igv/Cytoband"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3239">
-        <rdfs:label>CopasiML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3166"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>CopasiML, the native format of COPASI.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.copasi.org/tiki-index.php?page_ref_id=128"/>
-        <documentation rdf:resource="http://www.copasi.org/tiki-index.php?page_ref_id=128"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3240">
-        <rdfs:label>CellML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>CellML, the format for mathematical models of biological and other networks.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <documentation rdf:resource="http://www.cellml.org"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.cellml.org"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3242">
-        <rdfs:label>PSI MI TAB (MITAB)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2054"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README"/>
-        <documentation rdf:resource="ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/README"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3243">
-        <rdfs:label>PSI-PAR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3158"/>
-        <oboInOwl:hasDefinition>Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.psidev.info/psi-par"/>
-        <documentation rdf:resource="http://www.psidev.info/psi-par"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3244 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3244">
-        <rdfs:label>mzML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3245"/>
-        <rdfs:comment>mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center.</rdfs:comment>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://psidev.info/mzml"/>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/mzml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3245">
-        <rdfs:label>Mass spectrometry data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2536"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Format for mass spectrometry data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3246">
-        <rdfs:label>TraML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3245"/>
-        <oboInOwl:hasDefinition>TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <documentation rdf:resource="http://psidev.info/traml"/>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/traml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3247">
-        <rdfs:label>mzIdentML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3245"/>
-        <oboInOwl:hasDefinition>mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/mzidentml"/>
-        <documentation rdf:resource="http://psidev.info/mzidentml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3248">
-        <rdfs:label>mzQuantML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3245"/>
-        <oboInOwl:hasDefinition>mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <documentation rdf:resource="http://psidev.info/mzquantml"/>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/mzquantml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3249 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3249">
-        <rdfs:label>GelML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info/gelml"/>
-        <documentation rdf:resource="http://psidev.info/gelml"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3250">
-        <rdfs:label>spML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3167"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://psidev.info"/>
-        <documentation rdf:resource="http://psidev.info"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3252">
-        <rdfs:label>OWL Functional Syntax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>A human-readable encoding for the Web Ontology Language (OWL).</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3253">
-        <rdfs:label>Manchester OWL Syntax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>A syntax for writing OWL class expressions.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <rdfs:comment>This format was influenced by the OWL Abstract Syntax and the DL style syntax.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3254">
-        <rdfs:label>KRSS2 Syntax</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:comment>This format is used in Protege 4.</rdfs:comment>
-        <oboInOwl:hasDefinition>A superset of the &quot;Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort&quot;.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3255 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3255">
-        <rdfs:label>Turtle</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <rdfs:comment>The SPARQL Query Language incorporates a very similar syntax.</rdfs:comment>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3256 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3256">
-        <rdfs:label>N-Triples</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <rdfs:comment>N-Triples should not be confused with Notation 3 which is a superset of Turtle.</rdfs:comment>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3257">
-        <rdfs:label>Notation3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <oboInOwl:hasExactSynonym>N3</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3261 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3261">
-        <rdfs:label>RDF/XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2376"/>
-        <oboInOwl:hasNarrowSynonym>RDF</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Resource Description Framework (RDF) XML format.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <rdfs:seeAlso>http://www.ebi.ac.uk/SWO/data/SWO_3000006</rdfs:seeAlso>
-        <rdfs:comment>RDF/XML is a serialization syntax for OWL DL, but not for OWL Full.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3262 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3262">
-        <rdfs:label>OWL/XML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2197"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>OWL ontology XML serialisation format.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasNarrowSynonym>OWL</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3281 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3281">
-        <rdfs:label>A2M</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://compbio.soe.ucsc.edu/a2m-desc.html"/>
-        <documentation rdf:resource="http://compbio.soe.ucsc.edu/a2m-desc.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3284">
-        <rdfs:label>SFF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2057"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <oboInOwl:hasExactSynonym>Standard flowgram format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&amp;f=formats&amp;m=doc&amp;s=format#sff"/>
-        <documentation rdf:resource="http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&amp;f=formats&amp;m=doc&amp;s=format#sff"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3285">
-        <rdfs:label>MAP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3288"/>
-        <oboInOwl:hasDefinition>The MAP file describes SNPs and is used by the Plink package.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Plink MAP</oboInOwl:hasExactSynonym>
-        <documentation rdf:resource="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3286 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3286">
-        <rdfs:label>PED</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3288"/>
-        <oboInOwl:hasExactSynonym>Plink PED</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The PED file describes individuals and genetic data and is used by the Plink package.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3287 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3287">
-        <rdfs:label>Individual genetic data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Data format for a metadata on an individual and their genetic data.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3288">
-        <rdfs:label>PED/MAP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3287"/>
-        <oboInOwl:hasDefinition>The PED/MAP file describes data used by the Plink package.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Plink PED/MAP</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <documentation rdf:resource="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3309">
-        <rdfs:label>CT</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>File format of a CT (Connectivity Table) file from the RNAstructure package.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Connect format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Connectivity Table file format</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://rna.urmc.rochester.edu/Text/File_Formats.html"/>
-        <documentation rdf:resource="http://www.ibi.vu.nl/programs/k2nwww/static/data_formats.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3310">
-        <rdfs:label>SS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>XRNA old input style format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://rna.ucsc.edu/rnacenter/xrna/xrna_faq.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3311">
-        <rdfs:label>RNAML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1921"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2076"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>RNA Markup Language.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www-lbit.iro.umontreal.ca/rnaml/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3312">
-        <rdfs:label>GDE</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <oboInOwl:hasDefinition>Format for the Genetic Data Environment (GDE).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <documentation rdf:resource="http://home.cc.umanitoba.ca/~psgendb/birchhomedir/local/pkg/gde/doc/GDE2.2_manual.pdf"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3313">
-        <rdfs:label>BLC</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Block file format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.compbio.dundee.ac.uk/manuals/amps/subsubsection3_18_2_5.html#SECTION00018250000000000000"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3326">
-        <rdfs:label>Data index format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3327">
-        <rdfs:label>BAI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3326"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>BAM indexing format</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://samtools.sourceforge.net/SAMv1.pdf"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3328">
-        <rdfs:label>HMMER2</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1370"/>
-        <oboInOwl:hasDefinition>HMMER profile HMM file for HMMER versions 2.x</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <documentation rdf:resource="ftp://selab.janelia.org/pub/software/hmmer/2.4i/Userguide.pdf"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3329">
-        <rdfs:label>HMMER3</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1370"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>HMMER profile HMM file for HMMER versions 3.x</oboInOwl:hasDefinition>
-        <documentation rdf:resource="ftp://selab.janelia.org/pub/software/hmmer/CURRENT/Userguide.pdf"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3330">
-        <rdfs:label>PO</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>EMBOSS simple sequence pair alignment format.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://sourceforge.net/projects/poamsa/files/latest/download?source=files"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3331">
-        <rdfs:label>BLAST XML results format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <oboInOwl:hasDefinition>XML format as produced by the NCBI Blast package</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3462 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3462">
-        <rdfs:label>CRAM</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2920"/>
-        <oboInOwl:hasDefinition>Reference-based compression of alignment format</oboInOwl:hasDefinition>
-        <documentation>http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf</documentation>
-        <oboInOwl:hasDbXref>http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf</oboInOwl:hasDbXref>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3464">
-        <rdfs:label>JSON</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Javascript Object Notation format; a lightweight, text-based format to represent structured data using key-value pairs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3466 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3466">
-        <rdfs:label>EPS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Encapsulated PostScript format</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3467">
-        <rdfs:label>GIF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Graphics Interchange Format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3468">
-        <rdfs:label>xls</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <oboInOwl:hasDefinition>Microsoft Excel spreadsheet format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microsoft Excel format</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3475">
-        <rdfs:label>TSV</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasExactSynonym>Tabular format</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://filext.com/file-extension/CSV</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.iana.org/assignments/media-types/text/csv</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Tabular data represented as tab-separated values in a text file.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:seeAlso>http://filext.com/file-extension/TSV</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>CSV</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3476">
-        <rdfs:label>Gene expression data format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.10</obsolete_since>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Format of a file of gene expression data, e.g. a gene expression matrix or profile.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/format_2058"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3477 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3477">
-        <rdfs:label>Cytoscape input file format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3484 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3484">
-        <rdfs:label>ebwt</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3326"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3210"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <documentation>https://github.com/BenLangmead/bowtie/blob/master/MANUAL</documentation>
-        <oboInOwl:hasExactSynonym>Bowtie index format</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Bowtie format for indexed reference genome for &quot;small&quot; genomes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3485">
-        <rdfs:label>RSF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3486"/>
-        <documentation>http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf</documentation>
-        <rdfs:comment>RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual).</rdfs:comment>
-        <oboInOwl:hasDefinition>Rich sequence format.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>GCG RSF</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3486">
-        <rdfs:label>GCG format variant</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2551"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Some format based on the GCG format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3487">
-        <rdfs:label>BSML</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2552"/>
-        <documentation>http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc</documentation>
-        <oboInOwl:hasDefinition>Bioinformatics Sequence Markup Language format.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3491">
-        <rdfs:label>ebwtl</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3326"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3210"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <documentation>https://github.com/BenLangmead/bowtie/blob/master/MANUAL</documentation>
-        <oboInOwl:hasExactSynonym>Bowtie long index format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Bowtie format for indexed reference genome for &quot;large&quot; genomes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3499">
-        <rdfs:label>Ensembl variation file format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2921"/>
-        <oboInOwl:hasDefinition>Ensembl standard format for variation data.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.ensembl.org/info/website/upload/var.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3506">
-        <rdfs:label>docx</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2332"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Microsoft Word format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>doc</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Microsoft Word format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3507">
-        <rdfs:label>Document format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Portable Document Format</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microsoft Word format</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Format of documents including word processor, spreadsheet and presentation.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>doc</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3508">
-        <rdfs:label>PDF</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Portable Document Format</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3547">
-        <rdfs:label>Image format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2968"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format used for images and image metadata.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3548">
-        <rdfs:label>DICOM format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard.
-
-</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://dicom.nema.org/"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3549">
-        <rdfs:label>nii</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>Medical image and metadata format of the Neuroimaging Informatics Technology Initiative.
-
-</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>NIfTI-1 format</oboInOwl:hasExactSynonym>
-        <created_in>1.9</created_in>
-        <documentation rdf:resource="http://nifti.nimh.nih.gov/nifti-1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3550">
-        <rdfs:label>mhd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasExactSynonym>Metalmage format</oboInOwl:hasExactSynonym>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Text-based tagged file format for medical images generated using the MetaImage software package.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.itk.org/Wiki/ITK/MetaIO/Documentation"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3551">
-        <rdfs:label>nrrd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Nearly Raw Rasta Data format designed to support scientific visualization and image processing involving N-dimensional raster data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://teem.sourceforge.net/nrrd/format.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3554">
-        <rdfs:label>R file format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics.
-</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3555">
-        <rdfs:label>SPSS</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>File format used for scripts for the Statistical Package for the Social Sciences.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3556">
-        <rdfs:label>MHT</rdfs:label>
-        <rdfs:label>MIME  HTML format for Web pages, which can include external resources, including images, Flash animations and so on. </rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2331"/>
-        <oboInOwl:hasDefinition>EMBL entry format wrapped in HTML elements.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasExactSynonym>MHTML</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3578">
-        <rdfs:label>IDAT</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3110"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3579">
-        <rdfs:label>JPG</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Joint Picture Group file format for lossy graphics file.
-</oboInOwl:hasDefinition>
-        <rdfs:comment>Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/jpeg/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3580 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3580">
-        <rdfs:label>rcc</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2058"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3581 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3581">
-        <rdfs:label>arff</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <oboInOwl:hasDefinition>ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <rdfs:comment>This file format is for machine learning.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.cs.waikato.ac.nz/ml/weka/arff.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.cs.waikato.ac.nz/ml/weka/arff.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3582 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3582">
-        <rdfs:label>afg</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2055"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>AFG is a single text-based file assembly format  that holds read and consensus information together</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="http://seqanswers.com/wiki/AFG"/>
-        <documentation rdf:resource="http://seqanswers.com/wiki/AFG"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3583 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3583">
-        <rdfs:label>bedgraph</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <rdfs:comment>Holds a tab-delimited chromosome /start /end / datavalue dataset.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.8"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1.8"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3584 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3584">
-        <rdfs:label>bedstrict</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3003"/>
-        <oboInOwl:hasDefinition>Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns.  </oboInOwl:hasDefinition>
-        <rdfs:comment>Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.  </rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format1"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3585 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3585">
-        <rdfs:label>bed6</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3584"/>
-        <rdfs:comment>Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6</rdfs:comment>
-        <oboInOwl:hasDefinition>BED file format where each feature is described by chromosome, start, end, name, score, and strand.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3586 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3586">
-        <rdfs:label>bed12</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3584"/>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12</rdfs:comment>
-        <oboInOwl:hasDefinition>A BED file where each feature is described by all twelve columns.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <documentation rdf:resource="http://bedtools.readthedocs.org/en/latest/content/general-usage.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3587 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3587">
-        <rdfs:label>chrominfo</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3003"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Tabular format of chromosome names and sizes used by Galaxy.</oboInOwl:hasDefinition>
-        <rdfs:comment>Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.  </rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables?hgsid=43553_onGgm5PMjz4VDV1NySxolABvN978&amp;hgta_doSchemaDb=mm10&amp;hgta_doSchemaTable=chromInfo"/>
-        <oboInOwl:hasDbXref rdf:resource="http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables?hgsid=43553_onGgm5PMjz4VDV1NySxolABvN978&amp;hgta_doSchemaDb=mm10&amp;hgta_doSchemaTable=chromInfo"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3588 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3588">
-        <rdfs:label>customtrack</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2919"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Custom Sequence annotation track format used by Galaxy.</oboInOwl:hasDefinition>
-        <rdfs:comment>Used for tracks/track views within galaxy.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://genome.ucsc.edu/goldenPath/help/customTrack.html"/>
-        <oboInOwl:hasDbXref rdf:resource="https://genome.ucsc.edu/goldenPath/help/customTrack.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3589 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3589">
-        <rdfs:label>csfasta</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2200"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2554"/>
-        <oboInOwl:hasDefinition>Color space FASTA format sequence variant.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <rdfs:comment>FASTA format extended for color space information.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.clcsupport.com/clcassemblycell/420/index.php?manual=Color_space_file_formats.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.clcsupport.com/clcassemblycell/420/index.php?manual=Color_space_file_formats.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3590 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3590">
-        <rdfs:label>hdf5</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:comment>An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. H5py uses straightforward NumPy and Python metaphors, like dictionary and NumPy array syntax.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasExactSynonym>h5</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Binary format used by Galaxy for hierarchical data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <oboInOwl:hasDbXref rdf:resource="https://www.hdfgroup.org/HDF5/doc/H5.format.html"/>
-        <documentation rdf:resource="https://www.hdfgroup.org/HDF5/doc/H5.format.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3591 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3591">
-        <rdfs:label>tiff</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>The TIFF format is perhaps the most versatile and diverse bitmap format in existence. Its extensible nature and support for numerous data compression schemes allow developers to customize the TIFF format to fit any peculiar data storage needs.
-</rdfs:comment>
-        <oboInOwl:hasDefinition>A versatile bitmap format.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/tiff/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3592 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3592">
-        <rdfs:label>bmp</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>Standard bitmap storage format in the Microsoft Windows environment.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Although it is based on Windows internal bitmap data structures, it is supported by many non-Windows and non-PC applications.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/bmp/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3593">
-        <rdfs:label>im</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>IM is a format used by LabEye and other applications based on the IFUNC image processing library.</oboInOwl:hasDefinition>
-        <rdfs:comment>IFUNC library reads and writes most uncompressed interchange versions of this format.
-</rdfs:comment>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://pillow.readthedocs.org/en/latest/handbook/image-file-formats.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3594">
-        <rdfs:label>pcd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>PCD was developed by Kodak. A PCD file contains five different resolution (ranging from low to high) of a slide or film negative. Due to it PCD is often used by many photographers and graphics professionals for high-end printed applications.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Photo CD format, which is the highest resolution format for images on a CD.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://www.coolutils.com/Formats/PCD"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3595">
-        <rdfs:label>pcx</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>PCX is an image file format that uses a simple form of run-length encoding. It is lossless.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://www.coolutils.com/Formats/PCX"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3596 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3596">
-        <rdfs:label>ppm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>The PPM format is a lowest common denominator color image file format.
-</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://netpbm.sourceforge.net/doc/ppm.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3597 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3597">
-        <rdfs:label>psd</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>PSD (Photoshop Document) is a proprietary file that allows the user to work with the images’ individual layers even after the file has been saved.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/psd/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3598">
-        <rdfs:label>xbm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>The XBM format was replaced by XPM for X11 in 1989.</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI. </oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/xbm/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3599 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3599">
-        <rdfs:label>xpm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.</rdfs:comment>
-        <oboInOwl:hasDefinition>X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/xpm/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3600 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3600">
-        <rdfs:label>rgb</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>RGB file format is the native raster graphics file format for Silicon Graphics workstations.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.fileformat.info/format/jpeg/egff.htm"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3601">
-        <rdfs:label>pbm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters.
-</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://netpbm.sourceforge.net/doc/pbm.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3602">
-        <rdfs:label>pgm</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>It is designed to be extremely easy to learn and write programs for.</rdfs:comment>
-        <oboInOwl:hasDefinition>The PGM format is a lowest common denominator grayscale file format.
-</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://netpbm.sourceforge.net/doc/pgm.html"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3603 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3603">
-        <rdfs:label>png</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>PNG is a file format for image compression.
-</oboInOwl:hasDefinition>
-        <rdfs:comment>It iis expected to replace the Graphics Interchange Format (GIF).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.w3.org/TR/PNG/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3604 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3604">
-        <rdfs:label>svg</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment> The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.</rdfs:comment>
-        <oboInOwl:hasDefinition>Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.w3.org/Graphics/SVG/"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3605">
-        <rdfs:label>rast</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <rdfs:comment> The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="https://en.wikipedia.org/wiki/Sun_Raster"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3606">
-        <rdfs:label>Sequence quality report format (text)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2330"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2048"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Textual report format for sequence quality for reports from sequencing machines.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3607">
-        <rdfs:label>qual</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2182"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3606"/>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <created_in>1.11</created_in>
-        <rdfs:comment>Phred quality scores  are defined as a property which is logarithmically related to the base-calling error probabilities.</rdfs:comment>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3608">
-        <rdfs:label>qualsolexa</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1933"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <rdfs:comment>Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)</rdfs:comment>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3609 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3609">
-        <rdfs:label>qualillumina</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_1931"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <rdfs:comment>Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 &quot;B&quot;, is used also at the end of reads as a Read Segment Quality Control Indicator.</rdfs:comment>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3610">
-        <rdfs:label>qualsolid</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <rdfs:comment>For SOLiD data, the sequence is in color space, except the first position. The quality values are those of the Sanger format.</rdfs:comment>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3611">
-        <rdfs:label>qual454</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3607"/>
-        <documentation>http://en.wikipedia.org/wiki/Phred_quality_score</documentation>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3612">
-        <rdfs:label>ENCODE peak format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3585"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Human ENCODE peak format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Format that covers both the broad peak format and narrow peak format from ENCODE.</rdfs:comment>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format13"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format13"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3613">
-        <rdfs:label>ENCODE narrow peak format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3612"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Human ENCODE narrow peak format.</oboInOwl:hasDefinition>
-        <rdfs:comment>Format that covers both the broad peak format and narrow peak format from ENCODE.</rdfs:comment>
-        <oboInOwl:hasDbXref rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?"/>
-        <documentation rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3614 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3614">
-        <rdfs:label>ENCODE broad peak format </rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3612"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Human ENCODE broad peak format.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format12"/>
-        <oboInOwl:hasDbXref rdf:resource="http://genome.ucsc.edu/FAQ/FAQformat#format12"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3615 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3615">
-        <rdfs:label>bgzip</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <rdfs:comment>BAM files are compressed using a variant of GZIP (GNU ZIP), into a format called BGZF (Blocked GNU Zip Format).</rdfs:comment>
-        <oboInOwl:hasDefinition>Blocked GNU Zip format.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.htslib.org/doc/tabix.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3616">
-        <rdfs:label>tabix</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3547"/>
-        <oboInOwl:hasDefinition>TAB-delimited genome position file index format.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-        <documentation rdf:resource="http://www.htslib.org/doc/tabix.html"/>
-        <oboInOwl:hasDbXref rdf:resource="http://www.htslib.org/doc/tabix.html"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3617">
-        <rdfs:label>Graph format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <oboInOwl:hasDefinition>Data format for graph data.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3618">
-        <rdfs:label>xgmml</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3617"/>
-        <oboInOwl:hasDefinition>XML-based format used to store graph descriptions within Galaxy.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <documentation rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?highlight=datatypes%20graph#module-galaxy.datatypes.graph"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3619 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3619">
-        <rdfs:label>sif</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2013"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape.</oboInOwl:hasDefinition>
-        <documentation rdf:resource="http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?highlight=datatypes%20graph#module-galaxy.datatypes.graph"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3620">
-        <rdfs:label>xlsx</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3507"/>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3621">
-        <rdfs:label>SQLite</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <documentation>https://www.sqlite.org/fileformat2.html</documentation>
-        <oboInOwl:hasDefinition>Data format used by the SQLite database.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3622">
-        <rdfs:label>GeminiSQLite</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <documentation>https://gemini.readthedocs.org/en/latest/content/quick_start.html</documentation>
-        <created_in>1.11</created_in>
-        <oboInOwl:hasDefinition>Data format used by the SQLite database conformant to the Gemini schema.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3623 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3623">
-        <rdfs:label>Index format</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2333"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_2350"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/is_format_of"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Format of a data index of some type.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/format_3624 -->
-
-    <owl:Class rdf:about="http://edamontology.org/format_3624">
-        <rdfs:label>snpeffdb</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/format_3623"/>
-        <oboInOwl:hasDefinition>An index of a genome database, indexed for use by the snpeff tool.</oboInOwl:hasDefinition>
-        <created_in>1.11</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#formats"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0004 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0004">
-        <rdfs:label>Operation</rdfs:label>
-        <owl:disjointWith rdf:resource="http://edamontology.org/topic_0003"/>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <oboInOwl:hasRelatedSynonym>Computational tool</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Function</oboInOwl:hasBroadSynonym>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#Function</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Function</rdfs:seeAlso>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Function_(mathematics)</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Computational method</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000017</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ebi.ac.uk/swo/SWO_0000003</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Mathematical operation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasRelatedSynonym>sumo:Function</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasRelatedSynonym>Process</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasNarrowSynonym>Computational operation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Computational subroutine</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://semanticscience.org/resource/SIO_000649</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/span#Process</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Computational procedure</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Mathematical function</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Lambda abstraction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Function (programming)</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Process</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://wsio.org/operation_001</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Function</rdfs:seeAlso>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Function_(computer_science)</rdfs:seeAlso>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Subroutine</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedTarget>Process</owl:annotatedTarget>
-        <rdfs:comment>Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <rdfs:comment>Computational tool provides one or more operations.</rdfs:comment>
-        <owl:annotatedTarget>Computational tool</owl:annotatedTarget>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasRelatedSynonym"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedTarget>Function</owl:annotatedTarget>
-        <rdfs:comment>Operation is a function that is computational. It typically has input(s) and output(s), which are always data.</rdfs:comment>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_0004"/>
-        <owl:annotatedProperty rdf:resource="&oboInOwl;hasBroadSynonym"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/operation_0224 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0224">
-        <rdfs:label>Query and retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0090"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Query</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Retrieval</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Search or query a data resource and retrieve entries and / or annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0225 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0225">
-        <rdfs:label>Data retrieval (database cross-reference)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search database to retrieve all relevant references to a particular entity or entry.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0226 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0226">
-        <rdfs:label>Annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0089"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0582"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0227 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0227">
-        <rdfs:label>Indexing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Data indexing</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate an index of (typically a file of) biological data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database indexing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0228 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0228">
-        <rdfs:label>Data index analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Database index analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse an index of biological data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0227"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0229 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0229">
-        <rdfs:label>Annotation retrieval (sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Retrieve basic information about a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_1813"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0230 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0230">
-        <rdfs:label>Sequence generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a molecular sequence by some means.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0231 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0231">
-        <rdfs:label>Sequence editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <oboInOwl:hasDefinition>Edit or change a molecular sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0232 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0232">
-        <rdfs:label>Sequence merging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Merge two or more (typically overlapping) molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence splicing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0233">
-        <rdfs:label>Sequence conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3434"/>
-        <oboInOwl:hasDefinition>Convert a molecular sequence from one type to another.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0234 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0234">
-        <rdfs:label>Sequence complexity calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1259"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate sequence complexity, for example to find low-complexity regions in sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0235 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0235">
-        <rdfs:label>Sequence ambiguity calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1260"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0236 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0236">
-        <rdfs:label>Sequence composition calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1261"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate character or word composition or frequency of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0237">
-        <rdfs:label>Repeat sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Find and/or analyse repeat sequences in (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0238">
-        <rdfs:label>Sequence motif discovery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Motifs and patterns might be conserved or over-represented (occur with improbable frequency).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Motif discovery</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0239">
-        <rdfs:label>Sequence signature recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Motif search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence motif search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Motif detection</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence motif recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequence signature detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence profile search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Sequence motif detection</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Motif recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0240 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0240">
-        <rdfs:label>Sequence motif comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0858"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find motifs shared by molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0241">
-        <rdfs:label>Transcription regulatory sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0438"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0242 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0242">
-        <rdfs:label>Conserved transcription regulatory sequence identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:comment>For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0243 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0243">
-        <rdfs:label>Protein property calculation (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0250"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein structural property calculation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0244 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0244">
-        <rdfs:label>Protein flexibility and motion analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2476"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse flexibility and motion in protein structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0245 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0245">
-        <rdfs:label>Protein structural motif recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0166"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or screen for 3D structural motifs in protein structure(s).</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein structural feature identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0246">
-        <rdfs:label>Protein domain recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0736"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify structural domains in a protein structure from first principles (for example calculations on structural compactness).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0247 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0247">
-        <rdfs:label>Protein architecture analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0248 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0248">
-        <rdfs:label>Residue interaction calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1540"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDbXref>WHATIF: SymShellTenXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ListContactsRelaxed</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: SymShellTwoXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ListSideChainContactsRelaxed</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ListSideChainContactsNormal</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ListContactsNormal</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: SymShellFiveXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF: SymShellOneXML</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0249 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0249">
-        <rdfs:label>Torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2991"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate, visualise or analyse phi/psi angles of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0250 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0250">
-        <rdfs:label>Protein property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods to render and visualise the properties of a protein sequence.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein property rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0252 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0252">
-        <rdfs:label>Peptide immunogenicity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1534"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0253 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0253">
-        <rdfs:label>Sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1255"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence feature prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence feature recognition</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Motif database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasRelatedSynonym>SO:0000110</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0254 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0254">
-        <rdfs:label>Data retrieval (feature table)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Extract a sequence feature table from a sequence database entry.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0255 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0255">
-        <rdfs:label>Feature table query</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query the features (in a feature table) of molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0256 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0256">
-        <rdfs:label>Sequence feature comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1270"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare the feature tables of two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Feature comparison</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Feature table comparison</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0257">
-        <rdfs:label>Data retrieval (sequence alignment)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Display basic information about a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0258">
-        <rdfs:label>Sequence alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0259">
-        <rdfs:label>Sequence alignment comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <oboInOwl:hasDefinition>Compare (typically by aligning) two molecular sequence alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>See also &apos;Sequence profile alignment&apos;.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0260 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0260">
-        <rdfs:label>Sequence alignment conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3081"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3434"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0261 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0261">
-        <rdfs:label>Nucleic acid property processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) physicochemical property data of nucleic acids.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0262"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0262 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0262">
-        <rdfs:label>Nucleic acid property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0912"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0264">
-        <rdfs:label>Splice transcript prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2499"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict splicing alternatives or transcript isoforms from analysis of sequence data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0265">
-        <rdfs:label>Frameshift detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3195"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3202"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Frameshift error detection</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods include sequence alignment (if related sequences are available) and word-based sequence comparison.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0266 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0266">
-        <rdfs:label>Vector sequence detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0267 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0267">
-        <rdfs:label>Protein secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0172"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict secondary structure of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Secondary structure prediction (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0268 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0268">
-        <rdfs:label>Protein super-secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1277"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict super-secondary structure of protein sequence(s).</oboInOwl:hasDefinition>
-        <rdfs:comment>Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0269">
-        <rdfs:label>Transmembrane protein prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0270"/>
-        <oboInOwl:hasDefinition>Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0270 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0270">
-        <rdfs:label>Transmembrane protein analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0820"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions.</oboInOwl:hasDefinition>
-        <rdfs:comment>Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0271 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0271">
-        <rdfs:label>Structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict tertiary structure of a molecular (biopolymer) sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0272 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0272">
-        <rdfs:label>Residue interaction prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2506"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Methods usually involve multiple sequence alignment analysis.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0273 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0273">
-        <rdfs:label>Protein interaction raw data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2949"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0905"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0274 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0274">
-        <rdfs:label>Protein-protein interaction prediction (from protein sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1777"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2464"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0275 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0275">
-        <rdfs:label>Protein-protein interaction prediction (from protein structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2464"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0276 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0276">
-        <rdfs:label>Protein interaction network analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2497"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2949"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse a network of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0277">
-        <rdfs:label>Protein interaction network comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0276"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1778"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more networks of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0278">
-        <rdfs:label>RNA secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0279"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0279 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0279">
-        <rdfs:label>Nucleic acid folding prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2481"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1596"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid folding modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid folding</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0280">
-        <rdfs:label>Data retrieval (restriction enzyme annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Restriction enzyme information retrieval</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Retrieve information on restriction enzymes or restriction enzyme sites.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0281 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0281">
-        <rdfs:label>Genetic marker identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Identify genetic markers in DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0415"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0282 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0282">
-        <rdfs:label>Genetic mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2520"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1278"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>QTL mapping</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Linkage mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genetic map generation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genetic map construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Functional mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0283 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0283">
-        <rdfs:label>Linkage analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0927"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse genetic linkage.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0284">
-        <rdfs:label>Codon usage table generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2433"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate codon usage statistics and create a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Codon usage table construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0285 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0285">
-        <rdfs:label>Codon usage table comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2433"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more codon usage tables.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0286 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0286">
-        <rdfs:label>Codon usage analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0914"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>synon: Codon usage data analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>synon: Codon usage table analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0287 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0287">
-        <rdfs:label>Base position variability plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1263"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify and plot third base position variability in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0288 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0288">
-        <rdfs:label>Sequence word comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <oboInOwl:hasDefinition>Find exact character or word matches between molecular sequences without full sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0289">
-        <rdfs:label>Sequence distance matrix generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0870"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence distance matrix construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phylogenetic distance matrix generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0290 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0290">
-        <rdfs:label>Sequence redundancy removal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0291 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0291">
-        <rdfs:label>Sequence clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3432"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>The clusters may be output or used internally for some other purpose.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence cluster construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence cluster generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0292">
-        <rdfs:label>Sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align (identify equivalent sites within) molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment computation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0293">
-        <rdfs:label>Hybrid sequence alignment construction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Hybrid sequence alignment</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Hybrid sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0294 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0294">
-        <rdfs:label>Structure-based sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Structure-based sequence alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (structure-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure-based sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment (structure-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure-based sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align molecular sequences using sequence and structural information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0295">
-        <rdfs:label>Structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0886"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Align (superimpose) molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0296 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0296">
-        <rdfs:label>Sequence profile generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence profile construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0297">
-        <rdfs:label>3D profile generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0886"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structural profile generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate some type of structural (3D) profile or template from a structure or structure alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structural profile construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0298">
-        <rdfs:label>Profile-to-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0868"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>See also &apos;Sequence alignment comparison&apos;.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align sequence profiles (representing sequence alignments).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0299">
-        <rdfs:label>3D profile-to-3D profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0890"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>3D profile alignment (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>3D profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple 3D profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align structural (3D) profiles or templates (representing structures or structure alignments).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0300">
-        <rdfs:label>Sequence-to-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0869"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1354"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence-profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence-profile alignment generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align molecular sequence(s) to sequence profile(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence-profile alignment</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0301">
-        <rdfs:label>Sequence-to-3D-profile alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0303"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0893"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0889"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence-3D profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence-3D profile alignment generation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence-3D profile alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0302">
-        <rdfs:label>Protein threading</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0303"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2928"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0893"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align molecular sequence to structure in 3D space (threading).</oboInOwl:hasDefinition>
-        <rdfs:comment>Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence-structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0303">
-        <rdfs:label>Protein fold recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0180"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein domain prediction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.</rdfs:comment>
-        <oboInOwl:hasDefinition>Recognize (predict and identify) known protein structural domains or folds in protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein fold prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0304">
-        <rdfs:label>Metadata retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2422"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2337"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Data retrieval (documentation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Data retrieval (metadata)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes documentation, general information and other metadata on entities such as databases, database entries and tools.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0305">
-        <rdfs:label>Literature search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0970"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3068"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Query the biomedical and informatics literature.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0306">
-        <rdfs:label>Text mining</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2048"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0972"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0218"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Text data mining</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process and analyse text (typically the biomedical and informatics literature) to extract information from it.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0307">
-        <rdfs:label>Virtual PCR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform in-silico (virtual) PCR.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0308">
-        <rdfs:label>PCR primer design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2419"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1240"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>PCR primer prediction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set.</rdfs:comment>
-        <oboInOwl:hasDefinition>Design or predict oligonucleotide primers for PCR and DNA amplification etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0309 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0309">
-        <rdfs:label>Microarray probe design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2419"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2717"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray probe prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0310 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0310">
-        <rdfs:label>Sequence assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3433"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0925"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.</rdfs:comment>
-        <oboInOwl:hasDefinition>Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0311">
-        <rdfs:label>Microarray data standardization and normalization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3435"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3117"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3117"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Standardize or normalize microarray data.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0312">
-        <rdfs:label>Sequencing-based expression profile data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) SAGE, MPSS or SBS experimental data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0313 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0313">
-        <rdfs:label>Gene expression profile clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0315"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3432"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0314">
-        <rdfs:label>Gene expression profiling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0928"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Expression profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene expression profile construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Functional profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a gene expression profile or pattern, for example from microarray data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression profile generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0315">
-        <rdfs:label>Gene expression profile comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3111"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare gene expression profiles or patterns.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0316">
-        <rdfs:label>Functional profiling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Interpret (in functional terms) and annotate gene expression data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0532"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0317 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0317">
-        <rdfs:label>EST and cDNA sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse EST or cDNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2403"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0318">
-        <rdfs:label>Structural genomics target selection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identify and select targets for protein structural determination.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods will typically navigate a graph of protein families of known structure.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2406"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0319 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0319">
-        <rdfs:label>Protein secondary structure assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign secondary structure from protein coordinate or experimental data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0320">
-        <rdfs:label>Protein structure assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign a protein tertiary structure (3D coordinates) from raw experimental data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0321">
-        <rdfs:label>Protein model validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1539"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0172"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2275"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Evaluate the quality or correctness a protein three-dimensional model.</oboInOwl:hasDefinition>
-        <rdfs:comment>Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF: CorrectedPDBasXML</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Protein structure validation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>WHATIF: UseFileDB</oboInOwl:hasDbXref>
-        <rdfs:comment>The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0322">
-        <rdfs:label>Molecular model refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2425"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <oboInOwl:hasNarrowSynonym>Protein model refinement</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>WHATIF: CorrectedPDBasXML</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0323">
-        <rdfs:label>Phylogenetic tree generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0324 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0324">
-        <rdfs:label>Phylogenetic tree analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2523"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0325">
-        <rdfs:label>Phylogenetic tree comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0326 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0326">
-        <rdfs:label>Phylogenetic tree editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Edit a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0327 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0327">
-        <rdfs:label>Phylogenetic footprinting / shadowing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0540"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0194"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>A phylogenetic &apos;shadow&apos; represents the additive differences between individual sequences. By masking or &apos;shadowing&apos; variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0328 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0328">
-        <rdfs:label>Protein folding simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2415"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simulate the folding of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0329 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0329">
-        <rdfs:label>Protein folding pathway prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <oboInOwl:hasDefinition>Predict the folding pathway(s) or non-native structural intermediates of a protein.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0330 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0330">
-        <rdfs:label>Protein SNP mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0331"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2277"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0331 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0331">
-        <rdfs:label>Protein modelling (mutation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Methods might predict silent or pathological mutations.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Protein mutation modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0332">
-        <rdfs:label>Immunogen design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Design molecules that elicit an immune response (immunogens).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0559"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0333 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0333">
-        <rdfs:label>Zinc finger prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0334">
-        <rdfs:label>Enzyme kinetics calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2024"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0821"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate Km, Vmax and derived data for an enzyme reaction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0335">
-        <rdfs:label>Formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Reformat a file of data (or equivalent entity in memory).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Format conversion</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File formatting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Reformatting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File reformatting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File format conversion</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0336">
-        <rdfs:label>Format validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <oboInOwl:hasDefinition>Test and validate the format and content of a data file.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>File format validation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0337">
-        <rdfs:label>Visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2968"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2968"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0092"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0338">
-        <rdfs:label>Sequence database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0857"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Search a sequence database by sequence comparison and retrieve similar sequences.
-
-sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This excludes direct retrieval methods (e.g. the dbfetch program).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0339">
-        <rdfs:label>Structure database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0081"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0340">
-        <rdfs:label>Protein secondary database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_3087"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0341">
-        <rdfs:label>Motif database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Screen a sequence against a motif or pattern database.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0253"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0342">
-        <rdfs:label>Sequence profile database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a database of sequence profiles with a query sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0239"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0343">
-        <rdfs:label>Transmembrane protein database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Search a database of transmembrane proteins, for example for sequence or structural similarities.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2421"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0344">
-        <rdfs:label>Sequence retrieval (by code)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query a database and retrieve sequences with a given entry code or accession number.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0345">
-        <rdfs:label>Sequence retrieval (by keyword)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query a database and retrieve sequences containing a given keyword.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0346">
-        <rdfs:label>Sequence similarity search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2421"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <oboInOwl:hasNarrowSynonym>Structure database search (by sequence)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence database search (by sequence)</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences that are similar to a query sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0347 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0347">
-        <rdfs:label>Sequence database search (by motif or pattern)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0239"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0348">
-        <rdfs:label>Sequence database search (by amino acid composition)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences of a given amino acid composition.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0349">
-        <rdfs:label>Sequence database search (by property)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0350">
-        <rdfs:label>Sequence database search (by sequence using word-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (word-based methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0351 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0351">
-        <rdfs:label>Sequence database search (by sequence using profile-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (profile-based methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes tools based on PSI-BLAST.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0352">
-        <rdfs:label>Sequence database search (by sequence using local alignment-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (local alignment-based methods) </oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes tools based on the Smith-Waterman algorithm or FASTA.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0353">
-        <rdfs:label>Sequence database search (by sequence using global alignment-based methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes tools based on the Needleman and Wunsch algorithm.</rdfs:comment>
-        <oboInOwl:hasDefinition>Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (global alignment-based methods)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0354 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0354">
-        <rdfs:label>Sequence database search (by sequence for primer sequences)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <rdfs:comment>STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence similarity search (primer sequences)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0355 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0355">
-        <rdfs:label>Sequence database search (by molecular weight)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Protein fingerprinting</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide mass fingerprinting</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0356 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0356">
-        <rdfs:label>Sequence database search (by isoelectric point)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search sequence(s) or a sequence database for sequences of a given isoelectric point.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0338"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0357">
-        <rdfs:label>Structure retrieval (by code)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query a tertiary structure database and retrieve entries with a given entry code or accession number.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0358 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0358">
-        <rdfs:label>Structure retrieval (by keyword)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Query a tertiary structure database and retrieve entries containing a given keyword.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0359">
-        <rdfs:label>Structure database search (by sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0346"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0360">
-        <rdfs:label>Structural similarity search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0339"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Search a database of molecular structure and retrieve structures that are similar to a query structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Structure database search (by structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure retrieval by structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0361 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0361">
-        <rdfs:label>Sequence annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0849"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotate a molecular sequence record with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0362 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0362">
-        <rdfs:label>Genome annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0361"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Annotate a genome sequence with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0363 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0363">
-        <rdfs:label>Nucleic acid sequence reverse and complement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2513"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate the reverse and / or complement of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0364 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0364">
-        <rdfs:label>Random sequence generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <oboInOwl:hasDefinition>Generate a random sequence, for example, with a specific character composition.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0365">
-        <rdfs:label>Nucleic acid restriction digest</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2513"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1239"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate digest fragments for a nucleotide sequence containing restriction sites.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0366">
-        <rdfs:label>Protein sequence cleavage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2514"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1238"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0367 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0367">
-        <rdfs:label>Sequence mutation and randomization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0368">
-        <rdfs:label>Sequence masking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:hasDefinition>Mask characters in a molecular sequence (replacing those characters with a mask character).</oboInOwl:hasDefinition>
-        <rdfs:comment>For example, SNPs or repeats in a DNA sequence might be masked.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0369">
-        <rdfs:label>Sequence cutting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:hasDefinition>Cut (remove) characters or a region from a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0370">
-        <rdfs:label>Restriction site creation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:hasDefinition>Create (or remove) restriction sites in sequences, for example using silent mutations.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0371">
-        <rdfs:label>DNA translation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0108"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Translate a DNA sequence into protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0372">
-        <rdfs:label>DNA transcription</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Transcribe a nucleotide sequence into mRNA sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0377 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0377">
-        <rdfs:label>Sequence composition calculation (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Calculate base frequency or word composition of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0236"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0378">
-        <rdfs:label>Sequence composition calculation (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Calculate amino acid frequency or word composition of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0236"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0379">
-        <rdfs:label>Repeat sequence detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0237"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0380 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0380">
-        <rdfs:label>Repeat sequence organisation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0237"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse repeat sequence organization such as periodicity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0383">
-        <rdfs:label>Protein hydropathy calculation (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2574"/>
-        <oboInOwl:hasDefinition>Analyse the hydrophobic, hydrophilic or charge properties of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0384">
-        <rdfs:label>Protein solvent accessibility calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1542"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate solvent accessible or buried surface areas in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0385">
-        <rdfs:label>Protein hydropathy cluster calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0383"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0393"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify clusters of hydrophobic or charged residues in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0386">
-        <rdfs:label>Protein dipole moment calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1545"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate whether a protein structure has an unusually large net charge (dipole moment).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0387">
-        <rdfs:label>Protein surface and interior calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0384"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0166"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0388">
-        <rdfs:label>Protein binding site prediction (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0245"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2575"/>
-        <oboInOwl:hasDefinition>Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ligand-binding and active site prediction (from structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Binding site prediction (from structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0389 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0389">
-        <rdfs:label>Protein-nucleic acid binding site analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2949"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse RNA or DNA-binding sites in protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0390">
-        <rdfs:label>Protein peeling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0246"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Decompose a structure into compact or globular fragments (protein peeling).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0391">
-        <rdfs:label>Protein distance matrix calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1546"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0392 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0392">
-        <rdfs:label>Protein contact map calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1547"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0393">
-        <rdfs:label>Protein residue cluster calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1548"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Cluster of contacting residues might be key structural residues.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate clusters of contacting residues in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0394 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0394">
-        <rdfs:label>Hydrogen bond calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1549"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDbXref>WHATIF:ShowHydrogenBonds</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:HasHydrogenBonds</oboInOwl:hasDbXref>
-        <rdfs:comment>The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ShowHydrogenBondsM</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identify potential hydrogen bonds between amino acids and other groups.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0395">
-        <rdfs:label>Residue non-canonical interaction detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate non-canonical atomic interactions in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0396">
-        <rdfs:label>Ramachandran plot calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1544"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate a Ramachandran plot of a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0397">
-        <rdfs:label>Ramachandran plot validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1844"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1544"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1539"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Validate a Ramachandran plot of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0398">
-        <rdfs:label>Protein molecular weight calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1519"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate the molecular weight of a protein sequence or fragments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0399">
-        <rdfs:label>Protein extinction coefficient calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1531"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict extinction coefficients or optical density of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0400">
-        <rdfs:label>Protein pH-dependent property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate pH-dependent properties from pKa calculations of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0401">
-        <rdfs:label>Protein hydropathy calculation (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2574"/>
-        <oboInOwl:hasDefinition>Hydropathy calculation on a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0402">
-        <rdfs:label>Protein titration curve plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0400"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1527"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Plot a protein titration curve.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0403">
-        <rdfs:label>Protein isoelectric point calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0400"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1528"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate isoelectric point of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0404">
-        <rdfs:label>Protein hydrogen exchange rate calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0400"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1530"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Estimate hydrogen exchange rate of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0405">
-        <rdfs:label>Protein hydrophobic region calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <oboInOwl:hasDefinition>Calculate hydrophobic or hydrophilic / charged regions of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0406">
-        <rdfs:label>Protein aliphatic index calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1521"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0407">
-        <rdfs:label>Protein hydrophobic moment plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1520"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0408">
-        <rdfs:label>Protein globularity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1526"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0409">
-        <rdfs:label>Protein solubility prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1524"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict the solubility or atomic solvation energy of a protein sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0410">
-        <rdfs:label>Protein crystallizability prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0401"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1525"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict crystallizability of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0411">
-        <rdfs:label>Protein signal peptide detection (eukaryotes)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0418"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0412">
-        <rdfs:label>Protein signal peptide detection (bacteria)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0418"/>
-        <oboInOwl:hasDefinition>Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0413">
-        <rdfs:label>MHC peptide immunogenicity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0252"/>
-        <oboInOwl:hasDefinition>Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0414">
-        <rdfs:label>Protein feature prediction (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>Methods typically involve scanning for known motifs, patterns and regular expressions.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence feature detection (protein)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_3092"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0415">
-        <rdfs:label>Nucleic acid feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1276"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence feature detection (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods typically involve scanning for known motifs, patterns and regular expressions.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid feature recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid feature prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0416">
-        <rdfs:label>Epitope mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict antigenic determinant sites (epitopes) in protein sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Epitope mapping is commonly done during vaccine design.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0417">
-        <rdfs:label>Protein post-translation modification site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0601"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict post-translation modification sites in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0418 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0418">
-        <rdfs:label>Protein signal peptide detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2489"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0140"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Detect or predict signal peptides and signal peptide cleavage sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0419">
-        <rdfs:label>Protein binding site prediction (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2575"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <oboInOwl:hasExactSynonym>Binding site prediction (from sequence)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict catalytic residues, active sites or other ligand-binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ligand-binding and active site prediction (from sequence)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein binding site detection</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0420">
-        <rdfs:label>Protein-nucleic acid binding prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0419"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict RNA and DNA-binding binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0421">
-        <rdfs:label>Protein folding site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2415"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <oboInOwl:hasDefinition>Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0422">
-        <rdfs:label>Protein cleavage site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3087"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect or predict cleavage sites (enzymatic or chemical) in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0423">
-        <rdfs:label>Epitope mapping (MHC Class I)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict epitopes that bind to MHC class I molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0416"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0424">
-        <rdfs:label>Epitope mapping (MHC Class II)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Predict epitopes that bind to MHC class II molecules.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0416"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0425">
-        <rdfs:label>Whole gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2454"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0426">
-        <rdfs:label>Gene component prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2454"/>
-        <rdfs:comment>Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0427">
-        <rdfs:label>Transposon prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect or predict transposons, retrotransposons / retrotransposition signatures etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0428">
-        <rdfs:label>PolyA signal detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <oboInOwl:hasDefinition>Detect polyA signals in nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0429">
-        <rdfs:label>Quadruplex formation site detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Quadruplex structure prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Detect quadruplex-forming motifs in nucleotide sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0430">
-        <rdfs:label>CpG island and isochore detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0157"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>An isochore is long region (&gt; 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find CpG rich regions in a nucleotide sequence or isochores in genome sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>CpG island and isochores rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>CpG island and isochores detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0431 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0431">
-        <rdfs:label>Restriction site recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0432">
-        <rdfs:label>Nucleosome formation or exclusion sequence prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0433">
-        <rdfs:label>Splice site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify, predict or analyse splice sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods might require a pre-mRNA or genomic DNA sequence.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0434">
-        <rdfs:label>Integrated gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0425"/>
-        <oboInOwl:hasDefinition>Predict whole gene structure using a combination of multiple methods to achieve better predictions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0435">
-        <rdfs:label>Operon prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0425"/>
-        <oboInOwl:hasDefinition>Find operons (operators, promoters and genes) in bacteria genes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0436">
-        <rdfs:label>Coding region prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0426"/>
-        <oboInOwl:hasDefinition>Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ORF prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>ORF finding</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0437">
-        <rdfs:label>Selenocysteine insertion sequence (SECIS) prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict selenocysteine insertion sequence (SECIS) in a DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0438">
-        <rdfs:label>Regulatory element prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0749"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Translational regulatory element prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Transcription regulatory element prediction</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0439">
-        <rdfs:label>Translation initiation site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0436"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0108"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict translation initiation sites, possibly by searching a database of sites.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0440">
-        <rdfs:label>Promoter prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <oboInOwl:hasDefinition>Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods might recognize CG content, CpG islands, splice sites, polyA signals etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0441">
-        <rdfs:label>Transcription regulatory element prediction (DNA-cis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5&apos; promoter region of the gene, in an intron, or in the 3&apos; untranslated region. Cis-elements are often binding sites of one or more trans-acting factors.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0442">
-        <rdfs:label>Transcription regulatory element prediction (RNA-cis)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:comment>Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene&apos;s activity.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0443">
-        <rdfs:label>Transcription regulatory element prediction (trans)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Trans-regulatory elements regulate genes distant from the gene from which they were transcribed.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Functional RNA identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0444">
-        <rdfs:label>Matrix/scaffold attachment site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0438"/>
-        <rdfs:comment>MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0445">
-        <rdfs:label>Transcription factor binding site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0440"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict transcription factor binding sites in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0446">
-        <rdfs:label>Exonic splicing enhancer prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0440"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify or predict exonic splicing enhancers (ESE) in exons.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0447">
-        <rdfs:label>Sequence alignment validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:comment>Evaluation might be purely sequence-based or use structural information.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequence alignment quality evaluation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Evaluate molecular sequence alignment accuracy.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0448">
-        <rdfs:label>Sequence alignment analysis (conservation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Residue conservation analysis</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0449 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0449">
-        <rdfs:label>Sequence alignment analysis (site correlation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3465"/>
-        <oboInOwl:hasDefinition>Analyse correlations between sites in a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <rdfs:comment>This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0450 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0450">
-        <rdfs:label>Chimeric sequence detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles.</rdfs:comment>
-        <oboInOwl:hasDefinition>Detects chimeric sequences (chimeras) from a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (chimeric sequence detection)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0451">
-        <rdfs:label>Recombination detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (recombination detection)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment.</oboInOwl:hasDefinition>
-        <rdfs:comment>Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0452">
-        <rdfs:label>Indel detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (indel detection)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify insertion, deletion and duplication events from a sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0453">
-        <rdfs:label>Nucleosome formation potential prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Predict nucleosome formation potential of DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0432"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0455 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0455">
-        <rdfs:label>Nucleic acid thermodynamic property calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2985"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0456">
-        <rdfs:label>Nucleic acid melting profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1583"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA melting profile.</oboInOwl:hasDefinition>
-        <rdfs:comment>A melting profile is used to visualise and analyse partly melted DNA conformations.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0457">
-        <rdfs:label>Nucleic acid stitch profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1587"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA stitch profile.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0458 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0458">
-        <rdfs:label>Nucleic acid melting curve plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2958"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA melting curve.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0459">
-        <rdfs:label>Nucleic acid probability profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2959"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA probability profile.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0460">
-        <rdfs:label>Nucleic acid temperature profile plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0456"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2960"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate and plot a DNA or DNA/RNA temperature profile.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0461">
-        <rdfs:label>Nucleic acid curvature calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0262"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0912"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate curvature and flexibility / stiffness of a nucleotide sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes properties such as.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0463">
-        <rdfs:label>microRNA detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0443"/>
-        <oboInOwl:hasDefinition>Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0464">
-        <rdfs:label>tRNA gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0425"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or predict tRNA genes in genomic sequences (tRNA).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0465">
-        <rdfs:label>siRNA binding specificity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0467">
-        <rdfs:label>Protein secondary structure prediction (integrated)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <oboInOwl:hasDefinition>Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0468">
-        <rdfs:label>Protein secondary structure prediction (helices)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict helical secondary structure of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0469">
-        <rdfs:label>Protein secondary structure prediction (turns)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <oboInOwl:hasDefinition>Predict turn structure (for example beta hairpin turns) of protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0470">
-        <rdfs:label>Protein secondary structure prediction (coils)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0471">
-        <rdfs:label>Protein secondary structure prediction (disulfide bonds)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0267"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict cysteine bonding state and disulfide bond partners in protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0472">
-        <rdfs:label>GPCR prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0269"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0473"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>G protein-coupled receptor (GPCR) prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict G protein-coupled receptors (GPCR).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0473">
-        <rdfs:label>GPCR analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0270"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0820"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse G-protein coupled receptor proteins (GPCRs).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>G protein-coupled receptor (GPCR) analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0474">
-        <rdfs:label>Protein structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0271"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0172"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict tertiary structure (backbone and side-chain conformation) of protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0475">
-        <rdfs:label>Nucleic acid structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0271"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1459"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might identify thermodynamically stable or evolutionarily conserved structures.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict tertiary structure of DNA or RNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0476">
-        <rdfs:label>Ab initio structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0474"/>
-        <oboInOwl:hasDefinition>Predict tertiary structure of protein sequence(s) without homologs of known structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>de novo structure prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0477 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0477">
-        <rdfs:label>Protein modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0474"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2275"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Comparative modelling</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Build a three-dimensional protein model based on known (for example homologs) structures.</oboInOwl:hasDefinition>
-        <rdfs:comment>The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Homology modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Homology structure modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein structure comparative modelling</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0478">
-        <rdfs:label>Molecular docking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0177"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1461"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2877"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Model the structure of a protein in complex with a small molecule or another macromolecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Docking simulation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein docking</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0479">
-        <rdfs:label>Protein modelling (backbone)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <oboInOwl:hasDefinition>Model protein backbone conformation.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods might require a preliminary C(alpha) trace.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0480">
-        <rdfs:label>Protein modelling (side chains)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods might use a residue rotamer library.</rdfs:comment>
-        <oboInOwl:hasDefinition>Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0481">
-        <rdfs:label>Protein modelling (loops)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0477"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Model loop conformation in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0482">
-        <rdfs:label>Protein-ligand docking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1461"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Ligand-binding simulation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Virtual ligand screening</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0483">
-        <rdfs:label>Structured RNA prediction and optimisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3095"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1234"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Nucleic acid folding family identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA inverse folding</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0484 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0484">
-        <rdfs:label>SNP detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3202"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <oboInOwl:hasDefinition>Find single nucleotide polymorphisms (SNPs) between sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Single nucleotide polymorphism detection</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0485">
-        <rdfs:label>Radiation Hybrid Mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2870"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0486">
-        <rdfs:label>Functional mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).</rdfs:comment>
-        <oboInOwl:hasDefinition>Map the genetic architecture of dynamic complex traits.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0282"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0487">
-        <rdfs:label>Haplotype mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0282"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0283"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Haplotype map generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Haplotype inference</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual&apos;s haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Haplotype reconstruction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0488">
-        <rdfs:label>Linkage disequilibrium calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0283"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0927"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0489">
-        <rdfs:label>Genetic code prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1598"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict genetic code from analysis of codon usage data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0490">
-        <rdfs:label>Dotplot plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0288"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0565"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0862"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Draw a dotplot of sequence similarities identified from word-matching or character comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0491">
-        <rdfs:label>Pairwise sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1381"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasDefinition>Align exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0492">
-        <rdfs:label>Multiple sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0493 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0493">
-        <rdfs:label>Pairwise sequence alignment generation (local)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Local pairwise sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Locally align exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment (local)</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Local alignment methods identify regions of local similarity.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment construction (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0491"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0494 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0494">
-        <rdfs:label>Pairwise sequence alignment generation (global)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Global pairwise sequence alignment construction</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Globally align exactly two molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Global alignment methods identify similarity across the entire length of the sequences.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise sequence alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0491"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0496"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0495">
-        <rdfs:label>Local sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Local multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Local alignment methods identify regions of local similarity.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Locally align two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0496">
-        <rdfs:label>Global sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Global multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (global)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Globally align two or more molecular sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (global)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Global alignment methods identify similarity across the entire length of the sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0497">
-        <rdfs:label>Constrained sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences with user-defined constraints.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment (constrained)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Constrained multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0498">
-        <rdfs:label>Consensus-based sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasExactSynonym>Consensus multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence alignment (consensus)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align two or more molecular sequences using multiple methods to achieve higher quality.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0499">
-        <rdfs:label>Tree-based sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is supposed to give a more biologically meaningful alignment than standard alignments.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree-based multiple sequence alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence alignment (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment construction (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence alignment (phylogenetic tree-based)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0500">
-        <rdfs:label>Secondary structure alignment generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Align molecular secondary structure (represented as a 1D string).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2928"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0501">
-        <rdfs:label>Protein secondary structure alignment generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2488"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0878"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Protein secondary structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align protein secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein secondary structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0502">
-        <rdfs:label>RNA secondary structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0881"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>RNA secondary structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA secondary structure alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align RNA secondary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA secondary structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Secondary structure alignment (RNA)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0503">
-        <rdfs:label>Pairwise structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align (superimpose) exactly two molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0504">
-        <rdfs:label>Multiple structure alignment construction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Align (superimpose) two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that use an existing alignment.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0505">
-        <rdfs:label>Structure alignment (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align protein tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0506">
-        <rdfs:label>Structure alignment (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Align RNA tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0507">
-        <rdfs:label>Pairwise structure alignment generation (local)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Locally align (superimpose) exactly two molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment (local)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Local alignment methods identify regions of local similarity, common substructures etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment construction (local)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Local pairwise structure alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0509"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0508">
-        <rdfs:label>Pairwise structure alignment generation (global)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Global pairwise structure alignment construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Global alignment methods identify similarity across the entire structures.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Globally align (superimpose) exactly two molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pairwise structure alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0510"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0509">
-        <rdfs:label>Local structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:hasExactSynonym>Local multiple structure alignment construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Local alignment methods identify regions of local similarity, common substructures etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Structure alignment construction (local)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Locally align (superimpose) two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment construction (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure alignment generation (local)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0510 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0510">
-        <rdfs:label>Global structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:hasExactSynonym>Structure alignment construction (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structure alignment generation (global)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple structure alignment construction (global)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Global alignment methods identify similarity across the entire structures.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Global multiple structure alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Globally align (superimpose) two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0511">
-        <rdfs:label>Profile-to-profile alignment (pairwise)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0298"/>
-        <oboInOwl:hasExactSynonym>Sequence alignment generation (pairwise profile)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise sequence profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment construction (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment (pairwise)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Align exactly two molecular profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment generation (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0512">
-        <rdfs:label>Sequence alignment generation (multiple profile)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Align two or more molecular profiles.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment generation (multiple)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence profile alignment construction (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Multiple sequence profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0298"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0513 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0513">
-        <rdfs:label>3D profile-to-3D profile alignment (pairwise)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0299"/>
-        <rdfs:comment>Methods might perform one-to-one, one-to-many or many-to-many comparisons.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Pairwise structural (3D) profile alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural (3D) profile alignment (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align exactly two molecular Structural (3D) profiles.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structural profile alignment generation (pairwise)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0514">
-        <rdfs:label>Structural profile alignment generation (multiple)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Structural profile alignment construction (multiple)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align two or more molecular 3D profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Multiple structural (3D) profile alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structural (3D) profile alignment (multiple)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0299"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0515">
-        <rdfs:label>Data retrieval (tool metadata)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Data retrieval (tool annotation)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Tool information retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0304"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0516">
-        <rdfs:label>Data retrieval (database metadata)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Data retrieval (database annotation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database information retrieval</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0304"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0517 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0517">
-        <rdfs:label>PCR primer design (for large scale sequencing)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict primers for large scale sequencing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0518 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0518">
-        <rdfs:label>PCR primer design (for genotyping polymorphisms)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0519">
-        <rdfs:label>PCR primer design (for gene transcription profiling)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict primers for gene transcription profiling.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0520">
-        <rdfs:label>PCR primer design (for conserved primers)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <oboInOwl:hasDefinition>Predict primers that are conserved across multiple genomes or species.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0521">
-        <rdfs:label>PCR primer design (based on gene structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict primers based on gene structure, promoters, exon-exon junctions etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0522">
-        <rdfs:label>PCR primer design (for methylation PCRs)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0308"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict primers for methylation PCRs.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0523">
-        <rdfs:label>Sequence assembly (mapping assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0524">
-        <rdfs:label>Sequence assembly (de-novo assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Sequence assembly by combining fragments without the aid of a reference sequence or genome.</oboInOwl:hasDefinition>
-        <rdfs:comment>De-novo assemblers are much slower and more memory intensive than mapping assemblers.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0525">
-        <rdfs:label>Sequence assembly (genome assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Sequence assembly capable on a very large scale such as assembly of whole genomes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0526">
-        <rdfs:label>Sequence assembly (EST assembly)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Sequence assembly for EST sequences (transcribed mRNA).</oboInOwl:hasDefinition>
-        <rdfs:comment>Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0527">
-        <rdfs:label>Tag mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2520"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0936"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Tag to gene assignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0528">
-        <rdfs:label>SAGE data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Serial analysis of gene expression data processing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) serial analysis of gene expression (SAGE) data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0529">
-        <rdfs:label>MPSS data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) massively parallel signature sequencing (MPSS) data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Massively parallel signature sequencing data processing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0530">
-        <rdfs:label>SBS data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequencing by synthesis data processing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) sequencing by synthesis (SBS) data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0531">
-        <rdfs:label>Heat map generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1636"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Heat map construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a heat map of gene expression from microarray data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0532 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0532">
-        <rdfs:label>Gene expression profile analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Functional profiling</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse one or more gene expression profiles, typically to interpret them in functional terms.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0533">
-        <rdfs:label>Gene expression profile pathway mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2497"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0534">
-        <rdfs:label>Protein secondary structure assignment (from coordinate data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0319"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2406"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign secondary structure from protein coordinate data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0535 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0535">
-        <rdfs:label>Protein secondary structure assignment (from CD data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0319"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0939"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Assign secondary structure from circular dichroism (CD) spectroscopic data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0536">
-        <rdfs:label>Protein structure assignment (from X-ray crystallographic data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0320"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0537">
-        <rdfs:label>Protein structure assignment (from NMR data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0320"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0538 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0538">
-        <rdfs:label>Phylogenetic tree generation (data centric)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (data centric)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree from a specific type of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0539">
-        <rdfs:label>Phylogenetic tree generation (method centric)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (method centric)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree using a specific method.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0540">
-        <rdfs:label>Phylogenetic tree generation (from molecular sequences)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (from molecular sequences)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0541 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0541">
-        <rdfs:label>Phylogenetic tree generation (from continuous quantitative characters)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1426"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (from continuous quantitative characters)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from continuous quantitative character data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0542">
-        <rdfs:label>Phylogenetic tree generation (from gene frequencies)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2873"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (from gene frequencies)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from gene frequency data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0543">
-        <rdfs:label>Phylogenetic tree construction (from polymorphism data)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0538"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0199"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree generation (from polymorphism data)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0544 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0544">
-        <rdfs:label>Phylogenetic species tree construction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0540"/>
-        <oboInOwl:hasDefinition>Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic species tree generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0545">
-        <rdfs:label>Phylogenetic tree generation (parsimony methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (parsimony methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes evolutionary parsimony (invariants) methods.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0546 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0546">
-        <rdfs:label>Phylogenetic tree generation (minimum distance methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <rdfs:comment>This includes neighbor joining (NJ) clustering method.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (minimum distance methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0547 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0547">
-        <rdfs:label>Phylogenetic tree generation (maximum likelihood and Bayesian methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (maximum likelihood and Bayesian methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution.</oboInOwl:hasDefinition>
-        <rdfs:comment>Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0548 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0548">
-        <rdfs:label>Phylogenetic tree generation (quartet methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (quartet methods)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0549 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0549">
-        <rdfs:label>Phylogenetic tree generation (AI methods)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
-        <oboInOwl:hasDefinition>Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (AI methods)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0550 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0550">
-        <rdfs:label>DNA substitution modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2507"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1439"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (phylogenetic modelling)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify a plausible model of DNA substitution that explains a DNA sequence alignment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0551 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0551">
-        <rdfs:label>Phylogenetic tree analysis (shape)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree topology analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse the shape (topology) of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0552">
-        <rdfs:label>Phylogenetic tree bootstrapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <oboInOwl:hasDefinition>Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0553">
-        <rdfs:label>Phylogenetic tree analysis (gene family prediction)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0194"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict families of genes and gene function based on their position in a phylogenetic tree.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0554 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0554">
-        <rdfs:label>Phylogenetic tree analysis (natural selection)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0324"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0555 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0555">
-        <rdfs:label>Phylogenetic tree generation (consensus)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0325"/>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees to produce a consensus tree.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods typically test for topological similarity between trees using for example a congruence index.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree construction (consensus)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0556 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0556">
-        <rdfs:label>Phylogenetic sub/super tree detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0325"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees to detect subtrees or supertrees.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0557">
-        <rdfs:label>Phylogenetic tree distances calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0325"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1442"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more phylogenetic trees to calculate distances between trees.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0558 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0558">
-        <rdfs:label>Phylogenetic tree annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Annotate a phylogenetic tree with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0559">
-        <rdfs:label>Immunogenicity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0252"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Peptide immunogen prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict and optimise peptide ligands that elicit an immunological response.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0560">
-        <rdfs:label>DNA vaccine design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2430"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3095"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0173"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0804"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict or optimise DNA to elicit (via DNA vaccination) an immunological response.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0561">
-        <rdfs:label>Sequence formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Reformat (a file or other report of) molecular sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence file format conversion</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0562 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0562">
-        <rdfs:label>Sequence alignment formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Reformat (a file or other report of) molecular sequence alignment(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0563">
-        <rdfs:label>Codon usage table formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2433"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1597"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Reformat a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0564">
-        <rdfs:label>Sequence visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2969"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render a molecular sequence, possibly with sequence features or properties shown.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0565">
-        <rdfs:label>Sequence alignment visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0863"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1711"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence alignment rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise, format or print a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0566">
-        <rdfs:label>Sequence cluster visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1235"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Sequence cluster rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render sequence clusters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0567 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0567">
-        <rdfs:label>Phylogenetic tree visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0872"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Render or visualise a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Phylogenetic tree rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0568 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0568">
-        <rdfs:label>RNA secondary structure visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0880"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>RNA secondary structure rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise RNA secondary structure, knots, pseudoknots etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0569">
-        <rdfs:label>Protein secondary structure rendering</rdfs:label>
-        <rdfs:label>Protein secondary structure visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Render and visualise protein secondary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0570">
-        <rdfs:label>Structure visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1710"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structure rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0571">
-        <rdfs:label>Microarray data rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3117"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise microarray data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0572">
-        <rdfs:label>Protein interaction network rendering</rdfs:label>
-        <rdfs:label>Protein interaction network visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3083"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym></oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify and analyse networks of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0573">
-        <rdfs:label>Map drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>DNA map drawing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Map rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Draw or visualise a DNA map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0574">
-        <rdfs:label>Sequence motif rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Render a sequence with motifs.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0575">
-        <rdfs:label>Restriction map drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0431"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0573"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1289"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Draw or visualise restriction maps in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0577 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0577">
-        <rdfs:label>DNA linear map rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Draw a linear maps of DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0573"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0578 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0578">
-        <rdfs:label>Plasmid map drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0573"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasBroadSynonym>DNA circular map rendering</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Draw a circular maps of DNA, for example a plasmid map.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_0579 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_0579">
-        <rdfs:label>Operon drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0573"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise operon structure etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Operon rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1768 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1768">
-        <rdfs:label>Nucleic acid folding family identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Identify folding families of related RNAs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0483"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1769 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1769">
-        <rdfs:label>Nucleic acid folding energy calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0279"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1774 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1774">
-        <rdfs:label>Annotation retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations.</rdfs:comment>
-        <oboInOwl:hasDefinition>Retrieve existing annotation (or documentation), typically annotation on a database entity.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1777 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1777">
-        <rdfs:label>Protein function prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2414"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict general functional properties of a protein.</oboInOwl:hasDefinition>
-        <rdfs:comment>For functional properties that can be mapped to a sequence, use &apos;Sequence feature detection (protein)&apos; instead.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1778 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1778">
-        <rdfs:label>Protein function comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2414"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare the functional properties of two or more proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1780 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1780">
-        <rdfs:label>Sequence submission</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Submit a molecular sequence to a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_3431"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1781 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1781">
-        <rdfs:label>Gene regulatory network analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2497"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2846"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse a known network of gene regulation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_1781"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1812 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1812">
-        <rdfs:label>Loading</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0842"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Data loading</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>WHATIF:UploadPDB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Prepare or load a user-specified data file so that it is available for use.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1813 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1813">
-        <rdfs:label>Sequence retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Data retrieval (sequences)</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1814 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1814">
-        <rdfs:label>Structure retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDbXref>WHATIF:EchoPDB</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:DownloadPDB</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes direct retrieval methods but not those that perform calculations on the sequence or structure.</rdfs:comment>
-        <oboInOwl:hasDefinition>Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1816 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1816">
-        <rdfs:label>Surface rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0570"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2462"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:GetSurfaceDots</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate the positions of dots that are homogeneously distributed over the surface of a molecule.</oboInOwl:hasDefinition>
-        <rdfs:comment>A dot has three coordinates (x,y,z) and (typically) a color.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1817 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1817">
-        <rdfs:label>Protein atom surface calculation (accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilitySolventPlus</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilitySolvent</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible surface&apos;) for each atom in a structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>Waters are not considered.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1818 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1818">
-        <rdfs:label>Protein atom surface calculation (accessible molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2460"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible molecular surface&apos;) for each atom in a structure.</oboInOwl:hasDefinition>
-        <rdfs:comment>Waters are not considered.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilityMolecular</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:AtomAccessibilityMolecularPlus</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1819 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1819">
-        <rdfs:label>Protein residue surface calculation (accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilitySolvent</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible surface&apos;) for each residue in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1820 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1820">
-        <rdfs:label>Protein residue surface calculation (vacuum accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;vacuum accessible surface&apos;) for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilityVacuum</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1821 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1821">
-        <rdfs:label>Protein residue surface calculation (accessible molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible molecular surface&apos;) for each residue in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilityMolecular</oboInOwl:hasDbXref>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1822 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1822">
-        <rdfs:label>Protein residue surface calculation (vacuum molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2461"/>
-        <rdfs:comment>Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;vacuum molecular surface&apos;) for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueAccessibilityVacuumMolecular</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1823 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1823">
-        <rdfs:label>Protein surface calculation (accessible molecular)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2462"/>
-        <oboInOwl:hasDbXref>WHATIF:TotAccessibilityMolecular</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible molecular surface&apos;) for a structure as a whole.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1824 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1824">
-        <rdfs:label>Protein surface calculation (accessible)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2462"/>
-        <oboInOwl:hasDbXref>WHATIF:TotAccessibilitySolvent</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility (&apos;accessible surface&apos;) for a structure as a whole.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1825 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1825">
-        <rdfs:label>Backbone torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ResidueTorsionsBB</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate for each residue in a protein structure all its backbone torsion angles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1826 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1826">
-        <rdfs:label>Full torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate for each residue in a protein structure all its torsion angles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ResidueTorsions</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1827 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1827">
-        <rdfs:label>Cysteine torsion angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate for each cysteine (bridge) all its torsion angles.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:CysteineTorsions</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1828 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1828">
-        <rdfs:label>Tau angle calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0249"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowTauAngle</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Tau is the backbone angle N-Calpha-C (angle over the C-alpha).</rdfs:comment>
-        <oboInOwl:hasDefinition>For each amino acid in a protein structure calculate the backbone angle tau.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1829 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1829">
-        <rdfs:label>Cysteine bridge detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1850"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowCysteineBridge</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Detect cysteine bridges (from coordinate data) in a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1830 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1830">
-        <rdfs:label>Free cysteine detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1850"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal.</rdfs:comment>
-        <oboInOwl:hasDefinition>Detect free cysteines in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ShowCysteineFree</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1831 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1831">
-        <rdfs:label>Metal-bound cysteine detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1850"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ShowCysteineMetal</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Detect cysteines that are bound to metal in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1832 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1832">
-        <rdfs:label>Residue contact calculation (residue-nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0245"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0389"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:ShowProteiNucleicContacts</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate protein residue contacts with nucleic acids in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:HasNucleicContacts</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1834 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1834">
-        <rdfs:label>Residue contact calculation (residue-metal)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0388"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <oboInOwl:hasDbXref>WHATIF:HasMetalContacts</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate protein residue contacts with metal in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:HasMetalContactsPlus</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1835 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1835">
-        <rdfs:label>Residue contact calculation (residue-negative ion)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <oboInOwl:hasDefinition>Calculate ion contacts in a structure (all ions for all side chain atoms).</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:HasNegativeIonContactsPlus</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:HasNegativeIonContacts</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1836 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1836">
-        <rdfs:label>Residue bump detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0395"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowBumps</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect &apos;bumps&apos; between residues in a structure, i.e. those with pairs of atoms whose Van der Waals&apos; radii interpenetrate more than a defined distance.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1837 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1837">
-        <rdfs:label>Residue symmetry contact calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <oboInOwl:hasDefinition>Calculate the number of symmetry contacts made by residues in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:SymmetryContact</oboInOwl:hasDbXref>
-        <rdfs:comment>A symmetry contact is a contact between two atoms in different asymmetric unit.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1838 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1838">
-        <rdfs:label>Residue contact calculation (residue-ligand)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0388"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate contacts between residues and ligands in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ShowDrugContactsShort</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLigandContacts</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowDrugContacts</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1839 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1839">
-        <rdfs:label>Salt bridge calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <rdfs:comment>Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF:HasSaltBridgePlus</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowSaltBridges</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF:HasSaltBridge</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowSaltBridgesH</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Calculate (and possibly score) salt bridges in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1841 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1841">
-        <rdfs:label>Rotamer likelihood prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0480"/>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers500</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers800</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers600</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers900</oboInOwl:hasDbXref>
-        <rdfs:comment>Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.</rdfs:comment>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers700</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers400</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers300</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers200</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>WHATIF:ShowLikelyRotamers100</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1842 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1842">
-        <rdfs:label>Proline mutation value calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0331"/>
-        <oboInOwl:hasDefinition>Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF:ProlineMutationValue</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1843 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1843">
-        <rdfs:label>Residue packing validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0395"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify poorly packed residues in protein structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: PackingQuality</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1844 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1844">
-        <rdfs:label>Dihedral angle validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <oboInOwl:hasDbXref>WHATIF: ImproperQualitySum</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Identify for each residue in a protein structure any improper dihedral (phi/psi) angles.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: ImproperQualityMax</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1845 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1845">
-        <rdfs:label>PDB file sequence retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Extract a molecular sequence from a PDB file.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDbXref>WHATIF: PDB_sequence</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0344"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1846 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1846">
-        <rdfs:label>HET group detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1838"/>
-        <oboInOwl:hasDefinition>Identify HET groups in PDB files.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>WHATIF: HETGroupNames</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1847 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1847">
-        <rdfs:label>DSSP secondary structure assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Determine for residue the DSSP determined secondary structure in three-state (HSC).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: ResidueDSSP</oboInOwl:hasDbXref>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0534"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1848 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1848">
-        <rdfs:label>Structure formatting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0335"/>
-        <oboInOwl:hasDefinition>Reformat (a file or other report of) tertiary structure data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: PDBasXML</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1850 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1850">
-        <rdfs:label>Protein cysteine and disulfide bond assignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0534"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Assign cysteine bonding state and disulfide bond partners in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1913 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1913">
-        <rdfs:label>Residue validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <oboInOwl:hasDefinition>Identify poor quality amino acid positions in protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>WHATIF: UseResidueDB</oboInOwl:hasDbXref>
-        <rdfs:comment>The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_1914 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_1914">
-        <rdfs:label>Structure retrieval (water)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDbXref>WHATIF:MovedWaterPDB</oboInOwl:hasDbXref>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query a tertiary structure database and retrieve water molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2008 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2008">
-        <rdfs:label>siRNA duplex prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0659"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify or predict siRNA duplexes in RNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2089 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2089">
-        <rdfs:label>Sequence alignment refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2425"/>
-        <oboInOwl:hasDefinition>Refine an existing sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2120 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2120">
-        <rdfs:label>Listfile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2121 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2121">
-        <rdfs:label>Sequence file editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0231"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2122">
-        <rdfs:label>Sequence alignment file processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2123">
-        <rdfs:label>Small molecule data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) physicochemical property data for small molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2222 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2222">
-        <rdfs:label>Data retrieval (ontology annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Ontology information retrieval</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Search and retrieve documentation on a bioinformatics ontology.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2224 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2224">
-        <rdfs:label>Data retrieval (ontology concept)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query an ontology and retrieve concepts or relations.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Ontology retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2233">
-        <rdfs:label>Representative sequence identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2234 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2234">
-        <rdfs:label>Structure file processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Perform basic (non-analytical) operations on a file of molecular tertiary structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2237">
-        <rdfs:label>Data retrieval (sequence profile)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Query a profile data resource and retrieve one or more profile(s) and / or associated annotation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>This includes direct retrieval methods that retrieve a profile by, e.g. the profile name.</rdfs:comment>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2238 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2238">
-        <rdfs:label>Statistical calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3438"/>
-        <oboInOwl:hasExactSynonym>Statistical analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Perform a statistical data operation of some type, e.g. calibration or validation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2239 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2239">
-        <rdfs:label>3D-1D scoring matrix generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1499"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>3D-1D scoring matrix construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2241 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2241">
-        <rdfs:label>Transmembrane protein visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0270"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0569"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2992"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise transmembrane proteins, typically the transmembrane regions within a sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Transmembrane protein rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2246 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2246">
-        <rdfs:label>Demonstration</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>An operation performing purely illustrative (pedagogical) purposes.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2264 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2264">
-        <rdfs:label>Data retrieval (pathway or network)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Query a biological pathways database and retrieve annotation on one or more pathways.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2265 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2265">
-        <rdfs:label>Data retrieval (identifier)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Query a database and retrieve one or more data identifiers.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2284 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2284">
-        <rdfs:label>Nucleic acid density plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate a density plot (of base composition) for a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2403">
-        <rdfs:label>Sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse one or more known molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence analysis (general)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2404">
-        <rdfs:label>Sequence motif processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular sequence motifs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0239"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2405">
-        <rdfs:label>Protein interaction data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) protein interaction data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2949"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2406">
-        <rdfs:label>Protein structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Structure analysis (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse protein tertiary structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2407">
-        <rdfs:label>Annotation processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2408">
-        <rdfs:label>Sequence feature analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Analyse features in molecular sequences.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0253"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2409">
-        <rdfs:label>Utility operation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0220"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Basic (non-analytical) operations of some data, either a file or equivalent entity in memory.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>File processing</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Report handling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File handling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data file processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2410">
-        <rdfs:label>Gene expression analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse gene expression and regulation data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2411">
-        <rdfs:label>Structural profile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>3D profile processing</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2952"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2412">
-        <rdfs:label>Data index processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Database index processing</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) an index of (typically a file of) biological data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0227"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2413">
-        <rdfs:label>Sequence profile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) some type of sequence profile.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2463"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2414">
-        <rdfs:label>Protein function analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2415">
-        <rdfs:label>Protein folding analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0130"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1537"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein folding modelling</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2416">
-        <rdfs:label>Protein secondary structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2814"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2956"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse known protein secondary structure data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Secondary structure analysis (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2417">
-        <rdfs:label>Physicochemical property data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) data on the physicochemical property of a molecule.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2419">
-        <rdfs:label>Primer and probe design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3095"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0632"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Primer and probe prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict oligonucleotide primers or probes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2420">
-        <rdfs:label>Operation (typed)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <oboInOwl:hasExactSynonym>Computation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Calculation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) data of a specific type, for example applying analytical methods.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2421">
-        <rdfs:label>Database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0224"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2080"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database.</rdfs:comment>
-        <oboInOwl:hasDefinition>Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2422">
-        <rdfs:label>Data retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0224"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0842"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasBroadSynonym>Information retrieval</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2423">
-        <rdfs:label>Prediction and recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise, detect or identify some properties of a biomolecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Detection</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2424 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2424">
-        <rdfs:label>Comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more things to identify similarities.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2425 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2425">
-        <rdfs:label>Optimisation and refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Refine or optimise some data model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2426 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2426">
-        <rdfs:label>Modelling and simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2275"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Model or simulate some biological entity or system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2427 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2427">
-        <rdfs:label>Data handling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Perform basic operations on some data or a database.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2428 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2428">
-        <rdfs:label>Validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Validation and standardisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Validate some data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2429">
-        <rdfs:label>Mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.</rdfs:comment>
-        <oboInOwl:hasDefinition>Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2430">
-        <rdfs:label>Design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Design a biological entity (typically a molecular sequence or structure) with specific properties.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2432">
-        <rdfs:label>Microarray data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) microarray data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2433">
-        <rdfs:label>Codon usage table processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a codon usage table.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2434">
-        <rdfs:label>Data retrieval (codon usage table)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve a codon usage table and / or associated annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2435">
-        <rdfs:label>Gene expression profile processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) a gene expression profile.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2436">
-        <rdfs:label>Functional enrichment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene expression profile annotation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The Gene Ontology (GO) is invariably used, the input is a set of Gene IDs and the output of the analysis is typically a ranked list of GO terms, each associated with a p-value.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse a set of genes (genes corresponding to an expression profile, or any other set) with respect to concepts from an ontology of gene functions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>GO term enrichment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2437">
-        <rdfs:label>Gene regulatory network prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2846"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict a network of gene regulation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2438">
-        <rdfs:label>Pathway or network processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Generate, analyse or handle a biological pathway or network.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2439">
-        <rdfs:label>RNA secondary structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2481"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) RNA secondary structure data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2440">
-        <rdfs:label>Structure processing (RNA)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) RNA tertiary structure data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2519"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2441">
-        <rdfs:label>RNA structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0475"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1465"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict RNA tertiary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2442 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2442">
-        <rdfs:label>DNA structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0475"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1464"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict DNA tertiary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2443">
-        <rdfs:label>Phylogenetic tree processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a phylogenetic tree.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2444">
-        <rdfs:label>Protein secondary structure processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) protein secondary structure data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2416"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2445">
-        <rdfs:label>Protein interaction network processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a network of protein interactions.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0276"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2446">
-        <rdfs:label>Sequence processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence processing (general)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) one or more molecular sequences and associated annotation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2403"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2447">
-        <rdfs:label>Sequence processing (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a protein sequence and associated annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2446"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2448">
-        <rdfs:label>Sequence processing (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a nucleotide sequence and associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2446"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2451 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2451">
-        <rdfs:label>Sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2955"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0159"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare two or more molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2452">
-        <rdfs:label>Sequence cluster processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a sequence cluster.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0291"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2453">
-        <rdfs:label>Feature table processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a sequence feature table.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2446"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2454 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2454">
-        <rdfs:label>Gene prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Gene and gene component prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect, predict and identify genes or components of genes in DNA sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene finding</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2456">
-        <rdfs:label>GPCR classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0473"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2995"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0907"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>G protein-coupled receptor (GPCR) classification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Classify G-protein coupled receptors (GPCRs) into families and subfamilies.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2457">
-        <rdfs:label>GPCR coupling selectivity prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0473"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3088"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0896"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict G-protein coupled receptor (GPCR) coupling selectivity.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2459">
-        <rdfs:label>Structure processing (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a protein tertiary structure.</oboInOwl:hasDefinition>
-        <rdfs:comment rdf:resource="http://edamontology.org/operation_2406"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2460">
-        <rdfs:label>Protein atom surface calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0387"/>
-        <rdfs:comment>Waters are not considered.</rdfs:comment>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility for each atom in a structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2461">
-        <rdfs:label>Protein residue surface calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0387"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility for each residue in a structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2462 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2462">
-        <rdfs:label>Protein surface calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0387"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the solvent accessibility of a structure as a whole.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2463">
-        <rdfs:label>Sequence alignment processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular sequence alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2464 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2464">
-        <rdfs:label>Protein-protein interaction prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Identify or predict protein-protein interactions, interfaces, binding sites etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2465">
-        <rdfs:label>Structure processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular tertiary structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2480"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2466 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2466">
-        <rdfs:label>Map annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Annotate a DNA map of some type with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0362"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2467 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2467">
-        <rdfs:label>Data retrieval (protein annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve information on a protein.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Protein information retrieval</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2468 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2468">
-        <rdfs:label>Data retrieval (phylogenetic tree)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Retrieve a phylogenetic tree from a data resource.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2469">
-        <rdfs:label>Data retrieval (protein interaction annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve information on a protein interaction.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2470">
-        <rdfs:label>Data retrieval (protein family annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein family information retrieval</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Retrieve information on a protein family.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2471">
-        <rdfs:label>Data retrieval (RNA family annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Retrieve information on an RNA family.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>RNA family information retrieval</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2472">
-        <rdfs:label>Data retrieval (gene annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene information retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Retrieve information on a specific gene.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2473">
-        <rdfs:label>Data retrieval (genotype and phenotype annotation)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Retrieve information on a specific genotype or phenotype.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genotype and phenotype information retrieval</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2422"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2474">
-        <rdfs:label>Protein architecture comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0247"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2488"/>
-        <oboInOwl:hasDefinition>Compare the architecture of two or more protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2475 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2475">
-        <rdfs:label>Protein architecture recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0247"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2996"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify the architecture of a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2476 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2476">
-        <rdfs:label>Molecular dynamics simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0176"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0082"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2478">
-        <rdfs:label>Nucleic acid sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2977"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence analysis (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2479 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2479">
-        <rdfs:label>Protein sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2976"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a protein sequence (using methods that are only applicable to protein sequences).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence analysis (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2480">
-        <rdfs:label>Structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0081"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse known molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2481">
-        <rdfs:label>Nucleic acid structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1459"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse nucleic acid tertiary structural data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2482">
-        <rdfs:label>Secondary structure processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular secondary structure.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2465"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2483 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2483">
-        <rdfs:label>Structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more molecular tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2485 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2485">
-        <rdfs:label>Helical wheel drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0569"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2162"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Helical wheel rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Render a helical wheel representation of protein secondary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2486 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2486">
-        <rdfs:label>Topology diagram drawing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0569"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2992"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Topology diagram rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Render a topology diagram of protein secondary structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2487 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2487">
-        <rdfs:label>Protein structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1460"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure comparison (protein)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Methods might identify structural neighbors, find structural similarities or define a structural core.</rdfs:comment>
-        <oboInOwl:hasDefinition>Compare protein tertiary structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2488 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2488">
-        <rdfs:label>Protein secondary structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2416"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2931"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <oboInOwl:hasDefinition>Compare protein secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Secondary structure comparison (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein secondary structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2489">
-        <rdfs:label>Protein subcellular localization prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_1777"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0140"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict the subcellular localization of a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein targeting prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2490 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2490">
-        <rdfs:label>Residue contact calculation (residue-residue)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2950"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate contacts between residues in a protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2491 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2491">
-        <rdfs:label>Hydrogen bond calculation (inter-residue)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0394"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2490"/>
-        <oboInOwl:hasDefinition>Identify potential hydrogen bonds between amino acid residues.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2492 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2492">
-        <rdfs:label>Protein interaction prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Predict the interactions of proteins with other molecules.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2493 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2493">
-        <rdfs:label>Codon usage data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasDefinition>Process (read and / or write) codon usage data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0286"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2495 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2495">
-        <rdfs:label>Gene expression data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0203"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider>Gene expression profile analysis</oboInOwl:consider>
-        <oboInOwl:hasExactSynonym>Gene expression (microarray) data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene expression data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2496 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2496">
-        <rdfs:label>Gene regulatory network processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) a network of gene regulation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2497 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2497">
-        <rdfs:label>Pathway or network analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a known biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Network analysis</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2498 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2498">
-        <rdfs:label>Sequencing-based expression profile data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2499 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2499">
-        <rdfs:label>Splicing model analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0114"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Splicing analysis</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2500">
-        <rdfs:label>Microarray raw data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Analyse raw microarray data.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2495"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2501">
-        <rdfs:label>Nucleic acid analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Process (read and / or write) nucleic acid sequence or structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid data processing</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2502">
-        <rdfs:label>Protein analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0078"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) protein sequence or structural data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2503">
-        <rdfs:label>Sequence data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular sequence data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2504">
-        <rdfs:label>Structural data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular structural data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2465"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2505 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2505">
-        <rdfs:label>Text processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) text.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0306"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2506 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2506">
-        <rdfs:label>Protein sequence alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1384"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a protein sequence alignment, typically to detect features or make predictions.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2507 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2507">
-        <rdfs:label>Nucleic acid sequence alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0258"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2501"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3024"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1383"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence alignment analysis (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse a protein sequence alignment, typically to detect features or make predictions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2508 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2508">
-        <rdfs:label>Nucleic acid sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <oboInOwl:hasExactSynonym>Sequence comparison (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Compare two or more nucleic acid sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2509 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2509">
-        <rdfs:label>Protein sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2451"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence comparison (protein)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Compare two or more protein sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2510 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2510">
-        <rdfs:label>DNA back-translation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0233"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0108"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Back-translate a protein sequence into DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2511">
-        <rdfs:label>Sequence editing (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Edit or change a nucleic acid sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2512">
-        <rdfs:label>Sequence editing (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Edit or change a protein sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0231"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2513 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2513">
-        <rdfs:label>Sequence generation (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <oboInOwl:hasDefinition>Generate a nucleic acid sequence by some means.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2514">
-        <rdfs:label>Sequence generation (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <oboInOwl:hasDefinition>Generate a protein sequence by some means.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2515">
-        <rdfs:label>Nucleic acid sequence visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Visualise, format or render a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.</rdfs:comment>
-        <obsolete_since>1.8</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2516">
-        <rdfs:label>Protein sequence visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render a protein sequence.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <rdfs:comment>Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2518 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2518">
-        <rdfs:label>Nucleic acid structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2481"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2998"/>
-        <oboInOwl:hasDefinition>Compare nucleic acid tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Structure comparison (nucleic acid)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2519">
-        <rdfs:label>Structure processing (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) nucleic acid tertiary structure data.</oboInOwl:hasDefinition>
-        <rdfs:comment rdf:resource="http://edamontology.org/operation_2481"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2520">
-        <rdfs:label>DNA mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1274"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a map of a DNA sequence annotated with positional or non-positional features of some type.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2521">
-        <rdfs:label>Map data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>DNA map data processing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Process (read and / or write) a DNA map of some type.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2520"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2574">
-        <rdfs:label>Protein hydropathy calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0250"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0123"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2970"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2575">
-        <rdfs:label>Protein binding site prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2492"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Ligand-binding and active site prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Binding site prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2871 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2871">
-        <rdfs:label>Sequence tagged site (STS) mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1279"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Sequence mapping</oboInOwl:hasExactSynonym>
-        <rdfs:comment>An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2928 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2928">
-        <rdfs:label>Alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1916"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Alignment generation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Alignment construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2929 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2929">
-        <rdfs:label>Protein fragment weight comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0398"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2930"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2930 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2930">
-        <rdfs:label>Protein property comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2997"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0897"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare the physicochemical properties of two or more proteins (or reference data).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2931 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2931">
-        <rdfs:label>Secondary structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1770"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compare two or more molecular secondary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2932 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2932">
-        <rdfs:label>Hopp and Woods plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0252"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a Hopp and Woods plot of antigenicity of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2934 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2934">
-        <rdfs:label>Microarray cluster textual view generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise gene clusters with gene names.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2935 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2935">
-        <rdfs:label>Microarray wave graph plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasExactSynonym>Microarray wave graph rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray cluster temporal graph rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This view can be rendered as a pie graph.  The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades.</rdfs:comment>
-        <oboInOwl:hasDefinition>Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2936 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2936">
-        <rdfs:label>Microarray dendrograph plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasNarrowSynonym>Microarray dendrograph rendering</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Generate a dendrograph of raw, preprocessed or clustered microarray data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray checks view rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Microarray view rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2937 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2937">
-        <rdfs:label>Microarray proximity map plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray distance map rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a plot of distances (distance matrix) between genes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microarray proximity map rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2938 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2938">
-        <rdfs:label>Microarray tree or dendrogram rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasNarrowSynonym>Microarray 2-way dendrogram rendering</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Microarray matrix tree plot rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2939 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2939">
-        <rdfs:label>Microarray principal component plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray principal component rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2940 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2940">
-        <rdfs:label>Microarray scatter plot plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasDefinition>Generate a scatter plot of microarray data, typically after principal component analysis.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Microarray scatter plot rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2941 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2941">
-        <rdfs:label>Whole microarray graph plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <oboInOwl:hasDefinition>Visualise gene expression data where each band (or line graph) corresponds to a sample.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Whole microarray graph rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2942 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2942">
-        <rdfs:label>Microarray tree-map rendering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise gene expression data after hierarchical clustering for representing hierarchical relationships.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2943 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2943">
-        <rdfs:label>Microarray Box-Whisker plot plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0571"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2944 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2944">
-        <rdfs:label>Physical mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2520"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1280"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0102"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2945 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2945">
-        <rdfs:label>Analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <oboInOwl:hasDefinition>Apply analytical methods to existing data of a specific type.</oboInOwl:hasDefinition>
-        <rdfs:comment>For non-analytical operations, see the &apos;Processing&apos; branch.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2420"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2946 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2946">
-        <rdfs:label>Alignment analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process or analyse an alignment of molecular sequences or structures.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>1.8</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2928"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2947 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2947">
-        <rdfs:label>Article analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0306"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3068"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2526"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0971"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Analyse a body of scientific text (typically a full text article from a scientific journal.)</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Article analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2948 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2948">
-        <rdfs:label>Molecular interaction analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2949 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2949">
-        <rdfs:label>Protein interaction analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2950 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2950">
-        <rdfs:label>Residue contact calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0248"/>
-        <oboInOwl:hasDefinition>Calculate contacts between residues and some other group in a protein structure.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2951 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2951">
-        <rdfs:label>Alignment processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2463"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2952"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2952 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2952">
-        <rdfs:label>Structure alignment processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Process (read and / or write) a molecular tertiary (3D) structure alignment.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2962 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2962">
-        <rdfs:label>Codon usage bias calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2865"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate codon usage bias.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2963 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2963">
-        <rdfs:label>Codon usage bias plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2962"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Generate a codon usage bias plot.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2964 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2964">
-        <rdfs:label>Codon usage fraction calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0286"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1602"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2990 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2990">
-        <rdfs:label>Classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2993 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2993">
-        <rdfs:label>Molecular interaction data processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Process (read and / or write) molecular interaction data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2995 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2995">
-        <rdfs:label>Sequence classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2990"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Assign molecular sequence(s) to a group or category.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2996 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2996">
-        <rdfs:label>Structure classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2990"/>
-        <oboInOwl:hasDefinition>Assign molecular structure(s) to a group or category.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2997 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2997">
-        <rdfs:label>Protein comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <oboInOwl:hasDefinition>Compare two or more proteins (or some aspect) to identify similarities.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_2998 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_2998">
-        <rdfs:label>Nucleic acid comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Compare two or more nucleic acids to identify similarities.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3023 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3023">
-        <rdfs:label>Prediction and recognition (protein)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict, recognise, detect or identify some properties of proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3024 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3024">
-        <rdfs:label>Prediction and recognition (nucleic acid)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Predict, recognise, detect or identify some properties of nucleic acids.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3080">
-        <rdfs:label>Structure editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0883"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Edit, convert or otherwise change a  molecular tertiary structure, either randomly or specifically.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3081">
-        <rdfs:label>Sequence alignment editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3096"/>
-        <oboInOwl:hasDefinition>Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3083">
-        <rdfs:label>Pathway or network visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2438"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2600"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Render (visualise) a biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway or network rendering</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3084">
-        <rdfs:label>Protein function prediction (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Predict general (non-positional) functional properties of a protein from analysing its sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>For functional properties that are positional, use &apos;Protein site detection&apos; instead.</rdfs:comment>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_1777"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3087 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3087">
-        <rdfs:label>Protein sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3092"/>
-        <oboInOwl:hasNarrowSynonym>Protein site recognition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein site prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence profile database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein site detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary database search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequence feature detection (protein)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3088 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3088">
-        <rdfs:label>Protein property calculation (from sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0250"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2479"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3090 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3090">
-        <rdfs:label>Protein feature prediction (from structure)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.6</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in proteins from analysing protein structure.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_3092"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3092">
-        <rdfs:label>Protein feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2502"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3023"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_1277"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0160"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group.
-</rdfs:comment>
-        <oboInOwl:hasDefinition>Predict, recognise and identify positional features in proteins from analysing protein sequences or structures.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Protein feature recognition</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein feature prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3093 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3093">
-        <rdfs:label>Database search (by sequence)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence screening</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <oboInOwl:hasDefinition>Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_2421"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3094">
-        <rdfs:label>Protein interaction network prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3439"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0128"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0906"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Predict a network of protein interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3095 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3095">
-        <rdfs:label>Nucleic acid design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2430"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Design (or predict) nucleic acid sequences with specific chemical or physical properties.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3096 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3096">
-        <rdfs:label>Editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Edit a data entity, either randomly or specifically.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3180">
-        <rdfs:label>Sequence assembly validation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0925"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3181"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Evaluate a DNA sequence assembly, typically for purposes of quality control.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3182">
-        <rdfs:label>Genome alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <oboInOwl:hasDefinition>Align two or more (tpyically huge) molecular sequences that represent genomes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome alignment construction</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Genome alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3183">
-        <rdfs:label>Localized reassembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <oboInOwl:hasDefinition>Reconstruction of a sequence assembly in a localised area.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3184">
-        <rdfs:label>Sequence assembly visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0564"/>
-        <oboInOwl:hasExactSynonym>Assembly rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence assembly rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Render and visualise a DNA sequence assembly.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Assembly visualisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3185 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3185">
-        <rdfs:label>Base-calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2513"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Phred base calling</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Identify base (nucleobase) sequence from a fluorescence &apos;trace&apos; data generated by an automated DNA sequencer.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Base calling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Phred base-calling</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3186 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3186">
-        <rdfs:label>Bisulfite mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected.</rdfs:comment>
-        <oboInOwl:hasDefinition>The mapping of methylation sites in a DNA (genome) sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Bisulfite sequence alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Bisulfite sequence mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3187 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3187">
-        <rdfs:label>Sequence contamination filtering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3189 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3189">
-        <rdfs:label>Trim ends</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3192"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Trim sequences (typically from an automated DNA sequencer) to remove misleading ends.</oboInOwl:hasDefinition>
-        <rdfs:comment>For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3190 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3190">
-        <rdfs:label>Trim vector</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3192"/>
-        <oboInOwl:hasDefinition>Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3191">
-        <rdfs:label>Trim to reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3192"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3192 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3192">
-        <rdfs:label>Sequence trimming</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0369"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Cut (remove) the end from a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3194">
-        <rdfs:label>Genome feature comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0256"/>
-        <rdfs:comment>Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Compare the features of two genome sequences.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3195">
-        <rdfs:label>Sequencing error detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3168"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Short read error correction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Short-read error correction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Detect errors in DNA sequences generated from sequencing projects).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3196">
-        <rdfs:label>Genotyping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual&apos;s or a reference sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3197 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3197">
-        <rdfs:label>Genetic variation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Sequence variation analysis</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Genetic variation annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3198 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3198">
-        <rdfs:label>Read mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0292"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <oboInOwl:hasExactSynonym>Short oligonucleotide alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Oligonucleotide mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Oligonucleotide alignment generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Short read mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Oligonucleotide alignment construction</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Oligonucleotide alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Read alignment</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Short read alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Short sequence read mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3199 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3199">
-        <rdfs:label>Split read mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3198"/>
-        <oboInOwl:hasDefinition>A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3200">
-        <rdfs:label>DNA barcoding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasDefinition>Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Sample barcoding</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3201 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3201">
-        <rdfs:label>SNP calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0484"/>
-        <oboInOwl:hasDefinition>Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism.</oboInOwl:hasDefinition>
-        <rdfs:comment>Operations usually score confidence in the prediction or some other statistical measure of evidence.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3202">
-        <rdfs:label>Mutation detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasExactSynonym>Polymorphism detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3203">
-        <rdfs:label>Chromatogram visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <oboInOwl:hasDefinition>Visualise, format or render an image of a Chromatogram.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Chromatogram viewing</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3204">
-        <rdfs:label>Methylation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Determine cytosine methylation states in nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3205 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3205">
-        <rdfs:label>Methylation calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2944"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3204"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Determine cytosine methylation status of specific positions in a nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3206 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3206">
-        <rdfs:label>Methylation level analysis (global)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3205"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Global methylation analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3207 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3207">
-        <rdfs:label>Methylation level analysis (gene-specific)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3205"/>
-        <oboInOwl:hasExactSynonym>Gene-specific methylation analysis</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Many different techniques are available for this.</rdfs:comment>
-        <oboInOwl:hasDefinition>Measure the level of methyl cytosines in specific genes.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3208">
-        <rdfs:label>Genome visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0564"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Genome visualization</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome visualisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome viewing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genome browsing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3209">
-        <rdfs:label>Genome comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2508"/>
-        <oboInOwl:hasDefinition>Compare the sequence or features of two or more genomes, for example, to find matching regions.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Genomic region matching</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3211">
-        <rdfs:label>Genome indexing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0227"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3210"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate an index of a genome sequence.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3212 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3212">
-        <rdfs:label>Genome indexing (Burrows-Wheeler)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3211"/>
-        <rdfs:comment>The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm.</rdfs:comment>
-        <oboInOwl:hasDefinition>Generate an index of a genome sequence using the Burrows-Wheeler algorithm.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3213">
-        <rdfs:label>Genome indexing (suffix arrays)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3211"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Generate an index of a genome sequence using a suffix arrays algorithm.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>suffix arrays</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A suffix array consists of the lexicographically sorted list of suffixes of a genome.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3214 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3214">
-        <rdfs:label>Spectral analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasExactSynonym>Spectral analysis</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Spectrum analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse a spectrum from a mass spectrometry (or other) experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Mass spectrum analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3215">
-        <rdfs:label>Peak detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3214"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0943"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Peak finding</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Peak assignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3216 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3216">
-        <rdfs:label>Scaffolding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Scaffold construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length.  The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Scaffold may be positioned along a chromosome physical map to create a &quot;golden path&quot;.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Scaffold generation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3217">
-        <rdfs:label>Scaffold gap completion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3216"/>
-        <oboInOwl:hasDefinition>Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used.  For large (&gt;20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3218">
-        <rdfs:label>Sequencing quality control</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasDefinition>Raw sequence data quality control.</oboInOwl:hasDefinition>
-        <rdfs:comment>Analyse raw sequence data from a sequencing pipeline and identify problems.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Sequencing QC</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3219">
-        <rdfs:label>Read pre-processing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2428"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasExactSynonym>Sequence read pre-processing</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This is a broad concept and is used a placeholder for other, more specific concepts.  For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Pre-process sequence reads to ensure (or improve) quality and reliability.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3221 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3221">
-        <rdfs:label>Species frequency estimation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3174"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3222 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3222">
-        <rdfs:label>Peak calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3430"/>
-        <rdfs:comment>Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence.  The enriched areas contain the binding sites of DNA-associated proteins.  For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation (&apos;ChIP&apos;) with microarray (&apos;chip&apos;).</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein binding peak detection</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3223 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3223">
-        <rdfs:label>Differential expression analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0315"/>
-        <oboInOwl:hasDefinition>Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Differentially expressed gene identification</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3224 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3224">
-        <rdfs:label>Gene set testing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Gene sets can be defined beforehand by biological function, chromosome locations and so on.</rdfs:comment>
-        <oboInOwl:hasDefinition>Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3225 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3225">
-        <rdfs:label>Variant classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2995"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasDefinition>Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.)</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3226 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3226">
-        <rdfs:label>Variant prioritization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <rdfs:comment>Variant prioritization can be used for example to produce a list of variants responsible for &apos;knocking out&apos; genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes.</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3227 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3227">
-        <rdfs:label>Variant calling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasExactSynonym>Variant mapping</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods often utilise a database of aligned reads.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3228 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3228">
-        <rdfs:label>Structural variation discovery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <oboInOwl:hasDefinition>Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s).</oboInOwl:hasDefinition>
-        <created_in>1.1</created_in>
-        <rdfs:comment>Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3229 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3229">
-        <rdfs:label>Exome analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>Targeted exome capture</oboInOwl:hasExactSynonym>
-        <rdfs:comment>Exome sequencing is considered a cheap alternative to whole genome sequencing.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Exome sequence analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3230 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3230">
-        <rdfs:label>Read depth analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3232 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3232">
-        <rdfs:label>Gene expression QTL analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2984"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>expression quantitative trait loci profiling</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasExactSynonym>eQTL profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>expression QTL profiling</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3233 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3233">
-        <rdfs:label>Copy number estimation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <rdfs:comment>Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number).</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Transcript copy number estimation</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3237 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3237">
-        <rdfs:label>Primer removal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0369"/>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3258">
-        <rdfs:label>Transcriptome assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0925"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0196"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Infer a transcriptome sequence by analysis of short sequence reads.</oboInOwl:hasDefinition>
-        <created_in>1.2</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3259">
-        <rdfs:label>Transcriptome assembly (de novo)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>de novo transcriptome assembly</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>1.2</created_in>
-        <oboInOwl:hasDefinition>Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0524"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3260 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3260">
-        <rdfs:label>Transcriptome assembly (mapping)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Infer a transcriptome sequence by mapping short reads to a reference genome.</oboInOwl:hasDefinition>
-        <obsolete_since>1.6</obsolete_since>
-        <created_in>1.2</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/operation_0523"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3267 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3267">
-        <rdfs:label>Sequence coordinate conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3434"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2012"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2012"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3278">
-        <rdfs:label>Document similarity calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3437"/>
-        <oboInOwl:hasDefinition>Calculate similarity between 2 or more documents.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3279 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3279">
-        <rdfs:label>Document clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3432"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3437"/>
-        <oboInOwl:hasDefinition>Cluster (group) documents on the basis of their calculated similarity.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3280">
-        <rdfs:label>Named entity recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0306"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <oboInOwl:hasExactSynonym>Entity identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Entity chunking</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Entity extraction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Recognise named entities (text tokens) within documents.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3282 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3282">
-        <rdfs:label>ID mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <oboInOwl:hasExactSynonym>Identifier mapping</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Accession mapping</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3283 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3283">
-        <rdfs:label>Anonymisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:hasDefinition>Process data in such a way that makes it hard to trace to the person which the data concerns.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Data anonymisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3289 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3289">
-        <rdfs:label>ID retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0304"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0842"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>id retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data retrieval (accession)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data retrieval (ID)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Identifier retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data retrieval (id)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Accession retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Search for and retrieve a data identifier of some kind, e.g. a database entry accession.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3348 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3348">
-        <rdfs:label>Sequence checksum generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_2044"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3077"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Generate a checksum of a molecular sequence.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3349 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3349">
-        <rdfs:label>Bibliography generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3505"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Bibliography construction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Construct a bibliography from the scientific literature.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3350 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3350">
-        <rdfs:label>Protein quaternary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0474"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Predict the structure of a multi-subunit protein and particularly how the subunits fit together.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3351 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3351">
-        <rdfs:label>Protein surface analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0243"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Analyse the surface properties of proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3352 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3352">
-        <rdfs:label>Ontology comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Compare two or more ontologies, e.g. identify differences.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3353 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3353">
-        <rdfs:label>Ontology comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Compare two or more ontologies, e.g. identify differences.</oboInOwl:hasDefinition>
-        <obsolete_since>1.9</obsolete_since>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/operation_3352"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3357 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3357">
-        <rdfs:label>Format detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_input"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_0006"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_output"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/data_3358"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Recognition of which format the given data is in.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Format identification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Format recognition</oboInOwl:hasExactSynonym>
-        <rdfs:comment>&apos;Format recognition&apos; is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Format inference</oboInOwl:hasExactSynonym>
-        <noClue rdf:resource="http://edamontology.org/noClue"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    <owl:Axiom>
-        <rdfs:comment>The has_input &quot;Data&quot; (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs.</rdfs:comment>
-        <owl:annotatedProperty rdf:resource="http://edamontology.org/noClue"/>
-        <owl:annotatedTarget rdf:resource="http://edamontology.org/noClue"/>
-        <owl:annotatedSource rdf:resource="http://edamontology.org/operation_3357"/>
-    </owl:Axiom>
-    
-
-
-    <!-- http://edamontology.org/operation_3359 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3359">
-        <rdfs:label>Splitting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:hasExactSynonym>File splitting</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Split a file containing multiple data items into many files, each containing one item</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3429 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3429">
-        <rdfs:label>Generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasExactSynonym>Construction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>For non-analytical operations, see the &apos;Processing&apos; branch.</rdfs:comment>
-        <oboInOwl:hasDefinition>Construct some data entity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3430 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3430">
-        <rdfs:label>Nucleic acid sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0253"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0415"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid site prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid site recognition</oboInOwl:hasExactSynonym>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid site detection</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3431 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3431">
-        <rdfs:label>Deposition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
-        <oboInOwl:hasDefinition>Deposit some data in a database or some other type of repository or software system.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasExactSynonym>Database submission</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Submission</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data submission</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Data deposition</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Database deposition</oboInOwl:hasExactSynonym>
-        <rdfs:comment>For non-analytical operations, see the &apos;Processing&apos; branch.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3432 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3432">
-        <rdfs:label>Clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3433 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3433">
-        <rdfs:label>Assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Construct some entity (typically a molecule sequence) from component pieces.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3434 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3434">
-        <rdfs:label>Conversion</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Non-analytical data conversion.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3435 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3435">
-        <rdfs:label>Standardization and normalization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Standardize or normalize data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3436 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3436">
-        <rdfs:label>Aggregation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2409"/>
-        <oboInOwl:hasDefinition>Combine multiple files or data items into a single file or object.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3437 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3437">
-        <rdfs:label>Article comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <oboInOwl:hasDefinition>Compare two or more scientific articles.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3438 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3438">
-        <rdfs:label>Calculation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasDefinition>Mathemetical determination of the value of something, typically a properly of a  molecule.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3439 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3439">
-        <rdfs:label>Pathway or network prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2438"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>Predict a molecular pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3440 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3440">
-        <rdfs:label>Genome assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0310"/>
-        <created_in>1.6</created_in>
-        <oboInOwl:hasDefinition>The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3441 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3441">
-        <rdfs:label>Plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <oboInOwl:hasDefinition>Generate a graph, or other visual representation, of data, showing the relationship between two or more variables.</oboInOwl:hasDefinition>
-        <created_in>1.6</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3443 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3443">
-        <rdfs:label>Image analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2420"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3382"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>The analysis of a image (typically a digital image) of some type in order to extract information from it.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Image processing</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3445 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3445">
-        <rdfs:label>Diffraction data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Analysis of data from a diffraction experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3446 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3446">
-        <rdfs:label>Cell migration analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2229"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3447 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3447">
-        <rdfs:label>Diffraction data reduction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3445"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Processing of diffraction data into a corrected, ordered, and simplified form.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3450 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3450">
-        <rdfs:label>Neurite measurement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2229"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3453 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3453">
-        <rdfs:label>Diffraction data integration</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3445"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasNarrowSynonym>Diffraction summation integration</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Diffraction profile fitting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3454 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3454">
-        <rdfs:label>Phasing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3445"/>
-        <oboInOwl:hasDefinition>Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3455 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3455">
-        <rdfs:label>Molecular replacement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0322"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form.</oboInOwl:hasDefinition>
-        <rdfs:comment>The technique solves the phase problem, i.e. retrieve information concern phases of the structure.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3456">
-        <rdfs:label>Rigid body refinement</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0322"/>
-        <created_in>1.7</created_in>
-        <rdfs:comment>Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data.</rdfs:comment>
-        <oboInOwl:hasDefinition>A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3457 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3457">
-        <rdfs:label>Single particle analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2480"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3443"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1317"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:comment>Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM).</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3458 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3458">
-        <rdfs:label>Single particle alignment and classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2990"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3457"/>
-        <oboInOwl:hasDefinition>Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle. </oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:comment>A micrograph can include particles in multiple different orientations and/or conformations.  Particles are compared and organised into sets based on their similarity.  Typically iterations of classification and alignment and are performed to optimise the final image; average images produced by classification are used as a reference image for subsequent alignment of the whole image set.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3459 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3459">
-        <rdfs:label>Functional clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0291"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Functional sequence clustering</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3460 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3460">
-        <rdfs:label>Taxonomic classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2995"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Classifiication of molecular sequences by assignment to some taxonomic hierarchy.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3461 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3461">
-        <rdfs:label>Virulence prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3301"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasExactSynonym>Pathogenicity prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3463 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3463">
-        <rdfs:label>Gene expression correlation analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0315"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3465"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>Gene co-expression network analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Analyse the correlation patterns among genes across across a variety of experiments, microarray samples etc.
- </oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3465 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3465">
-        <rdfs:label>Correlation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0121"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3469 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3469">
-        <rdfs:label>RNA structure covariance model generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2439"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0097"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Compute the covariance model for (a family of) RNA secondary structures.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3470 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3470">
-        <rdfs:label>RNA secondary structure prediction (shape-based)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0278"/>
-        <oboInOwl:hasExactSynonym>RNA shape prediction</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3471 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3471">
-        <rdfs:label>Nucleic acid alignment folding prediction (alignment-based)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0279"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Prediction of nucleic-acid folding using sequence alignments as a source of data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3472 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3472">
-        <rdfs:label>k-mer counting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0236"/>
-        <oboInOwl:hasDefinition>Count k-mers (substrings of length k) in DNA sequence data.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <rdfs:comment>k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads. </rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3478 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3478">
-        <rdfs:label>Phylogenetic tree reconstruction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_0084"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Reconstructing the inner node labels of a phylogenetic tree from its leafes.</oboInOwl:hasDefinition>
-        <rdfs:comment>Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one.</rdfs:comment>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3480 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3480">
-        <rdfs:label>Probabilistic data generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3429"/>
-        <oboInOwl:hasDefinition>Generate some data from a choosen probibalistic model, possibly to evaluate algorithms.</oboInOwl:hasDefinition>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3481 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3481">
-        <rdfs:label>Probabilistic sequence generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0230"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3480"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Generate sequences from some probabilistic model, e.g. a model that simulates evolution.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3482 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3482">
-        <rdfs:label>Antimicrobial resistance prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2403"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2423"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3301"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDefinition>Identify or predict causes for antibiotic resistance from molecular sequence analysis.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3501 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3501">
-        <rdfs:label>Enrichment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2945"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <rdfs:comment>A relevant ontology will be used. The input is typically a set of identifiers or other data, and the output of the analysis is typically a ranked list of ontology terms, each associated with a p-value.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Term enrichment</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Analyse a dataset with respect to concepts from an ontology.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3502 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3502">
-        <rdfs:label>Chemical class enrichment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2495"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3501"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_1775"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Analyse a dataset with respect to concepts from an ontology of chemical structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3503 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3503">
-        <rdfs:label>Incident curve plotting</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3441"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Plot an incident curve such as a survival curve, death curve, mortality curve.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3504 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3504">
-        <rdfs:label>Variant pattern analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_3197"/>
-        <rdfs:comment>Methods often utilise a database of aligned reads.</rdfs:comment>
-        <oboInOwl:hasDefinition>Identify and map patterns of genomic variations.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3545 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3545">
-        <rdfs:label>Mathematical modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <oboInOwl:hasDefinition>Model some biological system using mathematical techniques including  dynamical systems, statistical models, differential equations, and game theoretic models.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3552 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3552">
-        <rdfs:label>Microscope image visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_3382"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Visualise images resulting from various types of microscopy.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasExactSynonym>Microscopy image visualisation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3553 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3553">
-        <rdfs:label>Image annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0226"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Annotate an image of some sort, typically with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3557 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3557">
-        <rdfs:label>Imputation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2238"/>
-        <oboInOwl:hasExactSynonym>Data imputation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Replace missing data with substituted values, usually by using some statistical or other mathematical approach.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3559 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3559">
-        <rdfs:label>Ontology visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0337"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Visualise, format or render data from an ontology, typically a tree of terms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Ontology browsing</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3560 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3560">
-        <rdfs:label>Maximum occurence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0321"/>
-        <oboInOwl:hasDefinition>A method for making numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data. </oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3561 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3561">
-        <rdfs:label>Database comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2424"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2429"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasNarrowSynonym>Data model comparison</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Compare the models or schemas used by two or more databases, or any other general comparison of databases rather than a detailed comparison of the entries themselves.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Schema comparison</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3562 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3562">
-        <rdfs:label>Network simulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://edamontology.org/has_topic"/>
-                <owl:someValuesFrom rdf:resource="http://edamontology.org/topic_2259"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
-        <oboInOwl:hasDefinition>Simulate the bevaviour of a biological pathway or network.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway simulation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Network topology simulation</oboInOwl:hasExactSynonym>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3563 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3563">
-        <rdfs:label>RNA-seq read count analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <oboInOwl:hasDefinition>Analyze read counts from RNA-seq experiments.</oboInOwl:hasDefinition>
-        <created_in>1.9</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3564 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3564">
-        <rdfs:label>Chemical redundancy removal</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2483"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Identify and remove redudancy from a set of small molecule structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3565 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3565">
-        <rdfs:label>RNA-seq time series data analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2478"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Analyze time series data from an RNA-seq experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/operation_3566 -->
-
-    <owl:Class rdf:about="http://edamontology.org/operation_3566">
-        <rdfs:label>Simulated gene expression data generation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/operation_2426"/>
-        <created_in>1.9</created_in>
-        <oboInOwl:hasDefinition>Simulate gene expression data, e.g. for purposes of benchmarking.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#operations"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0003 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0003">
-        <rdfs:label>Topic</rdfs:label>
-        <owl:disjointWith rdf:resource="&owl;DeprecatedClass"/>
-        <rdfs:seeAlso>http://purl.org/biotop/biotop.owl#Quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Category</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Quality</rdfs:seeAlso>
-        <rdfs:seeAlso>http://www.onto-med.de/ontologies/gfo.owl#Perpetuant</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://www.ifomis.org/bfo/1.1/snap#Continuant</rdfs:seeAlso>
-        <oboInOwl:hasRelatedSynonym>sumo:FieldOfStudy</oboInOwl:hasRelatedSynonym>
-        <rdfs:seeAlso>http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0077">
-        <rdfs:label>Nucleic acids</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <oboInOwl:hasDefinition>The processing and analysis of nucleic acid sequence, structural and other data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid bioinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid informatics</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D017423</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid properties</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid physicochemistry</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D017422</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0078">
-        <rdfs:label>Proteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <oboInOwl:hasExactSynonym>Protein bioinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein databases</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein analysis</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D020539</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Archival, processing and analysis of protein data, typically molecular sequence and structural data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0079 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0079">
-        <rdfs:label>Metabolites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <oboInOwl:hasExactSynonym>Metabolite structures</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This concept excludes macromolecules such as proteins and nucleic acids.</rdfs:comment>
-        <oboInOwl:hasDefinition>The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0080 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0080">
-        <rdfs:label>Sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3307"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Sequence databases</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Sequences</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D017421</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0081 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0081">
-        <rdfs:label>Structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3307"/>
-        <oboInOwl:hasNarrowSynonym>Computational structural biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015394</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Structure analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Structural bioinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Structure databases</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes related concepts such as structural properties, alignments and structural motifs.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Structure data resources</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0082 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0082">
-        <rdfs:label>Structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The prediction of molecular (secondary or tertiary) structure.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0083 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0083">
-        <rdfs:label>Alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0183"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0184"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0084 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0084">
-        <rdfs:label>Phylogeny</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3299"/>
-        <oboInOwl:hasNarrowSynonym>Phylogeny reconstruction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic stratigraphy</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic dating</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic clocks</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D010802</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The study of evolutionary relationships amongst organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Phylogenetic simulation</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0085 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0085">
-        <rdfs:label>Functional genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1775"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0089 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0089">
-        <rdfs:label>Ontology and terminology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasNarrowSynonym>Terminology</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D002965</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Applied ontology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Ontology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Ontologies</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0090 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0090">
-        <rdfs:label>Information retrieval</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Data retrieval</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes, for example, search, query and retrieval of molecular sequences and associated data.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Data search</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.3.3 Information retrieval</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Data query</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0091 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0091">
-        <rdfs:label>Bioinformatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <rdfs:comment>This includes data  processing in general, including basic handling of files and databases, datatypes, workflows and annotation.</rdfs:comment>
-        <oboInOwl:hasDbXref>VT 1.5.6 Bioinformatics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The archival, curation, processing and analysis of complex biological data.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D016247</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0092 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0092">
-        <rdfs:label>Data visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasExactSynonym>Data rendering</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.2.5 Computer graphics</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasBroadSynonym>Computer graphics</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0094 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0094">
-        <rdfs:label>Nucleic acid thermodynamics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The study of the thermodynamic properties of a nucleic acid.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0097 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0097">
-        <rdfs:label>Nucleic acid structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <rdfs:comment>Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>DNA melting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid denaturation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>RNA alignment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>RNA structure alignment</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid thermodynamics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>RNA structure</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0099 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0099">
-        <rdfs:label>RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0077"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>RNA sequences and structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0100 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0100">
-        <rdfs:label>Nucleic acid restriction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0747"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0102 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0102">
-        <rdfs:label>Mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Genetic linkage</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Linkage</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Linkage mapping</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Synteny</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>DNA mapping</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The mapping of complete (typically nucleotide) sequences.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0107 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0107">
-        <rdfs:label>Genetic codes and codon usage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Codon usage analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The study of codon usage in nucleotide sequence(s), genetic codes and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0108 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0108">
-        <rdfs:label>Protein expression</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <oboInOwl:hasNarrowSynonym>Translation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The translation of mRNA into protein and subsequent protein processing in the cell.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0109 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0109">
-        <rdfs:label>Gene finding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:comment>This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Gene discovery</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene prediction</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0110 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0110">
-        <rdfs:label>Transcription</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>The transcription of DNA into mRNA.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0111 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0111">
-        <rdfs:label>Promoters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins).</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0749"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0112 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0112">
-        <rdfs:label>Nucleic acid folding</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>The folding (in 3D space) of nucleic acid molecules.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0173"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0114 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0114">
-        <rdfs:label>Gene structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3321"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <rdfs:comment>This includes the study of promoters, coding regions etc.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene features</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc.
-</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0121 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0121">
-        <rdfs:label>Proteomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3391"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Protein and peptide identification, especially in the study of whole proteomes of organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein and peptide identification</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Peptide identification</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D040901</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Protein expression</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0122 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0122">
-        <rdfs:label>Structural genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The elucidation of the three dimensional structure for all (available) proteins in a given organism.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0123">
-        <rdfs:label>Protein properties</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <oboInOwl:hasDefinition>The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein hydropathy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein physicochemistry</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0128 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0128">
-        <rdfs:label>Protein interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein-nucleic acid interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein-RNA interaction</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Protein-protein interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein-ligand interactions</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein-DNA interaction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0130 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0130">
-        <rdfs:label>Protein folding, stability and design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:hasNarrowSynonym>Protein folding</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein stability</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Protein stability, folding (in 3D space) and protein sequence-structure-function relationships.  This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein residue interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Rational protein design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0133 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0133">
-        <rdfs:label>Two-dimensional gel electrophoresis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Two-dimensional gel electrophoresis image and related data.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0121"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0134 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0134">
-        <rdfs:label>Mass spectrometry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3520"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>An analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0135">
-        <rdfs:label>Protein microarrays</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Protein microarray data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0121"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0137 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0137">
-        <rdfs:label>Protein hydropathy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The study of the hydrophobic, hydrophilic and charge properties of a protein.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0123"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0140 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0140">
-        <rdfs:label>Protein targeting and localization</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0108"/>
-        <oboInOwl:hasNarrowSynonym>Protein targeting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein sorting</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein localization</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0141 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0141">
-        <rdfs:label>Protein cleavage sites and proteolysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0767"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0143 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0143">
-        <rdfs:label>Protein structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The comparison of two or more protein structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Use this concept for methods that are exclusively for protein structure.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0698"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0144 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0144">
-        <rdfs:label>Protein residue interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein residue interactions</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0130"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0147 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0147">
-        <rdfs:label>Protein-protein interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasNarrowSynonym>Protein interaction networks</oboInOwl:hasNarrowSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0148 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0148">
-        <rdfs:label>Protein-ligand interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein-ligand (small molecule) interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0149 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0149">
-        <rdfs:label>Protein-nucleic acid interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein-DNA/RNA interactions.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0150 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0150">
-        <rdfs:label>Protein design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0130"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0151 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0151">
-        <rdfs:label>G protein-coupled receptors (GPCR)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>G-protein coupled receptors (GPCRs).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0152 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0152">
-        <rdfs:label>Carbohydrates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Carbohydrates, typically including structural information.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0153 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0153">
-        <rdfs:label>Lipids</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Lipids and their structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0154 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0154">
-        <rdfs:label>Small molecules</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3292"/>
-        <oboInOwl:hasDefinition>Small molecules of biological significance, typically archival, curation, processing and analysis of structural information.</oboInOwl:hasDefinition>
-        <rdfs:comment>Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides.  Structural data is usually included.</rdfs:comment>
-        <oboInOwl:hasRelatedSynonym>CHEBI:23367</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0156 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0156">
-        <rdfs:label>Sequence editing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Edit, convert or otherwise change a molecular sequence, either randomly or specifically.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0091"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0157 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0157">
-        <rdfs:label>Sequence composition, complexity and repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Sequence complexity</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Repeat sequences</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Sequence repeats</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Low complexity sequences</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence composition</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0158 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0158">
-        <rdfs:label>Sequence motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Motifs</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0159 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0159">
-        <rdfs:label>Sequence comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <rdfs:comment>The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The comparison of two or more molecular sequences, for example sequence alignment and clustering.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0160 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0160">
-        <rdfs:label>Sequence sites, features and motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Sequence features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The archival, detection, prediction and analysis of
-positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Functional sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence motifs</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence profiles</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Sequence sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>HMMs</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0163 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0163">
-        <rdfs:label>Sequence database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>The query is a sequence-based entity such as another sequence, a motif or profile.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0164 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0164">
-        <rdfs:label>Sequence clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes systems that generate, process and analyse sequence clusters.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>The comparison and grouping together of molecular sequences on the basis of their similarities.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence clusters</oboInOwl:hasExactSynonym>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0166 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0166">
-        <rdfs:label>Protein structural motifs and surfaces</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <rdfs:comment>This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Protein structural features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Structural motifs</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Protein 3D motifs</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein structural motifs</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein surfaces</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0167 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0167">
-        <rdfs:label>Structural (3D) profiles</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Structural profiles</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0172">
-        <rdfs:label>Protein structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0173">
-        <rdfs:label>Nucleic acid structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:hasDefinition>The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>DNA structure prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>RNA structure prediction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid folding</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0174">
-        <rdfs:label>Ab initio structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>The prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0082"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0175">
-        <rdfs:label>Homology modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.4</obsolete_since>
-        <oboInOwl:hasDefinition>The modelling of the three-dimensional structure of a protein using known sequence and structural data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2275"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0176">
-        <rdfs:label>Molecular dynamics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:comment>This includes resources concerning flexibility and motion in protein and other molecular structures.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Protein dynamics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Molecular flexibility</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Molecular motions</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0177">
-        <rdfs:label>Molecular docking</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The modelling the structure of proteins in complex with small molecules or other macromolecules.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0178">
-        <rdfs:label>Protein secondary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>The prediction of secondary or supersecondary structure of protein sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0172"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0694"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0179">
-        <rdfs:label>Protein tertiary structure prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The prediction of tertiary structure of protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0172"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0698"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0180 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0180">
-        <rdfs:label>Protein fold recognition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <rdfs:comment>For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).</rdfs:comment>
-        <oboInOwl:hasDefinition>The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0182 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0182">
-        <rdfs:label>Sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasDefinition>The alignment of molecular sequences or sequence profiles (representing sequence alignments).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0183 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0183">
-        <rdfs:label>Structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes the generation, storage, analysis, rendering etc. of structure alignments.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.7</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0184 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0184">
-        <rdfs:label>Threading</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Sequence-structure alignment</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0180"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0188 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0188">
-        <rdfs:label>Sequence profiles and HMMs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Sequence profiles; typically a positional, numerical matrix representing a sequence alignment.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:comment>Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0191 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0191">
-        <rdfs:label>Phylogeny reconstruction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>Currently too specific for the topic sub-ontology (but might be unobsoleted).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3293"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0194 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0194">
-        <rdfs:label>Phylogenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0195 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0195">
-        <rdfs:label>Virtual PCR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <oboInOwl:hasExactSynonym>Polymerase chain reaction</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Simulated polymerase chain reaction (PCR).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>PCR</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0077"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0196 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0196">
-        <rdfs:label>Sequence assembly</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Assembly</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The assembly of fragments of a DNA sequence to reconstruct the original sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0199 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0199">
-        <rdfs:label>Genetic variation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0625"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D014644</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>DNA variation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Mutation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Polymorphism</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0200 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0200">
-        <rdfs:label>Microarrays</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D046228</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>Microarrays, for example, to process microarray data or design probes and experiments.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasNarrowSynonym>DNA microarrays</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0202 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0202">
-        <rdfs:label>Pharmacology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasNarrowSynonym>Computational pharmacology</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Pharmacoinformatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of drugs and their effects or responses in living systems. </oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.7 Pharmacology and pharmacy</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0203 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0203">
-        <rdfs:label>Gene expression</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <rdfs:comment>This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Gene expression profiling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Expression profiling</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasAlternativeId>http://edamontology.org/topic_0197</oboInOwl:hasAlternativeId>
-        <rdfs:comment>Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015870</rdfs:seeAlso>
-        <oboInOwl:hasExactSynonym>Gene expression analysis</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>DNA microarrays</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Codon usage</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0204 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0204">
-        <rdfs:label>Gene regulation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0203"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The regulation of gene expression.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0208 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0208">
-        <rdfs:label>Pharmacogenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0202"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0209 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0209">
-        <rdfs:label>Medicinal chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3336"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3371"/>
-        <oboInOwl:hasDbXref>VT 3.1.4 Medicinal chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Drug design</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0210 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0210">
-        <rdfs:label>Fish</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Information on a specific fish genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0211 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0211">
-        <rdfs:label>Flies</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a specific fly genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2819"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0213 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0213">
-        <rdfs:label>Mice or rats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2820"/>
-        <oboInOwl:hasDefinition>Information on a specific mouse or rat genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <rdfs:comment>The resource may be specific to a group of mice / rats or all mice / rats.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0215 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0215">
-        <rdfs:label>Worms</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Information on a specific worm genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2819"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0217 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0217">
-        <rdfs:label>Literature analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0218"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0218 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0218">
-        <rdfs:label>Data mining</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3068"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Text data mining</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The analysis of the biomedical and informatics literature.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Literature analysis</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Text mining</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Literature mining</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0219 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0219">
-        <rdfs:label>Data deposition, annotation and curation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>Deposition and curation of database accessions, including annotation, typically with terms from a controlled vocabulary.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Database curation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0220 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0220">
-        <rdfs:label>Document, record and content management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasExactSynonym>Document management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>File management</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Content management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The management and manipulation of digital documents, including database records, files and reports.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.3.6 Multimedia, hypermedia</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Record management</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0221 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0221">
-        <rdfs:label>Sequence annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Annotation of a molecular sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0219"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0222 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0222">
-        <rdfs:label>Genome annotation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Annotation of a genome.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0219"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0593 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0593">
-        <rdfs:label>NMR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasNarrowSynonym>ROESY</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>NOESY</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nuclear Overhauser Effect Spectroscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>HOESY</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Heteronuclear Overhauser Effect Spectroscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nuclear magnetic resonance spectroscopy</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Spectroscopy</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>NMR spectroscopy</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Rotational Frame Nuclear Overhauser Effect Spectroscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0594 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0594">
-        <rdfs:label>Sequence classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The classification of molecular sequences based on some measure of their similarity.</oboInOwl:hasDefinition>
-        <rdfs:comment>Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0595 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0595">
-        <rdfs:label>Protein classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0598 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0598">
-        <rdfs:label>Sequence motif or profile</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes comparison, discovery, recognition etc. of sequence motifs.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0158"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0188"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0601 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0601">
-        <rdfs:label>Protein modifications</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0108"/>
-        <oboInOwl:hasRelatedSynonym>GO:0006464</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:hasDefinition>Protein chemical modifications, e.g. post-translational modifications.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein post-translational modification</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>MOD:00000</oboInOwl:hasRelatedSynonym>
-        <rdfs:comment>EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000)</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0602 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0602">
-        <rdfs:label>Molecular interactions, pathways and networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasNarrowSynonym>Biological networks</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Network or pathway analysis</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasNarrowSynonym>Molecular interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Biological models</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Molecular interactions, biological pathways, networks and other models.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Biological pathways</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasAlternativeId>http://edamontology.org/topic_3076</oboInOwl:hasAlternativeId>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0605 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0605">
-        <rdfs:label>Informatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The study and practice of information processing and use of computer information systems.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.3.99 Other</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Knowledge management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.3.4 Information management</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Information management</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.3.5 Knowledge management</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.3.3 Information retrieval</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.3 Information sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Information science</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0606 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0606">
-        <rdfs:label>Literature data resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Data resources for the biological or biomedical literature, either a primary source of literature or some derivative.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3068"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0607 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0607">
-        <rdfs:label>Laboratory information management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasDefinition>Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Laboratory resources</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0608 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0608">
-        <rdfs:label>Cell and tissue culture</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasNarrowSynonym>Tissue culture</oboInOwl:hasNarrowSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>General cell culture or data on a specific cell lines.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Cell culture</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2229"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0610 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0610">
-        <rdfs:label>Ecology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDefinition>The ecological and environmental sciences and especially the application of information technology (ecoinformatics).</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D004777</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Ecological informatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.15 Ecology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Computational ecology</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Ecoinformatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Environmental science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0611 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0611">
-        <rdfs:label>Electron microscopy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasNarrowSynonym>SEM</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Scanning electron microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>TEM</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light.
-</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Transmission electron microscopy</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Electron crystallography</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Electron diffraction experiment</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Single particle electron microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0612 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0612">
-        <rdfs:label>Cell cycle</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The cell cycle including key genes and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2229"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0613 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0613">
-        <rdfs:label>Peptides and amino acids</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The physicochemical, biochemical or structural properties of amino acids or peptides.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Amino acids</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Peptides</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0616 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0616">
-        <rdfs:label>Organelles</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasNarrowSynonym>Cell membrane</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Cytoplasm</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Organelle genes and proteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Smooth endoplasmic reticulum</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Lysosome</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Centriole</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Ribosome</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nucleus</oboInOwl:hasNarrowSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Mitochondria</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Golgi apparatus</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Rough endoplasmic reticulum</oboInOwl:hasNarrowSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2229"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0617 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0617">
-        <rdfs:label>Ribosomes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Ribosomes, typically of ribosome-related genes and proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Ribosome genes and proteins</oboInOwl:hasNarrowSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0616"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0618 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0618">
-        <rdfs:label>Scents</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A database about scents.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0154"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0620 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0620">
-        <rdfs:label>Drugs and target structures</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3336"/>
-        <oboInOwl:hasNarrowSynonym>Drug structures</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The structures of drugs, drug target, their interactions and binding affinities.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Target structures</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0621 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0621">
-        <rdfs:label>Model organisms</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:comment>This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>A specific organism, or group of organisms, used to study a particular aspect of biology.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Organisms</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0622 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0622">
-        <rdfs:label>Genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3391"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D023281</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0623 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0623">
-        <rdfs:label>Gene families</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasDefinition>Particular gene(s), gene family or other gene group or system and their encoded proteins.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Gene family</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene system</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Genes, gene family or system</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Gene and protein families</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0624 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0624">
-        <rdfs:label>Chromosomes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Study of chromosomes.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0625 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0625">
-        <rdfs:label>Genotype and phenotype</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasExactSynonym>Genotype and phenotype resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Genotyping</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Phenotyping</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0629 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0629">
-        <rdfs:label>Gene expression and microarray</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0200"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0632 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0632">
-        <rdfs:label>Sequence design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:hasNarrowSynonym>Probes</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes the design of primers for PCR and DNA amplification or the design of molecular probes.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D015335</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Gene design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Probe design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>in silico cloning</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Primer design</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Primers</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0634 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0634">
-        <rdfs:label>Pathology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Diseases</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.1.6 Pathology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0635 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0635">
-        <rdfs:label>Specific protein resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>A particular protein, protein family or other group of proteins.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Specific protein</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0637 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0637">
-        <rdfs:label>Taxonomy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3299"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.25 Taxonomy</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Organism classification, identification and naming.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0639 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0639">
-        <rdfs:label>Protein sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0640 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0640">
-        <rdfs:label>Nucleic acid sequence analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0641 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0641">
-        <rdfs:label>Repeat sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The repetitive nature of molecular sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0157"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0642 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0642">
-        <rdfs:label>Low complexity sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The (character) complexity of molecular sequences, particularly regions of low complexity.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0157"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0644 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0644">
-        <rdfs:label>Proteome</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A specific proteome including protein sequences and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0654 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0654">
-        <rdfs:label>DNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0077"/>
-        <oboInOwl:hasExactSynonym>DNA analysis</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA sequences and structure, including processes such as methylation and replication.</oboInOwl:hasDefinition>
-        <rdfs:comment>The DNA sequences might be coding or non-coding sequences.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0655 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0655">
-        <rdfs:label>Coding RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <oboInOwl:hasNarrowSynonym>EST</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>cDNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>mRNA</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes expressed sequence tag (EST) or complementary DNA (cDNA) sequences.</rdfs:comment>
-        <oboInOwl:hasDefinition>Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0659 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0659">
-        <rdfs:label>Functional, regulatory and non-coding RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasNarrowSynonym>ncRNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Non-coding RNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Functional RNA</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Regulatory RNA</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>Non-coding RNA includes  piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA).  Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA).</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0660 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0660">
-        <rdfs:label>rRNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>One or more ribosomal RNA (rRNA) sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0659"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0663 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0663">
-        <rdfs:label>tRNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>One or more transfer RNA (tRNA) sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0659"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0694 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0694">
-        <rdfs:label>Protein secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.8</obsolete_since>
-        <oboInOwl:hasDefinition>Protein secondary structure or secondary structure alignments.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data.</rdfs:comment>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0697 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0697">
-        <rdfs:label>RNA structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>RNA secondary or tertiary structure and alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0698 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0698">
-        <rdfs:label>Protein tertiary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.8</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Protein tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0722 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0722">
-        <rdfs:label>Nucleic acid classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Classification of nucleic acid sequences and structures.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0623"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0724 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0724">
-        <rdfs:label>Protein families</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0078"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein sequence classification</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein secondary databases</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>A protein families database might include the classifier (e.g. a sequence profile) used to build the classification.</rdfs:comment>
-        <oboInOwl:hasDefinition>Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0736 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0736">
-        <rdfs:label>Protein domains and folds</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein folds</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Protein tertiary structural domains and folds.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein domains</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0740 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0740">
-        <rdfs:label>Nucleic acid sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Nucleotide sequence alignments.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0741 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0741">
-        <rdfs:label>Protein sequence alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein sequence alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <rdfs:comment>A sequence profile typically represents a sequence alignment.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0159"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0747 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0747">
-        <rdfs:label>Nucleic acid sites and features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The archival, detection, prediction and analysis of
-positional features such as functional sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0640"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0748 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0748">
-        <rdfs:label>Protein sites and features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The detection, identification and analysis of positional features in proteins, such as functional sites.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0639"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0749 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0749">
-        <rdfs:label>Transcription factors and regulatory sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1312"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3125"/>
-        <rdfs:comment>Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase.  Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators.</rdfs:comment>
-        <oboInOwl:hasDefinition>Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Transcriptional regulatory sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>TFBS</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Transcription factors</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Transcription factor binding sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0751 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0751">
-        <rdfs:label>Phosphorylation sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:hasDefinition>Protein phosphorylation and phosphorylation sites in protein sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0601"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0748"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0753 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0753">
-        <rdfs:label>Metabolic pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Metabolic pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0754 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0754">
-        <rdfs:label>Signaling pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Signaling pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Signal transduction pathways</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0767 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0767">
-        <rdfs:label>Protein and peptide identification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0121"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0769 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0769">
-        <rdfs:label>Workflows</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Biological or biomedical analytical workflows or pipelines.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.0</obsolete_since>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0770 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0770">
-        <rdfs:label>Data types and objects</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Structuring data into basic types and (computational) objects.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.0</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0091"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0771 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0771">
-        <rdfs:label>Theoretical biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3307"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0779 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0779">
-        <rdfs:label>Mitochondria</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Mitochondria, typically of mitochondrial genes and proteins.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0616"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0780 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0780">
-        <rdfs:label>Plants</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <rdfs:comment>The resource may be specific to a plant, a group of plants or all plants.</rdfs:comment>
-        <oboInOwl:hasBroadSynonym>Plant science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Plant biology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Botany</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.22 Plant science</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Plant</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.10 Botany</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0781 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0781">
-        <rdfs:label>Viruses</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:hasBroadSynonym>Virology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.28 Virology</oboInOwl:hasDbXref>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <rdfs:comment>The resource may be specific to a virus, a group of viruses or all viruses.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0782 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0782">
-        <rdfs:label>Fungi</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <oboInOwl:hasBroadSynonym>Mycology</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The resource may be specific to a fungus, a group of fungi or all fungi.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Yeast</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.21 Mycology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0783 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0783">
-        <rdfs:label>Pathogens</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:hasDefinition>Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The resource may be specific to a pathogen, a group of pathogens or all pathogens.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0786 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0786">
-        <rdfs:label>Arabidopsis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Arabidopsis-specific data.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0780"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0787 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0787">
-        <rdfs:label>Rice</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Rice-specific data.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0780"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0796 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0796">
-        <rdfs:label>Genetic mapping and linkage</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Linkage mapping</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Genetic linkage</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0102"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0797 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0797">
-        <rdfs:label>Comparative genomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <oboInOwl:hasDefinition>The study (typically comparison) of the sequence, structure or function of multiple genomes.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0798 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0798">
-        <rdfs:label>Mobile genetic elements</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <oboInOwl:hasNarrowSynonym>Transposons</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0803 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0803">
-        <rdfs:label>Human disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Human diseases, typically describing the genes, mutations and proteins implicated in disease.</oboInOwl:hasDefinition>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0804 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0804">
-        <rdfs:label>Immunology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDbXref>VT 3.1.3 Immunology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Immunoinformatics</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D007120</rdfs:seeAlso>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D007125</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Computational immunology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0820 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0820">
-        <rdfs:label>Membrane and  lipoproteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:hasDefinition>Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Membrane proteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Lipoproteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Transmembrane proteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0821 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0821">
-        <rdfs:label>Enzymes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <oboInOwl:hasDefinition>Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Enzymology</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_0922 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_0922">
-        <rdfs:label>Primers</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <oboInOwl:hasDefinition>PCR primers and hybridization oligos in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (primers)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Primer binding sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_0922"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1302">
-        <rdfs:label>PolyA signal or sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (PolyA signal or site)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>PolyA signal</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>PolyA site</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1302"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1304">
-        <rdfs:label>CpG island and isochores</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (CpG island and isochore)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>CpG rich regions (isochores) in a nucleotide sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1304"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1305">
-        <rdfs:label>Restriction sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3125"/>
-        <oboInOwl:hasDefinition>Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (restriction sites)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid restriction sites (report)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1305"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1307">
-        <rdfs:label>Splice sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3320"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (splice sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (RNA splicing)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Splice sites in a nucleotide sequence or alternative RNA splicing events.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid report (RNA splice model)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1307"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1308">
-        <rdfs:label>Matrix/scaffold attachment sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (matrix/scaffold attachment sites)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1308"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1311 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1311">
-        <rdfs:label>Operon</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasExactSynonym>Gene features (operon)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (operon)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query.</rdfs:comment>
-        <oboInOwl:hasDefinition>Operons (operators, promoters and genes) from a bacterial genome.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1311"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1312 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1312">
-        <rdfs:label>Promoters</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2399"/>
-        <oboInOwl:hasDefinition>Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (promoters)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1312"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1317 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1317">
-        <rdfs:label>Structural biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasNarrowSynonym>Structural assignment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Structure determination</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:consider>This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy.  Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen.</oboInOwl:consider>
-        <oboInOwl:hasDefinition>The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.5.24 Structural biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Structural determination</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1456 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1456">
-        <rdfs:label>Protein membrane regions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0736"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3539"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (membrane regions)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Intramembrane regions</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein transmembrane regions</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Transmembrane regions</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_1456"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1770 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1770">
-        <rdfs:label>Structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <rdfs:comment>This might involve comparison of secondary or tertiary (3D) structural information.</rdfs:comment>
-        <oboInOwl:hasDefinition>The comparison of two or more molecular structures, for example structure alignment and clustering.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1775 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1775">
-        <rdfs:label>Function analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3307"/>
-        <oboInOwl:hasNarrowSynonym>Protein function prediction</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of gene and protein function including the prediction of functional properties of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Protein function analysis</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_1811 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_1811">
-        <rdfs:label>Prokaryotes and archae</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <rdfs:comment>The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes.</rdfs:comment>
-        <oboInOwl:hasDbXref>VT 1.5.2 Bacteriology</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Bacteriology</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2225 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2225">
-        <rdfs:label>Protein databases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Protein data resources.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Protein data resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0078"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2226 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2226">
-        <rdfs:label>Structure determination</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1317"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2229 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2229">
-        <rdfs:label>Cell biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.11 Cell biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Cells, such as key genes and proteins involved in the cell cycle.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2230 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2230">
-        <rdfs:label>Classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta13</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0089"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2232 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2232">
-        <rdfs:label>Lipoproteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Lipoproteins (protein-lipid assemblies).</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2257 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2257">
-        <rdfs:label>Phylogeny visualisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Visualise a phylogeny, for example, render a phylogenetic tree.</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0084"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2258 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2258">
-        <rdfs:label>Cheminformatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasDefinition>The application of information technology to chemistry in biological research environment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Chemical informatics</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Chemoinformatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2259 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2259">
-        <rdfs:label>Systems biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Systems_biology</rdfs:seeAlso>
-        <rdfs:comment>This includes databases of models and methods to construct or analyse a model.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Biological models</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D049490</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Biological modelling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Biological system modelling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The holistic modelling and analysis of complex biological systems and the interactions therein.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2269 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2269">
-        <rdfs:label>Statistics and probability</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3315"/>
-        <oboInOwl:hasNarrowSynonym>Biostatistics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The application of statistical methods to biological problems.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://en.wikipedia.org/wiki/Biostatistics</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D056808</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2271 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2271">
-        <rdfs:label>Structure database search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template.</rdfs:comment>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure).</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2275 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2275">
-        <rdfs:label>Molecular modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0082"/>
-        <oboInOwl:hasNarrowSynonym>Homology modeling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Comparative modeling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Comparative modelling</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Homology modelling</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Molecular modeling</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2276 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2276">
-        <rdfs:label>Protein function prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.2</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The prediction of functional properties of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1775"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2277">
-        <rdfs:label>SNP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <oboInOwl:hasDefinition>Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Single nucleotide polymorphism</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2278 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2278">
-        <rdfs:label>Transmembrane protein prediction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Predict transmembrane domains and topology in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0172"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2280 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2280">
-        <rdfs:label>Nucleic acid structure comparison</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <rdfs:comment>Use this concept for methods that are exclusively for nucleic acid structures.</rdfs:comment>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2397">
-        <rdfs:label>Exons</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0655"/>
-        <oboInOwl:hasExactSynonym>Gene features (exon)</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Exons in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2397"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2399">
-        <rdfs:label>Gene transcription features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasNarrowSynonym>GC signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>CAAT signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>-35 signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Gene transcriptional features</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Enhancers (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Terminators (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Transcription of DNA into RNA including the regulation of transcription.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Ribosome binding sites (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>-10 signals (report)</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>TATA signals (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Attenuators (report)</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2399"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2533">
-        <rdfs:label>DNA mutation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0199"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <oboInOwl:hasExactSynonym>Mutation annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA mutation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (mutation)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2533"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2640 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2640">
-        <rdfs:label>Oncology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDbXref>VT 3.2.16 Oncology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Cancer</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of cancer, for example, genes and proteins implicated in cancer.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Cancer biology</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2661 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2661">
-        <rdfs:label>Toxins and targets</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0154"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2840"/>
-        <oboInOwl:hasNarrowSynonym>Toxins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Targets</oboInOwl:hasNarrowSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Structural and associated data for toxic chemical substances.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2754 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2754">
-        <rdfs:label>Introns</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <oboInOwl:hasExactSynonym>Gene features (intron)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (intron)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Introns in a nucleotide sequences.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2754"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2807 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2807">
-        <rdfs:label>Tool topic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2809 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2809">
-        <rdfs:label>Study topic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2811 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2811">
-        <rdfs:label>Nomenclature</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Biological nomenclature (naming), symbols and terminology.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0089"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2813 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2813">
-        <rdfs:label>Disease genes and proteins</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>The genes, gene variations and proteins involved in one or more specific diseases.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2814 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2814">
-        <rdfs:label>Protein structure analysis</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0081"/>
-        <oboInOwl:hasExactSynonym>Protein structure</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Protein secondary or tertiary structural data and/or associated annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId>http://edamontology.org/topic_3040</oboInOwl:hasAlternativeId>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2815 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2815">
-        <rdfs:label>Humans</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2820"/>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>The human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2816 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2816">
-        <rdfs:label>Gene resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Gene resource</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Informatics resource (typically a database) primarily focussed on genes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Gene database</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2817 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2817">
-        <rdfs:label>Yeast</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0782"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2818 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2818">
-        <rdfs:label>Eukaryotes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0621"/>
-        <oboInOwl:hasExactSynonym>Eukaryote</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <rdfs:comment>The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2819 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2819">
-        <rdfs:label>Invertebrates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3500"/>
-        <rdfs:comment>The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates.</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2820 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2820">
-        <rdfs:label>Vertebrates</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3500"/>
-        <rdfs:comment>The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates.</rdfs:comment>
-        <oboInOwl:hasDefinition>Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2821 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2821">
-        <rdfs:label>Unicellular eukaryotes</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <oboInOwl:hasDefinition>Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <rdfs:comment>The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2826 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2826">
-        <rdfs:label>Protein structure alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Protein secondary or tertiary structure alignments.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0183"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2828 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2828">
-        <rdfs:label>X-ray diffraction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>X-ray microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Crystallography</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>X-ray crystallography</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2829 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2829">
-        <rdfs:label>Ontologies, nomenclature and classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D002965</rdfs:seeAlso>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0089"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2830 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2830">
-        <rdfs:label>Immunoproteins, genes and antigens</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0724"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0804"/>
-        <oboInOwl:hasNarrowSynonym>Immunopeptides</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Immunity-related genes, proteins and their ligands.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Antigens</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc.&quot;</rdfs:comment>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Immunoproteins</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Immunogenes</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2839 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2839">
-        <rdfs:label>Molecules</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasRelatedSynonym>CHEBI:23367</oboInOwl:hasRelatedSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <oboInOwl:hasDefinition>Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3047"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2840 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2840">
-        <rdfs:label>Toxicology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3377"/>
-        <oboInOwl:hasDefinition>Toxins and the adverse effects of these chemical substances on living organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.9 Toxicology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Toxicoinformatics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasBroadSynonym>Toxicology</oboInOwl:hasBroadSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasNarrowSynonym>Computational toxicology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2842 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2842">
-        <rdfs:label>High-throughput sequencing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Next-generation sequencing</oboInOwl:hasExactSynonym>
-        <obsolete_since>beta13</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>Parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3168"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2844 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2844">
-        <rdfs:label>Structural clustering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters.</oboInOwl:hasDefinition>
-        <obsolete_since>1.7</obsolete_since>
-        <oboInOwl:hasExactSynonym>Structure classification</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:replacedBy rdf:resource="http://edamontology.org/topic_1770"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2846 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2846">
-        <rdfs:label>Gene regulatory networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0204"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Gene regulatory networks.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2847 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2847">
-        <rdfs:label>Disease (specific)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Informatics resources dedicated to one or more specific diseases (not diseases in general).</oboInOwl:hasDefinition>
-        <obsolete_since>beta12orEarlier</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2867 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2867">
-        <rdfs:label>VNTR</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (VNTR)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Variable number of tandem repeat polymorphism</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>VNTR annotation</oboInOwl:hasExactSynonym>
-        <rdfs:comment>VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times.</rdfs:comment>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2867"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2868 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2868">
-        <rdfs:label>Microsatellites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (microsatellite)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Microsatellite annotation</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Microsatellite polymorphism in a DNA sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2868"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2869 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2869">
-        <rdfs:label>RFLP</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2885"/>
-        <oboInOwl:hasDefinition>Restriction fragment length polymorphisms (RFLP) in a DNA sequence.</oboInOwl:hasDefinition>
-        <rdfs:comment>An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>RFLP annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (RFLP)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2869"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2885 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2885">
-        <rdfs:label>DNA polymorphism</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0199"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (polymorphism)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>DNA polymorphism.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Polymorphism annotation</oboInOwl:hasExactSynonym>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_2885"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_2953 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_2953">
-        <rdfs:label>Nucleic acid design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Topic for the design of nucleic acid sequences with specific conformations.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta12orEarlier</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0173"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3032 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3032">
-        <rdfs:label>Primer or probe design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The design of primers for PCR and DNA amplification or the design of molecular probes.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0632"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3038 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3038">
-        <rdfs:label>Structure databases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.2</obsolete_since>
-        <oboInOwl:hasExactSynonym>Structure data resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0081"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3039 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3039">
-        <rdfs:label>Nucleic acid structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation.</oboInOwl:hasDefinition>
-        <obsolete_since>1.2</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0097"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3041 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3041">
-        <rdfs:label>Sequence databases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Molecular sequence data resources, including sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Sequence data resources</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence data</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Sequence data resource</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0080"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3042 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3042">
-        <rdfs:label>Nucleic acid sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Nucleotide sequences</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0640"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3043 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3043">
-        <rdfs:label>Protein sequences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0639"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3044 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3044">
-        <rdfs:label>Protein interaction networks</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0147"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3047 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3047">
-        <rdfs:label>Molecular biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDbXref>VT 1.5.4 Biochemistry and molecular biology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3048 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3048">
-        <rdfs:label>Mammals</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2820"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3050 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3050">
-        <rdfs:label>Biodiversity</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0610"/>
-        <oboInOwl:hasDefinition>The degree of variation of life forms within a given ecosystem, biome or an entire planet.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.5 Biodiversity conservation</oboInOwl:hasDbXref>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D044822</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3052 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3052">
-        <rdfs:label>Sequence clusters and classification</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:comment>This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>The comparison, grouping together and classification of macromolecules on the basis of sequence similarity.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Sequence families</oboInOwl:hasExactSynonym>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasExactSynonym>Sequence clusters</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0594"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3053 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3053">
-        <rdfs:label>Genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D005823</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The study of genes, genetic variation and heredity in living organisms.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasNarrowSynonym>Heredity</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3055 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3055">
-        <rdfs:label>Quantitative genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0625"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3056 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3056">
-        <rdfs:label>Population genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasDefinition>The distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3060 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3060">
-        <rdfs:label>Regulatory RNA</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0659"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3061 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3061">
-        <rdfs:label>Documentation and help</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3068"/>
-        <oboInOwl:hasDefinition>The documentation of resources such as tools, services and databases and how to get help.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Help</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasNarrowSynonym>Documentation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3062 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3062">
-        <rdfs:label>Genetic organisation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The structural and functional organisation of genes and other genetic elements.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>beta13</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3063 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3063">
-        <rdfs:label>Medical informatics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasExactSynonym>Health informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Clinical informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Biomedical informatics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Translational medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>The application of information technology to health, disease and biomedicine.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Healthcare informatics</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Health and disease</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Molecular medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3064 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3064">
-        <rdfs:label>Developmental biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDbXref>VT 1.5.14 Developmental biology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>How organisms grow and develop.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3065 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3065">
-        <rdfs:label>Embryology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3064"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3067 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3067">
-        <rdfs:label>Anatomy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDbXref>VT 3.1.1 Anatomy and morphology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The form and function of the structures of living organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3068 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3068">
-        <rdfs:label>Literature and reference</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasNarrowSynonym>Literature search</oboInOwl:hasNarrowSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The scientific literature, reference information and documentation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Literature sources</oboInOwl:hasNarrowSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D011642</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3070 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3070">
-        <rdfs:label>Biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDbXref>VT 1.5.8 Biology</oboInOwl:hasDbXref>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDbXref>VT 1.5 Biological sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.23 Reproductive biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Cryobiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Biological rhythms</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>A particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.5.7 Biological rhythm</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Biological science</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Aerobiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.99 Other</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Chronobiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.13 Cryobiology
-</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.1 Aerobiology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.3 Behavioural biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Reproductive biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Behavioural biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3071 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3071">
-        <rdfs:label>Data management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0605"/>
-        <oboInOwl:hasDefinition>The development and use of architectures, policies, practices and procedures for management of data.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Data handling</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D030541</rdfs:seeAlso>
-        <oboInOwl:hasDbXref>VT 1.3.1 Data management</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3072 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3072">
-        <rdfs:label>Sequence feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>The detection of the positional features, such as functional and other key sites, in molecular sequences.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D058977</rdfs:seeAlso>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3073 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3073">
-        <rdfs:label>Nucleic acid feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The detection of positional features such as functional sites in nucleotide sequences.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition rdf:resource="http://edamontology.org/topic_0747"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3074 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3074">
-        <rdfs:label>Protein feature detection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The detection, identification and analysis of positional protein sequence features, such as functional sites.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3075 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3075">
-        <rdfs:label>Biological system modelling</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.2</obsolete_since>
-        <owl:deprecated>true</owl:deprecated>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasDefinition>Topic for modelling biological systems in mathematical terms.</oboInOwl:hasDefinition>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_2259"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3077 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3077">
-        <rdfs:label>Data acquisition</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#data"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3078 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3078">
-        <rdfs:label>Genes and proteins resources</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Gene family</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Gene and protein families</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins.</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0623"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3118 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3118">
-        <rdfs:label>Protein topological domains</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0736"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3539"/>
-        <oboInOwl:hasDefinition>Topological domains such as cytoplasmic regions in a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (topological domains)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3118"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3120 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3120">
-        <rdfs:label>Protein variants</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <oboInOwl:hasDefinition>protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.</oboInOwl:hasDefinition>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3120"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3123 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3123">
-        <rdfs:label>Expression signals</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0203"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (expression signal)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Regions within a nucleic acid sequence containing a signal that alters a biological function.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3123"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3125 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3125">
-        <rdfs:label>DNA binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <rdfs:comment>This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes).</rdfs:comment>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (binding)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Nucleic acids binding to some other molecule.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3125"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3126 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3126">
-        <rdfs:label>Nucleic acid repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <created_in>beta13</created_in>
-        <rdfs:comment>This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at  both ends of a defined sequence and other types of repeating unit.</rdfs:comment>
-        <oboInOwl:hasDefinition>Repetitive elements within a nucleic acid sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3126"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3127 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3127">
-        <rdfs:label>DNA replication and recombination</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3125"/>
-        <oboInOwl:hasDefinition>DNA replication or recombination.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Nucleosome exclusion sequences</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (replication and recombination)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3127"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3135 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3135">
-        <rdfs:label>Signal or transit peptide</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3512"/>
-        <created_in>beta13</created_in>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (signal or transit peptide)</oboInOwl:hasExactSynonym>
-        <rdfs:comment>A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle.</rdfs:comment>
-        <oboInOwl:hasDefinition>Coding sequences for a signal or transit peptide.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3135"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3139 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3139">
-        <rdfs:label>Sequence tagged sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3511"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (STS)</oboInOwl:hasExactSynonym>
-        <created_in>beta13</created_in>
-        <rdfs:comment>Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs.</rdfs:comment>
-        <oboInOwl:hasDefinition>Sequence tagged sites (STS) in nucleic acid sequences.</oboInOwl:hasDefinition>
-        <oboInOwl:hasAlternativeId rdf:resource="http://edamontology.org/data_3139"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3168 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3168">
-        <rdfs:label>Sequencing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D059014</rdfs:seeAlso>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasNarrowSynonym>NGS</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Next generation sequencing</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Next gen sequencing</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3169 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3169">
-        <rdfs:label>ChIP-seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>Chip sequencing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Chip seq</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>The analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Chip-sequencing</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3170 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3170">
-        <rdfs:label>RNA-Seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasExactSynonym>Small RNA-seq</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Whole transcriptome shotgun sequencing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>RNA-seq</oboInOwl:hasExactSynonym>
-        <created_in>1.1</created_in>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasDefinition>A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Small RNA-Seq</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>WTSS</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs.</rdfs:comment>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0203"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3171 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3171">
-        <rdfs:label>DNA methylation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:hasDefinition>DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D019175</rdfs:seeAlso>
-        <created_in>1.1</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3295"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3172 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3172">
-        <rdfs:label>Metabolomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3391"/>
-        <oboInOwl:hasDefinition>The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D055432</rdfs:seeAlso>
-        <created_in>1.1</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3173 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3173">
-        <rdfs:label>Epigenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3295"/>
-        <rdfs:comment>Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation.</rdfs:comment>
-        <created_in>1.1</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D057890</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The study of the epigenetic modifications of a whole cell, tissue, organism etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3174 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3174">
-        <rdfs:label>Metagenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0610"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D056186</rdfs:seeAlso>
-        <oboInOwl:hasBroadSynonym>Ecogenomics</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Community genomics</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Environmental genomics</oboInOwl:hasBroadSynonym>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>The study of genetic material recovered from environmental samples, and associated environmental data.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3175 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3175">
-        <rdfs:label>Structural variation</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0199"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0624"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genomic structural variation</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3176 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3176">
-        <rdfs:label>DNA packaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0654"/>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:hasDefinition>DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures.</oboInOwl:hasDefinition>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D042003</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3177 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3177">
-        <rdfs:label>DNA-Seq</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements.</oboInOwl:hasDefinition>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>DNA-seq</oboInOwl:hasExactSynonym>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3168"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3178 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3178">
-        <rdfs:label>RNA-Seq alignment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <oboInOwl:hasExactSynonym>RNA-seq alignment</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The alignment of sequences of (typically millions) of short reads to a reference genome.  This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing.</oboInOwl:hasDefinition>
-        <created_in>beta12orEarlier</created_in>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0196"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3179 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3179">
-        <rdfs:label>ChIP-on-chip</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <owl:deprecated>true</owl:deprecated>
-        <obsolete_since>1.3</obsolete_since>
-        <created_in>1.1</created_in>
-        <oboInOwl:hasDefinition>Experimental techniques that combine chromatin immunoprecipitation (&apos;ChIP&apos;) with microarray (&apos;chip&apos;). ChIP-on-chip is used for high-throughput study protein-DNA interactions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>ChIP-chip</oboInOwl:hasExactSynonym>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3263 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3263">
-        <rdfs:label>Data security</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Data privacy</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The protection of data, such as patient health data, from damage or unwanted access from unauthorized users.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3277 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3277">
-        <rdfs:label>Sample collections</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasNarrowSynonym>samples</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>biobanking</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>biosamples</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Biological samples and specimens.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Specimen collections</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3292 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3292">
-        <rdfs:label>Biochemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <oboInOwl:hasDbXref>VT 1.5.4 Biochemistry and molecular biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Chemical biology</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Biological chemistry</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Chemical substances and physico-chemical processes and that occur within living organisms.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3293 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3293">
-        <rdfs:label>Phylogenetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0084"/>
-        <oboInOwl:hasDefinition>The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences).</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D010802</rdfs:seeAlso>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3295 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3295">
-        <rdfs:label>Epigenetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3321"/>
-        <oboInOwl:hasNarrowSynonym>Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence.</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>DNA methylation</oboInOwl:hasNarrowSynonym>
-        <rdfs:comment>This includes sub-topics such as histone modification and DNA methylation.</rdfs:comment>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D019175</rdfs:seeAlso>
-        <oboInOwl:hasNarrowSynonym>Histone modification</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3297 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3297">
-        <rdfs:label>Biotechnology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3298 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3298">
-        <rdfs:label>Phenomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0625"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3299"/>
-        <oboInOwl:hasDefinition>Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. </oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3299 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3299">
-        <rdfs:label>Evolutionary biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDbXref>VT 1.5.16 Evolutionary biology</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3300 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3300">
-        <rdfs:label>Physiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The functions of living organisms and their constituent parts.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 3.1.8 Physiology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3301 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3301">
-        <rdfs:label>Microbiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDefinition>The biology of microorganisms.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.20 Microbiology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3302 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3302">
-        <rdfs:label>Parasitology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The biology of parasites.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3303 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3303">
-        <rdfs:label>Medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasNarrowSynonym>General medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Research in support of healing by diagnosis, treatment, and prevention of disease.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 3.1 Basic medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.2.9 General and internal medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Experimental medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Biomedical research</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Clinical medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.2 Clinical medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Internal medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3304 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3304">
-        <rdfs:label>Neurobiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasBroadSynonym>Neuroscience</oboInOwl:hasBroadSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The study of the nervous system and brain; its anatomy, physiology and function.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.5 Neuroscience</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3305 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3305">
-        <rdfs:label>Public health and epidemiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.3.1 Epidemiology</oboInOwl:hasDbXref>
-        <oboInOwl:hasAlternativeId>Topic concerning the the patterns, cause, and effect of disease within populations.</oboInOwl:hasAlternativeId>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>Public health</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Epidemiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3306 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3306">
-        <rdfs:label>Biophysics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3318"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.9 Biophysics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The use of physics to study biological system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3307 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3307">
-        <rdfs:label>Computational biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasDbXref>VT 1.5.19 Mathematical biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.5.12 Computational biology</oboInOwl:hasDbXref>
-        <rdfs:comment>This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology).</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Mathematical biology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.26 Theoretical biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Theoretical biology</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Biomathematics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3308 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3308">
-        <rdfs:label>Transcriptomics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0203"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0622"/>
-        <oboInOwl:hasDefinition>The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Transcriptome</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3314 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3314">
-        <rdfs:label>Chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasBroadSynonym>VT 1.7.10 Polymer science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.7 Mathematical chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.7.3 Colloid chemistry</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>Mathematical chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Physical chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.9 Physical chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Polymer science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Chemical science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Organic chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.6 Inorganic and nuclear chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.7 Chemical sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.7.5 Electrochemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Inorganic chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.2 Chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Nuclear chemistry</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.7.8 Organic chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The composition and properties of matter, reactions, and the use of reactions to create new substances.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3315 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3315">
-        <rdfs:label>Mathematics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The study of numbers (quantity) and other topics including structure, space, and change.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT:1.1 Mathematics</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Maths</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.1.99 Other</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3316 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3316">
-        <rdfs:label>Computer science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.2 Computer sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 1.2.99 Other</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The theory and practical use of computer systems.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3318 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3318">
-        <rdfs:label>Physics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The study of matter, space and time, and related concepts such as energy and force.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3320 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3320">
-        <rdfs:label>RNA splicing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3321"/>
-        <oboInOwl:hasDefinition>RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3321 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3321">
-        <rdfs:label>Molecular genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The structure and function of genes at a molecular level.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3322 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3322">
-        <rdfs:label>Respiratory medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.25 Respiratory systems</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Pulmonology</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The study of respiratory system.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pulmonary medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Respiratory disease</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasNarrowSynonym>Pulmonary disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3323 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3323">
-        <rdfs:label>Metabolic disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <oboInOwl:hasDefinition>The study of metabolic diseases.</oboInOwl:hasDefinition>
-        <obsolete_since>1.4</obsolete_since>
-        <created_in>1.3</created_in>
-        <owl:deprecated>true</owl:deprecated>
-        <oboInOwl:consider rdf:resource="http://edamontology.org/topic_3407"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#obsolete"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3324 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3324">
-        <rdfs:label>Infectious disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0634"/>
-        <oboInOwl:hasExactSynonym>Transmissable disease</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.3.4 Infectious diseases</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Communicable disease</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions).</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3325 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3325">
-        <rdfs:label>Rare diseases</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0634"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The study of rare diseases.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3332 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3332">
-        <rdfs:label>Computational chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDbXref>VT 1.7.4 Computational chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems.</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3334 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3334">
-        <rdfs:label>Neurology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Neurological disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the anatomy, functions and disorders of the nervous system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3335 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3335">
-        <rdfs:label>Cardiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Cardiovascular disease</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.4 Cardiac and Cardiovascular systems</oboInOwl:hasDbXref>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Cardiovascular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Heart disease</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.22 Peripheral vascular disease</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The diseases and abnormalities of the heart and circulatory system.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3336 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3336">
-        <rdfs:label>Drug discovery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The discovery and design of drugs or potential drug compounds.</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.</rdfs:comment>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3337 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3337">
-        <rdfs:label>Biobank</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <oboInOwl:hasExactSynonym>biobanking</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Repositories of biological samples, typically human, for basic biological and clinical research.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Tissue collection</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3338 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3338">
-        <rdfs:label>Mouse clinic</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3339 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3339">
-        <rdfs:label>Microbial collection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <oboInOwl:hasDefinition>Collections of microbial cells including bacteria, yeasts and moulds.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3340 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3340">
-        <rdfs:label>Cell culture collection</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3341 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3341">
-        <rdfs:label>Clone library</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3277"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasDefinition>Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3342 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3342">
-        <rdfs:label>Translational medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>&apos;translating&apos; the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice.</oboInOwl:hasDefinition>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3343 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3343">
-        <rdfs:label>Compound libraries and screening</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3336"/>
-        <oboInOwl:hasBroadSynonym>Translational medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Chemical library</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Collections of chemicals, typically for use in high-throughput screening experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Compound library</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Chemical screening</oboInOwl:hasNarrowSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3344 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3344">
-        <rdfs:label>Biomedical science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Topic concerning biological science that is (typically) performed in the context of medicine.</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.3 Health sciences</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Health science</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3345 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3345">
-        <rdfs:label>Data identity and mapping</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasExactSynonym>Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases.</oboInOwl:hasExactSynonym>
-        <created_in>1.3</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3346 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3346">
-        <rdfs:label>Sequence search</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0080"/>
-        <created_in>1.3</created_in>
-        <oboInOwl:hasExactSynonym>Sequence database search</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The search and retrieval from a database on the basis of molecular sequence similarity.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3360 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3360">
-        <rdfs:label>Biomarkers</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasExactSynonym>Diagnostic markers</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>Objective indicators of biological state often used to assess health, and determinate treatment.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3361 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3361">
-        <rdfs:label>Laboratory techniques</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0003"/>
-        <oboInOwl:hasDefinition>The procedures used to conduct an experiment.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Lab techniques</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3365 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3365">
-        <rdfs:label>Data architecture, analysis and design</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>The development of policies, models and standards that cover data acquisitioin, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Data analysis</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data design</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Data architecture</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3366 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3366">
-        <rdfs:label>Data integration and warehousing</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasDefinition>The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data.
-
-</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Data integration</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Data warehousing</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3368 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3368">
-        <rdfs:label>Biomaterials</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3297"/>
-        <oboInOwl:hasDefinition>Any matter, surface or construct that interacts with a biological system.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Diagnostic markers</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3369 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3369">
-        <rdfs:label>Chemical biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3371"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The use of synthetic chemistry to study and manipulate biological systems.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3370 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3370">
-        <rdfs:label>Analytical chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The study of the separation, identification, and quantification of the chemical components of natural and artificial materials.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 1.7.1 Analytical chemistry</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3371 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3371">
-        <rdfs:label>Synthetic chemistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3314"/>
-        <oboInOwl:hasExactSynonym>Synthetic organic chemistry</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The use of chemistry to create new compounds.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3372 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3372">
-        <rdfs:label>Software engineering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasDbXref>VT 1.2.1 Algorithms</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym> Programming languages</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.2.7 Data structures</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Software development</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>Software engineering</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Computer programming</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>1.2.12 Programming languages</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The process that leads from an original formulation of a computing problem to executable programs.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Data structures</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Algorithms</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 1.2.14 Software engineering</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3373 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3373">
-        <rdfs:label>Drug development</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Medicine development</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The process of bringing a new drug to market once a lead compounds has been identified through drug discovery.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Drug development science</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Medicines development</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3374 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3374">
-        <rdfs:label>Drug formulation and delivery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Drug delivery</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Drug formulation</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3375 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3375">
-        <rdfs:label>Pharmacokinetics and pharmacodynamics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasNarrowSynonym>Pharmacodynamics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Pharmacokinetics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Drug distribution</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Drug excretion</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of how a drug interacts with the body.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Drug absorption</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>ADME</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Drug metabolism</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasNarrowSynonym>Drug metabolism</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3376 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3376">
-        <rdfs:label>Medicines research and development</rdfs:label>
-        <rdfs:label>Medicine research and development</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasDefinition>The discovery, development and approval of medicines.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Health care research</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>Drug discovery and development</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasBroadSynonym>Health care science</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3377 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3377">
-        <rdfs:label>Safety sciences</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Drug safety</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The safety (or lack) of drugs and other medical interventions.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3378 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3378">
-        <rdfs:label>Pharmacovigilence</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3377"/>
-        <created_in>1.4</created_in>
-        <rdfs:comment>Pharmacovigilence concerns safety once a drug has gone to market.</rdfs:comment>
-        <oboInOwl:hasDefinition>The detection, assesment, understanding and prevention of adverse effects of medicines.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3379 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3379">
-        <rdfs:label>Preclinical and clinical studies</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Preclinical studies</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Clinical studies</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3382 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3382">
-        <rdfs:label>Imaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <rdfs:comment>This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as  X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Microscopy imaging</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Diffraction experiment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The visual representation of an object.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3383 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3383">
-        <rdfs:label>Biological imaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The use of imaging techniques to understand biology.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3384 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3384">
-        <rdfs:label>Medical imaging</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDbXref>VT 3.2.24 Radiology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The use of imaging techniques for clinical purposes for medical research.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Radiology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.14 Nuclear medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Nuclear medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.13 Medical imaging</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3385 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3385">
-        <rdfs:label>Light microscopy</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The use of optical instruments to magnify the image of an object.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3386 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3386">
-        <rdfs:label>Laboratory animal science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The use of animals and alternatives in experimental research.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3387 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3387">
-        <rdfs:label>Marine biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.18 Marine and Freshwater biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The study of organisms in the ocean or brackish waters.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3388 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3388">
-        <rdfs:label>Molecular medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3342"/>
-        <oboInOwl:hasDefinition>The identification of molecular and genetic causes of disease and the development of interventions to correct them.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3390 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3390">
-        <rdfs:label>Nutritional science</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 3.3.7 Nutrition and Dietetics</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Dietetics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals.  It also includes the study of human behaviours related to food choices.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Nutrition science</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3391 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3391">
-        <rdfs:label>Omics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <oboInOwl:hasDefinition>The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3393 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3393">
-        <rdfs:label>Quality affairs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The processes that need to be in place to ensure the quality of products for human or animal use.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Good clinical practice</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Good manufacturing practice</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Quality assurance</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Good laboratory practice</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3394 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3394">
-        <rdfs:label>Regulatory affairs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3376"/>
-        <oboInOwl:hasDefinition>The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3395 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3395">
-        <rdfs:label>Regnerative medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3344"/>
-        <oboInOwl:hasExactSynonym>Stem cell research</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Biomedical approaches to clinical interventions that involve the use of stem cells.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3396 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3396">
-        <rdfs:label>Systems medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3397 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3397">
-        <rdfs:label>Veterinary medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasAlternativeId>Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals.</oboInOwl:hasAlternativeId>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3398 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3398">
-        <rdfs:label>Bioengineering</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3297"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The application of biological concepts and methods to the analytical and synthetic methodologies of engineering.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Diagnostic markers</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3399 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3399">
-        <rdfs:label>Geriatric medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.10 Geriatrics and gerontology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Ageing</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Aging</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasBroadSynonym>Gerontology</oboInOwl:hasBroadSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Geriatrics</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3400 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3400">
-        <rdfs:label>Allergy, clinical immunology and immunotherapeutics.</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.1 Allergy</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>Health issues related to the immune system and their prevention, diagnosis and mangement.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Immune disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Clinical immunology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Immunomodulators</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Allergy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Immunotherapeutics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3401 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3401">
-        <rdfs:label>Pain medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Ageing</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasExactSynonym>Algiatry</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3402 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3402">
-        <rdfs:label>Anaesthesiology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Anaesthetics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Anaesthesia and anaesthetics.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 3.2.2 Anaesthesiology</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3403 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3403">
-        <rdfs:label>Critical care medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Acute medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Geriatrics</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.5 Critical care/Emergency medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Emergency medicine</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The multidisciplinary that cares for patients with acute, life-threatening illness or injury.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3404 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3404">
-        <rdfs:label>Dermatology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Dermatological disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDbXref>VT 3.2.7 Dermatology and venereal diseases</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3405 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3405">
-        <rdfs:label>Dentistry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3406 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3406">
-        <rdfs:label>Ear, nose and throat medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Otolaryngology</oboInOwl:hasExactSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Otorhinolaryngology</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Head and neck disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.20 Otorhinolaryngology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Audiovestibular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3407 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3407">
-        <rdfs:label>Endocrinology and metabolism</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Metabolic disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Metabolism</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Endocrinology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Endocrine disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3408 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3408">
-        <rdfs:label>Haematology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.11 Hematology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the blood, blood-forming organs and blood diseases.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Haematological disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Blood disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3409 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3409">
-        <rdfs:label>Gastroenterology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Gastrointestinal disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.8 Gastroenterology and hepatology</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3410 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3410">
-        <rdfs:label>Gender medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3411 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3411">
-        <rdfs:label>Gynaecology and obstetrics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDbXref>VT 3.2.15 Obstetrics and gynaecology</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Gynaecology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Gynaecological disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Obstetrics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3412 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3412">
-        <rdfs:label>Hepatic and biliary medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasExactSynonym>Hepatobiliary medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasNarrowSynonym>Liver disorders</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the liver, gallbladder, bile ducts and bile.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3413 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3413">
-        <rdfs:label>Infectious tropical disease</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3324"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the infectious diseases of the tropics. </oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3414 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3414">
-        <rdfs:label>Trauma medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3415 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3415">
-        <rdfs:label>Medical toxicology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3416 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3416">
-        <rdfs:label>Musculoskeletal medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue.  It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.26 Rheumatology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.2.19 Orthopaedics</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Musculoskeletal disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Orthopaedics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Rheumatology</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3417 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3417">
-        <rdfs:label>Opthalmology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Eye disoders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.18 Optometry</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasBroadSynonym>Optometry</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.17 Ophthalmology</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Audiovestibular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3418 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3418">
-        <rdfs:label>Paediatrics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the medical care of infants, children and adolescents.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.21 Paediatrics</oboInOwl:hasDbXref>
-        <oboInOwl:hasExactSynonym>Child health</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3419 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3419">
-        <rdfs:label>Psychiatry</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Psychiatric disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.23 Psychiatry</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Mental health</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3420 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3420">
-        <rdfs:label>Reproductive health</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Reproductive disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Audiovestibular medicine</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.3 Andrology</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Andrology</oboInOwl:hasNarrowSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Family planning</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The health of the reproductive processes, functions and systems at all stages of life.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Fertility medicine</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3421 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3421">
-        <rdfs:label>Surgery</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasNarrowSynonym>Transplantation</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.2.28 Transplantation</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance.</oboInOwl:hasDefinition>
-        <created_in>1.4</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3422 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3422">
-        <rdfs:label>Urology and nephrology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.29 Urology and nephrology</oboInOwl:hasDbXref>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasNarrowSynonym>Urology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Kidney disease</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Urological disorders</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Nephrology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3423 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3423">
-        <rdfs:label>Complementary medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <oboInOwl:hasDefinition>Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.2.12 Integrative and Complementary medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasBroadSynonym>Holistic medicine</oboInOwl:hasBroadSynonym>
-        <created_in>1.4</created_in>
-        <oboInOwl:hasBroadSynonym>Alternative medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Integrative medicine</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3444 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3444">
-        <rdfs:label>MRI</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasExactSynonym>Nuclear magnetic resonance imaging</oboInOwl:hasExactSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>MRT</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Magnetic resonance tomography</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>NMRI</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Magnetic resonance imaging
-</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3448 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3448">
-        <rdfs:label>Neutron diffraction</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_1317"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasDefinition>The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Neutron microscopy</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Elastic neutron scattering</oboInOwl:hasNarrowSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasExactSynonym>Neutron diffraction experiment</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3452 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3452">
-        <rdfs:label>Tomography</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3382"/>
-        <oboInOwl:hasNarrowSynonym>X-ray tomography</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram).</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Electron tomography</oboInOwl:hasNarrowSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3473 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3473">
-        <rdfs:label>Data mining</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDbXref>VT 1.3.2 Data mining</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>KDD</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasBroadSynonym>Knowledge discovery in databases</oboInOwl:hasBroadSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3474 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3474">
-        <rdfs:label>Machine learning</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3316"/>
-        <oboInOwl:hasDefinition>A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Artificial Intelligence</oboInOwl:hasBroadSynonym>
-        <created_in>1.7</created_in>
-        <oboInOwl:hasDbXref>VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics)</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3489 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3489">
-        <rdfs:label>Database management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasNarrowSynonym>Data maintenance</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasExactSynonym>Databases</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Database administration</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources.
-</oboInOwl:hasDefinition>
-        <rdfs:comment>This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature.</rdfs:comment>
-        <oboInOwl:hasNarrowSynonym>Biological databases</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3500 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3500">
-        <rdfs:label>Animals</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2818"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasBroadSynonym>Animal biology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasDefinition>Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation.</oboInOwl:hasDefinition>
-        <oboInOwl:hasBroadSynonym>Zoology</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym>Animal</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDbXref>VT 1.5.29 Zoology</oboInOwl:hasDbXref>
-        <rdfs:comment>The resource may be specific to a plant, a group of plants or all plants.</rdfs:comment>
-        <oboInOwl:hasExactSynonym>Metazoa</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3510 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3510">
-        <rdfs:label>Protein sites, features and motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:hasNarrowSynonym>Protein sequence features</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Protein functional sites</oboInOwl:hasNarrowSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3511 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3511">
-        <rdfs:label>Nucleic acid sites, features and motifs</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0160"/>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid sequence features</oboInOwl:hasNarrowSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasNarrowSynonym>Nucleic acid functional sites</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3512 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3512">
-        <rdfs:label>Gene transcript features</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0099"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0114"/>
-        <oboInOwl:hasExactSynonym>Nucleic acid features (mRNA features)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>mRNA features</oboInOwl:hasExactSynonym>
-        <rdfs:comment>This includes 5&apos;untranslated region (5&apos;UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3&apos;untranslated regions (3&apos;UTR).</rdfs:comment>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3514 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3514">
-        <rdfs:label>Protein-ligand interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0128"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Protein-ligand (small molecule) interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3515 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3515">
-        <rdfs:label>Protein-drug interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3514"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Protein-drug interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3516 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3516">
-        <rdfs:label>Genotyping experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3517 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3517">
-        <rdfs:label>GWAS study</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Genome-wide association study experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Genome-wide association study</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3518 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3518">
-        <rdfs:label>Microarray experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <rdfs:comment>This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates.</rdfs:comment>
-        <oboInOwl:hasDefinition>Microarray experiments including conditions, protocol, sample:data relationships etc.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3519 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3519">
-        <rdfs:label>PCR experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>PCR experiments, e.g. quantitative real-time PCR.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3520 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3520">
-        <rdfs:label>Proteomics experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <oboInOwl:hasDefinition>Proteomics experiments.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3521 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3521">
-        <rdfs:label>2D PAGE experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3520"/>
-        <oboInOwl:hasDefinition>Two-dimensional gel electrophoresis experiments, gels or spots in a gel.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3522 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3522">
-        <rdfs:label>Northern blot experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3520"/>
-        <oboInOwl:hasDefinition>Northern Blot experiments.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3523 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3523">
-        <rdfs:label>RNAi experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3168"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>RNAi experiments.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3524 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3524">
-        <rdfs:label>Simulation experiment</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3361"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3525 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3525">
-        <rdfs:label>Protein-nucleic acid interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0128"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Protein-DNA/RNA interaction(s).</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3526 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3526">
-        <rdfs:label>Protein-protein interactions</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0128"/>
-        <oboInOwl:hasNarrowSynonym>Domain-domain interactions</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Protein-protein interaction(s), including interactions between protein domains.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasNarrowSynonym>Protein interaction networks</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3527 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3527">
-        <rdfs:label>Cellular process pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Cellular process pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3528 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3528">
-        <rdfs:label>Disease pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Disease pathways, typically of human disease.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Pathway or network (disease)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3529 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3529">
-        <rdfs:label>Environmental information processing pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasDefinition>Environmental information processing pathways.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Pathway or network (environmental information processing)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3530 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3530">
-        <rdfs:label>Genetic information processing pathways</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0602"/>
-        <oboInOwl:hasExactSynonym>Pathway or network (genetic information processing)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Genetic information processing pathways.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3531 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3531">
-        <rdfs:label>Protein super-secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasDefinition>Super-secondary structure of protein sequence(s).</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (super-secondary)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <rdfs:comment>Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.</rdfs:comment>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3533 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3533">
-        <rdfs:label>Protein active sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasExactSynonym>Enzyme active site</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (active sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Catalytic residues (active site) of an enzyme.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3534 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3534">
-        <rdfs:label>Protein binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasDefinition>Ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (binding sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3535 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3535">
-        <rdfs:label>Protein-nucleic acid binding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0166"/>
-        <oboInOwl:hasDefinition>RNA and DNA-binding proteins and binding sites in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (nucleic acid binding sites)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3536 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3536">
-        <rdfs:label>Protein cleavage sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasDefinition>Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (cleavage sites)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3537 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3537">
-        <rdfs:label>Protein chemical modifications</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasDefinition>Chemical modification of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (chemical modifications)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasRelatedSynonym>MOD:00000</oboInOwl:hasRelatedSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasRelatedSynonym>GO:0006464</oboInOwl:hasRelatedSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3538 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3538">
-        <rdfs:label>Protein disordered structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasDefinition>Disordered structure in a protein.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (disordered structure)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3539 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3539">
-        <rdfs:label>Protein domains</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0736"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <rdfs:comment>The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc.</rdfs:comment>
-        <oboInOwl:hasDefinition>Structural domains or 3D folds in a protein or polypeptide chain.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein structural domains</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Protein features (domains)</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3540 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3540">
-        <rdfs:label>Protein key folding sites</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_0130"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasExactSynonym>Protein features (key folding sites)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasDefinition>Key residues involved in protein folding.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3541 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3541">
-        <rdfs:label>Protein post-translational modifications</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasExactSynonym>Protein features (post-translation modifications)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasExactSynonym>Post-translation modifications</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Post-translation modifications in a protein sequence, typically describing the specific sites involved.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3542 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3542">
-        <rdfs:label>Protein secondary structure</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_2814"/>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <rdfs:comment>The location and size of the secondary structure elements and intervening loop regions is typically given.  The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks).</rdfs:comment>
-        <oboInOwl:hasDefinition>Secondary structure (predicted or real) of a protein.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein features (secondary structure)</oboInOwl:hasExactSynonym>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3543 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3543">
-        <rdfs:label>Protein sequence repeats</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <created_in>1.8</created_in>
-        <oboInOwl:hasExactSynonym>Protein features (repeats)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Short repetitive subsequences (repeat sequences) in a protein sequence.</oboInOwl:hasDefinition>
-        <oboInOwl:hasExactSynonym>Protein repeats</oboInOwl:hasExactSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3544 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3544">
-        <rdfs:label>Protein signal peptides</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3510"/>
-        <oboInOwl:hasExactSynonym>Protein features (signal peptides)</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasDefinition>Signal peptides or signal peptide cleavage sites in protein sequences.</oboInOwl:hasDefinition>
-        <created_in>1.8</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3569 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3569">
-        <rdfs:label>Applied mathematics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3315"/>
-        <oboInOwl:hasDbXref>VT 1.1.1 Applied mathematics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3570 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3570">
-        <rdfs:label>Pure mathematics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3315"/>
-        <oboInOwl:hasDbXref>VT 1.1.1 Pure mathematics</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The study of abstract mathematical concepts.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3571 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3571">
-        <rdfs:label>Data governance</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <oboInOwl:hasExactSynonym>Data handling</oboInOwl:hasExactSynonym>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D030541</rdfs:seeAlso>
-        <oboInOwl:hasDefinition>The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints.</oboInOwl:hasDefinition>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasNarrowSynonym>Data stewardship</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3572 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3572">
-        <rdfs:label>Data quality management</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3071"/>
-        <rdfs:seeAlso>http://purl.bioontology.org/ontology/MSH/D030541</rdfs:seeAlso>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasNarrowSynonym>Data quality</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data integrity</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data clean-up</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasNarrowSynonym>Data enrichment</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>The quality, integrity, cleaning up and enrichment of data. </oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3573 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3573">
-        <rdfs:label>Freshwater biology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3070"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDbXref>VT 1.5.18 Marine and Freshwater biology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDefinition>The study of organisms in freshwater ecosystems.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3574 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3574">
-        <rdfs:label>Human genetics</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3053"/>
-        <oboInOwl:hasDefinition>The study of inheritatnce in human beings.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.1.2 Human genetics</oboInOwl:hasDbXref>
-        <created_in>1.10</created_in>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3575 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3575">
-        <rdfs:label>Tropical medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Health problems that are prevalent in tropical and subtropical regions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasDbXref>VT 3.3.14 Tropical medicine</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3576 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3576">
-        <rdfs:label>Medical biotechnology</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3297"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDbXref>VT 3.4.1 Biomedical devices</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.4.2 Health-related biotechnology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.4 Medical biotechnology</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>VT 3.3.14 Tropical medicine</oboInOwl:hasDbXref>
-        <oboInOwl:hasNarrowSynonym>Pharmaceutical biotechnology</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDefinition>Biotechnology applied to the medical sciences and the development of medicines.</oboInOwl:hasDefinition>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://edamontology.org/topic_3577 -->
-
-    <owl:Class rdf:about="http://edamontology.org/topic_3577">
-        <rdfs:label>Personalized medicine</rdfs:label>
-        <rdfs:subClassOf rdf:resource="http://edamontology.org/topic_3303"/>
-        <created_in>1.10</created_in>
-        <oboInOwl:hasDefinition>Health problems that are prevalent in tropical and subtropical regions.</oboInOwl:hasDefinition>
-        <oboInOwl:hasNarrowSynonym>Molecular diagnostics</oboInOwl:hasNarrowSynonym>
-        <oboInOwl:hasDbXref>VT 3.4.5 Molecular diagnostics</oboInOwl:hasDbXref>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#edam"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#events"/>
-        <oboInOwl:inSubset rdf:resource="&oboOther;edam#topics"/>
-    </owl:Class>
-    
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#ObsoleteClass -->
-
-    <owl:Class rdf:about="&oboInOwl;ObsoleteClass">
-        <rdfs:label>Obsolete concept (EDAM)</rdfs:label>
-        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>
-        <rdfs:subClassOf rdf:resource="&owl;DeprecatedClass"/>
-        <created_in>1.2</created_in>
-        <rdfs:comment>Needed for conversion to the OBO format.</rdfs:comment>
-        <oboInOwl:hasDefinition>An obsolete concept (redefined in EDAM).</oboInOwl:hasDefinition>
-        <owl:deprecated>true</owl:deprecated>
-    </owl:Class>
-    
-
-
-    <!-- http://www.w3.org/2002/07/owl#DeprecatedClass -->
-
-    <owl:Class rdf:about="&owl;DeprecatedClass"/>
-</rdf:RDF>
-
-
-
-<!-- Generated by the OWL API (version 3.4.2) http://owlapi.sourceforge.net -->
-
diff --git a/cwl/src/test/resources/cwl/ontology/gx_edam.ttl b/cwl/src/test/resources/cwl/ontology/gx_edam.ttl
deleted file mode 100644
index 8182f719d21..00000000000
--- a/cwl/src/test/resources/cwl/ontology/gx_edam.ttl
+++ /dev/null
@@ -1,7 +0,0 @@
-@prefix gx: <http://galaxyproject.org/formats/> .
-@prefix owl: <http://www.w3.org/2002/07/owl#> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix edam: <http://edamontology.org/> .
-
-gx:fasta a owl:Class .
-gx:fasta owl:equivalentClass edam:format_1929 .
diff --git a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/complex_workflow/expected_result.json
deleted file mode 100644
index fd297c8da92..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/expected_result.json
+++ /dev/null
@@ -1,204 +0,0 @@
-{
-  "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2",
-  "class" : "Workflow",
-  "requirements" : [
-    {
-      "class" : "StepInputExpressionRequirement"
-    }
-  ],
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/tool"
-    }
-  ],
-  "outputs" : [
-  ],
-  "steps" : [
-    {
-      "run" : {
-        "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1",
-        "class" : "Workflow",
-        "requirements" : [
-          {
-            "class" : "StepInputExpressionRequirement"
-          }
-        ],
-        "inputs" : [
-          {
-            "type" : "File",
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/tool"
-          }
-        ],
-        "outputs" : [
-        ],
-        "steps" : [
-          {
-            "run" : {
-              "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1",
-              "class" : "Workflow",
-              "requirements" : [
-                {
-                  "class" : "StepInputExpressionRequirement"
-                }
-              ],
-              "inputs" : [
-                {
-                  "type" : "File",
-                  "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool"
-                }
-              ],
-              "outputs" : [
-              ],
-              "steps" : [
-                {
-                  "run" : {
-                    "cwlVersion" : "v1.0",
-                    "class" : "CommandLineTool",
-                    "baseCommand" : [
-                      "echo"
-                    ],
-                    "inputs" : [
-                      {
-                        "type" : "string",
-                        "inputBinding" : {
-                          "position" : 1
-                        },
-                        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-                      }
-                    ],
-                    "outputs" : [
-                      {
-                        "type" : "string",
-                        "valueFrom" : "hello",
-                        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-                      }
-                    ],
-                    "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-                  },
-                  "in" : [
-                    {
-                      "valueFrom" : "$(inputs.tool.nameroot)",
-                      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/in"
-                    },
-                    {
-                      "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool",
-                      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/tool"
-                    }
-                  ],
-                  "out" : [
-                    "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/out"
-                  ],
-                  "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root"
-                }
-              ]
-            },
-            "in" : [
-              {
-                "valueFrom" : "$(inputs.tool.nameroot)",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root/in"
-              },
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/tool",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root/tool"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root/out"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/sub/sub_workflow.cwl#sub-echo-workflow-1/root"
-          }
-        ]
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/tool",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root1"
-    },
-    {
-      "run" : {
-        "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1",
-        "class" : "Workflow",
-        "requirements" : [
-          {
-            "class" : "StepInputExpressionRequirement"
-          }
-        ],
-        "inputs" : [
-          {
-            "type" : "File",
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool"
-          }
-        ],
-        "outputs" : [
-        ],
-        "steps" : [
-          {
-            "run" : {
-              "cwlVersion" : "v1.0",
-              "class" : "CommandLineTool",
-              "baseCommand" : [
-                "echo"
-              ],
-              "inputs" : [
-                {
-                  "type" : "string",
-                  "inputBinding" : {
-                    "position" : 1
-                  },
-                  "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-                }
-              ],
-              "outputs" : [
-                {
-                  "type" : "string",
-                  "valueFrom" : "hello",
-                  "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-                }
-              ],
-              "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-            },
-            "in" : [
-              {
-                "valueFrom" : "$(inputs.tool.nameroot)",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/in"
-              },
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/tool",
-                "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/tool"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root/out"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-1/root"
-          }
-        ]
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/tool",
-          "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/complex_workflow/root_workflow.cwl#echo-workflow-2/root2"
-    }
-  ]
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/complex_workflow/root_workflow.cwl
deleted file mode 100644
index 6aa8f741dad..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/root_workflow.cwl
+++ /dev/null
@@ -1,41 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root1:
-      run: "sub/sub_workflow.cwl#sub-echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-    root2:
-      run: "#echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: echo-workflow-1
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: ../echo_tool.cwl
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/sub/sub_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/complex_workflow/sub/sub_workflow.cwl
deleted file mode 100644
index de293ab19ce..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/complex_workflow/sub/sub_workflow.cwl
+++ /dev/null
@@ -1,34 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: sub-echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: ../../echo_tool.cwl
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: sub-echo-workflow-1
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "../root_workflow.cwl#echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/expected_result.json
deleted file mode 100644
index 59fea901d3b..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/expected_result.json
+++ /dev/null
@@ -1,132 +0,0 @@
-{
-  "class" : "Workflow",
-  "cwlVersion" : "v1.0",
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#file1"
-    }
-  ],
-  "outputs" : [
-    {
-      "type" : "int",
-      "outputSource" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/count_output",
-      "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#count_output"
-    }
-  ],
-  "requirements" : [
-    {
-      "class" : "SubworkflowFeatureRequirement"
-    }
-  ],
-  "steps" : [
-    {
-      "in" : [
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#file1",
-          "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/file1"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/count_output"
-      ],
-      "run" : {
-        "class" : "Workflow",
-        "inputs" : [
-          {
-            "type" : "File",
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/file1"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "int",
-            "outputSource" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2/output",
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/count_output"
-          }
-        ],
-        "steps" : [
-          {
-            "run" : {
-              "class" : "CommandLineTool",
-              "cwlVersion" : "v1.0",
-              "inputs" : [
-                {
-                  "type" : "File",
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/wc-tool.cwl#file1"
-                }
-              ],
-              "outputs" : [
-                {
-                  "type" : "File",
-                  "outputBinding" : {
-                    "glob" : "output"
-                  },
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/wc-tool.cwl#output"
-                }
-              ],
-              "baseCommand" : [
-                "wc",
-                "-l"
-              ],
-              "stdin" : "$(inputs.file1.path)",
-              "stdout" : "output",
-              "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/wc-tool.cwl"
-            },
-            "in" : [
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/file1",
-                "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1/file1"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1/output"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1"
-          },
-          {
-            "run" : {
-              "class" : "ExpressionTool",
-              "requirements" : [
-                {
-                  "class" : "InlineJavascriptRequirement"
-                }
-              ],
-              "cwlVersion" : "v1.0",
-              "inputs" : [
-                {
-                  "type" : "File",
-                  "inputBinding" : {
-                    "loadContents" : true
-                  },
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/parseInt-tool.cwl#file1"
-                }
-              ],
-              "outputs" : [
-                {
-                  "type" : "int",
-                  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/parseInt-tool.cwl#output"
-                }
-              ],
-              "expression" : "$({'output': parseInt(inputs.file1.contents)})",
-              "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/parseInt-tool.cwl"
-            },
-            "in" : [
-              {
-                "source" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step1/output",
-                "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2/file1"
-              }
-            ],
-            "out" : [
-              "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2/output"
-            ],
-            "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>/step2"
-          }
-        ],
-        "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0/<<RANDOM_UUID>>"
-      },
-      "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl#step0"
-    }
-  ],
-  "id" : "file://<<RESOURCES_ROOT>>/deep_nesting/root_workflow.cwl"
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/parseInt-tool.cwl b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/parseInt-tool.cwl
deleted file mode 100644
index 15460db136b..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/parseInt-tool.cwl
+++ /dev/null
@@ -1,14 +0,0 @@
-class: ExpressionTool
-requirements:
-  - class: InlineJavascriptRequirement
-cwlVersion: v1.0
-
-inputs:
-  file1:
-    type: File
-    inputBinding: { loadContents: true }
-
-outputs:
-  output: int
-
-expression: "$({'output': parseInt(inputs.file1.contents)})"
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/root_workflow.cwl
deleted file mode 100644
index 9d3d313c348..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/root_workflow.cwl
+++ /dev/null
@@ -1,21 +0,0 @@
-class: Workflow
-cwlVersion: v1.0
-inputs:
-  file1: File
-outputs:
-  count_output: {type: int, outputSource: step0/count_output}
-requirements:
-  SubworkflowFeatureRequirement: {}
-steps:
-  step0:
-    in: {file1: file1}
-    out: [count_output]
-    run:
-      class: Workflow
-      inputs:
-        file1: File
-      outputs:
-        count_output: {type: int, outputSource: step2/output}
-      steps:
-        step1: {run: wc-tool.cwl, in: {file1: file1}, out: [output]}
-        step2: {run: parseInt-tool.cwl, in: {file1: step1/output}, out: [output]}
diff --git a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/wc-tool.cwl b/cwl/src/test/resources/cwl/preprocessor/deep_nesting/wc-tool.cwl
deleted file mode 100644
index 3eb09378514..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/deep_nesting/wc-tool.cwl
+++ /dev/null
@@ -1,15 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-
-inputs:
-  file1: File
-
-outputs:
-  output:
-    type: File
-    outputBinding: { glob: output }
-
-baseCommand: [wc, -l]
-
-stdin: $(inputs.file1.path)
-stdout: output
diff --git a/cwl/src/test/resources/cwl/preprocessor/echo_tool.cwl b/cwl/src/test/resources/cwl/preprocessor/echo_tool.cwl
deleted file mode 100644
index f253c2a435f..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/echo_tool.cwl
+++ /dev/null
@@ -1,13 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: [echo]
-inputs:
-  in:
-    type: string
-    inputBinding:
-      position: 1
-outputs:
-  out:
-    type: string
-    valueFrom: "hello"
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/same_file_cyclic_dependency/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/same_file_cyclic_dependency/root_workflow.cwl
deleted file mode 100644
index fddea7eb644..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/same_file_cyclic_dependency/root_workflow.cwl
+++ /dev/null
@@ -1,34 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "#echo-workflow-1"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: echo-workflow-1
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "#echo-workflow-2"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/self_reference/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/self_reference/expected_result.json
deleted file mode 100644
index f6c98537192..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/self_reference/expected_result.json
+++ /dev/null
@@ -1,58 +0,0 @@
-{
-  "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2",
-  "class" : "Workflow",
-  "requirements" : [
-    {
-      "class" : "StepInputExpressionRequirement"
-    }
-  ],
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/tool"
-    }
-  ],
-  "outputs" : [
-  ],
-  "steps" : [
-    {
-      "run" : {
-        "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-tool",
-        "class" : "CommandLineTool",
-        "baseCommand" : [
-          "echo"
-        ],
-        "inputs" : [
-          {
-            "type" : "string",
-            "inputBinding" : {
-              "position" : 1
-            },
-            "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-tool/in"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "string",
-            "valueFrom" : "hello",
-            "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-tool/out"
-          }
-        ]
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/tool",
-          "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/self_reference/root_workflow.cwl#echo-workflow-2/root"
-    }
-  ]
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/self_reference/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/self_reference/root_workflow.cwl
deleted file mode 100644
index 06a70f19f01..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/self_reference/root_workflow.cwl
+++ /dev/null
@@ -1,31 +0,0 @@
-cwlVersion: v1.0
-$graph:
-- id: echo-workflow-2
-  class: Workflow
-  requirements:
-    - class: StepInputExpressionRequirement
-  inputs:
-    tool: File
-  outputs: []
-  steps:
-    root:
-      run: "#echo-tool"
-      in:
-        tool: tool
-        in:
-          valueFrom: $(inputs.tool.nameroot)
-      out: [out]
-
-- id: echo-tool
-  class: CommandLineTool
-  baseCommand: [echo]
-  inputs:
-    in:
-      type: string
-      inputBinding:
-        position: 1
-  outputs:
-    out:
-      type: string
-      valueFrom: "hello"
-      
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/expected_result.json b/cwl/src/test/resources/cwl/preprocessor/simple_workflow/expected_result.json
deleted file mode 100644
index 82176bc4177..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/expected_result.json
+++ /dev/null
@@ -1,100 +0,0 @@
-{
-  "cwlVersion" : "v1.0",
-  "class" : "Workflow",
-  "requirements" : [
-    {
-      "class" : "StepInputExpressionRequirement"
-    }
-  ],
-  "inputs" : [
-    {
-      "type" : "File",
-      "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#tool"
-    }
-  ],
-  "outputs" : [
-  ],
-  "steps" : [
-    {
-      "run" : {
-        "cwlVersion" : "v1.0",
-        "class" : "CommandLineTool",
-        "baseCommand" : [
-          "echo"
-        ],
-        "inputs" : [
-          {
-            "type" : "string",
-            "inputBinding" : {
-              "position" : 1
-            },
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "string",
-            "valueFrom" : "hello",
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-          }
-        ],
-        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#tool",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step1"
-    },
-    {
-      "run" : {
-        "cwlVersion" : "v1.0",
-        "class" : "CommandLineTool",
-        "baseCommand" : [
-          "echo"
-        ],
-        "inputs" : [
-          {
-            "type" : "string",
-            "inputBinding" : {
-              "position" : 1
-            },
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#in"
-          }
-        ],
-        "outputs" : [
-          {
-            "type" : "string",
-            "valueFrom" : "hello",
-            "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl#out"
-          }
-        ],
-        "id" : "file://<<RESOURCES_ROOT>>/echo_tool.cwl"
-      },
-      "in" : [
-        {
-          "valueFrom" : "$(inputs.tool.nameroot)",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2/in"
-        },
-        {
-          "source" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#tool",
-          "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2/tool"
-        }
-      ],
-      "out" : [
-        "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2/out"
-      ],
-      "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl#step2"
-    }
-  ],
-  "id" : "file://<<RESOURCES_ROOT>>/simple_workflow/root_workflow.cwl"
-}
diff --git a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/simple_workflow/root_workflow.cwl
deleted file mode 100644
index 86ba8b08658..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/simple_workflow/root_workflow.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-   tool: File
-outputs: []
-steps:
-  step1:
-    run: ../echo_tool.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-  step2:
-    run: ../echo_tool.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/root_workflow.cwl b/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/root_workflow.cwl
deleted file mode 100644
index 8871f99a932..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/root_workflow.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-  tool: File
-outputs: []
-steps:
-  root:
-    run: sub_workflow_1.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_1.cwl b/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_1.cwl
deleted file mode 100644
index 13f85d169b5..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_1.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-  tool: File
-outputs: []
-steps:
-  root:
-    run: sub_workflow_2.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_2.cwl b/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_2.cwl
deleted file mode 100644
index 0d8c5a49691..00000000000
--- a/cwl/src/test/resources/cwl/preprocessor/transitive_cyclic_dependency/sub_workflow_2.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-requirements:
-  - class: StepInputExpressionRequirement
-inputs:
-  tool: File
-outputs: []
-steps:
-  root:
-    run: root_workflow.cwl
-    in:
-      tool: tool
-      in:
-        valueFrom: $(inputs.tool.nameroot)
-    out: [out]
-    
\ No newline at end of file
diff --git a/cwl/src/test/resources/dir_example.cwl b/cwl/src/test/resources/dir_example.cwl
deleted file mode 100644
index 70efc02596a..00000000000
--- a/cwl/src/test/resources/dir_example.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-requirements:
-  - class: ShellCommandRequirement
-inputs:
-  - id: indir
-    type: Directory
-    default:
-      class: Directory
-      location: exampledir
-outputs:
-  outlist:
-    type: File
-    outputBinding:
-      glob: output.txt
-arguments: ["echo", "$(inputs.indir.basename)"]
-stdout: output.txt
diff --git a/cwl/src/test/resources/env.cwl b/cwl/src/test/resources/env.cwl
deleted file mode 100644
index 19a23e77948..00000000000
--- a/cwl/src/test/resources/env.cwl
+++ /dev/null
@@ -1,10 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: env
-requirements:
-  EnvVarRequirement:
-    envDef:
-      HELLO: $(inputs.message)
-inputs:
-  message: string
-outputs: []
diff --git a/cwl/src/test/resources/exampledir/example.txt b/cwl/src/test/resources/exampledir/example.txt
deleted file mode 100644
index 3b18e512dba..00000000000
--- a/cwl/src/test/resources/exampledir/example.txt
+++ /dev/null
@@ -1 +0,0 @@
-hello world
diff --git a/cwl/src/test/resources/file_example.cwl b/cwl/src/test/resources/file_example.cwl
deleted file mode 100644
index 6245d3232be..00000000000
--- a/cwl/src/test/resources/file_example.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-requirements:
-  - class: ShellCommandRequirement
-inputs:
-  - id: infile
-    type: File
-    default:
-      class: File
-      location: exampledir/example.txt
-outputs:
-  outlist:
-    type: File
-    outputBinding:
-      glob: output.txt
-arguments: ["echo", "$(inputs.infile.basename)"]
-stdout: output.txt
diff --git a/cwl/src/test/resources/file_size_example.cwl b/cwl/src/test/resources/file_size_example.cwl
deleted file mode 100644
index 3b24a1f5cdd..00000000000
--- a/cwl/src/test/resources/file_size_example.cwl
+++ /dev/null
@@ -1,18 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-requirements:
-  - class: ShellCommandRequirement
-inputs:
-  - id: infile
-    type: File
-    default:
-      class: File
-      location: exampledir/example.txt
-outputs:
-  outlist:
-    type: File
-    outputBinding:
-      glob: output.txt
-# size is optional according to the spec, however there are real world CWLs using it
-arguments: ["echo", "$(inputs.infile.size)"]
-stdout: output.txt
diff --git a/cwl/src/test/resources/links_dont_parse.cwl b/cwl/src/test/resources/links_dont_parse.cwl
deleted file mode 100644
index 2cab593fce8..00000000000
--- a/cwl/src/test/resources/links_dont_parse.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-inputs:
-  inp: File
-  ex: string
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classfile
-
-steps:
-  untar:
-    run: bad.cwl
-    in:
-      tarfile: inp
-      extractfile: ex
-    out: [example_out]
-
-  compile:
-    run: bad2.cwl
-    in:
-      src: untar/example_out
-    out: [classfile]
diff --git a/cwl/src/test/resources/logback-test.xml b/cwl/src/test/resources/logback-test.xml
deleted file mode 100644
index 5ef34ca9aad..00000000000
--- a/cwl/src/test/resources/logback-test.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<configuration>
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-            <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n</pattern>
-        </encoder>
-    </appender>
-
-    <root level="info">
-        <appender-ref ref="STDOUT"/>
-    </root>
-
-    <logger name="org.mockserver" level="WARN"/>
-    <logger name="liquibase" level="WARN"/>
-    <logger name="com.zaxxer.hikari" level="ERROR"/>
-    <logger name="HikariPool" level="ERROR"/>
-    <logger name="com.google.cloud.hadoop.gcsio.GoogleCloudStorageReadChannel" level="ERROR"/>
-</configuration>
diff --git a/cwl/src/test/resources/nestedworkflows.cwl b/cwl/src/test/resources/nestedworkflows.cwl
deleted file mode 100644
index 3963109e630..00000000000
--- a/cwl/src/test/resources/nestedworkflows.cwl
+++ /dev/null
@@ -1,52 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-
-inputs: []
-
-outputs:
-  classout:
-    type: File
-    outputSource: compile/classout
-
-requirements:
-  - class: SubworkflowFeatureRequirement
-
-steps:
-  compile:
-    run: 1st-workflow.cwl
-    in:
-      inp:
-        source: create-tar/tar
-      ex:
-        default: "Hello.java"
-    out: [classout]
-
-  create-tar:
-    requirements:
-      - class: InitialWorkDirRequirement
-        listing:
-          - entryname: Hello.java
-            entry: |
-              public class Hello {
-                public static void main(String[] argv) {
-                    System.out.println("Hello from Java");
-                }
-              }
-    in: []
-    out: [tar]
-    run:
-      class: CommandLineTool
-      requirements:
-        - class: ShellCommandRequirement
-      arguments:
-        - shellQuote: false
-          valueFrom: |
-            date
-            tar cf hello.tar Hello.java
-            date
-      inputs: []
-      outputs:
-        tar:
-          type: File
-          outputBinding:
-            glob: "hello.tar"
diff --git a/cwl/src/test/resources/tar-param.cwl b/cwl/src/test/resources/tar-param.cwl
deleted file mode 100644
index 39e9aa07016..00000000000
--- a/cwl/src/test/resources/tar-param.cwl
+++ /dev/null
@@ -1,17 +0,0 @@
-cwlVersion: "v1.0"
-class: "CommandLineTool"
-baseCommand: ["tar", "xf"]
-inputs: 
-  - type: "string"
-    inputBinding: 
-      position: 2
-    id: "extractfile"
-  - type: "File"
-    inputBinding: 
-      position: 1
-    id: "tarfile"
-outputs: 
-  - type: "File"
-    outputBinding: 
-      glob: "$(inputs.extractfile)"
-    id: "example_out"
diff --git a/cwl/src/test/resources/three_step.cwl b/cwl/src/test/resources/three_step.cwl
deleted file mode 100644
index e9cd1267b86..00000000000
--- a/cwl/src/test/resources/three_step.cwl
+++ /dev/null
@@ -1,112 +0,0 @@
-cwlVersion: v1.0
-class: Workflow
-id: three_step
-hints:
-# hints can be anything (CwlAny)
-- fee: fi
-  fo: fum
-- eenie: meenie
-  minie: mo
-- 42
-- class: DockerRequirement
-  dockerPull: "ubuntu:latest"
-inputs:
-- id: pattern
-  type: string
-outputs:
-- id: cgrep-count
-  outputSource: "#cgrep/cgrep-count"
-  type: int
-- id: wc-count
-  outputSource: "#wc/wc-count"
-  type: int
-steps:
-- id: ps
-  in: []
-  out:
-  - id: ps-stdOut
-  run:
-    inputs: []
-    outputs:
-    - id: ps-stdOut
-      outputBinding:
-        glob: ps-stdOut.txt
-      type: File
-    class: CommandLineTool
-    requirements:
-    - class: DockerRequirement
-      dockerPull: "debian:wheezy"
-    baseCommand: ps
-    stdout: ps-stdOut.txt
-- id: cgrep
-  in:
-  - id: pattern
-    source: "#pattern"
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: cgrep-count
-  run:
-    inputs:
-    - id: pattern
-      type: string
-    - id: file
-      type: File
-    outputs:
-    - id: cgrep-count
-      outputBinding:
-        glob: cgrep-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: grep
-      shellQuote: false
-    - valueFrom: $(inputs.pattern)
-      shellQuote: false
-    - valueFrom: ${return inputs.file}
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: cgrep-stdOut.txt
-- id: wc
-  in:
-  - id: file
-    source: "#ps/ps-stdOut"
-  out:
-  - id: wc-count
-  run:
-    inputs:
-    - id: file
-      type: File
-    outputs:
-    - id: wc-count
-      outputBinding:
-        glob: wc-stdOut.txt
-        loadContents: true
-        outputEval: $(parseInt(self[0].contents))
-      type: int
-    class: CommandLineTool
-    requirements:
-    - class: ShellCommandRequirement
-    - class: InlineJavascriptRequirement
-    arguments:
-    - valueFrom: cat
-      shellQuote: false
-    - valueFrom: $(inputs.file)
-      shellQuote: false
-    - valueFrom: '|'
-      shellQuote: false
-    - valueFrom: wc
-      shellQuote: false
-    - valueFrom: -l
-      shellQuote: false
-    stdout: wc-stdOut.txt
diff --git a/cwl/src/test/scala/cwl/CommandLineToolSpec.scala b/cwl/src/test/scala/cwl/CommandLineToolSpec.scala
deleted file mode 100644
index b466f1f3e90..00000000000
--- a/cwl/src/test/scala/cwl/CommandLineToolSpec.scala
+++ /dev/null
@@ -1,279 +0,0 @@
-package cwl
-import cats.syntax.traverse._
-import cats.instances.list._
-import common.assertion.CromwellTimeoutSpec
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.ParallelTestExecution
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.callable.Callable.RequiredInputDefinition
-import wom.callable.RuntimeEnvironment
-import wom.expression.NoIoFunctionSet
-import wom.types._
-import wom.values.{WomArray, WomBoolean, WomEvaluatedCallInputs, WomInteger, WomObject, WomSingleFile, WomString, WomValue}
-
-class CommandLineToolSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ParallelTestExecution {
-
-  behavior of "CommandLineTool"
-
-  val inputs: WomEvaluatedCallInputs = Map(
-    RequiredInputDefinition("a", WomStringType) -> WomString("helloA"),
-    RequiredInputDefinition("b", WomStringType) -> WomString("helloB"),
-    RequiredInputDefinition("c", WomStringType) -> WomString("helloC"),
-    RequiredInputDefinition("d", WomArrayType(WomStringType)) -> WomArray(WomArrayType(WomStringType), List(WomString("helloD0"), WomString("helloD1"))),
-    RequiredInputDefinition("e", WomCompositeType(Map("fa" -> WomSingleFileType, "fb" -> WomIntegerType)))
-      -> WomObject.withTypeUnsafe(Map("fa" -> WomSingleFile("helloEfa"), "fb" -> WomInteger(0)), WomCompositeType(Map("fa" -> WomSingleFileType, "fb" -> WomIntegerType))),
-    RequiredInputDefinition("f", WomBooleanType) -> WomBoolean.True,
-    RequiredInputDefinition("g", WomBooleanType) -> WomBoolean.False,
-    RequiredInputDefinition("h", WomIntegerType) -> WomInteger(0),
-    RequiredInputDefinition("i", WomSingleFileType) -> WomSingleFile("ifile")
-  )
-  
-  val localNameValues = inputs.map({ case (k, v) => k.localName -> v })
-  
-  val noIoFunctionSet = NoIoFunctionSet
-  
-  val runtimeEnv = RuntimeEnvironment("", "", refineMV[Positive](1), 0D, 0L, 0L)
-  
-  def validate(tool: String, expectation: List[String]) = {
-    val cltFile = better.files.File.newTemporaryFile()().write(tool)
-
-    val clt = CwlDecoder.decodeCwlFile(cltFile, None).value.unsafeRunSync() match {
-      case Left(errors) => fail("Cannot parse command line tool " + errors.toList.mkString(", "))
-      case Right(cwlFile) => cwlFile.select[CommandLineTool].get
-    }
-
-    val template = clt
-      .buildCommandTemplate.run((RequirementsAndHints(List.empty), Vector.empty,inputs))
-      .valueOr(errors => fail(errors.toList.mkString(", ")))
-    template
-      .flatTraverse(_.instantiate(localNameValues, noIoFunctionSet, identity[WomValue], runtimeEnv).map(_.map(_.commandString)))
-      .valueOr(errors => fail(errors.toList.mkString(", "))) shouldBe expectation
-    
-    cltFile.delete(true)
-  }
-  
-  it should "filter input arguments when not bound to command line" in {
-    val tool = """
-      |class: CommandLineTool
-      |cwlVersion: v1.0
-      |inputs:
-      |  - id: a
-      |    type: string
-      |    inputBinding: { position: 2 }
-      |
-      |  - id: b
-      |    type: string
-      |
-      |baseCommand: echo
-      |outputs: []
-    """.stripMargin
-
-    validate(tool, List("'echo'", "'helloA'"))
-  }
-
-  it should "order input arguments that are bound to command line" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  - id: b
-                 |    type: string
-                 |    inputBinding: { position: 2 }
-                 |    
-                 |  - id: c
-                 |    type: string
-                 |    inputBinding: { position: 3 }
-                 |
-                 |  - id: a
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'helloA'", "'helloB'", "'helloC'"))
-  }
-
-  it should "include arguments and sort them" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  - id: b
-                 |    type: string
-                 |    inputBinding: { position: 4 }
-                 |    
-                 |  - id: c
-                 |    type: string
-                 |    inputBinding: { position: 5 }
-                 |
-                 |  - id: a
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |arguments:
-                 |  - arg0
-                 |  - valueFrom: "arg2"
-                 |    position: 3
-                 |  - valueFrom: "arg1"
-                 |    position: 2
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'arg0'", "'helloA'", "'arg1'", "'arg2'", "'helloB'", "'helloC'"))
-  }
-
-  it should "handle array types" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  - id: d
-                 |    type:
-                 |      type: array
-                 |      items: string
-                 |      inputBinding: { prefix: "-YYY" }
-                 |    inputBinding: { position: 3, prefix: "-XXX" }
-                 |    
-                 |  - id: a
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |arguments:
-                 |  - valueFrom: "arg2"
-                 |    position: 2
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'helloA'", "'arg2'", "'-XXX'", "'-YYY'", "'helloD0'", "'-YYY'", "'helloD1'"))
-  }
-
-  it should "handle record schema" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  e:
-                 |    type:
-                 |      name: e
-                 |      type: record
-                 |      fields:
-                 |      - name: fa
-                 |        type: File
-                 |        inputBinding:
-                 |          position: 2
-                 |          prefix: "--prefixFa"
-                 |      - name: fb
-                 |        type: int
-                 |        inputBinding:
-                 |          position: 4
-                 |          prefix: "--prefixFb"
-                 |    inputBinding:      
-                 |      prefix: "--prefixRecord"
-                 |  a:
-                 |    type: string
-                 |    inputBinding: { position: 1 }
-                 |
-                 |baseCommand: echo
-                 |arguments:
-                 |  - valueFrom: "arg2"
-                 |    position: 3
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--prefixRecord'", "'--prefixFa'", "'helloEfa'", "'--prefixFb'", "'0'", "'helloA'", "'arg2'"))
-  }
-
-  it should "handle prefixes properly for primitive types" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  a:
-                 |    type: string
-                 |    inputBinding: { position: 1, prefix: --aprefix }
-                 |  f:
-                 |    type: boolean
-                 |    inputBinding: { position: 2, prefix: --show }
-                 |  g:
-                 |    type: boolean
-                 |    inputBinding: { position: 3, prefix: --noshow }
-                 |  h:
-                 |    type: string
-                 |    inputBinding: { position: 4, prefix: --hprefix }
-                 |  i:
-                 |    type: File
-                 |    inputBinding: { position: 5, prefix: --iprefix }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--aprefix'", "'helloA'", "'--show'", "'--hprefix'", "'0'", "'--iprefix'", "'ifile'"))
-  }
-
-  it should "handle arrays with item separator" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  d:
-                 |    type:
-                 |      type: array
-                 |      items: string
-                 |      inputBinding: { position: 2, prefix: --item }
-                 |    inputBinding: { position: 2, prefix: --array, itemSeparator: ", " }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--array'", "'helloD0, helloD1'"))
-  }
-
-  it should "handle arrays with valueFrom" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  d:
-                 |    type:
-                 |      type: array
-                 |      items: string
-                 |      inputBinding: { position: 2, prefix: --item }
-                 |    inputBinding: { position: 2, prefix: --array, valueFrom: "hello" }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--array'", "'hello'"))
-  }
-
-  it should "handle the separate field" in {
-    val tool = """
-                 |class: CommandLineTool
-                 |cwlVersion: v1.0
-                 |inputs:
-                 |  a:
-                 |    type: string
-                 |    inputBinding: { position: 0, prefix: --prefix, separate: false }
-                 |
-                 |baseCommand: echo
-                 |outputs: []
-               """.stripMargin
-
-    validate(tool, List("'echo'", "'--prefixhelloA'"))
-  }
-
-  it should "pull expression libs from all requirements" in {
-    val list = List(Coproduct[Requirement](InlineJavascriptRequirement(`class` = "InlineJavascriptRequirement", expressionLib = Some(Array("a")))))
-    Tool.inlineJavascriptRequirements(list).head shouldBe "a"
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CommandOutputExpressionSpec.scala b/cwl/src/test/scala/cwl/CommandOutputExpressionSpec.scala
deleted file mode 100644
index f2cc446e65f..00000000000
--- a/cwl/src/test/scala/cwl/CommandOutputExpressionSpec.scala
+++ /dev/null
@@ -1,57 +0,0 @@
-package cwl
-
-import java.util.concurrent.Executors
-
-import cats.syntax.all._
-import common.assertion.CromwellTimeoutSpec
-import cwl.CommandLineTool.CommandOutputParameter
-import cwl.ExpressionEvaluator._
-import eu.timepit.refined._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.expression.{EmptyIoFunctionSet, FileEvaluation, NoIoFunctionSet}
-import wom.types.WomIntegerType
-import wom.values._
-
-import scala.concurrent.{ExecutionContext, Future}
-
-
-class CommandOutputExpressionSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "CommandOutputExpression"
-
-  def ioFunctionSet(data: String) =
-    new EmptyIoFunctionSet {
-      override implicit def ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(1))
-      override def readFile(path: String, maxBytes: Option[Int] = None, failOnOverflow: Boolean = false) = Future.successful(data)
-      // For this test just "match" the submitted file.
-      override def glob(pattern: String): Future[Seq[String]] = Future.successful(List(pattern))
-    }
-
-  it should "evaluateValue" in {
-    val data = "41.1"
-    val tempFile = better.files.File.newTemporaryFile("glob.", ".txt").write(data)
-    val globExpression = Coproduct[Expression](refineMV[MatchesECMAScriptExpression]("$(inputs.myTempFile)"))
-    val outputEvalExpression = Coproduct[Expression](refineMV[MatchesECMAScriptExpression](
-      "$((parseInt(self[0].contents) + 1).toFixed())"))
-    val glob = Coproduct[Glob](Coproduct[StringOrExpression](globExpression))
-    val outputEval = Coproduct[StringOrExpression](outputEvalExpression)
-    val outputBinding = CommandOutputBinding(Option(glob), Option(true), Option(outputEval))
-    val commandOutputParameter = CommandOutputParameter("id", outputBinding = Option(outputBinding))
-    val commandOutputExpression = OutputParameterExpression(commandOutputParameter, WomIntegerType, Set.empty, Vector.empty, SchemaDefRequirement())
-    val inputValues = Map("myTempFile" -> WomString(tempFile.pathAsString))
-    val result = commandOutputExpression.evaluateValue(inputValues, ioFunctionSet(data))
-    result should be(WomInteger(42).valid)
-  }
-
-  it should "figure out stdout" in {
-    val glob = Coproduct[Glob](Coproduct[StringOrExpression]("stdout"))
-    val outputBinding = CommandOutputBinding(Option(glob))
-    val commandOutputParameter = CommandOutputParameter("id", outputBinding = Option(outputBinding))
-    val commandOutputExpression = OutputParameterExpression(commandOutputParameter, WomIntegerType, Set.empty, Vector.empty, SchemaDefRequirement())
-    val result = commandOutputExpression.evaluateFiles(Map.empty, NoIoFunctionSet, WomIntegerType)
-    // TODO: This should be a glob. See [[cwl.CommandOutputBinding.dependingIfGlobLike]]
-    result shouldBe Set(FileEvaluation.requiredFile(WomSingleFile("stdout"))).valid
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlDecoderSpec.scala b/cwl/src/test/scala/cwl/CwlDecoderSpec.scala
deleted file mode 100644
index c206c116a84..00000000000
--- a/cwl/src/test/scala/cwl/CwlDecoderSpec.scala
+++ /dev/null
@@ -1,48 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class CwlDecoderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "cwl decoder"
-
-  import TestSetup._
-
-  it should "read nested workflow" in {
-      decodeCwlFile(rootPath / "nestedworkflows.cwl").
-        value.
-        unsafeRunSync() match {
-        case Right(cwl) =>
-          val wf = cwl.select[Workflow].get
-          wf.steps.flatMap(_.run.select[String].toList).length shouldBe 0
-        case Left(other) => fail(other.toList.mkString(", "))
-      }
-  }
-
-  it should "fail to parse broken linked cwl" in {
-    val result: Either[NonEmptyList[String], Cwl] = decodeCwlFile(rootPath / "brokenlinks.cwl").
-      value.
-      unsafeRunSync()
-
-    result.isLeft shouldBe true
-    withClue(s"Actual message: ${result.swap.toOption.get.head}") {
-      "Field `run` contains undefined reference to `file://.+/wrong.cwl`".r.findAllIn(result.swap.toOption.get.head).size shouldBe 1
-      "Field `run` contains undefined reference to `file://.+/wrong2.cwl`".r.findAllIn(result.swap.toOption.get.head).size shouldBe 1
-    }
-  }
-
-  it should "fail to parse invalid linked cwl" in {
-      decodeCwlFile(rootPath/"links_dont_parse.cwl").
-        value.
-        unsafeRunSync() match {
-        case Left(errors) =>
-          errors.filter(_.contains("bad.cwl")).size + errors.filter(_.contains("bad2.cwl")).size shouldBe 1
-        case Right(_) => fail("should not have passed!")
-      }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlEcmaScriptDecoderSpec.scala b/cwl/src/test/scala/cwl/CwlEcmaScriptDecoderSpec.scala
deleted file mode 100644
index 6c6918efaaa..00000000000
--- a/cwl/src/test/scala/cwl/CwlEcmaScriptDecoderSpec.scala
+++ /dev/null
@@ -1,77 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.internal.{EcmaScriptEncoder, EcmaScriptUtil}
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.values.{WomFloat, WomMaybePopulatedFile, WomString, WomValue}
-
-
-class CwlEcmaScriptDecoderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-  behavior of "CwlJsDecoder"
-
-  val decodeTests= Table[String, String, Map[String, Map[String, WomValue]], WomValue](
-    (
-      "description",
-      "expr",
-      "values",
-      "expected"
-    ),
-    (
-      "a passed through file",
-      "inputMap",
-      Map("inputMap" -> Map(
-        "class" -> WomString("File"),
-        "location" -> WomString("path/to/file.txt"),
-        "checksum" -> WomString("hash_here"),
-        "size" -> WomFloat(Double.box(123.4)),
-        "format" -> WomString("file_format"),
-        "contents" -> WomString("file_contents")
-      )),
-      WomMaybePopulatedFile(
-        valueOption = Option("path/to/file.txt"),
-        checksumOption = Option("hash_here"),
-        sizeOption = Option(123L),
-        formatOption = Option("file_format"),
-        contentsOption = Option("file_contents"),
-        secondaryFiles = Vector()
-      )
-    ),
-    (
-      "a script generated file",
-      """|var result = {
-         |"class": "File",
-         |"path": "other/dir/img.jpg",
-         |"checksum": "check_sum",
-         |"size": 567.8,
-         |"format": "more_jpeg",
-         |"contents": "lol_cat"
-         |};
-         |result;
-         |""".stripMargin,
-      Map(),
-      WomMaybePopulatedFile(
-        valueOption = Option("other/dir/img.jpg"),
-        checksumOption = Option("check_sum"),
-        sizeOption = Option(567L),
-        formatOption = Option("more_jpeg"),
-        contentsOption = Option("lol_cat"),
-        secondaryFiles = Vector()
-      )
-    )
-  )
-
-  forAll(decodeTests) { (description, expr, values: Map[String, Map[String, WomValue]], expected) =>
-    it should s"decode $description" in {
-      val result = EcmaScriptUtil.evalStructish(
-        expr,
-        "fake" -> WomString("unused"),
-        values,
-        new EcmaScriptEncoder()
-      ).toTry.get
-      result should be(expected)
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlEcmaScriptEncoderSpec.scala b/cwl/src/test/scala/cwl/CwlEcmaScriptEncoderSpec.scala
deleted file mode 100644
index 9119f75c421..00000000000
--- a/cwl/src/test/scala/cwl/CwlEcmaScriptEncoderSpec.scala
+++ /dev/null
@@ -1,35 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.internal.EcmaScriptUtil.{ESArray, ESObject, ESPrimitive}
-import cwl.internal.{EcmaScriptEncoder, EcmaScriptUtil}
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.values.WomMaybePopulatedFile
-
-
-class CwlEcmaScriptEncoderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "EcmaScriptEncoder"
-
-  it should "encode" in {
-    val encoder = new EcmaScriptEncoder()
-    val file = WomMaybePopulatedFile("path/to/file.txt")
-    val expected = Map(
-      "class" -> ESPrimitive("File"),
-      "location" -> ESPrimitive("path/to/file.txt"),
-      "path" -> ESPrimitive("path/to/file.txt"),
-      "dirname" -> ESPrimitive("path/to"),
-      "basename" -> ESPrimitive("file.txt"),
-      "nameroot" -> ESPrimitive("file"),
-      "nameext" -> ESPrimitive(".txt")
-    )
-    val result: EcmaScriptUtil.ECMAScriptVariable = encoder.encode(file)
-    val resultMap = result.asInstanceOf[ESObject].fields
-    resultMap.view.filterKeys(_ != "secondaryFiles").toList should contain theSameElementsAs expected
-    resultMap("secondaryFiles") should be(a[ESArray])
-    resultMap("secondaryFiles").asInstanceOf[ESArray].array should be(empty)
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/CwlExpressionCommandPartSpec.scala b/cwl/src/test/scala/cwl/CwlExpressionCommandPartSpec.scala
deleted file mode 100644
index 0d675397a11..00000000000
--- a/cwl/src/test/scala/cwl/CwlExpressionCommandPartSpec.scala
+++ /dev/null
@@ -1,34 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.ExpressionEvaluator._
-import eu.timepit.refined._
-import eu.timepit.refined.numeric.Positive
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.callable.RuntimeEnvironment
-import wom.expression.NoIoFunctionSet
-import wom.graph.LocalName
-import wom.values.WomString
-
-
-class CwlExpressionCommandPartSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "CwlExpressionCommandPart"
-
-  val emptyEnvironment = RuntimeEnvironment("","",refineMV[Positive](1),1,1,1)
-
-  it should "instantiate" in {
-    // NOTE: toFixed used to remove the fraction part of ECMAScript numbers
-    // https://stackoverflow.com/questions/25989642/why-does-java-8-nashorn-javascript-modulo-returns-0-0-double-instead-of-0-i#answer-25991982
-    // https://community.apigee.com/questions/33936/javascript-parseint-not-converting-to-int-value-ne.html
-    val commandPart = CwlExpressionCommandPart(Coproduct[Expression](refineMV[MatchesECMAScriptExpression](
-      "$(parseInt(inputs.myStringInt).toFixed())"
-    )))(false, Vector.empty)
-    val result = commandPart.instantiate(Map(LocalName("myStringInt") -> WomString("3")), NoIoFunctionSet, identity, emptyEnvironment).toTry.get.head.commandString
-    result should be("'3'")
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/CwlInputValidationSpec.scala b/cwl/src/test/scala/cwl/CwlInputValidationSpec.scala
deleted file mode 100644
index c9d5272b07b..00000000000
--- a/cwl/src/test/scala/cwl/CwlInputValidationSpec.scala
+++ /dev/null
@@ -1,203 +0,0 @@
-package cwl
-
-import better.files.{File => BFile}
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder.decodeCwlFile
-import org.scalatest.BeforeAndAfterAll
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import shapeless.Coproduct
-import wom.expression.NoIoFunctionSet
-import wom.graph.Graph.ResolvedExecutableInput
-import wom.graph.GraphNodePort
-import wom.types.{WomArrayType, WomStringType}
-import wom.values._
-
-
-class CwlInputValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks with BeforeAndAfterAll {
-  behavior of "CWL Wom executable"
-
-  var cwlFile: BFile = _
-  var inputTempFile: BFile = _
-
-  override def beforeAll(): Unit = {
-    inputTempFile = BFile.newTemporaryFile()
-    cwlFile = BFile.newTemporaryFile().write(
-      """
-        |cwlVersion: v1.0
-        |class: Workflow
-        |inputs:
-        | w0:
-        |   type: string
-        |   default: "hi w0 !"
-        | w1: File
-        | w2:
-        |   type: string
-        |   default: "hi w2 !"
-        | w3: int
-        | w4: long
-        | w5: double
-        | w6: float
-        | w7: boolean
-        | w8:
-        |   type:
-        |     type: array
-        |     items:
-        |       type: array
-        |       items: string
-        | # enable this when InputRecordSchemas are enabled
-        | #w9:
-        | #  type:
-        | #    name: w9
-        | #    type: record
-        | #    fields:
-        | #    - name: w9a
-        | #      type: record
-        | #      fields:
-        | #      - name: w9aa
-        | #        type: string
-        | w10: Directory
-        |steps: []
-        |outputs: []
-      """.stripMargin
-    )
-  }
-
-  override def afterAll(): Unit = {
-    cwlFile.delete()
-    inputTempFile.delete()
-    ()
-  }
-
-  lazy val cwlWorkflow = decodeCwlFile(cwlFile).map {
-    _.select[Workflow].get
-  }.value.unsafeRunSync().fold(error => throw new RuntimeException(s"broken parse! msg was $error"), identity)
-
-  lazy val graph = cwlWorkflow.womDefinition(AcceptAllRequirements, Vector.empty) match {
-    case Left(errors) => fail(s"Failed to build wom definition: ${errors.toList.mkString(", ")}")
-    case Right(womDef) => womDef.graph
-  }
-
-  def getOutputPort(n: Int) = graph.inputNodes.find(_.localName == s"w$n").getOrElse(fail(s"Failed to find an input node for w$n")).singleOutputPort
-
-  lazy val w0OutputPort = getOutputPort(0)
-  lazy val w1OutputPort = getOutputPort(1)
-  lazy val w2OutputPort = getOutputPort(2)
-  lazy val w3OutputPort = getOutputPort(3)
-  lazy val w4OutputPort = getOutputPort(4)
-  lazy val w5OutputPort = getOutputPort(5)
-  lazy val w6OutputPort = getOutputPort(6)
-  lazy val w7OutputPort = getOutputPort(7)
-  lazy val w8OutputPort = getOutputPort(8)
-//  lazy val w9OutputPort = getOutputPort(9)
-  lazy val w10OutputPort = getOutputPort(10)
-
-  def validate(inputFile: String): Map[GraphNodePort.OutputPort, ResolvedExecutableInput] = {
-    cwlWorkflow.womExecutable(AcceptAllRequirements, Option(inputFile), LocalIoFunctionSet, strictValidation = false) match {
-      case Left(errors) => fail(s"Failed to build a wom executable: ${errors.toList.mkString(", ")}")
-      case Right(executable) => executable.resolvedExecutableInputs
-    }
-  }
-
-  it should "parse and validate a valid input file" in {
-    val inputFile =
-      s"""
-        w1:
-          class: File
-          path: ${inputTempFile.toString()}
-          secondaryFiles:
-            - class: File
-              path: secondaryFile.txt
-        w2: hello !
-        w3: 3
-        w4: 4
-        w5: 5.1
-        w6: 6.1
-        w7: true
-        w8: [
-          ["a", "b"],
-          ["c", "d"]
-        ]
-        w10:
-          class: Directory
-          location: "directory_location"
-          listing:
-            - class: Directory
-              path: "innerDirectory"
-            - class: File
-              location: "innerFile"
-      """.stripMargin
-    // TODO: With record schema, re-add:
-    //        w9:
-    //          w9a:
-    //            w9aa: "hello"
-
-    val validInputs = validate(inputFile).map {
-      case (port, resolvedInput) => (port.name, resolvedInput)
-    }
-
-    // w0 has no input value in the input file, so it should fallback to the default value
-    validInputs(w0OutputPort.name).select[WomValue].get.valueString shouldBe "hi w0 !"
-    validInputs(w1OutputPort.name) shouldBe
-      Coproduct[ResolvedExecutableInput](WomMaybePopulatedFile(
-        valueOption = Option(inputTempFile.toString()),
-        secondaryFiles = List(WomMaybePopulatedFile("secondaryFile.txt")),
-        sizeOption = Option(0)
-      ): WomValue)
-    validInputs(w2OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomString("hello !"): WomValue)
-    validInputs(w3OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomInteger(3): WomValue)
-    validInputs(w4OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomLong(4): WomValue)
-    validInputs(w5OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomFloat(5.1D): WomValue)
-    validInputs(w6OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomFloat(6.1D): WomValue)
-    validInputs(w7OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](WomBoolean(true): WomValue)
-    validInputs(w8OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](
-      WomArray(
-        WomArrayType(WomArrayType(WomStringType)),
-        List(
-          WomArray(WomArrayType(WomStringType), List(WomString("a"), WomString("b"))),
-          WomArray(WomArrayType(WomStringType), List(WomString("c"), WomString("d")))
-        )
-      ): WomValue
-    )
-    // Enable this when InputRecordSchema is enabled
-//    validInputs(w9OutputPort.name) shouldBe Coproduct[ResolvedExecutableInput](
-//      WomObject(
-//        Map(
-//          "w9a" -> WomObject(Map("w9aa" -> WomString("hello")))
-//        )
-//      ): WomValue
-//    )
-    validInputs(w10OutputPort.name) shouldBe
-      Coproduct[ResolvedExecutableInput](WomMaybeListedDirectory(
-        valueOption = Option("directory_location"),
-        listingOption = Option(
-          List(
-            WomMaybeListedDirectory("innerDirectory"),
-            WomMaybePopulatedFile("innerFile")
-          )
-        )
-      ): WomValue)
-  }
-
-  it should "not validate when required inputs are missing" in {
-    val inputFile =
-      """
-        w2: hello !
-      """.stripMargin
-
-    cwlWorkflow.womExecutable(AcceptAllRequirements, Option(inputFile), NoIoFunctionSet, strictValidation = false) match {
-      case Right(booh) => fail(s"Expected failed validation but got valid input map: $booh")
-      case Left(errors) => errors.toList.toSet shouldBe Set(
-        "Required workflow input 'w1' not specified",
-        "Required workflow input 'w3' not specified",
-        "Required workflow input 'w4' not specified",
-        "Required workflow input 'w5' not specified",
-        "Required workflow input 'w6' not specified",
-        "Required workflow input 'w7' not specified",
-        "Required workflow input 'w8' not specified",
-        "Required workflow input 'w10' not specified"
-      )
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/CwlWorkflowWomSpec.scala b/cwl/src/test/scala/cwl/CwlWorkflowWomSpec.scala
deleted file mode 100644
index 52f511fd9b7..00000000000
--- a/cwl/src/test/scala/cwl/CwlWorkflowWomSpec.scala
+++ /dev/null
@@ -1,216 +0,0 @@
-package cwl
-
-import cats.syntax.either._
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder._
-import cwl.ExpressionEvaluator._
-import cwl.command.ParentName
-import eu.timepit.refined._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import shapeless._
-import wom.WomMatchers._
-import wom.callable.{Callable, CommandTaskDefinition, WorkflowDefinition}
-import wom.graph.GraphNodePort.OutputPort
-import wom.graph._
-import wom.graph.expression.ExpressionNode
-import wom.types.{WomMaybePopulatedFileType, WomStringType, WomType}
-
-
-class CwlWorkflowWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-  import TestSetup._
-
-  implicit val parentName = ParentName.empty
-
-  "A Cwl object for 1st-tool" should "convert to WOM" in {
-    def validateWom(callable: Callable): Unit = callable match {
-      case taskDefinition: CommandTaskDefinition =>
-        val inputDef = taskDefinition.inputs.head
-        inputDef.name shouldBe "message"
-        inputDef.womType shouldBe WomStringType
-        ()
-
-      case _ => fail("not a task definition")
-    }
-
-    import cats.syntax.validated._
-    (for {
-      clt <- decodeCwlFile(rootPath/"1st-tool.cwl").
-              map(_.select[CommandLineTool].get).
-              value.
-              unsafeRunSync()
-      taskDef <- clt.buildTaskDefinition(_.validNel, Vector.empty)
-    } yield validateWom(taskDef)).leftMap(e => throw new RuntimeException(s"error! $e"))
-  }
-
-  "Cwl for 1st workflow" should "convert to WOM" in {
-    (for {
-      wf <- decodeCwlFile(rootPath/"1st-workflow.cwl").
-              value.
-              unsafeRunSync().
-              map(_.select[Workflow].get)
-
-      womDefinition <- wf.womDefinition(AcceptAllRequirements, Vector.empty)
-    } yield validateWom(womDefinition)).leftMap(e => throw new RuntimeException(s"error! ${e.toList.mkString("\n")}"))
-
-    def shouldBeRequiredGraphInputNode(node: GraphNode, localName: String, womType: WomType): Unit = {
-      node.isInstanceOf[RequiredGraphInputNode] shouldBe true
-      val requiredGraphInputNode = node.asInstanceOf[RequiredGraphInputNode]
-      requiredGraphInputNode.localName shouldBe localName
-      requiredGraphInputNode.womType shouldBe womType
-      ()
-    }
-
-    def validateWom(callable: Callable) = {
-      callable match {
-        case wf: WorkflowDefinition =>
-          val nodes = wf.innerGraph.nodes
-
-          nodes collect {
-            case gin: GraphInputNode => gin.localName
-          } should be(Set("ex", "inp"))
-
-          nodes collect {
-            case cn: CallNode => cn.localName
-          } should be(Set("compile", "untar"))
-
-          val untarUpstream = nodes.collectFirst {
-            case tarParam: CallNode if tarParam.localName == s"untar" => tarParam
-          }.get.
-            upstream
-
-          untarUpstream should have size 2
-          untarUpstream.collectFirst({
-            case exprNode: ExpressionNode if exprNode.localName == s"file://$rootPath/1st-workflow.cwl#untar/extractfile.merge" =>
-              shouldBeRequiredGraphInputNode(exprNode.inputPorts.head.upstream.graphNode, "ex", WomStringType)
-          }).getOrElse(fail("Can't find expression node for ex"))
-
-          untarUpstream.collectFirst({
-            case exprNode: ExpressionNode if exprNode.localName == s"file://$rootPath/1st-workflow.cwl#untar/tarfile.merge" =>
-              exprNode.inputPorts.map(_.upstream.graphNode).count {
-                case rgin: RequiredGraphInputNode =>
-                  rgin.identifier.localName == LocalName("inp") &&
-                    rgin.womType == WomMaybePopulatedFileType
-              }  shouldBe 1
-          }).getOrElse(fail("Can't find expression node for inp"))
-
-          val compileUpstreamExpressionPort = nodes.collectFirst {
-            case compile: CallNode if compile.localName == s"compile" => compile
-          }.get.inputPorts.map(_.upstream).head
-
-          compileUpstreamExpressionPort.name shouldBe s"file://$rootPath/1st-workflow.cwl#compile/src.merge"
-          compileUpstreamExpressionPort.graphNode.asInstanceOf[ExpressionNode].inputPorts.map(_.upstream.internalName).count(_ == "example_out") shouldBe 1
-
-          nodes.collect {
-            case c: PortBasedGraphOutputNode => c
-          }.map(_.localName) shouldBe Set("classout")
-        case wth: Any => fail(s"Parsed unexpected Callable: $wth")
-      }
-    }
-  }
-
-  behavior of "A decoded CWL 3step"
-
-  private val stringOrExpressionTests = Table(
-    ("index", "result"),
-    (0, Coproduct[StringOrExpression]("grep")),
-    (1, Coproduct[StringOrExpression](Coproduct[Expression](refineMV[MatchesECMAScriptExpression]("$(inputs.pattern)")))),
-    (2, Coproduct[StringOrExpression](Coproduct[Expression](refineMV[MatchesECMAScriptFunction]("$" + "{return inputs.file}")))),
-    (3, Coproduct[StringOrExpression]("|")),
-    (4, Coproduct[StringOrExpression]("wc")),
-    (5, Coproduct[StringOrExpression]("-l"))
-  )
-
-  private def getTestName(stringOrExpression: StringOrExpression): String = stringOrExpression match {
-    case StringOrExpression.String(s) => s"string $s"
-    // Although these two cases look the same, they're actually calling different 'value' functions. So we
-    // can't collapse this to a single "case StringOrExpression.Expression(e) => e.value":
-    case StringOrExpression.ECMAScriptExpression(e) => e.value
-    case StringOrExpression.ECMAScriptFunction(f) => f.value
-    case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-  }
-
-  private lazy val commandLineTool: CommandLineTool = {
-    val wf = decodeCwlFile(rootPath / "three_step.cwl").map { wf =>
-      wf.select[Workflow].get
-    }.value.unsafeRunSync().fold(error => throw new RuntimeException(s"broken parse! msg was ${error.toList.mkString(", ")}"), identity)
-
-    wf.id should include("three_step")
-
-    // The second step (aka 1) step should be cgrep
-    val run: WorkflowStep.Run = wf.steps.apply(1).run
-    val commandLineTool: CommandLineTool = run.select[CommandLineTool].getOrElse(fail(s"$run wasn't a CommandLineTool"))
-
-    commandLineTool.id should include("cgrep")
-    commandLineTool
-  }
-
-  forAll(stringOrExpressionTests) { (index, expected) =>
-    it should s"correctly identify the ${getTestName(expected)}" in {
-      val argument: CommandLineTool.Argument = commandLineTool.arguments.get.apply(index)
-      val commandLineBinding: ArgumentCommandLineBinding = argument.select[ArgumentCommandLineBinding]
-        .getOrElse(fail(s"$argument wasn't a CommandLineBinding"))
-      val stringOrExpression: StringOrExpression = commandLineBinding.valueFrom
-      stringOrExpression should be(expected)
-    }
-  }
-
-  "A CwlNamespace for 3step" should "provide conversion to WOM" in {
-
-    val wf = decodeCwlFile(rootPath/"three_step.cwl").map {
-      _.select[Workflow].get
-    }.value.unsafeRunSync().fold(error => throw new RuntimeException(s"broken parse: $error"), identity)
-
-    wf.id should include("three_step")
-
-    val wfd = wf.womDefinition(AcceptAllRequirements, Vector.empty) match {
-      case Right(wf: WorkflowDefinition) => wf
-      case Left(o) => fail(s"Workflow definition was not produced correctly: ${o.toList.mkString(", ")}")
-      case Right(callable) => fail(s"produced $callable when a Workflow Definition was expected!")
-    }
-
-    val nodes = wfd.innerGraph.nodes
-
-    val graphInputNodes = nodes collect { case gin: GraphInputNode => gin }
-    graphInputNodes should have size 1
-    val patternInputNode = graphInputNodes.head
-    patternInputNode.localName should be("pattern")
-
-    nodes collect { case gon: GraphOutputNode => gon.localName } should be(Set(
-      "cgrep-count",
-      "wc-count"
-    ))
-
-    nodes collect { case cn: CallNode => cn.localName } should be(Set("ps", "cgrep", "wc"))
-
-    val ps = nodes.collectFirst({ case ps: CallNode if ps.localName == "ps" => ps }).get
-    val cgrep = nodes.collectFirst({ case cgrep: CallNode if cgrep.localName == "cgrep" => cgrep }).get
-    val cgrepFileExpression = nodes.collectFirst({ case cgrepInput: ExpressionNode if s"${FileStepAndId(cgrepInput.localName).stepId}/${FileStepAndId(cgrepInput.localName).id}" == "cgrep/file.merge" => cgrepInput }).get
-    val cgrepPatternExpression = nodes.collectFirst({ case cgrepInput: ExpressionNode if s"${FileStepAndId(cgrepInput.localName).stepId}/${FileStepAndId(cgrepInput.localName).id}" == "cgrep/pattern.merge" => cgrepInput }).get
-    val wc = nodes.collectFirst({ case wc: CallNode if wc.localName == "wc" => wc }).get
-    val wcFileExpression = nodes.collectFirst({ case wcInput: ExpressionNode if s"${FileStepAndId(wcInput.localName).stepId}/${FileStepAndId(wcInput.localName).id}" == "wc/file.merge" => wcInput }).get
-
-    ps.upstream shouldBe empty
-
-    cgrep.upstream should contain theSameElementsAs Set(cgrepFileExpression, cgrepPatternExpression)
-    wc.upstream should contain theSameElementsAs Set(wcFileExpression)
-
-    // Check that expressions input ports point to the right output port
-    cgrepPatternExpression.inputPorts.head.upstream should be theSameInstanceAs patternInputNode.singleOutputPort
-    cgrepFileExpression.inputPorts.map(_.upstream).count(_ eq ps.outputPorts.head) shouldBe 1
-    wcFileExpression.inputPorts.map(_.upstream).count(_ eq ps.outputPorts.head) shouldBe 1
-
-    // Check that the inputDefinitionMappings are correct
-    ps.inputDefinitionMappings shouldBe empty
-    cgrep.inputDefinitionMappings should have size 2
-
-    val cgrepInputs = cgrep.inputDefinitionMappings.toMap
-    val cgrepFileInputDef = cgrep.callable.inputs.find(_.name == "file").get
-    cgrepInputs(cgrepFileInputDef).select[OutputPort].get should be theSameInstanceAs cgrepFileExpression.singleOutputPort
-
-    val cgrepPatternInputDef = cgrep.callable.inputs.find(_.name == "pattern").get
-    cgrepInputs(cgrepPatternInputDef).select[OutputPort].get should be theSameInstanceAs cgrepPatternExpression.singleOutputPort
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/DirectorySpec.scala b/cwl/src/test/scala/cwl/DirectorySpec.scala
deleted file mode 100644
index 1e7db881753..00000000000
--- a/cwl/src/test/scala/cwl/DirectorySpec.scala
+++ /dev/null
@@ -1,41 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.CwlDecoder.decodeCwlFile
-import cwl.TestSetup.rootPath
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.callable.Callable.InputDefinition
-import wom.callable.{CallableTaskDefinition, RuntimeEnvironment}
-import wom.expression.NoIoFunctionSet
-import wom.graph.OptionalGraphInputNodeWithDefault
-import wom.values.WomValue
-
-
-class DirectorySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "Directory"
-
-  it should "dir_example" in {
-    val cwl = decodeCwlFile(rootPath / "dir_example.cwl").value.unsafeRunSync().toOption.get
-    val executable = cwl.womExecutable(AcceptAllRequirements, None, NoIoFunctionSet, strictValidation = false).toOption.get
-    val call = executable.graph.calls.head
-    val runtimeEnvironment = RuntimeEnvironment("output/path", "temp/path",refineMV[Positive](1), 2e10, 100, 100)
-    val defaultCallInputs = executable.graph.nodes.collect({
-      case oginwd: OptionalGraphInputNodeWithDefault =>
-        val key: InputDefinition = call.inputDefinitionMappings.toMap.keys.find(
-          _.localName == oginwd.identifier.localName
-        ).get
-        val value: WomValue = oginwd.default.evaluateValue(Map.empty, NoIoFunctionSet).toTry.get
-        key -> value
-    }).toMap
-    val command = call.callable.asInstanceOf[CallableTaskDefinition].instantiateCommand(
-      defaultCallInputs, NoIoFunctionSet, identity, runtimeEnvironment
-    ).toTry.get
-    command.commandString should be("""   'echo' 'exampledir'   """.trim)
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/ExportCwlSamplesSpec.scala b/cwl/src/test/scala/cwl/ExportCwlSamplesSpec.scala
deleted file mode 100644
index e18c95a9966..00000000000
--- a/cwl/src/test/scala/cwl/ExportCwlSamplesSpec.scala
+++ /dev/null
@@ -1,146 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.CommandLineTool.{BaseCommand, CommandInputParameter}
-import cwl.Workflow.{WorkflowInputParameter, WorkflowOutputParameter}
-import cwl.WorkflowStep.WorkflowStepOutputInnerType
-import cwl.WorkflowStepInput.InputSource
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-
-
-
-  /**
-   * BROKEN
-   *
-   * (DB)Ability to write JSON removed due to conflicting circe-yaml cats dependency.
-   * See issue https://github.com/broadinstitute/wdl4s/issues/216 for more information.
-   */
-class ExportCwlSamplesSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  def assertCorrectJson(cwl: Cwl, expectedYaml: String) = throw new UnsupportedOperationException // shouldBe expectedYaml
-
-  it should "encode sample CWL command line tool" ignore {
-    val tool =
-      CommandLineTool(
-        id = "echo",
-        inputs =  Array(CommandInputParameter(
-          id = "message",
-          inputBinding = Option(InputCommandLineBinding(
-            position = Option(1)
-          ))
-        )),
-        baseCommand = Option(Coproduct[BaseCommand]("echo"))
-      )
-    val expectedToolJsonString =
-"""inputs:
-- id: message
-  inputBinding:
-    position: 1
-outputs: []
-class: CommandLineTool
-cwlVersion: v1.0
-baseCommand: echo
-"""
-    assertCorrectJson(tool.asCwl, expectedToolJsonString)
-  }
-
-  it should "encode sample CWL workflow" ignore {
-    val workflow = Workflow(
-      id = "MyCwlWorkflow",
-      inputs = Array(
-          WorkflowInputParameter(id = "inp", `type` = Option(Coproduct[MyriadInputType](Coproduct[MyriadInputInnerType](CwlType.File)))),
-          WorkflowInputParameter(id = "ex", `type` = Option(Coproduct[MyriadInputType](Coproduct[MyriadInputInnerType](CwlType.String))))
-        ),
-      outputs = Array(
-        WorkflowOutputParameter(
-          id = "classout",
-          `type` = Option(Coproduct[MyriadOutputType](Coproduct[MyriadOutputInnerType](CwlType.File))),
-          outputSource = Option(Coproduct[WorkflowOutputParameter#OutputSource]("compile/classfile"))
-        )
-      ),
-      steps =
-        Array(
-           WorkflowStep(
-            id = "untar",
-            run = Coproduct[WorkflowStep.Run]("tar-param.cwl"),
-            in =
-              Array(
-                WorkflowStepInput(id = "tarfile", source = Option(Coproduct[InputSource]("inp"))),
-                WorkflowStepInput(id = "extractfile", source =  Option(Coproduct[InputSource]("ex")))
-              ),
-            out = Array(Coproduct[WorkflowStepOutputInnerType](WorkflowStepOutput("example_out")))
-          ),
-          WorkflowStep(
-            id = "compile",
-            run = Coproduct[WorkflowStep.Run]("arguments.cwl"),
-            in = Array(
-                 WorkflowStepInput(id = "src", source = Option(Coproduct[InputSource]("untar/example_out")))
-              ),
-            out = Array(Coproduct[WorkflowStepOutputInnerType](WorkflowStepOutput("classfile")))
-          )
-        )
-      )
-    val expectedWorkflowJsonString =
-      """cwlVersion: v1.0
-class: Workflow
-inputs:
-- id: inp
-  type: File
-- id: ex
-  type: string
-outputs:
-- id: classout
-  outputSource: compile/classfile
-  type: File
-steps:
-- id: untar
-  in:
-  - id: tarfile
-    source: inp
-  - id: extractfile
-    source: ex
-  out:
-  - example_out
-  run: tar-param.cwl
-- id: compile
-  in:
-  - id: src
-    source: untar/example_out
-  out:
-  - classfile
-  run: arguments.cwl
-""".stripMargin
-    assertCorrectJson(workflow.asCwl, expectedWorkflowJsonString)
-  }
-
-  it should "encode sample CWL env" ignore {
-    val tool = CommandLineTool(
-      id = "env",
-      baseCommand = Option(Coproduct[BaseCommand]("env")),
-      requirements = Option(Array(Coproduct[Requirement](EnvVarRequirement(
-        envDef = Array(EnvironmentDef("HELLO", Coproduct[StringOrExpression]("$(inputs.message)")))
-      )))),
-      inputs = Array(
-        CommandInputParameter(id =  "message", `type` = Option(Coproduct[MyriadInputType](Coproduct[MyriadInputInnerType](CwlType.String))))
-      )
-    )
-    val expectedToolJsonString =
-"""inputs:
-- id: message
-  type: string
-outputs: []
-class: CommandLineTool
-requirements:
-- class: EnvVarRequirement
-  envDef:
-  - envName: HELLO
-    envValue: $(inputs.message)
-cwlVersion: v1.0
-baseCommand: env
-""".stripMargin
-    assertCorrectJson(tool.asCwl, expectedToolJsonString)
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/ExpressionEvaluatorSpec.scala b/cwl/src/test/scala/cwl/ExpressionEvaluatorSpec.scala
deleted file mode 100644
index c723d923901..00000000000
--- a/cwl/src/test/scala/cwl/ExpressionEvaluatorSpec.scala
+++ /dev/null
@@ -1,24 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.expression.DefaultSizeIoFunctionSet
-import wom.values.{WomBoolean, WomString, WomValue}
-
-
-class ExpressionEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "ExpressionEvaluator"
-
-  it should "eval inputs of different types" in {
-    val values: Map[String, WomValue] = Map(
-      "myName" -> WomString("hi"),
-      "someother" -> WomBoolean(false)
-    )
-    val parameterContext = ParameterContext(DefaultSizeIoFunctionSet, Vector.empty, values)
-    ExpressionEvaluator.eval("inputs.myName", parameterContext).toTry.get should be(WomString("hi"))
-    ExpressionEvaluator.eval("inputs.someother", parameterContext).toTry.get should be(WomBoolean(false))
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ExpressionInterpolatorSpec.scala b/cwl/src/test/scala/cwl/ExpressionInterpolatorSpec.scala
deleted file mode 100644
index df27b5736e1..00000000000
--- a/cwl/src/test/scala/cwl/ExpressionInterpolatorSpec.scala
+++ /dev/null
@@ -1,121 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.ErrorOr._
-import common.validation.Validation._
-import cwl.ExpressionInterpolator.SubstitutionException
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.callable.RuntimeEnvironment
-import wom.expression.DefaultSizeIoFunctionSet
-import wom.values._
-
-
-class ExpressionInterpolatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "ExpressionInterpolator"
-
-  private lazy val expressionLib = Vector(
-    better.files.File(getClass.getResource("lodash.js").getPath).contentAsString,
-    "var t = function(s) { return _.template(s, {variable: 'data'})({'inputs': inputs}); };"
-  )
-
-  private lazy val parameterContext = {
-    val runtime = RuntimeEnvironment("out", "tmp", refineMV[Positive](1), 2.0D, 100L, 200L)
-    val inputs = Map(
-      "cram" -> WomSingleFile("/path/to/my.cram"),
-      "file1" -> WomSingleFile("/path/to/my.file.txt")
-    )
-    ParameterContext(DefaultSizeIoFunctionSet, expressionLib, inputs = inputs, runtimeOption = Option(runtime))
-  }
-
-  private def evaluator(string: String): ErrorOr[WomValue] = {
-    ExpressionEvaluator.eval(string, parameterContext)
-  }
-
-  private val validTests = Table(
-    ("description", "expression", "expected"),
-    ("an empty string", "", WomString("")),
-    ("a space", " ", WomString("")),
-    ("two spaces", "  ", WomString("")),
-    ("whitespace string", " \n \t", WomString("")),
-    ("a regular string", "hello world", WomString("hello world")),
-    ("a dollar sign", "$6.28", WomString("$6.28")),
-    ("two dollar signs", "$$(6.28)", WomString("$$(6.28)")),
-    ("three dollar signs", "$$$(6.28)", WomString("$$6.28")),
-    ("a backslash and a dollar sign", """\$(6.28)""", WomString("$(6.28)")),
-    ("two backslashes and a dollar sign", """\\$(6.28)""", WomString("""\6.28""")),
-    ("a underscore and a dollar sign", "_$(6.28)", WomString("_6.28")),
-    ("nested parens", """$(parseInt("6")).$(parseInt(("2")) + "" + parseInt(((("8")))))""", WomString("6.28")),
-    ("missing open parens", """$(parseInt("6")).$(parseInt(("2")) + "" + parseInt((("8")))))""", WomString("6.28)")),
-    ("quoted open parens", """$("(")""", WomString("(")),
-    ("quoted closing parens", """$(")")""", WomString(")")),
-    ("prefixed/suffixed nested parens",
-      """6.$(parseInt("2"))$(parseInt(("8")) + "" + parseInt(((("3")))))1""",
-      WomString("6.2831")),
-    ("expressions using libs",
-      """$(t("The file is <%= data.inputs.file1.path.split('/').slice(-1)[0] %>\n"))""",
-      WomString("The file is my.file.txt\n")),
-    ("two expressions", """$(runtime.outdir)/$(inputs.cram.basename)""", WomString("out/my.cram")),
-    ("two expressions suffixed", "$(runtime.outdir)/$(inputs.cram.basename).crai", WomString("out/my.cram.crai")),
-    ("two expressions prefixed/suffixed",
-      "/path/to/$(runtime.outdir)/$(inputs.cram.basename).crai",
-      WomString("/path/to/out/my.cram.crai")),
-    ("a replacement that must be escaped", """$("$(hello)")""", WomString("$(hello)")),
-    ("a string containing a start prefix", """$("$(")""", WomString("$(")),
-    ("a replacement returning a json object",
-      "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})",
-      WomObject(Map("output" -> WomInteger(2))))
-  )
-
-  forAll(validTests) { (description, expression, expected) =>
-    it should s"interpolate $description" in {
-      ExpressionInterpolator.interpolate(expression, evaluator).toTry.get should be(expected)
-    }
-  }
-
-  private val substitutionErrorTests = Table(
-    ("description", "expression", "expected"),
-    ("a missing closing paren", "$(", "0: $("),
-    ("a missing quote", """$("))""", """0: $("))"""),
-    ("complex missing closing parens",
-      """$(parseInt("6")).$(parseInt(("2")) + "" + parseInt(((("8"))))""",
-      """1: $(parseInt(("2")) + "" + parseInt(((("8"))))""")
-  )
-
-  forAll(substitutionErrorTests) { (description, expression, expected) =>
-    it should s"throw a substitution error for $description" in {
-      the[SubstitutionException] thrownBy {
-        ExpressionInterpolator.interpolate(expression, evaluator)
-      } should have message s"Substitution error, unfinished block starting at position $expected"
-    }
-  }
-
-  /**
-    * Tests that sorta work but do not generate the same _exact_ responses as cwltool.
-    *
-    * See docs at top of [[ExpressionInterpolator]].
-    *
-    * According to cwltool's expression.py when an interpolated string contains more than just an expression,
-    * `json.dumps` should be used to serialize Arrays and Maps, and Maps should sort their keys.
-    *
-    * We don't even test maps with multiple keys here as WomMap does not guarantee key order.
-    */
-  private val semiSupportedTests = Table(
-    ("description", "expression", "expected"),
-    ("an array", """$(["hello", "world"])""", """["hello", "world"]"""),
-    ("a map", """$({"hello": "world"})""", """object {hello: "world"}"""),
-    ("an array of maps", """$([{"hello": "world"}])""", """[object {hello: "world"}]"""),
-    ("a map of arrays", """$({"hello": ["world"]})""", """object {hello: ["world"]}""")
-  )
-
-  forAll(semiSupportedTests) { (description, expression, expected) =>
-    it should s"semi-interpolate a string plus $description" in {
-      val actual = ExpressionInterpolator.interpolate("_" + expression, evaluator).map(_.valueString).toTry.get
-      actual should be("_" + expected)
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/FileSpec.scala b/cwl/src/test/scala/cwl/FileSpec.scala
deleted file mode 100644
index 814c164bc16..00000000000
--- a/cwl/src/test/scala/cwl/FileSpec.scala
+++ /dev/null
@@ -1,54 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import cwl.CwlDecoder.decodeCwlFile
-import cwl.TestSetup.rootPath
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import wom.callable.Callable.InputDefinition
-import wom.callable.{CallableTaskDefinition, RuntimeEnvironment}
-import wom.graph.OptionalGraphInputNodeWithDefault
-import wom.values.WomValue
-
-
-class FileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "File"
-
-  private val fileTests = Table(
-    ("description", "filePath", "ioFunctionSet", "expectedCommand"),
-    ("get the basename of a file", "file_example.cwl", LocalIoFunctionSet, """   'echo' 'example.txt'   """.trim),
-    ("get the size of a file", "file_size_example.cwl", LocalIoFunctionSet, """   'echo' '12'   """.trim)
-  )
-
-  forAll(fileTests) { (description, filePath, ioFunctionSet, expectedCommand) =>
-    it should description in {
-      val cwl = decodeCwlFile(rootPath / filePath).value.unsafeRunSync().toOption.get
-      val executable = cwl.womExecutable(AcceptAllRequirements, None, ioFunctionSet, strictValidation = false).toOption.get
-      val call = executable.graph.calls.head
-      val runtimeEnvironment = RuntimeEnvironment("output/path", "temp/path", refineMV[Positive](1), 2e10, 100, 100)
-      val defaultCallInputs = executable.graph.nodes.collect({
-        case oginwd: OptionalGraphInputNodeWithDefault =>
-          val key: InputDefinition = call.inputDefinitionMappings.toMap.keys.find(
-            _.localName == oginwd.identifier.localName
-          ).get
-          val value: WomValue = key
-            .valueMapper(ioFunctionSet)(oginwd.default.evaluateValue(Map.empty, ioFunctionSet).toTry.get)
-            .value.unsafeRunSync()
-            .toOption.get
-
-          key -> value
-      }).toMap
-      val commandEither = call.callable.asInstanceOf[CallableTaskDefinition].instantiateCommand(
-        defaultCallInputs, ioFunctionSet, identity, runtimeEnvironment
-      ).toEither
-      val command = commandEither.toOption.get.commandString
-      command should be(expectedCommand)
-    }
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/FullyQualifiedNameSpec.scala b/cwl/src/test/scala/cwl/FullyQualifiedNameSpec.scala
deleted file mode 100644
index 9c3babfc634..00000000000
--- a/cwl/src/test/scala/cwl/FullyQualifiedNameSpec.scala
+++ /dev/null
@@ -1,27 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.command.ParentName
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class FullyQualifiedNameSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  implicit val parentName = ParentName.empty
-  
-  "workflow input id " should "get filename and id" in {
-    val wfid = FileAndId("file#id")
-
-    wfid.fileName shouldBe "file"
-    wfid.id shouldBe "id"
-  }
-
-  "workflow step output id " should "get filename, id, and step" in {
-    val wfid = FileStepAndId("file#step/id")
-
-    wfid.fileName shouldBe "file"
-    wfid.id shouldBe "id"
-    wfid.stepId shouldBe "step"
-  }
-}
diff --git a/cwl/src/test/scala/cwl/LocalIoFunctionSet.scala b/cwl/src/test/scala/cwl/LocalIoFunctionSet.scala
deleted file mode 100644
index b3ab33a5809..00000000000
--- a/cwl/src/test/scala/cwl/LocalIoFunctionSet.scala
+++ /dev/null
@@ -1,48 +0,0 @@
-package cwl
-
-import java.nio.file.{Files, Paths}
-import java.util.concurrent.Executors
-
-import wom.expression.EmptyIoFunctionSet
-
-import scala.jdk.CollectionConverters._
-import scala.concurrent.{ExecutionContext, Future}
-import scala.util.Try
-
-/**
-  * Test io functions that can read from local file systems.
-  */
-object LocalIoFunctionSet extends EmptyIoFunctionSet {
-  override implicit def ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(1))
-
-  private def stripLocalPrefix(path: String): String = {
-    path.stripPrefix("file://")
-  }
-
-  private def fileSize(path: String): Long = {
-    Files.size(Paths.get(stripLocalPrefix(path)))
-  }
-
-  private def contentsAsString(path: String): String = {
-    Files.readAllLines(Paths.get(stripLocalPrefix(path))).asScala.mkString("\n")
-  }
-
-  override def readFile(path: String, maxBytesOption: Option[Int] = None,
-                        failOnOverflow: Boolean = false): Future[String] = {
-    Future.fromTry(Try {
-      maxBytesOption match {
-        case Some(maxBytes) if failOnOverflow && fileSize(path) > maxBytes =>
-          throw new RuntimeException(s"overflow while reading $path: ${fileSize(path)} > $maxBytes")
-        case Some(maxBytes) => contentsAsString(path).take(maxBytes)
-        case None => contentsAsString(path)
-      }
-    })
-  }
-
-  override def size(params: String): Future[Long] = {
-    Future.fromTry(Try {
-        fileSize(params)
-    }
-    )
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ParseBigThreeSpec.scala b/cwl/src/test/scala/cwl/ParseBigThreeSpec.scala
deleted file mode 100644
index e5ac02e80f4..00000000000
--- a/cwl/src/test/scala/cwl/ParseBigThreeSpec.scala
+++ /dev/null
@@ -1,34 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.CwlDecoder._
-import cwl.TestSetup._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class ParseBigThreeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  val namespace = "cwl"
-
-  it should "parse 1st tool" in {
-
-  decodeCwlFile(rootPath/"1st-tool.cwl").
-    value.
-    unsafeRunSync().
-    isRight shouldBe true
-  }
-
-  it should "parse first workflow" in {
-    decodeCwlFile(rootPath/"1st-workflow.cwl").
-      value.
-      unsafeRunSync().
-      isRight shouldBe true
-  }
-
-  it should "parse env cwl" in {
-    decodeCwlFile(rootPath/"env.cwl").
-      value.
-      unsafeRunSync().
-      isRight shouldBe true
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ParsingSpec.scala b/cwl/src/test/scala/cwl/ParsingSpec.scala
deleted file mode 100644
index 92c454a0964..00000000000
--- a/cwl/src/test/scala/cwl/ParsingSpec.scala
+++ /dev/null
@@ -1,63 +0,0 @@
-package cwl
-
-import CwlDecoder._
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-
-class WorkflowParsingSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "Workflow Json Parser"
-
-  def workflowJson(classValue: String) = s"""{"class":"$classValue", "cwlVersion": "v1.0", "id": "MyCwlWorkflow", "inputs":[], "outputs":[], "steps":[]}"""
-
-  it should "accept the Workflow argument" in {
-     decodeCwlString(workflowJson("Workflow")).value.unsafeRunSync() match {
-       case Right(_) => // great!
-       case Left(e) => fail(s"Workflow rejected because: ${e.toList.mkString(", ")}")
-     }
-  }
-
-  it should "not parse w/something other than Workflow as class" in {
-    decodeCwlString(workflowJson("wrong")).value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(wf) => fail(s"workflow unexpectedly accepted: $wf")
-    }
-  }
-
-  it should "not parse when class argument is missing" in {
-    decodeCwlString("""{"cwlVersion": "v1.0", "inputs":[], "outputs":[], "steps":[]}""").value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(wf) => fail(s"workflow unexpectedly accepted: $wf")
-    }
-  }
-}
-
-class CommandLineToolParsingSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "CommandLineTool Json Parser"
-
-  def commandLineToolJson(classValue: String) = s"""{"class":"$classValue", "cwlVersion":"v1.0", "id": "MyCwlTask", "inputs":[], "outputs":[]}"""
-
-  it should "accept the CommandLineTool argument for class" in {
-    decodeCwlString(commandLineToolJson("CommandLineTool")).value.unsafeRunSync() match {
-      case Right(_) => // great!
-      case Left(e) => fail(s"CommandLineTool rejected because: $e")
-    }
-  }
-
-  it should "not parse w/something other than CommandLineTool" in {
-    decodeCwlString(commandLineToolJson("wrong")).value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(clt) => fail(s"CommandLineTool unexpectedly accepted: $clt")
-    }
-  }
-
-  it should "doesn't parse when class argument is missing" in {
-    decodeCwlString("""{"inputs":[], "outputs":[]}""").value.unsafeRunSync() match {
-      case Left(_) => // great!
-      case Right(clt) => fail(s"CommandLineTool unexpectedly accepted: $clt")
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/ScatterLogicSpec.scala b/cwl/src/test/scala/cwl/ScatterLogicSpec.scala
deleted file mode 100644
index 8afd3c9df16..00000000000
--- a/cwl/src/test/scala/cwl/ScatterLogicSpec.scala
+++ /dev/null
@@ -1,140 +0,0 @@
-package cwl
-
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.BeforeAndAfterEach
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import spray.json.DefaultJsonProtocol
-import wom.graph.ScatterNode.ScatterVariableAndValue
-import wom.graph.expression.PlainAnonymousExpressionNode
-import wom.graph.{ScatterNode, ScatterVariableNode, WomIdentifier}
-import wom.types.{WomArrayType, WomStringType}
-import wom.values.{WomArray, WomString, WomValue}
-
-class ScatterLogicSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks
-  with DefaultJsonProtocol with BeforeAndAfterEach {
-  private val expressionNode = PlainAnonymousExpressionNode(WomIdentifier("name"), null, WomStringType, Map.empty)
-  private val arrayStringType = WomArrayType(WomStringType)
-
-  private val emptyArray = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List.empty)
-  )
-  private val simpleArray2 = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List(WomString("a"), WomString("b")))
-  )
-  private val simpleArray3 = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List(WomString("a"), WomString("b"), WomString("c")))
-  )
-  private val simpleArray4 = ScatterVariableAndValue(
-    ScatterVariableNode(null, expressionNode, WomStringType),
-    WomArray(arrayStringType, List(WomString("a"), WomString("b"), WomString("c"), WomString("d")))
-  )
-
-  override def beforeEach(): Unit = {
-    // The index length of the SVN is a mutable value, to avoid tests stepping on each others reset it to the default value
-    // before each test
-    emptyArray.scatterVariableNode.withRelativeIndexLength(1)
-    simpleArray2.scatterVariableNode.withRelativeIndexLength(1)
-    simpleArray3.scatterVariableNode.withRelativeIndexLength(1)
-    simpleArray4.scatterVariableNode.withRelativeIndexLength(1)
-  }
-
-  private val valueA = WomString("a")
-  private val valueB = WomString("b")
-  private val valueC = WomString("c")
-  private val valueD = WomString("d")
-
-  private def validateScatterCombinations(list: List[ScatterNode.ScatterVariableAndValue],
-                                  scatterSize: Int,
-                                  expected: List[List[Int]]) = {
-    // Go through all the variable nodes and feed all the shard numbers to the indexForShard function
-    val combinations = list.map({
-      case ScatterVariableAndValue(node, values) =>
-        (0 until scatterSize).map(node.indexForShard(_, values.size)).toList
-    })
-
-    combinations should contain theSameElementsInOrderAs expected
-  }
-
-  "CrossProduct scattering function" should "generate correct results" in {
-    val nonEmptyVariables = Table(
-      // None for the index length means "don't check because irrelevant"
-      ("variablesAndValues", "scatterSize", "arrayIndexes"),
-      (List(simpleArray2), 2, List(List(0, 1))),
-      (List(simpleArray2, simpleArray3), 6, List(List(0, 0, 0, 1, 1, 1), List(0, 1, 2, 0, 1, 2))),
-      (List(simpleArray2, simpleArray3, simpleArray4), 24, List(
-        List(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
-        List(0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2),
-        List(0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3))
-      )
-    )
-
-    forAll(nonEmptyVariables) { case (list, scatterSize, expected) =>
-      ScatterLogic.CrossProductScatterProcessingFunction(list) shouldBe Right(scatterSize)
-      validateScatterCombinations(list, scatterSize, expected)
-    }
-
-    List(List(emptyArray), List(emptyArray, simpleArray2), List(simpleArray2, emptyArray)) foreach { list =>
-      ScatterLogic.CrossProductScatterProcessingFunction(list) shouldBe Right(0)
-    }
-  }
-
-  "DotProduct scattering function" should "generate correct results" in {
-    import common.validation.Checked._
-    val simpleArray2Duplicate = ScatterVariableAndValue(
-      ScatterVariableNode(null, expressionNode, WomStringType),
-      WomArray(arrayStringType, List(WomString("a"), WomString("b")))
-    )
-    val nonEmptyVariables = Table(
-      // None for the index length means "don't check because irrelevant"
-      ("variablesAndValues", "scatterSize", "arrayIndexes"),
-      (List(simpleArray2, simpleArray2Duplicate), 2.validNelCheck, List(List(0, 1), List(0, 1))),
-      (List(simpleArray2, simpleArray3), "All arrays must have the same number of element when using the dot product scatter method".invalidNelCheck, List.empty)
-    )
-
-    forAll(nonEmptyVariables) { case (list, expectedScatterSize, expected) =>
-      ScatterLogic.DotProductScatterProcessingFunction(list) shouldBe expectedScatterSize
-
-      expectedScatterSize match {
-        case Right(scatterSize) => validateScatterCombinations(list, scatterSize, expected)
-        case _ => // Only verify combinations if the scatter is valid
-      }
-    }
-  }
-
-  "NestedCrossProduct collecting function builder" should "generate correct results" in {
-    import spray.json._
-
-    val arrayString = arrayStringType
-    val nestedArrayString = WomArrayType(arrayString)
-    val nestedArrayString2 = WomArrayType(nestedArrayString)
-
-    val variables = Table(
-      ("arraySizes", "shards", "valueType", "result"),
-      (List(0), List.empty, arrayString, "[]"),
-      (List(0, 2), List.empty, nestedArrayString, "[]"),
-      (List(2, 0), List.empty, nestedArrayString, "[[], []]"),
-      (List(2, 3, 0), List.empty, nestedArrayString2, "[[[], [], []], [[], [], []]]"),
-      (List(2, 0, 3), List.empty, nestedArrayString2, "[[], []]"),
-      // This technically should not happen since to have a cross product we need at least 2 scatter variables but..
-      (List(2), List(valueA, valueB), arrayString, """["a", "b"]"""),
-      (List(2, 2), List(valueA, valueB, valueC, valueD), nestedArrayString, """[["a", "b"], ["c", "d"]]"""),
-      (List(3, 2), List(valueA, valueB, valueC, valueD, valueA, valueB), nestedArrayString, """[["a", "b"], ["c", "d"], ["a", "b"]]"""),
-      (List(2, 3), List(valueA, valueB, valueC, valueC, valueB, valueA), nestedArrayString, """[["a", "b", "c"], ["c", "b", "a"]]"""),
-      (List(2, 3, 2), List(
-        valueA, valueB, valueA, valueB, valueA, valueB,
-        valueC, valueD, valueC, valueD, valueC, valueD
-      ), nestedArrayString2, """[[["a", "b"], ["a", "b"], ["a", "b"]], [["c", "d"], ["c", "d"], ["c", "d"]]]""")
-    )
-
-    forAll(variables) { case (arraySizes, shards, valueType, result) =>
-      val collection = ScatterLogic.NestedCrossProductScatterCollectionFunctionBuilder(arraySizes)(shards, valueType)
-      collection.arrayType shouldBe valueType
-      (collection: WomValue).toJson(WomValueJsonFormatter.WomValueJsonFormat) shouldBe result.parseJson
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/TestSetup.scala b/cwl/src/test/scala/cwl/TestSetup.scala
deleted file mode 100644
index 14e5dbe9b05..00000000000
--- a/cwl/src/test/scala/cwl/TestSetup.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cwl
-
-import better.files.File.currentWorkingDirectory
-
-object TestSetup {
-
-  val rootPath = currentWorkingDirectory/"cwl"/"src"/"test"/"resources"
-
-}
diff --git a/cwl/src/test/scala/cwl/WomTypeConversionSpec.scala b/cwl/src/test/scala/cwl/WomTypeConversionSpec.scala
deleted file mode 100644
index e7b76b153dc..00000000000
--- a/cwl/src/test/scala/cwl/WomTypeConversionSpec.scala
+++ /dev/null
@@ -1,134 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.types._
-import mouse.`try`._
-
-import scala.util.Try
-
-class WomTypeConversionSpec extends AnyFlatSpec with Matchers {
-  behavior of "WomTypeConversion"
-
-  /* ******** Inputs *********** */
-  it should "convert ArrayInputSchema" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val x = InputArraySchema(items = Coproduct[MyriadInputType](y))
-    val z = Coproduct[MyriadInputInnerType](x)
-    Coproduct[MyriadInputType](z).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomArrayType(WomStringType)
-  }
-
-  it should "convert Cwl Input String" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    Coproduct[MyriadInputType](y).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe WomStringType
-  }
-
-  it should "convert Array of a single type is actually one type not in an array" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    Coproduct[MyriadInputType](Array(y)).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomStringType
-  }
-
-  it should "convert Array of more than one type becomes a coproduct" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Boolean)
-    Coproduct[MyriadInputType](Array(y, z)).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType))
-  }
-
-  it should "convert Array of more than one type and a null becomes an optional coproduct" in {
-    val x = Coproduct[MyriadInputInnerType](CwlType.Null)
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Boolean)
-    Coproduct[MyriadInputType](Array(x, y, z)).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomOptionalType(WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType)))
-  }
-
-  it should "convert a 2-element Input Array of a single type accompanied by a null is an optional type" in {
-    val y = Coproduct[MyriadInputInnerType](CwlType.String)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Null)
-    testInputArray(Array(y,z), WomOptionalType(WomStringType))
-  }
-
-  private def testInputArray(array: Array[MyriadInputInnerType], assertedType: WomType ) = {
-    def f(array: Array[MyriadInputInnerType]) =
-      Try(Coproduct[MyriadInputType](array).fold(MyriadInputTypeToWomType).apply(SchemaDefRequirement())).cata(
-        success => withClue("input should evaluate to an optional array of files type")(success shouldBe assertedType),
-        failure => fail(s"expected an optional array of files type but received a failure: $failure")
-      )
-    f(array)
-    f(array.reverse)
-  }
-
-  it should "convert Optional Array of a type is interpreted correctly as input type" in {
-    val miit = Coproduct[MyriadInputInnerType](CwlType.File)
-    val mit = Coproduct[MyriadInputType](miit)
-    val ias =  InputArraySchema(items = mit)
-    val y = Coproduct[MyriadInputInnerType](ias)
-    val z = Coproduct[MyriadInputInnerType](CwlType.Null)
-    testInputArray(Array(y, z), WomOptionalType(WomMaybeEmptyArrayType(WomMaybePopulatedFileType)))
-  }
-
-  /* ******** Outputs *********** */
-  it should "convert ArrayOutputSchema" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val x = OutputArraySchema(items = Coproduct[MyriadOutputType](y))
-    val z = Coproduct[MyriadOutputInnerType](x)
-    Coproduct[MyriadOutputType](z).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomArrayType(WomStringType)
-  }
-
-  it should "convert Cwl Output String" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    Coproduct[MyriadOutputType](y).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe WomStringType
-  }
-
-  it should "convert Array of a single type is the same as one type not in an array" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    Coproduct[MyriadOutputType](Array(y)).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomStringType
-  }
-
-  it should "convert Output Array of more than one type becomes a coproduct" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val z = Coproduct[MyriadOutputInnerType](CwlType.Boolean)
-    Coproduct[MyriadOutputType](Array(y, z)).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType))
-  }
-
-  it should "convert Output Array of more than one types including a null is an optional coproduct" in {
-    val x = Coproduct[MyriadOutputInnerType](CwlType.Null)
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val z = Coproduct[MyriadOutputInnerType](CwlType.Boolean)
-    Coproduct[MyriadOutputType](Array(x, y, z)).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement()) shouldBe
-      WomOptionalType(WomCoproductType(NonEmptyList.of(WomStringType, WomBooleanType)))
-  }
-
-  private def testOutputArray(array: Array[MyriadOutputInnerType], assertedType: WomType) = {
-    def f(array: Array[MyriadOutputInnerType]) =
-      Try(Coproduct[MyriadOutputType](array).fold(MyriadOutputTypeToWomType).apply(SchemaDefRequirement())).cata(
-        success => withClue("input should evaluate to an optional string type")(success shouldBe assertedType),
-        failure => fail(s"expected an optional string type but received a failure: $failure")
-      )
-    f(array)
-    f(array.reverse)
-  }
-
-  it should "convert a 2-element Output Array of a single type accompanied by a null is an optional type" in {
-    val y = Coproduct[MyriadOutputInnerType](CwlType.String)
-    val z = Coproduct[MyriadOutputInnerType](CwlType.Null)
-    testOutputArray(Array(y,z), WomOptionalType(WomStringType))
-  }
-
-  it should "convert Optional Array of a type is interpreted correctly as output type" in {
-    val moit = Coproduct[MyriadOutputInnerType](CwlType.File)
-    val mot = Coproduct[MyriadOutputType](moit)
-    val oas =  OutputArraySchema(items = mot)
-    val moit2 = Coproduct[MyriadOutputInnerType](oas)
-    val moit3 = Coproduct[MyriadOutputInnerType](CwlType.Null)
-    testOutputArray(Array(moit2,moit3), WomOptionalType(WomMaybeEmptyArrayType(WomMaybePopulatedFileType)))
-  }
-}
diff --git a/cwl/src/test/scala/cwl/WomValueJsonFormatter.scala b/cwl/src/test/scala/cwl/WomValueJsonFormatter.scala
deleted file mode 100644
index 7939a076dc2..00000000000
--- a/cwl/src/test/scala/cwl/WomValueJsonFormatter.scala
+++ /dev/null
@@ -1,27 +0,0 @@
-package cwl
-
-import spray.json.{JsArray, JsBoolean, JsNull, JsNumber, JsObject, JsString, JsValue, RootJsonFormat}
-import wom.values.{WomArray, WomBoolean, WomFile, WomFloat, WomInteger, WomMap, WomObjectLike, WomOptionalValue, WomPair, WomString, WomValue}
-
-// Sometimes it's hard for compiler plugins to find this in ScatterLogicSpec, so here it is again:
-object WomValueJsonFormatter {
-  implicit object WomValueJsonFormat extends RootJsonFormat[WomValue] {
-    def write(value: WomValue): JsValue = value match {
-      case s: WomString => JsString(s.value)
-      case i: WomInteger => JsNumber(i.value)
-      case f: WomFloat => JsNumber(f.value)
-      case b: WomBoolean => JsBoolean(b.value)
-      case f: WomFile => JsString(f.value)
-      case o: WomObjectLike => new JsObject(o.values map {case(k, v) => k -> write(v)})
-      case a: WomArray => new JsArray(a.value.map(write).toVector)
-      case m: WomMap => new JsObject(m.value map {case(k,v) => k.valueString -> write(v)})
-      case q: WomPair => new JsObject(Map("left" -> write(q.left), "right" -> write(q.right)))
-      case WomOptionalValue(_, Some(innerValue)) => write(innerValue)
-      case WomOptionalValue(_, None) => JsNull
-      // handles WdlExpression
-      case v: WomValue => JsString(v.toWomString)
-
-    }
-    def read(value: JsValue): WomValue = throw new UnsupportedOperationException
-  }
-}
diff --git a/cwl/src/test/scala/cwl/WorkflowStepInputExpressionSpec.scala b/cwl/src/test/scala/cwl/WorkflowStepInputExpressionSpec.scala
deleted file mode 100644
index 122156b4f4e..00000000000
--- a/cwl/src/test/scala/cwl/WorkflowStepInputExpressionSpec.scala
+++ /dev/null
@@ -1,59 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import cats.data.Validated._
-import cwl.WorkflowStepInput.InputSource
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import shapeless.Coproduct
-import wom.graph.GraphNodePort.GraphNodeOutputPort
-import wom.graph.WomIdentifier
-import wom.types._
-import wom.values.{WomArray, WomInteger, WomString}
-
-class WorkflowStepInputExpressionSpec extends AnyFlatSpec with Matchers {
-  behavior of "WorkflowStepInputExpression"
-
-  it should "assert source arrays are concatenated when merge_flattened LinkMergeMethod is used" in {
-    val inputSource = Coproduct[InputSource](Array("i1", "i2"))
-    val i1OutputPort = GraphNodeOutputPort(WomIdentifier("i1"), WomStringType, null)
-    val i2OutputPort = GraphNodeOutputPort(WomIdentifier("i2"), WomStringType, null)
-    val wsi = WorkflowStepInput("s#h", source = Option(inputSource), linkMerge = Option(LinkMergeMethod.MergeFlattened))
-
-    val mergeTpeEither = wsi.determineMergeType(
-      sources = Map("i1" -> WomArrayType(WomStringType), "i2" -> WomArrayType(WomStringType)),
-      expectedTypeAsWom = Option(WomArrayType(WomStringType)))
-
-    val tpe: WomType = fromEither(mergeTpeEither).getOrElse(throw new RuntimeException("expected a womType but evaluation of determineType failed"))
-
-    val expression = WorkflowStepInputMergeExpression(wsi, tpe, NonEmptyList.of("i1" -> i1OutputPort, "i2" -> i2OutputPort), Vector.empty)
-
-    val r = expression.evaluateValue(Map("i1" -> WomString("1"), "i2" -> WomString("2")), null)
-    r shouldBe Valid(WomArray(Seq(WomString("1"), WomString("2"))))
-  }
-
-  it should "array of one entry for each input link when merge_nested is used" in {
-    val inputSource =  Coproduct[InputSource](Array("i1", "i2"))
-    val i1OutputPort = GraphNodeOutputPort(WomIdentifier("i1"), WomStringType, null)
-    val i2OutputPort = GraphNodeOutputPort(WomIdentifier("i2"), WomStringType, null)
-    val wsi = WorkflowStepInput("s#h", source = Option(inputSource))
-    val expression = WorkflowStepInputMergeExpression(wsi, null, NonEmptyList.of("i1" -> i1OutputPort, "i2" -> i2OutputPort), Vector.empty)
-
-    expression.evaluateValue(Map("i1" -> WomInteger(1), "i2" -> WomInteger(2)), null) shouldBe
-      Valid(WomArray(Seq(
-        WomInteger(1),
-        WomInteger(2)
-      )))
-  }
-
-  it should "list of one entry for when there is only one input link and when merge_nested is used" in {
-    val inputSource =  Coproduct[InputSource]("i1")
-    val wsi = WorkflowStepInput("s#h", source = Option(inputSource))
-    val i1OutputPort = GraphNodeOutputPort(WomIdentifier("i1"), WomStringType, null)
-    val expression = WorkflowStepInputMergeExpression(wsi, null, NonEmptyList.of("i1" -> i1OutputPort), Vector.empty)
-
-    expression.evaluateValue(Map("i1" -> WomInteger(1), "i2" -> WomInteger(2)), null) shouldBe
-      Valid(WomInteger(1))
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/WorkflowStepInputSpec.scala b/cwl/src/test/scala/cwl/WorkflowStepInputSpec.scala
deleted file mode 100644
index 5592e2ffddd..00000000000
--- a/cwl/src/test/scala/cwl/WorkflowStepInputSpec.scala
+++ /dev/null
@@ -1,109 +0,0 @@
-package cwl
-
-import cats.data.NonEmptyList
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.types._
-
-class WorkflowStepInputSpec extends AnyFlatSpec with Matchers {
-  behavior of "WorkflowStepInput"
-
-  it should "use single source type if no default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = false
-    ) shouldBe
-      Right(WomStringType)
-  }
-
-  it should "use optional single source type if no default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomOptionalType(WomStringType)),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe
-      Right(WomOptionalType(WomStringType))
-  }
-
-  it should "use single source type if there's a default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = true,
-    ) shouldBe
-      Right(WomStringType)
-  }
-
-  it should "use unpacked single source type if there's a default value and no merge method is specified" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomOptionalType(WomStringType)),
-      linkMerge = None,
-      expectedTypeAsWom = None,
-      hasDefault = true,
-    ) shouldBe
-      Right(WomStringType)
-  }
-
-  it should "wrap single source type in an array if merge method is nested" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType),
-      linkMerge = Option(LinkMergeMethod.MergeNested),
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe
-      Right(WomArrayType(WomStringType))
-  }
-
-  it should "find the closest common type to all sources if merge method is nested" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType, "s#in2" -> WomIntegerType),
-      linkMerge = Option(LinkMergeMethod.MergeNested),
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe
-      Right(WomMaybeEmptyArrayType(WomStringType))
-  }
-
-  it should "validate array inner type against target type if merge method is flattened" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType, "s#in2" -> WomStringType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = Option(WomArrayType(WomStringType)),
-      hasDefault = false,
-    ) shouldBe Right(WomArrayType(WomStringType))
-  }
-
-  it should "validate type against target type if merge method is flattened" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomStringType, "s#in2" -> WomStringType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = Option(WomStringType),
-      hasDefault = false,
-    ) shouldBe Right(WomArrayType(WomStringType))
-  }
-
-  it should "fail if target type does not conform to source types if merge method is flattened" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomObjectType, "s#in2" -> WomObjectType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = Option(WomStringType),
-      hasDefault = false,
-    ) shouldBe Left(NonEmptyList.one(
-      "could not verify that types Map(s#in -> WomObjectType, s#in2 -> WomObjectType)" +
-        " and the items type of the run's InputArraySchema WomStringType were compatible"
-    ))
-  }
-
-  it should "fall back to the closest common type" in {
-    WorkflowStepInput.determineMergeType(
-      sources = Map("s#in" -> WomBooleanType, "s#in2" -> WomIntegerType),
-      linkMerge = Option(LinkMergeMethod.MergeFlattened),
-      expectedTypeAsWom = None,
-      hasDefault = false,
-    ) shouldBe Right(WomStringType)
-  }
-}
diff --git a/cwl/src/test/scala/cwl/internal/EcmaScriptUtilSpec.scala b/cwl/src/test/scala/cwl/internal/EcmaScriptUtilSpec.scala
deleted file mode 100644
index adf482c2e82..00000000000
--- a/cwl/src/test/scala/cwl/internal/EcmaScriptUtilSpec.scala
+++ /dev/null
@@ -1,96 +0,0 @@
-package cwl.internal
-
-import common.assertion.CromwellTimeoutSpec
-import common.validation.Validation._
-import delight.rhinosandox.exceptions.ScriptDurationException
-import org.mozilla.javascript.{EcmaError, EvaluatorException}
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wom.types._
-import wom.values._
-
-class EcmaScriptUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "EcmaScriptUtil"
-
-  private lazy val encoder = new EcmaScriptEncoder()
-
-  it should "lookup a map entry with a string key" in {
-    val values =
-      "myName" -> WomMap(
-        WomMapType(WomBooleanType, WomArrayType(WomStringType)),
-        Map(WomBoolean(true) -> WomArray(WomArrayType(WomStringType), Seq(WomString("myValue"))))
-      )
-    val expr = """myName["true"][0] + 'Plus'"""
-    val result: WomValue = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(WomString("myValuePlus"))
-  }
-
-  it should "lookup a map entry with a boolean key" in {
-    val values =
-      "myName" -> WomMap(
-        WomMapType(WomBooleanType, WomArrayType(WomStringType)),
-        Map(WomBoolean(true) -> WomArray(WomArrayType(WomStringType), Seq(WomString("myValue"))))
-      )
-    val expr = "myName[true][0] + 'PlusPlus'"
-    val result = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(WomString("myValuePlusPlus"))
-  }
-
-  it should "JSON.stringify" in {
-    val values =
-      "myName" -> WomMap(
-        WomMapType(WomBooleanType, WomArrayType(WomStringType)),
-        Map(WomBoolean(true) -> WomArray(WomArrayType(WomStringType), Seq(WomString("myValue"))))
-      )
-    val expr = "JSON.stringify(myName)"
-    val result: WomValue = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(WomString("""{"true":["myValue"]}"""))
-  }
-
-  it should "Array.prototype.sort" in {
-    val values = "myName" -> WomArray(List("hello", "world", "alpha", "zulu", "indigo").map(WomString))
-    val expr = "myName.sort()"
-    val expected = WomArray(List("alpha", "hello", "indigo", "world", "zulu").map(WomString))
-    val result = EcmaScriptUtil.evalStructish(expr, values, encoder = encoder).toTry.get
-    result should be(expected)
-  }
-
-  it should "run in strict mode" in {
-    the[EvaluatorException] thrownBy {
-      EcmaScriptUtil.evalRaw(
-        """|function sum(a, a, c) { // !!! syntax error
-           |  return a + a + c; // wrong if this code ran
-           |}
-           |""".stripMargin) { (_, _) => () }
-    } should have message
-      """Parameter "a" already declared in this function. (<ecmascript>#1)"""
-  }
-
-  it should "not run java code" in {
-    the[EcmaError] thrownBy {
-      EcmaScriptUtil.evalRaw(
-        """|var path = java.nio.file.Paths.get("/etc/passwd");
-           |java.nio.file.Files.exists(path);
-           |// Or even... java.lang.System.exit(42);
-           |""".stripMargin) { (_, _) => () }
-    } should have message
-      """ReferenceError: "java" is not defined. (<ecmascript>#1)"""
-  }
-
-  it should "not run forever" in {
-    a[ScriptDurationException] should be thrownBy {
-      EcmaScriptUtil.evalRaw(
-        """|function sleep(milliseconds) {
-           |  var start = new Date().getTime();
-           |  while(true) {
-           |    if ((new Date().getTime() - start) > milliseconds){
-           |      break;
-           |    }
-           |  }
-           |}
-           |sleep(120 * 1000);
-           |""".stripMargin) { (_, _) => () }
-    }
-  }
-}
diff --git a/cwl/src/test/scala/cwl/internal/EnhancedRhinoSandboxSpec.scala b/cwl/src/test/scala/cwl/internal/EnhancedRhinoSandboxSpec.scala
deleted file mode 100644
index 01409d3c546..00000000000
--- a/cwl/src/test/scala/cwl/internal/EnhancedRhinoSandboxSpec.scala
+++ /dev/null
@@ -1,141 +0,0 @@
-package cwl.internal
-
-import java.util.concurrent.{CountDownLatch, TimeUnit}
-
-import common.assertion.CromwellTimeoutSpec
-import cwl.internal.EnhancedRhinoSandboxSpec.CachedClassLoader
-import org.apache.commons.io.IOUtils
-import org.mozilla.javascript.ContextFactory
-import org.scalatest.concurrent.ScaledTimeSpans
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-import scala.concurrent.duration._
-
-class EnhancedRhinoSandboxSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScaledTimeSpans {
-
-  behavior of "EnhancedRhinoSandbox"
-
-  it should "synchronize global ContextFactory initialization" in {
-    // Initialize the context factory here to be sure that our loaded runner is actually using a fresh ContextFactory
-    new EnhancedRhinoSandbox(true).assertContextFactory()
-
-    val threadCount = 10
-
-    // A custom loader that will contain our fresh static ContextFactory
-    val cachedClassLoader = new CachedClassLoader
-    // A latch that lets this test know the threads are ready
-    val threadReadyLatch = new CountDownLatch(threadCount)
-    // A latch to ensure that all threads try to run at the same time
-    val threadGoLatch = new CountDownLatch(1)
-
-    class Runner(name: String) extends Thread {
-      var success = false
-
-      override def run(): Unit = {
-        EnhancedRhinoSandboxSpec.runClassLoaded(
-          cachedClassLoader,
-          threadReadyLatch = threadReadyLatch,
-          threadGoLatch = threadGoLatch
-        )
-        success = true
-      }
-    }
-
-    val threads = (0 until threadCount).map(i => new Runner(i.toString))
-    // move all the threads to the starting line...
-    threads.foreach(_.start())
-    // Wait for threads to say they're ready
-    threadReadyLatch.await(scaled(10.seconds).toMillis, TimeUnit.MILLISECONDS)
-    // go!
-    threadGoLatch.countDown()
-    // Maximum time to wait for each runner to finish
-    threads.foreach(_.join(scaled(10.seconds).toMillis))
-
-    withClue("all threads did not complete successfully:") {
-      threads.map(_.success) should contain only true
-    }
-  }
-}
-
-object EnhancedRhinoSandboxSpec extends ScaledTimeSpans {
-  /**
-    * Runs a runner loaded from a custom class loader.
-    */
-  private def runClassLoaded(ecmaScriptUtilClassLoader: CachedClassLoader,
-                             threadReadyLatch: CountDownLatch,
-                             threadGoLatch: CountDownLatch): Unit = {
-    val cls = ecmaScriptUtilClassLoader.loadClass(classOf[LatchedRunner].getName)
-    val obj = cls.getDeclaredConstructor().newInstance()
-    cls
-      .getMethod("run", classOf[CountDownLatch], classOf[CountDownLatch])
-      .invoke(obj, threadReadyLatch, threadGoLatch)
-    ()
-  }
-
-  /**
-    * Waits for a shared latch and then quickly tries to run the EcmaScriptUtil.
-    * Before running, there is a test that ensures that the ContextFactory has _not_ been initialized.
-    *
-    * Inspired by: https://stackoverflow.com/questions/13263079/run-two-thread-at-the-same-time-in-java#13263273
-    */
-  class LatchedRunner {
-    def run(threadReadyLatch: CountDownLatch, threadGoLatch: CountDownLatch): Unit = {
-      require(!ContextFactory.hasExplicitGlobal, "The ContextFactory within this classloader is already initialized")
-      // Notify the test we're at the starting line.
-      threadReadyLatch.countDown()
-      // This await is for the time between all the threads `start()`-ing up, and the `countDownLatch.countDown()`
-      threadGoLatch.await(scaled(5.seconds).toMillis, TimeUnit.MILLISECONDS)
-      new EnhancedRhinoSandbox(true).assertContextFactory()
-      ()
-    }
-  }
-
-  /**
-    * Locates a class but instead of returning the class from the original classloader it instead returns a cached copy.
-    *
-    * This is needed when we want to ensure that a static variable has NOT been initialized on a class instance.
-    *
-    * Parent class loader must be the current thread's class loader since the system class loader is NOT sufficient
-    * under sbt.
-    *
-    * Inspired by: https://stackoverflow.com/questions/14316996/how-to-replace-classes-in-a-running-application-in-java#14317506
-    */
-  class CachedClassLoader extends ClassLoader(Thread.currentThread.getContextClassLoader) {
-
-    override def loadClass(name: String): Class[_] = {
-      loadedClasses synchronized {
-        loadedClasses.getOrElseUpdate(name, internalLoadClass(name))
-      }
-    }
-
-    /** Classes to always load from the parent. */
-    private val parentPackages = List("scala", "java", "sun")
-    /** Synchronized mutable map of our already loaded classes. */
-    private val loadedClasses = scala.collection.mutable.Map.empty[String, Class[_]]
-
-    /**
-      * Locates a class but returns our _own_ copy of it. Classes under "scala", "java", and "sun" will use the parent.
-      * If a class cannot be located for any reason, the parent is also returned.
-      *
-      * @param name Name of the class to load.
-      * @return The loaded class.
-      */
-    private def internalLoadClass(name: String): Class[_] = {
-      if (!parentPackages.exists(pkg => name.startsWith(pkg + "."))) {
-        val inputStream = getParent.getResourceAsStream(name.replace(".", "/").concat(".class"))
-        try {
-          val bytes = IOUtils.toByteArray(inputStream)
-          return defineClass(name, bytes, 0, bytes.length)
-        } catch {
-          case _: Throwable => /* ignore and fall through to loading from the parent */
-        } finally {
-          if (inputStream != null)
-            inputStream.close()
-        }
-      }
-      getParent.loadClass(name)
-    }
-  }
-
-}
diff --git a/cwl/src/test/scala/cwl/ontology/SchemaSpec.scala b/cwl/src/test/scala/cwl/ontology/SchemaSpec.scala
deleted file mode 100644
index 06f552797a8..00000000000
--- a/cwl/src/test/scala/cwl/ontology/SchemaSpec.scala
+++ /dev/null
@@ -1,114 +0,0 @@
-package cwl.ontology
-
-import com.typesafe.config.ConfigFactory
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks
-import org.semanticweb.owlapi.apibinding.OWLManager
-
-class SchemaSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
-
-  behavior of "Schema"
-
-  val resolveTests = Table(
-    ("base", "iri", "expected"),
-    ("file:///hello/world", "custom.owl", "file:/hello/custom.owl"),
-    ("file:///hello/world", "file:./custom.owl", "file:./custom.owl"),
-    ("file:///hello/world", "file:///custom.owl", "file:///custom.owl"),
-    ("http://hello/world", "custom.owl", "http://hello/custom.owl"),
-    ("http://hello/world", "file:./custom.owl", "file:./custom.owl"),
-    ("http://hello/world", "file:///custom.owl", "file:///custom.owl"),
-  )
-
-  forAll(resolveTests) { (base, iri, expected) =>
-    it should s"resolve $iri relative to $base to create $expected" in {
-      Schema.getIriPath(base, iri) should be(expected)
-    }
-  }
-
-  val fullIriTests = Table(
-    ("schemaDescription", "schema", "iri", "fullIri"),
-    ("galaxy", galaxySchema, "edam:format_1929", "http://edamontology.org/format_1929"),
-    ("galaxy", galaxySchema, "<edam:format_1929>", "edam:format_1929"),
-    ("galaxy", galaxySchema, "edam:format_2200", "http://edamontology.org/format_2200"),
-    ("galaxy", galaxySchema, "http://galaxyproject.org/formats/fasta", "http://galaxyproject.org/formats/fasta"),
-    ("galaxy", galaxySchema, "gx:fasta", "http://galaxyproject.org/formats/fasta"),
-    ("galaxy", galaxySchema, "not:real", "not:real"),
-    ("galaxy", galaxySchema, "owl:Thing", "http://www.w3.org/2002/07/owl#Thing"),
-    ("galaxy", galaxySchema, "owl:Nothing", "http://www.w3.org/2002/07/owl#Nothing"),
-    ("edam", edamSchema, "edam:format_1929", "http://purl.obolibrary.org/obo/edam#format_1929"),
-    ("edam w/ namespace", edamNamespaceSchema, "edam:format_1929", "http://edamontology.org/format_1929"),
-  )
-
-  forAll(fullIriTests) { (schemaDescription, schema, iri, fullIri) =>
-    it should s"expand $iri to $fullIri using schema $schemaDescription" in {
-      schema.fullIri(iri) should be(fullIri)
-    }
-  }
-
-  val subClassTests = Table(
-    ("isSubClass", "schemaDescription", "schema", "child", "ancestor"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "http://galaxyproject.org/formats/fasta"),
-    (true, "galaxy", galaxySchema, "http://galaxyproject.org/formats/fasta", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "gx:fasta", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "gx:fasta", "edam:format_2330"),
-    (false, "galaxy", galaxySchema, "not:real", "edam:format_1929"),
-    (false, "galaxy", galaxySchema, "edam:format_1929", "not:real"),
-    (false, "galaxy", galaxySchema, "owl:Thing", "owl:Nothing"),
-    (true, "galaxy", galaxySchema, "owl:Nothing", "owl:Thing"),
-    (false, "galaxy", galaxySchema, "owl:Thing", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "owl:Thing"),
-    (false, "galaxy", galaxySchema, "edam:format_1929", "owl:Nothing"),
-    (true, "galaxy", galaxySchema, "owl:Nothing", "edam:format_1929"),
-    (true, "galaxy", galaxySchema, "edam:format_1929", "http://edamontology.org/format_2330"),
-    (false, "edam", edamSchema, "edam:format_1929", "http://edamontology.org/format_2330"),
-    (true, "edam w/ namespace", edamNamespaceSchema, "edam:format_1929", "http://edamontology.org/format_2330"),
-  )
-
-  forAll(subClassTests) { (isSubClass, schemaDescription, schema, child, ancestor) =>
-    it should s"return $isSubClass that $child is a sub class of $ancestor when checking schema $schemaDescription" in {
-      schema.isSubClass(child, ancestor) should be(isSubClass)
-    }
-  }
-  
-  it should "cache ontologies" in {
-    val cache = Schema.makeOntologyCache(ConfigFactory.parseString("max-size=5"))
-    val ontologyManager1 = OWLManager.createOWLOntologyManager
-    val ontologyManager2 = OWLManager.createOWLOntologyManager
-    val ontology1 = Schema.loadOntologyFromIri(ontologyManager1, Option(cache))(getClass.getResource("EDAM.owl").toExternalForm)
-    ontology1.isValid shouldBe true
-    val ontology2 = Schema.loadOntologyFromIri(ontologyManager2, Option(cache))(getClass.getResource("EDAM.owl").toExternalForm)
-    ontology2.isValid shouldBe true
-    ontology2.getOrElse(fail()).getOWLOntologyManager shouldBe ontologyManager2
-  }
-
-  private lazy val galaxySchema = {
-    Schema(
-      List(
-        getClass.getResource("EDAM.owl").toExternalForm,
-        getClass.getResource("gx_edam.ttl").toExternalForm
-      ),
-      Map.empty
-    )
-  }
-
-  private lazy val edamSchema = {
-    Schema(
-      List(
-        getClass.getResource("EDAM.owl").toExternalForm
-      ),
-      Map.empty
-    )
-  }
-
-  private lazy val edamNamespaceSchema = {
-    Schema(
-      List(
-        getClass.getResource("EDAM.owl").toExternalForm
-      ),
-      Map("edam" -> "http://edamontology.org/")
-    )
-  }
-}
diff --git a/cwl/src/test/scala/cwl/preprocessor/CwlPreProcessorSpec.scala b/cwl/src/test/scala/cwl/preprocessor/CwlPreProcessorSpec.scala
deleted file mode 100644
index c0aba9c975d..00000000000
--- a/cwl/src/test/scala/cwl/preprocessor/CwlPreProcessorSpec.scala
+++ /dev/null
@@ -1,125 +0,0 @@
-package cwl.preprocessor
-
-import better.files.File
-import cats.data.NonEmptyList
-import common.assertion.CromwellTimeoutSpec
-import common.mock.MockSugar
-import cwl.preprocessor.CwlPreProcessor.SaladFunction
-import io.circe.Printer
-import org.mockito.ArgumentMatchers._
-import org.mockito.Mockito._
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-class CwlPreProcessorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with MockSugar {
-  behavior of "CwlPreProcessor"
-
-  private val resourcesRoot = File(getClass.getResource(".").getPath)
-  private val echoFileTool = CwlFileReference(resourcesRoot / "echo_tool.cwl", None)
-
-  it should "flatten a simple file" in {
-    validate(makeTestRoot("simple_workflow"), None) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(echoFileTool)
-    }
-  }
-
-  it should "flatten file with a self reference" in {
-    validate(makeTestRoot("self_reference"), Option("echo-workflow-2")) { _ => }
-  }
-
-  /*
-    * A "valid" cyclic dependency means for example
-    * file_1
-    *   - workflow_1 -> depends on workflow_3
-    *   - workflow_2
-    * file_2
-    *   - workflow_3 -> depends on workflow_2
-    * workflow_1 (in file_1) references a workflow in file_2 that references a workflow in file_1,
-    * but that's ok since the cycle is only over the file, not the workflows themselves.
-   */
-  it should "flatten file with sub workflow, self reference and valid cyclic dependency" in {
-    val testRoot = makeTestRoot("complex_workflow")
-    val subWorkflow =  CwlFileReference(testRoot / "sub" / "sub_workflow.cwl", Option("sub-echo-workflow-1"))
-
-    validate(testRoot, Option("echo-workflow-2")) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(echoFileTool)
-      verify(mockSaladingFunction).apply(subWorkflow)
-    }
-  }
-
-  it should "detect invalid cyclic dependencies in the same file and fail" in {
-    val testRoot = makeTestRoot("same_file_cyclic_dependency")
-
-    validate(testRoot, Option("echo-workflow-2"),
-      expectedFailure = Option(
-        NonEmptyList.one(s"Found a circular dependency on file://$testRoot/root_workflow.cwl#echo-workflow-2")
-      )
-    ) { _ => }
-  }
-
-  it should "detect invalid transitive cyclic dependencies (A => B => C => A) and fail" in {
-    val testRoot = makeTestRoot("transitive_cyclic_dependency")
-
-    val subWorkflow1 = CwlFileReference(testRoot / "sub_workflow_1.cwl", None)
-    val subWorkflow2 =  CwlFileReference(testRoot / "sub_workflow_2.cwl", None)
-
-    validate(testRoot, None,
-      expectedFailure = Option(
-        NonEmptyList.one(s"Found a circular dependency on file://$testRoot/root_workflow.cwl")
-      )
-    ) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(subWorkflow1)
-      verify(mockSaladingFunction).apply(subWorkflow2)
-    }
-  }
-
-  it should "pre-process inlined workflows" in {
-    val testRoot = makeTestRoot("deep_nesting")
-
-    val subWorkflow1 = CwlFileReference(testRoot / "wc-tool.cwl", None)
-    val subWorkflow2 =  CwlFileReference(testRoot / "parseInt-tool.cwl", None)
-
-    validate(testRoot, None, uuidExtractor = Option("step0/([0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12})/")) { mockSaladingFunction =>
-      verify(mockSaladingFunction).apply(subWorkflow1)
-      verify(mockSaladingFunction).apply(subWorkflow2)
-    }
-  }
-
-  private def makeTestRoot(testDirectoryName: String) = resourcesRoot / testDirectoryName
-
-  def validate[T](testRoot: File,
-                  root: Option[String],
-                  expectedFailure: Option[NonEmptyList[String]] = None,
-                  uuidExtractor: Option[String] = None
-                 )(additionalValidation: SaladFunction => T): Unit = {
-    val rootWorkflowReference = CwlFileReference(testRoot / "root_workflow.cwl", root)
-
-    // Mocking the salad function allows us to validate how many times it is called exactly and with which parameters
-    val mockSaladingFunction = mock[SaladFunction]
-    when(mockSaladingFunction.apply(any[CwlReference])) thenAnswer {
-      invocationOnMock =>
-        CwlPreProcessor.saladCwlFile(invocationOnMock.getArgument[CwlReference](0))
-    }
-    val preProcessor = new CwlPreProcessor(mockSaladingFunction)
-
-    val process = preProcessor.preProcessCwl(rootWorkflowReference).value.unsafeRunSync()
-    // Asserts that dependencies are only saladed once and exactly once
-    verify(mockSaladingFunction).apply(rootWorkflowReference)
-    additionalValidation(mockSaladingFunction)
-
-    (process, expectedFailure) match {
-      case (Left(errors), Some(failures)) => errors shouldBe failures
-      case (Left(errors), None) => fail("Unexpected failure to pre-process workflow: " + errors.toList.mkString(", "))
-      case (Right(result), None) =>
-        val content = (testRoot / "expected_result.json").contentAsString
-        val uuid = uuidExtractor.flatMap(_.r.findFirstMatchIn(result.printWith(Printer.noSpaces)).map(_.group(1)))
-        val expectationContent = content
-          .replaceAll("<<RESOURCES_ROOT>>", resourcesRoot.pathAsString)
-          .replaceAll("<<RANDOM_UUID>>", uuid.getOrElse(""))
-
-        result shouldBe io.circe.parser.parse(expectationContent).getOrElse(fail("Failed to parse expectation. Your test is broken !"))
-      case (Right(_), Some(failures)) => fail("Unexpected success to pre-process workflow, was expecting failures: " + failures.toList.mkString(", "))
-    }
-    ()
-  }
-}
diff --git a/cwl/src/test/scala/cwl/preprocessor/CwlReferenceSpec.scala b/cwl/src/test/scala/cwl/preprocessor/CwlReferenceSpec.scala
deleted file mode 100644
index a2c382c5bc9..00000000000
--- a/cwl/src/test/scala/cwl/preprocessor/CwlReferenceSpec.scala
+++ /dev/null
@@ -1,79 +0,0 @@
-package cwl.preprocessor
-
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-class CwlReferenceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  behavior of "CwlReference.apply"
-
-  it should "identify a pointerless local file reference" in {
-
-    val reference = "file:///blah/di/blah.cwl"
-    val cwlReference = CwlReference.fromString(reference)
-
-    cwlReference match {
-      case Some(ref @ CwlFileReference(file, _)) =>
-        file.pathAsString should be ("/blah/di/blah.cwl")
-        ref.pathAsString should be (reference)
-        ref.pointerWithinFile should be(None)
-        ref.fullReference should be (reference)
-      case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-      case None => fail("Failed to identify reference")
-    }
-  }
-
-  it should "identify a local file reference with a pointer" in {
-
-    val filePath = "/blah/di/blah.cwl"
-    val pointer = "1st-tool"
-    val reference = s"file://$filePath#$pointer"
-    val cwlReference = CwlReference.fromString(reference)
-
-    cwlReference match {
-      case Some(ref @ CwlFileReference(file, _)) =>
-        file.pathAsString should be (filePath)
-        ref.pathAsString should be (s"file://$filePath")
-        ref.pointerWithinFile should be(Some(pointer))
-        ref.fullReference should be (reference)
-      case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-      case None => fail("Failed to identify reference")
-    }
-  }
-
-  List("http://", "https://") foreach { scheme =>
-    it should s"identify a pointerless $scheme reference" in {
-
-      val reference = s"$scheme/blah.com/di/blah.cwl"
-      val cwlReference = CwlReference.fromString(reference)
-
-      cwlReference match {
-        case Some(ref @ CwlHttpReference(pathAsString, _)) =>
-          pathAsString should be (reference)
-          ref.pathAsString should be (reference)
-          ref.pointerWithinFile should be(None)
-          ref.fullReference should be (reference)
-        case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-        case None => fail("Failed to identify reference")
-      }
-    }
-
-    it should s"identify $scheme references with pointers" in {
-
-      val referencePath = s"$scheme/blah.com/di/blah.cwl"
-      val pointer = "1st-tool"
-      val reference = s"$referencePath#$pointer"
-      val cwlReference = CwlReference.fromString(reference)
-
-      cwlReference match {
-        case Some(ref @ CwlHttpReference(pathAsString, _)) =>
-          pathAsString should be (referencePath)
-          ref.pathAsString should be (referencePath)
-          ref.pointerWithinFile should be(Some(pointer))
-          ref.fullReference should be (reference)
-        case Some(ref) => fail(s"Unexpected pointer type ${ref.getClass.getSimpleName}")
-        case None => fail("Failed to identify reference")
-      }
-    }
-  }
-}
diff --git a/database/migration/src/main/resources/changelog.xml b/database/migration/src/main/resources/changelog.xml
index 5d711061c31..49d568766b3 100644
--- a/database/migration/src/main/resources/changelog.xml
+++ b/database/migration/src/main/resources/changelog.xml
@@ -87,6 +87,9 @@
     <include file="changesets/enlarge_call_caching_detritus_entry_id.xml" relativeToChangelogFile="true" />
     <include file="changesets/enlarge_call_caching_simpleton_entry_id.xml" relativeToChangelogFile="true" />
     <include file="changesets/reset_call_caching_hash_entry_id_autoincrement.xml" relativeToChangelogFile="true" />
+    <include file="changesets/enlarge_docker_hash_store_entry_id.xml" relativeToChangelogFile="true" />
+    <include file="changesets/enlarge_workflow_store_entry_id.xml" relativeToChangelogFile="true" />
+    <include file="changesets/enlarge_sub_workflow_store_entry_id.xml" relativeToChangelogFile="true" />
     <!-- REMINDER!
       Before appending here, did you remember to include the 'objectQuotingStrategy="QUOTE_ALL_OBJECTS"' line in your changeset/xyz.xml...?
     -->
diff --git a/database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml b/database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml
new file mode 100644
index 00000000000..fc7992268e6
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/enlarge_docker_hash_store_entry_id.xml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- BEGIN DOCKER_HASH_STORE_ENTRY_ID PK widening -->
+    <!-- For Postgresql there are 2 changesets: one for modifying the table column type, and another one for altering the autoincrementing sequence.
+         The other DBs can be refactored similarly with a single addAutoIncrement changeset. -->
+    <changeSet author="sshah" id="enlarge_docker_hash_store_entry_id" dbms="mysql,hsqldb,mariadb">
+        <addAutoIncrement
+                columnName="DOCKER_HASH_STORE_ENTRY_ID"
+                columnDataType="BIGINT"
+                incrementBy="1"
+                tableName="DOCKER_HASH_STORE_ENTRY"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_docker_hash_store_entry_id" dbms="postgresql">
+        <modifyDataType
+                columnName="DOCKER_HASH_STORE_ENTRY_ID"
+                tableName="DOCKER_HASH_STORE_ENTRY"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_docker_hash_store_entry_id_seq" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- idempotency check (noop if the sequence is present and already consistent what the alter would do) -->
+            <sqlCheck expectedResult="0">
+                SELECT count(*)
+                FROM information_schema.sequences
+                WHERE sequence_name = 'DOCKER_HASH_STORE_ENTRY_DOCKER_HASH_STORE_ENTRY_ID_seq'
+                AND data_type = 'bigint';
+            </sqlCheck>
+        </preConditions>
+        <sql>alter sequence "DOCKER_HASH_STORE_ENTRY_DOCKER_HASH_STORE_ENTRY_ID_seq" as bigint;</sql>
+    </changeSet>
+    <!-- END DOCKER_HASH_STORE_ENTRY_ID PK widening -->
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml b/database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml
new file mode 100644
index 00000000000..57894db824b
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/enlarge_sub_workflow_store_entry_id.xml
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- BEGIN SUB_WORKFLOW_STORE_ENTRY_ID PK widening -->
+    <!-- For Postgresql there are 2 changesets: one for modifying the table column type, and another one for altering the autoincrementing sequence.
+         The other DBs can be refactored similarly with a single addAutoIncrement changeset. -->
+    <changeSet author="sshah" id="enlarge_sub_workflow_store_entry_id" dbms="mysql,hsqldb,mariadb">
+        <addAutoIncrement
+                columnName="SUB_WORKFLOW_STORE_ENTRY_ID"
+                columnDataType="BIGINT"
+                incrementBy="1"
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_sub_workflow_store_entry_id" dbms="postgresql">
+        <modifyDataType
+                columnName="SUB_WORKFLOW_STORE_ENTRY_ID"
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_sub_workflow_store_entry_id_seq" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- idempotency check (noop if the sequence is present and already consistent what the alter would do) -->
+            <sqlCheck expectedResult="0">
+                SELECT count(*)
+                FROM information_schema.sequences
+                WHERE sequence_name = 'SUB_WORKFLOW_STORE_ENTRY_SUB_WORKFLOW_STORE_ENTRY_ID_seq'
+                AND data_type = 'bigint';
+            </sqlCheck>
+        </preConditions>
+        <sql>alter sequence "SUB_WORKFLOW_STORE_ENTRY_SUB_WORKFLOW_STORE_ENTRY_ID_seq" as bigint;</sql>
+    </changeSet>
+    <!-- END SUB_WORKFLOW_STORE_ENTRY_ID PK widening -->
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml b/database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml
new file mode 100644
index 00000000000..ea2b498fd51
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/enlarge_workflow_store_entry_id.xml
@@ -0,0 +1,82 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- Drop the foreign key constraint from SUB_WORKFLOW_STORE_ENTRY to WORKFLOW_STORE_ENTRY to allow for the latter's PK to be widened. -->
+    <changeSet author="sshah" id="drop_sub_workflow_store_entry_root_workflow_id_fk" dbms="mysql,hsqldb,postgresql,mariadb">
+        <dropForeignKeyConstraint
+                baseTableName="SUB_WORKFLOW_STORE_ENTRY"
+                constraintName="FK_SUB_WORKFLOW_STORE_ENTRY_ROOT_WORKFLOW_ID"
+        />
+    </changeSet>
+
+    <!-- BEGIN WORKFLOW_STORE_ENTRY_ID PK widening -->
+    <!-- For Postgresql there are 2 changesets: one for modifying the table column type, and another one for altering the autoincrementing sequence.
+         The other DBs can be refactored similarly with a single addAutoIncrement changeset. -->
+    <changeSet author="sshah" id="enlarge_workflow_store_entry_id" dbms="mysql,hsqldb,mariadb">
+        <addAutoIncrement
+                columnName="WORKFLOW_STORE_ENTRY_ID"
+                columnDataType="BIGINT"
+                incrementBy="1"
+                tableName="WORKFLOW_STORE_ENTRY"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_workflow_store_entry_id" dbms="postgresql">
+        <modifyDataType
+                columnName="WORKFLOW_STORE_ENTRY_ID"
+                tableName="WORKFLOW_STORE_ENTRY"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+
+    <changeSet author="sshah" id="postgresql_enlarge_workflow_store_entry_id_seq" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- idempotency check (noop if the sequence is present and already consistent what the alter would do) -->
+            <sqlCheck expectedResult="0">
+                SELECT count(*)
+                FROM information_schema.sequences
+                WHERE sequence_name = 'WORKFLOW_STORE_ENTRY_WORKFLOW_STORE_ENTRY_ID_seq'
+                AND data_type = 'bigint';
+            </sqlCheck>
+        </preConditions>
+        <sql>alter sequence "WORKFLOW_STORE_ENTRY_WORKFLOW_STORE_ENTRY_ID_seq" as bigint;</sql>
+    </changeSet>
+    <!-- END WORKFLOW_STORE_ENTRY_ID PK widening -->
+
+    <!-- BEGIN widening FK to match PK -->
+    <changeSet author="sshah" id="enlarge_sub_workflow_store_entry_fk" dbms="mysql,hsqldb,postgresql,mariadb">
+        <modifyDataType
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+                columnName="ROOT_WORKFLOW_ID"
+                newDataType="BIGINT"
+        />
+    </changeSet>
+    <!-- END widening FK to match PK -->
+
+    <!-- MariaDB's FK NotNull constraint does not survive the widening above and must be recreated explicitly. -->
+    <!-- BEGIN Restoring FK NotNull constraint -->
+    <changeSet author="sshah" id="mariadb_not_null_constraint_sub_workflow_store_entry_fk" dbms="mariadb,mysql">
+        <addNotNullConstraint
+                tableName="SUB_WORKFLOW_STORE_ENTRY"
+                columnName="ROOT_WORKFLOW_ID"
+                columnDataType="BIGINT"
+        />
+    </changeSet>
+    <!-- END Restoring FK NotNull constraint -->
+
+    <!-- Restoring the FK -->
+    <changeSet author="sshah" id="recreate_sub_workflow_store_entry_root_workflow_id_fk" dbms="mysql,hsqldb,postgresql,mariadb">
+        <addForeignKeyConstraint
+                constraintName="FK_SUB_WORKFLOW_STORE_ENTRY_ROOT_WORKFLOW_ID"
+                baseColumnNames="ROOT_WORKFLOW_ID"
+                baseTableName="SUB_WORKFLOW_STORE_ENTRY"
+                referencedTableName="WORKFLOW_STORE_ENTRY"
+                referencedColumnNames="WORKFLOW_STORE_ENTRY_ID"
+                onDelete="CASCADE"
+        />
+    </changeSet>
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala b/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala
index 20a77f58c02..e4823b8b0ac 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala
@@ -1,7 +1,5 @@
 package cromwell.database.migration.liquibase
 
-import java.sql.Connection
-
 import liquibase.changelog.{ChangeLogParameters, ChangeSet, DatabaseChangeLog}
 import liquibase.database.jvm.{HsqlConnection, JdbcConnection}
 import liquibase.database.{Database, DatabaseConnection, DatabaseFactory, ObjectQuotingStrategy}
@@ -10,12 +8,21 @@ import liquibase.diff.{DiffGeneratorFactory, DiffResult}
 import liquibase.parser.ChangeLogParserFactory
 import liquibase.resource.ClassLoaderResourceAccessor
 import liquibase.snapshot.{DatabaseSnapshot, SnapshotControl, SnapshotGeneratorFactory}
-import liquibase.{Contexts, LabelExpression, Liquibase}
+import liquibase.ui.LoggerUIService
+import liquibase.{Contexts, LabelExpression, Liquibase, Scope}
 import org.hsqldb.persist.HsqlDatabaseProperties
 
+import java.sql.Connection
 import scala.jdk.CollectionConverters._
 
 object LiquibaseUtils {
+
+  /*
+  Move liquibase calls to System.out.println to a logger.
+  Workaround for issue: https://github.com/liquibase/liquibase/issues/1741#issuecomment-853742652
+   */
+  Scope.enter(Map(Scope.Attr.ui.name -> new LoggerUIService().asInstanceOf[AnyRef]).asJava)
+
   // Paranoia: Create our own mutex. https://stackoverflow.com/questions/442564/avoid-synchronizedthis-in-java
   private val mutex = new Object
   private val DefaultContexts = new Contexts()
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
index e258b40f3b7..5929b2e5a6a 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
@@ -9,7 +9,7 @@ trait DockerHashStoreEntryComponent {
   import driver.api._
 
   class DockerHashStoreEntries(tag: Tag) extends Table[DockerHashStoreEntry](tag, "DOCKER_HASH_STORE_ENTRY") {
-    def dockerHashStoreEntryId = column[Int]("DOCKER_HASH_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
+    def dockerHashStoreEntryId = column[Long]("DOCKER_HASH_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def workflowExecutionUuid = column[String]("WORKFLOW_EXECUTION_UUID", O.Length(255))
 
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
index 2ea7b36782c..11fa2191cb2 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
@@ -10,9 +10,9 @@ trait SubWorkflowStoreEntryComponent {
   import driver.api._
 
   class SubWorkflowStoreEntries(tag: Tag) extends Table[SubWorkflowStoreEntry](tag, "SUB_WORKFLOW_STORE_ENTRY") {
-    def subWorkflowStoreEntryId = column[Int]("SUB_WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
+    def subWorkflowStoreEntryId = column[Long]("SUB_WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
-    def rootWorkflowId = column[Int]("ROOT_WORKFLOW_ID")
+    def rootWorkflowId = column[Long]("ROOT_WORKFLOW_ID")
     
     def parentWorkflowExecutionUuid = column[String]("PARENT_WORKFLOW_EXECUTION_UUID", O.Length(255))
 
@@ -40,7 +40,7 @@ trait SubWorkflowStoreEntryComponent {
   val subWorkflowStoreEntryIdsAutoInc = subWorkflowStoreEntries returning subWorkflowStoreEntries.map(_.subWorkflowStoreEntryId)
 
   val subWorkflowStoreEntriesForRootWorkflowId = Compiled(
-    (rootWorkflowId: Rep[Int]) => for {
+    (rootWorkflowId: Rep[Long]) => for {
       subWorkflowStoreEntry <- subWorkflowStoreEntries
       if subWorkflowStoreEntry.rootWorkflowId === rootWorkflowId
     } yield subWorkflowStoreEntry
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
index 0e29cee651f..847fa862405 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
@@ -11,7 +11,7 @@ trait WorkflowStoreEntryComponent {
   import driver.api._
 
   class WorkflowStoreEntries(tag: Tag) extends Table[WorkflowStoreEntry](tag, "WORKFLOW_STORE_ENTRY") {
-    def workflowStoreEntryId = column[Int]("WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
+    def workflowStoreEntryId = column[Long]("WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def workflowExecutionUuid = column[String]("WORKFLOW_EXECUTION_UUID", O.Length(255))
 
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
index a4a5b1247ee..542558324f5 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
@@ -6,5 +6,5 @@ case class DockerHashStoreEntry
   dockerTag: String,
   dockerHash: String,
   dockerSize: Option[Long],
-  dockerHashStoreEntryId: Option[Int] = None
+  dockerHashStoreEntryId: Option[Long] = None
 )
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
index 96ac39aa672..4cf89381ad0 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
@@ -2,11 +2,11 @@ package cromwell.database.sql.tables
 
 case class SubWorkflowStoreEntry
 (
-  rootWorkflowId: Option[Int],
+  rootWorkflowId: Option[Long],
   parentWorkflowExecutionUuid: String,
   callFullyQualifiedName: String,
   callIndex: Int,
   callAttempt: Int,
   subWorkflowExecutionUuid: String,
-  subWorkflowStoreEntryId: Option[Int] = None
+  subWorkflowStoreEntryId: Option[Long] = None
 )
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
index 6c03db87014..efb594444d4 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
@@ -21,5 +21,5 @@ case class WorkflowStoreEntry
   cromwellId: Option[String],
   heartbeatTimestamp: Option[Timestamp],
   hogGroup: Option[String],
-  workflowStoreEntryId: Option[Int] = None
+  workflowStoreEntryId: Option[Long] = None
 )
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
index 67e1d2fcd28..384f9f09e72 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
@@ -5,8 +5,8 @@ import cats.effect.IO
 import cats.syntax.either._
 import common.validation.Validation._
 import cromwell.docker.DockerInfoActor._
+import cromwell.docker._
 import cromwell.docker.registryv2.DockerRegistryV2Abstract._
-import cromwell.docker.{DockerHashResult, DockerImageIdentifier, DockerRegistry, DockerRegistryConfig}
 import io.circe.Decoder
 import io.circe.generic.auto._
 import org.http4s.Uri.{Authority, Scheme}
@@ -27,19 +27,27 @@ object DockerRegistryV2Abstract {
   }
 
   val DigestHeaderName = CaseInsensitiveString("Docker-Content-Digest")
-  val ManifestV2MediaType = "application/vnd.docker.distribution.manifest.v2+json"
-  val ManifestListV2MediaType = "application/vnd.docker.distribution.manifest.list.v2+json"
+  val DockerManifestV2MediaType = "application/vnd.docker.distribution.manifest.v2+json"
+  val DockerManifestListV2MediaType = "application/vnd.docker.distribution.manifest.list.v2+json"
+  // See https://github.com/opencontainers/image-spec/blob/main/image-index.md
+  // This is the media type that current images of Ubuntu use, https://github.com/docker-library/official-images/pull/13950
+  val OCIIndexV1MediaType = "application/vnd.oci.image.index.v1+json"
 
   // If one of those fails it means someone changed one of the strings above to an invalid one.
-  val ManifestV2MediaRange = MediaRange.parse(ManifestV2MediaType)
+  val DockerManifestV2MediaRange = MediaRange.parse(DockerManifestV2MediaType)
     .unsafe("Cannot parse invalid manifest v2 content type. Please report this error.")
-  val ManifestListV2MediaRange = MediaRange.parse(ManifestListV2MediaType)
+  val DockerManifestListV2MediaRange = MediaRange.parse(DockerManifestListV2MediaType)
     .unsafe("Cannot parse invalid manifest list v2 content type. Please report this error.")
-  val AcceptManifestV2Header = Accept.parse(ManifestV2MediaType)
+  val AcceptDockerManifestV2Header = Accept.parse(DockerManifestV2MediaType)
     .unsafe("Cannot parse invalid manifest v2 Accept header. Please report this error.")
 
-  implicit val entityManifestDecoder = jsonEntityDecoder[DockerManifest](ManifestV2MediaRange)
-  implicit val entityManifestListDecoder = jsonEntityDecoder[DockerManifestList](ManifestListV2MediaRange)
+  val OCIIndexV1MediaRange = MediaRange.parse(OCIIndexV1MediaType)
+    .unsafe("Cannot parse invalid OCI index v1 content type. Please report this error.")
+  val AcceptOCIIndexV1Header = Accept.parse(OCIIndexV1MediaType)
+    .unsafe("Cannot parse invalid OCI index v1 Accept header. Please report this error.")
+
+  implicit val entityManifestDecoder = jsonEntityDecoder[DockerManifest](DockerManifestV2MediaRange)
+  implicit val entityManifestListDecoder = jsonEntityDecoder[DockerManifestList](DockerManifestListV2MediaRange)
   implicit val entityTokenDecoder = jsonOf[IO, DockerAccessToken]
 
   /**
@@ -123,8 +131,12 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * @return docker info response
     */
   protected def getDockerResponse(token: Option[String], dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]): IO[DockerInfoSuccessResponse] = {
-    val request = manifestRequest(token, dockerInfoContext.dockerImageID)
-    executeRequest(request, handleManifestResponse(dockerInfoContext, token))
+    val requestDockerManifest = manifestRequest(token, dockerInfoContext.dockerImageID, AcceptDockerManifestV2Header)
+    lazy val requestOCIManifest = manifestRequest(token, dockerInfoContext.dockerImageID, AcceptOCIIndexV1Header)
+    def tryOCIManifest(err: Throwable) = executeRequest(requestOCIManifest, handleManifestResponse(dockerInfoContext, token))
+    // Try to execute a request using the Docker Manifest format, and if that fails, try using the newer OCI manifest format
+    executeRequest(requestDockerManifest, handleManifestResponse(dockerInfoContext, token))
+      .handleErrorWith(tryOCIManifest)
   }
 
   /**
@@ -205,12 +217,12 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
   /**
     * Request to get the manifest, using the auth token if provided
     */
-  private def manifestRequest(token: Option[String], imageId: DockerImageIdentifier): IO[Request[IO]] = {
-    val authorizationHeader = token.map(t => Authorization(Credentials.Token(authorizationScheme, t)))
+  private def manifestRequest(token: Option[String], imageId: DockerImageIdentifier, manifestHeader: Accept): IO[Request[IO]] = {
+    val authorizationHeader = token.map(t => Authorization(Credentials.Token(AuthScheme.Bearer, t)))
     val request = Method.GET(
       buildManifestUri(imageId),
       List(
-        Option(AcceptManifestV2Header),
+        Option(manifestHeader),
         authorizationHeader
       ).flatten: _*
     )
@@ -246,9 +258,9 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * If that assumption turns out to be incorrect, a smarter decision may need to be made to choose the manifest to lookup.
     */
   private def parseManifest(dockerImageIdentifier: DockerImageIdentifier, token: Option[String])(response: Response[IO])(implicit client: Client[IO]): IO[Option[DockerManifest]] = response match {
-    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(ManifestV2MediaType)) =>
+    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(DockerManifestV2MediaType)) =>
       r.as[DockerManifest].map(Option.apply)
-    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(ManifestListV2MediaType)) =>
+    case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(DockerManifestListV2MediaType)) =>
       r.as[DockerManifestList].flatMap({ dockerManifestList =>
         obtainManifestFromList(dockerManifestList, dockerImageIdentifier, token)
       })
@@ -262,7 +274,7 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
       .map(_.digest)
       .map(dockerImageIdentifier.swapReference) match {
       case Some(identifierWithNewHash) =>
-        val request = manifestRequest(token, identifierWithNewHash)
+        val request = manifestRequest(token, identifierWithNewHash, AcceptDockerManifestV2Header)
         executeRequest(request, parseManifest(dockerImageIdentifier, token))
       case None =>
         logger.error(s"The manifest list for ${dockerImageIdentifier.fullName} was empty. Cannot proceed to obtain the size of image")
diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
index e567aa540cd..e99383ac131 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
@@ -3,10 +3,10 @@ package cromwell.docker.registryv2
 import cats.effect.{IO, Resource}
 import common.assertion.CromwellTimeoutSpec
 import cromwell.docker.DockerInfoActor.{DockerInfoContext, DockerInfoFailedResponse}
-import cromwell.docker.{DockerImageIdentifier, DockerInfoActor, DockerInfoRequest, DockerRegistryConfig}
+import cromwell.docker._
+import org.http4s._
 import org.http4s.client.Client
 import org.http4s.headers.`Content-Type`
-import org.http4s.{Header, Headers, MediaType, Request, Response}
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
@@ -20,7 +20,7 @@ class DockerRegistryV2AbstractSpec extends AnyFlatSpec with CromwellTimeoutSpec
       override protected def buildTokenRequestHeaders(dockerInfoContext: DockerInfoActor.DockerInfoContext) = List.empty
     }
 
-    val mediaType = MediaType.parse(DockerRegistryV2Abstract.ManifestV2MediaType).toOption.get
+    val mediaType = MediaType.parse(DockerRegistryV2Abstract.DockerManifestV2MediaType).toOption.get
     val contentType: Header = `Content-Type`(mediaType)
 
     val mockClient = Client({ _: Request[IO] =>
diff --git a/docs/LanguageSupport.md b/docs/LanguageSupport.md
index d14d6751a42..ff7a64164f9 100644
--- a/docs/LanguageSupport.md
+++ b/docs/LanguageSupport.md
@@ -22,13 +22,6 @@ Cromwell also supports WDL version 1.0.
 
 As well as the changes to the WDL spec between draft-2 and 1.0, Cromwell also supports nested scatters and the [localization_optional](optimizations/FileLocalization.md) optimization in WDL 1.0.  
 
-
-### CWL 1.0
-
-Cromwell provides support for Common Workflow Language (CWL), beginning with the core spec, and most heavily used requirements.
-If you spot a CWL feature that Cromwell doesn't support, please notify us using an issue on our [Jira page](https://broadworkbench.atlassian.net/secure/RapidBoard.jspa?rapidView=39&view=planning.nodetail&issueLimit=100)!
-
-
 ## Future Language Support
 
 ### WDL 'development'
diff --git a/docs/RuntimeAttributes.md b/docs/RuntimeAttributes.md
index 1f16e125eff..8b318b617a2 100644
--- a/docs/RuntimeAttributes.md
+++ b/docs/RuntimeAttributes.md
@@ -30,18 +30,29 @@ workflow jes_workflow {
 
 Cromwell recognizes certain runtime attributes and has the ability to format these for some [Backends](/backends/Backends). See the table below for common attributes that apply to _most_ backends.
 
-| Runtime Attribute    | LOCAL |  Google Cloud  | AWS Batch |  HPC  |
-| -------------------- |:-----:|:-----:|:-----:|:------:|
-| [cpu](#cpu)                  |       |   x   |   x   |  `cpu`  |
-| [memory](#memory)                              |       |   x   |   x   |  `memory_mb` / `memory_gb`  |
-| [disks](#disks)                                |       |   x   |       |  *  |
-| [docker](#docker)                              |   x   |   x   |   x   |  `docker` (see below)  |
-| [maxRetries](#maxretries)                      |   x   |   x   |   x   | * |
-| [continueOnReturnCode](#continueonreturncode) |   x   |   x   |   x   | * |
-| [failOnStderr](#failonstderr)                  |   x   |   x   |   x   |  *  |
-
-
-> `*` The HPC [Shared Filesystem backend](/backends/HPC#shared-filesystem) (SFS) is fully configurable and any number of attributes can be exposed. Cromwell recognizes some of these attributes (`cpu`, `memory` and `docker`) and parses them into the attribute listed in the table which can be used within the HPC backend configuration.
+| Runtime Attribute                               | Local | Google Cloud | TES       | AWS Batch |            HPC            |
+|-------------------------------------------------|:-----:|:------------:|-----------|:---------:|:-------------------------:|
+| [`cpu`](#cpu)                                   |       |      ✅       |           |     ✅     |           `cpu`           |
+| [`memory`](#memory)                             |       |      ✅       |           |     ✅     | `memory_mb` / `memory_gb` |
+| [`disks`](#disks)                               |       |      ✅       | ⚠️ Note 1 | ⚠️ Note 2 |         ℹ️ Note 3         |
+| [`disk`](#disk)                                 |       |              | ✅         |           |                           |
+| [`docker`](#docker)                             |   ✅   |      ✅       |           |     ✅     |    `docker` ℹ️ Note 3     |
+| [`maxRetries`](#maxretries)                     |   ✅   |      ✅       |           |     ✅     |         ℹ️ Note 3         |
+| [`continueOnReturnCode`](#continueonreturncode) |   ✅   |      ✅       |           |     ✅     |         ℹ️ Note 3         |
+| [`failOnStderr`](#failonstderr)                 |   ✅   |      ✅       |           |     ✅     |         ℹ️ Note 3         |
+
+
+> **Note 1**
+> 
+> Partial support. See [TES documentation](/backends/TES) for details. 
+ 
+> **Note 2**
+>
+> Partial support. See [`disks`](#disks) for details.
+
+> **Note 3**
+> 
+> The HPC [Shared Filesystem backend](/backends/HPC#shared-filesystem) (SFS) is fully configurable and any number of attributes can be exposed. Cromwell recognizes some of these attributes (`cpu`, `memory` and `docker`) and parses them into the attribute listed in the table which can be used within the HPC backend configuration.
 
 
 ### Google Cloud Specific Attributes
@@ -156,15 +167,6 @@ runtime {
 }
 ```
 
-
-#### CWL
-
-CWL splits the `cpu` requirement into `cpuMin` and `cpuMax`. If one of them is provided, `cpu` will inherit this value. If both of them are provided, `cpu` will take the value of `cpuMin`.
-If none is provided, `cpu` will default to its default value.
-
-Note: If provided, `cpuMin` and/or `cpuMax` will be available to the [HPC runtime attribute configuration](/tutorials/HPCIntro.md#specifying-the-runtime-attributes-for-your-hpc-tasks).
-
-
 ### `memory`
 *Default: "2G"*
 
@@ -183,12 +185,6 @@ runtime {
 
 Within the SFS backend, you can additionally specify `memory_mb` or `memory_gb` as runtime attributes within the configuration. More information can be found [here](https://cromwell.readthedocs.io/en/stable/tutorials/HPCIntro/#specifying-the-runtime-attributes-for-your-hpc-tasks).
 
-#### CWL
-
-CWL splits the `memory` requirement into `ramMin` and `ramMax`. If one of them is provided, `memory` will inherit this value. If both of them are provided, `memory` will take the value of `ramMin`. If none is provided, `memory` will default to its default value.
-
-Note: If provided, `ramMin` and/or `ramMax` will be available to the [HPC runtime attribute configuration](/tutorials/HPCIntro.md#specifying-the-runtime-attributes-for-your-hpc-tasks).
-
 
 ### `disks`
 
@@ -224,6 +220,16 @@ runtime {
 }
 ```
 
+### `disk`
+
+Specific to the TES backend, sets the `disk_gb` resource.
+
+```
+runtime {
+  disk: "25 GB"
+}
+```
+
 ### `docker`
 
 When specified, Cromwell will run your task within the specified Docker image. 
diff --git a/docs/WOMtool.md b/docs/WOMtool.md
index fc8c16c7897..5b88e5a21a6 100644
--- a/docs/WOMtool.md
+++ b/docs/WOMtool.md
@@ -59,9 +59,9 @@ graph <WDL file>
   otherwise. Note that graph currently DOES NOT WORK on
   version 1.0 workflows.
 
-womgraph <WDL or CWL file> [ancillary files]
+womgraph <WDL file> [ancillary files]
 
-  Reads a WDL or CWL file from the first argument and
+  Reads a WDL file from the first argument and
   converts it to a WOM representation then prints out a graph
   of the WOM produced.
   Any imported files can be supplied as subsequent arguments.
diff --git a/docs/api/RESTAPI.md b/docs/api/RESTAPI.md
index b15072f6407..ffb2af329de 100644
--- a/docs/api/RESTAPI.md
+++ b/docs/api/RESTAPI.md
@@ -1,5 +1,5 @@
 <!--
-This file was generated by `sbt generateRestApiDocs` on Thu, 9 Jun 2022 13:29:46 -0400
+This file was generated by `sbt generateRestApiDocs` on Wed, 8 Feb 2023 09:46:32 -0500
 
 !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
 
@@ -32,6 +32,63 @@ Describes the REST API provided by a Cromwell server
 
 
 
+<a name="runworkflow"></a>
+## Run workflow
+```
+POST /api/ga4gh/wes/v1/runs
+```
+
+
+#### Description
+This endpoint creates a new workflow run and returns a `RunId` to monitor its progress.
+
+The `workflow_attachment` array may be used to upload files that are required to execute the workflow, including the primary workflow, tools imported by the workflow, other files referenced by the workflow, or files which are part of the input.  The implementation should stage these files to a temporary directory and execute the workflow from there. These parts must have a Content-Disposition header with a "filename" provided for each part.  Filenames may include subdirectories, but must not include references to parent directories with '..' -- implementations should guard against maliciously constructed filenames.
+
+The `workflow_url` is either an absolute URL to a workflow file that is accessible by the WES endpoint, or a relative URL corresponding to one of the files attached using `workflow_attachment`.
+
+The `workflow_params` JSON object specifies input parameters, such as input files.  The exact format of the JSON object depends on the conventions of the workflow language being used.  Input files should either be absolute URLs, or relative URLs corresponding to files uploaded using `workflow_attachment`.  The WES endpoint must understand and be able to access URLs supplied in the input.  This is implementation specific.
+
+The `workflow_type` is the type of workflow language and must be "WDL" currently (or another alternative supported by this WES instance).
+
+The `workflow_type_version` is the version of the workflow language submitted and must be one supported by this WES instance.
+
+See the `RunRequest` documentation for details about other fields.
+
+
+#### Parameters
+
+|Type|Name|Schema|
+|---|---|---|
+|**FormData**|**tags**  <br>*optional*|string|
+|**FormData**|**workflow_attachment**  <br>*optional*|< file (binary) > array|
+|**FormData**|**workflow_engine_parameters**  <br>*optional*|string|
+|**FormData**|**workflow_params**  <br>*optional*|string|
+|**FormData**|**workflow_type**  <br>*optional*|string|
+|**FormData**|**workflow_type_version**  <br>*optional*|string|
+|**FormData**|**workflow_url**  <br>*optional*|string|
+
+
+#### Responses
+
+|HTTP Code|Description|Schema|
+|---|---|---|
+|**201**|Successful Request|[RunId](#runid)|
+|**400**|Malformed Workflow ID|No Content|
+|**401**|Invalid submission request|No Content|
+|**403**|Workflow in terminal status|No Content|
+|**500**|Internal Error|No Content|
+
+
+#### Consumes
+
+* `multipart/form-data`
+
+
+#### Tags
+
+* GA4GH Workflow Execution Service (WES) - Alpha preview
+
+
 <a name="listruns"></a>
 ## List runs
 ```
@@ -207,8 +264,8 @@ POST /api/womtool/{version}/describe
 |**Path**|**version**  <br>*required*|Cromwell API Version|string|`"v1"`|
 |**FormData**|**workflowInputs**  <br>*optional*|JSON or YAML file containing the inputs as an object.|file||
 |**FormData**|**workflowSource**  <br>*optional*|The workflow source file to submit for execution. Either workflow source or workflow url is required.|file||
-|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.|enum (WDL, CWL)||
-|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.|enum (draft-2, 1.0, v1.0)||
+|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL.|enum (WDL)||
+|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.|enum (draft-2, 1.0)||
 |**FormData**|**workflowUrl**  <br>*optional*|URL which points to the workflow. Either workflow source or workflow url is required.|string||
 
 
@@ -255,10 +312,9 @@ Submits a workflow to Cromwell. Note that this endpoint can accept an unlimited
 |**FormData**|**workflowInputs_5**  <br>*optional*|A fifth JSON or YAML file containing inputs.|file||
 |**FormData**|**workflowOnHold**  <br>*optional*|Put workflow on hold upon submission. By default, it is taken as false.|boolean||
 |**FormData**|**workflowOptions**  <br>*optional*|JSON file containing configuration options for the execution of this workflow.|file||
-|**FormData**|**workflowRoot**  <br>*optional*|The root object to be run. Only necessary for CWL submissions containing multiple objects (in an array).|string||
 |**FormData**|**workflowSource**  <br>*optional*|The workflow source file to submit for execution. Either workflow source or workflow url is required.|file||
-|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.|enum (WDL, CWL)||
-|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.|enum (draft-2, 1.0, v1.0)||
+|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL.|enum (WDL)||
+|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.|enum (draft-2, 1.0)||
 |**FormData**|**workflowUrl**  <br>*optional*|URL which points to the workflow. Either workflow source or workflow url is required.|string||
 
 
@@ -334,8 +390,8 @@ In instances where you want to run the same workflow multiple times with varying
 |**FormData**|**workflowOnHold**  <br>*optional*|Put workflow on hold upon submission. By default, it is taken as false.|boolean||
 |**FormData**|**workflowOptions**  <br>*optional*|JSON file containing configuration options for the execution of this workflow.|file||
 |**FormData**|**workflowSource**  <br>*optional*|The workflow source file to submit for execution. Either workflow source or workflow url is required.|file||
-|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.|enum (WDL, CWL)||
-|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.|enum (draft-2, 1.0, v1.0)||
+|**FormData**|**workflowType**  <br>*optional*|The workflow language for the file you submitted. Cromwell currently supports WDL.|enum (WDL)||
+|**FormData**|**workflowTypeVersion**  <br>*optional*|The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.|enum (draft-2, 1.0)||
 |**FormData**|**workflowUrl**  <br>*optional*|URL which points to the workflow. Either workflow source or workflow url is required.|string||
 
 
@@ -852,9 +908,9 @@ Call level metadata
 |**backendLogs**  <br>*optional*|Paths to backend specific logs for this call|object|
 |**backendStatus**  <br>*optional*|Status in backend-specific terms.  Currently this will only be defined for the JES backend.|string|
 |**end**  <br>*optional*|End datetime of the call execution in ISO8601 format with milliseconds|string (date-time)|
-|**executionStatus**  <br>*required*|Status in Cromwell execution terms.|string|
-|**failures**  <br>*optional*||[FailureMessage](#failuremessage)|
-|**inputs**  <br>*required*|Mapping of input fully qualified names to stringified values|object|
+|**executionStatus**  <br>*optional*|Status in Cromwell execution terms.|string|
+|**failures**  <br>*optional*||< [FailureMessage](#failuremessage) > array|
+|**inputs**  <br>*optional*|Mapping of input fully qualified names to stringified values|object|
 |**jobId**  <br>*optional*|Backend-specific job ID|string|
 |**returnCode**  <br>*optional*|Call execution return code|integer|
 |**start**  <br>*optional*|Start datetime of the call execution in ISO8601 format with milliseconds|string (date-time)|
@@ -876,9 +932,9 @@ A message that allows one to describe default parameters for a workflow engine.
 
 <a name="descriptortype"></a>
 ### DescriptorType
-One from a list of descriptor type strings (e.g. CWL, WDL). Note that these files can also include associated Docker/container files and test parameters that further describe a version of a tool
+One from a list of descriptor type strings (e.g. WDL). Note that these files can also include associated Docker/container files and test parameters that further describe a version of a tool
 
-*Type* : enum (CWL, WDL)
+*Type* : enum (WDL)
 
 
 <a name="descriptortypeandversion"></a>
@@ -899,8 +955,8 @@ Failure messages
 
 |Name|Description|Schema|
 |---|---|---|
-|**failure**  <br>*required*|The failure message|string|
-|**timestamp**  <br>*required*|The time at which this failure occurred|string (date-time)|
+|**causedBy**  <br>*optional*||< [FailureMessage](#failuremessage) > array|
+|**message**  <br>*optional*|The failure message|string|
 
 
 <a name="labelsresponse"></a>
@@ -981,9 +1037,9 @@ To execute a workflow, send a run request including all the details needed to be
 |**tags**  <br>*optional*||< string, string > map|
 |**workflow_engine_parameters**  <br>*optional*||< string, string > map|
 |**workflow_params**  <br>*optional*|REQUIRED The workflow run parameterizations (JSON encoded), including input and output file locations|object|
-|**workflow_type**  <br>*optional*|REQUIRED The workflow descriptor type, must be "CWL" or "WDL" currently (or another alternative supported by this WES instance)|string|
+|**workflow_type**  <br>*optional*|REQUIRED The workflow descriptor type, must be "WDL" currently (or another alternative supported by this WES instance)|string|
 |**workflow_type_version**  <br>*optional*|REQUIRED The workflow descriptor type version, must be one supported by this WES instance|string|
-|**workflow_url**  <br>*optional*|REQUIRED The workflow CWL or WDL document. When `workflow_attachments` is used to attach files, the `workflow_url` may be a relative path to one of the attachments.|string|
+|**workflow_url**  <br>*optional*|REQUIRED The workflow WDL document. When `workflow_attachments` is used to attach files, the `workflow_url` may be a relative path to one of the attachments.|string|
 
 
 <a name="runstatus"></a>
@@ -1191,10 +1247,14 @@ Returns the version of Cromwell
 |Name|Description|Schema|
 |---|---|---|
 |**errors**  <br>*required*|The set of validation failure messages  <br>**Example** : `[ "The 'errors' field will be filled if 'valid' is false", "We might also provide warnings to a 'valid' workflow here", "Otherwise, 'errors' will be the empty array" ]`|< string > array|
+|**images**  <br>*optional*||< string > array|
+|**importedDescriptorTypes**  <br>*optional*||< [DescriptorTypeAndVersion](#descriptortypeandversion) > array|
 |**inputs**  <br>*required*|A list of inputs for this tool  <br>**Example** : `[ {<br>  "name" : "my_wf.string_input",<br>  "valueType" : {<br>    "typeName" : "String"<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "String"<br>}, {<br>  "name" : "my_wf.array_input",<br>  "valueType" : {<br>    "typeName" : "Array",<br>    "arrayType" : {<br>      "typeName" : "String"<br>    }<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Array[String]"<br>}, {<br>  "name" : "my_wf.optional_input",<br>  "valueType" : {<br>    "typeName" : "Optional",<br>    "optionalType" : {<br>      "typeName" : "String"<br>    }<br>  },<br>  "optional" : true,<br>  "default" : "hello",<br>  "typeDisplayName" : "String?"<br>}, {<br>  "name" : "my_wf.map_input",<br>  "valueType" : {<br>    "typeName" : "Map",<br>    "mapType" : {<br>      "keyType" : {<br>        "typeName" : "String"<br>      },<br>      "valueType" : {<br>        "typeName" : "Int"<br>      }<br>    }<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Map[String, Int]"<br>}, {<br>  "name" : "my_wf.object_input",<br>  "valueType" : {<br>    "typeName" : "Object",<br>    "objectFieldTypes" : [ {<br>      "fieldName" : "int_field",<br>      "fieldType" : {<br>        "typeName" : "Int"<br>      }<br>    }, {<br>      "fieldName" : "int_array_field",<br>      "fieldType" : {<br>        "typeName" : "Array",<br>        "arrayType" : {<br>          "typeName" : "Int"<br>        }<br>      }<br>    } ]<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Object"<br>}, {<br>  "name" : "my_wf.int_string_pair_input",<br>  "valueType" : {<br>    "typeName" : "Pair",<br>    "pairTypes" : [ {<br>      "leftType" : [ {<br>        "typeName" : "Int"<br>      } ]<br>    }, {<br>      "rightType" : [ {<br>        "typeName" : "String"<br>      } ]<br>    } ]<br>  },<br>  "optional" : false,<br>  "default" : null,<br>  "typeDisplayName" : "Pair[Int, String]"<br>} ]`|< [ToolInputParameter](#toolinputparameter) > array|
 |**isRunnableWorkflow**  <br>*required*|Indicates whether this file can be run on its own (e.g. a WDL workflow)|boolean|
+|**meta**  <br>*optional*||object|
 |**name**  <br>*required*|For a source file with one workflow and zero or more tasks, the name of the workflow. For a single task, the name of the task. For a source file with multiple tasks but no workflows, the empty string.|string|
 |**outputs**  <br>*required*|A list of outputs for this tool  <br>**Example** : `[ {<br>  "name" : "my_wf.string_output",<br>  "valueType" : {<br>    "typeName" : "String"<br>  },<br>  "typeDisplayName" : "String"<br>}, {<br>  "name" : "my_wf.array_output",<br>  "valueType" : {<br>    "typeName" : "Array",<br>    "arrayType" : {<br>      "typeName" : "String"<br>    }<br>  },<br>  "typeDisplayName" : "Array[String]"<br>}, {<br>  "name" : "my_wf.map_output",<br>  "valueType" : {<br>    "typeName" : "Map",<br>    "mapType" : {<br>      "keyType" : {<br>        "typeName" : "String"<br>      },<br>      "valueType" : {<br>        "typeName" : "Int"<br>      }<br>    }<br>  },<br>  "typeDisplayName" : "Map[String, Int]"<br>}, {<br>  "name" : "my_wf.object_output",<br>  "valueType" : {<br>    "typeName" : "Object",<br>    "objectFieldTypes" : [ {<br>      "fieldName" : "int_field",<br>      "fieldType" : {<br>        "typeName" : "Int"<br>      }<br>    }, {<br>      "fieldName" : "int_array_field",<br>      "fieldType" : {<br>        "typeName" : "Array",<br>        "arrayType" : {<br>          "typeName" : "Int"<br>        }<br>      }<br>    } ]<br>  },<br>  "typeDisplayName" : "Object"<br>}, {<br>  "name" : "my_wf.int_string_pair_output",<br>  "valueType" : {<br>    "typeName" : "Pair",<br>    "tupleTypes" : [ {<br>      "typeName" : "Int"<br>    }, {<br>      "typeName" : "String"<br>    } ]<br>  },<br>  "typeDisplayName" : "Pair[Int, String]"<br>} ]`|< [ToolOutputParameter](#tooloutputparameter) > array|
+|**parameterMeta**  <br>*optional*||object|
 |**submittedDescriptorType**  <br>*required*||[DescriptorTypeAndVersion](#descriptortypeandversion)|
 |**valid**  <br>*required*|Indicates that the workflow is valid and that the inputs, if provided, are compatible with the workflow.|boolean|
 |**validWorkflow**  <br>*required*|Indicates whether the workflow file is valid by itself. If inputs are provided, they are not considered when calculating this field; if inputs are not provided, the value is identical to `valid`.|boolean|
@@ -1218,13 +1278,13 @@ Workflow and call level metadata
 |---|---|---|
 |**calls**  <br>*optional*||[CallMetadata](#callmetadata)|
 |**end**  <br>*optional*|End datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
-|**failures**  <br>*optional*||[FailureMessage](#failuremessage)|
-|**id**  <br>*required*|The identifier of the workflow|string|
+|**failures**  <br>*optional*||< [FailureMessage](#failuremessage) > array|
+|**id**  <br>*optional*|The identifier of the workflow|string|
 |**inputs**  <br>*optional*|Map of input keys to input values|object|
 |**outputs**  <br>*optional*|Map of output keys to output values|object|
 |**start**  <br>*optional*|Start datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
-|**status**  <br>*required*|The status of the workflow|string|
-|**submission**  <br>*required*|Submission datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
+|**status**  <br>*optional*|The status of the workflow|string|
+|**submission**  <br>*optional*|Submission datetime of the workflow in ISO8601 format with milliseconds|string (date-time)|
 
 
 <a name="workflowqueryparameter"></a>
@@ -1267,7 +1327,8 @@ Result for an individual workflow returned by a workflow query
 |---|---|---|
 |**end**  <br>*optional*|Workflow end datetime|string (date-time)|
 |**id**  <br>*required*|Workflow ID|string|
-|**name**  <br>*required*|Workflow name|string|
+|**metadataArchiveStatus**  <br>*optional*|Status in metadata archives|string|
+|**name**  <br>*optional*|Workflow name|string|
 |**start**  <br>*optional*|Workflow start datetime|string (date-time)|
 |**status**  <br>*required*|Workflow status|string|
 |**submission**  <br>*optional*|Workflow submission datetime|string (date-time)|
diff --git a/docs/backends/TES.md b/docs/backends/TES.md
index e19917ec126..b90fa30bc3d 100644
--- a/docs/backends/TES.md
+++ b/docs/backends/TES.md
@@ -1,4 +1,4 @@
-**TES Backend**
+## TES Backend
 
 The TES backend submits jobs to a server that complies with the protocol described by the [GA4GH schema](https://github.com/ga4gh/task-execution-schemas).
 
@@ -19,7 +19,7 @@ echo $? > rc
 
 `<container_call_root>` would be equal to the runtime attribute `dockerWorkingDir`  or `/cromwell-executions/<workflow_uuid>/call-<call_name>/execution` if this attribute is not supplied.
 
-**Configuring**
+### Configuring
 
 Configuring the TES backend is straightforward; one must only provide the TES API endpoint for the service.
 
@@ -40,18 +40,18 @@ backend {
 }
 ```
 
-**Supported File Systems**  
+### Supported File Systems
 
 Currently this backend only works with files on a Local or Shared File System.
 
-**Docker**
+### Docker
 
 This backend supports the following optional [Runtime Attributes](../RuntimeAttributes) and [Workflow Options](../wf_options/Overview/) for working with Docker:
 
 * `docker`: Docker image to use such as "Ubuntu".
 * `dockerWorkingDir`: defines the working directory in the container.
 
-**CPU, Memory and Disk**
+### CPU, Memory and Disk
 
 This backend supports CPU, memory and disk size configuration through the use of the following [Runtime Attributes](../RuntimeAttributes) and [Workflow Options](../wf_options/Overview/):  
 
@@ -61,16 +61,29 @@ This backend supports CPU, memory and disk size configuration through the use of
     * Type: String (ex: "4 GB" or "4096 MB")
 * `disk` defines the amount of disk to use.
     * Type: String (ex: "1 GB" or "1024 MB")
+* `disks` accepts a GCP-style disk declaration and attempts to translate it for use on TES
+    * See table below for supported translations 
 * `preemptible` defines whether or not to use preemptible VMs.
     * Type: Boolean (ex: "true" or "false")
     * Integers are accepted and will be converted to boolean (true if > 0)
 
 If they are not set, the TES backend may use default values.
 
-**Azure**
+#### GCP `disks` to TES `disk` compatibility
+
+| GCP `disks` value                     | Supported | TES translation | Remark                            |
+|---------------------------------------|-----------|-----------------|-----------------------------------|
+| `local-disk 25 HDD`                   | ✅        | 25 GB disk      |                                   |
+| `local-disk 25 SSD`                   | ✅        | 25 GB disk      | Disk type info is dropped         |
+| `/some/mnt 25 SSD`                    | ❌        |                 | Custom mount points not supported | 
+| `local-disk 25 HDD, /some/mnt 50 SSD` | ❌        |                 | Multiple disks are not supported  | 
+            
+> Note: if both `disk` and `disks` attributes are specified, the TES backend will automatically use the value in `disk` and not attempt to translate `disks`.
+
+### Azure
 [Azure](Azure) is an implementation of Cromwell that uses the TES interface for orchestrating the tasks on Azure.
 
-**TESK**
+### TESK
 
 [TESK](https://github.com/EMBL-EBI-TSI/TESK) is an implementation of the TES interface that uses Kubernetes and FTP.
 When running Cromwell with a TESK backend, you will want to customize the way Cromwell process globs, as kubernetes will not work well with hard links in a lot of cases which is the default behavior in Cromwell.
diff --git a/docs/cromwell_features/HogFactors.md b/docs/cromwell_features/HogFactors.md
index c2d5f1b968f..aed82d5ebc9 100644
--- a/docs/cromwell_features/HogFactors.md
+++ b/docs/cromwell_features/HogFactors.md
@@ -2,7 +2,7 @@
 
 ## Introduction
 
-Cromwell has only a finite amount of resources at its disposal. WDL and CWL workflows allow scattered tasks to be
+Cromwell has only a finite amount of resources at its disposal. WDL workflows allow scattered tasks to be
 run a huge number of times with very simple syntax.
 This makes it easy for a very small number of workflows to hog all of the resources of Cromwell, forcing all other 
 workflows (even a simple 'hello_world') to wait in line behind them. 
diff --git a/docs/developers/CwlParsing.md b/docs/developers/CwlParsing.md
deleted file mode 100644
index c3982f784e5..00000000000
--- a/docs/developers/CwlParsing.md
+++ /dev/null
@@ -1,66 +0,0 @@
-# How CWL is Parsed
-
-The ultimate entry point to parsing CWL is in `CwlV1_0LanguageFactory.validateNamespace`. 
-
-Within that method, the process of parsing CWL can be thought of as performing these 4 steps:
-
-1. Produce a canonical one-file representation of the CWL as a JSON object in memory
-    - For the entrypoint into this process, see `CwlPreprocessor.preProcessCwl`
-2. Use Circe to turn that representation into scala case classes
-3. Convert the case classes into an appropriate WOM representations
-4. Mix in inputs to produce a WOM Executable.
-
-## Getting a canonical flat file
-
-### From a source file and dependencies zip:
-
-Note that the recursive implementation of `SALAD and flatten` in code can be found in: `CwlPreprocessor.preProcessCwl`.
-
-The process looks like:
-
-1. Write the workflow source file to disk
-2. Make sure the dependencies are unzipped next to it
-3. `SALAD and flatten` (see `CwlCanonicalizer.getCanonicalCwl`):
-    - Run `cwltool --print-pre` against the source file to get a canonicalize JSON representation (aka `SALAD`) it.
-        - NB: `cwltool --print-pre` must be able to resolve dependencies but it does not flatten them into the file.
-    - Recursively `SALAD and flatten` any references into their own JSON representations of the contents.
-    - Replace every reference in-place with the expanded JSON content.
-4. At the end of this process we will have:
-    - A single flat JSON 
-    - Every imported step expanded to contain an in-line description
-    - No more external references - everything required is provided in-line
-
-### From a workflow URL:
-
-The process looks similar to "source file and dependencies" except we never write anything locally:
-
-1. `SALAD and flatten`:
-    - Run `cwltool --print-pre` against the URL to get a canonicalize JSON representation (aka `SALAD`) it.
-        - NB: `cwltool --print-pre` must be able to resolve dependencies but it does not flatten them into the file.
-    - Recursively `SALAD and flatten` any references into their own JSON representations of the contents.
-    - Replace every reference in-place with the expanded JSON content.
-2. At the end of this process we will have:
-    - A single flat JSON 
-    - Every imported step expanded to contain an in-line description
-    - No more external references - everything required is provided in-line
-
-
-## Using Circe to get case classes
-
-This process is more or less automatic - the case classes define the fields which they anticipate existing in the JSON.
-and Circe does the rest.
-    - Optional fields in case classes are allowed to not exist in the JSON
-    - All fields in the JSON must be represented by fields in the appropriate case classes
-    - In cases where the JSON may be structured in one of several ways, we use Shapeless coproducts to specify "one of" many options.
-
-If a file is failing to parse the first stop should always be to double-check that the case classes accurately represent
-the range of possible CWL JSON.
-
-## Convert the case classes into WOM representations
-
-- This is a recursive process of examining the CWL case classes and creating WOM values instead.
-- Note that the CWL Language Factory (at least as of November 2018) does not implement the provision of WOM Bundles for 
-imports. Instead, CWL Language Factory implements only the all-in-one method of converting CWL source and inputs files 
-together into a WOM Executable.
-    - Pragmatically, this just means that using the CWL language factory to process an import statement in a WDL file 
-    is currently impossible (ie we cannot import CWL from WDL... yet).
diff --git a/docs/developers/bitesize/workflowParsing/cwlParsingOverview.md b/docs/developers/bitesize/workflowParsing/cwlParsingOverview.md
deleted file mode 100644
index 3ba5b13c494..00000000000
--- a/docs/developers/bitesize/workflowParsing/cwlParsingOverview.md
+++ /dev/null
@@ -1 +0,0 @@
-Coming soon.
diff --git a/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md b/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md
index 178ec2f3e8f..666e331334d 100644
--- a/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md
+++ b/docs/developers/bitesize/workflowParsing/wdlParsingOverview.md
@@ -31,7 +31,7 @@ You can think of WDL parsing in Cromwell in terms of the following major steps:
         * Including custom type references, variable references, task calls, subworkflow calls 
 * **WOM Bundle**:
     * A set of tasks, workflows and custom types, and the fully qualified names by which they can be referenced.
-    * In Cromwell's WOM format (the WOM format is the ultimate destination for _all_ languages, including WDL and CWL)
+    * In Cromwell's WOM format (the WOM format is the ultimate destination for _all_ languages, including WDL)
 * **Validated WOM Namespace**:
     * The conjunction of a WOM bundle with an input set.
-    * The entry point workflow (or sometimes task, in CWL) is known.
+    * The entry point workflow is known.
diff --git a/docs/filesystems/DataRepositoryService.md b/docs/filesystems/DataRepositoryService.md
index 21a33f8a668..770fc65207f 100644
--- a/docs/filesystems/DataRepositoryService.md
+++ b/docs/filesystems/DataRepositoryService.md
@@ -6,12 +6,12 @@ The Cromwell configuration for DRS is as follows:
 
 ```hocon
 drs {
-    # A reference to a potentially different auth required to contact Martha service.
+    # A reference to a potentially different auth required to contact DRS Resolution service.
     auth = "application-default"
 }
 ```
 
-The `auth` field refers to the authentication schema that should be used to authenticate requests to Martha service.
+The `auth` field refers to the authentication schema that should be used to authenticate requests to DRS Resolution service.
 
 The `drs` section needs to be added to
 - `engine.filesystems` block
diff --git a/docs/filesystems/Filesystems.md b/docs/filesystems/Filesystems.md
index d5a66de7eba..0630e421c0b 100644
--- a/docs/filesystems/Filesystems.md
+++ b/docs/filesystems/Filesystems.md
@@ -18,8 +18,8 @@ filesystems {
         # Class to instantiate and propagate to all factories. Takes a single typesafe config argument
         class = "cromwell.filesystems.drs.DrsFileSystemConfig"
         config {
-          martha {
-            url = "https://martha-url-here"
+          resolver {
+            url = "https://martha-url-here or https://drshub-url-here"
             # The number of times to retry failures connecting or HTTP 429 or HTTP 5XX responses, default 3.
             num-retries = 3
             # How long to wait between retrying HTTP 429 or HTTP 5XX responses, default 10 seconds.
@@ -150,11 +150,6 @@ engine {
 }
 ```
 
-#### Engine filesystems and CWL
-
-Note that CWL *always* needs to access file attributes from within the engine, so if you are using CWL, please make sure
-that **every filesystem you might use** is added to the `engine.filesystems` stanza.
-
 ### Backend Filesystems
 
 Similarly to the engine, you can also configure backend filesystems individually. Some backends might require the use of a specific filesystem.
diff --git a/docs/tutorials/Containers.md b/docs/tutorials/Containers.md
index 3934f7a4579..595f8305acc 100644
--- a/docs/tutorials/Containers.md
+++ b/docs/tutorials/Containers.md
@@ -2,7 +2,7 @@
 
 Containers are encapsulated environments that include an operating system, libraries, and software. For example, if you have a host machine running Centos, you can run an isolated container with Ubuntu 18.04. At a high level, it's useful to think of a container as a program or binary.
  
-To promote reproducibility and portability, it's considered best practice to define containers for a WDL and CWL task to run in - this ensures that running the same task on a different system will run the exact same software. 
+To promote reproducibility and portability, it's considered best practice to define containers for a WDL task to run in - this ensures that running the same task on a different system will run the exact same software. 
 
 Docker images are the most common container format, but it is not advisable for certain systems to run Docker itself, and for this reason Cromwell can be configured to support a number of alternatives.
 
@@ -71,26 +71,6 @@ workflow hello {
 }
 ```
 
-Similarly in CWL, you can specify a [`DockerRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#DockerRequirement) inside the requirements section:
-
-```cwl
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-inputs:
-    name:
-        type: string
-        default: "World"
-        inputBinding:
-          prefix: "Hello, "
-outputs:
-    out: stdout
-
-requirements:
-    DockerRequirement:
-        dockerPull: "ubuntu:latest"
-``` 
-___
 ### Docker
 
 [Docker](https://www.docker.com) is a popular container technology that is natively supported by Cromwell and WDL.
diff --git a/docs/tutorials/FiveMinuteIntro.md b/docs/tutorials/FiveMinuteIntro.md
index 87a9acd125d..2e203354bee 100644
--- a/docs/tutorials/FiveMinuteIntro.md
+++ b/docs/tutorials/FiveMinuteIntro.md
@@ -3,9 +3,10 @@
 ### Prerequisites:
 
 * A Unix-based operating system (yes, that includes Mac!)
-* A Java 8 runtime environment 
-	* You can see what you have by running `$ java -version` on a terminal. You're looking for a version that's at least `1.8` or higher.
-	* If not, you can download Java [here](http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html).
+* A Java 11 runtime environment 
+	* You can see what you have by running `$ java -version` on a terminal. 
+	* If not, you can download Java [here](https://adoptopenjdk.net/).
+	* You might need to update the `export JAVA_HOME` in your bash profile to point to your JAVA install location.
 * A sense of adventure!
 
 ### Goals
@@ -41,14 +42,17 @@ This bit is easy, you're just going to copy and paste something from the interne
 Open your favorite editor. Paste in the following content and save it as `myWorkflow.wdl` in your new `cromwell` directory:
 
 ```wdl
+# Example workflow
+# Declare WDL version 1.0 if working in Terra
+version 1.0
 workflow myWorkflow {
 	call myTask
 }
 
 task myTask {
-	command {
+	command <<<
 		echo "hello world"
-	}
+	>>>
 	output {
 		String out = read_string(stdout())
 	}
diff --git a/docs/tutorials/PipelinesApi101.md b/docs/tutorials/PipelinesApi101.md
index 6cc7bf72db4..ef94d111d04 100644
--- a/docs/tutorials/PipelinesApi101.md
+++ b/docs/tutorials/PipelinesApi101.md
@@ -2,22 +2,11 @@
 
 ## Pipelines API v2
 
-### Basic Information
-
-Initial support for Google [Pipelines API version 2](https://cloud.google.com/genomics/reference/rest/) was added in Cromwell 32.
-Expect feature parity with v1 except:
-
-* PAPI v2 private Docker support is equivalent to that in PAPI v1 but the configuration differs, please see [Docker configuration](http://cromwell.readthedocs.io/en/develop/filesystems/Google#Docker) for more details.
-* The "refresh token" authentication mode is **NOT** supported on PAPI V2.
-
-In addition, the following changes are to be expected:
-
-* Error messages for failed jobs might differ from V1
-* The Pipelines API log file content might differ from V1
-
 ### Setting up PAPIv2
 
-For now the easiest way to try PAPIv2 is to migrate an existing set up from PAPIv1 (see below). After that, copy the PAPIv2 sample configuration in [cromwell.examples.conf](https://github.com/broadinstitute/cromwell/blob/develop/cromwell.example.backends/PAPIv2.conf) in place of the PAPIv1 backend.
+For now the easiest way to try PAPIv2 is to start with the sample configuration in
+[cromwell.examples.conf](https://github.com/broadinstitute/cromwell/blob/develop/cromwell.example.backends/PAPIv2.conf)
+and adjust it to fit your needs.
 
 #### Permissions:
 
@@ -49,12 +38,6 @@ gsutil acl ch -u "$EMAIL":W gs://"$RANDOM_BUCKET_NAME"
 gcloud iam service-accounts keys create sa.json --iam-account "$EMAIL"
 ```
 
-## Pipelines API v1
-
-### Deprecation warning
-
-Please note that Google intends to deprecate PAPIv1 in the near future (circa mid 2019 or perhaps earlier). 
-
 ### Prerequisites
 
 This tutorial page relies on completing the previous tutorial:
diff --git a/docs/wf_options/Overview.md b/docs/wf_options/Overview.md
index 17ef2dd9f5f..9fcd7317eea 100644
--- a/docs/wf_options/Overview.md
+++ b/docs/wf_options/Overview.md
@@ -11,7 +11,7 @@ You provide workflow options to Cromwell in a JSON format. This can be supplied
 }
 ```
 
-Unless otherwise specified you can expect workflow options to override any hard-coded defaults in Cromwell or defaults provided in the [configuration file](../Configuring.md), but to be overridden by any values provided in the workflow definition file itself (WDL or CWL).
+Unless otherwise specified you can expect workflow options to override any hard-coded defaults in Cromwell or defaults provided in the [configuration file](../Configuring.md), but to be overridden by any values provided in the workflow definition file itself (WDL).
 
 Some workflow options apply only to tasks running on the [Google Pipelines API backend](Google).
 
@@ -27,7 +27,7 @@ Some options allow you to override or set defaults for runtime attributes.
 
 You can supply a default for any [Runtime Attributes](../RuntimeAttributes.md) by adding a `default_runtime_attributes` map to your workflow options file. Use the key to provide the attribute name and the value to supply the default. 
 
-These defaults replace any defaults in the Cromwell configuration file but are themselves replaced by any values explicitly provided by the task in the WDL or CWL file.
+These defaults replace any defaults in the Cromwell configuration file but are themselves replaced by any values explicitly provided by the task in the WDL file.
 
 Example `options.json`:
 ```json
diff --git a/engine/src/main/resources/swagger/cromwell.yaml b/engine/src/main/resources/swagger/cromwell.yaml
index 69fe3df4a71..6e840160d36 100644
--- a/engine/src/main/resources/swagger/cromwell.yaml
+++ b/engine/src/main/resources/swagger/cromwell.yaml
@@ -71,11 +71,6 @@ paths:
           type: file
           in: formData
         - $ref: '#/parameters/workflowTypeParam'
-        - name: workflowRoot
-          description: The root object to be run. Only necessary for CWL submissions containing multiple objects (in an array).
-          required: false
-          type: string
-          in: formData
         - $ref: '#/parameters/workflowTypeVersionParam'
         - name: labels
           description: JSON object of labels to apply to this workflow.
@@ -607,7 +602,7 @@ paths:
         '400':
           $ref: '#/responses/BadRequest'
         '404':
-           description: No matching cache entry. Cromwell versions prior to 28 will not have recorded information necessary for this endpoint and thus will also appear to not exist.
+          description: No matching cache entry. Cromwell versions prior to 28 will not have recorded information necessary for this endpoint and thus will also appear to not exist.
         '500':
           $ref: '#/responses/ServerError'
   '/api/workflows/{version}/backends':
@@ -753,6 +748,109 @@ paths:
         '500':
           description: An unexpected error occurred.
           $ref: '#/responses/ServerError'
+    post:
+      tags:
+        - GA4GH Workflow Execution Service (WES) - Alpha preview
+      summary: Run workflow
+      description: >-
+        This endpoint creates a new workflow run and returns a `RunId` to
+        monitor its progress.
+        
+        
+        The `workflow_attachment` array may be used to upload files that are
+        required to execute the workflow, including the primary workflow, tools
+        imported by the workflow, other files referenced by the workflow, or
+        files which are part of the input.  The implementation should stage
+        these files to a temporary directory and execute the workflow from
+        there. These parts must have a Content-Disposition header with a
+        "filename" provided for each part.  Filenames may include
+        subdirectories, but must not include references to parent directories
+        with '..' -- implementations should guard against maliciously
+        constructed filenames.
+        
+        
+        The `workflow_url` is either an absolute URL to a workflow file that is
+        accessible by the WES endpoint, or a relative URL corresponding to one
+        of the files attached using `workflow_attachment`.
+        
+        
+        The `workflow_params` JSON object specifies input parameters, such as
+        input files.  The exact format of the JSON object depends on the
+        conventions of the workflow language being used.  Input files should
+        either be absolute URLs, or relative URLs corresponding to files
+        uploaded using `workflow_attachment`.  The WES endpoint must understand
+        and be able to access URLs supplied in the input.  This is
+        implementation specific.
+        
+        
+        The `workflow_type` is the type of workflow language and must be "WDL"
+        currently (or another alternative supported by this WES instance).
+        
+        
+        The `workflow_type_version` is the version of the workflow language
+        submitted and must be one supported by this WES instance.
+        
+        
+        See the `RunRequest` documentation for details about other fields.
+      operationId: RunWorkflow
+      consumes:
+        - multipart/form-data
+      parameters:
+        - name: workflow_params
+          description: ""
+          required: false
+          type: string
+          in: formData
+        - name: workflow_type
+          description: ""
+          required: false
+          type: string
+          in: formData
+        - name: workflow_type_version
+          description: ""
+          required: false
+          type: string
+          in: formData
+        - name: tags
+          description: ''
+          required: false
+          type: string
+          in: formData
+        - name: workflow_engine_parameters
+          description: ''
+          required: false
+          type: string
+          in: formData
+        - name: workflow_url
+          description: ''
+          required: false
+          type: string
+          in: formData
+        - name: workflow_attachment
+          description: ''
+          required: false
+          type: array
+          items:
+            type: file
+            format: binary
+          in: formData
+      responses:
+        '201':
+          description: Successful Request
+          schema:
+            $ref: '#/definitions/RunId'
+        '400':
+          description: The request is malformed.
+          $ref: '#/responses/BadRequest'
+        '401':
+          description: The request is unauthorized.
+          $ref: '#/responses/InvalidSubmission'
+        '403':
+          description: The requester is not authorized to perform this action.
+          $ref: '#/responses/Forbidden'
+        '500':
+          description: An unexpected error occurred.
+          $ref: '#/responses/ServerError'
   '/api/ga4gh/wes/v1/runs/{run_id}':
     get:
       tags:
@@ -884,16 +982,16 @@ parameters:
   workflowTypeParam:
     name: workflowType
     type: string
-    description: The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.
-    enum: [WDL, CWL]
+    description: The workflow language for the file you submitted. Cromwell currently supports WDL.
+    enum: [WDL]
     required: false
     in: formData
   workflowTypeVersionParam:
     name: workflowTypeVersion
-    description: The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.
+    description: The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0.
     required: false
     type: string
-    enum: ["draft-2", "1.0", "v1.0"]
+    enum: ["draft-2", "1.0"]
     in: formData
   versionParam:
     name: version
@@ -931,10 +1029,6 @@ definitions:
         example: Submitted
   WorkflowMetadataResponse:
     description: Workflow and call level metadata
-    required:
-      - id
-      - status
-      - submission
     properties:
       id:
         type: string
@@ -963,12 +1057,11 @@ definitions:
       calls:
         $ref: '#/definitions/CallMetadata'
       failures:
-        $ref: '#/definitions/FailureMessage'
+        type: array
+        items:
+          $ref: '#/definitions/FailureMessage'
   CallMetadata:
     description: Call level metadata
-    required:
-      - inputs
-      - executionStatus
     properties:
       inputs:
         type: object
@@ -994,7 +1087,9 @@ definitions:
         type: string
         description: Backend-specific job ID
       failures:
-        $ref: '#/definitions/FailureMessage'
+        type: array
+        items:
+          $ref: '#/definitions/FailureMessage'
       returnCode:
         type: integer
         description: Call execution return code
@@ -1009,17 +1104,14 @@ definitions:
         description: Paths to backend specific logs for this call
   FailureMessage:
     description: Failure messages
-    required:
-      - failure
-      - timestamp
     properties:
-      failure:
+      message:
         type: string
         description: The failure message
-      timestamp:
-        type: string
-        format: date-time
-        description: The time at which this failure occurred
+      causedBy:
+        type: array
+        items:
+          $ref: '#/definitions/FailureMessage'
   WorkflowDescription:
     required:
       - valid
@@ -1108,9 +1200,9 @@ definitions:
               typeName: Pair
               pairTypes:
                 - leftType:
-                  -  typeName: Int
+                    -  typeName: Int
                 - rightType:
-                  -  typeName: String
+                    -  typeName: String
             optional: false
             default: null
             typeDisplayName: Pair[Int, String]
@@ -1159,8 +1251,20 @@ definitions:
                 - typeName: Int
                 - typeName: String
             typeDisplayName: Pair[Int, String]
+      images:
+        type: array
+        items:
+          type: string
       submittedDescriptorType:
         $ref: '#/definitions/DescriptorTypeAndVersion'
+      importedDescriptorTypes:
+        type: array
+        items:
+          $ref: '#/definitions/DescriptorTypeAndVersion'
+      meta:
+        type: object
+      parameterMeta:
+        type: object
       isRunnableWorkflow:
         description: Indicates whether this file can be run on its own (e.g. a WDL workflow)
         type: boolean
@@ -1276,12 +1380,11 @@ definitions:
   DescriptorType:
     type: string
     description: >-
-      One from a list of descriptor type strings (e.g. CWL, WDL).
+      One from a list of descriptor type strings (e.g. WDL).
       Note that these files can also include associated Docker/container files
       and test parameters that further describe a version of a tool
     example: "WDL"
     enum:
-      - CWL
       - WDL
   WorkflowQueryParameter:
     description: Workflow query parameters
@@ -1374,7 +1477,6 @@ definitions:
     description: Result for an individual workflow returned by a workflow query
     required:
       - id
-      - name
       - status
     properties:
       id:
@@ -1390,6 +1492,9 @@ definitions:
         type: string
         format: date-time
         description: Workflow submission datetime
+      metadataArchiveStatus:
+        type: string
+        description: Status in metadata archives
       start:
         type: string
         format: date-time
@@ -1678,7 +1783,7 @@ definitions:
         type: string
         description: >-
           REQUIRED
-          The workflow descriptor type, must be "CWL" or "WDL" currently (or
+          The workflow descriptor type, must be "WDL" currently (or
           another alternative supported by this WES instance)
       workflow_type_version:
         type: string
@@ -1698,7 +1803,7 @@ definitions:
         type: string
         description: >-
           REQUIRED
-          The workflow CWL or WDL document. When `workflow_attachments` is
+          The workflow WDL document. When `workflow_attachments` is
           used to attach files, the `workflow_url` may be a relative path to
           one of the attachments.
     description: >-
@@ -1853,4 +1958,3 @@ definitions:
           are also allowed. The version should be changed whenever the service
           is updated.
         example: 1.0.0
-
diff --git a/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala b/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
index 296d227d39f..c648261a7f4 100644
--- a/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
+++ b/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
@@ -8,19 +8,23 @@ import cromwell.core.filesystem.CromwellFileSystems
 import cromwell.core.path.{DefaultPathBuilderFactory, PathBuilder, PathBuilderFactory}
 import net.ceedubs.ficus.Ficus._
 
+import scala.collection.immutable.SortedMap
 import scala.concurrent.Future
 
 object EngineFilesystems {
   private val config: Config = ConfigFactory.load
 
-  private val defaultFileSystemFactory: Map[String, PathBuilderFactory] =
+  private val defaultFileSystemFactory: SortedMap[String, PathBuilderFactory] =
     Option(DefaultPathBuilderFactory.tuple)
       .filter(_ => config.as[Boolean]("engine.filesystems.local.enabled"))
-      .toMap
+      .to(collection.immutable.SortedMap)
 
-  private val pathBuilderFactories: Map[String, PathBuilderFactory] = {
-    CromwellFileSystems.instance.factoriesFromConfig(config.as[Config]("engine"))
-      .unsafe("Failed to instantiate engine filesystem") ++ defaultFileSystemFactory
+  private val pathBuilderFactories: SortedMap[String, PathBuilderFactory] = {
+    // Unordered maps are a classical source of randomness injection into a system
+    (
+      CromwellFileSystems.instance.factoriesFromConfig(config.as[Config]("engine"))
+        .unsafe("Failed to instantiate engine filesystem") ++ defaultFileSystemFactory
+    ).to(collection.immutable.SortedMap)
   }
 
   def configuredPathBuilderFactories: List[PathBuilderFactory] = pathBuilderFactories.values.toList
diff --git a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
index 0598e154f2d..012e771b5a0 100644
--- a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
+++ b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
@@ -12,6 +12,7 @@ import cromwell.core.path.Path
 import cromwell.engine.io.IoActor._
 import cromwell.engine.io.RetryableRequestSupport.{isInfinitelyRetryable, isRetryable}
 import cromwell.engine.io.{IoAttempts, IoCommandContext, IoCommandStalenessBackpressuring}
+import cromwell.filesystems.blob.BlobPath
 import cromwell.filesystems.drs.DrsPath
 import cromwell.filesystems.gcs.GcsPath
 import cromwell.filesystems.s3.S3Path
@@ -128,21 +129,33 @@ class NioFlow(parallelism: Int,
 
     def readFileAndChecksum: IO[String] = {
       for {
-        fileHash <- getHash(command.file)
+        fileHash <- getStoredHash(command.file)
         uncheckedValue <- readFile
-        checksumResult <- checkHash(uncheckedValue, fileHash)
+        checksumResult <- fileHash match {
+          case Some(hash) => checkHash(uncheckedValue, hash)
+          // If there is no stored checksum, don't attempt to validate.
+          // If the missing checksum is itself an error condition, that
+          // should be detected by the code that gets the FileHash.
+          case None => IO.pure(ChecksumSkipped())
+        }
         verifiedValue <- checksumResult match {
           case _: ChecksumSkipped => IO.pure(uncheckedValue)
           case _: ChecksumSuccess => IO.pure(uncheckedValue)
           case failure: ChecksumFailure => IO.raiseError(
             ChecksumFailedException(
-              s"Failed checksum for '${command.file}'. Expected '${fileHash.hashType}' hash of '${fileHash.hash}'. Calculated hash '${failure.calculatedHash}'"))
+              fileHash match {
+                case Some(hash) => s"Failed checksum for '${command.file}'. Expected '${hash.hashType}' hash of '${hash.hash}'. Calculated hash '${failure.calculatedHash}'"
+                case None => s"Failed checksum for '${command.file}'. Couldn't find stored file hash." // This should never happen
+              }
+            )
+          )
         }
       } yield verifiedValue
     }
 
     val fileContentIo = command.file match {
-      case _: DrsPath => readFileAndChecksum
+      case _: DrsPath  => readFileAndChecksum
+      case _: BlobPath => readFileAndChecksum
       case _ => readFile
     }
     fileContentIo.map(_.replaceAll("\\r\\n", "\\\n"))
@@ -153,19 +166,27 @@ class NioFlow(parallelism: Int,
   }
 
   private def hash(hash: IoHashCommand): IO[String] = {
-    getHash(hash.file).map(_.hash)
+    // If there is no hash accessible from the file storage system,
+    // we'll read the file and generate the hash ourselves.
+    getStoredHash(hash.file).flatMap {
+      case Some(storedHash) => IO.pure(storedHash)
+      case None => generateMd5FileHashForPath(hash.file)
+    }.map(_.hash)
   }
 
-  private def getHash(file: Path): IO[FileHash] = {
+  private def getStoredHash(file: Path): IO[Option[FileHash]] = {
     file match {
-      case gcsPath: GcsPath => getFileHashForGcsPath(gcsPath)
+      case gcsPath: GcsPath => getFileHashForGcsPath(gcsPath).map(Option(_))
+      case blobPath: BlobPath => getFileHashForBlobPath(blobPath)
       case drsPath: DrsPath => IO {
+        // We assume all DRS files have a stored hash; this will throw
+        // if the file does not.
         drsPath.getFileHash
-      }
+      }.map(Option(_))
       case s3Path: S3Path => IO {
-        FileHash(HashType.S3Etag, s3Path.eTag)
+        Option(FileHash(HashType.S3Etag, s3Path.eTag))
       }
-      case path => getMd5FileHashForPath(path)
+      case _ => IO.pure(None)
     }
   }
 
@@ -201,7 +222,11 @@ class NioFlow(parallelism: Int,
     gcsPath.objectBlobId.map(id => FileHash(HashType.GcsCrc32c, gcsPath.cloudStorage.get(id).getCrc32c))
   }
 
-  private def getMd5FileHashForPath(path: Path): IO[FileHash] = delayedIoFromTry {
+  private def getFileHashForBlobPath(blobPath: BlobPath): IO[Option[FileHash]] = delayedIoFromTry {
+    blobPath.md5HexString.map(md5 => md5.map(FileHash(HashType.Md5, _)))
+  }
+
+  private def generateMd5FileHashForPath(path: Path): IO[FileHash] = delayedIoFromTry {
     tryWithResource(() => path.newInputStream) { inputStream =>
       FileHash(HashType.Md5, org.apache.commons.codec.digest.DigestUtils.md5Hex(inputStream))
     }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
index ba82bab3e96..b4ccf3de53b 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
@@ -135,6 +135,12 @@ object WorkflowActor {
 
   case class StateCheckpoint(state: WorkflowActorState, failures: Option[List[Throwable]] = None)
 
+  /**
+    * Message sent from WorkflowActor to itself to trigger the initialization to start. Allows us to idle
+    * in the initializing state without an assigned actor for a few seconds if the first attempt fails.
+    */
+  case object StartInitializing
+
   /**
     * @param currentLifecycleStateActor The current lifecycle stage, represented by an ActorRef.
     */
@@ -145,7 +151,8 @@ object WorkflowActor {
                                effectiveStartableState: StartableState,
                                workflowFinalOutputs: Set[WomValue] = Set.empty,
                                workflowAllOutputs: Set[WomValue] = Set.empty,
-                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty)
+                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty,
+                               failedInitializationAttempts: Int = 0)
   object WorkflowActorData {
     def apply(startableState: StartableState): WorkflowActorData = WorkflowActorData(
       currentLifecycleStateActor = None,
@@ -255,6 +262,9 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
 
   protected val pathBuilderFactories: List[PathBuilderFactory] = EngineFilesystems.configuredPathBuilderFactories
 
+  protected val maxInitializationAttempts: Int = 16
+  protected val initializationRetryInterval: FiniteDuration = 1.minute
+
   startWith(WorkflowUnstartedState, WorkflowActorData(initialStartableState))
 
   pushCurrentStateToMetadataService(workflowId, WorkflowUnstartedState.workflowState)
@@ -299,18 +309,8 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
 
   when(MaterializingWorkflowDescriptorState) {
     case Event(MaterializeWorkflowDescriptorSuccessResponse(workflowDescriptor), data) =>
-      val initializerActor = context.actorOf(
-        WorkflowInitializationActor.props(
-          workflowIdForLogging,
-          rootWorkflowIdForLogging,
-          workflowDescriptor,
-          ioActor,
-          serviceRegistryActor,
-          restarting
-        ),
-        name = s"WorkflowInitializationActor-$workflowId")
-      initializerActor ! StartInitializationCommand
-      goto(InitializingWorkflowState) using data.copy(currentLifecycleStateActor = Option(initializerActor), workflowDescriptor = Option(workflowDescriptor))
+      self ! StartInitializing
+      goto(InitializingWorkflowState) using data.copy(workflowDescriptor = Option(workflowDescriptor))
     case Event(MaterializeWorkflowDescriptorFailureResponse(reason: Throwable), data) =>
       goto(WorkflowFailedState) using data.copy(lastStateReached = StateCheckpoint(MaterializingWorkflowDescriptorState, Option(List(reason))))
     // If the workflow is not being restarted then we can abort it immediately as nothing happened yet
@@ -320,40 +320,45 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   /* ************************** */
   /* ****** Initializing ****** */
   /* ************************** */
-
-  when(InitializingWorkflowState) {
-    case Event(WorkflowInitializationSucceededResponse(initializationData), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
-      val executionActor = context.actorOf(WorkflowExecutionActor.props(
+  protected def createInitializationActor(workflowDescriptor: EngineWorkflowDescriptor, name: String): ActorRef = {
+    context.actorOf(
+      WorkflowInitializationActor.props(
+        workflowIdForLogging,
+        rootWorkflowIdForLogging,
         workflowDescriptor,
-        ioActor = ioActor,
-        serviceRegistryActor = serviceRegistryActor,
-        jobStoreActor = jobStoreActor,
-        subWorkflowStoreActor = subWorkflowStoreActor,
-        callCacheReadActor = callCacheReadActor,
-        callCacheWriteActor = callCacheWriteActor,
-        workflowDockerLookupActor = workflowDockerLookupActor,
-        jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
-        jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
-        backendSingletonCollection,
-        initializationData,
-        startState = data.effectiveStartableState,
-        rootConfig = conf,
-        totalJobsByRootWf = totalJobsByRootWf,
-        fileHashCacheActor = fileHashCacheActorProps map context.system.actorOf,
-        blacklistCache = blacklistCache), name = s"WorkflowExecutionActor-$workflowId")
+        ioActor,
+        serviceRegistryActor,
+        restarting
+      ),
+      name)
+  }
 
+  when(InitializingWorkflowState) {
+    case Event(StartInitializing, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+      val initializerActor = createInitializationActor(workflowDescriptor, s"WorkflowInitializationActor-$workflowId-${data.failedInitializationAttempts + 1}")
+      initializerActor ! StartInitializationCommand
+      goto(InitializingWorkflowState) using data.copy(currentLifecycleStateActor = Option(initializerActor), workflowDescriptor = Option(workflowDescriptor))
+    case Event(WorkflowInitializationSucceededResponse(initializationData), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+      val dataWithInitializationData = data.copy(initializationData = initializationData)
+      val executionActor = createWorkflowExecutionActor(workflowDescriptor, dataWithInitializationData)
       executionActor ! ExecuteWorkflowCommand
-
       val nextState = data.effectiveStartableState match {
         case RestartableAborting => WorkflowAbortingState
         case _ => ExecutingWorkflowState
       }
-      goto(nextState) using data.copy(currentLifecycleStateActor = Option(executionActor), initializationData = initializationData)
-    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
-      finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
+      goto(nextState) using dataWithInitializationData.copy(currentLifecycleStateActor = Option(executionActor))
+    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+      val failedInitializationAttempts = data.failedInitializationAttempts + 1
+      if (failedInitializationAttempts < maxInitializationAttempts) {
+        workflowLogger.info(s"Initialization failed on attempt $failedInitializationAttempts. Will retry up to $maxInitializationAttempts times. Next retry is in $initializationRetryInterval", CromwellAggregatedException(reason, "Initialization Failure"))
+        context.system.scheduler.scheduleOnce(initializationRetryInterval) { self ! StartInitializing}
+        stay() using data.copy(currentLifecycleStateActor = None, failedInitializationAttempts = failedInitializationAttempts)
+      } else {
+        finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
+      }
 
     // If the workflow is not restarting, handle the Abort command normally and send an abort message to the init actor
-    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) if !restarting =>
+    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) if !restarting =>
       handleAbortCommand(data, workflowDescriptor)
   }
 
@@ -361,24 +366,45 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   /* ****** Running ****** */
   /* ********************* */
 
+  def createWorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor, data: WorkflowActorData): ActorRef = {
+    context.actorOf(WorkflowExecutionActor.props(
+      workflowDescriptor,
+      ioActor = ioActor,
+      serviceRegistryActor = serviceRegistryActor,
+      jobStoreActor = jobStoreActor,
+      subWorkflowStoreActor = subWorkflowStoreActor,
+      callCacheReadActor = callCacheReadActor,
+      callCacheWriteActor = callCacheWriteActor,
+      workflowDockerLookupActor = workflowDockerLookupActor,
+      jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
+      jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
+      backendSingletonCollection,
+      data.initializationData,
+      startState = data.effectiveStartableState,
+      rootConfig = conf,
+      totalJobsByRootWf = totalJobsByRootWf,
+      fileHashCacheActor = fileHashCacheActorProps map context.system.actorOf,
+      blacklistCache = blacklistCache), name = s"WorkflowExecutionActor-$workflowId")
+  }
+
   // Handles workflow completion events from the WEA and abort command
   val executionResponseHandler: StateFunction = {
     // Workflow responses
     case Event(WorkflowExecutionSucceededResponse(jobKeys, rootAndSubworklowIds, finalOutputs, allOutputs),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, finalOutputs, None, allOutputs, rootAndSubworklowIds)
     case Event(WorkflowExecutionFailedResponse(jobKeys, failures),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, CallOutputs.empty, Option(List(failures)))
     case Event(WorkflowExecutionAbortedResponse(jobKeys),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, StateCheckpoint(_, failures), _, _, _, _)) =>
+    data @ WorkflowActorData(_, Some(workflowDescriptor), _, StateCheckpoint(_, failures), _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, CallOutputs.empty, failures)
 
     // Whether we're running or aborting, restarting or not, pass along the abort command.
     // Note that aborting a workflow multiple times will result in as many abort commands sent to the execution actor
-    case Event(AbortWorkflowWithExceptionCommand(ex), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(AbortWorkflowWithExceptionCommand(ex), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       handleAbortCommand(data, workflowDescriptor, Option(ex))
-    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       handleAbortCommand(data, workflowDescriptor)
   }
 
@@ -391,12 +417,16 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   // Handles initialization responses we can get if the abort came in when we were initializing the workflow
   val abortHandler: StateFunction = {
     // If the initialization failed, record the failure in the data and finalize the workflow
-    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
 
     // Otherwise (success or abort), finalize the workflow without failures
-    case Event(_: WorkflowInitializationResponse, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _)) =>
+    case Event(_: WorkflowInitializationResponse, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, failures = None)
+
+    case Event(StartInitializing, _) =>
+      // An initialization trigger we no longer need to action. Ignore:
+      stay()
   }
 
   // In aborting state, we can receive initialization responses or execution responses.
@@ -413,6 +443,9 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
       val failures = data.lastStateReached.failures.getOrElse(List.empty) ++ finalizationFailures
       goto(WorkflowFailedState) using data.copy(lastStateReached = StateCheckpoint(FinalizingWorkflowState, Option(failures)))
     case Event(AbortWorkflowCommand, _) => stay()
+    case Event(StartInitializing, _) =>
+      // An initialization trigger we no longer need to action. Ignore:
+      stay()
   }
 
   when(MetadataIntegrityValidationState) {
@@ -431,13 +464,18 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   }
 
   def handleAbortCommand(data: WorkflowActorData, workflowDescriptor: EngineWorkflowDescriptor, exceptionCausedAbortOpt: Option[Throwable] = None) = {
+    val updatedData = data.copy(lastStateReached = StateCheckpoint(stateName, exceptionCausedAbortOpt.map(List(_))))
     data.currentLifecycleStateActor match {
       case Some(currentActor) =>
         currentActor ! EngineLifecycleActorAbortCommand
-        goto(WorkflowAbortingState) using data.copy(lastStateReached = StateCheckpoint(stateName, exceptionCausedAbortOpt.map(List(_))))
+        goto(WorkflowAbortingState) using updatedData
       case None =>
-        workflowLogger.warn(s"Received an abort command in state $stateName but there's no lifecycle actor associated. This is an abnormal state, finalizing the workflow anyway.")
-        finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, None)
+        if (stateName == InitializingWorkflowState) {
+          workflowLogger.info(s"Received an abort command in state $stateName (while awaiting an initialization retry). Finalizing the workflow.")
+        } else {
+          workflowLogger.warn(s"Received an abort command in state $stateName but there's no lifecycle actor associated. This is an abnormal state, finalizing the workflow anyway.")
+        }
+        finalizeWorkflow(updatedData, workflowDescriptor, Map.empty, CallOutputs.empty, failures = None, lastStateOverride = Option(WorkflowAbortingState))
     }
   }
 
@@ -645,11 +683,12 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
                                workflowFinalOutputs: CallOutputs,
                                failures: Option[List[Throwable]],
                                workflowAllOutputs: Set[WomValue] = Set.empty,
-                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty) = {
+                               rootAndSubworkflowIds: Set[WorkflowId] = Set.empty,
+                               lastStateOverride: Option[WorkflowActorState] = None) = {
     val finalizationActor = makeFinalizationActor(workflowDescriptor, jobExecutionMap, workflowFinalOutputs)
     finalizationActor ! StartFinalizationCommand
     goto(FinalizingWorkflowState) using data.copy(
-      lastStateReached = StateCheckpoint (stateName, failures),
+      lastStateReached = StateCheckpoint (lastStateOverride.getOrElse(stateName), failures),
       workflowFinalOutputs = workflowFinalOutputs.outputs.values.toSet,
       workflowAllOutputs = workflowAllOutputs,
       rootAndSubworkflowIds = rootAndSubworkflowIds
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
index 0eef565caf2..89745e6523d 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
@@ -37,7 +37,7 @@ class FetchCachedResultsActor(cacheResultId: CallCachingEntryId, replyTo: ActorR
 
         val sourceCacheDetails = Seq(result.callCachingEntry.workflowExecutionUuid,
           result.callCachingEntry.callFullyQualifiedName,
-          result.callCachingEntry.jobIndex).mkString(":")
+          result.callCachingEntry.jobIndex.toString).mkString(":")
 
         CachedOutputLookupSucceeded(simpletons, jobDetritusFiles.toMap,
           result.callCachingEntry.returnCode,
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
index 0f9eec73ef4..57da64de3ce 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
@@ -753,7 +753,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
   private def logCacheHitSuccessAndNotifyMetadata(data: ResponsePendingData): Unit = {
 
-    val metadataMap = Map(callCachingHitResultMetadataKey -> true) ++ data.ejeaCacheHit.flatMap(_.details).map(details => callCachingReadResultMetadataKey -> s"Cache Hit: $details").toMap
+    val metadataMap = Map[String, Any](callCachingHitResultMetadataKey -> true) ++ data.ejeaCacheHit.flatMap(_.details).map(details => callCachingReadResultMetadataKey -> s"Cache Hit: $details").toMap
 
     writeToMetadata(metadataMap)
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
index e913e5c6b3b..a5c1d6fc995 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
@@ -27,12 +27,13 @@ object ValueStore {
 case class ValueStore(store: Table[OutputPort, ExecutionIndex, WomValue]) {
 
   override def toString: String = {
+    import common.util.StringUtil.EnhancedToStringable
     import io.circe.syntax._
     import io.circe.Printer
 
     val values = store.valuesTriplet.map {
-      case (node, None, value) => node.name -> value.valueString
-      case (node, index, value) => s"${node.name}:${index.fromIndex}" -> value.valueString
+      case (node, None, value) => node.name -> value.toPrettyElidedString(limit = 100)
+      case (node, index, value) => s"${node.name}:${index.fromIndex}" -> value.toPrettyElidedString(limit = 100)
     }.toMap
 
     values.asJson.printWith(Printer.spaces2.copy(dropNullValues = true, colonLeft = ""))
diff --git a/engine/src/main/scala/cromwell/server/CromwellServer.scala b/engine/src/main/scala/cromwell/server/CromwellServer.scala
index b5705b91dae..76f784875fc 100644
--- a/engine/src/main/scala/cromwell/server/CromwellServer.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellServer.scala
@@ -11,7 +11,6 @@ import cromwell.services.instrumentation.CromwellInstrumentationActor
 import cromwell.webservice.SwaggerService
 import cromwell.webservice.routes.CromwellApiService
 import cromwell.webservice.routes.wes.WesRouteSupport
-import cromwell.webservice.routes.wes.WesRunRoutes
 
 import scala.concurrent.Future
 import scala.util.{Failure, Success}
@@ -37,7 +36,6 @@ class CromwellServerActor(cromwellSystem: CromwellSystem, gracefulShutdown: Bool
     with CromwellApiService
     with CromwellInstrumentationActor
     with WesRouteSupport
-    with WesRunRoutes
     with SwaggerService
     with ActorLogging {
   implicit val actorSystem = context.system
@@ -53,7 +51,7 @@ class CromwellServerActor(cromwellSystem: CromwellSystem, gracefulShutdown: Bool
     * cromwell.yaml is broken unless the swagger index.html is patched. Copy/paste the code from rawls or cromiam if
     * actual cromwell+swagger+oauth+/api support is needed.
     */
-  val apiRoutes: Route = pathPrefix("api")(concat(workflowRoutes, womtoolRoutes, wesRoutes, runRoutes))
+  val apiRoutes: Route = pathPrefix("api")(concat(workflowRoutes, womtoolRoutes, wesRoutes))
   val nonApiRoutes: Route = concat(engineRoutes, swaggerUiResourceRoute)
   val allRoutes: Route = concat(apiRoutes, nonApiRoutes)
 
diff --git a/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala b/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
index 9b23ec62311..a1c4f023135 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
@@ -81,81 +81,81 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
     path("workflows" / Segment / "backends") { _ =>
       get { instrumentRequest { complete(ToResponseMarshallable(backendResponse)) } }
     } ~
-    path("workflows" / Segment / "callcaching" / "diff") { _ =>
-      parameterSeq { parameters =>
-        get {
-          instrumentRequest {
-            CallCacheDiffQueryParameter.fromParameters(parameters) match {
-              case Valid(queryParameter) =>
-                val diffActor = actorRefFactory.actorOf(CallCacheDiffActor.props(serviceRegistryActor), "CallCacheDiffActor-" + UUID.randomUUID())
-                onComplete(diffActor.ask(queryParameter).mapTo[CallCacheDiffActorResponse]) {
-                  case Success(r: SuccessfulCallCacheDiffResponse) => complete(r)
-                  case Success(r: FailedCallCacheDiffResponse) => r.reason.errorRequest(StatusCodes.InternalServerError)
-                  case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
-                  case Failure(e: CachedCallNotFoundException) => e.errorRequest(StatusCodes.NotFound)
-                  case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
-                  case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
-                }
-              case Invalid(errors) =>
-                val e = AggregatedMessageException("Wrong parameters for call cache diff query", errors.toList)
-                e.errorRequest(StatusCodes.BadRequest)
+      path("workflows" / Segment / "callcaching" / "diff") { _ =>
+        parameterSeq { parameters =>
+          get {
+            instrumentRequest {
+              CallCacheDiffQueryParameter.fromParameters(parameters) match {
+                case Valid(queryParameter) =>
+                  val diffActor = actorRefFactory.actorOf(CallCacheDiffActor.props(serviceRegistryActor), "CallCacheDiffActor-" + UUID.randomUUID())
+                  onComplete(diffActor.ask(queryParameter).mapTo[CallCacheDiffActorResponse]) {
+                    case Success(r: SuccessfulCallCacheDiffResponse) => complete(r)
+                    case Success(r: FailedCallCacheDiffResponse) => r.reason.errorRequest(StatusCodes.InternalServerError)
+                    case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
+                    case Failure(e: CachedCallNotFoundException) => e.errorRequest(StatusCodes.NotFound)
+                    case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
+                    case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
+                  }
+                case Invalid(errors) =>
+                  val e = AggregatedMessageException("Wrong parameters for call cache diff query", errors.toList)
+                  e.errorRequest(StatusCodes.BadRequest)
+              }
             }
           }
         }
-      }
-    } ~
-    path("workflows" / Segment / Segment / "timing") { (_, possibleWorkflowId) =>
-      instrumentRequest {
-        onComplete(validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor)) {
-          case Success(workflowId) => completeTimingRouteResponse(metadataLookupForTimingRoute(workflowId))
-          case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
-          case Failure(e: InvalidWorkflowException) => e.failRequest(StatusCodes.BadRequest)
-          case Failure(e) => e.failRequest(StatusCodes.InternalServerError)
-        }
-      }
-    } ~
-    path("workflows" / Segment / Segment / "abort") { (_, possibleWorkflowId) =>
-      post {
+      } ~
+      path("workflows" / Segment / Segment / "timing") { (_, possibleWorkflowId) =>
         instrumentRequest {
-          abortWorkflow(possibleWorkflowId, workflowStoreActor, workflowManagerActor)
+          onComplete(validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor)) {
+            case Success(workflowId) => completeTimingRouteResponse(metadataLookupForTimingRoute(workflowId))
+            case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
+            case Failure(e: InvalidWorkflowException) => e.failRequest(StatusCodes.BadRequest)
+            case Failure(e) => e.failRequest(StatusCodes.InternalServerError)
+          }
         }
-      }
-    } ~
-  path("workflows" / Segment) { _ =>
-      post {
-        instrumentRequest {
-          entity(as[Multipart.FormData]) { formData =>
-            submitRequest(formData, isSingleSubmission = true)
+      } ~
+      path("workflows" / Segment / Segment / "abort") { (_, possibleWorkflowId) =>
+        post {
+          instrumentRequest {
+            abortWorkflow(possibleWorkflowId, workflowStoreActor, workflowManagerActor)
           }
         }
-      }
-    } ~
-  path("workflows" / Segment / "batch") { _ =>
-    post {
-      instrumentRequest {
-        entity(as[Multipart.FormData]) { formData =>
-          submitRequest(formData, isSingleSubmission = false)
+      } ~
+      path("workflows" / Segment) { _ =>
+        post {
+          instrumentRequest {
+            entity(as[Multipart.FormData]) { formData =>
+              submitRequest(formData, isSingleSubmission = true)
+            }
+          }
         }
-      }
-    }
-  } ~
-  path("workflows" / Segment / Segment / "releaseHold") { (_, possibleWorkflowId) =>
-    post {
-      instrumentRequest {
-        val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor) flatMap { workflowId =>
-          workflowStoreActor.ask(WorkflowStoreActor.WorkflowOnHoldToSubmittedCommand(workflowId)).mapTo[WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedResponse]
+      } ~
+      path("workflows" / Segment / "batch") { _ =>
+        post {
+          instrumentRequest {
+            entity(as[Multipart.FormData]) { formData =>
+              submitRequest(formData, isSingleSubmission = false)
+            }
+          }
         }
-        onComplete(response){
-          case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e: NotInOnHoldStateException)) => e.errorRequest(StatusCodes.Forbidden)
-          case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e)) => e.errorRequest(StatusCodes.InternalServerError)
-          case Success(r: WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedSuccess) => completeResponse(StatusCodes.OK, toResponse(r.workflowId, WorkflowSubmitted), Seq.empty)
-          case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
-          case Failure(e: InvalidWorkflowException) => e.failRequest(StatusCodes.BadRequest)
-          case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
+      } ~
+      path("workflows" / Segment / Segment / "releaseHold") { (_, possibleWorkflowId) =>
+        post {
+          instrumentRequest {
+            val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor) flatMap { workflowId =>
+              workflowStoreActor.ask(WorkflowStoreActor.WorkflowOnHoldToSubmittedCommand(workflowId)).mapTo[WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedResponse]
+            }
+            onComplete(response){
+              case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e: NotInOnHoldStateException)) => e.errorRequest(StatusCodes.Forbidden)
+              case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e)) => e.errorRequest(StatusCodes.InternalServerError)
+              case Success(r: WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedSuccess) => completeResponse(StatusCodes.OK, toResponse(r.workflowId, WorkflowSubmitted), Seq.empty)
+              case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
+              case Failure(e: InvalidWorkflowException) => e.failRequest(StatusCodes.BadRequest)
+              case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
+            }
+          }
         }
-      }
-    }
-  } ~ metadataRoutes
+      } ~ metadataRoutes
 
 
   private def metadataLookupForTimingRoute(workflowId: WorkflowId): Future[MetadataJsonResponse] = {
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
index 32e221272e0..58313cb5946 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
@@ -2,8 +2,7 @@ package cromwell.webservice.routes.wes
 
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport
 import cromwell.webservice.routes.wes.WesState.WesState
-import spray.json.{DefaultJsonProtocol, RootJsonFormat}
-import cromwell.webservice.routes.wes.WesRunLog
+import spray.json.{DefaultJsonProtocol, JsObject, RootJsonFormat}
 
 sealed trait WesResponse extends Product with Serializable
 final case class WesErrorResponse(msg: String, status_code: Int) extends WesResponse
@@ -12,6 +11,18 @@ final case class WesRunStatus(run_id: String, state: WesState) extends WesRespon
 final case class WesResponseRunList(runs: List[WesRunStatus]) extends WesResponse
 final case class WesResponseWorkflowMetadata(workflowLog: WesRunLog) extends WesResponse
 
+final case class WesRunLog(run_id: String,
+                           request: WesRunRequest,
+                           state: WesState,
+                           run_log: Option[WesLog],
+                           task_logs: Option[List[WesLog]],
+                           outputs: Option[JsObject]
+                          ) extends WesResponse
+
+object WesRunLog {
+  def fromJson(json: String): WesRunLog = CromwellMetadata.fromJson(json).wesRunLog
+}
+
 
 final case class WesStatusInfoResponse(workflow_type_version: Map[String, Iterable[String]],
                                     supported_wes_versions: Iterable[String],
@@ -48,6 +59,7 @@ object WesResponseJsonSupport extends SprayJsonSupport with DefaultJsonProtocol
         case i: WesStatusInfoResponse => i.toJson
         case l: WesResponseRunList => l.toJson
         case m: WesResponseWorkflowMetadata => m.toJson
+        case w: WesRunLog => w.toJson
       }
     }
 
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
index e4969702460..41973bb8981 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
@@ -1,34 +1,47 @@
 package cromwell.webservice.routes.wes
 
 import akka.actor.ActorRef
+import akka.http.scaladsl.model.{Multipart, StatusCode, StatusCodes}
 import akka.http.scaladsl.server.Directives._
-import akka.http.scaladsl.server.Route
+import akka.http.scaladsl.server.directives.RouteDirectives.complete
+import akka.http.scaladsl.server.{Directive1, Route}
 import akka.pattern.{AskTimeoutException, ask}
+import akka.stream.ActorMaterializer
 import akka.util.Timeout
-import cromwell.engine.instrumentation.HttpInstrumentation
-import cromwell.services.metadata.MetadataService.{GetStatus, MetadataServiceResponse, StatusLookupFailed}
-import cromwell.webservice.routes.CromwellApiService.{UnrecognizedWorkflowException, validateWorkflowIdInMetadata}
-import cromwell.webservice.WebServiceUtils.EnhancedThrowable
-
-import scala.concurrent.ExecutionContext
-import scala.util.{Failure, Success}
-import WesResponseJsonSupport._
-import akka.http.scaladsl.model.{StatusCode, StatusCodes}
-import akka.http.scaladsl.server.directives.RouteDirectives.complete
-import WesRouteSupport._
+import cats.data.NonEmptyList
+import com.typesafe.config.ConfigFactory
 import cromwell.core.abort.SuccessfulAbortResponse
+import cromwell.core.{WorkflowId, WorkflowOnHold, WorkflowState, WorkflowSubmitted}
+import cromwell.engine.instrumentation.HttpInstrumentation
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
+import cromwell.engine.workflow.workflowstore.{WorkflowStoreActor, WorkflowStoreSubmitActor}
 import cromwell.server.CromwellShutdown
-import cromwell.services.SuccessfulMetadataJsonResponse
+import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, GetSingleWorkflowMetadataAction, GetStatus, MetadataServiceResponse, StatusLookupFailed}
+import cromwell.services.{FailedMetadataJsonResponse, SuccessfulMetadataJsonResponse}
+import cromwell.webservice.PartialWorkflowSources
+import cromwell.webservice.WebServiceUtils.{EnhancedThrowable, completeResponse, materializeFormData}
 import cromwell.webservice.routes.CromwellApiService
+import cromwell.webservice.routes.CromwellApiService.{UnrecognizedWorkflowException, validateWorkflowIdInMetadata}
+import cromwell.webservice.routes.MetadataRouteSupport.{metadataBuilderActorRequest, metadataQueryRequest}
+import cromwell.webservice.routes.wes.WesResponseJsonSupport._
+import cromwell.webservice.routes.wes.WesRouteSupport.{respondWithWesError, _}
+import net.ceedubs.ficus.Ficus._
+
+import scala.concurrent.duration.FiniteDuration
+import scala.concurrent.{ExecutionContext, Future, TimeoutException}
+import scala.util.{Failure, Success}
+
+
 
 trait WesRouteSupport extends HttpInstrumentation {
+
   val serviceRegistryActor: ActorRef
   val workflowManagerActor: ActorRef
   val workflowStoreActor: ActorRef
 
   implicit val ec: ExecutionContext
   implicit val timeout: Timeout
+  implicit val materializer: ActorMaterializer
 
   /*
     Defines routes intended to sit alongside the primary Cromwell REST endpoints. For instance, we'll now have:
@@ -49,44 +62,125 @@ trait WesRouteSupport extends HttpInstrumentation {
         pathPrefix("ga4gh" / "wes" / "v1") {
           concat(
             path("service-info") {
-              complete(ServiceInfo.toWesResponse(workflowStoreActor))
+              get {
+                complete(ServiceInfo.toWesResponse(workflowStoreActor))
+              }
             },
-            pathPrefix("runs") {
-              concat(
-                path(Segment / "status") { possibleWorkflowId =>
-                  val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor).flatMap(w => serviceRegistryActor.ask(GetStatus(w)).mapTo[MetadataServiceResponse])
-                  // WES can also return a 401 or a 403 but that requires user auth knowledge which Cromwell doesn't currently have
-                  onComplete(response) {
-                    case Success(SuccessfulMetadataJsonResponse(_, jsObject)) =>
-                      val wesState = WesState.fromCromwellStatusJson(jsObject)
-                      complete(WesRunStatus(possibleWorkflowId, wesState))
-                    case Success(r: StatusLookupFailed) => r.reason.errorRequest(StatusCodes.InternalServerError)
-                    case Success(m: MetadataServiceResponse) =>
-                      // This should never happen, but ....
-                      val error = new IllegalStateException("Unexpected response from Metadata service: " + m)
-                      error.errorRequest(StatusCodes.InternalServerError)
-                    case Failure(_: UnrecognizedWorkflowException) => complete(NotFoundError)
-                    case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
-                  }
-                },
-                path(Segment / "cancel") { possibleWorkflowId =>
-                  post {
-                    CromwellApiService.abortWorkflow(possibleWorkflowId,
-                      workflowStoreActor,
-                      workflowManagerActor,
-                      successHandler = WesAbortSuccessHandler,
-                      errorHandler = WesAbortErrorHandler)
+            path("runs") {
+              get {
+                parameters(("page_size".as[Int].?, "page_token".?)) { (pageSize, pageToken) =>
+                  completeCromwellResponse(listRuns(pageSize, pageToken, serviceRegistryActor))
+                }
+              } ~
+                post {
+                  extractSubmission() { submission =>
+                    wesSubmitRequest(submission.entity,
+                      isSingleSubmission = true)
                   }
                 }
-              )
+            },
+            path("runs" / Segment) { workflowId =>
+              get {
+                // this is what it was like in code found in the project… it perhaps isn’t ideal but doesn’t seem to hurt, so leaving it like this for now.
+                completeCromwellResponse(runLog(workflowId, (w: WorkflowId) => GetSingleWorkflowMetadataAction(w, None, None, expandSubWorkflows = false), serviceRegistryActor))
+              }
+            },
+            path("runs" / Segment / "status") { possibleWorkflowId =>
+              val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor).flatMap(w => serviceRegistryActor.ask(GetStatus(w)).mapTo[MetadataServiceResponse])
+              // WES can also return a 401 or a 403 but that requires user auth knowledge which Cromwell doesn't currently have
+              onComplete(response) {
+                case Success(SuccessfulMetadataJsonResponse(_, jsObject)) =>
+                  val wesState = WesState.fromCromwellStatusJson(jsObject)
+                  complete(WesRunStatus(possibleWorkflowId, wesState))
+                case Success(r: StatusLookupFailed) => r.reason.errorRequest(StatusCodes.InternalServerError)
+                case Success(m: MetadataServiceResponse) =>
+                  // This should never happen, but ....
+                  val error = new IllegalStateException("Unexpected response from Metadata service: " + m)
+                  error.errorRequest(StatusCodes.InternalServerError)
+                case Failure(_: UnrecognizedWorkflowException) => complete(NotFoundError)
+                case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
+              }
+            },
+            path("runs" / Segment / "cancel") { possibleWorkflowId =>
+              post {
+                CromwellApiService.abortWorkflow(possibleWorkflowId,
+                  workflowStoreActor,
+                  workflowManagerActor,
+                  successHandler = WesAbortSuccessHandler,
+                  errorHandler = WesAbortErrorHandler)
+              }
             }
           )
         }
       )
     }
+
+  def toWesResponse(workflowId: WorkflowId, workflowState: WorkflowState):  WesRunStatus = {
+    WesRunStatus(workflowId.toString, WesState.fromCromwellStatus(workflowState))
+  }
+
+  def toWesResponseId(workflowId: WorkflowId): WesRunId ={
+    WesRunId(workflowId.toString)
+  }
+
+  def wesSubmitRequest(formData: Multipart.FormData, isSingleSubmission: Boolean): Route = {
+    def getWorkflowState(workflowOnHold: Boolean): WorkflowState = {
+      if (workflowOnHold)
+        WorkflowOnHold
+      else WorkflowSubmitted
+    }
+
+    def sendToWorkflowStore(command: WorkflowStoreActor.WorkflowStoreActorSubmitCommand, warnings: Seq[String], workflowState: WorkflowState): Route = {
+      // NOTE: Do not blindly copy the akka-http -to- ask-actor pattern below without knowing the pros and cons.
+      onComplete(workflowStoreActor.ask(command).mapTo[WorkflowStoreSubmitActor.WorkflowStoreSubmitActorResponse]) {
+        case Success(w) =>
+          w match {
+            case WorkflowStoreSubmitActor.WorkflowSubmittedToStore(workflowId, _) =>
+              completeResponse(StatusCodes.Created, toWesResponseId(workflowId), warnings)
+            case WorkflowStoreSubmitActor.WorkflowsBatchSubmittedToStore(workflowIds, _) =>
+              completeResponse(StatusCodes.Created, workflowIds.toList.map(toWesResponse(_, workflowState)), warnings)
+            case WorkflowStoreSubmitActor.WorkflowSubmitFailed(throwable) =>
+              respondWithWesError(throwable.getLocalizedMessage, StatusCodes.BadRequest)
+          }
+        case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => respondWithWesError("Cromwell service is shutting down", StatusCodes.InternalServerError)
+        case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
+        case Failure(e) => e.failRequest(StatusCodes.InternalServerError, warnings)
+      }
+    }
+
+    onComplete(materializeFormData(formData)) {
+      case Success(data) =>
+        PartialWorkflowSources.fromSubmitRoute(data, allowNoInputs = isSingleSubmission) match {
+          case Success(workflowSourceFiles) if isSingleSubmission && workflowSourceFiles.size == 1 =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            sendToWorkflowStore(WorkflowStoreActor.SubmitWorkflow(workflowSourceFiles.head), warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+          // Catches the case where someone has gone through the single submission endpoint w/ more than one workflow
+          case Success(workflowSourceFiles) if isSingleSubmission =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            val e = new IllegalArgumentException("To submit more than one workflow at a time, use the batch endpoint.")
+            e.failRequest(StatusCodes.BadRequest, warnings)
+          case Success(workflowSourceFiles) =>
+            val warnings = workflowSourceFiles.flatMap(_.warnings)
+            sendToWorkflowStore(
+              WorkflowStoreActor.BatchSubmitWorkflows(NonEmptyList.fromListUnsafe(workflowSourceFiles.toList)),
+              warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+          case Failure(t) => t.failRequest(StatusCodes.BadRequest)
+        }
+      case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
+      case Failure(e) => respondWithWesError(e.getLocalizedMessage, StatusCodes.InternalServerError)
+    }
+  }
 }
 
+
+
 object WesRouteSupport {
+  import WesResponseJsonSupport._
+
+  implicit lazy val duration: FiniteDuration = ConfigFactory.load().as[FiniteDuration]("akka.http.server.request-timeout")
+  implicit lazy val timeout: Timeout = duration
+  import scala.concurrent.ExecutionContext.Implicits.global
+
   val NotFoundError = WesErrorResponse("The requested workflow run wasn't found", StatusCodes.NotFound.intValue)
 
   def WesAbortSuccessHandler: PartialFunction[SuccessfulAbortResponse, Route] = {
@@ -104,4 +198,38 @@ object WesRouteSupport {
   private def respondWithWesError(errorMsg: String, status: StatusCode): Route = {
     complete((status, WesErrorResponse(errorMsg, status.intValue)))
   }
-}
+
+  def extractSubmission(): Directive1[WesSubmission] = {
+    formFields((
+      "workflow_params".?,
+      "workflow_type".?,
+      "workflow_type_version".?,
+      "tags".?,
+      "workflow_engine_parameters".?,
+      "workflow_url".?,
+      "workflow_attachment".as[String].*
+    )).as(WesSubmission)
+  }
+
+  def completeCromwellResponse(future: => Future[WesResponse]): Route = {
+    onComplete(future) {
+      case Success(response: WesResponse) => complete(response)
+      case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
+    }
+  }
+
+  def listRuns(pageSize: Option[Int], pageToken: Option[String], serviceRegistryActor: ActorRef): Future[WesResponse] = {
+    // FIXME: to handle - page_size, page_token
+    // FIXME: How to handle next_page_token in response?
+    metadataQueryRequest(Seq.empty[(String, String)], serviceRegistryActor).map(RunListResponse.fromMetadataQueryResponse)
+  }
+
+  def runLog(workflowId: String, request: WorkflowId => BuildMetadataJsonAction, serviceRegistryActor: ActorRef): Future[WesResponse] = {
+    val metadataJsonResponse = metadataBuilderActorRequest(workflowId, request, serviceRegistryActor)
+
+    metadataJsonResponse.map {
+      case SuccessfulMetadataJsonResponse(_, responseJson) => WesRunLog.fromJson(responseJson.toString())
+      case FailedMetadataJsonResponse(_, reason) => WesErrorResponse(reason.getMessage, StatusCodes.InternalServerError.intValue)
+    }
+  }
+}
\ No newline at end of file
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
index 344498e51ab..c882ebf4f8b 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
@@ -1,6 +1,5 @@
 package cromwell.webservice.routes.wes
 
-import cromwell.webservice.routes.wes.WesState.WesState
 import spray.json.JsObject
 
 
@@ -20,15 +19,3 @@ final case class WesRunRequest(workflow_params: Option[JsObject],
                                workflow_engine_parameters: Option[JsObject],
                                workflow_url: Option[String]
                               )
-
-final case class WesRunLog(run_id: String,
-                           request: WesRunRequest,
-                           state: WesState,
-                           run_log: Option[WesLog],
-                           task_logs: Option[List[WesLog]],
-                           outputs: Option[JsObject]
-                          )
-
-object WesRunLog {
-  def fromJson(json: String): WesRunLog = CromwellMetadata.fromJson(json).wesRunLog
-}
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala
deleted file mode 100644
index ce4d60fe78e..00000000000
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunRoutes.scala
+++ /dev/null
@@ -1,74 +0,0 @@
-package cromwell.webservice.routes.wes
-
-import akka.actor.ActorRef
-import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
-import akka.http.scaladsl.model.StatusCodes
-import akka.http.scaladsl.server.Directives._
-import akka.http.scaladsl.server.Route
-import akka.http.scaladsl.server.directives.RouteDirectives.complete
-import akka.util.Timeout
-import com.typesafe.config.ConfigFactory
-import cromwell.core.WorkflowId
-import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, GetSingleWorkflowMetadataAction}
-import cromwell.services.{FailedMetadataJsonResponse, SuccessfulMetadataJsonResponse}
-import cromwell.webservice.routes.MetadataRouteSupport.{metadataBuilderActorRequest, metadataQueryRequest}
-import cromwell.webservice.routes.wes.WesResponseJsonSupport.{WesResponseErrorFormat, WesResponseFormat}
-import cromwell.webservice.routes.wes.WesRunRoutes.{completeCromwellResponse, runLog}
-import net.ceedubs.ficus.Ficus._
-
-import scala.concurrent.ExecutionContext.Implicits.global
-import scala.concurrent.Future
-import scala.concurrent.duration.FiniteDuration
-import scala.util.{Failure, Success}
-
-trait WesRunRoutes {
-
-  val serviceRegistryActor: ActorRef
-
-  lazy val runRoutes: Route =
-    pathPrefix("ga4gh" / "wes" / "v1") {
-      concat(
-        pathPrefix("runs") {
-          get {
-            parameters(("page_size".as[Int].?, "page_token".?)) { (pageSize, pageToken) =>
-              WesRunRoutes.completeCromwellResponse(WesRunRoutes.listRuns(pageSize, pageToken, serviceRegistryActor))
-            }
-          }
-          path(Segment) { workflowId =>
-            get {
-              // this is what it was like in code found in the project… it perhaps isn’t ideal but doesn’t seem to hurt, so leaving it like this for now.
-              completeCromwellResponse(runLog(workflowId, (w: WorkflowId) => GetSingleWorkflowMetadataAction(w, None, None, expandSubWorkflows = false), serviceRegistryActor))
-            }
-          }
-        }
-      )
-    }
-}
-
-object WesRunRoutes {
-
-  implicit lazy val duration: FiniteDuration = ConfigFactory.load().as[FiniteDuration]("akka.http.server.request-timeout")
-  implicit lazy val timeout: Timeout = duration
-
-  def completeCromwellResponse(future: => Future[WesResponse]): Route = {
-    onComplete(future) {
-      case Success(response: WesResponse) => complete(response)
-      case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
-    }
-  }
-
-  def listRuns(pageSize: Option[Int], pageToken: Option[String], serviceRegistryActor: ActorRef): Future[WesResponse] = {
-    // FIXME: to handle - page_size, page_token
-    // FIXME: How to handle next_page_token in response?
-    metadataQueryRequest(Seq.empty[(String, String)], serviceRegistryActor).map(RunListResponse.fromMetadataQueryResponse)
-  }
-
-  def runLog(workflowId: String, request: WorkflowId => BuildMetadataJsonAction, serviceRegistryActor: ActorRef): Future[WesResponse] = {
-    val metadataJsonResponse = metadataBuilderActorRequest(workflowId, request, serviceRegistryActor)
-
-    metadataJsonResponse.map {
-      case SuccessfulMetadataJsonResponse(_, responseJson) => WesResponseWorkflowMetadata(WesRunLog.fromJson(responseJson.toString()))
-      case FailedMetadataJsonResponse(_, reason) => WesErrorResponse(reason.getMessage, StatusCodes.InternalServerError.intValue)
-    }
-  }
-}
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala
new file mode 100644
index 00000000000..1db2cd801b8
--- /dev/null
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala
@@ -0,0 +1,44 @@
+package cromwell.webservice.routes.wes
+
+import akka.http.scaladsl.model.{HttpEntity, MediaTypes, Multipart}
+import cromwell.webservice.PartialWorkflowSources._
+
+final case class WesSubmission(workflowParams: Option[String],
+                               workflowType: Option[String],
+                               workflowTypeVersion: Option[String],
+                               tags: Option[String],
+                               workflowEngineParameters: Option[String],
+                               workflowUrl: Option[String],
+                               workflowAttachment: Iterable[String]
+                              ) {
+  val entity: Multipart.FormData = {
+    /*
+      FIXME:
+
+      Super oversimplification going on here as Cromwell's API is expected to normalize w/ WES a bit over the course
+      of the quarter and it's not worth doing it here and throwing it out later (there's close to a 0% chance this will
+      be used between now and then)
+
+      At the moment, just taking the head of workflowAttachment (if it exists) and dropping that into the workflow source,
+      and we're ignoring the possible existence of a zip bundle. Eventually the way this will work is that there'll be
+      an Iterable of workflow files and workflowUrl will point to which one is the source and the rest goes into the bundle.
+
+      NB: I think we've already lost too much information for the above to happen as there's an optional use of
+      Content-Disposition headers on each of these files which can be used to describe directory structure and such
+      for relative import resolution
+     */
+    val sourcePart = workflowAttachment.headOption map { a => Multipart.FormData.BodyPart(WorkflowSourceKey, HttpEntity(MediaTypes.`application/json`, a)) }
+
+    val urlPart = workflowUrl map { u => Multipart.FormData.BodyPart(WorkflowUrlKey, HttpEntity(MediaTypes.`application/json`, u)) }
+
+    val typePart = workflowType map { w => Multipart.FormData.BodyPart(WorkflowTypeKey, HttpEntity(MediaTypes.`application/json`, w)) }
+    val typeVersionPart = workflowTypeVersion map { v => Multipart.FormData.BodyPart(WorkflowTypeVersionKey, HttpEntity(MediaTypes.`application/json`, v)) }
+    val inputsPart = workflowParams map { p => Multipart.FormData.BodyPart(WorkflowInputsKey, HttpEntity(MediaTypes.`application/json`, p)) }
+    val optionsPart = workflowEngineParameters map { o => Multipart.FormData.BodyPart(WorkflowOptionsKey, HttpEntity(MediaTypes.`application/json`, o)) }
+    val labelsPart = tags map { t => Multipart.FormData.BodyPart(labelsKey, HttpEntity(MediaTypes.`application/json`, t)) }
+
+    val parts = List(sourcePart, urlPart, typePart, typeVersionPart, inputsPart, optionsPart, labelsPart).flatten
+
+    Multipart.FormData(parts: _*)
+  }
+}
diff --git a/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala b/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
index 4b3461ae7d3..b01d52eece0 100644
--- a/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
@@ -20,13 +20,14 @@ import org.mockito.Mockito.{times, verify, when}
 import org.scalatest.flatspec.AsyncFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import common.mock.MockSugar
+import cromwell.filesystems.blob.BlobPath
 
 import java.nio.file.NoSuchFileException
 import java.util.UUID
 import scala.concurrent.ExecutionContext
 import scala.concurrent.duration._
 import scala.language.postfixOps
-import scala.util.Failure
+import scala.util.{Failure, Success, Try}
 import scala.util.control.NoStackTrace
 
 class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with MockSugar {
@@ -127,6 +128,23 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     }
   }
 
+  it should "get hash from a BlobPath when stored hash exists" in {
+    val testPath = mock[BlobPath]
+    val hashString = "2d01d5d9c24034d54fe4fba0ede5182d" // echo "hello there" | md5sum
+    testPath.md5HexString returns Try(Option(hashString))
+
+    val context = DefaultCommandContext(hashCommand(testPath).get, replyTo)
+    val testSource = Source.single(context)
+
+    val stream = testSource.via(flow).toMat(readSink)(Keep.right)
+
+    stream.run() map {
+      case (success: IoSuccess[_], _) => assert(success.result.asInstanceOf[String] == hashString)
+      case (ack, _) =>
+        fail(s"read returned an unexpected message:\n$ack\n\n")
+    }
+  }
+
   it should "fail if DrsPath hash doesn't match checksum" in {
     val testPath = mock[DrsPath]
     when(testPath.limitFileContent(any[Option[Int]], any[Boolean])(any[ExecutionContext])).thenReturn("hello".getBytes)
@@ -171,6 +189,25 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     }
   }
 
+  it should "succeed if a BlobPath is missing a stored hash" in {
+    val testPath = mock[BlobPath]
+    when(testPath.limitFileContent(any[Option[Int]], any[Boolean])(any[ExecutionContext]))
+      .thenReturn("hello there".getBytes)
+    when(testPath.md5HexString)
+      .thenReturn(Success(None))
+
+    val context = DefaultCommandContext(contentAsStringCommand(testPath, Option(100), failOnOverflow = true).get, replyTo)
+    val testSource = Source.single(context)
+
+    val stream = testSource.via(flow).toMat(readSink)(Keep.right)
+
+    stream.run() map {
+      case (success: IoSuccess[_], _) => assert(success.result.asInstanceOf[String] == "hello there")
+      case (ack, _) =>
+        fail(s"read returned an unexpected message:\n$ack\n\n")
+    }
+  }
+
   it should "copy Nio paths" in {
     val testPath = DefaultPathBuilder.createTempFile()
     val testCopyPath = testPath.sibling(UUID.randomUUID().toString)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
index 40b628a700d..095721569e7 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
@@ -11,7 +11,7 @@ import scala.util.{Failure, Success, Try}
 class ValidatingCachingConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
 
     it should "run config tests" in {
-      val cases = Table(
+      val cases = Table[String, Any](
         ("config"                 , "exceptionMessage"                                                              ),
         ("enabled = not-a-boolean", "String: 1: enabled has type STRING rather than BOOLEAN"                        ),
         ("enabled = true"         , true                                                                            ),
diff --git a/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
index ed4e588cfd1..24cce8ae932 100644
--- a/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
@@ -11,7 +11,7 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 import org.yaml.snakeyaml.constructor.Constructor
 import org.yaml.snakeyaml.error.YAMLException
 import org.yaml.snakeyaml.nodes.MappingNode
-import org.yaml.snakeyaml.{Yaml => SnakeYaml}
+import org.yaml.snakeyaml.{LoaderOptions, Yaml => SnakeYaml}
 
 import scala.jdk.CollectionConverters._
 
@@ -28,7 +28,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
         status should be(StatusCodes.OK)
 
         val body = responseAs[String]
-        val yaml = new SnakeYaml(new UniqueKeyConstructor()).loadAs(body, classOf[java.util.Map[String, AnyRef]])
+        val yaml = new SnakeYaml(new UniqueKeyConstructor(new LoaderOptions)).loadAs(body, classOf[java.util.Map[String, AnyRef]])
 
         yaml.get("swagger") should be("2.0")
       }
@@ -100,7 +100,7 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
   * Adapted from:
   * https://bitbucket.org/asomov/snakeyaml/src/e9cd9f5e8d76c61eb983e29b3dc039c1fac9c393/src/test/java/org/yaml/snakeyaml/issues/issue139/UniqueKeyTest.java?fileviewer=file-view-default#UniqueKeyTest.java-43:62
   */
-class UniqueKeyConstructor extends Constructor {
+class UniqueKeyConstructor(val loaderOptions: LoaderOptions) extends Constructor(loaderOptions) {
 
   import java.util.{Map => JMap}
 
diff --git a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
index 2a3b11a41c5..c40c84397f7 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
@@ -1,7 +1,5 @@
 package cromwell.webservice.routes
 
-import java.time.OffsetDateTime
-
 import akka.actor.{Actor, ActorLogging, ActorSystem, Props}
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
 import akka.http.scaladsl.model.ContentTypes._
@@ -17,13 +15,13 @@ import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor._
 import cromwell.engine.workflow.workflowstore.WorkflowStoreEngineActor.{WorkflowOnHoldToSubmittedFailure, WorkflowOnHoldToSubmittedSuccess}
 import cromwell.engine.workflow.workflowstore.WorkflowStoreSubmitActor.{WorkflowSubmittedToStore, WorkflowsBatchSubmittedToStore}
+import cromwell.services._
 import cromwell.services.healthmonitor.ProtoHealthMonitorServiceActor.{GetCurrentStatus, StatusCheckResponse, SubsystemStatus}
 import cromwell.services.instrumentation.InstrumentationService.InstrumentationServiceMessage
 import cromwell.services.metadata.MetadataArchiveStatus._
 import cromwell.services.metadata.MetadataService._
 import cromwell.services.metadata._
 import cromwell.services.metadata.impl.builder.MetadataBuilderActor
-import cromwell.services._
 import cromwell.services.womtool.WomtoolServiceMessages.{DescribeFailure, DescribeRequest, DescribeSuccess}
 import cromwell.services.womtool.models.WorkflowDescription
 import cromwell.util.SampleWdl.HelloWorld
@@ -34,6 +32,7 @@ import org.scalatest.flatspec.AsyncFlatSpec
 import org.scalatest.matchers.should.Matchers
 import spray.json._
 
+import java.time.OffsetDateTime
 import scala.concurrent.duration._
 
 class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with Matchers {
@@ -529,6 +528,7 @@ object CromwellApiServiceSpec {
   val WorkflowIdExistingOnlyInSummaryTable = WorkflowId.fromString("f0000000-0000-0000-0000-000000000011")
   val ArchivedWorkflowId = WorkflowId.fromString("c4c6339c-2145-47fb-acc5-b5cb8d2809f5")
   val ArchivedAndDeletedWorkflowId = WorkflowId.fromString("abc1234d-2145-47fb-acc5-b5cb8d2809f5")
+  val wesWorkflowId = WorkflowId.randomId()
   val SummarizedWorkflowIds = Set(
     SummarizedWorkflowId,
     WorkflowIdExistingOnlyInSummaryTable,
@@ -545,7 +545,8 @@ object CromwellApiServiceSpec {
     FailedWorkflowId,
     SummarizedWorkflowId,
     ArchivedWorkflowId,
-    ArchivedAndDeletedWorkflowId
+    ArchivedAndDeletedWorkflowId,
+    wesWorkflowId
   )
 
   class MockApiService()(implicit val system: ActorSystem) extends CromwellApiService {
@@ -564,13 +565,21 @@ object CromwellApiServiceSpec {
       List(
         MetadataEvent(MetadataKey(workflowId, None, "testKey1a"), MetadataValue("myValue1a", MetadataString)),
         MetadataEvent(MetadataKey(workflowId, None, "testKey1b"), MetadataValue("myValue1b", MetadataString)),
-        MetadataEvent(MetadataKey(workflowId, None, "testKey2a"), MetadataValue("myValue2a", MetadataString))
+        MetadataEvent(MetadataKey(workflowId, None, "testKey2a"), MetadataValue("myValue2a", MetadataString)),
+      )
+    }
+    private def wesFullMetadataResponse(workflowId: WorkflowId) = {
+      List(
+        MetadataEvent(MetadataKey(workflowId, None, "status"), MetadataValue("Running", MetadataString)),
+        MetadataEvent(MetadataKey(workflowId, None, "submittedFiles:workflow"), MetadataValue("myValue2a", MetadataString)),
+
       )
     }
 
     def responseMetadataValues(workflowId: WorkflowId, withKeys: List[String], withoutKeys: List[String]): JsObject = {
       def keyFilter(keys: List[String])(m: MetadataEvent) = keys.exists(k => m.key.key.startsWith(k))
-      val events = fullMetadataResponse(workflowId)
+      val metadataEvents = if (workflowId == wesWorkflowId) wesFullMetadataResponse(workflowId) else fullMetadataResponse(workflowId)
+      val events = metadataEvents
         .filter(m => withKeys.isEmpty || keyFilter(withKeys)(m))
         .filter(m => withoutKeys.isEmpty || !keyFilter(withoutKeys)(m))
 
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
index b4d775f7389..e32316f3649 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
@@ -22,7 +22,7 @@ class ServiceInfoSpec extends AsyncFlatSpec with ScalatestRouteTest with Matcher
 
   behavior of "ServiceInfo"
 
-  val expectedResponse = WesStatusInfoResponse(Map("CWL" -> Set("v1.0"), "WDL" -> Set("draft-2", "1.0", "biscayne")),
+  val expectedResponse = WesStatusInfoResponse(Map("WDL" -> Set("draft-2", "1.0", "biscayne")),
     List("1.0"),
     Set("ftp", "s3", "drs", "gcs", "http"),
     Map("Cromwell" -> CromwellApiService.cromwellVersion),
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
index 0c0fe1c8054..00a361a3174 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
@@ -1,22 +1,27 @@
 package cromwell.webservice.routes.wes
 
 import akka.actor.Props
-import akka.http.scaladsl.model.StatusCodes
 import akka.http.scaladsl.model.HttpMethods.POST
-import akka.http.scaladsl.testkit.ScalatestRouteTest
+import akka.http.scaladsl.model._
+import akka.http.scaladsl.server.MethodRejection
+import akka.http.scaladsl.testkit.{RouteTestTimeout, ScalatestRouteTest}
+import cromwell.util.SampleWdl.HelloWorld
 import cromwell.webservice.routes.CromwellApiServiceSpec
-
-import scala.concurrent.duration._
 import cromwell.webservice.routes.CromwellApiServiceSpec.{MockServiceRegistryActor, MockWorkflowManagerActor, MockWorkflowStoreActor}
+import cromwell.webservice.routes.wes.WesResponseJsonSupport._
 import org.scalatest.flatspec.AsyncFlatSpec
 import org.scalatest.matchers.should.Matchers
-import WesResponseJsonSupport._
-import akka.http.scaladsl.server.MethodRejection
+import spray.json._
+
+import scala.concurrent.duration._
 
 class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Matchers with WesRouteSupport {
+
   val actorRefFactory = system
   override implicit val ec = system.dispatcher
-  override implicit val timeout = 5.seconds
+  override val timeout = routeTestTimeout.duration
+  implicit def routeTestTimeout = RouteTestTimeout(5.seconds)
+
 
   override val workflowStoreActor = actorRefFactory.actorOf(Props(new MockWorkflowStoreActor()))
   override val serviceRegistryActor = actorRefFactory.actorOf(Props(new MockServiceRegistryActor()))
@@ -149,4 +154,52 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
         rejection shouldEqual MethodRejection(POST)
       }
   }
-}
+
+  behavior of "WES API /runs POST endpoint"
+  it should "return 201 for a successful workflow submission" in {
+    val workflowSource = Multipart.FormData.BodyPart("workflow_url", HttpEntity(MediaTypes.`application/json`, "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"))
+    val workflowInputs = Multipart.FormData.BodyPart("workflow_params", HttpEntity(MediaTypes.`application/json`, HelloWorld.rawInputs.toJson.toString()))
+    val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
+    Post(s"/ga4gh/wes/$version/runs", formData) ~>
+      wesRoutes ~>
+      check {
+        assertResult(
+          s"""{
+             |  "run_id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}"
+             |}""".stripMargin) {
+          responseAs[String].parseJson.prettyPrint
+        }
+        assertResult(StatusCodes.Created) {
+          status
+        }
+        headers should be(Seq.empty)
+      }
+  }
+
+
+  behavior of "WES API /runs GET endpoint"
+  it should "return results for a good query" in {
+    Get(s"/ga4gh/wes/v1/runs") ~>
+      wesRoutes ~>
+      check {
+        status should be(StatusCodes.OK)
+        contentType should be(ContentTypes.`application/json`)
+        val results = responseAs[JsObject].fields("runs").convertTo[Seq[JsObject]]
+        results.head.fields("run_id") should be(JsString(CromwellApiServiceSpec.ExistingWorkflowId.toString))
+        results.head.fields("state") should be(JsString("COMPLETE"))
+      }
+  }
+
+  behavior of "WES API /runs/{run_id} endpoint"
+  it should "return valid metadata when supplied a run_id" in {
+    Get(s"/ga4gh/wes/v1/runs/${CromwellApiServiceSpec.wesWorkflowId}") ~>
+      wesRoutes ~>
+      check {
+        status should be(StatusCodes.OK)
+        val result = responseAs[JsObject]
+        result.fields.keys should contain allOf("request", "run_id", "state")
+        result.fields("state") should be(JsString("RUNNING"))
+        result.fields("run_id") should be(JsString(CromwellApiServiceSpec.wesWorkflowId.toString))
+      }
+  }
+}
\ No newline at end of file
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
new file mode 100644
index 00000000000..ae84e39adbe
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
@@ -0,0 +1,52 @@
+package cromwell.filesystems.blob
+
+import cats.implicits.catsSyntaxValidatedId
+import com.azure.core.credential.TokenRequestContext
+import com.azure.core.management.AzureEnvironment
+import com.azure.core.management.profile.AzureProfile
+import com.azure.identity.DefaultAzureCredentialBuilder
+import common.validation.ErrorOr.ErrorOr
+
+import scala.concurrent.duration._
+import scala.jdk.DurationConverters._
+
+import scala.util.{Failure, Success, Try}
+
+/**
+  * Strategy for obtaining an access token in an environment with available Azure identity.
+  * If you need to disambiguate among multiple active user-assigned managed identities, pass
+  * in the client id of the identity that should be used.
+  */
+case object AzureCredentials {
+
+  final val tokenAcquisitionTimeout = 5.seconds
+
+  val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
+  val tokenScope = "https://management.azure.com/.default"
+
+  private def tokenRequestContext: TokenRequestContext = {
+    val trc = new TokenRequestContext()
+    trc.addScopes(tokenScope)
+    trc
+  }
+
+  private def defaultCredentialBuilder: DefaultAzureCredentialBuilder =
+    new DefaultAzureCredentialBuilder()
+      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
+
+  def getAccessToken(identityClientId: Option[String]): ErrorOr[String] = {
+    val credentials = identityClientId.foldLeft(defaultCredentialBuilder) {
+      (builder, clientId) => builder.managedIdentityClientId(clientId)
+    }.build()
+
+    Try(
+      credentials
+        .getToken(tokenRequestContext)
+        .block(tokenAcquisitionTimeout.toJava)
+    ) match {
+      case Success(null) => "null token value attempting to obtain access token".invalidNel
+      case Success(token) => token.getToken.validNel
+      case Failure(error) => s"Failed to refresh access token: ${error.getMessage}".invalidNel
+    }
+  }
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
new file mode 100644
index 00000000000..f68bf7f5176
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
@@ -0,0 +1,75 @@
+package cromwell.filesystems.blob
+
+import cats.implicits.catsSyntaxValidatedId
+import cats.syntax.apply._
+import com.typesafe.config.Config
+import common.validation.Validation._
+import net.ceedubs.ficus.Ficus._
+
+import java.util.UUID
+
+// WSM config is needed for accessing WSM-managed blob containers created in Terra workspaces.
+// If the identity executing Cromwell has native access to the blob container, this can be ignored.
+final case class WorkspaceManagerConfig(url: WorkspaceManagerURL,
+                                        workspaceId: WorkspaceId,
+                                        containerResourceId: ContainerResourceId,
+                                        overrideWsmAuthToken: Option[String]) // dev-only
+
+final case class BlobFileSystemConfig(endpointURL: EndpointURL,
+                                      blobContainerName: BlobContainerName,
+                                      subscriptionId: Option[SubscriptionId],
+                                      expiryBufferMinutes: Long,
+                                      workspaceManagerConfig: Option[WorkspaceManagerConfig])
+
+object BlobFileSystemConfig {
+
+  final val defaultExpiryBufferMinutes = 10L
+
+  def apply(config: Config): BlobFileSystemConfig = {
+    val endpointURL = parseString(config, "endpoint").map(EndpointURL)
+    val blobContainer = parseString(config, "container").map(BlobContainerName)
+    val subscriptionId = parseUUIDOpt(config, "subscription").map(_.map(SubscriptionId))
+    val expiryBufferMinutes =
+      parseLongOpt(config, "expiry-buffer-minutes")
+        .map(_.getOrElse(defaultExpiryBufferMinutes))
+
+    val wsmConfig =
+      if (config.hasPath("workspace-manager")) {
+        val wsmConf = config.getConfig("workspace-manager")
+        val wsmURL = parseString(wsmConf, "url").map(WorkspaceManagerURL)
+        val workspaceId = parseUUID(wsmConf, "workspace-id").map(WorkspaceId)
+        val containerResourceId = parseUUID(wsmConf, "container-resource-id").map(ContainerResourceId)
+        val overrideWsmAuthToken = parseStringOpt(wsmConf, "b2cToken")
+
+        (wsmURL, workspaceId, containerResourceId, overrideWsmAuthToken)
+          .mapN(WorkspaceManagerConfig)
+          .map(Option(_))
+      }
+      else None.validNel
+
+    (endpointURL, blobContainer, subscriptionId, expiryBufferMinutes, wsmConfig)
+      .mapN(BlobFileSystemConfig.apply)
+      .unsafe("Couldn't parse blob filesystem config")
+  }
+
+  private def parseString(config: Config, path: String) =
+    validate[String] { config.as[String](path) }
+
+  private def parseStringOpt(config: Config, path: String) =
+    validate[Option[String]] { config.as[Option[String]](path) }
+
+  private def parseUUID(config: Config, path: String) =
+    validate[UUID] { UUID.fromString(config.as[String](path)) }
+
+  private def parseUUIDOpt(config: Config, path: String) =
+    validate[Option[UUID]] { config.as[Option[String]](path).map(UUID.fromString) }
+
+  private def parseLongOpt(config: Config, path: String) =
+    validate[Option[Long]] { config.as[Option[Long]](path) }
+}
+
+// Our filesystem setup magic can't use BlobFileSystemConfig.apply directly, so we need this
+// wrapper class.
+class BlobFileSystemConfigWrapper(val config: BlobFileSystemConfig) {
+  def this(config: Config) = this(BlobFileSystemConfig(config))
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
new file mode 100644
index 00000000000..7b198f09f6f
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -0,0 +1,267 @@
+package cromwell.filesystems.blob
+
+import com.azure.core.credential.AzureSasCredential
+import com.azure.core.management.AzureEnvironment
+import com.azure.core.management.profile.AzureProfile
+import com.azure.identity.DefaultAzureCredentialBuilder
+import com.azure.resourcemanager.AzureResourceManager
+import com.azure.resourcemanager.storage.models.StorageAccountKey
+import com.azure.storage.blob.nio.AzureFileSystem
+import com.azure.storage.blob.sas.{BlobContainerSasPermission, BlobServiceSasSignatureValues}
+import com.azure.storage.blob.{BlobContainerClient, BlobContainerClientBuilder}
+import com.azure.storage.common.StorageSharedKeyCredential
+import com.typesafe.config.Config
+import com.typesafe.scalalogging.LazyLogging
+import common.validation.Validation._
+
+import java.net.URI
+import java.nio.file.{FileSystem, FileSystemNotFoundException, FileSystems}
+import java.time.temporal.ChronoUnit
+import java.time.{Duration, Instant, OffsetDateTime}
+import scala.jdk.CollectionConverters._
+import scala.util.{Failure, Success, Try}
+
+// We encapsulate this functionality here so that we can easily mock it out, to allow for testing without
+// actually connecting to Blob storage.
+case class FileSystemAPI() {
+  def getFileSystem(uri: URI): Try[FileSystem] = Try(FileSystems.getFileSystem(uri))
+  def newFileSystem(uri: URI, config: Map[String, Object]): FileSystem = FileSystems.newFileSystem(uri, config.asJava)
+  def closeFileSystem(uri: URI): Option[Unit] = getFileSystem(uri).toOption.map(_.close)
+}
+/**
+  * The BlobFileSystemManager is an object that is responsible for managing the open filesystem,
+  * and refreshing the SAS token that is used to access the blob container containing that filesystem.
+  *
+  * See BlobSasTokenGenerator for more information on how a SAS token is generated
+  */
+object BlobFileSystemManager {
+  def parseTokenExpiry(token: AzureSasCredential): Option[Instant] = for {
+    expiryString <- token.getSignature.split("&").find(_.startsWith("se")).map(_.replaceFirst("se=","")).map(_.replace("%3A", ":"))
+    instant = Instant.parse(expiryString)
+  } yield instant
+
+  def buildConfigMap(credential: AzureSasCredential, container: BlobContainerName): Map[String, Object] = {
+    Map((AzureFileSystem.AZURE_STORAGE_SAS_TOKEN_CREDENTIAL, credential),
+      (AzureFileSystem.AZURE_STORAGE_FILE_STORES, container.value),
+      (AzureFileSystem.AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK, java.lang.Boolean.TRUE))
+  }
+  def hasTokenExpired(tokenExpiry: Instant, buffer: Duration): Boolean = Instant.now.plus(buffer).isAfter(tokenExpiry)
+  def uri(endpoint: EndpointURL) = new URI("azb://?endpoint=" + endpoint)
+}
+
+class BlobFileSystemManager(val container: BlobContainerName,
+                            val endpoint: EndpointURL,
+                            val expiryBufferMinutes: Long,
+                            val blobTokenGenerator: BlobSasTokenGenerator,
+                            val fileSystemAPI: FileSystemAPI = FileSystemAPI(),
+                            private val initialExpiration: Option[Instant] = None) extends LazyLogging {
+
+  def this(config: BlobFileSystemConfig) = {
+    this(
+      config.blobContainerName,
+      config.endpointURL,
+      config.expiryBufferMinutes,
+      BlobSasTokenGenerator.createBlobTokenGeneratorFromConfig(config)
+    )
+  }
+
+  def this(rawConfig: Config) = this(BlobFileSystemConfig(rawConfig))
+
+  val buffer: Duration = Duration.of(expiryBufferMinutes, ChronoUnit.MINUTES)
+  private var expiry: Option[Instant] = initialExpiration
+
+  def getExpiry: Option[Instant] = expiry
+  def uri: URI = BlobFileSystemManager.uri(endpoint)
+  def isTokenExpired: Boolean = expiry.exists(BlobFileSystemManager.hasTokenExpired(_, buffer))
+  def shouldReopenFilesystem: Boolean = isTokenExpired || expiry.isEmpty
+  def retrieveFilesystem(): Try[FileSystem] = {
+    synchronized {
+      shouldReopenFilesystem match {
+        case false => fileSystemAPI.getFileSystem(uri).recoverWith {
+          // If no filesystem already exists, this will create a new connection, with the provided configs
+          case _: FileSystemNotFoundException =>
+            logger.info(s"Creating new blob filesystem for URI $uri")
+            blobTokenGenerator.generateBlobSasToken.flatMap(generateFilesystem(uri, container, _))
+        }
+        // If the token has expired, OR there is no token record, try to close the FS and regenerate
+        case true =>
+          logger.info(s"Closing & regenerating token for existing blob filesystem at URI $uri")
+          fileSystemAPI.closeFileSystem(uri)
+          blobTokenGenerator.generateBlobSasToken.flatMap(generateFilesystem(uri, container, _))
+      }
+    }
+  }
+
+  private def generateFilesystem(uri: URI, container: BlobContainerName, token: AzureSasCredential): Try[FileSystem] = {
+    expiry = BlobFileSystemManager.parseTokenExpiry(token)
+    if (expiry.isEmpty) return Failure(new Exception("Could not reopen filesystem, no expiration found"))
+    Try(fileSystemAPI.newFileSystem(uri, BlobFileSystemManager.buildConfigMap(token, container)))
+  }
+
+}
+
+sealed trait BlobSasTokenGenerator { def generateBlobSasToken: Try[AzureSasCredential] }
+object BlobSasTokenGenerator {
+
+  /**
+    * Creates the correct BlobSasTokenGenerator based on config inputs. This generator is responsible for producing
+    * a valid SAS token for use in accessing a Azure blob storage container.
+    * Two types of generators can be produced here:
+    * > Workspace Manager (WSM) mediated SAS token generator, used to create SAS tokens that allow access for
+    * blob containers mediated by the WSM, and is enabled when a WSM config is provided. This is what is intended
+    * for use inside Terra
+    *    OR
+    * > Native SAS token generator, which obtains a valid SAS token from your local environment to reach blob containers
+    * your local azure identity has access to and is the default if a WSM config is not found. This is intended for
+    * use outside of Terra
+    *
+    * Both of these generators require an authentication token to authorize the generation of the SAS token.
+    * See BlobSasTokenGenerator for more information on how these generators work.
+    *
+    * @param config A BlobFileSystemConfig object
+    * @return An appropriate BlobSasTokenGenerator
+    */
+  def createBlobTokenGeneratorFromConfig(config: BlobFileSystemConfig): BlobSasTokenGenerator =
+    config.workspaceManagerConfig.map { wsmConfig =>
+      val wsmClient: WorkspaceManagerApiClientProvider = new HttpWorkspaceManagerClientProvider(wsmConfig.url)
+
+      // WSM-mediated mediated SAS token generator
+      // parameterizing client instead of URL to make injecting mock client possible
+      BlobSasTokenGenerator.createBlobTokenGenerator(
+        config.blobContainerName,
+        config.endpointURL,
+        wsmConfig.workspaceId,
+        wsmConfig.containerResourceId,
+        wsmClient,
+        wsmConfig.overrideWsmAuthToken
+      )
+    }.getOrElse(
+      // Native SAS token generator
+      BlobSasTokenGenerator.createBlobTokenGenerator(config.blobContainerName, config.endpointURL, config.subscriptionId)
+    )
+
+  /**
+    * Native SAS token generator, uses the DefaultAzureCredentialBuilder in the local environment
+    * to produce a SAS token.
+    *
+    * @param container The BlobContainerName of the blob container to be accessed by the generated SAS token
+    * @param endpoint The EndpointURL containing the storage account of the blob container to be accessed by
+    * this SAS token
+    * @param subscription Optional subscription parameter to use for local authorization.
+    * If one is not provided the default subscription is used
+    * @return A NativeBlobTokenGenerator, able to produce a valid SAS token for accessing the provided blob
+    * container and endpoint locally
+    */
+  def createBlobTokenGenerator(container: BlobContainerName,
+                               endpoint: EndpointURL,
+                               subscription: Option[SubscriptionId]): BlobSasTokenGenerator = {
+    NativeBlobSasTokenGenerator(container, endpoint, subscription)
+  }
+
+  /**
+    * WSM-mediated SAS token generator, uses the DefaultAzureCredentialBuilder in the cloud environment
+    * to request a SAS token from the WSM to access the given blob container. If an overrideWsmAuthToken
+    * is provided this is used instead.
+    *
+    * @param container The BlobContainerName of the blob container to be accessed by the generated SAS token
+    * @param endpoint The EndpointURL containing the storage account of the blob container to be accessed by
+    * this SAS token
+    * @param workspaceId The WorkspaceId of the account to authenticate against
+    * @param containerResourceId The ContainterResourceId of the blob container as WSM knows it
+    * @param workspaceManagerClient The client for making requests against WSM
+    * @param overrideWsmAuthToken An optional WsmAuthToken used for authenticating against the WSM for a valid
+    * SAS token to access the given container and endpoint. This is a dev only option that is only intended
+    * for local testing of the WSM interface
+    * @return A WSMBlobTokenGenerator, able to produce a valid SAS token for accessing the provided blob
+    * container and endpoint that is managed by WSM
+    */
+  def createBlobTokenGenerator(container: BlobContainerName,
+                               endpoint: EndpointURL,
+                               workspaceId: WorkspaceId,
+                               containerResourceId: ContainerResourceId,
+                               workspaceManagerClient: WorkspaceManagerApiClientProvider,
+                               overrideWsmAuthToken: Option[String]): BlobSasTokenGenerator = {
+    WSMBlobSasTokenGenerator(container, endpoint, workspaceId, containerResourceId, workspaceManagerClient, overrideWsmAuthToken)
+  }
+
+}
+
+case class WSMBlobSasTokenGenerator(container: BlobContainerName,
+                                    endpoint: EndpointURL,
+                                    workspaceId: WorkspaceId,
+                                    containerResourceId: ContainerResourceId,
+                                    wsmClientProvider: WorkspaceManagerApiClientProvider,
+                                    overrideWsmAuthToken: Option[String]) extends BlobSasTokenGenerator {
+
+  /**
+    * Generate a BlobSasToken by using the available authorization information
+    * If an overrideWsmAuthToken is provided, use this in the wsmClient request
+    * Else try to use the environment azure identity to request the SAS token
+    *
+    * @return an AzureSasCredential for accessing a blob container
+    */
+  def generateBlobSasToken: Try[AzureSasCredential] = {
+    val wsmAuthToken: Try[String] = overrideWsmAuthToken match {
+      case Some(t) => Success(t)
+      case None => AzureCredentials.getAccessToken(None).toTry
+    }
+
+    for {
+      wsmAuth <- wsmAuthToken
+      wsmClient = wsmClientProvider.getControlledAzureResourceApi(wsmAuth)
+      sasToken <- Try(  // Java library throws
+        wsmClient.createAzureStorageContainerSasToken(
+          workspaceId.value,
+          containerResourceId.value,
+          null,
+          null,
+          null,
+          null
+        ).getToken)
+    } yield new AzureSasCredential(sasToken)
+  }
+}
+
+case class NativeBlobSasTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId] = None) extends BlobSasTokenGenerator {
+  private val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
+  private def azureCredentialBuilder = new DefaultAzureCredentialBuilder()
+      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
+      .build
+  private def authenticateWithSubscription(sub: SubscriptionId) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub.toString)
+  private def authenticateWithDefaultSubscription = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withDefaultSubscription()
+  private def azure = subscription.map(authenticateWithSubscription(_)).getOrElse(authenticateWithDefaultSubscription)
+
+  private def findAzureStorageAccount(name: StorageAccountName) = azure.storageAccounts.list.asScala.find(_.name.equals(name.value))
+      .map(Success(_)).getOrElse(Failure(new Exception("Azure Storage Account not found")))
+  private def buildBlobContainerClient(credential: StorageSharedKeyCredential, endpoint: EndpointURL, container: BlobContainerName): BlobContainerClient = {
+    new BlobContainerClientBuilder()
+        .credential(credential)
+        .endpoint(endpoint.value)
+        .containerName(container.value)
+        .buildClient()
+  }
+  private val bcsp = new BlobContainerSasPermission()
+    .setReadPermission(true)
+    .setCreatePermission(true)
+    .setListPermission(true)
+    .setWritePermission(true)
+
+  /**
+    * Generate a BlobSasToken by using the local environment azure identity
+    * This will use a default subscription if one is not provided.
+    *
+    * @return an AzureSasCredential for accessing a blob container
+    */
+  def generateBlobSasToken: Try[AzureSasCredential] = for {
+    uri <- BlobPathBuilder.parseURI(endpoint.value)
+    configuredAccount <- BlobPathBuilder.parseStorageAccount(uri)
+    azureAccount <- findAzureStorageAccount(configuredAccount)
+    keys = azureAccount.getKeys.asScala
+    key <- keys.headOption.fold[Try[StorageAccountKey]](Failure(new Exception("Storage account has no keys")))(Success(_))
+    first = key.value
+    sskc = new StorageSharedKeyCredential(configuredAccount.value, first)
+    bcc = buildBlobContainerClient(sskc, endpoint, container)
+    bsssv = new BlobServiceSasSignatureValues(OffsetDateTime.now.plusDays(1), bcsp)
+    asc = new AzureSasCredential(bcc.generateSas(bsssv))
+  } yield asc
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 038936ec46e..1be6bb8e13b 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -1,20 +1,14 @@
 package cromwell.filesystems.blob
 
-import com.azure.core.credential.AzureSasCredential
-import com.azure.storage.blob.nio.AzureFileSystem
+import com.azure.storage.blob.nio.{AzureBlobFileAttributes}
 import com.google.common.net.UrlEscapers
-import cromwell.core.path.NioPath
-import cromwell.core.path.Path
-import cromwell.core.path.PathBuilder
+import cromwell.core.path.{NioPath, Path, PathBuilder}
 import cromwell.filesystems.blob.BlobPathBuilder._
 
-import java.net.MalformedURLException
-import java.net.URI
-import java.nio.file.FileSystems
-import scala.jdk.CollectionConverters._
+import java.net.{MalformedURLException, URI}
 import scala.language.postfixOps
-import scala.util.Failure
-import scala.util.Try
+import scala.util.{Failure, Success, Try}
+import java.nio.file.Files
 
 object BlobPathBuilder {
 
@@ -22,9 +16,10 @@ object BlobPathBuilder {
   case class ValidBlobPath(path: String) extends BlobPathValidation
   case class UnparsableBlobPath(errorMessage: Throwable) extends BlobPathValidation
 
-  def invalidBlobPathMessage(container: String, endpoint: String) = s"Malformed Blob URL for this builder. Expecting a URL for a container $container and endpoint $endpoint"
-  def parseURI(string: String) = URI.create(UrlEscapers.urlFragmentEscaper().escape(string))
-  def parseStorageAccount(uri: URI) = uri.getHost().split("\\.").filter(!_.isEmpty()).headOption
+  def invalidBlobPathMessage(container: BlobContainerName, endpoint: EndpointURL) = s"Malformed Blob URL for this builder. Expecting a URL for a container $container and endpoint $endpoint"
+  def parseURI(string: String): Try[URI] = Try(URI.create(UrlEscapers.urlFragmentEscaper().escape(string)))
+  def parseStorageAccount(uri: URI): Try[StorageAccountName] = uri.getHost.split("\\.").find(_.nonEmpty).map(StorageAccountName(_))
+      .map(Success(_)).getOrElse(Failure(new Exception("Could not parse storage account")))
 
   /**
     * Validates a that a path from a string is a valid BlobPath of the format:
@@ -44,46 +39,84 @@ object BlobPathBuilder {
     *
     * If the configured container and storage account do not match, the string is considered unparsable
     */
-  def validateBlobPath(string: String, container: String, endpoint: String): BlobPathValidation = {
-    Try {
-      val uri = parseURI(string)
-      val storageAccount = parseStorageAccount(parseURI(endpoint))
-      val hasContainer = uri.getPath().split("/").filter(!_.isEmpty()).headOption.contains(container)
-      def hasEndpoint = parseStorageAccount(uri).contains(storageAccount.get)
-      if (hasContainer && !storageAccount.isEmpty && hasEndpoint) {
-        ValidBlobPath(uri.getPath.replaceFirst("/" + container, ""))
-      } else {
-        UnparsableBlobPath(new MalformedURLException(invalidBlobPathMessage(container, endpoint)))
+  def validateBlobPath(string: String, container: BlobContainerName, endpoint: EndpointURL): BlobPathValidation = {
+    val blobValidation = for {
+      testUri <- parseURI(string)
+      endpointUri <- parseURI(endpoint.value)
+      testStorageAccount <- parseStorageAccount(testUri)
+      endpointStorageAccount <- parseStorageAccount(endpointUri)
+      hasContainer = testUri.getPath.split("/").find(_.nonEmpty).contains(container.value)
+      hasEndpoint = testStorageAccount.equals(endpointStorageAccount)
+      blobPathValidation = (hasContainer && hasEndpoint) match {
+        case true => ValidBlobPath(testUri.getPath.replaceFirst("/" + container, ""))
+        case false => UnparsableBlobPath(new MalformedURLException(invalidBlobPathMessage(container, endpoint)))
       }
-    } recover { case t => UnparsableBlobPath(t) } get
+    } yield blobPathValidation
+    blobValidation recover { case t => UnparsableBlobPath(t) } get
   }
 }
 
-class BlobPathBuilder(credential: AzureSasCredential, container: String, endpoint: String) extends PathBuilder {
-
-  val fileSystemConfig: Map[String, Object] = Map((AzureFileSystem.AZURE_STORAGE_SAS_TOKEN_CREDENTIAL, credential),
-                                                  (AzureFileSystem.AZURE_STORAGE_FILE_STORES, container))
+class BlobPathBuilder(container: BlobContainerName, endpoint: EndpointURL)(private val fsm: BlobFileSystemManager) extends PathBuilder {
 
   def build(string: String): Try[BlobPath] = {
     validateBlobPath(string, container, endpoint) match {
-      case ValidBlobPath(path) =>
-        Try {
-          val fileSystem = FileSystems.newFileSystem(new URI("azb://?endpoint=" + endpoint), fileSystemConfig.asJava)
-          val blobStoragePath = fileSystem.getPath(path)
-          BlobPath(blobStoragePath, endpoint, container)
-        }
+      case ValidBlobPath(path) => Try(BlobPath(path, endpoint, container)(fsm))
       case UnparsableBlobPath(errorMessage: Throwable) => Failure(errorMessage)
     }
   }
-
   override def name: String = "Azure Blob Storage"
 }
 
-// Add args for container, storage account name
-case class BlobPath private[blob](nioPath: NioPath, endpoint: String, container: String) extends Path {
-  override protected def newPath(nioPath: NioPath): Path = BlobPath(nioPath, endpoint, container)
+object BlobPath {
+  // The Azure NIO library uses `{containerName}:` as the root of the path.
+  // This doesn't work well for our need to easily transfer back and forth
+  // to and from the blob URL format. This method removes anything up to and including
+  // the first colon, to create a path string useful for working with BlobPath.
+  // This is safe because the NIO library enforces no colons except to mark
+  // the root container name.
+  private def nioPathString(nioPath: NioPath): String = {
+    val pathStr = nioPath.toString
+    pathStr.substring(pathStr.indexOf(":")+1)
+  }
+
+  def apply(nioPath: NioPath,
+            endpoint: EndpointURL,
+            container: BlobContainerName,
+            fsm: BlobFileSystemManager): BlobPath = {
+    BlobPath(nioPathString(nioPath), endpoint, container)(fsm)
+  }
+}
+
+case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, container: BlobContainerName)(private val fsm: BlobFileSystemManager) extends Path {
+  override def nioPath: NioPath = findNioPath(pathString)
 
-  override def pathAsString: String = List(endpoint, container, nioPath.toString()).mkString("/")
+  override protected def newPath(nioPath: NioPath): Path = BlobPath(nioPath, endpoint, container, fsm)
 
-  override def pathWithoutScheme: String = parseURI(endpoint).getHost + "/" + container + "/" + nioPath.toString()
+  override def pathAsString: String = List(endpoint, container, pathString.stripPrefix("/")).mkString("/")
+
+  //This is purposefully an unprotected get because if the endpoint cannot be parsed this should fail loudly rather than quietly
+  override def pathWithoutScheme: String = parseURI(endpoint.value).map(u => List(u.getHost, container, pathString).mkString("/")).get
+
+  private def findNioPath(path: String): NioPath = (for {
+    fileSystem <- fsm.retrieveFilesystem()
+    // The Azure NIO library uses `{container}:` to represent the root of the path
+    nioPath = fileSystem.getPath(s"${container.value}:", path)
+  // This is purposefully an unprotected get because the NIO API needing an unwrapped path object.
+  // If an error occurs the api expects a thrown exception
+  } yield nioPath).get
+
+  def blobFileAttributes: Try[AzureBlobFileAttributes] =
+    Try(Files.readAttributes(nioPath, classOf[AzureBlobFileAttributes]))
+
+  def md5HexString: Try[Option[String]] = {
+    blobFileAttributes.map(h =>
+      Option(h.blobHttpHeaders().getContentMd5) match {
+        case None => None
+        case Some(arr) if arr.isEmpty => None
+        // Convert the bytes to a hex-encoded string. Note that this value
+        // is rendered in base64 in the Azure web portal.
+        case Some(bytes) => Option(bytes.map("%02x".format(_)).mkString)
+      }
+    )
+  }
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index ca5e24fe3d7..c263841dc8a 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -1,22 +1,29 @@
 package cromwell.filesystems.blob
 
 import akka.actor.ActorSystem
-import com.azure.core.credential.AzureSasCredential
 import com.typesafe.config.Config
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.PathBuilderFactory
-import cromwell.filesystems.blob.BlobPathBuilder
+import cromwell.core.path.PathBuilderFactory.PriorityBlob
 
-import scala.concurrent.ExecutionContext
-import scala.concurrent.Future
+import java.util.UUID
+import scala.concurrent.{ExecutionContext, Future}
+
+final case class SubscriptionId(value: UUID) {override def toString: String = value.toString}
+final case class BlobContainerName(value: String) {override def toString: String = value}
+final case class StorageAccountName(value: String) {override def toString: String = value}
+final case class EndpointURL(value: String) {override def toString: String = value}
+final case class WorkspaceId(value: UUID) {override def toString: String = value.toString}
+final case class ContainerResourceId(value: UUID) {override def toString: String = value.toString}
+final case class WorkspaceManagerURL(value: String) {override def toString: String = value}
+
+final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, fsm: BlobFileSystemManager) extends PathBuilderFactory {
 
-final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config) extends PathBuilderFactory {
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[BlobPathBuilder] = {
-    val sasToken: String = instanceConfig.getString("sasToken")
-    val container: String = instanceConfig.getString("store")
-    val endpoint: String = instanceConfig.getString("endpoint")
     Future {
-      new BlobPathBuilder(new AzureSasCredential(sasToken), container, endpoint)
+      new BlobPathBuilder(fsm.container, fsm.endpoint)(fsm)
     }
   }
+
+  override def priority: Int = PriorityBlob
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
new file mode 100644
index 00000000000..a9f52d92a91
--- /dev/null
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
@@ -0,0 +1,30 @@
+package cromwell.filesystems.blob
+
+import bio.terra.workspace.api.ControlledAzureResourceApi
+import bio.terra.workspace.client.ApiClient
+
+/**
+  * Represents a way to get a client for interacting with workspace manager controlled resources.
+  * Additional WSM clients can be added here if needed.
+  *
+  * Pared down from `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.WorkspaceManagerApiClientProvider`
+  *
+  * For testing, create an anonymous subclass as in `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.HttpWorkspaceManagerDAOSpec`
+  */
+trait WorkspaceManagerApiClientProvider {
+  def getControlledAzureResourceApi(token: String): ControlledAzureResourceApi
+}
+
+class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManagerURL) extends WorkspaceManagerApiClientProvider {
+  private def getApiClient: ApiClient = {
+    val client: ApiClient = new ApiClient()
+    client.setBasePath(baseWorkspaceManagerUrl.value)
+    client
+  }
+
+  def getControlledAzureResourceApi(token: String): ControlledAzureResourceApi = {
+    val apiClient = getApiClient
+    apiClient.setAccessToken(token)
+    new ControlledAzureResourceApi(apiClient)
+  }
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
new file mode 100644
index 00000000000..607ad5606f7
--- /dev/null
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
@@ -0,0 +1,75 @@
+package cromwell.filesystems.blob
+
+import com.typesafe.config.ConfigFactory
+import common.exception.AggregatedMessageException
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import java.util.UUID
+
+class BlobFileSystemConfigSpec extends AnyFlatSpec with Matchers {
+
+  private val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+  private val container = BlobContainerName("storageContainer")
+  private val workspaceId = WorkspaceId(UUID.fromString("B0BAFE77-0000-0000-0000-000000000000"))
+  private val containerResourceId = ContainerResourceId(UUID.fromString("F00B4911-0000-0000-0000-000000000000"))
+  private val workspaceManagerURL = WorkspaceManagerURL("https://wsm.example.com")
+  private val b2cToken = "b0gus-t0ken"
+
+  it should "parse configs for a minimal functioning factory with native blob access" in {
+    val config = BlobFileSystemConfig(
+      ConfigFactory.parseString(
+      s"""
+         |container = "$container"
+         |endpoint = "$endpoint"
+      """.stripMargin)
+    )
+    config.blobContainerName should equal(container)
+    config.endpointURL should equal(endpoint)
+    config.expiryBufferMinutes should equal(BlobFileSystemConfig.defaultExpiryBufferMinutes)
+  }
+
+  it should "parse configs for a functioning factory with WSM-mediated blob access" in {
+    val config = BlobFileSystemConfig(
+      ConfigFactory.parseString(
+        s"""
+           |container = "$container"
+           |endpoint = "$endpoint"
+           |expiry-buffer-minutes = "20"
+           |workspace-manager {
+           |  url = "$workspaceManagerURL"
+           |  workspace-id = "$workspaceId"
+           |  container-resource-id = "$containerResourceId"
+           |  b2cToken = "$b2cToken"
+           |}
+           |
+        """.stripMargin)
+    )
+    config.blobContainerName should equal(container)
+    config.endpointURL should equal(endpoint)
+    config.expiryBufferMinutes should equal(20L)
+    config.workspaceManagerConfig.isDefined shouldBe true
+    config.workspaceManagerConfig.get.url shouldBe workspaceManagerURL
+    config.workspaceManagerConfig.get.workspaceId shouldBe workspaceId
+    config.workspaceManagerConfig.get.containerResourceId shouldBe containerResourceId
+    config.workspaceManagerConfig.get.overrideWsmAuthToken.contains(b2cToken) shouldBe true
+  }
+
+  it should "fail when partial WSM config is supplied" in {
+    val rawConfig =
+      ConfigFactory.parseString(
+        s"""
+         |container = "$container"
+         |endpoint = "$endpoint"
+         |expiry-buffer-minutes = "10"
+         |workspace-manager {
+         |  url = "$workspaceManagerURL"
+         |  container-resource-id = "$containerResourceId"
+         |}
+         |
+        """.stripMargin)
+
+    val error = intercept[AggregatedMessageException](BlobFileSystemConfig(rawConfig))
+    error.getMessage should include("No configuration setting found for key 'workspace-id'")
+  }
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
new file mode 100644
index 00000000000..611a50f5603
--- /dev/null
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
@@ -0,0 +1,50 @@
+package cromwell.filesystems.blob
+
+import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
+import au.com.dius.pact.core.model.RequestResponsePact
+import io.circe.Json
+import io.circe.syntax._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import pact4s.circe.implicits._
+import pact4s.scalatest.RequestResponsePactForger
+
+class BlobFileSystemContractSpec extends AnyFlatSpec with Matchers with RequestResponsePactForger {
+
+  val resourceId = "";
+  val workspaceId = "";
+  /**
+   * we can define the folder that the pact contracts get written to upon completion of this test suite.
+   */
+  override val pactTestExecutionContext: PactTestExecutionContext = new PactTestExecutionContext(
+    "./filesystems/blob/target/pacts"
+  )
+
+  /**
+   * The following is an outline for what a RequestResponsePact might look like for requesting
+   * from WSM form the blob filesystem. To generate a pact file however tests must be written
+   * against this pact to validate that the agreement is met. These tests get run with other
+   * scala tests on build and if the tests pass when run a pact file will be generated locally
+   */
+  override def pact: RequestResponsePact = ConsumerPactBuilder
+      .consumer("cromwell-blob-filesystem-consumer")
+      .hasPactWith("wsm-provider")
+      .`given`(
+        "resource exists",
+        Map("id" -> resourceId.asJson, "value" -> 123.asJson) // we can use parameters to specify details about the provider state
+      )
+      .`given`(
+        "workspace exists",
+        Map("id" -> workspaceId, "value" -> 123) // we can use parameters to specify details about the provider state
+      )
+      .uponReceiving("Request to fetch SAS Token")
+      .method("POST")
+      .path(s"/api/workspaces/v1/${workspaceId}/resources/controlled/azure/storageContainer/${resourceId}/getSasToken")
+      .headers("Authorization" -> "sampleToken")
+      .willRespondWith()
+      .status(200)
+      .body(
+        Json.obj("id" -> "".asJson, "value" -> 123.asJson)
+      ).toPact()
+
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
new file mode 100644
index 00000000000..881cd3669a1
--- /dev/null
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
@@ -0,0 +1,166 @@
+package cromwell.filesystems.blob
+
+import com.azure.core.credential.AzureSasCredential
+import common.mock.MockSugar
+import org.mockito.Mockito._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import java.nio.file.{FileSystem, FileSystemNotFoundException}
+import java.time.format.DateTimeFormatter
+import java.time.temporal.ChronoUnit
+import java.time.{Duration, Instant, ZoneId}
+import scala.util.{Failure, Try}
+
+
+object BlobPathBuilderFactorySpec {
+  def buildExampleSasToken(expiry: Instant): AzureSasCredential = {
+    val formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd").withZone(ZoneId.systemDefault())
+    val sv = formatter.format(expiry)
+    val se = expiry.toString().replace(":","%3A")
+    new AzureSasCredential(s"sv=$sv&se=$se&sr=c&sp=rcl")
+  }
+}
+class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSugar {
+  def generateTokenExpiration(minutes: Long) = Instant.now.plus(minutes, ChronoUnit.MINUTES)
+
+  it should "build an example sas token of the correct format" in {
+    val testToken = BlobPathBuilderFactorySpec.buildExampleSasToken(Instant.ofEpochMilli(1603794041000L))
+    val sourceToken = "sv=2020-10-27&se=2020-10-27T10%3A20%3A41Z&sr=c&sp=rcl"
+    testToken.getSignature should equal(sourceToken)
+  }
+
+  it should "parse an expiration time from a sas token" in {
+    val expiryTime = generateTokenExpiration(20L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(expiryTime)
+    val expiry = BlobFileSystemManager.parseTokenExpiry(sasToken)
+    expiry should contain(expiryTime)
+  }
+
+  it should "verify an unexpired token will be processed as unexpired" in {
+    val expiryTime = generateTokenExpiration(11L)
+    val expired = BlobFileSystemManager.hasTokenExpired(expiryTime, Duration.ofMinutes(10L))
+    expired shouldBe false
+  }
+
+  it should "test an expired token will be processed as expired" in {
+    val expiryTime = generateTokenExpiration(9L)
+    val expired = BlobFileSystemManager.hasTokenExpired(expiryTime, Duration.ofMinutes(10L))
+    expired shouldBe true
+  }
+
+  it should "test that a filesystem gets closed correctly" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+    val fileSystems = mock[FileSystemAPI]
+    val fileSystem = mock[FileSystem]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(fileSystem))
+    when(fileSystems.closeFileSystem(azureUri)).thenCallRealMethod()
+
+    fileSystems.closeFileSystem(azureUri)
+    verify(fileSystem, times(1)).close()
+  }
+
+  it should "test retrieveFileSystem with expired filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val expiredToken = generateTokenExpiration(9L)
+    val refreshedToken = generateTokenExpiration(69L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+
+    val fileSystems = mock[FileSystemAPI]
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(expiredToken))
+    fsm.getExpiry should contain(expiredToken)
+    fsm.isTokenExpired shouldBe true
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(refreshedToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, never()).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
+    verify(fileSystems, times(1)).closeFileSystem(azureUri)
+  }
+
+  it should "test retrieveFileSystem with an unexpired fileSystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val initialToken = generateTokenExpiration(11L)
+    val refreshedToken = generateTokenExpiration(71L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+    // Need a fake filesystem to supply the getFileSystem simulated try
+    val dummyFileSystem = mock[FileSystem]
+
+    val fileSystems = mock[FileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(dummyFileSystem))
+
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(initialToken))
+    fsm.getExpiry should contain(initialToken)
+    fsm.isTokenExpired shouldBe false
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(initialToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, times(1)).getFileSystem(azureUri)
+    verify(fileSystems, never()).newFileSystem(azureUri, configMap)
+    verify(fileSystems, never()).closeFileSystem(azureUri)
+  }
+
+  it should "test retrieveFileSystem with an uninitialized filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val refreshedToken = generateTokenExpiration(71L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+
+    val fileSystems = mock[FileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Failure(new FileSystemNotFoundException))
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(refreshedToken))
+    fsm.getExpiry.isDefined shouldBe true
+    fsm.isTokenExpired shouldBe false
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(refreshedToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, times(1)).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
+    verify(fileSystems, never()).closeFileSystem(azureUri)
+  }
+
+  it should "test retrieveFileSystem with an unknown filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val refreshedToken = generateTokenExpiration(71L)
+    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
+    val container = BlobContainerName("storageContainer")
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.uri(endpoint)
+
+    val fileSystems = mock[FileSystemAPI]
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+
+    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems)
+    fsm.getExpiry.isDefined shouldBe false
+    fsm.isTokenExpired shouldBe false
+    fsm.retrieveFilesystem()
+
+    fsm.getExpiry should contain(refreshedToken)
+    fsm.isTokenExpired shouldBe false
+    verify(fileSystems, never()).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
+    verify(fileSystems, times(1)).closeFileSystem(azureUri)
+  }
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index 454b8f5adaf..2aa9b2b43aa 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -1,23 +1,22 @@
 package cromwell.filesystems.blob
-
-import com.azure.core.credential.AzureSasCredential
-import cromwell.filesystems.blob.BlobPathBuilder
+import common.mock.MockSugar
+import org.mockito.Mockito.when
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-import java.nio.file.Files
+import scala.util.{Failure, Try}
 
 object BlobPathBuilderSpec {
-  def buildEndpoint(storageAccount: String) = s"https://$storageAccount.blob.core.windows.net"
+  def buildEndpoint(storageAccount: String) = EndpointURL(s"https://$storageAccount.blob.core.windows.net")
 }
 
-class BlobPathBuilderSpec extends AnyFlatSpec with Matchers{
-
+class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
+  // ValidateBlobPath
   it should "parse a URI into a path" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = "container"
+    val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
-    val testString = endpoint + "/" + container + evalPath
+    val testString = endpoint.value + "/" + container + evalPath
     BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
       case BlobPathBuilder.ValidBlobPath(path) => path should equal(evalPath)
       case BlobPathBuilder.UnparsableBlobPath(errorMessage) => fail(errorMessage)
@@ -26,40 +25,83 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers{
 
   it should "bad storage account fails causes URI to fail parse into a path" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = "container"
+    val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
-    val testString = BlobPathBuilderSpec.buildEndpoint("badStorageAccount") + container + evalPath
+    val testString = BlobPathBuilderSpec.buildEndpoint("badStorageAccount").value + container.value + evalPath
     BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
       case BlobPathBuilder.ValidBlobPath(path) => fail(s"Valid path: $path found when verifying mismatched storage account")
-      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage() should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
+      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
     }
   }
 
   it should "bad container fails causes URI to fail parse into a path" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = "container"
+    val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
-    val testString = endpoint + "badContainer" + evalPath
+    val testString = endpoint.value + "badContainer" + evalPath
     BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
       case BlobPathBuilder.ValidBlobPath(path) => fail(s"Valid path: $path found when verifying mismatched container")
-      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage() should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
+      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
     }
   }
 
+  it should "provide a readable error when getting an illegal nioPath" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val container = BlobContainerName("container")
+    val evalPath = "/path/to/file"
+    val exception = new Exception("Failed to do the thing")
+    val fsm = mock[BlobFileSystemManager]
+    when(fsm.retrieveFilesystem()).thenReturn(Failure(exception))
+    val path = BlobPath(evalPath, endpoint, container)(fsm)
+    val testException = Try(path.nioPath).failed.toOption
+    testException should contain(exception)
+  }
+
   ignore should "build a blob path from a test string and read a file" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
-    val endpointHost = BlobPathBuilder.parseURI(endpoint).getHost
-    val store = "inputs"
+    val endpointHost = BlobPathBuilder.parseURI(endpoint.value).map(_.getHost).getOrElse(fail("Could not parse URI"))
+    val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
-    val sas = "{SAS TOKEN HERE}"
-    val testString = endpoint + "/" + store + evalPath
-    val blobPath: BlobPath = new BlobPathBuilder(new AzureSasCredential(sas), store, endpoint) build testString getOrElse fail()
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
+    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10L, blobTokenGenerator)
+    val testString = endpoint.value + "/" + store + evalPath
+    val blobPath: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
+
     blobPath.container should equal(store)
     blobPath.endpoint should equal(endpoint)
     blobPath.pathAsString should equal(testString)
     blobPath.pathWithoutScheme should equal(endpointHost + "/" + store + evalPath)
-    val is = Files.newInputStream(blobPath.nioPath)
+    val is = blobPath.newInputStream()
     val fileText = (is.readAllBytes.map(_.toChar)).mkString
     fileText should include ("This is my test file!!!! Did it work?")
   }
+
+  ignore should "build duplicate blob paths in the same filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
+    val store = BlobContainerName("inputs")
+    val evalPath = "/test/inputFile.txt"
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
+    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
+    val testString = endpoint.value + "/" + store + evalPath
+    val blobPath1: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
+    blobPath1.nioPath.getFileSystem.close()
+    val blobPath2: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
+    blobPath1 should equal(blobPath2)
+    val is = blobPath1.newInputStream()
+    val fileText = (is.readAllBytes.map(_.toChar)).mkString
+    fileText should include ("This is my test file!!!! Did it work?")
+  }
+
+  ignore should "resolve a path without duplicating container name" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
+    val store = BlobContainerName("inputs")
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
+    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
+
+    val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
+    val blobRoot: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build rootString getOrElse fail()
+    blobRoot.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution")
+    val otherFile = blobRoot.resolve("test/inputFile.txt")
+    otherFile.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
+  }
 }
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
index 4f899c318bb..5856e41f97b 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
@@ -28,7 +28,7 @@ case class DrsPath(drsPath: CloudNioPath, requesterPaysProjectIdOption: Option[S
       case Some(fileAttributes) =>
         fileAttributes.fileHash match {
           case Some(fileHash) => fileHash
-          case None => throw new IOException(s"Error while resolving DRS path $this. The response from Martha doesn't contain the 'md5' hash for the file.")
+          case None => throw new IOException(s"Error while resolving DRS path $this. The response from DRS Resolver doesn't contain the 'md5' hash for the file.")
         }
       case None => throw new IOException(s"Error getting file hash of DRS path $this. Reason: File attributes class DrsCloudNioRegularFileAttributes wasn't defined in DrsCloudNioFileProvider.")
     }
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
index f22023c87fd..b464772eec8 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
@@ -60,7 +60,7 @@ case class DrsPathBuilder(fileSystemProvider: DrsCloudNioFileSystemProvider,
     val gcsPathOption = for {
       // Right now, only pre-resolving GCS. In the future, could pull others like FTP, HTTP, S3, SRA, etc.
       gsUriOption <- logAttempt(
-        "resolve the uri through Martha",
+        "resolve the uri through DRS Resolver",
         DrsResolver.getSimpleGsUri(pathAsString, fileSystemProvider.drsPathResolver).unsafeRunSync()
       )
       gcsUrlWithNoCreds <- gsUriOption
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
index bc7fb598a81..873874912a0 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
@@ -2,13 +2,12 @@ package cromwell.filesystems.drs
 
 import akka.actor.ActorSystem
 import cats.data.Validated.{Invalid, Valid}
-import cloud.nio.impl.drs.{AzureDrsCredentials, DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import cloud.nio.impl.drs.{AzureDrsCredentials, DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.api.services.oauth2.Oauth2Scopes
 import com.typesafe.config.Config
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.{PathBuilder, PathBuilderFactory}
-import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -24,26 +23,23 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
   private lazy val googleConfiguration: GoogleConfiguration = GoogleConfiguration(globalConfig)
   private lazy val scheme = instanceConfig.getString("auth")
 
-  // For Azure support
+  // For Azure support - this should be the UAMI client id
   private val dataAccessIdentityKey = "data_access_identity"
-  private lazy val azureKeyVault = instanceConfig.as[Option[String]]("azure-keyvault-name")
-  private lazy val azureSecretName = instanceConfig.as[Option[String]]("azure-token-secret")
 
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] = {
     Future {
-      val marthaScopes = List(
-        // Profile and Email scopes are requirements for interacting with Martha
+      val drsResolverScopes = List(
+        // Profile and Email scopes are requirements for interacting with DRS Resolvers
         Oauth2Scopes.USERINFO_EMAIL,
         Oauth2Scopes.USERINFO_PROFILE
       )
 
-      val (googleAuthMode, drsCredentials) = (scheme, azureKeyVault, azureSecretName) match {
-        case ("azure", Some(vaultName), Some(secretName)) => (None, AzureDrsCredentials(options.get(dataAccessIdentityKey).toOption, vaultName, secretName))
-        case ("azure", _, _) => throw new RuntimeException(s"Error while instantiating DRS path builder factory. Couldn't find azure-keyvault-name and azure-token-secret in config.")
-        case (googleAuthScheme, _, _) => googleConfiguration.auth(googleAuthScheme) match {
+      val (googleAuthMode, drsCredentials) = scheme match {
+        case "azure" => (None, AzureDrsCredentials(options.get(dataAccessIdentityKey).toOption))
+        case googleAuthScheme => googleConfiguration.auth(googleAuthScheme) match {
           case Valid(auth) => (
             Option(auth),
-            GoogleDrsCredentials(auth.credentials(options.get(_).get, marthaScopes), singletonConfig.config)
+            GoogleOauthDrsCredentials(auth.credentials(options.get(_).get, drsResolverScopes), singletonConfig.config)
           )
           case Invalid(error) => throw new RuntimeException(s"Error while instantiating DRS path builder factory. Errors: ${error.toString}")
         }
@@ -54,7 +50,7 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
       val requesterPaysProjectIdOption = options.get("google_project").toOption
 
       /*
-      `override_preresolve_for_test` is a workflow option to override the default `martha.preresolve` specified in the
+      `override_preresolve_for_test` is a workflow option to override the default `resolver.preresolve` specified in the
       global config. This is only used for testing purposes.
        */
       val preResolve: Boolean =
@@ -64,7 +60,7 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
           .getOrElse(
             singletonConfig
               .config
-              .getBoolean("martha.preresolve")
+              .getBoolean("resolver.preresolve")
           )
 
       DrsPathBuilder(
@@ -82,4 +78,4 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
 
 case class UrlNotFoundException(scheme: String) extends Exception(s"No $scheme url associated with given DRS path.")
 
-case class MarthaResponseMissingKeyException(missingKey: String) extends Exception(s"The response from Martha doesn't contain the key '$missingKey'.")
+case class DrsResolverResponseMissingKeyException(missingKey: String) extends Exception(s"The response from the DRS Resolver doesn't contain the key '$missingKey'.")
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
index 3cc1cc3530a..3256d6da248 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
@@ -1,8 +1,8 @@
 package cromwell.filesystems.drs
 
 import cats.effect.IO
-import cloud.nio.impl.drs.MarthaResponseSupport.getGcsBucketAndName
-import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, MarthaResponse, SADataObject}
+import cloud.nio.impl.drs.DrsResolverResponseSupport.getGcsBucketAndName
+import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, DrsResolverResponse, SADataObject}
 import com.google.api.services.storage.StorageScopes
 import com.google.auth.oauth2.OAuth2Credentials
 import com.google.cloud.storage.Storage.BlobGetOption
@@ -21,8 +21,8 @@ object DrsReader {
              options: WorkflowOptions,
              requesterPaysProjectIdOption: Option[String],
              drsPathResolver: DrsPathResolver,
-             marthaResponse: MarthaResponse): IO[DrsReader] = {
-    (marthaResponse.accessUrl, marthaResponse.gsUri, googleAuthMode) match {
+             drsResolverResponse: DrsResolverResponse): IO[DrsReader] = {
+    (drsResolverResponse.accessUrl, drsResolverResponse.gsUri, googleAuthMode) match {
       case (Some(accessUrl), _, _) =>
         IO.pure(AccessUrlReader(drsPathResolver, accessUrl))
       case (_, Some(gcsPath), Some(authMode)) =>
@@ -31,10 +31,10 @@ object DrsReader {
           options,
           requesterPaysProjectIdOption,
           gcsPath,
-          marthaResponse.googleServiceAccount,
+          drsResolverResponse.googleServiceAccount,
         ))
       case (_, Some(_), _) =>
-        IO.raiseError(new RuntimeException("GCS URI found in Martha response, but no Google auth found!"))
+        IO.raiseError(new RuntimeException("GCS URI found in the DRS Resolver response, but no Google auth found!"))
       case _ =>
         IO.raiseError(new RuntimeException(DrsPathResolver.ExtractUriErrorMsg))
     }
@@ -44,9 +44,9 @@ object DrsReader {
                       options: WorkflowOptions,
                       requesterPaysProjectIdOption: Option[String])
                      (drsPathResolver: DrsPathResolver,
-                      marthaResponse: MarthaResponse): IO[ReadableByteChannel] = {
+                      drsResolverResponse: DrsResolverResponse): IO[ReadableByteChannel] = {
     for {
-      reader <- reader(googleAuthMode, options, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      reader <- reader(googleAuthMode, options, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
       channel <- reader.read()
     } yield channel
   }
@@ -69,7 +69,7 @@ case class GcsReader(googleAuthMode: GoogleAuthMode,
     val credentialsIo = googleServiceAccount match {
       case Some(googleSA) =>
         IO(
-          UserServiceAccountMode("martha_service_account").credentials(
+          UserServiceAccountMode("drs_resolver_service_account").credentials(
             Map(GoogleAuthMode.UserServiceAccountKey -> googleSA.data.noSpaces),
             readScopes,
           )
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
index 0f24e803480..4aa760f17e1 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
@@ -2,7 +2,7 @@ package cromwell.filesystems.drs
 
 import cats.data.NonEmptyList
 import cats.effect.IO
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, DrsPathResolver, MarthaField}
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, DrsPathResolver, DrsResolverField}
 import common.exception._
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import org.apache.commons.lang3.exception.ExceptionUtils
@@ -34,31 +34,31 @@ object DrsResolver {
     } yield drsFileSystemProvider.drsPathResolver
   }
 
-  case class MarthaLocalizationData(gsUri: Option[String],
-                                    fileName: Option[String],
-                                    bondProvider: Option[String],
-                                    localizationPath: Option[String])
+  case class DrsResolverLocalizationData(gsUri: Option[String],
+                                         fileName: Option[String],
+                                         bondProvider: Option[String],
+                                         localizationPath: Option[String])
 
-  private def getMarthaLocalizationData(pathAsString: String,
-                                        drsPathResolver: DrsPathResolver): IO[MarthaLocalizationData] = {
-    val fields = NonEmptyList.of(MarthaField.GsUri, MarthaField.FileName, MarthaField.BondProvider, MarthaField.LocalizationPath)
+  private def getDrsResolverLocalizationData(pathAsString: String,
+                                        drsPathResolver: DrsPathResolver): IO[DrsResolverLocalizationData] = {
+    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.FileName, DrsResolverField.BondProvider, DrsResolverField.LocalizationPath)
 
-    drsPathResolver.resolveDrsThroughMartha(pathAsString, fields) map { r =>
-      MarthaLocalizationData(r.gsUri, r.fileName, r.bondProvider, r.localizationPath)
+    drsPathResolver.resolveDrs(pathAsString, fields) map { r =>
+      DrsResolverLocalizationData(r.gsUri, r.fileName, r.bondProvider, r.localizationPath)
     }
   }
 
   /** Returns the `gsUri` if it ends in the `fileName` and the `bondProvider` is empty. */
-  private def getSimpleGsUri(localizationData: MarthaLocalizationData): Option[String] = {
+  private def getSimpleGsUri(localizationData: DrsResolverLocalizationData): Option[String] = {
     localizationData match {
       // `gsUri` not defined so no gsUri can be returned.
-      case MarthaLocalizationData(None, _, _, _) => None
+      case DrsResolverLocalizationData(None, _, _, _) => None
       // `bondProvider` defined, cannot "preresolve" to GCS.
-      case MarthaLocalizationData(_, _, Some(_), _) => None
+      case DrsResolverLocalizationData(_, _, Some(_), _) => None
       // Do not return the simple GS URI if the `fileName` from metadata is mismatched to the filename in the `gsUri`.
-      case MarthaLocalizationData(Some(gsUri), Some(fileName), _, _) if !gsUri.endsWith(s"/$fileName") => None
+      case DrsResolverLocalizationData(Some(gsUri), Some(fileName), _, _) if !gsUri.endsWith(s"/$fileName") => None
       // Barring any of the situations above return the `gsUri`.
-      case MarthaLocalizationData(Some(gsUri), _, _, _) => Option(gsUri)
+      case DrsResolverLocalizationData(Some(gsUri), _, _, _) => Option(gsUri)
     }
   }
 
@@ -66,7 +66,7 @@ object DrsResolver {
   def getSimpleGsUri(pathAsString: String,
                      drsPathResolver: DrsPathResolver): IO[Option[String]] = {
 
-    val gsUriIO = getMarthaLocalizationData(pathAsString, drsPathResolver) map getSimpleGsUri
+    val gsUriIO = getDrsResolverLocalizationData(pathAsString, drsPathResolver) map getSimpleGsUri
 
     gsUriIO.handleErrorWith(resolveError(pathAsString))
   }
@@ -82,15 +82,15 @@ object DrsResolver {
   def getContainerRelativePath(drsPath: DrsPath): IO[String] = {
     val pathIO = for {
       drsPathResolver <- getDrsPathResolver(drsPath)
-      localizationData <- getMarthaLocalizationData(drsPath.pathAsString, drsPathResolver)
+      localizationData <- getDrsResolverLocalizationData(drsPath.pathAsString, drsPathResolver)
       containerRelativePath <- buildContainerRelativePath(localizationData, drsPath)
     } yield containerRelativePath.pathAsString
 
     pathIO.handleErrorWith(resolveError(drsPath.pathAsString))
   }
 
-  // Return the container relative path built from the Martha-specified localization path, file name, or gs URI.
-  private def buildContainerRelativePath(localizationData: MarthaLocalizationData, drsPath: Path): IO[Path] = {
+  // Return the container relative path built from the DRS Resolver-specified localization path, file name, or gs URI.
+  private def buildContainerRelativePath(localizationData: DrsResolverLocalizationData, drsPath: Path): IO[Path] = {
     // Return a relative path constructed from the DRS path minus the leading scheme.
     // In the DOS/DRS spec file names are safe for file systems but not necessarily the DRS URIs.
     // Reuse the regex defined for ContentsObject.name, plus add "/" for directory separators.
@@ -99,13 +99,13 @@ object DrsResolver {
       DefaultPathBuilder.get(drsPath.pathWithoutScheme.replaceAll("[^/A-Za-z0-9._-]", "_"))
 
     localizationData match {
-      case MarthaLocalizationData(_, _, _, Some(localizationPath)) =>
+      case DrsResolverLocalizationData(_, _, _, Some(localizationPath)) =>
         // TDR may return an explicit localization path and if so we should not use the `drsPathRelativePath`.
         // We want to end up with something like /cromwell_root/drs_localization_paths/tdr/specified/path/foo.bam.
         // Calling code will add the `/cromwell_root/`, so strip any leading slashes to make this a relative path:
         val relativeLocalizationPath = if (localizationPath.startsWith("/")) localizationPath.tail else localizationPath
         IO.fromTry(DefaultPathBuilder.build(DrsLocalizationPathsContainer).map(_.resolve(relativeLocalizationPath)))
-      case MarthaLocalizationData(_, Some(fileName), _, _) =>
+      case DrsResolverLocalizationData(_, Some(fileName), _, _) =>
         // Paths specified by filename only are made relative to `drsPathRelativePath`.
         IO(drsPathRelativePath.resolve(fileName))
       case _ =>
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
index 1d941b5f6b2..d207bba8d86 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
@@ -18,8 +18,8 @@ class DrsPathBuilderFactorySpec extends AnyFlatSpec with CromwellTimeoutSpec wit
          |    global {
          |      class = "cromwell.filesystems.drs.DrsFileSystemConfig"
          |      config {
-         |        martha {
-         |          url = "http://martha-url"
+         |        resolver {
+         |          url = "http://drshub-url"
          |        }
          |      }
          |    }
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
index 242b662d5ea..315e51b5d04 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
@@ -1,7 +1,7 @@
 package cromwell.filesystems.drs
 
 import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.cloud.NoCredentials
 import com.typesafe.config.{Config, ConfigFactory}
 import cromwell.core.TestKitSuite
@@ -313,7 +313,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       isAbsolute = false,
     ),
 
-    // No spec says this is illegal... so pass it to Martha's various GCFs JIC
+    // No spec says this is illegal... so pass it to the DRS Resolver's various GCFs JIC
     GoodPath(
       description = "a bucketless path",
       path = s"drs://",
@@ -377,9 +377,9 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   private val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
     throw new UnsupportedOperationException("Currently DrsPathBuilderSpec doesn't need to use drs read interpreter.")
 
-  private val marthaConfig: Config = ConfigFactory.parseString(
-    """martha {
-      |   url = "http://martha-url"
+  private val drsResolverConfig: Config = ConfigFactory.parseString(
+    """resolver {
+      |   url = "http://drshub-url"
       |}
       |""".stripMargin
   )
@@ -387,7 +387,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   private lazy val fakeCredentials = NoCredentials.getInstance
 
   private lazy val drsPathBuilder = DrsPathBuilder(
-    new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+    new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
     None,
   )
 }
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
index fbcd900f371..b5bee55b301 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
@@ -1,6 +1,6 @@
 package cromwell.filesystems.drs
 
-import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, MarthaResponse, MockEngineDrsPathResolver}
+import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, DrsResolverResponse, MockEngineDrsPathResolver}
 import common.assertion.CromwellTimeoutSpec
 import cromwell.cloudsupport.gcp.auth.MockAuthMode
 import cromwell.core.WorkflowOptions
@@ -29,9 +29,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val drsPathResolver = new MockEngineDrsPathResolver()
     val gsUri = "gs://bucket/object"
     val googleServiceAccount = None
-    val marthaResponse = MarthaResponse(gsUri = Option(gsUri), googleServiceAccount = googleServiceAccount)
+    val drsResolverResponse = DrsResolverResponse(gsUri = Option(gsUri), googleServiceAccount = googleServiceAccount)
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
     readerIo.unsafeRunSync() should be(
       GcsReader(googleAuthMode, workflowOptions, requesterPaysProjectIdOption, gsUri, googleServiceAccount)
     )
@@ -43,9 +43,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val requesterPaysProjectIdOption = None
     val drsPathResolver = new MockEngineDrsPathResolver()
     val accessUrl = AccessUrl("https://host/object/path", Option(Map("hello" -> "world")))
-    val marthaResponse = MarthaResponse(accessUrl = Option(accessUrl))
+    val drsResolverResponse = DrsResolverResponse(accessUrl = Option(accessUrl))
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
     readerIo.unsafeRunSync() should be(
       AccessUrlReader(drsPathResolver, accessUrl)
     )
@@ -56,9 +56,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val workflowOptions = WorkflowOptions.empty
     val requesterPaysProjectIdOption = None
     val drsPathResolver = new MockEngineDrsPathResolver()
-    val marthaResponse = MarthaResponse()
+    val drsResolverResponse = DrsResolverResponse()
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, marthaResponse)
+      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
     the[RuntimeException] thrownBy {
       readerIo.unsafeRunSync()
     } should have message DrsPathResolver.ExtractUriErrorMsg
@@ -78,9 +78,9 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val drsPathResolver = new MockEngineDrsPathResolver(httpClientBuilderOverride = Option(httpClientBuilder))
 
     val accessUrl = AccessUrl("https://host/object/path", Option(Map("hello" -> "world")))
-    val marthaResponse = MarthaResponse(accessUrl = Option(accessUrl))
+    val drsResolverResponse = DrsResolverResponse(accessUrl = Option(accessUrl))
     val channelIo =
-      DrsReader.readInterpreter(Option(MockAuthMode("unused")), WorkflowOptions.empty, None)(drsPathResolver, marthaResponse)
+      DrsReader.readInterpreter(Option(MockAuthMode("unused")), WorkflowOptions.empty, None)(drsPathResolver, drsResolverResponse)
     val channel = channelIo.unsafeRunSync()
 
     val buffer = ByteBuffer.allocate(exampleBytes.length)
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
index 98d4140029b..23dcb1bcd66 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
@@ -11,14 +11,14 @@ import scala.jdk.CollectionConverters._
 
 class DrsResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
-  private val marthaConfig: Config = ConfigFactory.parseMap(
+  private val drsResolverConfig: Config = ConfigFactory.parseMap(
     Map(
-      "martha.url" -> "https://martha-url/martha_v3",
+      "resolver.url" -> "https://drshub-url/drshub_v4",
       "access-token-acceptable-ttl" -> "1 minute"
     ).asJava
   )
 
-  private val mockFileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = marthaConfig)
+  private val mockFileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = drsResolverConfig)
   private val drsPathBuilder = DrsPathBuilder(mockFileSystemProvider, None)
 
 
@@ -62,14 +62,14 @@ class DrsResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     } should have message s"Error while resolving DRS path: ${drsPath.pathAsString}. Error: UrlNotFoundException: No gs url associated with given DRS path."
   }
 
-  it should "throw Runtime Exception when Martha can't find the given DRS path " in {
-    val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathNotExistingInMartha).get.asInstanceOf[DrsPath]
+  it should "throw Runtime Exception when the DRS Resolver can't find the given DRS path " in {
+    val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathNotExistingInDrsResolver).get.asInstanceOf[DrsPath]
 
     the[RuntimeException] thrownBy {
       DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
     } should have message
       s"Error while resolving DRS path: ${drsPath.pathAsString}. " +
         s"Error: RuntimeException: Unexpected response resolving ${drsPath.pathAsString} " +
-        s"through Martha url https://martha-url/martha_v3. Error: 404 Not Found."
+        s"through DRS Resolver url https://drshub-url/drshub_v4. Error: 404 Not Found."
   }
 }
diff --git a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
index 645600d1613..306f39337dd 100644
--- a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
+++ b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
@@ -30,11 +30,12 @@
  */
 package cromwell.filesystems.s3.batch
 
-import cromwell.core.io.{IoCommandBuilder, IoContentAsStringCommand, IoIsDirectoryCommand, IoReadLinesCommand, IoWriteCommand, PartialIoCommandBuilder}
+import cromwell.core.io.{IoCommandBuilder, IoHashCommand, IoContentAsStringCommand, IoIsDirectoryCommand, IoReadLinesCommand, IoWriteCommand, PartialIoCommandBuilder}
 import cromwell.core.path.BetterFileMethods.OpenOptions
 import cromwell.core.path.Path
 import cromwell.filesystems.s3.S3Path
 import org.slf4j.{Logger, LoggerFactory}
+import cromwell.core.io.DefaultIoCommand.DefaultIoHashCommand
 
 import scala.util.Try
 
@@ -77,8 +78,9 @@ private case object PartialS3BatchCommandBuilder extends PartialIoCommandBuilder
     case (src: S3Path, dest: S3Path) => Try(S3BatchCopyCommand(src, dest))
   }
 
-  override def hashCommand: PartialFunction[Path, Try[S3BatchEtagCommand]] = {
-    case path: S3Path => Try(S3BatchEtagCommand(path))
+  override def hashCommand: PartialFunction[Path, Try[IoHashCommand]] = {
+    case s3_path: S3Path => Try(S3BatchEtagCommand(s3_path).asInstanceOf[IoHashCommand])
+    case local_path: Path => Try(DefaultIoHashCommand(local_path))
   }
 
   override def touchCommand: PartialFunction[Path, Try[S3BatchTouchCommand]] = {
diff --git a/languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala b/languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala
deleted file mode 100644
index e3a6387c739..00000000000
--- a/languageFactories/cwl-v1-0/src/main/scala/languages/cwl/CwlV1_0LanguageFactory.scala
+++ /dev/null
@@ -1,75 +0,0 @@
-package languages.cwl
-
-import better.files.File
-import cats.data.EitherT.fromEither
-import cats.effect.IO
-import com.typesafe.config.Config
-import common.Checked
-import common.validation.Checked._
-import common.validation.IOChecked.IOChecked
-import cromwell.core.{WorkflowId, WorkflowOptions, WorkflowSourceFilesCollection}
-import cromwell.languages.util.ImportResolver.ImportResolver
-import cromwell.languages.util.LanguageFactoryUtil
-import cromwell.languages.{LanguageFactory, ValidatedWomNamespace}
-import cwl.preprocessor.CwlReference
-import cwl.{Cwl, CwlDecoder}
-import wom.ResolvedImportRecord
-import wom.core.{WorkflowJson, WorkflowOptionsJson, WorkflowSource}
-import wom.executable.WomBundle
-import wom.expression.IoFunctionSet
-
-class CwlV1_0LanguageFactory(override val config: Config) extends LanguageFactory {
-
-  override val languageName: String = "CWL"
-  override val languageVersionName: String = "v1.0"
-
-  override def validateNamespace(source: WorkflowSourceFilesCollection,
-                                 workflowSource: WorkflowSource,
-                                 workflowOptions: WorkflowOptions,
-                                 importLocalFilesystem: Boolean,
-                                 workflowIdForLogging: WorkflowId,
-                                 ioFunctions: IoFunctionSet,
-                                 importResolvers: List[ImportResolver]): IOChecked[ValidatedWomNamespace] = {
-
-    def parse(): IOChecked[Cwl] = {
-      val decodedCwlReference =
-        for {
-          url <- source.workflowUrl
-          reference <- CwlReference.fromString(url)
-        } yield CwlDecoder.decodeCwlReference(reference.changePointer(source.workflowRoot))
-
-      decodedCwlReference
-        .getOrElse(
-          CwlDecoder.decodeCwlString(
-            workflowSource,
-            source.importsZipFileOption.map(File.newTemporaryFile().appendByteArray(_)),
-            source.workflowRoot,
-            cwlFilename = s"cwl_temp_file_$workflowIdForLogging"
-          ))
-    }
-
-    import cwl.AcceptAllRequirements
-    for {
-      _ <- fromEither[IO](enabledCheck)
-      cwl <- parse()
-      executable <- fromEither[IO](cwl.womExecutable(AcceptAllRequirements, Option(source.inputsJson), ioFunctions, strictValidation))
-      validatedWomNamespace <- fromEither[IO](LanguageFactoryUtil.validateWomNamespace(executable, ioFunctions))
-    } yield validatedWomNamespace
-  }
-
-  override def getWomBundle(workflowSource: WorkflowSource,
-                            workflowSourceOrigin: Option[ResolvedImportRecord],
-                            workflowOptionsJson: WorkflowOptionsJson,
-                            importResolvers: List[ImportResolver],
-                            languageFactories: List[LanguageFactory],
-                            convertNestedScatterToSubworkflow : Boolean = true): Checked[WomBundle] =
-    enabledCheck flatMap { _ => "No getWomBundle method implemented in CWL v1".invalidNelCheck }
-
-  override def createExecutable(womBundle: WomBundle, inputs: WorkflowJson, ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace] =
-    enabledCheck flatMap { _ => "No createExecutable method implemented in CWL v1".invalidNelCheck }
-
-  override def looksParsable(content: String): Boolean = content.linesIterator.exists { l =>
-    val trimmed = l.trim.stripSuffix(",")
-    trimmed == """"cwlVersion": "v1.0"""" || trimmed == "cwlVersion: v1.0"
-  }
-}
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
index 01c5db23084..f7fd70cfc56 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
@@ -9,12 +9,14 @@ import cats.syntax.either._
 import cats.syntax.validated._
 import com.softwaremill.sttp._
 import com.softwaremill.sttp.asynchttpclient.cats.AsyncHttpClientCatsBackend
+import com.typesafe.config.ConfigFactory
 import common.Checked
 import common.transforms.CheckedAtoB
 import common.validation.ErrorOr._
 import common.validation.Checked._
 import common.validation.Validation._
 import cromwell.core.path.{DefaultPathBuilder, Path}
+import net.ceedubs.ficus.Ficus._
 
 import java.nio.file.{Path => NioPath}
 import java.security.MessageDigest
@@ -157,7 +159,9 @@ object ImportResolver {
     }
   }
 
-  case class HttpResolver(relativeTo: Option[String] = None, headers: Map[String, String] = Map.empty) extends ImportResolver {
+  case class HttpResolver(relativeTo: Option[String],
+                          headers: Map[String, String],
+                          hostAllowlist: Option[List[String]]) extends ImportResolver {
     import HttpResolver._
 
     override def name: String = relativeTo match {
@@ -169,7 +173,7 @@ object ImportResolver {
     def newResolverList(newRoot: String): List[ImportResolver] = {
       val rootWithoutFilename = newRoot.split('/').init.mkString("", "/", "/")
       List(
-        HttpResolver(relativeTo = Some(canonicalize(rootWithoutFilename)), headers)
+        HttpResolver(relativeTo = Some(canonicalize(rootWithoutFilename)), headers, hostAllowlist)
       )
     }
 
@@ -183,18 +187,20 @@ object ImportResolver {
         else "Relative path".invalidNelCheck
     }
 
+    def isAllowed(uri: Uri): Boolean = hostAllowlist match {
+      case Some(hosts) => hosts.contains(uri.host)
+      case None => true
+    }
+
     override def innerResolver(str: String, currentResolvers: List[ImportResolver]): Checked[ResolvedImportBundle] = {
-      pathToLookup(str) flatMap { toLookup =>
+      pathToLookup(str) flatMap { toLookup: WorkflowSource =>
         (Try {
-          implicit val sttpBackend = HttpResolver.sttpBackend()
-          val responseIO: IO[Response[String]] = sttp.get(uri"$toLookup").headers(headers).send()
-
-          // temporary situation to get functionality working before
-          // starting in on async-ifying the entire WdlNamespace flow
-          val result: Checked[String] = Await.result(responseIO.unsafeToFuture(), 15.seconds).body.leftMap { e => NonEmptyList(e.toString.trim, List.empty) }
+          val uri: Uri = uri"$toLookup"
 
-          result map {
-            ResolvedImportBundle(_, newResolverList(toLookup), ResolvedImportRecord(toLookup))
+          if (isAllowed(uri)) {
+            getUri(toLookup)
+          } else {
+            s"Disallowed domain in URI. ${uri.toString()}".invalidNelCheck
           }
         } match {
           case Success(result) => result
@@ -203,6 +209,19 @@ object ImportResolver {
       }
     }
 
+    private def getUri(toLookup: WorkflowSource): Either[NonEmptyList[WorkflowSource], ResolvedImportBundle] = {
+      implicit val sttpBackend = HttpResolver.sttpBackend()
+      val responseIO: IO[Response[WorkflowSource]] = sttp.get(uri"$toLookup").headers(headers).send()
+
+      // temporary situation to get functionality working before
+      // starting in on async-ifying the entire WdlNamespace flow
+      val result: Checked[WorkflowSource] = Await.result(responseIO.unsafeToFuture(), 15.seconds).body.leftMap { e => NonEmptyList(e.toString.trim, List.empty) }
+
+      result map {
+        ResolvedImportBundle(_, newResolverList(toLookup), ResolvedImportRecord(toLookup))
+      }
+    }
+
     override def cleanupIfNecessary(): ErrorOr[Unit] = ().validNel
 
     override def hashKey: ErrorOr[String] = relativeTo.toString.md5Sum.validNel
@@ -213,6 +232,18 @@ object ImportResolver {
     import common.util.IntrospectableLazy
     import common.util.IntrospectableLazy._
 
+    def apply(relativeTo: Option[String] = None,
+              headers: Map[String, String] = Map.empty): HttpResolver = {
+      val config = ConfigFactory.load().getConfig("languages.WDL.http-allow-list")
+      val allowListEnabled = config.as[Option[Boolean]]("enabled").getOrElse(false)
+      val allowList: Option[List[String]] =
+        if (allowListEnabled)
+          config.as[Option[List[String]]]("allowed-http-hosts")
+        else None
+
+      new HttpResolver(relativeTo, headers, allowList)
+    }
+
     val sttpBackend: IntrospectableLazy[SttpBackend[IO, Nothing]] = lazily {
       // 2.13 Beginning with sttp 1.6.x a `ContextShift` parameter is now required to construct an
       // `AsyncHttpClientCatsBackend`. There may be a more appropriate choice for backing this than the global
diff --git a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
index 26249b02da1..813a688a573 100644
--- a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
+++ b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
@@ -1,7 +1,8 @@
 package cromwell.languages.util
 
-import java.nio.file.{Files, Paths}
+import com.softwaremill.sttp._
 
+import java.nio.file.{Files, Paths}
 import common.assertion.CromwellTimeoutSpec
 import common.assertion.ErrorOrAssertions._
 import cromwell.core.WorkflowId
@@ -41,13 +42,13 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   it should "resolve a path from no initial root" in {
-    val resolver = HttpResolver()
+    val resolver = HttpResolver(None, Map.empty, None)
     val toResolve = resolver.pathToLookup("http://abc.com:8000/blah1/blah2.wdl")
     toResolve shouldBeValid "http://abc.com:8000/blah1/blah2.wdl"
   }
 
   it should "resolve a path and store the import in ResolvedImportRecord" in {
-    val resolver = HttpResolver()
+    val resolver = HttpResolver(None, Map.empty, None)
     val importUri = "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.wdl"
     val resolvedBundle = resolver.innerResolver(importUri, List(resolver))
 
@@ -57,10 +58,42 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     }
   }
 
+  behavior of "HttpResolver with allowList"
+
+  val allowList = Option(List("my.favorite.wdls.com", "anotherwdlsite.org"))
+  val pathEnd = "bob/loblaw/blah/blah.wdl"
+
+  it should "allow any import when there is no allow list" in {
+    val resolver = HttpResolver(None, Map.empty, None)
+    resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"http://some-garbage.whatever.eu/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"localhost:8080/my/secrets") shouldBe true
+  }
+
+  it should "allow any import that's on the allow list" in {
+    val resolver = HttpResolver(None, Map.empty, allowList)
+    resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"http://anotherwdlsite.org/$pathEnd") shouldBe true
+    resolver.isAllowed(uri"https://yetanotherwdlsite.org/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://FOO.my.favorite.wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"localhost:8080/my/secrets") shouldBe false
+  }
+
+  it should "allow nothing with an empty allow list" in {
+    val resolver = HttpResolver(None, Map.empty, Option(List.empty))
+    resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"http://anotherwdlsite.org/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://yetanotherwdlsite.org/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://FOO.my.favorite.wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"https://wdls.com/$pathEnd") shouldBe false
+    resolver.isAllowed(uri"localhost:8080/my/secrets") shouldBe false
+  }
+
   behavior of "HttpResolver with a 'relativeTo' value"
 
-  val relativeHttpResolver = HttpResolver(relativeTo = Some("http://abc.com:8000/blah1/blah2/"))
-  val relativeToGithubHttpResolver = HttpResolver(relativeTo = Some(relativeToGithubRoot))
+  val relativeHttpResolver = HttpResolver(relativeTo = Some("http://abc.com:8000/blah1/blah2/"), Map.empty, None)
+  val relativeToGithubHttpResolver = HttpResolver(relativeTo = Some(relativeToGithubRoot), Map.empty, None)
 
   it should "resolve an absolute path from a different initial root" in {
     val pathToLookup = relativeHttpResolver.pathToLookup("http://def.org:8080/blah3.wdl")
diff --git a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
index df87f2fa644..b96cfa5c2f6 100644
--- a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
+++ b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
@@ -61,7 +61,7 @@ class NamespaceCacheSpec extends AnyFlatSpec with CromwellTimeoutSpec with Befor
     )
 
     var lookupCount = 0
-    val countingResolver = new HttpResolver() {
+    val countingResolver = new HttpResolver(None, Map.empty, None) {
       override def pathToLookup(str: String): Checked[String] = {
         lookupCount = lookupCount + 1
         super.pathToLookup(str)
diff --git a/mkdocs.yml b/mkdocs.yml
index 68e73560774..7aea4302d34 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -79,7 +79,6 @@ nav:
     - Integration tests: developers/Centaur.md
     - Security: developers/Security.md
     - Contribute to docs: developers/Contribute.md
-    - CWL Parsing: developers/CwlParsing.md
     - Bitesize Design Docs:
         - Workflow Parsing & Graph Construction:
             - What is WOM?: developers/bitesize/workflowParsing/whatIsWom.md
@@ -87,7 +86,6 @@ nav:
                 - Overview: developers/bitesize/workflowParsing/wdlParsingOverview.md
                 - From WDL to WDLOM: developers/bitesize/workflowParsing/wdlToWdlom.md
                 - Adding new WDL Engine Functions: developers/bitesize/workflowParsing/engineFunctionAddition.md
-            - From CWL Source to WOM: developers/bitesize/workflowParsing/cwlParsingOverview.md
         - Cromwell Actor System:
             - High level view: developers/bitesize/majorActorSystem/5000FtActorSystem.md
             - Workflow Execution:
diff --git a/processes/release_processes/README.MD b/processes/release_processes/README.MD
index d16f97fddef..5dffe3224a5 100644
--- a/processes/release_processes/README.MD
+++ b/processes/release_processes/README.MD
@@ -2,30 +2,31 @@
 
 ## How to update these processes
 
-Have a better idea about how the deployment processes should work? 
+Have a better idea about how the deployment processes should work?
 See our "updating the process" [process](../README.MD)!
 
 ## Core Process: How to Publish and Release Cromwell
 
-If you're the lucky "Release Rotation Engineer" this time, you should do the following four things:
+Cromwell versions are updated on a weekly cadence automatically. For more information see [here](https://support.terra.bio/hc/en-us/articles/9512163608731-Faster-Cromwell-updates-in-Terra-)
 
-1. Create a Jira ticket for the release (look at previous release tickets if you're not sure how). In the Suggested 
+Manually cutting a numeric release is expected to continue being done on a cadence of every ~6 months. If you're the lucky "Release Rotation Engineer" this time, you should do the following four things:
+
+1. Create a Jira ticket for the release (look at previous release tickets if you're not sure how). In the Suggested
 Release Notes field, add "Terra is now running Cromwell <version>" along with any other release notes relevant to Terra
 users.
-1. Check that all most recent executions of Cromwell's Jenkins tests have succeeded, and that all those executions were 
-against the most recent commit in "develop" branch. There are 2 groups of Jenkins tests which have to be checked (you 
+1. Check that all most recent executions of Cromwell's Jenkins tests have succeeded, and that all those executions were
+against the most recent commit in "develop" branch. There are 2 groups of Jenkins tests which have to be checked (you
 will need to be on the Broad internal network or VPN to open the following links):
     1. Tests for various backends supported by Cromwell. Log into Jenkins [here](https://fc-jenkins.dsp-techops.broadinstitute.org), check the tests [here](https://fc-jenkins.dsp-techops.broadinstitute.org/job/cromwell-cron-parent/).
     1. Tests for Cromwell in Terra environment. Log into Jenkins [here](https://fc-jenkins.dsp-techops.broadinstitute.org), check the tests [here](https://fc-jenkins.dsp-techops.broadinstitute.org/view/Batch/).
-1. [Run the publish script to create a new version of Cromwell](#how-to-publish-a-new-cromwell-version)  
-1. [Run through the "How to Release Cromwell into Firecloud/Terra" process](#how-to-release-cromwell-into-firecloud--terra)  
-1. [Run through the "How to Deploy Cromwell in CaaS prod" process](#how-to-deploy-cromwell-in-caas-staging-and-caas-prod)  
+1. [Run the publish script to create a new version of Cromwell](#how-to-publish-a-new-cromwell-version)
+1. [Run through the "How to Deploy Cromwell in CaaS prod" process](#how-to-deploy-cromwell-in-caas-staging-and-caas-prod)
 
 ### How to publish a new Cromwell version
 
 #### Announce your intentions
 
-Post a message in `#dsp-batch-private` letting people know that a publish is imminent in case there are PRs they want to get
+Post a message in `#dsp-workflows-private` letting people know that a publish is imminent in case there are PRs they want to get
 wrapped up and merged to `develop` to go out in the forthcoming version of Cromwell.
 
 #### Get a Github token
@@ -45,7 +46,8 @@ The release WDL uses a github token to perform actions on your behalf.
 Make or copy the following files into a temporary `release/` directory outside the Cromwell repository. This removes any chance of committing your token.
 
 * A copy of the workflow file to run (https://github.com/broadinstitute/cromwell/blob/develop/publish/publish_workflow.wdl)
-* An inputs json like this:
+* An inputs json like this one.
+  * `publishHomebrew` is `false` due to Homebrew taking on this part themselves. Homebrew remains an active distribution channel.
 
 ```json
 {
@@ -82,7 +84,7 @@ The workflow outputs its status to the console.
 
 #### Make sure it all went swimmingly
 
-* Check that the workflow succeeded. 
+* Check that the workflow succeeded.
 * Check that there's now a new Cromwell release listed [here](https://github.com/broadinstitute/cromwell/releases).
 * Look [in Travis](https://app.travis-ci.com/github/broadinstitute/cromwell/branches) for the release tag build that will publish Docker images for the new version.
 * Let `#dsp-batch-private` know that it's okay to resume merges to `develop`.
@@ -92,17 +94,6 @@ The workflow outputs its status to the console.
     * See the `cromwell::build::publish_artifacts()` function for details
 * **One business day later,** confirm that [the Homebrew package](https://formulae.brew.sh/formula/cromwell) has the latest version. If it doesn't, start investigation by looking at [Homebrew PR's](https://github.com/Homebrew/homebrew-core/pulls?q=is%3Apr+cromwell).
 
-### How to Release Cromwell into Firecloud / Terra
-
-**Note:** If the Cromwell CHANGELOG indicates that the upgrade might take some time (e.g., because of a database migration), checking in with the release engineer
-and user support/comms to let them know that the upgrade may involve downtime is also required. You may need to help draft an impact statement and co-ordinate timing
-the deploy to make sure user impact in minimized.
-
-**Note:** How to accomplish some of these steps might be non-obvious to you (e.g., generating the release notes).
-If so, refer to the additional details in the [full document](https://docs.google.com/document/d/1EEzwemE8IedCplIwL506fiqXr0262Pz4G0x6Cr6V-5E). 
-
-![firecloud-develop](firecloud-develop.dot.png) 
-
 ### How to Deploy Cromwell in CaaS staging and CaaS prod
 
 CaaS is "Cromwell as a Service". It is used by a couple of Broad teams (Pipelines and Epigenomics), though the long-term plan is for those teams to migrate to using Terra.
@@ -110,7 +101,7 @@ CaaS is "Cromwell as a Service". It is used by a couple of Broad teams (Pipeline
 **Note:** If the Cromwell CHANGELOG indicates that the upgrade might take some time (e.g., because of a database migration), checking in with the CaaS users
 to let them know that the upgrade is about to happen is a good idea.
 
-Deploying to CaaS is detailed in the [Quick CaaS Deployment Guide](https://docs.google.com/document/d/1s0YC-oohJ7o-OGcgnH_-YBtIEKmLIPTRpG36yvWxUpE) 
+Deploying to CaaS is detailed in the [Quick CaaS Deployment Guide](https://docs.google.com/document/d/1s0YC-oohJ7o-OGcgnH_-YBtIEKmLIPTRpG36yvWxUpE)
 
 ### How to be Sure You're Done
 
@@ -139,7 +130,7 @@ This generates the client library and runs the generated tests as well.  A succe
 [success] Total time: 4 s, completed Jun 26, 2019 3:01:19 PM
 ```
 
-To publish to artifactory, first obtain the artifactory username and credentials.  Then run
+To publish to artifactory, first obtain the artifactory username and credentials. Credentials are located in Vault at path `secret/dsde/cromwell/common/cromwell-artifactory`. Then run
 
 ```
 export ARTIFACTORY_USERNAME=<the-username>
@@ -147,8 +138,10 @@ export ARTIFACTORY_PASSWORD=<the-password>
 ./scripts/publish-client.sh
 ```
 
+A SNAP version of the client library will be published in jFrog at [this path](https://broadinstitute.jfrog.io/ui/repos/tree/General/libs-release-local/org/broadinstitute/cromwell).
+
 ## Cromwell setup for publishing
 
 One can run a publishing-friendly Cromwell using a containerized MySQL server and config files
-from Cromwell's CI. See the `start_publish_mysql_docker.sh` and `start_publish_cromwell.sh` 
+from Cromwell's CI. See the `start_publish_mysql_docker.sh` and `start_publish_cromwell.sh`
 scripts under `release_processes/scripts`.
diff --git a/project/ContinuousIntegration.scala b/project/ContinuousIntegration.scala
index 321ac0a69ab..e2b61994c22 100644
--- a/project/ContinuousIntegration.scala
+++ b/project/ContinuousIntegration.scala
@@ -67,9 +67,7 @@ object ContinuousIntegration {
   /**
     * For "reasons" these projects are excluded from the root aggregation in build.sbt.
     */
-  private val unaggregatedProjects = Map(
-    "cwlEncoder" -> "not sure what this is"
-  )
+  private val unaggregatedProjects = Map.empty
 
   /**
     * Get the list of projects defined in build.sbt excluding the passed in root project.
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 519c13d4c37..5be942f6d38 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -6,13 +6,12 @@ object Dependencies {
   private val akkaV = "2.5.32" // scala-steward:off (CROM-6637)
   private val ammoniteOpsV = "2.4.1"
   private val apacheHttpClientV = "4.5.13"
-  private val awsSdkV = "2.17.152"
+  private val awsSdkV = "2.17.265"
   // We would like to use the BOM to manage Azure SDK versions, but SBT doesn't support it.
   // https://github.com/Azure/azure-sdk-for-java/tree/main/sdk/boms/azure-sdk-bom
   // https://github.com/sbt/sbt/issues/4531
-  private val azureStorageBlobNioV = "12.0.0-beta.18"
-  private val azureIdentitySdkV = "1.4.2"
-  private val azureKeyVaultSdkV = "4.3.7"
+  private val azureStorageBlobNioV = "12.0.0-beta.19"
+  private val azureIdentitySdkV = "1.4.6"
   private val betterFilesV = "3.9.1"
   /*
   cats-effect, fs2, http4s, and sttp (also to v3) should all be upgraded at the same time to use cats-effect 3.x.
@@ -30,11 +29,11 @@ object Dependencies {
   private val commonsLang3V = "3.12.0"
   private val commonsMathV = "3.6.1"
   private val commonNetV = "3.8.0" // via: https://commons.apache.org/proper/commons-net/
-  private val commonsTextV = "1.9"
+  private val commonsTextV = "1.10.0"
   private val configsV = "0.6.1"
   private val delightRhinoSandboxV = "0.0.15"
   private val diffsonSprayJsonV = "4.1.1"
-  private val ficusV = "1.5.1"
+  private val ficusV = "1.5.2"
   private val fs2V = "2.5.9" // scala-steward:off (CROM-6564)
   private val googleApiClientV = "1.33.2"
   private val googleCloudBigQueryV = "2.10.0"
@@ -43,7 +42,7 @@ object Dependencies {
   private val googleCloudMonitoringV = "3.2.5"
   private val googleCloudNioV = "0.124.8"
   private val googleCloudStorageV = "2.9.2"
-  private val googleGaxGrpcV = "2.12.2"
+  private val googleGaxGrpcV = "2.19.0"
   // latest date via: https://mvnrepository.com/artifact/com.google.apis/google-api-services-genomics
   private val googleGenomicsServicesV2Alpha1ApiV = "v2alpha1-rev20210811-1.32.1"
   private val googleHttpClientApacheV = "2.1.2"
@@ -53,19 +52,24 @@ object Dependencies {
   private val googleOauth2V = "1.5.3"
   private val googleOauthClientV = "1.33.1"
   private val googleCloudResourceManagerV = "1.2.5"
-  private val grpcV = "1.45.0"
+  private val grpcV = "1.45.1"
   private val guavaV = "31.0.1-jre"
   private val heterodonV = "1.0.0-beta3"
   private val hsqldbV = "2.6.1"
   private val http4sV = "0.21.31" // this release is EOL. We need to upgrade further for cats3. https://http4s.org/versions/
   private val jacksonV = "2.13.3"
-  private val janinoV = "3.1.6"
+  private val jakartaActivationV = "1.2.1"
+  private val jakartaAnnotationV = "1.3.5"
+  private val jakartaInjectV = "2.6.1"
+  private val jakartaXmlBindApiV = "2.3.2"
+  private val janinoV = "3.1.7"
+  private val jerseyV = "2.32" // Use a jersey compatible with WSM. See notes in wsmDependencies below.
   private val jsr305V = "3.0.2"
   private val junitV = "4.13.2"
   private val kindProjectorV = "0.13.2"
   private val kittensV = "2.3.2"
   private val liquibaseV = "4.8.0"
-  private val logbackV = "1.2.10"
+  private val logbackV = "1.2.11"
   private val lz4JavaV = "1.8.0"
   private val mariadbV = "2.7.4"
   /*
@@ -75,9 +79,10 @@ object Dependencies {
   private val metrics4ScalaV = "4.2.8"
   private val metrics3StatsdV = "4.2.0"
   private val mockFtpServerV = "3.0.0"
-  private val mockitoV = "3.11.2"
-  private val mockserverNettyV = "5.11.2"
-  private val mouseV = "1.0.10"
+  private val mockitoV = "3.12.4"
+  private val mockserverNettyV = "5.14.0"
+  private val mouseV = "1.0.11"
+
   /*
   Newer version 8.0.29 fails `Control characters should work with metadata` Centaur tests, has charset changes mentioned in release notes
   https://dev.mysql.com/doc/relnotes/mysql/8.0/en/news-8-0-29.html#mysqld-8-0-29-charset
@@ -85,22 +90,23 @@ object Dependencies {
   private val mysqlV = "8.0.28"
   private val nettyV = "4.1.72.Final"
   private val owlApiV = "5.1.19"
-  private val postgresV = "42.3.3"
-  private val pprintV = "0.7.1"
+  private val postgresV = "42.4.1"
+  private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
-  private val refinedV = "0.9.28"
-  private val rhinoV = "1.7.13"
+  private val refinedV = "0.10.1"
+  private val rhinoV = "1.7.14"
+
   private val scalaCollectionCompatV = "2.5.0"
   private val scalaGraphV = "1.13.1"
-  private val scalaLoggingV = "3.9.4"
+  private val scalaLoggingV = "3.9.5"
   private val scalaPoolV = "0.4.3"
-  private val scalacticV = "3.2.10"
-  private val scalameterV = "0.19"
+  private val scalacticV = "3.2.13"
+  private val scalameterV = "0.21"
   private val scalatestV = "3.2.10"
   private val scalatestScalacheckV = scalatestV + ".0"
-  private val scoptV = "4.0.1"
-  private val sentryLogbackV = "5.2.4"
-  private val shapelessV = "2.3.7"
+  private val scoptV = "4.1.0"
+  private val sentryLogbackV = "5.7.4"
+  private val shapelessV = "2.3.9"
   private val simulacrumV = "1.0.1"
   private val slf4jV = "1.7.32"
   private val slickCatsV = "0.10.4"
@@ -116,14 +122,14 @@ object Dependencies {
     * https://github.com/slick/slick/pull/2201
   */
   private val slickV = "3.4.0-M1"
-  private val snakeyamlV = "1.30"
+  private val snakeyamlV = "1.33"
   private val sprayJsonV = "1.3.6"
   private val sttpV = "1.7.2"
   private val swaggerParserV = "1.0.56"
-  private val swaggerUiV = "4.5.0"
-  private val testContainersScalaV = "0.40.2"
+  private val swaggerUiV = "4.5.2"
+  private val testContainersScalaV = "0.40.10"
   private val tikaV = "2.3.0"
-  private val typesafeConfigV = "1.4.1"
+  private val typesafeConfigV = "1.4.2"
   private val workbenchGoogleV = "0.21-5c9c4f6" // via: https://github.com/broadinstitute/workbench-libs/blob/develop/google/CHANGELOG.md
   private val workbenchModelV = "0.15-f9f0d4c" // via: https://github.com/broadinstitute/workbench-libs/blob/develop/model/CHANGELOG.md
   private val workbenchUtilV = "0.6-65bba14" // via: https://github.com/broadinstitute/workbench-libs/blob/develop/util/CHANGELOG.md
@@ -141,7 +147,8 @@ object Dependencies {
     "generic",
     "shapes",
     "refined",
-    "literal"
+    "literal",
+    "optics"
   ).map(m => "io.circe" %% s"circe-$m" % circeV) :+ circeYamlDependency :+
   "io.circe" %% "circe-generic-extras" % circeGenericExtrasV :+
   "io.circe" %% "circe-config" % circeConfigV
@@ -170,6 +177,16 @@ object Dependencies {
     "com.google.api-client" % "google-api-client-jackson2" % googleApiClientV
       exclude("com.google.guava", "guava-jdk5"),
     "com.google.cloud" % "google-cloud-resourcemanager" % googleCloudResourceManagerV,
+    /*
+    The google-cloud-java dependencies have similar issues with using an older javax.* vs. jakarta.* as guice.
+    google-cloud-java is still using javax.annotation and guice is sticking with javax.inject:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/google-cloud-java/blob/v0.201.0/google-cloud-jar-parent/pom.xml#L131-L136
+
+     Globally use of jakarta instead of javax until Google does themselves.
+     The javax.annotation exclusion is below in cromwellExcludeDependencies.
+     */
+    "jakarta.annotation" % "jakarta.annotation-api" % jakartaAnnotationV,
   )
 
   val spiDependencies: List[ModuleID] = List(
@@ -188,9 +205,38 @@ object Dependencies {
     "com.azure" % "azure-identity" % azureIdentitySdkV
       exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
       exclude("jakarta.activation", "jakarta.activation-api"),
-    "com.azure" % "azure-security-keyvault-secrets" % azureKeyVaultSdkV
-      exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
-      exclude("jakarta.activation", "jakarta.activation-api")
+    "com.azure" % "azure-core-management" % "1.7.1",
+    "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0"
+  )
+
+  val wsmDependencies: List[ModuleID] = List(
+    "bio.terra" % "workspace-manager-client" % "0.254.452-SNAPSHOT"
+      exclude("com.sun.activation", "jakarta.activation"),
+    /*
+    1. WSM is looking for the rs-api under javax.*.
+
+    Jersey 3.x switched to jakarta.ws.rs-api 3.x. If one uses jakarta's rs-api, 3.x will automatically evict 2.x.
+
+    However, jakarta's rs-api 2.x provides packages javax.* while 3.x provides jakarta.* instead.
+     - https://javadoc.io/doc/jakarta.ws.rs/jakarta.ws.rs-api/2.1.6/javax/ws/rs/package-summary.html
+     - https://javadoc.io/doc/jakarta.ws.rs/jakarta.ws.rs-api/3.1.0/jakarta.ws.rs/module-summary.html
+
+    TODO: Perhaps coordinate with the WSM team to use the jakarta 3.x rs-api and jakarta.* instead of javax.*.
+
+    2. Use the exact version of jersey that WSM is using.
+
+    Jersey libraries cannot be mixed and matched as the various modules cannot be mixed and matched.
+    For example jersey-client 2.32 is not compatible with jersey-common 2.37.
+
+    If needed one may also explicitly enumerate the list of jersey artifacts and explicitly set the versions similar to
+    catsDepeendencies, akkaHttpDependencies, etc.
+     - https://broadinstitute.jfrog.io/ui/repos/tree/PomView/libs-snapshot-local/bio/terra/workspace-manager-client/0.254.452-SNAPSHOT/workspace-manager-client-0.254.452-20221114.190249-1.pom
+     - https://github.com/eclipse-ee4j/jersey/blob/2.32/core-client/src/main/java/org/glassfish/jersey/client/ClientExecutorProvidersConfigurator.java#L139
+     - https://github.com/eclipse-ee4j/jersey/blob/2.37/core-client/src/main/java/org/glassfish/jersey/client/ClientExecutorProvidersConfigurator.java#L136-L137
+     */
+    "org.glassfish.jersey.inject" % "jersey-hk2" % jerseyV
+      exclude("com.sun.activation", "jakarta.activation"),
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
   )
 
   val implFtpDependencies = List(
@@ -236,7 +282,13 @@ object Dependencies {
     "org.codehaus.janino" % "janino" % janinoV,
     // Replace all log4j usage with slf4j
     // https://www.slf4j.org/legacy.html#log4j-over-slf4j
-    "org.slf4j" % "log4j-over-slf4j" % slf4jV
+    "org.slf4j" % "log4j-over-slf4j" % slf4jV,
+    // Replace all commons-logging usage with slf4j
+    // https://www.slf4j.org/legacy.html#jcl-over-slf4j
+    "org.slf4j" % "jcl-over-slf4j" % slf4jV,
+    // Enable runtime replacing of java.util.logging usage with slf4j
+    // https://www.slf4j.org/legacy.html#jul-to-slf4j
+    "org.slf4j" % "jul-to-slf4j" % slf4jV,
   ) ++ slf4jFacadeDependencies
 
   private val slickDependencies = List(
@@ -246,7 +298,11 @@ object Dependencies {
   )
 
   private val liquibaseDependencies = List(
+    // The XML bind API replacement below may be removed when this ticket is addressed:
+    // https://github.com/liquibase/liquibase/issues/2991
     "org.liquibase" % "liquibase-core" % liquibaseV
+      exclude("javax.xml.bind", "jaxb-api"),
+    "jakarta.xml.bind" % "jakarta.xml.bind-api" % jakartaXmlBindApiV,
   )
 
   private val akkaDependencies = List(
@@ -319,15 +375,24 @@ object Dependencies {
   private val googleCloudDependencies = List(
     "io.grpc" % "grpc-core" % grpcV,
     "com.google.guava" % "guava" % guavaV,
+    /*
+    The google-cloud-nio has the same problems with an ancient inject as guice:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/java-storage-nio/blob/v0.124.20/google-cloud-nio/pom.xml#L49-L53
+
+     Force use of jakarta instead of javax until Google does themselves.
+     */
     "com.google.cloud" % "google-cloud-nio" % googleCloudNioV
       exclude("com.google.api.grpc", "grpc-google-common-protos")
       exclude("com.google.cloud.datastore", "datastore-v1-protos")
+      exclude("javax.inject", "javax.inject")
       exclude("org.apache.httpcomponents", "httpclient"),
     "org.broadinstitute.dsde.workbench" %% "workbench-google" % workbenchGoogleV
       exclude("com.google.apis", "google-api-services-genomics"),
     "org.apache.httpcomponents" % "httpclient" % apacheHttpClientV,
     "com.google.apis" % "google-api-services-cloudkms" % googleCloudKmsV
-      exclude("com.google.guava", "guava-jdk5")
+      exclude("com.google.guava", "guava-jdk5"),
+    "org.glassfish.hk2.external" % "jakarta.inject" % jakartaInjectV,
   ) ++ googleGenomicsV2Alpha1Dependency ++ googleLifeSciencesV2BetaDependency
 
   private val dbmsDependencies = List(
@@ -403,7 +468,7 @@ object Dependencies {
     List("scalatest", "mysql", "mariadb", "postgresql")
       .map(name => "com.dimafeng" %% s"testcontainers-scala-$name" % testContainersScalaV % Test)
 
-  val blobFileSystemDependencies: List[ModuleID] = azureDependencies
+  val blobFileSystemDependencies: List[ModuleID] = azureDependencies ++ wsmDependencies
 
   val s3FileSystemDependencies: List[ModuleID] = junitDependencies
 
@@ -427,56 +492,23 @@ object Dependencies {
   val languageFactoryDependencies = List(
     "com.softwaremill.sttp" %% "core" % sttpV,
     "com.softwaremill.sttp" %% "async-http-client-backend-cats" % sttpV
+      exclude("com.sun.activation", "javax.activation"),
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
   )
 
   val draft2LanguageFactoryDependencies = List(
     "org.mock-server" % "mockserver-netty" % mockserverNettyV % Test
   )
 
-  /*
-  The distro artifact contains the actual impl, but transitively includes OSGI bundles that conflict with assembly:
-  - https://github.com/owlcs/owlapi/wiki/Documentation/45d8f63d055f820c6ac2ca6c4679a2a7b705449b#howto
-  - https://github.com/owlcs/owlapi/issues/455
-  - https://github.com/owlcs/owlapi/issues/603
-
-  jcl-over-slf4j.jar is a replacement for commons-logging 1.1.1. Meanwhile our extensive transitive use of apache's
-  httpclient has been including commons-logging 1.2 for a while. Now the owl api dependency jcl-over-slf4j is
-  conflicting during assembly. As there have been no reported errors AFAIK with commons-logging leaving it in for now.
-  However as we use slf4j for cromwell log configuration the correct thing might actually be to exclude commons-logging
-  whenever importing httpclient and include jcl-over-slf4j. That way we can control all of our logging in one place.
-
-  - https://www.slf4j.org/legacy.html#jclOverSLF4J
-   */
-  val owlApiDependencies = List(
-    "net.sourceforge.owlapi" % "owlapi-distribution" % owlApiV
-      exclude("org.apache.httpcomponents", "httpclient-osgi")
-      exclude("org.apache.httpcomponents", "httpcore-osgi")
-      exclude("org.slf4j", "jcl-over-slf4j"),
-    "org.apache.httpcomponents" % "httpclient-cache" % apacheHttpClientV,
-    "org.apache.httpcomponents" % "httpclient" % apacheHttpClientV
-  )
-
-  val cwlDependencies: List[ModuleID] = List(
-    "com.lihaoyi" %% "ammonite-ops" % ammoniteOpsV,
-    "org.broadinstitute" % "heterodon" % heterodonV classifier "single",
-    "org.scalactic" %% "scalactic" % scalacticV,
-    "io.circe" %% "circe-optics" % circeOpticsV,
-    "org.mozilla" % "rhino" % rhinoV,
-    "org.javadelight" % "delight-rhino-sandbox" % delightRhinoSandboxV,
-    "commons-io" % "commons-io" % commonsIoV % Test
-  ) ++ betterFilesDependencies ++ owlApiDependencies
-
   val womtoolDependencies: List[ModuleID] = catsDependencies ++ slf4jBindingDependencies
 
-  val centaurCwlRunnerDependencies: List[ModuleID] = List(
-    "com.github.scopt" %% "scopt" % scoptV,
-    "io.circe" %% "circe-optics" % circeOpticsV
-  ) ++ slf4jBindingDependencies
-
   val coreDependencies: List[ModuleID] = List(
     "com.google.auth" % "google-auth-library-oauth2-http" % googleOauth2V,
     "com.chuusai" %% "shapeless" % shapelessV,
-    "com.storm-enroute" %% "scalameter" % scalameterV % Test,
+    // NOTE: See scalameter comment under engineDependencies
+    "com.storm-enroute" %% "scalameter" % scalameterV % Test
+      exclude("com.fasterxml.jackson.module", "jackson-module-scala_2.13")
+      exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.github.scopt" %% "scopt" % scoptV,
   ) ++ akkaStreamDependencies ++ configDependencies ++ catsDependencies ++ circeDependencies ++
     googleApiClientDependencies ++ statsDDependencies ++ betterFilesDependencies ++
@@ -502,10 +534,24 @@ object Dependencies {
   val engineDependencies: List[ModuleID] = List(
     "commons-codec" % "commons-codec" % commonsCodecV,
     "commons-io" % "commons-io" % commonsIoV,
+    /*
+    Maybe ScalaMeter should be used, but is anyone?
+
+    For now keep its dependencies from breaking jackson for other libraries. If someone wants to use it they can
+    re-fight with dependency-hell at that point.
+
+    Avoid:
+    "com.fasterxml.jackson.databind.JsonMappingException: Scala module 2.11.3 requires Jackson Databind
+    version >= 2.11.0 and < 2.12.0":
+     - https://scalameter.github.io/home/gettingstarted/0.7/sbt/index.html
+     - https://github.com/FasterXML/jackson-module-scala/blob/jackson-module-scala-2.11.3/src/main/scala/com/fasterxml/jackson/module/scala/JacksonModule.scala#L53-L62
+     */
     "com.storm-enroute" %% "scalameter" % scalameterV
       exclude("com.fasterxml.jackson.core", "jackson-databind")
       exclude("com.fasterxml.jackson.module", "jackson-module-scala")
-      exclude("org.scala-tools.testing", "test-interface"),
+      exclude("com.fasterxml.jackson.module", "jackson-module-scala_2.13")
+      exclude("org.scala-tools.testing", "test-interface")
+      exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.fasterxml.jackson.core" % "jackson-databind" % jacksonV,
     "io.github.andrebeat" %% "scala-pool" % scalaPoolV
   ) ++ swaggerUiDependencies ++ akkaHttpDependencies ++ akkaHttpCirceIntegrationDependency ++ circeDependencies ++
@@ -519,11 +565,24 @@ object Dependencies {
   val serverDependencies: List[ModuleID] = slf4jBindingDependencies
 
   val cromiamDependencies: List[ModuleID] = List(
+    /*
+    sttp 1.x was last released in 2019
+    See above comment regarding "cats-effect, fs2, http4s, and sttp" all needing to update together.
+    For now, replace sttp 1.x's com.sun.activation usage with the jakarta version.
+
+    NOTE when upgrading: sttp 3.x no longer requires an async-http-client-backend-future so jakarta.activation can
+    probably be removed from the dependencies:
+     - https://sttp.softwaremill.com/en/v3/backends/future.html#using-async-http-client
+     - https://sttp.softwaremill.com/en/v2/backends/future.html#using-async-http-client
+     - https://sttp.softwaremill.com/en/v1/backends/asynchttpclient.html
+     */
     "com.softwaremill.sttp" %% "core" % sttpV,
-    "com.softwaremill.sttp" %% "async-http-client-backend-future" % sttpV,
+    "com.softwaremill.sttp" %% "async-http-client-backend-future" % sttpV
+      exclude("com.sun.activation", "javax.activation"),
     "com.typesafe.scala-logging" %% "scala-logging" % scalaLoggingV,
     "org.broadinstitute.dsde.workbench" %% "workbench-model" % workbenchModelV,
-    "org.broadinstitute.dsde.workbench" %% "workbench-util" % workbenchUtilV
+    "org.broadinstitute.dsde.workbench" %% "workbench-util" % workbenchUtilV,
+    "jakarta.activation" % "jakarta.activation-api" % jakartaActivationV,
   ) ++ akkaHttpDependencies ++ swaggerUiDependencies ++ slf4jBindingDependencies
 
   val wes2cromwellDependencies: List[ModuleID] = coreDependencies ++ akkaHttpDependencies
@@ -542,7 +601,9 @@ object Dependencies {
     "org.scalatest" %% "scalatest" % scalatestV,
     // Use mockito Java DSL directly instead of the numerous and often hard to keep updated Scala DSLs.
     // See also scaladoc in common.mock.MockSugar and that trait's various usages.
-    "org.mockito" % "mockito-core" % mockitoV
+    "org.mockito" % "mockito-core" % mockitoV,
+    "io.github.jbwheatley" %% "pact4s-scalatest"  % "0.7.0",
+    "io.github.jbwheatley" %% "pact4s-circe" %  "0.7.0"
   ) ++ slf4jBindingDependencies // During testing, add an slf4j binding for _all_ libraries.
 
   val kindProjectorPlugin = "org.typelevel" % "kind-projector" % kindProjectorV cross CrossVersion.full
@@ -560,18 +621,17 @@ object Dependencies {
     "com.iheart" %% "ficus" % ficusV,
     "com.softwaremill.sttp" %% "circe" % sttpV,
     "com.github.scopt" %% "scopt" % scoptV,
+    "org.apache.commons" % "commons-csv" % commonsCsvV,
   ) ++ circeDependencies ++ catsDependencies ++ slf4jBindingDependencies ++ languageFactoryDependencies ++ azureDependencies
 
   val allProjectDependencies: List[ModuleID] =
     backendDependencies ++
-      centaurCwlRunnerDependencies ++
       centaurDependencies ++
       cloudSupportDependencies ++
       commonDependencies ++
       coreDependencies ++
       cromiamDependencies ++
       cromwellApiClientDependencies ++
-      cwlDependencies ++
       databaseMigrationDependencies ++
       databaseSqlDependencies ++
       draft2LanguageFactoryDependencies ++
@@ -722,4 +782,22 @@ object Dependencies {
       nimbusdsOverrides ++
       bouncyCastleOverrides ++
       protobufJavaOverrides
+
+  /*
+  Libraries that should be globally excluded.
+   */
+  val cromwellExcludeDependencies: List[ExclusionRule] = List(
+    // Replaced with jcl-over-slf4j
+    ExclusionRule("commons-logging", "commons-logging"),
+    /*
+    The google-cloud-java dependencies have similar issues with using an older javax.* vs. jakarta.* as guice.
+    google-cloud-java is still using javax.annotation and guice is sticking with javax.inject:
+     - https://github.com/google/guice/issues/1383
+     - https://github.com/googleapis/google-cloud-java/blob/v0.201.0/google-cloud-jar-parent/pom.xml#L131-L136
+
+     Globally use of jakarta instead of javax until Google does themselves.
+     The jakarta.annotation inclusion is above in googleApiClientDependencies.
+     */
+    ExclusionRule("javax.annotation", "javax.annotation-api"),
+  )
 }
diff --git a/project/GenerateRestApiDocs.scala b/project/GenerateRestApiDocs.scala
index afb1168fa5c..9173a25c3c5 100644
--- a/project/GenerateRestApiDocs.scala
+++ b/project/GenerateRestApiDocs.scala
@@ -1,13 +1,12 @@
-import java.time.OffsetDateTime
-import java.time.format.DateTimeFormatter
-
-import io.github.swagger2markup.Swagger2MarkupConverter
 import io.github.swagger2markup.builder.Swagger2MarkupConfigBuilder
-import io.github.swagger2markup.markup.builder.MarkupLanguage
+import io.github.swagger2markup.{MarkupLanguage, Swagger2MarkupConverter}
 import org.apache.commons.lang3.{ClassUtils, StringUtils}
 import sbt.Keys._
 import sbt._
 
+import java.time.OffsetDateTime
+import java.time.format.DateTimeFormatter
+
 /**
   * Provides a task to generate the REST API markdown from the Swagger YAML.
   *
diff --git a/project/Publishing.scala b/project/Publishing.scala
index 150c30ca293..1d4143fc13e 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -36,7 +36,20 @@ object Publishing {
       ArrayBuffer(broadinstitute/cromwell:dev, broadinstitute/cromwell:develop)
     */
     dockerTags := {
-      val versionsCsv = if (Version.isSnapshot) version.value else s"$cromwellVersion,${version.value}"
+      val versionsCsv = if (Version.isSnapshot) {
+        // Tag looks like `85-443a6fc-SNAP`
+        version.value
+      } else {
+        if (Version.isRelease) {
+          // Tags look like `85`, `85-443a6fc`
+          s"$cromwellVersion,${version.value}"
+        } else {
+          // Tag looks like `85-443a6fc`
+          version.value
+        }
+      }
+
+      // Travis applies (as of 10/22) the `dev` and `develop` tags on merge to `develop`
       sys.env.getOrElse("CROMWELL_SBT_DOCKER_TAGS", versionsCsv).split(",")
     },
     docker / imageNames := dockerTags.value map { tag =>
@@ -137,6 +150,10 @@ object Publishing {
     "Broad Artifactory" at
       "https://broadinstitute.jfrog.io/broadinstitute/libs-release/"
 
+  private val broadArtifactoryResolverSnap: Resolver =
+    "Broad Artifactory Snapshots" at
+      "https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot-local/"
+
   // https://stackoverflow.com/questions/9819965/artifactory-snapshot-filename-handling
   private val buildTimestamp = System.currentTimeMillis() / 1000
 
@@ -146,6 +163,7 @@ object Publishing {
 
   val additionalResolvers = List(
     broadArtifactoryResolver,
+    broadArtifactoryResolverSnap,
     Resolver.sonatypeRepo("releases")
   )
 
diff --git a/project/Settings.scala b/project/Settings.scala
index 79242733583..797d7917dd9 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -70,7 +70,7 @@ object Settings {
     assembly / assemblyMergeStrategy := customMergeStrategy.value,
   )
 
-  val Scala2_13Version = "2.13.8"
+  val Scala2_13Version = "2.13.9"
   private val ScalaVersion: String = Scala2_13Version
   private val sharedSettings: Seq[Setting[_]] =
     cromwellVersionWithGit ++ publishingSettings ++ List(
@@ -86,6 +86,7 @@ object Settings {
       Tags.limit(Tags.Test, 1)
     ),
     dependencyOverrides ++= cromwellDependencyOverrides,
+    excludeDependencies ++= cromwellExcludeDependencies,
     scalacOptions ++= baseSettings ++ warningSettings ++ consoleHostileSettings,
     // http://stackoverflow.com/questions/31488335/scaladoc-2-11-6-fails-on-throws-tag-with-unable-to-find-any-member-to-link#31497874
     Compile / doc / scalacOptions ++= baseSettings ++ List("-no-link-warnings"),
diff --git a/project/Version.scala b/project/Version.scala
index 80f74d66d3f..ca782b990e2 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -1,19 +1,31 @@
 import Dependencies._
-import com.typesafe.sbt.SbtGit._
+import com.github.sbt.git.SbtGit._
 import sbt.Keys._
 import sbt._
+import com.github.sbt.git.SbtGit
 
 object Version {
   // Upcoming release, or current if we're on a master / hotfix branch
-  val cromwellVersion = "83"
+  val cromwellVersion = "85"
 
   /**
     * Returns true if this project should be considered a snapshot.
     *
     * The value is read in directly from the system property `project.isSnapshot` as there were confusing issues with
     * the multi-project and sbt.Keys#isSnapshot().
+    *
+    * Default `true`.
+    */
+  val isSnapshot: Boolean = sys.props.get("project.isSnapshot").forall(_.toBoolean)
+
+  /**
+    * Returns `true` if this project should tag a release like `85` in addition to a hash like `85-443a6fc`.
+    *
+    * Has no effect when `isSnapshot` is `true`.
+    *
+    * Default `true`.
     */
-  val isSnapshot = sys.props.get("project.isSnapshot").forall(_.toBoolean)
+  val isRelease: Boolean = sys.props.get("project.isRelease").forall(_.toBoolean)
 
   // Adapted from SbtGit.versionWithGit
   def cromwellVersionWithGit: Seq[Setting[_]] =
diff --git a/project/plugins.sbt b/project/plugins.sbt
index 51289a45e53..bdb54f675bf 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1,5 +1,6 @@
 addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.9.0")
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.0")
-addSbtPlugin("com.typesafe.sbt" % "sbt-git" % "1.0.2")
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.9.3")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.1")
+addSbtPlugin("com.github.sbt" % "sbt-git" % "2.0.0")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.4")
+addSbtPlugin("com.github.cb372" % "sbt-explicit-dependencies" % "0.2.16")
 addDependencyTreePlugin
diff --git a/project/swagger2markup.sbt b/project/swagger2markup.sbt
index 96f836bcc72..1fa882328f1 100644
--- a/project/swagger2markup.sbt
+++ b/project/swagger2markup.sbt
@@ -14,7 +14,7 @@ val jacksonV = "2.8.4"
 val javaslangV = "2.0.5"
 val plexusUtilsV = "3.0.22"
 val slf4jV = "1.7.21"
-val swagger2markupV = "1.3.3"
+val swagger2markupV = "1.3.4"
 
 resolvers ++= List(
   "JCenter" at "https://jcenter.bintray.com"
diff --git a/publish/publish_inputs.json b/publish/publish_inputs.json
index e9c54b9f3d6..ea877b9c34e 100644
--- a/publish/publish_inputs.json
+++ b/publish/publish_inputs.json
@@ -1,7 +1,7 @@
 {
-  "publish_workflow.githubToken": "<<REQUIRED: GithubAPIToken (value, not path)>>",
-  "publish_workflow.organization": "<<REQUIRED: broadinstitute for a real release, your github username if testing>>",
-  "publish_workflow.publishDocker": <<OPTIONAL: the docker image to use for publishing, default broadinstitute/cromwell-publish:latest>>,
-  "publish_workflow.majorRelease": <<OPTIONAL: true for a major release, false for a minor release, default true>>,
-  "publish_workflow.publishHomebrew": <<OPTIONAL: true to publish release to homebrew, false to skip, default true>>
+  "publish_workflow.githubToken": "<<GITHUB TOKEN VALUE>>",
+  "publish_workflow.majorRelease": true,
+  "publish_workflow.publishHomebrew": false,
+  "publish_workflow.publishDocker": "broadinstitute/cromwell-publish:latest",
+  "publish_workflow.organization": "broadinstitute"
 }
diff --git a/runConfigurations/Repo template_ CromIAM.run.xml b/runConfigurations/Repo template_ CromIAM.run.xml
index 420ee26cae1..7fa2a61acd7 100644
--- a/runConfigurations/Repo template_ CromIAM.run.xml	
+++ b/runConfigurations/Repo template_ CromIAM.run.xml	
@@ -7,4 +7,4 @@
       <option name="Make" enabled="true" />
     </method>
   </configuration>
-</component>
\ No newline at end of file
+</component>
diff --git a/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml b/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml
index 1ca941fbfa9..91b36d9277e 100644
--- a/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml	
+++ b/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml	
@@ -1,11 +1,11 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="Repo template: Cromwell DRS Localizer" type="Application" factoryName="Application">
     <envs>
-      <env name="MARTHA_URL" value="https://us-central1-broad-dsde-dev.cloudfunctions.net/martha_v3" />
+      <env name="DRS_RESOLVER_URL" value="https://drshub.dsde-dev.broadinstitute.org/api/v4/drs/resolve" />
     </envs>
     <option name="MAIN_CLASS_NAME" value="drs.localizer.DrsLocalizerMain" />
     <module name="cromwell-drs-localizer" />
-    <option name="PROGRAM_PARAMETERS" value="--access-token-strategy azure drs://jade.datarepo-dev.broadinstitute.org/v1_f3c32ddd-20eb-4033-9716-46866521a3a4_8d651e95-38ce-4bc8-a8a4-8a4cd9513db1 $USER_HOME$/Downloads/NA12878_PLUMBING_wgs.g.vcf.gz.tbi --vault-name vault --secret-name secret --identity-client-id identity" />
+    <option name="PROGRAM_PARAMETERS" value="--access-token-strategy azure drs://jade.datarepo-dev.broadinstitute.org/v1_f3c32ddd-20eb-4033-9716-46866521a3a4_8d651e95-38ce-4bc8-a8a4-8a4cd9513db1 $USER_HOME$/Downloads/NA12878_PLUMBING_wgs.g.vcf.gz.tbi --identity-client-id identity" />
     <method v="2">
       <option name="Make" enabled="true" />
     </method>
diff --git a/runConfigurations/Repo template_ Cromwell server TES.run.xml b/runConfigurations/Repo template_ Cromwell server TES.run.xml
new file mode 100644
index 00000000000..9cb1818a004
--- /dev/null
+++ b/runConfigurations/Repo template_ Cromwell server TES.run.xml	
@@ -0,0 +1,21 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="Repo template: Cromwell server TES" type="Application" factoryName="Application">
+    <option name="ALTERNATIVE_JRE_PATH" value="$USER_HOME$/.sdkman/candidates/java/current" />
+    <envs>
+      <env name="CROMWELL_BUILD_CENTAUR_SLICK_PROFILE" value="slick.jdbc.MySQLProfile$" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_DRIVER" value="com.mysql.cj.jdbc.Driver" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_URL" value="jdbc:mysql://localhost:3306/cromwell_test?allowPublicKeyRetrieval=true&amp;useSSL=false&amp;rewriteBatchedStatements=true&amp;serverTimezone=UTC&amp;useInformationSchema=true" />
+      <env name="CROMWELL_BUILD_RESOURCES_DIRECTORY" value="target/ci/resources" />
+      <env name="CROMWELL_BUILD_PAPI_JSON_FILE" value="target/ci/resources/cromwell-centaur-service-account.json" />
+      <env name="CROMWELL_BUILD_CENTAUR_READ_LINES_LIMIT" value="128000" />
+      <env name="CROMWELL_BUILD_CENTAUR_256_BITS_KEY" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA=" />
+    </envs>
+    <option name="MAIN_CLASS_NAME" value="cromwell.CromwellApp" />
+    <module name="cromwell" />
+    <option name="PROGRAM_PARAMETERS" value="server" />
+    <option name="VM_PARAMETERS" value="-Dconfig.file=target/ci/resources/tes_application.conf" />
+    <method v="2">
+      <option name="Make" enabled="true" />
+    </method>
+  </configuration>
+</component>
\ No newline at end of file
diff --git a/scripts/gen_java_client.sh b/scripts/gen_java_client.sh
index 409af51a83f..59642098b1d 100755
--- a/scripts/gen_java_client.sh
+++ b/scripts/gen_java_client.sh
@@ -4,6 +4,7 @@ BASE_PACKAGE="cromwell.client"
 
 ORIGINAL_API_YAML=engine/src/main/resources/swagger/cromwell.yaml
 API_YAML=codegen_java/cromwell.nofile.yaml
+OPENAPI_DOCKER="openapitools/openapi-generator-cli@sha256:ddd1b01cbe8f494c6612c548e91f983938164ab713a4d18d099a1fc4a77c651d"
 
 # Cromwell doesn't specify the OAuth configuration in its swagger, and
 # without it the client doesn't support authentication.
@@ -37,7 +38,7 @@ cat $ORIGINAL_API_YAML | sed s/type:\ file/type:\ string/g >> $API_YAML
 # generator's build.sbt with ours.
 # 1. Hide our build.sbt
 mv codegen_java/build.sbt codegen_java/build.sbt.bak
-docker run --rm -v ${PWD}:/local openapitools/openapi-generator-cli generate \
+docker run --rm -v ${PWD}:/local ${OPENAPI_DOCKER} generate \
   -i /local/$API_YAML \
   -g java \
   -o /local/codegen_java \
diff --git a/server/src/main/resources/application.conf b/server/src/main/resources/application.conf
index e0769277a6b..e80cd716b4e 100644
--- a/server/src/main/resources/application.conf
+++ b/server/src/main/resources/application.conf
@@ -1,6 +1,6 @@
 akka {
   log-dead-letters = "off"
-  loggers = ["akka.event.slf4j.Slf4jLogger"]
+  loggers = ["cromwell.core.logging.EnhancedSlf4jLogger"]
   logging-filter = "cromwell.server.CromwellAkkaLogFilter"
   actor.guardian-supervisor-strategy = "cromwell.core.CromwellUserGuardianStrategy"
 
diff --git a/server/src/main/resources/logback.xml b/server/src/main/resources/logback.xml
index 4868962f994..006ca3953f4 100644
--- a/server/src/main/resources/logback.xml
+++ b/server/src/main/resources/logback.xml
@@ -1,5 +1,15 @@
 <configuration>
 
+    <!-- Enhanced thread and date reporting. -->
+    <conversionRule
+            conversionWord="et"
+            converterClass="cromwell.core.logging.EnhancedThreadConverter"
+    />
+    <conversionRule
+            conversionWord="ed"
+            converterClass="cromwell.core.logging.EnhancedDateConverter"
+    />
+
     <!-- default properties for FILEROLLER need to be set upfront -->
 
     <if condition='property("FILEROLLER_DIR").equals("")'>
@@ -18,7 +28,7 @@
         <then>
             <appender name="STANDARD_APPENDER" class="ch.qos.logback.core.ConsoleAppender">
                 <encoder>
-                    <pattern>%date %X{sourceThread} %-5level - %msg%n</pattern>
+                    <pattern>%ed{yyyy-MM-dd HH:mm:ss,SSS} %et %-5level - %msg%n</pattern>
                 </encoder>
             </appender>
         </then>
@@ -68,7 +78,7 @@
 
                 </rollingPolicy>
                 <encoder>
-                    <pattern>%d{yyyy-MM-dd HH:mm:ss,SSS} [%thread] %-5level %logger{35} - %msg%n</pattern>
+                    <pattern>%ed{yyyy-MM-dd HH:mm:ss,SSS} [%et] %-5level %logger{35} - %msg%n</pattern>
                 </encoder>
             </appender>
         </then>
@@ -96,4 +106,7 @@
     <logger name="HikariPool" level="ERROR"/>
     <logger name="com.google.cloud.hadoop.gcsio.GoogleCloudStorageReadChannel" level="ERROR"/>
     <logger name="org.semanticweb.owlapi.utilities.Injector" level="ERROR"/>
+
+    <!-- Guilty of logging ERROR under non-erroneous conditions -->
+    <logger name="com.azure.storage.blob.nio" level="OFF"/>
 </configuration>
diff --git a/server/src/main/scala/cromwell/CommandLineArguments.scala b/server/src/main/scala/cromwell/CommandLineArguments.scala
index 8064c115b78..986a33a4dc2 100644
--- a/server/src/main/scala/cromwell/CommandLineArguments.scala
+++ b/server/src/main/scala/cromwell/CommandLineArguments.scala
@@ -5,21 +5,17 @@ import java.nio.file.InvalidPathException
 
 import better.files.File
 import cats.syntax.apply._
-import cats.syntax.either._
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
-import common.validation.IOChecked._
 import common.validation.Validation._
 import cromwell.CommandLineArguments._
 import cromwell.CromwellApp.Command
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import cromwell.webservice.PartialWorkflowSources
-import cwl.preprocessor.CwlFileReference
-import cwl.preprocessor.CwlPreProcessor
 import org.slf4j.Logger
 
-import scala.util.{Failure, Success, Try}
+import scala.util.{Failure, Success}
 
 object CommandLineArguments {
   val DefaultCromwellHost = new URL("http://localhost:8000")
@@ -46,41 +42,10 @@ case class CommandLineArguments(command: Option[Command] = None,
                                 metadataOutput: Option[Path] = None,
                                 host: URL = CommandLineArguments.DefaultCromwellHost
                                ) {
-  private lazy val cwlPreProcessor = new CwlPreProcessor()
-  private lazy val isCwl = workflowType.exists(_.equalsIgnoreCase("cwl"))
-
-  /*
-    * If the file is a relative local path, resolve it against the path of the input json.
-   */
-  private def inputFilesMapper(inputJsonPath: Path)(file: String) = {
-    DefaultPathBuilder.build(file) match {
-      case Success(path) if !path.isAbsolute => inputJsonPath.sibling(file).pathAsString
-      case _ => file
-    }
-  }
-
-  private def preProcessCwlInputFile(path: Path): ErrorOr[String] = {
-    cwlPreProcessor.preProcessInputFiles(path.contentAsString, inputFilesMapper(path)).toErrorOr
-  }
-
   def validateSubmission(logger: Logger): ErrorOr[ValidSubmission] = {
-    def preProcessCwlWorkflowSource(workflowSourcePath: Path): ErrorOr[String] = {
-      val workflowPath = File(workflowSourcePath.pathAsString)
-
-      logger.info("Pre Processing Workflow...")
-      lazy val preProcessedCwl = cwlPreProcessor.preProcessCwlToString(CwlFileReference(workflowPath, workflowRoot))
-
-      Try(preProcessedCwl.value.unsafeRunSync())
-        .toChecked
-        .flatMap(identity)
-        .toValidated
-    }
 
     def getWorkflowSourceFromPath(workflowPath: Path): ErrorOr[WorkflowSourceOrUrl] = {
-      (isCwl, imports) match {
-        case (true, None) => preProcessCwlWorkflowSource(workflowPath).map(src => WorkflowSourceOrUrl(Option(src), None))
-        case (true, Some(_)) | (false, _) => WorkflowSourceOrUrl(None, Option(workflowPath.pathAsString)).validNel
-      }
+      WorkflowSourceOrUrl(None, Option(workflowPath.pathAsString)).validNel
     }
 
     val workflowSourceAndUrl: ErrorOr[WorkflowSourceOrUrl] = DefaultPathBuilder.build(workflowSource.get) match {
@@ -93,10 +58,7 @@ case class CommandLineArguments(command: Option[Command] = None,
       case Failure(_) => PartialWorkflowSources.validateWorkflowUrl(workflowSource.get).map(validUrl => WorkflowSourceOrUrl(None, Option(validUrl)))
     }
 
-    val inputsJson: ErrorOr[String] = if (isCwl) {
-      logger.info("Pre Processing Inputs...")
-      workflowInputs.map(preProcessCwlInputFile).getOrElse(readOptionContent("Workflow inputs", workflowInputs))
-    } else readOptionContent("Workflow inputs", workflowInputs)
+    val inputsJson: ErrorOr[String] = readOptionContent("Workflow inputs", workflowInputs)
 
     import common.validation.ErrorOr.ShortCircuitingFlatMap
     val optionsJson = readOptionContent("Workflow options", workflowOptions).flatMap { WorkflowOptions.fromJsonString(_).toErrorOr }
diff --git a/server/src/main/scala/cromwell/CromwellEntryPoint.scala b/server/src/main/scala/cromwell/CromwellEntryPoint.scala
index 5acddd75ce9..a1707db6488 100644
--- a/server/src/main/scala/cromwell/CromwellEntryPoint.scala
+++ b/server/src/main/scala/cromwell/CromwellEntryPoint.scala
@@ -16,6 +16,7 @@ import cromwell.CommandLineArguments.{ValidSubmission, WorkflowSourceOrUrl}
 import cromwell.CromwellApp._
 import cromwell.api.CromwellClient
 import cromwell.api.model.{Label, LabelsJsonFormatter, WorkflowSingleSubmission}
+import cromwell.core.logging.JavaLoggingBridge
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import cromwell.core.{WorkflowSourceFilesCollection, WorkflowSourceFilesWithDependenciesZip, WorkflowSourceFilesWithoutImports}
 import cromwell.engine.workflow.SingleWorkflowRunnerActor
@@ -166,6 +167,13 @@ object CromwellEntryPoint extends GracefulStopSupport {
     Make sure that the next time one uses the ConfigFactory that our updated system properties are loaded.
      */
     ConfigFactory.invalidateCaches()
+
+    /*
+    Replace java.util.logging with SLF4J.
+    https://www.slf4j.org/api/org/slf4j/bridge/SLF4JBridgeHandler.html
+     */
+    JavaLoggingBridge.init()
+
     ()
   }
 
diff --git a/server/src/test/resources/cwl_glob_sort.cwl b/server/src/test/resources/cwl_glob_sort.cwl
deleted file mode 100644
index 330c896eea6..00000000000
--- a/server/src/test/resources/cwl_glob_sort.cwl
+++ /dev/null
@@ -1,16 +0,0 @@
-cwlVersion: v1.0
-class: CommandLineTool
-requirements:
-  - class: InlineJavascriptRequirement
-hints:
-  DockerRequirement:
-    dockerPull: "debian:stretch-slim"
-inputs: []
-baseCommand: [touch, z, y, x, w, c, b, a]
-outputs:
-  letters:
-    type: string
-    outputBinding:
-      glob: '?'
-      outputEval: |
-        ${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(" ") }
diff --git a/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala b/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
index 58d2154f9b7..41b1edccb36 100644
--- a/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
+++ b/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
@@ -95,32 +95,6 @@ class CromwellCommandLineSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     validation.get.workflowUrl shouldBe Option(url)
   }
 
-  it should "run single when supplying cwl workflow" in {
-    val source = raw"""{"cwlVersion":"v1.0","class":"CommandLineTool","requirements":[{"class":"InlineJavascriptRequirement"}],"hints":[{"dockerPull":"debian:stretch-slim","class":"DockerRequirement"}],"inputs":[],"baseCommand":["touch","z","y","x","w","c","b","a"],"outputs":[{"type":"string","outputBinding":{"glob":"?","outputEval":"$${ return self.sort(function(a,b) { return a.location > b.location ? 1 : (a.location < b.location ? -1 : 0) }).map(f => f.basename).join(\" \") }\n""""
-    val command = parser.parse(Array("run", "server/src/test/resources/cwl_glob_sort.cwl", "--type", "CWL"), CommandLineArguments()).get
-
-    command.command shouldBe Some(Run)
-    command.workflowSource.get shouldBe "server/src/test/resources/cwl_glob_sort.cwl"
-
-    val validation = Try(CromwellEntryPoint.validateRunArguments(command))
-    validation.isSuccess shouldBe true
-    validation.get.workflowSource.get should include(source)
-    validation.get.workflowUrl shouldBe None
-  }
-
-  it should "run single when supplying cwl workflow using url" in {
-    val url = "https://path_to_url"
-    val command = parser.parse(Array("run", url, "--type", "CWL"), CommandLineArguments()).get
-
-    command.command shouldBe Some(Run)
-    command.workflowSource.get shouldBe url
-
-    val validation = Try(CromwellEntryPoint.validateRunArguments(command))
-    validation.isSuccess shouldBe true
-    validation.get.workflowSource shouldBe None
-    validation.get.workflowUrl shouldBe Option(url)
-  }
-
   it should "run single when supplying wdl and inputs and options" in {
     val optionsLast = parser.parse(Array("run", "3step.wdl", "--inputs", "3step.inputs", "--options", "3step.options"), CommandLineArguments()).get
     optionsLast.command shouldBe Some(Run)
diff --git a/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala b/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
index ab47dedeb5c..d9de71b9125 100644
--- a/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
@@ -2,7 +2,6 @@ package cromwell.engine.workflow
 
 import java.time.OffsetDateTime
 import java.util.concurrent.atomic.AtomicInteger
-
 import akka.actor.{Actor, ActorRef, ActorSystem, Kill, Props}
 import akka.testkit.{EventFilter, TestActorRef, TestFSMRef, TestProbe}
 import com.typesafe.config.{Config, ConfigFactory}
@@ -15,10 +14,10 @@ import cromwell.engine.backend.BackendSingletonCollection
 import cromwell.engine.workflow.WorkflowActor._
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowActorWorkComplete
 import cromwell.engine.workflow.lifecycle.EngineLifecycleActorAbortCommand
-import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{WorkflowExecutionAbortedResponse, WorkflowExecutionFailedResponse, WorkflowExecutionSucceededResponse}
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{ExecuteWorkflowCommand, WorkflowExecutionAbortedResponse, WorkflowExecutionFailedResponse, WorkflowExecutionSucceededResponse}
 import cromwell.engine.workflow.lifecycle.finalization.CopyWorkflowLogsActor
 import cromwell.engine.workflow.lifecycle.finalization.WorkflowFinalizationActor.{StartFinalizationCommand, WorkflowFinalizationSucceededResponse}
-import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{WorkflowInitializationAbortedResponse, WorkflowInitializationFailedResponse}
+import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{StartInitializationCommand, WorkflowInitializationAbortedResponse, WorkflowInitializationFailedResponse, WorkflowInitializationSucceededResponse}
 import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.MaterializeWorkflowDescriptorFailureResponse
 import cromwell.engine.workflow.workflowstore.{StartableState, Submitted, WorkflowHeartbeatConfig, WorkflowToStart}
 import cromwell.engine.{EngineFilesystems, EngineWorkflowDescriptor}
@@ -60,6 +59,8 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
     createMaterializedEngineWorkflowDescriptor(WorkflowId.randomId(), workflowSources = workflowSources)
   val supervisorProbe: TestProbe = TestProbe("supervisorProbe")
   val deathwatch: TestProbe = TestProbe("deathwatch")
+  val initializationProbe: TestProbe = TestProbe("initializationProbe")
+  val executionProbe: TestProbe = TestProbe("executionProbe")
   val finalizationProbe: TestProbe = TestProbe("finalizationProbe")
   var copyWorkflowLogsProbe: TestProbe = _
   val AwaitAlmostNothing: FiniteDuration = 100.milliseconds
@@ -78,7 +79,7 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 
   private val workflowHeartbeatConfig = WorkflowHeartbeatConfig(ConfigFactory.load())
 
-  private def createWorkflowActor(state: WorkflowActorState, extraPathBuilderFactory: Option[PathBuilderFactory] = None) = {
+  private def createWorkflowActor(state: WorkflowActorState, extraPathBuilderFactory: Option[PathBuilderFactory] = None, initializationMaxRetries: Int = 3, initializationInterval: FiniteDuration = 10.millis) = {
     val actor = TestFSMRef(
       factory = new WorkflowActorWithTestAddons(
         finalizationProbe = finalizationProbe,
@@ -102,7 +103,11 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
         workflowStoreActor = system.actorOf(Props.empty, s"workflowStoreActor-$currentWorkflowId"),
         workflowHeartbeatConfig = workflowHeartbeatConfig,
         totalJobsByRootWf = initialJobCtByRootWf,
-        extraPathBuilderFactory = extraPathBuilderFactory
+        extraPathBuilderFactory = extraPathBuilderFactory,
+        initializationMaxRetries = initializationMaxRetries,
+        initializationInterval = initializationInterval,
+        workflowInitializationActorProbe = initializationProbe,
+        workflowExecutionActorProbe = executionProbe
       ),
       supervisor = supervisorProbe.ref,
       name = s"workflowActor-$currentWorkflowId",
@@ -124,10 +129,17 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 
   "WorkflowActor" should {
 
-    "run Finalization actor if Initialization fails" in {
-      val actor = createWorkflowActor(InitializingWorkflowState)
+    "run Finalization actor if Initialization repeatedly fails" in {
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationMaxRetries = 3)
       deathwatch watch actor
-      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Materialization Failed")))
+
+      // Expect the WorkflowActor to retry up to three times:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (2)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (3)")))
+
       finalizationProbe.expectMsg(StartFinalizationCommand)
       actor.stateName should be(FinalizingWorkflowState)
       actor ! WorkflowFinalizationSucceededResponse
@@ -136,6 +148,24 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       deathwatch.expectTerminated(actor)
     }
 
+    "begin execution if Initialization eventually succeeds" in {
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationMaxRetries = 3)
+      deathwatch watch actor
+
+      // Expect the WorkflowActor to retry up to three times:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (2)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationSucceededResponse(AllBackendInitializationData(Map.empty))
+
+      executionProbe.expectMsg(ExecuteWorkflowCommand)
+      actor.stateName should be(ExecutingWorkflowState)
+      // Tidy up (and satisfy the deathwatch):
+      system.stop(actor)
+      deathwatch.expectTerminated(actor)
+    }
+
     "run Finalization actor if Initialization is aborted" in {
       val actor = createWorkflowActor(InitializingWorkflowState)
       deathwatch watch actor
@@ -151,6 +181,56 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       deathwatch.expectTerminated(actor)
     }
 
+    "run Finalization actor if Initialization is aborted during a retry" in {
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationInterval = 1.second)
+      deathwatch watch actor
+
+      // Set the stage with a few unfortunate retries:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (2)")))
+      initializationProbe.expectMsg(StartInitializationCommand)
+
+      actor ! AbortWorkflowCommand
+      eventually { actor.stateName should be(WorkflowAbortingState) }
+      // Because we failed a few times, the actor test's initial "currentLifecycleActor will have been replaced by this
+      // new initializationProbe:
+      initializationProbe.expectMsgPF(TimeoutDuration) {
+        case EngineLifecycleActorAbortCommand => actor ! WorkflowInitializationAbortedResponse
+      }
+
+      finalizationProbe.expectMsg(StartFinalizationCommand)
+      actor.stateName should be(FinalizingWorkflowState)
+      actor ! WorkflowFinalizationSucceededResponse
+      workflowManagerActorExpectsSingleWorkCompleteNotification(WorkflowAborted)
+      deathwatch.expectTerminated(actor)
+    }
+
+    "run Finalization actor if Initialization is aborted between retries" in {
+      // Set the interval long so that we can guarantee the "between retries" part
+      val actor = createWorkflowActor(InitializingWorkflowState, initializationInterval = 10.seconds)
+      deathwatch watch actor
+
+      // Set the stage with a few unfortunate retries:
+      actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
+      eventually { actor.stateData.currentLifecycleStateActor should be(None) }
+
+      actor ! AbortWorkflowCommand
+      // Because there are no active lifecycle actors, this actor should jump to Finalizing without
+      // needing any further input:
+      eventually { actor.stateName should be(FinalizingWorkflowState) }
+
+      // Expect the mailboxes for the initialization actor to be empty (and check "currentLifecycleActor" for good measure)
+      currentLifecycleActor.expectNoMessage(10.millis)
+      initializationProbe.expectNoMessage(10.millis)
+
+      finalizationProbe.expectMsg(StartFinalizationCommand)
+      actor.stateName should be(FinalizingWorkflowState)
+      actor ! WorkflowFinalizationSucceededResponse
+      workflowManagerActorExpectsSingleWorkCompleteNotification(WorkflowAborted)
+      deathwatch.expectTerminated(actor)
+    }
+
     "run Finalization if Execution fails" in {
       val actor = createWorkflowActor(ExecutingWorkflowState)
       deathwatch watch actor
@@ -283,7 +363,11 @@ class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
                                   workflowStoreActor: ActorRef,
                                   workflowHeartbeatConfig: WorkflowHeartbeatConfig,
                                   totalJobsByRootWf: AtomicInteger,
-                                  extraPathBuilderFactory: Option[PathBuilderFactory]) extends WorkflowActor(
+                                  extraPathBuilderFactory: Option[PathBuilderFactory],
+                                  initializationMaxRetries: Int,
+                                  initializationInterval: FiniteDuration,
+                                  workflowInitializationActorProbe: TestProbe,
+                                  workflowExecutionActorProbe: TestProbe) extends WorkflowActor(
   workflowToStart = WorkflowToStart(id = workflowId,
     submissionTime = OffsetDateTime.now,
     state = startState,
@@ -310,6 +394,12 @@ class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
   fileHashCacheActorProps = None,
   blacklistCache = None) {
 
+  override def createInitializationActor(workflowDescriptor: EngineWorkflowDescriptor, name: String): ActorRef = workflowInitializationActorProbe.ref
+  override def createWorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor, data: WorkflowActorData): ActorRef = workflowExecutionActorProbe.ref
+
+  override val initializationRetryInterval: FiniteDuration = initializationInterval
+  override val maxInitializationAttempts: Int = initializationMaxRetries
+
   override val pathBuilderFactories: List[PathBuilderFactory] = extraPathBuilderFactory match {
     case Some(pbf) => EngineFilesystems.configuredPathBuilderFactories :+ pbf
     case None => EngineFilesystems.configuredPathBuilderFactories
diff --git a/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala b/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
index fd1864d45f0..4df3f966db6 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
@@ -143,7 +143,7 @@ object SelectiveTsvInstrumentationServiceActor {
 
       val header = (List("timestamp") ++ interestingFields).mkString("\t")
       val rows = stateHistory.map { case (timestamp, fieldMap) =>
-        (Vector(timestamp.toString) ++ interestingFields.map(f => fieldMap.getOrElse(f, 0))).mkString("\t")
+        (Vector(timestamp.toString) ++ interestingFields.map(f => fieldMap.getOrElse(f, 0).toString)).mkString("\t")
       }
       Vector(header) ++ rows
     }
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
index 8e6029140e9..2a812419775 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
@@ -287,7 +287,7 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         }
         // Filter by workflow id within random Ids
         _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          (randomIds :+ workflow1Id).map(id => WorkflowQueryKey.Id.name -> id.toString))) map { case (response, _) =>
+          (randomIds :+ workflow1Id.toString).map(id => WorkflowQueryKey.Id.name -> id))) map { case (response, _) =>
           val resultsById = response.results groupBy {
             _.name
           }
diff --git a/src/ci/bin/testSingleWorkflowRunner.sh b/src/ci/bin/testSingleWorkflowRunner.sh
index ce8e3e4c65e..fcf0f626822 100755
--- a/src/ci/bin/testSingleWorkflowRunner.sh
+++ b/src/ci/bin/testSingleWorkflowRunner.sh
@@ -92,26 +92,3 @@ if [ $retVal -eq 0 ]; then
 else
     grep "Error: Unknown argument" console_output.txt
 fi
-
-# Test 5: application should run cwl with inputs
-STANDARD_TEST_CASES="$PWD/centaur/src/main/resources/standardTestCases/cwl_run"
-pushd "$STANDARD_TEST_CASES" > /dev/null
-
-java -jar ${CROMWELL_BUILD_CROMWELL_JAR} run ./1st-tool.cwl --inputs ./echo-job.yml --metadata-output ./run_mode_metadata.json | tee console_output.txt
-
-cat > expected.json <<FIN
-{
-  "actualWorkflowLanguage": "CWL",
-  "actualWorkflowLanguageVersion": "v1.0",
-  "status": "Succeeded"
-}
-FIN
-
-jq '{
-  actualWorkflowLanguage,
-  actualWorkflowLanguageVersion,
-  status
-}' run_mode_metadata.json > actual.json
-
-cmp <(jq -cS . actual.json) <(jq -cS . expected.json)
-popd > /dev/null
diff --git a/src/ci/resources/papi_application.inc.conf.ctmpl b/src/ci/resources/papi_application.inc.conf.ctmpl
index 9d6a06428dd..04d6690a6ba 100644
--- a/src/ci/resources/papi_application.inc.conf.ctmpl
+++ b/src/ci/resources/papi_application.inc.conf.ctmpl
@@ -63,7 +63,7 @@ services {
   }
 }
 
-filesystems.drs.global.config.martha.url = "https://us-central1-broad-dsde-dev.cloudfunctions.net/martha_v3"
+filesystems.drs.global.config.resolver.url = "https://drshub.dsde-dev.broadinstitute.org/api/v4/drs/resolve"
 
 drs {
   localization {
diff --git a/src/ci/resources/papi_v2_reference_image_manifest.conf b/src/ci/resources/papi_v2_reference_image_manifest.conf
index 8c15fc44636..ef12cef1b66 100644
--- a/src/ci/resources/papi_v2_reference_image_manifest.conf
+++ b/src/ci/resources/papi_v2_reference_image_manifest.conf
@@ -1,4819 +1,346 @@
 reference-disk-localization-manifests = [
   {
-    "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/broad-references-disk-image",
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-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03722.disc.txt.gz",
-      "crc32c" : 3830060763
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.sift.ndb",
+      "crc32c" : 2786880382
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03850.split.txt.gz",
-      "crc32c" : 2027997385
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20220512.nsi",
+      "crc32c" : 3787486272
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG01607.disc.txt.gz.tbi",
-      "crc32c" : 3618792688
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa",
+      "crc32c" : 3105778103
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00150.split.txt.gz.tbi",
-      "crc32c" : 3924662460
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa",
+      "crc32c" : 1821283507
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19001.split.txt.gz.tbi",
-      "crc32c" : 2885759998
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa",
+      "crc32c" : 1393836085
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18507.split.txt.gz",
-      "crc32c" : 878012894
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa",
+      "crc32c" : 2730251112
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG03694.disc.txt.gz",
-      "crc32c" : 4263331124
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.transcripts.ndb",
+      "crc32c" : 2114520493
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA20869.split.txt.gz",
-      "crc32c" : 1886106057
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MultiZ100Way_20171006.pcs",
+      "crc32c" : 1251171842
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG00129.disc.txt.gz.tbi",
-      "crc32c" : 3192168410
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_155.nsa.idx",
+      "crc32c" : 2183408606
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA18995.split.txt.gz",
-      "crc32c" : 4228428215
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsa",
+      "crc32c" : 482110804
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/NA19443.disc.txt.gz",
-      "crc32c" : 2064476647
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_155.nsa",
+      "crc32c" : 1654978963
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/pesr/HG02010.split.txt.gz",
-      "crc32c" : 2709469910
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/Cache/GRCh38/Both.polyphen.ndb",
+      "crc32c" : 3178180885
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-159.tar.gz",
-      "crc32c" : 1399388866
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/TOPMed_freeze_5.nsa.idx",
+      "crc32c" : 3807477399
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-137.tar.gz",
-      "crc32c" : 2834363733
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_SV_2.1.nsi",
+      "crc32c" : 2600275374
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-144.tar.gz",
-      "crc32c" : 3432942434
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_disease_validity_curations_20220512.nga",
+      "crc32c" : 4116422668
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-32.tar.gz",
-      "crc32c" : 688658120
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/OMIM_20220516.nga",
+      "crc32c" : 1767833806
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-84.tar.gz",
-      "crc32c" : 2362020576
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa",
+      "crc32c" : 710316739
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-66.tar.gz",
-      "crc32c" : 373531354
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/GME_20160618.nsa.idx",
+      "crc32c" : 1732177354
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-241.tar.gz",
-      "crc32c" : 1320364908
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa.idx",
+      "crc32c" : 245207854
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-107.tar.gz",
-      "crc32c" : 462909423
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa",
+      "crc32c" : 4136875677
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-134.tar.gz",
-      "crc32c" : 1188579016
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsi",
+      "crc32c" : 1056818502
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-43.tar.gz",
-      "crc32c" : 2098432647
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/GME_20160618.nsa",
+      "crc32c" : 1210977352
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-47.tar.gz",
-      "crc32c" : 1722109761
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus.nsa.idx",
+      "crc32c" : 870728029
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-28.tar.gz",
-      "crc32c" : 3161256248
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_LCR_2.1.lcr",
+      "crc32c" : 3602069872
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-197.tar.gz",
-      "crc32c" : 852592090
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/PrimateAI_0.2.nsa.idx",
+      "crc32c" : 2835194789
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-140.tar.gz",
-      "crc32c" : 4051126385
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_Dosage_Sensitivity_Map_20220512.nga",
+      "crc32c" : 2485206803
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-121.tar.gz",
-      "crc32c" : 623697692
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_SV_20200819.nsi",
+      "crc32c" : 1378887803
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-182.tar.gz",
-      "crc32c" : 2255237725
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/REVEL_20200205.nsa.idx",
+      "crc32c" : 302652747
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-273.tar.gz",
-      "crc32c" : 2368431717
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinGen_20160414.nsi",
+      "crc32c" : 1181611304
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-269.tar.gz",
-      "crc32c" : 3912509849
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/SpliceAi_1.3.nsa.idx",
+      "crc32c" : 980438557
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-4.tar.gz",
-      "crc32c" : 1832890207
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DECIPHER_201509.nsi",
+      "crc32c" : 2426309371
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-194.tar.gz",
-      "crc32c" : 2371872678
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/DANN_20200205.gsa",
+      "crc32c" : 3457097933
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-232.tar.gz",
-      "crc32c" : 645276377
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_3.1.2.nsa.idx",
+      "crc32c" : 3582543830
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-81.tar.gz",
-      "crc32c" : 615405862
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/COSMIC_GeneFusions_94.gfj",
+      "crc32c" : 429830169
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-61.tar.gz",
-      "crc32c" : 3254549888
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/dbSNP_151_globalMinor.nsa.idx",
+      "crc32c" : 37093822
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/sv-resources/ref-panel/1KG/gcnv/case-gcnv-model-files-256.tar.gz",
-      "crc32c" : 2225664241
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/FusionCatcher_1.33.gfs",
+      "crc32c" : 1420426876
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/genomestrip/Homo_sapiens_assembly38.vdjregions.bed",
-      "crc32c" : 665778154
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_(SV)_Phase_3_v5a.nsi",
+      "crc32c" : 2492681982
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/genomestrip/Homo_sapiens_assembly38.gcprof.zip",
-      "crc32c" : 954030109
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa.idx",
+      "crc32c" : 2375984948
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0008_of_50/scattered.interval_list",
-      "crc32c" : 2145467013
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/ClinVar_20220505.nsa.idx",
+      "crc32c" : 1539516090
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0038_of_50/scattered.interval_list",
-      "crc32c" : 1218417681
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma",
+      "crc32c" : 1696693985
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0019_of_50/scattered.interval_list",
-      "crc32c" : 2638902162
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/Gerp_20110522.gsa.idx",
+      "crc32c" : 3139541733
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/scattered_calling_intervals/temp_0047_of_50/scattered.interval_list",
-      "crc32c" : 1761876709
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/MITOMAP_20200819.nsa",
+      "crc32c" : 1721491427
     }, {
-      "path" : "gcp-public-data--broad-references/hg38/v0/CrossSpeciesContamination/CrossSpeciesContaminant/pathseq_microbe.fa.img",
-      "crc32c" : 2373170979
+      "path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/gnomAD_3.1.2.nsa",
+      "crc32c" : 4247114985
     } ]
   }
 ]
diff --git a/src/ci/resources/tes_application.conf b/src/ci/resources/tes_application.conf
index 018c13829d8..7f4c42a7d58 100644
--- a/src/ci/resources/tes_application.conf
+++ b/src/ci/resources/tes_application.conf
@@ -1,16 +1,68 @@
 include required(classpath("application.conf"))
 include "build_application.inc.conf"
 
+filesystems {
+  blob {
+    class = "cromwell.filesystems.blob.BlobPathBuilderFactory"
+    global {
+      # One BFSM is shared across all BlobPathBuilders
+      class = "cromwell.filesystems.blob.BlobFileSystemManager"
+      config {
+        container: "cromwell"
+        endpoint: "https://<storage-account>.blob.core.windows.net"
+        subscription: "00001111-2222-3333-aaaa-bbbbccccdddd"
+        # WSM config is needed for accessing WSM-managed blob containers
+        # created in Terra workspaces.
+        workspace-manager {
+          url: "https://workspace.dsde-dev.broadinstitute.org"
+          workspace-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
+          container-resource-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
+          b2cToken: "Zardoz"
+        }
+      }
+    }
+  }
+}
+
+engine {
+  filesystems {
+    local {
+      enabled: true
+    }
+    http {
+      enabled: true
+    }
+    blob {
+      enabled: false
+    }
+  }
+}
+
+
 backend {
   default = "TES"
   providers {
     TES {
       actor-factory = "cromwell.backend.impl.tes.TesBackendLifecycleActorFactory"
       config {
+        # Use for running on blob storage
+        #root = "https://<storage-account>.blob.core.windows.net/cromwell/cromwell-executions"
         root = "cromwell-executions"
         dockerRoot = "/cromwell-executions"
         endpoint = "http://127.0.0.1:9000/v1/tasks"
         concurrent-job-limit = 1000
+        transform-blob-to-local-path = false
+        filesystems {
+          blob {
+            enabled: false
+          }
+          local {
+            enabled: true
+          }
+          http {
+            enabled: true
+          }
+        }
       }
 
       # Have the engine (maybe) authenticate to docker.io. See BT-141 for more info.
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 8d2464a8ee3..87ef19e80cb 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -33,6 +33,7 @@ package cromwell.backend.impl.aws
 
 import java.net.SocketTimeoutException
 import java.io.FileNotFoundException
+import java.nio.file.Paths
 
 import akka.actor.ActorRef
 import akka.pattern.AskSupport
@@ -46,11 +47,12 @@ import common.util.StringUtil._
 import common.validation.Validation._
 
 import cromwell.backend._
-import cromwell.backend.async._ //{ExecutionHandle, PendingExecutionHandle}
+import cromwell.backend.async._ 
 import cromwell.backend.impl.aws.IntervalLimitedAwsJobSubmitActor.SubmitAwsJobRequest
 import cromwell.backend.impl.aws.OccasionalStatusPollingActor.{NotifyOfStatus, WhatsMyStatus}
 import cromwell.backend.impl.aws.RunStatus.{Initializing, TerminalRunStatus}
 import cromwell.backend.impl.aws.io._
+
 import cromwell.backend.io.DirectoryFunctions
 import cromwell.backend.io.JobPaths
 import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
@@ -80,6 +82,7 @@ import scala.concurrent.duration._
 import scala.language.postfixOps
 import scala.util.control.NoStackTrace
 import scala.util.{Success, Try, Failure}
+
 /**
   * The `AwsBatchAsyncBackendJobExecutionActor` creates and manages a job. The job itself is encapsulated by the
   * functionality in `AwsBatchJob`
@@ -175,6 +178,10 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
    * commandScriptContents here
    */
 
+   /* part of the full commandScriptContents is overriden here, in the context of mixed S3/EFS support with globbing. 
+      we'll see how much we need...
+    */ 
+
   lazy val cmdScript = configuration.fileSystem match {
      case AWSBatchStorageSystems.s3 => commandScriptContents.toEither.toOption.get
      case _ => execScript
@@ -239,6 +246,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         }
         Seq(AwsBatchFileInput(s"$namePrefix-$index", remotePath.valueString, DefaultPathBuilder.get(localPathString), workingDisk))
     }
+    
   }
 
   /**
@@ -250,12 +258,17 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   override protected def relativeLocalizationPath(file: WomFile): WomFile = {
     file.mapFile(value =>
       getPath(value) match {
-        case Success(path) =>
+        // for s3 paths :
+        case Success(path: S3Path) =>
           configuration.fileSystem match  {
-            case AWSBatchStorageSystems.s3 => path.pathWithoutScheme
-            case _ =>  path.toString
+            case AWSBatchStorageSystems.s3 => 
+                path.pathWithoutScheme
+            case _ =>  
+                path.toString
           }
-        case _ => value
+        // non-s3 paths
+        case _ => 
+            value
       }
     )
   }
@@ -287,11 +300,11 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
           case womFile: WomFile => womFile
         }
     }
-
+    
     val callInputInputs = callInputFiles flatMap {
       case (name, files) => inputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor, true)
     }
-
+    // this is a list : AwsBatchInput(name_in_wf, origin_such_as_s3, target_in_docker_relative, target_in_docker_disk[name mount] )
     val scriptInput: AwsBatchInput = AwsBatchFileInput(
       "script",
       jobPaths.script.pathAsString,
@@ -313,11 +326,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     def getAbsolutePath(path: Path) = {
       configuration.fileSystem match {
         case AWSBatchStorageSystems.s3 => AwsBatchWorkingDisk.MountPoint.resolve(path)
-        // case _ => DefaultPathBuilder.get(configuration.root).resolve(path)
-        case _ => 
-            Log.info("non-s3 path detected")
-            Log.info(path.toString)
-            AwsBatchWorkingDisk.MountPoint.resolve(path)
+        case _ => AwsBatchWorkingDisk.MountPoint.resolve(path)
       }
     }
     
@@ -325,7 +334,6 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       case p if !p.isAbsolute => getAbsolutePath(p)
       case p => p
     }
-
     disks.find(d => absolutePath.startsWith(d.mountPoint)) match {
       case Some(disk) => (disk.mountPoint.relativize(absolutePath), disk)
       case None =>
@@ -350,10 +358,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       ).getOrElse(List.empty[WomFile].validNel)
        .getOrElse(List.empty)
     }
-
     val womFileOutputs = jobDescriptor.taskCall.callable.outputs.flatMap(evaluateFiles) map relativeLocalizationPath
-    Log.debug("WomFileOutputs:")
-    Log.debug(womFileOutputs.toString())
     val outputs: Seq[AwsBatchFileOutput] = womFileOutputs.distinct flatMap {
       _.flattenFiles flatMap {
         case unlistedDirectory: WomUnlistedDirectory => generateUnlistedDirectoryOutputs(unlistedDirectory)
@@ -363,17 +368,17 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     }
 
     val additionalGlobOutput = jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateAwsBatchGlobFileOutputs).toSet
-
+    
     outputs.toSet ++ additionalGlobOutput
   }
 
+
   // used by generateAwsBatchOutputs, could potentially move this def within that function
   private def generateUnlistedDirectoryOutputs(womFile: WomUnlistedDirectory): List[AwsBatchFileOutput] = {
     val directoryPath = womFile.value.ensureSlashed
     val directoryListFile = womFile.value.ensureUnslashed + ".list"
     val dirDestinationPath = callRootPath.resolve(directoryPath).pathAsString
     val listDestinationPath = callRootPath.resolve(directoryListFile).pathAsString
-
     val (_, directoryDisk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
 
     // We need both the collection directory and the collection list:
@@ -397,6 +402,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
   // used by generateAwsBatchOutputs, could potentially move this def within that function
   private def generateAwsBatchSingleFileOutputs(womFile: WomSingleFile): List[AwsBatchFileOutput] = {
+    // rewrite this to create more flexibility
+    // 
     val destination = configuration.fileSystem match {
       case  AWSBatchStorageSystems.s3 =>  callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
       case _ => DefaultPathBuilder.get(womFile.valueString) match {
@@ -406,26 +413,65 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
     }
     val (relpath, disk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
-    val output = AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), destination, relpath, disk)
+    
+    val output = if (configuration.efsMntPoint.isDefined && 
+                     configuration.efsMntPoint.getOrElse("").equals(disk.toString.split(" ")(1)) &&
+                     ! runtimeAttributes.efsDelocalize) {
+            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), makeSafeAwsBatchReferenceName(womFile.value), relpath, disk)
+        } else {
+            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), destination, relpath, disk)
+        }
     List(output)
   }
+  
+  // get a unique glob name locations & paths.
+  //  1. globName :md5 hash of local PATH and WF_ID
+  //  2. globbedDir : local path of the directory being globbed.
+  //  3. volume on which the globbed data is located (eg root, efs, ...)
+  //  4. target path for delocalization for globDir
+  //  5. target path for delocalization for globList
+  private def generateGlobPaths(womFile: WomGlobFile): (String, String, AwsBatchVolume,String, String) = {
+    // add workflow id to hash for better conflict prevention
+    val wfid = standardParams.jobDescriptor.toString.split(":")(0)
+    val globName = GlobFunctions.globName(s"${womFile.value}-${wfid}")
+    val globbedDir = Paths.get(womFile.value).getParent.toString
+    // generalize folder and list file
+    val globDirectory = DefaultPathBuilder.get(globbedDir + "/." + globName + "/")
+    val globListFile = DefaultPathBuilder.get(globbedDir + "/." + globName + ".list")
+
+    // locate the disk where the globbed data resides
+    val (_, globDirectoryDisk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
 
+    
+    val (globDirectoryDestinationPath, globListFileDestinationPath) = if (configuration.efsMntPoint.isDefined && 
+                     configuration.efsMntPoint.getOrElse("").equals(globDirectoryDisk.toString.split(" ")(1)) &&
+                     ! runtimeAttributes.efsDelocalize) {
+                        (globDirectory, globListFile)
+                     } else {
+                        (callRootPath.resolve(globDirectory).pathAsString, callRootPath.resolve(globListFile).pathAsString)
+                     }
+    // return results
+    return (
+        globName,
+        globbedDir,
+        globDirectoryDisk,
+        globDirectoryDestinationPath.toString,
+        globListFileDestinationPath.toString
+    )
+    
+  }
   // used by generateAwsBatchOutputs, could potentially move this def within that function
   private def generateAwsBatchGlobFileOutputs(womFile: WomGlobFile): List[AwsBatchFileOutput] = {
-    val globName = GlobFunctions.globName(womFile.value)
-    val globDirectory = globName + "/"
-    val globListFile = globName + ".list"
-    val globDirectoryDestinationPath = callRootPath.resolve(globDirectory).pathAsString
-    val globListFileDestinationPath = callRootPath.resolve(globListFile).pathAsString
-
-    val (_, globDirectoryDisk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
-
+    
+    val (globName, globbedDir, globDirectoryDisk, globDirectoryDestinationPath, globListFileDestinationPath) = generateGlobPaths(womFile)
+    val (relpathDir,_) = relativePathAndVolume(DefaultPathBuilder.get(globbedDir + "/." + globName + "/" + "*").toString,runtimeAttributes.disks)
+    val (relpathList,_) = relativePathAndVolume(DefaultPathBuilder.get(globbedDir + "/." + globName + ".list").toString,runtimeAttributes.disks)
     // We need both the glob directory and the glob list:
     List(
-      // The glob directory:
-      AwsBatchFileOutput(makeSafeAwsBatchReferenceName(globDirectory), globDirectoryDestinationPath, DefaultPathBuilder.get(globDirectory + "*"), globDirectoryDisk),
+      // The glob directory:.
+      AwsBatchFileOutput(DefaultPathBuilder.get(globbedDir.toString + "/." + globName + "/" + "*").toString,globDirectoryDestinationPath, relpathDir, globDirectoryDisk),
       // The glob list file:
-      AwsBatchFileOutput(makeSafeAwsBatchReferenceName(globListFile), globListFileDestinationPath, DefaultPathBuilder.get(globListFile), globDirectoryDisk)
+      AwsBatchFileOutput(DefaultPathBuilder.get(globbedDir.toString + "/." + globName + ".list").toString, globListFileDestinationPath, relpathList, globDirectoryDisk)
     )
   }
 
@@ -805,4 +851,57 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     }
   }
 
+
+
+  // overrides for globbing
+  /**
+    * Returns the shell scripting for linking a glob results file.
+    *
+    * @param globFile The glob.
+    * @return The shell scripting.
+    */
+  override def globScript(globFile: WomGlobFile): String = {
+    
+    val (globName, globbedDir, _, _, _) = generateGlobPaths(globFile) 
+    val controlFileName = "cromwell_glob_control_file"
+    val absoluteGlobValue = commandDirectory.resolve(globFile.value).pathAsString
+    val globDirectory = globbedDir + "/." + globName + "/"
+    val globList = globbedDir + "/." + globName + ".list"
+    val globLinkCommand: String = (if (configuration.globLinkCommand.isDefined) {
+       "( " + configuration.globLinkCommand.getOrElse("").toString + " )"
+
+    } else {
+        "( ln -L GLOB_PATTERN GLOB_DIRECTORY 2> /dev/null ) || ( ln GLOB_PATTERN GLOB_DIRECTORY )"
+    }).toString
+      .replaceAll("GLOB_PATTERN", absoluteGlobValue)
+      .replaceAll("GLOB_DIRECTORY", globDirectory)
+    // if on EFS : remove the globbing dir first, to remove leftover links from previous globs. 
+    val mkDirCmd : String = if (configuration.efsMntPoint.isDefined && globDirectory.startsWith(configuration.efsMntPoint.getOrElse(""))) {
+        jobLogger.warn("Globbing on EFS has risks.")
+        jobLogger.warn(s"The globbing target (${globbedDir}/.${globName}/) will be overwritten when existing!")
+        jobLogger.warn("Consider keeping globbed outputs in the cromwell-root folder")
+        s"rm -Rf $globDirectory $globList && mkdir"
+    } else {
+        "mkdir"
+    }
+ 
+    val controlFileContent =
+      """This file is used by Cromwell to allow for globs that would not match any file.
+        |By its presence it works around the limitation of some backends that do not allow empty globs.
+        |Regardless of the outcome of the glob, this file will not be part of the final list of globbed files.
+      """.stripMargin
+    
+    s"""|# make the directory which will keep the matching files
+        |$mkDirCmd $globDirectory
+        |
+        |# create the glob control file that will allow for the globbing to succeed even if there is 0 match
+        |echo "${controlFileContent.trim}" > $globDirectory/$controlFileName
+        |
+        |# hardlink or symlink all the files into the glob directory
+        |$globLinkCommand
+        |
+        |# list all the files (except the control file) that match the glob into a file called glob-[md5 of glob].list
+        |ls -1 $globDirectory | grep -v $controlFileName > $globList
+        |""".stripMargin
+  }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index cc019f51004..ecb6c87a457 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -61,7 +61,9 @@ case class AwsBatchAttributes(fileSystem: String,
                               fsxMntPoint: Option[List[String]],
                               efsMntPoint: Option[String],
                               efsMakeMD5: Option[Boolean],
-                              efsDelocalize: Option[Boolean]
+                              efsDelocalize: Option[Boolean],
+                              globLinkCommand: Option[String],
+                              checkSiblingMd5: Option[Boolean]
                               )
 
 object AwsBatchAttributes {
@@ -84,13 +86,11 @@ object AwsBatchAttributes {
     "numCreateDefinitionAttempts",
     "numSubmitAttempts",
     "default-runtime-attributes.scriptBucketName",
-    //"default-runtime-attributes.efsMountPoint",
-    //"default-runtime-attributes.efsMakeMD5",
-    //"default-runtime-attributes.efsDelocalize",
     "awsBatchRetryAttempts",
     "ulimits",
     "efsDelocalize",
-    "efsMakeMD5"
+    "efsMakeMD5",
+    "glob-link-command"
   )
 
   private val deprecatedAwsBatchKeys: Map[String, String] = Map(
@@ -108,7 +108,6 @@ object AwsBatchAttributes {
       val deprecatedKeys = keys.intersect(deprecated.keySet)
       deprecatedKeys foreach { key => logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}") }
     }
-
     def parseFSx(config: List[String]): Option[List[String]] = {
       config.isEmpty match {
         case true => None
@@ -116,7 +115,7 @@ object AwsBatchAttributes {
       }
     }
 
-    def parseEFS(config: String): Option[String] = {
+    def parseConfigString(config: String): Option[String] = {
       config.isEmpty match {
         case true => None
         case false => Some(config)
@@ -165,7 +164,7 @@ object AwsBatchAttributes {
 
     // EFS settings:
     val efsMntPoint:ErrorOr[Option[String]] = validate {backendConfig.hasPath("filesystems.local.efs") match {
-        case true => parseEFS(backendConfig.getString("filesystems.local.efs"))
+        case true => parseConfigString(backendConfig.getString("filesystems.local.efs"))
         case false => None
       }
     }
@@ -181,6 +180,20 @@ object AwsBatchAttributes {
             case false => None
       }
     }
+    // from config if set.
+    val globLinkCommand:ErrorOr[Option[String]] = validate {
+        backendConfig.hasPath("glob-link-command") match {
+            case true => Some(backendConfig.getString("glob-link-command"))
+            case false => None
+      }
+    }
+    // from config if set:
+    val checkSiblingMd5:ErrorOr[Option[Boolean]] = validate {
+        backendConfig.hasPath("filesystems.local.caching.check-sibling-md5") match {
+            case true => Some(backendConfig.getBoolean("filesystems.local.caching.check-sibling-md5"))
+            case false => None
+      }
+    }
 
     (
       fileSysStr,
@@ -192,7 +205,9 @@ object AwsBatchAttributes {
       fsxMntPoint,
       efsMntPoint,
       efsMakeMD5,
-      efsDelocalize
+      efsDelocalize,
+      globLinkCommand,
+      checkSiblingMd5
     ).tupled.map((AwsBatchAttributes.apply _).tupled) match {
       case Valid(r) => r
       case Invalid(f) =>
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala
index edfbd560362..bff8848e037 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala
@@ -33,6 +33,7 @@ package cromwell.backend.impl.aws
 
 import cromwell.backend.standard.{StandardInitializationData, StandardValidatedRuntimeAttributesBuilder}
 import software.amazon.awssdk.auth.credentials.AwsCredentialsProvider
+import cromwell.backend.impl.aws.io.AwsBatchWorkflowPaths
 
 case class AwsBatchBackendInitializationData
 (
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
index c0ae9210852..acb066d7332 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
@@ -36,7 +36,8 @@ import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationDa
 import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardFinalizationActor, StandardFinalizationActorParams, StandardInitializationActor, StandardInitializationActorParams, StandardLifecycleActorFactory}
 import cromwell.core.CallOutputs
 import wom.graph.CommandCallNode
-
+import cromwell.backend.impl.aws.callcaching.{AwsBatchBackendCacheHitCopyingActor, AwsBatchBackendFileHashingActor}
+import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardFileHashingActor}
 /**
   * Factory to create `Actor` objects to manage the lifecycle of a backend job on AWS Batch. This factory provides an
   * object from the `AwsBatchAsyncBackendJobExecutionActor` class to create and manage the job.
@@ -89,6 +90,12 @@ case class AwsBatchBackendLifecycleActorFactory(
     AwsBatchFinalizationActorParams(workflowDescriptor, ioActor, calls, configuration, jobExecutionMap, workflowOutputs, initializationDataOption)
   }
 
+  override lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] = {
+    Option(classOf[AwsBatchBackendCacheHitCopyingActor])
+  }
+
+  override lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(classOf[AwsBatchBackendFileHashingActor])
+
   override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] = {
     Option(AwsBatchSingletonActor.props(configuration.awsConfig.region, Option(configuration.awsAuth)))
   }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
index 5f6d9eaf17a..8a019110509 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
@@ -60,6 +60,8 @@ class AwsBatchConfiguration(val configurationDescriptor: BackendConfigurationDes
   val efsMntPoint = batchAttributes.efsMntPoint
   val efsMakeMD5 = batchAttributes.efsMakeMD5
   val efsDelocalize = batchAttributes.efsDelocalize
+  val globLinkCommand = batchAttributes.globLinkCommand
+  val checkSiblingMd5 = batchAttributes.checkSiblingMd5
 }
 
 object AWSBatchStorageSystems {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala
index b75d4d6b00f..248ee90e8e3 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala
@@ -37,9 +37,13 @@ import cromwell.filesystems.s3.S3PathBuilder
 import cromwell.filesystems.s3.S3PathBuilder.{InvalidS3Path, PossiblyValidRelativeS3Path, ValidFullS3Path}
 import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
 import cromwell.core.path.{DefaultPath, Path}
+import cromwell.backend.impl.aws.io._
 
-class AwsBatchExpressionFunctions(standardParams: StandardExpressionFunctionsParams)
-  extends StandardExpressionFunctions(standardParams) {
+
+
+class AwsBatchExpressionFunctions(override val standardParams: StandardExpressionFunctionsParams)
+  extends StandardExpressionFunctions(standardParams) with AwsBatchGlobFunctions {
+  
   override lazy val ioCommandBuilder: IoCommandBuilder = S3BatchCommandBuilder
 
   override def preMapping(str: String) = {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
index 16241dbb8ce..5078b5b87f8 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
@@ -47,6 +47,7 @@ import wom.graph.CommandCallNode
 import org.apache.commons.codec.binary.Base64
 import spray.json.{JsObject, JsString}
 import org.slf4j.{Logger, LoggerFactory}
+import cromwell.backend.impl.aws.io.AwsBatchWorkflowPaths
 
 import scala.concurrent.Future
 import scala.jdk.CollectionConverters._
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 283b97ebd97..48f286dc436 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -305,7 +305,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     val outputCopyCommand = outputs.map {
       case output: AwsBatchFileOutput if output.local.pathAsString.contains("*") => "" //filter out globs
       case output: AwsBatchFileOutput if output.name.endsWith(".list") && output.name.contains("glob-") =>
-
+        Log.debug("Globbing : check for EFS settings.")
         val s3GlobOutDirectory = output.s3key.replace(".list", "")
         val globDirectory = output.name.replace(".list", "")
         /*
@@ -313,16 +313,60 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          * if it doesn't exist then 'touch' it so that it can be copied otherwise later steps will get upset
          * about the missing file
          */
-        s"""
-           |touch ${output.name}
-           |_s3_delocalize_with_retry ${output.name} ${output.s3key}
-           |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi""".stripMargin
-           
+        if ( efsMntPoint.isDefined && output.mount.mountPoint.pathAsString == efsMntPoint.get ) {
+           Log.debug("EFS glob output file detected: "+ output.s3key + s" / ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}")
+           val test_cmd = if (efsDelocalize.isDefined && efsDelocalize.getOrElse(false)) {
+                    Log.debug("delocalization on EFS is enabled")
+                    s"""
+                        |touch ${output.name}
+                        |_s3_delocalize_with_retry ${output.name} ${output.s3key}
+                        |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi
+                        |""".stripMargin
+                } else {
+                    
+                    // check file for existence
+                    s"""
+                        |# test the glob list
+                        |test -e ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && exit 1)
+                        |# test individual files.
+                        |for F in $$(cat ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}); do
+                        |   test -e "${globDirectory}/$$F" || (echo 'globbed file: "${globDirectory}/$$F" does not exist' && exit 1)
+                        |done
+                        |"""
+                }
+           // need to make md5sum? 
+           val md5_cmd = if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
+                    Log.debug("Add cmd to create MD5 sibling.")
+                    // this does NOT regenerate the md5 in case the file is overwritten ! 
+                    s"""
+                        |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
+                        |   # the glob list
+                        |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && exit 1 ); 
+                        |   # globbed files, using specified number of cpus for parallel processing.
+                        |   cat ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} | xargs -I% -P${runtimeAttributes.cpu.##.toString} bash -c "md5sum ${globDirectory}/% > ${globDirectory}/%.md5"
+                        |fi
+                        |""".stripMargin 
+                } else {
+                    Log.debug("MD5 not enabled: "+efsMakeMD5.get.toString())
+                    ""
+                }
+           // return combined result
+           s"""
+          |${test_cmd}
+          |${md5_cmd}
+          | """.stripMargin
+        } else {
+          // default delocalization command.
+          s"""
+             |touch ${output.name}
+             |_s3_delocalize_with_retry ${output.name} ${output.s3key}
+             |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi""".stripMargin
+        }
 
       // files on /cromwell/ working dir must be delocalized
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
         //output is on working disk mount
-        Log.info("output Data on working disk mount" + output.local.pathAsString)
+        Log.debug("output Data on working disk mount" + output.local.pathAsString)
         s"""_s3_delocalize_with_retry $workDir/${output.local.pathAsString} ${output.s3key}""".stripMargin
 
       // file(name (full path), s3key (delocalized path), local (file basename), mount (disk details))
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
index a3c693855be..35ca4d0c17c 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
@@ -32,7 +32,7 @@
 package cromwell.backend.impl.aws
 
 import akka.actor.Actor
-import cromwell.backend.impl.aws.io.{AwsBatchVolume, AwsBatchWorkingDisk}
+import cromwell.backend.impl.aws.io.{AwsBatchVolume, AwsBatchWorkingDisk,AwsBatchJobPaths}
 import cromwell.backend.standard.StandardCachingActorHelper
 import cromwell.core.logging.JobLogging
 import cromwell.core.path.Path
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala
index e8d93570dbc..219b264cc93 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala
@@ -29,10 +29,13 @@
  *  POSSIBILITY OF SUCH DAMAGE.
  */
 
-package cromwell.backend.impl.aws
+package cromwell.backend.impl.aws.io
 
 import cromwell.backend.BackendJobDescriptorKey
 import cromwell.backend.io.JobPaths
+import cromwell.core.path.Path
+import cromwell.core.JobKey
+
 
 object AwsBatchJobPaths {
   val AwsBatchLogPathKey = "cromwellLog"
@@ -60,4 +63,19 @@ final case class AwsBatchJobPaths(override val workflowPaths: AwsBatchWorkflowPa
   override def defaultStderrFilename: String = s"$logBasename-stderr.log"
 
   override def forCallCacheCopyAttempts: JobPaths = this.copy(isCallCacheCopyAttempt = true)
+  override lazy val callRoot = callPathBuilder(workflowPaths.workflowRoot, jobKey, isCallCacheCopyAttempt)
+
+  def callPathBuilder(root: Path, jobKey: JobKey, isCallCacheCopyAttempt: Boolean) = {
+    val callName = jobKey.node.localName
+    val call = s"${JobPaths.CallPrefix}-${callName}"
+    val shard = jobKey.index map { s => s"${JobPaths.ShardPrefix}-$s" } getOrElse ""
+
+    val retryOrCallCache =
+      if (isCallCacheCopyAttempt) JobPaths.CacheCopyPrefix
+      else if (jobKey.attempt > 1) s"${JobPaths.AttemptPrefix}-${jobKey.attempt}"
+      else ""
+
+    List(call, shard, retryOrCallCache).foldLeft(root)((path, dir) => path.resolve(dir))
+    
+  }  
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala
index 45d3eafe75d..fb2f3675951 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala
@@ -29,7 +29,7 @@
  *  POSSIBILITY OF SUCH DAMAGE.
  */
 
-package cromwell.backend.impl.aws
+package cromwell.backend.impl.aws.io
 
 import akka.actor.ActorSystem
 import com.typesafe.config.Config
@@ -39,6 +39,7 @@ import cromwell.core.WorkflowOptions
 import cromwell.core.path.PathBuilder
 import cromwell.filesystems.s3.S3PathBuilderFactory
 import software.amazon.awssdk.auth.credentials.AwsCredentialsProvider
+import cromwell.backend.impl.aws.{AwsBatchConfiguration,AWSBatchStorageSystems}
 
 object AwsBatchWorkflowPaths {
   private val RootOptionKey = "aws_s3_root"
@@ -70,8 +71,15 @@ case class AwsBatchWorkflowPaths(workflowDescriptor: BackendWorkflowDescriptor,
   override def config: Config = configuration.configurationDescriptor.backendConfig
   override def pathBuilders: List[PathBuilder] = {
     if (configuration.fileSystem == "s3") {
-      List(configuration.pathBuilderFactory.asInstanceOf[S3PathBuilderFactory].fromProvider(workflowOptions, provider))
+      // if efs is activated : add the default (local) pathbuilders.
+      if (configuration.batchAttributes.efsMntPoint.isDefined) {
+        List(configuration.pathBuilderFactory.asInstanceOf[S3PathBuilderFactory].fromProvider(workflowOptions, provider) ) ++ WorkflowPaths.DefaultPathBuilders
+      }
+      else {
+        List(configuration.pathBuilderFactory.asInstanceOf[S3PathBuilderFactory].fromProvider(workflowOptions, provider) )
+      }
     } else {
-      WorkflowPaths.DefaultPathBuilders}
+      WorkflowPaths.DefaultPathBuilders
+    }
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 8576dcb6de9..a1cdce0ba1b 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -258,7 +258,7 @@ Cromwell EC2 instances can be equipped with a shared elastic filesystem, termed
 
 1.  Setup an EFS filesystem: 
 
-Following the [GenomicsWorkFlows](https://docs.opendata.aws/genomics-workflows/orchestration/cromwell/cromwell-overview.html) deployment stack and selecting "Create EFS", you will end up with an EFS filesystem accessible within the provided subnets. It is mounted by default in EC2 workers under /mnt/efs. This is specified in the launch templates USER_DATA if you want to change this. 
+Following the [GenomicsWorkFlows](https://docs.opendata.aws/genomics-workflows/orchestration/cromwell/cromwell-overview.html) deployment stack and selecting "Create EFS", you will end up with an EFS filesystem accessible within the provided subnets. It is mounted by default in EC2 workers under /mnt/efs. This is specified in the launch templates USER_DATA if you want to change this. *BEWARE* : For globbing to work on EFS, the mountpoint must be left as "/mnt/efs" ! 
 
 Next, it is recommended to change the EFS setup (in console : select EFS service, then the "SharedDataGenomics" volume, edit). Change performance settings to Enhanced/Elastic, because the bursting throughput is usually insufficient. Optionally set the lifecycle to archive infrequently accessed data and reduce costs. 
 
@@ -271,13 +271,18 @@ backend {
     providers {
         AWSBatch {
             config{
+                // ALTER THE GLOBBING COMMAND: 
+                // use symlinks instad of hardlinks (not allowed on EFS)
+                //  "shopt -s nullglob" prevents issues with empty globbed folders.  
+                glob-link-command = " shopt -s nullglob; ln -fs GLOB_PATTERN GLOB_DIRECTORY "
+
                 default-runtime-attributes {
                     // keep you other settings as they are (queueArn etc)
 
                     // DEFAULT EFS CONFIG
                     // delocalize output files under /mnt/efs to the cromwell tmp bucket
                     efsDelocalize = false
-                    // make md5 sums of output files under /mnt/efs as part of the job 
+                    // make sibling-md5 files of output files under /mnt/efs as part of the job. see local.caching!
                     efsMakeMD5 = false
                 }
                 filesystems {
@@ -288,6 +293,11 @@ backend {
                     local {
                         // the mountpoint of the EFS volume within the HOST (specified in EC2 launch template)
                         efs = "/mnt/efs"
+                        caching {
+                            // sibling-md5 files reduce traffic on the EFS share. By default, files are streamed & hashed in cromwell itself
+                            // NOTE: beware on overwriting files. the md5-siblings are not automatically cleaned up or updated !! 
+                            check-sibling-md5 : true
+                        }
                     }
 
                 }
@@ -298,22 +308,31 @@ backend {
 
 ```
 
-Now, Cromwell is able to correctly handle output files both located in the cromwell working directory (delocalized to S3), and on the EFS volume (kept, and optionally delocalized).
+Now, Cromwell is able to : 
+
+- take input from localized files in temp-bucket (default) 
+- take input from files stored on EFS (no localization performed) 
+- generate output files located in the cromwell working directory : delocalized to S3 tmp bucket
+- generate output files located on the EFS volume : checked for presence, kept, and optionally delocalized
+- generate sibling md5 files for default output files and globbed output files
+- detect valid cached job outputs from previous runs, both on S3/tmp-bucket and EFS, for single files and globbed files. 
+
+Note: generating sibling md5 files for globbed output utilized the amount of vCPUs specified for the job.
 
 3. Current limitations:
 
-- To read an task output file in wdl using eg read_tsv(), it must be set to output type 'String' OR 'efsDelocalize' must be enabled for the job.
-- Call caching is not yet possible when using input files located on EFS.  Cromwell does not crash but issues errors and skips callcaching for that task. 
 - There is no unique temp/scratch folder generated per workflow ID. Data collision prevention is left to the user. 
 - Cleanup must be done manually
+- Globbing only works if efs is mounted under "/mnt/efs" (see config above)
 
 4. Example Workflow
 
 The following workflow highlights the following features: 
  
  - take input data from an s3 bucket. 
- - keep intermediate data on efs
- - delocalize output from efs volume 
+ - generate & keep intermediate data on efs
+ - glob files on s3
+ - delocalize output from efs volume to s3
  - read a file on efs in the main wdl cromwell process.
 
  
@@ -324,28 +343,40 @@ workflow TestEFS {
         # input file for WF is located on S3
         File s3_file = 's3://aws-quickstart/quickstart-aws-vpc/templates/aws-vpc.template.yaml'
         # set an input parameter holding the working dir on EFS
-        String efs_wd = "/mnt/efs/MyProject"
+        String efs_wd = "/mnt/efs/MyTestProject"
     }
-    # task one : create a file on efs.
+    # task one : create a file and a glob on efs. do not delocalize
     call task_one {input:
         infile = s3_file,
         wd = efs_wd    
     }
-    # read the outfile straight in a wdl structure
-    Array[Array[String]] myOutString_info = read_tsv(task_one.outfile)
+    # read the outfile on EFS straight in a wdl structure
+    Array[Array[String]] step1_info = read_tsv(task_one.efs_file)
 
-    # task two : reuse the file on the wd and delocalize to s3
+    # task two : reuse the file on the wd and delocalize to s3 (via runtime setting)
     call task_two {input:
         wd = efs_wd,
-        infile = task_one.outfile
+        infile = task_one.efs_file
+    }
+    Array[Array[String]] step2_info = read_tsv(task_two.outfile)
+
+    # run a task on the various files (get md5).
+    call task_three {input:
+        wd = efs_wd,
+        infiles = task_one.file_list,
+        f = task_two.outfile
     }
-    Array[Array[String]] myOutFile_info = read_tsv(task_two.outfile)
+    Array[String] step3_md5s = task_three.md5
 
     ## outputs
     output{
-        Array[Array[String]] wf_out_info_returned_as_string = myOutString_info
-        Array[Array[String]] wf_out_info_returned_as_file = myOutFile_info
-        String wf_out_file = task_two.outfile
+        Array[Array[String]] wf_out_info_step1 = step1_info
+        File wf_out_efs_file = task_one.efs_file
+        File wf_out_s3_file = task_one.s3_file
+        Array[File] wf_out_globList_out = task_one.file_list
+
+        File wf_out_file_step2 = task_two.outfile
+        Array[String] wf_out_step3 = step3_md5s    
     }
 }
 
@@ -356,21 +387,28 @@ task task_one {
     }
     command {
         # mk the wd:
-        mkdir -p ~{wd}
+        mkdir -p ~{wd}/StuffToGlob
+        # create files
+        for i in A B C D E F G H I F K L M N O P Q R; do 
+            echo $i > ~{wd}/StuffToGlob/$i.txt
+        done
         # mv the infile to wd
         mv ~{infile} ~{wd}/
-        # generate an outfile for output Testing
+        # generate an outfile for output Testing on EFS
         ls -alh ~{wd} > ~{wd}/MyOutFile
+        # and on the temp bucket.
+        ls -alh ~{wd} > MyRegularS3File.txt
     }
      runtime {
         docker: "ubuntu:22.04"
         cpu : "1"
-        memory: "500M" 
+        memory: "500M"         
      }
      output {
-        # to read a file in cromwell/wdl : pass it back as a string or delocalize (see task_two)
-        String outfile = '~{wd}/MyOutFile'
-     }
+        File efs_file = '~{wd}/MyOutFile'
+        File s3_file = "MyRegularS3File.txt"
+        Array[File] file_list = glob("~{wd}/StuffToGlob/*.txt")
+     }   
 }
 
 task task_two {
@@ -379,18 +417,38 @@ task task_two {
         File infile
     }
     command {
-        # put something new in the file:
-        ls -alh /tmp > ~{infile}
-        
+        # another derived file:
+        ls -alh /tmp > ~{infile}.step2
     }
      runtime {
         docker: "ubuntu:22.04"
         cpu : "1"
         memory: "500M" 
         efsDelocalize: true
+        
+     }
+     output {
+        File outfile = "~{infile}.step2"
+     }   
+}
+
+task task_three {
+    input {
+        String wd
+        Array[File] infiles
+        File f
+    }
+    command {    
+        #get checksums for globbed + extra infile
+        md5sum ~{sep=' ' infiles} ~{f}
+    }
+    runtime {
+        docker: "ubuntu:22.04"
+        cpu : "1"
+        memory: "500M"         
      }
      output {
-        File outfile = "~{infile}"
+        Array[String] md5 = read_lines(stdout())
      }
 }
 ```
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
index 86bfd46e754..1495e480358 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
@@ -30,10 +30,9 @@
  */
 package cromwell.backend.impl.aws.callcaching
 
-import com.google.cloud.storage.contrib.nio.CloudStorageOptions
 import common.util.TryUtil
 import cromwell.backend.BackendInitializationData
-import cromwell.backend.impl.aws.{AWSBatchStorageSystems, AwsBatchBackendInitializationData}
+import cromwell.backend.impl.aws.{AWSBatchStorageSystems, AwsBatchBackendInitializationData,AwsBatchJobCachingActorHelper}
 import cromwell.backend.io.JobPaths
 import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardCacheHitCopyingActorParams}
 import cromwell.core.CallOutputs
@@ -46,7 +45,7 @@ import wom.values.WomFile
 import scala.language.postfixOps
 import scala.util.Try
 
-class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams) extends StandardCacheHitCopyingActor(standardParams) {
+class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams) extends StandardCacheHitCopyingActor(standardParams) with AwsBatchJobCachingActorHelper{
   private val batchAttributes = BackendInitializationData
     .as[AwsBatchBackendInitializationData](standardParams.backendInitializationDataOption)
     .configuration.batchAttributes
@@ -74,8 +73,9 @@ class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyin
     }
   }
 
+  // detritus files : job script, stdout, stderr and RC files.
   override def processDetritus(sourceJobDetritusFiles: Map[String, String]
-                              ): Try[(Map[String, Path], Set[IoCommand[_]])] =
+                              ): Try[(Map[String, Path], Set[IoCommand[_]])] = {
     (batchAttributes.fileSystem, cachingStrategy) match {
       case (AWSBatchStorageSystems.s3, UseOriginalCachedOutputs) =>
         // apply getPath on each detritus string file
@@ -93,7 +93,7 @@ class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyin
         }
       case (_, _) => super.processDetritus(sourceJobDetritusFiles)
    }
-
+  }
   override protected def additionalIoCommands(sourceCallRootPath: Path,
                                               originalSimpletons: Seq[WomValueSimpleton],
                                               newOutputs: CallOutputs,
@@ -113,7 +113,7 @@ class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyin
           S3BatchCommandBuilder.writeCommand(
             path = jobPaths.forCallCacheCopyAttempts.callExecutionRoot / "call_caching_placeholder.txt",
             content = content,
-            options = Seq(CloudStorageOptions.withMimeType("text/plain")),
+            options = Seq(),
           ).get
         ))
        case (AWSBatchStorageSystems.s3, CopyCachedOutputs) => List.empty
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
index f731fb1b44a..41cb1dae97f 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
@@ -36,6 +36,9 @@ import cromwell.backend.BackendInitializationData
 import cromwell.backend.impl.aws.AwsBatchBackendInitializationData
 import cromwell.backend.impl.aws.AWSBatchStorageSystems
 import cromwell.core.io.DefaultIoCommandBuilder
+import scala.util.Try
+import cromwell.backend.standard.callcaching.StandardFileHashingActor.SingleFileHashRequest
+import cromwell.core.path.DefaultPathBuilder
 
 class AwsBatchBackendFileHashingActor(standardParams: StandardFileHashingActorParams) extends StandardFileHashingActor(standardParams) {
 
@@ -44,4 +47,27 @@ class AwsBatchBackendFileHashingActor(standardParams: StandardFileHashingActorPa
        case AWSBatchStorageSystems.s3  => S3BatchCommandBuilder
        case _ =>  DefaultIoCommandBuilder
   }
+  // get backend config.
+  val aws_config = BackendInitializationData.as[AwsBatchBackendInitializationData](standardParams.backendInitializationDataOption).configuration
+  
+  // custom strategy to handle efs (local) files, in case sibling-md5 file is present. 
+  override def customHashStrategy(fileRequest: SingleFileHashRequest): Option[Try[String]] = {
+    val file = DefaultPathBuilder.get(fileRequest.file.valueString)
+    if (aws_config.efsMntPoint.isDefined && file.toString.startsWith(aws_config.efsMntPoint.getOrElse("--")) && aws_config.checkSiblingMd5.getOrElse(false)) {
+            // check existence of the sibling file
+            val md5 = file.sibling(s"${file.toString}.md5")
+            if (md5.exists) {
+                // read the file.
+                val md5_value: Option[String] = Some(md5.contentAsString.split("\\s+")(0))
+                md5_value.map(str => Try(str))
+            } else {
+                // No sibling found, fall back to default.
+                None
+            }
+            
+    } else {
+        // Detected non-EFS file: return None
+        None  
+    }
+  }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
new file mode 100644
index 00000000000..18505f6d866
--- /dev/null
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
@@ -0,0 +1,96 @@
+/*
+ * Copyright 2018 Amazon.com, Inc. or its affiliates.
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions are met:
+ *
+ *  1. Redistributions of source code must retain the above copyright notice,
+ *  this list of conditions and the following disclaimer.
+ *
+ *  2. Redistributions in binary form must reproduce the above copyright
+ *  notice, this list of conditions and the following disclaimer in the
+ *  documentation and/or other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its
+ *  contributors may be used to endorse or promote products derived from
+ *  this software without specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ *  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
+ *  BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+ *  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+ *  THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ *  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ *  (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ *  STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+ *  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ *  POSSIBILITY OF SUCH DAMAGE.
+ */
+package cromwell.backend.impl.aws.io
+
+
+//import cats.implicits._
+//import common.validation.ErrorOr.ErrorOr
+//import cromwell.backend.BackendJobDescriptor
+//import cromwell.core.CallContext
+//import cromwell.core.io.AsyncIoFunctions
+//import wom.expression.{IoFunctionSet, IoFunctionSetAdapter}
+//import wom.graph.CommandCallNode
+import wom.values._
+import cromwell.backend.io._
+import cromwell.backend.standard._
+import scala.concurrent.Future
+import java.nio.file.Paths
+import cromwell.core.path.DefaultPathBuilder
+
+//import cromwell.backend.impl.aws.AwsBatchAttributes
+//import cromwell.backend.impl.aws._
+
+trait AwsBatchGlobFunctions extends GlobFunctions {
+    
+  def standardParams: StandardExpressionFunctionsParams
+
+  
+
+  /**
+    * Returns a list of path from the glob.
+    *
+    * The paths are read from a list file based on the pattern.
+    *
+    * @param pattern The pattern of the glob. This is the same "glob" passed to globPath().
+    * @return The paths that match the pattern.
+    */
+  override def glob(pattern: String): Future[Seq[String]] = {
+    // get access to globName()
+    import GlobFunctions._
+    
+    // GOAL : 
+    //  - get config (backend / runtime / ...) here to evaluate if efsMntPoint is set & if efs delocalization is set. 
+    //  - according to those values : write the pattern as s3:// or as local path. 
+    //  - get the wf id from the config settings.
+
+    // for now : hard coded as local at mount point /mnt/efs.
+    val wfid_regex = ".{8}-.{4}-.{4}-.{4}-.{12}".r
+    val wfid = callContext.root.toString.split("/").toList.filter(element => wfid_regex.pattern.matcher(element).matches()).lastOption.getOrElse("")
+    val globPatternName = globName(s"${pattern}-${wfid}")
+    val globbedDir = Paths.get(pattern).getParent.toString
+    val listFilePath = if (pattern.startsWith("/mnt/efs/")) {
+        DefaultPathBuilder.get(globbedDir + "/." + globPatternName + ".list")
+    } else {
+        callContext.root.resolve(s"${globPatternName}.list")
+    }
+    asyncIo.readLinesAsync(listFilePath.toRealPath()) map { lines =>
+      lines.toList map { fileName =>
+        // again : this should be config based...
+        if (pattern.startsWith("/mnt/efs/")) {
+            s"${globbedDir}/.${globPatternName}/${fileName}"
+        } else {
+            s"${callContext.root}/${globPatternName}/${fileName}"
+        }
+      }
+    }
+  }
+  
+}
\ No newline at end of file
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
index e79ef867a54..745e11bee35 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -452,7 +452,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
 
         val inputFilePaths = inputOutputParameters.jobInputParameters.map(_.cloudPath.pathAsString).toSet
         val referenceDisksToMount =
-          jesAttributes.referenceFileToDiskImageMappingOpt.map(getReferenceDisksToMount(_, inputFilePaths))
+          if (useReferenceDisks)
+            jesAttributes.referenceFileToDiskImageMappingOpt.map(getReferenceDisksToMount(_, inputFilePaths))
+          else None
 
         val workflowOptions = workflowDescriptor.workflowOptions
 
@@ -542,6 +544,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     Future.successful(PendingExecutionHandle(jobDescriptor, jobForResumption, Option(Run(jobForResumption)), previousState = None))
   }
 
+  protected def uploadDrsLocalizationManifest(createPipelineParameters: CreatePipelineParameters, cloudPath: Path): Future[Unit] = Future.successful(())
+
   protected def uploadGcsTransferLibrary(createPipelineParameters: CreatePipelineParameters, cloudPath: Path, gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = Future.successful(())
 
   protected def uploadGcsLocalizationScript(createPipelineParameters: CreatePipelineParameters,
@@ -639,6 +643,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
       customLabels <- Future.fromTry(GoogleLabels.fromWorkflowOptions(workflowDescriptor.workflowOptions))
       jesParameters <- generateInputOutputParameters
       createParameters = createPipelineParameters(jesParameters, customLabels)
+      drsLocalizationManifestCloudPath = jobPaths.callExecutionRoot / PipelinesApiJobPaths.DrsLocalizationManifestName
+      _ <- uploadDrsLocalizationManifest(createParameters, drsLocalizationManifestCloudPath)
       gcsTransferConfiguration = initializationData.papiConfiguration.papiAttributes.gcsTransferConfiguration
       gcsTransferLibraryCloudPath = jobPaths.callExecutionRoot / PipelinesApiJobPaths.GcsTransferLibraryName
       transferLibraryContainerPath = createParameters.commandScriptContainerPath.sibling(GcsTransferLibraryName)
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
index 2e6682c2e69..353e33a5019 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
@@ -75,7 +75,7 @@ trait PipelinesApiJobCachingActorHelper extends StandardCachingActorHelper {
       .get(WorkflowOptionKeys.GoogleProject)
       .getOrElse(jesAttributes.project)
 
-    Map(
+    Map[String, Any](
       PipelinesApiMetadataKeys.GoogleProject -> googleProject,
       PipelinesApiMetadataKeys.ExecutionBucket -> initializationData.workflowPaths.executionRootString,
       PipelinesApiMetadataKeys.EndpointUrl -> jesAttributes.endpointUrl,
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
index 0fc9a8ff49d..ae047187825 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
@@ -13,6 +13,7 @@ object PipelinesApiJobPaths {
   val GcsTransferLibraryName = "gcs_transfer.sh"
   val GcsLocalizationScriptName = "gcs_localization.sh"
   val GcsDelocalizationScriptName = "gcs_delocalization.sh"
+  val DrsLocalizationManifestName = "drs_manifest"
 }
 
 // Non-`final` as this is mocked for testing since using a real instance proved too difficult.
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
index 09fb0713de0..7710f3de98e 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
@@ -126,7 +126,7 @@ case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, en
             ComputeScopes.COMPUTE,
             StorageScopes.DEVSTORAGE_FULL_CONTROL,
             GoogleCloudScopes.KmsScope,
-            // Profile and Email scopes are requirements for interacting with Martha
+            // Profile and Email scopes are requirements for interacting with DRS Resolver
             Oauth2Scopes.USERINFO_EMAIL,
             Oauth2Scopes.USERINFO_PROFILE,
             // Monitoring scope as POC
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
index a0f899a26ff..481f7d6c5a8 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -141,9 +141,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       }
 
       val optional = Option(output) collectFirst { case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
-      val contentType = output.contentType.getOrElse("")
+      val contentType = output.contentType.map(_.toString).getOrElse("")
 
-      List(kind, output.cloudPath, output.containerPath, optional, contentType)
+      List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
     } mkString("\"", "\"\n|  \"", "\"")
 
     val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(
@@ -179,11 +179,12 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
                                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
+    import cromwell.backend.google.pipelines.common.action.ActionUtils.shellEscaped
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
         referenceInputsToMountedPaths map {
           case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${input.containerPath.parent.pathAsString} && ln -s $absolutePathOnRefDisk ${input.containerPath.pathAsString}"
+            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }
 
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
index b445f4786f8..19774a4cc41 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
@@ -38,12 +38,12 @@ trait PipelinesParameterConversions {
           val drsCommand =
             List(fileInput.cloudPath.pathAsString, fileInput.containerPath.pathAsString) ++
               drsPath.requesterPaysProjectIdOption.toList
-          val marthaEnv = DrsConfig.toEnv(drsFileSystemProvider.drsConfig)
+          val drsResolverEnv = DrsConfig.toEnv(drsFileSystemProvider.drsConfig)
           val localizationAction = ActionBuilder
             .withImage(drsDockerImage)
             .withCommand(drsCommand: _*)
             .withMounts(mounts)
-            .setEnvironment(marthaEnv.asJava)
+            .setEnvironment(drsResolverEnv.asJava)
             .withLabels(labels)
           List(ActionBuilder.describeParameter(fileInput, labels), localizationAction)
         case sraPath: SraPath =>
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
index 3535f1db8d8..18c84ee66eb 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
@@ -1,7 +1,7 @@
 package cromwell.backend.google.pipelines.v2alpha1
 
 import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.cloud.NoCredentials
 import com.typesafe.config.{Config, ConfigFactory}
 import common.assertion.CromwellTimeoutSpec
@@ -24,9 +24,9 @@ class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   implicit val gcsTransferConfiguration: GcsTransferConfiguration =
     GcsTransferConfiguration(transferAttempts = refineMV(1), parallelCompositeUploadThreshold = "0")
 
-  private val marthaConfig: Config = ConfigFactory.parseString(
-    """martha {
-      |   url = "http://martha-url"
+  private val drsResolverConfig: Config = ConfigFactory.parseString(
+    """resolver {
+      |   url = "http://drshub-url"
       |}
       |""".stripMargin
   )
@@ -39,7 +39,7 @@ class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   it should "create a DRS input parameter" in {
 
     val drsPathBuilder = DrsPathBuilder(
-      new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+      new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
       None,
     )
     val drsPath = drsPathBuilder.build("drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba").get
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
index 1c936e76317..7f10580b700 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
@@ -82,9 +82,9 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
-          "virtualMachine" -> Map(
+          "virtualMachine" -> Map[String, Any](
             "machineType" -> "custom-1-1024",
             "preemptible" -> false
           ).asJava
@@ -117,7 +117,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
           "virtualMachine" -> Map(
             "machineType" -> "custom-1-1024",
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
index e4c95dcb1e0..8d8f52d3773 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
@@ -119,7 +119,7 @@ case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode
             ComputeScopes.COMPUTE,
             StorageScopes.DEVSTORAGE_FULL_CONTROL,
             GoogleCloudScopes.KmsScope,
-            // Profile and Email scopes are requirements for interacting with Martha
+            // Profile and Email scopes are requirements for interacting with DRS Resolvers
             Oauth2Scopes.USERINFO_EMAIL,
             Oauth2Scopes.USERINFO_PROFILE,
             // Monitoring scope as POC
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
index 77370cabc92..3c0f5ca63f9 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -12,14 +12,19 @@ import cromwell.backend.google.pipelines.common.io.PipelinesApiWorkingDisk
 import cromwell.backend.google.pipelines.v2beta.PipelinesApiAsyncBackendJobExecutionActor._
 import cromwell.backend.standard.StandardAsyncExecutionActorParams
 import cromwell.core.path.{DefaultPathBuilder, Path}
+import cromwell.filesystems.drs.DrsPath
 import cromwell.filesystems.gcs.GcsPathBuilder.ValidFullGcsPath
 import cromwell.filesystems.gcs.{GcsPath, GcsPathBuilder}
 import org.apache.commons.codec.digest.DigestUtils
+import org.apache.commons.csv.{CSVFormat, CSVPrinter}
+import org.apache.commons.io.output.ByteArrayOutputStream
 import wom.core.FullyQualifiedName
 import wom.expression.FileEvaluation
 import wom.values.{GlobFunctions, WomFile, WomGlobFile, WomMaybeListedDirectory, WomMaybePopulatedFile, WomSingleFile, WomUnlistedDirectory}
 
-import java.io.FileNotFoundException
+import java.nio.charset.Charset
+
+import java.io.{FileNotFoundException, OutputStreamWriter}
 import scala.concurrent.Future
 import scala.io.Source
 import scala.language.postfixOps
@@ -141,9 +146,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       }
 
       val optional = Option(output) collectFirst { case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
-      val contentType = output.contentType.getOrElse("")
+      val contentType = output.contentType.map(_.toString).getOrElse("")
 
-      List(kind, output.cloudPath, output.containerPath, optional, contentType)
+      List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
     } mkString("\"", "\"\n|  \"", "\"")
 
     val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(
@@ -174,16 +179,25 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
 
   import mouse.all._
 
+  override def uploadDrsLocalizationManifest(createPipelineParameters: CreatePipelineParameters, cloudPath: Path): Future[Unit] = {
+    val content = generateDrsLocalizerManifest(createPipelineParameters.inputOutputParameters.fileInputParameters)
+    if (content.nonEmpty)
+      asyncIo.writeAsync(cloudPath, content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+    else
+      Future.unit
+  }
+
   private def generateGcsLocalizationScript(inputs: List[PipelinesApiInput],
                                             referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]])
                                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
+    import cromwell.backend.google.pipelines.common.action.ActionUtils.shellEscaped
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
         referenceInputsToMountedPaths map {
           case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${input.containerPath.parent.pathAsString} && ln -s $absolutePathOnRefDisk ${input.containerPath.pathAsString}"
+            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }
 
@@ -396,4 +410,17 @@ object PipelinesApiAsyncBackendJobExecutionActor {
       }
     } combineAll
   }
+
+  private [v2beta] def generateDrsLocalizerManifest(inputs: List[PipelinesApiInput]): String = {
+    val outputStream = new ByteArrayOutputStream()
+    val csvPrinter = new CSVPrinter(new OutputStreamWriter(outputStream), CSVFormat.DEFAULT)
+    val drsFileInputs = inputs collect {
+      case drsInput@PipelinesApiFileInput(_, drsPath: DrsPath, _, _) => (drsInput, drsPath)
+    }
+    drsFileInputs foreach { case (drsInput, drsPath) =>
+      csvPrinter.printRecord(drsPath.pathAsString, drsInput.containerPath.pathAsString)
+    }
+    csvPrinter.close(true)
+    outputStream.toString(Charset.defaultCharset())
+  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
index 505c23edb9c..64365fe404f 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
@@ -1,6 +1,5 @@
 package cromwell.backend.google.pipelines.v2beta
 
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, DrsConfig}
 import com.google.api.services.lifesciences.v2beta.model.{Action, Mount}
 import com.typesafe.config.ConfigFactory
 import cromwell.backend.google.pipelines.common.action.ActionCommands._
@@ -27,25 +26,6 @@ trait PipelinesParameterConversions {
 
       val labels = ActionBuilder.parameterLabels(fileInput)
       fileInput.cloudPath match {
-        case drsPath: DrsPath =>
-
-          import scala.jdk.CollectionConverters._
-
-          val drsFileSystemProvider = drsPath.drsPath.getFileSystem.provider.asInstanceOf[DrsCloudNioFileSystemProvider]
-
-          val drsDockerImage = config.getString("drs.localization.docker-image")
-          // Note: Don't ShellPath.escape the paths as we are directly invoking the localizer and NOT launching a shell.
-          val drsCommand =
-            List(fileInput.cloudPath.pathAsString, fileInput.containerPath.pathAsString) ++
-              drsPath.requesterPaysProjectIdOption.toList
-          val marthaEnv = DrsConfig.toEnv(drsFileSystemProvider.drsConfig)
-          val localizationAction = ActionBuilder
-            .withImage(drsDockerImage)
-            .withCommand(drsCommand: _*)
-            .withMounts(mounts)
-            .setEnvironment(marthaEnv.asJava)
-            .withLabels(labels)
-          List(ActionBuilder.describeParameter(fileInput, labels), localizationAction)
         case sraPath: SraPath =>
           val sraConfig = config.getConfig("filesystems.sra")
 
@@ -78,6 +58,9 @@ trait PipelinesParameterConversions {
         case _: GcsPath =>
           // GCS paths will be localized with a separate localization script.
           Nil
+        case _: DrsPath =>
+          // DRS paths will be localized with a single call to cromwell-drs-localizer with a manifest
+          Nil
       }
     }
   }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
index 4aa52f89801..3b470b9096b 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
@@ -1,14 +1,21 @@
 package cromwell.backend.google.pipelines.v2beta.api
 
+import cloud.nio.impl.drs.DrsConfig
 import com.google.api.services.lifesciences.v2beta.model.{Action, Mount}
+import com.typesafe.config.ConfigFactory
 import cromwell.backend.google.pipelines.common.action.ActionCommands.localizeFile
 import cromwell.backend.google.pipelines.common.action.ActionLabels._
 import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.pipelines.common.PipelinesApiFileInput
 import cromwell.backend.google.pipelines.common.PipelinesApiJobPaths._
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.CreatePipelineParameters
 import cromwell.backend.google.pipelines.v2beta.PipelinesConversions._
 import cromwell.backend.google.pipelines.v2beta.ToParameter.ops._
-import cromwell.backend.google.pipelines.v2beta.api.ActionBuilder.cloudSdkShellAction
+import cromwell.backend.google.pipelines.v2beta.api.ActionBuilder.{EnhancedAction, cloudSdkShellAction}
+import cromwell.core.path.Path
+import cromwell.filesystems.drs.DrsPath
+
+import scala.jdk.CollectionConverters._
 
 
 trait Localization {
@@ -34,15 +41,59 @@ trait Localization {
     val runGcsLocalizationScript = cloudSdkShellAction(
       s"/bin/bash $gcsLocalizationContainerPath")(mounts = mounts, labels = localizationLabel)
 
+    val drsInputs: List[DrsPath] = createPipelineParameters.inputOutputParameters.fileInputParameters.collect {
+      case PipelinesApiFileInput(_, drsPath: DrsPath, _, _) => drsPath
+    }
+
+    val drsLocalizationActions = if (drsInputs.nonEmpty) {
+      val drsLocalizationManifestContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(DrsLocalizationManifestName)
+      val localizeDrsLocalizationManifest = cloudSdkShellAction(localizeFile(
+        cloudPath = createPipelineParameters.cloudCallRoot / DrsLocalizationManifestName,
+        containerPath = drsLocalizationManifestContainerPath))(mounts = mounts, labels = localizationLabel)
+
+      // Requester pays project id is stored on each DrsPath, but will be the same for all DRS inputs to a
+      // particular workflow because it's determined by the Google project set in workflow options.
+      val requesterPaysProjectId: Option[String] = drsInputs.flatMap(_.requesterPaysProjectIdOption).headOption
+      val runDrsLocalization = Localization.drsAction(drsLocalizationManifestContainerPath, mounts, localizationLabel, requesterPaysProjectId)
+      List(localizeDrsLocalizationManifest, runDrsLocalization)
+    } else List[Action]()
+
     // Any "classic" PAPI v2 one-at-a-time localizations for non-GCS inputs.
     val singletonLocalizations = createPipelineParameters.inputOutputParameters.fileInputParameters.flatMap(_.toActions(mounts).toList)
 
     val localizations =
       localizeGcsTransferLibrary ::
         localizeGcsLocalizationScript :: runGcsLocalizationScript ::
+        drsLocalizationActions :::
         localizeGcsDelocalizationScript ::
         singletonLocalizations
 
     ActionBuilder.annotateTimestampedActions("localization", Value.Localization)(localizations)
   }
 }
+
+object Localization {
+
+  def drsAction(manifestPath: Path,
+                mounts: List[Mount],
+                labels: Map[String, String],
+                requesterPaysProjectId: Option[String]
+               ): Action = {
+    val config = ConfigFactory.load
+    val drsResolverConfig = config.getConfig("filesystems.drs.global.config.resolver")
+    val drsConfig = DrsConfig.fromConfig(drsResolverConfig)
+    val drsDockerImage = config.getString("drs.localization.docker-image")
+
+    val manifestArg = List("-m", manifestPath.pathAsString)
+    val requesterPaysArg = requesterPaysProjectId.map(r => List("-r", r)).getOrElse(List.empty)
+    val drsCommand = manifestArg ++ requesterPaysArg
+
+    val drsResolverEnv = DrsConfig.toEnv(drsConfig)
+    ActionBuilder
+      .withImage(drsDockerImage)
+      .withCommand(drsCommand: _*)
+      .withMounts(mounts)
+      .setEnvironment(drsResolverEnv.asJava)
+      .withLabels(labels)
+  }
+}
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
index 9b93a976e22..e7189d453ad 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
@@ -2,14 +2,22 @@ package cromwell.backend.google.pipelines.v2beta
 
 import java.nio.file.Paths
 import cats.data.NonEmptyList
+import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
+import com.google.cloud.NoCredentials
+import com.typesafe.config.{Config, ConfigFactory}
 import common.assertion.CromwellTimeoutSpec
 import common.mock.MockSugar
 import cromwell.backend.google.pipelines.common.PipelinesApiFileInput
+import cromwell.backend.google.pipelines.common.io.{DiskType, PipelinesApiWorkingDisk}
 import cromwell.core.path.DefaultPathBuilder
+import cromwell.filesystems.drs.DrsPathBuilder
 import org.mockito.Mockito._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
+import scala.concurrent.duration.DurationInt
+
 class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   with MockSugar {
   behavior of "PipelinesParameterConversions"
@@ -44,4 +52,45 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Cro
 
     PipelinesApiAsyncBackendJobExecutionActor.groupParametersByGcsBucket(inputs) shouldEqual expected
   }
+
+  it should "generate a CSV manifest for DRS inputs, ignoring non-DRS inputs" in {
+    def makeDrsPathBuilder: DrsPathBuilder = {
+      val drsResolverConfig: Config = ConfigFactory.parseString(
+        """resolver {
+          |   url = "http://drshub-url"
+          |}
+          |""".stripMargin
+      )
+
+      val fakeCredentials = NoCredentials.getInstance
+
+      val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
+        throw new UnsupportedOperationException("PipelinesApiAsyncBackendJobExecutionActorSpec doesn't need to use drs read interpreter.")
+
+      DrsPathBuilder(
+        new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
+        None,
+      )
+    }
+
+    val mount = PipelinesApiWorkingDisk(DiskType.LOCAL, 1)
+
+    def makeDrsInput(name: String, drsUri: String, containerPath: String): PipelinesApiFileInput = {
+      val drsPath = makeDrsPathBuilder.build(drsUri).get
+      val containerRelativePath = DefaultPathBuilder.get(containerPath)
+      PipelinesApiFileInput(name, drsPath, containerRelativePath, mount)
+    }
+
+    val nonDrsInput: PipelinesApiFileInput = PipelinesApiFileInput("nnn",
+      DefaultPathBuilder.get("/local/nnn.bai"), DefaultPathBuilder.get("/path/to/nnn.bai"), mount)
+
+    val inputs = List(
+      makeDrsInput("aaa", "drs://drs.example.org/aaa", "path/to/aaa.bai"),
+      nonDrsInput,
+      makeDrsInput("bbb", "drs://drs.example.org/bbb", "path/to/bbb.bai")
+    )
+
+    PipelinesApiAsyncBackendJobExecutionActor.generateDrsLocalizerManifest(inputs) shouldEqual
+      "drs://drs.example.org/aaa,/cromwell_root/path/to/aaa.bai\r\ndrs://drs.example.org/bbb,/cromwell_root/path/to/bbb.bai\r\n"
+  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala
deleted file mode 100644
index c3ed9d27b02..00000000000
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesConversionsSpec.scala
+++ /dev/null
@@ -1,96 +0,0 @@
-package cromwell.backend.google.pipelines.v2beta
-
-import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
-import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleDrsCredentials}
-import com.google.cloud.NoCredentials
-import com.typesafe.config.{Config, ConfigFactory}
-import common.assertion.CromwellTimeoutSpec
-import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.GcsTransferConfiguration
-import cromwell.backend.google.pipelines.common.PipelinesApiFileInput
-import cromwell.backend.google.pipelines.common.action.ActionUtils
-import cromwell.backend.google.pipelines.common.io.{DiskType, PipelinesApiWorkingDisk}
-import cromwell.core.path.DefaultPathBuilder
-import cromwell.filesystems.drs.DrsPathBuilder
-import eu.timepit.refined.refineMV
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-import scala.jdk.CollectionConverters._
-import scala.concurrent.duration.DurationInt
-
-class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  behavior of "PipelinesConversions"
-  implicit val gcsTransferConfiguration: GcsTransferConfiguration =
-    GcsTransferConfiguration(transferAttempts = refineMV(1), parallelCompositeUploadThreshold = "0")
-
-  private val marthaConfig: Config = ConfigFactory.parseString(
-    """martha {
-      |   url = "http://martha-url"
-      |}
-      |""".stripMargin
-  )
-
-  private lazy val fakeCredentials = NoCredentials.getInstance
-
-  private val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
-    throw new UnsupportedOperationException("Currently PipelinesConversionsSpec doesn't need to use drs read interpreter.")
-
-  it should "create a DRS input parameter" in {
-
-    val drsPathBuilder = DrsPathBuilder(
-      new DrsCloudNioFileSystemProvider(marthaConfig, GoogleDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
-      None,
-    )
-    val drsPath = drsPathBuilder.build("drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba").get
-    val containerRelativePath = DefaultPathBuilder.get("path/to/file.bai")
-    val mount = PipelinesApiWorkingDisk(DiskType.LOCAL, 1)
-    val input = PipelinesApiFileInput("example", drsPath, containerRelativePath, mount)
-    val actions = PipelinesConversions.inputToParameter.toActions(input, Nil)
-    actions.size should be(2)
-
-    val logging = actions.head
-
-    logging.keySet.asScala should contain theSameElementsAs
-      Set("entrypoint", "commands", "imageUri", "labels", "mounts", "timeout")
-
-    logging.get("commands") should be(a[java.util.List[_]])
-    logging.get("commands").asInstanceOf[java.util.List[_]] should contain(
-      """printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" """ +
-        """Localizing\ input\ drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba\ """ +
-        """-\>\ /cromwell_root/path/to/file.bai"""
-    )
-
-    logging.get("mounts") should be(a[java.util.List[_]])
-    logging.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
-
-    logging.get("imageUri") should be(ActionUtils.CloudSdkImage)
-
-    val loggingLabels = logging.get("labels").asInstanceOf[java.util.Map[_, _]]
-    loggingLabels.keySet.asScala should contain theSameElementsAs List("logging", "inputName")
-    loggingLabels.get("logging") should be("Localization")
-    loggingLabels.get("inputName") should be("example")
-
-    val action = actions.tail.head
-
-    action.keySet.asScala should contain theSameElementsAs
-      Set("commands", "environment", "imageUri", "labels", "mounts")
-
-    action.get("commands") should be(a[java.util.List[_]])
-    action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
-      "drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba",
-      "/cromwell_root/path/to/file.bai"
-    )
-
-    action.get("mounts") should be(a[java.util.List[_]])
-    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
-
-    action.get("imageUri") should be("somerepo/drs-downloader:tagged")
-
-    val actionLabels = action.get("labels").asInstanceOf[java.util.Map[_, _]]
-    actionLabels.keySet.asScala should contain theSameElementsAs List("tag", "inputName")
-    actionLabels.get("tag") should be("Localization")
-    actionLabels.get("inputName") should be("example")
-  }
-
-}
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
index 37020b0b0d6..6afd75adbd6 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
@@ -81,9 +81,9 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
-          "virtualMachine" -> Map(
+          "virtualMachine" -> Map[String, Any](
             "machineType" -> "custom-1-1024",
             "preemptible" -> false
           ).asJava
@@ -115,7 +115,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
           "virtualMachine" -> Map(
             "machineType" -> "custom-1-1024",
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala
new file mode 100644
index 00000000000..f815ceebd14
--- /dev/null
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala
@@ -0,0 +1,67 @@
+package cromwell.backend.google.pipelines.v2beta.api
+
+import common.assertion.CromwellTimeoutSpec
+import cromwell.backend.google.pipelines.common.PipelinesApiJobPaths.DrsLocalizationManifestName
+import cromwell.core.path.DefaultPathBuilder
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import scala.jdk.CollectionConverters._
+
+class LocalizationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  behavior of "Localization"
+
+  it should "create the right action to localize DRS files using a manifest" in {
+
+    val manifestPathString = s"path/to/${DrsLocalizationManifestName}"
+    val manifestPath = DefaultPathBuilder.get(manifestPathString)
+    val tagKey = "tag"
+    val tagLabel = "myLabel"
+
+    val action = Localization.drsAction(manifestPath, Nil, Map(tagKey -> tagLabel), None)
+    action.keySet.asScala should contain theSameElementsAs
+      Set("commands", "environment", "imageUri", "labels", "mounts")
+
+    action.get("commands") should be(a[java.util.List[_]])
+    action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
+      "-m", manifestPathString
+    )
+
+    action.get("mounts") should be(a[java.util.List[_]])
+    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+
+    action.get("imageUri") should be("somerepo/drs-downloader:tagged")
+
+    val actionLabels = action.get("labels").asInstanceOf[java.util.Map[_, _]]
+    actionLabels.keySet.asScala should contain theSameElementsAs List("tag")
+    actionLabels.get(tagKey) should be(tagLabel)
+  }
+
+  it should "create the right action to localize DRS files using a manifest with requester pays" in {
+
+    val manifestPathString = s"path/to/${DrsLocalizationManifestName}"
+    val manifestPath = DefaultPathBuilder.get(manifestPathString)
+    val tagKey = "tag"
+    val tagLabel = "myLabel"
+    val requesterPaysProjectId = "123"
+
+    val action = Localization.drsAction(manifestPath, Nil, Map(tagKey -> tagLabel), Option(requesterPaysProjectId))
+    action.keySet.asScala should contain theSameElementsAs
+      Set("commands", "environment", "imageUri", "labels", "mounts")
+
+    action.get("commands") should be(a[java.util.List[_]])
+    action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
+      "-m", manifestPathString, "-r", requesterPaysProjectId
+    )
+
+    action.get("mounts") should be(a[java.util.List[_]])
+    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+
+    action.get("imageUri") should be("somerepo/drs-downloader:tagged")
+
+    val actionLabels = action.get("labels").asInstanceOf[java.util.Map[_, _]]
+    actionLabels.keySet.asScala should contain theSameElementsAs List("tag")
+    actionLabels.get(tagKey) should be(tagLabel)
+  }
+}
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 1fe5b743465..1e5637fff0e 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -1,5 +1,6 @@
 package cromwell.backend.impl.tes
 
+import common.exception.AggregatedMessageException
 import java.io.FileNotFoundException
 import java.nio.file.FileAlreadyExistsException
 import cats.syntax.apply._
@@ -30,6 +31,7 @@ import scala.util.{Failure, Success}
 
 sealed trait TesRunStatus {
   def isTerminal: Boolean
+  def sysLogs: Seq[String] = Seq.empty[String]
 }
 
 case object Running extends TesRunStatus {
@@ -40,8 +42,14 @@ case object Complete extends TesRunStatus {
   def isTerminal = true
 }
 
-case object FailedOrError extends TesRunStatus {
+case class Error(override val sysLogs: Seq[String] = Seq.empty[String]) extends TesRunStatus {
   def isTerminal = true
+  override def toString = "SYSTEM_ERROR"
+}
+
+case class Failed(override val sysLogs: Seq[String] = Seq.empty[String]) extends TesRunStatus {
+  def isTerminal = true
+  override def toString = "EXECUTOR_ERROR"
 }
 
 case object Cancelled extends TesRunStatus {
@@ -80,6 +88,14 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
 
   private val tesEndpoint = workflowDescriptor.workflowOptions.getOrElse("endpoint", tesConfiguration.endpointURL)
 
+  // Temporary support for configuring the format we use to send BlobPaths to TES.
+  // Added 10/2022 as a workaround for the CromwellOnAzure TES server expecting
+  // blob containers to be mounted via blobfuse rather than addressed natively.
+  private val transformBlobToLocalPaths: Boolean =
+    configurationDescriptor.backendConfig
+      .getAs[Boolean]("transform-blob-to-local-path")
+      .getOrElse(false)
+
   override lazy val jobTag: String = jobDescriptor.key.tag
 
   private val outputMode = validate {
@@ -148,7 +164,7 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
         mode)
     })
 
-    tesTask.map(TesTask.makeTask)
+    tesTask.map(TesTask.makeTask(_, transformBlobToLocalPaths))
   }
 
   def writeScriptFile(): Future[Unit] = {
@@ -209,6 +225,21 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
   override def requestsAbortAndDiesImmediately: Boolean = false
 
   override def pollStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[TesRunStatus] = {
+    for {
+      status <- queryStatusAsync(handle)
+      errorLog <- status match {
+          case Error(_) | Failed(_) => getErrorLogs(handle)
+          case _ => Future.successful(Seq.empty[String])
+      }
+      statusWithLog = status match {
+        case Error(_) => Error(errorLog)
+        case Failed(_) => Failed(errorLog)
+        case _ => status
+      }
+    } yield statusWithLog
+  }
+
+  private def queryStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[TesRunStatus] = {
     makeRequest[MinimalTaskView](HttpRequest(uri = s"$tesEndpoint/${handle.pendingJob.jobId}?view=MINIMAL")) map {
       response =>
         val state = response.state
@@ -221,24 +252,40 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
             jobLogger.info(s"Job ${handle.pendingJob.jobId} was canceled")
             Cancelled
 
-          case s if s.contains("ERROR") =>
+          case s if s.contains("EXECUTOR_ERROR") =>
+            jobLogger.info(s"TES reported a failure for Job ${handle.pendingJob.jobId}: '$s'")
+            Failed()
+
+          case s if s.contains("SYSTEM_ERROR") =>
             jobLogger.info(s"TES reported an error for Job ${handle.pendingJob.jobId}: '$s'")
-            FailedOrError
+            Error()
 
           case _ => Running
         }
     }
   }
 
+  private def getErrorLogs(handle: StandardAsyncPendingExecutionHandle): Future[Seq[String]] = {
+    makeRequest[Task](HttpRequest(uri = s"$tesEndpoint/${handle.pendingJob.jobId}?view=FULL")) map { response =>
+      response.logs.flatMap(_.lastOption).flatMap(_.system_logs).getOrElse(Seq.empty[String])
+    }
+  }
+
   override def customPollStatusFailure: PartialFunction[(ExecutionHandle, Exception), ExecutionHandle] = {
     case (oldHandle: StandardAsyncPendingExecutionHandle@unchecked, e: Exception) =>
       jobLogger.error(s"$tag TES Job ${oldHandle.pendingJob.jobId} has not been found, failing call")
       FailedNonRetryableExecutionHandle(e, kvPairsToSave = None)
   }
 
+  private def handleExecutionError(status: TesRunStatus, returnCode: Option[Int]): Future[ExecutionHandle] = {
+    val exception = new AggregatedMessageException(s"Task ${jobDescriptor.key.tag} failed for unknown reason: ${status.toString()}", status.sysLogs)
+    Future.successful(FailedNonRetryableExecutionHandle(exception, returnCode, None))
+  }
+
   override def handleExecutionFailure(status: StandardAsyncRunState, returnCode: Option[Int]) = {
     status match {
       case Cancelled => Future.successful(AbortedExecutionHandle)
+      case Error(_) | Failed(_) => handleExecutionError(status, returnCode)
       case _ => super.handleExecutionFailure(status, returnCode)
     }
   }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
index 3d55a9f3a1c..264ba6299bd 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
@@ -11,10 +11,10 @@ class TesConfiguration(val configurationDescriptor: BackendConfigurationDescript
   val useBackendParameters =
     configurationDescriptor
       .backendConfig
-      .as[Option[Boolean]](TesConfiguration.useBackendParamtersKey)
+      .as[Option[Boolean]](TesConfiguration.useBackendParametersKey)
       .getOrElse(false)
 }
 
 object TesConfiguration {
-  final val useBackendParamtersKey = "use_tes_11_preview_backend_parameters"
+  final val useBackendParametersKey = "use_tes_11_preview_backend_parameters"
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
index 4212ff4be67..c5b3c4df66d 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
@@ -3,10 +3,13 @@ package cromwell.backend.impl.tes
 import cats.syntax.validated._
 import com.typesafe.config.Config
 import common.validation.ErrorOr.ErrorOr
+import cromwell.backend.google.pipelines.common.DisksValidation
+import cromwell.backend.google.pipelines.common.io.{PipelinesApiAttachedDisk, PipelinesApiEmptyMountedDisk, PipelinesApiWorkingDisk}
 import cromwell.backend.standard.StandardValidatedRuntimeAttributesBuilder
 import cromwell.backend.validation._
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
+import wdl4s.parser.MemoryUnit
 import wom.RuntimeAttributesKeys
 import wom.format.MemorySize
 import wom.types.{WomIntegerType, WomStringType}
@@ -36,6 +39,9 @@ object TesRuntimeAttributes {
 
   private def diskSizeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[MemorySize] = MemoryValidation.optional(DiskSizeKey)
 
+  private def diskSizeCompatValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Seq[PipelinesApiAttachedDisk]] =
+    DisksValidation.optional
+
   private def memoryValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[MemorySize] = MemoryValidation.optional(RuntimeAttributesKeys.MemoryKey)
 
   private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
@@ -45,10 +51,14 @@ object TesRuntimeAttributes {
   private def preemptibleValidation(runtimeConfig: Option[Config]) = PreemptibleValidation.default(runtimeConfig)
 
   def runtimeAttributesBuilder(backendRuntimeConfig: Option[Config]): StandardValidatedRuntimeAttributesBuilder =
+    // !! NOTE !! If new validated attributes are added to TesRuntimeAttributes, be sure to include
+    // their validations here so that they will be handled correctly with backendParameters.
+    // Location 2 of 2
     StandardValidatedRuntimeAttributesBuilder.default(backendRuntimeConfig).withValidation(
       cpuValidation(backendRuntimeConfig),
       memoryValidation(backendRuntimeConfig),
       diskSizeValidation(backendRuntimeConfig),
+      diskSizeCompatValidation(backendRuntimeConfig),
       dockerValidation,
       dockerWorkingDirValidation,
       preemptibleValidation(backendRuntimeConfig),
@@ -71,13 +81,45 @@ object TesRuntimeAttributes {
       Map.empty
   }
 
+  private def detectDiskFormat(backendRuntimeConfig: Option[Config], validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[MemorySize] = {
+
+    def adaptPapiDisks(disks: Seq[PipelinesApiAttachedDisk]): MemorySize = {
+      disks match {
+        case disk :: Nil if disk.isInstanceOf[PipelinesApiWorkingDisk] =>
+            MemorySize(disk.sizeGb.toDouble, MemoryUnit.GB)
+        case _ :: _ =>
+          // When a user specifies only a custom disk, we add the default disk in the background, so we technically have multiple disks.
+          // But we don't want to confuse the user with `multiple disks` message when they only put one.
+          if (disks.exists(_.isInstanceOf[PipelinesApiEmptyMountedDisk]))
+            throw new IllegalArgumentException("Disks with custom mount points are not supported by this backend")
+          else
+            // Multiple `local-disk` is not legal, but possible and should be detected
+            throw new IllegalArgumentException("Expecting exactly one disk definition on this backend, found multiple")
+      }
+    }
+
+    val maybeTesDisk: Option[MemorySize] =
+      RuntimeAttributesValidation.extractOption(diskSizeValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+    val maybePapiDisk: Option[Seq[PipelinesApiAttachedDisk]] =
+      RuntimeAttributesValidation.extractOption(diskSizeCompatValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+
+    (maybeTesDisk, maybePapiDisk) match {
+      case (Some(tesDisk: MemorySize), _) =>
+        Option(tesDisk) // If WDLs are in circulation with both `disk` and `disks`, pick the one intended for this backend
+      case (None, Some(papiDisks: Seq[PipelinesApiAttachedDisk])) =>
+        Option(adaptPapiDisks(papiDisks))
+      case _ =>
+        None
+    }
+  }
+
   def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes, rawRuntimeAttributes: Map[String, WomValue], config: TesConfiguration): TesRuntimeAttributes = {
     val backendRuntimeConfig = config.runtimeConfig
     val docker: String = RuntimeAttributesValidation.extract(dockerValidation, validatedRuntimeAttributes)
     val dockerWorkingDir: Option[String] = RuntimeAttributesValidation.extractOption(dockerWorkingDirValidation.key, validatedRuntimeAttributes)
     val cpu: Option[Int Refined Positive] = RuntimeAttributesValidation.extractOption(cpuValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
     val memory: Option[MemorySize] = RuntimeAttributesValidation.extractOption(memoryValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
-    val disk: Option[MemorySize] = RuntimeAttributesValidation.extractOption(diskSizeValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+    val disk: Option[MemorySize] = detectDiskFormat(backendRuntimeConfig, validatedRuntimeAttributes)
     val failOnStderr: Boolean =
       RuntimeAttributesValidation.extract(failOnStderrValidation(backendRuntimeConfig), validatedRuntimeAttributes)
     val continueOnReturnCode: ContinueOnReturnCode =
@@ -87,12 +129,14 @@ object TesRuntimeAttributes {
 
     // !! NOTE !! If new validated attributes are added to TesRuntimeAttributes, be sure to include
     // their validations here so that they will be handled correctly with backendParameters.
+    // Location 1 of 2
     val validations = Set(
       dockerValidation,
       dockerWorkingDirValidation,
       cpuValidation(backendRuntimeConfig),
       memoryValidation(backendRuntimeConfig),
       diskSizeValidation(backendRuntimeConfig),
+      diskSizeCompatValidation(backendRuntimeConfig),
       failOnStderrValidation(backendRuntimeConfig),
       continueOnReturnCodeValidation(backendRuntimeConfig),
       preemptibleValidation(backendRuntimeConfig)
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index 52fdd7c3fce..5d1a844bb83 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -3,9 +3,14 @@ package cromwell.backend.impl.tes
 import common.collections.EnhancedCollections._
 import common.util.StringUtil._
 import cromwell.backend.impl.tes.OutputMode.OutputMode
-import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendWorkflowDescriptor}
+import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor}
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.{DefaultPathBuilder, Path}
+import net.ceedubs.ficus.Ficus._
+
+import scala.language.postfixOps
+import scala.util.Try
+
 import wdl.draft2.model.FullyQualifiedName
 import wdl4s.parser.MemoryUnit
 import wom.InstantiatedCommand
@@ -13,9 +18,8 @@ import wom.callable.Callable.OutputDefinition
 import wom.expression.NoIoFunctionSet
 import wom.values._
 
-import scala.language.postfixOps
-import scala.util.Try
-
+final case class WorkflowExecutionIdentityConfig(value: String) {override def toString: String = value.toString}
+final case class WorkflowExecutionIdentityOption(value: String) {override def toString: String = value}
 final case class TesTask(jobDescriptor: BackendJobDescriptor,
                          configurationDescriptor: BackendConfigurationDescriptor,
                          jobLogger: JobLogger,
@@ -32,6 +36,16 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
   private val workflowDescriptor = jobDescriptor.workflowDescriptor
   private val workflowName = workflowDescriptor.callable.name
   private val fullyQualifiedTaskName = jobDescriptor.taskCall.fullyQualifiedName
+  private val workflowExecutionIdentityConfig: Option[WorkflowExecutionIdentityConfig] =
+    configurationDescriptor.backendConfig
+      .getAs[String]("workflow-execution-identity")
+      .map(WorkflowExecutionIdentityConfig)
+  private val workflowExecutionIdentityOption: Option[WorkflowExecutionIdentityOption] =
+    workflowDescriptor
+      .workflowOptions
+      .get(TesWorkflowOptionKeys.WorkflowExecutionIdentity)
+      .toOption
+      .map(WorkflowExecutionIdentityOption)
   val name: String = fullyQualifiedTaskName
   val description: String = jobDescriptor.toString
 
@@ -212,7 +226,15 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
     result
   }
 
-  val resources: Resources = TesTask.makeResources(runtimeAttributes, workflowDescriptor)
+  val preferedWorkflowExecutionIdentity = TesTask.getPreferredWorkflowExecutionIdentity(
+      workflowExecutionIdentityConfig,
+      workflowExecutionIdentityOption
+  )
+
+  val resources: Resources = TesTask.makeResources(
+    runtimeAttributes,
+    preferedWorkflowExecutionIdentity
+  )
 
   val executors = Seq(Executor(
     image = dockerImageUsed,
@@ -226,21 +248,22 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
 }
 
 object TesTask {
+  // Helper to determine which source to use for a workflowExecutionIdentity
+  def getPreferredWorkflowExecutionIdentity(configIdentity: Option[WorkflowExecutionIdentityConfig],
+                                           workflowOptionsIdentity: Option[WorkflowExecutionIdentityOption]): Option[String] = {
+    configIdentity.map(_.value).orElse(workflowOptionsIdentity.map(_.value))
+  }
   def makeResources(runtimeAttributes: TesRuntimeAttributes,
-                    workflowDescriptor: BackendWorkflowDescriptor): Resources = {
+                    workflowExecutionId: Option[String]): Resources = {
 
     // This was added in BT-409 to let us pass information to an Azure
     // TES server about which user identity to run tasks as.
     // Note that we validate the type of WorkflowExecutionIdentity
     // in TesInitializationActor.
     val backendParameters = runtimeAttributes.backendParameters ++
-      workflowDescriptor
-        .workflowOptions
-        .get(TesWorkflowOptionKeys.WorkflowExecutionIdentity)
-        .toOption
+      workflowExecutionId
         .map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option(_))
         .toMap
-
     val disk :: ram :: _ = Seq(runtimeAttributes.disk, runtimeAttributes.memory) map {
       case Some(x) =>
         Option(x.to(MemoryUnit.GB).amount)
@@ -258,14 +281,16 @@ object TesTask {
     )
   }
 
-  def makeTask(tesTask: TesTask): Task = {
+  def makeTask(tesTask: TesTask, transformBlobToLocalPath: Boolean = false): Task = {
+    val inputs = if (transformBlobToLocalPath) transformInputs(tesTask.inputs) else tesTask.inputs
+    val outputs = if (transformBlobToLocalPath) transformOutputs(tesTask.outputs) else tesTask.outputs
     Task(
       id = None,
       state = None,
       name = Option(tesTask.name),
       description = Option(tesTask.description),
-      inputs = Option(tesTask.inputs),
-      outputs = Option(tesTask.outputs),
+      inputs = Option(inputs),
+      outputs = Option(outputs),
       resources = Option(tesTask.resources),
       executors = tesTask.executors,
       volumes = None,
@@ -273,6 +298,20 @@ object TesTask {
       logs = None
     )
   }
+
+  def transformInputs(inputs: Seq[Input]): Seq[Input] = inputs.map(i =>
+    i.copy(url=i.url.map(transformBlobString))
+  )
+
+  def transformOutputs(outputs: Seq[Output]): Seq[Output] = outputs.map(i =>
+    i.copy(url=i.url.map(transformBlobString))
+  )
+
+  val blobSegment = ".blob.core.windows.net"
+  def transformBlobString(s: String): String = if (s.contains(blobSegment)) {
+    s.replaceFirst("https:/", "").replaceFirst(blobSegment, "")
+  } else s
+
 }
 
 // Field requirements in classes below based off GA4GH schema
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
index 1b3b3b7aea8..e1984fb65dc 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
@@ -160,6 +160,54 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
       assertFailure(runtimeAttributes, "Expecting disk runtime attribute to be an Integer or String with format '8 GB'")
     }
 
+    "parse an HDD definition" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 HDD"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(disk = Option(MemorySize.parse("10 GB").get))
+      assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "parse an SSD definition" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 SSD"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(disk = Option(MemorySize.parse("10 GB").get))
+      assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "refuse multiple `local-disk` instances" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 SSD, local-disk 20 SSD"))
+      assertFailure(runtimeAttributes, "Expecting exactly one disk definition on this backend, found multiple")
+    }
+
+    "refuse custom mount points" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("/some/mnt 20 SSD"))
+      assertFailure(runtimeAttributes, "Disks with custom mount points are not supported by this backend")
+    }
+
+    "refuse custom AND multiple mount points" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("/mnt/tmp 10 LOCAL, local-disk 20 HDD"))
+      assertFailure(runtimeAttributes, "Disks with custom mount points are not supported by this backend")
+    }
+
+    "not accept a single comma" ignore {
+      // Surprisingly, the PAPI code we call under the covers validates `,` and give the user a default disk.
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString(","))
+      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: ','")
+    }
+
+    "not accept empty string" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString(""))
+      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: ''")
+    }
+
+    "not accept `banana`" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("banana"))
+      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: 'banana'")
+    }
+
+    "not accept a random number (chosen by fair dice roll)" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomInteger(4))
+      assertFailure(runtimeAttributes, "Expecting disks runtime attribute to be a comma separated String or Array[String]")
+    }
+
     "validate a valid dockerWorkingDir entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "dockerWorkingDir" -> WomString("/tmp"))
       val expectedRuntimeAttributes = expectedDefaults.copy(dockerWorkingDir = Option("/tmp"))
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index 0e8440f2a1d..3e5a79b33c9 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -2,15 +2,15 @@ package cromwell.backend.impl.tes
 
 import common.assertion.CromwellTimeoutSpec
 import common.mock.MockSugar
-import cromwell.backend.{BackendSpec, TestConfig}
 import cromwell.backend.validation.ContinueOnReturnCodeSet
+import cromwell.backend.{BackendSpec, TestConfig}
 import cromwell.core.WorkflowOptions
 import cromwell.core.labels.Labels
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.DefaultPathBuilder
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
-import spray.json.{JsObject, JsString, JsValue}
+import spray.json.{JsObject, JsValue}
 import wom.InstantiatedCommand
 
 class TesTaskSpec
@@ -32,32 +32,44 @@ class TesTaskSpec
     Map.empty
   )
 
-  def workflowDescriptorWithIdentity(excIdentity: Option[String]) = {
-    val optionsMap: Map[String, JsValue] = excIdentity.map(i => TesWorkflowOptionKeys.WorkflowExecutionIdentity -> JsString(i)).toMap
-    buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld, None, WorkflowOptions(JsObject(optionsMap)))
-  }
-
   it should "create the correct resources when an identity is passed in WorkflowOptions" in {
-    val wd = workflowDescriptorWithIdentity(Option("abc123"))
-    TesTask.makeResources(runtimeAttributes, wd) shouldEqual
+    val wei = Option("abc123")
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
         Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123")))
     )
   }
 
   it should "create the correct resources when an empty identity is passed in WorkflowOptions" in {
-    val wd = workflowDescriptorWithIdentity(Option(""))
-    TesTask.makeResources(runtimeAttributes, wd) shouldEqual
+    val wei = Option("")
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
         Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("")))
     )
   }
 
   it should "create the correct resources when no identity is passed in WorkflowOptions" in {
-    val wd = workflowDescriptorWithIdentity(None)
-    TesTask.makeResources(runtimeAttributes, wd) shouldEqual
+    val wei = None
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
         Resources(None, None, None, Option(false), None, Option(Map.empty[String, Option[String]])
     )
   }
 
+  it should "create the correct resources when an identity is passed in via backend config" in {
+    val weic = Option(WorkflowExecutionIdentityConfig("abc123"))
+    val weio = Option(WorkflowExecutionIdentityOption("def456"))
+    val wei = TesTask.getPreferredWorkflowExecutionIdentity(weic, weio)
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
+        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123")))
+    )
+  }
+
+  it should "create the correct resources when no identity is passed in via backend config" in {
+    val weic = None
+    val weio = Option(WorkflowExecutionIdentityOption("def456"))
+    val wei = TesTask.getPreferredWorkflowExecutionIdentity(weic, weio)
+    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
+        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("def456")))
+    )
+  }
 
   it should "copy labels to tags" in {
     val jobLogger = mock[JobLogger]
@@ -88,4 +100,28 @@ class TesTaskSpec
 
     task.tags shouldBe Option(Map("foo" -> "bar"))
   }
+
+  it should "apply the correct transformation to a blob path" in {
+    val orig = "https://coaexternalstorage.blob.core.windows.net/cromwell/mydir/myfile.txt"
+    TesTask.transformBlobString(orig) shouldBe "/coaexternalstorage/cromwell/mydir/myfile.txt"
+  }
+
+  it should "not transform a non-blob path" in {
+    val orig = "https://some-bogus-url.test/cromwell/mydir/myfile.txt"
+    TesTask.transformBlobString(orig) shouldBe orig
+  }
+
+  it should "transform inputs" in {
+    val baseInput = Input(
+      Option("name"),
+      Option("descr"),
+      Option("https://coaexternalstorage.blob.core.windows.net/cromwell/mydir/myfile.txt"),
+      "path",
+      Option("type"),
+      Option("content"),
+    )
+    val inputs = Option(Seq(baseInput))
+    val outcome = inputs.map(TesTask.transformInputs)
+    outcome.get.head.url.get shouldBe "/coaexternalstorage/cromwell/mydir/myfile.txt"
+  }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
index c1f3c18242b..24194807f17 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
@@ -196,7 +196,7 @@ object AstTools {
           val pairType = womType.asInstanceOf[WomPairType]
           WomPair(subElements.head.womValue(pairType.leftType, wdlSyntaxErrorFormatter), subElements(1).womValue(pairType.rightType, wdlSyntaxErrorFormatter))
         } else {
-          throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).getOrElse("No AST").toString})")
+          throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})")
         }
       }
 
@@ -224,7 +224,7 @@ object AstTools {
         case a: Ast if a.getName == "TupleLiteral" => astTupleToValue(a)
         case a: Ast if a.getName == "MapLiteral" && womType.isInstanceOf[WomMapType] => astToMap(a)
         case a: Ast if a.getName == "ObjectLiteral" && womType == WomObjectType => astToObject(a)
-        case _ => throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).getOrElse("No AST").toString})")
+        case _ => throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})")
       }
     }
   }
diff --git a/wom/src/main/scala/wom/util/YamlUtils.scala b/wom/src/main/scala/wom/util/YamlUtils.scala
index b4e0f063c9b..50dffc0457d 100644
--- a/wom/src/main/scala/wom/util/YamlUtils.scala
+++ b/wom/src/main/scala/wom/util/YamlUtils.scala
@@ -38,7 +38,7 @@ object YamlUtils {
             maxDepth: Int Refined NonNegative = defaultMaxDepth
            ): Either[ParsingFailure, Json] = {
     try {
-      val yamlConstructor = new SafeConstructor()
+      val yamlConstructor = new SafeConstructor(loaderOptions)
       val yamlComposer = new MaxDepthComposer(yaml, maxDepth)
       yamlConstructor.setComposer(yamlComposer)
       val parsed = yamlConstructor.getSingleData(classOf[AnyRef])
@@ -76,12 +76,14 @@ object YamlUtils {
   // org.yaml.snakeyaml.error.YAMLException: Number of aliases for non-scalar nodes exceeds the specified max=50
   // that comes from the SnakeYAML library.
   private val loaderOptions = new LoaderOptions()
+  loaderOptions.setAllowRecursiveKeys(true)
+  loaderOptions.setNestingDepthLimit(1000)
   loaderOptions.setMaxAliasesForCollections(Integer.MAX_VALUE)
 
   /** Extends SnakeYaml's Composer checking for a maximum depth before a StackOverflowError occurs. */
   private class MaxDepthComposer(yaml: String, maxDepth: Int Refined NonNegative)
     extends Composer(
-      new ParserImpl(new StreamReader(new StringReader(yaml))),
+      new ParserImpl(new StreamReader(new StringReader(yaml)), loaderOptions),
       new Resolver(),
       loaderOptions
     ) {
diff --git a/wom/src/test/scala/wom/types/WomFileTypeSpec.scala b/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
index 217c15964cc..c4a90fadb07 100644
--- a/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
@@ -65,7 +65,7 @@ class WomFileTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     }
   }
 
-  lazy val failedCoercionTests = Table(
+  lazy val failedCoercionTests = Table[String, WomType, Any, String](
     ("description", "womFileType", "value", "expected"),
 
     ("a double to a dir", WomUnlistedDirectoryType, 6.28318,
diff --git a/wom/src/test/scala/wom/types/WomTypeSpec.scala b/wom/src/test/scala/wom/types/WomTypeSpec.scala
index 01c5030806d..4d3c7befeb5 100644
--- a/wom/src/test/scala/wom/types/WomTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomTypeSpec.scala
@@ -10,6 +10,7 @@ import wom.values._
 
 import scala.runtime.ScalaRunTime
 import scala.util.Random
+import scala.util.matching.Regex
 
 
 class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
@@ -32,7 +33,7 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     WomSingleFileType.stableName shouldEqual "File"
   }
 
-  val rawValuesCoercedToType = Table(
+  val rawValuesCoercedToType = Table[Any, WomType, Any, Regex](
     (
       "Raw Value",
       "WomType",
@@ -43,33 +44,33 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       WomString("hello"),
       WomIntegerType,
       classOf[NumberFormatException],
-      "For input string: \"hello\""
+      "For input string: \"hello\"".r
     ),
     (
       WomInteger(0),
       WomBooleanType,
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '0' of type 'Int' to 'Boolean'."""
+      """No coercion defined from wom value\(s\) '0' of type 'Int' to 'Boolean'.""".r
     ),
     (
       0,
       WomBooleanType,
       classOf[IllegalArgumentException],
-      "No coercion defined from '0' of type 'java.lang.Integer' to 'Boolean'."
+      "No coercion defined from '0' of type 'java.lang.Integer' to 'Boolean'.".r
     ),
     (
       Array(0, 1, 2, 3, 4),
       WomBooleanType,
       classOf[IllegalArgumentException],
-      """No coercion defined from 'Array\(0, 1, 2\)' of type 'int\[\]' to 'Boolean'."""
+      """No coercion defined from 'Array\(0, 1, 2\)' of type 'int\[\]' to 'Boolean'.""".r
     ),
     (
       new AnyRef {},
       WomBooleanType,
       classOf[IllegalArgumentException],
-      "No coercion defined from" +
+      ("No coercion defined from" +
         """ 'wom.types.WomTypeSpec\$\$anon\$(.*)@.*' of type""" +
-        """ 'wom.types.WomTypeSpec\$\$anon\$\1' to 'Boolean'."""
+        """ 'wom.types.WomTypeSpec\$\$anon\$\1' to 'Boolean'.""").r
     ),
     (
       WomArray(WomArrayType(WomOptionalType(WomIntegerType)), Seq(
@@ -81,19 +82,19 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       ),
       WomOptionalType(WomMaybeEmptyArrayType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '\[0, 1, 2\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'."""
+      """No coercion defined from wom value\(s\) '\[0, 1, 2\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'.""".r
     ),
     (
       WomArray(WomArrayType(WomOptionalType(WomIntegerType)), Seq(WomOptionalValue.none(WomIntegerType))),
       WomOptionalType(WomMaybeEmptyArrayType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '\[null\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'."""
+      """No coercion defined from wom value\(s\) '\[null\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'.""".r
     ),
     (
       WomOptionalValue.none(WomArrayType(WomIntegerType)),
       WomMaybeEmptyArrayType(WomOptionalType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) 'null' of type 'Array\[Int\]\?' to 'Array\[Int\?\]'."""
+      """No coercion defined from wom value\(s\) 'null' of type 'Array\[Int\]\?' to 'Array\[Int\?\]'.""".r
     )
   )
 
diff --git a/womtool/src/main/scala/womtool/graph/WomGraph.scala b/womtool/src/main/scala/womtool/graph/WomGraph.scala
index d81f36e5538..b1957a1545c 100644
--- a/womtool/src/main/scala/womtool/graph/WomGraph.scala
+++ b/womtool/src/main/scala/womtool/graph/WomGraph.scala
@@ -10,8 +10,6 @@ import common.Checked
 import common.transforms.CheckedAtoB
 import common.validation.Validation._
 import common.collections.EnhancedCollections._
-import cwl.CwlDecoder
-import cwl.preprocessor.CwlPreProcessor
 import spray.json.{JsArray, JsBoolean, JsNull, JsNumber, JsObject, JsString, JsValue}
 import wdl.draft2.model.{WdlNamespace, WdlNamespaceWithWorkflow}
 import wdl.transforms.base.wdlom2wom.FileElementToWomBundleInputs
@@ -21,7 +19,6 @@ import wdl.draft3.transforms.parsing.fileToAst
 import wdl.transforms.draft2.wdlom2wom.WdlDraft2WomBundleMakers._
 import wom.callable.WorkflowDefinition
 import wom.executable.WomBundle
-import wom.expression.NoIoFunctionSet
 import wom.graph._
 import wom.transforms.WomBundleMaker.ops._
 import wom.types._
@@ -161,8 +158,6 @@ class WomGraph(graphName: String, graph: Graph) {
 
 object WomGraph {
 
-  implicit val cwlPreProcessor = CwlPreProcessor.noLogging
-
   final case class WorkflowDigraph(workflowName: String, digraph: NodesAndLinks)
   final case class NodesAndLinks(nodes: Set[String], links: Set[String]) {
     def wrapNodes(f: Set[String] => String) = this.copy(Set(f(nodes)), links)
@@ -174,7 +169,7 @@ object WomGraph {
   }
 
   def fromFiles(mainFile: String) = {
-    val graph = if (mainFile.toLowerCase().endsWith("wdl")) womExecutableFromWdl(mainFile) else womExecutableFromCwl(mainFile)
+    val graph = womExecutableFromWdl(mainFile)
     new WomGraph("workflow", graph)
   }
 
@@ -204,21 +199,6 @@ object WomGraph {
     }
   }
 
-  private def womExecutableFromCwl(filePath: String): Graph = {
-    import cwl.AcceptAllRequirements
-    (for {
-      clt <- CwlDecoder.decodeCwlFile(File(filePath)).
-        value.
-        unsafeRunSync()
-      inputs = clt.requiredInputs
-      fakedInputs = JsObject(inputs map { i => i._1 -> fakeInput(i._2) })
-      wom <- clt.womExecutable(AcceptAllRequirements, Option(fakedInputs.prettyPrint), NoIoFunctionSet, strictValidation = false)
-    } yield wom) match {
-      case Right(womExecutable) => womExecutable.graph
-      case Left(e) => throw new Exception(s"Can't build WOM executable from CWL: ${e.toList.mkString("\n", "\n", "\n")}")
-    }
-  }
-
   def fakeInput(womType: WomType): JsValue = womType match {
     case WomStringType => JsString("hio")
     case WomIntegerType | WomFloatType | WomLongType => JsNumber(25)
diff --git a/womtool/src/main/scala/womtool/input/WomGraphMaker.scala b/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
index 50749640bcc..f0d238392fa 100644
--- a/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
+++ b/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
@@ -8,7 +8,6 @@ import common.validation.Validation._
 import cromwell.core.path.Path
 import cromwell.languages.LanguageFactory
 import cromwell.languages.util.ImportResolver._
-import languages.cwl.CwlV1_0LanguageFactory
 import languages.wdl.biscayne.WdlBiscayneLanguageFactory
 import languages.wdl.draft2.WdlDraft2LanguageFactory
 import languages.wdl.draft3.WdlDraft3LanguageFactory
@@ -32,8 +31,7 @@ object WomGraphMaker {
       val languageFactory =
         List(
           new WdlDraft3LanguageFactory(ConfigFactory.empty()),
-          new WdlBiscayneLanguageFactory(ConfigFactory.empty()),
-          new CwlV1_0LanguageFactory(ConfigFactory.empty()))
+          new WdlBiscayneLanguageFactory(ConfigFactory.empty()))
           .find(_.looksParsable(mainFileContents))
           .getOrElse(new WdlDraft2LanguageFactory(ConfigFactory.empty()))
 

From 17efd599d541a096dc5704991daeaefdd794fefd Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 10 May 2023 11:43:54 -0400
Subject: [PATCH 166/326] WX-1103 Accelerate TES CI (#7130)

---
 centaur/test_cromwell.sh     | 2 +-
 src/ci/bin/testCentaurTes.sh | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/centaur/test_cromwell.sh b/centaur/test_cromwell.sh
index 2f330f1feb0..9161f2da5ad 100755
--- a/centaur/test_cromwell.sh
+++ b/centaur/test_cromwell.sh
@@ -37,7 +37,7 @@ Arguments:
 INITIAL_DIR=$(pwd)
 RUN_DIR=$(pwd)
 LOG_DIR="${RUN_DIR}"/logs
-TEST_THREAD_COUNT=16
+TEST_THREAD_COUNT=16  # Note that most users of this script override this value
 CENTAUR_SBT_COVERAGE=false
 CROMWELL_TIMEOUT=10s
 SUITE=""
diff --git a/src/ci/bin/testCentaurTes.sh b/src/ci/bin/testCentaurTes.sh
index 8822a727b24..7cad5b26832 100755
--- a/src/ci/bin/testCentaurTes.sh
+++ b/src/ci/bin/testCentaurTes.sh
@@ -58,9 +58,10 @@ startup_funnel
 # read_file_limits:          Fail only in Travis for unknown reason (Note that the draft 3 version does not fail)
 # docker_hash_dockerhub:     Prone to request rate limiting by Dockerhub
 
-# Limiting Centaur to 4 threads here in order to try to prevent exceeding the OS's max open files limit: BA-6153
+# Setting threads to 8 upon moving from Travis to Github Actions. If we run into problems with
+# exceeding the OS's max open files limit, reduce. See BA-6153.
 cromwell::build::run_centaur \
-    -p 2 \
+    -p 8 \
     -e docker_hash_dockerhub \
     -e call_cache_capoeira_local \
     -e draft3_call_cache_capoeira_local \

From 62509afab0a8f8b19c70a271df904d13b47a2fcc Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 12 May 2023 09:21:38 -0400
Subject: [PATCH 167/326] Fix Horicromtal Deadlock Test (#7131)

---
 src/ci/bin/get_cromwell_hosts.py | 4 ++--
 src/ci/bin/test-deadlock.sh      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/ci/bin/get_cromwell_hosts.py b/src/ci/bin/get_cromwell_hosts.py
index bfea186519c..e894a5b1db1 100644
--- a/src/ci/bin/get_cromwell_hosts.py
+++ b/src/ci/bin/get_cromwell_hosts.py
@@ -1,9 +1,9 @@
 # Based on https://stackoverflow.com/a/39895650
 from __future__ import print_function
-from docker import Client
+from docker import APIClient
 import os
 
-cli = Client(base_url='unix://var/run/docker.sock')
+cli = APIClient(base_url='unix://var/run/docker.sock')
 
 our_hostname = os.environ.get("HOSTNAME")
 
diff --git a/src/ci/bin/test-deadlock.sh b/src/ci/bin/test-deadlock.sh
index 9cddbb65ade..7cde84c173d 100755
--- a/src/ci/bin/test-deadlock.sh
+++ b/src/ci/bin/test-deadlock.sh
@@ -2,7 +2,7 @@
 
 set -euo pipefail
 
-pip3 install docker-py
+pip3 install docker
 
 cromwell_hosts_file="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/cromwell_hosts.txt"
 

From 3db13d4bbd285611142a563e185b03f0ccfa0348 Mon Sep 17 00:00:00 2001
From: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Date: Mon, 15 May 2023 16:46:28 -0400
Subject: [PATCH 168/326] WM-1963: Validate PRs begin with Jira tags (#7127)

---
 .github/workflows/validate_pr_name.yml | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 .github/workflows/validate_pr_name.yml

diff --git a/.github/workflows/validate_pr_name.yml b/.github/workflows/validate_pr_name.yml
new file mode 100644
index 00000000000..db26bbd95c6
--- /dev/null
+++ b/.github/workflows/validate_pr_name.yml
@@ -0,0 +1,23 @@
+# A github action to validate the name of a pull request contains a Jira tag:
+
+name: Validate PR name
+
+on:
+  pull_request:
+    types: [opened, edited, synchronize]
+
+jobs:
+  validate_pr_name:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Validate PR title
+        id: validate
+        uses: actions/github-script@v3
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const title = context.payload.pull_request.title;
+            const regex = /[A-Z][A-Z]+-\d+/;
+            if (!regex.test(title)) {
+              core.setFailed("PR title must contain a Jira tag");
+            }

From 90af36d1e8ff4c7630d90689aed582f2a9fc379a Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Thu, 18 May 2023 11:00:05 -0400
Subject: [PATCH 169/326] WX-1106 Add logging for failed docker manifest pulls
 (#7135)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 .../registryv2/DockerRegistryV2Abstract.scala    | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
index 1a5a02d95bd..a7cc1969903 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
@@ -70,8 +70,9 @@ object DockerRegistryV2Abstract {
   }
 
   // Placeholder exceptions that can be carried through IO before being converted to a DockerInfoFailedResponse
-  private class Unauthorized() extends Exception
-  private class NotFound() extends Exception
+  private class Unauthorized(message: String) extends Exception(message)
+  private class NotFound(message: String) extends Exception(message)
+  private class UnknownError(message: String) extends Exception(message)
 }
 
 /**
@@ -131,7 +132,10 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
   protected def getDockerResponse(token: Option[String], dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]): IO[DockerInfoSuccessResponse] = {
     val requestDockerManifest = manifestRequest(token, dockerInfoContext.dockerImageID, AcceptDockerManifestV2Header)
     lazy val requestOCIManifest = manifestRequest(token, dockerInfoContext.dockerImageID, AcceptOCIIndexV1Header)
-    def tryOCIManifest(err: Throwable) = executeRequest(requestOCIManifest, handleManifestResponse(dockerInfoContext, token))
+    def tryOCIManifest(err: Throwable) = {
+      logger.info(s"Manifest request failed for docker manifest V2, falling back to OCI manifest. Image: ${dockerInfoContext.dockerImageID}", err)
+      executeRequest(requestOCIManifest, handleManifestResponse(dockerInfoContext, token))
+    }
     // Try to execute a request using the Docker Manifest format, and if that fails, try using the newer OCI manifest format
     executeRequest(requestDockerManifest, handleManifestResponse(dockerInfoContext, token))
       .handleErrorWith(tryOCIManifest)
@@ -282,9 +286,9 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
 
   private def getDigestFromResponse(response: Response[IO]): IO[DockerHashResult] = response match {
     case Status.Successful(r) => extractDigestFromHeaders(r.headers)
-    case Status.Unauthorized(_) => IO.raiseError(new Unauthorized)
-    case Status.NotFound(_) => IO.raiseError(new NotFound)
-    case failed => failed.as[String].flatMap(body => IO.raiseError(new Exception(s"Failed to get manifest: $body"))
+    case Status.Unauthorized(r) => r.as[String].flatMap(body => IO.raiseError(new Unauthorized(r.status.toString + " " + body)))
+    case Status.NotFound(r) => r.as[String].flatMap(body => IO.raiseError(new NotFound(r.status.toString + " " + body)))
+    case failed => failed.as[String].flatMap(body => IO.raiseError(new UnknownError(failed.status.toString + " " + body))
     )
   }
 

From eb2e4a31fbae3bf19201be83b335103dd1ff827b Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 23 May 2023 11:42:16 -0400
Subject: [PATCH 170/326] [WX-1108] Disable drs tests (#7145)

---
 src/ci/bin/testCentaurHoricromtalPapiV2beta.sh | 2 ++
 src/ci/bin/testCentaurPapiV2beta.sh            | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
index 9dba2f6f8ce..b331eda6962 100755
--- a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
+++ b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
@@ -25,5 +25,7 @@ cromwell::build::run_centaur \
     -e relative_output_paths_colliding \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
+    -e drs_usa_jdr \
+    -e drs_usa_jdr_preresolve
 
 cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testCentaurPapiV2beta.sh b/src/ci/bin/testCentaurPapiV2beta.sh
index b3a1ef2a61e..98db25c54b9 100755
--- a/src/ci/bin/testCentaurPapiV2beta.sh
+++ b/src/ci/bin/testCentaurPapiV2beta.sh
@@ -23,5 +23,7 @@ cromwell::build::run_centaur \
     -e relative_output_paths_colliding \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
+    -e drs_usa_jdr \
+    -e drs_usa_jdr_preresolve
 
 cromwell::build::generate_code_coverage

From 9bddbcfdb54099ddcaf2dc9f2f3ee0abc0f4b15c Mon Sep 17 00:00:00 2001
From: Tristan Garwood <tristan.garwood@gmail.com>
Date: Tue, 23 May 2023 14:02:37 -0400
Subject: [PATCH 171/326] ID-377 Setup pact for consumer contract testing.
 (#7123)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .github/workflows/consumer_contract_tests.yml | 145 ++++++++++++
 build.sbt                                     |   6 +
 pact4s/README.md                              |  51 +++++
 .../cromwell/consumer/DrsHubClient.scala      |  93 ++++++++
 .../workbench/cromwell/consumer/Helper.scala  | 207 ++++++++++++++++++
 pact4s/src/test/resources/logback.xml         |  14 ++
 .../BlobFileSystemContractSpec.scala          |   2 +-
 .../cromwell/consumer/DrsHubClientSpec.scala  | 170 ++++++++++++++
 project/Dependencies.scala                    |  29 ++-
 project/Settings.scala                        |  16 ++
 project/build.properties                      |   2 +-
 project/plugins.sbt                           |   2 +-
 12 files changed, 728 insertions(+), 9 deletions(-)
 create mode 100644 .github/workflows/consumer_contract_tests.yml
 create mode 100644 pact4s/README.md
 create mode 100644 pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
 create mode 100644 pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
 create mode 100644 pact4s/src/test/resources/logback.xml
 rename {filesystems/blob/src/test/scala/cromwell/filesystems/blob => pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer}/BlobFileSystemContractSpec.scala (97%)
 create mode 100644 pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala

diff --git a/.github/workflows/consumer_contract_tests.yml b/.github/workflows/consumer_contract_tests.yml
new file mode 100644
index 00000000000..27889230d1b
--- /dev/null
+++ b/.github/workflows/consumer_contract_tests.yml
@@ -0,0 +1,145 @@
+name: Consumer contract tests
+# The purpose of this workflow is to run a suite of Cromwell contract tests against mock service provider(s) using Pact framework.
+#
+# More details about Contract Testing can be found in our handbook
+#
+# https://broadworkbench.atlassian.net/wiki/spaces/IRT/pages/2660368406/Getting+Started+with+Pact+Contract+Testing
+#
+# This workflow involves Cromwell as a consumer, and ANY provider (e.g. Sam) Cromwell consumes.
+# Each party owns a set of tests (aka contract tests).
+#
+#   Consumer contract tests (aka consumer tests) runs on a mock provider service and does not require a real provider service.
+#   Provider contract tests (aka provider verification tests) runs independently of any consumer.
+#
+# Specifically:
+#   Cromwell runs consumer tests against mock service. Upon success, publish consumer pacts to
+#   Pact Broker https://pact-broker.dsp-eng-tools.broadinstitute.org/.
+#
+#   Pact Broker is the source of truth to forge contractual obligations between consumer and provider.
+#
+#   This workflow meets the criteria of Pact Broker *Platinum* as described in https://docs.pact.io/pact_nirvana/step_6.
+#   The can-i-deploy job has been added to this workflow to support *Platinum* and gate the code for promotion to default branch.
+#
+#   This is how it works.
+#
+#     Consumer makes a change that results in a new pact published to Pact Broker.
+#     Pact Broker notifies provider(s) of the changed pact and trigger corresponding verification workflows.
+#     Provider downloads relevant versions of consumer pacts from Pact Broker and kicks off verification tests against the consumer pacts.
+#     Provider updates Pact Broker with verification status.
+#     Consumer kicks off can-i-deploy on process to determine if changes can be promoted and used for deployment.
+#
+# NOTE: The publish-contracts workflow will use the latest commit of the branch that triggers this workflow to publish the unique consumer contract version to Pact Broker.
+
+on:
+  pull_request:
+    branches:
+      - develop
+    paths-ignore:
+      - 'README.md'
+  push:
+    branches:
+      - develop
+    paths-ignore:
+      - 'README.md'
+  merge_group:
+    branches:
+      - develop
+
+jobs:
+  init-github-context:
+    runs-on: ubuntu-latest
+    outputs:
+      repo-branch: ${{ steps.extract-branch.outputs.repo-branch }}
+      repo-version: ${{ steps.extract-branch.outputs.repo-version }}
+      fork: ${{ steps.extract-branch.outputs.fork }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Obtain branch properties
+        id: extract-branch
+        run: |
+          FORK=false
+          GITHUB_EVENT_NAME=${{ github.event_name }}
+          if [[ "$GITHUB_EVENT_NAME" == "push" ]]; then
+            GITHUB_REF=${{ github.ref }}
+            GITHUB_SHA=${{ github.sha }}
+          elif [[ "$GITHUB_EVENT_NAME" == "pull_request" ]]; then
+            FORK=${{ github.event.pull_request.head.repo.fork }}
+            GITHUB_REF=refs/heads/${{ github.head_ref }}
+            GITHUB_SHA=${{ github.event.pull_request.head.sha }}
+          elif [[ "$GITHUB_EVENT_NAME" == "merge_group" ]]; then
+            GITHUB_REF=refs/heads/${{ github.head_ref }}
+          else
+            echo "Failed to extract branch information"
+            exit 1
+          fi
+          echo "repo-branch=${GITHUB_REF/refs\/heads\//""}" >> $GITHUB_OUTPUT
+          echo "repo-version=${GITHUB_SHA}" >> $GITHUB_OUTPUT
+          echo "fork=${FORK}" >> $GITHUB_OUTPUT
+
+      - name: Is PR triggered by forked repo?
+        if: ${{ steps.extract-branch.outputs.fork == 'true' }}
+        run: |
+          echo "PR was triggered by forked repo"
+
+      - name: Echo repo and branch information
+        run: |
+          echo "repo-owner=${{ github.repository_owner }}"
+          echo "repo-name=${{ github.event.repository.name }}"
+          echo "repo-branch=${{ steps.extract-branch.outputs.repo-branch }}"
+          echo "repo-version=${{ steps.extract-branch.outputs.repo-version }}"
+
+  cromwell-consumer-contract-tests:
+    runs-on: ubuntu-latest
+    needs: [init-github-context]
+    outputs:
+      pact-b64: ${{ steps.encode-pact.outputs.pact-b64 }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Run consumer tests
+        run: |
+          docker run --rm -v $PWD:/working \
+                          -v jar-cache:/root/.ivy \
+                          -v jar-cache:/root/.ivy2 \
+                          -w /working \
+                          sbtscala/scala-sbt:openjdk-17.0.2_1.7.2_2.13.10 \
+                          sbt "project pact4s" clean test
+
+      - name: Output consumer contract as non-breaking base64 string
+        id: encode-pact
+        run: |
+          cd pact4s
+          NON_BREAKING_B64=$(cat target/pacts/cromwell-consumer-drshub-provider.json | base64 -w 0)
+          echo "pact-b64=${NON_BREAKING_B64}" >> $GITHUB_OUTPUT
+
+  # Prevent untrusted sources from using PRs to publish contracts
+  # since access to secrets is not allowed.
+  publish-contracts:
+    runs-on: ubuntu-latest
+    if: ${{ needs.init-github-context.outputs.fork == 'false' }}
+    needs: [init-github-context, cromwell-consumer-contract-tests]
+    steps:
+      - name: Dispatch to terra-github-workflows
+        uses: broadinstitute/workflow-dispatch@v3
+        with:
+          workflow: .github/workflows/publish-contracts.yaml
+          repo: broadinstitute/terra-github-workflows
+          ref: refs/heads/main
+          token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # github token for access to kick off a job in the private repo
+          inputs: '{ "pact-b64": "${{ needs.cromwell-consumer-contract-tests.outputs.pact-b64 }}", "repo-owner": "${{ github.repository_owner }}", "repo-name": "${{ github.event.repository.name }}", "repo-branch": "${{ needs.init-github-context.outputs.repo-branch }}" }'
+
+  can-i-deploy:
+    runs-on: ubuntu-latest
+    if: ${{ needs.init-github-context.outputs.fork == 'false' && false}} # Disabling this step for now until there is a webhook setup
+    needs: [ init-github-context, publish-contracts ]
+    steps:
+      - name: Dispatch to terra-github-workflows
+        uses: broadinstitute/workflow-dispatch@v3
+        with:
+          workflow: .github/workflows/can-i-deploy.yaml
+          repo: broadinstitute/terra-github-workflows
+          ref: refs/heads/main
+          token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # github token for access to kick off a job in the private repo
+          inputs: '{ "pacticipant": "cromwell-consumer", "version": "${{ needs.init-github-context.outputs.repo-version }}" }'
diff --git a/build.sbt b/build.sbt
index a12a94b3b82..edb6d2811e4 100644
--- a/build.sbt
+++ b/build.sbt
@@ -354,6 +354,11 @@ lazy val `cromwell-drs-localizer` = project
   .dependsOn(common)
   .dependsOn(`cloud-nio-impl-drs` % "test->test")
 
+lazy val pact4s = project.in(file("pact4s"))
+  .settings(pact4sSettings)
+  .dependsOn(services)
+  .disablePlugins(sbtassembly.AssemblyPlugin)
+
 lazy val server = project
   .withExecutableSettings("cromwell", serverDependencies)
   .dependsOn(engine)
@@ -419,4 +424,5 @@ lazy val root = (project in file("."))
   .aggregate(wes2cromwell)
   .aggregate(wom)
   .aggregate(womtool)
+  .aggregate(pact4s)
   .withAggregateSettings()
diff --git a/pact4s/README.md b/pact4s/README.md
new file mode 100644
index 00000000000..d33447f7356
--- /dev/null
+++ b/pact4s/README.md
@@ -0,0 +1,51 @@
+c# pact4s [Under construction]
+
+pact4s is used for contract testing.
+
+# Dependencies
+
+```scala
+  val pact4sDependencies = Seq(
+    pact4sScalaTest,
+    pact4sCirce,
+    http4sEmberClient,
+    http4sDsl,
+    http4sEmberServer,
+    http4sCirce,
+    circeCore,
+    typelevelCat,
+    scalaTest
+  )
+
+lazy val pact4s = project.in(file("pact4s"))
+  .settings(pact4sSettings)
+  .dependsOn(http % "test->test;compile->compile")
+```
+
+## Building and running contract tests
+Clone the repo.
+```
+$ git clone https://github.com/broadinstitute/cromwell.git 
+$ cd cromwell
+```
+
+If you are already using OpenJDK 11, run the following command. 
+```
+$ sbt "project pact4s" clean test  
+```
+
+Otherwise, you can run the command inside a docker container with OpenJDK 11 installed. 
+This is especially useful when automating contract tests in a GitHub Action runner which does not guarantee the correct OpenJDK version.
+```
+docker run --rm -v $PWD:/working \
+                -v jar-cache:/root/.ivy \
+                -v jar-cache:/root/.ivy2 \
+                -w /working \
+                sbtscala/scala-sbt:openjdk-11.0.16_1.8.1_2.13.10 \
+                sbt "project pact4s" clean test
+```
+
+The generated contracts can be found in the `./target/pacts` folder
+- `cromwell-consumer-drshub-provider.json`
+- `cromwell-consumer-fake-provider.json`
+
diff --git a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
new file mode 100644
index 00000000000..3fa11515118
--- /dev/null
+++ b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
@@ -0,0 +1,93 @@
+package org.broadinstitute.dsde.workbench.cromwell.consumer
+
+import cats.effect.Concurrent
+import cats.syntax.all._
+import com.typesafe.scalalogging.LazyLogging
+import io.circe.{Decoder, Encoder}
+import org.http4s._
+import org.http4s.circe.CirceEntityCodec.{circeEntityDecoder, circeEntityEncoder}
+import org.http4s.client.Client
+
+case class AccessUrl(url: String, headers: List[String])
+
+case class ResourceMetadataRequest(url: String, fields: List[String])
+
+case class ResourceMetadata(contentType: String,
+                            size: Long,
+                            timeCreated: String,
+                            timeUpdated: String,
+                            bucket: Option[String],
+                            name: Option[String],
+                            gsUri: Option[String],
+                            googleServiceAccount: Option[Map[String, Map[String, String]]],
+                            fileName: Option[String],
+                            accessUrl: Option[AccessUrl],
+                            hashes: Map[String, String],
+                            localizationPath: Option[String],
+                            bondProvider: Option[String]
+)
+trait DrsHubClient[F[_]] extends LazyLogging {
+  def fetchSystemStatus(): F[Boolean]
+
+  def resolveDrsObject(drsPath: String, fields: List[String]): F[ResourceMetadata]
+
+}
+
+/*
+ This class represents the consumer (Cromwell) view of the DrsHub provider that implements the following endpoints:
+  - GET /status
+  - GET /api/v4/drs/resolve
+ */
+class DrsHubClientImpl[F[_]: Concurrent](client: Client[F], baseUrl: Uri) extends DrsHubClient[F] {
+  val apiVersion = "v4"
+
+  implicit val accessUrlDecoder: Decoder[AccessUrl] = Decoder.forProduct2("url", "headers")(AccessUrl.apply)
+  implicit val resourceMetadataDecoder: Decoder[ResourceMetadata] = Decoder.forProduct13(
+    "contentType",
+    "size",
+    "timeCreated",
+    "timeUpdated",
+    "bucket",
+    "name",
+    "gsUri",
+    "googleServiceAccount",
+    "fileName",
+    "accessUrl",
+    "hashes",
+    "localizationPath",
+    "bondProvider"
+  )(ResourceMetadata.apply)
+  implicit val resourceMetadataRequestEncoder: Encoder[ResourceMetadataRequest] = Encoder.forProduct2("url", "fields")(x =>
+    (x.url, x.fields)
+  )
+  implicit val resourceMetadataRequestEntityEncoder: EntityEncoder[F, ResourceMetadataRequest] = circeEntityEncoder[F, ResourceMetadataRequest]
+  override def fetchSystemStatus(): F[Boolean] = {
+    val request = Request[F](uri = baseUrl / "status").withHeaders(
+      org.http4s.headers.Accept(MediaType.application.json)
+    )
+    client.run(request).use { resp =>
+      resp.status match {
+        case Status.Ok                  => true.pure[F]
+        case Status.InternalServerError => false.pure[F]
+        case _                          => UnknownError.raiseError
+      }
+    }
+  }
+
+  override def resolveDrsObject(drsPath: String, fields: List[String]): F[ResourceMetadata] = {
+    val body = ResourceMetadataRequest(url = drsPath, fields = fields)
+    val entityBody: EntityBody[F] = EntityEncoder[F, ResourceMetadataRequest].toEntity(body).body
+    val request = Request[F](uri = baseUrl / "api" / apiVersion / "drs" / "resolve", method=Method.POST, body=entityBody).withHeaders(
+      org.http4s.headers.`Content-Type`(MediaType.application.json)
+    )
+    client.run(request).use { resp =>
+      resp.status match {
+        case Status.Ok                  => resp.as[ResourceMetadata]
+        case _                          => UnknownError.raiseError
+      }
+    }
+  }
+
+}
+
+
diff --git a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
new file mode 100644
index 00000000000..ceeefc7479f
--- /dev/null
+++ b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
@@ -0,0 +1,207 @@
+package org.broadinstitute.dsde.workbench.cromwell.consumer
+
+import au.com.dius.pact.consumer.dsl.{DslPart, PactDslResponse, PactDslWithProvider}
+import pact4s.algebras.PactBodyJsonEncoder
+case object UnknownError extends Exception
+
+object PactHelper {
+  def buildInteraction(builder: PactDslResponse,
+                       state: String,
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int,
+                       responseHeaders: Seq[(String, String)],
+                       body: DslPart
+                      ): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+      .body(body)
+
+  def buildInteraction(builder: PactDslResponse,
+                       state: String,
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int,
+                       responseHeaders: Seq[(String, String)],
+                      ): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+
+  def buildInteraction(builder: PactDslResponse,
+                       state: String,
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int
+                      ): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+
+  def buildInteraction(builder: PactDslResponse,
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int
+                      ): PactDslResponse =
+    builder
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+
+  def buildInteraction(builder: PactDslWithProvider,
+                       state: String,
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int,
+                       responseHeaders: Seq[(String, String)],
+                       body: DslPart
+                      ): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+      .body(body)
+
+  def buildInteraction(builder: PactDslWithProvider,
+                       state: String,
+                       stateParams: Map[String, Any],
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       requestBody: DslPart,
+                       status: Int,
+                       responseHeaders: Seq[(String, String)],
+                       responsBody: DslPart
+                      ): PactDslResponse =
+    builder
+      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .body(requestBody)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+      .body(responsBody)
+
+  def buildInteraction(builder: PactDslResponse,
+                       state: String,
+                       stateParams: Map[String, Any],
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int,
+                       responseHeaders: Seq[(String, String)],
+                       body: DslPart
+                      ): PactDslResponse =
+    builder
+      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+      .body(body)
+
+  def buildInteraction[A](builder: PactDslWithProvider,
+                          state: String,
+                          stateParams: Map[String, Any],
+                          uponReceiving: String,
+                          method: String,
+                          path: String,
+                          requestHeaders: Seq[(String, String)],
+                          status: Int,
+                          responseHeaders: Seq[(String, String)],
+                          body: A
+                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
+    builder
+      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+      .body(ev.toJsonString(body))
+
+  def buildInteraction[A](builder: PactDslResponse,
+                          state: String,
+                          uponReceiving: String,
+                          method: String,
+                          path: String,
+                          requestHeaders: Seq[(String, String)],
+                          requestBody: A,
+                          status: Int
+                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .body(ev.toJsonString(requestBody))
+      .willRespondWith()
+      .status(status)
+
+  def buildInteraction[A](builder: PactDslResponse,
+                          state: String,
+                          stateParams: Map[String, Any],
+                          uponReceiving: String,
+                          method: String,
+                          path: String,
+                          requestHeaders: Seq[(String, String)],
+                          requestBody: A,
+                          status: Int
+                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
+    builder
+      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .body(ev.toJsonString(requestBody))
+      .willRespondWith()
+      .status(status)
+}
diff --git a/pact4s/src/test/resources/logback.xml b/pact4s/src/test/resources/logback.xml
new file mode 100644
index 00000000000..24316805e7e
--- /dev/null
+++ b/pact4s/src/test/resources/logback.xml
@@ -0,0 +1,14 @@
+<configuration>
+    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder>
+            <pattern>%d [%thread] %-5level  %logger{35} - %msg%n</pattern>
+        </encoder>
+    </appender>
+    <logger name="io.github.jbwheatley.pact4s.Pact4sLogger" level="INFO" />
+    <logger name="au.com.dius.pact.consumer" level="DEBUG"/>
+    <logger name="au.com.dius.pact.provider" level="DEBUG"/>
+
+    <root level="INFO">
+        <appender-ref ref="STDOUT" />
+    </root>
+</configuration>
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
similarity index 97%
rename from filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
rename to pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
index 611a50f5603..f023257fef9 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
+++ b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
@@ -1,4 +1,4 @@
-package cromwell.filesystems.blob
+package org.broadinstitute.dsde.workbench.cromwell.consumer
 
 import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
 import au.com.dius.pact.core.model.RequestResponsePact
diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
new file mode 100644
index 00000000000..a4ebe56d76a
--- /dev/null
+++ b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
@@ -0,0 +1,170 @@
+package org.broadinstitute.dsde.workbench.cromwell.consumer
+
+import au.com.dius.pact.consumer.dsl.LambdaDsl.newJsonBody
+import au.com.dius.pact.consumer.dsl._
+import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
+import au.com.dius.pact.core.model.RequestResponsePact
+import cats.effect.IO
+import org.broadinstitute.dsde.workbench.cromwell.consumer.PactHelper._
+import org.http4s.Uri
+import org.http4s.blaze.client.BlazeClientBuilder
+import org.http4s.client.Client
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import pact4s.scalatest.RequestResponsePactForger
+
+import java.util.concurrent.Executors
+import scala.concurrent.ExecutionContext
+
+class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePactForger {
+  val ec = ExecutionContext.fromExecutorService(Executors.newCachedThreadPool())
+  implicit val cs = IO.contextShift(ec)
+  /*
+    Define the folder that the pact contracts get written to upon completion of this test suite.
+   */
+  override val pactTestExecutionContext: PactTestExecutionContext =
+    new PactTestExecutionContext(
+      "./target/pacts"
+    )
+
+  private val requestFields = List(
+      "bucket",
+      "accessUrl",
+      "googleServiceAccount",
+      "fileName",
+      "hashes",
+      "localizationPath",
+      "bondProvider",
+      "name",
+      "size",
+      "timeCreated",
+      "timeUpdated",
+      "gsUri",
+      "contentType",
+  )
+
+  val filesize = 123L
+  val timeCreated = "2021-03-04T20:00:00.000Z"
+  val bucket = "fc-secure-1234567890"
+  val filename = "my-file.bam"
+  val bondProvider = "anvil"
+  val fileHash = "a2317edbd2eb6cf6b0ee49cb81e3a556"
+  val accessUrl = f"gs://${bucket}/${filename}"
+
+
+  val drsResourceResponsePlaceholder: ResourceMetadata = ResourceMetadata(
+    "application/octet-stream",
+    filesize,
+    timeCreated,
+    timeCreated,
+    None,
+    None,
+    None,
+    None,
+    None,
+    Option(AccessUrl(accessUrl, List("Header", "Example"))),
+    Map("md5" -> fileHash),
+    None,
+    Option(bondProvider)
+  )
+
+  val resourceMetadataResponseDsl: DslPart = newJsonBody { o =>
+    o.stringType("contentType", "application/octet-stream")
+      o.numberType("size", filesize)
+      o.stringType("timeCreated", timeCreated)
+      o.stringType("timeUpdated", timeCreated)
+      o.nullValue("gsUri")
+      o.nullValue("googleServiceAccount")
+      o.nullValue("fileName")
+      o.`object`("accessUrl" , { a =>
+        a.stringType("url", accessUrl)
+          a.`array`("headers", { h =>
+            h.stringType("Header")
+            h.stringType("Example")
+            ()
+          })
+        ()
+      })
+      o.`object`("hashes", { o =>
+        o.stringType("md5", fileHash)
+        ()
+      })
+      o.nullValue("localizationPath")
+      o.stringType("bondProvider", bondProvider)
+    ()
+  }.build
+
+  val fileId = "1234567890"
+
+  val resourceRequestDsl = newJsonBody { o =>
+    o.stringType("url", f"drs://test.theanvil.io/${fileId}")
+    o.array("fields", { a =>
+      requestFields.map(a.stringType)
+      ()
+    })
+    ()
+  }.build
+
+  val consumerPactBuilder: ConsumerPactBuilder = ConsumerPactBuilder
+    .consumer("cromwell-consumer")
+
+  val pactProvider: PactDslWithProvider = consumerPactBuilder
+    .hasPactWith("drshub-provider")
+
+  var pactDslResponse: PactDslResponse = buildInteraction(
+    pactProvider,
+    state = "resolve Drs url",
+    stateParams = Map[String, String](
+      "fileId" -> fileId,
+      "bucket" -> bucket,
+      "filename" -> filename,
+      "bondProvider" -> bondProvider,
+      "fileHash" -> fileHash,
+      "accessUrl" -> accessUrl,
+      "fileSize" -> filesize.toString,
+      "timeCreated" -> timeCreated
+    ),
+    uponReceiving = "Request to resolve drs url",
+    method = "POST",
+    path = "/api/v4/drs/resolve",
+    requestHeaders = Seq("Content-type" -> "application/json"),
+    requestBody = resourceRequestDsl,
+    status = 200,
+    responseHeaders = Seq(),
+    responsBody = resourceMetadataResponseDsl
+  )
+
+  pactDslResponse = buildInteraction(
+    pactDslResponse,
+    state = "Drshub is ok",
+    uponReceiving = "Request for drshub api status",
+    method = "GET",
+    path = "/status",
+    requestHeaders = Seq(),
+    status = 200,
+    responseHeaders = Seq()
+  )
+
+  override val pact: RequestResponsePact = pactDslResponse.toPact
+
+  val client: Client[IO] = {
+    BlazeClientBuilder[IO](ExecutionContext.global).resource.allocated.unsafeRunSync()._1
+  }
+
+  /*
+  we should use these tests to ensure that our client class correctly handles responses from the provider - i.e. decoding, error mapping, validation
+   */
+  it should "get DrsHub ok status" in {
+    new DrsHubClientImpl[IO](client, Uri.unsafeFromString(mockServer.getUrl))
+      .fetchSystemStatus()
+      .attempt
+      .unsafeRunSync() shouldBe Right(true)
+  }
+
+  it should "resolve drs object" in {
+    new DrsHubClientImpl[IO](client, Uri.unsafeFromString(mockServer.getUrl))
+      .resolveDrsObject("drs://drs.example.com/1234567890", requestFields)
+      .attempt
+      .unsafeRunSync() shouldBe Right(drsResourceResponsePlaceholder)
+  }
+}
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 405ecd2d3c4..ef829d6f780 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -91,6 +91,7 @@ object Dependencies {
   private val mysqlV = "8.0.28"
   private val nettyV = "4.1.72.Final"
   private val owlApiV = "5.1.19"
+  private val pact4sV = "0.9.0"
   private val postgresV = "42.4.1"
   private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
@@ -103,7 +104,7 @@ object Dependencies {
   private val scalaPoolV = "0.4.3"
   private val scalacticV = "3.2.13"
   private val scalameterV = "0.21"
-  private val scalatestV = "3.2.10"
+  private val scalatestV = "3.2.15"
   private val scalatestScalacheckV = scalatestV + ".0"
   private val scoptV = "4.1.0"
   private val sentryLogbackV = "5.7.4"
@@ -442,7 +443,7 @@ object Dependencies {
     - https://www.scalatest.org/user_guide/generator_driven_property_checks
     - https://www.scalatest.org/user_guide/writing_scalacheck_style_properties
    */
-  private val scalacheckBaseV = "1.15"
+  private val scalacheckBaseV = "1.17"
   private val scalacheckDependencies = List(
     "org.scalatestplus" %% s"scalacheck-${scalacheckBaseV.replace(".", "-")}" % scalatestScalacheckV % Test,
   )
@@ -594,14 +595,12 @@ object Dependencies {
   val sfsBackendDependencies = List (
     "org.lz4" % "lz4-java" % lz4JavaV
   )
-
+  val scalaTest = "org.scalatest" %% "scalatest" % scalatestV
   val testDependencies: List[ModuleID] = List(
-    "org.scalatest" %% "scalatest" % scalatestV,
+    scalaTest,
     // Use mockito Java DSL directly instead of the numerous and often hard to keep updated Scala DSLs.
     // See also scaladoc in common.mock.MockSugar and that trait's various usages.
     "org.mockito" % "mockito-core" % mockitoV,
-    "io.github.jbwheatley" %% "pact4s-scalatest"  % "0.7.0",
-    "io.github.jbwheatley" %% "pact4s-circe" %  "0.7.0"
   ) ++ slf4jBindingDependencies // During testing, add an slf4j binding for _all_ libraries.
 
   val kindProjectorPlugin = "org.typelevel" % "kind-projector" % kindProjectorV cross CrossVersion.full
@@ -797,5 +796,23 @@ object Dependencies {
      The jakarta.annotation inclusion is above in googleApiClientDependencies.
      */
     ExclusionRule("javax.annotation", "javax.annotation-api"),
+    ExclusionRule("javax.activation"),
+  )
+
+  val http4sDsl = "org.http4s" %% "http4s-dsl" % http4sV
+  val http4sEmberClient = "org.http4s" %% "http4s-ember-client" % http4sV
+  val http4sEmberServer = "org.http4s" %% "http4s-ember-server" % http4sV
+  val http4sCirce = "org.http4s" %% "http4s-circe" % http4sV
+  val pact4sScalaTest = "io.github.jbwheatley" %% "pact4s-scalatest" % pact4sV % Test
+  val pact4sCirce = "io.github.jbwheatley" %% "pact4s-circe" % pact4sV
+
+  val pact4sDependencies = Seq(
+    pact4sScalaTest,
+    pact4sCirce,
+    http4sEmberClient,
+    http4sDsl,
+    http4sEmberServer,
+    http4sCirce,
+    scalaTest,
   )
 }
diff --git a/project/Settings.scala b/project/Settings.scala
index 797d7917dd9..32559422066 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -98,6 +98,22 @@ object Settings {
     )
   )
 
+  val pact4sSettings = sharedSettings ++ List(
+    libraryDependencies ++= pact4sDependencies,
+
+    /**
+      * Invoking pact tests from root project (sbt "project pact" test)
+      * will launch tests in a separate JVM context that ensures contracts
+      * are written to the pact/target/pacts folder. Otherwise, contracts
+      * will be written to the root folder.
+      */
+    Test / fork := true
+
+  ) ++ assemblySettings
+
+  lazy val pact4s = project.in(file("pact4s"))
+    .settings(pact4sSettings)
+
   /*
       Docker instructions to install Google Cloud SDK image in docker image. It also installs `crcmod` which
       is needed while downloading large files using `gsutil`.
diff --git a/project/build.properties b/project/build.properties
index 2b4cbe4d584..54f486b9dc3 100644
--- a/project/build.properties
+++ b/project/build.properties
@@ -1,2 +1,2 @@
 # scala-steward:off
-sbt.version=1.5.5
+sbt.version=1.8.1
diff --git a/project/plugins.sbt b/project/plugins.sbt
index bdb54f675bf..151ba4b87e3 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1,5 +1,5 @@
 addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.9.0")
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.1")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "2.1.1")
 addSbtPlugin("com.github.sbt" % "sbt-git" % "2.0.0")
 addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.4")
 addSbtPlugin("com.github.cb372" % "sbt-explicit-dependencies" % "0.2.16")

From 24e67fd62a5b83419241e37188d764d2c644e620 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Tue, 23 May 2023 16:13:04 -0400
Subject: [PATCH 172/326] WX-1092 Support `size` engine function for public
 HTTP files (#7128)

---
 CHANGELOG.md                                  |  6 ++++
 build.sbt                                     |  1 +
 core/src/main/resources/reference.conf        |  9 +++++
 .../scala/cromwell/engine/io/IoActor.scala    |  3 +-
 .../cromwell/engine/io/nio/NioFlow.scala      | 16 ++++++---
 .../cromwell/engine/io/nio/NioFlowSpec.scala  | 33 +++++++++++++++++--
 .../filesystems/http/HttpPathBuilder.scala    | 18 +++++++++-
 7 files changed, 77 insertions(+), 9 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0084c05171b..b1190ef951a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Cromwell Change Log
 
+## 86 Release Notes
+
+### HTTPFilesystem Improvements
+
+ * WDL `size` engine function now works for HTTP files. 
+
 ## 85 Release Notes
 
 ### Migration of PKs to BIGINT
diff --git a/build.sbt b/build.sbt
index edb6d2811e4..3754a92305d 100644
--- a/build.sbt
+++ b/build.sbt
@@ -249,6 +249,7 @@ lazy val engine = project
   .dependsOn(backend)
   .dependsOn(gcsFileSystem)
   .dependsOn(drsFileSystem)
+  .dependsOn(httpFileSystem)
   .dependsOn(sraFileSystem)
   .dependsOn(awsS3FileSystem)
   .dependsOn(azureBlobFileSystem)
diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index 4ecdf1ce233..b341682f1db 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -15,6 +15,15 @@ webservice {
 }
 
 akka {
+
+  http {
+    client {
+      parsing {
+        illegal-header-warnings = off
+      }
+    }
+  }
+
   actor.default-dispatcher.fork-join-executor {
     # Number of threads = min(parallelism-factor * cpus, parallelism-max)
     # Below are the default values set by Akka, uncomment to tune these
diff --git a/engine/src/main/scala/cromwell/engine/io/IoActor.scala b/engine/src/main/scala/cromwell/engine/io/IoActor.scala
index 40a6f81c4aa..b4b3a0b191f 100644
--- a/engine/src/main/scala/cromwell/engine/io/IoActor.scala
+++ b/engine/src/main/scala/cromwell/engine/io/IoActor.scala
@@ -1,7 +1,7 @@
 package cromwell.engine.io
 
 import akka.NotUsed
-import akka.actor.{Actor, ActorLogging, ActorRef, Props, Timers}
+import akka.actor.{Actor, ActorLogging, ActorRef, ActorSystem, Props, Timers}
 import akka.dispatch.ControlMessage
 import akka.stream._
 import akka.stream.scaladsl.{Flow, GraphDSL, Merge, Partition, Sink, Source, SourceQueueWithComplete}
@@ -40,6 +40,7 @@ final class IoActor(ioConfig: IoConfig,
                     applicationName: String)(implicit val materializer: ActorMaterializer)
   extends Actor with ActorLogging with StreamActorHelper[IoCommandContext[_]] with IoInstrumentation with Timers {
   implicit val ec: ExecutionContext = context.dispatcher
+  implicit val system: ActorSystem = context.system
 
   // IntelliJ disapproves of mutable state in Actors, but this should be safe as long as access occurs only in
   // the `receive` method. Alternatively IntelliJ does suggest a `become` workaround we might try in the future.
diff --git a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
index 012e771b5a0..b6ce3ee7cc2 100644
--- a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
+++ b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
@@ -1,7 +1,8 @@
 package cromwell.engine.io.nio
 
+import akka.actor.ActorSystem
 import akka.stream.scaladsl.Flow
-import cats.effect.{IO, Timer}
+import cats.effect._
 
 import scala.util.Try
 import cloud.nio.spi.{ChecksumFailure, ChecksumResult, ChecksumSkipped, ChecksumSuccess, FileHash, HashType}
@@ -15,6 +16,7 @@ import cromwell.engine.io.{IoAttempts, IoCommandContext, IoCommandStalenessBackp
 import cromwell.filesystems.blob.BlobPath
 import cromwell.filesystems.drs.DrsPath
 import cromwell.filesystems.gcs.GcsPath
+import cromwell.filesystems.http.HttpPath
 import cromwell.filesystems.s3.S3Path
 import cromwell.util.TryWithResource._
 import net.ceedubs.ficus.Ficus._
@@ -34,9 +36,11 @@ class NioFlow(parallelism: Int,
               onBackpressure: Option[Double] => Unit,
               numberOfAttempts: Int,
               commandBackpressureStaleness: FiniteDuration
-              )(implicit ec: ExecutionContext) extends IoCommandStalenessBackpressuring {
+              )(implicit system: ActorSystem) extends IoCommandStalenessBackpressuring {
 
+  implicit private val ec: ExecutionContext = system.dispatcher
   implicit private val timer: Timer[IO] = IO.timer(ec)
+  implicit private val contextShift: ContextShift[IO] = IO.contextShift(ec)
 
   override def maxStaleness: FiniteDuration = commandBackpressureStaleness
 
@@ -161,9 +165,11 @@ class NioFlow(parallelism: Int,
     fileContentIo.map(_.replaceAll("\\r\\n", "\\\n"))
   }
 
-  private def size(size: IoSizeCommand) = IO {
-    size.file.size
-  }
+  private def size(size: IoSizeCommand) =
+    size.file match {
+      case httpPath: HttpPath => IO.fromFuture(IO(httpPath.fetchSize))
+      case nioPath => IO(nioPath.size)
+    }
 
   private def hash(hash: IoHashCommand): IO[String] = {
     // If there is no hash accessible from the file storage system,
diff --git a/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala b/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
index b01d52eece0..41c121da0cc 100644
--- a/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
@@ -21,6 +21,7 @@ import org.scalatest.flatspec.AsyncFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import common.mock.MockSugar
 import cromwell.filesystems.blob.BlobPath
+import cromwell.filesystems.http.HttpPathBuilder
 
 import java.nio.file.NoSuchFileException
 import java.util.UUID
@@ -42,7 +43,7 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     onRetryCallback = NoopOnRetry,
     onBackpressure = NoopOnBackpressure,
     numberOfAttempts = 3,
-    commandBackpressureStaleness = 5 seconds)(system.dispatcher).flow
+    commandBackpressureStaleness = 5 seconds)(system).flow
 
   implicit val materializer: ActorMaterializer = ActorMaterializer()
   private val replyTo = mock[ActorRef]
@@ -96,6 +97,34 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     }
   }
 
+  it should "fail with an UnknownHost error when trying to get size for a bogus HTTP path" in {
+    val httpPath = new HttpPathBuilder().build("http://ex000mple.c0m/bogus/url/fake.html").get
+
+    val context = DefaultCommandContext(sizeCommand(httpPath).get, replyTo)
+    val testSource = Source.single(context)
+
+    val stream = testSource.via(flow).toMat(readSink)(Keep.right)
+    stream.run() map {
+      case (IoFailure(_, EnhancedCromwellIoException(_, receivedException)), _) =>
+        receivedException.getMessage should include ("UnknownHost")
+      case (ack, _) => fail(s"size should have failed with UnknownHost but didn't:\n$ack\n\n")
+    }
+  }
+
+  it should "fail when trying to get size for a bogus HTTP path" in {
+    val httpPath = new HttpPathBuilder().build("http://google.com/bogus/je8934hufe832489uihewuihf").get
+
+    val context = DefaultCommandContext(sizeCommand(httpPath).get, replyTo)
+    val testSource = Source.single(context)
+
+    val stream = testSource.via(flow).toMat(readSink)(Keep.right)
+    stream.run() map {
+      case (IoFailure(_, EnhancedCromwellIoException(_, receivedException)), _) =>
+        receivedException.getMessage should include ("Couldn't fetch size")
+      case (ack, _) => fail(s"size should have failed but didn't:\n$ack\n\n")
+    }
+  }
+
   it should "get hash from a Nio Path" in {
     val testPath = DefaultPathBuilder.createTempFile()
     testPath.write("hello")
@@ -304,7 +333,7 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
       onRetryCallback = NoopOnRetry,
       onBackpressure = NoopOnBackpressure,
       numberOfAttempts = 3,
-      commandBackpressureStaleness = 5 seconds)(system.dispatcher) {
+      commandBackpressureStaleness = 5 seconds)(system) {
 
       private var tries = 0
       override def handleSingleCommand(ioSingleCommand: IoCommand[_]): IO[IoSuccess[_]] = {
diff --git a/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala b/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala
index d1c3f19ad61..89bb22021df 100644
--- a/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala
+++ b/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala
@@ -3,7 +3,7 @@ import java.nio.file.Paths
 
 import akka.actor.{ActorContext, ActorSystem}
 import akka.http.scaladsl.Http
-import akka.http.scaladsl.model.HttpRequest
+import akka.http.scaladsl.model.{HttpMethods, HttpRequest}
 import akka.stream.scaladsl.{FileIO, Keep}
 import akka.stream.{ActorAttributes, ActorMaterializer}
 import cromwell.core.Dispatcher
@@ -53,4 +53,20 @@ case class HttpPath(nioPath: NioPath) extends Path {
   override def pathAsString: String = nioPath.toString.replaceFirst("/", "//")
 
   override def pathWithoutScheme: String = pathAsString.replaceFirst("http[s]?://", "")
+
+  def fetchSize(implicit executionContext: ExecutionContext, actorSystem: ActorSystem): Future[Long] = {
+    Http().singleRequest(HttpRequest(uri = pathAsString, method = HttpMethods.HEAD)).map { response =>
+      response.discardEntityBytes()
+      val length = if (response.status.isSuccess())
+        response.entity.contentLengthOption
+      else
+        None
+      length.getOrElse(
+        throw new RuntimeException(
+          s"Couldn't fetch size for $pathAsString, missing Content-Length header or path doesn't exist (HTTP ${response.status.toString()})."
+        )
+      )
+    }
+  }
+
 }

From d80efee4fbe75ca950d4ffc6d85170272b1df451 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 24 May 2023 09:24:30 -0400
Subject: [PATCH 173/326] WX-1105 Fix interpretation of full http blob paths
 (#7138)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 .../filesystems/blob/BlobPathBuilder.scala    | 28 ++++++----
 .../blob/BlobPathBuilderSpec.scala            | 54 +++++++++++++++++--
 .../TesAsyncBackendJobExecutionActor.scala    | 13 ++++-
 .../backend/impl/tes/TesConfiguration.scala   |  9 ++++
 4 files changed, 90 insertions(+), 14 deletions(-)

diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 1906cc2f911..cc0e112806a 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -68,14 +68,22 @@ class BlobPathBuilder(container: BlobContainerName, endpoint: EndpointURL)(priva
 }
 
 object BlobPath {
-  // The Azure NIO library uses `{containerName}:` as the root of the path.
-  // This doesn't work well for our need to easily transfer back and forth
-  // to and from the blob URL format. This method removes anything up to and including
-  // the first colon, to create a path string useful for working with BlobPath.
-  // This is safe because the NIO library enforces no colons except to mark
-  // the root container name.
-  private def nioPathString(nioPath: NioPath): String = {
-    val pathStr = nioPath.toString
+  // The Azure NIO library uses `{containerName}:` as the root of the path (treating the blob container within
+  // the storage account similarly to a drive within a computer). This doesn't work well for our need to easily
+  // transfer back and forth to and from the blob URL format. It also causes the library to garble full http://
+  // paths that it receives (it interprets `http` as the container name); it transforms them to http:/<remainder of path>
+  //
+  // We transform these library-generated paths in two steps:
+  // 1) If the path starts with http:/ (single slash!) transform it to the containerName:<path inside container>
+  //    format the library expects
+  // 2) If the path looks like <container>:<path>, strip off the <container>: to leave the absolute path inside the container.
+  private val brokenPathRegex = "https:/([a-z0-9]+).blob.core.windows.net/([-a-zA-Z0-9]+)/(.*)".r
+  def cleanedNioPathString(nioString: String): String = {
+    val pathStr = nioString match {
+      case brokenPathRegex(_, containerName, pathInContainer) =>
+        s"${containerName}:/${pathInContainer}"
+      case _ => nioString
+    }
     pathStr.substring(pathStr.indexOf(":")+1)
   }
 
@@ -83,7 +91,7 @@ object BlobPath {
             endpoint: EndpointURL,
             container: BlobContainerName,
             fsm: BlobFileSystemManager): BlobPath = {
-    BlobPath(nioPathString(nioPath), endpoint, container)(fsm)
+    BlobPath(cleanedNioPathString(nioPath.toString), endpoint, container)(fsm)
   }
 }
 
@@ -95,7 +103,7 @@ case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, con
   override def pathAsString: String = List(endpoint, container, pathString.stripPrefix("/")).mkString("/")
 
   //This is purposefully an unprotected get because if the endpoint cannot be parsed this should fail loudly rather than quietly
-  override def pathWithoutScheme: String = parseURI(endpoint.value).map(u => List(u.getHost, container, pathString).mkString("/")).get
+  override def pathWithoutScheme: String = parseURI(endpoint.value).map(u => List(u.getHost, container, pathString.stripPrefix("/")).mkString("/")).get
 
   private def findNioPath(path: String): NioPath = (for {
     fileSystem <- fsm.retrieveFilesystem()
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index 2aa9b2b43aa..11ffc11354e 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -4,6 +4,7 @@ import org.mockito.Mockito.when
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
+import java.util.UUID
 import scala.util.{Failure, Try}
 
 object BlobPathBuilderSpec {
@@ -57,12 +58,59 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     testException should contain(exception)
   }
 
+  private def testBlobNioStringCleaning(input: String, expected: String) =
+    BlobPath.cleanedNioPathString(input) shouldBe expected
+
+  it should "clean the NIO path string when it has a garbled http protocol" in {
+    testBlobNioStringCleaning(
+      "https:/lz43.blob.core.windows.net/sc-ebda3e/workspace-services/cbas/terra-app-4628d0e1/test_all_engine_functions/4bb6a0a2-3b07/call-run_read_string/execution/stdout",
+      "/workspace-services/cbas/terra-app-4628d0e1/test_all_engine_functions/4bb6a0a2-3b07/call-run_read_string/execution/stdout"
+    )
+  }
+
+  it should "clean the NIO path string when it has a container name with colon prefix" in {
+    testBlobNioStringCleaning(
+      "sc-ebda3e:/workspace-services/cbas/terra-app-4628d0e1/test_all_engine_functions/4bb6a0a2-3b07/call-run_read_string/execution/stdout",
+      "/workspace-services/cbas/terra-app-4628d0e1/test_all_engine_functions/4bb6a0a2-3b07/call-run_read_string/execution/stdout"
+    )
+  }
+
+  it should "clean the NIO path string when it's an in-container absolute path" in {
+    testBlobNioStringCleaning(
+      "/workspace-services/cbas/terra-app-4628d0e1/test_all_engine_functions/4bb6a0a2-3b07/call-run_read_string/execution/stdout",
+      "/workspace-services/cbas/terra-app-4628d0e1/test_all_engine_functions/4bb6a0a2-3b07/call-run_read_string/execution/stdout"
+    )
+  }
+
+  it should "clean the NIO path string when it's the root directory only" in {
+    testBlobNioStringCleaning(
+      "sc-ebda3e:",
+      ""
+    )
+  }
+
+  //// The below tests are IGNORED because they depend on Azure auth information being present in the environment ////
+  val subscriptionId = SubscriptionId(UUID.fromString("62b22893-6bc1-46d9-8a90-806bb3cce3c9"))
+
+  ignore should "resolve an absolute path string correctly to a path" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
+    val store = BlobContainerName("inputs")
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint, Some(subscriptionId))
+    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
+
+    val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
+    val blobRoot: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build rootString getOrElse fail()
+    blobRoot.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution")
+    val otherFile = blobRoot.resolve("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
+    otherFile.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
+  }
+
   ignore should "build a blob path from a test string and read a file" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
     val endpointHost = BlobPathBuilder.parseURI(endpoint.value).map(_.getHost).getOrElse(fail("Could not parse URI"))
     val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
-    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint, Some(subscriptionId))
     val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10L, blobTokenGenerator)
     val testString = endpoint.value + "/" + store + evalPath
     val blobPath: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
@@ -80,7 +128,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
     val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
-    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint, Some(subscriptionId))
     val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
     val testString = endpoint.value + "/" + store + evalPath
     val blobPath1: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
@@ -95,7 +143,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   ignore should "resolve a path without duplicating container name" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
     val store = BlobContainerName("inputs")
-    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint)
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint, Some(subscriptionId))
     val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
 
     val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index f4259de90d8..0582997eef8 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -1,12 +1,14 @@
 package cromwell.backend.impl.tes
 
 import common.exception.AggregatedMessageException
+
 import java.io.FileNotFoundException
 import java.nio.file.FileAlreadyExistsException
 import cats.syntax.apply._
 import akka.http.scaladsl.Http
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
 import akka.http.scaladsl.marshalling.Marshal
+import akka.http.scaladsl.model.HttpHeader.ParsingResult.Ok
 import akka.http.scaladsl.model._
 import akka.http.scaladsl.unmarshalling.{Unmarshal, Unmarshaller}
 import akka.stream.ActorMaterializer
@@ -295,9 +297,18 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
     }
   }
 
+  // Headers that should be included with all requests to the TES server
+  private def requestHeaders: List[HttpHeader] =
+    tesConfiguration.token.flatMap { t =>
+      HttpHeader.parse("Authorization", t) match {
+        case Ok(header, _) => Some(header)
+        case _ => None
+      }
+    }.toList
+
   private def makeRequest[A](request: HttpRequest)(implicit um: Unmarshaller[ResponseEntity, A]): Future[A] = {
     for {
-      response <- withRetry(() => Http().singleRequest(request))
+      response <- withRetry(() => Http().singleRequest(request.withHeaders(requestHeaders)))
       data <- if (response.status.isFailure()) {
         response.entity.dataBytes.runFold(ByteString(""))(_ ++ _).map(_.utf8String) flatMap { errorBody =>
           Future.failed(new RuntimeException(s"Failed TES request: Code ${response.status.intValue()}, Body = $errorBody"))
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
index 7c7809d127f..253f60114be 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
@@ -32,6 +32,15 @@ class TesConfiguration(val configurationDescriptor: BackendConfigurationDescript
       .map(SimpleExponentialBackoff(_))
       .getOrElse(TesConfiguration.defaultExecOrRecoverBackoff)
 
+  // Used for testing only. Include a bearer token for authenticating with the TES server
+  final val bearerPrefix: String = "Bearer "
+  val token: Option[String] = {
+    configurationDescriptor.backendConfig.as[Option[String]]("bearer-token").map { t =>
+      if (!t.startsWith(bearerPrefix))
+        s"${bearerPrefix}${t}"
+      else t
+    }
+  }
 }
 
 object TesConfiguration {

From c01120207f241c55acbaa3cc49d4a757ad340f6d Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 24 May 2023 12:31:39 -0400
Subject: [PATCH 174/326] Revert "ID-377 Setup pact for consumer contract
 testing." (#7146)

---
 .github/workflows/consumer_contract_tests.yml | 145 ------------
 build.sbt                                     |   6 -
 .../blob}/BlobFileSystemContractSpec.scala    |   2 +-
 pact4s/README.md                              |  51 -----
 .../cromwell/consumer/DrsHubClient.scala      |  93 --------
 .../workbench/cromwell/consumer/Helper.scala  | 207 ------------------
 pact4s/src/test/resources/logback.xml         |  14 --
 .../cromwell/consumer/DrsHubClientSpec.scala  | 170 --------------
 project/Dependencies.scala                    |  29 +--
 project/Settings.scala                        |  16 --
 project/build.properties                      |   2 +-
 project/plugins.sbt                           |   2 +-
 12 files changed, 9 insertions(+), 728 deletions(-)
 delete mode 100644 .github/workflows/consumer_contract_tests.yml
 rename {pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer => filesystems/blob/src/test/scala/cromwell/filesystems/blob}/BlobFileSystemContractSpec.scala (97%)
 delete mode 100644 pact4s/README.md
 delete mode 100644 pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
 delete mode 100644 pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
 delete mode 100644 pact4s/src/test/resources/logback.xml
 delete mode 100644 pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala

diff --git a/.github/workflows/consumer_contract_tests.yml b/.github/workflows/consumer_contract_tests.yml
deleted file mode 100644
index 27889230d1b..00000000000
--- a/.github/workflows/consumer_contract_tests.yml
+++ /dev/null
@@ -1,145 +0,0 @@
-name: Consumer contract tests
-# The purpose of this workflow is to run a suite of Cromwell contract tests against mock service provider(s) using Pact framework.
-#
-# More details about Contract Testing can be found in our handbook
-#
-# https://broadworkbench.atlassian.net/wiki/spaces/IRT/pages/2660368406/Getting+Started+with+Pact+Contract+Testing
-#
-# This workflow involves Cromwell as a consumer, and ANY provider (e.g. Sam) Cromwell consumes.
-# Each party owns a set of tests (aka contract tests).
-#
-#   Consumer contract tests (aka consumer tests) runs on a mock provider service and does not require a real provider service.
-#   Provider contract tests (aka provider verification tests) runs independently of any consumer.
-#
-# Specifically:
-#   Cromwell runs consumer tests against mock service. Upon success, publish consumer pacts to
-#   Pact Broker https://pact-broker.dsp-eng-tools.broadinstitute.org/.
-#
-#   Pact Broker is the source of truth to forge contractual obligations between consumer and provider.
-#
-#   This workflow meets the criteria of Pact Broker *Platinum* as described in https://docs.pact.io/pact_nirvana/step_6.
-#   The can-i-deploy job has been added to this workflow to support *Platinum* and gate the code for promotion to default branch.
-#
-#   This is how it works.
-#
-#     Consumer makes a change that results in a new pact published to Pact Broker.
-#     Pact Broker notifies provider(s) of the changed pact and trigger corresponding verification workflows.
-#     Provider downloads relevant versions of consumer pacts from Pact Broker and kicks off verification tests against the consumer pacts.
-#     Provider updates Pact Broker with verification status.
-#     Consumer kicks off can-i-deploy on process to determine if changes can be promoted and used for deployment.
-#
-# NOTE: The publish-contracts workflow will use the latest commit of the branch that triggers this workflow to publish the unique consumer contract version to Pact Broker.
-
-on:
-  pull_request:
-    branches:
-      - develop
-    paths-ignore:
-      - 'README.md'
-  push:
-    branches:
-      - develop
-    paths-ignore:
-      - 'README.md'
-  merge_group:
-    branches:
-      - develop
-
-jobs:
-  init-github-context:
-    runs-on: ubuntu-latest
-    outputs:
-      repo-branch: ${{ steps.extract-branch.outputs.repo-branch }}
-      repo-version: ${{ steps.extract-branch.outputs.repo-version }}
-      fork: ${{ steps.extract-branch.outputs.fork }}
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Obtain branch properties
-        id: extract-branch
-        run: |
-          FORK=false
-          GITHUB_EVENT_NAME=${{ github.event_name }}
-          if [[ "$GITHUB_EVENT_NAME" == "push" ]]; then
-            GITHUB_REF=${{ github.ref }}
-            GITHUB_SHA=${{ github.sha }}
-          elif [[ "$GITHUB_EVENT_NAME" == "pull_request" ]]; then
-            FORK=${{ github.event.pull_request.head.repo.fork }}
-            GITHUB_REF=refs/heads/${{ github.head_ref }}
-            GITHUB_SHA=${{ github.event.pull_request.head.sha }}
-          elif [[ "$GITHUB_EVENT_NAME" == "merge_group" ]]; then
-            GITHUB_REF=refs/heads/${{ github.head_ref }}
-          else
-            echo "Failed to extract branch information"
-            exit 1
-          fi
-          echo "repo-branch=${GITHUB_REF/refs\/heads\//""}" >> $GITHUB_OUTPUT
-          echo "repo-version=${GITHUB_SHA}" >> $GITHUB_OUTPUT
-          echo "fork=${FORK}" >> $GITHUB_OUTPUT
-
-      - name: Is PR triggered by forked repo?
-        if: ${{ steps.extract-branch.outputs.fork == 'true' }}
-        run: |
-          echo "PR was triggered by forked repo"
-
-      - name: Echo repo and branch information
-        run: |
-          echo "repo-owner=${{ github.repository_owner }}"
-          echo "repo-name=${{ github.event.repository.name }}"
-          echo "repo-branch=${{ steps.extract-branch.outputs.repo-branch }}"
-          echo "repo-version=${{ steps.extract-branch.outputs.repo-version }}"
-
-  cromwell-consumer-contract-tests:
-    runs-on: ubuntu-latest
-    needs: [init-github-context]
-    outputs:
-      pact-b64: ${{ steps.encode-pact.outputs.pact-b64 }}
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Run consumer tests
-        run: |
-          docker run --rm -v $PWD:/working \
-                          -v jar-cache:/root/.ivy \
-                          -v jar-cache:/root/.ivy2 \
-                          -w /working \
-                          sbtscala/scala-sbt:openjdk-17.0.2_1.7.2_2.13.10 \
-                          sbt "project pact4s" clean test
-
-      - name: Output consumer contract as non-breaking base64 string
-        id: encode-pact
-        run: |
-          cd pact4s
-          NON_BREAKING_B64=$(cat target/pacts/cromwell-consumer-drshub-provider.json | base64 -w 0)
-          echo "pact-b64=${NON_BREAKING_B64}" >> $GITHUB_OUTPUT
-
-  # Prevent untrusted sources from using PRs to publish contracts
-  # since access to secrets is not allowed.
-  publish-contracts:
-    runs-on: ubuntu-latest
-    if: ${{ needs.init-github-context.outputs.fork == 'false' }}
-    needs: [init-github-context, cromwell-consumer-contract-tests]
-    steps:
-      - name: Dispatch to terra-github-workflows
-        uses: broadinstitute/workflow-dispatch@v3
-        with:
-          workflow: .github/workflows/publish-contracts.yaml
-          repo: broadinstitute/terra-github-workflows
-          ref: refs/heads/main
-          token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # github token for access to kick off a job in the private repo
-          inputs: '{ "pact-b64": "${{ needs.cromwell-consumer-contract-tests.outputs.pact-b64 }}", "repo-owner": "${{ github.repository_owner }}", "repo-name": "${{ github.event.repository.name }}", "repo-branch": "${{ needs.init-github-context.outputs.repo-branch }}" }'
-
-  can-i-deploy:
-    runs-on: ubuntu-latest
-    if: ${{ needs.init-github-context.outputs.fork == 'false' && false}} # Disabling this step for now until there is a webhook setup
-    needs: [ init-github-context, publish-contracts ]
-    steps:
-      - name: Dispatch to terra-github-workflows
-        uses: broadinstitute/workflow-dispatch@v3
-        with:
-          workflow: .github/workflows/can-i-deploy.yaml
-          repo: broadinstitute/terra-github-workflows
-          ref: refs/heads/main
-          token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # github token for access to kick off a job in the private repo
-          inputs: '{ "pacticipant": "cromwell-consumer", "version": "${{ needs.init-github-context.outputs.repo-version }}" }'
diff --git a/build.sbt b/build.sbt
index 3754a92305d..44a67721e42 100644
--- a/build.sbt
+++ b/build.sbt
@@ -355,11 +355,6 @@ lazy val `cromwell-drs-localizer` = project
   .dependsOn(common)
   .dependsOn(`cloud-nio-impl-drs` % "test->test")
 
-lazy val pact4s = project.in(file("pact4s"))
-  .settings(pact4sSettings)
-  .dependsOn(services)
-  .disablePlugins(sbtassembly.AssemblyPlugin)
-
 lazy val server = project
   .withExecutableSettings("cromwell", serverDependencies)
   .dependsOn(engine)
@@ -425,5 +420,4 @@ lazy val root = (project in file("."))
   .aggregate(wes2cromwell)
   .aggregate(wom)
   .aggregate(womtool)
-  .aggregate(pact4s)
   .withAggregateSettings()
diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
similarity index 97%
rename from pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
rename to filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
index f023257fef9..611a50f5603 100644
--- a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.dsde.workbench.cromwell.consumer
+package cromwell.filesystems.blob
 
 import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
 import au.com.dius.pact.core.model.RequestResponsePact
diff --git a/pact4s/README.md b/pact4s/README.md
deleted file mode 100644
index d33447f7356..00000000000
--- a/pact4s/README.md
+++ /dev/null
@@ -1,51 +0,0 @@
-c# pact4s [Under construction]
-
-pact4s is used for contract testing.
-
-# Dependencies
-
-```scala
-  val pact4sDependencies = Seq(
-    pact4sScalaTest,
-    pact4sCirce,
-    http4sEmberClient,
-    http4sDsl,
-    http4sEmberServer,
-    http4sCirce,
-    circeCore,
-    typelevelCat,
-    scalaTest
-  )
-
-lazy val pact4s = project.in(file("pact4s"))
-  .settings(pact4sSettings)
-  .dependsOn(http % "test->test;compile->compile")
-```
-
-## Building and running contract tests
-Clone the repo.
-```
-$ git clone https://github.com/broadinstitute/cromwell.git 
-$ cd cromwell
-```
-
-If you are already using OpenJDK 11, run the following command. 
-```
-$ sbt "project pact4s" clean test  
-```
-
-Otherwise, you can run the command inside a docker container with OpenJDK 11 installed. 
-This is especially useful when automating contract tests in a GitHub Action runner which does not guarantee the correct OpenJDK version.
-```
-docker run --rm -v $PWD:/working \
-                -v jar-cache:/root/.ivy \
-                -v jar-cache:/root/.ivy2 \
-                -w /working \
-                sbtscala/scala-sbt:openjdk-11.0.16_1.8.1_2.13.10 \
-                sbt "project pact4s" clean test
-```
-
-The generated contracts can be found in the `./target/pacts` folder
-- `cromwell-consumer-drshub-provider.json`
-- `cromwell-consumer-fake-provider.json`
-
diff --git a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
deleted file mode 100644
index 3fa11515118..00000000000
--- a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
+++ /dev/null
@@ -1,93 +0,0 @@
-package org.broadinstitute.dsde.workbench.cromwell.consumer
-
-import cats.effect.Concurrent
-import cats.syntax.all._
-import com.typesafe.scalalogging.LazyLogging
-import io.circe.{Decoder, Encoder}
-import org.http4s._
-import org.http4s.circe.CirceEntityCodec.{circeEntityDecoder, circeEntityEncoder}
-import org.http4s.client.Client
-
-case class AccessUrl(url: String, headers: List[String])
-
-case class ResourceMetadataRequest(url: String, fields: List[String])
-
-case class ResourceMetadata(contentType: String,
-                            size: Long,
-                            timeCreated: String,
-                            timeUpdated: String,
-                            bucket: Option[String],
-                            name: Option[String],
-                            gsUri: Option[String],
-                            googleServiceAccount: Option[Map[String, Map[String, String]]],
-                            fileName: Option[String],
-                            accessUrl: Option[AccessUrl],
-                            hashes: Map[String, String],
-                            localizationPath: Option[String],
-                            bondProvider: Option[String]
-)
-trait DrsHubClient[F[_]] extends LazyLogging {
-  def fetchSystemStatus(): F[Boolean]
-
-  def resolveDrsObject(drsPath: String, fields: List[String]): F[ResourceMetadata]
-
-}
-
-/*
- This class represents the consumer (Cromwell) view of the DrsHub provider that implements the following endpoints:
-  - GET /status
-  - GET /api/v4/drs/resolve
- */
-class DrsHubClientImpl[F[_]: Concurrent](client: Client[F], baseUrl: Uri) extends DrsHubClient[F] {
-  val apiVersion = "v4"
-
-  implicit val accessUrlDecoder: Decoder[AccessUrl] = Decoder.forProduct2("url", "headers")(AccessUrl.apply)
-  implicit val resourceMetadataDecoder: Decoder[ResourceMetadata] = Decoder.forProduct13(
-    "contentType",
-    "size",
-    "timeCreated",
-    "timeUpdated",
-    "bucket",
-    "name",
-    "gsUri",
-    "googleServiceAccount",
-    "fileName",
-    "accessUrl",
-    "hashes",
-    "localizationPath",
-    "bondProvider"
-  )(ResourceMetadata.apply)
-  implicit val resourceMetadataRequestEncoder: Encoder[ResourceMetadataRequest] = Encoder.forProduct2("url", "fields")(x =>
-    (x.url, x.fields)
-  )
-  implicit val resourceMetadataRequestEntityEncoder: EntityEncoder[F, ResourceMetadataRequest] = circeEntityEncoder[F, ResourceMetadataRequest]
-  override def fetchSystemStatus(): F[Boolean] = {
-    val request = Request[F](uri = baseUrl / "status").withHeaders(
-      org.http4s.headers.Accept(MediaType.application.json)
-    )
-    client.run(request).use { resp =>
-      resp.status match {
-        case Status.Ok                  => true.pure[F]
-        case Status.InternalServerError => false.pure[F]
-        case _                          => UnknownError.raiseError
-      }
-    }
-  }
-
-  override def resolveDrsObject(drsPath: String, fields: List[String]): F[ResourceMetadata] = {
-    val body = ResourceMetadataRequest(url = drsPath, fields = fields)
-    val entityBody: EntityBody[F] = EntityEncoder[F, ResourceMetadataRequest].toEntity(body).body
-    val request = Request[F](uri = baseUrl / "api" / apiVersion / "drs" / "resolve", method=Method.POST, body=entityBody).withHeaders(
-      org.http4s.headers.`Content-Type`(MediaType.application.json)
-    )
-    client.run(request).use { resp =>
-      resp.status match {
-        case Status.Ok                  => resp.as[ResourceMetadata]
-        case _                          => UnknownError.raiseError
-      }
-    }
-  }
-
-}
-
-
diff --git a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
deleted file mode 100644
index ceeefc7479f..00000000000
--- a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
+++ /dev/null
@@ -1,207 +0,0 @@
-package org.broadinstitute.dsde.workbench.cromwell.consumer
-
-import au.com.dius.pact.consumer.dsl.{DslPart, PactDslResponse, PactDslWithProvider}
-import pact4s.algebras.PactBodyJsonEncoder
-case object UnknownError extends Exception
-
-object PactHelper {
-  def buildInteraction(builder: PactDslResponse,
-                       state: String,
-                       uponReceiving: String,
-                       method: String,
-                       path: String,
-                       requestHeaders: Seq[(String, String)],
-                       status: Int,
-                       responseHeaders: Seq[(String, String)],
-                       body: DslPart
-                      ): PactDslResponse =
-    builder
-      .`given`(state)
-      .uponReceiving(uponReceiving)
-      .method(method)
-      .path(path)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
-      .willRespondWith()
-      .status(status)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
-      .body(body)
-
-  def buildInteraction(builder: PactDslResponse,
-                       state: String,
-                       uponReceiving: String,
-                       method: String,
-                       path: String,
-                       requestHeaders: Seq[(String, String)],
-                       status: Int,
-                       responseHeaders: Seq[(String, String)],
-                      ): PactDslResponse =
-    builder
-      .`given`(state)
-      .uponReceiving(uponReceiving)
-      .method(method)
-      .path(path)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
-      .willRespondWith()
-      .status(status)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
-
-  def buildInteraction(builder: PactDslResponse,
-                       state: String,
-                       uponReceiving: String,
-                       method: String,
-                       path: String,
-                       requestHeaders: Seq[(String, String)],
-                       status: Int
-                      ): PactDslResponse =
-    builder
-      .`given`(state)
-      .uponReceiving(uponReceiving)
-      .method(method)
-      .path(path)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
-      .willRespondWith()
-      .status(status)
-
-  def buildInteraction(builder: PactDslResponse,
-                       uponReceiving: String,
-                       method: String,
-                       path: String,
-                       requestHeaders: Seq[(String, String)],
-                       status: Int
-                      ): PactDslResponse =
-    builder
-      .uponReceiving(uponReceiving)
-      .method(method)
-      .path(path)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
-      .willRespondWith()
-      .status(status)
-
-  def buildInteraction(builder: PactDslWithProvider,
-                       state: String,
-                       uponReceiving: String,
-                       method: String,
-                       path: String,
-                       requestHeaders: Seq[(String, String)],
-                       status: Int,
-                       responseHeaders: Seq[(String, String)],
-                       body: DslPart
-                      ): PactDslResponse =
-    builder
-      .`given`(state)
-      .uponReceiving(uponReceiving)
-      .method(method)
-      .path(path)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
-      .willRespondWith()
-      .status(status)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
-      .body(body)
-
-  def buildInteraction(builder: PactDslWithProvider,
-                       state: String,
-                       stateParams: Map[String, Any],
-                       uponReceiving: String,
-                       method: String,
-                       path: String,
-                       requestHeaders: Seq[(String, String)],
-                       requestBody: DslPart,
-                       status: Int,
-                       responseHeaders: Seq[(String, String)],
-                       responsBody: DslPart
-                      ): PactDslResponse =
-    builder
-      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
-      .uponReceiving(uponReceiving)
-      .method(method)
-      .path(path)
-      .body(requestBody)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
-      .willRespondWith()
-      .status(status)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
-      .body(responsBody)
-
-  def buildInteraction(builder: PactDslResponse,
-                       state: String,
-                       stateParams: Map[String, Any],
-                       uponReceiving: String,
-                       method: String,
-                       path: String,
-                       requestHeaders: Seq[(String, String)],
-                       status: Int,
-                       responseHeaders: Seq[(String, String)],
-                       body: DslPart
-                      ): PactDslResponse =
-    builder
-      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
-      .uponReceiving(uponReceiving)
-      .method(method)
-      .path(path)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
-      .willRespondWith()
-      .status(status)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
-      .body(body)
-
-  def buildInteraction[A](builder: PactDslWithProvider,
-                          state: String,
-                          stateParams: Map[String, Any],
-                          uponReceiving: String,
-                          method: String,
-                          path: String,
-                          requestHeaders: Seq[(String, String)],
-                          status: Int,
-                          responseHeaders: Seq[(String, String)],
-                          body: A
-                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
-    builder
-      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
-      .uponReceiving(uponReceiving)
-      .method(method)
-      .path(path)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
-      .willRespondWith()
-      .status(status)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
-      .body(ev.toJsonString(body))
-
-  def buildInteraction[A](builder: PactDslResponse,
-                          state: String,
-                          uponReceiving: String,
-                          method: String,
-                          path: String,
-                          requestHeaders: Seq[(String, String)],
-                          requestBody: A,
-                          status: Int
-                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
-    builder
-      .`given`(state)
-      .uponReceiving(uponReceiving)
-      .method(method)
-      .path(path)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
-      .body(ev.toJsonString(requestBody))
-      .willRespondWith()
-      .status(status)
-
-  def buildInteraction[A](builder: PactDslResponse,
-                          state: String,
-                          stateParams: Map[String, Any],
-                          uponReceiving: String,
-                          method: String,
-                          path: String,
-                          requestHeaders: Seq[(String, String)],
-                          requestBody: A,
-                          status: Int
-                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
-    builder
-      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
-      .uponReceiving(uponReceiving)
-      .method(method)
-      .path(path)
-      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
-      .body(ev.toJsonString(requestBody))
-      .willRespondWith()
-      .status(status)
-}
diff --git a/pact4s/src/test/resources/logback.xml b/pact4s/src/test/resources/logback.xml
deleted file mode 100644
index 24316805e7e..00000000000
--- a/pact4s/src/test/resources/logback.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<configuration>
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-        <encoder>
-            <pattern>%d [%thread] %-5level  %logger{35} - %msg%n</pattern>
-        </encoder>
-    </appender>
-    <logger name="io.github.jbwheatley.pact4s.Pact4sLogger" level="INFO" />
-    <logger name="au.com.dius.pact.consumer" level="DEBUG"/>
-    <logger name="au.com.dius.pact.provider" level="DEBUG"/>
-
-    <root level="INFO">
-        <appender-ref ref="STDOUT" />
-    </root>
-</configuration>
diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
deleted file mode 100644
index a4ebe56d76a..00000000000
--- a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
+++ /dev/null
@@ -1,170 +0,0 @@
-package org.broadinstitute.dsde.workbench.cromwell.consumer
-
-import au.com.dius.pact.consumer.dsl.LambdaDsl.newJsonBody
-import au.com.dius.pact.consumer.dsl._
-import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
-import au.com.dius.pact.core.model.RequestResponsePact
-import cats.effect.IO
-import org.broadinstitute.dsde.workbench.cromwell.consumer.PactHelper._
-import org.http4s.Uri
-import org.http4s.blaze.client.BlazeClientBuilder
-import org.http4s.client.Client
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import pact4s.scalatest.RequestResponsePactForger
-
-import java.util.concurrent.Executors
-import scala.concurrent.ExecutionContext
-
-class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePactForger {
-  val ec = ExecutionContext.fromExecutorService(Executors.newCachedThreadPool())
-  implicit val cs = IO.contextShift(ec)
-  /*
-    Define the folder that the pact contracts get written to upon completion of this test suite.
-   */
-  override val pactTestExecutionContext: PactTestExecutionContext =
-    new PactTestExecutionContext(
-      "./target/pacts"
-    )
-
-  private val requestFields = List(
-      "bucket",
-      "accessUrl",
-      "googleServiceAccount",
-      "fileName",
-      "hashes",
-      "localizationPath",
-      "bondProvider",
-      "name",
-      "size",
-      "timeCreated",
-      "timeUpdated",
-      "gsUri",
-      "contentType",
-  )
-
-  val filesize = 123L
-  val timeCreated = "2021-03-04T20:00:00.000Z"
-  val bucket = "fc-secure-1234567890"
-  val filename = "my-file.bam"
-  val bondProvider = "anvil"
-  val fileHash = "a2317edbd2eb6cf6b0ee49cb81e3a556"
-  val accessUrl = f"gs://${bucket}/${filename}"
-
-
-  val drsResourceResponsePlaceholder: ResourceMetadata = ResourceMetadata(
-    "application/octet-stream",
-    filesize,
-    timeCreated,
-    timeCreated,
-    None,
-    None,
-    None,
-    None,
-    None,
-    Option(AccessUrl(accessUrl, List("Header", "Example"))),
-    Map("md5" -> fileHash),
-    None,
-    Option(bondProvider)
-  )
-
-  val resourceMetadataResponseDsl: DslPart = newJsonBody { o =>
-    o.stringType("contentType", "application/octet-stream")
-      o.numberType("size", filesize)
-      o.stringType("timeCreated", timeCreated)
-      o.stringType("timeUpdated", timeCreated)
-      o.nullValue("gsUri")
-      o.nullValue("googleServiceAccount")
-      o.nullValue("fileName")
-      o.`object`("accessUrl" , { a =>
-        a.stringType("url", accessUrl)
-          a.`array`("headers", { h =>
-            h.stringType("Header")
-            h.stringType("Example")
-            ()
-          })
-        ()
-      })
-      o.`object`("hashes", { o =>
-        o.stringType("md5", fileHash)
-        ()
-      })
-      o.nullValue("localizationPath")
-      o.stringType("bondProvider", bondProvider)
-    ()
-  }.build
-
-  val fileId = "1234567890"
-
-  val resourceRequestDsl = newJsonBody { o =>
-    o.stringType("url", f"drs://test.theanvil.io/${fileId}")
-    o.array("fields", { a =>
-      requestFields.map(a.stringType)
-      ()
-    })
-    ()
-  }.build
-
-  val consumerPactBuilder: ConsumerPactBuilder = ConsumerPactBuilder
-    .consumer("cromwell-consumer")
-
-  val pactProvider: PactDslWithProvider = consumerPactBuilder
-    .hasPactWith("drshub-provider")
-
-  var pactDslResponse: PactDslResponse = buildInteraction(
-    pactProvider,
-    state = "resolve Drs url",
-    stateParams = Map[String, String](
-      "fileId" -> fileId,
-      "bucket" -> bucket,
-      "filename" -> filename,
-      "bondProvider" -> bondProvider,
-      "fileHash" -> fileHash,
-      "accessUrl" -> accessUrl,
-      "fileSize" -> filesize.toString,
-      "timeCreated" -> timeCreated
-    ),
-    uponReceiving = "Request to resolve drs url",
-    method = "POST",
-    path = "/api/v4/drs/resolve",
-    requestHeaders = Seq("Content-type" -> "application/json"),
-    requestBody = resourceRequestDsl,
-    status = 200,
-    responseHeaders = Seq(),
-    responsBody = resourceMetadataResponseDsl
-  )
-
-  pactDslResponse = buildInteraction(
-    pactDslResponse,
-    state = "Drshub is ok",
-    uponReceiving = "Request for drshub api status",
-    method = "GET",
-    path = "/status",
-    requestHeaders = Seq(),
-    status = 200,
-    responseHeaders = Seq()
-  )
-
-  override val pact: RequestResponsePact = pactDslResponse.toPact
-
-  val client: Client[IO] = {
-    BlazeClientBuilder[IO](ExecutionContext.global).resource.allocated.unsafeRunSync()._1
-  }
-
-  /*
-  we should use these tests to ensure that our client class correctly handles responses from the provider - i.e. decoding, error mapping, validation
-   */
-  it should "get DrsHub ok status" in {
-    new DrsHubClientImpl[IO](client, Uri.unsafeFromString(mockServer.getUrl))
-      .fetchSystemStatus()
-      .attempt
-      .unsafeRunSync() shouldBe Right(true)
-  }
-
-  it should "resolve drs object" in {
-    new DrsHubClientImpl[IO](client, Uri.unsafeFromString(mockServer.getUrl))
-      .resolveDrsObject("drs://drs.example.com/1234567890", requestFields)
-      .attempt
-      .unsafeRunSync() shouldBe Right(drsResourceResponsePlaceholder)
-  }
-}
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index ef829d6f780..405ecd2d3c4 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -91,7 +91,6 @@ object Dependencies {
   private val mysqlV = "8.0.28"
   private val nettyV = "4.1.72.Final"
   private val owlApiV = "5.1.19"
-  private val pact4sV = "0.9.0"
   private val postgresV = "42.4.1"
   private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
@@ -104,7 +103,7 @@ object Dependencies {
   private val scalaPoolV = "0.4.3"
   private val scalacticV = "3.2.13"
   private val scalameterV = "0.21"
-  private val scalatestV = "3.2.15"
+  private val scalatestV = "3.2.10"
   private val scalatestScalacheckV = scalatestV + ".0"
   private val scoptV = "4.1.0"
   private val sentryLogbackV = "5.7.4"
@@ -443,7 +442,7 @@ object Dependencies {
     - https://www.scalatest.org/user_guide/generator_driven_property_checks
     - https://www.scalatest.org/user_guide/writing_scalacheck_style_properties
    */
-  private val scalacheckBaseV = "1.17"
+  private val scalacheckBaseV = "1.15"
   private val scalacheckDependencies = List(
     "org.scalatestplus" %% s"scalacheck-${scalacheckBaseV.replace(".", "-")}" % scalatestScalacheckV % Test,
   )
@@ -595,12 +594,14 @@ object Dependencies {
   val sfsBackendDependencies = List (
     "org.lz4" % "lz4-java" % lz4JavaV
   )
-  val scalaTest = "org.scalatest" %% "scalatest" % scalatestV
+
   val testDependencies: List[ModuleID] = List(
-    scalaTest,
+    "org.scalatest" %% "scalatest" % scalatestV,
     // Use mockito Java DSL directly instead of the numerous and often hard to keep updated Scala DSLs.
     // See also scaladoc in common.mock.MockSugar and that trait's various usages.
     "org.mockito" % "mockito-core" % mockitoV,
+    "io.github.jbwheatley" %% "pact4s-scalatest"  % "0.7.0",
+    "io.github.jbwheatley" %% "pact4s-circe" %  "0.7.0"
   ) ++ slf4jBindingDependencies // During testing, add an slf4j binding for _all_ libraries.
 
   val kindProjectorPlugin = "org.typelevel" % "kind-projector" % kindProjectorV cross CrossVersion.full
@@ -796,23 +797,5 @@ object Dependencies {
      The jakarta.annotation inclusion is above in googleApiClientDependencies.
      */
     ExclusionRule("javax.annotation", "javax.annotation-api"),
-    ExclusionRule("javax.activation"),
-  )
-
-  val http4sDsl = "org.http4s" %% "http4s-dsl" % http4sV
-  val http4sEmberClient = "org.http4s" %% "http4s-ember-client" % http4sV
-  val http4sEmberServer = "org.http4s" %% "http4s-ember-server" % http4sV
-  val http4sCirce = "org.http4s" %% "http4s-circe" % http4sV
-  val pact4sScalaTest = "io.github.jbwheatley" %% "pact4s-scalatest" % pact4sV % Test
-  val pact4sCirce = "io.github.jbwheatley" %% "pact4s-circe" % pact4sV
-
-  val pact4sDependencies = Seq(
-    pact4sScalaTest,
-    pact4sCirce,
-    http4sEmberClient,
-    http4sDsl,
-    http4sEmberServer,
-    http4sCirce,
-    scalaTest,
   )
 }
diff --git a/project/Settings.scala b/project/Settings.scala
index 32559422066..797d7917dd9 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -98,22 +98,6 @@ object Settings {
     )
   )
 
-  val pact4sSettings = sharedSettings ++ List(
-    libraryDependencies ++= pact4sDependencies,
-
-    /**
-      * Invoking pact tests from root project (sbt "project pact" test)
-      * will launch tests in a separate JVM context that ensures contracts
-      * are written to the pact/target/pacts folder. Otherwise, contracts
-      * will be written to the root folder.
-      */
-    Test / fork := true
-
-  ) ++ assemblySettings
-
-  lazy val pact4s = project.in(file("pact4s"))
-    .settings(pact4sSettings)
-
   /*
       Docker instructions to install Google Cloud SDK image in docker image. It also installs `crcmod` which
       is needed while downloading large files using `gsutil`.
diff --git a/project/build.properties b/project/build.properties
index 54f486b9dc3..2b4cbe4d584 100644
--- a/project/build.properties
+++ b/project/build.properties
@@ -1,2 +1,2 @@
 # scala-steward:off
-sbt.version=1.8.1
+sbt.version=1.5.5
diff --git a/project/plugins.sbt b/project/plugins.sbt
index 151ba4b87e3..bdb54f675bf 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -1,5 +1,5 @@
 addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.9.0")
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "2.1.1")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.1")
 addSbtPlugin("com.github.sbt" % "sbt-git" % "2.0.0")
 addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.4")
 addSbtPlugin("com.github.cb372" % "sbt-explicit-dependencies" % "0.2.16")

From 28cdba7b09e9dd4c16abe490929ff884bde1a0eb Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Wed, 24 May 2023 23:49:09 -0400
Subject: [PATCH 175/326] WX-966 Add Cascades, remove Directory from Biscayne
 (#7105)

---
 build.sbt                                     |   26 +
 .../biscayne_prohibits_directory.test         |   13 +
 .../directory_type_local.test                 |    6 +-
 .../directory_type_output_papi.test           |    4 +-
 .../directory_type_papi.test                  |    4 +-
 .../biscayne_http_relative_imports.wdl        |    4 +-
 .../biscayne_new_engine_functions.wdl         |    2 +-
 .../directory_type.wdl                        |   49 +
 .../directory_type_local_inputs.json          |    0
 .../default_default/default_default.wdl       |    2 +-
 .../read_functions_windows_line_endings.wdl   |    2 +-
 .../directory_type/directory_type.wdl         |    0
 .../directory_type_local_inputs.json          |    3 +
 .../directory_type_output.wdl                 |    0
 core/src/main/resources/reference.conf        |   10 +-
 .../routes/wes/ServiceInfoSpec.scala          |    2 +-
 .../languages/util/LanguageFactoryUtil.scala  |    2 +-
 .../biscayne/WdlBiscayneLanguageFactory.scala |    2 +-
 .../cascades/WdlCascadesLanguageFactory.scala |   87 +
 project/Merging.scala                         |    2 +-
 .../relative_url_imports/description.json     |    2 +-
 .../java/wdl/biscayne/parser/WdlParser.java   | 1744 ++--
 .../biscayne/src/main/resources/CHANGELOG.txt |    4 +
 .../biscayne/src/main/resources/grammar.hgr   |  444 +
 .../biscayne/ast2wdlom/ast2wdlom.scala        |    3 +-
 .../biscayne/src/test/cases/afters.wdl        |    2 +-
 .../src/test/cases/biscayne_escaping.wdl      |    2 +-
 .../cases/no_input_no_output_workflow.wdl     |    2 +-
 .../src/test/cases/simple_first_test.wdl      |    2 +-
 .../transforms/biscayne/Ast2WdlomSpec.scala   |    2 +-
 .../java/wdl/cascades/parser/WdlParser.java   | 7874 +++++++++++++++++
 .../cascades/src/main/resources/CHANGELOG.txt |    5 +
 .../cascades/src/main/resources/grammar.hgr   |  444 +
 .../AstToNewExpressionElements.scala          |   26 +
 .../ast2wdlom/CascadesGenericAstNode.scala    |   36 +
 .../cascades/ast2wdlom/ast2wdlom.scala        |   65 +
 .../CascadesExpressionValueConsumers.scala    |   57 +
 .../expression/consumed/consumed.scala        |  110 +
 .../files/CascadesFileEvaluators.scala        |   20 +
 .../linking/expression/files/files.scala      |  119 +
 .../types/CascadesTypeEvaluators.scala        |   97 +
 .../linking/expression/types/types.scala      |  118 +
 .../values/CascadesValueEvaluators.scala      |  169 +
 .../linking/expression/values/values.scala    |  124 +
 .../cascades/parsing/CascadesParser.scala     |   32 +
 .../WdlCascadesSyntaxErrorFormatter.scala     |   64 +
 .../transforms/cascades/parsing/package.scala |   10 +
 .../cascades/wdlom2wom/package.scala          |   18 +
 .../cascades/src/test/cases/afters.wdl        |   15 +
 .../src/test/cases/cascades_escaping.wdl      |   25 +
 .../cases/no_input_no_output_workflow.wdl     |   30 +
 .../src/test/cases/simple_first_test.wdl      |   24 +
 .../transforms/cascades/Ast2WdlomSpec.scala   |   97 +
 .../ast2wdlom/WdlFileToWdlomSpec.scala        |  212 +
 ...CascadesExpressionValueConsumersSpec.scala |   60 +
 .../files/CascadesFileEvaluatorSpec.scala     |   43 +
 .../types/CascadesTypeEvaluatorSpec.scala     |   59 +
 .../values/CascadesValueEvaluatorSpec.scala   |  189 +
 .../scala/womtool/input/WomGraphMaker.scala   |    5 +-
 .../expected_imports.txt                      |    6 +-
 .../invalid/after_circle/after_circle.wdl     |    2 +-
 .../biscayne/invalid/bad_after/bad_after.wdl  |    2 +-
 .../biscayne/invalid/bad_task/bad_task.wdl    |    2 +-
 .../directory_type/directory_type.wdl         |    2 +-
 .../invalid/object_struct/object_struct.wdl   |    2 +-
 .../invalid/object_type/object_type.wdl       |    2 +-
 .../read_and_write_object.wdl                 |    2 +-
 .../invalid/trailing_if/trailing_if.wdl       |    2 +-
 .../validate/biscayne/valid/afters/afters.wdl |    2 +-
 .../valid/afters_and_ifs/afters_and_ifs.wdl   |    2 +-
 .../afters_and_scatters.wdl                   |    2 +-
 .../http_relative_imports.wdl                 |    4 +-
 .../valid/object_struct/object_struct.wdl     |    2 +-
 .../pre_version_comments.wdl                  |    2 +-
 .../relative_imports/relative_imports.wdl     |    2 +-
 .../relative_imports/structs/my_struct.wdl    |    2 +-
 .../valid/relative_imports/sub_wfs/foo.wdl    |    2 +-
 .../relative_imports/sub_wfs/tasks/add5.wdl   |    2 +-
 .../valid/sep_function/sep_function.wdl       |    2 +-
 .../sep_function/sep_function_no_command.wdl  |    2 +-
 .../biscayne/valid/use_nones/use_nones.wdl    |    2 +-
 .../validate/biscayne/valid/utf8/utf8.wdl     |    2 +-
 .../version_variables/version_variables.wdl   |    2 +-
 83 files changed, 11702 insertions(+), 926 deletions(-)
 create mode 100644 centaur/src/main/resources/standardTestCases/biscayne_prohibits_directory.test
 create mode 100644 centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_prohibits_directory/directory_type.wdl
 rename centaur/src/main/resources/standardTestCases/wdl_biscayne/{directory_type => biscayne_prohibits_directory}/directory_type_local_inputs.json (100%)
 rename centaur/src/main/resources/standardTestCases/{wdl_biscayne => wdl_cascades}/directory_type/directory_type.wdl (100%)
 create mode 100644 centaur/src/main/resources/standardTestCases/wdl_cascades/directory_type/directory_type_local_inputs.json
 rename centaur/src/main/resources/standardTestCases/{wdl_biscayne => wdl_cascades}/directory_type_output/directory_type_output.wdl (100%)
 create mode 100644 languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala
 create mode 100644 wdl/transforms/biscayne/src/main/resources/CHANGELOG.txt
 create mode 100644 wdl/transforms/biscayne/src/main/resources/grammar.hgr
 create mode 100644 wdl/transforms/cascades/src/main/java/wdl/cascades/parser/WdlParser.java
 create mode 100644 wdl/transforms/cascades/src/main/resources/CHANGELOG.txt
 create mode 100644 wdl/transforms/cascades/src/main/resources/grammar.hgr
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/CascadesGenericAstNode.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/ast2wdlom.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/CascadesParser.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/WdlCascadesSyntaxErrorFormatter.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/package.scala
 create mode 100644 wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala
 create mode 100644 wdl/transforms/cascades/src/test/cases/afters.wdl
 create mode 100644 wdl/transforms/cascades/src/test/cases/cascades_escaping.wdl
 create mode 100644 wdl/transforms/cascades/src/test/cases/no_input_no_output_workflow.wdl
 create mode 100644 wdl/transforms/cascades/src/test/cases/simple_first_test.wdl
 create mode 100644 wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
 create mode 100644 wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala
 create mode 100644 wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
 create mode 100644 wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
 create mode 100644 wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
 create mode 100644 wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
 rename womtool/src/test/resources/validate/biscayne/{valid => invalid}/directory_type/directory_type.wdl (96%)

diff --git a/build.sbt b/build.sbt
index 44a67721e42..90e092d802d 100644
--- a/build.sbt
+++ b/build.sbt
@@ -37,6 +37,11 @@ lazy val wdlModelBiscayne = (project in wdlModelRoot / "biscayne")
   .dependsOn(wdlModelDraft3)
   .dependsOn(common % "test->test")
 
+lazy val wdlModelCascades = (project in wdlModelRoot / "cascades")
+  .withLibrarySettings("cromwell-wdl-model-cascades")
+  .dependsOn(wdlSharedModel)
+  .dependsOn(common % "test->test")
+
 lazy val wdlTransformsRoot = wdlRoot / "transforms"
 
 lazy val wdlSharedTransforms = (project in wdlTransformsRoot / "shared")
@@ -74,6 +79,13 @@ lazy val wdlTransformsBiscayne = (project in wdlTransformsRoot / "biscayne")
   .dependsOn(common % "test->test")
   .dependsOn(wom % "test->test")
 
+lazy val wdlTransformsCascades = (project in wdlTransformsRoot / "cascades")
+  .withLibrarySettings("cromwell-wdl-transforms-cascades", wdlDependencies)
+  .dependsOn(wdlNewBaseTransforms)
+  .dependsOn(languageFactoryCore)
+  .dependsOn(common % "test->test")
+  .dependsOn(wom % "test->test")
+
 lazy val core = project
   .withLibrarySettings("cromwell-core", coreDependencies)
   .dependsOn(wom)
@@ -178,6 +190,7 @@ lazy val services = project
   .dependsOn(wdlDraft2LanguageFactory % "test->test") // because the WaaS tests init language config with all languages
   .dependsOn(wdlDraft3LanguageFactory % "test->test")
   .dependsOn(wdlBiscayneLanguageFactory % "test->test")
+  .dependsOn(wdlCascadesLanguageFactory % "test->test")
   .dependsOn(core % "test->test")
   .dependsOn(ftpFileSystem % "test->test")
   .dependsOn(common % "test->test")
@@ -263,6 +276,7 @@ lazy val engine = project
   .dependsOn(wdlDraft2LanguageFactory % "test->test")
   .dependsOn(wdlDraft3LanguageFactory % "test->test")
   .dependsOn(wdlBiscayneLanguageFactory % "test->test")
+  .dependsOn(wdlCascadesLanguageFactory % "test->test")
   .dependsOn(common % "test->test")
   .dependsOn(core % "test->test")
   .dependsOn(backend % "test->test")
@@ -279,6 +293,7 @@ lazy val womtool = project
   .dependsOn(wdlDraft2LanguageFactory)
   .dependsOn(wdlDraft3LanguageFactory)
   .dependsOn(wdlBiscayneLanguageFactory)
+  .dependsOn(wdlCascadesLanguageFactory)
   .dependsOn(wom % "test->test")
   .dependsOn(common % "test->test")
 
@@ -324,6 +339,13 @@ lazy val wdlBiscayneLanguageFactory = (project in languageFactoryRoot / "wdl-bis
   .dependsOn(wdlTransformsBiscayne)
   .dependsOn(common % "test->test")
 
+lazy val wdlCascadesLanguageFactory = (project in languageFactoryRoot / "wdl-cascades")
+  .withLibrarySettings("wdl-cascades")
+  .dependsOn(languageFactoryCore)
+  .dependsOn(wdlModelCascades)
+  .dependsOn(wdlTransformsCascades)
+  .dependsOn(common % "test->test")
+
 lazy val `cloud-nio-spi` = (project in cloudNio / "cloud-nio-spi")
   .withLibrarySettings(libraryName = "cloud-nio-spi", dependencies = spiDependencies)
   .dependsOn(common % "test->test")
@@ -366,6 +388,7 @@ lazy val server = project
   .dependsOn(wdlDraft2LanguageFactory)
   .dependsOn(wdlDraft3LanguageFactory)
   .dependsOn(wdlBiscayneLanguageFactory)
+  .dependsOn(wdlCascadesLanguageFactory)
   .dependsOn(engine % "test->test")
   .dependsOn(common % "test->test")
 
@@ -406,15 +429,18 @@ lazy val root = (project in file("."))
   .aggregate(sraFileSystem)
   .aggregate(tesBackend)
   .aggregate(wdlBiscayneLanguageFactory)
+  .aggregate(wdlCascadesLanguageFactory)
   .aggregate(wdlDraft2LanguageFactory)
   .aggregate(wdlDraft3LanguageFactory)
   .aggregate(wdlModelBiscayne)
+  .aggregate(wdlModelCascades)
   .aggregate(wdlModelDraft2)
   .aggregate(wdlModelDraft3)
   .aggregate(wdlNewBaseTransforms)
   .aggregate(wdlSharedModel)
   .aggregate(wdlSharedTransforms)
   .aggregate(wdlTransformsBiscayne)
+  .aggregate(wdlTransformsCascades)
   .aggregate(wdlTransformsDraft2)
   .aggregate(wdlTransformsDraft3)
   .aggregate(wes2cromwell)
diff --git a/centaur/src/main/resources/standardTestCases/biscayne_prohibits_directory.test b/centaur/src/main/resources/standardTestCases/biscayne_prohibits_directory.test
new file mode 100644
index 00000000000..d2d9bfc9ddf
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/biscayne_prohibits_directory.test
@@ -0,0 +1,13 @@
+name: directory_type_local_denied
+testFormat: workflowfailure
+tags: [localdockertest, "wdl_biscayne"]
+backends: [Local, LocalNoDocker]
+
+files {
+  workflow: wdl_biscayne/biscayne_prohibits_directory/directory_type.wdl
+  inputs: wdl_biscayne/biscayne_prohibits_directory/directory_type_local_inputs.json
+}
+
+metadata {
+  status: Failed
+}
diff --git a/centaur/src/main/resources/standardTestCases/directory_type_local.test b/centaur/src/main/resources/standardTestCases/directory_type_local.test
index f2db3398d96..ae0f90dcc72 100644
--- a/centaur/src/main/resources/standardTestCases/directory_type_local.test
+++ b/centaur/src/main/resources/standardTestCases/directory_type_local.test
@@ -1,11 +1,11 @@
 name: directory_type_local
 testFormat: workflowsuccess
-tags: [localdockertest, "wdl_biscayne"]
+tags: [localdockertest, "wdl_cascades"]
 backends: [Local, LocalNoDocker]
 
 files {
-  workflow: wdl_biscayne/directory_type/directory_type.wdl
-  inputs: wdl_biscayne/directory_type/directory_type_local_inputs.json
+  workflow: wdl_cascades/directory_type/directory_type.wdl
+  inputs: wdl_cascades/directory_type/directory_type_local_inputs.json
 }
 
 metadata {
diff --git a/centaur/src/main/resources/standardTestCases/directory_type_output_papi.test b/centaur/src/main/resources/standardTestCases/directory_type_output_papi.test
index f66dfd656b3..67e435db619 100644
--- a/centaur/src/main/resources/standardTestCases/directory_type_output_papi.test
+++ b/centaur/src/main/resources/standardTestCases/directory_type_output_papi.test
@@ -1,10 +1,10 @@
 name: directory_type_output_papi
 testFormat: workflowsuccess
-tags: ["wdl_biscayne"]
+tags: ["wdl_cascades"]
 backends: [Papi]
 
 files {
-  workflow: wdl_biscayne/directory_type_output/directory_type_output.wdl
+  workflow: wdl_cascades/directory_type_output/directory_type_output.wdl
 }
 
 metadata {
diff --git a/centaur/src/main/resources/standardTestCases/directory_type_papi.test b/centaur/src/main/resources/standardTestCases/directory_type_papi.test
index 988a609d237..4d953e03c4e 100644
--- a/centaur/src/main/resources/standardTestCases/directory_type_papi.test
+++ b/centaur/src/main/resources/standardTestCases/directory_type_papi.test
@@ -1,10 +1,10 @@
 name: directory_type_papi
 testFormat: workflowsuccess
-tags: ["wdl_biscayne"]
+tags: ["wdl_cascades"]
 backends: [Papi]
 
 files {
-  workflow: wdl_biscayne/directory_type/directory_type.wdl
+  workflow: wdl_cascades/directory_type/directory_type.wdl
 }
 
 metadata {
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_http_relative_imports/biscayne_http_relative_imports.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_http_relative_imports/biscayne_http_relative_imports.wdl
index c75ffacc8a8..e68de3ef339 100644
--- a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_http_relative_imports/biscayne_http_relative_imports.wdl
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_http_relative_imports/biscayne_http_relative_imports.wdl
@@ -1,7 +1,7 @@
-version development
+version development-1.1
 
 # Is there a better way to test this?
-import "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/cromwell/aen_wx_966/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl"
 
 workflow biscayne_http_relative_imports {
   call foo.foo_wf
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
index 979ef6e998a..220fcb535e5 100644
--- a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow biscayne_new_engine_functions {
 
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_prohibits_directory/directory_type.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_prohibits_directory/directory_type.wdl
new file mode 100644
index 00000000000..7bd7f5583c3
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_prohibits_directory/directory_type.wdl
@@ -0,0 +1,49 @@
+version development-1.1
+
+workflow directory_type {
+  input {
+    String text2loc = "text2"
+  }
+  call make_directory { input: text2loc = text2loc }
+  call read_from_directory { input: d = make_directory.d, text2loc = text2loc }
+
+  output {
+    Array[String] out = read_from_directory.contents
+  }
+}
+
+task make_directory {
+  input {
+    String text2loc
+  }
+  String text2dir = sub("foo/~{text2loc}", "/[^/]*$", "")
+  command {
+    mkdir foo
+    mkdir -p ~{text2dir}
+    echo "foo text" > foo/text
+    echo "foo text2" > foo/~{text2loc}
+  }
+  runtime {
+    docker: "ubuntu:latest"
+  }
+  output {
+    Directory d = "foo/"
+  }
+}
+
+task read_from_directory {
+  input {
+    String text2loc
+    Directory d
+  }
+  command {
+    cat ~{d}/text
+    cat ~{d}/~{text2loc}
+  }
+  runtime {
+    docker: "ubuntu:latest"
+  }
+  output {
+    Array[String] contents = read_lines(stdout())
+  }
+}
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/directory_type/directory_type_local_inputs.json b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_prohibits_directory/directory_type_local_inputs.json
similarity index 100%
rename from centaur/src/main/resources/standardTestCases/wdl_biscayne/directory_type/directory_type_local_inputs.json
rename to centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_prohibits_directory/directory_type_local_inputs.json
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/default_default/default_default.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/default_default/default_default.wdl
index 20958128db5..a73b3736fdf 100644
--- a/centaur/src/main/resources/standardTestCases/wdl_biscayne/default_default/default_default.wdl
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/default_default/default_default.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow default_default {
   call default_default_task
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/read_functions_windows_line_endings/read_functions_windows_line_endings.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/read_functions_windows_line_endings/read_functions_windows_line_endings.wdl
index 033bdfc4d97..64b792fd5dd 100644
--- a/centaur/src/main/resources/standardTestCases/wdl_biscayne/read_functions_windows_line_endings/read_functions_windows_line_endings.wdl
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/read_functions_windows_line_endings/read_functions_windows_line_endings.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 struct JsonObj {
     String field1
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/directory_type/directory_type.wdl b/centaur/src/main/resources/standardTestCases/wdl_cascades/directory_type/directory_type.wdl
similarity index 100%
rename from centaur/src/main/resources/standardTestCases/wdl_biscayne/directory_type/directory_type.wdl
rename to centaur/src/main/resources/standardTestCases/wdl_cascades/directory_type/directory_type.wdl
diff --git a/centaur/src/main/resources/standardTestCases/wdl_cascades/directory_type/directory_type_local_inputs.json b/centaur/src/main/resources/standardTestCases/wdl_cascades/directory_type/directory_type_local_inputs.json
new file mode 100644
index 00000000000..cfe1a8bb688
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/wdl_cascades/directory_type/directory_type_local_inputs.json
@@ -0,0 +1,3 @@
+{
+  "directory_type.text2loc": "bar/text2"
+}
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/directory_type_output/directory_type_output.wdl b/centaur/src/main/resources/standardTestCases/wdl_cascades/directory_type_output/directory_type_output.wdl
similarity index 100%
rename from centaur/src/main/resources/standardTestCases/wdl_biscayne/directory_type_output/directory_type_output.wdl
rename to centaur/src/main/resources/standardTestCases/wdl_cascades/directory_type_output/directory_type_output.wdl
diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index b341682f1db..a3ac76e949c 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -470,13 +470,21 @@ languages {
         }
       }
       "biscayne" {
-        # WDL biscayne is our in-progress name for what will (probably) become WDL 1.1
+        # WDL biscayne is our in-progress name for what will become WDL 1.1
         language-factory = "languages.wdl.biscayne.WdlBiscayneLanguageFactory"
         config {
           strict-validation: true
           enabled: true
         }
       }
+      "cascades" {
+        # WDL cascades is our in-progress name for what will (probably) become WDL 2.0
+        language-factory = "languages.wdl.cascades.WdlCascadesLanguageFactory"
+        config {
+          strict-validation: true
+          enabled: true
+        }
+      }
     }
   }
 }
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
index e32316f3649..ba60258476c 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
@@ -22,7 +22,7 @@ class ServiceInfoSpec extends AsyncFlatSpec with ScalatestRouteTest with Matcher
 
   behavior of "ServiceInfo"
 
-  val expectedResponse = WesStatusInfoResponse(Map("WDL" -> Set("draft-2", "1.0", "biscayne")),
+  val expectedResponse = WesStatusInfoResponse(Map("WDL" -> Set("draft-2", "1.0", "biscayne", "cascades")),
     List("1.0"),
     Set("ftp", "s3", "drs", "gcs", "http"),
     Map("Cromwell" -> CromwellApiService.cromwellVersion),
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala
index b7e87034861..83183d6cd26 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala
@@ -94,7 +94,7 @@ object LanguageFactoryUtil {
     }
 
     val firstCodeLine = fileWithoutInitialWhitespace.headOption.map(_.dropWhile(_.isWhitespace))
-    firstCodeLine.exists { line => startsWithOptions.exists(line.startsWith) }
+    firstCodeLine.exists { line => startsWithOptions.contains(line) }
   }
 
   def chooseFactory(workflowSource: WorkflowSource, wsfc: WorkflowSourceFilesCollection): ErrorOr[LanguageFactory] = {
diff --git a/languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala b/languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala
index 431b0238fba..355a637439b 100644
--- a/languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala
+++ b/languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala
@@ -83,5 +83,5 @@ class WdlBiscayneLanguageFactory(override val config: Config) extends LanguageFa
     } yield validated
   }
 
-  override def looksParsable(content: String): Boolean = LanguageFactoryUtil.simpleLooksParseable(List("version development"), List("#"))(content)
+  override def looksParsable(content: String): Boolean = LanguageFactoryUtil.simpleLooksParseable(List("version development-1.1"), List("#"))(content)
 }
diff --git a/languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala b/languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala
new file mode 100644
index 00000000000..d7757e83e71
--- /dev/null
+++ b/languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala
@@ -0,0 +1,87 @@
+package languages.wdl.cascades
+
+import java.util.concurrent.Callable
+
+import cats.syntax.either._
+import cats.instances.either._
+import cats.data.EitherT.fromEither
+import cats.effect.IO
+import com.typesafe.config.Config
+import common.Checked
+import common.transforms.CheckedAtoB
+import common.validation.ErrorOr.ErrorOr
+import common.validation.IOChecked.IOChecked
+import cromwell.core._
+import cromwell.languages.util.ImportResolver._
+import cromwell.languages.util.{LanguageFactoryUtil, ParserCache}
+import cromwell.languages.util.ParserCache.ParserCacheInputs
+import cromwell.languages.{LanguageFactory, ValidatedWomNamespace}
+import wdl.transforms.base.wdlom2wom.WomBundleToWomExecutable._
+import wdl.transforms.base.wdlom2wom._
+import wdl.transforms.cascades.ast2wdlom._
+import wdl.transforms.cascades.parsing._
+import wdl.transforms.cascades.wdlom2wom._
+import wom.ResolvedImportRecord
+import wom.core.{WorkflowJson, WorkflowOptionsJson, WorkflowSource}
+import wom.executable.WomBundle
+import wom.expression.IoFunctionSet
+import wom.transforms.WomExecutableMaker.ops._
+
+class WdlCascadesLanguageFactory(override val config: Config) extends LanguageFactory with ParserCache[WomBundle] {
+
+  override val languageName: String = "WDL"
+  override val languageVersionName: String = "Cascades"
+
+  override def validateNamespace(source: WorkflowSourceFilesCollection,
+                                 workflowSource: WorkflowSource,
+                                 workflowOptions: WorkflowOptions,
+                                 importLocalFilesystem: Boolean,
+                                 workflowIdForLogging: WorkflowId,
+                                 ioFunctions: IoFunctionSet,
+                                 importResolvers: List[ImportResolver]): IOChecked[ValidatedWomNamespace] = {
+
+    val factories: List[LanguageFactory] = List(this)
+
+    val checked: Checked[ValidatedWomNamespace] = for {
+      _ <- enabledCheck
+      bundle <- getWomBundle(workflowSource, workflowSourceOrigin = None, source.workflowOptions.asPrettyJson, importResolvers, factories)
+      executable <- createExecutable(bundle, source.inputsJson, ioFunctions)
+    } yield executable
+
+    fromEither[IO](checked)
+
+  }
+
+  override def getWomBundle(workflowSource: WorkflowSource,
+                            workflowSourceOrigin: Option[ResolvedImportRecord],
+                            workflowOptionsJson: WorkflowOptionsJson,
+                            importResolvers: List[ImportResolver],
+                            languageFactories: List[LanguageFactory],
+                            convertNestedScatterToSubworkflow : Boolean = true): Checked[WomBundle] = {
+
+    val converter: CheckedAtoB[FileStringParserInput, WomBundle] = stringToAst andThen wrapAst andThen astToFileElement.map(FileElementToWomBundleInputs(_, workflowOptionsJson, convertNestedScatterToSubworkflow, importResolvers, languageFactories, workflowDefinitionElementToWomWorkflowDefinition, taskDefinitionElementToWomTaskDefinition)) andThen fileElementToWomBundle
+
+    lazy val validationCallable = new Callable[ErrorOr[WomBundle]] {
+      def call: ErrorOr[WomBundle] = converter
+        .run(FileStringParserInput(workflowSource, workflowSourceOrigin.map(_.importPath).getOrElse("input.wdl")))
+        .map(b => b.copyResolvedImportRecord(b, workflowSourceOrigin)).toValidated
+    }
+
+    lazy val parserCacheInputs = ParserCacheInputs(Option(workflowSource), workflowSourceOrigin.map(_.importPath), None, importResolvers)
+
+    for {
+      _ <- enabledCheck
+      womBundle <- retrieveOrCalculate(parserCacheInputs, validationCallable).toEither
+    } yield womBundle
+  }
+
+  override def createExecutable(womBundle: WomBundle, inputsJson: WorkflowJson, ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace] = {
+    for {
+      _ <- enabledCheck
+      executable <- womBundle.toWomExecutable(Option(inputsJson), ioFunctions, strictValidation)
+      validated <- LanguageFactoryUtil.validateWomNamespace(executable, ioFunctions)
+    } yield validated
+  }
+
+  override def looksParsable(content: String): Boolean = LanguageFactoryUtil.simpleLooksParseable(List("version development"), List("#"))(content)
+}
diff --git a/project/Merging.scala b/project/Merging.scala
index 053370d2d7b..046380a367c 100644
--- a/project/Merging.scala
+++ b/project/Merging.scala
@@ -53,7 +53,7 @@ object Merging {
           val oldStrategy = (assembly / assemblyMergeStrategy).value
           oldStrategy(x)
       }
-    case "asm-license.txt" | "module-info.class" | "overview.html" | "cobertura.properties" =>
+    case "asm-license.txt" | "module-info.class" | "overview.html" | "cobertura.properties" | "grammar.hgr" | "CHANGELOG.txt" =>
       MergeStrategy.discard
     // inspired by https://github.com/ergoplatform/explorer-backend/blob/7364ecfdeabeb691f0f25525e577d6c48240c672/build.sbt#L14-L15
     case other if other.contains("scala/annotation/nowarn.class")  => MergeStrategy.discard
diff --git a/services/src/test/resources/describe/wdl_1_0/relative_url_imports/description.json b/services/src/test/resources/describe/wdl_1_0/relative_url_imports/description.json
index ddfbba00517..7a8725ab631 100644
--- a/services/src/test/resources/describe/wdl_1_0/relative_url_imports/description.json
+++ b/services/src/test/resources/describe/wdl_1_0/relative_url_imports/description.json
@@ -19,7 +19,7 @@
   ],
   "submittedDescriptorType" : {
     "descriptorType" : "WDL",
-    "descriptorTypeVersion" : "Biscayne"
+    "descriptorTypeVersion" : "Cascades"
   },
   "importedDescriptorTypes" : [
   ],
diff --git a/wdl/transforms/biscayne/src/main/java/wdl/biscayne/parser/WdlParser.java b/wdl/transforms/biscayne/src/main/java/wdl/biscayne/parser/WdlParser.java
index b1274ba6237..26a2ea35d2e 100644
--- a/wdl/transforms/biscayne/src/main/java/wdl/biscayne/parser/WdlParser.java
+++ b/wdl/transforms/biscayne/src/main/java/wdl/biscayne/parser/WdlParser.java
@@ -1,9 +1,9 @@
 
 /*
- * This file was generated by Hermes Parser Generator on Mon Apr  1 17:17:23 2019
- *
- * Hermes command: hermes generate grammar.hgr --language=java --directory=./ --name=wdl --java-package=wdl.biscayne.parser --java-use-apache-commons --java-imports=org.apache.commons.lang3.StringEscapeUtils --header
- * Run from: . (relative to this file)
+ * This file was generated by Hermes Parser Generator on Wed Mar 22 19:44:20 2023
+ * 
+ * Hermes command: hermes generate resources/grammar.hgr --language=java --directory=./java --name=wdl --java-package=wdl.biscayne.parser --java-use-apache-commons --java-imports=org.apache.commons.lang3.StringEscapeUtils --header
+ * Run from: .. (relative to this file)
  * Hermes version: hermes-parser 2.0rc6
  * 
  * !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
@@ -516,73 +516,73 @@ public interface TerminalIdentifier {
         public String string();
     }
     public enum WdlTerminalIdentifier implements TerminalIdentifier {
-        TERMINAL_AFTER(52, "after"),
-        TERMINAL_ALIAS(17, "alias"),
-        TERMINAL_AS(51, "as"),
-        TERMINAL_ASTERISK(28, "asterisk"),
-        TERMINAL_BOOLEAN(45, "boolean"),
-        TERMINAL_CALL(10, "call"),
-        TERMINAL_CMD_ATTR_HINT(9, "cmd_attr_hint"),
-        TERMINAL_CMD_PART(8, "cmd_part"),
-        TERMINAL_COLON(57, "colon"),
-        TERMINAL_COMMA(66, "comma"),
-        TERMINAL_DASH(27, "dash"),
-        TERMINAL_DOT(62, "dot"),
-        TERMINAL_DOUBLE_AMPERSAND(61, "double_ampersand"),
-        TERMINAL_DOUBLE_EQUAL(15, "double_equal"),
-        TERMINAL_DOUBLE_PIPE(42, "double_pipe"),
-        TERMINAL_E(64, "e"),
-        TERMINAL_ELSE(44, "else"),
-        TERMINAL_EQUAL(46, "equal"),
-        TERMINAL_ESCAPE(23, "escape"),
-        TERMINAL_EXPRESSION_PLACEHOLDER_END(49, "expression_placeholder_end"),
-        TERMINAL_EXPRESSION_PLACEHOLDER_START(43, "expression_placeholder_start"),
-        TERMINAL_FLOAT(33, "float"),
-        TERMINAL_FQN(55, "fqn"),
-        TERMINAL_GT(19, "gt"),
-        TERMINAL_GTEQ(24, "gteq"),
-        TERMINAL_IDENTIFIER(31, "identifier"),
-        TERMINAL_IF(29, "if"),
-        TERMINAL_IMPORT(48, "import"),
-        TERMINAL_IN(53, "in"),
-        TERMINAL_INPUT(2, "input"),
-        TERMINAL_INTEGER(1, "integer"),
-        TERMINAL_LBRACE(41, "lbrace"),
-        TERMINAL_LPAREN(14, "lparen"),
-        TERMINAL_LSQUARE(39, "lsquare"),
-        TERMINAL_LT(16, "lt"),
-        TERMINAL_LTEQ(25, "lteq"),
-        TERMINAL_META(32, "meta"),
-        TERMINAL_META_VALUE(6, "meta_value"),
-        TERMINAL_NONE(37, "none"),
-        TERMINAL_NOT(36, "not"),
-        TERMINAL_NOT_EQUAL(5, "not_equal"),
-        TERMINAL_NULL(50, "null"),
-        TERMINAL_OBJECT(22, "object"),
-        TERMINAL_OUTPUT(54, "output"),
-        TERMINAL_PARAMETER_META(60, "parameter_meta"),
-        TERMINAL_PERCENT(3, "percent"),
-        TERMINAL_PLUS(34, "plus"),
-        TERMINAL_QMARK(12, "qmark"),
-        TERMINAL_QUOTE(58, "quote"),
-        TERMINAL_RAW_CMD_END(35, "raw_cmd_end"),
-        TERMINAL_RAW_CMD_START(59, "raw_cmd_start"),
-        TERMINAL_RAW_COMMAND(63, "raw_command"),
-        TERMINAL_RBRACE(65, "rbrace"),
-        TERMINAL_RPAREN(30, "rparen"),
-        TERMINAL_RSQUARE(7, "rsquare"),
-        TERMINAL_RUNTIME(11, "runtime"),
-        TERMINAL_SCATTER(0, "scatter"),
-        TERMINAL_SLASH(47, "slash"),
-        TERMINAL_STRING(26, "string"),
-        TERMINAL_STRUCT(18, "struct"),
-        TERMINAL_TASK(4, "task"),
-        TERMINAL_THEN(20, "then"),
-        TERMINAL_TYPE(13, "type"),
-        TERMINAL_TYPE_E(38, "type_e"),
-        TERMINAL_VERSION(56, "version"),
-        TERMINAL_VERSION_NAME(40, "version_name"),
-        TERMINAL_WORKFLOW(21, "workflow"),
+        TERMINAL_AFTER(23, "after"),
+        TERMINAL_ALIAS(27, "alias"),
+        TERMINAL_AS(10, "as"),
+        TERMINAL_ASTERISK(18, "asterisk"),
+        TERMINAL_BOOLEAN(13, "boolean"),
+        TERMINAL_CALL(60, "call"),
+        TERMINAL_CMD_ATTR_HINT(50, "cmd_attr_hint"),
+        TERMINAL_CMD_PART(11, "cmd_part"),
+        TERMINAL_COLON(28, "colon"),
+        TERMINAL_COMMA(19, "comma"),
+        TERMINAL_DASH(32, "dash"),
+        TERMINAL_DOT(42, "dot"),
+        TERMINAL_DOUBLE_AMPERSAND(29, "double_ampersand"),
+        TERMINAL_DOUBLE_EQUAL(53, "double_equal"),
+        TERMINAL_DOUBLE_PIPE(45, "double_pipe"),
+        TERMINAL_E(22, "e"),
+        TERMINAL_ELSE(57, "else"),
+        TERMINAL_EQUAL(31, "equal"),
+        TERMINAL_ESCAPE(1, "escape"),
+        TERMINAL_EXPRESSION_PLACEHOLDER_END(14, "expression_placeholder_end"),
+        TERMINAL_EXPRESSION_PLACEHOLDER_START(65, "expression_placeholder_start"),
+        TERMINAL_FLOAT(49, "float"),
+        TERMINAL_FQN(34, "fqn"),
+        TERMINAL_GT(2, "gt"),
+        TERMINAL_GTEQ(52, "gteq"),
+        TERMINAL_IDENTIFIER(46, "identifier"),
+        TERMINAL_IF(63, "if"),
+        TERMINAL_IMPORT(55, "import"),
+        TERMINAL_IN(39, "in"),
+        TERMINAL_INPUT(44, "input"),
+        TERMINAL_INTEGER(16, "integer"),
+        TERMINAL_LBRACE(59, "lbrace"),
+        TERMINAL_LPAREN(15, "lparen"),
+        TERMINAL_LSQUARE(17, "lsquare"),
+        TERMINAL_LT(36, "lt"),
+        TERMINAL_LTEQ(40, "lteq"),
+        TERMINAL_META(61, "meta"),
+        TERMINAL_META_VALUE(48, "meta_value"),
+        TERMINAL_NONE(43, "none"),
+        TERMINAL_NOT(12, "not"),
+        TERMINAL_NOT_EQUAL(51, "not_equal"),
+        TERMINAL_NULL(24, "null"),
+        TERMINAL_OBJECT(58, "object"),
+        TERMINAL_OUTPUT(7, "output"),
+        TERMINAL_PARAMETER_META(54, "parameter_meta"),
+        TERMINAL_PERCENT(64, "percent"),
+        TERMINAL_PLUS(33, "plus"),
+        TERMINAL_QMARK(21, "qmark"),
+        TERMINAL_QUOTE(20, "quote"),
+        TERMINAL_RAW_CMD_END(9, "raw_cmd_end"),
+        TERMINAL_RAW_CMD_START(26, "raw_cmd_start"),
+        TERMINAL_RAW_COMMAND(47, "raw_command"),
+        TERMINAL_RBRACE(66, "rbrace"),
+        TERMINAL_RPAREN(6, "rparen"),
+        TERMINAL_RSQUARE(3, "rsquare"),
+        TERMINAL_RUNTIME(8, "runtime"),
+        TERMINAL_SCATTER(62, "scatter"),
+        TERMINAL_SLASH(37, "slash"),
+        TERMINAL_STRING(0, "string"),
+        TERMINAL_STRUCT(5, "struct"),
+        TERMINAL_TASK(56, "task"),
+        TERMINAL_THEN(41, "then"),
+        TERMINAL_TYPE(30, "type"),
+        TERMINAL_TYPE_E(25, "type_e"),
+        TERMINAL_VERSION(4, "version"),
+        TERMINAL_VERSION_NAME(38, "version_name"),
+        TERMINAL_WORKFLOW(35, "workflow"),
         END_SENTINAL(-3, "END_SENTINAL");
         private final int id;
         private final String string;
@@ -595,112 +595,112 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
     }
     /* table[nonterminal][terminal] = rule */
     private static final int[][] table = {
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 83, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, 19, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 19, 19, -1, -1, 19, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 19, -1, -1, 18, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 44, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 49, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 23, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 21, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { 14, 15, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 84, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 46, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 85, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { 71, -1, 71, -1, -1, -1, -1, -1, -1, -1, 71, -1, -1, 71, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 71, -1, 71, 71, -1, -1, -1, -1, -1, 71, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 70, 71, -1, 71, -1, -1, -1, -1, -1, 71, -1, -1, -1, -1, 71, -1 },
+        { -1, -1, -1, -1, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 34, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 9, -1, -1, -1, -1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 82, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 59, -1, -1, -1, -1, 59, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 59, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 82, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, 71, -1, -1, 70, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 71, -1, 71, -1, -1, -1, -1, 71, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 71, -1, 71, -1, -1, -1, -1, -1, -1, -1, 71, -1, -1, -1, -1, -1, 71, 71, 71, 71, -1, -1, 71 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, 42, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, 74, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 74, -1, -1, -1, -1, 74, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 74, -1, 74, -1, -1, -1, -1, -1, -1, -1, 74, -1, -1, -1, -1, 73, 74, 74, 74, 74, -1, -1, 74 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 21, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 53, -1, -1, -1, -1, 53, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 53, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
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         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { 65, -1, 66, -1, -1, -1, -1, -1, -1, -1, 62, -1, -1, 63, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 64, -1, 63, 69, -1, -1, -1, -1, -1, 63, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 67, -1, -1, -1, -1, -1, 68, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 5, -1, -1, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 9, -1, -1, -1, -1, -1, -1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { 16, 16, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 17, -1 },
+        { -1, -1, -1, -1, -1, 19, -1, -1, -1, -1, 18, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 19, -1, -1, -1, -1, -1, -1, -1, 19, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 19, 19, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 55, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 38, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 39, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 61, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, 39, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 11, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 81, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, 76, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 77, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 46, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, 67, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 63, -1, -1, -1, -1, 63, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 66, -1, 63, -1, -1, -1, -1, -1, -1, -1, 68, -1, -1, -1, -1, -1, 62, 69, 65, 64, -1, -1, -1 },
+        { -1, -1, -1, -1, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 13, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 49, -1, -1, -1, -1, -1, -1, -1 },
     };
     static {
         Map<Integer, List<TerminalIdentifier>> map = new HashMap<Integer, List<TerminalIdentifier>>();
-        map.put(96, Arrays.asList(new TerminalIdentifier[] {
+        map.put(75, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
         }));
-        map.put(84, Arrays.asList(new TerminalIdentifier[] {
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+        map.put(115, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(114, Arrays.asList(new TerminalIdentifier[] {
+        map.put(68, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+        map.put(76, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(118, Arrays.asList(new TerminalIdentifier[] {
+        map.put(117, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_EQUAL,
         }));
-        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+        map.put(89, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(105, Arrays.asList(new TerminalIdentifier[] {
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -712,27 +712,27 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(80, Arrays.asList(new TerminalIdentifier[] {
+        map.put(79, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(115, Arrays.asList(new TerminalIdentifier[] {
+        map.put(95, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
         }));
-        map.put(93, Arrays.asList(new TerminalIdentifier[] {
+        map.put(81, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(140, Arrays.asList(new TerminalIdentifier[] {
+        map.put(88, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INPUT,
         }));
-        map.put(94, Arrays.asList(new TerminalIdentifier[] {
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+        map.put(87, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(81, Arrays.asList(new TerminalIdentifier[] {
+        map.put(91, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_FLOAT,
             WdlTerminalIdentifier.TERMINAL_INTEGER,
@@ -742,15 +742,15 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_NULL,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+        map.put(110, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(82, Arrays.asList(new TerminalIdentifier[] {
+        map.put(70, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(107, Arrays.asList(new TerminalIdentifier[] {
+        map.put(108, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -767,10 +767,10 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(73, Arrays.asList(new TerminalIdentifier[] {
+        map.put(119, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -787,22 +787,22 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(74, Arrays.asList(new TerminalIdentifier[] {
+        map.put(92, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(124, Arrays.asList(new TerminalIdentifier[] {
+        map.put(114, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(68, Arrays.asList(new TerminalIdentifier[] {
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(97, Arrays.asList(new TerminalIdentifier[] {
+        map.put(102, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
         }));
-        map.put(91, Arrays.asList(new TerminalIdentifier[] {
+        map.put(104, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -813,44 +813,44 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(141, Arrays.asList(new TerminalIdentifier[] {
+        map.put(140, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
         }));
-        map.put(76, Arrays.asList(new TerminalIdentifier[] {
+        map.put(109, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
         }));
-        map.put(139, Arrays.asList(new TerminalIdentifier[] {
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
         }));
-        map.put(83, Arrays.asList(new TerminalIdentifier[] {
+        map.put(78, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
         }));
-        map.put(117, Arrays.asList(new TerminalIdentifier[] {
+        map.put(86, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INPUT,
         }));
-        map.put(106, Arrays.asList(new TerminalIdentifier[] {
+        map.put(118, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(108, Arrays.asList(new TerminalIdentifier[] {
+        map.put(72, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
         }));
-        map.put(92, Arrays.asList(new TerminalIdentifier[] {
+        map.put(99, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
         }));
-        map.put(102, Arrays.asList(new TerminalIdentifier[] {
+        map.put(93, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(109, Arrays.asList(new TerminalIdentifier[] {
+        map.put(138, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_VERSION,
         }));
-        map.put(99, Arrays.asList(new TerminalIdentifier[] {
+        map.put(107, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -867,44 +867,44 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(135, Arrays.asList(new TerminalIdentifier[] {
+        map.put(97, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
         }));
-        map.put(137, Arrays.asList(new TerminalIdentifier[] {
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
         }));
-        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(79, Arrays.asList(new TerminalIdentifier[] {
+        map.put(94, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IF,
         }));
-        map.put(75, Arrays.asList(new TerminalIdentifier[] {
+        map.put(82, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
         }));
-        map.put(72, Arrays.asList(new TerminalIdentifier[] {
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
         }));
-        map.put(101, Arrays.asList(new TerminalIdentifier[] {
+        map.put(96, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(113, Arrays.asList(new TerminalIdentifier[] {
+        map.put(83, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(89, Arrays.asList(new TerminalIdentifier[] {
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(111, Arrays.asList(new TerminalIdentifier[] {
+        map.put(106, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INPUT,
         }));
-        map.put(95, Arrays.asList(new TerminalIdentifier[] {
+        map.put(116, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(103, Arrays.asList(new TerminalIdentifier[] {
+        map.put(100, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -921,16 +921,16 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(78, Arrays.asList(new TerminalIdentifier[] {
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_META,
         }));
-        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+        map.put(112, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(70, Arrays.asList(new TerminalIdentifier[] {
+        map.put(141, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(116, Arrays.asList(new TerminalIdentifier[] {
+        map.put(120, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_FLOAT,
             WdlTerminalIdentifier.TERMINAL_INTEGER,
@@ -940,59 +940,59 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_NULL,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(86, Arrays.asList(new TerminalIdentifier[] {
+        map.put(90, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+        map.put(77, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(120, Arrays.asList(new TerminalIdentifier[] {
+        map.put(84, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_OUTPUT,
         }));
-        map.put(100, Arrays.asList(new TerminalIdentifier[] {
+        map.put(105, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
         }));
-        map.put(69, Arrays.asList(new TerminalIdentifier[] {
+        map.put(85, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(85, Arrays.asList(new TerminalIdentifier[] {
+        map.put(80, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RUNTIME,
         }));
-        map.put(88, Arrays.asList(new TerminalIdentifier[] {
+        map.put(121, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_SCATTER,
         }));
-        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+        map.put(101, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_EQUAL,
         }));
-        map.put(138, Arrays.asList(new TerminalIdentifier[] {
+        map.put(98, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(110, Arrays.asList(new TerminalIdentifier[] {
+        map.put(69, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(87, Arrays.asList(new TerminalIdentifier[] {
+        map.put(139, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(104, Arrays.asList(new TerminalIdentifier[] {
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(71, Arrays.asList(new TerminalIdentifier[] {
+        map.put(74, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
         }));
-        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+        map.put(73, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(112, Arrays.asList(new TerminalIdentifier[] {
+        map.put(113, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_TASK,
         }));
-        map.put(98, Arrays.asList(new TerminalIdentifier[] {
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1003,15 +1003,15 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(119, Arrays.asList(new TerminalIdentifier[] {
+        map.put(67, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(121, Arrays.asList(new TerminalIdentifier[] {
+        map.put(71, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_VERSION,
         }));
-        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+        map.put(137, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1023,48 +1023,48 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(77, Arrays.asList(new TerminalIdentifier[] {
+        map.put(103, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_META,
         }));
-        map.put(67, Arrays.asList(new TerminalIdentifier[] {
+        map.put(111, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
         }));
-        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
         nonterminal_first = Collections.unmodifiableMap(map);
     }
     static {
         Map<Integer, List<TerminalIdentifier>> map = new HashMap<Integer, List<TerminalIdentifier>>();
-        map.put(96, Arrays.asList(new TerminalIdentifier[] {
+        map.put(75, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(84, Arrays.asList(new TerminalIdentifier[] {
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
         }));
-        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+        map.put(115, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(114, Arrays.asList(new TerminalIdentifier[] {
+        map.put(68, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+        map.put(76, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(118, Arrays.asList(new TerminalIdentifier[] {
+        map.put(117, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+        map.put(89, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(105, Arrays.asList(new TerminalIdentifier[] {
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(80, Arrays.asList(new TerminalIdentifier[] {
+        map.put(79, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1078,7 +1078,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(115, Arrays.asList(new TerminalIdentifier[] {
+        map.put(95, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1092,7 +1092,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(93, Arrays.asList(new TerminalIdentifier[] {
+        map.put(81, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1105,60 +1105,60 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(140, Arrays.asList(new TerminalIdentifier[] {
+        map.put(88, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(94, Arrays.asList(new TerminalIdentifier[] {
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+        map.put(87, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(81, Arrays.asList(new TerminalIdentifier[] {
+        map.put(91, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+        map.put(110, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(82, Arrays.asList(new TerminalIdentifier[] {
+        map.put(70, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(107, Arrays.asList(new TerminalIdentifier[] {
+        map.put(108, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RPAREN,
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(73, Arrays.asList(new TerminalIdentifier[] {
+        map.put(119, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(74, Arrays.asList(new TerminalIdentifier[] {
+        map.put(92, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(124, Arrays.asList(new TerminalIdentifier[] {
+        map.put(114, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(68, Arrays.asList(new TerminalIdentifier[] {
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(97, Arrays.asList(new TerminalIdentifier[] {
+        map.put(102, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(91, Arrays.asList(new TerminalIdentifier[] {
+        map.put(104, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(141, Arrays.asList(new TerminalIdentifier[] {
+        map.put(140, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
         }));
-        map.put(76, Arrays.asList(new TerminalIdentifier[] {
+        map.put(109, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -1175,7 +1175,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(139, Arrays.asList(new TerminalIdentifier[] {
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1189,7 +1189,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1202,7 +1202,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(83, Arrays.asList(new TerminalIdentifier[] {
+        map.put(78, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1217,10 +1217,10 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(117, Arrays.asList(new TerminalIdentifier[] {
+        map.put(86, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(106, Arrays.asList(new TerminalIdentifier[] {
+        map.put(118, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1233,7 +1233,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(108, Arrays.asList(new TerminalIdentifier[] {
+        map.put(72, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1245,12 +1245,12 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(92, Arrays.asList(new TerminalIdentifier[] {
+        map.put(99, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
         }));
-        map.put(102, Arrays.asList(new TerminalIdentifier[] {
+        map.put(93, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1265,9 +1265,9 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(109, Arrays.asList(new TerminalIdentifier[] {
+        map.put(138, Arrays.asList(new TerminalIdentifier[] {
         }));
-        map.put(99, Arrays.asList(new TerminalIdentifier[] {
+        map.put(107, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ASTERISK,
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_CALL,
@@ -1315,7 +1315,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(135, Arrays.asList(new TerminalIdentifier[] {
+        map.put(97, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
@@ -1323,7 +1323,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(137, Arrays.asList(new TerminalIdentifier[] {
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
             WdlTerminalIdentifier.TERMINAL_DASH,
@@ -1341,12 +1341,12 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(79, Arrays.asList(new TerminalIdentifier[] {
+        map.put(94, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1359,37 +1359,37 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(75, Arrays.asList(new TerminalIdentifier[] {
+        map.put(82, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(72, Arrays.asList(new TerminalIdentifier[] {
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(101, Arrays.asList(new TerminalIdentifier[] {
+        map.put(96, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(113, Arrays.asList(new TerminalIdentifier[] {
+        map.put(83, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(89, Arrays.asList(new TerminalIdentifier[] {
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(111, Arrays.asList(new TerminalIdentifier[] {
+        map.put(106, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1404,15 +1404,15 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(95, Arrays.asList(new TerminalIdentifier[] {
+        map.put(116, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(103, Arrays.asList(new TerminalIdentifier[] {
+        map.put(100, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(78, Arrays.asList(new TerminalIdentifier[] {
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1424,12 +1424,12 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+        map.put(112, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(70, Arrays.asList(new TerminalIdentifier[] {
+        map.put(141, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1444,23 +1444,23 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(116, Arrays.asList(new TerminalIdentifier[] {
+        map.put(120, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(86, Arrays.asList(new TerminalIdentifier[] {
+        map.put(90, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+        map.put(77, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(120, Arrays.asList(new TerminalIdentifier[] {
+        map.put(84, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1475,7 +1475,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(100, Arrays.asList(new TerminalIdentifier[] {
+        map.put(105, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1487,7 +1487,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(69, Arrays.asList(new TerminalIdentifier[] {
+        map.put(85, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1499,7 +1499,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(85, Arrays.asList(new TerminalIdentifier[] {
+        map.put(80, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1511,7 +1511,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(88, Arrays.asList(new TerminalIdentifier[] {
+        map.put(121, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1524,7 +1524,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+        map.put(101, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1539,7 +1539,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(138, Arrays.asList(new TerminalIdentifier[] {
+        map.put(98, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1550,13 +1550,13 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(110, Arrays.asList(new TerminalIdentifier[] {
+        map.put(69, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(87, Arrays.asList(new TerminalIdentifier[] {
+        map.put(139, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ASTERISK,
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_CALL,
@@ -1604,29 +1604,29 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(104, Arrays.asList(new TerminalIdentifier[] {
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(71, Arrays.asList(new TerminalIdentifier[] {
+        map.put(74, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+        map.put(73, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(112, Arrays.asList(new TerminalIdentifier[] {
+        map.put(113, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(98, Arrays.asList(new TerminalIdentifier[] {
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1638,15 +1638,15 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(119, Arrays.asList(new TerminalIdentifier[] {
+        map.put(67, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(121, Arrays.asList(new TerminalIdentifier[] {
+        map.put(71, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
         }));
-        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+        map.put(137, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1659,7 +1659,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(77, Arrays.asList(new TerminalIdentifier[] {
+        map.put(103, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1672,7 +1672,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(67, Arrays.asList(new TerminalIdentifier[] {
+        map.put(111, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1685,7 +1685,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
@@ -2407,218 +2407,218 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
     }
     static {
         Map<Integer, List<String>> map = new HashMap<Integer, List<String>>();
-        map.put(96, new ArrayList<String>());
-        map.put(84, new ArrayList<String>());
-        map.put(129, new ArrayList<String>());
-        map.put(114, new ArrayList<String>());
-        map.put(90, new ArrayList<String>());
-        map.put(118, new ArrayList<String>());
-        map.put(133, new ArrayList<String>());
-        map.put(105, new ArrayList<String>());
-        map.put(80, new ArrayList<String>());
-        map.put(115, new ArrayList<String>());
-        map.put(93, new ArrayList<String>());
-        map.put(140, new ArrayList<String>());
-        map.put(94, new ArrayList<String>());
-        map.put(122, new ArrayList<String>());
-        map.put(81, new ArrayList<String>());
-        map.put(136, new ArrayList<String>());
-        map.put(82, new ArrayList<String>());
-        map.put(107, new ArrayList<String>());
+        map.put(75, new ArrayList<String>());
         map.put(128, new ArrayList<String>());
-        map.put(73, new ArrayList<String>());
-        map.put(74, new ArrayList<String>());
-        map.put(124, new ArrayList<String>());
+        map.put(115, new ArrayList<String>());
         map.put(68, new ArrayList<String>());
-        map.put(97, new ArrayList<String>());
-        map.put(91, new ArrayList<String>());
-        map.put(141, new ArrayList<String>());
         map.put(76, new ArrayList<String>());
-        map.put(139, new ArrayList<String>());
-        map.put(127, new ArrayList<String>());
-        map.put(83, new ArrayList<String>());
         map.put(117, new ArrayList<String>());
-        map.put(106, new ArrayList<String>());
+        map.put(89, new ArrayList<String>());
+        map.put(132, new ArrayList<String>());
+        map.put(79, new ArrayList<String>());
+        map.put(95, new ArrayList<String>());
+        map.put(81, new ArrayList<String>());
+        map.put(88, new ArrayList<String>());
+        map.put(129, new ArrayList<String>());
+        map.put(87, new ArrayList<String>());
+        map.put(91, new ArrayList<String>());
+        map.put(110, new ArrayList<String>());
+        map.put(70, new ArrayList<String>());
         map.put(108, new ArrayList<String>());
+        map.put(135, new ArrayList<String>());
+        map.put(119, new ArrayList<String>());
         map.put(92, new ArrayList<String>());
+        map.put(114, new ArrayList<String>());
+        map.put(131, new ArrayList<String>());
         map.put(102, new ArrayList<String>());
+        map.put(104, new ArrayList<String>());
+        map.put(140, new ArrayList<String>());
         map.put(109, new ArrayList<String>());
-        map.put(99, new ArrayList<String>());
-        map.put(135, new ArrayList<String>());
-        map.put(137, new ArrayList<String>());
-        map.put(131, new ArrayList<String>());
-        map.put(79, new ArrayList<String>());
-        map.put(75, new ArrayList<String>());
-        map.put(72, new ArrayList<String>());
-        map.put(101, new ArrayList<String>());
-        map.put(113, new ArrayList<String>());
-        map.put(89, new ArrayList<String>());
-        map.put(111, new ArrayList<String>());
-        map.put(95, new ArrayList<String>());
-        map.put(103, new ArrayList<String>());
+        map.put(126, new ArrayList<String>());
+        map.put(124, new ArrayList<String>());
         map.put(78, new ArrayList<String>());
+        map.put(86, new ArrayList<String>());
+        map.put(118, new ArrayList<String>());
+        map.put(72, new ArrayList<String>());
+        map.put(99, new ArrayList<String>());
+        map.put(93, new ArrayList<String>());
+        map.put(138, new ArrayList<String>());
+        map.put(107, new ArrayList<String>());
+        map.put(97, new ArrayList<String>());
+        map.put(133, new ArrayList<String>());
+        map.put(127, new ArrayList<String>());
+        map.put(94, new ArrayList<String>());
+        map.put(82, new ArrayList<String>());
         map.put(125, new ArrayList<String>());
-        map.put(70, new ArrayList<String>());
+        map.put(96, new ArrayList<String>());
+        map.put(83, new ArrayList<String>());
+        map.put(122, new ArrayList<String>());
+        map.put(106, new ArrayList<String>());
         map.put(116, new ArrayList<String>());
-        map.put(86, new ArrayList<String>());
-        map.put(126, new ArrayList<String>());
-        map.put(120, new ArrayList<String>());
         map.put(100, new ArrayList<String>());
-        map.put(69, new ArrayList<String>());
-        map.put(85, new ArrayList<String>());
-        map.put(88, new ArrayList<String>());
-        map.put(134, new ArrayList<String>());
-        map.put(138, new ArrayList<String>());
-        map.put(110, new ArrayList<String>());
-        map.put(87, new ArrayList<String>());
-        map.put(104, new ArrayList<String>());
-        map.put(71, new ArrayList<String>());
-        map.put(132, new ArrayList<String>());
+        map.put(136, new ArrayList<String>());
         map.put(112, new ArrayList<String>());
-        map.put(98, new ArrayList<String>());
-        map.put(119, new ArrayList<String>());
+        map.put(141, new ArrayList<String>());
+        map.put(120, new ArrayList<String>());
+        map.put(90, new ArrayList<String>());
+        map.put(77, new ArrayList<String>());
+        map.put(84, new ArrayList<String>());
+        map.put(105, new ArrayList<String>());
+        map.put(85, new ArrayList<String>());
+        map.put(80, new ArrayList<String>());
         map.put(121, new ArrayList<String>());
+        map.put(101, new ArrayList<String>());
+        map.put(98, new ArrayList<String>());
+        map.put(69, new ArrayList<String>());
+        map.put(139, new ArrayList<String>());
         map.put(130, new ArrayList<String>());
-        map.put(77, new ArrayList<String>());
-        map.put(67, new ArrayList<String>());
+        map.put(74, new ArrayList<String>());
+        map.put(73, new ArrayList<String>());
+        map.put(113, new ArrayList<String>());
         map.put(123, new ArrayList<String>());
-        map.get(96).add("$_gen0 = list($import)");
-        map.get(84).add("$_gen1 = list($file_body_element)");
-        map.get(129).add("$_gen10 = list($input_declaration)");
-        map.get(114).add("$_gen11 = list($kv)");
-        map.get(90).add("$_gen12 = list($meta_kv)");
-        map.get(118).add("$_gen13 = $setter");
-        map.get(118).add("$_gen13 = :_empty");
-        map.get(133).add("$_gen14 = list($output_kv)");
-        map.get(105).add("$_gen15 = list($wf_body_element)");
-        map.get(80).add("$_gen16 = $alias");
-        map.get(80).add("$_gen16 = :_empty");
-        map.get(115).add("$_gen17 = list($call_after)");
-        map.get(93).add("$_gen18 = $call_brace_block");
-        map.get(93).add("$_gen18 = :_empty");
-        map.get(140).add("$_gen19 = $call_body");
-        map.get(140).add("$_gen19 = :_empty");
-        map.get(94).add("$_gen2 = list($struct_declaration)");
-        map.get(122).add("$_gen20 = list($input_kv, :comma)");
-        map.get(81).add("$_gen21 = list($meta_value, :comma)");
-        map.get(136).add("$_gen22 = list($meta_kv, :comma)");
-        map.get(82).add("$_gen23 = list($type_e, :comma)");
-        map.get(107).add("$_gen24 = list($e, :comma)");
-        map.get(128).add("$_gen25 = list($object_kv, :comma)");
-        map.get(73).add("$_gen26 = list($map_kv, :comma)");
-        map.get(74).add("$_gen3 = list($static_string_piece)");
-        map.get(124).add("$_gen4 = list($string_piece)");
-        map.get(68).add("$_gen5 = $import_namespace");
-        map.get(68).add("$_gen5 = :_empty");
-        map.get(97).add("$_gen6 = list($import_alias)");
-        map.get(91).add("$_gen7 = list($task_sections)");
-        map.get(141).add("$_gen8 = list($command_part)");
-        map.get(76).add("$_gen9 = list($expression_placeholder_kv)");
-        map.get(139).add("$alias = :as :identifier -> $1");
-        map.get(127).add("$call = :call :fqn $_gen16 $_gen17 $_gen18 -> Call( task=$1, alias=$2, after=$3, body=$4 )");
-        map.get(83).add("$call_after = :after :identifier -> $1");
-        map.get(117).add("$call_body = :input :colon $_gen20 -> CallBody( inputs=$2 )");
-        map.get(106).add("$call_brace_block = :lbrace $_gen19 :rbrace -> $1");
-        map.get(108).add("$command = :raw_command :raw_cmd_start $_gen8 :raw_cmd_end -> RawCommand( parts=$2 )");
-        map.get(92).add("$command_part = $expression_placeholder");
-        map.get(92).add("$command_part = :cmd_part");
-        map.get(102).add("$declaration = $type_e :identifier $setter -> Declaration( type=$0, name=$1, expression=$2 )");
-        map.get(109).add("$document = $version $_gen0 $_gen1 -> Draft3File( version=$0, imports=$1, body=$2 )");
-        map.get(99).add("$e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :plus $e -> Add( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e :slash $e -> Divide( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
-        map.get(99).add("$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
-        map.get(99).add("$e = $string_literal");
-        map.get(99).add("$e = :boolean");
-        map.get(99).add("$e = :dash $e -> UnaryNegation( expression=$1 )");
-        map.get(99).add("$e = :float");
-        map.get(99).add("$e = :identifier");
-        map.get(99).add("$e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 )");
-        map.get(99).add("$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
-        map.get(99).add("$e = :integer");
-        map.get(99).add("$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
-        map.get(99).add("$e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 )");
-        map.get(99).add("$e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 )");
-        map.get(99).add("$e = :none");
-        map.get(99).add("$e = :not $e -> LogicalNot( expression=$1 )");
-        map.get(99).add("$e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 )");
-        map.get(99).add("$e = :plus $e -> UnaryPlus( expression=$1 )");
-        map.get(135).add("$expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 )");
-        map.get(137).add("$expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 )");
-        map.get(131).add("$file_body_element = $struct");
-        map.get(131).add("$file_body_element = $task");
-        map.get(131).add("$file_body_element = $workflow");
-        map.get(79).add("$if_stmt = :if :lparen $e :rparen :lbrace $_gen15 :rbrace -> If( expression=$2, body=$5 )");
-        map.get(75).add("$import = :import $static_string $_gen5 $_gen6 -> Import( uri=$1, namespace=$2, aliases=$3 )");
-        map.get(72).add("$import_alias = :alias :identifier :as :identifier -> ImportAlias( old_name=$1, new_name=$3 )");
-        map.get(101).add("$import_namespace = :as :identifier -> $1");
-        map.get(113).add("$input_declaration = $type_e :identifier $_gen13 -> InputDeclaration( type=$0, name=$1, expression=$2 )");
-        map.get(89).add("$input_kv = :identifier :equal $e -> ObjectKV( key=$0, value=$2 )");
-        map.get(111).add("$inputs = :input :lbrace $_gen10 :rbrace -> Inputs( inputs=$2 )");
-        map.get(95).add("$kv = :identifier :colon $e -> RuntimeAttribute( key=$0, value=$2 )");
-        map.get(103).add("$map_kv = $e :colon $e -> MapLiteralKv( key=$0, value=$2 )");
-        map.get(78).add("$meta = :meta $meta_map -> Meta( map=$1 )");
-        map.get(125).add("$meta_kv = :identifier :colon $meta_value -> MetaKvPair( key=$0, value=$2 )");
-        map.get(70).add("$meta_map = :lbrace $_gen12 :rbrace -> $1");
-        map.get(116).add("$meta_value = $static_string");
-        map.get(116).add("$meta_value = :boolean");
-        map.get(116).add("$meta_value = :float");
-        map.get(116).add("$meta_value = :integer");
-        map.get(116).add("$meta_value = :lbrace $_gen22 :rbrace -> MetaObject( map=$1 )");
-        map.get(116).add("$meta_value = :lsquare $_gen21 :rsquare -> MetaArray( values=$1 )");
-        map.get(116).add("$meta_value = :null");
-        map.get(86).add("$object_kv = :identifier :colon $e -> ObjectKV( key=$0, value=$2 )");
-        map.get(126).add("$output_kv = $type_e :identifier :equal $e -> Output( type=$0, name=$1, expression=$3 )");
-        map.get(120).add("$outputs = :output :lbrace $_gen14 :rbrace -> Outputs( outputs=$2 )");
-        map.get(100).add("$parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
-        map.get(69).add("$rt_map = :lbrace $_gen11 :rbrace -> $1");
-        map.get(85).add("$runtime = :runtime $rt_map -> Runtime( map=$1 )");
-        map.get(88).add("$scatter = :scatter :lparen :identifier :in $e :rparen :lbrace $_gen15 :rbrace -> Scatter( item=$2, collection=$4, body=$7 )");
-        map.get(134).add("$setter = :equal $e -> $1");
-        map.get(138).add("$static_string = :quote $_gen3 :quote -> StaticString( value=$1 )");
-        map.get(110).add("$static_string_piece = :escape");
-        map.get(110).add("$static_string_piece = :string");
-        map.get(87).add("$string_literal = :quote $_gen4 :quote -> StringLiteral( pieces=$1 )");
-        map.get(104).add("$string_piece = $expression_placeholder");
-        map.get(104).add("$string_piece = $static_string_piece");
-        map.get(71).add("$struct = :struct :identifier :lbrace $_gen2 :rbrace -> Struct( name=$1, entries=$3 )");
-        map.get(132).add("$struct_declaration = $type_e :identifier -> StructEntry( type=$0, name=$1 )");
-        map.get(112).add("$task = :task :identifier :lbrace $_gen7 :rbrace -> Task( name=$1, sections=$3 )");
-        map.get(98).add("$task_sections = $command");
-        map.get(98).add("$task_sections = $declaration");
-        map.get(98).add("$task_sections = $inputs");
-        map.get(98).add("$task_sections = $meta");
-        map.get(98).add("$task_sections = $outputs");
-        map.get(98).add("$task_sections = $parameter_meta");
-        map.get(98).add("$task_sections = $runtime");
-        map.get(119).add("$type_e = :identifier");
-        map.get(119).add("$type_e = :type");
-        map.get(119).add("$type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 )");
-        map.get(119).add("$type_e = :type <=> :plus -> NonEmptyType( innerType=$0 )");
-        map.get(119).add("$type_e = :type <=> :qmark -> OptionalType( innerType=$0 )");
-        map.get(121).add("$version = :version :version_name -> VersionDeclaration( v=$1 )");
-        map.get(130).add("$wf_body_element = $call");
-        map.get(130).add("$wf_body_element = $declaration");
-        map.get(130).add("$wf_body_element = $if_stmt");
-        map.get(130).add("$wf_body_element = $inputs");
-        map.get(130).add("$wf_body_element = $outputs");
-        map.get(130).add("$wf_body_element = $scatter");
-        map.get(130).add("$wf_body_element = $wf_meta");
-        map.get(130).add("$wf_body_element = $wf_parameter_meta");
-        map.get(77).add("$wf_meta = :meta $meta_map -> Meta( map=$1 )");
-        map.get(67).add("$wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
-        map.get(123).add("$workflow = :workflow :identifier :lbrace $_gen15 :rbrace -> Workflow( name=$1, body=$3 )");
+        map.put(67, new ArrayList<String>());
+        map.put(71, new ArrayList<String>());
+        map.put(137, new ArrayList<String>());
+        map.put(103, new ArrayList<String>());
+        map.put(111, new ArrayList<String>());
+        map.put(134, new ArrayList<String>());
+        map.get(75).add("$_gen0 = list($import)");
+        map.get(128).add("$_gen1 = list($file_body_element)");
+        map.get(115).add("$_gen10 = list($input_declaration)");
+        map.get(68).add("$_gen11 = list($kv)");
+        map.get(76).add("$_gen12 = list($meta_kv)");
+        map.get(117).add("$_gen13 = $setter");
+        map.get(117).add("$_gen13 = :_empty");
+        map.get(89).add("$_gen14 = list($output_kv)");
+        map.get(132).add("$_gen15 = list($wf_body_element)");
+        map.get(79).add("$_gen16 = $alias");
+        map.get(79).add("$_gen16 = :_empty");
+        map.get(95).add("$_gen17 = list($call_after)");
+        map.get(81).add("$_gen18 = $call_brace_block");
+        map.get(81).add("$_gen18 = :_empty");
+        map.get(88).add("$_gen19 = $call_body");
+        map.get(88).add("$_gen19 = :_empty");
+        map.get(129).add("$_gen2 = list($struct_declaration)");
+        map.get(87).add("$_gen20 = list($input_kv, :comma)");
+        map.get(91).add("$_gen21 = list($meta_value, :comma)");
+        map.get(110).add("$_gen22 = list($meta_kv, :comma)");
+        map.get(70).add("$_gen23 = list($type_e, :comma)");
+        map.get(108).add("$_gen24 = list($e, :comma)");
+        map.get(135).add("$_gen25 = list($object_kv, :comma)");
+        map.get(119).add("$_gen26 = list($map_kv, :comma)");
+        map.get(92).add("$_gen3 = list($static_string_piece)");
+        map.get(114).add("$_gen4 = list($string_piece)");
+        map.get(131).add("$_gen5 = $import_namespace");
+        map.get(131).add("$_gen5 = :_empty");
+        map.get(102).add("$_gen6 = list($import_alias)");
+        map.get(104).add("$_gen7 = list($task_sections)");
+        map.get(140).add("$_gen8 = list($command_part)");
+        map.get(109).add("$_gen9 = list($expression_placeholder_kv)");
+        map.get(126).add("$alias = :as :identifier -> $1");
+        map.get(124).add("$call = :call :fqn $_gen16 $_gen17 $_gen18 -> Call( task=$1, alias=$2, after=$3, body=$4 )");
+        map.get(78).add("$call_after = :after :identifier -> $1");
+        map.get(86).add("$call_body = :input :colon $_gen20 -> CallBody( inputs=$2 )");
+        map.get(118).add("$call_brace_block = :lbrace $_gen19 :rbrace -> $1");
+        map.get(72).add("$command = :raw_command :raw_cmd_start $_gen8 :raw_cmd_end -> RawCommand( parts=$2 )");
+        map.get(99).add("$command_part = $expression_placeholder");
+        map.get(99).add("$command_part = :cmd_part");
+        map.get(93).add("$declaration = $type_e :identifier $setter -> Declaration( type=$0, name=$1, expression=$2 )");
+        map.get(138).add("$document = $version $_gen0 $_gen1 -> Draft3File( version=$0, imports=$1, body=$2 )");
+        map.get(107).add("$e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :plus $e -> Add( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e :slash $e -> Divide( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
+        map.get(107).add("$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
+        map.get(107).add("$e = $string_literal");
+        map.get(107).add("$e = :boolean");
+        map.get(107).add("$e = :dash $e -> UnaryNegation( expression=$1 )");
+        map.get(107).add("$e = :float");
+        map.get(107).add("$e = :identifier");
+        map.get(107).add("$e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 )");
+        map.get(107).add("$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
+        map.get(107).add("$e = :integer");
+        map.get(107).add("$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
+        map.get(107).add("$e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 )");
+        map.get(107).add("$e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 )");
+        map.get(107).add("$e = :none");
+        map.get(107).add("$e = :not $e -> LogicalNot( expression=$1 )");
+        map.get(107).add("$e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 )");
+        map.get(107).add("$e = :plus $e -> UnaryPlus( expression=$1 )");
+        map.get(97).add("$expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 )");
+        map.get(133).add("$expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 )");
+        map.get(127).add("$file_body_element = $struct");
+        map.get(127).add("$file_body_element = $task");
+        map.get(127).add("$file_body_element = $workflow");
+        map.get(94).add("$if_stmt = :if :lparen $e :rparen :lbrace $_gen15 :rbrace -> If( expression=$2, body=$5 )");
+        map.get(82).add("$import = :import $static_string $_gen5 $_gen6 -> Import( uri=$1, namespace=$2, aliases=$3 )");
+        map.get(125).add("$import_alias = :alias :identifier :as :identifier -> ImportAlias( old_name=$1, new_name=$3 )");
+        map.get(96).add("$import_namespace = :as :identifier -> $1");
+        map.get(83).add("$input_declaration = $type_e :identifier $_gen13 -> InputDeclaration( type=$0, name=$1, expression=$2 )");
+        map.get(122).add("$input_kv = :identifier :equal $e -> ObjectKV( key=$0, value=$2 )");
+        map.get(106).add("$inputs = :input :lbrace $_gen10 :rbrace -> Inputs( inputs=$2 )");
+        map.get(116).add("$kv = :identifier :colon $e -> RuntimeAttribute( key=$0, value=$2 )");
+        map.get(100).add("$map_kv = $e :colon $e -> MapLiteralKv( key=$0, value=$2 )");
+        map.get(136).add("$meta = :meta $meta_map -> Meta( map=$1 )");
+        map.get(112).add("$meta_kv = :identifier :colon $meta_value -> MetaKvPair( key=$0, value=$2 )");
+        map.get(141).add("$meta_map = :lbrace $_gen12 :rbrace -> $1");
+        map.get(120).add("$meta_value = $static_string");
+        map.get(120).add("$meta_value = :boolean");
+        map.get(120).add("$meta_value = :float");
+        map.get(120).add("$meta_value = :integer");
+        map.get(120).add("$meta_value = :lbrace $_gen22 :rbrace -> MetaObject( map=$1 )");
+        map.get(120).add("$meta_value = :lsquare $_gen21 :rsquare -> MetaArray( values=$1 )");
+        map.get(120).add("$meta_value = :null");
+        map.get(90).add("$object_kv = :identifier :colon $e -> ObjectKV( key=$0, value=$2 )");
+        map.get(77).add("$output_kv = $type_e :identifier :equal $e -> Output( type=$0, name=$1, expression=$3 )");
+        map.get(84).add("$outputs = :output :lbrace $_gen14 :rbrace -> Outputs( outputs=$2 )");
+        map.get(105).add("$parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
+        map.get(85).add("$rt_map = :lbrace $_gen11 :rbrace -> $1");
+        map.get(80).add("$runtime = :runtime $rt_map -> Runtime( map=$1 )");
+        map.get(121).add("$scatter = :scatter :lparen :identifier :in $e :rparen :lbrace $_gen15 :rbrace -> Scatter( item=$2, collection=$4, body=$7 )");
+        map.get(101).add("$setter = :equal $e -> $1");
+        map.get(98).add("$static_string = :quote $_gen3 :quote -> StaticString( value=$1 )");
+        map.get(69).add("$static_string_piece = :escape");
+        map.get(69).add("$static_string_piece = :string");
+        map.get(139).add("$string_literal = :quote $_gen4 :quote -> StringLiteral( pieces=$1 )");
+        map.get(130).add("$string_piece = $expression_placeholder");
+        map.get(130).add("$string_piece = $static_string_piece");
+        map.get(74).add("$struct = :struct :identifier :lbrace $_gen2 :rbrace -> Struct( name=$1, entries=$3 )");
+        map.get(73).add("$struct_declaration = $type_e :identifier -> StructEntry( type=$0, name=$1 )");
+        map.get(113).add("$task = :task :identifier :lbrace $_gen7 :rbrace -> Task( name=$1, sections=$3 )");
+        map.get(123).add("$task_sections = $command");
+        map.get(123).add("$task_sections = $declaration");
+        map.get(123).add("$task_sections = $inputs");
+        map.get(123).add("$task_sections = $meta");
+        map.get(123).add("$task_sections = $outputs");
+        map.get(123).add("$task_sections = $parameter_meta");
+        map.get(123).add("$task_sections = $runtime");
+        map.get(67).add("$type_e = :identifier");
+        map.get(67).add("$type_e = :type");
+        map.get(67).add("$type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 )");
+        map.get(67).add("$type_e = :type <=> :plus -> NonEmptyType( innerType=$0 )");
+        map.get(67).add("$type_e = :type <=> :qmark -> OptionalType( innerType=$0 )");
+        map.get(71).add("$version = :version :version_name -> VersionDeclaration( v=$1 )");
+        map.get(137).add("$wf_body_element = $call");
+        map.get(137).add("$wf_body_element = $declaration");
+        map.get(137).add("$wf_body_element = $if_stmt");
+        map.get(137).add("$wf_body_element = $inputs");
+        map.get(137).add("$wf_body_element = $outputs");
+        map.get(137).add("$wf_body_element = $scatter");
+        map.get(137).add("$wf_body_element = $wf_meta");
+        map.get(137).add("$wf_body_element = $wf_parameter_meta");
+        map.get(103).add("$wf_meta = :meta $meta_map -> Meta( map=$1 )");
+        map.get(111).add("$wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
+        map.get(134).add("$workflow = :workflow :identifier :lbrace $_gen15 :rbrace -> Workflow( name=$1, body=$3 )");
         nonterminal_rules = Collections.unmodifiableMap(map);
     }
     static {
@@ -2803,29 +2803,29 @@ private static Terminal expect(ParserContext ctx, TerminalIdentifier expecting)
     private static Map<Integer, Integer> prefix_binding_power_e;
     static {
         Map<Integer, Integer> map = new HashMap<Integer, Integer>();
-        map.put(42, 4000); /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
-        map.put(61, 5000); /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
-        map.put(15, 6000); /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
-        map.put(5, 6000); /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
-        map.put(16, 7000); /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
-        map.put(25, 7000); /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
-        map.put(19, 7000); /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
-        map.put(24, 7000); /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
-        map.put(34, 8000); /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
-        map.put(27, 8000); /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
-        map.put(28, 9000); /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
-        map.put(47, 9000); /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
-        map.put(3, 9000); /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
-        map.put(14, 11000); /* $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall( name=$0, params=$2 ) */
-        map.put(39, 12000); /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
-        map.put(62, 13000); /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
+        map.put(45, 4000); /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
+        map.put(29, 5000); /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
+        map.put(53, 6000); /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
+        map.put(51, 6000); /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
+        map.put(36, 7000); /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
+        map.put(40, 7000); /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
+        map.put(2, 7000); /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
+        map.put(52, 7000); /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
+        map.put(33, 8000); /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
+        map.put(32, 8000); /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
+        map.put(18, 9000); /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
+        map.put(37, 9000); /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
+        map.put(64, 9000); /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
+        map.put(15, 11000); /* $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall( name=$0, params=$2 ) */
+        map.put(17, 12000); /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
+        map.put(42, 13000); /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
         infix_binding_power_e = Collections.unmodifiableMap(map);
     }
     static {
         Map<Integer, Integer> map = new HashMap<Integer, Integer>();
-        map.put(36, 10000); /* $e = :not $e -> LogicalNot( expression=$1 ) */
-        map.put(34, 10000); /* $e = :plus $e -> UnaryPlus( expression=$1 ) */
-        map.put(27, 10000); /* $e = :dash $e -> UnaryNegation( expression=$1 ) */
+        map.put(12, 10000); /* $e = :not $e -> LogicalNot( expression=$1 ) */
+        map.put(33, 10000); /* $e = :plus $e -> UnaryPlus( expression=$1 ) */
+        map.put(32, 10000); /* $e = :dash $e -> UnaryNegation( expression=$1 ) */
         prefix_binding_power_e = Collections.unmodifiableMap(map);
     }
     static int get_infix_binding_power_e(int terminal_id) {
@@ -2862,7 +2862,7 @@ public static ParseTree parse_e_internal(ParserContext ctx, int rbp) throws Synt
         return left;
     }
     private static ParseTree nud_e(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(99, "e") );
+        ParseTree tree = new ParseTree( new NonTerminal(107, "e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "e";
         if (current == null) {
@@ -2876,7 +2876,7 @@ else if (rule_first.get(117).contains(terminal_map.get(current.getId()))) {
             tree.setAstTransformation(new AstTransformNodeCreator("LogicalNot", parameters));
             tree.setNudMorphemeCount(2);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NOT));
-            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(36)));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(12)));
             tree.setPrefix(true);
         }
         else if (rule_first.get(118).contains(terminal_map.get(current.getId()))) {
@@ -2887,7 +2887,7 @@ else if (rule_first.get(118).contains(terminal_map.get(current.getId()))) {
             tree.setAstTransformation(new AstTransformNodeCreator("UnaryPlus", parameters));
             tree.setNudMorphemeCount(2);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PLUS));
-            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(34)));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(33)));
             tree.setPrefix(true);
         }
         else if (rule_first.get(119).contains(terminal_map.get(current.getId()))) {
@@ -2898,7 +2898,7 @@ else if (rule_first.get(119).contains(terminal_map.get(current.getId()))) {
             tree.setAstTransformation(new AstTransformNodeCreator("UnaryNegation", parameters));
             tree.setNudMorphemeCount(2);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DASH));
-            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(27)));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(32)));
             tree.setPrefix(true);
         }
         else if (rule_first.get(121).contains(terminal_map.get(current.getId()))) {
@@ -3014,11 +3014,11 @@ else if (rule_first.get(136).contains(terminal_map.get(current.getId()))) {
         return tree;
     }
     private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(99, "e") );
+        ParseTree tree = new ParseTree( new NonTerminal(107, "e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "e";
         int modifier;
-        if (current.getId() == 42) {
+        if (current.getId() == 45) {
             /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(104);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3030,10 +3030,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_PIPE));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(42) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(45) - modifier));
             return tree;
         }
-        if (current.getId() == 61) {
+        if (current.getId() == 29) {
             /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(105);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3045,10 +3045,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_AMPERSAND));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(61) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(29) - modifier));
             return tree;
         }
-        if (current.getId() == 15) {
+        if (current.getId() == 53) {
             /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(106);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3060,10 +3060,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_EQUAL));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(15) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(53) - modifier));
             return tree;
         }
-        if (current.getId() == 5) {
+        if (current.getId() == 51) {
             /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(107);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3075,10 +3075,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NOT_EQUAL));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(5) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(51) - modifier));
             return tree;
         }
-        if (current.getId() == 16) {
+        if (current.getId() == 36) {
             /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(108);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3090,10 +3090,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LT));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(16) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(36) - modifier));
             return tree;
         }
-        if (current.getId() == 25) {
+        if (current.getId() == 40) {
             /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(109);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3105,10 +3105,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LTEQ));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(25) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(40) - modifier));
             return tree;
         }
-        if (current.getId() == 19) {
+        if (current.getId() == 2) {
             /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(110);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3120,10 +3120,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_GT));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(19) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(2) - modifier));
             return tree;
         }
-        if (current.getId() == 24) {
+        if (current.getId() == 52) {
             /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(111);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3135,10 +3135,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_GTEQ));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(24) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(52) - modifier));
             return tree;
         }
-        if (current.getId() == 34) {
+        if (current.getId() == 33) {
             /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(112);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3150,10 +3150,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PLUS));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(34) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(33) - modifier));
             return tree;
         }
-        if (current.getId() == 27) {
+        if (current.getId() == 32) {
             /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(113);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3165,10 +3165,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DASH));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(27) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(32) - modifier));
             return tree;
         }
-        if (current.getId() == 28) {
+        if (current.getId() == 18) {
             /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(114);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3180,10 +3180,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_ASTERISK));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(28) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(18) - modifier));
             return tree;
         }
-        if (current.getId() == 47) {
+        if (current.getId() == 37) {
             /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(115);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3195,10 +3195,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_SLASH));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(47) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(37) - modifier));
             return tree;
         }
-        if (current.getId() == 3) {
+        if (current.getId() == 64) {
             /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(116);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3210,10 +3210,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PERCENT));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(3) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(64) - modifier));
             return tree;
         }
-        if (current.getId() == 14) {
+        if (current.getId() == 15) {
             /* $e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 ) */
             ctx.rule = rules.get(121);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3226,7 +3226,7 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RPAREN));
             return tree;
         }
-        if (current.getId() == 39) {
+        if (current.getId() == 17) {
             /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(122);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3237,11 +3237,11 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(left);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LSQUARE));
             modifier = 0;
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(39) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(17) - modifier));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
             return tree;
         }
-        if (current.getId() == 62) {
+        if (current.getId() == 42) {
             /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
             ctx.rule = rules.get(123);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3300,7 +3300,7 @@ public static ParseTree parse_meta_value_internal(ParserContext ctx, int rbp) th
         return left;
     }
     private static ParseTree nud_meta_value(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(116, "meta_value") );
+        ParseTree tree = new ParseTree( new NonTerminal(120, "meta_value") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "meta_value";
         if (current == null) {
@@ -3366,7 +3366,7 @@ else if (rule_first.get(97).contains(terminal_map.get(current.getId()))) {
         return tree;
     }
     private static ParseTree led_meta_value(ParseTree left, ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(116, "meta_value") );
+        ParseTree tree = new ParseTree( new NonTerminal(120, "meta_value") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "meta_value";
         int modifier;
@@ -3376,9 +3376,9 @@ private static ParseTree led_meta_value(ParseTree left, ParserContext ctx) throw
     private static Map<Integer, Integer> prefix_binding_power_type_e;
     static {
         Map<Integer, Integer> map = new HashMap<Integer, Integer>();
-        map.put(39, 1000); /* $type_e = :type <=> :lsquare list($type_e, :comma) :rsquare -> Type( name=$0, subtype=$2 ) */
-        map.put(12, 2000); /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
-        map.put(34, 3000); /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
+        map.put(17, 1000); /* $type_e = :type <=> :lsquare list($type_e, :comma) :rsquare -> Type( name=$0, subtype=$2 ) */
+        map.put(21, 2000); /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
+        map.put(33, 3000); /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
         infix_binding_power_type_e = Collections.unmodifiableMap(map);
     }
     static {
@@ -3419,7 +3419,7 @@ public static ParseTree parse_type_e_internal(ParserContext ctx, int rbp) throws
         return left;
     }
     private static ParseTree nud_type_e(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(119, "type_e") );
+        ParseTree tree = new ParseTree( new NonTerminal(67, "type_e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "type_e";
         if (current == null) {
@@ -3463,11 +3463,11 @@ else if (rule_first.get(103).contains(terminal_map.get(current.getId()))) {
         return tree;
     }
     private static ParseTree led_type_e(ParseTree left, ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(119, "type_e") );
+        ParseTree tree = new ParseTree( new NonTerminal(67, "type_e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "type_e";
         int modifier;
-        if (current.getId() == 39) {
+        if (current.getId() == 17) {
             /* $type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 ) */
             ctx.rule = rules.get(99);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3480,7 +3480,7 @@ private static ParseTree led_type_e(ParseTree left, ParserContext ctx) throws Sy
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
             return tree;
         }
-        if (current.getId() == 12) {
+        if (current.getId() == 21) {
             /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
             ctx.rule = rules.get(100);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3490,7 +3490,7 @@ private static ParseTree led_type_e(ParseTree left, ParserContext ctx) throws Sy
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_QMARK));
             return tree;
         }
-        if (current.getId() == 34) {
+        if (current.getId() == 33) {
             /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
             ctx.rule = rules.get(101);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3507,12 +3507,12 @@ public ParseTree parse__gen0(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen0(ctx);
     }
     private static ParseTree parse__gen0(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(96, "_gen0"));
+        ParseTree tree = new ParseTree(new NonTerminal(75, "_gen0"));
         tree.setList(true);
         ctx.nonterminal = "_gen0";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(96).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(96).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(75).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(75).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3521,7 +3521,7 @@ private static ParseTree parse__gen0(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(96).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(75).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_import(ctx));
             ctx.nonterminal = "_gen0"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3533,12 +3533,12 @@ public ParseTree parse__gen1(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen1(ctx);
     }
     private static ParseTree parse__gen1(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(84, "_gen1"));
+        ParseTree tree = new ParseTree(new NonTerminal(128, "_gen1"));
         tree.setList(true);
         ctx.nonterminal = "_gen1";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(84).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(84).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(128).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(128).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3547,7 +3547,7 @@ private static ParseTree parse__gen1(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(84).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(128).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_file_body_element(ctx));
             ctx.nonterminal = "_gen1"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3559,12 +3559,12 @@ public ParseTree parse__gen10(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen10(ctx);
     }
     private static ParseTree parse__gen10(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(129, "_gen10"));
+        ParseTree tree = new ParseTree(new NonTerminal(115, "_gen10"));
         tree.setList(true);
         ctx.nonterminal = "_gen10";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(115).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(115).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3573,7 +3573,7 @@ private static ParseTree parse__gen10(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(115).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_input_declaration(ctx));
             ctx.nonterminal = "_gen10"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3585,12 +3585,12 @@ public ParseTree parse__gen11(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen11(ctx);
     }
     private static ParseTree parse__gen11(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(114, "_gen11"));
+        ParseTree tree = new ParseTree(new NonTerminal(68, "_gen11"));
         tree.setList(true);
         ctx.nonterminal = "_gen11";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(114).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(114).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(68).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(68).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3599,7 +3599,7 @@ private static ParseTree parse__gen11(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(114).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(68).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_kv(ctx));
             ctx.nonterminal = "_gen11"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3611,12 +3611,12 @@ public ParseTree parse__gen12(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen12(ctx);
     }
     private static ParseTree parse__gen12(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(90, "_gen12"));
+        ParseTree tree = new ParseTree(new NonTerminal(76, "_gen12"));
         tree.setList(true);
         ctx.nonterminal = "_gen12";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(90).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(90).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(76).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(76).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3625,7 +3625,7 @@ private static ParseTree parse__gen12(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(90).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(76).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_meta_kv(ctx));
             ctx.nonterminal = "_gen12"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3637,12 +3637,12 @@ public ParseTree parse__gen14(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen14(ctx);
     }
     private static ParseTree parse__gen14(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(133, "_gen14"));
+        ParseTree tree = new ParseTree(new NonTerminal(89, "_gen14"));
         tree.setList(true);
         ctx.nonterminal = "_gen14";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(133).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(133).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(89).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(89).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3651,7 +3651,7 @@ private static ParseTree parse__gen14(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(133).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(89).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_output_kv(ctx));
             ctx.nonterminal = "_gen14"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3663,12 +3663,12 @@ public ParseTree parse__gen15(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen15(ctx);
     }
     private static ParseTree parse__gen15(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(105, "_gen15"));
+        ParseTree tree = new ParseTree(new NonTerminal(132, "_gen15"));
         tree.setList(true);
         ctx.nonterminal = "_gen15";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(105).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(105).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(132).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(132).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3677,7 +3677,7 @@ private static ParseTree parse__gen15(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(105).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(132).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_wf_body_element(ctx));
             ctx.nonterminal = "_gen15"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3689,12 +3689,12 @@ public ParseTree parse__gen17(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen17(ctx);
     }
     private static ParseTree parse__gen17(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(115, "_gen17"));
+        ParseTree tree = new ParseTree(new NonTerminal(95, "_gen17"));
         tree.setList(true);
         ctx.nonterminal = "_gen17";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(115).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(115).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(95).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(95).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3703,7 +3703,7 @@ private static ParseTree parse__gen17(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(115).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(95).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_call_after(ctx));
             ctx.nonterminal = "_gen17"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3715,12 +3715,12 @@ public ParseTree parse__gen2(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen2(ctx);
     }
     private static ParseTree parse__gen2(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(94, "_gen2"));
+        ParseTree tree = new ParseTree(new NonTerminal(129, "_gen2"));
         tree.setList(true);
         ctx.nonterminal = "_gen2";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(94).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(94).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3729,7 +3729,7 @@ private static ParseTree parse__gen2(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(94).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_struct_declaration(ctx));
             ctx.nonterminal = "_gen2"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3741,13 +3741,13 @@ public ParseTree parse__gen20(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen20(ctx);
     }
     private static ParseTree parse__gen20(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(122, "_gen20"));
+        ParseTree tree = new ParseTree(new NonTerminal(87, "_gen20"));
         tree.setList(true);
-        tree.setListSeparator(66);
+        tree.setListSeparator(19);
         ctx.nonterminal = "_gen20";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(122).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(122).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(87).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(87).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3756,7 +3756,7 @@ private static ParseTree parse__gen20(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(122).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(87).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_input_kv(ctx));
             ctx.nonterminal = "_gen20"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3782,13 +3782,13 @@ public ParseTree parse__gen21(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen21(ctx);
     }
     private static ParseTree parse__gen21(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(81, "_gen21"));
+        ParseTree tree = new ParseTree(new NonTerminal(91, "_gen21"));
         tree.setList(true);
-        tree.setListSeparator(66);
+        tree.setListSeparator(19);
         ctx.nonterminal = "_gen21";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(81).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(81).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(91).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(91).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3797,7 +3797,7 @@ private static ParseTree parse__gen21(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(81).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(91).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_meta_value(ctx));
             ctx.nonterminal = "_gen21"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3823,13 +3823,13 @@ public ParseTree parse__gen22(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen22(ctx);
     }
     private static ParseTree parse__gen22(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(136, "_gen22"));
+        ParseTree tree = new ParseTree(new NonTerminal(110, "_gen22"));
         tree.setList(true);
-        tree.setListSeparator(66);
+        tree.setListSeparator(19);
         ctx.nonterminal = "_gen22";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(136).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(136).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(110).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(110).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3838,7 +3838,7 @@ private static ParseTree parse__gen22(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(136).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(110).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_meta_kv(ctx));
             ctx.nonterminal = "_gen22"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3864,13 +3864,13 @@ public ParseTree parse__gen23(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen23(ctx);
     }
     private static ParseTree parse__gen23(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(82, "_gen23"));
+        ParseTree tree = new ParseTree(new NonTerminal(70, "_gen23"));
         tree.setList(true);
-        tree.setListSeparator(66);
+        tree.setListSeparator(19);
         ctx.nonterminal = "_gen23";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(82).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(82).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(70).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(70).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3879,7 +3879,7 @@ private static ParseTree parse__gen23(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(82).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(70).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_type_e(ctx));
             ctx.nonterminal = "_gen23"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3905,13 +3905,13 @@ public ParseTree parse__gen24(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen24(ctx);
     }
     private static ParseTree parse__gen24(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(107, "_gen24"));
+        ParseTree tree = new ParseTree(new NonTerminal(108, "_gen24"));
         tree.setList(true);
-        tree.setListSeparator(66);
+        tree.setListSeparator(19);
         ctx.nonterminal = "_gen24";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(107).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(107).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(108).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(108).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3920,7 +3920,7 @@ private static ParseTree parse__gen24(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(107).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(108).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_e(ctx));
             ctx.nonterminal = "_gen24"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3946,13 +3946,13 @@ public ParseTree parse__gen25(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen25(ctx);
     }
     private static ParseTree parse__gen25(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(128, "_gen25"));
+        ParseTree tree = new ParseTree(new NonTerminal(135, "_gen25"));
         tree.setList(true);
-        tree.setListSeparator(66);
+        tree.setListSeparator(19);
         ctx.nonterminal = "_gen25";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(128).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(128).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(135).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(135).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3961,7 +3961,7 @@ private static ParseTree parse__gen25(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(128).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(135).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_object_kv(ctx));
             ctx.nonterminal = "_gen25"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3987,13 +3987,13 @@ public ParseTree parse__gen26(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen26(ctx);
     }
     private static ParseTree parse__gen26(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(73, "_gen26"));
+        ParseTree tree = new ParseTree(new NonTerminal(119, "_gen26"));
         tree.setList(true);
-        tree.setListSeparator(66);
+        tree.setListSeparator(19);
         ctx.nonterminal = "_gen26";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(73).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(73).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(119).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(119).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4002,7 +4002,7 @@ private static ParseTree parse__gen26(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(73).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(119).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_map_kv(ctx));
             ctx.nonterminal = "_gen26"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -4028,12 +4028,12 @@ public ParseTree parse__gen3(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen3(ctx);
     }
     private static ParseTree parse__gen3(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(74, "_gen3"));
+        ParseTree tree = new ParseTree(new NonTerminal(92, "_gen3"));
         tree.setList(true);
         ctx.nonterminal = "_gen3";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(74).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(74).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(92).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(92).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4042,7 +4042,7 @@ private static ParseTree parse__gen3(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(74).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(92).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_static_string_piece(ctx));
             ctx.nonterminal = "_gen3"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4054,12 +4054,12 @@ public ParseTree parse__gen4(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen4(ctx);
     }
     private static ParseTree parse__gen4(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(124, "_gen4"));
+        ParseTree tree = new ParseTree(new NonTerminal(114, "_gen4"));
         tree.setList(true);
         ctx.nonterminal = "_gen4";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(124).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(124).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(114).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(114).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4068,7 +4068,7 @@ private static ParseTree parse__gen4(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(124).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(114).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_string_piece(ctx));
             ctx.nonterminal = "_gen4"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4080,12 +4080,12 @@ public ParseTree parse__gen6(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen6(ctx);
     }
     private static ParseTree parse__gen6(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(97, "_gen6"));
+        ParseTree tree = new ParseTree(new NonTerminal(102, "_gen6"));
         tree.setList(true);
         ctx.nonterminal = "_gen6";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(97).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(97).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(102).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(102).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4094,7 +4094,7 @@ private static ParseTree parse__gen6(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(97).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(102).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_import_alias(ctx));
             ctx.nonterminal = "_gen6"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4106,12 +4106,12 @@ public ParseTree parse__gen7(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen7(ctx);
     }
     private static ParseTree parse__gen7(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(91, "_gen7"));
+        ParseTree tree = new ParseTree(new NonTerminal(104, "_gen7"));
         tree.setList(true);
         ctx.nonterminal = "_gen7";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(91).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(91).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(104).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(104).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4120,7 +4120,7 @@ private static ParseTree parse__gen7(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(91).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(104).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_task_sections(ctx));
             ctx.nonterminal = "_gen7"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4132,12 +4132,12 @@ public ParseTree parse__gen8(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen8(ctx);
     }
     private static ParseTree parse__gen8(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(141, "_gen8"));
+        ParseTree tree = new ParseTree(new NonTerminal(140, "_gen8"));
         tree.setList(true);
         ctx.nonterminal = "_gen8";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(141).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(141).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(140).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(140).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4146,7 +4146,7 @@ private static ParseTree parse__gen8(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(141).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(140).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_command_part(ctx));
             ctx.nonterminal = "_gen8"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4158,12 +4158,12 @@ public ParseTree parse__gen9(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen9(ctx);
     }
     private static ParseTree parse__gen9(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(76, "_gen9"));
+        ParseTree tree = new ParseTree(new NonTerminal(109, "_gen9"));
         tree.setList(true);
         ctx.nonterminal = "_gen9";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(76).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(76).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4172,7 +4172,7 @@ private static ParseTree parse__gen9(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(76).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_expression_placeholder_kv(ctx));
             ctx.nonterminal = "_gen9"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4187,12 +4187,12 @@ private static ParseTree parse__gen13(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[51][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(118, "_gen13"));
+        int rule = (current != null) ? table[50][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(117, "_gen13"));
         ctx.nonterminal = "_gen13";
         if ( current != null &&
-             !nonterminal_first.get(118).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(118).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(117).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(117).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4216,12 +4216,12 @@ private static ParseTree parse__gen16(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[13][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(80, "_gen16"));
+        int rule = (current != null) ? table[12][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(79, "_gen16"));
         ctx.nonterminal = "_gen16";
         if ( current != null &&
-             !nonterminal_first.get(80).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(80).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(79).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(79).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4245,12 +4245,12 @@ private static ParseTree parse__gen18(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[26][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(93, "_gen18"));
+        int rule = (current != null) ? table[14][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(81, "_gen18"));
         ctx.nonterminal = "_gen18";
         if ( current != null &&
-             !nonterminal_first.get(93).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(93).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(81).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(81).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4274,12 +4274,12 @@ private static ParseTree parse__gen19(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[73][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(140, "_gen19"));
+        int rule = (current != null) ? table[21][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(88, "_gen19"));
         ctx.nonterminal = "_gen19";
         if ( current != null &&
-             !nonterminal_first.get(140).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(140).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(88).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(88).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4303,12 +4303,12 @@ private static ParseTree parse__gen5(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[1][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(68, "_gen5"));
+        int rule = (current != null) ? table[64][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(131, "_gen5"));
         ctx.nonterminal = "_gen5";
         if ( current != null &&
-             !nonterminal_first.get(68).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(68).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(131).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(131).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4332,14 +4332,14 @@ private static ParseTree parse_alias(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[72][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(139, "alias"));
+        int rule = (current != null) ? table[59][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(126, "alias"));
         ctx.nonterminal = "alias";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "alias",
-                nonterminal_first.get(139),
-                nonterminal_rules.get(139)
+                nonterminal_first.get(126),
+                nonterminal_rules.get(126)
             ));
         }
         if (rule == 81) {
@@ -4355,7 +4355,7 @@ private static ParseTree parse_alias(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "alias",
             current,
-            nonterminal_first.get(139),
+            nonterminal_first.get(126),
             rules.get(81)
         ));
     }
@@ -4367,14 +4367,14 @@ private static ParseTree parse_call(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[60][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(127, "call"));
+        int rule = (current != null) ? table[57][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(124, "call"));
         ctx.nonterminal = "call";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call",
-                nonterminal_first.get(127),
-                nonterminal_rules.get(127)
+                nonterminal_first.get(124),
+                nonterminal_rules.get(124)
             ));
         }
         if (rule == 75) {
@@ -4401,7 +4401,7 @@ private static ParseTree parse_call(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call",
             current,
-            nonterminal_first.get(127),
+            nonterminal_first.get(124),
             rules.get(75)
         ));
     }
@@ -4413,14 +4413,14 @@ private static ParseTree parse_call_after(ParserContext ctx) throws SyntaxError
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[16][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(83, "call_after"));
+        int rule = (current != null) ? table[11][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(78, "call_after"));
         ctx.nonterminal = "call_after";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call_after",
-                nonterminal_first.get(83),
-                nonterminal_rules.get(83)
+                nonterminal_first.get(78),
+                nonterminal_rules.get(78)
             ));
         }
         if (rule == 82) {
@@ -4436,7 +4436,7 @@ private static ParseTree parse_call_after(ParserContext ctx) throws SyntaxError
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call_after",
             current,
-            nonterminal_first.get(83),
+            nonterminal_first.get(78),
             rules.get(82)
         ));
     }
@@ -4448,14 +4448,14 @@ private static ParseTree parse_call_body(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[50][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(117, "call_body"));
+        int rule = (current != null) ? table[19][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(86, "call_body"));
         ctx.nonterminal = "call_body";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call_body",
-                nonterminal_first.get(117),
-                nonterminal_rules.get(117)
+                nonterminal_first.get(86),
+                nonterminal_rules.get(86)
             ));
         }
         if (rule == 80) {
@@ -4475,7 +4475,7 @@ private static ParseTree parse_call_body(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call_body",
             current,
-            nonterminal_first.get(117),
+            nonterminal_first.get(86),
             rules.get(80)
         ));
     }
@@ -4487,14 +4487,14 @@ private static ParseTree parse_call_brace_block(ParserContext ctx) throws Syntax
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[39][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(106, "call_brace_block"));
+        int rule = (current != null) ? table[51][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(118, "call_brace_block"));
         ctx.nonterminal = "call_brace_block";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call_brace_block",
-                nonterminal_first.get(106),
-                nonterminal_rules.get(106)
+                nonterminal_first.get(118),
+                nonterminal_rules.get(118)
             ));
         }
         if (rule == 78) {
@@ -4512,7 +4512,7 @@ private static ParseTree parse_call_brace_block(ParserContext ctx) throws Syntax
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call_brace_block",
             current,
-            nonterminal_first.get(106),
+            nonterminal_first.get(118),
             rules.get(78)
         ));
     }
@@ -4524,14 +4524,14 @@ private static ParseTree parse_command(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[41][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(108, "command"));
+        int rule = (current != null) ? table[5][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(72, "command"));
         ctx.nonterminal = "command";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "command",
-                nonterminal_first.get(108),
-                nonterminal_rules.get(108)
+                nonterminal_first.get(72),
+                nonterminal_rules.get(72)
             ));
         }
         if (rule == 34) {
@@ -4553,7 +4553,7 @@ private static ParseTree parse_command(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "command",
             current,
-            nonterminal_first.get(108),
+            nonterminal_first.get(72),
             rules.get(34)
         ));
     }
@@ -4565,14 +4565,14 @@ private static ParseTree parse_command_part(ParserContext ctx) throws SyntaxErro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[25][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(92, "command_part"));
+        int rule = (current != null) ? table[32][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(99, "command_part"));
         ctx.nonterminal = "command_part";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "command_part",
-                nonterminal_first.get(92),
-                nonterminal_rules.get(92)
+                nonterminal_first.get(99),
+                nonterminal_rules.get(99)
             ));
         }
         if (rule == 35) {
@@ -4594,7 +4594,7 @@ else if (rule == 36) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "command_part",
             current,
-            nonterminal_first.get(92),
+            nonterminal_first.get(99),
             rules.get(36)
         ));
     }
@@ -4606,14 +4606,14 @@ private static ParseTree parse_declaration(ParserContext ctx) throws SyntaxError
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[35][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(102, "declaration"));
+        int rule = (current != null) ? table[26][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(93, "declaration"));
         ctx.nonterminal = "declaration";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "declaration",
-                nonterminal_first.get(102),
-                nonterminal_rules.get(102)
+                nonterminal_first.get(93),
+                nonterminal_rules.get(93)
             ));
         }
         if (rule == 54) {
@@ -4635,7 +4635,7 @@ private static ParseTree parse_declaration(ParserContext ctx) throws SyntaxError
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "declaration",
             current,
-            nonterminal_first.get(102),
+            nonterminal_first.get(93),
             rules.get(54)
         ));
     }
@@ -4647,14 +4647,14 @@ private static ParseTree parse_document(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[42][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(109, "document"));
+        int rule = (current != null) ? table[71][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(138, "document"));
         ctx.nonterminal = "document";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "document",
-                nonterminal_first.get(109),
-                nonterminal_rules.get(109)
+                nonterminal_first.get(138),
+                nonterminal_rules.get(138)
             ));
         }
         if (rule == 2) {
@@ -4676,7 +4676,7 @@ private static ParseTree parse_document(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "document",
             current,
-            nonterminal_first.get(109),
+            nonterminal_first.get(138),
             rules.get(2)
         ));
     }
@@ -4688,14 +4688,14 @@ private static ParseTree parse_expression_placeholder(ParserContext ctx) throws
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[68][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(135, "expression_placeholder"));
+        int rule = (current != null) ? table[30][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(97, "expression_placeholder"));
         ctx.nonterminal = "expression_placeholder";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "expression_placeholder",
-                nonterminal_first.get(135),
-                nonterminal_rules.get(135)
+                nonterminal_first.get(97),
+                nonterminal_rules.get(97)
             ));
         }
         if (rule == 38) {
@@ -4718,7 +4718,7 @@ private static ParseTree parse_expression_placeholder(ParserContext ctx) throws
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "expression_placeholder",
             current,
-            nonterminal_first.get(135),
+            nonterminal_first.get(97),
             rules.get(38)
         ));
     }
@@ -4730,14 +4730,14 @@ private static ParseTree parse_expression_placeholder_kv(ParserContext ctx) thro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[70][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(137, "expression_placeholder_kv"));
+        int rule = (current != null) ? table[66][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(133, "expression_placeholder_kv"));
         ctx.nonterminal = "expression_placeholder_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "expression_placeholder_kv",
-                nonterminal_first.get(137),
-                nonterminal_rules.get(137)
+                nonterminal_first.get(133),
+                nonterminal_rules.get(133)
             ));
         }
         if (rule == 39) {
@@ -4760,7 +4760,7 @@ private static ParseTree parse_expression_placeholder_kv(ParserContext ctx) thro
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "expression_placeholder_kv",
             current,
-            nonterminal_first.get(137),
+            nonterminal_first.get(133),
             rules.get(39)
         ));
     }
@@ -4772,14 +4772,14 @@ private static ParseTree parse_file_body_element(ParserContext ctx) throws Synta
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[64][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(131, "file_body_element"));
+        int rule = (current != null) ? table[60][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(127, "file_body_element"));
         ctx.nonterminal = "file_body_element";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "file_body_element",
-                nonterminal_first.get(131),
-                nonterminal_rules.get(131)
+                nonterminal_first.get(127),
+                nonterminal_rules.get(127)
             ));
         }
         if (rule == 3) {
@@ -4809,7 +4809,7 @@ else if (rule == 5) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "file_body_element",
             current,
-            nonterminal_first.get(131),
+            nonterminal_first.get(127),
             rules.get(5)
         ));
     }
@@ -4821,14 +4821,14 @@ private static ParseTree parse_if_stmt(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[12][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(79, "if_stmt"));
+        int rule = (current != null) ? table[27][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(94, "if_stmt"));
         ctx.nonterminal = "if_stmt";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "if_stmt",
-                nonterminal_first.get(79),
-                nonterminal_rules.get(79)
+                nonterminal_first.get(94),
+                nonterminal_rules.get(94)
             ));
         }
         if (rule == 85) {
@@ -4857,7 +4857,7 @@ private static ParseTree parse_if_stmt(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "if_stmt",
             current,
-            nonterminal_first.get(79),
+            nonterminal_first.get(94),
             rules.get(85)
         ));
     }
@@ -4869,14 +4869,14 @@ private static ParseTree parse_import(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[8][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(75, "import"));
+        int rule = (current != null) ? table[15][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(82, "import"));
         ctx.nonterminal = "import";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "import",
-                nonterminal_first.get(75),
-                nonterminal_rules.get(75)
+                nonterminal_first.get(82),
+                nonterminal_rules.get(82)
             ));
         }
         if (rule == 21) {
@@ -4900,7 +4900,7 @@ private static ParseTree parse_import(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "import",
             current,
-            nonterminal_first.get(75),
+            nonterminal_first.get(82),
             rules.get(21)
         ));
     }
@@ -4912,14 +4912,14 @@ private static ParseTree parse_import_alias(ParserContext ctx) throws SyntaxErro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[5][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(72, "import_alias"));
+        int rule = (current != null) ? table[58][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(125, "import_alias"));
         ctx.nonterminal = "import_alias";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "import_alias",
-                nonterminal_first.get(72),
-                nonterminal_rules.get(72)
+                nonterminal_first.get(125),
+                nonterminal_rules.get(125)
             ));
         }
         if (rule == 23) {
@@ -4942,7 +4942,7 @@ private static ParseTree parse_import_alias(ParserContext ctx) throws SyntaxErro
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "import_alias",
             current,
-            nonterminal_first.get(72),
+            nonterminal_first.get(125),
             rules.get(23)
         ));
     }
@@ -4954,14 +4954,14 @@ private static ParseTree parse_import_namespace(ParserContext ctx) throws Syntax
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[34][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(101, "import_namespace"));
+        int rule = (current != null) ? table[29][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(96, "import_namespace"));
         ctx.nonterminal = "import_namespace";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "import_namespace",
-                nonterminal_first.get(101),
-                nonterminal_rules.get(101)
+                nonterminal_first.get(96),
+                nonterminal_rules.get(96)
             ));
         }
         if (rule == 22) {
@@ -4977,7 +4977,7 @@ private static ParseTree parse_import_namespace(ParserContext ctx) throws Syntax
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "import_namespace",
             current,
-            nonterminal_first.get(101),
+            nonterminal_first.get(96),
             rules.get(22)
         ));
     }
@@ -4989,14 +4989,14 @@ private static ParseTree parse_input_declaration(ParserContext ctx) throws Synta
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[46][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(113, "input_declaration"));
+        int rule = (current != null) ? table[16][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(83, "input_declaration"));
         ctx.nonterminal = "input_declaration";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "input_declaration",
-                nonterminal_first.get(113),
-                nonterminal_rules.get(113)
+                nonterminal_first.get(83),
+                nonterminal_rules.get(83)
             ));
         }
         if (rule == 53) {
@@ -5018,7 +5018,7 @@ private static ParseTree parse_input_declaration(ParserContext ctx) throws Synta
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "input_declaration",
             current,
-            nonterminal_first.get(113),
+            nonterminal_first.get(83),
             rules.get(53)
         ));
     }
@@ -5030,14 +5030,14 @@ private static ParseTree parse_input_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[22][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(89, "input_kv"));
+        int rule = (current != null) ? table[55][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(122, "input_kv"));
         ctx.nonterminal = "input_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "input_kv",
-                nonterminal_first.get(89),
-                nonterminal_rules.get(89)
+                nonterminal_first.get(122),
+                nonterminal_rules.get(122)
             ));
         }
         if (rule == 88) {
@@ -5058,7 +5058,7 @@ private static ParseTree parse_input_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "input_kv",
             current,
-            nonterminal_first.get(89),
+            nonterminal_first.get(122),
             rules.get(88)
         ));
     }
@@ -5070,14 +5070,14 @@ private static ParseTree parse_inputs(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[44][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(111, "inputs"));
+        int rule = (current != null) ? table[39][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(106, "inputs"));
         ctx.nonterminal = "inputs";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "inputs",
-                nonterminal_first.get(111),
-                nonterminal_rules.get(111)
+                nonterminal_first.get(106),
+                nonterminal_rules.get(106)
             ));
         }
         if (rule == 41) {
@@ -5099,7 +5099,7 @@ private static ParseTree parse_inputs(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "inputs",
             current,
-            nonterminal_first.get(111),
+            nonterminal_first.get(106),
             rules.get(41)
         ));
     }
@@ -5111,14 +5111,14 @@ private static ParseTree parse_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[28][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(95, "kv"));
+        int rule = (current != null) ? table[49][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(116, "kv"));
         ctx.nonterminal = "kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "kv",
-                nonterminal_first.get(95),
-                nonterminal_rules.get(95)
+                nonterminal_first.get(116),
+                nonterminal_rules.get(116)
             ));
         }
         if (rule == 45) {
@@ -5139,7 +5139,7 @@ private static ParseTree parse_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "kv",
             current,
-            nonterminal_first.get(95),
+            nonterminal_first.get(116),
             rules.get(45)
         ));
     }
@@ -5151,14 +5151,14 @@ private static ParseTree parse_map_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[36][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(103, "map_kv"));
+        int rule = (current != null) ? table[33][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(100, "map_kv"));
         ctx.nonterminal = "map_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "map_kv",
-                nonterminal_first.get(103),
-                nonterminal_rules.get(103)
+                nonterminal_first.get(100),
+                nonterminal_rules.get(100)
             ));
         }
         if (rule == 56) {
@@ -5179,7 +5179,7 @@ private static ParseTree parse_map_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "map_kv",
             current,
-            nonterminal_first.get(103),
+            nonterminal_first.get(100),
             rules.get(56)
         ));
     }
@@ -5191,14 +5191,14 @@ private static ParseTree parse_meta(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[11][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(78, "meta"));
+        int rule = (current != null) ? table[69][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(136, "meta"));
         ctx.nonterminal = "meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "meta",
-                nonterminal_first.get(78),
-                nonterminal_rules.get(78)
+                nonterminal_first.get(136),
+                nonterminal_rules.get(136)
             ));
         }
         if (rule == 46) {
@@ -5216,7 +5216,7 @@ private static ParseTree parse_meta(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "meta",
             current,
-            nonterminal_first.get(78),
+            nonterminal_first.get(136),
             rules.get(46)
         ));
     }
@@ -5228,14 +5228,14 @@ private static ParseTree parse_meta_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[58][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(125, "meta_kv"));
+        int rule = (current != null) ? table[45][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(112, "meta_kv"));
         ctx.nonterminal = "meta_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "meta_kv",
-                nonterminal_first.get(125),
-                nonterminal_rules.get(125)
+                nonterminal_first.get(112),
+                nonterminal_rules.get(112)
             ));
         }
         if (rule == 50) {
@@ -5256,7 +5256,7 @@ private static ParseTree parse_meta_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "meta_kv",
             current,
-            nonterminal_first.get(125),
+            nonterminal_first.get(112),
             rules.get(50)
         ));
     }
@@ -5268,14 +5268,14 @@ private static ParseTree parse_meta_map(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[3][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(70, "meta_map"));
+        int rule = (current != null) ? table[74][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(141, "meta_map"));
         ctx.nonterminal = "meta_map";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "meta_map",
-                nonterminal_first.get(70),
-                nonterminal_rules.get(70)
+                nonterminal_first.get(141),
+                nonterminal_rules.get(141)
             ));
         }
         if (rule == 49) {
@@ -5293,7 +5293,7 @@ private static ParseTree parse_meta_map(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "meta_map",
             current,
-            nonterminal_first.get(70),
+            nonterminal_first.get(141),
             rules.get(49)
         ));
     }
@@ -5305,14 +5305,14 @@ private static ParseTree parse_object_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[19][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(86, "object_kv"));
+        int rule = (current != null) ? table[23][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(90, "object_kv"));
         ctx.nonterminal = "object_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "object_kv",
-                nonterminal_first.get(86),
-                nonterminal_rules.get(86)
+                nonterminal_first.get(90),
+                nonterminal_rules.get(90)
             ));
         }
         if (rule == 87) {
@@ -5333,7 +5333,7 @@ private static ParseTree parse_object_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "object_kv",
             current,
-            nonterminal_first.get(86),
+            nonterminal_first.get(90),
             rules.get(87)
         ));
     }
@@ -5345,14 +5345,14 @@ private static ParseTree parse_output_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[59][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(126, "output_kv"));
+        int rule = (current != null) ? table[10][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(77, "output_kv"));
         ctx.nonterminal = "output_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "output_kv",
-                nonterminal_first.get(126),
-                nonterminal_rules.get(126)
+                nonterminal_first.get(77),
+                nonterminal_rules.get(77)
             ));
         }
         if (rule == 59) {
@@ -5376,7 +5376,7 @@ private static ParseTree parse_output_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "output_kv",
             current,
-            nonterminal_first.get(126),
+            nonterminal_first.get(77),
             rules.get(59)
         ));
     }
@@ -5388,14 +5388,14 @@ private static ParseTree parse_outputs(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[53][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(120, "outputs"));
+        int rule = (current != null) ? table[17][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(84, "outputs"));
         ctx.nonterminal = "outputs";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "outputs",
-                nonterminal_first.get(120),
-                nonterminal_rules.get(120)
+                nonterminal_first.get(84),
+                nonterminal_rules.get(84)
             ));
         }
         if (rule == 58) {
@@ -5417,7 +5417,7 @@ private static ParseTree parse_outputs(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "outputs",
             current,
-            nonterminal_first.get(120),
+            nonterminal_first.get(84),
             rules.get(58)
         ));
     }
@@ -5429,14 +5429,14 @@ private static ParseTree parse_parameter_meta(ParserContext ctx) throws SyntaxEr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[33][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(100, "parameter_meta"));
+        int rule = (current != null) ? table[38][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(105, "parameter_meta"));
         ctx.nonterminal = "parameter_meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "parameter_meta",
-                nonterminal_first.get(100),
-                nonterminal_rules.get(100)
+                nonterminal_first.get(105),
+                nonterminal_rules.get(105)
             ));
         }
         if (rule == 47) {
@@ -5454,7 +5454,7 @@ private static ParseTree parse_parameter_meta(ParserContext ctx) throws SyntaxEr
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "parameter_meta",
             current,
-            nonterminal_first.get(100),
+            nonterminal_first.get(105),
             rules.get(47)
         ));
     }
@@ -5466,14 +5466,14 @@ private static ParseTree parse_rt_map(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[2][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(69, "rt_map"));
+        int rule = (current != null) ? table[18][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(85, "rt_map"));
         ctx.nonterminal = "rt_map";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "rt_map",
-                nonterminal_first.get(69),
-                nonterminal_rules.get(69)
+                nonterminal_first.get(85),
+                nonterminal_rules.get(85)
             ));
         }
         if (rule == 44) {
@@ -5491,7 +5491,7 @@ private static ParseTree parse_rt_map(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "rt_map",
             current,
-            nonterminal_first.get(69),
+            nonterminal_first.get(85),
             rules.get(44)
         ));
     }
@@ -5503,14 +5503,14 @@ private static ParseTree parse_runtime(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[18][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(85, "runtime"));
+        int rule = (current != null) ? table[13][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(80, "runtime"));
         ctx.nonterminal = "runtime";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "runtime",
-                nonterminal_first.get(85),
-                nonterminal_rules.get(85)
+                nonterminal_first.get(80),
+                nonterminal_rules.get(80)
             ));
         }
         if (rule == 42) {
@@ -5528,7 +5528,7 @@ private static ParseTree parse_runtime(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "runtime",
             current,
-            nonterminal_first.get(85),
+            nonterminal_first.get(80),
             rules.get(42)
         ));
     }
@@ -5540,14 +5540,14 @@ private static ParseTree parse_scatter(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[21][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(88, "scatter"));
+        int rule = (current != null) ? table[54][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(121, "scatter"));
         ctx.nonterminal = "scatter";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "scatter",
-                nonterminal_first.get(88),
-                nonterminal_rules.get(88)
+                nonterminal_first.get(121),
+                nonterminal_rules.get(121)
             ));
         }
         if (rule == 86) {
@@ -5581,7 +5581,7 @@ private static ParseTree parse_scatter(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "scatter",
             current,
-            nonterminal_first.get(88),
+            nonterminal_first.get(121),
             rules.get(86)
         ));
     }
@@ -5593,14 +5593,14 @@ private static ParseTree parse_setter(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[67][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(134, "setter"));
+        int rule = (current != null) ? table[34][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(101, "setter"));
         ctx.nonterminal = "setter";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "setter",
-                nonterminal_first.get(134),
-                nonterminal_rules.get(134)
+                nonterminal_first.get(101),
+                nonterminal_rules.get(101)
             ));
         }
         if (rule == 55) {
@@ -5616,7 +5616,7 @@ private static ParseTree parse_setter(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "setter",
             current,
-            nonterminal_first.get(134),
+            nonterminal_first.get(101),
             rules.get(55)
         ));
     }
@@ -5628,14 +5628,14 @@ private static ParseTree parse_static_string(ParserContext ctx) throws SyntaxErr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[71][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(138, "static_string"));
+        int rule = (current != null) ? table[31][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(98, "static_string"));
         ctx.nonterminal = "static_string";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "static_string",
-                nonterminal_first.get(138),
-                nonterminal_rules.get(138)
+                nonterminal_first.get(98),
+                nonterminal_rules.get(98)
             ));
         }
         if (rule == 11) {
@@ -5655,7 +5655,7 @@ private static ParseTree parse_static_string(ParserContext ctx) throws SyntaxErr
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "static_string",
             current,
-            nonterminal_first.get(138),
+            nonterminal_first.get(98),
             rules.get(11)
         ));
     }
@@ -5667,14 +5667,14 @@ private static ParseTree parse_static_string_piece(ParserContext ctx) throws Syn
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[43][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(110, "static_string_piece"));
+        int rule = (current != null) ? table[2][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(69, "static_string_piece"));
         ctx.nonterminal = "static_string_piece";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "static_string_piece",
-                nonterminal_first.get(110),
-                nonterminal_rules.get(110)
+                nonterminal_first.get(69),
+                nonterminal_rules.get(69)
             ));
         }
         if (rule == 14) {
@@ -5696,7 +5696,7 @@ else if (rule == 15) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "static_string_piece",
             current,
-            nonterminal_first.get(110),
+            nonterminal_first.get(69),
             rules.get(15)
         ));
     }
@@ -5708,14 +5708,14 @@ private static ParseTree parse_string_literal(ParserContext ctx) throws SyntaxEr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[20][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(87, "string_literal"));
+        int rule = (current != null) ? table[72][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(139, "string_literal"));
         ctx.nonterminal = "string_literal";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "string_literal",
-                nonterminal_first.get(87),
-                nonterminal_rules.get(87)
+                nonterminal_first.get(139),
+                nonterminal_rules.get(139)
             ));
         }
         if (rule == 13) {
@@ -5735,7 +5735,7 @@ private static ParseTree parse_string_literal(ParserContext ctx) throws SyntaxEr
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "string_literal",
             current,
-            nonterminal_first.get(87),
+            nonterminal_first.get(139),
             rules.get(13)
         ));
     }
@@ -5747,14 +5747,14 @@ private static ParseTree parse_string_piece(ParserContext ctx) throws SyntaxErro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[37][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(104, "string_piece"));
+        int rule = (current != null) ? table[63][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(130, "string_piece"));
         ctx.nonterminal = "string_piece";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "string_piece",
-                nonterminal_first.get(104),
-                nonterminal_rules.get(104)
+                nonterminal_first.get(130),
+                nonterminal_rules.get(130)
             ));
         }
         if (rule == 16) {
@@ -5776,7 +5776,7 @@ else if (rule == 17) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "string_piece",
             current,
-            nonterminal_first.get(104),
+            nonterminal_first.get(130),
             rules.get(17)
         ));
     }
@@ -5788,14 +5788,14 @@ private static ParseTree parse_struct(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[4][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(71, "struct"));
+        int rule = (current != null) ? table[7][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(74, "struct"));
         ctx.nonterminal = "struct";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "struct",
-                nonterminal_first.get(71),
-                nonterminal_rules.get(71)
+                nonterminal_first.get(74),
+                nonterminal_rules.get(74)
             ));
         }
         if (rule == 8) {
@@ -5820,7 +5820,7 @@ private static ParseTree parse_struct(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "struct",
             current,
-            nonterminal_first.get(71),
+            nonterminal_first.get(74),
             rules.get(8)
         ));
     }
@@ -5832,14 +5832,14 @@ private static ParseTree parse_struct_declaration(ParserContext ctx) throws Synt
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[65][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(132, "struct_declaration"));
+        int rule = (current != null) ? table[6][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(73, "struct_declaration"));
         ctx.nonterminal = "struct_declaration";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "struct_declaration",
-                nonterminal_first.get(132),
-                nonterminal_rules.get(132)
+                nonterminal_first.get(73),
+                nonterminal_rules.get(73)
             ));
         }
         if (rule == 9) {
@@ -5858,7 +5858,7 @@ private static ParseTree parse_struct_declaration(ParserContext ctx) throws Synt
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "struct_declaration",
             current,
-            nonterminal_first.get(132),
+            nonterminal_first.get(73),
             rules.get(9)
         ));
     }
@@ -5870,14 +5870,14 @@ private static ParseTree parse_task(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[45][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(112, "task"));
+        int rule = (current != null) ? table[46][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(113, "task"));
         ctx.nonterminal = "task";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "task",
-                nonterminal_first.get(112),
-                nonterminal_rules.get(112)
+                nonterminal_first.get(113),
+                nonterminal_rules.get(113)
             ));
         }
         if (rule == 25) {
@@ -5902,7 +5902,7 @@ private static ParseTree parse_task(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "task",
             current,
-            nonterminal_first.get(112),
+            nonterminal_first.get(113),
             rules.get(25)
         ));
     }
@@ -5914,14 +5914,14 @@ private static ParseTree parse_task_sections(ParserContext ctx) throws SyntaxErr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[31][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(98, "task_sections"));
+        int rule = (current != null) ? table[56][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(123, "task_sections"));
         ctx.nonterminal = "task_sections";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "task_sections",
-                nonterminal_first.get(98),
-                nonterminal_rules.get(98)
+                nonterminal_first.get(123),
+                nonterminal_rules.get(123)
             ));
         }
         if (rule == 26) {
@@ -5983,7 +5983,7 @@ else if (rule == 32) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "task_sections",
             current,
-            nonterminal_first.get(98),
+            nonterminal_first.get(123),
             rules.get(32)
         ));
     }
@@ -5995,14 +5995,14 @@ private static ParseTree parse_version(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[54][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(121, "version"));
+        int rule = (current != null) ? table[4][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(71, "version"));
         ctx.nonterminal = "version";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "version",
-                nonterminal_first.get(121),
-                nonterminal_rules.get(121)
+                nonterminal_first.get(71),
+                nonterminal_rules.get(71)
             ));
         }
         if (rule == 6) {
@@ -6020,7 +6020,7 @@ private static ParseTree parse_version(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "version",
             current,
-            nonterminal_first.get(121),
+            nonterminal_first.get(71),
             rules.get(6)
         ));
     }
@@ -6032,14 +6032,14 @@ private static ParseTree parse_wf_body_element(ParserContext ctx) throws SyntaxE
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[63][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(130, "wf_body_element"));
+        int rule = (current != null) ? table[70][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(137, "wf_body_element"));
         ctx.nonterminal = "wf_body_element";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "wf_body_element",
-                nonterminal_first.get(130),
-                nonterminal_rules.get(130)
+                nonterminal_first.get(137),
+                nonterminal_rules.get(137)
             ));
         }
         if (rule == 62) {
@@ -6109,7 +6109,7 @@ else if (rule == 69) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "wf_body_element",
             current,
-            nonterminal_first.get(130),
+            nonterminal_first.get(137),
             rules.get(69)
         ));
     }
@@ -6121,14 +6121,14 @@ private static ParseTree parse_wf_meta(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[10][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(77, "wf_meta"));
+        int rule = (current != null) ? table[36][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(103, "wf_meta"));
         ctx.nonterminal = "wf_meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "wf_meta",
-                nonterminal_first.get(77),
-                nonterminal_rules.get(77)
+                nonterminal_first.get(103),
+                nonterminal_rules.get(103)
             ));
         }
         if (rule == 84) {
@@ -6146,7 +6146,7 @@ private static ParseTree parse_wf_meta(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "wf_meta",
             current,
-            nonterminal_first.get(77),
+            nonterminal_first.get(103),
             rules.get(84)
         ));
     }
@@ -6158,14 +6158,14 @@ private static ParseTree parse_wf_parameter_meta(ParserContext ctx) throws Synta
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[0][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(67, "wf_parameter_meta"));
+        int rule = (current != null) ? table[44][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(111, "wf_parameter_meta"));
         ctx.nonterminal = "wf_parameter_meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "wf_parameter_meta",
-                nonterminal_first.get(67),
-                nonterminal_rules.get(67)
+                nonterminal_first.get(111),
+                nonterminal_rules.get(111)
             ));
         }
         if (rule == 83) {
@@ -6183,7 +6183,7 @@ private static ParseTree parse_wf_parameter_meta(ParserContext ctx) throws Synta
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "wf_parameter_meta",
             current,
-            nonterminal_first.get(67),
+            nonterminal_first.get(111),
             rules.get(83)
         ));
     }
@@ -6195,14 +6195,14 @@ private static ParseTree parse_workflow(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[56][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(123, "workflow"));
+        int rule = (current != null) ? table[67][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(134, "workflow"));
         ctx.nonterminal = "workflow";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "workflow",
-                nonterminal_first.get(123),
-                nonterminal_rules.get(123)
+                nonterminal_first.get(134),
+                nonterminal_rules.get(134)
             ));
         }
         if (rule == 61) {
@@ -6227,7 +6227,7 @@ private static ParseTree parse_workflow(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "workflow",
             current,
-            nonterminal_first.get(123),
+            nonterminal_first.get(134),
             rules.get(61)
         ));
     }
@@ -7167,7 +7167,7 @@ private void lexer_init() throws SyntaxError {
                 })
             ),
             new HermesRegex(
-                Pattern.compile("development"),
+                Pattern.compile("development-1.1"),
                 Arrays.asList(new LexerOutput[] {
                     new LexerRegexOutput(
                         WdlTerminalIdentifier.TERMINAL_VERSION_NAME,
diff --git a/wdl/transforms/biscayne/src/main/resources/CHANGELOG.txt b/wdl/transforms/biscayne/src/main/resources/CHANGELOG.txt
new file mode 100644
index 00000000000..af2ba7d94e7
--- /dev/null
+++ b/wdl/transforms/biscayne/src/main/resources/CHANGELOG.txt
@@ -0,0 +1,4 @@
+2023-03-16
+Synced grammar from OpenWDL `development` version, which is actually development of 2.0. There is no 1.1 Hermes grammar, develop it here.
+Changed version declaration to `development1_1`.
+This disallows `version 1.1` workflows to run with incomplete support. Once development is finished, change to `1.1`.
\ No newline at end of file
diff --git a/wdl/transforms/biscayne/src/main/resources/grammar.hgr b/wdl/transforms/biscayne/src/main/resources/grammar.hgr
new file mode 100644
index 00000000000..e12ad170e60
--- /dev/null
+++ b/wdl/transforms/biscayne/src/main/resources/grammar.hgr
@@ -0,0 +1,444 @@
+grammar {
+  lexer {
+    partials {
+      r'[a-zA-Z]' -> _identifier_start
+      r'[a-zA-Z0-9_]' -> _identifier_follow
+      r'(Array|Map|Pair|Boolean|Int|Float|File|Directory|String)(?!{%_identifier_follow%})' -> _type
+      r'{%_identifier_start%}({%_identifier_follow%})*' -> _identifier
+    }
+
+    r'#.*' -> null
+    r'\s+' -> null
+    r'^version(?!{%_identifier_follow%})' -> :version @awaiting_version_name
+
+    mode<main> {
+
+      r'\s+' -> null
+
+      enum {
+        python: r'/\*(.*?)\*/' (DOTALL)
+        c: r'/\*(.*?)\*/' (PCRE_DOTALL)
+        java: r'/\*(.*?)\*/' (DOTALL)
+        javascript: r'/\*(.*?)\*/' (m)
+      } -> null
+
+      r'#.*' -> null
+      r'task(?!{%_identifier_follow%})' -> task(:task)
+      r'(call)\s+' -> :call[1] @task_fqn
+      r'after(?!{%_identifier_follow%})' -> :after
+      r'workflow(?!{%_identifier_follow%})' -> workflow(:workflow)
+      r'struct(?!{%_identifier_follow%})' -> :struct
+      r'import(?!{%_identifier_follow%})' -> :import
+      r'alias(?!{%_identifier_follow%})' -> :alias
+      r'input(?!{%_identifier_follow%})' -> :input
+      r'output(?!{%_identifier_follow%})' -> :output
+      r'as(?!{%_identifier_follow%})' -> :as
+      r'if(?!{%_identifier_follow%})' -> :if
+      r'then(?!{%_identifier_follow%})' -> :then
+      r'else(?!{%_identifier_follow%})' -> :else
+      r'runtime(?!{%_identifier_follow%})' -> :runtime
+      r'scatter(?!{%_identifier_follow%})' -> :scatter @scatter
+      r'command\s*(?=<<<)' -> :raw_command  @raw_command2
+      r'command\s*(?=\{)' -> :raw_command  @raw_command
+      r'parameter_meta(?!{%_identifier_follow%})' -> :parameter_meta
+      r'meta(?!{%_identifier_follow%})' -> :meta
+      r'(true|false)(?!{%_identifier_follow%})' -> :boolean
+      r'(object)\s*(\{)' -> :object :lbrace
+      r'{%_type%}(?!{%_identifier_follow%})' -> :type
+      r'None' -> :none
+      r'{%_identifier%}' -> :identifier
+      r'null' -> :null
+
+      r':' -> :colon
+      r',' -> :comma
+      r'==' -> :double_equal
+      r'\|\|' -> :double_pipe
+      r'\&\&' -> :double_ampersand
+      r'!=' -> :not_equal
+      r'=' -> :equal
+      r'\.' -> :dot
+      r'\{' -> :lbrace
+      r'\}' -> :rbrace
+      r'\(' -> :lparen
+      r'\)' -> :rparen
+      r'\[' -> :lsquare
+      r'\]' -> :rsquare
+      r'\+' -> :plus
+      r'\*' -> :asterisk
+      r'-' -> :dash
+      r'/' -> :slash
+      r'%' -> :percent
+      r'<=' -> :lteq
+      r'<' -> :lt
+      r'>=' -> :gteq
+      r'>' -> :gt
+      r'!' -> :not
+
+      enum {
+        python: r'\"'
+        java: "\""
+        javascript:"\""
+      } -> :quote @dquote_string
+      r'\'' -> :quote @squote_string
+      enum {
+        python: r'\?'
+        java: "\\?"
+        javascript: "\\?"
+      } -> :qmark
+      r'-?[0-9]+\.[0-9]+' -> :float
+      r'[0-9]+' -> :integer
+    }
+
+    mode<dquote_string> {
+      # String ends immediately (empty)
+      enum {
+        python: r'\"'
+        java: "\""
+        javascript:"\""
+      } -> :quote %pop
+
+      # String is an expression placeholder
+      r'\$\{' -> :expression_placeholder_start @expression_placeholder
+      r'~\{' -> :expression_placeholder_start @expression_placeholder
+
+      # Escape sequences
+      r'\\[0-7][0-7][0-7]' -> :escape
+      r'\\x[0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+      r'\\u[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+      r'\\U[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+
+      enum {
+        python: r'\\.'
+        java: "\\\\."
+        javascript: "\\."
+      } -> :escape
+
+      # String with ordinary contents
+      enum {
+        python: r'[^\\\"\n(\$\{)(~\{)]*'
+        java: "(.*?)(?=\\\\|\\$\\{|~\\{|\")"
+        javascript: "[^\\\"\\n(${)(~{)]*"
+      } -> :string
+    }
+
+    mode<squote_string> {
+      # String ends immediately (empty)
+      r'\'' -> :quote %pop
+      r'\$\{' -> :expression_placeholder_start @expression_placeholder
+      r'~\{' -> :expression_placeholder_start @expression_placeholder
+
+      # Escape sequences
+      r'\\[0-7][0-7][0-7]' -> :escape
+      r'\\x[0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+      r'\\u[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+      r'\\U[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+
+      enum {
+        python: r'\\.'
+        java: "\\\\."
+        javascript: "\\."
+      } -> :escape
+
+      # String with ordinary contents
+      enum {
+        python: r'[^\\\'\n(\$\{)(~\{)]*'
+        java: "(.*?)(?=\\\\|\\$\\{|~\\{|\')"
+        javascript: "[^\\\'\\n(${)(~{)]*"
+      } -> :string
+    }
+
+    mode<awaiting_version_name> {
+      r'\s+' -> null
+      r'development-1.1' -> :version_name @main
+    }
+    mode<task_fqn> {
+      r'\s+' -> null
+      enum {
+        python: r'{%_identifier%}(\.{%_identifier%})*'
+        java: "{%_identifier%}(\\.{%_identifier%})*"
+        javascript: "{%_identifier%}(\\.{%_identifier%})*"
+      } -> :fqn %pop
+    }
+    mode<scatter> {
+      r'\s+' -> null
+      r'\(' -> :lparen
+      r'in(?!{%_identifier_follow%})' -> :in %pop
+      r'{%_identifier%}' -> :identifier
+    }
+    mode<raw_command> {
+      r'\{' -> :raw_cmd_start
+      r'\}' -> :raw_cmd_end %pop
+      r'\$\{' -> :expression_placeholder_start @expression_placeholder
+      r'~\{' -> :expression_placeholder_start @expression_placeholder
+      enum {
+        python: r'(.*?)(?=\$\{|~\{|\})' (DOTALL)
+        c: r'(.*?)(?=\$\{|~\{|\})' (PCRE_DOTALL)
+        java: r'(.*?)(?=\$\{|~\{|\})' (DOTALL)
+        javascript: r'([\s\S]*?)(?=\$\{|~\{|\})' (m)
+      } -> :cmd_part
+    }
+    mode<raw_command2> {
+      r'<<<' -> :raw_cmd_start
+      r'>>>' -> :raw_cmd_end %pop
+      r'~\{' -> :expression_placeholder_start @expression_placeholder
+      enum {
+        python: r'(.*?)(?=~\{|>>>)' (DOTALL)
+        c: r'(.*?)(?=~\{|>>>)' (PCRE_DOTALL)
+        java: r'(.*?)(?=~\{|>>>)' (DOTALL)
+        javascript: r'([\s\S]*?)(?=~\{|>>>)' (m)
+      } -> :cmd_part
+    }
+    mode<expression_placeholder> {
+      r'\s+' -> null
+      r'\}' -> :expression_placeholder_end %pop
+      r'\[' -> :lsquare
+      r'\]' -> :rsquare
+      r'=' -> :equal
+      r'\+' -> :plus
+      r'\*' -> :asterisk
+      r'[0-9]+' -> :integer
+      r'if' -> :if
+      r'else' -> :else
+      r'then' -> :then
+      r'{%_identifier%}(?=\s*=)' -> :cmd_attr_hint[] :identifier
+      r'(true|false)(?!{%_identifier_follow%})' -> :boolean
+      r'{%_type%}(?!{%_identifier_follow%})' -> :type
+      r'None' -> :none
+      r'{%_identifier%}' -> :identifier
+
+      # Expression tokens
+      r':' -> :colon
+      r',' -> :comma
+      r'\.' -> :dot
+      r'==' -> :double_equal
+      r'\|\|' -> :double_pipe
+      r'\&\&' -> :double_ampersand
+      r'!=' -> :not_equal
+      r'=' -> :equal
+      r'\.' -> :dot
+      r'\{' -> :lbrace
+      r'\(' -> :lparen
+      r'\)' -> :rparen
+      r'\[' -> :lsquare
+      r'\]' -> :rsquare
+      r'\+' -> :plus
+      r'\*' -> :asterisk
+      r'-' -> :dash
+      r'/' -> :slash
+      r'%' -> :percent
+      r'<=' -> :lteq
+      r'<' -> :lt
+      r'>=' -> :gteq
+      r'>' -> :gt
+      r'!' -> :not
+
+      # Literals
+      enum {
+        python: r'\"'
+        java: "\""
+        javascript: "\\\\\\\""
+      } -> :quote @dquote_string
+      r'\'' -> :quote @squote_string
+      r'-?[0-9]+\.[0-9]+' -> :float
+      r'[0-9]+' -> :integer
+    }
+
+    code<python> << PYTHON
+    def init():
+        return {
+            'context': None,
+            'replacements': {
+                re.compile(r"\\n"): 0x000A,
+                re.compile(r"\\r"): 0x000D,
+                re.compile(r"\\b"): 0x0008,
+                re.compile(r"\\t"): 0x0009,
+                re.compile(r"\\a"): 0x0007,
+                re.compile(r"\\v"): 0x000B,
+                re.compile(r'\\"'): 0x0022,
+                re.compile(r"\\'"): 0x0027,
+                re.compile(r"\\\?"): 0x003F
+            },
+            'escapes': {
+                re.compile(r'(\\([0-7]{1,3}))'): 8,
+                re.compile(r'(\\[xX]([0-9a-fA-F]{1,4}))'): 16,
+                re.compile(r'(\\[uU]([0-9a-fA-F]{4}))'): 16
+            }
+        }
+    def workflow(ctx, terminal, source_string, line, col):
+        ctx.user_context['context'] = 'workflow'
+        default_action(ctx, terminal, source_string, line, col)
+    def task(ctx, terminal, source_string, line, col):
+        ctx.user_context['context'] = 'task'
+        default_action(ctx, terminal, source_string, line, col)
+    def output(ctx, terminal, source_string, line, col):
+        if ctx.user_context['context'] == 'workflow':
+            ctx.stack.append('wf_output')
+        default_action(ctx, terminal, source_string, line, col)
+    PYTHON
+
+    code<java> << JAVA
+    private class WdlContext {
+        public String wf_or_task = null;
+    }
+    public Object init() {
+        return new WdlContext();
+    }
+    public void workflow(LexerContext ctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+        ((WdlContext) ctx.context).wf_or_task = "workflow";
+        default_action(ctx, terminal, source_string, line, col);
+    }
+    public void task(LexerContext ctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+        ((WdlContext) ctx.context).wf_or_task = "task";
+        default_action(ctx, terminal, source_string, line, col);
+    }
+    public void output(LexerContext ctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+        WdlContext user_ctx = (WdlContext) ctx.context;
+        if (user_ctx.wf_or_task != null && user_ctx.wf_or_task.equals("workflow")) {
+            ctx.stack.push("wf_output");
+        }
+        default_action(ctx, terminal, source_string, line, col);
+    }
+    JAVA
+
+    code<javascript> << JAVASCRIPT
+        function init() {
+            return {wf_or_task: null};
+        }
+        function workflow(ctx, terminal, source_string, line, col) {
+            ctx.user_context.wf_or_task = "workflow";
+            default_action(ctx, terminal, source_string, line, col);
+        }
+        function task(ctx, terminal, source_string, line, col) {
+            ctx.user_context.wf_or_task = "task";
+            default_action(ctx, terminal, source_string, line, col);
+        }
+        function output(ctx, terminal, source_string, line, col) {
+            const user_ctx = ctx.user_context;
+            if (user_ctx.wf_or_task != null && user_ctx.wf_or_task === "workflow") {
+                ctx.mode_stack.push("wf_output");
+            }
+            default_action(ctx, terminal, source_string, line, col);
+        }
+        JAVASCRIPT
+  }
+  parser {
+    # Document: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#document
+    $document = $version list($import) list($file_body_element) -> Draft3File(version=$0, imports=$1, body=$2)
+    $file_body_element = $workflow | $task | $struct
+
+    # Version declaration:
+    $version = :version :version_name -> VersionDeclaration(v = $1)
+
+    $struct = :struct :identifier :lbrace list($struct_declaration) :rbrace -> Struct(name=$1, entries=$3)
+    $struct_declaration = $type_e :identifier -> StructEntry(type=$0, name=$1)
+
+    $static_string = :quote list($static_string_piece) :quote -> StaticString(value=$1)
+    $string_literal = :quote list($string_piece) :quote -> StringLiteral(pieces=$1)
+    $static_string_piece = :string | :escape
+    $string_piece = $static_string_piece | $expression_placeholder
+
+    # Import Statements: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#import-statements
+    $import = :import $static_string optional($import_namespace) list($import_alias) -> Import(uri=$1, namespace=$2, aliases=$3)
+    $import_namespace = :as :identifier -> $1
+    $import_alias = :alias :identifier :as :identifier -> ImportAlias(old_name=$1, new_name=$3)
+
+    # Task Definition: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#task-definition
+    $task = :task :identifier :lbrace list($task_sections) :rbrace -> Task(name=$1, sections=$3)
+    $task_sections = $command | $inputs | $outputs | $runtime | $parameter_meta | $meta | $declaration
+    $command = :raw_command :raw_cmd_start list($command_part) :raw_cmd_end -> RawCommand(parts=$2)
+    $command_part = :cmd_part | $expression_placeholder
+    $expression_placeholder = :expression_placeholder_start list($expression_placeholder_kv) $e :expression_placeholder_end -> ExpressionPlaceholder(attributes=$1, expr=$2)
+    $expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr(key=$1, value=$3)
+    $inputs = :input :lbrace list($input_declaration) :rbrace -> Inputs(inputs=$2)
+    $runtime = :runtime $rt_map -> Runtime(map=$1)
+    $rt_map = :lbrace list($kv) :rbrace -> $1
+    $kv = :identifier :colon $e -> RuntimeAttribute(key=$0, value=$2)
+
+    # Meta sections
+    $meta = :meta $meta_map -> Meta(map=$1)
+    $parameter_meta = :parameter_meta $meta_map -> ParameterMeta(map=$1)
+    $meta_map = :lbrace list($meta_kv) :rbrace -> $1
+    $meta_kv = :identifier :colon $meta_value -> MetaKvPair(key=$0, value=$2)
+    $meta_value = parser<expression> {
+      $meta_value = $static_string
+      $meta_value = :boolean
+      $meta_value = :integer
+      $meta_value = :float
+      $meta_value = :null
+      $meta_value = :lsquare list($meta_value, :comma) :rsquare -> MetaArray(values=$1)
+      $meta_value = :lbrace list($meta_kv, :comma) :rbrace -> MetaObject(map=$1)
+    }
+
+    # Declarations: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#declarations
+    $input_declaration = $type_e :identifier optional($setter) -> InputDeclaration(type=$0, name=$1, expression=$2)
+    $declaration = $type_e :identifier $setter -> Declaration(type=$0, name=$1, expression=$2)
+    $setter = :equal $e -> $1
+
+    # Types: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#types
+    $type_e = parser<expression> {
+      (*:left) $type_e = :type <=> :lsquare list($type_e, :comma) :rsquare -> Type(name=$0, subtype=$2)
+      (*:left) $type_e = :type <=> :qmark -> OptionalType(innerType=$0)
+      (*:left) $type_e = :type <=> :plus -> NonEmptyType(innerType=$0)
+      $type_e = :type
+      $type_e = :identifier
+    }
+
+    # Expressions: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#expressions
+    $e = parser<expression> {
+      (*:left) $e = $e :double_pipe $e -> LogicalOr(lhs=$0, rhs=$2)
+      (*:left) $e = $e :double_ampersand $e -> LogicalAnd(lhs=$0, rhs=$2)
+      (*:left) $e = $e :double_equal $e -> Equals(lhs=$0, rhs=$2)
+      (-:left) $e = $e :not_equal $e -> NotEquals(lhs=$0, rhs=$2)
+      (*:left) $e = $e :lt $e -> LessThan(lhs=$0, rhs=$2)
+      (-:left) $e = $e :lteq $e -> LessThanOrEqual(lhs=$0, rhs=$2)
+      (-:left) $e = $e :gt $e -> GreaterThan(lhs=$0, rhs=$2)
+      (-:left) $e = $e :gteq $e -> GreaterThanOrEqual(lhs=$0, rhs=$2)
+      (*:left) $e = $e :plus $e -> Add(lhs=$0, rhs=$2)
+      (-:left) $e = $e :dash $e -> Subtract(lhs=$0, rhs=$2)
+      (*:left) $e = $e :asterisk $e -> Multiply(lhs=$0, rhs=$2)
+      (-:left) $e = $e :slash $e -> Divide(lhs=$0, rhs=$2)
+      (-:left) $e = $e :percent $e -> Remainder(lhs=$0, rhs=$2)
+      (*:unary) $e = :not $e -> LogicalNot(expression=$1)
+      (-:unary) $e = :plus $e -> UnaryPlus(expression=$1)
+      (-:unary) $e = :dash $e -> UnaryNegation(expression=$1)
+      (*:left) $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall(name=$0, params=$2)
+      (*:left) $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup(lhs=$0, rhs=$2)
+      (*:left) $e = $e <=> :dot :identifier -> MemberAccess(value=$0, member=$2)
+      # TODO: is there a better object literal syntax?
+      (*:left) $e = :object :lbrace list($object_kv, :comma) :rbrace -> ObjectLiteral(map=$2)
+      (*:left) $e = :lsquare list($e, :comma) :rsquare -> ArrayLiteral(values=$1)
+      (*:left) $e = :lbrace list($map_kv, :comma) :rbrace -> MapLiteral(map=$1)
+      (*:left) $e = :lparen list($e, :comma) :rparen -> TupleLiteral(values=$1)
+      (*:left) $e = :if $e :then $e :else $e -> TernaryIf(cond=$1, iftrue=$3, iffalse=$5)
+      $e = $string_literal
+      $e = :identifier
+      $e = :boolean
+      $e = :integer
+      $e = :float
+      $e = :none
+    }
+    $map_kv = $e :colon $e -> MapLiteralKv(key=$0, value=$2)
+
+    # Outputs
+    $outputs = :output :lbrace list($output_kv) :rbrace -> Outputs(outputs=$2)
+    $output_kv = $type_e :identifier :equal $e -> Output(type=$0, name=$1, expression=$3)
+
+    # Workflows: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#workflow-definition
+    $workflow = :workflow :identifier :lbrace list($wf_body_element) :rbrace -> Workflow(name=$1, body=$3)
+    $wf_body_element = $call | $declaration | $if_stmt | $scatter | $inputs | $outputs | $wf_parameter_meta | $wf_meta
+    $call = :call :fqn optional($alias) list($call_after) optional($call_brace_block) -> Call(task=$1, alias=$2, after=$3, body=$4)
+    $call_brace_block = :lbrace optional($call_body) :rbrace -> $1
+    $call_body = :input :colon list($input_kv, :comma) -> CallBody(inputs=$2)
+    $alias = :as :identifier -> $1
+    $call_after = :after :identifier -> $1
+    $wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta(map=$1)
+    $wf_meta = :meta $meta_map -> Meta(map=$1)
+    $if_stmt = :if :lparen $e :rparen :lbrace list($wf_body_element) :rbrace -> If(expression=$2, body=$5)
+
+    $scatter = :scatter :lparen :identifier :in $e :rparen :lbrace list($wf_body_element) :rbrace
+        -> Scatter(item=$2, collection=$4, body=$7)
+
+    $object_kv = :identifier :colon $e -> ObjectKV(key=$0, value=$2)
+    $input_kv = :identifier :equal $e -> ObjectKV(key=$0, value=$2)
+  }
+}
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/ast2wdlom.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/ast2wdlom.scala
index 18b560bd99f..6bc3bcd94bc 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/ast2wdlom.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/ast2wdlom.scala
@@ -10,7 +10,6 @@ import wdl.model.draft3.elements._
 import wdl.transforms.base.ast2wdlom._
 import wdl.transforms.biscayne.parsing.fileToAst
 import wom.callable.MetaKvPair
-import wom.types.WomUnlistedDirectoryType
 
 package object ast2wdlom {
 
@@ -27,7 +26,7 @@ package object ast2wdlom {
   implicit val astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement] = AstNodeToExpressionElement.astNodeToExpressionElement(customEngineFunctionMakers = AstToNewExpressionElements.newBiscayneEngineFunctionMakers)
   implicit val astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair] = AstNodeToKvPair.astNodeToKvPair(astNodeToExpressionElement)
 
-  implicit val astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement] = AstNodeToTypeElement.astNodeToTypeElement(Map("Directory" -> WomUnlistedDirectoryType))
+  implicit val astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement] = AstNodeToTypeElement.astNodeToTypeElement(Map.empty)
   implicit val astToStructElement: CheckedAtoB[GenericAst, StructElement] = AstToStructElement.astToStructElement
   implicit val astNodeToImportElement: CheckedAtoB[GenericAstNode, ImportElement] = astNodeToAst andThen AstToImportElement.astToImportElement
 
diff --git a/wdl/transforms/biscayne/src/test/cases/afters.wdl b/wdl/transforms/biscayne/src/test/cases/afters.wdl
index 3ba709da26e..8c18609a52d 100644
--- a/wdl/transforms/biscayne/src/test/cases/afters.wdl
+++ b/wdl/transforms/biscayne/src/test/cases/afters.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow afters {
   call foo { input: i = 5 }
diff --git a/wdl/transforms/biscayne/src/test/cases/biscayne_escaping.wdl b/wdl/transforms/biscayne/src/test/cases/biscayne_escaping.wdl
index 4dbfdaa10ee..8439c864b16 100644
--- a/wdl/transforms/biscayne/src/test/cases/biscayne_escaping.wdl
+++ b/wdl/transforms/biscayne/src/test/cases/biscayne_escaping.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow escapes {
     String backslash = " \\ "
diff --git a/wdl/transforms/biscayne/src/test/cases/no_input_no_output_workflow.wdl b/wdl/transforms/biscayne/src/test/cases/no_input_no_output_workflow.wdl
index 55e74a730f1..e0f9aa413ab 100644
--- a/wdl/transforms/biscayne/src/test/cases/no_input_no_output_workflow.wdl
+++ b/wdl/transforms/biscayne/src/test/cases/no_input_no_output_workflow.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow no_input_no_output {
   call no_inputs as noi1
diff --git a/wdl/transforms/biscayne/src/test/cases/simple_first_test.wdl b/wdl/transforms/biscayne/src/test/cases/simple_first_test.wdl
index adde2b1639f..098e2cb096b 100644
--- a/wdl/transforms/biscayne/src/test/cases/simple_first_test.wdl
+++ b/wdl/transforms/biscayne/src/test/cases/simple_first_test.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 task in_n_out {
   input {
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
index 183c0141c02..e5d7a2f9249 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
@@ -31,7 +31,7 @@ object Ast2WdlomSpec {
                    (implicit converter: CheckedAtoB[GenericAstNode, A]): Checked[A] = {
 
     // Add the "version development" to force the lexer into "main" mode.
-    val versionedExpression = "version development\n" + expression
+    val versionedExpression = "version development-1.1\n" + expression
     // That "version development" means we'll have 2 unwanted tokens at the start of the list, so drop 'em:
     val tokens = parser.lex(versionedExpression, "string").asScala.drop(2).asJava
     val terminalMap = (tokens.asScala.toVector map {(_, versionedExpression)}).toMap
diff --git a/wdl/transforms/cascades/src/main/java/wdl/cascades/parser/WdlParser.java b/wdl/transforms/cascades/src/main/java/wdl/cascades/parser/WdlParser.java
new file mode 100644
index 00000000000..678bef21092
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/java/wdl/cascades/parser/WdlParser.java
@@ -0,0 +1,7874 @@
+
+/*
+ * This file was generated by Hermes Parser Generator on Mon Mar 27 20:16:01 2023
+ * 
+ * Hermes command: hermes generate resources/grammar.hgr --language=java --directory=java --name=wdl --java-package=wdl.cascades.parser --java-use-apache-commons --java-imports=org.apache.commons.lang3.StringEscapeUtils --header
+ * Run from: .. (relative to this file)
+ * Hermes version: hermes-parser 2.0rc6
+ * 
+ * !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
+ * 
+ * If you wish to change something in this file, either change the grammar and
+ * re-generate this file, or change the templates in Hermes and regenerate.
+ * See the Hermes repository: http://github.com/scottfrazer/hermes
+ */
+package wdl.cascades.parser;
+import java.util.*;
+import java.io.IOException;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStreamReader;
+import java.util.Arrays;
+import java.nio.*;
+import java.nio.channels.FileChannel;
+import java.nio.charset.Charset;
+import org.apache.commons.codec.binary.Base64;
+import org.apache.commons.lang3.StringEscapeUtils;
+import java.util.regex.Pattern;
+import java.util.regex.Matcher;
+import java.lang.reflect.Method;
+public class WdlParser {
+    private static Map<Integer, List<TerminalIdentifier>> nonterminal_first;
+    private static Map<Integer, List<TerminalIdentifier>> nonterminal_follow;
+    private static Map<Integer, List<TerminalIdentifier>> rule_first;
+    private static Map<Integer, List<String>> nonterminal_rules;
+    private static Map<Integer, String> rules;
+    public static WdlTerminalMap terminal_map = new WdlTerminalMap(WdlTerminalIdentifier.values());
+    public WdlParser() {
+        try {
+            lexer_init();
+        } catch(Exception e) {}
+    }
+    public static String join(Collection<?> s, String delimiter) {
+        StringBuilder builder = new StringBuilder();
+        Iterator iter = s.iterator();
+        while (iter.hasNext()) {
+            builder.append(iter.next());
+            if (!iter.hasNext()) {
+                break;
+            }
+            builder.append(delimiter);
+        }
+        return builder.toString();
+    }
+    public static String getIndentString(int spaces) {
+        StringBuilder sb = new StringBuilder();
+        for(int i = 0; i < spaces; i++) {
+            sb.append(' ');
+        }
+        return sb.toString();
+    }
+    public static String readStdin() throws IOException {
+        InputStreamReader stream = new InputStreamReader(System.in, "utf-8");
+        char buffer[] = new char[System.in.available()];
+        try {
+            stream.read(buffer, 0, System.in.available());
+        } finally {
+            stream.close();
+        }
+        return new String(buffer);
+    }
+    public static String readFile(String path) throws IOException {
+        FileInputStream stream = new FileInputStream(new File(path));
+        try {
+            FileChannel fc = stream.getChannel();
+            MappedByteBuffer bb = fc.map(FileChannel.MapMode.READ_ONLY, 0, fc.size());
+            /* Instead of using default, pass in a decoder. */
+            return Charset.defaultCharset().decode(bb).toString();
+        }
+        finally {
+            stream.close();
+        }
+    }
+    public static class SyntaxError extends Exception {
+        public SyntaxError(String message) {
+            super(message);
+        }
+    }
+    public interface SyntaxErrorFormatter {
+        /* Called when the parser runs out of tokens but isn't finished parsing. */
+        String unexpectedEof(String method, List<TerminalIdentifier> expected, List<String> nt_rules);
+        /* Called when the parser finished parsing but there are still tokens left in the stream. */
+        String excessTokens(String method, Terminal terminal);
+        /* Called when the parser is expecting one token and gets another. */
+        String unexpectedSymbol(String method, Terminal actual, List<TerminalIdentifier> expected, String rule);
+        /* Called when the parser is expecing a tokens but there are no more tokens. */
+        String noMoreTokens(String method, TerminalIdentifier expecting, Terminal last);
+        /* Invalid terminal is found in the token stream. */
+        String invalidTerminal(String method, Terminal invalid);
+        /* For lists that have a minimum required size which is not met */
+        String missingListItems(String method, int required, int found, Terminal last);
+        /* For lists that require a terminal to terminate each element in the list */
+        String missingTerminator(String method, TerminalIdentifier terminator, Terminal last);
+    }
+    public static class TokenStream extends ArrayList<Terminal> {
+        private int index;
+        public TokenStream(List<Terminal> terminals) {
+            super(terminals);
+            reset();
+        }
+        public TokenStream() {
+            reset();
+        }
+        public void reset() {
+            this.index = 0;
+        }
+        public Terminal advance() {
+            this.index += 1;
+            return this.current();
+        }
+        public Terminal current() {
+            try {
+                return this.get(this.index);
+            } catch (IndexOutOfBoundsException e) {
+                return null;
+            }
+        }
+        public Terminal last() {
+          return this.get(this.size() - 1);
+        }
+    }
+    public static class NonTerminal {
+        private int id;
+        private String string;
+        NonTerminal(int id, String string) {
+            this.id = id;
+            this.string = string;
+        }
+        public int getId() {
+            return this.id;
+        }
+        public String getString() {
+            return this.string;
+        }
+        public String toString() {
+            return this.string;
+        }
+    }
+    public interface AstTransform {}
+    public static class AstTransformNodeCreator implements AstTransform {
+        private String name;
+        private LinkedHashMap<String, Integer> parameters;
+        AstTransformNodeCreator(String name, LinkedHashMap<String, Integer> parameters) {
+            this.name = name;
+            this.parameters = parameters;
+        }
+        public Map<String, Integer> getParameters() {
+            return this.parameters;
+        }
+        public String getName() {
+            return this.name;
+        }
+        public String toString() {
+            LinkedList<String> items = new LinkedList<String>();
+            for (final Map.Entry<String, Integer> entry : this.parameters.entrySet()) {
+                items.add(entry.getKey() + "=$" + entry.getValue().toString());
+            }
+            return "AstNodeCreator: " + this.name + "( " + join(items, ", ") + " )";
+        }
+    }
+    public static class AstTransformSubstitution implements AstTransform {
+        private int index;
+        AstTransformSubstitution(int index) {
+            this.index = index;
+        }
+        public int getIndex() {
+            return this.index;
+        }
+        public String toString() {
+            return "AstSubstitution: $" + Integer.toString(this.index);
+        }
+    }
+    public interface AstNode {
+        public String toString();
+        public String toPrettyString();
+        public String toPrettyString(int indent);
+    }
+    public static class AstList extends ArrayList<AstNode> implements AstNode {
+        public String toString() {
+            return "[" + join(this, ", ") + "]";
+        }
+        public String toPrettyString() {
+            return toPrettyString(0);
+        }
+        public String toPrettyString(int indent) {
+            String spaces = getIndentString(indent);
+            if (this.size() == 0) {
+                return spaces + "[]";
+            }
+            ArrayList<String> elements = new ArrayList<String>();
+            for ( AstNode node : this ) {
+                elements.add(node.toPrettyString(indent + 2));
+            }
+            return spaces + "[\n" + join(elements, ",\n") + "\n" + spaces + "]";
+        }
+    }
+    public static class Ast implements AstNode {
+        private String name;
+        private Map<String, AstNode> attributes;
+        Ast(String name, Map<String, AstNode> attributes) {
+            this.name = name;
+            this.attributes = attributes;
+        }
+        public AstNode getAttribute(String name) {
+            return this.attributes.get(name);
+        }
+        public Map<String, AstNode> getAttributes() {
+            return this.attributes;
+        }
+        public String getName() {
+            return this.name;
+        }
+        public String toString() {
+            Formatter formatter = new Formatter(new StringBuilder(), Locale.US);
+            LinkedList<String> attributes = new LinkedList<String>();
+            for (final Map.Entry<String, AstNode> attribute : this.attributes.entrySet()) {
+                final String name = attribute.getKey();
+                final AstNode node = attribute.getValue();
+                final String nodeStr = (node == null) ? "None" : node.toString();
+                attributes.add(name + "=" + nodeStr);
+            }
+            formatter.format("(%s: %s)", this.name, join(attributes, ", "));
+            return formatter.toString();
+        }
+        public String toPrettyString() {
+            return toPrettyString(0);
+        }
+        public String toPrettyString(int indent) {
+            String spaces = getIndentString(indent);
+            ArrayList<String> children = new ArrayList<String>();
+            for( Map.Entry<String, AstNode> attribute : this.attributes.entrySet() ) {
+                String valueString = attribute.getValue() == null ? "None" : attribute.getValue().toPrettyString(indent + 2).trim();
+                children.add(spaces + "  " + attribute.getKey() + "=" + valueString);
+            }
+            return spaces + "(" + this.name + ":\n" + join(children, ",\n") + "\n" + spaces + ")";
+        }
+    }
+    public interface ParseTreeNode {
+        public AstNode toAst();
+        public String toString();
+        public String toPrettyString();
+        public String toPrettyString(int indent);
+    }
+    public static class Terminal implements AstNode, ParseTreeNode
+    {
+        public int id;
+        public String terminal_str;
+        public String source_string;
+        public String resource;
+        public int line;
+        public int col;
+        public Terminal(int id, String terminal_str, String source_string, String resource, int line, int col) {
+            this.id = id;
+            this.terminal_str = terminal_str;
+            this.source_string = source_string;
+            this.resource = resource;
+            this.line = line;
+            this.col = col;
+        }
+        public int getId() {
+            return this.id;
+        }
+        public String getTerminalStr() {
+            return this.terminal_str;
+        }
+        public String getSourceString() {
+            return this.source_string;
+        }
+        public String getResource() {
+            return this.resource;
+        }
+        public int getLine() {
+            return this.line;
+        }
+        public int getColumn() {
+            return this.col;
+        }
+        public String toString() {
+            byte[] source_string_bytes;
+            try {
+                source_string_bytes = this.getSourceString().getBytes("UTF-8");
+            } catch (java.io.UnsupportedEncodingException e) {
+                source_string_bytes = this.getSourceString().getBytes();
+            }
+            return String.format("<%s:%d:%d %s \"%s\">",
+                this.getResource(),
+                this.getLine(),
+                this.getColumn(),
+                this.getTerminalStr(),
+                Base64.encodeBase64String(source_string_bytes)
+            );
+        }
+        public String toPrettyString() {
+            return toPrettyString(0);
+        }
+        public String toPrettyString(int indent) {
+            return getIndentString(indent) + this.toString();
+        }
+        public AstNode toAst() { return this; }
+    }
+    public static class ParseTree implements ParseTreeNode {
+        private NonTerminal nonterminal;
+        private ArrayList<ParseTreeNode> children;
+        private boolean isExpr, isNud, isPrefix, isInfix, isExprNud;
+        private int nudMorphemeCount;
+        private int listSeparatorId;
+        private boolean list;
+        private AstTransform astTransform;
+        ParseTree(NonTerminal nonterminal) {
+            this.nonterminal = nonterminal;
+            this.children = new ArrayList<ParseTreeNode>();
+            this.astTransform = null;
+            this.isExpr = false;
+            this.isNud = false;
+            this.isPrefix = false;
+            this.isInfix = false;
+            this.isExprNud = false;
+            this.nudMorphemeCount = 0;
+            this.listSeparatorId = -1;
+            this.list = false;
+        }
+        public void setExpr(boolean value) { this.isExpr = value; }
+        public void setNud(boolean value) { this.isNud = value; }
+        public void setPrefix(boolean value) { this.isPrefix = value; }
+        public void setInfix(boolean value) { this.isInfix = value; }
+        public void setExprNud(boolean value) { this.isExprNud = value; }
+        public void setAstTransformation(AstTransform value) { this.astTransform = value; }
+        public void setNudMorphemeCount(int value) { this.nudMorphemeCount = value; }
+        public void setList(boolean value) { this.list = value; }
+        public void setListSeparator(int value) { this.listSeparatorId = value; }
+        public int getNudMorphemeCount() { return this.nudMorphemeCount; }
+        public List<ParseTreeNode> getChildren() { return this.children; }
+        public boolean isInfix() { return this.isInfix; }
+        public boolean isPrefix() { return this.isPrefix; }
+        public boolean isExpr() { return this.isExpr; }
+        public boolean isNud() { return this.isNud; }
+        public boolean isExprNud() { return this.isExprNud; }
+        public void add(ParseTreeNode tree) {
+            if (this.children == null) {
+                this.children = new ArrayList<ParseTreeNode>();
+            }
+            this.children.add(tree);
+        }
+        private boolean isCompoundNud() {
+            if ( this.children.size() > 0 && this.children.get(0) instanceof ParseTree ) {
+                ParseTree child = (ParseTree) this.children.get(0);
+                if ( child.isNud() && !child.isPrefix() && !this.isExprNud() && !this.isInfix() ) {
+                    return true;
+                }
+            }
+            return false;
+        }
+        public AstNode toAst() {
+            if ( this.list == true ) {
+                AstList astList = new AstList();
+                if ( this.children.size() == 0 ) {
+                    return astList;
+                }
+                for (int i = 0; i < this.children.size(); i++) {
+                    if (this.children.get(i) instanceof Terminal && this.listSeparatorId >= 0 &&
+                        ((Terminal) this.children.get(i)).id == this.listSeparatorId) {
+                        continue;
+                    }
+                    astList.add(this.children.get(i).toAst());
+                }
+                return astList;
+            } else if ( this.isExpr ) {
+                if ( this.astTransform instanceof AstTransformSubstitution ) {
+                    AstTransformSubstitution astSubstitution = (AstTransformSubstitution) astTransform;
+                    return this.children.get(astSubstitution.getIndex()).toAst();
+                } else if ( this.astTransform instanceof AstTransformNodeCreator ) {
+                    AstTransformNodeCreator astNodeCreator = (AstTransformNodeCreator) this.astTransform;
+                    LinkedHashMap<String, AstNode> parameters = new LinkedHashMap<String, AstNode>();
+                    ParseTreeNode child;
+                    for ( final Map.Entry<String, Integer> parameter : astNodeCreator.getParameters().entrySet() ) {
+                        String name = parameter.getKey();
+                        int index = parameter.getValue().intValue();
+                        if ( index == '$' ) {
+                            child = this.children.get(0);
+                        } else if ( this.isCompoundNud() ) {
+                            ParseTree firstChild = (ParseTree) this.children.get(0);
+                            if ( index < firstChild.getNudMorphemeCount() ) {
+                                child = firstChild.getChildren().get(index);
+                            } else {
+                                index = index - firstChild.getNudMorphemeCount() + 1;
+                                child = this.children.get(index);
+                            }
+                        } else if ( this.children.size() == 1 && !(this.children.get(0) instanceof ParseTree) && !(this.children.get(0) instanceof List) ) {
+                            // TODO: I don't think this should ever be called
+                            child = this.children.get(0);
+                        } else {
+                            child = this.children.get(index);
+                        }
+                        parameters.put(name, child.toAst());
+                    }
+                    return new Ast(astNodeCreator.getName(), parameters);
+                }
+            } else {
+                AstTransformSubstitution defaultAction = new AstTransformSubstitution(0);
+                AstTransform action = this.astTransform != null ? this.astTransform : defaultAction;
+                if (this.children.size() == 0) return null;
+                if (action instanceof AstTransformSubstitution) {
+                    AstTransformSubstitution astSubstitution = (AstTransformSubstitution) action;
+                    return this.children.get(astSubstitution.getIndex()).toAst();
+                } else if (action instanceof AstTransformNodeCreator) {
+                    AstTransformNodeCreator astNodeCreator = (AstTransformNodeCreator) action;
+                    LinkedHashMap<String, AstNode> evaluatedParameters = new LinkedHashMap<String, AstNode>();
+                    for ( Map.Entry<String, Integer> baseParameter : astNodeCreator.getParameters().entrySet() ) {
+                        String name = baseParameter.getKey();
+                        int index2 = baseParameter.getValue().intValue();
+                        evaluatedParameters.put(name, this.children.get(index2).toAst());
+                    }
+                    return new Ast(astNodeCreator.getName(), evaluatedParameters);
+                }
+            }
+            return null;
+        }
+        public String toString() {
+          ArrayList<String> children = new ArrayList<String>();
+          for (ParseTreeNode child : this.children) {
+            children.add(child.toString());
+          }
+          return "(" + this.nonterminal.getString() + ": " + join(children, ", ") + ")";
+        }
+        public String toPrettyString() {
+          return toPrettyString(0);
+        }
+        public String toPrettyString(int indent) {
+          if (this.children.size() == 0) {
+            return "(" + this.nonterminal.toString() + ": )";
+          }
+          String spaces = getIndentString(indent);
+          ArrayList<String> children = new ArrayList<String>();
+          for ( ParseTreeNode node : this.children ) {
+            String sub = node.toPrettyString(indent + 2).trim();
+            children.add(spaces + "  " +  sub);
+          }
+          return spaces + "(" + this.nonterminal.toString() + ":\n" + join(children, ",\n") + "\n" + spaces + ")";
+        }
+    }
+    private static class ParserContext {
+        public TokenStream tokens;
+        public SyntaxErrorFormatter error_formatter;
+        public String nonterminal;
+        public String rule;
+        public ParserContext(TokenStream tokens, SyntaxErrorFormatter error_formatter) {
+            this.tokens = tokens;
+            this.error_formatter = error_formatter;
+        }
+    }
+    private static class DefaultSyntaxErrorFormatter implements SyntaxErrorFormatter {
+        public String unexpectedEof(String method, List<TerminalIdentifier> expected, List<String> nt_rules) {
+            return "Error: unexpected end of file";
+        }
+        public String excessTokens(String method, Terminal terminal) {
+            return "Finished parsing without consuming all tokens.";
+        }
+        public String unexpectedSymbol(String method, Terminal actual, List<TerminalIdentifier> expected, String rule) {
+            ArrayList<String> expected_terminals = new ArrayList<String>();
+            for ( TerminalIdentifier e : expected ) {
+                expected_terminals.add(e.string());
+            }
+            return String.format(
+                "Unexpected symbol (line %d, col %d) when parsing parse_%s.  Expected %s, got %s.",
+                actual.getLine(), actual.getColumn(), method, join(expected_terminals, ", "), actual.toPrettyString()
+            );
+        }
+        public String noMoreTokens(String method, TerminalIdentifier expecting, Terminal last) {
+            return "No more tokens.  Expecting " + expecting.string();
+        }
+        public String invalidTerminal(String method, Terminal invalid) {
+            return "Invalid symbol ID: "+invalid.getId()+" ("+invalid.getTerminalStr()+")";
+        }
+        public String missingListItems(String method, int required, int found, Terminal last) {
+            return "List for "+method+" requires "+required+" items but only "+found+" were found.";
+        }
+        public String missingTerminator(String method, TerminalIdentifier terminator, Terminal last) {
+            return "List for "+method+" is missing a terminator";
+        }
+    }
+    public interface TerminalMap {
+        TerminalIdentifier get(String string);
+        TerminalIdentifier get(int id);
+        boolean isValid(String string);
+        boolean isValid(int id);
+    }
+    public static class WdlTerminalMap implements TerminalMap {
+        private Map<Integer, TerminalIdentifier> id_to_term;
+        private Map<String, TerminalIdentifier> str_to_term;
+        WdlTerminalMap(WdlTerminalIdentifier[] terminals) {
+            id_to_term = new HashMap<Integer, TerminalIdentifier>();
+            str_to_term = new HashMap<String, TerminalIdentifier>();
+            for( WdlTerminalIdentifier terminal : terminals ) {
+                Integer id = new Integer(terminal.id());
+                String str = terminal.string();
+                id_to_term.put(id, terminal);
+                str_to_term.put(str, terminal);
+            }
+        }
+        public TerminalIdentifier get(String string) { return this.str_to_term.get(string); }
+        public TerminalIdentifier get(int id) { return this.id_to_term.get(id); }
+        public boolean isValid(String string) { return this.str_to_term.containsKey(string); }
+        public boolean isValid(int id) { return this.id_to_term.containsKey(id); }
+    }
+    public interface TerminalIdentifier {
+        public int id();
+        public String string();
+    }
+    public enum WdlTerminalIdentifier implements TerminalIdentifier {
+        TERMINAL_AFTER(11, "after"),
+        TERMINAL_ALIAS(18, "alias"),
+        TERMINAL_AS(7, "as"),
+        TERMINAL_ASTERISK(3, "asterisk"),
+        TERMINAL_BOOLEAN(30, "boolean"),
+        TERMINAL_CALL(19, "call"),
+        TERMINAL_CMD_ATTR_HINT(33, "cmd_attr_hint"),
+        TERMINAL_CMD_PART(46, "cmd_part"),
+        TERMINAL_COLON(37, "colon"),
+        TERMINAL_COMMA(38, "comma"),
+        TERMINAL_DASH(63, "dash"),
+        TERMINAL_DOT(62, "dot"),
+        TERMINAL_DOUBLE_AMPERSAND(13, "double_ampersand"),
+        TERMINAL_DOUBLE_EQUAL(24, "double_equal"),
+        TERMINAL_DOUBLE_PIPE(25, "double_pipe"),
+        TERMINAL_E(36, "e"),
+        TERMINAL_ELSE(41, "else"),
+        TERMINAL_EQUAL(53, "equal"),
+        TERMINAL_ESCAPE(31, "escape"),
+        TERMINAL_EXPRESSION_PLACEHOLDER_END(35, "expression_placeholder_end"),
+        TERMINAL_EXPRESSION_PLACEHOLDER_START(42, "expression_placeholder_start"),
+        TERMINAL_FLOAT(56, "float"),
+        TERMINAL_FQN(22, "fqn"),
+        TERMINAL_GT(4, "gt"),
+        TERMINAL_GTEQ(21, "gteq"),
+        TERMINAL_IDENTIFIER(23, "identifier"),
+        TERMINAL_IF(61, "if"),
+        TERMINAL_IMPORT(6, "import"),
+        TERMINAL_IN(17, "in"),
+        TERMINAL_INPUT(49, "input"),
+        TERMINAL_INTEGER(48, "integer"),
+        TERMINAL_LBRACE(32, "lbrace"),
+        TERMINAL_LPAREN(12, "lparen"),
+        TERMINAL_LSQUARE(51, "lsquare"),
+        TERMINAL_LT(65, "lt"),
+        TERMINAL_LTEQ(1, "lteq"),
+        TERMINAL_META(45, "meta"),
+        TERMINAL_META_VALUE(16, "meta_value"),
+        TERMINAL_NONE(44, "none"),
+        TERMINAL_NOT(60, "not"),
+        TERMINAL_NOT_EQUAL(14, "not_equal"),
+        TERMINAL_NULL(40, "null"),
+        TERMINAL_OBJECT(59, "object"),
+        TERMINAL_OUTPUT(28, "output"),
+        TERMINAL_PARAMETER_META(15, "parameter_meta"),
+        TERMINAL_PERCENT(5, "percent"),
+        TERMINAL_PLUS(9, "plus"),
+        TERMINAL_QMARK(57, "qmark"),
+        TERMINAL_QUOTE(50, "quote"),
+        TERMINAL_RAW_CMD_END(58, "raw_cmd_end"),
+        TERMINAL_RAW_CMD_START(27, "raw_cmd_start"),
+        TERMINAL_RAW_COMMAND(39, "raw_command"),
+        TERMINAL_RBRACE(0, "rbrace"),
+        TERMINAL_RPAREN(52, "rparen"),
+        TERMINAL_RSQUARE(8, "rsquare"),
+        TERMINAL_RUNTIME(54, "runtime"),
+        TERMINAL_SCATTER(66, "scatter"),
+        TERMINAL_SLASH(29, "slash"),
+        TERMINAL_STRING(26, "string"),
+        TERMINAL_STRUCT(34, "struct"),
+        TERMINAL_TASK(10, "task"),
+        TERMINAL_THEN(2, "then"),
+        TERMINAL_TYPE(43, "type"),
+        TERMINAL_TYPE_E(20, "type_e"),
+        TERMINAL_VERSION(64, "version"),
+        TERMINAL_VERSION_NAME(55, "version_name"),
+        TERMINAL_WORKFLOW(47, "workflow"),
+        END_SENTINAL(-3, "END_SENTINAL");
+        private final int id;
+        private final String string;
+        WdlTerminalIdentifier(int id, String string) {
+            this.id = id;
+            this.string = string;
+        }
+        public int id() {return id;}
+        public String string() {return string;}
+    }
+    /* table[nonterminal][terminal] = rule */
+    private static final int[][] table = {
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 25, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 85, -1, -1, -1, -1, -1 },
+        { 52, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 52, -1, -1, 52, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 52, -1, -1, -1, -1, -1, -1, -1, -1, -1, 51, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 68, -1, -1, -1, 62, 63, -1, -1, 63, -1, -1, -1, -1, 67, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 63, -1, 69, -1, -1, -1, 66, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 64, -1, -1, -1, -1, 65 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 47, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 75, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 88, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 50, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { 74, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 74, -1, -1, -1, 74, 74, -1, -1, 74, -1, -1, -1, -1, 74, -1, -1, -1, 73, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 74, -1, 74, -1, -1, -1, 74, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 74, -1, -1, -1, -1, 74 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 45, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { 71, -1, -1, -1, -1, -1, -1, 70, -1, -1, -1, 71, -1, -1, -1, 71, -1, -1, -1, 71, 71, -1, -1, 71, -1, -1, -1, -1, 71, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 71, -1, 71, -1, -1, -1, 71, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 71, -1, -1, -1, -1, 71 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 23, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 41, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 6, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, 56, -1, -1, 56, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 56, -1, -1, -1, -1, -1, -1, 56, -1, 56, -1, -1, -1, 56, -1, -1, -1, -1, -1, -1, -1, 56, -1, -1, -1, 56, -1, 56, 56, -1, -1, -1, -1, 56, -1, -1, 56, 56, 56, -1, 56, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, 21, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 39, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 36, -1, -1, -1, 35, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, 22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
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+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 82, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 2, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 42, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 38, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 80, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 30, -1, -1, -1, -1, 32, -1, -1, 32, -1, -1, -1, -1, 28, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 26, -1, -1, -1, 32, -1, 31, -1, -1, -1, 27, -1, -1, -1, -1, 29, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 84, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 54, -1, -1, 54, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 54, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+    };
+    static {
+        Map<Integer, List<TerminalIdentifier>> map = new HashMap<Integer, List<TerminalIdentifier>>();
+        map.put(96, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+        }));
+        map.put(98, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(121, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(74, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(110, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(70, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_EQUAL,
+        }));
+        map.put(67, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(81, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AS,
+        }));
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AFTER,
+        }));
+        map.put(78, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+        }));
+        map.put(117, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+        }));
+        map.put(140, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(119, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(104, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_META_VALUE,
+            WdlTerminalIdentifier.TERMINAL_NULL,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(89, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(80, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(92, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(109, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(141, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AS,
+        }));
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ALIAS,
+        }));
+        map.put(120, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(100, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CMD_PART,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+        }));
+        map.put(73, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
+        }));
+        map.put(116, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AS,
+        }));
+        map.put(75, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+        }));
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AFTER,
+        }));
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+        }));
+        map.put(105, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+        }));
+        map.put(95, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+        }));
+        map.put(88, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CMD_PART,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+        }));
+        map.put(139, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_VERSION,
+        }));
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+        }));
+        map.put(87, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
+        }));
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(69, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IF,
+        }));
+        map.put(86, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+        }));
+        map.put(82, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ALIAS,
+        }));
+        map.put(91, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AS,
+        }));
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(76, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(83, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+        }));
+        map.put(79, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(85, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_META,
+        }));
+        map.put(77, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(115, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+        }));
+        map.put(113, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_META_VALUE,
+            WdlTerminalIdentifier.TERMINAL_NULL,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(114, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(107, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(111, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+        }));
+        map.put(72, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+        }));
+        map.put(93, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+        }));
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+        }));
+        map.put(103, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+        }));
+        map.put(99, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_EQUAL,
+        }));
+        map.put(106, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(118, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(97, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(102, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+        }));
+        map.put(112, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(68, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_TASK,
+        }));
+        map.put(137, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(101, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(84, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_VERSION,
+        }));
+        map.put(71, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(138, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_META,
+        }));
+        map.put(108, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+        }));
+        map.put(94, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        nonterminal_first = Collections.unmodifiableMap(map);
+    }
+    static {
+        Map<Integer, List<TerminalIdentifier>> map = new HashMap<Integer, List<TerminalIdentifier>>();
+        map.put(96, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(98, Arrays.asList(new TerminalIdentifier[] {
+        }));
+        map.put(121, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(74, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(110, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(70, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(67, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(81, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AFTER,
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(78, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(117, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(140, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(119, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(104, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RSQUARE,
+        }));
+        map.put(89, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RSQUARE,
+        }));
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RPAREN,
+            WdlTerminalIdentifier.TERMINAL_RSQUARE,
+        }));
+        map.put(80, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(92, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(109, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(141, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ALIAS,
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(120, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(100, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
+        }));
+        map.put(73, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(116, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AFTER,
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(75, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AFTER,
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(105, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(95, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(88, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CMD_PART,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+            WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
+        }));
+        map.put(139, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+        }));
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ASTERISK,
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
+            WdlTerminalIdentifier.TERMINAL_COLON,
+            WdlTerminalIdentifier.TERMINAL_COMMA,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_DOT,
+            WdlTerminalIdentifier.TERMINAL_DOUBLE_AMPERSAND,
+            WdlTerminalIdentifier.TERMINAL_DOUBLE_EQUAL,
+            WdlTerminalIdentifier.TERMINAL_DOUBLE_PIPE,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_ELSE,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_END,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_GT,
+            WdlTerminalIdentifier.TERMINAL_GTEQ,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_LT,
+            WdlTerminalIdentifier.TERMINAL_LTEQ,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_NOT_EQUAL,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_PERCENT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RPAREN,
+            WdlTerminalIdentifier.TERMINAL_RSQUARE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_SLASH,
+            WdlTerminalIdentifier.TERMINAL_THEN,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CMD_PART,
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+            WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(87, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(69, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(86, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(82, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ALIAS,
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(91, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ALIAS,
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(76, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_COMMA,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(83, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(79, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(85, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_COMMA,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(77, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_COMMA,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(115, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(113, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_COMMA,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RSQUARE,
+        }));
+        map.put(114, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_COMMA,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(107, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(111, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(72, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(93, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(103, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(99, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(106, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AS,
+            WdlTerminalIdentifier.TERMINAL_COMMA,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RSQUARE,
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(118, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(97, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ASTERISK,
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
+            WdlTerminalIdentifier.TERMINAL_COLON,
+            WdlTerminalIdentifier.TERMINAL_COMMA,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_DOT,
+            WdlTerminalIdentifier.TERMINAL_DOUBLE_AMPERSAND,
+            WdlTerminalIdentifier.TERMINAL_DOUBLE_EQUAL,
+            WdlTerminalIdentifier.TERMINAL_DOUBLE_PIPE,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_ELSE,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_END,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_GT,
+            WdlTerminalIdentifier.TERMINAL_GTEQ,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_LT,
+            WdlTerminalIdentifier.TERMINAL_LTEQ,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_NOT_EQUAL,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_PERCENT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RPAREN,
+            WdlTerminalIdentifier.TERMINAL_RSQUARE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_SLASH,
+            WdlTerminalIdentifier.TERMINAL_THEN,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(102, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(112, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(68, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(137, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(101, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_COMMA,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_RSQUARE,
+        }));
+        map.put(84, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+        }));
+        map.put(71, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(138, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(108, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(94, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        nonterminal_follow = Collections.unmodifiableMap(map);
+    }
+    static {
+        Map<Integer, List<TerminalIdentifier>> map = new HashMap<Integer, List<TerminalIdentifier>>();
+        map.put(0, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+        }));
+        map.put(1, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+            WdlTerminalIdentifier.TERMINAL_TASK,
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(40, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(43, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(48, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(51, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_EQUAL,
+        }));
+        map.put(52, Arrays.asList(new TerminalIdentifier[] {
+        }));
+        map.put(57, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(60, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(70, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AS,
+        }));
+        map.put(71, Arrays.asList(new TerminalIdentifier[] {
+        }));
+        map.put(72, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AFTER,
+        }));
+        map.put(73, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+        }));
+        map.put(74, Arrays.asList(new TerminalIdentifier[] {
+        }));
+        map.put(76, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+        }));
+        map.put(77, Arrays.asList(new TerminalIdentifier[] {
+        }));
+        map.put(7, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(79, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(94, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_META_VALUE,
+            WdlTerminalIdentifier.TERMINAL_NULL,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(96, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(98, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(120, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(10, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(12, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(18, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AS,
+        }));
+        map.put(19, Arrays.asList(new TerminalIdentifier[] {
+        }));
+        map.put(20, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ALIAS,
+        }));
+        map.put(24, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+            WdlTerminalIdentifier.TERMINAL_META,
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(33, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CMD_PART,
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+        }));
+        map.put(37, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
+        }));
+        map.put(81, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AS,
+        }));
+        map.put(75, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+        }));
+        map.put(82, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AFTER,
+        }));
+        map.put(80, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+        }));
+        map.put(78, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+        }));
+        map.put(34, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+        }));
+        map.put(36, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+        }));
+        map.put(35, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CMD_PART,
+        }));
+        map.put(54, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(2, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_VERSION,
+        }));
+        map.put(114, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(113, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(105, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(106, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(104, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(110, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(111, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(108, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(109, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(107, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(116, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(112, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(115, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+        }));
+        map.put(119, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_DASH,
+        }));
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+        }));
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(121, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IF,
+        }));
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+        }));
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+        }));
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+        }));
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+        }));
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_NONE,
+        }));
+        map.put(117, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_NOT,
+        }));
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+        }));
+        map.put(118, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+        }));
+        map.put(38, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+        }));
+        map.put(39, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
+        }));
+        map.put(5, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+        }));
+        map.put(4, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_TASK,
+        }));
+        map.put(3, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        map.put(85, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IF,
+        }));
+        map.put(21, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IMPORT,
+        }));
+        map.put(23, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ALIAS,
+        }));
+        map.put(22, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_AS,
+        }));
+        map.put(53, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(88, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(41, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+        }));
+        map.put(45, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(56, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+            WdlTerminalIdentifier.TERMINAL_DASH,
+            WdlTerminalIdentifier.TERMINAL_E,
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_IF,
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+            WdlTerminalIdentifier.TERMINAL_LPAREN,
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+            WdlTerminalIdentifier.TERMINAL_NONE,
+            WdlTerminalIdentifier.TERMINAL_NOT,
+            WdlTerminalIdentifier.TERMINAL_OBJECT,
+            WdlTerminalIdentifier.TERMINAL_PLUS,
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(46, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_META,
+        }));
+        map.put(50, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(49, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+        }));
+        map.put(89, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+        }));
+        map.put(92, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_FLOAT,
+        }));
+        map.put(91, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_INTEGER,
+        }));
+        map.put(97, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+        }));
+        map.put(95, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LSQUARE,
+        }));
+        map.put(93, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_NULL,
+        }));
+        map.put(87, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(59, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(58, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+        }));
+        map.put(47, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+        }));
+        map.put(44, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_LBRACE,
+        }));
+        map.put(42, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+        }));
+        map.put(86, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+        }));
+        map.put(55, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_EQUAL,
+        }));
+        map.put(11, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(15, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+        }));
+        map.put(14, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(13, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_QUOTE,
+        }));
+        map.put(17, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+        }));
+        map.put(16, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_ESCAPE,
+            WdlTerminalIdentifier.TERMINAL_STRING,
+        }));
+        map.put(8, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_STRUCT,
+        }));
+        map.put(9, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(25, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_TASK,
+        }));
+        map.put(26, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+        }));
+        map.put(32, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(27, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+        }));
+        map.put(31, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_META,
+        }));
+        map.put(28, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+        }));
+        map.put(30, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+        }));
+        map.put(29, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RUNTIME,
+        }));
+        map.put(103, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(102, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+        }));
+        map.put(99, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+        }));
+        map.put(101, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+        }));
+        map.put(100, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+        }));
+        map.put(6, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_VERSION,
+        }));
+        map.put(62, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_CALL,
+        }));
+        map.put(63, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+            WdlTerminalIdentifier.TERMINAL_TYPE,
+            WdlTerminalIdentifier.TERMINAL_TYPE_E,
+        }));
+        map.put(64, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IF,
+        }));
+        map.put(66, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_INPUT,
+        }));
+        map.put(67, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_OUTPUT,
+        }));
+        map.put(65, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_SCATTER,
+        }));
+        map.put(69, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_META,
+        }));
+        map.put(68, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+        }));
+        map.put(84, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_META,
+        }));
+        map.put(83, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+        }));
+        map.put(61, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+        }));
+        rule_first = Collections.unmodifiableMap(map);
+    }
+    static {
+        Map<Integer, List<String>> map = new HashMap<Integer, List<String>>();
+        map.put(96, new ArrayList<String>());
+        map.put(98, new ArrayList<String>());
+        map.put(121, new ArrayList<String>());
+        map.put(74, new ArrayList<String>());
+        map.put(110, new ArrayList<String>());
+        map.put(70, new ArrayList<String>());
+        map.put(67, new ArrayList<String>());
+        map.put(123, new ArrayList<String>());
+        map.put(81, new ArrayList<String>());
+        map.put(132, new ArrayList<String>());
+        map.put(78, new ArrayList<String>());
+        map.put(117, new ArrayList<String>());
+        map.put(140, new ArrayList<String>());
+        map.put(119, new ArrayList<String>());
+        map.put(104, new ArrayList<String>());
+        map.put(89, new ArrayList<String>());
+        map.put(129, new ArrayList<String>());
+        map.put(127, new ArrayList<String>());
+        map.put(80, new ArrayList<String>());
+        map.put(92, new ArrayList<String>());
+        map.put(109, new ArrayList<String>());
+        map.put(141, new ArrayList<String>());
+        map.put(122, new ArrayList<String>());
+        map.put(124, new ArrayList<String>());
+        map.put(120, new ArrayList<String>());
+        map.put(100, new ArrayList<String>());
+        map.put(73, new ArrayList<String>());
+        map.put(116, new ArrayList<String>());
+        map.put(75, new ArrayList<String>());
+        map.put(128, new ArrayList<String>());
+        map.put(136, new ArrayList<String>());
+        map.put(105, new ArrayList<String>());
+        map.put(95, new ArrayList<String>());
+        map.put(88, new ArrayList<String>());
+        map.put(139, new ArrayList<String>());
+        map.put(130, new ArrayList<String>());
+        map.put(135, new ArrayList<String>());
+        map.put(133, new ArrayList<String>());
+        map.put(87, new ArrayList<String>());
+        map.put(134, new ArrayList<String>());
+        map.put(69, new ArrayList<String>());
+        map.put(86, new ArrayList<String>());
+        map.put(82, new ArrayList<String>());
+        map.put(91, new ArrayList<String>());
+        map.put(125, new ArrayList<String>());
+        map.put(76, new ArrayList<String>());
+        map.put(83, new ArrayList<String>());
+        map.put(79, new ArrayList<String>());
+        map.put(85, new ArrayList<String>());
+        map.put(126, new ArrayList<String>());
+        map.put(77, new ArrayList<String>());
+        map.put(115, new ArrayList<String>());
+        map.put(113, new ArrayList<String>());
+        map.put(114, new ArrayList<String>());
+        map.put(107, new ArrayList<String>());
+        map.put(111, new ArrayList<String>());
+        map.put(72, new ArrayList<String>());
+        map.put(93, new ArrayList<String>());
+        map.put(131, new ArrayList<String>());
+        map.put(103, new ArrayList<String>());
+        map.put(99, new ArrayList<String>());
+        map.put(106, new ArrayList<String>());
+        map.put(118, new ArrayList<String>());
+        map.put(97, new ArrayList<String>());
+        map.put(102, new ArrayList<String>());
+        map.put(90, new ArrayList<String>());
+        map.put(112, new ArrayList<String>());
+        map.put(68, new ArrayList<String>());
+        map.put(137, new ArrayList<String>());
+        map.put(101, new ArrayList<String>());
+        map.put(84, new ArrayList<String>());
+        map.put(71, new ArrayList<String>());
+        map.put(138, new ArrayList<String>());
+        map.put(108, new ArrayList<String>());
+        map.put(94, new ArrayList<String>());
+        map.get(96).add("$_gen0 = list($import)");
+        map.get(98).add("$_gen1 = list($file_body_element)");
+        map.get(121).add("$_gen10 = list($input_declaration)");
+        map.get(74).add("$_gen11 = list($kv)");
+        map.get(110).add("$_gen12 = list($meta_kv)");
+        map.get(70).add("$_gen13 = $setter");
+        map.get(70).add("$_gen13 = :_empty");
+        map.get(67).add("$_gen14 = list($output_kv)");
+        map.get(123).add("$_gen15 = list($wf_body_element)");
+        map.get(81).add("$_gen16 = $alias");
+        map.get(81).add("$_gen16 = :_empty");
+        map.get(132).add("$_gen17 = list($call_after)");
+        map.get(78).add("$_gen18 = $call_brace_block");
+        map.get(78).add("$_gen18 = :_empty");
+        map.get(117).add("$_gen19 = $call_body");
+        map.get(117).add("$_gen19 = :_empty");
+        map.get(140).add("$_gen2 = list($struct_declaration)");
+        map.get(119).add("$_gen20 = list($input_kv, :comma)");
+        map.get(104).add("$_gen21 = list($meta_value, :comma)");
+        map.get(89).add("$_gen22 = list($meta_kv, :comma)");
+        map.get(129).add("$_gen23 = list($type_e, :comma)");
+        map.get(127).add("$_gen24 = list($e, :comma)");
+        map.get(80).add("$_gen25 = list($object_kv, :comma)");
+        map.get(92).add("$_gen26 = list($map_kv, :comma)");
+        map.get(109).add("$_gen3 = list($static_string_piece)");
+        map.get(141).add("$_gen4 = list($string_piece)");
+        map.get(122).add("$_gen5 = $import_namespace");
+        map.get(122).add("$_gen5 = :_empty");
+        map.get(124).add("$_gen6 = list($import_alias)");
+        map.get(120).add("$_gen7 = list($task_sections)");
+        map.get(100).add("$_gen8 = list($command_part)");
+        map.get(73).add("$_gen9 = list($expression_placeholder_kv)");
+        map.get(116).add("$alias = :as :identifier -> $1");
+        map.get(75).add("$call = :call :fqn $_gen16 $_gen17 $_gen18 -> Call( task=$1, alias=$2, after=$3, body=$4 )");
+        map.get(128).add("$call_after = :after :identifier -> $1");
+        map.get(136).add("$call_body = :input :colon $_gen20 -> CallBody( inputs=$2 )");
+        map.get(105).add("$call_brace_block = :lbrace $_gen19 :rbrace -> $1");
+        map.get(95).add("$command = :raw_command :raw_cmd_start $_gen8 :raw_cmd_end -> RawCommand( parts=$2 )");
+        map.get(88).add("$command_part = $expression_placeholder");
+        map.get(88).add("$command_part = :cmd_part");
+        map.get(139).add("$declaration = $type_e :identifier $setter -> Declaration( type=$0, name=$1, expression=$2 )");
+        map.get(130).add("$document = $version $_gen0 $_gen1 -> Draft3File( version=$0, imports=$1, body=$2 )");
+        map.get(135).add("$e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :plus $e -> Add( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e :slash $e -> Divide( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
+        map.get(135).add("$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
+        map.get(135).add("$e = $string_literal");
+        map.get(135).add("$e = :boolean");
+        map.get(135).add("$e = :dash $e -> UnaryNegation( expression=$1 )");
+        map.get(135).add("$e = :float");
+        map.get(135).add("$e = :identifier");
+        map.get(135).add("$e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 )");
+        map.get(135).add("$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
+        map.get(135).add("$e = :integer");
+        map.get(135).add("$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
+        map.get(135).add("$e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 )");
+        map.get(135).add("$e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 )");
+        map.get(135).add("$e = :none");
+        map.get(135).add("$e = :not $e -> LogicalNot( expression=$1 )");
+        map.get(135).add("$e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 )");
+        map.get(135).add("$e = :plus $e -> UnaryPlus( expression=$1 )");
+        map.get(133).add("$expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 )");
+        map.get(87).add("$expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 )");
+        map.get(134).add("$file_body_element = $struct");
+        map.get(134).add("$file_body_element = $task");
+        map.get(134).add("$file_body_element = $workflow");
+        map.get(69).add("$if_stmt = :if :lparen $e :rparen :lbrace $_gen15 :rbrace -> If( expression=$2, body=$5 )");
+        map.get(86).add("$import = :import $static_string $_gen5 $_gen6 -> Import( uri=$1, namespace=$2, aliases=$3 )");
+        map.get(82).add("$import_alias = :alias :identifier :as :identifier -> ImportAlias( old_name=$1, new_name=$3 )");
+        map.get(91).add("$import_namespace = :as :identifier -> $1");
+        map.get(125).add("$input_declaration = $type_e :identifier $_gen13 -> InputDeclaration( type=$0, name=$1, expression=$2 )");
+        map.get(76).add("$input_kv = :identifier :equal $e -> ObjectKV( key=$0, value=$2 )");
+        map.get(83).add("$inputs = :input :lbrace $_gen10 :rbrace -> Inputs( inputs=$2 )");
+        map.get(79).add("$kv = :identifier :colon $e -> RuntimeAttribute( key=$0, value=$2 )");
+        map.get(85).add("$map_kv = $e :colon $e -> MapLiteralKv( key=$0, value=$2 )");
+        map.get(126).add("$meta = :meta $meta_map -> Meta( map=$1 )");
+        map.get(77).add("$meta_kv = :identifier :colon $meta_value -> MetaKvPair( key=$0, value=$2 )");
+        map.get(115).add("$meta_map = :lbrace $_gen12 :rbrace -> $1");
+        map.get(113).add("$meta_value = $static_string");
+        map.get(113).add("$meta_value = :boolean");
+        map.get(113).add("$meta_value = :float");
+        map.get(113).add("$meta_value = :integer");
+        map.get(113).add("$meta_value = :lbrace $_gen22 :rbrace -> MetaObject( map=$1 )");
+        map.get(113).add("$meta_value = :lsquare $_gen21 :rsquare -> MetaArray( values=$1 )");
+        map.get(113).add("$meta_value = :null");
+        map.get(114).add("$object_kv = :identifier :colon $e -> ObjectKV( key=$0, value=$2 )");
+        map.get(107).add("$output_kv = $type_e :identifier :equal $e -> Output( type=$0, name=$1, expression=$3 )");
+        map.get(111).add("$outputs = :output :lbrace $_gen14 :rbrace -> Outputs( outputs=$2 )");
+        map.get(72).add("$parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
+        map.get(93).add("$rt_map = :lbrace $_gen11 :rbrace -> $1");
+        map.get(131).add("$runtime = :runtime $rt_map -> Runtime( map=$1 )");
+        map.get(103).add("$scatter = :scatter :lparen :identifier :in $e :rparen :lbrace $_gen15 :rbrace -> Scatter( item=$2, collection=$4, body=$7 )");
+        map.get(99).add("$setter = :equal $e -> $1");
+        map.get(106).add("$static_string = :quote $_gen3 :quote -> StaticString( value=$1 )");
+        map.get(118).add("$static_string_piece = :escape");
+        map.get(118).add("$static_string_piece = :string");
+        map.get(97).add("$string_literal = :quote $_gen4 :quote -> StringLiteral( pieces=$1 )");
+        map.get(102).add("$string_piece = $expression_placeholder");
+        map.get(102).add("$string_piece = $static_string_piece");
+        map.get(90).add("$struct = :struct :identifier :lbrace $_gen2 :rbrace -> Struct( name=$1, entries=$3 )");
+        map.get(112).add("$struct_declaration = $type_e :identifier -> StructEntry( type=$0, name=$1 )");
+        map.get(68).add("$task = :task :identifier :lbrace $_gen7 :rbrace -> Task( name=$1, sections=$3 )");
+        map.get(137).add("$task_sections = $command");
+        map.get(137).add("$task_sections = $declaration");
+        map.get(137).add("$task_sections = $inputs");
+        map.get(137).add("$task_sections = $meta");
+        map.get(137).add("$task_sections = $outputs");
+        map.get(137).add("$task_sections = $parameter_meta");
+        map.get(137).add("$task_sections = $runtime");
+        map.get(101).add("$type_e = :identifier");
+        map.get(101).add("$type_e = :type");
+        map.get(101).add("$type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 )");
+        map.get(101).add("$type_e = :type <=> :plus -> NonEmptyType( innerType=$0 )");
+        map.get(101).add("$type_e = :type <=> :qmark -> OptionalType( innerType=$0 )");
+        map.get(84).add("$version = :version :version_name -> VersionDeclaration( v=$1 )");
+        map.get(71).add("$wf_body_element = $call");
+        map.get(71).add("$wf_body_element = $declaration");
+        map.get(71).add("$wf_body_element = $if_stmt");
+        map.get(71).add("$wf_body_element = $inputs");
+        map.get(71).add("$wf_body_element = $outputs");
+        map.get(71).add("$wf_body_element = $scatter");
+        map.get(71).add("$wf_body_element = $wf_meta");
+        map.get(71).add("$wf_body_element = $wf_parameter_meta");
+        map.get(138).add("$wf_meta = :meta $meta_map -> Meta( map=$1 )");
+        map.get(108).add("$wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
+        map.get(94).add("$workflow = :workflow :identifier :lbrace $_gen15 :rbrace -> Workflow( name=$1, body=$3 )");
+        nonterminal_rules = Collections.unmodifiableMap(map);
+    }
+    static {
+        Map<Integer, String> map = new HashMap<Integer, String>();
+        map.put(new Integer(0), "$_gen0 = list($import)");
+        map.put(new Integer(1), "$_gen1 = list($file_body_element)");
+        map.put(new Integer(40), "$_gen10 = list($input_declaration)");
+        map.put(new Integer(43), "$_gen11 = list($kv)");
+        map.put(new Integer(48), "$_gen12 = list($meta_kv)");
+        map.put(new Integer(51), "$_gen13 = $setter");
+        map.put(new Integer(52), "$_gen13 = :_empty");
+        map.put(new Integer(57), "$_gen14 = list($output_kv)");
+        map.put(new Integer(60), "$_gen15 = list($wf_body_element)");
+        map.put(new Integer(70), "$_gen16 = $alias");
+        map.put(new Integer(71), "$_gen16 = :_empty");
+        map.put(new Integer(72), "$_gen17 = list($call_after)");
+        map.put(new Integer(73), "$_gen18 = $call_brace_block");
+        map.put(new Integer(74), "$_gen18 = :_empty");
+        map.put(new Integer(76), "$_gen19 = $call_body");
+        map.put(new Integer(77), "$_gen19 = :_empty");
+        map.put(new Integer(7), "$_gen2 = list($struct_declaration)");
+        map.put(new Integer(79), "$_gen20 = list($input_kv, :comma)");
+        map.put(new Integer(94), "$_gen21 = list($meta_value, :comma)");
+        map.put(new Integer(96), "$_gen22 = list($meta_kv, :comma)");
+        map.put(new Integer(98), "$_gen23 = list($type_e, :comma)");
+        map.put(new Integer(120), "$_gen24 = list($e, :comma)");
+        map.put(new Integer(124), "$_gen25 = list($object_kv, :comma)");
+        map.put(new Integer(127), "$_gen26 = list($map_kv, :comma)");
+        map.put(new Integer(10), "$_gen3 = list($static_string_piece)");
+        map.put(new Integer(12), "$_gen4 = list($string_piece)");
+        map.put(new Integer(18), "$_gen5 = $import_namespace");
+        map.put(new Integer(19), "$_gen5 = :_empty");
+        map.put(new Integer(20), "$_gen6 = list($import_alias)");
+        map.put(new Integer(24), "$_gen7 = list($task_sections)");
+        map.put(new Integer(33), "$_gen8 = list($command_part)");
+        map.put(new Integer(37), "$_gen9 = list($expression_placeholder_kv)");
+        map.put(new Integer(81), "$alias = :as :identifier -> $1");
+        map.put(new Integer(75), "$call = :call :fqn $_gen16 $_gen17 $_gen18 -> Call( task=$1, alias=$2, after=$3, body=$4 )");
+        map.put(new Integer(82), "$call_after = :after :identifier -> $1");
+        map.put(new Integer(80), "$call_body = :input :colon $_gen20 -> CallBody( inputs=$2 )");
+        map.put(new Integer(78), "$call_brace_block = :lbrace $_gen19 :rbrace -> $1");
+        map.put(new Integer(34), "$command = :raw_command :raw_cmd_start $_gen8 :raw_cmd_end -> RawCommand( parts=$2 )");
+        map.put(new Integer(36), "$command_part = $expression_placeholder");
+        map.put(new Integer(35), "$command_part = :cmd_part");
+        map.put(new Integer(54), "$declaration = $type_e :identifier $setter -> Declaration( type=$0, name=$1, expression=$2 )");
+        map.put(new Integer(2), "$document = $version $_gen0 $_gen1 -> Draft3File( version=$0, imports=$1, body=$2 )");
+        map.put(new Integer(114), "$e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 )");
+        map.put(new Integer(113), "$e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 )");
+        map.put(new Integer(105), "$e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 )");
+        map.put(new Integer(106), "$e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 )");
+        map.put(new Integer(104), "$e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 )");
+        map.put(new Integer(110), "$e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 )");
+        map.put(new Integer(111), "$e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 )");
+        map.put(new Integer(108), "$e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 )");
+        map.put(new Integer(109), "$e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 )");
+        map.put(new Integer(107), "$e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 )");
+        map.put(new Integer(116), "$e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 )");
+        map.put(new Integer(112), "$e = $e :plus $e -> Add( lhs=$0, rhs=$2 )");
+        map.put(new Integer(115), "$e = $e :slash $e -> Divide( lhs=$0, rhs=$2 )");
+        map.put(new Integer(123), "$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
+        map.put(new Integer(122), "$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
+        map.put(new Integer(131), "$e = $string_literal");
+        map.put(new Integer(133), "$e = :boolean");
+        map.put(new Integer(119), "$e = :dash $e -> UnaryNegation( expression=$1 )");
+        map.put(new Integer(135), "$e = :float");
+        map.put(new Integer(132), "$e = :identifier");
+        map.put(new Integer(121), "$e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 )");
+        map.put(new Integer(130), "$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
+        map.put(new Integer(134), "$e = :integer");
+        map.put(new Integer(128), "$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
+        map.put(new Integer(129), "$e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 )");
+        map.put(new Integer(126), "$e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 )");
+        map.put(new Integer(136), "$e = :none");
+        map.put(new Integer(117), "$e = :not $e -> LogicalNot( expression=$1 )");
+        map.put(new Integer(125), "$e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 )");
+        map.put(new Integer(118), "$e = :plus $e -> UnaryPlus( expression=$1 )");
+        map.put(new Integer(38), "$expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 )");
+        map.put(new Integer(39), "$expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 )");
+        map.put(new Integer(5), "$file_body_element = $struct");
+        map.put(new Integer(4), "$file_body_element = $task");
+        map.put(new Integer(3), "$file_body_element = $workflow");
+        map.put(new Integer(85), "$if_stmt = :if :lparen $e :rparen :lbrace $_gen15 :rbrace -> If( expression=$2, body=$5 )");
+        map.put(new Integer(21), "$import = :import $static_string $_gen5 $_gen6 -> Import( uri=$1, namespace=$2, aliases=$3 )");
+        map.put(new Integer(23), "$import_alias = :alias :identifier :as :identifier -> ImportAlias( old_name=$1, new_name=$3 )");
+        map.put(new Integer(22), "$import_namespace = :as :identifier -> $1");
+        map.put(new Integer(53), "$input_declaration = $type_e :identifier $_gen13 -> InputDeclaration( type=$0, name=$1, expression=$2 )");
+        map.put(new Integer(88), "$input_kv = :identifier :equal $e -> ObjectKV( key=$0, value=$2 )");
+        map.put(new Integer(41), "$inputs = :input :lbrace $_gen10 :rbrace -> Inputs( inputs=$2 )");
+        map.put(new Integer(45), "$kv = :identifier :colon $e -> RuntimeAttribute( key=$0, value=$2 )");
+        map.put(new Integer(56), "$map_kv = $e :colon $e -> MapLiteralKv( key=$0, value=$2 )");
+        map.put(new Integer(46), "$meta = :meta $meta_map -> Meta( map=$1 )");
+        map.put(new Integer(50), "$meta_kv = :identifier :colon $meta_value -> MetaKvPair( key=$0, value=$2 )");
+        map.put(new Integer(49), "$meta_map = :lbrace $_gen12 :rbrace -> $1");
+        map.put(new Integer(89), "$meta_value = $static_string");
+        map.put(new Integer(90), "$meta_value = :boolean");
+        map.put(new Integer(92), "$meta_value = :float");
+        map.put(new Integer(91), "$meta_value = :integer");
+        map.put(new Integer(97), "$meta_value = :lbrace $_gen22 :rbrace -> MetaObject( map=$1 )");
+        map.put(new Integer(95), "$meta_value = :lsquare $_gen21 :rsquare -> MetaArray( values=$1 )");
+        map.put(new Integer(93), "$meta_value = :null");
+        map.put(new Integer(87), "$object_kv = :identifier :colon $e -> ObjectKV( key=$0, value=$2 )");
+        map.put(new Integer(59), "$output_kv = $type_e :identifier :equal $e -> Output( type=$0, name=$1, expression=$3 )");
+        map.put(new Integer(58), "$outputs = :output :lbrace $_gen14 :rbrace -> Outputs( outputs=$2 )");
+        map.put(new Integer(47), "$parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
+        map.put(new Integer(44), "$rt_map = :lbrace $_gen11 :rbrace -> $1");
+        map.put(new Integer(42), "$runtime = :runtime $rt_map -> Runtime( map=$1 )");
+        map.put(new Integer(86), "$scatter = :scatter :lparen :identifier :in $e :rparen :lbrace $_gen15 :rbrace -> Scatter( item=$2, collection=$4, body=$7 )");
+        map.put(new Integer(55), "$setter = :equal $e -> $1");
+        map.put(new Integer(11), "$static_string = :quote $_gen3 :quote -> StaticString( value=$1 )");
+        map.put(new Integer(15), "$static_string_piece = :escape");
+        map.put(new Integer(14), "$static_string_piece = :string");
+        map.put(new Integer(13), "$string_literal = :quote $_gen4 :quote -> StringLiteral( pieces=$1 )");
+        map.put(new Integer(17), "$string_piece = $expression_placeholder");
+        map.put(new Integer(16), "$string_piece = $static_string_piece");
+        map.put(new Integer(8), "$struct = :struct :identifier :lbrace $_gen2 :rbrace -> Struct( name=$1, entries=$3 )");
+        map.put(new Integer(9), "$struct_declaration = $type_e :identifier -> StructEntry( type=$0, name=$1 )");
+        map.put(new Integer(25), "$task = :task :identifier :lbrace $_gen7 :rbrace -> Task( name=$1, sections=$3 )");
+        map.put(new Integer(26), "$task_sections = $command");
+        map.put(new Integer(32), "$task_sections = $declaration");
+        map.put(new Integer(27), "$task_sections = $inputs");
+        map.put(new Integer(31), "$task_sections = $meta");
+        map.put(new Integer(28), "$task_sections = $outputs");
+        map.put(new Integer(30), "$task_sections = $parameter_meta");
+        map.put(new Integer(29), "$task_sections = $runtime");
+        map.put(new Integer(103), "$type_e = :identifier");
+        map.put(new Integer(102), "$type_e = :type");
+        map.put(new Integer(99), "$type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 )");
+        map.put(new Integer(101), "$type_e = :type <=> :plus -> NonEmptyType( innerType=$0 )");
+        map.put(new Integer(100), "$type_e = :type <=> :qmark -> OptionalType( innerType=$0 )");
+        map.put(new Integer(6), "$version = :version :version_name -> VersionDeclaration( v=$1 )");
+        map.put(new Integer(62), "$wf_body_element = $call");
+        map.put(new Integer(63), "$wf_body_element = $declaration");
+        map.put(new Integer(64), "$wf_body_element = $if_stmt");
+        map.put(new Integer(66), "$wf_body_element = $inputs");
+        map.put(new Integer(67), "$wf_body_element = $outputs");
+        map.put(new Integer(65), "$wf_body_element = $scatter");
+        map.put(new Integer(69), "$wf_body_element = $wf_meta");
+        map.put(new Integer(68), "$wf_body_element = $wf_parameter_meta");
+        map.put(new Integer(84), "$wf_meta = :meta $meta_map -> Meta( map=$1 )");
+        map.put(new Integer(83), "$wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
+        map.put(new Integer(61), "$workflow = :workflow :identifier :lbrace $_gen15 :rbrace -> Workflow( name=$1, body=$3 )");
+        rules = Collections.unmodifiableMap(map);
+    }
+    public static boolean is_terminal(int id) {
+        return 0 <= id && id <= 66;
+    }
+    public ParseTree parse(TokenStream tokens) throws SyntaxError {
+        return parse(tokens, new DefaultSyntaxErrorFormatter());
+    }
+    public ParseTree parse(List<Terminal> tokens) throws SyntaxError {
+        return parse(new TokenStream(tokens));
+    }
+    public ParseTree parse(TokenStream tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(tokens, error_formatter);
+        ParseTree tree = parse_document(ctx);
+        if (ctx.tokens.current() != null) {
+            StackTraceElement[] stack = Thread.currentThread().getStackTrace();
+            throw new SyntaxError(ctx.error_formatter.excessTokens(stack[1].getMethodName(), ctx.tokens.current()));
+        }
+        return tree;
+    }
+    public ParseTree parse(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        return parse(new TokenStream(tokens), error_formatter);
+    }
+    private static Terminal expect(ParserContext ctx, TerminalIdentifier expecting) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.noMoreTokens(ctx.nonterminal, expecting, ctx.tokens.last()));
+        }
+        if (current.getId() != expecting.id()) {
+            ArrayList<TerminalIdentifier> expectedList = new ArrayList<TerminalIdentifier>();
+            expectedList.add(expecting);
+            throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(ctx.nonterminal, current, expectedList, ctx.rule));
+        }
+        Terminal next = ctx.tokens.advance();
+        if ( next != null && !is_terminal(next.getId()) ) {
+            throw new SyntaxError(ctx.error_formatter.invalidTerminal(ctx.nonterminal, next));
+        }
+        return current;
+    }
+    private static Map<Integer, Integer> infix_binding_power_e;
+    private static Map<Integer, Integer> prefix_binding_power_e;
+    static {
+        Map<Integer, Integer> map = new HashMap<Integer, Integer>();
+        map.put(25, 4000); /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
+        map.put(13, 5000); /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
+        map.put(24, 6000); /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
+        map.put(14, 6000); /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
+        map.put(65, 7000); /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
+        map.put(1, 7000); /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
+        map.put(4, 7000); /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
+        map.put(21, 7000); /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
+        map.put(9, 8000); /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
+        map.put(63, 8000); /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
+        map.put(3, 9000); /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
+        map.put(29, 9000); /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
+        map.put(5, 9000); /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
+        map.put(12, 11000); /* $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall( name=$0, params=$2 ) */
+        map.put(51, 12000); /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
+        map.put(62, 13000); /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
+        infix_binding_power_e = Collections.unmodifiableMap(map);
+    }
+    static {
+        Map<Integer, Integer> map = new HashMap<Integer, Integer>();
+        map.put(60, 10000); /* $e = :not $e -> LogicalNot( expression=$1 ) */
+        map.put(9, 10000); /* $e = :plus $e -> UnaryPlus( expression=$1 ) */
+        map.put(63, 10000); /* $e = :dash $e -> UnaryNegation( expression=$1 ) */
+        prefix_binding_power_e = Collections.unmodifiableMap(map);
+    }
+    static int get_infix_binding_power_e(int terminal_id) {
+        if (infix_binding_power_e.containsKey(terminal_id)) {
+            return infix_binding_power_e.get(terminal_id);
+        }
+        return 0;
+    }
+    static int get_prefix_binding_power_e(int terminal_id) {
+        if (prefix_binding_power_e.containsKey(terminal_id)) {
+            return prefix_binding_power_e.get(terminal_id);
+        }
+        return 0;
+    }
+    public ParseTree parse_e(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_e_internal(ctx, 0);
+    }
+    public static ParseTree parse_e(ParserContext ctx) throws SyntaxError {
+        return parse_e_internal(ctx, 0);
+    }
+    public static ParseTree parse_e_internal(ParserContext ctx, int rbp) throws SyntaxError {
+        ParseTree left = nud_e(ctx);
+        if ( left instanceof ParseTree ) {
+            left.setExpr(true);
+            left.setNud(true);
+        }
+        while (ctx.tokens.current() != null && rbp < get_infix_binding_power_e(ctx.tokens.current().getId())) {
+            left = led_e(left, ctx);
+        }
+        if (left != null) {
+            left.setExpr(true);
+        }
+        return left;
+    }
+    private static ParseTree nud_e(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree( new NonTerminal(135, "e") );
+        Terminal current = ctx.tokens.current();
+        ctx.nonterminal = "e";
+        if (current == null) {
+            return tree;
+        }
+        else if (rule_first.get(117).contains(terminal_map.get(current.getId()))) {
+            /* (117) $e = :not $e -> LogicalNot( expression=$1 ) */
+            ctx.rule = rules.get(117);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("expression", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("LogicalNot", parameters));
+            tree.setNudMorphemeCount(2);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NOT));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(60)));
+            tree.setPrefix(true);
+        }
+        else if (rule_first.get(118).contains(terminal_map.get(current.getId()))) {
+            /* (118) $e = :plus $e -> UnaryPlus( expression=$1 ) */
+            ctx.rule = rules.get(118);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("expression", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("UnaryPlus", parameters));
+            tree.setNudMorphemeCount(2);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PLUS));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(9)));
+            tree.setPrefix(true);
+        }
+        else if (rule_first.get(119).contains(terminal_map.get(current.getId()))) {
+            /* (119) $e = :dash $e -> UnaryNegation( expression=$1 ) */
+            ctx.rule = rules.get(119);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("expression", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("UnaryNegation", parameters));
+            tree.setNudMorphemeCount(2);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DASH));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(63)));
+            tree.setPrefix(true);
+        }
+        else if (rule_first.get(121).contains(terminal_map.get(current.getId()))) {
+            /* (121) $e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 ) */
+            ctx.rule = rules.get(121);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
+        }
+        else if (rule_first.get(125).contains(terminal_map.get(current.getId()))) {
+            /* (125) $e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 ) */
+            ctx.rule = rules.get(125);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("map", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("ObjectLiteral", parameters));
+            tree.setNudMorphemeCount(4);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_OBJECT));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE));
+            tree.add(parse__gen25(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE));
+        }
+        else if (rule_first.get(126).contains(terminal_map.get(current.getId()))) {
+            /* (126) $e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 ) */
+            ctx.rule = rules.get(126);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("values", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("ArrayLiteral", parameters));
+            tree.setNudMorphemeCount(3);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LSQUARE));
+            tree.add(parse__gen24(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
+        }
+        else if (rule_first.get(128).contains(terminal_map.get(current.getId()))) {
+            /* (128) $e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 ) */
+            ctx.rule = rules.get(128);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("map", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("MapLiteral", parameters));
+            tree.setNudMorphemeCount(3);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE));
+            tree.add(parse__gen26(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE));
+        }
+        else if (rule_first.get(129).contains(terminal_map.get(current.getId()))) {
+            /* (129) $e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 ) */
+            ctx.rule = rules.get(129);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("values", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("TupleLiteral", parameters));
+            tree.setNudMorphemeCount(3);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LPAREN));
+            tree.add(parse__gen24(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RPAREN));
+        }
+        else if (rule_first.get(130).contains(terminal_map.get(current.getId()))) {
+            /* (130) $e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 ) */
+            ctx.rule = rules.get(130);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("cond", 1);
+            parameters.put("iftrue", 3);
+            parameters.put("iffalse", 5);
+            tree.setAstTransformation(new AstTransformNodeCreator("TernaryIf", parameters));
+            tree.setNudMorphemeCount(6);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IF));
+            tree.add(parse_e(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_THEN));
+            tree.add(parse_e(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_ELSE));
+            tree.add(parse_e(ctx));
+        }
+        else if (rule_first.get(131).contains(terminal_map.get(current.getId()))) {
+            /* (131) $e = $string_literal */
+            ctx.rule = rules.get(131);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(parse_string_literal(ctx));
+        }
+        else if (rule_first.get(132).contains(terminal_map.get(current.getId()))) {
+            /* (132) $e = :identifier */
+            ctx.rule = rules.get(132);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
+        }
+        else if (rule_first.get(133).contains(terminal_map.get(current.getId()))) {
+            /* (133) $e = :boolean */
+            ctx.rule = rules.get(133);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_BOOLEAN));
+        }
+        else if (rule_first.get(134).contains(terminal_map.get(current.getId()))) {
+            /* (134) $e = :integer */
+            ctx.rule = rules.get(134);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_INTEGER));
+        }
+        else if (rule_first.get(135).contains(terminal_map.get(current.getId()))) {
+            /* (135) $e = :float */
+            ctx.rule = rules.get(135);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_FLOAT));
+        }
+        else if (rule_first.get(136).contains(terminal_map.get(current.getId()))) {
+            /* (136) $e = :none */
+            ctx.rule = rules.get(136);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NONE));
+        }
+        return tree;
+    }
+    private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree( new NonTerminal(135, "e") );
+        Terminal current = ctx.tokens.current();
+        ctx.nonterminal = "e";
+        int modifier;
+        if (current.getId() == 25) {
+            /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(104);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("LogicalOr", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_PIPE));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(25) - modifier));
+            return tree;
+        }
+        if (current.getId() == 13) {
+            /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(105);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("LogicalAnd", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_AMPERSAND));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(13) - modifier));
+            return tree;
+        }
+        if (current.getId() == 24) {
+            /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(106);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Equals", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_EQUAL));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(24) - modifier));
+            return tree;
+        }
+        if (current.getId() == 14) {
+            /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(107);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("NotEquals", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NOT_EQUAL));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(14) - modifier));
+            return tree;
+        }
+        if (current.getId() == 65) {
+            /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(108);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("LessThan", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LT));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(65) - modifier));
+            return tree;
+        }
+        if (current.getId() == 1) {
+            /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(109);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("LessThanOrEqual", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LTEQ));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(1) - modifier));
+            return tree;
+        }
+        if (current.getId() == 4) {
+            /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(110);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("GreaterThan", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_GT));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(4) - modifier));
+            return tree;
+        }
+        if (current.getId() == 21) {
+            /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(111);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("GreaterThanOrEqual", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_GTEQ));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(21) - modifier));
+            return tree;
+        }
+        if (current.getId() == 9) {
+            /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(112);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Add", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PLUS));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(9) - modifier));
+            return tree;
+        }
+        if (current.getId() == 63) {
+            /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(113);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Subtract", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DASH));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(63) - modifier));
+            return tree;
+        }
+        if (current.getId() == 3) {
+            /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(114);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Multiply", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_ASTERISK));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(3) - modifier));
+            return tree;
+        }
+        if (current.getId() == 29) {
+            /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(115);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Divide", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_SLASH));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(29) - modifier));
+            return tree;
+        }
+        if (current.getId() == 5) {
+            /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(116);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Remainder", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PERCENT));
+            modifier = 0;
+            tree.setInfix(true);
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(5) - modifier));
+            return tree;
+        }
+        if (current.getId() == 12) {
+            /* $e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 ) */
+            ctx.rule = rules.get(121);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("name", 0);
+            parameters.put("params", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("FunctionCall", parameters));
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LPAREN));
+            tree.add(parse__gen24(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RPAREN));
+            return tree;
+        }
+        if (current.getId() == 51) {
+            /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
+            ctx.rule = rules.get(122);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("lhs", 0);
+            parameters.put("rhs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("ArrayOrMapLookup", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LSQUARE));
+            modifier = 0;
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(51) - modifier));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
+            return tree;
+        }
+        if (current.getId() == 62) {
+            /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
+            ctx.rule = rules.get(123);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("value", 0);
+            parameters.put("member", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("MemberAccess", parameters));
+            tree.setExprNud(true);
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOT));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
+            return tree;
+        }
+        return tree;
+    }
+    private static Map<Integer, Integer> infix_binding_power_meta_value;
+    private static Map<Integer, Integer> prefix_binding_power_meta_value;
+    static {
+        Map<Integer, Integer> map = new HashMap<Integer, Integer>();
+        infix_binding_power_meta_value = Collections.unmodifiableMap(map);
+    }
+    static {
+        Map<Integer, Integer> map = new HashMap<Integer, Integer>();
+        prefix_binding_power_meta_value = Collections.unmodifiableMap(map);
+    }
+    static int get_infix_binding_power_meta_value(int terminal_id) {
+        if (infix_binding_power_meta_value.containsKey(terminal_id)) {
+            return infix_binding_power_meta_value.get(terminal_id);
+        }
+        return 0;
+    }
+    static int get_prefix_binding_power_meta_value(int terminal_id) {
+        if (prefix_binding_power_meta_value.containsKey(terminal_id)) {
+            return prefix_binding_power_meta_value.get(terminal_id);
+        }
+        return 0;
+    }
+    public ParseTree parse_meta_value(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_meta_value_internal(ctx, 0);
+    }
+    public static ParseTree parse_meta_value(ParserContext ctx) throws SyntaxError {
+        return parse_meta_value_internal(ctx, 0);
+    }
+    public static ParseTree parse_meta_value_internal(ParserContext ctx, int rbp) throws SyntaxError {
+        ParseTree left = nud_meta_value(ctx);
+        if ( left instanceof ParseTree ) {
+            left.setExpr(true);
+            left.setNud(true);
+        }
+        while (ctx.tokens.current() != null && rbp < get_infix_binding_power_meta_value(ctx.tokens.current().getId())) {
+            left = led_meta_value(left, ctx);
+        }
+        if (left != null) {
+            left.setExpr(true);
+        }
+        return left;
+    }
+    private static ParseTree nud_meta_value(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree( new NonTerminal(113, "meta_value") );
+        Terminal current = ctx.tokens.current();
+        ctx.nonterminal = "meta_value";
+        if (current == null) {
+            return tree;
+        }
+        if (rule_first.get(89).contains(terminal_map.get(current.getId()))) {
+            /* (89) $meta_value = $static_string */
+            ctx.rule = rules.get(89);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(parse_static_string(ctx));
+        }
+        else if (rule_first.get(90).contains(terminal_map.get(current.getId()))) {
+            /* (90) $meta_value = :boolean */
+            ctx.rule = rules.get(90);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_BOOLEAN));
+        }
+        else if (rule_first.get(91).contains(terminal_map.get(current.getId()))) {
+            /* (91) $meta_value = :integer */
+            ctx.rule = rules.get(91);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_INTEGER));
+        }
+        else if (rule_first.get(92).contains(terminal_map.get(current.getId()))) {
+            /* (92) $meta_value = :float */
+            ctx.rule = rules.get(92);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_FLOAT));
+        }
+        else if (rule_first.get(93).contains(terminal_map.get(current.getId()))) {
+            /* (93) $meta_value = :null */
+            ctx.rule = rules.get(93);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NULL));
+        }
+        else if (rule_first.get(95).contains(terminal_map.get(current.getId()))) {
+            /* (95) $meta_value = :lsquare $_gen21 :rsquare -> MetaArray( values=$1 ) */
+            ctx.rule = rules.get(95);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("values", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("MetaArray", parameters));
+            tree.setNudMorphemeCount(3);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LSQUARE));
+            tree.add(parse__gen21(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
+        }
+        else if (rule_first.get(97).contains(terminal_map.get(current.getId()))) {
+            /* (97) $meta_value = :lbrace $_gen22 :rbrace -> MetaObject( map=$1 ) */
+            ctx.rule = rules.get(97);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("map", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("MetaObject", parameters));
+            tree.setNudMorphemeCount(3);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE));
+            tree.add(parse__gen22(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE));
+        }
+        return tree;
+    }
+    private static ParseTree led_meta_value(ParseTree left, ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree( new NonTerminal(113, "meta_value") );
+        Terminal current = ctx.tokens.current();
+        ctx.nonterminal = "meta_value";
+        int modifier;
+        return tree;
+    }
+    private static Map<Integer, Integer> infix_binding_power_type_e;
+    private static Map<Integer, Integer> prefix_binding_power_type_e;
+    static {
+        Map<Integer, Integer> map = new HashMap<Integer, Integer>();
+        map.put(51, 1000); /* $type_e = :type <=> :lsquare list($type_e, :comma) :rsquare -> Type( name=$0, subtype=$2 ) */
+        map.put(57, 2000); /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
+        map.put(9, 3000); /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
+        infix_binding_power_type_e = Collections.unmodifiableMap(map);
+    }
+    static {
+        Map<Integer, Integer> map = new HashMap<Integer, Integer>();
+        prefix_binding_power_type_e = Collections.unmodifiableMap(map);
+    }
+    static int get_infix_binding_power_type_e(int terminal_id) {
+        if (infix_binding_power_type_e.containsKey(terminal_id)) {
+            return infix_binding_power_type_e.get(terminal_id);
+        }
+        return 0;
+    }
+    static int get_prefix_binding_power_type_e(int terminal_id) {
+        if (prefix_binding_power_type_e.containsKey(terminal_id)) {
+            return prefix_binding_power_type_e.get(terminal_id);
+        }
+        return 0;
+    }
+    public ParseTree parse_type_e(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_type_e_internal(ctx, 0);
+    }
+    public static ParseTree parse_type_e(ParserContext ctx) throws SyntaxError {
+        return parse_type_e_internal(ctx, 0);
+    }
+    public static ParseTree parse_type_e_internal(ParserContext ctx, int rbp) throws SyntaxError {
+        ParseTree left = nud_type_e(ctx);
+        if ( left instanceof ParseTree ) {
+            left.setExpr(true);
+            left.setNud(true);
+        }
+        while (ctx.tokens.current() != null && rbp < get_infix_binding_power_type_e(ctx.tokens.current().getId())) {
+            left = led_type_e(left, ctx);
+        }
+        if (left != null) {
+            left.setExpr(true);
+        }
+        return left;
+    }
+    private static ParseTree nud_type_e(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree( new NonTerminal(101, "type_e") );
+        Terminal current = ctx.tokens.current();
+        ctx.nonterminal = "type_e";
+        if (current == null) {
+            return tree;
+        }
+        if (rule_first.get(99).contains(terminal_map.get(current.getId()))) {
+            /* (99) $type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 ) */
+            ctx.rule = rules.get(99);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_TYPE));
+        }
+        else if (rule_first.get(100).contains(terminal_map.get(current.getId()))) {
+            /* (100) $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
+            ctx.rule = rules.get(100);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_TYPE));
+        }
+        else if (rule_first.get(101).contains(terminal_map.get(current.getId()))) {
+            /* (101) $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
+            ctx.rule = rules.get(101);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_TYPE));
+        }
+        else if (rule_first.get(102).contains(terminal_map.get(current.getId()))) {
+            /* (102) $type_e = :type */
+            ctx.rule = rules.get(102);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_TYPE));
+        }
+        else if (rule_first.get(103).contains(terminal_map.get(current.getId()))) {
+            /* (103) $type_e = :identifier */
+            ctx.rule = rules.get(103);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
+        }
+        return tree;
+    }
+    private static ParseTree led_type_e(ParseTree left, ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree( new NonTerminal(101, "type_e") );
+        Terminal current = ctx.tokens.current();
+        ctx.nonterminal = "type_e";
+        int modifier;
+        if (current.getId() == 51) {
+            /* $type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 ) */
+            ctx.rule = rules.get(99);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("name", 0);
+            parameters.put("subtype", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Type", parameters));
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LSQUARE));
+            tree.add(parse__gen23(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
+            return tree;
+        }
+        if (current.getId() == 57) {
+            /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
+            ctx.rule = rules.get(100);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("innerType", 0);
+            tree.setAstTransformation(new AstTransformNodeCreator("OptionalType", parameters));
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_QMARK));
+            return tree;
+        }
+        if (current.getId() == 9) {
+            /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
+            ctx.rule = rules.get(101);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("innerType", 0);
+            tree.setAstTransformation(new AstTransformNodeCreator("NonEmptyType", parameters));
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PLUS));
+            return tree;
+        }
+        return tree;
+    }
+    public ParseTree parse__gen0(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen0(ctx);
+    }
+    private static ParseTree parse__gen0(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(96, "_gen0"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen0";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(96).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(96).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(96).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_import(ctx));
+            ctx.nonterminal = "_gen0"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen1(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen1(ctx);
+    }
+    private static ParseTree parse__gen1(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(98, "_gen1"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen1";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(98).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(98).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(98).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_file_body_element(ctx));
+            ctx.nonterminal = "_gen1"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen10(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen10(ctx);
+    }
+    private static ParseTree parse__gen10(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(121, "_gen10"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen10";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(121).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(121).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(121).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_input_declaration(ctx));
+            ctx.nonterminal = "_gen10"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen11(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen11(ctx);
+    }
+    private static ParseTree parse__gen11(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(74, "_gen11"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen11";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(74).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(74).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(74).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_kv(ctx));
+            ctx.nonterminal = "_gen11"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen12(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen12(ctx);
+    }
+    private static ParseTree parse__gen12(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(110, "_gen12"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen12";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(110).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(110).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(110).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_meta_kv(ctx));
+            ctx.nonterminal = "_gen12"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen14(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen14(ctx);
+    }
+    private static ParseTree parse__gen14(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(67, "_gen14"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen14";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(67).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(67).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(67).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_output_kv(ctx));
+            ctx.nonterminal = "_gen14"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen15(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen15(ctx);
+    }
+    private static ParseTree parse__gen15(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(123, "_gen15"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen15";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(123).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(123).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(123).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_wf_body_element(ctx));
+            ctx.nonterminal = "_gen15"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen17(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen17(ctx);
+    }
+    private static ParseTree parse__gen17(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(132, "_gen17"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen17";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(132).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(132).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(132).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_call_after(ctx));
+            ctx.nonterminal = "_gen17"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen2(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen2(ctx);
+    }
+    private static ParseTree parse__gen2(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(140, "_gen2"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen2";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(140).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(140).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(140).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_struct_declaration(ctx));
+            ctx.nonterminal = "_gen2"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen20(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen20(ctx);
+    }
+    private static ParseTree parse__gen20(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(119, "_gen20"));
+        tree.setList(true);
+        tree.setListSeparator(38);
+        ctx.nonterminal = "_gen20";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(119).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(119).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(119).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_input_kv(ctx));
+            ctx.nonterminal = "_gen20"; // because parse_* can reset this
+            if (ctx.tokens.current() != null &&
+                ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
+              tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_COMMA));
+            } else {
+              if (minimum > 1) {
+                  throw new SyntaxError(ctx.error_formatter.missingListItems(
+                      "_gen20",
+                      0,
+                      0 - minimum + 1,
+                      null
+                  ));
+              }
+              break;
+            }
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen21(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen21(ctx);
+    }
+    private static ParseTree parse__gen21(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(104, "_gen21"));
+        tree.setList(true);
+        tree.setListSeparator(38);
+        ctx.nonterminal = "_gen21";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(104).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(104).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(104).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_meta_value(ctx));
+            ctx.nonterminal = "_gen21"; // because parse_* can reset this
+            if (ctx.tokens.current() != null &&
+                ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
+              tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_COMMA));
+            } else {
+              if (minimum > 1) {
+                  throw new SyntaxError(ctx.error_formatter.missingListItems(
+                      "_gen21",
+                      0,
+                      0 - minimum + 1,
+                      null
+                  ));
+              }
+              break;
+            }
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen22(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen22(ctx);
+    }
+    private static ParseTree parse__gen22(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(89, "_gen22"));
+        tree.setList(true);
+        tree.setListSeparator(38);
+        ctx.nonterminal = "_gen22";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(89).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(89).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(89).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_meta_kv(ctx));
+            ctx.nonterminal = "_gen22"; // because parse_* can reset this
+            if (ctx.tokens.current() != null &&
+                ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
+              tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_COMMA));
+            } else {
+              if (minimum > 1) {
+                  throw new SyntaxError(ctx.error_formatter.missingListItems(
+                      "_gen22",
+                      0,
+                      0 - minimum + 1,
+                      null
+                  ));
+              }
+              break;
+            }
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen23(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen23(ctx);
+    }
+    private static ParseTree parse__gen23(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(129, "_gen23"));
+        tree.setList(true);
+        tree.setListSeparator(38);
+        ctx.nonterminal = "_gen23";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_type_e(ctx));
+            ctx.nonterminal = "_gen23"; // because parse_* can reset this
+            if (ctx.tokens.current() != null &&
+                ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
+              tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_COMMA));
+            } else {
+              if (minimum > 1) {
+                  throw new SyntaxError(ctx.error_formatter.missingListItems(
+                      "_gen23",
+                      0,
+                      0 - minimum + 1,
+                      null
+                  ));
+              }
+              break;
+            }
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen24(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen24(ctx);
+    }
+    private static ParseTree parse__gen24(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(127, "_gen24"));
+        tree.setList(true);
+        tree.setListSeparator(38);
+        ctx.nonterminal = "_gen24";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(127).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(127).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(127).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_e(ctx));
+            ctx.nonterminal = "_gen24"; // because parse_* can reset this
+            if (ctx.tokens.current() != null &&
+                ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
+              tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_COMMA));
+            } else {
+              if (minimum > 1) {
+                  throw new SyntaxError(ctx.error_formatter.missingListItems(
+                      "_gen24",
+                      0,
+                      0 - minimum + 1,
+                      null
+                  ));
+              }
+              break;
+            }
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen25(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen25(ctx);
+    }
+    private static ParseTree parse__gen25(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(80, "_gen25"));
+        tree.setList(true);
+        tree.setListSeparator(38);
+        ctx.nonterminal = "_gen25";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(80).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(80).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(80).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_object_kv(ctx));
+            ctx.nonterminal = "_gen25"; // because parse_* can reset this
+            if (ctx.tokens.current() != null &&
+                ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
+              tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_COMMA));
+            } else {
+              if (minimum > 1) {
+                  throw new SyntaxError(ctx.error_formatter.missingListItems(
+                      "_gen25",
+                      0,
+                      0 - minimum + 1,
+                      null
+                  ));
+              }
+              break;
+            }
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen26(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen26(ctx);
+    }
+    private static ParseTree parse__gen26(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(92, "_gen26"));
+        tree.setList(true);
+        tree.setListSeparator(38);
+        ctx.nonterminal = "_gen26";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(92).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(92).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(92).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_map_kv(ctx));
+            ctx.nonterminal = "_gen26"; // because parse_* can reset this
+            if (ctx.tokens.current() != null &&
+                ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
+              tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_COMMA));
+            } else {
+              if (minimum > 1) {
+                  throw new SyntaxError(ctx.error_formatter.missingListItems(
+                      "_gen26",
+                      0,
+                      0 - minimum + 1,
+                      null
+                  ));
+              }
+              break;
+            }
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen3(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen3(ctx);
+    }
+    private static ParseTree parse__gen3(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(109, "_gen3"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen3";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_static_string_piece(ctx));
+            ctx.nonterminal = "_gen3"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen4(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen4(ctx);
+    }
+    private static ParseTree parse__gen4(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(141, "_gen4"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen4";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(141).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(141).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(141).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_string_piece(ctx));
+            ctx.nonterminal = "_gen4"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen6(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen6(ctx);
+    }
+    private static ParseTree parse__gen6(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(124, "_gen6"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen6";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(124).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(124).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(124).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_import_alias(ctx));
+            ctx.nonterminal = "_gen6"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen7(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen7(ctx);
+    }
+    private static ParseTree parse__gen7(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(120, "_gen7"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen7";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(120).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(120).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(120).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_task_sections(ctx));
+            ctx.nonterminal = "_gen7"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen8(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen8(ctx);
+    }
+    private static ParseTree parse__gen8(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(100, "_gen8"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen8";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(100).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(100).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(100).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_command_part(ctx));
+            ctx.nonterminal = "_gen8"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen9(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen9(ctx);
+    }
+    private static ParseTree parse__gen9(ParserContext ctx) throws SyntaxError {
+        ParseTree tree = new ParseTree(new NonTerminal(73, "_gen9"));
+        tree.setList(true);
+        ctx.nonterminal = "_gen9";
+        if ( ctx.tokens.current() != null &&
+             !nonterminal_first.get(73).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(73).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+            return tree;
+        }
+        if (ctx.tokens.current() == null) {
+            return tree;
+        }
+        int minimum = 0;
+        while (minimum > 0 ||
+               (ctx.tokens.current() != null &&
+               nonterminal_first.get(73).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_expression_placeholder_kv(ctx));
+            ctx.nonterminal = "_gen9"; // because parse_* can reset this
+            minimum = Math.max(minimum - 1, 0);
+        }
+        return tree;
+    }
+    public ParseTree parse__gen13(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen13(ctx);
+    }
+    private static ParseTree parse__gen13(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[3][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(70, "_gen13"));
+        ctx.nonterminal = "_gen13";
+        if ( current != null &&
+             !nonterminal_first.get(70).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(70).contains(terminal_map.get(current.getId())) ) {
+            return tree;
+        }
+        if (current == null) {
+            return tree;
+        }
+        if (rule == 51) {
+            /* $_gen13 = $setter */
+            ctx.rule = rules.get(51);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_setter(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        return tree;
+    }
+    public ParseTree parse__gen16(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen16(ctx);
+    }
+    private static ParseTree parse__gen16(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[14][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(81, "_gen16"));
+        ctx.nonterminal = "_gen16";
+        if ( current != null &&
+             !nonterminal_first.get(81).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(81).contains(terminal_map.get(current.getId())) ) {
+            return tree;
+        }
+        if (current == null) {
+            return tree;
+        }
+        if (rule == 70) {
+            /* $_gen16 = $alias */
+            ctx.rule = rules.get(70);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_alias(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        return tree;
+    }
+    public ParseTree parse__gen18(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen18(ctx);
+    }
+    private static ParseTree parse__gen18(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[11][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(78, "_gen18"));
+        ctx.nonterminal = "_gen18";
+        if ( current != null &&
+             !nonterminal_first.get(78).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(78).contains(terminal_map.get(current.getId())) ) {
+            return tree;
+        }
+        if (current == null) {
+            return tree;
+        }
+        if (rule == 73) {
+            /* $_gen18 = $call_brace_block */
+            ctx.rule = rules.get(73);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_call_brace_block(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        return tree;
+    }
+    public ParseTree parse__gen19(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen19(ctx);
+    }
+    private static ParseTree parse__gen19(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[50][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(117, "_gen19"));
+        ctx.nonterminal = "_gen19";
+        if ( current != null &&
+             !nonterminal_first.get(117).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(117).contains(terminal_map.get(current.getId())) ) {
+            return tree;
+        }
+        if (current == null) {
+            return tree;
+        }
+        if (rule == 76) {
+            /* $_gen19 = $call_body */
+            ctx.rule = rules.get(76);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_call_body(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        return tree;
+    }
+    public ParseTree parse__gen5(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse__gen5(ctx);
+    }
+    private static ParseTree parse__gen5(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[55][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(122, "_gen5"));
+        ctx.nonterminal = "_gen5";
+        if ( current != null &&
+             !nonterminal_first.get(122).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(122).contains(terminal_map.get(current.getId())) ) {
+            return tree;
+        }
+        if (current == null) {
+            return tree;
+        }
+        if (rule == 18) {
+            /* $_gen5 = $import_namespace */
+            ctx.rule = rules.get(18);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_import_namespace(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        return tree;
+    }
+    public ParseTree parse_alias(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_alias(ctx);
+    }
+    private static ParseTree parse_alias(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[49][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(116, "alias"));
+        ctx.nonterminal = "alias";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "alias",
+                nonterminal_first.get(116),
+                nonterminal_rules.get(116)
+            ));
+        }
+        if (rule == 81) {
+            /* $alias = :as :identifier -> $1 */
+            ctx.rule = rules.get(81);
+            tree.setAstTransformation(new AstTransformSubstitution(1));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_AS);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "alias",
+            current,
+            nonterminal_first.get(116),
+            rules.get(81)
+        ));
+    }
+    public ParseTree parse_call(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_call(ctx);
+    }
+    private static ParseTree parse_call(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[8][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(75, "call"));
+        ctx.nonterminal = "call";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "call",
+                nonterminal_first.get(75),
+                nonterminal_rules.get(75)
+            ));
+        }
+        if (rule == 75) {
+            /* $call = :call :fqn $_gen16 $_gen17 $_gen18 -> Call( task=$1, alias=$2, after=$3, body=$4 ) */
+            ctx.rule = rules.get(75);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("task", 1);
+            parameters.put("alias", 2);
+            parameters.put("after", 3);
+            parameters.put("body", 4);
+            tree.setAstTransformation(new AstTransformNodeCreator("Call", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_CALL);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_FQN);
+            tree.add(next);
+            subtree = parse__gen16(ctx);
+            tree.add(subtree);
+            subtree = parse__gen17(ctx);
+            tree.add(subtree);
+            subtree = parse__gen18(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "call",
+            current,
+            nonterminal_first.get(75),
+            rules.get(75)
+        ));
+    }
+    public ParseTree parse_call_after(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_call_after(ctx);
+    }
+    private static ParseTree parse_call_after(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[61][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(128, "call_after"));
+        ctx.nonterminal = "call_after";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "call_after",
+                nonterminal_first.get(128),
+                nonterminal_rules.get(128)
+            ));
+        }
+        if (rule == 82) {
+            /* $call_after = :after :identifier -> $1 */
+            ctx.rule = rules.get(82);
+            tree.setAstTransformation(new AstTransformSubstitution(1));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_AFTER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "call_after",
+            current,
+            nonterminal_first.get(128),
+            rules.get(82)
+        ));
+    }
+    public ParseTree parse_call_body(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_call_body(ctx);
+    }
+    private static ParseTree parse_call_body(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[69][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(136, "call_body"));
+        ctx.nonterminal = "call_body";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "call_body",
+                nonterminal_first.get(136),
+                nonterminal_rules.get(136)
+            ));
+        }
+        if (rule == 80) {
+            /* $call_body = :input :colon $_gen20 -> CallBody( inputs=$2 ) */
+            ctx.rule = rules.get(80);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("inputs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("CallBody", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_INPUT);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_COLON);
+            tree.add(next);
+            subtree = parse__gen20(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "call_body",
+            current,
+            nonterminal_first.get(136),
+            rules.get(80)
+        ));
+    }
+    public ParseTree parse_call_brace_block(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_call_brace_block(ctx);
+    }
+    private static ParseTree parse_call_brace_block(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[38][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(105, "call_brace_block"));
+        ctx.nonterminal = "call_brace_block";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "call_brace_block",
+                nonterminal_first.get(105),
+                nonterminal_rules.get(105)
+            ));
+        }
+        if (rule == 78) {
+            /* $call_brace_block = :lbrace $_gen19 :rbrace -> $1 */
+            ctx.rule = rules.get(78);
+            tree.setAstTransformation(new AstTransformSubstitution(1));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE);
+            tree.add(next);
+            subtree = parse__gen19(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "call_brace_block",
+            current,
+            nonterminal_first.get(105),
+            rules.get(78)
+        ));
+    }
+    public ParseTree parse_command(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_command(ctx);
+    }
+    private static ParseTree parse_command(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[28][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(95, "command"));
+        ctx.nonterminal = "command";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "command",
+                nonterminal_first.get(95),
+                nonterminal_rules.get(95)
+            ));
+        }
+        if (rule == 34) {
+            /* $command = :raw_command :raw_cmd_start $_gen8 :raw_cmd_end -> RawCommand( parts=$2 ) */
+            ctx.rule = rules.get(34);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("parts", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("RawCommand", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RAW_COMMAND);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RAW_CMD_START);
+            tree.add(next);
+            subtree = parse__gen8(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RAW_CMD_END);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "command",
+            current,
+            nonterminal_first.get(95),
+            rules.get(34)
+        ));
+    }
+    public ParseTree parse_command_part(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_command_part(ctx);
+    }
+    private static ParseTree parse_command_part(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[21][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(88, "command_part"));
+        ctx.nonterminal = "command_part";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "command_part",
+                nonterminal_first.get(88),
+                nonterminal_rules.get(88)
+            ));
+        }
+        if (rule == 35) {
+            /* $command_part = :cmd_part */
+            ctx.rule = rules.get(35);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_CMD_PART);
+            tree.add(next);
+            return tree;
+        }
+        else if (rule == 36) {
+            /* $command_part = $expression_placeholder */
+            ctx.rule = rules.get(36);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_expression_placeholder(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "command_part",
+            current,
+            nonterminal_first.get(88),
+            rules.get(36)
+        ));
+    }
+    public ParseTree parse_declaration(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_declaration(ctx);
+    }
+    private static ParseTree parse_declaration(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[72][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(139, "declaration"));
+        ctx.nonterminal = "declaration";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "declaration",
+                nonterminal_first.get(139),
+                nonterminal_rules.get(139)
+            ));
+        }
+        if (rule == 54) {
+            /* $declaration = $type_e :identifier $setter -> Declaration( type=$0, name=$1, expression=$2 ) */
+            ctx.rule = rules.get(54);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("type", 0);
+            parameters.put("name", 1);
+            parameters.put("expression", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Declaration", parameters));
+            subtree = parse_type_e(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            subtree = parse_setter(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "declaration",
+            current,
+            nonterminal_first.get(139),
+            rules.get(54)
+        ));
+    }
+    public ParseTree parse_document(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_document(ctx);
+    }
+    private static ParseTree parse_document(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[63][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(130, "document"));
+        ctx.nonterminal = "document";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "document",
+                nonterminal_first.get(130),
+                nonterminal_rules.get(130)
+            ));
+        }
+        if (rule == 2) {
+            /* $document = $version $_gen0 $_gen1 -> Draft3File( version=$0, imports=$1, body=$2 ) */
+            ctx.rule = rules.get(2);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("version", 0);
+            parameters.put("imports", 1);
+            parameters.put("body", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Draft3File", parameters));
+            subtree = parse_version(ctx);
+            tree.add(subtree);
+            subtree = parse__gen0(ctx);
+            tree.add(subtree);
+            subtree = parse__gen1(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "document",
+            current,
+            nonterminal_first.get(130),
+            rules.get(2)
+        ));
+    }
+    public ParseTree parse_expression_placeholder(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_expression_placeholder(ctx);
+    }
+    private static ParseTree parse_expression_placeholder(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[66][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(133, "expression_placeholder"));
+        ctx.nonterminal = "expression_placeholder";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "expression_placeholder",
+                nonterminal_first.get(133),
+                nonterminal_rules.get(133)
+            ));
+        }
+        if (rule == 38) {
+            /* $expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 ) */
+            ctx.rule = rules.get(38);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("attributes", 1);
+            parameters.put("expr", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("ExpressionPlaceholder", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START);
+            tree.add(next);
+            subtree = parse__gen9(ctx);
+            tree.add(subtree);
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_END);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "expression_placeholder",
+            current,
+            nonterminal_first.get(133),
+            rules.get(38)
+        ));
+    }
+    public ParseTree parse_expression_placeholder_kv(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_expression_placeholder_kv(ctx);
+    }
+    private static ParseTree parse_expression_placeholder_kv(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[20][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(87, "expression_placeholder_kv"));
+        ctx.nonterminal = "expression_placeholder_kv";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "expression_placeholder_kv",
+                nonterminal_first.get(87),
+                nonterminal_rules.get(87)
+            ));
+        }
+        if (rule == 39) {
+            /* $expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 ) */
+            ctx.rule = rules.get(39);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("key", 1);
+            parameters.put("value", 3);
+            tree.setAstTransformation(new AstTransformNodeCreator("ExpressionPlaceholderAttr", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_EQUAL);
+            tree.add(next);
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "expression_placeholder_kv",
+            current,
+            nonterminal_first.get(87),
+            rules.get(39)
+        ));
+    }
+    public ParseTree parse_file_body_element(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_file_body_element(ctx);
+    }
+    private static ParseTree parse_file_body_element(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[67][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(134, "file_body_element"));
+        ctx.nonterminal = "file_body_element";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "file_body_element",
+                nonterminal_first.get(134),
+                nonterminal_rules.get(134)
+            ));
+        }
+        if (rule == 3) {
+            /* $file_body_element = $workflow */
+            ctx.rule = rules.get(3);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_workflow(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 4) {
+            /* $file_body_element = $task */
+            ctx.rule = rules.get(4);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_task(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 5) {
+            /* $file_body_element = $struct */
+            ctx.rule = rules.get(5);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_struct(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "file_body_element",
+            current,
+            nonterminal_first.get(134),
+            rules.get(5)
+        ));
+    }
+    public ParseTree parse_if_stmt(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_if_stmt(ctx);
+    }
+    private static ParseTree parse_if_stmt(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[2][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(69, "if_stmt"));
+        ctx.nonterminal = "if_stmt";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "if_stmt",
+                nonterminal_first.get(69),
+                nonterminal_rules.get(69)
+            ));
+        }
+        if (rule == 85) {
+            /* $if_stmt = :if :lparen $e :rparen :lbrace $_gen15 :rbrace -> If( expression=$2, body=$5 ) */
+            ctx.rule = rules.get(85);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("expression", 2);
+            parameters.put("body", 5);
+            tree.setAstTransformation(new AstTransformNodeCreator("If", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IF);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LPAREN);
+            tree.add(next);
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RPAREN);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE);
+            tree.add(next);
+            subtree = parse__gen15(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "if_stmt",
+            current,
+            nonterminal_first.get(69),
+            rules.get(85)
+        ));
+    }
+    public ParseTree parse_import(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_import(ctx);
+    }
+    private static ParseTree parse_import(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[19][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(86, "import"));
+        ctx.nonterminal = "import";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "import",
+                nonterminal_first.get(86),
+                nonterminal_rules.get(86)
+            ));
+        }
+        if (rule == 21) {
+            /* $import = :import $static_string $_gen5 $_gen6 -> Import( uri=$1, namespace=$2, aliases=$3 ) */
+            ctx.rule = rules.get(21);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("uri", 1);
+            parameters.put("namespace", 2);
+            parameters.put("aliases", 3);
+            tree.setAstTransformation(new AstTransformNodeCreator("Import", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IMPORT);
+            tree.add(next);
+            subtree = parse_static_string(ctx);
+            tree.add(subtree);
+            subtree = parse__gen5(ctx);
+            tree.add(subtree);
+            subtree = parse__gen6(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "import",
+            current,
+            nonterminal_first.get(86),
+            rules.get(21)
+        ));
+    }
+    public ParseTree parse_import_alias(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_import_alias(ctx);
+    }
+    private static ParseTree parse_import_alias(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[15][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(82, "import_alias"));
+        ctx.nonterminal = "import_alias";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "import_alias",
+                nonterminal_first.get(82),
+                nonterminal_rules.get(82)
+            ));
+        }
+        if (rule == 23) {
+            /* $import_alias = :alias :identifier :as :identifier -> ImportAlias( old_name=$1, new_name=$3 ) */
+            ctx.rule = rules.get(23);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("old_name", 1);
+            parameters.put("new_name", 3);
+            tree.setAstTransformation(new AstTransformNodeCreator("ImportAlias", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_ALIAS);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_AS);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "import_alias",
+            current,
+            nonterminal_first.get(82),
+            rules.get(23)
+        ));
+    }
+    public ParseTree parse_import_namespace(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_import_namespace(ctx);
+    }
+    private static ParseTree parse_import_namespace(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[24][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(91, "import_namespace"));
+        ctx.nonterminal = "import_namespace";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "import_namespace",
+                nonterminal_first.get(91),
+                nonterminal_rules.get(91)
+            ));
+        }
+        if (rule == 22) {
+            /* $import_namespace = :as :identifier -> $1 */
+            ctx.rule = rules.get(22);
+            tree.setAstTransformation(new AstTransformSubstitution(1));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_AS);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "import_namespace",
+            current,
+            nonterminal_first.get(91),
+            rules.get(22)
+        ));
+    }
+    public ParseTree parse_input_declaration(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_input_declaration(ctx);
+    }
+    private static ParseTree parse_input_declaration(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[58][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(125, "input_declaration"));
+        ctx.nonterminal = "input_declaration";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "input_declaration",
+                nonterminal_first.get(125),
+                nonterminal_rules.get(125)
+            ));
+        }
+        if (rule == 53) {
+            /* $input_declaration = $type_e :identifier $_gen13 -> InputDeclaration( type=$0, name=$1, expression=$2 ) */
+            ctx.rule = rules.get(53);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("type", 0);
+            parameters.put("name", 1);
+            parameters.put("expression", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("InputDeclaration", parameters));
+            subtree = parse_type_e(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            subtree = parse__gen13(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "input_declaration",
+            current,
+            nonterminal_first.get(125),
+            rules.get(53)
+        ));
+    }
+    public ParseTree parse_input_kv(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_input_kv(ctx);
+    }
+    private static ParseTree parse_input_kv(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[9][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(76, "input_kv"));
+        ctx.nonterminal = "input_kv";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "input_kv",
+                nonterminal_first.get(76),
+                nonterminal_rules.get(76)
+            ));
+        }
+        if (rule == 88) {
+            /* $input_kv = :identifier :equal $e -> ObjectKV( key=$0, value=$2 ) */
+            ctx.rule = rules.get(88);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("key", 0);
+            parameters.put("value", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("ObjectKV", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_EQUAL);
+            tree.add(next);
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "input_kv",
+            current,
+            nonterminal_first.get(76),
+            rules.get(88)
+        ));
+    }
+    public ParseTree parse_inputs(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_inputs(ctx);
+    }
+    private static ParseTree parse_inputs(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[16][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(83, "inputs"));
+        ctx.nonterminal = "inputs";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "inputs",
+                nonterminal_first.get(83),
+                nonterminal_rules.get(83)
+            ));
+        }
+        if (rule == 41) {
+            /* $inputs = :input :lbrace $_gen10 :rbrace -> Inputs( inputs=$2 ) */
+            ctx.rule = rules.get(41);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("inputs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Inputs", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_INPUT);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE);
+            tree.add(next);
+            subtree = parse__gen10(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "inputs",
+            current,
+            nonterminal_first.get(83),
+            rules.get(41)
+        ));
+    }
+    public ParseTree parse_kv(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_kv(ctx);
+    }
+    private static ParseTree parse_kv(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[12][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(79, "kv"));
+        ctx.nonterminal = "kv";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "kv",
+                nonterminal_first.get(79),
+                nonterminal_rules.get(79)
+            ));
+        }
+        if (rule == 45) {
+            /* $kv = :identifier :colon $e -> RuntimeAttribute( key=$0, value=$2 ) */
+            ctx.rule = rules.get(45);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("key", 0);
+            parameters.put("value", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("RuntimeAttribute", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_COLON);
+            tree.add(next);
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "kv",
+            current,
+            nonterminal_first.get(79),
+            rules.get(45)
+        ));
+    }
+    public ParseTree parse_map_kv(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_map_kv(ctx);
+    }
+    private static ParseTree parse_map_kv(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[18][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(85, "map_kv"));
+        ctx.nonterminal = "map_kv";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "map_kv",
+                nonterminal_first.get(85),
+                nonterminal_rules.get(85)
+            ));
+        }
+        if (rule == 56) {
+            /* $map_kv = $e :colon $e -> MapLiteralKv( key=$0, value=$2 ) */
+            ctx.rule = rules.get(56);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("key", 0);
+            parameters.put("value", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("MapLiteralKv", parameters));
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_COLON);
+            tree.add(next);
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "map_kv",
+            current,
+            nonterminal_first.get(85),
+            rules.get(56)
+        ));
+    }
+    public ParseTree parse_meta(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_meta(ctx);
+    }
+    private static ParseTree parse_meta(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[59][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(126, "meta"));
+        ctx.nonterminal = "meta";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "meta",
+                nonterminal_first.get(126),
+                nonterminal_rules.get(126)
+            ));
+        }
+        if (rule == 46) {
+            /* $meta = :meta $meta_map -> Meta( map=$1 ) */
+            ctx.rule = rules.get(46);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("map", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("Meta", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_META);
+            tree.add(next);
+            subtree = parse_meta_map(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "meta",
+            current,
+            nonterminal_first.get(126),
+            rules.get(46)
+        ));
+    }
+    public ParseTree parse_meta_kv(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_meta_kv(ctx);
+    }
+    private static ParseTree parse_meta_kv(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[10][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(77, "meta_kv"));
+        ctx.nonterminal = "meta_kv";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "meta_kv",
+                nonterminal_first.get(77),
+                nonterminal_rules.get(77)
+            ));
+        }
+        if (rule == 50) {
+            /* $meta_kv = :identifier :colon $meta_value -> MetaKvPair( key=$0, value=$2 ) */
+            ctx.rule = rules.get(50);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("key", 0);
+            parameters.put("value", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("MetaKvPair", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_COLON);
+            tree.add(next);
+            subtree = parse_meta_value(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "meta_kv",
+            current,
+            nonterminal_first.get(77),
+            rules.get(50)
+        ));
+    }
+    public ParseTree parse_meta_map(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_meta_map(ctx);
+    }
+    private static ParseTree parse_meta_map(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[48][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(115, "meta_map"));
+        ctx.nonterminal = "meta_map";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "meta_map",
+                nonterminal_first.get(115),
+                nonterminal_rules.get(115)
+            ));
+        }
+        if (rule == 49) {
+            /* $meta_map = :lbrace $_gen12 :rbrace -> $1 */
+            ctx.rule = rules.get(49);
+            tree.setAstTransformation(new AstTransformSubstitution(1));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE);
+            tree.add(next);
+            subtree = parse__gen12(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "meta_map",
+            current,
+            nonterminal_first.get(115),
+            rules.get(49)
+        ));
+    }
+    public ParseTree parse_object_kv(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_object_kv(ctx);
+    }
+    private static ParseTree parse_object_kv(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[47][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(114, "object_kv"));
+        ctx.nonterminal = "object_kv";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "object_kv",
+                nonterminal_first.get(114),
+                nonterminal_rules.get(114)
+            ));
+        }
+        if (rule == 87) {
+            /* $object_kv = :identifier :colon $e -> ObjectKV( key=$0, value=$2 ) */
+            ctx.rule = rules.get(87);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("key", 0);
+            parameters.put("value", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("ObjectKV", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_COLON);
+            tree.add(next);
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "object_kv",
+            current,
+            nonterminal_first.get(114),
+            rules.get(87)
+        ));
+    }
+    public ParseTree parse_output_kv(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_output_kv(ctx);
+    }
+    private static ParseTree parse_output_kv(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[40][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(107, "output_kv"));
+        ctx.nonterminal = "output_kv";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "output_kv",
+                nonterminal_first.get(107),
+                nonterminal_rules.get(107)
+            ));
+        }
+        if (rule == 59) {
+            /* $output_kv = $type_e :identifier :equal $e -> Output( type=$0, name=$1, expression=$3 ) */
+            ctx.rule = rules.get(59);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("type", 0);
+            parameters.put("name", 1);
+            parameters.put("expression", 3);
+            tree.setAstTransformation(new AstTransformNodeCreator("Output", parameters));
+            subtree = parse_type_e(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_EQUAL);
+            tree.add(next);
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "output_kv",
+            current,
+            nonterminal_first.get(107),
+            rules.get(59)
+        ));
+    }
+    public ParseTree parse_outputs(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_outputs(ctx);
+    }
+    private static ParseTree parse_outputs(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[44][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(111, "outputs"));
+        ctx.nonterminal = "outputs";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "outputs",
+                nonterminal_first.get(111),
+                nonterminal_rules.get(111)
+            ));
+        }
+        if (rule == 58) {
+            /* $outputs = :output :lbrace $_gen14 :rbrace -> Outputs( outputs=$2 ) */
+            ctx.rule = rules.get(58);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("outputs", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("Outputs", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_OUTPUT);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE);
+            tree.add(next);
+            subtree = parse__gen14(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "outputs",
+            current,
+            nonterminal_first.get(111),
+            rules.get(58)
+        ));
+    }
+    public ParseTree parse_parameter_meta(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_parameter_meta(ctx);
+    }
+    private static ParseTree parse_parameter_meta(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[5][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(72, "parameter_meta"));
+        ctx.nonterminal = "parameter_meta";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "parameter_meta",
+                nonterminal_first.get(72),
+                nonterminal_rules.get(72)
+            ));
+        }
+        if (rule == 47) {
+            /* $parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 ) */
+            ctx.rule = rules.get(47);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("map", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("ParameterMeta", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_PARAMETER_META);
+            tree.add(next);
+            subtree = parse_meta_map(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "parameter_meta",
+            current,
+            nonterminal_first.get(72),
+            rules.get(47)
+        ));
+    }
+    public ParseTree parse_rt_map(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_rt_map(ctx);
+    }
+    private static ParseTree parse_rt_map(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[26][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(93, "rt_map"));
+        ctx.nonterminal = "rt_map";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "rt_map",
+                nonterminal_first.get(93),
+                nonterminal_rules.get(93)
+            ));
+        }
+        if (rule == 44) {
+            /* $rt_map = :lbrace $_gen11 :rbrace -> $1 */
+            ctx.rule = rules.get(44);
+            tree.setAstTransformation(new AstTransformSubstitution(1));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE);
+            tree.add(next);
+            subtree = parse__gen11(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "rt_map",
+            current,
+            nonterminal_first.get(93),
+            rules.get(44)
+        ));
+    }
+    public ParseTree parse_runtime(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_runtime(ctx);
+    }
+    private static ParseTree parse_runtime(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[64][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(131, "runtime"));
+        ctx.nonterminal = "runtime";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "runtime",
+                nonterminal_first.get(131),
+                nonterminal_rules.get(131)
+            ));
+        }
+        if (rule == 42) {
+            /* $runtime = :runtime $rt_map -> Runtime( map=$1 ) */
+            ctx.rule = rules.get(42);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("map", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("Runtime", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RUNTIME);
+            tree.add(next);
+            subtree = parse_rt_map(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "runtime",
+            current,
+            nonterminal_first.get(131),
+            rules.get(42)
+        ));
+    }
+    public ParseTree parse_scatter(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_scatter(ctx);
+    }
+    private static ParseTree parse_scatter(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[36][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(103, "scatter"));
+        ctx.nonterminal = "scatter";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "scatter",
+                nonterminal_first.get(103),
+                nonterminal_rules.get(103)
+            ));
+        }
+        if (rule == 86) {
+            /* $scatter = :scatter :lparen :identifier :in $e :rparen :lbrace $_gen15 :rbrace -> Scatter( item=$2, collection=$4, body=$7 ) */
+            ctx.rule = rules.get(86);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("item", 2);
+            parameters.put("collection", 4);
+            parameters.put("body", 7);
+            tree.setAstTransformation(new AstTransformNodeCreator("Scatter", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_SCATTER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LPAREN);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IN);
+            tree.add(next);
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RPAREN);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE);
+            tree.add(next);
+            subtree = parse__gen15(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "scatter",
+            current,
+            nonterminal_first.get(103),
+            rules.get(86)
+        ));
+    }
+    public ParseTree parse_setter(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_setter(ctx);
+    }
+    private static ParseTree parse_setter(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[32][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(99, "setter"));
+        ctx.nonterminal = "setter";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "setter",
+                nonterminal_first.get(99),
+                nonterminal_rules.get(99)
+            ));
+        }
+        if (rule == 55) {
+            /* $setter = :equal $e -> $1 */
+            ctx.rule = rules.get(55);
+            tree.setAstTransformation(new AstTransformSubstitution(1));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_EQUAL);
+            tree.add(next);
+            subtree = parse_e(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "setter",
+            current,
+            nonterminal_first.get(99),
+            rules.get(55)
+        ));
+    }
+    public ParseTree parse_static_string(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_static_string(ctx);
+    }
+    private static ParseTree parse_static_string(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[39][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(106, "static_string"));
+        ctx.nonterminal = "static_string";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "static_string",
+                nonterminal_first.get(106),
+                nonterminal_rules.get(106)
+            ));
+        }
+        if (rule == 11) {
+            /* $static_string = :quote $_gen3 :quote -> StaticString( value=$1 ) */
+            ctx.rule = rules.get(11);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("value", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("StaticString", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_QUOTE);
+            tree.add(next);
+            subtree = parse__gen3(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_QUOTE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "static_string",
+            current,
+            nonterminal_first.get(106),
+            rules.get(11)
+        ));
+    }
+    public ParseTree parse_static_string_piece(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_static_string_piece(ctx);
+    }
+    private static ParseTree parse_static_string_piece(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[51][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(118, "static_string_piece"));
+        ctx.nonterminal = "static_string_piece";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "static_string_piece",
+                nonterminal_first.get(118),
+                nonterminal_rules.get(118)
+            ));
+        }
+        if (rule == 14) {
+            /* $static_string_piece = :string */
+            ctx.rule = rules.get(14);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_STRING);
+            tree.add(next);
+            return tree;
+        }
+        else if (rule == 15) {
+            /* $static_string_piece = :escape */
+            ctx.rule = rules.get(15);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_ESCAPE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "static_string_piece",
+            current,
+            nonterminal_first.get(118),
+            rules.get(15)
+        ));
+    }
+    public ParseTree parse_string_literal(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_string_literal(ctx);
+    }
+    private static ParseTree parse_string_literal(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[30][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(97, "string_literal"));
+        ctx.nonterminal = "string_literal";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "string_literal",
+                nonterminal_first.get(97),
+                nonterminal_rules.get(97)
+            ));
+        }
+        if (rule == 13) {
+            /* $string_literal = :quote $_gen4 :quote -> StringLiteral( pieces=$1 ) */
+            ctx.rule = rules.get(13);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("pieces", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("StringLiteral", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_QUOTE);
+            tree.add(next);
+            subtree = parse__gen4(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_QUOTE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "string_literal",
+            current,
+            nonterminal_first.get(97),
+            rules.get(13)
+        ));
+    }
+    public ParseTree parse_string_piece(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_string_piece(ctx);
+    }
+    private static ParseTree parse_string_piece(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[35][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(102, "string_piece"));
+        ctx.nonterminal = "string_piece";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "string_piece",
+                nonterminal_first.get(102),
+                nonterminal_rules.get(102)
+            ));
+        }
+        if (rule == 16) {
+            /* $string_piece = $static_string_piece */
+            ctx.rule = rules.get(16);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_static_string_piece(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 17) {
+            /* $string_piece = $expression_placeholder */
+            ctx.rule = rules.get(17);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_expression_placeholder(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "string_piece",
+            current,
+            nonterminal_first.get(102),
+            rules.get(17)
+        ));
+    }
+    public ParseTree parse_struct(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_struct(ctx);
+    }
+    private static ParseTree parse_struct(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[23][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(90, "struct"));
+        ctx.nonterminal = "struct";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "struct",
+                nonterminal_first.get(90),
+                nonterminal_rules.get(90)
+            ));
+        }
+        if (rule == 8) {
+            /* $struct = :struct :identifier :lbrace $_gen2 :rbrace -> Struct( name=$1, entries=$3 ) */
+            ctx.rule = rules.get(8);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("name", 1);
+            parameters.put("entries", 3);
+            tree.setAstTransformation(new AstTransformNodeCreator("Struct", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_STRUCT);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE);
+            tree.add(next);
+            subtree = parse__gen2(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "struct",
+            current,
+            nonterminal_first.get(90),
+            rules.get(8)
+        ));
+    }
+    public ParseTree parse_struct_declaration(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_struct_declaration(ctx);
+    }
+    private static ParseTree parse_struct_declaration(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[45][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(112, "struct_declaration"));
+        ctx.nonterminal = "struct_declaration";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "struct_declaration",
+                nonterminal_first.get(112),
+                nonterminal_rules.get(112)
+            ));
+        }
+        if (rule == 9) {
+            /* $struct_declaration = $type_e :identifier -> StructEntry( type=$0, name=$1 ) */
+            ctx.rule = rules.get(9);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("type", 0);
+            parameters.put("name", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("StructEntry", parameters));
+            subtree = parse_type_e(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "struct_declaration",
+            current,
+            nonterminal_first.get(112),
+            rules.get(9)
+        ));
+    }
+    public ParseTree parse_task(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_task(ctx);
+    }
+    private static ParseTree parse_task(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[1][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(68, "task"));
+        ctx.nonterminal = "task";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "task",
+                nonterminal_first.get(68),
+                nonterminal_rules.get(68)
+            ));
+        }
+        if (rule == 25) {
+            /* $task = :task :identifier :lbrace $_gen7 :rbrace -> Task( name=$1, sections=$3 ) */
+            ctx.rule = rules.get(25);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("name", 1);
+            parameters.put("sections", 3);
+            tree.setAstTransformation(new AstTransformNodeCreator("Task", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_TASK);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE);
+            tree.add(next);
+            subtree = parse__gen7(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "task",
+            current,
+            nonterminal_first.get(68),
+            rules.get(25)
+        ));
+    }
+    public ParseTree parse_task_sections(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_task_sections(ctx);
+    }
+    private static ParseTree parse_task_sections(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[70][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(137, "task_sections"));
+        ctx.nonterminal = "task_sections";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "task_sections",
+                nonterminal_first.get(137),
+                nonterminal_rules.get(137)
+            ));
+        }
+        if (rule == 26) {
+            /* $task_sections = $command */
+            ctx.rule = rules.get(26);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_command(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 27) {
+            /* $task_sections = $inputs */
+            ctx.rule = rules.get(27);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_inputs(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 28) {
+            /* $task_sections = $outputs */
+            ctx.rule = rules.get(28);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_outputs(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 29) {
+            /* $task_sections = $runtime */
+            ctx.rule = rules.get(29);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_runtime(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 30) {
+            /* $task_sections = $parameter_meta */
+            ctx.rule = rules.get(30);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_parameter_meta(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 31) {
+            /* $task_sections = $meta */
+            ctx.rule = rules.get(31);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_meta(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 32) {
+            /* $task_sections = $declaration */
+            ctx.rule = rules.get(32);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_declaration(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "task_sections",
+            current,
+            nonterminal_first.get(137),
+            rules.get(32)
+        ));
+    }
+    public ParseTree parse_version(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_version(ctx);
+    }
+    private static ParseTree parse_version(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[17][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(84, "version"));
+        ctx.nonterminal = "version";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "version",
+                nonterminal_first.get(84),
+                nonterminal_rules.get(84)
+            ));
+        }
+        if (rule == 6) {
+            /* $version = :version :version_name -> VersionDeclaration( v=$1 ) */
+            ctx.rule = rules.get(6);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("v", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("VersionDeclaration", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_VERSION);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_VERSION_NAME);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "version",
+            current,
+            nonterminal_first.get(84),
+            rules.get(6)
+        ));
+    }
+    public ParseTree parse_wf_body_element(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_wf_body_element(ctx);
+    }
+    private static ParseTree parse_wf_body_element(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[4][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(71, "wf_body_element"));
+        ctx.nonterminal = "wf_body_element";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "wf_body_element",
+                nonterminal_first.get(71),
+                nonterminal_rules.get(71)
+            ));
+        }
+        if (rule == 62) {
+            /* $wf_body_element = $call */
+            ctx.rule = rules.get(62);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_call(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 63) {
+            /* $wf_body_element = $declaration */
+            ctx.rule = rules.get(63);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_declaration(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 64) {
+            /* $wf_body_element = $if_stmt */
+            ctx.rule = rules.get(64);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_if_stmt(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 65) {
+            /* $wf_body_element = $scatter */
+            ctx.rule = rules.get(65);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_scatter(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 66) {
+            /* $wf_body_element = $inputs */
+            ctx.rule = rules.get(66);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_inputs(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 67) {
+            /* $wf_body_element = $outputs */
+            ctx.rule = rules.get(67);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_outputs(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 68) {
+            /* $wf_body_element = $wf_parameter_meta */
+            ctx.rule = rules.get(68);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_wf_parameter_meta(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        else if (rule == 69) {
+            /* $wf_body_element = $wf_meta */
+            ctx.rule = rules.get(69);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            subtree = parse_wf_meta(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "wf_body_element",
+            current,
+            nonterminal_first.get(71),
+            rules.get(69)
+        ));
+    }
+    public ParseTree parse_wf_meta(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_wf_meta(ctx);
+    }
+    private static ParseTree parse_wf_meta(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[71][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(138, "wf_meta"));
+        ctx.nonterminal = "wf_meta";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "wf_meta",
+                nonterminal_first.get(138),
+                nonterminal_rules.get(138)
+            ));
+        }
+        if (rule == 84) {
+            /* $wf_meta = :meta $meta_map -> Meta( map=$1 ) */
+            ctx.rule = rules.get(84);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("map", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("Meta", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_META);
+            tree.add(next);
+            subtree = parse_meta_map(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "wf_meta",
+            current,
+            nonterminal_first.get(138),
+            rules.get(84)
+        ));
+    }
+    public ParseTree parse_wf_parameter_meta(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_wf_parameter_meta(ctx);
+    }
+    private static ParseTree parse_wf_parameter_meta(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[41][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(108, "wf_parameter_meta"));
+        ctx.nonterminal = "wf_parameter_meta";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "wf_parameter_meta",
+                nonterminal_first.get(108),
+                nonterminal_rules.get(108)
+            ));
+        }
+        if (rule == 83) {
+            /* $wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 ) */
+            ctx.rule = rules.get(83);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("map", 1);
+            tree.setAstTransformation(new AstTransformNodeCreator("ParameterMeta", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_PARAMETER_META);
+            tree.add(next);
+            subtree = parse_meta_map(ctx);
+            tree.add(subtree);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "wf_parameter_meta",
+            current,
+            nonterminal_first.get(108),
+            rules.get(83)
+        ));
+    }
+    public ParseTree parse_workflow(List<Terminal> tokens, SyntaxErrorFormatter error_formatter) throws SyntaxError {
+        ParserContext ctx = new ParserContext(new TokenStream(tokens), error_formatter);
+        return parse_workflow(ctx);
+    }
+    private static ParseTree parse_workflow(ParserContext ctx) throws SyntaxError {
+        Terminal current = ctx.tokens.current();
+        Terminal next;
+        ParseTree subtree;
+        int rule = (current != null) ? table[27][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(94, "workflow"));
+        ctx.nonterminal = "workflow";
+        if (current == null) {
+            throw new SyntaxError(ctx.error_formatter.unexpectedEof(
+                "workflow",
+                nonterminal_first.get(94),
+                nonterminal_rules.get(94)
+            ));
+        }
+        if (rule == 61) {
+            /* $workflow = :workflow :identifier :lbrace $_gen15 :rbrace -> Workflow( name=$1, body=$3 ) */
+            ctx.rule = rules.get(61);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("name", 1);
+            parameters.put("body", 3);
+            tree.setAstTransformation(new AstTransformNodeCreator("Workflow", parameters));
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_WORKFLOW);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER);
+            tree.add(next);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE);
+            tree.add(next);
+            subtree = parse__gen15(ctx);
+            tree.add(subtree);
+            next = expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE);
+            tree.add(next);
+            return tree;
+        }
+        throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
+            "workflow",
+            current,
+            nonterminal_first.get(94),
+            rules.get(61)
+        ));
+    }
+    /* Section: Lexer */
+    private Map<String, List<HermesRegex>> regex = null;
+    private interface LexerOutput {}
+    private class LexerRegexOutput implements LexerOutput {
+        public WdlTerminalIdentifier terminal;
+        public int group;
+        public Method function;
+        LexerRegexOutput(WdlTerminalIdentifier terminal, int group, Method function) {
+            this.terminal = terminal;
+            this.group = group;
+            this.function = function;
+        }
+        public String toString() {
+            return String.format("<LexerRegexOutput terminal=%s, group=%d, func=%s>", this.terminal, this.group, this.function);
+        }
+    }
+    private class LexerStackPush implements LexerOutput {
+        public String mode;
+        LexerStackPush(String mode) {
+            this.mode = mode;
+        }
+    }
+    private class LexerAction implements LexerOutput {
+        public String action;
+        LexerAction(String action) {
+            this.action = action;
+        }
+    }
+    private class HermesRegex {
+        public Pattern pattern;
+        public List<LexerOutput> outputs;
+        HermesRegex(Pattern pattern, List<LexerOutput> outputs) {
+            this.pattern = pattern;
+            this.outputs = outputs;
+        }
+        public String toString() {
+            return String.format("<HermesRegex pattern=%s, outputs=%s>", this.pattern, this.outputs);
+        }
+    }
+    private class LineColumn {
+        public int line, col;
+        public LineColumn(int line, int col) {
+            this.line = line;
+            this.col = col;
+        }
+        public String toString() {
+            return String.format("<LineColumn: line=%d column=%d>", this.line, this.col);
+        }
+    }
+    private class LexerContext {
+        public String string;
+        public String resource;
+        public int line;
+        public int col;
+        public Stack<String> stack;
+        public Object context;
+        public List<Terminal> terminals;
+        LexerContext(String string, String resource) {
+            this.string = string;
+            this.resource = resource;
+            this.line = 1;
+            this.col = 1;
+            this.stack = new Stack<String>();
+            this.stack.push("default");
+            this.terminals = new ArrayList<Terminal>();
+        }
+        public void advance(String match) {
+            LineColumn lc = advance_line_col(match, match.length());
+            this.line = lc.line;
+            this.col = lc.col;
+            this.string = this.string.substring(match.length());
+        }
+        public LineColumn advance_line_col(String match, int length) {
+            LineColumn lc = new LineColumn(this.line, this.col);
+            for (int i = 0; i < length && i < match.length(); i++) {
+                if (match.charAt(i) == '\n') {
+                    lc.line += 1;
+                    lc.col = 1;
+                } else {
+                    lc.col += 1;
+                }
+            }
+            return lc;
+        }
+    }
+    private void emit(LexerContext lctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+        lctx.terminals.add(new Terminal(terminal.id(), terminal.string(), source_string, lctx.resource, line, col));
+    }
+    /**
+     * The default function that is called on every regex match during lexical analysis.
+     * By default, this simply calls the emit() function with all of the same parameters.
+     * This can be overridden in the grammar file to provide a different default action.
+     *
+     * @param lctx The current state of the lexical analyzer
+     * @param terminal The current terminal that was matched
+     * @param source_string The source code that was matched
+     * @param line The line where the match happened
+     * @param col The column where the match happened
+     * @return void
+     */
+    public void default_action(LexerContext lctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+        emit(lctx, terminal, source_string, line, col);
+    }
+    /* START USER CODE */
+    private class WdlContext {
+    public String wf_or_task = null;
+}
+public Object init() {
+    return new WdlContext();
+}
+public void workflow(LexerContext ctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+    ((WdlContext) ctx.context).wf_or_task = "workflow";
+    default_action(ctx, terminal, source_string, line, col);
+}
+public void task(LexerContext ctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+    ((WdlContext) ctx.context).wf_or_task = "task";
+    default_action(ctx, terminal, source_string, line, col);
+}
+public void output(LexerContext ctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+    WdlContext user_ctx = (WdlContext) ctx.context;
+    if (user_ctx.wf_or_task != null && user_ctx.wf_or_task.equals("workflow")) {
+        ctx.stack.push("wf_output");
+    }
+    default_action(ctx, terminal, source_string, line, col);
+}
+    /* END USER CODE */
+    public List<Terminal> post_filter(List<Terminal> terminals) {
+        return terminals;
+    }
+    public void destroy(Object context) {
+        return;
+    }
+    private Method getFunction(String name) throws SyntaxError {
+        try {
+            return getClass().getMethod(
+                name,
+                LexerContext.class,
+                TerminalIdentifier.class,
+                String.class,
+                int.class,
+                int.class
+            );
+        } catch (NoSuchMethodException e) {
+            throw new SyntaxError("No such method: " + name);
+        }
+    }
+    private void lexer_init() throws SyntaxError {
+        this.regex = new HashMap<String, List<HermesRegex>>();
+        this.regex.put("default", Arrays.asList(new HermesRegex[] {
+            new HermesRegex(
+                Pattern.compile("#.*"),
+                Arrays.asList(new LexerOutput[] {
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\s+"),
+                Arrays.asList(new LexerOutput[] {
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("^version(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_VERSION,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("awaiting_version_name"),
+                })
+            ),
+        }));
+        this.regex.put("main", Arrays.asList(new HermesRegex[] {
+            new HermesRegex(
+                Pattern.compile("\\s+"),
+                Arrays.asList(new LexerOutput[] {
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("/\\*(.*?)\\*/", Pattern.DOTALL),
+                Arrays.asList(new LexerOutput[] {
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("#.*"),
+                Arrays.asList(new LexerOutput[] {
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("task(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_TASK,
+                        0,
+                        getFunction("task")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("(call)\\s+"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_CALL,
+                        1,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("task_fqn"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("after(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_AFTER,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("workflow(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_WORKFLOW,
+                        0,
+                        getFunction("workflow")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("struct(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_STRUCT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("import(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_IMPORT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("alias(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ALIAS,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("input(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_INPUT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("output(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_OUTPUT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("as(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_AS,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("if(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_IF,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("then(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_THEN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("else(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ELSE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("runtime(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RUNTIME,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("scatter(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_SCATTER,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("scatter"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("command\\s*(?=<<<)"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("raw_command2"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("command\\s*(?=\\{)"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("raw_command"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("parameter_meta(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("meta(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_META,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("(true|false)(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("(object)\\s*(\\{)"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_OBJECT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LBRACE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("(Array|Map|Pair|Boolean|Int|Float|File|Directory|String)(?![a-zA-Z0-9_])(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_TYPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("None"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_NONE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("[a-zA-Z]([a-zA-Z0-9_])*"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("null"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_NULL,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile(":"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_COLON,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile(","),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_COMMA,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("=="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DOUBLE_EQUAL,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\|\\|"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DOUBLE_PIPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\&\\&"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DOUBLE_AMPERSAND,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("!="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_NOT_EQUAL,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EQUAL,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\."),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DOT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\{"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LBRACE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\}"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RBRACE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\("),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LPAREN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\)"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RPAREN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\["),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LSQUARE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RSQUARE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\+"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_PLUS,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\*"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ASTERISK,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("-"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DASH,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("/"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_SLASH,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("%"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_PERCENT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("<="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LTEQ,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("<"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile(">="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_GTEQ,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile(">"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_GT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("!"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_NOT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\""),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_QUOTE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("dquote_string"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\'"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_QUOTE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("squote_string"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\?"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_QMARK,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("-?[0-9]+\\.[0-9]+"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_FLOAT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("[0-9]+"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_INTEGER,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+        }));
+        this.regex.put("dquote_string", Arrays.asList(new HermesRegex[] {
+            new HermesRegex(
+                Pattern.compile("\""),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_QUOTE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerAction("pop"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\$\\{"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("expression_placeholder"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("~\\{"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("expression_placeholder"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\\\[0-7][0-7][0-7]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ESCAPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\\\x[0-9A-Fa-f][0-9A-Fa-f]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ESCAPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\\\u[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ESCAPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\\\U[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ESCAPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\\\."),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ESCAPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("(.*?)(?=\\\\|\\$\\{|~\\{|\")"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_STRING,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+        }));
+        this.regex.put("squote_string", Arrays.asList(new HermesRegex[] {
+            new HermesRegex(
+                Pattern.compile("\\'"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_QUOTE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerAction("pop"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\$\\{"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("expression_placeholder"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("~\\{"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("expression_placeholder"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\\\[0-7][0-7][0-7]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ESCAPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\\\x[0-9A-Fa-f][0-9A-Fa-f]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ESCAPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\\\u[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ESCAPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\\\U[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ESCAPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\\\."),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ESCAPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("(.*?)(?=\\\\|\\$\\{|~\\{|\')"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_STRING,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+        }));
+        this.regex.put("awaiting_version_name", Arrays.asList(new HermesRegex[] {
+            new HermesRegex(
+                Pattern.compile("\\s+"),
+                Arrays.asList(new LexerOutput[] {
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("development"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_VERSION_NAME,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("main"),
+                })
+            ),
+        }));
+        this.regex.put("task_fqn", Arrays.asList(new HermesRegex[] {
+            new HermesRegex(
+                Pattern.compile("\\s+"),
+                Arrays.asList(new LexerOutput[] {
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("[a-zA-Z]([a-zA-Z0-9_])*(\\.[a-zA-Z]([a-zA-Z0-9_])*)*"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_FQN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerAction("pop"),
+                })
+            ),
+        }));
+        this.regex.put("scatter", Arrays.asList(new HermesRegex[] {
+            new HermesRegex(
+                Pattern.compile("\\s+"),
+                Arrays.asList(new LexerOutput[] {
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\("),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LPAREN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("in(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_IN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerAction("pop"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("[a-zA-Z]([a-zA-Z0-9_])*"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+        }));
+        this.regex.put("raw_command", Arrays.asList(new HermesRegex[] {
+            new HermesRegex(
+                Pattern.compile("\\{"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RAW_CMD_START,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\}"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerAction("pop"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\$\\{"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("expression_placeholder"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("~\\{"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("expression_placeholder"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("(.*?)(?=\\$\\{|~\\{|\\})", Pattern.DOTALL),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_CMD_PART,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+        }));
+        this.regex.put("raw_command2", Arrays.asList(new HermesRegex[] {
+            new HermesRegex(
+                Pattern.compile("<<<"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RAW_CMD_START,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile(">>>"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerAction("pop"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("~\\{"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("expression_placeholder"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("(.*?)(?=~\\{|>>>)", Pattern.DOTALL),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_CMD_PART,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+        }));
+        this.regex.put("expression_placeholder", Arrays.asList(new HermesRegex[] {
+            new HermesRegex(
+                Pattern.compile("\\s+"),
+                Arrays.asList(new LexerOutput[] {
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\}"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_END,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerAction("pop"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\["),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LSQUARE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RSQUARE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EQUAL,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\+"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_PLUS,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\*"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ASTERISK,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("[0-9]+"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_INTEGER,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("if"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_IF,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("else"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ELSE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("then"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_THEN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("[a-zA-Z]([a-zA-Z0-9_])*(?=\\s*=)"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
+                        -1,
+                        getFunction("default_action")
+                    ),
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("(true|false)(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_BOOLEAN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("(Array|Map|Pair|Boolean|Int|Float|File|Directory|String)(?![a-zA-Z0-9_])(?![a-zA-Z0-9_])"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_TYPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("None"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_NONE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("[a-zA-Z]([a-zA-Z0-9_])*"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile(":"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_COLON,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile(","),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_COMMA,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\."),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DOT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("=="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DOUBLE_EQUAL,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\|\\|"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DOUBLE_PIPE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\&\\&"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DOUBLE_AMPERSAND,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("!="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_NOT_EQUAL,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_EQUAL,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\."),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DOT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\{"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LBRACE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\("),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LPAREN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\)"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RPAREN,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\["),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LSQUARE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\]"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_RSQUARE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\+"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_PLUS,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\*"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_ASTERISK,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("-"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_DASH,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("/"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_SLASH,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("%"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_PERCENT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("<="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LTEQ,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("<"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_LT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile(">="),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_GTEQ,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile(">"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_GT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("!"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_NOT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\""),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_QUOTE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("dquote_string"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("\\'"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_QUOTE,
+                        0,
+                        getFunction("default_action")
+                    ),
+                    new LexerStackPush("squote_string"),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("-?[0-9]+\\.[0-9]+"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_FLOAT,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+            new HermesRegex(
+                Pattern.compile("[0-9]+"),
+                Arrays.asList(new LexerOutput[] {
+                    new LexerRegexOutput(
+                        WdlTerminalIdentifier.TERMINAL_INTEGER,
+                        0,
+                        getFunction("default_action")
+                    ),
+                })
+            ),
+        }));
+    }
+    private void unrecognized_token(String string, int line, int col) throws SyntaxError {
+        String[] a = string.split("\n");
+        String bad_line = string.split("\n")[line-1];
+        StringBuffer spaces = new StringBuffer();
+        for (int i = 0; i < col-1; i++) {
+          spaces.append(' ');
+        }
+        String message = String.format(
+            "Unrecognized token on line %d, column %d:\n\n%s\n%s^",
+            line, col, bad_line, spaces
+        );
+        throw new SyntaxError(message);
+    }
+    private int next(LexerContext lctx) throws SyntaxError {
+        String mode = lctx.stack.peek();
+        for (int i = 0; i < this.regex.get(mode).size(); i++) {
+            HermesRegex regex = this.regex.get(mode).get(i);
+            Matcher matcher = regex.pattern.matcher(lctx.string);
+            if (matcher.lookingAt()) {
+                for (LexerOutput output : regex.outputs) {
+                    if (output instanceof LexerStackPush) {
+                        lctx.stack.push(((LexerStackPush) output).mode);
+                    } else if (output instanceof LexerAction) {
+                        LexerAction action = (LexerAction) output;
+                        if (!action.action.equals("pop")) {
+                            throw new SyntaxError("Invalid action");
+                        }
+                        if (action.action.equals("pop")) {
+                            if (lctx.stack.empty()) {
+                                throw new SyntaxError("Stack empty, cannot pop");
+                            }
+                            lctx.stack.pop();
+                        }
+                    } else if (output instanceof LexerRegexOutput) {
+                        LexerRegexOutput regex_output = (LexerRegexOutput) output;
+                        int group_line = lctx.line;
+                        int group_col = lctx.col;
+                        if (regex_output.group > 0) {
+                            LineColumn lc = lctx.advance_line_col(matcher.group(0), matcher.start(regex_output.group));
+                            group_line = lc.line;
+                            group_col = lc.col;
+                        }
+                        try {
+                            String source_string = (regex_output.group >= 0) ? matcher.group(regex_output.group) : "";
+                            regex_output.function.invoke(
+                                this,
+                                lctx,
+                                regex_output.terminal,
+                                source_string,
+                                group_line,
+                                group_col
+                            );
+                        } catch (Exception e) {
+                            e.printStackTrace();
+                            throw new SyntaxError("Invalid method: " + regex_output.function);
+                        }
+                    }
+                }
+                lctx.advance(matcher.group(0));
+                return matcher.group(0).length();
+            }
+        }
+        return 0;
+    }
+    /**
+     * Lexically analyze WDL source code, return a sequence of tokens.  Output of this
+     * method should be used to construct a TerminalStream and then pass that to parse()
+     *
+     * @param string The WDL source code to analyze
+     * @param resource A descriptor of where this code came from (usually a file path)
+     * @return List of Terminal objects.
+     * @throws SyntaxError If part of the source code could not lexically analyzed
+     */
+    public List<Terminal> lex(String string, String resource) throws SyntaxError {
+        LexerContext lctx = new LexerContext(string, resource);
+        Object context = this.init();
+        lctx.context = context;
+        String string_copy = new String(string);
+        if (this.regex == null) {
+            lexer_init();
+        }
+        while (lctx.string.length() > 0) {
+            int match_length = this.next(lctx);
+            if (match_length == 0) {
+                this.unrecognized_token(string_copy, lctx.line, lctx.col);
+            }
+        }
+        this.destroy(context);
+        List<Terminal> filtered = post_filter(lctx.terminals);
+        return filtered;
+    }
+    /* Section: Main */
+}
diff --git a/wdl/transforms/cascades/src/main/resources/CHANGELOG.txt b/wdl/transforms/cascades/src/main/resources/CHANGELOG.txt
new file mode 100644
index 00000000000..b407769cba8
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/resources/CHANGELOG.txt
@@ -0,0 +1,5 @@
+2023-03-16
+
+Duplicated Cromwell `biscayne` into `cascades` to serve as new home for OpenWDL `development` version. Grammar synced from OpenWDL.
+Will become WDL 1.2 or 2.0.
+Some Terra users run `version development` WDLs, we don't officially support it, but shouldn't break it too badly if possible.
\ No newline at end of file
diff --git a/wdl/transforms/cascades/src/main/resources/grammar.hgr b/wdl/transforms/cascades/src/main/resources/grammar.hgr
new file mode 100644
index 00000000000..0b17648d925
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/resources/grammar.hgr
@@ -0,0 +1,444 @@
+grammar {
+  lexer {
+    partials {
+      r'[a-zA-Z]' -> _identifier_start
+      r'[a-zA-Z0-9_]' -> _identifier_follow
+      r'(Array|Map|Pair|Boolean|Int|Float|File|Directory|String)(?!{%_identifier_follow%})' -> _type
+      r'{%_identifier_start%}({%_identifier_follow%})*' -> _identifier
+    }
+
+    r'#.*' -> null
+    r'\s+' -> null
+    r'^version(?!{%_identifier_follow%})' -> :version @awaiting_version_name
+
+    mode<main> {
+
+      r'\s+' -> null
+
+      enum {
+        python: r'/\*(.*?)\*/' (DOTALL)
+        c: r'/\*(.*?)\*/' (PCRE_DOTALL)
+        java: r'/\*(.*?)\*/' (DOTALL)
+        javascript: r'/\*(.*?)\*/' (m)
+      } -> null
+
+      r'#.*' -> null
+      r'task(?!{%_identifier_follow%})' -> task(:task)
+      r'(call)\s+' -> :call[1] @task_fqn
+      r'after(?!{%_identifier_follow%})' -> :after
+      r'workflow(?!{%_identifier_follow%})' -> workflow(:workflow)
+      r'struct(?!{%_identifier_follow%})' -> :struct
+      r'import(?!{%_identifier_follow%})' -> :import
+      r'alias(?!{%_identifier_follow%})' -> :alias
+      r'input(?!{%_identifier_follow%})' -> :input
+      r'output(?!{%_identifier_follow%})' -> :output
+      r'as(?!{%_identifier_follow%})' -> :as
+      r'if(?!{%_identifier_follow%})' -> :if
+      r'then(?!{%_identifier_follow%})' -> :then
+      r'else(?!{%_identifier_follow%})' -> :else
+      r'runtime(?!{%_identifier_follow%})' -> :runtime
+      r'scatter(?!{%_identifier_follow%})' -> :scatter @scatter
+      r'command\s*(?=<<<)' -> :raw_command  @raw_command2
+      r'command\s*(?=\{)' -> :raw_command  @raw_command
+      r'parameter_meta(?!{%_identifier_follow%})' -> :parameter_meta
+      r'meta(?!{%_identifier_follow%})' -> :meta
+      r'(true|false)(?!{%_identifier_follow%})' -> :boolean
+      r'(object)\s*(\{)' -> :object :lbrace
+      r'{%_type%}(?!{%_identifier_follow%})' -> :type
+      r'None' -> :none
+      r'{%_identifier%}' -> :identifier
+      r'null' -> :null
+
+      r':' -> :colon
+      r',' -> :comma
+      r'==' -> :double_equal
+      r'\|\|' -> :double_pipe
+      r'\&\&' -> :double_ampersand
+      r'!=' -> :not_equal
+      r'=' -> :equal
+      r'\.' -> :dot
+      r'\{' -> :lbrace
+      r'\}' -> :rbrace
+      r'\(' -> :lparen
+      r'\)' -> :rparen
+      r'\[' -> :lsquare
+      r'\]' -> :rsquare
+      r'\+' -> :plus
+      r'\*' -> :asterisk
+      r'-' -> :dash
+      r'/' -> :slash
+      r'%' -> :percent
+      r'<=' -> :lteq
+      r'<' -> :lt
+      r'>=' -> :gteq
+      r'>' -> :gt
+      r'!' -> :not
+
+      enum {
+        python: r'\"'
+        java: "\""
+        javascript:"\""
+      } -> :quote @dquote_string
+      r'\'' -> :quote @squote_string
+      enum {
+        python: r'\?'
+        java: "\\?"
+        javascript: "\\?"
+      } -> :qmark
+      r'-?[0-9]+\.[0-9]+' -> :float
+      r'[0-9]+' -> :integer
+    }
+
+    mode<dquote_string> {
+      # String ends immediately (empty)
+      enum {
+        python: r'\"'
+        java: "\""
+        javascript:"\""
+      } -> :quote %pop
+
+      # String is an expression placeholder
+      r'\$\{' -> :expression_placeholder_start @expression_placeholder
+      r'~\{' -> :expression_placeholder_start @expression_placeholder
+
+      # Escape sequences
+      r'\\[0-7][0-7][0-7]' -> :escape
+      r'\\x[0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+      r'\\u[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+      r'\\U[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+
+      enum {
+        python: r'\\.'
+        java: "\\\\."
+        javascript: "\\."
+      } -> :escape
+
+      # String with ordinary contents
+      enum {
+        python: r'[^\\\"\n(\$\{)(~\{)]*'
+        java: "(.*?)(?=\\\\|\\$\\{|~\\{|\")"
+        javascript: "[^\\\"\\n(${)(~{)]*"
+      } -> :string
+    }
+
+    mode<squote_string> {
+      # String ends immediately (empty)
+      r'\'' -> :quote %pop
+      r'\$\{' -> :expression_placeholder_start @expression_placeholder
+      r'~\{' -> :expression_placeholder_start @expression_placeholder
+
+      # Escape sequences
+      r'\\[0-7][0-7][0-7]' -> :escape
+      r'\\x[0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+      r'\\u[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+      r'\\U[0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f][0-9A-Fa-f]' -> :escape
+
+      enum {
+        python: r'\\.'
+        java: "\\\\."
+        javascript: "\\."
+      } -> :escape
+
+      # String with ordinary contents
+      enum {
+        python: r'[^\\\'\n(\$\{)(~\{)]*'
+        java: "(.*?)(?=\\\\|\\$\\{|~\\{|\')"
+        javascript: "[^\\\'\\n(${)(~{)]*"
+      } -> :string
+    }
+
+    mode<awaiting_version_name> {
+      r'\s+' -> null
+      r'development' -> :version_name @main
+    }
+    mode<task_fqn> {
+      r'\s+' -> null
+      enum {
+        python: r'{%_identifier%}(\.{%_identifier%})*'
+        java: "{%_identifier%}(\\.{%_identifier%})*"
+        javascript: "{%_identifier%}(\\.{%_identifier%})*"
+      } -> :fqn %pop
+    }
+    mode<scatter> {
+      r'\s+' -> null
+      r'\(' -> :lparen
+      r'in(?!{%_identifier_follow%})' -> :in %pop
+      r'{%_identifier%}' -> :identifier
+    }
+    mode<raw_command> {
+      r'\{' -> :raw_cmd_start
+      r'\}' -> :raw_cmd_end %pop
+      r'\$\{' -> :expression_placeholder_start @expression_placeholder
+      r'~\{' -> :expression_placeholder_start @expression_placeholder
+      enum {
+        python: r'(.*?)(?=\$\{|~\{|\})' (DOTALL)
+        c: r'(.*?)(?=\$\{|~\{|\})' (PCRE_DOTALL)
+        java: r'(.*?)(?=\$\{|~\{|\})' (DOTALL)
+        javascript: r'([\s\S]*?)(?=\$\{|~\{|\})' (m)
+      } -> :cmd_part
+    }
+    mode<raw_command2> {
+      r'<<<' -> :raw_cmd_start
+      r'>>>' -> :raw_cmd_end %pop
+      r'~\{' -> :expression_placeholder_start @expression_placeholder
+      enum {
+        python: r'(.*?)(?=~\{|>>>)' (DOTALL)
+        c: r'(.*?)(?=~\{|>>>)' (PCRE_DOTALL)
+        java: r'(.*?)(?=~\{|>>>)' (DOTALL)
+        javascript: r'([\s\S]*?)(?=~\{|>>>)' (m)
+      } -> :cmd_part
+    }
+    mode<expression_placeholder> {
+      r'\s+' -> null
+      r'\}' -> :expression_placeholder_end %pop
+      r'\[' -> :lsquare
+      r'\]' -> :rsquare
+      r'=' -> :equal
+      r'\+' -> :plus
+      r'\*' -> :asterisk
+      r'[0-9]+' -> :integer
+      r'if' -> :if
+      r'else' -> :else
+      r'then' -> :then
+      r'{%_identifier%}(?=\s*=)' -> :cmd_attr_hint[] :identifier
+      r'(true|false)(?!{%_identifier_follow%})' -> :boolean
+      r'{%_type%}(?!{%_identifier_follow%})' -> :type
+      r'None' -> :none
+      r'{%_identifier%}' -> :identifier
+
+      # Expression tokens
+      r':' -> :colon
+      r',' -> :comma
+      r'\.' -> :dot
+      r'==' -> :double_equal
+      r'\|\|' -> :double_pipe
+      r'\&\&' -> :double_ampersand
+      r'!=' -> :not_equal
+      r'=' -> :equal
+      r'\.' -> :dot
+      r'\{' -> :lbrace
+      r'\(' -> :lparen
+      r'\)' -> :rparen
+      r'\[' -> :lsquare
+      r'\]' -> :rsquare
+      r'\+' -> :plus
+      r'\*' -> :asterisk
+      r'-' -> :dash
+      r'/' -> :slash
+      r'%' -> :percent
+      r'<=' -> :lteq
+      r'<' -> :lt
+      r'>=' -> :gteq
+      r'>' -> :gt
+      r'!' -> :not
+
+      # Literals
+      enum {
+        python: r'\"'
+        java: "\""
+        javascript: "\\\\\\\""
+      } -> :quote @dquote_string
+      r'\'' -> :quote @squote_string
+      r'-?[0-9]+\.[0-9]+' -> :float
+      r'[0-9]+' -> :integer
+    }
+
+    code<python> << PYTHON
+    def init():
+        return {
+            'context': None,
+            'replacements': {
+                re.compile(r"\\n"): 0x000A,
+                re.compile(r"\\r"): 0x000D,
+                re.compile(r"\\b"): 0x0008,
+                re.compile(r"\\t"): 0x0009,
+                re.compile(r"\\a"): 0x0007,
+                re.compile(r"\\v"): 0x000B,
+                re.compile(r'\\"'): 0x0022,
+                re.compile(r"\\'"): 0x0027,
+                re.compile(r"\\\?"): 0x003F
+            },
+            'escapes': {
+                re.compile(r'(\\([0-7]{1,3}))'): 8,
+                re.compile(r'(\\[xX]([0-9a-fA-F]{1,4}))'): 16,
+                re.compile(r'(\\[uU]([0-9a-fA-F]{4}))'): 16
+            }
+        }
+    def workflow(ctx, terminal, source_string, line, col):
+        ctx.user_context['context'] = 'workflow'
+        default_action(ctx, terminal, source_string, line, col)
+    def task(ctx, terminal, source_string, line, col):
+        ctx.user_context['context'] = 'task'
+        default_action(ctx, terminal, source_string, line, col)
+    def output(ctx, terminal, source_string, line, col):
+        if ctx.user_context['context'] == 'workflow':
+            ctx.stack.append('wf_output')
+        default_action(ctx, terminal, source_string, line, col)
+    PYTHON
+
+    code<java> << JAVA
+    private class WdlContext {
+        public String wf_or_task = null;
+    }
+    public Object init() {
+        return new WdlContext();
+    }
+    public void workflow(LexerContext ctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+        ((WdlContext) ctx.context).wf_or_task = "workflow";
+        default_action(ctx, terminal, source_string, line, col);
+    }
+    public void task(LexerContext ctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+        ((WdlContext) ctx.context).wf_or_task = "task";
+        default_action(ctx, terminal, source_string, line, col);
+    }
+    public void output(LexerContext ctx, TerminalIdentifier terminal, String source_string, int line, int col) {
+        WdlContext user_ctx = (WdlContext) ctx.context;
+        if (user_ctx.wf_or_task != null && user_ctx.wf_or_task.equals("workflow")) {
+            ctx.stack.push("wf_output");
+        }
+        default_action(ctx, terminal, source_string, line, col);
+    }
+    JAVA
+
+    code<javascript> << JAVASCRIPT
+        function init() {
+            return {wf_or_task: null};
+        }
+        function workflow(ctx, terminal, source_string, line, col) {
+            ctx.user_context.wf_or_task = "workflow";
+            default_action(ctx, terminal, source_string, line, col);
+        }
+        function task(ctx, terminal, source_string, line, col) {
+            ctx.user_context.wf_or_task = "task";
+            default_action(ctx, terminal, source_string, line, col);
+        }
+        function output(ctx, terminal, source_string, line, col) {
+            const user_ctx = ctx.user_context;
+            if (user_ctx.wf_or_task != null && user_ctx.wf_or_task === "workflow") {
+                ctx.mode_stack.push("wf_output");
+            }
+            default_action(ctx, terminal, source_string, line, col);
+        }
+        JAVASCRIPT
+  }
+  parser {
+    # Document: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#document
+    $document = $version list($import) list($file_body_element) -> Draft3File(version=$0, imports=$1, body=$2)
+    $file_body_element = $workflow | $task | $struct
+
+    # Version declaration:
+    $version = :version :version_name -> VersionDeclaration(v = $1)
+
+    $struct = :struct :identifier :lbrace list($struct_declaration) :rbrace -> Struct(name=$1, entries=$3)
+    $struct_declaration = $type_e :identifier -> StructEntry(type=$0, name=$1)
+
+    $static_string = :quote list($static_string_piece) :quote -> StaticString(value=$1)
+    $string_literal = :quote list($string_piece) :quote -> StringLiteral(pieces=$1)
+    $static_string_piece = :string | :escape
+    $string_piece = $static_string_piece | $expression_placeholder
+
+    # Import Statements: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#import-statements
+    $import = :import $static_string optional($import_namespace) list($import_alias) -> Import(uri=$1, namespace=$2, aliases=$3)
+    $import_namespace = :as :identifier -> $1
+    $import_alias = :alias :identifier :as :identifier -> ImportAlias(old_name=$1, new_name=$3)
+
+    # Task Definition: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#task-definition
+    $task = :task :identifier :lbrace list($task_sections) :rbrace -> Task(name=$1, sections=$3)
+    $task_sections = $command | $inputs | $outputs | $runtime | $parameter_meta | $meta | $declaration
+    $command = :raw_command :raw_cmd_start list($command_part) :raw_cmd_end -> RawCommand(parts=$2)
+    $command_part = :cmd_part | $expression_placeholder
+    $expression_placeholder = :expression_placeholder_start list($expression_placeholder_kv) $e :expression_placeholder_end -> ExpressionPlaceholder(attributes=$1, expr=$2)
+    $expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr(key=$1, value=$3)
+    $inputs = :input :lbrace list($input_declaration) :rbrace -> Inputs(inputs=$2)
+    $runtime = :runtime $rt_map -> Runtime(map=$1)
+    $rt_map = :lbrace list($kv) :rbrace -> $1
+    $kv = :identifier :colon $e -> RuntimeAttribute(key=$0, value=$2)
+
+    # Meta sections
+    $meta = :meta $meta_map -> Meta(map=$1)
+    $parameter_meta = :parameter_meta $meta_map -> ParameterMeta(map=$1)
+    $meta_map = :lbrace list($meta_kv) :rbrace -> $1
+    $meta_kv = :identifier :colon $meta_value -> MetaKvPair(key=$0, value=$2)
+    $meta_value = parser<expression> {
+      $meta_value = $static_string
+      $meta_value = :boolean
+      $meta_value = :integer
+      $meta_value = :float
+      $meta_value = :null
+      $meta_value = :lsquare list($meta_value, :comma) :rsquare -> MetaArray(values=$1)
+      $meta_value = :lbrace list($meta_kv, :comma) :rbrace -> MetaObject(map=$1)
+    }
+
+    # Declarations: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#declarations
+    $input_declaration = $type_e :identifier optional($setter) -> InputDeclaration(type=$0, name=$1, expression=$2)
+    $declaration = $type_e :identifier $setter -> Declaration(type=$0, name=$1, expression=$2)
+    $setter = :equal $e -> $1
+
+    # Types: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#types
+    $type_e = parser<expression> {
+      (*:left) $type_e = :type <=> :lsquare list($type_e, :comma) :rsquare -> Type(name=$0, subtype=$2)
+      (*:left) $type_e = :type <=> :qmark -> OptionalType(innerType=$0)
+      (*:left) $type_e = :type <=> :plus -> NonEmptyType(innerType=$0)
+      $type_e = :type
+      $type_e = :identifier
+    }
+
+    # Expressions: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#expressions
+    $e = parser<expression> {
+      (*:left) $e = $e :double_pipe $e -> LogicalOr(lhs=$0, rhs=$2)
+      (*:left) $e = $e :double_ampersand $e -> LogicalAnd(lhs=$0, rhs=$2)
+      (*:left) $e = $e :double_equal $e -> Equals(lhs=$0, rhs=$2)
+      (-:left) $e = $e :not_equal $e -> NotEquals(lhs=$0, rhs=$2)
+      (*:left) $e = $e :lt $e -> LessThan(lhs=$0, rhs=$2)
+      (-:left) $e = $e :lteq $e -> LessThanOrEqual(lhs=$0, rhs=$2)
+      (-:left) $e = $e :gt $e -> GreaterThan(lhs=$0, rhs=$2)
+      (-:left) $e = $e :gteq $e -> GreaterThanOrEqual(lhs=$0, rhs=$2)
+      (*:left) $e = $e :plus $e -> Add(lhs=$0, rhs=$2)
+      (-:left) $e = $e :dash $e -> Subtract(lhs=$0, rhs=$2)
+      (*:left) $e = $e :asterisk $e -> Multiply(lhs=$0, rhs=$2)
+      (-:left) $e = $e :slash $e -> Divide(lhs=$0, rhs=$2)
+      (-:left) $e = $e :percent $e -> Remainder(lhs=$0, rhs=$2)
+      (*:unary) $e = :not $e -> LogicalNot(expression=$1)
+      (-:unary) $e = :plus $e -> UnaryPlus(expression=$1)
+      (-:unary) $e = :dash $e -> UnaryNegation(expression=$1)
+      (*:left) $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall(name=$0, params=$2)
+      (*:left) $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup(lhs=$0, rhs=$2)
+      (*:left) $e = $e <=> :dot :identifier -> MemberAccess(value=$0, member=$2)
+      # TODO: is there a better object literal syntax?
+      (*:left) $e = :object :lbrace list($object_kv, :comma) :rbrace -> ObjectLiteral(map=$2)
+      (*:left) $e = :lsquare list($e, :comma) :rsquare -> ArrayLiteral(values=$1)
+      (*:left) $e = :lbrace list($map_kv, :comma) :rbrace -> MapLiteral(map=$1)
+      (*:left) $e = :lparen list($e, :comma) :rparen -> TupleLiteral(values=$1)
+      (*:left) $e = :if $e :then $e :else $e -> TernaryIf(cond=$1, iftrue=$3, iffalse=$5)
+      $e = $string_literal
+      $e = :identifier
+      $e = :boolean
+      $e = :integer
+      $e = :float
+      $e = :none
+    }
+    $map_kv = $e :colon $e -> MapLiteralKv(key=$0, value=$2)
+
+    # Outputs
+    $outputs = :output :lbrace list($output_kv) :rbrace -> Outputs(outputs=$2)
+    $output_kv = $type_e :identifier :equal $e -> Output(type=$0, name=$1, expression=$3)
+
+    # Workflows: https://github.com/broadinstitute/wdl/blob/wdl2/SPEC.md#workflow-definition
+    $workflow = :workflow :identifier :lbrace list($wf_body_element) :rbrace -> Workflow(name=$1, body=$3)
+    $wf_body_element = $call | $declaration | $if_stmt | $scatter | $inputs | $outputs | $wf_parameter_meta | $wf_meta
+    $call = :call :fqn optional($alias) list($call_after) optional($call_brace_block) -> Call(task=$1, alias=$2, after=$3, body=$4)
+    $call_brace_block = :lbrace optional($call_body) :rbrace -> $1
+    $call_body = :input :colon list($input_kv, :comma) -> CallBody(inputs=$2)
+    $alias = :as :identifier -> $1
+    $call_after = :after :identifier -> $1
+    $wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta(map=$1)
+    $wf_meta = :meta $meta_map -> Meta(map=$1)
+    $if_stmt = :if :lparen $e :rparen :lbrace list($wf_body_element) :rbrace -> If(expression=$2, body=$5)
+
+    $scatter = :scatter :lparen :identifier :in $e :rparen :lbrace list($wf_body_element) :rbrace
+        -> Scatter(item=$2, collection=$4, body=$7)
+
+    $object_kv = :identifier :colon $e -> ObjectKV(key=$0, value=$2)
+    $input_kv = :identifier :equal $e -> ObjectKV(key=$0, value=$2)
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
new file mode 100644
index 00000000000..edcd6204f6c
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
@@ -0,0 +1,26 @@
+package wdl.transforms.cascades.ast2wdlom
+
+import cats.syntax.validated._
+import common.validation.ErrorOr.ErrorOr
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.elements.ExpressionElement.{Keys, AsMap, AsPairs, CollectByKey, Min, Max, Sep}
+import wdl.transforms.base.ast2wdlom.AstNodeToExpressionElement
+
+object AstToNewExpressionElements {
+  val newcascadesEngineFunctionMakers: Map[String, Vector[ExpressionElement] => ErrorOr[ExpressionElement]] = Map(
+    "keys" -> AstNodeToExpressionElement.validateOneParamEngineFunction(Keys, "keys"),
+    "as_map" -> AstNodeToExpressionElement.validateOneParamEngineFunction(AsMap, "as_map"),
+    "as_pairs" -> AstNodeToExpressionElement.validateOneParamEngineFunction(AsPairs, "as_pairs"),
+    "collect_by_key" -> AstNodeToExpressionElement.validateOneParamEngineFunction(CollectByKey, "collect_by_key"),
+
+    "min" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Min, "min"),
+    "max" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Max, "max"),
+
+    "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
+
+    "read_object" -> (_ => "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel),
+    "read_objects" -> (_ => "read_objects is no longer available in this WDL version. Consider using read_json instead".invalidNel),
+    "write_object" -> (_ => "write_object is no longer available in this WDL version. Consider using write_json instead".invalidNel),
+    "write_objects" -> (_ => "write_objects is no longer available in this WDL version. Consider using write_json instead".invalidNel),
+  )
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/CascadesGenericAstNode.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/CascadesGenericAstNode.scala
new file mode 100644
index 00000000000..a503ca897be
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/CascadesGenericAstNode.scala
@@ -0,0 +1,36 @@
+package wdl.transforms.cascades.ast2wdlom
+
+import wdl.cascades.parser.WdlParser.{Ast, AstList, AstNode, Terminal}
+import wdl.transforms.base.ast2wdlom.{GenericAst, GenericAstList, GenericAstNode, GenericTerminal}
+import scala.jdk.CollectionConverters._
+
+case class cascadesGenericAst(ast: Ast) extends GenericAst {
+  override def getAttribute(attr: String): GenericAstNode = Option(ast.getAttribute(attr)).map(cascadesGenericAstNode.apply).orNull
+  override def getAttributes: Map[String, GenericAstNode] = ast.getAttributes.asScala.toMap collect {
+    case (key, value) if value != null => key -> cascadesGenericAstNode(value)
+  }
+  override def getName: String = ast.getName
+}
+
+case class cascadesGenericTerminal(terminal: Terminal) extends GenericTerminal {
+  override def getSourceString: String = terminal.getSourceString
+  override def getTerminalStr: String = terminal.getTerminalStr
+  override def getLine: Int = terminal.getLine
+  override def getColumn: Int = terminal.getColumn
+
+  override def toString: String = s"cascadesGenericTerminal($getTerminalStr: $getSourceString)"
+}
+
+case class cascadesGenericAstList(astList: AstList) extends GenericAstList {
+  override def astNodeList: Seq[GenericAstNode] = astList.asScala.toSeq map cascadesGenericAstNode.apply
+}
+
+object cascadesGenericAstNode {
+  def apply(astNode: AstNode): GenericAstNode = astNode match {
+    case list: AstList => cascadesGenericAstList(list)
+    case ast: Ast => cascadesGenericAst(ast)
+    case terminal: Terminal => cascadesGenericTerminal(terminal)
+    case null =>
+      throw new Exception()
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/ast2wdlom.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/ast2wdlom.scala
new file mode 100644
index 00000000000..3bda86048ef
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/ast2wdlom.scala
@@ -0,0 +1,65 @@
+package wdl.transforms.cascades
+
+import cats.instances.either._
+import better.files.File
+import common.transforms.CheckedAtoB
+import common.validation.Checked._
+import wdl.cascades.parser.WdlParser.{Ast, AstNode}
+import wdl.model.draft3.elements.ExpressionElement.KvPair
+import wdl.model.draft3.elements._
+import wdl.transforms.base.ast2wdlom._
+import wdl.transforms.cascades.parsing.fileToAst
+import wom.callable.MetaKvPair
+import wom.types.WomUnlistedDirectoryType
+
+package object ast2wdlom {
+
+  val wrapAst: CheckedAtoB[Ast, GenericAst] = CheckedAtoB.fromCheck { a => cascadesGenericAst(a).validNelCheck }
+  val wrapAstNode: CheckedAtoB[AstNode, GenericAstNode] = CheckedAtoB.fromCheck { a => cascadesGenericAstNode(a).validNelCheck }
+
+  implicit val astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString] = AstNodeToStaticString.astNodeToStaticStringElement()
+
+  // meta sections
+  implicit val astNodeToMetaKvPair: CheckedAtoB[GenericAstNode, MetaKvPair] = AstNodeToMetaKvPair.astNodeToMetaKvPair
+  implicit val astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement] = astNodeToAst andThen AstToMetaSectionElement.astToMetaSectionElement
+  implicit val astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement] = astNodeToAst andThen AstToParameterMetaSectionElement.astToParameterMetaSectionElement
+
+  implicit val astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement] = AstNodeToExpressionElement.astNodeToExpressionElement(customEngineFunctionMakers = AstToNewExpressionElements.newcascadesEngineFunctionMakers)
+  implicit val astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair] = AstNodeToKvPair.astNodeToKvPair(astNodeToExpressionElement)
+
+  implicit val astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement] = AstNodeToTypeElement.astNodeToTypeElement(Map("Directory" -> WomUnlistedDirectoryType))
+  implicit val astToStructElement: CheckedAtoB[GenericAst, StructElement] = AstToStructElement.astToStructElement
+  implicit val astNodeToImportElement: CheckedAtoB[GenericAstNode, ImportElement] = astNodeToAst andThen AstToImportElement.astToImportElement
+
+  implicit val astNodeToInputDeclarationElement: CheckedAtoB[GenericAstNode, InputDeclarationElement] = astNodeToAst andThen AstToInputDeclarationElement.astToInputDeclarationElement
+  implicit val astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement] = astNodeToAst andThen AstToInputsSectionElement.astToInputsSectionElement
+
+  implicit val astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent] = astNodeToAst andThen AstToDeclarationContent.astToDeclarationContent
+  implicit val astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement] = astNodeToAst andThen AstToOutputsSectionElement.astToOutputSectionElement
+
+  val astToWorkflowGraphNodeElementConverterMaker = new AstToWorkflowGraphNodeElementConverterMaker()
+  implicit val astNodeToGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement] = astNodeToAst andThen astToWorkflowGraphNodeElementConverterMaker.converter
+  implicit val astNodeToCallElement: CheckedAtoB[GenericAstNode, CallElement] = astNodeToAst andThen AstToCallElement.astToCallElement
+  implicit val astNodeToScatterElement: CheckedAtoB[GenericAstNode, ScatterElement] = astNodeToAst andThen AstToScatterElement.astToScatterElement
+  implicit val astNodeToIfElement: CheckedAtoB[GenericAstNode, IfElement] = astNodeToAst andThen AstToIfElement.astToIfElement
+  astToWorkflowGraphNodeElementConverterMaker.astNodeToScatterElement = Some(astNodeToScatterElement)
+  astToWorkflowGraphNodeElementConverterMaker.astNodeToIfElement = Some(astNodeToIfElement)
+  astToWorkflowGraphNodeElementConverterMaker.astNodeToCallElement = Some(astNodeToCallElement)
+  astToWorkflowGraphNodeElementConverterMaker.astNodeToDeclarationContent = Some(astNodeToDeclarationContent)
+
+  implicit val astNodeToWorkflowBodyElement: CheckedAtoB[GenericAstNode, WorkflowBodyElement] = astNodeToAst andThen AstToWorkflowBodyElement.astToWorkflowBodyElement
+  implicit val astToWorkflowDefinitionElement: CheckedAtoB[GenericAst, WorkflowDefinitionElement] = AstToWorkflowDefinitionElement.astToWorkflowDefinitionElement
+
+  implicit val astNodeToPlaceholderAttributeSet: CheckedAtoB[GenericAstNode, PlaceholderAttributeSet] = astNodeToAstList andThen AstNodeToPlaceholderAttributeSet.attributeKvpConverter
+  implicit val astNodeToCommandPartElement: CheckedAtoB[GenericAstNode, CommandPartElement] = AstNodeToCommandPartElement.astNodeToCommandPartElement
+  implicit val astNodeToCommandSectionElement: CheckedAtoB[GenericAstNode, CommandSectionElement] = astNodeToAst andThen AstToCommandSectionElement.astToCommandSectionElement
+  implicit val astNodeToRuntimeAttributesSectionElement: CheckedAtoB[GenericAstNode, RuntimeAttributesSectionElement] = astNodeToAst andThen AstToRuntimeAttributesSectionElement.astToRuntimeSectionElement
+  implicit val astNodeToTaskSectionElement: CheckedAtoB[GenericAstNode, TaskSectionElement] = astNodeToAst andThen AstToTaskSectionElement.astToTaskSectionElement
+  implicit val astToTaskDefinitionElement: CheckedAtoB[GenericAst, TaskDefinitionElement] = AstToTaskDefinitionElement.astToTaskDefinitionElement
+
+  implicit val astToFileBodyElement: CheckedAtoB[GenericAstNode, FileBodyElement] = astNodeToAst andThen AstToFileBodyElement.astToFileBodyElement(astToWorkflowDefinitionElement, astToTaskDefinitionElement, astToStructElement)
+
+  implicit val astToFileElement: CheckedAtoB[GenericAst, FileElement] = AstToFileElement.astToFileElement
+  implicit val fileToFileElement: CheckedAtoB[File, FileElement] = fileToAst andThen wrapAst andThen astToFileElement
+
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
new file mode 100644
index 00000000000..196005fdb84
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
@@ -0,0 +1,57 @@
+package wdl.transforms.cascades.linking.expression.consumed
+
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.elements.ExpressionElement._
+import wdl.model.draft3.graph.{ExpressionValueConsumer, UnlinkedConsumedValueHook}
+
+object cascadesExpressionValueConsumers {
+  implicit val keysExpressionValueConsumer: ExpressionValueConsumer[Keys] = new ExpressionValueConsumer[Keys] {
+    override def expressionConsumedValueHooks(a: Keys)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+    }
+  }
+
+  implicit val asMapExpressionValueConsumer: ExpressionValueConsumer[AsMap] = new ExpressionValueConsumer[AsMap] {
+    override def expressionConsumedValueHooks(a: AsMap)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+    }
+  }
+
+  implicit val asPairsExpressionValueConsumer: ExpressionValueConsumer[AsPairs] = new ExpressionValueConsumer[AsPairs] {
+    override def expressionConsumedValueHooks(a: AsPairs)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+    }
+  }
+
+  implicit val collectByKeyExpressionValueConsumer: ExpressionValueConsumer[CollectByKey] = new ExpressionValueConsumer[CollectByKey] {
+    override def expressionConsumedValueHooks(a: CollectByKey)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+    }
+  }
+
+  implicit val minExpressionValueConsumer: ExpressionValueConsumer[Min] = new ExpressionValueConsumer[Min] {
+    override def expressionConsumedValueHooks(a: Min)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++ expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
+    }
+  }
+
+  implicit val maxExpressionValueConsumer: ExpressionValueConsumer[Max] = new ExpressionValueConsumer[Max] {
+    override def expressionConsumedValueHooks(a: Max)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++ expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
+    }
+  }
+
+  implicit val sepExpressionValueConsumer: ExpressionValueConsumer[Sep] = new ExpressionValueConsumer[Sep] {
+    override def expressionConsumedValueHooks(a: Sep)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++
+        expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
+    }
+  }
+
+  implicit val noneLiteralExpressionValueConsumer: ExpressionValueConsumer[NoneLiteralElement.type] = new ExpressionValueConsumer[NoneLiteralElement.type] {
+    override def expressionConsumedValueHooks(a: NoneLiteralElement.type)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+      // None literals consume no values:
+      Set.empty[UnlinkedConsumedValueHook]
+    }
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
new file mode 100644
index 00000000000..d689d2a175a
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
@@ -0,0 +1,110 @@
+package wdl.transforms.cascades.linking.expression
+
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.elements.ExpressionElement._
+import wdl.model.draft3.graph.ExpressionValueConsumer.ops._
+import wdl.model.draft3.graph.{ExpressionValueConsumer, UnlinkedConsumedValueHook}
+import wdl.transforms.base.linking.expression.consumed.BinaryOperatorEvaluators._
+import wdl.transforms.base.linking.expression.consumed.EngineFunctionEvaluators._
+import wdl.transforms.base.linking.expression.consumed.LiteralEvaluators._
+import wdl.transforms.base.linking.expression.consumed.LookupEvaluators._
+import wdl.transforms.base.linking.expression.consumed.TernaryIfEvaluator._
+import wdl.transforms.base.linking.expression.consumed.UnaryOperatorEvaluators._
+import wdl.transforms.cascades.linking.expression.consumed.cascadesExpressionValueConsumers._
+
+package object consumed {
+
+  implicit val expressionElementUnlinkedValueConsumer: ExpressionValueConsumer[ExpressionElement] = new ExpressionValueConsumer[ExpressionElement] {
+    override def expressionConsumedValueHooks(a: ExpressionElement)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = a match {
+      case _: PrimitiveLiteralExpressionElement | _: StringLiteral => Set.empty[UnlinkedConsumedValueHook]
+      case a: NoneLiteralElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      case a: StringExpression => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ObjectLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: PairLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ArrayLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: MapLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      // Member access:
+      case a: IdentifierLookup => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: IdentifierMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ExpressionMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: IndexAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      // Unary operators:
+      case a: UnaryNegation => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: UnaryPlus => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: LogicalNot => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      // Binary operators:
+      case a: LogicalOr => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: LogicalAnd => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Equals => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: NotEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: LessThan => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: LessThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: GreaterThan => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: GreaterThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Add => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Subtract => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Multiply => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Divide => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Remainder => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      case a: TernaryIf => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      // Engine functions:
+      case a: StdoutElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: StderrElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      case a: ReadLines => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ReadTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ReadMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ReadObject => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ReadObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ReadJson => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ReadInt => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ReadString => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ReadFloat => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: ReadBoolean => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: WriteLines => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: WriteTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: WriteMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: WriteObject => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: WriteObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: WriteJson => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Range => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Transpose => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Length => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Flatten => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Prefix => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: SelectFirst => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: SelectAll => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Defined => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Floor => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Ceil => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Round => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Glob => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      case a: Size => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Basename => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      case a: Zip => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Cross => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      case a: Sub => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      // New WDL biscayne expressions:
+      case a: Keys => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: AsMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: AsPairs => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: CollectByKey => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Sep => sepExpressionValueConsumer.expressionConsumedValueHooks(a)(expressionValueConsumer)
+
+      case a: Min => a.expressionConsumedValueHooks(expressionValueConsumer)
+      case a: Max => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+      case other => throw new Exception(s"Cannot generate consumed values for ExpressionElement ${other.getClass.getSimpleName}")
+    }
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
new file mode 100644
index 00000000000..f1e63de78cc
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
@@ -0,0 +1,20 @@
+package wdl.transforms.cascades.linking.expression.files
+
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep}
+import wdl.model.draft3.graph.expression.FileEvaluator
+import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators
+import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.twoParameterFunctionPassthroughFileEvaluator
+
+object cascadesFileEvaluators {
+
+  implicit val keysFileEvaluator: FileEvaluator[Keys] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val asMapFileEvaluator: FileEvaluator[AsMap] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val asPairsFileEvaluator: FileEvaluator[AsPairs] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val collectByKeyFileEvaluator: FileEvaluator[CollectByKey] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+
+  implicit val sepFunctionEvaluator: FileEvaluator[Sep] = twoParameterFunctionPassthroughFileEvaluator[Sep]
+
+  implicit val minFunctionEvaluator: FileEvaluator[Min] = twoParameterFunctionPassthroughFileEvaluator[Min]
+  implicit val maxFunctionEvaluator: FileEvaluator[Max] = twoParameterFunctionPassthroughFileEvaluator[Max]
+
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
new file mode 100644
index 00000000000..1c9da7b2d60
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
@@ -0,0 +1,119 @@
+package wdl.transforms.cascades.linking.expression
+
+import cats.syntax.validated._
+import common.validation.ErrorOr.ErrorOr
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.elements.ExpressionElement._
+import wdl.model.draft3.graph.expression.{FileEvaluator, ValueEvaluator}
+import wdl.model.draft3.graph.expression.FileEvaluator.ops._
+import wdl.transforms.base.linking.expression.files.BinaryOperatorEvaluators._
+import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators._
+import wdl.transforms.base.linking.expression.files.LiteralEvaluators._
+import wdl.transforms.base.linking.expression.files.LookupEvaluators._
+import wdl.transforms.base.linking.expression.files.TernaryIfEvaluator.ternaryIfEvaluator
+import wdl.transforms.base.linking.expression.files.UnaryOperatorEvaluators._
+import wom.expression.IoFunctionSet
+import wom.types.WomType
+import wom.values.{WomFile, WomValue}
+import wdl.transforms.cascades.linking.expression.files.cascadesFileEvaluators._
+
+package object files {
+
+  implicit val expressionFileEvaluator: FileEvaluator[ExpressionElement] = new FileEvaluator[ExpressionElement] {
+
+    override def predictFilesNeededToEvaluate(a: ExpressionElement, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
+                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
+                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+
+      a match {
+        // Literals:
+        case a: PrimitiveLiteralExpressionElement => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: StringLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ObjectLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: MapLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ArrayLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: PairLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        // Lookups and member accesses:
+        case a: IdentifierLookup => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ExpressionMemberAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IdentifierMemberAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IndexAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        // Unary operators:
+        case a: UnaryNegation => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: UnaryPlus => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalNot => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        // Binary operators (at some point we might want to split these into separate cases):
+        case a: LogicalOr => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalAnd => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Equals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: NotEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LessThan => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LessThanOrEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: GreaterThan => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: GreaterThanOrEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Add => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Subtract => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Multiply => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Divide => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Remainder => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        case a: TernaryIf => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        // Engine functions:
+        case StdoutElement => StdoutElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case StderrElement => StderrElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        case a: ReadLines => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadTsv => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadObject => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadObjects => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadJson => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadInt => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadString => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadFloat => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadBoolean => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteLines => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteTsv => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteObject => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteObjects => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteJson => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Range => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Transpose => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Length => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Flatten => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Prefix => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SelectFirst => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SelectAll => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Defined => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Floor => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Ceil => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Round => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Glob => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        case a: Size => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Basename => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        case a: Zip => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Cross => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        case a: Sub => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        case a: Keys => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: AsMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: AsPairs => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: CollectByKey => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Sep => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        case a: Min => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Max => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        case other => s"No implementation of FileEvaluator[${other.getClass.getSimpleName}]".invalidNel
+      }
+    }
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
new file mode 100644
index 00000000000..4a2e389c25a
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
@@ -0,0 +1,97 @@
+package wdl.transforms.biscayne.linking.expression.types
+
+import cats.syntax.validated._
+import common.validation.ErrorOr._
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.elements.ExpressionElement._
+import wdl.model.draft3.graph.expression.TypeEvaluator
+import wdl.model.draft3.graph.{GeneratedValueHandle, UnlinkedConsumedValueHook}
+import wdl.transforms.base.linking.expression.types.EngineFunctionEvaluators.validateParamType
+import wom.types._
+
+object cascadesTypeEvaluators {
+  implicit val keysFunctionEvaluator: TypeEvaluator[Keys] = new TypeEvaluator[Keys] {
+    override def evaluateType(a: Keys, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
+                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)) flatMap {
+        case WomMapType(keyType, _) => WomArrayType(keyType).validNel
+        case other => s"Cannot invoke 'keys' on type '${other.stableName}'. Expected a map".invalidNel
+      }
+    }
+  }
+
+  implicit val asMapFunctionEvaluator: TypeEvaluator[AsMap] = new TypeEvaluator[AsMap] {
+    override def evaluateType(a: AsMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
+                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
+        case WomArrayType(WomPairType(x: WomPrimitiveType, y)) => WomMapType(x, y).validNel
+        case other @ WomArrayType(WomPairType(x, _)) => s"Cannot invoke 'as_map' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
+        case other => s"Cannot invoke 'as_map' on type '${other.stableName}'. Expected an array of pairs".invalidNel
+      }
+    }
+  }
+
+  implicit val asPairsFunctionEvaluator: TypeEvaluator[AsPairs] = new TypeEvaluator[AsPairs] {
+    override def evaluateType(a: AsPairs, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
+                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)) flatMap {
+        case WomMapType(x, y) => WomArrayType(WomPairType(x, y)).validNel
+        case other => s"Cannot invoke 'as_pairs' on type '${other.stableName}'. Expected a map".invalidNel
+      }
+    }
+  }
+
+  implicit val collectByKeyFunctionEvaluator: TypeEvaluator[CollectByKey] = new TypeEvaluator[CollectByKey] {
+    override def evaluateType(a: CollectByKey, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
+                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
+        case WomArrayType(WomPairType(x: WomPrimitiveType, y)) => WomMapType(x, WomArrayType(y)).validNel
+        case other @ WomArrayType(WomPairType(x, _)) => s"Cannot invoke 'collect_by_key' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
+        case other => s"Cannot invoke 'collect_by_key' on type '${other.stableName}'. Expected an array of pairs".invalidNel
+      }
+    }
+  }
+
+  private def resultTypeOfIntVsFloat(functionName: String)(type1: WomType, type2: WomType): ErrorOr[WomType] = (type1, type2) match {
+    case (WomIntegerType, WomIntegerType) => WomIntegerType.validNel
+    case (WomIntegerType, WomFloatType) => WomFloatType.validNel
+    case (WomFloatType, WomIntegerType) => WomFloatType.validNel
+    case (WomFloatType, WomFloatType) => WomFloatType.validNel
+    case (other1, other2) => s"Cannot call '$functionName' with arguments (${other1.friendlyName}, ${other2.friendlyName}). Must be Int or Long.".invalidNel
+  }
+
+  implicit val minFunctionEvaluator: TypeEvaluator[Min] = new TypeEvaluator[Min] {
+    override def evaluateType(a: Min,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
+                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+      val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
+      val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
+
+      (type1, type2) flatMapN resultTypeOfIntVsFloat("min")
+    }
+  }
+
+  implicit val maxFunctionEvaluator: TypeEvaluator[Max] = new TypeEvaluator[Max] {
+    override def evaluateType(a: Max,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
+                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+      val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
+      val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
+
+      (type1, type2) flatMapN resultTypeOfIntVsFloat("max")
+    }
+  }
+
+  implicit val sepFunctionEvaluator: TypeEvaluator[Sep] = new TypeEvaluator[Sep] {
+    override def evaluateType(a: Sep, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
+                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+      validateParamType(a.arg2, linkedValues, WomArrayType(WomAnyType)) flatMap {
+        case WomArrayType(WomArrayType(_)) => s"Cannot invoke 'sep' on type 'Array[Array[_]]'. Expected an Array[String].".invalidNel
+        case WomArrayType(_) => WomStringType.validNel
+
+        case other => s"Cannot invoke 'sep' on type '${other.stableName}'. Expected an Array[String].".invalidNel
+
+      }
+    }
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
new file mode 100644
index 00000000000..367967b91be
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
@@ -0,0 +1,118 @@
+package wdl.transforms.cascades.linking.expression
+
+import cats.syntax.validated._
+import common.validation.ErrorOr.ErrorOr
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.elements.ExpressionElement._
+import wdl.model.draft3.graph.expression.TypeEvaluator
+import wdl.model.draft3.graph.expression.TypeEvaluator.ops._
+import wdl.model.draft3.graph.{GeneratedValueHandle, UnlinkedConsumedValueHook}
+import wdl.transforms.base.linking.expression.types.BinaryOperatorEvaluators._
+import wdl.transforms.base.linking.expression.types.EngineFunctionEvaluators._
+import wdl.transforms.base.linking.expression.types.LiteralEvaluators._
+import wdl.transforms.base.linking.expression.types.LookupEvaluators._
+import wdl.transforms.base.linking.expression.types.TernaryIfEvaluator._
+import wdl.transforms.base.linking.expression.types.UnaryOperatorEvaluators._
+import wom.types.WomType
+import wdl.transforms.biscayne.linking.expression.types.cascadesTypeEvaluators._
+
+package object types {
+  implicit val expressionTypeEvaluator: TypeEvaluator[ExpressionElement] = new TypeEvaluator[ExpressionElement] {
+    override def evaluateType(a: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
+                             (implicit typeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+
+      a match {
+        // Literals:
+        case a: PrimitiveLiteralExpressionElement => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: NoneLiteralElement.type => a.evaluateType(linkedValues)(typeEvaluator)
+
+        case a: StringLiteral => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: StringExpression => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ObjectLiteral => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: MapLiteral => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ArrayLiteral => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: PairLiteral => a.evaluateType(linkedValues)(typeEvaluator)
+
+        // Lookups and member accesses:
+        case a: IdentifierLookup => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ExpressionMemberAccess => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: IdentifierMemberAccess => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: IndexAccess => a.evaluateType(linkedValues)(typeEvaluator)
+
+        // Unary operators:
+        case a: UnaryNegation => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: UnaryPlus => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: LogicalNot => a.evaluateType(linkedValues)(typeEvaluator)
+
+        // Binary operators (at some point we might want to split these into separate cases):
+        case a: LogicalOr => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: LogicalAnd => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Equals => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: NotEquals => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: LessThan => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: LessThanOrEquals => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: GreaterThan => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: GreaterThanOrEquals => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Add => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Subtract => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Multiply => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Divide => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Remainder => a.evaluateType(linkedValues)(typeEvaluator)
+
+        case a: TernaryIf => a.evaluateType(linkedValues)(typeEvaluator)
+
+        // Engine functions:
+        case a: ReadLines => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadTsv => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadMap => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadObject => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadObjects => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadJson => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadInt => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadString => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadFloat => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadBoolean => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: WriteLines => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: WriteTsv => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: WriteMap => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: WriteObject => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: WriteObjects => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: WriteJson => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Range => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Transpose => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Length => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Flatten => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Prefix => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: SelectFirst => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: SelectAll => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Defined => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Floor => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Ceil => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Round => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Glob => a.evaluateType(linkedValues)(typeEvaluator)
+
+        case a: Size => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Basename => a.evaluateType(linkedValues)(typeEvaluator)
+
+        case a: Zip => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Cross => a.evaluateType(linkedValues)(typeEvaluator)
+
+        case a: Sub => a.evaluateType(linkedValues)(typeEvaluator)
+
+        case a: StdoutElement.type => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: StderrElement.type => a.evaluateType(linkedValues)(typeEvaluator)
+
+        case a: Keys => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: AsMap => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: AsPairs => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: CollectByKey => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Sep => a.evaluateType(linkedValues)(typeEvaluator)
+
+        case a: Min => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Max => a.evaluateType(linkedValues)(typeEvaluator)
+
+        case other => s"Unable to process ${other.getClass.getSimpleName}: No evaluateType exists for that type.".invalidNel
+      }
+    }
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
new file mode 100644
index 00000000000..4a02ed221f1
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
@@ -0,0 +1,169 @@
+package wdl.transforms.biscayne.linking.expression.values
+
+import cats.data.NonEmptyList
+import cats.syntax.validated._
+import cats.syntax.traverse._
+import cats.instances.list._
+import common.validation.ErrorOr._
+import common.collections.EnhancedCollections._
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.elements.ExpressionElement._
+import wdl.model.draft3.graph.expression.{EvaluatedValue, ForCommandInstantiationOptions, ValueEvaluator}
+import wdl.transforms.base.linking.expression.values.EngineFunctionEvaluators.{processValidatedSingleValue, processTwoValidatedValues}
+import wom.expression.IoFunctionSet
+import wom.types._
+import wom.values.{WomArray, WomInteger, WomFloat, WomMap, WomOptionalValue, WomPair, WomValue, WomString}
+import wom.types.coercion.defaults._
+
+object cascadesValueEvaluators {
+
+  implicit val noneLiteralEvaluator: ValueEvaluator[NoneLiteralElement.type] = new ValueEvaluator[ExpressionElement.NoneLiteralElement.type] {
+    override def evaluateValue(a: ExpressionElement.NoneLiteralElement.type, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+      EvaluatedValue(
+        value = WomOptionalValue(WomNothingType, None),
+        sideEffectFiles = Seq.empty).validNel
+    }
+  }
+
+  implicit val asMapFunctionEvaluator: ValueEvaluator[AsMap] = new ValueEvaluator[AsMap] {
+    override def evaluateValue(a: AsMap, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
+                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+      processValidatedSingleValue[WomArray, WomMap](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
+        case WomArray(WomArrayType(WomPairType(_: WomPrimitiveType, _)), values) =>
+          val validPairs: ErrorOr[List[(WomValue, WomValue)]] = values.toList traverse {
+            case WomPair(l, r) => (l, r).validNel
+            case other => s"Unexpected array element. Expected a Pair[X, Y] but array contained ${other.toWomString}]".invalidNel
+          } leftMap {
+            errors => NonEmptyList.fromListUnsafe(errors.toList.distinct)
+          }
+          validPairs flatMap { pairs =>
+            val grouped = pairs.groupBy(_._1)
+            val tooManyKeyErrors = grouped collect {
+              case (name, list) if list.length != 1 => s"keys can only appear once but ${name.toWomString} appeared ${list.size} times."
+            }
+            if (tooManyKeyErrors.isEmpty) {
+              val pairs = grouped map { case (key, value) => (key -> value.head._2) }
+
+              EvaluatedValue(WomMap(pairs), Seq.empty).validNel
+            } else {
+              s"Cannot evaluate 'as_map' with duplicated keys: ${tooManyKeyErrors.mkString(", ")}".invalidNel
+            }
+          }
+
+        case WomArray(womType@WomArrayType(WomPairType(x, _)), _) => s"Cannot evaluate 'as_map' on type ${womType.stableName}. Keys must be primitive but got ${x.stableName}.".invalidNel
+        case other => s"Invalid call of 'as_map' on parameter of type '${other.womType.stableName}' (expected Array[Pair[X, Y]])".invalidNel
+      } (coercer = WomArrayType(WomPairType(WomAnyType, WomAnyType)))
+    }
+  }
+
+  implicit val keysFunctionEvaluator: ValueEvaluator[Keys] = new ValueEvaluator[Keys] {
+    override def evaluateValue(a: Keys,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
+                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
+
+      processValidatedSingleValue[WomMap, WomArray](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
+        case WomMap(WomMapType(keyType, _), values) => EvaluatedValue(WomArray(WomArrayType(keyType), values.keys.toList), Seq.empty).validNel
+        case other => s"Invalid call of 'keys' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
+      }
+    }
+  }
+
+  implicit val asPairsFunctionEvaluator: ValueEvaluator[AsPairs] = new ValueEvaluator[AsPairs] {
+    override def evaluateValue(a: AsPairs, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
+                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+      processValidatedSingleValue[WomMap, WomArray](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
+        case WomMap(WomMapType(keyType, valueType), values) =>
+          val validPairs: List[WomPair] = values.toList map {
+            case (l, r) => WomPair(l, r)
+          }
+          EvaluatedValue(WomArray(WomArrayType(WomPairType(keyType, valueType)), validPairs), Seq.empty).validNel
+
+        case other => s"Invalid call of 'as_pairs' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
+      }
+    }
+  }
+
+  implicit val collectByKeyFunctionEvaluator: ValueEvaluator[CollectByKey] = new ValueEvaluator[CollectByKey] {
+    override def evaluateValue(a: CollectByKey, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
+                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+      processValidatedSingleValue[WomArray, WomMap](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
+        case WomArray(WomArrayType(WomPairType(_: WomPrimitiveType, _)), values) =>
+          val validPairs: ErrorOr[List[(WomValue, WomValue)]] = values.toList traverse {
+            case WomPair(l, r) => (l, r).validNel
+            case other => s"Unexpected array element. Expected a Pair[X, Y] but array contained ${other.toWomString}]".invalidNel
+          }
+          validPairs flatMap { kvpairs =>
+            val grouped: Map[WomValue, WomArray] = kvpairs.groupBy(_._1).safeMapValues(v => WomArray(v.map(_._2)))
+            EvaluatedValue(WomMap(grouped), Seq.empty).validNel
+
+          }
+
+        case WomArray(womType@WomArrayType(WomPairType(x, _)), _) => s"Cannot evaluate 'collect_by_key' on type ${womType.stableName}. Keys must be primitive but got ${x.stableName}.".invalidNel
+        case other => s"Invalid call of 'collect_by_key' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
+      } (coercer = WomArrayType(WomPairType(WomAnyType, WomAnyType)))
+    }
+  }
+
+  private def resultOfIntVsFloat(functionName: String,
+                                 intFunc: (Int, Int) => Int,
+                                 doubleFunc: (Double, Double) => Double)
+                                (value1: EvaluatedValue[_], value2: EvaluatedValue[_]): ErrorOr[EvaluatedValue[WomValue]] = {
+    val newValue = (value1.value, value2.value) match {
+      case (WomInteger(i1), WomInteger(i2)) => WomInteger(intFunc(i1, i2)).validNel
+      case (WomInteger(i1), WomFloat(l2)) => WomFloat(doubleFunc(i1.doubleValue, l2)).validNel
+      case (WomFloat(l1), WomInteger(i2)) => WomFloat(doubleFunc(l1, i2.doubleValue)).validNel
+      case (WomFloat(l1), WomFloat(l2)) => WomFloat(doubleFunc(l1, l2)).validNel
+      case (other1, other2) => s"Invalid arguments to '$functionName':(${other1.typeName}, ${other2.typeName})".invalidNel
+    }
+    newValue map { v => EvaluatedValue(v, value1.sideEffectFiles ++ value2.sideEffectFiles) }
+  }
+
+  implicit val minFunctionEvaluator: ValueEvaluator[Min] = new ValueEvaluator[Min] {
+    override def evaluateValue(a: Min,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
+                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
+      val value1 = expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+      val value2 = expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+      val intFunc = (i1: Int, i2: Int) => Math.min(i1, i2)
+      val doubleFunc = (l1: Double, l2: Double) => Math.min(l1, l2)
+
+      (value1, value2) flatMapN resultOfIntVsFloat("min", intFunc, doubleFunc)
+    }
+  }
+
+  implicit val maxFunctionEvaluator: ValueEvaluator[Max] = new ValueEvaluator[Max] {
+    override def evaluateValue(a: Max,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
+      val value1 = expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+      val value2 = expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+      val intFunc = (i1: Int, i2: Int) => Math.max(i1, i2)
+      val doubleFunc = (l1: Double, l2: Double) => Math.max(l1, l2)
+
+      (value1, value2) flatMapN resultOfIntVsFloat("max", intFunc, doubleFunc)
+    }
+  }
+
+  implicit val sepFunctionEvaluator: ValueEvaluator[Sep] = new ValueEvaluator[Sep] {
+    override def evaluateValue(a: Sep,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
+                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] = {
+
+      processTwoValidatedValues[WomString, WomArray, WomString](
+        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator),
+        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+      ) { (sepvalue, arr) =>
+        EvaluatedValue(WomString(arr.value.map(v => v.valueString).mkString(sepvalue.value)), Seq.empty).validNel
+      }
+    }
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
new file mode 100644
index 00000000000..24b21928f4b
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
@@ -0,0 +1,124 @@
+package wdl.transforms.cascades.linking.expression
+
+import cats.syntax.validated._
+import common.validation.ErrorOr.ErrorOr
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.elements.ExpressionElement._
+import wdl.model.draft3.graph.expression.ValueEvaluator.ops._
+import wdl.model.draft3.graph.expression.{EvaluatedValue, ForCommandInstantiationOptions, ValueEvaluator}
+import wdl.transforms.base.linking.expression.values.BinaryOperatorEvaluators._
+import wdl.transforms.base.linking.expression.values.EngineFunctionEvaluators._
+import wdl.transforms.base.linking.expression.values.LiteralEvaluators._
+import wdl.transforms.base.linking.expression.values.LookupEvaluators._
+import wdl.transforms.base.linking.expression.values.TernaryIfEvaluator.ternaryIfEvaluator
+import wdl.transforms.base.linking.expression.values.UnaryOperatorEvaluators._
+import wdl.transforms.biscayne.linking.expression.values.cascadesValueEvaluators._
+import wom.expression.IoFunctionSet
+import wom.values.WomValue
+import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
+import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.expressionElementWriter
+
+package object values {
+
+  implicit val expressionEvaluator: ValueEvaluator[ExpressionElement] = new ValueEvaluator[ExpressionElement] {
+    override def evaluateValue(a: ExpressionElement,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
+                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+
+      a match {
+        // Literals:
+        case a: PrimitiveLiteralExpressionElement => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: NoneLiteralElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: StringLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: StringExpression => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ObjectLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: MapLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ArrayLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: PairLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        // Lookups and member accesses:
+        case a: IdentifierLookup => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ExpressionMemberAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: IdentifierMemberAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: IndexAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        // Unary operators:
+        case a: UnaryNegation => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: UnaryPlus => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LogicalNot => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        // Binary operators (at some point we might want to split these into separate cases):
+        case a: LogicalOr => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LogicalAnd => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Equals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: NotEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LessThan => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LessThanOrEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: GreaterThan => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: GreaterThanOrEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Add => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Subtract => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Multiply => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Divide => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Remainder => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: TernaryIf => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        // Engine functions:
+        case a: StdoutElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: StderrElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: ReadLines => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadTsv => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadMap => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadObject => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadObjects => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadJson => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadInt => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadString => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadFloat => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadBoolean => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteLines => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteTsv => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteMap => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteObject => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteObjects => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteJson => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Range => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Transpose => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Length => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Flatten => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Prefix => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: SelectFirst => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: SelectAll => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Defined => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Floor => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Ceil => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Round => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Glob => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: Size => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Basename => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: Zip => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Cross => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: Sub => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: Keys => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: AsMap => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: AsPairs => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: CollectByKey => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Sep => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: Min => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Max => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case other => s"Unable to process ${other.toWdlV1}: No evaluateValue exists for that type in WDL 1.1".invalidNel
+      }
+    }
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/CascadesParser.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/CascadesParser.scala
new file mode 100644
index 00000000000..ed0bd20e2e9
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/CascadesParser.scala
@@ -0,0 +1,32 @@
+package wdl.transforms.cascades.parsing
+
+import better.files.File
+import common.Checked
+import common.validation.Validation.TryValidation
+import wdl.cascades.parser.WdlParser
+import wdl.cascades.parser.WdlParser.Ast
+import wom.core.WorkflowSource
+
+import scala.jdk.CollectionConverters._
+import scala.util.Try
+
+object StringParser {
+
+  def convert(a: FileStringParserInput): Checked[Ast] = Try {
+    val parser = new WdlParser()
+    val tokens = parser.lex(a.workflowSource, a.resource)
+    val terminalMap = (tokens.asScala.toVector map {(_, a.workflowSource)}).toMap
+    val syntaxErrorFormatter = WdlCascadesSyntaxErrorFormatter(terminalMap)
+    parser.parse(tokens, syntaxErrorFormatter).toAst.asInstanceOf[Ast]
+  }.toChecked
+}
+
+final case class FileStringParserInput(workflowSource: WorkflowSource, resource: String)
+
+object FileParser {
+
+  def convert(a: File): Checked[Ast] = {
+    val parserInput = FileStringParserInput(a.contentAsString, a.name)
+    StringParser.convert(parserInput)
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/WdlCascadesSyntaxErrorFormatter.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/WdlCascadesSyntaxErrorFormatter.scala
new file mode 100644
index 00000000000..175adf8f1af
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/WdlCascadesSyntaxErrorFormatter.scala
@@ -0,0 +1,64 @@
+package wdl.transforms.cascades.parsing
+
+import wdl.cascades.parser.WdlParser._
+import wom.core.WorkflowSource
+
+import scala.jdk.CollectionConverters._
+
+case class WdlCascadesSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) extends SyntaxErrorFormatter {
+
+  private def pointToSource(t: Terminal): String = s"${line(t)}\n${" " * (t.getColumn - 1)}^"
+
+  private def getTerminal(t: Terminal) = t match {
+    case classicTerminal => terminalMap.get(classicTerminal)
+  }
+
+  private def line(t: Terminal): String = getTerminal(t).map(_.split("\n")(t.getLine - 1)).getOrElse(s"Cannot highlight line. It was probably in an imported file.")
+
+  def unexpectedEof(method: String, expected: java.util.List[TerminalIdentifier], nt_rules: java.util.List[String]): String = "ERROR: Unexpected end of file"
+
+  def excessTokens(method: String, terminal: Terminal): String = {
+    s"""ERROR: Finished parsing without consuming all tokens.
+       |
+        |${pointToSource(terminal)}
+     """.stripMargin
+  }
+
+  def unexpectedSymbol(method: String, actual: Terminal, expected: java.util.List[TerminalIdentifier], rule: String): String = {
+    val expectedTokens = expected.asScala.map(_.string).mkString(", ")
+    s"""ERROR: Unexpected symbol (line ${actual.getLine}, col ${actual.getColumn}) when parsing '$method'.
+       |
+        |Expected $expectedTokens, got "${actual.getSourceString}".
+       |
+        |${pointToSource(actual)}
+       |
+        |$rule
+     """.stripMargin
+  }
+
+  def noMoreTokens(method: String, expecting: TerminalIdentifier, last: Terminal): String = {
+    s"""ERROR: No more tokens.  Expecting ${expecting.string}
+       |
+        |${pointToSource(last)}
+     """.stripMargin
+  }
+
+  def invalidTerminal(method: String, invalid: Terminal): String = {
+    s"""ERROR: Invalid symbol ID: ${invalid.getId} (${invalid.getTerminalStr})
+       |
+        |${pointToSource(invalid)}
+     """.stripMargin
+  }
+
+  // TODO: these next two methods won't be called by the parser because there are no lists in the WDL grammar that
+  // cause these to be triggered.  Currently the parser is passing in 'null' for the value of 'last' and when that
+  // changes, these errors can be made more helpful.
+
+  def missingListItems(method: String, required: Int, found: Int, last: Terminal): String = {
+    s"ERROR: $method requires $required items, but only found $found"
+  }
+
+  def missingTerminator(method: String, terminal: TerminalIdentifier, last: Terminal): String = {
+    s"ERROR: $method requires a terminator after each element"
+  }
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/package.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/package.scala
new file mode 100644
index 00000000000..507ec139deb
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/package.scala
@@ -0,0 +1,10 @@
+package wdl.transforms.cascades
+
+import better.files.File
+import common.transforms.CheckedAtoB
+import wdl.cascades.parser.WdlParser.Ast
+
+package object parsing {
+  val fileToAst: CheckedAtoB[File, Ast] = CheckedAtoB.fromCheck(FileParser.convert)
+  val stringToAst: CheckedAtoB[FileStringParserInput, Ast] = CheckedAtoB.fromCheck(StringParser.convert)
+}
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala
new file mode 100644
index 00000000000..6f2f084867f
--- /dev/null
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala
@@ -0,0 +1,18 @@
+package wdl.transforms.cascades
+
+import common.transforms.CheckedAtoB
+import wdl.transforms.base.wdlom2wom.TaskDefinitionElementToWomTaskDefinition.TaskDefinitionElementToWomInputs
+import wdl.transforms.base.wdlom2wom.WorkflowDefinitionElementToWomWorkflowDefinition.WorkflowDefinitionConvertInputs
+import wdl.transforms.base.wdlom2wom.{FileElementToWomBundle, FileElementToWomBundleInputs, TaskDefinitionElementToWomTaskDefinition, WorkflowDefinitionElementToWomWorkflowDefinition}
+import wom.callable.{CallableTaskDefinition, WorkflowDefinition}
+import wom.executable.WomBundle
+import wdl.transforms.cascades.linking.expression.consumed._
+import wdl.transforms.cascades.linking.expression.files._
+import wdl.transforms.cascades.linking.expression.types._
+import wdl.transforms.cascades.linking.expression.values._
+
+package object wdlom2wom {
+  val taskDefinitionElementToWomTaskDefinition: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition] = CheckedAtoB.fromErrorOr(TaskDefinitionElementToWomTaskDefinition.convert)
+  val workflowDefinitionElementToWomWorkflowDefinition: CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition] = CheckedAtoB.fromErrorOr(WorkflowDefinitionElementToWomWorkflowDefinition.convert)
+  val fileElementToWomBundle: CheckedAtoB[FileElementToWomBundleInputs, WomBundle] = CheckedAtoB.fromCheck(FileElementToWomBundle.convert)
+}
diff --git a/wdl/transforms/cascades/src/test/cases/afters.wdl b/wdl/transforms/cascades/src/test/cases/afters.wdl
new file mode 100644
index 00000000000..3ba709da26e
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/cases/afters.wdl
@@ -0,0 +1,15 @@
+version development
+
+workflow afters {
+  call foo { input: i = 5 }
+  call foo as foo2 after foo { input: i = 6 }
+}
+
+task foo {
+  input {
+    Int i
+  }
+  command <<<
+    cat "hello ~{i}" > /tmp/helloFile
+  >>>
+}
diff --git a/wdl/transforms/cascades/src/test/cases/cascades_escaping.wdl b/wdl/transforms/cascades/src/test/cases/cascades_escaping.wdl
new file mode 100644
index 00000000000..4dbfdaa10ee
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/cases/cascades_escaping.wdl
@@ -0,0 +1,25 @@
+version development
+
+workflow escapes {
+    String backslash = " \\ "
+    String n = " \n "
+    String t = " \t "
+
+    String q1 = "leading text \" trailing text"
+    String q2 =              "\""
+    String q3 =            "  \"  "
+    String q4 = "leading text \' trailing text"
+    String q5 =              "\'"
+    String q6 =            "  \'  "
+
+    String sq1 = 'leading text \" trailing text'
+    String sq2 =              '\"'
+    String sq3 =            '  \"  '
+    String sq4 = 'leading text \' trailing text'
+    String sq5 =              '\''
+    String sq6 =            '  \'  '
+
+    String octal_hello = "\150\145\154\154\157"
+    String hex_hello = "\x68\x65\x6C\x6c\x6F"
+    String unicode_hello = "\u0068\U00000065\u006C\U0000006C\u006F"
+}
diff --git a/wdl/transforms/cascades/src/test/cases/no_input_no_output_workflow.wdl b/wdl/transforms/cascades/src/test/cases/no_input_no_output_workflow.wdl
new file mode 100644
index 00000000000..4e720f81521
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/cases/no_input_no_output_workflow.wdl
@@ -0,0 +1,30 @@
+version development
+
+# This workflow has been arbitrarily selected to test that tabs and spaces work interchangeably as whitespace.
+# Be very careful while editing, as many editors automatically convert spaces to tabs.
+
+workflow no_input_no_output {
+  call no_inputs as noi1
+
+  call no_inputs{}
+
+	call no_inputs as noi2 {}
+
+	call no_inputs as noi3 {
+
+	}
+
+  call no_inputs as noi4
+  {
+  }
+
+  call no_inputs as noi5 {
+    # A comment does not mess up the works
+  }
+
+}
+
+task no_inputs {
+  command { echo Hello World }
+
+}
diff --git a/wdl/transforms/cascades/src/test/cases/simple_first_test.wdl b/wdl/transforms/cascades/src/test/cases/simple_first_test.wdl
new file mode 100644
index 00000000000..adde2b1639f
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/cases/simple_first_test.wdl
@@ -0,0 +1,24 @@
+version development
+
+task in_n_out {
+  input {
+    Int total
+    String amount
+  }
+  command { echo ${total} }
+  output {
+    Int out = read_int(stdout()) + 1
+  }
+}
+
+workflow order {
+  input {
+    Int n = 4
+    String more = "more"
+  }
+  call in_n_out { input: total = n, amount = more }
+
+  output {
+    Int out = in_n_out.out
+  }
+}
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
new file mode 100644
index 00000000000..7633624bede
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
@@ -0,0 +1,97 @@
+package wdl.transforms.cascades
+
+import java.util
+
+import common.Checked
+import common.assertion.ErrorOrAssertions._
+import common.transforms.CheckedAtoB
+import cats.instances.either._
+import common.assertion.CromwellTimeoutSpec
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import wdl.cascades.parser.WdlParser
+import wdl.cascades.parser.WdlParser.{ParseTree, SyntaxErrorFormatter}
+import wdl.model.draft3.elements.ExpressionElement._
+import wdl.model.draft3.elements._
+import wdl.transforms.base.ast2wdlom.{GenericAstNode, _}
+import wdl.transforms.cascades.Ast2WdlomSpec._
+import wdl.transforms.cascades.ast2wdlom._
+import wdl.transforms.cascades.parsing.WdlCascadesSyntaxErrorFormatter
+import wom.callable.MetaValueElement.MetaValueElementInteger
+import wom.types.WomIntegerType
+import wom.values.WomInteger
+
+import scala.jdk.CollectionConverters._
+
+object Ast2WdlomSpec {
+  val parser = new WdlParser()
+
+  def fromString[A](expression: String,
+                    parseFunction: (util.List[WdlParser.Terminal], SyntaxErrorFormatter) => ParseTree)
+                   (implicit converter: CheckedAtoB[GenericAstNode, A]): Checked[A] = {
+
+    // Add the "version development" to force the lexer into "main" mode.
+    val versionedExpression = "version development\n" + expression
+    // That "version development" means we'll have 2 unwanted tokens at the start of the list, so drop 'em:
+    val tokens = parser.lex(versionedExpression, "string").asScala.drop(2).asJava
+    val terminalMap = (tokens.asScala.toVector map {(_, versionedExpression)}).toMap
+    val parseTree = parseFunction(tokens, WdlCascadesSyntaxErrorFormatter(terminalMap))
+    (wrapAstNode andThen converter).run(parseTree.toAst)
+  }
+}
+
+class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+
+
+  it should "parse a simple expression" in {
+    val str = "3 + 3"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid Add(PrimitiveLiteralExpressionElement(WomInteger(3)), PrimitiveLiteralExpressionElement(WomInteger(3)))
+  }
+
+  it should "parse a map expression" in {
+    val str = "{3: 3}"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid MapLiteral(Map(PrimitiveLiteralExpressionElement(WomInteger(3)) -> PrimitiveLiteralExpressionElement(WomInteger(3))))
+  }
+
+  it should "parse a simple meta section" in {
+    val str = "meta { five: 5 }"
+    val metaKvPair = fromString[MetaSectionElement](str, parser.parse_meta)
+    metaKvPair shouldBeValid MetaSectionElement(Map("five" -> MetaValueElementInteger(5)))
+  }
+
+  it should "parse a struct element" in {
+    val str = "struct Foo { Int five\n Int six }"
+    val struct = fromString[StructElement](str, parser.parse_struct)(astNodeToAst andThen astToStructElement)
+    struct shouldBeValid StructElement("Foo", Seq(
+      StructEntryElement("five", PrimitiveTypeElement(WomIntegerType)),
+      StructEntryElement("six", PrimitiveTypeElement(WomIntegerType)))
+    )
+  }
+
+  it should "parse the new as_map function" in {
+    val str = "as_map(some_pairs)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid(AsMap(IdentifierLookup("some_pairs")))
+  }
+
+  it should "parse the new as_pairs function" in {
+    val str = "as_pairs(some_map)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid(AsPairs(IdentifierLookup("some_map")))
+  }
+
+  it should "parse the new collect_by_key function" in {
+    val str = "collect_by_key(some_map)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid(CollectByKey(IdentifierLookup("some_map")))
+  }
+
+  it should "parse the new None keyword" in {
+    val str = "None"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid(NoneLiteralElement)
+  }
+}
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala
new file mode 100644
index 00000000000..5d2cb2991e8
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala
@@ -0,0 +1,212 @@
+package wdl.transforms.cascades.ast2wdlom
+
+import better.files.File
+import common.assertion.CromwellTimeoutSpec
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import wdl.model.draft3.elements.CommandPartElement.{PlaceholderCommandPartElement, StringCommandPartElement}
+import wdl.model.draft3.elements.ExpressionElement._
+import wdl.model.draft3.elements._
+import wdl.transforms.cascades.ast2wdlom.WdlFileToWdlomSpec._
+import wom.SourceFileLocation
+import wom.types._
+import wom.values.WomInteger
+
+
+class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  behavior of "WDL File to WDLOM"
+
+  val testCases = File("wdl/transforms/cascades/src/test/cases")
+
+  it should "be set up for testing" in {
+    testCases.exists shouldBe true
+    testCases.list.nonEmpty shouldBe true
+  }
+
+  testCases.list.filter(x => x.isRegularFile && x.extension.contains(".wdl")) foreach { testCase =>
+
+    val fileName = testCase.name
+    val testName = testCase.name.split("\\.").head
+
+    val itShouldString = s"create the correct Element structure for $fileName"
+    val testOrIgnore: (=>Any) => Unit = if (fileName.endsWith(".ignored.wdl")) {
+      (it should itShouldString).ignore _
+    } else {
+      (it should itShouldString).in _
+    }
+
+    testOrIgnore {
+
+      val expected = expectations.getOrElse(testName, fail(s"No Element expectation defined for $testName"))
+      fileToFileElement.run(testCase) match {
+        case Right(actual) => actual shouldBe expected
+        case Left(errors) =>
+          val formattedErrors = errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
+          fail(s"Failed to create WDLOM:$formattedErrors")
+      }
+
+    }
+  }
+}
+
+object WdlFileToWdlomSpec {
+
+  val expectations: Map[String, FileElement] = Map(
+    "no_input_no_output_workflow" ->
+      FileElement(
+        imports = Vector.empty,
+        structs = Vector.empty,
+        workflows = Vector(WorkflowDefinitionElement(
+          name = "no_input_no_output",
+          inputsSection = None,
+          graphElements = Set(
+            CallElement("no_inputs", Some("noi1"), Vector.empty, None, Some(SourceFileLocation(7))),
+            CallElement("no_inputs", Some("noi5"), Vector.empty, None, Some(SourceFileLocation(21))),
+            CallElement("no_inputs", Some("noi2"), Vector.empty, None, Some(SourceFileLocation(11))),
+            CallElement("no_inputs", Some("noi3"), Vector.empty, None, Some(SourceFileLocation(13))),
+            CallElement("no_inputs", Some("noi4"), Vector.empty, None, Some(SourceFileLocation(17))),
+            CallElement("no_inputs", None, Vector.empty, None, Some(SourceFileLocation(9)))
+          ),
+          outputsSection = None,
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(6)))
+        ),
+        tasks = Vector(
+          TaskDefinitionElement(
+            name = "no_inputs",
+            inputsSection = None,
+            declarations = Vector.empty,
+            outputsSection = None,
+            commandSection = CommandSectionElement(List(CommandSectionLine(Vector(StringCommandPartElement("echo Hello World "))))),
+            runtimeSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(27))
+          )
+        )
+      ),
+    "simple_first_test" ->
+      FileElement(
+        imports = Vector.empty,
+        structs = Vector.empty,
+        workflows = Vector(WorkflowDefinitionElement(
+          name = "order",
+          inputsSection = Some(InputsSectionElement(Vector(
+            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "n", Some(PrimitiveLiteralExpressionElement(WomInteger(4)))),
+            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", Some(StringLiteral("more")))))),
+          graphElements = Set(CallElement("in_n_out", None, Vector.empty, Some(CallBodyElement(Vector(KvPair("total", IdentifierLookup("n")), KvPair("amount", IdentifierLookup("more"))))), Some(SourceFileLocation(19)))),
+          outputsSection = Some(OutputsSectionElement(Vector(
+            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "out", IdentifierMemberAccess("in_n_out", "out", List.empty))))),
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(14)))
+        ),
+        tasks = Vector(TaskDefinitionElement(
+          name = "in_n_out",
+          inputsSection = Some(InputsSectionElement(Vector(
+            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "total", None),
+            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "amount", None)))),
+          declarations = Vector.empty,
+          outputsSection = Some(OutputsSectionElement(Vector(
+            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "out", Add(ReadInt(StdoutElement), PrimitiveLiteralExpressionElement(WomInteger(1))))))),
+          commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(
+            StringCommandPartElement("echo "),
+            PlaceholderCommandPartElement(IdentifierLookup("total"), PlaceholderAttributeSet.empty),
+            StringCommandPartElement(" ")
+          )))),
+          runtimeSection = None,
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(3))
+        ))
+      ),
+    "afters" ->
+      FileElement(
+        imports = Vector.empty,
+        structs = Vector.empty,
+        workflows = Vector(WorkflowDefinitionElement(
+          name = "afters",
+          inputsSection = None,
+          graphElements = Set(
+            CallElement("foo", None, Vector.empty, Some(CallBodyElement(Vector(KvPair("i", ExpressionElement.PrimitiveLiteralExpressionElement(WomInteger(5)))))),
+                        Some(SourceFileLocation(4))),
+            CallElement("foo", Some("foo2"), Vector("foo"), Some(CallBodyElement(Vector(KvPair("i", ExpressionElement.PrimitiveLiteralExpressionElement(WomInteger(6)))))),
+                        Some(SourceFileLocation(5)))
+          ),
+          outputsSection = None,
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(3)))
+        ),
+        tasks = Vector(TaskDefinitionElement(
+          name = "foo",
+          inputsSection = Some(InputsSectionElement(Vector(
+            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", None)))),
+          declarations = Vector.empty,
+          outputsSection = None,
+          commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(
+            StringCommandPartElement("cat \"hello "),
+            PlaceholderCommandPartElement(IdentifierLookup("i"), PlaceholderAttributeSet.empty),
+            StringCommandPartElement("\" > /tmp/helloFile")
+          )))),
+          runtimeSection = None,
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(8))
+        ))
+      ),
+    "cascades_escaping" ->
+      FileElement(
+        imports = Vector.empty,
+        structs = Vector.empty,
+        workflows = Vector(WorkflowDefinitionElement(
+          name = "escapes",
+          inputsSection = None,
+          graphElements = Set(
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"backslash",StringExpression(Vector(StringLiteral(" "), BackslashEscape, StringLiteral(" ")))),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"n",StringExpression(Vector(StringLiteral(" "), NewlineEscape, StringLiteral(" ")))),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"t",StringExpression(Vector(StringLiteral(" "), TabEscape, StringLiteral(" ")))),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q1",StringExpression(Vector(StringLiteral("leading text "), DoubleQuoteEscape, StringLiteral(" trailing text")))),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q2",StringLiteral("\"")),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q3",StringExpression(Vector(StringLiteral("  "), DoubleQuoteEscape, StringLiteral("  ")))),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q4",StringExpression(Vector(StringLiteral("leading text "), SingleQuoteEscape, StringLiteral(" trailing text")))),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q5",StringLiteral("'")),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q6",StringExpression(Vector(StringLiteral("  "), SingleQuoteEscape, StringLiteral("  ")))),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq1",StringExpression(Vector(StringLiteral("leading text "), DoubleQuoteEscape, StringLiteral(" trailing text")))),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq2",StringLiteral("\"")),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq3",StringExpression(Vector(StringLiteral("  "), DoubleQuoteEscape, StringLiteral("  ")))),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq4",StringExpression(Vector(StringLiteral("leading text "), SingleQuoteEscape, StringLiteral(" trailing text")))),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq5",StringLiteral("'")),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq6",StringExpression(Vector(StringLiteral("  "), SingleQuoteEscape, StringLiteral("  ")))),
+            IntermediateValueDeclarationElement(
+              PrimitiveTypeElement(WomStringType),
+              "octal_hello",
+              StringExpression(Vector(UnicodeCharacterEscape(104), UnicodeCharacterEscape(101), UnicodeCharacterEscape(108), UnicodeCharacterEscape(108), UnicodeCharacterEscape(111)))
+            ),
+            IntermediateValueDeclarationElement(
+              PrimitiveTypeElement(WomStringType),
+              "hex_hello",
+              StringExpression(Vector(UnicodeCharacterEscape(104), UnicodeCharacterEscape(101), UnicodeCharacterEscape(108), UnicodeCharacterEscape(108), UnicodeCharacterEscape(111)))
+            ),
+            IntermediateValueDeclarationElement(
+              PrimitiveTypeElement(WomStringType),
+              "unicode_hello",
+              StringExpression(Vector(
+                UnicodeCharacterEscape(104),
+                UnicodeCharacterEscape(101),
+                UnicodeCharacterEscape(108),
+                UnicodeCharacterEscape(108),
+                UnicodeCharacterEscape(111)
+              ))
+            )
+          ),
+          outputsSection = None,
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(3))
+        )),
+        tasks = Vector.empty)
+  )
+}
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
new file mode 100644
index 00000000000..4276d882b46
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
@@ -0,0 +1,60 @@
+package wdl.transforms.cascades.linking.expression.consumed
+
+import common.assertion.CromwellTimeoutSpec
+import common.assertion.ErrorOrAssertions._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.graph.ExpressionValueConsumer.ops._
+import wdl.model.draft3.graph.{UnlinkedCallOutputOrIdentifierAndMemberAccessHook, UnlinkedIdentifierHook}
+import wdl.transforms.cascades.Ast2WdlomSpec._
+import wdl.transforms.cascades.ast2wdlom._
+
+class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+  behavior of "WDL Cascades' expressionValueConsumer"
+
+  it should "return nothing from static integer addition" in {
+    val str = "3 + 3"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.expressionConsumedValueHooks should be(Set.empty)
+    }
+  }
+
+  it should "find the variable lookup within an integer addition" in {
+    val str = "3 + three"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("three")))
+    }
+  }
+
+  it should "find the variable lookup within as_map(...) called on a task output" in {
+    val str = "as_map(my_task.out)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedCallOutputOrIdentifierAndMemberAccessHook("my_task", "out")))
+    }
+  }
+
+  it should "find the variable lookup within as_pairs(as_map(...)), called on a task output" in {
+    val str = "as_pairs(as_map(my_task.out))"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedCallOutputOrIdentifierAndMemberAccessHook("my_task", "out")))
+    }
+  }
+
+  it should "discover the variable lookups within a sep() call" in {
+    val str = """ sep(my_separator, ["a", "b", c]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_separator"), UnlinkedIdentifierHook("c")))
+    }
+  }
+}
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
new file mode 100644
index 00000000000..a65bd73c8a9
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
@@ -0,0 +1,43 @@
+package wdl.transforms.cascades.linking.expression.files
+
+import common.assertion.CromwellTimeoutSpec
+import common.assertion.ErrorOrAssertions._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.graph.expression.FileEvaluator.ops._
+import wdl.transforms.cascades.Ast2WdlomSpec.{fromString, parser}
+import wdl.transforms.cascades.ast2wdlom._
+import wdl.transforms.cascades.linking.expression.values.expressionEvaluator
+import wom.expression.NoIoFunctionSet
+import wom.types.{WomArrayType, WomIntegerType, WomPairType, WomStringType}
+import wom.values.WomSingleFile
+
+class CascadesFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+  it should "return nothing from static integer addition" in {
+    val str = "3 + 3"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomIntegerType) shouldBeValid Set.empty
+    }
+  }
+
+  it should "find the map to read" in {
+    val str = """as_pairs(read_map("my_map.txt"))"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomArrayType(WomPairType(WomStringType, WomStringType))) shouldBeValid Set(WomSingleFile("my_map.txt"))
+    }
+  }
+
+  it should "discover the file which would be required to evaluate a sep() function" in {
+    val str = """ sep(' ', read_lines("foo.txt")) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(WomSingleFile("foo.txt"))
+    }
+  }
+}
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
new file mode 100644
index 00000000000..b6944e4485a
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
@@ -0,0 +1,59 @@
+package wdl.transforms.cascades.linking.expression.types
+
+import common.assertion.CromwellTimeoutSpec
+import common.assertion.ErrorOrAssertions._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.graph.expression.TypeEvaluator.ops._
+import wdl.transforms.cascades.Ast2WdlomSpec.{fromString, parser}
+import wdl.transforms.cascades.ast2wdlom._
+import wom.types._
+
+class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+  it should "return nothing from static integer addition" in {
+    val str = "3 + 3"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.evaluateType(Map.empty) shouldBeValid WomIntegerType
+    }
+  }
+
+  it should "evaluate the right map type from as_map" in {
+    val str = """as_map([(1,2), (3,4)])"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.evaluateType(Map.empty) shouldBeValid WomMapType(WomIntegerType, WomIntegerType)
+    }
+  }
+
+  it should "evaluate the right Array[Pair[X, Y]] type from as_pairs" in {
+    val str = """as_pairs({ "one": 1, "two": 2, "three": 3 })"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomPairType(WomStringType, WomIntegerType))
+    }
+  }
+
+  it should "evaluate the type of a sep() function as String" in {
+    val str = """ sep(' ', ["a", "b", "c"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.evaluateType(Map.empty) shouldBeValid WomStringType
+    }
+  }
+
+  it should "evaluate the type of a sep() function with a sub-call to prefix as String" in {
+    val str = """ sep(' ', prefix("-i ", ["a", "b", "c"])) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.evaluateType(Map.empty) shouldBeValid WomStringType
+    }
+  }
+
+}
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
new file mode 100644
index 00000000000..7055da1c1ae
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
@@ -0,0 +1,189 @@
+package wdl.transforms.cascades.linking.expression.values
+
+import common.assertion.CromwellTimeoutSpec
+import common.assertion.ErrorOrAssertions._
+import common.assertion.ManyTimes.intWithTimes
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.graph.expression.EvaluatedValue
+import wdl.model.draft3.graph.expression.ValueEvaluator.ops._
+import wdl.transforms.cascades.Ast2WdlomSpec.{fromString, parser}
+import wdl.transforms.cascades.ast2wdlom._
+import wom.expression.NoIoFunctionSet
+import wom.types.{WomIntegerType, WomMapType, WomOptionalType, WomStringType}
+import wom.values.{WomArray, WomInteger, WomMap, WomOptionalValue, WomPair, WomString}
+
+class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  behavior of "cascades value evaluator"
+
+  // The "did we bring in the base transforms" sanity check:
+  it should "return a static integer from static integer addition" in {
+    val str = "3 + 3"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF {
+      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomInteger(6), Seq.empty)
+    }
+  }
+
+  it should "evaluate an 'as_map' expression correctly" in {
+    val str = """ as_map( [("x", 1), ("y", 2), ("z", 3)] ) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedMap: WomMap = WomMap(Map (
+      WomString("x") -> WomInteger(1),
+      WomString("y") -> WomInteger(2),
+      WomString("z") -> WomInteger(3)
+    ))
+
+    expr.shouldBeValidPF {
+      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
+    }
+  }
+
+  it should "evaluate an 'as_pairs' expression correctly" in {
+    // Repeat this a few times ensure we aren't occasionally reordering by accident:
+    10 times {
+      val str = """ as_pairs( { 1: "one", 2: "two", 3: three } ) """
+      val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+      val inputs = Map("three" -> WomString("three"))
+      val expectedPairs: WomArray = WomArray(Seq(
+        WomPair(WomInteger(1), WomString("one")),
+        WomPair(WomInteger(2), WomString("two")),
+        WomPair(WomInteger(3), WomString("three"))
+      ))
+
+      expr.shouldBeValidPF {
+        case e => e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPairs, Seq.empty)
+      }
+      ()
+    }
+  }
+
+  // TODO: Sort out stable map ordering
+  // We cannot run this test yet because the map reorders the pairs
+  it should "echo correctly via as_pairs(as_map(...))" ignore {
+
+    // Repeat this a few times ensure we aren't occasionally reordering by accident:
+    10 times {
+      // A value lookup expression:
+      val str = """ as_pairs(as_map(echo_me)) """
+      val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+      val expectedPairs: WomArray = WomArray(Seq(
+        WomPair(WomInteger(1), WomString("one")),
+        WomPair(WomInteger(2), WomString("two")),
+        WomPair(WomInteger(3), WomString("three"))
+      ))
+
+      val inputs = Map("echo_me" -> expectedPairs)
+
+      expr.shouldBeValidPF {
+        case e => e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPairs, Seq.empty)
+      }
+      ()
+    }
+  }
+
+  it should "fail to evaluate 'as_map' if keys are duplicated" in {
+
+    // Repeat this a few times ensure we aren't occasionally reordering by accident:
+    10 times {
+      val str = """ as_map( [("x", 1), ("y", 2), ("x", 3)] ) """
+      val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+      expr.shouldBeValidPF {
+        case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None).shouldBeInvalid("""Cannot evaluate 'as_map' with duplicated keys: keys can only appear once but "x" appeared 2 times.""")
+      }
+      ()
+    }
+  }
+
+  it should "collect by key when keys are duplicated" in {
+
+    // Repeat this a few times ensure we aren't occasionally reordering by accident:
+    10 times {
+      val str = """ collect_by_key( [("x", 1), ("y", 2), ("x", 3)] ) """
+      val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+      val expectedMap: WomMap = WomMap(Map(
+        WomString("x") -> WomArray(Seq(WomInteger(1), WomInteger(3))),
+        WomString("y") -> WomArray(Seq(WomInteger(2)))
+      ))
+
+      expr.shouldBeValidPF {
+        case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
+      }
+      ()
+    }
+  }
+
+  it should "evaluate a map literal mixing String?s and Int?s" in {
+    val str = """ { "i": i_in, "s": s_in } """
+    val inputs = Map(
+      "i_in" -> WomOptionalValue(WomIntegerType, Some(WomInteger(1))),
+      "s_in" -> WomOptionalValue(WomStringType, Some(WomString("two")))
+    )
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedMap: WomMap = WomMap(WomMapType(WomStringType, WomOptionalType(WomStringType)), Map (
+      WomString("i") -> WomOptionalValue(WomStringType, Some(WomString("1"))),
+      WomString("s") -> WomOptionalValue(WomStringType, Some(WomString("two")))
+    ))
+
+    expr.shouldBeValidPF {
+      case e => e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
+    }
+  }
+
+  val escapeTests = Map(
+    "\\\\" -> "\\",
+    "\\n" -> System.lineSeparator,
+    "\\t" -> "\t",
+    "\\'" -> "'",
+    "\\\"" -> "\"",
+    "\\150\\145\\154\\154\\157" -> "hello",
+    "\\x68\\x65\\x6C\\x6c\\x6F" -> "hello",
+    "\\u0068\\U00000065\\u006C\\U0000006C\\u006F" -> "hello",
+    "\\u03A9 (omega)" -> "Ω (omega)"
+  )
+
+  escapeTests foreach { case (sequence, expected) =>
+    List("\"", "'") foreach { quote =>
+      it should s"evaluate the escaping string $quote$sequence$quote as: $expected" in {
+        val str = s"$quote$sequence$quote"
+        val expectedEvaluation = WomString(expected)
+        val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+        expr.shouldBeValidPF {
+          case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedEvaluation, Seq.empty)
+        }
+      }
+    }
+  }
+
+  it should "evaluate a simple sep expression correctly" in {
+    val str = """ sep(" ", ["a", "b", "c"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedString: WomString = WomString("a b c")
+
+    expr.shouldBeValidPF {
+      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
+    }
+  }
+
+  it should "evaluate a sep expression containing a sub-call to prefix correctly" in {
+    val str = """ sep(" ", prefix("-i ", ["a", "b", "c"])) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedString: WomString = WomString("-i a -i b -i c")
+
+    expr.shouldBeValidPF {
+      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
+    }
+  }
+}
diff --git a/womtool/src/main/scala/womtool/input/WomGraphMaker.scala b/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
index f0d238392fa..bd3ef65e09b 100644
--- a/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
+++ b/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
@@ -1,7 +1,6 @@
 package womtool.input
 
 import java.nio.file.{Files, Paths}
-
 import com.typesafe.config.ConfigFactory
 import common.Checked
 import common.validation.Validation._
@@ -9,6 +8,7 @@ import cromwell.core.path.Path
 import cromwell.languages.LanguageFactory
 import cromwell.languages.util.ImportResolver._
 import languages.wdl.biscayne.WdlBiscayneLanguageFactory
+import languages.wdl.cascades.WdlCascadesLanguageFactory
 import languages.wdl.draft2.WdlDraft2LanguageFactory
 import languages.wdl.draft3.WdlDraft3LanguageFactory
 import wom.ResolvedImportRecord
@@ -31,7 +31,8 @@ object WomGraphMaker {
       val languageFactory =
         List(
           new WdlDraft3LanguageFactory(ConfigFactory.empty()),
-          new WdlBiscayneLanguageFactory(ConfigFactory.empty()))
+          new WdlBiscayneLanguageFactory(ConfigFactory.empty()),
+          new WdlCascadesLanguageFactory(ConfigFactory.empty()))
           .find(_.looksParsable(mainFileContents))
           .getOrElse(new WdlDraft2LanguageFactory(ConfigFactory.empty()))
 
diff --git a/womtool/src/test/resources/validate-with-imports/biscayne/http_relative_imports/expected_imports.txt b/womtool/src/test/resources/validate-with-imports/biscayne/http_relative_imports/expected_imports.txt
index f1845d36f99..afd8c5729e4 100644
--- a/womtool/src/test/resources/validate-with-imports/biscayne/http_relative_imports/expected_imports.txt
+++ b/womtool/src/test/resources/validate-with-imports/biscayne/http_relative_imports/expected_imports.txt
@@ -1,5 +1,5 @@
 Success!
 List of Workflow dependencies is:
-https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/biscayne/valid/relative_imports/structs/my_struct.wdl
-https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/tasks/add5.wdl
-https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl
+https://raw.githubusercontent.com/broadinstitute/cromwell/aen_wx_966/womtool/src/test/resources/validate/biscayne/valid/relative_imports/structs/my_struct.wdl
+https://raw.githubusercontent.com/broadinstitute/cromwell/aen_wx_966/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/tasks/add5.wdl
+https://raw.githubusercontent.com/broadinstitute/cromwell/aen_wx_966/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl
diff --git a/womtool/src/test/resources/validate/biscayne/invalid/after_circle/after_circle.wdl b/womtool/src/test/resources/validate/biscayne/invalid/after_circle/after_circle.wdl
index c1dbd773dbf..86f7afb70c5 100644
--- a/womtool/src/test/resources/validate/biscayne/invalid/after_circle/after_circle.wdl
+++ b/womtool/src/test/resources/validate/biscayne/invalid/after_circle/after_circle.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow after_circle {
   call foo as foo1 after foo2 { input: i = 5 }
diff --git a/womtool/src/test/resources/validate/biscayne/invalid/bad_after/bad_after.wdl b/womtool/src/test/resources/validate/biscayne/invalid/bad_after/bad_after.wdl
index b9cc5fbc0f4..3401fbc1142 100644
--- a/womtool/src/test/resources/validate/biscayne/invalid/bad_after/bad_after.wdl
+++ b/womtool/src/test/resources/validate/biscayne/invalid/bad_after/bad_after.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow bad_after {
   call foo { input: i = 5 }
diff --git a/womtool/src/test/resources/validate/biscayne/invalid/bad_task/bad_task.wdl b/womtool/src/test/resources/validate/biscayne/invalid/bad_task/bad_task.wdl
index 6d3f4825e5b..1f1bdb22c3d 100644
--- a/womtool/src/test/resources/validate/biscayne/invalid/bad_task/bad_task.wdl
+++ b/womtool/src/test/resources/validate/biscayne/invalid/bad_task/bad_task.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow oops {
   call oopsie
diff --git a/womtool/src/test/resources/validate/biscayne/valid/directory_type/directory_type.wdl b/womtool/src/test/resources/validate/biscayne/invalid/directory_type/directory_type.wdl
similarity index 96%
rename from womtool/src/test/resources/validate/biscayne/valid/directory_type/directory_type.wdl
rename to womtool/src/test/resources/validate/biscayne/invalid/directory_type/directory_type.wdl
index 4d33536fac1..21f73d23257 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/directory_type/directory_type.wdl
+++ b/womtool/src/test/resources/validate/biscayne/invalid/directory_type/directory_type.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow use_directory {
   call make_directory
diff --git a/womtool/src/test/resources/validate/biscayne/invalid/object_struct/object_struct.wdl b/womtool/src/test/resources/validate/biscayne/invalid/object_struct/object_struct.wdl
index c74fb2d4b66..22c4dcefed0 100644
--- a/womtool/src/test/resources/validate/biscayne/invalid/object_struct/object_struct.wdl
+++ b/womtool/src/test/resources/validate/biscayne/invalid/object_struct/object_struct.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 struct Object {
   String field
diff --git a/womtool/src/test/resources/validate/biscayne/invalid/object_type/object_type.wdl b/womtool/src/test/resources/validate/biscayne/invalid/object_type/object_type.wdl
index 63f636399e3..0741a2cd1d7 100644
--- a/womtool/src/test/resources/validate/biscayne/invalid/object_type/object_type.wdl
+++ b/womtool/src/test/resources/validate/biscayne/invalid/object_type/object_type.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow object_type {
   input {
diff --git a/womtool/src/test/resources/validate/biscayne/invalid/read_and_write_object/read_and_write_object.wdl b/womtool/src/test/resources/validate/biscayne/invalid/read_and_write_object/read_and_write_object.wdl
index 96d8dba0252..dc76c757676 100644
--- a/womtool/src/test/resources/validate/biscayne/invalid/read_and_write_object/read_and_write_object.wdl
+++ b/womtool/src/test/resources/validate/biscayne/invalid/read_and_write_object/read_and_write_object.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow read_and_write_object {
   File foo = write_object( { "a": "b" } )
diff --git a/womtool/src/test/resources/validate/biscayne/invalid/trailing_if/trailing_if.wdl b/womtool/src/test/resources/validate/biscayne/invalid/trailing_if/trailing_if.wdl
index 7dad0400c84..71e32f74b3d 100644
--- a/womtool/src/test/resources/validate/biscayne/invalid/trailing_if/trailing_if.wdl
+++ b/womtool/src/test/resources/validate/biscayne/invalid/trailing_if/trailing_if.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow trailing_if {
   input {
diff --git a/womtool/src/test/resources/validate/biscayne/valid/afters/afters.wdl b/womtool/src/test/resources/validate/biscayne/valid/afters/afters.wdl
index a27224fc620..363a43e338a 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/afters/afters.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/afters/afters.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow afters {
   call foo { input: i = 5 }
diff --git a/womtool/src/test/resources/validate/biscayne/valid/afters_and_ifs/afters_and_ifs.wdl b/womtool/src/test/resources/validate/biscayne/valid/afters_and_ifs/afters_and_ifs.wdl
index 2bd89d8180d..b03e761cf57 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/afters_and_ifs/afters_and_ifs.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/afters_and_ifs/afters_and_ifs.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow afters {
   input {
diff --git a/womtool/src/test/resources/validate/biscayne/valid/afters_and_scatters/afters_and_scatters.wdl b/womtool/src/test/resources/validate/biscayne/valid/afters_and_scatters/afters_and_scatters.wdl
index 8cb07333b79..d4aff77c238 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/afters_and_scatters/afters_and_scatters.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/afters_and_scatters/afters_and_scatters.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow afters {
   input {
diff --git a/womtool/src/test/resources/validate/biscayne/valid/http_relative_imports/http_relative_imports.wdl b/womtool/src/test/resources/validate/biscayne/valid/http_relative_imports/http_relative_imports.wdl
index 3c517119984..26c750e8b64 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/http_relative_imports/http_relative_imports.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/http_relative_imports/http_relative_imports.wdl
@@ -1,7 +1,7 @@
-version development
+version development-1.1
 
 # Is there a better way to test this?
-import "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/cromwell/aen_wx_966/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl"
 
 workflow http_relative_imports {
   call foo.foo_wf
diff --git a/womtool/src/test/resources/validate/biscayne/valid/object_struct/object_struct.wdl b/womtool/src/test/resources/validate/biscayne/valid/object_struct/object_struct.wdl
index c74fb2d4b66..22c4dcefed0 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/object_struct/object_struct.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/object_struct/object_struct.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 struct Object {
   String field
diff --git a/womtool/src/test/resources/validate/biscayne/valid/pre_version_comments/pre_version_comments.wdl b/womtool/src/test/resources/validate/biscayne/valid/pre_version_comments/pre_version_comments.wdl
index bc31812f266..16aa23591f7 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/pre_version_comments/pre_version_comments.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/pre_version_comments/pre_version_comments.wdl
@@ -6,7 +6,7 @@
 ##
 #
 
-version development
+version development-1.1
 
 workflow foo {
   output {
diff --git a/womtool/src/test/resources/validate/biscayne/valid/relative_imports/relative_imports.wdl b/womtool/src/test/resources/validate/biscayne/valid/relative_imports/relative_imports.wdl
index 8d3c65eff9c..5b26d0cbade 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/relative_imports/relative_imports.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/relative_imports/relative_imports.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 import "sub_wfs/foo.wdl"
 
diff --git a/womtool/src/test/resources/validate/biscayne/valid/relative_imports/structs/my_struct.wdl b/womtool/src/test/resources/validate/biscayne/valid/relative_imports/structs/my_struct.wdl
index a70b2619ccd..e15367731b2 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/relative_imports/structs/my_struct.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/relative_imports/structs/my_struct.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 struct MyStruct {
   Int a
diff --git a/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl b/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl
index 106a7c7cc78..88376fa05ed 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 import "../structs/my_struct.wdl"
 import "tasks/add5.wdl" as a5
diff --git a/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/tasks/add5.wdl b/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/tasks/add5.wdl
index ca731fc4e5e..c3d0e3b676a 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/tasks/add5.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/tasks/add5.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 import "../../structs/my_struct.wdl"
 
diff --git a/womtool/src/test/resources/validate/biscayne/valid/sep_function/sep_function.wdl b/womtool/src/test/resources/validate/biscayne/valid/sep_function/sep_function.wdl
index 36a4165fcb5..8375d550c43 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/sep_function/sep_function.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/sep_function/sep_function.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow SepWorkflow {
   input {}
diff --git a/womtool/src/test/resources/validate/biscayne/valid/sep_function/sep_function_no_command.wdl b/womtool/src/test/resources/validate/biscayne/valid/sep_function/sep_function_no_command.wdl
index 4fd26c1f824..d491a74a556 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/sep_function/sep_function_no_command.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/sep_function/sep_function_no_command.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow SepWorkflow2 {
   input {}
diff --git a/womtool/src/test/resources/validate/biscayne/valid/use_nones/use_nones.wdl b/womtool/src/test/resources/validate/biscayne/valid/use_nones/use_nones.wdl
index d304a3b9189..ccdf67fe330 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/use_nones/use_nones.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/use_nones/use_nones.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow use_nones {
   input {
diff --git a/womtool/src/test/resources/validate/biscayne/valid/utf8/utf8.wdl b/womtool/src/test/resources/validate/biscayne/valid/utf8/utf8.wdl
index 0ae539e35a8..74e11ba2b40 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/utf8/utf8.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/utf8/utf8.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow foo {
   String omega = "Ω"
diff --git a/womtool/src/test/resources/validate/biscayne/valid/version_variables/version_variables.wdl b/womtool/src/test/resources/validate/biscayne/valid/version_variables/version_variables.wdl
index aa06f9f63d3..33dd50b3dcf 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/version_variables/version_variables.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/version_variables/version_variables.wdl
@@ -1,4 +1,4 @@
-version development
+version development-1.1
 
 workflow version_variables {
   input {

From c5d615121f4ee3b144410a281934abc6c54df6a4 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 25 May 2023 17:09:00 -0400
Subject: [PATCH 176/326] WX-966 Post-merge branch cleanup + test fix (#7149)

---
 .../biscayne_http_relative_imports.wdl                      | 2 +-
 .../describe/wdl_1_0/relative_url_imports/description.json  | 2 +-
 .../biscayne/http_relative_imports/expected_imports.txt     | 6 +++---
 .../valid/http_relative_imports/http_relative_imports.wdl   | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_http_relative_imports/biscayne_http_relative_imports.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_http_relative_imports/biscayne_http_relative_imports.wdl
index e68de3ef339..dbe4fdee0f8 100644
--- a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_http_relative_imports/biscayne_http_relative_imports.wdl
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_http_relative_imports/biscayne_http_relative_imports.wdl
@@ -1,7 +1,7 @@
 version development-1.1
 
 # Is there a better way to test this?
-import "https://raw.githubusercontent.com/broadinstitute/cromwell/aen_wx_966/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl"
 
 workflow biscayne_http_relative_imports {
   call foo.foo_wf
diff --git a/services/src/test/resources/describe/wdl_1_0/relative_url_imports/description.json b/services/src/test/resources/describe/wdl_1_0/relative_url_imports/description.json
index 7a8725ab631..ddfbba00517 100644
--- a/services/src/test/resources/describe/wdl_1_0/relative_url_imports/description.json
+++ b/services/src/test/resources/describe/wdl_1_0/relative_url_imports/description.json
@@ -19,7 +19,7 @@
   ],
   "submittedDescriptorType" : {
     "descriptorType" : "WDL",
-    "descriptorTypeVersion" : "Cascades"
+    "descriptorTypeVersion" : "Biscayne"
   },
   "importedDescriptorTypes" : [
   ],
diff --git a/womtool/src/test/resources/validate-with-imports/biscayne/http_relative_imports/expected_imports.txt b/womtool/src/test/resources/validate-with-imports/biscayne/http_relative_imports/expected_imports.txt
index afd8c5729e4..f1845d36f99 100644
--- a/womtool/src/test/resources/validate-with-imports/biscayne/http_relative_imports/expected_imports.txt
+++ b/womtool/src/test/resources/validate-with-imports/biscayne/http_relative_imports/expected_imports.txt
@@ -1,5 +1,5 @@
 Success!
 List of Workflow dependencies is:
-https://raw.githubusercontent.com/broadinstitute/cromwell/aen_wx_966/womtool/src/test/resources/validate/biscayne/valid/relative_imports/structs/my_struct.wdl
-https://raw.githubusercontent.com/broadinstitute/cromwell/aen_wx_966/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/tasks/add5.wdl
-https://raw.githubusercontent.com/broadinstitute/cromwell/aen_wx_966/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl
+https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/biscayne/valid/relative_imports/structs/my_struct.wdl
+https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/tasks/add5.wdl
+https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl
diff --git a/womtool/src/test/resources/validate/biscayne/valid/http_relative_imports/http_relative_imports.wdl b/womtool/src/test/resources/validate/biscayne/valid/http_relative_imports/http_relative_imports.wdl
index 26c750e8b64..7b2a728a068 100644
--- a/womtool/src/test/resources/validate/biscayne/valid/http_relative_imports/http_relative_imports.wdl
+++ b/womtool/src/test/resources/validate/biscayne/valid/http_relative_imports/http_relative_imports.wdl
@@ -1,7 +1,7 @@
 version development-1.1
 
 # Is there a better way to test this?
-import "https://raw.githubusercontent.com/broadinstitute/cromwell/aen_wx_966/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl"
+import "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/biscayne/valid/relative_imports/sub_wfs/foo.wdl"
 
 workflow http_relative_imports {
   call foo.foo_wf

From 0119ac6cb9a81db6fcd86d1f6e8e081d44fcf623 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 26 May 2023 13:11:07 -0400
Subject: [PATCH 177/326] WX-1122 Enable Azure ApplicationInsights (#7143)

---
 .gitignore                                        |  1 +
 CHANGELOG.md                                      |  7 ++++++-
 project/Dependencies.scala                        |  4 +++-
 .../src/main/resources/applicationinsights.json   |  7 +++++++
 .../main/scala/cromwell/CromwellEntryPoint.scala  | 15 +++++++++++++++
 5 files changed, 32 insertions(+), 2 deletions(-)
 create mode 100644 server/src/main/resources/applicationinsights.json

diff --git a/.gitignore b/.gitignore
index a5b72f6b263..d67639e9ef1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -55,3 +55,4 @@ tesk_application.conf
 **/venv/
 exome_germline_single_sample_v1.3/
 **/*.pyc
+applicationinsights.log
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b1190ef951a..3a7c097699e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,12 @@
 
 ### HTTPFilesystem Improvements
 
- * WDL `size` engine function now works for HTTP files. 
+WDL `size` engine function now works for HTTP files. 
+
+### Azure Instrumentation Support
+Cromwell can now send logs and process information to Azure Application Insights. To enable, set environment 
+variable `APPLICATIONINSIGHTS_CONNECTION_STRING` to your connection string. [See here for information.](https://learn.microsoft.com/en-us/azure/azure-monitor/app/sdk-connection-string)
+
 
 ## 85 Release Notes
 
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 405ecd2d3c4..110faf925e4 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -12,6 +12,7 @@ object Dependencies {
   // https://github.com/sbt/sbt/issues/4531
   private val azureStorageBlobNioV = "12.0.0-beta.19"
   private val azureIdentitySdkV = "1.9.0-beta.2"
+  private val azureAppInsightsV = "3.4.12"
   private val betterFilesV = "3.9.1"
   private val jsonSmartV = "2.4.10"
   /*
@@ -210,7 +211,8 @@ object Dependencies {
     "com.azure" % "azure-core-management" % "1.7.1",
     "com.fasterxml.jackson.dataformat" % "jackson-dataformat-xml" % jacksonV,
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0",
-    "net.minidev" % "json-smart" % jsonSmartV
+    "net.minidev" % "json-smart" % jsonSmartV,
+    "com.microsoft.azure" % "applicationinsights-runtime-attach" % azureAppInsightsV,
   )
 
   val wsmDependencies: List[ModuleID] = List(
diff --git a/server/src/main/resources/applicationinsights.json b/server/src/main/resources/applicationinsights.json
new file mode 100644
index 00000000000..e90407242bf
--- /dev/null
+++ b/server/src/main/resources/applicationinsights.json
@@ -0,0 +1,7 @@
+{
+  "instrumentation": {
+    "jdbc": {
+      "enabled": false
+    }
+  }
+}
diff --git a/server/src/main/scala/cromwell/CromwellEntryPoint.scala b/server/src/main/scala/cromwell/CromwellEntryPoint.scala
index a1707db6488..9f6ce82a127 100644
--- a/server/src/main/scala/cromwell/CromwellEntryPoint.scala
+++ b/server/src/main/scala/cromwell/CromwellEntryPoint.scala
@@ -9,6 +9,7 @@ import cats.data.Validated._
 import cats.effect.{ContextShift, IO}
 import cats.syntax.apply._
 import cats.syntax.validated._
+import com.microsoft.applicationinsights.attach.ApplicationInsights
 import com.typesafe.config.{Config, ConfigFactory}
 import common.exception.MessageAggregation
 import common.validation.ErrorOr._
@@ -45,6 +46,11 @@ object CromwellEntryPoint extends GracefulStopSupport {
   private val dnsCacheTtl = config.getOrElse("system.dns-cache-ttl", 3 minutes)
   java.security.Security.setProperty("networkaddress.cache.ttl", dnsCacheTtl.toSeconds.toString)
 
+  // The presence of this env var tells us that the user is trying to send instrumentation data and
+  // logs to Azure Application Insights. If it's present, we'll attach the ApplicationInsights agent.
+  // To configure the behavior of this agent, see server/src/main/resources/applicationinsights.json
+  private lazy val useAzureInstrumentation = sys.env.contains("APPLICATIONINSIGHTS_CONNECTION_STRING")
+
   /**
     * Run Cromwell in server mode.
     */
@@ -140,8 +146,17 @@ object CromwellEntryPoint extends GracefulStopSupport {
     *
     * Also copies variables from config/system/environment/defaults over to the system properties.
     * Fixes issue where users are trying to specify Java properties as environment variables.
+    *
+    * Also also enables Azure log handling when appropriate
     */
   private def initLogging(command: Command): Unit = {
+
+    // Enable Azure instrumentation and log-slurping if desired. Running ApplicationInsights.attach()
+    // without checking for the presence of the relevant env var doesn't cause any failures, but does
+    // print an error that would be confusing for non-Azure users.
+    if (useAzureInstrumentation)
+      ApplicationInsights.attach()
+
     val logbackSetting = command match {
       case Server => "STANDARD"
       case Submit => "PRETTY"

From f931c25d7c55423e70f0cb5a20f0b70789142116 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 30 May 2023 15:59:32 -0400
Subject: [PATCH 178/326] [WX-1108] Add tests back (#7148)

---
 project/Settings.scala                         | 4 ++--
 src/ci/bin/testCentaurHoricromtalPapiV2beta.sh | 2 --
 src/ci/bin/testCentaurPapiV2beta.sh            | 2 --
 3 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/project/Settings.scala b/project/Settings.scala
index 797d7917dd9..11867e74017 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -127,9 +127,9 @@ object Settings {
       Instructions.Run("""mkdir -p /usr/local/gcloud \
                          | && tar -C /usr/local/gcloud -xvf /tmp/google-cloud-sdk.tar.gz \
                          | && /usr/local/gcloud/google-cloud-sdk/install.sh""".stripMargin),
-      // instructions to install `getm`. Pin to version 0.0.4 as the behaviors of future versions with respect to
+      // instructions to install `getm`. Pin to version 0.0.5 as the behaviors of future versions with respect to
       // messages or exit codes may change.
-      Instructions.Run("pip3 install getm==0.0.4")
+      Instructions.Run("pip3 install getm==0.0.5")
     )
   )
 
diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
index b331eda6962..9dba2f6f8ce 100755
--- a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
+++ b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
@@ -25,7 +25,5 @@ cromwell::build::run_centaur \
     -e relative_output_paths_colliding \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
-    -e drs_usa_jdr \
-    -e drs_usa_jdr_preresolve
 
 cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testCentaurPapiV2beta.sh b/src/ci/bin/testCentaurPapiV2beta.sh
index 98db25c54b9..b3a1ef2a61e 100755
--- a/src/ci/bin/testCentaurPapiV2beta.sh
+++ b/src/ci/bin/testCentaurPapiV2beta.sh
@@ -23,7 +23,5 @@ cromwell::build::run_centaur \
     -e relative_output_paths_colliding \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
-    -e drs_usa_jdr \
-    -e drs_usa_jdr_preresolve
 
 cromwell::build::generate_code_coverage

From f03adf0aad87af7499516b688464a9fae12ce28f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 31 May 2023 16:10:06 -0400
Subject: [PATCH 179/326] [WX-1136] Docker Build Test (#7151)

---
 .github/workflows/chart_update_on_merge.yml |  1 +
 .github/workflows/docker_build_test.yml     | 37 +++++++++++++++++++++
 2 files changed, 38 insertions(+)
 create mode 100644 .github/workflows/docker_build_test.yml

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index 0eb8facd927..107e9d5de4a 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -49,6 +49,7 @@ jobs:
         username: dsdejenkins
         password: ${{ secrets.DSDEJENKINS_PASSWORD }}
     # Build & push `cromwell`, `womtool`, `cromiam`, and `cromwell-drs-localizer`
+    # This step is validated in the GHA 'docker_build_test.yml' without the accompanying docker push
     - name: Build Cromwell Docker
       run: |
         set -e
diff --git a/.github/workflows/docker_build_test.yml b/.github/workflows/docker_build_test.yml
new file mode 100644
index 00000000000..01c2ea502c9
--- /dev/null
+++ b/.github/workflows/docker_build_test.yml
@@ -0,0 +1,37 @@
+name: 'Docker Build Test'
+
+# This test verifies that we can successfully build the same docker images that we release.
+# Includes `cromwell`, `womtool`, `cromiam`, and `cromwell-drs-localizer`
+# See chart_update_on_merge.yml for the actual release workflow.
+
+run-name: ${{ github.actor }} Docker Build Test
+
+on:
+  workflow_dispatch:
+  push:
+  merge_group:
+
+permissions:
+  contents: read
+
+jobs:
+  sbt-build:
+    name: sbt docker build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone Cromwell
+        uses: actions/checkout@v2
+        with:
+          repository: broadinstitute/cromwell
+          token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+          path: cromwell
+      - uses: olafurpg/setup-scala@v10
+        with:
+          java-version: adopt@1.11
+      # The following invocation should be as similar as possible to the one in chart_update_on_merge.yml
+      # To state the obvious: This test should not publish anything. It should simply verify that the build completes.
+      - name: Build Cromwell Docker
+        run: |
+          set -e
+          cd cromwell
+          sbt -Dproject.isSnapshot=false -Dproject.isRelease=false docker

From bbf45bf8c7eb5acdb9b110880a73dd2d3e7dbd5a Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 1 Jun 2023 09:40:54 -0400
Subject: [PATCH 180/326] [WX-1136] Self Hosted (#7152)

---
 .github/workflows/docker_build_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker_build_test.yml b/.github/workflows/docker_build_test.yml
index 01c2ea502c9..15517cce919 100644
--- a/.github/workflows/docker_build_test.yml
+++ b/.github/workflows/docker_build_test.yml
@@ -17,7 +17,7 @@ permissions:
 jobs:
   sbt-build:
     name: sbt docker build
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     steps:
       - name: Clone Cromwell
         uses: actions/checkout@v2

From 012d16b55c92b580b3d18d891940c00d279b5762 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 5 Jun 2023 20:24:39 -0400
Subject: [PATCH 181/326] WX-1145 Fix minor regression introduced in WDL 1.1
 foundation (#7153)

---
 .../languages/util/LanguageFactoryUtil.scala  |  2 +-
 .../languages/util/LooksParseableSpec.scala   | 81 +++++++++++++++++++
 2 files changed, 82 insertions(+), 1 deletion(-)
 create mode 100644 languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/LooksParseableSpec.scala

diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala
index 83183d6cd26..da0860c3a86 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala
@@ -94,7 +94,7 @@ object LanguageFactoryUtil {
     }
 
     val firstCodeLine = fileWithoutInitialWhitespace.headOption.map(_.dropWhile(_.isWhitespace))
-    firstCodeLine.exists { line => startsWithOptions.contains(line) }
+    firstCodeLine.exists { line => startsWithOptions.contains(line.trim) }
   }
 
   def chooseFactory(workflowSource: WorkflowSource, wsfc: WorkflowSourceFilesCollection): ErrorOr[LanguageFactory] = {
diff --git a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/LooksParseableSpec.scala b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/LooksParseableSpec.scala
new file mode 100644
index 00000000000..a6bee26ac19
--- /dev/null
+++ b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/LooksParseableSpec.scala
@@ -0,0 +1,81 @@
+package cromwell.languages.util
+
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+class LooksParseableSpec extends AnyFlatSpec with Matchers {
+  behavior of "simpleLooksParseable"
+
+  it should "work with `version 1.0` followed by whitespace" in {
+
+    val source =
+      """
+        |version 1.0              
+        |# Programmer warning: make sure your editor does not trim the whitespace in the line above.
+        |""".stripMargin
+
+    LanguageFactoryUtil.simpleLooksParseable(List("version 1.0"), List("#"))(source) shouldBe true
+  }
+
+  it should "work with `version 1.0` preceded by whitespace" in {
+
+    val source =
+      """
+        |              version 1.0
+        |# Programmer warning: make sure your editor does not trim the whitespace in the line above.
+        |""".stripMargin
+
+    LanguageFactoryUtil.simpleLooksParseable(List("version 1.0"), List("#"))(source) shouldBe true
+  }
+
+  it should "work with `version 1.0` surrounded by whitespace" in {
+
+    val source =
+      """
+        |              version 1.0              
+        |# Programmer warning: make sure your editor does not trim the whitespace in the line above.
+        |""".stripMargin
+
+    LanguageFactoryUtil.simpleLooksParseable(List("version 1.0"), List("#"))(source) shouldBe true
+  }
+
+  it should "work with `version 1.0` surrounded by whitespace on all sides" in {
+
+    val source =
+      """
+        |              
+        |              version 1.0              
+        |              
+        |# Programmer warning: make sure your editor does not trim the whitespace in the line above.
+        |""".stripMargin
+
+    LanguageFactoryUtil.simpleLooksParseable(List("version 1.0"), List("#"))(source) shouldBe true
+  }
+
+  // This test technically contradicts the spec [0] but there is better hope of receiving a useful
+  // error if we try & fail to parse as 1.0, than if we fall back to the server default, `draft-2`
+  // > From draft-3 forward, the first line of all WDL files must be a version statement
+  // [0] https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#versioning
+  it should "work with `version 1.0` surrounded by comments" in {
+
+    val source =
+      """
+        |# My WDL does a cool thing
+        |version 1.0
+        |# Here we go...
+        |""".stripMargin
+
+    LanguageFactoryUtil.simpleLooksParseable(List("version 1.0"), List("#"))(source) shouldBe true
+  }
+
+  it should "reject Chris's idea of a version declaration" in {
+
+    val source =
+      """
+        |# Thank goodness this WDL is not version 1.1!
+        |""".stripMargin
+
+    LanguageFactoryUtil.simpleLooksParseable(List("version 1.0"), List("#"))(source) shouldBe false
+  }
+
+}

From 89718976b5a7b9bdd2f5cb63a1d0ef70517accf0 Mon Sep 17 00:00:00 2001
From: Tristan Garwood <tristan.garwood@gmail.com>
Date: Tue, 6 Jun 2023 15:10:22 -0400
Subject: [PATCH 182/326] ID-377 Setup pact for consumer contract testing.
 Retry (#7147)

Co-authored-by: Tom Wiseman <twiseman@broadinstitute.org>
Co-authored-by: Ivan <ichang@broadinstitute.org>
---
 .github/workflows/consumer_contract_tests.yml | 143 ++++++++++++
 build.sbt                                     |   6 +
 pact4s/README.md                              |  51 +++++
 .../cromwell/consumer/DrsHubClient.scala      |  93 ++++++++
 .../workbench/cromwell/consumer/Helper.scala  | 207 ++++++++++++++++++
 pact4s/src/test/resources/logback.xml         |  14 ++
 .../BlobFileSystemContractSpec.scala          |   2 +-
 .../cromwell/consumer/DrsHubClientSpec.scala  | 170 ++++++++++++++
 project/Dependencies.scala                    |  29 ++-
 project/Settings.scala                        |  15 ++
 project/build.properties                      |   2 +-
 11 files changed, 724 insertions(+), 8 deletions(-)
 create mode 100644 .github/workflows/consumer_contract_tests.yml
 create mode 100644 pact4s/README.md
 create mode 100644 pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
 create mode 100644 pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
 create mode 100644 pact4s/src/test/resources/logback.xml
 rename {filesystems/blob/src/test/scala/cromwell/filesystems/blob => pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer}/BlobFileSystemContractSpec.scala (97%)
 create mode 100644 pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala

diff --git a/.github/workflows/consumer_contract_tests.yml b/.github/workflows/consumer_contract_tests.yml
new file mode 100644
index 00000000000..0970e45e863
--- /dev/null
+++ b/.github/workflows/consumer_contract_tests.yml
@@ -0,0 +1,143 @@
+name: Consumer contract tests
+# The purpose of this workflow is to run a suite of Cromwell contract tests against mock service provider(s) using Pact framework.
+#
+# More details about Contract Testing can be found in our handbook
+#
+# https://broadworkbench.atlassian.net/wiki/spaces/IRT/pages/2660368406/Getting+Started+with+Pact+Contract+Testing
+#
+# This workflow involves Cromwell as a consumer, and ANY provider (e.g. Sam) Cromwell consumes.
+# Each party owns a set of tests (aka contract tests).
+#
+#   Consumer contract tests (aka consumer tests) runs on a mock provider service and does not require a real provider service.
+#   Provider contract tests (aka provider verification tests) runs independently of any consumer.
+#
+# Specifically:
+#   Cromwell runs consumer tests against mock service. Upon success, publish consumer pacts to
+#   Pact Broker https://pact-broker.dsp-eng-tools.broadinstitute.org/.
+#
+#   Pact Broker is the source of truth to forge contractual obligations between consumer and provider.
+#
+#   This workflow meets the criteria of Pact Broker *Platinum* as described in https://docs.pact.io/pact_nirvana/step_6.
+#   The can-i-deploy job has been added to this workflow to support *Platinum* and gate the code for promotion to default branch.
+#
+#   This is how it works.
+#
+#     Consumer makes a change that results in a new pact published to Pact Broker.
+#     Pact Broker notifies provider(s) of the changed pact and trigger corresponding verification workflows.
+#     Provider downloads relevant versions of consumer pacts from Pact Broker and kicks off verification tests against the consumer pacts.
+#     Provider updates Pact Broker with verification status.
+#     Consumer kicks off can-i-deploy on process to determine if changes can be promoted and used for deployment.
+#
+# NOTE: The publish-contracts workflow will use the latest commit of the branch that triggers this workflow to publish the unique consumer contract version to Pact Broker.
+
+on:
+  pull_request:
+    paths-ignore:
+      - 'README.md'
+  push:
+    paths-ignore:
+      - 'README.md'
+  merge_group:
+    branches:
+      - develop
+
+jobs:
+  init-github-context:
+    runs-on: ubuntu-latest
+    outputs:
+      repo-branch: ${{ steps.extract-branch.outputs.repo-branch }}
+      repo-version: ${{ steps.extract-branch.outputs.repo-version }}
+      fork: ${{ steps.extract-branch.outputs.fork }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Extract branch
+        id: extract-branch
+        run: |
+          GITHUB_EVENT_NAME=${{ github.event_name }}
+          if [[ "$GITHUB_EVENT_NAME" == "push" ]]; then
+            GITHUB_REF=${{ github.ref }}
+            GITHUB_SHA=${{ github.sha }}
+          elif [[ "$GITHUB_EVENT_NAME" == "pull_request" ]]; then
+            GITHUB_REF=refs/heads/${{ github.head_ref }}
+            GITHUB_SHA=${{ github.event.pull_request.head.sha }}
+          elif [[ "$GITHUB_EVENT_NAME" == "merge_group" ]]; then
+            GITHUB_REF=refs/heads/${{ github.head_ref }}
+          else
+            echo "Failed to extract branch information"
+            exit 1
+          fi
+          echo "CURRENT_BRANCH=${GITHUB_REF/refs\/heads\//""}" >> $GITHUB_ENV
+          echo "CURRENT_SHA=$GITHUB_SHA" >> $GITHUB_ENV
+          
+          echo "repo-branch=${GITHUB_REF/refs\/heads\//""}" >> $GITHUB_OUTPUT
+          echo "repo-version=${GITHUB_SHA}" >> $GITHUB_OUTPUT
+          echo "fork=${FORK}" >> $GITHUB_OUTPUT
+
+      - name: Is PR triggered by forked repo?
+        if: ${{ steps.extract-branch.outputs.fork == 'true' }}
+        run: |
+          echo "PR was triggered by forked repo"
+
+      - name: Echo repo and branch information
+        run: |
+          echo "repo-owner=${{ github.repository_owner }}"
+          echo "repo-name=${{ github.event.repository.name }}"
+          echo "repo-branch=${{ steps.extract-branch.outputs.repo-branch }}"
+          echo "repo-version=${{ steps.extract-branch.outputs.repo-version }}"
+          echo "fork=${{ steps.extract-branch.outputs.fork }}"
+
+  cromwell-consumer-contract-tests:
+    runs-on: ubuntu-latest
+    needs: [init-github-context]
+    outputs:
+      pact-b64: ${{ steps.encode-pact.outputs.pact-b64 }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Run consumer tests
+        run: |
+          docker run --rm -v $PWD:/working \
+                          -v jar-cache:/root/.ivy \
+                          -v jar-cache:/root/.ivy2 \
+                          -w /working \
+                          sbtscala/scala-sbt:openjdk-17.0.2_1.7.2_2.13.10 \
+                          sbt "project pact4s" clean test
+
+      - name: Output consumer contract as non-breaking base64 string
+        id: encode-pact
+        run: |
+          cd pact4s
+          NON_BREAKING_B64=$(cat target/pacts/cromwell-consumer-drshub-provider.json | base64 -w 0)
+          echo "pact-b64=${NON_BREAKING_B64}" >> $GITHUB_OUTPUT
+
+  # Prevent untrusted sources from using PRs to publish contracts
+  # since access to secrets is not allowed.
+  publish-contracts:
+    runs-on: ubuntu-latest
+    if: ${{ needs.init-github-context.outputs.fork == 'false' ||  needs.init-github-context.outputs.fork == ''}}
+    needs: [init-github-context, cromwell-consumer-contract-tests]
+    steps:
+      - name: Dispatch to terra-github-workflows
+        uses: broadinstitute/workflow-dispatch@v3
+        with:
+          workflow: .github/workflows/publish-contracts.yaml
+          repo: broadinstitute/terra-github-workflows
+          ref: refs/heads/main
+          token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # github token for access to kick off a job in the private repo
+          inputs: '{ "pact-b64": "${{ needs.cromwell-consumer-contract-tests.outputs.pact-b64 }}", "repo-owner": "${{ github.repository_owner }}", "repo-name": "${{ github.event.repository.name }}", "repo-branch": "${{ needs.init-github-context.outputs.repo-branch }}" }'
+
+  can-i-deploy:
+    runs-on: ubuntu-latest
+    if: ${{ needs.init-github-context.outputs.fork == 'false' ||  needs.init-github-context.outputs.fork == ''}}
+    needs: [ init-github-context, publish-contracts ]
+    steps:
+      - name: Dispatch to terra-github-workflows
+        uses: broadinstitute/workflow-dispatch@v3
+        with:
+          workflow: .github/workflows/can-i-deploy.yaml
+          repo: broadinstitute/terra-github-workflows
+          ref: refs/heads/main
+          token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # github token for access to kick off a job in the private repo
+          inputs: '{ "pacticipant": "cromwell-consumer", "version": "${{ needs.init-github-context.outputs.repo-version }}" }'
diff --git a/build.sbt b/build.sbt
index 90e092d802d..f8d32f2f5a7 100644
--- a/build.sbt
+++ b/build.sbt
@@ -377,6 +377,11 @@ lazy val `cromwell-drs-localizer` = project
   .dependsOn(common)
   .dependsOn(`cloud-nio-impl-drs` % "test->test")
 
+lazy val pact4s = project.in(file("pact4s"))
+  .settings(pact4sSettings)
+  .dependsOn(services)
+  .disablePlugins(sbtassembly.AssemblyPlugin)
+
 lazy val server = project
   .withExecutableSettings("cromwell", serverDependencies)
   .dependsOn(engine)
@@ -446,4 +451,5 @@ lazy val root = (project in file("."))
   .aggregate(wes2cromwell)
   .aggregate(wom)
   .aggregate(womtool)
+  .aggregate(pact4s)
   .withAggregateSettings()
diff --git a/pact4s/README.md b/pact4s/README.md
new file mode 100644
index 00000000000..d33447f7356
--- /dev/null
+++ b/pact4s/README.md
@@ -0,0 +1,51 @@
+c# pact4s [Under construction]
+
+pact4s is used for contract testing.
+
+# Dependencies
+
+```scala
+  val pact4sDependencies = Seq(
+    pact4sScalaTest,
+    pact4sCirce,
+    http4sEmberClient,
+    http4sDsl,
+    http4sEmberServer,
+    http4sCirce,
+    circeCore,
+    typelevelCat,
+    scalaTest
+  )
+
+lazy val pact4s = project.in(file("pact4s"))
+  .settings(pact4sSettings)
+  .dependsOn(http % "test->test;compile->compile")
+```
+
+## Building and running contract tests
+Clone the repo.
+```
+$ git clone https://github.com/broadinstitute/cromwell.git 
+$ cd cromwell
+```
+
+If you are already using OpenJDK 11, run the following command. 
+```
+$ sbt "project pact4s" clean test  
+```
+
+Otherwise, you can run the command inside a docker container with OpenJDK 11 installed. 
+This is especially useful when automating contract tests in a GitHub Action runner which does not guarantee the correct OpenJDK version.
+```
+docker run --rm -v $PWD:/working \
+                -v jar-cache:/root/.ivy \
+                -v jar-cache:/root/.ivy2 \
+                -w /working \
+                sbtscala/scala-sbt:openjdk-11.0.16_1.8.1_2.13.10 \
+                sbt "project pact4s" clean test
+```
+
+The generated contracts can be found in the `./target/pacts` folder
+- `cromwell-consumer-drshub-provider.json`
+- `cromwell-consumer-fake-provider.json`
+
diff --git a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
new file mode 100644
index 00000000000..3fa11515118
--- /dev/null
+++ b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
@@ -0,0 +1,93 @@
+package org.broadinstitute.dsde.workbench.cromwell.consumer
+
+import cats.effect.Concurrent
+import cats.syntax.all._
+import com.typesafe.scalalogging.LazyLogging
+import io.circe.{Decoder, Encoder}
+import org.http4s._
+import org.http4s.circe.CirceEntityCodec.{circeEntityDecoder, circeEntityEncoder}
+import org.http4s.client.Client
+
+case class AccessUrl(url: String, headers: List[String])
+
+case class ResourceMetadataRequest(url: String, fields: List[String])
+
+case class ResourceMetadata(contentType: String,
+                            size: Long,
+                            timeCreated: String,
+                            timeUpdated: String,
+                            bucket: Option[String],
+                            name: Option[String],
+                            gsUri: Option[String],
+                            googleServiceAccount: Option[Map[String, Map[String, String]]],
+                            fileName: Option[String],
+                            accessUrl: Option[AccessUrl],
+                            hashes: Map[String, String],
+                            localizationPath: Option[String],
+                            bondProvider: Option[String]
+)
+trait DrsHubClient[F[_]] extends LazyLogging {
+  def fetchSystemStatus(): F[Boolean]
+
+  def resolveDrsObject(drsPath: String, fields: List[String]): F[ResourceMetadata]
+
+}
+
+/*
+ This class represents the consumer (Cromwell) view of the DrsHub provider that implements the following endpoints:
+  - GET /status
+  - GET /api/v4/drs/resolve
+ */
+class DrsHubClientImpl[F[_]: Concurrent](client: Client[F], baseUrl: Uri) extends DrsHubClient[F] {
+  val apiVersion = "v4"
+
+  implicit val accessUrlDecoder: Decoder[AccessUrl] = Decoder.forProduct2("url", "headers")(AccessUrl.apply)
+  implicit val resourceMetadataDecoder: Decoder[ResourceMetadata] = Decoder.forProduct13(
+    "contentType",
+    "size",
+    "timeCreated",
+    "timeUpdated",
+    "bucket",
+    "name",
+    "gsUri",
+    "googleServiceAccount",
+    "fileName",
+    "accessUrl",
+    "hashes",
+    "localizationPath",
+    "bondProvider"
+  )(ResourceMetadata.apply)
+  implicit val resourceMetadataRequestEncoder: Encoder[ResourceMetadataRequest] = Encoder.forProduct2("url", "fields")(x =>
+    (x.url, x.fields)
+  )
+  implicit val resourceMetadataRequestEntityEncoder: EntityEncoder[F, ResourceMetadataRequest] = circeEntityEncoder[F, ResourceMetadataRequest]
+  override def fetchSystemStatus(): F[Boolean] = {
+    val request = Request[F](uri = baseUrl / "status").withHeaders(
+      org.http4s.headers.Accept(MediaType.application.json)
+    )
+    client.run(request).use { resp =>
+      resp.status match {
+        case Status.Ok                  => true.pure[F]
+        case Status.InternalServerError => false.pure[F]
+        case _                          => UnknownError.raiseError
+      }
+    }
+  }
+
+  override def resolveDrsObject(drsPath: String, fields: List[String]): F[ResourceMetadata] = {
+    val body = ResourceMetadataRequest(url = drsPath, fields = fields)
+    val entityBody: EntityBody[F] = EntityEncoder[F, ResourceMetadataRequest].toEntity(body).body
+    val request = Request[F](uri = baseUrl / "api" / apiVersion / "drs" / "resolve", method=Method.POST, body=entityBody).withHeaders(
+      org.http4s.headers.`Content-Type`(MediaType.application.json)
+    )
+    client.run(request).use { resp =>
+      resp.status match {
+        case Status.Ok                  => resp.as[ResourceMetadata]
+        case _                          => UnknownError.raiseError
+      }
+    }
+  }
+
+}
+
+
diff --git a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
new file mode 100644
index 00000000000..ceeefc7479f
--- /dev/null
+++ b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
@@ -0,0 +1,207 @@
+package org.broadinstitute.dsde.workbench.cromwell.consumer
+
+import au.com.dius.pact.consumer.dsl.{DslPart, PactDslResponse, PactDslWithProvider}
+import pact4s.algebras.PactBodyJsonEncoder
+case object UnknownError extends Exception
+
+object PactHelper {
+  def buildInteraction(builder: PactDslResponse,
+                       state: String,
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int,
+                       responseHeaders: Seq[(String, String)],
+                       body: DslPart
+                      ): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+      .body(body)
+
+  def buildInteraction(builder: PactDslResponse,
+                       state: String,
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int,
+                       responseHeaders: Seq[(String, String)],
+                      ): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+
+  def buildInteraction(builder: PactDslResponse,
+                       state: String,
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int
+                      ): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+
+  def buildInteraction(builder: PactDslResponse,
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int
+                      ): PactDslResponse =
+    builder
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+
+  def buildInteraction(builder: PactDslWithProvider,
+                       state: String,
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int,
+                       responseHeaders: Seq[(String, String)],
+                       body: DslPart
+                      ): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+      .body(body)
+
+  def buildInteraction(builder: PactDslWithProvider,
+                       state: String,
+                       stateParams: Map[String, Any],
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       requestBody: DslPart,
+                       status: Int,
+                       responseHeaders: Seq[(String, String)],
+                       responsBody: DslPart
+                      ): PactDslResponse =
+    builder
+      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .body(requestBody)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+      .body(responsBody)
+
+  def buildInteraction(builder: PactDslResponse,
+                       state: String,
+                       stateParams: Map[String, Any],
+                       uponReceiving: String,
+                       method: String,
+                       path: String,
+                       requestHeaders: Seq[(String, String)],
+                       status: Int,
+                       responseHeaders: Seq[(String, String)],
+                       body: DslPart
+                      ): PactDslResponse =
+    builder
+      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+      .body(body)
+
+  def buildInteraction[A](builder: PactDslWithProvider,
+                          state: String,
+                          stateParams: Map[String, Any],
+                          uponReceiving: String,
+                          method: String,
+                          path: String,
+                          requestHeaders: Seq[(String, String)],
+                          status: Int,
+                          responseHeaders: Seq[(String, String)],
+                          body: A
+                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
+    builder
+      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .willRespondWith()
+      .status(status)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
+      .body(ev.toJsonString(body))
+
+  def buildInteraction[A](builder: PactDslResponse,
+                          state: String,
+                          uponReceiving: String,
+                          method: String,
+                          path: String,
+                          requestHeaders: Seq[(String, String)],
+                          requestBody: A,
+                          status: Int
+                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .body(ev.toJsonString(requestBody))
+      .willRespondWith()
+      .status(status)
+
+  def buildInteraction[A](builder: PactDslResponse,
+                          state: String,
+                          stateParams: Map[String, Any],
+                          uponReceiving: String,
+                          method: String,
+                          path: String,
+                          requestHeaders: Seq[(String, String)],
+                          requestBody: A,
+                          status: Int
+                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
+    builder
+      .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .body(ev.toJsonString(requestBody))
+      .willRespondWith()
+      .status(status)
+}
diff --git a/pact4s/src/test/resources/logback.xml b/pact4s/src/test/resources/logback.xml
new file mode 100644
index 00000000000..24316805e7e
--- /dev/null
+++ b/pact4s/src/test/resources/logback.xml
@@ -0,0 +1,14 @@
+<configuration>
+    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+        <encoder>
+            <pattern>%d [%thread] %-5level  %logger{35} - %msg%n</pattern>
+        </encoder>
+    </appender>
+    <logger name="io.github.jbwheatley.pact4s.Pact4sLogger" level="INFO" />
+    <logger name="au.com.dius.pact.consumer" level="DEBUG"/>
+    <logger name="au.com.dius.pact.provider" level="DEBUG"/>
+
+    <root level="INFO">
+        <appender-ref ref="STDOUT" />
+    </root>
+</configuration>
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
similarity index 97%
rename from filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
rename to pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
index 611a50f5603..f023257fef9 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemContractSpec.scala
+++ b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
@@ -1,4 +1,4 @@
-package cromwell.filesystems.blob
+package org.broadinstitute.dsde.workbench.cromwell.consumer
 
 import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
 import au.com.dius.pact.core.model.RequestResponsePact
diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
new file mode 100644
index 00000000000..a4ebe56d76a
--- /dev/null
+++ b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
@@ -0,0 +1,170 @@
+package org.broadinstitute.dsde.workbench.cromwell.consumer
+
+import au.com.dius.pact.consumer.dsl.LambdaDsl.newJsonBody
+import au.com.dius.pact.consumer.dsl._
+import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
+import au.com.dius.pact.core.model.RequestResponsePact
+import cats.effect.IO
+import org.broadinstitute.dsde.workbench.cromwell.consumer.PactHelper._
+import org.http4s.Uri
+import org.http4s.blaze.client.BlazeClientBuilder
+import org.http4s.client.Client
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import pact4s.scalatest.RequestResponsePactForger
+
+import java.util.concurrent.Executors
+import scala.concurrent.ExecutionContext
+
+class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePactForger {
+  val ec = ExecutionContext.fromExecutorService(Executors.newCachedThreadPool())
+  implicit val cs = IO.contextShift(ec)
+  /*
+    Define the folder that the pact contracts get written to upon completion of this test suite.
+   */
+  override val pactTestExecutionContext: PactTestExecutionContext =
+    new PactTestExecutionContext(
+      "./target/pacts"
+    )
+
+  private val requestFields = List(
+      "bucket",
+      "accessUrl",
+      "googleServiceAccount",
+      "fileName",
+      "hashes",
+      "localizationPath",
+      "bondProvider",
+      "name",
+      "size",
+      "timeCreated",
+      "timeUpdated",
+      "gsUri",
+      "contentType",
+  )
+
+  val filesize = 123L
+  val timeCreated = "2021-03-04T20:00:00.000Z"
+  val bucket = "fc-secure-1234567890"
+  val filename = "my-file.bam"
+  val bondProvider = "anvil"
+  val fileHash = "a2317edbd2eb6cf6b0ee49cb81e3a556"
+  val accessUrl = f"gs://${bucket}/${filename}"
+
+
+  val drsResourceResponsePlaceholder: ResourceMetadata = ResourceMetadata(
+    "application/octet-stream",
+    filesize,
+    timeCreated,
+    timeCreated,
+    None,
+    None,
+    None,
+    None,
+    None,
+    Option(AccessUrl(accessUrl, List("Header", "Example"))),
+    Map("md5" -> fileHash),
+    None,
+    Option(bondProvider)
+  )
+
+  val resourceMetadataResponseDsl: DslPart = newJsonBody { o =>
+    o.stringType("contentType", "application/octet-stream")
+      o.numberType("size", filesize)
+      o.stringType("timeCreated", timeCreated)
+      o.stringType("timeUpdated", timeCreated)
+      o.nullValue("gsUri")
+      o.nullValue("googleServiceAccount")
+      o.nullValue("fileName")
+      o.`object`("accessUrl" , { a =>
+        a.stringType("url", accessUrl)
+          a.`array`("headers", { h =>
+            h.stringType("Header")
+            h.stringType("Example")
+            ()
+          })
+        ()
+      })
+      o.`object`("hashes", { o =>
+        o.stringType("md5", fileHash)
+        ()
+      })
+      o.nullValue("localizationPath")
+      o.stringType("bondProvider", bondProvider)
+    ()
+  }.build
+
+  val fileId = "1234567890"
+
+  val resourceRequestDsl = newJsonBody { o =>
+    o.stringType("url", f"drs://test.theanvil.io/${fileId}")
+    o.array("fields", { a =>
+      requestFields.map(a.stringType)
+      ()
+    })
+    ()
+  }.build
+
+  val consumerPactBuilder: ConsumerPactBuilder = ConsumerPactBuilder
+    .consumer("cromwell-consumer")
+
+  val pactProvider: PactDslWithProvider = consumerPactBuilder
+    .hasPactWith("drshub-provider")
+
+  var pactDslResponse: PactDslResponse = buildInteraction(
+    pactProvider,
+    state = "resolve Drs url",
+    stateParams = Map[String, String](
+      "fileId" -> fileId,
+      "bucket" -> bucket,
+      "filename" -> filename,
+      "bondProvider" -> bondProvider,
+      "fileHash" -> fileHash,
+      "accessUrl" -> accessUrl,
+      "fileSize" -> filesize.toString,
+      "timeCreated" -> timeCreated
+    ),
+    uponReceiving = "Request to resolve drs url",
+    method = "POST",
+    path = "/api/v4/drs/resolve",
+    requestHeaders = Seq("Content-type" -> "application/json"),
+    requestBody = resourceRequestDsl,
+    status = 200,
+    responseHeaders = Seq(),
+    responsBody = resourceMetadataResponseDsl
+  )
+
+  pactDslResponse = buildInteraction(
+    pactDslResponse,
+    state = "Drshub is ok",
+    uponReceiving = "Request for drshub api status",
+    method = "GET",
+    path = "/status",
+    requestHeaders = Seq(),
+    status = 200,
+    responseHeaders = Seq()
+  )
+
+  override val pact: RequestResponsePact = pactDslResponse.toPact
+
+  val client: Client[IO] = {
+    BlazeClientBuilder[IO](ExecutionContext.global).resource.allocated.unsafeRunSync()._1
+  }
+
+  /*
+  we should use these tests to ensure that our client class correctly handles responses from the provider - i.e. decoding, error mapping, validation
+   */
+  it should "get DrsHub ok status" in {
+    new DrsHubClientImpl[IO](client, Uri.unsafeFromString(mockServer.getUrl))
+      .fetchSystemStatus()
+      .attempt
+      .unsafeRunSync() shouldBe Right(true)
+  }
+
+  it should "resolve drs object" in {
+    new DrsHubClientImpl[IO](client, Uri.unsafeFromString(mockServer.getUrl))
+      .resolveDrsObject("drs://drs.example.com/1234567890", requestFields)
+      .attempt
+      .unsafeRunSync() shouldBe Right(drsResourceResponsePlaceholder)
+  }
+}
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 110faf925e4..b5fad373834 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -92,6 +92,7 @@ object Dependencies {
   private val mysqlV = "8.0.28"
   private val nettyV = "4.1.72.Final"
   private val owlApiV = "5.1.19"
+  private val pact4sV = "0.9.0"
   private val postgresV = "42.4.1"
   private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
@@ -104,7 +105,7 @@ object Dependencies {
   private val scalaPoolV = "0.4.3"
   private val scalacticV = "3.2.13"
   private val scalameterV = "0.21"
-  private val scalatestV = "3.2.10"
+  private val scalatestV = "3.2.15"
   private val scalatestScalacheckV = scalatestV + ".0"
   private val scoptV = "4.1.0"
   private val sentryLogbackV = "5.7.4"
@@ -444,7 +445,7 @@ object Dependencies {
     - https://www.scalatest.org/user_guide/generator_driven_property_checks
     - https://www.scalatest.org/user_guide/writing_scalacheck_style_properties
    */
-  private val scalacheckBaseV = "1.15"
+  private val scalacheckBaseV = "1.17"
   private val scalacheckDependencies = List(
     "org.scalatestplus" %% s"scalacheck-${scalacheckBaseV.replace(".", "-")}" % scalatestScalacheckV % Test,
   )
@@ -596,14 +597,12 @@ object Dependencies {
   val sfsBackendDependencies = List (
     "org.lz4" % "lz4-java" % lz4JavaV
   )
-
+  val scalaTest = "org.scalatest" %% "scalatest" % scalatestV
   val testDependencies: List[ModuleID] = List(
-    "org.scalatest" %% "scalatest" % scalatestV,
+    scalaTest,
     // Use mockito Java DSL directly instead of the numerous and often hard to keep updated Scala DSLs.
     // See also scaladoc in common.mock.MockSugar and that trait's various usages.
     "org.mockito" % "mockito-core" % mockitoV,
-    "io.github.jbwheatley" %% "pact4s-scalatest"  % "0.7.0",
-    "io.github.jbwheatley" %% "pact4s-circe" %  "0.7.0"
   ) ++ slf4jBindingDependencies // During testing, add an slf4j binding for _all_ libraries.
 
   val kindProjectorPlugin = "org.typelevel" % "kind-projector" % kindProjectorV cross CrossVersion.full
@@ -799,5 +798,23 @@ object Dependencies {
      The jakarta.annotation inclusion is above in googleApiClientDependencies.
      */
     ExclusionRule("javax.annotation", "javax.annotation-api"),
+    ExclusionRule("javax.activation"),
+  )
+
+  val http4sDsl = "org.http4s" %% "http4s-dsl" % http4sV
+  val http4sEmberClient = "org.http4s" %% "http4s-ember-client" % http4sV
+  val http4sEmberServer = "org.http4s" %% "http4s-ember-server" % http4sV
+  val http4sCirce = "org.http4s" %% "http4s-circe" % http4sV
+  val pact4sScalaTest = "io.github.jbwheatley" %% "pact4s-scalatest" % pact4sV % Test
+  val pact4sCirce = "io.github.jbwheatley" %% "pact4s-circe" % pact4sV
+
+  val pact4sDependencies = Seq(
+    pact4sScalaTest,
+    pact4sCirce,
+    http4sEmberClient,
+    http4sDsl,
+    http4sEmberServer,
+    http4sCirce,
+    scalaTest,
   )
 }
diff --git a/project/Settings.scala b/project/Settings.scala
index 11867e74017..fd07a4c6bcc 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -98,6 +98,21 @@ object Settings {
     )
   )
 
+  val pact4sSettings = sharedSettings ++ List(
+    libraryDependencies ++= pact4sDependencies,
+
+    /**
+      * Invoking pact tests from root project (sbt "project pact" test)
+      * will launch tests in a separate JVM context that ensures contracts
+      * are written to the pact/target/pacts folder. Otherwise, contracts
+      * will be written to the root folder.
+      */
+    Test / fork := true
+  ) ++ assemblySettings
+
+  lazy val pact4s = project.in(file("pact4s"))
+    .settings(pact4sSettings)
+
   /*
       Docker instructions to install Google Cloud SDK image in docker image. It also installs `crcmod` which
       is needed while downloading large files using `gsutil`.
diff --git a/project/build.properties b/project/build.properties
index 2b4cbe4d584..54f486b9dc3 100644
--- a/project/build.properties
+++ b/project/build.properties
@@ -1,2 +1,2 @@
 # scala-steward:off
-sbt.version=1.5.5
+sbt.version=1.8.1

From fe0da4b2d43ae77a42dadc7b2e1b6b8052d97dff Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Thu, 8 Jun 2023 09:16:17 -0400
Subject: [PATCH 183/326] WX-1133 Shorten TES localized blob paths (#7150)

---
 build.sbt                                     |  1 +
 .../filesystems/blob/BlobPathBuilder.scala    | 14 ++++
 .../blob/BlobPathBuilderSpec.scala            | 64 ++++++++++++-------
 .../TesAsyncBackendJobExecutionActor.scala    | 15 +++++
 4 files changed, 70 insertions(+), 24 deletions(-)

diff --git a/build.sbt b/build.sbt
index f8d32f2f5a7..48f986badd7 100644
--- a/build.sbt
+++ b/build.sbt
@@ -252,6 +252,7 @@ lazy val tesBackend = (project in backendRoot / "tes")
   .dependsOn(sfsBackend)
   .dependsOn(ftpFileSystem)
   .dependsOn(drsFileSystem)
+  .dependsOn(azureBlobFileSystem)
   // TES backend provides a compatibility layer to run WDLs with PAPI runtime attributes [WX-769]
   .dependsOn(googlePipelinesCommon)
   .dependsOn(backend % "test->test")
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index cc0e112806a..9e7b230286c 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -128,5 +128,19 @@ case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, con
     )
   }
 
+  /**
+    * Return the pathString of this BlobPath, with the given prefix removed if this path shares that
+    * prefix.
+    */
+  def pathStringWithoutPrefix(prefix: Path): String = {
+    if (this.startsWith(prefix)) {
+      prefix.relativize(this) match {
+        case b: BlobPath => b.pathString // path inside the blob container
+        case p: Path => p.pathAsString // full path
+      }
+    }
+    else pathString
+  }
+
   override def getSymlinkSafePath(options: LinkOption*): Path  = toAbsolutePath
 }
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index 11ffc11354e..4012e241eb3 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -90,30 +90,31 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   //// The below tests are IGNORED because they depend on Azure auth information being present in the environment ////
-  val subscriptionId = SubscriptionId(UUID.fromString("62b22893-6bc1-46d9-8a90-806bb3cce3c9"))
+  private val subscriptionId: SubscriptionId = SubscriptionId(UUID.fromString("62b22893-6bc1-46d9-8a90-806bb3cce3c9"))
+  private val endpoint: EndpointURL = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
+  private val store: BlobContainerName = BlobContainerName("inputs")
+
+  def makeBlobPathBuilder(blobEndpoint: EndpointURL, container: BlobContainerName): BlobPathBuilder = {
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(container, blobEndpoint, Some(subscriptionId))
+    val fsm = new BlobFileSystemManager(container, blobEndpoint, 10, blobTokenGenerator)
+    new BlobPathBuilder(store, endpoint)(fsm)
+  }
 
   ignore should "resolve an absolute path string correctly to a path" in {
-    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
-    val store = BlobContainerName("inputs")
-    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint, Some(subscriptionId))
-    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
-
+    val builder = makeBlobPathBuilder(endpoint, store)
     val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
-    val blobRoot: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build rootString getOrElse fail()
+    val blobRoot: BlobPath = builder build rootString getOrElse fail()
     blobRoot.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution")
     val otherFile = blobRoot.resolve("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
     otherFile.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
   }
 
   ignore should "build a blob path from a test string and read a file" in {
-    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
+    val builder = makeBlobPathBuilder(endpoint, store)
     val endpointHost = BlobPathBuilder.parseURI(endpoint.value).map(_.getHost).getOrElse(fail("Could not parse URI"))
-    val store = BlobContainerName("inputs")
     val evalPath = "/test/inputFile.txt"
-    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint, Some(subscriptionId))
-    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10L, blobTokenGenerator)
     val testString = endpoint.value + "/" + store + evalPath
-    val blobPath: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
+    val blobPath: BlobPath = builder build testString getOrElse fail()
 
     blobPath.container should equal(store)
     blobPath.endpoint should equal(endpoint)
@@ -125,15 +126,12 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   ignore should "build duplicate blob paths in the same filesystem" in {
-    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
-    val store = BlobContainerName("inputs")
+    val builder = makeBlobPathBuilder(endpoint, store)
     val evalPath = "/test/inputFile.txt"
-    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint, Some(subscriptionId))
-    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
     val testString = endpoint.value + "/" + store + evalPath
-    val blobPath1: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
+    val blobPath1: BlobPath = builder build testString getOrElse fail()
     blobPath1.nioPath.getFileSystem.close()
-    val blobPath2: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build testString getOrElse fail()
+    val blobPath2: BlobPath = builder build testString getOrElse fail()
     blobPath1 should equal(blobPath2)
     val is = blobPath1.newInputStream()
     val fileText = (is.readAllBytes.map(_.toChar)).mkString
@@ -141,15 +139,33 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   ignore should "resolve a path without duplicating container name" in {
-    val endpoint = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
-    val store = BlobContainerName("inputs")
-    val blobTokenGenerator = NativeBlobSasTokenGenerator(store, endpoint, Some(subscriptionId))
-    val fsm: BlobFileSystemManager = new BlobFileSystemManager(store, endpoint, 10, blobTokenGenerator)
-
+    val builder = makeBlobPathBuilder(endpoint, store)
     val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
-    val blobRoot: BlobPath = new BlobPathBuilder(store, endpoint)(fsm) build rootString getOrElse fail()
+    val blobRoot: BlobPath = builder build rootString getOrElse fail()
     blobRoot.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution")
     val otherFile = blobRoot.resolve("test/inputFile.txt")
     otherFile.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
   }
+
+  ignore should "correctly remove a prefix from the blob path" in {
+    val builder = makeBlobPathBuilder(endpoint, store)
+    val rootString = s"${endpoint.value}/${store.value}/cromwell-execution/"
+    val execDirString = s"${endpoint.value}/${store.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/"
+    val fileString = s"${endpoint.value}/${store.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
+    val blobRoot: BlobPath = builder build rootString getOrElse fail()
+    val execDir: BlobPath = builder build execDirString getOrElse fail()
+    val blobFile: BlobPath = builder build fileString getOrElse fail()
+    blobFile.pathStringWithoutPrefix(blobRoot) should equal ("abc123/myworkflow/task1/def4356/execution/stdout")
+    blobFile.pathStringWithoutPrefix(execDir) should equal ("stdout")
+    blobFile.pathStringWithoutPrefix(blobFile) should equal ("")
+  }
+
+  ignore should "not change a path if it doesn't start with a prefix" in {
+    val builder = makeBlobPathBuilder(endpoint, store)
+    val otherRootString = s"${endpoint.value}/${store.value}/foobar/"
+    val fileString = s"${endpoint.value}/${store.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
+    val otherBlobRoot: BlobPath = builder build otherRootString getOrElse fail()
+    val blobFile: BlobPath = builder build fileString getOrElse fail()
+    blobFile.pathStringWithoutPrefix(otherBlobRoot) should equal ("/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout")
+  }
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 0582997eef8..7ff507e63f2 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -22,6 +22,7 @@ import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardAsyncExec
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import cromwell.core.retry.SimpleExponentialBackoff
 import cromwell.core.retry.Retry._
+import cromwell.filesystems.blob.BlobPath
 import cromwell.filesystems.drs.{DrsPath, DrsResolver}
 import wom.values.WomFile
 import net.ceedubs.ficus.Ficus._
@@ -115,6 +116,20 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
           tesJobPaths.containerExec(commandDirectory, path.name)
         case Success(path: Path) if path.startsWith(tesJobPaths.callRoot) =>
           tesJobPaths.callDockerRoot.resolve(path.name).pathAsString
+        case Success(path: BlobPath) if path.startsWith(tesJobPaths.workflowPaths.workflowRoot) =>
+          // Blob paths can get really long, which causes problems for some tools. If this input file
+          // lives in the workflow execution directory, strip off that prefix from the path we're
+          // generating inside `inputs/` to keep the total path length under control.
+          // In Terra on Azure, this saves us 200+ characters.
+          tesJobPaths.callInputsDockerRoot.resolve(
+            path.pathStringWithoutPrefix(tesJobPaths.workflowPaths.workflowRoot)
+          ).pathAsString
+        case Success(path: BlobPath) if path.startsWith(tesJobPaths.workflowPaths.executionRoot) =>
+          // See comment above... if this file is in the execution root, strip that off.
+          // In Terra on Azure, this saves us 160+ characters.
+          tesJobPaths.callInputsDockerRoot.resolve(
+            path.pathStringWithoutPrefix(tesJobPaths.workflowPaths.executionRoot)
+          ).pathAsString
         case Success(path: Path) =>
           tesJobPaths.callInputsDockerRoot.resolve(path.pathWithoutScheme.stripPrefix("/")).pathAsString
         case _ =>

From adb8d2ad87cba307e5b1eccd1a3e21857cc9b81c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 13 Jun 2023 16:40:06 -0400
Subject: [PATCH 184/326] WX-1154 Fix Slack Messaging  (#7159)

---
 .github/workflows/integration_tests.yml       | 32 +++++--------------
 .../workflows/nightly_integration_tests.yml   | 23 -------------
 2 files changed, 8 insertions(+), 47 deletions(-)
 delete mode 100644 .github/workflows/nightly_integration_tests.yml

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 94d3a6611a3..f82a5020ef3 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -2,33 +2,15 @@ name: 'Integration Tests'
 
 #This github action runs all of Cromwell's integration tests.
 
-#This is what shows up in the github workflows page as the title.
-run-name: ${{ github.actor }} Integration Testing.
+# This is what shows up in the github workflows page as the title. Using github ternary syntax & format() function.
+run-name: ${{ github.event_name == 'schedule' && 'Nightly Integration Testing' || format('{0} Integration Testing', github.actor) }}
 
 #What will trigger the workflow to run.
 on:
-  workflow_call:
-    inputs:
-      target-branch:
-        description: 'The branch to run integration tests against'
-        required: false
-        type: string
-      slack-alert:
-        description: 'A flag to enable slack alerts. True if this should alert via slack'
-        required: true
-        default: false
-        type: boolean
-    secrets:
-      VAULT_ROLE_ID_CI:
-        required: true
-      VAULT_SECRET_ID_CI:
-        required: true
-      BROADBOT_GITHUB_TOKEN:
-        required: true
-      SLACK_WEBHOOK_URL:
-        required: false
   workflow_dispatch: #Manual trigger from GitHub UI
-  push: #git push
+  push:
+  schedule:
+    - cron: '0 0 * * 1-5'
   merge_group:
 
 permissions:
@@ -115,8 +97,10 @@ jobs:
         set -e
         echo Running test.sh
         ./src/ci/bin/test.sh
+    # always() is some github magic that forces the following step to run, even when the previous fails.
+    # Without it, the if statement won't be evaluated on a test failure.
     - uses: ravsamhq/notify-slack-action@v2
-      if: inputs.slack-alert
+      if: always() && github.ref == 'refs/heads/develop' #only report on failures against develop.
       with:
         status: ${{ job.status }}
         notify_when: "failure"
diff --git a/.github/workflows/nightly_integration_tests.yml b/.github/workflows/nightly_integration_tests.yml
deleted file mode 100644
index 024588b4ac5..00000000000
--- a/.github/workflows/nightly_integration_tests.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-#This github action runs all of Cromwell's integration tests nightly.
-name: 'Nightly Integration Tests'
-
-#This is what shows up in the github workflows page as the title.
-run-name: Nightly ${{ github.actor }} Integration Testing.
-
-#What will trigger the workflow to run.
-on:
-  workflow_dispatch:
-  schedule:
-    - cron: '0 0 * * 1-5'
-
-permissions:
-  contents: read
-
-# Use if as arg to only send slack notifications on nightly
-jobs:
-  integration-tests:
-    uses: broadinstitute/cromwell/.github/workflows/integration_tests.yml@develop
-    with:
-      target-branch: 'develop'
-      slack-alert: true
-    secrets: inherit

From 473321fc08cf784a3e9f2e4352f14036e714523b Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Thu, 15 Jun 2023 13:11:15 +0200
Subject: [PATCH 185/326] efs fixes : support paths with over 127 characters,
 fix delocalization of efs-based globs (#32)

---
 .../AwsBatchAsyncBackendJobExecutionActor.scala |  7 +++++--
 .../cromwell/backend/impl/aws/AwsBatchJob.scala | 17 +++++++++++------
 .../impl/aws/io/AwsBatchGlobFunctions.scala     |  6 ++++--
 3 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 87ef19e80cb..498bd2ec4fe 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -417,8 +417,10 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     val output = if (configuration.efsMntPoint.isDefined && 
                      configuration.efsMntPoint.getOrElse("").equals(disk.toString.split(" ")(1)) &&
                      ! runtimeAttributes.efsDelocalize) {
-            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), makeSafeAwsBatchReferenceName(womFile.value), relpath, disk)
+            // name: String, s3key: String, local: Path, mount: AwsBatchVolume
+            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), womFile.value, relpath, disk)
         } else {
+            // if efs is not enabled, OR efs delocalization IS enabled, keep the s3 path as destination.
             AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), destination, relpath, disk)
         }
     List(output)
@@ -448,7 +450,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
                      ! runtimeAttributes.efsDelocalize) {
                         (globDirectory, globListFile)
                      } else {
-                        (callRootPath.resolve(globDirectory).pathAsString, callRootPath.resolve(globListFile).pathAsString)
+                        // cannot resolve absolute paths : strip the leading '/'
+                        (callRootPath.resolve(globDirectory.toString.stripPrefix("/")).pathAsString, callRootPath.resolve(globListFile.toString.stripPrefix("/")).pathAsString)
                      }
     // return results
     return (
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 48f286dc436..97302357175 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -259,7 +259,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  b=$$(( 5 * 1024 * 1024 ))
          |  chunk_size=$$(( a > b ? a : b ))
          |  echo $$chunk_size
-         }
+         |}
+         |
          |function _check_data_integrity() {
          |  local local_path=$$1
          |  local s3_path=$$2
@@ -276,7 +277,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
          |        { echo "Attempt to get head of object failed for $$s3_path." && return 1 ; }
          |  # local
-         |  local_content_length=$$(LC_ALL=C ls -dn -- "$$local_path" | awk '{print $$5; exit}' ) || 
+         |  local_content_length=$$(LC_ALL=C ls -dnL -- "$$local_path" | awk '{print $$5; exit}' ) || 
          |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }   
          |  # compare
          |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
@@ -303,10 +304,12 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
 
     //generate a series of s3 commands to delocalize artifacts from the container to storage at the end of the task
     val outputCopyCommand = outputs.map {
+      // local is relative path, no mountpoint disk in front.
       case output: AwsBatchFileOutput if output.local.pathAsString.contains("*") => "" //filter out globs
-      case output: AwsBatchFileOutput if output.name.endsWith(".list") && output.name.contains("glob-") =>
-        Log.debug("Globbing : check for EFS settings.")
+      case output: AwsBatchFileOutput if output.s3key.endsWith(".list") && output.s3key.contains("glob-") =>
+        Log.debug("Globbing  : check for EFS settings.")
         val s3GlobOutDirectory = output.s3key.replace(".list", "")
+        // glob paths are not generated with 127 char limit, using generateGlobPaths(). name can be used safely 
         val globDirectory = output.name.replace(".list", "")
         /*
          * Need to process this list and de-localize each file if the list file actually exists
@@ -317,9 +320,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
            Log.debug("EFS glob output file detected: "+ output.s3key + s" / ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}")
            val test_cmd = if (efsDelocalize.isDefined && efsDelocalize.getOrElse(false)) {
                     Log.debug("delocalization on EFS is enabled")
+                    Log.debug(s"Delocalizing $globDirectory to $s3GlobOutDirectory\n")
                     s"""
-                        |touch ${output.name}
-                        |_s3_delocalize_with_retry ${output.name} ${output.s3key}
+                        |touch ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}
+                        |_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}
                         |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi
                         |""".stripMargin
                 } else {
@@ -357,6 +361,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
           | """.stripMargin
         } else {
           // default delocalization command.
+          Log.debug(s"Delocalize from ${output.name} to ${output.s3key}\n")
           s"""
              |touch ${output.name}
              |_s3_delocalize_with_retry ${output.name} ${output.s3key}
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
index 18505f6d866..e94e1fe9ea8 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
@@ -71,6 +71,8 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
     //  - according to those values : write the pattern as s3:// or as local path. 
     //  - get the wf id from the config settings.
 
+    // this function reads in the globfile and locates globbed files : "local" or NIO access is needed to the files. 
+
     // for now : hard coded as local at mount point /mnt/efs.
     val wfid_regex = ".{8}-.{4}-.{4}-.{4}-.{12}".r
     val wfid = callContext.root.toString.split("/").toList.filter(element => wfid_regex.pattern.matcher(element).matches()).lastOption.getOrElse("")
@@ -79,7 +81,7 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
     val listFilePath = if (pattern.startsWith("/mnt/efs/")) {
         DefaultPathBuilder.get(globbedDir + "/." + globPatternName + ".list")
     } else {
-        callContext.root.resolve(s"${globPatternName}.list")
+        callContext.root.resolve(s"${globbedDir}/.${globPatternName}.list".stripPrefix("/"))
     }
     asyncIo.readLinesAsync(listFilePath.toRealPath()) map { lines =>
       lines.toList map { fileName =>
@@ -87,7 +89,7 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
         if (pattern.startsWith("/mnt/efs/")) {
             s"${globbedDir}/.${globPatternName}/${fileName}"
         } else {
-            s"${callContext.root}/${globPatternName}/${fileName}"
+            callContext.root.resolve(s"${globbedDir}/.${globPatternName}/${fileName}".stripPrefix("/")).pathAsString
         }
       }
     }

From 76719fed08cacb9ee06305c8d1f7aeb939d48986 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Thu, 15 Jun 2023 14:51:45 -0400
Subject: [PATCH 186/326] WX-1160 Fix bad MariaDB version assumptions (#7160)

---
 .../scala/cromwell/services/database/QueryTimeoutSpec.scala     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/services/src/test/scala/cromwell/services/database/QueryTimeoutSpec.scala b/services/src/test/scala/cromwell/services/database/QueryTimeoutSpec.scala
index 621b14c8441..ad3277f4ae0 100644
--- a/services/src/test/scala/cromwell/services/database/QueryTimeoutSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/QueryTimeoutSpec.scala
@@ -102,7 +102,7 @@ class QueryTimeoutSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
               Either way, we just need to make sure the sleep was interrupted and don't care if it was via an exception
               or returning `1`.
                */
-              case (major, minor) if major >= 10 && minor >= 3 =>
+              case (major, minor) if (major >= 10 && minor >= 3) || major >= 11 =>
                 RegexErrorMessage(
                     """(\(conn=\d+\) )?Query execution was interrupted \(max_statement_time exceeded\)""".r
                 )

From e266135d0ebdb1c3ab99ac14d190e9ed2254b8e1 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 21 Jun 2023 10:07:16 -0400
Subject: [PATCH 187/326] WX-1126 Upgrade to modern Python, 3.8 not available
 in package repo anymore (#7164)

---
 project/Settings.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Settings.scala b/project/Settings.scala
index fd07a4c6bcc..0257cbac06b 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -130,7 +130,7 @@ object Settings {
       Instructions.Env("PATH", "$PATH:/usr/local/gcloud/google-cloud-sdk/bin"),
       // instructions to install `crcmod`
       Instructions.Run("apt-get -y update"),
-      Instructions.Run("apt-get -y install python3.8"),
+      Instructions.Run("apt-get -y install python3.11"),
       Instructions.Run("apt -y install python3-pip"),
       Instructions.Run("apt-get -y install gcc python3-dev python3-setuptools"),
       Instructions.Run("pip3 uninstall crcmod"),

From 23e391912cf6477cc80155f8430d246d4305e1d8 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 21 Jun 2023 16:21:56 -0400
Subject: [PATCH 188/326] WX-1122 Use legacy AppInsights to get better control
 over logging (#7157)

---
 .gitignore                                           |  1 -
 CHANGELOG.md                                         |  6 +++---
 project/Dependencies.scala                           |  9 +++++++--
 project/Merging.scala                                |  3 +++
 server/src/main/resources/applicationinsights.json   |  7 -------
 server/src/main/resources/logback.xml                |  3 +++
 .../src/main/scala/cromwell/CromwellEntryPoint.scala | 12 ------------
 7 files changed, 16 insertions(+), 25 deletions(-)
 delete mode 100644 server/src/main/resources/applicationinsights.json

diff --git a/.gitignore b/.gitignore
index d67639e9ef1..a5b72f6b263 100644
--- a/.gitignore
+++ b/.gitignore
@@ -55,4 +55,3 @@ tesk_application.conf
 **/venv/
 exome_germline_single_sample_v1.3/
 **/*.pyc
-applicationinsights.log
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3a7c097699e..526c244da03 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,9 +6,9 @@
 
 WDL `size` engine function now works for HTTP files. 
 
-### Azure Instrumentation Support
-Cromwell can now send logs and process information to Azure Application Insights. To enable, set environment 
-variable `APPLICATIONINSIGHTS_CONNECTION_STRING` to your connection string. [See here for information.](https://learn.microsoft.com/en-us/azure/azure-monitor/app/sdk-connection-string)
+### Azure ApplicationInsights Logging Support
+Cromwell can now send logs to Azure Application Insights. To enable, set environment 
+variable `APPLICATIONINSIGHTS_INSTRUMENTATIONKEY` to your account's key. [See here for information.](https://learn.microsoft.com/en-us/azure/azure-monitor/app/sdk-connection-string)
 
 
 ## 85 Release Notes
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index b5fad373834..d90ab1956c0 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -12,7 +12,12 @@ object Dependencies {
   // https://github.com/sbt/sbt/issues/4531
   private val azureStorageBlobNioV = "12.0.0-beta.19"
   private val azureIdentitySdkV = "1.9.0-beta.2"
-  private val azureAppInsightsV = "3.4.12"
+  // We are using the older AppInsights 2 because we want to use the
+  // logback appender to send logs. AppInsights 3 does not have a standalone
+  // appender, and its auto-hoovering of logs didn't meet our needs.
+  // (Specifically, the side-by-side root logger and workflow logger resulted in
+  // duplicate messages in AI. See WX-1122.)
+  private val azureAppInsightsLogbackV = "2.6.4"
   private val betterFilesV = "3.9.1"
   private val jsonSmartV = "2.4.10"
   /*
@@ -213,7 +218,7 @@ object Dependencies {
     "com.fasterxml.jackson.dataformat" % "jackson-dataformat-xml" % jacksonV,
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0",
     "net.minidev" % "json-smart" % jsonSmartV,
-    "com.microsoft.azure" % "applicationinsights-runtime-attach" % azureAppInsightsV,
+    "com.microsoft.azure" % "applicationinsights-logging-logback" % azureAppInsightsLogbackV,
   )
 
   val wsmDependencies: List[ModuleID] = List(
diff --git a/project/Merging.scala b/project/Merging.scala
index 046380a367c..5ecd951014b 100644
--- a/project/Merging.scala
+++ b/project/Merging.scala
@@ -9,6 +9,9 @@ object Merging {
       MergeStrategy.filterDistinctLines
     case PathList(ps@_*) if ps.last == "logback.xml" =>
       MergeStrategy.first
+    // Merge mozilla/public-suffix-list.txt if duplicated
+    case PathList(ps@_*) if ps.last == "public-suffix-list.txt" =>
+      MergeStrategy.last
     // AWS SDK v2 configuration files - can be discarded
     case PathList(ps@_*) if Set("codegen.config" , "service-2.json" , "waiters-2.json" , "customization.config" , "examples-1.json" , "paginators-1.json").contains(ps.last) =>
       MergeStrategy.discard
diff --git a/server/src/main/resources/applicationinsights.json b/server/src/main/resources/applicationinsights.json
deleted file mode 100644
index e90407242bf..00000000000
--- a/server/src/main/resources/applicationinsights.json
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-  "instrumentation": {
-    "jdbc": {
-      "enabled": false
-    }
-  }
-}
diff --git a/server/src/main/resources/logback.xml b/server/src/main/resources/logback.xml
index 006ca3953f4..29582f140d3 100644
--- a/server/src/main/resources/logback.xml
+++ b/server/src/main/resources/logback.xml
@@ -94,11 +94,14 @@
         </filter>
     </appender>
 
+    <appender name="AppInsightsAppender" class="com.microsoft.applicationinsights.logback.ApplicationInsightsAppender" />
+
     <root level="${LOG_LEVEL}">
         <appender-ref ref="STANDARD_APPENDER" />
         <appender-ref ref="PRETTY_APPENDER" />
         <appender-ref ref="FILEROLLER_APPENDER" />
         <appender-ref ref="Sentry" />
+        <appender-ref ref="AppInsightsAppender" />
     </root>
 
     <logger name="liquibase" level="WARN"/>
diff --git a/server/src/main/scala/cromwell/CromwellEntryPoint.scala b/server/src/main/scala/cromwell/CromwellEntryPoint.scala
index 9f6ce82a127..d712ea71b28 100644
--- a/server/src/main/scala/cromwell/CromwellEntryPoint.scala
+++ b/server/src/main/scala/cromwell/CromwellEntryPoint.scala
@@ -9,7 +9,6 @@ import cats.data.Validated._
 import cats.effect.{ContextShift, IO}
 import cats.syntax.apply._
 import cats.syntax.validated._
-import com.microsoft.applicationinsights.attach.ApplicationInsights
 import com.typesafe.config.{Config, ConfigFactory}
 import common.exception.MessageAggregation
 import common.validation.ErrorOr._
@@ -46,11 +45,6 @@ object CromwellEntryPoint extends GracefulStopSupport {
   private val dnsCacheTtl = config.getOrElse("system.dns-cache-ttl", 3 minutes)
   java.security.Security.setProperty("networkaddress.cache.ttl", dnsCacheTtl.toSeconds.toString)
 
-  // The presence of this env var tells us that the user is trying to send instrumentation data and
-  // logs to Azure Application Insights. If it's present, we'll attach the ApplicationInsights agent.
-  // To configure the behavior of this agent, see server/src/main/resources/applicationinsights.json
-  private lazy val useAzureInstrumentation = sys.env.contains("APPLICATIONINSIGHTS_CONNECTION_STRING")
-
   /**
     * Run Cromwell in server mode.
     */
@@ -151,12 +145,6 @@ object CromwellEntryPoint extends GracefulStopSupport {
     */
   private def initLogging(command: Command): Unit = {
 
-    // Enable Azure instrumentation and log-slurping if desired. Running ApplicationInsights.attach()
-    // without checking for the presence of the relevant env var doesn't cause any failures, but does
-    // print an error that would be confusing for non-Azure users.
-    if (useAzureInstrumentation)
-      ApplicationInsights.attach()
-
     val logbackSetting = command match {
       case Server => "STANDARD"
       case Submit => "PRETTY"

From 8a1297fb0e44a11421eed98c5885188972337ce9 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 30 Jun 2023 10:29:24 -0400
Subject: [PATCH 189/326] WX-1137 Replace 4-byte unicode chars in PAPI event
 descriptions (#7166)

---
 .../v2beta/PipelinesUtilityConversions.scala  | 16 +++++++++++-
 .../PipelinesUtilityConversionsSpec.scala     | 26 +++++++++++++++++++
 2 files changed, 41 insertions(+), 1 deletion(-)
 create mode 100644 supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversionsSpec.scala

diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala
index cb472b86bd9..09359428d01 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala
@@ -60,8 +60,16 @@ trait PipelinesUtilityConversions {
       Option(event.getDescription) collect { case d if d.startsWith(s"$k pulling") => "Pulling" + d.substring(s"$k pulling".length)}
     } headOption
 
+    // See WX-1137. ContainerStoppedEvent descriptions contain the stderr, which may include 4-byte unicode
+    // characters (typically emoji). Some databases have trouble storing these; replace them with the standard
+    // "unknown character" unicode symbol.
+    val name = Option(event.getContainerStopped) match {
+      case Some(_) => cleanUtf8mb4(event.getDescription)
+      case _ => event.getDescription
+    }
+
     ExecutionEvent(
-      name = event.getDescription,
+      name = name,
       offsetDateTime = OffsetDateTime.parse(event.getTimestamp),
       grouping = groupingFromAction.orElse(groupingFromPull)
     )
@@ -91,4 +99,10 @@ object PipelinesUtilityConversions {
       }
     }
   }
+
+  lazy val utf8mb4Regex = "[\\x{10000}-\\x{FFFFF}]"
+  lazy val utf8mb3Replacement = "\uFFFD"  // This is the standard char for replacing invalid/unknown unicode chars
+  def cleanUtf8mb4(in: String): String = {
+    in.replaceAll(utf8mb4Regex, utf8mb3Replacement)
+  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversionsSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversionsSpec.scala
new file mode 100644
index 00000000000..eeef482a740
--- /dev/null
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversionsSpec.scala
@@ -0,0 +1,26 @@
+package cromwell.backend.google.pipelines.v2beta
+
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+class PipelinesUtilityConversionsSpec extends AnyFlatSpec with Matchers {
+  behavior of "PipelinesUtilityConversions"
+
+  it should "not modify strings that contain only ascii characters" in {
+    val input = "hi there!?"
+    PipelinesUtilityConversions.cleanUtf8mb4(input) shouldBe input
+  }
+
+  it should "not modify strings with 3-byte unicode characters" in {
+    val input = "Here is my non-ascii character: \u1234 Do you like it?"
+    PipelinesUtilityConversions.cleanUtf8mb4(input) shouldBe input
+  }
+
+  it should "replace 4-byte unicode characters" in {
+    val cry = new String(Character.toChars(Integer.parseInt("1F62D", 16)))
+    val barf = new String(Character.toChars(Integer.parseInt("1F92E", 16)))
+    val input = s"When I try to put an emoji in the database it $barf and then I $cry"
+    val cleaned = "When I try to put an emoji in the database it \uFFFD and then I \uFFFD"
+    PipelinesUtilityConversions.cleanUtf8mb4(input) shouldBe cleaned
+  }
+}

From 4ea3a054acb2dbfdebd41ca6a60ff77a99d887bd Mon Sep 17 00:00:00 2001
From: dspeck1 <dspeck@burwood.com>
Date: Thu, 6 Jul 2023 13:15:49 -0500
Subject: [PATCH 190/326] WX-1101 Update library versions to support batch
 (#7155)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .../filesystems/gcs/GcsPathBuilderSpec.scala   |  2 +-
 project/Dependencies.scala                     | 18 +++++++++---------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala
index c6ea1e2e12b..22e63ea0f32 100644
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala
+++ b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala
@@ -323,7 +323,7 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       val storageOptionsField = cloudFilesystemProvider.getClass.getDeclaredField("storageOptions")
       storageOptionsField.setAccessible(true)
       val storageOptions = storageOptionsField.get(cloudFilesystemProvider)
-      val credentialsField = storageOptions.getClass.getSuperclass.getDeclaredField("credentials")
+      val credentialsField = storageOptions.getClass.getSuperclass.getSuperclass.getDeclaredField("credentials")
       credentialsField.setAccessible(true)
       credentialsField.get(storageOptions).asInstanceOf[Credentials]
     }
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index d90ab1956c0..ad1e4961b6a 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -42,24 +42,24 @@ object Dependencies {
   private val diffsonSprayJsonV = "4.1.1"
   private val ficusV = "1.5.2"
   private val fs2V = "2.5.9" // scala-steward:off (CROM-6564)
-  private val googleApiClientV = "1.33.2"
-  private val googleCloudBigQueryV = "2.10.0"
+  private val googleApiClientV = "2.1.4"
+  private val googleCloudBigQueryV = "2.25.0"
   // latest date via: https://github.com/googleapis/google-api-java-client-services/blob/main/clients/google-api-services-cloudkms/v1.metadata.json
-  private val googleCloudKmsV = "v1-rev20220104-1.32.1"
+  private val googleCloudKmsV = "v1-rev20230421-2.0.0"
   private val googleCloudMonitoringV = "3.2.5"
   private val googleCloudNioV = "0.124.8"
-  private val googleCloudStorageV = "2.9.2"
-  private val googleGaxGrpcV = "2.19.0"
+  private val googleCloudStorageV = "2.17.2"
+  private val googleGaxGrpcV = "2.25.0"
   // latest date via: https://mvnrepository.com/artifact/com.google.apis/google-api-services-genomics
   private val googleGenomicsServicesV2Alpha1ApiV = "v2alpha1-rev20210811-1.32.1"
   private val googleHttpClientApacheV = "2.1.2"
-  private val googleHttpClientV = "1.38.0"
+  private val googleHttpClientV = "1.42.3"
   // latest date via: https://mvnrepository.com/artifact/com.google.apis/google-api-services-lifesciences
-  private val googleLifeSciencesServicesV2BetaApiV = "v2beta-rev20210813-1.32.1"
+  private val googleLifeSciencesServicesV2BetaApiV = "v2beta-rev20220916-2.0.0"
   private val googleOauth2V = "1.5.3"
   private val googleOauthClientV = "1.33.1"
-  private val googleCloudResourceManagerV = "1.2.5"
-  private val grpcV = "1.45.1"
+  private val googleCloudResourceManagerV = "1.17.0"
+  private val grpcV = "1.54.1"
   private val guavaV = "31.0.1-jre"
   private val heterodonV = "1.0.0-beta3"
   private val hsqldbV = "2.6.1"

From cb5da0aabfc94a53a04539d80a3cfb2c22569e06 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Tue, 11 Jul 2023 09:47:37 -0400
Subject: [PATCH 191/326] WX-1195 Update Azure identity libs (#7173)

---
 project/Dependencies.scala | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index ad1e4961b6a..6a8d73db01f 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -11,7 +11,9 @@ object Dependencies {
   // https://github.com/Azure/azure-sdk-for-java/tree/main/sdk/boms/azure-sdk-bom
   // https://github.com/sbt/sbt/issues/4531
   private val azureStorageBlobNioV = "12.0.0-beta.19"
-  private val azureIdentitySdkV = "1.9.0-beta.2"
+  private val azureIdentitySdkV = "1.9.1"
+  private val azureIdentityExtensionsV = "1.1.4"
+  private val azureCoreManagementV = "1.7.1"
   // We are using the older AppInsights 2 because we want to use the
   // logback appender to send logs. AppInsights 3 does not have a standalone
   // appender, and its auto-hoovering of logs didn't meet our needs.
@@ -214,7 +216,8 @@ object Dependencies {
       exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
       exclude("jakarta.activation", "jakarta.activation-api")
       exclude("net.minidev", "json-smart"),
-    "com.azure" % "azure-core-management" % "1.7.1",
+    "com.azure" % "azure-identity-extensions" % azureIdentityExtensionsV,
+    "com.azure" % "azure-core-management" % azureCoreManagementV,
     "com.fasterxml.jackson.dataformat" % "jackson-dataformat-xml" % jacksonV,
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0",
     "net.minidev" % "json-smart" % jsonSmartV,

From 63b035f6d74a8dbe47c328de2b0da8a820f5260a Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Thu, 13 Jul 2023 11:52:56 -0400
Subject: [PATCH 192/326] WX-1114 Initial inclusion of Azure NIO 'fork' (#7168)

---
 azure-blob-nio/README.md                      |    5 +
 azure-blob-nio/assets.json                    |    6 +
 .../blob/nio/AzureBasicFileAttributeView.java |   69 +
 .../blob/nio/AzureBasicFileAttributes.java    |  165 +++
 .../blob/nio/AzureBlobFileAttributeView.java  |  157 +++
 .../blob/nio/AzureBlobFileAttributes.java     |  369 +++++
 .../blob/nio/AzureDirectoryStream.java        |  189 +++
 .../storage/blob/nio/AzureFileStore.java      |  194 +++
 .../storage/blob/nio/AzureFileSystem.java     |  492 +++++++
 .../blob/nio/AzureFileSystemProvider.java     | 1182 +++++++++++++++++
 .../com/azure/storage/blob/nio/AzurePath.java |  836 ++++++++++++
 .../azure/storage/blob/nio/AzureResource.java |  284 ++++
 .../blob/nio/AzureSeekableByteChannel.java    |  245 ++++
 .../storage/blob/nio/DirectoryStatus.java     |   23 +
 .../storage/blob/nio/LoggingUtility.java      |   16 +
 .../storage/blob/nio/NioBlobInputStream.java  |  211 +++
 .../storage/blob/nio/NioBlobOutputStream.java |   99 ++
 .../azure/storage/blob/nio/package-info.java  |    7 +
 .../java.nio.file.spi.FileSystemProvider      |    1 +
 .../azure-storage-blob-nio.properties         |    2 +
 .../azure/storage/blob/nio/ReadmeSamples.java |  129 ++
 build.sbt                                     |    5 +
 project/Dependencies.scala                    |   25 +-
 project/Merging.scala                         |    5 +
 24 files changed, 4711 insertions(+), 5 deletions(-)
 create mode 100644 azure-blob-nio/README.md
 create mode 100644 azure-blob-nio/assets.json
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBasicFileAttributeView.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBasicFileAttributes.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBlobFileAttributeView.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBlobFileAttributes.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureDirectoryStream.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileStore.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystemProvider.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzurePath.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureResource.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureSeekableByteChannel.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/DirectoryStatus.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/LoggingUtility.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/NioBlobInputStream.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/NioBlobOutputStream.java
 create mode 100644 azure-blob-nio/src/main/java/com/azure/storage/blob/nio/package-info.java
 create mode 100644 azure-blob-nio/src/main/resources/META-INF/services/java.nio.file.spi.FileSystemProvider
 create mode 100644 azure-blob-nio/src/main/resources/azure-storage-blob-nio.properties
 create mode 100644 azure-blob-nio/src/samples/java/com/azure/storage/blob/nio/ReadmeSamples.java

diff --git a/azure-blob-nio/README.md b/azure-blob-nio/README.md
new file mode 100644
index 00000000000..ad6c553eabf
--- /dev/null
+++ b/azure-blob-nio/README.md
@@ -0,0 +1,5 @@
+# Azure Storage Blob NIO FileSystemProvider
+
+[This is a copy of the NIO Filesystem implementation version 12.0.0-beta.19](https://github.com/Azure/azure-sdk-for-java/tree/2490e1e19e8531fe0a6378f40e299e7ec64cf3aa/sdk/storage/azure-storage-blob-nio)
+
+For more information on the initial design and commit history see the Azure SDK repository linked above. Changes to this repo were necessary to support some of the specific needs Cromwell as an App on Azure has as a system in Terra. This is something that has some precedent as it has been done for other filesystems in the past.
diff --git a/azure-blob-nio/assets.json b/azure-blob-nio/assets.json
new file mode 100644
index 00000000000..c262f7ebafc
--- /dev/null
+++ b/azure-blob-nio/assets.json
@@ -0,0 +1,6 @@
+{
+  "AssetsRepo": "Azure/azure-sdk-assets",
+  "AssetsRepoPrefixPath": "java",
+  "TagPrefix": "java/storage/azure-storage-blob-nio",
+  "Tag": "java/storage/azure-storage-blob-nio_b2a0ce219e"
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBasicFileAttributeView.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBasicFileAttributeView.java
new file mode 100644
index 00000000000..43744893ccb
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBasicFileAttributeView.java
@@ -0,0 +1,69 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import com.azure.core.util.logging.ClientLogger;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributeView;
+import java.nio.file.attribute.FileTime;
+
+/**
+ * Provides support for basic file attributes.
+ * <p>
+ * The operations supported by this view and the attributes it reads are a strict subset of
+ * {@link AzureBlobFileAttributeView} and has the same network behavior. Therefore, while this type is offered for
+ * compliance with the NIO spec, {@link AzureBlobFileAttributeView} is generally preferred.
+ * <p>
+ * {@link #setTimes(FileTime, FileTime, FileTime)} is not supported.
+ */
+public final class AzureBasicFileAttributeView implements BasicFileAttributeView {
+    private static final ClientLogger LOGGER = new ClientLogger(AzureBasicFileAttributeView.class);
+
+    static final String NAME = "azureBasic";
+
+    private final Path path;
+
+    AzureBasicFileAttributeView(Path path) {
+        this.path = path;
+    }
+
+    /**
+     * Returns the name of the attribute view: {@code "azureBasic"}
+     *
+     * @return the name of the attribute view: {@code "azureBasic"}
+     */
+    @Override
+    public String name() {
+        return NAME;
+    }
+
+    /**
+     * Reads the basic file attributes as a bulk operation.
+     * <p>
+     * All file attributes are read as an atomic operation with respect to other file system operations.
+     *
+     * @return {@link AzureBasicFileAttributes}
+     */
+    @Override
+    public AzureBasicFileAttributes readAttributes() throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        return new AzureBasicFileAttributes(path);
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @param lastModifiedTime the new last modified time, or null to not change the value
+     * @param lastAccessTime the last access time, or null to not change the value
+     * @param createTime the file's create time, or null to not change the value
+     * @throws UnsupportedOperationException Operation not supported.
+     * @throws IOException never
+     */
+    @Override
+    public void setTimes(FileTime lastModifiedTime, FileTime lastAccessTime, FileTime createTime) throws IOException {
+        throw LoggingUtility.logError(LOGGER, new UnsupportedOperationException());
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBasicFileAttributes.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBasicFileAttributes.java
new file mode 100644
index 00000000000..d1ab6d28562
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBasicFileAttributes.java
@@ -0,0 +1,165 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.nio.file.attribute.FileAttribute;
+import java.nio.file.attribute.FileTime;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * Provides support for basic file attributes.
+ * <p>
+ * The properties available on this type are a strict subset of {@link AzureBlobFileAttributes}, and the two types have
+ * the same network behavior. Therefore, while this type is offered for compliance with the NIO spec,
+ * {@link AzureBlobFileAttributes} is generally preferred.
+ * <p>
+ * Some attributes are not supported. Refer to the javadocs on each method for more information.
+ * <p>
+ * If the target file is a virtual directory, most attributes will be set to null.
+ */
+public final class AzureBasicFileAttributes implements BasicFileAttributes {
+    // For verifying parameters on FileSystemProvider.readAttributes
+    static final Set<String> ATTRIBUTE_STRINGS;
+    static {
+        Set<String> set = new HashSet<>();
+        set.add("lastModifiedTime");
+        set.add("isRegularFile");
+        set.add("isDirectory");
+        set.add("isVirtualDirectory");
+        set.add("isSymbolicLink");
+        set.add("isOther");
+        set.add("size");
+        set.add("creationTime");
+        ATTRIBUTE_STRINGS = Collections.unmodifiableSet(set);
+    }
+
+    private final AzureBlobFileAttributes internalAttributes;
+
+    /*
+    In order to support Files.exist() and other methods like Files.walkFileTree() which depend on it, we have had to add
+    support for virtual directories. This is not ideal as customers will have to now perform null checks when inspecting
+    attributes (or at least check if it is a virtual directory before inspecting properties). It also incurs extra
+    network requests as we have to call a checkDirectoryExists() after receiving the initial 404. This is two
+    additional network requests, though they only happen in the case when a file doesn't exist or is virtual, so it
+    shouldn't happen in the majority of api calls.
+     */
+    AzureBasicFileAttributes(Path path) throws IOException {
+        this.internalAttributes = new AzureBlobFileAttributes(path);
+    }
+
+    /**
+     * Returns the time of last modification or null if this is a virtual directory.
+     *
+     * @return the time of last modification or null if this is a virtual directory
+     */
+    @Override
+    public FileTime lastModifiedTime() {
+        return this.internalAttributes.lastModifiedTime();
+    }
+
+    /**
+     * Returns the time of last modification or null if this is a virtual directory
+     * <p>
+     * Last access time is not supported by the blob service. In this case, it is typical for implementations to return
+     * the {@link #lastModifiedTime()}.
+     *
+     * @return the time of last modification or null if this is a virtual directory
+     */
+    @Override
+    public FileTime lastAccessTime() {
+        return this.internalAttributes.lastAccessTime();
+    }
+
+    /**
+     * Returns the creation time. The creation time is the time that the file was created. Returns null if this is a
+     * virtual directory.
+     *
+     * @return The creation time or null if this is a virtual directory
+     */
+    @Override
+    public FileTime creationTime() {
+        return this.internalAttributes.creationTime();
+    }
+
+    /**
+     * Tells whether the file is a regular file with opaque content.
+     *
+     * @return whether the file is a regular file.
+     */
+    @Override
+    public boolean isRegularFile() {
+        return this.internalAttributes.isRegularFile();
+    }
+
+    /**
+     * Tells whether the file is a directory.
+     * <p>
+     * Will only return true if the directory is a concrete directory. See
+     * {@link AzureFileSystemProvider#createDirectory(Path, FileAttribute[])} for more information on virtual and
+     * concrete directories.
+     *
+     * @return whether the file is a directory
+     */
+    @Override
+    public boolean isDirectory() {
+        return this.internalAttributes.isDirectory();
+    }
+
+    /**
+     * Tells whether the file is a virtual directory.
+     * <p>
+     * See {@link AzureFileSystemProvider#createDirectory(Path, FileAttribute[])} for more information on virtual and
+     * concrete directories.
+     *
+     * @return whether the file is a virtual directory
+     */
+    public boolean isVirtualDirectory() {
+        return this.internalAttributes.isVirtualDirectory();
+    }
+
+    /**
+     * Tells whether the file is a symbolic link.
+     *
+     * @return false. Symbolic links are not supported.
+     */
+    @Override
+    public boolean isSymbolicLink() {
+        return this.internalAttributes.isSymbolicLink();
+    }
+
+    /**
+     * Tells whether the file is something other than a regular file, directory, or symbolic link.
+     *
+     * @return false. No other object types are supported.
+     */
+    @Override
+    public boolean isOther() {
+        return this.internalAttributes.isOther();
+    }
+
+    /**
+     * Returns the size of the file (in bytes).
+     *
+     * @return the size of the file
+     */
+    @Override
+    public long size() {
+        return this.internalAttributes.size();
+    }
+
+    /**
+     * Returns the url of the resource.
+     *
+     * @return The file key, which is the url.
+     */
+    @Override
+    public Object fileKey() {
+        return this.internalAttributes.fileKey();
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBlobFileAttributeView.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBlobFileAttributeView.java
new file mode 100644
index 00000000000..d9366e22417
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBlobFileAttributeView.java
@@ -0,0 +1,157 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.models.AccessTier;
+import com.azure.storage.blob.models.BlobHttpHeaders;
+import com.azure.storage.blob.models.BlobStorageException;
+import com.azure.storage.blob.specialized.BlobClientBase;
+
+import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributeView;
+import java.nio.file.attribute.FileTime;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.function.Consumer;
+
+/**
+ * A file attribute view that provides a view of attributes specific to files stored as blobs in Azure Storage.
+ * <p>
+ * All attributes are retrieved from the file system as a bulk operation.
+ * <p>
+ * {@link #setTimes(FileTime, FileTime, FileTime)} is not supported.
+ */
+public final class AzureBlobFileAttributeView implements BasicFileAttributeView {
+    private static final ClientLogger LOGGER = new ClientLogger(AzureBlobFileAttributeView.class);
+
+    static final String ATTR_CONSUMER_ERROR = "Exception thrown by attribute consumer";
+    static final String NAME = "azureBlob";
+
+    private final Path path;
+
+    AzureBlobFileAttributeView(Path path) {
+        this.path = path;
+    }
+
+    @SuppressWarnings("unchecked")
+    static Map<String, Consumer<Object>> setAttributeConsumers(AzureBlobFileAttributeView view) {
+        Map<String, Consumer<Object>> map = new HashMap<>();
+        map.put("blobHttpHeaders", obj -> {
+            try {
+                view.setBlobHttpHeaders((BlobHttpHeaders) obj);
+            } catch (IOException e) {
+                throw LoggingUtility.logError(LOGGER, new UncheckedIOException(ATTR_CONSUMER_ERROR, e));
+            }
+        });
+        map.put("metadata", obj -> {
+            try {
+                Map<String, String> m = (Map<String, String>) obj;
+                if (m == null) {
+                    throw LoggingUtility.logError(LOGGER, new ClassCastException());
+                }
+                view.setMetadata(m);
+            } catch (IOException e) {
+                throw LoggingUtility.logError(LOGGER, new UncheckedIOException(ATTR_CONSUMER_ERROR, e));
+            }
+        });
+        map.put("tier", obj -> {
+            try {
+                view.setTier((AccessTier) obj);
+            } catch (IOException e) {
+                throw LoggingUtility.logError(LOGGER, new UncheckedIOException(ATTR_CONSUMER_ERROR, e));
+            }
+        });
+
+        return map;
+    }
+
+    /**
+     * Returns the name of the attribute view: {@code "azureBlob"}
+     *
+     * @return the name of the attribute view: {@code "azureBlob"}
+     */
+    @Override
+    public String name() {
+        return NAME;
+    }
+
+    /**
+     * Reads the file attributes as a bulk operation.
+     * <p>
+     * All file attributes are read as an atomic operation with respect to other file system operations. A fresh copy is
+     * retrieved every time this method is called.
+     * @return {@link AzureBlobFileAttributes}
+     * @throws IOException if an IOException occurs.
+     */
+    @Override
+    public AzureBlobFileAttributes readAttributes() throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        return new AzureBlobFileAttributes(path);
+    }
+
+    /**
+     * Sets the {@link BlobHttpHeaders} as an atomic operation.
+     * <p>
+     * See {@link BlobClientBase#setHttpHeaders(BlobHttpHeaders)} for more information.
+     * @param headers {@link BlobHttpHeaders}
+     * @throws IOException if an IOException occurs.
+     */
+    public void setBlobHttpHeaders(BlobHttpHeaders headers) throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            new AzureResource(this.path).getBlobClient().setHttpHeaders(headers);
+        } catch (BlobStorageException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    /**
+     * Sets the metadata as an atomic operation.
+     * <p>
+     * See {@link BlobClientBase#setMetadata(Map)} for more information.
+     * @param metadata The metadata to associate with the blob
+     * @throws IOException if an IOException occurs.
+     */
+    public void setMetadata(Map<String, String> metadata) throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            new AzureResource(this.path).getBlobClient().setMetadata(metadata);
+        } catch (BlobStorageException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    /**
+     * Sets the {@link AccessTier} on the file.
+     * <p>
+     * See {@link BlobClientBase#setAccessTier(AccessTier)} for more information.
+     * @param tier {@link AccessTier}
+     * @throws IOException if an IOException occurs.
+     */
+    public void setTier(AccessTier tier) throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            new AzureResource(this.path).getBlobClient().setAccessTier(tier);
+        } catch (BlobStorageException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @param lastModifiedTime the new last modified time, or null to not change the value
+     * @param lastAccessTime the last access time, or null to not change the value
+     * @param createTime the file's create time, or null to not change the value
+     * @throws UnsupportedOperationException Operation not supported.
+     * @throws IOException never
+     */
+    @Override
+    public void setTimes(FileTime lastModifiedTime, FileTime lastAccessTime, FileTime createTime) throws IOException {
+        throw LoggingUtility.logError(LOGGER, new UnsupportedOperationException());
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBlobFileAttributes.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBlobFileAttributes.java
new file mode 100644
index 00000000000..c73d062e117
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureBlobFileAttributes.java
@@ -0,0 +1,369 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.nio.file.attribute.FileAttribute;
+import java.nio.file.attribute.FileTime;
+import java.time.OffsetDateTime;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.function.Supplier;
+
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.models.AccessTier;
+import com.azure.storage.blob.models.ArchiveStatus;
+import com.azure.storage.blob.models.BlobHttpHeaders;
+import com.azure.storage.blob.models.BlobProperties;
+import com.azure.storage.blob.models.BlobStorageException;
+import com.azure.storage.blob.models.BlobType;
+import com.azure.storage.blob.models.CopyStatusType;
+
+/**
+ * Provides support for attributes associated with a file stored as a blob in Azure Storage.
+ * <p>
+ * Some of the attributes inherited from {@link BasicFileAttributes} are not supported. See the docs on each method for
+ * more information.
+ * <p>
+ * If the target file is a virtual directory, most attributes will be set to null.
+ */
+public final class AzureBlobFileAttributes implements BasicFileAttributes {
+    /*
+    Some blob properties do not have getters as they do not make sense in the context of nio. These properties are:
+        - incremental snapshot related properties (only for page blobs)
+        - lease related properties (leases not currently supported)
+        - sequence number (only for page blobs)
+        - encryption key sha256 (cpk not supported)
+        - committed block count (only for append blobs)
+     */
+
+    private static final ClientLogger LOGGER = new ClientLogger(AzureBlobFileAttributes.class);
+
+    private final BlobProperties properties;
+    private final AzureResource resource;
+    private final boolean isVirtualDirectory;
+
+    AzureBlobFileAttributes(Path path) throws IOException {
+        this.resource = new AzureResource(path);
+        BlobProperties props = null;
+        try {
+            props = resource.getBlobClient().getProperties();
+        } catch (BlobStorageException e) {
+            if (e.getStatusCode() == 404 && this.resource.checkVirtualDirectoryExists()) {
+                this.isVirtualDirectory = true;
+                this.properties = null;
+                return;
+            } else {
+                throw LoggingUtility.logError(LOGGER, new IOException("Path: " + path.toString(), e));
+            }
+        }
+        this.properties = props;
+        this.isVirtualDirectory = false;
+    }
+
+    static Map<String, Supplier<Object>> getAttributeSuppliers(AzureBlobFileAttributes attributes) {
+        Map<String, Supplier<Object>> map = new HashMap<>();
+        map.put("creationTime", attributes::creationTime);
+        map.put("lastModifiedTime", attributes::lastModifiedTime);
+        map.put("eTag", attributes::eTag);
+        map.put("blobHttpHeaders", attributes::blobHttpHeaders);
+        map.put("blobType", attributes::blobType);
+        map.put("copyId", attributes::copyId);
+        map.put("copyStatus", attributes::copyStatus);
+        map.put("copySource", attributes::copySource);
+        map.put("copyProgress", attributes::copyProgress);
+        map.put("copyCompletionTime", attributes::copyCompletionTime);
+        map.put("copyStatusDescription", attributes::copyStatusDescription);
+        map.put("isServerEncrypted", attributes::isServerEncrypted);
+        map.put("accessTier", attributes::accessTier);
+        map.put("isAccessTierInferred", attributes::isAccessTierInferred);
+        map.put("archiveStatus", attributes::archiveStatus);
+        map.put("accessTierChangeTime", attributes::accessTierChangeTime);
+        map.put("metadata", attributes::metadata);
+        map.put("isRegularFile", attributes::isRegularFile);
+        map.put("isDirectory", attributes::isDirectory);
+        map.put("isVirtualDirectory", attributes::isVirtualDirectory);
+        map.put("isSymbolicLink", attributes::isSymbolicLink);
+        map.put("isOther", attributes::isOther);
+        map.put("size", attributes::size);
+        return map;
+    }
+
+    /**
+     * Returns the creation time. The creation time is the time that the file was created. Returns null if this is a
+     * virtual directory.
+     *
+     * @return The creation time or null if this is a virtual directory
+     */
+    @Override
+    public FileTime creationTime() {
+        return !this.isVirtualDirectory ? FileTime.from(this.properties.getCreationTime().toInstant()) : null;
+    }
+
+    /**
+     * Returns the time of last modification. Returns null if this is a virtual directory
+     *
+     * @return the time of last modification or null if this is a virtual directory
+     */
+    @Override
+    public FileTime lastModifiedTime() {
+        return !this.isVirtualDirectory ? FileTime.from(this.properties.getLastModified().toInstant()) : null;
+    }
+
+    /**
+     * Returns the eTag of the blob or null if this is a virtual directory
+     *
+     * @return the eTag of the blob or null if this is a virtual directory
+     */
+    public String eTag() {
+        return !this.isVirtualDirectory ? this.properties.getETag() : null;
+    }
+
+    /**
+     * Returns the {@link BlobHttpHeaders} of the blob or null if this is a virtual directory.
+     *
+     * @return {@link BlobHttpHeaders} or null if this is a virtual directory
+     */
+    public BlobHttpHeaders blobHttpHeaders() {
+        if (this.isVirtualDirectory) {
+            return null;
+        }
+        /*
+        We return these all as one value, so it's consistent with the way of setting, especially the setAttribute method
+        that accepts a string argument for the name of the property. Returning them individually would mean we have to
+        support setting them individually as well, which is not possible due to service constraints.
+         */
+        return new BlobHttpHeaders()
+            .setContentType(this.properties.getContentType())
+            .setContentLanguage(this.properties.getContentLanguage())
+            .setContentMd5(this.properties.getContentMd5())
+            .setContentDisposition(this.properties.getContentDisposition())
+            .setContentEncoding(this.properties.getContentEncoding())
+            .setCacheControl(this.properties.getCacheControl());
+    }
+
+    /**
+     * Returns the type of the blob or null if this is a virtual directory
+     *
+     * @return the type of the blob or null if this is a virtual directory
+     */
+    public BlobType blobType() {
+        return !this.isVirtualDirectory ? this.properties.getBlobType() : null;
+    }
+
+    /**
+     * Returns the identifier of the last copy operation. If this blob hasn't been the target of a copy operation or has
+     * been modified since this won't be set. Returns null if this is a virtual directory
+     *
+     * @return the identifier of the last copy operation or null if this is a virtual directory
+     */
+    public String copyId() {
+        return !this.isVirtualDirectory ? this.properties.getCopyId() : null;
+    }
+
+    /**
+     * Returns the status of the last copy operation. If this blob hasn't been the target of a copy operation or has
+     * been modified since this won't be set. Returns null if this is a virtual directory
+     *
+     * @return the status of the last copy operation or null if this is a virtual directory
+     */
+    public CopyStatusType copyStatus() {
+        return !this.isVirtualDirectory ? this.properties.getCopyStatus() : null;
+    }
+
+    /**
+     * Returns the source blob URL from the last copy operation. If this blob hasn't been the target of a copy operation
+     * or has been modified since this won't be set. Returns null if this is a virtual directory
+     *
+     * @return the source blob URL from the last copy operation or null if this is a virtual directory
+     */
+    public String copySource() {
+        return !this.isVirtualDirectory ? this.properties.getCopySource() : null;
+    }
+
+    /**
+     * Returns the number of bytes copied and total bytes in the source from the last copy operation (bytes copied/total
+     * bytes). If this blob hasn't been the target of a copy operation or has been modified since this won't be set.
+     * Returns null if this is a virtual directory
+     *
+     * @return the number of bytes copied and total bytes in the source from the last copy operation null if this is a
+     * virtual directory
+     */
+    public String copyProgress() {
+        return !this.isVirtualDirectory ? this.properties.getCopyProgress() : null;
+    }
+
+    /**
+     * Returns the completion time of the last copy operation. If this blob hasn't been the target of a copy operation
+     * or has been modified since this won't be set. Returns null if this is a virtual directory.
+     *
+     * @return the completion time of the last copy operation or null if this is a virtual directory
+     */
+    public OffsetDateTime copyCompletionTime() {
+        return !this.isVirtualDirectory ? this.properties.getCopyCompletionTime() : null;
+    }
+
+    /**
+     * Returns the description of the last copy failure, this is set when the {@link #copyStatus() getCopyStatus} is
+     * {@link CopyStatusType#FAILED failed} or {@link CopyStatusType#ABORTED aborted}. If this blob hasn't been the
+     * target of a copy operation or has been modified since this won't be set. Returns null if this is a virtual
+     * directory.
+     *
+     * @return the description of the last copy failure or null if this is a virtual directory
+     */
+    public String copyStatusDescription() {
+        return !this.isVirtualDirectory ? this.properties.getCopyStatusDescription() : null;
+    }
+
+    /**
+     * Returns the status of the blob being encrypted on the server or null if this is a virtual directory.
+     *
+     * @return the status of the blob being encrypted on the server or null if this is a virtual directory
+     */
+    public Boolean isServerEncrypted() {
+        return !this.isVirtualDirectory ? this.properties.isServerEncrypted() : null;
+    }
+
+    /**
+     * Returns the tier of the blob. This is only set for Page blobs on a premium storage account or for Block blobs on
+     * blob storage or general purpose V2 account. Returns null if this is a virtual directory.
+     *
+     * @return the tier of the blob or null if this is a virtual directory
+     */
+    public AccessTier accessTier() {
+        return !this.isVirtualDirectory ? this.properties.getAccessTier() : null;
+    }
+
+    /**
+     * Returns the status of the tier being inferred for the blob. This is only set for Page blobs on a premium storage
+     * account or for Block blobs on blob storage or general purpose V2 account. Returns null if this is a virtual
+     * directory.
+     *
+     * @return the status of the tier being inferred for the blob or null if this is a virtual directory
+     */
+    public Boolean isAccessTierInferred() {
+        return !this.isVirtualDirectory ? this.properties.isAccessTierInferred() : null;
+    }
+
+    /**
+     * Returns the archive status of the blob. This is only for blobs on a blob storage and general purpose v2 account.
+     * Returns null if this is a virtual directory.
+     *
+     * @return the archive status of the blob or null if this is a virtual directory
+     */
+    public ArchiveStatus archiveStatus() {
+        return !this.isVirtualDirectory ? this.properties.getArchiveStatus() : null;
+    }
+
+    /**
+     * Returns the time when the access tier for the blob was last changed or null if this is a virtual directory.
+     *
+     * @return the time when the access tier for the blob was last changed or null if this is a virtual directory
+     */
+    public OffsetDateTime accessTierChangeTime() {
+        return !this.isVirtualDirectory ? this.properties.getAccessTierChangeTime() : null;
+    }
+
+    /**
+     * Returns the metadata associated with this blob or null if this is a virtual directory.
+     *
+     * @return the metadata associated with this blob or null if this is a virtual directory
+     */
+    public Map<String, String> metadata() {
+        return !this.isVirtualDirectory ? Collections.unmodifiableMap(this.properties.getMetadata()) : null;
+    }
+
+    /**
+     * Returns the time of last modification or null if this is a virtual directory.
+     * <p>
+     * Last access time is not supported by the blob service. In this case, it is typical for implementations to return
+     * the {@link #lastModifiedTime()}.
+     *
+     * @return the time of last modification or null if this is a virtual directory
+     */
+    @Override
+    public FileTime lastAccessTime() {
+        return !this.isVirtualDirectory ? FileTime.from(this.properties.getLastAccessedTime().toInstant()) : null;
+    }
+
+    /**
+     * Tells whether the file is a regular file with opaque content.
+     *
+     * @return whether the file is a regular file.
+     */
+    @Override
+    public boolean isRegularFile() {
+        return !this.isVirtualDirectory
+            && !this.properties.getMetadata().getOrDefault(AzureResource.DIR_METADATA_MARKER, "false").equals("true");
+    }
+
+    /**
+     * Tells whether the file is a directory.
+     * <p>
+     * Will return true if the directory is a concrete or virtual directory. See
+     * {@link AzureFileSystemProvider#createDirectory(Path, FileAttribute[])} for more information on virtual and
+     * concrete directories.
+     *
+     * @return whether the file is a directory
+     */
+    @Override
+    public boolean isDirectory() {
+        return !this.isRegularFile();
+    }
+
+    /**
+     * Tells whether the file is a virtual directory.
+     * <p>
+     * See {@link AzureFileSystemProvider#createDirectory(Path, FileAttribute[])} for more information on virtual and
+     * concrete directories.
+     *
+     * @return whether the file is a virtual directory
+     */
+    public boolean isVirtualDirectory() {
+        return this.isVirtualDirectory;
+    }
+
+    /**
+     * Tells whether the file is a symbolic link.
+     *
+     * @return false. Symbolic links are not supported.
+     */
+    @Override
+    public boolean isSymbolicLink() {
+        return false;
+    }
+
+    /**
+     * Tells whether the file is something other than a regular file, directory, or symbolic link.
+     *
+     * @return false. No other object types are supported.
+     */
+    @Override
+    public boolean isOther() {
+        return false;
+    }
+
+    /**
+     * Returns the size of the file (in bytes).
+     *
+     * @return the size of the file
+     */
+    @Override
+    public long size() {
+        return !this.isVirtualDirectory ? properties.getBlobSize() : 0;
+    }
+
+    /**
+     * Returns the url of the resource.
+     *
+     * @return The file key, which is the url.
+     */
+    @Override
+    public Object fileKey() {
+        return resource.getBlobClient().getBlobUrl();
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureDirectoryStream.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureDirectoryStream.java
new file mode 100644
index 00000000000..917f712ddfc
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureDirectoryStream.java
@@ -0,0 +1,189 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.BlobContainerClient;
+import com.azure.storage.blob.models.BlobItem;
+import com.azure.storage.blob.models.BlobListDetails;
+import com.azure.storage.blob.models.ListBlobsOptions;
+
+import java.io.IOException;
+import java.nio.file.DirectoryIteratorException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import java.util.Set;
+
+/**
+ * A type for iterating over the contents of a directory.
+ *
+ * This type is asynchronously closeable, i.e. closing the stream from any thread will cause the stream to stop
+ * returning elements at that point.
+ *
+ * {@inheritDoc}
+ */
+public final class AzureDirectoryStream implements DirectoryStream<Path> {
+    private static final ClientLogger LOGGER = new ClientLogger(AzureDirectoryStream.class);
+
+    private final AzurePath path;
+    private final DirectoryStream.Filter<? super Path> filter;
+    private boolean iteratorRequested = false;
+    private final AzureDirectoryIterator iterator;
+    boolean closed = false;
+
+    AzureDirectoryStream(AzurePath path, DirectoryStream.Filter<? super Path> filter) throws IOException {
+        this.path = path;
+        this.filter = filter;
+        this.iterator = new AzureDirectoryIterator(this, this.path, this.filter);
+    }
+
+    @Override
+    public Iterator<Path> iterator() {
+        if (this.iteratorRequested) {
+            throw LoggingUtility.logError(LOGGER,
+                new IllegalStateException("Only one iterator may be requested from a given directory stream"));
+        }
+        this.iteratorRequested = true;
+        return this.iterator;
+    }
+
+    @Override
+    public void close() throws IOException {
+        this.closed = true;
+    }
+
+    private static class AzureDirectoryIterator implements Iterator<Path> {
+        private static final ClientLogger LOGGER = new ClientLogger(AzureDirectoryIterator.class);
+
+        private final AzureDirectoryStream parentStream;
+        private final DirectoryStream.Filter<? super Path> filter;
+        private final Iterator<BlobItem> blobIterator;
+        private final AzurePath path;
+        private final Path withoutRoot;
+        private Path bufferedNext = null;
+        private final Set<String> directoryPaths;
+
+        AzureDirectoryIterator(AzureDirectoryStream parentStream, AzurePath path,
+            DirectoryStream.Filter<? super Path> filter) throws IOException {
+            this.parentStream = parentStream;
+            this.filter = filter;
+            this.path = path;
+
+            /*
+            Resolving two paths requires that either both have a root or neither does. Because the paths returned from
+            listing will never have a root, we prepare a copy of the list path without a root for quick resolving later.
+             */
+            Path root = this.path.getRoot();
+            this.withoutRoot = root == null ? this.path : root.relativize(this.path);
+
+            directoryPaths = new HashSet<>();
+
+            BlobContainerClient containerClient;
+            ListBlobsOptions listOptions = new ListBlobsOptions()
+                .setDetails(new BlobListDetails().setRetrieveMetadata(true));
+            if (path.isRoot()) {
+                String containerName = path.toString().substring(0, path.toString().length() - 1);
+                AzureFileSystem afs = ((AzureFileSystem) path.getFileSystem());
+                containerClient = ((AzureFileStore) afs.getFileStore(containerName)).getContainerClient();
+            } else {
+                AzureResource azureResource = new AzureResource(path);
+                listOptions.setPrefix(azureResource.getBlobClient().getBlobName() + AzureFileSystem.PATH_SEPARATOR);
+                containerClient = azureResource.getContainerClient();
+            }
+            this.blobIterator = containerClient
+                .listBlobsByHierarchy(AzureFileSystem.PATH_SEPARATOR, listOptions, null).iterator();
+        }
+
+        @Override
+        public boolean hasNext() {
+            AzurePath.ensureFileSystemOpen(path);
+
+            // Closing the parent stream halts iteration.
+            if (parentStream.closed) {
+                return false;
+            }
+
+            // In case a customer calls hasNext multiple times in a row. If we've buffered an element, we have a next.
+            if (this.bufferedNext != null) {
+                return true;
+            }
+
+            /*
+            Search for a new element that passes the filter and buffer it when found. If no such element is found,
+            return false.
+             */
+            while (this.blobIterator.hasNext()) {
+                BlobItem nextBlob = this.blobIterator.next();
+                Path nextPath = getNextListResult(nextBlob);
+                try {
+                    if (this.filter.accept(nextPath) && isNotDuplicate(nextPath, nextBlob)) {
+                        this.bufferedNext = nextPath;
+                        return true;
+                    }
+                } catch (IOException e) {
+                    throw LoggingUtility.logError(LOGGER, new DirectoryIteratorException(e));
+                }
+            }
+            return false;
+        }
+
+        @Override
+        public Path next() {
+            if (this.bufferedNext == null) {
+                if (!this.hasNext()) { // This will populate bufferedNext in the process.
+                    throw LoggingUtility.logError(LOGGER, new NoSuchElementException());
+                }
+            }
+            Path next = this.bufferedNext; // bufferedNext will have been populated by hasNext()
+            this.bufferedNext = null;
+            return next;
+        }
+
+        @Override
+        public void remove() {
+            throw LoggingUtility.logError(LOGGER, new UnsupportedOperationException());
+        }
+
+        private Path getNextListResult(BlobItem blobItem) {
+            /*
+            Listing results return the full blob path, and we don't want to duplicate the path we listed off of, so
+            we relativize to remove it.
+             */
+            String blobName = blobItem.getName();
+            Path relativeResult = this.withoutRoot.relativize(
+                this.path.getFileSystem().getPath(blobName));
+
+            // Resolve the cleaned list result against the original path for the final result.
+            return this.path.resolve(relativeResult);
+        }
+
+        /*
+        If there is a concrete directory with children, a given path will be returned twice: once as the marker blob
+        and once as the prefix for its children. We don't want to return the item twice, and we have no guarantees on
+        result ordering, so we have to maintain a cache of directory paths we've seen in order to de-dup.
+         */
+        private boolean isNotDuplicate(Path path, BlobItem blob) {
+            /*
+            If the blob is not a prefix and the blob does not contain the directory metadata marker, it is a normal blob
+            and therefore will not be duplicated.
+             */
+            if (!(blob.isPrefix() != null && blob.isPrefix())
+                && !(blob.getMetadata() != null && blob.getMetadata().containsKey(AzureResource.DIR_METADATA_MARKER))) {
+                return true;
+            }
+
+            // If the set contains this path, it means we've seen it before and we shouldn't return it again.
+            if (this.directoryPaths.contains(path.toString())) {
+                return false;
+            }
+
+            // We haven't seen this before. Track it and indicate it should be returned.
+            this.directoryPaths.add(path.toString());
+            return true;
+        }
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileStore.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileStore.java
new file mode 100644
index 00000000000..bbe361864bc
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileStore.java
@@ -0,0 +1,194 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.BlobContainerClient;
+
+import java.io.IOException;
+import java.nio.file.FileStore;
+import java.nio.file.attribute.FileAttributeView;
+import java.nio.file.attribute.FileStoreAttributeView;
+import java.util.Objects;
+
+/**
+ * An {@code AzureFileStore} is a {@link FileStore} backed by an Azure Blob Storage container.
+ */
+public final class AzureFileStore extends FileStore {
+    private static final ClientLogger LOGGER = new ClientLogger(AzureFileStore.class);
+
+    private static final String AZURE_FILE_STORE_TYPE = "AzureBlobContainer";
+
+    private final AzureFileSystem parentFileSystem;
+    private final BlobContainerClient containerClient;
+
+
+    AzureFileStore(AzureFileSystem parentFileSystem, String containerName, Boolean skipConnectionCheck)
+        throws IOException {
+        // A FileStore should only ever be created by a FileSystem.
+        if (Objects.isNull(parentFileSystem)) {
+            throw LoggingUtility.logError(LOGGER, new IllegalStateException("AzureFileStore cannot be instantiated "
+                + "without a parent FileSystem"));
+        }
+        this.parentFileSystem = parentFileSystem;
+        this.containerClient = this.parentFileSystem.getBlobServiceClient().getBlobContainerClient(containerName);
+
+        if (skipConnectionCheck == null || !skipConnectionCheck) {
+            try {
+                // This also serves as our connection check.
+                if (!this.containerClient.exists()) {
+                    this.containerClient.create();
+                }
+            } catch (Exception e) {
+                throw LoggingUtility.logError(LOGGER, new IOException("There was an error in establishing the existence of "
+                    + "container: " + containerName, e));
+            }
+        }
+    }
+
+    /**
+     * Returns the name of the container that underlies this file store.
+     *
+     * @return the name of the container that underlies this file store.
+     */
+    @Override
+    public String name() {
+        return this.containerClient.getBlobContainerName();
+    }
+
+    /**
+     * Returns the {@code String "AzureBlobContainer"} to indicate that the file store is backed by a remote blob
+     * container in Azure Storage.
+     *
+     * @return {@code "AzureBlobContainer"}
+     */
+    @Override
+    public String type() {
+        return AZURE_FILE_STORE_TYPE;
+    }
+
+    /**
+     * Always returns false.
+     * <p>
+     * It may be the case that the authentication method provided to this file system only
+     * supports read operations and hence the file store is implicitly read only in this view, but that does not
+     * imply the underlying container/file store is inherently read only. Creating/specifying read only file stores
+     * is not currently supported.
+     *
+     * @return false.
+     */
+    @Override
+    public boolean isReadOnly() {
+        return false;
+    }
+
+    /**
+     * Returns the size, in bytes, of the file store.
+     * <p>
+     * Containers do not limit the amount of data stored. This method will always return max long.
+     *
+     * @return the size of the file store.
+     * @throws IOException If an I/O error occurs.
+     */
+    @Override
+    public long getTotalSpace() throws IOException {
+        return Long.MAX_VALUE;
+    }
+
+    /**
+     * Returns the number of bytes available to this Java virtual machine on the file store.
+     * <p>
+     * Containers do not limit the amount of data stored. This method will always return max long.
+     *
+     * @return the number of bytes available on the file store.
+     * @throws IOException If an I/O error occurs.
+     */
+    @Override
+    public long getUsableSpace() throws IOException {
+        return Long.MAX_VALUE;
+    }
+
+    /**
+     * Returns the number of unallocated bytes in the file store.
+     * <p>
+     * Containers do not limit the amount of data stored. This method will always return max long.
+     *
+     * @return the number of unallocated bytes in the file store.
+     * @throws IOException If an I/O error occurs.
+     */
+    @Override
+    public long getUnallocatedSpace() throws IOException {
+        return Long.MAX_VALUE;
+    }
+
+    /**
+     * Tells whether this file store supports the file attributes identified by the given file attribute view.
+     * <p>
+     * All file stores in this file system support the following views:
+     * <ul>
+     *     <li>{@link java.nio.file.attribute.BasicFileAttributeView}</li>
+     *     <li>{@link AzureBasicFileAttributeView}</li>
+     *     <li>{@link AzureBlobFileAttributeView}</li>
+     * </ul>
+     *
+     * @param type the file attribute view type
+     * @return Whether the file attribute view is supported.
+     */
+    @Override
+    public boolean supportsFileAttributeView(Class<? extends FileAttributeView> type) {
+        return AzureFileSystem.SUPPORTED_ATTRIBUTE_VIEWS.containsKey(type);
+    }
+
+    /**
+     * Tells whether this file store supports the file attributes identified by the given file attribute view.
+     * <p>
+     * All file stores in this file system support the following views:
+     * <ul>
+     *     <li>{@link java.nio.file.attribute.BasicFileAttributeView}</li>
+     *     <li>{@link AzureBasicFileAttributeView}</li>
+     *     <li>{@link AzureBlobFileAttributeView}</li>
+     * </ul>
+     *
+     * @param name the name of the file attribute view
+     * @return whether the file attribute view is supported.
+     */
+    @Override
+    public boolean supportsFileAttributeView(String name) {
+        return AzureFileSystem.SUPPORTED_ATTRIBUTE_VIEWS.containsValue(name);
+    }
+
+    /**
+     * Returns a FileStoreAttributeView of the given type.
+     * <p>
+     * This method always returns null as no {@link FileStoreAttributeView} is currently supported.
+     *
+     * @param aClass a class
+     * @return null
+     */
+    @Override
+    public <V extends FileStoreAttributeView> V getFileStoreAttributeView(Class<V> aClass) {
+        return null;
+    }
+
+    /**
+     * Unsupported.
+     * <p>
+     * This method always throws an {@code UnsupportedOperationException} as no {@link FileStoreAttributeView} is
+     * currently supported.
+     *
+     * @param s a string
+     * @return The attribute value.
+     * @throws UnsupportedOperationException unsupported
+     * @throws IOException never
+     */
+    @Override
+    public Object getAttribute(String s) throws IOException {
+        throw LoggingUtility.logError(LOGGER, new UnsupportedOperationException("FileStoreAttributeViews aren't"
+            + " supported."));
+    }
+
+    BlobContainerClient getContainerClient() {
+        return this.containerClient;
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
new file mode 100644
index 00000000000..6f981b1b45e
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
@@ -0,0 +1,492 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import com.azure.core.credential.AzureSasCredential;
+import com.azure.core.http.HttpClient;
+import com.azure.core.http.policy.HttpLogDetailLevel;
+import com.azure.core.http.policy.HttpPipelinePolicy;
+import com.azure.core.util.CoreUtils;
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.BlobServiceClient;
+import com.azure.storage.blob.BlobServiceClientBuilder;
+import com.azure.storage.blob.implementation.util.BlobUserAgentModificationPolicy;
+import com.azure.storage.common.StorageSharedKeyCredential;
+import com.azure.storage.common.policy.RequestRetryOptions;
+import com.azure.storage.common.policy.RetryPolicyType;
+
+import java.io.IOException;
+import java.nio.file.FileStore;
+import java.nio.file.FileSystem;
+import java.nio.file.InvalidPathException;
+import java.nio.file.Path;
+import java.nio.file.PathMatcher;
+import java.nio.file.WatchService;
+import java.nio.file.attribute.BasicFileAttributeView;
+import java.nio.file.attribute.FileAttributeView;
+import java.nio.file.attribute.UserPrincipalLookupService;
+import java.nio.file.spi.FileSystemProvider;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Set;
+import java.util.regex.PatternSyntaxException;
+import java.util.stream.Collectors;
+
+/**
+ * Implement's Java's {@link FileSystem} interface for Azure Blob Storage.
+ * <p>
+ * The following behavior is specific to this FileSystem:
+ * <p>
+ * In the hierarchy of this file system, an {@code AzureFileSystem} corresponds to an Azure Blob Storage account. A
+ * file store is represented by a container in the storage account. Each container has one root directory.
+ * <p>
+ * Closing the file system will not block on outstanding operations. Any operations in progress will be allowed to
+ * terminate naturally after the file system is closed, though no further operations may be started after the parent
+ * file system is closed.
+ * <p>
+ * All instance of {@code AzureFileSystem} are opened for read-write access.
+ * <p>
+ * For a more complete description of the uses for the constants described here, please see the instructions for opening
+ * and configuring a FileSystem in the docs of {@link FileSystemProvider}.
+ */
+public final class AzureFileSystem extends FileSystem {
+    private static final ClientLogger LOGGER = new ClientLogger(AzureFileSystem.class);
+
+    // Configuration constants for blob clients.
+    /**
+     * Expected type: String
+     */
+    public static final String AZURE_STORAGE_SHARED_KEY_CREDENTIAL = "AzureStorageSharedKeyCredential";
+
+    /**
+     * Expected type: String
+     */
+    public static final String AZURE_STORAGE_SAS_TOKEN_CREDENTIAL = "AzureStorageSasTokenCredential";
+
+    /**
+     * Expected type: com.azure.core.http.policy.HttpLogLevelDetail
+     */
+    public static final String AZURE_STORAGE_HTTP_LOG_DETAIL_LEVEL = "AzureStorageHttpLogDetailLevel";
+
+    /**
+     * Expected type: Integer
+     */
+    public static final String AZURE_STORAGE_MAX_TRIES = "AzureStorageMaxTries";
+
+    /**
+     * Expected type: Integer
+     */
+    public static final String AZURE_STORAGE_TRY_TIMEOUT = "AzureStorageTryTimeout";
+
+    /**
+     * Expected type: Long
+     */
+    public static final String AZURE_STORAGE_RETRY_DELAY_IN_MS = "AzureStorageRetryDelayInMs";
+
+    /**
+     * Expected type: Long
+     */
+    public static final String AZURE_STORAGE_MAX_RETRY_DELAY_IN_MS = "AzureStorageMaxRetryDelayInMs";
+
+    /**
+     * Expected type: com.azure.storage.common.policy.RetryPolicyType
+     */
+    public static final String AZURE_STORAGE_RETRY_POLICY_TYPE = "AzureStorageRetryPolicyType";
+
+    /**
+     * Expected type: String
+     */
+    public static final String AZURE_STORAGE_SECONDARY_HOST = "AzureStorageSecondaryHost";
+
+    /**
+     * Expected type: Long
+     */
+    public static final String AZURE_STORAGE_UPLOAD_BLOCK_SIZE = "AzureStorageUploadBlockSize";
+
+    /**
+     * Expected type: Integer
+     */
+    public static final String AZURE_STORAGE_MAX_CONCURRENCY_PER_REQUEST = "AzureStorageMaxConcurrencyPerRequest";
+
+    /**
+     * Expected type: Long
+     */
+    public static final String AZURE_STORAGE_PUT_BLOB_THRESHOLD = "AzureStoragePutBlobThreshold";
+
+    /**
+     * Expected type: Integer
+     */
+    public static final String AZURE_STORAGE_DOWNLOAD_RESUME_RETRIES = "AzureStorageDownloadResumeRetries";
+
+    static final String AZURE_STORAGE_HTTP_CLIENT = "AzureStorageHttpClient"; // undocumented; for test.
+    static final String AZURE_STORAGE_HTTP_POLICIES = "AzureStorageHttpPolicies"; // undocumented; for test.
+
+    /**
+     * Expected type: String
+     */
+    public static final String AZURE_STORAGE_FILE_STORES = "AzureStorageFileStores";
+
+    /**
+     * Expected type: Boolean
+     */
+    public static final String AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK = "AzureStorageSkipInitialContainerCheck";
+
+    static final String PATH_SEPARATOR = "/";
+
+    private static final Map<String, String> PROPERTIES =
+        CoreUtils.getProperties("azure-storage-blob-nio.properties");
+    private static final String SDK_NAME = "name";
+    private static final String SDK_VERSION = "version";
+    private static final String CLIENT_NAME = PROPERTIES.getOrDefault(SDK_NAME, "UnknownName");
+    private static final String CLIENT_VERSION = PROPERTIES.getOrDefault(SDK_VERSION, "UnknownVersion");
+
+    static final Map<Class<? extends FileAttributeView>, String> SUPPORTED_ATTRIBUTE_VIEWS;
+    static {
+        Map<Class<? extends FileAttributeView>, String> map = new HashMap<>();
+        map.put(BasicFileAttributeView.class, "basic");
+        map.put(AzureBasicFileAttributeView.class, "azureBasic");
+        map.put(AzureBlobFileAttributeView.class, "azureBlob");
+        SUPPORTED_ATTRIBUTE_VIEWS = Collections.unmodifiableMap(map);
+    }
+
+    private final AzureFileSystemProvider parentFileSystemProvider;
+    private final BlobServiceClient blobServiceClient;
+    private final Long blockSize;
+    private final Long putBlobThreshold;
+    private final Integer maxConcurrencyPerRequest;
+    private final Integer downloadResumeRetries;
+    private final Map<String, FileStore> fileStores;
+    private FileStore defaultFileStore;
+    private boolean closed;
+
+    AzureFileSystem(AzureFileSystemProvider parentFileSystemProvider, String endpoint, Map<String, ?> config)
+            throws IOException {
+        // A FileSystem should only ever be instantiated by a provider.
+        if (Objects.isNull(parentFileSystemProvider)) {
+            throw LoggingUtility.logError(LOGGER, new IllegalArgumentException("AzureFileSystem cannot be instantiated"
+                + " without a parent FileSystemProvider"));
+        }
+        this.parentFileSystemProvider = parentFileSystemProvider;
+
+        // Read configurations and build client.
+        try {
+            this.blobServiceClient = this.buildBlobServiceClient(endpoint, config);
+            this.blockSize = (Long) config.get(AZURE_STORAGE_UPLOAD_BLOCK_SIZE);
+            this.putBlobThreshold = (Long) config.get(AZURE_STORAGE_PUT_BLOB_THRESHOLD);
+            this.maxConcurrencyPerRequest = (Integer) config.get(AZURE_STORAGE_MAX_CONCURRENCY_PER_REQUEST);
+            this.downloadResumeRetries = (Integer) config.get(AZURE_STORAGE_DOWNLOAD_RESUME_RETRIES);
+
+            // Initialize and ensure access to FileStores.
+            this.fileStores = this.initializeFileStores(config);
+        } catch (RuntimeException e) {
+            throw LoggingUtility.logError(LOGGER, new IllegalArgumentException("There was an error parsing the "
+                + "configurations map. Please ensure all fields are set to a legal value of the correct type.", e));
+        } catch (IOException e) {
+            throw LoggingUtility.logError(LOGGER,
+                new IOException("Initializing FileStores failed. FileSystem could not be opened.", e));
+        }
+
+        this.closed = false;
+    }
+
+    /**
+     * Returns the provider that created this file system.
+     *
+     * @return the provider that created this file system.
+     */
+    @Override
+    public FileSystemProvider provider() {
+        return this.parentFileSystemProvider;
+    }
+
+    /**
+     * Closes this file system.
+     * <p>
+     * After a file system is closed then all subsequent access to the file system, either by methods defined by this
+     * class or on objects associated with this file system, throw ClosedFileSystemException. If the file system is
+     * already closed then invoking this method has no effect.
+     * <p>
+     * Closing the file system will not block on outstanding operations. Any operations in progress will be allowed to
+     * terminate naturally after the file system is closed, though no further operations may be started after the
+     * parent file system is closed.
+     * <p>
+     * Once closed, a file system with the same identifier as the one closed may be re-opened.
+     *
+     * @throws IOException If an I/O error occurs.
+     */
+    @Override
+    public void close() throws IOException {
+        this.closed = true;
+        this.parentFileSystemProvider.closeFileSystem(this.getFileSystemUrl());
+    }
+
+    /**
+     * Tells whether this file system is open.
+     *
+     * @return whether this file system is open.
+     */
+    @Override
+    public boolean isOpen() {
+        return !this.closed;
+    }
+
+    /**
+     * Tells whether this file system allows only read-only access to its file stores.
+     * <p>
+     * Always returns false. It may be the case that the authentication method provided to this file system only
+     * supports read operations and hence the file system is implicitly read only in this view, but that does not
+     * imply the underlying account/file system is inherently read only. Creating/specifying read only file
+     * systems is not supported.
+     *
+     * @return false
+     */
+    @Override
+    public boolean isReadOnly() {
+        return false;
+    }
+
+    /**
+     * Returns the name separator, represented as a string.
+     * <p>
+     * The separator used in this file system is {@code "/"}.
+     *
+     * @return "/"
+     */
+    @Override
+    public String getSeparator() {
+        return AzureFileSystem.PATH_SEPARATOR;
+    }
+
+    /**
+     * Returns an object to iterate over the paths of the root directories.
+     * <p>
+     * The list of root directories corresponds to the list of available file stores and therefore containers specified
+     * upon initialization. A root directory always takes the form {@code "<file-store-name>:"}. This list will
+     * respect the parameters provided during initialization.
+     * <p>
+     * If a finite list of containers was provided on start up, this list will not change during the lifetime of this
+     * object. If containers are added to the account after initialization, they will be ignored. If a container is
+     * deleted or otherwise becomes unavailable, its root directory will still be returned but operations to it will
+     * fail.
+     *
+     * @return an object to iterate over the paths of the root directories
+     */
+    @Override
+    public Iterable<Path> getRootDirectories() {
+        /*
+        Should we add different initialization options later:
+        If the file system was set to use all containers in the account, the account will be re-queried and the
+        list may grow or shrink if containers were added or deleted.
+         */
+        return fileStores.keySet().stream()
+            .map(name -> this.getPath(name + AzurePath.ROOT_DIR_SUFFIX))
+            .collect(Collectors.toList());
+    }
+
+    /**
+     * Returns an object to iterate over the underlying file stores
+     * <p>
+     * This list will respect the parameters provided during initialization.
+     * <p>
+     * If a finite list of containers was provided on start up, this list will not change during the lifetime of this
+     * object. If containers are added to the account after initialization, they will be ignored. If a container is
+     * deleted or otherwise becomes unavailable, its root directory will still be returned but operations to it will
+     * fail.
+     */
+    @Override
+    public Iterable<FileStore> getFileStores() {
+        /*
+        Should we add different initialization options later:
+        If the file system was set to use all containers in the account, the account will be re-queried and the
+        list may grow or shrink if containers were added or deleted.
+         */
+        return this.fileStores.values();
+    }
+
+    /**
+     * Returns the set of the names of the file attribute views supported by this FileSystem.
+     * <p>
+     * This file system supports the following views:
+     * <ul>
+     *     <li>{@link java.nio.file.attribute.BasicFileAttributeView}</li>
+     *     <li>{@link AzureBasicFileAttributeView}</li>
+     *     <li>{@link AzureBlobFileAttributeView}</li>
+     * </ul>
+     */
+    @Override
+    public Set<String> supportedFileAttributeViews() {
+        return new HashSet<>(SUPPORTED_ATTRIBUTE_VIEWS.values());
+    }
+
+    /**
+     * Converts a path string, or a sequence of more that when joined form a path string, to a Path.
+     * <p>
+     * If more does not specify any elements then the value of the first parameter is the path string to convert. If
+     * more specifies one or more elements than each non-empty string, including first, is considered to be a sequence
+     * of name elements (see Path) and is joined to form a path string. The more will be joined using the name
+     * separator.
+     * <p>
+     * Each name element will be {@code String}-joined to the other elements by this file system's first path separator.
+     * Naming conventions and allowed characters are as
+     * <a href="https://docs.microsoft.com/en-us/rest/api/storageservices/Naming-and-Referencing-Containers--Blobs--and-Metadata">defined</a>
+     * by the Azure Blob Storage service. The root component is interpreted as the container name and all name elements
+     * are interpreted as a part of the blob name. The character {@code ':'} is only allowed in the root component and
+     * must be the last character of the root component.
+     *
+     * @param first the path string or initial part of the path string
+     * @param more additional strings to be joined to form the path string
+     * @throws InvalidPathException if the path string cannot be converted.
+     */
+    @Override
+    public Path getPath(String first, String... more) {
+        return new AzurePath(this, first, more);
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @param s the matcher
+     * @throws UnsupportedOperationException unsupported.
+     * @throws IllegalArgumentException never
+     * @throws PatternSyntaxException never
+     */
+    @Override
+    public PathMatcher getPathMatcher(String s) throws IllegalArgumentException, PatternSyntaxException {
+        throw LoggingUtility.logError(LOGGER, new UnsupportedOperationException());
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @throws UnsupportedOperationException unsupported.
+     */
+    @Override
+    public UserPrincipalLookupService getUserPrincipalLookupService() {
+        throw LoggingUtility.logError(LOGGER, new UnsupportedOperationException());
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @throws UnsupportedOperationException unsupported.
+     * @throws IOException Never thrown.
+     */
+    @Override
+    public WatchService newWatchService() throws IOException {
+        throw LoggingUtility.logError(LOGGER, new UnsupportedOperationException());
+    }
+
+    String getFileSystemUrl() {
+        return this.blobServiceClient.getAccountUrl();
+    }
+
+    BlobServiceClient getBlobServiceClient() {
+        return this.blobServiceClient;
+    }
+
+    private BlobServiceClient buildBlobServiceClient(String endpoint, Map<String, ?> config) {
+        BlobServiceClientBuilder builder = new BlobServiceClientBuilder()
+                .endpoint(endpoint);
+
+        // Set the credentials.
+        if (config.containsKey(AZURE_STORAGE_SHARED_KEY_CREDENTIAL)) {
+            builder.credential((StorageSharedKeyCredential) config.get(AZURE_STORAGE_SHARED_KEY_CREDENTIAL));
+        } else if (config.containsKey(AZURE_STORAGE_SAS_TOKEN_CREDENTIAL)) {
+            builder.credential((AzureSasCredential) config.get(AZURE_STORAGE_SAS_TOKEN_CREDENTIAL));
+        } else {
+            throw LoggingUtility.logError(LOGGER, new IllegalArgumentException(String.format("No credentials were "
+                    + "provided. Please specify one of the following when constructing an AzureFileSystem: %s, %s.",
+                AZURE_STORAGE_SHARED_KEY_CREDENTIAL, AZURE_STORAGE_SAS_TOKEN_CREDENTIAL)));
+        }
+
+        // Configure options and client.
+        builder.httpLogOptions(BlobServiceClientBuilder.getDefaultHttpLogOptions()
+            .setLogLevel((HttpLogDetailLevel) config.get(AZURE_STORAGE_HTTP_LOG_DETAIL_LEVEL)));
+
+        RequestRetryOptions retryOptions = new RequestRetryOptions(
+            (RetryPolicyType) config.get(AZURE_STORAGE_RETRY_POLICY_TYPE),
+            (Integer) config.get(AZURE_STORAGE_MAX_TRIES),
+            (Integer) config.get(AZURE_STORAGE_TRY_TIMEOUT),
+            (Long) config.get(AZURE_STORAGE_RETRY_DELAY_IN_MS),
+            (Long) config.get(AZURE_STORAGE_MAX_RETRY_DELAY_IN_MS),
+            (String) config.get(AZURE_STORAGE_SECONDARY_HOST));
+        builder.retryOptions(retryOptions);
+
+        builder.httpClient((HttpClient) config.get(AZURE_STORAGE_HTTP_CLIENT));
+
+        // Add BlobUserAgentModificationPolicy
+        builder.addPolicy(new BlobUserAgentModificationPolicy(CLIENT_NAME, CLIENT_VERSION));
+
+        if (config.containsKey(AZURE_STORAGE_HTTP_POLICIES)) {
+            for (HttpPipelinePolicy policy : (HttpPipelinePolicy[]) config.get(AZURE_STORAGE_HTTP_POLICIES)) {
+                builder.addPolicy(policy);
+            }
+        }
+
+        return builder.buildClient();
+    }
+
+    private Map<String, FileStore> initializeFileStores(Map<String, ?> config) throws IOException {
+        String fileStoreNames = (String) config.get(AZURE_STORAGE_FILE_STORES);
+        if (CoreUtils.isNullOrEmpty(fileStoreNames)) {
+            throw LoggingUtility.logError(LOGGER, new IllegalArgumentException("The list of FileStores cannot be "
+                + "null."));
+        }
+
+        Boolean skipConnectionCheck = (Boolean) config.get(AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK);
+        Map<String, FileStore> fileStores = new HashMap<>();
+        for (String fileStoreName : fileStoreNames.split(",")) {
+            FileStore fs = new AzureFileStore(this, fileStoreName, skipConnectionCheck);
+            if (this.defaultFileStore == null) {
+                this.defaultFileStore = fs;
+            }
+            fileStores.put(fileStoreName, fs);
+        }
+        return fileStores;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
+        AzureFileSystem that = (AzureFileSystem) o;
+        return Objects.equals(this.getFileSystemUrl(), that.getFileSystemUrl());
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(this.getFileSystemUrl());
+    }
+
+    Path getDefaultDirectory() {
+        return this.getPath(this.defaultFileStore.name() + AzurePath.ROOT_DIR_SUFFIX);
+    }
+
+    FileStore getFileStore(String name) throws IOException {
+        FileStore store = this.fileStores.get(name);
+        if (store == null) {
+            throw LoggingUtility.logError(LOGGER, new IOException("Invalid file store: " + name));
+        }
+        return store;
+    }
+
+    Long getBlockSize() {
+        return this.blockSize;
+    }
+
+    Long getPutBlobThreshold() {
+        return this.putBlobThreshold;
+    }
+
+    Integer getMaxConcurrencyPerRequest() {
+        return this.maxConcurrencyPerRequest;
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystemProvider.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystemProvider.java
new file mode 100644
index 00000000000..6881341d218
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystemProvider.java
@@ -0,0 +1,1182 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.UncheckedIOException;
+import java.net.HttpURLConnection;
+import java.net.URI;
+import java.nio.channels.SeekableByteChannel;
+import java.nio.file.AccessDeniedException;
+import java.nio.file.AccessMode;
+import java.nio.file.CopyOption;
+import java.nio.file.DirectoryNotEmptyException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.FileAlreadyExistsException;
+import java.nio.file.FileStore;
+import java.nio.file.FileSystem;
+import java.nio.file.FileSystemAlreadyExistsException;
+import java.nio.file.FileSystemNotFoundException;
+import java.nio.file.Files;
+import java.nio.file.LinkOption;
+import java.nio.file.NoSuchFileException;
+import java.nio.file.NotDirectoryException;
+import java.nio.file.OpenOption;
+import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
+import java.nio.file.StandardOpenOption;
+import java.nio.file.attribute.BasicFileAttributeView;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.nio.file.attribute.FileAttribute;
+import java.nio.file.attribute.FileAttributeView;
+import java.nio.file.spi.FileSystemProvider;
+import java.time.Duration;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentMap;
+import java.util.function.Consumer;
+import java.util.function.Supplier;
+
+import com.azure.core.util.CoreUtils;
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.core.util.polling.SyncPoller;
+import com.azure.storage.blob.models.BlobCopyInfo;
+import com.azure.storage.blob.models.BlobErrorCode;
+import com.azure.storage.blob.models.BlobRequestConditions;
+import com.azure.storage.blob.models.BlobStorageException;
+import com.azure.storage.blob.models.ParallelTransferOptions;
+
+import reactor.core.publisher.Flux;
+import reactor.core.publisher.Mono;
+
+/**
+ * The {@code AzureFileSystemProvider} is Azure Storage's implementation of the nio interface on top of Azure Blob
+ * Storage.
+ * <p>
+ * Particular care should be taken when working with a remote storage service. This implementation makes no guarantees
+ * on behavior or state should other processes operate on the same data concurrently; file systems from this provider
+ * will assume they have exclusive access to their data and will behave without regard for potential of interfering
+ * applications. Moreover, remote file stores introduce higher latencies. Therefore, additional consideration should be
+ * given to managing concurrency: race conditions are more likely to manifest and network failures occur more frequently
+ * than disk failures. These and other such distributed application scenarios must be considered when working with this
+ * file system. While the {@code AzureFileSystem} will ensure it takes appropriate steps towards robustness and
+ * reliability, the application developer must design around these failure scenarios and have fallback and retry options
+ * available.
+ * <p>
+ * The Azure Blob Storage service backing these APIs is not a true FileSystem, nor is it the goal of this implementation
+ * to force Azure Blob Storage to act like a full-fledged file system. Some APIs and scenarios will remain unsupported
+ * indefinitely until they may be sensibly implemented. Other APIs may experience lower performance than is expected
+ * because of the number of network requests needed to ensure correctness. The javadocs for each type and method should
+ * also be read carefully to understand what guarantees are made and how they may differ from the contract defined by
+ * {@link FileSystemProvider}.
+ * <p>
+ * The scheme for this provider is {@code "azb"}, and the format of the URI to identify an {@code AzureFileSystem} is
+ * {@code "azb://?endpoint=<endpoint>"}. The endpoint of the Storage account is used to uniquely identify the
+ * filesystem.
+ * <p>
+ * An {@link AzureFileSystem} is backed by an account. An {@link AzureFileStore} is backed by a container. Any number of
+ * containers may be specified as file stores upon creation of the file system. When a file system is created,
+ * it will try to retrieve the properties of each container to ensure connection to the account. If any of the
+ * containers does not exist, it will be created. Failure to access or create containers as necessary will result in
+ * an exception and failure to create the file system. Any data existing in the containers will be preserved and
+ * accessible via the file system, though customers should be aware that it must be in a format understandable by
+ * the types in this package or behavior will be undefined.
+ * <p>
+ * {@link #newFileSystem(URI, Map)} will check for the following keys in the configuration map and expect the named
+ * types. Any entries not listed here will be ignored. Note that {@link AzureFileSystem} has public constants defined
+ * for each of the keys for convenience. Most values are documented in the blob package. Any values which are unique to
+ * nio will be documented here.
+ * <ul>
+ *     <li>{@code AzureStorageSharedKeyCredential:}{@link com.azure.storage.common.StorageSharedKeyCredential}</li>
+ *     <li>{@code AzureStorageSasTokenCredential:}{@link com.azure.core.credential.AzureSasCredential}</li>
+ *     <li>{@code AzureStorageHttpLogDetailLevel:}{@link com.azure.core.http.policy.HttpLogDetailLevel}</li>
+ *     <li>{@code AzureStorageMaxTries:}{@link Integer}</li>
+ *     <li>{@code AzureStorageTryTimeout:}{@link Integer}</li>
+ *     <li>{@code AzureStorageRetryDelayInMs:}{@link Long}</li>
+ *     <li>{@code AzureStorageMaxRetryDelayInMs:}{@link Long}</li>
+ *     <li>{@code AzureStorageRetryPolicyType:}{@link com.azure.storage.common.policy.RetryPolicyType}</li>
+ *     <li>{@code AzureStorageSecondaryHost:}{@link String}</li>
+ *     <li>{@code AzureStorageSecondaryHost:}{@link Integer}</li>
+ *     <li>{@code AzureStorageBlockSize:}{@link Long}</li>
+ *     <li>{@code AzureStoragePutBlobThreshold:}{@link Long}</li>
+ *     <li>{@code AzureStorageMaxConcurrencyPerRequest:}{@link Integer}</li>
+ *     <li>{@code AzureStorageDownloadResumeRetries:}{@link Integer}</li>
+ *     <li>{@code AzureStorageFileStores:}{@link String}</li>
+ *     <li>{@code AzureStorageSkipInitialContainerCheck:}{@link Boolean}. Indicates that the initial check which
+ *     confirms the existence of the containers meant to act as file stores should be skipped. This can be useful in
+ *     cases where a sas token that is scoped to only one file is used to authenticate.</li>
+ * </ul>
+ * <p>
+ * Either an account key or a sas token must be specified. If both are provided, the account key will be preferred. If
+ * a sas token is specified, the customer must take care that it has appropriate permissions to perform the actions
+ * demanded of the file system in a given workflow, including the initial connection check specified above. The same
+ * token will be applied to all operations.
+ * <p>
+ * An iterable of file stores must also be provided; each entry should simply be the name of a container. The first
+ * container listed will be considered the default file store and the root directory of which will be the file system's
+ * default directory. All other values listed are used to configure the underlying
+ * {@link com.azure.storage.blob.BlobServiceClient}. Please refer to that type for more information on these values.
+ *
+ * @see FileSystemProvider
+ */
+public final class AzureFileSystemProvider extends FileSystemProvider {
+    /*
+     * A static inner class is used to hold the ClientLogger for AzureFileSystemProvider to defer creating the
+     * ClientLogger until logging is needed. Some implementations of SLF4J may make calls to load FileSystemProviders
+     * which results in a load FileSystemProviders to occur during a call to load FileSystemProviders. This results in
+     * the JVM to throw an exception that a circular call to load FileSystemProviders has occurred.
+     */
+    private static final class ClientLoggerHolder {
+        private static final ClientLogger LOGGER = new ClientLogger(AzureFileSystemProvider.class);
+    }
+
+    /**
+     * A helper for setting the HTTP properties when creating a directory.
+     */
+    public static final String CONTENT_TYPE = "Content-Type";
+
+    /**
+     * A helper for setting the HTTP properties when creating a directory.
+     */
+    public static final String CONTENT_DISPOSITION = "Content-Disposition";
+
+    /**
+     * A helper for setting the HTTP properties when creating a directory.
+     */
+    public static final String CONTENT_LANGUAGE = "Content-Language";
+
+    /**
+     * A helper for setting the HTTP properties when creating a directory.
+     */
+    public static final String CONTENT_ENCODING = "Content-Encoding";
+
+    /**
+     * A helper for setting the HTTP properties when creating a directory.
+     */
+    public static final String CONTENT_MD5 = "Content-MD5";
+
+    /**
+     * A helper for setting the HTTP properties when creating a directory.
+     */
+    public static final String CACHE_CONTROL = "Cache-Control";
+
+    private static final String ENDPOINT_QUERY_KEY = "endpoint";
+    private static final int COPY_TIMEOUT_SECONDS = 30;
+    private static final Set<OpenOption> OUTPUT_STREAM_DEFAULT_OPTIONS =
+        Collections.unmodifiableSet(new HashSet<>(Arrays.asList(StandardOpenOption.CREATE,
+            StandardOpenOption.WRITE,
+            StandardOpenOption.TRUNCATE_EXISTING)));
+    private static final Set<OpenOption> OUTPUT_STREAM_SUPPORTED_OPTIONS =
+        Collections.unmodifiableSet(new HashSet<>(Arrays.asList(
+            StandardOpenOption.CREATE_NEW,
+            StandardOpenOption.CREATE,
+            StandardOpenOption.WRITE,
+            // Though we don't actually truncate, the same result is achieved by overwriting the destination.
+            StandardOpenOption.TRUNCATE_EXISTING)));
+
+    private final ConcurrentMap<String, FileSystem> openFileSystems;
+
+
+    // Specs require a public zero argument constructor.
+    /**
+     * Creates an AzureFileSystemProvider.
+     */
+    public AzureFileSystemProvider() {
+        this.openFileSystems = new ConcurrentHashMap<>();
+    }
+
+    /**
+     * Returns the URI scheme that identifies this provider: {@code "azb".}
+     *
+     * @return {@code "azb"}
+     */
+    @Override
+    public String getScheme() {
+        return "azb";
+    }
+
+    /**
+     * Constructs a new FileSystem object identified by a URI.
+     * <p>
+     * The format of a {@code URI} identifying a file system is {@code "azb://?endpoint=<endpoint>"}.
+     * <p>
+     * Once closed, a file system with the same identifier may be reopened.
+     *
+     * @param uri URI reference
+     * @param config A map of provider specific properties to configure the file system
+     * @return a new file system.
+     * @throws IllegalArgumentException If the pre-conditions for the uri parameter aren't met, or the env parameter
+     * does not contain properties required by the provider, or a property value is invalid.
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     * @throws FileSystemAlreadyExistsException If the file system has already been created.
+     */
+    @Override
+    public FileSystem newFileSystem(URI uri, Map<String, ?> config) throws IOException {
+        String endpoint = extractAccountEndpoint(uri);
+
+        if (this.openFileSystems.containsKey(endpoint)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new FileSystemAlreadyExistsException("Name: " + endpoint));
+        }
+
+        AzureFileSystem afs = new AzureFileSystem(this, endpoint, config);
+        this.openFileSystems.put(endpoint, afs);
+
+        return afs;
+    }
+
+    /**
+     * Returns an existing FileSystem created by this provider.
+     * <p>
+     * The format of a {@code URI} identifying a file system is {@code "azb://?endpoint=&lt;endpoint&gt;"}.
+     * <p>
+     * Trying to retrieve a closed file system will throw a {@link FileSystemNotFoundException}. Once closed, a
+     * file system with the same identifier may be reopened.
+     *
+     * @param uri URI reference
+     * @return the file system
+     * @throws IllegalArgumentException If the pre-conditions for the uri parameter aren't met
+     * @throws FileSystemNotFoundException If the file system already exists
+     * @throws SecurityException never
+     */
+    @Override
+    public FileSystem getFileSystem(URI uri) {
+        String endpoint = extractAccountEndpoint(uri);
+        if (!this.openFileSystems.containsKey(endpoint)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new FileSystemNotFoundException("Name: " + endpoint));
+        }
+        return this.openFileSystems.get(endpoint);
+    }
+
+    /**
+     * Return a Path object by converting the given URI. The resulting Path is associated with a FileSystem that already
+     * exists.
+     *
+     * @param uri The URI to convert
+     * @return The path identified by the URI.
+     * @throws IllegalArgumentException If the URI scheme does not identify this provider or other preconditions on the
+     * uri parameter do not hold
+     * @throws FileSystemNotFoundException if the file system identified by the query does not exist
+     * @throws SecurityException never
+     *
+     * @see #getFileSystem(URI) for information on the URI format
+     */
+    @Override
+    public Path getPath(URI uri) {
+        return getFileSystem(uri).getPath(uri.getPath());
+    }
+
+    /**
+     * Opens or creates a file, returning a seekable byte channel to access the file.
+     * <p>
+     * This method is primarily offered to support some jdk convenience methods such as
+     * {@link Files#createFile(Path, FileAttribute[])} which requires opening a channel and closing it. A channel may
+     * only be opened in read mode OR write mode. It may not be opened in read/write mode. Seeking is supported for
+     * reads, but not for writes. Modifications to existing files is not permitted--only creating new files or
+     * overwriting existing files.
+     * <p>
+     * This type is not threadsafe to prevent having to hold locks across network calls.
+     *
+     * @param path the path of the file to open
+     * @param set options specifying how the file should be opened
+     * @param fileAttributes an optional list of file attributes to set atomically when creating the directory
+     * @return a new seekable byte channel
+     * @throws UnsupportedOperationException Operation is not supported.
+     * @throws IllegalArgumentException if the set contains an invalid combination of options
+     * @throws FileAlreadyExistsException if a file of that name already exists and the CREATE_NEW option is specified
+     * (optional specific exception)
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public SeekableByteChannel newByteChannel(Path path, Set<? extends OpenOption> set,
+            FileAttribute<?>... fileAttributes) throws IOException {
+        if (Objects.isNull(set)) {
+            set = Collections.emptySet();
+        }
+
+        if (set.contains(StandardOpenOption.WRITE)) {
+            return new AzureSeekableByteChannel(
+                (NioBlobOutputStream) this.newOutputStreamInternal(path, set, fileAttributes), path);
+        } else {
+            return new AzureSeekableByteChannel(
+                (NioBlobInputStream) this.newInputStream(path, set.toArray(new OpenOption[0])), path);
+        }
+    }
+
+    /**
+     * Opens an {@link InputStream} to the given path.
+     * <p>
+     * The stream will not attempt to read or buffer the entire file. However, when fetching data, it will always
+     * request the same size chunk of several MB to prevent network thrashing on small reads. Mark and reset are
+     * supported.
+     * <p>
+     * Only {@link StandardOpenOption#READ} is supported. Any other option will throw.
+     *
+     * @param path the path to the file to open
+     * @param options options specifying how the file is opened
+     * @return a new input stream
+     * @throws IllegalArgumentException if an invalid combination of options is specified
+     * @throws UnsupportedOperationException if an unsupported option is specified
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public InputStream newInputStream(Path path, OpenOption... options) throws IOException {
+        // Validate options. Only read is supported.
+        if (options.length > 1 || (options.length > 0 && !options[0].equals(StandardOpenOption.READ))) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new UnsupportedOperationException("Only the read option is supported."));
+        }
+
+        AzureResource resource = new AzureResource(path);
+        AzurePath.ensureFileSystemOpen(resource.getPath());
+
+        // Ensure the path points to a file.
+        if (!resource.checkDirStatus().equals(DirectoryStatus.NOT_A_DIRECTORY)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IOException("Path either does not exist or points to a directory."
+                    + "Path must point to a file. Path: " + path.toString()));
+        }
+
+        // Note that methods on BlobInputStream are already synchronized.
+        return new NioBlobInputStream(resource.getBlobClient().openInputStream(), resource.getPath());
+    }
+
+    /**
+     * Opens an {@link OutputStream} to the given path. The resulting file will be stored as a block blob.
+     * <p>
+     * The only supported options are {@link StandardOpenOption#CREATE}, {@link StandardOpenOption#CREATE_NEW},
+     * {@link StandardOpenOption#WRITE}, {@link StandardOpenOption#TRUNCATE_EXISTING}. Any other options will throw an
+     * {@link UnsupportedOperationException}. {@code WRITE} and {@code TRUNCATE_EXISTING} must be specified or an
+     * {@link IllegalArgumentException} will be thrown. Hence, files cannot be updated, only overwritten completely.
+     * <p>
+     * This stream will not attempt to buffer the entire file, however some buffering will be done for potential
+     * optimizations and to avoid network thrashing. Specifically, up to
+     * {@link AzureFileSystem#AZURE_STORAGE_PUT_BLOB_THRESHOLD} bytes will be buffered initially. If that threshold is
+     * exceeded, the data will be broken into chunks and sent in blocks, and writes will be buffered into sizes of
+     * {@link AzureFileSystem#AZURE_STORAGE_UPLOAD_BLOCK_SIZE}. The maximum number of buffers of this size to be
+     * allocated is defined by {@link AzureFileSystem#AZURE_STORAGE_MAX_CONCURRENCY_PER_REQUEST}, which also configures
+     * the level of parallelism with which we may write and thus may affect write speeds as well.
+     * <p>
+     * The data is only committed when the steam is closed. Hence, data cannot be read from the destination until the
+     * stream is closed. When the close method returns, it is guaranteed that, barring any errors, the data is finalized
+     * and available for reading.
+     * <p>
+     * Writing happens asynchronously. Bytes passed for writing are stored until either the threshold or block size are
+     * met at which time they are sent to the service. When the write method returns, there is no guarantee about which
+     * phase of this process the data is in other than it has been accepted and will be written. Again, closing will
+     * guarantee that the data is written and available.
+     * <p>
+     * Flush is a no-op as regards data transfers, but it can be used to check the state of the stream for errors.
+     * This can be a useful tool because writing happens asynchronously, and therefore an error from a previous write
+     * may not otherwise be thrown unless the stream is flushed, closed, or written to again.
+     *
+     * @param path the path to the file to open or create
+     * @param options options specifying how the file is opened
+     * @return a new output stream
+     * @throws IllegalArgumentException if an invalid combination of options is specified
+     * @throws UnsupportedOperationException if an unsupported option is specified
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public OutputStream newOutputStream(Path path, OpenOption... options) throws IOException {
+        return newOutputStreamInternal(path, new HashSet<>(Arrays.asList(options)));
+    }
+
+    OutputStream newOutputStreamInternal(Path path, Set<? extends OpenOption> optionsSet,
+        FileAttribute<?>... fileAttributes) throws IOException {
+        // If options are empty, add Create, Write, TruncateExisting as defaults per nio docs.
+        if (optionsSet == null || optionsSet.size() == 0) {
+            optionsSet = OUTPUT_STREAM_DEFAULT_OPTIONS;
+        }
+
+        // Check for unsupported options.
+        for (OpenOption option : optionsSet) {
+            if (!OUTPUT_STREAM_SUPPORTED_OPTIONS.contains(option)) {
+                throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                    new UnsupportedOperationException("Unsupported option: " + option.toString()));
+            }
+        }
+
+        /*
+        Write must be specified. Either create_new or truncate must be specified. This is to ensure that no edits or
+        appends are allowed.
+         */
+        if (!optionsSet.contains(StandardOpenOption.WRITE)
+            || !(optionsSet.contains(StandardOpenOption.TRUNCATE_EXISTING)
+            || optionsSet.contains(StandardOpenOption.CREATE_NEW))) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IllegalArgumentException("Write and either CreateNew or TruncateExisting must be specified to open "
+                    + "an OutputStream"));
+        }
+
+        AzureResource resource = new AzureResource(path);
+        AzurePath.ensureFileSystemOpen(resource.getPath());
+        DirectoryStatus status = resource.checkDirStatus();
+
+        // Cannot write to a directory.
+        if (DirectoryStatus.isDirectory(status)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IOException("Cannot open an OutputStream to a directory. Path: " + path.toString()));
+        }
+
+        // Writing to an empty location requires a create option.
+        if (status.equals(DirectoryStatus.DOES_NOT_EXIST)
+            && !(optionsSet.contains(StandardOpenOption.CREATE)
+            || optionsSet.contains(StandardOpenOption.CREATE_NEW))) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IOException("Writing to an empty location requires a create option. Path: " + path.toString()));
+        }
+
+        // Cannot write to an existing file if create new was specified.
+        if (status.equals(DirectoryStatus.NOT_A_DIRECTORY) && optionsSet.contains(StandardOpenOption.CREATE_NEW)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IOException("A file already exists at this location and "
+                    + "CREATE_NEW was specified. Path: " + path.toString()));
+        }
+
+        // Create options based on file system config
+        AzureFileSystem fs = (AzureFileSystem) (path.getFileSystem());
+        Integer blockSize = fs.getBlockSize() == null ? null : fs.getBlockSize().intValue();
+        Integer putBlobThreshold = fs.getPutBlobThreshold() == null ? null : fs.getPutBlobThreshold().intValue();
+        ParallelTransferOptions pto = new ParallelTransferOptions(blockSize, fs.getMaxConcurrencyPerRequest(), null,
+            putBlobThreshold);
+
+        // Add an extra etag check for create new
+        BlobRequestConditions rq = null;
+        if (optionsSet.contains(StandardOpenOption.CREATE_NEW)) {
+            rq = new BlobRequestConditions().setIfNoneMatch("*");
+        }
+
+        // For parsing properties and metadata
+        if (fileAttributes == null) {
+            fileAttributes = new FileAttribute<?>[0];
+        }
+        resource.setFileAttributes(Arrays.asList(fileAttributes));
+
+        return new NioBlobOutputStream(resource.getBlobOutputStream(pto, rq), resource.getPath());
+    }
+
+    /**
+     * Returns an {@link AzureDirectoryStream} for iterating over the contents of a directory. The elements returned by
+     * the directory stream's iterator are of type Path, each one representing an entry in the directory. The Path
+     * objects are obtained as if by resolving the name of the directory entry against dir. The entries returned by the
+     * iterator are filtered by the given filter.
+     * <p>
+     * When not using the try-with-resources construct, then directory stream's close method should be invoked after
+     * iteration is completed to free any resources held for the open directory.
+     * <p>
+     * Where the filter terminates due to an uncaught error or runtime exception then it is propagated to the hasNext or
+     * next method. Where an IOException is thrown, it results in the hasNext or next method throwing a
+     * DirectoryIteratorException with the IOException as the cause.
+     *
+     * @param path the path to the directory
+     * @param filter the directory stream filter
+     * @return a new and open {@code DirectoryStream} object
+     * @throws IllegalArgumentException If the path type is not an instance of {@link AzurePath}.
+     * @throws NotDirectoryException if the file could not otherwise be opened because it is not a directory
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public DirectoryStream<Path> newDirectoryStream(Path path, DirectoryStream.Filter<? super Path> filter)
+        throws IOException {
+        if (!(path instanceof AzurePath)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IllegalArgumentException("This provider cannot operate on subtypes of Path other than AzurePath"));
+        }
+        AzurePath.ensureFileSystemOpen(path);
+
+        /*
+        Ensure the path is a directory. Note that roots are always directories. The case of an invalid root will be
+        caught in instantiating the stream below.
+
+        Possible optimization later is to save the result of the list call to use as the first list call inside the
+        stream rather than a list call for checking the status and a list call for listing.
+         */
+        if (!((AzurePath) path).isRoot() && !(new AzureResource(path).checkDirectoryExists())) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new NotDirectoryException(path.toString()));
+        }
+
+        return new AzureDirectoryStream((AzurePath) path, filter);
+    }
+
+    /**
+     * Creates a new directory at the specified path.
+     * <p>
+     * The existence of a directory in the {@code AzureFileSystem} is defined on two levels. <i>Weak existence</i> is
+     * defined by the presence of a non-zero number of blobs prefixed with the directory's path. This concept is also
+     * known as a  <i>virtual directory</i> and enables the file system to work with containers that were pre-loaded
+     * with data by another source but need to be accessed by this file system. <i>Strong existence</i> is defined as
+     * the presence of an actual storage resource at the given path, which in the case of directories, is a zero-length
+     * blob whose name is the directory path with a particular metadata field indicating the blob's status as a
+     * directory. This is also known as a <i>concrete directory</i>. Directories created by this file system will
+     * strongly exist. Operations targeting directories themselves as the object (e.g. setting properties) will target
+     * marker blobs underlying concrete directories. Other operations (e.g. listing) will operate on the blob-name
+     * prefix.
+     * <p>
+     * This method fulfills the nio contract of: "The check for the existence of the file and the creation of the
+     * directory if it does not exist are a single operation that is atomic with respect to all other filesystem
+     * activities that might affect the directory." More specifically, this method will atomically check for <i>strong
+     * existence</i> of another file or directory at the given path and fail if one is present. On the other hand, we
+     * only check for <i>weak existence</i> of the parent to determine if the given path is valid. Additionally, the
+     * action of checking whether the parent exists, is <i>not</i> atomic with the creation of the directory. Note that
+     * while it is possible that the parent may be deleted between when the parent is determined to exist and the
+     * creation of the child, the creation of the child will always ensure the existence of a virtual parent, so the
+     * child will never be left floating and unreachable. The different checks on parent and child is due to limitations
+     * in the Storage service API.
+     * <p>
+     * There may be some unintuitive behavior when working with directories in this file system, particularly virtual
+     * directories (usually those not created by this file system). A virtual directory will disappear as soon as all
+     * its children have been deleted. Furthermore, if a directory with the given path weakly exists at the time of
+     * calling this method, this method will still return success and create a concrete directory at the target
+     * location. In other words, it is possible to "double create" a directory if it first weakly exists and then is
+     * strongly created. This is both because it is impossible to atomically check if a virtual directory exists while
+     * creating a concrete directory and because such behavior will have minimal side effects--no files will be
+     * overwritten and the directory will still be available for writing as intended, though it may not be empty. This
+     * is not a complete list of such unintuitive behavior.
+     * <p>
+     * This method will attempt to extract standard HTTP content headers from the list of file attributes to set them
+     * as blob headers. All other attributes will be set as blob metadata. The value of every attribute will be
+     * converted to a {@code String} except the Content-MD5 attribute which expects a {@code byte[]}.
+     * When extracting the content headers, the following strings will be used for comparison (constants for these
+     * values can be found on this type):
+     * <ul>
+     *     <li>{@code Content-Type}</li>
+     *     <li>{@code Content-Disposition}</li>
+     *     <li>{@code Content-Language}</li>
+     *     <li>{@code Content-Encoding}</li>
+     *     <li>{@code Content-MD5}</li>
+     *     <li>{@code Cache-Control}</li>
+     * </ul>
+     * Note that these properties also have a particular semantic in that if one is specified, all are updated. In other
+     * words, if any of the above is set, all those that are not set will be cleared. See the
+     * <a href="https://docs.microsoft.com/en-us/rest/api/storageservices/set-blob-properties">Azure Docs</a> for more
+     * information.
+     *
+     * @param path the directory to create
+     * @param fileAttributes an optional list of file attributes to set atomically when creating the directory
+     * @throws IllegalArgumentException If the path type is not an instance of {@link AzurePath}.
+     * @throws UnsupportedOperationException if the array contains an attribute that cannot be set atomically when
+     * creating the directory
+     * @throws FileAlreadyExistsException if a directory could not otherwise be created because a file of that name
+     * already exists
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public void createDirectory(Path path, FileAttribute<?>... fileAttributes) throws IOException {
+        fileAttributes = fileAttributes == null ? new FileAttribute<?>[0] : fileAttributes;
+
+        // Get the destination for the directory. Will throw if path is a root.
+        AzureResource azureResource = new AzureResource(path);
+        AzurePath.ensureFileSystemOpen(azureResource.getPath());
+
+        // Check if parent exists. If it does, atomically check if a file already exists and create a new dir if not.
+        if (azureResource.checkParentDirectoryExists()) {
+            try {
+                azureResource.setFileAttributes(Arrays.asList(fileAttributes))
+                    .putDirectoryBlob(new BlobRequestConditions().setIfNoneMatch("*"));
+            } catch (BlobStorageException e) {
+                if (e.getStatusCode() == HttpURLConnection.HTTP_CONFLICT
+                    && e.getErrorCode().equals(BlobErrorCode.BLOB_ALREADY_EXISTS)) {
+                    throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                        new FileAlreadyExistsException(azureResource.getPath().toString()));
+                } else {
+                    throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                        new IOException("An error occurred when creating the directory", e));
+                }
+            }
+        } else {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IOException("Parent directory does not exist for path: " + azureResource.getPath()));
+        }
+    }
+
+    /**
+     * Deletes the specified resource.
+     * <p>
+     * This method is not atomic with respect to other file system operations. It is possible to delete a file in use by
+     * another process, and doing so will not immediately invalidate any channels open to that file--they will simply
+     * start to fail. Root directories cannot be deleted even when empty.
+     *
+     * @param path the path to the file to delete
+     * @throws IllegalArgumentException If the path type is not an instance of {@link AzurePath}.
+     * @throws NoSuchFileException if the file does not exist
+     * @throws DirectoryNotEmptyException if the file is a directory and could not otherwise be deleted because the
+     * directory is not empty
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public void delete(Path path) throws IOException {
+        // Basic validation. Must be an AzurePath. Cannot be a root.
+        AzureResource azureResource = new AzureResource(path);
+        AzurePath.ensureFileSystemOpen(azureResource.getPath());
+
+        // Check directory status--possibly throw DirectoryNotEmpty or NoSuchFile.
+        DirectoryStatus dirStatus = azureResource.checkDirStatus();
+        if (dirStatus.equals(DirectoryStatus.DOES_NOT_EXIST)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new NoSuchFileException(path.toString()));
+        }
+        if (dirStatus.equals(DirectoryStatus.NOT_EMPTY)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new DirectoryNotEmptyException(path.toString()));
+        }
+
+        // After all validation has completed, delete the resource.
+        try {
+            azureResource.getBlobClient().delete();
+        } catch (BlobStorageException e) {
+            if (e.getErrorCode().equals(BlobErrorCode.BLOB_NOT_FOUND)) {
+                throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new NoSuchFileException(path.toString()));
+            }
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new IOException(e));
+        }
+    }
+
+    /**
+     * Copies the resource at the source location to the destination.
+     * <p>
+     * This method is not atomic with respect to other file system operations. More specifically, the checks necessary
+     * to validate the inputs and state of the file system are not atomic with the actual copying of data. If the copy
+     * is triggered, the copy itself is atomic and only a complete copy will ever be left at the destination.
+     * <p>
+     * In addition to those in the docs for {@link FileSystemProvider#copy(Path, Path, CopyOption...)}, this method has
+     * the following requirements for successful completion. {@link StandardCopyOption#COPY_ATTRIBUTES} must be passed
+     * as it is impossible not to copy blob properties; if this option is not passed, an
+     * {@link UnsupportedOperationException} will be thrown. Neither the source nor the destination can be a root
+     * directory; if either is a root directory, an {@link IllegalArgumentException} will be thrown. The parent
+     * directory of the destination must at least weakly exist; if it does not, an {@link IOException} will be thrown.
+     * The only supported option other than {@link StandardCopyOption#COPY_ATTRIBUTES} is
+     * {@link StandardCopyOption#REPLACE_EXISTING}; the presence of any other option will result in an
+     * {@link UnsupportedOperationException}.
+     * <p>
+     * This method supports both virtual and concrete directories as both the source and destination. Unlike when
+     * creating a directory, the existence of a virtual directory at the destination will cause this operation to fail.
+     * This is in order to prevent the possibility of overwriting a non-empty virtual directory with a file. Still, as
+     * mentioned above, this check is not atomic with the creation of the resultant directory.
+     *
+     * @param source the path to the file to copy
+     * @param destination the path to the target file
+     * @param copyOptions specifying how the copy should be done
+     * @throws UnsupportedOperationException if the array contains a copy option that is not supported
+     * @throws FileAlreadyExistsException if the target file exists but cannot be replaced because the REPLACE_EXISTING
+     * option is not specified
+     * @throws DirectoryNotEmptyException the REPLACE_EXISTING option is specified but the file cannot be replaced
+     * because it is a non-empty directory
+     * @throws IOException If an I/O error occurs.
+     * @throws IllegalArgumentException If the path type is not an instance of {@link AzurePath}.
+     * @throws SecurityException never
+     * @see #createDirectory(Path, FileAttribute[]) for more information about directory existence.
+     */
+    @Override
+    public void copy(Path source, Path destination, CopyOption... copyOptions) throws IOException {
+        // If paths point to the same file, operation is a no-op.
+        if (source.equals(destination)) {
+            return;
+        }
+
+        // Read and validate options.
+        // Remove accepted options as we find them. Anything left we don't support.
+        boolean replaceExisting = false;
+        List<CopyOption> optionsList = new ArrayList<>(Arrays.asList(copyOptions));
+        if (!optionsList.contains(StandardCopyOption.COPY_ATTRIBUTES)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new UnsupportedOperationException(
+                "StandardCopyOption.COPY_ATTRIBUTES must be specified as the service will always copy "
+                    + "file attributes."));
+        }
+        optionsList.remove(StandardCopyOption.COPY_ATTRIBUTES);
+        if (optionsList.contains(StandardCopyOption.REPLACE_EXISTING)) {
+            replaceExisting = true;
+            optionsList.remove(StandardCopyOption.REPLACE_EXISTING);
+        }
+        if (!optionsList.isEmpty()) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new UnsupportedOperationException("Unsupported copy option found. Only "
+                    + "StandardCopyOption.COPY_ATTRIBUTES and StandardCopyOption.REPLACE_EXISTING are supported."));
+        }
+
+        // Validate paths. Build resources.
+        // Copying a root directory or attempting to create/overwrite a root directory is illegal.
+        AzureResource sourceRes = new AzureResource(source);
+        AzurePath.ensureFileSystemOpen(sourceRes.getPath());
+        AzureResource destinationRes = new AzureResource(destination);
+        AzurePath.ensureFileSystemOpen(destinationRes.getPath());
+
+        // Check destination is not a directory with children.
+        DirectoryStatus destinationStatus = destinationRes.checkDirStatus();
+        if (destinationStatus.equals(DirectoryStatus.NOT_EMPTY)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new DirectoryNotEmptyException(destination.toString()));
+        }
+
+        /*
+        Set request conditions if we should not overwrite. We can error out here if we know something already exists,
+        but we will also create request conditions as a safeguard against overwriting something that was created
+        between our check and put.
+         */
+        BlobRequestConditions requestConditions = null;
+        if (!replaceExisting) {
+            if (!destinationStatus.equals(DirectoryStatus.DOES_NOT_EXIST)) {
+                throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                    new FileAlreadyExistsException(destinationRes.getPath().toString()));
+            }
+            requestConditions = new BlobRequestConditions().setIfNoneMatch("*");
+        }
+
+        /*
+        More path validation
+
+        Check that the parent for the destination exists. We only need to perform this check if there is nothing
+        currently at the destination, for if the destination exists, its parent at least weakly exists and we
+        can skip a service call.
+         */
+        if (destinationStatus.equals(DirectoryStatus.DOES_NOT_EXIST) && !destinationRes.checkParentDirectoryExists()) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IOException("Parent directory of destination location does not exist. The destination path is "
+                    + "therefore invalid. Destination: " + destinationRes.getPath()));
+        }
+
+        /*
+        Try to copy the resource at the source path.
+
+        There is an optimization here where we try to do the copy first and only check for a virtual directory if
+        there's a 404. In the cases of files and concrete directories, this only requires one request. For virtual
+        directories, however, this requires three requests: failed copy, check status, create directory. Depending on
+        customer scenarios and how many virtual directories they copy, it could be better to check the directory status
+        first and then do a copy or createDir, which would always be two requests for all resource types.
+         */
+        try {
+            SyncPoller<BlobCopyInfo, Void> pollResponse =
+                destinationRes.getBlobClient().beginCopy(sourceRes.getBlobClient().getBlobUrl(), null, null, null,
+                    null, requestConditions, null);
+            pollResponse.waitForCompletion(Duration.ofSeconds(COPY_TIMEOUT_SECONDS));
+        } catch (BlobStorageException e) {
+            // If the source was not found, it could be because it's a virtual directory. Check the status.
+            // If a non-dir resource existed, it would have been copied above. This check is therefore sufficient.
+            if (e.getErrorCode().equals(BlobErrorCode.BLOB_NOT_FOUND)
+                && !sourceRes.checkDirStatus().equals(DirectoryStatus.DOES_NOT_EXIST)) {
+                /*
+                We already checked that the parent exists and validated the paths above, so we can put the blob
+                directly.
+                 */
+                destinationRes.putDirectoryBlob(requestConditions);
+            } else {
+                throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new IOException(e));
+            }
+        } catch (RuntimeException e) { // To better log possible timeout from poller.
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new IOException(e));
+        }
+    }
+
+    // Used for checking the status of the root directory. To be implemented later when needed.
+    /*int checkRootDirStatus(BlobContainerClient rootClient) {
+
+    }*/
+
+    /**
+     * Unsupported.
+     *
+     * @param path path
+     * @param path1 path
+     * @param copyOptions options
+     * @throws UnsupportedOperationException Operation is not supported.
+     */
+    @Override
+    public void move(Path path, Path path1, CopyOption... copyOptions) throws IOException {
+        throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new UnsupportedOperationException());
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @param path path
+     * @param path1 path
+     * @throws UnsupportedOperationException Operation is not supported.
+     */
+    @Override
+    public boolean isSameFile(Path path, Path path1) throws IOException {
+        throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new UnsupportedOperationException());
+    }
+
+    /**
+     * Always returns false as hidden files are not supported.
+     *
+     * @param path the path
+     * @return false
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public boolean isHidden(Path path) throws IOException {
+        return false;
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @param path path
+     * @return the file store where the file is stored.
+     * @throws UnsupportedOperationException Operation is not supported.
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public FileStore getFileStore(Path path) throws IOException {
+        throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new UnsupportedOperationException());
+    }
+
+    /**
+     * Checks the existence, and optionally the accessibility, of a file.
+     * <p>
+     * This method may only be used to check the existence of a file. It is not possible to determine the permissions
+     * granted to a given client, so if any mode argument is specified, an {@link UnsupportedOperationException} will be
+     * thrown.
+     *
+     * @param path the path to the file to check
+     * @param accessModes The access modes to check; may have zero elements
+     * @throws NoSuchFileException if a file does not exist
+     * @throws java.nio.file.AccessDeniedException the requested access would be denied or the access cannot be
+     * determined because the Java virtual machine has insufficient privileges or other reasons
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public void checkAccess(Path path, AccessMode... accessModes) throws IOException {
+        if (accessModes != null && accessModes.length != 0) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new AccessDeniedException("The access cannot be determined."));
+        }
+        AzurePath.ensureFileSystemOpen(path);
+
+        /*
+        Some static utility methods in the jdk require checking access on a root. ReadAttributes is not supported on
+        roots as they are containers. Furthermore, we always assume that roots exist as they are verified at creation
+        and cannot be deleted by the file system. Thus, we prefer a short circuit for roots.
+         */
+        if (path instanceof AzurePath && ((AzurePath) path).isRoot()) {
+            return;
+        }
+
+        // Read attributes already wraps BlobStorageException in an IOException.
+        try {
+            readAttributes(path, BasicFileAttributes.class);
+        } catch (IOException e) {
+            Throwable cause = e.getCause();
+            if (cause instanceof BlobStorageException
+                && BlobErrorCode.BLOB_NOT_FOUND.equals(((BlobStorageException) cause).getErrorCode())) {
+                throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new NoSuchFileException(path.toString()));
+            } else {
+                throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, e);
+            }
+        }
+    }
+
+    /**
+     * Returns a file attribute view of a given type.
+     * <p>
+     * See {@link AzureBasicFileAttributeView} and {@link AzureBlobFileAttributeView} for more information.
+     * <p>
+     * Reading attributes on a virtual directory will return {@code null} for most properties other than
+     * {@link AzureBlobFileAttributes#isVirtualDirectory()}, which will return true. See
+     * {@link #createDirectory(Path, FileAttribute[])} for more information on virtual directories.
+     *
+     * @param path the path to the file
+     * @param type the Class object corresponding to the file attribute view
+     * @param linkOptions ignored
+     * @return a file attribute view of the specified type, or null if the attribute view type is not available
+     */
+    @Override
+    @SuppressWarnings("unchecked")
+    public <V extends FileAttributeView> V getFileAttributeView(Path path, Class<V> type, LinkOption... linkOptions) {
+        /*
+        No resource validation is necessary here. That can happen at the time of making a network requests internal to
+        the view object.
+         */
+        if (type == BasicFileAttributeView.class || type == AzureBasicFileAttributeView.class) {
+            return (V) new AzureBasicFileAttributeView(path);
+        } else if (type == AzureBlobFileAttributeView.class) {
+            return (V) new AzureBlobFileAttributeView(path);
+        } else {
+            return null;
+        }
+    }
+
+    /**
+     * Reads a file's attributes as a bulk operation.
+     * <p>
+     * See {@link AzureBasicFileAttributes} and {@link AzureBlobFileAttributes} for more information.
+     * <p>
+     * Reading attributes on a virtual directory will return {@code null} for most properties other than
+     * {@link AzureBlobFileAttributes#isVirtualDirectory()}, which will return true. See
+     * {@link #createDirectory(Path, FileAttribute[])} for more information on virtual directories.
+     *
+     * @param path the path to the file
+     * @param type the Class of the file attributes required to read
+     * @param linkOptions ignored
+     * @return the file attributes
+     * @throws UnsupportedOperationException if an attributes of the given type are not supported
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    @SuppressWarnings("unchecked")
+    public <A extends BasicFileAttributes> A readAttributes(Path path, Class<A> type, LinkOption... linkOptions)
+        throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+
+        Class<? extends BasicFileAttributeView> view;
+        if (type == BasicFileAttributes.class || type == AzureBasicFileAttributes.class) {
+            view = AzureBasicFileAttributeView.class;
+        } else if (type == AzureBlobFileAttributes.class) {
+            view = AzureBlobFileAttributeView.class;
+        } else {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new UnsupportedOperationException());
+        }
+
+        /*
+        Resource validation will happen in readAttributes of the view. We don't want to double-check, and checking
+        internal to the view ensures it is always checked no matter which code path is taken.
+         */
+        return (A) getFileAttributeView(path, view, linkOptions).readAttributes();
+    }
+
+    /**
+     * Reads a set of file attributes as a bulk operation.
+     * <p>
+     * See {@link AzureBasicFileAttributes} and {@link AzureBlobFileAttributes} for more information.
+     * <p>
+     * Reading attributes on a virtual directory will return {@code null} for all properties other than
+     * {@link AzureBlobFileAttributes#isVirtualDirectory()}, which will return true. See
+     * {@link #createDirectory(Path, FileAttribute[])} for more information on virtual directories.
+     *
+     * @param path the path to the file
+     * @param attributes the attributes to read
+     * @param linkOptions ignored
+     * @return a map of the attributes returned; may be empty. The map's keys are the attribute names, its values are
+     * the attribute values
+     * @throws UnsupportedOperationException if an attributes of the given type are not supported
+     * @throws IllegalArgumentException if no attributes are specified or an unrecognized attributes is specified
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public Map<String, Object> readAttributes(Path path, String attributes, LinkOption... linkOptions)
+        throws IOException {
+        if (attributes == null) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IllegalArgumentException("Attribute string cannot be null."));
+        }
+
+        AzurePath.ensureFileSystemOpen(path);
+
+        Map<String, Object> results = new HashMap<>();
+
+        /*
+        AzureBlobFileAttributes can do everything the basic attributes can do and more. There's no need to instantiate
+        one of each if both are specified somewhere in the list as that will waste a network call. This can be
+        generified later if we need to add more attribute types, but for now we can stick to just caching the supplier
+        for a single attributes object.
+         */
+        Map<String, Supplier<Object>> attributeSuppliers = null; // Initialized later as needed.
+        String viewType;
+        String attributeList;
+        String[] parts = attributes.split(":");
+
+        if (parts.length > 2) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IllegalArgumentException("Invalid format for attribute string: " + attributes));
+        }
+
+        if (parts.length == 1) {
+            viewType = "basic"; // Per jdk docs.
+            attributeList = attributes;
+        } else {
+            viewType = parts[0];
+            attributeList = parts[1];
+        }
+
+        /*
+        For specificity, our basic implementation of BasicFileAttributes uses the name azureBasic. However, the docs
+        state that "basic" must be supported, so we funnel to azureBasic.
+         */
+        if ("basic".equals(viewType)) {
+            viewType = AzureBasicFileAttributeView.NAME;
+        }
+        if (!viewType.equals(AzureBasicFileAttributeView.NAME) && !viewType.equals(AzureBlobFileAttributeView.NAME)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new UnsupportedOperationException("Invalid attribute view: " + viewType));
+        }
+
+        for (String attributeName : attributeList.split(",")) {
+            /*
+            We rely on the azureBlobFAV to actually do the work here as mentioned above, but if basic is specified, we
+            should at least validate that the attribute is available on a basic view.
+             */
+            // TODO: Put these strings in constants
+            if (viewType.equals(AzureBasicFileAttributeView.NAME)) {
+                if (!AzureBasicFileAttributes.ATTRIBUTE_STRINGS.contains(attributeName) && !"*".equals(attributeName)) {
+                    throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                        new IllegalArgumentException("Invalid attribute. View: " + viewType
+                            + ". Attribute: " + attributeName));
+                }
+            }
+
+            // As mentioned, azure blob can fulfill requests to both kinds of views.
+            // Populate the supplier if we haven't already.
+            if (attributeSuppliers == null) {
+                attributeSuppliers = AzureBlobFileAttributes.getAttributeSuppliers(
+                    this.readAttributes(path, AzureBlobFileAttributes.class, linkOptions));
+            }
+
+            // If "*" is specified, add all the attributes from the specified set.
+            if ("*".equals(attributeName)) {
+                if (viewType.equals(AzureBasicFileAttributeView.NAME)) {
+                    for (String attr : AzureBasicFileAttributes.ATTRIBUTE_STRINGS) {
+                        results.put(attr, attributeSuppliers.get(attr).get());
+                    }
+                } else {
+                    // attributeSuppliers is guaranteed to have been set by this point.
+                    for (Map.Entry<String, Supplier<Object>> entry: attributeSuppliers.entrySet()) {
+                        results.put(entry.getKey(), entry.getValue().get());
+                    }
+                }
+
+            } else if (!attributeSuppliers.containsKey(attributeName)) {
+                // Validate that the attribute is legal and add the value returned by the supplier to the results.
+                throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                    new IllegalArgumentException("Invalid attribute. View: " + viewType
+                        + ". Attribute: " + attributeName));
+            } else {
+                results.put(attributeName, attributeSuppliers.get(attributeName).get());
+
+            }
+        }
+
+        // Throw if nothing specified per jdk docs.
+        if (results.isEmpty()) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IllegalArgumentException("No attributes were specified. Attributes: " + attributes));
+        }
+
+        return results;
+    }
+
+    /**
+     * Sets the value of a file attribute.
+     * <p>
+     * See {@link AzureBlobFileAttributeView} for more information.
+     * <p>
+     * Setting attributes on a virtual directory is not supported and will throw an {@link IOException}. See
+     * {@link #createDirectory(Path, FileAttribute[])} for more information on virtual directories.
+     *
+     * @param path the path to the file
+     * @param attributes the attribute to set
+     * @param value the attribute value
+     * @param linkOptions ignored
+     * @throws UnsupportedOperationException if an attribute view is not available
+     * @throws IllegalArgumentException if the attribute name is not specified, or is not recognized, or the attribute
+     * value is of the correct type but has an inappropriate value
+     * @throws ClassCastException If the attribute value is not of the expected type or is a collection containing
+     * elements that are not of the expected type
+     * @throws IOException If an I/O error occurs.
+     * @throws SecurityException never
+     */
+    @Override
+    public void setAttribute(Path path, String attributes, Object value, LinkOption... linkOptions) throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        String viewType;
+        String attributeName;
+        String[] parts = attributes.split(":");
+        if (parts.length > 2) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IllegalArgumentException("Invalid format for attribute string: " + attributes));
+        }
+        if (parts.length == 1) {
+            viewType = "basic"; // Per jdk docs.
+            attributeName = attributes;
+        } else {
+            viewType = parts[0];
+            attributeName = parts[1];
+        }
+
+        /*
+        For specificity, our basic implementation of BasicFileAttributes uses the name azureBasic. However, the docs
+        state that "basic" must be supported, so we funnel to azureBasic.
+         */
+        if ("basic".equals(viewType)) {
+            viewType = AzureBasicFileAttributeView.NAME;
+        }
+
+        // We don't actually support any setters on the basic view.
+        if (viewType.equals(AzureBasicFileAttributeView.NAME)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IllegalArgumentException("Invalid attribute. View: " + viewType
+                    + ". Attribute: " + attributeName));
+        } else if (viewType.equals(AzureBlobFileAttributeView.NAME)) {
+            Map<String, Consumer<Object>> attributeConsumers = AzureBlobFileAttributeView.setAttributeConsumers(
+                this.getFileAttributeView(path, AzureBlobFileAttributeView.class, linkOptions));
+            if (!attributeConsumers.containsKey(attributeName)) {
+                // Validate that the attribute is legal and add the value returned by the supplier to the results.
+                throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                    new IllegalArgumentException("Invalid attribute. View: " + viewType
+                        + ". Attribute: " + attributeName));
+            }
+            try {
+                attributeConsumers.get(attributeName).accept(value);
+            } catch (UncheckedIOException e) {
+                if (e.getMessage().equals(AzureBlobFileAttributeView.ATTR_CONSUMER_ERROR)) {
+                    throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, e.getCause());
+                }
+            }
+        } else {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new UnsupportedOperationException("Invalid attribute view: " + viewType));
+        }
+    }
+
+    void closeFileSystem(String fileSystemName) {
+        this.openFileSystems.remove(fileSystemName);
+    }
+
+    private String extractAccountEndpoint(URI uri) {
+        if (!uri.getScheme().equals(this.getScheme())) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new IllegalArgumentException(
+                "URI scheme does not match this provider"));
+        }
+        if (CoreUtils.isNullOrEmpty(uri.getQuery())) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IllegalArgumentException("URI does not contain a query component. FileSystems require a URI of "
+                    + "the format \"azb://?endpoint=<account_endpoint>\"."));
+        }
+
+        String endpoint = Flux.fromArray(uri.getQuery().split("&"))
+                .filter(s -> s.startsWith(ENDPOINT_QUERY_KEY + "="))
+                .switchIfEmpty(Mono.defer(() -> Mono.error(LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                    new IllegalArgumentException("URI does not contain an \"" + ENDPOINT_QUERY_KEY + "=\" parameter. "
+                        + "FileSystems require a URI of the format \"azb://?endpoint=<endpoint>\"")))))
+                .map(s -> s.substring(ENDPOINT_QUERY_KEY.length() + 1)) // Trim the query key and =
+                .blockLast();
+
+        if (CoreUtils.isNullOrEmpty(endpoint)) {
+            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
+                new IllegalArgumentException("No account endpoint provided in URI query."));
+        }
+
+        return endpoint;
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzurePath.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzurePath.java
new file mode 100644
index 00000000000..9742af1f696
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzurePath.java
@@ -0,0 +1,836 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.file.ClosedFileSystemException;
+import java.nio.file.FileSystem;
+import java.nio.file.InvalidPathException;
+import java.nio.file.LinkOption;
+import java.nio.file.Path;
+import java.nio.file.WatchEvent;
+import java.nio.file.WatchKey;
+import java.nio.file.WatchService;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Deque;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Objects;
+import java.util.stream.Stream;
+
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.BlobClient;
+import com.azure.storage.blob.BlobContainerClient;
+import com.azure.storage.blob.BlobUrlParts;
+
+/**
+ * An object that may be used to locate a file in a file system.
+ * <p>
+ * The root component, if it is present, is the first element of the path and is denoted by a {@code ':'} as the last
+ * character. Hence, only one instance of {@code ':'} may appear in a path string, and it may only be the last character
+ * of the first element in the path. The root component is used to identify which container a path belongs to. All other
+ * path elements, including separators, are considered as the blob name. {@link AzurePath#fromBlobUrl} may
+ * be used to convert a typical http url pointing to a blob into an {@code AzurePath} object pointing to the same
+ * resource.
+ * <p>
+ * Constructing a syntactically valid path does not ensure a resource exists at the given path. An error will
+ * not be thrown until trying to access an invalid resource, e.g. trying to access a resource that does not exist.
+ * <p>
+ * Path names are case-sensitive.
+ * <p>
+ * If a resource is accessed via a relative path, it will be resolved against the default directory of the file system.
+ * The default directory is as defined in the {@link AzureFileSystem} docs.
+ * <p>
+ * Leading and trailing separators will be stripped from each component passed to
+ * {@link AzureFileSystem#getPath(String, String...)}. This has the effect of treating "foo/" as though it were simply
+ * "foo".
+ */
+public final class AzurePath implements Path {
+    private static final ClientLogger LOGGER = new ClientLogger(AzurePath.class);
+    static final String ROOT_DIR_SUFFIX = ":";
+
+    private final AzureFileSystem parentFileSystem;
+    private final String pathString;
+
+    AzurePath(AzureFileSystem parentFileSystem, String first, String... more) {
+        this.parentFileSystem = parentFileSystem;
+
+        /*
+        Break all strings into their respective elements and remove empty elements. This has the effect of stripping
+        any trailing, leading, or internal delimiters so there are no duplicates/empty elements when we join.
+         */
+        List<String> elements = new ArrayList<>(Arrays.asList(first.split(parentFileSystem.getSeparator())));
+        if (more != null) {
+            for (String next : more) {
+                elements.addAll(Arrays.asList(next.split(parentFileSystem.getSeparator())));
+            }
+        }
+        elements.removeIf(String::isEmpty);
+
+        this.pathString = String.join(this.parentFileSystem.getSeparator(), elements);
+
+        // Validate the path string by checking usage of the reserved character ROOT_DIR_SUFFIX.
+        for (int i = 0; i < elements.size(); i++) {
+            String element = elements.get(i);
+            /*
+            If there is a root component, it must be the first element. A root component takes the format of
+            "<fileStoreName>:". The ':', or ROOT_DIR_SUFFIX, if present, can only appear once, and can only be the last
+            character of the first element.
+             */
+            if (i == 0) {
+                if (element.contains(ROOT_DIR_SUFFIX) && element.indexOf(ROOT_DIR_SUFFIX) < element.length() - 1) {
+                    throw LoggingUtility.logError(LOGGER, new InvalidPathException(this.pathString, ROOT_DIR_SUFFIX
+                        + " may only be used as the last character in the root component of a path"));
+                }
+            // No element besides the first may contain the ROOT_DIR_SUFFIX, as only the first element may be the root.
+            } else if (element.contains(ROOT_DIR_SUFFIX)) {
+                throw LoggingUtility.logError(LOGGER, new InvalidPathException(this.pathString, ROOT_DIR_SUFFIX
+                    + " is an invalid character except to identify the root element of this path if there is one."));
+            }
+        }
+    }
+
+    /**
+     * Returns the file system that created this object.
+     *
+     * @return the file system that created this object
+     */
+    @Override
+    public FileSystem getFileSystem() {
+        return this.parentFileSystem;
+    }
+
+    /**
+     * Tells whether this path is absolute.
+     * <p>
+     * An absolute path is complete in that it doesn't need to be combined with other path information in order to
+     * locate a file. A path is considered absolute in this file system if it contains a root component.
+     *
+     * @return whether the path is absolute
+     */
+    @Override
+    public boolean isAbsolute() {
+        return this.getRoot() != null;
+    }
+
+    /**
+     * Returns the root component of this path as a Path object, or null if this path does not have a root component.
+     * <p>
+     * The root component of this path also identifies the Azure Storage Container in which the file is stored. This
+     * method will not validate that the root component corresponds to an actual file store/container in this
+     * file system. It will simply return the root component of the path if one is present and syntactically valid.
+     *
+     * @return a path representing the root component of this path, or null
+     */
+    @Override
+    public Path getRoot() {
+        // Check if the first element of the path is formatted like a root directory.
+        String[] elements = this.splitToElements();
+        if (elements.length > 0 && elements[0].endsWith(ROOT_DIR_SUFFIX)) {
+            return this.parentFileSystem.getPath(elements[0]);
+        }
+        return null;
+    }
+
+    /**
+     * Returns the name of the file or directory denoted by this path as a Path object. The file name is the farthest
+     * element from the root in the directory hierarchy.
+     *
+     * @return a path representing the name of the file or directory, or null if this path has zero elements
+     */
+    @Override
+    public Path getFileName() {
+        if (this.isRoot()) {
+            return null;
+        } else if (this.pathString.isEmpty()) {
+            return this;
+        } else {
+            List<String> elements = Arrays.asList(this.splitToElements());
+            return this.parentFileSystem.getPath(elements.get(elements.size() - 1));
+        }
+    }
+
+    /**
+     * Returns the parent path, or null if this path does not have a parent.
+     * <p>
+     * The parent of this path object consists of this path's root component, if any, and each element in the path
+     * except for the farthest from the root in the directory hierarchy. This method does not access the file system;
+     * the path or its parent may not exist. Furthermore, this method does not eliminate special names such as "." and
+     * ".." that may be used in some implementations. On UNIX for example, the parent of "/a/b/c" is "/a/b", and the
+     * parent of "x/y/." is "x/y". This method may be used with the normalize method, to eliminate redundant names, for
+     * cases where shell-like navigation is required.
+     * <p>
+     * If this path has one or more elements, and no root component, then this method is equivalent to evaluating the
+     * expression:
+     *
+     *  {@code subpath(0, getNameCount()-1);}
+     *
+     * @return a path representing the path's parent
+     */
+    @Override
+    public Path getParent() {
+        /*
+        If this path only has one element or is empty, there is no parent. Note the root is included in the parent, so
+        we don't use getNameCount here.
+         */
+        String[] elements = this.splitToElements();
+        if (elements.length == 1 || elements.length == 0) {
+            return null;
+        }
+
+        return this.parentFileSystem.getPath(
+            this.pathString.substring(0, this.pathString.lastIndexOf(this.parentFileSystem.getSeparator())));
+    }
+
+    /**
+     * Returns the number of name elements in the path.
+     *
+     * @return the number of elements in the path, or 0 if this path only represents a root component
+     */
+    @Override
+    public int getNameCount() {
+        if (this.pathString.isEmpty()) {
+            return 1;
+        }
+        return this.splitToElements(this.withoutRoot()).length;
+    }
+
+    /**
+     * Returns a name element of this path as a Path object.
+     * <p>
+     * The index parameter is the index of the name element to return. The element that is closest to the root in the
+     * directory hierarchy has index 0. The element that is farthest from the root has index {@code count-1}.
+     *
+     * @param index the index of the element
+     * @return the name element
+     * @throws IllegalArgumentException if index is negative, index is greater than or equal to the number of elements,
+     * or this path has zero name elements
+     */
+    @Override
+    public Path getName(int index) {
+        if (index < 0 || index >= this.getNameCount()) {
+            throw LoggingUtility.logError(LOGGER, new IllegalArgumentException(String.format("Index %d is out of "
+                + "bounds", index)));
+        }
+        // If the path is empty, the only valid option is also an empty path.
+        if (this.pathString.isEmpty()) {
+            return this;
+        }
+
+        return this.parentFileSystem.getPath(this.splitToElements(this.withoutRoot())[index]);
+    }
+
+    /**
+     * Returns a relative Path that is a subsequence of the name elements of this path.
+     * <p>
+     * The beginIndex and endIndex parameters specify the subsequence of name elements. The name that is closest to the
+     * root in the directory hierarchy has index 0. The name that is farthest from the root has index {@code count-1}.
+     * The returned Path object has the name elements that begin at beginIndex and extend to the element at index
+     * {@code endIndex-1}.
+     *
+     * @param begin the index of the first element, inclusive
+     * @param end the index of the last element, exclusive
+     * @return a new Path object that is a subsequence of the name elements in this Path
+     */
+    @Override
+    public Path subpath(int begin, int end) {
+        if (begin < 0 || begin >= this.getNameCount()
+            || end <= begin || end > this.getNameCount()) {
+            throw LoggingUtility.logError(LOGGER,
+                new IllegalArgumentException(String.format("Values of begin: %d and end: %d are invalid", begin, end)));
+        }
+
+        String[] subnames = Stream.of(this.splitToElements(this.withoutRoot()))
+            .skip(begin)
+            .limit(end - begin)
+            .toArray(String[]::new);
+
+        return this.parentFileSystem.getPath(String.join(this.parentFileSystem.getSeparator(), subnames));
+    }
+
+    /**
+     * Tests if this path starts with the given path.
+     * <p>
+     * This path starts with the given path if this path's root component starts with the root component of the given
+     * path, and this path starts with the same name elements as the given path. If the given path has more name
+     * elements than this path then false is returned.
+     * <p>
+     * If this path does not have a root component and the given path has a root component then this path does not start
+     * with the given path.
+     * <p>
+     * If the given path is associated with a different FileSystem to this path then false is returned.
+     * <p>
+     * In this implementation, a root component starts with another root component if the two root components are
+     * equivalent strings. In other words, if the files are stored in the same container.
+     *
+     * @param path the given path
+     * @return true if this path starts with the given path; otherwise false
+     */
+    @Override
+    public boolean startsWith(Path path) {
+        if (!path.getFileSystem().equals(this.parentFileSystem)) {
+            return false;
+        }
+
+        // An empty path never starts with another path and is never the start of another path.
+        if (this.pathString.isEmpty() ^ ((AzurePath) path).pathString.isEmpty()) {
+            return false;
+        }
+
+        String[] thisPathElements = this.splitToElements();
+        String[] otherPathElements = ((AzurePath) path).splitToElements();
+        if (otherPathElements.length > thisPathElements.length) {
+            return false;
+        }
+        for (int i = 0; i < otherPathElements.length; i++) {
+            if (!otherPathElements[i].equals(thisPathElements[i])) {
+                return false;
+            }
+        }
+
+        return true;
+    }
+
+    /**
+     * Tests if this path starts with a Path, constructed by converting the given path string, in exactly the manner
+     * specified by the startsWith(Path) method.
+     *
+     * @param path the given path string
+     * @return true if this path starts with the given path; otherwise false
+     * @throws InvalidPathException If the path string cannot be converted to a Path.
+     */
+    @Override
+    public boolean startsWith(String path) {
+        return this.startsWith(this.parentFileSystem.getPath(path));
+    }
+
+    /**
+     * Tests if this path ends with the given path.
+     * <p>
+     * If the given path has N elements, and no root component, and this path has N or more elements, then this path
+     * ends with the given path if the last N elements of each path, starting at the element farthest from the root,
+     * are equal.
+     * <p>
+     * If the given path has a root component then this path ends with the given path if the root component of this path
+     * ends with the root component of the given path, and the corresponding elements of both paths are equal. If this
+     * path does not have a root component and the given path has a root component then this path does not end with the
+     * given path.
+     * <p>
+     * If the given path is associated with a different FileSystem to this path then false is returned.
+     * <p>
+     * In this implementation, a root component ends with another root component if the two root components are
+     * equivalent strings. In other words, if the files are stored in the same container.
+     *
+     * @param path the given path
+     * @return true if this path ends with the given path; otherwise false
+     */
+    @Override
+    public boolean endsWith(Path path) {
+        /*
+        There can only be one instance of a file system with a given id, so comparing object identity is equivalent
+        to checking ids here.
+         */
+        if (path.getFileSystem() != this.parentFileSystem) {
+            return false;
+        }
+
+        // An empty path never ends with another path and is never the end of another path.
+        if (this.pathString.isEmpty() ^ ((AzurePath) path).pathString.isEmpty()) {
+            return false;
+        }
+
+        String[] thisPathElements = this.splitToElements();
+        String[] otherPathElements = ((AzurePath) path).splitToElements();
+        if (otherPathElements.length > thisPathElements.length) {
+            return false;
+        }
+        // If the given path has a root component, the paths must be equal.
+        if (path.getRoot() != null && otherPathElements.length != thisPathElements.length) {
+            return false;
+        }
+        for (int i = 1; i <= otherPathElements.length; i++) {
+            if (!otherPathElements[otherPathElements.length - i]
+                .equals(thisPathElements[thisPathElements.length - i])) {
+                return false;
+            }
+        }
+        return true;
+    }
+
+    /**
+     * Tests if this path ends with a Path, constructed by converting the given path string, in exactly the manner
+     * specified by the endsWith(Path) method.
+     *
+     * @param path the given path string
+     * @return true if this path starts with the given path; otherwise false
+     * @throws InvalidPathException If the path string cannot be converted to a Path.
+     */
+    @Override
+    public boolean endsWith(String path) {
+        return this.endsWith(this.parentFileSystem.getPath(path));
+    }
+
+    /**
+     * Returns a path that is this path with redundant name elements eliminated.
+     * <p>
+     * It derives from this path, a path that does not contain redundant name elements. The "." and ".." are special
+     * names used to indicate the current directory and parent directory. All occurrences of "." are considered
+     * redundant. If a ".." is preceded by a non-".." name then both names are considered redundant (the process to
+     * identify such names is repeated until is it no longer applicable).
+     * <p>
+     * This method does not access the file system; the path may not locate a file that exists. Eliminating ".." and a
+     * preceding name from a path may result in the path that locates a different file than the original path
+     *
+     * @return the resulting path or this path if it does not contain redundant name elements; an empty path is returned
+     * if this path does have a root component and all name elements are redundant
+     *
+     */
+    @Override
+    public Path normalize() {
+        Deque<String> stack = new ArrayDeque<>();
+        String[] pathElements = this.splitToElements();
+        Path root = this.getRoot();
+        String rootStr = root == null ? null : root.toString();
+        for (String element : pathElements) {
+            if (".".equals(element)) {
+                continue;
+            } else if ("..".equals(element)) {
+                if (rootStr != null) {
+                    // Root path. We never push "..".
+                    if (!stack.isEmpty() && stack.peekLast().equals(rootStr)) {
+                        // Cannot go higher than root. Ignore.
+                        continue;
+                    } else {
+                        stack.removeLast();
+                    }
+                } else {
+                    // Relative paths can have an arbitrary number of ".." at the beginning.
+                    if (stack.isEmpty()) {
+                        stack.addLast(element);
+                    } else if (stack.peek().equals("..")) {
+                        stack.addLast(element);
+                    } else {
+                        stack.removeLast();
+                    }
+                }
+            } else {
+                stack.addLast(element);
+            }
+        }
+
+        return this.parentFileSystem.getPath("", stack.toArray(new String[0]));
+    }
+
+    /**
+     * Resolve the given path against this path.
+     * <p>
+     * If the other parameter is an absolute path then this method trivially returns other. If other is an empty path
+     * then this method trivially returns this path. Otherwise, this method considers this path to be a directory and
+     * resolves the given path against this path. In the simplest case, the given path does not have a root component,
+     * in which case this method joins the given path to this path and returns a resulting path that ends with the given
+     * path. Where the given path has a root component then resolution is highly implementation dependent and therefore
+     * unspecified.
+     *
+     * @param path the path to resolve against this path
+     * @return the resulting path
+     */
+    @Override
+    public Path resolve(Path path) {
+        if (path.isAbsolute()) {
+            return path;
+        }
+        if (path.getNameCount() == 0) {
+            return this;
+        }
+        return this.parentFileSystem.getPath(this.toString(), path.toString());
+    }
+
+    /**
+     * Converts a given path string to a Path and resolves it against this Path in exactly the manner specified by the
+     * {@link #resolve(Path) resolve} method.
+     *
+     * @param path the path string to resolve against this path
+     * @return the resulting path
+     * @throws InvalidPathException if the path string cannot be converted to a Path.
+     */
+    @Override
+    public Path resolve(String path) {
+        return this.resolve(this.parentFileSystem.getPath(path));
+    }
+
+    /**
+     * Resolves the given path against this path's parent path. This is useful where a file name needs to be replaced
+     * with another file name. For example, suppose that the name separator is "/" and a path represents
+     * "dir1/dir2/foo", then invoking this method with the Path "bar" will result in the Path "dir1/dir2/bar". If this
+     * path does not have a parent path, or other is absolute, then this method returns other. If other is an empty path
+     * then this method returns this path's parent, or where this path doesn't have a parent, the empty path.
+     *
+     * @param path the path to resolve against this path's parent
+     * @return the resulting path
+     */
+    @Override
+    public Path resolveSibling(Path path) {
+        if (path.isAbsolute()) {
+            return path;
+        }
+
+        Path parent = this.getParent();
+        return parent == null ? path : parent.resolve(path);
+    }
+
+    /**
+     * Converts a given path string to a Path and resolves it against this path's parent path in exactly the manner
+     * specified by the resolveSibling method.
+     *
+     * @param path the path string to resolve against this path's parent
+     * @return the resulting path
+     * @throws InvalidPathException if the path string cannot be converted to a Path.
+     */
+    @Override
+    public Path resolveSibling(String path) {
+        return this.resolveSibling(this.parentFileSystem.getPath(path));
+    }
+
+    /**
+     * Constructs a relative path between this path and a given path.
+     * <p>
+     * Relativization is the inverse of resolution. This method attempts to construct a relative path that when resolved
+     * against this path, yields a path that locates the same file as the given path.
+     * <p>
+     * A relative path cannot be constructed if only one of the paths have a root component. If both paths have a root
+     * component, it is still possible to relativize one against the other. If this path and the given path are equal
+     * then an empty path is returned.
+     * <p>
+     * For any two normalized paths p and q, where q does not have a root component,
+     *     {@code p.relativize(p.resolve(q)).equals(q)}
+     *
+     * @param path the path to relativize against this path
+     * @return the resulting relative path, or an empty path if both paths are equal
+     * @throws IllegalArgumentException if other is not a Path that can be relativized against this path
+     */
+    @Override
+    public Path relativize(Path path) {
+        if (path.getRoot() == null ^ this.getRoot() == null) {
+            throw LoggingUtility.logError(LOGGER,
+                new IllegalArgumentException("Both paths must be absolute or neither can be"));
+        }
+
+        AzurePath thisNormalized = (AzurePath) this.normalize();
+        Path otherNormalized = path.normalize();
+
+        Deque<String> deque = new ArrayDeque<>(
+            Arrays.asList(otherNormalized.toString().split(this.parentFileSystem.getSeparator())));
+
+        int i = 0;
+        String[] thisElements = thisNormalized.splitToElements();
+        while (i < thisElements.length && !deque.isEmpty() && thisElements[i].equals(deque.peekFirst())) {
+            deque.removeFirst();
+            i++;
+        }
+        while (i < thisElements.length) {
+            deque.addFirst("..");
+            i++;
+        }
+
+        return this.parentFileSystem.getPath("", deque.toArray(new String[0]));
+    }
+
+    /**
+     * Returns a URI to represent this path.
+     * <p>
+     * This method constructs an absolute URI with a scheme equal to the URI scheme that identifies the provider.
+     * <p>
+     * No authority component is defined for the {@code URI} returned by this method. This implementation offers the
+     * same equivalence guarantee as the default provider.
+     *
+     * @return the URI representing this path
+     * @throws SecurityException never
+     */
+    @Override
+    public URI toUri() {
+        try {
+            return new URI(this.parentFileSystem.provider().getScheme(), null, "/" + this.toAbsolutePath(),
+                null, null);
+        } catch (URISyntaxException e) {
+            throw LoggingUtility.logError(LOGGER, new IllegalStateException("Unable to create valid URI from path", e));
+        }
+    }
+
+    /**
+     * Returns a Path object representing the absolute path of this path.
+     * <p>
+     * If this path is already absolute then this method simply returns this path. Otherwise, this method resolves the
+     * path against the default directory.
+     *
+     * @return a Path object representing the absolute path
+     * @throws SecurityException never
+     */
+    @Override
+    public Path toAbsolutePath() {
+        if (this.isAbsolute()) {
+            return this;
+        }
+        return this.parentFileSystem.getDefaultDirectory().resolve(this);
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @param linkOptions options
+     * @return the real path
+     * @throws UnsupportedOperationException operation not supported.
+     */
+    @Override
+    public Path toRealPath(LinkOption... linkOptions) throws IOException {
+        throw new UnsupportedOperationException("Symbolic links are not supported.");
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @return the file
+     * @throws UnsupportedOperationException operation not supported.
+     */
+    @Override
+    public File toFile() {
+        throw new UnsupportedOperationException();
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @param watchService watchService
+     * @param kinds kinds
+     * @param modifiers modifiers
+     * @return the watch key
+     * @throws UnsupportedOperationException operation not supported.
+     */
+    @Override
+    public WatchKey register(WatchService watchService, WatchEvent.Kind<?>[] kinds, WatchEvent.Modifier... modifiers)
+        throws IOException {
+        throw new UnsupportedOperationException("WatchEvents are not supported.");
+    }
+
+    /**
+     * Unsupported.
+     *
+     * @param watchService watchService
+     * @param kinds kinds
+     * @return the watch key
+     * @throws UnsupportedOperationException operation not supported.
+     */
+    @Override
+    public WatchKey register(WatchService watchService, WatchEvent.Kind<?>... kinds) throws IOException {
+        throw new UnsupportedOperationException("WatchEvents are not supported.");
+    }
+
+    /**
+     * Returns an iterator over the name elements of this path.
+     * <p>
+     * The first element returned by the iterator represents the name element that is closest to the root in the
+     * directory hierarchy, the second element is the next closest, and so on. The last element returned is the name of
+     * the file or directory denoted by this path. The root component, if present, is not returned by the iterator.
+     *
+     * @return an iterator over the name elements of this path.
+     */
+    @Override
+    public Iterator<Path> iterator() {
+        if (this.pathString.isEmpty()) {
+            return Collections.singletonList((Path) this).iterator();
+        }
+        return Arrays.asList(Stream.of(this.splitToElements(this.withoutRoot()))
+            .map(s -> this.parentFileSystem.getPath(s))
+            .toArray(Path[]::new))
+            .iterator();
+    }
+
+    /**
+     * Compares two abstract paths lexicographically. This method does not access the file system and neither file is
+     * required to exist.
+     * <p>
+     * This method may not be used to compare paths that are associated with different file system providers.
+     * <p>
+     * This result of this method is identical to a string comparison on the underlying path strings.
+     *
+     * @return zero if the argument is equal to this path, a value less than zero if this path is lexicographically less
+     * than the argument, or a value greater than zero if this path is lexicographically greater than the argument
+     * @throws ClassCastException if the paths are associated with different providers
+     */
+    @Override
+    public int compareTo(Path path) {
+        if (!(path instanceof AzurePath)) {
+            throw LoggingUtility.logError(LOGGER, new ClassCastException("Other path is not an instance of "
+                + "AzurePath."));
+        }
+
+        return this.pathString.compareTo(((AzurePath) path).pathString);
+    }
+
+    /**
+     * Returns the string representation of this path.
+     * <p>
+     * If this path was created by converting a path string using the getPath method then the path string returned by
+     * this method may differ from the original String used to create the path.
+     * <p>
+     * The returned path string uses the default name separator to separate names in the path.
+     *
+     * @return the string representation of this path
+     */
+    @Override
+    public String toString() {
+        return this.pathString;
+    }
+
+    /**
+     * A path is considered equal to another path if it is associated with the same file system instance and if the
+     * path strings are equivalent.
+     *
+     * @return true if, and only if, the given object is a Path that is identical to this Path
+     */
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
+        AzurePath paths = (AzurePath) o;
+        return Objects.equals(parentFileSystem, paths.parentFileSystem)
+            && Objects.equals(pathString, paths.pathString);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(parentFileSystem, pathString);
+    }
+
+    /**
+     * Returns a {@link BlobClient} which references a blob pointed to by this path. Note that this does not guarantee
+     * the existence of the blob at this location.
+     *
+     * @return a {@link BlobClient}.
+     * @throws IOException If the path only contains a root component or is empty
+     */
+    public BlobClient toBlobClient() throws IOException {
+        /*
+        We don't store the blob client because unlike other types in this package, a Path does not actually indicate the
+        existence or even validity of any remote resource. It is purely a representation of a path. Therefore, we do not
+        construct the client or perform any validation until it is requested.
+        */
+        // Converting to an absolute path ensures there is a container to operate on even if it is the default.
+        // Normalizing ensures the path is clean.
+        Path root = this.normalize().toAbsolutePath().getRoot();
+        if (root == null) {
+            throw LoggingUtility.logError(LOGGER,
+                new IllegalStateException("Root should never be null after calling toAbsolutePath."));
+        }
+        String fileStoreName = this.rootToFileStore(root.toString());
+
+        BlobContainerClient containerClient =
+            ((AzureFileStore) this.parentFileSystem.getFileStore(fileStoreName)).getContainerClient();
+
+        String blobName = this.withoutRoot();
+        if (blobName.isEmpty()) {
+            throw LoggingUtility.logError(LOGGER, new IOException("Cannot get a blob client to a path that only "
+                + "contains the root or is an empty path"));
+        }
+
+        return containerClient.getBlobClient(blobName);
+    }
+
+    /**
+     * A utility method to conveniently convert from a URL to a storage resource to an {@code AzurePath} pointing to the
+     * same resource.
+     *
+     * The url must be well formatted. There must be an open filesystem corresponding to the account which contains the
+     * blob. Otherwise, a {@link java.nio.file.FileSystemNotFoundException} will be thrown.
+     *
+     * The url may point to either an account, container, or blob. If it points to an account, the path will be empty,
+     * but it will have an internal reference to the file system containing it, meaning instance methods may be
+     * performed on the path to construct a reference to another object. If it points to a container, there will be one
+     * element, which is the root element. Everything after the container, that is the blob name, will then be appended
+     * after the root element.
+     *
+     * IP style urls are not currently supported.
+     *
+     * The {@link AzureFileSystemProvider} can typically be obtained via {@link AzureFileSystem#provider()}.
+     *
+     * @param provider The installed {@link AzureFileSystemProvider} that manages open file systems for this jvm.
+     * @param url The url to the desired resource.
+     * @return An {@link AzurePath} which points to the resource identified by the url.
+     * @throws URISyntaxException If the url contains elements which are not well formatted.
+     */
+    public static AzurePath fromBlobUrl(AzureFileSystemProvider provider, String url) throws URISyntaxException {
+        BlobUrlParts parts = BlobUrlParts.parse(url);
+        URI fileSystemUri = hostToFileSystemUri(provider, parts.getScheme(), parts.getHost());
+        FileSystem parentFileSystem = provider.getFileSystem(fileSystemUri);
+        return new AzurePath((AzureFileSystem) parentFileSystem, fileStoreToRoot(parts.getBlobContainerName()),
+            parts.getBlobName() == null ? "" : parts.getBlobName());
+    }
+
+    /**
+     * @return Whether this path consists of only a root component.
+     */
+    boolean isRoot() {
+        return this.equals(this.getRoot());
+    }
+
+    private String withoutRoot() {
+        Path root = this.getRoot();
+        String str = this.pathString;
+        if (root != null) {
+            str = this.pathString.substring(root.toString().length());
+        }
+        if (str.startsWith(this.parentFileSystem.getSeparator())) {
+            str = str.substring(1);
+        }
+
+        return str;
+    }
+
+    private String[] splitToElements() {
+        return this.splitToElements(this.pathString);
+    }
+
+    private String[] splitToElements(String str) {
+        String[] arr = str.split(this.parentFileSystem.getSeparator());
+        /*
+        This is a special case where we split after removing the root from a path that is just the root. Or otherwise
+        have an empty path.
+         */
+        if (arr.length == 1 && arr[0].isEmpty()) {
+            return new String[0];
+        }
+        return arr;
+    }
+
+    private String rootToFileStore(String root) {
+        return root.substring(0, root.length() - 1); // Remove the ROOT_DIR_SUFFIX
+    }
+
+    private static String fileStoreToRoot(String fileStore) {
+        if (fileStore == null || "".equals(fileStore)) {
+            return "";
+        }
+        return fileStore + ROOT_DIR_SUFFIX;
+    }
+
+    private static URI hostToFileSystemUri(AzureFileSystemProvider provider, String scheme, String host)
+        throws URISyntaxException {
+        return new URI(provider.getScheme() + "://?endpoint=" + scheme + "://" + host);
+    }
+
+    static void ensureFileSystemOpen(Path p) {
+        if (!p.getFileSystem().isOpen()) {
+            throw LoggingUtility.logError(LOGGER, new ClosedFileSystemException());
+        }
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureResource.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureResource.java
new file mode 100644
index 00000000000..92fb14a62cc
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureResource.java
@@ -0,0 +1,284 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.BlobContainerClient;
+import com.azure.storage.blob.BlobClient;
+import com.azure.storage.blob.BlobContainerClientBuilder;
+import com.azure.storage.blob.models.BlobHttpHeaders;
+import com.azure.storage.blob.models.BlobItem;
+import com.azure.storage.blob.models.BlobListDetails;
+import com.azure.storage.blob.models.BlobProperties;
+import com.azure.storage.blob.models.BlobRequestConditions;
+import com.azure.storage.blob.models.BlobStorageException;
+import com.azure.storage.blob.models.ListBlobsOptions;
+import com.azure.storage.blob.models.ParallelTransferOptions;
+import com.azure.storage.blob.options.BlockBlobOutputStreamOptions;
+import com.azure.storage.blob.specialized.BlobOutputStream;
+import com.azure.storage.common.implementation.Constants;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.attribute.FileAttribute;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+/**
+ * This type is meant to be a logical grouping of operations and data associated with an azure resource. It is NOT
+ * intended to serve as a local cache for any data related to remote resources. It is agnostic to whether the resource
+ * is a directory or a file and will not perform any validation of the resource type, though root directories are not
+ * supported as they are backed by containers and do not support many file system apis.
+ *
+ * It also serves as the interface to Storage clients. Any operation that needs to use a client should first build an
+ * AzureResource using a path and then use the getter to access the client.
+ */
+final class AzureResource {
+    private static final ClientLogger LOGGER = new ClientLogger(AzureResource.class);
+
+    static final String DIR_METADATA_MARKER = Constants.HeaderConstants.DIRECTORY_METADATA_KEY;
+
+    private final AzurePath path;
+    private final BlobClient blobClient;
+
+    // The following are not kept consistent with the service. They are only held here between parsing and putting.
+    private BlobHttpHeaders blobHeaders;
+    private Map<String, String> blobMetadata;
+
+    AzureResource(Path path) throws IOException {
+        Objects.requireNonNull(path, "path");
+        this.path = validatePathInstanceType(path);
+        this.validateNotRoot();
+        this.blobClient = this.path.toBlobClient();
+    }
+
+    /**
+     * Checks for the existence of the parent of the given path. We do not check for the actual marker blob as parents
+     * need only weakly exist.
+     *
+     * If the parent is a root (container), it will be assumed to exist, so it must be validated elsewhere that the
+     * container is a legitimate root within this file system.
+     */
+    boolean checkParentDirectoryExists() throws IOException {
+        /*
+        If the parent is just the root (or null, which means the parent is implicitly the default directory which is a
+        root), that means we are checking a container, which is always considered to exist. Otherwise, perform normal
+        existence check.
+         */
+        Path parent = this.path.getParent();
+        return (parent == null || parent.equals(path.getRoot()))
+            || new AzureResource(this.path.getParent()).checkDirectoryExists();
+    }
+
+    /**
+     * Checks whether a directory exists by either being empty or having children.
+     */
+    boolean checkDirectoryExists() throws IOException {
+        DirectoryStatus dirStatus = this.checkDirStatus();
+        return dirStatus.equals(DirectoryStatus.EMPTY) || dirStatus.equals(DirectoryStatus.NOT_EMPTY);
+    }
+
+    /*
+    This method will check specifically whether there is a virtual directory at this location. It must be known before
+    that there is no file present at the destination.
+     */
+    boolean checkVirtualDirectoryExists() throws IOException {
+        DirectoryStatus dirStatus = this.checkDirStatus(false);
+        return dirStatus.equals(DirectoryStatus.NOT_EMPTY); // Virtual directories cannot be empty
+    }
+
+    /**
+     * This method will check if a directory is extant and/or empty and accommodates virtual directories. This method
+     * will not check the status of root directories.
+     */
+    DirectoryStatus checkDirStatus() throws IOException {
+        if (this.blobClient == null) {
+            throw LoggingUtility.logError(LOGGER, new IllegalArgumentException("The blob client was null."));
+        }
+
+        /*
+         * Do a get properties first on the directory name. This will determine if it is concrete&&exists or is either
+         * virtual or doesn't exist.
+         */
+        BlobProperties props = null;
+        boolean exists = false;
+        try {
+            props = this.getBlobClient().getProperties();
+            exists = true;
+        } catch (BlobStorageException e) {
+            if (e.getStatusCode() != 404) {
+                throw LoggingUtility.logError(LOGGER, new IOException(e));
+            }
+        }
+
+        // Check if the resource is a file or directory before listing
+        if (exists && !props.getMetadata().containsKey(AzureResource.DIR_METADATA_MARKER)) {
+            return DirectoryStatus.NOT_A_DIRECTORY;
+        }
+
+        return checkDirStatus(exists);
+    }
+
+    /*
+    This method will determine the status of the directory given it is already known whether or not there is an object
+    at the target.
+     */
+    DirectoryStatus checkDirStatus(boolean exists) throws IOException {
+        BlobContainerClient containerClient = this.getContainerClient();
+
+        // List on the directory name + '/' so that we only get things under the directory if any
+        ListBlobsOptions listOptions = new ListBlobsOptions().setMaxResultsPerPage(2)
+            .setPrefix(this.blobClient.getBlobName() + AzureFileSystem.PATH_SEPARATOR)
+            .setDetails(new BlobListDetails().setRetrieveMetadata(true));
+
+        /*
+         * If listing returns anything, then it is not empty. If listing returns nothing and exists() was true, then it's
+         * empty Else it does not exist
+         */
+        try {
+            Iterator<BlobItem> blobIterator = containerClient.listBlobsByHierarchy(AzureFileSystem.PATH_SEPARATOR,
+                listOptions, null).iterator();
+            if (blobIterator.hasNext()) {
+                return DirectoryStatus.NOT_EMPTY;
+            } else if (exists) {
+                return DirectoryStatus.EMPTY;
+            } else {
+                return DirectoryStatus.DOES_NOT_EXIST;
+            }
+        } catch (BlobStorageException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    /**
+     * Creates the actual directory marker. This method should only be used when any necessary checks for proper
+     * conditions of directory creation (e.g. parent existence) have already been performed. Otherwise,
+     * {@link AzureFileSystemProvider#createDirectory(Path, FileAttribute[])} should be preferred.
+     *
+     * @param requestConditions Any necessary request conditions to pass when creating the directory blob.
+     */
+    void putDirectoryBlob(BlobRequestConditions requestConditions) {
+        this.blobClient.getBlockBlobClient().commitBlockListWithResponse(Collections.emptyList(), this.blobHeaders,
+            this.prepareMetadataForDirectory(), null, requestConditions, null, null);
+    }
+
+    /*
+    Note that this will remove the properties from the list of attributes as it finds them.
+     */
+    private void extractHttpHeaders(List<FileAttribute<?>> fileAttributes) {
+        BlobHttpHeaders headers = new BlobHttpHeaders();
+        for (Iterator<FileAttribute<?>> it = fileAttributes.iterator(); it.hasNext();) {
+            FileAttribute<?> attr = it.next();
+            boolean propertyFound = true;
+            switch (attr.name()) {
+                case AzureFileSystemProvider.CONTENT_TYPE:
+                    headers.setContentType(attr.value().toString());
+                    break;
+                case AzureFileSystemProvider.CONTENT_LANGUAGE:
+                    headers.setContentLanguage(attr.value().toString());
+                    break;
+                case AzureFileSystemProvider.CONTENT_DISPOSITION:
+                    headers.setContentDisposition(attr.value().toString());
+                    break;
+                case AzureFileSystemProvider.CONTENT_ENCODING:
+                    headers.setContentEncoding(attr.value().toString());
+                    break;
+                case AzureFileSystemProvider.CONTENT_MD5:
+                    if ((attr.value() instanceof byte[])) {
+                        headers.setContentMd5((byte[]) attr.value());
+                    } else {
+                        throw LoggingUtility.logError(LOGGER,
+                            new UnsupportedOperationException("Content-MD5 attribute must be a byte[]"));
+                    }
+                    break;
+                case AzureFileSystemProvider.CACHE_CONTROL:
+                    headers.setCacheControl(attr.value().toString());
+                    break;
+                default:
+                    propertyFound = false;
+                    break;
+            }
+
+            if (propertyFound) {
+                it.remove();
+            }
+        }
+
+        this.blobHeaders = headers;
+    }
+
+    /**
+     * Note this should only be used after the headers have been extracted.
+     *
+     * @param fileAttributes The attributes to convert to metadata.
+     */
+    private void convertAttributesToMetadata(List<FileAttribute<?>> fileAttributes) {
+        Map<String, String> metadata = new HashMap<>();
+        for (FileAttribute<?> attr : fileAttributes) {
+            metadata.put(attr.name(), attr.value().toString());
+        }
+
+        // If no attributes are set, return null so existing metadata is not cleared.
+        this.blobMetadata = metadata.isEmpty() ? null : metadata;
+    }
+
+    private void validateNotRoot() {
+        if (this.path.isRoot()) {
+            throw LoggingUtility.logError(LOGGER, new IllegalArgumentException(
+                "Root directory not supported. Path: " + this.path));
+        }
+    }
+
+    private AzurePath validatePathInstanceType(Path path) {
+        if (!(path instanceof AzurePath)) {
+            throw LoggingUtility.logError(LOGGER, new IllegalArgumentException("This provider cannot operate on "
+                + "subtypes of Path other than AzurePath"));
+        }
+        return (AzurePath) path;
+    }
+
+    BlobContainerClient getContainerClient() {
+        return new BlobContainerClientBuilder().endpoint(this.blobClient.getBlobUrl())
+            .pipeline(this.blobClient.getHttpPipeline())
+            .buildClient();
+    }
+
+    AzureResource setFileAttributes(List<FileAttribute<?>> attributes) {
+        attributes = new ArrayList<>(attributes); // To ensure removing header values from the list is supported.
+        extractHttpHeaders(attributes);
+        convertAttributesToMetadata(attributes);
+
+        return this;
+    }
+
+    AzurePath getPath() {
+        return this.path;
+    }
+
+    BlobClient getBlobClient() {
+        return this.blobClient;
+    }
+
+    BlobOutputStream getBlobOutputStream(ParallelTransferOptions pto, BlobRequestConditions rq) {
+        BlockBlobOutputStreamOptions options = new BlockBlobOutputStreamOptions()
+            .setHeaders(this.blobHeaders)
+            .setMetadata(this.blobMetadata)
+            .setParallelTransferOptions(pto)
+            .setRequestConditions(rq);
+        return this.blobClient.getBlockBlobClient().getBlobOutputStream(options);
+    }
+
+    private Map<String, String> prepareMetadataForDirectory() {
+        if (this.blobMetadata == null) {
+            this.blobMetadata = new HashMap<>();
+        }
+        this.blobMetadata.put(DIR_METADATA_MARKER, "true");
+        return this.blobMetadata;
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureSeekableByteChannel.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureSeekableByteChannel.java
new file mode 100644
index 00000000000..e51e727450b
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureSeekableByteChannel.java
@@ -0,0 +1,245 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import com.azure.core.util.logging.ClientLogger;
+
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.channels.ClosedChannelException;
+import java.nio.channels.NonReadableChannelException;
+import java.nio.channels.NonWritableChannelException;
+import java.nio.channels.SeekableByteChannel;
+import java.nio.file.Path;
+
+/**
+ * A byte channel that maintains a current position.
+ * <p>
+ * A channel may only be opened in read mode OR write mode. It may not be opened in read/write mode. Seeking is
+ * supported for reads, but not for writes. Modifications to existing files is not permitted--only creating new files or
+ * overwriting existing files.
+ * <p>
+ * This type is not threadsafe to prevent having to hold locks across network calls.
+ */
+public final class AzureSeekableByteChannel implements SeekableByteChannel {
+    private static final ClientLogger LOGGER = new ClientLogger(AzureSeekableByteChannel.class);
+
+    private final NioBlobInputStream reader;
+    private final NioBlobOutputStream writer;
+    private long position;
+    private boolean closed = false;
+    private final Path path;
+    /*
+    If this type needs to be made threadsafe, closed should be volatile. We need to add a lock to guard updates to
+    position or make it an atomicLong. If we have a lock, we have to be careful about holding while doing io ops and at
+    least ensure timeouts are set. We probably have to duplicate or copy the buffers for at least writing to ensure they
+     don't get overwritten.
+     */
+
+    AzureSeekableByteChannel(NioBlobInputStream inputStream, Path path) {
+        this.reader = inputStream;
+        /*
+        We mark at the beginning (we always construct a stream to the beginning of the blob) to support seeking. We can
+        effectively seek anywhere by always marking at the beginning of the blob and then a seek is resetting to that
+        mark and skipping.
+         */
+        inputStream.mark(Integer.MAX_VALUE);
+        this.writer = null;
+        this.position = 0;
+        this.path = path;
+    }
+
+    AzureSeekableByteChannel(NioBlobOutputStream outputStream, Path path) {
+        this.writer = outputStream;
+        this.reader = null;
+        this.position = 0;
+        this.path = path;
+    }
+
+    @Override
+    public int read(ByteBuffer dst) throws IOException {
+        AzurePath.ensureFileSystemOpen(this.path);
+        validateOpen();
+        validateReadMode();
+
+        // See comments in position(), remember that position is 0-based and size() is exclusive
+        if (this.position >= this.size()) {
+            return -1; // at or past EOF
+        }
+
+        // If the buffer is backed by an array, we can write directly to that instead of allocating new memory.
+        int pos;
+        final int limit;
+        final byte[] buf;
+        if (dst.hasArray()) {
+            // ByteBuffer has a position and limit that define the bounds of the writeable area, and that
+            // area can be both smaller than the backing array and might not begin at array index 0.
+            pos = dst.position();
+            limit = pos + dst.remaining();
+            buf = dst.array();
+        } else {
+            pos = 0;
+            limit = dst.remaining();
+            buf = new byte[limit];
+        }
+
+        while (pos < limit) {
+            int byteCount = this.reader.read(buf, pos, limit - pos);
+            if (byteCount == -1) {
+                break;
+            }
+            pos += byteCount;
+        }
+
+        /*
+        Either write to the destination if we had to buffer separately or just set the position correctly if we wrote
+        underneath the buffer
+         */
+        int count;
+        if (dst.hasArray()) {
+            count = pos - dst.position();
+            dst.position(pos);
+        } else {
+            count = pos; // original position was 0
+            dst.put(buf, 0, count);
+        }
+
+        this.position += count;
+        return count;
+    }
+
+    @Override
+    public int write(ByteBuffer src) throws IOException {
+        AzurePath.ensureFileSystemOpen(this.path);
+        validateOpen();
+        validateWriteMode();
+
+        final int length = src.remaining();
+        this.position += length;
+
+        /*
+        If the buffer is backed by an array, we can read directly from that instead of allocating new memory.
+        Set the position correctly if we read from underneath the buffer
+         */
+        int pos;
+        byte[] buf;
+        if (src.hasArray()) {
+            // ByteBuffer has a position and limit that define the bounds of the readable area, and that
+            // area can be both smaller than the backing array and might not begin at array index 0.
+            pos = src.position();
+            buf = src.array();
+            src.position(pos + length);
+        } else {
+            pos = 0;
+            buf = new byte[length];
+            src.get(buf); // advances src.position()
+        }
+        // Either way, the src.position() and this.position have been updated before we know if this write
+        // will succeed. (Original behavior.) It may be better to update position(s) only *after* success,
+        // but then on IOException would we know if there was a partial write, and if so how much?
+        this.writer.write(buf, pos, length);
+        return length;
+    }
+
+    @Override
+    public long position() throws IOException {
+        AzurePath.ensureFileSystemOpen(this.path);
+        validateOpen();
+
+        return this.position;
+    }
+
+    @Override
+    public AzureSeekableByteChannel position(long newPosition) throws IOException {
+        AzurePath.ensureFileSystemOpen(this.path);
+        validateOpen();
+        validateReadMode();
+
+        if (newPosition < 0) {
+            throw LoggingUtility.logError(LOGGER, new IllegalArgumentException("Seek position cannot be negative"));
+        }
+
+        /*
+        The javadoc says seeking past the end for reading is legal and that it should indicate the end of the file on
+        the next read. StorageInputStream doesn't allow this, but we can get around that by modifying the
+        position variable and skipping the actual read (when read is called next); we'll check in read if we've seeked
+        past the end and short circuit there as well.
+
+        Because we are in read mode this will always give us the size from properties.
+         */
+        if (newPosition > this.size()) {
+            this.position = newPosition;
+            return this;
+        }
+        this.reader.reset(); // Because we always mark at the beginning, this will reset us back to the beginning.
+        this.reader.mark(Integer.MAX_VALUE);
+        long skipAmount = this.reader.skip(newPosition);
+        if (skipAmount < newPosition) {
+            throw new IOException("Could not set desired position");
+        }
+        this.position = newPosition;
+
+        return this;
+    }
+
+    @Override
+    public long size() throws IOException {
+        AzurePath.ensureFileSystemOpen(this.path);
+        validateOpen();
+
+        /*
+        If we are in read mode, the size is the size of the file.
+        If we are in write mode, the size is the amount of data written so far.
+         */
+        if (reader != null) {
+            return reader.getBlobInputStream().getProperties().getBlobSize();
+        } else {
+            return position;
+        }
+    }
+
+    @Override
+    public AzureSeekableByteChannel truncate(long size) throws IOException {
+        throw LoggingUtility.logError(LOGGER, new UnsupportedOperationException());
+    }
+
+    @Override
+    public boolean isOpen() {
+        AzurePath.ensureFileSystemOpen(this.path);
+        return !this.closed;
+    }
+
+    @Override
+    public void close() throws IOException {
+        AzurePath.ensureFileSystemOpen(this.path);
+        if (this.reader != null) {
+            this.reader.close();
+        } else {
+            this.writer.close();
+        }
+        this.closed = true;
+    }
+
+    Path getPath() {
+        return this.path;
+    }
+
+    private void validateOpen() throws ClosedChannelException {
+        if (this.closed) {
+            throw LoggingUtility.logError(LOGGER, new ClosedChannelException());
+        }
+    }
+
+    private void validateReadMode() {
+        if (this.reader == null) {
+            throw LoggingUtility.logError(LOGGER, new NonReadableChannelException());
+        }
+    }
+
+    private void validateWriteMode() {
+        if (this.writer == null) {
+            throw LoggingUtility.logError(LOGGER, new NonWritableChannelException());
+        }
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/DirectoryStatus.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/DirectoryStatus.java
new file mode 100644
index 00000000000..8356a7ebeb1
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/DirectoryStatus.java
@@ -0,0 +1,23 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+/**
+ * RESERVED FOR INTERNAL USE.
+ *
+ * An enum to indicate the status of a directory.
+ */
+enum DirectoryStatus {
+    EMPTY, // The directory at least weakly exists and is empty.
+
+    NOT_EMPTY, // The directory at least weakly exists and has one or more children.
+
+    DOES_NOT_EXIST, // There is no resource at this path.
+
+    NOT_A_DIRECTORY; // A resource exists at this path, but it is not a directory.
+
+    static boolean isDirectory(DirectoryStatus status) {
+        return EMPTY.equals(status) || NOT_EMPTY.equals(status);
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/LoggingUtility.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/LoggingUtility.java
new file mode 100644
index 00000000000..3cd503f98c2
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/LoggingUtility.java
@@ -0,0 +1,16 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import com.azure.core.util.logging.ClientLogger;
+
+/**
+ * Only a minimal Utility class to get around a shortcoming in Core's logging.
+ */
+final class LoggingUtility {
+    public static <T extends Exception> T logError(ClientLogger logger, T e) {
+        logger.error(e.getMessage());
+        return e;
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/NioBlobInputStream.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/NioBlobInputStream.java
new file mode 100644
index 00000000000..676972dc93a
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/NioBlobInputStream.java
@@ -0,0 +1,211 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.specialized.BlobInputStream;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Path;
+
+/**
+ * Provides an InputStream to read a file stored as an Azure Blob.
+ */
+public final class NioBlobInputStream extends InputStream {
+    private static final ClientLogger LOGGER = new ClientLogger(NioBlobInputStream.class);
+
+    private final BlobInputStream blobInputStream;
+    private final Path path;
+
+    NioBlobInputStream(BlobInputStream blobInputStream, Path path) {
+        this.blobInputStream = blobInputStream;
+        this.path = path;
+    }
+
+    /**
+     * Returns an estimate of the number of bytes that can be read (or skipped over) from this input stream without
+     * blocking by the next invocation of a method for this input stream. The next invocation might be the same thread
+     * or another thread. A single read or skip of this many bytes will not block, but may read or skip fewer bytes.
+     *
+     * @return An <code>int</code> which represents an estimate of the number of bytes that can be read (or skipped
+     * over) from this input stream without blocking, or 0 when it reaches the end of the input stream.
+     */
+    @Override
+    public synchronized int available() throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        return this.blobInputStream.available();
+    }
+
+    /**
+     * Closes this input stream and releases any system resources associated with the stream.
+     */
+    @Override
+    public synchronized void close() throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        this.blobInputStream.close();
+    }
+
+    /**
+     * Marks the current position in this input stream. A subsequent call to the reset method repositions this stream at
+     * the last marked position so that subsequent reads re-read the same bytes.
+     *
+     * @param readlimit An <code>int</code> which represents the maximum limit of bytes that can be read before the mark
+     * position becomes invalid.
+     */
+    @Override
+    public synchronized void mark(final int readlimit) {
+        this.blobInputStream.mark(readlimit);
+    }
+
+    /**
+     * Tests if this input stream supports the mark and reset methods.
+     *
+     * @return Returns {@code true}
+     */
+    @Override
+    public boolean markSupported() {
+        return this.blobInputStream.markSupported();
+    }
+
+    /**
+     * Reads the next byte of data from the input stream. The value byte is returned as an int in the range 0 to 255. If
+     * no byte is available because the end of the stream has been reached, the value -1 is returned. This method blocks
+     * until input data is available, the end of the stream is detected, or an exception is thrown.
+     *
+     * @return An <code>int</code> which represents the total number of bytes read into the buffer, or -1 if there is no
+     * more data because the end of the stream has been reached.
+     * @throws IOException If an I/O error occurs.
+     */
+    @Override
+    public int read() throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            return this.blobInputStream.read();
+            /*
+            BlobInputStream only throws RuntimeException, and it doesn't preserve the cause, it only takes the message,
+            so we can't do any better than re-wrapping it in an IOException.
+             */
+        } catch (RuntimeException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    /**
+     * Reads some number of bytes from the input stream and stores them into the buffer array <code>b</code>. The number
+     * of bytes actually read is returned as an integer. This method blocks until input data is available, end of file
+     * is detected, or an exception is thrown. If the length of <code>b</code> is zero, then no bytes are read and 0 is
+     * returned; otherwise, there is an attempt to read at least one byte. If no byte is available because the stream is
+     * at the end of the file, the value -1 is returned; otherwise, at least one byte is read and stored into
+     * <code>b</code>.
+     *
+     * The first byte read is stored into element <code>b[0]</code>, the next one into <code>b[1]</code>, and so on. The
+     * number of bytes read is, at most, equal to the length of <code>b</code>. Let <code>k</code> be the number of
+     * bytes actually read; these bytes will be stored in elements <code>b[0]</code> through <code>b[k-1]</code>,
+     * leaving elements <code>b[k]</code> through
+     * <code>b[b.length-1]</code> unaffected.
+     *
+     * The <code>read(b)</code> method for class {@link InputStream} has the same effect as:
+     *
+     * <code>read(b, 0, b.length)</code>
+     *
+     * @param b A <code>byte</code> array which represents the buffer into which the data is read.
+     * @throws IOException If the first byte cannot be read for any reason other than the end of the file, if the input
+     * stream has been closed, or if some other I/O error occurs.
+     * @throws NullPointerException If the <code>byte</code> array <code>b</code> is null.
+     */
+    @Override
+    public int read(final byte[] b) throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            return this.blobInputStream.read(b);
+        } catch (RuntimeException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    /**
+     * Reads up to <code>len</code> bytes of data from the input stream into an array of bytes. An attempt is made to
+     * read as many as <code>len</code> bytes, but a smaller number may be read. The number of bytes actually read is
+     * returned as an integer. This method blocks until input data is available, end of file is detected, or an
+     * exception is thrown.
+     *
+     * If <code>len</code> is zero, then no bytes are read and 0 is returned; otherwise, there is an attempt to read at
+     * least one byte. If no byte is available because the stream is at end of file, the value -1 is returned;
+     * otherwise, at least one byte is read and stored into <code>b</code>.
+     *
+     * The first byte read is stored into element <code>b[off]</code>, the next one into <code>b[off+1]</code>, and so
+     * on. The number of bytes read is, at most, equal to <code>len</code>. Let <code>k</code> be the number of bytes
+     * actually read; these bytes will be stored in elements <code>b[off]</code> through <code>b[off+k-1]</code>,
+     * leaving elements <code>b[off+k]</code> through
+     * <code>b[off+len-1]</code> unaffected.
+     *
+     * In every case, elements <code>b[0]</code> through <code>b[off]</code> and elements <code>b[off+len]</code>
+     * through <code>b[b.length-1]</code> are unaffected.
+     *
+     * @param b A <code>byte</code> array which represents the buffer into which the data is read.
+     * @param off An <code>int</code> which represents the start offset in the <code>byte</code> array at which the data
+     * is written.
+     * @param len An <code>int</code> which represents the maximum number of bytes to read.
+     * @return An <code>int</code> which represents the total number of bytes read into the buffer, or -1 if there is no
+     * more data because the end of the stream has been reached.
+     * @throws IOException If the first byte cannot be read for any reason other than end of file, or if the input
+     * stream has been closed, or if some other I/O error occurs.
+     * @throws NullPointerException If the <code>byte</code> array <code>b</code> is null.
+     * @throws IndexOutOfBoundsException If <code>off</code> is negative, <code>len</code> is negative, or
+     * <code>len</code> is greater than
+     * <code>b.length - off</code>.
+     */
+    @Override
+    public int read(final byte[] b, final int off, final int len) throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        if (off < 0 || len < 0 || len > b.length - off) {
+            throw LOGGER.logExceptionAsError(new IndexOutOfBoundsException());
+        }
+        try {
+            return this.blobInputStream.read(b, off, len);
+        } catch (RuntimeException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    /**
+     * Repositions this stream to the position at the time the mark method was last called on this input stream. Note
+     * repositioning the blob read stream will disable blob MD5 checking.
+     *
+     * @throws IOException If this stream has not been marked or if the mark has been invalidated.
+     */
+    @Override
+    public synchronized void reset() throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            this.blobInputStream.reset();
+        } catch (RuntimeException e) {
+            if (e.getMessage().equals("Stream mark expired.")) {
+                throw LoggingUtility.logError(LOGGER, new IOException(e));
+            }
+            throw LoggingUtility.logError(LOGGER, e);
+        }
+    }
+
+    /**
+     * Skips over and discards n bytes of data from this input stream. The skip method may, for a variety of reasons,
+     * end up skipping over some smaller number of bytes, possibly 0. This may result from any of a number of
+     * conditions; reaching end of file before n bytes have been skipped is only one possibility. The actual number of
+     * bytes skipped is returned. If n is negative, no bytes are skipped.
+     *
+     * Note repositioning the blob read stream will disable blob MD5 checking.
+     *
+     * @param n A <code>long</code> which represents the number of bytes to skip.
+     */
+    @Override
+    public synchronized long skip(final long n) throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        return this.blobInputStream.skip(n);
+    }
+
+    BlobInputStream getBlobInputStream() {
+        return blobInputStream;
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/NioBlobOutputStream.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/NioBlobOutputStream.java
new file mode 100644
index 00000000000..ae5c0fa02b1
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/NioBlobOutputStream.java
@@ -0,0 +1,99 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+package com.azure.storage.blob.nio;
+
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.specialized.BlobOutputStream;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.file.Path;
+
+/**
+ * Provides an OutputStream to write to a file stored as an Azure Blob.
+ */
+public final class NioBlobOutputStream extends OutputStream {
+    private static final ClientLogger LOGGER = new ClientLogger(NioBlobOutputStream.class);
+
+    private final BlobOutputStream blobOutputStream;
+    private final Path path;
+
+    NioBlobOutputStream(BlobOutputStream blobOutputStream, Path path) {
+        this.blobOutputStream = blobOutputStream;
+        this.path = path;
+    }
+
+    @Override
+    public synchronized void write(int i) throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            this.blobOutputStream.write(i);
+            /*
+            BlobOutputStream only throws RuntimeException, and it doesn't preserve the cause, it only takes the message,
+            so we can't do any better than re-wrapping it in an IOException.
+             */
+        } catch (RuntimeException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    @Override
+    public synchronized void write(byte[] b) throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            this.blobOutputStream.write(b);
+            /*
+            BlobOutputStream only throws RuntimeException, and it doesn't preserve the cause, it only takes the message,
+            so we can't do any better than re-wrapping it in an IOException.
+             */
+        } catch (RuntimeException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    @Override
+    public synchronized void write(byte[] b, int off, int len) throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            this.blobOutputStream.write(b, off, len);
+            /*
+            BlobOutputStream only throws RuntimeException, and it doesn't preserve the cause, it only takes the message,
+            so we can't do any better than re-wrapping it in an IOException.
+             */
+        } catch (RuntimeException e) {
+            if (e instanceof IndexOutOfBoundsException) {
+                throw LoggingUtility.logError(LOGGER, e);
+            }
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    @Override
+    public synchronized void flush() throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            this.blobOutputStream.flush();
+            /*
+            BlobOutputStream only throws RuntimeException, and it doesn't preserve the cause, it only takes the message,
+            so we can't do any better than re-wrapping it in an IOException.
+             */
+        } catch (RuntimeException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+
+    @Override
+    public synchronized void close() throws IOException {
+        AzurePath.ensureFileSystemOpen(path);
+        try {
+            this.blobOutputStream.close();
+            /*
+            BlobOutputStream only throws RuntimeException, and it doesn't preserve the cause, it only takes the message,
+            so we can't do any better than re-wrapping it in an IOException.
+             */
+        } catch (RuntimeException e) {
+            throw LoggingUtility.logError(LOGGER, new IOException(e));
+        }
+    }
+}
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/package-info.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/package-info.java
new file mode 100644
index 00000000000..96cd1fbd627
--- /dev/null
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/package-info.java
@@ -0,0 +1,7 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+
+/**
+ * Package containing the classes for loading the AzureFileSystemProvider based on Azure Storage Blobs.
+ */
+package com.azure.storage.blob.nio;
diff --git a/azure-blob-nio/src/main/resources/META-INF/services/java.nio.file.spi.FileSystemProvider b/azure-blob-nio/src/main/resources/META-INF/services/java.nio.file.spi.FileSystemProvider
new file mode 100644
index 00000000000..5cc2b4ead14
--- /dev/null
+++ b/azure-blob-nio/src/main/resources/META-INF/services/java.nio.file.spi.FileSystemProvider
@@ -0,0 +1 @@
+com.azure.storage.blob.nio.AzureFileSystemProvider
diff --git a/azure-blob-nio/src/main/resources/azure-storage-blob-nio.properties b/azure-blob-nio/src/main/resources/azure-storage-blob-nio.properties
new file mode 100644
index 00000000000..ca812989b4f
--- /dev/null
+++ b/azure-blob-nio/src/main/resources/azure-storage-blob-nio.properties
@@ -0,0 +1,2 @@
+name=${project.artifactId}
+version=${project.version}
diff --git a/azure-blob-nio/src/samples/java/com/azure/storage/blob/nio/ReadmeSamples.java b/azure-blob-nio/src/samples/java/com/azure/storage/blob/nio/ReadmeSamples.java
new file mode 100644
index 00000000000..6c8c5e06e0b
--- /dev/null
+++ b/azure-blob-nio/src/samples/java/com/azure/storage/blob/nio/ReadmeSamples.java
@@ -0,0 +1,129 @@
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License.
+package com.azure.storage.blob.nio;
+
+import com.azure.storage.blob.models.BlobHttpHeaders;
+import com.azure.storage.common.StorageSharedKeyCredential;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.file.FileSystem;
+import java.nio.file.FileSystems;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * WARNING: MODIFYING THIS FILE WILL REQUIRE CORRESPONDING UPDATES TO README.md FILE. LINE NUMBERS
+ * ARE USED TO EXTRACT APPROPRIATE CODE SEGMENTS FROM THIS FILE. ADD NEW CODE AT THE BOTTOM TO AVOID CHANGING
+ * LINE NUMBERS OF EXISTING CODE SAMPLES.
+ *
+ * Code samples for the README.md
+ */
+public class ReadmeSamples {
+
+    private static final String CONTAINER_STORES = "container1,container2"; // A comma separated list of container names
+    private static final StorageSharedKeyCredential SHARE_KEY_CREDENTIAL
+        = new StorageSharedKeyCredential("<account_name>", "<account_key>");
+    private static final Map<String, Object> CONFIG = new HashMap<String, Object>() {
+        {
+            put(AzureFileSystem.AZURE_STORAGE_SHARED_KEY_CREDENTIAL, SHARE_KEY_CREDENTIAL);
+            put(AzureFileSystem.AZURE_STORAGE_FILE_STORES, CONTAINER_STORES);
+        }
+    };
+    private FileSystem myFs = FileSystems.newFileSystem(new URI("azb://?endpoint=<your_account_name"),
+        Collections.emptyMap());
+    private Path dirPath = myFs.getPath("dir");
+    private Path filePath = myFs.getPath("file");
+
+    public ReadmeSamples() throws URISyntaxException, IOException {
+    }
+
+    public void createAFileSystem() throws URISyntaxException, IOException {
+        // BEGIN: readme-sample-createAFileSystem
+        Map<String, Object> config = new HashMap<>();
+        String stores = "<container_name>,<another_container_name>"; // A comma separated list of container names
+        StorageSharedKeyCredential credential = new StorageSharedKeyCredential("<account_name", "account_key");
+        config.put(AzureFileSystem.AZURE_STORAGE_SHARED_KEY_CREDENTIAL, credential);
+        config.put(AzureFileSystem.AZURE_STORAGE_FILE_STORES, stores);
+        FileSystem myFs = FileSystems.newFileSystem(new URI("azb://?endpoint=<account_endpoint"), config);
+        // END: readme-sample-createAFileSystem
+    }
+
+    public void createADirectory() throws IOException {
+        // BEGIN: readme-sample-createADirectory
+        Path dirPath = myFs.getPath("dir");
+        Files.createDirectory(dirPath);
+        // END: readme-sample-createADirectory
+    }
+
+    public void iterateOverDirectoryContents() throws IOException {
+        // BEGIN: readme-sample-iterateOverDirectoryContents
+        for (Path p : Files.newDirectoryStream(dirPath)) {
+            System.out.println(p.toString());
+        }
+        // END: readme-sample-iterateOverDirectoryContents
+    }
+
+    public void readAFile() throws IOException {
+        // BEGIN: readme-sample-readAFile
+        Path filePath = myFs.getPath("file");
+        try (InputStream is = Files.newInputStream(filePath)) {
+            is.read();
+        }
+        // END: readme-sample-readAFile
+    }
+
+    public void writeToAFile() throws IOException {
+        // BEGIN: readme-sample-writeToAFile
+        try (OutputStream os = Files.newOutputStream(filePath)) {
+            os.write(0);
+        }
+        // END: readme-sample-writeToAFile
+    }
+
+    public void copyAFile() throws IOException {
+        // BEGIN: readme-sample-copyAFile
+        Path destinationPath = myFs.getPath("destinationFile");
+        Files.copy(filePath, destinationPath, StandardCopyOption.COPY_ATTRIBUTES);
+        // END: readme-sample-copyAFile
+    }
+
+    public void deleteAFile() throws IOException {
+        // BEGIN: readme-sample-deleteAFile
+        Files.delete(filePath);
+        // END: readme-sample-deleteAFile
+    }
+
+    public void readAttributesOnAFile() throws IOException {
+        // BEGIN: readme-sample-readAttributesOnAFile
+        AzureBlobFileAttributes attr = Files.readAttributes(filePath, AzureBlobFileAttributes.class);
+        BlobHttpHeaders headers = attr.blobHttpHeaders();
+        // END: readme-sample-readAttributesOnAFile
+    }
+
+    public void readAttributesOnAFileString() throws IOException {
+        // BEGIN: readme-sample-readAttributesOnAFileString
+        Map<String, Object> attributes = Files.readAttributes(filePath, "azureBlob:metadata,headers");
+        // END: readme-sample-readAttributesOnAFileString
+    }
+
+    public void writeAttributesToAFile() throws IOException {
+        // BEGIN: readme-sample-writeAttributesToAFile
+        AzureBlobFileAttributeView view = Files.getFileAttributeView(filePath, AzureBlobFileAttributeView.class);
+        view.setMetadata(Collections.emptyMap());
+        // END: readme-sample-writeAttributesToAFile
+    }
+
+    public void writeAttributesToAFileString() throws IOException {
+        // BEGIN: readme-sample-writeAttributesToAFileString
+        Files.setAttribute(filePath, "azureBlob:blobHttpHeaders", new BlobHttpHeaders());
+        // END: readme-sample-writeAttributesToAFileString
+    }
+}
diff --git a/build.sbt b/build.sbt
index 48f986badd7..6b2641e024f 100644
--- a/build.sbt
+++ b/build.sbt
@@ -97,12 +97,16 @@ lazy val cloudSupport = project
   .dependsOn(common)
   .dependsOn(common % "test->test")
 
+lazy val azureBlobNio = (project in file("azure-blob-nio"))
+  .withLibrarySettings("cromwell-azure-blobNio", azureBlobNioDependencies)
+
 lazy val azureBlobFileSystem = (project in file("filesystems/blob"))
   .withLibrarySettings("cromwell-azure-blobFileSystem", blobFileSystemDependencies)
   .dependsOn(core)
   .dependsOn(core % "test->test")
   .dependsOn(common % "test->test")
   .dependsOn(cloudSupport)
+  .dependsOn(azureBlobNio)
 
 lazy val awsS3FileSystem = (project in file("filesystems/s3"))
   .withLibrarySettings("cromwell-aws-s3filesystem", s3FileSystemDependencies)
@@ -408,6 +412,7 @@ lazy val root = (project in file("."))
   .aggregate(`cromwell-drs-localizer`)
   .aggregate(awsBackend)
   .aggregate(awsS3FileSystem)
+  .aggregate(azureBlobNio)
   .aggregate(azureBlobFileSystem)
   .aggregate(backend)
   .aggregate(centaur)
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 6a8d73db01f..1a7681da1e3 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -10,7 +10,6 @@ object Dependencies {
   // We would like to use the BOM to manage Azure SDK versions, but SBT doesn't support it.
   // https://github.com/Azure/azure-sdk-for-java/tree/main/sdk/boms/azure-sdk-bom
   // https://github.com/sbt/sbt/issues/4531
-  private val azureStorageBlobNioV = "12.0.0-beta.19"
   private val azureIdentitySdkV = "1.9.1"
   private val azureIdentityExtensionsV = "1.1.4"
   private val azureCoreManagementV = "1.7.1"
@@ -208,10 +207,26 @@ object Dependencies {
     "org.typelevel" %% "cats-effect" % catsEffectV,
   )
 
+  /*
+   Due to complications with the public preview Nio filesystem for azure,
+  we include this FS implementation locally and include its dependencies
+   */
+  val azureBlobNioDependencies = List(
+    "com.azure" % "azure-core" % "1.40.0",
+    "com.azure" % "azure-storage-blob" % "12.23.0-beta.1",
+    "com.azure" % "azure-storage-common" % "12.22.0-beta.1",
+    "com.azure" % "azure-core-test" % "1.18.0",
+    "org.junit.jupiter" % "junit-jupiter-params" % "5.9.3",
+    "org.junit.jupiter" % "junit-jupiter-engine" % "5.9.3",
+    "org.junit.jupiter" % "junit-jupiter-api" % "5.9.3",
+    "io.projectreactor" % "reactor-test" % "3.4.29",
+    "cglib" % "cglib-nodep" % "3.2.7",
+    "com.azure" % "azure-core-http-okhttp" % "1.11.10",
+    "org.mockito" % "mockito-core" % "4.11.0",
+    "com.github.sbt" % "junit-interface" % "0.13.2"
+  )
+
   val azureDependencies: List[ModuleID] = List(
-    "com.azure" % "azure-storage-blob-nio" % azureStorageBlobNioV
-      exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
-      exclude("jakarta.activation", "jakarta.activation-api"),
     "com.azure" % "azure-identity" % azureIdentitySdkV
       exclude("jakarta.xml.bind", "jakarta.xml.bind-api")
       exclude("jakarta.activation", "jakarta.activation-api")
@@ -222,7 +237,7 @@ object Dependencies {
     "com.azure.resourcemanager" % "azure-resourcemanager" % "2.18.0",
     "net.minidev" % "json-smart" % jsonSmartV,
     "com.microsoft.azure" % "applicationinsights-logging-logback" % azureAppInsightsLogbackV,
-  )
+  ) ++ azureBlobNioDependencies
 
   val wsmDependencies: List[ModuleID] = List(
     "bio.terra" % "workspace-manager-client" % "0.254.452-SNAPSHOT"
diff --git a/project/Merging.scala b/project/Merging.scala
index 5ecd951014b..91b135e59eb 100644
--- a/project/Merging.scala
+++ b/project/Merging.scala
@@ -12,6 +12,11 @@ object Merging {
     // Merge mozilla/public-suffix-list.txt if duplicated
     case PathList(ps@_*) if ps.last == "public-suffix-list.txt" =>
       MergeStrategy.last
+    // Merge kotlin modules if duplicated
+    case PathList(ps@_*) if ps.last == "kotlin-stdlib-common.kotlin_module" =>
+      MergeStrategy.last
+    case PathList(ps@_*) if ps.last == "kotlin-stdlib.kotlin_module" =>
+      MergeStrategy.last
     // AWS SDK v2 configuration files - can be discarded
     case PathList(ps@_*) if Set("codegen.config" , "service-2.json" , "waiters-2.json" , "customization.config" , "examples-1.json" , "paginators-1.json").contains(ps.last) =>
       MergeStrategy.discard

From af9660ee714309250b7373de75fb6fad513e6ba4 Mon Sep 17 00:00:00 2001
From: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Date: Mon, 17 Jul 2023 10:36:12 -0400
Subject: [PATCH 193/326] WX-1110[risk=low] Added endpoint to fetch failed
 tasks by root workflow id (#7165)

---
 .../slick/MetadataSlickDatabase.scala         |   5 +
 .../slick/tables/MetadataEntryComponent.scala |  78 ++++++++++
 .../database/sql/MetadataSqlDatabase.scala    |   2 +
 docs/api/RESTAPI.md                           |  32 +++-
 .../src/main/resources/swagger/cromwell.yaml  |  20 +++
 .../routes/MetadataRouteSupport.scala         |  14 +-
 .../webservice/MetadataBuilderActorSpec.scala | 140 +++++++++++++-----
 .../routes/CromwellApiServiceSpec.scala       |   4 +
 .../routes/MetadataRouteSupportSpec.scala     |  14 ++
 .../services/metadata/MetadataQuery.scala     |   2 +
 .../services/metadata/MetadataService.scala   |   5 +-
 .../impl/MetadataDatabaseAccess.scala         |   5 +-
 .../ReadDatabaseMetadataWorkerActor.scala     |  16 +-
 .../impl/ReadMetadataRegulatorActor.scala     |  12 +-
 .../impl/builder/MetadataBuilderActor.scala   |  13 ++
 .../database/MetadataSlickDatabaseSpec.scala  | 125 +++++++++++++++-
 .../impl/WriteMetadataActorSpec.scala         |   2 +
 17 files changed, 443 insertions(+), 46 deletions(-)

diff --git a/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
index 1405f7d101f..0a33e4b6b72 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
@@ -515,4 +515,9 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
   override def getMetadataTableSizeInformation()(implicit ec: ExecutionContext): Future[Option[InformationSchemaEntry]] = {
     runAction(dataAccess.metadataTableSizeInformation())
   }
+
+  override def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: String)(implicit ec: ExecutionContext): Future[Vector[MetadataEntry]] = {
+    val isPostgres = databaseConfig.getValue("db.driver").toString.toLowerCase().contains("postgres")
+    runLobAction(dataAccess.failedJobsMetadataWithWorkflowId(rootWorkflowId, isPostgres))
+  }
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
index 32256c448fb..f4b2724b6a7 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
@@ -310,6 +310,84 @@ trait MetadataEntryComponent {
     }).headOption
   }
 
+  def failedJobsMetadataWithWorkflowId(rootWorkflowId: String, isPostgres: Boolean) = {
+    val getMetadataEntryResult = GetResult(r => {
+      MetadataEntry(r.<<, r.<<, r.<<, r.<<, r.<<, r.nextClobOption().map(clob => new SerialClob(clob)), r.<<, r.<<, r.<<)
+    })
+
+    def dbIdentifierWrapper(identifier: String, isPostgres: Boolean) = {
+      if(isPostgres) s"${'"'}$identifier${'"'}" else identifier
+    }
+
+    def dbMetadataValueColCheckName(isPostgres: Boolean): String = {
+      if(isPostgres) "obj.data" else "METADATA_VALUE"
+    }
+
+    def targetCallsSelectStatement(callFqn: String, scatterIndex: String, retryAttempt: String): String = {
+      s"SELECT ${callFqn}, MAX(COALESCE(${scatterIndex}, 0)) as maxScatter, MAX(COALESCE(${retryAttempt}, 0)) AS maxRetry"
+    }
+
+    def pgObjectInnerJoinStatement(isPostgres: Boolean, metadataValColName: String): String = {
+      if(isPostgres) s"INNER JOIN pg_largeobject obj ON me.${metadataValColName} = cast(obj.loid as text)" else ""
+    }
+
+    val workflowUuid = dbIdentifierWrapper("WORKFLOW_EXECUTION_UUID", isPostgres)
+    val callFqn = dbIdentifierWrapper("CALL_FQN", isPostgres)
+    val scatterIndex = dbIdentifierWrapper("JOB_SCATTER_INDEX", isPostgres)
+    val retryAttempt = dbIdentifierWrapper("JOB_RETRY_ATTEMPT", isPostgres)
+    val metadataKey = dbIdentifierWrapper("METADATA_KEY", isPostgres)
+    val metadataValueType = dbIdentifierWrapper("METADATA_VALUE_TYPE", isPostgres)
+    val metadataTimestamp = dbIdentifierWrapper("METADATA_TIMESTAMP", isPostgres)
+    val metadataJournalId = dbIdentifierWrapper("METADATA_JOURNAL_ID", isPostgres)
+    val rootUuid = dbIdentifierWrapper("ROOT_WORKFLOW_EXECUTION_UUID", isPostgres)
+    val metadataValue = dbIdentifierWrapper("METADATA_VALUE", isPostgres)
+    val metadataEntry = dbIdentifierWrapper("METADATA_ENTRY", isPostgres)
+    val wmse = dbIdentifierWrapper("WORKFLOW_METADATA_SUMMARY_ENTRY", isPostgres)
+    val resultSetColumnNames = s"me.${workflowUuid}, me.${callFqn}, me.${scatterIndex}, me.${retryAttempt}, me.${metadataKey}, me.${metadataValue}, me.${metadataValueType}, me.${metadataTimestamp}, me.${metadataJournalId}"
+
+    val query = sql"""
+      SELECT #${resultSetColumnNames}
+      FROM #${metadataEntry} me
+      INNER JOIN (
+        #${targetCallsSelectStatement(callFqn, scatterIndex, retryAttempt)}
+        FROM #${metadataEntry} me
+        INNER JOIN #${wmse} wmse
+        ON wmse.#${workflowUuid} = me.#${workflowUuid}
+        WHERE (wmse.#${rootUuid} = $rootWorkflowId OR wmse.#${workflowUuid} = $rootWorkflowId)
+        AND #${callFqn} IS NOT NULL
+        GROUP BY #${callFqn}
+      ) AS targetCalls
+      ON me.#${callFqn} = targetCalls.#${callFqn}
+      LEFT JOIN (
+        SELECT DISTINCT #${callFqn}
+        FROM #${metadataEntry} me
+        INNER JOIN #${wmse} wmse
+        ON wmse.#${workflowUuid} = me.#${workflowUuid}
+        WHERE (wmse.#${rootUuid} = $rootWorkflowId OR wmse.#${workflowUuid} = $rootWorkflowId)
+        AND me.#${metadataKey} = 'subWorkflowId'
+        GROUP BY #${callFqn}
+      ) AS avoidedCalls
+      ON me.#${callFqn} = avoidedCalls.#${callFqn}
+      INNER JOIN #${wmse} wmse
+      ON wmse.#${workflowUuid} = me.#${workflowUuid}
+      #${pgObjectInnerJoinStatement(isPostgres, metadataValue)}
+      WHERE avoidedCalls.#${callFqn} IS NULL
+      AND (me.#${metadataKey} in ('executionStatus', 'backendStatus') AND #${dbMetadataValueColCheckName(isPostgres)} = 'Failed')
+      AND (
+        (COALESCE(me.#${retryAttempt}, 0) = targetCalls.maxRetry AND me.#${scatterIndex} IS NULL)
+        OR (COALESCE(me.#${retryAttempt}, 0) = targetCalls.maxRetry AND me.#${scatterIndex} = targetCalls.maxScatter)
+       )
+      GROUP BY #${resultSetColumnNames}
+      HAVING me.#${workflowUuid} IN (
+        SELECT DISTINCT wmse.#${workflowUuid}
+        FROM #${wmse} wmse
+        WHERE wmse.#${rootUuid} = $rootWorkflowId OR wmse.#${workflowUuid} = $rootWorkflowId
+      )
+    """
+
+    query.as(getMetadataEntryResult)
+  }
+
   private[this] def metadataEntryHasMetadataKeysLike(metadataEntry: MetadataEntries,
                                                      metadataKeysToFilterFor: List[String],
                                                      metadataKeysToFilterOut: List[String]): Rep[Boolean] = {
diff --git a/database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala
index 30534818f85..9139c819999 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala
@@ -197,4 +197,6 @@ trait MetadataSqlDatabase extends SqlDatabase {
   def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold: Timestamp)(implicit ec: ExecutionContext): Future[Int]
 
   def getMetadataTableSizeInformation()(implicit ec: ExecutionContext): Future[Option[InformationSchemaEntry]]
+
+  def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: String)(implicit ec: ExecutionContext): Future[Vector[MetadataEntry]]
 }
diff --git a/docs/api/RESTAPI.md b/docs/api/RESTAPI.md
index 7a0585ca08e..64ffe19a3fd 100644
--- a/docs/api/RESTAPI.md
+++ b/docs/api/RESTAPI.md
@@ -1,5 +1,5 @@
 <!--
-This file was generated by `sbt generateRestApiDocs` on Mon, 27 Feb 2023 15:52:59 -0500
+This file was generated by `sbt generateRestApiDocs` on Wed, 12 Jul 2023 15:55:37 -0400
 
 !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
 
@@ -699,6 +699,36 @@ GET /api/workflows/{version}/{id}/metadata
 * Workflows
 
 
+<a name="failed-jobs"></a>
+## Get call-level metadata of failed tasks for a specified root workflow
+```
+GET /api/workflows/{version}/{id}/metadata/failed-jobs
+```
+
+
+#### Parameters
+
+|Type|Name|Description|Schema|Default|
+|---|---|---|---|---|
+|**Path**|**id**  <br>*required*|A workflow ID|string||
+|**Path**|**version**  <br>*required*|Cromwell API Version|string|`"v1"`|
+
+
+#### Responses
+
+|HTTP Code|Description|Schema|
+|---|---|---|
+|**200**|Successful request|[WorkflowMetadataResponse](#workflowmetadataresponse)|
+|**400**|Malformed Workflow ID|No Content|
+|**404**|Workflow ID Not Found|No Content|
+|**500**|Internal Error|No Content|
+
+
+#### Tags
+
+* Workflows
+
+
 <a name="outputs"></a>
 ## Get the outputs for a workflow
 ```
diff --git a/engine/src/main/resources/swagger/cromwell.yaml b/engine/src/main/resources/swagger/cromwell.yaml
index bc34cb6476b..dca96b20ceb 100644
--- a/engine/src/main/resources/swagger/cromwell.yaml
+++ b/engine/src/main/resources/swagger/cromwell.yaml
@@ -510,6 +510,26 @@ paths:
           $ref: '#/responses/NotFound'
         '500':
           $ref: '#/responses/ServerError'
+  '/api/workflows/{version}/{id}/metadata/failed-jobs':
+    get:
+      operationId: failed-jobs
+      summary: Get call-level metadata of failed tasks for a specified root workflow
+      parameters:
+        - $ref: '#/parameters/versionParam'
+        - $ref: '#/parameters/singleId'
+      tags:
+        - Workflows
+      responses:
+        '200':
+          description: Successful request
+          schema:
+            $ref: '#/definitions/WorkflowMetadataResponse'
+        '400':
+          $ref: '#/responses/BadRequest'
+        '404':
+          $ref: '#/responses/NotFound'
+        '500':
+          $ref: '#/responses/ServerError'
   '/api/workflows/{version}/{id}/metadata':
     get:
       operationId: metadata
diff --git a/engine/src/main/scala/cromwell/webservice/routes/MetadataRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/MetadataRouteSupport.scala
index 237e21a2edd..b84ff59d5a3 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/MetadataRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/MetadataRouteSupport.scala
@@ -69,6 +69,17 @@ trait MetadataRouteSupport extends HttpInstrumentation {
         }
       }
     },
+    encodeResponse {
+      path("workflows" / Segment / Segment / "metadata" / "failed-jobs") { (_, possibleWorkflowId) =>
+        instrumentRequest {
+          metadataLookup(
+            possibleWorkflowId,
+            (w: WorkflowId) => FetchFailedJobsMetadataWithWorkflowId(w),
+            serviceRegistryActor
+          )
+        }
+      }
+    },
     encodeResponse {
       path("workflows" / Segment / Segment / "metadata") { (_, possibleWorkflowId) =>
         instrumentRequest {
@@ -212,8 +223,7 @@ object MetadataRouteSupport {
   }
 
   def completeMetadataBuilderResponse(response: Future[MetadataJsonResponse]): Route = {
-    onComplete(response) {
-      case Success(r: SuccessfulMetadataJsonResponse) => complete(r.responseJson)
+    onComplete(response) { case Success(r: SuccessfulMetadataJsonResponse) => complete(r.responseJson)
       case Success(r: FailedMetadataJsonResponse) => r.reason.errorRequest(StatusCodes.InternalServerError)
       case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
       case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
diff --git a/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala b/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala
index a520faee1f2..700c0274026 100644
--- a/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala
@@ -36,6 +36,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
                              events: Seq[MetadataEvent],
                              expectedRes: String,
                              metadataBuilderActorName: String,
+                             failedTasks: Boolean = false
                             ): Future[Assertion] = {
     val mockReadMetadataWorkerActor = TestProbe("mockReadMetadataWorkerActor")
     def readMetadataWorkerMaker = () => mockReadMetadataWorkerActor.props
@@ -45,13 +46,17 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       props = MetadataBuilderActor.props(readMetadataWorkerMaker, 1000000),
       name = metadataBuilderActorName,
     )
+
     val response = mba.ask(action).mapTo[MetadataJsonResponse]
     mockReadMetadataWorkerActor.expectMsg(defaultTimeout, action)
-    mockReadMetadataWorkerActor.reply(MetadataLookupResponse(queryReply, events))
+    mockReadMetadataWorkerActor.reply(
+      if(failedTasks) FetchFailedJobsMetadataLookupResponse(events) else MetadataLookupResponse(queryReply, events)
+    )
     response map { r => r shouldBe a [SuccessfulMetadataJsonResponse] }
     response.mapTo[SuccessfulMetadataJsonResponse] map { b => b.responseJson shouldBe expectedRes.parseJson}
   }
 
+
   def assertMetadataFailureResponse(action: MetadataServiceAction,
                                     metadataServiceResponse: MetadataServiceResponse,
                                     expectedException: Exception,
@@ -95,37 +100,37 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     // We'll use a Query instead of a SingleWorkflowMetadataGet, so we expect the WorkflowID this time:
     val expectedRes =
       s"""{
-        |  "calls": {
-        |    "callB": [{
-        |      "attempt": 1,
-        |      "NOT_CHECKED": "NOT_CHECKED",
-        |      "shardIndex": -1
-        |    }, {
-        |      "attempt": 1,
-        |      "NOT_CHECKED": "NOT_CHECKED",
-        |      "shardIndex": 0
-        |    }, {
-        |      "attempt": 1,
-        |      "NOT_CHECKED": "NOT_CHECKED",
-        |      "shardIndex": 1
-        |    }, {
-        |      "attempt": 2,
-        |      "NOT_CHECKED": "NOT_CHECKED",
-        |      "shardIndex": 1
-        |    }, {
-        |      "attempt": 3,
-        |      "NOT_CHECKED": "NOT_CHECKED",
-        |      "shardIndex": 1
-        |    }],
-        |    "callA": [{
-        |      "attempt": 1,
-        |      "NOT_CHECKED": "NOT_CHECKED",
-        |      "shardIndex": -1
-        |    }]
-        |  },
-        |  "NOT_CHECKED": "NOT_CHECKED",
-        |  "id": "$workflowA"
-      |}""".stripMargin
+         |  "calls": {
+         |    "callB": [{
+         |      "attempt": 1,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": -1
+         |    }, {
+         |      "attempt": 1,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": 0
+         |    }, {
+         |      "attempt": 1,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": 1
+         |    }, {
+         |      "attempt": 2,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": 1
+         |    }, {
+         |      "attempt": 3,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": 1
+         |    }],
+         |    "callA": [{
+         |      "attempt": 1,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": -1
+         |    }]
+         |  },
+         |  "NOT_CHECKED": "NOT_CHECKED",
+         |  "id": "$workflowA"
+         |}""".stripMargin
 
     val mdQuery = MetadataQuery(workflowA, None, None, None, None, expandSubWorkflows = false)
     val queryAction = GetMetadataAction(mdQuery)
@@ -134,7 +139,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       queryReply = mdQuery,
       events = workflowAEvents,
       expectedRes = expectedRes,
-      metadataBuilderActorName = "mba-scope-tree",
+      metadataBuilderActorName = "mba-scope-tree"
     )
   }
 
@@ -162,6 +167,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
                                  eventMaker: WorkflowId => (String, MetadataValue, OffsetDateTime) => MetadataEvent =
                                  makeEvent,
                                  metadataBuilderActorName: String,
+                                 isFailedTaskFetch: Boolean = false
                                 ): Future[Assertion] = {
 
     val events = eventList map { e => (e._1, MetadataValue(e._2), e._3) } map Function.tupled(eventMaker(workflow))
@@ -172,6 +178,74 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     assertMetadataResponse(queryAction, mdQuery, events, expectedRes, metadataBuilderActorName)
   }
 
+  it should "build the call list for failed tasks when prompted" in {
+
+    def makeEvent(workflow: WorkflowId, key: Option[MetadataJobKey]) = {
+      MetadataEvent(MetadataKey(workflow, key, "NOT_CHECKED"), MetadataValue("NOT_CHECKED"))
+    }
+
+    val workflowA = WorkflowId.randomId()
+
+    val workflowACalls = List(
+      Option(MetadataJobKey("callB", Option(1), 3)),
+      Option(MetadataJobKey("callB", None, 1)),
+      Option(MetadataJobKey("callB", Option(1), 2)),
+      Option(MetadataJobKey("callA", None, 1)),
+      Option(MetadataJobKey("callB", Option(1), 1)),
+      Option(MetadataJobKey("callB", Option(0), 1)),
+      None
+    )
+    val workflowAEvents = workflowACalls map {
+      makeEvent(workflowA, _)
+    }
+
+    val expectedRes =
+      s"""{
+         |"${workflowA}": {
+         |  "calls": {
+         |    "callB": [{
+         |      "attempt": 1,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": -1
+         |    }, {
+         |      "attempt": 1,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": 0
+         |    }, {
+         |      "attempt": 1,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": 1
+         |    }, {
+         |      "attempt": 2,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": 1
+         |    }, {
+         |      "attempt": 3,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": 1
+         |    }],
+         |    "callA": [{
+         |      "attempt": 1,
+         |      "NOT_CHECKED": "NOT_CHECKED",
+         |      "shardIndex": -1
+         |    }]
+         |  },
+         |  "NOT_CHECKED": "NOT_CHECKED"
+         | }
+         |}""".stripMargin
+
+    val mdQuery = MetadataQuery(workflowA, None, None, None, None, expandSubWorkflows = false)
+    val queryAction = GetMetadataAction(mdQuery)
+    assertMetadataResponse(
+      action = queryAction,
+      queryReply = mdQuery,
+      events = workflowAEvents,
+      expectedRes = expectedRes,
+      failedTasks = true,
+      metadataBuilderActorName = "mba-failed-tasks",
+    )
+  }
+
   it should "assume the event list is ordered and keep last event if 2 events have same key" in {
     val eventBuilderList = List(
       ("a", "aLater", OffsetDateTime.parse("2000-01-02T12:00:00Z")),
diff --git a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
index c40c84397f7..4e7caf932ef 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
@@ -568,6 +568,7 @@ object CromwellApiServiceSpec {
         MetadataEvent(MetadataKey(workflowId, None, "testKey2a"), MetadataValue("myValue2a", MetadataString)),
       )
     }
+
     private def wesFullMetadataResponse(workflowId: WorkflowId) = {
       List(
         MetadataEvent(MetadataKey(workflowId, None, "status"), MetadataValue("Running", MetadataString)),
@@ -576,6 +577,7 @@ object CromwellApiServiceSpec {
       )
     }
 
+
     def responseMetadataValues(workflowId: WorkflowId, withKeys: List[String], withoutKeys: List[String]): JsObject = {
       def keyFilter(keys: List[String])(m: MetadataEvent) = keys.exists(k => m.key.key.startsWith(k))
       val metadataEvents = if (workflowId == wesWorkflowId) wesFullMetadataResponse(workflowId) else fullMetadataResponse(workflowId)
@@ -645,6 +647,8 @@ object CromwellApiServiceSpec {
         sender() ! SuccessfulMetadataJsonResponse(request, MetadataBuilderActor.processOutputsResponse(id, event))
       case request @ GetLogs(id) =>
         sender() ! SuccessfulMetadataJsonResponse(request, MetadataBuilderActor.workflowMetadataResponse(id, logsEvents(id), includeCallsIfEmpty = false, Map.empty))
+      case request @ FetchFailedJobsMetadataWithWorkflowId(id) =>
+        sender() ! SuccessfulMetadataJsonResponse(request, responseMetadataValues(id, List.empty, List.empty))
       case request @ GetMetadataAction(MetadataQuery(id, _, _, withKeys, withoutKeys, _), _) =>
         val withKeysList = withKeys.map(_.toList).getOrElse(List.empty)
         val withoutKeysList = withoutKeys.map(_.toList).getOrElse(List.empty)
diff --git a/engine/src/test/scala/cromwell/webservice/routes/MetadataRouteSupportSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/MetadataRouteSupportSpec.scala
index 07b780a3aaf..73cc257e828 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/MetadataRouteSupportSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/MetadataRouteSupportSpec.scala
@@ -313,6 +313,20 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       }
   }
 
+  it should "return 200 with metadata for failed tasks on a workflow" in {
+    Get(s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/metadata/failed-jobs") ~>
+      akkaHttpService.metadataRoutes ~>
+      check {
+        status should be(StatusCodes.OK)
+        val result = responseAs[JsObject]
+        result.fields.keys should contain allOf("testKey1a", "testKey1b", "testKey2a")
+        result.fields.keys shouldNot contain("testKey3")
+        result.fields("testKey1a") should be(JsString("myValue1a"))
+        result.fields("testKey1b") should be(JsString("myValue1b"))
+        result.fields("testKey2a") should be(JsString("myValue2a"))
+      }
+  }
+
   behavior of "REST API /query GET endpoint"
   it should "return good results for a good query" in {
     Get(s"/workflows/$version/query?status=Succeeded&id=${CromwellApiServiceSpec.ExistingWorkflowId}") ~>
diff --git a/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala b/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala
index d3264b839c3..1b38bd2f479 100644
--- a/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala
+++ b/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala
@@ -26,7 +26,9 @@ object MetadataKey {
 
 object MetadataEvent {
   def apply(key: MetadataKey, value: MetadataValue) = new MetadataEvent(key, Option(value), OffsetDateTime.now)
+
   def apply(key: MetadataKey, optionalValue: Option[MetadataValue]) = new MetadataEvent(key, optionalValue, OffsetDateTime.now)
+
   def empty(key: MetadataKey) = new MetadataEvent(key, None, OffsetDateTime.now)
 
   def labelsToMetadataEvents(labels: Labels, workflowId: WorkflowId): Iterable[MetadataEvent] = {
diff --git a/services/src/main/scala/cromwell/services/metadata/MetadataService.scala b/services/src/main/scala/cromwell/services/metadata/MetadataService.scala
index 61acd8052c8..dd45cf5535d 100644
--- a/services/src/main/scala/cromwell/services/metadata/MetadataService.scala
+++ b/services/src/main/scala/cromwell/services/metadata/MetadataService.scala
@@ -127,6 +127,7 @@ object MetadataService {
   final case class ValidateWorkflowIdInMetadata(possibleWorkflowId: WorkflowId) extends MetadataServiceAction
   final case class ValidateWorkflowIdInMetadataSummaries(possibleWorkflowId: WorkflowId) extends MetadataServiceAction
   final case class FetchWorkflowMetadataArchiveStatusAndEndTime(workflowId: WorkflowId) extends MetadataServiceAction
+  final case class FetchFailedJobsMetadataWithWorkflowId(workflowId: WorkflowId) extends BuildWorkflowMetadataJsonAction
 
   /**
     * Responses
@@ -140,8 +141,10 @@ object MetadataService {
   final case class MetadataLookupStreamFailed(id: WorkflowId, reason: Throwable) extends MetadataServiceResponse
   final case class MetadataLookupFailedTooLargeResponse(query: MetadataQuery, metadataSizeRows: Int) extends MetadataServiceResponse
   final case class MetadataLookupFailedTimeoutResponse(query: MetadataQuery) extends MetadataServiceResponse
-
+  final case class FetchFailedTasksTimeoutResponse(workflowId: WorkflowId) extends MetadataServiceResponse
   final case class MetadataLookupResponse(query: MetadataQuery, eventList: Seq[MetadataEvent]) extends MetadataServiceResponse
+  final case class FetchFailedJobsMetadataLookupResponse(events: Seq[MetadataEvent]) extends MetadataServiceResponse
+  final case class FetchFailedJobsMetadataLookupFailed(workflowId: WorkflowId, reason: Throwable) extends MetadataServiceFailure
   final case class MetadataServiceKeyLookupFailed(query: MetadataQuery, reason: Throwable) extends MetadataServiceFailure
 
   final case class StatusLookupResponse(workflowId: WorkflowId, status: WorkflowState) extends MetadataServiceResponse
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala b/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala
index 271251bcdd7..0069ffe8821 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala
@@ -114,7 +114,7 @@ trait MetadataDatabaseAccess {
       labelMetadataKey = WorkflowMetadataKeys.Labels)
   }
 
-  private def metadataToMetadataEvents(workflowId: WorkflowId)(metadata: Seq[MetadataEntry]): Seq[MetadataEvent] = {
+  def metadataToMetadataEvents(workflowId: WorkflowId)(metadata: Seq[MetadataEntry]): Seq[MetadataEvent] = {
     metadata map { m =>
       // If callFullyQualifiedName is non-null then attempt will also be non-null and there is a MetadataJobKey.
       val metadataJobKey: Option[MetadataJobKey] = for {
@@ -382,4 +382,7 @@ trait MetadataDatabaseAccess {
     metadataDatabaseInterface.countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold.toSystemTimestamp)
 
   def getMetadataTableSizeInformation()(implicit ec: ExecutionContext): Future[Option[InformationSchemaEntry]] = metadataDatabaseInterface.getMetadataTableSizeInformation()
+
+  def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Vector[MetadataEntry]] =
+    metadataDatabaseInterface.getFailedJobsMetadataWithWorkflowId(rootWorkflowId.toString)
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/ReadDatabaseMetadataWorkerActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/ReadDatabaseMetadataWorkerActor.scala
index 3a67ad504ec..165c1bc2f14 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/ReadDatabaseMetadataWorkerActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/ReadDatabaseMetadataWorkerActor.scala
@@ -1,13 +1,12 @@
 package cromwell.services.metadata.impl
 
 import java.sql.SQLTimeoutException
-
 import akka.actor.{Actor, ActorLogging, ActorRef, PoisonPill, Props}
 import cromwell.core.Dispatcher.ServiceDispatcher
 import cromwell.core.{WorkflowId, WorkflowSubmitted}
 import cromwell.services.MetadataServicesStore
 import cromwell.services.metadata.MetadataService._
-import cromwell.services.metadata.{MetadataQuery, WorkflowQueryParameters}
+import cromwell.services.metadata.{MetadataEvent, MetadataQuery, WorkflowQueryParameters}
 
 import scala.concurrent.Future
 import scala.concurrent.duration.Duration
@@ -27,6 +26,9 @@ class ReadDatabaseMetadataWorkerActor(metadataReadTimeout: Duration, metadataRea
   implicit val ec = context.dispatcher
 
   def receive = {
+    case FetchFailedJobsMetadataWithWorkflowId(w: WorkflowId) => {
+      evaluateRespondAndStop(sender(), getFailedJobs(w))
+    }
     case GetMetadataAction(query: MetadataQuery, checkTotalMetadataRowNumberBeforeQuerying: Boolean) =>
       evaluateRespondAndStop(sender(), getMetadata(query, checkTotalMetadataRowNumberBeforeQuerying))
     case GetMetadataStreamAction(workflowId) =>
@@ -84,6 +86,16 @@ class ReadDatabaseMetadataWorkerActor(metadataReadTimeout: Duration, metadataRea
       case t => MetadataServiceKeyLookupFailed(query, t)
     }
 
+  private def getFailedJobs(workflowId: WorkflowId): Future[MetadataServiceResponse] = {
+   val futureEvents: Future[Seq[MetadataEvent]] = getFailedJobsMetadataWithWorkflowId(workflowId) map metadataToMetadataEvents(workflowId)
+    futureEvents map {
+      m => FetchFailedJobsMetadataLookupResponse(m)
+    } recover {
+      case _: SQLTimeoutException => FetchFailedTasksTimeoutResponse(workflowId)
+      case t => FetchFailedJobsMetadataLookupFailed(workflowId, t)
+    }
+  }
+
   private def getStatus(id: WorkflowId): Future[MetadataServiceResponse] = {
 
     getWorkflowStatus(id) map {
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataRegulatorActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataRegulatorActor.scala
index 1c50cb00404..869ae79e10f 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataRegulatorActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataRegulatorActor.scala
@@ -1,12 +1,11 @@
 package cromwell.services.metadata.impl
 
 import java.util.UUID
-
 import akka.actor.{Actor, ActorLogging, ActorRef, Props}
 import cromwell.core.Dispatcher.ApiDispatcher
 import cromwell.services.MetadataJsonResponse
 import cromwell.services.metadata.MetadataService
-import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, BuildWorkflowMetadataJsonAction, GetMetadataStreamAction, MetadataLookupStreamSuccess, MetadataQueryResponse, MetadataServiceAction, MetadataServiceResponse, RootAndSubworkflowLabelsLookupResponse}
+import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, BuildWorkflowMetadataJsonAction, FetchFailedJobsMetadataWithWorkflowId, GetMetadataStreamAction, MetadataLookupStreamSuccess, MetadataQueryResponse, MetadataServiceAction, MetadataServiceResponse, RootAndSubworkflowLabelsLookupResponse}
 import cromwell.services.metadata.impl.ReadMetadataRegulatorActor.PropsMaker
 import cromwell.services.metadata.impl.builder.MetadataBuilderActor
 
@@ -28,11 +27,18 @@ class ReadMetadataRegulatorActor(metadataBuilderActorProps: PropsMaker, readMeta
     // This indirection via 'MetadataReadAction' lets the compiler make sure we cover all cases in the sealed trait:
     case action: BuildMetadataJsonAction =>
       action match {
+        case fetchFailedJobsMetadataAction: FetchFailedJobsMetadataWithWorkflowId =>
+          val currentRequesters = apiRequests.getOrElse(fetchFailedJobsMetadataAction, Set.empty)
+          apiRequests.put(fetchFailedJobsMetadataAction, currentRequesters + sender())
+          if (currentRequesters.isEmpty) {
+            val builderActor = context.actorOf(metadataBuilderActorProps().withDispatcher(ApiDispatcher), MetadataBuilderActor.uniqueActorName(fetchFailedJobsMetadataAction.workflowId.toString))
+            builderRequests.put(builderActor, fetchFailedJobsMetadataAction)
+            builderActor ! fetchFailedJobsMetadataAction
+          }
         case singleWorkflowAction: BuildWorkflowMetadataJsonAction =>
           val currentRequesters = apiRequests.getOrElse(singleWorkflowAction, Set.empty)
           apiRequests.put(singleWorkflowAction, currentRequesters + sender())
           if (currentRequesters.isEmpty) {
-
             val builderActor = context.actorOf(metadataBuilderActorProps().withDispatcher(ApiDispatcher), MetadataBuilderActor.uniqueActorName(singleWorkflowAction.workflowId.toString))
             builderRequests.put(builderActor, singleWorkflowAction)
             builderActor ! singleWorkflowAction
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala
index cc77522811f..05e494680a3 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala
@@ -278,6 +278,8 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props, metadataReadRow
       allDone()
     case Event(MetadataLookupResponse(query, metadata), HasWorkData(target, originalRequest)) =>
       processMetadataResponse(query, metadata, target, originalRequest)
+    case Event(FetchFailedJobsMetadataLookupResponse(metadata), HasWorkData(target, originalRequest)) =>
+      processFailedJobsMetadataResponse(metadata, target, originalRequest)
     case Event(MetadataLookupFailedTooLargeResponse(query, metadataSizeRows), HasWorkData(target, originalRequest)) =>
       val metadataTooLargeNumberOfRowsException = new MetadataTooLargeNumberOfRowsException(query.workflowId, metadataSizeRows, metadataReadRowNumberSafetyThreshold)
       target ! FailedMetadataJsonResponse(originalRequest, metadataTooLargeNumberOfRowsException)
@@ -286,6 +288,10 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props, metadataReadRow
       val metadataTooLargeTimeoutException = new MetadataTooLargeTimeoutException(query.workflowId)
       target ! FailedMetadataJsonResponse(originalRequest, metadataTooLargeTimeoutException)
       allDone()
+    case Event(FetchFailedTasksTimeoutResponse(workflowId), HasWorkData(target, originalRequest)) =>
+      val metadataTooLargeTimeoutException = new MetadataTooLargeTimeoutException(workflowId)
+      target ! FailedMetadataJsonResponse(originalRequest, metadataTooLargeTimeoutException)
+      allDone()
     case Event(failure: MetadataServiceFailure, HasWorkData(target, originalRequest)) =>
       target ! FailedMetadataJsonResponse(originalRequest, failure.reason)
       allDone()
@@ -371,4 +377,11 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props, metadataReadRow
       buildAndStop(query, eventsList, Map.empty, target, originalRequest)
     }
   }
+
+  def processFailedJobsMetadataResponse(eventsList: Seq[MetadataEvent], target: ActorRef, originalRequest: BuildMetadataJsonAction) = {
+    val groupedEvents = groupEvents(eventsList)
+    val res = MetadataBuilderActor.parse(groupedEvents, Map.empty)
+    target ! SuccessfulMetadataJsonResponse(originalRequest, res)
+    allDone()
+  }
 }
diff --git a/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala b/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala
index 3a8a320e1d2..86167977050 100644
--- a/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala
@@ -1,7 +1,6 @@
 package cromwell.services.database
 
 import java.time.OffsetDateTime
-
 import com.dimafeng.testcontainers.Container
 import common.assertion.CromwellTimeoutSpec
 import cromwell.core.Tags.DbmsTest
@@ -17,8 +16,9 @@ import org.scalatest.concurrent.ScalaFutures
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
+import javax.sql.rowset.serial.SerialClob
 import scala.concurrent.duration._
-import scala.concurrent.{ExecutionContext, ExecutionContextExecutor}
+import scala.concurrent.{ExecutionContext, ExecutionContextExecutor, Future}
 import scala.language.postfixOps
 
 class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalaFutures {
@@ -46,6 +46,15 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
 
     val subSubWorkflowCountableId = "subsubworkflow id: countable stuff"
 
+    val failedParentWorkflowId = "bbf4c25b-282b-4a18-a914-441f9684b69e"
+    val successfulParentWorkflowId = "4c1cf43d-1fbd-47af-944c-c63216f293ae"
+
+    val failedChildWorkflowId = "9ff3d855-0585-48e4-b3a1-189101f611e5"
+    val successfulChildWorkflowId = "73886096-2e06-48f6-ba42-f365dbf23de5"
+
+    val failedStatusMetadataValue = Option(new SerialClob("Failed".toCharArray()))
+    val doneStatusMetadataValue = Option(new SerialClob("Done".toCharArray()))
+
     it should "set up the test data" taggedAs DbmsTest in {
       database.runTestTransaction(
         database.dataAccess.metadataEntries ++= Seq(
@@ -116,7 +125,7 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
 
           WorkflowMetadataSummaryEntry(rootCountableId, Option("workflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), None, None, None, None),
           WorkflowMetadataSummaryEntry(subWorkflowCountableId, Option("subworkflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), Option(rootCountableId), Option(rootCountableId), None, None),
-          WorkflowMetadataSummaryEntry(subSubWorkflowCountableId, Option("subsubworkflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), Option(subWorkflowCountableId), Option(rootCountableId), None, None)
+          WorkflowMetadataSummaryEntry(subSubWorkflowCountableId, Option("subsubworkflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), Option(subWorkflowCountableId), Option(rootCountableId), None, None),
         )
       ).futureValue(Timeout(10.seconds))
     }
@@ -198,6 +207,116 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       }
     }
 
+    it should "fetch failed tasks from a failed workflow" taggedAs DbmsTest in {
+      database.runTestTransaction(
+        database.dataAccess.metadataEntries ++= Seq(
+          //Failed parent workflow calls (successful calls and older attempts and runs mixed in for negative checks)
+          MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(0), Option(0), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(0), Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(1), Option(0), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(1), Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedParentWorkflowId, Option("successfulWorkflowCall"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedParentWorkflowId, Option("successfulSubWorkflowCall"), Option(0), Option(0), "subWorkflowId", Option(new SerialClob(failedChildWorkflowId.toCharArray)), Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+
+          //child workflow calls (successful calls and previous failed attempts/shards are mixed in for negative checks)
+          //notFailedSubWorkflowCall should not be returned since it succeeded on the last attempt and has no scatters
+          MetadataEntry(failedChildWorkflowId, Option("notActuallyFailedSubWorkflowCall"), None, Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("notActuallyFailedSubWorkflowCall"), None, Option(2), "backendStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+
+          //Failed child workflow calls (successful calls and previous failed attempts/shards are mixed in for negative checks)
+          //failedSubWorkflowCall2 should be returned since it never succeeded
+          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall"), None, Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall"), None, Option(2), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall2"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+
+          //Third set of child workflow calls, similar to above however this set consists of retries and scatters
+          //It's safe to assume that if one scatter fails then they all fail, so pull the last scatter on the last attempt
+          //failedSubWorkflowCall2 should return since the scatters failed on the last attempt
+          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(1), Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(2), Option(1), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(1), Option(2), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(2), Option(2), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall3"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+
+          //Fourth set of child workflow calls
+          //This set should not return anything since the scatters succeeded on the last attempt
+          MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(1), Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(2), Option(1), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(1), Option(2), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(2), Option(2), "backendStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall4"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+
+          //Successful parent workflow call (negative check)
+          MetadataEntry(successfulParentWorkflowId, Option("successfulWorkflowCall"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+
+          //Successful child workflow calls (negative check)
+          MetadataEntry(successfulChildWorkflowId, Option("successfulSubWorkflowCall"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(successfulChildWorkflowId, Option("successfulSubWorkflowCall"), Option(0), Option(0), "subWorkflowId", Option(new SerialClob(successfulParentWorkflowId.toCharArray)), Option("String"), OffsetDateTime.now().toSystemTimestamp, None)
+        )
+      ).futureValue(Timeout(10.seconds))
+
+      database.runTestTransaction(
+        database.dataAccess.workflowMetadataSummaryEntries ++= Seq(
+          //Failed WorkflowMetadataSummaryEntry setup
+          WorkflowMetadataSummaryEntry(failedParentWorkflowId, Option("failedParentWorkflow"), Option("Failed"), Option(now), Option(now), Option(now), None, None, None, None),
+          WorkflowMetadataSummaryEntry(failedChildWorkflowId, Option("failedChildWorkflow"), Option("Failed"), Option(now), Option(now), Option(now), Option(failedParentWorkflowId), Option(failedParentWorkflowId), None, None),
+          WorkflowMetadataSummaryEntry(successfulParentWorkflowId, Option("successfulParentWorkflow"), Option("Succeeded"), Option(now), Option(now), Option(now), None, None, None, None),
+          WorkflowMetadataSummaryEntry(successfulChildWorkflowId, Option("successfulChildWorkflow"), Option("Succeeded"), Option(now), Option(now), Option(now), Option(successfulParentWorkflowId), Option(successfulParentWorkflowId), None, None)
+        )
+      ).futureValue(Timeout(10.seconds))
+
+      val futureEntries: Future[Seq[MetadataEntry]] = database.getFailedJobsMetadataWithWorkflowId(failedParentWorkflowId)
+      var entriesFound = false
+
+      val recordCount = Map(
+        failedParentWorkflowId -> scala.collection.mutable.Map(
+          "expected" -> 1,
+          "actual" -> 0
+        ),
+        failedChildWorkflowId -> scala.collection.mutable.Map(
+          "expected" -> 2,
+          "actual" -> 0
+        )
+      )
+
+      whenReady(futureEntries, timeout(scaled(5 seconds))) {
+        entries =>
+          entries.foreach(entry => {
+            entriesFound = true
+            val workflowId = entry.workflowExecutionUuid
+            recordCount.getOrElse(workflowId, None) should not be(None)
+            recordCount(workflowId)("actual") += 1
+            val metadataValueClob = entry.metadataValue.get
+            val metadataValueString = metadataValueClob.getSubString(1, metadataValueClob.length().toInt)
+            metadataValueString should be("Failed")
+            entry.metadataKey should not be("subWorkflowId")
+            entry.callFullyQualifiedName.getOrElse("") match {
+              case "failedWorkflowCall" => {
+                entry.jobIndex.get should be(1)
+                entry.jobAttempt.get should be(1)
+                entry.metadataKey should be("executionStatus")
+              }
+              case "failedSubWorkflowCall" => {
+                entry.jobIndex should be(None)
+                entry.jobAttempt.get should be(2)
+                entry.metadataKey should be("backendStatus")
+              }
+              case "failedSubWorkflowCall2" => {
+                entry.jobIndex.get should be(2)
+                entry.jobAttempt.get should be(2)
+                entry.metadataKey should be("executionStatus")
+              }
+              case _ => fail(s"Entry ${entry.callFullyQualifiedName.getOrElse("N/A")} | Index: ${entry.jobIndex.get} | Attempt: ${entry.jobAttempt.get} should not be in result set")
+            }
+          })
+          entriesFound should be(true)
+          recordCount.foreach(record => {
+            record._2("actual") should be(record._2("expected"))
+          })
+      }
+    }
+
     it should "clean up & close the database" taggedAs DbmsTest in {
       // Not relevant in Travis where all state gets nuked but useful for testing locally
       database.runTestTransaction(database.dataAccess.metadataEntries.delete).futureValue(Timeout(10.seconds))
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala
index 0df5efab18b..6ed7fa6c402 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala
@@ -308,6 +308,8 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     override def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold: Timestamp)(implicit ec: ExecutionContext): Future[Int] = notImplemented()
 
     override def getMetadataTableSizeInformation()(implicit ec: ExecutionContext): Future[Option[InformationSchemaEntry]] = notImplemented()
+
+    override def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: String)(implicit ec: ExecutionContext): Future[Vector[MetadataEntry]] = notImplemented()
   }
 }
 

From 4ca252c5f403b25d557a4fa02647f11a6bd61f39 Mon Sep 17 00:00:00 2001
From: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Date: Thu, 20 Jul 2023 10:39:58 -0400
Subject: [PATCH 194/326] WX-1210 Added JIRA ID for Cromwhelm auto commit
 message (#7180)

---
 .github/workflows/chart_update_on_merge.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index 107e9d5de4a..ac1c9e79141 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -11,6 +11,12 @@ jobs:
     if: github.event.pull_request.merged == true
     runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
     steps:
+    - name: Fetch Jira ID from the commit message
+      id: fetch-jira-id
+      run: |
+        JIRA_ID=$(echo '${{ github.event.head_commit.message }}' | grep -Eo '\[?[A-Z][A-Z]+-[0-9]+\]?')
+        [[ -z "$JIRA_ID" ]] && { echo "No Jira ID found in $1" ; exit 1; }
+        echo "JIRA_ID=$JIRA_ID" >> $GITHUB_OUTPUT
     - name: Clone Cromwell
       uses: actions/checkout@v2
       with:
@@ -82,5 +88,5 @@ jobs:
         git diff
         git config --global user.name "broadbot"
         git config --global user.email "broadbot@broadinstitute.org"
-        git commit -am "Auto update to Cromwell $CROMWELL_VERSION"
+        git commit -am "${{ steps.fetch-jira-id.outputs.JIRA_ID }}: Auto update to Cromwell $CROMWELL_VERSION"
         git push https://broadbot:$BROADBOT_GITHUB_TOKEN@github.com/broadinstitute/cromwhelm.git main

From d1ef074a7f12e690c4d3f60f3cb102fcc377fc3a Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 20 Jul 2023 15:44:15 -0400
Subject: [PATCH 195/326] WX-1179 DRS image build updates, remove self-hosted
 runners (#7179)

---
 .github/workflows/chart_update_on_merge.yml                 | 2 +-
 .github/workflows/docker_build_test.yml                     | 2 +-
 .github/workflows/make_publish_prs.yml                      | 3 +--
 .../resources/standardTestCases/drs_tests/drs_usa_jdr.wdl   | 6 +++---
 project/Settings.scala                                      | 6 +++---
 5 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index ac1c9e79141..883bd557a1f 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -9,7 +9,7 @@ jobs:
   chart-update:
     name: Cromwhelm Chart Auto Updater
     if: github.event.pull_request.merged == true
-    runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
+    runs-on: ubuntu-latest
     steps:
     - name: Fetch Jira ID from the commit message
       id: fetch-jira-id
diff --git a/.github/workflows/docker_build_test.yml b/.github/workflows/docker_build_test.yml
index 15517cce919..01c2ea502c9 100644
--- a/.github/workflows/docker_build_test.yml
+++ b/.github/workflows/docker_build_test.yml
@@ -17,7 +17,7 @@ permissions:
 jobs:
   sbt-build:
     name: sbt docker build
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     steps:
       - name: Clone Cromwell
         uses: actions/checkout@v2
diff --git a/.github/workflows/make_publish_prs.yml b/.github/workflows/make_publish_prs.yml
index 4a25210dd6e..e4e98a7f2f0 100644
--- a/.github/workflows/make_publish_prs.yml
+++ b/.github/workflows/make_publish_prs.yml
@@ -16,7 +16,7 @@ on:
 jobs:
   make-firecloud-develop-pr:
     name: Create firecloud-develop PR
-    runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners
+    runs-on: ubuntu-latest
     steps:
       - name: Clone firecloud-develop
         uses: actions/checkout@v2
@@ -70,4 +70,3 @@ jobs:
                 'It updates cromwell from version ${{ github.event.inputs.old_cromwell_version }} to ${{ github.event.inputs.new_cromwell_version }}.'
               ].join('\n')
             });
-
diff --git a/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.wdl b/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.wdl
index ba2a17f292d..e9b56af98d2 100644
--- a/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.wdl
+++ b/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.wdl
@@ -61,7 +61,7 @@ task localize_jdr_drs_with_usa {
     }
 
     runtime {
-        docker: "ubuntu"
+        docker: "ubuntu:latest"
         backend: "papi-v2-usa"
     }
 }
@@ -88,7 +88,7 @@ task skip_localize_jdr_drs_with_usa {
     }
 
     runtime {
-        docker: "ubuntu"
+        docker: "ubuntu:latest"
         backend: "papi-v2-usa"
     }
 }
@@ -109,7 +109,7 @@ task read_drs_with_usa {
     }
 
     runtime {
-        docker: "ubuntu"
+        docker: "ubuntu:latest"
         backend: "papi-v2-usa"
     }
 }
diff --git a/project/Settings.scala b/project/Settings.scala
index 0257cbac06b..ea775ed2bf5 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -131,14 +131,14 @@ object Settings {
       // instructions to install `crcmod`
       Instructions.Run("apt-get -y update"),
       Instructions.Run("apt-get -y install python3.11"),
-      Instructions.Run("apt -y install python3-pip"),
-      Instructions.Run("apt-get -y install gcc python3-dev python3-setuptools"),
+      Instructions.Run("apt-get -y install python3-pip"),
+      Instructions.Run("apt-get -y install wget gcc python3-dev python3-setuptools"),
       Instructions.Run("pip3 uninstall crcmod"),
       Instructions.Run("pip3 install --no-cache-dir -U crcmod"),
       Instructions.Run("update-alternatives --install /usr/bin/python python /usr/bin/python3 1"),
       Instructions.Env("CLOUDSDK_PYTHON", "python3"),
       // instructions to install Google Cloud SDK
-      Instructions.Run("curl https://dl.google.com/dl/cloudsdk/release/google-cloud-sdk.tar.gz > /tmp/google-cloud-sdk.tar.gz"),
+      Instructions.Run("wget https://dl.google.com/dl/cloudsdk/release/google-cloud-sdk.tar.gz -O /tmp/google-cloud-sdk.tar.gz"),
       Instructions.Run("""mkdir -p /usr/local/gcloud \
                          | && tar -C /usr/local/gcloud -xvf /tmp/google-cloud-sdk.tar.gz \
                          | && /usr/local/gcloud/google-cloud-sdk/install.sh""".stripMargin),

From b44554a2a64638619d2cdcf3fda69e93e273ca34 Mon Sep 17 00:00:00 2001
From: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Date: Mon, 24 Jul 2023 10:21:06 -0400
Subject: [PATCH 196/326] WX-1210-action-fix Use PR title to find JIRA ID for
 cromwhelm commit message (#7184)

---
 .github/workflows/chart_update_on_merge.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index 883bd557a1f..72a3486b24b 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -14,7 +14,7 @@ jobs:
     - name: Fetch Jira ID from the commit message
       id: fetch-jira-id
       run: |
-        JIRA_ID=$(echo '${{ github.event.head_commit.message }}' | grep -Eo '\[?[A-Z][A-Z]+-[0-9]+\]?')
+        JIRA_ID=$(echo '${{ github.event.pull_request.title }}' | grep -Eo '\[?[A-Z][A-Z]+-[0-9]+\]?')
         [[ -z "$JIRA_ID" ]] && { echo "No Jira ID found in $1" ; exit 1; }
         echo "JIRA_ID=$JIRA_ID" >> $GITHUB_OUTPUT
     - name: Clone Cromwell

From d89e4affaab70e5a89a6e3f8bbf0e1ded02c4bc2 Mon Sep 17 00:00:00 2001
From: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Date: Thu, 27 Jul 2023 07:28:45 -0400
Subject: [PATCH 197/326] WX-1110-query-fix Corrected Query to pull in
 attributes outside of executionStatus and backendStatus (#7185)

---
 .../slick/tables/MetadataEntryComponent.scala | 39 +++++++++++-----
 .../database/MetadataSlickDatabaseSpec.scala  | 46 +++++++++++++++----
 2 files changed, 65 insertions(+), 20 deletions(-)

diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
index f4b2724b6a7..1c1225c195d 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
@@ -323,14 +323,18 @@ trait MetadataEntryComponent {
       if(isPostgres) "obj.data" else "METADATA_VALUE"
     }
 
-    def targetCallsSelectStatement(callFqn: String, scatterIndex: String, retryAttempt: String): String = {
-      s"SELECT ${callFqn}, MAX(COALESCE(${scatterIndex}, 0)) as maxScatter, MAX(COALESCE(${retryAttempt}, 0)) AS maxRetry"
+    def attemptAndIndexSelectStatement(callFqn: String, scatterIndex: String, retryAttempt: String, variablePrefix: String): String = {
+      s"SELECT ${callFqn}, MAX(COALESCE(${scatterIndex}, 0)) as ${variablePrefix}Scatter, MAX(COALESCE(${retryAttempt}, 0)) AS ${variablePrefix}Retry"
     }
 
     def pgObjectInnerJoinStatement(isPostgres: Boolean, metadataValColName: String): String = {
       if(isPostgres) s"INNER JOIN pg_largeobject obj ON me.${metadataValColName} = cast(obj.loid as text)" else ""
     }
 
+    def failedTaskGroupByClause(metadataValue: String, callFqn: String): String = {
+      return s"GROUP BY ${callFqn}, ${metadataValue}"
+    }
+
     val workflowUuid = dbIdentifierWrapper("WORKFLOW_EXECUTION_UUID", isPostgres)
     val callFqn = dbIdentifierWrapper("CALL_FQN", isPostgres)
     val scatterIndex = dbIdentifierWrapper("JOB_SCATTER_INDEX", isPostgres)
@@ -345,19 +349,32 @@ trait MetadataEntryComponent {
     val wmse = dbIdentifierWrapper("WORKFLOW_METADATA_SUMMARY_ENTRY", isPostgres)
     val resultSetColumnNames = s"me.${workflowUuid}, me.${callFqn}, me.${scatterIndex}, me.${retryAttempt}, me.${metadataKey}, me.${metadataValue}, me.${metadataValueType}, me.${metadataTimestamp}, me.${metadataJournalId}"
 
-    val query = sql"""
+    val query =
+      sql"""
       SELECT #${resultSetColumnNames}
       FROM #${metadataEntry} me
       INNER JOIN (
-        #${targetCallsSelectStatement(callFqn, scatterIndex, retryAttempt)}
+       #${attemptAndIndexSelectStatement(callFqn, scatterIndex, retryAttempt, "failed")}
+        FROM #${metadataEntry} me
+        INNER JOIN #${wmse} wmse
+        ON wmse.#${workflowUuid} = me.#${workflowUuid}
+        #${pgObjectInnerJoinStatement(isPostgres, metadataValue)}
+        WHERE (wmse.#${rootUuid} = $rootWorkflowId OR wmse.#${workflowUuid} = $rootWorkflowId)
+        AND (me.#${metadataKey} in ('executionStatus', 'backendStatus') AND #${dbMetadataValueColCheckName(isPostgres)} = 'Failed')
+        #${failedTaskGroupByClause(dbMetadataValueColCheckName(isPostgres), callFqn)}
+        HAVING #${dbMetadataValueColCheckName(isPostgres)} = 'Failed'
+      ) AS failedCalls
+      ON me.#${callFqn} = failedCalls.#${callFqn}
+      INNER JOIN (
+        #${attemptAndIndexSelectStatement(callFqn, scatterIndex, retryAttempt, "max")}
         FROM #${metadataEntry} me
         INNER JOIN #${wmse} wmse
         ON wmse.#${workflowUuid} = me.#${workflowUuid}
         WHERE (wmse.#${rootUuid} = $rootWorkflowId OR wmse.#${workflowUuid} = $rootWorkflowId)
         AND #${callFqn} IS NOT NULL
         GROUP BY #${callFqn}
-      ) AS targetCalls
-      ON me.#${callFqn} = targetCalls.#${callFqn}
+      ) maxCalls
+      ON me.#${callFqn} = maxCalls.#${callFqn}
       LEFT JOIN (
         SELECT DISTINCT #${callFqn}
         FROM #${metadataEntry} me
@@ -370,13 +387,11 @@ trait MetadataEntryComponent {
       ON me.#${callFqn} = avoidedCalls.#${callFqn}
       INNER JOIN #${wmse} wmse
       ON wmse.#${workflowUuid} = me.#${workflowUuid}
-      #${pgObjectInnerJoinStatement(isPostgres, metadataValue)}
       WHERE avoidedCalls.#${callFqn} IS NULL
-      AND (me.#${metadataKey} in ('executionStatus', 'backendStatus') AND #${dbMetadataValueColCheckName(isPostgres)} = 'Failed')
-      AND (
-        (COALESCE(me.#${retryAttempt}, 0) = targetCalls.maxRetry AND me.#${scatterIndex} IS NULL)
-        OR (COALESCE(me.#${retryAttempt}, 0) = targetCalls.maxRetry AND me.#${scatterIndex} = targetCalls.maxScatter)
-       )
+      AND COALESCE(me.#${scatterIndex}, 0) = maxCalls.maxScatter
+      AND COALESCE(me.#${retryAttempt}, 0) = maxCalls.maxRetry
+      AND failedCalls.failedScatter = maxCalls.maxScatter
+      AND failedCalls.failedRetry = maxCalls.maxRetry
       GROUP BY #${resultSetColumnNames}
       HAVING me.#${workflowUuid} IN (
         SELECT DISTINCT wmse.#${workflowUuid}
diff --git a/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala b/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala
index 86167977050..33dd2a73b66 100644
--- a/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala
@@ -47,6 +47,8 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val subSubWorkflowCountableId = "subsubworkflow id: countable stuff"
 
     val failedParentWorkflowId = "bbf4c25b-282b-4a18-a914-441f9684b69e"
+    val ignoredFailedParentWorkflowId = "ccccc-ddddd-3333-42242"
+    val ignoredFailedChildWorkflowId = "eeeeeee-ggggggg-33333-22222"
     val successfulParentWorkflowId = "4c1cf43d-1fbd-47af-944c-c63216f293ae"
 
     val failedChildWorkflowId = "9ff3d855-0585-48e4-b3a1-189101f611e5"
@@ -54,6 +56,7 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
 
     val failedStatusMetadataValue = Option(new SerialClob("Failed".toCharArray()))
     val doneStatusMetadataValue = Option(new SerialClob("Done".toCharArray()))
+    val stdErrValue = Option(new SerialClob("test value".toCharArray()))
 
     it should "set up the test data" taggedAs DbmsTest in {
       database.runTestTransaction(
@@ -215,19 +218,26 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
           MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(0), Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(1), Option(0), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(1), Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(1), Option(1), "stderr", stdErrValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedParentWorkflowId, Option("successfulWorkflowCall"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedParentWorkflowId, Option("successfulSubWorkflowCall"), Option(0), Option(0), "subWorkflowId", Option(new SerialClob(failedChildWorkflowId.toCharArray)), Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
 
+          //ignored failed workflow calls. These should not be fetched since it's not part of the target workflow tree
+          MetadataEntry(ignoredFailedParentWorkflowId, Option("failedWorkflowCall"), Option(0), Option(0), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(ignoredFailedChildWorkflowId, Option("failedSubWorkflowCall"), None, Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+
           //child workflow calls (successful calls and previous failed attempts/shards are mixed in for negative checks)
           //notFailedSubWorkflowCall should not be returned since it succeeded on the last attempt and has no scatters
           MetadataEntry(failedChildWorkflowId, Option("notActuallyFailedSubWorkflowCall"), None, Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedChildWorkflowId, Option("notActuallyFailedSubWorkflowCall"), None, Option(2), "backendStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("notActuallyFailedSubWorkflowCall"), None, Option(2), "stderr", stdErrValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
 
           //Failed child workflow calls (successful calls and previous failed attempts/shards are mixed in for negative checks)
-          //failedSubWorkflowCall2 should be returned since it never succeeded
+          //failedSubWorkflowCall should be returned since it never succeeded
           MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall"), None, Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall"), None, Option(2), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall"), None, Option(2), "stderr", stdErrValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall2"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
 
           //Third set of child workflow calls, similar to above however this set consists of retries and scatters
@@ -237,6 +247,7 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
           MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(2), Option(1), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(1), Option(2), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(2), Option(2), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(2), Option(2), "stderr", stdErrValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall3"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
 
           //Fourth set of child workflow calls
@@ -245,6 +256,7 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
           MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(2), Option(1), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(1), Option(2), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(2), Option(2), "backendStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
+          MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(2), Option(2), "stderr", stdErrValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
           MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall4"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
 
           //Successful parent workflow call (negative check)
@@ -262,7 +274,9 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
           WorkflowMetadataSummaryEntry(failedParentWorkflowId, Option("failedParentWorkflow"), Option("Failed"), Option(now), Option(now), Option(now), None, None, None, None),
           WorkflowMetadataSummaryEntry(failedChildWorkflowId, Option("failedChildWorkflow"), Option("Failed"), Option(now), Option(now), Option(now), Option(failedParentWorkflowId), Option(failedParentWorkflowId), None, None),
           WorkflowMetadataSummaryEntry(successfulParentWorkflowId, Option("successfulParentWorkflow"), Option("Succeeded"), Option(now), Option(now), Option(now), None, None, None, None),
-          WorkflowMetadataSummaryEntry(successfulChildWorkflowId, Option("successfulChildWorkflow"), Option("Succeeded"), Option(now), Option(now), Option(now), Option(successfulParentWorkflowId), Option(successfulParentWorkflowId), None, None)
+          WorkflowMetadataSummaryEntry(successfulChildWorkflowId, Option("successfulChildWorkflow"), Option("Succeeded"), Option(now), Option(now), Option(now), Option(successfulParentWorkflowId), Option(successfulParentWorkflowId), None, None),
+          WorkflowMetadataSummaryEntry(ignoredFailedParentWorkflowId, Option("ignoredFailedParentWorkflow"), Option("Failed"), Option(now), Option(now), Option(now), Option(ignoredFailedParentWorkflowId), Option(ignoredFailedParentWorkflowId), None, None),
+          WorkflowMetadataSummaryEntry(ignoredFailedChildWorkflowId, Option("ignoredFailedChildWorkflow"), Option("Failed"), Option(now), Option(now), Option(now), Option(ignoredFailedChildWorkflowId), Option(ignoredFailedChildWorkflowId), None, None)
         )
       ).futureValue(Timeout(10.seconds))
 
@@ -271,11 +285,11 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
 
       val recordCount = Map(
         failedParentWorkflowId -> scala.collection.mutable.Map(
-          "expected" -> 1,
+          "expected" -> 2,
           "actual" -> 0
         ),
         failedChildWorkflowId -> scala.collection.mutable.Map(
-          "expected" -> 2,
+          "expected" -> 4,
           "actual" -> 0
         )
       )
@@ -289,23 +303,39 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
             recordCount(workflowId)("actual") += 1
             val metadataValueClob = entry.metadataValue.get
             val metadataValueString = metadataValueClob.getSubString(1, metadataValueClob.length().toInt)
-            metadataValueString should be("Failed")
+
+            entry.metadataKey match {
+              case "stderr" => {
+                metadataValueString should be("test value")
+              }
+              case "backendStatus" => {
+                metadataValueString should be("Failed")
+              }
+              case "executionStatus" => {
+                metadataValueString should be("Failed")
+              }
+              case _ => fail(s"Unexpected key ${entry.metadataKey} was included in result set")
+            }
+
             entry.metadataKey should not be("subWorkflowId")
             entry.callFullyQualifiedName.getOrElse("") match {
               case "failedWorkflowCall" => {
                 entry.jobIndex.get should be(1)
                 entry.jobAttempt.get should be(1)
-                entry.metadataKey should be("executionStatus")
+                val isValidKey = List("executionStatus", "stderr").contains(entry.metadataKey)
+                isValidKey should be(true)
               }
               case "failedSubWorkflowCall" => {
                 entry.jobIndex should be(None)
                 entry.jobAttempt.get should be(2)
-                entry.metadataKey should be("backendStatus")
+                val isValidKey = List("backendStatus", "stderr").contains(entry.metadataKey)
+                isValidKey should be(true)
               }
               case "failedSubWorkflowCall2" => {
                 entry.jobIndex.get should be(2)
                 entry.jobAttempt.get should be(2)
-                entry.metadataKey should be("executionStatus")
+                val isValidKey = List("executionStatus", "stderr").contains(entry.metadataKey)
+                isValidKey should be(true)
               }
               case _ => fail(s"Entry ${entry.callFullyQualifiedName.getOrElse("N/A")} | Index: ${entry.jobIndex.get} | Attempt: ${entry.jobAttempt.get} should not be in result set")
             }

From d2319527819350532fea36bbcb1928a9c0b473de Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 31 Jul 2023 12:18:25 -0400
Subject: [PATCH 198/326] WX-1179 GCP Batch new base (#7177)

Co-authored-by: dspeck <dspeck@burwood.com>
Co-authored-by: jarroyo28 <johnarroyo45@gmail.com>
Co-authored-by: Jacob Jennings <53196131+jakejennings@users.noreply.github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Tom Wiseman <twiseman@broadinstitute.org>
Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Co-authored-by: Christian Freitas <cfreitas@broadinstitute.org>
Co-authored-by: Tristan Garwood <tristan.garwood@gmail.com>
---
 .github/workflows/integration_tests.yml       |    4 +
 build.sbt                                     |   15 +
 .../draft3_read_file_limits.test              |    1 +
 .../resources/standardTestCases/long_cmd.test |    1 +
 .../standardTestCases/read_file_limits.test   |    1 +
 .../relative_output_paths_colliding.test      |    1 +
 ...dard_output_paths_colliding_prevented.test |    1 +
 cromwell.example.backends/GCPBATCH.conf       |  104 ++
 docs/backends/GCPBatch.md                     |  473 +++++++
 docs/tutorials/Batch101.md                    |  227 ++++
 project/Dependencies.scala                    |   14 +-
 src/ci/bin/testCentaurGcpBatch.sh             |   27 +
 src/ci/bin/test_gcpbatch.inc.sh               |  118 ++
 src/ci/bin/test_papi.inc.sh                   |    2 +-
 src/ci/resources/gcp_batch_application.conf   |   12 +
 .../gcp_batch_application.inc.conf.ctmpl      |   73 ++
 .../gcp_batch_provider_config.inc.conf        |   20 +
 .../gcp_batch_shared_application.inc.conf     |   34 +
 ...GcpBatchBackendLifecycleActorFactory.scala |  115 ++
 .../batch/actors/BatchApiAbortClient.scala    |   23 +
 .../batch/actors/BatchApiFetchJobClient.scala |   47 +
 .../actors/BatchApiRunCreationClient.scala    |   50 +
 ...cpBatchAsyncBackendJobExecutionActor.scala | 1086 +++++++++++++++++
 .../GcpBatchBackendSingletonActor.scala       |  122 ++
 .../actors/GcpBatchFinalizationActor.scala    |   35 +
 .../actors/GcpBatchInitializationActor.scala  |  254 ++++
 .../GcpBatchJobCachingActorHelper.scala       |   87 ++
 .../batch/api/GcpBatchApiRequestHandler.scala |   34 +
 .../batch/api/GcpBatchRequestFactory.scala    |  102 ++
 .../api/GcpBatchRequestFactoryImpl.scala      |  232 ++++
 .../batch/authentication/GcpBatchAuths.scala  |    5 +
 .../GcpBatchVMAuthentication.scala            |   60 +
 .../BatchBackendCacheHitCopyingActor.scala    |   88 ++
 .../BatchBackendFileHashingActor.scala        |    8 +
 .../BatchCacheHitDuplicationStrategy.scala    |    7 +
 ...validGcsPathsInManifestFileException.scala |    7 +
 .../backend/google/batch/io/DiskType.java     |   15 +
 .../batch/io/GcpBatchAttachedDisk.scala       |   98 ++
 .../backend/google/batch/io/package.scala     |   31 +
 .../models/CreateGcpBatchParameters.scala     |   10 +
 .../models/GcpBackendInitializationData.scala |   16 +
 .../batch/models/GcpBatchConfiguration.scala  |   38 +
 .../GcpBatchConfigurationAttributes.scala     |  465 +++++++
 .../models/GcpBatchCustomMachineType.scala    |  184 +++
 .../batch/models/GcpBatchJobPaths.scala       |   43 +
 .../batch/models/GcpBatchParameters.scala     |   83 ++
 .../google/batch/models/GcpBatchRequest.scala |    9 +
 .../models/GcpBatchRuntimeAttributes.scala    |  294 +++++
 .../batch/models/GcpBatchWorkflowPaths.scala  |   86 ++
 .../google/batch/models/GcpLabel.scala        |  102 ++
 .../google/batch/models/ManifestFile.scala    |    3 +
 .../batch/models/PreviousRetryReasons.scala   |   44 +
 .../google/batch/models/ProjectLabels.scala   |    3 +
 .../google/batch/models/ReferenceFile.scala   |    3 +
 .../backend/google/batch/models/Run.scala     |    5 +
 .../google/batch/models/RunStatus.scala       |   62 +
 .../VpcAndSubnetworkProjectLabelValues.scala  |   30 +
 .../monitoring/BatchInstrumentation.scala     |   32 +
 .../CheckpointingConfiguration.scala          |   75 ++
 .../backend/google/batch/monitoring/Env.scala |   24 +
 .../batch/monitoring/MonitoringImage.scala    |   47 +
 .../runnable/CheckpointingRunnable.scala      |   49 +
 .../batch/runnable/ContainerSetup.scala       |   25 +
 .../batch/runnable/Delocalization.scala       |  116 ++
 .../batch/runnable/GcpBatchMetadataKeys.scala |   11 +
 .../google/batch/runnable/Localization.scala  |  101 ++
 .../runnable/MemoryRetryCheckRunnable.scala   |   14 +
 .../batch/runnable/MonitoringRunnable.scala   |   66 +
 .../batch/runnable/RunnableBuilder.scala      |  318 +++++
 .../batch/runnable/RunnableCommands.scala     |  185 +++
 .../google/batch/runnable/RunnableFlag.scala  |    9 +
 .../batch/runnable/RunnableLabels.scala       |   22 +
 .../google/batch/runnable/RunnableUtils.scala |   83 ++
 .../google/batch/runnable/UserRunnable.scala  |   25 +
 .../batch/runnable/WorkflowOptionKeys.scala   |   13 +
 .../batch/util/BatchExpressionFunctions.scala |   38 +
 .../util/BatchParameterConversions.scala      |  149 +++
 .../batch/util/BatchUtilityConversions.scala  |  102 ++
 ...GcpBatchDockerCacheMappingOperations.scala |   81 ++
 .../util/GcpBatchExpressionFunctions.scala    |   38 +
 .../util/GcpBatchMachineConstraints.scala     |   31 +
 ...BatchReferenceFilesMappingOperations.scala |  119 ++
 .../google/batch/util/GpuTypeValidation.scala |   25 +
 .../google/batch/util/GpuValidation.scala     |   40 +
 .../batch/util/RuntimeOutputMapping.scala     |   33 +
 .../batch/src/test/resources/reference.conf   |    1 +
 .../backend/google/batch/GcpBatchIoSpec.scala |   34 +
 ...tchAsyncBackendJobExecutionActorSpec.scala |  800 ++++++++++++
 ...atchBackendLifecycleActorFactorySpec.scala |   64 +
 .../GcpBatchInitializationActorSpec.scala     |  185 +++
 .../batch/io/GcpBatchAttachedDiskSpec.scala   |   47 +
 .../batch/models/GcpBatchAttributeSpec.scala  |   80 ++
 .../GcpBatchConfigurationAttributesSpec.scala |  469 +++++++
 .../models/GcpBatchConfigurationSpec.scala    |  124 ++
 .../batch/models/GcpBatchJobPathsSpec.scala   |   81 ++
 .../batch/models/GcpBatchLabelSpec.scala      |   38 +
 .../GcpBatchRuntimeAttributesSpec.scala       |  298 +++++
 .../batch/models/GcpBatchTestConfig.scala     |  114 ++
 ...cAndSubnetworkProjectLabelValuesSpec.scala |   42 +
 .../batch/runnable/LocalizationSpec.scala     |   67 +
 .../batch/runnable/RunnableBuilderSpec.scala  |   94 ++
 .../batch/runnable/RunnableCommandSpec.scala  |   67 +
 .../util/GcpBatchMachineConstraintsSpec.scala |   90 ++
 103 files changed, 9676 insertions(+), 4 deletions(-)
 create mode 100644 cromwell.example.backends/GCPBATCH.conf
 create mode 100644 docs/backends/GCPBatch.md
 create mode 100644 docs/tutorials/Batch101.md
 create mode 100755 src/ci/bin/testCentaurGcpBatch.sh
 create mode 100644 src/ci/bin/test_gcpbatch.inc.sh
 create mode 100644 src/ci/resources/gcp_batch_application.conf
 create mode 100644 src/ci/resources/gcp_batch_application.inc.conf.ctmpl
 create mode 100644 src/ci/resources/gcp_batch_provider_config.inc.conf
 create mode 100644 src/ci/resources/gcp_batch_shared_application.inc.conf
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiAbortClient.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiFetchJobClient.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiRunCreationClient.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchBackendSingletonActor.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchFinalizationActor.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActor.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchJobCachingActorHelper.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchApiRequestHandler.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchAuths.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchVMAuthentication.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendCacheHitCopyingActor.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendFileHashingActor.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchCacheHitDuplicationStrategy.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/errors/InvalidGcsPathsInManifestFileException.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/DiskType.java
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/package.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/CreateGcpBatchParameters.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBackendInitializationData.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfiguration.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributes.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchCustomMachineType.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchJobPaths.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchParameters.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRequest.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchWorkflowPaths.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ManifestFile.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/PreviousRetryReasons.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ProjectLabels.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ReferenceFile.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/Run.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/RunStatus.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/VpcAndSubnetworkProjectLabelValues.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/BatchInstrumentation.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/CheckpointingConfiguration.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/Env.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/MonitoringImage.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/CheckpointingRunnable.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/ContainerSetup.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Delocalization.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/GcpBatchMetadataKeys.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Localization.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MemoryRetryCheckRunnable.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MonitoringRunnable.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableCommands.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableFlag.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableLabels.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/WorkflowOptionKeys.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchExpressionFunctions.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchParameterConversions.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchDockerCacheMappingOperations.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchExpressionFunctions.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraints.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchReferenceFilesMappingOperations.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuTypeValidation.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala
 create mode 100644 supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/RuntimeOutputMapping.scala
 create mode 100644 supportedBackends/google/batch/src/test/resources/reference.conf
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/GcpBatchIoSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchBackendLifecycleActorFactorySpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActorSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDiskSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchAttributeSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributesSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchJobPathsSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchLabelSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchTestConfig.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchVpcAndSubnetworkProjectLabelValuesSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/LocalizationSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableCommandSpec.scala
 create mode 100644 supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraintsSpec.scala

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index f82a5020ef3..98185b3d1b3 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -24,7 +24,11 @@ jobs:
       #Each will be launched on its own runner so they can occur in parallel.
       #Friendly names are displayed on the Github UI and aren't used anywhere else.
       matrix:
+        # Batch test fixes to land later
         include:
+          # - build_type: centaurGcpBatch
+          #   build_mysql: 5.7
+          #   friendly_name: Centaur GCP Batch with MySQL 5.7
           - build_type: centaurPapiV2beta
             build_mysql: 5.7
             friendly_name: Centaur Papi V2 Beta with MySQL 5.7
diff --git a/build.sbt b/build.sbt
index 6b2641e024f..9bdd086d731 100644
--- a/build.sbt
+++ b/build.sbt
@@ -233,6 +233,19 @@ lazy val googlePipelinesV2Beta = (project in backendRoot / "google" / "pipelines
   .dependsOn(core % "test->test")
   .dependsOn(common % "test->test")
 
+lazy val googleBatch = (project in backendRoot / "google" / "batch")
+  .withLibrarySettings("cromwell-google-batch-backend")
+  .dependsOn(backend)
+  .dependsOn(gcsFileSystem)
+  .dependsOn(drsFileSystem)
+  .dependsOn(sraFileSystem)
+  .dependsOn(httpFileSystem)
+  .dependsOn(backend % "test->test")
+  .dependsOn(gcsFileSystem % "test->test")
+  .dependsOn(services % "test->test")
+  .dependsOn(common % "test->test")
+  .dependsOn(core % "test->test")
+
 lazy val awsBackend = (project in backendRoot / "aws")
   .withLibrarySettings("cromwell-aws-backend")
   .dependsOn(backend)
@@ -392,6 +405,7 @@ lazy val server = project
   .dependsOn(engine)
   .dependsOn(googlePipelinesV2Alpha1)
   .dependsOn(googlePipelinesV2Beta)
+  .dependsOn(googleBatch)
   .dependsOn(awsBackend)
   .dependsOn(tesBackend)
   .dependsOn(cromwellApiClient)
@@ -431,6 +445,7 @@ lazy val root = (project in file("."))
   .aggregate(googlePipelinesCommon)
   .aggregate(googlePipelinesV2Alpha1)
   .aggregate(googlePipelinesV2Beta)
+  .aggregate(googleBatch)
   .aggregate(httpFileSystem)
   .aggregate(languageFactoryCore)
   .aggregate(perf)
diff --git a/centaur/src/main/resources/standardTestCases/draft3_read_file_limits.test b/centaur/src/main/resources/standardTestCases/draft3_read_file_limits.test
index 4a9af0c8813..4bcbdd38db7 100644
--- a/centaur/src/main/resources/standardTestCases/draft3_read_file_limits.test
+++ b/centaur/src/main/resources/standardTestCases/draft3_read_file_limits.test
@@ -2,6 +2,7 @@ name: draft3_read_file_limits
 testFormat: workflowfailure
 workflowType: WDL
 workflowTypeVersion: 1.0
+tags: [batchexclude]
 
 files {
   workflow: wdl_draft3/read_file_limits/read_file_limits.wdl
diff --git a/centaur/src/main/resources/standardTestCases/long_cmd.test b/centaur/src/main/resources/standardTestCases/long_cmd.test
index 40b6110b629..cef5fda2177 100644
--- a/centaur/src/main/resources/standardTestCases/long_cmd.test
+++ b/centaur/src/main/resources/standardTestCases/long_cmd.test
@@ -9,6 +9,7 @@
 
 name: long_cmd
 testFormat: workflowsuccess
+tags: [batchexclude]
 
 files {
   workflow: long_cmd/long_cmd.wdl
diff --git a/centaur/src/main/resources/standardTestCases/read_file_limits.test b/centaur/src/main/resources/standardTestCases/read_file_limits.test
index 0079401812a..734ab809b92 100644
--- a/centaur/src/main/resources/standardTestCases/read_file_limits.test
+++ b/centaur/src/main/resources/standardTestCases/read_file_limits.test
@@ -1,5 +1,6 @@
 name: read_file_limits
 testFormat: workflowfailure
+tags: [batchexclude]
 
 files {
   workflow: read_file_limits/read_file_limits.wdl
diff --git a/centaur/src/main/resources/standardTestCases/relative_output_paths_colliding.test b/centaur/src/main/resources/standardTestCases/relative_output_paths_colliding.test
index 82b01c6399d..2a6fca6793e 100644
--- a/centaur/src/main/resources/standardTestCases/relative_output_paths_colliding.test
+++ b/centaur/src/main/resources/standardTestCases/relative_output_paths_colliding.test
@@ -1,5 +1,6 @@
 name: relative_output_paths_colliding
 testFormat: workflowfailure
+tags: [batchexclude]
 
 files {
   workflow: relative_output_paths_colliding/workflow_output_paths_colliding.wdl
diff --git a/centaur/src/main/resources/standardTestCases/standard_output_paths_colliding_prevented.test b/centaur/src/main/resources/standardTestCases/standard_output_paths_colliding_prevented.test
index 6c5a5b51476..d8d37b4b2d0 100644
--- a/centaur/src/main/resources/standardTestCases/standard_output_paths_colliding_prevented.test
+++ b/centaur/src/main/resources/standardTestCases/standard_output_paths_colliding_prevented.test
@@ -1,5 +1,6 @@
 name: standard_output_paths_colliding_prevented
 testFormat: workflowsuccess
+tags: [batchexclude]
 
 files {
   workflow: standard_output_paths_colliding_prevented/workflow_output_paths_colliding.wdl
diff --git a/cromwell.example.backends/GCPBATCH.conf b/cromwell.example.backends/GCPBATCH.conf
new file mode 100644
index 00000000000..ba554e3322d
--- /dev/null
+++ b/cromwell.example.backends/GCPBATCH.conf
@@ -0,0 +1,104 @@
+# This is an example of how you can use the Google Cloud Batch backend
+# provider. *This is not a complete configuration file!* The
+# content here should be copy pasted into the backend -> providers section
+# of cromwell.example.backends/cromwell.examples.conf in the root of the repository.
+# You should uncomment lines that you want to define, and read carefully to customize
+# the file.
+
+# Documentation
+# https://cromwell.readthedocs.io/en/stable/backends/Google/
+
+backend {
+  default = GCPBATCH
+
+  providers {
+    GCPBATCH {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory"
+      config {
+        # Google project
+        project = "my-cromwell-workflows"
+
+        # Base bucket for workflow executions
+        root = "gs://my-cromwell-workflows-bucket"
+
+        # Polling for completion backs-off gradually for slower-running jobs.
+        # This is the maximum polling interval (in seconds):
+        maximum-polling-interval = 600
+
+        # Optional Dockerhub Credentials. Can be used to access private docker images.
+        dockerhub {
+          # account = ""
+          # token = ""
+        }
+
+        # Optional configuration to use high security network (Virtual Private Cloud) for running jobs.
+        # See https://cromwell.readthedocs.io/en/stable/backends/Google/ for more details.
+        # virtual-private-cloud {
+        #  network-label-key = "network-key"
+        #  auth = "application-default"
+        # }
+
+        # Global pipeline timeout
+        # Defaults to 7 days; max 30 days
+        # batch-timeout = 7 days
+
+        genomics {
+          # A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
+          # Batch Jobs and manipulate auth JSONs.
+          auth = "application-default"
+
+
+          // alternative service account to use on the launched compute instance
+          // NOTE: If combined with service account authorization, both that service account and this service account
+          // must be able to read and write to the 'root' GCS path
+          compute-service-account = "default"
+
+          # Location to submit jobs to Batch and store job metadata.
+          location = "us-central1"
+
+          # Specifies the minimum file size for `gsutil cp` to use parallel composite uploads during delocalization.
+          # Parallel composite uploads can result in a significant improvement in delocalization speed for large files
+          # but may introduce complexities in downloading such files from GCS, please see
+          # https://cloud.google.com/storage/docs/gsutil/commands/cp#parallel-composite-uploads for more information.
+          #
+          # If set to 0 parallel composite uploads are turned off. The default Cromwell configuration turns off
+          # parallel composite uploads, this sample configuration turns it on for files of 150M or larger.
+          parallel-composite-upload-threshold="150M"
+        }
+
+        filesystems {
+          gcs {
+            # A reference to a potentially different auth for manipulating files via engine functions.
+            auth = "application-default"
+            # Google project which will be billed for the requests
+            project = "google-billing-project"
+
+            caching {
+              # When a cache hit is found, the following duplication strategy will be followed to use the cached outputs
+              # Possible values: "copy", "reference". Defaults to "copy"
+              # "copy": Copy the output files
+              # "reference": DO NOT copy the output files but point to the original output files instead.
+              #              Will still make sure than all the original output files exist and are accessible before
+              #              going forward with the cache hit.
+              duplication-strategy = "copy"
+            }
+          }
+        }
+
+        default-runtime-attributes {
+          cpu: 1
+          failOnStderr: false
+          continueOnReturnCode: 0
+          memory: "2048 MB"
+          bootDiskSizeGb: 10
+          # Allowed to be a String, or a list of Strings
+          disks: "local-disk 10 SSD"
+          noAddress: false
+          preemptible: 0
+          zones: ["us-central1-a", "us-central1-b"]
+        }
+
+      }
+    }
+  }
+}
diff --git a/docs/backends/GCPBatch.md b/docs/backends/GCPBatch.md
new file mode 100644
index 00000000000..766719af8c5
--- /dev/null
+++ b/docs/backends/GCPBatch.md
@@ -0,0 +1,473 @@
+**Google Cloud Backend**
+
+[//]:
+Google Cloud Batch is a fully managed service that lets you schedule, queue, and execute batch processing workloads on Google Cloud resources. Batch provisions resources and manages capacity on your behalf, allowing your batch workloads to run at scale.
+
+This section offers detailed configuration instructions for using Cromwell with the Batch API in all supported
+authentication modes. Before reading further in this section please see the
+[Getting started on Google Batch API](../tutorials/Batch101) for instructions common to all authentication modes
+and detailed instructions for the application default authentication scheme in particular.
+The instructions below assume you have created a Google Cloud Storage bucket and a Google project enabled for the appropriate APIs.
+
+**Configuring Authentication**
+
+The `google` stanza in the Cromwell configuration file defines how to authenticate to Google.  There are four different
+authentication schemes that might be used:
+
+* `application_default` (default, recommended) - Use [application default](https://developers.google.com/identity/protocols/application-default-credentials) credentials.
+* `service_account` - Use a specific service account and key file (in PEM format) to authenticate.
+* `user_account` - Authenticate as a user.
+* `user_service_account` - Authenticate each individual workflow using service account credentials supplied in the workflow options.
+
+The `auths` block in the `google` stanza defines the authentication schemes within a Cromwell deployment:
+
+
+```hocon
+google {
+  application-name = "cromwell"
+  auths = [
+    {
+      name = "application-default"
+      scheme = "application_default"
+    },
+    {
+      name = "service-account"
+      scheme = "service_account"
+      service-account-id = "my-service-account"
+      pem-file = "/path/to/file.pem"
+    },
+    {
+      name = "user-service-account"
+      scheme = "user_service_account"
+    }
+  ]
+}
+```
+
+These authentication schemes can be referenced by name within other portions of the configuration file.  For example, both
+the `GCPBATCH` and `filesystems.gcs` sections within a Google configuration block must reference an auth defined in this block.
+The auth for the `GCPBATCH` section governs the interactions with Google itself, while `filesystems.gcs` governs the localization
+of data into and out of GCE VMs.
+
+**Application Default Credentials**
+
+By default, application default credentials will be used.  Only `name` and `scheme` are required for application default credentials.
+
+To authenticate, run the following commands from your command line (requires [gcloud](https://cloud.google.com/sdk/gcloud/)):
+
+```
+$ gcloud auth login
+$ gcloud config set project my-project
+```
+
+**Service Account**
+
+First create a new service account through the [API Credentials](https://console.developers.google.com/apis/credentials) page.  Go to **Create credentials -> Service account key**.  Then in the **Service account** dropdown select **New service account**.  Fill in a name (e.g. `my-account`), and select key type of JSON.
+
+Creating the account will cause the JSON file to be downloaded.  The structure of this file is roughly like this (account name is `my-account`):
+
+```
+{
+  "type": "service_account",
+  "project_id": "my-project",
+  "private_key_id": "OMITTED",
+  "private_key": "-----BEGIN PRIVATE KEY-----\nBASE64 ENCODED KEY WITH \n TO REPRESENT NEWLINES\n-----END PRIVATE KEY-----\n",
+  "client_email": "my-account@my-project.iam.gserviceaccount.com",
+  "client_id": "22377410244549202395",
+  "auth_uri": "https://accounts.google.com/o/oauth2/auth",
+  "token_uri": "https://accounts.google.com/o/oauth2/token",
+  "auth_provider_x509_cert_url": "https://www.googleapis.com/oauth2/v1/certs",
+  "client_x509_cert_url": "https://www.googleapis.com/robot/v1/metadata/x509/my-account%40my-project.iam.gserviceaccount.com"
+}
+```
+
+Most importantly, the value of the `client_email` field should go into the `service-account-id` field in the configuration (see below).  The
+`private_key` portion needs to be pulled into its own file (e.g. `my-key.pem`).  The `\n`s in the string need to be converted to newline characters.
+
+While technically not part of Service Account authentication mode, one can also override the default service account that the compute VM is started with via the configuration option `GCPBATCH.config.genomics.compute-service-account` or through the workflow options parameter `google_compute_service_account`.  The service account you provide must have been granted Service Account Actor role to Cromwell's primary service account. As this only affects Google Batch API and not GCS, it's important that this service account, and the service account specified in `GCPBATCH.config.genomics.auth` can both read/write the location specified by `GCPBATCH.config.root`
+
+**User Service Account**
+
+A [JSON key file for the service account](../wf_options/Google.md) must be passed in via the `user_service_account_json` field in the [Workflow Options](../wf_options/Google.md) when submitting the job. Omitting this field will cause the workflow to fail. The JSON should be passed as a string and will need to have no newlines and all instances of `"` and `\n` escaped. 
+
+[//]: # (TODO: is jes_gcs_root the correct workflow option?)
+In the likely event that this service account does not have access to Cromwell's default google project the `google_project` workflow option must be set. In the similarly likely case that this service account can not access Cromwell's default google bucket, the `jes_gcs_root` workflow option should be set appropriately.
+
+For information on the interaction of `user_service_account_json` with private Docker images please see the `Docker` section below.  
+
+**Docker**
+
+It's possible to reference private Docker images to which only particular Docker Hub accounts have access:
+
+```
+task mytask {
+  command {
+    ...
+  }
+  runtime {
+    docker: "private_repo/image"
+    memory: "8 GB"
+    cpu: "1"
+  }
+  ...
+}
+```
+
+In order for a private image to be used the appropriate Docker configuration must be provided. If the Docker images being used
+are public there is no need to add this configuration.
+
+For Batch
+
+[//]: # (TODO: Is this the correct way to configure Docker for batch?)
+[//]: # (5-4-23: Leave alone for now)
+```
+backend {
+  default = GCPBATCH
+  providers {
+    GCPBATCH {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory"
+      config {
+        dockerhub {
+          token = "base64-encoded-docker-hub-username:password"
+          key-name = "name/of/the/kms/key/used/for/encrypting/and/decrypting/the/docker/hub/token"
+          auth = "reference-to-the-auth-cromwell-should-use-for-kms-encryption"
+        }
+      }
+    }
+  }
+}       
+```
+
+`token` is the standard base64-encoded username:password for the appropriate Docker Hub account.
+
+`key-name` is the name of the Google KMS key Cromwell should use for encrypting the Docker `token` before including it
+in the PAPI job execution request. This `key-name` will also be included in the PAPI job execution
+request and will be used by Batch to decrypt the Docker token used by `docker login` to enable access to the private Docker image.
+ 
+`auth` is a reference to the name of an authorization in the `auths` block of Cromwell's `google` config.
+Cromwell will use this authorization for encrypting the Google KMS key.
+
+The equivalents of `key-name`, `token` and `auth` can also be specified in workflow options which take
+precedence over values specified in configuration. The corresponding workflow options are named `docker_credentials_key_name`,
+`docker_credentials_token`, and `user_service_account_json`. While the config value `auth` refers to an auth defined in the 
+`google.auths` stanza elsewhere in Cromwell's
+configuration, `user_service_account_json` is expected to be a literal escaped Google service account auth JSON.
+See the `User Service Account` section above for more information on using user service accounts.
+If the key, token or auth value is provided in workflow options then the corresponding private Docker configuration value
+is not required, and vice versa. Also note that for the `user_service_account_json` workflow option to work an auth of type `user_service_account`
+must be defined in Cromwell's `google.auths` stanza; more details in the `User Service Account` section above.
+
+Example Batch workflow options for private Docker configuration:
+
+```
+{
+  "docker_credentials_key_name": "name/of/the/kms/key/used/for/encrypting/and/decrypting/the/docker/hub/token",
+  "docker_credentials_token": "base64_username:password",
+  "user_service_account_json": "<properly escaped user service account JSON file>"
+}
+```
+
+Important
+
+If any of the three private Docker configuration values of key name, auth, or Docker token are missing, Batch will not perform a `docker login`.
+If the Docker image to be pulled is not public the `docker pull` will fail which will cause the overall job to fail.
+
+If using any of these private Docker workflow options it is advisable to add
+them to the `workflow-options.encrypted-fields` list in Cromwell configuration.
+
+
+**Monitoring**
+
+In order to monitor metrics (CPU, Memory, Disk usage...) about the VM during Call Runtime, a workflow option can be used to specify the path to a script that will run in the background and write its output to a log file.
+
+```
+{
+  "monitoring_script": "gs://cromwell/monitoring/script.sh"
+}
+```
+
+The output of this script will be written to a `monitoring.log` file that will be available in the call gcs bucket when the call completes.  This feature is meant to run a script in the background during long-running processes.  It's possible that if the task is very short that the log file does not flush before de-localization happens and you will end up with a zero byte file.
+
+**Google Cloud Storage Filesystem**
+
+On the Google Batch backend the GCS (Google Cloud Storage) filesystem is used for the root of the workflow execution.
+On the Local, SGE, and associated backends any GCS URI will be downloaded locally.  For the Google backend the `jes_gcs_root` [Workflow Option](../wf_options/Google) will take
+precedence over the `root` specified at `backend.providers.JES.config.root` in the configuration file. Google Cloud Storage URIs are the only acceptable values for `File` inputs for
+workflows using the Google backend.
+
+**Batch timeout**
+
+Google sets a default pipeline timeout of 7 days, after which the pipeline will abort. Setting `batch-timeout` overrides this limit to a maximum of 30 days.
+
+```hocon
+backend.providers.GCPBATCH.config {
+    batch-timeout: 14 days
+}
+```
+
+#### Google Labels
+
+Every call run on the Batch API backend is given certain labels by default, so that Google resources can be queried by these labels later. 
+The current default label set automatically applied is:
+
+| Key | Value | Example | Notes |
+|-----|-------|---------|-------|
+| cromwell-workflow-id | The Cromwell ID given to the root workflow (i.e. the ID returned by Cromwell on submission) | cromwell-d4b412c5-bf3d-4169-91b0-1b635ce47a26 | To fit the required [format](#label-format), we prefix with 'cromwell-' |
+| cromwell-sub-workflow-name | The name of this job's sub-workflow | my-sub-workflow | Only present if the task is called in a subworkflow. |
+| wdl-task-name | The name of the WDL task | my-task | |
+| wdl-call-alias | The alias of the WDL call that created this job | my-task-1 | Only present if the task was called with an alias. |
+
+Any custom labels provided as '`google_labels`' in the [workflow options](../wf_options/Google) are also applied to Google resources by the Batch API.
+
+### Virtual Private Network
+
+Cromwell can arrange for jobs to run in specific GCP private networks via the `config.virtual-private-cloud` stanza of a Batch backend.
+There are two ways of specifying private networks:
+
+* [Literal network and subnetwork values](#virtual-private-network-via-literals) that will apply to all projects
+* [Google project labels](#virtual-private-network-via-labels) whose values in a particular Google project will specify the network and subnetwork
+
+#### Virtual Private Network via Literals
+
+```hocon
+backend {
+  ...
+  providers {
+    ...
+    GCPBATCH {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchLifecycleActorFactory"
+      config {
+        ...
+        virtual-private-cloud {
+          network-name = "vpc-network"
+          subnetwork-name = "vpc-subnetwork"
+        }
+        ...
+      }
+    }
+  }
+}
+```
+
+The `network-name` and `subnetwork-name` should reference the name of your private network and subnetwork within that
+network respectively. The `subnetwork-name` is an optional config.
+
+For example, if your `virtual-private-cloud` config looks like the one above, then Cromwell will use the value of the
+configuration key, which is `vpc-network` here, as the name of private network and run the jobs on this network.
+If the network name is not present in the config Cromwell will fall back to trying to run jobs on the default network.
+
+If the `network-name` or `subnetwork-name` values contain the string `${projectId}` then that value will be replaced
+by Cromwell with the name of the project running the Batch API.
+
+If the `network-name` does not contain a `/` then it will be prefixed with `projects/${projectId}/global/networks/`.
+
+Cromwell will then pass the network and subnetwork values to the Batch API. See the documentation for the
+[Batch API](https://cloud.google.com/batch/docs/networking-overview)
+for more information on the various formats accepted for `network` and `subnetwork`.
+
+#### Virtual Private Network via Labels
+
+```hocon
+backend {
+  ...
+  providers {
+    ...
+    GCPBATCH {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchLifecycleActorFactory"
+      config {
+        ...
+        virtual-private-cloud {
+          network-label-key = "my-private-network"
+          subnetwork-label-key = "my-private-subnetwork"
+          auth = "reference-to-auth-scheme"
+        }
+        ...
+      }
+    }
+  }
+}
+```
+
+
+The `network-label-key` and `subnetwork-label-key` should reference the keys in your project's labels whose value is the name of your private network
+and subnetwork within that network respectively. `auth` should reference an auth scheme in the `google` stanza which will be used to get the project metadata from Google Cloud.
+The `subnetwork-label-key` is an optional config.
+
+For example, if your `virtual-private-cloud` config looks like the one above, and one of the labels in your project is
+
+```
+"my-private-network" = "vpc-network"
+```
+
+Cromwell will get labels from the project's metadata and look for a label whose key is `my-private-network`.
+Then it will use the value of the label, which is `vpc-network` here, as the name of private network and run the jobs on this network.
+If the network key is not present in the project's metadata Cromwell will fall back to trying to run jobs using literal
+network labels, and then fall back to running on the default network.
+
+### Custom Google Cloud SDK container
+
+[//]: # (TODO: need to test this section as well)
+Cromwell can't use Google's container registry if VPC Perimeter is used in project.
+Own repository can be used by adding `cloud-sdk-image-url` reference to used container:
+
+```
+google {
+  ...
+  cloud-sdk-image-url = "eu.gcr.io/your-project-id/cloudsdktool/cloud-sdk:354.0.0-alpine"
+  cloud-sdk-image-size-gb = 1
+}
+```
+
+### Parallel Composite Uploads 
+
+[//]: # (TODO: Need to test parallel composite uploads)
+
+Cromwell can be configured to use GCS parallel composite uploads which can greatly improve delocalization performance. This feature
+is turned off by default but can be enabled backend-wide by specifying a `gsutil`-compatible memory specification for the key
+`genomics.parallel-composite-upload-threshold` in backend configuration. This memory value represents the minimum size an output file
+must have to be a candidate for `gsutil` parallel composite uploading:
+
+```
+backend {
+  ...
+  providers {
+    ...
+    GCPBATCH {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchLifecycleActorFactory"
+      config {
+        ...
+        genomics {
+          ...
+          parallel-composite-upload-threshold = 150M
+          ...
+        }
+        ...
+      }
+    }
+  }
+}
+```
+
+Alternatively this threshold can be specified in workflow options using the key `parallel-composite-upload-threshold`,
+which takes precedence over a setting in configuration. The default setting for this threshold is `0` which turns off
+parallel composite uploads; a value of `0` can also be used in workflow options to turn off parallel composite uploads
+in a Cromwell deployment where they are turned on in config.
+
+#### Issues with composite files
+
+Please see the [Google documentation](https://cloud.google.com/storage/docs/gsutil/commands/cp#parallel-composite-uploads)
+describing the benefits and drawbacks of parallel composite uploads.
+
+The actual error message observed when attempting to download a composite file on a system without a compiled `crcmod`
+looks like the following:
+
+```
+/ # gsutil -o GSUtil:parallel_composite_upload_threshold=150M cp gs://my-bucket/composite.bam .
+Copying gs://my-bucket/composite.bam...
+==> NOTE: You are downloading one or more large file(s), which would
+run significantly faster if you enabled sliced object downloads. This
+feature is enabled by default but requires that compiled crcmod be
+installed (see "gsutil help crcmod").
+
+CommandException:
+Downloading this composite object requires integrity checking with CRC32c,
+but your crcmod installation isn't using the module's C extension, so the
+hash computation will likely throttle download performance. For help
+installing the extension, please see "gsutil help crcmod".
+
+To download regardless of crcmod performance or to skip slow integrity
+checks, see the "check_hashes" option in your boto config file.
+
+NOTE: It is strongly recommended that you not disable integrity checks. Doing so
+could allow data corruption to go undetected during uploading/downloading.
+/ #
+```
+
+As the message states, the best option would be to have a compiled `crcmod` installed on the system.
+Turning off integrity checks on downloads does get around this issue but really isn't a great idea.
+
+#### Parallel composite uploads and call caching
+
+Because the parallel composite upload threshold is not considered part of the hash used for call caching purposes, calls
+which would be expected to generate non-composite outputs may call cache to results that did generate composite
+outputs. Calls which are executed and not cached will always honor the parallel composite upload setting at the time of
+their execution.
+
+
+### Migration from Google Cloud Genomics v2alpha1 to Google Cloud Life Sciences v2beta
+
+1. If you currently run your workflows using Cloud Genomics v2beta and would like to switch to Google Batch, you will need to do a few changes to your configuration file: `actor-factory` value should be changed 
+from `cromwell.backend.google.pipelines.v2beta.PipelinesApiLifecycleActorFactory` to `cromwell.backend.google.batch.GcpBatchLifecycleActorFactory`.
+
+2. You will need to remove the parameter `genomics.endpoint-url` and generate a new config file.
+
+3. Google Batch is now available in a variety of regions. Please see the [Batch Locations](https://cloud.google.com/batch/docs/locations) for a list of supported regions
+
+
+### Reference Disk Support
+
+[//]: # (TODO: follow up later)
+
+Cromwell 55 and later support mounting reference disks from prebuilt GCP disk images as an alternative to localizing large
+input reference files on Batch. Please note the configuration of reference disk manifests has changed starting with
+Cromwell 57 and now uses the format documented below. 
+
+Within the `config` stanza of a Batch backend the `reference-disk-localization-manifests`
+key specifies an array of reference disk manifests:  
+
+```hocon
+backend {
+  ...
+  providers {
+    ...
+    GCPBATCH {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchLifecycleActorFactory"
+      config {
+        ...
+        reference-disk-localization-manifests = [
+          {
+            "imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/broad-references-disk-image",
+            "diskSizeGb" : 500,
+            "files" : [ {
+              "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.nhr",
+              "crc32c" : 407769621
+            }, {
+              "path" : "gcp-public-data--broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.sa",
+              "crc32c" : 1902048083
+            },
+            ...
+          },
+          ...
+        ]
+        ...
+      }
+    }
+  }
+}
+```
+
+Reference disk usage is an opt-in feature, so workflow submissions must specify this workflow option:
+
+```json
+{
+  ...
+  "use_reference_disks": true,
+  ...
+}
+```
+
+Using the first file in the manifest above as an example, assume a Batch backend is configured to use this manifest and the appropriate
+`use_reference_disks` workflow option is set to `true` in the workflow submission. If a call in that workflow 
+specifies the input `gs://my-references/enormous_reference.bam` and because that input matches the path of a file on the
+reference image without the leading `gs://`, Cromwell would
+arrange for a reference disk based on this image to be mounted and for the call's input to refer to the 
+copy of the file on the reference disk, bypassing localization of the input.     
+
+The Cromwell git repository includes a Java-based tool to facilitate the creation of manifests called
+[CromwellRefdiskManifestCreatorApp](https://github.com/broadinstitute/cromwell/tree/develop/CromwellRefdiskManifestCreator).
+Please see the help command of that tool for more details.
+
+Alternatively for public data stored under `gs://gcp-public-data--broad-references` there exists a shell script to
+extract reference data to a new disk and then convert that disk to a public image. For more information see
+[create_images.sh](https://github.com/broadinstitute/cromwell/tree/develop/scripts/reference_disks/create_images.sh).
+
diff --git a/docs/tutorials/Batch101.md b/docs/tutorials/Batch101.md
new file mode 100644
index 00000000000..4c31d910ab1
--- /dev/null
+++ b/docs/tutorials/Batch101.md
@@ -0,0 +1,227 @@
+## Getting started on Google Cloud with Batch
+
+## Batch
+
+### Basic Information
+
+Google Cloud Batch is a fully managed service that lets you schedule, queue, and execute batch processing workloads on Google Cloud resources. 
+Batch provisions resources and manages capacity on your behalf, allowing your batch workloads to run at scale.
+
+### Setting up Batch
+
+#### Permissions:
+
+### Prerequisites
+
+This tutorial page relies on completing the previous tutorial:
+
+* [Downloading Prerequisites](FiveMinuteIntro.md)
+
+### Goals
+
+At the end of this tutorial you'll have run your first workflow against the Google Batch API.
+
+### Let's get started!
+
+
+**Configuring a Google Project**
+
+Install the <a href="https://cloud.google.com/sdk/downloads" target="_blank">Google Cloud SDK</a>.
+Create a <a href="https://cloud.google.com/resource-manager/docs/creating-managing-projects" target="_blank">Google Cloud Project</a> and give it a project id (e.g. sample-project).  We’ll refer to this as `<google-project-id>` and your user login (e.g. username@gmail.com) as `<google-user-id>`.
+
+On your Google project, open up the <a href="https://console.developers.google.com/apis/library" target="_blank">API Manager</a> and enable the following APIs:
+
+* Google Compute Engine API
+* Cloud Storage
+* Google Cloud Batch API
+
+Authenticate to Google Cloud Platform  
+`gcloud auth login <google-user-id>`
+
+Set your default account (will require to login again)  
+`gcloud auth application-default login`
+
+Set your default project  
+`gcloud config set project <google-project-id>`
+
+Create a Google Cloud Storage (GCS) bucket to hold Cromwell execution directories.
+We will refer to this bucket as `google-bucket-name`, and the full identifier as `gs://google-bucket-name`.  
+`gsutil mb gs://<google-bucket-name>`
+
+
+**Workflow Source Files**
+
+Copy over the sample `hello.wdl` and `hello.inputs` files to the same directory as the Cromwell jar.
+This workflow takes a string value as specified in the inputs file and writes it to stdout.
+
+
+***hello.wdl***
+```
+task hello {
+  String addressee  
+  command {
+    echo "Hello ${addressee}! Welcome to Cromwell . . . on Google Cloud!"  
+  }
+  output {
+    String message = read_string(stdout())
+  }
+  runtime {
+    docker: "ubuntu:latest"
+  }
+}
+
+workflow wf_hello {
+  call hello
+
+  output {
+     hello.message
+  }
+}
+```
+
+***hello.inputs***
+```
+{
+  "wf_hello.hello.addressee": "World"
+}
+```
+
+**Google Configuration File**
+
+Copy over the sample `google.conf` file utilizing <a href="https://developers.google.com/identity/protocols/application-default-credentials" target="_blank">Application Default credentials</a> to the same directory that contains your sample WDL, inputs and Cromwell jar.
+Replace `<google-project-id>` and `<google-bucket-name>`in the configuration file with the project id and bucket name. Replace `<google-billing-project-id>` with the project id that has to be billed for the request (more information for Requester Pays can be found at:
+<a href="https://cloud.google.com/storage/docs/requester-pays" target="_blank">Requester Pays</a>)
+
+***google.conf***
+```
+include required(classpath("application"))
+
+google {
+
+  application-name = "cromwell"
+
+  auths = [
+    {
+      name = "application-default"
+      scheme = "application_default"
+    }
+  ]
+}
+
+engine {
+  filesystems {
+    gcs {
+      auth = "application-default"
+      project = "<google-billing-project-id>"
+    }
+  }
+}
+
+backend {
+  default = batch
+
+  providers {
+    batch {
+      actor-factory = "cromwell.backend.google.pipelines.batch.GcpBatchBackendLifecycleActorFactory"
+      config {
+        # Google project
+        project = "my-cromwell-workflows"
+
+        # Base bucket for workflow executions
+        root = "gs://my-cromwell-workflows-bucket"
+
+        # Polling for completion backs-off gradually for slower-running jobs.
+        # This is the maximum polling interval (in seconds):
+        maximum-polling-interval = 600
+
+        # Optional Dockerhub Credentials. Can be used to access private docker images.
+        dockerhub {
+          # account = ""
+          # token = ""
+        }
+
+        # Optional configuration to use high security network (Virtual Private Cloud) for running jobs.
+        # See https://cromwell.readthedocs.io/en/stable/backends/Google/ for more details.
+        # virtual-private-cloud {
+        #  network-label-key = "network-key"
+        #  auth = "application-default"
+        # }
+
+        # Global pipeline timeout
+        # Defaults to 7 days; max 30 days
+        # batch-timeout = 7 days
+
+        genomics {
+          # A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
+          # Batch Jobs and manipulate auth JSONs.
+          auth = "application-default"
+
+
+          // alternative service account to use on the launched compute instance
+          // NOTE: If combined with service account authorization, both that service account and this service account
+          // must be able to read and write to the 'root' GCS path
+          compute-service-account = "default"
+
+          # Location to submit jobs to Batch and store job metadata.
+          location = "us-central1"
+
+          # Specifies the minimum file size for `gsutil cp` to use parallel composite uploads during delocalization.
+          # Parallel composite uploads can result in a significant improvement in delocalization speed for large files
+          # but may introduce complexities in downloading such files from GCS, please see
+          # https://cloud.google.com/storage/docs/gsutil/commands/cp#parallel-composite-uploads for more information.
+          #
+          # If set to 0 parallel composite uploads are turned off. The default Cromwell configuration turns off
+          # parallel composite uploads, this sample configuration turns it on for files of 150M or larger.
+          parallel-composite-upload-threshold="150M"
+        }
+
+        filesystems {
+          gcs {
+            # A reference to a potentially different auth for manipulating files via engine functions.
+            auth = "application-default"
+            # Google project which will be billed for the requests
+            project = "google-billing-project"
+
+            caching {
+              # When a cache hit is found, the following duplication strategy will be followed to use the cached outputs
+              # Possible values: "copy", "reference". Defaults to "copy"
+              # "copy": Copy the output files
+              # "reference": DO NOT copy the output files but point to the original output files instead.
+              #              Will still make sure than all the original output files exist and are accessible before
+              #              going forward with the cache hit.
+              duplication-strategy = "copy"
+            }
+          }
+        }
+      }
+    }
+  }
+}
+```
+
+**Run Workflow**
+
+`java -Dconfig.file=google.conf -jar cromwell-67.jar run hello.wdl -i hello.inputs`
+
+**Outputs**
+
+The end of your workflow logs should report the workflow outputs.
+
+```
+[info] SingleWorkflowRunnerActor workflow finished with status 'Succeeded'.
+{
+  "outputs": {
+    "wf_hello.hello.message": "Hello World! Welcome to Cromwell . . . on Google Cloud!"
+  },
+  "id": "08213b40-bcf5-470d-b8b7-1d1a9dccb10e"
+}
+```
+
+Success!
+
+### Next steps
+
+You might find the following tutorials interesting to tackle next:
+
+* [Persisting Data Between Restarts](PersistentServer)
+* [Server Mode](ServerMode.md)
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 1a7681da1e3..b2e94cc7470 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -55,6 +55,7 @@ object Dependencies {
   private val googleGenomicsServicesV2Alpha1ApiV = "v2alpha1-rev20210811-1.32.1"
   private val googleHttpClientApacheV = "2.1.2"
   private val googleHttpClientV = "1.42.3"
+  private val googleCloudBatchV1 = "0.18.0"
   // latest date via: https://mvnrepository.com/artifact/com.google.apis/google-api-services-lifesciences
   private val googleLifeSciencesServicesV2BetaApiV = "v2beta-rev20220916-2.0.0"
   private val googleOauth2V = "1.5.3"
@@ -373,6 +374,12 @@ object Dependencies {
       exclude("com.google.guava", "guava-jdk5")
   )
 
+  private val googleBatchv1Dependency = List(
+    "com.google.cloud" % "google-cloud-batch" % googleCloudBatchV1,
+    "com.google.api.grpc" % "proto-google-cloud-batch-v1" % googleCloudBatchV1,
+    "com.google.api.grpc" % "proto-google-cloud-resourcemanager-v3" % "1.17.0"
+  )
+
   /*
   Used instead of `"org.lerch" % "s3fs" % s3fsV exclude("org.slf4j", "jcl-over-slf4j")`
   org.lerch:s3fs:1.0.1 depends on a preview release of software.amazon.awssdk:s3.
@@ -417,7 +424,7 @@ object Dependencies {
     "com.google.apis" % "google-api-services-cloudkms" % googleCloudKmsV
       exclude("com.google.guava", "guava-jdk5"),
     "org.glassfish.hk2.external" % "jakarta.inject" % jakartaInjectV,
-  ) ++ googleGenomicsV2Alpha1Dependency ++ googleLifeSciencesV2BetaDependency
+  ) ++ googleGenomicsV2Alpha1Dependency ++ googleLifeSciencesV2BetaDependency ++ googleBatchv1Dependency
 
   private val dbmsDependencies = List(
     "org.hsqldb" % "hsqldb" % hsqldbV,
@@ -621,11 +628,12 @@ object Dependencies {
     "org.lz4" % "lz4-java" % lz4JavaV
   )
   val scalaTest = "org.scalatest" %% "scalatest" % scalatestV
+  
   val testDependencies: List[ModuleID] = List(
-    scalaTest,
+    "org.scalatest" %% "scalatest" % scalatestV,
     // Use mockito Java DSL directly instead of the numerous and often hard to keep updated Scala DSLs.
     // See also scaladoc in common.mock.MockSugar and that trait's various usages.
-    "org.mockito" % "mockito-core" % mockitoV,
+    "org.mockito" % "mockito-core" % mockitoV
   ) ++ slf4jBindingDependencies // During testing, add an slf4j binding for _all_ libraries.
 
   val kindProjectorPlugin = "org.typelevel" % "kind-projector" % kindProjectorV cross CrossVersion.full
diff --git a/src/ci/bin/testCentaurGcpBatch.sh b/src/ci/bin/testCentaurGcpBatch.sh
new file mode 100755
index 00000000000..ad5da44eacb
--- /dev/null
+++ b/src/ci/bin/testCentaurGcpBatch.sh
@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+set -o errexit -o nounset -o pipefail
+export CROMWELL_BUILD_REQUIRES_SECURE=true
+# import in shellcheck / CI / IntelliJ compatible ways
+# shellcheck source=/dev/null
+source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
+# shellcheck source=/dev/null
+source "${BASH_SOURCE%/*}/test_gcpbatch.inc.sh" || source test_gcpbatch.inc.sh
+
+cromwell::build::setup_common_environment
+
+cromwell::build::setup_centaur_environment
+
+cromwell::build::batch::setup_batch_centaur_environment
+
+cromwell::build::assemble_jars
+
+cromwell::build::run_centaur \
+    -p 100 \
+    -e localdockertest \
+    -e relative_output_paths \
+    -e relative_output_paths_colliding \
+    -e standard_output_paths_colliding_prevented \
+    -e papi_v2alpha1_gcsa \
+
+cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/test_gcpbatch.inc.sh b/src/ci/bin/test_gcpbatch.inc.sh
new file mode 100644
index 00000000000..f75764b6006
--- /dev/null
+++ b/src/ci/bin/test_gcpbatch.inc.sh
@@ -0,0 +1,118 @@
+#!/usr/bin/env bash
+
+set -o errexit -o nounset -o pipefail
+# import in shellcheck / CI / IntelliJ compatible ways
+# shellcheck source=/dev/null
+source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
+
+# A set of common Gcp Batch functions for use in other scripts.
+#
+# Functions:
+#
+#   - cromwell::build::batch::*
+#     Functions for use in other Papi scripts
+#
+#   - cromwell::private::batch::batch::*
+#     Functions for use only within this file by cromwell::build::batch::* functions
+#
+
+cromwell::private::batch::setup_batch_gcloud() {
+    CROMWELL_BUILD_BATCH_AUTH_JSON="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/cromwell-service-account.json"
+    CROMWELL_BUILD_BATCH_CLIENT_EMAIL="$(jq --exit-status --raw-output .client_email "${CROMWELL_BUILD_BATCH_AUTH_JSON}")"
+    CROMWELL_BUILD_BATCH_PROJECT_ID="$(jq --exit-status --raw-output .project_id "${CROMWELL_BUILD_BATCH_AUTH_JSON}")"
+    CROMWELL_BUILD_BATCH_GCR_IMAGES="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/cromwell_build_batch_gcloud_images_temporary.$$"
+    CROMWELL_BUILD_BATCH_CLOUDSDK_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/cromwell_build_batch_gcloud_config.$$"
+
+    export CROMWELL_BUILD_BATCH_AUTH_JSON
+    export CROMWELL_BUILD_BATCH_CLIENT_EMAIL
+    export CROMWELL_BUILD_BATCH_CLOUDSDK_CONFIG
+    export CROMWELL_BUILD_BATCH_GCR_IMAGES
+    export CROMWELL_BUILD_BATCH_PROJECT_ID
+
+    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_TRAVIS}" ]]; then
+        cromwell::private::batch::install_gcloud
+    fi
+
+    # All `gcloud` commands should use this configuration directory.
+    # https://stackoverflow.com/questions/34883810/how-to-authenticate-google-apis-with-different-service-account-credentials
+    # https://github.com/googleapis/google-auth-library-java/issues/58
+    export CLOUDSDK_CONFIG="${CROMWELL_BUILD_BATCH_CLOUDSDK_CONFIG}"
+
+    cromwell::build::add_exit_function cromwell::private::batch::teardown_batch_gcloud
+
+    gcloud auth activate-service-account --key-file="${CROMWELL_BUILD_BATCH_AUTH_JSON}"
+    export GOOGLE_APPLICATION_CREDENTIALS="${CROMWELL_BUILD_BATCH_AUTH_JSON}"
+    gcloud config set account "${CROMWELL_BUILD_BATCH_CLIENT_EMAIL}"
+    gcloud config set project "${CROMWELL_BUILD_BATCH_PROJECT_ID}"
+}
+
+cromwell::private::batch::teardown_batch_gcloud() {
+    cromwell::build::delete_docker_images cromwell::private::batch::gcr_image_delete "${CROMWELL_BUILD_BATCH_GCR_IMAGES}"
+}
+
+cromwell::private::batch::install_gcloud() {
+    echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main" \
+        | sudo tee -a /etc/apt/sources.list.d/google-cloud-sdk.list
+    sudo apt-get install -y apt-transport-https ca-certificates
+    curl https://packages.cloud.google.com/apt/doc/apt-key.gpg \
+        | sudo apt-key --keyring /usr/share/keyrings/cloud.google.gpg add -
+    sudo apt-get update
+    sudo apt-get install -y google-cloud-sdk
+}
+
+cromwell::private::batch::gcr_image_push() {
+    local executable_name
+    local docker_image
+
+    executable_name="${1:?gcr_image_push called without an executable_name}"
+    docker_image="${2:?gcr_image_push called without an docker_image}"
+    shift
+    shift
+
+    cromwell::build::build_docker_image "${executable_name}" "${docker_image}"
+    echo "${docker_image}" >> "${CROMWELL_BUILD_BATCH_GCR_IMAGES}"
+    # Use cat to quiet docker: https://github.com/moby/moby/issues/36655#issuecomment-375136087
+    docker push "${docker_image}" | cat
+}
+
+cromwell::private::batch::gcr_image_delete() {
+    local docker_image_name
+    docker_image_name="${1:?gcr_image_delete called without a docker_image_name}"
+    shift
+    gcloud container images delete "${docker_image_name}" --force-delete-tags --quiet
+}
+
+cromwell::private::batch::setup_batch_gcr() {
+    # Build a DOS/DRS localizer image from source, or for faster local debugging use an already provided image
+    if [[ -n "${CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS:+set}" ]]; then
+        # If CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS is already set then use that image
+        echo "Using CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS='${CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS}'"
+    elif command -v docker; then
+        # Upload images built from this commit
+        gcloud auth configure-docker --quiet
+        CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS="gcr.io/${CROMWELL_BUILD_BATCH_PROJECT_ID}/cromwell-drs-localizer:${CROMWELL_BUILD_DOCKER_TAG}-batch"
+        cromwell::private::batch::gcr_image_push cromwell-drs-localizer "${CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS}"
+        export CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS
+    else
+        echo "Error: BA-6546 The environment variable CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS must be set/export pointing to a valid docker image" >&2
+        exit 1
+    fi
+}
+
+cromwell::private::batch::setup_batch_service_account() {
+    CROMWELL_BUILD_BATCH_AUTH_MODE="service-account"
+    export CROMWELL_BUILD_BATCH_AUTH_MODE
+}
+
+cromwell::build::batch::setup_batch_centaur_environment() {
+    cromwell::private::batch::setup_batch_gcloud
+    if [[ "${CROMWELL_BUILD_PROVIDER}" != "${CROMWELL_BUILD_PROVIDER_JENKINS}" ]]
+    then
+        cromwell::private::batch::setup_batch_gcr
+    fi
+    cromwell::private::batch::setup_batch_service_account
+}
+
+cromwell::build::batch::setup_batch_conformance_environment() {
+    cromwell::private::batch::setup_batch_service_account
+}
diff --git a/src/ci/bin/test_papi.inc.sh b/src/ci/bin/test_papi.inc.sh
index 51f33a459b3..e3c253d7455 100644
--- a/src/ci/bin/test_papi.inc.sh
+++ b/src/ci/bin/test_papi.inc.sh
@@ -89,7 +89,7 @@ cromwell::private::papi::setup_papi_gcr() {
     elif command -v docker; then
         # Upload images built from this commit
         gcloud auth configure-docker --quiet
-        CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS="gcr.io/${CROMWELL_BUILD_PAPI_PROJECT_ID}/cromwell-drs-localizer:${CROMWELL_BUILD_DOCKER_TAG}"
+        CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS="gcr.io/${CROMWELL_BUILD_PAPI_PROJECT_ID}/cromwell-drs-localizer:${CROMWELL_BUILD_DOCKER_TAG}-papi"
         cromwell::private::papi::gcr_image_push cromwell-drs-localizer "${CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS}"
         export CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS
     else
diff --git a/src/ci/resources/gcp_batch_application.conf b/src/ci/resources/gcp_batch_application.conf
new file mode 100644
index 00000000000..61c6ffee36b
--- /dev/null
+++ b/src/ci/resources/gcp_batch_application.conf
@@ -0,0 +1,12 @@
+include "gcp_batch_shared_application.inc.conf"
+
+backend {
+  providers {
+    GCPBATCH {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory"
+      config {
+        include "gcp_batch_provider_config.inc.conf"
+      }
+    }
+  }
+}
diff --git a/src/ci/resources/gcp_batch_application.inc.conf.ctmpl b/src/ci/resources/gcp_batch_application.inc.conf.ctmpl
new file mode 100644
index 00000000000..aebdd7ea377
--- /dev/null
+++ b/src/ci/resources/gcp_batch_application.inc.conf.ctmpl
@@ -0,0 +1,73 @@
+backend {
+  providers {
+    Local.config.filesystems.gcs.auth = "service_account"
+  }
+}
+
+engine {
+  filesystems {
+    gcs {
+      auth = "service_account"
+      project = "broad-dsde-cromwell-dev"
+    }
+    drs {
+      auth = "service_account"
+    }
+  }
+}
+
+google {
+  application-name = "cromwell"
+  json-dir = "Error: BA-6546 The environment variable CROMWELL_BUILD_RESOURCES_DIRECTORY must be set/export pointing to a valid path such as '${YOUR_CROMWELL_DIR}/target/ci/resources'"
+  json-dir = ${?CROMWELL_BUILD_RESOURCES_DIRECTORY}
+  auths = [
+    {
+      name = "service_account"
+      scheme = "service_account"
+      json-file = ${google.json-dir}/cromwell-centaur-service-account.json
+    }
+    {
+      name = "requester_pays_service_account"
+      scheme = "service_account"
+      # This service account does have billing permission and can be used for requester pays
+      json-file = ${google.json-dir}/cromwell-centaur-requester-pays-service-account.json
+    }
+    {
+      name = "google_compute_service_account"
+      scheme = "service_account"
+      # This service account has only:
+      # 1. The role "Genomics Pipelines Runner"
+      # 2. Has been added a "Service Account User" on cromwell@broad-dsde-cromwell-dev.iam.gserviceaccount.com
+      json-file = ${google.json-dir}/cromwell-centaur-google-compute-service-account.json
+    }
+    {
+      name = "user_service_account"
+      scheme = "user_service_account"
+    }
+  ]
+}
+
+services {
+  HealthMonitor {
+    class = "cromwell.services.healthmonitor.impl.HealthMonitorServiceActor"
+	config {
+
+      //check-papi-backends: [ Papi ]
+      check-gcs: true
+      check-engine-database: true
+      check-dockerhub: true
+
+	  google-auth-name = "service_account"
+	  gcs-bucket-to-check = "cloud-cromwell-dev"
+	}
+  }
+}
+
+filesystems.drs.global.config.resolver.url = "https://drshub.dsde-dev.broadinstitute.org/api/v4/drs/resolve"
+
+drs {
+  localization {
+    docker-image = "Error: BA-6546 The environment variable CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS must be set/export pointing to a valid docker image"
+    docker-image = ${?CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS}
+  }
+}
diff --git a/src/ci/resources/gcp_batch_provider_config.inc.conf b/src/ci/resources/gcp_batch_provider_config.inc.conf
new file mode 100644
index 00000000000..a7f92e41e8c
--- /dev/null
+++ b/src/ci/resources/gcp_batch_provider_config.inc.conf
@@ -0,0 +1,20 @@
+project = "broad-dsde-cromwell-dev"
+root = "gs://cloud-cromwell-dev-self-cleaning/cromwell_execution/ci"
+maximum-polling-interval = 600
+concurrent-job-limit = 1000
+
+genomics {
+  auth = "service_account"
+  location = "us-central1"
+}
+
+filesystems {
+  gcs {
+    auth = "service_account"
+    project = "broad-dsde-cromwell-dev"
+  }
+}
+
+slow-job-warning-time: 20 minutes
+
+checkpointing-interval: "10 seconds"
diff --git a/src/ci/resources/gcp_batch_shared_application.inc.conf b/src/ci/resources/gcp_batch_shared_application.inc.conf
new file mode 100644
index 00000000000..09124a5bb28
--- /dev/null
+++ b/src/ci/resources/gcp_batch_shared_application.inc.conf
@@ -0,0 +1,34 @@
+include required(classpath("application.conf"))
+include "build_application.inc.conf"
+include "gcp_batch_application.inc.conf"
+
+services {
+  HealthMonitor.config {
+    check-gcpbatch-backends: [
+      "GCPBATCH",
+    ]
+  }
+}
+
+backend {
+  default = "GCPBATCH"
+  enabled = ["GCPBATCH"]
+  providers {
+    # Default gcp batch backend
+    GCPBATCH {
+      actor-factory = "cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory"
+      config {
+        # When importing: Remember to also include an appropriate provider_config.inc.conf here.
+
+        # TODO: Should not need because already included.  testing.
+        include "gcp_batch_provider_config.inc.conf"
+
+        include "dockerhub_provider_config_v2.inc.conf"
+        # This SA does not have permission to bill this project when accessing RP buckets.
+        # This is on purpose so that we can assert the failure (see requester_pays_localization_negative)
+        genomics.compute-service-account = "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com"
+        filesystems.http {}
+      }
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala
new file mode 100644
index 00000000000..1bf708e8f8c
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala
@@ -0,0 +1,115 @@
+package cromwell.backend.google.batch
+
+import akka.actor.{ActorRef, Props}
+import com.google.api.client.util.ExponentialBackOff
+import com.typesafe.scalalogging.StrictLogging
+import cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory.{preemptionCountKey, robustBuildAttributes, unexpectedRetryCountKey}
+import cromwell.backend.google.batch.actors._
+import cromwell.backend.google.batch.api.{GcpBatchApiRequestHandler, GcpBatchRequestFactoryImpl}
+import cromwell.backend.google.batch.models.{GcpBatchConfiguration, GcpBatchConfigurationAttributes}
+import cromwell.backend.google.batch.callcaching.{BatchBackendCacheHitCopyingActor, BatchBackendFileHashingActor}
+import cromwell.backend.standard._
+import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardFileHashingActor}
+import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor, JobExecutionMap}
+import cromwell.cloudsupport.gcp.GoogleConfiguration
+import cromwell.core.CallOutputs
+import wom.graph.CommandCallNode
+
+import scala.util.{Failure, Try}
+
+class GcpBatchBackendLifecycleActorFactory(override val name: String, override val configurationDescriptor: BackendConfigurationDescriptor)
+  extends StandardLifecycleActorFactory {
+
+  override val requestedKeyValueStoreKeys: Seq[String] = Seq(preemptionCountKey, unexpectedRetryCountKey)
+
+  override def jobIdKey: String = "__gcp_batch"
+  protected val googleConfig: GoogleConfiguration = GoogleConfiguration(configurationDescriptor.globalConfig)
+
+  override lazy val initializationActorClass: Class[_ <: StandardInitializationActor] = classOf[GcpBatchInitializationActor]
+
+  override def asyncExecutionActorClass: Class[_ <: StandardAsyncExecutionActor] =
+    classOf[GcpBatchAsyncBackendJobExecutionActor]
+
+  override lazy val finalizationActorClassOption: Option[Class[_ <: StandardFinalizationActor]] =
+    Option(classOf[GcpBatchFinalizationActor])
+
+
+
+  protected val batchAttributes: GcpBatchConfigurationAttributes = {
+    def defaultBuildAttributes()=
+      GcpBatchConfigurationAttributes(googleConfig, configurationDescriptor.backendConfig, "batchConfig")
+    robustBuildAttributes(defaultBuildAttributes)
+  }
+
+  val batchConfiguration = new GcpBatchConfiguration(configurationDescriptor, googleConfig, batchAttributes)
+
+  override def workflowInitializationActorParams(
+
+                                                  workflowDescriptor: BackendWorkflowDescriptor,
+                                                  ioActor: ActorRef,
+                                                  calls: Set[CommandCallNode],
+                                                  serviceRegistryActor: ActorRef,
+                                                  restart: Boolean): StandardInitializationActorParams = {
+    GcpBatchInitializationActorParams(workflowDescriptor, ioActor , calls, batchConfiguration, serviceRegistryActor, restart)
+  }
+
+  override def workflowFinalizationActorParams(
+                                           workflowDescriptor: BackendWorkflowDescriptor,
+                                           ioActor: ActorRef,
+                                           //batchConfiguration: GcpBatchConfiguration,
+                                           calls: Set[CommandCallNode],
+                                           jobExecutionMap: JobExecutionMap,
+                                           workflowOutputs: CallOutputs,
+                                           initializationDataOption: Option[BackendInitializationData]): StandardFinalizationActorParams = {
+    GcpBatchFinalizationActorParams(workflowDescriptor, ioActor, batchConfiguration, calls, jobExecutionMap, workflowOutputs, initializationDataOption)
+  }
+
+  override lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] = {
+    Option(classOf[BatchBackendCacheHitCopyingActor])
+  }
+
+  override lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(classOf[BatchBackendFileHashingActor])
+
+  override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] = {
+    val requestHandler = new GcpBatchApiRequestHandler
+    val requestFactory = new GcpBatchRequestFactoryImpl()(batchConfiguration.batchAttributes.gcsTransferConfiguration)
+    Option(GcpBatchBackendSingletonActor.props(requestFactory, serviceRegistryActor = serviceRegistryActor)(requestHandler))
+  }
+}
+
+object GcpBatchBackendLifecycleActorFactory extends StrictLogging {
+  val preemptionCountKey = "PreemptionCount"
+  val unexpectedRetryCountKey = "UnexpectedRetryCount"
+
+
+  private [batch] def robustBuildAttributes(buildAttributes: () => GcpBatchConfigurationAttributes,
+                                            maxAttempts: Int = 3,
+                                            initialIntervalMillis: Int = 5000,
+                                            maxIntervalMillis: Int = 10000,
+                                            multiplier: Double = 1.5,
+                                            randomizationFactor: Double = 0.5): GcpBatchConfigurationAttributes = {
+    val backoff = new ExponentialBackOff.Builder()
+      .setInitialIntervalMillis(initialIntervalMillis)
+      .setMaxIntervalMillis(maxIntervalMillis)
+      .setMultiplier(multiplier)
+      .setRandomizationFactor(randomizationFactor)
+      .build()
+
+    // `attempt` is 1-based
+    def build(attempt: Int): Try[GcpBatchConfigurationAttributes] = {
+      Try {
+        buildAttributes()
+      } recoverWith {
+        // Try again if this was an Exception (as opposed to an Error) and we have not hit maxAttempts
+        case ex: Exception if attempt < maxAttempts =>
+          logger
+            .warn(s"Failed to build GcpBatchConfigurationAttributes on attempt $attempt of $maxAttempts, retrying.", ex)
+          Thread.sleep(backoff.nextBackOffMillis())
+          build(attempt + 1)
+        case e => Failure(new RuntimeException(s"Failed to build GcpBatchConfigurationAttributes on attempt $attempt of $maxAttempts", e))
+      }
+    }
+    // This intentionally throws if the final result of `build` is a `Failure`.
+    build(attempt = 1).get
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiAbortClient.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiAbortClient.scala
new file mode 100644
index 00000000000..f025ae05282
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiAbortClient.scala
@@ -0,0 +1,23 @@
+package cromwell.backend.google.batch.actors
+
+import akka.actor.{Actor, ActorLogging, ActorRef}
+import com.google.cloud.batch.v1.JobName
+import cromwell.backend.google.batch.monitoring.BatchInstrumentation
+
+trait BatchApiAbortClient { this: Actor with ActorLogging with BatchInstrumentation =>
+
+  def abortJob(jobName: JobName, backendSingletonActor: ActorRef): Unit = {
+    backendSingletonActor ! GcpBatchBackendSingletonActor.Action.AbortJob(jobName)
+  }
+
+  def abortActorClientReceive: Actor.Receive = {
+    case GcpBatchBackendSingletonActor.Event.JobAbortRequestSent(job) =>
+      log.info(s"Job aborted on GCP: ${job.getName}")
+      abortSuccess()
+
+    case GcpBatchBackendSingletonActor.Event.ActionFailed(jobName, cause) =>
+      val msg = s"Failed to abort job ($jobName) from GCP"
+      log.error(cause, msg)
+      abortFailed()
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiFetchJobClient.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiFetchJobClient.scala
new file mode 100644
index 00000000000..e502bb18c2e
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiFetchJobClient.scala
@@ -0,0 +1,47 @@
+package cromwell.backend.google.batch.actors
+
+import akka.actor.{Actor, ActorLogging, ActorRef}
+import com.google.cloud.batch.v1.{Job, JobName}
+import cromwell.backend.google.batch.monitoring.BatchInstrumentation
+
+import scala.concurrent.{Future, Promise}
+import scala.util.{Failure, Success, Try}
+
+/**
+  * Allows fetching a job
+  */
+trait BatchApiFetchJobClient { this: Actor with ActorLogging with BatchInstrumentation =>
+
+  private var pollingActorClientPromise: Option[Promise[Job]] = None
+
+  // handles messages produced from GcpBatchBackendSingletonActor
+  def pollingActorClientReceive: Actor.Receive = {
+    case GcpBatchBackendSingletonActor.Event.JobStatusRetrieved(job) =>
+      log.info(s"Job retrieved from GCP: ${job.getName}: ${job.getStatus}")
+      pollSuccess()
+      completePromise(Success(job))
+
+    case GcpBatchBackendSingletonActor.Event.ActionFailed(jobName, cause) =>
+      val msg = s"Failed to query job ($jobName) from GCP"
+      log.error(cause, msg)
+      pollFailed()
+      completePromise(Failure(cause))
+  }
+
+  private def completePromise(result: Try[Job]): Unit = {
+    pollingActorClientPromise foreach { _.complete(result) }
+    pollingActorClientPromise = None
+  }
+
+  def fetchJob(jobName: JobName, backendSingletonActor: ActorRef): Future[Job] = {
+    pollingActorClientPromise match {
+      case Some(p) => p.future
+      case None =>
+        backendSingletonActor ! GcpBatchBackendSingletonActor.Action.QueryJob(jobName)
+
+        val newPromise = Promise[Job]()
+        pollingActorClientPromise = Option(newPromise)
+        newPromise.future
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiRunCreationClient.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiRunCreationClient.scala
new file mode 100644
index 00000000000..0763369dc50
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiRunCreationClient.scala
@@ -0,0 +1,50 @@
+package cromwell.backend.google.batch.actors
+
+import akka.actor.{Actor, ActorLogging, ActorRef}
+import cromwell.backend.google.batch.models.GcpBatchRequest
+import cromwell.backend.google.batch.monitoring.BatchInstrumentation
+import cromwell.backend.standard.StandardAsyncJob
+
+import scala.concurrent.{Future, Promise}
+import scala.util.{Failure, Success, Try}
+
+/**
+  * Handles the flow for submitting a single job to GCP, we can't do anything when that fails
+  */
+trait BatchApiRunCreationClient { this: Actor with ActorLogging with BatchInstrumentation =>
+  private var runCreationClientPromise: Option[Promise[StandardAsyncJob]] = None
+
+  // handles messages produced from GcpBatchBackendSingletonActor
+  def runCreationClientReceive: Actor.Receive = {
+    case GcpBatchBackendSingletonActor.Event.JobSubmitted(job) =>
+      log.info(s"Job submitted to GCP: ${job.getName}")
+      runSuccess()
+      completePromise(Success(StandardAsyncJob(job.getName)))
+
+    case GcpBatchBackendSingletonActor.Event.ActionFailed(jobName, cause) =>
+      val msg = s"Failed to submit job ($jobName) to GCP"
+      log.error(cause, msg)
+      runFailed()
+      completePromise(Failure(cause))
+  }
+
+  private def completePromise(job: Try[StandardAsyncJob]): Unit = {
+    runCreationClientPromise.foreach {
+      _.complete(job)
+    }
+    runCreationClientPromise = None
+  }
+
+  def runBatchJob(request: GcpBatchRequest, backendSingletonActor: ActorRef): Future[StandardAsyncJob] = {
+    runCreationClientPromise match {
+      case Some(p) =>
+        p.future
+      case None =>
+        log.info(s"Asking singleton actor to submit a job: ${request.jobName}")
+        backendSingletonActor ! GcpBatchBackendSingletonActor.Action.SubmitJob(request)
+        val newPromise = Promise[StandardAsyncJob]()
+        runCreationClientPromise = Option(newPromise)
+        newPromise.future
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
new file mode 100644
index 00000000000..b2b10d92afb
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
@@ -0,0 +1,1086 @@
+package cromwell.backend.google.batch.actors
+
+import akka.actor.{ActorLogging, ActorRef}
+import akka.http.scaladsl.model.{ContentType, ContentTypes}
+import akka.pattern.AskSupport
+import cats.data.NonEmptyList
+import cats.data.Validated.Valid
+import cats.implicits._
+import com.google.cloud.batch.v1.JobName
+import com.google.cloud.storage.contrib.nio.CloudStorageOptions
+import common.util.StringUtil._
+import common.validation.ErrorOr.ErrorOr
+import cromwell.backend._
+import cromwell.backend.async.{ExecutionHandle, PendingExecutionHandle}
+import cromwell.backend.google.batch.api.GcpBatchRequestFactory._
+import cromwell.backend.google.batch.io._
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.batch.models.GcpBatchJobPaths.GcsTransferLibraryName
+import cromwell.backend.google.batch.models.RunStatus.TerminalRunStatus
+import cromwell.backend.google.batch.models._
+import cromwell.backend.google.batch.monitoring.{BatchInstrumentation, CheckpointingConfiguration, MonitoringImage}
+import cromwell.backend.google.batch.runnable.WorkflowOptionKeys
+import cromwell.backend.google.batch.util.{GcpBatchReferenceFilesMappingOperations, RuntimeOutputMapping}
+import cromwell.filesystems.gcs.GcsPathBuilder
+import cromwell.filesystems.gcs.GcsPathBuilder.ValidFullGcsPath
+import java.io.FileNotFoundException
+import cromwell.backend.standard.{StandardAdHocValue, StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
+import cromwell.core._
+import cromwell.core.io.IoCommandBuilder
+import cromwell.core.path.{DefaultPathBuilder, Path}
+import cromwell.core.retry.SimpleExponentialBackoff
+import cromwell.filesystems.drs.{DrsPath, DrsResolver}
+import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
+import cromwell.filesystems.gcs.GcsPath
+import cromwell.filesystems.http.HttpPath
+import cromwell.filesystems.sra.SraPath
+import cromwell.services.instrumentation.CromwellInstrumentation
+import cromwell.services.metadata.CallMetadataKeys
+import mouse.all._
+import shapeless.Coproduct
+import org.apache.commons.codec.digest.DigestUtils
+import org.apache.commons.csv.{CSVFormat, CSVPrinter}
+import org.apache.commons.io.output.ByteArrayOutputStream
+import wdl4s.parser.MemoryUnit
+import wom.callable.Callable.OutputDefinition
+import wom.callable.MetaValueElement.{MetaValueElementBoolean, MetaValueElementObject}
+import wom.callable.{AdHocValue, RuntimeEnvironment}
+import wom.core.FullyQualifiedName
+import wom.expression.{FileEvaluation, NoIoFunctionSet}
+import wom.format.MemorySize
+import wom.values._
+import java.io.OutputStreamWriter
+import java.nio.charset.Charset
+import java.util.Base64
+import scala.concurrent.Future
+import scala.concurrent.duration._
+import scala.io.Source
+import scala.language.postfixOps
+import scala.util.{Failure, Success, Try}
+import scala.util.control.NoStackTrace
+
+object GcpBatchAsyncBackendJobExecutionActor {
+
+  // GCS path regexes comments:
+  // - The (?s) option at the start makes '.' expression to match any symbol, including '\n'
+  // - All valid GCS paths start with gs://
+  // - Bucket names:
+  //  - The bucket name is matched inside a set of '()'s so it can be used later.
+  //  - The bucket name must start with a letter or number (https://cloud.google.com/storage/docs/naming)
+  //  - Then, anything that is not a '/' is part of the bucket name
+  // - Allow zero or more subdirectories, with (/[^/]+)*
+  // - Then, for files:
+  //  - There must be at least one '/', followed by some content in the file name.
+  // - Or, then, for directories:
+  //  - If we got this far, we already have a valid directory path. Allow it to optionally end with a `/` character.
+  private val gcsFilePathMatcher = "(?s)^gs://([a-zA-Z0-9][^/]+)(/[^/]+)*/[^/]+$".r
+  private val gcsDirectoryPathMatcher = "(?s)^gs://([a-zA-Z0-9][^/]+)(/[^/]+)*/?$".r
+
+  val GcpBatchOperationIdKey = "__gcp_batch_operation_id"
+
+  type GcpBatchPendingExecutionHandle = PendingExecutionHandle[StandardAsyncJob, Run, RunStatus]
+
+  val plainTextContentType: Option[ContentType.WithCharset] = Option(ContentTypes.`text/plain(UTF-8)`)
+
+  private[batch] def groupParametersByGcsBucket[T <: BatchParameter](parameters: List[T]): Map[String, NonEmptyList[T]] = {
+    parameters.map { param =>
+      def pathTypeString = if (param.isFileParameter) "File" else "Directory"
+      val regexToUse = if (param.isFileParameter) gcsFilePathMatcher else gcsDirectoryPathMatcher
+
+      param.cloudPath.pathAsString match {
+        case regexToUse(bucket) => Map(bucket -> NonEmptyList.of(param))
+        case regexToUse(bucket, _) => Map(bucket -> NonEmptyList.of(param))
+        case other =>
+          throw new Exception(s"$pathTypeString path '$other' did not match the expected regex: ${regexToUse.pattern.toString}")  with NoStackTrace
+      }
+    } combineAll
+  }
+
+  private[batch] def generateDrsLocalizerManifest(inputs: List[GcpBatchInput]): String = {
+    val outputStream = new ByteArrayOutputStream()
+    val csvPrinter = new CSVPrinter(new OutputStreamWriter(outputStream), CSVFormat.DEFAULT)
+    val drsFileInputs = inputs collect {
+      case drsInput@GcpBatchFileInput(_, drsPath: DrsPath, _, _) => (drsInput, drsPath)
+    }
+    drsFileInputs foreach { case (drsInput, drsPath) =>
+      csvPrinter.printRecord(drsPath.pathAsString, drsInput.containerPath.pathAsString)
+    }
+    csvPrinter.close(true)
+    outputStream.toString(Charset.defaultCharset())
+  }
+
+}
+
+class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
+  extends BackendJobLifecycleActor
+    with StandardAsyncExecutionActor
+    with BatchApiRunCreationClient
+    with BatchApiFetchJobClient
+    with BatchApiAbortClient
+    with AskSupport
+    with GcpBatchJobCachingActorHelper
+    with GcpBatchReferenceFilesMappingOperations
+    with BatchInstrumentation
+    with ActorLogging
+    with CromwellInstrumentation {
+
+  import GcpBatchAsyncBackendJobExecutionActor._
+  override lazy val ioCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder
+
+  lazy val workflowId: WorkflowId = jobDescriptor.workflowDescriptor.id
+
+  /** The type of the run info when a job is started. */
+  override type StandardAsyncRunInfo = Run
+
+  /** The type of the run status returned during each poll. */
+  override type StandardAsyncRunState = RunStatus
+
+  override def receive: Receive = runCreationClientReceive orElse pollingActorClientReceive orElse abortActorClientReceive orElse kvClientReceive orElse super.receive
+
+  /** Should return true if the status contained in `thiz` is equivalent to `that`, delta any other data that might be carried around
+   * in the state type.
+   */
+  def statusEquivalentTo(thiz: StandardAsyncRunState)(that: StandardAsyncRunState): Boolean = thiz == that
+
+  protected lazy val cmdInput: GcpBatchFileInput =
+    GcpBatchFileInput(GcpBatchJobPaths.BatchExecParamName, gcpBatchCallPaths.script, DefaultPathBuilder.get(gcpBatchCallPaths.scriptFilename), workingDisk)
+
+  private lazy val jobDockerImage = jobDescriptor.maybeCallCachingEligible.dockerHash
+    .getOrElse(runtimeAttributes.dockerImage)
+
+  override def dockerImageUsed: Option[String] = Option(jobDockerImage)
+
+  //noinspection ActorMutableStateInspection
+
+  // Need to add previousRetryReasons and preemptible in order to get preemptible to work in the tests
+  protected val previousRetryReasons: ErrorOr[PreviousRetryReasons] = PreviousRetryReasons.tryApply(jobDescriptor.prefetchedKvStoreEntries, jobDescriptor.key.attempt)
+
+  lazy val preemptible: Boolean = previousRetryReasons match {
+    case Valid(PreviousRetryReasons(p, _)) => p < maxPreemption
+    case _ => false
+  }
+
+  override def tryAbort(job: StandardAsyncJob): Unit = abortJob(JobName.parse(job.jobId), backendSingletonActor)
+
+  val backendSingletonActor: ActorRef = standardParams.backendSingletonActorOption
+    .getOrElse(throw new RuntimeException("GCP Batch actor cannot exist without its backend singleton 2"))
+
+
+  /**
+   * Takes two arrays of remote and local WOM File paths and generates the necessary `GcpBatchInput`s.
+   */
+  protected def gcpBatchInputsFromWomFiles(inputName: String,
+                                           remotePathArray: Seq[WomFile],
+                                           localPathArray: Seq[WomFile],
+                                           jobDescriptor: BackendJobDescriptor): Iterable[GcpBatchInput] = {
+        (remotePathArray zip localPathArray) flatMap {
+          case (remotePath: WomMaybeListedDirectory, localPath) =>
+            maybeListedDirectoryToBatchParameters(inputName, remotePath, localPath.valueString)
+          case (remotePath: WomUnlistedDirectory, localPath) =>
+            Seq(GcpBatchDirectoryInput(inputName, getPath(remotePath.valueString).get, DefaultPathBuilder.get(localPath.valueString), workingDisk))
+          case (remotePath: WomMaybePopulatedFile, localPath) =>
+            maybePopulatedFileToBatchParameters(inputName, remotePath, localPath.valueString)
+          case (remotePath, localPath) =>
+            Seq(GcpBatchFileInput(inputName, getPath(remotePath.valueString).get, DefaultPathBuilder.get(localPath.valueString), workingDisk))
+        }
+  }
+
+  private def maybePopulatedFileToBatchParameters(inputName: String, maybePopulatedFile: WomMaybePopulatedFile, localPath: String) = {
+    val secondaryFiles = maybePopulatedFile.secondaryFiles.flatMap({ secondaryFile =>
+      gcpBatchInputsFromWomFiles(secondaryFile.valueString, List(secondaryFile), List(relativeLocalizationPath(secondaryFile)), jobDescriptor)
+    })
+
+    Seq(GcpBatchFileInput(inputName, getPath(maybePopulatedFile.valueString).get, DefaultPathBuilder.get(localPath), workingDisk)) ++ secondaryFiles
+  }
+
+  /**
+   * Turns WomFiles into relative paths.  These paths are relative to the working disk.
+   *
+   * relativeLocalizationPath("foo/bar.txt") -> "foo/bar.txt"
+   * relativeLocalizationPath("gs://some/bucket/foo.txt") -> "some/bucket/foo.txt"
+   */
+  override protected def relativeLocalizationPath(file: WomFile): WomFile = {
+    file.mapFile(value =>
+      getPath(value) match {
+        case Success(drsPath: DrsPath) => DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
+        case Success(path) => path.pathWithoutScheme
+        case _ => value
+      }
+    )
+  }
+
+  lazy val localMonitoringImageScriptPath: Path =
+    DefaultPathBuilder.get(gcpBatchCallPaths.batchMonitoringImageScriptFilename)
+
+  override protected def fileName(file: WomFile): WomFile = {
+    file.mapFile(value =>
+      getPath(value) match {
+        case Success(drsPath: DrsPath) => DefaultPathBuilder
+          .get(DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()).name
+        case Success(path) => path.name
+        case _ => value
+      }
+    )
+  }
+
+  override lazy val inputsToNotLocalize: Set[WomFile] = {
+    val localizeOptional = jobDescriptor.findInputFilesByParameterMeta {
+      case MetaValueElementObject(values) => values.get("localization_optional").contains(MetaValueElementBoolean(true))
+      case _ => false
+    }
+    val localizeSkipped = localizeOptional.filter(canSkipLocalize)
+    val localizeMapped = localizeSkipped.map(cloudResolveWomFile)
+    localizeSkipped ++ localizeMapped
+  }
+
+  private def canSkipLocalize(womFile: WomFile): Boolean = {
+    var canSkipLocalize = true
+    womFile.mapFile { value =>
+      getPath(value) match {
+        case Success(drsPath: DrsPath) =>
+          val gsUriOption = DrsResolver.getSimpleGsUri(drsPath).unsafeRunSync()
+          if (gsUriOption.isEmpty) {
+            canSkipLocalize = false
+          }
+        case _ => /* ignore */
+      }
+      value
+    }
+    canSkipLocalize
+  }
+
+  // The original implementation recursively finds all non directory files, in V2 we can keep directory as is
+  protected lazy val callInputFiles: Map[FullyQualifiedName, Seq[WomFile]] = {
+
+    // NOTE: This causes the tests to fail
+      jobDescriptor.localInputs map {
+        case (key, womFile) =>
+          key -> womFile.collectAsSeq({
+            case womFile: WomFile if !inputsToNotLocalize.contains(womFile) => womFile
+          })
+      }
+  }
+
+  private lazy val gcsTransferLibrary =
+    Source.fromInputStream(Thread.currentThread.getContextClassLoader.getResourceAsStream("gcs_transfer.sh")).mkString
+
+  private def gcsLocalizationTransferBundle[T <: GcpBatchInput](gcsTransferConfiguration: GcsTransferConfiguration)(bucket: String, inputs: NonEmptyList[T]): String = {
+    val project = inputs.head.cloudPath.asInstanceOf[GcsPath].projectId
+    val maxAttempts = gcsTransferConfiguration.transferAttempts
+
+    // Split files and directories out so files can possibly benefit from a `gsutil -m cp -I ...` optimization
+    // on a per-container-parent-directory basis.
+    val (files, directories) = inputs.toList partition {
+      _.isInstanceOf[GcpBatchFileInput]
+    }
+
+    // Files with different names between cloud and container are not eligible for bulk copying.
+    val (filesWithSameNames, filesWithDifferentNames) = files partition { f =>
+      f.cloudPath.asInstanceOf[GcsPath].nioPath.getFileName.toString == f.containerPath.getFileName.toString
+    }
+
+    val filesByContainerParentDirectory = filesWithSameNames.groupBy(_.containerPath.parent.toString)
+    // Deduplicate any inputs since parallel localization can't deal with this.
+    val uniqueFilesByContainerParentDirectory = filesByContainerParentDirectory map { case (p, fs) => p -> fs.toSet }
+
+    val filesWithSameNamesTransferBundles: List[String] = uniqueFilesByContainerParentDirectory.toList map { case (containerParent, filesWithSameParent) =>
+      val arrayIdentifier = s"files_to_localize_" + DigestUtils.md5Hex(bucket + containerParent)
+      val entries = filesWithSameParent.map(_.cloudPath) mkString("\"", "\"\n|  \"", "\"")
+
+      s"""
+         |# Localize files from source bucket '$bucket' to container parent directory '$containerParent'.
+         |$arrayIdentifier=(
+         |  "$project"   # project to use if requester pays
+         |  "$maxAttempts" # max transfer attempts
+         |  "${containerParent.ensureSlashed}" # container parent directory
+         |  $entries
+         |)
+         |
+         |localize_files "$${$arrayIdentifier[@]}"
+       """.stripMargin
+    }
+
+    val filesWithDifferentNamesTransferBundles = filesWithDifferentNames map { f =>
+      val arrayIdentifier = s"singleton_file_to_localize_" + DigestUtils.md5Hex(f.cloudPath.pathAsString + f.containerPath.pathAsString)
+      s"""
+         |# Localize singleton file '${f.cloudPath.pathAsString}' to '${f.containerPath.pathAsString}'.
+         |$arrayIdentifier=(
+         |  "$project"
+         |  "$maxAttempts"
+         |  "${f.cloudPath}"
+         |  "${f.containerPath}"
+         |)
+         |
+         |localize_singleton_file "$${$arrayIdentifier[@]}"
+       """.stripMargin
+    }
+
+    // Only write a transfer bundle for directories if there are directories to be localized. Emptiness isn't a concern
+    // for files since there is always at least the command script to be localized.
+    val directoryTransferBundle = if (directories.isEmpty) "" else {
+      val entries = directories flatMap { i => List(i.cloudPath, i.containerPath) } mkString("\"", "\"\n|  \"", "\"")
+
+      val arrayIdentifier = s"directories_to_localize_" + DigestUtils.md5Hex(bucket)
+
+      s"""
+         |# Directories from source bucket '$bucket'.
+         |$arrayIdentifier=(
+         |  "$project"    # project to use if requester pays
+         |  "$maxAttempts" # max transfer attempts
+         |  $entries
+         |)
+         |
+         |localize_directories "$${$arrayIdentifier[@]}"
+       """.stripMargin
+    }
+
+    (directoryTransferBundle :: (filesWithSameNamesTransferBundles ++ filesWithDifferentNamesTransferBundles)) mkString "\n\n"
+  }
+
+  private def gcsDelocalizationTransferBundle[T <: GcpBatchOutput](transferConfiguration: GcsTransferConfiguration)(bucket: String, outputs: NonEmptyList[T]): String = {
+    val project = outputs.head.cloudPath.asInstanceOf[GcsPath].projectId
+    val maxAttempts = transferConfiguration.transferAttempts
+
+    val transferItems = outputs.toList.flatMap { output =>
+      val kind = output match {
+        case o: GcpBatchFileOutput if o.secondary => "file_or_directory" // if secondary the type is unknown
+        case _: GcpBatchFileOutput => "file" // a primary file
+        case _: GcpBatchDirectoryOutput => "directory" // a primary directory
+      }
+
+      val optional = Option(output) collectFirst { case o: GcpBatchFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
+      val contentType = output.contentType.map(_.toString).getOrElse("")
+
+      List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
+    } mkString("\"", "\"\n|  \"", "\"")
+
+    val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(
+      "parallel_composite_upload_threshold", transferConfiguration.parallelCompositeUploadThreshold)
+
+    // Use a digest as bucket names can contain characters that are not legal in bash identifiers.
+    val arrayIdentifier = s"delocalize_" + DigestUtils.md5Hex(bucket)
+    s"""
+       |# $bucket
+       |$arrayIdentifier=(
+       |  "$project"       # project
+       |  "$maxAttempts"   # max attempts
+       |  "$parallelCompositeUploadThreshold" # parallel composite upload threshold, will not be used for directory types
+       |  $transferItems
+       |)
+       |
+       |delocalize "$${$arrayIdentifier[@]}"
+      """.stripMargin
+  }
+
+  private def bracketTransfersWithMessages(activity: String)(transferBody: String): String = {
+    List(
+      s"timestamped_message '$activity script execution started...'",
+      transferBody,
+      s"timestamped_message '$activity script execution complete.'"
+    ) mkString "\n"
+  }
+
+  def uploadDrsLocalizationManifest(createParameters: CreateBatchJobParameters, cloudPath: Path): Future[Unit] = {
+    val content = generateDrsLocalizerManifest(createParameters.inputOutputParameters.fileInputParameters)
+    if (content.nonEmpty)
+      asyncIo.writeAsync(cloudPath, content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+    else
+      Future.unit
+  }
+
+  def uploadScriptFile(): Future[Unit] = {
+    commandScriptContents
+      .fold(
+        errors => Future
+          .failed(new RuntimeException(errors
+            .toList
+            .mkString(", "))),
+        asyncIo
+          .writeAsync(jobPaths
+            .script, _, Seq(CloudStorageOptions.withMimeType("text/plain")))
+      )
+  }
+
+  def sendGoogleLabelsToMetadata(customLabels: Seq[GcpLabel]): Unit = {
+    lazy val backendLabelEvents: Map[String, String] = ((backendLabels ++ customLabels) map { l => s"${CallMetadataKeys.BackendLabels}:${l.key}" -> l.value }).toMap
+    tellMetadata(backendLabelEvents)
+  }
+
+  protected val useReferenceDisks: Boolean = {
+    val optionName = WorkflowOptions.UseReferenceDisks.name
+    workflowDescriptor.workflowOptions.getBoolean(optionName) match {
+      case Success(value) => value
+      case Failure(OptionNotFoundException(_)) => false
+      case Failure(f) =>
+        // Should not happen, this case should have been screened for and fast-failed during workflow materialization.
+        log.error(f, s"Programmer error: unexpected failure attempting to read value for workflow option '$optionName' as a Boolean")
+        false
+    }
+  }
+
+
+  def getReferenceInputsToMountedPathsOpt(createParameters: CreateBatchJobParameters): Option[Map[GcpBatchInput, String]] = {
+    if (useReferenceDisks) {
+      batchAttributes
+        .referenceFileToDiskImageMappingOpt
+        .map(getReferenceInputsToMountedPathMappings(_, createParameters.inputOutputParameters.fileInputParameters))
+    } else {
+      None
+    }
+  }
+
+  private def generateGcsLocalizationScript(inputs: List[GcpBatchInput],
+                                            referenceInputsToMountedPathsOpt: Option[Map[GcpBatchInput, String]])
+                                           (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+    // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
+    // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
+    import cromwell.backend.google.batch.runnable.RunnableUtils.shellEscaped
+
+    val referenceFilesLocalizationScript = {
+      val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
+        referenceInputsToMountedPaths map {
+          case (input, absolutePathOnRefDisk) =>
+            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
+        }
+      }
+
+      if (symlinkCreationCommandsOpt.exists(_.nonEmpty)) {
+        s"""
+           |# Faux-localizing reference files (if any) by creating symbolic links to the files located on the mounted reference disk
+           |${symlinkCreationCommandsOpt.get.mkString("\n")}
+           |""".stripMargin
+      } else {
+        "\n# No reference disks mounted / no symbolic links created since no matching reference files found in the inputs to this call.\n"
+      }
+    }
+
+    val maybeReferenceFilesLocalizationScript =
+      if (useReferenceDisks) {
+        referenceFilesLocalizationScript
+      } else {
+        "\n# No reference disks mounted since not requested in workflow options.\n"
+      }
+
+    val regularFilesLocalizationScript = {
+      val regularFiles = referenceInputsToMountedPathsOpt.map(maybeReferenceInputsToMountedPaths =>
+        inputs diff maybeReferenceInputsToMountedPaths.keySet.toList
+      ).getOrElse(inputs)
+      if (regularFiles.nonEmpty) {
+        val bundleFunction = (gcsLocalizationTransferBundle(gcsTransferConfiguration) _).tupled
+        generateGcsTransferScript(regularFiles, bundleFunction)
+      } else {
+        ""
+      }
+    }
+
+    val combinedLocalizationScript =
+      s"""
+         |$maybeReferenceFilesLocalizationScript
+         |
+         |$regularFilesLocalizationScript
+         |""".stripMargin
+
+    combinedLocalizationScript |> bracketTransfersWithMessages("Localization")
+  }
+
+  private def generateGcsDelocalizationScript(outputs: List[GcpBatchOutput])(implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+    val bundleFunction = (gcsDelocalizationTransferBundle(gcsTransferConfiguration) _).tupled
+    generateGcsTransferScript(outputs, bundleFunction) |> bracketTransfersWithMessages("Delocalization")
+  }
+
+  private def generateGcsTransferScript[T <: BatchParameter](items: List[T], bundleFunction: ((String, NonEmptyList[T])) => String): String = {
+    val gcsItems = items collect { case i if i.cloudPath.isInstanceOf[GcsPath] => i }
+    groupParametersByGcsBucket(gcsItems) map bundleFunction mkString "\n"
+  }
+
+  def uploadGcsLocalizationScript(createParameters: CreateBatchJobParameters,
+                                  cloudPath: Path,
+                                  transferLibraryContainerPath: Path,
+                                  gcsTransferConfiguration: GcsTransferConfiguration,
+                                  referenceInputsToMountedPathsOpt: Option[Map[GcpBatchInput, String]]): Future[Unit] = {
+    val content = generateGcsLocalizationScript(createParameters.inputOutputParameters.fileInputParameters, referenceInputsToMountedPathsOpt)(gcsTransferConfiguration)
+    asyncIo.writeAsync(cloudPath, s"source '$transferLibraryContainerPath'\n\n" + content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+  }
+
+  def uploadGcsDelocalizationScript(createParameters: CreateBatchJobParameters,
+                                    cloudPath: Path,
+                                    transferLibraryContainerPath: Path,
+                                    gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = {
+    val content = generateGcsDelocalizationScript(createParameters.inputOutputParameters.fileOutputParameters)(gcsTransferConfiguration)
+    asyncIo.writeAsync(cloudPath, s"source '$transferLibraryContainerPath'\n\n" + content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+  }
+
+
+  // TAG DISK
+  private def createBatchParameters(inputOutputParameters: InputOutputParameters,
+                                       customLabels: Seq[GcpLabel],
+                                      ): CreateBatchJobParameters = {
+    standardParams.backendInitializationDataOption match {
+      case Some(data: GcpBackendInitializationData) =>
+        val dockerKeyAndToken: Option[CreateBatchDockerKeyAndToken] = for {
+          key <- data.privateDockerEncryptionKeyName
+          token <- data.privateDockerEncryptedToken
+        } yield CreateBatchDockerKeyAndToken(key, token)
+
+        /*
+           * Right now this doesn't cost anything, because sizeOption returns the size if it was previously already fetched
+           * for some reason (expression evaluation for instance), but otherwise does not retrieve it and returns None.
+           * In CWL-land we tend to be aggressive in pre-fetching the size in order to be able to evaluate JS expressions,
+           * but less in WDL as we can get it last minute and on demand because size is a WDL function, whereas in CWL
+           * we don't inspect the JS to know if size is called and therefore always pre-fetch it.
+           *
+           * We could decide to call withSize before in which case we would retrieve the size for all files and have
+           * a guaranteed more accurate total size, but there might be performance impacts ?
+           */
+        val inputFileSize = Option(callInputFiles.values.flatMap(_.flatMap(_.sizeOption)).sum)
+
+        // Attempt to adjust the disk size by taking into account the size of input files
+        val adjustedSizeDisks = inputFileSize.map(size => MemorySize.apply(size.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB)) map { inputFileSizeInformation =>
+          runtimeAttributes.disks.adjustWorkingDiskWithNewMin(
+            inputFileSizeInformation,
+            jobLogger.info(s"Adjusted working disk size to ${inputFileSizeInformation.amount} GB to account for input files")
+          )
+        } getOrElse runtimeAttributes.disks
+
+        val inputFilePaths = inputOutputParameters.jobInputParameters.map(_.cloudPath.pathAsString).toSet
+
+        val referenceDisksToMount =
+          batchAttributes.referenceFileToDiskImageMappingOpt.map(getReferenceDisksToMount(_, inputFilePaths))
+
+        val dockerhubCredentials: (String, String) = {
+          new String(Base64.getDecoder.decode(batchAttributes.dockerhubToken), "UTF-8").split(":", 2) match {
+            case Array(username, password) => (username, password)
+            case _ => ("", "")
+          }
+        }
+
+        val workflowOptions = workflowDescriptor.workflowOptions
+
+        val monitoringImage = new MonitoringImage(
+          jobDescriptor = jobDescriptor,
+          workflowOptions = workflowOptions,
+          workflowPaths = workflowPaths,
+          commandDirectory = commandDirectory,
+          workingDisk = workingDisk,
+          localMonitoringImageScriptPath = localMonitoringImageScriptPath,
+        )
+
+        val checkpointingConfiguration =
+          new CheckpointingConfiguration(
+            jobDescriptor = jobDescriptor,
+            workflowPaths = workflowPaths,
+            commandDirectory = commandDirectory,
+            batchConfiguration.batchAttributes.checkpointingInterval
+          )
+
+        val enableSshAccess = workflowOptions.getBoolean(WorkflowOptionKeys.EnableSSHAccess).toOption.contains(true)
+
+        // if the `memory_retry_multiplier` is not present in the workflow options there is no need to check whether or
+        // not the `stderr` file contained memory retry error keys
+        val retryWithMoreMemoryKeys: Option[List[String]] = memoryRetryFactor.flatMap(_ => memoryRetryErrorKeys)
+
+        CreateBatchJobParameters(
+          jobDescriptor = jobDescriptor,
+          runtimeAttributes = runtimeAttributes,
+          dockerImage = jobDockerImage,
+          cloudWorkflowRoot = workflowPaths.workflowRoot,
+          cloudCallRoot = callRootPath,
+          commandScriptContainerPath = cmdInput.containerPath,
+          logGcsPath = gcpBatchLogPath,
+          inputOutputParameters = inputOutputParameters,
+          projectId = googleProject(jobDescriptor.workflowDescriptor),
+          computeServiceAccount = computeServiceAccount(jobDescriptor.workflowDescriptor),
+          googleLabels = backendLabels ++ customLabels,
+          preemptible = preemptible,
+          batchTimeout = batchConfiguration.batchTimeout,
+          jobShell = batchConfiguration.jobShell,
+          privateDockerKeyAndEncryptedToken = dockerKeyAndToken,
+          womOutputRuntimeExtractor = jobDescriptor.workflowDescriptor.outputRuntimeExtractor,
+          adjustedSizeDisks = adjustedSizeDisks,
+          virtualPrivateCloudConfiguration = batchAttributes.virtualPrivateCloudConfiguration,
+          retryWithMoreMemoryKeys = retryWithMoreMemoryKeys,
+          fuseEnabled = fuseEnabled(jobDescriptor.workflowDescriptor),
+          referenceDisksForLocalizationOpt = referenceDisksToMount,
+          monitoringImage = monitoringImage,
+          checkpointingConfiguration,
+          enableSshAccess = enableSshAccess,
+          vpcNetworkAndSubnetworkProjectLabels = data.vpcNetworkAndSubnetworkProjectLabels,
+          dockerhubCredentials = dockerhubCredentials
+        )
+      case Some(other) =>
+        throw new RuntimeException(s"Unexpected initialization data: $other")
+      case None =>
+        throw new RuntimeException("No batch backend initialization data found?")
+    }
+  }
+
+  protected def relativePathAndAttachedDisk(path: String, disks: Seq[GcpBatchAttachedDisk]): (Path, GcpBatchAttachedDisk) = {
+    val absolutePath = DefaultPathBuilder.get(path) match {
+      case p if !p.isAbsolute => GcpBatchWorkingDisk.MountPoint.resolve(p)
+      case p => p
+    }
+
+    disks.find(d => absolutePath.startsWith(d.mountPoint)) match {
+      case Some(disk) => (disk.mountPoint.relativize(absolutePath), disk)
+      case None =>
+        throw new Exception(s"Absolute path $path doesn't appear to be under any mount points: ${disks.map(_.toString).mkString(", ")}")
+    }
+  }
+
+  protected def makeSafeReferenceName(referenceName: String): String = {
+    if (referenceName.length <= 127) referenceName else referenceName.md5Sum
+  }
+
+  // De-localize the glob directory as a GcpBatchDirectoryOutput instead of using * pattern match
+  protected def generateGlobFileOutputs(womFile: WomGlobFile): List[GcpBatchOutput] = {
+    val globName = GlobFunctions.globName(womFile.value)
+    val globDirectory = globName + "/"
+    val globListFile = globName + ".list"
+    val gcsGlobDirectoryDestinationPath = callRootPath.resolve(globDirectory)
+    val gcsGlobListFileDestinationPath = callRootPath.resolve(globListFile)
+
+    val (_, globDirectoryDisk) = relativePathAndAttachedDisk(womFile.value, runtimeAttributes.disks)
+
+    // We need both the glob directory and the glob list:
+    List(
+      // The glob directory:
+      GcpBatchDirectoryOutput(makeSafeReferenceName(globDirectory), gcsGlobDirectoryDestinationPath, DefaultPathBuilder.get(globDirectory), globDirectoryDisk, optional = false, secondary = false),
+      // The glob list file:
+      GcpBatchFileOutput(makeSafeReferenceName(globListFile), gcsGlobListFileDestinationPath, DefaultPathBuilder.get(globListFile), globDirectoryDisk, optional = false, secondary = false)
+    )
+  }
+
+  lazy val batchMonitoringParamName: String = GcpBatchJobPaths.BatchMonitoringKey
+  lazy val localMonitoringLogPath: Path = DefaultPathBuilder.get(gcpBatchCallPaths.batchMonitoringLogFilename)
+  lazy val localMonitoringScriptPath: Path = DefaultPathBuilder.get(gcpBatchCallPaths.batchMonitoringScriptFilename)
+
+  lazy val monitoringScript: Option[GcpBatchFileInput] = {
+    gcpBatchCallPaths.workflowPaths.monitoringScriptPath map { path =>
+      GcpBatchFileInput(s"$batchMonitoringParamName-in", path, localMonitoringScriptPath, workingDisk)
+    }
+  }
+
+  private val DockerMonitoringLogPath: Path = GcpBatchWorkingDisk.MountPoint.resolve(gcpBatchCallPaths.batchMonitoringLogFilename)
+  private val DockerMonitoringScriptPath: Path = GcpBatchWorkingDisk.MountPoint.resolve(gcpBatchCallPaths.batchMonitoringScriptFilename)
+
+  override def scriptPreamble: String = {
+    if (monitoringOutput.isDefined) {
+      s"""|touch $DockerMonitoringLogPath
+          |chmod u+x $DockerMonitoringScriptPath
+          |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin
+    } else ""
+  }
+
+  private[actors] def generateInputs(jobDescriptor: BackendJobDescriptor): Set[GcpBatchInput] = {
+    // We need to tell PAPI about files that were created as part of command instantiation (these need to be defined
+    // as inputs that will be localized down to the VM). Make up 'names' for these files that are just the short
+    // md5's of their paths.
+    val writeFunctionFiles = instantiatedCommand.createdFiles map { f => f.file.value.md5SumShort -> List(f) } toMap
+
+    val writeFunctionInputs = writeFunctionFiles flatMap {
+      case (name, files) => gcpBatchInputsFromWomFiles(name, files.map(_.file), files.map(localizationPath), jobDescriptor)
+    }
+
+    val callInputInputs = callInputFiles flatMap {
+      case (name, files) => gcpBatchInputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor)
+    }
+
+    (writeFunctionInputs ++ callInputInputs).toSet
+  }
+
+  // Simply create a GcpBatchDirectoryOutput instead of globbing
+  protected def generateUnlistedDirectoryOutputs(unlistedDirectory: WomUnlistedDirectory, fileEvaluation: FileEvaluation): List[GcpBatchOutput] = {
+    val destination = callRootPath.resolve(unlistedDirectory.value.stripPrefix("/"))
+    val (relpath, disk) = relativePathAndAttachedDisk(unlistedDirectory.value, runtimeAttributes.disks)
+    val directoryOutput = GcpBatchDirectoryOutput(makeSafeReferenceName(unlistedDirectory.value), destination, relpath, disk, fileEvaluation.optional, fileEvaluation.secondary)
+    List(directoryOutput)
+  }
+
+  private def maybeListedDirectoryToBatchParameters(inputName: String, womMaybeListedDirectory: WomMaybeListedDirectory, localPath: String) = womMaybeListedDirectory match {
+    // If there is a path, simply localize as a directory
+    case WomMaybeListedDirectory(Some(path), _, _, _) =>
+      List(GcpBatchDirectoryInput(inputName, getPath(path).get, DefaultPathBuilder.get(localPath), workingDisk))
+
+    // If there is a listing, recurse and call gcpBatchInputsFromWomFiles on all the listed files
+    case WomMaybeListedDirectory(_, Some(listing), _, _) if listing.nonEmpty =>
+      listing.flatMap({
+        case womFile: WomFile if isAdHocFile(womFile) =>
+          gcpBatchInputsFromWomFiles(makeSafeReferenceName(womFile.valueString), List(womFile), List(fileName(womFile)), jobDescriptor)
+        case womFile: WomFile =>
+          gcpBatchInputsFromWomFiles(makeSafeReferenceName(womFile.valueString), List(womFile), List(relativeLocalizationPath(womFile)), jobDescriptor)
+      })
+    case _ => List.empty
+  }
+
+  def generateSingleFileOutputs(womFile: WomSingleFile, fileEvaluation: FileEvaluation): List[GcpBatchFileOutput] = {
+    val (relpath, disk) = relativePathAndAttachedDisk(womFile.value, runtimeAttributes.disks)
+    // If the file is on a custom mount point, resolve it so that the full mount path will show up in the cloud path
+    // For the default one (cromwell_root), the expectation is that it does not appear
+    val mountedPath = if (!disk.mountPoint.isSamePathAs(GcpBatchWorkingDisk.Default.mountPoint)) disk.mountPoint.resolve(relpath) else relpath
+    // Normalize the local path (to get rid of ".." and "."). Also strip any potential leading / so that it gets appended to the call root
+    val normalizedPath = mountedPath.normalize().pathAsString.stripPrefix("/")
+    val destination = callRootPath.resolve(normalizedPath)
+    val batchFileOutput = GcpBatchFileOutput(makeSafeReferenceName(womFile.value), destination, relpath, disk, fileEvaluation.optional, fileEvaluation.secondary)
+    List(batchFileOutput)
+  }
+
+  private[actors] def generateOutputs(jobDescriptor: BackendJobDescriptor): Set[GcpBatchOutput] = {
+    def evaluateFiles(output: OutputDefinition): List[FileEvaluation] = {
+      Try(
+        output.expression.evaluateFiles(jobDescriptor.localInputs, NoIoFunctionSet, output.womType).map(_.toList)
+      ).getOrElse(List.empty[FileEvaluation].validNel)
+        .getOrElse(List.empty)
+    }
+
+    def relativeFileEvaluation(evaluation: FileEvaluation): FileEvaluation = {
+      evaluation.copy(file = relativeLocalizationPath(evaluation.file))
+    }
+
+    val womFileOutputs = jobDescriptor.taskCall.callable.outputs.flatMap(evaluateFiles) map relativeFileEvaluation
+
+    val outputs: Seq[GcpBatchOutput] = womFileOutputs.distinct flatMap { fileEvaluation =>
+      fileEvaluation.file.flattenFiles flatMap {
+        case unlistedDirectory: WomUnlistedDirectory => generateUnlistedDirectoryOutputs(unlistedDirectory, fileEvaluation)
+        case singleFile: WomSingleFile => generateSingleFileOutputs(singleFile, fileEvaluation)
+        case globFile: WomGlobFile => generateGlobFileOutputs(globFile) // Assumes optional = false for globs.
+      }
+    }
+
+    val additionalGlobOutput = jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateGlobFileOutputs).toSet
+
+    outputs.toSet ++ additionalGlobOutput
+  }
+
+  protected def uploadGcsTransferLibrary(createBatchParameters: CreateBatchJobParameters,
+                                         cloudPath: Path,
+                                         gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = {
+
+    asyncIo.writeAsync(cloudPath, gcsTransferLibrary, Seq(CloudStorageOptions.withMimeType("text/plain")))
+  }
+
+
+  lazy val monitoringOutput: Option[GcpBatchFileOutput] = monitoringScript map { _ =>
+    GcpBatchFileOutput(s"$batchMonitoringParamName-out",
+      gcpBatchCallPaths.batchMonitoringLogPath, localMonitoringLogPath, workingDisk, optional = false, secondary = false,
+      contentType = plainTextContentType)
+  }
+
+  override lazy val commandDirectory: Path = GcpBatchWorkingDisk.MountPoint
+
+
+  // Primary entry point for cromwell to run GCP Batch job
+  override def executeAsync(): Future[ExecutionHandle] = {
+
+    // Want to force runtimeAttributes to evaluate so we can fail quickly now if we need to:
+    def evaluateRuntimeAttributes = Future.fromTry(Try(runtimeAttributes))
+
+    def generateInputOutputParameters: Future[InputOutputParameters] = Future.fromTry(Try {
+      val rcFileOutput = GcpBatchFileOutput(returnCodeFilename, returnCodeGcsPath, DefaultPathBuilder.get(returnCodeFilename), workingDisk, optional = false, secondary = false,
+        contentType = plainTextContentType)
+
+      val memoryRetryRCFileOutput = GcpBatchFileOutput(
+        memoryRetryRCFilename,
+        memoryRetryRCGcsPath,
+        DefaultPathBuilder.get(memoryRetryRCFilename),
+        workingDisk,
+        optional = true,
+        secondary = false,
+        contentType = plainTextContentType
+      )
+
+      case class StandardStream(name: String, f: StandardPaths => Path) {
+        val filename: String = f(gcpBatchCallPaths.standardPaths).name
+      }
+
+      val standardStreams = List(
+        StandardStream("stdout", _.output),
+        StandardStream("stderr", _.error)
+      ) map { s =>
+        GcpBatchFileOutput(s.name, returnCodeGcsPath.sibling(s.filename), DefaultPathBuilder.get(s.filename),
+          workingDisk, optional = false, secondary = false, uploadPeriod = batchAttributes.logFlushPeriod, contentType = plainTextContentType)
+      }
+
+      InputOutputParameters(
+        DetritusInputParameters(
+          executionScriptInputParameter = cmdInput,
+          monitoringScriptInputParameter = monitoringScript
+        ),
+        generateInputs(jobDescriptor).toList,
+        standardStreams ++ generateOutputs(jobDescriptor).toList,
+        DetritusOutputParameters(
+          monitoringScriptOutputParameter = monitoringOutput,
+          rcFileOutputParameter = rcFileOutput,
+          memoryRetryRCFileOutputParameter = memoryRetryRCFileOutput
+        ),
+        List.empty
+      )
+
+    })
+
+
+    val gcpBatchParameters = CreateGcpBatchParameters(
+      jobDescriptor = jobDescriptor,
+      runtimeAttributes = runtimeAttributes,
+      batchAttributes = batchAttributes,
+      projectId = batchAttributes.project,
+      region = batchAttributes.location)
+
+    val runBatchResponse = for {
+      _ <- evaluateRuntimeAttributes
+      _ <- uploadScriptFile()
+      customLabels <- Future.fromTry(GcpLabel.fromWorkflowOptions(workflowDescriptor.workflowOptions))
+      _ = customLabels.foreach(x => println(s"ZZZ Custom Labels - $x"))
+      batchParameters <- generateInputOutputParameters
+      _ = batchParameters.fileInputParameters.foreach(x => println(s"ZZZ File InputParameters - $x"))
+      _ = batchParameters.jobInputParameters.foreach(x => println(s"ZZZ InputParameters - $x"))
+      _ = batchParameters.fileOutputParameters.foreach(x => println(s"ZZZ File OutputParameters - $x"))
+      _ = batchParameters.jobOutputParameters.foreach(x => println(s"ZZZ OutputParameters - $x"))
+      createParameters = createBatchParameters(batchParameters, customLabels)
+      drsLocalizationManifestCloudPath = jobPaths.callExecutionRoot / GcpBatchJobPaths.DrsLocalizationManifestName
+      _ <- uploadDrsLocalizationManifest(createParameters, drsLocalizationManifestCloudPath)
+      gcsTransferConfiguration = initializationData.gcpBatchConfiguration.batchAttributes.gcsTransferConfiguration
+      gcsTransferLibraryCloudPath = jobPaths.callExecutionRoot / GcpBatchJobPaths.GcsTransferLibraryName
+      transferLibraryContainerPath = createParameters.commandScriptContainerPath.sibling(GcsTransferLibraryName)
+      _ <- uploadGcsTransferLibrary(createParameters, gcsTransferLibraryCloudPath, gcsTransferConfiguration)
+      gcsLocalizationScriptCloudPath = jobPaths.callExecutionRoot / GcpBatchJobPaths.GcsLocalizationScriptName
+      referenceInputsToMountedPathsOpt = getReferenceInputsToMountedPathsOpt(createParameters)
+      _ <- uploadGcsLocalizationScript(createParameters, gcsLocalizationScriptCloudPath, transferLibraryContainerPath, gcsTransferConfiguration, referenceInputsToMountedPathsOpt)
+      gcsDelocalizationScriptCloudPath = jobPaths.callExecutionRoot / GcpBatchJobPaths.GcsDelocalizationScriptName
+      _ <- uploadGcsDelocalizationScript(createParameters, gcsDelocalizationScriptCloudPath, transferLibraryContainerPath, gcsTransferConfiguration)
+      _ = createParameters.privateDockerKeyAndEncryptedToken.isDefined
+      jobName = "job-" + java.util.UUID.randomUUID.toString
+      request = GcpBatchRequest(workflowId, createParameters, jobName = jobName, gcpBatchParameters)
+      response <- runBatchJob(request = request, backendSingletonActor = backendSingletonActor)
+      _ = sendGoogleLabelsToMetadata(customLabels)
+      _ = sendIncrementMetricsForReferenceFiles(referenceInputsToMountedPathsOpt.map(_.keySet))
+
+    } yield response
+
+    // TODO: Handle when the job gets aborted before it starts being processed
+    runBatchResponse.map { runId =>
+      PendingExecutionHandle(
+        jobDescriptor = jobDescriptor,
+        pendingJob = runId,
+        runInfo = Option(Run(runId)),
+        previousState = None)
+    }
+  }
+
+  override def reconnectAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] = {
+    log.info("reconnect async runs") // in for debugging remove later
+    val handle = PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState](jobDescriptor, jobId, Option(Run(jobId)), previousState = None)
+    Future.successful(handle)
+  }
+
+  override lazy val pollBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(5
+    .second, 5
+    .minutes, 1.1)
+
+  override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(
+    initialInterval = 5
+      .seconds, maxInterval = 20
+      .seconds, multiplier = 1.1)
+
+  override lazy val runtimeEnvironment: RuntimeEnvironment = {
+    RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes, GcpBatchWorkingDisk.MountPoint, GcpBatchWorkingDisk.MountPoint)(standardParams.minimumRuntimeSettings)
+  }
+
+  protected def sendIncrementMetricsForReferenceFiles(referenceInputFilesOpt: Option[Set[GcpBatchInput]]): Unit = {
+    referenceInputFilesOpt match {
+      case Some(referenceInputFiles) =>
+        referenceInputFiles.foreach { referenceInputFile =>
+          increment(NonEmptyList.of("referencefiles", referenceInputFile.relativeHostPath.pathAsString))
+        }
+      case _ =>
+      // do nothing - reference disks feature is either not configured in Cromwell or disabled in workflow options
+    }
+  }
+
+  protected def sendIncrementMetricsForDockerImageCache(dockerImageCacheDiskOpt: Option[String],
+                                                        dockerImageAsSpecifiedByUser: String,
+                                                        isDockerImageCacheUsageRequested: Boolean): Unit = {
+    (isDockerImageCacheUsageRequested, dockerImageCacheDiskOpt) match {
+      case (true, None) => increment(NonEmptyList("docker", List("image", "cache", "image_not_in_cache", dockerImageAsSpecifiedByUser)))
+      case (true, Some(_)) => increment(NonEmptyList("docker", List("image", "cache", "used_image_from_cache", dockerImageAsSpecifiedByUser)))
+      case (false, Some(_)) => increment(NonEmptyList("docker", List("image", "cache", "cached_image_not_used", dockerImageAsSpecifiedByUser)))
+      case _ => // docker image cache not requested and image is not in cache anyway - do nothing
+    }
+  }
+
+  override def pollStatusAsync(handle: GcpBatchPendingExecutionHandle): Future[RunStatus] = {
+    // yes, we use the whole jobName as the id
+    val jobNameStr = handle.pendingJob.jobId
+
+    for {
+      _ <- Future.unit // trick to get into a future context
+      _ = log.info(s"started polling for $jobNameStr")
+      jobName = JobName.parse(jobNameStr)
+      job <- fetchJob(jobName, backendSingletonActor)
+    } yield RunStatus.fromJobStatus(job.getStatus.getState)
+  }
+
+  override def isTerminal(runStatus: RunStatus): Boolean = {
+    runStatus match {
+      case _: RunStatus.TerminalRunStatus =>
+        log.info(s"isTerminal match terminal run status with $runStatus")
+        true
+      case other =>
+        log.info(f"isTerminal match _ running with status $other")
+        false
+    }
+  }
+
+  override def isDone(runStatus: RunStatus): Boolean = {
+    runStatus match {
+      case _: RunStatus.Succeeded =>
+        log.info("GCP batch job succeeded matched isDone")
+        true
+      case _: RunStatus.UnsuccessfulRunStatus =>
+        log.info("GCP batch job unsuccessful matched isDone")
+        false
+      case _ =>
+        log.info(s"did not match isDone: $runStatus")
+        throw new RuntimeException(s"Cromwell programmer blunder: isDone was called on an incomplete RunStatus ($runStatus).")
+    }
+  }
+
+  override def getTerminalEvents(runStatus: RunStatus): Seq[ExecutionEvent] = {
+    runStatus match {
+      case t: RunStatus.TerminalRunStatus =>
+        log.warning(s"Tried to get terminal events on a terminal status without events: $runStatus")
+        t.eventList
+
+      case unknown =>
+        throw new RuntimeException(s"handleExecutionSuccess not called with RunStatus.Success. Instead got $unknown")
+    }
+  }
+
+  override lazy val startMetadataKeyValues: Map[String, Any] = super[GcpBatchJobCachingActorHelper].startMetadataKeyValues
+
+  // TODO: review sending machine and Instance type
+  override def getTerminalMetadata(runStatus: RunStatus): Map[String, Any] = {
+    runStatus match {
+      case _: TerminalRunStatus => Map()
+      case unknown => throw new RuntimeException(s"Attempt to get terminal metadata from non terminal status: $unknown")
+    }
+  }
+
+  override def mapOutputWomFile(womFile: WomFile): WomFile = {
+    womFileToGcsPath(generateOutputs(jobDescriptor))(womFile)
+  }
+
+
+  override def globParentDirectory(womGlobFile: WomGlobFile): Path = {
+    val (_, disk) = relativePathAndAttachedDisk(womGlobFile.value, runtimeAttributes.disks)
+    disk.mountPoint
+  }
+
+
+  protected def googleProject(descriptor: BackendWorkflowDescriptor): String = {
+    descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleProject, batchAttributes.project)
+  }
+
+  protected def computeServiceAccount(descriptor: BackendWorkflowDescriptor): String = {
+    descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleComputeServiceAccount, batchAttributes.computeServiceAccount)
+  }
+
+  protected def fuseEnabled(descriptor: BackendWorkflowDescriptor): Boolean = {
+    descriptor.workflowOptions.getBoolean(WorkflowOptionKeys.EnableFuse).toOption.getOrElse(batchAttributes.enableFuse)
+  }
+
+  protected def useDockerImageCache(descriptor: BackendWorkflowDescriptor): Boolean = {
+    descriptor.workflowOptions.getBoolean(WorkflowOptionKeys.UseDockerImageCache).getOrElse(false)
+  }
+
+  override def cloudResolveWomFile(womFile: WomFile): WomFile = {
+    womFile.mapFile { value =>
+      getPath(value) match {
+        case Success(drsPath: DrsPath) => DrsResolver.getSimpleGsUri(drsPath).unsafeRunSync().getOrElse(value)
+        case Success(path) => path.pathAsString
+        case _ => value
+      }
+    }
+  }
+
+  override def mapCommandLineWomFile(womFile: WomFile): WomFile = {
+    womFile.mapFile { value =>
+      (getPath(value), asAdHocFile(womFile)) match {
+        case (Success(gcsPath: GcsPath), Some(adHocFile)) =>
+          // Ad hoc files will be placed directly at the root ("/cromwell_root/ad_hoc_file.txt") unlike other input files
+          // for which the full path is being propagated ("/cromwell_root/path/to/input_file.txt")
+          workingDisk.mountPoint.resolve(adHocFile.alternativeName.getOrElse(gcsPath.name)).pathAsString
+        case (Success(path@(_: GcsPath | _: HttpPath)), _) =>
+          workingDisk.mountPoint.resolve(path.pathWithoutScheme).pathAsString
+        case (Success(drsPath: DrsPath), _) =>
+          val filePath = DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
+          workingDisk.mountPoint.resolve(filePath).pathAsString
+        case (Success(sraPath: SraPath), _) =>
+          workingDisk.mountPoint.resolve(s"sra-${sraPath.accession}/${sraPath.pathWithoutScheme}").pathAsString
+        case _ => value
+      }
+    }
+  }
+
+  override def mapCommandLineJobInputWomFile(womFile: WomFile): WomFile = {
+    womFile.mapFile(value =>
+      getPath(value) match {
+        case Success(gcsPath: GcsPath) => workingDisk.mountPoint.resolve(gcsPath.pathWithoutScheme).pathAsString
+        case Success(drsPath: DrsPath) =>
+          val filePath = DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
+          workingDisk.mountPoint.resolve(filePath).pathAsString
+        case _ => value
+      }
+    )
+  }
+
+  def womFileToGcsPath(batchOutputs: Set[GcpBatchOutput])(womFile: WomFile): WomFile = {
+    womFile mapFile { path =>
+      batchOutputs collectFirst {
+        case batchOutput if batchOutput.name == makeSafeReferenceName(path) =>
+          val pathAsString = batchOutput.cloudPath.pathAsString
+          if (batchOutput.isFileParameter && !batchOutput.cloudPath.exists) {
+            // This is not an error if the path represents a `File?` optional output (the Batch delocalization script
+            // should have failed if this file output was not optional but missing). Throw to produce the correct "empty
+            // optional" value for a missing optional file output.
+            throw new FileNotFoundException(s"GCS output file not found: $pathAsString")
+          }
+          pathAsString
+      } getOrElse {
+        GcsPathBuilder.validateGcsPath(path) match {
+          case _: ValidFullGcsPath => path
+
+          /*
+            * Strip the prefixes in RuntimeOutputMapping.prefixFilters from the path, one at a time.
+            * For instance
+            * file:///cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt will progressively become
+            *
+            * /cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
+            * bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
+            * call-A/file.txt
+            *
+            * This code is called as part of a path mapper that will be applied to the WOMified cwl.output.json.
+            * The cwl.output.json when it's being read by Cromwell from the bucket still contains local paths
+            * (as they were created by the cwl tool).
+            * In order to keep things working we need to map those local paths to where they were actually delocalized,
+            * which is determined in cromwell.backend.google.pipelines.v2beta.api.Delocalization.
+            */
+          case _ => (callRootPath /
+            RuntimeOutputMapping
+              .prefixFilters(workflowPaths.workflowRoot)
+              .foldLeft(path)({
+                case (newPath, prefix) => newPath.stripPrefix(prefix)
+              })
+            ).pathAsString
+        }
+      }
+    }
+  }
+
+  // No need for Cromwell-performed localization in the PAPI backend, ad hoc values are localized directly from GCS to the VM by PAPI.
+  override lazy val localizeAdHocValues: List[AdHocValue] => ErrorOr[List[StandardAdHocValue]] = _.map(Coproduct[StandardAdHocValue](_)).validNel
+}
+
+
+
+
+
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchBackendSingletonActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchBackendSingletonActor.scala
new file mode 100644
index 00000000000..66e74b3f2c8
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchBackendSingletonActor.scala
@@ -0,0 +1,122 @@
+package cromwell.backend.google.batch.actors
+
+import akka.actor.{Actor, ActorLogging, ActorRef, Props, Timers}
+import com.google.cloud.batch.v1.JobName
+import com.google.longrunning.Operation
+import cromwell.backend.BackendSingletonActorAbortWorkflow
+import cromwell.backend.google.batch.api.{GcpBatchApiRequestHandler, GcpBatchRequestFactory}
+import cromwell.backend.google.batch.models.GcpBatchRequest
+import cromwell.backend.google.batch.monitoring.BatchInstrumentation
+import cromwell.core.Dispatcher.BackendDispatcher
+import cromwell.services.instrumentation.CromwellInstrumentationScheduler
+
+import scala.concurrent.{ExecutionContext, Future}
+import scala.util.{Failure, Success}
+
+object GcpBatchBackendSingletonActor {
+  def props(requestFactory: GcpBatchRequestFactory, serviceRegistryActor: ActorRef)(implicit requestHandler: GcpBatchApiRequestHandler): Props = {
+    Props(new GcpBatchBackendSingletonActor(requestFactory, serviceRegistryActor = serviceRegistryActor))
+      .withDispatcher(BackendDispatcher)
+  }
+
+  // This is the only type of messages that can be processed by this actor from this actor
+  sealed trait Action extends Product with Serializable
+  object Action {
+    final case class SubmitJob(request: GcpBatchRequest) extends Action
+    final case class QueryJob(jobName: JobName) extends Action
+    final case class AbortJob(jobName: JobName) extends Action
+  }
+
+  // This is the only type of messages produced from this actor while reacting to received messages
+  sealed trait Event extends Product with Serializable
+  object Event {
+    final case class JobSubmitted(job: com.google.cloud.batch.v1.Job) extends Event
+    final case class JobStatusRetrieved(job: com.google.cloud.batch.v1.Job) extends Event
+    final case class JobAbortRequestSent(operation: Operation) extends Event
+    final case class ActionFailed(jobName: String, cause: Throwable) extends Event
+  }
+
+}
+
+final class GcpBatchBackendSingletonActor(requestFactory: GcpBatchRequestFactory, override val serviceRegistryActor: ActorRef)(implicit requestHandler: GcpBatchApiRequestHandler)
+  extends Actor
+    with ActorLogging
+    with BatchInstrumentation
+    with CromwellInstrumentationScheduler
+    with Timers {
+
+  import GcpBatchBackendSingletonActor._
+
+  private implicit val ec: ExecutionContext = context.dispatcher
+
+  override def preStart() = {
+    startInstrumentationTimer()
+    super.preStart()
+  }
+
+  private def normalReceive: Receive = {
+    case Action.SubmitJob(request) =>
+      val replyTo = sender()
+      log.info(s"Submitting job (${request.jobName}) to GCP, workflowId = ${request.workflowId}")
+      Future {
+        requestHandler.submit(requestFactory.submitRequest(request))
+      }.onComplete {
+        case Failure(exception) =>
+          log.error(exception, s"Failed to submit job (${request.jobName}) to GCP, workflowId = ${request.workflowId}")
+          replyTo ! Event.ActionFailed(request.jobName, exception)
+
+        case Success(job) =>
+          log.info(s"Job (${request.jobName}) submitted to GCP, workflowId = ${request.workflowId}, id = ${job.getUid}")
+          replyTo ! Event.JobSubmitted(job)
+      }
+
+    case Action.QueryJob(jobName) =>
+      val replyTo = sender()
+
+      Future {
+        requestHandler.query(requestFactory.queryRequest(jobName))
+      }.onComplete {
+        case Success(job) =>
+          log.info(s"Job ($jobName) retrieved from GCP, state = ${job.getStatus.getState}")
+          replyTo ! Event.JobStatusRetrieved(job)
+
+        case Failure(exception) =>
+          log.error(exception,  s"Failed to query job status ($jobName) from GCP")
+          replyTo ! Event.ActionFailed(jobName.toString ,exception)
+      }
+
+    case Action.AbortJob(jobName) =>
+      val replyTo = sender()
+
+      Future {
+        requestHandler.abort(requestFactory.abortRequest(jobName))
+      }.onComplete {
+        case Success(operation) =>
+          log.info(s"Job ($jobName) aborted from GCP")
+          replyTo ! Event.JobAbortRequestSent(operation)
+
+        case Failure(exception) =>
+          log.error(exception, s"Failed to abort job ($jobName) from GCP")
+          replyTo ! Event.ActionFailed(jobName.toString, exception)
+      }
+
+    // Cromwell sends this message
+    case BackendSingletonActorAbortWorkflow(workflowId) =>
+      // It seems that AbortJob(jobName) is processed before this message, hence, we don't need to do anything else.
+      // If it ever becomes necessary, we'll need to create link submitted jobs to its workflow id, which require
+      // us to be cautious because batch deletes jobs instead of canceling them, hence, we should not delete jobs
+      // that are on a final state.
+      log.info(s"Cromwell requested to abort workflow $workflowId")
+
+    case other => log.error(s"Unexpected message from {} to ${this.getClass.getSimpleName}: {}", sender().path.name, other)
+  }
+
+  override def receive = instrumentationReceive(loadMetricHandler _).orElse(normalReceive)
+
+  private def loadMetricHandler() = {
+    // TODO: Implement this once we have details to expose
+//    val load = if (workQueue.size > LoadConfig.PAPIThreshold) HighLoad else NormalLoad
+//    serviceRegistryActor ! LoadMetric("PAPIQueryManager", load)
+//    updateQueueSize(workQueue.size)
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchFinalizationActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchFinalizationActor.scala
new file mode 100644
index 00000000000..dd57edc8b4e
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchFinalizationActor.scala
@@ -0,0 +1,35 @@
+package cromwell.backend.google.batch.actors
+
+import akka.actor.ActorRef
+import cromwell.backend._
+import cromwell.backend.google.batch.models.GcpBatchConfiguration
+import cromwell.backend.standard.{StandardFinalizationActor, StandardFinalizationActorParams}
+import cromwell.core.CallOutputs
+import cromwell.core.io.AsyncIoActorClient
+import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
+import wom.graph.CommandCallNode
+
+case class GcpBatchFinalizationActorParams
+(
+  workflowDescriptor: BackendWorkflowDescriptor,
+  ioActor: ActorRef,
+  batchConfiguration: GcpBatchConfiguration,
+  calls: Set[CommandCallNode],
+  jobExecutionMap: JobExecutionMap,
+  workflowOutputs: CallOutputs,
+  initializationDataOption: Option[BackendInitializationData]
+) extends StandardFinalizationActorParams {
+  override def configurationDescriptor: BackendConfigurationDescriptor = batchConfiguration.configurationDescriptor
+}
+
+class GcpBatchFinalizationActor(val batchParams: GcpBatchFinalizationActorParams) extends StandardFinalizationActor(batchParams) with AsyncIoActorClient {
+
+  lazy val batchConfiguration: GcpBatchConfiguration = batchParams.batchConfiguration
+
+  override lazy val ioCommandBuilder = GcsBatchCommandBuilder
+  override def ioActor: ActorRef = batchParams.ioActor
+}
+
+object GcpBatchFinalizationActor {
+
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActor.scala
new file mode 100644
index 00000000000..466a4f20d7e
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActor.scala
@@ -0,0 +1,254 @@
+package cromwell.backend.google.batch.actors
+
+import _root_.io.circe.Decoder
+import _root_.io.circe.generic.semiauto.deriveDecoder
+import _root_.io.circe.parser.decode
+import akka.actor.ActorRef
+import com.google.api.client.http.{HttpRequest, HttpResponse}
+import com.google.api.services.cloudkms.v1.model.EncryptRequest
+import com.google.api.services.cloudkms.v1.{CloudKMS, CloudKMSScopes}
+import com.google.api.services.cloudresourcemanager.{CloudResourceManager, CloudResourceManagerScopes}
+import com.google.api.services.genomics.v2alpha1.GenomicsScopes
+import com.google.api.services.lifesciences.v2beta.CloudLifeSciencesScopes
+import com.google.api.services.storage.StorageScopes
+import com.google.auth.Credentials
+import com.google.auth.http.HttpCredentialsAdapter
+import com.google.auth.oauth2.OAuth2Credentials
+import cromwell.backend.google.batch._
+import cromwell.backend.google.batch.actors.GcpBatchInitializationActor._
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.{VirtualPrivateCloudConfiguration, VirtualPrivateCloudLabels, VirtualPrivateCloudLiterals}
+import cromwell.backend.google.batch.models._
+import cromwell.backend.google.batch.runnable.WorkflowOptionKeys
+import cromwell.backend.standard.{StandardInitializationActor, StandardInitializationActorParams, StandardValidatedRuntimeAttributesBuilder}
+import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor}
+import cromwell.cloudsupport.gcp.auth.GoogleAuthMode.{httpTransport, jsonFactory}
+import cromwell.cloudsupport.gcp.auth.{GoogleAuthMode, UserServiceAccountMode}
+import cromwell.core.io.AsyncIoActorClient
+import cromwell.core.{Dispatcher, WorkflowOptions}
+import cromwell.filesystems.gcs.GoogleUtil._
+import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
+import org.apache.commons.codec.binary.Base64
+import org.apache.commons.lang3.exception.ExceptionUtils
+import spray.json.{JsObject, JsString}
+import wom.graph.CommandCallNode
+
+import scala.concurrent.Future
+import scala.util.Try
+import scala.util.control.NonFatal
+
+case class GcpBatchInitializationActorParams
+(
+  workflowDescriptor: BackendWorkflowDescriptor,
+  ioActor: ActorRef,
+  calls: Set[CommandCallNode],
+  batchConfiguration: GcpBatchConfiguration,
+  serviceRegistryActor: ActorRef,
+  restarting: Boolean
+) extends StandardInitializationActorParams {
+  override val configurationDescriptor: BackendConfigurationDescriptor = batchConfiguration.configurationDescriptor
+
+}
+class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams) extends StandardInitializationActor(batchParams) with AsyncIoActorClient {
+
+  override lazy val ioActor: ActorRef = batchParams.ioActor
+  protected val gcpBatchConfiguration: GcpBatchConfiguration = batchParams.batchConfiguration
+  protected val workflowOptions: WorkflowOptions = workflowDescriptor.workflowOptions
+  private lazy val ioEc = context.system.dispatchers.lookup(Dispatcher.IoDispatcher)
+
+  override lazy val runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder =
+    GcpBatchRuntimeAttributes
+      .runtimeAttributesBuilder(gcpBatchConfiguration)
+
+  // Credentials object for the GCS API
+  private lazy val gcsCredentials: Future[Credentials] = gcpBatchConfiguration.batchAttributes.auths.gcs
+    .retryCredentials(workflowOptions, List(StorageScopes.DEVSTORAGE_FULL_CONTROL))
+
+  // Credentials object for the Genomics API
+  private lazy val genomicsCredentials: Future[Credentials] = gcpBatchConfiguration.batchAttributes.auths.genomics
+                                                                                    .retryCredentials(workflowOptions, List(
+                                                                                      CloudLifeSciencesScopes
+                                                                                        .CLOUD_PLATFORM,
+                                                                                      GenomicsScopes.GENOMICS
+                                                                                    ))
+
+  val privateDockerEncryptionKeyName: Option[String] = {
+    val optionsEncryptionKey = workflowOptions.get(GoogleAuthMode.DockerCredentialsEncryptionKeyNameKey).toOption
+    optionsEncryptionKey.orElse(gcpBatchConfiguration.dockerEncryptionKeyName)
+  }
+
+  val privateDockerToken: Option[String] = {
+    val optionsDockerToken = workflowOptions.get(GoogleAuthMode.DockerCredentialsTokenKey).toOption
+    optionsDockerToken.orElse(gcpBatchConfiguration.dockerToken)
+  }
+
+  lazy val privateDockerEncryptedToken: Option[String] = {
+    val effectiveAuth: Option[GoogleAuthMode] = {
+      // Use the user service account if a user service account value is provided in the workflow options and there's
+      // a user service account auth in the list of auths.
+      // TODO is it okay that this would silently ignore user auths if there isn't one defined in the config list of auths?
+      // That doesn't seem great but it's effectively what the existing code around user service accounts appears to be doing.
+      val userServiceAccountAuth: Option[GoogleAuthMode] = for {
+        _ <- workflowOptions.get(GoogleAuthMode.UserServiceAccountKey).toOption
+        usaAuth <- gcpBatchConfiguration.googleConfig.authsByName.values collectFirst { case u: UserServiceAccountMode => u }
+      } yield usaAuth
+
+      def encryptionAuthFromConfig: Option[GoogleAuthMode] = gcpBatchConfiguration.dockerEncryptionAuthName.flatMap { name =>
+        gcpBatchConfiguration.googleConfig.auth(name).toOption
+      }
+      // If there's no user service account auth in the workflow options fall back to an auth specified in config.
+      userServiceAccountAuth orElse encryptionAuthFromConfig
+    }
+
+    val unencrypted: Option[String] = privateDockerToken flatMap { dockerToken =>
+      new String(Base64.decodeBase64(dockerToken)).split(':') match {
+        case Array(username, password) =>
+          // unencrypted tokens are base64-encoded username:password
+          Option(JsObject(
+            Map(
+              "username" -> JsString(username),
+              "password" -> JsString(password)
+            )).compactPrint)
+        case _ => throw new RuntimeException(s"provided dockerhub token '$dockerToken' is not a base64-encoded username:password")
+      }
+    }
+
+    for {
+      plain <- unencrypted
+      auth <- effectiveAuth
+      key <- privateDockerEncryptionKeyName
+      credentials = auth.credentials(workflowOptions.get(_).get, List(CloudKMSScopes.CLOUD_PLATFORM))
+      encrypted = encryptKms(key, credentials, plain)
+    } yield encrypted
+  }
+
+  private def vpcNetworkAndSubnetworkProjectLabelsFuture(): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
+    def googleProject(descriptor: BackendWorkflowDescriptor): String = {
+      descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleProject, batchParams.batchConfiguration.batchAttributes.project)
+    }
+
+    def projectMetadataRequest(vpcConfig: VirtualPrivateCloudLabels): Future[HttpRequest] = {
+      Future {
+        val credentials = vpcConfig.auth.credentials(workflowOptions.get(_).getOrElse(throw new RuntimeException("Unable to find the necessary workflow option for auth credentials")), List(CloudResourceManagerScopes.CLOUD_PLATFORM))
+
+        val httpCredentialsAdapter = new HttpCredentialsAdapter(credentials)
+        val cloudResourceManagerBuilder = new CloudResourceManager
+        .Builder(GoogleAuthMode.httpTransport, GoogleAuthMode.jsonFactory, httpCredentialsAdapter)
+          .setApplicationName(gcpBatchConfiguration.googleConfig.applicationName)
+          .build()
+
+        val project = cloudResourceManagerBuilder.projects().get(googleProject(workflowDescriptor))
+
+        project.buildHttpRequest()
+      }
+    }
+
+    def projectMetadataResponseToLabels(httpResponse: HttpResponse): Future[ProjectLabels] = {
+      implicit val googleProjectMetadataLabelDecoder: Decoder[ProjectLabels] = deriveDecoder
+      Future.fromTry(decode[ProjectLabels](httpResponse.parseAsString()).toTry).recoverWith {
+        case NonFatal(e) => Future.failed(new RuntimeException(s"Failed to parse labels from project metadata response from Google Cloud Resource Manager API. " +
+          s"${ExceptionUtils.getMessage(e)}", e))
+      }
+    }
+
+    def networkLabelsFromProjectLabels(vpcConfig: VirtualPrivateCloudLabels,
+                                       projectLabels: ProjectLabels,
+                                      ): Option[VpcAndSubnetworkProjectLabelValues] = {
+      projectLabels.labels.get(vpcConfig.network) map { vpcNetworkLabelValue =>
+        val subnetworkLabelOption = vpcConfig.subnetwork.flatMap { s =>
+          projectLabels.labels.collectFirst {
+            case (labelName, labelValue) if labelName.equals(s) => labelValue
+          }
+        }
+
+        VpcAndSubnetworkProjectLabelValues(vpcNetworkLabelValue, subnetworkLabelOption)
+      }
+    }
+
+    def fetchVpcLabelsFromProjectMetadata(vpcConfig: VirtualPrivateCloudLabels
+                                         ): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
+      for {
+        projectMetadataResponse <- projectMetadataRequest(vpcConfig).map(_.executeAsync().get())
+        projectLabels <- projectMetadataResponseToLabels(projectMetadataResponse)
+      } yield networkLabelsFromProjectLabels(vpcConfig, projectLabels)
+    }
+
+    /*
+    First, try to fetch the network information from labels, where that fetch may still return None.
+    Then, if we did not discover a network via labels for whatever reason try to look for literal values.
+     */
+    def fetchVpcLabels(vpcConfig: VirtualPrivateCloudConfiguration
+                      ): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
+      // Added explicit types to hopefully help future devs who stumble across this two-step code
+      val fetchedFromLabels: Future[Option[VpcAndSubnetworkProjectLabelValues]] = vpcConfig.labelsOption match {
+        case Some(labels: VirtualPrivateCloudLabels) => fetchVpcLabelsFromProjectMetadata(labels)
+        case None => Future.successful(None)
+      }
+      fetchedFromLabels map {
+        _ orElse {
+          vpcConfig.literalsOption map { literals: VirtualPrivateCloudLiterals =>
+            VpcAndSubnetworkProjectLabelValues(literals.network, literals.subnetwork)
+          }
+        }
+      }
+    }
+
+    val vpcConfig: VirtualPrivateCloudConfiguration =
+      gcpBatchConfiguration.batchAttributes.virtualPrivateCloudConfiguration
+    fetchVpcLabels(vpcConfig)
+  }
+
+  override lazy val workflowPaths: Future[GcpBatchWorkflowPaths] = for {
+    gcsCred <- gcsCredentials
+    genomicsCred <- genomicsCredentials
+    validatedPathBuilders <- pathBuilders
+  } yield new GcpBatchWorkflowPaths(
+      workflowDescriptor, gcsCred, genomicsCred, gcpBatchConfiguration, validatedPathBuilders, standardStreamNameToFileNameMetadataMapper)(ioEc)
+
+
+  override lazy val initializationData: Future[GcpBackendInitializationData] = for {
+    batchWorkflowPaths <- workflowPaths
+    gcsCreds <- gcsCredentials
+    vpcNetworkAndSubnetworkProjectLabels <- vpcNetworkAndSubnetworkProjectLabelsFuture()
+  } yield models.GcpBackendInitializationData(
+    workflowPaths = batchWorkflowPaths,
+    runtimeAttributesBuilder = runtimeAttributesBuilder,
+    gcpBatchConfiguration = gcpBatchConfiguration,
+    gcsCredentials = gcsCreds,
+    privateDockerEncryptionKeyName = privateDockerEncryptionKeyName,
+    privateDockerEncryptedToken = privateDockerEncryptedToken,
+    vpcNetworkAndSubnetworkProjectLabels = vpcNetworkAndSubnetworkProjectLabels
+  )
+
+  override def validateWorkflowOptions(): Try[Unit] = GcpLabel.fromWorkflowOptions(workflowOptions).map(_ => ())
+
+  override def beforeAll(): Future[Option[BackendInitializationData]] = {
+    for {
+      paths <- workflowPaths
+      _ = publishWorkflowRoot(paths.workflowRoot.pathAsString)
+      data <- initializationData
+    } yield Option(data)
+  }
+
+  def standardStreamNameToFileNameMetadataMapper(gcpBatchJobPaths: GcpBatchJobPaths, streamName: String): String =
+    GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper(gcpBatchJobPaths, streamName)
+
+  override lazy val ioCommandBuilder: GcsBatchCommandBuilder.type = GcsBatchCommandBuilder
+
+}
+
+object GcpBatchInitializationActor {
+  // For metadata publishing purposes default to using the name of a standard stream as the stream's filename.
+  def defaultStandardStreamNameToFileNameMetadataMapper(gcpBatchJobPaths: GcpBatchJobPaths, streamName: String): String = streamName
+
+  def encryptKms(keyName: String, credentials: OAuth2Credentials, plainText: String): String = {
+    val httpCredentialsAdapter = new HttpCredentialsAdapter(credentials)
+    val kms = new CloudKMS.Builder(httpTransport, jsonFactory, httpCredentialsAdapter)
+      .setApplicationName("cromwell")
+      .build()
+
+    val request = new EncryptRequest().encodePlaintext(plainText.toCharArray.map(_.toByte))
+    val response = kms.projects.locations.keyRings.cryptoKeys.encrypt(keyName, request).execute
+    response.getCiphertext
+  }
+
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchJobCachingActorHelper.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchJobCachingActorHelper.scala
new file mode 100644
index 00000000000..e86404bef1e
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchJobCachingActorHelper.scala
@@ -0,0 +1,87 @@
+package cromwell.backend.google.batch.actors
+
+import cromwell.backend.google.batch.io.{GcpBatchAttachedDisk, GcpBatchWorkingDisk}
+import cromwell.backend.google.batch.runnable.{GcpBatchMetadataKeys, WorkflowOptionKeys}
+import cromwell.backend.google.batch.models._
+import cromwell.backend.standard.StandardCachingActorHelper
+import cromwell.core.labels.Labels
+import cromwell.core.logging.JobLogging
+import cromwell.core.path.Path
+import cromwell.services.metadata.CallMetadataKeys
+
+import scala.language.postfixOps
+
+trait GcpBatchJobCachingActorHelper extends StandardCachingActorHelper {
+  this: GcpBatchAsyncBackendJobExecutionActor with JobLogging =>
+
+  lazy val initializationData: GcpBackendInitializationData = {
+    backendInitializationDataAs[GcpBackendInitializationData]
+  }
+  lazy val batchConfiguration: GcpBatchConfiguration = initializationData.gcpBatchConfiguration
+
+  lazy val gcpBatchCallPaths: GcpBatchJobPaths = jobPaths.asInstanceOf[GcpBatchJobPaths]
+
+  lazy val runtimeAttributes = GcpBatchRuntimeAttributes(
+    validatedRuntimeAttributes,
+    batchConfiguration
+      .runtimeConfig
+  )
+
+  lazy val maxPreemption: Int = runtimeAttributes.preemptible
+
+
+  lazy val workingDisk: GcpBatchAttachedDisk = runtimeAttributes.disks.find(_.name == GcpBatchWorkingDisk.Name).get
+
+  lazy val callRootPath: Path = gcpBatchCallPaths.callExecutionRoot
+  lazy val returnCodeFilename: String = gcpBatchCallPaths.returnCodeFilename
+  lazy val returnCodeGcsPath: Path = gcpBatchCallPaths.returnCode
+  lazy val gcpBatchLogPath: Path = gcpBatchCallPaths.batchLogPath
+  lazy val memoryRetryRCFilename: String = gcpBatchCallPaths.memoryRetryRCFilename
+  lazy val memoryRetryRCGcsPath: Path = gcpBatchCallPaths.memoryRetryRC
+
+  lazy val batchAttributes: GcpBatchConfigurationAttributes = batchConfiguration.batchAttributes
+
+  lazy val defaultLabels: Labels = {
+    val workflow = jobDescriptor.workflowDescriptor
+    val call = jobDescriptor.taskCall
+    val subWorkflow = workflow.callable
+    val subWorkflowLabels = if (!subWorkflow.equals(workflow.rootWorkflow))
+      Labels("cromwell-sub-workflow-name" -> subWorkflow.name)
+    else
+      Labels.empty
+
+    val alias = call.localName
+    val aliasLabels = if (!alias.equals(call.callable.name))
+      Labels("wdl-call-alias" -> alias)
+    else
+      Labels.empty
+
+    Labels(
+      "cromwell-workflow-id" -> s"cromwell-${workflow.rootWorkflowId}",
+      "wdl-task-name" -> call.callable.name
+    ) ++ subWorkflowLabels ++ aliasLabels
+  }
+
+
+  lazy val originalLabels: Labels = defaultLabels
+
+  lazy val backendLabels: Seq[GcpLabel] = GcpLabel.safeLabels(originalLabels.asTuple: _*)
+
+  lazy val originalLabelEvents: Map[String, String] = originalLabels.value map { l => s"${CallMetadataKeys.Labels}:${l.key}" -> l.value } toMap
+
+  override protected def nonStandardMetadata: Map[String, Any] = {
+    val googleProject = initializationData
+      .workflowPaths
+      .workflowDescriptor
+      .workflowOptions
+      .get(WorkflowOptionKeys.GoogleProject)
+      .getOrElse(batchAttributes.project)
+
+    Map[String, Any](
+      GcpBatchMetadataKeys.GoogleProject -> googleProject,
+      GcpBatchMetadataKeys.ExecutionBucket -> initializationData.workflowPaths.executionRootString,
+      "preemptible" -> preemptible
+    ) ++ originalLabelEvents
+  }
+
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchApiRequestHandler.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchApiRequestHandler.scala
new file mode 100644
index 00000000000..1a877558942
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchApiRequestHandler.scala
@@ -0,0 +1,34 @@
+package cromwell.backend.google.batch.api
+
+import com.google.api.gax.rpc.FixedHeaderProvider
+import com.google.cloud.batch.v1._
+import com.google.common.collect.ImmutableMap
+import com.google.longrunning.Operation
+
+class GcpBatchApiRequestHandler {
+  def submit(request: CreateJobRequest): Job = withClient { client =>
+    client.createJobCallable
+      .call(request)
+  }
+
+  def query(request: GetJobRequest): Job = withClient { client =>
+    client.getJob(request)
+  }
+
+  def abort(request: DeleteJobRequest): Operation = withClient { client =>
+    client.deleteJobCallable().call(request)
+  }
+
+  private def withClient[T](f: BatchServiceClient => T): T = {
+    // set user agent to cromwell so requests can be differentiated on batch
+    val headers = ImmutableMap.of("user-agent", "cromwell")
+    val headerProvider = FixedHeaderProvider.create(headers)
+    val batchSettings = BatchServiceSettings.newBuilder.setHeaderProvider(headerProvider).build
+    val client = BatchServiceClient.create(batchSettings)
+    try {
+      f(client)
+    } finally {
+      client.close()
+    }
+  }
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala
new file mode 100644
index 00000000000..6976bd09867
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala
@@ -0,0 +1,102 @@
+package cromwell.backend.google.batch.api
+
+import com.google.cloud.batch.v1.{CreateJobRequest, DeleteJobRequest, GetJobRequest, JobName}
+import cromwell.backend.BackendJobDescriptor
+import cromwell.backend.google.batch.io.GcpBatchAttachedDisk
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.VirtualPrivateCloudConfiguration
+import cromwell.backend.google.batch.models._
+import cromwell.backend.google.batch.monitoring.{CheckpointingConfiguration, MonitoringImage}
+import cromwell.core.path.Path
+import wom.runtime.WomOutputRuntimeExtractor
+
+import scala.concurrent.duration.FiniteDuration
+
+trait GcpBatchRequestFactory {
+  def submitRequest(data: GcpBatchRequest): CreateJobRequest
+
+  def queryRequest(jobName: JobName): GetJobRequest
+
+  def abortRequest(jobName: JobName): DeleteJobRequest
+
+}
+
+object GcpBatchRequestFactory {
+
+  type MountsToEnv = List[String] => Map[String, String]
+
+  /**
+    * Input parameters that are not strictly needed by the user's command but are Cromwell byproducts.
+    */
+  case class DetritusInputParameters(
+                                      executionScriptInputParameter: GcpBatchFileInput,
+                                      monitoringScriptInputParameter: Option[GcpBatchFileInput]
+                                    ) {
+    def all: List[GcpBatchFileInput] = List(executionScriptInputParameter) ++ monitoringScriptInputParameter
+  }
+
+  /**
+    * Output parameters that are not produced by the user's command but are Cromwell byproducts.
+    */
+  case class DetritusOutputParameters(
+                                       monitoringScriptOutputParameter: Option[GcpBatchFileOutput],
+                                       rcFileOutputParameter: GcpBatchFileOutput,
+                                       memoryRetryRCFileOutputParameter: GcpBatchFileOutput
+                                     ) {
+    def all: List[GcpBatchFileOutput] = memoryRetryRCFileOutputParameter :: List(rcFileOutputParameter) ++ monitoringScriptOutputParameter
+  }
+
+  /**
+    * Bundle containing all input and output parameters to a PAPI job
+    * Detrituses and actual inputs / outputs to the job are separated for more clarity and to leave open the possibility
+    * to treat them differently.
+    */
+  case class InputOutputParameters(
+                                    detritusInputParameters: DetritusInputParameters,
+                                    jobInputParameters: List[GcpBatchInput],
+                                    jobOutputParameters: List[GcpBatchOutput],
+                                    detritusOutputParameters: DetritusOutputParameters,
+                                    literalInputParameters: List[GcpBatchLiteralInput]
+                                  ) {
+    lazy val fileInputParameters: List[GcpBatchInput] = jobInputParameters ++ detritusInputParameters.all
+    lazy val fileOutputParameters: List[GcpBatchOutput] = detritusOutputParameters.all ++ jobOutputParameters
+  }
+
+  case class CreateBatchDockerKeyAndToken(key: String, encryptedToken: String)
+
+  case class CreateBatchJobParameters(jobDescriptor: BackendJobDescriptor,
+                                      runtimeAttributes: GcpBatchRuntimeAttributes,
+                                      dockerImage: String,
+                                      cloudWorkflowRoot: Path,
+                                      cloudCallRoot: Path,
+                                      commandScriptContainerPath: Path,
+                                      logGcsPath: Path,
+                                      inputOutputParameters: InputOutputParameters,
+                                      projectId: String,
+                                      computeServiceAccount: String,
+                                      googleLabels: Seq[GcpLabel],
+                                      preemptible: Boolean,
+                                      batchTimeout: FiniteDuration,
+                                      jobShell: String,
+                                      privateDockerKeyAndEncryptedToken: Option[CreateBatchDockerKeyAndToken],
+                                      womOutputRuntimeExtractor: Option[WomOutputRuntimeExtractor],
+                                      adjustedSizeDisks: Seq[GcpBatchAttachedDisk],
+                                      virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
+                                      retryWithMoreMemoryKeys: Option[List[String]],
+                                      fuseEnabled: Boolean,
+                                      referenceDisksForLocalizationOpt: Option[List[GcpBatchAttachedDisk]],
+                                      monitoringImage: MonitoringImage,
+                                      checkpointingConfiguration: CheckpointingConfiguration,
+                                      enableSshAccess: Boolean,
+                                      vpcNetworkAndSubnetworkProjectLabels: Option[VpcAndSubnetworkProjectLabelValues],
+                                      dockerhubCredentials: (String, String)
+                                     ) {
+    def literalInputs = inputOutputParameters.literalInputParameters
+
+    def inputParameters = inputOutputParameters.fileInputParameters
+
+    def outputParameters = inputOutputParameters.fileOutputParameters
+
+    def allParameters = inputParameters ++ outputParameters
+  }
+
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
new file mode 100644
index 00000000000..435992b8cd8
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
@@ -0,0 +1,232 @@
+package cromwell.backend.google.batch.api
+
+import com.google.cloud.batch.v1.AllocationPolicy.Accelerator
+import com.google.cloud.batch.v1.{DeleteJobRequest, GetJobRequest, JobName}
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.batch.models.GcpBatchRequest
+import cromwell.backend.google.batch.runnable._
+import cromwell.backend.google.batch.util.BatchUtilityConversions
+import com.google.cloud.batch.v1.AllocationPolicy.{AttachedDisk, InstancePolicy, InstancePolicyOrTemplate, LocationPolicy, NetworkInterface, NetworkPolicy, ProvisioningModel}
+import com.google.cloud.batch.v1.LogsPolicy.Destination
+import com.google.cloud.batch.v1.{AllocationPolicy, ComputeResource, CreateJobRequest, Job, LogsPolicy, Runnable, ServiceAccount, TaskGroup, TaskSpec, Volume}
+import com.google.protobuf.Duration
+import cromwell.backend.google.batch.io.GcpBatchAttachedDisk
+import cromwell.backend.google.batch.models.VpcAndSubnetworkProjectLabelValues
+
+import scala.jdk.CollectionConverters._
+
+class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransferConfiguration) extends GcpBatchRequestFactory
+  with BatchUtilityConversions
+  with UserRunnable
+  with ContainerSetup
+  with Localization
+  with Delocalization
+  with MemoryRetryCheckRunnable
+  with MonitoringRunnable
+  with CheckpointingRunnable {
+
+  override def queryRequest(jobName: JobName): GetJobRequest = GetJobRequest.newBuilder.setName(jobName.toString).build
+
+  override def abortRequest(jobName: JobName): DeleteJobRequest = DeleteJobRequest.newBuilder.setName(jobName.toString).build()
+
+
+  def createNetworkWithVPC(vpcAndSubnetworkProjectLabelValues: VpcAndSubnetworkProjectLabelValues, data: GcpBatchRequest): NetworkInterface.Builder = {
+
+    val network = NetworkInterface
+      .newBuilder
+      .setNoExternalIpAddress(data.gcpBatchParameters.runtimeAttributes.noAddress)
+      .setNetwork(vpcAndSubnetworkProjectLabelValues.networkName(data.gcpBatchParameters.projectId))
+
+    vpcAndSubnetworkProjectLabelValues
+      .subnetNameOption(data.gcpBatchParameters.projectId)
+      .foreach(network.setSubnetwork)
+
+    network
+
+  }
+
+  def createNetwork(data: GcpBatchRequest): NetworkInterface.Builder = {
+    data.createParameters.vpcNetworkAndSubnetworkProjectLabels match {
+      case Some(vpcAndSubnetworkProjectLabelValues) => createNetworkWithVPC(vpcAndSubnetworkProjectLabelValues, data)
+      case _ => NetworkInterface.newBuilder().setNoExternalIpAddress(data.createParameters.runtimeAttributes.noAddress)
+    }
+  }
+
+  private def createComputeResource(cpu: Long, memory: Long, bootDiskSizeMb: Long) = {
+    ComputeResource
+      .newBuilder
+      .setCpuMilli(cpu)
+      .setMemoryMib(memory)
+      .setBootDiskMib(bootDiskSizeMb)
+      .build
+  }
+
+  private def createInstancePolicy(cpuPlatform: String, spotModel: ProvisioningModel, accelerators: Option[Accelerator.Builder], attachedDisks: List[AttachedDisk]) = {
+
+    //set GPU count to 0 if not included in workflow
+    val gpuAccelerators = accelerators.getOrElse(Accelerator.newBuilder.setCount(0).setType(""))
+    val instancePolicy = InstancePolicy
+      .newBuilder
+      .setProvisioningModel(spotModel)
+      .addAllDisks(attachedDisks.asJava)
+      .setMinCpuPlatform(cpuPlatform)
+      .buildPartial()
+
+    //add GPUs if GPU count is greater than 1
+    if (gpuAccelerators.getCount >= 1) {
+      val instancePolicyGpu = instancePolicy.toBuilder
+      instancePolicyGpu.addAccelerators(gpuAccelerators).build
+      instancePolicyGpu
+    } else {
+      instancePolicy.toBuilder
+    }
+
+  }
+
+
+  private def createNetworkPolicy(networkInterface: NetworkInterface): NetworkPolicy = {
+    NetworkPolicy
+      .newBuilder
+      .addNetworkInterfaces(0, networkInterface)
+      .build
+  }
+
+  private def createTaskSpec(runnables: List[Runnable], computeResource: ComputeResource, retryCount: Int, durationInSeconds: Long, volumes: List[Volume]) = {
+    TaskSpec
+      .newBuilder
+      .addAllRunnables(runnables.asJava)
+      .setComputeResource(computeResource)
+      .addAllVolumes(volumes.asJava)
+      .setMaxRetryCount(retryCount)
+      .setMaxRunDuration(Duration
+        .newBuilder
+        .setSeconds(durationInSeconds)
+        .build)
+  }
+
+  private def createTaskGroup(taskCount: Long, task: TaskSpec.Builder): TaskGroup = {
+    TaskGroup
+      .newBuilder
+      .setTaskCount(taskCount)
+      .setTaskSpec(task)
+      .build
+
+  }
+
+  private def createAllocationPolicy(data: GcpBatchRequest, locationPolicy: LocationPolicy, instancePolicy: InstancePolicy, networkPolicy: NetworkPolicy, serviceAccount: ServiceAccount) = {
+    AllocationPolicy
+      .newBuilder
+      .setLocation(locationPolicy)
+      .setNetwork(networkPolicy)
+      .putLabels("cromwell-workflow-id", toLabel(data.workflowId.toString)) //label for workflow from WDL
+      .putLabels("goog-batch-worker", "true")
+      .putAllLabels((data.createParameters.googleLabels.map(label => label.key -> label.value).toMap.asJava))
+      .setServiceAccount(serviceAccount)
+      .addInstances(InstancePolicyOrTemplate
+        .newBuilder
+        .setPolicy(instancePolicy)
+        .build)
+      .build
+  }
+
+  override def submitRequest(data: GcpBatchRequest): CreateJobRequest = {
+
+    val batchAttributes = data.gcpBatchParameters.batchAttributes
+    val runtimeAttributes = data.gcpBatchParameters.runtimeAttributes
+    val createParameters = data.createParameters
+    val retryCount = data.gcpBatchParameters.runtimeAttributes.preemptible
+    val allDisksToBeMounted: Seq[GcpBatchAttachedDisk] = createParameters.adjustedSizeDisks ++ createParameters.referenceDisksForLocalizationOpt.getOrElse(List.empty)
+    val gcpBootDiskSizeMb = convertGbToMib(runtimeAttributes)
+
+    // set parent for metadata storage of job information
+    lazy val parent = s"projects/${data.gcpBatchParameters.projectId}/locations/${data.gcpBatchParameters.region}"
+    val gcpSa = ServiceAccount.newBuilder.setEmail(batchAttributes.computeServiceAccount).build
+
+    // make zones path
+    val zones = toZonesPath(runtimeAttributes.zones)
+
+    // convert to millicores for Batch
+    val cpu = runtimeAttributes.cpu
+    val cpuCores = toCpuCores(cpu.toString.toLong)
+
+    val cpuPlatform = runtimeAttributes.cpuPlatform.getOrElse("")
+
+    // convert memory to MiB for Batch
+    val memory = toMemMib(runtimeAttributes.memory)
+
+    // Determine max runtime for Batch
+    val durationInSeconds: Long = data.gcpBatchParameters.batchAttributes.batchTimeout.toSeconds
+
+    // Batch defaults to 1 task
+    val taskCount: Long = 1
+
+    println(f"command script container path ${data.createParameters.commandScriptContainerPath}")
+    println(f"cloud workflow root ${data.createParameters.cloudWorkflowRoot}")
+    println(f"all parameters:\n ${data.createParameters.allParameters.mkString("\n")}")
+
+    // parse preemption value and set value for Spot. Spot is replacement for preemptible
+    val spotModel = toProvisioningModel(runtimeAttributes.preemptible)
+
+    // Set GPU accelerators
+    val accelerators = runtimeAttributes.gpuResource.map(toAccelerator)
+
+    val networkInterface = createNetwork(data = data)
+    val networkPolicy = createNetworkPolicy(networkInterface.build())
+    val allDisks = toDisks(allDisksToBeMounted)
+    val allVolumes = toVolumes(allDisksToBeMounted)
+
+    val containerSetup: List[Runnable] = containerSetupRunnables(allVolumes)
+    val localization: List[Runnable] = localizeRunnables(createParameters, allVolumes)
+    val userRunnable: List[Runnable] = userRunnables(data.createParameters, allVolumes)
+    val memoryRetryRunnable: List[Runnable] = checkForMemoryRetryRunnables(createParameters, allVolumes)
+    val deLocalization: List[Runnable] = deLocalizeRunnables(createParameters, allVolumes)
+    val monitoringSetup: List[Runnable] = monitoringSetupRunnables(createParameters, allVolumes)
+    val monitoringShutdown: List[Runnable] = monitoringShutdownRunnables(createParameters)
+    val checkpointingStart: List[Runnable] = checkpointingSetupRunnables(createParameters, allVolumes)
+    val checkpointingShutdown: List[Runnable] = checkpointingShutdownRunnables(createParameters, allVolumes)
+    val sshAccess: List[Runnable] = List.empty //sshAccessActions(createPipelineParameters, mounts)
+
+    val sortedRunnables: List[Runnable] = RunnableUtils.sortRunnables(
+      containerSetup = containerSetup,
+        localization = localization,
+        userRunnable = userRunnable,
+        memoryRetryRunnable = memoryRetryRunnable,
+        deLocalization = deLocalization,
+        monitoringSetup = monitoringSetup,
+        monitoringShutdown = monitoringShutdown,
+        checkpointingStart = checkpointingStart,
+        checkpointingShutdown = checkpointingShutdown,
+        sshAccess = sshAccess,
+        isBackground = _.getBackground,
+      )
+
+    val computeResource = createComputeResource(cpuCores, memory, gcpBootDiskSizeMb)
+    val taskSpec = createTaskSpec(sortedRunnables, computeResource, retryCount, durationInSeconds, allVolumes)
+    val taskGroup: TaskGroup = createTaskGroup(taskCount, taskSpec)
+    val instancePolicy = createInstancePolicy(cpuPlatform, spotModel, accelerators, allDisks)
+    val locationPolicy = LocationPolicy.newBuilder.addAllowedLocations(zones).build
+    val allocationPolicy = createAllocationPolicy(data, locationPolicy, instancePolicy.build, networkPolicy, gcpSa)
+    val job = Job
+      .newBuilder
+      .addTaskGroups(taskGroup)
+      .setAllocationPolicy(allocationPolicy)
+      .putLabels("submitter", "cromwell") // label to signify job submitted by cromwell for larger tracking purposes within GCP batch
+      .putLabels("goog-batch-worker", "true")
+      .putAllLabels((data.createParameters.googleLabels.map(label => label.key -> label.value).toMap.asJava))
+      .setLogsPolicy(LogsPolicy
+        .newBuilder
+        .setDestination(Destination.CLOUD_LOGGING)
+        .build)
+
+    println(f"job shell ${data.createParameters.jobShell}")
+    println(f"script container path ${data.createParameters.commandScriptContainerPath}")
+    println(f"labels ${data.createParameters.googleLabels}")
+
+    CreateJobRequest
+      .newBuilder
+      .setParent(parent)
+      .setJob(job)
+      .setJobId(data.jobName)
+      .build()
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchAuths.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchAuths.scala
new file mode 100644
index 00000000000..7dabe4ca46d
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchAuths.scala
@@ -0,0 +1,5 @@
+package cromwell.backend.google.batch.authentication
+
+import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
+
+case class GcpBatchAuths(genomics: GoogleAuthMode, gcs: GoogleAuthMode)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchVMAuthentication.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchVMAuthentication.scala
new file mode 100644
index 00000000000..4f14d1b92b1
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchVMAuthentication.scala
@@ -0,0 +1,60 @@
+package cromwell.backend.google.batch.authentication
+
+import cats.data.Validated.{Invalid, Valid}
+import cats.syntax.validated._
+import common.validation.ErrorOr._
+import common.validation.Validation._
+import cromwell.cloudsupport.gcp.GoogleConfiguration
+import cromwell.core.DockerCredentials
+import spray.json.{JsString, JsValue}
+
+/**
+  * Interface for Authentication information that can be included as a json object in the file uploaded to GCS
+  * upon workflow creation and used in the VM.
+  */
+sealed trait GcpBatchAuthObject {
+  def context: String
+
+  def map: Map[String, JsValue]
+
+  def toMap: Map[String, Map[String, JsValue]] = Map(context -> map)
+}
+
+object GcpBatchDockerCredentials {
+
+  def apply(dockerCredentials: DockerCredentials, googleConfig: GoogleConfiguration): GcpBatchDockerCredentials = {
+    // If there's an encryption key defined there must be a valid auth defined to encrypt it.
+    val authValidation = dockerCredentials.keyName match {
+      case None => ().validNel // fine
+      case _ =>
+        for {
+          authName <- dockerCredentials.authName.toErrorOr("KMS Encryption key defined for private Docker but no auth specified")
+          _ <- googleConfig.auth(authName)
+        } yield ()
+    }
+
+    authValidation match {
+      case Invalid(errors) =>
+        throw new RuntimeException(errors.toList.mkString(", "))
+      case Valid(_) =>
+        new GcpBatchDockerCredentials(
+          token = dockerCredentials.token,
+          keyName = dockerCredentials.keyName,
+          authName = dockerCredentials.authName)
+    }
+  }
+}
+
+/**
+  * Authentication information to pull docker images as the user.
+  */
+case class GcpBatchDockerCredentials(override val token: String,
+                                     override val keyName: Option[String],
+                                     override val authName: Option[String])
+  extends DockerCredentials(token = token, keyName = keyName, authName = authName) with GcpBatchAuthObject {
+
+  override val context = "docker"
+  override val map = Map(
+    "token" -> JsString(token)
+  )
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendCacheHitCopyingActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendCacheHitCopyingActor.scala
new file mode 100644
index 00000000000..a0fc2e96317
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendCacheHitCopyingActor.scala
@@ -0,0 +1,88 @@
+package cromwell.backend.google.batch.callcaching
+
+import com.google.cloud.storage.contrib.nio.CloudStorageOptions
+import common.util.TryUtil
+import cromwell.backend.BackendInitializationData
+import cromwell.backend.google.batch.models.GcpBackendInitializationData
+import cromwell.backend.io.JobPaths
+import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardCacheHitCopyingActorParams}
+import cromwell.core.CallOutputs
+import cromwell.core.io.{IoCommand, IoTouchCommand}
+import cromwell.core.path.Path
+import cromwell.core.simpleton.{WomValueBuilder, WomValueSimpleton}
+import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
+import wom.values.WomFile
+
+import scala.language.postfixOps
+import scala.util.Try
+
+class BatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams) extends StandardCacheHitCopyingActor(standardParams){
+  override protected val commandBuilder: GcsBatchCommandBuilder.type = GcsBatchCommandBuilder
+  private val cachingStrategy: BatchCacheHitDuplicationStrategy = BackendInitializationData
+    .as[GcpBackendInitializationData](standardParams.backendInitializationDataOption)
+    .gcpBatchConfiguration.batchAttributes.cacheHitDuplicationStrategy
+
+  override def processSimpletons(womValueSimpletons: Seq[WomValueSimpleton],
+                                 sourceCallRootPath: Path,
+                                ): Try[(CallOutputs, Set[IoCommand[_]])] =
+    cachingStrategy match {
+      case CopyCachedOutputs => super.processSimpletons(womValueSimpletons, sourceCallRootPath)
+      case UseOriginalCachedOutputs =>
+        val touchCommands: Seq[Try[IoTouchCommand]] = womValueSimpletons collect {
+          case WomValueSimpleton(_, wdlFile: WomFile) => getPath(wdlFile.value) flatMap GcsBatchCommandBuilder.touchCommand
+        }
+
+        TryUtil.sequence(touchCommands) map {
+          WomValueBuilder.toJobOutputs(jobDescriptor.taskCall.outputPorts, womValueSimpletons) -> _.toSet
+        }
+    }
+
+  override def extractBlacklistPrefix(path: String): Option[String] = Option(path.stripPrefix("gs://").takeWhile(_ != '/'))
+
+  override def processDetritus(sourceJobDetritusFiles: Map[String, String]
+                              ): Try[(Map[String, Path], Set[IoCommand[_]])] =
+    cachingStrategy match {
+      case CopyCachedOutputs => super.processDetritus(sourceJobDetritusFiles)
+      case UseOriginalCachedOutputs =>
+        // apply getPath on each detritus string file
+        val detritusAsPaths = detritusFileKeys(sourceJobDetritusFiles).toSeq map { key =>
+          key -> getPath(sourceJobDetritusFiles(key))
+        } toMap
+
+        // Don't forget to re-add the CallRootPathKey that has been filtered out by detritusFileKeys
+        TryUtil.sequenceMap(detritusAsPaths, "Failed to make paths out of job detritus") flatMap { newDetritus =>
+          Try {
+            // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
+            (newDetritus + (JobPaths.CallRootPathKey -> destinationCallRootPath)) ->
+              newDetritus.values.map(GcsBatchCommandBuilder.touchCommand(_).get).toSet
+          }
+        }
+    }
+
+  override protected def additionalIoCommands(sourceCallRootPath: Path,
+                                              originalSimpletons: Seq[WomValueSimpleton],
+                                              newOutputs: CallOutputs,
+                                              originalDetritus: Map[String, String],
+                                              newDetritus: Map[String, Path]): Try[List[Set[IoCommand[_]]]] = Try {
+    cachingStrategy match {
+      case UseOriginalCachedOutputs =>
+        val content =
+          s"""
+             |This directory does not contain any output files because this job matched an identical job that was previously run, thus it was a cache-hit.
+             |Cromwell is configured to not copy outputs during call caching. To change this, edit the filesystems.gcs.caching.duplication-strategy field in your backend configuration.
+             |The original outputs can be found at this location: ${sourceCallRootPath.pathAsString}
+    """.stripMargin
+
+        // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
+        List(Set(
+          GcsBatchCommandBuilder.writeCommand(
+            path = jobPaths.forCallCacheCopyAttempts.callExecutionRoot / "call_caching_placeholder.txt",
+            content = content,
+            options = Seq(CloudStorageOptions.withMimeType("text/plain")),
+          ).get
+        ))
+      case CopyCachedOutputs => List.empty
+    }
+  }
+
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendFileHashingActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendFileHashingActor.scala
new file mode 100644
index 00000000000..a3f000e7085
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendFileHashingActor.scala
@@ -0,0 +1,8 @@
+package cromwell.backend.google.batch.callcaching
+
+import cromwell.backend.standard.callcaching.{StandardFileHashingActor, StandardFileHashingActorParams}
+import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
+
+class BatchBackendFileHashingActor(standardParams: StandardFileHashingActorParams) extends StandardFileHashingActor(standardParams) {
+  override val ioCommandBuilder = GcsBatchCommandBuilder
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchCacheHitDuplicationStrategy.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchCacheHitDuplicationStrategy.scala
new file mode 100644
index 00000000000..778a0c2fefe
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchCacheHitDuplicationStrategy.scala
@@ -0,0 +1,7 @@
+package cromwell.backend.google.batch.callcaching
+
+sealed trait BatchCacheHitDuplicationStrategy
+
+case object CopyCachedOutputs extends BatchCacheHitDuplicationStrategy
+case object UseOriginalCachedOutputs extends BatchCacheHitDuplicationStrategy
+
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/errors/InvalidGcsPathsInManifestFileException.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/errors/InvalidGcsPathsInManifestFileException.scala
new file mode 100644
index 00000000000..708906e8f17
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/errors/InvalidGcsPathsInManifestFileException.scala
@@ -0,0 +1,7 @@
+package cromwell.backend.google.batch.errors
+
+import scala.util.control.NoStackTrace
+
+class InvalidGcsPathsInManifestFileException(paths: List[String]) extends Exception with NoStackTrace {
+  override def getMessage: String = s"Some of the paths in manifest file are not valid GCS paths: \n${paths.mkString("\n")}"
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/DiskType.java b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/DiskType.java
new file mode 100644
index 00000000000..1adfa3e53b9
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/DiskType.java
@@ -0,0 +1,15 @@
+package cromwell.backend.google.batch.io;
+
+public enum DiskType {
+    LOCAL("LOCAL", "LOCAL_SSD"),
+    SSD("SSD", "PERSISTENT_SSD"),
+    HDD("HDD", "PERSISTENT_HDD");
+
+    public final String diskTypeName;
+    public final String googleTypeName;
+
+    DiskType(final String diskTypeName, final String googleTypeName) {
+        this.diskTypeName = diskTypeName;
+        this.googleTypeName = googleTypeName;
+    }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala
new file mode 100644
index 00000000000..0e49985e24f
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala
@@ -0,0 +1,98 @@
+package cromwell.backend.google.batch.io
+
+import cats.data.Validated._
+import cats.syntax.apply._
+import cats.syntax.validated._
+import common.exception.MessageAggregation
+import common.validation.ErrorOr._
+import cromwell.backend.DiskPatterns._
+import cromwell.core.path.{DefaultPathBuilder, Path}
+import wdl4s.parser.MemoryUnit
+import wom.format.MemorySize
+import wom.values._
+
+import scala.util.Try
+
+object GcpBatchAttachedDisk {
+  def parse(s: String): Try[GcpBatchAttachedDisk] = {
+
+    def sizeGbValidation(sizeGbString: String): ErrorOr[Int] = validateLong(sizeGbString).map(_.toInt)
+
+    def diskTypeValidation(diskTypeString: String): ErrorOr[DiskType] = validateDiskType(diskTypeString)
+
+    val validation: ErrorOr[GcpBatchAttachedDisk] = s match {
+      case WorkingDiskPattern(sizeGb, diskType) => (validateDiskType(diskType), sizeGbValidation(sizeGb)) mapN {
+        GcpBatchWorkingDisk.apply
+      }
+      case MountedDiskPattern(mountPoint, sizeGb, diskType) => (sizeGbValidation(sizeGb), diskTypeValidation(diskType)) mapN { (s, dt) => PipelinesApiEmptyMountedDisk(dt, s, DefaultPathBuilder.get(mountPoint)) }
+      case _ => s"Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: '$s'".invalidNel
+    }
+
+    Try(validation match {
+      case Valid(localDisk) => localDisk
+      case Invalid(nels) =>
+        throw new UnsupportedOperationException with MessageAggregation {
+          val exceptionContext = ""
+          val errorMessages: List[String] = nels.toList
+        }
+    })
+  }
+
+  private def validateDiskType(diskTypeName: String): ErrorOr[DiskType] = {
+    DiskType.values().find(_.diskTypeName == diskTypeName) match {
+      case Some(diskType) => diskType.validNel
+      case None =>
+        val diskTypeNames = DiskType.values.map(_.diskTypeName).mkString(", ")
+        s"Disk TYPE $diskTypeName should be one of $diskTypeNames".invalidNel
+    }
+  }
+
+  private def validateLong(value: String): ErrorOr[Long] = {
+    try {
+      value.toLong.validNel
+    } catch {
+      case _: IllegalArgumentException => s"$value not convertible to a Long".invalidNel
+    }
+  }
+
+  implicit class EnhancedDisks(val disks: Seq[GcpBatchAttachedDisk]) extends AnyVal {
+    def adjustWorkingDiskWithNewMin(minimum: MemorySize, onAdjustment: => Unit): Seq[GcpBatchAttachedDisk] = disks map {
+      case disk: GcpBatchWorkingDisk if disk == GcpBatchWorkingDisk.Default && disk.sizeGb < minimum.to(MemoryUnit.GB).amount.toInt =>
+        onAdjustment
+        disk.copy(sizeGb = minimum.to(MemoryUnit.GB).amount.toInt)
+      case other => other
+    }
+  }
+}
+
+trait GcpBatchAttachedDisk {
+  def name: String
+  def diskType: DiskType
+  def sizeGb: Int
+  def mountPoint: Path
+}
+
+case class PipelinesApiEmptyMountedDisk(diskType: DiskType, sizeGb: Int, mountPoint: Path) extends GcpBatchAttachedDisk {
+  val name = s"d-${mountPoint.pathAsString.md5Sum}"
+
+  override def toString: String = s"$mountPoint $sizeGb ${diskType.diskTypeName}"
+}
+
+object GcpBatchWorkingDisk {
+  val MountPoint: Path = DefaultPathBuilder.get("/mnt/disks/cromwell_root")
+  val Name = "local-disk"
+  val Default = GcpBatchWorkingDisk(DiskType.SSD, 10)
+}
+
+case class GcpBatchWorkingDisk(diskType: DiskType, sizeGb: Int) extends GcpBatchAttachedDisk {
+  val mountPoint: Path = GcpBatchWorkingDisk.MountPoint
+  val name: String = GcpBatchWorkingDisk.Name
+
+  override def toString: String = s"$name $sizeGb ${diskType.diskTypeName}"
+}
+
+case class GcpBatchReferenceFilesDisk(image: String, sizeGb: Int) extends GcpBatchAttachedDisk {
+  val mountPoint: Path = DefaultPathBuilder.get(s"/mnt/${image.md5Sum}")
+  val name: String = s"d-${mountPoint.pathAsString.md5Sum}"
+  val diskType: DiskType = DiskType.HDD
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/package.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/package.scala
new file mode 100644
index 00000000000..25489ff6869
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/package.scala
@@ -0,0 +1,31 @@
+
+package cromwell.backend.google.batch
+
+import com.google.api.client.http.HttpResponseException
+import com.google.cloud.storage.contrib.nio.CloudStorageOptions
+import cromwell.core.path.Path
+
+package object io {
+  implicit class PathEnhanced(val path: Path) extends AnyVal {
+
+    def writeAsJson(content: String): Path = {
+      path.writeBytes(content.getBytes.iterator)(Seq(CloudStorageOptions.withMimeType("application/json")))
+    }
+
+    def writeAsText(content: String): Path = {
+      path.writeBytes(content.getBytes.iterator)(Seq(CloudStorageOptions.withMimeType("text/plain")))
+    }
+  }
+
+  private [batch] def isFatalJesException(t: Throwable): Boolean = t match {
+    case e: HttpResponseException if e.getStatusCode == 403 => true
+    case e: HttpResponseException if e.getStatusCode == 400 && e.getContent.contains("INVALID_ARGUMENT") => true
+    case _ => false
+  }
+
+  private [batch] def isTransientJesException(t: Throwable): Boolean = t match {
+    // Quota exceeded
+    case e: HttpResponseException if e.getStatusCode == 429 => true
+    case _ => false
+  }
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/CreateGcpBatchParameters.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/CreateGcpBatchParameters.scala
new file mode 100644
index 00000000000..d6258169fa8
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/CreateGcpBatchParameters.scala
@@ -0,0 +1,10 @@
+package cromwell.backend.google.batch.models
+
+import cromwell.backend.BackendJobDescriptor
+
+case class CreateGcpBatchParameters(jobDescriptor: BackendJobDescriptor,
+                                    runtimeAttributes: GcpBatchRuntimeAttributes,
+                                    batchAttributes: GcpBatchConfigurationAttributes,
+                                    projectId: String,
+                                    region: String
+                                   )
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBackendInitializationData.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBackendInitializationData.scala
new file mode 100644
index 00000000000..47169b30f0a
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBackendInitializationData.scala
@@ -0,0 +1,16 @@
+package cromwell.backend.google.batch.models
+
+import com.google.auth.Credentials
+import cromwell.backend.google.batch.util.BatchExpressionFunctions
+import cromwell.backend.standard.{StandardInitializationData, StandardValidatedRuntimeAttributesBuilder}
+
+case class GcpBackendInitializationData(
+                                         override val workflowPaths: GcpBatchWorkflowPaths,
+                                         override val runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder,
+                                         gcpBatchConfiguration: GcpBatchConfiguration,
+                                         gcsCredentials: Credentials,
+                                         privateDockerEncryptionKeyName: Option[String],
+                                         privateDockerEncryptedToken: Option[String],
+                                         vpcNetworkAndSubnetworkProjectLabels: Option[VpcAndSubnetworkProjectLabelValues]
+
+                                       ) extends StandardInitializationData(workflowPaths, runtimeAttributesBuilder, classOf[BatchExpressionFunctions] )
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfiguration.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfiguration.scala
new file mode 100644
index 00000000000..dc397c5755e
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfiguration.scala
@@ -0,0 +1,38 @@
+package cromwell.backend.google.batch.models
+
+import com.typesafe.config.Config
+import cromwell.backend.BackendConfigurationDescriptor
+import cromwell.backend.google.batch.authentication.{GcpBatchAuths, GcpBatchDockerCredentials}
+import cromwell.cloudsupport.gcp.GoogleConfiguration
+import cromwell.core.BackendDockerConfiguration
+import net.ceedubs.ficus.Ficus._
+import spray.json._
+
+import scala.concurrent.duration.FiniteDuration
+
+
+class GcpBatchConfiguration(val configurationDescriptor: BackendConfigurationDescriptor,
+                            val googleConfig: GoogleConfiguration,
+                            val batchAttributes: GcpBatchConfigurationAttributes
+                           ) extends DefaultJsonProtocol {
+
+  val batchAuths: GcpBatchAuths = batchAttributes.auths
+  val root: String = configurationDescriptor.backendConfig.getString("root")
+  val batchTimeout: FiniteDuration = batchAttributes.batchTimeout
+  val runtimeConfig: Option[Config] = configurationDescriptor.backendRuntimeAttributesConfig
+
+
+  val dockerCredentials: Option[GcpBatchDockerCredentials] = {
+    BackendDockerConfiguration.build(configurationDescriptor.backendConfig).dockerCredentials map { creds =>
+      GcpBatchDockerCredentials.apply(creds, googleConfig)
+   }
+  }
+
+  val dockerEncryptionKeyName: Option[String] = dockerCredentials flatMap { _.keyName }
+  val dockerEncryptionAuthName: Option[String] = dockerCredentials flatMap { _.authName }
+  val dockerToken: Option[String] = dockerCredentials map { _.token }
+
+  val jobShell: String = configurationDescriptor.backendConfig.as[Option[String]]("job-shell").getOrElse(
+    configurationDescriptor.globalConfig.getOrElse("system.job-shell", "/bin/bash"))
+
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributes.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributes.scala
new file mode 100644
index 00000000000..0a57b0a2a5e
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributes.scala
@@ -0,0 +1,465 @@
+package cromwell.backend.google.batch.models
+
+import cats.data.Validated._
+import cats.data.{NonEmptyList, Validated}
+import cats.implicits._
+import com.typesafe.config.{Config, ConfigValue}
+import com.typesafe.scalalogging.StrictLogging
+import common.exception.MessageAggregation
+import common.validation.ErrorOr._
+import common.validation.Validation._
+import cromwell.backend.CommonBackendConfigurationAttributes
+import cromwell.backend.google.batch._
+import cromwell.backend.google.batch.authentication.GcpBatchAuths
+import cromwell.backend.google.batch.callcaching.{BatchCacheHitDuplicationStrategy, CopyCachedOutputs, UseOriginalCachedOutputs}
+import cromwell.backend.google.batch.io.GcpBatchReferenceFilesDisk
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.{BatchRequestTimeoutConfiguration, GcsTransferConfiguration, VirtualPrivateCloudConfiguration}
+import cromwell.backend.google.batch.util.{DockerImageCacheEntry, GcpBatchDockerCacheMappingOperations, GcpBatchReferenceFilesMappingOperations}
+import cromwell.cloudsupport.gcp.GoogleConfiguration
+import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
+import cromwell.filesystems.gcs.GcsPathBuilder
+import cromwell.filesystems.gcs.GcsPathBuilder.ValidFullGcsPath
+import eu.timepit.refined.api.Refined
+import eu.timepit.refined.numeric.Positive
+import eu.timepit.refined.{refineMV, refineV}
+import net.ceedubs.ficus.Ficus._
+import org.slf4j.{Logger, LoggerFactory}
+
+import scala.concurrent.duration._
+import scala.jdk.CollectionConverters._
+import scala.util.matching.Regex
+import scala.util.{Failure, Success, Try}
+
+case class GcpBatchConfigurationAttributes(project: String,
+                                           computeServiceAccount: String,
+                                           auths: GcpBatchAuths,
+                                           restrictMetadataAccess: Boolean,
+                                           dockerhubToken: String,
+                                           enableFuse: Boolean,
+                                           executionBucket: String,
+                                           location: String,
+                                           maxPollingInterval: Int,
+                                           qps: Int Refined Positive,
+                                           cacheHitDuplicationStrategy: BatchCacheHitDuplicationStrategy,
+                                           requestWorkers: Int Refined Positive,
+                                           batchTimeout: FiniteDuration,
+                                           logFlushPeriod: Option[FiniteDuration],
+                                           gcsTransferConfiguration: GcsTransferConfiguration,
+                                           virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
+                                           batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration,
+                                           referenceFileToDiskImageMappingOpt: Option[Map[String, GcpBatchReferenceFilesDisk]],
+                                           dockerImageToCacheDiskImageMappingOpt: Option[Map[String, DockerImageCacheEntry]],
+                                           checkpointingInterval: FiniteDuration
+                                          )
+
+object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperations with GcpBatchReferenceFilesMappingOperations with StrictLogging {
+
+  /**
+    * param transferAttempts This is the number of attempts, not retries, hence it is positive.
+    */
+  case class GcsTransferConfiguration(transferAttempts: Int Refined Positive, parallelCompositeUploadThreshold: String)
+
+  final case class VirtualPrivateCloudLabels(network: String, subnetwork: Option[String], auth: GoogleAuthMode)
+
+  final case class VirtualPrivateCloudLiterals(network: String, subnetwork: Option[String])
+
+  final case class VirtualPrivateCloudConfiguration(labelsOption: Option[VirtualPrivateCloudLabels],
+                                                    literalsOption: Option[VirtualPrivateCloudLiterals],
+                                                   )
+
+  final case class BatchRequestTimeoutConfiguration(readTimeoutMillis: Option[Int Refined Positive], connectTimeoutMillis: Option[Int Refined Positive])
+
+
+  lazy val Logger: Logger = LoggerFactory.getLogger("BatchConfiguration")
+
+  val BatchApiDefaultQps = 1000
+  val DefaultGcsTransferAttempts: Refined[Int, Positive] = refineMV[Positive](3)
+
+  val checkpointingIntervalKey = "checkpointing-interval"
+
+  private val batchKeys = CommonBackendConfigurationAttributes.commonValidConfigurationAttributeKeys ++ Set(
+    "project",
+    "root",
+    "maximum-polling-interval",
+    "genomics",
+    "genomics.location",
+    "genomics.compute-service-account",
+    "genomics.auth",
+    "genomics.restrict-metadata-access",
+    "genomics.enable-fuse",
+    "genomics-api-queries-per-100-seconds",
+    "genomics.localization-attempts",
+    "genomics.parallel-composite-upload-threshold",
+    "filesystems",
+    "filesystems.drs.auth",
+    "filesystems.gcs.auth",
+    "filesystems.gcs.project",
+    "filesystems.gcs.caching.duplication-strategy",
+    "concurrent-job-limit",
+    "request-workers",
+    "batch-timeout",
+    "batch-requests.timeouts.read",
+    "batch-requests.timeouts.connect",
+    "default-runtime-attributes.bootDiskSizeGb",
+    "default-runtime-attributes.noAddress",
+    "default-runtime-attributes.preemptible",
+    "default-runtime-attributes.zones",
+    "virtual-private-cloud",
+    "virtual-private-cloud.network-name",
+    "virtual-private-cloud.subnetwork-name",
+    "virtual-private-cloud.network-label-key",
+    "virtual-private-cloud.subnetwork-label-key",
+    "virtual-private-cloud.auth",
+    "reference-disk-localization-manifests",
+    "docker-image-cache-manifest-file",
+    checkpointingIntervalKey
+  )
+
+  private val deprecatedJesKeys: Map[String, String] = Map(
+    "genomics.default-zones" -> "default-runtime-attributes.zones"
+  )
+
+  def apply(googleConfig: GoogleConfiguration, backendConfig: Config, backendName: String): GcpBatchConfigurationAttributes = {
+
+
+    def vpcErrorMessage(missingKeys: List[String]) = s"Virtual Private Cloud configuration is invalid. Missing keys: `${missingKeys.mkString(",")}`.".invalidNel
+
+    def validateVPCLabelsConfig(networkOption: Option[String],
+                                subnetworkOption: Option[String],
+                                authOption: Option[String],
+                               ): ErrorOr[Option[VirtualPrivateCloudLabels]] = {
+      (networkOption, subnetworkOption, authOption) match {
+        case (Some(network), _, Some(auth)) => googleConfig.auth(auth) match {
+          case Valid(validAuth) =>
+            Option(VirtualPrivateCloudLabels(network, subnetworkOption, validAuth)).validNel
+          case Invalid(error) => s"Auth $auth is not valid for Virtual Private Cloud configuration. Reason: $error".invalidNel
+        }
+        case (Some(_), _, None) => vpcErrorMessage(List("auth"))
+        case (None, _, Some(_)) => vpcErrorMessage(List("network-label-key"))
+        case (None, Some(_), None) => vpcErrorMessage(List("network-label-key", "auth"))
+        case (None, None, None) => None.validNel
+      }
+    }
+
+
+    def validateVPCLiteralsConfig(networkNameOption: Option[String],
+                                  subnetworkNameOption: Option[String],
+                                 ): ErrorOr[Option[VirtualPrivateCloudLiterals]] = {
+      (networkNameOption, subnetworkNameOption) match {
+        case (None, Some(_)) => vpcErrorMessage(List("network-name"))
+        case (Some(networkName), _) => Option(VirtualPrivateCloudLiterals(networkName, subnetworkNameOption)).valid
+        case (None, None) => None.valid
+      }
+    }
+
+    def validateVPCConfig(networkNameOption: Option[String],
+                          subnetworkNameOption: Option[String],
+                          networkLabelOption: Option[String],
+                          subnetworkLabelOption: Option[String],
+                          authOption: Option[String],
+                         ): ErrorOr[VirtualPrivateCloudConfiguration] = {
+      val vpcLabelsValidation =
+        validateVPCLabelsConfig(networkLabelOption, subnetworkLabelOption, authOption)
+      val vpcLiteralsValidation =
+        validateVPCLiteralsConfig(networkNameOption, subnetworkNameOption)
+      (vpcLabelsValidation, vpcLiteralsValidation) mapN VirtualPrivateCloudConfiguration
+    }
+
+    val configKeys = backendConfig.entrySet().asScala.toSet map { entry: java.util.Map.Entry[String, ConfigValue] => entry.getKey }
+    warnNotRecognized(configKeys, batchKeys, backendName, Logger)
+
+
+    def warnDeprecated(keys: Set[String], deprecated: Map[String, String], logger: Logger): Unit = {
+      val deprecatedKeys = keys.intersect(deprecated.keySet)
+      deprecatedKeys foreach { key => logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}") }
+    }
+
+    warnDeprecated(configKeys, deprecatedJesKeys, Logger)
+
+
+    val project: ErrorOr[String] = validate {
+      backendConfig.as[String]("project")
+    }
+    val executionBucket: ErrorOr[String] = validate {
+      backendConfig.as[String]("root")
+    }
+    val location: ErrorOr[String] = validate {
+      backendConfig.as[String]("genomics.location")
+    }
+    val maxPollingInterval: Int = backendConfig.as[Option[Int]]("maximum-polling-interval").getOrElse(600)
+    val computeServiceAccount: String = backendConfig.as[Option[String]]("genomics.compute-service-account").getOrElse("default")
+    val genomicsAuthName: ErrorOr[String] = validate {
+      backendConfig.as[String]("genomics.auth")
+    }
+    val genomicsRestrictMetadataAccess: ErrorOr[Boolean] = validate {
+      backendConfig.as[Option[Boolean]]("genomics.restrict-metadata-access").getOrElse(false)
+    }
+    val genomicsEnableFuse: ErrorOr[Boolean] = validate {
+      backendConfig.as[Option[Boolean]]("genomics.enable-fuse").getOrElse(false)
+    }
+
+    val dockerhubToken: ErrorOr[String] = validate {
+      backendConfig.as[Option[String]]("dockerhub.token").getOrElse("")
+    }
+
+    val gcsFilesystemAuthName: ErrorOr[String] = validate {
+      backendConfig.as[String]("filesystems.gcs.auth")
+    }
+    val qpsValidation = validateQps(backendConfig)
+    val duplicationStrategy = validate {
+      backendConfig.as[Option[String]]("filesystems.gcs.caching.duplication-strategy").getOrElse("copy") match {
+        case "copy" => CopyCachedOutputs
+        case "reference" => UseOriginalCachedOutputs
+        case other => throw new IllegalArgumentException(s"Unrecognized caching duplication strategy: $other. Supported strategies are copy and reference. See reference.conf for more details.")
+      }
+    }
+    val requestWorkers: ErrorOr[Int Refined Positive] = validatePositiveInt(backendConfig.as[Option[Int]]("request-workers").getOrElse(3), "request-workers")
+
+    val batchTimeout: FiniteDuration = backendConfig.getOrElse("batch-timeout", 7.days)
+
+    val logFlushPeriod: Option[FiniteDuration] = backendConfig.as[Option[FiniteDuration]]("log-flush-period") match {
+      case Some(duration) if duration.isFinite => Option(duration)
+      // "Inf" disables upload
+      case Some(_) => None
+      // Defaults to 1 minute
+      case None => Option(1.minute)
+    }
+
+    val parallelCompositeUploadThreshold = validateGsutilMemorySpecification(backendConfig, "genomics.parallel-composite-upload-threshold")
+
+    val localizationAttempts: ErrorOr[Int Refined Positive] = backendConfig.as[Option[Int]]("genomics.localization-attempts")
+      .map(attempts => validatePositiveInt(attempts, "genomics.localization-attempts"))
+      .getOrElse(DefaultGcsTransferAttempts.validNel)
+
+    val gcsTransferConfiguration: ErrorOr[GcsTransferConfiguration] =
+      (localizationAttempts, parallelCompositeUploadThreshold) mapN GcsTransferConfiguration.apply
+
+    val vpcNetworkName: ErrorOr[Option[String]] = validate {
+      backendConfig.getAs[String]("virtual-private-cloud.network-name")
+    }
+    val vpcSubnetworkName: ErrorOr[Option[String]] = validate {
+      backendConfig.getAs[String]("virtual-private-cloud.subnetwork-name")
+    }
+    val vpcNetworkLabel: ErrorOr[Option[String]] = validate {
+      backendConfig.getAs[String]("virtual-private-cloud.network-label-key")
+    }
+    val vpcSubnetworkLabel: ErrorOr[Option[String]] = validate {
+      backendConfig.getAs[String]("virtual-private-cloud.subnetwork-label-key")
+    }
+    val vpcAuth: ErrorOr[Option[String]] = validate {
+      backendConfig.getAs[String]("virtual-private-cloud.auth")
+    }
+
+    val virtualPrivateCloudConfiguration: ErrorOr[VirtualPrivateCloudConfiguration] = {
+      (vpcNetworkName, vpcSubnetworkName, vpcNetworkLabel, vpcSubnetworkLabel, vpcAuth) flatMapN validateVPCConfig
+    }
+
+    val batchRequestsReadTimeout = readOptionalPositiveMillisecondsIntFromDuration(backendConfig, "batch-requests.timeouts.read")
+    val batchRequestsConnectTimeout = readOptionalPositiveMillisecondsIntFromDuration(backendConfig, "batch-requests.timeouts.connect")
+
+    val batchRequestTimeoutConfigurationValidation = (batchRequestsReadTimeout, batchRequestsConnectTimeout) mapN { (read, connect) =>
+      BatchRequestTimeoutConfiguration(readTimeoutMillis = read, connectTimeoutMillis = connect)
+    }
+
+    val referenceDiskLocalizationManifestFiles: ErrorOr[Option[List[ManifestFile]]] = validateReferenceDiskManifestConfigs(backendConfig, backendName)
+
+    val dockerImageCacheManifestFile: ErrorOr[Option[ValidFullGcsPath]] = validateGcsPathToDockerImageCacheManifestFile(backendConfig)
+
+    val checkpointingInterval: FiniteDuration = backendConfig.getOrElse(checkpointingIntervalKey, 10.minutes)
+
+    def authGoogleConfigForBatchConfigurationAttributes(project: String,
+                                                        bucket: String,
+                                                        genomicsName: String,
+                                                        location: String,
+                                                        restrictMetadata: Boolean,
+                                                        dockerhubToken: String,
+                                                        enableFuse: Boolean,
+                                                        gcsName: String,
+                                                        qps: Int Refined Positive,
+                                                        cacheHitDuplicationStrategy: BatchCacheHitDuplicationStrategy,
+                                                        requestWorkers: Int Refined Positive,
+                                                        gcsTransferConfiguration: GcsTransferConfiguration,
+                                                        virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
+                                                        batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration,
+                                                        referenceDiskLocalizationManifestFilesOpt: Option[List[ManifestFile]],
+                                                        dockerImageCacheManifestFileOpt: Option[ValidFullGcsPath]): ErrorOr[GcpBatchConfigurationAttributes] =
+      (googleConfig.auth(genomicsName), googleConfig.auth(gcsName)) mapN {
+        (genomicsAuth, gcsAuth) =>
+          val generatedReferenceFilesMappingOpt = referenceDiskLocalizationManifestFilesOpt map {
+            generateReferenceFilesMapping(genomicsAuth, _)
+          }
+          val dockerImageToCacheDiskImageMappingOpt = dockerImageCacheManifestFileOpt map {
+            generateDockerImageToDiskImageMapping(genomicsAuth, _)
+          }
+          models.GcpBatchConfigurationAttributes(
+            project = project,
+            computeServiceAccount = computeServiceAccount,
+            auths = GcpBatchAuths(genomicsAuth, gcsAuth),
+            restrictMetadataAccess = restrictMetadata,
+            dockerhubToken = dockerhubToken,
+            enableFuse = enableFuse,
+            executionBucket = bucket,
+            location = location,
+            maxPollingInterval = maxPollingInterval,
+            qps = qps,
+            cacheHitDuplicationStrategy = cacheHitDuplicationStrategy,
+            requestWorkers = requestWorkers,
+            batchTimeout = batchTimeout,
+            logFlushPeriod = logFlushPeriod,
+            gcsTransferConfiguration = gcsTransferConfiguration,
+            virtualPrivateCloudConfiguration = virtualPrivateCloudConfiguration,
+            batchRequestTimeoutConfiguration = batchRequestTimeoutConfiguration,
+            referenceFileToDiskImageMappingOpt = generatedReferenceFilesMappingOpt,
+            dockerImageToCacheDiskImageMappingOpt = dockerImageToCacheDiskImageMappingOpt,
+            checkpointingInterval = checkpointingInterval
+          )
+      }
+
+
+    (project,
+      executionBucket,
+      genomicsAuthName,
+      location,
+      genomicsRestrictMetadataAccess,
+      dockerhubToken,
+      genomicsEnableFuse,
+      gcsFilesystemAuthName,
+      qpsValidation,
+      duplicationStrategy,
+      requestWorkers,
+      gcsTransferConfiguration,
+      virtualPrivateCloudConfiguration,
+      batchRequestTimeoutConfigurationValidation,
+      referenceDiskLocalizationManifestFiles,
+      dockerImageCacheManifestFile
+    ) flatMapN authGoogleConfigForBatchConfigurationAttributes match {
+      case Valid(r) => r
+      case Invalid(f) =>
+        throw new IllegalArgumentException with MessageAggregation {
+          override val exceptionContext = "Google Cloud Batch configuration is not valid: Errors"
+          override val errorMessages: List[String] = f.toList
+        }
+    }
+  }
+
+  private def validateSingleGcsPath(gcsPath: String): ErrorOr[ValidFullGcsPath] = {
+    GcsPathBuilder.validateGcsPath(gcsPath) match {
+      case validPath: ValidFullGcsPath => validPath.validNel
+      case invalidPath => s"Invalid GCS path: $invalidPath".invalidNel
+    }
+  }
+
+  private[batch] def validateGcsPathToDockerImageCacheManifestFile(backendConfig: Config): ErrorOr[Option[ValidFullGcsPath]] = {
+    backendConfig.getAs[String]("docker-image-cache-manifest-file") match {
+      case Some(gcsPath) => validateSingleGcsPath(gcsPath).map(Option.apply)
+      case None => None.validNel
+    }
+  }
+
+  /**
+    * Validate that the entries corresponding to "reference-disk-localization-manifests" in the specified
+    * backend are parseable as `ManifestFile`s.
+    */
+  private[batch] def validateReferenceDiskManifestConfigs(backendConfig: Config, backendName: String): ErrorOr[Option[List[ManifestFile]]] = {
+    Try(backendConfig.getAs[List[Config]]("reference-disk-localization-manifests")) match {
+      case Failure(e) =>
+        ("Error attempting to parse value for 'reference-disk-localization-manifests' as List[Config]: " +
+          e.getMessage).invalidNel
+      case Success(s) =>
+        s match {
+          case Some(configs) =>
+            import _root_.io.circe.config.parser
+            import _root_.io.circe.generic.auto._
+
+            // Unfortunately the `as` method of `config` collides with the Ficus method of the same name, so invoke its
+            // equivalent using clunkier syntax:
+            configs traverse parser.decode[ManifestFile] match {
+              case Right(manifests) =>
+                logger.info(s"Reference disks feature for $backendName backend is configured with the following reference images: ${manifests.map(_.imageIdentifier).mkString(", ")}.")
+                Option(manifests).validNel
+              case Left(err) =>
+                val message = s"Reference disks misconfigured for backend $backendName, could not parse as List[ManifestFile]"
+                logger.error(message, err.getCause)
+                s"$message: ${err.getMessage}".invalidNel
+            }
+          case None =>
+            logger.info(s"Reference disks feature for $backendName backend is not configured.")
+            None.validNel
+        }
+    }
+  }
+
+  def validateQps(config: Config): ErrorOr[Int Refined Positive] = {
+    import eu.timepit.refined._
+
+    val qp100s = config.as[Option[Int]]("genomics-api-queries-per-100-seconds").getOrElse(BatchApiDefaultQps)
+    val qpsCandidate = qp100s / 100
+
+    refineV[Positive](qpsCandidate) match {
+      case Left(_) => s"Calculated QPS for Google Genomics API ($qpsCandidate/s) was not a positive integer (supplied value was $qp100s per 100s)".invalidNel
+      case Right(refined) => refined.validNel
+    }
+  }
+
+  def validateGsutilMemorySpecification(config: Config, configPath: String): ErrorOr[String] = {
+    val entry = config.as[Option[String]](configPath)
+    entry match {
+      case None => "0".validNel
+      case Some(v@GsutilHumanBytes(_, _)) => v.validNel
+      case Some(bad) => s"Invalid gsutil memory specification in Cromwell configuration at path '$configPath': '$bad'".invalidNel
+    }
+  }
+
+  def validatePositiveInt(n: Int, configPath: String): Validated[NonEmptyList[String], Refined[Int, Positive]] = {
+    refineV[Positive](n) match {
+      case Left(_) => s"Value $n for $configPath is not strictly positive".invalidNel
+      case Right(refined) => refined.validNel
+    }
+  }
+
+  def readOptionalPositiveMillisecondsIntFromDuration(backendConfig: Config, configPath: String): ErrorOr[Option[Int Refined Positive]] = {
+
+    def validate(n: FiniteDuration) = {
+      val result: ErrorOr[Int Refined Positive] = Try(n.toMillis.toInt).toErrorOr flatMap { millisInt =>
+        refineV[Positive](millisInt) match {
+          case Left(_) => s"Value $n for $configPath is not strictly positive".invalidNel
+          case Right(refined) => refined.validNel
+        }
+      }
+
+      result.contextualizeErrors(s"Parse '$configPath' value $n as a positive Int (in milliseconds)")
+    }
+
+    backendConfig.as[Option[FiniteDuration]](configPath) match {
+      case Some(value) => validate(value).map(Option.apply)
+      case None => None.validNel
+    }
+  }
+
+  // Copy/port of gsutil's "_GenerateSuffixRegex"
+  private[batch] lazy val GsutilHumanBytes: Regex = {
+    val _EXP_STRINGS = List(
+      List("B", "bit"),
+      List("KiB", "Kibit", "K"),
+      List("MiB", "Mibit", "M"),
+      List("GiB", "Gibit", "G"),
+      List("TiB", "Tibit", "T"),
+      List("PiB", "Pibit", "P"),
+      List("EiB", "Eibit", "E"),
+    )
+
+    val suffixes = for {
+      unit <- _EXP_STRINGS
+      name <- unit
+    } yield name
+
+    // Differs from the Python original in a couple of ways:
+    //* The Python original uses named groups which are not supported in Scala regexes.
+    //   (?P<num>\d*\.\d+|\d+)\s*(?P<suffix>%s)?
+    //
+    // * The Python original lowercases both the units and the human string before running the matcher.
+    //   This Scala version turns on the (?i) case insensitive matching regex option instead.
+    val orSuffixes = suffixes.mkString("|")
+    "(?i)(\\d*\\.\\d+|\\d+)\\s*(%s)?".format(orSuffixes).r
+  }
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchCustomMachineType.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchCustomMachineType.scala
new file mode 100644
index 00000000000..84366f4e969
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchCustomMachineType.scala
@@ -0,0 +1,184 @@
+package cromwell.backend.google.batch.models
+
+import cromwell.backend.google.batch.models.CustomMachineType._
+import eu.timepit.refined.api.Refined
+import eu.timepit.refined.numeric.Positive
+import eu.timepit.refined.refineV
+import mouse.all._
+import org.slf4j.Logger
+import wdl4s.parser.MemoryUnit
+import wom.format.MemorySize
+
+import scala.math.{log, pow}
+
+/**
+  * Adjusts memory and cpu for custom machine types.
+  *
+  * For more info see:
+  * - https://cloud.google.com/compute/docs/instances/creating-instance-with-custom-machine-type
+  * - https://cloud.google.com/compute/docs/instances/creating-instance-with-custom-machine-type#specifications
+  * - https://cloud.google.com/compute/docs/instances/creating-instance-with-custom-machine-type#gcloud
+  * - https://cloud.google.com/sdk/gcloud/reference/compute/instances/create#--custom-vm-type
+  */
+trait CustomMachineType {
+  /**
+    * The vm prefix to create this custom machine type.
+    */
+  def vmTypePrefix: String
+
+  /**
+    * The minimum memory per cpu.
+    */
+  def minMemoryPerCpu: MemorySize
+
+  /**
+    * The maximum memory per cpu.
+    */
+  def maxMemoryPerCpu: MemorySize
+
+  /**
+    * The total memory for a custom machine type must be a multiple of this value.
+    */
+  def memoryFactor: MemorySize
+
+  /**
+    * Increase the cpu to the next valid amount for this machine type.
+    */
+  def validateCpu(cpu: Int Refined Positive): Int
+
+  /**
+    * Increase the memory to the next valid amount for this machine type.
+    */
+  def validateMemory(memory: MemorySize): MemorySize
+
+  /**
+    * Generates a custom machine type based on the requested memory and cpu
+    */
+  def machineType(requestedMemory: MemorySize,
+                  requestedCpu: Int Refined Positive,
+                  jobLogger: Logger,
+                 ): String = {
+    val memory = requestedMemory |> validateMemory
+    val cpu = requestedCpu |> validateCpu
+
+    val memoryPerCpuRatio = memory.bytes / cpu.toDouble
+
+    lazy val adjustedMemory = MemorySize(minMemoryPerCpu.amount * cpu.toDouble, minMemoryPerCpu.unit) |> validateMemory
+
+    lazy val adjustedCpu = refineV[Positive]((memory.bytes / maxMemoryPerCpu.bytes).ceil.toInt) match {
+      // If for some reason the above yields 0, keep the cpu value unchanged
+      case Left(_) => cpu
+      case Right(adjusted) => adjusted |> validateCpu
+    }
+
+    val (validCpu, validMemory) =
+      if (memoryPerCpuRatio < minMemoryPerCpu.bytes) {
+        // If we're under the ratio, top up the memory. Because validMemory will only increase memory (if needed),
+        // there's no risk that the call to validMemory will make the ratio invalid
+        (cpu, adjustedMemory)
+      } else if (memoryPerCpuRatio > maxMemoryPerCpu.bytes) {
+        // If we're over the ratio, top up the CPU. Because validCpu will only increase CPU (if needed), there's no risk
+        // that the call to validCpu will make the ratio invalid
+        (adjustedCpu, memory)
+      } else {
+        //
+        (cpu, memory)
+      }
+    logAdjustment(requestedCpu.value, validCpu, requestedMemory, validMemory, jobLogger)
+    s"${vmTypePrefix}custom-$validCpu-${validMemory.to(MemoryUnit.MB).amount.intValue()}"
+  }
+
+  private def logAdjustment(originalCpu: Int,
+                            adjustedCpu: Int,
+                            originalMemory: MemorySize,
+                            adjustedMemory: MemorySize,
+                            logger: Logger,
+                           ): Unit = {
+    def memoryAdjustmentLog = s"memory was adjusted from ${originalMemory.toMBString} to ${adjustedMemory.toMBString}"
+
+    def cpuAdjustmentLog = s"cpu was adjusted from $originalCpu to $adjustedCpu"
+
+    val messageOption =
+      (
+        originalCpu == adjustedCpu,
+        originalMemory.to(MemoryUnit.MB).amount == adjustedMemory.to(MemoryUnit.MB).amount,
+      ) match {
+        case (true, false) => Option(memoryAdjustmentLog)
+        case (false, true) => Option(cpuAdjustmentLog)
+        case (false, false) => Option(memoryAdjustmentLog + " and " + cpuAdjustmentLog)
+        case _ => None
+      }
+
+    messageOption foreach { message => logger.info("To comply with GCE custom machine requirements, " + message) }
+  }
+}
+
+object CustomMachineType {
+  implicit class EnhancedInformation(val information: MemorySize) extends AnyVal {
+    def asMultipleOf(factor: MemorySize): MemorySize =
+      MemorySize(factor.amount * (information.bytes / factor.bytes).ceil, factor.unit)
+
+    def toMBString: String = information.to(MemoryUnit.MB).toString
+  }
+}
+
+case object N1CustomMachineType extends CustomMachineType {
+  // For now using the legacy empty prefix that implies "n1-"
+  override val vmTypePrefix: String = ""
+  override val minMemoryPerCpu: MemorySize = MemorySize(0.9, MemoryUnit.GB)
+  override val maxMemoryPerCpu: MemorySize = MemorySize(6.5, MemoryUnit.GB)
+  override val memoryFactor: MemorySize = MemorySize(256, MemoryUnit.MB)
+
+  override def validateCpu(cpu: Refined[Int, Positive]): Int = {
+    // Either one cpu, or an even number of cpus
+    cpu.value match {
+      case 1 => 1
+      case cpu => cpu + (cpu % 2)
+    }
+  }
+
+  override def validateMemory(memory: MemorySize): MemorySize = {
+    memory.asMultipleOf(memoryFactor)
+  }
+}
+
+case object N2CustomMachineType extends CustomMachineType {
+  override val vmTypePrefix: String = "n2-"
+  override val minMemoryPerCpu: MemorySize = MemorySize(1.0, MemoryUnit.GB)
+  override val maxMemoryPerCpu: MemorySize = MemorySize(8.0, MemoryUnit.GB)
+  override val memoryFactor: MemorySize = MemorySize(256, MemoryUnit.MB)
+
+  override def validateCpu(cpu: Refined[Int, Positive]): Int = {
+    // cpus must be divisible by 2 up to 32, and higher numbers must be divisible by 4
+    cpu.value match {
+      case cpu if cpu <= 32 => cpu + (cpu % 2)
+      case cpu if cpu % 4 == 0 => cpu
+      case cpu => cpu + (4 - (cpu % 4))
+    }
+  }
+
+  override def validateMemory(memory: MemorySize): MemorySize = {
+    memory.asMultipleOf(memoryFactor)
+  }
+}
+
+case object N2DCustomMachineType extends CustomMachineType {
+  override val vmTypePrefix: String = "n2d-"
+  override val minMemoryPerCpu: MemorySize = MemorySize(0.5, MemoryUnit.GB)
+  override val maxMemoryPerCpu: MemorySize = MemorySize(8.0, MemoryUnit.GB)
+  override val memoryFactor: MemorySize = MemorySize(256, MemoryUnit.MB)
+  
+  override def validateCpu(cpu: Refined[Int, Positive]): Int = {
+    cpu.value match {
+      case cpu if cpu <= 16 => 2 max pow(2, (log(cpu.toDouble)/log(2)).ceil).toInt
+      case cpu if cpu > 16 && cpu <= 96 && cpu % 16 == 0 => cpu
+      case cpu if cpu > 16 && cpu <= 96 => cpu + 16 - (cpu % 16)
+      case cpu if cpu > 96 => 96
+    }
+  }
+
+  override def validateMemory(memory: MemorySize): MemorySize = {
+    memory.asMultipleOf(memoryFactor)
+  }
+}
+
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchJobPaths.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchJobPaths.scala
new file mode 100644
index 00000000000..923e5dc16f5
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchJobPaths.scala
@@ -0,0 +1,43 @@
+package cromwell.backend.google.batch.models
+
+import cromwell.backend.BackendJobDescriptorKey
+import cromwell.backend.io.JobPaths
+import cromwell.core.path.Path
+
+object GcpBatchJobPaths {
+
+  val BatchLogPathKey = "jesLog"
+  val BatchMonitoringKey = "monitoring"
+  val BatchMonitoringImageKey = "monitoringImage"
+  val BatchExecParamName = "exec"
+  val GcsTransferLibraryName = "gcs_transfer.sh"
+  val GcsLocalizationScriptName = "gcs_localization.sh"
+  val GcsDelocalizationScriptName = "gcs_delocalization.sh"
+  val DrsLocalizationManifestName = "drs_manifest"
+
+}
+case class GcpBatchJobPaths(override val workflowPaths: GcpBatchWorkflowPaths, jobKey: BackendJobDescriptorKey, override val isCallCacheCopyAttempt: Boolean = false) extends JobPaths {
+
+  def batchLogBasename = {
+    val index = jobKey
+      .index
+      .map(s => s"-$s")
+      .getOrElse("")
+    s"${
+      jobKey
+        .node
+        .localName
+    }$index"
+  }
+
+  val batchLogFilename: String = s"$batchLogBasename.log"
+  lazy val batchLogPath: Path = callExecutionRoot.resolve(batchLogFilename)
+
+  val batchMonitoringLogFilename: String = s"${GcpBatchJobPaths.BatchMonitoringKey}.log"
+  lazy val batchMonitoringLogPath: Path = callExecutionRoot.resolve(batchMonitoringLogFilename)
+
+  val batchMonitoringScriptFilename: String = s"${GcpBatchJobPaths.BatchMonitoringKey}.sh"
+  val batchMonitoringImageScriptFilename: String = s"${GcpBatchJobPaths.BatchMonitoringImageKey}.sh"
+
+  override def forCallCacheCopyAttempts: JobPaths = this.copy(isCallCacheCopyAttempt = true)
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchParameters.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchParameters.scala
new file mode 100644
index 00000000000..c2c75ce5667
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchParameters.scala
@@ -0,0 +1,83 @@
+package cromwell.backend.google.batch.models
+
+import akka.http.scaladsl.model.ContentType
+import cromwell.backend.google.batch.io.GcpBatchAttachedDisk
+import cromwell.core.path.Path
+
+import scala.concurrent.duration.FiniteDuration
+
+sealed trait BatchParameter {
+  def name: String
+
+  def mount: GcpBatchAttachedDisk
+
+  /**
+    * The Path where the input file resides.  The backend-specific localization
+    * code handles creating actions for each specific filesystem
+    * implementation.
+    *
+    * e.g: gs://root_bucket/input_data/my_input.bam
+    */
+  def cloudPath: Path
+
+  /**
+    * Relative path on the host machine where the file should be localized to / delocalized from.
+    * Note that the actual localization / delocalization happens in a docker container, therefore
+    * [[containerPath]] should be used as the actual source / destination path when localizing / delocalizing
+    *
+    * e.g: root_bucket/input_data/my_input.bam
+    */
+  def relativeHostPath: Path
+
+  /**
+    * Path in the docker container. It must be mounted on the docker from / to its hostPath
+    *
+    * e.g: /cromwell_root/root_bucket/input_data/my_input.bam
+    */
+  def containerPath: Path = mount.mountPoint.resolve(relativeHostPath)
+
+  /**
+    * True if this parameter represents a file; false if it represents a directory.
+    */
+  def isFileParameter: Boolean = this match {
+    case _: GcpBatchFileInput => true
+    case _: GcpBatchFileOutput => true
+    case _: GcpBatchDirectoryInput => false
+    case _: GcpBatchDirectoryOutput => false
+  }
+}
+
+sealed trait GcpBatchInput extends BatchParameter
+sealed trait GcpBatchOutput extends BatchParameter {
+  def contentType: Option[ContentType] = None
+}
+
+final case class GcpBatchFileInput(name: String,
+                                       cloudPath: Path,
+                                       relativeHostPath: Path,
+                                       mount: GcpBatchAttachedDisk) extends GcpBatchInput
+
+final case class GcpBatchDirectoryInput(name: String,
+                                            cloudPath: Path,
+                                            relativeHostPath: Path,
+                                            mount: GcpBatchAttachedDisk) extends GcpBatchInput
+
+final case class GcpBatchFileOutput(name: String,
+                                        cloudPath: Path,
+                                        relativeHostPath: Path,
+                                        mount: GcpBatchAttachedDisk,
+                                        optional: Boolean,
+                                        secondary: Boolean,
+                                        uploadPeriod: Option[FiniteDuration] = None,
+                                        override val contentType: Option[ContentType] = None) extends GcpBatchOutput
+
+final case class GcpBatchDirectoryOutput(name: String,
+                                             cloudPath: Path,
+                                             relativeHostPath: Path,
+                                             mount: GcpBatchAttachedDisk,
+                                             optional: Boolean,
+                                             secondary: Boolean,
+                                             override val contentType: Option[ContentType] = None) extends GcpBatchOutput
+
+// TODO: Remove when support for V1 is stopped, this is only used to pass the extra_param auth file
+final case class GcpBatchLiteralInput(name: String, value: String)
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRequest.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRequest.scala
new file mode 100644
index 00000000000..3c616c0ba4e
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRequest.scala
@@ -0,0 +1,9 @@
+package cromwell.backend.google.batch.models
+
+import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobParameters
+import cromwell.core.WorkflowId
+
+case class GcpBatchRequest(workflowId: WorkflowId,
+                           createParameters: CreateBatchJobParameters,
+                           jobName: String,
+                           gcpBatchParameters: CreateGcpBatchParameters)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
new file mode 100644
index 00000000000..9fe3327f35d
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
@@ -0,0 +1,294 @@
+package cromwell.backend.google.batch.models
+
+import cats.implicits.{catsSyntaxValidatedId, toTraverseOps}
+import com.typesafe.config.Config
+import common.validation.ErrorOr.ErrorOr
+import cromwell.backend.google.batch.io.{GcpBatchAttachedDisk, GcpBatchWorkingDisk}
+import cromwell.backend.google.batch.models.GpuResource.GpuType
+import cromwell.backend.google.batch.util.{GpuTypeValidation, GpuValidation}
+import cromwell.backend.standard.StandardValidatedRuntimeAttributesBuilder
+import cromwell.backend.validation._
+import eu.timepit.refined._
+import eu.timepit.refined.api.Refined
+import eu.timepit.refined.numeric.Positive
+import wdl4s.parser.MemoryUnit
+import wom.RuntimeAttributesKeys
+import wom.format.MemorySize
+import wom.types.{WomArrayType, WomStringType, WomType}
+import wom.values.{WomArray, WomBoolean, WomInteger, WomString, WomValue}
+
+object GpuResource {
+
+  final case class GpuType(name: String) {
+    override def toString: String = name
+  }
+
+  object GpuType {
+    val NVIDIATeslaP100 = GpuType("nvidia-tesla-p100")
+    val NVIDIATeslaK80 = GpuType("nvidia-tesla-k80")
+
+    val DefaultGpuType: GpuType = NVIDIATeslaK80
+    val DefaultGpuCount: Int Refined Positive = refineMV[Positive](1)
+    val MoreDetailsURL = "https://cloud.google.com/compute/docs/gpus/"
+  }
+}
+
+final case class GpuResource(gpuType: GpuType, gpuCount: Int Refined Positive)
+
+final case class GcpBatchRuntimeAttributes(
+                                      cpu: Int Refined Positive,
+                                      cpuPlatform: Option[String],
+                                      gpuResource: Option[GpuResource],
+                                      zones: Vector[String],
+                                      preemptible: Int,
+                                      bootDiskSize: Int,
+                                      memory: MemorySize,
+                                      disks: Seq[GcpBatchAttachedDisk],
+                                      dockerImage: String,
+                                      failOnStderr: Boolean,
+                                      continueOnReturnCode: ContinueOnReturnCode,
+                                      noAddress: Boolean,
+                                      useDockerImageCache: Option[Boolean],
+                                      checkpointFilename: Option[String])
+
+object GcpBatchRuntimeAttributes {
+
+  val ZonesKey = "zones"
+  private val ZonesDefaultValue = WomString("us-central1-b")
+
+  val PreemptibleKey = "preemptible"
+  private val preemptibleValidationInstance = new IntRuntimeAttributesValidation(PreemptibleKey)
+  private val PreemptibleDefaultValue = WomInteger(0)
+
+  val BootDiskSizeKey = "bootDiskSizeGb"
+  private val bootDiskValidationInstance = new IntRuntimeAttributesValidation(BootDiskSizeKey)
+  private val BootDiskDefaultValue = WomInteger(10)
+
+  val NoAddressKey = "noAddress"
+  private val noAddressValidationInstance = new BooleanRuntimeAttributesValidation(NoAddressKey)
+  private val NoAddressDefaultValue = WomBoolean(false)
+
+  val DisksKey = "disks"
+  private val DisksDefaultValue = WomString(s"${GcpBatchWorkingDisk.Name} 10 SSD")
+
+  val CpuPlatformKey = "cpuPlatform"
+  private val cpuPlatformValidationInstance = new StringRuntimeAttributesValidation(CpuPlatformKey)
+    .optional
+  // via `gcloud compute zones describe us-central1-a`
+  val CpuPlatformIntelCascadeLakeValue = "Intel Cascade Lake"
+  val CpuPlatformAMDRomeValue = "AMD Rome"
+
+  private def cpuMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] = CpuValidation
+    .instanceMin
+    .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
+
+  val UseDockerImageCacheKey = "useDockerImageCache"
+  private val useDockerImageCacheValidationInstance = new BooleanRuntimeAttributesValidation(UseDockerImageCacheKey)
+    .optional
+
+  val CheckpointFileKey = "checkpointFile"
+  private val checkpointFileValidationInstance = new StringRuntimeAttributesValidation(CheckpointFileKey).optional
+
+  private val MemoryDefaultValue = "2048 MB"
+
+  private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] = CpuValidation
+    .instance
+    .withDefault(CpuValidation
+      .configDefaultWomValue(runtimeConfig) getOrElse CpuValidation
+      .defaultMin)
+  private def cpuPlatformValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] = cpuPlatformValidationInstance
+  private def gpuTypeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[GpuType] = GpuTypeValidation.optional
+
+  private def gpuCountValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optional
+  private def gpuMinValidation(runtimeConfig: Option[Config]):OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optionalMin
+
+  private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
+
+  private def failOnStderrValidation(runtimeConfig: Option[Config]) = FailOnStderrValidation.default(runtimeConfig)
+
+  private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) = ContinueOnReturnCodeValidation.default(runtimeConfig)
+
+  private def disksValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Seq[GcpBatchAttachedDisk]] = DisksValidation
+    .withDefault(DisksValidation.configDefaultWomValue(runtimeConfig) getOrElse DisksDefaultValue)
+
+  private def zonesValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[String]] = ZonesValidation
+    .withDefault(ZonesValidation
+      .configDefaultWomValue(runtimeConfig) getOrElse ZonesDefaultValue)
+
+  private def preemptibleValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = preemptibleValidationInstance
+    .withDefault(preemptibleValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse PreemptibleDefaultValue)
+
+  private def memoryValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] = {
+    MemoryValidation.withDefaultMemory(
+      RuntimeAttributesKeys.MemoryKey,
+      MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, runtimeConfig) getOrElse MemoryDefaultValue)
+  }
+
+  private def memoryMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] = {
+    MemoryValidation.withDefaultMemory(
+      RuntimeAttributesKeys.MemoryMinKey,
+      MemoryValidation
+        .configDefaultString(RuntimeAttributesKeys.MemoryMinKey, runtimeConfig) getOrElse MemoryDefaultValue)
+  }
+
+
+  private def bootDiskSizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = bootDiskValidationInstance
+    .withDefault(bootDiskValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse BootDiskDefaultValue)
+
+  private def noAddressValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = noAddressValidationInstance
+    .withDefault(noAddressValidationInstance
+      .configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue)
+
+  private def useDockerImageCacheValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Boolean] =
+    useDockerImageCacheValidationInstance
+
+  private val outDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] = {
+    InformationValidation.optional(RuntimeAttributesKeys.OutDirMinKey, MemoryUnit.MB, allowZero = true)
+  }
+
+  private val tmpDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] = {
+    InformationValidation.optional(RuntimeAttributesKeys.TmpDirMinKey, MemoryUnit.MB, allowZero = true)
+  }
+
+  private val inputDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] = {
+    InformationValidation.optional(RuntimeAttributesKeys.DnaNexusInputDirMinKey, MemoryUnit.MB, allowZero = true)
+  }
+
+  def runtimeAttributesBuilder(batchConfiguration: GcpBatchConfiguration): StandardValidatedRuntimeAttributesBuilder = {
+    val runtimeConfig = batchConfiguration.runtimeConfig
+    StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
+      gpuCountValidation(runtimeConfig),
+      gpuTypeValidation(runtimeConfig),
+      cpuValidation(runtimeConfig),
+      cpuPlatformValidation(runtimeConfig),
+      cpuMinValidation(runtimeConfig),
+      gpuMinValidation(runtimeConfig),
+      disksValidation(runtimeConfig),
+      noAddressValidation(runtimeConfig),
+      zonesValidation(runtimeConfig),
+      preemptibleValidation(runtimeConfig),
+      memoryValidation(runtimeConfig),
+      memoryMinValidation(runtimeConfig),
+      bootDiskSizeValidation(runtimeConfig),
+      useDockerImageCacheValidation(runtimeConfig),
+      checkpointFileValidationInstance,
+      dockerValidation,
+      outDirMinValidation,
+      tmpDirMinValidation,
+      inputDirMinValidation
+    )
+  }
+
+  def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes, runtimeAttrsConfig: Option[Config]): GcpBatchRuntimeAttributes = {
+    val cpu: Int Refined Positive = RuntimeAttributesValidation.extract(cpuValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val cpuPlatform: Option[String] = RuntimeAttributesValidation.extractOption(cpuPlatformValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+    val checkpointFileName: Option[String] = RuntimeAttributesValidation.extractOption(checkpointFileValidationInstance.key, validatedRuntimeAttributes)
+
+    //GPU
+    lazy val gpuType: Option[GpuType] = RuntimeAttributesValidation
+      .extractOption(gpuTypeValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+    lazy val gpuCount: Option[Int Refined Positive] = RuntimeAttributesValidation
+      .extractOption(gpuCountValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+
+    val gpuResource: Option[GpuResource] = if (gpuType.isDefined || gpuCount.isDefined) {
+      Option(GpuResource(gpuType.getOrElse(GpuType.DefaultGpuType), gpuCount
+        .getOrElse(GpuType.DefaultGpuCount)))
+    } else {
+      None
+    }
+
+
+    val docker: String = RuntimeAttributesValidation.extract(dockerValidation, validatedRuntimeAttributes)
+    val failOnStderr: Boolean = RuntimeAttributesValidation.extract(failOnStderrValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val continueOnReturnCode: ContinueOnReturnCode = RuntimeAttributesValidation.extract(continueOnReturnCodeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val noAddress: Boolean = RuntimeAttributesValidation.extract(noAddressValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val zones: Vector[String] = RuntimeAttributesValidation.extract(ZonesValidation, validatedRuntimeAttributes)
+    val preemptible: Int = RuntimeAttributesValidation.extract(preemptibleValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val bootDiskSize: Int = RuntimeAttributesValidation.extract(bootDiskSizeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val memory: MemorySize = RuntimeAttributesValidation.extract(memoryValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val disks: Seq[GcpBatchAttachedDisk] = RuntimeAttributesValidation.extract(disksValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val useDockerImageCache: Option[Boolean] = RuntimeAttributesValidation.extractOption(useDockerImageCacheValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+
+    val outDirMin: Option[MemorySize] = RuntimeAttributesValidation
+      .extractOption(outDirMinValidation.key, validatedRuntimeAttributes)
+    val tmpDirMin: Option[MemorySize] = RuntimeAttributesValidation
+      .extractOption(tmpDirMinValidation.key, validatedRuntimeAttributes)
+    val inputDirMin: Option[MemorySize] = RuntimeAttributesValidation
+      .extractOption(inputDirMinValidation.key, validatedRuntimeAttributes)
+
+
+    val totalExecutionDiskSizeBytes = List(inputDirMin.map(_.bytes), outDirMin.map(_.bytes), tmpDirMin.map(_.bytes))
+      .flatten.fold(MemorySize(0, MemoryUnit.Bytes).bytes)(_ + _)
+    val totalExecutionDiskSize = MemorySize(totalExecutionDiskSizeBytes, MemoryUnit.Bytes)
+
+    val adjustedDisks = disks.adjustWorkingDiskWithNewMin(totalExecutionDiskSize, ())
+
+    new GcpBatchRuntimeAttributes(
+      cpu,
+      cpuPlatform,
+      gpuResource,
+      zones,
+      preemptible,
+      bootDiskSize,
+      memory,
+      adjustedDisks,
+      docker,
+      failOnStderr,
+      continueOnReturnCode,
+      noAddress,
+      useDockerImageCache,
+      checkpointFileName)
+  }
+
+
+}
+
+object ZonesValidation extends RuntimeAttributesValidation[Vector[String]] {
+  override def key: String = GcpBatchRuntimeAttributes.ZonesKey
+
+  override def coercion: Iterable[WomType] = Set(WomStringType, WomArrayType(WomStringType))
+
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[Vector[String]]] = {
+    case WomString(s) => s.split("\\s+").toVector.validNel
+    case WomArray(womType, value) if womType.memberType == WomStringType =>
+      value.map(_.valueString).toVector.validNel
+  }
+
+  override protected def missingValueMessage: String =
+    s"Expecting $key runtime attribute to be either a whitespace separated String or an Array[String]"
+}
+
+object DisksValidation extends RuntimeAttributesValidation[Seq[GcpBatchAttachedDisk]] {
+  override def key: String = GcpBatchRuntimeAttributes.DisksKey
+
+  override def coercion: Iterable[WomType] = Set(WomStringType, WomArrayType(WomStringType))
+
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[Seq[GcpBatchAttachedDisk]]] = {
+    case WomString(value) => validateLocalDisks(value.split(",\\s*").toSeq)
+    case WomArray(womType, values) if womType.memberType == WomStringType =>
+      validateLocalDisks(values.map(_.valueString))
+  }
+
+  private def validateLocalDisks(disks: Seq[String]): ErrorOr[Seq[GcpBatchAttachedDisk]] = {
+    val diskNels: ErrorOr[Seq[GcpBatchAttachedDisk]] = disks.toList.traverse[ErrorOr, GcpBatchAttachedDisk](validateLocalDisk)
+    val defaulted: ErrorOr[Seq[GcpBatchAttachedDisk]] = addDefault(diskNels)
+    defaulted
+  }
+
+  private def validateLocalDisk(disk: String): ErrorOr[GcpBatchAttachedDisk] = {
+    GcpBatchAttachedDisk.parse(disk) match {
+      case scala.util.Success(attachedDisk) => attachedDisk.validNel
+      case scala.util.Failure(ex) => ex.getMessage.invalidNel
+    }
+  }
+
+  private def addDefault(disksNel: ErrorOr[Seq[GcpBatchAttachedDisk]]): ErrorOr[Seq[GcpBatchAttachedDisk]] = {
+    disksNel map {
+      case disks if disks.exists(_.name == GcpBatchWorkingDisk.Name) => disks
+      case disks => disks :+ GcpBatchWorkingDisk.Default
+    }
+  }
+
+  override protected def missingValueMessage: String =
+    s"Expecting $key runtime attribute to be a comma separated String or Array[String]"
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchWorkflowPaths.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchWorkflowPaths.scala
new file mode 100644
index 00000000000..fcb80241b21
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchWorkflowPaths.scala
@@ -0,0 +1,86 @@
+package cromwell.backend.google.batch.models
+
+import com.google.api.gax.retrying.RetrySettings
+import com.google.auth.Credentials
+import com.typesafe.config.Config
+import cromwell.backend.google.batch.models.GcpBatchWorkflowPaths.callCachePathPrefixFromExecutionRoot
+import cromwell.backend.google.batch.runnable.WorkflowOptionKeys
+import cromwell.backend.io.WorkflowPaths
+import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
+import cromwell.cloudsupport.gcp.gcs.GcsStorage
+import cromwell.core.WorkflowOptions
+import cromwell.core.path.Path
+import cromwell.core.path.PathFactory.PathBuilders
+import cromwell.filesystems.gcs.GcsPathBuilder
+
+import scala.concurrent.ExecutionContext
+import scala.language.postfixOps
+
+object GcpBatchWorkflowPaths {
+  val GcsRootOptionKey = "gcp_batch_gcs_root"
+  private val AuthFilePathOptionKey = "auth_bucket"
+  private val GcsPrefix = "gs://"
+
+  private def callCachePathPrefixFromExecutionRoot(executionRoot: String): String = {
+    // If the root looks like gs://bucket/stuff-under-bucket this should return gs://bucket
+    GcsPrefix + executionRoot.substring(GcsPrefix.length).takeWhile(_ != '/')
+  }
+}
+case class GcpBatchWorkflowPaths(workflowDescriptor: BackendWorkflowDescriptor,
+                                 gcsCredentials: Credentials,
+                                 genomicsCredentials: Credentials,
+                                 gcpBatchConfiguration: GcpBatchConfiguration,
+                                 override val pathBuilders: PathBuilders,
+                                 // This allows for the adjustment of the standard stream file names in PAPI v1 to match the
+                                 // combined controller + job standard output and error files. PAPI v1 controls the periodic
+                                 // delocalization of these files so the metadata Cromwell publishes for these files needs
+                                 // to match the PAPI v1 names.
+                                 standardStreamNameToFileNameMetadataMapper: (GcpBatchJobPaths, String) => String)(implicit ec: ExecutionContext) extends WorkflowPaths {
+
+  override lazy val executionRootString: String = workflowDescriptor.workflowOptions.getOrElse(GcpBatchWorkflowPaths.GcsRootOptionKey, gcpBatchConfiguration.root)
+  override lazy val callCacheRootPrefix: Option[String] = Option(callCachePathPrefixFromExecutionRoot(executionRootString))
+
+  private val workflowOptions: WorkflowOptions = workflowDescriptor.workflowOptions
+
+  val gcsAuthFilePath: Path = {
+    // The default auth file bucket is always at the root of the root workflow
+    val defaultBucket = executionRoot.resolve(workflowDescriptor.rootWorkflow.name)
+                                     .resolve(workflowDescriptor.rootWorkflowId.toString)
+    val bucket = workflowDescriptor.workflowOptions
+                                   .get(GcpBatchWorkflowPaths.AuthFilePathOptionKey) getOrElse defaultBucket
+      .pathAsString
+
+    /*
+     * This is an "exception". The filesystem used here is built from genomicsAuth
+     * unlike everywhere else where the filesystem used is built from gcsFileSystemAuth
+     */
+    val pathBuilderWithGenomicsAuth = GcsPathBuilder.fromCredentials(
+      genomicsCredentials,
+      gcpBatchConfiguration.googleConfig.applicationName,
+      RetrySettings.newBuilder().build(),
+      GcsStorage.DefaultCloudStorageConfiguration,
+      workflowOptions,
+      Option(gcpBatchConfiguration.batchAttributes.project)
+    )
+
+    val authBucket = pathBuilderWithGenomicsAuth.build(bucket) recover {
+      case ex => throw new Exception(s"Invalid gcs auth_bucket path $bucket", ex)
+    } get
+
+    authBucket.resolve(s"${workflowDescriptor.rootWorkflowId}_auth.json")
+  }
+
+  val monitoringScriptPath: Option[Path] = workflowOptions.get(WorkflowOptionKeys.MonitoringScript)
+                                                          .toOption map { path =>
+    // Fail here if the path exists but can't be built
+    getPath(path).get
+  }
+  override def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): GcpBatchJobPaths = {
+    new GcpBatchJobPaths(workflowPaths.asInstanceOf[GcpBatchWorkflowPaths], jobKey)
+  }
+  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths = this.copy(workflowDescriptor = workflowDescriptor)
+  override def config: Config = gcpBatchConfiguration.configurationDescriptor.backendConfig
+}
+
+
+
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala
new file mode 100644
index 00000000000..49e2941bf59
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala
@@ -0,0 +1,102 @@
+package cromwell.backend.google.batch.models
+
+import cats.data.Validated.{Invalid, Valid}
+import cats.instances.list._
+import cats.syntax.apply._
+import cats.syntax.traverse._
+import cats.syntax.validated._
+import common.exception.AggregatedMessageException
+import common.validation.ErrorOr.ErrorOr
+import cromwell.core.{CromwellFatalExceptionMarker, WorkflowOptions}
+import spray.json.{JsObject, JsString}
+
+import scala.util.control.NoStackTrace
+import scala.util.{Failure, Success, Try}
+
+final case class GcpLabel(key: String, value: String)
+
+object GcpLabel {
+
+  val MaxLabelLength = 63
+  val GoogleLabelRegexPattern = "[a-z]([-a-z0-9]*[a-z0-9])?"
+  val GoogleLabelRegex = GoogleLabelRegexPattern.r
+
+  // This function is used to coerce a string into one that meets the requirements for a label submission to Google Pipelines API.
+  // See 'labels' in https://cloud.google.com/genomics/reference/rpc/google.genomics.v1alpha2#google.genomics.v1alpha2.RunPipelineArgs
+  def safeGoogleName(mainText: String, emptyAllowed: Boolean = false): String = {
+
+    validateLabelRegex(mainText) match {
+      case Valid(labelText) => labelText
+      case invalid @ _ if mainText.equals("") && emptyAllowed => mainText
+      case invalid @ _ =>
+        def appendSafe(current: String, nextChar: Char): String = {
+          nextChar match {
+            case c if c.isLetterOrDigit || c == '-' => current + c.toLower
+            case _ => current + '-'
+          }
+        }
+
+        val foldResult = mainText.toCharArray.foldLeft("")(appendSafe)
+
+        val startsValid = foldResult.headOption.exists(_.isLetter)
+        val endsValid = foldResult.lastOption.exists(_.isLetterOrDigit)
+
+        val validStart = if (startsValid) foldResult else "x--" + foldResult
+        val validStartAndEnd = if (endsValid) validStart else validStart + "--x"
+
+        val length = validStartAndEnd.length
+        val tooLong = length > MaxLabelLength
+
+        if (tooLong) {
+          val middleSeparator = "---"
+          val subSectionLength = (MaxLabelLength - middleSeparator.length) / 2
+          validStartAndEnd.substring(0, subSectionLength) + middleSeparator + validStartAndEnd.substring(length - subSectionLength, length)
+        } else {
+          validStartAndEnd
+        }
+    }
+  }
+
+  def validateLabelRegex(s: String): ErrorOr[String] = {
+    (GoogleLabelRegex.pattern.matcher(s).matches, s.length <= MaxLabelLength) match {
+      case (true, true) => s.validNel
+      case (false, false) => s"Invalid label field: `$s` did not match regex '$GoogleLabelRegexPattern' and it is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
+      case (false, _) => s"Invalid label field: `$s` did not match the regex '$GoogleLabelRegexPattern'".invalidNel
+      case (_, false) => s"Invalid label field: `$s` is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
+    }
+  }
+
+
+  def safeLabels(values: (String, String)*): Seq[GcpLabel] = {
+    def safeGoogleLabel(kvp: (String, String)): GcpLabel = {
+      GcpLabel(safeGoogleName(kvp._1), safeGoogleName(kvp._2, emptyAllowed = true))
+    }
+    values.map(safeGoogleLabel)
+  }
+
+  def validateLabel(key: String, value: String): ErrorOr[GcpLabel] = {
+    (validateLabelRegex(key), validateLabelRegex(value)).mapN { (validKey, validValue) => GcpLabel(validKey, validValue)  }
+  }
+
+  def fromWorkflowOptions(workflowOptions: WorkflowOptions): Try[Seq[GcpLabel]] = {
+
+    def extractGoogleLabelsFromJsObject(jsObject: JsObject): Try[Seq[GcpLabel]] = {
+      val asErrorOr = jsObject.fields.toList.traverse {
+        case (key: String, value: JsString) => GcpLabel.validateLabel(key, value.value)
+        case (key, other) => s"Bad label value type for '$key'. Expected simple string but got $other".invalidNel : ErrorOr[GcpLabel]
+      }
+
+      asErrorOr match {
+        case Valid(value) => Success(value)
+        case Invalid(errors) => Failure(new AggregatedMessageException("Invalid 'google_labels' in workflow options", errors.toList) with CromwellFatalExceptionMarker with NoStackTrace)
+      }
+    }
+
+    workflowOptions.toMap.get("google_labels") match {
+      case Some(obj: JsObject) => extractGoogleLabelsFromJsObject(obj)
+      case Some(other) => Failure(new Exception(s"Invalid 'google_labels' in workflow options. Must be a simple JSON object mapping string keys to string values. Got $other") with NoStackTrace with CromwellFatalExceptionMarker)
+      case None => Success(Seq.empty)
+    }
+  }
+
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ManifestFile.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ManifestFile.scala
new file mode 100644
index 00000000000..9b8d1fcafc8
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ManifestFile.scala
@@ -0,0 +1,3 @@
+package cromwell.backend.google.batch.models
+
+case class ManifestFile(imageIdentifier: String, diskSizeGb: Int, files: List[ReferenceFile])
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/PreviousRetryReasons.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/PreviousRetryReasons.scala
new file mode 100644
index 00000000000..521dec4ee57
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/PreviousRetryReasons.scala
@@ -0,0 +1,44 @@
+package cromwell.backend.google.batch.models
+
+import cats.syntax.apply._
+import cats.syntax.validated._
+import common.validation.ErrorOr.ErrorOr
+import cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory.{preemptionCountKey, unexpectedRetryCountKey}
+import cromwell.services.keyvalue.KeyValueServiceActor._
+
+import scala.util.{Failure, Success, Try}
+
+case class PreviousRetryReasons(preempted: Int, unexpectedRetry: Int)
+
+object PreviousRetryReasons {
+
+  def tryApply(prefetchedKvEntries: Map[String, KvResponse], attemptNumber: Int): ErrorOr[PreviousRetryReasons] = {
+    val validatedPreemptionCount = validatedKvResponse(prefetchedKvEntries.get(preemptionCountKey), preemptionCountKey)
+    val validatedUnexpectedRetryCount = validatedKvResponse(prefetchedKvEntries.get(unexpectedRetryCountKey), unexpectedRetryCountKey)
+
+    (validatedPreemptionCount, validatedUnexpectedRetryCount) mapN { PreviousRetryReasons.apply }
+  }
+
+  def apply(knownPreemptedCount: Int, knownUnexpectedRetryCount: Int, attempt: Int): PreviousRetryReasons = {
+    // If we have anything unaccounted for, we can top up the unexpected retry count.
+    // NB: 'attempt' is 1-indexed, so, magic number:
+    // NB2: for sanity's sake, I won't let this unaccounted for drop below 0, just in case...
+    val unaccountedFor = Math.max(attempt - 1 - knownPreemptedCount - knownUnexpectedRetryCount, 0)
+    PreviousRetryReasons(knownPreemptedCount, knownUnexpectedRetryCount + unaccountedFor)
+  }
+
+  private def validatedKvResponse(r: Option[KvResponse], fromKey: String): ErrorOr[Int] = r match {
+    case Some(KvPair(_, v)) => validatedInt(v, fromKey)
+    case Some(_: KvKeyLookupFailed) => 0.validNel
+    case Some(KvFailure(_, failure)) => s"Failed to get key $fromKey: ${failure.getMessage}".invalidNel
+    case Some(_: KvPutSuccess) => s"Programmer Error: Got a KvPutSuccess from a Get request...".invalidNel
+    case None => s"Programmer Error: Engine made no effort to prefetch $fromKey".invalidNel
+  }
+
+  private def validatedInt(s: String, fromKey: String): ErrorOr[Int] = {
+    Try(s.toInt) match {
+      case Success(i) => i.validNel
+      case Failure(_) => s"Unexpected value found in the KV store: $fromKey='$s'".invalidNel
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ProjectLabels.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ProjectLabels.scala
new file mode 100644
index 00000000000..88c8e1aab57
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ProjectLabels.scala
@@ -0,0 +1,3 @@
+package cromwell.backend.google.batch.models
+
+final case class ProjectLabels(labels: Map[String, String])
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ReferenceFile.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ReferenceFile.scala
new file mode 100644
index 00000000000..21e280d318f
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/ReferenceFile.scala
@@ -0,0 +1,3 @@
+package cromwell.backend.google.batch.models
+
+case class ReferenceFile(path: String, crc32c: Long)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/Run.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/Run.scala
new file mode 100644
index 00000000000..418d8ee2a35
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/Run.scala
@@ -0,0 +1,5 @@
+package cromwell.backend.google.batch.models
+
+import cromwell.backend.standard.StandardAsyncJob
+
+case class Run(job: StandardAsyncJob)
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/RunStatus.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/RunStatus.scala
new file mode 100644
index 00000000000..f5631ef6afa
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/RunStatus.scala
@@ -0,0 +1,62 @@
+package cromwell.backend.google.batch.models
+
+import com.google.cloud.batch.v1.JobStatus
+import cromwell.core.ExecutionEvent
+import org.slf4j.{Logger, LoggerFactory}
+
+sealed trait RunStatus
+
+object RunStatus {
+
+    private val log: Logger = LoggerFactory.getLogger(RunStatus.toString)
+
+    def fromJobStatus(status: JobStatus.State): RunStatus = status match {
+        case JobStatus.State.QUEUED =>
+            log.info("job queued")
+            Running
+        case JobStatus.State.SCHEDULED =>
+            log.info("job scheduled")
+            Running
+        case JobStatus.State.RUNNING =>
+            log.info("job running")
+            Running
+        case JobStatus.State.SUCCEEDED =>
+            log.info("job scheduled")
+            Succeeded(List(ExecutionEvent("complete in GCP Batch"))) //update to more specific
+        case JobStatus.State.FAILED =>
+            log.info("job failed")
+            Failed(List.empty)
+        case JobStatus.State.DELETION_IN_PROGRESS =>
+            log.info("deletion in progress")
+            DeletionInProgress
+        case JobStatus.State.STATE_UNSPECIFIED =>
+            log.info("state unspecified")
+            StateUnspecified
+        case JobStatus.State.UNRECOGNIZED =>
+            log.info("state unrecognized")
+            Unrecognized
+        case _ =>
+            log.info(s"job status not matched: $status")
+            Running
+    }
+
+
+    sealed trait TerminalRunStatus extends RunStatus {
+        def eventList: Seq[ExecutionEvent]
+    }
+
+    sealed trait UnsuccessfulRunStatus extends TerminalRunStatus
+
+    case object Running extends RunStatus
+    case object DeletionInProgress extends RunStatus
+    case object StateUnspecified extends RunStatus
+    case object Unrecognized extends RunStatus
+
+    case class Succeeded(override val eventList: Seq[ExecutionEvent]) extends TerminalRunStatus {
+        override def toString = "Succeeded"
+    }
+
+    final case class Failed(override val eventList: Seq[ExecutionEvent]) extends UnsuccessfulRunStatus {
+        override def toString = "Failed"
+    }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/VpcAndSubnetworkProjectLabelValues.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/VpcAndSubnetworkProjectLabelValues.scala
new file mode 100644
index 00000000000..a77bcd96d87
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/VpcAndSubnetworkProjectLabelValues.scala
@@ -0,0 +1,30 @@
+package cromwell.backend.google.batch.models
+
+import cromwell.backend.google.batch.models.VpcAndSubnetworkProjectLabelValues._
+
+final case class VpcAndSubnetworkProjectLabelValues(vpcName: String, subnetNameOpt: Option[String]) {
+  /**
+   * Returns a qualified network name replacing the string `\${projectId}` in the network name if found.
+   */
+  def networkName(projectId: String): String = {
+    val networkNameTemplate =
+      if (vpcName.contains("/")) {
+        vpcName
+      } else {
+        s"projects/$ProjectIdToken/global/networks/$vpcName/"
+      }
+
+    networkNameTemplate.replace(ProjectIdToken, projectId)
+  }
+
+  /**
+   * Replaces the string `\${projectId}` in the subnet name if found.
+   */
+  def subnetNameOption(projectId: String): Option[String] = {
+    subnetNameOpt map { _.replace(ProjectIdToken, projectId) }
+  }
+}
+
+object VpcAndSubnetworkProjectLabelValues {
+  private val ProjectIdToken = s"$${projectId}"
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/BatchInstrumentation.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/BatchInstrumentation.scala
new file mode 100644
index 00000000000..a09cd9d5fed
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/BatchInstrumentation.scala
@@ -0,0 +1,32 @@
+package cromwell.backend.google.batch.monitoring
+
+import cats.data.NonEmptyList
+import cromwell.core.instrumentation.InstrumentationKeys._
+import cromwell.core.instrumentation.InstrumentationPrefixes._
+import cromwell.services.instrumentation.CromwellInstrumentation
+import cromwell.services.instrumentation.CromwellInstrumentation._
+
+object BatchInstrumentation {
+  private val BatchKey = NonEmptyList.of("batch")
+  private val BatchPollKey = BatchKey.concatNel("poll")
+  private val BatchRunKey = BatchKey.concatNel("run")
+  private val BatchAbortKey = BatchKey.concatNel("abort")
+
+  private val BatchPollFailedKey = BatchPollKey.concatNel(FailureKey)
+  private val BatchRunFailedKey = BatchRunKey.concatNel(FailureKey)
+  private val BatchAbortFailedKey = BatchAbortKey.concatNel(FailureKey)
+}
+
+trait BatchInstrumentation extends CromwellInstrumentation {
+  import BatchInstrumentation._
+
+  def pollSuccess() = increment(BatchPollKey.concatNel(SuccessKey), BackendPrefix)
+  def pollFailed() = increment(BatchPollFailedKey.concatNel(FailureKey), BackendPrefix)
+
+  def runSuccess() = increment(BatchRunKey.concatNel(SuccessKey), BackendPrefix)
+  def runFailed() = increment(BatchRunFailedKey.concatNel(FailureKey), BackendPrefix)
+
+  def abortSuccess() = increment(BatchAbortKey.concatNel(SuccessKey), BackendPrefix)
+  def abortFailed() = increment(BatchAbortFailedKey.concatNel(FailureKey), BackendPrefix)
+
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/CheckpointingConfiguration.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/CheckpointingConfiguration.scala
new file mode 100644
index 00000000000..ab04a4a71a9
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/CheckpointingConfiguration.scala
@@ -0,0 +1,75 @@
+package cromwell.backend.google.batch.monitoring
+
+import cromwell.backend.BackendJobDescriptor
+import cromwell.backend.io.WorkflowPaths
+import cromwell.core.path.Path
+
+import scala.concurrent.duration.FiniteDuration
+
+final class CheckpointingConfiguration(jobDescriptor: BackendJobDescriptor,
+                                       workflowPaths: WorkflowPaths,
+                                       commandDirectory: Path,
+                                       checkpointInterval: FiniteDuration
+                                      ) {
+  def checkpointFileCloud(checkpointFileName: String): String = {
+    // The checkpoint file for ANY attempt always goes in the "attempt 1" directory. That way we guarantee that
+    // every attempt is able to recover from the single source of checkpointing truth.
+    workflowPaths.toJobPaths(jobDescriptor.key.copy(attempt = 1), jobDescriptor.workflowDescriptor)
+      .callExecutionRoot.resolve("__checkpointing").resolve(checkpointFileName).toAbsolutePath.pathAsString
+  }
+  def tmpCheckpointFileCloud(checkpointFileName: String): String = checkpointFileCloud(checkpointFileName) + "-tmp"
+
+  def checkpointFileLocal(checkpointFileName: String): String = {
+    commandDirectory.resolve(checkpointFileName).toAbsolutePath.pathAsString
+  }
+  def tmpCheckpointFileLocal(checkpointFileName: String): String = checkpointFileLocal(checkpointFileName) + "-tmp"
+
+  def localizePreviousCheckpointCommand(checkpointFileName: String): String = {
+    val local = checkpointFileLocal(checkpointFileName)
+    val cloud = checkpointFileCloud(checkpointFileName)
+
+    s"gsutil cp $cloud $local || touch $local"
+  }
+
+  def checkpointingCommand(checkpointFilename: String, multilineActionSquasher: String => String): List[String] = {
+    val local = checkpointFileLocal(checkpointFilename)
+    val localTmp = tmpCheckpointFileLocal(checkpointFilename)
+    val cloud = checkpointFileCloud(checkpointFilename)
+    val cloudTmp = tmpCheckpointFileCloud(checkpointFilename)
+
+    val checkpointUploadScript =
+      s"""touch $local
+         |while true
+         |do
+         |  # Attempt to make a local copy of the checkpoint file
+         |  echo "CHECKPOINTING: Making local copy of $local"
+         |  COPY_SUCCESS="false"
+         |  while [ "$$COPY_SUCCESS" != "true" ]
+         |  do
+         |    PRE_COPY_TIMESTAMP="$$(stat -c'%Z' $local)"
+         |    cp $local $localTmp
+         |    if [ "$$PRE_COPY_TIMESTAMP" == "$$(stat -c'%Z' $local)" ]
+         |    then
+         |      COPY_SUCCESS="true"
+         |    else
+         |      echo "CHECKPOINTING: $local was modified while trying to make a local copy. Will retry in 10s..."
+         |      sleep 10
+         |    fi
+         |  done
+         |
+         |  # Perform the upload:
+         |  echo "CHECKPOINTING: Uploading new checkpoint content"
+         |  gsutil -m mv $localTmp $cloudTmp
+         |  echo "CHECKPOINTING: Replacing cloud checkpoint file with new content"
+         |  gsutil -m mv $cloudTmp $cloud
+         |  echo "CHECKPOINTING: Sleeping for ${checkpointInterval.toString} before next checkpoint"
+         |  sleep ${checkpointInterval.toSeconds}
+         |done""".stripMargin
+
+    List(
+      "/bin/bash",
+      "-c",
+      multilineActionSquasher(checkpointUploadScript)
+    )
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/Env.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/Env.scala
new file mode 100644
index 00000000000..df0cb3b070c
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/Env.scala
@@ -0,0 +1,24 @@
+package cromwell.backend.google.batch.monitoring
+
+import cromwell.backend.BackendJobDescriptor
+
+object Env {
+  /**
+   * Name of an environmental variable
+   */
+  val WorkflowId = "WORKFLOW_ID"
+  val TaskCallName = "TASK_CALL_NAME"
+  val TaskCallIndex = "TASK_CALL_INDEX"
+  val TaskCallAttempt = "TASK_CALL_ATTEMPT"
+  val DiskMounts = "DISK_MOUNTS"
+
+  def monitoringImageEnvironment(jobDescriptor: BackendJobDescriptor)
+                                (mountPaths: List[String]): Map[String, String] =
+    Map(
+      Env.WorkflowId -> jobDescriptor.workflowDescriptor.id.toString,
+      Env.TaskCallName -> jobDescriptor.taskCall.localName,
+      Env.TaskCallIndex -> jobDescriptor.key.index.map(_.toString).getOrElse("NA"),
+      Env.TaskCallAttempt -> jobDescriptor.key.attempt.toString,
+      Env.DiskMounts -> mountPaths.mkString(" "),
+    )
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/MonitoringImage.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/MonitoringImage.scala
new file mode 100644
index 00000000000..578081dc46f
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/MonitoringImage.scala
@@ -0,0 +1,47 @@
+package cromwell.backend.google.batch.monitoring
+
+import cromwell.backend.BackendJobDescriptor
+import cromwell.backend.google.batch.io.GcpBatchAttachedDisk
+import cromwell.backend.google.batch.runnable.WorkflowOptionKeys
+import cromwell.backend.google.batch.api.GcpBatchRequestFactory.MountsToEnv
+import cromwell.backend.io.WorkflowPaths
+import cromwell.core.WorkflowOptions
+import cromwell.core.path.{Path, PathFactory}
+
+final class MonitoringImage(jobDescriptor: BackendJobDescriptor,
+                            workflowOptions: WorkflowOptions,
+                            workflowPaths: WorkflowPaths,
+                            commandDirectory: Path,
+                            workingDisk: GcpBatchAttachedDisk,
+                            localMonitoringImageScriptPath: Path,
+                           ) {
+
+  val monitoringImageOption: Option[String] = workflowOptions.get(WorkflowOptionKeys.MonitoringImage).toOption
+
+  val monitoringImageScriptContainerPath: Path = workingDisk.mountPoint.resolve(localMonitoringImageScriptPath)
+
+  val monitoringImageScriptOption: Option[Path] =
+    for {
+      _ <- monitoringImageOption // Only use the monitoring_image_script when monitoring_image provided
+      monitoringImageScript <- workflowOptions.get(WorkflowOptionKeys.MonitoringImageScript).toOption
+    } yield {
+      PathFactory.buildPath(
+        monitoringImageScript,
+        workflowPaths.pathBuilders,
+      )
+    }
+
+  val monitoringImageCommand: List[String] =
+    monitoringImageScriptOption match {
+      case Some(_) => List(
+        "/bin/sh",
+        "-c",
+        s"cd '${commandDirectory.pathAsString}' && " +
+          s"chmod +x '${monitoringImageScriptContainerPath.pathAsString}' && " +
+          s"'${monitoringImageScriptContainerPath.pathAsString}'"
+      )
+      case None => Nil
+    }
+
+  val monitoringImageEnvironment: MountsToEnv = Env.monitoringImageEnvironment(jobDescriptor)
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/CheckpointingRunnable.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/CheckpointingRunnable.scala
new file mode 100644
index 00000000000..5ad8d2b21f9
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/CheckpointingRunnable.scala
@@ -0,0 +1,49 @@
+package cromwell.backend.google.batch.runnable
+
+import com.google.cloud.batch.v1.{Runnable, Volume}
+import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobParameters
+
+trait CheckpointingRunnable {
+  def checkpointingSetupRunnables(createParameters: CreateBatchJobParameters,
+                                  volumes: List[Volume]
+                               ): List[Runnable] = {
+    val result = createParameters.runtimeAttributes.checkpointFilename.map { checkpointFilename =>
+      val checkpointingImage = RunnableUtils.CloudSdkImage
+      val checkpointingCommand = createParameters.checkpointingConfiguration.checkpointingCommand(checkpointFilename, RunnableCommands.multiLineBinBashCommand)
+      val checkpointingEnvironment = Map.empty[String, String]
+
+      // Initial sync from cloud:
+      val initialCheckpointSyncRunnable = RunnableBuilder.cloudSdkShellRunnable(
+        createParameters.checkpointingConfiguration.localizePreviousCheckpointCommand(checkpointFilename)
+      )(volumes = volumes, flags = List.empty, labels = Map.empty)
+      val describeInitialCheckpointingSyncRunnable = RunnableBuilder.describeDocker("initial checkpointing sync", initialCheckpointSyncRunnable)
+
+      // Background upload runnable:
+      val backgroundCheckpointingRunnable = RunnableBuilder.backgroundRunnable(
+        image = checkpointingImage,
+        command = checkpointingCommand,
+        environment = checkpointingEnvironment,
+        volumes = volumes
+      )
+      val describeBackgroundCheckpointingRunnable = RunnableBuilder.describeDocker("begin checkpointing background runnable", backgroundCheckpointingRunnable)
+
+      List(describeInitialCheckpointingSyncRunnable, initialCheckpointSyncRunnable, describeBackgroundCheckpointingRunnable, backgroundCheckpointingRunnable)
+    }.getOrElse(Nil)
+
+    result.map(_.build)
+  }
+
+  def checkpointingShutdownRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume]): List[Runnable] = {
+    val result = createParameters.runtimeAttributes.checkpointFilename.map { checkpointFilename =>
+      val terminationRunnable = RunnableBuilder.terminateBackgroundRunnablesRunnable()
+      val describeTerminationRunnable = RunnableBuilder.describeDocker("terminate checkpointing runnable", terminationRunnable)
+
+      val deleteCheckpointRunnable = RunnableBuilder.gcsFileDeletionRunnable(createParameters.checkpointingConfiguration.checkpointFileCloud(checkpointFilename), volumes)
+      val deleteTmpCheckpointRunnable = RunnableBuilder.gcsFileDeletionRunnable(createParameters.checkpointingConfiguration.tmpCheckpointFileCloud(checkpointFilename), volumes)
+
+      List(describeTerminationRunnable, terminationRunnable, deleteCheckpointRunnable, deleteTmpCheckpointRunnable)
+    }.getOrElse(Nil)
+
+    result.map(_.build)
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/ContainerSetup.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/ContainerSetup.scala
new file mode 100644
index 00000000000..8c7badc37ba
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/ContainerSetup.scala
@@ -0,0 +1,25 @@
+package cromwell.backend.google.batch.runnable
+
+import com.google.cloud.batch.v1.{Runnable, Volume}
+import cromwell.backend.google.batch.io.GcpBatchWorkingDisk
+
+trait ContainerSetup {
+  import RunnableLabels._
+
+  def containerSetupRunnables(volumes: List[Volume]): List[Runnable] = {
+    val containerRoot = GcpBatchWorkingDisk.MountPoint.pathAsString
+
+    // As opposed to V1, the container root does not have a 777 umask, which can cause issues for docker running as non root
+    // Run a first action to create the root and give it the right permissions
+    val containerRootSetup = RunnableBuilder
+      .cloudSdkShellRunnable(s"mkdir -p $containerRoot && chmod -R a+rwx $containerRoot")(
+        volumes = volumes,
+        labels = Map(Key.Tag -> Value.ContainerSetup),
+        flags = List.empty
+      )
+
+    RunnableBuilder
+      .annotateTimestampedRunnable("container setup", Value.ContainerSetup)(volumes, List(containerRootSetup))
+      .map(_.build())
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Delocalization.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Delocalization.scala
new file mode 100644
index 00000000000..f1b28598a28
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Delocalization.scala
@@ -0,0 +1,116 @@
+package cromwell.backend.google.batch.runnable
+
+import com.google.cloud.batch.v1.{Runnable, Volume}
+import common.util.StringUtil._
+import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobParameters
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.batch.models.GcpBatchJobPaths.GcsDelocalizationScriptName
+import cromwell.backend.google.batch.util.GcpBatchParameterConversions._
+import cromwell.backend.google.batch.util.RuntimeOutputMapping
+import cromwell.backend.google.batch.util.ToParameter.ops._
+import cromwell.core.path.Path
+import wom.runtime.WomOutputRuntimeExtractor
+
+import java.util.UUID
+
+trait Delocalization {
+
+  import RunnableBuilder._
+  import RunnableCommands._
+  import RunnableLabels._
+  import RunnableUtils._
+
+  private def runtimeOutputExtractorRunnable(containerCallRoot: String,
+                                           outputFile: String,
+                                           womOutputRuntimeExtractor: WomOutputRuntimeExtractor): Runnable.Builder = {
+    val commands = List(
+      "-c",
+      // Create the directory where the fofn will be written
+      s"mkdir -p $$(dirname $outputFile) && " +
+        s"cd $containerCallRoot && " +
+        """echo "Runtime output files to be delocalized:" && """ +
+        s"${womOutputRuntimeExtractor.command} | tee $outputFile"
+    )
+
+    RunnableBuilder
+      .withImage(womOutputRuntimeExtractor.dockerImage.getOrElse(CloudSdkImage))
+      .withCommand(commands: _*)
+      .withEntrypointCommand("/bin/bash")
+      .withLabels(Map(Key.Tag -> Value.Delocalization))
+  }
+
+  private def delocalizeRuntimeOutputsScript(fofnPath: String, workflowRoot: Path, cloudCallRoot: Path)(implicit gcsTransferConfiguration: GcsTransferConfiguration) = {
+    val gsutilCommand: String => String = { flag =>
+      s"""rm -f $$HOME/.config/gcloud/gce && gsutil -m $flag cp -r $$line "${cloudCallRoot.pathAsString.ensureSlashed}$$gcs_path""""
+    }
+
+    def sedStripPrefix(prefix: String) = s"""sed -e "s/^${prefix.ensureSedEscaped}//""""
+
+    // See RuntimeOutputMapping.prefixFilters for more info on why this is needed
+    val prefixFilters = RuntimeOutputMapping
+      .prefixFilters(workflowRoot)
+      .map(sedStripPrefix)
+      .mkString(" | ")
+
+    /*
+     * Delocalize all the files returned by the runtime output extractor
+     */
+    s"""|#!/bin/bash
+        |
+        |set -x
+        |
+        |if [ -f $fofnPath ]; then
+        |  while IFS= read line
+        |  do
+        |    gcs_path=$$(echo $$line | $prefixFilters)
+        |    (
+        |       ${retry(recoverRequesterPaysError(cloudCallRoot)(gsutilCommand))}
+        |    )
+        |  done  <$fofnPath
+        |fi""".stripMargin
+  }
+
+  private def delocalizeRuntimeOutputsRunnable(cloudCallRoot: Path, inputFile: String, workflowRoot: Path, volumes: List[Volume])(implicit gcsTransferConfiguration: GcsTransferConfiguration): Runnable.Builder = {
+    val command = multiLineCommand(delocalizeRuntimeOutputsScript(inputFile, workflowRoot, cloudCallRoot))
+    RunnableBuilder.cloudSdkShellRunnable(command)(volumes = volumes, labels = Map(Key.Tag -> Value.Delocalization), flags = List.empty)
+  }
+
+  def deLocalizeRunnables(createParameters: CreateBatchJobParameters,
+                          volumes: List[Volume])(implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable] = {
+    val cloudCallRoot = createParameters.cloudCallRoot
+    val callExecutionContainerRoot = createParameters.commandScriptContainerPath.parent
+
+    /*
+     * Ideally temporaryFofnForRuntimeOutputFiles should be somewhere else than the execution directory (we could mount anther directory)
+     * However because it runs after everything else there's no risk of polluting the task's results and the random ID ensures we don't override anything
+     */
+    val temporaryFofnDirectoryForRuntimeOutputFiles = callExecutionContainerRoot.pathAsString.ensureSlashed + UUID.randomUUID().toString.split("-")(0)
+    val temporaryFofnForRuntimeOutputFiles = temporaryFofnDirectoryForRuntimeOutputFiles + "/runtime_output_files.txt"
+
+    val runtimeExtractionRunnables = createParameters.womOutputRuntimeExtractor.toList flatMap { extractor =>
+      List (
+        runtimeOutputExtractorRunnable(callExecutionContainerRoot.pathAsString, temporaryFofnForRuntimeOutputFiles, extractor),
+        delocalizeRuntimeOutputsRunnable(cloudCallRoot, temporaryFofnForRuntimeOutputFiles, createParameters.cloudWorkflowRoot, volumes)
+      )
+    }
+
+    val gcsDelocalizationContainerPath = createParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
+
+    val delocalizationLabel = Map(Key.Tag -> Value.Delocalization)
+    val runGcsDelocalizationScript = cloudSdkShellRunnable(
+      s"/bin/bash $gcsDelocalizationContainerPath")(volumes = volumes, labels = delocalizationLabel, flags = List.empty)
+
+    val annotatedRunnables: List[Runnable.Builder] = runGcsDelocalizationScript ::
+      createParameters.outputParameters.flatMap(_.toRunnables(volumes)) ++
+        runtimeExtractionRunnables
+
+    // NOTE: papiv2 delocalizes logs from /google but such logs are not available on batch
+    // See: https://cloud.google.com/life-sciences/docs/reference/rpc/google.cloud.lifesciences.v2beta
+    val all = RunnableBuilder.annotateTimestampedRunnable("delocalization", Value.Delocalization)(
+      volumes,
+      annotatedRunnables
+    )
+
+    all.map(_.build)
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/GcpBatchMetadataKeys.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/GcpBatchMetadataKeys.scala
new file mode 100644
index 00000000000..f7c0302a98f
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/GcpBatchMetadataKeys.scala
@@ -0,0 +1,11 @@
+package cromwell.backend.google.batch.runnable
+
+object GcpBatchMetadataKeys {
+  val GoogleProject = "gcpBatch:googleProject"
+  val ExecutionBucket = "gcpBatch:executionBucket"
+  val MonitoringScript = "gcpBatch:monitoringScript"
+  val MachineType = "gcpBatch:machineType"
+  val Zone = "gcpBatch:zone"
+  val InstanceName = "gcpBatch:instanceName"
+  val MonitoringLog = "monitoringLog"
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Localization.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Localization.scala
new file mode 100644
index 00000000000..07fe3e848c4
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Localization.scala
@@ -0,0 +1,101 @@
+package cromwell.backend.google.batch.runnable
+
+import cloud.nio.impl.drs.DrsConfig
+import com.google.cloud.batch.v1.{Runnable, Volume}
+import com.typesafe.config.ConfigFactory
+import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobParameters
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.batch.models.{GcpBatchFileInput, GcpBatchJobPaths}
+import cromwell.backend.google.batch.util.GcpBatchParameterConversions._
+import cromwell.backend.google.batch.util.ToParameter.ops._
+import cromwell.core.path.Path
+import cromwell.filesystems.drs.DrsPath
+
+trait Localization {
+  import GcpBatchJobPaths._
+  import RunnableBuilder._
+  import RunnableCommands._
+  import RunnableLabels._
+
+  def localizeRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume])
+                       (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable] = {
+    val localizationLabel = Map(Key.Tag -> Value.Localization)
+
+    val gcsTransferLibraryContainerPath = createParameters.commandScriptContainerPath.sibling(GcsTransferLibraryName)
+    val localizeGcsTransferLibrary = cloudSdkShellRunnable(localizeFile(
+      cloudPath = createParameters.cloudCallRoot / GcsTransferLibraryName,
+      containerPath = gcsTransferLibraryContainerPath))(volumes = volumes, labels = localizationLabel, flags = List.empty)
+
+    val gcsLocalizationContainerPath = createParameters.commandScriptContainerPath.sibling(GcsLocalizationScriptName)
+    val localizeGcsLocalizationScript = cloudSdkShellRunnable(localizeFile(
+      cloudPath = createParameters.cloudCallRoot / GcsLocalizationScriptName,
+      containerPath = gcsLocalizationContainerPath))(volumes = volumes, labels = localizationLabel, flags = List.empty)
+
+    val gcsDelocalizationContainerPath = createParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
+    val localizeGcsDelocalizationScript = cloudSdkShellRunnable(localizeFile(
+      cloudPath = createParameters.cloudCallRoot / GcsDelocalizationScriptName,
+      containerPath = gcsDelocalizationContainerPath))(volumes = volumes, labels = localizationLabel, flags = List.empty)
+
+    val runGcsLocalizationScript = cloudSdkShellRunnable(
+      s"/bin/bash $gcsLocalizationContainerPath")(volumes = volumes, labels = localizationLabel, flags = List.empty)
+
+    val drsInputs: List[DrsPath] = createParameters.inputOutputParameters.fileInputParameters.collect {
+      case GcpBatchFileInput(_, drsPath: DrsPath, _, _) => drsPath
+    }
+
+    val drsLocalizationRunnable = if (drsInputs.nonEmpty) {
+      val drsLocalizationManifestContainerPath = createParameters.commandScriptContainerPath.sibling(DrsLocalizationManifestName)
+      val localizeDrsLocalizationManifest = cloudSdkShellRunnable(localizeFile(
+        cloudPath = createParameters.cloudCallRoot / DrsLocalizationManifestName,
+        containerPath = drsLocalizationManifestContainerPath))(volumes = volumes, labels = localizationLabel, flags = List.empty)
+
+      // Requester pays project id is stored on each DrsPath, but will be the same for all DRS inputs to a
+      // particular workflow because it's determined by the Google project set in workflow options.
+      val requesterPaysProjectId: Option[String] = drsInputs.flatMap(_.requesterPaysProjectIdOption).headOption
+      val runDrsLocalization = Localization.drsRunnable(drsLocalizationManifestContainerPath, localizationLabel, requesterPaysProjectId)
+      List(localizeDrsLocalizationManifest, runDrsLocalization)
+    } else List[Runnable.Builder]()
+
+    // Any "classic" PAPI v2 one-at-a-time localizations for non-GCS inputs.
+    val singletonLocalizations = createParameters.inputOutputParameters.fileInputParameters.flatMap(_.toRunnables(volumes))
+
+    val localizations =
+      localizeGcsTransferLibrary ::
+        localizeGcsLocalizationScript :: runGcsLocalizationScript ::
+        drsLocalizationRunnable :::
+        localizeGcsDelocalizationScript ::
+        singletonLocalizations
+
+    RunnableBuilder
+      .annotateTimestampedRunnable("localization", Value.Localization)(volumes, localizations)
+      .map(_.build)
+  }
+}
+
+object Localization {
+
+  private lazy val config = ConfigFactory.load
+
+  def drsRunnable(manifestPath: Path,
+                  labels: Map[String, String],
+                  requesterPaysProjectId: Option[String]
+                 ): Runnable.Builder = {
+    import RunnableBuilder.EnhancedRunnableBuilder
+
+    val drsResolverConfig = config.getConfig("filesystems.drs.global.config.resolver")
+    val drsConfig = DrsConfig.fromConfig(drsResolverConfig)
+    val drsDockerImage = config.getString("drs.localization.docker-image")
+
+    val manifestArg = List("-m", manifestPath.pathAsString)
+    val requesterPaysArg = requesterPaysProjectId.map(r => List("-r", r)).getOrElse(List.empty)
+    val drsCommand = manifestArg ++ requesterPaysArg
+
+    val drsResolverEnv = DrsConfig.toEnv(drsConfig)
+
+    RunnableBuilder
+      .withImage(drsDockerImage)
+      .withCommand(drsCommand: _*)
+      .withEnvironment(drsResolverEnv)
+      .withLabels(labels)
+  }
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MemoryRetryCheckRunnable.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MemoryRetryCheckRunnable.scala
new file mode 100644
index 00000000000..3c728b21775
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MemoryRetryCheckRunnable.scala
@@ -0,0 +1,14 @@
+package cromwell.backend.google.batch.runnable
+
+import com.google.cloud.batch.v1.{Runnable, Volume}
+import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobParameters
+
+trait MemoryRetryCheckRunnable {
+
+  def checkForMemoryRetryRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume]): List[Runnable] = {
+    createParameters.retryWithMoreMemoryKeys match {
+      case Some(keys) => List(RunnableBuilder.checkForMemoryRetryRunnable(keys, volumes)).map(_.build)
+      case None => List.empty[Runnable]
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MonitoringRunnable.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MonitoringRunnable.scala
new file mode 100644
index 00000000000..b48918610b2
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MonitoringRunnable.scala
@@ -0,0 +1,66 @@
+package cromwell.backend.google.batch.runnable
+
+import com.google.cloud.batch.v1.{Runnable, Volume}
+import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobParameters
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
+
+trait MonitoringRunnable {
+  def monitoringSetupRunnables(createParameters: CreateBatchJobParameters,
+                               volumes: List[Volume]
+                            )(implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable] = {
+
+    val monitoringImageScriptRunnables =
+      createParameters.monitoringImage.monitoringImageScriptOption match {
+        case Some(script) =>
+          val localizeScriptRunnable =
+            RunnableBuilder.monitoringImageScriptRunnable(
+              script,
+              createParameters.monitoringImage.monitoringImageScriptContainerPath,
+              volumes
+            )
+          val describeLocalizeScriptRunnable =
+            RunnableBuilder.describeDocker(
+              "localizing monitoring image script runnable",
+              localizeScriptRunnable,
+            )
+          List(describeLocalizeScriptRunnable, localizeScriptRunnable)
+        case None => Nil
+      }
+
+    val monitoringImageRunnables =
+      createParameters.monitoringImage.monitoringImageOption match {
+        case Some(image) =>
+
+          val monitoringImage = image
+          val monitoringImageCommand = createParameters.monitoringImage.monitoringImageCommand
+          val monitoringImageEnvironment = createParameters.monitoringImage.monitoringImageEnvironment
+
+          val monitoringRunnable = RunnableBuilder.backgroundRunnable(
+            monitoringImage,
+            monitoringImageCommand,
+            monitoringImageEnvironment(volumes.map(_.getMountPath)),
+            volumes
+          )
+
+          val describeMonitoringRunnable = RunnableBuilder.describeDocker("monitoring runnable", monitoringRunnable)
+
+          List(describeMonitoringRunnable, monitoringRunnable)
+
+        case None => Nil
+      }
+
+    (monitoringImageScriptRunnables ++ monitoringImageRunnables).map(_.build)
+  }
+
+  def monitoringShutdownRunnables(createParameters: CreateBatchJobParameters): List[Runnable] = {
+    createParameters.monitoringImage.monitoringImageOption match {
+      case Some(_) =>
+        val terminationRunnable = RunnableBuilder.terminateBackgroundRunnablesRunnable()
+
+        val describeTerminationRunnable = RunnableBuilder.describeDocker("terminate monitoring runnable", terminationRunnable)
+
+        List(describeTerminationRunnable, terminationRunnable).map(_.build)
+      case None => Nil
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala
new file mode 100644
index 00000000000..c68e3dbdd29
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala
@@ -0,0 +1,318 @@
+package cromwell.backend.google.batch.runnable
+
+import com.google.cloud.batch.v1.Runnable.Container
+import com.google.cloud.batch.v1.{Environment,Runnable, Volume}
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.batch.models.{BatchParameter, GcpBatchInput, GcpBatchOutput}
+//import cromwell.backend.google.batch.runnable.RunnableLabels._
+import cromwell.core.path.Path
+import mouse.all.anySyntaxMouse
+
+import scala.concurrent.duration.{Duration, DurationInt, FiniteDuration}
+import scala.jdk.CollectionConverters._
+
+/**
+ * Utility singleton to create high level batch runnables.
+ */
+object RunnableBuilder {
+
+  import RunnableLabels._
+  import RunnableUtils._
+
+  implicit class EnhancedRunnableBuilder(val builder: Runnable.Builder) extends AnyVal {
+    /**
+      * Only for use with docker images KNOWN to not have entrypoints already set,
+      * or used with accompanying call to setEntrypoint("non-empty-string").
+      *
+      * Otherwise use the withEntrypointCommand() workaround below since the google issue listed in BA-6406 is not being
+      * fixed.
+      */
+    def withCommand(command: String*): Runnable.Builder = {
+      val container = builder.getContainerBuilder.addAllCommands(command.toList.asJava)
+      builder.setContainer(container)
+    }
+
+    def withEntrypointCommand(command: String*): Runnable.Builder = {
+      builder
+        .setContainer(
+          builder.getContainerBuilder
+            .setEntrypoint(command.headOption.getOrElse(""))  //set to blank string instead of null because batch does not support null
+            .addAllCommands(
+              command.drop(1).asJava
+            )
+        )
+    }
+
+    def withFlags(flags: List[RunnableFlag]): Runnable.Builder = {
+      flags.foldLeft(builder) {
+        case (acc, RunnableFlag.IgnoreExitStatus) => acc.setIgnoreExitStatus(true)
+        case (acc, RunnableFlag.RunInBackground) => acc.setBackground(true)
+        case (acc, RunnableFlag.AlwaysRun) => acc.setAlwaysRun(true)
+      }
+    }
+
+    def withEnvironment(environment: Map[String, String]): Runnable.Builder = {
+      val env = Environment.newBuilder.putAllVariables(environment.asJava)
+      builder.setEnvironment(env)
+    }
+
+
+    def withVolumes(volumes: List[Volume]): Runnable.Builder = {
+      val formattedVolumes = volumes.map { volume =>
+        val mountPath = volume.getMountPath
+        val mountOptions = Option(volume.getMountOptionsList).map(_.asScala.toList).getOrElse(List.empty)
+        s"$mountPath:$mountPath:${mountOptions.mkString(",")}"
+      }
+
+      builder.setContainer(
+        builder.getContainerBuilder.addAllVolumes(formattedVolumes.asJava)
+      )
+    }
+
+    def withLabels(labels: Map[String, String]): Runnable.Builder = builder.putAllLabels(labels.asJava)
+
+    def withTimeout(timeout: Duration): Runnable.Builder = timeout match {
+      case _: FiniteDuration =>
+        builder.setTimeout(
+          com.google.protobuf.Duration.newBuilder().setSeconds(timeout.toSeconds).build()
+        )
+
+      case _ => builder
+    }
+
+    def withAlwaysRun(alwaysRun: Boolean): Runnable.Builder = builder.setAlwaysRun(alwaysRun)
+
+    def withRunInBackground(runInBackground: Boolean): Runnable.Builder = builder.setBackground(runInBackground)
+
+    def scalaLabels: Map[String, String] = {
+      val list = for {
+        keyValueList <- Option(builder.getLabelsMap).toList
+        keyValue <- keyValueList.asScala
+      } yield keyValue
+      list.toMap
+    }
+  }
+
+  def withImage(image: String): Runnable.Builder = {
+    Runnable.newBuilder()
+      .setContainer(Container.newBuilder.setImageUri(image))
+  }
+
+  private def cloudSdkContainerBuilder: Container.Builder = {
+    Container.newBuilder.setImageUri(CloudSdkImage)
+  }
+
+  def monitoringImageScriptRunnable(cloudPath: Path, containerPath: Path, volumes: List[Volume])
+                                 (implicit gcsTransferConfiguration: GcsTransferConfiguration): Runnable.Builder = {
+    val command = RunnableCommands.localizeFile(cloudPath, containerPath)
+    val labels = Map(Key.Tag -> Value.Localization)
+    cloudSdkShellRunnable(command)(volumes = volumes, flags = List.empty, labels = labels)
+  }
+
+  def backgroundRunnable(image: String,
+                         command: List[String],
+                         environment: Map[String, String],
+                         volumes: List[Volume]
+                      ): Runnable.Builder = {
+    withImage(image)
+      .withEntrypointCommand(command: _*)
+      .withRunInBackground(true)
+      .withVolumes(volumes)
+      .withEnvironment(environment)
+      .withFlags(List(RunnableFlag.RunInBackground, RunnableFlag.IgnoreExitStatus))
+      .withLabels(Map(Key.Tag -> Value.Monitoring))
+  }
+
+
+  def terminateBackgroundRunnablesRunnable(): Runnable.Builder = {
+    cloudSdkShellRunnable(terminateAllBackgroundRunnablesCommand)(
+      volumes = List.empty,
+      flags = List(RunnableFlag.AlwaysRun),
+      labels = Map(Key.Tag -> Value.Monitoring)
+    )
+  }
+
+  def gcsFileDeletionRunnable(cloudPath: String, volumes: List[Volume]): Runnable.Builder = {
+    cloudSdkShellRunnable(
+      s"""gsutil rm '$cloudPath'"""
+    )(
+      volumes = volumes,
+      flags = List(RunnableFlag.IgnoreExitStatus),
+      labels = Map(Key.Tag -> Value.Monitoring)
+    )
+  }
+
+  def userRunnable(docker: String,
+                   scriptContainerPath: String,
+                   jobShell: String,
+                   volumes: List[Volume],
+                   dockerhubCredentials: (String, String)): Runnable.Builder = {
+
+    val container = (dockerhubCredentials._1, dockerhubCredentials._2) match {
+      case (username, password) if username.nonEmpty && password.nonEmpty =>
+        Container.newBuilder
+          .setImageUri(docker)
+          .setEntrypoint(jobShell)
+          .addCommands(scriptContainerPath)
+          .setUsername(username)
+          .setPassword(password)
+      case _ =>
+        Container.newBuilder
+          .setImageUri(docker)
+          .setEntrypoint(jobShell)
+          .addCommands(scriptContainerPath)
+    }
+    Runnable.newBuilder()
+      .setContainer(container)
+      .withVolumes(volumes)
+      .putLabels(Key.Tag, Value.UserRunnable)
+  }
+
+  def checkForMemoryRetryRunnable(retryLookupKeys: List[String], volumes: List[Volume]): Runnable.Builder = {
+    cloudSdkShellRunnable(RunnableCommands.checkIfStderrContainsRetryKeys(retryLookupKeys))(
+      volumes = volumes,
+      flags = List(RunnableFlag.AlwaysRun),
+      labels = Map(Key.Tag -> Value.RetryWithMoreMemory)
+    ).withAlwaysRun(true)
+  }
+
+  // Creates a Runnable that logs the docker command for the passed in runnable.
+  def describeDocker(description: String, runnable: Runnable.Builder): Runnable.Builder = {
+    logTimestampedRunnable(
+      s"Running $description: ${toDockerRun(runnable)}",
+      List.empty,
+      List.empty,
+      runnable.scalaLabels
+    )
+  }
+
+  private def timestampedMessage(message: String): String =
+    s"""printf '%s %s\\n' "$$(date -u '+%Y/%m/%d %H:%M:%S')" ${shellEscaped(message)}"""
+
+  private def logTimestampedRunnable(message: String, volumes: List[Volume], flags: List[RunnableFlag], runnableLabels: Map[String, String]): Runnable.Builder = {
+    // Uses the cloudSdk image as that image will be used for other operations as well.
+    cloudSdkShellRunnable(
+      timestampedMessage(message)
+    )(volumes, flags, labels = runnableLabels collect {
+      case (key, value) if key == Key.Tag => Key.Logging -> value
+      case (key, value) => key -> value
+    }).withTimeout(timeout = 300.seconds)
+  }
+
+  def cloudSdkRunnable: Runnable.Builder = Runnable.newBuilder.setContainer(cloudSdkContainerBuilder)
+
+  def cloudSdkShellRunnable(shellCommand: String)(
+    volumes: List[Volume],
+    flags: List[RunnableFlag],
+    labels: Map[String, String],
+    timeout: Duration = Duration.Inf): Runnable.Builder = {
+
+    Runnable.newBuilder.setContainer(cloudSdkContainerBuilder)
+      .withVolumes(volumes)
+      .withLabels(labels)
+      .withEntrypointCommand(
+        "/bin/sh",
+        "-c",
+        if (shellCommand.contains("\n")) shellCommand |> RunnableCommands.multiLineCommand else shellCommand
+      )
+      .withFlags(flags)
+      .withTimeout(timeout)
+  }
+
+    def annotateTimestampedRunnable(description: String,
+                                    loggingLabelValue: String,
+                                    isAlwaysRun: Boolean = false)(
+                                    volumes: List[Volume],
+                                    runnables: List[Runnable.Builder]): List[Runnable.Builder] = {
+
+      val flags = if (isAlwaysRun) List(RunnableFlag.AlwaysRun) else List()
+      val labels = Map(Key.Logging -> loggingLabelValue)
+      val starting = logTimestampedRunnable(s"Starting $description.", volumes, flags, labels)
+      val done = logTimestampedRunnable(s"Done $description.", volumes, flags, labels)
+      List(starting) ++ runnables ++ List(done)
+  }
+
+  /**
+    * Returns a set of labels for a parameter.
+    *
+    * @param parameter Input or output parameter to label.
+    * @return The labels.
+    */
+  def parameterLabels(parameter: BatchParameter): Map[String, String] = {
+    parameter match {
+      case _: GcpBatchInput =>
+        Map(
+          Key.Tag -> Value.Localization,
+          Key.InputName -> parameter.name
+        )
+      case _: GcpBatchOutput =>
+        Map(
+          Key.Tag -> Value.Delocalization,
+          Key.OutputName -> parameter.name
+        )
+    }
+  }
+
+  /** Creates a Runnable that describes the parameter localization or delocalization. */
+  def describeParameter(parameter: BatchParameter, volumes: List[Volume], labels: Map[String, String]): Runnable.Builder = {
+    parameter match {
+      case _: GcpBatchInput =>
+        val message = "Localizing input %s -> %s".format(
+          shellEscaped(parameter.cloudPath),
+          shellEscaped(parameter.containerPath),
+        )
+        logTimestampedRunnable(message, volumes, List.empty, labels)
+      case _: GcpBatchOutput =>
+        val message = "Delocalizing output %s -> %s".format(
+          shellEscaped(parameter.containerPath),
+          shellEscaped(parameter.cloudPath),
+        )
+        logTimestampedRunnable(message, volumes, List(RunnableFlag.AlwaysRun), labels)
+    }
+  }
+
+  // Converts an Runnable to a `docker run ...` command runnable in the shell.
+  private[runnable] def toDockerRun(runnable: Runnable.Builder): String = {
+    runnable.getContainer
+      .getCommandsList
+      .asScala
+      .toList
+      .map { cmd => shellEscaped(cmd) }
+      .mkString(" ")
+
+    val commandArgs: String = Option(runnable.getContainerBuilder.getCommandsList) match {
+      case Some(commands) =>
+        commands.asScala map {
+          case command if Option(command).isDefined => s" ${shellEscaped(command)}"
+          case _ => ""
+        } mkString ""
+      case None => ""
+    }
+
+    val entrypointArg: String = Option(runnable.getContainerBuilder.getEntrypoint).filter(_.nonEmpty) match {
+      case Some(entrypoint) => s" --entrypoint=${shellEscaped(entrypoint)}"
+      case None => ""
+    }
+
+    val imageArg: String = Option(runnable.getContainerBuilder.getImageUri) match {
+      case None => " <no docker image specified>"
+      case Some(imageUri) => s" ${shellEscaped(imageUri)}"
+    }
+
+    val mountArgs: String = Option(runnable.getContainerBuilder.getVolumesList) match {
+      case None => ""
+      case Some(volumes) =>
+        volumes.asScala map {
+          case volume if Option(volume).isEmpty => ""
+          case volume => s" -v ${shellEscaped(volume).replaceAll(":r[o|w]", "")}"
+        } mkString ""
+    }
+
+    List("docker run",
+      mountArgs,
+      entrypointArg,
+      imageArg,
+      commandArgs,
+    ).mkString
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableCommands.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableCommands.scala
new file mode 100644
index 00000000000..0bbd1c50d53
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableCommands.scala
@@ -0,0 +1,185 @@
+package cromwell.backend.google.batch.runnable
+
+import akka.http.scaladsl.model.ContentType
+import common.util.StringUtil._
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
+import cromwell.core.path.Path
+import cromwell.filesystems.gcs.GcsPath
+import cromwell.filesystems.gcs.RequesterPaysErrors._
+import mouse.all._
+import org.apache.commons.codec.binary.Base64
+import org.apache.commons.text.StringEscapeUtils
+
+import java.nio.charset.StandardCharsets
+import java.util.UUID
+import scala.concurrent.duration._
+
+object RunnableCommands {
+
+  import RunnableUtils._
+
+  implicit val waitBetweenRetries: FiniteDuration = 5.seconds
+
+  implicit class EnhancedCromwellPath(val path: Path) extends AnyVal {
+    def projectId: String = path match {
+      case gcs: GcsPath => gcs.projectId
+      case _ => ""
+    }
+  }
+
+  implicit class ShellPath(val path: Path) extends AnyVal {
+    // The command String runs in Bourne shell so shell metacharacters in filenames must be escaped
+    def escape: String = StringEscapeUtils.escapeXSI(path.pathAsString)
+  }
+
+  private def makeContentTypeFlag(contentType: Option[ContentType]) = contentType.map(ct => s"""-h "Content-Type: $ct"""").getOrElse("")
+
+  def makeContainerDirectory(containerPath: Path) = s"mkdir -p ${containerPath.escape}"
+
+  def delocalizeDirectory(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
+                         (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+    retry {
+      recoverRequesterPaysError(cloudPath) { flag =>
+        s"rm -f $$HOME/.config/gcloud/gce && " +
+          s"gsutil $flag ${contentType |> makeContentTypeFlag} -m rsync -r ${containerPath.escape} ${cloudPath.escape}"
+      }
+    }
+  }
+
+  /**
+    * As per https://cloud.google.com/storage/docs/gsutil/addlhelp/HowSubdirectoriesWork, rule #2
+    * If one attempts a
+    * gsutil cp /local/file.txt gs://bucket/subdir/file.txt
+    * AND
+    * there exists a folder gs://bucket/subdir/file.txt_thisCouldBeAnything
+    * then gs://bucket/subdir/file.txt will be treated as a directory, and /local/file.txt will be copied under gs://bucket/subdir/file.txt/file.txt
+    * and not gs://bucket/subdir/file.txt.
+    *
+    * By instead using the parent directory (and ensuring it ends with a slash), gsutil will treat that as a directory and put the file under it.
+    * So the final gsutil command will look something like gsutil cp /local/file.txt gs://bucket/subdir/
+    */
+  def delocalizeFile(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
+                    (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+    retry {
+      recoverRequesterPaysError(cloudPath) { flag =>
+        s"rm -f $$HOME/.config/gcloud/gce && " +
+          s"gsutil $flag ${contentType |> makeContentTypeFlag} cp ${containerPath.escape} ${cloudPath.parent.escape.ensureSlashed}"
+      }
+    }
+  }
+
+  /**
+    * delocalizeFile necessarily copies the file to the same name. Use this if you want to to specify a name different from the original
+    * Make sure that there's no object named "yourfinalname_something" (see above) in the same cloud directory.
+    */
+  def delocalizeFileTo(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
+                      (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+    retry {
+      recoverRequesterPaysError(cloudPath) { flag =>
+        s"rm -f $$HOME/.config/gcloud/gce && " +
+          s"gsutil $flag ${contentType |> makeContentTypeFlag} cp ${containerPath.escape} ${cloudPath.escape}"
+      }
+    }
+  }
+
+  def ifExist(containerPath: Path)(f: => String) = s"if [ -e ${containerPath.escape} ]; then $f; fi"
+
+  def every(duration: FiniteDuration)(f: => String): String =
+    s"""while true; do
+       |  (
+       |    $f
+       |  ) > /dev/null 2>&1
+       |  sleep ${duration.toSeconds}
+       |done""".stripMargin
+
+  def retry(f: => String)(implicit gcsTransferConfiguration: GcsTransferConfiguration, wait: FiniteDuration): String = {
+    s"""for i in $$(seq ${gcsTransferConfiguration.transferAttempts}); do
+       |  (
+       |    $f
+       |  )
+       |  RC=$$?
+       |  if [ "$$RC" = "0" ]; then
+       |    break
+       |  fi
+       |  if [ $$i -lt ${gcsTransferConfiguration.transferAttempts} ]; then
+       |    ${s"""Waiting ${wait.toSeconds} seconds and retrying""" |> timestampedMessage}
+       |    sleep ${wait.toSeconds}
+       |  fi
+       |done
+       |exit "$$RC"""".stripMargin
+  }
+
+  def delocalizeFileOrDirectory(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
+                               (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+    s"""if [ -d ${containerPath.escape} ]; then
+       |  ${delocalizeDirectory(containerPath, cloudPath, contentType)}
+       |else
+       |  ${delocalizeFile(containerPath, cloudPath, contentType)}
+       |fi""".stripMargin
+  }
+
+  def localizeDirectory(cloudPath: Path, containerPath: Path)
+                       (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+    retry {
+      recoverRequesterPaysError(cloudPath) { flag =>
+        s"${containerPath |> makeContainerDirectory} && " +
+          s"rm -f $$HOME/.config/gcloud/gce && gsutil $flag -m rsync -r ${cloudPath.escape} ${containerPath.escape}"
+      }
+    }
+  }
+
+  def localizeFile(cloudPath: Path, containerPath: Path)
+                  (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+    retry {
+      recoverRequesterPaysError(cloudPath) { flag =>
+        s"rm -f $$HOME/.config/gcloud/gce && gsutil $flag cp ${cloudPath.escape} ${containerPath.escape}"
+      }
+    }
+  }
+
+  def recoverRequesterPaysError(path: Path)(f: String => String): String = {
+    val commandWithoutProject = f("")
+    val commandWithProject = f(s"-u ${path.projectId}")
+
+    s"""$commandWithoutProject > gsutil_output.txt 2>&1
+       |# Record the exit code of the gsutil command without project flag
+       |RC_GSUTIL=$$?
+       |if [ "$$RC_GSUTIL" != "0" ]; then
+       |  ${s"$commandWithoutProject failed" |> timestampedMessage}
+       |  # Print the reason of the failure
+       |  cat gsutil_output.txt
+       |
+       |  # Check if it matches the BucketIsRequesterPaysErrorMessage
+       |  if grep -q "$BucketIsRequesterPaysErrorMessage" gsutil_output.txt; then
+       |    ${"Retrying with user project" |> timestampedMessage}
+       |    $commandWithProject
+       |  else
+       |    exit "$$RC_GSUTIL"
+       |  fi
+       |else
+       |  exit 0
+       |fi""".stripMargin
+  }
+
+  def checkIfStderrContainsRetryKeys(retryLookupKeys: List[String]): String = {
+    val lookupKeysAsString = retryLookupKeys.mkString("|")
+    s"grep -E -q '$lookupKeysAsString' /cromwell_root/stderr ; echo $$? > /cromwell_root/memory_retry_rc"
+  }
+
+  def multiLineCommandTransformer(shell: String)(commandString: String): String = {
+    val randomUuid = UUID.randomUUID().toString
+    val withBashShebang = s"#!/bin/bash\n\n$commandString"
+    val base64EncodedScript = Base64.encodeBase64String(withBashShebang.getBytes(StandardCharsets.UTF_8))
+    val scriptPath = s"/tmp/$randomUuid.sh"
+
+    s"""python3 -c 'import base64; print(base64.b64decode("$base64EncodedScript").decode("utf-8"));' """ +
+      s"""> $scriptPath && """ +
+      s"chmod u+x $scriptPath && " +
+      s"$shell $scriptPath"
+  }
+
+  def multiLineCommand(commandString: String): String = multiLineCommandTransformer("sh")(commandString)
+
+  def multiLineBinBashCommand(commandString: String): String = multiLineCommandTransformer("/bin/bash")(commandString)
+
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableFlag.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableFlag.scala
new file mode 100644
index 00000000000..f2007c65226
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableFlag.scala
@@ -0,0 +1,9 @@
+package cromwell.backend.google.batch.runnable
+
+sealed trait RunnableFlag
+
+object RunnableFlag {
+  case object IgnoreExitStatus extends RunnableFlag
+  case object RunInBackground extends RunnableFlag
+  case object AlwaysRun extends RunnableFlag
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableLabels.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableLabels.scala
new file mode 100644
index 00000000000..7d9978c42c1
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableLabels.scala
@@ -0,0 +1,22 @@
+package cromwell.backend.google.batch.runnable
+
+object RunnableLabels {
+  object Key {
+    /**
+      * Very short description of the runnable
+      */
+    val Tag = "tag"
+    val Logging = "logging"
+    val InputName = "inputName"
+    val OutputName = "outputName"
+  }
+  object Value {
+    val ContainerSetup = "ContainerSetup"
+    val UserRunnable = "UserRunnable"
+    val Localization = "Localization"
+    val Delocalization = "Delocalization"
+    val Monitoring = "Monitoring"
+    val Background = "Background"
+    val RetryWithMoreMemory = "CheckingForMemoryRetry"
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala
new file mode 100644
index 00000000000..7df2a4bff79
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala
@@ -0,0 +1,83 @@
+package cromwell.backend.google.batch.runnable
+
+import com.google.cloud.batch.v1.Runnable
+import com.typesafe.config.ConfigFactory
+import net.ceedubs.ficus.Ficus._
+import org.apache.commons.text.StringEscapeUtils
+
+object RunnableUtils {
+  /** Image to use for ssh access. */
+  val sshImage = "gcr.io/cloud-genomics-pipelines/tools"
+
+  /** Entry point on the ssh image. */
+  val sshEntryPoint = "ssh-server"
+
+  /** Port mappings for the ssh container. */
+  val sshPortMappings = Map("22" -> Int.box(22))
+
+  /*
+   * At the moment, cloud-sdk (924MB for 276.0.0-slim) and stedolan/jq (182MB) decompressed ~= 1.1 GB
+   */
+  val cromwellImagesSizeRoundedUpInGB = 1
+
+  private val config = ConfigFactory.load().getConfig("google")
+
+  /**
+    * An image with the Google Cloud SDK installed.
+    * http://gcr.io/google.com/cloudsdktool/cloud-sdk
+    *
+    * FYI additional older versions are available on DockerHub at:
+    * https://hub.docker.com/r/google/cloud-sdk
+    *
+    * When updating this value, also consider updating the CromwellImagesSizeRoundedUpInGB below.
+    */
+  val CloudSdkImage: String =
+    //config.getOrElse("cloud-sdk-image-url", "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine")
+    config.getOrElse("cloud-sdk-image-url", "gcr.io/google.com/cloudsdktool/cloud-sdk:434.0.0-alpine")
+  /*
+   * At the moment, cloud-sdk (584MB for 354.0.0-alpine) and stedolan/jq (182MB) decompressed ~= 0.8 GB
+   */
+  val CromwellImagesSizeRoundedUpInGB: Int =
+    config.getOrElse("cloud-sdk-image-size-gb", 1)
+
+  /** Quotes a string such that it's compatible as a string argument in the shell. */
+  def shellEscaped(any: Any): String = {
+    val str = String.valueOf(any)
+    /*
+    NOTE: escapeXSI is more compact than wrapping in single quotes. Newlines are also stripped by the shell, as they
+    are by escapeXSI. If for some reason escapeXSI doesn't 100% work, say because it ends up stripping some required
+    newlines, then consider adding a check for newlines and then using:
+
+    "'" + str.replace("'", "'\"'\"'") + "'"
+     */
+    StringEscapeUtils.escapeXSI(str)
+  }
+
+  private val backgroundRunnableTerminationGraceTime = 10
+
+  val terminateAllBackgroundRunnablesCommand: String = s"kill -TERM -1 && sleep $backgroundRunnableTerminationGraceTime || true"
+
+  def timestampedMessage(message: String): String =
+    s"""printf '%s %s\\n' "$$(date -u '+%Y/%m/%d %H:%M:%S')" ${shellEscaped(message)}"""
+
+  /** Start background runnables first, leave the rest as is */
+  def sortRunnables(containerSetup: List[Runnable],
+                            localization: List[Runnable],
+                            userRunnable: List[Runnable],
+                            memoryRetryRunnable: List[Runnable],
+                            deLocalization: List[Runnable],
+                            monitoringSetup: List[Runnable],
+                            monitoringShutdown: List[Runnable],
+                            checkpointingStart: List[Runnable],
+                            checkpointingShutdown: List[Runnable],
+                            sshAccess: List[Runnable],
+                            isBackground: Runnable => Boolean,
+                         ): List[Runnable] = {
+    val toBeSortedRunnables = localization ++ userRunnable ++ memoryRetryRunnable ++ deLocalization
+    val sortedRunnables = toBeSortedRunnables.sortWith {
+      case (runnable, _) => isBackground(runnable)
+    }
+
+    sshAccess ++ containerSetup ++ monitoringSetup ++ checkpointingStart ++ sortedRunnables ++ checkpointingShutdown ++ monitoringShutdown
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala
new file mode 100644
index 00000000000..b7f5a026476
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala
@@ -0,0 +1,25 @@
+package cromwell.backend.google.batch.runnable
+
+import com.google.cloud.batch.v1.{Runnable, Volume}
+import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobParameters
+
+
+trait UserRunnable {
+
+  def userRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume]): List[Runnable] = {
+
+    println(f"job shell ${createParameters.jobShell}")
+    println(f"script container path ${createParameters.commandScriptContainerPath}")
+
+    val userRunnable = RunnableBuilder.userRunnable(
+      docker = createParameters.dockerImage,
+      scriptContainerPath = createParameters.commandScriptContainerPath.pathAsString,
+      jobShell = "/bin/bash",
+      volumes = volumes,
+      dockerhubCredentials = createParameters.dockerhubCredentials
+    )
+
+    val describeRunnable = RunnableBuilder.describeDocker("user runnable", userRunnable)
+    List(describeRunnable, userRunnable).map(_.build)
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/WorkflowOptionKeys.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/WorkflowOptionKeys.scala
new file mode 100644
index 00000000000..34f22acbd8b
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/WorkflowOptionKeys.scala
@@ -0,0 +1,13 @@
+package cromwell.backend.google.batch.runnable
+
+object WorkflowOptionKeys {
+  val MonitoringScript = "monitoring_script"
+  val MonitoringImage = "monitoring_image"
+  val MonitoringImageScript = "monitoring_image_script"
+  val EnableSSHAccess = "enable_ssh_access"
+  val GoogleProject = "google_project"
+  val GoogleComputeServiceAccount = "google_compute_service_account"
+  val EnableFuse = "enable_fuse"
+  val GoogleLegacyMachineSelection = "google_legacy_machine_selection"
+  val UseDockerImageCache = "use_docker_image_cache"
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchExpressionFunctions.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchExpressionFunctions.scala
new file mode 100644
index 00000000000..4ad6cc45b61
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchExpressionFunctions.scala
@@ -0,0 +1,38 @@
+package cromwell.backend.google.batch.util
+
+import com.google.cloud.storage.contrib.nio.CloudStorageOptions
+import cromwell.backend.standard.{StandardExpressionFunctions, StandardExpressionFunctionsParams}
+import cromwell.core.CallContext
+import cromwell.core.io.{CallCorePathFunctionSet, IoCommandBuilder}
+import cromwell.core.path.Path
+import cromwell.core.path.PathFactory.PathBuilders
+import cromwell.filesystems.gcs.GcsPathBuilder
+import cromwell.filesystems.gcs.GcsPathBuilder.{InvalidGcsPath, PossiblyValidRelativeGcsPath, ValidFullGcsPath}
+import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
+
+class BatchPathFunctions(pathBuilders: PathBuilders, callContext: CallContext) extends CallCorePathFunctionSet(pathBuilders, callContext) {
+  override def relativeToHostCallRoot(path: String) = {
+    GcsPathBuilder.validateGcsPath(path) match {
+      case _: ValidFullGcsPath => path
+      case _ => callContext.root.resolve(path.stripPrefix("file://").stripPrefix("/")).pathAsString
+    }
+  }
+}
+
+class BatchExpressionFunctions(standardParams: StandardExpressionFunctionsParams)
+  extends StandardExpressionFunctions(standardParams) {
+  override lazy val ioCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder
+
+  override def preMapping(str: String) = {
+    GcsPathBuilder.validateGcsPath(str) match {
+      case _: ValidFullGcsPath => str
+      case PossiblyValidRelativeGcsPath => callContext.root.resolve(str.stripPrefix("/")).pathAsString
+      case _: InvalidGcsPath => str
+    }
+  }
+
+  override lazy val pathFunctions = new BatchPathFunctions(pathBuilders, callContext)
+
+  override protected def writeAsync(file: Path, content: String) =
+    asyncIo.writeAsync(file, content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchParameterConversions.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchParameterConversions.scala
new file mode 100644
index 00000000000..ad7c942b4f9
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchParameterConversions.scala
@@ -0,0 +1,149 @@
+package cromwell.backend.google.batch.util
+
+import com.google.cloud.batch.v1.{Runnable, Volume}
+//import com.typesafe.config.ConfigFactory
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.batch.models._
+import cromwell.backend.google.batch.runnable._
+import cromwell.filesystems.drs.DrsPath
+import cromwell.filesystems.gcs.GcsPath
+import cromwell.filesystems.http.HttpPath
+//import cromwell.filesystems.sra.SraPath
+import simulacrum.typeclass
+
+@typeclass trait ToParameter[A <: BatchParameter] {
+  def toRunnables(p: A, volumes: List[Volume])(implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable.Builder]
+}
+
+trait GcpBatchParameterConversions {
+  import RunnableBuilder._
+  import RunnableCommands._
+  import RunnableLabels._
+
+
+  implicit val fileInputToParameter: ToParameter[GcpBatchFileInput] = new ToParameter[GcpBatchFileInput] {
+    override def toRunnables(fileInput: GcpBatchFileInput, volumes: List[Volume])
+                          (implicit retryPolicy: GcsTransferConfiguration): List[Runnable.Builder] = {
+
+      val labels = RunnableBuilder.parameterLabels(fileInput)
+      fileInput.cloudPath match {
+        case _: HttpPath =>
+          val command = s"curl --silent --create-dirs --output ${fileInput.containerPath} ${fileInput.cloudPath}"
+          val localizationRunnables = RunnableBuilder.cloudSdkShellRunnable(command)(volumes = volumes, labels = labels, flags = List.empty)
+          List(RunnableBuilder.describeParameter(fileInput, volumes, labels), localizationRunnables)
+
+        case _: GcsPath =>
+          // GCS paths will be localized with a separate localization script.
+          Nil
+        case _: DrsPath =>
+          // DRS paths will be localized with a single call to cromwell-drs-localizer with a manifest
+          Nil
+      }
+    }
+  }
+
+  implicit val directoryInputToParameter: ToParameter[GcpBatchDirectoryInput] =
+    new ToParameter[GcpBatchDirectoryInput] {
+      override def toRunnables(directoryInput: GcpBatchDirectoryInput, volumes: List[Volume])
+                            (implicit retryPolicy: GcsTransferConfiguration): List[Runnable.Builder] = {
+        directoryInput.cloudPath match {
+          case _: GcsPath => Nil // GCS paths will be localized with a separate localization script.
+          case _ =>
+            val labels = RunnableBuilder.parameterLabels(directoryInput)
+            val describeRunnables = RunnableBuilder.describeParameter(directoryInput, volumes, labels)
+            val localizationRunnables = RunnableBuilder.cloudSdkShellRunnable(
+              RunnableCommands.localizeDirectory(directoryInput.cloudPath, directoryInput.containerPath)
+            )(volumes = volumes, labels = labels, flags = List.empty)
+            List(describeRunnables, localizationRunnables)
+        }
+      }
+    }
+
+  implicit val fileOutputToParameter: ToParameter[GcpBatchFileOutput] = new ToParameter[GcpBatchFileOutput] {
+    override def toRunnables(fileOutput: GcpBatchFileOutput, volumes: List[Volume])
+                          (implicit retryPolicy: GcsTransferConfiguration): List[Runnable.Builder] = {
+
+      // If the output is a "secondary file", it actually could be a directory but we won't know before runtime.
+      // The fileOrDirectory method will generate a command that can cover both cases
+      lazy val copy = if (fileOutput.secondary)
+        RunnableCommands.delocalizeFileOrDirectory(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
+      else
+        RunnableCommands.delocalizeFile(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
+
+      lazy val copyOnlyIfExists = RunnableCommands.ifExist(fileOutput.containerPath) {
+        copy
+      }
+
+      lazy val copyCommand = if (fileOutput.optional || fileOutput.secondary) copyOnlyIfExists else copy
+      lazy val labels = RunnableBuilder.parameterLabels(fileOutput)
+
+      // The delocalization runnables to take once the user command has terminated (i.e., the non-periodic uploads).
+      val finalDelocalizationRunnables = fileOutput.cloudPath match {
+        case _: GcsPath => Nil // GCS files are delocalized with a separate delocalization script.
+        case _ =>
+          val describeRunnable = RunnableBuilder.describeParameter(fileOutput, volumes, labels)
+          val delocalizationRunnable = RunnableBuilder
+            .cloudSdkShellRunnable(copyCommand)(volumes = volumes, labels = labels, flags = List.empty)
+            .withAlwaysRun(true)
+
+          List(describeRunnable, delocalizationRunnable)
+      }
+
+      fileOutput.uploadPeriod match {
+        // If the file should be uploaded periodically, create a background upload runnable in addition to any normal ones
+        // that run at the end to make sure we get the most up to date version of the file.
+        case Some(period) =>
+          val periodicLabels = labels collect {
+            case (key, _) if key == Key.Tag => key -> Value.Background
+            case (key, value) => key -> value
+          }
+          val periodic = RunnableBuilder.cloudSdkShellRunnable(
+            every(period) {
+              copyCommand
+            }
+          )(volumes = volumes, labels = periodicLabels, flags = List.empty).withRunInBackground(true)
+
+          finalDelocalizationRunnables :+ periodic
+
+        case None => finalDelocalizationRunnables
+      }
+    }
+  }
+
+  implicit val directoryOutputToParameter: ToParameter[GcpBatchDirectoryOutput] =
+    new ToParameter[GcpBatchDirectoryOutput] {
+      override def toRunnables(directoryOutput: GcpBatchDirectoryOutput, volumes: List[Volume])
+                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable.Builder] = {
+        directoryOutput.cloudPath match {
+          case _: GcsPath => Nil // GCS paths will be delocalized with a separate delocalization script.
+          case _ =>
+            val labels = RunnableBuilder.parameterLabels(directoryOutput)
+            val describeRunnable = RunnableBuilder.describeParameter(directoryOutput, volumes, labels)
+            val delocalizationRunnable = RunnableBuilder.cloudSdkShellRunnable(
+              delocalizeDirectory(directoryOutput.containerPath, directoryOutput.cloudPath, None)
+            )(volumes = volumes, labels = labels, flags = List.empty)
+              .withAlwaysRun(true)
+
+            List(describeRunnable, delocalizationRunnable)
+        }
+      }
+    }
+
+  implicit val inputToParameter: ToParameter[GcpBatchInput] = new ToParameter[GcpBatchInput] {
+    override def toRunnables(p: GcpBatchInput, volumes: List[Volume])
+                          (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable.Builder] = p match {
+      case fileInput: GcpBatchFileInput => fileInputToParameter.toRunnables(fileInput, volumes)
+      case directoryInput: GcpBatchDirectoryInput => directoryInputToParameter.toRunnables(directoryInput, volumes)
+    }
+  }
+
+  implicit val outputToParameter: ToParameter[GcpBatchOutput] = new ToParameter[GcpBatchOutput] {
+    override def toRunnables(p: GcpBatchOutput, volumes: List[Volume])
+                          (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable.Builder] = p match {
+      case fileOutput: GcpBatchFileOutput => fileOutputToParameter.toRunnables(fileOutput, volumes)
+      case directoryOutput: GcpBatchDirectoryOutput => directoryOutputToParameter.toRunnables(directoryOutput, volumes)
+    }
+  }
+}
+
+object GcpBatchParameterConversions extends GcpBatchParameterConversions
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala
new file mode 100644
index 00000000000..87b4762f5a5
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala
@@ -0,0 +1,102 @@
+package cromwell.backend.google.batch.util
+
+import com.google.cloud.batch.v1.AllocationPolicy.{Accelerator, AttachedDisk, Disk, ProvisioningModel}
+import com.google.cloud.batch.v1.Volume
+import cromwell.backend.google.batch.io.{DiskType, GcpBatchAttachedDisk, GcpBatchReferenceFilesDisk}
+import cromwell.backend.google.batch.models.{GcpBatchRuntimeAttributes, GpuResource}
+import wom.format.MemorySize
+
+trait BatchUtilityConversions {
+
+
+  // construct zones string
+  def toZonesPath(zones: Vector[String]): String = {
+    "zones/" + zones.mkString(",")
+  }
+
+  // lowercase text to match gcp label requirements
+  def toLabel(text: String): String = {
+    text.toLowerCase
+  }
+
+  // creates batch run time location from zones entered in runtime.  This is needed if network not defined by user to place on right network.
+  def toBatchRunLocation(zones: Vector[String]): String = {
+    val parts = zones.mkString(",").split("-")
+    parts(0) + "-" + parts(1)
+  }
+
+  // convert cpu cores to millicores that Batch expects
+  def toCpuCores(cpu: Long): Long = {
+    cpu * 1000
+  }
+
+  // convert memory to MiB that Batch expects
+  def toMemMib(memory: MemorySize): Long = {
+    (memory.amount * 1024).toLong
+  }
+
+  // set Standard or Spot instances
+  def toProvisioningModel(preemption: Int): ProvisioningModel = preemption compare 0 match {
+    case 0 => ProvisioningModel.STANDARD
+    case 1 => ProvisioningModel.SPOT
+  }
+
+  def toDisks(disks: Seq[GcpBatchAttachedDisk]): List[AttachedDisk] = disks.map(toDisk).toList
+
+  def toVolumes(disks: Seq[GcpBatchAttachedDisk]): List[Volume] = disks.map(toVolume).toList
+
+  def toVolume(disk: GcpBatchAttachedDisk): Volume = {
+    val volume = Volume
+      .newBuilder
+      .setDeviceName(disk.name)
+      .setMountPath(disk.mountPoint.pathAsString)
+
+
+    disk match {
+      case _: GcpBatchReferenceFilesDisk =>
+        volume
+          .addMountOptions("async, rw")
+          .build
+      case _ =>
+        volume
+          .build
+    }
+  }
+
+  private def toDisk(disk: GcpBatchAttachedDisk): AttachedDisk = {
+    val googleDisk = Disk
+      .newBuilder
+      .setSizeGb(disk.sizeGb.toLong)
+      .setType(toBatchDiskType(disk.diskType))
+
+    disk match {
+      case refDisk: GcpBatchReferenceFilesDisk =>
+        googleDisk.setImage(refDisk.image)
+          .build
+      case _ =>
+        googleDisk.build
+    }
+
+    val googleAttachedDisk = AttachedDisk
+      .newBuilder
+      .setDeviceName(disk.name)
+      .setNewDisk(googleDisk)
+      .build
+    googleAttachedDisk
+
+  }
+
+  private def toBatchDiskType(diskType: DiskType) = diskType match {
+    case DiskType.HDD => "pd-standard"
+    case DiskType.SSD => "pd-ssd"
+    case DiskType.LOCAL => "local-ssd"
+  }
+
+  def convertGbToMib(runtimeAttributes: GcpBatchRuntimeAttributes): Long = {
+    (runtimeAttributes.bootDiskSize * 953.7).toLong
+  }
+
+  // Create accelerators for GPUs
+  def toAccelerator(gpuResource: GpuResource): Accelerator.Builder = Accelerator.newBuilder.setCount(gpuResource.gpuCount.value.toLong).setType(gpuResource.gpuType.toString)
+
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchDockerCacheMappingOperations.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchDockerCacheMappingOperations.scala
new file mode 100644
index 00000000000..e7ca7a0e6a8
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchDockerCacheMappingOperations.scala
@@ -0,0 +1,81 @@
+package cromwell.backend.google.batch.util
+
+import _root_.io.circe.generic.auto._
+import _root_.io.circe.parser._
+import cats.effect.IO
+import com.google.api.services.storage.StorageScopes
+import com.google.cloud.storage.{BlobId, Storage, StorageOptions}
+import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
+import cromwell.core.logging.JobLogger
+import cromwell.filesystems.gcs.GcsPathBuilder.ValidFullGcsPath
+
+import scala.util.control.NoStackTrace
+
+case class DockerImageCacheEntry(dockerImageDigest: String, diskImageName: String)
+case class DockerImageCacheManifest(manifestFormatVersion: Int, dockerImageCacheMap: Map[String, DockerImageCacheEntry])
+
+trait GcpBatchDockerCacheMappingOperations {
+
+  private val CURRENT_SUPPORTED_MANIFEST_FORMAT_VERSION = 2
+  private class DockerImageManifestVersionError(message: String) extends RuntimeException(message) with NoStackTrace
+
+  def generateDockerImageToDiskImageMapping(auth: GoogleAuthMode,
+                                            dockerImageCacheManifestFile: ValidFullGcsPath): Map[String, DockerImageCacheEntry] = {
+
+    val gcsClient = StorageOptions
+      .newBuilder()
+      .setCredentials(auth.credentials(Set(StorageScopes.DEVSTORAGE_READ_ONLY)))
+      .build
+      .getService
+    val mappingsFromManifestIO = readDockerImageCacheManifestFileFromGCS(gcsClient, dockerImageCacheManifestFile)
+    mappingsFromManifestIO.map(_.dockerImageCacheMap).unsafeRunSync()
+  }
+
+  def getDockerCacheDiskImageForAJob(dockerImageToCacheDiskImageMappingOpt: Option[Map[String, DockerImageCacheEntry]],
+                                     dockerImageAsSpecifiedByUser: String,
+                                     dockerImageWithDigest: String,
+                                     jobLogger: JobLogger): Option[String] = {
+    dockerImageToCacheDiskImageMappingOpt
+      .flatMap(_.get(dockerImageAsSpecifiedByUser))
+      .filter { cachedDockerImageDigestAndDiskName =>
+        val hashStartingPositionInActualDockerImage = dockerImageWithDigest.indexOf('@')
+        if (hashStartingPositionInActualDockerImage != -1) {
+          val actualDigestOfDesiredDockerImage = dockerImageWithDigest.substring(hashStartingPositionInActualDockerImage + 1)
+          if (cachedDockerImageDigestAndDiskName.dockerImageDigest == actualDigestOfDesiredDockerImage) {
+            true
+          } else {
+            jobLogger.info(s"Cached Docker image digest mismatch. Requested docker image $dockerImageAsSpecifiedByUser has different digest than " +
+              s"corresponding cached image located at the ${cachedDockerImageDigestAndDiskName.diskImageName} disk image. " +
+              s"Digest of requested image is $actualDigestOfDesiredDockerImage, but digest of cached image is ${cachedDockerImageDigestAndDiskName.dockerImageDigest}. " +
+              s"Docker image cache feature will not be used for this task.")
+
+            false
+          }
+        } else {
+          jobLogger.error(s"Programmer error ! Odd docker image name where supposed to be name with digest: $dockerImageWithDigest")
+          false
+        }
+      }
+      .map(_.diskImageName)
+  }
+
+  private[batch] def readDockerImageCacheManifestFileFromGCS(gcsClient: Storage, gcsPath: ValidFullGcsPath): IO[DockerImageCacheManifest] = {
+    val manifestFileBlobIo = IO { gcsClient.get(BlobId.of(gcsPath.bucket, gcsPath.path.substring(1))) }
+    manifestFileBlobIo flatMap { manifestFileBlob =>
+      val jsonStringIo = IO { manifestFileBlob.getContent().map(_.toChar).mkString }
+      jsonStringIo.flatMap { jsonStr =>
+        decode[DockerImageCacheManifest](jsonStr) match {
+          case Left(error) => IO.raiseError(error)
+          case Right(parsedManifest) =>
+            if (parsedManifest.manifestFormatVersion == CURRENT_SUPPORTED_MANIFEST_FORMAT_VERSION) {
+              IO.pure(parsedManifest)
+            } else {
+              IO.raiseError(new DockerImageManifestVersionError(s"Current supported docker image cache manifest format version " +
+                s"is $CURRENT_SUPPORTED_MANIFEST_FORMAT_VERSION, but got ${parsedManifest.manifestFormatVersion}"))
+            }
+        }
+      }
+    }
+  }
+
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchExpressionFunctions.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchExpressionFunctions.scala
new file mode 100644
index 00000000000..2cb2b86b34c
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchExpressionFunctions.scala
@@ -0,0 +1,38 @@
+package cromwell.backend.google.batch.util
+
+import com.google.cloud.storage.contrib.nio.CloudStorageOptions
+import cromwell.backend.standard.{StandardExpressionFunctions, StandardExpressionFunctionsParams}
+import cromwell.core.CallContext
+import cromwell.core.io.{CallCorePathFunctionSet, IoCommandBuilder}
+import cromwell.core.path.Path
+import cromwell.core.path.PathFactory.PathBuilders
+import cromwell.filesystems.gcs.GcsPathBuilder
+import cromwell.filesystems.gcs.GcsPathBuilder.{InvalidGcsPath, PossiblyValidRelativeGcsPath, ValidFullGcsPath}
+import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
+
+class GcpBatchPathFunctions(pathBuilders: PathBuilders, callContext: CallContext) extends CallCorePathFunctionSet(pathBuilders, callContext) {
+  override def relativeToHostCallRoot(path: String) = {
+    GcsPathBuilder.validateGcsPath(path) match {
+      case _: ValidFullGcsPath => path
+      case _ => callContext.root.resolve(path.stripPrefix("file://").stripPrefix("/")).pathAsString
+    }
+  }
+}
+
+class GcpBatchExpressionFunctions(standardParams: StandardExpressionFunctionsParams)
+  extends StandardExpressionFunctions(standardParams) {
+  override lazy val ioCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder
+
+  override def preMapping(str: String) = {
+    GcsPathBuilder.validateGcsPath(str) match {
+      case _: ValidFullGcsPath => str
+      case PossiblyValidRelativeGcsPath => callContext.root.resolve(str.stripPrefix("/")).pathAsString
+      case _: InvalidGcsPath => str
+    }
+  }
+
+  override lazy val pathFunctions = new GcpBatchPathFunctions(pathBuilders, callContext)
+
+  override protected def writeAsync(file: Path, content: String) =
+    asyncIo.writeAsync(file, content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraints.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraints.scala
new file mode 100644
index 00000000000..83b4796e039
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraints.scala
@@ -0,0 +1,31 @@
+package cromwell.backend.google.batch.util
+
+import cromwell.backend.google.batch.models.{GcpBatchRuntimeAttributes, N1CustomMachineType, N2CustomMachineType, N2DCustomMachineType}
+import eu.timepit.refined.api.Refined
+import eu.timepit.refined.numeric.Positive
+import org.slf4j.Logger
+import wdl4s.parser.MemoryUnit
+import wom.format.MemorySize
+
+object GcpBatchMachineConstraints {
+  def machineType(memory: MemorySize,
+                  cpu: Int Refined Positive,
+                  cpuPlatformOption: Option[String],
+                  googleLegacyMachineSelection: Boolean,
+                  jobLogger: Logger,
+                 ): String = {
+    if (googleLegacyMachineSelection) {
+      s"predefined-$cpu-${memory.to(MemoryUnit.MB).amount.intValue()}"
+    } else {
+      // If someone requests Intel Cascade Lake as their CPU platform then switch the machine type to n2.
+      // Similarly, CPU platform of AMD Rome corresponds to the machine type n2d.  
+      val customMachineType =
+        cpuPlatformOption match {
+          case Some(GcpBatchRuntimeAttributes.CpuPlatformIntelCascadeLakeValue) => N2CustomMachineType
+          case Some(GcpBatchRuntimeAttributes.CpuPlatformAMDRomeValue)          => N2DCustomMachineType
+          case _ => N1CustomMachineType
+        }
+      customMachineType.machineType(memory, cpu, jobLogger)
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchReferenceFilesMappingOperations.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchReferenceFilesMappingOperations.scala
new file mode 100644
index 00000000000..f472263f51c
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchReferenceFilesMappingOperations.scala
@@ -0,0 +1,119 @@
+package cromwell.backend.google.batch.util
+
+import cats.effect.IO
+import cats.implicits._
+import com.google.api.services.storage.StorageScopes
+import com.google.cloud.storage.Storage.{BlobField, BlobGetOption}
+import com.google.cloud.storage.{BlobId, Storage, StorageOptions}
+import com.google.common.io.BaseEncoding
+import com.google.common.primitives.Longs
+import cromwell.backend.google.batch.errors.InvalidGcsPathsInManifestFileException
+import cromwell.backend.google.batch.io.GcpBatchReferenceFilesDisk
+import cromwell.backend.google.batch.models.{GcpBatchInput, ManifestFile, ReferenceFile}
+import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
+import cromwell.filesystems.gcs.GcsPathBuilder.{InvalidFullGcsPath, ValidFullGcsPath}
+import cromwell.filesystems.gcs.{GcsPath, GcsPathBuilder}
+import org.slf4j.{Logger, LoggerFactory}
+
+import java.util
+
+trait GcpBatchReferenceFilesMappingOperations {
+  private val logger: Logger = LoggerFactory.getLogger(getClass)
+
+  /**
+    * This method validates reference files' CRC32Cs. Depending on the number of manifests and their sizes this
+    * may take a significant amount of time.
+    */
+  def generateReferenceFilesMapping(auth: GoogleAuthMode,
+                                    referenceDiskLocalizationManifests: List[ManifestFile]): Map[String, GcpBatchReferenceFilesDisk] = {
+    val gcsClient = StorageOptions
+      .newBuilder()
+      .setCredentials(auth.credentials(Set(StorageScopes.DEVSTORAGE_READ_ONLY)))
+      .build
+      .getService
+
+    val validReferenceFilesMapIO = referenceDiskLocalizationManifests
+      .traverse(manifestFile => getMapOfValidReferenceFilePathsToDisks(gcsClient, manifestFile))
+      .map(_.flatten.toMap)
+
+    validReferenceFilesMapIO.unsafeRunSync()
+  }
+
+  def getReferenceInputsToMountedPathMappings(referenceFileToDiskImageMapping: Map[String, GcpBatchReferenceFilesDisk],
+                                              inputFiles: List[GcpBatchInput]): Map[GcpBatchInput, String] = {
+    val gcsPathsToInputs = inputFiles.collect { case i if i.cloudPath.isInstanceOf[GcsPath] => (i.cloudPath.asInstanceOf[GcsPath].pathAsString, i) }.toMap
+    referenceFileToDiskImageMapping.collect {
+      case (path, disk) if gcsPathsToInputs.keySet.contains(s"gs://$path")  =>
+        (gcsPathsToInputs(s"gs://$path"), s"${disk.mountPoint.pathAsString}/$path")
+    }
+  }
+
+  def getReferenceDisksToMount(referenceFileToDiskImageMapping: Map[String, GcpBatchReferenceFilesDisk],
+                               inputFilePaths: Set[String]): List[GcpBatchReferenceFilesDisk] = {
+    referenceFileToDiskImageMapping.view.filterKeys(key => inputFilePaths.contains(s"gs://$key")).values.toList.distinct
+  }
+
+  private def getReferenceFileToValidatedGcsPathMap(referenceFiles: Set[ReferenceFile]): IO[Map[ReferenceFile, ValidFullGcsPath]] = {
+    val filesAndValidatedPaths = referenceFiles.map {
+      referenceFile => (referenceFile, GcsPathBuilder.validateGcsPath(s"gs://${referenceFile.path}"))
+    }.toMap
+
+    val filesWithValidPaths = filesAndValidatedPaths.collect {
+      case (referenceFile, validPath: ValidFullGcsPath) => (referenceFile, validPath)
+    }
+    val filesWithInvalidPaths = filesAndValidatedPaths.collect {
+      case (referenceFile, invalidPath: InvalidFullGcsPath) => (referenceFile, invalidPath)
+    }
+
+    if (filesWithInvalidPaths.nonEmpty) {
+      IO.raiseError(new InvalidGcsPathsInManifestFileException(filesWithInvalidPaths.keySet.map(_.path).toList))
+    } else {
+      IO.pure(filesWithValidPaths)
+    }
+  }
+
+  protected def bulkValidateCrc32cs(gcsClient: Storage,
+                                    filesWithValidPaths: Map[ReferenceFile, ValidFullGcsPath]): IO[Map[ReferenceFile, Boolean]] = {
+    IO {
+      val gcsBatch = gcsClient.batch()
+      val filesAndBlobResults = filesWithValidPaths map {
+        case (referenceFile, ValidFullGcsPath(bucket, path)) =>
+          val blobGetResult = gcsBatch.get(BlobId.of(bucket, path.substring(1)), BlobGetOption.fields(BlobField.CRC32C))
+          (referenceFile, blobGetResult)
+      }
+      gcsBatch.submit()
+
+      filesAndBlobResults map {
+        case (referenceFile, blobGetResult) =>
+          val crc32cFromManifest = BaseEncoding.base64.encode(
+            // drop 4 leading bytes from Long crc32c value
+            // https://stackoverflow.com/a/25111119/1794750
+            util.Arrays.copyOfRange(Longs.toByteArray(referenceFile.crc32c), 4, 8)
+          )
+
+          (referenceFile, crc32cFromManifest === blobGetResult.get().getCrc32c)
+      }
+    }
+  }
+
+  private def getMapOfValidReferenceFilePathsToDisks(gcsClient: Storage, manifestFile: ManifestFile): IO[Map[String, GcpBatchReferenceFilesDisk]] = {
+    val refDisk = GcpBatchReferenceFilesDisk(manifestFile.imageIdentifier, manifestFile.diskSizeGb)
+    val allReferenceFilesFromManifestMap = manifestFile.files.map(refFile => (refFile, refDisk)).toMap
+
+    val validReferenceFilesFromManifestMapIo =
+      for {
+        referenceFilesWithValidPaths <- getReferenceFileToValidatedGcsPathMap(allReferenceFilesFromManifestMap.keySet)
+        filesWithValidatedCrc32cs <- bulkValidateCrc32cs(gcsClient, referenceFilesWithValidPaths)
+      } yield allReferenceFilesFromManifestMap.view.filterKeys(key => filesWithValidatedCrc32cs.getOrElse(key, false))
+
+    validReferenceFilesFromManifestMapIo map { validReferenceFilesFromManifestMap =>
+      val invalidReferenceFiles = allReferenceFilesFromManifestMap.keySet -- validReferenceFilesFromManifestMap.keySet
+      if (invalidReferenceFiles.nonEmpty) {
+        logger.warn(s"The following files listed in references manifest have checksum mismatch with actual files in GCS: ${invalidReferenceFiles.mkString(",")}")
+      }
+      validReferenceFilesFromManifestMap.map {
+        case (refFile, disk) => (refFile.path, disk)
+      }.toMap
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuTypeValidation.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuTypeValidation.scala
new file mode 100644
index 00000000000..e7ade1bc46a
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuTypeValidation.scala
@@ -0,0 +1,25 @@
+package cromwell.backend.google.batch.util
+
+import cats.syntax.validated._
+import common.validation.ErrorOr.ErrorOr
+import cromwell.backend.google.batch.models.GpuResource.GpuType
+import cromwell.backend.validation.{OptionalRuntimeAttributesValidation, RuntimeAttributesValidation}
+import wom.RuntimeAttributesKeys
+import wom.types.{WomStringType, WomType}
+import wom.values.{WomString, WomValue}
+
+
+object GpuTypeValidation {
+  lazy val instance: RuntimeAttributesValidation[GpuType] = new GpuTypeValidation
+  lazy val optional: OptionalRuntimeAttributesValidation[GpuType] = instance.optional
+}
+
+class GpuTypeValidation extends RuntimeAttributesValidation[GpuType] {
+  override def key = RuntimeAttributesKeys.GpuTypeKey
+
+  override def coercion: Iterable[WomType] = Set(WomStringType)
+  override def validateValue: PartialFunction[WomValue, ErrorOr[GpuType]] = {
+    case WomString(s) => GpuType(s).validNel
+    case other => s"Invalid '$key': String value required but got ${other.womType.friendlyName}. See ${GpuType.MoreDetailsURL} for a list of options".invalidNel
+  }
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala
new file mode 100644
index 00000000000..4b24c9aeacf
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala
@@ -0,0 +1,40 @@
+package cromwell.backend.google.batch.util
+
+import cats.data.NonEmptyList
+import cats.syntax.either._
+import cats.syntax.validated._
+import com.typesafe.config.Config
+import common.validation.ErrorOr.ErrorOr
+import cromwell.backend.validation.{OptionalRuntimeAttributesValidation, PositiveIntRuntimeAttributesValidation, RuntimeAttributesValidation}
+import eu.timepit.refined.api.Refined
+import eu.timepit.refined.numeric.Positive
+import eu.timepit.refined.refineV
+import wom.RuntimeAttributesKeys.{GpuKey, GpuMaxKey, GpuMinKey}
+import wom.types.WomIntegerType
+import wom.values.{WomInteger, WomValue}
+
+object GpuValidation {
+  lazy val instance: RuntimeAttributesValidation[Int Refined Positive] = new GpuValidation(GpuKey)
+  lazy val optional: OptionalRuntimeAttributesValidation[Int Refined Positive] = instance.optional
+  lazy val instanceMin: RuntimeAttributesValidation[Int Refined Positive] = new GpuValidation(GpuMinKey)
+  lazy val optionalMin: OptionalRuntimeAttributesValidation[Int Refined Positive] = instanceMin.optional
+  lazy val instanceMax: RuntimeAttributesValidation[Int Refined Positive] = new GpuValidation(GpuMaxKey)
+  lazy val optionalMax: OptionalRuntimeAttributesValidation[Int Refined Positive] = instanceMax.optional
+
+  lazy val defaultMin: WomValue = WomInteger(0)
+  def configDefaultWomValue(config: Option[Config]): Option[WomValue] = instance.configDefaultWomValue(config)
+}
+
+class GpuValidation(attributeName: String) extends PositiveIntRuntimeAttributesValidation(attributeName) {
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[Int Refined Positive]] = {
+    case womValue if WomIntegerType.coerceRawValue(womValue).isSuccess =>
+      WomIntegerType.coerceRawValue(womValue).get match {
+        case WomInteger(value) =>
+          refineV[Positive](value.toInt)
+            .leftMap(_ => NonEmptyList.one(s"Expecting $key runtime attribute value greater than 0"))
+            .toValidated
+      }
+    case other =>
+      s"Invalid gpu count. Expected positive Int but got ${other.womType.friendlyName} ${other.toWomString}".invalidNel
+  }
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/RuntimeOutputMapping.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/RuntimeOutputMapping.scala
new file mode 100644
index 00000000000..4177c09dc6a
--- /dev/null
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/RuntimeOutputMapping.scala
@@ -0,0 +1,33 @@
+package cromwell.backend.google.batch.util
+
+import common.util.StringUtil._
+import cromwell.backend.google.batch.io.GcpBatchWorkingDisk
+import cromwell.core.path.Path
+
+object RuntimeOutputMapping {
+
+  /**
+   * List of prefixes to be stripped away from runtime output paths before
+   * appending them to the cloud call root to generate the delocalization path.
+   * The goal is to reduce unnecessary long paths which keep repeating the workflow root
+   * as the workflow progresses
+   *
+   * For instance:
+   *
+   * file:///cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
+   * ->
+   * call-A/file.txt
+   *
+   * Which will be delocalized to
+   * gs://bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-B/call-A/file.txt
+   * instead of
+   * gs://bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-B/cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
+   */
+  def prefixFilters(workflowRoot: Path): List[String] = List(
+    "file://",
+    "/",
+    GcpBatchWorkingDisk.MountPoint.pathAsString.relativeDirectory,
+    workflowRoot.pathWithoutScheme.relativeDirectory
+  )
+
+}
diff --git a/supportedBackends/google/batch/src/test/resources/reference.conf b/supportedBackends/google/batch/src/test/resources/reference.conf
new file mode 100644
index 00000000000..3685305454d
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/resources/reference.conf
@@ -0,0 +1 @@
+drs.localization.docker-image = "somerepo/drs-downloader:tagged"
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/GcpBatchIoSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/GcpBatchIoSpec.scala
new file mode 100644
index 00000000000..186152c0768
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/GcpBatchIoSpec.scala
@@ -0,0 +1,34 @@
+package cromwell.backend.google.batch
+
+import com.google.api.client.http.HttpResponseException
+import com.google.api.client.testing.http.{HttpTesting, MockHttpTransport, MockLowLevelHttpRequest, MockLowLevelHttpResponse}
+import common.assertion.CromwellTimeoutSpec
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+class GcpBatchIoSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  behavior of "io"
+
+  it should "consider 403 as a fatal exception" in {
+    val transport = mockTransport(403)
+    val request = transport.createRequestFactory().buildGetRequest(HttpTesting.SIMPLE_GENERIC_URL)
+    val mockedResponse = intercept[HttpResponseException](request.execute())
+    io.isFatalJesException(mockedResponse) should be(true)
+  }
+
+  it should "consider 429 as a transient exception" in {
+    val transport = mockTransport(429)
+    val request = transport.createRequestFactory().buildGetRequest(HttpTesting.SIMPLE_GENERIC_URL)
+    val mockedResponse = intercept[HttpResponseException](request.execute())
+    io.isTransientJesException(mockedResponse) should be(true)
+  }
+
+  private def mockTransport(statusCode: Int) = new MockHttpTransport() {
+    override def buildRequest(method: String, url: String) = {
+      new MockLowLevelHttpRequest() {
+        override def execute() = new MockLowLevelHttpResponse().setStatusCode(statusCode)
+      }
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
new file mode 100644
index 00000000000..711f59d6845
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
@@ -0,0 +1,800 @@
+package cromwell.backend.google.batch
+package actors
+
+import _root_.io.grpc.Status
+import _root_.wdl.draft2.model._
+import akka.actor.{ActorRef, Props}
+import akka.testkit.{ImplicitSender, TestActorRef, TestDuration, TestProbe}
+import cats.data.NonEmptyList
+import com.google.cloud.NoCredentials
+import com.google.cloud.batch.v1.{Job, JobName}
+import common.collections.EnhancedCollections._
+import cromwell.backend.BackendJobExecutionActor.BackendJobExecutionResponse
+import cromwell.backend._
+import cromwell.backend.async.AsyncBackendJobExecutionActor.{Execute, ExecutionMode}
+import cromwell.backend.async.{ExecutionHandle, FailedNonRetryableExecutionHandle}
+import cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.GcpBatchPendingExecutionHandle
+import cromwell.backend.google.batch.io.{DiskType, GcpBatchWorkingDisk}
+import cromwell.backend.google.batch.models._
+import cromwell.backend.google.batch.util.BatchExpressionFunctions
+import cromwell.backend.io.JobPathsSpecHelper._
+import cromwell.backend.standard.{DefaultStandardAsyncExecutionActorParams, StandardAsyncExecutionActorParams, StandardAsyncJob, StandardExpressionFunctionsParams}
+import cromwell.core._
+import cromwell.core.callcaching.NoDocker
+import cromwell.core.labels.Labels
+import cromwell.core.logging.JobLogger
+import cromwell.core.path.{DefaultPathBuilder, PathBuilder}
+import cromwell.filesystems.gcs.{GcsPath, GcsPathBuilder, MockGcsPathBuilder}
+import cromwell.services.instrumentation.InstrumentationService.InstrumentationServiceMessage
+import cromwell.services.instrumentation.{CromwellBucket, CromwellIncrement}
+import cromwell.services.keyvalue.InMemoryKvServiceActor
+import cromwell.services.keyvalue.KeyValueServiceActor.{KvJobKey, KvPair, ScopedKey}
+import cromwell.util.JsonFormatting.WomValueJsonFormatter._
+import cromwell.util.SampleWdl
+import org.scalatest._
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.matchers.should.Matchers
+import org.slf4j.Logger
+import spray.json._
+import wdl.transforms.draft2.wdlom2wom.WdlDraft2WomExecutableMakers._
+import wdl.transforms.draft2.wdlom2wom._
+import wom.WomFileMapper
+import wom.expression.NoIoFunctionSet
+import wom.graph.CommandCallNode
+import wom.transforms.WomExecutableMaker.ops._
+import wom.transforms.WomWorkflowDefinitionMaker.ops._
+import wom.values._
+
+import java.nio.file.Paths
+import java.util.UUID
+import scala.concurrent.duration._
+import scala.concurrent.{Await, ExecutionContext, Future, Promise}
+import scala.language.postfixOps
+import common.mock.MockSugar
+import org.mockito.Mockito._
+
+class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
+  with AnyFlatSpecLike
+  with Matchers
+  with ImplicitSender
+  with BackendSpec
+  with BeforeAndAfter
+  with MockSugar
+  with DefaultJsonProtocol {
+
+  val mockPathBuilder: GcsPathBuilder = MockGcsPathBuilder.instance
+  import MockGcsPathBuilder._
+  var kvService: ActorRef = system.actorOf(Props(new InMemoryKvServiceActor), "kvService")
+
+  private def gcsPath(str: String) = mockPathBuilder.build(str).getOrElse(fail(s"Invalid gcs path: $str"))
+
+  //import GcpBatchTestConfig._
+  import cromwell.backend.google.batch.models.GcpBatchTestConfig._
+
+  implicit val Timeout: FiniteDuration = 25.seconds.dilated
+
+  val YoSup: String =
+    s"""
+       |task sup {
+       |  String addressee
+       |  command {
+       |    echo "yo sup $${addressee}!"
+       |  }
+       |  output {
+       |    String salutation = read_string(stdout())
+       |  }
+       |  runtime {
+       |    docker: "ubuntu:latest"
+       |    [PREEMPTIBLE]
+       |  }
+       |}
+       |
+       |workflow wf_sup {
+       |  call sup
+       |}
+    """.stripMargin
+
+  val Inputs: Map[FullyQualifiedName, WomValue] = Map("wf_sup.sup.addressee" -> WomString("dog"))
+
+  private val NoOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))
+
+  private lazy val TestableCallContext = CallContext(mockPathBuilder.build("gs://root").get, DummyStandardPaths, isDocker = false)
+
+  private lazy val TestableStandardExpressionFunctionsParams: StandardExpressionFunctionsParams
+  = new StandardExpressionFunctionsParams {
+    override lazy val pathBuilders: List[PathBuilder] = List(mockPathBuilder)
+    override lazy val callContext: CallContext = TestableCallContext
+    override val ioActorProxy: ActorRef = simpleIoActor
+    override val executionContext: ExecutionContext = system.dispatcher
+  }
+
+  lazy val TestableGcpBatchExpressionFunctions: BatchExpressionFunctions = {
+    new BatchExpressionFunctions(TestableStandardExpressionFunctionsParams)
+  }
+
+  private def buildInitializationData(jobDescriptor: BackendJobDescriptor, configuration: GcpBatchConfiguration) = {
+    val pathBuilders = Await.result(configuration.configurationDescriptor.pathBuilders(WorkflowOptions.empty), 5.seconds)
+    val workflowPaths = GcpBatchWorkflowPaths(
+      jobDescriptor.workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), configuration, pathBuilders, GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+    val runtimeAttributesBuilder = GcpBatchRuntimeAttributes.runtimeAttributesBuilder(configuration)
+
+    GcpBackendInitializationData(workflowPaths, runtimeAttributesBuilder, configuration, null, None, None, None)
+  }
+
+  class TestableGcpBatchJobExecutionActor(params: StandardAsyncExecutionActorParams, functions: BatchExpressionFunctions)
+    extends GcpBatchAsyncBackendJobExecutionActor(params) {
+
+    def this(jobDescriptor: BackendJobDescriptor,
+             promise: Promise[BackendJobExecutionResponse],
+             batchConfiguration: GcpBatchConfiguration,
+             functions: BatchExpressionFunctions = TestableGcpBatchExpressionFunctions,
+             batchSingletonActor: ActorRef = emptyActor,
+             ioActor: ActorRef = mockIoActor,
+             serviceRegistryActor: ActorRef = kvService) = {
+
+      this(
+        DefaultStandardAsyncExecutionActorParams(
+          jobIdKey = GcpBatchAsyncBackendJobExecutionActor.GcpBatchOperationIdKey,
+          serviceRegistryActor = serviceRegistryActor,
+          ioActor = ioActor,
+          jobDescriptor = jobDescriptor,
+          configurationDescriptor = batchConfiguration.configurationDescriptor,
+          backendInitializationDataOption = Option(buildInitializationData(jobDescriptor, batchConfiguration)),
+          backendSingletonActorOption = Option(batchSingletonActor),
+          completionPromise = promise,
+          minimumRuntimeSettings = MinimumRuntimeSettings()
+        ),
+        functions
+      )
+    }
+
+    override lazy val jobLogger: JobLogger = new JobLogger(
+      loggerName = "TestLogger",
+      workflowIdForLogging = workflowId.toPossiblyNotRoot,
+      rootWorkflowIdForLogging = workflowId.toRoot,
+      jobTag = jobTag,
+      akkaLogger = Option(log)
+    ) {
+      override def tag: String = s"$name [UUID(${workflowId.shortString})$jobTag]"
+      override val slf4jLoggers: Set[Logger] = Set.empty
+    }
+
+    override lazy val backendEngineFunctions: BatchExpressionFunctions = functions
+  }
+
+
+  private val runtimeAttributesBuilder = GcpBatchRuntimeAttributes.runtimeAttributesBuilder(gcpBatchConfiguration)
+  private val workingDisk = GcpBatchWorkingDisk(DiskType.SSD, 200)
+
+  val DockerAndDiskRuntime: String =
+    """
+      |runtime {
+      |  docker: "ubuntu:latest"
+      |  disks: "local-disk 200 SSD"
+      |}
+    """.stripMargin
+
+  private def buildPreemptibleJobDescriptor(preemptible: Int, previousPreemptions: Int, previousUnexpectedRetries: Int, failedRetriesCountOpt: Option[Int] = None): BackendJobDescriptor = {
+    val attempt = previousPreemptions + previousUnexpectedRetries + 1
+    val wdlNamespace = WdlNamespaceWithWorkflow.load(YoSup.replace("[PREEMPTIBLE]", s"preemptible: $preemptible"),
+      Seq.empty[Draft2ImportResolver]).get
+    val womDefinition = wdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+
+    wdlNamespace.toWomExecutable(Option(Inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
+      case Right(womExecutable) =>
+        val inputs = for {
+          combined <- womExecutable.resolvedExecutableInputs
+          (port, resolvedInput) = combined
+          value <- resolvedInput.select[WomValue]
+        } yield port -> value
+
+        val workflowDescriptor = BackendWorkflowDescriptor(
+          WorkflowId.randomId(),
+          womDefinition,
+          inputs,
+          NoOptions,
+          Labels.empty,
+          HogGroup("foo"),
+          List.empty,
+          None
+        )
+
+        val job = workflowDescriptor.callable.taskCallNodes.head
+        val key = BackendJobDescriptorKey(job, None, attempt)
+        val runtimeAttributes = makeRuntimeAttributes(job)
+        val prefetchedKvEntries = Map(
+          GcpBatchBackendLifecycleActorFactory.preemptionCountKey -> KvPair(ScopedKey(workflowDescriptor.id, KvJobKey(key), GcpBatchBackendLifecycleActorFactory.preemptionCountKey), previousPreemptions.toString),
+          GcpBatchBackendLifecycleActorFactory.unexpectedRetryCountKey -> KvPair(ScopedKey(workflowDescriptor.id, KvJobKey(key), GcpBatchBackendLifecycleActorFactory.unexpectedRetryCountKey), previousUnexpectedRetries.toString))
+        val prefetchedKvEntriesUpd = if(failedRetriesCountOpt.isEmpty) {
+          prefetchedKvEntries
+        } else {
+          prefetchedKvEntries + (BackendLifecycleActorFactory.FailedRetryCountKey -> KvPair(ScopedKey(workflowDescriptor.id, KvJobKey(key), BackendLifecycleActorFactory.FailedRetryCountKey), failedRetriesCountOpt.get.toString ))
+        }
+        BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(Inputs), NoDocker, None, prefetchedKvEntriesUpd)
+      case Left(badtimes) => fail(badtimes.toList.mkString(", "))
+    }
+  }
+
+  private case class DockerImageCacheTestingParameters(dockerImageCacheDiskOpt: Option[String],
+                                                       dockerImageAsSpecifiedByUser: String,
+                                                       isDockerImageCacheUsageRequested: Boolean)
+
+  private def executionActor(jobDescriptor: BackendJobDescriptor,
+                             promise: Promise[BackendJobExecutionResponse],
+                             batchSingletonActor: ActorRef,
+                             shouldBePreemptible: Boolean,
+                             serviceRegistryActor: ActorRef = kvService,
+                             referenceInputFilesOpt: Option[Set[GcpBatchInput]] = None,
+                             dockerImageCacheTestingParamsOpt: Option[DockerImageCacheTestingParameters] = None
+                            ): ActorRef = {
+
+    val job = generateStandardAsyncJob
+    val run = Run(job)
+    val handle = new GcpBatchPendingExecutionHandle(jobDescriptor, run.job, Option(run), None)
+
+    class ExecuteOrRecoverActor extends TestableGcpBatchJobExecutionActor(jobDescriptor, promise, gcpBatchConfiguration, batchSingletonActor = batchSingletonActor, serviceRegistryActor = serviceRegistryActor) {
+      override def executeOrRecover(mode: ExecutionMode)(implicit ec: ExecutionContext): Future[ExecutionHandle] = {
+        sendIncrementMetricsForReferenceFiles(referenceInputFilesOpt)
+        dockerImageCacheTestingParamsOpt.foreach { dockerImageCacheTestingParams =>
+          sendIncrementMetricsForDockerImageCache(
+            dockerImageCacheTestingParams.dockerImageCacheDiskOpt,
+            dockerImageCacheTestingParams.dockerImageAsSpecifiedByUser,
+            dockerImageCacheTestingParams.isDockerImageCacheUsageRequested
+          )
+        }
+
+        if (preemptible == shouldBePreemptible) Future.successful(handle)
+        else Future.failed(new Exception(s"Test expected preemptible to be $shouldBePreemptible but got $preemptible"))
+      }
+    }
+
+    system.actorOf(Props(new ExecuteOrRecoverActor), "ExecuteOrRecoverActor-" + UUID.randomUUID)
+  }
+
+  def runAndFail(previousPreemptions: Int, previousUnexpectedRetries: Int, preemptible: Int, errorCode: Status, innerErrorMessage: String, expectPreemptible: Boolean): BackendJobExecutionResponse = {
+
+    val runStatus: RunStatus = RunStatus.Failed(List.empty)
+    //    val runStatus = UnsuccessfulRunStatus(errorCode, Option(innerErrorMessage), Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), expectPreemptible)
+    val statusPoller = TestProbe("statusPoller")
+
+    val promise = Promise[BackendJobExecutionResponse]()
+    val jobDescriptor =  buildPreemptibleJobDescriptor(preemptible, previousPreemptions, previousUnexpectedRetries)
+
+    // TODO: Use this to check the new KV entries are there!  From PAPI
+    //val kvProbe = TestProbe("kvProbe")
+
+    val backend = executionActor(jobDescriptor, promise, statusPoller.ref, expectPreemptible)
+    backend ! Execute
+    statusPoller.expectMsgPF(max = Timeout, hint = "awaiting status poll") {
+      case GcpBatchBackendSingletonActor.Action.QueryJob(jobName) =>
+        println(s"Message received to query job: $jobName")
+        val internalStatus = runStatus match {
+          case RunStatus.Failed(_) => com.google.cloud.batch.v1.JobStatus.State.FAILED
+          case RunStatus.Succeeded(_) => com.google.cloud.batch.v1.JobStatus.State.SUCCEEDED
+          case RunStatus.Running => com.google.cloud.batch.v1.JobStatus.State.RUNNING
+          case RunStatus.DeletionInProgress => com.google.cloud.batch.v1.JobStatus.State.DELETION_IN_PROGRESS
+          case RunStatus.StateUnspecified => com.google.cloud.batch.v1.JobStatus.State.STATE_UNSPECIFIED
+          case RunStatus.Unrecognized => com.google.cloud.batch.v1.JobStatus.State.UNRECOGNIZED
+        }
+
+        backend ! GcpBatchBackendSingletonActor.Event.JobStatusRetrieved(Job.newBuilder.setStatus(com.google.cloud.batch.v1.JobStatus.newBuilder.setState(internalStatus).build()).build())
+    }
+
+    Await.result(promise.future, Timeout)
+  }
+
+  def buildPreemptibleTestActorRef(attempt: Int, preemptible: Int, failedRetriesCountOpt: Option[Int] = None): TestActorRef[TestableGcpBatchJobExecutionActor] = {
+    // For this test we say that all previous attempts were preempted:
+    val jobDescriptor = buildPreemptibleJobDescriptor(preemptible, attempt - 1, previousUnexpectedRetries = 0, failedRetriesCountOpt = failedRetriesCountOpt)
+    val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(),
+      gcpBatchConfiguration,
+      TestableGcpBatchExpressionFunctions,
+      emptyActor,
+      failIoActor))
+    TestActorRef(props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+  }
+
+  behavior of "GcpBatchAsyncBackendJobExecutionActor"
+
+  private val timeout = 25 seconds
+
+  it should "group files by bucket" in {
+
+    def makeInput(bucket: String, name: String): GcpBatchFileInput = {
+      val mockCloudPath = mock[cromwell.core.path.Path]
+      when(mockCloudPath.pathAsString) thenReturn s"gs://$bucket/$name"
+
+      GcpBatchFileInput(
+        name = name,
+        cloudPath = mockCloudPath,
+        relativeHostPath = DefaultPathBuilder.build(Paths.get(s"$bucket/$name")),
+        mount = null
+      )
+    }
+
+    val inputs: List[GcpBatchFileInput] = List(
+      ("foo", "file1"),
+      ("foo", "file2"),
+      ("bar", "file1"),
+      ("bar", "file2"),
+      ("bar", "file3"),
+      ("baz", "file1")
+    ) map (makeInput _).tupled.apply
+
+    val expected =
+      Map("foo" -> (NonEmptyList.of(0, 1) map inputs.apply)) ++
+        Map("bar" -> (NonEmptyList.of(2, 3, 4) map inputs.apply)) ++
+        Map("baz" -> NonEmptyList.of(inputs(5)))
+
+    GcpBatchAsyncBackendJobExecutionActor.groupParametersByGcsBucket(inputs) shouldEqual expected
+  }
+
+  it should "send proper value for \"number of reference files used gauge\" metric, or don't send anything if reference disks feature is disabled" in {
+
+    val expectedInput1 = GcpBatchFileInput(name = "testfile1", relativeHostPath = DefaultPathBuilder.build(Paths.get(s"test/reference/path/file1")), mount = null, cloudPath = null)
+    val expectedInput2 = GcpBatchFileInput(name = "testfile2", relativeHostPath = DefaultPathBuilder.build(Paths.get(s"test/reference/path/file2")), mount = null, cloudPath = null)
+    val expectedReferenceInputFiles = Set[GcpBatchInput](expectedInput1, expectedInput2)
+
+    val expectedMsg1 = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList.of("referencefiles", expectedInput1.relativeHostPath.pathAsString))))
+    val expectedMsg2 = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList.of("referencefiles", expectedInput2.relativeHostPath.pathAsString))))
+
+    val jobDescriptor = buildPreemptibleJobDescriptor(0, 0, 0)
+    val serviceRegistryProbe = TestProbe()
+
+    val backend1 = executionActor(
+      jobDescriptor,
+      Promise[BackendJobExecutionResponse](),
+      TestProbe().ref,
+      shouldBePreemptible = false,
+      serviceRegistryActor = serviceRegistryProbe.ref,
+      referenceInputFilesOpt = Option(expectedReferenceInputFiles)
+    )
+    backend1 ! Execute
+    serviceRegistryProbe.expectMsgAllOf(expectedMsg1, expectedMsg2)
+
+    val backend2 = executionActor(
+      jobDescriptor,
+      Promise[BackendJobExecutionResponse](),
+      TestProbe().ref,
+      shouldBePreemptible = false,
+      serviceRegistryActor = serviceRegistryProbe.ref,
+      referenceInputFilesOpt = None
+    )
+    backend2 ! Execute
+    serviceRegistryProbe.expectNoMessage(timeout)
+  }
+
+  it should "sends proper metrics for docker image cache feature" in {
+
+    val jobDescriptor = buildPreemptibleJobDescriptor(0, 0, 0)
+    val serviceRegistryProbe = TestProbe()
+    val madeUpDockerImageName = "test_madeup_docker_image_name"
+
+    val expectedMessageWhenRequestedNotFound = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList("docker", List("image", "cache", "image_not_in_cache", madeUpDockerImageName)))))
+    val backendDockerCacheRequestedButNotFound = executionActor(
+      jobDescriptor,
+      Promise[BackendJobExecutionResponse](),
+      TestProbe().ref,
+      shouldBePreemptible = false,
+      serviceRegistryActor = serviceRegistryProbe.ref,
+      dockerImageCacheTestingParamsOpt =
+        Option(
+          DockerImageCacheTestingParameters(
+            None,
+            "test_madeup_docker_image_name",
+            isDockerImageCacheUsageRequested = true
+          )
+        )
+    )
+    backendDockerCacheRequestedButNotFound ! Execute
+    serviceRegistryProbe.expectMsg(expectedMessageWhenRequestedNotFound)
+
+    val expectedMessageWhenRequestedAndFound = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList("docker", List("image", "cache", "used_image_from_cache", madeUpDockerImageName)))))
+    val backendDockerCacheRequestedAndFound = executionActor(
+      jobDescriptor,
+      Promise[BackendJobExecutionResponse](),
+      TestProbe().ref,
+      shouldBePreemptible = false,
+      serviceRegistryActor = serviceRegistryProbe.ref,
+      dockerImageCacheTestingParamsOpt =
+        Option(
+          DockerImageCacheTestingParameters(
+            Option("test_madeup_disk_image_name"),
+            "test_madeup_docker_image_name",
+            isDockerImageCacheUsageRequested = true
+          )
+        )
+    )
+    backendDockerCacheRequestedAndFound ! Execute
+    serviceRegistryProbe.expectMsg(expectedMessageWhenRequestedAndFound)
+
+    val expectedMessageWhenNotRequestedButFound = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList("docker", List("image", "cache", "cached_image_not_used", madeUpDockerImageName)))))
+    val backendDockerCacheNotRequestedButFound = executionActor(
+      jobDescriptor,
+      Promise[BackendJobExecutionResponse](),
+      TestProbe().ref,
+      shouldBePreemptible = false,
+      serviceRegistryActor = serviceRegistryProbe.ref,
+      dockerImageCacheTestingParamsOpt =
+        Option(
+          DockerImageCacheTestingParameters(
+            Option("test_madeup_disk_image_name"),
+            "test_madeup_docker_image_name",
+            isDockerImageCacheUsageRequested = false
+          )
+        )
+    )
+    backendDockerCacheNotRequestedButFound ! Execute
+    serviceRegistryProbe.expectMsg(expectedMessageWhenNotRequestedButFound)
+
+    val backendDockerCacheNotRequestedNotFound = executionActor(
+      jobDescriptor,
+      Promise[BackendJobExecutionResponse](),
+      TestProbe().ref,
+      shouldBePreemptible = false,
+      serviceRegistryActor = serviceRegistryProbe.ref,
+      dockerImageCacheTestingParamsOpt =
+        Option(
+          DockerImageCacheTestingParameters(
+            None,
+            "test_madeup_docker_image_name",
+            isDockerImageCacheUsageRequested = false
+          )
+        )
+    )
+    backendDockerCacheNotRequestedNotFound ! Execute
+    serviceRegistryProbe.expectNoMessage(timeout)
+  }
+
+  it should "not restart 2 of 1 unexpected shutdowns without another preemptible VM" in {
+
+    val actorRef = buildPreemptibleTestActorRef(2, 1)
+    val batchBackend = actorRef.underlyingActor
+    val runId = generateStandardAsyncJob
+    val handle = new GcpBatchPendingExecutionHandle(null, runId, None, None)
+
+    val failedStatus = RunStatus.Failed(List.empty)
+    val executionResult = batchBackend.handleExecutionResult(failedStatus, handle)
+    val result = Await.result(executionResult, timeout)
+    result.isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
+    val failedHandle = result.asInstanceOf[FailedNonRetryableExecutionHandle]
+    failedHandle.returnCode shouldBe None
+  }
+
+  it should "handle Failure Status for various errors" in {
+
+    val actorRef = buildPreemptibleTestActorRef(1, 1)
+    val batchBackend = actorRef.underlyingActor
+    val runId = generateStandardAsyncJob
+    val handle = new GcpBatchPendingExecutionHandle(null, runId, None, None)
+
+    def checkFailedResult(errorCode: Status, errorMessage: Option[String]): ExecutionHandle = {
+      val failed = RunStatus.Failed(List.empty)
+      Await.result(batchBackend.handleExecutionResult(failed, handle), timeout)
+    }
+
+    checkFailedResult(Status.ABORTED, Option("15: Other type of error."))
+      .isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
+    checkFailedResult(Status.OUT_OF_RANGE, Option("14: Wrong errorCode.")).isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
+    checkFailedResult(Status.ABORTED, Option("Weird error message.")).isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
+    checkFailedResult(Status.ABORTED, Option("UnparsableInt: Even weirder error message."))
+      .isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
+    checkFailedResult(Status.ABORTED, None).isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
+    actorRef.stop()
+  }
+
+  it should "map GCS paths and *only* GCS paths to local" in {
+    val wdlString =
+      s"""|workflow wf {
+          |  call t
+          |}
+          |
+          |task t {
+          |  String abc
+          |  File lf
+          |  File gcsf
+          |  command {}
+          |  runtime { docker: "ubuntu" }
+          |}
+          |""".stripMargin
+
+    val stringKey = "wf.t.abc"
+    val stringVal = WomString("abc")
+    val localFileKey = "wf.t.lf"
+    val localFileVal = WomSingleFile("/blah/abc")
+    val gcsFileKey = "wf.t.gcsf"
+    val gcsFileVal = WomSingleFile("gs://blah/abc")
+
+    val inputs: Map[String, WomValue] = Map(
+      stringKey -> stringVal,
+      localFileKey -> localFileVal,
+      gcsFileKey -> gcsFileVal
+    )
+
+    val wdlNamespace = WdlNamespaceWithWorkflow.load(
+      wdlString,
+      Seq.empty[Draft2ImportResolver],
+    ).get
+    val womWorkflow = wdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    wdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
+      case Right(womExecutable) =>
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+
+        val workflowDescriptor = BackendWorkflowDescriptor(
+          WorkflowId.randomId(),
+          womWorkflow,
+          wdlInputs,
+          NoOptions,
+          Labels.empty,
+          HogGroup("foo"),
+          List.empty,
+          None
+        )
+
+        val call: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst({ case t: CommandCallNode => t }).get
+        val key = BackendJobDescriptorKey(call, None, 1)
+        val runtimeAttributes = makeRuntimeAttributes(call)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+
+        val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
+        val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
+          props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+
+
+        def gcsPathToLocal(womValue: WomValue): WomValue = {
+          WomFileMapper.mapWomFiles(testActorRef.underlyingActor.mapCommandLineWomFile)(womValue).get
+        }
+
+        val mappedInputs = jobDescriptor.localInputs safeMapValues gcsPathToLocal
+
+        mappedInputs(stringKey) match {
+          case WomString(v) => assert(v.equalsIgnoreCase(stringVal.value))
+          case _ => fail("test setup error")
+        }
+
+        mappedInputs(localFileKey) match {
+          case wdlFile: WomSingleFile => assert(wdlFile.value.equalsIgnoreCase(localFileVal.value))
+          case _ => fail("test setup error")
+        }
+
+        mappedInputs(gcsFileKey) match {
+          case wdlFile: WomSingleFile => wdlFile.value shouldBe "/mnt/disks/cromwell_root/blah/abc"
+          case _ => fail("test setup error")
+        }
+      case Left(badtimes) => fail(badtimes.toList.mkString(", "))
+    }
+  }
+
+  it should "create a GcpBatchFileInput for the monitoring script, when specified" in {
+
+    val workflowDescriptor = BackendWorkflowDescriptor(
+      WorkflowId.randomId(),
+      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      Map.empty,
+      WorkflowOptions.fromJsonString("""{"monitoring_script": "gs://path/to/script"}""").get,
+      Labels.empty,
+      HogGroup("foo"),
+      List.empty,
+      None
+    )
+
+    val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
+    val runtimeAttributes = makeRuntimeAttributes(job)
+    val key = BackendJobDescriptorKey(job, None, 1)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+
+    val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
+    val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
+      props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+
+    testActorRef.underlyingActor.monitoringScript shouldBe
+      Option(GcpBatchFileInput("monitoring-in", gcsPath("gs://path/to/script"), DefaultPathBuilder.get("monitoring.sh"), workingDisk))
+  }
+
+  it should "not create a GcpBatchFileInput for the monitoring script, when not specified" in {
+
+    val workflowDescriptor = BackendWorkflowDescriptor(
+      WorkflowId.randomId(),
+      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      Map.empty,
+      NoOptions,
+      Labels.empty,
+      HogGroup("foo"),
+      List.empty,
+      None
+    )
+
+    val job: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst({case t: CommandCallNode => t}).get
+    val key = BackendJobDescriptorKey(job, None, 1)
+    val runtimeAttributes = makeRuntimeAttributes(job)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+
+    val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
+    val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
+      props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+
+    testActorRef.underlyingActor.monitoringScript shouldBe None
+  }
+
+  it should "return GCP Batch log paths for non-scattered call" in {
+
+    val workflowDescriptor = BackendWorkflowDescriptor(
+      WorkflowId(UUID.fromString("e6236763-c518-41d0-9688-432549a8bf7c")),
+      WdlNamespaceWithWorkflow.load(
+        SampleWdl.HelloWorld.asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
+        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      Map.empty,
+      WorkflowOptions.fromJsonString(s""" {"${GcpBatchWorkflowPaths.GcsRootOptionKey}": "gs://path/to/gcs_root"} """).get,
+      Labels.empty,
+      HogGroup("foo"),
+      List.empty,
+      None
+    )
+
+    val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "hello").get
+    val key = BackendJobDescriptorKey(call, None, 1)
+    val runtimeAttributes = makeRuntimeAttributes(call)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+
+    val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
+    val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
+      props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+
+    val batchBackend = testActorRef.underlyingActor
+
+    batchBackend.gcpBatchCallPaths.stdout should be(a[GcsPath])
+    batchBackend.gcpBatchCallPaths.stdout.pathAsString shouldBe
+      "gs://path/to/gcs_root/wf_hello/e6236763-c518-41d0-9688-432549a8bf7c/call-hello/stdout"
+    batchBackend.gcpBatchCallPaths.stderr should be(a[GcsPath])
+    batchBackend.gcpBatchCallPaths.stderr.pathAsString shouldBe
+      "gs://path/to/gcs_root/wf_hello/e6236763-c518-41d0-9688-432549a8bf7c/call-hello/stderr"
+    batchBackend.gcpBatchCallPaths.batchLogPath should be(a[GcsPath])
+    batchBackend.gcpBatchCallPaths.batchLogPath.pathAsString shouldBe
+      "gs://path/to/gcs_root/wf_hello/e6236763-c518-41d0-9688-432549a8bf7c/call-hello/hello.log"
+  }
+
+  it should "return Batch log paths for scattered call" in {
+
+    val workflowDescriptor = BackendWorkflowDescriptor(
+      WorkflowId(UUID.fromString("e6236763-c518-41d0-9688-432549a8bf7d")),
+      WdlNamespaceWithWorkflow.load(
+        new SampleWdl.ScatterWdl().asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
+        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      Map.empty,
+      WorkflowOptions.fromJsonString(s""" {"${GcpBatchWorkflowPaths.GcsRootOptionKey}": "gs://path/to/gcs_root"} """).get,
+      Labels.empty,
+      HogGroup("foo"),
+      List.empty,
+      None
+    )
+
+    val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "B").get
+    val key = BackendJobDescriptorKey(call, Option(2), 1)
+    val runtimeAttributes = makeRuntimeAttributes(call)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+
+    val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
+    val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
+      props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+
+    val batchBackend = testActorRef.underlyingActor
+
+    batchBackend.gcpBatchCallPaths.stdout should be(a[GcsPath])
+    batchBackend.gcpBatchCallPaths.stdout.pathAsString shouldBe
+      "gs://path/to/gcs_root/w/e6236763-c518-41d0-9688-432549a8bf7d/call-B/shard-2/stdout"
+    batchBackend.gcpBatchCallPaths.stderr should be(a[GcsPath])
+    batchBackend.gcpBatchCallPaths.stderr.pathAsString shouldBe
+      "gs://path/to/gcs_root/w/e6236763-c518-41d0-9688-432549a8bf7d/call-B/shard-2/stderr"
+    batchBackend.gcpBatchCallPaths.batchLogPath should be(a[GcsPath])
+    batchBackend.gcpBatchCallPaths.batchLogPath.pathAsString shouldBe
+      "gs://path/to/gcs_root/w/e6236763-c518-41d0-9688-432549a8bf7d/call-B/shard-2/B-2.log"
+  }
+
+  it should "return preemptible = true only in the correct cases" in {
+
+    def attempt(max: Int, attempt: Int): GcpBatchAsyncBackendJobExecutionActor = {
+      buildPreemptibleTestActorRef(attempt, max).underlyingActor
+    }
+    def attempt1(max: Int) = attempt(max, 1)
+    def attempt2(max: Int) = attempt(max, 2)
+
+    val descriptorWithMax0AndKey1 = attempt1(max = 0)
+    descriptorWithMax0AndKey1.preemptible shouldBe false
+
+    val descriptorWithMax1AndKey1 = attempt1(max = 1)
+    descriptorWithMax1AndKey1.preemptible shouldBe true
+
+    val descriptorWithMax2AndKey1 = attempt1(max = 2)
+    descriptorWithMax2AndKey1.preemptible shouldBe true
+
+    val descriptorWithMax1AndKey2 = attempt2(max = 1)
+    descriptorWithMax1AndKey2.preemptible shouldBe false
+
+    val descriptorWithMax2AndKey2 = attempt2(max = 2)
+    descriptorWithMax2AndKey2.preemptible shouldBe true
+  }
+
+  it should "return the project from the workflow options in the start metadata" in {
+
+    val googleProject = "baa-ram-ewe"
+    val batchGcsRoot = "gs://anorexic/duck"
+    val workflowId = WorkflowId.randomId()
+    val workflowDescriptor = BackendWorkflowDescriptor(
+      workflowId,
+      WdlNamespaceWithWorkflow
+        .load(
+          SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+          Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      Map.empty,
+      WorkflowOptions.fromJsonString(
+        s"""|{
+            |  "google_project": "$googleProject",
+            |  "${GcpBatchWorkflowPaths.GcsRootOptionKey}": "$batchGcsRoot"
+            |}
+            |""".stripMargin
+      ).get,
+      Labels.empty,
+      HogGroup("foo"),
+      List.empty,
+      None
+    )
+
+    val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "goodbye").get
+    val key = BackendJobDescriptorKey(call, None, 1)
+    val runtimeAttributes = makeRuntimeAttributes(call)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+
+    val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
+    val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
+      props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+
+    val batchBackend = testActorRef.underlyingActor
+
+    // NOTE: The commented lines are not provided by batch yet, we need to check whether those are necessary
+    val actual = batchBackend.startMetadataKeyValues.safeMapValues(_.toString)
+    actual should be(
+      Map(
+        //       "backendLogs:log" -> s"$batchGcsRoot/wf_hello/$workflowId/call-goodbye/goodbye.log",
+        "callRoot" -> s"$batchGcsRoot/wf_hello/$workflowId/call-goodbye",
+        "gcpBatch:executionBucket" -> batchGcsRoot,
+        "gcpBatch:googleProject" -> googleProject,
+        "labels:cromwell-workflow-id" -> s"cromwell-$workflowId",
+        "labels:wdl-task-name" -> "goodbye",
+        "preemptible" -> "false",
+        "runtimeAttributes:bootDiskSizeGb" -> "10",
+        "runtimeAttributes:continueOnReturnCode" -> "0",
+        "runtimeAttributes:cpu" -> "1",
+        "runtimeAttributes:cpuMin" -> "1",
+        "runtimeAttributes:disks" -> "local-disk 200 SSD",
+        "runtimeAttributes:docker" -> "ubuntu:latest",
+        "runtimeAttributes:failOnStderr" -> "false",
+        "runtimeAttributes:memory" -> "2 GB",
+        "runtimeAttributes:memoryMin" -> "2 GB",
+        "runtimeAttributes:noAddress" -> "false",
+        "runtimeAttributes:preemptible" -> "0",
+        "runtimeAttributes:zones" -> "us-central1-b,us-central1-a",
+        "runtimeAttributes:maxRetries" -> "0",
+        "stderr" -> s"$batchGcsRoot/wf_hello/$workflowId/call-goodbye/stderr",
+        "stdout" -> s"$batchGcsRoot/wf_hello/$workflowId/call-goodbye/stdout"
+      )
+    )
+
+  }
+
+  private def makeRuntimeAttributes(job: CommandCallNode) = {
+    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(job.callable.runtimeAttributes, null, Map.empty)
+    RuntimeAttributeDefinition.addDefaultsToAttributes(
+      runtimeAttributesBuilder.definitions.toSet, NoOptions)(evaluatedAttributes.getOrElse(fail("Failed to evaluate runtime attributes")))
+  }
+
+  private def generateStandardAsyncJob = {
+    StandardAsyncJob(JobName.newBuilder().setJob(UUID.randomUUID().toString).setProject("test").setLocation("local").build().toString)
+  }
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchBackendLifecycleActorFactorySpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchBackendLifecycleActorFactorySpec.scala
new file mode 100644
index 00000000000..d3bf3a7a3d1
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchBackendLifecycleActorFactorySpec.scala
@@ -0,0 +1,64 @@
+package cromwell.backend.google.batch.actors
+
+import cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory;
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes;
+import eu.timepit.refined.numeric.Positive
+import eu.timepit.refined.refineV
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.prop.TableDrivenPropertyChecks
+
+import scala.concurrent.duration._
+import scala.language.postfixOps
+
+
+class GcpBatchBackendLifecycleActorFactorySpec extends AnyFlatSpecLike with Matchers with TableDrivenPropertyChecks {
+
+  "GcpBatchBackendLifecycleActorFactory" should "robustly build configuration attributes" in {
+
+    val attributes = new GcpBatchConfigurationAttributes(
+      project = "project",
+      computeServiceAccount = "computeServiceAccount",
+      auths = null,
+      restrictMetadataAccess = true,
+      dockerhubToken = "test",
+      enableFuse = true,
+      executionBucket = "executionBucket",
+      location = "location",
+      maxPollingInterval = 0,
+      qps = refineV[Positive](1).toOption.get,
+      cacheHitDuplicationStrategy = null,
+      requestWorkers = refineV[Positive](1).toOption.get,
+      batchTimeout = 1 second,
+      logFlushPeriod = Option(1 second),
+      gcsTransferConfiguration = null,
+      virtualPrivateCloudConfiguration = null,
+      batchRequestTimeoutConfiguration = null,
+      referenceFileToDiskImageMappingOpt = None,
+      dockerImageToCacheDiskImageMappingOpt = None,
+      checkpointingInterval = 1 second)
+
+    GcpBatchBackendLifecycleActorFactory.robustBuildAttributes(() => attributes) shouldBe attributes
+  }
+
+  {
+    // The message string actually observed during construction failure.
+    val actualRetryMessage = s"We encountered an internal error. Please try again."
+    val fails = Table(
+      ("attempts", "description", "function"),
+      (3, "no exception message", () => throw new RuntimeException()),
+      (3, "exception message", () => throw new RuntimeException(actualRetryMessage)),
+      (1, "error not exception, no message", () => throw new Error()),
+      (1, "error not exception", () => throw new Error(actualRetryMessage))
+    )
+    forAll(fails) { (attempts, description, function) =>
+      it should s"$description: make $attempts attribute creation attempts before giving up" in {
+        val e = the[RuntimeException] thrownBy {
+          GcpBatchBackendLifecycleActorFactory.robustBuildAttributes(function, initialIntervalMillis = 1, maxIntervalMillis = 5)
+        }
+        e.getMessage should startWith(s"Failed to build GcpBatchConfigurationAttributes on attempt $attempts of 3")
+      }
+    }
+  }
+
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActorSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActorSpec.scala
new file mode 100644
index 00000000000..c57902531c8
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActorSpec.scala
@@ -0,0 +1,185 @@
+package cromwell.backend.google.batch.actors
+
+import java.util.UUID
+import akka.actor.Props
+import akka.testkit._
+import com.typesafe.config.{Config, ConfigFactory}
+import cromwell.backend.BackendWorkflowInitializationActor.{InitializationFailed, InitializationSuccess, Initialize}
+import cromwell.backend.async.RuntimeAttributeValidationFailures
+import cromwell.backend.google.batch.models.GcpBatchConfiguration
+import cromwell.backend.google.batch.actors.GcpBatchInitializationActorSpec._
+import cromwell.backend.google.batch.models.GcpBatchTestConfig.{BatchGlobalConfig, googleConfiguration, batchAttributes}
+import cromwell.backend.{BackendConfigurationDescriptor, BackendSpec, BackendWorkflowDescriptor}
+import cromwell.core.Dispatcher.BackendDispatcher
+import cromwell.core.TestKitSuite
+import cromwell.core.filesystem.CromwellFileSystems
+import cromwell.core.logging.LoggingTest._
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.matchers.should.Matchers
+import wom.graph.CommandCallNode
+
+import scala.concurrent.duration._
+
+class GcpBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
+  with ImplicitSender {
+  val Timeout: FiniteDuration = 30.second.dilated
+
+  import BackendSpec._
+
+  val HelloWorld: String =
+    s"""
+       |task hello {
+       |  String addressee = "you"
+       |  command {
+       |    echo "Hello $${addressee}!"
+       |  }
+       |  output {
+       |    String salutation = read_string(stdout())
+       |  }
+       |
+       |  RUNTIME
+       |}
+       |
+       |workflow wf_hello {
+       |  call hello
+       |}
+    """.stripMargin
+
+  private def getJesBackendProps(workflowDescriptor: BackendWorkflowDescriptor,
+                                 calls: Set[CommandCallNode],
+                                 jesConfiguration: GcpBatchConfiguration): Props = {
+    val ioActor = mockIoActor
+    val params = GcpBatchInitializationActorParams(workflowDescriptor, ioActor, calls, jesConfiguration, emptyActor, restarting = false)
+    Props(new GcpBatchInitializationActor(params)).withDispatcher(BackendDispatcher)
+  }
+
+  private def getJesBackend(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[CommandCallNode], conf: BackendConfigurationDescriptor) = {
+    val props = getJesBackendProps(workflowDescriptor, calls, new GcpBatchConfiguration(conf, googleConfiguration, batchAttributes))
+    system.actorOf(props, "TestableJesInitializationActor-" + UUID.randomUUID)
+  }
+
+  behavior of "GcpBatchInitializationActor"
+
+  it should "log a warning message when there are unsupported runtime attributes" in {
+
+    within(Timeout) {
+      val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld,
+        runtime = """runtime { docker: "ubuntu/latest" test: true }""")
+      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes,
+        defaultBackendConfig)
+      val eventPattern =
+        "Key/s [test] is/are not supported by backend. Unsupported attributes will not be part of job executions."
+      EventFilter.warning(pattern = escapePattern(eventPattern), occurrences = 1) intercept {
+        backend ! Initialize
+      }
+      expectMsgPF() {
+        case InitializationSuccess(_) => //Docker entry is present.
+        case InitializationFailed(failure) => fail(s"InitializationSuccess was expected but got $failure")
+      }
+    }
+  }
+
+  it should "return InitializationFailed when docker runtime attribute key is not present" in {
+    within(Timeout) {
+      val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld, runtime = """runtime { }""")
+      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes,
+        defaultBackendConfig)
+      backend ! Initialize
+      expectMsgPF() {
+        case InitializationFailed(failure) =>
+          failure match {
+            case exception: RuntimeAttributeValidationFailures =>
+              if (!exception.getMessage.equals("Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!"))
+                fail("Exception message is not equal to 'Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!'.")
+          }
+      }
+    }
+  }
+}
+
+object GcpBatchInitializationActorSpec {
+  val globalConfig: Config = ConfigFactory.parseString(
+    """
+      |google {
+      |
+      |  application-name = "cromwell"
+      |
+      |  auths = [
+      |    {
+      |      name = "application-default"
+      |      scheme = "mock"
+      |    }
+      |  ]
+      |}
+      |""".stripMargin)
+
+  val backendConfigTemplate: String =
+    """
+      |  // Google project
+      |  project = "my-cromwell-workflows"
+      |
+      |  // Base bucket for workflow executions
+      |  root = "gs://my-cromwell-workflows-bucket"
+      |
+      |  // Polling for completion backs-off gradually for slower-running jobs.
+      |  // This is the maximum polling interval (in seconds):
+      |  maximum-polling-interval = 600
+      |
+      |  genomics {
+      |  // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
+      |  // Pipelines and manipulate auth JSONs.
+      |     auth = "application-default"
+      |     // Endpoint for APIs, no reason to change this unless directed by Google.
+      |     endpoint-url = "https://genomics.googleapis.com/"
+      |  }
+      |
+      |  default-runtime-attributes {
+      |     cpu: 1
+      |     failOnStderr: false
+      |     # Allowed to be a boolean, or a list of Ints, or an Int
+      |     continueOnReturnCode: 0
+      |     memory: "2 GB"
+      |     bootDiskSizeGb: 10
+      |     # Allowed to be a String, or a list of Strings
+      |     disks: "local-disk 10 SSD"
+      |     noAddress: false
+      |     preemptible: 0
+      |     zones: ["us-central1-a", "us-central1-b"]
+      |  }
+      |  filesystems {
+      |    gcs {
+      |      // A reference to a potentially different auth for manipulating files via engine functions.
+      |      auth = "application-default"
+      |    }
+      |  }
+      |
+      |[VPCCONFIG]
+      |
+      |[DOCKERHUBCONFIG]
+      |""".stripMargin
+
+  val backendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[VPCCONFIG]", "").replace("[DOCKERHUBCONFIG]", ""))
+
+  val dockerBackendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[VPCCONFIG]", "").replace("[DOCKERHUBCONFIG]",
+    """
+      |dockerhub {
+      |  account = "my@docker.account"
+      |  # no secrets here guys this is just `echo -n username:password | base64`
+      |  token = "dXNlcm5hbWU6cGFzc3dvcmQ="
+      |}
+      | """.stripMargin))
+
+  val vpcBackendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[DOCKERHUBCONFIG]", "").replace("[VPCCONFIG]",
+    """
+      |virtual-private-cloud {
+      |  network-label-key = "cromwell-ci-network"
+      |  subnetwork-label-key = "cromwell-ci-subnetwork"
+      |  auth = "service_account"
+      |}
+      | """.stripMargin))
+
+  private val defaultBackendConfig = new BackendConfigurationDescriptor(backendConfig, globalConfig) {
+    override private[backend] lazy val cromwellFileSystems = new CromwellFileSystems(BatchGlobalConfig)
+  }
+}
+
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDiskSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDiskSpec.scala
new file mode 100644
index 00000000000..a168743db8f
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDiskSpec.scala
@@ -0,0 +1,47 @@
+package cromwell.backend.google.batch.io
+
+import common.assertion.CromwellTimeoutSpec
+import cromwell.core.path.DefaultPathBuilder
+import org.scalatest.TryValues
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.prop.TableDrivenPropertyChecks._
+import org.scalatest.prop.Tables.Table
+
+import scala.util.Failure
+
+class GcpBatchAttachedDiskSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TryValues {
+  val validTable = Table(
+    ("unparsed", "parsed"),
+    ("/mnt 3 SSD", PipelinesApiEmptyMountedDisk(DiskType.SSD, 3, DefaultPathBuilder.get("/mnt"))),
+    ("/mnt/my_path 10 HDD", PipelinesApiEmptyMountedDisk(DiskType.HDD, 10, DefaultPathBuilder.get("/mnt/my_path"))),
+    ("local-disk 100 SSD", GcpBatchWorkingDisk(DiskType.SSD, 100)),
+    ("local-disk 100 LOCAL", GcpBatchWorkingDisk(DiskType.LOCAL, 100))
+  )
+
+  it should "parse" in {
+    forAll(validTable) { (unparsed, parsed) =>
+      GcpBatchAttachedDisk.parse(unparsed).get shouldEqual parsed
+    }
+  }
+
+  it should "stringify" in {
+    forAll(validTable) { (unparsed, parsed) =>
+      parsed.toString shouldEqual unparsed
+    }
+  }
+
+  val invalidTable = Table(
+    "unparsed",
+    "local-disk BAD HDD",
+    "local-disk 10 BAD",
+    "BAD 100 SSD",
+    "foobar"
+  )
+
+  it should "reject malformed disk mounts" in {
+    forAll(invalidTable) { (unparsed) =>
+      GcpBatchAttachedDisk.parse(unparsed) should be(a[Failure[_]])
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchAttributeSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchAttributeSpec.scala
new file mode 100644
index 00000000000..6743962a4e0
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchAttributeSpec.scala
@@ -0,0 +1,80 @@
+package cromwell.backend.google.batch.models
+
+import cromwell.backend.google.batch.models.GpuResource.GpuType
+import cromwell.backend.google.batch.models.GcpBatchTestConfig.gcpBatchConfiguration
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.wordspec.AnyWordSpecLike
+import wom.values.{WomFloat, WomInteger, WomSingleFile, WomString, WomValue}
+
+class GcpBatchGpuAttributesSpec
+  extends AnyWordSpecLike
+    with Matchers
+    with GcpBatchRuntimeAttributesSpecsMixin {
+
+  val validGpuTypes = List(
+    (Option(WomString("nvidia-tesla-k80")), Option(GpuType.NVIDIATeslaK80)),
+    (Option(WomString("nvidia-tesla-p100")), Option( GpuType.NVIDIATeslaP100)),
+    (Option(WomString("custom-gpu-24601")), Option( GpuType("custom-gpu-24601"))),
+    (None, None))
+  val invalidGpuTypes = List(
+    WomSingleFile("nvidia-tesla-k80"),
+    WomInteger(100))
+
+  val validGpuCounts = List(
+    (Option(WomInteger(1)), Option(1)),
+    (Option(WomInteger(100)), Option(100)),
+    (None, None)
+  )
+  val invalidGpuCounts = List(
+    WomString("ten"),
+    WomFloat(1.0))
+
+  validGpuTypes foreach { case (validGpuType, expectedGpuTypeValue) =>
+    validGpuCounts foreach { case (validGpuCount, expectedGpuCountValue) =>
+      s"validate the valid gpu type '$validGpuType' and count '$validGpuCount'" in {
+        val runtimeAttributes = Map(
+          "docker" -> WomString("ubuntu:latest")
+        ) ++ validGpuType.map(t => "gpuType" -> t) ++ validGpuCount.map(c => "gpuCount" -> c)
+
+        val actualRuntimeAttributes = toBatchRuntimeAttributes(runtimeAttributes, emptyWorkflowOptions, gcpBatchConfiguration)
+
+        expectedGpuTypeValue match {
+          case Some(v) => actualRuntimeAttributes.gpuResource.exists(_.gpuType == v)
+          case None => actualRuntimeAttributes.gpuResource.foreach(_.gpuType == GpuType.DefaultGpuType)
+        }
+
+        expectedGpuCountValue match {
+          case Some(v) => actualRuntimeAttributes.gpuResource.exists(_.gpuCount.value == v)
+          case None => actualRuntimeAttributes.gpuResource.foreach(_.gpuCount.value == GpuType.DefaultGpuCount.value)
+        }
+
+      }
+    }
+
+    invalidGpuCounts foreach { invalidGpuCount =>
+      s"not validate a valid gpu type '$validGpuType' but an invalid gpu count '$invalidGpuCount'" in {
+        val runtimeAttributes: Map[String, WomValue] = Map(
+          "docker" -> WomString("ubuntu:latest")
+        ) ++ validGpuType.map(t => "gpuType" -> t) + ("gpuCount" -> invalidGpuCount)
+
+        assertBatchRuntimeAttributesFailedCreation(
+          runtimeAttributes,
+          s"Invalid gpu count. Expected positive Int but got")
+      }
+    }
+  }
+
+  invalidGpuTypes foreach { invalidGpuType =>
+    invalidGpuCounts foreach { invalidGpuCount =>
+      s"not validate a invalid gpu type '$invalidGpuType' and invalid gpu count '$invalidGpuCount'" in {
+        val runtimeAttributes: Map[String, WomValue] = Map(
+          "docker" -> WomString("ubuntu:latest")
+        ) + ("gpuType" -> invalidGpuType) + ("gpuCount" -> invalidGpuCount)
+
+        assertBatchRuntimeAttributesFailedCreation(
+          runtimeAttributes,
+          s"Invalid gpu count. Expected positive Int but got")
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributesSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributesSpec.scala
new file mode 100644
index 00000000000..d914e9f2978
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributesSpec.scala
@@ -0,0 +1,469 @@
+package cromwell.backend.google.batch.models
+
+import cats.data.Validated.{Invalid, Valid}
+import cats.syntax.validated._
+import com.typesafe.config.{Config, ConfigFactory}
+import common.assertion.CromwellTimeoutSpec
+import common.exception.MessageAggregation
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes._
+import cromwell.backend.google.batch.models.GcpBatchTestConfig.BatchGlobalConfig
+import cromwell.cloudsupport.gcp.GoogleConfiguration
+import cromwell.cloudsupport.gcp.auth.MockAuthMode
+import cromwell.filesystems.gcs.GcsPathBuilder
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.prop.TableDrivenPropertyChecks
+
+//import java.net.URL
+import scala.concurrent.duration._
+
+class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
+  with TableDrivenPropertyChecks {
+
+  behavior of "GcpBatchAttributes"
+
+  val googleConfig: GoogleConfiguration = GoogleConfiguration(BatchGlobalConfig)
+  val runtimeConfig: Config = ConfigFactory.load()
+
+  it should "parse correct Batch config" in {
+
+    val backendConfig = ConfigFactory.parseString(configString())
+    println(backendConfig)
+
+    val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+    println(gcpBatchAttributes)
+    gcpBatchAttributes.project should be("myProject")
+    gcpBatchAttributes.executionBucket should be("gs://myBucket")
+    gcpBatchAttributes.maxPollingInterval should be(600)
+    gcpBatchAttributes.computeServiceAccount should be("default")
+    gcpBatchAttributes.restrictMetadataAccess should be(false)
+    gcpBatchAttributes.referenceFileToDiskImageMappingOpt.isEmpty should be(true)
+  }
+
+  it should "parse correct preemptible config" in {
+
+    val backendConfig = ConfigFactory.parseString(configString(customContent = "preemptible = 3"))
+
+    val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+    gcpBatchAttributes.project should be("myProject")
+    gcpBatchAttributes.executionBucket should be("gs://myBucket")
+    gcpBatchAttributes.maxPollingInterval should be(600)
+  }
+
+  it should "parse batch-requests.timeouts values correctly" in  {
+
+    val customContent =
+      """
+        |batch-requests {
+        |  timeouts {
+        |    read = 100 hours
+        |    connect = 10 seconds
+        |  }
+        |}
+      """.stripMargin
+
+    val backendConfig = ConfigFactory.parseString(configString(customContent = customContent))
+    val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+
+    gcpBatchAttributes.batchRequestTimeoutConfiguration.readTimeoutMillis.get.value should be(100.hours.toMillis.toInt)
+    gcpBatchAttributes.batchRequestTimeoutConfiguration.connectTimeoutMillis.get.value should be(10.seconds.toMillis.toInt)
+  }
+
+  it should "parse an empty batch-requests.timeouts section correctly" in {
+
+    val customContent =
+      """
+        |batch-requests {
+        |  timeouts {
+        |    # read = 100 hours
+        |    # connect = 10 seconds
+        |  }
+        |}
+      """.stripMargin
+
+    val backendConfig = ConfigFactory.parseString(configString(customContent = customContent))
+    val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+
+    gcpBatchAttributes.batchRequestTimeoutConfiguration should be(BatchRequestTimeoutConfiguration(None, None))
+  }
+
+  it should "parse batch-timeout" in {
+
+    val backendConfig = ConfigFactory.parseString(configString(customContent = "batch-timeout = 3 days"))
+    val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+
+    gcpBatchAttributes.batchTimeout should be(3.days)
+  }
+
+  it should "parse an undefined batch-timeout" in {
+
+    val backendConfig = ConfigFactory.parseString(configString())
+    val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+
+    gcpBatchAttributes.batchTimeout should be(7.days)
+  }
+
+  it should "parse compute service account" in {
+
+    val backendConfig = ConfigFactory.parseString(configString(genomics = """compute-service-account = "testing" """))
+
+    val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+    gcpBatchAttributes.computeServiceAccount should be("testing")
+  }
+
+  it should "parse restrict-metadata-access" in {
+
+    val backendConfig = ConfigFactory.parseString(configString(genomics = "restrict-metadata-access = true"))
+
+    val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+    gcpBatchAttributes.restrictMetadataAccess should be(true)
+
+  }
+
+  it should "parse localization-attempts" in {
+
+    val backendConfig = ConfigFactory.parseString(configString(genomics = "localization-attempts = 31380"))
+
+    val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+    gcpBatchAttributes.gcsTransferConfiguration.transferAttempts.value should be(31380)
+  }
+
+  private val mockAuth = MockAuthMode("mock")
+
+  private val validVpcConfigTests = Table(
+    ("description", "customConfig", "vpcConfig"),
+    ("empty body", "virtual-private-cloud {}", VirtualPrivateCloudConfiguration(None, None)),
+    (
+      "labels config",
+      """virtual-private-cloud {
+        |  network-label-key = my-network
+        |  subnetwork-label-key = my-subnetwork
+        |  auth = mock
+        |}
+        |""".stripMargin,
+      VirtualPrivateCloudConfiguration(
+        Option(VirtualPrivateCloudLabels("my-network", Option("my-subnetwork"), mockAuth)),
+        None,
+      ),
+    ),
+    (
+      "labels config without subnetwork key",
+      """virtual-private-cloud {
+        |  network-label-key = my-network
+        |  auth = mock
+        |}
+        |""".stripMargin,
+      VirtualPrivateCloudConfiguration(
+        Option(VirtualPrivateCloudLabels("my-network", None, mockAuth)),
+        None,
+      ),
+    ),
+    (
+      "literal config",
+      """virtual-private-cloud {
+        |  network-name = my-network
+        |  subnetwork-name = my-subnetwork
+        |}
+        |""".stripMargin,
+      VirtualPrivateCloudConfiguration(
+        None,
+        Option(VirtualPrivateCloudLiterals("my-network", Option("my-subnetwork"))),
+      ),
+    ),
+    (
+      "literal config without subnetwork name",
+      """virtual-private-cloud {
+        |  network-name = my-network
+        |}
+        |""".stripMargin,
+      VirtualPrivateCloudConfiguration(
+        None,
+        Option(VirtualPrivateCloudLiterals("my-network", None)),
+      ),
+    ),
+  )
+
+  private val invalidVPCConfigTests = Table(
+    ("description", "customConfig", "messages"),
+    (
+      "without auth",
+      """virtual-private-cloud {
+        |  network-label-key = my-network
+        |}
+        |""".stripMargin,
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `auth`."),
+    ),
+    (
+      "without network label-key",
+      """virtual-private-cloud {
+        |  auth = mock
+        |}
+        |""".stripMargin,
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key`."),
+    ),
+    (
+      "with just a subnetwork label key",
+      """virtual-private-cloud {
+        |  subnetwork-label-key = my-subnetwork
+        |}
+        |""".stripMargin,
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key,auth`."),
+    ),
+    (
+      "with subnetwork label network key and auth",
+      """ virtual-private-cloud {
+        |   subnetwork-label-key = my-subnetwork
+        |   auth = mock
+        | }
+        |""".stripMargin,
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key`."),
+    ),
+  )
+
+  forAll(validVpcConfigTests) { (description, customConfig, vpcConfig) =>
+    it should s"parse virtual-private-cloud $description" in {
+
+      val backendConfig = ConfigFactory.parseString(configString(customConfig))
+      val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+      gcpBatchAttributes.virtualPrivateCloudConfiguration should be(vpcConfig)
+    }
+  }
+
+  forAll(invalidVPCConfigTests) { (description, customConfig, errorMessages) =>
+    it should s"not parse invalid virtual-private-cloud config $description" in {
+
+      val backendConfig = ConfigFactory.parseString(configString(customConfig))
+      val exception = intercept[IllegalArgumentException with MessageAggregation] {
+        GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
+      }
+      exception.errorMessages.toList should be(errorMessages)
+    }
+  }
+
+  it should "not parse invalid config" in {
+
+    val nakedConfig =
+      ConfigFactory.parseString(
+        """
+          |{
+          |   genomics {
+          |
+          |   }
+          |}
+        """.stripMargin)
+
+    val exception = intercept[IllegalArgumentException with MessageAggregation] {
+      GcpBatchConfigurationAttributes(googleConfig, nakedConfig, "batch")
+    }
+    val errorsList = exception.errorMessages.toList
+    errorsList should contain("String: 2: No configuration setting found for key 'project'")
+    errorsList should contain("String: 2: No configuration setting found for key 'root'")
+    errorsList should contain("String: 3: No configuration setting found for key 'genomics.auth'")
+    errorsList should contain("String: 2: No configuration setting found for key 'filesystems'")
+  }
+
+  def configString(customContent: String = "", genomics: String = ""): String =
+    s"""
+       |{
+       |   project = "myProject"
+       |   root = "gs://myBucket"
+       |   maximum-polling-interval = 600
+       |   $customContent
+       |   genomics {
+       |     // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
+       |     // Pipelines and manipulate auth JSONs.
+       |     auth = "mock"
+       |    $genomics
+       |     endpoint-url = "http://myEndpoint"
+       |     location = "us-central1"
+       |   }
+       |
+       |   filesystems = {
+       |     gcs {
+       |       // A reference to a potentially different auth for manipulating files via engine functions.
+       |       auth = "mock"
+       |     }
+       |   }
+       |}
+       | """.stripMargin
+
+  it should "parse gsutil memory specifications" in {
+
+    val valids = List("0", "150M", "14   PIBIT", "6kib")
+
+    valids foreach {
+      case GcpBatchConfigurationAttributes.GsutilHumanBytes(_, _) =>
+      case bad => fail(s"'$bad' was expected to be a valid gsutil memory specification")
+    }
+  }
+
+  it should "reject invalid memory specifications" in {
+
+    val invalids = List("-1", "150MB", "14PB")
+
+    invalids foreach {
+      case invalid@GcpBatchConfigurationAttributes.GsutilHumanBytes(_, _) => fail(s"Memory specification $invalid not expected to be accepted")
+      case _ =>
+    }
+  }
+
+  it should "parse a missing \"reference-disk-localization-manifests\"" in {
+
+    val backendConfig = ConfigFactory.parseString(configString())
+
+    val validation = GcpBatchConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "batch")
+
+    validation shouldBe None.validNel
+  }
+
+  it should "parse a present but empty \"reference-disk-localization-manifests\"" in {
+
+    val manifestConfig = "reference-disk-localization-manifests = []"
+
+    val backendConfig = ConfigFactory.parseString(configString(customContent = manifestConfig))
+
+    val validation = GcpBatchConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "batch")
+
+    validation shouldBe Option(List.empty).validNel
+  }
+
+  it should "parse a present and populated \"reference-disk-localization-manifests\"" in {
+
+    // Highly abridged versions of hg19 and hg38 manifests just to test for correctness
+    // of parsing.
+    val manifestConfig =
+    """
+      |reference-disk-localization-manifests = [
+      |{
+      |  "imageIdentifier" : "hg19-public-2020-10-26",
+      |  "diskSizeGb" : 10,
+      |  "files" : [ {
+      |    "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
+      |    "crc32c" : 159565724
+      |  }, {
+      |    "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
+      |    "crc32c" : 1679459712
+      |  }]
+      |},
+      |{
+      |  "imageIdentifier" : "hg38-public-2020-10-26",
+      |  "diskSizeGb" : 20,
+      |  "files" : [ {
+      |    "path" : "gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
+      |    "crc32c" : 930173616
+      |  }, {
+      |    "path" : "gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
+      |    "crc32c" : 289077232
+      |  }]
+      |}
+      |]
+      |""".stripMargin
+    val backendConfig = ConfigFactory.parseString(configString(manifestConfig))
+    val validation = GcpBatchConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "batch")
+    val manifests: List[ManifestFile] = validation.toEither.toOption.get.get
+
+    manifests shouldBe List(
+      ManifestFile(
+        imageIdentifier = "hg19-public-2020-10-26",
+        diskSizeGb = 10,
+        files = List(
+          ReferenceFile(
+            path = "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
+            crc32c = 159565724
+          ),
+          ReferenceFile(
+            path = "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
+            crc32c = 1679459712
+          )
+        )
+      ),
+      ManifestFile(
+        imageIdentifier = "hg38-public-2020-10-26",
+        diskSizeGb = 20,
+        files = List(
+          ReferenceFile(
+            path = "gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
+            crc32c = 930173616
+          ),
+          ReferenceFile(
+            path = "gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
+            crc32c = 289077232
+          )
+        )
+      )
+    )
+  }
+
+  it should "parse a present and invalid \"reference-disk-localization-manifests\"" in {
+
+    val badValues = List(
+      "\"foo\"",
+      "{ foo: bar }",
+      s"""
+         |[{
+         |   # missing imageIdentifier
+         |   "diskSizeGb" : 10,
+         |   "files" : [ {
+         |     "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
+         |     "crc32c" : 159565724
+         |     }]
+         |}]""",
+      s"""
+         |[{
+         |   "imageIdentifier" : "hg19-public-2020-10-26",
+         |   # missing diskSizeGb
+         |   "files" : [ {
+         |     "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
+         |     "crc32c" : 159565724
+         |     }]
+         |}]""",
+      s"""
+         |[{
+         |   "imageIdentifier" : "hg19-public-2020-10-26",
+         |   "diskSizeGb" : 10,
+         |   # missing files
+         |}]""",
+    )
+
+    badValues foreach { badValue =>
+      val customContent = s""""reference-disk-localization-manifests" = $badValue"""
+      val backendConfig = ConfigFactory.parseString(configString(customContent))
+      val validation = GcpBatchConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "batch")
+      validation.isInvalid shouldBe true
+    }
+  }
+
+
+  it should "parse correct existing docker-image-cache-manifest-file config" in {
+
+    val dockerImageCacheManifest1Path = "gs://bucket/manifest1.json"
+    val dockerImageCacheManifestConfigStr = s"""docker-image-cache-manifest-file = "$dockerImageCacheManifest1Path""""
+    val backendConfig = ConfigFactory.parseString(configString(dockerImageCacheManifestConfigStr))
+
+    val validatedGcsPathToDockerImageCacheManifestFileErrorOr = GcpBatchConfigurationAttributes.validateGcsPathToDockerImageCacheManifestFile(backendConfig)
+    validatedGcsPathToDockerImageCacheManifestFileErrorOr match {
+      case Valid(validatedGcsPathToDockerImageCacheManifestFileOpt) =>
+        validatedGcsPathToDockerImageCacheManifestFileOpt match {
+          case Some(validatedGcsPathToDockerCacheManifestFile) =>
+            validatedGcsPathToDockerCacheManifestFile shouldBe GcsPathBuilder.validateGcsPath(dockerImageCacheManifest1Path)
+          case None =>
+            fail("GCS paths to docker image cache manifest files, parsed from config, should not be empty")
+        }
+      case Invalid(ex) =>
+        fail(s"Error while parsing GCS paths to docker image cache manifest files from config: $ex")
+    }
+  }
+
+  it should "parse correct missing docker-image-cache-manifest-file config" in {
+
+    val backendConfig = ConfigFactory.parseString(configString())
+
+    val validatedGcsPathsToDockerImageCacheManifestFilesErrorOr = GcpBatchConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "unit-test-backend")
+    validatedGcsPathsToDockerImageCacheManifestFilesErrorOr match {
+      case Valid(validatedGcsPathsToDockerImageCacheManifestFilesOpt) =>
+        validatedGcsPathsToDockerImageCacheManifestFilesOpt shouldBe None
+      case Invalid(ex) =>
+        fail(s"Error while parsing GCS paths to docker image cache manifest files from config: $ex")
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala
new file mode 100644
index 00000000000..46b7c147b34
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala
@@ -0,0 +1,124 @@
+package cromwell.backend.google.batch.models
+
+import com.typesafe.config.ConfigFactory
+import common.assertion.CromwellTimeoutSpec
+import cromwell.backend.BackendConfigurationDescriptor
+import cromwell.backend.google.batch.models.GcpBatchTestConfig._
+import cromwell.cloudsupport.gcp.GoogleConfiguration
+import cromwell.core.path.DefaultPathBuilder
+import org.scalatest.BeforeAndAfterAll
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.prop.TableDrivenPropertyChecks
+
+class GcpBatchConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks with BeforeAndAfterAll {
+
+  behavior of "GcpBatchConfigurationSpec"
+
+  val mockFile = DefaultPathBuilder.createTempFile()
+
+  override def afterAll(): Unit = {
+    mockFile.delete(swallowIOExceptions = true)
+    ()
+  }
+
+  val globalConfig = ConfigFactory.parseString(
+    s"""
+       |google {
+       |
+       |  application-name = "cromwell"
+       |
+       |  auths = [
+       |    {
+       |      name = "application-default"
+       |      scheme = "application_default"
+       |    },
+       |    {
+       |      name = "service-account"
+       |      scheme = "service_account"
+       |      service-account-id = "my-service-account"
+       |      pem-file = "${mockFile.pathAsString}"
+       |    }
+       |  ]
+       |}
+       |
+    """.stripMargin)
+
+  val backendConfig = ConfigFactory.parseString(
+    """
+      |  // Google project
+      |  project = "my-cromwell-workflows"
+      |
+      |  // Base bucket for workflow executions
+      |  root = "gs://my-cromwell-workflows-bucket"
+      |
+      |  // Polling for completion backs-off gradually for slower-running jobs.
+      |  // This is the maximum polling interval (in seconds):
+      |  maximum-polling-interval = 600
+      |
+      |  genomics {
+      |  // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
+      |  // Pipelines and manipulate auth JSONs.
+      |     auth = "application-default"
+      |     location = "us-central1"
+      |  }
+      |
+      |  default-runtime-attributes {
+      |      failOnStderr: false
+      |      continueOnReturnCode: 0
+      |      cpu: 1
+      |      memory: "2 GB"
+      |      bootDiskSizeGb: 10
+      |      disks: "local-disk 10 SSD"
+      |      noAddress: false
+      |      preemptible: 3
+      |      zones:["us-central1-a", "us-central1-b"]
+      |  }
+      |
+      |  dockerhub {
+      |    account = "dockerAccount"
+      |    token = "dockerToken"
+      |  }
+      |
+      |  filesystems {
+      |    gcs {
+      |      // A reference to a potentially different auth for manipulating files via engine functions.
+      |      auth = "application-default"
+      |    }
+      |  }
+      |
+    """.stripMargin)
+
+  it should "fail to instantiate if any required configuration is missing" in {
+
+    val configs = Table(
+      ("backendConfig", "globalConfig"),
+      (backendConfig, globalConfig.withoutPath("google")),
+      (backendConfig.withoutPath("project"), globalConfig),
+      (backendConfig.withoutPath("root"), globalConfig),
+      (backendConfig.withoutPath("genomics"), globalConfig),
+      (backendConfig.withoutPath("genomics.location"), globalConfig),
+      (backendConfig.withoutPath("filesystems"), globalConfig),
+      (backendConfig.withoutPath("filesystems.gcs"), globalConfig),
+      (backendConfig.withoutPath("filesystems.gcs.auth"), globalConfig)
+    )
+
+    forAll(configs) { (backend, global) =>
+      an[Exception] shouldBe thrownBy {
+        val failingGoogleConf = GoogleConfiguration(global)
+        val failingAttributes = GcpBatchConfigurationAttributes(failingGoogleConf, backend, "papi")
+        new GcpBatchConfiguration(BackendConfigurationDescriptor(backend, global), failingGoogleConf, failingAttributes)
+      }
+    }
+  }
+
+  it should "have correct root" in {
+    new GcpBatchConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig), googleConfiguration, batchAttributes).root shouldBe "gs://my-cromwell-workflows-bucket"
+  }
+
+  //it should "have correct docker" in {
+  //  val dockerConf = new GcpBatchConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig), googleConfiguration, batchAttributes).dockerCredentials
+  //  dockerConf shouldBe defined
+  //  dockerConf.get.token shouldBe "dockerToken"
+  //}
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchJobPathsSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchJobPathsSpec.scala
new file mode 100644
index 00000000000..ed2baf4fd06
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchJobPathsSpec.scala
@@ -0,0 +1,81 @@
+package cromwell.backend.google.batch.models
+
+import com.google.cloud.NoCredentials
+import common.collections.EnhancedCollections._
+import cromwell.backend.BackendSpec
+import cromwell.backend.google.batch.actors.GcpBatchInitializationActor
+import cromwell.backend.google.batch.models.GcpBatchTestConfig.{gcpBatchConfiguration, pathBuilders}
+import cromwell.backend.io.JobPathsSpecHelper._
+import cromwell.core.TestKitSuite
+import cromwell.util.SampleWdl
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.matchers.should.Matchers
+import spray.json.{JsObject, JsString}
+
+import scala.concurrent.ExecutionContext.Implicits.global
+
+class GcpBatchJobPathsSpec extends TestKitSuite with AnyFlatSpecLike with Matchers {
+
+  import BackendSpec._
+
+  behavior of "GcpBatchCallPaths"
+
+  it should "map the correct filenames" in {
+    val workflowDescriptor = buildWdlWorkflowDescriptor(
+      SampleWdl.HelloWorld.workflowSource(),
+      inputFileAsJson = Option(JsObject(SampleWdl.HelloWorld.rawInputs.safeMapValues(JsString.apply)).compactPrint)
+    )
+    val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
+
+    val workflowPaths = GcpBatchWorkflowPaths(workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), gcpBatchConfiguration, pathBuilders(), GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+
+    val callPaths = GcpBatchJobPaths(workflowPaths, jobDescriptorKey)
+
+    callPaths.returnCodeFilename should be("rc")
+    callPaths.stderr.getFileName.pathAsString should be("gs://my-cromwell-workflows-bucket/stderr")
+    callPaths.stdout.getFileName.pathAsString should be("gs://my-cromwell-workflows-bucket/stdout")
+    callPaths.batchLogFilename should be("hello.log")
+  }
+
+  it should "map the correct paths" in {
+    val workflowDescriptor = buildWdlWorkflowDescriptor(
+      SampleWdl.HelloWorld.workflowSource(),
+      inputFileAsJson = Option(JsObject(SampleWdl.HelloWorld.rawInputs.safeMapValues(JsString.apply)).compactPrint)
+    )
+    val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
+
+    val workflowPaths = GcpBatchWorkflowPaths(workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), gcpBatchConfiguration, pathBuilders(), GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+
+    val callPaths = GcpBatchJobPaths(workflowPaths, jobDescriptorKey)
+
+    callPaths.returnCode.pathAsString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello/rc")
+    callPaths.stdout.pathAsString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello/stdout")
+    callPaths.stderr.pathAsString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello/stderr")
+    callPaths.batchLogPath.pathAsString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello/hello.log")
+  }
+
+  it should "map the correct call context" in {
+
+    val workflowDescriptor = buildWdlWorkflowDescriptor(
+      SampleWdl.HelloWorld.workflowSource(),
+      inputFileAsJson = Option(JsObject(SampleWdl.HelloWorld.rawInputs.safeMapValues(JsString.apply)).compactPrint)
+    )
+    val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
+
+    val workflowPaths = GcpBatchWorkflowPaths(workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), gcpBatchConfiguration, pathBuilders(), GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+
+    val callPaths = GcpBatchJobPaths(workflowPaths, jobDescriptorKey)
+
+    callPaths.callContext.root.pathAsString should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello")
+    callPaths.callContext.stdout should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello/stdout")
+    callPaths.callContext.stderr should
+      be(s"gs://my-cromwell-workflows-bucket/wf_hello/${workflowDescriptor.id}/call-hello/stderr")
+  }
+
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchLabelSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchLabelSpec.scala
new file mode 100644
index 00000000000..8ae97f4d0ca
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchLabelSpec.scala
@@ -0,0 +1,38 @@
+package cromwell.backend.google.batch.models
+
+import cats.data.Validated.{Invalid, Valid}
+import common.assertion.CromwellTimeoutSpec
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+class GcpBatchLabelSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  behavior of "GoogleLabels"
+
+  /**
+    * In the format 'to validate', 'expected result'
+    */
+  val googleLabelConversions = List(
+    "11f2468c-39d6-4be3-85c8-32735c01e66b" -> "x--11f2468c-39d6-4be3-85c8-32735c01e66b",
+    "0-cromwell-root-workflow-id" -> "x--0-cromwell-root-workflow-id",
+    "cromwell-root-workflow-id-" -> "cromwell-root-workflow-id---x",
+    "0-cromwell-root-workflow-id-" -> "x--0-cromwell-root-workflow-id---x",
+    "Cromwell-root-workflow-id" -> "cromwell-root-workflow-id",
+    "cromwell_root_workflow_id" -> "cromwell-root-workflow-id",
+    "too-long-too-long-too-long-too-long-too-long-too-long-too-long-t" -> "too-long-too-long-too-long-too---g-too-long-too-long-too-long-t",
+    "0-too-long-and-invalid-too-long-and-invalid-too-long-and-invali+" -> "x--0-too-long-and-invalid-too----nvalid-too-long-and-invali---x"
+  )
+
+  googleLabelConversions foreach { case (label: String, conversion: String) =>
+    it should s"not validate the bad label key '$label'" in {
+      GcpLabel.validateLabelRegex(label) match {
+        case Invalid(_) => // Good!
+        case Valid(_) => fail(s"Label validation succeeded but should have failed.")
+      }
+    }
+
+    it should s"convert the bad label string '$label' into the safe label string '$conversion'" in {
+      GcpLabel.safeGoogleName(label) should be(conversion)
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
new file mode 100644
index 00000000000..569a2af58eb
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
@@ -0,0 +1,298 @@
+package cromwell.backend.google.batch.models
+
+import cats.data.NonEmptyList
+import cromwell.backend.RuntimeAttributeDefinition
+import cromwell.backend.google.batch.models.GcpBatchTestConfig._
+import cromwell.backend.validation.ContinueOnReturnCodeSet
+//import cromwell.backend.google.batch.io.{DiskType, GcpBatchAttachedDisk}
+import cromwell.backend.google.batch.io.{DiskType, GcpBatchWorkingDisk}
+import cromwell.core.WorkflowOptions
+import eu.timepit.refined.refineMV
+import org.scalatest.TestSuite
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.wordspec.AnyWordSpecLike
+import org.slf4j.helpers.NOPLogger
+import spray.json._
+import wdl4s.parser.MemoryUnit
+import wom.format.MemorySize
+import wom.types._
+import wom.values._
+
+import scala.util.{Failure, Success, Try}
+
+final class GcpBatchRuntimeAttributesSpec
+  extends AnyWordSpecLike
+    with Matchers
+    with GcpBatchRuntimeAttributesSpecsMixin {
+
+  "GcpBatchRuntimeAttributes" should {
+
+    "throw an exception when there are no runtime attributes defined." in {
+      val runtimeAttributes = Map.empty[String, WomValue]
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Can't find an attribute value for key docker")
+    }
+
+    "use hardcoded defaults if not declared in task, workflow options, or config (except for docker)" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"))
+      val expectedRuntimeAttributes = expectedDefaults
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes, batchConfiguration = noDefaultsBatchConfiguration)
+    }
+
+    "validate a valid Docker entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"))
+      val expectedRuntimeAttributes = expectedDefaults
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid Docker entry" in {
+      pending
+      val runtimeAttributes = Map("docker" -> WomInteger(1))
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting docker runtime attribute to be String")
+    }
+
+    "validate a valid failOnStderr entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "failOnStderr" -> WomBoolean(true))
+      val expectedRuntimeAttributes = expectedDefaults.copy(failOnStderr = true)
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid failOnStderr entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "failOnStderr" -> WomString("yes"))
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'")
+    }
+
+    "fail to validate an invalid continueOnReturnCode entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomString("value"))
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]")
+    }
+
+    "validate a valid cpu entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "cpu" -> WomInteger(2))
+      val expectedRuntimeAttributes = expectedDefaults.copy(cpu = refineMV(2))
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "validate a valid cpu string entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "cpu" -> WomString("2"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(cpu = refineMV(2))
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid cpu entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "cpu" -> WomString("value"))
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting cpu runtime attribute to be an Integer")
+    }
+
+    "validate a valid zones entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "zones" -> WomString("us-central-z"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(zones = Vector("us-central-z"))
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid zones entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "zones" -> WomInteger(1))
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]")
+    }
+
+    "validate a valid array zones entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "zones" -> WomArray(WomArrayType(WomStringType), List(WomString("us-central1-y"), WomString("us-central1-z"))))
+      val expectedRuntimeAttributes = expectedDefaults.copy(zones = Vector("us-central1-y", "us-central1-z"))
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid array zones entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "zones" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2))))
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]")
+    }
+
+    "validate a valid preemptible entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "preemptible" -> WomInteger(3))
+      val expectedRuntimeAttributes = expectedDefaults.copy(preemptible = 3)
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid preemptible entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "preemptible" -> WomString("value"))
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+        "Expecting preemptible runtime attribute to be an Integer")
+    }
+
+    "validate a valid bootDiskSizeGb entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "bootDiskSizeGb" -> WomInteger(4))
+      val expectedRuntimeAttributes = expectedDefaults.copy(bootDiskSize = 4)
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid bootDiskSizeGb entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "bootDiskSizeGb" -> WomString("4GB"))
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting bootDiskSizeGb runtime attribute to be an Integer")
+    }
+
+    //    "validate a valid disks entry" in {
+    //      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 20 SSD"))
+    //      val expectedRuntimeAttributes = expectedDefaults.copy(disks = Seq(GcpBatchAttachedDisk.parse("local-disk 20 SSD").get))
+    //      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    //    }
+
+    //"fail to validate an invalid disks entry" in {
+    //  val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomInteger(10))
+    //  assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting disks runtime attribute to be a comma separated String or Array[String]")
+    //}
+
+    //"fail to validate a valid disks array entry" in {
+    //  val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomArray(WomArrayType(WomStringType), List(WomString("blah"), WomString("blah blah"))))
+    //  assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE'")
+    //}
+
+    "validate a valid memory entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "memory" -> WomString("1 GB"))
+      val expectedRuntimeAttributes = expectedDefaults.copy(memory = MemorySize.parse("1 GB").get)
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid memory entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "memory" -> WomString("blah"))
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting memory runtime attribute to be an Integer or String with format '8 GB'")
+    }
+
+    "validate a valid noAddress entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "noAddress" -> WomBoolean(true))
+      val expectedRuntimeAttributes = expectedDefaults.copy(noAddress = true)
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid noAddress entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "noAddress" -> WomInteger(1))
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+        "Expecting noAddress runtime attribute to be a Boolean")
+    }
+
+    "override config default attributes with default attributes declared in workflow options" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"))
+
+      val workflowOptionsJson =
+        """{
+          |  "default_runtime_attributes": { "cpu": 2 }
+          |}
+        """.stripMargin.parseJson.asInstanceOf[JsObject]
+
+      val workflowOptions = WorkflowOptions.fromJsonObject(workflowOptionsJson).get
+      val expectedRuntimeAttributes = expectedDefaults.copy(cpu = refineMV(2))
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes, workflowOptions)
+    }
+
+    "override config default runtime attributes with task runtime attributes" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "cpu" -> WomInteger(4))
+
+      val workflowOptionsJson =
+        """{
+          |  "default_runtime_attributes": { "cpu": 2 }
+          |}
+        """.stripMargin.parseJson.asInstanceOf[JsObject]
+
+      val workflowOptions = WorkflowOptions.fromJsonObject(workflowOptionsJson).get
+      val expectedRuntimeAttributes = expectedDefaults.copy(cpu = refineMV(4))
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes, workflowOptions)
+    }
+
+    "override invalid config default attributes with task runtime attributes" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "cpu" -> WomInteger(4))
+
+      val workflowOptionsJson =
+        """{
+          |  "default_runtime_attributes": { "cpu": 2.2 }
+          |}
+        """.stripMargin.parseJson.asInstanceOf[JsObject]
+
+      val workflowOptions = WorkflowOptions.fromJsonObject(workflowOptionsJson).get
+      val expectedRuntimeAttributes = expectedDefaults.copy(cpu = refineMV(4))
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes, workflowOptions)
+    }
+
+    "parse cpuPlatform correctly" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"))
+      val workflowOptionsJson =
+        """{
+          |  "default_runtime_attributes": { "cpuPlatform": "the platform" }
+          |}
+        """.stripMargin.parseJson.asInstanceOf[JsObject]
+      val workflowOptions = WorkflowOptions.fromJsonObject(workflowOptionsJson).get
+      val expectedRuntimeAttributes = expectedDefaults.copy(cpuPlatform = Option("the platform"))
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes, workflowOptions)
+    }
+  }
+}
+
+trait GcpBatchRuntimeAttributesSpecsMixin {
+  this: TestSuite =>
+
+  def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]): WorkflowOptions = {
+    WorkflowOptions(JsObject(Map(
+      "default_runtime_attributes" -> JsObject(defaults)
+    )))
+  }
+
+  val expectedDefaults = new GcpBatchRuntimeAttributes(
+    cpu = refineMV(1),
+    cpuPlatform = None,
+    gpuResource = None,
+    zones = Vector("us-central1-b", "us-central1-a"),
+    preemptible = 0,
+    bootDiskSize = 10,
+    memory = MemorySize(2, MemoryUnit.GB),
+    disks = Vector(GcpBatchWorkingDisk(DiskType.SSD, 10)),
+    dockerImage = "ubuntu:latest",
+    failOnStderr = false,
+    continueOnReturnCode = ContinueOnReturnCodeSet(Set(0)),
+    noAddress = false,
+    useDockerImageCache = None,
+    checkpointFilename = None
+  )
+
+  def assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes: Map[String, WomValue],
+                                                     expectedRuntimeAttributes: GcpBatchRuntimeAttributes,
+                                                     workflowOptions: WorkflowOptions = emptyWorkflowOptions,
+                                                     defaultZones: NonEmptyList[String] = defaultZones,
+                                                     batchConfiguration: GcpBatchConfiguration = gcpBatchConfiguration): Unit = {
+    try {
+      val actualRuntimeAttributes = toBatchRuntimeAttributes(runtimeAttributes, workflowOptions, batchConfiguration)
+      assert(actualRuntimeAttributes == expectedRuntimeAttributes)
+    } catch {
+      case ex: RuntimeException => fail(s"Exception was not expected but received: ${ex.getMessage}")
+    }
+    ()
+  }
+
+  def assertBatchRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue],
+                                                 exMsgs: List[String],
+                                                 workflowOptions: WorkflowOptions): Unit = {
+    Try(toBatchRuntimeAttributes(runtimeAttributes, workflowOptions, gcpBatchConfiguration)) match {
+      case Success(oops) =>
+        fail(s"Expected error containing strings: ${exMsgs.map(s => s"'$s'").mkString(", ")} but instead got Success($oops)")
+      case Failure(ex) => exMsgs foreach { exMsg => assert(ex.getMessage.contains(exMsg)) }
+    }
+    ()
+  }
+
+  def assertBatchRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue],
+                                                 exMsg: String,
+                                                 workflowOptions: WorkflowOptions = emptyWorkflowOptions): Unit = {
+    assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, List(exMsg), workflowOptions)
+  }
+
+  def toBatchRuntimeAttributes(runtimeAttributes: Map[String, WomValue],
+                               workflowOptions: WorkflowOptions,
+                               batchConfiguration: GcpBatchConfiguration): GcpBatchRuntimeAttributes = {
+    val runtimeAttributesBuilder = GcpBatchRuntimeAttributes.runtimeAttributesBuilder(batchConfiguration)
+    val defaultedAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(
+      staticRuntimeAttributeDefinitions, workflowOptions)(runtimeAttributes)
+    val validatedRuntimeAttributes = runtimeAttributesBuilder.build(defaultedAttributes, NOPLogger.NOP_LOGGER)
+    GcpBatchRuntimeAttributes(validatedRuntimeAttributes, batchConfiguration.runtimeConfig)
+  }
+
+  val emptyWorkflowOptions: WorkflowOptions = WorkflowOptions.fromMap(Map.empty).get
+  val defaultZones: NonEmptyList[String] = NonEmptyList.of("us-central1-b", "us-central1-a")
+  val noDefaultsBatchConfiguration = new GcpBatchConfiguration(GcpBatchTestConfig.NoDefaultsConfigurationDescriptor, googleConfiguration, batchAttributes)
+  val staticRuntimeAttributeDefinitions: Set[RuntimeAttributeDefinition] =
+    GcpBatchRuntimeAttributes.runtimeAttributesBuilder(GcpBatchTestConfig.gcpBatchConfiguration).definitions.toSet
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchTestConfig.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchTestConfig.scala
new file mode 100644
index 00000000000..fc8b1333170
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchTestConfig.scala
@@ -0,0 +1,114 @@
+package cromwell.backend.google.batch.models
+
+import akka.actor.ActorSystem
+import com.typesafe.config.{Config, ConfigFactory}
+import cromwell.backend.BackendConfigurationDescriptor
+import cromwell.cloudsupport.gcp.GoogleConfiguration
+import cromwell.core.WorkflowOptions
+import cromwell.core.filesystem.CromwellFileSystems
+import cromwell.core.path.PathBuilder
+
+import scala.concurrent.Await
+import scala.concurrent.duration._
+
+object GcpBatchTestConfig {
+
+  private val BatchBackendConfigString =
+    """
+      |project = "my-cromwell-workflows"
+      |root = "gs://my-cromwell-workflows-bucket"
+      |
+      |genomics {
+      |  auth = "application-default"
+      |  location = "us-central1"
+      |}
+      |
+      |filesystems.gcs.auth = "application-default"
+      |
+      |request-workers = 1
+      |
+      |default-runtime-attributes {
+      |    cpu: 1
+      |    failOnStderr: false
+      |    continueOnReturnCode: 0
+      |    docker: "ubuntu:latest"
+      |    memory: "2048 MB"
+      |    bootDiskSizeGb: 10
+      |    disks: "local-disk 10 SSD"
+      |    noAddress: false
+      |    preemptible: 0
+      |    zones:["us-central1-b", "us-central1-a"]
+      |}
+      |
+      |""".stripMargin
+
+  private val NoDefaultsConfigString =
+    """
+      |project = "my-cromwell-workflows"
+      |root = "gs://my-cromwell-workflows-bucket"
+      |
+      |genomics {
+      |  auth = "application-default"
+      |}
+      |
+      |filesystems {
+      |  gcs {
+      |    auth = "application-default"
+      |  }
+      |}
+      |""".stripMargin
+
+  private val BatchGlobalConfigString =
+    s"""
+       |google {
+       |  application-name = "cromwell"
+       |  auths = [
+       |    {
+       |      name = mock
+       |      scheme = mock
+       |    }
+       |    {
+       |      # legacy `application-default` auth that actually just mocks
+       |      name = "application-default"
+       |      scheme = "mock"
+       |    }
+       |  ]
+       |}
+       |
+       |filesystems {
+       |  gcs {
+       |    class = "cromwell.filesystems.gcs.GcsPathBuilderFactory"
+       |  }
+       |}
+       |
+       |backend {
+       |  default = "batch"
+       |  providers {
+       |    batch {
+       |      actor-factory = "cromwell.backend.google.pipelines.batch.GcpBatchBackendLifecycleActorFactory"
+       |      config {
+       |      $BatchBackendConfigString
+       |      }
+       |    }
+       |  }
+       |}
+       |
+       |""".stripMargin
+
+  val BatchBackendConfig: Config = ConfigFactory.parseString(BatchBackendConfigString)
+  val BatchGlobalConfig: Config = ConfigFactory.parseString(BatchGlobalConfigString)
+  val BatchBackendNoDefaultConfig: Config = ConfigFactory.parseString(NoDefaultsConfigString)
+  val BatchBackendConfigurationDescriptor: BackendConfigurationDescriptor = {
+    new BackendConfigurationDescriptor(BatchBackendConfig, BatchGlobalConfig) {
+      override private[backend] lazy val cromwellFileSystems = new CromwellFileSystems(BatchGlobalConfig)
+    }
+  }
+  val NoDefaultsConfigurationDescriptor: BackendConfigurationDescriptor =
+    BackendConfigurationDescriptor(BatchBackendNoDefaultConfig, BatchGlobalConfig)
+  def pathBuilders()(implicit as: ActorSystem): List[PathBuilder] =
+    Await.result(BatchBackendConfigurationDescriptor.pathBuilders(WorkflowOptions.empty), 5.seconds)
+  val googleConfiguration: GoogleConfiguration = GoogleConfiguration(BatchGlobalConfig)
+  val batchAttributes: GcpBatchConfigurationAttributes =
+    GcpBatchConfigurationAttributes(googleConfiguration, BatchBackendConfig, "batch")
+  val gcpBatchConfiguration = new GcpBatchConfiguration(BatchBackendConfigurationDescriptor, googleConfiguration,batchAttributes)
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchVpcAndSubnetworkProjectLabelValuesSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchVpcAndSubnetworkProjectLabelValuesSpec.scala
new file mode 100644
index 00000000000..e24b3fc809e
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchVpcAndSubnetworkProjectLabelValuesSpec.scala
@@ -0,0 +1,42 @@
+package cromwell.backend.google.batch.models
+
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.prop.TableDrivenPropertyChecks
+
+class GcpBatchVpcAndSubnetworkProjectLabelValuesSpec extends AnyFlatSpec with Matchers with TableDrivenPropertyChecks {
+
+  behavior of "VpcAndSubnetworkProjectLabelValues"
+
+  private val myProjectId = "my-project"
+
+  private val labelsTests = Table(
+    ("description", "network", "subnetOption", "networkName", "subnetNameOption"),
+    ("a network with a slash", "slash/net", None, "slash/net", None),
+    ("a network without a slash", "net", None, "projects/my-project/global/networks/net/", None),
+    ("a subnet with a slash", "slashed/net", Option("slashed/sub"), "slashed/net", Option("slashed/sub")),
+    ("a subnet without a slash", "slashed/net", Option("sub"), "slashed/net", Option("sub")),
+    (
+      "a network with a project token",
+      s"slashed/$${projectId}/net",
+      None,
+      "slashed/my-project/net",
+      None,
+    ),
+    (
+      "a subnet with a project token",
+      "slashed/net",
+      Option(s"slashed/$${projectId}/sub"),
+      "slashed/net",
+      Option("slashed/my-project/sub"),
+    ),
+  )
+
+  forAll(labelsTests) { (description, network, subnetOption, networkName, subnetNameOption) =>
+    it should description in {
+      val labels = VpcAndSubnetworkProjectLabelValues(network, subnetOption)
+      labels.networkName(myProjectId) should be(networkName)
+      labels.subnetNameOption(myProjectId) should be(subnetNameOption)
+    }
+  }
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/LocalizationSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/LocalizationSpec.scala
new file mode 100644
index 00000000000..12be65744e0
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/LocalizationSpec.scala
@@ -0,0 +1,67 @@
+package cromwell.backend.google.batch.runnable
+
+import common.assertion.CromwellTimeoutSpec
+import cromwell.backend.google.batch.models.GcpBatchJobPaths
+import cromwell.core.path.DefaultPathBuilder
+import org.scalatest.OptionValues._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import scala.jdk.CollectionConverters._
+
+class LocalizationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  behavior of "Localization"
+
+  it should "create the right runnable to localize DRS files using a manifest" in {
+    val manifestPathString = s"path/to/${GcpBatchJobPaths.DrsLocalizationManifestName}"
+    val manifestPath = DefaultPathBuilder.get(manifestPathString)
+    val tagKey = "tag"
+    val tagLabel = "myLabel"
+
+    val container = Localization.drsRunnable(manifestPath, Map(tagKey -> tagLabel), None).getContainer
+    val fields = container.getAllFields.asScala
+    fields.keySet.map(_.getName) should contain theSameElementsAs Set("commands", "image_uri")
+    //      Set("commands", "environment", "imageUri", "labels", "mounts")
+
+    fields.find(_._1.getName == "commands").value.asInstanceOf[(_, java.util.List[_])]._2 should contain theSameElementsAs List(
+      "-m", manifestPathString
+    )
+
+    //    runnable.get("mounts") should be(a[java.util.List[_]])
+    //    runnable.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+    //
+    fields.find(_._1.getName == "image_uri").value.asInstanceOf[(_, String)]._2 should be("somerepo/drs-downloader:tagged")
+    //
+    //    val actionLabels = runnable.get("labels").asInstanceOf[java.util.Map[_, _]]
+    //    actionLabels.keySet.asScala should contain theSameElementsAs List("tag")
+    //    actionLabels.get(tagKey) should be(tagLabel)
+  }
+
+  it should "create the right runnable to localize DRS files using a manifest with requester pays" in {
+
+    val manifestPathString = s"path/to/${GcpBatchJobPaths.DrsLocalizationManifestName}"
+    val manifestPath = DefaultPathBuilder.get(manifestPathString)
+    val tagKey = "tag"
+    val tagLabel = "myLabel"
+    val requesterPaysProjectId = "123"
+
+    val container = Localization.drsRunnable(manifestPath, Map(tagKey -> tagLabel), Option(requesterPaysProjectId)).getContainer
+    val fields = container.getAllFields.asScala
+    fields.keySet.map(_.getName) should contain theSameElementsAs Set("commands", "image_uri")
+    //      Set("commands", "environment", "imageUri", "labels", "mounts")
+
+    fields.find(_._1.getName == "commands").value.asInstanceOf[(_, java.util.List[_])]._2 should contain theSameElementsAs List(
+      "-m", manifestPathString, "-r", requesterPaysProjectId
+    )
+
+    //    runnable.get("mounts") should be(a[java.util.List[_]])
+    //    runnable.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+
+    fields.find(_._1.getName == "image_uri").value.asInstanceOf[(_, String)]._2 should be("somerepo/drs-downloader:tagged")
+
+    //    val actionLabels = runnable.get("labels").asInstanceOf[java.util.Map[_, _]]
+    //    actionLabels.keySet.asScala should contain theSameElementsAs List("tag")
+    //    actionLabels.get(tagKey) should be(tagLabel)
+  }
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala
new file mode 100644
index 00000000000..d0e4eac0b87
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala
@@ -0,0 +1,94 @@
+package cromwell.backend.google.batch.runnable
+
+import com.google.cloud.batch.v1.{Runnable, Volume}
+import common.assertion.CromwellTimeoutSpec
+import cromwell.backend.google.batch.runnable.RunnableBuilder.EnhancedRunnableBuilder
+import cromwell.backend.google.batch.runnable.RunnableLabels._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.prop.TableDrivenPropertyChecks
+
+import scala.jdk.CollectionConverters._
+
+class RunnableBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
+
+  behavior of "RunnableBuilder"
+
+  private val dockerRunRunnables = Table(
+    ("description", "runnable", "command"),
+    ("a cloud sdk runnable", RunnableBuilder.cloudSdkRunnable, s"docker run ${RunnableUtils.CloudSdkImage}"),
+    ("a cloud sdk runnable with args",
+      RunnableBuilder.cloudSdkRunnable.withCommand("bash", "-c", "echo hello"),
+      s"docker run ${RunnableUtils.CloudSdkImage} bash -c echo\\ hello"
+    ),
+    ("a cloud sdk runnable with quotes in the args",
+      RunnableBuilder.cloudSdkRunnable.withCommand("bash", "-c", "echo hello m'lord"),
+      s"docker run ${RunnableUtils.CloudSdkImage} bash -c echo\\ hello\\ m\\'lord"
+    ),
+    ("a cloud sdk runnable with a newline in the args",
+      RunnableBuilder.cloudSdkRunnable.withCommand("bash", "-c", "echo hello\\\nworld"),
+      s"docker run ${RunnableUtils.CloudSdkImage} bash -c echo\\ hello\\\\world"
+    ),
+    ("an runnable with multiple args",
+      Runnable.newBuilder()
+        .setContainer(Runnable.Container.newBuilder.setImageUri("ubuntu"))
+        .withEntrypointCommand("")
+        .withCommand("bash", "-c", "echo hello")
+        .withAlwaysRun(true)
+        .withVolumes(List(
+          Volume.newBuilder().setDeviceName("read-only-disk").setMountPath("/mnt/read/only/container").addMountOptions("ro"),
+          Volume.newBuilder().setDeviceName("read-write-disk").setMountPath("/mnt/read/write/container").addMountOptions("rw"),
+        ).map(_.build())),
+      "docker run" +
+        " -v /mnt/read/only/container:/mnt/read/only/container -v /mnt/read/write/container:/mnt/read/write/container" +
+        " ubuntu bash -c echo\\ hello"
+    ),
+  )
+
+  forAll(dockerRunRunnables) { (description, runnable, command) =>
+    it should s"convert $description" in {
+      RunnableBuilder.toDockerRun(runnable) should be(command)
+    }
+  }
+
+  private val memoryRetryExpectedEntrypoint = "/bin/sh"
+
+  def memoryRetryExpectedCommand(lookupString: String): List[String] = {
+    List(
+      "-c",
+      s"grep -E -q '$lookupString' /cromwell_root/stderr ; echo $$? > /cromwell_root/memory_retry_rc"
+    )
+  }
+
+  val volumes = List(
+    Volume.newBuilder().setDeviceName("read-only-disk").setMountPath("/mnt/read/only/container")/*.addMountOptions("ro")*/
+  ).map(_.build())
+
+  private val memoryRetryRunnableExpectedLabels = Map(Key.Tag -> Value.RetryWithMoreMemory).asJava
+
+  it should "return cloud sdk runnable for one key in retry-with-double-memory" in {
+    val lookupKeyList = List("OutOfMemory")
+    val expectedCommand = memoryRetryExpectedCommand(lookupKeyList.mkString("|"))
+
+    val runnable = RunnableBuilder.checkForMemoryRetryRunnable(lookupKeyList, volumes)
+
+    runnable.getContainer.getEntrypoint shouldBe memoryRetryExpectedEntrypoint
+    runnable.getContainer.getCommandsList.asScala shouldBe expectedCommand
+    runnable.getAlwaysRun shouldBe true
+    runnable.getLabelsMap shouldBe memoryRetryRunnableExpectedLabels
+    runnable.getContainer.getVolumesList.asScala.toList shouldBe volumes.map(v => s"${v.getMountPath}:${v.getMountPath}:")
+  }
+
+  it should "return cloud sdk runnable for multiple keys in retry-with-double-memory" in {
+    val lookupKeyList = List("OutOfMemory", "Killed", "Exit123")
+    val expectedCommand = memoryRetryExpectedCommand(lookupKeyList.mkString("|"))
+
+    val runnable = RunnableBuilder.checkForMemoryRetryRunnable(lookupKeyList, volumes)
+
+    runnable.getContainer.getEntrypoint shouldBe memoryRetryExpectedEntrypoint
+    runnable.getContainer.getCommandsList.asScala shouldBe expectedCommand
+    runnable.getAlwaysRun shouldBe true
+    runnable.getLabelsMap shouldBe memoryRetryRunnableExpectedLabels
+    runnable.getContainer.getVolumesList.asScala.toList shouldBe volumes.map(v => s"${v.getMountPath}:${v.getMountPath}:")
+  }
+}
\ No newline at end of file
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableCommandSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableCommandSpec.scala
new file mode 100644
index 00000000000..6e6c9f2d0af
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableCommandSpec.scala
@@ -0,0 +1,67 @@
+package cromwell.backend.google.batch.runnable
+
+
+import java.nio.file.Path
+import common.assertion.CromwellTimeoutSpec
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.batch.runnable.RunnableCommands._
+import cromwell.filesystems.gcs.GcsPath
+import eu.timepit.refined.refineMV
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import common.mock.MockSugar
+
+class RunnableCommandsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with MockSugar {
+  behavior of "ActionCommands"
+
+  it should "inject project flag when request fails because of requester pays" in {
+    val path = GcsPath(
+      mock[Path],
+      mock[com.google.api.services.storage.Storage],
+      mock[com.google.cloud.storage.Storage],
+      "my-project",
+    )
+    val recovered = recoverRequesterPaysError(path) { flag =>
+      s"flag is $flag"
+    }
+
+    recovered shouldBe """flag is  > gsutil_output.txt 2>&1
+                         |# Record the exit code of the gsutil command without project flag
+                         |RC_GSUTIL=$?
+                         |if [ "$RC_GSUTIL" != "0" ]; then
+                         |  printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" flag\ is\ \ failed
+                         |  # Print the reason of the failure
+                         |  cat gsutil_output.txt
+                         |
+                         |  # Check if it matches the BucketIsRequesterPaysErrorMessage
+                         |  if grep -q "requester pays bucket but no user project" gsutil_output.txt; then
+                         |    printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" Retrying\ with\ user\ project
+                         |    flag is -u my-project
+                         |  else
+                         |    exit "$RC_GSUTIL"
+                         |  fi
+                         |else
+                         |  exit 0
+                         |fi""".stripMargin
+  }
+
+  it should "use GcsTransferConfiguration to set the number of localization retries" in {
+    implicit val gcsTransferConfiguration: GcsTransferConfiguration = GcsTransferConfiguration(
+      transferAttempts = refineMV(31380), parallelCompositeUploadThreshold = "0")
+    retry("I'm very flaky") shouldBe """for i in $(seq 31380); do
+                                       |  (
+                                       |    I'm very flaky
+                                       |  )
+                                       |  RC=$?
+                                       |  if [ "$RC" = "0" ]; then
+                                       |    break
+                                       |  fi
+                                       |  if [ $i -lt 31380 ]; then
+                                       |    printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" Waiting\ 5\ seconds\ and\ retrying
+                                       |    sleep 5
+                                       |  fi
+                                       |done
+                                       |exit "$RC"""".stripMargin
+  }
+}
+
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraintsSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraintsSpec.scala
new file mode 100644
index 00000000000..968ab545cbf
--- /dev/null
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraintsSpec.scala
@@ -0,0 +1,90 @@
+package cromwell.backend.google.batch.util
+
+import common.assertion.CromwellTimeoutSpec
+import cromwell.backend.google.batch.models.GcpBatchRuntimeAttributes
+import eu.timepit.refined.numeric.Positive
+import eu.timepit.refined.refineMV
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.prop.TableDrivenPropertyChecks._
+import org.scalatest.prop.Tables.Table
+import org.slf4j.helpers.NOPLogger
+import wdl4s.parser.MemoryUnit
+import wom.format.MemorySize
+
+class GcpBatchMachineConstraintsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+  behavior of "MachineConstraints"
+
+  private val n2Option = Option(GcpBatchRuntimeAttributes.CpuPlatformIntelCascadeLakeValue)
+
+  private val n2dOption = Option(GcpBatchRuntimeAttributes.CpuPlatformAMDRomeValue)
+
+  it should "generate valid machine types" in {
+    val validTypes = Table(
+      ("memory", "cpu", "cpuPlatformOption", "googleLegacyMachineSelection", "machineTypeString"),
+      // Already ok tuple
+      (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), None, false, "custom-1-1024"),
+      // CPU must be even (except if it's 1)
+      (MemorySize(4, MemoryUnit.GB), refineMV[Positive](3), None, false, "custom-4-4096"),
+      // Memory must be a multiple of 256
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](1), None, false, "custom-1-1024"),
+      // Memory / cpu ratio must be > 0.9GB, increase memory
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](4), None, false, "custom-4-3840"),
+      (MemorySize(14, MemoryUnit.GB), refineMV[Positive](16), None, false, "custom-16-14848"),
+      // Memory / cpu ratio must be < 6.5GB, increase CPU
+      (MemorySize(13.65, MemoryUnit.GB), refineMV[Positive](1), None, false, "custom-4-14080"),
+      // Memory should be an int
+      (MemorySize(1520.96, MemoryUnit.MB), refineMV[Positive](1), None, false, "custom-1-1536"),
+      (MemorySize(1024.0, MemoryUnit.MB), refineMV[Positive](1), None, false, "custom-1-1024"),
+      // Increase to a cpu selection not valid for n2 below
+      (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), None, false, "custom-34-31488"),
+
+      // Same tests as above but with legacy machine type selection (cpu and memory as specified. No 'custom machine
+      // requirement' adjustments are expected this time, except float->int)
+
+      (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), None, true, "predefined-1-1024"),
+      (MemorySize(4, MemoryUnit.GB), refineMV[Positive](3), None, true, "predefined-3-4096"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](1), None, true, "predefined-1-1024"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](4), None, true, "predefined-4-1024"),
+      (MemorySize(14, MemoryUnit.GB), refineMV[Positive](16), None, true, "predefined-16-14336"),
+      (MemorySize(13.65, MemoryUnit.GB), refineMV[Positive](1), None, true, "predefined-1-13977"),
+      (MemorySize(1520.96, MemoryUnit.MB), refineMV[Positive](1), None, true, "predefined-1-1520"),
+      (MemorySize(1024.0, MemoryUnit.MB), refineMV[Positive](1), None, true, "predefined-1-1024"),
+      (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), None, true, "predefined-33-2048"),
+
+      // Same tests but with cascade lake (n2)
+      (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), n2Option, false, "n2-custom-2-2048"),
+      (MemorySize(4, MemoryUnit.GB), refineMV[Positive](3), n2Option, false, "n2-custom-4-4096"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](1), n2Option, false, "n2-custom-2-2048"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](4), n2Option, false, "n2-custom-4-4096"),
+      (MemorySize(14, MemoryUnit.GB), refineMV[Positive](16), n2Option, false, "n2-custom-16-16384"),
+      (MemorySize(13.65, MemoryUnit.GB), refineMV[Positive](1), n2Option, false, "n2-custom-2-14080"),
+      (MemorySize(1520.96, MemoryUnit.MB), refineMV[Positive](1), n2Option, false, "n2-custom-2-2048"),
+      (MemorySize(1024.0, MemoryUnit.MB), refineMV[Positive](1), n2Option, false, "n2-custom-2-2048"),
+      (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), n2Option, false, "n2-custom-36-36864"),
+
+      // Same tests but with AMD Rome (n2d) #cpu > 16 are in increments of 16
+      (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1024"),
+      (MemorySize(4,  MemoryUnit.GB), refineMV[Positive](3), n2dOption, false, "n2d-custom-4-4096"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1024"),
+      (MemorySize(1 , MemoryUnit.GB), refineMV[Positive](4), n2dOption, false, "n2d-custom-4-2048"),
+      (MemorySize(14, MemoryUnit.GB), refineMV[Positive](16), n2dOption, false, "n2d-custom-16-14336"),
+      (MemorySize(13.65, MemoryUnit.GB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-14080"),
+      (MemorySize(1520.96, MemoryUnit.MB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1536"),
+      (MemorySize(1024.0, MemoryUnit.MB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1024"),
+      (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), n2dOption, false, "n2d-custom-48-24576"),
+      (MemorySize(2, MemoryUnit.GB), refineMV[Positive](81), n2dOption, false, "n2d-custom-96-49152"),
+      (MemorySize(256, MemoryUnit.GB), refineMV[Positive](128), n2dOption, false, "n2d-custom-96-262144")
+    )
+
+    forAll(validTypes) { (memory, cpu, cpuPlatformOption, googleLegacyMachineSelection, expected) =>
+      GcpBatchMachineConstraints.machineType(
+        memory = memory,
+        cpu = cpu,
+        cpuPlatformOption = cpuPlatformOption,
+        googleLegacyMachineSelection = googleLegacyMachineSelection,
+        jobLogger = NOPLogger.NOP_LOGGER,
+      ) shouldBe expected
+    }
+  }
+}

From 7fed469ca0a7bf83ebce37de8172e30049ba092b Mon Sep 17 00:00:00 2001
From: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Date: Mon, 31 Jul 2023 16:33:44 -0400
Subject: [PATCH 199/326] WM-2100: Update terra-helmfile on publish (#7187)

---
 .github/workflows/chart_update_on_merge.yml | 45 ++++++++++++++++++++-
 1 file changed, 44 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index 72a3486b24b..b00ab5e2766 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -75,7 +75,7 @@ jobs:
         repository: broadinstitute/terra-helmfile
         event-type: update-service
         client-payload: '{"service": "cromiam", "version": "${{ env.CROMWELL_VERSION }}", "dev_only": false}'
-    - name: Edit & push chart
+    - name: Edit & push cromwhelm chart
       env:
         BROADBOT_GITHUB_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
       run: |
@@ -90,3 +90,46 @@ jobs:
         git config --global user.email "broadbot@broadinstitute.org"
         git commit -am "${{ steps.fetch-jira-id.outputs.JIRA_ID }}: Auto update to Cromwell $CROMWELL_VERSION"
         git push https://broadbot:$BROADBOT_GITHUB_TOKEN@github.com/broadinstitute/cromwhelm.git main
+        cd -
+
+    - name: Clone terra-helmfile
+      uses: actions/checkout@v3
+      with:
+        repository: broadinstitute/terra-helmfile
+        token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
+        path: terra-helmfile
+
+    - name: Update workflows-app in terra-helmfile
+      run: |
+        set -e
+        cd terra-helmfile
+        sed -i "s|image: broadinstitute/cromwell:.*|image: broadinstitute/cromwell:$CROMWELL_VERSION|" charts/workflows-app/values.yaml
+        cd -
+
+    - name: Update cromwell-runner-app in terra-helmfile
+      run: |
+        set -e
+        cd terra-helmfile
+        sed -i "s|image: broadinstitute/cromwell:.*|image: broadinstitute/cromwell:$CROMWELL_VERSION|" charts/cromwell-runner-app/values.yaml
+        cd -
+        
+
+    - name: Make PR in terra-helmfile
+      env:
+        BROADBOT_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+        GH_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+      run: |
+        set -e
+        JIRA_ID=${{ steps.fetch-jira-id.outputs.JIRA_ID }}
+        if [[ $JIRA_ID == "missing" ]]; then
+          echo "JIRA_ID missing, PR to terra-helmfile will not be created"
+          exit 0;
+        fi
+        cd terra-helmfile
+        git checkout -b ${JIRA_ID}-cromwell-update-$CROMWELL_VERSION
+        git config --global user.name "broadbot"
+        git config --global user.email "broadbot@broadinstitute.org"
+        git commit -am "${JIRA_ID}: Auto update Cromwell to $CROMWELL_VERSION in workflows-app"
+        git push -u origin ${JIRA_ID}-cromwell-update-$CROMWELL_VERSION
+        gh pr create --title "${JIRA_ID}: auto update Cromwell version to $CROMWELL_VERSION in workflows-app" --body "${JIRA_ID} helm chart update" --label "automerge"
+        cd -

From 0b232dd6a2a2f5bfbaaf606f708151dae603f968 Mon Sep 17 00:00:00 2001
From: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Date: Tue, 1 Aug 2023 13:59:53 -0400
Subject: [PATCH 200/326] WM-2100: Correct commit and PR description of
 terra-helmfile auto update (#7188)

---
 .github/workflows/chart_update_on_merge.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index b00ab5e2766..00995f5178b 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -129,7 +129,7 @@ jobs:
         git checkout -b ${JIRA_ID}-cromwell-update-$CROMWELL_VERSION
         git config --global user.name "broadbot"
         git config --global user.email "broadbot@broadinstitute.org"
-        git commit -am "${JIRA_ID}: Auto update Cromwell to $CROMWELL_VERSION in workflows-app"
+        git commit -am "${JIRA_ID}: Auto update Cromwell to $CROMWELL_VERSION in workflows-app and cromwell-runner-app"
         git push -u origin ${JIRA_ID}-cromwell-update-$CROMWELL_VERSION
-        gh pr create --title "${JIRA_ID}: auto update Cromwell version to $CROMWELL_VERSION in workflows-app" --body "${JIRA_ID} helm chart update" --label "automerge"
+        gh pr create --title "${JIRA_ID}: auto update Cromwell version to $CROMWELL_VERSION in workflows-app and cromwell-runner-app" --body "${JIRA_ID} helm chart update" --label "automerge"
         cd -

From d616608ad328c999c8821ace3af578ecde2567ae Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 8 Aug 2023 15:56:43 -0400
Subject: [PATCH 201/326] WX-1230 Ignore
 `invalidate_bad_caches_use_good_local.test` (#7197)

---
 .../invalidate_bad_caches_use_good_local.test                 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/centaur/src/main/resources/standardTestCases/invalidate_bad_caches_use_good_local.test b/centaur/src/main/resources/standardTestCases/invalidate_bad_caches_use_good_local.test
index 2d3bc8a4e31..4249e041c47 100644
--- a/centaur/src/main/resources/standardTestCases/invalidate_bad_caches_use_good_local.test
+++ b/centaur/src/main/resources/standardTestCases/invalidate_bad_caches_use_good_local.test
@@ -3,6 +3,10 @@ testFormat: workflowsuccess
 backends: [Local]
 tags: [localdockertest]
 
+# This test stopped working 8/23 but its cloud equivalent that we care about is fine [0]
+# [0] `invalidate_bad_caches_use_good_jes.test`
+ignore: true
+
 files {
   workflow: invalidate_bad_caches/invalidate_bad_caches_use_good.wdl
   inputs: invalidate_bad_caches/local.inputs

From f469ecbbd448d6fce8d731f4fd825ef968140522 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Wed, 9 Aug 2023 16:23:10 -0400
Subject: [PATCH 202/326] WX-1078 ACR support (#7192)

---
 build.sbt                                     |   1 +
 .../azure}/AzureCredentials.scala             |   3 +-
 core/src/main/resources/reference.conf        |   9 ++
 .../docker/DockerImageIdentifier.scala        |  11 +-
 .../cromwell/docker/DockerInfoActor.scala     |   2 +
 .../registryv2/DockerRegistryV2Abstract.scala |   6 +-
 .../flows/azure/AcrAccessToken.scala          |   3 +
 .../flows/azure/AcrRefreshToken.scala         |   3 +
 .../flows/azure/AzureContainerRegistry.scala  | 149 ++++++++++++++++++
 .../docker/DockerImageIdentifierSpec.scala    |   2 +
 .../cromwell/docker/DockerInfoActorSpec.scala |  14 +-
 .../blob/BlobFileSystemManager.scala          |   2 +-
 12 files changed, 197 insertions(+), 8 deletions(-)
 rename {filesystems/blob/src/main/scala/cromwell/filesystems/blob => cloudSupport/src/main/scala/cromwell/cloudsupport/azure}/AzureCredentials.scala (98%)
 create mode 100644 dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AcrAccessToken.scala
 create mode 100644 dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AcrRefreshToken.scala
 create mode 100644 dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AzureContainerRegistry.scala

diff --git a/build.sbt b/build.sbt
index 9bdd086d731..814e966b364 100644
--- a/build.sbt
+++ b/build.sbt
@@ -165,6 +165,7 @@ lazy val databaseMigration = (project in file("database/migration"))
 
 lazy val dockerHashing = project
   .withLibrarySettings("cromwell-docker-hashing", dockerHashingDependencies)
+  .dependsOn(cloudSupport)
   .dependsOn(core)
   .dependsOn(core % "test->test")
   .dependsOn(common % "test->test")
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala
similarity index 98%
rename from filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
rename to cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala
index ae84e39adbe..c29155056a9 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/AzureCredentials.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala
@@ -1,4 +1,4 @@
-package cromwell.filesystems.blob
+package cromwell.cloudsupport.azure
 
 import cats.implicits.catsSyntaxValidatedId
 import com.azure.core.credential.TokenRequestContext
@@ -9,7 +9,6 @@ import common.validation.ErrorOr.ErrorOr
 
 import scala.concurrent.duration._
 import scala.jdk.DurationConverters._
-
 import scala.util.{Failure, Success, Try}
 
 /**
diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index a3ac76e949c..d2cc9c5171f 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -411,6 +411,15 @@ docker {
     max-retries = 3
 
     // Supported registries (Docker Hub, Google, Quay) can have additional configuration set separately
+    azure {
+      // Worst case `ReadOps per minute` value from official docs
+      // https://github.com/MicrosoftDocs/azure-docs/blob/main/includes/container-registry-limits.md
+      throttle {
+        number-of-requests = 1000
+        per = 60 seconds
+      }      
+      num-threads = 10
+    }
     google {
       // Example of how to configure throttling, available for all supported registries
       throttle {
diff --git a/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala b/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala
index 9fbd173303b..a798f351f17 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala
@@ -1,5 +1,7 @@
 package cromwell.docker
 
+import cromwell.docker.registryv2.flows.azure.AzureContainerRegistry
+
 import scala.util.{Failure, Success, Try}
 
 sealed trait DockerImageIdentifier {
@@ -14,7 +16,14 @@ sealed trait DockerImageIdentifier {
   lazy val name = repository map { r => s"$r/$image" } getOrElse image
   // The name of the image with a repository prefix if a repository was specified, or with a default repository prefix of
   // "library" if no repository was specified.
-  lazy val nameWithDefaultRepository = repository.getOrElse("library") + s"/$image"
+  lazy val nameWithDefaultRepository = {
+    // In ACR, the repository is part of the registry domain instead of the path
+    // e.g. `terrabatchdev.azurecr.io`
+    if (host.exists(_.contains(AzureContainerRegistry.domain)))
+      image
+    else
+      repository.getOrElse("library") + s"/$image"
+  }
   lazy val hostAsString = host map { h => s"$h/" } getOrElse ""
   // The full name of this image, including a repository prefix only if a repository was explicitly specified.
   lazy val fullName = s"$hostAsString$name:$reference"
diff --git a/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala b/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala
index 40a4c74cb9b..3ebb8d98f39 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala
@@ -14,6 +14,7 @@ import cromwell.core.actor.StreamIntegration.{BackPressure, StreamContext}
 import cromwell.core.{Dispatcher, DockerConfiguration}
 import cromwell.docker.DockerInfoActor._
 import cromwell.docker.registryv2.DockerRegistryV2Abstract
+import cromwell.docker.registryv2.flows.azure.AzureContainerRegistry
 import cromwell.docker.registryv2.flows.dockerhub.DockerHubRegistry
 import cromwell.docker.registryv2.flows.google.GoogleRegistry
 import cromwell.docker.registryv2.flows.quay.QuayRegistry
@@ -232,6 +233,7 @@ object DockerInfoActor {
 
     // To add a new registry, simply add it to that list
     List(
+      ("azure", { c: DockerRegistryConfig => new AzureContainerRegistry(c) }),
       ("dockerhub", { c: DockerRegistryConfig => new DockerHubRegistry(c) }),
       ("google", { c: DockerRegistryConfig => new GoogleRegistry(c) }),
       ("quay", { c: DockerRegistryConfig => new QuayRegistry(c) })
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
index a7cc1969903..bb25cb4bc3d 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
@@ -107,7 +107,7 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
   }
 
   // Execute a request. No retries because they're expected to already be handled by the client
-  private def executeRequest[A](request: IO[Request[IO]], handler: Response[IO] => IO[A])(implicit client: Client[IO]): IO[A] = {
+  protected def executeRequest[A](request: IO[Request[IO]], handler: Response[IO] => IO[A])(implicit client: Client[IO]): IO[A] = {
     request.flatMap(client.run(_).use[IO, A](handler))
   }
 
@@ -188,7 +188,7 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
   /**
     * Builds the token request
     */
-  private def buildTokenRequest(dockerInfoContext: DockerInfoContext): IO[Request[IO]] = {
+  protected def buildTokenRequest(dockerInfoContext: DockerInfoContext): IO[Request[IO]] = {
     val request = Method.GET(
       buildTokenRequestUri(dockerInfoContext.dockerImageID),
       buildTokenRequestHeaders(dockerInfoContext): _*
@@ -220,7 +220,7 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * Request to get the manifest, using the auth token if provided
     */
   private def manifestRequest(token: Option[String], imageId: DockerImageIdentifier, manifestHeader: Accept): IO[Request[IO]] = {
-    val authorizationHeader = token.map(t => Authorization(Credentials.Token(AuthScheme.Bearer, t)))
+    val authorizationHeader: Option[Authorization] = token.map(t => Authorization(Credentials.Token(AuthScheme.Bearer, t)))
     val request = Method.GET(
       buildManifestUri(imageId),
       List(
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AcrAccessToken.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AcrAccessToken.scala
new file mode 100644
index 00000000000..bf0841e2547
--- /dev/null
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AcrAccessToken.scala
@@ -0,0 +1,3 @@
+package cromwell.docker.registryv2.flows.azure
+
+case class AcrAccessToken(access_token: String)
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AcrRefreshToken.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AcrRefreshToken.scala
new file mode 100644
index 00000000000..aa6a6d17eb5
--- /dev/null
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AcrRefreshToken.scala
@@ -0,0 +1,3 @@
+package cromwell.docker.registryv2.flows.azure
+
+case class AcrRefreshToken(refresh_token: String)
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AzureContainerRegistry.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AzureContainerRegistry.scala
new file mode 100644
index 00000000000..46dfd116bc6
--- /dev/null
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AzureContainerRegistry.scala
@@ -0,0 +1,149 @@
+package cromwell.docker.registryv2.flows.azure
+
+import cats.data.Validated.{Invalid, Valid}
+import cats.effect.IO
+import com.typesafe.scalalogging.LazyLogging
+import common.validation.ErrorOr.ErrorOr
+import cromwell.cloudsupport.azure.AzureCredentials
+import cromwell.docker.DockerInfoActor.DockerInfoContext
+import cromwell.docker.{DockerImageIdentifier, DockerRegistryConfig}
+import cromwell.docker.registryv2.DockerRegistryV2Abstract
+import org.http4s.{Header, Request, Response, Status}
+import cromwell.docker.registryv2.flows.azure.AzureContainerRegistry.domain
+import org.http4s.circe.jsonOf
+import org.http4s.client.Client
+import io.circe.generic.auto._
+import org.http4s._
+
+
+class AzureContainerRegistry(config: DockerRegistryConfig) extends DockerRegistryV2Abstract(config) with LazyLogging {
+
+  /**
+    * (e.g registry-1.docker.io)
+    */
+  override protected def registryHostName(dockerImageIdentifier: DockerImageIdentifier): String =
+    dockerImageIdentifier.host.getOrElse("")
+
+  override def accepts(dockerImageIdentifier: DockerImageIdentifier): Boolean =
+    dockerImageIdentifier.hostAsString.contains(domain) 
+
+  override protected def authorizationServerHostName(dockerImageIdentifier: DockerImageIdentifier): String =
+    dockerImageIdentifier.host.getOrElse("")
+
+  /**
+    * In Azure, service name does not exist at the registry level, it varies per repo, e.g. `terrabatchdev.azurecr.io`
+    */
+  override def serviceName: Option[String] =
+    throw new Exception("ACR service name is host of user-defined registry, must derive from `DockerImageIdentifier`")
+  
+  /**
+    * Builds the list of headers for the token request
+    */
+  override protected def buildTokenRequestHeaders(dockerInfoContext: DockerInfoContext): List[Header] = {
+    List(contentTypeHeader)
+  }
+
+  private val contentTypeHeader: Header = {
+    import org.http4s.headers.`Content-Type`
+    import org.http4s.MediaType
+
+    `Content-Type`(MediaType.application.`x-www-form-urlencoded`)
+  }
+  
+  private def getRefreshToken(authServerHostname: String, defaultAccessToken: String): IO[Request[IO]] = {
+    import org.http4s.Uri.{Authority, Scheme}
+    import org.http4s.client.dsl.io._
+    import org.http4s._
+
+    val uri = Uri.apply(
+      scheme = Option(Scheme.https),
+      authority = Option(Authority(host = Uri.RegName(authServerHostname))),
+      path = "/oauth2/exchange",
+      query = Query.empty
+    )
+
+    org.http4s.Method.POST(
+      UrlForm(
+        "service" -> authServerHostname,
+        "access_token" -> defaultAccessToken,
+        "grant_type" -> "access_token"
+      ),
+      uri,
+      List(contentTypeHeader): _* 
+    )
+  }
+
+  /*
+  Unlike other repositories, Azure reserves `GET /oauth2/token` for Basic Authentication [0]
+  In order to use Oauth we must `POST /oauth2/token` [1]
+  
+  [0] https://github.com/Azure/acr/blob/main/docs/Token-BasicAuth.md#using-the-token-api
+  [1] https://github.com/Azure/acr/blob/main/docs/AAD-OAuth.md#calling-post-oauth2token-to-get-an-acr-access-token 
+   */
+  private def getDockerAccessToken(hostname: String, repository: String, refreshToken: String): IO[Request[IO]] = {
+    import org.http4s.Uri.{Authority, Scheme}
+    import org.http4s.client.dsl.io._
+    import org.http4s._
+
+    val uri = Uri.apply(
+      scheme = Option(Scheme.https),
+      authority = Option(Authority(host = Uri.RegName(hostname))),
+      path = "/oauth2/token",
+      query = Query.empty
+    )
+
+    org.http4s.Method.POST(
+      UrlForm(
+        // Tricky behavior - invalid `repository` values return a 200 with a valid-looking token.
+        // However, the token will cause 401s on all subsequent requests.
+        "scope" -> s"repository:$repository:pull",
+        "service" -> hostname,
+        "refresh_token" -> refreshToken,
+        "grant_type" -> "refresh_token"
+      ),
+      uri,
+      List(contentTypeHeader): _* 
+    )
+  }
+
+  override protected def getToken(dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]): IO[Option[String]] = {
+    val hostname = authorizationServerHostName(dockerInfoContext.dockerImageID)
+    val maybeAadAccessToken: ErrorOr[String] = AzureCredentials.getAccessToken(None) // AAD token suitable for get-refresh-token request
+    val repository = dockerInfoContext.dockerImageID.image // ACR uses what we think of image name, as the repository 
+
+    // Top-level flow: AAD access token -> refresh token -> ACR access token
+    maybeAadAccessToken match {
+      case Valid(accessToken) =>
+        (for {
+          refreshToken <- executeRequest(getRefreshToken(hostname, accessToken), parseRefreshToken)
+          dockerToken <- executeRequest(getDockerAccessToken(hostname, repository, refreshToken), parseAccessToken)
+        } yield dockerToken).map(Option.apply)
+      case Invalid(errors) =>
+        IO.raiseError(
+          new Exception(s"Could not obtain AAD token to exchange for ACR refresh token. Error(s): ${errors}")
+        )
+    }
+  }
+
+  implicit val refreshTokenDecoder: EntityDecoder[IO, AcrRefreshToken] = jsonOf[IO, AcrRefreshToken]
+  implicit val accessTokenDecoder: EntityDecoder[IO, AcrAccessToken] = jsonOf[IO, AcrAccessToken]
+
+  private def parseRefreshToken(response: Response[IO]): IO[String] = response match {
+    case Status.Successful(r) => r.as[AcrRefreshToken].map(_.refresh_token)
+    case r =>
+      r.as[String].flatMap(b => IO.raiseError(new Exception(s"Request failed with status ${r.status.code} and body $b")))
+  }
+
+  private def parseAccessToken(response: Response[IO]): IO[String] = response match {
+    case Status.Successful(r) => r.as[AcrAccessToken].map(_.access_token)
+    case r =>
+      r.as[String].flatMap(b => IO.raiseError(new Exception(s"Request failed with status ${r.status.code} and body $b")))
+  }
+
+}
+
+object AzureContainerRegistry {
+  
+  def domain: String = "azurecr.io"
+  
+}
diff --git a/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala
index 00c738dbede..41353934fc6 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala
@@ -18,6 +18,7 @@ class DockerImageIdentifierSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       ("broad/cromwell/submarine",                None,               Option("broad/cromwell"), "submarine",  "latest"),
       ("gcr.io/google/slim",              Option("gcr.io"),         Option("google"),         "slim",     "latest"),
       ("us-central1-docker.pkg.dev/google/slim", Option("us-central1-docker.pkg.dev"), Option("google"), "slim", "latest"),
+      ("terrabatchdev.azurecr.io/postgres",      Option("terrabatchdev.azurecr.io"),         None,     "postgres", "latest"),
       // With tags
       ("ubuntu:latest",                           None,               None,                   "ubuntu",     "latest"),
       ("ubuntu:1235-SNAP",                        None,               None,                   "ubuntu",     "1235-SNAP"),
@@ -25,6 +26,7 @@ class DockerImageIdentifierSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       ("index.docker.io:9999/ubuntu:170904",  Option("index.docker.io:9999"), None,             "ubuntu",    "170904"),
       ("localhost:5000/capture/transwf:170904", Option("localhost:5000"), Option("capture"),      "transwf",    "170904"),
       ("quay.io/biocontainers/platypus-variant:0.8.1.1--htslib1.5_0", Option("quay.io"), Option("biocontainers"), "platypus-variant", "0.8.1.1--htslib1.5_0"),
+      ("terrabatchdev.azurecr.io/postgres:latest", Option("terrabatchdev.azurecr.io"), None, "postgres", "latest"),
       // Very long tags with trailing spaces cause problems for the re engine
       ("someuser/someimage:supercalifragilisticexpialidociouseventhoughthesoundofitissomethingquiteatrociousifyousayitloudenoughyoullalwayssoundprecocious ",              None,         Some("someuser"),         "someimage",     "supercalifragilisticexpialidociouseventhoughthesoundofitissomethingquiteatrociousifyousayitloudenoughyoullalwayssoundprecocious")
     )
diff --git a/dockerHashing/src/test/scala/cromwell/docker/DockerInfoActorSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/DockerInfoActorSpec.scala
index e41be33f762..72baec70825 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/DockerInfoActorSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/DockerInfoActorSpec.scala
@@ -2,6 +2,7 @@ package cromwell.docker
 
 import cromwell.core.Tags.IntegrationTest
 import cromwell.docker.DockerInfoActor._
+import cromwell.docker.registryv2.flows.azure.AzureContainerRegistry
 import cromwell.docker.registryv2.flows.dockerhub.DockerHubRegistry
 import cromwell.docker.registryv2.flows.google.GoogleRegistry
 import cromwell.docker.registryv2.flows.quay.QuayRegistry
@@ -18,7 +19,8 @@ class DockerInfoActorSpec extends DockerRegistrySpec with AnyFlatSpecLike with M
   override protected lazy val registryFlows = List(
     new DockerHubRegistry(DockerRegistryConfig.default),
     new GoogleRegistry(DockerRegistryConfig.default),
-    new QuayRegistry(DockerRegistryConfig.default)
+    new QuayRegistry(DockerRegistryConfig.default),
+    new AzureContainerRegistry(DockerRegistryConfig.default)
   )
 
   it should "retrieve a public docker hash" taggedAs IntegrationTest in {
@@ -50,6 +52,16 @@ class DockerInfoActorSpec extends DockerRegistrySpec with AnyFlatSpecLike with M
         hash should not be empty
     }
   }
+
+  it should "retrieve a private docker hash on acr" taggedAs IntegrationTest in {
+    dockerActor ! makeRequest("terrabatchdev.azurecr.io/postgres:latest")
+
+    expectMsgPF(15 second) {
+      case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
+        alg shouldBe "sha256"
+        hash should not be empty
+    }
+  }
   
   it should "send image not found message back if the image does not exist" taggedAs IntegrationTest in {
     val notFound = makeRequest("ubuntu:nonexistingtag")
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index e50446ea294..ed22d1b55f5 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -6,7 +6,7 @@ import com.azure.storage.blob.sas.{BlobContainerSasPermission, BlobServiceSasSig
 import com.typesafe.config.Config
 import com.typesafe.scalalogging.LazyLogging
 import common.validation.Validation._
-import cromwell.cloudsupport.azure.AzureUtils
+import cromwell.cloudsupport.azure.{AzureCredentials, AzureUtils}
 
 import java.net.URI
 import java.nio.file.{FileSystem, FileSystemNotFoundException, FileSystems}

From 9a140549636114431de8261d8f3169a27a16968b Mon Sep 17 00:00:00 2001
From: dspeck1 <dspeck@burwood.com>
Date: Wed, 9 Aug 2023 17:47:45 -0500
Subject: [PATCH 203/326] WX-1179 Enable GCP Batch Integration Tests (#7199)

Co-authored-by: Adam Nichols <aednichols@gmail.com>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 .github/workflows/integration_tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 98185b3d1b3..ebafe51064c 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -26,9 +26,9 @@ jobs:
       matrix:
         # Batch test fixes to land later
         include:
-          # - build_type: centaurGcpBatch
-          #   build_mysql: 5.7
-          #   friendly_name: Centaur GCP Batch with MySQL 5.7
+          - build_type: centaurGcpBatch
+            build_mysql: 5.7
+            friendly_name: Centaur GCP Batch with MySQL 5.7
           - build_type: centaurPapiV2beta
             build_mysql: 5.7
             friendly_name: Centaur Papi V2 Beta with MySQL 5.7

From acf584099b68c35083bffa1815404b36bc7c363e Mon Sep 17 00:00:00 2001
From: dspeck1 <dspeck@burwood.com>
Date: Fri, 11 Aug 2023 13:14:11 -0500
Subject: [PATCH 204/326] WX-1179 GCP Batch Docs Update (#7196)

Co-authored-by: Jacob Jennings <53196131+jakejennings@users.noreply.github.com>
Co-authored-by: Adam Nichols <aednichols@gmail.com>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 docs/backends/GCPBatch.md | 68 +++++++--------------------------------
 1 file changed, 11 insertions(+), 57 deletions(-)

diff --git a/docs/backends/GCPBatch.md b/docs/backends/GCPBatch.md
index 766719af8c5..d626356223f 100644
--- a/docs/backends/GCPBatch.md
+++ b/docs/backends/GCPBatch.md
@@ -3,9 +3,9 @@
 [//]:
 Google Cloud Batch is a fully managed service that lets you schedule, queue, and execute batch processing workloads on Google Cloud resources. Batch provisions resources and manages capacity on your behalf, allowing your batch workloads to run at scale.
 
-This section offers detailed configuration instructions for using Cromwell with the Batch API in all supported
+This section offers detailed configuration instructions for using Cromwell with the Google Cloud Batch in all supported
 authentication modes. Before reading further in this section please see the
-[Getting started on Google Batch API](../tutorials/Batch101) for instructions common to all authentication modes
+[Getting started on Google Cloud Batch](../tutorials/Batch101) for instructions common to all authentication modes
 and detailed instructions for the application default authentication scheme in particular.
 The instructions below assume you have created a Google Cloud Storage bucket and a Google project enabled for the appropriate APIs.
 
@@ -90,7 +90,6 @@ While technically not part of Service Account authentication mode, one can also
 
 A [JSON key file for the service account](../wf_options/Google.md) must be passed in via the `user_service_account_json` field in the [Workflow Options](../wf_options/Google.md) when submitting the job. Omitting this field will cause the workflow to fail. The JSON should be passed as a string and will need to have no newlines and all instances of `"` and `\n` escaped. 
 
-[//]: # (TODO: is jes_gcs_root the correct workflow option?)
 In the likely event that this service account does not have access to Cromwell's default google project the `google_project` workflow option must be set. In the similarly likely case that this service account can not access Cromwell's default google bucket, the `jes_gcs_root` workflow option should be set appropriately.
 
 For information on the interaction of `user_service_account_json` with private Docker images please see the `Docker` section below.  
@@ -113,13 +112,11 @@ task mytask {
 }
 ```
 
-In order for a private image to be used the appropriate Docker configuration must be provided. If the Docker images being used
+In order for a private image to be used, Docker Hub credentials must be provided. If the Docker images being used
 are public there is no need to add this configuration.
 
 For Batch
 
-[//]: # (TODO: Is this the correct way to configure Docker for batch?)
-[//]: # (5-4-23: Leave alone for now)
 ```
 backend {
   default = GCPBATCH
@@ -129,8 +126,6 @@ backend {
       config {
         dockerhub {
           token = "base64-encoded-docker-hub-username:password"
-          key-name = "name/of/the/kms/key/used/for/encrypting/and/decrypting/the/docker/hub/token"
-          auth = "reference-to-the-auth-cromwell-should-use-for-kms-encryption"
         }
       }
     }
@@ -140,42 +135,6 @@ backend {
 
 `token` is the standard base64-encoded username:password for the appropriate Docker Hub account.
 
-`key-name` is the name of the Google KMS key Cromwell should use for encrypting the Docker `token` before including it
-in the PAPI job execution request. This `key-name` will also be included in the PAPI job execution
-request and will be used by Batch to decrypt the Docker token used by `docker login` to enable access to the private Docker image.
- 
-`auth` is a reference to the name of an authorization in the `auths` block of Cromwell's `google` config.
-Cromwell will use this authorization for encrypting the Google KMS key.
-
-The equivalents of `key-name`, `token` and `auth` can also be specified in workflow options which take
-precedence over values specified in configuration. The corresponding workflow options are named `docker_credentials_key_name`,
-`docker_credentials_token`, and `user_service_account_json`. While the config value `auth` refers to an auth defined in the 
-`google.auths` stanza elsewhere in Cromwell's
-configuration, `user_service_account_json` is expected to be a literal escaped Google service account auth JSON.
-See the `User Service Account` section above for more information on using user service accounts.
-If the key, token or auth value is provided in workflow options then the corresponding private Docker configuration value
-is not required, and vice versa. Also note that for the `user_service_account_json` workflow option to work an auth of type `user_service_account`
-must be defined in Cromwell's `google.auths` stanza; more details in the `User Service Account` section above.
-
-Example Batch workflow options for private Docker configuration:
-
-```
-{
-  "docker_credentials_key_name": "name/of/the/kms/key/used/for/encrypting/and/decrypting/the/docker/hub/token",
-  "docker_credentials_token": "base64_username:password",
-  "user_service_account_json": "<properly escaped user service account JSON file>"
-}
-```
-
-Important
-
-If any of the three private Docker configuration values of key name, auth, or Docker token are missing, Batch will not perform a `docker login`.
-If the Docker image to be pulled is not public the `docker pull` will fail which will cause the overall job to fail.
-
-If using any of these private Docker workflow options it is advisable to add
-them to the `workflow-options.encrypted-fields` list in Cromwell configuration.
-
-
 **Monitoring**
 
 In order to monitor metrics (CPU, Memory, Disk usage...) about the VM during Call Runtime, a workflow option can be used to specify the path to a script that will run in the background and write its output to a log file.
@@ -207,7 +166,7 @@ backend.providers.GCPBATCH.config {
 
 #### Google Labels
 
-Every call run on the Batch API backend is given certain labels by default, so that Google resources can be queried by these labels later. 
+Every call run on the GCP Batch backend is given certain labels by default, so that Google resources can be queried by these labels later. 
 The current default label set automatically applied is:
 
 | Key | Value | Example | Notes |
@@ -217,7 +176,7 @@ The current default label set automatically applied is:
 | wdl-task-name | The name of the WDL task | my-task | |
 | wdl-call-alias | The alias of the WDL call that created this job | my-task-1 | Only present if the task was called with an alias. |
 
-Any custom labels provided as '`google_labels`' in the [workflow options](../wf_options/Google) are also applied to Google resources by the Batch API.
+Any custom labels provided as '`google_labels`' in the [workflow options](../wf_options/Google) are also applied to Google resources by GCP Batch.
 
 ### Virtual Private Network
 
@@ -257,12 +216,12 @@ configuration key, which is `vpc-network` here, as the name of private network a
 If the network name is not present in the config Cromwell will fall back to trying to run jobs on the default network.
 
 If the `network-name` or `subnetwork-name` values contain the string `${projectId}` then that value will be replaced
-by Cromwell with the name of the project running the Batch API.
+by Cromwell with the name of the project running GCP Batch.
 
 If the `network-name` does not contain a `/` then it will be prefixed with `projects/${projectId}/global/networks/`.
 
-Cromwell will then pass the network and subnetwork values to the Batch API. See the documentation for the
-[Batch API](https://cloud.google.com/batch/docs/networking-overview)
+Cromwell will then pass the network and subnetwork values to GCP Batch. See the documentation for
+[GCP Batch](https://cloud.google.com/batch/docs/networking-overview)
 for more information on the various formats accepted for `network` and `subnetwork`.
 
 #### Virtual Private Network via Labels
@@ -306,7 +265,6 @@ network labels, and then fall back to running on the default network.
 
 ### Custom Google Cloud SDK container
 
-[//]: # (TODO: need to test this section as well)
 Cromwell can't use Google's container registry if VPC Perimeter is used in project.
 Own repository can be used by adding `cloud-sdk-image-url` reference to used container:
 
@@ -320,8 +278,6 @@ google {
 
 ### Parallel Composite Uploads 
 
-[//]: # (TODO: Need to test parallel composite uploads)
-
 Cromwell can be configured to use GCS parallel composite uploads which can greatly improve delocalization performance. This feature
 is turned off by default but can be enabled backend-wide by specifying a `gsutil`-compatible memory specification for the key
 `genomics.parallel-composite-upload-threshold` in backend configuration. This memory value represents the minimum size an output file
@@ -394,20 +350,18 @@ outputs. Calls which are executed and not cached will always honor the parallel
 their execution.
 
 
-### Migration from Google Cloud Genomics v2alpha1 to Google Cloud Life Sciences v2beta
+### Migration from Google Cloud Life Sciences v2beta to Google Cloud Batch
 
-1. If you currently run your workflows using Cloud Genomics v2beta and would like to switch to Google Batch, you will need to do a few changes to your configuration file: `actor-factory` value should be changed 
+1. If you currently run your workflows using Cloud Genomics v2beta and would like to switch to Google Cloud Batch, you will need to do a few changes to your configuration file: `actor-factory` value should be changed 
 from `cromwell.backend.google.pipelines.v2beta.PipelinesApiLifecycleActorFactory` to `cromwell.backend.google.batch.GcpBatchLifecycleActorFactory`.
 
 2. You will need to remove the parameter `genomics.endpoint-url` and generate a new config file.
 
-3. Google Batch is now available in a variety of regions. Please see the [Batch Locations](https://cloud.google.com/batch/docs/locations) for a list of supported regions
+3. Google Cloud Batch is now available in a variety of regions. Please see the [Batch Locations](https://cloud.google.com/batch/docs/locations) for a list of supported regions
 
 
 ### Reference Disk Support
 
-[//]: # (TODO: follow up later)
-
 Cromwell 55 and later support mounting reference disks from prebuilt GCP disk images as an alternative to localizing large
 input reference files on Batch. Please note the configuration of reference disk manifests has changed starting with
 Cromwell 57 and now uses the format documented below. 

From 29d3810988ece6ccc85feed631bca6b881c7b7d5 Mon Sep 17 00:00:00 2001
From: Trevyn Langsford <tlangs@broadinstitute.org>
Date: Mon, 14 Aug 2023 11:41:27 -0400
Subject: [PATCH 205/326] ID-734 Increase Timeout for DRSHub Communication
 (#7198)

---
 .../scala/cloud/nio/impl/drs/DrsConfig.scala  |  6 ++---
 .../cloud/nio/impl/drs/DrsPathResolver.scala  | 24 +++++++++++++------
 .../nio/impl/drs/EngineDrsPathResolver.scala  |  2 +-
 docs/filesystems/Filesystems.md               |  8 +++----
 4 files changed, 25 insertions(+), 15 deletions(-)

diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
index c8333a57a66..a2b0a385680 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
@@ -17,9 +17,9 @@ final case class DrsConfig(drsResolverUrl: String,
 object DrsConfig {
   // If you update these values also update Filesystems.md!
   private val DefaultNumRetries = 3
-  private val DefaultWaitInitial = 10 seconds
-  private val DefaultWaitMaximum = 30 seconds
-  private val DefaultWaitMultiplier = 1.5d
+  private val DefaultWaitInitial = 30 seconds
+  private val DefaultWaitMaximum = 60 seconds
+  private val DefaultWaitMultiplier = 1.25d
   private val DefaultWaitRandomizationFactor = 0.1
 
   private val EnvDrsResolverUrl = "DRS_RESOLVER_URL"
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
index f9ae5b62e03..22d86c31726 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
@@ -17,6 +17,7 @@ import org.apache.commons.lang3.exception.ExceptionUtils
 import org.apache.http.client.methods.{HttpGet, HttpPost}
 import org.apache.http.entity.{ContentType, StringEntity}
 import org.apache.http.impl.client.HttpClientBuilder
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager
 import org.apache.http.util.EntityUtils
 import org.apache.http.{HttpResponse, HttpStatus, StatusLine}
 
@@ -24,16 +25,16 @@ import java.nio.ByteBuffer
 import java.nio.channels.{Channels, ReadableByteChannel}
 import scala.util.Try
 
-abstract class DrsPathResolver(drsConfig: DrsConfig, retryInternally: Boolean = true) {
+abstract class DrsPathResolver(drsConfig: DrsConfig) {
 
   protected lazy val httpClientBuilder: HttpClientBuilder = {
     val clientBuilder = HttpClientBuilder.create()
-    if (retryInternally) {
-      val retryHandler = new DrsResolverHttpRequestRetryStrategy(drsConfig)
-      clientBuilder
-        .setRetryHandler(retryHandler)
-        .setServiceUnavailableRetryStrategy(retryHandler)
-    }
+    val retryHandler = new DrsResolverHttpRequestRetryStrategy(drsConfig)
+    clientBuilder
+      .setRetryHandler(retryHandler)
+      .setServiceUnavailableRetryStrategy(retryHandler)
+    clientBuilder.setConnectionManager(connectionManager)
+    clientBuilder.setConnectionManagerShared(true)
     clientBuilder
   }
 
@@ -241,4 +242,13 @@ object DrsResolverResponseSupport {
         baseMessage + "(empty response)"
     }
   }
+
+  lazy val connectionManager = {
+    val connManager = new PoolingHttpClientConnectionManager()
+    connManager.setMaxTotal(250)
+    // Since the HttpClient is always talking to DRSHub,
+    // make the max connections per route the same as max total connections
+    connManager.setDefaultMaxPerRoute(250)
+    connManager
+  }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala
index a62ce7971c2..01f7a488eb3 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala
@@ -5,7 +5,7 @@ import common.validation.ErrorOr.ErrorOr
 case class EngineDrsPathResolver(drsConfig: DrsConfig,
                                  drsCredentials: DrsCredentials,
                                 )
-  extends DrsPathResolver(drsConfig, retryInternally = false) {
+  extends DrsPathResolver(drsConfig) {
 
   override def getAccessToken: ErrorOr[String] = drsCredentials.getAccessToken
 }
diff --git a/docs/filesystems/Filesystems.md b/docs/filesystems/Filesystems.md
index 0630e421c0b..8ca03825c6e 100644
--- a/docs/filesystems/Filesystems.md
+++ b/docs/filesystems/Filesystems.md
@@ -23,12 +23,12 @@ filesystems {
             # The number of times to retry failures connecting or HTTP 429 or HTTP 5XX responses, default 3.
             num-retries = 3
             # How long to wait between retrying HTTP 429 or HTTP 5XX responses, default 10 seconds.
-            wait-initial = 10 seconds
+            wait-initial = 30 seconds
             # The maximum amount of time to wait between retrying HTTP 429 or HTTP 5XX responses, default 30 seconds.
-            wait-maximum = 30 seconds
+            wait-maximum = 60 seconds
             # The amount to multiply the amount of time to wait between retrying HTTP or 429 or HTTP 5XX responses.
-            # Default 2.0, and will never multiply the wait time more than wait-maximum.
-            wait-mulitiplier = 2.0
+            # Default 1.25, and will never multiply the wait time more than wait-maximum.
+            wait-mulitiplier = 1.25
             # The randomization factor to use for creating a range around the wait interval.
             # A randomization factor of 0.5 results in a random period ranging between 50% below and 50% above the wait
             # interval. Default 0.1.

From 2a69691ec56ba0e8f279b8f006ba796bb9cfaf05 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 15 Aug 2023 15:01:14 -0400
Subject: [PATCH 206/326] [WX-1156] internal_path_prefix for TES 4.4 (#7190)

---
 .../backend/impl/tes/TesJobPaths.scala        |  9 +++
 .../cromwell/backend/impl/tes/TesTask.scala   | 34 +++++-----
 .../backend/impl/tes/TesTaskSpec.scala        | 63 +++++++++++++++----
 3 files changed, 81 insertions(+), 25 deletions(-)

diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
index 0b75cfc0f3a..f1797d9bc58 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
@@ -28,6 +28,15 @@ case class TesJobPaths private[tes] (override val workflowPaths: TesWorkflowPath
   val callInputsDockerRoot = callDockerRoot.resolve("inputs")
   val callInputsRoot = callRoot.resolve("inputs")
 
+  /*
+   * tesTaskRoot: This is the root directory that TES will use for files related to this task.
+   * We provide it to TES as a k/v pair where the key is "internal_path_prefix" (specified in TesWorkflowOptionKeys.scala)
+   * and the value is a blob path.
+   * This is not a standard TES feature, but rather related to the Azure TES implementation that Terra uses.
+   * While passing it outside of terra won't do any harm, we could consider making this optional and/or configurable.
+   */
+  val tesTaskRoot : Path = callExecutionRoot.resolve("tes_task")
+
   // Given an output path, return a path localized to the storage file system
   def storageOutput(path: String): String = {
     callExecutionRoot.resolve(path).toString
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index f7674c377e7..66f0f508d77 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -1,5 +1,4 @@
 package cromwell.backend.impl.tes
-
 import common.collections.EnhancedCollections._
 import common.util.StringUtil._
 import cromwell.backend.impl.tes.OutputMode.OutputMode
@@ -71,7 +70,6 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
     path = tesPaths.callExecutionDockerRoot.resolve("script").toString,
     `type` = Option("FILE")
   )
-
   private def writeFunctionFiles: Map[FullyQualifiedName, Seq[WomFile]] =
     instantiatedCommand.createdFiles map { f => f.file.value.md5SumShort -> List(f.file) } toMap
 
@@ -231,11 +229,6 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
       workflowExecutionIdentityOption
   )
 
-  val resources: Resources = TesTask.makeResources(
-    runtimeAttributes,
-    preferedWorkflowExecutionIdentity
-  )
-
   val executors = Seq(Executor(
     image = dockerImageUsed,
     command = Seq(jobShell, commandScript.path),
@@ -245,6 +238,12 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
     stdin = None,
     env = None
   ))
+
+  val resources: Resources = TesTask.makeResources(
+    runtimeAttributes,
+    preferedWorkflowExecutionIdentity,
+    Option(tesPaths.tesTaskRoot.pathAsString)
+  )
 }
 
 object TesTask {
@@ -254,15 +253,22 @@ object TesTask {
     configIdentity.map(_.value).orElse(workflowOptionsIdentity.map(_.value))
   }
   def makeResources(runtimeAttributes: TesRuntimeAttributes,
-                    workflowExecutionId: Option[String]): Resources = {
-
-    // This was added in BT-409 to let us pass information to an Azure
-    // TES server about which user identity to run tasks as.
-    // Note that we validate the type of WorkflowExecutionIdentity
-    // in TesInitializationActor.
-    val backendParameters = runtimeAttributes.backendParameters ++
+                    workflowExecutionId: Option[String], internalPathPrefix: Option[String]): Resources = {
+    /*
+     * workflowExecutionId: This was added in BT-409 to let us pass information to an Azure
+     * TES server about which user identity to run tasks as.
+     * Note that we validate the type of WorkflowExecutionIdentity in TesInitializationActor.
+     *
+     * internalPathPrefix: Added in WX-1156 to support the azure TES implementation. Specifies
+     * a working directory that the TES task can use.
+     */
+    val internalPathPrefixKey = "internal_path_prefix"
+    val backendParameters : Map[String, Option[String]] = runtimeAttributes.backendParameters ++
       workflowExecutionId
         .map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option(_))
+        .toMap ++
+      internalPathPrefix
+        .map(internalPathPrefixKey -> Option(_))
         .toMap
     val disk :: ram :: _ = Seq(runtimeAttributes.disk, runtimeAttributes.memory) map {
       case Some(x) =>
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index e2c743bb718..5bfa916086d 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -31,34 +31,40 @@ class TesTaskSpec
     false,
     Map.empty
   )
+  val internalPathPrefix = Option("mock/path/to/tes/task")
+  val expectedTuple = "internal_path_prefix" -> internalPathPrefix
 
   it should "create the correct resources when an identity is passed in WorkflowOptions" in {
     val wei = Option("abc123")
-    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
-        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123")))
+    TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
+        Resources(None, None, None, Option(false), None,
+          Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"),
+            expectedTuple))
     )
   }
 
   it should "create the correct resources when an empty identity is passed in WorkflowOptions" in {
     val wei = Option("")
-    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
-        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("")))
+    TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
+      Resources(None, None, None, Option(false), None,
+        Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option(""),
+          expectedTuple))
     )
   }
 
   it should "create the correct resources when no identity is passed in WorkflowOptions" in {
     val wei = None
-    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
-        Resources(None, None, None, Option(false), None, Option(Map.empty[String, Option[String]])
-    )
+    TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
+      Resources(None, None, None, Option(false), None, Option(Map(expectedTuple)))
   }
 
   it should "create the correct resources when an identity is passed in via backend config" in {
     val weic = Option(WorkflowExecutionIdentityConfig("abc123"))
     val weio = Option(WorkflowExecutionIdentityOption("def456"))
     val wei = TesTask.getPreferredWorkflowExecutionIdentity(weic, weio)
-    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
-        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123")))
+    TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
+        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"),
+          expectedTuple))
     )
   }
 
@@ -66,11 +72,46 @@ class TesTaskSpec
     val weic = None
     val weio = Option(WorkflowExecutionIdentityOption("def456"))
     val wei = TesTask.getPreferredWorkflowExecutionIdentity(weic, weio)
-    TesTask.makeResources(runtimeAttributes, wei) shouldEqual
-        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("def456")))
+    TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
+        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("def456"),
+          expectedTuple))
     )
   }
 
+  it should "correctly set the internal path prefix when provided as a backend parameter" in {
+    val wei = Option("abc123")
+    val internalPathPrefix = Option("mock/path/to/tes/task")
+    TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
+      Resources(None, None, None, Option(false), None,
+        Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"),
+          "internal_path_prefix" -> internalPathPrefix)
+      ))
+  }
+
+  it should "correctly resolve the path to .../tes_task and add the k/v pair to backend parameters" in {
+    val emptyWorkflowOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))
+    val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld,
+      labels = Labels("foo" -> "bar"))
+    val jobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+      Map.empty,
+      emptyWorkflowOptions,
+      Set.empty)
+    val tesPaths = TesJobPaths(jobDescriptor.key,
+      jobDescriptor.workflowDescriptor,
+      TestConfig.emptyConfig)
+
+    val expectedKey = "internal_path_prefix"
+    val expectedValue = Option(tesPaths.tesTaskRoot.pathAsString)
+
+    //Assert path correctly ends up in the resources
+    val wei = Option("abc123")
+    TesTask.makeResources(runtimeAttributes, wei, expectedValue) shouldEqual
+      Resources(None, None, None, Option(false), None,
+        Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"),
+          expectedKey -> expectedValue))
+      )
+  }
+
   it should "copy labels to tags" in {
     val jobLogger = mock[JobLogger]
     val emptyWorkflowOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))

From 2fc467e2be4ba7930a386ea43f12b06432d60c29 Mon Sep 17 00:00:00 2001
From: Dillon Scott <67511512+dillydally414@users.noreply.github.com>
Date: Thu, 17 Aug 2023 15:51:28 -0400
Subject: [PATCH 207/326] [WM-2184] Remove brackets from Jira ID (#7206)

---
 .github/workflows/chart_update_on_merge.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index 00995f5178b..a2b14f2ec65 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -14,7 +14,7 @@ jobs:
     - name: Fetch Jira ID from the commit message
       id: fetch-jira-id
       run: |
-        JIRA_ID=$(echo '${{ github.event.pull_request.title }}' | grep -Eo '\[?[A-Z][A-Z]+-[0-9]+\]?')
+        JIRA_ID=$(echo '${{ github.event.pull_request.title }}' | grep -Eo '[A-Z][A-Z]+-[0-9]+' | xargs echo -n | tr '[:space:]' ',')
         [[ -z "$JIRA_ID" ]] && { echo "No Jira ID found in $1" ; exit 1; }
         echo "JIRA_ID=$JIRA_ID" >> $GITHUB_OUTPUT
     - name: Clone Cromwell

From c025756c349e45f1d7cd4939869106368d217d17 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 17 Aug 2023 18:00:49 -0400
Subject: [PATCH 208/326] WX-1153 Azure blob read md5 from metadata for large
 files (#7204)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .github/workflows/cromwell_unit_tests.yml     |   4 +
 .../blob/BlobFileSystemManager.scala          |  11 +-
 .../filesystems/blob/BlobPathBuilder.scala    |  48 +++++++--
 .../blob/BlobPathBuilderSpec.scala            | 100 ++++++++++++------
 4 files changed, 117 insertions(+), 46 deletions(-)

diff --git a/.github/workflows/cromwell_unit_tests.yml b/.github/workflows/cromwell_unit_tests.yml
index 797f38efd96..88951871d8f 100644
--- a/.github/workflows/cromwell_unit_tests.yml
+++ b/.github/workflows/cromwell_unit_tests.yml
@@ -28,6 +28,10 @@ jobs:
   
     #Invoke SBT to run all unit tests for Cromwell. 
     - name: Run tests
+      env:
+        AZURE_CLIENT_ID: ${{ secrets.VAULT_AZURE_CENTAUR_CLIENT_ID }}
+        AZURE_CLIENT_SECRET: ${{ secrets.VAULT_AZURE_CENTAUR_CLIENT_SECRET }}
+        AZURE_TENANT_ID: ${{ secrets.VAULT_AZURE_CENTAUR_TENANT_ID }}
       run: |
         set -e
         sbt "test"
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index ed22d1b55f5..ac8f01d2cc7 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -1,7 +1,7 @@
 package cromwell.filesystems.blob
 
 import com.azure.core.credential.AzureSasCredential
-import com.azure.storage.blob.nio.AzureFileSystem
+import com.azure.storage.blob.nio.{AzureFileSystem, AzureFileSystemProvider}
 import com.azure.storage.blob.sas.{BlobContainerSasPermission, BlobServiceSasSignatureValues}
 import com.typesafe.config.Config
 import com.typesafe.scalalogging.LazyLogging
@@ -9,7 +9,8 @@ import common.validation.Validation._
 import cromwell.cloudsupport.azure.{AzureCredentials, AzureUtils}
 
 import java.net.URI
-import java.nio.file.{FileSystem, FileSystemNotFoundException, FileSystems}
+import java.nio.file.spi.FileSystemProvider
+import java.nio.file.{FileSystem, FileSystemNotFoundException}
 import java.time.temporal.ChronoUnit
 import java.time.{Duration, Instant, OffsetDateTime}
 import scala.jdk.CollectionConverters._
@@ -17,9 +18,9 @@ import scala.util.{Failure, Success, Try}
 
 // We encapsulate this functionality here so that we can easily mock it out, to allow for testing without
 // actually connecting to Blob storage.
-case class FileSystemAPI() {
-  def getFileSystem(uri: URI): Try[FileSystem] = Try(FileSystems.getFileSystem(uri))
-  def newFileSystem(uri: URI, config: Map[String, Object]): FileSystem = FileSystems.newFileSystem(uri, config.asJava)
+case class FileSystemAPI(private val provider: FileSystemProvider = new AzureFileSystemProvider()) {
+  def getFileSystem(uri: URI): Try[FileSystem] = Try(provider.getFileSystem(uri))
+  def newFileSystem(uri: URI, config: Map[String, Object]): FileSystem = provider.newFileSystem(uri, config.asJava)
   def closeFileSystem(uri: URI): Option[Unit] = getFileSystem(uri).toOption.map(_.close)
 }
 /**
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 9e7b230286c..aa6445fa779 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -7,6 +7,7 @@ import cromwell.filesystems.blob.BlobPathBuilder._
 
 import java.net.{MalformedURLException, URI}
 import java.nio.file.{Files, LinkOption}
+import scala.jdk.CollectionConverters._
 import scala.language.postfixOps
 import scala.util.{Failure, Success, Try}
 
@@ -78,6 +79,20 @@ object BlobPath {
   //    format the library expects
   // 2) If the path looks like <container>:<path>, strip off the <container>: to leave the absolute path inside the container.
   private val brokenPathRegex = "https:/([a-z0-9]+).blob.core.windows.net/([-a-zA-Z0-9]+)/(.*)".r
+
+  // Blob files larger than 5 GB upload in parallel parts [0][1] and do not get a native `CONTENT-MD5` property.
+  // Instead, some uploaders such as TES [2] calculate the md5 themselves and store it under this key in metadata.
+  // They do this for all files they touch, regardless of size, and the root/metadata property is authoritative over native.
+  //
+  // N.B. most if not virtually all large files in the wild will NOT have this key populated because they were not created
+  // by TES or its associated upload utility [4].
+  //
+  // [0] https://learn.microsoft.com/en-us/azure/storage/blobs/scalability-targets
+  // [1] https://learn.microsoft.com/en-us/rest/api/storageservices/version-2019-12-12
+  // [2] https://github.com/microsoft/ga4gh-tes/blob/03feb746bb961b72fa91266a56db845e3b31be27/src/Tes.Runner/Transfer/BlobBlockApiHttpUtils.cs#L25
+  // [4] https://github.com/microsoft/ga4gh-tes/blob/main/src/Tes.RunnerCLI/scripts/roothash.sh
+  private val largeBlobFileMetadataKey = "md5_4mib_hashlist_root_hash"
+
   def cleanedNioPathString(nioString: String): String = {
     val pathStr = nioString match {
       case brokenPathRegex(_, containerName, pathInContainer) =>
@@ -116,16 +131,33 @@ case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, con
   def blobFileAttributes: Try[AzureBlobFileAttributes] =
     Try(Files.readAttributes(nioPath, classOf[AzureBlobFileAttributes]))
 
+  def blobFileMetadata: Try[Option[Map[String, String]]] = blobFileAttributes.map { attrs =>
+    // `metadata()` has a documented `null` case
+    Option(attrs.metadata()).map(_.asScala.toMap)
+  }
+
   def md5HexString: Try[Option[String]] = {
-    blobFileAttributes.map(h =>
-      Option(h.blobHttpHeaders().getContentMd5) match {
-        case None => None
-        case Some(arr) if arr.isEmpty => None
-        // Convert the bytes to a hex-encoded string. Note that this value
-        // is rendered in base64 in the Azure web portal.
-        case Some(bytes) => Option(bytes.map("%02x".format(_)).mkString)
+    def md5FromMetadata: Option[String] = (blobFileMetadata map { maybeMetadataMap: Option[Map[String, String]] =>
+      maybeMetadataMap flatMap { metadataMap: Map[String, String] =>
+        metadataMap.get(BlobPath.largeBlobFileMetadataKey)
       }
-    )
+    }).toOption.flatten
+
+    // Convert the bytes to a hex-encoded string. Note that the value
+    // is rendered in base64 in the Azure web portal.
+    def hexString(bytes: Array[Byte]): String = bytes.map("%02x".format(_)).mkString
+
+    blobFileAttributes.map { attr: AzureBlobFileAttributes =>
+      (Option(attr.blobHttpHeaders().getContentMd5), md5FromMetadata) match {
+        case (None, None) => None
+        // (Some, Some) will happen for all <5 GB files uploaded by TES. Per Microsoft 2023-08-15 the
+        // root/metadata algorithm emits different values than the native algorithm and we should
+        // always choose metadata for consistency with larger files that only have that one.
+        case (_, Some(metadataMd5)) => Option(metadataMd5)
+        case (Some(headerMd5Bytes), None) if headerMd5Bytes.isEmpty => None
+        case (Some(headerMd5Bytes), None) => Option(hexString(headerMd5Bytes))
+      }
+    }
   }
 
   /**
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index 4012e241eb3..eef6db8e942 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -89,46 +89,80 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     )
   }
 
-  //// The below tests are IGNORED because they depend on Azure auth information being present in the environment ////
+  // The following tests use the `centaurtesting` account injected into CI. They depend on access to the
+  // container specified below. You may need to log in to az cli locally to get them to pass.
   private val subscriptionId: SubscriptionId = SubscriptionId(UUID.fromString("62b22893-6bc1-46d9-8a90-806bb3cce3c9"))
-  private val endpoint: EndpointURL = BlobPathBuilderSpec.buildEndpoint("coaexternalstorage")
-  private val store: BlobContainerName = BlobContainerName("inputs")
+  private val endpoint: EndpointURL = BlobPathBuilderSpec.buildEndpoint("centaurtesting")
+  private val container: BlobContainerName = BlobContainerName("test-blob")
 
-  def makeBlobPathBuilder(blobEndpoint: EndpointURL, container: BlobContainerName): BlobPathBuilder = {
+  def makeBlobPathBuilder(blobEndpoint: EndpointURL,
+                          container: BlobContainerName): BlobPathBuilder = {
     val blobTokenGenerator = NativeBlobSasTokenGenerator(container, blobEndpoint, Some(subscriptionId))
     val fsm = new BlobFileSystemManager(container, blobEndpoint, 10, blobTokenGenerator)
-    new BlobPathBuilder(store, endpoint)(fsm)
+    new BlobPathBuilder(container, blobEndpoint)(fsm)
   }
 
-  ignore should "resolve an absolute path string correctly to a path" in {
-    val builder = makeBlobPathBuilder(endpoint, store)
-    val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
+  it should "read md5 from small files <5g" in {
+    val builder = makeBlobPathBuilder(endpoint, container)
+    val evalPath = "/testRead.txt"
+    val testString = endpoint.value + "/" + container + evalPath
+    val blobPath1: BlobPath = (builder build testString).get
+    blobPath1.md5HexString.get should equal(Option("31ae06882d06a20e01ba1ac961ce576c"))
+  }
+
+  it should "read md5 from large files >5g" in {
+    val builder = makeBlobPathBuilder(endpoint, container)
+    val evalPath = "/Rocky-9.2-aarch64-dvd.iso"
+    val testString = endpoint.value + "/" + container + evalPath
+    val blobPath1: BlobPath = (builder build testString).get
+    blobPath1.md5HexString.toOption.get should equal(Some("13cb09331d2d12c0f476f81c672a4319"))
+  }
+
+  it should "choose the root/metadata md5 over the native md5 for files that have both" in {
+    val builder = makeBlobPathBuilder(endpoint, container)
+    val evalPath = "/redundant_md5_test.txt"
+    val testString = endpoint.value + "/" + container + evalPath
+    val blobPath1: BlobPath = (builder build testString).get
+    blobPath1.md5HexString.toOption.get should equal(Some("021c7cc715ec82292bb9b925f9ca44d3"))
+  }
+
+  it should "gracefully return `None` when neither hash is found" in {
+    val builder = makeBlobPathBuilder(endpoint, container)
+    val evalPath = "/no_md5_test.txt"
+    val testString = endpoint.value + "/" + container + evalPath
+    val blobPath1: BlobPath = (builder build testString).get
+    blobPath1.md5HexString.get should equal(None)
+  }
+
+  it should "resolve an absolute path string correctly to a path" in {
+    val builder = makeBlobPathBuilder(endpoint, container)
+    val rootString = s"${endpoint.value}/${container.value}/cromwell-execution"
     val blobRoot: BlobPath = builder build rootString getOrElse fail()
-    blobRoot.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution")
-    val otherFile = blobRoot.resolve("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
-    otherFile.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
+    blobRoot.toAbsolutePath.pathAsString should equal ("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution")
+    val otherFile = blobRoot.resolve("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution/test/inputFile.txt")
+    otherFile.toAbsolutePath.pathAsString should equal ("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution/test/inputFile.txt")
   }
 
-  ignore should "build a blob path from a test string and read a file" in {
-    val builder = makeBlobPathBuilder(endpoint, store)
+  it should "build a blob path from a test string and read a file" in {
+    val builder = makeBlobPathBuilder(endpoint, container)
     val endpointHost = BlobPathBuilder.parseURI(endpoint.value).map(_.getHost).getOrElse(fail("Could not parse URI"))
     val evalPath = "/test/inputFile.txt"
-    val testString = endpoint.value + "/" + store + evalPath
+    val testString = endpoint.value + "/" + container + evalPath
     val blobPath: BlobPath = builder build testString getOrElse fail()
 
-    blobPath.container should equal(store)
+    blobPath.container should equal(container)
     blobPath.endpoint should equal(endpoint)
     blobPath.pathAsString should equal(testString)
-    blobPath.pathWithoutScheme should equal(endpointHost + "/" + store + evalPath)
+    blobPath.pathWithoutScheme should equal(endpointHost + "/" + container + evalPath)
     val is = blobPath.newInputStream()
     val fileText = (is.readAllBytes.map(_.toChar)).mkString
     fileText should include ("This is my test file!!!! Did it work?")
   }
 
-  ignore should "build duplicate blob paths in the same filesystem" in {
-    val builder = makeBlobPathBuilder(endpoint, store)
+  it should "build duplicate blob paths in the same filesystem" in {
+    val builder = makeBlobPathBuilder(endpoint, container)
     val evalPath = "/test/inputFile.txt"
-    val testString = endpoint.value + "/" + store + evalPath
+    val testString = endpoint.value + "/" + container + evalPath
     val blobPath1: BlobPath = builder build testString getOrElse fail()
     blobPath1.nioPath.getFileSystem.close()
     val blobPath2: BlobPath = builder build testString getOrElse fail()
@@ -138,20 +172,20 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     fileText should include ("This is my test file!!!! Did it work?")
   }
 
-  ignore should "resolve a path without duplicating container name" in {
-    val builder = makeBlobPathBuilder(endpoint, store)
-    val rootString = s"${endpoint.value}/${store.value}/cromwell-execution"
+  it should "resolve a path without duplicating container name" in {
+    val builder = makeBlobPathBuilder(endpoint, container)
+    val rootString = s"${endpoint.value}/${container.value}/cromwell-execution"
     val blobRoot: BlobPath = builder build rootString getOrElse fail()
-    blobRoot.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution")
+    blobRoot.toAbsolutePath.pathAsString should equal ("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution")
     val otherFile = blobRoot.resolve("test/inputFile.txt")
-    otherFile.toAbsolutePath.pathAsString should equal ("https://coaexternalstorage.blob.core.windows.net/inputs/cromwell-execution/test/inputFile.txt")
+    otherFile.toAbsolutePath.pathAsString should equal ("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution/test/inputFile.txt")
   }
 
-  ignore should "correctly remove a prefix from the blob path" in {
-    val builder = makeBlobPathBuilder(endpoint, store)
-    val rootString = s"${endpoint.value}/${store.value}/cromwell-execution/"
-    val execDirString = s"${endpoint.value}/${store.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/"
-    val fileString = s"${endpoint.value}/${store.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
+  it should "correctly remove a prefix from the blob path" in {
+    val builder = makeBlobPathBuilder(endpoint, container)
+    val rootString = s"${endpoint.value}/${container.value}/cromwell-execution/"
+    val execDirString = s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/"
+    val fileString = s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
     val blobRoot: BlobPath = builder build rootString getOrElse fail()
     val execDir: BlobPath = builder build execDirString getOrElse fail()
     val blobFile: BlobPath = builder build fileString getOrElse fail()
@@ -160,10 +194,10 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     blobFile.pathStringWithoutPrefix(blobFile) should equal ("")
   }
 
-  ignore should "not change a path if it doesn't start with a prefix" in {
-    val builder = makeBlobPathBuilder(endpoint, store)
-    val otherRootString = s"${endpoint.value}/${store.value}/foobar/"
-    val fileString = s"${endpoint.value}/${store.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
+  it should "not change a path if it doesn't start with a prefix" in {
+    val builder = makeBlobPathBuilder(endpoint, container)
+    val otherRootString = s"${endpoint.value}/${container.value}/foobar/"
+    val fileString = s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
     val otherBlobRoot: BlobPath = builder build otherRootString getOrElse fail()
     val blobFile: BlobPath = builder build fileString getOrElse fail()
     blobFile.pathStringWithoutPrefix(otherBlobRoot) should equal ("/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout")

From c12aaba2e082f1dadfdb52c6e78a36764a12808a Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 18 Aug 2023 11:21:16 -0400
Subject: [PATCH 209/326] WX-1156 Fix internal_path_prefix (#7208)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .../cromwell/filesystems/blob/BlobPathBuilder.scala   |  8 ++++++++
 .../scala/cromwell/backend/impl/tes/TesJobPaths.scala | 11 ++++++++---
 .../scala/cromwell/backend/impl/tes/TesTask.scala     |  2 +-
 .../scala/cromwell/backend/impl/tes/TesTaskSpec.scala |  2 +-
 4 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index aa6445fa779..35c518c0a43 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -174,5 +174,13 @@ case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, con
     else pathString
   }
 
+  /**
+    * Returns the path relative to the container root.
+    * For example, https://{storageAccountName}.blob.core.windows.net/{containerid}/path/to/my/file
+    * will be returned as path/to/my/file.
+    * @return Path string relative to the container root.
+    */
+  def pathWithoutContainer : String = pathString
+  
   override def getSymlinkSafePath(options: LinkOption*): Path  = toAbsolutePath
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
index f1797d9bc58..a624a16328a 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
@@ -4,6 +4,7 @@ import com.typesafe.config.Config
 import cromwell.backend.io.{JobPaths, WorkflowPaths}
 import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
 import cromwell.core.path._
+import cromwell.filesystems.blob.BlobPath
 
 object TesJobPaths {
   def apply(jobKey: BackendJobDescriptorKey,
@@ -30,12 +31,16 @@ case class TesJobPaths private[tes] (override val workflowPaths: TesWorkflowPath
 
   /*
    * tesTaskRoot: This is the root directory that TES will use for files related to this task.
-   * We provide it to TES as a k/v pair where the key is "internal_path_prefix" (specified in TesWorkflowOptionKeys.scala)
-   * and the value is a blob path.
+   * TES expects a path relative to the root of the storage container.
+   * We provide it to TES as a k/v pair where the key is "internal_path_prefix" and the value is the relative path string.
    * This is not a standard TES feature, but rather related to the Azure TES implementation that Terra uses.
    * While passing it outside of terra won't do any harm, we could consider making this optional and/or configurable.
    */
-  val tesTaskRoot : Path = callExecutionRoot.resolve("tes_task")
+  private val taskFullPath = callRoot./("tes_task")
+  val tesTaskRoot : String = taskFullPath match {
+    case blob: BlobPath => blob.pathWithoutContainer
+    case anyOtherPath: Path => anyOtherPath.pathAsString
+  }
 
   // Given an output path, return a path localized to the storage file system
   def storageOutput(path: String): String = {
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index 66f0f508d77..a345e87ebf7 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -242,7 +242,7 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
   val resources: Resources = TesTask.makeResources(
     runtimeAttributes,
     preferedWorkflowExecutionIdentity,
-    Option(tesPaths.tesTaskRoot.pathAsString)
+    Option(tesPaths.tesTaskRoot)
   )
 }
 
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index 5bfa916086d..25a8f55f682 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -101,7 +101,7 @@ class TesTaskSpec
       TestConfig.emptyConfig)
 
     val expectedKey = "internal_path_prefix"
-    val expectedValue = Option(tesPaths.tesTaskRoot.pathAsString)
+    val expectedValue = Option(tesPaths.tesTaskRoot)
 
     //Assert path correctly ends up in the resources
     val wei = Option("abc123")

From 3affdc3541bfe92633b770b1302b056cd2b46f1a Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Mon, 21 Aug 2023 13:05:09 -0400
Subject: [PATCH 210/326] WX-1256 Temporarily turn off engine hashing for blob
 files (#7209)

Co-authored-by: Adam Nichols <aednichols@gmail.com>
---
 engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
index b6ce3ee7cc2..69e5551b8a9 100644
--- a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
+++ b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
@@ -159,7 +159,9 @@ class NioFlow(parallelism: Int,
 
     val fileContentIo = command.file match {
       case _: DrsPath  => readFileAndChecksum
-      case _: BlobPath => readFileAndChecksum
+      // Temporarily disable since our hashing algorithm doesn't match the stored hash
+      // https://broadworkbench.atlassian.net/browse/WX-1257
+      case _: BlobPath => readFile//readFileAndChecksum
       case _ => readFile
     }
     fileContentIo.map(_.replaceAll("\\r\\n", "\\\n"))

From bdc1ab3b6becb4b496e44ea7faa1d69db64a43aa Mon Sep 17 00:00:00 2001
From: Christian Freitas <cfreitas@broadinstitute.org>
Date: Tue, 22 Aug 2023 10:07:15 -0400
Subject: [PATCH 211/326] WX-1173 Reopen filesystem for blob storage outside
 workspace (#7178)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Tom Wiseman <twiseman@broadinstitute.org>
Co-authored-by: Adam Nichols <aednichols@gmail.com>
---
 .../blob/nio/AzureDirectoryStream.java        |  14 +-
 .../storage/blob/nio/AzureFileSystem.java     | 100 ++++++----
 .../com/azure/storage/blob/nio/AzurePath.java |   2 +-
 build.sbt                                     |   5 +-
 .../blob/BlobFileSystemConfig.scala           |  17 +-
 .../blob/BlobFileSystemManager.scala          | 166 ++++++++--------
 .../filesystems/blob/BlobPathBuilder.scala    |  34 ++--
 .../blob/BlobPathBuilderFactory.scala         |  21 +-
 .../WorkspaceManagerApiClientProvider.scala   |  46 ++++-
 .../org.mockito.plugins.MockMaker             |   1 +
 .../blob/AzureFileSystemSpec.scala            |  25 +++
 .../blob/BlobFileSystemConfigSpec.scala       |  25 +--
 .../blob/BlobPathBuilderFactorySpec.scala     | 185 +++++++++++-------
 .../blob/BlobPathBuilderSpec.scala            |  61 ++----
 14 files changed, 399 insertions(+), 303 deletions(-)
 create mode 100644 filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
 create mode 100644 filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala

diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureDirectoryStream.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureDirectoryStream.java
index 917f712ddfc..817121e958e 100644
--- a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureDirectoryStream.java
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureDirectoryStream.java
@@ -3,12 +3,6 @@
 
 package com.azure.storage.blob.nio;
 
-import com.azure.core.util.logging.ClientLogger;
-import com.azure.storage.blob.BlobContainerClient;
-import com.azure.storage.blob.models.BlobItem;
-import com.azure.storage.blob.models.BlobListDetails;
-import com.azure.storage.blob.models.ListBlobsOptions;
-
 import java.io.IOException;
 import java.nio.file.DirectoryIteratorException;
 import java.nio.file.DirectoryStream;
@@ -18,6 +12,12 @@
 import java.util.NoSuchElementException;
 import java.util.Set;
 
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.BlobContainerClient;
+import com.azure.storage.blob.models.BlobItem;
+import com.azure.storage.blob.models.BlobListDetails;
+import com.azure.storage.blob.models.ListBlobsOptions;
+
 /**
  * A type for iterating over the contents of a directory.
  *
@@ -88,7 +88,7 @@ private static class AzureDirectoryIterator implements Iterator<Path> {
             if (path.isRoot()) {
                 String containerName = path.toString().substring(0, path.toString().length() - 1);
                 AzureFileSystem afs = ((AzureFileSystem) path.getFileSystem());
-                containerClient = ((AzureFileStore) afs.getFileStore(containerName)).getContainerClient();
+                containerClient = ((AzureFileStore) afs.getFileStore()).getContainerClient();
             } else {
                 AzureResource azureResource = new AzureResource(path);
                 listOptions.setPrefix(azureResource.getBlobClient().getBlobName() + AzureFileSystem.PATH_SEPARATOR);
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
index 6f981b1b45e..381ed0289d7 100644
--- a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
@@ -3,19 +3,6 @@
 
 package com.azure.storage.blob.nio;
 
-import com.azure.core.credential.AzureSasCredential;
-import com.azure.core.http.HttpClient;
-import com.azure.core.http.policy.HttpLogDetailLevel;
-import com.azure.core.http.policy.HttpPipelinePolicy;
-import com.azure.core.util.CoreUtils;
-import com.azure.core.util.logging.ClientLogger;
-import com.azure.storage.blob.BlobServiceClient;
-import com.azure.storage.blob.BlobServiceClientBuilder;
-import com.azure.storage.blob.implementation.util.BlobUserAgentModificationPolicy;
-import com.azure.storage.common.StorageSharedKeyCredential;
-import com.azure.storage.common.policy.RequestRetryOptions;
-import com.azure.storage.common.policy.RetryPolicyType;
-
 import java.io.IOException;
 import java.nio.file.FileStore;
 import java.nio.file.FileSystem;
@@ -27,14 +14,31 @@
 import java.nio.file.attribute.FileAttributeView;
 import java.nio.file.attribute.UserPrincipalLookupService;
 import java.nio.file.spi.FileSystemProvider;
+import java.time.Duration;
+import java.time.Instant;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
 import java.util.Objects;
+import java.util.Optional;
 import java.util.Set;
 import java.util.regex.PatternSyntaxException;
-import java.util.stream.Collectors;
+
+import com.azure.core.credential.AzureSasCredential;
+import com.azure.core.http.HttpClient;
+import com.azure.core.http.policy.HttpLogDetailLevel;
+import com.azure.core.http.policy.HttpPipelinePolicy;
+import com.azure.core.util.CoreUtils;
+import com.azure.core.util.logging.ClientLogger;
+import com.azure.storage.blob.BlobServiceClient;
+import com.azure.storage.blob.BlobServiceClientBuilder;
+import com.azure.storage.blob.implementation.util.BlobUserAgentModificationPolicy;
+import com.azure.storage.common.StorageSharedKeyCredential;
+import com.azure.storage.common.policy.RequestRetryOptions;
+import com.azure.storage.common.policy.RetryPolicyType;
 
 /**
  * Implement's Java's {@link FileSystem} interface for Azure Blob Storage.
@@ -67,6 +71,11 @@ public final class AzureFileSystem extends FileSystem {
      */
     public static final String AZURE_STORAGE_SAS_TOKEN_CREDENTIAL = "AzureStorageSasTokenCredential";
 
+    /**
+     * Expected type: String
+     */
+    public static final String AZURE_STORAGE_PUBLIC_ACCESS_CREDENTIAL = "AzureStoragePublicAccessCredential";
+
     /**
      * Expected type: com.azure.core.http.policy.HttpLogLevelDetail
      */
@@ -159,9 +168,9 @@ public final class AzureFileSystem extends FileSystem {
     private final Long putBlobThreshold;
     private final Integer maxConcurrencyPerRequest;
     private final Integer downloadResumeRetries;
-    private final Map<String, FileStore> fileStores;
     private FileStore defaultFileStore;
     private boolean closed;
+    private Instant expiry;
 
     AzureFileSystem(AzureFileSystemProvider parentFileSystemProvider, String endpoint, Map<String, ?> config)
             throws IOException {
@@ -181,7 +190,7 @@ public final class AzureFileSystem extends FileSystem {
             this.downloadResumeRetries = (Integer) config.get(AZURE_STORAGE_DOWNLOAD_RESUME_RETRIES);
 
             // Initialize and ensure access to FileStores.
-            this.fileStores = this.initializeFileStores(config);
+            this.defaultFileStore = this.initializeFileStore(config);
         } catch (RuntimeException e) {
             throw LoggingUtility.logError(LOGGER, new IllegalArgumentException("There was an error parsing the "
                 + "configurations map. Please ensure all fields are set to a legal value of the correct type.", e));
@@ -221,7 +230,7 @@ public FileSystemProvider provider() {
     @Override
     public void close() throws IOException {
         this.closed = true;
-        this.parentFileSystemProvider.closeFileSystem(this.getFileSystemUrl());
+        this.parentFileSystemProvider.closeFileSystem(this.getFileSystemUrl() + "/" + defaultFileStore.name());
     }
 
     /**
@@ -282,9 +291,7 @@ public Iterable<Path> getRootDirectories() {
         If the file system was set to use all containers in the account, the account will be re-queried and the
         list may grow or shrink if containers were added or deleted.
          */
-        return fileStores.keySet().stream()
-            .map(name -> this.getPath(name + AzurePath.ROOT_DIR_SUFFIX))
-            .collect(Collectors.toList());
+        return Arrays.asList(this.getPath(defaultFileStore.name() + AzurePath.ROOT_DIR_SUFFIX));
     }
 
     /**
@@ -304,7 +311,7 @@ public Iterable<FileStore> getFileStores() {
         If the file system was set to use all containers in the account, the account will be re-queried and the
         list may grow or shrink if containers were added or deleted.
          */
-        return this.fileStores.values();
+        return Arrays.asList(defaultFileStore);
     }
 
     /**
@@ -397,6 +404,12 @@ private BlobServiceClient buildBlobServiceClient(String endpoint, Map<String, ?>
             builder.credential((StorageSharedKeyCredential) config.get(AZURE_STORAGE_SHARED_KEY_CREDENTIAL));
         } else if (config.containsKey(AZURE_STORAGE_SAS_TOKEN_CREDENTIAL)) {
             builder.credential((AzureSasCredential) config.get(AZURE_STORAGE_SAS_TOKEN_CREDENTIAL));
+            this.setExpiryFromSAS((AzureSasCredential) config.get(AZURE_STORAGE_SAS_TOKEN_CREDENTIAL));
+        } else if (config.containsKey(AZURE_STORAGE_PUBLIC_ACCESS_CREDENTIAL)) {
+            // The Blob Service Client Builder requires at least one kind of authentication to make requests
+            // For public files however, this is unnecessary. This key-value pair is to denote the case
+            // explicitly when we supply a placeholder SAS credential to bypass this requirement.
+            builder.credential((AzureSasCredential) config.get(AZURE_STORAGE_PUBLIC_ACCESS_CREDENTIAL));
         } else {
             throw LoggingUtility.logError(LOGGER, new IllegalArgumentException(String.format("No credentials were "
                     + "provided. Please specify one of the following when constructing an AzureFileSystem: %s, %s.",
@@ -430,23 +443,17 @@ private BlobServiceClient buildBlobServiceClient(String endpoint, Map<String, ?>
         return builder.buildClient();
     }
 
-    private Map<String, FileStore> initializeFileStores(Map<String, ?> config) throws IOException {
-        String fileStoreNames = (String) config.get(AZURE_STORAGE_FILE_STORES);
-        if (CoreUtils.isNullOrEmpty(fileStoreNames)) {
+    private FileStore initializeFileStore(Map<String, ?> config) throws IOException {
+        String fileStoreName = (String) config.get(AZURE_STORAGE_FILE_STORES);
+        if (CoreUtils.isNullOrEmpty(fileStoreName)) {
             throw LoggingUtility.logError(LOGGER, new IllegalArgumentException("The list of FileStores cannot be "
                 + "null."));
         }
 
         Boolean skipConnectionCheck = (Boolean) config.get(AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK);
         Map<String, FileStore> fileStores = new HashMap<>();
-        for (String fileStoreName : fileStoreNames.split(",")) {
-            FileStore fs = new AzureFileStore(this, fileStoreName, skipConnectionCheck);
-            if (this.defaultFileStore == null) {
-                this.defaultFileStore = fs;
-            }
-            fileStores.put(fileStoreName, fs);
-        }
-        return fileStores;
+        this.defaultFileStore = new AzureFileStore(this, fileStoreName, skipConnectionCheck);
+        return this.defaultFileStore;
     }
 
     @Override
@@ -470,12 +477,11 @@ Path getDefaultDirectory() {
         return this.getPath(this.defaultFileStore.name() + AzurePath.ROOT_DIR_SUFFIX);
     }
 
-    FileStore getFileStore(String name) throws IOException {
-        FileStore store = this.fileStores.get(name);
-        if (store == null) {
-            throw LoggingUtility.logError(LOGGER, new IOException("Invalid file store: " + name));
+    FileStore getFileStore() throws IOException {
+        if (this.defaultFileStore == null) {
+            throw LoggingUtility.logError(LOGGER, new IOException("FileStore not initialized"));
         }
-        return store;
+        return defaultFileStore;
     }
 
     Long getBlockSize() {
@@ -489,4 +495,24 @@ Long getPutBlobThreshold() {
     Integer getMaxConcurrencyPerRequest() {
         return this.maxConcurrencyPerRequest;
     }
+
+    public Optional<Instant> getExpiry() {
+        return Optional.ofNullable(expiry);
+    }
+
+    private void setExpiryFromSAS(AzureSasCredential token) {
+        List<String> strings = Arrays.asList(token.getSignature().split("&"));
+        Optional<String> expiryString = strings.stream()
+            .filter(s -> s.startsWith("se"))
+            .findFirst()
+            .map(s -> s.replaceFirst("se=",""))
+            .map(s -> s.replace("%3A", ":"));
+        this.expiry = expiryString.map(es -> Instant.parse(es)).orElse(null);
+    }
+
+    public boolean isExpired(Duration buffer) {
+        return Optional.ofNullable(this.expiry)
+            .map(e -> Instant.now().plus(buffer).isAfter(e))
+            .orElse(true);
+    }
 }
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzurePath.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzurePath.java
index 9742af1f696..917895ba39e 100644
--- a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzurePath.java
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzurePath.java
@@ -735,7 +735,7 @@ public BlobClient toBlobClient() throws IOException {
         String fileStoreName = this.rootToFileStore(root.toString());
 
         BlobContainerClient containerClient =
-            ((AzureFileStore) this.parentFileSystem.getFileStore(fileStoreName)).getContainerClient();
+            ((AzureFileStore) this.parentFileSystem.getFileStore()).getContainerClient();
 
         String blobName = this.withoutRoot();
         if (blobName.isEmpty()) {
diff --git a/build.sbt b/build.sbt
index 814e966b364..2c9a8068992 100644
--- a/build.sbt
+++ b/build.sbt
@@ -103,10 +103,11 @@ lazy val azureBlobNio = (project in file("azure-blob-nio"))
 lazy val azureBlobFileSystem = (project in file("filesystems/blob"))
   .withLibrarySettings("cromwell-azure-blobFileSystem", blobFileSystemDependencies)
   .dependsOn(core)
-  .dependsOn(core % "test->test")
-  .dependsOn(common % "test->test")
   .dependsOn(cloudSupport)
   .dependsOn(azureBlobNio)
+  .dependsOn(core % "test->test")
+  .dependsOn(common % "test->test")
+  .dependsOn(azureBlobNio % "test->test")
 
 lazy val awsS3FileSystem = (project in file("filesystems/s3"))
   .withLibrarySettings("cromwell-aws-s3filesystem", s3FileSystemDependencies)
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
index f68bf7f5176..c5467c78ffe 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
@@ -11,13 +11,9 @@ import java.util.UUID
 // WSM config is needed for accessing WSM-managed blob containers created in Terra workspaces.
 // If the identity executing Cromwell has native access to the blob container, this can be ignored.
 final case class WorkspaceManagerConfig(url: WorkspaceManagerURL,
-                                        workspaceId: WorkspaceId,
-                                        containerResourceId: ContainerResourceId,
                                         overrideWsmAuthToken: Option[String]) // dev-only
 
-final case class BlobFileSystemConfig(endpointURL: EndpointURL,
-                                      blobContainerName: BlobContainerName,
-                                      subscriptionId: Option[SubscriptionId],
+final case class BlobFileSystemConfig(subscriptionId: Option[SubscriptionId],
                                       expiryBufferMinutes: Long,
                                       workspaceManagerConfig: Option[WorkspaceManagerConfig])
 
@@ -26,8 +22,6 @@ object BlobFileSystemConfig {
   final val defaultExpiryBufferMinutes = 10L
 
   def apply(config: Config): BlobFileSystemConfig = {
-    val endpointURL = parseString(config, "endpoint").map(EndpointURL)
-    val blobContainer = parseString(config, "container").map(BlobContainerName)
     val subscriptionId = parseUUIDOpt(config, "subscription").map(_.map(SubscriptionId))
     val expiryBufferMinutes =
       parseLongOpt(config, "expiry-buffer-minutes")
@@ -37,17 +31,15 @@ object BlobFileSystemConfig {
       if (config.hasPath("workspace-manager")) {
         val wsmConf = config.getConfig("workspace-manager")
         val wsmURL = parseString(wsmConf, "url").map(WorkspaceManagerURL)
-        val workspaceId = parseUUID(wsmConf, "workspace-id").map(WorkspaceId)
-        val containerResourceId = parseUUID(wsmConf, "container-resource-id").map(ContainerResourceId)
         val overrideWsmAuthToken = parseStringOpt(wsmConf, "b2cToken")
 
-        (wsmURL, workspaceId, containerResourceId, overrideWsmAuthToken)
+        (wsmURL, overrideWsmAuthToken)
           .mapN(WorkspaceManagerConfig)
           .map(Option(_))
       }
       else None.validNel
 
-    (endpointURL, blobContainer, subscriptionId, expiryBufferMinutes, wsmConfig)
+    (subscriptionId, expiryBufferMinutes, wsmConfig)
       .mapN(BlobFileSystemConfig.apply)
       .unsafe("Couldn't parse blob filesystem config")
   }
@@ -58,9 +50,6 @@ object BlobFileSystemConfig {
   private def parseStringOpt(config: Config, path: String) =
     validate[Option[String]] { config.as[Option[String]](path) }
 
-  private def parseUUID(config: Config, path: String) =
-    validate[UUID] { UUID.fromString(config.as[String](path)) }
-
   private def parseUUIDOpt(config: Config, path: String) =
     validate[Option[UUID]] { config.as[Option[String]](path).map(UUID.fromString) }
 
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index ac8f01d2cc7..6b6088c7689 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -1,5 +1,6 @@
 package cromwell.filesystems.blob
 
+import bio.terra.workspace.client.ApiException
 import com.azure.core.credential.AzureSasCredential
 import com.azure.storage.blob.nio.{AzureFileSystem, AzureFileSystemProvider}
 import com.azure.storage.blob.sas.{BlobContainerSasPermission, BlobServiceSasSignatureValues}
@@ -9,18 +10,19 @@ import common.validation.Validation._
 import cromwell.cloudsupport.azure.{AzureCredentials, AzureUtils}
 
 import java.net.URI
+import java.nio.file._
 import java.nio.file.spi.FileSystemProvider
-import java.nio.file.{FileSystem, FileSystemNotFoundException}
 import java.time.temporal.ChronoUnit
 import java.time.{Duration, Instant, OffsetDateTime}
+import java.util.UUID
 import scala.jdk.CollectionConverters._
 import scala.util.{Failure, Success, Try}
 
 // We encapsulate this functionality here so that we can easily mock it out, to allow for testing without
 // actually connecting to Blob storage.
-case class FileSystemAPI(private val provider: FileSystemProvider = new AzureFileSystemProvider()) {
-  def getFileSystem(uri: URI): Try[FileSystem] = Try(provider.getFileSystem(uri))
-  def newFileSystem(uri: URI, config: Map[String, Object]): FileSystem = provider.newFileSystem(uri, config.asJava)
+case class AzureFileSystemAPI(private val provider: FileSystemProvider = new AzureFileSystemProvider()) {
+  def getFileSystem(uri: URI): Try[AzureFileSystem] = Try(provider.getFileSystem(uri).asInstanceOf[AzureFileSystem])
+  def newFileSystem(uri: URI, config: Map[String, Object]): Try[AzureFileSystem] = Try(provider.newFileSystem(uri, config.asJava).asInstanceOf[AzureFileSystem])
   def closeFileSystem(uri: URI): Option[Unit] = getFileSystem(uri).toOption.map(_.close)
 }
 /**
@@ -36,25 +38,25 @@ object BlobFileSystemManager {
   } yield instant
 
   def buildConfigMap(credential: AzureSasCredential, container: BlobContainerName): Map[String, Object] = {
-    Map((AzureFileSystem.AZURE_STORAGE_SAS_TOKEN_CREDENTIAL, credential),
-      (AzureFileSystem.AZURE_STORAGE_FILE_STORES, container.value),
-      (AzureFileSystem.AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK, java.lang.Boolean.TRUE))
+    // Special handling is done here to provide a special key value pair if the placeholder token is provided
+    // This is due to the BlobClient requiring an auth token even for public blob paths.
+    val sasTuple = if (credential == PLACEHOLDER_TOKEN) (AzureFileSystem.AZURE_STORAGE_PUBLIC_ACCESS_CREDENTIAL, PLACEHOLDER_TOKEN)
+    else (AzureFileSystem.AZURE_STORAGE_SAS_TOKEN_CREDENTIAL, credential)
+
+    Map(sasTuple, (AzureFileSystem.AZURE_STORAGE_FILE_STORES, container.value),
+        (AzureFileSystem.AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK, java.lang.Boolean.TRUE))
   }
-  def hasTokenExpired(tokenExpiry: Instant, buffer: Duration): Boolean = Instant.now.plus(buffer).isAfter(tokenExpiry)
-  def uri(endpoint: EndpointURL) = new URI("azb://?endpoint=" + endpoint)
+  def combinedEnpointContainerUri(endpoint: EndpointURL, container: BlobContainerName) = new URI("azb://?endpoint=" + endpoint + "/" + container.value)
+
+  val PLACEHOLDER_TOKEN = new AzureSasCredential("this-is-a-public-sas")
 }
 
-class BlobFileSystemManager(val container: BlobContainerName,
-                            val endpoint: EndpointURL,
-                            val expiryBufferMinutes: Long,
+class BlobFileSystemManager(val expiryBufferMinutes: Long,
                             val blobTokenGenerator: BlobSasTokenGenerator,
-                            val fileSystemAPI: FileSystemAPI = FileSystemAPI(),
-                            private val initialExpiration: Option[Instant] = None) extends LazyLogging {
+                            val fileSystemAPI: AzureFileSystemAPI = AzureFileSystemAPI()) extends LazyLogging {
 
   def this(config: BlobFileSystemConfig) = {
     this(
-      config.blobContainerName,
-      config.endpointURL,
       config.expiryBufferMinutes,
       BlobSasTokenGenerator.createBlobTokenGeneratorFromConfig(config)
     )
@@ -63,39 +65,46 @@ class BlobFileSystemManager(val container: BlobContainerName,
   def this(rawConfig: Config) = this(BlobFileSystemConfig(rawConfig))
 
   val buffer: Duration = Duration.of(expiryBufferMinutes, ChronoUnit.MINUTES)
-  private var expiry: Option[Instant] = initialExpiration
 
-  def getExpiry: Option[Instant] = expiry
-  def uri: URI = BlobFileSystemManager.uri(endpoint)
-  def isTokenExpired: Boolean = expiry.exists(BlobFileSystemManager.hasTokenExpired(_, buffer))
-  def shouldReopenFilesystem: Boolean = isTokenExpired || expiry.isEmpty
-  def retrieveFilesystem(): Try[FileSystem] = {
+  def retrieveFilesystem(endpoint: EndpointURL, container: BlobContainerName): Try[FileSystem] = {
+    val uri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
     synchronized {
-      shouldReopenFilesystem match {
-        case false => fileSystemAPI.getFileSystem(uri).recoverWith {
-          // If no filesystem already exists, this will create a new connection, with the provided configs
-          case _: FileSystemNotFoundException =>
-            logger.info(s"Creating new blob filesystem for URI $uri")
-            blobTokenGenerator.generateBlobSasToken.flatMap(generateFilesystem(uri, container, _))
+      fileSystemAPI.getFileSystem(uri).filter(!_.isExpired(buffer)).recoverWith {
+        // If no filesystem already exists, this will create a new connection, with the provided configs
+        case _: FileSystemNotFoundException => {
+          logger.info(s"Creating new blob filesystem for URI $uri")
+          generateFilesystem(uri, container, endpoint)
         }
-        // If the token has expired, OR there is no token record, try to close the FS and regenerate
-        case true =>
+        case _ : NoSuchElementException => {
+          // When the filesystem expires, the above filter results in a
+          // NoSuchElementException. If expired, close the filesystem
+          // and reopen the filesystem with the fresh token
           logger.info(s"Closing & regenerating token for existing blob filesystem at URI $uri")
           fileSystemAPI.closeFileSystem(uri)
-          blobTokenGenerator.generateBlobSasToken.flatMap(generateFilesystem(uri, container, _))
+          generateFilesystem(uri, container, endpoint)
+        }
       }
     }
   }
 
-  private def generateFilesystem(uri: URI, container: BlobContainerName, token: AzureSasCredential): Try[FileSystem] = {
-    expiry = BlobFileSystemManager.parseTokenExpiry(token)
-    if (expiry.isEmpty) return Failure(new Exception("Could not reopen filesystem, no expiration found"))
-    Try(fileSystemAPI.newFileSystem(uri, BlobFileSystemManager.buildConfigMap(token, container)))
+  /**
+    * Create a new filesystem pointing to a particular container and storage account,
+    * generating a SAS token from WSM as needed
+    *
+    * @param uri a URI formatted to include the scheme, storage account endpoint and container
+    * @param container the container to open as a filesystem
+    * @param endpoint the endpoint containing the storage account for the container to open
+    * @return a try with either the successfully created filesystem, or a failure containing the exception
+    */
+  private def generateFilesystem(uri: URI, container: BlobContainerName, endpoint: EndpointURL): Try[AzureFileSystem] = {
+    blobTokenGenerator.generateBlobSasToken(endpoint, container)
+      .flatMap((token: AzureSasCredential) => {
+        fileSystemAPI.newFileSystem(uri, BlobFileSystemManager.buildConfigMap(token, container))
+      })
   }
-
 }
 
-sealed trait BlobSasTokenGenerator { def generateBlobSasToken: Try[AzureSasCredential] }
+sealed trait BlobSasTokenGenerator { def generateBlobSasToken(endpoint: EndpointURL, container: BlobContainerName): Try[AzureSasCredential] }
 object BlobSasTokenGenerator {
 
   /**
@@ -122,35 +131,23 @@ object BlobSasTokenGenerator {
 
       // WSM-mediated mediated SAS token generator
       // parameterizing client instead of URL to make injecting mock client possible
-      BlobSasTokenGenerator.createBlobTokenGenerator(
-        config.blobContainerName,
-        config.endpointURL,
-        wsmConfig.workspaceId,
-        wsmConfig.containerResourceId,
-        wsmClient,
-        wsmConfig.overrideWsmAuthToken
-      )
+      BlobSasTokenGenerator.createBlobTokenGenerator(wsmClient, wsmConfig.overrideWsmAuthToken)
     }.getOrElse(
       // Native SAS token generator
-      BlobSasTokenGenerator.createBlobTokenGenerator(config.blobContainerName, config.endpointURL, config.subscriptionId)
+      BlobSasTokenGenerator.createBlobTokenGenerator(config.subscriptionId)
     )
 
   /**
     * Native SAS token generator, uses the DefaultAzureCredentialBuilder in the local environment
     * to produce a SAS token.
     *
-    * @param container The BlobContainerName of the blob container to be accessed by the generated SAS token
-    * @param endpoint The EndpointURL containing the storage account of the blob container to be accessed by
-    * this SAS token
     * @param subscription Optional subscription parameter to use for local authorization.
     * If one is not provided the default subscription is used
     * @return A NativeBlobTokenGenerator, able to produce a valid SAS token for accessing the provided blob
     * container and endpoint locally
     */
-  def createBlobTokenGenerator(container: BlobContainerName,
-                               endpoint: EndpointURL,
-                               subscription: Option[SubscriptionId]): BlobSasTokenGenerator = {
-    NativeBlobSasTokenGenerator(container, endpoint, subscription)
+  def createBlobTokenGenerator(subscription: Option[SubscriptionId]): BlobSasTokenGenerator = {
+    NativeBlobSasTokenGenerator(subscription)
   }
 
   /**
@@ -158,11 +155,6 @@ object BlobSasTokenGenerator {
     * to request a SAS token from the WSM to access the given blob container. If an overrideWsmAuthToken
     * is provided this is used instead.
     *
-    * @param container The BlobContainerName of the blob container to be accessed by the generated SAS token
-    * @param endpoint The EndpointURL containing the storage account of the blob container to be accessed by
-    * this SAS token
-    * @param workspaceId The WorkspaceId of the account to authenticate against
-    * @param containerResourceId The ContainterResourceId of the blob container as WSM knows it
     * @param workspaceManagerClient The client for making requests against WSM
     * @param overrideWsmAuthToken An optional WsmAuthToken used for authenticating against the WSM for a valid
     * SAS token to access the given container and endpoint. This is a dev only option that is only intended
@@ -170,54 +162,56 @@ object BlobSasTokenGenerator {
     * @return A WSMBlobTokenGenerator, able to produce a valid SAS token for accessing the provided blob
     * container and endpoint that is managed by WSM
     */
-  def createBlobTokenGenerator(container: BlobContainerName,
-                               endpoint: EndpointURL,
-                               workspaceId: WorkspaceId,
-                               containerResourceId: ContainerResourceId,
-                               workspaceManagerClient: WorkspaceManagerApiClientProvider,
+  def createBlobTokenGenerator(workspaceManagerClient: WorkspaceManagerApiClientProvider,
                                overrideWsmAuthToken: Option[String]): BlobSasTokenGenerator = {
-    WSMBlobSasTokenGenerator(container, endpoint, workspaceId, containerResourceId, workspaceManagerClient, overrideWsmAuthToken)
+    WSMBlobSasTokenGenerator(workspaceManagerClient, overrideWsmAuthToken)
   }
 
 }
 
-case class WSMBlobSasTokenGenerator(container: BlobContainerName,
-                                    endpoint: EndpointURL,
-                                    workspaceId: WorkspaceId,
-                                    containerResourceId: ContainerResourceId,
-                                    wsmClientProvider: WorkspaceManagerApiClientProvider,
+case class WSMBlobSasTokenGenerator(wsmClientProvider: WorkspaceManagerApiClientProvider,
                                     overrideWsmAuthToken: Option[String]) extends BlobSasTokenGenerator {
 
   /**
     * Generate a BlobSasToken by using the available authorization information
     * If an overrideWsmAuthToken is provided, use this in the wsmClient request
     * Else try to use the environment azure identity to request the SAS token
+    * @param endpoint The EndpointURL of the blob container to be accessed by the generated SAS token
+    * @param container The BlobContainerName of the blob container to be accessed by the generated SAS token
     *
     * @return an AzureSasCredential for accessing a blob container
     */
-  def generateBlobSasToken: Try[AzureSasCredential] = {
+  def generateBlobSasToken(endpoint: EndpointURL, container: BlobContainerName): Try[AzureSasCredential] = {
     val wsmAuthToken: Try[String] = overrideWsmAuthToken match {
       case Some(t) => Success(t)
       case None => AzureCredentials.getAccessToken(None).toTry
     }
+    container.workspaceId match {
+      // If this is a Terra workspace, request a token from WSM
+      case Success(workspaceId) => {
+        (for {
+          wsmAuth <- wsmAuthToken
+          wsmAzureResourceClient = wsmClientProvider.getControlledAzureResourceApi(wsmAuth)
+          resourceId <- getContainerResourceId(workspaceId, container, wsmAuth)
+          sasToken <- wsmAzureResourceClient.createAzureStorageContainerSasToken(workspaceId, resourceId)
+        } yield sasToken).recoverWith {
+          // If the storage account was still not found in WSM, this may be a public filesystem
+          case exception: ApiException if exception.getCode == 404 => Try(BlobFileSystemManager.PLACEHOLDER_TOKEN)
+        }
+      }
+      // Otherwise assume that the container is public and use a placeholder
+      // SAS token to bypass the BlobClient authentication requirement
+      case Failure(_) => Try(BlobFileSystemManager.PLACEHOLDER_TOKEN)
+    }
+  }
 
-    for {
-      wsmAuth <- wsmAuthToken
-      wsmClient = wsmClientProvider.getControlledAzureResourceApi(wsmAuth)
-      sasToken <- Try(  // Java library throws
-        wsmClient.createAzureStorageContainerSasToken(
-          workspaceId.value,
-          containerResourceId.value,
-          null,
-          null,
-          null,
-          null
-        ).getToken)
-    } yield new AzureSasCredential(sasToken)
+ def getContainerResourceId(workspaceId: UUID, container: BlobContainerName, wsmAuth : String): Try[UUID] = {
+    val wsmResourceClient = wsmClientProvider.getResourceApi(wsmAuth)
+    wsmResourceClient.findContainerResourceId(workspaceId, container)
   }
 }
 
-case class NativeBlobSasTokenGenerator(container: BlobContainerName, endpoint: EndpointURL, subscription: Option[SubscriptionId] = None) extends BlobSasTokenGenerator {
+case class NativeBlobSasTokenGenerator(subscription: Option[SubscriptionId] = None) extends BlobSasTokenGenerator {
   private val bcsp = new BlobContainerSasPermission()
     .setReadPermission(true)
     .setCreatePermission(true)
@@ -227,10 +221,12 @@ case class NativeBlobSasTokenGenerator(container: BlobContainerName, endpoint: E
   /**
     * Generate a BlobSasToken by using the local environment azure identity
     * This will use a default subscription if one is not provided.
+    * @param endpoint The EndpointURL of the blob container to be accessed by the generated SAS token
+    * @param container The BlobContainerName of the blob container to be accessed by the generated SAS token
     *
     * @return an AzureSasCredential for accessing a blob container
     */
-  def generateBlobSasToken: Try[AzureSasCredential] = for {
+  def generateBlobSasToken(endpoint: EndpointURL, container: BlobContainerName): Try[AzureSasCredential] = for {
     bcc <- AzureUtils.buildContainerClientFromLocalEnvironment(container.toString, endpoint.toString, subscription.map(_.toString))
     bsssv = new BlobServiceSasSignatureValues(OffsetDateTime.now.plusDays(1), bcsp)
     asc = new AzureSasCredential(bcc.generateSas(bsssv))
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 35c518c0a43..3aa26eb3c11 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -12,12 +12,13 @@ import scala.language.postfixOps
 import scala.util.{Failure, Success, Try}
 
 object BlobPathBuilder {
-
+  private val blobHostnameSuffix = ".blob.core.windows.net"
   sealed trait BlobPathValidation
-  case class ValidBlobPath(path: String) extends BlobPathValidation
+  case class ValidBlobPath(path: String, container: BlobContainerName, endpoint: EndpointURL) extends BlobPathValidation
   case class UnparsableBlobPath(errorMessage: Throwable) extends BlobPathValidation
 
-  def invalidBlobPathMessage(container: BlobContainerName, endpoint: EndpointURL) = s"Malformed Blob URL for this builder. Expecting a URL for a container $container and endpoint $endpoint"
+  def invalidBlobHostMessage(endpoint: EndpointURL) = s"Malformed Blob URL for this builder: The endpoint $endpoint doesn't contain the expected host string '{SA}.blob.core.windows.net/'"
+  def invalidBlobContainerMessage(endpoint: EndpointURL) = s"Malformed Blob URL for this builder: Could not parse container"
   def parseURI(string: String): Try[URI] = Try(URI.create(UrlEscapers.urlFragmentEscaper().escape(string)))
   def parseStorageAccount(uri: URI): Try[StorageAccountName] = uri.getHost.split("\\.").find(_.nonEmpty).map(StorageAccountName(_))
       .map(Success(_)).getOrElse(Failure(new Exception("Could not parse storage account")))
@@ -40,28 +41,31 @@ object BlobPathBuilder {
     *
     * If the configured container and storage account do not match, the string is considered unparsable
     */
-  def validateBlobPath(string: String, container: BlobContainerName, endpoint: EndpointURL): BlobPathValidation = {
+ def validateBlobPath(string: String): BlobPathValidation = {
     val blobValidation = for {
       testUri <- parseURI(string)
-      endpointUri <- parseURI(endpoint.value)
+      testEndpoint = EndpointURL(testUri.getScheme + "://" + testUri.getHost())
       testStorageAccount <- parseStorageAccount(testUri)
-      endpointStorageAccount <- parseStorageAccount(endpointUri)
-      hasContainer = testUri.getPath.split("/").find(_.nonEmpty).contains(container.value)
-      hasEndpoint = testStorageAccount.equals(endpointStorageAccount)
-      blobPathValidation = (hasContainer && hasEndpoint) match {
-        case true => ValidBlobPath(testUri.getPath.replaceFirst("/" + container, ""))
-        case false => UnparsableBlobPath(new MalformedURLException(invalidBlobPathMessage(container, endpoint)))
+      testContainer = testUri.getPath.split("/").find(_.nonEmpty)
+      isBlobHost = testUri.getHost().contains(blobHostnameSuffix) && testUri.getScheme().contains("https")
+      blobPathValidation = (isBlobHost, testContainer) match {
+        case (true, Some(container)) => ValidBlobPath(
+            testUri.getPath.replaceFirst("/" + container, ""),
+            BlobContainerName(container),
+            testEndpoint)
+        case (false, _) => UnparsableBlobPath(new MalformedURLException(invalidBlobHostMessage(testEndpoint)))
+        case (true, None) => UnparsableBlobPath(new MalformedURLException(invalidBlobContainerMessage(testEndpoint)))
       }
     } yield blobPathValidation
     blobValidation recover { case t => UnparsableBlobPath(t) } get
   }
 }
 
-class BlobPathBuilder(container: BlobContainerName, endpoint: EndpointURL)(private val fsm: BlobFileSystemManager) extends PathBuilder {
+class BlobPathBuilder()(private val fsm: BlobFileSystemManager) extends PathBuilder {
 
   def build(string: String): Try[BlobPath] = {
-    validateBlobPath(string, container, endpoint) match {
-      case ValidBlobPath(path) => Try(BlobPath(path, endpoint, container)(fsm))
+    validateBlobPath(string) match {
+      case ValidBlobPath(path, container, endpoint) => Try(BlobPath(path, endpoint, container)(fsm))
       case UnparsableBlobPath(errorMessage: Throwable) => Failure(errorMessage)
     }
   }
@@ -121,7 +125,7 @@ case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, con
   override def pathWithoutScheme: String = parseURI(endpoint.value).map(u => List(u.getHost, container, pathString.stripPrefix("/")).mkString("/")).get
 
   private def findNioPath(path: String): NioPath = (for {
-    fileSystem <- fsm.retrieveFilesystem()
+    fileSystem <- fsm.retrieveFilesystem(endpoint, container)
     // The Azure NIO library uses `{container}:` to represent the root of the path
     nioPath = fileSystem.getPath(s"${container.value}:", path)
   // This is purposefully an unprotected get because the NIO API needing an unwrapped path object.
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index c263841dc8a..47245552dc2 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -8,11 +8,26 @@ import cromwell.core.path.PathBuilderFactory.PriorityBlob
 
 import java.util.UUID
 import scala.concurrent.{ExecutionContext, Future}
+import scala.util.Try
 
 final case class SubscriptionId(value: UUID) {override def toString: String = value.toString}
-final case class BlobContainerName(value: String) {override def toString: String = value}
+final case class BlobContainerName(value: String) {
+  override def toString: String = value
+  lazy val workspaceId: Try[UUID] = {
+    Try(UUID.fromString(value.replaceFirst("sc-","")))
+  }
+}
 final case class StorageAccountName(value: String) {override def toString: String = value}
-final case class EndpointURL(value: String) {override def toString: String = value}
+final case class EndpointURL(value: String) {
+  override def toString: String = value
+  lazy val storageAccountName : Try[StorageAccountName] = {
+    val sa = for {
+      host <- value.split("//").findLast(_.nonEmpty)
+      storageAccountName <- host.split("\\.").find(_.nonEmpty)
+    } yield StorageAccountName(storageAccountName)
+    sa.toRight(new Exception(s"Storage account name could not be parsed from $value")).toTry
+  }
+}
 final case class WorkspaceId(value: UUID) {override def toString: String = value.toString}
 final case class ContainerResourceId(value: UUID) {override def toString: String = value.toString}
 final case class WorkspaceManagerURL(value: String) {override def toString: String = value}
@@ -21,7 +36,7 @@ final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Co
 
   override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[BlobPathBuilder] = {
     Future {
-      new BlobPathBuilder(fsm.container, fsm.endpoint)(fsm)
+      new BlobPathBuilder()(fsm)
     }
   }
 
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
index a9f52d92a91..276738c98b6 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
@@ -1,7 +1,13 @@
 package cromwell.filesystems.blob
 
-import bio.terra.workspace.api.ControlledAzureResourceApi
+import bio.terra.workspace.api._
 import bio.terra.workspace.client.ApiClient
+import bio.terra.workspace.model.{ResourceType, StewardshipType}
+import com.azure.core.credential.AzureSasCredential
+
+import java.util.UUID
+import scala.jdk.CollectionConverters._
+import scala.util.Try
 
 /**
   * Represents a way to get a client for interacting with workspace manager controlled resources.
@@ -12,7 +18,8 @@ import bio.terra.workspace.client.ApiClient
   * For testing, create an anonymous subclass as in `org.broadinstitute.dsde.rawls.dataaccess.workspacemanager.HttpWorkspaceManagerDAOSpec`
   */
 trait WorkspaceManagerApiClientProvider {
-  def getControlledAzureResourceApi(token: String): ControlledAzureResourceApi
+  def getControlledAzureResourceApi(token: String): WsmControlledAzureResourceApi
+  def getResourceApi(token: String): WsmResourceApi
 }
 
 class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManagerURL) extends WorkspaceManagerApiClientProvider {
@@ -22,9 +29,40 @@ class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManag
     client
   }
 
-  def getControlledAzureResourceApi(token: String): ControlledAzureResourceApi = {
+  def getResourceApi(token: String): WsmResourceApi = {
+    val apiClient = getApiClient
+    apiClient.setAccessToken(token)
+    WsmResourceApi(new ResourceApi(apiClient))
+  }
+
+  def getControlledAzureResourceApi(token: String): WsmControlledAzureResourceApi = {
     val apiClient = getApiClient
     apiClient.setAccessToken(token)
-    new ControlledAzureResourceApi(apiClient)
+    WsmControlledAzureResourceApi(new ControlledAzureResourceApi(apiClient))
+  }
+}
+
+case class WsmResourceApi(resourcesApi : ResourceApi) {
+  def findContainerResourceId(workspaceId : UUID, container: BlobContainerName): Try[UUID] = {
+    for {
+      workspaceResources <- Try(resourcesApi.enumerateResources(workspaceId, 0, 10, ResourceType.AZURE_STORAGE_CONTAINER, StewardshipType.CONTROLLED).getResources())
+      workspaceStorageContainerOption = workspaceResources.asScala.find(r => r.getMetadata().getName() == container.value)
+      workspaceStorageContainer <- workspaceStorageContainerOption.toRight(new Exception("No storage container found for this workspace")).toTry
+      resourceId = workspaceStorageContainer.getMetadata().getResourceId()
+    } yield resourceId
+  }
+}
+case class WsmControlledAzureResourceApi(controlledAzureResourceApi : ControlledAzureResourceApi) {
+  def createAzureStorageContainerSasToken(workspaceId: UUID, resourceId: UUID): Try[AzureSasCredential] = {
+    for {
+      sas <- Try(controlledAzureResourceApi.createAzureStorageContainerSasToken(
+        workspaceId,
+        resourceId,
+        null,
+        null,
+        null,
+        null
+      ).getToken)
+    } yield new AzureSasCredential(sas)
   }
 }
diff --git a/filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker b/filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
new file mode 100644
index 00000000000..1f0955d450f
--- /dev/null
+++ b/filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
@@ -0,0 +1 @@
+mock-maker-inline
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala
new file mode 100644
index 00000000000..e0463bab740
--- /dev/null
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala
@@ -0,0 +1,25 @@
+package cromwell.filesystems.blob
+
+import com.azure.storage.blob.nio.{AzureFileSystem, AzureFileSystemProvider}
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import java.time.Instant
+import scala.compat.java8.OptionConverters._
+import scala.jdk.CollectionConverters._
+
+class AzureFileSystemSpec extends AnyFlatSpec with Matchers {
+  val now = Instant.now()
+  val container = BlobContainerName("testConainer")
+  val exampleSas = BlobPathBuilderFactorySpec.buildExampleSasToken(now)
+  val exampleConfig = BlobFileSystemManager.buildConfigMap(exampleSas, container)
+  val exampleStorageEndpoint = BlobPathBuilderSpec.buildEndpoint("testStorageAccount")
+  val exampleCombinedEndpoint = BlobFileSystemManager.combinedEnpointContainerUri(exampleStorageEndpoint, container)
+
+  it should "parse an expiration from a sas token" in {
+    val provider = new AzureFileSystemProvider()
+    val filesystem : AzureFileSystem = provider.newFileSystem(exampleCombinedEndpoint, exampleConfig.asJava).asInstanceOf[AzureFileSystem]
+    filesystem.getExpiry.asScala shouldBe Some(now)
+    filesystem.getFileStores.asScala.map(_.name()).exists(_ == container.value) shouldBe true
+  }
+}
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
index 607ad5606f7..68804113763 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
@@ -5,14 +5,8 @@ import common.exception.AggregatedMessageException
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-import java.util.UUID
-
 class BlobFileSystemConfigSpec extends AnyFlatSpec with Matchers {
 
-  private val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-  private val container = BlobContainerName("storageContainer")
-  private val workspaceId = WorkspaceId(UUID.fromString("B0BAFE77-0000-0000-0000-000000000000"))
-  private val containerResourceId = ContainerResourceId(UUID.fromString("F00B4911-0000-0000-0000-000000000000"))
   private val workspaceManagerURL = WorkspaceManagerURL("https://wsm.example.com")
   private val b2cToken = "b0gus-t0ken"
 
@@ -20,12 +14,8 @@ class BlobFileSystemConfigSpec extends AnyFlatSpec with Matchers {
     val config = BlobFileSystemConfig(
       ConfigFactory.parseString(
       s"""
-         |container = "$container"
-         |endpoint = "$endpoint"
       """.stripMargin)
     )
-    config.blobContainerName should equal(container)
-    config.endpointURL should equal(endpoint)
     config.expiryBufferMinutes should equal(BlobFileSystemConfig.defaultExpiryBufferMinutes)
   }
 
@@ -33,25 +23,17 @@ class BlobFileSystemConfigSpec extends AnyFlatSpec with Matchers {
     val config = BlobFileSystemConfig(
       ConfigFactory.parseString(
         s"""
-           |container = "$container"
-           |endpoint = "$endpoint"
            |expiry-buffer-minutes = "20"
            |workspace-manager {
            |  url = "$workspaceManagerURL"
-           |  workspace-id = "$workspaceId"
-           |  container-resource-id = "$containerResourceId"
            |  b2cToken = "$b2cToken"
            |}
            |
         """.stripMargin)
     )
-    config.blobContainerName should equal(container)
-    config.endpointURL should equal(endpoint)
     config.expiryBufferMinutes should equal(20L)
     config.workspaceManagerConfig.isDefined shouldBe true
     config.workspaceManagerConfig.get.url shouldBe workspaceManagerURL
-    config.workspaceManagerConfig.get.workspaceId shouldBe workspaceId
-    config.workspaceManagerConfig.get.containerResourceId shouldBe containerResourceId
     config.workspaceManagerConfig.get.overrideWsmAuthToken.contains(b2cToken) shouldBe true
   }
 
@@ -59,17 +41,14 @@ class BlobFileSystemConfigSpec extends AnyFlatSpec with Matchers {
     val rawConfig =
       ConfigFactory.parseString(
         s"""
-         |container = "$container"
-         |endpoint = "$endpoint"
          |expiry-buffer-minutes = "10"
          |workspace-manager {
-         |  url = "$workspaceManagerURL"
-         |  container-resource-id = "$containerResourceId"
+         |  b2cToken = "$b2cToken"
          |}
          |
         """.stripMargin)
 
     val error = intercept[AggregatedMessageException](BlobFileSystemConfig(rawConfig))
-    error.getMessage should include("No configuration setting found for key 'workspace-id'")
+    error.getMessage should include("No configuration setting found for key 'url'")
   }
 }
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
index 881cd3669a1..c4ee102c58b 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
@@ -1,16 +1,18 @@
 package cromwell.filesystems.blob
 
 import com.azure.core.credential.AzureSasCredential
+import com.azure.storage.blob.nio.AzureFileSystem
 import common.mock.MockSugar
 import org.mockito.Mockito._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-import java.nio.file.{FileSystem, FileSystemNotFoundException}
+import java.nio.file.FileSystemNotFoundException
 import java.time.format.DateTimeFormatter
 import java.time.temporal.ChronoUnit
 import java.time.{Duration, Instant, ZoneId}
-import scala.util.{Failure, Try}
+import java.util.UUID
+import scala.util.{Failure, Success, Try}
 
 
 object BlobPathBuilderFactorySpec {
@@ -37,23 +39,12 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     expiry should contain(expiryTime)
   }
 
-  it should "verify an unexpired token will be processed as unexpired" in {
-    val expiryTime = generateTokenExpiration(11L)
-    val expired = BlobFileSystemManager.hasTokenExpired(expiryTime, Duration.ofMinutes(10L))
-    expired shouldBe false
-  }
-
-  it should "test an expired token will be processed as expired" in {
-    val expiryTime = generateTokenExpiration(9L)
-    val expired = BlobFileSystemManager.hasTokenExpired(expiryTime, Duration.ofMinutes(10L))
-    expired shouldBe true
-  }
-
   it should "test that a filesystem gets closed correctly" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val azureUri = BlobFileSystemManager.uri(endpoint)
-    val fileSystems = mock[FileSystemAPI]
-    val fileSystem = mock[FileSystem]
+    val container = BlobContainerName("test")
+    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
+    val fileSystems = mock[AzureFileSystemAPI]
+    val fileSystem = mock[AzureFileSystem]
     when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(fileSystem))
     when(fileSystems.closeFileSystem(azureUri)).thenCallRealMethod()
 
@@ -61,106 +52,156 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     verify(fileSystem, times(1)).close()
   }
 
-  it should "test retrieveFileSystem with expired filesystem" in {
+  it should "test retrieveFileSystem with expired Terra filesystem" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val expiredToken = generateTokenExpiration(9L)
+    //val expiredToken = generateTokenExpiration(9L)
     val refreshedToken = generateTokenExpiration(69L)
     val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
-    val container = BlobContainerName("storageContainer")
+    val container = BlobContainerName("sc-" + UUID.randomUUID().toString())
     val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
-    val azureUri = BlobFileSystemManager.uri(endpoint)
-
-    val fileSystems = mock[FileSystemAPI]
+    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
+
+    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    val azureFileSystem = mock[AzureFileSystem]
+    when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(true)
+    val fileSystems = mock[AzureFileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Success(azureFileSystem))
     val blobTokenGenerator = mock[BlobSasTokenGenerator]
-    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+    when(blobTokenGenerator.generateBlobSasToken(endpoint, container)).thenReturn(Try(sasToken))
 
-    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(expiredToken))
-    fsm.getExpiry should contain(expiredToken)
-    fsm.isTokenExpired shouldBe true
-    fsm.retrieveFilesystem()
+    val fsm = new BlobFileSystemManager(10L, blobTokenGenerator, fileSystems)
+    fsm.retrieveFilesystem(endpoint, container)
 
-    fsm.getExpiry should contain(refreshedToken)
-    fsm.isTokenExpired shouldBe false
-    verify(fileSystems, never()).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).getFileSystem(azureUri)
     verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
     verify(fileSystems, times(1)).closeFileSystem(azureUri)
   }
 
-  it should "test retrieveFileSystem with an unexpired fileSystem" in {
+  it should "test retrieveFileSystem with an unexpired Terra fileSystem" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val initialToken = generateTokenExpiration(11L)
+    //val initialToken = generateTokenExpiration(11L)
     val refreshedToken = generateTokenExpiration(71L)
     val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
-    val container = BlobContainerName("storageContainer")
+    val container = BlobContainerName("sc-" + UUID.randomUUID().toString())
     val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
-    val azureUri = BlobFileSystemManager.uri(endpoint)
-    // Need a fake filesystem to supply the getFileSystem simulated try
-    val dummyFileSystem = mock[FileSystem]
+    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint,container)
 
-    val fileSystems = mock[FileSystemAPI]
-    when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(dummyFileSystem))
+    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    val azureFileSystem = mock[AzureFileSystem]
+    when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(false)
+    val fileSystems = mock[AzureFileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(azureFileSystem))
 
     val blobTokenGenerator = mock[BlobSasTokenGenerator]
-    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+    when(blobTokenGenerator.generateBlobSasToken(endpoint, container)).thenReturn(Try(sasToken))
 
-    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(initialToken))
-    fsm.getExpiry should contain(initialToken)
-    fsm.isTokenExpired shouldBe false
-    fsm.retrieveFilesystem()
+    val fsm = new BlobFileSystemManager(10L, blobTokenGenerator, fileSystems)
+    fsm.retrieveFilesystem(endpoint, container)
 
-    fsm.getExpiry should contain(initialToken)
-    fsm.isTokenExpired shouldBe false
     verify(fileSystems, times(1)).getFileSystem(azureUri)
     verify(fileSystems, never()).newFileSystem(azureUri, configMap)
     verify(fileSystems, never()).closeFileSystem(azureUri)
   }
 
-  it should "test retrieveFileSystem with an uninitialized filesystem" in {
+  it should "test retrieveFileSystem with an uninitialized Terra filesystem" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
     val refreshedToken = generateTokenExpiration(71L)
     val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
-    val container = BlobContainerName("storageContainer")
+    val container = BlobContainerName("sc-" + UUID.randomUUID().toString())
     val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
-    val azureUri = BlobFileSystemManager.uri(endpoint)
+    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
 
-    val fileSystems = mock[FileSystemAPI]
+    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    val azureFileSystem = mock[AzureFileSystem]
+    when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(false)
+    val fileSystems = mock[AzureFileSystemAPI]
     when(fileSystems.getFileSystem(azureUri)).thenReturn(Failure(new FileSystemNotFoundException))
+    when(fileSystems.newFileSystem(azureUri, configMap)).thenReturn(Try(azureFileSystem))
     val blobTokenGenerator = mock[BlobSasTokenGenerator]
-    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+    when(blobTokenGenerator.generateBlobSasToken(endpoint, container)).thenReturn(Try(sasToken))
 
-    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems, Some(refreshedToken))
-    fsm.getExpiry.isDefined shouldBe true
-    fsm.isTokenExpired shouldBe false
-    fsm.retrieveFilesystem()
+    val fsm = new BlobFileSystemManager(0L, blobTokenGenerator, fileSystems)
+    fsm.retrieveFilesystem(endpoint, container)
 
-    fsm.getExpiry should contain(refreshedToken)
-    fsm.isTokenExpired shouldBe false
     verify(fileSystems, times(1)).getFileSystem(azureUri)
     verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
     verify(fileSystems, never()).closeFileSystem(azureUri)
   }
 
-  it should "test retrieveFileSystem with an unknown filesystem" in {
+  it should "test retrieveFileSystem with expired non-Terra filesystem" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val refreshedToken = generateTokenExpiration(71L)
-    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
-    val container = BlobContainerName("storageContainer")
+    val sasToken = BlobFileSystemManager.PLACEHOLDER_TOKEN
+    val container = BlobContainerName("sc-" + UUID.randomUUID().toString())
     val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
-    val azureUri = BlobFileSystemManager.uri(endpoint)
-
-    val fileSystems = mock[FileSystemAPI]
+    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
+
+    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    val azureFileSystem = mock[AzureFileSystem]
+    when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(true)
+    val fileSystems = mock[AzureFileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Success(azureFileSystem))
     val blobTokenGenerator = mock[BlobSasTokenGenerator]
-    when(blobTokenGenerator.generateBlobSasToken).thenReturn(Try(sasToken))
+    when(blobTokenGenerator.generateBlobSasToken(endpoint, container)).thenReturn(Try(sasToken))
 
-    val fsm = new BlobFileSystemManager(container, endpoint, 10L, blobTokenGenerator, fileSystems)
-    fsm.getExpiry.isDefined shouldBe false
-    fsm.isTokenExpired shouldBe false
-    fsm.retrieveFilesystem()
+    val fsm = new BlobFileSystemManager(10L, blobTokenGenerator, fileSystems)
+    fsm.retrieveFilesystem(endpoint, container)
 
-    fsm.getExpiry should contain(refreshedToken)
-    fsm.isTokenExpired shouldBe false
-    verify(fileSystems, never()).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).getFileSystem(azureUri)
     verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
     verify(fileSystems, times(1)).closeFileSystem(azureUri)
   }
+
+  it should "test retrieveFileSystem with an unexpired non-Terra fileSystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val sasToken = BlobFileSystemManager.PLACEHOLDER_TOKEN
+    val container = BlobContainerName("sc-" + UUID.randomUUID().toString())
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint,container)
+
+    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    val azureFileSystem = mock[AzureFileSystem]
+    when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(false)
+    val fileSystems = mock[AzureFileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Try(azureFileSystem))
+
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken(endpoint, container)).thenReturn(Try(sasToken))
+
+    val fsm = new BlobFileSystemManager(10L, blobTokenGenerator, fileSystems)
+    fsm.retrieveFilesystem(endpoint, container)
+
+    verify(fileSystems, times(1)).getFileSystem(azureUri)
+    verify(fileSystems, never()).newFileSystem(azureUri, configMap)
+    verify(fileSystems, never()).closeFileSystem(azureUri)
+  }
+
+  it should "test retrieveFileSystem with an uninitialized non-Terra filesystem" in {
+    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
+    val sasToken = BlobFileSystemManager.PLACEHOLDER_TOKEN
+    val container = BlobContainerName("sc-" + UUID.randomUUID().toString())
+    val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
+    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
+
+    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    val azureFileSystem = mock[AzureFileSystem]
+    when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(false)
+    val fileSystems = mock[AzureFileSystemAPI]
+    when(fileSystems.getFileSystem(azureUri)).thenReturn(Failure(new FileSystemNotFoundException))
+    when(fileSystems.newFileSystem(azureUri, configMap)).thenReturn(Try(azureFileSystem))
+    val blobTokenGenerator = mock[BlobSasTokenGenerator]
+    when(blobTokenGenerator.generateBlobSasToken(endpoint, container)).thenReturn(Try(sasToken))
+
+    val fsm = new BlobFileSystemManager(0L, blobTokenGenerator, fileSystems)
+    fsm.retrieveFilesystem(endpoint, container)
+
+    verify(fileSystems, times(1)).getFileSystem(azureUri)
+    verify(fileSystems, times(1)).newFileSystem(azureUri, configMap)
+    verify(fileSystems, never()).closeFileSystem(azureUri)
+  }
 }
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index eef6db8e942..a8ca7d58d6f 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -18,41 +18,23 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
     val testString = endpoint.value + "/" + container + evalPath
-    BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
-      case BlobPathBuilder.ValidBlobPath(path) => path should equal(evalPath)
+    BlobPathBuilder.validateBlobPath(testString) match {
+      case BlobPathBuilder.ValidBlobPath(path, parsedContainer, parsedEndpoint) => {
+        path should equal(evalPath)
+        parsedContainer should equal(container)
+        parsedEndpoint should equal(endpoint)
+      }
       case BlobPathBuilder.UnparsableBlobPath(errorMessage) => fail(errorMessage)
     }
   }
 
-  it should "bad storage account fails causes URI to fail parse into a path" in {
-    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = BlobContainerName("container")
-    val evalPath = "/path/to/file"
-    val testString = BlobPathBuilderSpec.buildEndpoint("badStorageAccount").value + container.value + evalPath
-    BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
-      case BlobPathBuilder.ValidBlobPath(path) => fail(s"Valid path: $path found when verifying mismatched storage account")
-      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
-    }
-  }
-
-  it should "bad container fails causes URI to fail parse into a path" in {
-    val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    val container = BlobContainerName("container")
-    val evalPath = "/path/to/file"
-    val testString = endpoint.value + "badContainer" + evalPath
-    BlobPathBuilder.validateBlobPath(testString, container, endpoint) match {
-      case BlobPathBuilder.ValidBlobPath(path) => fail(s"Valid path: $path found when verifying mismatched container")
-      case BlobPathBuilder.UnparsableBlobPath(errorMessage) => errorMessage.getMessage should equal(BlobPathBuilder.invalidBlobPathMessage(container, endpoint))
-    }
-  }
-
   it should "provide a readable error when getting an illegal nioPath" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
     val container = BlobContainerName("container")
     val evalPath = "/path/to/file"
     val exception = new Exception("Failed to do the thing")
     val fsm = mock[BlobFileSystemManager]
-    when(fsm.retrieveFilesystem()).thenReturn(Failure(exception))
+    when(fsm.retrieveFilesystem(endpoint, container)).thenReturn(Failure(exception))
     val path = BlobPath(evalPath, endpoint, container)(fsm)
     val testException = Try(path.nioPath).failed.toOption
     testException should contain(exception)
@@ -95,15 +77,14 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   private val endpoint: EndpointURL = BlobPathBuilderSpec.buildEndpoint("centaurtesting")
   private val container: BlobContainerName = BlobContainerName("test-blob")
 
-  def makeBlobPathBuilder(blobEndpoint: EndpointURL,
-                          container: BlobContainerName): BlobPathBuilder = {
-    val blobTokenGenerator = NativeBlobSasTokenGenerator(container, blobEndpoint, Some(subscriptionId))
-    val fsm = new BlobFileSystemManager(container, blobEndpoint, 10, blobTokenGenerator)
-    new BlobPathBuilder(container, blobEndpoint)(fsm)
+  def makeBlobPathBuilder(): BlobPathBuilder = {
+    val blobTokenGenerator = NativeBlobSasTokenGenerator(Some(subscriptionId))
+    val fsm = new BlobFileSystemManager(10, blobTokenGenerator)
+    new BlobPathBuilder()(fsm)
   }
 
   it should "read md5 from small files <5g" in {
-    val builder = makeBlobPathBuilder(endpoint, container)
+    val builder = makeBlobPathBuilder()
     val evalPath = "/testRead.txt"
     val testString = endpoint.value + "/" + container + evalPath
     val blobPath1: BlobPath = (builder build testString).get
@@ -111,7 +92,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   it should "read md5 from large files >5g" in {
-    val builder = makeBlobPathBuilder(endpoint, container)
+    val builder = makeBlobPathBuilder()
     val evalPath = "/Rocky-9.2-aarch64-dvd.iso"
     val testString = endpoint.value + "/" + container + evalPath
     val blobPath1: BlobPath = (builder build testString).get
@@ -119,7 +100,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   it should "choose the root/metadata md5 over the native md5 for files that have both" in {
-    val builder = makeBlobPathBuilder(endpoint, container)
+    val builder = makeBlobPathBuilder()
     val evalPath = "/redundant_md5_test.txt"
     val testString = endpoint.value + "/" + container + evalPath
     val blobPath1: BlobPath = (builder build testString).get
@@ -127,7 +108,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   it should "gracefully return `None` when neither hash is found" in {
-    val builder = makeBlobPathBuilder(endpoint, container)
+    val builder = makeBlobPathBuilder()
     val evalPath = "/no_md5_test.txt"
     val testString = endpoint.value + "/" + container + evalPath
     val blobPath1: BlobPath = (builder build testString).get
@@ -135,7 +116,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   it should "resolve an absolute path string correctly to a path" in {
-    val builder = makeBlobPathBuilder(endpoint, container)
+    val builder = makeBlobPathBuilder()
     val rootString = s"${endpoint.value}/${container.value}/cromwell-execution"
     val blobRoot: BlobPath = builder build rootString getOrElse fail()
     blobRoot.toAbsolutePath.pathAsString should equal ("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution")
@@ -144,7 +125,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   it should "build a blob path from a test string and read a file" in {
-    val builder = makeBlobPathBuilder(endpoint, container)
+    val builder = makeBlobPathBuilder()
     val endpointHost = BlobPathBuilder.parseURI(endpoint.value).map(_.getHost).getOrElse(fail("Could not parse URI"))
     val evalPath = "/test/inputFile.txt"
     val testString = endpoint.value + "/" + container + evalPath
@@ -160,7 +141,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   it should "build duplicate blob paths in the same filesystem" in {
-    val builder = makeBlobPathBuilder(endpoint, container)
+    val builder = makeBlobPathBuilder()
     val evalPath = "/test/inputFile.txt"
     val testString = endpoint.value + "/" + container + evalPath
     val blobPath1: BlobPath = builder build testString getOrElse fail()
@@ -173,7 +154,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   it should "resolve a path without duplicating container name" in {
-    val builder = makeBlobPathBuilder(endpoint, container)
+    val builder = makeBlobPathBuilder()
     val rootString = s"${endpoint.value}/${container.value}/cromwell-execution"
     val blobRoot: BlobPath = builder build rootString getOrElse fail()
     blobRoot.toAbsolutePath.pathAsString should equal ("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution")
@@ -182,7 +163,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   it should "correctly remove a prefix from the blob path" in {
-    val builder = makeBlobPathBuilder(endpoint, container)
+    val builder = makeBlobPathBuilder()
     val rootString = s"${endpoint.value}/${container.value}/cromwell-execution/"
     val execDirString = s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/"
     val fileString = s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
@@ -195,7 +176,7 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
   }
 
   it should "not change a path if it doesn't start with a prefix" in {
-    val builder = makeBlobPathBuilder(endpoint, container)
+    val builder = makeBlobPathBuilder()
     val otherRootString = s"${endpoint.value}/${container.value}/foobar/"
     val fileString = s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
     val otherBlobRoot: BlobPath = builder build otherRootString getOrElse fail()

From f64b3b97b53cc976ef7e46ebea042da0362a2ef8 Mon Sep 17 00:00:00 2001
From: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Date: Tue, 22 Aug 2023 13:19:48 -0400
Subject: [PATCH 212/326] WX-1174 Adjust NIO Copy functionality (#7207)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 .../storage/blob/nio/AzureFileSystem.java     | 11 ++++++++
 .../blob/nio/AzureFileSystemProvider.java     | 27 ++++++++++++++-----
 ...Repo template_ Cromwell server TES.run.xml |  3 ++-
 3 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
index 381ed0289d7..862352b06ee 100644
--- a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
@@ -170,6 +170,8 @@ public final class AzureFileSystem extends FileSystem {
     private final Integer downloadResumeRetries;
     private FileStore defaultFileStore;
     private boolean closed;
+
+    private AzureSasCredential currentActiveSasCredential;
     private Instant expiry;
 
     AzureFileSystem(AzureFileSystemProvider parentFileSystemProvider, String endpoint, Map<String, ?> config)
@@ -188,6 +190,7 @@ public final class AzureFileSystem extends FileSystem {
             this.putBlobThreshold = (Long) config.get(AZURE_STORAGE_PUT_BLOB_THRESHOLD);
             this.maxConcurrencyPerRequest = (Integer) config.get(AZURE_STORAGE_MAX_CONCURRENCY_PER_REQUEST);
             this.downloadResumeRetries = (Integer) config.get(AZURE_STORAGE_DOWNLOAD_RESUME_RETRIES);
+            this.currentActiveSasCredential = (AzureSasCredential) config.get(AZURE_STORAGE_SAS_TOKEN_CREDENTIAL);
 
             // Initialize and ensure access to FileStores.
             this.defaultFileStore = this.initializeFileStore(config);
@@ -496,6 +499,13 @@ Integer getMaxConcurrencyPerRequest() {
         return this.maxConcurrencyPerRequest;
     }
 
+    public String createSASAppendedURL(String url) throws IllegalStateException {
+        if (Objects.isNull(currentActiveSasCredential)) {
+            throw new IllegalStateException("No current active SAS credential present");
+        }
+        return url + "?" + currentActiveSasCredential.getSignature();
+    }
+
     public Optional<Instant> getExpiry() {
         return Optional.ofNullable(expiry);
     }
@@ -514,5 +524,6 @@ public boolean isExpired(Duration buffer) {
         return Optional.ofNullable(this.expiry)
             .map(e -> Instant.now().plus(buffer).isAfter(e))
             .orElse(true);
+
     }
 }
diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystemProvider.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystemProvider.java
index 6881341d218..2066acf89d5 100644
--- a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystemProvider.java
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystemProvider.java
@@ -47,6 +47,7 @@
 import java.util.concurrent.ConcurrentMap;
 import java.util.function.Consumer;
 import java.util.function.Supplier;
+import java.util.stream.Collectors;
 
 import com.azure.core.util.CoreUtils;
 import com.azure.core.util.logging.ClientLogger;
@@ -695,16 +696,23 @@ public void copy(Path source, Path destination, CopyOption... copyOptions) throw
         // Remove accepted options as we find them. Anything left we don't support.
         boolean replaceExisting = false;
         List<CopyOption> optionsList = new ArrayList<>(Arrays.asList(copyOptions));
-        if (!optionsList.contains(StandardCopyOption.COPY_ATTRIBUTES)) {
-            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new UnsupportedOperationException(
-                "StandardCopyOption.COPY_ATTRIBUTES must be specified as the service will always copy "
-                    + "file attributes."));
+//        NOTE: We're going to assume COPY_ATTRIBUTES as a default copy option (but can still be provided and handled safely)
+//        REPLACE_EXISTING must still be provided if you want to replace existing file
+
+//        if (!optionsList.contains(StandardCopyOption.COPY_ATTRIBUTES)) {
+//            throw LoggingUtility.logError(ClientLoggerHolder.LOGGER, new UnsupportedOperationException(
+//                "StandardCopyOption.COPY_ATTRIBUTES must be specified as the service will always copy "
+//                    + "file attributes."));
+//        }
+        if(optionsList.contains(StandardCopyOption.COPY_ATTRIBUTES)) {
+            optionsList.remove(StandardCopyOption.COPY_ATTRIBUTES);
         }
-        optionsList.remove(StandardCopyOption.COPY_ATTRIBUTES);
+
         if (optionsList.contains(StandardCopyOption.REPLACE_EXISTING)) {
             replaceExisting = true;
             optionsList.remove(StandardCopyOption.REPLACE_EXISTING);
         }
+
         if (!optionsList.isEmpty()) {
             throw LoggingUtility.logError(ClientLoggerHolder.LOGGER,
                 new UnsupportedOperationException("Unsupported copy option found. Only "
@@ -760,9 +768,16 @@ public void copy(Path source, Path destination, CopyOption... copyOptions) throw
         customer scenarios and how many virtual directories they copy, it could be better to check the directory status
         first and then do a copy or createDir, which would always be two requests for all resource types.
          */
+
         try {
+            /*
+            Format the url by appending the SAS token as a param, otherwise the copy request will fail.
+            AzureFileSystem has been updated to handle url transformation via createSASAuthorizedURL()
+            */
+            AzureFileSystem afs = (AzureFileSystem) sourceRes.getPath().getFileSystem();
+            String sasAppendedSourceUrl = afs.createSASAppendedURL(sourceRes.getBlobClient().getBlobUrl());
             SyncPoller<BlobCopyInfo, Void> pollResponse =
-                destinationRes.getBlobClient().beginCopy(sourceRes.getBlobClient().getBlobUrl(), null, null, null,
+                destinationRes.getBlobClient().beginCopy(sasAppendedSourceUrl, null, null, null,
                     null, requestConditions, null);
             pollResponse.waitForCompletion(Duration.ofSeconds(COPY_TIMEOUT_SECONDS));
         } catch (BlobStorageException e) {
diff --git a/runConfigurations/Repo template_ Cromwell server TES.run.xml b/runConfigurations/Repo template_ Cromwell server TES.run.xml
index 9cb1818a004..32127027ecc 100644
--- a/runConfigurations/Repo template_ Cromwell server TES.run.xml	
+++ b/runConfigurations/Repo template_ Cromwell server TES.run.xml	
@@ -1,6 +1,6 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="Repo template: Cromwell server TES" type="Application" factoryName="Application">
-    <option name="ALTERNATIVE_JRE_PATH" value="$USER_HOME$/.sdkman/candidates/java/current" />
+    <option name="ALTERNATIVE_JRE_PATH" value="$PROJECT_DIR$/../.sdkman/candidates/java/current" />
     <envs>
       <env name="CROMWELL_BUILD_CENTAUR_SLICK_PROFILE" value="slick.jdbc.MySQLProfile$" />
       <env name="CROMWELL_BUILD_CENTAUR_JDBC_DRIVER" value="com.mysql.cj.jdbc.Driver" />
@@ -16,6 +16,7 @@
     <option name="VM_PARAMETERS" value="-Dconfig.file=target/ci/resources/tes_application.conf" />
     <method v="2">
       <option name="Make" enabled="true" />
+      <option name="RunConfigurationTask" enabled="true" run_configuration_name="renderCiResources" run_configuration_type="SbtRunConfiguration" />
     </method>
   </configuration>
 </component>
\ No newline at end of file

From aea7343d3b256fcb42741d96dff99d0ce1ac0945 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 24 Aug 2023 14:43:45 -0400
Subject: [PATCH 213/326] [WX-1168] TES Log Paths (#7210)

---
 .../impl/tes/TesJobCachingActorHelper.scala        |  1 +
 .../cromwell/backend/impl/tes/TesJobPaths.scala    | 14 +++++++++++---
 .../backend/impl/tes/TesJobPathsSpec.scala         |  5 +++++
 3 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobCachingActorHelper.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobCachingActorHelper.scala
index d9be8f77b5d..6c4b495d362 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobCachingActorHelper.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobCachingActorHelper.scala
@@ -19,5 +19,6 @@ trait TesJobCachingActorHelper extends StandardCachingActorHelper {
   lazy val tesConfiguration: TesConfiguration = initializationData.tesConfiguration
 
   lazy val runtimeAttributes = TesRuntimeAttributes(validatedRuntimeAttributes, jobDescriptor.runtimeAttributes, tesConfiguration)
+  override protected def nonStandardMetadata: Map[String, Any] = super.nonStandardMetadata ++ tesJobPaths.azureLogPathsForMetadata
 
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
index a624a16328a..ab7b2b27916 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
@@ -30,9 +30,10 @@ case class TesJobPaths private[tes] (override val workflowPaths: TesWorkflowPath
   val callInputsRoot = callRoot.resolve("inputs")
 
   /*
-   * tesTaskRoot: This is the root directory that TES will use for files related to this task.
-   * TES expects a path relative to the root of the storage container.
-   * We provide it to TES as a k/v pair where the key is "internal_path_prefix" and the value is the relative path string.
+   * tesTaskRoot: The Azure TES implementation allows us to specify a working directory that it should use for its own files.
+   * Once the task finishes, this directory will contain stderr.txt, stdout.txt, and some other misc files.
+   * Unlike other paths we provide, this one is expected as a path relative to the root of the storage container.
+   * We provide it as a k/v pair where the key is "internal_path_prefix" and the value is the relative path string.
    * This is not a standard TES feature, but rather related to the Azure TES implementation that Terra uses.
    * While passing it outside of terra won't do any harm, we could consider making this optional and/or configurable.
    */
@@ -42,6 +43,13 @@ case class TesJobPaths private[tes] (override val workflowPaths: TesWorkflowPath
     case anyOtherPath: Path => anyOtherPath.pathAsString
   }
 
+  // Like above: Nothing should rely on these files existing, since only the Azure TES implementation will actually create them.
+  // Used to send the Azure TES log paths to the frontend.
+  val azureLogPathsForMetadata : Map[String, Any] = Map(
+    "tes_stdout" -> taskFullPath./("stdout.txt").pathAsString,
+    "tes_stderr" -> taskFullPath./("stderr.txt").pathAsString
+  )
+
   // Given an output path, return a path localized to the storage file system
   def storageOutput(path: String): String = {
     callExecutionRoot.resolve(path).toString
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesJobPathsSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesJobPathsSpec.scala
index 177331445c9..36bdd2a5015 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesJobPathsSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesJobPathsSpec.scala
@@ -35,6 +35,11 @@ class TesJobPathsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
       File(s"/cromwell-executions/wf_hello/$id/call-hello").pathAsString
     jobPaths.callExecutionDockerRoot.toString shouldBe
       File(s"/cromwell-executions/wf_hello/$id/call-hello/execution").pathAsString
+    jobPaths.azureLogPathsForMetadata shouldBe
+      Map(
+        "tes_stdout" -> File(s"local-cromwell-executions/wf_hello/$id/call-hello/tes_task/stdout.txt").pathAsString,
+        "tes_stderr" -> File(s"local-cromwell-executions/wf_hello/$id/call-hello/tes_task/stderr.txt").pathAsString
+      )
 
     val jobKeySharded = BackendJobDescriptorKey(call, Option(0), 1)
     val jobPathsSharded = TesJobPaths(jobKeySharded, wd, TesTestConfig.backendConfig)

From dfda93c5206162f696027fb2fb88201fe3f9821e Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Thu, 14 Sep 2023 19:55:41 +0200
Subject: [PATCH 214/326] Develop aws (#34)

* efs fixes : support paths with over 127 characters, fix delocalization of efs-based globs

* add deployment manual, fix issue with empty disks

* update documentation

* update documentation

* update documentation
---
 README.md                                     |  10 +-
 .../StandardCacheHitCopyingActor.scala        |   7 +-
 .../impl/aws/AwsBatchRuntimeAttributes.scala  |   7 +-
 .../scala/cromwell/backend/impl/aws/DEPLOY.md | 243 ++++++++++++++++++
 .../scala/cromwell/backend/impl/aws/README.md |  37 ++-
 .../AwsBatchBackendFileHashingActor.scala     |  11 +-
 .../backend/impl/aws/io/AwsBatchVolume.scala  |   4 +-
 7 files changed, 300 insertions(+), 19 deletions(-)
 create mode 100644 supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md

diff --git a/README.md b/README.md
index bbb38795420..d0d78091356 100644
--- a/README.md
+++ b/README.md
@@ -3,9 +3,15 @@
 
 ## Welcome to the "AWS-friendly" Cromwell
 
-More information regarding AWS features can be found [here](https://github.com/henriqueribeiro/cromwell/tree/master/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws)
+The AWS-friendly Cromwell is an optimized fork of the main cromwell release.  We try to keep it up-to-date with new releases, while keeping our additions functional. 
 
-Contact: henrique [at] loka [dot] com 
+* Information regarding AWS features can be found [here](supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md)
+* Information regarding deployment can be found [here](supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md)
+
+Contact: 
+* henrique [at] loka [dot] com 
+* geert [dot] vandeweyer [at] uza [dot] be
+* Join the #AWS channel at the [Cromwell Slack workspace](https://join.slack.com/t/cromwellhq/shared_invite/zt-dxmmrtye-JHxwKE53rfKE_ZWdOHIB4g).
 
 Cromwell is an open-source Workflow Management System for bioinformatics. Licensing is [BSD 3-Clause](LICENSE.txt).
 
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
index e23ecd277af..4b9eecc68a7 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
@@ -230,6 +230,8 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
               logCacheHitCopyCommand(command)
             case Some(command: IoTouchCommand) =>
               logCacheHitTouchCommand(command)
+            case Some(command: IoWriteCommand) =>
+              logCacheHitWriteCommand(command)
             case huh =>
               log.warning(s"BT-322 {} unexpected commandsToWaitFor: {}", jobTag, huh)
           }
@@ -310,7 +312,10 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
     }
 
   private def logCacheHitTouchCommand(command: IoTouchCommand): Unit =
-    log.info(s"BT-322 {} cache hit for file : {}", jobTag, command.toString)
+    log.info(s"BT-322 {} cache touch hit for file : {}", jobTag, command.toString)
+
+  private def logCacheHitWriteCommand(command: IoWriteCommand): Unit =
+    log.info(s"BT-322 {} cache write hit for file : {}", jobTag, command.toString)
                                 
   def succeedAndStop(returnCode: Option[Int], copiedJobOutputs: CallOutputs, detritusMap: DetritusMap): State = {
     import cromwell.services.metadata.MetadataService.implicits.MetadataAutoPutter
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index ceca53a7c85..235927ab07c 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -188,10 +188,11 @@ object AwsBatchRuntimeAttributes {
         rtc.getAnyRef(AwsBatchRuntimeAttributes.DisksKey).asInstanceOf[String] // just to prevent complaints about var/val
     } catch {
         case _: ConfigException.Missing => 
-           ""
+           "local-disk"
     }
-    // combine
-    val disks = s"${efs_disks},${rtc_disks}".split(",").toSet.mkString(",")
+    // combine and remove empty values
+    val disks = s"${efs_disks},${rtc_disks}".split(",").toSet.filterNot(_.isEmpty).mkString(",")
+    Log.debug(s"Disks: ${disks}")
     val runtimeConfig = Some(rtc.withValue(AwsBatchRuntimeAttributes.DisksKey, ConfigValueFactory.fromAnyRef(disks)))
     return runtimeConfig
   }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md
new file mode 100644
index 00000000000..856dd46af99
--- /dev/null
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md
@@ -0,0 +1,243 @@
+AWS/CROMWELL DEPLOYMENT
+=======================
+
+Overview
+--------
+
+AWS Cloudformation is used to deploy Cromwell-AWS.  As resources are created, costs might be generated along the way.  To make sure all generated data is cleaned, remove the stacks again using the CloudFormation Console.
+
+
+Deployment
+----------
+
+Deployment of the cromwell/AWS environment can be performed using the three cloudformation stacks:
+
+1. VPC : setup of the networks
+2. Resources : setup of the compute environment, job queues and storage solutions
+3. Cromwell : setup of an EC2 instance and RDS, hosting the cromwell server and submission tools. 
+
+Along the way, all necessary IAM rols are generated. 
+
+*Note:* This tutorial uses the eu-west-2 (London) region. Change where appropriate for you setup
+
+*Note:* Select "Preserve successfully provisioned resources" as failure option to review problems in depth. 
+
+### STEP 1 : SETUP VPC 
+
+The default VPC settings create both private and public subnets. Private subnets are used for the compute environment and database setup. Public subnets are used to host the cromwell server instance. 
+
+
+Used Template : 
+
+```
+https://cromwell-aws-cloudformation-templates.s3.eu-west-1.amazonaws.com/root-templates/aws-vpc.template.yaml
+```
+
+Steps:
+
+1. Go to the CloudFormation console in your region : https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/
+
+2. Select "Stacks" in the left menu, then "Create Stack" on the top right. Choose "With new resources" :[link](https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/stacks/create)
+
+3. Select "Template is ready", and use "Amazon S3 URL" as template source. Provide the yaml file URL provided above.
+
+4. Enter a stack name. 
+
+5. Select availability zones, more is better. This gives Batch more zones to find suitable instances. 
+
+6. Match "Number of availability zones" to your selection. 
+
+7. Other settings can be left as default. 
+
+8. Review, confirm and submit on final page. 
+
+
+
+### STEP 2 : SETUP COMPUTE RESOURCES
+
+The default setup configures a spot and on-demand queue, a cromwell-specific bucket and the necessary IAM roles to run BATCH jobs. See below for further configuration to extend this setup.
+
+Used Template : 
+
+```
+https://cromwell-aws-cloudformation-templates.s3.eu-west-1.amazonaws.com/root-templates/gwfcore-root.template.yaml
+```
+
+Steps:
+
+1. Go to the CloudFormation console in your region : https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/
+
+2. Select "Stacks" in the left menu, then "Create Stack" on the top right. Choose "With new resources" :[link](https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/stacks/create)
+
+3. Select "Template is ready", and use "Amazon S3 URL" as template source. Provide the yaml file URL provided above.
+
+4. Enter a stack name. 
+    * *Note:* This name is referred to as "GWFCORE NameSpace" in STEP 3
+    * *Note:* The name gets reflected in queue names etc. Keep it short. 
+
+5. Provide an s3 bucket name to host cromwell temp data, results and runtime requirements. 
+    * *Note:* If the bucket exists, it must be located in the same region. 
+    * *Note:* If the bucket exists, specify this in the next field
+
+6. Select the VPC ID generated in STEP 1
+
+7. Provide the PRIVATE subnets (all of them) from STEP 1, for the compute environment. Match the number of subnets to your selection
+
+8. Set the Max vCPU count for default (spot) and High Priority (on-demand) compute environment.
+    * *Note:*  Check your quota per region [here](https://eu-west-2.console.aws.amazon.com/servicequotas/home/services/ec2/quotas), look for "Standard"
+
+9. Set the maximal spot bidding price.
+
+10. Select the list of instance types to be used. Default "optimal" value is a safe bet. 
+    * *Note:*  To edit this, clone the compute environment in the [Batch dashboard](https://eu-west-2.console.aws.amazon.com/batch/home?region=eu-west-2#compute-environments), and play around with the options. 
+
+11. *Optional:* Create an EFS filesystem:
+    * *Note:* EFS is a distributed filesystem. Keeping large intermediate results on EFS can improve perforance by reducing S3/EC2 transfer times
+    * *Note:* By default, EFS performance is limited. Change the setup of the volume using the [console](https://eu-west-2.console.aws.amazon.com/efs/home?region=eu-west-2#/file-systems) to "Enhanced/Elastic" Performance. Consider the costs this implies! 
+    * *Note:* It's recommended to create a new EFS, to make sure that mounting and network settings are correctly setup. 
+
+
+12. *Optional:* Create an FSx filesystem:
+    * *Note:* see documentation in [README](README.md)
+
+13. Other settings can be left as default. 
+
+14. Review, confirm and submit on final page. 
+
+
+### STEP 3 : SETUP CROMWELL SERVER
+
+The default setup deploys a small t3.medium EC2 instance with 25Gb of storage and a RDS aurora-mysql database, to host cromwell, and some interaction tools. Although enough for testing, you'll probably have to scale up the instance for production runs. Alternatively, you can deploy cromwell on local infrastructure, preventing the RDS/EC2 costs.  See below for details.
+
+
+Used Template : 
+
+```
+https://cromwell-aws-cloudformation-templates.s3.eu-west-1.amazonaws.com/root-templates/cromwell-resources.template.yaml
+```
+
+Steps:
+
+1. Go to the CloudFormation console in your region : https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/
+
+2. Select "Stacks" in the left menu, then "Create Stack" on the top right. Choose "With new resources" :[link](https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/stacks/create)
+
+3. Select "Template is ready", and use "Amazon S3 URL" as template source. Provide the yaml file URL provided above.
+
+4. Provide a stack name.
+
+5. Provide a name space.
+    * *Note:* This name is reflected in the key name. Keep it short.
+
+6. Provide the GWFCORE Namespace from STEP 2
+
+7. Specify the VPC ID, from STEP 1
+
+8. Select a PUBLIC subnet for the cromwell server
+
+9. Select 2+ PRIVATE subnets for the RDS database
+
+10. Set the instance root volume size to 25+ Gb
+
+11. Set a password for the cromwell database
+
+12. Provide Filesystem details for EFS if specified in STEP 2:
+    * *Note:* Get the values from [the dashboard](https://eu-west-2.console.aws.amazon.com/efs/home?region=eu-west-2#/file-systems)
+    * *Note:* Accesspoint is listed under filesystem details, tab "Access Points"
+    * *Note:* Security Group is listed under filesystem details, tab "Network"
+
+13. Other settings can be left as default. 
+
+14. Review, confirm and submit on final page. 
+
+
+When the stack is ready, use the following commands to retrieve your SSH key. The exact name of the key can be retrieved from the EC2 instance "Connect" page. 
+
+```
+KEY_NAME=key-<stack_namespace>
+REGION=<region>
+
+# GET KEY ID :
+KEY_ID=$(aws ec2 describe-key-pairs --filters Name=key-name,Values=${KEY_NAME} --query KeyPairs[*].KeyPairId --output text --region ${REGION})
+
+# GET KEY CONTENTS
+mkdir -p ~/.ssh/.keys
+aws ssm get-parameter --region ${REGION} --name /ec2/keypair/${KEY_ID} --with-decryption --query Parameter.Value --output text > ~/.ssh/.keys/${KEY_NAME}.pem
+chmod 600 ~/.ssh/.keys/${KEY_NAME}.pem
+
+```
+
+
+
+Post Install Optimizations
+--------------------------
+
+### EFS 
+
+EFS data is not cleaned up automatically. Consider adding a "cleanup" step in your production WFs, to keep the storage footprint/costs low.
+
+Edit settings [here](https://eu-west-2.console.aws.amazon.com/efs/home?region=eu-west-2#/file-systems). Select the FS and "edit"
+
+* Performance : "Enhanced":"Elastic" Throughput mode is recommended for large workflows. consider extra costs
+* Lifecycle management : Consider moving data to infrequent access, to reduce costs of "forgotten" data. 
+
+### S3 
+
+The cromwell temporary data and results are located in the bucket specified in STEP 2. To reduce your storage footprint/costs, consider setting up lifecycle management. 
+
+* *cromwell-execution/* : Contains analysis results and logs for each executed workflow. 
+* *scripts/* : contains the runtime scripts for each executed task 
+
+To set up a lifecycle:
+
+* go to the [s3 console](https://s3.console.aws.amazon.com/s3/buckets?region=eu-west-2), and select the bucket from STEP 1
+* Select the "Management" tab and "Create Lifecycle rule"
+* analysis results:
+    * Set name : e.g. "Prune cromwell-execution"
+    * Set prefix "cromwell-execution"
+    * Choose actions : "Expire current versions of objects" and "Delete expired object delete markers or incomplete multipart uploads"
+    * Set time limits for  after which objects are deleted (expired).
+    * Enable "delete incomplete multipart upload" checkbox and set time. 
+* scripts:
+    * repeat steps above, with prefix "scripts"
+
+
+### LOCAL CROMWELL INSTANCE
+
+Running cromwell locally has the benefit of not running an EC2 instance 24/7.  However, consider the following points: 
+
+* Run cromwell as a user with a default AWS IAM profile set to the same region, and with sufficient permissions to interact with ECR, Batch and S3. 
+
+* Setup a local database, or setup ingress rules on the RDS security group. 
+
+* Consider load balancing by running multiple instances : see [here](https://cromwell.readthedocs.io/en/stable/Scaling/)
+
+* for EFS, there are specific concerns:
+    * expose EFS to your local network : 
+        * Run a cheap (e.g t4g.nano) instance mounting the EFS share, assign a PEM key to access it
+        * Setup sshfs to mount the EFS share from that instance to your local machine at "/mnt/efs"
+    * REDUCE network traffic by enabling the "check-sibling-md5" and "efsMakeMD5" settings
+
+
+### COMPUTE ENVIRONMENT
+
+* You might play around with the instance types to get more options:
+    * clone the compute environment
+    * double check all network settings ! 
+    * replace the "optimal" type by "*.family" types. There is maximal number of entries, so using whole families allows more types
+
+* Extra Queues : You might consider a dedicated queue for high disk/network jobs, by altering the launch template:
+    * Go to Batch console, select the spot compute environment and open the JSON tab. Look for "launchTemplateName" (eg lt-06fa9fee031254098)
+    * Go to EC2 console, select "Launch Templates" in the menu on the left, and search for your launch template
+    * On details, select "Modify Template (create new version)" in the top right under "Actions"
+    * On the resulting page, add a description (eg "HighNetwork"), and then open advanced settings at the bottom of the page
+    * At the bottom, look in "User Data". About halfway, set EBS_* settings. EBS_IOPS can go as high as 16,000 and EBS_THROUGHPUT can go as high as 1,000Mbs/s
+    * Now clone the compute environment (double check all network settings and roles)
+        * specify "exact" launch template version to the version you created. 
+        * set instance type to network/disk optimized machines (eg m5zn.6xlarge)
+        * have a blazing fast I/O machine (tests reached constant simultaneous 1Gb/s upload and 1gb/s download, while transferring novaseq data from basespace to AWS/S3)
+
+
+ 
+
+
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index a1cdce0ba1b..613607da42a 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -29,6 +29,21 @@ defined.
 This infrastructure and all the associated configuration still exists; however,
 it is moved out of the Cromwell configuration.
 
+Deployment
+----------
+
+Deployment of the cromwell/AWS environment can be performed using the three cloudformation stacks:
+
+1. VPC : setup of the networks
+2. Resources : setup of the compute environment, job queues and storage solutions
+3. Cromwell : setup of an EC2 instance and RDS, hosting the cromwell server and submission tools. 
+
+Along the way, all necessary IAM rols are generated. 
+
+The full documentation is available [here](DEPLOY.md)
+
+
+
 Features
 ---------------------
 ### Docker Hub Authentication
@@ -42,7 +57,7 @@ Docker Hub authentication for AWS Backend enable users to access and use private
 dockerhub { token = "<enconded-string-from-point-2>" }
 ```
 
-Stack must be deployed through https://github.com/aws-samples/aws-genomics-workflows.
+
 
 ### `awsBatchRetryAttempts`
 
@@ -154,11 +169,9 @@ backend {
 }
 
 // set the keys for Out-Of-Memory killing. 
-// system.io.memory-retry-error-keys
-system{
-    io{
-        memory-retry-error-keys = ["OutOfMemory","Killed"]
-    }
+// system.memory-retry-error-keys
+system {
+    memory-retry-error-keys = ["OutOfMemory","Killed"]
 }
 ```
 
@@ -169,6 +182,14 @@ Workflow specific runtime options : `workflow_options.json`:
 }
 ```
 
+Or specify it in the cromwell config as : 
+
+```
+workflow-options {
+    memory-retry-multiplier = 1.5
+}
+```
+
 When providing the options.json file during workflow submission, jobs that were terminated due to insufficient memory will be retried 6 times, with increasing memory allocation. For example 4Gb => 6Gb => 9Gb => 13.5Gb => ... 
 
 Note: Retries of jobs using the `awsBatchRetryAttempts` counter do *not* increase memory allocation. 
@@ -340,8 +361,8 @@ The following workflow highlights the following features:
 version 1.0
 workflow TestEFS {
     input {
-        # input file for WF is located on S3
-        File s3_file = 's3://aws-quickstart/quickstart-aws-vpc/templates/aws-vpc.template.yaml'
+        # input file for WF is located on a public S3
+        File s3_file = 's3://cromwell-aws-cloudformation-templates/root-templates/aws-vpc.template.yaml'
         # set an input parameter holding the working dir on EFS
         String efs_wd = "/mnt/efs/MyTestProject"
     }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
index 41cb1dae97f..66287a781af 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
@@ -54,14 +54,19 @@ class AwsBatchBackendFileHashingActor(standardParams: StandardFileHashingActorPa
   override def customHashStrategy(fileRequest: SingleFileHashRequest): Option[Try[String]] = {
     val file = DefaultPathBuilder.get(fileRequest.file.valueString)
     if (aws_config.efsMntPoint.isDefined && file.toString.startsWith(aws_config.efsMntPoint.getOrElse("--")) && aws_config.checkSiblingMd5.getOrElse(false)) {
-            // check existence of the sibling file
             val md5 = file.sibling(s"${file.toString}.md5")
-            if (md5.exists) {
+            // check existance of the file : 
+            if (!file.exists) {
+                // if missing, cache hit is invalid; return invalid md5
+                Some("File Missing").map(str => Try(str))
+            }
+            // check existence of the sibling file
+            else if (md5.exists) {
                 // read the file.
                 val md5_value: Option[String] = Some(md5.contentAsString.split("\\s+")(0))
                 md5_value.map(str => Try(str))
             } else {
-                // No sibling found, fall back to default.
+                // File present, but no sibling found, fall back to default.
                 None
             }
             
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala
index 769c2c2f5d8..563834e8d06 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala
@@ -56,7 +56,6 @@ object AwsBatchVolume {
   val LocalDiskPattern: Regex = raw"""^\s*local-disk\s*$$""".r
 
   def parse(s: String): Try[AwsBatchVolume] = {
-
     val validation: ErrorOr[AwsBatchVolume] = s match {
       case LocalDiskPattern() =>
         Valid(AwsBatchWorkingDisk())
@@ -69,8 +68,9 @@ object AwsBatchVolume {
         Valid(AwsBatchEmptyMountedDisk(DefaultPathBuilder.get(mountPoint),fsType))
       case _ =>
         s"Disk strings should be of the format 'local-disk' or '/mount/point' but got: '$s'".invalidNel
-    }
 
+    }
+    
     Try(validation match {
       case Valid(localDisk) => localDisk
       case Invalid(nels) =>

From 33e991f6960ddd37c2a4ed14b4d610e275b8d90b Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 15 Sep 2023 11:50:07 -0400
Subject: [PATCH 215/326] WX-1264 Don't expire an unexpirable filesystem
 (#7216)

---
 .../storage/blob/nio/AzureFileSystem.java     |  7 ++-
 .../blob/BlobFileSystemManager.scala          | 19 +++----
 .../blob/AzureFileSystemSpec.scala            | 56 +++++++++++++++----
 .../blob/BlobPathBuilderFactorySpec.scala     |  7 ---
 4 files changed, 61 insertions(+), 28 deletions(-)

diff --git a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
index 862352b06ee..8ca4361bd3e 100644
--- a/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
+++ b/azure-blob-nio/src/main/java/com/azure/storage/blob/nio/AzureFileSystem.java
@@ -520,10 +520,15 @@ private void setExpiryFromSAS(AzureSasCredential token) {
         this.expiry = expiryString.map(es -> Instant.parse(es)).orElse(null);
     }
 
+    /**
+     * Return true if this filesystem has SAS credentials with an expiration data attached, and we're within
+     * `buffer` of the expiration. Return false if our credentials don't come with an expiration, or we
+     * aren't within `buffer` of our expiration.
+     */
     public boolean isExpired(Duration buffer) {
         return Optional.ofNullable(this.expiry)
             .map(e -> Instant.now().plus(buffer).isAfter(e))
-            .orElse(true);
+            .orElse(false);
 
     }
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index 6b6088c7689..e3de6783d85 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -13,7 +13,7 @@ import java.net.URI
 import java.nio.file._
 import java.nio.file.spi.FileSystemProvider
 import java.time.temporal.ChronoUnit
-import java.time.{Duration, Instant, OffsetDateTime}
+import java.time.{Duration, OffsetDateTime}
 import java.util.UUID
 import scala.jdk.CollectionConverters._
 import scala.util.{Failure, Success, Try}
@@ -32,10 +32,6 @@ case class AzureFileSystemAPI(private val provider: FileSystemProvider = new Azu
   * See BlobSasTokenGenerator for more information on how a SAS token is generated
   */
 object BlobFileSystemManager {
-  def parseTokenExpiry(token: AzureSasCredential): Option[Instant] = for {
-    expiryString <- token.getSignature.split("&").find(_.startsWith("se")).map(_.replaceFirst("se=","")).map(_.replace("%3A", ":"))
-    instant = Instant.parse(expiryString)
-  } yield instant
 
   def buildConfigMap(credential: AzureSasCredential, container: BlobContainerName): Map[String, Object] = {
     // Special handling is done here to provide a special key value pair if the placeholder token is provided
@@ -226,9 +222,12 @@ case class NativeBlobSasTokenGenerator(subscription: Option[SubscriptionId] = No
     *
     * @return an AzureSasCredential for accessing a blob container
     */
-  def generateBlobSasToken(endpoint: EndpointURL, container: BlobContainerName): Try[AzureSasCredential] = for {
-    bcc <- AzureUtils.buildContainerClientFromLocalEnvironment(container.toString, endpoint.toString, subscription.map(_.toString))
-    bsssv = new BlobServiceSasSignatureValues(OffsetDateTime.now.plusDays(1), bcsp)
-    asc = new AzureSasCredential(bcc.generateSas(bsssv))
-  } yield asc
+  def generateBlobSasToken(endpoint: EndpointURL, container: BlobContainerName): Try[AzureSasCredential] = {
+    val c = AzureUtils.buildContainerClientFromLocalEnvironment(container.toString, endpoint.toString, subscription.map(_.toString))
+
+    c.map { bcc =>
+        val bsssv = new BlobServiceSasSignatureValues(OffsetDateTime.now.plusDays(1), bcsp)
+        new AzureSasCredential(bcc.generateSas(bsssv))
+      }.orElse(Try(BlobFileSystemManager.PLACEHOLDER_TOKEN))
+  }
 }
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala
index e0463bab740..9b8362ced80 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala
@@ -1,25 +1,61 @@
 package cromwell.filesystems.blob
 
+import com.azure.core.credential.AzureSasCredential
 import com.azure.storage.blob.nio.{AzureFileSystem, AzureFileSystemProvider}
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-import java.time.Instant
+import java.time.{Duration, Instant}
+import java.time.temporal.ChronoUnit
 import scala.compat.java8.OptionConverters._
 import scala.jdk.CollectionConverters._
 
 class AzureFileSystemSpec extends AnyFlatSpec with Matchers {
-  val now = Instant.now()
-  val container = BlobContainerName("testConainer")
-  val exampleSas = BlobPathBuilderFactorySpec.buildExampleSasToken(now)
-  val exampleConfig = BlobFileSystemManager.buildConfigMap(exampleSas, container)
-  val exampleStorageEndpoint = BlobPathBuilderSpec.buildEndpoint("testStorageAccount")
-  val exampleCombinedEndpoint = BlobFileSystemManager.combinedEnpointContainerUri(exampleStorageEndpoint, container)
 
-  it should "parse an expiration from a sas token" in {
+  val fiveMinutes: Duration = Duration.of(5, ChronoUnit.MINUTES)
+
+  private def makeFilesystemWithExpiration(expiration: Instant): AzureFileSystem =
+    makeFilesystemWithCreds(BlobPathBuilderFactorySpec.buildExampleSasToken(expiration))
+
+  private def makeFilesystemWithCreds(creds: AzureSasCredential): AzureFileSystem = {
+    val storageEndpoint = BlobPathBuilderSpec.buildEndpoint("testStorageAccount")
+    val container = BlobContainerName("testContainer")
+    val combinedEndpoint = BlobFileSystemManager.combinedEnpointContainerUri(storageEndpoint, container)
+
     val provider = new AzureFileSystemProvider()
-    val filesystem : AzureFileSystem = provider.newFileSystem(exampleCombinedEndpoint, exampleConfig.asJava).asInstanceOf[AzureFileSystem]
+    provider.newFileSystem(
+      combinedEndpoint,
+      BlobFileSystemManager.buildConfigMap(creds, container).asJava
+    ).asInstanceOf[AzureFileSystem]
+  }
+
+  it should "parse an expiration from a sas token" in {
+    val now = Instant.now()
+    val filesystem : AzureFileSystem = makeFilesystemWithExpiration(now)
     filesystem.getExpiry.asScala shouldBe Some(now)
-    filesystem.getFileStores.asScala.map(_.name()).exists(_ == container.value) shouldBe true
+    filesystem.getFileStores.asScala.map(_.name()).exists(_ == "testContainer") shouldBe true
+  }
+
+  it should "not be expired when the token is fresh" in {
+    val anHourFromNow = Instant.now().plusSeconds(3600)
+    val filesystem : AzureFileSystem = makeFilesystemWithExpiration(anHourFromNow)
+    filesystem.isExpired(fiveMinutes) shouldBe false
+  }
+
+  it should "be expired when we're within the buffer" in {
+    val threeMinutesFromNow = Instant.now().plusSeconds(180)
+    val filesystem : AzureFileSystem = makeFilesystemWithExpiration(threeMinutesFromNow)
+    filesystem.isExpired(fiveMinutes) shouldBe true
+  }
+
+  it should "be expired when the token is stale" in {
+    val anHourAgo = Instant.now().minusSeconds(3600)
+    val filesystem : AzureFileSystem = makeFilesystemWithExpiration(anHourAgo)
+    filesystem.isExpired(fiveMinutes) shouldBe true
+  }
+
+  it should "not be expired with public credentials" in {
+    val fileSystem = makeFilesystemWithCreds(BlobFileSystemManager.PLACEHOLDER_TOKEN)
+    fileSystem.isExpired(fiveMinutes) shouldBe false
   }
 }
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
index c4ee102c58b..24783c15780 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
@@ -32,13 +32,6 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     testToken.getSignature should equal(sourceToken)
   }
 
-  it should "parse an expiration time from a sas token" in {
-    val expiryTime = generateTokenExpiration(20L)
-    val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(expiryTime)
-    val expiry = BlobFileSystemManager.parseTokenExpiry(sasToken)
-    expiry should contain(expiryTime)
-  }
-
   it should "test that a filesystem gets closed correctly" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
     val container = BlobContainerName("test")

From a290e6d513ca953a23a8e77096e1e6eeb367e00e Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 15 Sep 2023 15:32:40 -0400
Subject: [PATCH 216/326] [WX-495] DRS Parallel Downloads (#7214)

---
 .../drs/localizer/DrsLocalizerMain.scala      | 242 ++++++----
 .../downloaders/AccessUrlDownloader.scala     |  91 ----
 .../downloaders/BulkAccessUrlDownloader.scala | 144 ++++++
 .../downloaders/DownloaderFactory.scala       |   8 +-
 .../downloaders/GcsUriDownloader.scala        |  43 +-
 .../localizer/downloaders/GetmChecksum.scala  |   2 +-
 .../drs/localizer/DrsLocalizerMainSpec.scala  | 415 ++++++++----------
 .../downloaders/AccessUrlDownloaderSpec.scala |  59 ---
 .../BulkAccessUrlDownloaderSpec.scala         | 114 +++++
 ...o template_ Cromwell DRS Localizer.run.xml |   2 +-
 10 files changed, 653 insertions(+), 467 deletions(-)
 delete mode 100644 cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/AccessUrlDownloader.scala
 create mode 100644 cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
 delete mode 100644 cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/AccessUrlDownloaderSpec.scala
 create mode 100644 cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala

diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
index 1858f395024..3d99538f614 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
@@ -2,13 +2,13 @@ package drs.localizer
 
 import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO, IOApp}
-import cats.implicits._
+import cats.implicits.toTraverseOps
 import cloud.nio.impl.drs.DrsPathResolver.{FatalRetryDisposition, RegularRetryDisposition}
 import cloud.nio.impl.drs._
 import cloud.nio.spi.{CloudNioBackoff, CloudNioSimpleExponentialBackoff}
 import com.typesafe.scalalogging.StrictLogging
 import drs.localizer.CommandLineParser.AccessTokenStrategy.{Azure, Google}
-import drs.localizer.downloaders.AccessUrlDownloader.Hashes
+import drs.localizer.DrsLocalizerMain.{defaultNumRetries, toValidatedUriType}
 import drs.localizer.downloaders._
 import org.apache.commons.csv.{CSVFormat, CSVParser}
 
@@ -17,7 +17,10 @@ import java.nio.charset.Charset
 import scala.concurrent.duration._
 import scala.jdk.CollectionConverters._
 import scala.language.postfixOps
+import drs.localizer.URIType.URIType
 
+case class UnresolvedDrsUrl(drsUrl: String, downloadDestinationPath: String)
+case class ResolvedDrsUrl(drsResponse: DrsResolverResponse, downloadDestinationPath: String, uriType: URIType)
 object DrsLocalizerMain extends IOApp with StrictLogging {
 
   override def run(args: List[String]): IO[ExitCode] = {
@@ -38,15 +41,18 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
 
   def buildParser(): scopt.OptionParser[CommandLineArguments] = new CommandLineParser()
 
+  // Default retry parameters for resolving a DRS url
+  val defaultNumRetries: Int = 5
   val defaultBackoff: CloudNioBackoff = CloudNioSimpleExponentialBackoff(
-    initialInterval = 10 seconds, maxInterval = 60 seconds, multiplier = 2)
+    initialInterval = 1 seconds, maxInterval = 60 seconds, multiplier = 2)
 
   val defaultDownloaderFactory: DownloaderFactory = new DownloaderFactory {
-    override def buildAccessUrlDownloader(accessUrl: AccessUrl, downloadLoc: String, hashes: Hashes): IO[Downloader] =
-      IO.pure(AccessUrlDownloader(accessUrl, downloadLoc, hashes))
+    override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader =
+      GcsUriDownloader(gcsPath, serviceAccountJsonOption, downloadLoc, requesterPaysProjectOption)
 
-    override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): IO[Downloader] =
-      IO.pure(GcsUriDownloader(gcsPath, serviceAccountJsonOption, downloadLoc, requesterPaysProjectOption))
+    override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+      BulkAccessUrlDownloader(urlsToDownload)
+    }
   }
 
   private def printUsage: IO[ExitCode] = {
@@ -54,35 +60,83 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
     IO.pure(ExitCode.Error)
   }
 
-  def runLocalizer(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials): IO[ExitCode] = {
-    commandLineArguments.manifestPath match {
-      case Some(manifestPath) =>
-        val manifestFile = new File(manifestPath)
-        val csvParser = CSVParser.parse(manifestFile, Charset.defaultCharset(), CSVFormat.DEFAULT)
-        val exitCodes: IO[List[ExitCode]] = csvParser.asScala.map(record => {
-          val drsObject = record.get(0)
-          val containerPath = record.get(1)
-          localizeFile(commandLineArguments, drsCredentials, drsObject, containerPath)
-        }).toList.sequence
-        exitCodes.map(_.find(_ != ExitCode.Success).getOrElse(ExitCode.Success))
-      case None =>
-        val drsObject = commandLineArguments.drsObject.get
-        val containerPath = commandLineArguments.containerPath.get
-        localizeFile(commandLineArguments, drsCredentials, drsObject, containerPath)
+  /**
+    * Helper function to read a CSV file as pairs of drsURL -> local download destination.
+    * @param csvManifestPath Path to a CSV file where each row is something like: drs://asdf.ghj, path/to/my/directory
+    */
+  def loadCSVManifest(csvManifestPath: String): IO[List[UnresolvedDrsUrl]] = {
+    IO {
+      val openFile = new File(csvManifestPath)
+      val csvParser = CSVParser.parse(openFile, Charset.defaultCharset(), CSVFormat.DEFAULT)
+      try{
+        csvParser.getRecords.asScala.map(record => UnresolvedDrsUrl(record.get(0), record.get(1))).toList
+      } finally {
+        csvParser.close()
+      }
     }
   }
 
-  private def localizeFile(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials, drsObject: String, containerPath: String) = {
-    new DrsLocalizerMain(drsObject, containerPath, drsCredentials, commandLineArguments.googleRequesterPaysProject).
-      resolveAndDownloadWithRetries(downloadRetries = 3, checksumRetries = 1, defaultDownloaderFactory, Option(defaultBackoff)).map(_.exitCode)
+  def runLocalizer(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials) : IO[ExitCode] = {
+    val urlList = (commandLineArguments.manifestPath, commandLineArguments.drsObject, commandLineArguments.containerPath) match {
+      case (Some(manifestPath), _, _) => {
+        loadCSVManifest(manifestPath)
+      }
+      case (_, Some(drsObject), Some(containerPath)) => {
+        IO.pure(List(UnresolvedDrsUrl(drsObject, containerPath)))
+      }
+      case(_,_,_) => {
+        throw new RuntimeException("Illegal command line arguments supplied to drs localizer.")
+      }
+    }
+    val main = new DrsLocalizerMain(urlList, defaultDownloaderFactory, drsCredentials, commandLineArguments.googleRequesterPaysProject)
+    main.resolveAndDownload().map(_.exitCode)
+    }
+
+  /**
+    * Helper function to decide which downloader to use based on data from the DRS response.
+    * Throws a runtime exception if the DRS response is invalid.
+    */
+  def toValidatedUriType(accessUrl: Option[AccessUrl], gsUri: Option[String]): URIType = {
+    // if both are provided, prefer using access urls
+    (accessUrl, gsUri) match {
+      case (Some(_), _) =>
+        if(!accessUrl.get.url.startsWith("https://")) { throw new RuntimeException("Resolved Access URL does not start with https://")}
+        URIType.ACCESS
+      case (_, Some(_)) =>
+        if(!gsUri.get.startsWith("gs://")) { throw new RuntimeException("Resolved Google URL does not start with gs://")}
+        URIType.GCS
+      case (_, _) =>
+        throw new RuntimeException("DRS response did not contain any URLs")
+    }
   }
+  }
+
+object URIType extends Enumeration {
+  type URIType = Value
+  val GCS, ACCESS, UNKNOWN = Value
 }
 
-class DrsLocalizerMain(drsUrl: String,
-                       downloadLoc: String,
+class DrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
+                       downloaderFactory: DownloaderFactory,
                        drsCredentials: DrsCredentials,
                        requesterPaysProjectIdOption: Option[String]) extends StrictLogging {
 
+  /**
+    * This will:
+    *   - resolve all URLS
+    *   - build downloader(s) for them
+    *   - Invoke the downloaders to localize the files.
+    * @return DownloadSuccess if all downloads succeed. An error otherwise.
+    */
+  def resolveAndDownload(): IO[DownloadResult] = {
+    val downloadResults = buildDownloaders().flatMap { downloaderList =>
+      downloaderList.map(downloader => downloader.download).traverse(identity)
+    }
+    downloadResults.map{list =>
+      list.find(result => result != DownloadSuccess).getOrElse(DownloadSuccess)
+    }
+  }
+
   def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] = {
     IO {
       val drsConfig = DrsConfig.fromEnv(sys.env)
@@ -91,76 +145,86 @@ class DrsLocalizerMain(drsUrl: String,
     }
   }
 
-  def resolveAndDownloadWithRetries(downloadRetries: Int,
-                                    checksumRetries: Int,
-                                    downloaderFactory: DownloaderFactory,
-                                    backoff: Option[CloudNioBackoff],
-                                    downloadAttempt: Int = 0,
-                                    checksumAttempt: Int = 0): IO[DownloadResult] = {
-
-    def maybeRetryForChecksumFailure(t: Throwable): IO[DownloadResult] = {
-      if (checksumAttempt < checksumRetries) {
-        backoff foreach { b => Thread.sleep(b.backoffMillis) }
-        logger.warn(s"Attempting retry $checksumAttempt of $checksumRetries checksum retries to download $drsUrl", t)
-        // In the event of a checksum failure reset the download attempt to zero.
-        resolveAndDownloadWithRetries(downloadRetries, checksumRetries, downloaderFactory, backoff map { _.next }, 0, checksumAttempt + 1)
-      } else {
-        IO.raiseError(new RuntimeException(s"Exhausted $checksumRetries checksum retries to resolve, download and checksum $drsUrl", t))
-      }
+  /**
+    * After resolving all of the URLs, this sorts them into an "Access" or "GCS" bucket.
+    * All access URLS will be downloaded as a batch with a single bulk downloader.
+    * All google URLs will be downloaded individually in their own google downloader.
+    * @return List of all downloaders required to fulfill the request.
+    */
+  def buildDownloaders() : IO[List[Downloader]] = {
+    resolveUrls(toResolveAndDownload).map { pendingDownloads =>
+      val accessUrls = pendingDownloads.filter(url => url.uriType == URIType.ACCESS)
+      val googleUrls = pendingDownloads.filter(url => url.uriType == URIType.GCS)
+      val bulkDownloader: List[Downloader] = if (accessUrls.isEmpty) List() else List(buildBulkAccessUrlDownloader(accessUrls))
+      val googleDownloaders: List[Downloader] = if (googleUrls.isEmpty) List() else buildGoogleDownloaders(googleUrls)
+      bulkDownloader ++ googleDownloaders
     }
+  }
 
-    def maybeRetryForDownloadFailure(t: Throwable): IO[DownloadResult] = {
-      t match {
-        case _: FatalRetryDisposition =>
-          IO.raiseError(t)
-        case _ if downloadAttempt < downloadRetries =>
-          backoff foreach { b => Thread.sleep(b.backoffMillis) }
-          logger.warn(s"Attempting retry $downloadAttempt of $downloadRetries download retries to download $drsUrl", t)
-          resolveAndDownloadWithRetries(downloadRetries, checksumRetries, downloaderFactory, backoff map { _.next }, downloadAttempt + 1, checksumAttempt)
-        case _ =>
-          IO.raiseError(new RuntimeException(s"Exhausted $downloadRetries download retries to resolve, download and checksum $drsUrl", t))
-      }
+  def buildGoogleDownloaders(resolvedGoogleUrls: List[ResolvedDrsUrl]) : List[Downloader] = {
+    resolvedGoogleUrls.map{url=>
+      downloaderFactory.buildGcsUriDownloader(
+        gcsPath = url.drsResponse.gsUri.get,
+        serviceAccountJsonOption = url.drsResponse.googleServiceAccount.map(_.data.spaces2),
+        downloadLoc = url.downloadDestinationPath,
+        requesterPaysProjectOption = requesterPaysProjectIdOption)
     }
+  }
+  def buildBulkAccessUrlDownloader(resolvedUrls: List[ResolvedDrsUrl]) : Downloader = {
+    downloaderFactory.buildBulkAccessUrlDownloader(resolvedUrls)
+  }
 
-    resolveAndDownload(downloaderFactory).redeemWith({
-      maybeRetryForDownloadFailure
-    },
-    {
-      case f: FatalDownloadFailure =>
-        IO.raiseError(new RuntimeException(s"Fatal error downloading DRS object: $f"))
-      case r: RetryableDownloadFailure =>
-        maybeRetryForDownloadFailure(
-          new RuntimeException(s"Retryable download error: $r for $drsUrl on retry attempt $downloadAttempt of $downloadRetries") with RegularRetryDisposition)
-      case ChecksumFailure =>
-        maybeRetryForChecksumFailure(new RuntimeException(s"Checksum failure for $drsUrl on checksum retry attempt $checksumAttempt of $checksumRetries"))
-      case o => IO.pure(o)
-    })
+  /**
+    * Runs a synchronous HTTP request to resolve the provided DRS URL with the provided resolver.
+    */
+  def resolveSingleUrl(resolverObject: DrsLocalizerDrsPathResolver, drsUrlToResolve: UnresolvedDrsUrl): IO[ResolvedDrsUrl] = {
+    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl, DrsResolverField.Hashes)
+    val drsResponse = resolverObject.resolveDrs(drsUrlToResolve.drsUrl, fields)
+    drsResponse.map(resp => ResolvedDrsUrl(resp, drsUrlToResolve.downloadDestinationPath, toValidatedUriType(resp.accessUrl, resp.gsUri)))
   }
 
-  private [localizer] def resolveAndDownload(downloaderFactory: DownloaderFactory): IO[DownloadResult] = {
-    resolve(downloaderFactory) flatMap { _.download }
+
+  val defaultBackoff: CloudNioBackoff = CloudNioSimpleExponentialBackoff(
+    initialInterval = 10 seconds, maxInterval = 60 seconds, multiplier = 2)
+
+  /**
+    * Runs synchronous HTTP requests to resolve all the DRS urls.
+    */
+  def resolveUrls(unresolvedUrls: IO[List[UnresolvedDrsUrl]]): IO[List[ResolvedDrsUrl]] = {
+    unresolvedUrls.flatMap { unresolvedList =>
+      getDrsPathResolver.flatMap { resolver =>
+        unresolvedList.map { unresolvedUrl =>
+          resolveWithRetries(resolver, unresolvedUrl, defaultNumRetries, Option(defaultBackoff))
+        }.traverse(identity)
+      }
+    }
   }
 
-  private [localizer] def resolve(downloaderFactory: DownloaderFactory): IO[Downloader] = {
-    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl, DrsResolverField.Hashes)
-    for {
-      resolver <- getDrsPathResolver
-      drsResolverResponse <- resolver.resolveDrs(drsUrl, fields)
-
-      // Currently DRS Resolver only supports resolving DRS paths to access URLs or GCS paths.
-      downloader <- (drsResolverResponse.accessUrl, drsResolverResponse.gsUri) match {
-        case (Some(accessUrl), _) =>
-          downloaderFactory.buildAccessUrlDownloader(accessUrl, downloadLoc, drsResolverResponse.hashes)
-        case (_, Some(gcsPath)) =>
-          val serviceAccountJsonOption = drsResolverResponse.googleServiceAccount.map(_.data.spaces2)
-          downloaderFactory.buildGcsUriDownloader(
-            gcsPath = gcsPath,
-            serviceAccountJsonOption = serviceAccountJsonOption,
-            downloadLoc = downloadLoc,
-            requesterPaysProjectOption = requesterPaysProjectIdOption)
-        case _ =>
-          IO.raiseError(new RuntimeException(DrsPathResolver.ExtractUriErrorMsg))
+  def resolveWithRetries(resolverObject: DrsLocalizerDrsPathResolver,
+                         drsUrlToResolve: UnresolvedDrsUrl,
+                         resolutionRetries: Int,
+                         backoff: Option[CloudNioBackoff],
+                        resolutionAttempt: Int = 0) : IO[ResolvedDrsUrl] = {
+
+    def maybeRetryForResolutionFailure(t: Throwable): IO[ResolvedDrsUrl] = {
+      if (resolutionAttempt < resolutionRetries) {
+        backoff foreach { b => Thread.sleep(b.backoffMillis) }
+        logger.warn(s"Attempting retry $resolutionAttempt of $resolutionRetries drs resolution retries to resolve ${drsUrlToResolve.drsUrl}", t)
+        resolveWithRetries(resolverObject, drsUrlToResolve, resolutionRetries, backoff map { _.next }, resolutionAttempt+1)
+      } else {
+        IO.raiseError(new RuntimeException(s"Exhausted $resolutionRetries resolution retries to resolve $drsUrlToResolve.drsUrl", t))
       }
-    } yield downloader
+    }
+
+    resolveSingleUrl(resolverObject, drsUrlToResolve).redeemWith(
+      recover = maybeRetryForResolutionFailure,
+      bind = {
+      case f: FatalRetryDisposition =>
+        IO.raiseError(new RuntimeException(s"Fatal error resolving DRS URL: $f"))
+      case _: RegularRetryDisposition =>
+        resolveWithRetries(resolverObject, drsUrlToResolve, resolutionRetries, backoff, resolutionAttempt+1)
+      case o => IO.pure(o)
+    })
   }
 }
+
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/AccessUrlDownloader.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/AccessUrlDownloader.scala
deleted file mode 100644
index ae6f2fa4f1e..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/AccessUrlDownloader.scala
+++ /dev/null
@@ -1,91 +0,0 @@
-package drs.localizer.downloaders
-
-import cats.data.Validated.{Invalid, Valid}
-import cats.effect.{ExitCode, IO}
-import cloud.nio.impl.drs.AccessUrl
-import com.typesafe.scalalogging.StrictLogging
-import common.exception.AggregatedMessageException
-import common.util.StringUtil._
-import common.validation.ErrorOr.ErrorOr
-import drs.localizer.downloaders.AccessUrlDownloader._
-
-import scala.sys.process.{Process, ProcessLogger}
-import scala.util.matching.Regex
-
-case class GetmResult(returnCode: Int, stderr: String)
-
-case class AccessUrlDownloader(accessUrl: AccessUrl, downloadLoc: String, hashes: Hashes) extends Downloader with StrictLogging {
-  def generateDownloadScript: ErrorOr[String] = {
-    val signedUrl = accessUrl.url
-    GetmChecksum(hashes, accessUrl).args map { checksumArgs =>
-      s"""mkdir -p $$(dirname '$downloadLoc') && rm -f '$downloadLoc' && getm $checksumArgs --filepath '$downloadLoc' '$signedUrl'"""
-    }
-  }
-
-  def runGetm: IO[GetmResult] = {
-    generateDownloadScript match {
-      case Invalid(errors) =>
-        IO.raiseError(AggregatedMessageException("Error generating access URL download script", errors.toList))
-      case Valid(script) => IO {
-        val copyCommand = Seq("bash", "-c", script)
-        val copyProcess = Process(copyCommand)
-
-        val stderr = new StringBuilder()
-        val errorCapture: String => Unit = { s => stderr.append(s); () }
-
-        // As of `getm` version 0.0.4 the contents of stdout do not appear to be interesting (only a progress bar
-        // with no option to suppress it), so ignore stdout for now. If stdout becomes interesting in future versions
-        // of `getm` it can be captured just like stderr is being captured here.
-        val returnCode = copyProcess ! ProcessLogger(_ => (), errorCapture)
-
-        GetmResult(returnCode, stderr.toString().trim())
-      }
-    }
-  }
-
-  override def download: IO[DownloadResult] = {
-    // We don't want to log the unmasked signed URL here. On a PAPI backend this log will end up under the user's
-    // workspace bucket, but that bucket may have visibility different than the data referenced by the signed URL.
-    val masked = accessUrl.url.maskSensitiveUri
-    logger.info(s"Attempting to download data to '$downloadLoc' from access URL '$masked'.")
-
-    runGetm map toDownloadResult
-  }
-
-  def toDownloadResult(getmResult: GetmResult): DownloadResult = {
-    getmResult match {
-      case GetmResult(0, stderr) if stderr.isEmpty =>
-        DownloadSuccess
-      case GetmResult(0, stderr) =>
-        stderr match {
-          case ChecksumFailureMessage() =>
-            ChecksumFailure
-          case _ =>
-            UnrecognizedRetryableDownloadFailure(ExitCode(0))
-        }
-      case GetmResult(rc, stderr) =>
-        stderr match {
-          case HttpStatusMessage(status) =>
-            Integer.parseInt(status) match {
-              case 408 | 429 =>
-                RecognizedRetryableDownloadFailure(ExitCode(rc))
-              case s if s / 100 == 4 =>
-                FatalDownloadFailure(ExitCode(rc))
-              case s if s / 100 == 5 =>
-                RecognizedRetryableDownloadFailure(ExitCode(rc))
-              case _ =>
-                UnrecognizedRetryableDownloadFailure(ExitCode(rc))
-            }
-          case _ =>
-            UnrecognizedRetryableDownloadFailure(ExitCode(rc))
-        }
-    }
-  }
-}
-
-object AccessUrlDownloader {
-  type Hashes = Option[Map[String, String]]
-
-  val ChecksumFailureMessage: Regex = raw""".*AssertionError: Checksum failed!.*""".r
-  val HttpStatusMessage: Regex = raw"""ERROR:getm\.cli.*"status_code":\s*(\d+).*""".r
-}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
new file mode 100644
index 00000000000..4668c5072ed
--- /dev/null
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
@@ -0,0 +1,144 @@
+package drs.localizer.downloaders
+
+import cats.effect.{ExitCode, IO}
+import cloud.nio.impl.drs.{AccessUrl, DrsResolverResponse}
+import com.typesafe.scalalogging.StrictLogging
+
+import java.nio.charset.StandardCharsets
+import java.nio.file.{Files, Path, Paths}
+import scala.sys.process.{Process, ProcessLogger}
+import scala.util.matching.Regex
+import drs.localizer.ResolvedDrsUrl
+case class GetmResult(returnCode: Int, stderr: String)
+/**
+  * Getm is a python tool that is used to download resolved DRS uris quickly and in parallel.
+  * This class builds a getm-manifest.json file that it uses for input, and builds/executes a shell command
+  * to invoke the Getm tool, which is expected to already be installed in the local environment.
+  * @param resolvedUrls
+  */
+case class BulkAccessUrlDownloader(resolvedUrls : List[ResolvedDrsUrl]) extends Downloader with StrictLogging {
+
+  val getmManifestPath: Path = Paths.get("getm-manifest.json")
+  /**
+    * Write a json manifest to disk that looks like:
+    * // [
+    * //  {
+    * //     "url" : "www.123.com",
+    * //     "filepath" : "path/to/where/123/should/be/downloaded",
+    * //     "checksum" : "sdfjndsfjkfsdjsdfkjsdf",
+    * //     "checksum-algorithm" : "md5"
+    * //  },
+    * //  {
+    * //     "url" : "www.567.com"
+    * //     "filepath" : "path/to/where/567/should/be/downloaded",
+    * //     "checksum" : "asdasdasfsdfsdfasdsdfasd",
+    * //     "checksum-algorithm" : "md5"
+    * //  }
+    * // ]
+    *
+    * @param resolvedUrls
+    * @return Filepath of a getm-manifest.json that Getm can use to download multiple files in parallel.
+    */
+  def generateJsonManifest(resolvedUrls : List[ResolvedDrsUrl]): IO[Path] = {
+    def toJsonString(drsResponse: DrsResolverResponse, destinationFilepath: String): String = {
+      //NB: trailing comma is being removed in generateJsonManifest
+      val accessUrl: AccessUrl = drsResponse.accessUrl.getOrElse(AccessUrl("missing", None))
+      drsResponse.hashes.map(_ => {
+        val checksum = GetmChecksum(drsResponse.hashes, accessUrl).value.getOrElse("error_calculating_checksum")
+        val checksumAlgorithm = GetmChecksum(drsResponse.hashes, accessUrl).getmAlgorithm
+        s"""  {
+           |    "url" : "${accessUrl.url}",
+           |    "filepath" : "$destinationFilepath",
+           |    "checksum" : "$checksum",
+           |    "checksum-algorithm" : "$checksumAlgorithm"
+           |  },
+           |""".stripMargin
+      }).getOrElse(
+        s"""  {
+           |    "url" : "${accessUrl.url}",
+           |    "filepath" : "$destinationFilepath"
+           |  },
+           |""".stripMargin
+      )
+    }
+    IO {
+      var jsonString: String = "[\n"
+      for (resolvedUrl <- resolvedUrls) {
+        jsonString += toJsonString(resolvedUrl.drsResponse, resolvedUrl.downloadDestinationPath)
+      }
+      if(jsonString.contains(',')) {
+        //remove trailing comma from array elements, but don't crash on empty list.
+        jsonString = jsonString.substring(0, jsonString.lastIndexOf(","))
+      }
+      jsonString += "\n]"
+      Files.write(getmManifestPath, jsonString.getBytes(StandardCharsets.UTF_8))
+    }
+  }
+
+  def deleteJsonManifest() = {
+    Files.deleteIfExists(getmManifestPath)
+  }
+
+  def generateGetmCommand(pathToMainfestJson : Path) : String = {
+    s"""getm --manifest ${pathToMainfestJson.toString}"""
+  }
+  def runGetm: IO[GetmResult] = {
+    generateJsonManifest(resolvedUrls).flatMap{ manifestPath =>
+      val script = generateGetmCommand(manifestPath)
+      val copyCommand : Seq[String] = Seq("bash", "-c", script)
+      logger.info(script)
+      val copyProcess = Process(copyCommand)
+      val stderr = new StringBuilder()
+      val errorCapture: String => Unit = { s => stderr.append(s); () }
+      val returnCode = copyProcess ! ProcessLogger(_ => (), errorCapture)
+      deleteJsonManifest()
+      logger.info(stderr.toString().trim())
+      IO(GetmResult(returnCode, stderr.toString().trim()))
+    }
+  }
+
+  override def download: IO[DownloadResult] = {
+    // We don't want to log the unmasked signed URL here. On a PAPI backend this log will end up under the user's
+    // workspace bucket, but that bucket may have visibility different than the data referenced by the signed URL.
+    logger.info(s"Attempting to download data")
+
+    runGetm map toDownloadResult
+  }
+
+  def toDownloadResult(getmResult: GetmResult): DownloadResult = {
+    getmResult match {
+      case GetmResult(0, stderr) if stderr.isEmpty =>
+        DownloadSuccess
+      case GetmResult(0, stderr) =>
+        stderr match {
+          case BulkAccessUrlDownloader.ChecksumFailureMessage() =>
+            ChecksumFailure
+          case _ =>
+            UnrecognizedRetryableDownloadFailure(ExitCode(0))
+        }
+      case GetmResult(rc, stderr) =>
+        stderr match {
+          case BulkAccessUrlDownloader.HttpStatusMessage(status) =>
+            Integer.parseInt(status) match {
+              case 408 | 429 =>
+                RecognizedRetryableDownloadFailure(ExitCode(rc))
+              case s if s / 100 == 4 =>
+                FatalDownloadFailure(ExitCode(rc))
+              case s if s / 100 == 5 =>
+                RecognizedRetryableDownloadFailure(ExitCode(rc))
+              case _ =>
+                UnrecognizedRetryableDownloadFailure(ExitCode(rc))
+            }
+          case _ =>
+            UnrecognizedRetryableDownloadFailure(ExitCode(rc))
+        }
+    }
+  }
+}
+
+object BulkAccessUrlDownloader{
+  type Hashes = Option[Map[String, String]]
+
+  val ChecksumFailureMessage: Regex = raw""".*AssertionError: Checksum failed!.*""".r
+  val HttpStatusMessage: Regex = raw"""ERROR:getm\.cli.*"status_code":\s*(\d+).*""".r
+}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/DownloaderFactory.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/DownloaderFactory.scala
index 8465ede0dd6..6c7f27e8a6e 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/DownloaderFactory.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/DownloaderFactory.scala
@@ -1,14 +1,12 @@
 package drs.localizer.downloaders
 
-import cats.effect.IO
-import cloud.nio.impl.drs.AccessUrl
-import drs.localizer.downloaders.AccessUrlDownloader.Hashes
+import drs.localizer.ResolvedDrsUrl
 
 trait DownloaderFactory {
-  def buildAccessUrlDownloader(accessUrl: AccessUrl, downloadLoc: String, hashes: Hashes): IO[Downloader]
+  def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]) : Downloader
 
   def buildGcsUriDownloader(gcsPath: String,
                             serviceAccountJsonOption: Option[String],
                             downloadLoc: String,
-                            requesterPaysProjectOption: Option[String]): IO[Downloader]
+                            requesterPaysProjectOption: Option[String]): Downloader
 }
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
index d4c81af6300..8991e79f5fd 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
@@ -1,10 +1,12 @@
 package drs.localizer.downloaders
 import cats.effect.{ExitCode, IO}
+import cloud.nio.spi.{CloudNioBackoff, CloudNioSimpleExponentialBackoff}
 import com.typesafe.scalalogging.StrictLogging
 import drs.localizer.downloaders.GcsUriDownloader.RequesterPaysErrorMsg
-
+import scala.language.postfixOps
 import java.nio.charset.StandardCharsets
 import java.nio.file.{Files, Path}
+import scala.concurrent.duration.DurationInt
 import scala.sys.process.{Process, ProcessLogger}
 
 case class GcsUriDownloader(gcsUrl: String,
@@ -12,7 +14,15 @@ case class GcsUriDownloader(gcsUrl: String,
                             downloadLoc: String,
                             requesterPaysProjectIdOption: Option[String]) extends Downloader with StrictLogging {
 
+  val defaultNumRetries: Int = 5
+  val defaultBackoff: CloudNioBackoff = CloudNioSimpleExponentialBackoff(
+    initialInterval = 1 seconds, maxInterval = 60 seconds, multiplier = 2)
+
   override def download: IO[DownloadResult] = {
+    downloadWithRetries(defaultNumRetries, Option(defaultBackoff))
+  }
+
+  def runDownloadCommand: IO[DownloadResult] = {
 
     logger.info(s"Requester Pays project ID is $requesterPaysProjectIdOption")
     logger.info(s"Attempting to download $gcsUrl to $downloadLoc")
@@ -40,6 +50,37 @@ case class GcsUriDownloader(gcsUrl: String,
     IO.pure(result)
   }
 
+  def downloadWithRetries(downloadRetries: Int,
+                          backoff: Option[CloudNioBackoff],
+                          downloadAttempt: Int = 0): IO[DownloadResult] =
+  {
+
+    def maybeRetryForDownloadFailure(t: Throwable): IO[DownloadResult] = {
+      if (downloadAttempt < downloadRetries) {
+        backoff foreach { b => Thread.sleep(b.backoffMillis) }
+        logger.warn(s"Attempting download retry $downloadAttempt of $downloadRetries for a GCS url", t)
+        downloadWithRetries(downloadRetries, backoff map {
+          _.next
+        }, downloadAttempt + 1)
+      } else {
+        IO.raiseError(new RuntimeException(s"Exhausted $downloadRetries resolution retries to download GCS file", t))
+      }
+    }
+
+    runDownloadCommand.redeemWith(
+      recover = maybeRetryForDownloadFailure,
+      bind = {
+        case s: DownloadSuccess.type =>
+          IO.pure(s)
+        case _: RecognizedRetryableDownloadFailure =>
+          downloadWithRetries(downloadRetries, backoff, downloadAttempt+1)
+        case _: UnrecognizedRetryableDownloadFailure =>
+          downloadWithRetries(downloadRetries, backoff, downloadAttempt+1)
+        case _ =>
+          downloadWithRetries(downloadRetries, backoff, downloadAttempt+1)
+      })
+  }
+
   /**
     * Bash to download the GCS file using `gsutil`.
     */
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
index 2a39a6543a3..2ca1bd3d2e3 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
@@ -3,7 +3,7 @@ package drs.localizer.downloaders
 import cats.syntax.validated._
 import cloud.nio.impl.drs.AccessUrl
 import common.validation.ErrorOr.ErrorOr
-import drs.localizer.downloaders.AccessUrlDownloader.Hashes
+import drs.localizer.downloaders.BulkAccessUrlDownloader.Hashes
 import org.apache.commons.codec.binary.Base64.encodeBase64String
 import org.apache.commons.codec.binary.Hex.decodeHex
 import org.apache.commons.text.StringEscapeUtils
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
index 66799fcc099..52fa4c99330 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
@@ -3,12 +3,11 @@ package drs.localizer
 import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO}
 import cats.syntax.validated._
-import cloud.nio.impl.drs.DrsPathResolver.FatalRetryDisposition
+import drs.localizer.MockDrsPaths.{fakeAccessUrls, fakeDrsUrlWithGcsResolutionOnly, fakeGoogleUrls}
 import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsCredentials, DrsResolverField, DrsResolverResponse}
 import common.assertion.CromwellTimeoutSpec
 import common.validation.ErrorOr.ErrorOr
 import drs.localizer.MockDrsLocalizerDrsPathResolver.{FakeAccessTokenStrategy, FakeHashes}
-import drs.localizer.downloaders.AccessUrlDownloader.Hashes
 import drs.localizer.downloaders._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
@@ -19,6 +18,28 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
   val fakeDownloadLocation = "/root/foo/foo-123.bam"
   val fakeRequesterPaysId = "fake-billing-project"
 
+  val fakeGoogleInput : IO[List[UnresolvedDrsUrl]] = IO(List(
+    UnresolvedDrsUrl(fakeDrsUrlWithGcsResolutionOnly, "/path/to/nowhere")
+  ))
+
+  val fakeAccessInput: IO[List[UnresolvedDrsUrl]] = IO(List(
+    UnresolvedDrsUrl("https://my-fake-access-url.com", "/path/to/somewhereelse")
+  ))
+
+  val fakeBulkGoogleInput: IO[List[UnresolvedDrsUrl]] = IO(List(
+    UnresolvedDrsUrl("drs://my-fake-google-url.com", "/path/to/nowhere"),
+    UnresolvedDrsUrl("drs://my-fake-google-url.com2", "/path/to/nowhere2"),
+    UnresolvedDrsUrl("drs://my-fake-google-url.com3", "/path/to/nowhere3"),
+    UnresolvedDrsUrl("drs://my-fake-google-url.com4", "/path/to/nowhere4")
+  ))
+
+  val fakeBulkAccessInput: IO[List[UnresolvedDrsUrl]] = IO(List(
+    UnresolvedDrsUrl("drs://my-fake-access-url.com", "/path/to/somewhereelse"),
+    UnresolvedDrsUrl("drs://my-fake-access-url2.com", "/path/to/somewhereelse2"),
+    UnresolvedDrsUrl("drs://my-fake-access-url3.com", "/path/to/somewhereelse3"),
+    UnresolvedDrsUrl("drs://my-fake-access-url4.com", "/path/to/somewhereelse4")
+  ))
+
   behavior of "DrsLocalizerMain"
 
   it should "fail if drs input is not passed" in {
@@ -29,264 +50,192 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     DrsLocalizerMain.run(List(MockDrsPaths.fakeDrsUrlWithGcsResolutionOnly)).unsafeRunSync() shouldBe ExitCode.Error
   }
 
-  it should "accept arguments and run successfully without Requester Pays ID" in {
-    val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithGcsResolutionOnly, fakeDownloadLocation, None)
-    val expected = GcsUriDownloader(
-      gcsUrl = "gs://abc/foo-123/abc123",
-      serviceAccountJson = None,
-      downloadLoc = fakeDownloadLocation,
-      requesterPaysProjectIdOption = None)
-    mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync() shouldBe expected
-  }
-
-  it should "run successfully with all 3 arguments" in {
-    val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithGcsResolutionOnly, fakeDownloadLocation, Option(fakeRequesterPaysId))
-    val expected = GcsUriDownloader(
-      gcsUrl = "gs://abc/foo-123/abc123",
-      serviceAccountJson = None,
-      downloadLoc = fakeDownloadLocation,
-      requesterPaysProjectIdOption = Option(fakeRequesterPaysId))
-    mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync() shouldBe expected
-  }
-
-  it should "fail and throw error if the DRS Resolver response does not have gs:// url" in {
-    val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithoutAnyResolution, fakeDownloadLocation, None)
-
-    the[RuntimeException] thrownBy {
-      mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync()
-    } should have message "No access URL nor GCS URI starting with 'gs://' found in the DRS Resolver response!"
-  }
-
-  it should "resolve to use the correct downloader for an access url" in {
-    val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithAccessUrlResolutionOnly, fakeDownloadLocation, None)
-    val expected = AccessUrlDownloader(
-      accessUrl = AccessUrl(url = "http://abc/def/ghi.bam", headers = None),
-      downloadLoc = fakeDownloadLocation,
-      hashes = FakeHashes
-    )
-    mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync() shouldBe expected
-  }
-
-  it should "resolve to use the correct downloader for an access url when the DRS Resolver response also contains a gs url" in {
-    val mockDrsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithAccessUrlAndGcsResolution, fakeDownloadLocation, None)
-    val expected = AccessUrlDownloader(
-      accessUrl = AccessUrl(url = "http://abc/def/ghi.bam", headers = None), downloadLoc = fakeDownloadLocation,
-      hashes = FakeHashes
-    )
-    mockDrsLocalizer.resolve(DrsLocalizerMain.defaultDownloaderFactory).unsafeRunSync() shouldBe expected
-  }
-
-  it should "not retry on access URL download success" in {
-    var actualAttempts = 0
+  it should "tolerate no URLs being provided" in {
+    val mockDownloadFactory = new DownloaderFactory {
+      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader = {
+        // This test path should never ask for the Google downloader
+        throw new RuntimeException("test failure111")
+      }
 
-    val drsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithAccessUrlResolutionOnly, fakeDownloadLocation, None) {
-      override def resolveAndDownload(downloaderFactory: DownloaderFactory): IO[DownloadResult] = {
-        actualAttempts = actualAttempts + 1
-        super.resolveAndDownload(downloaderFactory)
+      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+        // This test path should never ask for the Bulk downloader
+        throw new RuntimeException("test failure111")
       }
     }
-    val accessUrlDownloader = IO.pure(new Downloader {
-      override def download: IO[DownloadResult] =
-        IO.pure(DownloadSuccess)
-    })
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(List()), mockDownloadFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
+    downloaders.length shouldBe 0
+  }
 
-    val downloaderFactory = new DownloaderFactory {
-      override def buildAccessUrlDownloader(accessUrl: AccessUrl, downloadLoc: String, hashes: Hashes): IO[Downloader] = {
-        accessUrlDownloader
+  it should "build correct downloader(s) for a single google URL" in {
+    val mockDownloadFactory = new DownloaderFactory {
+      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader = {
+        GcsUriDownloader(gcsPath, serviceAccountJsonOption, downloadLoc, requesterPaysProjectOption)
       }
 
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): IO[Downloader] = {
-        // This test path should never ask for the GCS downloader
-        throw new RuntimeException("test failure")
+      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+        // This test path should never ask for the Bulk downloader
+        throw new RuntimeException("test failure111")
       }
     }
 
-    drsLocalizer.resolveAndDownloadWithRetries(
-      downloadRetries = 3,
-      checksumRetries = 1,
-      downloaderFactory = downloaderFactory,
-      backoff = None
-    ).unsafeRunSync() shouldBe DownloadSuccess
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(List(fakeGoogleUrls.head._1)), mockDownloadFactory,FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
+    downloaders.length shouldBe 1
 
-    actualAttempts shouldBe 1
-  }
-
-  it should "retry an appropriate number of times for regular retryable access URL download failures" in {
-    var actualAttempts = 0
-
-    val drsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithAccessUrlResolutionOnly, fakeDownloadLocation, None) {
-      override def resolveAndDownload(downloaderFactory: DownloaderFactory): IO[DownloadResult] = {
-        actualAttempts = actualAttempts + 1
-        super.resolveAndDownload(downloaderFactory)
-      }
+    val correct = downloaders.head match {
+      case _: GcsUriDownloader => true
+      case _ => false
     }
-    val accessUrlDownloader = IO.pure(new Downloader {
-      override def download: IO[DownloadResult] =
-        IO.pure(RecognizedRetryableDownloadFailure(exitCode = ExitCode(0)))
-    })
-
-    val downloaderFactory = new DownloaderFactory {
-      override def buildAccessUrlDownloader(accessUrl: AccessUrl, downloadLoc: String, hashes: Hashes): IO[Downloader] = {
-        accessUrlDownloader
-      }
+    correct shouldBe true
+  }
 
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): IO[Downloader] = {
+  it should "build correct downloader(s) for a single access URL" in {
+    val mockDownloadFactory = new DownloaderFactory {
+      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader = {
         // This test path should never ask for the GCS downloader
         throw new RuntimeException("test failure")
       }
-    }
-
-    assertThrows[Throwable] {
-      drsLocalizer.resolveAndDownloadWithRetries(
-        downloadRetries = 3,
-        checksumRetries = 1,
-        downloaderFactory = downloaderFactory,
-        backoff = None
-      ).unsafeRunSync()
-    }
-
-    actualAttempts shouldBe 4 // 1 initial attempt + 3 retries = 4 total attempts
-  }
 
-  it should "retry an appropriate number of times for fatal retryable access URL download failures" in {
-    var actualAttempts = 0
-
-    val drsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithAccessUrlResolutionOnly, fakeDownloadLocation, None) {
-      override def resolveAndDownload(downloaderFactory: DownloaderFactory): IO[DownloadResult] = {
-        actualAttempts = actualAttempts + 1
-        IO.raiseError(new RuntimeException("testing: fatal error") with FatalRetryDisposition)
+      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+        BulkAccessUrlDownloader(urlsToDownload)
       }
     }
 
-    val accessUrlDownloader = IO.pure(new Downloader {
-      override def download: IO[DownloadResult] =
-        IO.pure(RecognizedRetryableDownloadFailure(exitCode = ExitCode(0)))
-    })
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(List(fakeAccessUrls.head._1)), mockDownloadFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
+    downloaders.length shouldBe 1
+
+    val expected = BulkAccessUrlDownloader(
+      List(fakeAccessUrls.head._2)
+    )
+    expected shouldEqual downloaders.head
+  }
 
-    val downloaderFactory = new DownloaderFactory {
-      override def buildAccessUrlDownloader(accessUrl: AccessUrl, downloadLoc: String, hashes: Hashes): IO[Downloader] = {
-        accessUrlDownloader
+  it should "build correct downloader(s) for multiple google URLs" in {
+    val mockDownloadFactory = new DownloaderFactory {
+      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader = {
+        GcsUriDownloader(gcsPath, serviceAccountJsonOption, downloadLoc, requesterPaysProjectOption)
       }
 
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): IO[Downloader] = {
+      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
         // This test path should never ask for the GCS downloader
         throw new RuntimeException("test failure")
       }
     }
-
-    assertThrows[Throwable] {
-      drsLocalizer.resolveAndDownloadWithRetries(
-        downloadRetries = 3,
-        checksumRetries = 1,
-        downloaderFactory = downloaderFactory,
-        backoff = None
-      ).unsafeRunSync()
-    }
-
-    actualAttempts shouldBe 1 // 1 and done with a fatal exception
-  }
-
-  it should "not retry on GCS URI download success" in {
-    var actualAttempts = 0
-    val drsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithGcsResolutionOnly, fakeDownloadLocation, None) {
-      override def resolveAndDownload(downloaderFactory: DownloaderFactory): IO[DownloadResult] = {
-        actualAttempts = actualAttempts + 1
-        super.resolveAndDownload(downloaderFactory)
-      }
-    }
-    val gcsUriDownloader = IO.pure(new Downloader {
-      override def download: IO[DownloadResult] =
-        IO.pure(DownloadSuccess)
+    val unresolvedUrls : List[UnresolvedDrsUrl] = fakeGoogleUrls.map(pair => pair._1).toList
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(unresolvedUrls), mockDownloadFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
+    downloaders.length shouldBe unresolvedUrls.length
+
+    val countGoogleDownloaders = downloaders.count(downloader => downloader match {
+      case _: GcsUriDownloader => true
+      case _ => false
     })
+    // We expect one GCS downloader for each GCS uri provided
+    countGoogleDownloaders shouldBe downloaders.length
+  }
 
-    val downloaderFactory = new DownloaderFactory {
-      override def buildAccessUrlDownloader(accessUrl: AccessUrl, downloadLoc: String, hashes: Hashes): IO[Downloader] = {
-        // This test path should never ask for the access URL downloader
+  it should "build a single bulk downloader for multiple access URLs" in {
+    val mockDownloadFactory = new DownloaderFactory {
+      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader = {
+        // This test path should never ask for the GCS downloader
         throw new RuntimeException("test failure")
       }
 
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): IO[Downloader] = {
-        gcsUriDownloader
+      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+        BulkAccessUrlDownloader(urlsToDownload)
       }
     }
-
-    drsLocalizer.resolveAndDownloadWithRetries(
-      downloadRetries = 3,
-      checksumRetries = 1,
-      downloaderFactory = downloaderFactory,
-      backoff = None).unsafeRunSync()
-
-    actualAttempts shouldBe 1
+    val unresolvedUrls: List[UnresolvedDrsUrl] = fakeAccessUrls.map(pair => pair._1).toList
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(unresolvedUrls), mockDownloadFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
+    downloaders.length shouldBe 1
+
+    val countBulkDownloaders = downloaders.count(downloader => downloader match {
+      case _: BulkAccessUrlDownloader => true
+      case _ => false
+    })
+    // We expect one total Bulk downloader for all access URIs to share
+    countBulkDownloaders shouldBe 1
+    val expected = BulkAccessUrlDownloader(
+      fakeAccessUrls.map(pair => pair._2).toList
+    )
+    expected shouldEqual downloaders.head
   }
 
-  it should "retry an appropriate number of times for retryable GCS URI download failures" in {
-    var actualAttempts = 0
-    val drsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithGcsResolutionOnly, fakeDownloadLocation, None) {
-      override def resolveAndDownload(downloaderFactory: DownloaderFactory): IO[DownloadResult] = {
-        actualAttempts = actualAttempts + 1
-        super.resolveAndDownload(downloaderFactory)
-      }
-    }
-    val gcsUriDownloader = IO.pure(new Downloader {
-      override def download: IO[DownloadResult] =
-        IO.pure(RecognizedRetryableDownloadFailure(exitCode = ExitCode(1)))
-    })
+  it should "build 1 bulk downloader and 5 google downloaders for a mix of URLs" in {
+    val unresolvedUrls: List[UnresolvedDrsUrl] = fakeAccessUrls.map(pair => pair._1).toList ++ fakeGoogleUrls.map(pair => pair._1).toList
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(unresolvedUrls), DrsLocalizerMain.defaultDownloaderFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
 
-    val downloaderFactory = new DownloaderFactory {
-      override def buildAccessUrlDownloader(accessUrl: AccessUrl, downloadLoc: String, hashes: Hashes): IO[Downloader] = {
-        // This test path should never ask for the access URL downloader
-        throw new RuntimeException("test failure")
-      }
+    downloaders.length shouldBe 6
 
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): IO[Downloader] = {
-        gcsUriDownloader
-      }
-    }
+    //we expect a single bulk downloader despite 5 access URLs being provided
+    val countBulkDownloaders = downloaders.count(downloader => downloader match {
+      case _: BulkAccessUrlDownloader => true
+      case _ => false
+    })
+    // We expect one GCS downloader for each GCS uri provided
+    countBulkDownloaders shouldBe 1
+    val countGoogleDownloaders = downloaders.count(downloader => downloader match {
+      case _: GcsUriDownloader => true
+      case _ => false
+    })
+    // We expect one GCS downloader for each GCS uri provided
+    countBulkDownloaders shouldBe 1
+    countGoogleDownloaders shouldBe 5
+  }
 
-    assertThrows[Throwable] {
-      drsLocalizer.resolveAndDownloadWithRetries(
-        downloadRetries = 3,
-        checksumRetries = 1,
-        downloaderFactory = downloaderFactory,
-        backoff = None).unsafeRunSync()
-    }
+  it should "accept arguments and run successfully without Requester Pays ID" in {
+    val unresolved = fakeGoogleUrls.head._1
+    val mockDrsLocalizer = new MockDrsLocalizerMain(IO(List(unresolved)), DrsLocalizerMain.defaultDownloaderFactory, FakeAccessTokenStrategy, None)
+    val expected = GcsUriDownloader(
+      gcsUrl = fakeGoogleUrls.get(unresolved).get.drsResponse.gsUri.get,
+      serviceAccountJson = None,
+      downloadLoc = unresolved.downloadDestinationPath,
+      requesterPaysProjectIdOption = None)
+    val downloader: Downloader = mockDrsLocalizer.buildDownloaders().unsafeRunSync().head
+    downloader shouldBe expected
+  }
 
-    actualAttempts shouldBe 4 // 1 initial attempt + 3 retries = 4 total attempts
+  it should "run successfully with all 3 arguments" in {
+    val unresolved = fakeGoogleUrls.head._1
+    val mockDrsLocalizer = new MockDrsLocalizerMain(IO(List(unresolved)), DrsLocalizerMain.defaultDownloaderFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val expected = GcsUriDownloader(
+      gcsUrl = fakeGoogleUrls.get(unresolved).get.drsResponse.gsUri.get,
+      serviceAccountJson = None,
+      downloadLoc = unresolved.downloadDestinationPath,
+      requesterPaysProjectIdOption = Option(fakeRequesterPaysId))
+    val downloader: Downloader = mockDrsLocalizer.buildDownloaders().unsafeRunSync().head
+    downloader shouldBe expected
   }
 
-  it should "retry an appropriate number of times for checksum failures" in {
-    var actualAttempts = 0
-    val drsLocalizer = new MockDrsLocalizerMain(MockDrsPaths.fakeDrsUrlWithAccessUrlResolutionOnly, fakeDownloadLocation, None) {
-      override def resolveAndDownload(downloaderFactory: DownloaderFactory): IO[DownloadResult] = {
-        actualAttempts = actualAttempts + 1
-        super.resolveAndDownload(downloaderFactory)
-      }
-    }
-    val accessUrlDownloader = IO.pure(new Downloader {
-      override def download: IO[DownloadResult] =
-        IO.pure(ChecksumFailure)
-    })
+  it should "successfully identify uri types, preferring access" in {
+    val exampleAccessResponse = DrsResolverResponse(accessUrl = Option(AccessUrl("https://something.com", FakeHashes)))
+    val exampleGoogleResponse = DrsResolverResponse(gsUri = Option("gs://something"))
+    val exampleMixedResponse = DrsResolverResponse(accessUrl = Option(AccessUrl("https://something.com", FakeHashes)), gsUri = Option("gs://something"))
+    DrsLocalizerMain.toValidatedUriType(exampleAccessResponse.accessUrl, exampleAccessResponse.gsUri) shouldBe URIType.ACCESS
+    DrsLocalizerMain.toValidatedUriType(exampleGoogleResponse.accessUrl, exampleGoogleResponse.gsUri) shouldBe URIType.GCS
+    DrsLocalizerMain.toValidatedUriType(exampleMixedResponse.accessUrl, exampleMixedResponse.gsUri) shouldBe URIType.ACCESS
+  }
 
-    val downloaderFactory = new DownloaderFactory {
-      override def buildAccessUrlDownloader(accessUrl: AccessUrl, downloadLoc: String, hashes: Hashes): IO[Downloader] = {
-        accessUrlDownloader
-      }
+  it should "throw an exception if the DRS Resolver response is invalid" in {
+    val badAccessResponse = DrsResolverResponse(accessUrl = Option(AccessUrl("hQQps://something.com", FakeHashes)))
+    val badGoogleResponse = DrsResolverResponse(gsUri = Option("gQQs://something"))
+    val emptyResponse = DrsResolverResponse()
 
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): IO[Downloader] = {
-        // This test path should never ask for the GCS URI downloader.
-        throw new RuntimeException("test failure")
-      }
-    }
+    the[RuntimeException] thrownBy {
+      DrsLocalizerMain.toValidatedUriType(badAccessResponse.accessUrl, badAccessResponse.gsUri)
+    } should have message "Resolved Access URL does not start with https://"
 
-    assertThrows[Throwable] {
-      drsLocalizer.resolveAndDownloadWithRetries(
-        downloadRetries = 3,
-        checksumRetries = 1,
-        downloaderFactory = downloaderFactory,
-        backoff = None).unsafeRunSync()
-    }
+    the[RuntimeException] thrownBy {
+      DrsLocalizerMain.toValidatedUriType(badGoogleResponse.accessUrl, badGoogleResponse.gsUri)
+    } should have message "Resolved Google URL does not start with gs://"
 
-    actualAttempts shouldBe 2 // 1 initial attempt + 1 retry = 2 total attempts
+    the[RuntimeException] thrownBy {
+      DrsLocalizerMain.toValidatedUriType(emptyResponse.accessUrl, emptyResponse.gsUri)
+    } should have message "DRS response did not contain any URLs"
   }
 }
 
@@ -295,27 +244,53 @@ object MockDrsPaths {
   val fakeDrsUrlWithAccessUrlResolutionOnly = "drs://def/bar-456/def456"
   val fakeDrsUrlWithAccessUrlAndGcsResolution = "drs://ghi/baz-789/ghi789"
   val fakeDrsUrlWithoutAnyResolution = "drs://foo/bar/no-gcs-path"
+
+  val fakeGoogleUrls: Map[UnresolvedDrsUrl, ResolvedDrsUrl] = Map(
+    (UnresolvedDrsUrl("drs://abc/foo-123/google/0", "/path/to/google/local0"), ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri0")), "/path/to/google/local0", URIType.GCS)),
+    (UnresolvedDrsUrl("drs://abc/foo-123/google/1", "/path/to/google/local1"), ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri1")), "/path/to/google/local1", URIType.GCS)),
+    (UnresolvedDrsUrl("drs://abc/foo-123/google/2", "/path/to/google/local2"), ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri2")), "/path/to/google/local2", URIType.GCS)),
+    (UnresolvedDrsUrl("drs://abc/foo-123/google/3", "/path/to/google/local3"), ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri3")), "/path/to/google/local3", URIType.GCS)),
+    (UnresolvedDrsUrl("drs://abc/foo-123/google/4", "/path/to/google/local4"), ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri4")), "/path/to/google/local4", URIType.GCS))
+  )
+
+  val fakeAccessUrls: Map[UnresolvedDrsUrl, ResolvedDrsUrl] = Map(
+    (UnresolvedDrsUrl("drs://abc/foo-123/access/0", "/path/to/access/local0"), ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/0", FakeHashes))), "/path/to/access/local0", URIType.ACCESS)),
+    (UnresolvedDrsUrl("drs://abc/foo-123/access/1", "/path/to/access/local1"), ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/1", FakeHashes))), "/path/to/access/local1", URIType.ACCESS)),
+    (UnresolvedDrsUrl("drs://abc/foo-123/access/2", "/path/to/access/local2"), ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/2", FakeHashes))), "/path/to/access/local2", URIType.ACCESS)),
+    (UnresolvedDrsUrl("drs://abc/foo-123/access/3", "/path/to/access/local3"), ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/3", FakeHashes))), "/path/to/access/local3", URIType.ACCESS)),
+    (UnresolvedDrsUrl("drs://abc/foo-123/access/4", "/path/to/access/local4"), ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/4", FakeHashes))), "/path/to/access/local4", URIType.ACCESS))
+  )
 }
 
 
-class MockDrsLocalizerMain(drsUrl: String,
-                           downloadLoc: String,
-                           requesterPaysProjectIdOption: Option[String],
+class MockDrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
+                           downloaderFactory: DownloaderFactory,
+                           drsCredentials: DrsCredentials,
+                           requesterPaysProjectIdOption: Option[String]
                           )
-  extends DrsLocalizerMain(drsUrl, downloadLoc, FakeAccessTokenStrategy, requesterPaysProjectIdOption) {
+
+  extends DrsLocalizerMain(toResolveAndDownload, downloaderFactory, FakeAccessTokenStrategy, requesterPaysProjectIdOption) {
 
   override def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] = {
     IO {
       new MockDrsLocalizerDrsPathResolver(cloud.nio.impl.drs.MockDrsPaths.mockDrsConfig)
     }
   }
+  override def resolveSingleUrl(resolverObject: DrsLocalizerDrsPathResolver, drsUrlToResolve: UnresolvedDrsUrl): IO[ResolvedDrsUrl] = {
+    IO {
+      if (!fakeAccessUrls.contains(drsUrlToResolve) && !fakeGoogleUrls.contains(drsUrlToResolve)) {
+        throw new RuntimeException("Unexpected URI during testing")
+      }
+      fakeAccessUrls.getOrElse(drsUrlToResolve, fakeGoogleUrls.getOrElse(drsUrlToResolve, ResolvedDrsUrl(DrsResolverResponse(),"/12/3/", URIType.UNKNOWN)))
+    }
+  }
 }
 
-
 class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig) extends
   DrsLocalizerDrsPathResolver(drsConfig, FakeAccessTokenStrategy) {
 
   override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
+
     val drsResolverResponse = DrsResolverResponse(
       size = Option(1234),
       hashes = FakeHashes
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/AccessUrlDownloaderSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/AccessUrlDownloaderSpec.scala
deleted file mode 100644
index df7512dd81a..00000000000
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/AccessUrlDownloaderSpec.scala
+++ /dev/null
@@ -1,59 +0,0 @@
-package drs.localizer.downloaders
-
-import cats.effect.ExitCode
-import cats.syntax.validated._
-import cloud.nio.impl.drs.AccessUrl
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import org.scalatest.prop.TableDrivenPropertyChecks._
-
-class AccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  it should "return the correct download script for a url-only access URL, no requester pays" in {
-    val fakeDownloadLocation = "/root/foo/foo-123.bam"
-    val fakeAccessUrl = "http://abc/def/ghi.bam"
-
-    val downloader = AccessUrlDownloader(
-      accessUrl = AccessUrl(url = fakeAccessUrl, headers = None),
-      downloadLoc = fakeDownloadLocation,
-      hashes = None
-    )
-
-    val expected = s"""mkdir -p $$(dirname '$fakeDownloadLocation') && rm -f '$fakeDownloadLocation' && getm --checksum-algorithm 'null' --checksum null --filepath '$fakeDownloadLocation' '$fakeAccessUrl'""".validNel
-
-    downloader.generateDownloadScript shouldBe expected
-  }
-
-  {
-    val results = Table(
-      ("exitCode", "stderr", "download result"),
-      (0, "", DownloadSuccess),
-      // In `getm` version 0.0.4 checksum failures currently exit 0.
-      (0, "oh me oh my: AssertionError: Checksum failed!!!", ChecksumFailure),
-      // Unrecognized because of non-zero exit code without an HTTP status, despite what looks like a checksum failure.
-      (1, "oh me oh my: AssertionError: Checksum failed!!!", UnrecognizedRetryableDownloadFailure(ExitCode(1))),
-      // Unrecognized because of zero exit status with stderr that does not look like a checksum failure.
-      (0, "what the", UnrecognizedRetryableDownloadFailure(ExitCode(0))),
-      // Unrecognized because of non-zero exit code without an HTTP status.
-      (1, " foobar ", UnrecognizedRetryableDownloadFailure(ExitCode(1))),
-      // Unrecognized because of zero exit status with stderr that does not look like a checksum failure.
-      (0, """ERROR:getm.cli possibly some words "status_code": 503 words""", UnrecognizedRetryableDownloadFailure(ExitCode(0))),
-      // Recognized because of non-zero exit status and an HTTP status.
-      (1, """ERROR:getm.cli possibly some words "status_code": 503 words""", RecognizedRetryableDownloadFailure(ExitCode(1))),
-      // Recognized because of non-zero exit status and an HTTP status.
-      (1, """ERROR:getm.cli possibly some words "status_code": 408 more words""", RecognizedRetryableDownloadFailure(ExitCode(1))),
-      // Recognized and non-retryable because of non-zero exit status and 404 HTTP status.
-      (1, """ERROR:getm.cli possibly some words "status_code": 404 even more words""", FatalDownloadFailure(ExitCode(1))),
-      // Unrecognized because of zero exit status and 404 HTTP status.
-      (0, """ERROR:getm.cli possibly some words "status_code": 404 even more words""", UnrecognizedRetryableDownloadFailure(ExitCode(0))),
-    )
-
-    val accessUrlDownloader = AccessUrlDownloader(null, null, null)
-
-    forAll(results) { (exitCode, stderr, expected) =>
-      it should s"produce $expected for exitCode $exitCode and stderr '$stderr'" in {
-        accessUrlDownloader.toDownloadResult(GetmResult(exitCode, stderr)) shouldBe expected
-      }
-    }
-  }
-}
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
new file mode 100644
index 00000000000..7b96ece8d0a
--- /dev/null
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
@@ -0,0 +1,114 @@
+package drs.localizer.downloaders
+
+import cats.effect.{ExitCode, IO}
+import cloud.nio.impl.drs.{AccessUrl, DrsResolverResponse}
+import common.assertion.CromwellTimeoutSpec
+import org.scalatest.prop.TableDrivenPropertyChecks._
+import drs.localizer.{ResolvedDrsUrl, URIType}
+
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import java.nio.file.Path
+
+class BulkAccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+  val ex1 = ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://my.fake/url123", None))), "path/to/local/download/dest", URIType.ACCESS)
+  val ex2 = ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://my.fake/url1234", None))), "path/to/local/download/dest2", URIType.ACCESS)
+  val ex3 = ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://my.fake/url1235", None))), "path/to/local/download/dest3", URIType.ACCESS)
+  val emptyList : List[ResolvedDrsUrl] = List()
+  val oneElement: List[ResolvedDrsUrl] = List(ex1)
+  val threeElements: List[ResolvedDrsUrl] = List(ex1, ex2, ex3)
+
+  it should "correctly parse a collection of Access Urls into a manifest.json" in {
+    val expected: String =
+      s"""|[
+          |  {
+          |    "url" : "https://my.fake/url123",
+          |    "filepath" : "path/to/local/download/dest"
+          |  },
+          |  {
+          |    "url" : "https://my.fake/url1234",
+          |    "filepath" : "path/to/local/download/dest2"
+          |  },
+          |  {
+          |    "url" : "https://my.fake/url1235",
+          |    "filepath" : "path/to/local/download/dest3"
+          |  }
+          |]""".stripMargin
+
+    val downloader = BulkAccessUrlDownloader(threeElements)
+
+    val filepath: IO[Path] = downloader.generateJsonManifest(threeElements)
+    val source = scala.io.Source.fromFile(filepath.unsafeRunSync().toString)
+    val lines = try source.mkString finally source.close()
+    lines shouldBe expected
+  }
+
+  it should "properly construct empty JSON array from empty list." in {
+    val expected: String =
+      s"""|[
+          |
+          |]""".stripMargin
+
+    val downloader = BulkAccessUrlDownloader(emptyList)
+    val filepath: IO[Path] = downloader.generateJsonManifest(emptyList)
+    val source = scala.io.Source.fromFile(filepath.unsafeRunSync().toString)
+    val lines = try source.mkString finally source.close()
+    lines shouldBe expected
+  }
+
+  it should "properly construct JSON array from single element list." in {
+    val expected: String =
+      s"""|[
+          |  {
+          |    "url" : "https://my.fake/url123",
+          |    "filepath" : "path/to/local/download/dest"
+          |  }
+          |]""".stripMargin
+
+    val downloader = BulkAccessUrlDownloader(oneElement)
+    val filepath: IO[Path] = downloader.generateJsonManifest(oneElement)
+    val source = scala.io.Source.fromFile(filepath.unsafeRunSync().toString)
+    val lines = try source.mkString finally source.close()
+    lines shouldBe expected
+  }
+
+  it should "properly construct the invocation command" in {
+    val downloader = BulkAccessUrlDownloader(oneElement)
+    val filepath: Path = downloader.generateJsonManifest(threeElements).unsafeRunSync()
+    val expected = s"""getm --manifest ${filepath.toString}"""
+    downloader.generateGetmCommand(filepath) shouldBe expected
+  }
+
+  {
+    val results = Table(
+      ("exitCode", "stderr", "download result"),
+      (0, "", DownloadSuccess),
+      // In `getm` version 0.0.4 checksum failures currently exit 0.
+      (0, "oh me oh my: AssertionError: Checksum failed!!!", ChecksumFailure),
+      // Unrecognized because of non-zero exit code without an HTTP status, despite what looks like a checksum failure.
+      (1, "oh me oh my: AssertionError: Checksum failed!!!", UnrecognizedRetryableDownloadFailure(ExitCode(1))),
+      // Unrecognized because of zero exit status with stderr that does not look like a checksum failure.
+      (0, "what the", UnrecognizedRetryableDownloadFailure(ExitCode(0))),
+      // Unrecognized because of non-zero exit code without an HTTP status.
+      (1, " foobar ", UnrecognizedRetryableDownloadFailure(ExitCode(1))),
+      // Unrecognized because of zero exit status with stderr that does not look like a checksum failure.
+      (0, """ERROR:getm.cli possibly some words "status_code": 503 words""", UnrecognizedRetryableDownloadFailure(ExitCode(0))),
+      // Recognized because of non-zero exit status and an HTTP status.
+      (1, """ERROR:getm.cli possibly some words "status_code": 503 words""", RecognizedRetryableDownloadFailure(ExitCode(1))),
+      // Recognized because of non-zero exit status and an HTTP status.
+      (1, """ERROR:getm.cli possibly some words "status_code": 408 more words""", RecognizedRetryableDownloadFailure(ExitCode(1))),
+      // Recognized and non-retryable because of non-zero exit status and 404 HTTP status.
+      (1, """ERROR:getm.cli possibly some words "status_code": 404 even more words""", FatalDownloadFailure(ExitCode(1))),
+      // Unrecognized because of zero exit status and 404 HTTP status.
+      (0, """ERROR:getm.cli possibly some words "status_code": 404 even more words""", UnrecognizedRetryableDownloadFailure(ExitCode(0))),
+    )
+    val bulkDownloader = BulkAccessUrlDownloader(null)
+
+    forAll(results) { (exitCode, stderr, expected) =>
+      it should s"produce $expected for exitCode $exitCode and stderr '$stderr'" in {
+        bulkDownloader.toDownloadResult(GetmResult(exitCode, stderr)) shouldBe expected
+      }
+    }
+  }
+}
diff --git a/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml b/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml
index 91b36d9277e..12f01e0179e 100644
--- a/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml	
+++ b/runConfigurations/Repo template_ Cromwell DRS Localizer.run.xml	
@@ -5,7 +5,7 @@
     </envs>
     <option name="MAIN_CLASS_NAME" value="drs.localizer.DrsLocalizerMain" />
     <module name="cromwell-drs-localizer" />
-    <option name="PROGRAM_PARAMETERS" value="--access-token-strategy azure drs://jade.datarepo-dev.broadinstitute.org/v1_f3c32ddd-20eb-4033-9716-46866521a3a4_8d651e95-38ce-4bc8-a8a4-8a4cd9513db1 $USER_HOME$/Downloads/NA12878_PLUMBING_wgs.g.vcf.gz.tbi --identity-client-id identity" />
+    <option name="PROGRAM_PARAMETERS" value="--access-token-strategy google drs://drs.anv0:v1_e2151834-13cd-4156-9ea2-168a1b7abf60_0761203d-d2a1-448e-8f71-9f81d80ddd9d $USER_HOME$/Downloads/test/plumbing" />
     <method v="2">
       <option name="Make" enabled="true" />
     </method>

From 8395859bad1c44565f79f9494ad7d6c2301dc890 Mon Sep 17 00:00:00 2001
From: Henrique Ribeiro <henriqueribeiro@users.noreply.github.com>
Date: Mon, 18 Sep 2023 13:41:03 +0100
Subject: [PATCH 217/326] Develop AWS (#35)

* 85 release (#28)

* Update cromwell version from 83 to 84

* BW-1255 Implement POST /runs endpoint (#6779)

* Adding route

* Fixing HTTP method error

* All formFields made optional

* A compliling state

* Saving

* Saving

* All three endpoints functioning as expected; updated RESTAPI.md

* Updated response for submission from 200 to 201 to pass tests

* Test submission response

* Moved updated submission response to askSubmit

* test

* updating RESTAPI.md

* saving

* Adding utility file for submitRequest

* cleanup

* Update awssdkv from 2.17.152 to 2.17.194 (#6814)

* BW-1305 Swagger Update (#6818)

* Properly documenting metadataArchiveStatus in WorkflowQueryResult model

* Update docs

* BT-710 Add configs for BlobPathBuilderFactory (#6817)

BT-710 Add configs for BlobPathBuilderFactory

* BW-1305 Make "name" optional in workflow query response (#6821)

* BT-724 Fix BlobPathBuilder failing on retrieving existing filesystem (#6816)

Modify blobPathBuilder to fallback to creating a filesystem if one is not found

* Logging updates: (#6813)

* [BT-698] first pass on BlobTokenGenerator with E2E test (#6824)

* first pass on BlobTokenGenerator with E2E test

* update BlobPathBuilder constructor args in test

* account -> container level client

* [BT-687] specify correct types (#6829)

* specify correct types

* fix test with new type

* remove type declarations in function call

* remove unnecessary sas-token config

* BW-1206 - Combine all Wes Endpoints & add Tests (#6833)

* Add tests, getting frid of WesRunRoutes.scala

* wesWorkflowId fix, ec implicits errors gone

* Refactoring path for GET /runs

* Indentation fix

* Commit to rollback

* Revert "Indentation fix"

This reverts commit 63fc4842c9d4eff68ec9cb7c3ef19e110696598b.

* PR trigger

* Optimize imports

* Missed import

* BW-1354 - Porting CBAS preliminary step (#6837)

* Getting rid of shared utility file; Adding/Updating WES version of submit.

* Edit spec file

* Adding Wes-like error

* BW-1378 Addl CromIAM user enablement checks (#6826)

* Update cromwell version from 84 to 85

* BW-1393 Release doc updates (#6839)

* BT-732 Checksum validation for blobs read by engine (#6838)

* Draft support for optional FileHash

* Draft getMd5 for BlobPath

* Resolve non-parallel IO to fix tests

* Checksum validation for BlobPath

* Nicer error message

* Test for missing Blob hash

* Break attr acquisition into separate method

* Cleanup, comments

* In-progress tests of blob hash command

* Remove test

* Remove unused import

* BT-711 Refresh SAS token for filesystem on expiry (#6831)

* BT-711 Refresh SAS token for filesystem on expiry

* Rough cut of token refresh using exceptions

* Ignore tests, and minor cleanup

* Remove stray line

* Draft of manager class for handling expiring file systems

* Style fixes

* Refactor of blobfilesystemManager and tests covering its functionality

* Refined tests to validate close filesystem as separate unit

* Ignore connected tests

* Clean up of some things

* Refactor BlobFileSystemManager to separate file, and some other cleanup

* Some additional scala-ifying

* Small cleanup

* Correcting imports

* trigger tests

* trigger tests

* Batch 1 of scala steward updates (#6903)

* Batch 1 of scala steward updates

* Rollback snakeYAML

* Attempt 3, with only the passing dependancies

* Revert google API and Big Query udpates

* Winding back other google deps

* rollback remaining google updates

* trigger tests

* trigger tests

* [BW-1398] Migrate PKs to BIGINT (#6907)

* BT-745  Batch 2 of scala steward updates (#6906)

* Update SBT to 2.0.0

* Fix sbt-git import

* Update mouse to 1.0.11

* Update rhino 1.7.14

* SUP-692 Retry with more memory after RC 137 (#6912)

* Reorder execution result checks so 137 can retry with more memory

* Test for memory retry after 137 RC

* Fix test expectations

* Make memory retry checks consistent

* Revert changes to existing test

* Rename retryWithMoreMemory to outOfMemoryDetected

* Scala steward updates batch 3 (#6913)

* Scala steward updates batch 3

* WX-745 Batch 4 scala steward updates (#6916)

* WX-746 Localize all DRS inputs in a single Action (#6914)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* WX-755 Build all images instead of just Cromwell (#6919)

* WX-755 Add `isRelease` option for Docker builds (#6923)

* WX-755 Cromwell/CromIAM automatically board train (#6924)

* WX-755 Fix environment variable syntax (#6926)

* WX-743 Enable TES task creation with BlobPaths (#6921)

* Give blob SAS tokens write permission

* Case class wrapper for subscription id

* Resolve duplicate container name in absolute BlobPath

* Ignored test demonstrating correct absolute path generation

* Update filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala

Co-authored-by: Brian Reilly <breilly@broadinstitute.org>

* PR feedback

Co-authored-by: Brian Reilly <breilly@broadinstitute.org>

* [WX-765] Update snakeyaml to 1.33 (#6927)

* update snakeyaml to 1.33

* Don't use deprecated no-arg Constructor constructor

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* WM-1414 Refactoring WesRunLog to omit Cromwell's "workflowLog" object (#6925)

* Upgrade Postgres to 42.4.1 (#6932)

* WX-735 Fix incorrect and/or nondeterministic filesystem ordering (#6930)

* WX-772 Update Scala to 2.13.9 (#6928)

* Update Scala to 2.13.9

* Try updating sbt-scoverage

* Does this version exist anywhere we can see?

* This version actually exists

* Update library version to remove conflict

* Codegen version

* Fix fun new 2.13.9 compiler errors

* Resolve warnings

* Newest Scala?

* I guess not

* Does this please Travis?

* force ci

* Back out changes to generated code

Co-authored-by: Adam Nichols <aednichols@gmail.com>

* WX-781 Bump jackson-databind in /CromwellRefdiskManifestCreator (#6935)

Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.13.2.2 to 2.13.4.1.
- [Release notes](https://github.com/FasterXML/jackson/releases)
- [Commits](https://github.com/FasterXML/jackson/commits)

---
updated-dependencies:
- dependency-name: com.fasterxml.jackson.core:jackson-databind
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* WX-808 Host allowlist for HTTP imports (#6938)

* `hostAllowlist` that allows everything

* Refactor

* Stick allow list in HttpResolver

* Better default config

* Allow list tests

* Make it build

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Update commons text to 1.10.0 (#6937)

* WX-751 Token refresh signal for monitoring (#6939)

* Log messages

* `DEBUG` -> `INFO`

* WX-744 Optionally rewrite blob paths to appear as local paths (#6941)

* Modify blob paths for TES

* Make blob transformation configurable

* Update supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Apply PR feedback in second place

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Update changelog for wdl http allow list (#6944)

* WM-1491 Fixing Cromwell-client (#6943)

* More updated client for use in cbas

* Removing excess code

* Fix client build script (#6945)

* WX-837: Remove CWL references from documentation (#6949)

* wx-837 removed cwl references in markdown doc files

* wx-837 removed cwlParsingOverview.md, updated mkdocs.yml

* wx-837 updated cromwell.yaml, generated new RESTAPI file

* WX-728 Add configurable WSM client to Cromwell (#6948)

* Dependencies

* Compiles but no tests

* Formatting

* Moar exclusions

* Update to latest WSM

* Add additional dependency

* We need some UUID here to make the request

* Formatting

* Clarify what is fake

* Formatting

* Use our own version of Jersey and Jackson stuff

* Port-in Khalid's changes (thank you!)

Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>

* Test longevity

Don't break the test if someone decides to add a cert to `ws.org`

* Cleanup

* Cleanup

* Cleanup

* Adjust TES config file for CI

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>

* CROM-6554: Removed PAPIv1 references from doc (#6950)

* crom-6554 removed references to PAPI v1 from doc

* crom-6554 pr feedback, reworded doc to use example conf as a starting point

* WX-833 Real Azure DRS Credentials (#6952)

* Remove B2C reference from name

* Get token for current user rather than getting from KeyVault

* Remove KeyVault config for engine

* Remove KeyVault config for DRSLocalizer

* Remove KeyVault dependency

* Remove KeyVault support from localizer repo template

* Cleaned up and working Azure token acquisition for engine

* Collapse localizer's AccessTokenStrategy into DrsCredentials

* Cleanup

* WX-853 Remove most CWL (#6955)

* WX-696 Enable getting SAS token from WSM (#6954)

* WX-696 Enable getting SAS token from WSM

* Wire container resource id from config

* Move resource-container-id config path

* First pass at config for WSM

* Remove unused singleton config

* Tests for new config

* Fix config parsing

* Modified b2c token to be provided each time

* Remove singletonConfig arg from factory

* Restore types to factory configs

* Clean up comments and empty token default

* Default to config b2c before searching environment

* Fix token default on api client

* Fix test

* Refactor error handling for when there is no token

* Remove token constructor arg for clientProvider

* Move configs to global singleton config

* Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

* default -> override

* Add override token to test

* Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Parentheses

* Reduce token timeout

* Move AzureCredentials to separate file

* Make AzureCredentials an object

* WSM token cleanup

* Config refactor (#6960)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Initial blob token documentation

* Refine language in BlobSasTokenGenerator

* Update comment and formatting

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* WX-853 Remove CWL language factory, Centaur runner (#6961)

* WX-842 Add Pact Dependency for Cromwell (#6962)

* WX-842 Add Pact Dependency for Cromwell

* Remove incomplete test spec

* Initial Pact Test

* Fix pact so it compiles

* Add breadcrumb comment and clean up

* ID-125 Add support for drshub, rename all the things (#6959)

* Add support for drshub, rename all the things

* fallback to martha if resolver is not in config

* WX-867 Translate crc32c hashes to b64 for getm (#6970)

* Translate crc32c hashes to b64 for getm

* Update tests

* Remove obsolete b64 handling for md5, centralize hex validation

* Restore old test, fix other test

* WX-843 Workflow failure reason should accurately indicate issues opening blob filesystem (#6965)

* WX-859 Accept workflow execution identity in config (#6967)

* WX-892 Trim down `ValueStore` logging to prevent OOMs (#6981)

* Add Nirvana 3.18.1 reference image test, minor cleanup [VS-705] (#6975)

* WX-863 Turn off Azure NIO logging (#6982)

* Turn off Azure NIO logging

* Poke Travis

* WM-1616: Allow repeating attempts at initialization (take 2) (#6985)

* WX-878 Single shared BlobFileSystemManager (#6986)

* Make BlobFileSystemManager shared across all BlobPathBuilders

* Update TES conf file to reflect new singleton config

* Shell escape reference image  files [VS-796] [WX-910] (#6989)

* WX-769 `disks` compatibility for TES backend (#6991)

* Update FiveMinuteIntro.md (#6994)

* WX-906 Sbt Unit Tests as Github Actions (#6992)

* WX-926 Support falling back to OCI Manifest Format (#7003)

* WX-926 Support falling back to OCI Manifest Forma

* Only mount reference disks if requested [WX-925] (#7001)

* [WM-1646] Add missing fields for `WorkflowDescription` for WomTool /describe endpoint to Swagger (#7004)

* WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status (#6980)

* WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status

* Address feedback

* Address feedback (#6997)

* Address additional feedback (#7000)

* Fix copy/paste error (#7005)

* Address additional feedback

* Fix copy/paste error

* Trigger CI

---------

Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Centaur reference image test should validate symlinks [VS-796] (#6996)

* WX-903 Pre-GHA test suite disablement

* WX-877 Update CHANGELOG for release 85 (#7011)

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Katrina P <68349264+kpierre13@users.noreply.github.com>
Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Co-authored-by: Christian Freitas <christian.j.freitas@gmail.com>
Co-authored-by: Saloni Shah <salonipshah11@gmail.com>
Co-authored-by: kshakir <kshakir@broadinstitute.org>
Co-authored-by: mspector <michael.l.spector@gmail.com>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
Co-authored-by: Brian Reilly <breilly@broadinstitute.org>
Co-authored-by: Adam Nichols <aednichols@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Co-authored-by: Christian Freitas <cfreitas@broadinstitute.org>
Co-authored-by: Trevyn Langsford <tlangs@broadinstitute.org>
Co-authored-by: Miguel Covarrubias <mcovarr@users.noreply.github.com>
Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com>
Co-authored-by: Tom Wiseman <tom.h.wiseman@gmail.com>
Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>

* Develop aws (#29)

* stuck on globbing

* efs works, no callcaching

* update readme

* extended EFS support

* fix for globbing in nested scatters

* updated config for globbing, to prevent issues with empty folders

* efs fixes : support paths with over 127 characters, fix delocalization of efs-based globs (#32)

* Develop aws (#34)

* efs fixes : support paths with over 127 characters, fix delocalization of efs-based globs

* add deployment manual, fix issue with empty disks

* update documentation

* update documentation

* update documentation

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Katrina P <68349264+kpierre13@users.noreply.github.com>
Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Co-authored-by: Christian Freitas <christian.j.freitas@gmail.com>
Co-authored-by: Saloni Shah <salonipshah11@gmail.com>
Co-authored-by: kshakir <kshakir@broadinstitute.org>
Co-authored-by: mspector <michael.l.spector@gmail.com>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
Co-authored-by: Brian Reilly <breilly@broadinstitute.org>
Co-authored-by: Adam Nichols <aednichols@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Co-authored-by: Christian Freitas <cfreitas@broadinstitute.org>
Co-authored-by: Trevyn Langsford <tlangs@broadinstitute.org>
Co-authored-by: Miguel Covarrubias <mcovarr@users.noreply.github.com>
Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com>
Co-authored-by: Tom Wiseman <tom.h.wiseman@gmail.com>
Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>
Co-authored-by: geertvandeweyer <geertvandeweyer@gmail.com>
---
 README.md                                     |  10 +-
 .../StandardCacheHitCopyingActor.scala        |   7 +-
 ...wsBatchAsyncBackendJobExecutionActor.scala |   7 +-
 .../backend/impl/aws/AwsBatchJob.scala        |  17 +-
 .../impl/aws/AwsBatchRuntimeAttributes.scala  |   7 +-
 .../scala/cromwell/backend/impl/aws/DEPLOY.md | 243 ++++++++++++++++++
 .../scala/cromwell/backend/impl/aws/README.md |  37 ++-
 .../AwsBatchBackendFileHashingActor.scala     |  11 +-
 .../impl/aws/io/AwsBatchGlobFunctions.scala   |   5 +-
 .../backend/impl/aws/io/AwsBatchVolume.scala  |   4 +-
 10 files changed, 319 insertions(+), 29 deletions(-)
 create mode 100644 supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md

diff --git a/README.md b/README.md
index bbb38795420..d0d78091356 100644
--- a/README.md
+++ b/README.md
@@ -3,9 +3,15 @@
 
 ## Welcome to the "AWS-friendly" Cromwell
 
-More information regarding AWS features can be found [here](https://github.com/henriqueribeiro/cromwell/tree/master/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws)
+The AWS-friendly Cromwell is an optimized fork of the main cromwell release.  We try to keep it up-to-date with new releases, while keeping our additions functional. 
 
-Contact: henrique [at] loka [dot] com 
+* Information regarding AWS features can be found [here](supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md)
+* Information regarding deployment can be found [here](supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md)
+
+Contact: 
+* henrique [at] loka [dot] com 
+* geert [dot] vandeweyer [at] uza [dot] be
+* Join the #AWS channel at the [Cromwell Slack workspace](https://join.slack.com/t/cromwellhq/shared_invite/zt-dxmmrtye-JHxwKE53rfKE_ZWdOHIB4g).
 
 Cromwell is an open-source Workflow Management System for bioinformatics. Licensing is [BSD 3-Clause](LICENSE.txt).
 
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
index e23ecd277af..4b9eecc68a7 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
@@ -230,6 +230,8 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
               logCacheHitCopyCommand(command)
             case Some(command: IoTouchCommand) =>
               logCacheHitTouchCommand(command)
+            case Some(command: IoWriteCommand) =>
+              logCacheHitWriteCommand(command)
             case huh =>
               log.warning(s"BT-322 {} unexpected commandsToWaitFor: {}", jobTag, huh)
           }
@@ -310,7 +312,10 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
     }
 
   private def logCacheHitTouchCommand(command: IoTouchCommand): Unit =
-    log.info(s"BT-322 {} cache hit for file : {}", jobTag, command.toString)
+    log.info(s"BT-322 {} cache touch hit for file : {}", jobTag, command.toString)
+
+  private def logCacheHitWriteCommand(command: IoWriteCommand): Unit =
+    log.info(s"BT-322 {} cache write hit for file : {}", jobTag, command.toString)
                                 
   def succeedAndStop(returnCode: Option[Int], copiedJobOutputs: CallOutputs, detritusMap: DetritusMap): State = {
     import cromwell.services.metadata.MetadataService.implicits.MetadataAutoPutter
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 87ef19e80cb..498bd2ec4fe 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -417,8 +417,10 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     val output = if (configuration.efsMntPoint.isDefined && 
                      configuration.efsMntPoint.getOrElse("").equals(disk.toString.split(" ")(1)) &&
                      ! runtimeAttributes.efsDelocalize) {
-            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), makeSafeAwsBatchReferenceName(womFile.value), relpath, disk)
+            // name: String, s3key: String, local: Path, mount: AwsBatchVolume
+            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), womFile.value, relpath, disk)
         } else {
+            // if efs is not enabled, OR efs delocalization IS enabled, keep the s3 path as destination.
             AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), destination, relpath, disk)
         }
     List(output)
@@ -448,7 +450,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
                      ! runtimeAttributes.efsDelocalize) {
                         (globDirectory, globListFile)
                      } else {
-                        (callRootPath.resolve(globDirectory).pathAsString, callRootPath.resolve(globListFile).pathAsString)
+                        // cannot resolve absolute paths : strip the leading '/'
+                        (callRootPath.resolve(globDirectory.toString.stripPrefix("/")).pathAsString, callRootPath.resolve(globListFile.toString.stripPrefix("/")).pathAsString)
                      }
     // return results
     return (
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 48f286dc436..97302357175 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -259,7 +259,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  b=$$(( 5 * 1024 * 1024 ))
          |  chunk_size=$$(( a > b ? a : b ))
          |  echo $$chunk_size
-         }
+         |}
+         |
          |function _check_data_integrity() {
          |  local local_path=$$1
          |  local s3_path=$$2
@@ -276,7 +277,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
          |        { echo "Attempt to get head of object failed for $$s3_path." && return 1 ; }
          |  # local
-         |  local_content_length=$$(LC_ALL=C ls -dn -- "$$local_path" | awk '{print $$5; exit}' ) || 
+         |  local_content_length=$$(LC_ALL=C ls -dnL -- "$$local_path" | awk '{print $$5; exit}' ) || 
          |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }   
          |  # compare
          |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
@@ -303,10 +304,12 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
 
     //generate a series of s3 commands to delocalize artifacts from the container to storage at the end of the task
     val outputCopyCommand = outputs.map {
+      // local is relative path, no mountpoint disk in front.
       case output: AwsBatchFileOutput if output.local.pathAsString.contains("*") => "" //filter out globs
-      case output: AwsBatchFileOutput if output.name.endsWith(".list") && output.name.contains("glob-") =>
-        Log.debug("Globbing : check for EFS settings.")
+      case output: AwsBatchFileOutput if output.s3key.endsWith(".list") && output.s3key.contains("glob-") =>
+        Log.debug("Globbing  : check for EFS settings.")
         val s3GlobOutDirectory = output.s3key.replace(".list", "")
+        // glob paths are not generated with 127 char limit, using generateGlobPaths(). name can be used safely 
         val globDirectory = output.name.replace(".list", "")
         /*
          * Need to process this list and de-localize each file if the list file actually exists
@@ -317,9 +320,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
            Log.debug("EFS glob output file detected: "+ output.s3key + s" / ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}")
            val test_cmd = if (efsDelocalize.isDefined && efsDelocalize.getOrElse(false)) {
                     Log.debug("delocalization on EFS is enabled")
+                    Log.debug(s"Delocalizing $globDirectory to $s3GlobOutDirectory\n")
                     s"""
-                        |touch ${output.name}
-                        |_s3_delocalize_with_retry ${output.name} ${output.s3key}
+                        |touch ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}
+                        |_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}
                         |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi
                         |""".stripMargin
                 } else {
@@ -357,6 +361,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
           | """.stripMargin
         } else {
           // default delocalization command.
+          Log.debug(s"Delocalize from ${output.name} to ${output.s3key}\n")
           s"""
              |touch ${output.name}
              |_s3_delocalize_with_retry ${output.name} ${output.s3key}
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index ceca53a7c85..235927ab07c 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -188,10 +188,11 @@ object AwsBatchRuntimeAttributes {
         rtc.getAnyRef(AwsBatchRuntimeAttributes.DisksKey).asInstanceOf[String] // just to prevent complaints about var/val
     } catch {
         case _: ConfigException.Missing => 
-           ""
+           "local-disk"
     }
-    // combine
-    val disks = s"${efs_disks},${rtc_disks}".split(",").toSet.mkString(",")
+    // combine and remove empty values
+    val disks = s"${efs_disks},${rtc_disks}".split(",").toSet.filterNot(_.isEmpty).mkString(",")
+    Log.debug(s"Disks: ${disks}")
     val runtimeConfig = Some(rtc.withValue(AwsBatchRuntimeAttributes.DisksKey, ConfigValueFactory.fromAnyRef(disks)))
     return runtimeConfig
   }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md
new file mode 100644
index 00000000000..856dd46af99
--- /dev/null
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md
@@ -0,0 +1,243 @@
+AWS/CROMWELL DEPLOYMENT
+=======================
+
+Overview
+--------
+
+AWS Cloudformation is used to deploy Cromwell-AWS.  As resources are created, costs might be generated along the way.  To make sure all generated data is cleaned, remove the stacks again using the CloudFormation Console.
+
+
+Deployment
+----------
+
+Deployment of the cromwell/AWS environment can be performed using the three cloudformation stacks:
+
+1. VPC : setup of the networks
+2. Resources : setup of the compute environment, job queues and storage solutions
+3. Cromwell : setup of an EC2 instance and RDS, hosting the cromwell server and submission tools. 
+
+Along the way, all necessary IAM rols are generated. 
+
+*Note:* This tutorial uses the eu-west-2 (London) region. Change where appropriate for you setup
+
+*Note:* Select "Preserve successfully provisioned resources" as failure option to review problems in depth. 
+
+### STEP 1 : SETUP VPC 
+
+The default VPC settings create both private and public subnets. Private subnets are used for the compute environment and database setup. Public subnets are used to host the cromwell server instance. 
+
+
+Used Template : 
+
+```
+https://cromwell-aws-cloudformation-templates.s3.eu-west-1.amazonaws.com/root-templates/aws-vpc.template.yaml
+```
+
+Steps:
+
+1. Go to the CloudFormation console in your region : https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/
+
+2. Select "Stacks" in the left menu, then "Create Stack" on the top right. Choose "With new resources" :[link](https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/stacks/create)
+
+3. Select "Template is ready", and use "Amazon S3 URL" as template source. Provide the yaml file URL provided above.
+
+4. Enter a stack name. 
+
+5. Select availability zones, more is better. This gives Batch more zones to find suitable instances. 
+
+6. Match "Number of availability zones" to your selection. 
+
+7. Other settings can be left as default. 
+
+8. Review, confirm and submit on final page. 
+
+
+
+### STEP 2 : SETUP COMPUTE RESOURCES
+
+The default setup configures a spot and on-demand queue, a cromwell-specific bucket and the necessary IAM roles to run BATCH jobs. See below for further configuration to extend this setup.
+
+Used Template : 
+
+```
+https://cromwell-aws-cloudformation-templates.s3.eu-west-1.amazonaws.com/root-templates/gwfcore-root.template.yaml
+```
+
+Steps:
+
+1. Go to the CloudFormation console in your region : https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/
+
+2. Select "Stacks" in the left menu, then "Create Stack" on the top right. Choose "With new resources" :[link](https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/stacks/create)
+
+3. Select "Template is ready", and use "Amazon S3 URL" as template source. Provide the yaml file URL provided above.
+
+4. Enter a stack name. 
+    * *Note:* This name is referred to as "GWFCORE NameSpace" in STEP 3
+    * *Note:* The name gets reflected in queue names etc. Keep it short. 
+
+5. Provide an s3 bucket name to host cromwell temp data, results and runtime requirements. 
+    * *Note:* If the bucket exists, it must be located in the same region. 
+    * *Note:* If the bucket exists, specify this in the next field
+
+6. Select the VPC ID generated in STEP 1
+
+7. Provide the PRIVATE subnets (all of them) from STEP 1, for the compute environment. Match the number of subnets to your selection
+
+8. Set the Max vCPU count for default (spot) and High Priority (on-demand) compute environment.
+    * *Note:*  Check your quota per region [here](https://eu-west-2.console.aws.amazon.com/servicequotas/home/services/ec2/quotas), look for "Standard"
+
+9. Set the maximal spot bidding price.
+
+10. Select the list of instance types to be used. Default "optimal" value is a safe bet. 
+    * *Note:*  To edit this, clone the compute environment in the [Batch dashboard](https://eu-west-2.console.aws.amazon.com/batch/home?region=eu-west-2#compute-environments), and play around with the options. 
+
+11. *Optional:* Create an EFS filesystem:
+    * *Note:* EFS is a distributed filesystem. Keeping large intermediate results on EFS can improve perforance by reducing S3/EC2 transfer times
+    * *Note:* By default, EFS performance is limited. Change the setup of the volume using the [console](https://eu-west-2.console.aws.amazon.com/efs/home?region=eu-west-2#/file-systems) to "Enhanced/Elastic" Performance. Consider the costs this implies! 
+    * *Note:* It's recommended to create a new EFS, to make sure that mounting and network settings are correctly setup. 
+
+
+12. *Optional:* Create an FSx filesystem:
+    * *Note:* see documentation in [README](README.md)
+
+13. Other settings can be left as default. 
+
+14. Review, confirm and submit on final page. 
+
+
+### STEP 3 : SETUP CROMWELL SERVER
+
+The default setup deploys a small t3.medium EC2 instance with 25Gb of storage and a RDS aurora-mysql database, to host cromwell, and some interaction tools. Although enough for testing, you'll probably have to scale up the instance for production runs. Alternatively, you can deploy cromwell on local infrastructure, preventing the RDS/EC2 costs.  See below for details.
+
+
+Used Template : 
+
+```
+https://cromwell-aws-cloudformation-templates.s3.eu-west-1.amazonaws.com/root-templates/cromwell-resources.template.yaml
+```
+
+Steps:
+
+1. Go to the CloudFormation console in your region : https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/
+
+2. Select "Stacks" in the left menu, then "Create Stack" on the top right. Choose "With new resources" :[link](https://eu-west-2.console.aws.amazon.com/cloudformation/home?region=eu-west-2#/stacks/create)
+
+3. Select "Template is ready", and use "Amazon S3 URL" as template source. Provide the yaml file URL provided above.
+
+4. Provide a stack name.
+
+5. Provide a name space.
+    * *Note:* This name is reflected in the key name. Keep it short.
+
+6. Provide the GWFCORE Namespace from STEP 2
+
+7. Specify the VPC ID, from STEP 1
+
+8. Select a PUBLIC subnet for the cromwell server
+
+9. Select 2+ PRIVATE subnets for the RDS database
+
+10. Set the instance root volume size to 25+ Gb
+
+11. Set a password for the cromwell database
+
+12. Provide Filesystem details for EFS if specified in STEP 2:
+    * *Note:* Get the values from [the dashboard](https://eu-west-2.console.aws.amazon.com/efs/home?region=eu-west-2#/file-systems)
+    * *Note:* Accesspoint is listed under filesystem details, tab "Access Points"
+    * *Note:* Security Group is listed under filesystem details, tab "Network"
+
+13. Other settings can be left as default. 
+
+14. Review, confirm and submit on final page. 
+
+
+When the stack is ready, use the following commands to retrieve your SSH key. The exact name of the key can be retrieved from the EC2 instance "Connect" page. 
+
+```
+KEY_NAME=key-<stack_namespace>
+REGION=<region>
+
+# GET KEY ID :
+KEY_ID=$(aws ec2 describe-key-pairs --filters Name=key-name,Values=${KEY_NAME} --query KeyPairs[*].KeyPairId --output text --region ${REGION})
+
+# GET KEY CONTENTS
+mkdir -p ~/.ssh/.keys
+aws ssm get-parameter --region ${REGION} --name /ec2/keypair/${KEY_ID} --with-decryption --query Parameter.Value --output text > ~/.ssh/.keys/${KEY_NAME}.pem
+chmod 600 ~/.ssh/.keys/${KEY_NAME}.pem
+
+```
+
+
+
+Post Install Optimizations
+--------------------------
+
+### EFS 
+
+EFS data is not cleaned up automatically. Consider adding a "cleanup" step in your production WFs, to keep the storage footprint/costs low.
+
+Edit settings [here](https://eu-west-2.console.aws.amazon.com/efs/home?region=eu-west-2#/file-systems). Select the FS and "edit"
+
+* Performance : "Enhanced":"Elastic" Throughput mode is recommended for large workflows. consider extra costs
+* Lifecycle management : Consider moving data to infrequent access, to reduce costs of "forgotten" data. 
+
+### S3 
+
+The cromwell temporary data and results are located in the bucket specified in STEP 2. To reduce your storage footprint/costs, consider setting up lifecycle management. 
+
+* *cromwell-execution/* : Contains analysis results and logs for each executed workflow. 
+* *scripts/* : contains the runtime scripts for each executed task 
+
+To set up a lifecycle:
+
+* go to the [s3 console](https://s3.console.aws.amazon.com/s3/buckets?region=eu-west-2), and select the bucket from STEP 1
+* Select the "Management" tab and "Create Lifecycle rule"
+* analysis results:
+    * Set name : e.g. "Prune cromwell-execution"
+    * Set prefix "cromwell-execution"
+    * Choose actions : "Expire current versions of objects" and "Delete expired object delete markers or incomplete multipart uploads"
+    * Set time limits for  after which objects are deleted (expired).
+    * Enable "delete incomplete multipart upload" checkbox and set time. 
+* scripts:
+    * repeat steps above, with prefix "scripts"
+
+
+### LOCAL CROMWELL INSTANCE
+
+Running cromwell locally has the benefit of not running an EC2 instance 24/7.  However, consider the following points: 
+
+* Run cromwell as a user with a default AWS IAM profile set to the same region, and with sufficient permissions to interact with ECR, Batch and S3. 
+
+* Setup a local database, or setup ingress rules on the RDS security group. 
+
+* Consider load balancing by running multiple instances : see [here](https://cromwell.readthedocs.io/en/stable/Scaling/)
+
+* for EFS, there are specific concerns:
+    * expose EFS to your local network : 
+        * Run a cheap (e.g t4g.nano) instance mounting the EFS share, assign a PEM key to access it
+        * Setup sshfs to mount the EFS share from that instance to your local machine at "/mnt/efs"
+    * REDUCE network traffic by enabling the "check-sibling-md5" and "efsMakeMD5" settings
+
+
+### COMPUTE ENVIRONMENT
+
+* You might play around with the instance types to get more options:
+    * clone the compute environment
+    * double check all network settings ! 
+    * replace the "optimal" type by "*.family" types. There is maximal number of entries, so using whole families allows more types
+
+* Extra Queues : You might consider a dedicated queue for high disk/network jobs, by altering the launch template:
+    * Go to Batch console, select the spot compute environment and open the JSON tab. Look for "launchTemplateName" (eg lt-06fa9fee031254098)
+    * Go to EC2 console, select "Launch Templates" in the menu on the left, and search for your launch template
+    * On details, select "Modify Template (create new version)" in the top right under "Actions"
+    * On the resulting page, add a description (eg "HighNetwork"), and then open advanced settings at the bottom of the page
+    * At the bottom, look in "User Data". About halfway, set EBS_* settings. EBS_IOPS can go as high as 16,000 and EBS_THROUGHPUT can go as high as 1,000Mbs/s
+    * Now clone the compute environment (double check all network settings and roles)
+        * specify "exact" launch template version to the version you created. 
+        * set instance type to network/disk optimized machines (eg m5zn.6xlarge)
+        * have a blazing fast I/O machine (tests reached constant simultaneous 1Gb/s upload and 1gb/s download, while transferring novaseq data from basespace to AWS/S3)
+
+
+ 
+
+
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index a1cdce0ba1b..613607da42a 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -29,6 +29,21 @@ defined.
 This infrastructure and all the associated configuration still exists; however,
 it is moved out of the Cromwell configuration.
 
+Deployment
+----------
+
+Deployment of the cromwell/AWS environment can be performed using the three cloudformation stacks:
+
+1. VPC : setup of the networks
+2. Resources : setup of the compute environment, job queues and storage solutions
+3. Cromwell : setup of an EC2 instance and RDS, hosting the cromwell server and submission tools. 
+
+Along the way, all necessary IAM rols are generated. 
+
+The full documentation is available [here](DEPLOY.md)
+
+
+
 Features
 ---------------------
 ### Docker Hub Authentication
@@ -42,7 +57,7 @@ Docker Hub authentication for AWS Backend enable users to access and use private
 dockerhub { token = "<enconded-string-from-point-2>" }
 ```
 
-Stack must be deployed through https://github.com/aws-samples/aws-genomics-workflows.
+
 
 ### `awsBatchRetryAttempts`
 
@@ -154,11 +169,9 @@ backend {
 }
 
 // set the keys for Out-Of-Memory killing. 
-// system.io.memory-retry-error-keys
-system{
-    io{
-        memory-retry-error-keys = ["OutOfMemory","Killed"]
-    }
+// system.memory-retry-error-keys
+system {
+    memory-retry-error-keys = ["OutOfMemory","Killed"]
 }
 ```
 
@@ -169,6 +182,14 @@ Workflow specific runtime options : `workflow_options.json`:
 }
 ```
 
+Or specify it in the cromwell config as : 
+
+```
+workflow-options {
+    memory-retry-multiplier = 1.5
+}
+```
+
 When providing the options.json file during workflow submission, jobs that were terminated due to insufficient memory will be retried 6 times, with increasing memory allocation. For example 4Gb => 6Gb => 9Gb => 13.5Gb => ... 
 
 Note: Retries of jobs using the `awsBatchRetryAttempts` counter do *not* increase memory allocation. 
@@ -340,8 +361,8 @@ The following workflow highlights the following features:
 version 1.0
 workflow TestEFS {
     input {
-        # input file for WF is located on S3
-        File s3_file = 's3://aws-quickstart/quickstart-aws-vpc/templates/aws-vpc.template.yaml'
+        # input file for WF is located on a public S3
+        File s3_file = 's3://cromwell-aws-cloudformation-templates/root-templates/aws-vpc.template.yaml'
         # set an input parameter holding the working dir on EFS
         String efs_wd = "/mnt/efs/MyTestProject"
     }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
index 41cb1dae97f..66287a781af 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
@@ -54,14 +54,19 @@ class AwsBatchBackendFileHashingActor(standardParams: StandardFileHashingActorPa
   override def customHashStrategy(fileRequest: SingleFileHashRequest): Option[Try[String]] = {
     val file = DefaultPathBuilder.get(fileRequest.file.valueString)
     if (aws_config.efsMntPoint.isDefined && file.toString.startsWith(aws_config.efsMntPoint.getOrElse("--")) && aws_config.checkSiblingMd5.getOrElse(false)) {
-            // check existence of the sibling file
             val md5 = file.sibling(s"${file.toString}.md5")
-            if (md5.exists) {
+            // check existance of the file : 
+            if (!file.exists) {
+                // if missing, cache hit is invalid; return invalid md5
+                Some("File Missing").map(str => Try(str))
+            }
+            // check existence of the sibling file
+            else if (md5.exists) {
                 // read the file.
                 val md5_value: Option[String] = Some(md5.contentAsString.split("\\s+")(0))
                 md5_value.map(str => Try(str))
             } else {
-                // No sibling found, fall back to default.
+                // File present, but no sibling found, fall back to default.
                 None
             }
             
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
index 18505f6d866..1706f55370f 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
@@ -71,6 +71,7 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
     //  - according to those values : write the pattern as s3:// or as local path. 
     //  - get the wf id from the config settings.
 
+    // this function reads in the globfile and locates globbed files : "local" or NIO access is needed to the files. 
     // for now : hard coded as local at mount point /mnt/efs.
     val wfid_regex = ".{8}-.{4}-.{4}-.{4}-.{12}".r
     val wfid = callContext.root.toString.split("/").toList.filter(element => wfid_regex.pattern.matcher(element).matches()).lastOption.getOrElse("")
@@ -79,7 +80,7 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
     val listFilePath = if (pattern.startsWith("/mnt/efs/")) {
         DefaultPathBuilder.get(globbedDir + "/." + globPatternName + ".list")
     } else {
-        callContext.root.resolve(s"${globPatternName}.list")
+        callContext.root.resolve(s"${globbedDir}/.${globPatternName}.list".stripPrefix("/"))
     }
     asyncIo.readLinesAsync(listFilePath.toRealPath()) map { lines =>
       lines.toList map { fileName =>
@@ -87,7 +88,7 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
         if (pattern.startsWith("/mnt/efs/")) {
             s"${globbedDir}/.${globPatternName}/${fileName}"
         } else {
-            s"${callContext.root}/${globPatternName}/${fileName}"
+            callContext.root.resolve(s"${globbedDir}/.${globPatternName}/${fileName}".stripPrefix("/")).pathAsString
         }
       }
     }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala
index 769c2c2f5d8..563834e8d06 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala
@@ -56,7 +56,6 @@ object AwsBatchVolume {
   val LocalDiskPattern: Regex = raw"""^\s*local-disk\s*$$""".r
 
   def parse(s: String): Try[AwsBatchVolume] = {
-
     val validation: ErrorOr[AwsBatchVolume] = s match {
       case LocalDiskPattern() =>
         Valid(AwsBatchWorkingDisk())
@@ -69,8 +68,9 @@ object AwsBatchVolume {
         Valid(AwsBatchEmptyMountedDisk(DefaultPathBuilder.get(mountPoint),fsType))
       case _ =>
         s"Disk strings should be of the format 'local-disk' or '/mount/point' but got: '$s'".invalidNel
-    }
 
+    }
+    
     Try(validation match {
       case Valid(localDisk) => localDisk
       case Invalid(nels) =>

From 5456e40b08774b5c1bfca94f32198dfb656ae84d Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Thu, 21 Sep 2023 10:36:13 -0400
Subject: [PATCH 218/326] WX-1225 Print TES error messages to job logger
 (#7220)

---
 .../backend/impl/tes/TesAsyncBackendJobExecutionActor.scala   | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 7ff507e63f2..ad8daca6ec7 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -276,7 +276,9 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
   }
 
   private def handleExecutionError(status: TesRunStatus, returnCode: Option[Int]): Future[ExecutionHandle] = {
-    val exception = new AggregatedMessageException(s"Task ${jobDescriptor.key.tag} failed for unknown reason: ${status.toString()}", status.sysLogs)
+    val msg = s"Task ${jobDescriptor.key.tag} failed with ${status.toString}"
+    jobLogger.info(s"${msg}. Error messages: ${status.sysLogs}")
+    val exception = new AggregatedMessageException(msg, status.sysLogs)
     Future.successful(FailedNonRetryableExecutionHandle(exception, returnCode, None))
   }
 

From 660f6e39efd47e57a6738ff0998a51d4b2c92605 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 22 Sep 2023 16:52:14 -0400
Subject: [PATCH 219/326] WX-1217 Workflow completion callback (#7213)

Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
---
 CHANGELOG.md                                  |   5 +
 .../cloudsupport/azure/AzureCredentials.scala |   2 +-
 core/src/main/resources/reference.conf        |  16 +
 .../scala/cromwell/core/WorkflowOptions.scala |   1 +
 docs/cromwell_features/WorkflowCallback.md    |  58 ++++
 .../engine/workflow/WorkflowActor.scala       |  60 ++--
 .../workflow/WorkflowManagerActor.scala       |   4 +
 .../finalization/WorkflowCallbackActor.scala  | 216 ++++++++++++++
 .../WorkflowCallbackJsonSupport.scala         |  14 +
 .../cromwell/server/CromwellRootActor.scala   |  16 +-
 .../cromwell/server/CromwellShutdown.scala    |   3 +-
 .../WorkflowCallbackActorSpec.scala           | 278 ++++++++++++++++++
 .../cromwell/SimpleWorkflowActorSpec.scala    |   1 +
 .../engine/workflow/WorkflowActorSpec.scala   |  44 ++-
 14 files changed, 689 insertions(+), 29 deletions(-)
 create mode 100644 docs/cromwell_features/WorkflowCallback.md
 create mode 100644 engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
 create mode 100644 engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackJsonSupport.scala
 create mode 100644 engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 526c244da03..76746d972c8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,11 @@ WDL `size` engine function now works for HTTP files.
 Cromwell can now send logs to Azure Application Insights. To enable, set environment 
 variable `APPLICATIONINSIGHTS_INSTRUMENTATIONKEY` to your account's key. [See here for information.](https://learn.microsoft.com/en-us/azure/azure-monitor/app/sdk-connection-string)
 
+### Workflow Completion Callback
+
+Cromwell can be configured to send a POST request to a specified URL when a workflow completes. The request body
+includes the workflow id, terminal state, and (if applicable) final outputs or error message.
+See `WorkflowCallback` in [ReadTheDocs](https://cromwell.readthedocs.io/en/stable/) for more information.
 
 ## 85 Release Notes
 
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala
index c29155056a9..200b162c614 100644
--- a/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala
@@ -33,7 +33,7 @@ case object AzureCredentials {
     new DefaultAzureCredentialBuilder()
       .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
 
-  def getAccessToken(identityClientId: Option[String]): ErrorOr[String] = {
+  def getAccessToken(identityClientId: Option[String] = None): ErrorOr[String] = {
     val credentials = identityClientId.foldLeft(defaultCredentialBuilder) {
       (builder, clientId) => builder.managedIdentityClientId(clientId)
     }.build()
diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index d2cc9c5171f..6ec05cf6025 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -626,3 +626,19 @@ ga4gh {
     contact-info-url = "https://cromwell.readthedocs.io/en/stable/"
   }
 }
+
+workflow-state-callback {
+  enabled: false
+  ## The number of threads to allocate for performing callbacks
+  # num-threads: 5
+  # endpoint: "http://example.com/foo" # Can be overridden in workflow options
+  # auth.azure: true
+  ## Users can override default retry behavior if desired
+  # request-backoff {
+  #   min: "3 seconds"
+  #   max: "5 minutes"
+  #   multiplier: 1.1
+  # }
+  # max-retries = 10
+
+}
diff --git a/core/src/main/scala/cromwell/core/WorkflowOptions.scala b/core/src/main/scala/cromwell/core/WorkflowOptions.scala
index 010300b2d8b..91a7c30bbfe 100644
--- a/core/src/main/scala/cromwell/core/WorkflowOptions.scala
+++ b/core/src/main/scala/cromwell/core/WorkflowOptions.scala
@@ -62,6 +62,7 @@ object WorkflowOptions {
   case object WorkflowFailureMode extends WorkflowOption("workflow_failure_mode")
   case object UseReferenceDisks extends WorkflowOption("use_reference_disks")
   case object MemoryRetryMultiplier extends WorkflowOption("memory_retry_multiplier")
+  case object WorkflowCallbackUri extends WorkflowOption("workflow_callback_uri")
 
   private lazy val WorkflowOptionsConf = ConfigFactory.load.getConfig("workflow-options")
   private lazy val EncryptedFields: Seq[String] = WorkflowOptionsConf.getStringList("encrypted-fields").asScala.toList
diff --git a/docs/cromwell_features/WorkflowCallback.md b/docs/cromwell_features/WorkflowCallback.md
new file mode 100644
index 00000000000..275a6ede0a7
--- /dev/null
+++ b/docs/cromwell_features/WorkflowCallback.md
@@ -0,0 +1,58 @@
+The workflow callback is a simple way to integrate Cromwell with an external system. When each workflow reaches a terminal
+state, Cromwell will attempt to POST a message to a provided URL (see below for schema of this message). 
+Messages are sent for root workflows only, not subworkflows. Callback status information, including success or failure, 
+will be recorded in workflow metadata with keys containing `workflowCallback`.
+
+### Configuration
+
+This feature will only be used if enabled via config. All config items except `enabled` are optional.
+
+```
+workflow-state-callback {
+  enabled: true
+  num-threads: 5
+  endpoint: "http://example.com"
+  auth.azure: true
+  request-backoff {
+    min: "3 seconds",
+    max: "5 minutes",
+    multiplier: 1.1
+  }
+  max-retries = 10
+}
+```
+
+ * `enabled`: This boolean controls whether a callback will be attempted or not.
+ * `num-threads`: The number of threads Cromwell will allocate for performing callbacks.
+ * `endpoint`: This is the default URL to send the message to. If this is unset, and no URL is set in workflow options, no callback will be sent.
+ * `auth.azure`: If true, and if Cromwell is running in an Azure environment, Cromwell will include an auth header with bearer token generated from local Azure credentials.
+ * `request-backoff` and `max-retries`: Include these to override the default retry behavior (default behavior shown here).
+
+### Workflow Options
+
+You may choose to override the `endpoint` set in config by including this workflow option:
+```
+{
+  "workflow_callback_uri": "http://mywebsite.com"
+}
+```
+
+### Callback schema
+
+Below is an example of a callback request body.
+
+```
+{
+  "workflowId": "00001111-2222-3333-4444-555566667777",
+  "state": "Succeeded",
+  "outputs": {
+    "task1.out": 5,
+    "task2.out": "/some/file.txt"
+  }
+}
+```
+
+ * `workflowId`: The UUID of the workflow
+ * `state`: The terminal state of the workflow. The list of possible values is: `Succeeded`, `Failed`, `Aborted`
+ * `outputs`: The final outputs of the workflow, as would be returned from the `api/workflows/{version}/{id}/outputs` endpoint. Expected to be empty when the workflow is not successful..
+ * `failures`: A list of strings describing the workflow's failures. Expected to be empty if the workflow did not fail.
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
index b4ccf3de53b..3061e2e8a74 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
@@ -1,7 +1,6 @@
 package cromwell.engine.workflow
 
 import java.util.concurrent.atomic.AtomicInteger
-
 import akka.actor.SupervisorStrategy.Stop
 import akka.actor._
 import com.typesafe.config.Config
@@ -23,6 +22,7 @@ import cromwell.engine.workflow.lifecycle.deletion.DeleteWorkflowFilesActor
 import cromwell.engine.workflow.lifecycle.deletion.DeleteWorkflowFilesActor.{DeleteWorkflowFilesFailedResponse, DeleteWorkflowFilesSucceededResponse, StartWorkflowFilesDeletion}
 import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor
 import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor._
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackActor.PerformCallbackCommand
 import cromwell.engine.workflow.lifecycle.finalization.WorkflowFinalizationActor.{StartFinalizationCommand, WorkflowFinalizationFailedResponse, WorkflowFinalizationSucceededResponse}
 import cromwell.engine.workflow.lifecycle.finalization.{CopyWorkflowLogsActor, CopyWorkflowOutputsActor, WorkflowFinalizationActor}
 import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor
@@ -149,7 +149,7 @@ object WorkflowActor {
                                initializationData: AllBackendInitializationData,
                                lastStateReached: StateCheckpoint,
                                effectiveStartableState: StartableState,
-                               workflowFinalOutputs: Set[WomValue] = Set.empty,
+                               workflowFinalOutputs: Option[CallOutputs] = None,
                                workflowAllOutputs: Set[WomValue] = Set.empty,
                                rootAndSubworkflowIds: Set[WorkflowId] = Set.empty,
                                failedInitializationAttempts: Int = 0)
@@ -176,6 +176,7 @@ object WorkflowActor {
             ioActor: ActorRef,
             serviceRegistryActor: ActorRef,
             workflowLogCopyRouter: ActorRef,
+            workflowCallbackActor: Option[ActorRef],
             jobStoreActor: ActorRef,
             subWorkflowStoreActor: ActorRef,
             callCacheReadActor: ActorRef,
@@ -199,6 +200,7 @@ object WorkflowActor {
         ioActor = ioActor,
         serviceRegistryActor = serviceRegistryActor,
         workflowLogCopyRouter = workflowLogCopyRouter,
+        workflowCallbackActor = workflowCallbackActor,
         jobStoreActor = jobStoreActor,
         subWorkflowStoreActor = subWorkflowStoreActor,
         callCacheReadActor = callCacheReadActor,
@@ -226,6 +228,7 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
                     ioActor: ActorRef,
                     override val serviceRegistryActor: ActorRef,
                     workflowLogCopyRouter: ActorRef,
+                    workflowCallbackActor: Option[ActorRef],
                     jobStoreActor: ActorRef,
                     subWorkflowStoreActor: ActorRef,
                     callCacheReadActor: ActorRef,
@@ -534,26 +537,27 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
         case _ => // The WMA is waiting for the WorkflowActorWorkComplete message. No extra information needed here.
       }
 
-      // Copy/Delete workflow logs
-      if (WorkflowLogger.isEnabled) {
-        /*
-          * The submitted workflow options have been previously validated by the CromwellApiHandler. These are
-          * being recreated so that in case MaterializeWorkflowDescriptor fails, the workflow logs can still
-          * be copied by accessing the workflow options outside of the EngineWorkflowDescriptor.
-          */
-        def bruteForceWorkflowOptions: WorkflowOptions = sources.workflowOptions
-        val system = context.system
-        val ec = context.system.dispatcher
-        def bruteForcePathBuilders: Future[List[PathBuilder]] = {
-          // Protect against path builders that may throw an exception instead of returning a failed future
-          Future(EngineFilesystems.pathBuildersForWorkflow(bruteForceWorkflowOptions, pathBuilderFactories)(system))(ec).flatten
-        }
+      /*
+       * The submitted workflow options have been previously validated by the CromwellApiHandler. These are
+       * being recreated so that even if the MaterializeWorkflowDescriptor fails, the workflow options can still be
+       * accessed outside of the EngineWorkflowDescriptor. Used for both copying workflow log and sending workflow callbacks.
+       */
+      def bruteForceWorkflowOptions: WorkflowOptions = sources.workflowOptions
+
+      val system = context.system
+      val ec = context.system.dispatcher
+      def bruteForcePathBuilders: Future[List[PathBuilder]] = {
+        // Protect against path builders that may throw an exception instead of returning a failed future
+        Future(EngineFilesystems.pathBuildersForWorkflow(bruteForceWorkflowOptions, pathBuilderFactories)(system))(ec).flatten
+      }
 
-        val (workflowOptions, pathBuilders) = stateData.workflowDescriptor match {
-          case Some(wd) => (wd.backendDescriptor.workflowOptions, Future.successful(wd.pathBuilders))
-          case None => (bruteForceWorkflowOptions, bruteForcePathBuilders)
-        }
+      val (workflowOptions, pathBuilders) = stateData.workflowDescriptor match {
+        case Some(wd) => (wd.backendDescriptor.workflowOptions, Future.successful(wd.pathBuilders))
+        case None => (bruteForceWorkflowOptions, bruteForcePathBuilders)
+      }
 
+      // Copy/Delete workflow logs
+      if (WorkflowLogger.isEnabled) {
         workflowOptions.get(FinalWorkflowLogDir).toOption match {
           case Some(destinationDir) =>
             pathBuilders
@@ -566,6 +570,18 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
         }
       }
 
+      // Attempt to perform workflow completion callback
+      workflowCallbackActor.foreach { wca =>
+        val callbackUri = workflowOptions.get(WorkflowOptions.WorkflowCallbackUri).toOption
+        wca ! PerformCallbackCommand(
+          workflowId,
+          callbackUri,
+          terminalState.workflowState,
+          stateData.workflowFinalOutputs.getOrElse(CallOutputs.empty),
+          nextStateData.lastStateReached.failures.toList.flatMap(_.map(_.getMessage))
+        )
+      }
+
       // We can't transition from within another transition function, but we can instruct ourselves to with a message:
       self ! AwaitMetadataIntegrity
 
@@ -627,7 +643,7 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
         rootWorkflowId = rootWorkflowId,
         rootWorkflowRootPaths = data.initializationData.getWorkflowRoots(),
         rootAndSubworkflowIds = data.rootAndSubworkflowIds,
-        workflowFinalOutputs = data.workflowFinalOutputs,
+        workflowFinalOutputs = data.workflowFinalOutputs.map(out => out.outputs.values.toSet).getOrElse(Set.empty),
         workflowAllOutputs = data.workflowAllOutputs,
         pathBuilders = data.workflowDescriptor.get.pathBuilders,
         serviceRegistryActor = serviceRegistryActor,
@@ -689,7 +705,7 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
     finalizationActor ! StartFinalizationCommand
     goto(FinalizingWorkflowState) using data.copy(
       lastStateReached = StateCheckpoint (lastStateOverride.getOrElse(stateName), failures),
-      workflowFinalOutputs = workflowFinalOutputs.outputs.values.toSet,
+      workflowFinalOutputs = Option(workflowFinalOutputs),
       workflowAllOutputs = workflowAllOutputs,
       rootAndSubworkflowIds = rootAndSubworkflowIds
     )
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
index 15d0c4321a7..e84d9091ad0 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
@@ -57,6 +57,7 @@ object WorkflowManagerActor {
             ioActor: ActorRef,
             serviceRegistryActor: ActorRef,
             workflowLogCopyRouter: ActorRef,
+            workflowCallbackActor: Option[ActorRef],
             jobStoreActor: ActorRef,
             subWorkflowStoreActor: ActorRef,
             callCacheReadActor: ActorRef,
@@ -75,6 +76,7 @@ object WorkflowManagerActor {
       ioActor = ioActor,
       serviceRegistryActor = serviceRegistryActor,
       workflowLogCopyRouter = workflowLogCopyRouter,
+      workflowCallbackActor = workflowCallbackActor,
       jobStoreActor = jobStoreActor,
       subWorkflowStoreActor = subWorkflowStoreActor,
       callCacheReadActor = callCacheReadActor,
@@ -124,6 +126,7 @@ case class WorkflowManagerActorParams(config: Config,
                                       ioActor: ActorRef,
                                       serviceRegistryActor: ActorRef,
                                       workflowLogCopyRouter: ActorRef,
+                                      workflowCallbackActor: Option[ActorRef],
                                       jobStoreActor: ActorRef,
                                       subWorkflowStoreActor: ActorRef,
                                       callCacheReadActor: ActorRef,
@@ -313,6 +316,7 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
       ioActor = params.ioActor,
       serviceRegistryActor = params.serviceRegistryActor,
       workflowLogCopyRouter = params.workflowLogCopyRouter,
+      workflowCallbackActor = params.workflowCallbackActor,
       jobStoreActor = params.jobStoreActor,
       subWorkflowStoreActor = params.subWorkflowStoreActor,
       callCacheReadActor = params.callCacheReadActor,
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
new file mode 100644
index 00000000000..516184d023a
--- /dev/null
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
@@ -0,0 +1,216 @@
+package cromwell.engine.workflow.lifecycle.finalization
+
+import akka.Done
+import akka.actor.{Actor, ActorLogging, ActorRef, ActorSystem, Props}
+import akka.event.LoggingReceive
+import akka.http.scaladsl.Http
+import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
+import akka.http.scaladsl.marshalling.Marshal
+import akka.http.scaladsl.model._
+import akka.http.scaladsl.model.headers.RawHeader
+import akka.routing.Broadcast
+import akka.util.ByteString
+import cats.data.Validated.{Invalid, Valid}
+import cats.implicits.toTraverseOps
+import com.typesafe.config.Config
+import com.typesafe.scalalogging.LazyLogging
+import common.validation.ErrorOr
+import cromwell.cloudsupport.azure.AzureCredentials
+import cromwell.core.Dispatcher.IoDispatcher
+import cromwell.core.retry.Retry.withRetry
+import cromwell.core.retry.SimpleExponentialBackoff
+import cromwell.core.{CallOutputs, WorkflowId, WorkflowState}
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackActor.PerformCallbackCommand
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackJsonSupport._
+import net.ceedubs.ficus.Ficus._
+
+import scala.concurrent.{ExecutionContext, Future}
+import scala.concurrent.duration.DurationInt
+import scala.util.Try
+import cromwell.services.metadata.MetadataService.PutMetadataAction
+import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
+import cromwell.util.GracefulShutdownHelper.ShutdownCommand
+
+import java.net.URI
+import java.time.Instant
+import java.util.concurrent.Executors
+import scala.util.{Failure, Success}
+
+
+case class WorkflowCallbackConfig(enabled: Boolean,
+                                  numThreads: Int,
+                                  retryBackoff: SimpleExponentialBackoff,
+                                  maxRetries: Int,
+                                  defaultUri: Option[URI], // May be overridden by workflow options
+                                  authMethod: Option[WorkflowCallbackConfig.AuthMethod])
+
+object WorkflowCallbackConfig extends LazyLogging {
+  sealed trait AuthMethod { def getAccessToken:  ErrorOr.ErrorOr[String]  }
+  case object AzureAuth extends AuthMethod {
+    override def getAccessToken: ErrorOr.ErrorOr[String] = AzureCredentials.getAccessToken()
+  }
+
+  private lazy val defaultNumThreads = 5
+  private lazy val defaultRetryBackoff = SimpleExponentialBackoff(3.seconds, 5.minutes, 1.1)
+  private lazy val defaultMaxRetries = 10
+
+  def empty: WorkflowCallbackConfig = WorkflowCallbackConfig(
+    false, defaultNumThreads, defaultRetryBackoff, defaultMaxRetries, None, None
+  )
+
+  def apply(config: Config): WorkflowCallbackConfig = {
+    val enabled = config.as[Boolean]("enabled")
+    val numThreads = config.as[Option[Int]]("num-threads").getOrElse(defaultNumThreads)
+    val backoff = config.as[Option[Config]]("request-backoff").map(SimpleExponentialBackoff(_)).getOrElse(defaultRetryBackoff)
+    val maxRetries = config.as[Option[Int]]("max-retries").getOrElse(defaultMaxRetries)
+    val uri = config.as[Option[String]]("endpoint").flatMap(createAndValidateUri)
+
+    val authMethod = if (config.hasPath("auth.azure")) {
+      Option(AzureAuth)
+    } else None
+
+    WorkflowCallbackConfig(
+      enabled = enabled,
+      numThreads = numThreads,
+      retryBackoff = backoff,
+      maxRetries = maxRetries,
+      defaultUri = uri,
+      authMethod = authMethod
+    )
+  }
+
+  def createAndValidateUri(uriString: String): Option[URI] = {
+    Try(new URI(uriString)) match {
+      case Success(uri) => Option(uri)
+      case Failure(err) =>
+        logger.warn(s"Failed to parse provided workflow callback URI (${uriString}): $err")
+        None
+    }
+  }
+}
+
+/**
+  * The WorkflowCallbackActor is responsible for sending a message on workflow completion to a configured endpoint.
+  * This allows for users to build automation around workflow completion without needing to poll Cromwell for
+  * workflow status.
+  */
+object WorkflowCallbackActor {
+
+  final case class PerformCallbackCommand(workflowId: WorkflowId,
+                                          uri: Option[String],
+                                          terminalState: WorkflowState,
+                                          workflowOutputs: CallOutputs,
+                                          failureMessage: List[String])
+
+  def props(serviceRegistryActor: ActorRef,
+            callbackConfig: WorkflowCallbackConfig,
+            httpClient: CallbackHttpHandler = CallbackHttpHandlerImpl
+           ) = Props(
+    new WorkflowCallbackActor(
+      serviceRegistryActor,
+      callbackConfig,
+      httpClient)
+  ).withDispatcher(IoDispatcher)
+}
+
+class WorkflowCallbackActor(serviceRegistryActor: ActorRef,
+                            config: WorkflowCallbackConfig,
+                            httpClient: CallbackHttpHandler)
+  extends Actor with ActorLogging {
+
+  // Create a dedicated thread pool for this actor so its damage is limited if we end up with
+  // too many threads all taking a long time to do callbacks. If we're frequently saturating
+  // this thread pool, consider refactoring this actor to maintain a queue of callbacks and
+  // handle them one at a time, as opposed to starting a thread to perform each as soon as its
+  // received.
+  implicit val ec = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(config.numThreads))
+  implicit val system: ActorSystem = context.system
+
+  override def receive: Actor.Receive = LoggingReceive {
+    case PerformCallbackCommand(workflowId, requestedCallbackUri, terminalState, outputs, failures) =>
+      // If no uri was provided to us here, fall back to the one in config. If there isn't
+      // one there, do not perform a callback.
+      val callbackUri: Option[URI] = requestedCallbackUri.map(WorkflowCallbackConfig.createAndValidateUri).getOrElse(config.defaultUri)
+      callbackUri.map { uri =>
+        performCallback(workflowId, uri, terminalState, outputs, failures) onComplete {
+          case Success(_) =>
+            log.info(s"Successfully sent callback for workflow for workflow $workflowId in state $terminalState to $uri")
+            sendMetadata(workflowId, successful = true, uri)
+          case Failure(t) =>
+            log.warning(s"Permanently failed to send callback for workflow $workflowId in state $terminalState to $uri: ${t.getMessage}")
+            sendMetadata(workflowId, successful = false, uri)
+        }
+      }.getOrElse(())
+    case Broadcast(ShutdownCommand) | ShutdownCommand => context stop self
+    case other => log.warning(s"WorkflowCallbackActor received an unexpected message: $other")
+  }
+
+  private def makeHeaders: Future[List[HttpHeader]] = {
+    config.authMethod.toList.map(_.getAccessToken).map {
+      case Valid(header) => Future.successful(header)
+      case Invalid(err) => Future.failed(new RuntimeException(err.toString))
+    }
+      .map(t => t.map(t => RawHeader("Authorization", s"Bearer $t")))
+      .traverse(identity)
+  }
+
+  private def performCallback(workflowId: WorkflowId, callbackUri: URI, terminalState: WorkflowState, outputs: CallOutputs, failures: List[String]): Future[Done] = {
+    val callbackPostBody = CallbackMessage(workflowId.toString, terminalState.toString, outputs.outputs.map(entry => (entry._1.name, entry._2)), failures)
+    for {
+      entity <- Marshal(callbackPostBody).to[RequestEntity]
+      headers <- makeHeaders
+      request = HttpRequest(method = HttpMethods.POST, uri = callbackUri.toString, entity = entity).withHeaders(headers)
+      response <- withRetry(
+        () => sendRequestOrFail(request),
+        backoff = config.retryBackoff,
+        maxRetries = Option(config.maxRetries),
+        onRetry = err => log.warning(s"Will retry after failure to send workflow callback for workflow $workflowId in state $terminalState to $callbackUri : $err")
+      )
+      result <-
+        // Akka will get upset if we have a response body and leave it totally unread.
+        // Since there's nothing here we want to read, we need to deliberately discard it.
+        response.entity.discardBytes().future
+    } yield result
+  }
+
+  private def sendRequestOrFail(request: HttpRequest): Future[HttpResponse] =
+    httpClient.sendRequest(request).flatMap(response =>
+      if (response.status.isFailure()) {
+        response.entity.dataBytes.runFold(ByteString(""))(_ ++ _).map(_.utf8String) flatMap { errorBody =>
+          Future.failed(
+            new RuntimeException(s"HTTP ${response.status.value}: $errorBody")
+          )
+        }
+      } else Future.successful(response)
+    )
+
+  private def sendMetadata(workflowId: WorkflowId, successful: Boolean, uri: URI): Unit = {
+    val events = List(
+      MetadataEvent(
+        MetadataKey(workflowId, None, "workflowCallback", "successful"),
+        MetadataValue(successful)
+      ),
+      MetadataEvent(
+        MetadataKey(workflowId, None, "workflowCallback", "url"),
+        MetadataValue(uri.toString)
+      ),
+      MetadataEvent(
+        MetadataKey(workflowId, None, "workflowCallback", "timestamp"),
+        MetadataValue(Instant.now())
+      )
+    )
+    serviceRegistryActor ! PutMetadataAction(events)
+  }
+
+}
+
+// Wrap the http call in a trait so it can be easily mocked for testing
+trait CallbackHttpHandler {
+  def sendRequest(httpRequest: HttpRequest)(implicit actorSystem: ActorSystem): Future[HttpResponse]
+}
+
+object CallbackHttpHandlerImpl extends CallbackHttpHandler {
+  override def sendRequest(httpRequest: HttpRequest)(implicit actorSystem: ActorSystem): Future[HttpResponse] = {
+    Http().singleRequest(httpRequest)
+  }
+}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackJsonSupport.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackJsonSupport.scala
new file mode 100644
index 00000000000..eb9b1c7ea9e
--- /dev/null
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackJsonSupport.scala
@@ -0,0 +1,14 @@
+package cromwell.engine.workflow.lifecycle.finalization
+
+import cromwell.util.JsonFormatting.WomValueJsonFormatter.WomValueJsonFormat
+import spray.json.DefaultJsonProtocol
+import wom.values.WomValue
+
+final case class CallbackMessage(workflowId: String,
+                                 state: String,
+                                 outputs: Map[String, WomValue],
+                                 failures: List[String])
+
+object WorkflowCallbackJsonSupport extends DefaultJsonProtocol {
+  implicit val callbackMessageFormat = jsonFormat4(CallbackMessage)
+}
diff --git a/engine/src/main/scala/cromwell/server/CromwellRootActor.scala b/engine/src/main/scala/cromwell/server/CromwellRootActor.scala
index df4fc5b1207..c37d6466fcc 100644
--- a/engine/src/main/scala/cromwell/server/CromwellRootActor.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellRootActor.scala
@@ -20,7 +20,7 @@ import cromwell.engine.io.{IoActor, IoActorProxy}
 import cromwell.engine.workflow.WorkflowManagerActor
 import cromwell.engine.workflow.WorkflowManagerActor.AbortAllWorkflowsCommand
 import cromwell.engine.workflow.lifecycle.execution.callcaching.{CallCache, CallCacheReadActor, CallCacheWriteActor}
-import cromwell.engine.workflow.lifecycle.finalization.CopyWorkflowLogsActor
+import cromwell.engine.workflow.lifecycle.finalization.{CopyWorkflowLogsActor, WorkflowCallbackActor, WorkflowCallbackConfig}
 import cromwell.engine.workflow.tokens.{DynamicRateLimiter, JobTokenDispenserActor}
 import cromwell.engine.workflow.workflowstore.AbortRequestScanningActor.AbortConfig
 import cromwell.engine.workflow.workflowstore._
@@ -122,6 +122,18 @@ abstract class CromwellRootActor(terminator: CromwellTerminator,
     .props(CopyWorkflowLogsActor.props(serviceRegistryActor, ioActor)),
     "WorkflowLogCopyRouter")
 
+  private val workflowCallbackConfig = WorkflowCallbackConfig(config.getConfig("workflow-state-callback"))
+
+  lazy val workflowCallbackActor: Option[ActorRef] = {
+    if (workflowCallbackConfig.enabled) {
+      val props = WorkflowCallbackActor.props(
+        serviceRegistryActor,
+        workflowCallbackConfig
+      )
+      Option(context.actorOf(props, "WorkflowCallbackActor"))
+    } else None
+  }
+
   //Call-caching config validation
   lazy val callCachingConfig = config.getConfig("call-caching")
   lazy val callCachingEnabled = callCachingConfig.getBoolean("enabled")
@@ -174,6 +186,7 @@ abstract class CromwellRootActor(terminator: CromwellTerminator,
       ioActor = ioActorProxy,
       serviceRegistryActor = serviceRegistryActor,
       workflowLogCopyRouter = workflowLogCopyRouter,
+      workflowCallbackActor = workflowCallbackActor,
       jobStoreActor = jobStoreActor,
       subWorkflowStoreActor = subWorkflowStoreActor,
       callCacheReadActor = callCacheReadActor,
@@ -218,6 +231,7 @@ abstract class CromwellRootActor(terminator: CromwellTerminator,
       actorSystem = context.system,
       workflowManagerActor = workflowManagerActor,
       logCopyRouter = workflowLogCopyRouter,
+      workflowCallbackActor = workflowCallbackActor,
       jobStoreActor = jobStoreActor,
       jobTokenDispenser = jobExecutionTokenDispenserActor,
       workflowStoreActor = workflowStoreActor,
diff --git a/engine/src/main/scala/cromwell/server/CromwellShutdown.scala b/engine/src/main/scala/cromwell/server/CromwellShutdown.scala
index 99e4041db56..ce204249b1e 100644
--- a/engine/src/main/scala/cromwell/server/CromwellShutdown.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellShutdown.scala
@@ -1,7 +1,6 @@
 package cromwell.server
 
 import java.util.concurrent.atomic.AtomicBoolean
-
 import akka.Done
 import akka.actor._
 import akka.http.scaladsl.Http
@@ -83,6 +82,7 @@ object CromwellShutdown extends GracefulStopSupport {
                              actorSystem: ActorSystem,
                              workflowManagerActor: ActorRef,
                              logCopyRouter: ActorRef,
+                             workflowCallbackActor: Option[ActorRef],
                              jobTokenDispenser: ActorRef,
                              jobStoreActor: ActorRef,
                              workflowStoreActor: ActorRef,
@@ -180,6 +180,7 @@ object CromwellShutdown extends GracefulStopSupport {
 
     shutdownActor(workflowStoreActor, CoordinatedShutdown.PhaseServiceRequestsDone, ShutdownCommand)
     shutdownActor(logCopyRouter, CoordinatedShutdown.PhaseServiceRequestsDone, Broadcast(ShutdownCommand))
+    workflowCallbackActor.foreach(wca => shutdownActor(wca, CoordinatedShutdown.PhaseServiceRequestsDone, Broadcast(ShutdownCommand)))
     shutdownActor(jobTokenDispenser, CoordinatedShutdown.PhaseServiceRequestsDone, ShutdownCommand)
     
     /*
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
new file mode 100644
index 00000000000..c469d1dcaa2
--- /dev/null
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
@@ -0,0 +1,278 @@
+package cromwell.engine.workflow.lifecycle.finalization
+
+import akka.testkit._
+import akka.http.scaladsl.client.RequestBuilding.Post
+import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
+import akka.http.scaladsl.model.{HttpResponse, StatusCodes}
+import akka.testkit.TestProbe
+import common.mock.MockSugar
+import cromwell.core.retry.SimpleExponentialBackoff
+import org.mockito.Mockito._
+import cromwell.core.{CallOutputs, TestKitSuite, WorkflowFailed, WorkflowId, WorkflowSucceeded}
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackActor.PerformCallbackCommand
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackJsonSupport._
+import cromwell.services.metadata.MetadataService.PutMetadataAction
+import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
+import cromwell.util.{GracefulShutdownHelper, WomMocks}
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.matchers.should.Matchers
+import wom.values.WomString
+
+import java.net.URI
+import java.time.Instant
+import scala.concurrent.duration._
+import scala.concurrent.Future
+
+class WorkflowCallbackActorSpec
+  extends TestKitSuite with AnyFlatSpecLike with Matchers with MockSugar {
+
+  behavior of "WorkflowCallbackActor"
+
+  private implicit val ec = system.dispatcher
+
+  private val msgWait = 10.second.dilated
+  private val awaitAlmostNothing = 1.second
+  private val serviceRegistryActor = TestProbe("testServiceRegistryActor")
+  private val deathWatch = TestProbe("deathWatch")
+  private val mockUri = new URI("http://example.com")
+  private val basicConfig = WorkflowCallbackConfig.empty.copy(enabled = true)
+  private val basicOutputs = WomMocks.mockOutputExpectations(List("foo" -> WomString("bar")).toMap)
+
+  private val httpSuccess = Future.successful(HttpResponse.apply(StatusCodes.OK))
+  private val httpFailure = Future.successful(HttpResponse.apply(StatusCodes.GatewayTimeout))
+
+  private def metadataEvents(workflowId: WorkflowId, successful: Boolean) = (
+    MetadataEvent(
+      MetadataKey(workflowId, None, "workflowCallback", "successful"),
+      MetadataValue(successful)
+    ),
+    MetadataEvent(
+      MetadataKey(workflowId, None, "workflowCallback", "url"),
+      MetadataValue(mockUri.toString)
+    ),
+    MetadataEvent(
+      MetadataKey(workflowId, None, "workflowCallback", "timestamp"),
+      MetadataValue(Instant.now())
+    )
+  )
+
+  it should "send a command to the default URI and record the correct metadata" in {
+    // Setup
+    val workflowId = WorkflowId.randomId()
+    val mockHttpClient = mock[CallbackHttpHandler]
+
+    val expectedPostBody = CallbackMessage(
+      workflowId.toString,
+      WorkflowSucceeded.toString,
+      basicOutputs.outputs.map(entry => (entry._1.name, entry._2)),
+      List.empty
+    )
+    val expectedRequest = Post(mockUri.toString, expectedPostBody)
+    val (expectedResultMetadata, expectedUriMetadata, expectedTimestampMetadata) = metadataEvents(workflowId, true)
+
+    when(mockHttpClient.sendRequest(expectedRequest)).thenReturn(httpSuccess)
+
+    val props = WorkflowCallbackActor.props(
+      serviceRegistryActor.ref,
+      basicConfig.copy(defaultUri = Option(mockUri)),
+      httpClient = mockHttpClient
+    )
+    val workflowCallbackActor = system.actorOf(props, "testWorkflowCallbackActorSuccess")
+
+    // Do the thing
+    val cmd = PerformCallbackCommand(
+      workflowId = workflowId, uri = None, terminalState = WorkflowSucceeded, workflowOutputs = basicOutputs, List.empty
+    )
+    workflowCallbackActor ! cmd
+
+    // Check the result
+    serviceRegistryActor.expectMsgPF(msgWait) {
+      case PutMetadataAction(List(resultEvent, uriEvent, timestampEvent), _) =>
+        resultEvent.key shouldBe expectedResultMetadata.key
+        resultEvent.value shouldBe expectedResultMetadata.value
+        uriEvent.key shouldBe expectedUriMetadata.key
+        uriEvent.value shouldBe expectedUriMetadata.value
+        timestampEvent.key shouldBe expectedTimestampMetadata.key
+        // Not checking timestamp value because it won't match
+      case _ =>
+    }
+
+    verify(mockHttpClient, times(1)).sendRequest(expectedRequest)
+
+    // Shut it down
+    deathWatch.watch(workflowCallbackActor)
+    workflowCallbackActor ! GracefulShutdownHelper.ShutdownCommand
+    deathWatch.expectTerminated(workflowCallbackActor, msgWait)
+
+  }
+
+  it should "correctly handle a callback that fails, then succeeds" in {
+    // Setup
+    val workflowId = WorkflowId.randomId()
+    val mockHttpClient = mock[CallbackHttpHandler]
+
+    val expectedPostBody = CallbackMessage(
+      workflowId.toString,
+      WorkflowSucceeded.toString,
+      basicOutputs.outputs.map(entry => (entry._1.name, entry._2)),
+      List.empty
+    )
+    val expectedRequest = Post(mockUri.toString, expectedPostBody)
+
+    val (expectedResultMetadata, expectedUriMetadata, expectedTimestampMetadata) = metadataEvents(workflowId, true)
+
+    when(mockHttpClient.sendRequest(expectedRequest)).thenReturn(httpFailure, httpFailure, httpSuccess)
+
+    val props = WorkflowCallbackActor.props(
+      serviceRegistryActor.ref,
+      basicConfig.copy(defaultUri = Option(mockUri)),
+      httpClient = mockHttpClient
+    )
+    val workflowCallbackActor = system.actorOf(props, "testWorkflowCallbackActorFailThenSuccees")
+
+    // Do the thing
+    val cmd = PerformCallbackCommand(
+      workflowId = workflowId, uri = None, terminalState = WorkflowSucceeded, workflowOutputs = basicOutputs, List.empty
+    )
+    workflowCallbackActor ! cmd
+
+    // Check the result
+    serviceRegistryActor.expectMsgPF(msgWait) {
+      case PutMetadataAction(List(resultEvent, uriEvent, timestampEvent), _) =>
+        resultEvent.key shouldBe expectedResultMetadata.key
+        resultEvent.value shouldBe expectedResultMetadata.value
+        uriEvent.key shouldBe expectedUriMetadata.key
+        uriEvent.value shouldBe expectedUriMetadata.value
+        timestampEvent.key shouldBe expectedTimestampMetadata.key
+      // Not checking timestamp value because it won't match
+      case _ =>
+    }
+
+    verify(mockHttpClient, times(3)).sendRequest(expectedRequest)
+
+    // Shut it down
+    deathWatch.watch(workflowCallbackActor)
+    workflowCallbackActor ! GracefulShutdownHelper.ShutdownCommand
+    deathWatch.expectTerminated(workflowCallbackActor, msgWait)
+
+  }
+
+  it should "retry sending the callback for a failing workflow before failing" in {
+    // Setup
+    val workflowId = WorkflowId.randomId()
+    val mockHttpClient = mock[CallbackHttpHandler]
+
+    val errorMsg = "Something bad happened :("
+    val expectedPostBody = CallbackMessage(
+      workflowId.toString,
+      WorkflowFailed.toString,
+      Map.empty,
+      List(errorMsg)
+    )
+    val expectedRequest = Post(mockUri.toString, expectedPostBody)
+
+    val (expectedResultMetadata, expectedUriMetadata, expectedTimestampMetadata) = metadataEvents(workflowId, false)
+
+    when(mockHttpClient.sendRequest(expectedRequest)).thenReturn(httpFailure)
+
+    val props = WorkflowCallbackActor.props(
+      serviceRegistryActor.ref,
+      basicConfig.copy(
+        retryBackoff = SimpleExponentialBackoff(500.millis, 1.minute, 1.1),
+        maxRetries = 5,
+      ),
+      httpClient = mockHttpClient
+    )
+    val workflowCallbackActor = system.actorOf(props, "testWorkflowCallbackActorFail")
+
+    // Do the thing
+    val cmd = PerformCallbackCommand(
+      workflowId = workflowId,
+      uri = Option(mockUri.toString),
+      terminalState = WorkflowFailed,
+      workflowOutputs = CallOutputs.empty,
+      List(errorMsg)
+    )
+    workflowCallbackActor ! cmd
+
+    // Check the result
+    serviceRegistryActor.expectMsgPF(msgWait) {
+      case PutMetadataAction(List(resultEvent, uriEvent, timestampEvent), _) =>
+        resultEvent.key shouldBe expectedResultMetadata.key
+        resultEvent.value shouldBe expectedResultMetadata.value
+        uriEvent.key shouldBe expectedUriMetadata.key
+        uriEvent.value shouldBe expectedUriMetadata.value
+        timestampEvent.key shouldBe expectedTimestampMetadata.key
+      // Not checking timestamp value because it won't match
+      case _ =>
+    }
+
+    verify(mockHttpClient, times(5)).sendRequest(expectedRequest)
+
+    // Shut it down
+    deathWatch.watch(workflowCallbackActor)
+    workflowCallbackActor ! GracefulShutdownHelper.ShutdownCommand
+    deathWatch.expectTerminated(workflowCallbackActor, msgWait)
+
+  }
+
+  it should "not send a callback if no URI is provided" in {
+    // Setup
+    val workflowId = WorkflowId.randomId()
+    val mockHttpClient = mock[CallbackHttpHandler]
+
+    val props = WorkflowCallbackActor.props(
+      serviceRegistryActor.ref,
+      basicConfig,
+      httpClient = mockHttpClient
+    )
+    val workflowCallbackActor = system.actorOf(props, "testWorkflowCallbackActorNoUri")
+
+    // Do the thing
+    val cmd = PerformCallbackCommand(
+      workflowId = workflowId, uri = None, terminalState = WorkflowSucceeded, workflowOutputs = basicOutputs, List.empty
+    )
+    workflowCallbackActor ! cmd
+
+    // Check the result
+    serviceRegistryActor.expectNoMessage(awaitAlmostNothing)
+    verifyNoInteractions(mockHttpClient)
+
+    // Shut it down
+    deathWatch.watch(workflowCallbackActor)
+    workflowCallbackActor ! GracefulShutdownHelper.ShutdownCommand
+    deathWatch.expectTerminated(workflowCallbackActor, msgWait)
+  }
+
+  it should "do nothing when given a bogus URI" in {
+    // Setup
+    val workflowId = WorkflowId.randomId()
+    val mockHttpClient = mock[CallbackHttpHandler]
+
+    val props = WorkflowCallbackActor.props(
+      serviceRegistryActor.ref,
+      basicConfig,
+      httpClient = mockHttpClient
+    )
+    val workflowCallbackActor = system.actorOf(props, "testWorkflowCallbackActorBogusUri")
+
+    // Do the thing
+    val cmd = PerformCallbackCommand(
+      workflowId = workflowId,
+      uri = Option("this is not a very good URI, is it"),
+      terminalState = WorkflowSucceeded,
+      workflowOutputs = basicOutputs,
+      List.empty
+    )
+    workflowCallbackActor ! cmd
+
+    // Check the result
+    serviceRegistryActor.expectNoMessage(awaitAlmostNothing)
+    verifyNoInteractions(mockHttpClient)
+
+    // Shut it down
+    deathWatch.watch(workflowCallbackActor)
+    workflowCallbackActor ! GracefulShutdownHelper.ShutdownCommand
+    deathWatch.expectTerminated(workflowCallbackActor, msgWait)
+  }
+}
diff --git a/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala b/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
index 375c51e886b..b3f4df64d07 100644
--- a/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
+++ b/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
@@ -68,6 +68,7 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
         invalidateBadCacheResults = invalidateBadCacheResults,
         serviceRegistryActor = watchActor,
         workflowLogCopyRouter = system.actorOf(Props.empty, s"workflow-copy-log-router-$workflowId-${UUID.randomUUID()}"),
+        workflowCallbackActor = None,
         jobStoreActor = system.actorOf(AlwaysHappyJobStoreActor.props),
         subWorkflowStoreActor = system.actorOf(AlwaysHappySubWorkflowStoreActor.props),
         callCacheReadActor = system.actorOf(EmptyCallCacheReadActor.props),
diff --git a/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala b/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
index d9de71b9125..6f7c57ae985 100644
--- a/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
@@ -15,16 +15,18 @@ import cromwell.engine.workflow.WorkflowActor._
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowActorWorkComplete
 import cromwell.engine.workflow.lifecycle.EngineLifecycleActorAbortCommand
 import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{ExecuteWorkflowCommand, WorkflowExecutionAbortedResponse, WorkflowExecutionFailedResponse, WorkflowExecutionSucceededResponse}
-import cromwell.engine.workflow.lifecycle.finalization.CopyWorkflowLogsActor
-import cromwell.engine.workflow.lifecycle.finalization.WorkflowFinalizationActor.{StartFinalizationCommand, WorkflowFinalizationSucceededResponse}
+import cromwell.engine.workflow.lifecycle.finalization.{CopyWorkflowLogsActor, WorkflowCallbackActor}
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowFinalizationActor.{StartFinalizationCommand, WorkflowFinalizationFailedResponse, WorkflowFinalizationSucceededResponse}
 import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{StartInitializationCommand, WorkflowInitializationAbortedResponse, WorkflowInitializationFailedResponse, WorkflowInitializationSucceededResponse}
 import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.MaterializeWorkflowDescriptorFailureResponse
 import cromwell.engine.workflow.workflowstore.{StartableState, Submitted, WorkflowHeartbeatConfig, WorkflowToStart}
 import cromwell.engine.{EngineFilesystems, EngineWorkflowDescriptor}
 import cromwell.services.metadata.MetadataService.{MetadataWriteSuccess, PutMetadataActionAndRespond}
 import cromwell.util.SampleWdl.ThreeStep
+import cromwell.util.WomMocks
 import org.scalatest.BeforeAndAfter
 import org.scalatest.concurrent.Eventually
+import wom.values.WomString
 
 import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future}
@@ -50,7 +52,8 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
     )
 
   val mockDir: Path = DefaultPathBuilder.get("/where/to/copy/wf/logs")
-  val mockWorkflowOptions = s"""{ "final_workflow_log_dir" : "$mockDir" }"""
+  val mockUri: String = "http://example.com"
+  val mockWorkflowOptions = s"""{ "final_workflow_log_dir" : "$mockDir", "workflow_callback_uri": "$mockUri" }"""
 
   var currentWorkflowId: WorkflowId = _
   val currentLifecycleActor: TestProbe = TestProbe("currentLifecycleActor")
@@ -63,6 +66,7 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
   val executionProbe: TestProbe = TestProbe("executionProbe")
   val finalizationProbe: TestProbe = TestProbe("finalizationProbe")
   var copyWorkflowLogsProbe: TestProbe = _
+  val workflowCallbackProbe: TestProbe = TestProbe("workflowCallbackProbe")
   val AwaitAlmostNothing: FiniteDuration = 100.milliseconds
   val initialJobCtByRootWf = new AtomicInteger()
   val callCachingEnabled = true
@@ -79,7 +83,11 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 
   private val workflowHeartbeatConfig = WorkflowHeartbeatConfig(ConfigFactory.load())
 
-  private def createWorkflowActor(state: WorkflowActorState, extraPathBuilderFactory: Option[PathBuilderFactory] = None, initializationMaxRetries: Int = 3, initializationInterval: FiniteDuration = 10.millis) = {
+  private def createWorkflowActor(state: WorkflowActorState,
+                                  extraPathBuilderFactory: Option[PathBuilderFactory] = None,
+                                  workflowCallbackActor: Option[ActorRef] = None,
+                                  initializationMaxRetries: Int = 3,
+                                  initializationInterval: FiniteDuration = 10.millis) = {
     val actor = TestFSMRef(
       factory = new WorkflowActorWithTestAddons(
         finalizationProbe = finalizationProbe,
@@ -92,6 +100,7 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
         ioActor = system.actorOf(SimpleIoActor.props, s"ioActor-$currentWorkflowId"),
         serviceRegistryActor = mockServiceRegistryActor,
         workflowLogCopyRouter = copyWorkflowLogsProbe.ref,
+        workflowCallbackActor = workflowCallbackActor,
         jobStoreActor = system.actorOf(AlwaysHappyJobStoreActor.props, s"jobStoreActor-$currentWorkflowId"),
         subWorkflowStoreActor =
           system.actorOf(AlwaysHappySubWorkflowStoreActor.props, s"subWorkflowStoreActor-$currentWorkflowId"),
@@ -328,6 +337,31 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
         val _ = createWorkflowActor(WorkflowSucceededState, Option(new ThrowingPathBuilderFactory()))
       }
     }
+
+    "send a workflow callback message" in {
+      val actor = createWorkflowActor(ExecutingWorkflowState, workflowCallbackActor = Option(workflowCallbackProbe.ref))
+      deathwatch watch actor
+      val mockOutputs = WomMocks.mockOutputExpectations(Map("foo" -> WomString("bar")))
+      val msg = WorkflowCallbackActor.PerformCallbackCommand(currentWorkflowId, Some(mockUri), WorkflowSucceeded, mockOutputs, List.empty)
+
+      workflowCallbackProbe.expectNoMessage(AwaitAlmostNothing)
+      actor ! WorkflowExecutionSucceededResponse(Map.empty, Set(currentWorkflowId), mockOutputs, Set.empty)
+      actor ! WorkflowFinalizationSucceededResponse
+      workflowCallbackProbe.expectMsg(msg)
+      deathwatch.expectTerminated(actor)
+    }
+
+    "send a workflow callback message for a failing workflow" in {
+      val actor = createWorkflowActor(FinalizingWorkflowState, workflowCallbackActor = Option(workflowCallbackProbe.ref))
+      deathwatch watch actor
+      val errorText = "oh nooo :("
+      val msg = WorkflowCallbackActor.PerformCallbackCommand(currentWorkflowId, Some(mockUri), WorkflowFailed, CallOutputs.empty, List(errorText))
+
+      workflowCallbackProbe.expectNoMessage(AwaitAlmostNothing)
+      actor ! WorkflowFinalizationFailedResponse(Seq(new RuntimeException(errorText)))
+      workflowCallbackProbe.expectMsg(msg)
+      deathwatch.expectTerminated(actor)
+    }
   }
 }
 
@@ -353,6 +387,7 @@ class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
                                   ioActor: ActorRef,
                                   serviceRegistryActor: ActorRef,
                                   workflowLogCopyRouter: ActorRef,
+                                  workflowCallbackActor: Option[ActorRef],
                                   jobStoreActor: ActorRef,
                                   subWorkflowStoreActor: ActorRef,
                                   callCacheReadActor: ActorRef,
@@ -379,6 +414,7 @@ class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
   ioActor = ioActor,
   serviceRegistryActor = serviceRegistryActor,
   workflowLogCopyRouter = workflowLogCopyRouter,
+  workflowCallbackActor,
   jobStoreActor = jobStoreActor,
   subWorkflowStoreActor = subWorkflowStoreActor,
   callCacheReadActor = callCacheReadActor,

From 2fec07b2fde696e6f0d0849e27c9dd5ac5be4f38 Mon Sep 17 00:00:00 2001
From: Saloni Shah <salonipshah11@gmail.com>
Date: Wed, 27 Sep 2023 19:23:59 -0400
Subject: [PATCH 220/326] [WM-2199] Changeset for modifying ownership of tables
 for WORKFLOWS app (#7218)

Co-authored-by: Chris Llanwarne <cjllanwarne@gmail.com>
---
 .../metadata_changesets/set_table_role.xml    | 34 +++++++++++++++++++
 .../main/resources/sql_metadata_changelog.xml |  7 ++++
 2 files changed, 41 insertions(+)
 create mode 100644 database/migration/src/main/resources/metadata_changesets/set_table_role.xml

diff --git a/database/migration/src/main/resources/metadata_changesets/set_table_role.xml b/database/migration/src/main/resources/metadata_changesets/set_table_role.xml
new file mode 100644
index 00000000000..48a56bb6091
--- /dev/null
+++ b/database/migration/src/main/resources/metadata_changesets/set_table_role.xml
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- The 'sharedCromwellDbRole' can be set via JAVA_OPTS if desired (eg -DsharedCromwellDbRole=...). -->
+    <property  name="sharedCromwellDbRole" value=""/>
+
+    <!--
+        This changeset will be applied whenever the 'sharedCromwellDbRole' property is set.
+        It runs every time to ensure the role is set correctly after all other changesets.
+     -->
+    <changeSet runAlways="true" author="sshah" id="set_table_role" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- check that 'sharedCromwellDbRole' role is set, and matches something in the pg_roles table -->
+            <sqlCheck expectedResult="1">
+                SELECT count(1)
+                FROM pg_roles
+                where '${sharedCromwellDbRole}' != '' and pg_roles.rolname = '${sharedCromwellDbRole}';
+            </sqlCheck>
+        </preConditions>
+        <sql>
+            ALTER TABLE "CUSTOM_LABEL_ENTRY" OWNER TO ${sharedCromwellDbRole};
+            ALTER TABLE "METADATA_ENTRY" OWNER TO ${sharedCromwellDbRole};
+            ALTER TABLE "SUMMARY_QUEUE_ENTRY" OWNER TO ${sharedCromwellDbRole};
+            ALTER TABLE "SUMMARY_STATUS_ENTRY" OWNER TO ${sharedCromwellDbRole};
+            ALTER TABLE "WORKFLOW_METADATA_SUMMARY_ENTRY" OWNER TO ${sharedCromwellDbRole};
+            ALTER TABLE "sqlmetadatadatabasechangelog" OWNER TO ${sharedCromwellDbRole};
+            ALTER TABLE "sqlmetadatadatabasechangeloglock" OWNER TO ${sharedCromwellDbRole};
+        </sql>
+    </changeSet>
+
+</databaseChangeLog>
diff --git a/database/migration/src/main/resources/sql_metadata_changelog.xml b/database/migration/src/main/resources/sql_metadata_changelog.xml
index 1c5b0837a89..0989ec2199a 100644
--- a/database/migration/src/main/resources/sql_metadata_changelog.xml
+++ b/database/migration/src/main/resources/sql_metadata_changelog.xml
@@ -19,5 +19,12 @@
     <include file="metadata_changesets/remove_non_summarizable_metadata_from_queue.xml" relativeToChangelogFile="true" />
     <include file="metadata_changesets/update_metadata_archive_index.xml" relativeToChangelogFile="true" />
     <include file="metadata_changesets/reset_archive_statuses_to_null.xml" relativeToChangelogFile="true" />
+    <!-- WARNING!
+      This changeset should always be last.
+      It it always run (and should always run last) to set table ownership correctly.
+      If your changeset adds a new table, make sure it is also owned by the sharedCromwellDbRole.
+    -->
+    <include file="metadata_changesets/set_table_role.xml" relativeToChangelogFile="true" />
+
 </databaseChangeLog>
 <!-- See Dos and Don'ts in changelog.xml -->

From a83ec6e76a4cedd0a8f29e29a41940bb6064140f Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 29 Sep 2023 16:33:52 -0400
Subject: [PATCH 221/326] [WX-1234] Update CHANGELOG.md (#7227)

Merging past CI since this is doc only.
---
 CHANGELOG.md | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 76746d972c8..a581852c02e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,19 +2,17 @@
 
 ## 86 Release Notes
 
-### HTTPFilesystem Improvements
-
-WDL `size` engine function now works for HTTP files. 
-
-### Azure ApplicationInsights Logging Support
-Cromwell can now send logs to Azure Application Insights. To enable, set environment 
-variable `APPLICATIONINSIGHTS_INSTRUMENTATIONKEY` to your account's key. [See here for information.](https://learn.microsoft.com/en-us/azure/azure-monitor/app/sdk-connection-string)
+### GCP Batch
+Cromwell now supports the GCP Batch backend for running workflows. See `Backend` in [ReadTheDocs](https://cromwell.readthedocs.io/en/stable/) for more information.
 
 ### Workflow Completion Callback
+Cromwell can be configured to send a POST request to a specified URL when a workflow completes. The request body includes the workflow ID, terminal state,
+and (if applicable) final outputs or error message. See `WorkflowCallback` in [ReadTheDocs](https://cromwell.readthedocs.io/en/stable/) for more information.
 
-Cromwell can be configured to send a POST request to a specified URL when a workflow completes. The request body
-includes the workflow id, terminal state, and (if applicable) final outputs or error message.
-See `WorkflowCallback` in [ReadTheDocs](https://cromwell.readthedocs.io/en/stable/) for more information.
+### Other Improvements
+* Cromwell will now parallelize the downloads of DRS files that resolve to signed URLs. This significantly reduces the time localization takes in certain situations.
+* WDL size engine function now works for HTTP files
+* Improved Cromwell's handling of docker manifests. Additional logging information is emitted, and Cromwell will fall back to using OCI manifests if it encounters an error with a Docker Image Manifest V2. 
 
 ## 85 Release Notes
 

From fc9e3cc9ceb081396d3b17027b11ddef14dced93 Mon Sep 17 00:00:00 2001
From: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Date: Mon, 2 Oct 2023 10:35:30 -0400
Subject: [PATCH 222/326] WM-2252: Configurable metadata write role (#7225)

Co-authored-by: dvoet <dvoet@users.noreply.github.com>
---
 .../database/slick/MetadataSlickDatabase.scala         | 10 +++++++---
 .../finalization/WorkflowCallbackActorSpec.scala       |  2 +-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
index 0a33e4b6b72..eb87f88d101 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
@@ -1,7 +1,6 @@
 package cromwell.database.slick
 
 import java.sql.Timestamp
-
 import cats.syntax.functor._
 import cats.instances.future._
 import com.typesafe.config.{Config, ConfigFactory}
@@ -10,6 +9,7 @@ import cromwell.database.sql.MetadataSqlDatabase
 import cromwell.database.sql.SqlConverters._
 import cromwell.database.sql.joins.{CallOrWorkflowQuery, CallQuery, MetadataJobQueryValue, WorkflowQuery}
 import cromwell.database.sql.tables.{CustomLabelEntry, InformationSchemaEntry, MetadataEntry, WorkflowMetadataSummaryEntry}
+import net.ceedubs.ficus.Ficus._
 import slick.basic.DatabasePublisher
 import slick.jdbc.{ResultSetConcurrency, ResultSetType}
 
@@ -60,6 +60,8 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
   import dataAccess.driver.api._
   import MetadataSlickDatabase._
 
+  lazy val pgLargeObjectWriteRole: Option[String] = originalDatabaseConfig.as[Option[String]]("pgLargeObjectWriteRole")
+
   override def existsMetadataEntries()(implicit ec: ExecutionContext): Future[Boolean] = {
     val action = dataAccess.metadataEntriesExists.result
     runTransaction(action)
@@ -87,6 +89,8 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
         rootWorkflowIdKey,
         labelMetadataKey)
 
+    val roleSet = pgLargeObjectWriteRole.map(role => sqlu"""SET ROLE TO "#$role"""")
+
     // These entries also require a write to the summary queue.
     def writeSummarizable(): Future[Unit] = if (partitioned.summarizableMetadata.isEmpty) Future.successful(()) else {
       val batchesToWrite = partitioned.summarizableMetadata.grouped(insertBatchSize).toList
@@ -94,13 +98,13 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
         val insertMetadata = dataAccess.metadataEntryIdsAutoInc ++= batch
         insertMetadata.flatMap(ids => writeSummaryQueueEntries(ids))
       }
-      runTransaction(DBIO.sequence(insertActions)).void
+      runTransaction(DBIO.sequence(roleSet ++ insertActions)).void
     }
 
     // Non-summarizable metadata that only needs to go to the metadata table can be written much more efficiently
     // than summarizable metadata.
     def writeNonSummarizable(): Future[Unit] = if (partitioned.nonSummarizableMetadata.isEmpty) Future.successful(()) else {
-      val action = DBIO.sequence(partitioned.nonSummarizableMetadata.grouped(insertBatchSize).map(dataAccess.metadataEntries ++= _))
+      val action = DBIO.sequence(roleSet ++ partitioned.nonSummarizableMetadata.grouped(insertBatchSize).map(dataAccess.metadataEntries ++= _))
       runLobAction(action).void
     }
 
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
index c469d1dcaa2..97479d348ae 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
@@ -35,7 +35,7 @@ class WorkflowCallbackActorSpec
   private val serviceRegistryActor = TestProbe("testServiceRegistryActor")
   private val deathWatch = TestProbe("deathWatch")
   private val mockUri = new URI("http://example.com")
-  private val basicConfig = WorkflowCallbackConfig.empty.copy(enabled = true)
+  private val basicConfig = WorkflowCallbackConfig.empty.copy(enabled = true).copy(retryBackoff = SimpleExponentialBackoff(100.millis, 200.millis, 1.1))
   private val basicOutputs = WomMocks.mockOutputExpectations(List("foo" -> WomString("bar")).toMap)
 
   private val httpSuccess = Future.successful(HttpResponse.apply(StatusCodes.OK))

From d967bcdba2cf8d321c34837eceba2b48a62aa42b Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 2 Oct 2023 17:01:36 +0000
Subject: [PATCH 223/326] Update cromwell version from 86 to 87

---
 project/Version.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Version.scala b/project/Version.scala
index cfdd3352dc2..4de639d9d41 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -6,7 +6,7 @@ import com.github.sbt.git.SbtGit
 
 object Version {
   // Upcoming release, or current if we're on a master / hotfix branch
-  val cromwellVersion = "86"
+  val cromwellVersion = "87"
 
   /**
     * Returns true if this project should be considered a snapshot.

From c7b043b7b534454d49561f3e2a2b9cf99a3c661b Mon Sep 17 00:00:00 2001
From: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Date: Wed, 4 Oct 2023 11:48:35 -0400
Subject: [PATCH 224/326] WX-1282 Update failedJobs Query to use `lo_get`
 instead of INNER JOIN against pg_largeobject (#7228)

---
 .../slick/tables/MetadataEntryComponent.scala | 19 +++++--------------
 1 file changed, 5 insertions(+), 14 deletions(-)

diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
index 1c1225c195d..8c3c0aa27c9 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
@@ -319,22 +319,14 @@ trait MetadataEntryComponent {
       if(isPostgres) s"${'"'}$identifier${'"'}" else identifier
     }
 
-    def dbMetadataValueColCheckName(isPostgres: Boolean): String = {
-      if(isPostgres) "obj.data" else "METADATA_VALUE"
+    def evaluateMetadataValue(isPostgres: Boolean, colName: String): String = {
+      if(isPostgres) s"convert_from(lo_get(${colName}::oid), 'UTF8')" else colName
     }
 
     def attemptAndIndexSelectStatement(callFqn: String, scatterIndex: String, retryAttempt: String, variablePrefix: String): String = {
       s"SELECT ${callFqn}, MAX(COALESCE(${scatterIndex}, 0)) as ${variablePrefix}Scatter, MAX(COALESCE(${retryAttempt}, 0)) AS ${variablePrefix}Retry"
     }
 
-    def pgObjectInnerJoinStatement(isPostgres: Boolean, metadataValColName: String): String = {
-      if(isPostgres) s"INNER JOIN pg_largeobject obj ON me.${metadataValColName} = cast(obj.loid as text)" else ""
-    }
-
-    def failedTaskGroupByClause(metadataValue: String, callFqn: String): String = {
-      return s"GROUP BY ${callFqn}, ${metadataValue}"
-    }
-
     val workflowUuid = dbIdentifierWrapper("WORKFLOW_EXECUTION_UUID", isPostgres)
     val callFqn = dbIdentifierWrapper("CALL_FQN", isPostgres)
     val scatterIndex = dbIdentifierWrapper("JOB_SCATTER_INDEX", isPostgres)
@@ -358,11 +350,10 @@ trait MetadataEntryComponent {
         FROM #${metadataEntry} me
         INNER JOIN #${wmse} wmse
         ON wmse.#${workflowUuid} = me.#${workflowUuid}
-        #${pgObjectInnerJoinStatement(isPostgres, metadataValue)}
         WHERE (wmse.#${rootUuid} = $rootWorkflowId OR wmse.#${workflowUuid} = $rootWorkflowId)
-        AND (me.#${metadataKey} in ('executionStatus', 'backendStatus') AND #${dbMetadataValueColCheckName(isPostgres)} = 'Failed')
-        #${failedTaskGroupByClause(dbMetadataValueColCheckName(isPostgres), callFqn)}
-        HAVING #${dbMetadataValueColCheckName(isPostgres)} = 'Failed'
+        AND (me.#${metadataKey} in ('executionStatus', 'backendStatus') AND #${evaluateMetadataValue(isPostgres, metadataValue)} = 'Failed')
+        GROUP BY #${callFqn}, #${metadataValue} 
+        HAVING #${evaluateMetadataValue(isPostgres, metadataValue)} = 'Failed'
       ) AS failedCalls
       ON me.#${callFqn} = failedCalls.#${callFqn}
       INNER JOIN (

From 2634f2f34023075f8e0dda3794e3a3ec81f2c096 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 4 Oct 2023 14:12:04 -0400
Subject: [PATCH 225/326] [WX-1234] Update Release Process with Docker
 Instructions (#7231)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 processes/release_processes/README.MD | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/processes/release_processes/README.MD b/processes/release_processes/README.MD
index 146c2479620..0d2f4e9475e 100644
--- a/processes/release_processes/README.MD
+++ b/processes/release_processes/README.MD
@@ -90,6 +90,13 @@ The workflow outputs its status to the console.
 * Announce release in `#dsp-workflows`, set expectations about when the new version will be available in Terra.
 * **One business day later,** confirm that [the Homebrew package](https://formulae.brew.sh/formula/cromwell) has the latest version. If it doesn't, start investigation by looking at [Homebrew PR's](https://github.com/Homebrew/homebrew-core/pulls?q=is%3Apr+cromwell).
 
+### Publish Docker Image
+* If the release workflow went well, it's time to also publish Docker images for this release. 
+* `git checkout` the Cromwell hash that was just published (i.e. the one directly BEFORE the "Update Cromwell version from x to x+1" commit that the publish WDL makes). It's important that the image being built uses the exact same code as the .jar files published to github.
+* Run `sbt -Dproject.isSnapshot=false -Dproject.isRelease=true dockerBuildAndPush` from your local Cromwell directory. 
+* Grab a cup of coffee, and verify that all of the new images were pushed successfully. For example, you should now be able to do `docker pull broadinstitute/cromwell:{new version #}`
+  * The list of images is `cromwell`, `cromiam`, `cromwell-drs-localizer`, and `womtool`
+
 ### How to Deploy Cromwell in CaaS staging and CaaS prod
 
 CaaS is "Cromwell as a Service". It is used by a couple of Broad teams (Pipelines and Epigenomics), though the long-term plan is for those teams to migrate to using Terra.

From 4289ec1e78a6134b69c9502a282186a37f006886 Mon Sep 17 00:00:00 2001
From: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Date: Thu, 5 Oct 2023 17:24:36 -0400
Subject: [PATCH 226/326] WM-2294: Allow role-setter action to run on change
 (#7233)

---
 .../src/main/resources/metadata_changesets/set_table_role.xml   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/database/migration/src/main/resources/metadata_changesets/set_table_role.xml b/database/migration/src/main/resources/metadata_changesets/set_table_role.xml
index 48a56bb6091..67219feeca3 100644
--- a/database/migration/src/main/resources/metadata_changesets/set_table_role.xml
+++ b/database/migration/src/main/resources/metadata_changesets/set_table_role.xml
@@ -11,7 +11,7 @@
         This changeset will be applied whenever the 'sharedCromwellDbRole' property is set.
         It runs every time to ensure the role is set correctly after all other changesets.
      -->
-    <changeSet runAlways="true" author="sshah" id="set_table_role" dbms="postgresql">
+    <changeSet runAlways="true" runOnChange="true" author="sshah" id="set_table_role" dbms="postgresql">
         <preConditions onFail="MARK_RAN">
             <!-- check that 'sharedCromwellDbRole' role is set, and matches something in the pg_roles table -->
             <sqlCheck expectedResult="1">

From c4e7566ab65daf87b0a2982f0a3fe28d4f6a0846 Mon Sep 17 00:00:00 2001
From: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Date: Fri, 6 Oct 2023 10:28:42 -0400
Subject: [PATCH 227/326] WM-2296: Callback should supply fully qualified
 output names (#7234)

---
 .../finalization/WorkflowCallbackActor.scala  |  2 +-
 .../WorkflowCallbackActorSpec.scala           | 22 +++++++++++--------
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
index 516184d023a..c8eb1790365 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
@@ -155,7 +155,7 @@ class WorkflowCallbackActor(serviceRegistryActor: ActorRef,
   }
 
   private def performCallback(workflowId: WorkflowId, callbackUri: URI, terminalState: WorkflowState, outputs: CallOutputs, failures: List[String]): Future[Done] = {
-    val callbackPostBody = CallbackMessage(workflowId.toString, terminalState.toString, outputs.outputs.map(entry => (entry._1.name, entry._2)), failures)
+    val callbackPostBody = CallbackMessage(workflowId.toString, terminalState.toString, outputs.outputs.map(entry => (entry._1.identifier.fullyQualifiedName.value, entry._2)), failures)
     for {
       entity <- Marshal(callbackPostBody).to[RequestEntity]
       headers <- makeHeaders
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
index 97479d348ae..383e75458ff 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
@@ -1,27 +1,29 @@
 package cromwell.engine.workflow.lifecycle.finalization
 
-import akka.testkit._
 import akka.http.scaladsl.client.RequestBuilding.Post
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
 import akka.http.scaladsl.model.{HttpResponse, StatusCodes}
-import akka.testkit.TestProbe
+import akka.testkit.{TestProbe, _}
 import common.mock.MockSugar
 import cromwell.core.retry.SimpleExponentialBackoff
-import org.mockito.Mockito._
-import cromwell.core.{CallOutputs, TestKitSuite, WorkflowFailed, WorkflowId, WorkflowSucceeded}
+import cromwell.core._
 import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackActor.PerformCallbackCommand
 import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackJsonSupport._
 import cromwell.services.metadata.MetadataService.PutMetadataAction
 import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
-import cromwell.util.{GracefulShutdownHelper, WomMocks}
+import cromwell.util.GracefulShutdownHelper
+import org.mockito.Mockito._
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
+import wom.graph.GraphNodePort.GraphNodeOutputPort
+import wom.graph.WomIdentifier
+import wom.types.WomStringType
 import wom.values.WomString
 
 import java.net.URI
 import java.time.Instant
-import scala.concurrent.duration._
 import scala.concurrent.Future
+import scala.concurrent.duration._
 
 class WorkflowCallbackActorSpec
   extends TestKitSuite with AnyFlatSpecLike with Matchers with MockSugar {
@@ -36,7 +38,9 @@ class WorkflowCallbackActorSpec
   private val deathWatch = TestProbe("deathWatch")
   private val mockUri = new URI("http://example.com")
   private val basicConfig = WorkflowCallbackConfig.empty.copy(enabled = true).copy(retryBackoff = SimpleExponentialBackoff(100.millis, 200.millis, 1.1))
-  private val basicOutputs = WomMocks.mockOutputExpectations(List("foo" -> WomString("bar")).toMap)
+  private val basicOutputs = CallOutputs(Map(
+    GraphNodeOutputPort(WomIdentifier("foo", "wf.foo"), WomStringType, null) -> WomString("bar")
+  ))
 
   private val httpSuccess = Future.successful(HttpResponse.apply(StatusCodes.OK))
   private val httpFailure = Future.successful(HttpResponse.apply(StatusCodes.GatewayTimeout))
@@ -64,7 +68,7 @@ class WorkflowCallbackActorSpec
     val expectedPostBody = CallbackMessage(
       workflowId.toString,
       WorkflowSucceeded.toString,
-      basicOutputs.outputs.map(entry => (entry._1.name, entry._2)),
+      Map(("wf.foo", WomString("bar"))),
       List.empty
     )
     val expectedRequest = Post(mockUri.toString, expectedPostBody)
@@ -114,7 +118,7 @@ class WorkflowCallbackActorSpec
     val expectedPostBody = CallbackMessage(
       workflowId.toString,
       WorkflowSucceeded.toString,
-      basicOutputs.outputs.map(entry => (entry._1.name, entry._2)),
+      Map(("wf.foo", WomString("bar"))),
       List.empty
     )
     val expectedRequest = Post(mockUri.toString, expectedPostBody)

From b6aae148052fdc4773cba679f564eb5947cd8975 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 11 Oct 2023 08:59:51 -0400
Subject: [PATCH 228/326] [WX-499] DRS Parallel Downloads Follow-up (#7229)

---
 .../downloaders/BulkAccessUrlDownloader.scala | 55 ++++++++-----------
 .../BulkAccessUrlDownloaderSpec.scala         | 43 ++++++---------
 project/Dependencies.scala                    |  1 +
 3 files changed, 39 insertions(+), 60 deletions(-)

diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
index 4668c5072ed..f47265d7730 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
@@ -1,7 +1,7 @@
 package drs.localizer.downloaders
 
 import cats.effect.{ExitCode, IO}
-import cloud.nio.impl.drs.{AccessUrl, DrsResolverResponse}
+import cloud.nio.impl.drs.{AccessUrl}
 import com.typesafe.scalalogging.StrictLogging
 
 import java.nio.charset.StandardCharsets
@@ -9,6 +9,9 @@ import java.nio.file.{Files, Path, Paths}
 import scala.sys.process.{Process, ProcessLogger}
 import scala.util.matching.Regex
 import drs.localizer.ResolvedDrsUrl
+import spray.json.DefaultJsonProtocol.{StringJsonFormat, listFormat, mapFormat}
+import spray.json._
+
 case class GetmResult(returnCode: Int, stderr: String)
 /**
   * Getm is a python tool that is used to download resolved DRS uris quickly and in parallel.
@@ -40,39 +43,25 @@ case class BulkAccessUrlDownloader(resolvedUrls : List[ResolvedDrsUrl]) extends
     * @return Filepath of a getm-manifest.json that Getm can use to download multiple files in parallel.
     */
   def generateJsonManifest(resolvedUrls : List[ResolvedDrsUrl]): IO[Path] = {
-    def toJsonString(drsResponse: DrsResolverResponse, destinationFilepath: String): String = {
-      //NB: trailing comma is being removed in generateJsonManifest
-      val accessUrl: AccessUrl = drsResponse.accessUrl.getOrElse(AccessUrl("missing", None))
-      drsResponse.hashes.map(_ => {
-        val checksum = GetmChecksum(drsResponse.hashes, accessUrl).value.getOrElse("error_calculating_checksum")
-        val checksumAlgorithm = GetmChecksum(drsResponse.hashes, accessUrl).getmAlgorithm
-        s"""  {
-           |    "url" : "${accessUrl.url}",
-           |    "filepath" : "$destinationFilepath",
-           |    "checksum" : "$checksum",
-           |    "checksum-algorithm" : "$checksumAlgorithm"
-           |  },
-           |""".stripMargin
-      }).getOrElse(
-        s"""  {
-           |    "url" : "${accessUrl.url}",
-           |    "filepath" : "$destinationFilepath"
-           |  },
-           |""".stripMargin
-      )
-    }
-    IO {
-      var jsonString: String = "[\n"
-      for (resolvedUrl <- resolvedUrls) {
-        jsonString += toJsonString(resolvedUrl.drsResponse, resolvedUrl.downloadDestinationPath)
-      }
-      if(jsonString.contains(',')) {
-        //remove trailing comma from array elements, but don't crash on empty list.
-        jsonString = jsonString.substring(0, jsonString.lastIndexOf(","))
-      }
-      jsonString += "\n]"
-      Files.write(getmManifestPath, jsonString.getBytes(StandardCharsets.UTF_8))
+    def resolvedUrlToJsonMap(resolvedUrl: ResolvedDrsUrl): Map[String,String] = {
+      val accessUrl: AccessUrl = resolvedUrl.drsResponse.accessUrl.getOrElse(AccessUrl("missing", None))
+      resolvedUrl.drsResponse.hashes.map{_ =>
+        val checksum = GetmChecksum(resolvedUrl.drsResponse.hashes, accessUrl).value.getOrElse("error_calculating_checksum")
+        val checksumAlgorithm = GetmChecksum(resolvedUrl.drsResponse.hashes, accessUrl).getmAlgorithm
+        Map(
+          ("url", accessUrl.url),
+          ("filepath", resolvedUrl.downloadDestinationPath),
+          ("checksum", checksum),
+          ("checksum-algorithm", checksumAlgorithm)
+        )
+      }.getOrElse(Map(
+        ("url", accessUrl.url),
+        ("filepath", resolvedUrl.downloadDestinationPath)
+      ))
     }
+
+    val jsonArray: String = resolvedUrls.map(resolved => resolvedUrlToJsonMap(resolved)).toJson.prettyPrint
+    IO(Files.write(getmManifestPath, jsonArray.getBytes(StandardCharsets.UTF_8)))
   }
 
   def deleteJsonManifest() = {
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
index 7b96ece8d0a..0e0714febb8 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
@@ -20,22 +20,17 @@ class BulkAccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec w
   val threeElements: List[ResolvedDrsUrl] = List(ex1, ex2, ex3)
 
   it should "correctly parse a collection of Access Urls into a manifest.json" in {
-    val expected: String =
-      s"""|[
-          |  {
-          |    "url" : "https://my.fake/url123",
-          |    "filepath" : "path/to/local/download/dest"
-          |  },
-          |  {
-          |    "url" : "https://my.fake/url1234",
-          |    "filepath" : "path/to/local/download/dest2"
-          |  },
-          |  {
-          |    "url" : "https://my.fake/url1235",
-          |    "filepath" : "path/to/local/download/dest3"
-          |  }
-          |]""".stripMargin
-
+    val expected =
+      """[{
+        |  "url": "https://my.fake/url123",
+        |  "filepath": "path/to/local/download/dest"
+        |}, {
+        |  "url": "https://my.fake/url1234",
+        |  "filepath": "path/to/local/download/dest2"
+        |}, {
+        |  "url": "https://my.fake/url1235",
+        |  "filepath": "path/to/local/download/dest3"
+        |}]""".stripMargin
     val downloader = BulkAccessUrlDownloader(threeElements)
 
     val filepath: IO[Path] = downloader.generateJsonManifest(threeElements)
@@ -45,11 +40,7 @@ class BulkAccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec w
   }
 
   it should "properly construct empty JSON array from empty list." in {
-    val expected: String =
-      s"""|[
-          |
-          |]""".stripMargin
-
+    val expected: String = "[]"
     val downloader = BulkAccessUrlDownloader(emptyList)
     val filepath: IO[Path] = downloader.generateJsonManifest(emptyList)
     val source = scala.io.Source.fromFile(filepath.unsafeRunSync().toString)
@@ -59,12 +50,10 @@ class BulkAccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec w
 
   it should "properly construct JSON array from single element list." in {
     val expected: String =
-      s"""|[
-          |  {
-          |    "url" : "https://my.fake/url123",
-          |    "filepath" : "path/to/local/download/dest"
-          |  }
-          |]""".stripMargin
+      s"""|[{
+          |  "url": "https://my.fake/url123",
+          |  "filepath": "path/to/local/download/dest"
+          |}]""".stripMargin
 
     val downloader = BulkAccessUrlDownloader(oneElement)
     val filepath: IO[Path] = downloader.generateJsonManifest(oneElement)
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index b2e94cc7470..2bc4ec34f00 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -652,6 +652,7 @@ object Dependencies {
     "com.softwaremill.sttp" %% "circe" % sttpV,
     "com.github.scopt" %% "scopt" % scoptV,
     "org.apache.commons" % "commons-csv" % commonsCsvV,
+    "io.spray" %% "spray-json" % sprayJsonV,
   ) ++ circeDependencies ++ catsDependencies ++ slf4jBindingDependencies ++ languageFactoryDependencies ++ azureDependencies
 
   val allProjectDependencies: List[ModuleID] =

From aeacb3a41426c7971e5b5675d03bec4727d7bb12 Mon Sep 17 00:00:00 2001
From: dspeck1 <dspeck@burwood.com>
Date: Fri, 13 Oct 2023 12:29:30 -0500
Subject: [PATCH 229/326] WX-1318 gcp batch: Add GPU driver install (#7235)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 ...cpBatchAsyncBackendJobExecutionActor.scala |  5 --
 .../api/GcpBatchRequestFactoryImpl.scala      | 53 +++++++++----------
 .../models/GcpBatchRuntimeAttributes.scala    |  9 +++-
 .../google/batch/runnable/UserRunnable.scala  |  3 --
 4 files changed, 33 insertions(+), 37 deletions(-)

diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
index b2b10d92afb..ae228ad503b 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
@@ -829,12 +829,7 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       _ <- evaluateRuntimeAttributes
       _ <- uploadScriptFile()
       customLabels <- Future.fromTry(GcpLabel.fromWorkflowOptions(workflowDescriptor.workflowOptions))
-      _ = customLabels.foreach(x => println(s"ZZZ Custom Labels - $x"))
       batchParameters <- generateInputOutputParameters
-      _ = batchParameters.fileInputParameters.foreach(x => println(s"ZZZ File InputParameters - $x"))
-      _ = batchParameters.jobInputParameters.foreach(x => println(s"ZZZ InputParameters - $x"))
-      _ = batchParameters.fileOutputParameters.foreach(x => println(s"ZZZ File OutputParameters - $x"))
-      _ = batchParameters.jobOutputParameters.foreach(x => println(s"ZZZ OutputParameters - $x"))
       createParameters = createBatchParameters(batchParameters, customLabels)
       drsLocalizationManifestCloudPath = jobPaths.callExecutionRoot / GcpBatchJobPaths.DrsLocalizationManifestName
       _ <- uploadDrsLocalizationManifest(createParameters, drsLocalizationManifestCloudPath)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
index 435992b8cd8..9c482d852d1 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
@@ -1,17 +1,14 @@
 package cromwell.backend.google.batch.api
 
-import com.google.cloud.batch.v1.AllocationPolicy.Accelerator
-import com.google.cloud.batch.v1.{DeleteJobRequest, GetJobRequest, JobName}
-import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
-import cromwell.backend.google.batch.models.GcpBatchRequest
-import cromwell.backend.google.batch.runnable._
-import cromwell.backend.google.batch.util.BatchUtilityConversions
-import com.google.cloud.batch.v1.AllocationPolicy.{AttachedDisk, InstancePolicy, InstancePolicyOrTemplate, LocationPolicy, NetworkInterface, NetworkPolicy, ProvisioningModel}
+import com.google.cloud.batch.v1.AllocationPolicy._
 import com.google.cloud.batch.v1.LogsPolicy.Destination
-import com.google.cloud.batch.v1.{AllocationPolicy, ComputeResource, CreateJobRequest, Job, LogsPolicy, Runnable, ServiceAccount, TaskGroup, TaskSpec, Volume}
+import com.google.cloud.batch.v1.{AllocationPolicy, ComputeResource, CreateJobRequest, DeleteJobRequest, GetJobRequest, Job, JobName, LogsPolicy, Runnable, ServiceAccount, TaskGroup, TaskSpec, Volume}
 import com.google.protobuf.Duration
 import cromwell.backend.google.batch.io.GcpBatchAttachedDisk
-import cromwell.backend.google.batch.models.VpcAndSubnetworkProjectLabelValues
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
+import cromwell.backend.google.batch.models.{GcpBatchRequest, VpcAndSubnetworkProjectLabelValues}
+import cromwell.backend.google.batch.runnable._
+import cromwell.backend.google.batch.util.BatchUtilityConversions
 
 import scala.jdk.CollectionConverters._
 
@@ -61,10 +58,11 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
       .build
   }
 
-  private def createInstancePolicy(cpuPlatform: String, spotModel: ProvisioningModel, accelerators: Option[Accelerator.Builder], attachedDisks: List[AttachedDisk]) = {
+  private def createInstancePolicy(cpuPlatform: String, spotModel: ProvisioningModel, accelerators: Option[Accelerator.Builder], attachedDisks: List[AttachedDisk]): InstancePolicy.Builder = {
 
     //set GPU count to 0 if not included in workflow
-    val gpuAccelerators = accelerators.getOrElse(Accelerator.newBuilder.setCount(0).setType(""))
+    val gpuAccelerators = accelerators.getOrElse(Accelerator.newBuilder.setCount(0).setType("")) // TODO: Driver version
+
     val instancePolicy = InstancePolicy
       .newBuilder
       .setProvisioningModel(spotModel)
@@ -83,7 +81,6 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
 
   }
 
-
   private def createNetworkPolicy(networkInterface: NetworkInterface): NetworkPolicy = {
     NetworkPolicy
       .newBuilder
@@ -113,8 +110,9 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
 
   }
 
-  private def createAllocationPolicy(data: GcpBatchRequest, locationPolicy: LocationPolicy, instancePolicy: InstancePolicy, networkPolicy: NetworkPolicy, serviceAccount: ServiceAccount) = {
-    AllocationPolicy
+  private def createAllocationPolicy(data: GcpBatchRequest, locationPolicy: LocationPolicy, instancePolicy: InstancePolicy, networkPolicy: NetworkPolicy, serviceAccount: ServiceAccount, accelerators: Option[Accelerator.Builder]) = {
+
+    val allocationPolicy = AllocationPolicy
       .newBuilder
       .setLocation(locationPolicy)
       .setNetwork(networkPolicy)
@@ -122,13 +120,19 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
       .putLabels("goog-batch-worker", "true")
       .putAllLabels((data.createParameters.googleLabels.map(label => label.key -> label.value).toMap.asJava))
       .setServiceAccount(serviceAccount)
-      .addInstances(InstancePolicyOrTemplate
-        .newBuilder
-        .setPolicy(instancePolicy)
-        .build)
-      .build
+      .buildPartial()
+
+    val gpuAccelerators = accelerators.getOrElse(Accelerator.newBuilder.setCount(0).setType(""))
+
+    //add GPUs if GPU count is greater than or equal to 1
+    if (gpuAccelerators.getCount >= 1) {
+      allocationPolicy.toBuilder.addInstances(InstancePolicyOrTemplate.newBuilder.setPolicy(instancePolicy).setInstallGpuDrivers(true).build)
+    } else {
+      allocationPolicy.toBuilder.addInstances(InstancePolicyOrTemplate.newBuilder.setPolicy(instancePolicy).build)
+    }
   }
 
+
   override def submitRequest(data: GcpBatchRequest): CreateJobRequest = {
 
     val batchAttributes = data.gcpBatchParameters.batchAttributes
@@ -160,10 +164,6 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
     // Batch defaults to 1 task
     val taskCount: Long = 1
 
-    println(f"command script container path ${data.createParameters.commandScriptContainerPath}")
-    println(f"cloud workflow root ${data.createParameters.cloudWorkflowRoot}")
-    println(f"all parameters:\n ${data.createParameters.allParameters.mkString("\n")}")
-
     // parse preemption value and set value for Spot. Spot is replacement for preemptible
     val spotModel = toProvisioningModel(runtimeAttributes.preemptible)
 
@@ -205,11 +205,11 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
     val taskGroup: TaskGroup = createTaskGroup(taskCount, taskSpec)
     val instancePolicy = createInstancePolicy(cpuPlatform, spotModel, accelerators, allDisks)
     val locationPolicy = LocationPolicy.newBuilder.addAllowedLocations(zones).build
-    val allocationPolicy = createAllocationPolicy(data, locationPolicy, instancePolicy.build, networkPolicy, gcpSa)
+    val allocationPolicy = createAllocationPolicy(data, locationPolicy, instancePolicy.build, networkPolicy, gcpSa, accelerators)
     val job = Job
       .newBuilder
       .addTaskGroups(taskGroup)
-      .setAllocationPolicy(allocationPolicy)
+      .setAllocationPolicy(allocationPolicy.build())
       .putLabels("submitter", "cromwell") // label to signify job submitted by cromwell for larger tracking purposes within GCP batch
       .putLabels("goog-batch-worker", "true")
       .putAllLabels((data.createParameters.googleLabels.map(label => label.key -> label.value).toMap.asJava))
@@ -218,9 +218,6 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
         .setDestination(Destination.CLOUD_LOGGING)
         .build)
 
-    println(f"job shell ${data.createParameters.jobShell}")
-    println(f"script container path ${data.createParameters.commandScriptContainerPath}")
-    println(f"labels ${data.createParameters.googleLabels}")
 
     CreateJobRequest
       .newBuilder
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
index 9fe3327f35d..c9dc62b0cc7 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
@@ -19,6 +19,8 @@ import wom.values.{WomArray, WomBoolean, WomInteger, WomString, WomValue}
 
 object GpuResource {
 
+  val DefaultNvidiaDriverVersion = "418.87.00"
+
   final case class GpuType(name: String) {
     override def toString: String = name
   }
@@ -99,6 +101,9 @@ object GcpBatchRuntimeAttributes {
   private def cpuPlatformValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] = cpuPlatformValidationInstance
   private def gpuTypeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[GpuType] = GpuTypeValidation.optional
 
+  val GpuDriverVersionKey = "nvidiaDriverVersion"
+  private def gpuDriverValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] = new StringRuntimeAttributesValidation(GpuDriverVersionKey).optional
+
   private def gpuCountValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optional
   private def gpuMinValidation(runtimeConfig: Option[Config]):OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optionalMin
 
@@ -159,6 +164,7 @@ object GcpBatchRuntimeAttributes {
     StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
       gpuCountValidation(runtimeConfig),
       gpuTypeValidation(runtimeConfig),
+      gpuDriverValidation(runtimeConfig),
       cpuValidation(runtimeConfig),
       cpuPlatformValidation(runtimeConfig),
       cpuMinValidation(runtimeConfig),
@@ -189,8 +195,9 @@ object GcpBatchRuntimeAttributes {
       .extractOption(gpuTypeValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
     lazy val gpuCount: Option[Int Refined Positive] = RuntimeAttributesValidation
       .extractOption(gpuCountValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+    lazy val gpuDriver: Option[String] = RuntimeAttributesValidation.extractOption(gpuDriverValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
 
-    val gpuResource: Option[GpuResource] = if (gpuType.isDefined || gpuCount.isDefined) {
+    val gpuResource: Option[GpuResource] = if (gpuType.isDefined || gpuCount.isDefined || gpuDriver.isDefined) {
       Option(GpuResource(gpuType.getOrElse(GpuType.DefaultGpuType), gpuCount
         .getOrElse(GpuType.DefaultGpuCount)))
     } else {
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala
index b7f5a026476..d2d499b3127 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala
@@ -8,9 +8,6 @@ trait UserRunnable {
 
   def userRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume]): List[Runnable] = {
 
-    println(f"job shell ${createParameters.jobShell}")
-    println(f"script container path ${createParameters.commandScriptContainerPath}")
-
     val userRunnable = RunnableBuilder.userRunnable(
       docker = createParameters.dockerImage,
       scriptContainerPath = createParameters.commandScriptContainerPath.pathAsString,

From c9d4ce4287a5da9bff097244b664135171021f7e Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 13 Oct 2023 16:02:33 -0400
Subject: [PATCH 230/326] WX-1232 Include useful workflow ids in TES tags
 (#7221)

---
 .../main/scala/cromwell/backend/backend.scala |  1 +
 .../cromwell/backend/impl/tes/TesTask.scala   | 19 +++--
 .../backend/impl/tes/TesTaskSpec.scala        | 70 ++++++++++++++++++-
 3 files changed, 83 insertions(+), 7 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index ea413c10367..33d16f34b5a 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -84,6 +84,7 @@ case class BackendWorkflowDescriptor(id: WorkflowId,
   val rootWorkflow = breadCrumbs.headOption.map(_.callable).getOrElse(callable)
   val possiblyNotRootWorkflowId = id.toPossiblyNotRoot
   val rootWorkflowId = breadCrumbs.headOption.map(_.id).getOrElse(id).toRoot
+  val possibleParentWorkflowId = breadCrumbs.lastOption.map(_.id)
 
   override def toString: String = s"[BackendWorkflowDescriptor id=${id.shortString} workflowName=${callable.name}]"
   def getWorkflowOption(key: WorkflowOption) = workflowOptions.get(key).toOption
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index a345e87ebf7..4a6e77641e3 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -2,14 +2,13 @@ package cromwell.backend.impl.tes
 import common.collections.EnhancedCollections._
 import common.util.StringUtil._
 import cromwell.backend.impl.tes.OutputMode.OutputMode
-import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor}
+import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendWorkflowDescriptor}
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import net.ceedubs.ficus.Ficus._
 
 import scala.language.postfixOps
 import scala.util.Try
-
 import wdl.draft2.model.FullyQualifiedName
 import wdl4s.parser.MemoryUnit
 import wom.InstantiatedCommand
@@ -244,6 +243,8 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
     preferedWorkflowExecutionIdentity,
     Option(tesPaths.tesTaskRoot)
   )
+
+  val tags: Map[String, Option[String]] = TesTask.makeTags(jobDescriptor.workflowDescriptor)
 }
 
 object TesTask {
@@ -287,6 +288,16 @@ object TesTask {
     )
   }
 
+  def makeTags(workflowDescriptor: BackendWorkflowDescriptor): Map[String, Option[String]] = {
+    // In addition to passing through any workflow labels, include relevant workflow ids as tags.
+    val baseTags = workflowDescriptor.customLabels.asMap.map { case (k, v) => (k, Option(v)) }
+    baseTags ++ Map(
+      "workflow_id" -> Option(workflowDescriptor.id.toString),
+      "root_workflow_id" -> Option(workflowDescriptor.rootWorkflowId.toString),
+      "parent_workflow_id" -> workflowDescriptor.possibleParentWorkflowId.map(_.toString)
+    )
+  }
+
   def makeTask(tesTask: TesTask): Task = {
     Task(
       id = None,
@@ -298,7 +309,7 @@ object TesTask {
       resources = Option(tesTask.resources),
       executors = tesTask.executors,
       volumes = None,
-      tags = Option(tesTask.jobDescriptor.workflowDescriptor.customLabels.asMap),
+      tags = Option(tesTask.tags),
       logs = None
     )
   }
@@ -314,7 +325,7 @@ final case class Task(id: Option[String],
                       resources: Option[Resources],
                       executors: Seq[Executor],
                       volumes: Option[Seq[String]],
-                      tags: Option[Map[String, String]],
+                      tags: Option[Map[String, Option[String]]],
                       logs: Option[Seq[TaskLog]])
 
 final case class Executor(image: String,
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index 25a8f55f682..b7887b29944 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -3,8 +3,8 @@ package cromwell.backend.impl.tes
 import common.assertion.CromwellTimeoutSpec
 import common.mock.MockSugar
 import cromwell.backend.validation.ContinueOnReturnCodeSet
-import cromwell.backend.{BackendSpec, TestConfig}
-import cromwell.core.WorkflowOptions
+import cromwell.backend.{BackendSpec, BackendWorkflowDescriptor, TestConfig}
+import cromwell.core.{RootWorkflowId, WorkflowId, WorkflowOptions}
 import cromwell.core.labels.Labels
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.DefaultPathBuilder
@@ -13,6 +13,8 @@ import org.scalatest.matchers.should.Matchers
 import spray.json.{JsObject, JsValue}
 import wom.InstantiatedCommand
 
+import java.util.UUID
+
 class TesTaskSpec
   extends AnyFlatSpec
     with CromwellTimeoutSpec
@@ -117,6 +119,42 @@ class TesTaskSpec
     val emptyWorkflowOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))
     val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld,
                                                         labels = Labels("foo" -> "bar"))
+    val jobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+      Map.empty,
+      emptyWorkflowOptions,
+      Set.empty)
+    val tesPaths = TesJobPaths(jobDescriptor.key,
+      jobDescriptor.workflowDescriptor,
+      TestConfig.emptyConfig)
+    val tesTask = TesTask(jobDescriptor,
+      TestConfig.emptyBackendConfigDescriptor,
+      jobLogger,
+      tesPaths,
+      runtimeAttributes,
+      DefaultPathBuilder.build("").get,
+      "",
+      InstantiatedCommand("command"),
+      "",
+      Map.empty,
+      "",
+      OutputMode.ROOT)
+
+    val task = TesTask.makeTask(tesTask)
+
+    task.tags shouldBe Option(
+      Map(
+        "foo" -> Option("bar"),
+        "workflow_id" -> Option(workflowDescriptor.id.toString),
+        "root_workflow_id" -> Option(workflowDescriptor.id.toString),
+        "parent_workflow_id" -> None
+      )
+    )
+  }
+
+  it should "put workflow ids in tags" in {
+    val jobLogger = mock[JobLogger]
+    val emptyWorkflowOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))
+    val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld)
     val jobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
                                                             Map.empty,
                                                             emptyWorkflowOptions,
@@ -139,6 +177,32 @@ class TesTaskSpec
 
     val task = TesTask.makeTask(tesTask)
 
-    task.tags shouldBe Option(Map("foo" -> "bar"))
+    task.tags shouldBe Option(
+      Map(
+        "workflow_id" -> Option(workflowDescriptor.id.toString),
+        "root_workflow_id" -> Option(workflowDescriptor.id.toString),
+        "parent_workflow_id" -> None
+      )
+    )
+  }
+
+  it should "put non-root workflow ids in tags" in {
+    // Doing this test with mocks rather than real job/workflow descriptors as above because
+    // getting the subworkflow structure build was really hard.
+    val rootWorkflowId = RootWorkflowId(UUID.randomUUID())
+    val subWorkflowId = WorkflowId(UUID.randomUUID())
+    val subSubWorkflowId = WorkflowId(UUID.randomUUID())
+
+    val workflowDescriptor = mock[BackendWorkflowDescriptor]
+    workflowDescriptor.customLabels returns Labels.empty
+    workflowDescriptor.id returns subSubWorkflowId
+    workflowDescriptor.rootWorkflowId returns rootWorkflowId
+    workflowDescriptor.possibleParentWorkflowId returns Option(subWorkflowId)
+
+    TesTask.makeTags(workflowDescriptor) shouldBe Map(
+      "workflow_id" -> Option(subSubWorkflowId.toString),
+      "root_workflow_id" -> Option(rootWorkflowId.toString),
+      "parent_workflow_id" -> Option(subWorkflowId.toString)
+    )
   }
 }

From 3baa86912acc0d5c7d31168485b6e4643b95f8fb Mon Sep 17 00:00:00 2001
From: xquek <46759870+xquek@users.noreply.github.com>
Date: Mon, 16 Oct 2023 08:41:31 -0700
Subject: [PATCH 231/326] Options to publish status only (#36)

* add options to publish status only

* updated readme.md

---------

Co-authored-by: quekx <quekx@gene.com>
---
 .../metadata/impl/aws/SnsMetadataServiceActor.scala  | 12 ++++++++++--
 .../main/scala/cromwell/backend/impl/aws/README.md   |  4 +++-
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
index da66ae4f7f4..4fc9f43328e 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
@@ -46,7 +46,7 @@ import software.amazon.awssdk.services.sns.model.PublishRequest
 import spray.json.enrichAny
 
 import scala.concurrent.{ExecutionContextExecutor, Future}
-import scala.util.{Failure, Success}
+import scala.util.{Failure, Success, Try}
 
 
 /**
@@ -61,6 +61,10 @@ class AwsSnsMetadataServiceActor(serviceConfig: Config, globalConfig: Config, se
 
   //setup sns client
   val topicArn: String = serviceConfig.getString("aws.topicArn")
+  val publishStatusOnly: Boolean = Try(serviceConfig.getBoolean("aws.publishStatusOnly")) match {
+    case Failure(_) => false
+    case Success(value) => value
+  }
 
   val awsConfig: AwsConfiguration = AwsConfiguration(globalConfig)
   val credentialsProviderChain: AwsCredentialsProviderChain =
@@ -74,7 +78,11 @@ class AwsSnsMetadataServiceActor(serviceConfig: Config, globalConfig: Config, se
   def publishMessages(events: Iterable[MetadataEvent]): Future[Unit] = {
     import AwsSnsMetadataServiceActor.EnhancedMetadataEvents
 
-    val eventsJson = events.toJson
+    val eventsJson = if (publishStatusOnly) {
+      events.filter(_.key.key == "status").toJson
+    } else {
+      events.toJson
+    }
     //if there are no events then don't publish anything
     if( eventsJson.length < 1) { return Future(())}
     log.debug(f"Publishing to $topicArn : $eventsJson")
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 613607da42a..48bc3adc442 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -227,6 +227,7 @@ In the AWS backend those notifications can be send to **SNS Topic** or **EventBr
 #### AWS SNS
 
 1. Create an SNS topic, add the following to your `cromwell.conf` file and replace `topicArn` with the topic's ARN you just created:
+2. By default, all cromwell events will be publish to sns. Set `publishStatusOnly = true` if you only publish events that are `status` updates.
 
 ```
 services {
@@ -241,12 +242,13 @@ services {
                 }]
                 region = "us-east-1"
                 topicArn = "<topicARN>"
+                publishStatusOnly = true
             }
         }
     }
 }
 ```
-2. Add `sns:Publish` IAM policy to your Cromwell server IAM role. 
+3. Add `sns:Publish` IAM policy to your Cromwell server IAM role. 
 
 #### AWS EventBridge
 

From 4d16f01c9d969e726a9efc6debd19dcd968bdf01 Mon Sep 17 00:00:00 2001
From: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Date: Thu, 26 Oct 2023 15:33:33 -0400
Subject: [PATCH 232/326] WX-1307 Azure E2E test (#7239)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .github/workflows/azure_e2e_run_workflow.yml | 136 +++++++++++++++++++
 .gitignore                                   |   6 +
 2 files changed, 142 insertions(+)
 create mode 100644 .github/workflows/azure_e2e_run_workflow.yml

diff --git a/.github/workflows/azure_e2e_run_workflow.yml b/.github/workflows/azure_e2e_run_workflow.yml
new file mode 100644
index 00000000000..d2df9b38441
--- /dev/null
+++ b/.github/workflows/azure_e2e_run_workflow.yml
@@ -0,0 +1,136 @@
+name: 'Azure e2e - Run Workflow'
+on:
+  schedule:
+    - cron: '0 16 * * *' # UTC 4pm, EST 11am, EDT 12pm
+  workflow_dispatch:
+    inputs:
+      target-branch:
+        description: 'Branch name of dsp-reusable-workflows repo to run tests on'
+        required: true
+        default: 'main'
+        type: string
+      owner-subject:
+        description: 'Owner of billing project'
+        required: true
+        default: 'hermione.owner@quality.firecloud.org'
+        type: string
+      service-account:
+        description: 'Email address or unique identifier of the Google Cloud service account for which to generate credentials'
+        required: true
+        default: 'firecloud-qa@broad-dsde-qa.iam.gserviceaccount.com'
+        type: string
+
+env:
+  BROADBOT_TOKEN: '${{ secrets.BROADBOT_GITHUB_TOKEN }}' # github token for access to kick off a job in the private repo
+  RUN_NAME_SUFFIX: '${{ github.event.repository.name }}-${{ github.run_id }}-${{ github.run_attempt }}'
+
+jobs:
+
+  # This job provisions useful parameters for e2e tests
+  params-gen:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: 'read'
+      id-token: 'write'
+    outputs:
+      project-name: ${{ steps.gen.outputs.project_name }}
+      bee-name: '${{ github.event.repository.name }}-${{ github.run_id }}-${{ github.run_attempt}}-dev'
+    steps:
+      - name: Generate a random billing project name
+        id: 'gen'
+        run: |
+          project_name=$(echo "tmp-billing-project-$(uuidgen)" | cut -c -30)
+          echo "project_name=${project_name}" >> $GITHUB_OUTPUT
+  
+  create-bee-workflow:
+    runs-on: ubuntu-latest
+    needs: [params-gen]
+    permissions:
+      contents: 'read'
+      id-token: 'write'
+    steps:
+      - name: Dispatch to terra-github-workflows
+        uses: broadinstitute/workflow-dispatch@v3
+        with:
+          workflow: bee-create
+          repo: broadinstitute/terra-github-workflows
+          ref: refs/heads/main
+          token: ${{ env.BROADBOT_TOKEN }}
+          # NOTE: Opting to use "prod" instead of custom tag since I specifically want to test against the current prod state
+          # NOTE: For testing/development purposes I'm using dev
+          inputs: '{ "bee-name": "${{ needs.params-gen.outputs.bee-name }}", "version-template": "dev", "bee-template-name": "rawls-e2e-azure-tests"}'
+  
+  create-and-attach-billing-project-to-landing-zone-workflow:
+    runs-on: ubuntu-latest
+    needs: [create-bee-workflow, params-gen]
+    steps:
+      - name: dispatch to terra-github-workflows
+        uses: broadinstitute/workflow-dispatch@v3
+        with:
+          workflow: attach-billing-project-to-landing-zone.yaml
+          repo: broadinstitute/terra-github-workflows
+          ref: refs/heads/main
+          token: ${{ env.BROADBOT_TOKEN }}
+          inputs: '{
+            "run-name": "attach-billing-project-to-landing-zone-${{ env.RUN_NAME_SUFFIX }}",
+            "bee-name": "${{ needs.params-gen.outputs.bee-name }}",
+            "billing-project": "${{ needs.params-gen.outputs.project-name }}",
+            "billing-project-creator": "${{ inputs.owner-subject }}",
+            "service-account": "${{inputs.service-account}}" }'
+
+  run-cromwell-az-e2e:
+    needs: [params-gen, create-and-attach-billing-project-to-landing-zone-workflow]
+    permissions:
+      contents: read
+      id-token: write
+    uses: "broadinstitute/dsp-reusable-workflows/.github/workflows/cromwell-az-e2e-test.yaml@main"
+    with:
+      branch: "${{ inputs.target-branch }}"
+      bee-name: "${{ needs.params-gen.outputs.bee-name }}"
+      billing-project-name: "${{ needs.params-gen.outputs.project-name }}"
+
+  delete-billing-project-v2-from-bee-workflow:
+    continue-on-error: true
+    runs-on: ubuntu-latest
+    needs: [run-cromwell-az-e2e, create-and-attach-billing-project-to-landing-zone-workflow, params-gen]
+    if: always()
+    steps:
+      - name: dispatch to terra-github-workflows
+        uses: broadinstitute/workflow-dispatch@v3
+        with:
+          workflow: .github/workflows/delete-billing-project-v2-from-bee.yaml
+          repo: broadinstitute/terra-github-workflows
+          ref: refs/heads/main
+          token: ${{ env.BROADBOT_TOKEN }}
+          inputs: '{ 
+            "run-name": "delete-billing-project-v2-from-bee-${{ env.RUN_NAME_SUFFIX }}",
+            "bee-name": "${{ needs.params-gen.outputs.bee-name }}", 
+            "billing-project": "${{ needs.params-gen.outputs.project-name }}", 
+            "billing-project-owner": "${{ inputs.owner-subject }}", 
+            "service-account": "${{ inputs.service-account }}", 
+            "silent-on-failure": "false" }'
+
+  destroy-bee-workflow:
+    runs-on: ubuntu-latest
+    needs: [params-gen, create-bee-workflow, delete-billing-project-v2-from-bee-workflow]
+    if: always()
+    permissions:
+      contents: 'read'
+      id-token: 'write'
+    steps:
+      - name: dispatch to terra-github-workflows
+        uses: broadinstitute/workflow-dispatch@v3
+        with:
+          workflow: bee-destroy.yaml
+          repo: broadinstitute/terra-github-workflows
+          ref: refs/heads/main
+          token: ${{ env.BROADBOT_TOKEN }}
+          inputs: '{ "bee-name": "${{ needs.params-gen.outputs.bee-name }}" }'
+          wait-for-completion: true
+
+  report-workflow:
+    uses: broadinstitute/sherlock/.github/workflows/client-report-workflow.yaml@main
+    with:
+      notify-slack-channels-upon-workflow-failure: "#cromwell_jenkins_ci_errors"
+    permissions:
+      id-token: write
diff --git a/.gitignore b/.gitignore
index a5b72f6b263..250b6aa3c16 100644
--- a/.gitignore
+++ b/.gitignore
@@ -23,6 +23,9 @@ console_output.txt
 expected.json
 run_mode_metadata.json
 
+#bloop files
+/.bloop
+
 # custom config
 cromwell-executions
 cromwell-test-executions
@@ -55,3 +58,6 @@ tesk_application.conf
 **/venv/
 exome_germline_single_sample_v1.3/
 **/*.pyc
+
+# GHA credentials
+gha-creds-*.json

From 7bc78bde3b940e00a8cd161f8582bdc8274872e9 Mon Sep 17 00:00:00 2001
From: xquek <46759870+xquek@users.noreply.github.com>
Date: Mon, 30 Oct 2023 05:11:17 -0700
Subject: [PATCH 233/326] Fix aws unit tests (#39)

* checkpoint

* fix ecr and batch tests

* fix AwsBatchJobSpec.scala

---------

Co-authored-by: quekx <quekx@gene.com>
---
 .../flows/aws/AmazonEcrPublicSpec.scala       |  12 +-
 .../registryv2/flows/aws/AmazonEcrSpec.scala  |  13 +-
 .../backend/impl/aws/AwsBatchJob.scala        |  65 +++--
 ...tchAsyncBackendJobExecutionActorSpec.scala |   3 +-
 .../impl/aws/AwsBatchCallPathsSpec.scala      |   3 +-
 .../backend/impl/aws/AwsBatchJobSpec.scala    | 261 ++++++++++--------
 .../aws/AwsBatchRuntimeAttributesSpec.scala   |   7 +-
 .../impl/aws/AwsBatchWorkflowPathsSpec.scala  |   1 +
 8 files changed, 203 insertions(+), 162 deletions(-)

diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
index 18a0a23232e..f6f1520512f 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
@@ -1,5 +1,4 @@
 package cromwell.docker.registryv2.flows.aws
-
 import cats.effect.{IO, Resource}
 import cromwell.core.TestKitSuite
 import cromwell.docker.registryv2.DockerRegistryV2Abstract
@@ -12,20 +11,19 @@ import org.mockito.Mockito._
 import org.scalatest.{BeforeAndAfter, PrivateMethodTester}
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
-import org.scalatestplus.mockito.MockitoSugar
 import software.amazon.awssdk.services.ecrpublic.model.{AuthorizationData, GetAuthorizationTokenRequest, GetAuthorizationTokenResponse}
 import software.amazon.awssdk.services.ecrpublic.EcrPublicClient
 
-class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with MockitoSugar with BeforeAndAfter with PrivateMethodTester {
+class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with BeforeAndAfter with PrivateMethodTester {
   behavior of "AmazonEcrPublic"
 
   val goodUri = "public.ecr.aws/amazonlinux/amazonlinux:latest"
   val otherUri = "ubuntu:latest"
 
 
-  val mediaType: MediaType = MediaType.parse(DockerRegistryV2Abstract.ManifestV2MediaType).right.get
+  val mediaType: MediaType = MediaType.parse(DockerRegistryV2Abstract.DockerManifestV2MediaType).getOrElse(fail("Cant parse mediatype"))
   val contentType: Header = `Content-Type`(mediaType)
-  val mockEcrClient: EcrPublicClient = mock[EcrPublicClient]
+  val mockEcrClient: EcrPublicClient = mock(classOf[EcrPublicClient])
   implicit val mockIOClient: Client[IO] = Client({ _: Request[IO] =>
     // This response will have an empty body, so we need to be explicit about the typing:
     Resource.pure[IO, Response[IO]](Response(headers = Headers.of(contentType))) : Resource[IO, Response[IO]]
@@ -44,7 +42,7 @@ class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matcher
   }
 
   it should "have public.ecr.aws as registryHostName" in {
-    val registryHostNameMethod = PrivateMethod[String]('registryHostName)
+    val registryHostNameMethod = PrivateMethod[String](Symbol("registryHostName"))
     registry invokePrivate registryHostNameMethod(DockerImageIdentifier.fromString(goodUri).get) shouldEqual "public.ecr.aws"
   }
 
@@ -63,7 +61,7 @@ class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matcher
           .build())
         .build)
 
-    val getTokenMethod = PrivateMethod[IO[Option[String]]]('getToken)
+    val getTokenMethod = PrivateMethod[IO[Option[String]]](Symbol("getToken"))
     registry invokePrivate getTokenMethod(context, mockIOClient) ensuring(io => io.unsafeRunSync().get == token)
   }
 }
diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala
index 5ddf98c7ffa..c4f121188db 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala
@@ -11,19 +11,18 @@ import org.mockito.Mockito._
 import org.scalatest.{BeforeAndAfter, PrivateMethodTester}
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
-import org.scalatestplus.mockito.MockitoSugar
 import software.amazon.awssdk.services.ecr.EcrClient
 import software.amazon.awssdk.services.ecr.model.{AuthorizationData, GetAuthorizationTokenResponse}
 
-class AmazonEcrSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with MockitoSugar with BeforeAndAfter with PrivateMethodTester{
+class AmazonEcrSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with BeforeAndAfter with PrivateMethodTester{
   behavior of "AmazonEcr"
 
   val goodUri = "123456789012.dkr.ecr.us-east-1.amazonaws.com/amazonlinux/amazonlinux:latest"
   val otherUri = "ubuntu:latest"
 
-  val mediaType: MediaType = MediaType.parse(DockerRegistryV2Abstract.ManifestV2MediaType).right.get
+  val mediaType: MediaType = MediaType.parse(DockerRegistryV2Abstract.DockerManifestV2MediaType).getOrElse(fail("Can't parse media type"))
   val contentType: Header = `Content-Type`(mediaType)
-  val mockEcrClient: EcrClient = mock[EcrClient]
+  val mockEcrClient: EcrClient = mock(classOf[EcrClient])
   implicit val mockIOClient: Client[IO] = Client({ _: Request[IO] =>
     // This response will have an empty body, so we need to be explicit about the typing:
     Resource.pure[IO, Response[IO]](Response(headers = Headers.of(contentType))) : Resource[IO, Response[IO]]
@@ -42,12 +41,12 @@ class AmazonEcrSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with
   }
 
   it should "use Basic Auth Scheme" in {
-    val authSchemeMethod = PrivateMethod[AuthScheme]('authorizationScheme)
+    val authSchemeMethod = PrivateMethod[AuthScheme](Symbol("authorizationScheme"))
     registry invokePrivate authSchemeMethod() shouldEqual AuthScheme.Basic
   }
 
   it should "return 123456789012.dkr.ecr.us-east-1.amazonaws.com as registryHostName" in {
-    val registryHostNameMethod = PrivateMethod[String]('registryHostName)
+    val registryHostNameMethod = PrivateMethod[String](Symbol("registryHostName"))
     registry invokePrivate registryHostNameMethod(DockerImageIdentifier.fromString(goodUri).get) shouldEqual "123456789012.dkr.ecr.us-east-1.amazonaws.com"
   }
 
@@ -66,7 +65,7 @@ class AmazonEcrSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with
           .build())
         .build)
 
-    val getTokenMethod = PrivateMethod[IO[Option[String]]]('getToken)
+    val getTokenMethod = PrivateMethod[IO[Option[String]]](Symbol("getToken"))
     registry invokePrivate getTokenMethod(context, mockIOClient) ensuring(io => io.unsafeRunSync().get == token)
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 97302357175..d967e26659a 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -117,7 +117,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     */
   lazy val reconfiguredScript: String = {
     //this is the location of the aws cli mounted into the container by the ec2 launch template
-    val awsCmd = "/usr/local/aws-cli/v2/current/bin/aws "
+    val awsCmd = "/usr/local/aws-cli/v2/current/bin/aws"
     //internal to the container, therefore not mounted
     val workDir = "/tmp/scratch"
     //working in a mount will cause collisions in long running workers
@@ -125,7 +125,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     val insertionPoint = replaced.indexOf("\n", replaced.indexOf("#!")) +1 //just after the new line after the shebang!
     // load the config
     val conf : Config = ConfigFactory.load();
-    
+
     /* generate a series of s3 copy statements to copy any s3 files into the container. */
     val inputCopyCommand = inputs.map {
       case input: AwsBatchFileInput if input.s3key.startsWith("s3://") && input.s3key.endsWith(".tmp") =>
@@ -135,14 +135,11 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
            |sed -i 's#${AwsBatchWorkingDisk.MountPoint.pathAsString}#$workDir#g' $workDir/${input.local}
            |""".stripMargin
 
-      
       case input: AwsBatchFileInput if input.s3key.startsWith("s3://") => 
         // regular s3 objects : download to working dir.
         s"_s3_localize_with_retry ${input.s3key} ${input.mount.mountPoint.pathAsString}/${input.local}"
           .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
 
-      
-       
       case input: AwsBatchFileInput if efsMntPoint.isDefined && input.s3key.startsWith(efsMntPoint.get) =>  
         // EFS located file : test for presence on provided path.
         Log.debug("EFS input file detected: "+ input.s3key + " / "+ input.local.pathAsString)
@@ -187,11 +184,11 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
          |      exit 1
          |    fi
-         |    # copy  
+         |    # copy
          |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination"  ||
          |        { echo "attempt $$i to copy $$s3_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # check data integrity
-         |    _check_data_integrity $$destination $$s3_path || 
+         |    _check_data_integrity $$destination $$s3_path ||
          |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # copy succeeded
          |    break
@@ -207,7 +204,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  # get the multipart chunk size
          |  chunk_size=$$(_get_multipart_chunk_size $$local_path)
          |  local MP_THRESHOLD=${mp_threshold}
-         |  # then set them 
+         |  # then set them
          |  $awsCmd configure set default.s3.multipart_threshold $$MP_THRESHOLD
          |  $awsCmd configure set default.s3.multipart_chunksize $$chunk_size
          |
@@ -220,27 +217,27 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |        exit 2
          |    fi
          |    # if destination is not a bucket : abort
-         |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then 
+         |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then
          |     echo "$$destination is not an S3 path with a bucket and key. aborting"
          |      exit 1
          |    fi
          |    # copy ok or try again.
          |    if [[ -d "$$local_path" ]]; then
-         |       # make sure to strip the trailing / in destination 
+         |       # make sure to strip the trailing / in destination
          |       destination=$${destination%/}
          |       # glob directory. do recursive copy
-         |       $awsCmd s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" || 
-         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
+         |       $awsCmd s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" ||
+         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |       # check integrity for each of the files
          |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
-         |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE || 
+         |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE ||
          |               { echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2; }
          |       done
-         |    else 
-         |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" || 
-         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
+         |    else
+         |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" ||
+         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |      # check content length for data integrity
-         |      _check_data_integrity $$local_path $$destination || 
+         |      _check_data_integrity $$local_path $$destination ||
          |         { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    fi
          |    # copy succeeded
@@ -251,9 +248,9 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |function _get_multipart_chunk_size() {
          |  local file_path=$$1
          |  # file size
-         |  file_size=$$(stat --printf="%s" $$file_path) 
+         |  file_size=$$(stat --printf="%s" $$file_path)
          |  # chunk_size : you can have at most 10K parts with at least one 5MB part
-         |  # this reflects the formula in s3-copy commands of cromwell (S3FileSystemProvider.java) 
+         |  # this reflects the formula in s3-copy commands of cromwell (S3FileSystemProvider.java)
          |  #   => long partSize = Math.max((objectSize / 10000L) + 1, 5 * 1024 * 1024);
          |  a=$$(( ( file_size / 10000) + 1 ))
          |  b=$$(( 5 * 1024 * 1024 ))
@@ -264,9 +261,9 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |function _check_data_integrity() {
          |  local local_path=$$1
          |  local s3_path=$$2
-         |  
+         |
          |  # remote : use content_length
-         |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then 
+         |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
          |        bucket="$${BASH_REMATCH[1]}"
          |        key="$${BASH_REMATCH[2]}"
          |  else
@@ -274,16 +271,16 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
          |      exit 1
          |  fi
-         |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
-         |        { echo "Attempt to get head of object failed for $$s3_path." && return 1 ; }
+         |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') ||
+         |        { echo "Attempt to get head of object failed for $$s3_path." && return 1; }
          |  # local
-         |  local_content_length=$$(LC_ALL=C ls -dnL -- "$$local_path" | awk '{print $$5; exit}' ) || 
-         |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }   
+         |  local_content_length=$$(LC_ALL=C ls -dnL -- "$$local_path" | awk '{print $$5; exit}' ) ||
+         |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }
          |  # compare
          |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
          |       true
          |  else
-         |       false  
+         |       false
          |  fi
          |}
          |
@@ -375,8 +372,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         s"""_s3_delocalize_with_retry $workDir/${output.local.pathAsString} ${output.s3key}""".stripMargin
 
       // file(name (full path), s3key (delocalized path), local (file basename), mount (disk details))
-      // files on EFS mounts are optionally delocalized. 
-      case output: AwsBatchFileOutput if efsMntPoint.isDefined && output.mount.mountPoint.pathAsString == efsMntPoint.get =>  
+      // files on EFS mounts are optionally delocalized.
+      case output: AwsBatchFileOutput if efsMntPoint.isDefined && output.mount.mountPoint.pathAsString == efsMntPoint.get =>
         Log.debug("EFS output file detected: "+ output.s3key + s" / ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}")
         // EFS located file : test existence or delocalize.
         var test_cmd = ""
@@ -388,25 +385,25 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
             // check file for existence
             test_cmd = s"test -e ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && exit 1)"
         }
-        // need to make md5sum? 
+        // need to make md5sum?
         var md5_cmd = ""
         if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
             Log.debug("Add cmd to create MD5 sibling.")
             md5_cmd = s"""
-                            |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
-                            |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && exit 1 ); 
+                            |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then
+                            |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && exit 1 );
                             |fi
-                            |""".stripMargin 
+                            |""".stripMargin
         } else {
             Log.debug("MD5 not enabled: "+efsMakeMD5.get.toString())
             md5_cmd = ""
-        } 
+        }
         // return combined result
         s"""
           |${test_cmd}
           |${md5_cmd}
           | """.stripMargin
-      
+
       case output: AwsBatchFileOutput =>
         //output on a different mount
         Log.debug("output data on other mount")
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
index ba2e5580b3f..98af4f00282 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
@@ -32,7 +32,6 @@
 package cromwell.backend.impl.aws
 
 import java.util.UUID
-
 import akka.actor.{ActorRef, Props}
 import akka.testkit.{ImplicitSender, TestActorRef, TestDuration}
 import common.collections.EnhancedCollections._
@@ -41,7 +40,7 @@ import cromwell.backend._
 import cromwell.backend.async.{ExecutionHandle, FailedNonRetryableExecutionHandle, PendingExecutionHandle}
 import cromwell.backend.impl.aws.AwsBatchAsyncBackendJobExecutionActor.AwsBatchPendingExecutionHandle
 import cromwell.backend.impl.aws.RunStatus.UnsuccessfulRunStatus
-import cromwell.backend.impl.aws.io.AwsBatchWorkingDisk
+import cromwell.backend.impl.aws.io.{AwsBatchWorkflowPaths, AwsBatchWorkingDisk}
 import cromwell.backend.io.JobPathsSpecHelper._
 import cromwell.backend.standard.{DefaultStandardAsyncExecutionActorParams, StandardAsyncExecutionActorParams, StandardAsyncJob, StandardExpressionFunctions, StandardExpressionFunctionsParams}
 import cromwell.cloudsupport.aws.s3.S3Storage
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchCallPathsSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchCallPathsSpec.scala
index b250ab12ed4..131114c8921 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchCallPathsSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchCallPathsSpec.scala
@@ -33,7 +33,8 @@ package cromwell.backend.impl.aws
 
 import common.collections.EnhancedCollections._
 import cromwell.backend.BackendSpec
-import cromwell.backend.io.JobPathsSpecHelper._
+import cromwell.backend.impl.aws.io.{AwsBatchJobPaths, AwsBatchWorkflowPaths}
+import cromwell.backend.io.JobPathsSpecHelper.{EnhancedJobPaths, EnhancedCallContext}
 import org.scalatest.flatspec.AnyFlatSpecLike
 import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider
 import cromwell.core.Tags.AwsTest
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index 0e7172343cd..3c8e0382974 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -34,7 +34,7 @@ package cromwell.backend.impl.aws
 import common.collections.EnhancedCollections._
 import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
 import cromwell.backend.BackendSpec._
-import cromwell.backend.impl.aws.io.AwsBatchWorkingDisk
+import cromwell.backend.impl.aws.io.{AwsBatchJobPaths, AwsBatchWorkflowPaths, AwsBatchWorkingDisk}
 import cromwell.backend.validation.ContinueOnReturnCodeFlag
 import cromwell.core.path.DefaultPathBuilder
 import cromwell.core.TestKitSuite
@@ -118,6 +118,8 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
       scriptS3BucketName = "script-bucket",
       awsBatchRetryAttempts = 1,
       ulimits = Vector(Map.empty[String, String]),
+      efsDelocalize = false,
+      efsMakeMD5 = false,
       fileSystem = "s3")
 
   val containerDetail: ContainerDetail = ContainerDetail.builder().exitCode(0).build()
@@ -127,21 +129,21 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       Seq.empty[AwsBatchInput].toSet, Seq.empty[AwsBatchFileOutput].toSet,
-      jobPaths, Seq.empty[AwsBatchParameter], None, None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None)
     job
   }
   private def generateBasicJobForLocalFS: AwsBatchJob = {
     val job = AwsBatchJob(null, runtimeAttributes.copy(fileSystem="local"), "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       Seq.empty[AwsBatchInput].toSet, Seq.empty[AwsBatchFileOutput].toSet,
-      jobPaths, Seq.empty[AwsBatchParameter], None, None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None)
     job
   }
   private def generateJobWithS3InOut: AwsBatchJob = {
     val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       s3Inputs, s3Outputs,
-      jobPaths, Seq.empty[AwsBatchParameter], None, None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None)
     job
   }
 
@@ -180,109 +182,152 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
 
   it should "add s3 localize with retry function to reconfigured script" in {
     val job = generateBasicJob
-    val retryFunctionText = s"""
-                              |export AWS_METADATA_SERVICE_TIMEOUT=10
-                              |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
-                              |
-                              |function _s3_localize_with_retry() {
-                              |  local s3_path=$$1
-                              |  # destination must be the path to a file and not just the directory you want the file in
-                              |  local destination=$$2
-                              |
-                              |  for i in {1..6};
-                              |  do
-                              |    # abort if tries are exhausted
-                              |    if [ "$$i" -eq 6 ]; then
-                              |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts. aborting"
-                              |        exit 2
-                              |    fi
-                              |    # check validity of source path
-                              |    if ! [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
-                              |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
-                              |      exit 1
-                              |    fi
-                              |    # copy  
-                              |    /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$s3_path" "$$destination"  ||
-                              |        ( echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue)
-                              |    # check data integrity
-                              |    _check_data_integrity $$destination $$s3_path || 
-                              |       (echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
-                              |    # copy succeeded
-                              |    break
-                              |  done
-                              |}
-                              |
-                              |function _s3_delocalize_with_retry() {
-                              |  local local_path=$$1
-                              |  # destination must be the path to a file and not just the directory you want the file in
-                              |  local destination=$$2
-                              |
-                              |  for i in {1..6};
-                              |  do
-                              |    # if tries exceeded : abort
-                              |    if [ "$$i" -eq 6 ]; then
-                              |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts. aborting"
-                              |        exit 2
-                              |    fi
-                              |    # if destination is not a bucket : abort
-                              |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then 
-                              |     echo "$$destination is not an S3 path with a bucket and key. aborting"
-                              |      exit 1
-                              |    fi
-                              |    # copy ok or try again.
-                              |    if [[ -d "$$local_path" ]]; then
-                              |       # make sure to strip the trailing / in destination 
-                              |       destination=$${destination%/}
-                              |       # glob directory. do recursive copy
-                              |       /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" || 
-                              |         ( echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
-                              |       # check integrity for each of the files
-                              |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
-                              |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE || 
-                              |               ( echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2)
-                              |       done
-                              |    else 
-                              |      /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$local_path" "$$destination" || 
-                              |         ( echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
-                              |      # check content length for data integrity
-                              |      _check_data_integrity $$local_path $$destination || 
-                              |         ( echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
-                              |    fi
-                              |    # copy succeeded
-                              |    break
-                              |  done
-                              |}
-                              |
-                              |function _check_data_integrity() {
-                              |  local local_path=$$1
-                              |  local s3_path=$$2
-                              |  
-                              |  # remote : use content_length
-                              |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then 
-                              |        bucket="$${BASH_REMATCH[1]}"
-                              |        key="$${BASH_REMATCH[2]}"
-                              |  else
-                              |      # this is already checked in the caller function
-                              |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
-                              |      exit 1
-                              |  fi
-                              |  s3_content_length=$$(/usr/local/aws-cli/v2/current/bin/aws s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
-                              |        ( echo "Attempt to get head of object failed for $$s3_path." && return 1 )
-                              |  # local
-                              |  local_content_length=$$(LC_ALL=C ls -dn -- "$$local_path" | awk '{print $$5; exit}' ) || 
-                              |        ( echo "Attempt to get local content length failed for $$_local_path." && return 1 )   
-                              |  # compare
-                              |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
-                              |       true
-                              |  else
-                              |       false  
-                              |  fi
-                              |}
-                              |""".stripMargin
+    val retryFunctionText =
+      s"""
+          |export AWS_METADATA_SERVICE_TIMEOUT=10
+          |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
+          |
+          |function _s3_localize_with_retry() {
+          |  local s3_path=$$1
+          |  # destination must be the path to a file and not just the directory you want the file in
+          |  local destination=$$2
+          |
+          |  for i in {1..6};
+          |  do
+          |    # abort if tries are exhausted
+          |    if [ "$$i" -eq 6 ]; then
+          |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts. aborting"
+          |        exit 2
+          |    fi
+          |    # check validity of source path
+          |    if ! [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
+          |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+          |      exit 1
+          |    fi
+          |    # copy
+          |    /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$s3_path" "$$destination"  ||
+          |        { echo "attempt $$i to copy $$s3_path failed" && sleep $$((7 * "$$i")) && continue; }
+          |    # check data integrity
+          |    _check_data_integrity $$destination $$s3_path ||
+          |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+          |    # copy succeeded
+          |    break
+          |  done
+          |}""".stripMargin
 
     job.reconfiguredScript should include (retryFunctionText)
   }
 
+  it should "s3 delocalization with retry function in reconfigured script" in {
+    val job = generateBasicJob
+    val delocalizeText = s"""
+         |
+         |function _s3_delocalize_with_retry() {
+         |  # input variables
+         |  local local_path=$$1
+         |  # destination must be the path to a file and not just the directory you want the file in
+         |  local destination=$$2
+         |
+         |  # get the multipart chunk size
+         |  chunk_size=$$(_get_multipart_chunk_size $$local_path)
+         |  local MP_THRESHOLD=5368709120
+         |  # then set them
+         |  /usr/local/aws-cli/v2/current/bin/aws configure set default.s3.multipart_threshold $$MP_THRESHOLD
+         |  /usr/local/aws-cli/v2/current/bin/aws configure set default.s3.multipart_chunksize $$chunk_size
+         |
+         |  # try & validate upload 5 times
+         |  for i in {1..6};
+         |  do
+         |    # if tries exceeded : abort
+         |    if [ "$$i" -eq 6 ]; then
+         |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts. aborting"
+         |        exit 2
+         |    fi
+         |    # if destination is not a bucket : abort
+         |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then
+         |     echo "$$destination is not an S3 path with a bucket and key. aborting"
+         |      exit 1
+         |    fi
+         |    # copy ok or try again.
+         |    if [[ -d "$$local_path" ]]; then
+         |       # make sure to strip the trailing / in destination
+         |       destination=$${destination%/}
+         |       # glob directory. do recursive copy
+         |       /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" ||
+         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+         |       # check integrity for each of the files
+         |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
+         |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE ||
+         |               { echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2; }
+         |       done
+         |    else
+         |      /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$local_path" "$$destination" ||
+         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+         |      # check content length for data integrity
+         |      _check_data_integrity $$local_path $$destination ||
+         |         { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+         |    fi
+         |    # copy succeeded
+         |    break
+         |  done
+         |}""".stripMargin
+    job.reconfiguredScript should include (delocalizeText)
+  }
+
+  it should "generate check data integrity in reconfigured script" in {
+    val job = generateBasicJob
+    val checkDataIntegrityBlock =
+      s"""
+         |function _check_data_integrity() {
+         |  local local_path=$$1
+         |  local s3_path=$$2
+         |
+         |  # remote : use content_length
+         |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
+         |        bucket="$${BASH_REMATCH[1]}"
+         |        key="$${BASH_REMATCH[2]}"
+         |  else
+         |      # this is already checked in the caller function
+         |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+         |      exit 1
+         |  fi
+         |  s3_content_length=$$(/usr/local/aws-cli/v2/current/bin/aws s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') ||
+         |        { echo "Attempt to get head of object failed for $$s3_path." && return 1; }
+         |  # local
+         |  local_content_length=$$(LC_ALL=C ls -dnL -- "$$local_path" | awk '{print $$5; exit}' ) ||
+         |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }
+         |  # compare
+         |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
+         |       true
+         |  else
+         |       false
+         |  fi
+         |}
+         |""".stripMargin
+    job.reconfiguredScript should include (checkDataIntegrityBlock)
+  }
+
+  it should "generate get multipart chunk size in script" in {
+    val job = generateBasicJob
+    val getMultiplePartChunkSize =
+      s"""
+         |function _get_multipart_chunk_size() {
+         |  local file_path=$$1
+         |  # file size
+         |  file_size=$$(stat --printf="%s" $$file_path)
+         |  # chunk_size : you can have at most 10K parts with at least one 5MB part
+         |  # this reflects the formula in s3-copy commands of cromwell (S3FileSystemProvider.java)
+         |  #   => long partSize = Math.max((objectSize / 10000L) + 1, 5 * 1024 * 1024);
+         |  a=$$(( ( file_size / 10000) + 1 ))
+         |  b=$$(( 5 * 1024 * 1024 ))
+         |  chunk_size=$$(( a > b ? a : b ))
+         |  echo $$chunk_size
+         |}
+         |""".stripMargin
+
+    job.reconfiguredScript should include (getMultiplePartChunkSize)
+  }
+
   it should "generate postscript with output copy command in reconfigured script" in {
     val job = generateJobWithS3InOut
     val postscript =
@@ -290,13 +335,10 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
          |{
          |set -e
          |echo '*** DELOCALIZING OUTPUTS ***'
-         |
          |_s3_delocalize_with_retry /tmp/scratch/baa s3://bucket/somewhere/baa
          |
-         |
          |if [ -f /tmp/scratch/hello-rc.txt ]; then _s3_delocalize_with_retry /tmp/scratch/hello-rc.txt ${job.jobPaths.returnCode} ; fi
-         |
-         |if [ -f /tmp/scratch/hello-stderr.log ]; then _s3_delocalize_with_retrys /tmp/scratch/hello-stderr.log ${job.jobPaths.standardPaths.error}; fi
+         |if [ -f /tmp/scratch/hello-stderr.log ]; then _s3_delocalize_with_retry /tmp/scratch/hello-stderr.log ${job.jobPaths.standardPaths.error}; fi
          |if [ -f /tmp/scratch/hello-stdout.log ]; then _s3_delocalize_with_retry /tmp/scratch/hello-stdout.log ${job.jobPaths.standardPaths.output}; fi
          |
          |echo '*** COMPLETED DELOCALIZATION ***'
@@ -309,6 +351,8 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     job.reconfiguredScript should include (postscript)
   }
 
+
+
   it should "generate preamble with input copy command in reconfigured script" in {
     val job = generateJobWithS3InOut
     val preamble =
@@ -345,7 +389,4 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     val job = generateBasicJob
     job.rc(jobDetail) should be (0)
   }
-
-
-
 }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
index 3de9cac621b..7664c9dc748 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
@@ -66,7 +66,10 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     false,
     "my-stuff",
     1,
-    Vector(Map.empty[String, String]))
+    Vector(Map.empty[String, String]),
+    false,
+    false
+  )
 
   val expectedDefaultsLocalFS = new AwsBatchRuntimeAttributes(refineMV[Positive](1), Vector("us-east-1a", "us-east-1b"),
 
@@ -79,6 +82,8 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     "",
     1,
     Vector(Map.empty[String, String]),
+    false,
+    false,
     "local")
 
   "AwsBatchRuntimeAttributes" should {
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPathsSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPathsSpec.scala
index 2b2d0ea14d8..09a2223c0ac 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPathsSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPathsSpec.scala
@@ -33,6 +33,7 @@ package cromwell.backend.impl.aws
 
 import common.collections.EnhancedCollections._
 import cromwell.backend.BackendSpec
+import cromwell.backend.impl.aws.io.AwsBatchWorkflowPaths
 import org.scalatest.flatspec.AnyFlatSpecLike
 import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider
 import cromwell.core.Tags.AwsTest

From 0fd2cc87def59a0db5151e74f575e07f642e568a Mon Sep 17 00:00:00 2001
From: xquek <46759870+xquek@users.noreply.github.com>
Date: Wed, 1 Nov 2023 02:57:21 -0700
Subject: [PATCH 234/326] return bucket directly instead of listing and
 checking it (#38)

Co-authored-by: quekx <quekx@gene.com>
---
 filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
index 8e15999180a..5de7e89813b 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
@@ -99,10 +99,7 @@ public Bucket getBucket() {
     }
 
     private Bucket getBucket(String bucketName) {
-        for (Bucket buck : getClient().listBuckets().buckets())
-            if (buck.name().equals(bucketName))
-                return buck;
-        return null;
+        return Bucket.builder().name(bucketName).build();
     }
 
     private boolean hasBucket(String bucketName) {

From 5bc7ac314d1320e0a68c4fae7920993a711a80fe Mon Sep 17 00:00:00 2001
From: dspeck1 <dspeck@burwood.com>
Date: Wed, 1 Nov 2023 08:42:19 -0500
Subject: [PATCH 235/326] WX-1340 GCP Batch: Mount with extra colon issue and
 multiple zones support (#7240)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 .../google/batch/runnable/RunnableBuilder.scala       | 11 ++++++++---
 .../google/batch/util/BatchUtilityConversions.scala   |  3 +--
 .../google/batch/runnable/RunnableBuilderSpec.scala   |  4 ++--
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala
index c68e3dbdd29..7f35528fad3 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala
@@ -4,7 +4,6 @@ import com.google.cloud.batch.v1.Runnable.Container
 import com.google.cloud.batch.v1.{Environment,Runnable, Volume}
 import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
 import cromwell.backend.google.batch.models.{BatchParameter, GcpBatchInput, GcpBatchOutput}
-//import cromwell.backend.google.batch.runnable.RunnableLabels._
 import cromwell.core.path.Path
 import mouse.all.anySyntaxMouse
 
@@ -60,8 +59,14 @@ object RunnableBuilder {
     def withVolumes(volumes: List[Volume]): Runnable.Builder = {
       val formattedVolumes = volumes.map { volume =>
         val mountPath = volume.getMountPath
-        val mountOptions = Option(volume.getMountOptionsList).map(_.asScala.toList).getOrElse(List.empty)
-        s"$mountPath:$mountPath:${mountOptions.mkString(",")}"
+
+        val mountOptions = Option(volume.getMountOptionsList)
+          .map(_.asScala)
+          .filter(_.nonEmpty)
+          .map(_.mkString(":", ",", ""))
+          .getOrElse("")
+
+        s"$mountPath:$mountPath$mountOptions"
       }
 
       builder.setContainer(
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala
index 87b4762f5a5..612c95651e9 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala
@@ -8,10 +8,9 @@ import wom.format.MemorySize
 
 trait BatchUtilityConversions {
 
-
   // construct zones string
   def toZonesPath(zones: Vector[String]): String = {
-    "zones/" + zones.mkString(",")
+    zones.map(zone => "zones/" + zone).mkString(" ")
   }
 
   // lowercase text to match gcp label requirements
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala
index d0e4eac0b87..04d2c7d43f5 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala
@@ -76,7 +76,7 @@ class RunnableBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     runnable.getContainer.getCommandsList.asScala shouldBe expectedCommand
     runnable.getAlwaysRun shouldBe true
     runnable.getLabelsMap shouldBe memoryRetryRunnableExpectedLabels
-    runnable.getContainer.getVolumesList.asScala.toList shouldBe volumes.map(v => s"${v.getMountPath}:${v.getMountPath}:")
+    runnable.getContainer.getVolumesList.asScala.toList shouldBe volumes.map(v => s"${v.getMountPath}:${v.getMountPath}")
   }
 
   it should "return cloud sdk runnable for multiple keys in retry-with-double-memory" in {
@@ -89,6 +89,6 @@ class RunnableBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     runnable.getContainer.getCommandsList.asScala shouldBe expectedCommand
     runnable.getAlwaysRun shouldBe true
     runnable.getLabelsMap shouldBe memoryRetryRunnableExpectedLabels
-    runnable.getContainer.getVolumesList.asScala.toList shouldBe volumes.map(v => s"${v.getMountPath}:${v.getMountPath}:")
+    runnable.getContainer.getVolumesList.asScala.toList shouldBe volumes.map(v => s"${v.getMountPath}:${v.getMountPath}")
   }
 }
\ No newline at end of file

From e880371efd2f5f85bc4c9ef99b3cec78a3e94447 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Wed, 1 Nov 2023 20:40:40 -0400
Subject: [PATCH 236/326] WX-1339 Make `throwExceptionOnExecuteError` false for
 PAPI aborts (#7245)

---
 .../pipelines/v2beta/api/request/AbortRequestHandler.scala      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/AbortRequestHandler.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/AbortRequestHandler.scala
index 974c8710766..b4d9421b451 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/AbortRequestHandler.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/AbortRequestHandler.scala
@@ -35,7 +35,7 @@ trait AbortRequestHandler extends LazyLogging { this: RequestHandler =>
   // The Genomics batch endpoint doesn't seem to be able to handle abort requests on V2 operations at the moment
   // For now, don't batch the request and execute it on its own
   def handleRequest(abortQuery: PAPIAbortRequest, batch: BatchRequest, pollingManager: ActorRef)(implicit ec: ExecutionContext): Future[Try[Unit]] = {
-    Future(abortQuery.httpRequest.execute()) map {
+    Future(abortQuery.httpRequest.setThrowExceptionOnExecuteError(false).execute()) map {
       case response if response.isSuccessStatusCode =>
         abortQuery.requester ! PAPIAbortRequestSuccessful(abortQuery.jobId.jobId)
         Success(())

From 74de9e33d1c35885db1d084a4b2b1ac22c144796 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 3 Nov 2023 09:58:03 -0400
Subject: [PATCH 237/326] WX-1338 Fix cron invocation of E2E test (#7244)

---
 .github/workflows/azure_e2e_run_workflow.yml | 23 ++------------------
 1 file changed, 2 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/azure_e2e_run_workflow.yml b/.github/workflows/azure_e2e_run_workflow.yml
index d2df9b38441..5071fc37e8b 100644
--- a/.github/workflows/azure_e2e_run_workflow.yml
+++ b/.github/workflows/azure_e2e_run_workflow.yml
@@ -3,22 +3,6 @@ on:
   schedule:
     - cron: '0 16 * * *' # UTC 4pm, EST 11am, EDT 12pm
   workflow_dispatch:
-    inputs:
-      target-branch:
-        description: 'Branch name of dsp-reusable-workflows repo to run tests on'
-        required: true
-        default: 'main'
-        type: string
-      owner-subject:
-        description: 'Owner of billing project'
-        required: true
-        default: 'hermione.owner@quality.firecloud.org'
-        type: string
-      service-account:
-        description: 'Email address or unique identifier of the Google Cloud service account for which to generate credentials'
-        required: true
-        default: 'firecloud-qa@broad-dsde-qa.iam.gserviceaccount.com'
-        type: string
 
 env:
   BROADBOT_TOKEN: '${{ secrets.BROADBOT_GITHUB_TOKEN }}' # github token for access to kick off a job in the private repo
@@ -75,8 +59,7 @@ jobs:
             "run-name": "attach-billing-project-to-landing-zone-${{ env.RUN_NAME_SUFFIX }}",
             "bee-name": "${{ needs.params-gen.outputs.bee-name }}",
             "billing-project": "${{ needs.params-gen.outputs.project-name }}",
-            "billing-project-creator": "${{ inputs.owner-subject }}",
-            "service-account": "${{inputs.service-account}}" }'
+            "service-account": "firecloud-qa@broad-dsde-qa.iam.gserviceaccount.com" }'
 
   run-cromwell-az-e2e:
     needs: [params-gen, create-and-attach-billing-project-to-landing-zone-workflow]
@@ -85,7 +68,6 @@ jobs:
       id-token: write
     uses: "broadinstitute/dsp-reusable-workflows/.github/workflows/cromwell-az-e2e-test.yaml@main"
     with:
-      branch: "${{ inputs.target-branch }}"
       bee-name: "${{ needs.params-gen.outputs.bee-name }}"
       billing-project-name: "${{ needs.params-gen.outputs.project-name }}"
 
@@ -106,8 +88,7 @@ jobs:
             "run-name": "delete-billing-project-v2-from-bee-${{ env.RUN_NAME_SUFFIX }}",
             "bee-name": "${{ needs.params-gen.outputs.bee-name }}", 
             "billing-project": "${{ needs.params-gen.outputs.project-name }}", 
-            "billing-project-owner": "${{ inputs.owner-subject }}", 
-            "service-account": "${{ inputs.service-account }}", 
+            "service-account": "firecloud-qa@broad-dsde-qa.iam.gserviceaccount.com", 
             "silent-on-failure": "false" }'
 
   destroy-bee-workflow:

From 110ca3e3c1bcd205eb290b95dfc986581f6c5e3c Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 3 Nov 2023 13:06:19 -0400
Subject: [PATCH 238/326] WX-1341 Better logging when a runner stops picking up
 new workflows (#7246)

---
 .../engine/workflow/WorkflowManagerActor.scala        | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
index e84d9091ad0..c3b1b998a94 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
@@ -179,11 +179,16 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
       params.jobExecutionTokenDispenserActor ! FetchLimitedGroups
       stay()
     case Event(ReplyLimitedGroups(groups), stateData) =>
+      val wfCount = stateData.workflows.size
+      val swfCount = stateData.subWorkflows.size
+      val maxNewWorkflows = maxWorkflowsToLaunch min (maxWorkflowsRunning - wfCount - swfCount)
+      val fetchCountLog = s"Fetching $maxNewWorkflows new workflows ($wfCount workflows and $swfCount subworkflows in flight)"
       if (groups.nonEmpty)
-        log.info(s"Excluding groups from workflow launch: ${groups.mkString(", ")}")
+        log.info(s"${fetchCountLog}, excluding groups: ${groups.mkString(", ")}")
+      else if (maxNewWorkflows < 1)
+        log.info(s"${fetchCountLog}, no groups excluded from workflow launch.")
       else
-        log.debug("No groups excluded from workflow launch.")
-      val maxNewWorkflows = maxWorkflowsToLaunch min (maxWorkflowsRunning - stateData.workflows.size - stateData.subWorkflows.size)
+        log.debug(s"${fetchCountLog}, no groups excluded from workflow launch.")
       params.workflowStore ! WorkflowStoreActor.FetchRunnableWorkflows(maxNewWorkflows, excludedGroups = groups)
       stay()
     case Event(WorkflowStoreEngineActor.NoNewWorkflowsToStart, _) =>

From 465d8f59e5209dd59ac7610d7217d3eda7a35bc3 Mon Sep 17 00:00:00 2001
From: xquek <46759870+xquek@users.noreply.github.com>
Date: Mon, 13 Nov 2023 01:59:13 -0800
Subject: [PATCH 239/326] Add evaluteOnExit for aws batch retry (#40)

Co-authored-by: quekx <quekx@gene.com>
---
 .../main/scala/cromwell/backend/backend.scala |   1 +
 .../backend/impl/aws/AwsBatchAttributes.scala |   1 +
 .../impl/aws/AwsBatchJobDefinition.scala      |  29 +++-
 .../impl/aws/AwsBatchRuntimeAttributes.scala  | 134 +++++++++++++++++-
 .../scala/cromwell/backend/impl/aws/README.md |  31 ++++
 .../backend/impl/aws/AwsBatchJobSpec.scala    |  48 ++++++-
 .../aws/AwsBatchRuntimeAttributesSpec.scala   | 106 ++++++++++++--
 .../backend/impl/aws/AwsBatchTestConfig.scala |  90 ++++++++++++
 8 files changed, 419 insertions(+), 21 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index bf9f67e27a1..2f18f499f30 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -140,6 +140,7 @@ object CommonBackendConfigurationAttributes {
     "default-runtime-attributes.docker",
     "default-runtime-attributes.queueArn",
     "default-runtime-attributes.awsBatchRetryAttempts",
+    "default-runtime-attributes.awsBatchEvaluateOnExit",
     "default-runtime-attributes.ulimits",
     "default-runtime-attributes.efsDelocalize",
     "default-runtime-attributes.efsMakeMD5",
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index ecb6c87a457..1119e192262 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -87,6 +87,7 @@ object AwsBatchAttributes {
     "numSubmitAttempts",
     "default-runtime-attributes.scriptBucketName",
     "awsBatchRetryAttempts",
+    "awsBatchEvaluateOnExit",
     "ulimits",
     "efsDelocalize",
     "efsMakeMD5",
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index e1e5af42539..792fd6825d0 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -34,7 +34,7 @@ package cromwell.backend.impl.aws
 import scala.collection.mutable.ListBuffer
 import cromwell.backend.BackendJobDescriptor
 import cromwell.backend.io.JobPaths
-import software.amazon.awssdk.services.batch.model.{ContainerProperties, Host, KeyValuePair, MountPoint, ResourceRequirement, ResourceType, RetryStrategy, Ulimit, Volume}
+import software.amazon.awssdk.services.batch.model.{ContainerProperties, EvaluateOnExit, Host, KeyValuePair, MountPoint, ResourceRequirement, ResourceType, RetryAction, RetryStrategy, Ulimit, Volume}
 import cromwell.backend.impl.aws.io.AwsBatchVolume
 
 import scala.jdk.CollectionConverters._
@@ -183,9 +183,30 @@ trait AwsBatchJobDefinitionBuilder {
 
   def retryStrategyBuilder(context: AwsBatchJobDefinitionContext): (RetryStrategy.Builder, String) = {
     // We can add here the 'evaluateOnExit' statement
-    (RetryStrategy.builder()
-      .attempts(context.runtimeAttributes.awsBatchRetryAttempts),
-     context.runtimeAttributes.awsBatchRetryAttempts.toString)
+    var builder = RetryStrategy.builder()
+      .attempts(context.runtimeAttributes.awsBatchRetryAttempts)
+
+    var evaluations: Seq[EvaluateOnExit] = Seq()
+    context.runtimeAttributes.awsBatchEvaluateOnExit.foreach(
+      (evaluate) => {
+        val evaluateBuilder = evaluate.foldLeft(EvaluateOnExit.builder()) {
+          case (acc, (k, v)) => (k.toLowerCase, v.toLowerCase) match {
+            case ("action", "retry") => acc.action(RetryAction.RETRY)
+            case ("action", "exit") => acc.action(RetryAction.EXIT)
+            case ("onexitcode", _) => acc.onExitCode(v)
+            case ("onreason", _) => acc.onReason(v)
+            case ("onstatusreason", _) => acc.onStatusReason(v)
+            case _ => acc
+          }
+        }
+        evaluations = evaluations :+ evaluateBuilder.build()
+      }
+    )
+
+    builder = builder.evaluateOnExit(evaluations.asJava)
+
+    (builder,
+     s"${context.runtimeAttributes.awsBatchRetryAttempts.toString}${context.runtimeAttributes.awsBatchEvaluateOnExit.toString}")
   }
 
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index 235927ab07c..13137718354 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -44,11 +44,15 @@ import wom.RuntimeAttributesKeys
 import wom.format.MemorySize
 import wom.types._
 import wom.values._
-import com.typesafe.config.{ConfigException,ConfigValueFactory}
+import com.typesafe.config.{ConfigException, ConfigValueFactory}
 
 import scala.util.matching.Regex
 import org.slf4j.{Logger, LoggerFactory}
 
+import scala.util.{Failure, Success, Try}
+import scala.jdk.CollectionConverters._
+
+
 /**
  * Attributes that are provided to the job at runtime
  * @param cpu number of vCPU
@@ -63,6 +67,7 @@ import org.slf4j.{Logger, LoggerFactory}
  * @param scriptS3BucketName the s3 bucket where the execution command or script will be written and, from there, fetched into the container and executed
  * @param fileSystem the filesystem type, default is "s3"
  * @param awsBatchRetryAttempts number of attempts that AWS Batch will retry the task if it fails
+ * @param awsBatchEvaluateOnExit Evaluate on exit strategy setting for AWS batch retry
  * @param ulimits ulimit values to be passed to the container
  * @param efsDelocalize should we delocalize efs files to s3
  * @param efsMakeMD5 should we make a sibling md5 file as part of the job 
@@ -78,6 +83,7 @@ case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      noAddress: Boolean,
                                      scriptS3BucketName: String,
                                      awsBatchRetryAttempts: Int,
+                                     awsBatchEvaluateOnExit: Vector[Map[String, String]],
                                      ulimits: Vector[Map[String, String]],
                                      efsDelocalize: Boolean,
                                      efsMakeMD5 : Boolean,
@@ -91,6 +97,10 @@ object AwsBatchRuntimeAttributes {
 
   val awsBatchRetryAttemptsKey = "awsBatchRetryAttempts"
 
+  val awsBatchEvaluateOnExitKey = "awsBatchEvaluateOnExit"
+  private val awsBatchEvaluateOnExitDefault = WomArray(WomArrayType(WomMapType(WomStringType,WomStringType)), Vector(WomMap(Map.empty[WomValue, WomValue])))
+
+
   val awsBatchefsDelocalizeKey = "efsDelocalize"
   val awsBatchefsMakeMD5Key = "efsMakeMD5"
 
@@ -157,6 +167,11 @@ object AwsBatchRuntimeAttributes {
     .configDefaultWomValue(runtimeConfig).getOrElse(WomInteger(0)))
   }
 
+  def awsBatchEvaluateOnExitValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[Map[String, String]]] = {
+    AwsBatchEvaluateOnExitValidation
+      .withDefault(AwsBatchEvaluateOnExitValidation.fromConfig(runtimeConfig).getOrElse(awsBatchEvaluateOnExitDefault))
+  }
+
   private def awsBatchefsDelocalizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = {
     AwsBatchefsDelocalizeValidation(awsBatchefsDelocalizeKey).withDefault(AwsBatchefsDelocalizeValidation(awsBatchefsDelocalizeKey)
     .configDefaultWomValue(runtimeConfig).getOrElse(WomBoolean(false)))
@@ -199,7 +214,6 @@ object AwsBatchRuntimeAttributes {
 
   def runtimeAttributesBuilder(configuration: AwsBatchConfiguration): StandardValidatedRuntimeAttributesBuilder = {
     val runtimeConfig = aggregateDisksInRuntimeConfig(configuration)
-    
     def validationsS3backend = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
                         cpuValidation(runtimeConfig),
                         cpuMinValidation(runtimeConfig),
@@ -212,6 +226,7 @@ object AwsBatchRuntimeAttributes {
                         queueArnValidation(runtimeConfig),
                         scriptS3BucketNameValidation(runtimeConfig),
                         awsBatchRetryAttemptsValidation(runtimeConfig),
+                        awsBatchEvaluateOnExitValidation(runtimeConfig),
                         ulimitsValidation(runtimeConfig),
                         awsBatchefsDelocalizeValidation(runtimeConfig),
                         awsBatchefsMakeMD5Validation(runtimeConfig)
@@ -227,6 +242,7 @@ object AwsBatchRuntimeAttributes {
       dockerValidation,
       queueArnValidation(runtimeConfig),
       awsBatchRetryAttemptsValidation(runtimeConfig),
+      awsBatchEvaluateOnExitValidation(runtimeConfig),
       ulimitsValidation(runtimeConfig),
       awsBatchefsDelocalizeValidation(runtimeConfig),
       awsBatchefsMakeMD5Validation(runtimeConfig)
@@ -254,6 +270,8 @@ object AwsBatchRuntimeAttributes {
        case _ => ""
     }
     val awsBatchRetryAttempts: Int = RuntimeAttributesValidation.extract(awsBatchRetryAttemptsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val awsBatchEvaluateOnExit: Vector[Map[String, String]] = RuntimeAttributesValidation.extract(awsBatchEvaluateOnExitValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+
     val ulimits: Vector[Map[String, String]] = RuntimeAttributesValidation.extract(ulimitsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val efsDelocalize: Boolean = RuntimeAttributesValidation.extract(awsBatchefsDelocalizeValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
     val efsMakeMD5: Boolean = RuntimeAttributesValidation.extract(awsBatchefsMakeMD5Validation(runtimeAttrsConfig),validatedRuntimeAttributes)
@@ -270,6 +288,7 @@ object AwsBatchRuntimeAttributes {
       noAddress,
       scriptS3BucketName,
       awsBatchRetryAttempts,
+      awsBatchEvaluateOnExit,
       ulimits,
       efsDelocalize,
       efsMakeMD5,
@@ -473,6 +492,115 @@ class AwsBatchRetryAttemptsValidation(key: String) extends IntRuntimeAttributesV
   override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Integer"
 }
 
+object AwsBatchEvaluateOnExitValidation extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
+
+  val requiredKey = "action"
+  private val acceptedKeys = Set(requiredKey, "onExitCode", "onReason", "onStatusReason")
+
+
+  def fromConfig(runtimeConfig: Option[Config]): Option[WomValue]= {
+    val config = runtimeConfig match {
+      case Some(value) => Try(value.getObjectList(key)) match {
+        case Failure(_) => None
+        case Success(value) => Some(value.asScala.map {
+          _.unwrapped().asScala.toMap
+        }.toList)
+      }
+      case _ => None
+    }
+
+    config match {
+      case Some(value) => Some(AwsBatchEvaluateOnExitValidation
+        .coercion collectFirst {
+        case womType if womType.coerceRawValue(value).isSuccess => womType.coerceRawValue(value).get
+      } getOrElse {
+        BadDefaultAttribute(WomString(value.toString))
+      })
+      case None => None
+    }
+  }
+
+  override def coercion: Iterable[WomType] = {
+    Set(WomStringType, WomArrayType(WomMapType(WomStringType, WomStringType)))
+  }
+
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[Vector[Map[String, String]]]] = {
+    case WomArray(womType, value)
+      if womType.memberType == WomMapType(WomStringType, WomStringType) =>
+      check_maps(value.toVector)
+    case WomMap(_, _) => "!!! ERROR1".invalidNel
+  }
+
+  private def check_maps(
+                          maps: Vector[WomValue]
+                        ): ErrorOr[Vector[Map[String, String]]] = {
+    val entryNels: Vector[ErrorOr[Map[String, String]]] = maps.map {
+      case WomMap(_, value) => check_keys(value)
+      case _ => "!!! ERROR2".invalidNel
+    }
+    val sequenced: ErrorOr[Vector[Map[String, String]]] = sequenceNels(
+      entryNels
+    )
+    sequenced
+  }
+
+  private def validateActionKey(dict: Map[WomValue, WomValue]): ErrorOr[Map[String, String]] = {
+    val validCondition = Set("retry", "exit")
+    val convertedMap = dict
+      .map { case (WomString(k), WomString(v)) =>
+        (k, v)
+        // case _ => "!!! ERROR3".invalidNel
+      }
+    if (convertedMap.exists {
+      case (key, value) => key.toLowerCase == requiredKey && validCondition.contains(value.toLowerCase)
+    }) {
+      convertedMap.validNel
+    }
+    else {
+      s"Missing or invalid $requiredKey key/value for runtime attribute: $key. Refer to https://docs.aws.amazon.com/batch/latest/APIReference/API_RetryStrategy.html".invalidNel
+    }
+  }
+
+  private def check_keys(
+                          dict: Map[WomValue, WomValue]
+                        ): ErrorOr[Map[String, String]] = {
+    val map_keys = dict.keySet.map(_.valueString.toLowerCase)
+    val unrecognizedKeys =
+      map_keys.diff(acceptedKeys.map(x => x.toLowerCase))
+    if (!dict.nonEmpty) {
+      Map.empty[String, String].validNel
+    }
+    else if (unrecognizedKeys.nonEmpty) {
+      s"Invalid keys in $key runtime attribute: $unrecognizedKeys. Only $acceptedKeys are accepted. Refer to https://docs.aws.amazon.com/batch/latest/APIReference/API_RetryStrategy.html".invalidNel
+    }
+    else {
+      validateActionKey(dict)
+    }
+  }
+
+  private def sequenceNels(
+                            nels: Vector[ErrorOr[Map[String, String]]]
+                          ): ErrorOr[Vector[Map[String, String]]] = {
+    val emptyNel: ErrorOr[Vector[Map[String, String]]] =
+      Vector.empty[Map[String, String]].validNel
+    val seqNel: ErrorOr[Vector[Map[String, String]]] =
+      nels.foldLeft(emptyNel) { (acc, v) =>
+        (acc, v) mapN { (a, v) => a :+ v }
+      }
+    seqNel
+  }
+
+
+  override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be defined"
+
+  /**
+   * Returns the key of the runtime attribute.
+   *
+   * @return The key of the runtime attribute.
+   */
+  override def key: String = AwsBatchRuntimeAttributes.awsBatchEvaluateOnExitKey
+}
+
 object AwsBatchefsDelocalizeValidation {
   def apply(key: String): AwsBatchefsDelocalizeValidation = new AwsBatchefsDelocalizeValidation(key)
 }
@@ -531,7 +659,7 @@ object UlimitsValidation
       accepted_keys.diff(map_keys) union map_keys.diff(accepted_keys)
 
     if (!dict.nonEmpty){
-      Map.empty[String, String].validNel  
+      Map.empty[String, String].validNel
     }else if (unrecognizedKeys.nonEmpty) {
       s"Invalid keys in $key runtime attribute. Refer to 'ulimits' section on https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#containerProperties".invalidNel
     } else {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 48bc3adc442..f9c3670f67b 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -75,6 +75,37 @@ runtime {
 }
 ```
 
+### `awsBatchEvaluteOnExit`
+
+*Default: _[]_* - will always retry 
+
+This runtime attribute sets the `evaluateOnExit` for [*AWS Batch Automated Job Retries*](https://docs.aws.amazon.com/batch/latest/userguide/job_retries.html) and specify the retry condition for a failed job.
+
+This configuration works with `awsBatchRetryAttempts` and is useful if you only want to retry on certain failures. 
+
+For instance, if you will only like to retry during spot termination.
+
+```
+runtime {
+    awsBatchEvaluateOnExit: [
+        {  
+            Action: "RETRY",
+            onStatusReason: "Host EC2*"
+        },
+        {
+            onReason : "*"
+            Action: "EXIT"
+        }
+    ]
+}
+```
+
+For more information on the batch retry strategy, please refer to:
+
+* General Doc: [userguide/job_retries.html](https://docs.aws.amazon.com/batch/latest/userguide/job_retries.html)
+* Blog: [Introducing retry strategies](https://aws.amazon.com/blogs/compute/introducing-retry-strategies-for-aws-batch/)
+
+
 ### `ulimits`
 
 *Default: _empty_*
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index 3c8e0382974..0c202aa8946 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -32,7 +32,7 @@
 package cromwell.backend.impl.aws
 
 import common.collections.EnhancedCollections._
-import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
+import cromwell.backend.{BackendJobDescriptor, BackendJobDescriptorKey, BackendWorkflowDescriptor}
 import cromwell.backend.BackendSpec._
 import cromwell.backend.impl.aws.io.{AwsBatchJobPaths, AwsBatchWorkflowPaths, AwsBatchWorkingDisk}
 import cromwell.backend.validation.ContinueOnReturnCodeFlag
@@ -46,7 +46,7 @@ import org.scalatest.PrivateMethodTester
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider
-import software.amazon.awssdk.services.batch.model.{ContainerDetail, JobDetail, KeyValuePair}
+import software.amazon.awssdk.services.batch.model.{ContainerDetail, EvaluateOnExit, JobDetail, KeyValuePair, RetryAction, RetryStrategy}
 import spray.json.{JsObject, JsString}
 import wdl4s.parser.MemoryUnit
 import wom.format.MemorySize
@@ -100,6 +100,8 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
 
   val call: CommandCallNode = workFlowDescriptor.callable.taskCallNodes.head
   val jobKey: BackendJobDescriptorKey = BackendJobDescriptorKey(call, None, 1)
+  val jobDescriptor: BackendJobDescriptor = BackendJobDescriptor(null, null, null, Map.empty, null, null, null)
+
   val jobPaths: AwsBatchJobPaths = AwsBatchJobPaths(workflowPaths, jobKey)
   val s3Inputs: Set[AwsBatchInput] = Set(AwsBatchFileInput("foo", "s3://bucket/foo", DefaultPathBuilder.get("foo"), AwsBatchWorkingDisk()))
   val s3Outputs: Set[AwsBatchFileOutput] = Set(AwsBatchFileOutput("baa", "s3://bucket/somewhere/baa", DefaultPathBuilder.get("baa"), AwsBatchWorkingDisk()))
@@ -117,11 +119,19 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
       noAddress = false,
       scriptS3BucketName = "script-bucket",
       awsBatchRetryAttempts = 1,
+      awsBatchEvaluateOnExit = Vector(Map.empty[String, String]),
       ulimits = Vector(Map.empty[String, String]),
       efsDelocalize = false,
       efsMakeMD5 = false,
       fileSystem = "s3")
 
+  val batchJobDefintion = AwsBatchJobDefinitionContext(
+    runtimeAttributes = runtimeAttributes,
+    commandText = "", dockerRcPath = "", dockerStdoutPath = "", dockerStderrPath = "", jobDescriptor = jobDescriptor
+    , jobPaths = jobPaths, inputs = Set(), outputs = Set(), fsxMntPoint = None, None, None, None
+
+  )
+
   val containerDetail: ContainerDetail = ContainerDetail.builder().exitCode(0).build()
   val jobDetail: JobDetail = JobDetail.builder().container(containerDetail).build
 
@@ -351,8 +361,6 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     job.reconfiguredScript should include (postscript)
   }
 
-
-
   it should "generate preamble with input copy command in reconfigured script" in {
     val job = generateJobWithS3InOut
     val preamble =
@@ -389,4 +397,36 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     val job = generateBasicJob
     job.rc(jobDetail) should be (0)
   }
+
+  it should "use RetryStrategy" in {
+    val runtime = runtimeAttributes.copy(
+      awsBatchEvaluateOnExit = Vector(Map("action" -> "EXIT", "onStatusReason" -> "Failed")),
+    )
+
+    val builder = RetryStrategy.builder().attempts(1).evaluateOnExit(
+      EvaluateOnExit.builder().onStatusReason("Failed").action(RetryAction.EXIT).build()
+    ).build()
+
+    val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion.copy(runtimeAttributes = runtime))
+    val jobDefinitionName = jobDefinition.name
+    val expected = jobDefinition.retryStrategy
+    expected should equal (builder)
+    jobDefinitionName should equal ("cromwell_ubuntu_latest_656d5a7e7cd016d2360b27bc5ee75018d91a777a")
+  }
+
+  it should "use RetryStrategy evaluateOnExit should be case insensitive" in {
+    val runtime = runtimeAttributes.copy(
+      awsBatchEvaluateOnExit = Vector(Map("aCtIoN" -> "EXIT", "onStatusReason" -> "Failed")),
+    )
+
+    val builder = RetryStrategy.builder().attempts(1).evaluateOnExit(
+      EvaluateOnExit.builder().onStatusReason("Failed").action(RetryAction.EXIT).build()
+    ).build()
+
+    val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion.copy(runtimeAttributes = runtime))
+    val jobDefinitionName = jobDefinition.name
+    val expected = jobDefinition.retryStrategy
+    expected should equal(builder)
+    jobDefinitionName should equal("cromwell_ubuntu_latest_66a335d761780e64e6b154339c5f1db2f0783f96")
+  }
 }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
index 7664c9dc748..944577d229d 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
@@ -48,6 +48,8 @@ import wom.format.MemorySize
 import wom.types._
 import wom.values._
 
+import scala.util.{Failure, Success, Try}
+
 class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec with Matchers {
 
   def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]): WorkflowOptions = {
@@ -67,6 +69,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     "my-stuff",
     1,
     Vector(Map.empty[String, String]),
+    Vector(Map.empty[String, String]),
     false,
     false
   )
@@ -82,6 +85,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     "",
     1,
     Vector(Map.empty[String, String]),
+    Vector(Map.empty[String, String]),
     false,
     false,
     "local")
@@ -191,9 +195,9 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
     "validate a valid Filesystem string entry local Filesystem" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),"scriptBucketName" -> WomString(""), "filesystem" -> WomString("local"))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString(""), "filesystem" -> WomString("local"))
       val expectedRuntimeAttributes = expectedDefaultsLocalFS
-      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes,WorkflowOptions.fromMap(Map.empty).get,
+      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes, WorkflowOptions.fromMap(Map.empty).get,
         NonEmptyList.of("us-east-1a", "us-east-1b"), new AwsBatchConfiguration(AwsBatchTestConfigForLocalFS.AwsBatchBackendConfigurationDescriptor))
     }
 
@@ -307,7 +311,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     }
 
     "override config default attributes with default attributes declared in workflow options" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff") )
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"))
 
       val workflowOptionsJson =
         """{
@@ -321,7 +325,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     }
 
     "override config default runtime attributes with task runtime attributes" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"),  "cpu" -> WomInteger(4))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "cpu" -> WomInteger(4))
 
       val workflowOptionsJson =
         """{
@@ -335,7 +339,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     }
 
     "override invalid config default attributes with task runtime attributes" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),"scriptBucketName" -> WomString("my-stuff"),  "cpu" -> WomInteger(4))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "cpu" -> WomInteger(4))
 
       val workflowOptionsJson =
         """{
@@ -374,6 +378,89 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
       val expectedRuntimeAttributes = expectedDefaults.copy(awsBatchRetryAttempts = 0)
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
+
+    "validate a valid awsBatchEvaluateOnExit " in {
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "awsBatchRetryAttempts" -> WomInteger(0),
+        "scriptBucketName" -> WomString("my-stuff"),
+        "awsBatchEvaluateOnExit" -> WomArray(
+          Seq(WomMap(Map(WomString("action") -> WomString("RETRY"), WomString("onStatusReason") -> WomString("Host EC2*")))
+          )
+        )
+      )
+
+      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedDefaults.copy(
+        awsBatchRetryAttempts = 0,
+        awsBatchEvaluateOnExit = Vector(Map("action" -> "RETRY", "onStatusReason" -> "Host EC2*"))
+      ))
+    }
+
+    "if awsBatchEvaluteOnExit is empty, do not fail" in {
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "awsBatchRetryAttempts" -> WomInteger(0),
+        "scriptBucketName" -> WomString("my-stuff"),
+        "awsBatchEvaluateOnExit" -> WomArray(WomArrayType(WomMapType(WomStringType,WomStringType)), Vector(WomMap(Map.empty[WomValue, WomValue])))
+      )
+      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedDefaults.copy(
+        awsBatchRetryAttempts = 0,
+      ))
+    }
+
+    "missing or invalid action key result in an invalid awsBatchEvaluateOnExit" in {
+      val invalidEvaluateOnExit = List(
+        // missing action key
+        WomArray(
+          Seq(WomMap(Map(WomString("onStatusReason") -> WomString("Host EC2*")))
+          )
+        ),
+        // invalid value
+        WomArray(
+          Seq(WomMap(Map(WomString("action") -> WomString("TRYAGAIN"), WomString("onStatusReason") -> WomString("Host EC2*")))
+          )
+        )
+      )
+
+      invalidEvaluateOnExit foreach { invalidVal =>
+        val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "awsBatchEvaluateOnExit" -> invalidVal)
+        assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+          "Missing or invalid action key/value for runtime attribute: awsBatchEvaluateOnExit")
+      }
+    }
+  }
+
+  "Unrecognized keys for retry strategy should result in an invalid awsBatchEvaluateOnExit" in {
+    // invalid key
+    val invalidValue = WomArray(
+      Seq(WomMap(Map(WomString("action") -> WomString("RETRY"), WomString("onRandomStatus") -> WomString("Host EC2*")))
+      )
+    )
+    val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "awsBatchEvaluateOnExit" -> invalidValue)
+    assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+      s"""Invalid keys in awsBatchEvaluateOnExit runtime attribute: Set(onrandomstatus).
+         | Only Set(action, onExitCode, onReason, onStatusReason) are accepted.""".stripMargin.replace(
+        "\n", ""))
+  }
+
+  "Config with defined awsBatchEvaluateOnExit works" in {
+    val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"),
+    )
+    val batchConfig = new AwsBatchConfiguration(AwsBatchTestWithRetryConfig.AwsBatchBackendConfigurationDescriptor)
+    val workflowOptions = WorkflowOptions.fromMap(Map.empty).get
+    val expectedRuntimeAttributes = expectedDefaults.copy(
+      awsBatchEvaluateOnExit = Vector(
+        Map("Action" -> "RETRY", "onStatusReason" -> "Host EC2*"), Map("Action" -> "EXIT", "onReason" -> "*"))
+    )
+
+    val runtimeAttributesBuilder = AwsBatchRuntimeAttributes.runtimeAttributesBuilder(batchConfig)
+    val defaultedAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(
+      AwsBatchRuntimeAttributes.runtimeAttributesBuilder(batchConfig).definitions.toSet, workflowOptions)(runtimeAttributes)
+
+    val validatedRuntimeAttributes = runtimeAttributesBuilder.build(defaultedAttributes, NOPLogger.NOP_LOGGER)
+    val actualRuntimeAttributes = AwsBatchRuntimeAttributes(
+      validatedRuntimeAttributes, batchConfig.runtimeConfig, batchConfig.fileSystem)
+    assert(actualRuntimeAttributes == expectedRuntimeAttributes)
   }
 
   private def assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes: Map[String, WomValue],
@@ -393,11 +480,10 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
   private def assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue],
                                                        exMsg: String,
                                                        workflowOptions: WorkflowOptions = emptyWorkflowOptions): Unit = {
-    try {
-      toAwsBatchRuntimeAttributes(runtimeAttributes, workflowOptions, configuration)
-      fail(s"A RuntimeException was expected with message: $exMsg")
-    } catch {
-      case ex: RuntimeException => assert(ex.getMessage.contains(exMsg))
+
+    Try(toAwsBatchRuntimeAttributes(runtimeAttributes, workflowOptions, configuration)) match {
+      case Failure(exception) => assert(exception.getMessage.contains(exMsg))
+      case Success(_) => fail(s"A RuntimeException was expected with message: $exMsg")
     }
     ()
   }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
index 682714b225c..275f126765b 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
@@ -187,6 +187,96 @@ object AwsBatchTestConfigForLocalFS {
        |
        |""".stripMargin
 
+  val AwsBatchBackendConfig = ConfigFactory.parseString(AwsBatchBackendConfigString)
+  val AwsBatchGlobalConfig = ConfigFactory.parseString(AwsBatchGlobalConfigString)
+  val AwsBatchBackendNoDefaultConfig = ConfigFactory.parseString(NoDefaultsConfigString)
+  val AwsBatchBackendConfigurationDescriptor = BackendConfigurationDescriptor(AwsBatchBackendConfig, AwsBatchGlobalConfig)
+  val NoDefaultsConfigurationDescriptor = BackendConfigurationDescriptor(AwsBatchBackendNoDefaultConfig, AwsBatchGlobalConfig)
+}
+
+object AwsBatchTestWithRetryConfig {
+
+  private val AwsBatchBackendConfigString =
+    """
+      |root = "s3://my-cromwell-workflows-bucket"
+      |
+      |filesystems {
+      |  s3 {
+      |    auth = "default"
+      |  }
+      |}
+      |
+      |auth = "default"
+      |   numSubmitAttempts = 6
+      |   numCreateDefinitionAttempts = 6
+      |
+      |default-runtime-attributes {
+      |    cpu: 1
+      |    failOnStderr: false
+      |    continueOnReturnCode: 0
+      |    docker: "ubuntu:latest"
+      |    memory: "2 GB"
+      |    disks: "local-disk"
+      |    noAddress: false
+      |    zones:["us-east-1a", "us-east-1b"]
+      |    queueArn: "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue"
+      |    scriptBucketName: "my-bucket"
+      |    awsBatchRetryAttempts: 1
+      |    awsBatchEvaluateOnExit: [
+      |     {
+      |       Action: "RETRY",
+      |       onStatusReason: "Host EC2*"
+      |     },
+      |     {
+      |  		  onReason : "*"
+      |       Action: "EXIT"
+      |     }
+      |    ]
+      |}
+      |
+      |""".stripMargin
+
+  private val NoDefaultsConfigString =
+    """
+      |root = "s3://my-cromwell-workflows-bucket"
+      |
+      |auth = "default"
+      |   numSubmitAttempts = 6
+      |   numCreateDefinitionAttempts = 6
+      |
+      |filesystems {
+      |  s3 {
+      |    auth = "default"
+      |  }
+      |}
+      |""".stripMargin
+
+  private val AwsBatchGlobalConfigString =
+    s"""
+       |aws {
+       |  application-name = "cromwell"
+       |  auths = [
+       |    {
+       |      name = "default"
+       |      scheme = "default"
+       |    }
+       |  ]
+       |}
+       |
+       |backend {
+       |  default = "AWS"
+       |  providers {
+       |    AWS {
+       |      actor-factory = "cromwell.backend.impl.aws.AwsBatchBackendLifecycleFactory"
+       |      config {
+       |      $AwsBatchBackendConfigString
+       |      }
+       |    }
+       |  }
+       |}
+       |
+       |""".stripMargin
+
   val AwsBatchBackendConfig = ConfigFactory.parseString(AwsBatchBackendConfigString)
   val AwsBatchGlobalConfig = ConfigFactory.parseString(AwsBatchGlobalConfigString)
   val AwsBatchBackendNoDefaultConfig = ConfigFactory.parseString(NoDefaultsConfigString)

From 2a93f2810452b6c4b9ded2aa9bb2c183f930025b Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 13 Nov 2023 13:19:39 -0500
Subject: [PATCH 240/326] [WX-1260] Acquire sas token from task runner (#7241)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 .../StandardAsyncExecutionActor.scala         |   9 +-
 .../blob/BlobFileSystemManager.scala          |  70 ++++++--
 .../filesystems/blob/BlobPathBuilder.scala    |   5 +-
 .../WorkspaceManagerApiClientProvider.scala   |   2 +
 ...cpBatchAsyncBackendJobExecutionActor.scala |   6 +-
 ...inesApiAsyncBackendJobExecutionActor.scala |   4 +-
 .../TesAsyncBackendJobExecutionActor.scala    | 161 ++++++++++++++++--
 .../impl/tes/TesRuntimeAttributes.scala       |  39 ++++-
 .../cromwell/backend/impl/tes/TesTask.scala   |  42 +++--
 ...TesAsyncBackendJobExecutionActorSpec.scala | 155 +++++++++++++++++
 .../impl/tes/TesInitializationActorSpec.scala |   4 +-
 .../impl/tes/TesRuntimeAttributesSpec.scala   |  12 ++
 .../backend/impl/tes/TesTaskSpec.scala        |   1 +
 13 files changed, 455 insertions(+), 55 deletions(-)
 create mode 100644 supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index c98e429c63d..59eb7f08269 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -1,7 +1,6 @@
 package cromwell.backend.standard
 
 import java.io.IOException
-
 import akka.actor.{Actor, ActorLogging, ActorRef}
 import akka.event.LoggingReceive
 import cats.implicits._
@@ -329,7 +328,7 @@ trait StandardAsyncExecutionActor
   }
 
   /** Any custom code that should be run within commandScriptContents before the instantiated command. */
-  def scriptPreamble: String = ""
+  def scriptPreamble: ErrorOr[String] = "".valid
 
   def cwd: Path = commandDirectory
   def rcPath: Path = cwd./(jobPaths.returnCodeFilename)
@@ -427,10 +426,12 @@ trait StandardAsyncExecutionActor
            |find . -type d -exec sh -c '[ -z "$$(ls -A '"'"'{}'"'"')" ] && touch '"'"'{}'"'"'/.file' \\;
            |)""".stripMargin)
 
+    val errorOrPreamble: ErrorOr[String] = scriptPreamble
+
     // The `tee` trickery below is to be able to redirect to known filenames for CWL while also streaming
     // stdout and stderr for PAPI to periodically upload to cloud storage.
     // https://stackoverflow.com/questions/692000/how-do-i-write-stderr-to-a-file-while-using-tee-with-a-pipe
-    (errorOrDirectoryOutputs, errorOrGlobFiles).mapN((directoryOutputs, globFiles) =>
+    (errorOrDirectoryOutputs, errorOrGlobFiles, errorOrPreamble).mapN((directoryOutputs, globFiles, preamble) =>
     s"""|#!$jobShell
         |DOCKER_OUTPUT_DIR_LINK
         |cd ${cwd.pathAsString}
@@ -464,7 +465,7 @@ trait StandardAsyncExecutionActor
         |)
         |mv $rcTmpPath $rcPath
         |""".stripMargin
-      .replace("SCRIPT_PREAMBLE", scriptPreamble)
+      .replace("SCRIPT_PREAMBLE", preamble)
       .replace("ENVIRONMENT_VARIABLES", environmentVariables)
       .replace("INSTANTIATED_COMMAND", commandString)
       .replace("SCRIPT_EPILOGUE", scriptEpilogue)
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index e3de6783d85..8f03dbe7e33 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -15,6 +15,7 @@ import java.nio.file.spi.FileSystemProvider
 import java.time.temporal.ChronoUnit
 import java.time.{Duration, OffsetDateTime}
 import java.util.UUID
+import scala.collection.mutable
 import scala.jdk.CollectionConverters._
 import scala.util.{Failure, Success, Try}
 
@@ -160,12 +161,14 @@ object BlobSasTokenGenerator {
     */
   def createBlobTokenGenerator(workspaceManagerClient: WorkspaceManagerApiClientProvider,
                                overrideWsmAuthToken: Option[String]): BlobSasTokenGenerator = {
-    WSMBlobSasTokenGenerator(workspaceManagerClient, overrideWsmAuthToken)
+    new WSMBlobSasTokenGenerator(workspaceManagerClient, overrideWsmAuthToken)
   }
 
 }
 
-case class WSMBlobSasTokenGenerator(wsmClientProvider: WorkspaceManagerApiClientProvider,
+case class WSMTerraCoordinates(wsmEndpoint: String, workspaceId: UUID, containerResourceId: UUID)
+
+class WSMBlobSasTokenGenerator(wsmClientProvider: WorkspaceManagerApiClientProvider,
                                     overrideWsmAuthToken: Option[String]) extends BlobSasTokenGenerator {
 
   /**
@@ -178,17 +181,14 @@ case class WSMBlobSasTokenGenerator(wsmClientProvider: WorkspaceManagerApiClient
     * @return an AzureSasCredential for accessing a blob container
     */
   def generateBlobSasToken(endpoint: EndpointURL, container: BlobContainerName): Try[AzureSasCredential] = {
-    val wsmAuthToken: Try[String] = overrideWsmAuthToken match {
-      case Some(t) => Success(t)
-      case None => AzureCredentials.getAccessToken(None).toTry
-    }
+    val wsmAuthToken: Try[String] = getWsmAuth
     container.workspaceId match {
       // If this is a Terra workspace, request a token from WSM
       case Success(workspaceId) => {
         (for {
           wsmAuth <- wsmAuthToken
           wsmAzureResourceClient = wsmClientProvider.getControlledAzureResourceApi(wsmAuth)
-          resourceId <- getContainerResourceId(workspaceId, container, wsmAuth)
+          resourceId <- getContainerResourceId(workspaceId, container, Option(wsmAuth))
           sasToken <- wsmAzureResourceClient.createAzureStorageContainerSasToken(workspaceId, resourceId)
         } yield sasToken).recoverWith {
           // If the storage account was still not found in WSM, this may be a public filesystem
@@ -201,9 +201,59 @@ case class WSMBlobSasTokenGenerator(wsmClientProvider: WorkspaceManagerApiClient
     }
   }
 
- def getContainerResourceId(workspaceId: UUID, container: BlobContainerName, wsmAuth : String): Try[UUID] = {
-    val wsmResourceClient = wsmClientProvider.getResourceApi(wsmAuth)
-    wsmResourceClient.findContainerResourceId(workspaceId, container)
+  private val cachedContainerResourceIds = new mutable.HashMap[BlobContainerName, UUID]()
+
+  // Optionally provide wsmAuth to avoid acquiring it twice in generateBlobSasToken.
+  // In the case that the resourceId is not cached and no auth is provided, this function will acquire a new auth as necessary.
+  private def getContainerResourceId(workspaceId: UUID, container: BlobContainerName, precomputedWsmAuth: Option[String]): Try[UUID] = {
+    cachedContainerResourceIds.get(container) match {
+      case Some(id) => Try(id) //cache hit
+      case _ => { //cache miss
+        val auth: Try[String] = precomputedWsmAuth.map(auth => Try(auth)).getOrElse(getWsmAuth)
+        val resourceId = for {
+          wsmAuth <- auth
+          wsmResourceApi = wsmClientProvider.getResourceApi(wsmAuth)
+          resourceId <- wsmResourceApi.findContainerResourceId(workspaceId, container)
+        } yield resourceId
+        resourceId.map(id => cachedContainerResourceIds.put(container, id)) //NB: Modifying cache state here.
+        cachedContainerResourceIds.get(container) match {
+          case Some(uuid) => Try(uuid)
+          case _ => Failure(new NoSuchElementException("Could not retrieve container resource ID from WSM"))
+        }
+      }
+    }
+  }
+
+  private def getWsmAuth: Try[String] = {
+    overrideWsmAuthToken match {
+      case Some(t) => Success(t)
+      case None => AzureCredentials.getAccessToken(None).toTry
+    }
+  }
+
+  private def parseTerraWorkspaceIdFromPath(blobPath: BlobPath): Try[UUID] = {
+    if (blobPath.container.value.startsWith("sc-")) Try(UUID.fromString(blobPath.container.value.substring(3)))
+    else Failure(new Exception("Could not parse workspace ID from storage container. Are you sure this is a file in a Terra Workspace?"))
+  }
+
+  /**
+   * Return a REST endpoint that will reply with a sas token for the blob storage container associated with the provided blob path.
+   * @param blobPath A blob path of a file living in a blob container that WSM knows about (likely a workspace container).
+   * @param tokenDuration How long will the token last after being generated. Default is 8 hours. Sas tokens won't last longer than 24h.
+   * NOTE: If a blobPath is provided for a file in a container other than what this token generator was constructed for,
+   * this function will make two REST requests. Otherwise, the relevant data is already cached locally.
+   */
+  def getWSMSasFetchEndpoint(blobPath: BlobPath, tokenDuration: Option[Duration] = None): Try[String] = {
+    val wsmEndpoint = wsmClientProvider.getBaseWorkspaceManagerUrl
+    val lifetimeQueryParameters: String = tokenDuration.map(d => s"?sasExpirationDuration=${d.toSeconds.intValue}").getOrElse("")
+    val terraInfo: Try[WSMTerraCoordinates] = for {
+      workspaceId <- parseTerraWorkspaceIdFromPath(blobPath)
+      containerResourceId <- getContainerResourceId(workspaceId, blobPath.container, None)
+      coordinates = WSMTerraCoordinates(wsmEndpoint, workspaceId, containerResourceId)
+    } yield coordinates
+    terraInfo.map{terraCoordinates =>
+      s"${terraCoordinates.wsmEndpoint}/api/workspaces/v1/${terraCoordinates.workspaceId.toString}/resources/controlled/azure/storageContainer/${terraCoordinates.containerResourceId.toString}/getSasToken${lifetimeQueryParameters}"
+    }
   }
 }
 
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 3aa26eb3c11..3acb99857e0 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -185,6 +185,9 @@ case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, con
     * @return Path string relative to the container root.
     */
   def pathWithoutContainer : String = pathString
-  
+
+  def getFilesystemManager: BlobFileSystemManager = fsm
+
   override def getSymlinkSafePath(options: LinkOption*): Path  = toAbsolutePath
+
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
index 276738c98b6..490d0fcc704 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
@@ -20,6 +20,7 @@ import scala.util.Try
 trait WorkspaceManagerApiClientProvider {
   def getControlledAzureResourceApi(token: String): WsmControlledAzureResourceApi
   def getResourceApi(token: String): WsmResourceApi
+  def getBaseWorkspaceManagerUrl: String
 }
 
 class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManagerURL) extends WorkspaceManagerApiClientProvider {
@@ -40,6 +41,7 @@ class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManag
     apiClient.setAccessToken(token)
     WsmControlledAzureResourceApi(new ControlledAzureResourceApi(apiClient))
   }
+  def getBaseWorkspaceManagerUrl: String = baseWorkspaceManagerUrl.value
 }
 
 case class WsmResourceApi(resourcesApi : ResourceApi) {
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
index ae228ad503b..766a8f2552f 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
@@ -663,12 +663,12 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   private val DockerMonitoringLogPath: Path = GcpBatchWorkingDisk.MountPoint.resolve(gcpBatchCallPaths.batchMonitoringLogFilename)
   private val DockerMonitoringScriptPath: Path = GcpBatchWorkingDisk.MountPoint.resolve(gcpBatchCallPaths.batchMonitoringScriptFilename)
 
-  override def scriptPreamble: String = {
+  override def scriptPreamble: ErrorOr[String] = {
     if (monitoringOutput.isDefined) {
       s"""|touch $DockerMonitoringLogPath
           |chmod u+x $DockerMonitoringScriptPath
-          |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin
-    } else ""
+          |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin.valid
+    } else "".valid
   }
 
   private[actors] def generateInputs(jobDescriptor: BackendJobDescriptor): Set[GcpBatchInput] = {
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
index 745e11bee35..942838f8125 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -380,12 +380,12 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
 
   private lazy val isDockerImageCacheUsageRequested = runtimeAttributes.useDockerImageCache.getOrElse(useDockerImageCache(jobDescriptor.workflowDescriptor))
 
-  override def scriptPreamble: String = {
+  override def scriptPreamble: ErrorOr[String] = {
     if (monitoringOutput.isDefined) {
       s"""|touch $DockerMonitoringLogPath
           |chmod u+x $DockerMonitoringScriptPath
           |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin
-    } else ""
+    }.valid else "".valid
   }
 
   override def globParentDirectory(womGlobFile: WomGlobFile): Path = {
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index ad8daca6ec7..100ed6137e9 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -1,10 +1,5 @@
 package cromwell.backend.impl.tes
 
-import common.exception.AggregatedMessageException
-
-import java.io.FileNotFoundException
-import java.nio.file.FileAlreadyExistsException
-import cats.syntax.apply._
 import akka.http.scaladsl.Http
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
 import akka.http.scaladsl.marshalling.Marshal
@@ -13,23 +8,31 @@ import akka.http.scaladsl.model._
 import akka.http.scaladsl.unmarshalling.{Unmarshal, Unmarshaller}
 import akka.stream.ActorMaterializer
 import akka.util.ByteString
+import cats.implicits._
+import common.collections.EnhancedCollections._
+import common.exception.AggregatedMessageException
 import common.validation.ErrorOr.ErrorOr
 import common.validation.Validation._
 import cromwell.backend.BackendJobLifecycleActor
 import cromwell.backend.async.{AbortedExecutionHandle, ExecutionHandle, FailedNonRetryableExecutionHandle, PendingExecutionHandle}
+import cromwell.backend.impl.tes.TesAsyncBackendJobExecutionActor.{determineWSMSasEndpointFromInputs, generateLocalizedSasScriptPreamble}
 import cromwell.backend.impl.tes.TesResponseJsonFormatter._
 import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
+import cromwell.core.logging.JobLogger
 import cromwell.core.path.{DefaultPathBuilder, Path}
-import cromwell.core.retry.SimpleExponentialBackoff
 import cromwell.core.retry.Retry._
-import cromwell.filesystems.blob.BlobPath
+import cromwell.core.retry.SimpleExponentialBackoff
+import cromwell.filesystems.blob.{BlobPath, WSMBlobSasTokenGenerator}
 import cromwell.filesystems.drs.{DrsPath, DrsResolver}
-import wom.values.WomFile
 import net.ceedubs.ficus.Ficus._
+import wom.values.WomFile
 
+import java.io.FileNotFoundException
+import java.nio.file.FileAlreadyExistsException
+import java.time.Duration
+import java.time.temporal.ChronoUnit
 import scala.concurrent.Future
-import scala.util.{Failure, Success}
-
+import scala.util.{Failure, Success, Try}
 sealed trait TesRunStatus {
   def isTerminal: Boolean
   def sysLogs: Seq[String] = Seq.empty[String]
@@ -59,6 +62,110 @@ case object Cancelled extends TesRunStatus {
 
 object TesAsyncBackendJobExecutionActor {
   val JobIdKey = "tes_job_id"
+
+  def generateLocalizedSasScriptPreamble(environmentVariableName: String, getSasWsmEndpoint: String) : String = {
+    // BEARER_TOKEN: https://learn.microsoft.com/en-us/azure/active-directory/managed-identities-azure-resources/how-to-use-vm-token#get-a-token-using-http
+    // NB: Scala string interpolation and bash variable substitution use similar syntax. $$ is an escaped $, much like \\ is an escaped \.
+    s"""
+       |### BEGIN ACQUIRE LOCAL SAS TOKEN ###
+       |# Function to check if a command exists on this machine
+       |command_exists() {
+       |  command -v "$$1" > /dev/null 2>&1
+       |}
+       |
+       |# Check if curl exists; install if not
+       |if ! command_exists curl; then
+       |  if command_exists apt-get; then
+       |    apt-get -y update && apt-get -y install curl
+       |    if [ $$? -ne 0 ]; then
+       |      echo "Error: Failed to install curl via apt-get."
+       |      exit 1
+       |    fi
+       |  else
+       |    echo "Error: apt-get is not available, and curl is not installed."
+       |    exit 1
+       |  fi
+       |fi
+       |
+       |# Check if jq exists; install if not
+       |if ! command_exists jq; then
+       |  if command_exists apt-get; then
+       |    apt-get -y update && apt-get -y install jq
+       |    if [ $$? -ne 0 ]; then
+       |      echo "Error: Failed to install jq via apt-get."
+       |      exit 1
+       |    fi
+       |  else
+       |    echo "Error: apt-get is not available, and jq is not installed."
+       |    exit 1
+       |  fi
+       |fi
+       |
+       |# Acquire bearer token, relying on the User Assigned Managed Identity of this VM.
+       |echo Acquiring Bearer Token using User Assigned Managed Identity...
+       |BEARER_TOKEN=$$(curl 'http://169.254.169.254/metadata/identity/oauth2/token?api-version=2018-02-01&resource=https%3A%2F%2Fmanagement.azure.com%2F' -H Metadata:true -s | jq .access_token)
+       |
+       |# Remove the leading and trailing quotes
+       |BEARER_TOKEN="$${BEARER_TOKEN#\\"}"
+       |BEARER_TOKEN="$${BEARER_TOKEN%\\"}"
+       |
+       |# Use the precomputed endpoint from cromwell + WSM to acquire a sas token
+       |echo Requesting sas token from WSM...
+       |sas_response_json=$$(curl -s \\
+       |                    --retry 3 \\
+       |                    --retry-delay 2 \\
+       |                    -X POST "$getSasWsmEndpoint" \\
+       |                    -H "Content-Type: application/json" \\
+       |                    -H "accept: */*" \\
+       |                    -H "Authorization: Bearer $${BEARER_TOKEN}")
+       |
+       |# Store token as environment variable
+       |export $environmentVariableName=$$(echo "$${sas_response_json}" | jq -r '.token')
+       |
+       |# Echo the first characters for logging/debugging purposes. "null" indicates something went wrong.
+       |echo Saving sas token: $${$environmentVariableName:0:4}**** to environment variable $environmentVariableName...
+       |### END ACQUIRE LOCAL SAS TOKEN ###
+       |""".stripMargin
+  }
+
+  private def maybeConvertToBlob(pathToTest: Try[Path]): Try[BlobPath] = {
+    pathToTest.collect { case blob: BlobPath => blob }
+  }
+
+  /**
+   * Computes an endpoint that can be used to retrieve a sas token for a particular blob storage container.
+   * This assumes that some of the task inputs are blob files, all blob files are in the same container, and we can get a sas
+   * token for this container from WSM.
+   * The task VM will use the user assigned managed identity that it is running as in order to authenticate.
+   * @param taskInputs The inputs to this particular TesTask. If any are blob files, the first  will be used to
+   *                   determine the storage container to retrieve the sas token for.
+   * @param pathGetter A function to convert string filepath into a cromwell Path object.
+   * @param blobConverter A function to convert a Path into a Blob path, if possible. Provided for testing purposes.
+   * @return A URL endpoint that, when called with proper authentication, will return a sas token.
+   *         Returns 'None' if one should not be used for this task.
+   */
+  def determineWSMSasEndpointFromInputs(taskInputs: List[Input],
+                                        pathGetter: String => Try[Path],
+                                        logger: JobLogger,
+                                        blobConverter: Try[Path] => Try[BlobPath] = maybeConvertToBlob): Try[String] = {
+    // Collect all of the inputs that are valid blob paths
+    val blobFiles = taskInputs
+      .collect{ case Input(_, _, Some(url), _, _, _) => blobConverter(pathGetter(url)) }
+      .collect{ case Success(blob) => blob }
+
+    // Log if not all input files live in the same container.
+    if (blobFiles.map(_.container).distinct.size > 1) {
+      logger.info(s"While parsing blob inputs, found more than one container. Generating SAS token based on first file in the list.")
+    }
+
+    // We use the first blob file in the list to determine the correct blob container.
+    blobFiles.headOption.map{blobPath =>
+      blobPath.getFilesystemManager.blobTokenGenerator match {
+        case wsmGenerator: WSMBlobSasTokenGenerator => wsmGenerator.getWSMSasFetchEndpoint(blobPath, Some(Duration.of(24, ChronoUnit.HOURS)))
+        case _ => Failure(new UnsupportedOperationException("Blob file does not have an associated WSMBlobSasTokenGenerator"))
+      }
+    }.getOrElse(Failure(new NoSuchElementException("Could not infer blob storage container from task inputs: No valid blob files provided.")))
+  }
 }
 
 class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
@@ -71,7 +178,6 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
   override type StandardAsyncRunState = TesRunStatus
 
   def statusEquivalentTo(thiz: StandardAsyncRunState)(that: StandardAsyncRunState): Boolean = thiz == that
-
   override lazy val pollBackOff: SimpleExponentialBackoff = tesConfiguration.pollBackoff
   override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff = tesConfiguration.executeOrRecoverBackoff
 
@@ -90,6 +196,38 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
     )
   }
 
+  /**
+   * This script preamble is bash code that is executed at the start of a task inside the user's container.
+   * It is executed directly before the user's instantiated command is, which gives cromwell a chance to adjust the
+   * container environment before the actual task runs. See commandScriptContents in StandardAsyncExecutionActor for more context.
+   *
+   * For TES tasks, we sometimes want to acquire and save an azure sas token to an environment variable.
+   * If the user provides a value for runtimeAttributes.localizedSasEnvVar, we will add the relevant bash code to the preamble
+   * that acquires/exports the sas token to an environment variable. Once there, it will be visible to the user's task code.
+   *
+   * If runtimeAttributes.localizedSasEnvVar is provided in the WDL (and determineWSMSasEndpointFromInputs is successful),
+   * we will export the sas token to an environment variable named to be the value of runtimeAttributes.localizedSasEnvVar.
+   * Otherwise, we won't alter the preamble.
+   *
+   * See determineWSMSasEndpointFromInputs to see how we use taskInputs to infer *which* container to get a sas token for.
+   *
+   * @return Bash code to run at the start of a task.
+   */
+  override def scriptPreamble: ErrorOr[String] = {
+    runtimeAttributes.localizedSasEnvVar match {
+      case Some(environmentVariableName) => { // Case: user wants a sas token. Return the computed preamble or die trying.
+        val workflowName = workflowDescriptor.callable.name
+        val callInputFiles = jobDescriptor.fullyQualifiedInputs.safeMapValues {
+          _.collectAsSeq { case w: WomFile => w }
+        }
+        val taskInputs: List[Input] = TesTask.buildTaskInputs(callInputFiles, workflowName, mapCommandLineWomFile)
+        val computedEndpoint = determineWSMSasEndpointFromInputs(taskInputs, getPath, jobLogger)
+        computedEndpoint.map(endpoint => generateLocalizedSasScriptPreamble(environmentVariableName, endpoint))
+      }.toErrorOr
+      case _ => "".valid // Case: user doesn't want a sas token. Empty preamble is the correct preamble.
+    }
+  }
+
   override def mapCommandLineWomFile(womFile: WomFile): WomFile = {
     womFile.mapFile(value =>
       (getPath(value), asAdHocFile(womFile)) match {
@@ -173,7 +311,6 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
   }
 
   override def executeAsync(): Future[ExecutionHandle] = {
-
     // create call exec dir
     tesJobPaths.callExecutionRoot.createPermissionedDirectories()
     val taskMessageFuture = createTaskMessage().fold(
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
index c5b3c4df66d..48ade7b234a 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
@@ -1,5 +1,6 @@
 package cromwell.backend.impl.tes
 
+import cats.data.Validated
 import cats.syntax.validated._
 import com.typesafe.config.Config
 import common.validation.ErrorOr.ErrorOr
@@ -15,6 +16,8 @@ import wom.format.MemorySize
 import wom.types.{WomIntegerType, WomStringType}
 import wom.values._
 
+import java.util.regex.Pattern
+
 case class TesRuntimeAttributes(continueOnReturnCode: ContinueOnReturnCode,
                                 dockerImage: String,
                                 dockerWorkingDir: Option[String],
@@ -23,13 +26,14 @@ case class TesRuntimeAttributes(continueOnReturnCode: ContinueOnReturnCode,
                                 memory: Option[MemorySize],
                                 disk: Option[MemorySize],
                                 preemptible: Boolean,
+                                localizedSasEnvVar: Option[String],
                                 backendParameters: Map[String, Option[String]])
 
 object TesRuntimeAttributes {
-
   val DockerWorkingDirKey = "dockerWorkingDir"
   val DiskSizeKey = "disk"
   val PreemptibleKey = "preemptible"
+  val LocalizedSasKey = "azureSasEnvironmentVariable"
 
   private def cpuValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Int Refined Positive] = CpuValidation.optional
 
@@ -47,8 +51,8 @@ object TesRuntimeAttributes {
   private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
 
   private val dockerWorkingDirValidation: OptionalRuntimeAttributesValidation[String] = DockerWorkingDirValidation.optional
-
   private def preemptibleValidation(runtimeConfig: Option[Config]) = PreemptibleValidation.default(runtimeConfig)
+  private def localizedSasValidation: OptionalRuntimeAttributesValidation[String] = LocalizedSasValidation.optional
 
   def runtimeAttributesBuilder(backendRuntimeConfig: Option[Config]): StandardValidatedRuntimeAttributesBuilder =
     // !! NOTE !! If new validated attributes are added to TesRuntimeAttributes, be sure to include
@@ -62,6 +66,7 @@ object TesRuntimeAttributes {
       dockerValidation,
       dockerWorkingDirValidation,
       preemptibleValidation(backendRuntimeConfig),
+      localizedSasValidation
     )
 
   def makeBackendParameters(runtimeAttributes: Map[String, WomValue],
@@ -124,8 +129,10 @@ object TesRuntimeAttributes {
       RuntimeAttributesValidation.extract(failOnStderrValidation(backendRuntimeConfig), validatedRuntimeAttributes)
     val continueOnReturnCode: ContinueOnReturnCode =
       RuntimeAttributesValidation.extract(continueOnReturnCodeValidation(backendRuntimeConfig), validatedRuntimeAttributes)
-    val preemptible: Boolean =
+    val preemptible: Boolean = {
       RuntimeAttributesValidation.extract(preemptibleValidation(backendRuntimeConfig), validatedRuntimeAttributes)
+    }
+    val localizedSas: Option[String] = RuntimeAttributesValidation.extractOption(localizedSasValidation.key, validatedRuntimeAttributes)
 
     // !! NOTE !! If new validated attributes are added to TesRuntimeAttributes, be sure to include
     // their validations here so that they will be handled correctly with backendParameters.
@@ -139,7 +146,8 @@ object TesRuntimeAttributes {
       diskSizeCompatValidation(backendRuntimeConfig),
       failOnStderrValidation(backendRuntimeConfig),
       continueOnReturnCodeValidation(backendRuntimeConfig),
-      preemptibleValidation(backendRuntimeConfig)
+      preemptibleValidation(backendRuntimeConfig),
+      localizedSasValidation
     )
 
     // BT-458 any strings included in runtime attributes that aren't otherwise used should be
@@ -156,6 +164,7 @@ object TesRuntimeAttributes {
       memory,
       disk,
       preemptible,
+      localizedSas,
       backendParameters
     )
   }
@@ -218,3 +227,25 @@ class PreemptibleValidation extends BooleanRuntimeAttributesValidation(TesRuntim
   override protected def missingValueMessage: String =
     s"Expecting $key runtime attribute to be an Integer, Boolean, or a String with values of 'true' or 'false'"
 }
+
+object LocalizedSasValidation {
+  lazy val instance: RuntimeAttributesValidation[String] = new LocalizedSasValidation
+  lazy val optional: OptionalRuntimeAttributesValidation[String] = instance.optional
+}
+
+class LocalizedSasValidation extends StringRuntimeAttributesValidation(TesRuntimeAttributes.LocalizedSasKey) {
+  private def isValidBashVariableName(str: String): Boolean = {
+    // require string be only letters, numbers, and underscores
+    val pattern = Pattern.compile("^[a-zA-Z0-9_]+$", Pattern.CASE_INSENSITIVE)
+    val matcher = pattern.matcher(str)
+    matcher.find
+  }
+
+  override protected def invalidValueMessage(value: WomValue): String = {
+    s"Invalid Runtime Attribute value for ${TesRuntimeAttributes.LocalizedSasKey}. Value must be a string containing only letters, numbers, and underscores."
+  }
+
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = {
+    case WomString(value) => if(isValidBashVariableName(value)) value.validNel else Validated.invalidNel(invalidValueMessage(WomString(value)))
+  }
+}
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index 4a6e77641e3..d775367ac74 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -16,6 +16,8 @@ import wom.callable.Callable.OutputDefinition
 import wom.expression.NoIoFunctionSet
 import wom.values._
 
+import scala.collection.immutable.Map
+
 final case class WorkflowExecutionIdentityConfig(value: String) {override def toString: String = value.toString}
 final case class WorkflowExecutionIdentityOption(value: String) {override def toString: String = value}
 final case class TesTask(jobDescriptor: BackendJobDescriptor,
@@ -79,24 +81,7 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
     }
 
   lazy val inputs: Seq[Input] = {
-    val result = (callInputFiles ++ writeFunctionFiles).flatMap {
-      case (fullyQualifiedName, files) => files.flatMap(_.flattenFiles).zipWithIndex.map {
-        case (f, index) =>
-          val inputType = f match {
-            case _: WomUnlistedDirectory => "DIRECTORY"
-            case _: WomSingleFile => "FILE"
-            case _: WomGlobFile => "FILE"
-          }
-          Input(
-            name = Option(fullyQualifiedName + "." + index),
-            description = Option(workflowName + "." + fullyQualifiedName + "." + index),
-            url = Option(f.value),
-            path = mapCommandLineWomFile(f).value,
-            `type` = Option(inputType),
-            content = None
-          )
-      }
-    }.toList ++ Seq(commandScript)
+    val result = TesTask.buildTaskInputs(callInputFiles ++ writeFunctionFiles, workflowName, mapCommandLineWomFile) ++ Seq(commandScript)
     jobLogger.info(s"Calculated TES inputs (found ${result.size}): " + result.mkString(System.lineSeparator(),System.lineSeparator(),System.lineSeparator()))
     result
   }
@@ -288,6 +273,27 @@ object TesTask {
     )
   }
 
+  def buildTaskInputs(taskFiles: Map[FullyQualifiedName, Seq[WomFile]], workflowName: String, womMapFn: WomFile => WomFile): List[Input] = {
+    taskFiles.flatMap {
+      case (fullyQualifiedName, files) => files.flatMap(_.flattenFiles).zipWithIndex.map {
+        case (f, index) =>
+          val inputType = f match {
+            case _: WomUnlistedDirectory => "DIRECTORY"
+            case _: WomSingleFile => "FILE"
+            case _: WomGlobFile => "FILE"
+          }
+          Input(
+            name = Option(fullyQualifiedName + "." + index),
+            description = Option(workflowName + "." + fullyQualifiedName + "." + index),
+            url = Option(f.value),
+            path = womMapFn(f).value,
+            `type` = Option(inputType),
+            content = None
+          )
+      }
+    }.toList
+  }
+
   def makeTags(workflowDescriptor: BackendWorkflowDescriptor): Map[String, Option[String]] = {
     // In addition to passing through any workflow labels, include relevant workflow ids as tags.
     val baseTags = workflowDescriptor.customLabels.asMap.map { case (k, v) => (k, Option(v)) }
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
new file mode 100644
index 00000000000..a28fce3d445
--- /dev/null
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
@@ -0,0 +1,155 @@
+package cromwell.backend.impl.tes
+
+import common.mock.MockSugar
+import cromwell.core.logging.JobLogger
+import cromwell.core.path.NioPath
+import cromwell.filesystems.blob.{BlobFileSystemManager, BlobPath, WSMBlobSasTokenGenerator}
+import org.mockito.ArgumentMatchers.any
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import java.time.Duration
+import java.time.temporal.ChronoUnit
+import scala.util.{Failure, Try}
+
+class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers with MockSugar {
+  behavior of "TesAsyncBackendJobExecutionActor"
+
+  val fullyQualifiedName = "this.name.is.more.than.qualified"
+  val workflowName = "mockWorkflow"
+  val someBlobUrl = "https://lz813a3d637adefec2c6e88f.blob.core.windows.net/sc-d8143fd8-aa07-446d-9ba0-af72203f1794/nyxp6c/tes-internal/configuration/supported-vm-sizes"
+  val someNotBlobUrl = "https://www.google.com/path/to/exile"
+  var index = 0
+
+  val blobInput_0 = Input(
+    name = Option(fullyQualifiedName + "." + index),
+    description = Option(workflowName + "." + fullyQualifiedName + "." + index),
+    url = Option(someBlobUrl),
+    path = someBlobUrl,
+    `type` = Option("FILE"),
+    content = None
+  )
+  index = index+1
+
+  val blobInput_1 = Input(
+    name = Option(fullyQualifiedName + "." + index),
+    description = Option(workflowName + "." + fullyQualifiedName + "." + index),
+    url = Option(someBlobUrl),
+    path = someBlobUrl,
+    `type` = Option("FILE"),
+    content = None
+  )
+  index = index+1
+
+  val notBlobInput_1 = Input(
+    name = Option(fullyQualifiedName + "." + index),
+    description = Option(workflowName + "." + fullyQualifiedName + "." + index),
+    url = Option(someNotBlobUrl + index),
+    path = someNotBlobUrl + index,
+    `type` = Option("FILE"),
+    content = None
+  )
+  index = index+1
+
+  val notBlobInput_2 = Input(
+    name = Option(fullyQualifiedName + "." + index),
+    description = Option(workflowName + "." + fullyQualifiedName + "." + index),
+    url = Option(someNotBlobUrl + index),
+    path = someNotBlobUrl + index,
+    `type` = Option("FILE"),
+    content = None
+  )
+
+  // Mock blob path functionality.
+  val testWsmEndpoint = "https://wsm.mock.com/endpoint"
+  val testWorkspaceId = "e58ed763-928c-4155-0000-fdbaaadc15f3"
+  val testContainerResourceId = "e58ed763-928c-4155-1111-fdbaaadc15f3"
+
+  def generateMockWsmTokenGenerator: WSMBlobSasTokenGenerator = {
+    val mockTokenGenerator = mock[WSMBlobSasTokenGenerator]
+    val expectedTokenDuration: Duration = Duration.of(24, ChronoUnit.HOURS)
+    mockTokenGenerator.getWSMSasFetchEndpoint(any[BlobPath], any[Option[Duration]]) returns Try(s"$testWsmEndpoint/api/workspaces/v1/$testWorkspaceId/resources/controlled/azure/storageContainer/$testContainerResourceId/getSasToken?sasExpirationDuration=${expectedTokenDuration.getSeconds.toInt}")
+    mockTokenGenerator
+  }
+  def generateMockFsm: BlobFileSystemManager = {
+    val mockFsm: BlobFileSystemManager = mock[BlobFileSystemManager]
+    val mockGenerator: WSMBlobSasTokenGenerator = generateMockWsmTokenGenerator
+    mockFsm.blobTokenGenerator returns mockGenerator
+    mockFsm
+  }
+  //path to a blob file
+  def generateMockBlobPath: BlobPath = {
+    val mockBlobPath = mock[BlobPath]
+    mockBlobPath.pathAsString returns someBlobUrl
+
+    val mockFsm = generateMockFsm
+    mockBlobPath.getFilesystemManager returns mockFsm
+
+    val mockNioPath: NioPath = mock[NioPath]
+    mockBlobPath.nioPath returns mockNioPath
+    mockBlobPath
+  }
+
+  //Path to a file that isn't a blob file
+  def generateMockDefaultPath: cromwell.core.path.Path = {
+    val mockDefaultPath: cromwell.core.path.Path = mock[cromwell.core.path.Path]
+    mockDefaultPath.pathAsString returns someNotBlobUrl
+    mockDefaultPath
+  }
+  def pathGetter(pathString: String): Try[cromwell.core.path.Path] = {
+    val mockBlob: BlobPath = generateMockBlobPath
+    val mockDefault: cromwell.core.path.Path = generateMockDefaultPath
+    if(pathString.contains(someBlobUrl)) Try(mockBlob) else Try(mockDefault)
+  }
+
+  def blobConverter(pathToConvert: Try[cromwell.core.path.Path]): Try[BlobPath] = {
+    val mockBlob: BlobPath = generateMockBlobPath
+    if(pathToConvert.get.pathAsString.contains(someBlobUrl)) Try(mockBlob) else Failure(new Exception("failed"))
+  }
+
+  it should "not return sas endpoint when no blob paths are provided" in {
+    val mockLogger: JobLogger = mock[JobLogger]
+    val emptyInputs: List[Input] = List()
+    val bloblessInputs: List[Input] = List(notBlobInput_1, notBlobInput_2)
+    TesAsyncBackendJobExecutionActor.determineWSMSasEndpointFromInputs(emptyInputs, pathGetter, mockLogger, blobConverter).isFailure shouldBe true
+    TesAsyncBackendJobExecutionActor.determineWSMSasEndpointFromInputs(bloblessInputs, pathGetter, mockLogger, blobConverter).isFailure shouldBe true
+  }
+
+  it should "return a sas endpoint based on inputs when blob paths are provided" in {
+    val mockLogger: JobLogger = mock[JobLogger]
+    val expectedTokenLifetimeSeconds = 24 * 60 * 60 //assert that cromwell asks for 24h token duration.
+    val expected = s"$testWsmEndpoint/api/workspaces/v1/$testWorkspaceId/resources/controlled/azure/storageContainer/$testContainerResourceId/getSasToken?sasExpirationDuration=${expectedTokenLifetimeSeconds}"
+    val blobInput: List[Input] = List(blobInput_0)
+    val blobInputs: List[Input] = List(blobInput_0, blobInput_1)
+    val mixedInputs: List[Input] = List(notBlobInput_1, blobInput_0, blobInput_1)
+    TesAsyncBackendJobExecutionActor.determineWSMSasEndpointFromInputs(blobInput, pathGetter, mockLogger, blobConverter).get shouldEqual expected
+    TesAsyncBackendJobExecutionActor.determineWSMSasEndpointFromInputs(blobInputs, pathGetter, mockLogger, blobConverter).get shouldEqual expected
+    TesAsyncBackendJobExecutionActor.determineWSMSasEndpointFromInputs(mixedInputs, pathGetter, mockLogger,  blobConverter).get shouldEqual expected
+  }
+
+  it should "contain expected strings in the bash script" in {
+    val mockEnvironmentVariableNameFromWom = "mock_env_var_for_storing_sas_token"
+    val expectedEndpoint = s"$testWsmEndpoint/api/workspaces/v1/$testWorkspaceId/resources/controlled/azure/storageContainer/$testContainerResourceId/getSasToken"
+
+    val beginSubstring = "### BEGIN ACQUIRE LOCAL SAS TOKEN ###"
+    val endSubstring = "### END ACQUIRE LOCAL SAS TOKEN ###"
+    val curlCommandSubstring =
+      s"""
+        |sas_response_json=$$(curl -s \\
+        |                    --retry 3 \\
+        |                    --retry-delay 2 \\
+        |                    -X POST "$expectedEndpoint" \\
+        |                    -H "Content-Type: application/json" \\
+        |                    -H "accept: */*" \\
+        |                    -H "Authorization: Bearer $${BEARER_TOKEN}")
+        |""".stripMargin
+    val exportCommandSubstring = s"""export $mockEnvironmentVariableNameFromWom=$$(echo "$${sas_response_json}" | jq -r '.token')"""
+
+    val generatedBashScript = TesAsyncBackendJobExecutionActor.generateLocalizedSasScriptPreamble(mockEnvironmentVariableNameFromWom, expectedEndpoint)
+
+    generatedBashScript should include (beginSubstring)
+    generatedBashScript should include (endSubstring)
+    generatedBashScript should include (curlCommandSubstring)
+    generatedBashScript should include (exportCommandSubstring)
+  }
+}
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesInitializationActorSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesInitializationActorSpec.scala
index 731dd3c6c70..a081f26c910 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesInitializationActorSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesInitializationActorSpec.scala
@@ -63,6 +63,7 @@ class TesInitializationActorSpec extends TestKitSuite
       |    # The keys below have been commented out as they are optional runtime attributes.
       |    # dockerWorkingDir
       |    # docker
+      |    # azureSasEnvironmentVariable
       |}
       |""".stripMargin
 
@@ -107,6 +108,7 @@ class TesInitializationActorSpec extends TestKitSuite
     }
 
     def nonStringErrorMessage(key: String) = s"Workflow option $key must be a string"
+
     val bothRequiredErrorMessage = s"Workflow options ${TesWorkflowOptionKeys.WorkflowExecutionIdentity} and ${TesWorkflowOptionKeys.DataAccessIdentity} are both required if one is provided"
 
     "fail when WorkflowExecutionIdentity is not a string and DataAccessIdentity is missing" in {
@@ -120,7 +122,7 @@ class TesInitializationActorSpec extends TestKitSuite
           case InitializationFailed(failure) =>
             val expectedMsg = nonStringErrorMessage(TesWorkflowOptionKeys.WorkflowExecutionIdentity)
             if (!(failure.getMessage.contains(expectedMsg) &&
-                  failure.getMessage.contains(bothRequiredErrorMessage))) {
+              failure.getMessage.contains(bothRequiredErrorMessage))) {
               fail(s"Exception message did not contain both '$expectedMsg' and '$bothRequiredErrorMessage'. Was '$failure'")
             }
         }
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
index e1984fb65dc..830e0cbe70c 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
@@ -25,6 +25,7 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
     None,
     None,
     false,
+    None,
     Map.empty
   )
 
@@ -71,6 +72,17 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
       assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
     }
 
+    "validate a valid azureSasEnvironmentVariable entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), TesRuntimeAttributes.LocalizedSasKey -> WomString("THIS_IS_VALID"))
+      val expectedRuntimeAttributes = expectedDefaultsPlusUbuntuDocker.copy(localizedSasEnvVar = Some("THIS_IS_VALID"))
+      assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid azureSasEnvironmentVariable entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), TesRuntimeAttributes.LocalizedSasKey -> WomString("THIS IS INVALID"))
+      assertFailure(runtimeAttributes, "Value must be a string containing only letters, numbers, and underscores.")
+    }
+
     "convert a positive integer preemptible entry to true boolean" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "preemptible" -> WomInteger(3))
       val expectedRuntimeAttributes = expectedDefaultsPlusUbuntuDocker.copy(preemptible = true)
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index b7887b29944..a5fd3a3a7e2 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -31,6 +31,7 @@ class TesTaskSpec
     None,
     None,
     false,
+    None,
     Map.empty
   )
   val internalPathPrefix = Option("mock/path/to/tes/task")

From 9b7ad989c886c7f23a40bc4dfcdcf3f489d11bb2 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 14 Nov 2023 09:32:19 -0500
Subject: [PATCH 241/326] [WX-1183] Ice Lake (#7252)

---
 .../standardTestCases/papi_cpu_platform.test  |  3 +-
 .../papi_cpu_platform/papi_cpu_platform.wdl   |  9 ++---
 docs/RuntimeAttributes.md                     |  1 +
 .../pipelines/common/MachineConstraints.scala |  9 +++--
 .../PipelinesApiRuntimeAttributes.scala       |  1 +
 .../common/MachineConstraintsSpec.scala       | 36 ++++++++++++-------
 6 files changed, 40 insertions(+), 19 deletions(-)

diff --git a/centaur/src/main/resources/standardTestCases/papi_cpu_platform.test b/centaur/src/main/resources/standardTestCases/papi_cpu_platform.test
index 5aca2634edb..7b38c3a25d7 100644
--- a/centaur/src/main/resources/standardTestCases/papi_cpu_platform.test
+++ b/centaur/src/main/resources/standardTestCases/papi_cpu_platform.test
@@ -8,9 +8,10 @@ files {
 
 metadata {
   status: Succeeded
-  "outputs.cpus.cascadeLake.cpuPlatform": "Intel Cascade Lake"
   "outputs.cpus.broadwell.cpuPlatform": "Intel Broadwell"
   "outputs.cpus.haswell.cpuPlatform": "Intel Haswell"
+  "outputs.cpus.cascadeLake.cpuPlatform": "Intel Cascade Lake"
+  "outputs.cpus.iceLake.cpuPlatform": "Intel Ice Lake"
   "outputs.cpus.rome.cpuPlatform": "AMD Rome"
 }
 
diff --git a/centaur/src/main/resources/standardTestCases/papi_cpu_platform/papi_cpu_platform.wdl b/centaur/src/main/resources/standardTestCases/papi_cpu_platform/papi_cpu_platform.wdl
index 39d25e6fe47..3ec1bd77cae 100644
--- a/centaur/src/main/resources/standardTestCases/papi_cpu_platform/papi_cpu_platform.wdl
+++ b/centaur/src/main/resources/standardTestCases/papi_cpu_platform/papi_cpu_platform.wdl
@@ -24,8 +24,9 @@ task cpu_platform {
 }
 
 workflow cpus {
-   call cpu_platform as haswell { input: cpu_platform = "Intel Haswell" }
-   call cpu_platform as broadwell { input: cpu_platform = "Intel Broadwell" }
-   call cpu_platform as cascadeLake { input: cpu_platform = "Intel Cascade Lake" }
-   call cpu_platform as rome {input: cpu_platform = "AMD Rome" }
+    call cpu_platform as haswell { input: cpu_platform = "Intel Haswell" }
+    call cpu_platform as broadwell { input: cpu_platform = "Intel Broadwell" }
+    call cpu_platform as cascadeLake { input: cpu_platform = "Intel Cascade Lake" }
+    call cpu_platform as iceLake { input: cpu_platform = "Intel Ice Lake" }
+    call cpu_platform as rome { input: cpu_platform = "AMD Rome" }
 }
diff --git a/docs/RuntimeAttributes.md b/docs/RuntimeAttributes.md
index 3924c1de3e4..60216946a37 100644
--- a/docs/RuntimeAttributes.md
+++ b/docs/RuntimeAttributes.md
@@ -429,6 +429,7 @@ runtime {
 Note that when this options is specified, make sure the requested CPU platform is [available](https://cloud.google.com/compute/docs/regions-zones/#available) in the `zones` you selected.
 
 The following CPU platforms are currently supported by the Google Cloud backend:
+- `Intel Ice Lake`
 - `Intel Cascade Lake`
 - `Intel Skylake`     
 - `Intel Broadwell`   
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/MachineConstraints.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/MachineConstraints.scala
index fa1835dbad7..7e707f959e1 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/MachineConstraints.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/MachineConstraints.scala
@@ -16,10 +16,15 @@ object MachineConstraints {
     if (googleLegacyMachineSelection) {
       s"predefined-$cpu-${memory.to(MemoryUnit.MB).amount.intValue()}"
     } else {
-      // If someone requests Intel Cascade Lake as their CPU platform then switch the machine type to n2.
-      // Similarly, CPU platform of AMD Rome corresponds to the machine type n2d.  
+      // Users specify a CPU platform in their WDL, but GCP also needs to know which machine type to use.
+      // The below logic infers the machine type from the requested CPU.
+      // The heuristic we're using is: find the newest 'General Purpose' type that supports the given CPU.
+      // https://cloud.google.com/compute/docs/machine-resource
+      // For example, if someone requests Intel Cascade Lake as their CPU platform, then infer the n2 machine type.
+      // Infer n2d from AMD Rome, etc.
       val customMachineType =
         cpuPlatformOption match {
+          case Some(PipelinesApiRuntimeAttributes.CpuPlatformIntelIceLakeValue) => N2CustomMachineType
           case Some(PipelinesApiRuntimeAttributes.CpuPlatformIntelCascadeLakeValue) => N2CustomMachineType
           case Some(PipelinesApiRuntimeAttributes.CpuPlatformAMDRomeValue)          => N2DCustomMachineType 
           case _ => N1CustomMachineType
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala
index f1a8767ee5b..db87797de37 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala
@@ -78,6 +78,7 @@ object PipelinesApiRuntimeAttributes {
   // via `gcloud compute zones describe us-central1-a`
   val CpuPlatformIntelCascadeLakeValue = "Intel Cascade Lake"
   val CpuPlatformAMDRomeValue = "AMD Rome"
+  val CpuPlatformIntelIceLakeValue = "Intel Ice Lake"
 
   val UseDockerImageCacheKey = "useDockerImageCache"
   private val useDockerImageCacheValidationInstance = new BooleanRuntimeAttributesValidation(UseDockerImageCacheKey).optional
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/MachineConstraintsSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/MachineConstraintsSpec.scala
index 6eeb1102ec4..48ace9666e0 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/MachineConstraintsSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/MachineConstraintsSpec.scala
@@ -14,9 +14,11 @@ import wom.format.MemorySize
 class MachineConstraintsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "MachineConstraints"
 
-  private val n2Option = Option(PipelinesApiRuntimeAttributes.CpuPlatformIntelCascadeLakeValue)
+  private val n2OptionCascade = Option(PipelinesApiRuntimeAttributes.CpuPlatformIntelCascadeLakeValue)
 
-  private val n2dOption = Option(PipelinesApiRuntimeAttributes.CpuPlatformAMDRomeValue) 
+  private val n2dOption = Option(PipelinesApiRuntimeAttributes.CpuPlatformAMDRomeValue)
+
+  private val n2OptionIceLake = Option(PipelinesApiRuntimeAttributes.CpuPlatformIntelIceLakeValue)
 
   it should "generate valid machine types" in {
     val validTypes = Table(
@@ -40,7 +42,6 @@ class MachineConstraintsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
       // Same tests as above but with legacy machine type selection (cpu and memory as specified. No 'custom machine
       // requirement' adjustments are expected this time, except float->int)
-
       (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), None, true, "predefined-1-1024"),
       (MemorySize(4, MemoryUnit.GB), refineMV[Positive](3), None, true, "predefined-3-4096"),
       (MemorySize(1, MemoryUnit.GB), refineMV[Positive](1), None, true, "predefined-1-1024"),
@@ -52,15 +53,26 @@ class MachineConstraintsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
       (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), None, true, "predefined-33-2048"),
 
       // Same tests but with cascade lake (n2)
-      (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), n2Option, false, "n2-custom-2-2048"),
-      (MemorySize(4, MemoryUnit.GB), refineMV[Positive](3), n2Option, false, "n2-custom-4-4096"),
-      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](1), n2Option, false, "n2-custom-2-2048"),
-      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](4), n2Option, false, "n2-custom-4-4096"),
-      (MemorySize(14, MemoryUnit.GB), refineMV[Positive](16), n2Option, false, "n2-custom-16-16384"),
-      (MemorySize(13.65, MemoryUnit.GB), refineMV[Positive](1), n2Option, false, "n2-custom-2-14080"),
-      (MemorySize(1520.96, MemoryUnit.MB), refineMV[Positive](1), n2Option, false, "n2-custom-2-2048"),
-      (MemorySize(1024.0, MemoryUnit.MB), refineMV[Positive](1), n2Option, false, "n2-custom-2-2048"),
-      (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), n2Option, false, "n2-custom-36-36864"),
+      (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), n2OptionCascade, false, "n2-custom-2-2048"),
+      (MemorySize(4, MemoryUnit.GB), refineMV[Positive](3), n2OptionCascade, false, "n2-custom-4-4096"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](1), n2OptionCascade, false, "n2-custom-2-2048"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](4), n2OptionCascade, false, "n2-custom-4-4096"),
+      (MemorySize(14, MemoryUnit.GB), refineMV[Positive](16), n2OptionCascade, false, "n2-custom-16-16384"),
+      (MemorySize(13.65, MemoryUnit.GB), refineMV[Positive](1), n2OptionCascade, false, "n2-custom-2-14080"),
+      (MemorySize(1520.96, MemoryUnit.MB), refineMV[Positive](1), n2OptionCascade, false, "n2-custom-2-2048"),
+      (MemorySize(1024.0, MemoryUnit.MB), refineMV[Positive](1), n2OptionCascade, false, "n2-custom-2-2048"),
+      (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), n2OptionCascade, false, "n2-custom-36-36864"),
+
+      // Same tests, but with ice lake. Should produce same results as cascade lake since they're both n2.
+      (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), n2OptionIceLake, false, "n2-custom-2-2048"),
+      (MemorySize(4, MemoryUnit.GB), refineMV[Positive](3), n2OptionIceLake, false, "n2-custom-4-4096"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](1), n2OptionIceLake, false, "n2-custom-2-2048"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](4), n2OptionIceLake, false, "n2-custom-4-4096"),
+      (MemorySize(14, MemoryUnit.GB), refineMV[Positive](16), n2OptionIceLake, false, "n2-custom-16-16384"),
+      (MemorySize(13.65, MemoryUnit.GB), refineMV[Positive](1), n2OptionIceLake, false, "n2-custom-2-14080"),
+      (MemorySize(1520.96, MemoryUnit.MB), refineMV[Positive](1), n2OptionIceLake, false, "n2-custom-2-2048"),
+      (MemorySize(1024.0, MemoryUnit.MB), refineMV[Positive](1), n2OptionIceLake, false, "n2-custom-2-2048"),
+      (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), n2OptionIceLake, false, "n2-custom-36-36864"),
 
       // Same tests but with AMD Rome (n2d) #cpu > 16 are in increments of 16  
       (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1024"),

From 14c31840fddb6d7f7feea8c011b2a94fea6436af Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 16 Nov 2023 18:07:32 -0500
Subject: [PATCH 242/326] WX-1333 Improve logging visibility for load
 management (#7253)

---
 .../main/scala/cromwell/engine/io/IoActor.scala |  1 +
 .../services/ServiceRegistryActor.scala         | 14 +++++++++++++-
 .../common/api/PipelinesApiRequestManager.scala | 17 +++++++++++++----
 3 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/engine/src/main/scala/cromwell/engine/io/IoActor.scala b/engine/src/main/scala/cromwell/engine/io/IoActor.scala
index b4b3a0b191f..80a362a7b78 100644
--- a/engine/src/main/scala/cromwell/engine/io/IoActor.scala
+++ b/engine/src/main/scala/cromwell/engine/io/IoActor.scala
@@ -136,6 +136,7 @@ final class IoActor(ioConfig: IoConfig,
 
   override def onBackpressure(scale: Option[Double] = None): Unit = {
     incrementBackpressure()
+    log.warning("IoActor notifying HighLoad")
     serviceRegistryActor ! LoadMetric("IO", HighLoad)
 
     val uncappedDelay = scale.getOrElse(1.0d) * LoadConfig.IoNormalWindowMinimum
diff --git a/services/src/main/scala/cromwell/services/ServiceRegistryActor.scala b/services/src/main/scala/cromwell/services/ServiceRegistryActor.scala
index 0c613f307ba..2e43e651b2b 100644
--- a/services/src/main/scala/cromwell/services/ServiceRegistryActor.scala
+++ b/services/src/main/scala/cromwell/services/ServiceRegistryActor.scala
@@ -6,6 +6,7 @@ import akka.routing.Listen
 import cats.data.NonEmptyList
 import com.typesafe.config.{Config, ConfigFactory, ConfigObject}
 import cromwell.core.Dispatcher.ServiceDispatcher
+import cromwell.services.loadcontroller.LoadControllerService.LoadMetric
 import cromwell.util.GracefulShutdownHelper
 import cromwell.util.GracefulShutdownHelper.ShutdownCommand
 import net.ceedubs.ficus.Ficus._
@@ -82,7 +83,9 @@ class ServiceRegistryActor(globalConfig: Config) extends Actor with ActorLogging
   def receive = {
     case msg: ServiceRegistryMessage =>
       services.get(msg.serviceName) match {
-        case Some(ref) => ref.tell(transform(msg, sender()), sender())
+        case Some(ref) =>
+          debugLogLoadMessages(msg, sender())
+          ref.tell(transform(msg, sender()), sender())
         case None =>
           log.error("Received ServiceRegistryMessage requesting service '{}' for which no service is configured.  Message: {}", msg.serviceName, msg)
           sender() ! ServiceRegistryFailure(msg.serviceName)
@@ -107,6 +110,15 @@ class ServiceRegistryActor(globalConfig: Config) extends Actor with ActorLogging
       sender() ! ServiceRegistryFailure("Message is not a ServiceRegistryMessage: " + fool)
   }
 
+  private def debugLogLoadMessages(msg: ServiceRegistryMessage, sender: ActorRef): Unit = {
+    msg match {
+      case msg: LoadMetric =>
+        log.debug(s"Service Registry Actor receiving $msg message from $sender")
+      case _ =>
+        ()
+    }
+  }
+
   /**
     * Set the supervision strategy such that any of the individual service actors fails to initialize that we'll pass
     * the error up the chain
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManager.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManager.scala
index 02950e8bec8..81e3c2d9fda 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManager.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManager.scala
@@ -2,7 +2,6 @@ package cromwell.backend.google.pipelines.common.api
 
 import java.io.IOException
 import java.util.UUID
-
 import akka.actor.{Actor, ActorLogging, ActorRef, Props, SupervisorStrategy, Terminated, Timers}
 import akka.dispatch.ControlMessage
 import cats.data.NonEmptyList
@@ -18,7 +17,7 @@ import cromwell.core.Dispatcher.BackendDispatcher
 import cromwell.core.retry.SimpleExponentialBackoff
 import cromwell.core.{CromwellFatalExceptionMarker, LoadConfig, Mailbox, WorkflowId}
 import cromwell.services.instrumentation.CromwellInstrumentationScheduler
-import cromwell.services.loadcontroller.LoadControllerService.{HighLoad, LoadMetric, NormalLoad}
+import cromwell.services.loadcontroller.LoadControllerService.{HighLoad, LoadLevel, LoadMetric, NormalLoad}
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric._
 
@@ -89,6 +88,8 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
   protected[api] var statusPollers: Vector[ActorRef] = Vector.empty
   self ! ResetAllRequestWorkers
 
+  private var previousLoad: LoadLevel = NormalLoad
+
   override def preStart() = {
     log.info("Running with {} PAPI request workers", requestWorkers.value)
     startInstrumentationTimer()
@@ -96,8 +97,16 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
   }
 
   def monitorQueueSize() = {
-    val load = if (workQueue.size > LoadConfig.PAPIThreshold) HighLoad else NormalLoad
-    serviceRegistryActor ! LoadMetric("PAPIQueryManager", load)
+    val newLoad = if (workQueue.size > LoadConfig.PAPIThreshold) HighLoad else NormalLoad
+
+    if (previousLoad == NormalLoad && newLoad == HighLoad)
+      log.warning(s"PAPI Request Manager transitioned to HighLoad with queue size ${workQueue.size} exceeding limit of ${LoadConfig.PAPIThreshold}")
+    else if (previousLoad == HighLoad && newLoad == NormalLoad)
+      log.info("PAPI Request Manager transitioned back to NormaLoad")
+
+    previousLoad = newLoad
+
+    serviceRegistryActor ! LoadMetric("PAPIQueryManager", newLoad)
     updateQueueSize(workQueue.size)
   }
 

From 84b4480dbacf05ef3051fc1aab5c2f1789a46f00 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 1 Dec 2023 14:59:41 -0500
Subject: [PATCH 243/326] [WX-1391] Fix Bash Bug (#7326)

---
 .../StandardAsyncExecutionActor.scala         | 28 +++++++++++++++----
 ...cpBatchAsyncBackendJobExecutionActor.scala | 13 +++++----
 ...inesApiAsyncBackendJobExecutionActor.scala | 12 ++++----
 .../TesAsyncBackendJobExecutionActor.scala    | 10 +++----
 ...TesAsyncBackendJobExecutionActorSpec.scala |  3 +-
 5 files changed, 44 insertions(+), 22 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 59eb7f08269..3b116ae1b99 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -61,6 +61,10 @@ case class DefaultStandardAsyncExecutionActorParams
   override val minimumRuntimeSettings: MinimumRuntimeSettings
 ) extends StandardAsyncExecutionActorParams
 
+// Typically we want to "executeInSubshell" for encapsulation of bash code.
+// Override to `false` when we need the script to set an environment variable in the parent shell.
+case class ScriptPreambleData(bashString: String, executeInSubshell: Boolean = true)
+
 /**
   * An extension of the generic AsyncBackendJobExecutionActor providing a standard abstract implementation of an
   * asynchronous polling backend.
@@ -328,7 +332,7 @@ trait StandardAsyncExecutionActor
   }
 
   /** Any custom code that should be run within commandScriptContents before the instantiated command. */
-  def scriptPreamble: ErrorOr[String] = "".valid
+  def scriptPreamble: ErrorOr[ScriptPreambleData] = ScriptPreambleData("").valid
 
   def cwd: Path = commandDirectory
   def rcPath: Path = cwd./(jobPaths.returnCodeFilename)
@@ -426,7 +430,22 @@ trait StandardAsyncExecutionActor
            |find . -type d -exec sh -c '[ -z "$$(ls -A '"'"'{}'"'"')" ] && touch '"'"'{}'"'"'/.file' \\;
            |)""".stripMargin)
 
-    val errorOrPreamble: ErrorOr[String] = scriptPreamble
+    val errorOrPreamble: ErrorOr[String] = scriptPreamble.map{ preambleData =>
+        preambleData.executeInSubshell match {
+          case true =>
+            s"""
+               |(
+               |cd ${cwd.pathAsString}
+               |${preambleData.bashString}
+               |)
+               |""".stripMargin
+          case false =>
+            s"""
+               |cd ${cwd.pathAsString}
+               |${preambleData.bashString}
+               |""".stripMargin
+        }
+    }
 
     // The `tee` trickery below is to be able to redirect to known filenames for CWL while also streaming
     // stdout and stderr for PAPI to periodically upload to cloud storage.
@@ -440,10 +459,9 @@ trait StandardAsyncExecutionActor
         |export _JAVA_OPTIONS=-Djava.io.tmpdir="$$tmpDir"
         |export TMPDIR="$$tmpDir"
         |export HOME="$home"
-        |(
-        |cd ${cwd.pathAsString}
+        |
         |SCRIPT_PREAMBLE
-        |)
+        |
         |$out="$${tmpDir}/out.$$$$" $err="$${tmpDir}/err.$$$$"
         |mkfifo "$$$out" "$$$err"
         |trap 'rm "$$$out" "$$$err"' EXIT
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
index 766a8f2552f..b3f9d47d316 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
@@ -23,8 +23,9 @@ import cromwell.backend.google.batch.runnable.WorkflowOptionKeys
 import cromwell.backend.google.batch.util.{GcpBatchReferenceFilesMappingOperations, RuntimeOutputMapping}
 import cromwell.filesystems.gcs.GcsPathBuilder
 import cromwell.filesystems.gcs.GcsPathBuilder.ValidFullGcsPath
+
 import java.io.FileNotFoundException
-import cromwell.backend.standard.{StandardAdHocValue, StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
+import cromwell.backend.standard.{ScriptPreambleData, StandardAdHocValue, StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
 import cromwell.core._
 import cromwell.core.io.IoCommandBuilder
 import cromwell.core.path.{DefaultPathBuilder, Path}
@@ -49,6 +50,7 @@ import wom.core.FullyQualifiedName
 import wom.expression.{FileEvaluation, NoIoFunctionSet}
 import wom.format.MemorySize
 import wom.values._
+
 import java.io.OutputStreamWriter
 import java.nio.charset.Charset
 import java.util.Base64
@@ -663,12 +665,13 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   private val DockerMonitoringLogPath: Path = GcpBatchWorkingDisk.MountPoint.resolve(gcpBatchCallPaths.batchMonitoringLogFilename)
   private val DockerMonitoringScriptPath: Path = GcpBatchWorkingDisk.MountPoint.resolve(gcpBatchCallPaths.batchMonitoringScriptFilename)
 
-  override def scriptPreamble: ErrorOr[String] = {
-    if (monitoringOutput.isDefined) {
+  override def scriptPreamble: ErrorOr[ScriptPreambleData] = {
+    if (monitoringOutput.isDefined)
+      ScriptPreambleData(
       s"""|touch $DockerMonitoringLogPath
           |chmod u+x $DockerMonitoringScriptPath
-          |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin.valid
-    } else "".valid
+          |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin).valid
+    else ScriptPreambleData("").valid
   }
 
   private[actors] def generateInputs(jobDescriptor: BackendJobDescriptor): Set[GcpBatchInput] = {
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
index 942838f8125..fee63573ff1 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -1,7 +1,6 @@
 package cromwell.backend.google.pipelines.common
 
 import java.net.SocketTimeoutException
-
 import _root_.io.grpc.Status
 import akka.actor.ActorRef
 import akka.http.scaladsl.model.{ContentType, ContentTypes}
@@ -27,7 +26,7 @@ import cromwell.backend.google.pipelines.common.errors.FailedToDelocalizeFailure
 import cromwell.backend.google.pipelines.common.io._
 import cromwell.backend.google.pipelines.common.monitoring.{CheckpointingConfiguration, MonitoringImage}
 import cromwell.backend.io.DirectoryFunctions
-import cromwell.backend.standard.{StandardAdHocValue, StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
+import cromwell.backend.standard.{ScriptPreambleData, StandardAdHocValue, StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
 import cromwell.core._
 import cromwell.core.io.IoCommandBuilder
 import cromwell.core.path.{DefaultPathBuilder, Path}
@@ -380,12 +379,13 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
 
   private lazy val isDockerImageCacheUsageRequested = runtimeAttributes.useDockerImageCache.getOrElse(useDockerImageCache(jobDescriptor.workflowDescriptor))
 
-  override def scriptPreamble: ErrorOr[String] = {
-    if (monitoringOutput.isDefined) {
+  override def scriptPreamble: ErrorOr[ScriptPreambleData] = {
+    if (monitoringOutput.isDefined)
+      ScriptPreambleData(
       s"""|touch $DockerMonitoringLogPath
           |chmod u+x $DockerMonitoringScriptPath
-          |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin
-    }.valid else "".valid
+          |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin).valid
+     else ScriptPreambleData("").valid
   }
 
   override def globParentDirectory(womGlobFile: WomGlobFile): Path = {
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 100ed6137e9..92391296533 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -17,7 +17,7 @@ import cromwell.backend.BackendJobLifecycleActor
 import cromwell.backend.async.{AbortedExecutionHandle, ExecutionHandle, FailedNonRetryableExecutionHandle, PendingExecutionHandle}
 import cromwell.backend.impl.tes.TesAsyncBackendJobExecutionActor.{determineWSMSasEndpointFromInputs, generateLocalizedSasScriptPreamble}
 import cromwell.backend.impl.tes.TesResponseJsonFormatter._
-import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
+import cromwell.backend.standard.{ScriptPreambleData, StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import cromwell.core.retry.Retry._
@@ -123,7 +123,7 @@ object TesAsyncBackendJobExecutionActor {
        |export $environmentVariableName=$$(echo "$${sas_response_json}" | jq -r '.token')
        |
        |# Echo the first characters for logging/debugging purposes. "null" indicates something went wrong.
-       |echo Saving sas token: $${$environmentVariableName:0:4}**** to environment variable $environmentVariableName...
+       |echo "Saving sas token: $${$environmentVariableName:0:4}**** to environment variable $environmentVariableName..."
        |### END ACQUIRE LOCAL SAS TOKEN ###
        |""".stripMargin
   }
@@ -213,7 +213,7 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
    *
    * @return Bash code to run at the start of a task.
    */
-  override def scriptPreamble: ErrorOr[String] = {
+  override def scriptPreamble: ErrorOr[ScriptPreambleData] = {
     runtimeAttributes.localizedSasEnvVar match {
       case Some(environmentVariableName) => { // Case: user wants a sas token. Return the computed preamble or die trying.
         val workflowName = workflowDescriptor.callable.name
@@ -222,9 +222,9 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
         }
         val taskInputs: List[Input] = TesTask.buildTaskInputs(callInputFiles, workflowName, mapCommandLineWomFile)
         val computedEndpoint = determineWSMSasEndpointFromInputs(taskInputs, getPath, jobLogger)
-        computedEndpoint.map(endpoint => generateLocalizedSasScriptPreamble(environmentVariableName, endpoint))
+        computedEndpoint.map(endpoint => ScriptPreambleData(generateLocalizedSasScriptPreamble(environmentVariableName, endpoint), executeInSubshell =  false))
       }.toErrorOr
-      case _ => "".valid // Case: user doesn't want a sas token. Empty preamble is the correct preamble.
+      case _ => ScriptPreambleData("", executeInSubshell = false).valid // Case: user doesn't want a sas token. Empty preamble is the correct preamble.
     }
   }
 
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
index a28fce3d445..b9082d2e01f 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
@@ -144,12 +144,13 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
         |                    -H "Authorization: Bearer $${BEARER_TOKEN}")
         |""".stripMargin
     val exportCommandSubstring = s"""export $mockEnvironmentVariableNameFromWom=$$(echo "$${sas_response_json}" | jq -r '.token')"""
-
+    val echoCommandSubstring = s"""echo "Saving sas token: $${$mockEnvironmentVariableNameFromWom:0:4}**** to environment variable $mockEnvironmentVariableNameFromWom...""""
     val generatedBashScript = TesAsyncBackendJobExecutionActor.generateLocalizedSasScriptPreamble(mockEnvironmentVariableNameFromWom, expectedEndpoint)
 
     generatedBashScript should include (beginSubstring)
     generatedBashScript should include (endSubstring)
     generatedBashScript should include (curlCommandSubstring)
+    generatedBashScript should include (echoCommandSubstring)
     generatedBashScript should include (exportCommandSubstring)
   }
 }

From 408bc298f10e9a2ba8a9d05462658e75f61a0b6c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 4 Dec 2023 13:42:03 -0500
Subject: [PATCH 244/326] [WX-1393] Add Content Length to Curl request (#7328)

---
 .../impl/tes/TesAsyncBackendJobExecutionActor.scala       | 8 +++++---
 .../impl/tes/TesAsyncBackendJobExecutionActorSpec.scala   | 4 +++-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 92391296533..bd171d757b4 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -100,11 +100,11 @@ object TesAsyncBackendJobExecutionActor {
        |    exit 1
        |  fi
        |fi
-       |
+       |curl --version
+       |jq --version
        |# Acquire bearer token, relying on the User Assigned Managed Identity of this VM.
        |echo Acquiring Bearer Token using User Assigned Managed Identity...
        |BEARER_TOKEN=$$(curl 'http://169.254.169.254/metadata/identity/oauth2/token?api-version=2018-02-01&resource=https%3A%2F%2Fmanagement.azure.com%2F' -H Metadata:true -s | jq .access_token)
-       |
        |# Remove the leading and trailing quotes
        |BEARER_TOKEN="$${BEARER_TOKEN#\\"}"
        |BEARER_TOKEN="$${BEARER_TOKEN%\\"}"
@@ -117,7 +117,9 @@ object TesAsyncBackendJobExecutionActor {
        |                    -X POST "$getSasWsmEndpoint" \\
        |                    -H "Content-Type: application/json" \\
        |                    -H "accept: */*" \\
-       |                    -H "Authorization: Bearer $${BEARER_TOKEN}")
+       |                    -H "Authorization: Bearer $${BEARER_TOKEN}" \\
+       |                    -H "Content-Length: 0" \\
+       |                    -d "")
        |
        |# Store token as environment variable
        |export $environmentVariableName=$$(echo "$${sas_response_json}" | jq -r '.token')
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
index b9082d2e01f..11267d238cf 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
@@ -141,7 +141,9 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
         |                    -X POST "$expectedEndpoint" \\
         |                    -H "Content-Type: application/json" \\
         |                    -H "accept: */*" \\
-        |                    -H "Authorization: Bearer $${BEARER_TOKEN}")
+        |                    -H "Authorization: Bearer $${BEARER_TOKEN}" \\
+        |                    -H "Content-Length: 0" \\
+        |                    -d "")
         |""".stripMargin
     val exportCommandSubstring = s"""export $mockEnvironmentVariableNameFromWom=$$(echo "$${sas_response_json}" | jq -r '.token')"""
     val echoCommandSubstring = s"""echo "Saving sas token: $${$mockEnvironmentVariableNameFromWom:0:4}**** to environment variable $mockEnvironmentVariableNameFromWom...""""

From 9b98728520850b195f28cb02c652a8df24838f3e Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Mon, 4 Dec 2023 15:39:48 -0500
Subject: [PATCH 245/326] [WX-1346] Scalafmt  (#7257)

---
 .scalafmt.conf                                |   18 +
 .../main/scala/cromiam/auth/Collection.scala  |   23 +-
 .../src/main/scala/cromiam/auth/User.scala    |    1 -
 .../cromiam/cromwell/CromwellClient.scala     |   63 +-
 .../CromIamInstrumentation.scala              |   17 +-
 .../main/scala/cromiam/sam/SamClient.scala    |   66 +-
 .../scala/cromiam/server/CromIamServer.scala  |   20 +-
 .../server/config/CromIamServerConfig.scala   |   37 +-
 .../status/StatusCheckedSubsystem.scala       |    5 +-
 .../cromiam/server/status/StatusService.scala |    7 +-
 .../webservice/CromIamApiService.scala        |  127 +-
 .../webservice/EngineRouteSupport.scala       |    8 +-
 .../cromiam/webservice/QuerySupport.scala     |   27 +-
 .../cromiam/webservice/RequestSupport.scala   |   23 +-
 .../webservice/SubmissionSupport.scala        |  105 +-
 .../webservice/SwaggerUiHttpService.scala     |   19 +-
 .../scala/cromiam/auth/CollectionSpec.scala   |    1 -
 .../cromiam/cromwell/CromwellClientSpec.scala |   69 +-
 .../scala/cromiam/sam/SamClientSpec.scala     |   92 +-
 .../server/status/MockStatusService.scala     |    7 +-
 .../webservice/CromIamApiServiceSpec.scala    |  195 +-
 .../webservice/EngineRouteSupportSpec.scala   |    8 +-
 .../cromiam/webservice/MockClients.scala      |   67 +-
 .../cromiam/webservice/QuerySupportSpec.scala |   14 +-
 .../webservice/SubmissionSupportSpec.scala    |    9 +-
 .../webservice/SwaggerServiceSpec.scala       |   54 +-
 .../webservice/SwaggerUiHttpServiceSpec.scala |   42 +-
 .../webservice/WomtoolRouteSupportSpec.scala  |    8 +-
 .../backend/BackendCacheHitCopyingActor.scala |    8 +-
 .../backend/BackendInitializationData.scala   |    6 +-
 .../backend/BackendJobExecutionActor.scala    |   62 +-
 .../backend/BackendLifecycleActor.scala       |   11 +-
 .../BackendLifecycleActorFactory.scala        |   49 +-
 .../BackendWorkflowFinalizationActor.scala    |    4 +-
 .../BackendWorkflowInitializationActor.scala  |   71 +-
 .../main/scala/cromwell/backend/Command.scala |   13 +-
 .../cromwell/backend/FileSizeTooBig.scala     |    1 -
 .../cromwell/backend/OutputEvaluator.scala    |   68 +-
 .../backend/RuntimeAttributeDefinition.scala  |   16 +-
 .../cromwell/backend/RuntimeEnvironment.scala |   48 +-
 .../cromwell/backend/SlowJobWarning.scala     |   10 +-
 .../cromwell/backend/WriteFunctions.scala     |   14 +-
 .../async/AsyncBackendJobExecutionActor.scala |   33 +-
 .../backend/async/ExecutionHandle.scala       |   12 +-
 .../backend/async/ExecutionResult.scala       |    3 +-
 .../async/KnownJobFailureException.scala      |   52 +-
 .../cromwell/backend/async/package.scala      |    1 -
 .../main/scala/cromwell/backend/backend.scala |   43 +-
 .../dummy/DummyAsyncExecutionActor.scala      |   83 +-
 .../dummy/DummyInitializationActor.scala      |   15 +-
 .../dummy/DummyLifecycleActorFactory.scala    |   17 +-
 .../backend/dummy/DummySingletonActor.scala   |    5 +-
 .../backend/io/DirectoryFunctions.scala       |   45 +-
 .../io/FileEvaluationIoFunctionSet.scala      |    3 +-
 .../cromwell/backend/io/GlobFunctions.scala   |    7 +-
 .../scala/cromwell/backend/io/JobPaths.scala  |    4 +-
 .../backend/io/JobPathsWithDocker.scala       |   36 +-
 .../cromwell/backend/io/WorkflowPaths.scala   |   19 +-
 .../backend/io/WorkflowPathsWithDocker.scala  |   11 +-
 .../main/scala/cromwell/backend/package.scala |    1 +
 .../StandardAsyncExecutionActor.scala         |  738 +++---
 .../standard/StandardCachingActorHelper.scala |    8 +-
 .../StandardExpressionFunctions.scala         |   10 +-
 .../standard/StandardFinalizationActor.scala  |   19 +-
 .../StandardInitializationActor.scala         |   34 +-
 .../standard/StandardInitializationData.scala |    8 +-
 .../StandardJobExecutionActorParams.scala     |    8 +-
 .../StandardLifecycleActorFactory.scala       |  228 +-
 .../standard/StandardSyncExecutionActor.scala |   50 +-
 ...ardValidatedRuntimeAttributesBuilder.scala |   14 +-
 .../standard/callcaching/BlacklistCache.scala |   35 +-
 .../CallCachingBlacklistManager.scala         |   28 +-
 .../CopyingActorBlacklistCacheSupport.scala   |   36 +-
 .../RootWorkflowFileHashCacheActor.scala      |   42 +-
 .../StandardCacheHitCopyingActor.scala        |  278 ++-
 .../StandardFileHashingActor.scala            |   33 +-
 .../cromwell/backend/standard/package.scala   |    2 +-
 .../validation/ContinueOnReturnCode.scala     |    4 +-
 .../ContinueOnReturnCodeValidation.scala      |   13 +-
 .../backend/validation/DockerValidation.scala |    4 +-
 .../validation/FailOnStderrValidation.scala   |    7 +-
 .../validation/InformationValidation.scala    |   63 +-
 .../validation/MaxRetriesValidation.scala     |    4 +-
 .../backend/validation/MemoryValidation.scala |   16 +-
 ...PrimitiveRuntimeAttributesValidation.scala |   23 +-
 .../validation/RuntimeAttributesDefault.scala |   39 +-
 .../RuntimeAttributesValidation.scala         |  114 +-
 .../ValidatedRuntimeAttributesBuilder.scala   |   23 +-
 .../ValidationAggregatedException.scala       |    3 +-
 .../wfs/DefaultWorkflowPathBuilder.scala      |    1 -
 .../backend/wfs/WorkflowPathBuilder.scala     |   12 +-
 .../scala/cromwell/backend/BackendSpec.scala  |  153 +-
 ...ckendWorkflowInitializationActorSpec.scala |  105 +-
 .../cromwell/backend/MemorySizeSpec.scala     |    2 +-
 .../backend/OutputEvaluatorSpec.scala         |   85 +-
 .../RuntimeAttributeValidationSpec.scala      |   76 +-
 .../scala/cromwell/backend/TestConfig.scala   |    3 +-
 .../backend/io/DirectoryFunctionsSpec.scala   |   10 +-
 .../cromwell/backend/io/JobPathsSpec.scala    |    7 +-
 .../cromwell/backend/io/TestWorkflows.scala   |  109 +-
 .../backend/io/WorkflowPathsSpec.scala        |   18 +-
 ...alidatedRuntimeAttributesBuilderSpec.scala |  126 +-
 .../CallCachingBlacklistManagerSpec.scala     |    3 +-
 .../RootWorkflowHashCacheActorSpec.scala      |   47 +-
 .../StandardFileHashingActorSpec.scala        |   23 +-
 .../validation/ContinueOnReturnCodeSpec.scala |   15 +-
 .../RuntimeAttributesDefaultSpec.scala        |   12 +-
 .../RuntimeAttributesValidationSpec.scala     |  256 +-
 .../centaur/AbstractCentaurTestCaseSpec.scala |   60 +-
 ...llEngineOrBackendUpgradeTestCaseSpec.scala |   48 +-
 .../it/scala/centaur/CentaurTestSuite.scala   |   10 +-
 .../centaur/EngineUpgradeTestCaseSpec.scala   |    7 +-
 .../scala/centaur/ExternalTestCaseSpec.scala  |    7 +-
 .../centaur/PapiUpgradeTestCaseSpec.scala     |    2 +-
 .../scala/centaur/ParallelTestCaseSpec.scala  |    6 +-
 .../centaur/SequentialTestCaseSpec.scala      |    4 +-
 .../centaur/WdlUpgradeTestCaseSpec.scala      |    4 +-
 .../CromwellDatabaseCallCaching.scala         |    3 +-
 .../centaur/reporting/AggregatedIo.scala      |   19 +-
 .../centaur/reporting/BigQueryReporter.scala  |  125 +-
 .../centaur/reporting/CiEnvironment.scala     |    8 +-
 .../centaur/reporting/ErrorReporter.scala     |    8 +-
 .../ErrorReporterCromwellDatabase.scala       |   24 +-
 .../reporting/ErrorReporterParams.scala       |    3 +-
 .../centaur/reporting/ErrorReporters.scala    |   32 +-
 .../scala/centaur/reporting/GcsReporter.scala |   16 +-
 .../centaur/reporting/Slf4jReporter.scala     |   14 +-
 .../centaur/reporting/SuccessReporter.scala   |    8 +-
 .../main/scala/centaur/CentaurConfig.scala    |   11 +-
 .../main/scala/centaur/CromwellManager.scala  |   14 +-
 .../main/scala/centaur/CromwellTracker.scala  |   10 +-
 .../DockerComposeCromwellConfiguration.scala  |   17 +-
 .../centaur/JarCromwellConfiguration.scala    |   17 +-
 .../centaur/api/CentaurCromwellClient.scala   |  104 +-
 .../src/main/scala/centaur/api/Retry.scala    |   18 +-
 .../main/scala/centaur/json/JsonUtils.scala   |   18 +-
 .../centaur/test/CentaurTestException.scala   |   27 +-
 .../scala/centaur/test/ObjectCounter.scala    |   14 +-
 .../src/main/scala/centaur/test/Test.scala    |  589 +++--
 .../main/scala/centaur/test/TestOptions.scala |    8 +-
 .../centaur/test/formulas/TestFormulas.scala  |  161 +-
 .../centaur/test/markers/CallMarker.scala     |    3 +-
 .../test/metadata/CallAttemptFailure.scala    |   22 +-
 .../test/metadata/WorkflowFlatMetadata.scala  |   41 +-
 .../test/standard/CentaurTestCase.scala       |   33 +-
 .../test/standard/CentaurTestFormat.scala     |   69 +-
 .../centaur/test/submit/SubmitResponse.scala  |   16 +-
 .../workflow/DirectoryContentCountCheck.scala |   19 +-
 .../workflow/SubmittedWorkflowTracker.scala   |    3 +-
 .../centaur/test/workflow/Workflow.scala      |   60 +-
 .../centaur/test/workflow/WorkflowData.scala  |   57 +-
 .../DaemonizedDefaultThreadFactorySpec.scala  |    2 +-
 .../scala/centaur/json/JsonUtilsSpec.scala    |    8 +-
 .../centaur/test/CentaurOperationsSpec.scala  |   24 +-
 .../metadata/CallAttemptFailureSpec.scala     |    1 -
 ...actJobManagerStyleMetadataFieldsSpec.scala |    5 +-
 .../testfilecheck/FileCheckerSpec.scala       |   20 +-
 .../impl/drs/DrsCloudNioFileProvider.scala    |   47 +-
 .../drs/DrsCloudNioFileSystemProvider.scala   |    7 +-
 .../DrsCloudNioRegularFileAttributes.scala    |   45 +-
 .../scala/cloud/nio/impl/drs/DrsConfig.scala  |   21 +-
 .../cloud/nio/impl/drs/DrsCredentials.scala   |   24 +-
 .../cloud/nio/impl/drs/DrsPathResolver.scala  |   86 +-
 .../DrsResolverHttpRequestRetryStrategy.scala |   14 +-
 .../nio/impl/drs/EngineDrsPathResolver.scala  |    6 +-
 .../drs/DrsCloudNioFileProviderSpec.scala     |   31 +-
 .../DrsCloudNioFileSystemProviderSpec.scala   |    2 +-
 .../nio/impl/drs/DrsPathResolverSpec.scala    |  118 +-
 ...ResolverHttpRequestRetryStrategySpec.scala |    2 +-
 .../MockDrsCloudNioFileSystemProvider.scala   |   13 +-
 .../impl/drs/MockEngineDrsPathResolver.scala  |   16 +-
 .../cloud/nio/impl/ftp/FtpClientPool.scala    |   29 +-
 .../impl/ftp/FtpCloudNioFileProvider.scala    |   70 +-
 .../nio/impl/ftp/FtpCloudNioFileSystem.scala  |   11 +-
 .../ftp/FtpCloudNioFileSystemProvider.scala   |   24 +-
 .../cloud/nio/impl/ftp/FtpCredentials.scala   |    3 +-
 .../cloud/nio/impl/ftp/FtpFileSystems.scala   |   16 +-
 .../ftp/FtpFileSystemsConfiguration.scala     |    3 +-
 .../scala/cloud/nio/impl/ftp/FtpUtil.scala    |   16 +-
 .../nio/impl/ftp/InputOutputStreams.scala     |    8 +-
 .../nio/impl/ftp/LeasedInputStream.scala      |    6 +-
 .../nio/impl/ftp/LeasedOutputStream.scala     |    6 +-
 .../impl/ftp/operations/FtpOperation.scala    |   78 +-
 .../nio/impl/ftp/FtpClientPoolSpec.scala      |   10 +-
 .../ftp/FtpCloudNioFileProviderSpec.scala     |    3 +-
 .../FtpCloudNioFileSystemProviderSpec.scala   |   15 +-
 .../impl/ftp/FtpCloudNioFileSystemSpec.scala  |    8 +-
 .../nio/impl/ftp/FtpCredentialsSpec.scala     |   10 +-
 .../nio/impl/ftp/FtpFileSystemsSpec.scala     |    4 +-
 .../cloud/nio/impl/ftp/FtpUtilSpec.scala      |    6 +-
 .../nio/impl/ftp/LeaseInputStreamSpec.scala   |    6 +-
 .../nio/impl/ftp/LeaseOutputStreamSpec.scala  |    6 +-
 .../nio/impl/ftp/MockFtpFileSystem.scala      |   15 +-
 .../scala/cloud/nio/spi/CloudNioBackoff.scala |   26 +-
 .../nio/spi/CloudNioDirectoryStream.scala     |   13 +-
 .../nio/spi/CloudNioFileAttributeView.scala   |   10 +-
 .../cloud/nio/spi/CloudNioFileSystem.scala    |   31 +-
 .../nio/spi/CloudNioFileSystemProvider.scala  |   76 +-
 .../scala/cloud/nio/spi/CloudNioPath.scala    |   56 +-
 .../cloud/nio/spi/CloudNioReadChannel.scala   |   49 +-
 .../scala/cloud/nio/spi/CloudNioRetry.scala   |    8 +-
 .../cloud/nio/spi/CloudNioWriteChannel.scala  |    7 +-
 .../main/scala/cloud/nio/spi/UnixPath.scala   |   62 +-
 .../scala/cloud/nio/util/ChannelUtil.scala    |    3 +-
 .../scala/cloud/nio/util/CloudNioFiles.scala  |    3 +-
 .../scala/cloud/nio/util/CloudNioPaths.scala  |   21 +-
 .../main/scala/cloud/nio/util/IoUtil.scala    |   15 +-
 .../cloud/nio/util/TryWithResource.scala      |   16 +-
 .../scala/cloud/nio/util/VersionUtil.scala    |    9 +-
 .../cloudsupport/aws/AwsConfiguration.scala   |   19 +-
 .../cloudsupport/aws/auth/AwsAuthMode.scala   |   71 +-
 .../cloudsupport/aws/s3/S3Storage.scala       |    6 +-
 .../cloudsupport/azure/AzureCredentials.scala |    8 +-
 .../cloudsupport/azure/AzureUtils.scala       |   35 +-
 .../gcp/GoogleConfiguration.scala             |   24 +-
 .../gcp/auth/GoogleAuthMode.scala             |   60 +-
 .../cloudsupport/gcp/gcs/GcsStorage.scala     |   25 +-
 .../gcp/http/GoogleHttpTransportOptions.scala |    3 +-
 .../aws/AwsConfigurationSpec.scala            |   69 +-
 .../cloudsupport/aws/s3/S3StorageSpec.scala   |    1 -
 .../gcp/GoogleConfigurationSpec.scala         |   75 +-
 .../gcp/auth/ApplicationDefaultModeSpec.scala |    1 -
 .../gcp/auth/GoogleAuthModeSpec.scala         |    7 +-
 .../gcp/auth/MockAuthModeSpec.scala           |    1 -
 .../gcp/auth/ServiceAccountModeSpec.scala     |    6 +-
 .../gcp/auth/ServiceAccountTestSupport.scala  |   10 +-
 .../cloudsupport/gcp/auth/UserModeSpec.scala  |    1 -
 .../gcp/auth/UserServiceAccountModeSpec.scala |    1 -
 .../cloudsupport/gcp/gcs/GcsStorageSpec.scala |    4 +-
 codegen_java/project/Artifactory.scala        |    2 +-
 codegen_java/project/Publishing.scala         |   16 +-
 codegen_java/project/Version.scala            |   16 +-
 .../collections/EnhancedCollections.scala     |   51 +-
 .../main/scala/common/collections/Table.scala |    9 +-
 .../common/collections/WeightedQueue.scala    |   22 +-
 .../exception/ExceptionAggregation.scala      |   21 +-
 .../main/scala/common/exception/package.scala |    3 +-
 .../scala/common/numeric/IntegerUtil.scala    |    6 +-
 .../scala/common/transforms/package.scala     |   48 +-
 .../src/main/scala/common/util/Backoff.scala  |    2 +
 .../src/main/scala/common/util/IORetry.scala  |   18 +-
 .../common/util/IntrospectableLazy.scala      |   15 +-
 .../main/scala/common/util/StringUtil.scala   |    6 +-
 .../main/scala/common/util/TerminalUtil.scala |   14 +-
 .../src/main/scala/common/util/TimeUtil.scala |   10 +-
 .../src/main/scala/common/util/TryUtil.scala  |    3 +-
 .../src/main/scala/common/util/UriUtil.scala  |   25 +-
 .../main/scala/common/util/VersionUtil.scala  |    9 +-
 .../scala/common/validation/ErrorOr.scala     |  341 ++-
 .../scala/common/validation/IOChecked.scala   |   38 +-
 .../scala/common/validation/Validation.scala  |   53 +-
 .../assertion/CaseClassAssertions.scala       |    3 +-
 .../common/assertion/ErrorOrAssertions.scala  |    1 -
 .../scala/common/collections/TableSpec.scala  |   17 +-
 .../collections/WeightedQueueSpec.scala       |    4 +-
 .../exception/ExceptionAggregationSpec.scala  |    1 -
 .../scala/common/mock/MockImplicits.scala     |   38 +-
 .../test/scala/common/mock/MockSugar.scala    |   15 +-
 .../common/numeric/IntegerUtilSpec.scala      |   33 +-
 .../common/util/IntrospectableLazySpec.scala  |   12 +-
 .../test/scala/common/util/IoRetrySpec.scala  |    4 +-
 .../scala/common/util/StringUtilSpec.scala    |   46 +-
 .../scala/common/util/TerminalUtilSpec.scala  |    1 -
 .../test/scala/common/util/TryUtilSpec.scala  |   31 +-
 .../scala/common/util/VersionUtilSpec.scala   |    7 +-
 .../scala/common/validation/CheckedSpec.scala |    3 +-
 .../scala/common/validation/ErrorOrSpec.scala |  261 +-
 .../common/validation/ValidationSpec.scala    |    1 -
 .../core/BackendDockerConfiguration.scala     |    4 +-
 .../main/scala/cromwell/core/ConfigUtil.scala |   21 +-
 .../cromwell/core/DockerConfiguration.scala   |   43 +-
 .../main/scala/cromwell/core/Encryption.scala |   21 +-
 .../scala/cromwell/core/ExecutionIndex.scala  |    3 +-
 .../scala/cromwell/core/ExecutionStatus.scala |    5 +-
 .../main/scala/cromwell/core/HogGroup.scala   |   10 +-
 .../src/main/scala/cromwell/core/JobKey.scala |    4 +-
 .../core/MonitoringCompanionActor.scala       |   16 +-
 .../main/scala/cromwell/core/WorkflowId.scala |    6 +-
 .../scala/cromwell/core/WorkflowOptions.scala |   42 +-
 .../core/WorkflowProcessingEvents.scala       |    6 +-
 .../core/WorkflowSourceFilesCollection.scala  |   25 +-
 .../scala/cromwell/core/WorkflowState.scala   |   17 +-
 .../cromwell/core/actor/BatchActor.scala      |   16 +-
 .../core/actor/RobustClientHelper.scala       |   23 +-
 .../core/actor/StreamActorHelper.scala        |   45 +-
 .../cromwell/core/actor/ThrottlerActor.scala  |    3 +-
 .../core/callcaching/CallCachingMode.scala    |   14 +-
 .../core/callcaching/HashResultMessage.scala  |    1 -
 core/src/main/scala/cromwell/core/core.scala  |   18 +-
 .../core/filesystem/CromwellFileSystems.scala |  105 +-
 .../main/scala/cromwell/core/io/AsyncIo.scala |   31 +-
 .../cromwell/core/io/AsyncIoFunctions.scala   |    1 +
 .../core/io/CorePathFunctionSet.scala         |   11 +-
 .../cromwell/core/io/DefaultIoCommand.scala   |   30 +-
 .../main/scala/cromwell/core/io/IoAck.scala   |    8 +-
 .../cromwell/core/io/IoClientHelper.scala     |   17 +-
 .../scala/cromwell/core/io/IoCommand.scala    |   21 +-
 .../cromwell/core/io/IoCommandBuilder.scala   |   64 +-
 .../core/io/IoPromiseProxyActor.scala         |   16 +-
 .../scala/cromwell/core/io/Throttle.scala     |    3 +-
 .../scala/cromwell/core/labels/Label.scala    |    9 +-
 .../scala/cromwell/core/labels/Labels.scala   |    6 +-
 .../core/logging/EnhancedDateConverter.scala  |    7 +-
 .../core/logging/EnhancedSlf4jLogger.scala    |    1 +
 .../core/logging/JavaLoggingBridge.scala      |    1 +
 .../cromwell/core/logging/JobLogger.scala     |   16 +-
 .../cromwell/core/logging/LoggerWrapper.scala |   49 +-
 .../core/logging/WorkflowLogger.scala         |   54 +-
 .../core/path/BetterFileMethods.scala         |  164 +-
 .../core/path/CustomRetryParams.scala         |    5 +-
 .../core/path/DefaultPathBuilder.scala        |    6 +-
 .../core/path/DefaultPathBuilderFactory.scala |    3 +-
 .../core/path/EvenBetterPathMethods.scala     |   58 +-
 .../core/path/JavaWriterImplicits.scala       |    1 +
 .../cromwell/core/path/NioPathMethods.scala   |    6 +-
 .../scala/cromwell/core/path/Obsolete.scala   |    6 +-
 .../cromwell/core/path/PathBuilder.scala      |    7 +-
 .../core/path/PathBuilderFactory.scala        |    9 +-
 .../scala/cromwell/core/path/PathCopier.scala |    9 +-
 .../cromwell/core/path/PathFactory.scala      |   28 +-
 .../core/path/PathObjectMethods.scala         |    3 +-
 .../scala/cromwell/core/path/PathWriter.scala |    3 +-
 .../cromwell/core/retry/GoogleBackoff.scala   |   52 +-
 .../scala/cromwell/core/retry/Retry.scala     |   23 +-
 .../core/simpleton/WomValueBuilder.scala      |  118 +-
 .../core/simpleton/WomValueSimpleton.scala    |   31 +-
 .../scala/cromwell/util/DatabaseUtil.scala    |    2 +-
 .../util/GracefulShutdownHelper.scala         |    7 +-
 .../WomValueJsonFormatter.scala               |    9 +-
 .../scala/cromwell/util/PromiseActor.scala    |   12 +-
 .../cromwell/util/StopAndLogSupervisor.scala  |    9 +-
 .../scala/cromwell/util/TryWithResource.scala |   16 +-
 .../cromwell/core/DockerCredentialsSpec.scala |    6 +-
 .../scala/cromwell/core/LoadConfigSpec.scala  |    2 +-
 .../scala/cromwell/core/MockIoActor.scala     |    7 +-
 .../scala/cromwell/core/SimpleIoActor.scala   |   36 +-
 .../scala/cromwell/core/TestKitSuite.scala    |    3 +-
 .../cromwell/core/WorkflowOptionsSpec.scala   |    6 +-
 .../cromwell/core/actor/BatchActorSpec.scala  |   17 +-
 .../core/actor/RobustClientHelperSpec.scala   |   63 +-
 .../core/actor/StreamActorHelperSpec.scala    |   25 +-
 .../core/callcaching/HashKeySpec.scala        |    5 +-
 .../filesystem/CromwellFileSystemsSpec.scala  |  108 +-
 .../scala/cromwell/core/io/AsyncIoSpec.scala  |   13 +-
 .../cromwell/core/io/IoClientHelperSpec.scala |   34 +-
 .../cromwell/core/labels/LabelSpec.scala      |    2 +-
 .../core/logging/LoggerWrapperSpec.scala      |   66 +-
 .../core/path/DefaultPathBuilderSpec.scala    |   80 +-
 .../core/path/PathBuilderFactorySpec.scala    |   30 +-
 .../core/path/PathBuilderSpecUtils.scala      |    6 +-
 .../cromwell/core/retry/BackoffSpec.scala     |   15 +-
 .../scala/cromwell/core/retry/RetrySpec.scala |   24 +-
 .../core/simpleton/WomValueBuilderSpec.scala  |  271 ++-
 .../scala/cromwell/util/AkkaTestUtil.scala    |    6 +-
 .../scala/cromwell/util/EncryptionSpec.scala  |    3 +-
 .../util/GracefulShutdownHelperSpec.scala     |   12 +-
 .../test/scala/cromwell/util/SampleWdl.scala  |  881 +++----
 .../scala/cromwell/util/TestFileUtil.scala    |    4 +-
 .../cromwell/util/TryWithResourceSpec.scala   |   18 +-
 .../test/scala/cromwell/util/WomMocks.scala   |   73 +-
 .../util/WomValueJsonFormatterSpec.scala      |    4 +-
 .../drs/localizer/CommandLineParser.scala     |   46 +-
 .../DrsLocalizerDrsPathResolver.scala         |    4 +-
 .../drs/localizer/DrsLocalizerMain.scala      |  153 +-
 .../downloaders/BulkAccessUrlDownloader.scala |   59 +-
 .../downloaders/DownloaderFactory.scala       |    5 +-
 .../downloaders/GcsUriDownloader.scala        |   47 +-
 .../localizer/downloaders/GetmChecksum.scala  |   13 +-
 .../drs/localizer/CommandLineParserSpec.scala |   68 +-
 .../drs/localizer/DrsLocalizerMainSpec.scala  |  302 ++-
 .../BulkAccessUrlDownloaderSpec.scala         |   54 +-
 .../downloaders/GetmChecksumSpec.scala        |   31 +-
 .../scala/cromwell/api/CromwellClient.scala   |  171 +-
 .../cromwell/api/model/CallCacheDiff.scala    |   12 +-
 .../api/model/CromwellQueryResult.scala       |    8 +-
 .../main/scala/cromwell/api/model/Label.scala |    2 +-
 .../scala/cromwell/api/model/TimeUtil.scala   |   10 +-
 .../cromwell/api/model/WaasDescription.scala  |    9 +-
 .../api/model/WorkflowDescribeRequest.scala   |    3 +-
 .../scala/cromwell/api/model/WorkflowId.scala |    1 -
 .../cromwell/api/model/WorkflowStatus.scala   |    3 +-
 .../api/model/WorkflowSubmission.scala        |    6 +-
 .../scala/cromwell/api/model/package.scala    |   17 +-
 .../cromwell/api/CromwellClientSpec.scala     |  168 +-
 .../api/CromwellResponseFailedSpec.scala      |   26 +-
 ...CromwellQueryResultJsonFormatterSpec.scala |   77 +-
 .../api/model/LabelsJsonFormatterSpec.scala   |   11 +-
 .../WaasDescriptionJsonSupportSpec.scala      |    8 +-
 .../migration/WdlTransformation.scala         |    9 +-
 .../migration/custom/BatchedTaskChange.scala  |   46 +-
 .../custom/MigrationTaskChange.scala          |    3 +-
 .../migration/custom/QueryPaginator.scala     |    7 +-
 .../DeduplicateFailureMessageIds.scala        |    6 +-
 .../liquibase/DiffResultFilter.scala          |   64 +-
 .../migration/liquibase/LiquibaseUtils.scala  |   42 +-
 .../metadata/MetadataCustomSql.scala          |    8 +-
 .../table/ExecutionTableMigration.scala       |   50 +-
 .../table/FailureEventTableMigration.scala    |   47 +-
 ...cutionEventTableDescriptionMigration.scala |    3 +-
 .../ExecutionEventTableEndMigration.scala     |   47 +-
 .../ExecutionEventTableStartMigration.scala   |   50 +-
 .../CallOutputSymbolTableMigration.scala      |   17 +-
 .../symbol/InputSymbolTableMigration.scala    |   15 +-
 .../table/symbol/MetadataStatement.scala      |   22 +-
 .../table/symbol/SymbolTableMigration.scala   |   35 +-
 .../WorkflowOutputSymbolTableMigration.scala  |    3 +-
 .../WorkflowExecutionTableMigration.scala     |  194 +-
 .../table/JobStoreSimpletonMigration.scala    |   11 +-
 .../RenameWorkflowOptionKeysMigration.scala   |    4 +-
 .../ClearMetadataEntryWorkflowOptions.scala   |    3 +-
 .../RenameWorkflowOptionsInMetadata.scala     |    6 +-
 .../WorkflowOptionsChange.scala               |    8 +-
 .../WorkflowOptionsRenaming.scala             |    3 +-
 .../slick/CallCachingSlickDatabase.scala      |  158 +-
 .../slick/DockerHashStoreSlickDatabase.scala  |   14 +-
 .../database/slick/EngineSlickDatabase.scala  |    2 +-
 .../slick/JobKeyValueSlickDatabase.scala      |   50 +-
 .../slick/JobStoreSlickDatabase.scala         |   26 +-
 .../slick/MetadataSlickDatabase.scala         |  435 ++--
 .../database/slick/SlickDatabase.scala        |   58 +-
 .../slick/SubWorkflowStoreSlickDatabase.scala |   45 +-
 .../slick/SummaryQueueSlickDatabase.scala     |    9 +-
 .../slick/SummaryStatusSlickDatabase.scala    |   13 +-
 .../slick/WorkflowStoreSlickDatabase.scala    |   73 +-
 ...CallCachingAggregationEntryComponent.scala |   79 +-
 .../CallCachingDetritusEntryComponent.scala   |   13 +-
 .../tables/CallCachingEntryComponent.scala    |   53 +-
 .../CallCachingHashEntryComponent.scala       |   12 +-
 .../CallCachingSimpletonEntryComponent.scala  |   12 +-
 .../tables/CustomLabelEntryComponent.scala    |   56 +-
 .../DockerHashStoreEntryComponent.scala       |   19 +-
 .../slick/tables/DriverComponent.scala        |    7 +-
 .../tables/EngineDataAccessComponent.scala    |   25 +-
 .../tables/JobKeyValueEntryComponent.scala    |   45 +-
 .../slick/tables/JobStoreEntryComponent.scala |   27 +-
 .../JobStoreSimpletonEntryComponent.scala     |    8 +-
 .../tables/MetadataDataAccessComponent.scala  |   22 +-
 .../slick/tables/MetadataEntryComponent.scala |  349 +--
 .../SubWorkflowStoreEntryComponent.scala      |   41 +-
 .../tables/SummaryStatusEntryComponent.scala  |    4 +-
 ...orkflowMetadataSummaryEntryComponent.scala |  251 +-
 .../tables/WorkflowStoreEntryComponent.scala  |  104 +-
 .../database/sql/CallCachingSqlDatabase.scala |   30 +-
 .../sql/DockerHashStoreSqlDatabase.scala      |    8 +-
 .../database/sql/EngineSqlDatabase.scala      |   15 +-
 .../database/sql/JobKeyValueSqlDatabase.scala |   20 +-
 .../database/sql/JobStoreSqlDatabase.scala    |    5 +-
 .../database/sql/MetadataSqlDatabase.scala    |  135 +-
 .../cromwell/database/sql/SqlDatabase.scala   |    1 +
 .../sql/SubWorkflowStoreSqlDatabase.scala     |    8 +-
 .../sql/WorkflowStoreSqlDatabase.scala        |   27 +-
 .../sql/joins/CallCachingDiffJoin.scala       |    5 +-
 .../database/sql/joins/CallCachingJoin.scala  |    3 +-
 .../database/sql/joins/JobStoreJoin.scala     |    3 +-
 .../tables/CallCachingAggregationEntry.scala  |    3 +-
 .../sql/tables/CallCachingDetritusEntry.scala |    3 +-
 .../sql/tables/CallCachingEntry.scala         |    3 +-
 .../sql/tables/CallCachingHashEntry.scala     |    3 +-
 .../tables/CallCachingSimpletonEntry.scala    |    3 +-
 .../sql/tables/CustomLabelEntry.scala         |    3 +-
 .../sql/tables/DockerHashStoreEntry.scala     |    3 +-
 .../sql/tables/InformationSchemaEntry.scala   |    3 +-
 .../sql/tables/JobKeyValueEntry.scala         |    3 +-
 .../database/sql/tables/JobStoreEntry.scala   |    3 +-
 .../sql/tables/JobStoreSimpletonEntry.scala   |    3 +-
 .../database/sql/tables/MetadataEntry.scala   |    3 +-
 .../sql/tables/SubWorkflowStoreEntry.scala    |    3 +-
 .../sql/tables/SummaryStatusEntry.scala       |    3 +-
 .../tables/WorkflowMetadataSummaryEntry.scala |    3 +-
 .../sql/tables/WorkflowStoreEntry.scala       |    3 +-
 .../cromwell/docker/DockerClientHelper.scala  |   11 +-
 .../cromwell/docker/DockerHashResult.scala    |    8 +-
 .../docker/DockerImageIdentifier.scala        |   32 +-
 .../cromwell/docker/DockerInfoActor.scala     |   72 +-
 .../cromwell/docker/DockerRegistry.scala      |    4 +-
 .../docker/DockerRegistryConfig.scala         |    6 +-
 .../docker/local/DockerCliClient.scala        |   21 +-
 .../cromwell/docker/local/DockerCliFlow.scala |   47 +-
 .../docker/registryv2/DockerManifest.scala    |    2 +-
 .../registryv2/DockerRegistryV2Abstract.scala |  135 +-
 .../flows/azure/AzureContainerRegistry.scala  |   37 +-
 .../flows/dockerhub/DockerHubRegistry.scala   |    8 +-
 .../flows/google/GoogleRegistry.scala         |   36 +-
 .../registryv2/flows/quay/QuayRegistry.scala  |    7 +-
 .../cromwell/docker/DockerHashMocks.scala     |   33 +-
 .../docker/DockerImageIdentifierSpec.scala    |   51 +-
 .../cromwell/docker/DockerInfoActorSpec.scala |   53 +-
 .../cromwell/docker/DockerRegistrySpec.scala  |    5 +-
 .../docker/local/DockerCliClientSpec.scala    |   15 +-
 .../cromwell/docker/local/DockerCliSpec.scala |   23 +-
 .../docker/local/DockerCliTimeoutSpec.scala   |   62 +-
 .../DockerRegistryV2AbstractSpec.scala        |   11 +-
 .../src/main/scala/cromwell/Simpletons.scala  |    6 +-
 .../cromwell/engine/EngineFilesystems.scala   |   11 +-
 .../cromwell/engine/EngineIoFunctions.scala   |   23 +-
 .../engine/EngineWorkflowDescriptor.scala     |    3 +-
 .../engine/backend/BackendConfiguration.scala |   25 +-
 .../engine/backend/CromwellBackends.scala     |   16 +-
 .../main/scala/cromwell/engine/engine.scala   |    4 +-
 .../instrumentation/HttpInstrumentation.scala |   34 +-
 .../instrumentation/IoInstrumentation.scala   |   35 +-
 .../instrumentation/JobInstrumentation.scala  |   14 +-
 .../WorkflowInstrumentation.scala             |   25 +-
 .../scala/cromwell/engine/io/IoActor.scala    |   80 +-
 .../cromwell/engine/io/IoActorProxy.scala     |    5 +-
 .../scala/cromwell/engine/io/IoAttempts.scala |   17 +-
 .../io/IoCommandStalenessBackpressuring.scala |    7 +-
 .../engine/io/RetryableRequestSupport.scala   |   25 +-
 .../io/gcs/GcsBatchCommandContext.scala       |   41 +-
 .../cromwell/engine/io/gcs/GcsBatchFlow.scala |   66 +-
 .../cromwell/engine/io/gcs/GcsResponse.scala  |    9 +-
 .../engine/io/gcs/ParallelGcsBatchFlow.scala  |    9 +-
 .../cromwell/engine/io/nio/NioFlow.scala      |   73 +-
 .../main/scala/cromwell/engine/package.scala  |    4 +-
 .../workflow/SingleWorkflowRunnerActor.scala  |  112 +-
 .../engine/workflow/WorkflowActor.scala       |  372 ++-
 .../workflow/WorkflowDockerLookupActor.scala  |  196 +-
 .../workflow/WorkflowManagerActor.scala       |   74 +-
 .../workflow/WorkflowMetadataHelper.scala     |   22 +-
 .../WorkflowProcessingEventPublishing.scala   |   14 +-
 .../engine/workflow/lifecycle/TimedFSM.scala  |    9 +-
 .../lifecycle/WorkflowLifecycleActor.scala    |   30 +-
 .../deletion/DeleteWorkflowFilesActor.scala   |  182 +-
 .../execution/CallMetadataHelper.scala        |   62 +-
 .../execution/SubWorkflowExecutionActor.scala |  231 +-
 .../execution/WorkflowExecutionActor.scala    |  403 ++--
 .../WorkflowExecutionActorData.scala          |  105 +-
 .../execution/callcaching/CallCache.scala     |  155 +-
 .../callcaching/CallCacheDiffActor.scala      |  158 +-
 .../CallCacheDiffActorJsonFormatting.scala    |   22 +-
 .../CallCacheDiffQueryParameter.scala         |   38 +-
 .../CallCacheHashingJobActor.scala            |  159 +-
 .../CallCacheInvalidateActor.scala            |   13 +-
 .../callcaching/CallCacheReadActor.scala      |   31 +-
 .../CallCacheReadingJobActor.scala            |   51 +-
 .../callcaching/CallCacheWriteActor.scala     |   20 +-
 .../callcaching/EngineJobHashingActor.scala   |   84 +-
 .../callcaching/FetchCachedResultsActor.scala |   34 +-
 .../execution/callcaching/package.scala       |    5 +-
 .../job/EngineJobExecutionActor.scala         |  522 ++--
 .../job/preparation/CallPreparation.scala     |    8 +-
 .../job/preparation/JobPreparationActor.scala |  210 +-
 .../job/preparation/KeyValueLookups.scala     |    8 +-
 .../SubWorkflowPreparationActor.scala         |   48 +-
 .../keys/ConditionalCollectorKey.scala        |    8 +-
 .../execution/keys/ConditionalKey.scala       |   20 +-
 .../execution/keys/ExpressionKey.scala        |   18 +-
 .../execution/keys/ScatterCollectorKey.scala  |   10 +-
 .../lifecycle/execution/keys/ScatterKey.scala |   41 +-
 .../keys/ScatterVariableInputKey.scala        |    2 +-
 .../keys/ScatteredCallCompletionKey.scala     |    6 +-
 .../execution/keys/SubWorkflowKey.scala       |    3 +-
 .../lifecycle/execution/keys/package.scala    |    9 +-
 .../execution/stores/ExecutionStore.scala     |   90 +-
 .../execution/stores/ValueStore.scala         |   29 +-
 .../finalization/CopyWorkflowLogsActor.scala  |   70 +-
 .../CopyWorkflowOutputsActor.scala            |  103 +-
 .../finalization/WorkflowCallbackActor.scala  |  116 +-
 .../WorkflowCallbackJsonSupport.scala         |    3 +-
 .../WorkflowFinalizationActor.scala           |  127 +-
 .../WorkflowInitializationActor.scala         |   84 +-
 .../MaterializeWorkflowDescriptorActor.scala  |  269 ++-
 .../workflow/tokens/DynamicRateLimiter.scala  |    3 +-
 .../tokens/JobTokenDispenserActor.scala       |   67 +-
 .../tokens/RoundRobinQueueIterator.scala      |    7 +-
 .../workflow/tokens/TokenEventLogger.scala    |   13 +-
 .../engine/workflow/tokens/TokenQueue.scala   |   23 +-
 .../workflow/tokens/UnhoggableTokenPool.scala |   49 +-
 .../AbortRequestScanningActor.scala           |   21 +-
 .../InMemorySubWorkflowStore.scala            |   23 +-
 .../workflowstore/InMemoryWorkflowStore.scala |   55 +-
 .../workflowstore/SqlWorkflowStore.scala      |  122 +-
 .../WorkflowHeartbeatConfig.scala             |   22 +-
 .../workflowstore/WorkflowStore.scala         |   14 +-
 .../workflowstore/WorkflowStoreAccess.scala   |   91 +-
 .../workflowstore/WorkflowStoreActor.scala    |   71 +-
 .../WorkflowStoreCoordinatedAccessActor.scala |   13 +-
 .../WorkflowStoreEngineActor.scala            |  153 +-
 .../WorkflowStoreHeartbeatWriteActor.scala    |  131 +-
 .../WorkflowStoreSubmitActor.scala            |  140 +-
 .../workflowstore/workflowstore_.scala        |    3 +-
 .../jobstore/JobResultJsonFormatter.scala     |    8 +-
 .../scala/cromwell/jobstore/JobStore.scala    |    8 +-
 .../cromwell/jobstore/JobStoreActor.scala     |   22 +-
 .../jobstore/JobStoreReaderActor.scala        |   10 +-
 .../jobstore/JobStoreWriterActor.scala        |   79 +-
 .../scala/cromwell/jobstore/SqlJobStore.scala |   55 +-
 .../scala/cromwell/jobstore/jobstore_.scala   |   17 +-
 .../scala/cromwell/jobstore/package.scala     |    3 +-
 .../cromwell/logging/TerminalLayout.scala     |   13 +-
 .../server/CromwellAkkaLogFilter.scala        |   16 +-
 .../server/CromwellDeadLetterListener.scala   |   11 +-
 .../cromwell/server/CromwellRootActor.scala   |  154 +-
 .../cromwell/server/CromwellServer.scala      |   33 +-
 .../cromwell/server/CromwellShutdown.scala    |  185 +-
 .../cromwell/server/CromwellSystem.scala      |   17 +-
 .../EmptySubWorkflowStoreActor.scala          |    2 +-
 .../SqlSubWorkflowStore.scala                 |   16 +-
 .../subworkflowstore/SubWorkflowStore.scala   |    8 +-
 .../SubWorkflowStoreActor.scala               |   36 +-
 .../cromwell/webservice/ApiDataModels.scala   |   15 +-
 .../webservice/EngineStatsActor.scala         |    9 +-
 .../webservice/LabelsManagerActor.scala       |   11 +-
 .../webservice/PartialWorkflowSources.scala   |  148 +-
 .../webservice/SwaggerUiHttpService.scala     |   27 +-
 .../cromwell/webservice/WebServiceUtils.scala |   47 +-
 .../webservice/WorkflowJsonSupport.scala      |   18 +-
 .../routes/CromwellApiService.scala           |  136 +-
 .../routes/MetadataRouteSupport.scala         |  150 +-
 .../routes/WomtoolRouteSupport.scala          |    7 +-
 .../routes/wes/CromwellMetadata.scala         |   25 +-
 .../routes/wes/RunListResponse.scala          |    6 +-
 .../webservice/routes/wes/ServiceInfo.scala   |   19 +-
 .../webservice/routes/wes/WesResponse.scala   |   27 +-
 .../routes/wes/WesRouteSupport.scala          |  125 +-
 .../webservice/routes/wes/WesRunLog.scala     |    5 +-
 .../webservice/routes/wes/WesState.scala      |   48 +-
 .../webservice/routes/wes/WesSubmission.scala |   34 +-
 .../cromwell/webservice/webservice_.scala     |    2 +-
 .../scala/cromwell/MetadataWatchActor.scala   |   34 +-
 .../engine/MockCromwellTerminator.scala       |    3 +-
 .../DefaultBackendJobExecutionActor.scala     |   36 +-
 .../RetryableBackendJobExecutionActor.scala   |   31 +-
 ...etryableBackendLifecycleActorFactory.scala |   14 +-
 .../engine/backend/mock/package.scala         |    3 +-
 .../engine/io/IoActorProxyGcsBatchSpec.scala  |   34 +-
 .../cromwell/engine/io/IoActorSpec.scala      |   80 +-
 .../io/gcs/GcsBatchCommandContextSpec.scala   |   23 +-
 .../engine/io/gcs/GcsBatchFlowSpec.scala      |   38 +-
 .../cromwell/engine/io/nio/NioFlowSpec.scala  |   51 +-
 .../WorkflowDockerLookupActorSpec.scala       |  110 +-
 .../ValidatingCachingConfigSpec.scala         |   38 +-
 .../ValidatingCallCachingModeSpec.scala       |   61 +-
 .../DeleteWorkflowFilesActorSpec.scala        |  521 ++--
 .../execution/ExecutionStoreBenchmark.scala   |   17 +-
 .../SubWorkflowExecutionActorSpec.scala       |  137 +-
 .../callcaching/CallCacheDiffActorSpec.scala  |  134 +-
 .../CallCacheHashingJobActorDataSpec.scala    |   79 +-
 .../CallCacheHashingJobActorSpec.scala        |  174 +-
 .../CallCacheReadingJobActorSpec.scala        |  111 +-
 .../CallCachingSlickDatabaseSpec.scala        |   45 +-
 .../EngineJobHashingActorSpec.scala           |  103 +-
 .../job/preparation/CallPreparationSpec.scala |    3 +-
 .../preparation/JobPreparationActorSpec.scala |  136 +-
 .../JobPreparationTestHelper.scala            |   87 +-
 .../execution/stores/ExecutionStoreSpec.scala |   19 +-
 .../CopyWorkflowLogsActorSpec.scala           |   41 +-
 .../WorkflowCallbackActorSpec.scala           |   39 +-
 .../workflow/mocks/DeclarationMock.scala      |    4 +-
 .../engine/workflow/mocks/TaskMock.scala      |    6 +-
 .../tokens/JobTokenDispenserActorSpec.scala   |  177 +-
 .../tokens/RoundRobinQueueIteratorSpec.scala  |    4 +-
 .../tokens/TestTokenGrabbingActor.scala       |    8 +-
 .../workflow/tokens/TokenQueueSpec.scala      |    2 +-
 .../tokens/UnhoggableTokenPoolSpec.scala      |   21 +-
 ...LargeScaleJobTokenDispenserActorSpec.scala |  230 +-
 .../large/MultipleTokenUsingActor.scala       |   13 +-
 .../large/PatientTokenNeedingActor.scala      |    4 +-
 .../large/TokenDispenserBenchmark.scala       |    5 +-
 .../workflowstore/SqlWorkflowStoreSpec.scala  |  206 +-
 .../WorkflowHeartbeatConfigSpec.scala         |   54 +-
 ...kflowStoreCoordinatedAccessActorSpec.scala |   70 +-
 ...WorkflowStoreHeartbeatWriteActorSpec.scala |   28 +-
 .../cromwell/jobstore/JobResultSpec.scala     |   11 +-
 .../webservice/EngineStatsActorSpec.scala     |    4 +-
 .../webservice/MetadataBuilderActorSpec.scala |  265 +-
 .../PartialWorkflowSourcesSpec.scala          |   19 +-
 .../webservice/SwaggerServiceSpec.scala       |   53 +-
 .../webservice/SwaggerUiHttpServiceSpec.scala |   37 +-
 .../webservice/WorkflowJsonSupportSpec.scala  |    3 +-
 .../routes/CromwellApiServiceSpec.scala       |  747 +++---
 .../routes/MetadataRouteSupportSpec.scala     |  138 +-
 .../routes/WomtoolRouteSupportSpec.scala      |   63 +-
 .../routes/wes/ServiceInfoSpec.scala          |    7 +-
 .../routes/wes/WesRouteSupportSpec.scala      |   70 +-
 .../blob/BlobFileSystemConfig.scala           |   17 +-
 .../blob/BlobFileSystemManager.scala          |  122 +-
 .../filesystems/blob/BlobPathBuilder.scala    |   54 +-
 .../blob/BlobPathBuilderFactory.scala         |   25 +-
 .../WorkspaceManagerApiClientProvider.scala   |   47 +-
 .../blob/AzureFileSystemSpec.scala            |   18 +-
 .../blob/BlobFileSystemConfigSpec.scala       |   31 +-
 .../blob/BlobPathBuilderFactorySpec.scala     |   35 +-
 .../blob/BlobPathBuilderSpec.scala            |   49 +-
 .../cromwell/filesystems/drs/DrsPath.scala    |   14 +-
 .../filesystems/drs/DrsPathBuilder.scala      |   16 +-
 .../drs/DrsPathBuilderFactory.scala           |   40 +-
 .../cromwell/filesystems/drs/DrsReader.scala  |   61 +-
 .../filesystems/drs/DrsResolver.scala         |   28 +-
 .../drs/DrsPathBuilderFactorySpec.scala       |    2 +-
 .../filesystems/drs/DrsPathBuilderSpec.scala  |   71 +-
 .../filesystems/drs/DrsReaderSpec.scala       |   32 +-
 .../filesystems/drs/DrsResolverSpec.scala     |   20 +-
 .../ftp/CromwellFtpFileSystems.scala          |   16 +-
 .../ftp/FtpInstanceConfiguration.scala        |    8 +-
 .../filesystems/ftp/FtpPathBuilder.scala      |    3 +-
 .../ftp/FtpPathBuilderFactory.scala           |   39 +-
 .../ftp/CromwellFtpFileSystemsSpec.scala      |   15 +-
 .../ftp/FtpInstanceConfigurationSpec.scala    |   24 +-
 .../filesystems/ftp/FtpPathSpec.scala         |   74 +-
 .../filesystems/gcs/GcsEnhancedRequest.scala  |   31 +-
 .../filesystems/gcs/GcsPathBuilder.scala      |   71 +-
 .../gcs/GcsPathBuilderFactory.scala           |   12 +-
 .../cromwell/filesystems/gcs/GoogleUtil.scala |   22 +-
 .../filesystems/gcs/RequesterPaysErrors.scala |    2 +-
 .../gcs/batch/GcsBatchCommandBuilder.scala    |   26 +-
 .../gcs/batch/GcsBatchIoCommand.scala         |  136 +-
 .../gcs/GcsEnhancedRequestSpec.scala          |   22 +-
 .../filesystems/gcs/GcsPathBuilderSpec.scala  |  102 +-
 .../filesystems/gcs/MockGcsPathBuilder.scala  |    5 +-
 .../gcs/batch/GcsBatchIoCommandSpec.scala     |    4 +-
 .../filesystems/http/HttpPathBuilder.scala    |   23 +-
 .../http/HttpPathBuilderFactory.scala         |    6 +-
 .../filesystems/s3/S3PathBuilder.scala        |   35 +-
 .../filesystems/s3/S3PathBuilderFactory.scala |   15 +-
 .../s3/batch/S3BatchCommandBuilder.scala      |   16 +-
 .../s3/batch/S3BatchIoCommand.scala           |   48 +-
 .../filesystems/s3/S3PathBuilderSpec.scala    |   50 +-
 .../filesystems/sra/SraPathBuilder.scala      |    4 +-
 .../sra/SraPathBuilderFactory.scala           |    6 +-
 .../filesystems/sra/SraPathBuilderSpec.scala  |   35 +-
 .../cromwell/languages/LanguageFactory.scala  |   25 +-
 .../languages/ValidatedWomNamespace.scala     |    3 +-
 .../languages/config/CromwellLanguages.scala  |   18 +-
 .../config/LanguageConfiguration.scala        |   15 +-
 .../languages/util/ImportResolver.scala       |   61 +-
 .../languages/util/LanguageFactoryUtil.scala  |   61 +-
 .../cromwell/languages/util/ParserCache.scala |   33 +-
 .../util/ResolvedExecutableInputsPoly.scala   |   11 +-
 .../languages/util/ImportResolverSpec.scala   |   42 +-
 .../biscayne/WdlBiscayneLanguageFactory.scala |   43 +-
 .../cascades/WdlCascadesLanguageFactory.scala |   43 +-
 .../wdl/draft2/WdlDraft2LanguageFactory.scala |   63 +-
 .../ArrayCoercionsSpec.scala                  |   22 +-
 .../MapWorkflowSpec.scala                     |   34 +-
 .../NamespaceCacheSpec.scala                  |   20 +-
 .../WdlWorkflowHttpImportSpec.scala           |   67 +-
 .../wdl/draft3/WdlDraft3LanguageFactory.scala |   64 +-
 .../wdl/draft3/WdlDraft3CachingSpec.scala     |   20 +-
 .../cromwell/consumer/DrsHubClient.scala      |   26 +-
 .../workbench/cromwell/consumer/Helper.scala  |   22 +-
 .../consumer/BlobFileSystemContractSpec.scala |   42 +-
 .../cromwell/consumer/DrsHubClientSpec.scala  |   88 +-
 perf/src/main/scala/cromwell/perf/Call.scala  |   41 +-
 .../scala/cromwell/perf/CompareMetadata.scala |   59 +-
 .../main/scala/cromwell/perf/Metadata.scala   |   68 +-
 project/ContinuousIntegration.scala           |   37 +-
 project/GenerateRestApiDocs.scala             |   24 +-
 project/Merging.scala                         |   28 +-
 project/Publishing.scala                      |   41 +-
 project/Testing.scala                         |   19 +-
 project/Version.scala                         |   14 +-
 .../scala/cromwell/CommandLineArguments.scala |   33 +-
 .../scala/cromwell/CommandLineParser.scala    |   80 +-
 .../src/main/scala/cromwell/CromwellApp.scala |    5 +-
 .../scala/cromwell/CromwellEntryPoint.scala   |  150 +-
 .../cromwell/CromwellCommandLineSpec.scala    |   46 +-
 .../scala/cromwell/CromwellTestKitSpec.scala  |  163 +-
 .../cromwell/DeclarationWorkflowSpec.scala    |   13 +-
 .../cromwell/FilePassingWorkflowSpec.scala    |    2 +-
 ...ultipleFilesWithSameNameWorkflowSpec.scala |    2 +-
 .../cromwell/OptionalParamWorkflowSpec.scala  |   36 +-
 .../scala/cromwell/ReferenceConfSpec.scala    |   11 +-
 .../cromwell/SimpleWorkflowActorSpec.scala    |   83 +-
 .../scala/cromwell/WorkflowFailSlowSpec.scala |    5 +-
 .../scala/cromwell/WorkflowOutputsSpec.scala  |    8 +-
 .../engine/WorkflowManagerActorSpec.scala     |   18 +-
 .../engine/WorkflowStoreActorSpec.scala       |  171 +-
 ...CoordinatedWorkflowStoreActorBuilder.scala |    6 +-
 .../workflow/SqlWorkflowStoreBuilder.scala    |    7 +-
 .../engine/workflow/WorkflowActorSpec.scala   |  209 +-
 .../WorkflowDescriptorBuilderForSpecs.scala   |   57 +-
 ...terializeWorkflowDescriptorActorSpec.scala |  375 ++-
 .../WorkflowExecutionActorSpec.scala          |   83 +-
 ...jeaBackendIsCopyingCachedOutputsSpec.scala |  351 +--
 .../EjeaCheckingCacheEntryExistenceSpec.scala |   14 +-
 .../ejea/EjeaCheckingCallCacheSpec.scala      |   46 +-
 .../ejea/EjeaCheckingJobStoreSpec.scala       |   30 +-
 ...etchingCachedOutputsFromDatabaseSpec.scala |   96 +-
 .../ejea/EjeaInvalidatingCacheEntrySpec.scala |   47 +-
 ...jeaMultipleCallCacheCopyAttemptsSpec.scala |   54 +-
 .../execution/ejea/EjeaPendingSpec.scala      |   17 +-
 .../execution/ejea/EjeaPreparingJobSpec.scala |   55 +-
 .../EjeaRequestingExecutionTokenSpec.scala    |   12 +-
 .../EjeaRequestingRestartCheckTokenSpec.scala |    7 +-
 .../execution/ejea/EjeaRunningJobSpec.scala   |   70 +-
 .../ejea/EjeaUpdatingCallCacheSpec.scala      |    8 +-
 .../ejea/EjeaUpdatingJobStoreSpec.scala       |   14 +-
 .../ejea/EjeaWaitingForValueStoreSpec.scala   |   10 +-
 .../ejea/EngineJobExecutionActorSpec.scala    |   43 +-
 .../EngineJobExecutionActorSpecUtil.scala     |   46 +-
 ...gineJobExecutionActorTransitionsSpec.scala |   44 +-
 .../lifecycle/execution/ejea/ExpectOne.scala  |   14 +-
 .../execution/ejea/PerTestHelper.scala        |  217 +-
 .../jobstore/JobStoreServiceSpec.scala        |   36 +-
 .../jobstore/JobStoreWriterSpec.scala         |   50 +-
 .../SubWorkflowStoreSpec.scala                |   38 +-
 .../services/EnhancedBatchActor.scala         |    2 +-
 .../services/EnhancedThrottlerActor.scala     |    8 +-
 .../cromwell/services/IoActorRequester.scala  |    5 +-
 .../services/ServiceRegistryActor.scala       |   76 +-
 .../ProtoHealthMonitorServiceActor.scala      |   49 +-
 .../impl/HealthMonitorServiceActor.scala      |    6 +-
 .../impl/common/DockerHubMonitor.scala        |   11 +-
 .../impl/common/EngineDatabaseMonitor.scala   |    5 +-
 .../WorkbenchHealthMonitorServiceActor.scala  |   89 +-
 ...ynchronousThrottlingGaugeMetricActor.scala |   13 +-
 .../CromwellInstrumentation.scala             |   47 +-
 .../instrumentation/CromwellMetric.scala      |    9 +-
 .../InstrumentedBatchActor.scala              |   12 +-
 .../NoopInstrumentationServiceActor.scala     |    7 +-
 ...ectiveTsvInstrumentationServiceActor.scala |   46 +-
 .../impl/stackdriver/StackdriverConfig.scala  |   51 +-
 ...ackdriverInstrumentationServiceActor.scala |   91 +-
 .../impl/statsd/CromwellStatsD.scala          |    5 +-
 .../impl/statsd/StatsDConfig.scala            |   24 +-
 .../StatsDInstrumentationServiceActor.scala   |   25 +-
 .../services/keyvalue/KeyValueReadActor.scala |   13 +-
 .../keyvalue/KeyValueServiceActor.scala       |    4 +-
 .../keyvalue/KeyValueWriteActor.scala         |   30 +-
 .../cromwell/services/keyvalue/KvClient.scala |   17 +-
 .../impl/BackendKeyValueDatabaseAccess.scala  |   44 +-
 .../keyvalue/impl/SqlKeyValueReadActor.scala  |    6 +-
 .../impl/SqlKeyValueServiceActor.scala        |   11 +-
 .../keyvalue/impl/SqlKeyValueWriteActor.scala |   22 +-
 .../LoadControlledBatchActor.scala            |   18 +-
 .../impl/LoadControllerServiceActor.scala     |   39 +-
 .../metadata/MetadataArchiveStatus.scala      |   12 +-
 .../metadata/MetadataJsonSupport.scala        |   12 +-
 .../services/metadata/MetadataQuery.scala     |   58 +-
 .../services/metadata/MetadataService.scala   |  127 +-
 .../services/metadata/WorkflowQueryKey.scala  |   40 +-
 .../metadata/WorkflowQueryParameters.scala    |  122 +-
 .../impl/MetadataDatabaseAccess.scala         |  281 ++-
 .../metadata/impl/MetadataServiceActor.scala  |  136 +-
 .../impl/MetadataStatisticsRecorder.scala     |   84 +-
 .../impl/MetadataSummaryRefreshActor.scala    |   64 +-
 .../ReadDatabaseMetadataWorkerActor.scala     |  118 +-
 .../impl/ReadMetadataRegulatorActor.scala     |   52 +-
 .../metadata/impl/WriteMetadataActor.scala    |   38 +-
 .../impl/archiver/ArchiveMetadataConfig.scala |   34 +-
 .../ArchiveMetadataSchedulerActor.scala       |  194 +-
 .../impl/builder/MetadataBuilderActor.scala   |  232 +-
 .../impl/builder/MetadataComponent.scala      |   52 +-
 .../impl/deleter/DeleteMetadataActor.scala    |   83 +-
 .../impl/deleter/DeleteMetadataConfig.scala   |   12 +-
 .../HybridPubSubMetadataServiceActor.scala    |   11 +-
 .../pubsub/PubSubMetadataServiceActor.scala   |   34 +-
 .../cromwell/services/metadata/metadata.scala |    2 +-
 .../cromwell/services/metadata/package.scala  |   18 +-
 .../cromwell/services/womtool/Describer.scala |   17 +-
 .../impl/WomtoolServiceInCromwellActor.scala  |    8 +-
 .../womtool/models/InputDescription.scala     |    9 +-
 .../models/MetaValueElementJsonSupport.scala  |    9 +-
 .../womtool/models/OutputDescription.scala    |    2 +-
 .../womtool/models/WomTypeJsonSupport.scala   |   37 +-
 .../womtool/models/WorkflowDescription.scala  |  123 +-
 .../services/IoActorRequesterSpec.scala       |   23 +-
 .../cromwell/services/NooPServiceActor.scala  |    4 +-
 .../services/ServiceRegistryActorSpec.scala   |   67 +-
 .../cromwell/services/ServicesSpec.scala      |    3 +-
 .../database/ConnectionMetadata.scala         |    5 +-
 .../database/CromwellDatabaseType.scala       |    8 +-
 .../services/database/DatabaseSystem.scala    |    2 +-
 .../services/database/DatabaseTestKit.scala   |  142 +-
 .../HsqldbTransactionIsolationSpec.scala      |   11 +-
 .../database/LiquibaseChangeSetSpec.scala     |    4 +-
 .../database/LiquibaseComparisonSpec.scala    |  132 +-
 .../services/database/LiquibaseOrdering.scala |    3 +-
 .../cromwell/services/database/LobSpec.scala  |   16 +-
 .../database/MetadataSlickDatabaseSpec.scala  | 1215 ++++++++--
 .../services/database/QueryTimeoutSpec.scala  |   86 +-
 .../RootAndSubworkflowLabelsSpec.scala        |   48 +-
 .../services/database/SchemaManager.scala     |    2 +-
 .../services/database/SchemaManagerSpec.scala |   86 +-
 .../database/SlickDeadlocksSpec.scala         |   14 +-
 .../services/database/TestSlickDatabase.scala |    5 +-
 .../HealthMonitorServiceActorSpec.scala       |   20 +-
 .../ProtoHealthMonitorServiceActorSpec.scala  |   27 +-
 ...ronousThrottlingGaugeMetricActorSpec.scala |   49 +-
 .../stackdriver/StackdriverConfigSpec.scala   |    4 -
 ...riverInstrumentationServiceActorSpec.scala |   38 +-
 ...ackdriverInstrumentationServiceActor.scala |   17 +-
 .../impl/statsd/StatsDConfigSpec.scala        |    2 +-
 ...rumentationServiceActorBenchmarkSpec.scala |   21 +-
 ...tatsDInstrumentationServiceActorSpec.scala |  100 +-
 .../keyvalue/InMemoryKvServiceActor.scala     |    3 +-
 .../services/keyvalue/KvClientSpec.scala      |    2 -
 .../keyvalue/impl/KeyValueDatabaseSpec.scala  |   20 +-
 .../impl/KeyValueServiceActorSpec.scala       |   40 +-
 .../impl/LoadControllerServiceActorSpec.scala |    9 +-
 .../services/metadata/MetadataQuerySpec.scala |   42 +-
 .../metadata/MetadataServiceSpec.scala        |   54 +-
 .../MetadataStatisticsRecorderSpec.scala      |   94 +-
 ...ryForWorkflowsMatchingParametersSpec.scala |   12 +-
 .../impl/MetadataDatabaseAccessSpec.scala     |  442 ++--
 .../impl/MetadataServiceActorSpec.scala       |  175 +-
 .../impl/WriteMetadataActorBenchmark.scala    |   19 +-
 .../impl/WriteMetadataActorSpec.scala         |  291 ++-
 .../PubSubMetadataServiceActorSpec.scala      |   56 +-
 .../services/womtool/DescriberSpec.scala      |    6 +-
 .../WomtoolServiceInCromwellActorSpec.scala   |  111 +-
 ...wsBatchAsyncBackendJobExecutionActor.scala |  221 +-
 .../backend/impl/aws/AwsBatchAttributes.scala |   54 +-
 .../AwsBatchBackendInitializationData.scala   |   23 +-
 ...AwsBatchBackendLifecycleActorFactory.scala |   76 +-
 .../impl/aws/AwsBatchConfiguration.scala      |   17 +-
 .../aws/AwsBatchExpressionFunctions.scala     |   10 +-
 .../impl/aws/AwsBatchFinalizationActor.scala  |   12 +-
 .../aws/AwsBatchInitializationActor.scala     |   41 +-
 .../backend/impl/aws/AwsBatchJob.scala        |  530 ++--
 .../aws/AwsBatchJobCachingActorHelper.scala   |   19 +-
 .../impl/aws/AwsBatchJobDefinition.scala      |  152 +-
 .../backend/impl/aws/AwsBatchJobPaths.scala   |    5 +-
 .../impl/aws/AwsBatchMetadataKeys.scala       |    1 -
 .../backend/impl/aws/AwsBatchParameters.scala |    8 +-
 .../impl/aws/AwsBatchRuntimeAttributes.scala  |  205 +-
 .../impl/aws/AwsBatchSingletonActor.scala     |   18 +-
 .../impl/aws/AwsBatchWorkflowPaths.scala      |   21 +-
 .../IntervalLimitedAwsJobSubmitActor.scala    |   42 +-
 .../aws/OccasionalStatusPollingActor.scala    |   39 +-
 .../cromwell/backend/impl/aws/RunStatus.scala |   33 +-
 .../AwsBatchBackendCacheHitCopyingActor.scala |   67 +-
 .../AwsBatchBackendFileHashingActor.scala     |   14 +-
 .../AwsBatchCacheHitDuplicationStrategy.scala |    2 +-
 .../aws/errors/AwsBatchKnownJobFailure.scala  |    6 +-
 .../backend/impl/aws/io/AwsBatchVolume.scala  |   24 +-
 .../cromwell/backend/impl/aws/package.scala   |   11 +-
 ...tchAsyncBackendJobExecutionActorSpec.scala |  588 +++--
 .../impl/aws/AwsBatchAttachedDiskSpec.scala   |    7 +-
 .../impl/aws/AwsBatchAttributesSpec.scala     |   37 +-
 .../impl/aws/AwsBatchConfigurationSpec.scala  |   68 +-
 .../aws/AwsBatchInitializationActorSpec.scala |  138 +-
 .../aws/AwsBatchJobExecutionActorSpec.scala   |   68 +-
 .../backend/impl/aws/AwsBatchJobSpec.scala    |   83 +-
 .../aws/AwsBatchRuntimeAttributesSpec.scala   |  255 +-
 .../backend/impl/aws/AwsBatchTestConfig.scala |   14 +-
 ...GcpBatchBackendLifecycleActorFactory.scala |  112 +-
 .../batch/actors/BatchApiAbortClient.scala    |    3 +-
 .../batch/actors/BatchApiFetchJobClient.scala |    3 +-
 .../actors/BatchApiRunCreationClient.scala    |    3 +-
 ...cpBatchAsyncBackendJobExecutionActor.scala |  657 +++--
 .../GcpBatchBackendSingletonActor.scala       |   20 +-
 .../actors/GcpBatchFinalizationActor.scala    |   11 +-
 .../actors/GcpBatchInitializationActor.scala  |  124 +-
 .../GcpBatchJobCachingActorHelper.scala       |   35 +-
 .../batch/api/GcpBatchApiRequestHandler.scala |    7 +-
 .../batch/api/GcpBatchRequestFactory.scala    |   31 +-
 .../api/GcpBatchRequestFactoryImpl.scala      |  175 +-
 .../GcpBatchVMAuthentication.scala            |   19 +-
 .../BatchBackendCacheHitCopyingActor.scala    |   44 +-
 .../BatchBackendFileHashingActor.scala        |    3 +-
 .../BatchCacheHitDuplicationStrategy.scala    |    1 -
 ...validGcsPathsInManifestFileException.scala |    5 +-
 .../batch/io/GcpBatchAttachedDisk.scala       |   33 +-
 .../backend/google/batch/io/package.scala     |   13 +-
 .../models/CreateGcpBatchParameters.scala     |    2 +-
 .../models/GcpBackendInitializationData.scala |   17 +-
 .../batch/models/GcpBatchConfiguration.scala  |   14 +-
 .../GcpBatchConfigurationAttributes.scala     |  326 +--
 .../models/GcpBatchCustomMachineType.scala    |   35 +-
 .../batch/models/GcpBatchJobPaths.scala       |   14 +-
 .../batch/models/GcpBatchParameters.scala     |   43 +-
 .../google/batch/models/GcpBatchRequest.scala |    3 +-
 .../models/GcpBatchRuntimeAttributes.scala    |  257 +-
 .../batch/models/GcpBatchWorkflowPaths.scala  |   43 +-
 .../google/batch/models/GcpLabel.scala        |   49 +-
 .../batch/models/PreviousRetryReasons.scala   |    8 +-
 .../backend/google/batch/models/Run.scala     |    2 +-
 .../google/batch/models/RunStatus.scala       |  101 +-
 .../VpcAndSubnetworkProjectLabelValues.scala  |    4 +-
 .../CheckpointingConfiguration.scala          |   17 +-
 .../backend/google/batch/monitoring/Env.scala |    6 +-
 .../batch/monitoring/MonitoringImage.scala    |   29 +-
 .../runnable/CheckpointingRunnable.scala      |   86 +-
 .../batch/runnable/Delocalization.scala       |   53 +-
 .../google/batch/runnable/Localization.scala  |   64 +-
 .../runnable/MemoryRetryCheckRunnable.scala   |    3 +-
 .../batch/runnable/MonitoringRunnable.scala   |   15 +-
 .../batch/runnable/RunnableBuilder.scala      |  131 +-
 .../batch/runnable/RunnableCommands.scala     |   42 +-
 .../batch/runnable/RunnableLabels.scala       |    1 +
 .../google/batch/runnable/RunnableUtils.scala |   32 +-
 .../google/batch/runnable/UserRunnable.scala  |    1 -
 .../batch/util/BatchExpressionFunctions.scala |   11 +-
 .../util/BatchParameterConversions.scala      |   71 +-
 .../batch/util/BatchUtilityConversions.scala  |   34 +-
 ...GcpBatchDockerCacheMappingOperations.scala |   42 +-
 .../util/GcpBatchExpressionFunctions.scala    |   11 +-
 .../util/GcpBatchMachineConstraints.scala     |   16 +-
 ...BatchReferenceFilesMappingOperations.scala |   67 +-
 .../google/batch/util/GpuTypeValidation.scala |    6 +-
 .../google/batch/util/GpuValidation.scala     |    8 +-
 .../backend/google/batch/GcpBatchIoSpec.scala |   10 +-
 ...tchAsyncBackendJobExecutionActorSpec.scala |  448 ++--
 ...atchBackendLifecycleActorFactorySpec.scala |    9 +-
 .../GcpBatchInitializationActorSpec.scala     |  136 +-
 .../batch/io/GcpBatchAttachedDiskSpec.scala   |    2 +-
 .../batch/models/GcpBatchAttributeSpec.scala  |   37 +-
 .../GcpBatchConfigurationAttributesSpec.scala |  122 +-
 .../models/GcpBatchConfigurationSpec.scala    |   58 +-
 .../batch/models/GcpBatchJobPathsSpec.scala   |   27 +-
 .../GcpBatchRuntimeAttributesSpec.scala       |  101 +-
 .../batch/models/GcpBatchTestConfig.scala     |    8 +-
 ...cAndSubnetworkProjectLabelValuesSpec.scala |    6 +-
 .../batch/runnable/LocalizationSpec.scala     |   31 +-
 .../batch/runnable/RunnableBuilderSpec.scala  |   67 +-
 .../batch/runnable/RunnableCommandSpec.scala  |   38 +-
 .../util/GcpBatchMachineConstraintsSpec.scala |    6 +-
 .../pipelines/common/CustomMachineType.scala  |   35 +-
 .../pipelines/common/GoogleCloudScopes.scala  |    1 +
 .../pipelines/common/GoogleLabels.scala       |   49 +-
 .../pipelines/common/GpuTypeValidation.scala  |    3 +-
 .../pipelines/common/GpuValidation.scala      |    6 +-
 .../pipelines/common/MachineConstraints.scala |    7 +-
 .../common/PapiInstrumentation.scala          |   21 +-
 ...inesApiAsyncBackendJobExecutionActor.scala |  511 ++--
 ...ipelinesApiBackendInitializationData.scala |    3 +-
 ...linesApiBackendLifecycleActorFactory.scala |  117 +-
 .../PipelinesApiBackendSingletonActor.scala   |   19 +-
 .../common/PipelinesApiConfiguration.scala    |   11 +-
 .../PipelinesApiConfigurationAttributes.scala |  352 +--
 ...linesApiDockerCacheMappingOperations.scala |   40 +-
 .../PipelinesApiExpressionFunctions.scala     |   11 +-
 .../PipelinesApiFinalizationActor.scala       |    6 +-
 .../PipelinesApiInitializationActor.scala     |  123 +-
 .../PipelinesApiJobCachingActorHelper.scala   |   35 +-
 .../common/PipelinesApiJobPaths.scala         |   15 +-
 .../common/PipelinesApiParameters.scala       |   12 +-
 ...esApiReferenceFilesMappingOperations.scala |   74 +-
 .../PipelinesApiRuntimeAttributes.scala       |  232 +-
 .../common/PipelinesApiWorkflowPaths.scala    |   54 +-
 .../common/PreviousRetryReasons.scala         |   13 +-
 .../VpcAndSubnetworkProjectLabelValues.scala  |    4 +-
 .../common/action/ActionCommands.scala        |   42 +-
 .../common/action/ActionLabels.scala          |    1 +
 .../pipelines/common/action/ActionUtils.scala |   14 +-
 .../common/api/PipelinesApiBatchHandler.scala |    5 +-
 .../api/PipelinesApiFactoryInterface.scala    |    2 +-
 .../api/PipelinesApiRequestFactory.scala      |   31 +-
 .../api/PipelinesApiRequestHandler.scala      |   17 +-
 .../api/PipelinesApiRequestManager.scala      |  186 +-
 .../api/PipelinesApiRequestWorker.scala       |   45 +-
 .../pipelines/common/api/RunStatus.scala      |   51 +-
 .../api/clients/PipelinesApiAbortClient.scala |   13 +-
 .../PipelinesApiRunCreationClient.scala       |   22 +-
 .../PipelinesApiStatusRequestClient.scala     |    9 +-
 .../PipelinesApiVMAuthentication.scala        |   20 +-
 ...elinesApiBackendCacheHitCopyingActor.scala |   94 +-
 .../PipelinesApiBackendFileHashingActor.scala |    3 +-
 ...validGcsPathsInManifestFileException.scala |    3 +-
 .../errors/PipelinesApiKnownJobFailure.scala  |    2 +-
 .../common/io/PipelinesApiAttachedDisk.scala  |   40 +-
 .../google/pipelines/common/io/package.scala  |   10 +-
 .../CheckpointingConfiguration.scala          |   17 +-
 .../pipelines/common/monitoring/Env.scala     |    6 +-
 .../common/monitoring/MonitoringImage.scala   |   29 +-
 .../google/pipelines/common/IoSpec.scala      |   10 +-
 .../common/MachineConstraintsSpec.scala       |   10 +-
 ...ApiAsyncBackendJobExecutionActorSpec.scala | 1160 ++++++---
 .../common/PipelinesApiAttachedDiskSpec.scala |    9 +-
 ...sApiBackendLifecycleActorFactorySpec.scala |   15 +-
 .../common/PipelinesApiCallPathsSpec.scala    |   27 +-
 ...elinesApiConfigurationAttributesSpec.scala |  166 +-
 .../PipelinesApiConfigurationSpec.scala       |   67 +-
 ...sApiDockerCacheMappingOperationsSpec.scala |   53 +-
 .../PipelinesApiGpuAttributesSpec.scala       |   35 +-
 .../PipelinesApiInitializationActorSpec.scala |  171 +-
 .../PipelinesApiJobExecutionActorSpec.scala   |   69 +-
 ...iReferenceFilesMappingOperationsSpec.scala |   44 +-
 .../PipelinesApiRuntimeAttributesSpec.scala   |  160 +-
 .../common/PipelinesApiTestConfig.scala       |   19 +-
 .../PipelinesApiWorkflowPathsSpec.scala       |    9 +-
 ...cAndSubnetworkProjectLabelValuesSpec.scala |    6 +-
 .../api/PipelinesApiRequestManagerSpec.scala  |   83 +-
 .../api/PipelinesApiRequestWorkerSpec.scala   |   90 +-
 ...esApiBackendCacheHitCopyingActorSpec.scala |   89 +-
 .../pipelines/v2alpha1/GenomicsFactory.scala  |   77 +-
 ...inesApiAsyncBackendJobExecutionActor.scala |  315 ++-
 .../PipelinesApiLifecycleActorFactory.scala   |   12 +-
 .../PipelinesParameterConversions.scala       |   85 +-
 .../PipelinesUtilityConversions.scala         |    9 +-
 .../v2alpha1/api/ActionBuilder.scala          |   75 +-
 .../v2alpha1/api/CheckpointingAction.scala    |   33 +-
 .../v2alpha1/api/Delocalization.scala         |   90 +-
 .../v2alpha1/api/Deserialization.scala        |   45 +-
 .../pipelines/v2alpha1/api/Localization.scala |   52 +-
 .../v2alpha1/api/MemoryRetryCheckAction.scala |    5 +-
 .../v2alpha1/api/MonitoringAction.scala       |   16 +-
 .../v2alpha1/api/SSHAccessAction.scala        |    6 +-
 .../api/request/AbortRequestHandler.scala     |   41 +-
 .../v2alpha1/api/request/ErrorReporter.scala  |   69 +-
 .../api/request/GetRequestHandler.scala       |   61 +-
 .../v2alpha1/api/request/RequestHandler.scala |   23 +-
 .../api/request/RunRequestHandler.scala       |   19 +-
 ...ApiAsyncBackendJobExecutionActorSpec.scala |   11 +-
 .../v2alpha1/PipelinesConversionsSpec.scala   |   17 +-
 .../v2alpha1/api/ActionBuilderSpec.scala      |   52 +-
 .../v2alpha1/api/ActionCommandsSpec.scala     |   36 +-
 .../v2alpha1/api/DeserializationSpec.scala    |   30 +-
 .../api/request/GetRequestHandlerSpec.scala   |  494 ++--
 .../v2beta/LifeSciencesFactory.scala          |   78 +-
 ...inesApiAsyncBackendJobExecutionActor.scala |  325 ++-
 .../PipelinesApiLifecycleActorFactory.scala   |   12 +-
 .../PipelinesParameterConversions.scala       |   87 +-
 .../v2beta/PipelinesUtilityConversions.scala  |   17 +-
 .../pipelines/v2beta/api/ActionBuilder.scala  |   77 +-
 .../v2beta/api/CheckpointingAction.scala      |   36 +-
 .../pipelines/v2beta/api/Delocalization.scala |   88 +-
 .../v2beta/api/Deserialization.scala          |   31 +-
 .../pipelines/v2beta/api/Localization.scala   |   70 +-
 .../v2beta/api/MemoryRetryCheckAction.scala   |    5 +-
 .../v2beta/api/MonitoringAction.scala         |   16 +-
 .../v2beta/api/SSHAccessAction.scala          |    6 +-
 .../api/request/AbortRequestHandler.scala     |   41 +-
 .../v2beta/api/request/ErrorReporter.scala    |   72 +-
 .../api/request/GetRequestHandler.scala       |   63 +-
 .../v2beta/api/request/RequestHandler.scala   |   23 +-
 .../api/request/RunRequestHandler.scala       |   19 +-
 ...ApiAsyncBackendJobExecutionActorSpec.scala |   27 +-
 .../v2beta/api/ActionBuilderSpec.scala        |   53 +-
 .../v2beta/api/ActionCommandsSpec.scala       |   36 +-
 .../v2beta/api/DeserializationSpec.scala      |   33 +-
 .../v2beta/api/LocalizationSpec.scala         |   12 +-
 .../api/request/GetRequestHandlerSpec.scala   | 1229 +++++-----
 .../config/ConfigAsyncJobExecutionActor.scala |   79 +-
 .../sfs/config/ConfigBackendFileHashing.scala |    6 +-
 .../ConfigBackendFileHashingActor.scala       |   14 +-
 .../ConfigBackendLifecycleActorFactory.scala  |   16 +-
 .../sfs/config/ConfigHashingStrategy.scala    |   82 +-
 .../config/ConfigInitializationActor.scala    |   31 +-
 .../impl/sfs/config/ConfigWdlNamespace.scala  |   28 +-
 .../sfs/config/CpuDeclarationValidation.scala |    8 +-
 .../sfs/config/DeclarationValidation.scala    |   56 +-
 .../config/MemoryDeclarationValidation.scala  |   20 +-
 .../BackgroundAsyncJobExecutionActor.scala    |   44 +-
 .../backend/sfs/SharedFileSystem.scala        |  130 +-
 ...aredFileSystemAsyncJobExecutionActor.scala |   76 +-
 ...leSystemBackendLifecycleActorFactory.scala |    3 +-
 ...SharedFileSystemCacheHitCopyingActor.scala |   27 +-
 .../SharedFileSystemExpressionFunctions.scala |   30 +-
 .../SharedFileSystemInitializationActor.scala |   14 +-
 ...haredFileSystemJobCachingActorHelper.scala |    8 +-
 .../ConfigAsyncJobExecutionActorSpec.scala    |   10 +-
 .../config/ConfigHashingStrategySpec.scala    |   28 +-
 .../ConfigInitializationActorSpec.scala       |   44 +-
 .../MemoryDeclarationValidationSpec.scala     |   62 +-
 ...redFileSystemInitializationActorSpec.scala |   46 +-
 ...haredFileSystemJobExecutionActorSpec.scala |  242 +-
 .../backend/sfs/SharedFileSystemSpec.scala    |   32 +-
 .../sfs/TestLocalAsyncJobExecutionActor.scala |   35 +-
 .../config/DeclarationValidationSpec.scala    |   21 +-
 .../config/HttpFilesystemEnablementSpec.scala |   15 +-
 .../TesAsyncBackendJobExecutionActor.scala    |  198 +-
 .../tes/TesBackendInitializationData.scala    |    3 +-
 .../tes/TesBackendLifecycleActorFactory.scala |   11 +-
 .../backend/impl/tes/TesConfiguration.scala   |   12 +-
 .../impl/tes/TesExpressionFunctions.scala     |    6 +-
 .../impl/tes/TesInitializationActor.scala     |   22 +-
 .../impl/tes/TesJobCachingActorHelper.scala   |   10 +-
 .../backend/impl/tes/TesJobPaths.scala        |   20 +-
 .../impl/tes/TesRuntimeAttributes.scala       |  127 +-
 .../cromwell/backend/impl/tes/TesTask.scala   |  179 +-
 .../backend/impl/tes/TesWorkflowPaths.scala   |   12 +-
 ...TesAsyncBackendJobExecutionActorSpec.scala |   92 +-
 .../impl/tes/TesConfigurationSpec.scala       |   14 +-
 .../impl/tes/TesInitializationActorSpec.scala |   75 +-
 .../impl/tes/TesRuntimeAttributesSpec.scala   |  111 +-
 .../backend/impl/tes/TesTaskSpec.scala        |  145 +-
 .../backend/impl/tes/TesTestConfig.scala      |    1 -
 .../impl/tes/TesWorkflowPathsSpec.scala       |    4 +-
 .../backend/impl/tes/TestWorkflows.scala      |  115 +-
 .../scala/wdl/draft2/model/AstTools.scala     |  275 ++-
 .../scala/wdl/draft2/model/Declaration.scala  |   72 +-
 .../src/main/scala/wdl/draft2/model/If.scala  |    7 +-
 .../main/scala/wdl/draft2/model/Scatter.scala |    4 +-
 .../main/scala/wdl/draft2/model/Scope.scala   |  156 +-
 .../scala/wdl/draft2/model/TaskOutput.scala   |   15 +-
 .../main/scala/wdl/draft2/model/WdlCall.scala |   59 +-
 .../wdl/draft2/model/WdlExpression.scala      |  124 +-
 .../scala/wdl/draft2/model/WdlGraphNode.scala |   32 +-
 .../scala/wdl/draft2/model/WdlNamespace.scala |  394 +--
 .../draft2/model/WdlRuntimeAttributes.scala   |    3 +-
 .../model/WdlSyntaxErrorFormatter.scala       |  283 +--
 .../main/scala/wdl/draft2/model/WdlTask.scala |   32 +-
 .../scala/wdl/draft2/model/WdlWorkflow.scala  |   56 +-
 .../wdl/draft2/model/WorkflowOutput.scala     |    7 +-
 .../draft2/model/WorkflowOutputWildcard.scala |    3 +-
 .../wdl/draft2/model/WorkflowScoped.scala     |   10 +-
 .../model/command/ParameterCommandPart.scala  |   36 +-
 .../model/command/StringCommandPart.scala     |    7 +-
 .../draft2/model/command/WdlCommandPart.scala |   16 +-
 .../scala/wdl/draft2/model/examples/ex1.scala |   16 +-
 .../scala/wdl/draft2/model/examples/ex2.scala |   22 +-
 .../scala/wdl/draft2/model/examples/ex3.scala |   22 +-
 .../scala/wdl/draft2/model/examples/ex4.scala |   14 +-
 .../scala/wdl/draft2/model/examples/ex5.scala |   28 +-
 .../scala/wdl/draft2/model/examples/ex6.scala |   13 +-
 .../scala/wdl/draft2/model/examples/ex7.scala |   27 +-
 .../scala/wdl/draft2/model/examples/ex8.scala |    2 +-
 .../model/exception/LookupException.scala     |   20 +-
 .../exception/UnsatisfiedInputException.scala |    2 +-
 .../model/exception/ValidationException.scala |    2 +-
 .../draft2/model/expression/Evaluator.scala   |    1 -
 .../model/expression/FileEvaluator.scala      |   61 +-
 .../model/expression/TypeEvaluator.scala      |   71 +-
 .../model/expression/ValueEvaluator.scala     |  167 +-
 .../model/expression/WdlFunctions.scala       |   10 +-
 .../WdlStandardLibraryFunctions.scala         |  410 +++-
 .../model/formatter/SyntaxFormatter.scala     |  105 +-
 .../main/scala/wdl/draft2/model/package.scala |    3 +-
 .../types/WdlCallOutputsObjectType.scala      |    4 +-
 .../model/types/WdlFlavoredWomType.scala      |   16 +-
 .../draft2/model/types/WdlNamespaceType.scala |    4 +-
 .../draft2/src/test/scala/wdl/AstSpec.scala   |   10 +-
 .../src/test/scala/wdl/DeclarationSpec.scala  |   78 +-
 .../src/test/scala/wdl/NamespaceSpec.scala    |    5 +-
 .../wdl/ParameterWdlCommandPartSpec.scala     |   48 +-
 .../test/scala/wdl/RuntimeAttributeSpec.scala |   18 +-
 .../scala/wdl/SameNameParametersSpec.scala    |   21 +-
 .../draft2/src/test/scala/wdl/SampleWdl.scala |  367 ++-
 .../draft2/src/test/scala/wdl/ScopeSpec.scala |    6 +-
 .../src/test/scala/wdl/SyntaxErrorSpec.scala  |  140 +-
 .../test/scala/wdl/SyntaxHighlightSpec.scala  |  378 +--
 .../draft2/src/test/scala/wdl/TaskSpec.scala  |   66 +-
 .../src/test/scala/wdl/TestFileUtil.scala     |    3 +-
 .../wdl/ThreeStepImportNamespaceSpec.scala    |   90 +-
 .../test/scala/wdl/ThreeStepImportSpec.scala  |   88 +-
 .../src/test/scala/wdl/WdlCallSpec.scala      |  276 ++-
 .../draft2/src/test/scala/wdl/WdlTest.scala   |   13 +-
 .../src/test/scala/wdl/WdlWiringSpec.scala    |  109 +-
 .../scala/wdl/WdlWorkflowImportsSpec.scala    |  208 +-
 .../src/test/scala/wdl/WdlWorkflowSpec.scala  |  231 +-
 .../wdl/expression/DNAxTypeEvalTest.scala     |   20 +-
 .../expression/Draft2SizeFunctionSpec.scala   |   78 +-
 .../wdl/expression/FileEvaluatorSpec.scala    |   75 +-
 .../PureStandardLibraryFunctionsSpec.scala    |   73 +-
 .../wdl/expression/TypeEvaluatorSpec.scala    |   19 +-
 .../wdl/expression/ValueEvaluatorSpec.scala   |  326 +--
 .../WdlStandardLibraryFunctionsSpec.scala     |    2 -
 .../scala/wdl/types/WdlArrayTypeSpec.scala    |    2 +-
 .../test/scala/wdl/types/WdlMapTypeSpec.scala |   22 +-
 .../scala/wdl/types/WdlObjectTypeSpec.scala   |   29 +-
 .../scala/wdl/types/WdlPairTypeSpec.scala     |  105 +-
 .../scala/wdl/types/WomArrayTypeSpec.scala    |   38 +-
 .../test/scala/wdl/util/StringUtilSpec.scala  |    1 -
 .../test/scala/wdl/values/WdlValueSpec.scala  |  119 +-
 .../model/draft3/elements/CallElement.scala   |    5 +-
 .../draft3/elements/CommandPartElement.scala  |    4 +-
 .../draft3/elements/DeclarationElement.scala  |   33 +-
 .../draft3/elements/ExpressionElement.scala   |   62 +-
 .../model/draft3/elements/FileElement.scala   |    7 +-
 .../wdl/model/draft3/elements/IfElement.scala |    4 +-
 .../model/draft3/elements/ImportElement.scala |    5 +-
 .../elements/InputsSectionElement.scala       |    4 +-
 .../draft3/elements/LanguageElement.scala     |    2 +-
 .../draft3/elements/MetaSectionElement.scala  |    4 +-
 .../elements/OutputsSectionElement.scala      |    4 +-
 .../ParameterMetaSectionElement.scala         |    4 +-
 .../PlaceholderAttributeElement.scala         |    6 +-
 .../draft3/elements/ScatterElement.scala      |    6 +-
 .../elements/StringEscapeSequence.scala       |   11 +-
 .../elements/TaskDefinitionElement.scala      |    3 +-
 .../model/draft3/elements/TypeElement.scala   |    2 +-
 .../elements/WorkflowDefinitionElement.scala  |    3 +-
 .../draft3/graph/GeneratedValueHandle.scala   |    3 +-
 .../wdl/model/draft3/graph/LinkedGraph.scala  |    4 +-
 .../graph/UnlinkedConsumedValueHook.scala     |    4 +-
 .../draft3/graph/UnlinkedValueConsumer.scala  |   12 +-
 .../draft3/graph/UnlinkedValueGenerator.scala |    5 +-
 .../graph/expression/FileEvaluator.scala      |   17 +-
 .../graph/expression/TypeEvaluator.scala      |    6 +-
 .../graph/expression/ValueEvaluator.scala     |    5 +-
 .../graph/expression/WomExpressionMaker.scala |    3 +-
 .../wdl/shared/FileSizeLimitationConfig.scala |   17 +-
 .../model/expression/FileEvaluatorUtil.scala  |   15 +-
 .../model/expression/ValueEvaluation.scala    |   28 +-
 .../AstToNewExpressionElements.scala          |   21 +-
 .../ast2wdlom/BiscayneGenericAstNode.scala    |    3 +-
 .../biscayne/ast2wdlom/ast2wdlom.scala        |   83 +-
 .../BiscayneExpressionValueConsumers.scala    |   58 +-
 .../expression/consumed/consumed.scala        |  188 +-
 .../files/BiscayneFileEvaluators.scala        |    9 +-
 .../linking/expression/files/files.scala      |  165 +-
 .../types/BiscayneTypeEvaluators.scala        |   70 +-
 .../linking/expression/types/types.scala      |   10 +-
 .../values/BiscayneValueEvaluators.scala      |  167 +-
 .../linking/expression/values/values.scala    |  195 +-
 .../biscayne/parsing/BiscayneParser.scala     |    2 +-
 .../WdlBiscayneSyntaxErrorFormatter.scala     |   42 +-
 .../biscayne/wdlom2wom/package.scala          |   17 +-
 .../transforms/biscayne/Ast2WdlomSpec.scala   |   31 +-
 .../ast2wdlom/WdlFileToWdlomSpec.scala        |  408 +++-
 ...BiscayneExpressionValueConsumersSpec.scala |   20 +-
 .../files/BiscayneFileEvaluatorSpec.scala     |   17 +-
 .../types/BiscayneTypeEvaluatorSpec.scala     |   20 +-
 .../values/BiscayneValueEvaluatorSpec.scala   |  102 +-
 .../AstToNewExpressionElements.scala          |   21 +-
 .../ast2wdlom/CascadesGenericAstNode.scala    |    3 +-
 .../cascades/ast2wdlom/ast2wdlom.scala        |   83 +-
 .../CascadesExpressionValueConsumers.scala    |   58 +-
 .../expression/consumed/consumed.scala        |  188 +-
 .../files/CascadesFileEvaluators.scala        |    9 +-
 .../linking/expression/files/files.scala      |  165 +-
 .../types/CascadesTypeEvaluators.scala        |   70 +-
 .../linking/expression/types/types.scala      |   10 +-
 .../values/CascadesValueEvaluators.scala      |  167 +-
 .../linking/expression/values/values.scala    |  195 +-
 .../cascades/parsing/CascadesParser.scala     |    2 +-
 .../WdlCascadesSyntaxErrorFormatter.scala     |   42 +-
 .../cascades/wdlom2wom/package.scala          |   17 +-
 .../transforms/cascades/Ast2WdlomSpec.scala   |   31 +-
 .../ast2wdlom/WdlFileToWdlomSpec.scala        |  408 +++-
 ...CascadesExpressionValueConsumersSpec.scala |   20 +-
 .../files/CascadesFileEvaluatorSpec.scala     |   17 +-
 .../types/CascadesTypeEvaluatorSpec.scala     |   20 +-
 .../values/CascadesValueEvaluatorSpec.scala   |  102 +-
 .../wdlom2wom/WdlDraft2WomBundleMakers.scala  |   24 +-
 .../wdlom2wom/WdlDraft2WomCallNodeMaker.scala |  131 +-
 ...lDraft2WomCommandTaskDefinitionMaker.scala |   16 +-
 .../WdlDraft2WomConditionalNodeMaker.scala    |   65 +-
 .../WdlDraft2WomExecutableMakers.scala        |   35 +-
 .../wdlom2wom/WdlDraft2WomGraphMaker.scala    |   67 +-
 .../WdlDraft2WomScatterNodeMaker.scala        |   49 +-
 .../WdlDraft2WomWorkflowDefinitionMaker.scala |   21 +-
 .../wdlwom/Draft2ReadFileLimitsSpec.scala     |   12 +-
 .../transforms/wdlwom/WdlAliasWomSpec.scala   |   15 +-
 .../wdlwom/WdlConditionalWomSpec.scala        |   79 +-
 .../wdlwom/WdlInputValidationSpec.scala       |   68 +-
 .../wdlwom/WdlNamespaceWomSpec.scala          |   46 +-
 .../wdlwom/WdlNestedConditionalWomSpec.scala  |   10 +-
 .../transforms/wdlwom/WdlScatterWomSpec.scala |  133 +-
 .../wdlwom/WdlSubworkflowWomSpec.scala        |   57 +-
 .../WdlWomExpressionsAsInputsSpec.scala       |   10 +-
 .../ast2wdlom/Draft3GenericAstNode.scala      |    3 +-
 .../transforms/ast2wdlom/ast2wdlom.scala      |  115 +-
 .../linking/expression/consumed/package.scala |  148 +-
 .../linking/expression/files/package.scala    |  157 +-
 .../linking/expression/types/package.scala    |   10 +-
 .../linking/expression/values/package.scala   |   33 +-
 .../transforms/parsing/Draft3Parser.scala     |    2 +-
 .../WdlDraft3SyntaxErrorFormatter.scala       |   42 +-
 .../draft3/transforms/wdlom2wom/package.scala |   17 +-
 .../AstToWorkflowDefinitionElementSpec.scala  |   73 +-
 .../transforms/ast2wdlom/Ast2WdlomSpec.scala  |    8 +-
 .../transforms/ast2wdlom/ExpressionSet.scala  |   28 +-
 .../ast2wdlom/WdlFileToWdlomSpec.scala        | 2146 +++++++++++------
 .../MemberAccessTypeEvaluatorSpec.scala       |   22 +-
 .../MemberAccessValueEvaluatorSpec.scala      |   18 +-
 .../expression/TernaryIfEvaluatorSpec.scala   |    6 +-
 ...UnaryAndBinaryOperatorsEvaluatorSpec.scala |    5 -
 .../consumed/ValueConsumerSpec.scala          |    4 +-
 .../values/Draft3ReadFileLimitsSpec.scala     |   19 +-
 .../values/Draft3SizeFunctionSpec.scala       |  129 +-
 .../expression/files/FileEvaluatorSpec.scala  |    6 +-
 .../wdlom2wdl/WdlomToWdlFileSpec.scala        |   36 +-
 .../wdlom2wom/WdlFileToWomSpec.scala          |  146 +-
 .../AstNodeToCommandPartElement.scala         |   26 +-
 .../AstNodeToExpressionElement.scala          |  108 +-
 .../base/ast2wdlom/AstNodeToKvPair.scala      |    5 +-
 .../base/ast2wdlom/AstNodeToMetaKvPair.scala  |   22 +-
 .../AstNodeToPlaceholderAttributeSet.scala    |   64 +-
 .../ast2wdlom/AstNodeToStaticString.scala     |   54 +-
 .../base/ast2wdlom/AstNodeToTypeElement.scala |   61 +-
 .../base/ast2wdlom/AstToCallElement.scala     |   18 +-
 .../AstToCommandSectionElement.scala          |   20 +-
 .../ast2wdlom/AstToDeclarationContent.scala   |   16 +-
 .../base/ast2wdlom/AstToFileBodyElement.scala |   14 +-
 .../base/ast2wdlom/AstToFileElement.scala     |   14 +-
 .../base/ast2wdlom/AstToIfElement.scala       |   10 +-
 .../base/ast2wdlom/AstToImportElement.scala   |   16 +-
 .../AstToInputDeclarationElement.scala        |   11 +-
 .../ast2wdlom/AstToInputsSectionElement.scala |    6 +-
 .../ast2wdlom/AstToMetaSectionElement.scala   |    6 +-
 .../AstToOutputsSectionElement.scala          |   10 +-
 .../AstToParameterMetaSectionElement.scala    |   15 +-
 ...AstToRuntimeAttributesSectionElement.scala |   13 +-
 .../base/ast2wdlom/AstToScatterElement.scala  |   23 +-
 .../base/ast2wdlom/AstToStructElement.scala   |   13 +-
 .../AstToTaskDefinitionElement.scala          |   63 +-
 .../ast2wdlom/AstToTaskSectionElement.scala   |   17 +-
 .../ast2wdlom/AstToWorkflowBodyElement.scala  |   29 +-
 .../AstToWorkflowDefinitionElement.scala      |   79 +-
 .../AstToWorkflowGraphNodeElement.scala       |   35 +-
 .../base/ast2wdlom/GenericAst.scala           |   26 +-
 .../transforms/base/ast2wdlom/ast2wdlom.scala |   14 +-
 .../consumed/BinaryOperatorEvaluators.scala   |    6 +-
 .../consumed/EngineFunctionEvaluators.scala   |   60 +-
 .../consumed/LiteralEvaluators.scala          |   85 +-
 .../consumed/LookupEvaluators.scala           |   37 +-
 .../consumed/TernaryIfEvaluator.scala         |   12 +-
 .../consumed/UnaryOperatorEvaluators.scala    |    5 +-
 .../files/BinaryOperatorEvaluators.scala      |   15 +-
 .../files/EngineFunctionEvaluators.scala      |  161 +-
 .../expression/files/LiteralEvaluators.scala  |   76 +-
 .../expression/files/LookupEvaluators.scala   |   64 +-
 .../expression/files/TernaryIfEvaluator.scala |   14 +-
 .../files/UnaryOperatorEvaluators.scala       |    8 +-
 .../base/linking/expression/package.scala     |   16 +-
 .../types/BinaryOperatorEvaluators.scala      |   11 +-
 .../types/EngineFunctionEvaluators.scala      |  294 +--
 .../expression/types/LiteralEvaluators.scala  |   54 +-
 .../expression/types/LookupEvaluators.scala   |   79 +-
 .../expression/types/TernaryIfEvaluator.scala |    9 +-
 .../types/UnaryOperatorEvaluators.scala       |    6 +-
 .../values/BinaryOperatorEvaluators.scala     |   21 +-
 .../values/EngineFunctionEvaluators.scala     |  590 +++--
 .../expression/values/LiteralEvaluators.scala |   57 +-
 .../expression/values/LookupEvaluators.scala  |  119 +-
 .../values/TernaryIfEvaluator.scala           |   17 +-
 .../values/UnaryOperatorEvaluators.scala      |    5 +-
 .../base/linking/graph/LinkedGraphMaker.scala |   89 +-
 .../base/linking/graph/package.scala          |  263 +-
 .../base/linking/typemakers/package.scala     |   42 +-
 .../transforms/base/wdlom2wdl/WdlWriter.scala |    2 +-
 .../base/wdlom2wdl/WdlWriterImpl.scala        |  470 ++--
 .../CommandPartElementToWomCommandPart.scala  |   68 +-
 .../wdlom2wom/FileElementToWomBundle.scala    |  143 +-
 .../base/wdlom2wom/StructEvaluation.scala     |   17 +-
 ...DefinitionElementToWomTaskDefinition.scala |  232 +-
 .../wdlom2wom/WomBundleToWomExecutable.scala  |    6 +-
 ...nitionElementToWomWorkflowDefinition.scala |  161 +-
 .../expression/WdlomWomExpression.scala       |   51 +-
 .../renaming/BinaryOperatorEvaluators.scala   |   23 +-
 .../renaming/EngineFunctionEvaluators.scala   |   54 +-
 .../renaming/IdentifierLookupRenamer.scala    |    4 +-
 .../renaming/LiteralEvaluators.scala          |   92 +-
 .../renaming/LookupEvaluators.scala           |   74 +-
 .../renaming/TernaryIfEvaluator.scala         |    4 +-
 .../renaming/UnaryOperatorEvaluators.scala    |    4 +-
 .../expression/renaming/package.scala         |  151 +-
 .../graph/CallElementToGraphNode.scala        |  139 +-
 .../graph/IfElementToGraphNode.scala          |   93 +-
 .../InputDeclarationElementToGraphNode.scala  |   23 +-
 .../graph/ScatterElementToGraphNode.scala     |  207 +-
 .../WorkflowGraphElementToGraphNode.scala     |   70 +-
 .../GraphIdentifierLookupRenamer.scala        |    7 +-
 .../wdlom2wom/graph/renaming/package.scala    |  152 +-
 .../evaluation/values/EngineFunctions.scala   |   22 +-
 .../wdlom2wom/WdlSharedInputParsing.scala     |   19 +-
 .../wdlom2wom/WomGraphMakerTools.scala        |   26 +-
 wom/src/main/scala/wdl/util/StringUtil.scala  |    6 +-
 wom/src/main/scala/wom/CommandPart.scala      |    3 +-
 .../main/scala/wom/RuntimeAttributes.scala    |    3 +
 wom/src/main/scala/wom/WomFileMapper.scala    |   19 +-
 .../main/scala/wom/callable/Callable.scala    |  115 +-
 .../wom/callable/CommandTaskDefinition.scala  |  102 +-
 .../ContainerizedInputExpression.scala        |    3 +-
 .../wom/callable/RuntimeEnvironment.scala     |    4 +-
 .../wom/callable/WorkflowDefinition.scala     |    3 +-
 .../scala/wom/executable/Executable.scala     |   78 +-
 .../wom/executable/ExecutableValidation.scala |   21 +-
 .../main/scala/wom/executable/WomBundle.scala |    6 +-
 .../expression/InputPointerToWomValue.scala   |   44 +-
 .../wom/expression/IoFunctionSetAdapter.scala |    5 +-
 .../wom/expression/NoIoFunctionSet.scala      |   33 +-
 .../scala/wom/expression/WomExpression.scala  |   26 +-
 .../main/scala/wom/format/MemorySize.scala    |    9 +-
 wom/src/main/scala/wom/graph/CallNode.scala   |  234 +-
 .../scala/wom/graph/ConditionalNode.scala     |   18 +-
 wom/src/main/scala/wom/graph/Graph.scala      |   40 +-
 .../main/scala/wom/graph/GraphInputNode.scala |  131 +-
 wom/src/main/scala/wom/graph/GraphNode.scala  |   18 +-
 .../wom/graph/GraphNodeInputExpression.scala  |    9 +-
 .../main/scala/wom/graph/GraphNodePort.scala  |   36 +-
 .../graph/GraphNodeWithSingleOutputPort.scala |    1 +
 .../scala/wom/graph/GraphOutputNode.scala     |   10 +-
 .../main/scala/wom/graph/ScatterNode.scala    |   74 +-
 .../main/scala/wom/graph/WomIdentifier.scala  |    6 +-
 .../expression/AnonymousExpressionNode.scala  |   15 +-
 .../expression/ExposedExpressionNode.scala    |    7 +-
 .../wom/graph/expression/ExpressionNode.scala |   38 +-
 .../graph/expression/ExpressionNodeLike.scala |    4 +-
 wom/src/main/scala/wom/package.scala          |   16 +-
 .../runtime/WomOutputRuntimeExtractor.scala   |    4 +-
 .../wom/transforms/WomCallNodeMaker.scala     |    7 +-
 .../transforms/WomConditionalNodeMaker.scala  |    7 +-
 .../wom/transforms/WomExecutableMaker.scala   |    6 +-
 .../scala/wom/transforms/WomGraphMaker.scala  |    7 +-
 .../wom/transforms/WomScatterNodeMaker.scala  |    7 +-
 wom/src/main/scala/wom/types/WomAnyType.scala |   11 +-
 .../main/scala/wom/types/WomArrayType.scala   |   26 +-
 .../main/scala/wom/types/WomBooleanType.scala |    2 +-
 .../scala/wom/types/WomCompositeType.scala    |   33 +-
 .../scala/wom/types/WomCoproductType.scala    |   33 +-
 .../scala/wom/types/WomEnumerationType.scala  |   10 +-
 .../main/scala/wom/types/WomFileType.scala    |    4 +-
 .../main/scala/wom/types/WomFloatType.scala   |    2 +-
 .../main/scala/wom/types/WomIntegerLike.scala |    1 -
 .../main/scala/wom/types/WomIntegerType.scala |   14 +-
 .../main/scala/wom/types/WomNothingType.scala |    4 +-
 .../main/scala/wom/types/WomObjectType.scala  |   24 +-
 .../scala/wom/types/WomOptionalType.scala     |   13 +-
 .../main/scala/wom/types/WomPairType.scala    |   22 +-
 .../scala/wom/types/WomPrimitiveType.scala    |    3 +-
 .../main/scala/wom/types/WomStringType.scala  |    2 +-
 wom/src/main/scala/wom/types/WomType.scala    |   71 +-
 .../wom/types/WomTypeJsonFormatter.scala      |    4 +-
 .../wom/types/coercion/defaults/package.scala |   22 +-
 wom/src/main/scala/wom/util/YamlUtils.scala   |   50 +-
 wom/src/main/scala/wom/values/WomArray.scala  |   58 +-
 .../main/scala/wom/values/WomBoolean.scala    |   10 +-
 .../scala/wom/values/WomCoproductValue.scala  |    3 +-
 wom/src/main/scala/wom/values/WomFile.scala   |   93 +-
 wom/src/main/scala/wom/values/WomFloat.scala  |   66 +-
 .../main/scala/wom/values/WomInteger.scala    |   44 +-
 wom/src/main/scala/wom/values/WomLong.scala   |    2 +-
 wom/src/main/scala/wom/values/WomMap.scala    |   66 +-
 wom/src/main/scala/wom/values/WomObject.scala |   57 +-
 .../scala/wom/values/WomOptionalValue.scala   |   13 +-
 wom/src/main/scala/wom/values/WomPair.scala   |    3 +-
 wom/src/main/scala/wom/values/WomValue.scala  |   29 +-
 wom/src/main/scala/wom/views/GraphPrint.scala |   49 +-
 wom/src/test/scala/wom/WomMatchers.scala      |    2 +-
 .../callable/CommandTaskDefinitionSpec.scala  |   21 +-
 .../expression/PlaceholderWomExpression.scala |   13 +-
 .../scala/wom/format/MemorySizeSpec.scala     |    7 +-
 .../wom/graph/ExpressionAsCallInputSpec.scala |    8 +-
 .../scala/wom/graph/ExpressionNodeSpec.scala  |   17 +-
 .../scala/wom/graph/GraphOutputNodeSpec.scala |   14 +-
 wom/src/test/scala/wom/graph/GraphSpec.scala  |   76 +-
 .../scala/wom/graph/ScatterNodeSpec.scala     |   21 +-
 .../scala/wom/types/WomArrayTypeSpec.scala    |   18 +-
 .../scala/wom/types/WomCoercionSpec.scala     |   10 +-
 .../wom/types/WomCompositeTypeSpec.scala      |   62 +-
 .../scala/wom/types/WomCoproductSpec.scala    |    1 -
 .../scala/wom/types/WomFileTypeSpec.scala     |  176 +-
 .../test/scala/wom/types/WomMapTypeSpec.scala |   84 +-
 .../scala/wom/types/WomObjectTypeSpec.scala   |   48 +-
 .../scala/wom/types/WomOptionalTypeSpec.scala |   56 +-
 .../test/scala/wom/types/WomTypeSpec.scala    |   88 +-
 .../test/scala/wom/util/YamlUtilsSpec.scala   |   40 +-
 .../test/scala/wom/values/WomFileSpec.scala   |  250 +-
 .../test/scala/wom/values/WomObjectSpec.scala |    8 +-
 .../wom/values/WomOptionalValueSpec.scala     |    1 -
 .../src/main/scala/womtool/WomtoolMain.scala  |   71 +-
 .../PartialWomtoolCommandLineArguments.scala  |   12 +-
 .../cmdline/WomtoolCommandLineParser.scala    |   66 +-
 .../main/scala/womtool/graph/WomGraph.scala   |   66 +-
 .../main/scala/womtool/graph/package.scala    |    4 +-
 .../scala/womtool/input/WomGraphMaker.scala   |   11 +-
 .../main/scala/womtool/inputs/Inputs.scala    |   24 +-
 .../main/scala/womtool/outputs/Outputs.scala  |   19 +-
 .../scala/womtool/validate/Validate.scala     |    3 +-
 .../scala/womtool/wom2wdlom/WomToWdlom.scala  |  317 ++-
 .../src/test/scala/womtool/SampleWdl.scala    |    4 +-
 .../womtool/WomtoolJsonCommandSpec.scala      |   17 +-
 .../test/scala/womtool/WomtoolMainSpec.scala  |   16 +-
 .../scala/womtool/WomtoolValidateSpec.scala   |   73 +-
 .../ExpressionBasedGraphOutputNodeSpec.scala  |   16 +-
 .../womtool/graph/ExpressionNodeSpec.scala    |    6 +-
 .../graph/OutputNameCollisionSpec.scala       |    7 +-
 .../scala/womtool/graph/WomDotGraphTest.scala |   10 +-
 1553 files changed, 49441 insertions(+), 32619 deletions(-)
 create mode 100644 .scalafmt.conf

diff --git a/.scalafmt.conf b/.scalafmt.conf
new file mode 100644
index 00000000000..336b0fd7145
--- /dev/null
+++ b/.scalafmt.conf
@@ -0,0 +1,18 @@
+version = 3.7.17
+align.preset = none
+align.openParenCallSite = true
+align.openParenDefnSite = true
+maxColumn = 120
+continuationIndent.defnSite = 2
+assumeStandardLibraryStripMargin = true
+align.stripMargin = true
+danglingParentheses.preset = true
+rewrite.rules = [Imports, RedundantBraces, RedundantParens, SortModifiers]
+rewrite.imports.sort = scalastyle
+docstrings.style = keep
+project.excludeFilters = [
+  Dependencies.scala,
+  Settings.scala,
+  build.sbt
+]
+runner.dialect = scala213
diff --git a/CromIAM/src/main/scala/cromiam/auth/Collection.scala b/CromIAM/src/main/scala/cromiam/auth/Collection.scala
index 84e72194ab2..47785ae2005 100644
--- a/CromIAM/src/main/scala/cromiam/auth/Collection.scala
+++ b/CromIAM/src/main/scala/cromiam/auth/Collection.scala
@@ -9,6 +9,7 @@ import scala.util.{Success, Try}
 final case class Collection(name: String) extends AnyVal
 
 object Collection {
+
   /**
     * Parses a raw JSON string to make sure it fits the standard pattern (see below) for labels,
     * performs some CromIAM-specific checking to ensure the user isn't attempting to manipulate the
@@ -19,13 +20,14 @@ object Collection {
     */
   def validateLabels(labelsJson: Option[String]): Directive1[Option[Map[String, JsValue]]] = {
 
-      val labels = labelsJson map { l =>
-        Try(l.parseJson) match {
-          case Success(JsObject(json)) if json.keySet.contains(CollectionLabelName) => throw new LabelContainsCollectionException
-          case Success(JsObject(json)) => json
-          case _ => throw InvalidLabelsException(l)
-        }
+    val labels = labelsJson map { l =>
+      Try(l.parseJson) match {
+        case Success(JsObject(json)) if json.keySet.contains(CollectionLabelName) =>
+          throw new LabelContainsCollectionException
+        case Success(JsObject(json)) => json
+        case _ => throw InvalidLabelsException(l)
       }
+    }
 
     provide(labels)
   }
@@ -34,15 +36,16 @@ object Collection {
   val LabelsKey = "labels"
 
   // LabelContainsCollectionException is a class because of ScalaTest, some of the constructs don't play well w/ case objects
-  final class LabelContainsCollectionException extends Exception(s"Submitted labels contain the key $CollectionLabelName, which is not allowed\n")
-  final case class InvalidLabelsException(labels: String) extends Exception(s"Labels must be a valid JSON object, received: $labels\n")
+  final class LabelContainsCollectionException
+      extends Exception(s"Submitted labels contain the key $CollectionLabelName, which is not allowed\n")
+  final case class InvalidLabelsException(labels: String)
+      extends Exception(s"Labels must be a valid JSON object, received: $labels\n")
 
   /**
     * Returns the default collection for a user.
     */
-  def forUser(user: User): Collection = {
+  def forUser(user: User): Collection =
     Collection(user.userId.value)
-  }
 
   implicit val collectionJsonReader = new JsonReader[Collection] {
     import spray.json.DefaultJsonProtocol._
diff --git a/CromIAM/src/main/scala/cromiam/auth/User.scala b/CromIAM/src/main/scala/cromiam/auth/User.scala
index d123f8fa2f7..fec64ebc5f9 100644
--- a/CromIAM/src/main/scala/cromiam/auth/User.scala
+++ b/CromIAM/src/main/scala/cromiam/auth/User.scala
@@ -7,4 +7,3 @@ import org.broadinstitute.dsde.workbench.model.WorkbenchUserId
   * Wraps the concept of an authenticated workbench user including their numeric ID as well as their bearer token
   */
 final case class User(userId: WorkbenchUserId, authorization: Authorization)
-
diff --git a/CromIAM/src/main/scala/cromiam/cromwell/CromwellClient.scala b/CromIAM/src/main/scala/cromiam/cromwell/CromwellClient.scala
index a95b8df89b5..4a419b62255 100644
--- a/CromIAM/src/main/scala/cromiam/cromwell/CromwellClient.scala
+++ b/CromIAM/src/main/scala/cromiam/cromwell/CromwellClient.scala
@@ -25,10 +25,16 @@ import scala.concurrent.{ExecutionContextExecutor, Future}
   *
   * FIXME: Look for ways to synch this up with the mothership
   */
-class CromwellClient(scheme: String, interface: String, port: Int, log: LoggingAdapter, serviceRegistryActorRef: ActorRef)(implicit system: ActorSystem,
-                                                                                        ece: ExecutionContextExecutor,
-                                                                                        materializer: ActorMaterializer)
-  extends SprayJsonSupport with DefaultJsonProtocol with StatusCheckedSubsystem with CromIamInstrumentation{
+class CromwellClient(scheme: String,
+                     interface: String,
+                     port: Int,
+                     log: LoggingAdapter,
+                     serviceRegistryActorRef: ActorRef
+)(implicit system: ActorSystem, ece: ExecutionContextExecutor, materializer: ActorMaterializer)
+    extends SprayJsonSupport
+    with DefaultJsonProtocol
+    with StatusCheckedSubsystem
+    with CromIamInstrumentation {
 
   val cromwellUrl = new URL(s"$scheme://$interface:$port")
   val cromwellApiVersion = "v1"
@@ -41,21 +47,23 @@ class CromwellClient(scheme: String, interface: String, port: Int, log: LoggingA
 
   def collectionForWorkflow(workflowId: String,
                             user: User,
-                            cromIamRequest: HttpRequest): FailureResponseOrT[Collection] = {
+                            cromIamRequest: HttpRequest
+  ): FailureResponseOrT[Collection] = {
     import CromwellClient.EnhancedWorkflowLabels
 
     log.info("Requesting collection for " + workflowId + " for user " + user.userId + " from metadata")
 
     // Look up in Cromwell what the collection is for this workflow. If it doesn't exist, fail the Future
-    val cromwellApiLabelFunc = () => cromwellApiClient.labels(WorkflowId.fromString(workflowId), headers = List(user.authorization)) flatMap {
-      _.caasCollection match {
-        case Some(c) => FailureResponseOrT.pure[IO, HttpResponse](c)
-        case None =>
-          val exception = new IllegalArgumentException(s"Workflow $workflowId has no associated collection")
-          val failure = IO.raiseError[Collection](exception)
-          FailureResponseOrT.right[HttpResponse](failure)
+    val cromwellApiLabelFunc = () =>
+      cromwellApiClient.labels(WorkflowId.fromString(workflowId), headers = List(user.authorization)) flatMap {
+        _.caasCollection match {
+          case Some(c) => FailureResponseOrT.pure[IO, HttpResponse](c)
+          case None =>
+            val exception = new IllegalArgumentException(s"Workflow $workflowId has no associated collection")
+            val failure = IO.raiseError[Collection](exception)
+            FailureResponseOrT.right[HttpResponse](failure)
+        }
       }
-    }
 
     instrumentRequest(cromwellApiLabelFunc, cromIamRequest, wfCollectionPrefix)
   }
@@ -63,13 +71,14 @@ class CromwellClient(scheme: String, interface: String, port: Int, log: LoggingA
   def forwardToCromwell(httpRequest: HttpRequest): FailureResponseOrT[HttpResponse] = {
     val future = {
       // See CromwellClient's companion object for info on these header modifications
-      val headers = httpRequest.headers.filterNot(header => header.name == TimeoutAccessHeader || header.name == HostHeader)
+      val headers =
+        httpRequest.headers.filterNot(header => header.name == TimeoutAccessHeader || header.name == HostHeader)
       val cromwellRequest = httpRequest
         .copy(uri = httpRequest.uri.withAuthority(interface, port).withScheme(scheme))
         .withHeaders(headers)
       Http().singleRequest(cromwellRequest)
-    } recoverWith {
-      case e => Future.failed(CromwellConnectionFailure(e))
+    } recoverWith { case e =>
+      Future.failed(CromwellConnectionFailure(e))
     }
     future.asFailureResponseOrT
   }
@@ -86,7 +95,7 @@ class CromwellClient(scheme: String, interface: String, port: Int, log: LoggingA
           use the current workflow id.
 
           This is all called from inside the context of a Future, so exceptions will be properly caught.
-      */
+       */
       metadata.value.parseJson.asJsObject.fields.get("rootWorkflowId").map(_.convertTo[String]).getOrElse(workflowId)
     }
 
@@ -96,11 +105,13 @@ class CromwellClient(scheme: String, interface: String, port: Int, log: LoggingA
       Grab the metadata from Cromwell filtered down to the rootWorkflowId. Then transform the response to get just the
       root workflow ID itself
      */
-    val cromwellApiMetadataFunc = () => cromwellApiClient.metadata(
-      WorkflowId.fromString(workflowId),
-      args = Option(Map("includeKey" -> List("rootWorkflowId"))),
-      headers = List(user.authorization)).map(metadataToRootWorkflowId
-    )
+    val cromwellApiMetadataFunc = () =>
+      cromwellApiClient
+        .metadata(WorkflowId.fromString(workflowId),
+                  args = Option(Map("includeKey" -> List("rootWorkflowId"))),
+                  headers = List(user.authorization)
+        )
+        .map(metadataToRootWorkflowId)
 
     instrumentRequest(cromwellApiMetadataFunc, cromIamRequest, rootWfIdPrefix)
   }
@@ -120,14 +131,14 @@ object CromwellClient {
   // See: https://broadworkbench.atlassian.net/browse/DDO-2190
   val HostHeader = "Host"
 
-  final case class CromwellConnectionFailure(f: Throwable) extends Exception(s"Unable to connect to Cromwell (${f.getMessage})", f)
+  final case class CromwellConnectionFailure(f: Throwable)
+      extends Exception(s"Unable to connect to Cromwell (${f.getMessage})", f)
 
   implicit class EnhancedWorkflowLabels(val wl: WorkflowLabels) extends AnyVal {
 
-    import Collection.{CollectionLabelName, collectionJsonReader}
+    import Collection.{collectionJsonReader, CollectionLabelName}
 
-    def caasCollection: Option[Collection] = {
+    def caasCollection: Option[Collection] =
       wl.labels.fields.get(CollectionLabelName).map(_.convertTo[Collection])
-    }
   }
 }
diff --git a/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala b/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
index 65b164f00f6..c79e0b6e14c 100644
--- a/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
+++ b/CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala
@@ -27,10 +27,11 @@ trait CromIamInstrumentation extends CromwellInstrumentation {
   val rootWfIdPrefix = NonEmptyList.one("root-workflow-id")
   val wfCollectionPrefix = NonEmptyList.one("workflow-collection")
 
-
   def convertRequestToPath(httpRequest: HttpRequest): NonEmptyList[String] = NonEmptyList.of(
     // Returns the path of the URI only, without query parameters (e.g: api/engine/workflows/metadata)
-    httpRequest.uri.path.toString().stripPrefix("/")
+    httpRequest.uri.path
+      .toString()
+      .stripPrefix("/")
       // Replace UUIDs with [id] to keep paths same regardless of the workflow
       .replaceAll(CromIamInstrumentation.UUIDRegex, "[id]"),
     // Name of the method (e.g: GET)
@@ -43,15 +44,19 @@ trait CromIamInstrumentation extends CromwellInstrumentation {
   def makePathFromRequestAndResponse(httpRequest: HttpRequest, httpResponse: HttpResponse): InstrumentationPath =
     convertRequestToPath(httpRequest).concatNel(NonEmptyList.of(httpResponse.status.intValue.toString))
 
-  def sendTimingApi(statsDPath: InstrumentationPath, timing: FiniteDuration, prefixToStatsd: NonEmptyList[String]): Unit = {
+  def sendTimingApi(statsDPath: InstrumentationPath,
+                    timing: FiniteDuration,
+                    prefixToStatsd: NonEmptyList[String]
+  ): Unit =
     sendTiming(prefixToStatsd.concatNel(statsDPath), timing, CromIamPrefix)
-  }
 
-  def instrumentationPrefixForSam(methodPrefix: NonEmptyList[String]): NonEmptyList[String] = samPrefix.concatNel(methodPrefix)
+  def instrumentationPrefixForSam(methodPrefix: NonEmptyList[String]): NonEmptyList[String] =
+    samPrefix.concatNel(methodPrefix)
 
   def instrumentRequest[A](func: () => FailureResponseOrT[A],
                            httpRequest: HttpRequest,
-                           prefix: NonEmptyList[String]): FailureResponseOrT[A] = {
+                           prefix: NonEmptyList[String]
+  ): FailureResponseOrT[A] = {
     def now(): Deadline = Deadline.now
 
     val startTimestamp = now()
diff --git a/CromIAM/src/main/scala/cromiam/sam/SamClient.scala b/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
index d6a315f8241..8fa0cc8fd87 100644
--- a/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
+++ b/CromIAM/src/main/scala/cromiam/sam/SamClient.scala
@@ -33,20 +33,21 @@ class SamClient(scheme: String,
                 port: Int,
                 checkSubmitWhitelist: Boolean,
                 log: LoggingAdapter,
-                serviceRegistryActorRef: ActorRef)
-               (implicit system: ActorSystem, ece: ExecutionContextExecutor, materializer: ActorMaterializer) extends StatusCheckedSubsystem with CromIamInstrumentation {
+                serviceRegistryActorRef: ActorRef
+)(implicit system: ActorSystem, ece: ExecutionContextExecutor, materializer: ActorMaterializer)
+    extends StatusCheckedSubsystem
+    with CromIamInstrumentation {
 
-  private implicit val cs = IO.contextShift(ece)
+  implicit private val cs = IO.contextShift(ece)
 
   override val statusUri = uri"$samBaseUri/status"
   override val serviceRegistryActor: ActorRef = serviceRegistryActorRef
 
-  def isSubmitWhitelisted(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+  def isSubmitWhitelisted(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] =
     checkSubmitWhitelist.fold(
       isSubmitWhitelistedSam(user, cromIamRequest),
       FailureResponseOrT.pure(true)
     )
-  }
 
   def isSubmitWhitelistedSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
     val request = HttpRequest(
@@ -64,7 +65,7 @@ class SamClient(scheme: String,
       whitelisted <- response.status match {
         case StatusCodes.OK =>
           // Does not seem to be already provided?
-          implicit val entityToBooleanUnmarshaller : Unmarshaller[HttpEntity, Boolean] =
+          implicit val entityToBooleanUnmarshaller: Unmarshaller[HttpEntity, Boolean] =
             (Unmarshaller.stringUnmarshaller flatMap Unmarshaller.booleanFromStringUnmarshaller).asScala
           val unmarshal = IO.fromFuture(IO(Unmarshal(response.entity).to[Boolean]))
           FailureResponseOrT.right[HttpResponse](unmarshal)
@@ -95,14 +96,19 @@ class SamClient(scheme: String,
             userInfo.enabled
           }
         case _ =>
-          log.error("Could not verify access with Sam for user {}, error was {} {}", user.userId, response.status, response.toString().take(100))
+          log.error("Could not verify access with Sam for user {}, error was {} {}",
+                    user.userId,
+                    response.status,
+                    response.toString().take(100)
+          )
           FailureResponseOrT.pure[IO, HttpResponse](false)
       }
     } yield userEnabled
   }
 
   def collectionsForUser(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[List[Collection]] = {
-    val request = HttpRequest(method = HttpMethods.GET, uri = samBaseCollectionUri, headers = List[HttpHeader](user.authorization))
+    val request =
+      HttpRequest(method = HttpMethods.GET, uri = samBaseCollectionUri, headers = List[HttpHeader](user.authorization))
 
     for {
       response <- instrumentRequest(
@@ -120,24 +126,25 @@ class SamClient(scheme: String,
     * @return Successful future if the auth is accepted, a Failure otherwise.
     */
   def requestAuth(authorizationRequest: CollectionAuthorizationRequest,
-                  cromIamRequest: HttpRequest): FailureResponseOrT[Unit] = {
+                  cromIamRequest: HttpRequest
+  ): FailureResponseOrT[Unit] = {
     val logString = authorizationRequest.action + " access for user " + authorizationRequest.user.userId +
-      " on a request to " + authorizationRequest.action +  " for collection " + authorizationRequest.collection.name
+      " on a request to " + authorizationRequest.action + " for collection " + authorizationRequest.collection.name
 
-    def validateEntityBytes(byteString: ByteString): FailureResponseOrT[Unit] = {
+    def validateEntityBytes(byteString: ByteString): FailureResponseOrT[Unit] =
       if (byteString.utf8String == "true") {
         Monad[FailureResponseOrT].unit
       } else {
         log.warning("Sam denied " + logString)
         FailureResponseOrT[IO, HttpResponse, Unit](IO.raiseError(new SamDenialException))
       }
-    }
 
     log.info("Requesting authorization for " + logString)
 
     val request = HttpRequest(method = HttpMethods.GET,
-      uri = samAuthorizeActionUri(authorizationRequest),
-      headers = List[HttpHeader](authorizationRequest.user.authorization))
+                              uri = samAuthorizeActionUri(authorizationRequest),
+                              headers = List[HttpHeader](authorizationRequest.user.authorization)
+    )
 
     for {
       response <- instrumentRequest(
@@ -158,10 +165,7 @@ class SamClient(scheme: String,
             - If user has the 'add' permission we're ok
         - else fail the future
    */
-  def requestSubmission(user: User,
-                        collection: Collection,
-                        cromIamRequest: HttpRequest
-                       ): FailureResponseOrT[Unit] = {
+  def requestSubmission(user: User, collection: Collection, cromIamRequest: HttpRequest): FailureResponseOrT[Unit] = {
     log.info("Verifying user " + user.userId + " can submit a workflow to collection " + collection.name)
     val createCollection = registerCreation(user, collection, cromIamRequest)
 
@@ -169,15 +173,20 @@ class SamClient(scheme: String,
       case r if r.status == StatusCodes.NoContent => Monad[FailureResponseOrT].unit
       case r => FailureResponseOrT[IO, HttpResponse, Unit](IO.raiseError(SamRegisterCollectionException(r.status)))
     } recoverWith {
-      case r if r.status == StatusCodes.Conflict => requestAuth(CollectionAuthorizationRequest(user, collection, "add"), cromIamRequest)
+      case r if r.status == StatusCodes.Conflict =>
+        requestAuth(CollectionAuthorizationRequest(user, collection, "add"), cromIamRequest)
       case r => FailureResponseOrT[IO, HttpResponse, Unit](IO.raiseError(SamRegisterCollectionException(r.status)))
     }
   }
 
   protected def registerCreation(user: User,
                                  collection: Collection,
-                                 cromIamRequest: HttpRequest): FailureResponseOrT[HttpResponse] = {
-    val request = HttpRequest(method = HttpMethods.POST, uri = samRegisterUri(collection), headers = List[HttpHeader](user.authorization))
+                                 cromIamRequest: HttpRequest
+  ): FailureResponseOrT[HttpResponse] = {
+    val request = HttpRequest(method = HttpMethods.POST,
+                              uri = samRegisterUri(collection),
+                              headers = List[HttpHeader](user.authorization)
+    )
 
     instrumentRequest(
       () => Http().singleRequest(request).asFailureResponseOrT,
@@ -186,9 +195,9 @@ class SamClient(scheme: String,
     )
   }
 
-  private def samAuthorizeActionUri(authorizationRequest: CollectionAuthorizationRequest) = {
-    akka.http.scaladsl.model.Uri(s"${samBaseUriForWorkflow(authorizationRequest.collection)}/action/${authorizationRequest.action}")
-  }
+  private def samAuthorizeActionUri(authorizationRequest: CollectionAuthorizationRequest) =
+    akka.http.scaladsl.model
+      .Uri(s"${samBaseUriForWorkflow(authorizationRequest.collection)}/action/${authorizationRequest.action}")
 
   private def samRegisterUri(collection: Collection) = akka.http.scaladsl.model.Uri(samBaseUriForWorkflow(collection))
 
@@ -207,15 +216,18 @@ object SamClient {
 
   class SamDenialException extends Exception("Access Denied")
 
-  final case class SamConnectionFailure(phase: String, f: Throwable) extends Exception(s"Unable to connect to Sam during $phase (${f.getMessage})", f)
+  final case class SamConnectionFailure(phase: String, f: Throwable)
+      extends Exception(s"Unable to connect to Sam during $phase (${f.getMessage})", f)
 
-  final case class SamRegisterCollectionException(errorCode: StatusCode) extends Exception(s"Can't register collection with Sam. Status code: ${errorCode.value}")
+  final case class SamRegisterCollectionException(errorCode: StatusCode)
+      extends Exception(s"Can't register collection with Sam. Status code: ${errorCode.value}")
 
   final case class CollectionAuthorizationRequest(user: User, collection: Collection, action: String)
 
   val SamDenialResponse = HttpResponse(status = StatusCodes.Forbidden, entity = new SamDenialException().getMessage)
 
-  def SamRegisterCollectionExceptionResp(statusCode: StatusCode) = HttpResponse(status = statusCode, entity = SamRegisterCollectionException(statusCode).getMessage)
+  def SamRegisterCollectionExceptionResp(statusCode: StatusCode) =
+    HttpResponse(status = statusCode, entity = SamRegisterCollectionException(statusCode).getMessage)
 
   case class UserStatusInfo(adminEnabled: Boolean, enabled: Boolean, userEmail: String, userSubjectId: String)
 
diff --git a/CromIAM/src/main/scala/cromiam/server/CromIamServer.scala b/CromIAM/src/main/scala/cromiam/server/CromIamServer.scala
index 9f5af038b12..b18366490c5 100644
--- a/CromIAM/src/main/scala/cromiam/server/CromIamServer.scala
+++ b/CromIAM/src/main/scala/cromiam/server/CromIamServer.scala
@@ -15,7 +15,6 @@ import org.broadinstitute.dsde.workbench.util.health.Subsystems.{Cromwell, Sam}
 
 import scala.concurrent.{ExecutionContext, ExecutionContextExecutor, Future, Promise}
 
-
 object CromIamServer extends HttpApp with CromIamApiService with SwaggerService {
 
   final val rootConfig: Config = ConfigFactory.load()
@@ -35,21 +34,28 @@ object CromIamServer extends HttpApp with CromIamApiService with SwaggerService
     If there is a reason then leave a comment why there should be two actor systems.
     https://github.com/broadinstitute/cromwell/issues/3851
      */
-    CromIamServer.startServer(configuration.cromIamConfig.http.interface, configuration.cromIamConfig.http.port, configuration.cromIamConfig.serverSettings)
+    CromIamServer.startServer(configuration.cromIamConfig.http.interface,
+                              configuration.cromIamConfig.http.port,
+                              configuration.cromIamConfig.serverSettings
+    )
   }
 
-  override implicit val system: ActorSystem = ActorSystem()
-  override implicit lazy val executor: ExecutionContextExecutor = system.dispatcher
-  override implicit val materializer: ActorMaterializer = ActorMaterializer()
+  implicit override val system: ActorSystem = ActorSystem()
+  implicit override lazy val executor: ExecutionContextExecutor = system.dispatcher
+  implicit override val materializer: ActorMaterializer = ActorMaterializer()
 
   override val log = Logging(system, getClass)
 
   override val routes: Route = allRoutes ~ swaggerUiResourceRoute
 
-  override val statusService: StatusService = new StatusService(() => Map(Cromwell -> cromwellClient.subsystemStatus(), Sam -> samClient.subsystemStatus()))
+  override val statusService: StatusService = new StatusService(() =>
+    Map(Cromwell -> cromwellClient.subsystemStatus(), Sam -> samClient.subsystemStatus())
+  )
 
   // Override default shutdownsignal which was just "hit return/enter"
-  override def waitForShutdownSignal(actorSystem: ActorSystem)(implicit executionContext: ExecutionContext): Future[Done] = {
+  override def waitForShutdownSignal(
+    actorSystem: ActorSystem
+  )(implicit executionContext: ExecutionContext): Future[Done] = {
     val promise = Promise[Done]()
     sys.addShutdownHook {
       // we can add anything we want the server to do when someone shutdowns the server (Ctrl-c)
diff --git a/CromIAM/src/main/scala/cromiam/server/config/CromIamServerConfig.scala b/CromIAM/src/main/scala/cromiam/server/config/CromIamServerConfig.scala
index 8d27c7b980d..ce8c5934acd 100644
--- a/CromIAM/src/main/scala/cromiam/server/config/CromIamServerConfig.scala
+++ b/CromIAM/src/main/scala/cromiam/server/config/CromIamServerConfig.scala
@@ -15,7 +15,8 @@ import scala.util.{Failure, Success, Try}
 final case class CromIamServerConfig(cromIamConfig: CromIamConfig,
                                      cromwellConfig: ServiceConfig,
                                      samConfig: SamClientConfig,
-                                     swaggerOauthConfig: SwaggerOauthConfig)
+                                     swaggerOauthConfig: SwaggerOauthConfig
+)
 
 object CromIamServerConfig {
   def getFromConfig(conf: Config): ErrorOr[CromIamServerConfig] = {
@@ -27,22 +28,28 @@ object CromIamServerConfig {
     (cromIamConfig, cromwellConfig, samConfig, googleConfig) mapN CromIamServerConfig.apply
   }
 
-  private[config] def getValidatedConfigPath[A](conf: Config, path: String, getter: (Config, String) => A, default: Option[A] = None): ErrorOr[A] = {
+  private[config] def getValidatedConfigPath[A](conf: Config,
+                                                path: String,
+                                                getter: (Config, String) => A,
+                                                default: Option[A] = None
+  ): ErrorOr[A] =
     if (conf.hasPath(path)) {
       Try(getter.apply(conf, path)) match {
         case Success(s) => s.validNel
         case Failure(e) => s"Unable to read valid value at '$path': ${e.getMessage}".invalidNel
       }
-    } else default match {
-      case Some(d) => d.validNel
-      case None => s"Configuration does not have path $path".invalidNel
-    }
-  }
+    } else
+      default match {
+        case Some(d) => d.validNel
+        case None => s"Configuration does not have path $path".invalidNel
+      }
 
-  private[config] implicit final class ValidatingConfig(val conf: Config) extends AnyVal {
-    def getValidatedString(path: String, default: Option[String] = None): ErrorOr[String] = getValidatedConfigPath(conf, path, (c, p) => c.getString(p), default)
+  implicit final private[config] class ValidatingConfig(val conf: Config) extends AnyVal {
+    def getValidatedString(path: String, default: Option[String] = None): ErrorOr[String] =
+      getValidatedConfigPath(conf, path, (c, p) => c.getString(p), default)
     def getValidatedInt(path: String): ErrorOr[Int] = getValidatedConfigPath(conf, path, (c, p) => c.getInt(p))
-    def getValidatedStringList(path: String): ErrorOr[List[String]] = getValidatedConfigPath[List[String]](conf, path, (c, p) => c.getStringList(p).asScala.toList)
+    def getValidatedStringList(path: String): ErrorOr[List[String]] =
+      getValidatedConfigPath[List[String]](conf, path, (c, p) => c.getStringList(p).asScala.toList)
   }
 }
 
@@ -50,13 +57,12 @@ final case class CromIamConfig(http: ServiceConfig, serverSettings: ServerSettin
 
 object CromIamConfig {
 
-  private def getValidatedServerSettings(conf: Config): ErrorOr[ServerSettings] = {
+  private def getValidatedServerSettings(conf: Config): ErrorOr[ServerSettings] =
     Try(ServerSettings(conf)) match {
       case Success(serverSettings) => serverSettings.validNel
       case Failure(e) =>
         s"Unable to generate server settings from configuration file: ${e.getMessage}".invalidNel
     }
-  }
 
   private[config] def getFromConfig(conf: Config, basePath: String): ErrorOr[CromIamConfig] = {
     val serviceConfig = ServiceConfig.getFromConfig(conf, basePath)
@@ -94,6 +100,9 @@ object SwaggerOauthConfig {
   private[config] def getFromConfig(conf: Config, basePath: String): ErrorOr[SwaggerOauthConfig] = {
     def getValidatedOption(option: String) = conf.getValidatedString(s"$basePath.$option")
 
-    (getValidatedOption("client_id"), getValidatedOption("realm"), getValidatedOption("app_name")) mapN SwaggerOauthConfig.apply
-   }
+    (getValidatedOption("client_id"),
+     getValidatedOption("realm"),
+     getValidatedOption("app_name")
+    ) mapN SwaggerOauthConfig.apply
+  }
 }
diff --git a/CromIAM/src/main/scala/cromiam/server/status/StatusCheckedSubsystem.scala b/CromIAM/src/main/scala/cromiam/server/status/StatusCheckedSubsystem.scala
index 7aa6c0af752..b267b201bb0 100644
--- a/CromIAM/src/main/scala/cromiam/server/status/StatusCheckedSubsystem.scala
+++ b/CromIAM/src/main/scala/cromiam/server/status/StatusCheckedSubsystem.scala
@@ -1,7 +1,7 @@
 package cromiam.server.status
 
 import com.softwaremill.sttp.asynchttpclient.future.AsyncHttpClientFutureBackend
-import com.softwaremill.sttp.{Uri, sttp}
+import com.softwaremill.sttp.{sttp, Uri}
 import org.broadinstitute.dsde.workbench.util.health.SubsystemStatus
 
 import scala.concurrent.{ExecutionContext, Future}
@@ -18,12 +18,11 @@ trait StatusCheckedSubsystem {
     * Make a call to the status endpoint. If we receive a 200 OK fill in the SubsystemStatus w/ OK = true and no
     * error messages, otherwise OK = false and include the response body
     */
-  def subsystemStatus()(implicit ec: ExecutionContext): Future[SubsystemStatus] = {
+  def subsystemStatus()(implicit ec: ExecutionContext): Future[SubsystemStatus] =
     sttp.get(statusUri).send() map { x =>
       x.body match {
         case Right(_) => SubsystemStatus(true, None)
         case Left(errors) => SubsystemStatus(false, Option(List(errors)))
       }
     }
-  }
 }
diff --git a/CromIAM/src/main/scala/cromiam/server/status/StatusService.scala b/CromIAM/src/main/scala/cromiam/server/status/StatusService.scala
index 97b16e98a5e..c3f38865224 100644
--- a/CromIAM/src/main/scala/cromiam/server/status/StatusService.scala
+++ b/CromIAM/src/main/scala/cromiam/server/status/StatusService.scala
@@ -15,13 +15,14 @@ import scala.concurrent.duration._
   */
 class StatusService(checkStatus: () => Map[Subsystem, Future[SubsystemStatus]],
                     initialDelay: FiniteDuration = Duration.Zero,
-                    pollInterval: FiniteDuration = 1.minute)(implicit system: ActorSystem, executionContext: ExecutionContext) {
+                    pollInterval: FiniteDuration = 1.minute
+)(implicit system: ActorSystem, executionContext: ExecutionContext) {
   implicit val askTimeout = Timeout(5.seconds)
 
   private val healthMonitor = system.actorOf(HealthMonitor.props(Set(Cromwell, Sam))(checkStatus), "HealthMonitorActor")
 
   system.scheduler.schedule(initialDelay, pollInterval, healthMonitor, HealthMonitor.CheckAll)
 
-  def status(): Future[StatusCheckResponse] = healthMonitor.ask(GetCurrentStatus).asInstanceOf[Future[StatusCheckResponse]]
+  def status(): Future[StatusCheckResponse] =
+    healthMonitor.ask(GetCurrentStatus).asInstanceOf[Future[StatusCheckResponse]]
 }
-
diff --git a/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala b/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
index 7a16e5ea797..d046694b0f9 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/CromIamApiService.scala
@@ -16,7 +16,12 @@ import cromiam.auth.{Collection, User}
 import cromiam.cromwell.CromwellClient
 import cromiam.instrumentation.CromIamInstrumentation
 import cromiam.sam.SamClient
-import cromiam.sam.SamClient.{CollectionAuthorizationRequest, SamConnectionFailure, SamDenialException, SamDenialResponse}
+import cromiam.sam.SamClient.{
+  CollectionAuthorizationRequest,
+  SamConnectionFailure,
+  SamDenialException,
+  SamDenialResponse
+}
 import cromiam.server.config.CromIamServerConfig
 import cromiam.server.status.StatusService
 import cromiam.webservice.CromIamApiService._
@@ -30,12 +35,13 @@ trait SwaggerService extends SwaggerUiResourceHttpService {
 }
 
 // NB: collection name *must* follow label value rules in cromwell. This needs to be documented somewhere. (although those restrictions are soon to die)
-trait CromIamApiService extends RequestSupport
-  with EngineRouteSupport
-  with SubmissionSupport
-  with QuerySupport
-  with WomtoolRouteSupport
-  with CromIamInstrumentation {
+trait CromIamApiService
+    extends RequestSupport
+    with EngineRouteSupport
+    with SubmissionSupport
+    with QuerySupport
+    with WomtoolRouteSupport
+    with CromIamInstrumentation {
 
   implicit val system: ActorSystem
   implicit def executor: ExecutionContextExecutor
@@ -44,23 +50,23 @@ trait CromIamApiService extends RequestSupport
   protected def rootConfig: Config
   protected def configuration: CromIamServerConfig
 
-  override lazy val serviceRegistryActor: ActorRef = system.actorOf(ServiceRegistryActor.props(rootConfig), "ServiceRegistryActor")
+  override lazy val serviceRegistryActor: ActorRef =
+    system.actorOf(ServiceRegistryActor.props(rootConfig), "ServiceRegistryActor")
 
   val log: LoggingAdapter
 
-  val CromIamExceptionHandler: ExceptionHandler = {
-  ExceptionHandler {
-      case e: Exception =>
-        log.error(e, "Request failed {}", e)
-        complete(HttpResponse(InternalServerError, entity = e.getMessage)) // FIXME: use workbench-model ErrorReport
+  val CromIamExceptionHandler: ExceptionHandler =
+    ExceptionHandler { case e: Exception =>
+      log.error(e, "Request failed {}", e)
+      complete(HttpResponse(InternalServerError, entity = e.getMessage)) // FIXME: use workbench-model ErrorReport
     }
-  }
 
   lazy val cromwellClient = new CromwellClient(configuration.cromwellConfig.scheme,
-    configuration.cromwellConfig.interface,
-    configuration.cromwellConfig.port,
-    log,
-    serviceRegistryActor)
+                                               configuration.cromwellConfig.interface,
+                                               configuration.cromwellConfig.port,
+                                               log,
+                                               serviceRegistryActor
+  )
 
   lazy val samClient = new SamClient(
     configuration.samConfig.http.scheme,
@@ -68,7 +74,8 @@ trait CromIamApiService extends RequestSupport
     configuration.samConfig.http.port,
     configuration.samConfig.checkSubmitWhitelist,
     log,
-    serviceRegistryActor)
+    serviceRegistryActor
+  )
 
   val statusService: StatusService
 
@@ -76,8 +83,7 @@ trait CromIamApiService extends RequestSupport
     workflowLogsRoute ~ abortRoute ~ metadataRoute ~ timingRoute ~ statusRoute ~ backendRoute ~ labelPatchRoute ~
     callCacheDiffRoute ~ labelGetRoute ~ releaseHoldRoute
 
-
-  val allRoutes: Route = handleExceptions(CromIamExceptionHandler) { workflowRoutes ~ engineRoutes ~ womtoolRoutes }
+  val allRoutes: Route = handleExceptions(CromIamExceptionHandler)(workflowRoutes ~ engineRoutes ~ womtoolRoutes)
 
   def abortRoute: Route = path("api" / "workflows" / Segment / Segment / Abort) { (_, workflowId) =>
     post {
@@ -90,8 +96,8 @@ trait CromIamApiService extends RequestSupport
     }
   }
 
-  //noinspection MutatorLikeMethodIsParameterless
-  def releaseHoldRoute: Route =  path("api" / "workflows" / Segment / Segment / ReleaseHold) { (_, workflowId) =>
+  // noinspection MutatorLikeMethodIsParameterless
+  def releaseHoldRoute: Route = path("api" / "workflows" / Segment / Segment / ReleaseHold) { (_, workflowId) =>
     post {
       extractUserAndStrictRequest { (user, req) =>
         logUserWorkflowAction(user, workflowId, ReleaseHold)
@@ -109,22 +115,22 @@ trait CromIamApiService extends RequestSupport
   def statusRoute: Route = workflowGetRouteWithId("status")
   def labelGetRoute: Route = workflowGetRouteWithId(Labels)
 
-  def labelPatchRoute: Route = {
+  def labelPatchRoute: Route =
     path("api" / "workflows" / Segment / Segment / Labels) { (_, workflowId) =>
       patch {
         extractUserAndStrictRequest { (user, req) =>
           entity(as[String]) { labels =>
             logUserWorkflowAction(user, workflowId, Labels)
-            validateLabels(Option(labels)) { _ => // Not using the labels, just using this to verify they didn't specify labels we don't want them to
-              complete {
-                authorizeUpdateThenForwardToCromwell(user, workflowId, req).asHttpResponse
-              }
+            validateLabels(Option(labels)) {
+              _ => // Not using the labels, just using this to verify they didn't specify labels we don't want them to
+                complete {
+                  authorizeUpdateThenForwardToCromwell(user, workflowId, req).asHttpResponse
+                }
             }
           }
         }
       }
     }
-  }
 
   def backendRoute: Route = workflowGetRoute("backends")
 
@@ -137,7 +143,10 @@ trait CromIamApiService extends RequestSupport
           complete {
             (paramMap.get("workflowA"), paramMap.get("workflowB")) match {
               case (Some(a), Some(b)) => authorizeReadThenForwardToCromwell(user, List(a, b), req).asHttpResponse
-              case _ => HttpResponse(status = BadRequest, entity = "Must supply both workflowA and workflowB to the /callcaching/diff endpoint")
+              case _ =>
+                HttpResponse(status = BadRequest,
+                             entity = "Must supply both workflowA and workflowB to the /callcaching/diff endpoint"
+                )
             }
           }
         }
@@ -162,31 +171,31 @@ trait CromIamApiService extends RequestSupport
     */
   private def workflowGetRouteWithId(urlSuffix: String): Route = workflowRoute(urlSuffix, get)
 
-  private def workflowRoute(urlSuffix: String, method: Directive0): Route = path("api" / "workflows" / Segment / Segment / urlSuffix) { (_, workflowId) =>
-    method {
-      extractUserAndStrictRequest { (user, req) =>
-        logUserWorkflowAction(user, workflowId, urlSuffix)
-        complete {
-          authorizeReadThenForwardToCromwell(user, List(workflowId), req).asHttpResponse
+  private def workflowRoute(urlSuffix: String, method: Directive0): Route =
+    path("api" / "workflows" / Segment / Segment / urlSuffix) { (_, workflowId) =>
+      method {
+        extractUserAndStrictRequest { (user, req) =>
+          logUserWorkflowAction(user, workflowId, urlSuffix)
+          complete {
+            authorizeReadThenForwardToCromwell(user, List(workflowId), req).asHttpResponse
+          }
         }
       }
     }
-  }
 
   private def authorizeThenForwardToCromwell(user: User,
                                              workflowIds: List[String],
                                              action: String,
                                              request: HttpRequest,
-                                             cromwellClient: CromwellClient):
-  FailureResponseOrT[HttpResponse] = {
-    def authForCollection(collection: Collection): FailureResponseOrT[Unit] = {
+                                             cromwellClient: CromwellClient
+  ): FailureResponseOrT[HttpResponse] = {
+    def authForCollection(collection: Collection): FailureResponseOrT[Unit] =
       samClient.requestAuth(CollectionAuthorizationRequest(user, collection, action), request) mapErrorWith {
         case e: SamDenialException => IO.raiseError(e)
         case e =>
           log.error(e, "Unable to connect to Sam {}", e)
           IO.raiseError(SamConnectionFailure("authorization", e))
       }
-    }
 
     val cromwellResponseT = for {
       rootWorkflowIds <- workflowIds.traverse(cromwellClient.getRootWorkflow(_, user, request))
@@ -209,31 +218,29 @@ trait CromIamApiService extends RequestSupport
   private def authorizeReadThenForwardToCromwell(user: User,
                                                  workflowIds: List[String],
                                                  request: HttpRequest
-                                                ): FailureResponseOrT[HttpResponse] = {
-    authorizeThenForwardToCromwell(
-      user = user,
-      workflowIds = workflowIds,
-      action = "view",
-      request = request,
-      cromwellClient = cromwellClient)
-  }
+  ): FailureResponseOrT[HttpResponse] =
+    authorizeThenForwardToCromwell(user = user,
+                                   workflowIds = workflowIds,
+                                   action = "view",
+                                   request = request,
+                                   cromwellClient = cromwellClient
+    )
 
   private def authorizeUpdateThenForwardToCromwell(user: User,
                                                    workflowId: String,
                                                    request: HttpRequest
-                                                  ): FailureResponseOrT[HttpResponse] = {
-    authorizeThenForwardToCromwell(
-      user = user,
-      workflowIds = List(workflowId),
-      action = "update",
-      request = request,
-      cromwellClient = cromwellClient)
-  }
+  ): FailureResponseOrT[HttpResponse] =
+    authorizeThenForwardToCromwell(user = user,
+                                   workflowIds = List(workflowId),
+                                   action = "update",
+                                   request = request,
+                                   cromwellClient = cromwellClient
+    )
 
   private def authorizeAbortThenForwardToCromwell(user: User,
                                                   workflowId: String,
                                                   request: HttpRequest
-                                                 ): FailureResponseOrT[HttpResponse] = {
+  ): FailureResponseOrT[HttpResponse] =
     // Do all the authing for the abort with "this" cromwell instance (cromwellClient), but the actual abort command
     // must go to the dedicated abort server (cromwellAbortClient).
     authorizeThenForwardToCromwell(
@@ -243,13 +250,11 @@ trait CromIamApiService extends RequestSupport
       request = request,
       cromwellClient = cromwellClient
     )
-  }
 
   private def logUserAction(user: User, action: String) = log.info("User " + user.userId + " requesting " + action)
 
-  private def logUserWorkflowAction(user: User, wfId: String, action: String) = {
+  private def logUserWorkflowAction(user: User, wfId: String, action: String) =
     log.info("User " + user.userId + " requesting " + action + " with " + wfId)
-  }
 }
 
 object CromIamApiService {
diff --git a/CromIAM/src/main/scala/cromiam/webservice/EngineRouteSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/EngineRouteSupport.scala
index 5719bda3479..42f69ee6449 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/EngineRouteSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/EngineRouteSupport.scala
@@ -13,7 +13,6 @@ import org.broadinstitute.dsde.workbench.util.health.StatusJsonSupport._
 
 import scala.concurrent.ExecutionContextExecutor
 
-
 trait EngineRouteSupport extends RequestSupport with SprayJsonSupport {
   val statusService: StatusService
   val cromwellClient: CromwellClient
@@ -25,7 +24,7 @@ trait EngineRouteSupport extends RequestSupport with SprayJsonSupport {
   def versionRoute: Route = path("engine" / Segment / "version") { _ =>
     get {
       extractStrictRequest { req =>
-        complete { cromwellClient.forwardToCromwell(req).asHttpResponse }
+        complete(cromwellClient.forwardToCromwell(req).asHttpResponse)
       }
     }
   }
@@ -39,10 +38,11 @@ trait EngineRouteSupport extends RequestSupport with SprayJsonSupport {
     }
   }
 
-  def statsRoute: Route = path("engine" / Segment / "stats") { _ => complete(CromIamStatsForbidden) }
+  def statsRoute: Route = path("engine" / Segment / "stats")(_ => complete(CromIamStatsForbidden))
 
 }
 
 object EngineRouteSupport {
-  private[webservice] val CromIamStatsForbidden = HttpResponse(status = Forbidden, entity = "CromIAM does not allow access to the /stats endpoint")
+  private[webservice] val CromIamStatsForbidden =
+    HttpResponse(status = Forbidden, entity = "CromIAM does not allow access to the /stats endpoint")
 }
diff --git a/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala b/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
index e9397605c6a..68ad1f21230 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
@@ -43,7 +43,7 @@ trait QuerySupport extends RequestSupport {
     post {
       preprocessQuery { (user, collections, request) =>
         processLabelsForPostQuery(user, collections) { entity =>
-          complete { cromwellClient.forwardToCromwell(request.withEntity(entity)).asHttpResponse }
+          complete(cromwellClient.forwardToCromwell(request.withEntity(entity)).asHttpResponse)
         }
       }
     }
@@ -54,7 +54,7 @@ trait QuerySupport extends RequestSupport {
     * retrieves the collections for the user, grabs the underlying HttpRequest and forwards it on to the specific
     * directive
     */
-  private def preprocessQuery: Directive[(User, List[Collection], HttpRequest)] = {
+  private def preprocessQuery: Directive[(User, List[Collection], HttpRequest)] =
     extractUserAndStrictRequest tflatMap { case (user, cromIamRequest) =>
       log.info("Received query " + cromIamRequest.method.value + " request for user " + user.userId)
 
@@ -71,13 +71,12 @@ trait QuerySupport extends RequestSupport {
           throw new RuntimeException(s"Unable to look up collections for user ${user.userId}: ${e.getMessage}", e)
       }
     }
-  }
 
   /**
     * Will verify that none of the GET query parameters are specifying the collection label, and then tack
     * on query parameters for the user's collections on to the query URI
     */
-  private def processLabelsForGetQuery(user: User, collections: List[Collection]): Directive1[Uri] = {
+  private def processLabelsForGetQuery(user: User, collections: List[Collection]): Directive1[Uri] =
     extractUri flatMap { uri =>
       val query = uri.query()
 
@@ -95,7 +94,6 @@ trait QuerySupport extends RequestSupport {
 
       provide(uri.withQuery(newQueryBuilder.result()))
     }
-  }
 
   /**
     * Will verify that none of the POSTed query parameters are specifying the collection label, and then tack
@@ -115,7 +113,7 @@ trait QuerySupport extends RequestSupport {
               case jsObject if jsObject.fields.keySet.exists(key => key.equalsIgnoreCase(LabelOrKey)) =>
                 jsObject.fields.values.map(_.convertTo[String])
             }
-            ).flatten
+          ).flatten
           // DO NOT REMOVE THE NEXT LINE WITHOUT READING THE SCALADOC ON ensureNoLabelOrs
           ensureNoLabelOrs(user, labelOrs)
 
@@ -152,12 +150,11 @@ trait QuerySupport extends RequestSupport {
     * - https://github.com/persvr/rql#rql-rules
     * - https://github.com/jirutka/rsql-parser#grammar-and-semantic
     */
-  protected[this] def ensureNoLabelOrs(user: User, labelOrs: Iterable[String]): Unit = {
+  protected[this] def ensureNoLabelOrs(user: User, labelOrs: Iterable[String]): Unit =
     labelOrs.toList match {
       case Nil => ()
       case head :: tail => throw new LabelContainsOrException(user, NonEmptyList(head, tail))
     }
-  }
 
   /**
     * Returns the user's collections as a set of labels
@@ -169,12 +166,14 @@ trait QuerySupport extends RequestSupport {
 }
 
 object QuerySupport {
-  final case class InvalidQueryException(e: Throwable) extends
-    Exception(s"Invalid JSON in query POST body: ${e.getMessage}", e)
-
-  final class LabelContainsOrException(val user: User, val labelOrs: NonEmptyList[String]) extends
-    Exception(s"User ${user.userId} submitted a labels query containing an OR which CromIAM is blocking: " +
-      labelOrs.toList.mkString("LABELS CONTAIN '", "' OR LABELS CONTAIN '", "'"))
+  final case class InvalidQueryException(e: Throwable)
+      extends Exception(s"Invalid JSON in query POST body: ${e.getMessage}", e)
+
+  final class LabelContainsOrException(val user: User, val labelOrs: NonEmptyList[String])
+      extends Exception(
+        s"User ${user.userId} submitted a labels query containing an OR which CromIAM is blocking: " +
+          labelOrs.toList.mkString("LABELS CONTAIN '", "' OR LABELS CONTAIN '", "'")
+      )
 
   val LabelAndKey = "label"
   val LabelOrKey = "labelor"
diff --git a/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
index c9b6a196368..22575738ae7 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/RequestSupport.scala
@@ -15,32 +15,34 @@ import cromiam.sam.SamClient
 import scala.util.{Failure, Success}
 
 trait RequestSupport {
-  def extractStrictRequest: Directive1[HttpRequest] = {
+  def extractStrictRequest: Directive1[HttpRequest] =
     toStrictEntity(Timeout) tflatMap { _ =>
       extractRequest flatMap { request =>
         provide(request)
       }
     }
-  }
 
   /**
     * Obtain both the user id header from the proxy as well as the bearer token and pass that back
     * into the route logic as a User object
     */
-  def extractUser: Directive1[User] = {
-    (headerValueByName("OIDC_CLAIM_user_id") & headerValuePF { case a: Authorization => a }) tmap { case (userId, auth) =>
-      User(WorkbenchUserId(userId), auth)
+  def extractUser: Directive1[User] =
+    (headerValueByName("OIDC_CLAIM_user_id") & headerValuePF { case a: Authorization => a }) tmap {
+      case (userId, auth) =>
+        User(WorkbenchUserId(userId), auth)
     }
-  }
 
-  def extractUserAndStrictRequest: Directive[(User, HttpRequest)] = {
+  def extractUserAndStrictRequest: Directive[(User, HttpRequest)] =
     for {
       user <- extractUser
       request <- extractStrictRequest
     } yield (user, request)
-  }
 
-  def forwardIfUserEnabled(user: User, req: HttpRequest, cromwellClient: CromwellClient, samClient: SamClient): Route = {
+  def forwardIfUserEnabled(user: User,
+                           req: HttpRequest,
+                           cromwellClient: CromwellClient,
+                           samClient: SamClient
+  ): Route = {
     import cromwell.api.model.EnhancedFailureResponseOrHttpResponseT
 
     onComplete(samClient.isUserEnabledSam(user, req).value.unsafeToFuture()) {
@@ -52,7 +54,8 @@ trait RequestSupport {
           }
         }
       case Failure(e) =>
-        val message = s"Unable to look up enablement status for user ${user.userId}: ${e.getMessage}. Please try again later."
+        val message =
+          s"Unable to look up enablement status for user ${user.userId}: ${e.getMessage}. Please try again later."
         throw new RuntimeException(message, e)
     }
   }
diff --git a/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
index 52a05d1cdc7..79c66a77313 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
@@ -7,7 +7,7 @@ import akka.http.scaladsl.server._
 import akka.stream.ActorMaterializer
 import akka.util.ByteString
 import cats.effect.IO
-import cromiam.auth.Collection.{CollectionLabelName, LabelsKey, validateLabels}
+import cromiam.auth.Collection.{validateLabels, CollectionLabelName, LabelsKey}
 import cromiam.auth.{Collection, User}
 import cromiam.cromwell.CromwellClient
 import cromiam.sam.SamClient
@@ -57,16 +57,18 @@ trait SubmissionSupport extends RequestSupport {
 
   private def forwardSubmissionToCromwell(user: User,
                                           collection: Collection,
-                                          submissionRequest: HttpRequest): FailureResponseOrT[HttpResponse] = {
-    log.info("Forwarding submission request for " + user.userId + " with collection " + collection.name + " to Cromwell")
+                                          submissionRequest: HttpRequest
+  ): FailureResponseOrT[HttpResponse] = {
+    log.info(
+      "Forwarding submission request for " + user.userId + " with collection " + collection.name + " to Cromwell"
+    )
 
-    def registerWithSam(collection: Collection, httpRequest: HttpRequest): FailureResponseOrT[Unit] = {
+    def registerWithSam(collection: Collection, httpRequest: HttpRequest): FailureResponseOrT[Unit] =
       samClient.requestSubmission(user, collection, httpRequest) mapErrorWith {
         case e: SamDenialException => IO.raiseError(e)
         case SamRegisterCollectionException(statusCode) => IO.raiseError(SamRegisterCollectionException(statusCode))
         case e => IO.raiseError(SamConnectionFailure("new workflow registration", e))
       }
-    }
 
     FailureResponseOrT(
       (for {
@@ -81,36 +83,34 @@ trait SubmissionSupport extends RequestSupport {
 }
 
 object SubmissionSupport {
-  def extractCollection(user: User): Directive1[Collection] = {
+  def extractCollection(user: User): Directive1[Collection] =
     formField(CollectionNameKey.?) map { maybeCollectionName =>
       maybeCollectionName.map(Collection(_)).getOrElse(Collection.forUser(user))
     }
-  }
 
-  def extractSubmission(user: User): Directive1[WorkflowSubmission] = {
+  def extractSubmission(user: User): Directive1[WorkflowSubmission] =
     (
       extractCollection(user) &
-      formFields((
-        WorkflowSourceKey.?,
-        WorkflowUrlKey.?,
-        WorkflowTypeKey.?,
-        WorkflowTypeVersionKey.?,
-        WorkflowInputsKey.?,
-        WorkflowOptionsKey.?,
-        WorkflowOnHoldKey.as[Boolean].?,
-        WorkflowDependenciesKey.as[ByteString].?)) &
-      extractLabels &
-      extractInputAux
+        formFields(
+          (WorkflowSourceKey.?,
+           WorkflowUrlKey.?,
+           WorkflowTypeKey.?,
+           WorkflowTypeVersionKey.?,
+           WorkflowInputsKey.?,
+           WorkflowOptionsKey.?,
+           WorkflowOnHoldKey.as[Boolean].?,
+           WorkflowDependenciesKey.as[ByteString].?
+          )
+        ) &
+        extractLabels &
+        extractInputAux
     ).as(WorkflowSubmission)
-  }
 
-  def extractLabels: Directive1[Option[Map[String, JsValue]]] = {
+  def extractLabels: Directive1[Option[Map[String, JsValue]]] =
     formField(LabelsKey.?) flatMap validateLabels
-  }
 
-  def extractInputAux: Directive1[Map[String, String]] = {
+  def extractInputAux: Directive1[Map[String, String]] =
     formFieldMap.map(_.view.filterKeys(_.startsWith(WorkflowInputsAuxPrefix)).toMap)
-  }
 
   // FIXME: Much like CromwellClient see if there are ways of unifying this a bit w/ the mothership
   final case class WorkflowSubmission(collection: Collection,
@@ -123,32 +123,61 @@ object SubmissionSupport {
                                       workflowOnHold: Option[Boolean],
                                       workflowDependencies: Option[ByteString],
                                       origLabels: Option[Map[String, JsValue]],
-                                      workflowInputsAux: Map[String, String]) {
+                                      workflowInputsAux: Map[String, String]
+  ) {
     // For auto-validation, if origLabels defined, can't have CaaS collection label set. Was checked previously, but ...
     require(origLabels.forall(!_.keySet.contains(CollectionLabelName)))
 
     // Inject the collection name into the labels and convert to a String
     private val collectionLabels = Map(CollectionLabelName -> JsString(collection.name))
-    private val labels: String = JsObject(origLabels.map(o => o ++ collectionLabels).getOrElse(collectionLabels)).toString
+    private val labels: String = JsObject(
+      origLabels.map(o => o ++ collectionLabels).getOrElse(collectionLabels)
+    ).toString
 
     val entity: MessageEntity = {
-      val sourcePart = workflowSource map { s => Multipart.FormData.BodyPart(WorkflowSourceKey, HttpEntity(MediaTypes.`application/json`, s)) }
-      val urlPart = workflowUrl map { u => Multipart.FormData.BodyPart(WorkflowUrlKey, HttpEntity(MediaTypes.`application/json`, u))}
-      val typePart = workflowType map { t => Multipart.FormData.BodyPart(WorkflowTypeKey, HttpEntity(MediaTypes.`application/json`, t)) }
-      val typeVersionPart = workflowTypeVersion map { v => Multipart.FormData.BodyPart(WorkflowTypeVersionKey, HttpEntity(MediaTypes.`application/json`, v)) }
-      val inputsPart = workflowInputs map { i => Multipart.FormData.BodyPart(WorkflowInputsKey, HttpEntity(MediaTypes.`application/json`, i)) }
-      val optionsPart = workflowOptions map { o => Multipart.FormData.BodyPart(WorkflowOptionsKey, HttpEntity(MediaTypes.`application/json`, o)) }
-      val importsPart = workflowDependencies map { d => Multipart.FormData.BodyPart(WorkflowDependenciesKey, HttpEntity(MediaTypes.`application/octet-stream`, d)) }
-      val onHoldPart = workflowOnHold map { h => Multipart.FormData.BodyPart(WorkflowOnHoldKey, HttpEntity(h.toString)) }
+      val sourcePart = workflowSource map { s =>
+        Multipart.FormData.BodyPart(WorkflowSourceKey, HttpEntity(MediaTypes.`application/json`, s))
+      }
+      val urlPart = workflowUrl map { u =>
+        Multipart.FormData.BodyPart(WorkflowUrlKey, HttpEntity(MediaTypes.`application/json`, u))
+      }
+      val typePart = workflowType map { t =>
+        Multipart.FormData.BodyPart(WorkflowTypeKey, HttpEntity(MediaTypes.`application/json`, t))
+      }
+      val typeVersionPart = workflowTypeVersion map { v =>
+        Multipart.FormData.BodyPart(WorkflowTypeVersionKey, HttpEntity(MediaTypes.`application/json`, v))
+      }
+      val inputsPart = workflowInputs map { i =>
+        Multipart.FormData.BodyPart(WorkflowInputsKey, HttpEntity(MediaTypes.`application/json`, i))
+      }
+      val optionsPart = workflowOptions map { o =>
+        Multipart.FormData.BodyPart(WorkflowOptionsKey, HttpEntity(MediaTypes.`application/json`, o))
+      }
+      val importsPart = workflowDependencies map { d =>
+        Multipart.FormData.BodyPart(WorkflowDependenciesKey, HttpEntity(MediaTypes.`application/octet-stream`, d))
+      }
+      val onHoldPart = workflowOnHold map { h =>
+        Multipart.FormData.BodyPart(WorkflowOnHoldKey, HttpEntity(h.toString))
+      }
       val labelsPart = Multipart.FormData.BodyPart(LabelsKey, HttpEntity(MediaTypes.`application/json`, labels))
-      val parts = List(sourcePart, urlPart, typePart, typeVersionPart, inputsPart, optionsPart, importsPart, onHoldPart, Option(labelsPart)).flatten ++ auxParts
+      val parts = List(sourcePart,
+                       urlPart,
+                       typePart,
+                       typeVersionPart,
+                       inputsPart,
+                       optionsPart,
+                       importsPart,
+                       onHoldPart,
+                       Option(labelsPart)
+      ).flatten ++ auxParts
 
       Multipart.FormData(parts: _*).toEntity()
     }
 
-    private def auxParts = {
-      workflowInputsAux map { case (k, v) => Multipart.FormData.BodyPart(k, HttpEntity(MediaTypes.`application/json`, v)) }
-    }
+    private def auxParts =
+      workflowInputsAux map { case (k, v) =>
+        Multipart.FormData.BodyPart(k, HttpEntity(MediaTypes.`application/json`, v))
+      }
   }
 
   // FIXME: Unify these w/ Cromwell.PartialWorkflowSources (via common?)
diff --git a/CromIAM/src/main/scala/cromiam/webservice/SwaggerUiHttpService.scala b/CromIAM/src/main/scala/cromiam/webservice/SwaggerUiHttpService.scala
index 9fed12ca163..874949a5244 100644
--- a/CromIAM/src/main/scala/cromiam/webservice/SwaggerUiHttpService.scala
+++ b/CromIAM/src/main/scala/cromiam/webservice/SwaggerUiHttpService.scala
@@ -27,7 +27,7 @@ trait SwaggerUiHttpService extends Directives {
     s"META-INF/resources/webjars/swagger-ui/$swaggerUiVersion"
   }
 
-  private val serveIndex: server.Route = {
+  private val serveIndex: server.Route =
     mapResponseEntity { entityFromJar =>
       entityFromJar.transformDataBytes(Flow.fromFunction[ByteString, ByteString] { original: ByteString =>
         ByteString(rewriteSwaggerIndex(original.utf8String))
@@ -35,14 +35,13 @@ trait SwaggerUiHttpService extends Directives {
     } {
       getFromResource(s"$resourceDirectory/index.html")
     }
-  }
 
   /**
    * Serves up the swagger UI only. Redirects requests to the root of the UI path to the index.html.
    *
    * @return Route serving the swagger UI.
    */
-  final def swaggerUiRoute: Route = {
+  final def swaggerUiRoute: Route =
     pathEndOrSingleSlash {
       get {
         serveIndex
@@ -68,16 +67,15 @@ trait SwaggerUiHttpService extends Directives {
 
         }
       }
-  }
 
   /** Rewrite the swagger index.html. Default passes through the origin data. */
   protected def rewriteSwaggerIndex(original: String): String = {
     val swaggerOptions =
       s"""
-        |        validatorUrl: null,
-        |        apisSorter: "alpha",
-        |        oauth2RedirectUrl: window.location.origin + "/swagger/oauth2-redirect.html",
-        |        operationsSorter: "alpha"
+         |        validatorUrl: null,
+         |        apisSorter: "alpha",
+         |        oauth2RedirectUrl: window.location.origin + "/swagger/oauth2-redirect.html",
+         |        operationsSorter: "alpha"
       """.stripMargin
 
     val initOAuthOriginal = "window.ui = ui"
@@ -94,7 +92,6 @@ trait SwaggerUiHttpService extends Directives {
           |$initOAuthOriginal
           |""".stripMargin
 
-
     original
       .replace(initOAuthOriginal, initOAuthReplacement)
       .replace("""url: "https://petstore.swagger.io/v2/swagger.json"""", "url: 'cromiam.yaml'")
@@ -109,6 +106,7 @@ trait SwaggerUiHttpService extends Directives {
  * swagger UI, but defaults to "yaml". This is an alternative to spray-swagger's SwaggerHttpService.
  */
 trait SwaggerResourceHttpService {
+
   /**
    * @return The directory for the resource under the classpath, and in the url
    */
@@ -134,7 +132,8 @@ trait SwaggerResourceHttpService {
    */
   final def swaggerResourceRoute: Route = {
     // Serve CromIAM API docs from either `/swagger/cromiam.yaml` or just `cromiam.yaml`.
-    val swaggerDocsDirective = path(separateOnSlashes(swaggerDocsPath)) | path(s"$swaggerServiceName.$swaggerResourceType")
+    val swaggerDocsDirective =
+      path(separateOnSlashes(swaggerDocsPath)) | path(s"$swaggerServiceName.$swaggerResourceType")
     val route = get {
       swaggerDocsDirective {
         // Return /uiPath/serviceName.resourceType from the classpath resources.
diff --git a/CromIAM/src/test/scala/cromiam/auth/CollectionSpec.scala b/CromIAM/src/test/scala/cromiam/auth/CollectionSpec.scala
index 5f3f4fd3791..0ee89b9bbb6 100644
--- a/CromIAM/src/test/scala/cromiam/auth/CollectionSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/auth/CollectionSpec.scala
@@ -42,7 +42,6 @@ class CollectionSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     }
   }
 
-
   behavior of "validateLabels"
   it should "not throw exception when labels are valid" in {
     val labels = """{"key-1":"foo","key-2":"bar"}"""
diff --git a/CromIAM/src/test/scala/cromiam/cromwell/CromwellClientSpec.scala b/CromIAM/src/test/scala/cromiam/cromwell/CromwellClientSpec.scala
index ce6f16935d6..303aff01dc4 100644
--- a/CromIAM/src/test/scala/cromiam/cromwell/CromwellClientSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/cromwell/CromwellClientSpec.scala
@@ -39,25 +39,35 @@ class CromwellClientSpec extends AsyncFlatSpec with Matchers with BeforeAndAfter
   }
 
   "CromwellClient" should "eventually return a subworkflow's root workflow id" in {
-    cromwellClient.getRootWorkflow(SubworkflowId.id.toString, FictitiousUser, fakeHttpRequest).map(w => assert(w == RootWorkflowId.id.toString))
-      .asIo.unsafeToFuture()
+    cromwellClient
+      .getRootWorkflow(SubworkflowId.id.toString, FictitiousUser, fakeHttpRequest)
+      .map(w => assert(w == RootWorkflowId.id.toString))
+      .asIo
+      .unsafeToFuture()
   }
 
   it should "eventually return a top level workflow's ID when requesting root workflow id" in {
-    cromwellClient.getRootWorkflow(RootWorkflowId.id.toString, FictitiousUser, fakeHttpRequest).map(w => assert(w == RootWorkflowId.id.toString))
-      .asIo.unsafeToFuture()
+    cromwellClient
+      .getRootWorkflow(RootWorkflowId.id.toString, FictitiousUser, fakeHttpRequest)
+      .map(w => assert(w == RootWorkflowId.id.toString))
+      .asIo
+      .unsafeToFuture()
   }
 
   it should "properly fetch the collection for a workflow with a collection name" in {
-    cromwellClient.collectionForWorkflow(RootWorkflowId.id.toString, FictitiousUser, fakeHttpRequest).map(c =>
-      assert(c.name == CollectionName)
-    ).asIo.unsafeToFuture()
+    cromwellClient
+      .collectionForWorkflow(RootWorkflowId.id.toString, FictitiousUser, fakeHttpRequest)
+      .map(c => assert(c.name == CollectionName))
+      .asIo
+      .unsafeToFuture()
   }
 
   it should "throw an exception if the workflow doesn't have a collection" in {
     recoverToExceptionIf[IllegalArgumentException] {
-      cromwellClient.collectionForWorkflow(WorkflowIdWithoutCollection.id.toString, FictitiousUser, fakeHttpRequest)
-        .asIo.unsafeToFuture()
+      cromwellClient
+        .collectionForWorkflow(WorkflowIdWithoutCollection.id.toString, FictitiousUser, fakeHttpRequest)
+        .asIo
+        .unsafeToFuture()
     } map { exception =>
       assert(exception.getMessage == s"Workflow $WorkflowIdWithoutCollection has no associated collection")
     }
@@ -65,24 +75,25 @@ class CromwellClientSpec extends AsyncFlatSpec with Matchers with BeforeAndAfter
 }
 
 object CromwellClientSpec {
-  final class MockCromwellClient()(implicit system: ActorSystem,
-                                   ece: ExecutionContextExecutor,
-                                   materializer: ActorMaterializer)
-  extends CromwellClient("http", "bar", 1, NoLogging, ActorRef.noSender) {
+  final class MockCromwellClient()(implicit
+    system: ActorSystem,
+    ece: ExecutionContextExecutor,
+    materializer: ActorMaterializer
+  ) extends CromwellClient("http", "bar", 1, NoLogging, ActorRef.noSender) {
     override val cromwellApiClient: CromwellApiClient = new MockCromwellApiClient()
 
     override def sendTimingApi(statsDPath: InstrumentationPath,
                                timing: FiniteDuration,
                                prefixToStatsd: NonEmptyList[String]
-                              ): Unit = ()
+    ): Unit = ()
   }
 
   final class MockCromwellApiClient()(implicit actorSystem: ActorSystem, materializer: ActorMaterializer)
-    extends CromwellApiClient(new URL("http://foo.com"), "bar") {
+      extends CromwellApiClient(new URL("http://foo.com"), "bar") {
 
-
-    override def labels(workflowId: WorkflowId, headers: List[HttpHeader] = defaultHeaders)
-                       (implicit ec: ExecutionContext): FailureResponseOrT[WorkflowLabels] = {
+    override def labels(workflowId: WorkflowId, headers: List[HttpHeader] = defaultHeaders)(implicit
+      ec: ExecutionContext
+    ): FailureResponseOrT[WorkflowLabels] =
       if (workflowId == RootWorkflowId) {
         FailureResponseOrT.pure(FictitiousWorkflowLabelsWithCollection)
       } else if (workflowId == WorkflowIdWithoutCollection) {
@@ -92,18 +103,17 @@ object CromwellClientSpec {
           IO.raiseError(new RuntimeException("Unexpected workflow ID sent to MockCromwellApiClient"))
         }
       }
-    }
 
     override def metadata(workflowId: WorkflowId,
-                 args: Option[Map[String, List[String]]] = None,
-                 headers: List[HttpHeader] = defaultHeaders
-                )(implicit ec: ExecutionContext): FailureResponseOrT[WorkflowMetadata] = {
+                          args: Option[Map[String, List[String]]] = None,
+                          headers: List[HttpHeader] = defaultHeaders
+    )(implicit ec: ExecutionContext): FailureResponseOrT[WorkflowMetadata] =
       if (workflowId == RootWorkflowId) FailureResponseOrT.pure(RootWorkflowMetadata)
       else if (workflowId == SubworkflowId) FailureResponseOrT.pure(SubWorkflowMetadata)
-      else FailureResponseOrT[IO, HttpResponse, WorkflowMetadata] {
-        IO.raiseError(new RuntimeException("Unexpected workflow ID sent to MockCromwellApiClient"))
-      }
-    }
+      else
+        FailureResponseOrT[IO, HttpResponse, WorkflowMetadata] {
+          IO.raiseError(new RuntimeException("Unexpected workflow ID sent to MockCromwellApiClient"))
+        }
   }
 
   private val SubworkflowId = WorkflowId.fromString("58114f5c-f439-4488-8d73-092273cf92d9")
@@ -126,7 +136,8 @@ object CromwellClientSpec {
                                               }""")
 
   val CollectionName = "foo"
-  val FictitiousWorkflowLabelsWithCollection = WorkflowLabels(RootWorkflowId.id.toString, JsObject(Map("caas-collection-name" -> JsString(CollectionName))))
-  val FictitiousWorkflowLabelsWithoutCollection = WorkflowLabels(RootWorkflowId.id.toString, JsObject(Map("something" -> JsString("foo"))))
+  val FictitiousWorkflowLabelsWithCollection =
+    WorkflowLabels(RootWorkflowId.id.toString, JsObject(Map("caas-collection-name" -> JsString(CollectionName))))
+  val FictitiousWorkflowLabelsWithoutCollection =
+    WorkflowLabels(RootWorkflowId.id.toString, JsObject(Map("something" -> JsString("foo"))))
 }
-
diff --git a/CromIAM/src/test/scala/cromiam/sam/SamClientSpec.scala b/CromIAM/src/test/scala/cromiam/sam/SamClientSpec.scala
index 40f0cda2e86..95869718fb5 100644
--- a/CromIAM/src/test/scala/cromiam/sam/SamClientSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/sam/SamClientSpec.scala
@@ -28,7 +28,8 @@ class SamClientSpec extends AsyncFlatSpec with Matchers with BeforeAndAfterAll {
     HttpResponse(StatusCodes.InternalServerError, entity = HttpEntity("expected error"))
 
   private val authorization = Authorization(OAuth2BearerToken("my-token"))
-  private val authorizedUserWithCollection = User(WorkbenchUserId(MockSamClient.AuthorizedUserCollectionStr), authorization)
+  private val authorizedUserWithCollection =
+    User(WorkbenchUserId(MockSamClient.AuthorizedUserCollectionStr), authorization)
   private val unauthorizedUserWithNoCollection =
     User(WorkbenchUserId(MockSamClient.UnauthorizedUserCollectionStr), authorization)
   private val notWhitelistedUser = User(WorkbenchUserId(MockSamClient.NotWhitelistedUser), authorization)
@@ -47,25 +48,25 @@ class SamClientSpec extends AsyncFlatSpec with Matchers with BeforeAndAfterAll {
     super.afterAll()
   }
 
-
   behavior of "SamClient"
   it should "return true if user is whitelisted" in {
     val samClient = new MockSamClient()
-    samClient.isSubmitWhitelisted(authorizedUserWithCollection, emptyHttpRequest).map(v => assert(v))
-      .asIo.unsafeToFuture()
+    samClient
+      .isSubmitWhitelisted(authorizedUserWithCollection, emptyHttpRequest)
+      .map(v => assert(v))
+      .asIo
+      .unsafeToFuture()
   }
 
   it should "return false if user is not whitelisted" in {
     val samClient = new MockSamClient()
-    samClient.isSubmitWhitelisted(notWhitelistedUser, emptyHttpRequest).map(v => assert(!v))
-      .asIo.unsafeToFuture()
+    samClient.isSubmitWhitelisted(notWhitelistedUser, emptyHttpRequest).map(v => assert(!v)).asIo.unsafeToFuture()
   }
 
   it should "return sam errors while checking is whitelisted" in {
     val samClient = new MockSamClient() {
-      override def isSubmitWhitelistedSam(user: User, cromiamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+      override def isSubmitWhitelistedSam(user: User, cromiamRequest: HttpRequest): FailureResponseOrT[Boolean] =
         MockSamClient.returnResponse(expectedErrorResponse)
-      }
     }
     samClient.isSubmitWhitelisted(notWhitelistedUser, emptyHttpRequest).value.unsafeToFuture() map {
       _ should be(Left(expectedErrorResponse))
@@ -74,32 +75,33 @@ class SamClientSpec extends AsyncFlatSpec with Matchers with BeforeAndAfterAll {
 
   it should "eventually return the collection(s) of user" in {
     val samClient = new MockSamClient()
-    samClient.collectionsForUser(authorizedUserWithCollection, emptyHttpRequest).map(collectionList =>
-      assert(collectionList == MockSamClient.UserCollectionList)
-    ).asIo.unsafeToFuture()
+    samClient
+      .collectionsForUser(authorizedUserWithCollection, emptyHttpRequest)
+      .map(collectionList => assert(collectionList == MockSamClient.UserCollectionList))
+      .asIo
+      .unsafeToFuture()
   }
 
   it should "fail if user doesn't have any collections" in {
     val samClient = new MockSamClient()
     recoverToExceptionIf[Exception] {
-      samClient.collectionsForUser(unauthorizedUserWithNoCollection, emptyHttpRequest)
-        .asIo.unsafeToFuture()
-    } map(exception =>
-      assert(exception.getMessage == s"Unable to look up collections for user ${unauthorizedUserWithNoCollection.userId.value}!")
+      samClient.collectionsForUser(unauthorizedUserWithNoCollection, emptyHttpRequest).asIo.unsafeToFuture()
+    } map (exception =>
+      assert(
+        exception.getMessage == s"Unable to look up collections for user ${unauthorizedUserWithNoCollection.userId.value}!"
+      )
     )
   }
 
   it should "return true if user is authorized to perform action on collection" in {
     val samClient = new MockSamClient()
-    samClient.requestAuth(authorizedCollectionRequest, emptyHttpRequest).map(_ => succeed)
-      .asIo.unsafeToFuture()
+    samClient.requestAuth(authorizedCollectionRequest, emptyHttpRequest).map(_ => succeed).asIo.unsafeToFuture()
   }
 
   it should "throw SamDenialException if user is not authorized to perform action on collection" in {
     val samClient = new MockSamClient()
     recoverToExceptionIf[SamDenialException] {
-      samClient.requestAuth(unauthorizedCollectionRequest, emptyHttpRequest)
-        .asIo.unsafeToFuture()
+      samClient.requestAuth(unauthorizedCollectionRequest, emptyHttpRequest).asIo.unsafeToFuture()
     } map { exception =>
       assert(exception.getMessage == "Access Denied")
     }
@@ -107,15 +109,21 @@ class SamClientSpec extends AsyncFlatSpec with Matchers with BeforeAndAfterAll {
 
   it should "register collection to Sam if user has authorization to create/add to collection" in {
     val samClient = new MockSamClient()
-    samClient.requestSubmission(authorizedUserWithCollection, authorizedCollection, emptyHttpRequest).map(_ => succeed)
-      .asIo.unsafeToFuture()
+    samClient
+      .requestSubmission(authorizedUserWithCollection, authorizedCollection, emptyHttpRequest)
+      .map(_ => succeed)
+      .asIo
+      .unsafeToFuture()
   }
 
   it should "throw SamRegisterCollectionException if user doesn't have authorization to create/add to collection" in {
     val samClient = new MockSamClient()
     recoverToExceptionIf[SamRegisterCollectionException] {
-      samClient.requestSubmission(unauthorizedUserWithNoCollection, unauthorizedCollection, emptyHttpRequest).map(_ => succeed)
-        .asIo.unsafeToFuture()
+      samClient
+        .requestSubmission(unauthorizedUserWithNoCollection, unauthorizedCollection, emptyHttpRequest)
+        .map(_ => succeed)
+        .asIo
+        .unsafeToFuture()
     } map { exception =>
       assert(exception.getMessage == "Can't register collection with Sam. Status code: 400 Bad Request")
     }
@@ -125,15 +133,16 @@ class SamClientSpec extends AsyncFlatSpec with Matchers with BeforeAndAfterAll {
     val samClient = new BaseMockSamClient() {
       override protected def registerCreation(user: User,
                                               collection: Collection,
-                                              cromiamRequest: HttpRequest): FailureResponseOrT[HttpResponse] = {
+                                              cromiamRequest: HttpRequest
+      ): FailureResponseOrT[HttpResponse] = {
         val conflictResponse = HttpResponse(StatusCodes.Conflict, entity = HttpEntity("expected conflict"))
         returnResponse(conflictResponse)
       }
 
       override def requestAuth(authorizationRequest: CollectionAuthorizationRequest,
-                               cromiamRequest: HttpRequest): FailureResponseOrT[Unit] = {
+                               cromiamRequest: HttpRequest
+      ): FailureResponseOrT[Unit] =
         Monad[FailureResponseOrT].unit
-      }
     }
     samClient
       .requestSubmission(unauthorizedUserWithNoCollection, unauthorizedCollection, emptyHttpRequest)
@@ -146,19 +155,22 @@ class SamClientSpec extends AsyncFlatSpec with Matchers with BeforeAndAfterAll {
     val samClient = new BaseMockSamClient() {
       override protected def registerCreation(user: User,
                                               collection: Collection,
-                                              cromiamRequest: HttpRequest): FailureResponseOrT[HttpResponse] = {
+                                              cromiamRequest: HttpRequest
+      ): FailureResponseOrT[HttpResponse] = {
         val conflictResponse = HttpResponse(StatusCodes.Conflict, entity = HttpEntity("expected conflict"))
         returnResponse(conflictResponse)
       }
 
       override def requestAuth(authorizationRequest: CollectionAuthorizationRequest,
-                               cromiamRequest: HttpRequest): FailureResponseOrT[Unit] = {
+                               cromiamRequest: HttpRequest
+      ): FailureResponseOrT[Unit] =
         returnResponse(expectedErrorResponse)
-      }
     }
     recoverToExceptionIf[UnsuccessfulRequestException] {
-      samClient.requestSubmission(unauthorizedUserWithNoCollection, unauthorizedCollection, emptyHttpRequest)
-        .asIo.unsafeToFuture()
+      samClient
+        .requestSubmission(unauthorizedUserWithNoCollection, unauthorizedCollection, emptyHttpRequest)
+        .asIo
+        .unsafeToFuture()
     } map { exception =>
       assert(exception.getMessage == "expected error")
     }
@@ -168,14 +180,17 @@ class SamClientSpec extends AsyncFlatSpec with Matchers with BeforeAndAfterAll {
     val samClient = new BaseMockSamClient() {
       override protected def registerCreation(user: User,
                                               collection: Collection,
-                                              cromiamRequest: HttpRequest): FailureResponseOrT[HttpResponse] = {
+                                              cromiamRequest: HttpRequest
+      ): FailureResponseOrT[HttpResponse] = {
         val unexpectedOkResponse = HttpResponse(StatusCodes.OK, entity = HttpEntity("elided ok message"))
         returnResponse(unexpectedOkResponse)
       }
     }
     recoverToExceptionIf[SamRegisterCollectionException] {
-      samClient.requestSubmission(unauthorizedUserWithNoCollection, unauthorizedCollection, emptyHttpRequest)
-        .asIo.unsafeToFuture()
+      samClient
+        .requestSubmission(unauthorizedUserWithNoCollection, unauthorizedCollection, emptyHttpRequest)
+        .asIo
+        .unsafeToFuture()
     } map { exception =>
       exception.getMessage should be("Can't register collection with Sam. Status code: 200 OK")
     }
@@ -185,14 +200,17 @@ class SamClientSpec extends AsyncFlatSpec with Matchers with BeforeAndAfterAll {
     val samClient = new BaseMockSamClient() {
       override protected def registerCreation(user: User,
                                               collection: Collection,
-                                              cromiamRequest: HttpRequest): FailureResponseOrT[HttpResponse] = {
+                                              cromiamRequest: HttpRequest
+      ): FailureResponseOrT[HttpResponse] = {
         val unexpectedFailureResponse = HttpResponse(StatusCodes.ImATeapot, entity = HttpEntity("elided error message"))
         returnResponse(unexpectedFailureResponse)
       }
     }
     recoverToExceptionIf[SamRegisterCollectionException] {
-      samClient.requestSubmission(unauthorizedUserWithNoCollection, unauthorizedCollection, emptyHttpRequest)
-        .asIo.unsafeToFuture()
+      samClient
+        .requestSubmission(unauthorizedUserWithNoCollection, unauthorizedCollection, emptyHttpRequest)
+        .asIo
+        .unsafeToFuture()
     } map { exception =>
       exception.getMessage should be("Can't register collection with Sam. Status code: 418 I'm a teapot")
     }
diff --git a/CromIAM/src/test/scala/cromiam/server/status/MockStatusService.scala b/CromIAM/src/test/scala/cromiam/server/status/MockStatusService.scala
index 9010da8bda0..c7866c68089 100644
--- a/CromIAM/src/test/scala/cromiam/server/status/MockStatusService.scala
+++ b/CromIAM/src/test/scala/cromiam/server/status/MockStatusService.scala
@@ -6,8 +6,10 @@ import org.broadinstitute.dsde.workbench.util.health.Subsystems.{Cromwell, Sam,
 
 import scala.concurrent.{ExecutionContext, Future}
 
-class MockStatusService(checkStatus: () => Map[Subsystem, Future[SubsystemStatus]])(implicit system: ActorSystem, executionContext: ExecutionContext) extends
-  StatusService(checkStatus)(system, executionContext) {
+class MockStatusService(checkStatus: () => Map[Subsystem, Future[SubsystemStatus]])(implicit
+  system: ActorSystem,
+  executionContext: ExecutionContext
+) extends StatusService(checkStatus)(system, executionContext) {
 
   override def status(): Future[StatusCheckResponse] = {
     val subsystemStatus: SubsystemStatus = SubsystemStatus(ok = true, None)
@@ -16,4 +18,3 @@ class MockStatusService(checkStatus: () => Map[Subsystem, Future[SubsystemStatus
     Future.successful(StatusCheckResponse(ok = true, subsystems))
   }
 }
-
diff --git a/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
index 89945c5bfcb..e93acd51a2a 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/CromIamApiServiceSpec.scala
@@ -13,14 +13,23 @@ import cromiam.server.status.StatusService
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with CromIamApiService with ScalatestRouteTest {
+class CromIamApiServiceSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with CromIamApiService
+    with ScalatestRouteTest {
   override def testConfigSource = "akka.loglevel = DEBUG"
 
   val log = NoLogging
 
-  override def rootConfig: Config = throw new UnsupportedOperationException("This spec shouldn't need to access the real config")
+  override def rootConfig: Config = throw new UnsupportedOperationException(
+    "This spec shouldn't need to access the real config"
+  )
 
-  override def configuration = throw new UnsupportedOperationException("This spec shouldn't need to access the real interface/port")
+  override def configuration = throw new UnsupportedOperationException(
+    "This spec shouldn't need to access the real interface/port"
+  )
 
   override lazy val cromwellClient = new MockCromwellClient()
   override lazy val samClient = new MockSamClient()
@@ -29,13 +38,15 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   val version = "v1"
 
   val authorization = Authorization(OAuth2BearerToken("my-token"))
-  val badAuthHeaders: List[HttpHeader] = List(authorization, RawHeader("OIDC_CLAIM_user_id", cromwellClient.unauthorizedUserCollectionStr))
-  val goodAuthHeaders: List[HttpHeader] = List(authorization, RawHeader("OIDC_CLAIM_user_id", cromwellClient.authorizedUserCollectionStr))
-
+  val badAuthHeaders: List[HttpHeader] =
+    List(authorization, RawHeader("OIDC_CLAIM_user_id", cromwellClient.unauthorizedUserCollectionStr))
+  val goodAuthHeaders: List[HttpHeader] =
+    List(authorization, RawHeader("OIDC_CLAIM_user_id", cromwellClient.authorizedUserCollectionStr))
 
   behavior of "Status endpoint"
   it should "return 200 for authorized user who has collection associated with root workflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/status").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/status")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -43,7 +54,8 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 200 for authorized user who has collection associated with subworkflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/status").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/status")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -51,15 +63,19 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 500 for authorized user who doesn't have collection associated with workflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/status").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/status")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe InternalServerError
-      responseAs[String] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
+      responseAs[
+        String
+      ] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
   it should "return SamDenialException for user who doesn't have view permissions" in {
-    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/status").withHeaders(badAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/status")
+      .withHeaders(badAuthHeaders) ~> allRoutes ~> check {
       status shouldBe Forbidden
       responseAs[String] shouldBe "Access Denied"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -72,10 +88,10 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-
   behavior of "Outputs endpoint"
   it should "return 200 for authorized user who has collection associated with root workflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/outputs").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/outputs")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -83,7 +99,8 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 200 for authorized user who has collection associated with subworkflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/outputs").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/outputs")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -91,15 +108,19 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 500 for authorized user who doesn't have collection associated with workflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/outputs").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/outputs")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe InternalServerError
-      responseAs[String] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
+      responseAs[
+        String
+      ] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
   it should "return SamDenialException for user who doesn't have view permissions" in {
-    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/outputs").withHeaders(badAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/outputs")
+      .withHeaders(badAuthHeaders) ~> allRoutes ~> check {
       status shouldBe Forbidden
       responseAs[String] shouldBe "Access Denied"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -112,10 +133,10 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-
   behavior of "Metadata endpoint"
   it should "return 200 for authorized user who has collection associated with root workflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/metadata").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/metadata")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -123,7 +144,8 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 200 for authorized user who has collection associated with subworkflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/metadata").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/metadata")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -131,15 +153,19 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 500 for authorized user who doesn't have collection associated with workflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/metadata").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/metadata")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe InternalServerError
-      responseAs[String] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
+      responseAs[
+        String
+      ] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
   it should "return SamDenialException for user who doesn't have view permissions" in {
-    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/metadata").withHeaders(badAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/metadata")
+      .withHeaders(badAuthHeaders) ~> allRoutes ~> check {
       status shouldBe Forbidden
       responseAs[String] shouldBe "Access Denied"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -152,10 +178,10 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-
   behavior of "Logs endpoint"
   it should "return 200 for authorized user who has collection associated with root workflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/logs").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/logs")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -163,7 +189,8 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 200 for authorized user who has collection associated with subworkflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/logs").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/logs")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -171,15 +198,19 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 500 for authorized user who doesn't have collection associated with workflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/logs").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/logs")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe InternalServerError
-      responseAs[String] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
+      responseAs[
+        String
+      ] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
   it should "return SamDenialException for user who doesn't have view permissions" in {
-    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/logs").withHeaders(badAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/logs")
+      .withHeaders(badAuthHeaders) ~> allRoutes ~> check {
       status shouldBe Forbidden
       responseAs[String] shouldBe "Access Denied"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -192,10 +223,10 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-
   behavior of "GET Labels endpoint"
   it should "return 200 for authorized user who has collection associated with root workflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/labels").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/labels")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -203,7 +234,8 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 200 for authorized user who has collection associated with subworkflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/labels").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/labels")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -211,15 +243,19 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 500 for authorized user who doesn't have collection associated with workflow" in {
-    Get(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/labels").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/labels")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe InternalServerError
-      responseAs[String] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
+      responseAs[
+        String
+      ] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
   it should "return SamDenialException for user who doesn't have view permissions" in {
-    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/labels").withHeaders(badAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/${cromwellClient.subworkflowId}/labels")
+      .withHeaders(badAuthHeaders) ~> allRoutes ~> check {
       status shouldBe Forbidden
       responseAs[String] shouldBe "Access Denied"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -232,12 +268,13 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-
   behavior of "PATCH Labels endpoint"
   it should "successfully forward request to Cromwell if nothing is untoward" in {
     val labels = """{"key-1":"foo","key-2":"bar"}"""
     val labelEntity = HttpEntity(ContentTypes.`application/json`, labels)
-    Patch(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/labels").withHeaders(goodAuthHeaders).withEntity(labelEntity) ~> allRoutes ~> check {
+    Patch(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/labels")
+      .withHeaders(goodAuthHeaders)
+      .withEntity(labelEntity) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -248,7 +285,9 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     val labels = """{"key-1":"foo","caas-collection-name":"bar"}"""
     val labelEntity = HttpEntity(ContentTypes.`application/json`, labels)
 
-    Patch(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/labels").withHeaders(goodAuthHeaders).withEntity(labelEntity) ~> allRoutes ~> check {
+    Patch(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/labels")
+      .withHeaders(goodAuthHeaders)
+      .withEntity(labelEntity) ~> allRoutes ~> check {
       status shouldBe InternalServerError
       responseAs[String] shouldBe "Submitted labels contain the key caas-collection-name, which is not allowed\n"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -259,7 +298,9 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     val labels = """"key-1":"foo""""
     val labelEntity = HttpEntity(ContentTypes.`application/json`, labels)
 
-    Patch(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/labels").withHeaders(goodAuthHeaders).withEntity(labelEntity) ~> allRoutes ~> check {
+    Patch(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/labels")
+      .withHeaders(goodAuthHeaders)
+      .withEntity(labelEntity) ~> allRoutes ~> check {
       status shouldBe InternalServerError
       responseAs[String] shouldBe "Labels must be a valid JSON object, received: \"key-1\":\"foo\"\n"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -269,9 +310,13 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   it should "return 500 for authorized user who doesn't have collection associated with workflow" in {
     val labels = """{"key-1":"foo","key-2":"bar"}"""
     val labelEntity = HttpEntity(ContentTypes.`application/json`, labels)
-    Patch(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/labels").withHeaders(goodAuthHeaders).withEntity(labelEntity) ~> allRoutes ~> check {
+    Patch(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/labels")
+      .withHeaders(goodAuthHeaders)
+      .withEntity(labelEntity) ~> allRoutes ~> check {
       status shouldBe InternalServerError
-      responseAs[String] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
+      responseAs[
+        String
+      ] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
@@ -279,7 +324,9 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   it should "return SamDenialException for user who doesn't have update permissions" in {
     val labels = """{"key-1":"foo","key-2":"bar"}"""
     val labelEntity = HttpEntity(ContentTypes.`application/json`, labels)
-    Patch(s"/api/workflows/$version/${cromwellClient.subworkflowId}/labels").withHeaders(badAuthHeaders).withEntity(labelEntity) ~> allRoutes ~> check {
+    Patch(s"/api/workflows/$version/${cromwellClient.subworkflowId}/labels")
+      .withHeaders(badAuthHeaders)
+      .withEntity(labelEntity) ~> allRoutes ~> check {
       status shouldBe Forbidden
       responseAs[String] shouldBe "Access Denied"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -289,12 +336,12 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   it should "reject request if it doesn't contain OIDC_CLAIM_user_id in header" in {
     val labels = """{"key-1":"foo","key-2":"bar"}"""
     val labelEntity = HttpEntity(ContentTypes.`application/json`, labels)
-    Patch(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/labels").withEntity(labelEntity) ~> allRoutes ~> check {
+    Patch(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/labels")
+      .withEntity(labelEntity) ~> allRoutes ~> check {
       rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
     }
   }
 
-
   behavior of "Backends endpoint"
   it should "successfully forward request to Cromwell if auth header is provided" in {
     Get(s"/api/workflows/$version/backends").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
@@ -346,7 +393,8 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
 
   behavior of "ReleaseHold endpoint"
   it should "return 200 for authorized user who has collection associated with root workflow" in {
-    Post(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/releaseHold").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Post(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/releaseHold")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -354,15 +402,19 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 500 for authorized user who doesn't have collection associated with workflow" in {
-    Post(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/releaseHold").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Post(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/releaseHold")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe InternalServerError
-      responseAs[String] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
+      responseAs[
+        String
+      ] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
   it should "return SamDenialException for user who doesn't have update permissions" in {
-    Post(s"/api/workflows/$version/${cromwellClient.subworkflowId}/releaseHold").withHeaders(badAuthHeaders) ~> allRoutes ~> check {
+    Post(s"/api/workflows/$version/${cromwellClient.subworkflowId}/releaseHold")
+      .withHeaders(badAuthHeaders) ~> allRoutes ~> check {
       status shouldBe Forbidden
       responseAs[String] shouldBe "Access Denied"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -375,10 +427,10 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-
   behavior of "Abort endpoint"
   it should "return 200 for authorized user who has collection associated with root workflow" in {
-    Post(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/abort").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Post(s"/api/workflows/$version/${cromwellClient.rootWorkflowIdWithCollection}/abort")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -386,15 +438,19 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 500 for authorized user who doesn't have collection associated with workflow" in {
-    Post(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/abort").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Post(s"/api/workflows/$version/${cromwellClient.workflowIdWithoutCollection}/abort")
+      .withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
       status shouldBe InternalServerError
-      responseAs[String] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
+      responseAs[
+        String
+      ] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
   it should "return SamDenialException for user who doesn't have abort permissions" in {
-    Post(s"/api/workflows/$version/${cromwellClient.subworkflowId}/abort").withHeaders(badAuthHeaders) ~> allRoutes ~> check {
+    Post(s"/api/workflows/$version/${cromwellClient.subworkflowId}/abort")
+      .withHeaders(badAuthHeaders) ~> allRoutes ~> check {
       status shouldBe Forbidden
       responseAs[String] shouldBe "Access Denied"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -407,11 +463,13 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-
   behavior of "CallCacheDiff endpoint"
   it should "return 200 for authorized user who has collection associated with both workflows" in {
-    val callCacheDiffParams = s"workflowA=${cromwellClient.rootWorkflowIdWithCollection}&callA=helloCall&workflowB=${cromwellClient.anotherRootWorkflowIdWithCollection}&callB=helloCall"
-    Get(s"/api/workflows/$version/callcaching/diff?$callCacheDiffParams").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    val callCacheDiffParams =
+      s"workflowA=${cromwellClient.rootWorkflowIdWithCollection}&callA=helloCall&workflowB=${cromwellClient.anotherRootWorkflowIdWithCollection}&callB=helloCall"
+    Get(s"/api/workflows/$version/callcaching/diff?$callCacheDiffParams").withHeaders(
+      goodAuthHeaders
+    ) ~> allRoutes ~> check {
       status shouldBe OK
       responseAs[String] shouldBe "Response from Cromwell"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -420,7 +478,9 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
 
   it should "return BadRequest if request is malformed" in {
     val callCacheDiffParams = s"workflowA=${cromwellClient.rootWorkflowIdWithCollection}&callA=helloCall"
-    Get(s"/api/workflows/$version/callcaching/diff?$callCacheDiffParams").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    Get(s"/api/workflows/$version/callcaching/diff?$callCacheDiffParams").withHeaders(
+      goodAuthHeaders
+    ) ~> allRoutes ~> check {
       status shouldBe BadRequest
       responseAs[String] shouldBe "Must supply both workflowA and workflowB to the /callcaching/diff endpoint"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -428,17 +488,25 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "return 500 for authorized user who has doesn't have collection associated with any one workflow" in {
-    val callCacheDiffParams = s"workflowA=${cromwellClient.rootWorkflowIdWithCollection}&callA=helloCall&workflowB=${cromwellClient.workflowIdWithoutCollection}&callB=helloCall"
-    Get(s"/api/workflows/$version/callcaching/diff?$callCacheDiffParams").withHeaders(goodAuthHeaders) ~> allRoutes ~> check {
+    val callCacheDiffParams =
+      s"workflowA=${cromwellClient.rootWorkflowIdWithCollection}&callA=helloCall&workflowB=${cromwellClient.workflowIdWithoutCollection}&callB=helloCall"
+    Get(s"/api/workflows/$version/callcaching/diff?$callCacheDiffParams").withHeaders(
+      goodAuthHeaders
+    ) ~> allRoutes ~> check {
       status shouldBe InternalServerError
-      responseAs[String] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
+      responseAs[
+        String
+      ] shouldBe s"CromIAM unexpected error: java.lang.IllegalArgumentException: Workflow ${cromwellClient.workflowIdWithoutCollection} has no associated collection"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
     }
   }
 
   it should "return SamDenialException for user who doesn't have read permissions" in {
-    val callCacheDiffParams = s"workflowA=${cromwellClient.rootWorkflowIdWithCollection}&callA=helloCall&workflowB=${cromwellClient.anotherRootWorkflowIdWithCollection}&callB=helloCall"
-    Get(s"/api/workflows/$version/callcaching/diff?$callCacheDiffParams").withHeaders(badAuthHeaders) ~> allRoutes ~> check {
+    val callCacheDiffParams =
+      s"workflowA=${cromwellClient.rootWorkflowIdWithCollection}&callA=helloCall&workflowB=${cromwellClient.anotherRootWorkflowIdWithCollection}&callB=helloCall"
+    Get(s"/api/workflows/$version/callcaching/diff?$callCacheDiffParams").withHeaders(
+      badAuthHeaders
+    ) ~> allRoutes ~> check {
       status shouldBe Forbidden
       responseAs[String] shouldBe "Access Denied"
       contentType should be(ContentTypes.`text/plain(UTF-8)`)
@@ -446,7 +514,8 @@ class CromIamApiServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "reject request if it doesn't contain OIDC_CLAIM_user_id in header" in {
-    val callCacheDiffParams = s"workflowA=${cromwellClient.rootWorkflowIdWithCollection}&callA=helloCall&workflowB=${cromwellClient.anotherRootWorkflowIdWithCollection}&callB=helloCall"
+    val callCacheDiffParams =
+      s"workflowA=${cromwellClient.rootWorkflowIdWithCollection}&callA=helloCall&workflowB=${cromwellClient.anotherRootWorkflowIdWithCollection}&callB=helloCall"
     Get(s"/api/workflows/$version/callcaching/diff?$callCacheDiffParams") ~> allRoutes ~> check {
       rejection shouldEqual MissingHeaderRejection("OIDC_CLAIM_user_id")
     }
diff --git a/CromIAM/src/test/scala/cromiam/webservice/EngineRouteSupportSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/EngineRouteSupportSpec.scala
index f6f1e3b75de..9d431f6af05 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/EngineRouteSupportSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/EngineRouteSupportSpec.scala
@@ -9,8 +9,12 @@ import cromiam.server.status.{MockStatusService, StatusService}
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
-class EngineRouteSupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalatestRouteTest with EngineRouteSupport  {
+class EngineRouteSupportSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalatestRouteTest
+    with EngineRouteSupport {
   override val cromwellClient = new MockCromwellClient()
   val samClient = new MockSamClient()
   override val statusService: StatusService = new MockStatusService(() => Map.empty)
diff --git a/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala b/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
index 59e75347159..ff976e24b4b 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/MockClients.scala
@@ -16,10 +16,8 @@ import cromwell.api.model._
 
 import scala.concurrent.ExecutionContextExecutor
 
-class MockCromwellClient()(implicit system: ActorSystem,
-                                 ece: ExecutionContextExecutor,
-                                 materializer: ActorMaterializer)
-  extends CromwellClient("http", "bar", 1, NoLogging, ActorRef.noSender)(system, ece, materializer) {
+class MockCromwellClient()(implicit system: ActorSystem, ece: ExecutionContextExecutor, materializer: ActorMaterializer)
+    extends CromwellClient("http", "bar", 1, NoLogging, ActorRef.noSender)(system, ece, materializer) {
   val version = "v1"
 
   val unauthorizedUserCollectionStr: String = "987654321"
@@ -56,7 +54,7 @@ class MockCromwellClient()(implicit system: ActorSystem,
     val womtoolRoutePath = s"/api/womtool/$version/describe"
 
     httpRequest.uri.path.toString match {
-      //version endpoint doesn't require authentication
+      // version endpoint doesn't require authentication
       case `versionRoutePath` =>
         FailureResponseOrT.pure(HttpResponse(status = OK, entity = "Response from Cromwell"))
       // womtool endpoint requires authn which it gets for free from the proxy, does not care about authz
@@ -68,18 +66,19 @@ class MockCromwellClient()(implicit system: ActorSystem,
 
   override def getRootWorkflow(workflowId: String,
                                user: User,
-                               cromIamRequest: HttpRequest): FailureResponseOrT[String] = {
+                               cromIamRequest: HttpRequest
+  ): FailureResponseOrT[String] =
     workflowId match {
       case `subworkflowId` | `rootWorkflowIdWithCollection` =>
         FailureResponseOrT.pure(rootWorkflowIdWithCollection)
       case `anotherRootWorkflowIdWithCollection` => FailureResponseOrT.pure(anotherRootWorkflowIdWithCollection)
       case _ => FailureResponseOrT.pure(workflowIdWithoutCollection)
     }
-  }
 
   override def collectionForWorkflow(workflowId: String,
                                      user: User,
-                                     cromIamRequest: HttpRequest): FailureResponseOrT[Collection] = {
+                                     cromIamRequest: HttpRequest
+  ): FailureResponseOrT[Collection] =
     workflowId match {
       case `rootWorkflowIdWithCollection` | `anotherRootWorkflowIdWithCollection` =>
         FailureResponseOrT.pure(userCollection)
@@ -87,33 +86,32 @@ class MockCromwellClient()(implicit system: ActorSystem,
         val exception = new IllegalArgumentException(s"Workflow $workflowId has no associated collection")
         FailureResponseOrT.left(IO.raiseError[HttpResponse](exception))
     }
-  }
 }
 
 /**
   * Overrides some values, but doesn't override methods.
   */
-class BaseMockSamClient(checkSubmitWhitelist: Boolean = true)
-                   (implicit system: ActorSystem,
-                    ece: ExecutionContextExecutor,
-                    materializer: ActorMaterializer)
-  extends SamClient(
-    "http",
-    "bar",
-    1,
-    checkSubmitWhitelist,
-    NoLogging,
-    ActorRef.noSender
-  )(system, ece, materializer)
+class BaseMockSamClient(checkSubmitWhitelist: Boolean = true)(implicit
+  system: ActorSystem,
+  ece: ExecutionContextExecutor,
+  materializer: ActorMaterializer
+) extends SamClient(
+      "http",
+      "bar",
+      1,
+      checkSubmitWhitelist,
+      NoLogging,
+      ActorRef.noSender
+    )(system, ece, materializer)
 
 /**
   * Extends the base mock client with overriden methods.
   */
-class MockSamClient(checkSubmitWhitelist: Boolean = true)
-                   (implicit system: ActorSystem,
-                      ece: ExecutionContextExecutor,
-                      materializer: ActorMaterializer)
-  extends BaseMockSamClient(checkSubmitWhitelist) {
+class MockSamClient(checkSubmitWhitelist: Boolean = true)(implicit
+  system: ActorSystem,
+  ece: ExecutionContextExecutor,
+  materializer: ActorMaterializer
+) extends BaseMockSamClient(checkSubmitWhitelist) {
 
   override def collectionsForUser(user: User, httpRequest: HttpRequest): FailureResponseOrT[List[Collection]] = {
     val userId = user.userId.value
@@ -127,7 +125,8 @@ class MockSamClient(checkSubmitWhitelist: Boolean = true)
 
   override def requestSubmission(user: User,
                                  collection: Collection,
-                                 cromIamRequest: HttpRequest): FailureResponseOrT[Unit] = {
+                                 cromIamRequest: HttpRequest
+  ): FailureResponseOrT[Unit] =
     collection match {
       case c if c.name.equalsIgnoreCase(UnauthorizedUserCollectionStr) =>
         val exception = SamRegisterCollectionException(StatusCodes.BadRequest)
@@ -135,28 +134,25 @@ class MockSamClient(checkSubmitWhitelist: Boolean = true)
       case c if c.name.equalsIgnoreCase(AuthorizedUserCollectionStr) => Monad[FailureResponseOrT].unit
       case _ => Monad[FailureResponseOrT].unit
     }
-  }
 
-  override def isSubmitWhitelistedSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+  override def isSubmitWhitelistedSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] =
     FailureResponseOrT.pure(!user.userId.value.equalsIgnoreCase(NotWhitelistedUser))
-  }
 
-  override def isUserEnabledSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+  override def isUserEnabledSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] =
     if (user.userId.value == "enabled@example.com" || user.userId.value == MockSamClient.AuthorizedUserCollectionStr)
       FailureResponseOrT.pure(true)
     else if (user.userId.value == "disabled@example.com")
       FailureResponseOrT.pure(false)
     else
       throw new Exception("Misconfigured test")
-  }
 
   override def requestAuth(authorizationRequest: CollectionAuthorizationRequest,
-                           cromIamRequest: HttpRequest): FailureResponseOrT[Unit] = {
+                           cromIamRequest: HttpRequest
+  ): FailureResponseOrT[Unit] =
     authorizationRequest.user.userId.value match {
       case AuthorizedUserCollectionStr => Monad[FailureResponseOrT].unit
       case _ => FailureResponseOrT.left(IO.raiseError[HttpResponse](new SamDenialException))
     }
-  }
 }
 
 object MockSamClient {
@@ -165,7 +161,6 @@ object MockSamClient {
   val NotWhitelistedUser: String = "ABC123"
   val UserCollectionList: List[Collection] = List(Collection("col1"), Collection("col2"))
 
-  def returnResponse[T](response: HttpResponse): FailureResponseOrT[T] = {
+  def returnResponse[T](response: HttpResponse): FailureResponseOrT[T] =
     FailureResponseOrT.left(IO.pure(response))
-  }
 }
diff --git a/CromIAM/src/test/scala/cromiam/webservice/QuerySupportSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/QuerySupportSpec.scala
index 216691c1c35..57dedbaefdf 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/QuerySupportSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/QuerySupportSpec.scala
@@ -11,8 +11,12 @@ import org.broadinstitute.dsde.workbench.model.WorkbenchUserId
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
-class QuerySupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalatestRouteTest with QuerySupport {
+class QuerySupportSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalatestRouteTest
+    with QuerySupport {
   override val cromwellClient = new MockCromwellClient()
   override val samClient = new MockSamClient()
   override val log: LoggingAdapter = NoLogging
@@ -27,7 +31,8 @@ class QuerySupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
   val getQuery = s"$queryPath?status=Submitted&label=foo:bar&label=foo:baz"
   val badGetQuery = s"$queryPath?status=Submitted&labelor=foo:bar&label=foo:baz"
 
-  val goodPostEntity = HttpEntity(ContentTypes.`application/json`,
+  val goodPostEntity = HttpEntity(
+    ContentTypes.`application/json`,
     """|[
        |  {
        |    "start": "2015-11-01T00:00:00-04:00"
@@ -50,7 +55,8 @@ class QuerySupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
        |]
        |""".stripMargin
   )
-  val badPostEntity = HttpEntity(ContentTypes.`application/json`,
+  val badPostEntity = HttpEntity(
+    ContentTypes.`application/json`,
     """|[
        |  {
        |    "start": "2015-11-01T00:00:00-04:00"
diff --git a/CromIAM/src/test/scala/cromiam/webservice/SubmissionSupportSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/SubmissionSupportSpec.scala
index c4a424747e6..bfbd38075f5 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/SubmissionSupportSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/SubmissionSupportSpec.scala
@@ -12,8 +12,12 @@ import org.scalatest.matchers.should.Matchers
 
 import scala.concurrent.duration._
 
-
-class SubmissionSupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalatestRouteTest with SubmissionSupport {
+class SubmissionSupportSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalatestRouteTest
+    with SubmissionSupport {
   override val cromwellClient = new MockCromwellClient()
   override val samClient = new MockSamClient()
   override val log: LoggingAdapter = NoLogging
@@ -56,7 +60,6 @@ class SubmissionSupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   val workflowSource = Multipart.FormData.BodyPart("workflowSource", HttpEntity(helloWorldWdl))
   val formData = Multipart.FormData(workflowSource).toEntity()
 
-
   "Submit endpoint" should "forward the request to Cromwell for authorized SAM user" in {
     Post(submitPath).withHeaders(goodAuthHeaders).withEntity(formData) ~> submitRoute ~> check {
       status shouldEqual StatusCodes.OK
diff --git a/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
index 838a523f4eb..32a7511c6de 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
@@ -16,9 +16,13 @@ import org.yaml.snakeyaml.{LoaderOptions, Yaml => SnakeYaml}
 
 import scala.jdk.CollectionConverters._
 
-
-class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with SwaggerService with ScalatestRouteTest with Matchers
-  with TableDrivenPropertyChecks {
+class SwaggerServiceSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with SwaggerService
+    with ScalatestRouteTest
+    with Matchers
+    with TableDrivenPropertyChecks {
   def actorRefFactory = system
   override def oauthConfig: SwaggerOauthConfig = SwaggerOauthConfig("clientId", "realm", "appName")
   val yamlLoaderOptions = new LoaderOptions
@@ -33,7 +37,8 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
         contentType should be(ContentTypes.`application/octet-stream`)
 
         val body = responseAs[String]
-        val yaml = new SnakeYaml(new UniqueKeyConstructor(new LoaderOptions)).loadAs(body, classOf[java.util.Map[String, AnyRef]])
+        val yaml = new SnakeYaml(new UniqueKeyConstructor(new LoaderOptions))
+          .loadAs(body, classOf[java.util.Map[String, AnyRef]])
 
         yaml.get("swagger") should be("2.0")
       }
@@ -62,27 +67,42 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
 
         resultWithInfo.getSwagger.getDefinitions.asScala foreach {
           // If no properties, `getProperties` returns `null` instead of an empty map
-          case (defKey, defVal) => Option(defVal.getProperties).map(_.asScala).getOrElse(Map.empty) foreach {
-            /*
+          case (defKey, defVal) =>
+            Option(defVal.getProperties).map(_.asScala).getOrElse(Map.empty) foreach {
+              /*
             Two against one.
             Swagger parser implementation lets a RefProperty have descriptions.
             http://swagger.io/specification/#referenceObject & http://editor.swagger.io both say it's ref ONLY!
-             */
-            case (propKey, propVal: RefProperty) =>
-              withClue(s"RefProperty $defKey.$propKey has a description: ") {
-                propVal.getDescription should be(null)
-              }
-            case _ => /* ignore */
-          }
+               */
+              case (propKey, propVal: RefProperty) =>
+                withClue(s"RefProperty $defKey.$propKey has a description: ") {
+                  propVal.getDescription should be(null)
+                }
+              case _ => /* ignore */
+            }
         }
       }
   }
 
   it should "return status OK when getting OPTIONS on paths" in {
-    val pathExamples = Table("path", "/", "/swagger", "/swagger/cromwell.yaml", "/swagger/index.html", "/api",
-      "/api/workflows/", "/api/workflows/v1", "/workflows/v1/outputs", "/workflows/v1/status",
-      "/api/workflows/v1/validate", "/workflows", "/workflows/v1", "/workflows/v1/outputs", "/workflows/v1/status",
-      "/workflows/v1/validate")
+    val pathExamples = Table(
+      "path",
+      "/",
+      "/swagger",
+      "/swagger/cromwell.yaml",
+      "/swagger/index.html",
+      "/api",
+      "/api/workflows/",
+      "/api/workflows/v1",
+      "/workflows/v1/outputs",
+      "/workflows/v1/status",
+      "/api/workflows/v1/validate",
+      "/workflows",
+      "/workflows/v1",
+      "/workflows/v1/outputs",
+      "/workflows/v1/status",
+      "/workflows/v1/validate"
+    )
 
     forAll(pathExamples) { path =>
       Options(path) ~>
diff --git a/CromIAM/src/test/scala/cromiam/webservice/SwaggerUiHttpServiceSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/SwaggerUiHttpServiceSpec.scala
index 1d0103a09fd..b39466ec4f0 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/SwaggerUiHttpServiceSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/SwaggerUiHttpServiceSpec.scala
@@ -10,19 +10,38 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks
 
-
-trait SwaggerUiHttpServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalatestRouteTest with SwaggerUiHttpService {
+trait SwaggerUiHttpServiceSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalatestRouteTest
+    with SwaggerUiHttpService {
   def actorRefFactory = system
 }
 
-trait SwaggerResourceHttpServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalatestRouteTest with
-TableDrivenPropertyChecks with SwaggerResourceHttpService {
-
-  val testPathsForOptions = Table("endpoint", "/", "/swagger", "/swagger/index.html", "/api", "/api/example",
-    "/api/example?with=param", "/api/example/path")
+trait SwaggerResourceHttpServiceSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalatestRouteTest
+    with TableDrivenPropertyChecks
+    with SwaggerResourceHttpService {
+
+  val testPathsForOptions = Table("endpoint",
+                                  "/",
+                                  "/swagger",
+                                  "/swagger/index.html",
+                                  "/api",
+                                  "/api/example",
+                                  "/api/example?with=param",
+                                  "/api/example/path"
+  )
 }
 
-trait SwaggerUiResourceHttpServiceSpec extends SwaggerUiHttpServiceSpec with SwaggerResourceHttpServiceSpec with SwaggerUiResourceHttpService
+trait SwaggerUiResourceHttpServiceSpec
+    extends SwaggerUiHttpServiceSpec
+    with SwaggerResourceHttpServiceSpec
+    with SwaggerUiResourceHttpService
 
 object SwaggerUiHttpServiceSpec {
   // TODO: Re-common-ize swagger out of cromwell's engine and reuse.
@@ -40,7 +59,7 @@ class BasicSwaggerUiHttpServiceSpec extends SwaggerUiHttpServiceSpec {
   behavior of "SwaggerUiHttpService"
 
   override protected def rewriteSwaggerIndex(data: String): String =
-  // Replace same magic string used in SwaggerUiResourceHttpService.rewriteSwaggerIndex
+    // Replace same magic string used in SwaggerUiResourceHttpService.rewriteSwaggerIndex
     data.replace("window.ui = ui", "replaced-client-id")
 
   it should "redirect /swagger to /" in {
@@ -80,7 +99,9 @@ class BasicSwaggerUiHttpServiceSpec extends SwaggerUiHttpServiceSpec {
   }
 
   override def oauthConfig: SwaggerOauthConfig = SwaggerOauthConfig(
-    clientId = "test-client-id", realm = "test-realm", appName = "test-appname"
+    clientId = "test-client-id",
+    realm = "test-realm",
+    appName = "test-appname"
   )
 }
 
@@ -195,7 +216,6 @@ class YamlSwaggerUiResourceHttpServiceSpec extends SwaggerUiResourceHttpServiceS
   }
 }
 
-
 class JsonSwaggerUiResourceHttpServiceSpec extends SwaggerUiResourceHttpServiceSpec {
 
   override def oauthConfig: SwaggerOauthConfig = SwaggerOauthConfig("clientId", "realm", "appName")
diff --git a/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
index 785c887c374..a229f2db255 100644
--- a/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
+++ b/CromIAM/src/test/scala/cromiam/webservice/WomtoolRouteSupportSpec.scala
@@ -10,8 +10,12 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
-class WomtoolRouteSupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with WomtoolRouteSupport with ScalatestRouteTest {
+class WomtoolRouteSupportSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with WomtoolRouteSupport
+    with ScalatestRouteTest {
 
   override lazy val cromwellClient = new MockCromwellClient()
   override lazy val samClient = new MockSamClient()
diff --git a/backend/src/main/scala/cromwell/backend/BackendCacheHitCopyingActor.scala b/backend/src/main/scala/cromwell/backend/BackendCacheHitCopyingActor.scala
index 54849df4250..549bf761e38 100644
--- a/backend/src/main/scala/cromwell/backend/BackendCacheHitCopyingActor.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendCacheHitCopyingActor.scala
@@ -6,13 +6,19 @@ import cromwell.core.simpleton.WomValueSimpleton
 import cromwell.services.CallCaching.CallCachingEntryId
 
 object BackendCacheHitCopyingActor {
-  final case class CopyOutputsCommand(womValueSimpletons: Seq[WomValueSimpleton], jobDetritusFiles: Map[String, String], cacheHit: CallCachingEntryId, returnCode: Option[Int])
+  final case class CopyOutputsCommand(womValueSimpletons: Seq[WomValueSimpleton],
+                                      jobDetritusFiles: Map[String, String],
+                                      cacheHit: CallCachingEntryId,
+                                      returnCode: Option[Int]
+  )
 
   final case class CopyingOutputsFailedResponse(jobKey: JobKey, cacheCopyAttempt: Int, failure: CacheCopyFailure)
 
   sealed trait CacheCopyFailure
+
   /** A cache hit copy was attempted but failed.  */
   final case class CopyAttemptError(failure: Throwable) extends CacheCopyFailure
+
   /** Copying was requested for a blacklisted cache hit, however the cache hit copying actor found the hit had already
     * been blacklisted so no novel copy attempt was made. */
   final case class BlacklistSkip(failureCategory: MetricableCacheCopyErrorCategory) extends CacheCopyFailure
diff --git a/backend/src/main/scala/cromwell/backend/BackendInitializationData.scala b/backend/src/main/scala/cromwell/backend/BackendInitializationData.scala
index b1099b07155..8a9daa3cc39 100644
--- a/backend/src/main/scala/cromwell/backend/BackendInitializationData.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendInitializationData.scala
@@ -15,12 +15,11 @@ object BackendInitializationData {
     * @tparam A The type to cast the initialization data.
     * @return The initialization data as the type A.
     */
-  def as[A <: BackendInitializationData](initializationDataOption: Option[BackendInitializationData]): A = {
+  def as[A <: BackendInitializationData](initializationDataOption: Option[BackendInitializationData]): A =
     initializationDataOption match {
       case Some(initializationData) => initializationData.asInstanceOf[A]
       case None => throw new RuntimeException("Initialization data was not found.")
     }
-  }
 }
 
 object AllBackendInitializationData {
@@ -30,5 +29,6 @@ object AllBackendInitializationData {
 // Holds initialization data for all backends initialized for a workflow.
 case class AllBackendInitializationData(data: Map[String, Option[BackendInitializationData]]) {
   def get(backendName: String): Option[BackendInitializationData] = data.get(backendName).flatten
-  def getWorkflowRoots(): Set[Path] = data.values.collect({case Some(i: StandardInitializationData) => i.workflowPaths.workflowRoot}).toSet[Path]
+  def getWorkflowRoots(): Set[Path] =
+    data.values.collect { case Some(i: StandardInitializationData) => i.workflowPaths.workflowRoot }.toSet[Path]
 }
diff --git a/backend/src/main/scala/cromwell/backend/BackendJobExecutionActor.scala b/backend/src/main/scala/cromwell/backend/BackendJobExecutionActor.scala
index a58131363d3..493221ec3ce 100644
--- a/backend/src/main/scala/cromwell/backend/BackendJobExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendJobExecutionActor.scala
@@ -33,7 +33,8 @@ object BackendJobExecutionActor {
                                   jobDetritusFiles: Option[Map[String, Path]],
                                   executionEvents: Seq[ExecutionEvent],
                                   dockerImageUsed: Option[String],
-                                  resultGenerationMode: ResultGenerationMode) extends BackendJobExecutionResponse
+                                  resultGenerationMode: ResultGenerationMode
+  ) extends BackendJobExecutionResponse
 
   sealed trait ResultGenerationMode
   case object RunOnBackend extends ResultGenerationMode
@@ -41,25 +42,30 @@ object BackendJobExecutionActor {
   case object FetchedFromJobStore extends ResultGenerationMode
 
   case class JobAbortedResponse(jobKey: BackendJobDescriptorKey) extends BackendJobExecutionResponse
-  
-  sealed trait BackendJobFailedResponse extends BackendJobExecutionResponse {  def throwable: Throwable; def returnCode: Option[Int] }
-  case class JobFailedNonRetryableResponse(jobKey: JobKey, throwable: Throwable, returnCode: Option[Int]) extends BackendJobFailedResponse
-  case class JobFailedRetryableResponse(jobKey: BackendJobDescriptorKey,
-                                        throwable: Throwable,
-                                        returnCode: Option[Int]) extends BackendJobFailedResponse
-  
-  // Reconnection Exceptions
-  case class JobReconnectionNotSupportedException(jobKey: BackendJobDescriptorKey) extends Exception(
-    s"This backend does not support job reconnection. The status of the underlying job for ${jobKey.tag} cannot be known."
-  ) with CromwellFatalExceptionMarker
 
-  case class JobNotFoundException(jobKey: BackendJobDescriptorKey) extends Exception (
-    s"No backend job for ${jobKey.tag} could be found. The status of the underlying job cannot be known."
-  ) with CromwellFatalExceptionMarker
+  sealed trait BackendJobFailedResponse extends BackendJobExecutionResponse {
+    def throwable: Throwable; def returnCode: Option[Int]
+  }
+  case class JobFailedNonRetryableResponse(jobKey: JobKey, throwable: Throwable, returnCode: Option[Int])
+      extends BackendJobFailedResponse
+  case class JobFailedRetryableResponse(jobKey: BackendJobDescriptorKey, throwable: Throwable, returnCode: Option[Int])
+      extends BackendJobFailedResponse
 
-  def buildJobExecutionActorName(workflowId: WorkflowId, jobKey: BackendJobDescriptorKey) = {
+  // Reconnection Exceptions
+  case class JobReconnectionNotSupportedException(jobKey: BackendJobDescriptorKey)
+      extends Exception(
+        s"This backend does not support job reconnection. The status of the underlying job for ${jobKey.tag} cannot be known."
+      )
+      with CromwellFatalExceptionMarker
+
+  case class JobNotFoundException(jobKey: BackendJobDescriptorKey)
+      extends Exception(
+        s"No backend job for ${jobKey.tag} could be found. The status of the underlying job cannot be known."
+      )
+      with CromwellFatalExceptionMarker
+
+  def buildJobExecutionActorName(workflowId: WorkflowId, jobKey: BackendJobDescriptorKey) =
     s"$workflowId-BackendJobExecutionActor-${jobKey.tag}"
-  }
 }
 
 /**
@@ -92,7 +98,9 @@ trait BackendJobExecutionActor extends BackendJobLifecycleActor with ActorLoggin
     */
   def recover: Future[BackendJobExecutionResponse] = {
     log.warning("{} backend currently doesn't support recovering jobs. Starting {} again.",
-      jobTag, jobDescriptor.key.call.fullyQualifiedName)
+                jobTag,
+                jobDescriptor.key.call.fullyQualifiedName
+    )
     execute
   }
 
@@ -100,28 +108,24 @@ trait BackendJobExecutionActor extends BackendJobLifecycleActor with ActorLoggin
     * Tries to reconnect to a previously started job. This method differs from recover by sending a ReconnectionFailure
     * if it can't reconnect to the job for whatever reason. It should NOT execute the job if reconnection is impossible.
     */
-  def reconnect: Future[BackendJobExecutionResponse] = {
+  def reconnect: Future[BackendJobExecutionResponse] =
     Future.failed(JobReconnectionNotSupportedException(jobDescriptor.key))
-  }
 
   /**
     * Similar to reconnect, except that if the reconnection succeeds and the job is still running,
     * an abort attempt should be made.
     */
-  def reconnectToAborting: Future[BackendJobExecutionResponse] = {
+  def reconnectToAborting: Future[BackendJobExecutionResponse] =
     Future.failed(JobReconnectionNotSupportedException(jobDescriptor.key))
-  }
 
   /**
     * Abort a running job.
     */
-  def abort(): Unit = {
-    log.warning("{} backend currently doesn't support abort for {}.",
-      jobTag, jobDescriptor.key.call.fullyQualifiedName)
-  }
+  def abort(): Unit =
+    log.warning("{} backend currently doesn't support abort for {}.", jobTag, jobDescriptor.key.call.fullyQualifiedName)
 
-  def evaluateOutputs(wdlFunctions: IoFunctionSet,
-                      postMapper: WomValue => Try[WomValue] = v => Success(v))(implicit ec: ExecutionContext): EvaluatedJobOutputs = {
+  def evaluateOutputs(wdlFunctions: IoFunctionSet, postMapper: WomValue => Try[WomValue] = v => Success(v))(implicit
+    ec: ExecutionContext
+  ): EvaluatedJobOutputs =
     Await.result(OutputEvaluator.evaluateOutputs(jobDescriptor, wdlFunctions, postMapper), Duration.Inf)
-  }
 }
diff --git a/backend/src/main/scala/cromwell/backend/BackendLifecycleActor.scala b/backend/src/main/scala/cromwell/backend/BackendLifecycleActor.scala
index 72b0c24a800..450179c43e4 100644
--- a/backend/src/main/scala/cromwell/backend/BackendLifecycleActor.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendLifecycleActor.scala
@@ -30,7 +30,7 @@ trait BackendLifecycleActor extends Actor {
   /**
     * The execution context for the actor
     */
-  protected implicit def ec: ExecutionContext = context.dispatcher
+  implicit protected def ec: ExecutionContext = context.dispatcher
 
   /**
     * The configuration for the backend, in the context of the entire Cromwell configuration file.
@@ -39,7 +39,8 @@ trait BackendLifecycleActor extends Actor {
 
   protected def performActionThenRespond(operation: => Future[BackendWorkflowLifecycleActorResponse],
                                          onFailure: Throwable => BackendWorkflowLifecycleActorResponse,
-                                         andThen: => Unit = ()) = {
+                                         andThen: => Unit = ()
+  ) = {
     val respondTo: ActorRef = sender()
     operation onComplete {
       case Success(r) =>
@@ -54,9 +55,9 @@ trait BackendLifecycleActor extends Actor {
 
 trait BackendWorkflowLifecycleActor extends BackendLifecycleActor with WorkflowLogging {
 
-  //For Logging and boilerplate
-  override lazy final val workflowIdForLogging = workflowDescriptor.possiblyNotRootWorkflowId
-  override lazy final val rootWorkflowIdForLogging = workflowDescriptor.rootWorkflowId
+  // For Logging and boilerplate
+  final override lazy val workflowIdForLogging = workflowDescriptor.possiblyNotRootWorkflowId
+  final override lazy val rootWorkflowIdForLogging = workflowDescriptor.rootWorkflowId
 
   /**
     * The workflow descriptor for the workflow in which this Backend is being used
diff --git a/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala b/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala
index 0d38d87b01f..8be9a7f327c 100644
--- a/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala
@@ -25,7 +25,8 @@ trait BackendLifecycleActorFactory {
     */
   def name: String
 
-  def nameForCallCachingPurposes: String = configurationDescriptor.backendConfig.getOrElse("name-for-call-caching-purposes", name)
+  def nameForCallCachingPurposes: String =
+    configurationDescriptor.backendConfig.getOrElse("name-for-call-caching-purposes", name)
 
   /**
     * Config values for the backend, and a pointer to the global config.
@@ -44,7 +45,8 @@ trait BackendLifecycleActorFactory {
                                        ioActor: ActorRef,
                                        calls: Set[CommandCallNode],
                                        serviceRegistryActor: ActorRef,
-                                       restarting: Boolean): Option[Props] = None
+                                       restarting: Boolean
+  ): Option[Props] = None
 
   /* ****************************** */
   /*          Job Execution         */
@@ -54,7 +56,8 @@ trait BackendLifecycleActorFactory {
                              initializationData: Option[BackendInitializationData],
                              serviceRegistryActor: ActorRef,
                              ioActor: ActorRef,
-                             backendSingletonActor: Option[ActorRef]): Props
+                             backendSingletonActor: Option[ActorRef]
+  ): Props
 
   lazy val jobExecutionTokenType: JobTokenType = {
     val concurrentJobLimit = configurationDescriptor.backendConfig.as[Option[Int]]("concurrent-job-limit")
@@ -67,7 +70,8 @@ trait BackendLifecycleActorFactory {
   }
 
   lazy val jobRestartCheckTokenType: JobTokenType = {
-    val concurrentRestartCheckLimit = configurationDescriptor.globalConfig.as[Option[Int]]("system.job-restart-check-rate-control.max-jobs")
+    val concurrentRestartCheckLimit =
+      configurationDescriptor.globalConfig.as[Option[Int]]("system.job-restart-check-rate-control.max-jobs")
     // if defined, use per-backend hog-factor, otherwise use system-level value
     val hogFactor = configurationDescriptor.backendConfig.as[Option[Int]]("hog-factor") match {
       case Some(backendHogFactorValue) => backendHogFactorValue
@@ -85,13 +89,16 @@ trait BackendLifecycleActorFactory {
                                      calls: Set[CommandCallNode],
                                      jobExecutionMap: JobExecutionMap,
                                      workflowOutputs: CallOutputs,
-                                     initializationData: Option[BackendInitializationData]): Option[Props] = None
+                                     initializationData: Option[BackendInitializationData]
+  ): Option[Props] = None
 
   /* ****************************** */
   /*           Call Caching         */
   /* ****************************** */
 
-  def fileHashingActorProps: Option[(BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Option[ActorRef]) => Props] = None
+  def fileHashingActorProps
+    : Option[(BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Option[ActorRef]) => Props] =
+    None
 
   /**
     * Providing this method to generate Props for a cache hit copying actor is optional.
@@ -102,7 +109,9 @@ trait BackendLifecycleActorFactory {
     *
     * Simples!
     */
-  def cacheHitCopyingActorProps: Option[(BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Int, Option[BlacklistCache]) => Props] = None
+  def cacheHitCopyingActorProps: Option[
+    (BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Int, Option[BlacklistCache]) => Props
+  ] = None
 
   /* ****************************** */
   /*              Misc.             */
@@ -114,19 +123,26 @@ trait BackendLifecycleActorFactory {
                                   jobKey: BackendJobDescriptorKey,
                                   initializationData: Option[BackendInitializationData],
                                   ioActor: ActorRef,
-                                  ec: ExecutionContext): IoFunctionSet = NoIoFunctionSet
+                                  ec: ExecutionContext
+  ): IoFunctionSet = NoIoFunctionSet
 
   def pathBuilders(initializationDataOption: Option[BackendInitializationData]): PathBuilders = List.empty
 
-  def getExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor, backendConfig: Config, initializationData: Option[BackendInitializationData]): Path = {
+  def getExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor,
+                           backendConfig: Config,
+                           initializationData: Option[BackendInitializationData]
+  ): Path =
     new WorkflowPathsWithDocker(workflowDescriptor, backendConfig).executionRoot
-  }
 
-  def getWorkflowExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor, backendConfig: Config, initializationData: Option[BackendInitializationData]): Path = {
+  def getWorkflowExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor,
+                                   backendConfig: Config,
+                                   initializationData: Option[BackendInitializationData]
+  ): Path =
     new WorkflowPathsWithDocker(workflowDescriptor, backendConfig).workflowRoot
-  }
 
-  def runtimeAttributeDefinitions(initializationDataOption: Option[BackendInitializationData]): Set[RuntimeAttributeDefinition] = Set.empty
+  def runtimeAttributeDefinitions(
+    initializationDataOption: Option[BackendInitializationData]
+  ): Set[RuntimeAttributeDefinition] = Set.empty
 
   /**
     * A set of KV store keys that this backend requests that the engine lookup before running each job.
@@ -136,13 +152,16 @@ trait BackendLifecycleActorFactory {
   /**
     * A set of KV store keys that are requested and looked up on behalf of all backends before running each job.
     */
-  def defaultKeyValueStoreKeys: Seq[String] = Seq(BackendLifecycleActorFactory.FailedRetryCountKey, BackendLifecycleActorFactory.MemoryMultiplierKey)
+  def defaultKeyValueStoreKeys: Seq[String] =
+    Seq(BackendLifecycleActorFactory.FailedRetryCountKey, BackendLifecycleActorFactory.MemoryMultiplierKey)
 
   /*
    * Returns credentials that can be used to authenticate to a docker registry server
    * in order to obtain a docker hash.
    */
-  def dockerHashCredentials(workflowDescriptor: BackendWorkflowDescriptor, initializationDataOption: Option[BackendInitializationData]): List[Any] = List.empty
+  def dockerHashCredentials(workflowDescriptor: BackendWorkflowDescriptor,
+                            initializationDataOption: Option[BackendInitializationData]
+  ): List[Any] = List.empty
 }
 
 object BackendLifecycleActorFactory {
diff --git a/backend/src/main/scala/cromwell/backend/BackendWorkflowFinalizationActor.scala b/backend/src/main/scala/cromwell/backend/BackendWorkflowFinalizationActor.scala
index 2f77c2ebc2a..04abe76e372 100644
--- a/backend/src/main/scala/cromwell/backend/BackendWorkflowFinalizationActor.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendWorkflowFinalizationActor.scala
@@ -27,8 +27,8 @@ object BackendWorkflowFinalizationActor {
   */
 trait BackendWorkflowFinalizationActor extends BackendWorkflowLifecycleActor with ActorLogging {
 
-  def receive: Receive = LoggingReceive {
-    case Finalize => performActionThenRespond(afterAll() map { _ => FinalizationSuccess }, onFailure = FinalizationFailed)
+  def receive: Receive = LoggingReceive { case Finalize =>
+    performActionThenRespond(afterAll() map { _ => FinalizationSuccess }, onFailure = FinalizationFailed)
   }
 
   /**
diff --git a/backend/src/main/scala/cromwell/backend/BackendWorkflowInitializationActor.scala b/backend/src/main/scala/cromwell/backend/BackendWorkflowInitializationActor.scala
index bc3dd963f63..9f59a451478 100644
--- a/backend/src/main/scala/cromwell/backend/BackendWorkflowInitializationActor.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendWorkflowInitializationActor.scala
@@ -34,7 +34,8 @@ object BackendWorkflowInitializationActor {
   // Responses
   sealed trait BackendWorkflowInitializationActorResponse extends BackendWorkflowLifecycleActorResponse
   sealed trait InitializationResponse extends BackendWorkflowInitializationActorResponse
-  case class InitializationSuccess(backendInitializationData: Option[BackendInitializationData]) extends InitializationResponse
+  case class InitializationSuccess(backendInitializationData: Option[BackendInitializationData])
+      extends InitializationResponse
   case class InitializationFailed(reason: Throwable) extends Exception with InitializationResponse
 
   /**
@@ -70,24 +71,25 @@ object BackendWorkflowInitializationActor {
     * - It would be nice to memoize as much of the work that gets done here as possible so it doesn't have to all be
     *   repeated when the various `FooRuntimeAttributes` classes are created, in the spirit of #1076.
     */
-    def validateRuntimeAttributes(
-                                   taskName: String,
-                                   defaultRuntimeAttributes: Map[String, WomValue],
-                                   runtimeAttributes: Map[String, WomExpression],
-                                   runtimeAttributeValidators: Map[String, Option[WomExpression] => Boolean]
-                                 ): ValidatedNel[RuntimeAttributeValidationFailure, Unit] = {
-
-      //This map append will overwrite default key/values with runtime settings upon key collisions
-      val lookups = defaultRuntimeAttributes.safeMapValues(_.asWomExpression) ++ runtimeAttributes
-
-      runtimeAttributeValidators.toList.traverse{
-        case (attributeName, validator) =>
-          val runtimeAttributeValue: Option[WomExpression] = lookups.get(attributeName)
-          validator(runtimeAttributeValue).fold(
-            validNel(()),
-            Invalid(NonEmptyList.of(RuntimeAttributeValidationFailure(taskName, attributeName, runtimeAttributeValue)))
-          )
-      }.map(_ => ())
+  def validateRuntimeAttributes(
+    taskName: String,
+    defaultRuntimeAttributes: Map[String, WomValue],
+    runtimeAttributes: Map[String, WomExpression],
+    runtimeAttributeValidators: Map[String, Option[WomExpression] => Boolean]
+  ): ValidatedNel[RuntimeAttributeValidationFailure, Unit] = {
+
+    // This map append will overwrite default key/values with runtime settings upon key collisions
+    val lookups = defaultRuntimeAttributes.safeMapValues(_.asWomExpression) ++ runtimeAttributes
+
+    runtimeAttributeValidators.toList
+      .traverse { case (attributeName, validator) =>
+        val runtimeAttributeValue: Option[WomExpression] = lookups.get(attributeName)
+        validator(runtimeAttributeValue).fold(
+          validNel(()),
+          Invalid(NonEmptyList.of(RuntimeAttributeValidationFailure(taskName, attributeName, runtimeAttributeValue)))
+        )
+      }
+      .map(_ => ())
   }
 }
 
@@ -110,7 +112,9 @@ trait BackendWorkflowInitializationActor extends BackendWorkflowLifecycleActor w
     * declarations will fail evaluation and return `true` from this predicate, even if the type could be determined
     * to be wrong with consideration of task declarations or inputs.
     */
-  protected def womTypePredicate(valueRequired: Boolean, predicate: WomType => Boolean)(womExpressionMaybe: Option[WomExpression]): Boolean = {
+  protected def womTypePredicate(valueRequired: Boolean, predicate: WomType => Boolean)(
+    womExpressionMaybe: Option[WomExpression]
+  ): Boolean =
     womExpressionMaybe match {
       case None => !valueRequired
       case Some(womExpression: WomExpression) =>
@@ -119,29 +123,31 @@ trait BackendWorkflowInitializationActor extends BackendWorkflowLifecycleActor w
           case Invalid(_) => true // If we can't evaluate it, we'll let it pass for now...
         }
     }
-  }
 
   /**
     * This predicate is only appropriate for validation during workflow initialization.  The logic does not differentiate
     * between evaluation failures due to missing call inputs or evaluation failures due to malformed expressions, and will
     * return `true` in both cases.
     */
-  protected def continueOnReturnCodePredicate(valueRequired: Boolean)(womExpressionMaybe: Option[WomValue]): Boolean = {
-    ContinueOnReturnCodeValidation.default(configurationDescriptor.backendRuntimeAttributesConfig).validateOptionalWomValue(womExpressionMaybe)
-  }
+  protected def continueOnReturnCodePredicate(valueRequired: Boolean)(womExpressionMaybe: Option[WomValue]): Boolean =
+    ContinueOnReturnCodeValidation
+      .default(configurationDescriptor.backendRuntimeAttributesConfig)
+      .validateOptionalWomValue(womExpressionMaybe)
 
   protected def runtimeAttributeValidators: Map[String, Option[WomExpression] => Boolean]
 
   // FIXME: If a workflow executes jobs using multiple backends,
   // each backend will try to write its own workflow root and override any previous one.
   // They should be structured differently or at least be prefixed by the backend name
-  protected def publishWorkflowRoot(workflowRoot: String): Unit = {
-    serviceRegistryActor ! PutMetadataAction(MetadataEvent(MetadataKey(workflowDescriptor.id, None, WorkflowMetadataKeys.WorkflowRoot), MetadataValue(workflowRoot)))
-  }
+  protected def publishWorkflowRoot(workflowRoot: String): Unit =
+    serviceRegistryActor ! PutMetadataAction(
+      MetadataEvent(MetadataKey(workflowDescriptor.id, None, WorkflowMetadataKeys.WorkflowRoot),
+                    MetadataValue(workflowRoot)
+      )
+    )
 
   protected def coerceDefaultRuntimeAttributes(options: WorkflowOptions): Try[Map[String, WomValue]]
 
-
   def receive: Receive = LoggingReceive {
     case Initialize => performActionThenRespond(initSequence(), onFailure = InitializationFailed)
     case Abort => abortInitialization()
@@ -154,10 +160,11 @@ trait BackendWorkflowInitializationActor extends BackendWorkflowLifecycleActor w
     for {
       defaultRuntimeAttributes <- coerceDefaultRuntimeAttributes(workflowDescriptor.workflowOptions) |> Future.fromTry _
       taskList = calls.toList.map(_.callable).map(t => t.name -> t.runtimeAttributes.attributes)
-      _ <- taskList.
-            traverse{
-              case (name, runtimeAttributes) => validateRuntimeAttributes(name, defaultRuntimeAttributes, runtimeAttributes, runtimeAttributeValidators)
-            }.toFuture(errors => RuntimeAttributeValidationFailures(errors.toList))
+      _ <- taskList
+        .traverse { case (name, runtimeAttributes) =>
+          validateRuntimeAttributes(name, defaultRuntimeAttributes, runtimeAttributes, runtimeAttributeValidators)
+        }
+        .toFuture(errors => RuntimeAttributeValidationFailures(errors.toList))
       _ <- validate()
       data <- beforeAll()
     } yield InitializationSuccess(data)
diff --git a/backend/src/main/scala/cromwell/backend/Command.scala b/backend/src/main/scala/cromwell/backend/Command.scala
index 40310c68485..3a4eaf3b88a 100644
--- a/backend/src/main/scala/cromwell/backend/Command.scala
+++ b/backend/src/main/scala/cromwell/backend/Command.scala
@@ -24,11 +24,16 @@ object Command {
     */
   def instantiate(jobDescriptor: BackendJobDescriptor,
                   callEngineFunction: IoFunctionSet,
-                  inputsPreProcessor: WomEvaluatedCallInputs => Try[WomEvaluatedCallInputs] = (i: WomEvaluatedCallInputs) => Success(i),
+                  inputsPreProcessor: WomEvaluatedCallInputs => Try[WomEvaluatedCallInputs] =
+                    (i: WomEvaluatedCallInputs) => Success(i),
                   valueMapper: WomValue => WomValue,
-                  runtimeEnvironment: RuntimeEnvironment): ErrorOr[InstantiatedCommand] = {
+                  runtimeEnvironment: RuntimeEnvironment
+  ): ErrorOr[InstantiatedCommand] =
     inputsPreProcessor(jobDescriptor.evaluatedTaskInputs).toErrorOr flatMap { mappedInputs =>
-      jobDescriptor.taskCall.callable.instantiateCommand(mappedInputs, callEngineFunction, valueMapper, runtimeEnvironment)
+      jobDescriptor.taskCall.callable.instantiateCommand(mappedInputs,
+                                                         callEngineFunction,
+                                                         valueMapper,
+                                                         runtimeEnvironment
+      )
     }
-  }
 }
diff --git a/backend/src/main/scala/cromwell/backend/FileSizeTooBig.scala b/backend/src/main/scala/cromwell/backend/FileSizeTooBig.scala
index 2580d9218fc..79ccc698b05 100644
--- a/backend/src/main/scala/cromwell/backend/FileSizeTooBig.scala
+++ b/backend/src/main/scala/cromwell/backend/FileSizeTooBig.scala
@@ -1,4 +1,3 @@
 package cromwell.backend
 
 case class FileSizeTooBig(override val getMessage: String) extends Exception
-
diff --git a/backend/src/main/scala/cromwell/backend/OutputEvaluator.scala b/backend/src/main/scala/cromwell/backend/OutputEvaluator.scala
index 2bf215fb0fa..8c799e36ad5 100644
--- a/backend/src/main/scala/cromwell/backend/OutputEvaluator.scala
+++ b/backend/src/main/scala/cromwell/backend/OutputEvaluator.scala
@@ -26,15 +26,20 @@ object OutputEvaluator {
 
   def evaluateOutputs(jobDescriptor: BackendJobDescriptor,
                       ioFunctions: IoFunctionSet,
-                      postMapper: WomValue => Try[WomValue] = v => Success(v))(implicit ec: ExecutionContext): Future[EvaluatedJobOutputs] = {
+                      postMapper: WomValue => Try[WomValue] = v => Success(v)
+  )(implicit ec: ExecutionContext): Future[EvaluatedJobOutputs] = {
     val taskInputValues: Map[String, WomValue] = jobDescriptor.localInputs
 
-    def foldFunction(accumulatedOutputs: Try[ErrorOr[List[(OutputPort, WomValue)]]], output: ExpressionBasedOutputPort) = accumulatedOutputs flatMap { accumulated =>
+    def foldFunction(accumulatedOutputs: Try[ErrorOr[List[(OutputPort, WomValue)]]],
+                     output: ExpressionBasedOutputPort
+    ) = accumulatedOutputs flatMap { accumulated =>
       // Extract the valid pairs from the job outputs accumulated so far, and add to it the inputs (outputs can also reference inputs)
       val allKnownValues: Map[String, WomValue] = accumulated match {
         case Valid(outputs) =>
           // The evaluateValue methods needs a Map[String, WomValue], use the output port name for already computed outputs
-          outputs.toMap[OutputPort, WomValue].map({ case (port, value) => port.internalName -> value }) ++ taskInputValues
+          outputs.toMap[OutputPort, WomValue].map { case (port, value) =>
+            port.internalName -> value
+          } ++ taskInputValues
         case Invalid(_) => taskInputValues
       }
 
@@ -45,22 +50,24 @@ object OutputEvaluator {
         }
 
       // Attempt to coerce the womValue to the desired output type
-      def coerceOutputValue(womValue: WomValue, coerceTo: WomType): OutputResult[WomValue] = {
+      def coerceOutputValue(womValue: WomValue, coerceTo: WomType): OutputResult[WomValue] =
         fromEither[Try](
           // TODO WOM: coerceRawValue should return an ErrorOr
-          coerceTo.coerceRawValue(womValue).toEither.leftMap(t => NonEmptyList.one(t.getClass.getSimpleName + ": " + t.getMessage))
+          coerceTo
+            .coerceRawValue(womValue)
+            .toEither
+            .leftMap(t => NonEmptyList.one(t.getClass.getSimpleName + ": " + t.getMessage))
         )
-      }
 
       /*
-        * Go through evaluation, coercion and post processing.
-        * Transform the result to a validated Try[ErrorOr[(String, WomValue)]] with toValidated
-        * If we have a valid pair, add it to the previously accumulated outputs, otherwise combine the Nels of errors
+       * Go through evaluation, coercion and post processing.
+       * Transform the result to a validated Try[ErrorOr[(String, WomValue)]] with toValidated
+       * If we have a valid pair, add it to the previously accumulated outputs, otherwise combine the Nels of errors
        */
       val evaluated = for {
         evaluated <- evaluateOutputExpression
         coerced <- coerceOutputValue(evaluated, output.womType)
-        postProcessed <- EitherT { postMapper(coerced).map(_.validNelCheck) }: OutputResult[WomValue]
+        postProcessed <- EitherT(postMapper(coerced).map(_.validNelCheck)): OutputResult[WomValue]
         pair = output -> postProcessed
       } yield pair
 
@@ -73,24 +80,27 @@ object OutputEvaluator {
     val emptyValue = Success(List.empty[(OutputPort, WomValue)].validNel): Try[ErrorOr[List[(OutputPort, WomValue)]]]
 
     // Fold over the outputs to evaluate them in order, map the result to an EvaluatedJobOutputs
-    def fromOutputPorts: EvaluatedJobOutputs = jobDescriptor.taskCall.expressionBasedOutputPorts.foldLeft(emptyValue)(foldFunction) match {
-      case Success(Valid(outputs)) => ValidJobOutputs(CallOutputs(outputs.toMap))
-      case Success(Invalid(errors)) => InvalidJobOutputs(errors)
-      case Failure(exception) => JobOutputsEvaluationException(exception)
-    }
+    def fromOutputPorts: EvaluatedJobOutputs =
+      jobDescriptor.taskCall.expressionBasedOutputPorts.foldLeft(emptyValue)(foldFunction) match {
+        case Success(Valid(outputs)) => ValidJobOutputs(CallOutputs(outputs.toMap))
+        case Success(Invalid(errors)) => InvalidJobOutputs(errors)
+        case Failure(exception) => JobOutputsEvaluationException(exception)
+      }
 
     /*
-      * Because Cromwell doesn't trust anyone, if custom evaluation is provided,
-      * still make sure that all the output ports have been filled with values
+     * Because Cromwell doesn't trust anyone, if custom evaluation is provided,
+     * still make sure that all the output ports have been filled with values
      */
     def validateCustomEvaluation(outputs: Map[OutputPort, WomValue]): EvaluatedJobOutputs = {
-      def toError(outputPort: OutputPort) = s"Missing output value for ${outputPort.identifier.fullyQualifiedName.value}"
+      def toError(outputPort: OutputPort) =
+        s"Missing output value for ${outputPort.identifier.fullyQualifiedName.value}"
 
       jobDescriptor.taskCall.expressionBasedOutputPorts.diff(outputs.keySet.toList) match {
         case Nil =>
           val errorMessagePrefix = "Error applying postMapper in short-circuit output evaluation"
-          TryUtil.sequenceMap(outputs map { case (k, v) => (k, postMapper(v))}, errorMessagePrefix) match {
-            case Failure(e) => InvalidJobOutputs(NonEmptyList.of(e.getMessage, e.getStackTrace.take(5).toIndexedSeq.map(_.toString):_*))
+          TryUtil.sequenceMap(outputs map { case (k, v) => (k, postMapper(v)) }, errorMessagePrefix) match {
+            case Failure(e) =>
+              InvalidJobOutputs(NonEmptyList.of(e.getMessage, e.getStackTrace.take(5).toIndexedSeq.map(_.toString): _*))
             case Success(postMappedOutputs) => ValidJobOutputs(CallOutputs(postMappedOutputs))
           }
         case head :: tail => InvalidJobOutputs(NonEmptyList.of(toError(head), tail.map(toError): _*))
@@ -98,18 +108,20 @@ object OutputEvaluator {
     }
 
     /*
-      * See if the task definition has "short-circuit" for the default output evaluation.
-      * In the case of CWL for example, this gives a chance to look for cwl.output.json and use it as the output of the tool,
-      * instead of the default behavior of going over each output port of the task and evaluates their expression.
-      * If the "customOutputEvaluation" returns None (which will happen if the cwl.output.json is not there, as well as for all WDL workflows),
-      * we fallback to the default behavior.
+     * See if the task definition has "short-circuit" for the default output evaluation.
+     * In the case of CWL for example, this gives a chance to look for cwl.output.json and use it as the output of the tool,
+     * instead of the default behavior of going over each output port of the task and evaluates their expression.
+     * If the "customOutputEvaluation" returns None (which will happen if the cwl.output.json is not there, as well as for all WDL workflows),
+     * we fallback to the default behavior.
      */
-    jobDescriptor.taskCall.customOutputEvaluation(taskInputValues, ioFunctions, ec).value
-      .map({
+    jobDescriptor.taskCall
+      .customOutputEvaluation(taskInputValues, ioFunctions, ec)
+      .value
+      .map {
         case Some(Right(outputs)) => validateCustomEvaluation(outputs)
         case Some(Left(errors)) => InvalidJobOutputs(errors)
         // If it returns an empty value, fallback to canonical output evaluation
         case None => fromOutputPorts
-      })
+      }
   }
 }
diff --git a/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala b/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala
index 33e6e2db020..7e73301af71 100644
--- a/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala
+++ b/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala
@@ -22,7 +22,8 @@ object RuntimeAttributeDefinition {
 
   def evaluateRuntimeAttributes(unevaluated: RuntimeAttributes,
                                 wdlFunctions: IoFunctionSet,
-                                evaluatedInputs: Map[InputDefinition, WomValue]): ErrorOr[Map[String, WomValue]] = {
+                                evaluatedInputs: Map[InputDefinition, WomValue]
+  ): ErrorOr[Map[String, WomValue]] = {
     import common.validation.ErrorOr._
     val inputsMap = evaluatedInputs map { case (x, y) => x.name -> y }
     unevaluated.attributes.traverseValues(_.evaluateValue(inputsMap, wdlFunctions))
@@ -32,18 +33,23 @@ object RuntimeAttributeDefinition {
     val successfulEvaluations = evaluatedDeclarations collect {
       case (k, v) if v.isSuccess => k.name -> v.get
     }
-    successfulEvaluations.getOrElse(identifier, throw new WomExpressionException(s"Could not resolve variable $identifier as a task input"))
+    successfulEvaluations.getOrElse(
+      identifier,
+      throw new WomExpressionException(s"Could not resolve variable $identifier as a task input")
+    )
   }
 
-  def addDefaultsToAttributes(runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition], workflowOptions: WorkflowOptions)
-                             (specifiedAttributes: Map[LocallyQualifiedName, WomValue]): Map[LocallyQualifiedName, WomValue] = {
+  def addDefaultsToAttributes(runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition],
+                              workflowOptions: WorkflowOptions
+  )(specifiedAttributes: Map[LocallyQualifiedName, WomValue]): Map[LocallyQualifiedName, WomValue] = {
     import WomValueJsonFormatter._
 
     def isUnspecifiedAttribute(name: String) = !specifiedAttributes.contains(name)
 
     val missing = runtimeAttributeDefinitions filter { x => isUnspecifiedAttribute(x.name) }
     val defaults = missing map { x => (x, workflowOptions.getDefaultRuntimeOption(x.name)) } collect {
-      case (runtimeAttributeDefinition, Success(jsValue)) => runtimeAttributeDefinition.name -> jsValue.convertTo[WomValue]
+      case (runtimeAttributeDefinition, Success(jsValue)) =>
+        runtimeAttributeDefinition.name -> jsValue.convertTo[WomValue]
       case (RuntimeAttributeDefinition(name, Some(factoryDefault), _), _) => name -> factoryDefault
     }
     specifiedAttributes ++ defaults
diff --git a/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala b/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala
index c6c4cd22c21..40f8f1f7b07 100644
--- a/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala
+++ b/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala
@@ -15,31 +15,33 @@ import wom.values.WomValue
 
 object RuntimeEnvironmentBuilder {
 
-  def apply(runtimeAttributes: Map[String, WomValue], callRoot: Path, callExecutionRoot: Path): MinimumRuntimeSettings => RuntimeEnvironment = {
-    minimums =>
+  def apply(runtimeAttributes: Map[String, WomValue],
+            callRoot: Path,
+            callExecutionRoot: Path
+  ): MinimumRuntimeSettings => RuntimeEnvironment = { minimums =>
+    val outputPath: String = callExecutionRoot.pathAsString
 
-      val outputPath: String = callExecutionRoot.pathAsString
+    val tempPath: String = {
+      val uuid = UUID.randomUUID().toString
+      val hash = uuid.substring(0, uuid.indexOf('-'))
+      callRoot.resolve(s"tmp.$hash").pathAsString
+    }
 
-      val tempPath: String = {
-        val uuid = UUID.randomUUID().toString
-        val hash = uuid.substring(0, uuid.indexOf('-'))
-        callRoot.resolve(s"tmp.$hash").pathAsString
-      }
+    val cores: Int Refined Positive = CpuValidation.instanceMin.validate(runtimeAttributes).getOrElse(minimums.cores)
 
-      val cores: Int Refined Positive = CpuValidation.instanceMin.validate(runtimeAttributes).getOrElse(minimums.cores)
+    val memoryInMB: Double =
+      MemoryValidation
+        .instance()
+        .validate(runtimeAttributes)
+        .map(_.to(MemoryUnit.MB).amount)
+        .getOrElse(minimums.ram.amount)
 
-      val memoryInMB: Double =
-        MemoryValidation.instance().
-          validate(runtimeAttributes).
-          map(_.to(MemoryUnit.MB).amount).
-          getOrElse(minimums.ram.amount)
+    // TODO: Read these from somewhere else
+    val outputPathSize: Long = minimums.outputPathSize
 
-      //TODO: Read these from somewhere else
-      val outputPathSize: Long = minimums.outputPathSize
+    val tempPathSize: Long = minimums.outputPathSize
 
-      val tempPathSize: Long = minimums.outputPathSize
-
-      RuntimeEnvironment(outputPath, tempPath, cores, memoryInMB, outputPathSize, tempPathSize)
+    RuntimeEnvironment(outputPath, tempPath, cores, memoryInMB, outputPathSize, tempPathSize)
   }
 
   /**
@@ -48,12 +50,14 @@ object RuntimeEnvironmentBuilder {
     * "For cores, ram, outdirSize and tmpdirSize, if an implementation can't provide the actual number of reserved cores
     * during the expression evaluation time, it should report back the minimal requested amount."
     */
-  def apply(runtimeAttributes: Map[String, WomValue], jobPaths: JobPaths): MinimumRuntimeSettings => RuntimeEnvironment = {
+  def apply(runtimeAttributes: Map[String, WomValue],
+            jobPaths: JobPaths
+  ): MinimumRuntimeSettings => RuntimeEnvironment =
     this.apply(runtimeAttributes, jobPaths.callRoot, jobPaths.callExecutionRoot)
-  }
 }
 
 case class MinimumRuntimeSettings(cores: Int Refined Positive = refineMV(1),
                                   ram: MemorySize = MemorySize(4, MemoryUnit.GB),
                                   outputPathSize: Long = Long.MaxValue,
-                                  tempPathSize: Long = Long.MaxValue)
+                                  tempPathSize: Long = Long.MaxValue
+)
diff --git a/backend/src/main/scala/cromwell/backend/SlowJobWarning.scala b/backend/src/main/scala/cromwell/backend/SlowJobWarning.scala
index 074895e366a..22db6d7f92a 100644
--- a/backend/src/main/scala/cromwell/backend/SlowJobWarning.scala
+++ b/backend/src/main/scala/cromwell/backend/SlowJobWarning.scala
@@ -12,20 +12,21 @@ trait SlowJobWarning { this: Actor with ActorLogging =>
   def slowJobWarningReceive: Actor.Receive = {
     case WarnAboutSlownessAfter(jobId, duration) =>
       alreadyWarned = false
-      warningDetails = Option(WarningDetails(jobId, OffsetDateTime.now(), OffsetDateTime.now().plusSeconds(duration.toSeconds)))
+      warningDetails = Option(
+        WarningDetails(jobId, OffsetDateTime.now(), OffsetDateTime.now().plusSeconds(duration.toSeconds))
+      )
     case WarnAboutSlownessIfNecessary => handleWarnMessage()
   }
 
   var warningDetails: Option[WarningDetails] = None
   var alreadyWarned: Boolean = false
 
-  def warnAboutSlowJobIfNecessary(jobId: String) = {
+  def warnAboutSlowJobIfNecessary(jobId: String) =
     // Don't do anything here because we might need to update state.
     // Instead, send a message and handle this in the receive block.
     self ! WarnAboutSlownessIfNecessary
-  }
 
-  private def handleWarnMessage(): Unit = {
+  private def handleWarnMessage(): Unit =
     if (!alreadyWarned) {
       warningDetails match {
         case Some(WarningDetails(jobId, startTime, warningTime)) if OffsetDateTime.now().isAfter(warningTime) =>
@@ -34,7 +35,6 @@ trait SlowJobWarning { this: Actor with ActorLogging =>
         case _ => // Nothing to do
       }
     }
-  }
 
 }
 
diff --git a/backend/src/main/scala/cromwell/backend/WriteFunctions.scala b/backend/src/main/scala/cromwell/backend/WriteFunctions.scala
index 572a417c047..5a8224d37a6 100644
--- a/backend/src/main/scala/cromwell/backend/WriteFunctions.scala
+++ b/backend/src/main/scala/cromwell/backend/WriteFunctions.scala
@@ -24,13 +24,14 @@ trait WriteFunctions extends PathFactory with IoFunctionSet with AsyncIoFunction
     */
   def writeDirectory: Path
 
-  private lazy val _writeDirectory = if (isDocker) writeDirectory.createPermissionedDirectories() else writeDirectory.createDirectories()
+  private lazy val _writeDirectory =
+    if (isDocker) writeDirectory.createPermissionedDirectories() else writeDirectory.createDirectories()
 
   override def createTemporaryDirectory(name: Option[String]) = {
     val tempDirPath = _writeDirectory / name.getOrElse(UUID.randomUUID().toString)
     // This is evil, but has the added advantage to work both for cloud and local
     val tempDirHiddenFile = tempDirPath / ".file"
-    asyncIo.writeAsync(tempDirHiddenFile, "", OpenOptions.default) as { tempDirPath.pathAsString }
+    asyncIo.writeAsync(tempDirHiddenFile, "", OpenOptions.default) as tempDirPath.pathAsString
   }
 
   protected def writeAsync(file: Path, content: String) = asyncIo.writeAsync(file, content, OpenOptions.default)
@@ -38,21 +39,22 @@ trait WriteFunctions extends PathFactory with IoFunctionSet with AsyncIoFunction
   override def writeFile(path: String, content: String): Future[WomSingleFile] = {
     val file = _writeDirectory / path
     asyncIo.existsAsync(file) flatMap {
-      case false => writeAsync(file, content) as { WomSingleFile(file.pathAsString) }
+      case false => writeAsync(file, content) as WomSingleFile(file.pathAsString)
       case true => Future.successful(WomSingleFile(file.pathAsString))
     }
   }
 
   private val relativeToLocal = System.getProperty("user.dir").ensureSlashed
 
-  def relativeToAbsolutePath(pathFrom: String): String = if (buildPath(pathFrom).isAbsolute) pathFrom else relativeToLocal + pathFrom
+  def relativeToAbsolutePath(pathFrom: String): String =
+    if (buildPath(pathFrom).isAbsolute) pathFrom else relativeToLocal + pathFrom
 
   override def copyFile(pathFrom: String, targetName: String): Future[WomSingleFile] = {
     val source = buildPath(relativeToAbsolutePath(pathFrom))
     val destination = _writeDirectory / targetName
 
-    asyncIo.copyAsync(source, destination).as(WomSingleFile(destination.pathAsString)) recoverWith {
-      case e => Future.failed(new Exception(s"Could not copy ${source.toAbsolutePath} to ${destination.toAbsolutePath}", e))
+    asyncIo.copyAsync(source, destination).as(WomSingleFile(destination.pathAsString)) recoverWith { case e =>
+      Future.failed(new Exception(s"Could not copy ${source.toAbsolutePath} to ${destination.toAbsolutePath}", e))
     }
   }
 }
diff --git a/backend/src/main/scala/cromwell/backend/async/AsyncBackendJobExecutionActor.scala b/backend/src/main/scala/cromwell/backend/async/AsyncBackendJobExecutionActor.scala
index 241081f5a02..2872633d9bd 100644
--- a/backend/src/main/scala/cromwell/backend/async/AsyncBackendJobExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/async/AsyncBackendJobExecutionActor.scala
@@ -1,6 +1,5 @@
 package cromwell.backend.async
 
-
 import java.util.concurrent.ExecutionException
 
 import akka.actor.{Actor, ActorLogging, ActorRef}
@@ -18,10 +17,12 @@ import scala.util.{Failure, Success}
 object AsyncBackendJobExecutionActor {
 
   sealed trait AsyncBackendJobExecutionActorMessage
-  private final case class IssuePollRequest(executionHandle: ExecutionHandle) extends AsyncBackendJobExecutionActorMessage
-  private final case class PollResponseReceived(executionHandle: ExecutionHandle) extends AsyncBackendJobExecutionActorMessage
-  private final case class FailAndStop(reason: Throwable) extends AsyncBackendJobExecutionActorMessage
-  private final case class Finish(executionHandle: ExecutionHandle) extends AsyncBackendJobExecutionActorMessage
+  final private case class IssuePollRequest(executionHandle: ExecutionHandle)
+      extends AsyncBackendJobExecutionActorMessage
+  final private case class PollResponseReceived(executionHandle: ExecutionHandle)
+      extends AsyncBackendJobExecutionActorMessage
+  final private case class FailAndStop(reason: Throwable) extends AsyncBackendJobExecutionActorMessage
+  final private case class Finish(executionHandle: ExecutionHandle) extends AsyncBackendJobExecutionActorMessage
 
   trait JobId
 
@@ -57,27 +58,24 @@ trait AsyncBackendJobExecutionActor { this: Actor with ActorLogging with SlowJob
 
   def isTransient(throwable: Throwable): Boolean = false
 
-  private def withRetry[A](work: () => Future[A], backOff: SimpleExponentialBackoff): Future[A] = {
+  private def withRetry[A](work: () => Future[A], backOff: SimpleExponentialBackoff): Future[A] =
     Retry.withRetry(work, isTransient = isTransient, isFatal = isFatal, backoff = backOff)(context.system)
-  }
 
-  private def robustExecuteOrRecover(mode: ExecutionMode) = {
+  private def robustExecuteOrRecover(mode: ExecutionMode) =
     withRetry(() => executeOrRecover(mode), executeOrRecoverBackOff) onComplete {
       case Success(h) => self ! IssuePollRequest(h)
       case Failure(t) => self ! FailAndStop(t)
     }
-  }
 
   def pollBackOff: SimpleExponentialBackoff
 
   def executeOrRecoverBackOff: SimpleExponentialBackoff
 
-  private def robustPoll(handle: ExecutionHandle) = {
+  private def robustPoll(handle: ExecutionHandle) =
     withRetry(() => poll(handle), pollBackOff) onComplete {
       case Success(h) => self ! PollResponseReceived(h)
       case Failure(t) => self ! FailAndStop(t)
     }
-  }
 
   private def failAndStop(t: Throwable) = {
     completionPromise.success(JobFailedNonRetryableResponse(jobDescriptor.key, t, None))
@@ -94,7 +92,16 @@ trait AsyncBackendJobExecutionActor { this: Actor with ActorLogging with SlowJob
       context.system.scheduler.scheduleOnce(pollBackOff.backoffMillis.millis, self, IssuePollRequest(handle))
       ()
     case Finish(SuccessfulExecutionHandle(outputs, returnCode, jobDetritusFiles, executionEvents, _)) =>
-      completionPromise.success(JobSucceededResponse(jobDescriptor.key, Some(returnCode), outputs, Option(jobDetritusFiles), executionEvents, dockerImageUsed, resultGenerationMode = RunOnBackend))
+      completionPromise.success(
+        JobSucceededResponse(jobDescriptor.key,
+                             Some(returnCode),
+                             outputs,
+                             Option(jobDetritusFiles),
+                             executionEvents,
+                             dockerImageUsed,
+                             resultGenerationMode = RunOnBackend
+        )
+      )
       context.stop(self)
     case Finish(FailedNonRetryableExecutionHandle(throwable, returnCode, _)) =>
       completionPromise.success(JobFailedNonRetryableResponse(jobDescriptor.key, throwable, returnCode))
@@ -133,5 +140,5 @@ trait AsyncBackendJobExecutionActor { this: Actor with ActorLogging with SlowJob
 
   def jobDescriptor: BackendJobDescriptor
 
-  protected implicit def ec: ExecutionContext
+  implicit protected def ec: ExecutionContext
 }
diff --git a/backend/src/main/scala/cromwell/backend/async/ExecutionHandle.scala b/backend/src/main/scala/cromwell/backend/async/ExecutionHandle.scala
index ab1354e4323..ff6a088b1f9 100644
--- a/backend/src/main/scala/cromwell/backend/async/ExecutionHandle.scala
+++ b/backend/src/main/scala/cromwell/backend/async/ExecutionHandle.scala
@@ -15,8 +15,7 @@ sealed trait ExecutionHandle {
   def result: ExecutionResult
 }
 
-final case class PendingExecutionHandle[BackendJobId <: JobId, BackendRunInfo, BackendRunState]
-(
+final case class PendingExecutionHandle[BackendJobId <: JobId, BackendRunInfo, BackendRunState](
   jobDescriptor: BackendJobDescriptor,
   pendingJob: BackendJobId,
   runInfo: Option[BackendRunInfo],
@@ -30,7 +29,8 @@ final case class SuccessfulExecutionHandle(outputs: CallOutputs,
                                            returnCode: Int,
                                            jobDetritusFiles: Map[String, Path],
                                            executionEvents: Seq[ExecutionEvent],
-                                           resultsClonedFrom: Option[BackendJobDescriptor] = None) extends ExecutionHandle {
+                                           resultsClonedFrom: Option[BackendJobDescriptor] = None
+) extends ExecutionHandle {
   override val isDone = true
   override val result = SuccessfulExecution(outputs, returnCode, jobDetritusFiles, executionEvents, resultsClonedFrom)
 }
@@ -41,7 +41,8 @@ sealed trait FailedExecutionHandle extends ExecutionHandle {
 
 final case class FailedNonRetryableExecutionHandle(throwable: Throwable,
                                                    returnCode: Option[Int] = None,
-                                                   override val kvPairsToSave: Option[Seq[KvPair]]) extends FailedExecutionHandle {
+                                                   override val kvPairsToSave: Option[Seq[KvPair]]
+) extends FailedExecutionHandle {
 
   override val isDone = true
   override val result = NonRetryableExecution(throwable, returnCode)
@@ -49,7 +50,8 @@ final case class FailedNonRetryableExecutionHandle(throwable: Throwable,
 
 final case class FailedRetryableExecutionHandle(throwable: Throwable,
                                                 returnCode: Option[Int] = None,
-                                                override val kvPairsToSave: Option[Seq[KvPair]]) extends FailedExecutionHandle {
+                                                override val kvPairsToSave: Option[Seq[KvPair]]
+) extends FailedExecutionHandle {
 
   override val isDone = true
   override val result = RetryableExecution(throwable, returnCode)
diff --git a/backend/src/main/scala/cromwell/backend/async/ExecutionResult.scala b/backend/src/main/scala/cromwell/backend/async/ExecutionResult.scala
index fc8f95e049b..b3c4bcda692 100644
--- a/backend/src/main/scala/cromwell/backend/async/ExecutionResult.scala
+++ b/backend/src/main/scala/cromwell/backend/async/ExecutionResult.scala
@@ -16,7 +16,8 @@ final case class SuccessfulExecution(outputs: CallOutputs,
                                      returnCode: Int,
                                      jobDetritusFiles: Map[String, Path],
                                      executionEvents: Seq[ExecutionEvent],
-                                     resultsClonedFrom: Option[BackendJobDescriptor] = None) extends ExecutionResult
+                                     resultsClonedFrom: Option[BackendJobDescriptor] = None
+) extends ExecutionResult
 
 /**
  * A user-requested abort of the command.
diff --git a/backend/src/main/scala/cromwell/backend/async/KnownJobFailureException.scala b/backend/src/main/scala/cromwell/backend/async/KnownJobFailureException.scala
index 8dd9aef3544..e106f06fcd2 100644
--- a/backend/src/main/scala/cromwell/backend/async/KnownJobFailureException.scala
+++ b/backend/src/main/scala/cromwell/backend/async/KnownJobFailureException.scala
@@ -9,61 +9,77 @@ abstract class KnownJobFailureException extends Exception {
   def stderrPath: Option[Path]
 }
 
-final case class WrongReturnCode(jobTag: String, returnCode: Int, stderrPath: Option[Path]) extends KnownJobFailureException {
-  override def getMessage = s"Job $jobTag exited with return code $returnCode which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
+final case class WrongReturnCode(jobTag: String, returnCode: Int, stderrPath: Option[Path])
+    extends KnownJobFailureException {
+  override def getMessage =
+    s"Job $jobTag exited with return code $returnCode which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
 }
 
-final case class ReturnCodeIsNotAnInt(jobTag: String, returnCode: String, stderrPath: Option[Path]) extends KnownJobFailureException {
-  override def getMessage = {
+final case class ReturnCodeIsNotAnInt(jobTag: String, returnCode: String, stderrPath: Option[Path])
+    extends KnownJobFailureException {
+  override def getMessage =
     if (returnCode.isEmpty)
       s"The return code file for job $jobTag was empty."
     else
       s"Job $jobTag exited with return code $returnCode which couldn't be converted to an Integer."
-  }
 }
 
-final case class StderrNonEmpty(jobTag: String, stderrLength: Long, stderrPath: Option[Path]) extends KnownJobFailureException {
-  override def getMessage = s"stderr for job $jobTag has length $stderrLength and 'failOnStderr' runtime attribute was true."
+final case class StderrNonEmpty(jobTag: String, stderrLength: Long, stderrPath: Option[Path])
+    extends KnownJobFailureException {
+  override def getMessage =
+    s"stderr for job $jobTag has length $stderrLength and 'failOnStderr' runtime attribute was true."
 }
 
 final case class RetryWithMoreMemory(jobTag: String,
                                      stderrPath: Option[Path],
                                      memoryRetryErrorKeys: Option[List[String]],
-                                     logger: LoggingAdapter) extends KnownJobFailureException {
+                                     logger: LoggingAdapter
+) extends KnownJobFailureException {
   val errorKeysAsString = memoryRetryErrorKeys match {
     case None =>
       // this should not occur at this point as one would reach this error class only if Cromwell found one of the
       // `memory-retry-error-keys` in `stderr` of the task, which is only checked if the `memory-retry-error-keys`
       // are instantiated in Cromwell config
-      logger.error(s"Programmer error: found one of the `system.memory-retry-error-keys` in the `stderr` of task but " +
-        s"didn't find the error keys while generating the exception!")
+      logger.error(
+        s"Programmer error: found one of the `system.memory-retry-error-keys` in the `stderr` of task but " +
+          s"didn't find the error keys while generating the exception!"
+      )
       ""
     case Some(keys) => keys.mkString(": [", ",", "]")
   }
-  override def getMessage = s"stderr for job `$jobTag` contained one of the `memory-retry-error-keys${errorKeysAsString}` specified in " +
-    s"the Cromwell config. Job might have run out of memory."
+  override def getMessage =
+    s"stderr for job `$jobTag` contained one of the `memory-retry-error-keys${errorKeysAsString}` specified in " +
+      s"the Cromwell config. Job might have run out of memory."
 }
 
-
 object RuntimeAttributeValidationFailure {
   def apply(jobTag: String,
             runtimeAttributeName: String,
-            runtimeAttributeValue: Option[WomExpression]): RuntimeAttributeValidationFailure = RuntimeAttributeValidationFailure(jobTag, runtimeAttributeName, runtimeAttributeValue, None)
+            runtimeAttributeValue: Option[WomExpression]
+  ): RuntimeAttributeValidationFailure =
+    RuntimeAttributeValidationFailure(jobTag, runtimeAttributeName, runtimeAttributeValue, None)
 }
 
 final case class RuntimeAttributeValidationFailure private (jobTag: String,
                                                             runtimeAttributeName: String,
                                                             runtimeAttributeValue: Option[WomExpression],
-                                                            stderrPath: Option[Path]) extends KnownJobFailureException {
-  override def getMessage = s"Task $jobTag has an invalid runtime attribute $runtimeAttributeName = ${runtimeAttributeValue map { _.evaluateValue(Map.empty, NoIoFunctionSet)} getOrElse "!! NOT FOUND !!"}"
+                                                            stderrPath: Option[Path]
+) extends KnownJobFailureException {
+  override def getMessage =
+    s"Task $jobTag has an invalid runtime attribute $runtimeAttributeName = ${runtimeAttributeValue map {
+        _.evaluateValue(Map.empty, NoIoFunctionSet)
+      } getOrElse "!! NOT FOUND !!"}"
 }
 
-final case class RuntimeAttributeValidationFailures(throwables: List[RuntimeAttributeValidationFailure]) extends KnownJobFailureException with ThrowableAggregation {
+final case class RuntimeAttributeValidationFailures(throwables: List[RuntimeAttributeValidationFailure])
+    extends KnownJobFailureException
+    with ThrowableAggregation {
   override def exceptionContext = "Runtime validation failed"
   override val stderrPath: Option[Path] = None
 }
 
-final case class JobAlreadyFailedInJobStore(jobTag: String, originalErrorMessage: String) extends KnownJobFailureException {
+final case class JobAlreadyFailedInJobStore(jobTag: String, originalErrorMessage: String)
+    extends KnownJobFailureException {
   override def stderrPath: Option[Path] = None
   override def getMessage = originalErrorMessage
 }
diff --git a/backend/src/main/scala/cromwell/backend/async/package.scala b/backend/src/main/scala/cromwell/backend/async/package.scala
index b496126ef11..1f7037e711e 100644
--- a/backend/src/main/scala/cromwell/backend/async/package.scala
+++ b/backend/src/main/scala/cromwell/backend/async/package.scala
@@ -2,7 +2,6 @@ package cromwell.backend
 
 import scala.concurrent.{ExecutionContext, Future}
 
-
 package object async {
   implicit class EnhancedFutureFuture[A](val ffa: Future[Future[A]])(implicit ec: ExecutionContext) {
     def flatten: Future[A] = ffa flatMap identity
diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index 33d16f34b5a..ab7cdf602b6 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -26,9 +26,7 @@ import scala.util.Try
 /**
   * For uniquely identifying a job which has been or will be sent to the backend.
   */
-case class BackendJobDescriptorKey(call: CommandCallNode,
-                                   index: Option[Int],
-                                   attempt: Int) extends CallKey {
+case class BackendJobDescriptorKey(call: CommandCallNode, index: Option[Int], attempt: Int) extends CallKey {
   def node = call
   private val indexString = index map { _.toString } getOrElse "NA"
   lazy val tag = s"${call.fullyQualifiedName}:$indexString:$attempt"
@@ -44,15 +42,19 @@ final case class BackendJobDescriptor(workflowDescriptor: BackendWorkflowDescrip
                                       evaluatedTaskInputs: WomEvaluatedCallInputs,
                                       maybeCallCachingEligible: MaybeCallCachingEligible,
                                       dockerSize: Option[DockerSize],
-                                      prefetchedKvStoreEntries: Map[String, KvResponse]) {
+                                      prefetchedKvStoreEntries: Map[String, KvResponse]
+) {
 
   val fullyQualifiedInputs: Map[String, WomValue] = evaluatedTaskInputs map { case (declaration, value) =>
     key.call.identifier.combine(declaration.name).fullyQualifiedName.value -> value
   }
 
-  def findInputFilesByParameterMeta(filter: MetaValueElement => Boolean): Set[WomFile] = evaluatedTaskInputs.collect {
-    case (declaration, value) if declaration.parameterMeta.exists(filter) => findFiles(value)
-  }.flatten.toSet
+  def findInputFilesByParameterMeta(filter: MetaValueElement => Boolean): Set[WomFile] = evaluatedTaskInputs
+    .collect {
+      case (declaration, value) if declaration.parameterMeta.exists(filter) => findFiles(value)
+    }
+    .flatten
+    .toSet
 
   def findFiles(v: WomValue): Set[WomFile] = v match {
     case value: WomFile => Set(value)
@@ -79,7 +81,8 @@ case class BackendWorkflowDescriptor(id: WorkflowId,
                                      customLabels: Labels,
                                      hogGroup: HogGroup,
                                      breadCrumbs: List[BackendJobBreadCrumb],
-                                     outputRuntimeExtractor: Option[WomOutputRuntimeExtractor]) {
+                                     outputRuntimeExtractor: Option[WomOutputRuntimeExtractor]
+) {
 
   val rootWorkflow = breadCrumbs.headOption.map(_.callable).getOrElse(callable)
   val possiblyNotRootWorkflowId = id.toPossiblyNotRoot
@@ -100,33 +103,31 @@ case class BackendConfigurationDescriptor(backendConfig: Config, globalConfig: C
       Option(backendConfig.getConfig("default-runtime-attributes"))
     else
       None
-  
+
   // So it can be overridden in tests
-  private [backend] lazy val cromwellFileSystems = CromwellFileSystems.instance
+  private[backend] lazy val cromwellFileSystems = CromwellFileSystems.instance
 
-  lazy val configuredPathBuilderFactories: Map[String, PathBuilderFactory] = {
+  lazy val configuredPathBuilderFactories: Map[String, PathBuilderFactory] =
     cromwellFileSystems.factoriesFromConfig(backendConfig).unsafe("Failed to instantiate backend filesystem")
-  }
 
-  private lazy val configuredFactoriesWithDefault = if (configuredPathBuilderFactories.values.exists(_ == DefaultPathBuilderFactory)) {
-    configuredPathBuilderFactories
-  } else configuredPathBuilderFactories + DefaultPathBuilderFactory.tuple
+  private lazy val configuredFactoriesWithDefault =
+    if (configuredPathBuilderFactories.values.exists(_ == DefaultPathBuilderFactory)) {
+      configuredPathBuilderFactories
+    } else configuredPathBuilderFactories + DefaultPathBuilderFactory.tuple
 
   /**
     * Creates path builders using only the configured factories.
     */
-  def pathBuilders(workflowOptions: WorkflowOptions)(implicit as: ActorSystem) = {
+  def pathBuilders(workflowOptions: WorkflowOptions)(implicit as: ActorSystem) =
     PathBuilderFactory.instantiatePathBuilders(configuredPathBuilderFactories.values.toList, workflowOptions)
-  }
 
   /**
     * Creates path builders using only the configured factories + the default factory
     */
-  def pathBuildersWithDefault(workflowOptions: WorkflowOptions)(implicit as: ActorSystem) = {
+  def pathBuildersWithDefault(workflowOptions: WorkflowOptions)(implicit as: ActorSystem) =
     PathBuilderFactory.instantiatePathBuilders(configuredFactoriesWithDefault.values.toList, workflowOptions)
-  }
 
-  lazy val slowJobWarningAfter = backendConfig.as[Option[FiniteDuration]](path="slow-job-warning-time")
+  lazy val slowJobWarningAfter = backendConfig.as[Option[FiniteDuration]](path = "slow-job-warning-time")
 }
 
 object CommonBackendConfigurationAttributes {
@@ -147,7 +148,7 @@ object CommonBackendConfigurationAttributes {
     "dockerhub.token",
     "dockerhub.auth",
     "dockerhub.key-name",
-    "name-for-call-caching-purposes",
+    "name-for-call-caching-purposes"
   )
 }
 
diff --git a/backend/src/main/scala/cromwell/backend/dummy/DummyAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/dummy/DummyAsyncExecutionActor.scala
index 5c491c5a741..b84843fea5e 100644
--- a/backend/src/main/scala/cromwell/backend/dummy/DummyAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/dummy/DummyAsyncExecutionActor.scala
@@ -9,7 +9,12 @@ import cats.implicits._
 import common.exception.AggregatedMessageException
 import common.validation.ErrorOr.ErrorOr
 import cromwell.backend.BackendJobLifecycleActor
-import cromwell.backend.async.{ExecutionHandle, FailedNonRetryableExecutionHandle, PendingExecutionHandle, SuccessfulExecutionHandle}
+import cromwell.backend.async.{
+  ExecutionHandle,
+  FailedNonRetryableExecutionHandle,
+  PendingExecutionHandle,
+  SuccessfulExecutionHandle
+}
 import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
 import cromwell.core.CallOutputs
 import cromwell.core.retry.SimpleExponentialBackoff
@@ -22,12 +27,13 @@ import scala.concurrent.Future
 import scala.concurrent.duration._
 
 class DummyAsyncExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
-  extends BackendJobLifecycleActor
+    extends BackendJobLifecycleActor
     with StandardAsyncExecutionActor
     with CromwellInstrumentation {
 
   /** The type of the run info when a job is started. */
   override type StandardAsyncRunInfo = String
+
   /** The type of the run status returned during each poll. */
   override type StandardAsyncRunState = String
 
@@ -46,14 +52,17 @@ class DummyAsyncExecutionActor(override val standardParams: StandardAsyncExecuti
 
   override def dockerImageUsed: Option[String] = None
 
-  override def pollBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(initialInterval = 1.second, maxInterval = 300.seconds, multiplier = 1.1)
+  override def pollBackOff: SimpleExponentialBackoff =
+    SimpleExponentialBackoff(initialInterval = 1.second, maxInterval = 300.seconds, multiplier = 1.1)
 
-  override def executeOrRecoverBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(initialInterval = 1.second, maxInterval = 300.seconds, multiplier = 1.1)
+  override def executeOrRecoverBackOff: SimpleExponentialBackoff =
+    SimpleExponentialBackoff(initialInterval = 1.second, maxInterval = 300.seconds, multiplier = 1.1)
 
   override val logJobIds: Boolean = false
 
   val singletonActor = standardParams.backendSingletonActorOption.getOrElse(
-    throw new RuntimeException("Dummy Backend actor cannot exist without its singleton actor"))
+    throw new RuntimeException("Dummy Backend actor cannot exist without its singleton actor")
+  )
 
   var finishTime: Option[OffsetDateTime] = None
 
@@ -71,46 +80,54 @@ class DummyAsyncExecutionActor(override val standardParams: StandardAsyncExecuti
     )
   }
 
-  override def pollStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[String] = {
+  override def pollStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[String] =
     finishTime match {
-      case Some(ft) if (ft.isBefore(OffsetDateTime.now)) => Future.successful("done")
+      case Some(ft) if ft.isBefore(OffsetDateTime.now) => Future.successful("done")
       case Some(_) => Future.successful("running")
-      case None => Future.failed(new Exception("Dummy backend polling for status before finishTime is established(!!?)"))
+      case None =>
+        Future.failed(new Exception("Dummy backend polling for status before finishTime is established(!!?)"))
     }
 
-  }
-
-  override def handlePollSuccess(oldHandle: StandardAsyncPendingExecutionHandle, state: String): Future[ExecutionHandle] = {
-
+  override def handlePollSuccess(oldHandle: StandardAsyncPendingExecutionHandle,
+                                 state: String
+  ): Future[ExecutionHandle] =
     if (state == "done") {
 
       increment(NonEmptyList("jobs", List("dummy", "executing", "done")))
       singletonActor ! DummySingletonActor.MinusOne
 
-      val outputsValidation: ErrorOr[Map[OutputPort, WomValue]] = jobDescriptor.taskCall.outputPorts.toList.traverse {
-        case expressionBasedOutputPort: ExpressionBasedOutputPort =>
-          expressionBasedOutputPort.expression.evaluateValue(Map.empty, NoIoFunctionSet).map(expressionBasedOutputPort -> _)
-        case other => s"Unknown output port type for Dummy backend output evaluator: ${other.getClass.getSimpleName}".invalidNel
-      }.map(_.toMap)
+      val outputsValidation: ErrorOr[Map[OutputPort, WomValue]] = jobDescriptor.taskCall.outputPorts.toList
+        .traverse {
+          case expressionBasedOutputPort: ExpressionBasedOutputPort =>
+            expressionBasedOutputPort.expression
+              .evaluateValue(Map.empty, NoIoFunctionSet)
+              .map(expressionBasedOutputPort -> _)
+          case other =>
+            s"Unknown output port type for Dummy backend output evaluator: ${other.getClass.getSimpleName}".invalidNel
+        }
+        .map(_.toMap)
 
       outputsValidation match {
         case Valid(outputs) =>
-          Future.successful(SuccessfulExecutionHandle(
-            outputs = CallOutputs(outputs.toMap),
-            returnCode = 0,
-            jobDetritusFiles = Map.empty,
-            executionEvents = Seq.empty,
-            resultsClonedFrom = None
-          ))
+          Future.successful(
+            SuccessfulExecutionHandle(
+              outputs = CallOutputs(outputs.toMap),
+              returnCode = 0,
+              jobDetritusFiles = Map.empty,
+              executionEvents = Seq.empty,
+              resultsClonedFrom = None
+            )
+          )
         case Invalid(errors) =>
-          Future.successful(FailedNonRetryableExecutionHandle(
-            throwable = AggregatedMessageException("Evaluate outputs from dummy job", errors.toList),
-            returnCode = None,
-            kvPairsToSave = None
-          ))
+          Future.successful(
+            FailedNonRetryableExecutionHandle(
+              throwable = AggregatedMessageException("Evaluate outputs from dummy job", errors.toList),
+              returnCode = None,
+              kvPairsToSave = None
+            )
+          )
       }
-    }
-    else if (state == "running") {
+    } else if (state == "running") {
       Future.successful(
         PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState](
           jobDescriptor = jobDescriptor,
@@ -119,9 +136,7 @@ class DummyAsyncExecutionActor(override val standardParams: StandardAsyncExecuti
           previousState = Option(state)
         )
       )
-    }
-    else {
+    } else {
       Future.failed(new Exception(s"Unexpected Dummy state in handlePollSuccess: $state"))
     }
-  }
 }
diff --git a/backend/src/main/scala/cromwell/backend/dummy/DummyInitializationActor.scala b/backend/src/main/scala/cromwell/backend/dummy/DummyInitializationActor.scala
index 34fd2e8bc51..53a310d1dd8 100644
--- a/backend/src/main/scala/cromwell/backend/dummy/DummyInitializationActor.scala
+++ b/backend/src/main/scala/cromwell/backend/dummy/DummyInitializationActor.scala
@@ -2,16 +2,22 @@ package cromwell.backend.dummy
 
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
-import cromwell.backend.standard.{StandardInitializationActor, StandardInitializationActorParams, StandardValidatedRuntimeAttributesBuilder}
+import cromwell.backend.standard.{
+  StandardInitializationActor,
+  StandardInitializationActorParams,
+  StandardValidatedRuntimeAttributesBuilder
+}
 import cromwell.backend.validation.RuntimeAttributesValidation
 import wom.expression.WomExpression
 import wom.types.{WomStringType, WomType}
 import wom.values.{WomString, WomValue}
 
 class DummyInitializationActor(pipelinesParams: StandardInitializationActorParams)
-  extends StandardInitializationActor(pipelinesParams) {
+    extends StandardInitializationActor(pipelinesParams) {
 
-  override protected lazy val runtimeAttributeValidators: Map[String, Option[WomExpression] => Boolean] = Map("backend" -> { _ => true } )
+  override protected lazy val runtimeAttributeValidators: Map[String, Option[WomExpression] => Boolean] = Map(
+    "backend" -> { _ => true }
+  )
 
   // Specific validator for "backend" to let me specify it in test cases (to avoid accidentally submitting the workflow to real backends!)
   val backendAttributeValidation: RuntimeAttributesValidation[String] = new RuntimeAttributesValidation[String] {
@@ -25,5 +31,6 @@ class DummyInitializationActor(pipelinesParams: StandardInitializationActorParam
     }
   }
 
-  override def runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder = super.runtimeAttributesBuilder.withValidation(backendAttributeValidation)
+  override def runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder =
+    super.runtimeAttributesBuilder.withValidation(backendAttributeValidation)
 }
diff --git a/backend/src/main/scala/cromwell/backend/dummy/DummyLifecycleActorFactory.scala b/backend/src/main/scala/cromwell/backend/dummy/DummyLifecycleActorFactory.scala
index ee959513a36..492de4970a9 100644
--- a/backend/src/main/scala/cromwell/backend/dummy/DummyLifecycleActorFactory.scala
+++ b/backend/src/main/scala/cromwell/backend/dummy/DummyLifecycleActorFactory.scala
@@ -3,9 +3,15 @@ package cromwell.backend.dummy
 import akka.actor.{ActorRef, Props}
 import cromwell.backend.BackendConfigurationDescriptor
 import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardFileHashingActor}
-import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardInitializationActor, StandardLifecycleActorFactory}
+import cromwell.backend.standard.{
+  StandardAsyncExecutionActor,
+  StandardInitializationActor,
+  StandardLifecycleActorFactory
+}
 
-class DummyLifecycleActorFactory(override val name: String, override val configurationDescriptor: BackendConfigurationDescriptor) extends StandardLifecycleActorFactory {
+class DummyLifecycleActorFactory(override val name: String,
+                                 override val configurationDescriptor: BackendConfigurationDescriptor
+) extends StandardLifecycleActorFactory {
 
   /**
     * @return the key to use for storing and looking up the job id.
@@ -23,8 +29,11 @@ class DummyLifecycleActorFactory(override val name: String, override val configu
   // Don't hash files
   override lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = None
 
-  override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] = Option(Props(new DummySingletonActor()))
+  override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] = Option(
+    Props(new DummySingletonActor())
+  )
 
-  override lazy val initializationActorClass: Class[_ <: StandardInitializationActor] = classOf[DummyInitializationActor]
+  override lazy val initializationActorClass: Class[_ <: StandardInitializationActor] =
+    classOf[DummyInitializationActor]
 
 }
diff --git a/backend/src/main/scala/cromwell/backend/dummy/DummySingletonActor.scala b/backend/src/main/scala/cromwell/backend/dummy/DummySingletonActor.scala
index 35c689ae2b4..4ea2cf7951c 100644
--- a/backend/src/main/scala/cromwell/backend/dummy/DummySingletonActor.scala
+++ b/backend/src/main/scala/cromwell/backend/dummy/DummySingletonActor.scala
@@ -22,7 +22,7 @@ final class DummySingletonActor() extends Actor with StrictLogging {
     case PlusOne => count = count + 1
     case MinusOne => count = count - 1
     case PrintCount =>
-      if(countHistory.lastOption.exists(_._2 != count)) {
+      if (countHistory.lastOption.exists(_._2 != count)) {
         countHistory = countHistory :+ (OffsetDateTime.now() -> count)
         logger.info("The current count is now: " + count)
         if (count == 0) {
@@ -52,7 +52,7 @@ final class DummySingletonActor() extends Actor with StrictLogging {
     bw.close()
   }
 
-  context.system.scheduler.schedule(10.seconds, 1.second) { self ! PrintCount }
+  context.system.scheduler.schedule(10.seconds, 1.second)(self ! PrintCount)
 }
 
 object DummySingletonActor {
@@ -60,4 +60,3 @@ object DummySingletonActor {
   case object MinusOne
   case object PrintCount
 }
-
diff --git a/backend/src/main/scala/cromwell/backend/io/DirectoryFunctions.scala b/backend/src/main/scala/cromwell/backend/io/DirectoryFunctions.scala
index 7b68e2bf723..84d45d1ee61 100644
--- a/backend/src/main/scala/cromwell/backend/io/DirectoryFunctions.scala
+++ b/backend/src/main/scala/cromwell/backend/io/DirectoryFunctions.scala
@@ -11,7 +11,14 @@ import cromwell.core.path.{Path, PathFactory}
 import wom.expression.IoFunctionSet.{IoDirectory, IoElement, IoFile}
 import wom.expression.{IoFunctionSet, IoFunctionSetAdapter}
 import wom.graph.CommandCallNode
-import wom.values.{WomFile, WomGlobFile, WomMaybeListedDirectory, WomMaybePopulatedFile, WomSingleFile, WomUnlistedDirectory}
+import wom.values.{
+  WomFile,
+  WomGlobFile,
+  WomMaybeListedDirectory,
+  WomMaybePopulatedFile,
+  WomSingleFile,
+  WomUnlistedDirectory
+}
 
 import scala.concurrent.Future
 import scala.util.Try
@@ -21,13 +28,18 @@ trait DirectoryFunctions extends IoFunctionSet with PathFactory with AsyncIoFunc
   private lazy val evaluateFileFunctions = new IoFunctionSetAdapter(this) with FileEvaluationIoFunctionSet
 
   def findDirectoryOutputs(call: CommandCallNode,
-                           jobDescriptor: BackendJobDescriptor): ErrorOr[List[WomUnlistedDirectory]] = {
+                           jobDescriptor: BackendJobDescriptor
+  ): ErrorOr[List[WomUnlistedDirectory]] =
     call.callable.outputs.flatTraverse[ErrorOr, WomUnlistedDirectory] { outputDefinition =>
-      outputDefinition.expression.evaluateFiles(jobDescriptor.localInputs, evaluateFileFunctions, outputDefinition.womType) map {
-        _.toList.flatMap(_.file.flattenFiles) collect { case unlistedDirectory: WomUnlistedDirectory => unlistedDirectory }
+      outputDefinition.expression.evaluateFiles(jobDescriptor.localInputs,
+                                                evaluateFileFunctions,
+                                                outputDefinition.womType
+      ) map {
+        _.toList.flatMap(_.file.flattenFiles) collect { case unlistedDirectory: WomUnlistedDirectory =>
+          unlistedDirectory
+        }
       }
     }
-  }
 
   override def isDirectory(path: String) = asyncIo.isDirectory(buildPath(path))
 
@@ -39,7 +51,7 @@ trait DirectoryFunctions extends IoFunctionSet with PathFactory with AsyncIoFunc
    * implementation which lists files and directories children. What we need is the unix behavior, even for cloud filesystems.
    * 3) It uses the isDirectory function directly on the path, which cannot be trusted for GCS paths. It should use asyncIo.isDirectory instead.
    */
-  override def listDirectory(path: String)(visited: Vector[String] = Vector.empty): Future[Iterator[IoElement]] = {
+  override def listDirectory(path: String)(visited: Vector[String] = Vector.empty): Future[Iterator[IoElement]] =
     Future.fromTry(Try {
       val visitedPaths = visited.map(buildPath)
       val cromwellPath = buildPath(path.ensureSlashed)
@@ -47,21 +59,21 @@ trait DirectoryFunctions extends IoFunctionSet with PathFactory with AsyncIoFunc
       // To prevent infinite recursion through symbolic links make sure we don't visit the same directory twice
       def hasBeenVisited(other: Path) = visitedPaths.exists(_.isSameFileAs(other))
 
-      cromwellPath.list.collect({
-        case directory if directory.isDirectory &&
-          !cromwellPath.isSamePathAs(directory) &&
-          !hasBeenVisited(directory) => IoDirectory(directory.pathAsString)
+      cromwellPath.list.collect {
+        case directory
+            if directory.isDirectory &&
+              !cromwellPath.isSamePathAs(directory) &&
+              !hasBeenVisited(directory) =>
+          IoDirectory(directory.pathAsString)
         case file => IoFile(file.pathAsString)
-      })
+      }
     })
-  }
 
-  override def listAllFilesUnderDirectory(dirPath: String): Future[Seq[String]] = {
+  override def listAllFilesUnderDirectory(dirPath: String): Future[Seq[String]] =
     temporaryImplListPaths(dirPath)
-  }
 
   // TODO: WOM: WOMFILE: This will likely use a Tuple2(tar file, dir list file) for each dirPath.
-  private final def temporaryImplListPaths(dirPath: String): Future[Seq[String]] = {
+  final private def temporaryImplListPaths(dirPath: String): Future[Seq[String]] = {
     val errorOrPaths = for {
       dir <- validate(buildPath(dirPath.ensureSlashed))
       files <- listFiles(dir)
@@ -74,7 +86,7 @@ object DirectoryFunctions {
   def listFiles(path: Path): ErrorOr[List[Path]] = path.listRecursively.filterNot(_.isDirectory).toList.validNel
 
   def listWomSingleFiles(womFile: WomFile, pathFactory: PathFactory): ErrorOr[List[WomSingleFile]] = {
-    def listWomSingleFiles(womFile: WomFile): ErrorOr[List[WomSingleFile]] = {
+    def listWomSingleFiles(womFile: WomFile): ErrorOr[List[WomSingleFile]] =
       womFile match {
         case womSingleFile: WomSingleFile => List(womSingleFile).valid
 
@@ -99,7 +111,6 @@ object DirectoryFunctions {
 
         case _: WomGlobFile => s"Unexpected glob / unable to list glob files at this time: $womFile".invalidNel
       }
-    }
 
     listWomSingleFiles(womFile)
   }
diff --git a/backend/src/main/scala/cromwell/backend/io/FileEvaluationIoFunctionSet.scala b/backend/src/main/scala/cromwell/backend/io/FileEvaluationIoFunctionSet.scala
index f46ff9ce9e2..0408c590cb2 100644
--- a/backend/src/main/scala/cromwell/backend/io/FileEvaluationIoFunctionSet.scala
+++ b/backend/src/main/scala/cromwell/backend/io/FileEvaluationIoFunctionSet.scala
@@ -5,5 +5,6 @@ import wom.expression.IoFunctionSet
 import scala.concurrent.Future
 
 trait FileEvaluationIoFunctionSet { this: IoFunctionSet =>
-  override def glob(pattern: String) = Future.failed(new IllegalStateException("Cannot perform globing while evaluating files"))
+  override def glob(pattern: String) =
+    Future.failed(new IllegalStateException("Cannot perform globing while evaluating files"))
 }
diff --git a/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala b/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala
index 680c073bf45..5ed3b4a30ff 100644
--- a/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala
+++ b/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala
@@ -19,7 +19,10 @@ trait GlobFunctions extends IoFunctionSet with AsyncIoFunctions {
 
   def findGlobOutputs(call: CommandCallNode, jobDescriptor: BackendJobDescriptor): ErrorOr[List[WomGlobFile]] = {
     def fromOutputs = call.callable.outputs.flatTraverse[ErrorOr, WomGlobFile] { outputDefinition =>
-      outputDefinition.expression.evaluateFiles(jobDescriptor.localInputs, evaluateFileFunctions, outputDefinition.womType) map {
+      outputDefinition.expression.evaluateFiles(jobDescriptor.localInputs,
+                                                evaluateFileFunctions,
+                                                outputDefinition.womType
+      ) map {
         _.toList.flatMap(_.file.flattenFiles) collect { case glob: WomGlobFile => glob }
       }
     }
@@ -40,7 +43,7 @@ trait GlobFunctions extends IoFunctionSet with AsyncIoFunctions {
     val listFilePath = callContext.root.resolve(s"${globName(pattern)}.list")
     asyncIo.readLinesAsync(listFilePath.getSymlinkSafePath()) map { lines =>
       lines.toList map { fileName =>
-        (callContext.root /  globPatternName  / fileName).pathAsString
+        (callContext.root / globPatternName / fileName).pathAsString
       }
     }
   }
diff --git a/backend/src/main/scala/cromwell/backend/io/JobPaths.scala b/backend/src/main/scala/cromwell/backend/io/JobPaths.scala
index eb9e9ec31d7..05ad6a56dc1 100644
--- a/backend/src/main/scala/cromwell/backend/io/JobPaths.scala
+++ b/backend/src/main/scala/cromwell/backend/io/JobPaths.scala
@@ -54,16 +54,14 @@ trait JobPaths {
   /**
     * Return a host path corresponding to the specified container path.
     */
-  def hostPathFromContainerPath(string: String): Path = {
+  def hostPathFromContainerPath(string: String): Path =
     // No container here, just return a Path of the absolute path to the file.
     callExecutionRoot.resolve(string.stripPrefix(rootWithSlash))
-  }
 
   def hostPathFromContainerInputs(string: String): Path =
     // No container here, just return a Path of the absolute path to the file.
     callExecutionRoot.resolve(string.stripPrefix(rootWithSlash))
 
-
   def scriptFilename: String = "script"
   def dockerCidFilename: String = "docker_cid"
 
diff --git a/backend/src/main/scala/cromwell/backend/io/JobPathsWithDocker.scala b/backend/src/main/scala/cromwell/backend/io/JobPathsWithDocker.scala
index f6d8855f3fa..2fb81a44019 100644
--- a/backend/src/main/scala/cromwell/backend/io/JobPathsWithDocker.scala
+++ b/backend/src/main/scala/cromwell/backend/io/JobPathsWithDocker.scala
@@ -6,18 +6,19 @@ import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
 import cromwell.core.path.Path
 
 object JobPathsWithDocker {
-  def apply(jobKey: BackendJobDescriptorKey,
-            workflowDescriptor: BackendWorkflowDescriptor,
-            config: Config) = {
+  def apply(jobKey: BackendJobDescriptorKey, workflowDescriptor: BackendWorkflowDescriptor, config: Config) = {
     val workflowPaths = new WorkflowPathsWithDocker(workflowDescriptor, config, WorkflowPaths.DefaultPathBuilders)
     new JobPathsWithDocker(workflowPaths, jobKey)
   }
 }
 
-case class JobPathsWithDocker private[io] (override val workflowPaths: WorkflowPathsWithDocker, jobKey: BackendJobDescriptorKey, override val isCallCacheCopyAttempt: Boolean = false) extends JobPaths {
+case class JobPathsWithDocker private[io] (override val workflowPaths: WorkflowPathsWithDocker,
+                                           jobKey: BackendJobDescriptorKey,
+                                           override val isCallCacheCopyAttempt: Boolean = false
+) extends JobPaths {
   import JobPaths._
 
-  override lazy val callExecutionRoot = { callRoot.resolve("execution") }
+  override lazy val callExecutionRoot = callRoot.resolve("execution")
   override def isDocker: Boolean = true
   val callDockerRoot = callPathBuilder(workflowPaths.dockerWorkflowRoot, jobKey, isCallCacheCopyAttempt)
   val callExecutionDockerRoot = callDockerRoot.resolve("execution")
@@ -29,34 +30,31 @@ case class JobPathsWithDocker private[io] (override val workflowPaths: WorkflowP
 
   override def isInExecution(string: String): Boolean = string.startsWith(callExecutionDockerRootWithSlash)
 
-  override def hostPathFromContainerPath(string: String): Path = {
+  override def hostPathFromContainerPath(string: String): Path =
     callExecutionRoot.resolve(string.stripPrefix(callExecutionDockerRootWithSlash))
-  }
-
 
   override def hostPathFromContainerInputs(string: String): Path = {
     val stripped = string.stripPrefix(callInputsDockerRootWithSlash)
     callInputsRoot.resolve(stripped)
   }
 
-  def toDockerPath(path: Path): Path = {
+  def toDockerPath(path: Path): Path =
     path.toAbsolutePath match {
       case p if p.startsWith(workflowPaths.dockerRoot) => p
       case p =>
         /* For example:
-          *
-          * p = /abs/path/to/cromwell-executions/three-step/f00ba4/call-ps/stdout.txt
-          * localExecutionRoot = /abs/path/to/cromwell-executions
-          * subpath = three-step/f00ba4/call-ps/stdout.txt
-          *
-          * return value = /root/three-step/f00ba4/call-ps/stdout.txt
-          *
-          * TODO: this assumes that p.startsWith(localExecutionRoot)
-          */
+         *
+         * p = /abs/path/to/cromwell-executions/three-step/f00ba4/call-ps/stdout.txt
+         * localExecutionRoot = /abs/path/to/cromwell-executions
+         * subpath = three-step/f00ba4/call-ps/stdout.txt
+         *
+         * return value = /root/three-step/f00ba4/call-ps/stdout.txt
+         *
+         * TODO: this assumes that p.startsWith(localExecutionRoot)
+         */
         val subpath = p.subpath(workflowPaths.executionRoot.getNameCount, p.getNameCount)
         workflowPaths.dockerRoot.resolve(subpath)
     }
-  }
 
   override def forCallCacheCopyAttempts: JobPaths = this.copy(isCallCacheCopyAttempt = true)
 }
diff --git a/backend/src/main/scala/cromwell/backend/io/WorkflowPaths.scala b/backend/src/main/scala/cromwell/backend/io/WorkflowPaths.scala
index 8c233717898..228285dbd5d 100644
--- a/backend/src/main/scala/cromwell/backend/io/WorkflowPaths.scala
+++ b/backend/src/main/scala/cromwell/backend/io/WorkflowPaths.scala
@@ -20,7 +20,8 @@ trait WorkflowPaths extends PathFactory {
   /**
     * Path (as a String) of the root directory Cromwell should use for ALL workflows.
     */
-  protected lazy val executionRootString: String = config.as[Option[String]]("root").getOrElse(WorkflowPaths.DefaultExecutionRootString)
+  protected lazy val executionRootString: String =
+    config.as[Option[String]]("root").getOrElse(WorkflowPaths.DefaultExecutionRootString)
 
   /**
     * Implementers of this trait might override this to provide an appropriate prefix corresponding to the execution root
@@ -51,18 +52,17 @@ trait WorkflowPaths extends PathFactory {
   def getPath(url: String): Try[Path] = Try(buildPath(url))
 
   // Rebuild potential intermediate call directories in case of a sub workflow
-  protected def workflowPathBuilder(root: Path): Path = {
-    workflowDescriptor.breadCrumbs.foldLeft(root)((acc, breadCrumb) => {
-      breadCrumb.toPath(acc)
-    }).resolve(workflowDescriptor.callable.name).resolve(workflowDescriptor.id.toString + "/")
-  }
+  protected def workflowPathBuilder(root: Path): Path =
+    workflowDescriptor.breadCrumbs
+      .foldLeft(root)((acc, breadCrumb) => breadCrumb.toPath(acc))
+      .resolve(workflowDescriptor.callable.name)
+      .resolve(workflowDescriptor.id.toString + "/")
 
   lazy val finalCallLogsPath: Option[Path] =
     workflowDescriptor.getWorkflowOption(FinalCallLogsDir) map getPath map { _.get }
 
-  def toJobPaths(jobDescriptor: BackendJobDescriptor): JobPaths = {
+  def toJobPaths(jobDescriptor: BackendJobDescriptor): JobPaths =
     toJobPaths(jobDescriptor.key, jobDescriptor.workflowDescriptor)
-  }
 
   /**
     * Creates job paths using the key and workflow descriptor.
@@ -73,11 +73,10 @@ trait WorkflowPaths extends PathFactory {
     * @param jobWorkflowDescriptor The workflow descriptor for the job.
     * @return The paths for the job.
     */
-  def toJobPaths(jobKey: BackendJobDescriptorKey, jobWorkflowDescriptor: BackendWorkflowDescriptor): JobPaths = {
+  def toJobPaths(jobKey: BackendJobDescriptorKey, jobWorkflowDescriptor: BackendWorkflowDescriptor): JobPaths =
     // If the descriptors are the same, no need to create a new WorkflowPaths
     if (workflowDescriptor == jobWorkflowDescriptor) toJobPaths(this, jobKey)
     else toJobPaths(withDescriptor(jobWorkflowDescriptor), jobKey)
-  }
 
   protected def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): JobPaths
 
diff --git a/backend/src/main/scala/cromwell/backend/io/WorkflowPathsWithDocker.scala b/backend/src/main/scala/cromwell/backend/io/WorkflowPathsWithDocker.scala
index 78dc1ed77e3..38ea17fe61c 100644
--- a/backend/src/main/scala/cromwell/backend/io/WorkflowPathsWithDocker.scala
+++ b/backend/src/main/scala/cromwell/backend/io/WorkflowPathsWithDocker.scala
@@ -9,16 +9,19 @@ object WorkflowPathsWithDocker {
   val DefaultDockerRoot = "/cromwell-executions"
 }
 
-final case class WorkflowPathsWithDocker(workflowDescriptor: BackendWorkflowDescriptor, config: Config, pathBuilders: List[PathBuilder] = WorkflowPaths.DefaultPathBuilders) extends WorkflowPaths {
+final case class WorkflowPathsWithDocker(workflowDescriptor: BackendWorkflowDescriptor,
+                                         config: Config,
+                                         pathBuilders: List[PathBuilder] = WorkflowPaths.DefaultPathBuilders
+) extends WorkflowPaths {
   val dockerRoot: Path =
     DefaultPathBuilder.get(
       config.getOrElse[String]("dockerRoot", WorkflowPathsWithDocker.DefaultDockerRoot)
     )
   val dockerWorkflowRoot: Path = workflowPathBuilder(dockerRoot)
 
-  override def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): JobPathsWithDocker = {
+  override def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): JobPathsWithDocker =
     new JobPathsWithDocker(workflowPaths.asInstanceOf[WorkflowPathsWithDocker], jobKey, isCallCacheCopyAttempt = false)
-  }
 
-  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths = this.copy(workflowDescriptor = workflowDescriptor)
+  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths =
+    this.copy(workflowDescriptor = workflowDescriptor)
 }
diff --git a/backend/src/main/scala/cromwell/backend/package.scala b/backend/src/main/scala/cromwell/backend/package.scala
index 132fcf57887..ca58701641f 100644
--- a/backend/src/main/scala/cromwell/backend/package.scala
+++ b/backend/src/main/scala/cromwell/backend/package.scala
@@ -1,6 +1,7 @@
 package cromwell
 
 package object backend {
+
   /** Represents the jobKeys executed by a (potentially sub-) workflow at a given point in time */
   type JobExecutionMap = Map[BackendWorkflowDescriptor, List[BackendJobDescriptorKey]]
 }
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 3b116ae1b99..00b5f37513b 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -11,7 +11,11 @@ import common.util.TryUtil
 import common.validation.ErrorOr.{ErrorOr, ShortCircuitingFlatMap}
 import common.validation.IOChecked._
 import common.validation.Validation._
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, JobAbortedResponse, JobReconnectionNotSupportedException}
+import cromwell.backend.BackendJobExecutionActor.{
+  BackendJobExecutionResponse,
+  JobAbortedResponse,
+  JobReconnectionNotSupportedException
+}
 import cromwell.backend.BackendLifecycleActor.AbortJobCommand
 import cromwell.backend.BackendLifecycleActorFactory.{FailedRetryCountKey, MemoryMultiplierKey}
 import cromwell.backend.OutputEvaluator._
@@ -44,12 +48,12 @@ import scala.concurrent.duration._
 import scala.util.{Failure, Success, Try}
 
 trait StandardAsyncExecutionActorParams extends StandardJobExecutionActorParams {
+
   /** The promise that will be completed when the async run is complete. */
   def completionPromise: Promise[BackendJobExecutionResponse]
 }
 
-case class DefaultStandardAsyncExecutionActorParams
-(
+case class DefaultStandardAsyncExecutionActorParams(
   override val jobIdKey: String,
   override val serviceRegistryActor: ActorRef,
   override val ioActor: ActorRef,
@@ -76,7 +80,11 @@ case class ScriptPreambleData(bashString: String, executeInSubshell: Boolean = t
   * as the common behavior among the backends adjusts in unison.
   */
 trait StandardAsyncExecutionActor
-  extends AsyncBackendJobExecutionActor with StandardCachingActorHelper with AsyncIoActorClient with KvClient with SlowJobWarning {
+    extends AsyncBackendJobExecutionActor
+    with StandardCachingActorHelper
+    with AsyncIoActorClient
+    with KvClient
+    with SlowJobWarning {
   this: Actor with ActorLogging with BackendJobLifecycleActor =>
 
   override lazy val ioCommandBuilder: IoCommandBuilder = DefaultIoCommandBuilder
@@ -100,7 +108,8 @@ trait StandardAsyncExecutionActor
   def statusEquivalentTo(thiz: StandardAsyncRunState)(that: StandardAsyncRunState): Boolean
 
   /** The pending execution handle for each poll. */
-  type StandardAsyncPendingExecutionHandle = PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState]
+  type StandardAsyncPendingExecutionHandle =
+    PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState]
 
   /** Standard set of parameters passed to the backend. */
   def standardParams: StandardAsyncExecutionActorParams
@@ -150,39 +159,36 @@ trait StandardAsyncExecutionActor
   protected def cloudResolveWomFile(womFile: WomFile): WomFile = womFile
 
   /** Process files while resolving files that will not be localized to their actual cloud locations. */
-  private def mapOrCloudResolve(mapper: WomFile => WomFile): WomValue => Try[WomValue] = {
-    WomFileMapper.mapWomFiles(
-      womFile =>
-        if (inputsToNotLocalize.contains(womFile)) {
-          cloudResolveWomFile(womFile)
-        } else {
-          mapper(womFile)
-        }
+  private def mapOrCloudResolve(mapper: WomFile => WomFile): WomValue => Try[WomValue] =
+    WomFileMapper.mapWomFiles(womFile =>
+      if (inputsToNotLocalize.contains(womFile)) {
+        cloudResolveWomFile(womFile)
+      } else {
+        mapper(womFile)
+      }
     )
-  }
 
   /** Process files while ignoring files that will not be localized. */
-  private def mapOrNoResolve(mapper: WomFile => WomFile): WomValue => Try[WomValue] = {
-    WomFileMapper.mapWomFiles(
-      womFile =>
-        if (inputsToNotLocalize.contains(womFile)) {
-          womFile
-        } else {
-          mapper(womFile)
-        }
+  private def mapOrNoResolve(mapper: WomFile => WomFile): WomValue => Try[WomValue] =
+    WomFileMapper.mapWomFiles(womFile =>
+      if (inputsToNotLocalize.contains(womFile)) {
+        womFile
+      } else {
+        mapper(womFile)
+      }
     )
-  }
 
   /** @see [[Command.instantiate]] */
   final def commandLinePreProcessor(inputs: WomEvaluatedCallInputs): Try[WomEvaluatedCallInputs] = {
     val map = inputs map { case (k, v) => k -> mapOrCloudResolve(preProcessWomFile)(v) }
-    TryUtil.sequenceMap(map).
-      recoverWith {
-        case e => Failure(new IOException(e.getMessage) with CromwellFatalExceptionMarker)
-      }
+    TryUtil.sequenceMap(map).recoverWith { case e =>
+      Failure(new IOException(e.getMessage) with CromwellFatalExceptionMarker)
+    }
   }
 
-  final lazy val localizedInputs: Try[WomEvaluatedCallInputs] = commandLinePreProcessor(jobDescriptor.evaluatedTaskInputs)
+  final lazy val localizedInputs: Try[WomEvaluatedCallInputs] = commandLinePreProcessor(
+    jobDescriptor.evaluatedTaskInputs
+  )
 
   /**
     * Maps WomFile to a local path, for use in the commandLineValueMapper.
@@ -205,47 +211,58 @@ trait StandardAsyncExecutionActor
   def inputsToNotLocalize: Set[WomFile] = Set.empty
 
   /** @see [[Command.instantiate]] */
-  final lazy val commandLineValueMapper: WomValue => WomValue = {
-    womValue => mapOrNoResolve(mapCommandLineWomFile)(womValue).get
+  final lazy val commandLineValueMapper: WomValue => WomValue = { womValue =>
+    mapOrNoResolve(mapCommandLineWomFile)(womValue).get
   }
 
   /** @see [[Command.instantiate]] */
-  final lazy val commandLineJobInputValueMapper: WomValue => WomValue = {
-    womValue => mapOrNoResolve(mapCommandLineJobInputWomFile)(womValue).get
+  final lazy val commandLineJobInputValueMapper: WomValue => WomValue = { womValue =>
+    mapOrNoResolve(mapCommandLineJobInputWomFile)(womValue).get
   }
 
-  lazy val jobShell: String = configurationDescriptor.backendConfig.getOrElse("job-shell",
-    configurationDescriptor.globalConfig.getOrElse("system.job-shell", "/bin/bash"))
+  lazy val jobShell: String = configurationDescriptor.backendConfig.getOrElse(
+    "job-shell",
+    configurationDescriptor.globalConfig.getOrElse("system.job-shell", "/bin/bash")
+  )
 
-  lazy val abbreviateCommandLength: Int = configurationDescriptor.backendConfig.getOrElse("abbreviate-command-length",
-    configurationDescriptor.globalConfig.getOrElse("system.abbreviate-command-length", 0))
+  lazy val abbreviateCommandLength: Int = configurationDescriptor.backendConfig.getOrElse(
+    "abbreviate-command-length",
+    configurationDescriptor.globalConfig.getOrElse("system.abbreviate-command-length", 0)
+  )
 
   /**
     * The local path where the command will run.
     */
   lazy val commandDirectory: Path = jobPaths.callExecutionRoot
 
-  lazy val memoryRetryErrorKeys: Option[List[String]] = configurationDescriptor.globalConfig.as[Option[List[String]]]("system.memory-retry-error-keys")
+  lazy val memoryRetryErrorKeys: Option[List[String]] =
+    configurationDescriptor.globalConfig.as[Option[List[String]]]("system.memory-retry-error-keys")
 
-  lazy val memoryRetryFactor: Option[MemoryRetryMultiplierRefined] = {
+  lazy val memoryRetryFactor: Option[MemoryRetryMultiplierRefined] =
     jobDescriptor.workflowDescriptor.getWorkflowOption(WorkflowOptions.MemoryRetryMultiplier) flatMap { value: String =>
       Try(value.toDouble) match {
-        case Success(v) => refineV[MemoryRetryMultiplier](v.toDouble) match {
-          case Left(e) =>
-            // should not happen, this case should have been screened for and fast-failed during workflow materialization.
-            log.error(e, s"Programmer error: unexpected failure attempting to read value for workflow option " +
-              s"'${WorkflowOptions.MemoryRetryMultiplier.name}'. Expected value should be in range 1.0 ≤ n ≤ 99.0")
-            None
-          case Right(refined) => Option(refined)
-        }
+        case Success(v) =>
+          refineV[MemoryRetryMultiplier](v.toDouble) match {
+            case Left(e) =>
+              // should not happen, this case should have been screened for and fast-failed during workflow materialization.
+              log.error(
+                e,
+                s"Programmer error: unexpected failure attempting to read value for workflow option " +
+                  s"'${WorkflowOptions.MemoryRetryMultiplier.name}'. Expected value should be in range 1.0 ≤ n ≤ 99.0"
+              )
+              None
+            case Right(refined) => Option(refined)
+          }
         case Failure(e) =>
           // should not happen, this case should have been screened for and fast-failed during workflow materialization.
-          log.error(e, s"Programmer error: unexpected failure attempting to convert value for workflow option " +
-            s"'${WorkflowOptions.MemoryRetryMultiplier.name}' to Double.")
+          log.error(
+            e,
+            s"Programmer error: unexpected failure attempting to convert value for workflow option " +
+              s"'${WorkflowOptions.MemoryRetryMultiplier.name}' to Double."
+          )
           None
       }
     }
-  }
 
   lazy val memoryRetryRequested: Boolean = memoryRetryFactor.nonEmpty
 
@@ -305,7 +322,8 @@ trait StandardAsyncExecutionActor
     val globList = parentDirectory./(s"$globDir.list")
     val controlFileName = "cromwell_glob_control_file"
     val absoluteGlobValue = commandDirectory.resolve(globFile.value).pathAsString
-    val globLinkCommand: String = configurationDescriptor.backendConfig.getAs[String]("glob-link-command")
+    val globLinkCommand: String = configurationDescriptor.backendConfig
+      .getAs[String]("glob-link-command")
       .map("( " + _ + " )")
       .getOrElse("( ln -L GLOB_PATTERN GLOB_DIRECTORY 2> /dev/null ) || ( ln GLOB_PATTERN GLOB_DIRECTORY )")
       .replaceAll("GLOB_PATTERN", absoluteGlobValue)
@@ -350,13 +368,14 @@ trait StandardAsyncExecutionActor
   // Absolutize any redirect and overridden paths. All of these files must have absolute paths since the command script
   // references them outside a (cd "execution dir"; ...) subshell. The default names are known to be relative paths,
   // the names from redirections may or may not be relative.
-  private def absolutizeContainerPath(path: String): String = {
+  private def absolutizeContainerPath(path: String): String =
     if (path.startsWith(cwd.pathAsString)) path else cwd.resolve(path).pathAsString
-  }
 
   def executionStdin: Option[String] = instantiatedCommand.evaluatedStdinRedirection map absolutizeContainerPath
-  def executionStdout: String = instantiatedCommand.evaluatedStdoutOverride.getOrElse(jobPaths.defaultStdoutFilename) |> absolutizeContainerPath
-  def executionStderr: String = instantiatedCommand.evaluatedStderrOverride.getOrElse(jobPaths.defaultStderrFilename) |> absolutizeContainerPath
+  def executionStdout: String =
+    instantiatedCommand.evaluatedStdoutOverride.getOrElse(jobPaths.defaultStdoutFilename) |> absolutizeContainerPath
+  def executionStderr: String =
+    instantiatedCommand.evaluatedStderrOverride.getOrElse(jobPaths.defaultStderrFilename) |> absolutizeContainerPath
 
   /*
    * Ensures the standard paths are correct w.r.t overridden paths. This is called in two places: when generating the command and
@@ -408,9 +427,11 @@ trait StandardAsyncExecutionActor
     val errorOrGlobFiles: ErrorOr[List[WomGlobFile]] =
       backendEngineFunctions.findGlobOutputs(call, jobDescriptor)
 
-    lazy val environmentVariables = instantiatedCommand.environmentVariables map { case (k, v) => s"""export $k="$v"""" } mkString("", "\n", "\n")
+    lazy val environmentVariables = instantiatedCommand.environmentVariables map { case (k, v) =>
+      s"""export $k="$v""""
+    } mkString ("", "\n", "\n")
 
-    val home = jobDescriptor.taskCall.callable.homeOverride.map { _ (runtimeEnvironment) }.getOrElse("$HOME")
+    val home = jobDescriptor.taskCall.callable.homeOverride.map(_(runtimeEnvironment)).getOrElse("$HOME")
     val shortId = jobDescriptor.workflowDescriptor.id.shortString
     // Give the out and error FIFO variables names that are unlikely to conflict with anything the user is doing.
     val (out, err) = (s"out$shortId", s"err$shortId")
@@ -422,72 +443,73 @@ trait StandardAsyncExecutionActor
     // Only adjust the temporary directory permissions if this is executing under Docker.
     val tmpDirPermissionsAdjustment = if (isDockerRun) s"""chmod 777 "$$tmpDir"""" else ""
 
-    val emptyDirectoryFillCommand: String = configurationDescriptor.backendConfig.getAs[String]("empty-dir-fill-command")
-      .getOrElse(
-        s"""(
-           |# add a .file in every empty directory to facilitate directory delocalization on the cloud
-           |cd $cwd
-           |find . -type d -exec sh -c '[ -z "$$(ls -A '"'"'{}'"'"')" ] && touch '"'"'{}'"'"'/.file' \\;
-           |)""".stripMargin)
-
-    val errorOrPreamble: ErrorOr[String] = scriptPreamble.map{ preambleData =>
-        preambleData.executeInSubshell match {
-          case true =>
-            s"""
-               |(
-               |cd ${cwd.pathAsString}
-               |${preambleData.bashString}
-               |)
-               |""".stripMargin
-          case false =>
-            s"""
-               |cd ${cwd.pathAsString}
-               |${preambleData.bashString}
-               |""".stripMargin
-        }
+    val emptyDirectoryFillCommand: String = configurationDescriptor.backendConfig
+      .getAs[String]("empty-dir-fill-command")
+      .getOrElse(s"""(
+                    |# add a .file in every empty directory to facilitate directory delocalization on the cloud
+                    |cd $cwd
+                    |find . -type d -exec sh -c '[ -z "$$(ls -A '"'"'{}'"'"')" ] && touch '"'"'{}'"'"'/.file' \\;
+                    |)""".stripMargin)
+
+    val errorOrPreamble: ErrorOr[String] = scriptPreamble.map { preambleData =>
+      preambleData.executeInSubshell match {
+        case true =>
+          s"""
+             |(
+             |cd ${cwd.pathAsString}
+             |${preambleData.bashString}
+             |)
+             |""".stripMargin
+        case false =>
+          s"""
+             |cd ${cwd.pathAsString}
+             |${preambleData.bashString}
+             |""".stripMargin
+      }
     }
 
     // The `tee` trickery below is to be able to redirect to known filenames for CWL while also streaming
     // stdout and stderr for PAPI to periodically upload to cloud storage.
     // https://stackoverflow.com/questions/692000/how-do-i-write-stderr-to-a-file-while-using-tee-with-a-pipe
     (errorOrDirectoryOutputs, errorOrGlobFiles, errorOrPreamble).mapN((directoryOutputs, globFiles, preamble) =>
-    s"""|#!$jobShell
-        |DOCKER_OUTPUT_DIR_LINK
-        |cd ${cwd.pathAsString}
-        |tmpDir=$temporaryDirectory
-        |$tmpDirPermissionsAdjustment
-        |export _JAVA_OPTIONS=-Djava.io.tmpdir="$$tmpDir"
-        |export TMPDIR="$$tmpDir"
-        |export HOME="$home"
-        |
-        |SCRIPT_PREAMBLE
-        |
-        |$out="$${tmpDir}/out.$$$$" $err="$${tmpDir}/err.$$$$"
-        |mkfifo "$$$out" "$$$err"
-        |trap 'rm "$$$out" "$$$err"' EXIT
-        |touch $stdoutRedirection $stderrRedirection
-        |tee $stdoutRedirection < "$$$out" &
-        |tee $stderrRedirection < "$$$err" >&2 &
-        |(
-        |cd ${cwd.pathAsString}
-        |ENVIRONMENT_VARIABLES
-        |INSTANTIATED_COMMAND
-        |) $stdinRedirection > "$$$out" 2> "$$$err"
-        |echo $$? > $rcTmpPath
-        |$emptyDirectoryFillCommand
-        |(
-        |cd ${cwd.pathAsString}
-        |SCRIPT_EPILOGUE
-        |${globScripts(globFiles)}
-        |${directoryScripts(directoryOutputs)}
-        |)
-        |mv $rcTmpPath $rcPath
-        |""".stripMargin
-      .replace("SCRIPT_PREAMBLE", preamble)
-      .replace("ENVIRONMENT_VARIABLES", environmentVariables)
-      .replace("INSTANTIATED_COMMAND", commandString)
-      .replace("SCRIPT_EPILOGUE", scriptEpilogue)
-      .replace("DOCKER_OUTPUT_DIR_LINK", dockerOutputDir))
+      s"""|#!$jobShell
+          |DOCKER_OUTPUT_DIR_LINK
+          |cd ${cwd.pathAsString}
+          |tmpDir=$temporaryDirectory
+          |$tmpDirPermissionsAdjustment
+          |export _JAVA_OPTIONS=-Djava.io.tmpdir="$$tmpDir"
+          |export TMPDIR="$$tmpDir"
+          |export HOME="$home"
+          |
+          |SCRIPT_PREAMBLE
+          |
+          |$out="$${tmpDir}/out.$$$$" $err="$${tmpDir}/err.$$$$"
+          |mkfifo "$$$out" "$$$err"
+          |trap 'rm "$$$out" "$$$err"' EXIT
+          |touch $stdoutRedirection $stderrRedirection
+          |tee $stdoutRedirection < "$$$out" &
+          |tee $stderrRedirection < "$$$err" >&2 &
+          |(
+          |cd ${cwd.pathAsString}
+          |ENVIRONMENT_VARIABLES
+          |INSTANTIATED_COMMAND
+          |) $stdinRedirection > "$$$out" 2> "$$$err"
+          |echo $$? > $rcTmpPath
+          |$emptyDirectoryFillCommand
+          |(
+          |cd ${cwd.pathAsString}
+          |SCRIPT_EPILOGUE
+          |${globScripts(globFiles)}
+          |${directoryScripts(directoryOutputs)}
+          |)
+          |mv $rcTmpPath $rcPath
+          |""".stripMargin
+        .replace("SCRIPT_PREAMBLE", preamble)
+        .replace("ENVIRONMENT_VARIABLES", environmentVariables)
+        .replace("INSTANTIATED_COMMAND", commandString)
+        .replace("SCRIPT_EPILOGUE", scriptEpilogue)
+        .replace("DOCKER_OUTPUT_DIR_LINK", dockerOutputDir)
+    )
   }
 
   def runtimeEnvironmentPathMapper(env: RuntimeEnvironment): RuntimeEnvironment = {
@@ -495,9 +517,10 @@ trait StandardAsyncExecutionActor
     env.copy(outputPath = env.outputPath |> localize, tempPath = env.tempPath |> localize)
   }
 
-  lazy val runtimeEnvironment: RuntimeEnvironment = {
-    RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes, jobPaths)(standardParams.minimumRuntimeSettings) |> runtimeEnvironmentPathMapper
-  }
+  lazy val runtimeEnvironment: RuntimeEnvironment =
+    RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes, jobPaths)(
+      standardParams.minimumRuntimeSettings
+    ) |> runtimeEnvironmentPathMapper
 
   /**
    * Turns WomFiles into relative paths.  These paths are relative to the working disk.
@@ -507,23 +530,21 @@ trait StandardAsyncExecutionActor
    * relativeLocalizationPath("gs://some/bucket/foo.txt") -> "some/bucket/foo.txt"
    * etc
    */
-  protected def relativeLocalizationPath(file: WomFile): WomFile = {
+  protected def relativeLocalizationPath(file: WomFile): WomFile =
     file.mapFile(value =>
       getPath(value) match {
         case Success(path) => path.pathWithoutScheme
         case _ => value
       }
     )
-  }
 
-  protected def fileName(file: WomFile): WomFile = {
+  protected def fileName(file: WomFile): WomFile =
     file.mapFile(value =>
       getPath(value) match {
         case Success(path) => path.name
         case _ => value
       }
     )
-  }
 
   protected def localizationPath(f: CommandSetupSideEffectFile): WomFile = {
     val fileTransformer = if (isAdHocFile(f.file)) fileName _ else relativeLocalizationPath _
@@ -539,7 +560,6 @@ trait StandardAsyncExecutionActor
     * Maybe this should be the other way around: the default implementation is noop and SFS / TES override it ?
     */
   lazy val localizeAdHocValues: List[AdHocValue] => ErrorOr[List[StandardAdHocValue]] = { adHocValues =>
-
     // Localize an adhoc file to the callExecutionRoot as needed
     val localize: (AdHocValue, Path) => Future[LocalizedAdHocValue] = { (adHocValue, file) =>
       val actualName = adHocValue.alternativeName.getOrElse(file.name)
@@ -547,17 +567,19 @@ trait StandardAsyncExecutionActor
       // First check that it's not already there under execution root
       asyncIo.existsAsync(finalPath) flatMap {
         // If it's not then copy it
-        case false => asyncIo.copyAsync(file, finalPath) as { LocalizedAdHocValue(adHocValue, finalPath) }
+        case false => asyncIo.copyAsync(file, finalPath) as LocalizedAdHocValue(adHocValue, finalPath)
         case true => Future.successful(LocalizedAdHocValue(adHocValue, finalPath))
       }
     }
 
-    adHocValues.traverse[ErrorOr, (AdHocValue, Path)]({ adHocValue =>
-      // Build an actionable Path from the ad hoc file
-      getPath(adHocValue.womValue.value).toErrorOr.map(adHocValue -> _)
-    })
+    adHocValues
+      .traverse[ErrorOr, (AdHocValue, Path)] { adHocValue =>
+        // Build an actionable Path from the ad hoc file
+        getPath(adHocValue.womValue.value).toErrorOr.map(adHocValue -> _)
+      }
       // Localize the values if necessary
-      .map(_.traverse[Future, LocalizedAdHocValue](localize.tupled)).toEither
+      .map(_.traverse[Future, LocalizedAdHocValue](localize.tupled))
+      .toEither
       // TODO: Asynchronify
       // This is obviously sad but turning it into a Future has earth-shattering consequences, so synchronizing it for now
       .flatMap(future => Try(Await.result(future, 1.hour)).toChecked)
@@ -577,37 +599,41 @@ trait StandardAsyncExecutionActor
     val callable = jobDescriptor.taskCall.callable
 
     /*
-      * Try to map the command line values.
-      *
-      * May not work as the commandLineValueMapper was originally meant to modify paths in the later stages of command
-      * line instantiation. However, due to [[AdHocValue]] support the command line instantiation itself currently needs
-      * to use the commandLineValue mapper. So the commandLineValueMapper is attempted first, and if that fails then
-      * returns the original womValue.
-      */
-    def tryCommandLineValueMapper(womValue: WomValue): WomValue = {
+     * Try to map the command line values.
+     *
+     * May not work as the commandLineValueMapper was originally meant to modify paths in the later stages of command
+     * line instantiation. However, due to [[AdHocValue]] support the command line instantiation itself currently needs
+     * to use the commandLineValue mapper. So the commandLineValueMapper is attempted first, and if that fails then
+     * returns the original womValue.
+     */
+    def tryCommandLineValueMapper(womValue: WomValue): WomValue =
       Try(commandLineJobInputValueMapper(womValue)).getOrElse(womValue)
-    }
 
-    val unmappedInputs: Map[String, WomValue] = jobDescriptor.evaluatedTaskInputs.map({
+    val unmappedInputs: Map[String, WomValue] = jobDescriptor.evaluatedTaskInputs.map {
       case (inputDefinition, womValue) => inputDefinition.localName.value -> womValue
-    })
-
-    val mappedInputs: Checked[Map[String, WomValue]] = localizedInputs.toErrorOr.map(
-      _.map({
-        case (inputDefinition, value) => inputDefinition.localName.value -> tryCommandLineValueMapper(value)
-      })
-    ).toEither
-
-    val evaluateAndInitialize = (containerizedInputExpression: ContainerizedInputExpression) => for {
-      mapped <- mappedInputs
-      evaluated <- containerizedInputExpression.evaluate(unmappedInputs, mapped, backendEngineFunctions).toChecked
-      initialized <- evaluated.traverse[IOChecked, AdHocValue]({ adHocValue =>
-        adHocValue.womValue.initialize(backendEngineFunctions).map({
-          case file: WomFile => adHocValue.copy(womValue = file)
-          case _ => adHocValue
-        })
-      }).toChecked
-    } yield initialized
+    }
+
+    val mappedInputs: Checked[Map[String, WomValue]] = localizedInputs.toErrorOr
+      .map(
+        _.map { case (inputDefinition, value) =>
+          inputDefinition.localName.value -> tryCommandLineValueMapper(value)
+        }
+      )
+      .toEither
+
+    val evaluateAndInitialize = (containerizedInputExpression: ContainerizedInputExpression) =>
+      for {
+        mapped <- mappedInputs
+        evaluated <- containerizedInputExpression.evaluate(unmappedInputs, mapped, backendEngineFunctions).toChecked
+        initialized <- evaluated
+          .traverse[IOChecked, AdHocValue] { adHocValue =>
+            adHocValue.womValue.initialize(backendEngineFunctions).map {
+              case file: WomFile => adHocValue.copy(womValue = file)
+              case _ => adHocValue
+            }
+          }
+          .toChecked
+      } yield initialized
 
     callable.adHocFileCreation.toList
       .flatTraverse[ErrorOr, AdHocValue](evaluateAndInitialize.andThen(_.toValidated))
@@ -617,9 +643,10 @@ trait StandardAsyncExecutionActor
     .flatMap(localizeAdHocValues.andThen(_.toEither))
     .toValidated
 
-  protected def asAdHocFile(womFile: WomFile): Option[AdHocValue] = evaluatedAdHocFiles map { _.find({
-    case AdHocValue(file, _, _) => file.value == womFile.value
-  })
+  protected def asAdHocFile(womFile: WomFile): Option[AdHocValue] = evaluatedAdHocFiles map {
+    _.find { case AdHocValue(file, _, _) =>
+      file.value == womFile.value
+    }
   } getOrElse None
 
   protected def isAdHocFile(womFile: WomFile): Boolean = asAdHocFile(womFile).isDefined
@@ -629,18 +656,22 @@ trait StandardAsyncExecutionActor
     val callable = jobDescriptor.taskCall.callable
 
     // Replace input files with the ad hoc updated version
-    def adHocFilePreProcessor(in: WomEvaluatedCallInputs): Try[WomEvaluatedCallInputs] = {
+    def adHocFilePreProcessor(in: WomEvaluatedCallInputs): Try[WomEvaluatedCallInputs] =
       localizedAdHocValues.toTry("Error evaluating ad hoc files") map { adHocFiles =>
-        in map {
-          case (inputDefinition, originalWomValue) =>
-            inputDefinition -> adHocFiles.collectFirst({
-              case AsAdHocValue(AdHocValue(originalWomFile, _, Some(inputName))) if inputName == inputDefinition.localName.value => originalWomFile
-              case AsLocalizedAdHocValue(LocalizedAdHocValue(AdHocValue(originalWomFile, _, Some(inputName)), localizedPath)) if inputName == inputDefinition.localName.value =>
+        in map { case (inputDefinition, originalWomValue) =>
+          inputDefinition -> adHocFiles
+            .collectFirst {
+              case AsAdHocValue(AdHocValue(originalWomFile, _, Some(inputName)))
+                  if inputName == inputDefinition.localName.value =>
+                originalWomFile
+              case AsLocalizedAdHocValue(
+                    LocalizedAdHocValue(AdHocValue(originalWomFile, _, Some(inputName)), localizedPath)
+                  ) if inputName == inputDefinition.localName.value =>
                 originalWomFile.mapFile(_ => localizedPath.pathAsString)
-            }).getOrElse(originalWomValue)
+            }
+            .getOrElse(originalWomValue)
         }
       }
-    }
 
     // Gets the inputs that will be mutated by instantiating the command.
     val mutatingPreProcessor: WomEvaluatedCallInputs => Try[WomEvaluatedCallInputs] = { _ =>
@@ -658,12 +689,16 @@ trait StandardAsyncExecutionActor
       runtimeEnvironment
     )
 
-    def makeStringKeyedMap(list: List[(LocalName, WomValue)]): Map[String, WomValue] = list.toMap map { case (k, v) => k.value -> v }
+    def makeStringKeyedMap(list: List[(LocalName, WomValue)]): Map[String, WomValue] = list.toMap map { case (k, v) =>
+      k.value -> v
+    }
 
     val command = instantiatedCommandValidation flatMap { instantiatedCommand =>
       val valueMappedPreprocessedInputs = instantiatedCommand.valueMappedPreprocessedInputs |> makeStringKeyedMap
 
-      val adHocFileCreationSideEffectFiles: ErrorOr[List[CommandSetupSideEffectFile]] = localizedAdHocValues map { _.map(adHocValueToCommandSetupSideEffectFile) }
+      val adHocFileCreationSideEffectFiles: ErrorOr[List[CommandSetupSideEffectFile]] = localizedAdHocValues map {
+        _.map(adHocValueToCommandSetupSideEffectFile)
+      }
 
       def evaluateEnvironmentExpression(nameAndExpression: (String, WomExpression)): ErrorOr[(String, String)] = {
         val (name, expression) = nameAndExpression
@@ -674,16 +709,25 @@ trait StandardAsyncExecutionActor
 
       // Build a list of functions from a CommandTaskDefinition to an Option[WomExpression] representing a possible
       // redirection or override of the filename of a redirection. Evaluate that expression if present and stringify.
-      val List(stdinRedirect, stdoutOverride, stderrOverride) = List[CommandTaskDefinition => Option[WomExpression]](
-        _.stdinRedirection, _.stdoutOverride, _.stderrOverride) map {
-        _.apply(callable).traverse[ErrorOr, String] { _.evaluateValue(valueMappedPreprocessedInputs, backendEngineFunctions) map { _.valueString} }
-      }
+      val List(stdinRedirect, stdoutOverride, stderrOverride) =
+        List[CommandTaskDefinition => Option[WomExpression]](_.stdinRedirection,
+                                                             _.stdoutOverride,
+                                                             _.stderrOverride
+        ) map {
+          _.apply(callable).traverse[ErrorOr, String] {
+            _.evaluateValue(valueMappedPreprocessedInputs, backendEngineFunctions) map { _.valueString }
+          }
+        }
 
       (adHocFileCreationSideEffectFiles, environmentVariables, stdinRedirect, stdoutOverride, stderrOverride) mapN {
         (adHocFiles, env, in, out, err) =>
           instantiatedCommand.copy(
-            createdFiles = instantiatedCommand.createdFiles ++ adHocFiles, environmentVariables = env.toMap,
-            evaluatedStdinRedirection = in, evaluatedStdoutOverride = out, evaluatedStderrOverride = err)
+            createdFiles = instantiatedCommand.createdFiles ++ adHocFiles,
+            environmentVariables = env.toMap,
+            evaluatedStdinRedirection = in,
+            evaluatedStdoutOverride = out,
+            evaluatedStderrOverride = err
+          )
       }: ErrorOr[InstantiatedCommand]
     }
 
@@ -700,11 +744,10 @@ trait StandardAsyncExecutionActor
     *
     * If the `command` errors for some reason, put a "-1" into the rc file.
     */
-  def redirectOutputs(command: String): String = {
+  def redirectOutputs(command: String): String =
     // > 128 is the cutoff for signal-induced process deaths such as might be observed with abort.
     // http://www.tldp.org/LDP/abs/html/exitcodes.html
     s"""$command < /dev/null || { rc=$$?; if [ "$$rc" -gt "128" ]; then echo $$rc; else echo -1; fi } > ${jobPaths.returnCode}"""
-  }
 
   /** A tag that may be used for logging. */
   lazy val tag = s"${this.getClass.getSimpleName} [UUID(${workflowIdForLogging.shortString}):${jobDescriptor.key.tag}]"
@@ -714,42 +757,47 @@ trait StandardAsyncExecutionActor
     *
     * @return True if a non-empty `remoteStdErrPath` should fail the job.
     */
-  lazy val failOnStdErr: Boolean = RuntimeAttributesValidation.extract(
-    FailOnStderrValidation.instance, validatedRuntimeAttributes)
+  lazy val failOnStdErr: Boolean =
+    RuntimeAttributesValidation.extract(FailOnStderrValidation.instance, validatedRuntimeAttributes)
 
   /**
     * Returns the behavior for continuing on the return code, obtained by converting `returnCodeContents` to an Int.
     *
     * @return the behavior for continuing on the return code.
     */
-  lazy val continueOnReturnCode: ContinueOnReturnCode = RuntimeAttributesValidation.extract(
-    ContinueOnReturnCodeValidation.instance, validatedRuntimeAttributes)
+  lazy val continueOnReturnCode: ContinueOnReturnCode =
+    RuntimeAttributesValidation.extract(ContinueOnReturnCodeValidation.instance, validatedRuntimeAttributes)
 
   /**
     * Returns the max number of times that a failed job should be retried, obtained by converting `maxRetries` to an Int.
     */
-  lazy val maxRetries: Int = RuntimeAttributesValidation.extract(
-    MaxRetriesValidation.instance, validatedRuntimeAttributes)
+  lazy val maxRetries: Int =
+    RuntimeAttributesValidation.extract(MaxRetriesValidation.instance, validatedRuntimeAttributes)
 
-
-  lazy val previousFailedRetries: Int = jobDescriptor.prefetchedKvStoreEntries.get(BackendLifecycleActorFactory.FailedRetryCountKey) match {
-    case Some(KvPair(_,v)) => v.toInt
-    case _ => 0
-  }
+  lazy val previousFailedRetries: Int =
+    jobDescriptor.prefetchedKvStoreEntries.get(BackendLifecycleActorFactory.FailedRetryCountKey) match {
+      case Some(KvPair(_, v)) => v.toInt
+      case _ => 0
+    }
 
   /**
    * Returns the memory multiplier for previous attempt if available
    */
-  lazy val previousMemoryMultiplier: Option[Double] = jobDescriptor.prefetchedKvStoreEntries.get(BackendLifecycleActorFactory.MemoryMultiplierKey) match {
-    case Some(KvPair(_,v)) => Try(v.toDouble) match {
-      case Success(m) => Option(m)
-      case Failure(e) =>
-        // should not happen as Cromwell itself had written the value as a Double
-        log.error(e, s"Programmer error: unexpected failure attempting to convert value of MemoryMultiplierKey from JOB_KEY_VALUE_ENTRY table to Double.")
-        None
+  lazy val previousMemoryMultiplier: Option[Double] =
+    jobDescriptor.prefetchedKvStoreEntries.get(BackendLifecycleActorFactory.MemoryMultiplierKey) match {
+      case Some(KvPair(_, v)) =>
+        Try(v.toDouble) match {
+          case Success(m) => Option(m)
+          case Failure(e) =>
+            // should not happen as Cromwell itself had written the value as a Double
+            log.error(
+              e,
+              s"Programmer error: unexpected failure attempting to convert value of MemoryMultiplierKey from JOB_KEY_VALUE_ENTRY table to Double."
+            )
+            None
+        }
+      case _ => None
     }
-    case _ => None
-  }
 
   /**
     * Execute the job specified in the params. Should return a `StandardAsyncPendingExecutionHandle`, or a
@@ -757,9 +805,8 @@ trait StandardAsyncExecutionActor
     *
     * @return the execution handle for the job.
     */
-  def execute(): ExecutionHandle = {
+  def execute(): ExecutionHandle =
     throw new UnsupportedOperationException(s"Neither execute() nor executeAsync() implemented by $getClass")
-  }
 
   /**
     * Async execute the job specified in the params. Should return a `StandardAsyncPendingExecutionHandle`, or a
@@ -797,7 +844,8 @@ trait StandardAsyncExecutionActor
     * @param jobId The previously recorded job id.
     * @return the execution handle for the job.
     */
-  def reconnectToAbortAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] = Future.failed(JobReconnectionNotSupportedException(jobDescriptor.key))
+  def reconnectToAbortAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] =
+    Future.failed(JobReconnectionNotSupportedException(jobDescriptor.key))
 
   /**
     * This is in spirit similar to recover except it does not defaults back to running the job if not implemented.
@@ -809,7 +857,8 @@ trait StandardAsyncExecutionActor
     * @param jobId The previously recorded job id.
     * @return the execution handle for the job.
     */
-  def reconnectAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] = Future.failed(JobReconnectionNotSupportedException(jobDescriptor.key))
+  def reconnectAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] =
+    Future.failed(JobReconnectionNotSupportedException(jobDescriptor.key))
 
   /**
     * Returns the run status for the job.
@@ -817,9 +866,8 @@ trait StandardAsyncExecutionActor
     * @param handle The handle of the running job.
     * @return The status of the job.
     */
-  def pollStatus(handle: StandardAsyncPendingExecutionHandle): StandardAsyncRunState = {
+  def pollStatus(handle: StandardAsyncPendingExecutionHandle): StandardAsyncRunState =
     throw new UnsupportedOperationException(s"Neither pollStatus nor pollStatusAsync implemented by $getClass")
-  }
 
   /**
     * Returns the async run status for the job.
@@ -827,7 +875,8 @@ trait StandardAsyncExecutionActor
     * @param handle The handle of the running job.
     * @return The status of the job.
     */
-  def pollStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[StandardAsyncRunState] = Future.fromTry(Try(pollStatus(handle)))
+  def pollStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[StandardAsyncRunState] =
+    Future.fromTry(Try(pollStatus(handle)))
 
   /**
     * Adds custom behavior invoked when polling fails due to some exception. By default adds nothing.
@@ -838,9 +887,8 @@ trait StandardAsyncExecutionActor
     *
     * @return A partial function handler for exceptions after polling.
     */
-  def customPollStatusFailure: PartialFunction[(ExecutionHandle, Exception), ExecutionHandle] = {
+  def customPollStatusFailure: PartialFunction[(ExecutionHandle, Exception), ExecutionHandle] =
     PartialFunction.empty
-  }
 
   /**
     * Returns true when a job is complete, either successfully or unsuccessfully.
@@ -911,13 +959,12 @@ trait StandardAsyncExecutionActor
     *
     * By default handles the behavior of `requestsAbortAndDiesImmediately`.
     */
-  def postAbort(): Unit = {
+  def postAbort(): Unit =
     if (requestsAbortAndDiesImmediately) {
       tellMetadata(Map(CallMetadataKeys.BackendStatus -> "Aborted"))
       context.parent ! JobAbortedResponse(jobDescriptor.key)
       context.stop(self)
     }
-  }
 
   /**
     * Output value mapper.
@@ -925,19 +972,17 @@ trait StandardAsyncExecutionActor
     * @param womValue The original WOM value.
     * @return The Try wrapped and mapped WOM value.
     */
-  final def outputValueMapper(womValue: WomValue): Try[WomValue] = {
+  final def outputValueMapper(womValue: WomValue): Try[WomValue] =
     WomFileMapper.mapWomFiles(mapOutputWomFile)(womValue)
-  }
 
   /**
     * Used to convert to output paths.
     *
     */
   def mapOutputWomFile(womFile: WomFile): WomFile =
-    womFile.mapFile{
-      path =>
-        val pathFromContainerInputs = jobPaths.hostPathFromContainerInputs(path)
-        pathFromContainerInputs.toAbsolutePath.toString
+    womFile.mapFile { path =>
+      val pathFromContainerInputs = jobPaths.hostPathFromContainerInputs(path)
+      pathFromContainerInputs.toAbsolutePath.toString
     }
 
   /**
@@ -947,9 +992,8 @@ trait StandardAsyncExecutionActor
     *
     * @return A Try wrapping evaluated outputs.
     */
-  def evaluateOutputs()(implicit ec: ExecutionContext): Future[EvaluatedJobOutputs] = {
+  def evaluateOutputs()(implicit ec: ExecutionContext): Future[EvaluatedJobOutputs] =
     OutputEvaluator.evaluateOutputs(jobDescriptor, backendEngineFunctions, outputValueMapper)
-  }
 
   /**
     * Tests whether an attempted result of evaluateOutputs should possibly be retried.
@@ -965,7 +1009,7 @@ trait StandardAsyncExecutionActor
     * @param exception The exception, possibly an CromwellAggregatedException.
     * @return True if evaluateOutputs should be retried later.
     */
-  final def retryEvaluateOutputsAggregated(exception: Exception): Boolean = {
+  final def retryEvaluateOutputsAggregated(exception: Exception): Boolean =
     exception match {
       case aggregated: CromwellAggregatedException =>
         aggregated.throwables.collectFirst {
@@ -973,7 +1017,6 @@ trait StandardAsyncExecutionActor
         }.isDefined
       case _ => retryEvaluateOutputs(exception)
     }
-  }
 
   /**
     * Tests whether an attempted result of evaluateOutputs should possibly be retried.
@@ -999,7 +1042,8 @@ trait StandardAsyncExecutionActor
     */
   def handleExecutionSuccess(runStatus: StandardAsyncRunState,
                              handle: StandardAsyncPendingExecutionHandle,
-                             returnCode: Int)(implicit ec: ExecutionContext): Future[ExecutionHandle] = {
+                             returnCode: Int
+  )(implicit ec: ExecutionContext): Future[ExecutionHandle] =
     evaluateOutputs() map {
       case ValidJobOutputs(outputs) =>
         // Need to make sure the paths are up to date before sending the detritus back in the response
@@ -1016,7 +1060,6 @@ trait StandardAsyncExecutionActor
         handle
       case JobOutputsEvaluationException(ex) => FailedNonRetryableExecutionHandle(ex, kvPairsToSave = None)
     }
-  }
 
   /**
     * Process an unsuccessful run, as interpreted by `handleExecutionFailure`.
@@ -1024,18 +1067,18 @@ trait StandardAsyncExecutionActor
     * @return The execution handle.
     */
   def retryElseFail(backendExecutionStatus: Future[ExecutionHandle],
-                    retryWithMoreMemory: Boolean = false): Future[ExecutionHandle] = {
-
+                    retryWithMoreMemory: Boolean = false
+  ): Future[ExecutionHandle] =
     backendExecutionStatus flatMap {
       case failedRetryableOrNonRetryable: FailedExecutionHandle =>
-
         val kvsFromPreviousAttempt = jobDescriptor.prefetchedKvStoreEntries.collect {
           case (key: String, kvPair: KvPair) => key -> kvPair
         }
         val kvsForNextAttempt = failedRetryableOrNonRetryable.kvPairsToSave match {
-          case Some(kvPairs) => kvPairs.map {
-            case kvPair@KvPair(ScopedKey(_, _, key), _) => key -> kvPair
-          }.toMap
+          case Some(kvPairs) =>
+            kvPairs.map { case kvPair @ KvPair(ScopedKey(_, _, key), _) =>
+              key -> kvPair
+            }.toMap
           case None => Map.empty[String, KvPair]
         }
 
@@ -1045,23 +1088,35 @@ trait StandardAsyncExecutionActor
             (retryWithMoreMemory, memoryRetryFactor, previousMemoryMultiplier) match {
               case (true, Some(retryFactor), Some(previousMultiplier)) =>
                 val nextMemoryMultiplier = previousMultiplier * retryFactor.value
-                saveAttrsAndRetry(failed, kvsFromPreviousAttempt, kvsForNextAttempt, incFailedCount = true, Option(nextMemoryMultiplier))
+                saveAttrsAndRetry(failed,
+                                  kvsFromPreviousAttempt,
+                                  kvsForNextAttempt,
+                                  incFailedCount = true,
+                                  Option(nextMemoryMultiplier)
+                )
               case (true, Some(retryFactor), None) =>
-                saveAttrsAndRetry(failed, kvsFromPreviousAttempt, kvsForNextAttempt, incFailedCount = true, Option(retryFactor.value))
-              case (_, _, _) => saveAttrsAndRetry(failed, kvsFromPreviousAttempt, kvsForNextAttempt, incFailedCount = true)
+                saveAttrsAndRetry(failed,
+                                  kvsFromPreviousAttempt,
+                                  kvsForNextAttempt,
+                                  incFailedCount = true,
+                                  Option(retryFactor.value)
+                )
+              case (_, _, _) =>
+                saveAttrsAndRetry(failed, kvsFromPreviousAttempt, kvsForNextAttempt, incFailedCount = true)
             }
           case failedNonRetryable: FailedNonRetryableExecutionHandle => Future.successful(failedNonRetryable)
-          case failedRetryable: FailedRetryableExecutionHandle => saveAttrsAndRetry(failedRetryable, kvsFromPreviousAttempt, kvsForNextAttempt, incFailedCount = false)
+          case failedRetryable: FailedRetryableExecutionHandle =>
+            saveAttrsAndRetry(failedRetryable, kvsFromPreviousAttempt, kvsForNextAttempt, incFailedCount = false)
         }
       case _ => backendExecutionStatus
     }
-  }
 
   private def saveAttrsAndRetry(failedExecHandle: FailedExecutionHandle,
                                 kvPrev: Map[String, KvPair],
                                 kvNext: Map[String, KvPair],
                                 incFailedCount: Boolean,
-                                nextMemoryMultiplier: Option[Double] = None): Future[FailedRetryableExecutionHandle] = {
+                                nextMemoryMultiplier: Option[Double] = None
+  ): Future[FailedRetryableExecutionHandle] =
     failedExecHandle match {
       case failedNonRetryable: FailedNonRetryableExecutionHandle =>
         saveKvPairsForNextAttempt(kvPrev, kvNext, incFailedCount, nextMemoryMultiplier) map { _ =>
@@ -1070,7 +1125,6 @@ trait StandardAsyncExecutionActor
       case failedRetryable: FailedRetryableExecutionHandle =>
         saveKvPairsForNextAttempt(kvPrev, kvNext, incFailedCount, nextMemoryMultiplier) map (_ => failedRetryable)
     }
-  }
 
   /**
    * Merge key-value pairs from previous job execution attempt with incoming pairs from current attempt, which has just
@@ -1081,8 +1135,10 @@ trait StandardAsyncExecutionActor
   private def saveKvPairsForNextAttempt(kvsFromPreviousAttempt: Map[String, KvPair],
                                         kvsForNextAttempt: Map[String, KvPair],
                                         incrementFailedRetryCount: Boolean,
-                                        nextMemoryMultiplierOption: Option[Double]): Future[Seq[KvResponse]] = {
-    val nextKvJobKey = KvJobKey(jobDescriptor.key.call.fullyQualifiedName, jobDescriptor.key.index, jobDescriptor.key.attempt + 1)
+                                        nextMemoryMultiplierOption: Option[Double]
+  ): Future[Seq[KvResponse]] = {
+    val nextKvJobKey =
+      KvJobKey(jobDescriptor.key.call.fullyQualifiedName, jobDescriptor.key.index, jobDescriptor.key.attempt + 1)
 
     def getNextKvPair[A](key: String, value: String): Map[String, KvPair] = {
       val nextScopedKey = ScopedKey(jobDescriptor.workflowDescriptor.id, nextKvJobKey, key)
@@ -1090,7 +1146,8 @@ trait StandardAsyncExecutionActor
       Map(key -> nextKvPair)
     }
 
-    val kvsFromPreviousAttemptUpd = kvsFromPreviousAttempt.view.mapValues(kvPair => kvPair.copy(key = kvPair.key.copy(jobKey = nextKvJobKey)))
+    val kvsFromPreviousAttemptUpd =
+      kvsFromPreviousAttempt.view.mapValues(kvPair => kvPair.copy(key = kvPair.key.copy(jobKey = nextKvJobKey)))
 
     val failedRetryCountKvPair: Map[String, KvPair] =
       if (incrementFailedRetryCount) getNextKvPair(FailedRetryCountKey, (previousFailedRetries + 1).toString)
@@ -1108,8 +1165,10 @@ trait StandardAsyncExecutionActor
       if (failures.isEmpty) {
         respSeq
       } else {
-        throw new RuntimeException("Failed to save one or more job execution attributes to the database between " +
-          "attempts:\n " + failures.mkString("\n"))
+        throw new RuntimeException(
+          "Failed to save one or more job execution attributes to the database between " +
+            "attempts:\n " + failures.mkString("\n")
+        )
       }
     }
   }
@@ -1120,8 +1179,7 @@ trait StandardAsyncExecutionActor
     * @param runStatus The run status.
     * @return The execution handle.
     */
-  def handleExecutionFailure(runStatus: StandardAsyncRunState,
-                             returnCode: Option[Int]): Future[ExecutionHandle] = {
+  def handleExecutionFailure(runStatus: StandardAsyncRunState, returnCode: Option[Int]): Future[ExecutionHandle] = {
     val exception = new RuntimeException(s"Task ${jobDescriptor.key.tag} failed for unknown reason: $runStatus")
     Future.successful(FailedNonRetryableExecutionHandle(exception, returnCode, None))
   }
@@ -1150,30 +1208,33 @@ trait StandardAsyncExecutionActor
   }
 
   override def executeOrRecover(mode: ExecutionMode)(implicit ec: ExecutionContext): Future[ExecutionHandle] = {
-    val executeOrRecoverFuture = {
+    val executeOrRecoverFuture =
       mode match {
-        case Reconnect(jobId: StandardAsyncJob@unchecked) => reconnectAsync(jobId)
-        case ReconnectToAbort(jobId: StandardAsyncJob@unchecked) => reconnectToAbortAsync(jobId)
-        case Recover(jobId: StandardAsyncJob@unchecked) => recoverAsync(jobId)
+        case Reconnect(jobId: StandardAsyncJob @unchecked) => reconnectAsync(jobId)
+        case ReconnectToAbort(jobId: StandardAsyncJob @unchecked) => reconnectToAbortAsync(jobId)
+        case Recover(jobId: StandardAsyncJob @unchecked) => recoverAsync(jobId)
         case _ =>
           tellMetadata(startMetadataKeyValues)
           executeAsync()
       }
-    }
 
-    executeOrRecoverFuture flatMap executeOrRecoverSuccess recoverWith {
-      case throwable: Throwable => Future failed {
+    executeOrRecoverFuture flatMap executeOrRecoverSuccess recoverWith { case throwable: Throwable =>
+      Future failed {
         jobLogger.error(s"Error attempting to $mode", throwable)
         throwable
       }
     }
   }
 
-  private def executeOrRecoverSuccess(executionHandle: ExecutionHandle): Future[ExecutionHandle] = {
+  private def executeOrRecoverSuccess(executionHandle: ExecutionHandle): Future[ExecutionHandle] =
     executionHandle match {
-      case handle: PendingExecutionHandle[StandardAsyncJob@unchecked, StandardAsyncRunInfo@unchecked, StandardAsyncRunState@unchecked] =>
-
-        configurationDescriptor.slowJobWarningAfter foreach { duration => self ! WarnAboutSlownessAfter(handle.pendingJob.jobId, duration) }
+      case handle: PendingExecutionHandle[StandardAsyncJob @unchecked,
+                                          StandardAsyncRunInfo @unchecked,
+                                          StandardAsyncRunState @unchecked
+          ] =>
+        configurationDescriptor.slowJobWarningAfter foreach { duration =>
+          self ! WarnAboutSlownessAfter(handle.pendingJob.jobId, duration)
+        }
 
         tellKvJobId(handle.pendingJob) map { _ =>
           if (logJobIds) jobLogger.info(s"job id: ${handle.pendingJob.jobId}")
@@ -1183,34 +1244,31 @@ trait StandardAsyncExecutionActor
           the prior runnable to the thread pool this actor doesn't know the job id for aborting. These runnables are
           queued up and may still be run by the thread pool anytime in the future. Issue #1218 may address this
           inconsistency at a later time. For now, just go back and check if we missed the abort command.
-          */
+           */
           self ! CheckMissedAbort(handle.pendingJob)
           executionHandle
         }
       case _ => Future.successful(executionHandle)
     }
-  }
 
-  override def poll(previous: ExecutionHandle)(implicit ec: ExecutionContext): Future[ExecutionHandle] = {
+  override def poll(previous: ExecutionHandle)(implicit ec: ExecutionContext): Future[ExecutionHandle] =
     previous match {
-      case handle: PendingExecutionHandle[
-        StandardAsyncJob@unchecked, StandardAsyncRunInfo@unchecked, StandardAsyncRunState@unchecked] =>
-
+      case handle: PendingExecutionHandle[StandardAsyncJob @unchecked,
+                                          StandardAsyncRunInfo @unchecked,
+                                          StandardAsyncRunState @unchecked
+          ] =>
         jobLogger.debug(s"$tag Polling Job ${handle.pendingJob}")
-        pollStatusAsync(handle) flatMap {
-          backendRunStatus =>
-            self ! WarnAboutSlownessIfNecessary
-            handlePollSuccess(handle, backendRunStatus)
-        } recover {
-          case throwable =>
-            handlePollFailure(handle, throwable)
+        pollStatusAsync(handle) flatMap { backendRunStatus =>
+          self ! WarnAboutSlownessIfNecessary
+          handlePollSuccess(handle, backendRunStatus)
+        } recover { case throwable =>
+          handlePollFailure(handle, throwable)
         }
       case successful: SuccessfulExecutionHandle => Future.successful(successful)
       case failed: FailedNonRetryableExecutionHandle => Future.successful(failed)
       case failedRetryable: FailedRetryableExecutionHandle => Future.successful(failedRetryable)
       case badHandle => Future.failed(new IllegalArgumentException(s"Unexpected execution handle: $badHandle"))
     }
-  }
 
   /**
     * Process a poll success.
@@ -1220,7 +1278,8 @@ trait StandardAsyncExecutionActor
     * @return The updated execution handle.
     */
   def handlePollSuccess(oldHandle: StandardAsyncPendingExecutionHandle,
-                        state: StandardAsyncRunState): Future[ExecutionHandle] = {
+                        state: StandardAsyncRunState
+  ): Future[ExecutionHandle] = {
     val previousState = oldHandle.previousState
     if (!(previousState exists statusEquivalentTo(state))) {
       // If this is the first time checking the status, we log the transition as '-' to 'currentStatus'. Otherwise just use
@@ -1236,7 +1295,10 @@ trait StandardAsyncExecutionActor
         val metadata = getTerminalMetadata(state)
         tellMetadata(metadata)
         handleExecutionResult(state, oldHandle)
-      case s => Future.successful(oldHandle.copy(previousState = Option(s))) // Copy the current handle with updated previous status.
+      case s =>
+        Future.successful(
+          oldHandle.copy(previousState = Option(s))
+        ) // Copy the current handle with updated previous status.
     }
   }
 
@@ -1247,8 +1309,7 @@ trait StandardAsyncExecutionActor
     * @param throwable The cause of the polling failure.
     * @return The updated execution handle.
     */
-  def handlePollFailure(oldHandle: StandardAsyncPendingExecutionHandle,
-                        throwable: Throwable): ExecutionHandle = {
+  def handlePollFailure(oldHandle: StandardAsyncPendingExecutionHandle, throwable: Throwable): ExecutionHandle =
     throwable match {
       case exception: Exception =>
         val handler: PartialFunction[(ExecutionHandle, Exception), ExecutionHandle] =
@@ -1259,7 +1320,9 @@ trait StandardAsyncExecutionActor
               FailedNonRetryableExecutionHandle(exception, kvPairsToSave = None)
             case (handle: ExecutionHandle, exception: Exception) =>
               // Log exceptions and return the original handle to try again.
-              jobLogger.warn(s"Caught non-fatal ${exception.getClass.getSimpleName} exception trying to poll, retrying", exception)
+              jobLogger.warn(s"Caught non-fatal ${exception.getClass.getSimpleName} exception trying to poll, retrying",
+                             exception
+              )
               handle
           }
         handler((oldHandle, exception))
@@ -1268,7 +1331,6 @@ trait StandardAsyncExecutionActor
         // Someone has subclassed or instantiated Throwable directly. Kill the job. They should be using an Exception.
         FailedNonRetryableExecutionHandle(throwable, kvPairsToSave = None)
     }
-  }
 
   /**
     * Process an execution result.
@@ -1278,33 +1340,35 @@ trait StandardAsyncExecutionActor
     * @return The updated execution handle.
     */
   def handleExecutionResult(status: StandardAsyncRunState,
-                            oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
+                            oldHandle: StandardAsyncPendingExecutionHandle
+  ): Future[ExecutionHandle] = {
 
     // Returns true if the task has written an RC file that indicates OOM, false otherwise
     def memoryRetryRC: Future[Boolean] = {
-      def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean = {
+      def returnCodeAsBoolean(codeAsOption: Option[String]): Boolean =
         codeAsOption match {
           case Some(codeAsString) =>
             Try(codeAsString.trim.toInt) match {
-              case Success(code) => code match {
-                case StderrContainsRetryKeysCode => true
-                case _ => false
-              }
+              case Success(code) =>
+                code match {
+                  case StderrContainsRetryKeysCode => true
+                  case _ => false
+                }
               case Failure(e) =>
-                log.error(s"'CheckingForMemoryRetry' action exited with code '$codeAsString' which couldn't be " +
-                  s"converted to an Integer. Task will not be retried with more memory. Error: ${ExceptionUtils.getMessage(e)}")
+                log.error(
+                  s"'CheckingForMemoryRetry' action exited with code '$codeAsString' which couldn't be " +
+                    s"converted to an Integer. Task will not be retried with more memory. Error: ${ExceptionUtils.getMessage(e)}"
+                )
                 false
             }
           case None => false
         }
-      }
 
-      def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] = {
+      def readMemoryRetryRCFile(fileExists: Boolean): Future[Option[String]] =
         if (fileExists)
           asyncIo.contentAsStringAsync(jobPaths.memoryRetryRC, None, failOnOverflow = false).map(Option(_))
         else
           Future.successful(None)
-      }
 
       for {
         fileExists <- asyncIo.existsAsync(jobPaths.memoryRetryRC)
@@ -1324,47 +1388,73 @@ trait StandardAsyncExecutionActor
       outOfMemoryDetected <- memoryRetryRC
     } yield (stderrSize, returnCodeAsString, outOfMemoryDetected)
 
-    stderrSizeAndReturnCodeAndMemoryRetry flatMap {
-      case (stderrSize, returnCodeAsString, outOfMemoryDetected) =>
-        val tryReturnCodeAsInt = Try(returnCodeAsString.trim.toInt)
-
-        if (isDone(status)) {
-          tryReturnCodeAsInt match {
-            case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
-              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
-              retryElseFail(executionHandle)
-            case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
-              handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
-            // It's important that we check retryWithMoreMemory case before isAbort. RC could be 137 in either case;
-            // if it was caused by OOM killer, want to handle as OOM and not job abort.
-            case Success(returnCodeAsInt) if outOfMemoryDetected && memoryRetryRequested  =>
-              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
-              retryElseFail(executionHandle, outOfMemoryDetected)
-            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
-              Future.successful(AbortedExecutionHandle)
-            case Success(returnCodeAsInt) =>
-              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption), Option(returnCodeAsInt), None))
-              retryElseFail(executionHandle)
-            case Failure(_) =>
-              Future.successful(FailedNonRetryableExecutionHandle(ReturnCodeIsNotAnInt(jobDescriptor.key.tag, returnCodeAsString, stderrAsOption), kvPairsToSave = None))
-          }
-        } else {
-          tryReturnCodeAsInt match {
-            case Success(returnCodeAsInt) if outOfMemoryDetected && memoryRetryRequested && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
-              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
-              retryElseFail(executionHandle, outOfMemoryDetected)
-            case _ =>
-              val failureStatus = handleExecutionFailure(status, tryReturnCodeAsInt.toOption)
-              retryElseFail(failureStatus)
-          }
+    stderrSizeAndReturnCodeAndMemoryRetry flatMap { case (stderrSize, returnCodeAsString, outOfMemoryDetected) =>
+      val tryReturnCodeAsInt = Try(returnCodeAsString.trim.toInt)
+
+      if (isDone(status)) {
+        tryReturnCodeAsInt match {
+          case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
+            val executionHandle = Future.successful(
+              FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption),
+                                                Option(returnCodeAsInt),
+                                                None
+              )
+            )
+            retryElseFail(executionHandle)
+          case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
+            handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
+          // It's important that we check retryWithMoreMemory case before isAbort. RC could be 137 in either case;
+          // if it was caused by OOM killer, want to handle as OOM and not job abort.
+          case Success(returnCodeAsInt) if outOfMemoryDetected && memoryRetryRequested =>
+            val executionHandle = Future.successful(
+              FailedNonRetryableExecutionHandle(
+                RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log),
+                Option(returnCodeAsInt),
+                None
+              )
+            )
+            retryElseFail(executionHandle, outOfMemoryDetected)
+          case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) =>
+            Future.successful(AbortedExecutionHandle)
+          case Success(returnCodeAsInt) =>
+            val executionHandle = Future.successful(
+              FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption),
+                                                Option(returnCodeAsInt),
+                                                None
+              )
+            )
+            retryElseFail(executionHandle)
+          case Failure(_) =>
+            Future.successful(
+              FailedNonRetryableExecutionHandle(
+                ReturnCodeIsNotAnInt(jobDescriptor.key.tag, returnCodeAsString, stderrAsOption),
+                kvPairsToSave = None
+              )
+            )
         }
-    } recoverWith {
-      case exception =>
-        if (isDone(status)) Future.successful(FailedNonRetryableExecutionHandle(exception, kvPairsToSave = None))
-        else {
-          val failureStatus = handleExecutionFailure(status, None)
-          retryElseFail(failureStatus)
+      } else {
+        tryReturnCodeAsInt match {
+          case Success(returnCodeAsInt)
+              if outOfMemoryDetected && memoryRetryRequested && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
+            val executionHandle = Future.successful(
+              FailedNonRetryableExecutionHandle(
+                RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log),
+                Option(returnCodeAsInt),
+                None
+              )
+            )
+            retryElseFail(executionHandle, outOfMemoryDetected)
+          case _ =>
+            val failureStatus = handleExecutionFailure(status, tryReturnCodeAsInt.toOption)
+            retryElseFail(failureStatus)
         }
+      }
+    } recoverWith { case exception =>
+      if (isDone(status)) Future.successful(FailedNonRetryableExecutionHandle(exception, kvPairsToSave = None))
+      else {
+        val failureStatus = handleExecutionFailure(status, None)
+        retryElseFail(failureStatus)
+      }
     }
   }
 
@@ -1393,7 +1483,7 @@ trait StandardAsyncExecutionActor
     serviceRegistryActor.putMetadata(jobDescriptor.workflowDescriptor.id, Option(jobDescriptor.key), metadataKeyValues)
   }
 
-  override protected implicit lazy val ec: ExecutionContextExecutor = context.dispatcher
+  implicit override protected lazy val ec: ExecutionContextExecutor = context.dispatcher
 }
 
 /**
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala b/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
index a64c6a5439c..9d049ee8fff 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala
@@ -48,16 +48,16 @@ trait StandardCachingActorHelper extends JobCachingActorHelper {
 
   lazy val call: CommandCallNode = jobDescriptor.key.call
 
-  lazy val standardInitializationData: StandardInitializationData = BackendInitializationData.
-    as[StandardInitializationData](backendInitializationDataOption)
+  lazy val standardInitializationData: StandardInitializationData =
+    BackendInitializationData.as[StandardInitializationData](backendInitializationDataOption)
 
   lazy val validatedRuntimeAttributes: ValidatedRuntimeAttributes = {
     val builder = standardInitializationData.runtimeAttributesBuilder
     builder.build(jobDescriptor.runtimeAttributes, jobLogger)
   }
 
-  lazy val isDockerRun: Boolean = RuntimeAttributesValidation.extractOption(
-    DockerValidation.instance, validatedRuntimeAttributes).isDefined
+  lazy val isDockerRun: Boolean =
+    RuntimeAttributesValidation.extractOption(DockerValidation.instance, validatedRuntimeAttributes).isDefined
 
   /**
     * Returns the paths to the job.
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardExpressionFunctions.scala b/backend/src/main/scala/cromwell/backend/standard/StandardExpressionFunctions.scala
index 7782c2da901..ac4c39fc8d7 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardExpressionFunctions.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardExpressionFunctions.scala
@@ -24,11 +24,15 @@ case class DefaultStandardExpressionFunctionsParams(override val pathBuilders: P
                                                     override val callContext: CallContext,
                                                     override val ioActorProxy: ActorRef,
                                                     override val executionContext: ExecutionContext
-                                                   ) extends StandardExpressionFunctionsParams
+) extends StandardExpressionFunctionsParams
 
 // TODO: Once we figure out premapping and postmapping, maybe we can standardize that behavior. Currently that's the most important feature that subclasses override.
 class StandardExpressionFunctions(val standardParams: StandardExpressionFunctionsParams)
-  extends GlobFunctions with DirectoryFunctions with ReadLikeFunctions with WriteFunctions with CallCorePathFunctions {
+    extends GlobFunctions
+    with DirectoryFunctions
+    with ReadLikeFunctions
+    with WriteFunctions
+    with CallCorePathFunctions {
 
   override lazy val ec = standardParams.executionContext
 
@@ -41,6 +45,6 @@ class StandardExpressionFunctions(val standardParams: StandardExpressionFunction
   val callContext: CallContext = standardParams.callContext
 
   val writeDirectory: Path = callContext.root
-  
+
   val isDocker: Boolean = callContext.isDocker
 }
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardFinalizationActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardFinalizationActor.scala
index 22eb6763b53..4bac258312e 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardFinalizationActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardFinalizationActor.scala
@@ -24,8 +24,7 @@ trait StandardFinalizationActorParams {
   def configurationDescriptor: BackendConfigurationDescriptor
 }
 
-case class DefaultStandardFinalizationActorParams
-(
+case class DefaultStandardFinalizationActorParams(
   workflowDescriptor: BackendWorkflowDescriptor,
   calls: Set[CommandCallNode],
   jobExecutionMap: JobExecutionMap,
@@ -42,7 +41,7 @@ case class DefaultStandardFinalizationActorParams
   * @param standardParams Standard parameters.
   */
 class StandardFinalizationActor(val standardParams: StandardFinalizationActorParams)
-  extends BackendWorkflowFinalizationActor {
+    extends BackendWorkflowFinalizationActor {
 
   override lazy val workflowDescriptor: BackendWorkflowDescriptor = standardParams.workflowDescriptor
   override lazy val calls: Set[CommandCallNode] = standardParams.calls
@@ -59,7 +58,7 @@ class StandardFinalizationActor(val standardParams: StandardFinalizationActorPar
 
   override def afterAll(): Future[Unit] = copyCallLogs()
 
-  lazy val logPaths: Seq[Path] = {
+  lazy val logPaths: Seq[Path] =
     for {
       actualWorkflowPath <- workflowPaths.toSeq
       (backendWorkflowDescriptor, keys) <- jobExecutionMap.toSeq
@@ -67,9 +66,8 @@ class StandardFinalizationActor(val standardParams: StandardFinalizationActorPar
       jobPaths = actualWorkflowPath.toJobPaths(key, backendWorkflowDescriptor)
       logPath <- jobPaths.logPaths.values
     } yield logPath
-  }
 
-  protected def copyCallLogs(): Future[Unit] = {
+  protected def copyCallLogs(): Future[Unit] =
     /*
     NOTE: Only using one thread pool slot here to upload all the files for all the calls.
     Using the io-dispatcher defined in application.conf because this might take a while.
@@ -77,21 +75,18 @@ class StandardFinalizationActor(val standardParams: StandardFinalizationActorPar
     pool for parallel uploads.
 
     Measure and optimize as necessary. Will likely need retry code at some level as well.
-    */
+     */
     workflowPaths match {
       case Some(paths) => Future(paths.finalCallLogsPath foreach copyCallLogs)(ioExecutionContext)
       case _ => Future.successful(())
     }
-  }
 
-  private def copyCallLogs(callLogsPath: Path): Unit = {
+  private def copyCallLogs(callLogsPath: Path): Unit =
     copyLogs(callLogsPath, logPaths)
-  }
 
-  private def copyLogs(callLogsDirPath: Path, logPaths: Seq[Path]): Unit = {
+  private def copyLogs(callLogsDirPath: Path, logPaths: Seq[Path]): Unit =
     workflowPaths match {
       case Some(paths) => logPaths.foreach(PathCopier.copy(paths.executionRoot, _, callLogsDirPath))
       case None =>
     }
-  }
 }
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardInitializationActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardInitializationActor.scala
index 95e898d6711..c4adba3cd59 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardInitializationActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardInitializationActor.scala
@@ -4,7 +4,12 @@ import akka.actor.ActorRef
 import cromwell.backend.io.WorkflowPaths
 import cromwell.backend.validation.RuntimeAttributesDefault
 import cromwell.backend.wfs.WorkflowPathBuilder
-import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor, BackendWorkflowInitializationActor}
+import cromwell.backend.{
+  BackendConfigurationDescriptor,
+  BackendInitializationData,
+  BackendWorkflowDescriptor,
+  BackendWorkflowInitializationActor
+}
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.PathBuilder
 import wom.expression.WomExpression
@@ -24,8 +29,7 @@ trait StandardInitializationActorParams {
   def configurationDescriptor: BackendConfigurationDescriptor
 }
 
-case class DefaultInitializationActorParams
-(
+case class DefaultInitializationActorParams(
   workflowDescriptor: BackendWorkflowDescriptor,
   ioActor: ActorRef,
   calls: Set[CommandCallNode],
@@ -42,7 +46,7 @@ case class DefaultInitializationActorParams
   * @param standardParams Standard parameters
   */
 class StandardInitializationActor(val standardParams: StandardInitializationActorParams)
-  extends BackendWorkflowInitializationActor {
+    extends BackendWorkflowInitializationActor {
 
   implicit protected val system = context.system
 
@@ -50,16 +54,18 @@ class StandardInitializationActor(val standardParams: StandardInitializationActo
 
   override lazy val calls: Set[CommandCallNode] = standardParams.calls
 
-  override def beforeAll(): Future[Option[BackendInitializationData]] = {
+  override def beforeAll(): Future[Option[BackendInitializationData]] =
     initializationData map Option.apply
-  }
 
   lazy val initializationData: Future[StandardInitializationData] =
-    workflowPaths map { new StandardInitializationData(_, runtimeAttributesBuilder, classOf[StandardExpressionFunctions]) }
+    workflowPaths map {
+      new StandardInitializationData(_, runtimeAttributesBuilder, classOf[StandardExpressionFunctions])
+    }
 
   lazy val expressionFunctions: Class[_ <: StandardExpressionFunctions] = classOf[StandardExpressionFunctions]
 
-  lazy val pathBuilders: Future[List[PathBuilder]] = standardParams.configurationDescriptor.pathBuilders(workflowDescriptor.workflowOptions)
+  lazy val pathBuilders: Future[List[PathBuilder]] =
+    standardParams.configurationDescriptor.pathBuilders(workflowDescriptor.workflowOptions)
 
   lazy val workflowPaths: Future[WorkflowPaths] =
     pathBuilders map { WorkflowPathBuilder.workflowPaths(configurationDescriptor, workflowDescriptor, _) }
@@ -74,13 +80,11 @@ class StandardInitializationActor(val standardParams: StandardInitializationActo
   def runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder =
     StandardValidatedRuntimeAttributesBuilder.default(configurationDescriptor.backendRuntimeAttributesConfig)
 
-  override protected lazy val runtimeAttributeValidators: Map[String, (Option[WomExpression]) => Boolean] = {
+  override protected lazy val runtimeAttributeValidators: Map[String, (Option[WomExpression]) => Boolean] =
     runtimeAttributesBuilder.validatorMap
-  }
 
-  override protected def coerceDefaultRuntimeAttributes(options: WorkflowOptions): Try[Map[String, WomValue]] = {
+  override protected def coerceDefaultRuntimeAttributes(options: WorkflowOptions): Try[Map[String, WomValue]] =
     RuntimeAttributesDefault.workflowOptionsDefault(options, runtimeAttributesBuilder.coercionMap)
-  }
 
   def validateWorkflowOptions(): Try[Unit] = Success(())
 
@@ -93,19 +97,19 @@ class StandardInitializationActor(val standardParams: StandardInitializationActo
         val notSupportedAttrString = notSupportedAttributes mkString ", "
         workflowLogger.warn(
           s"Key/s [$notSupportedAttrString] is/are not supported by backend. " +
-            s"Unsupported attributes will not be part of job executions.")
+            s"Unsupported attributes will not be part of job executions."
+        )
       }
     }
   }
 
-  override def validate(): Future[Unit] = {
+  override def validate(): Future[Unit] =
     Future.fromTry(
       for {
         _ <- validateWorkflowOptions()
         _ <- checkForUnsupportedRuntimeAttributes()
       } yield ()
     )
-  }
 
   override protected lazy val workflowDescriptor: BackendWorkflowDescriptor = standardParams.workflowDescriptor
 
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardInitializationData.scala b/backend/src/main/scala/cromwell/backend/standard/StandardInitializationData.scala
index e2618818e50..d317af2ada2 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardInitializationData.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardInitializationData.scala
@@ -6,8 +6,7 @@ import cromwell.backend.io.{JobPaths, WorkflowPaths}
 
 import scala.concurrent.ExecutionContext
 
-class StandardInitializationData
-(
+class StandardInitializationData(
   val workflowPaths: WorkflowPaths,
   val runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder,
   val standardExpressionFunctionsClass: Class[_ <: StandardExpressionFunctions]
@@ -17,7 +16,10 @@ class StandardInitializationData
   private lazy val standardExpressionFunctionsConstructor =
     standardExpressionFunctionsClass.getConstructor(classOf[StandardExpressionFunctionsParams])
 
-  def expressionFunctions(jobPaths: JobPaths, ioActorProxy: ActorRef, ec: ExecutionContext): StandardExpressionFunctions = {
+  def expressionFunctions(jobPaths: JobPaths,
+                          ioActorProxy: ActorRef,
+                          ec: ExecutionContext
+  ): StandardExpressionFunctions = {
     val pathBuilders = jobPaths.workflowPaths.pathBuilders
     val standardParams = DefaultStandardExpressionFunctionsParams(pathBuilders, jobPaths.callContext, ioActorProxy, ec)
     standardExpressionFunctionsConstructor.newInstance(standardParams)
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardJobExecutionActorParams.scala b/backend/src/main/scala/cromwell/backend/standard/StandardJobExecutionActorParams.scala
index ac670617bb9..a595f589647 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardJobExecutionActorParams.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardJobExecutionActorParams.scala
@@ -1,12 +1,18 @@
 package cromwell.backend.standard
 
 import akka.actor.ActorRef
-import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendJobDescriptor, MinimumRuntimeSettings}
+import cromwell.backend.{
+  BackendConfigurationDescriptor,
+  BackendInitializationData,
+  BackendJobDescriptor,
+  MinimumRuntimeSettings
+}
 
 /**
   * Base trait for params passed to both the sync and async backend actors.
   */
 trait StandardJobExecutionActorParams {
+
   /** The service registry actor for key/value and metadata. */
   def serviceRegistryActor: ActorRef
 
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardLifecycleActorFactory.scala b/backend/src/main/scala/cromwell/backend/standard/StandardLifecycleActorFactory.scala
index 64f79f5ad7d..aec03977ad9 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardLifecycleActorFactory.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardLifecycleActorFactory.scala
@@ -16,6 +16,7 @@ import scala.concurrent.ExecutionContext
   * May be extended for using the standard sync/async backend pattern.
   */
 trait StandardLifecycleActorFactory extends BackendLifecycleActorFactory {
+
   /**
     * Config values for the backend, and a pointer to the global config.
     *
@@ -59,41 +60,65 @@ trait StandardLifecycleActorFactory extends BackendLifecycleActorFactory {
     *
     * @return the cache hit copying class.
     */
-  lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] = Option(classOf[DefaultStandardCacheHitCopyingActor])
+  lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] = Option(
+    classOf[DefaultStandardCacheHitCopyingActor]
+  )
 
   /**
     * Returns the cache hit copying class.
     *
     * @return the cache hit copying class.
     */
-  lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(classOf[DefaultStandardFileHashingActor])
+  lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(
+    classOf[DefaultStandardFileHashingActor]
+  )
 
   /**
     * Returns the finalization class.
     *
     * @return the finalization class.
     */
-  lazy val finalizationActorClassOption: Option[Class[_ <: StandardFinalizationActor]] = Option(classOf[StandardFinalizationActor])
+  lazy val finalizationActorClassOption: Option[Class[_ <: StandardFinalizationActor]] = Option(
+    classOf[StandardFinalizationActor]
+  )
 
-  override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor, ioActor: ActorRef, calls: Set[CommandCallNode],
-                                                serviceRegistryActor: ActorRef, restart: Boolean): Option[Props] = {
+  override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
+                                                ioActor: ActorRef,
+                                                calls: Set[CommandCallNode],
+                                                serviceRegistryActor: ActorRef,
+                                                restart: Boolean
+  ): Option[Props] = {
     val params = workflowInitializationActorParams(workflowDescriptor, ioActor, calls, serviceRegistryActor, restart)
     val props = Props(initializationActorClass, params).withDispatcher(Dispatcher.BackendDispatcher)
     Option(props)
   }
 
-  def workflowInitializationActorParams(workflowDescriptor: BackendWorkflowDescriptor, ioActor: ActorRef, calls: Set[CommandCallNode],
-                                        serviceRegistryActor: ActorRef, restarting: Boolean): StandardInitializationActorParams = {
-    DefaultInitializationActorParams(workflowDescriptor, ioActor, calls, serviceRegistryActor, configurationDescriptor, restarting)
-  }
+  def workflowInitializationActorParams(workflowDescriptor: BackendWorkflowDescriptor,
+                                        ioActor: ActorRef,
+                                        calls: Set[CommandCallNode],
+                                        serviceRegistryActor: ActorRef,
+                                        restarting: Boolean
+  ): StandardInitializationActorParams =
+    DefaultInitializationActorParams(workflowDescriptor,
+                                     ioActor,
+                                     calls,
+                                     serviceRegistryActor,
+                                     configurationDescriptor,
+                                     restarting
+    )
 
   override def jobExecutionActorProps(jobDescriptor: BackendJobDescriptor,
                                       initializationDataOption: Option[BackendInitializationData],
                                       serviceRegistryActor: ActorRef,
                                       ioActor: ActorRef,
-                                      backendSingletonActorOption: Option[ActorRef]): Props = {
-    val params = jobExecutionActorParams(jobDescriptor, initializationDataOption, serviceRegistryActor,
-      ioActor, backendSingletonActorOption)
+                                      backendSingletonActorOption: Option[ActorRef]
+  ): Props = {
+    val params = jobExecutionActorParams(jobDescriptor,
+                                         initializationDataOption,
+                                         serviceRegistryActor,
+                                         ioActor,
+                                         backendSingletonActorOption
+    )
     Props(new StandardSyncExecutionActor(params)).withDispatcher(Dispatcher.BackendDispatcher)
   }
 
@@ -101,25 +126,35 @@ trait StandardLifecycleActorFactory extends BackendLifecycleActorFactory {
                               initializationDataOption: Option[BackendInitializationData],
                               serviceRegistryActor: ActorRef,
                               ioActor: ActorRef,
-                              backendSingletonActorOption: Option[ActorRef]): StandardSyncExecutionActorParams = {
-    DefaultStandardSyncExecutionActorParams(jobIdKey, serviceRegistryActor, ioActor, jobDescriptor, configurationDescriptor,
-      initializationDataOption, backendSingletonActorOption, asyncExecutionActorClass, MinimumRuntimeSettings())
-  }
+                              backendSingletonActorOption: Option[ActorRef]
+  ): StandardSyncExecutionActorParams =
+    DefaultStandardSyncExecutionActorParams(
+      jobIdKey,
+      serviceRegistryActor,
+      ioActor,
+      jobDescriptor,
+      configurationDescriptor,
+      initializationDataOption,
+      backendSingletonActorOption,
+      asyncExecutionActorClass,
+      MinimumRuntimeSettings()
+    )
 
-  override def fileHashingActorProps:
-  Option[(BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Option[ActorRef]) => Props] = {
-    fileHashingActorClassOption map {
-      standardFileHashingActor => fileHashingActorInner(standardFileHashingActor) _
+  override def fileHashingActorProps
+    : Option[(BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Option[ActorRef]) => Props] =
+    fileHashingActorClassOption map { standardFileHashingActor =>
+      fileHashingActorInner(standardFileHashingActor) _
     }
-  }
-  
-  def fileHashingActorInner(standardFileHashingActor: Class[_ <: StandardFileHashingActor])
-                               (jobDescriptor: BackendJobDescriptor,
-                                initializationDataOption: Option[BackendInitializationData],
-                                serviceRegistryActor: ActorRef,
-                                ioActor: ActorRef,
-                                fileHashCacheActor: Option[ActorRef]): Props = {
-    val params = fileHashingActorParams(jobDescriptor, initializationDataOption, serviceRegistryActor, ioActor, fileHashCacheActor)
+
+  def fileHashingActorInner(standardFileHashingActor: Class[_ <: StandardFileHashingActor])(
+    jobDescriptor: BackendJobDescriptor,
+    initializationDataOption: Option[BackendInitializationData],
+    serviceRegistryActor: ActorRef,
+    ioActor: ActorRef,
+    fileHashCacheActor: Option[ActorRef]
+  ): Props = {
+    val params =
+      fileHashingActorParams(jobDescriptor, initializationDataOption, serviceRegistryActor, ioActor, fileHashCacheActor)
     Props(standardFileHashingActor, params).withDispatcher(BackendDispatcher)
   }
 
@@ -127,26 +162,38 @@ trait StandardLifecycleActorFactory extends BackendLifecycleActorFactory {
                              initializationDataOption: Option[BackendInitializationData],
                              serviceRegistryActor: ActorRef,
                              ioActor: ActorRef,
-                             fileHashCacheActor: Option[ActorRef]): StandardFileHashingActorParams = {
-    DefaultStandardFileHashingActorParams(
-      jobDescriptor, initializationDataOption, serviceRegistryActor, ioActor, configurationDescriptor, fileHashCacheActor)
-  }
+                             fileHashCacheActor: Option[ActorRef]
+  ): StandardFileHashingActorParams =
+    DefaultStandardFileHashingActorParams(jobDescriptor,
+                                          initializationDataOption,
+                                          serviceRegistryActor,
+                                          ioActor,
+                                          configurationDescriptor,
+                                          fileHashCacheActor
+    )
 
-  override def cacheHitCopyingActorProps:
-  Option[(BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Int, Option[BlacklistCache]) => Props] = {
-    cacheHitCopyingActorClassOption map {
-      standardCacheHitCopyingActor => cacheHitCopyingActorInner(standardCacheHitCopyingActor) _
+  override def cacheHitCopyingActorProps: Option[
+    (BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Int, Option[BlacklistCache]) => Props
+  ] =
+    cacheHitCopyingActorClassOption map { standardCacheHitCopyingActor =>
+      cacheHitCopyingActorInner(standardCacheHitCopyingActor) _
     }
-  }
 
-  def cacheHitCopyingActorInner(standardCacheHitCopyingActor: Class[_ <: StandardCacheHitCopyingActor])
-                               (jobDescriptor: BackendJobDescriptor,
-                                initializationDataOption: Option[BackendInitializationData],
-                                serviceRegistryActor: ActorRef,
-                                ioActor: ActorRef,
-                                cacheCopyAttempt: Int,
-                                blacklistCache: Option[BlacklistCache]): Props = {
-    val params = cacheHitCopyingActorParams(jobDescriptor, initializationDataOption, serviceRegistryActor, ioActor, cacheCopyAttempt, blacklistCache)
+  def cacheHitCopyingActorInner(standardCacheHitCopyingActor: Class[_ <: StandardCacheHitCopyingActor])(
+    jobDescriptor: BackendJobDescriptor,
+    initializationDataOption: Option[BackendInitializationData],
+    serviceRegistryActor: ActorRef,
+    ioActor: ActorRef,
+    cacheCopyAttempt: Int,
+    blacklistCache: Option[BlacklistCache]
+  ): Props = {
+    val params = cacheHitCopyingActorParams(jobDescriptor,
+                                            initializationDataOption,
+                                            serviceRegistryActor,
+                                            ioActor,
+                                            cacheCopyAttempt,
+                                            blacklistCache
+    )
     Props(standardCacheHitCopyingActor, params).withDispatcher(BackendDispatcher)
   }
 
@@ -155,71 +202,94 @@ trait StandardLifecycleActorFactory extends BackendLifecycleActorFactory {
                                  serviceRegistryActor: ActorRef,
                                  ioActor: ActorRef,
                                  cacheCopyAttempt: Int,
-                                 blacklistCache: Option[BlacklistCache]): StandardCacheHitCopyingActorParams = {
-    DefaultStandardCacheHitCopyingActorParams(
-      jobDescriptor, initializationDataOption, serviceRegistryActor, ioActor, configurationDescriptor, cacheCopyAttempt, blacklistCache)
-  }
+                                 blacklistCache: Option[BlacklistCache]
+  ): StandardCacheHitCopyingActorParams =
+    DefaultStandardCacheHitCopyingActorParams(jobDescriptor,
+                                              initializationDataOption,
+                                              serviceRegistryActor,
+                                              ioActor,
+                                              configurationDescriptor,
+                                              cacheCopyAttempt,
+                                              blacklistCache
+    )
 
-  override def workflowFinalizationActorProps(workflowDescriptor: BackendWorkflowDescriptor, ioActor: ActorRef, calls: Set[CommandCallNode],
-                                              jobExecutionMap: JobExecutionMap, workflowOutputs: CallOutputs,
-                                              initializationData: Option[BackendInitializationData]): Option[Props] = {
+  override def workflowFinalizationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
+                                              ioActor: ActorRef,
+                                              calls: Set[CommandCallNode],
+                                              jobExecutionMap: JobExecutionMap,
+                                              workflowOutputs: CallOutputs,
+                                              initializationData: Option[BackendInitializationData]
+  ): Option[Props] =
     finalizationActorClassOption map { finalizationActorClass =>
-      val params = workflowFinalizationActorParams(workflowDescriptor, ioActor, calls, jobExecutionMap, workflowOutputs,
-        initializationData)
+      val params = workflowFinalizationActorParams(workflowDescriptor,
+                                                   ioActor,
+                                                   calls,
+                                                   jobExecutionMap,
+                                                   workflowOutputs,
+                                                   initializationData
+      )
       Props(finalizationActorClass, params).withDispatcher(BackendDispatcher)
     }
-  }
 
-  def workflowFinalizationActorParams(workflowDescriptor: BackendWorkflowDescriptor, ioActor: ActorRef, calls: Set[CommandCallNode],
-                                      jobExecutionMap: JobExecutionMap, workflowOutputs: CallOutputs,
-                                      initializationDataOption: Option[BackendInitializationData]):
-  StandardFinalizationActorParams = {
-    DefaultStandardFinalizationActorParams(workflowDescriptor, calls, jobExecutionMap, workflowOutputs,
-      initializationDataOption, configurationDescriptor)
-  }
+  def workflowFinalizationActorParams(workflowDescriptor: BackendWorkflowDescriptor,
+                                      ioActor: ActorRef,
+                                      calls: Set[CommandCallNode],
+                                      jobExecutionMap: JobExecutionMap,
+                                      workflowOutputs: CallOutputs,
+                                      initializationDataOption: Option[BackendInitializationData]
+  ): StandardFinalizationActorParams =
+    DefaultStandardFinalizationActorParams(workflowDescriptor,
+                                           calls,
+                                           jobExecutionMap,
+                                           workflowOutputs,
+                                           initializationDataOption,
+                                           configurationDescriptor
+    )
 
   override def expressionLanguageFunctions(workflowDescriptor: BackendWorkflowDescriptor,
                                            jobKey: BackendJobDescriptorKey,
                                            initializationDataOption: Option[BackendInitializationData],
                                            ioActorProxy: ActorRef,
-                                           ec: ExecutionContext):
-  IoFunctionSet = {
+                                           ec: ExecutionContext
+  ): IoFunctionSet = {
     val standardInitializationData = BackendInitializationData.as[StandardInitializationData](initializationDataOption)
     val jobPaths = standardInitializationData.workflowPaths.toJobPaths(jobKey, workflowDescriptor)
     standardInitializationData.expressionFunctions(jobPaths, ioActorProxy, ec)
   }
-  
+
   override def pathBuilders(initializationDataOption: Option[BackendInitializationData]) = {
     val standardInitializationData = BackendInitializationData.as[StandardInitializationData](initializationDataOption)
     standardInitializationData.workflowPaths.pathBuilders
-  } 
+  }
 
-  override def getExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor, backendConfig: Config,
-                                    initializationData: Option[BackendInitializationData]): Path = {
+  override def getExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor,
+                                    backendConfig: Config,
+                                    initializationData: Option[BackendInitializationData]
+  ): Path =
     initializationData match {
       case Some(data) => data.asInstanceOf[StandardInitializationData].workflowPaths.executionRoot
       case None => super.getExecutionRootPath(workflowDescriptor, backendConfig, initializationData)
     }
-  }
 
-  override def getWorkflowExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor, backendConfig: Config,
-                                            initializationData: Option[BackendInitializationData]): Path = {
+  override def getWorkflowExecutionRootPath(workflowDescriptor: BackendWorkflowDescriptor,
+                                            backendConfig: Config,
+                                            initializationData: Option[BackendInitializationData]
+  ): Path =
     initializationData match {
       case Some(data) => data.asInstanceOf[StandardInitializationData].workflowPaths.workflowRoot
       case None => super.getWorkflowExecutionRootPath(workflowDescriptor, backendConfig, initializationData)
     }
-  }
 
-  override def runtimeAttributeDefinitions(initializationDataOption: Option[BackendInitializationData]): Set[RuntimeAttributeDefinition] = {
-    val initializationData = BackendInitializationData.
-      as[StandardInitializationData](initializationDataOption)
+  override def runtimeAttributeDefinitions(
+    initializationDataOption: Option[BackendInitializationData]
+  ): Set[RuntimeAttributeDefinition] = {
+    val initializationData = BackendInitializationData.as[StandardInitializationData](initializationDataOption)
 
     initializationData.runtimeAttributesBuilder.definitions.toSet
   }
 
   override def dockerHashCredentials(workflowDescriptor: BackendWorkflowDescriptor,
-                                     initializationDataOption: Option[BackendInitializationData],
-                                    ): List[Any] = {
+                                     initializationDataOption: Option[BackendInitializationData]
+  ): List[Any] =
     BackendDockerConfiguration.build(configurationDescriptor.backendConfig).dockerCredentials.toList
-  }
 }
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardSyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardSyncExecutionActor.scala
index 99e81fbf8b2..794602887e4 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardSyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardSyncExecutionActor.scala
@@ -13,12 +13,12 @@ import scala.concurrent.{Future, Promise}
 import scala.util.control.NoStackTrace
 
 trait StandardSyncExecutionActorParams extends StandardJobExecutionActorParams {
+
   /** The class for creating an async backend. */
   def asyncJobExecutionActorClass: Class[_ <: StandardAsyncExecutionActor]
 }
 
-case class DefaultStandardSyncExecutionActorParams
-(
+case class DefaultStandardSyncExecutionActorParams(
   override val jobIdKey: String,
   override val serviceRegistryActor: ActorRef,
   override val ioActor: ActorRef,
@@ -52,7 +52,7 @@ case class DefaultStandardSyncExecutionActorParams
   * - Asynchronous actor completes the promise with a success or failure.
   */
 class StandardSyncExecutionActor(val standardParams: StandardSyncExecutionActorParams)
-  extends BackendJobExecutionActor {
+    extends BackendJobExecutionActor {
 
   override val jobDescriptor: BackendJobDescriptor = standardParams.jobDescriptor
   override val configurationDescriptor: BackendConfigurationDescriptor = standardParams.configurationDescriptor
@@ -61,10 +61,9 @@ class StandardSyncExecutionActor(val standardParams: StandardSyncExecutionActorP
 
   context.become(startup orElse receive)
 
-  private def startup: Receive = {
-    case AbortJobCommand =>
-      context.parent ! JobAbortedResponse(jobDescriptor.key)
-      context.stop(self)
+  private def startup: Receive = { case AbortJobCommand =>
+    context.parent ! JobAbortedResponse(jobDescriptor.key)
+    context.stop(self)
   }
 
   private def running(executor: ActorRef): Receive = {
@@ -78,7 +77,7 @@ class StandardSyncExecutionActor(val standardParams: StandardSyncExecutionActorP
       completionPromise.tryFailure(e)
       throw new RuntimeException(s"Failure attempting to look up job id for key ${jobDescriptor.key}", e)
   }
-  
+
   private def recovering(executor: ActorRef): Receive = running(executor).orElse {
     case KvPair(key, jobId) if key.key == jobIdKey =>
       // Successful operation ID lookup.
@@ -131,20 +130,17 @@ class StandardSyncExecutionActor(val standardParams: StandardSyncExecutionActorP
     serviceRegistryActor ! kvGet
     completionPromise.future
   }
-  
-  override def recover: Future[BackendJobExecutionResponse] = {
+
+  override def recover: Future[BackendJobExecutionResponse] =
     onRestart(recovering)
-  }
-  
-  override def reconnectToAborting: Future[BackendJobExecutionResponse] = {
+
+  override def reconnectToAborting: Future[BackendJobExecutionResponse] =
     onRestart(reconnectingToAbort)
-  }
 
-  override def reconnect: Future[BackendJobExecutionResponse] = {
+  override def reconnect: Future[BackendJobExecutionResponse] =
     onRestart(reconnecting)
-  }
 
-  def createAsyncParams(): StandardAsyncExecutionActorParams = {
+  def createAsyncParams(): StandardAsyncExecutionActorParams =
     DefaultStandardAsyncExecutionActorParams(
       standardParams.jobIdKey,
       standardParams.serviceRegistryActor,
@@ -156,16 +152,14 @@ class StandardSyncExecutionActor(val standardParams: StandardSyncExecutionActorP
       completionPromise,
       standardParams.minimumRuntimeSettings
     )
-  }
 
   def createAsyncProps(): Props = {
     val asyncParams = createAsyncParams()
     Props(standardParams.asyncJobExecutionActorClass, asyncParams)
   }
 
-  def createAsyncRefName(): String = {
+  def createAsyncRefName(): String =
     standardParams.asyncJobExecutionActorClass.getSimpleName
-  }
 
   def createAsyncRef(): ActorRef = {
     val props = createAsyncProps().withDispatcher(Dispatcher.BackendDispatcher)
@@ -173,16 +167,18 @@ class StandardSyncExecutionActor(val standardParams: StandardSyncExecutionActorP
     context.actorOf(props, name)
   }
 
-  override def abort(): Unit = {
+  override def abort(): Unit =
     throw new UnsupportedOperationException("Abort is implemented via a custom receive of the message AbortJobCommand.")
-  }
 
   // Supervision strategy: if the async actor throws an exception, stop the actor and fail the job.
-  def jobFailingDecider: Decider = {
-    case exception: Exception =>
-      completionPromise.tryFailure(
-        new RuntimeException(s"${createAsyncRefName()} failed and didn't catch its exception. This condition has been handled and the job will be marked as failed.", exception) with NoStackTrace)
-      Stop
+  def jobFailingDecider: Decider = { case exception: Exception =>
+    completionPromise.tryFailure(
+      new RuntimeException(
+        s"${createAsyncRefName()} failed and didn't catch its exception. This condition has been handled and the job will be marked as failed.",
+        exception
+      ) with NoStackTrace
+    )
+    Stop
   }
 
   override val supervisorStrategy: OneForOneStrategy = OneForOneStrategy()(jobFailingDecider)
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilder.scala b/backend/src/main/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilder.scala
index 4160d9a8522..77f890b4a19 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilder.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilder.scala
@@ -17,8 +17,7 @@ import cromwell.backend.validation._
   */
 object StandardValidatedRuntimeAttributesBuilder {
 
-  private case class StandardValidatedRuntimeAttributesBuilderImpl
-  (
+  private case class StandardValidatedRuntimeAttributesBuilderImpl(
     override val requiredValidations: Seq[RuntimeAttributesValidation[_]],
     override val customValidations: Seq[RuntimeAttributesValidation[_]]
   ) extends StandardValidatedRuntimeAttributesBuilder
@@ -41,8 +40,8 @@ object StandardValidatedRuntimeAttributesBuilder {
   }
 
   private def withValidations(builder: StandardValidatedRuntimeAttributesBuilder,
-                              customValidations: Seq[RuntimeAttributesValidation[_]]):
-  StandardValidatedRuntimeAttributesBuilder = {
+                              customValidations: Seq[RuntimeAttributesValidation[_]]
+  ): StandardValidatedRuntimeAttributesBuilder = {
     val required = builder.requiredValidations
     val custom = builder.customValidations ++ customValidations
     StandardValidatedRuntimeAttributesBuilderImpl(custom, required)
@@ -50,19 +49,18 @@ object StandardValidatedRuntimeAttributesBuilder {
 }
 
 sealed trait StandardValidatedRuntimeAttributesBuilder extends ValidatedRuntimeAttributesBuilder {
+
   /**
     * Returns a new builder with the additional validation(s).
     *
     * @param validation Additional validation.
     * @return New builder with the validation.
     */
-  final def withValidation(validation: RuntimeAttributesValidation[_]*):
-  StandardValidatedRuntimeAttributesBuilder = {
+  final def withValidation(validation: RuntimeAttributesValidation[_]*): StandardValidatedRuntimeAttributesBuilder =
     StandardValidatedRuntimeAttributesBuilder.withValidations(this, validation)
-  }
 
   /** Returns all the validations, those required for the standard backend, plus custom addons for the subclass. */
-  override final lazy val validations: Seq[RuntimeAttributesValidation[_]] = requiredValidations ++ customValidations
+  final override lazy val validations: Seq[RuntimeAttributesValidation[_]] = requiredValidations ++ customValidations
 
   private[standard] def requiredValidations: Seq[RuntimeAttributesValidation[_]]
 
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/BlacklistCache.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/BlacklistCache.scala
index ff3248123ff..fa5207c99c6 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/BlacklistCache.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/BlacklistCache.scala
@@ -11,19 +11,20 @@ case object UntestedCacheResult extends BlacklistStatus
 
 sealed abstract class BlacklistCache(bucketCacheConfig: CacheConfig,
                                      hitCacheConfig: CacheConfig,
-                                     val name: Option[String]) {
+                                     val name: Option[String]
+) {
   val bucketCache = {
     // Queries to the bucket blacklist cache return UntestedCacheResult by default.
     val unknownLoader = new CacheLoader[String, BlacklistStatus]() {
       override def load(key: String): BlacklistStatus = UntestedCacheResult
     }
 
-    CacheBuilder.
-      newBuilder().
-      concurrencyLevel(bucketCacheConfig.concurrency).
-      maximumSize(bucketCacheConfig.size).
-      expireAfterWrite(bucketCacheConfig.ttl.length, bucketCacheConfig.ttl.unit).
-      build[String, BlacklistStatus](unknownLoader)
+    CacheBuilder
+      .newBuilder()
+      .concurrencyLevel(bucketCacheConfig.concurrency)
+      .maximumSize(bucketCacheConfig.size)
+      .expireAfterWrite(bucketCacheConfig.ttl.length, bucketCacheConfig.ttl.unit)
+      .build[String, BlacklistStatus](unknownLoader)
   }
 
   val hitCache = {
@@ -32,12 +33,12 @@ sealed abstract class BlacklistCache(bucketCacheConfig: CacheConfig,
       override def load(key: CallCachingEntryId): BlacklistStatus = UntestedCacheResult
     }
 
-    CacheBuilder.
-      newBuilder().
-      concurrencyLevel(hitCacheConfig.concurrency).
-      maximumSize(hitCacheConfig.size).
-      expireAfterWrite(hitCacheConfig.ttl.length, hitCacheConfig.ttl.unit).
-      build[CallCachingEntryId, BlacklistStatus](unknownLoader)
+    CacheBuilder
+      .newBuilder()
+      .concurrencyLevel(hitCacheConfig.concurrency)
+      .maximumSize(hitCacheConfig.size)
+      .expireAfterWrite(hitCacheConfig.ttl.length, hitCacheConfig.ttl.unit)
+      .build[CallCachingEntryId, BlacklistStatus](unknownLoader)
   }
 
   def getBlacklistStatus(hit: CallCachingEntryId): BlacklistStatus = hitCache.get(hit)
@@ -53,8 +54,8 @@ sealed abstract class BlacklistCache(bucketCacheConfig: CacheConfig,
   def whitelist(bucket: String): Unit = bucketCache.put(bucket, GoodCacheResult)
 }
 
-class RootWorkflowBlacklistCache(bucketCacheConfig: CacheConfig, hitCacheConfig: CacheConfig) extends
-  BlacklistCache(bucketCacheConfig = bucketCacheConfig, hitCacheConfig = hitCacheConfig, name = None)
+class RootWorkflowBlacklistCache(bucketCacheConfig: CacheConfig, hitCacheConfig: CacheConfig)
+    extends BlacklistCache(bucketCacheConfig = bucketCacheConfig, hitCacheConfig = hitCacheConfig, name = None)
 
-class GroupingBlacklistCache(bucketCacheConfig: CacheConfig, hitCacheConfig: CacheConfig, val group: String) extends
-  BlacklistCache(bucketCacheConfig = bucketCacheConfig, hitCacheConfig = hitCacheConfig, name = Option(group))
+class GroupingBlacklistCache(bucketCacheConfig: CacheConfig, hitCacheConfig: CacheConfig, val group: String)
+    extends BlacklistCache(bucketCacheConfig = bucketCacheConfig, hitCacheConfig = hitCacheConfig, name = Option(group))
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/CallCachingBlacklistManager.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/CallCachingBlacklistManager.scala
index a22631aeeb4..f1c6a988021 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/CallCachingBlacklistManager.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/CallCachingBlacklistManager.scala
@@ -47,7 +47,7 @@ class CallCachingBlacklistManager(rootConfig: Config, logger: LoggingAdapter) {
     import CallCachingBlacklistManager.Defaults.Groupings._
     for {
       _ <- blacklistGroupingWorkflowOptionKey
-      groupingsOption = rootConfig.as[Option[Config]] ("call-caching.blacklist-cache.groupings")
+      groupingsOption = rootConfig.as[Option[Config]]("call-caching.blacklist-cache.groupings")
       conf = CacheConfig.config(groupingsOption, defaultConcurrency = Concurrency, defaultSize = Size, defaultTtl = Ttl)
     } yield conf
   }
@@ -74,7 +74,10 @@ class CallCachingBlacklistManager(rootConfig: Config, logger: LoggingAdapter) {
 
   // If configuration allows, build a cache of blacklist groupings to BlacklistCaches.
   private val blacklistGroupingsCache: Option[LoadingCache[String, BlacklistCache]] = {
-    def buildBlacklistGroupingsCache(groupingConfig: CacheConfig, bucketConfig: CacheConfig, hitConfig: CacheConfig): LoadingCache[String, BlacklistCache] = {
+    def buildBlacklistGroupingsCache(groupingConfig: CacheConfig,
+                                     bucketConfig: CacheConfig,
+                                     hitConfig: CacheConfig
+    ): LoadingCache[String, BlacklistCache] = {
       val emptyBlacklistCacheLoader = new CacheLoader[String, BlacklistCache]() {
         override def load(key: String): BlacklistCache = new GroupingBlacklistCache(
           bucketCacheConfig = bucketConfig,
@@ -83,12 +86,12 @@ class CallCachingBlacklistManager(rootConfig: Config, logger: LoggingAdapter) {
         )
       }
 
-      CacheBuilder.
-        newBuilder().
-        concurrencyLevel(groupingConfig.concurrency).
-        maximumSize(groupingConfig.size).
-        expireAfterWrite(groupingConfig.ttl.length, groupingConfig.ttl.unit).
-        build[String, BlacklistCache](emptyBlacklistCacheLoader)
+      CacheBuilder
+        .newBuilder()
+        .concurrencyLevel(groupingConfig.concurrency)
+        .maximumSize(groupingConfig.size)
+        .expireAfterWrite(groupingConfig.ttl.length, groupingConfig.ttl.unit)
+        .build[String, BlacklistCache](emptyBlacklistCacheLoader)
     }
 
     for {
@@ -121,8 +124,13 @@ class CallCachingBlacklistManager(rootConfig: Config, logger: LoggingAdapter) {
     val maybeCache = groupBlacklistCache orElse rootWorkflowBlacklistCache
     maybeCache collect {
       case group: GroupingBlacklistCache =>
-        logger.info("Workflow {} using group blacklist cache '{}' containing blacklist status for {} hits and {} buckets.",
-          workflow.id, group.group, group.hitCache.size(), group.bucketCache.size())
+        logger.info(
+          "Workflow {} using group blacklist cache '{}' containing blacklist status for {} hits and {} buckets.",
+          workflow.id,
+          group.group,
+          group.hitCache.size(),
+          group.bucketCache.size()
+        )
       case _: RootWorkflowBlacklistCache =>
         logger.info("Workflow {} using root workflow blacklist cache.", workflow.id)
     }
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/CopyingActorBlacklistCacheSupport.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/CopyingActorBlacklistCacheSupport.scala
index 8ad88ae4f49..d90bba7ee90 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/CopyingActorBlacklistCacheSupport.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/CopyingActorBlacklistCacheSupport.scala
@@ -4,7 +4,6 @@ import cromwell.backend.BackendCacheHitCopyingActor.CopyOutputsCommand
 import cromwell.core.io.{IoCommand, IoCopyCommand}
 import cromwell.services.CallCaching.CallCachingEntryId
 
-
 object CopyingActorBlacklistCacheSupport {
   trait HasFormatting {
     def metricFormat: String = getClass.getName.toLowerCase.split('$').last
@@ -52,13 +51,12 @@ trait CopyingActorBlacklistCacheSupport {
   }
 
   def publishBlacklistMetric(verb: Verb, entityType: EntityType, value: BlacklistStatus): Unit = {
-    val metricPath = NonEmptyList.of(
-      "job",
-      "callcaching", "blacklist", verb.metricFormat, entityType.metricFormat, value.toString)
+    val metricPath =
+      NonEmptyList.of("job", "callcaching", "blacklist", verb.metricFormat, entityType.metricFormat, value.toString)
     increment(metricPath)
   }
 
-  def blacklistAndMetricHit(blacklistCache: BlacklistCache, hit: CallCachingEntryId): Unit = {
+  def blacklistAndMetricHit(blacklistCache: BlacklistCache, hit: CallCachingEntryId): Unit =
     blacklistCache.getBlacklistStatus(hit) match {
       case UntestedCacheResult =>
         blacklistCache.blacklist(hit)
@@ -71,13 +69,13 @@ trait CopyingActorBlacklistCacheSupport {
         // mark the hit as BadCacheResult and log this strangeness.
         log.warning(
           "Cache hit {} found in GoodCacheResult blacklist state, but cache hit copying has failed for permissions reasons. Overwriting status to BadCacheResult state.",
-          hit.id)
+          hit.id
+        )
         blacklistCache.blacklist(hit)
         publishBlacklistMetric(Write, Hit, value = BadCacheResult)
     }
-  }
 
-  def blacklistAndMetricBucket(blacklistCache: BlacklistCache, bucket: String): Unit = {
+  def blacklistAndMetricBucket(blacklistCache: BlacklistCache, bucket: String): Unit =
     blacklistCache.getBlacklistStatus(bucket) match {
       case UntestedCacheResult =>
         blacklistCache.blacklist(bucket)
@@ -90,13 +88,13 @@ trait CopyingActorBlacklistCacheSupport {
         // mark the bucket as BadCacheResult and log this strangeness.
         log.warning(
           "Bucket {} found in GoodCacheResult blacklist state, but cache hit copying has failed for permissions reasons. Overwriting status to BadCacheResult state.",
-          bucket)
+          bucket
+        )
         blacklistCache.blacklist(bucket)
         publishBlacklistMetric(Write, Bucket, value = BadCacheResult)
     }
-  }
 
-  def whitelistAndMetricHit(blacklistCache: BlacklistCache, hit: CallCachingEntryId): Unit = {
+  def whitelistAndMetricHit(blacklistCache: BlacklistCache, hit: CallCachingEntryId): Unit =
     blacklistCache.getBlacklistStatus(hit) match {
       case UntestedCacheResult =>
         blacklistCache.whitelist(hit)
@@ -107,11 +105,11 @@ trait CopyingActorBlacklistCacheSupport {
         // Don't overwrite this to GoodCacheResult, hopefully there are less weird cache hits out there.
         log.warning(
           "Cache hit {} found in BadCacheResult blacklist state, not overwriting to GoodCacheResult despite successful copy.",
-          hit.id)
+          hit.id
+        )
     }
-  }
 
-  def whitelistAndMetricBucket(blacklistCache: BlacklistCache, bucket: String): Unit = {
+  def whitelistAndMetricBucket(blacklistCache: BlacklistCache, bucket: String): Unit =
     blacklistCache.getBlacklistStatus(bucket) match {
       case UntestedCacheResult =>
         blacklistCache.whitelist(bucket)
@@ -122,11 +120,11 @@ trait CopyingActorBlacklistCacheSupport {
         // of a successful copy. Don't overwrite this to GoodCacheResult, hopefully there are less weird cache hits out there.
         log.warning(
           "Bucket {} found in BadCacheResult blacklist state, not overwriting to GoodCacheResult despite successful copy.",
-          bucket)
+          bucket
+        )
     }
-  }
 
-  def publishBlacklistReadMetrics(command: CopyOutputsCommand, cacheHit: CallCachingEntryId, cacheReadType: Product) = {
+  def publishBlacklistReadMetrics(command: CopyOutputsCommand, cacheHit: CallCachingEntryId, cacheReadType: Product) =
     for {
       c <- standardParams.blacklistCache
       hitBlacklistStatus = c.getBlacklistStatus(cacheHit)
@@ -139,7 +137,6 @@ trait CopyingActorBlacklistCacheSupport {
       bucketBlacklistStatus = c.getBlacklistStatus(prefix)
       _ = publishBlacklistMetric(Read, Bucket, bucketBlacklistStatus)
     } yield ()
-  }
 
   def isSourceBlacklisted(command: CopyOutputsCommand): Boolean = {
     val path = sourcePathFromCopyOutputsCommand(command)
@@ -150,10 +147,9 @@ trait CopyingActorBlacklistCacheSupport {
     } yield value == BadCacheResult).getOrElse(false)
   }
 
-  def isSourceBlacklisted(hit: CallCachingEntryId): Boolean = {
+  def isSourceBlacklisted(hit: CallCachingEntryId): Boolean =
     (for {
       cache <- standardParams.blacklistCache
       value = cache.getBlacklistStatus(hit)
     } yield value == BadCacheResult).getOrElse(false)
-  }
 }
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
index c3d1452660e..3ab77bdf778 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
@@ -11,8 +11,10 @@ import cromwell.core.WorkflowId
 import cromwell.core.actor.RobustClientHelper.RequestTimeout
 import cromwell.core.io._
 
-
-class RootWorkflowFileHashCacheActor private[callcaching](override val ioActor: ActorRef, workflowId: WorkflowId) extends Actor with ActorLogging with IoClientHelper {
+class RootWorkflowFileHashCacheActor private[callcaching] (override val ioActor: ActorRef, workflowId: WorkflowId)
+    extends Actor
+    with ActorLogging
+    with IoClientHelper {
   case class FileHashRequester(replyTo: ActorRef, fileHashContext: FileHashContext, ioCommand: IoCommand[_])
 
   sealed trait FileHashValue
@@ -25,8 +27,9 @@ class RootWorkflowFileHashCacheActor private[callcaching](override val ioActor:
   // Hashing failed.
   case class FileHashFailure(error: String) extends FileHashValue
 
-  val cache: LoadingCache[String, FileHashValue] = CacheBuilder.newBuilder().build(
-    new CacheLoader[String, FileHashValue] {
+  val cache: LoadingCache[String, FileHashValue] = CacheBuilder
+    .newBuilder()
+    .build(new CacheLoader[String, FileHashValue] {
       override def load(key: String): FileHashValue = FileHashValueNotRequested
     })
 
@@ -66,44 +69,49 @@ class RootWorkflowFileHashCacheActor private[callcaching](override val ioActor:
         requesters foreach { case FileHashRequester(replyTo, fileHashContext, ioCommand) =>
           replyTo ! Tuple2(fileHashContext, IoFailure(ioCommand, failure.failure))
         }
-        cache.put(hashContext.file, FileHashFailure(s"Error hashing file '${hashContext.file}': ${failure.failure.getMessage}"))
+        cache.put(hashContext.file,
+                  FileHashFailure(s"Error hashing file '${hashContext.file}': ${failure.failure.getMessage}")
+        )
       }
     case other =>
       log.warning(s"Root workflow file hash caching actor received unexpected message: $other")
   }
 
   // Invoke the supplied block on the happy path, handle unexpected states for IoSuccess and IoFailure with common code.
-  private def handleHashResult(ioAck: IoAck[_], fileHashContext: FileHashContext)
-                              (notifyRequestersAndCacheValue: List[FileHashRequester] => Unit): Unit = {
+  private def handleHashResult(ioAck: IoAck[_], fileHashContext: FileHashContext)(
+    notifyRequestersAndCacheValue: List[FileHashRequester] => Unit
+  ): Unit =
     cache.get(fileHashContext.file) match {
       case FileHashValueRequested(requesters) => notifyRequestersAndCacheValue(requesters.toList)
       case FileHashValueNotRequested =>
         log.info(msgIoAckWithNoRequesters.format(fileHashContext.file))
         notifyRequestersAndCacheValue(List.empty[FileHashRequester])
       case _ =>
-        // IoAck arrived when hash result is already saved in cache. This is a result of benign race condition.
-        // No further action is required.
+      // IoAck arrived when hash result is already saved in cache. This is a result of benign race condition.
+      // No further action is required.
     }
-  }
 
-  override protected def onTimeout(message: Any, to: ActorRef): Unit = {
+  override protected def onTimeout(message: Any, to: ActorRef): Unit =
     message match {
       case (fileHashContext: FileHashContext, _) =>
         // Send this message to all requestors.
         cache.get(fileHashContext.file) match {
           case FileHashValueRequested(requesters) =>
-            requesters.toList foreach { case FileHashRequester(replyTo, requestContext, ioCommand) => replyTo ! RequestTimeout(Tuple2(requestContext, ioCommand), replyTo) }
+            requesters.toList foreach { case FileHashRequester(replyTo, requestContext, ioCommand) =>
+              replyTo ! RequestTimeout(Tuple2(requestContext, ioCommand), replyTo)
+            }
             // Allow for the possibility of trying again on a timeout.
             cache.put(fileHashContext.file, FileHashValueNotRequested)
           case FileHashValueNotRequested =>
-            // Due to race condition, timeout came after the actual response. This is fine and no further action required.
+          // Due to race condition, timeout came after the actual response. This is fine and no further action required.
           case v =>
             log.info(msgTimeoutAfterIoAck.format(v, fileHashContext.file))
         }
       case other =>
-        log.error(s"Programmer error! Root workflow file hash caching actor received unexpected timeout message: $other")
+        log.error(
+          s"Programmer error! Root workflow file hash caching actor received unexpected timeout message: $other"
+        )
     }
-  }
 
   override def preRestart(reason: Throwable, message: Option[Any]): Unit = {
     log.error(reason, s"RootWorkflowFileHashCacheActor for workflow '$workflowId' is unexpectedly being restarted")
@@ -121,5 +129,7 @@ object RootWorkflowFileHashCacheActor {
 
   case class IoHashCommandWithContext(ioHashCommand: IoHashCommand, fileHashContext: FileHashContext)
 
-  def props(ioActor: ActorRef, workflowId: WorkflowId): Props = Props(new RootWorkflowFileHashCacheActor(ioActor, workflowId))
+  def props(ioActor: ActorRef, workflowId: WorkflowId): Props = Props(
+    new RootWorkflowFileHashCacheActor(ioActor, workflowId)
+  )
 }
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
index f1662db858b..3c052f69f8e 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardCacheHitCopyingActor.scala
@@ -9,7 +9,12 @@ import cromwell.backend.io.JobPaths
 import cromwell.backend.standard.StandardCachingActorHelper
 import cromwell.backend.standard.callcaching.CopyingActorBlacklistCacheSupport._
 import cromwell.backend.standard.callcaching.StandardCacheHitCopyingActor._
-import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendJobDescriptor, MetricableCacheCopyErrorCategory}
+import cromwell.backend.{
+  BackendConfigurationDescriptor,
+  BackendInitializationData,
+  BackendJobDescriptor,
+  MetricableCacheCopyErrorCategory
+}
 import cromwell.core.CallOutputs
 import cromwell.core.io._
 import cromwell.core.logging.JobLogging
@@ -46,8 +51,7 @@ trait StandardCacheHitCopyingActorParams {
 }
 
 /** A default implementation of the cache hit copying params. */
-case class DefaultStandardCacheHitCopyingActorParams
-(
+case class DefaultStandardCacheHitCopyingActorParams(
   override val jobDescriptor: BackendJobDescriptor,
   override val backendInitializationDataOption: Option[BackendInitializationData],
   override val serviceRegistryActor: ActorRef,
@@ -81,32 +85,33 @@ object StandardCacheHitCopyingActor {
                                               newDetritus: DetritusMap,
                                               cacheHit: CallCachingEntryId,
                                               returnCode: Option[Int]
-                                             ) {
+  ) {
 
     /**
       * Removes the command from commandsToWaitFor
       * returns a pair of the new state data and CommandSetState giving information about what to do next
       */
-    def commandComplete(command: IoCommand[_]): (StandardCacheHitCopyingActorData, CommandSetState) = commandsToWaitFor match {
-      // If everything was already done send back current data and AllCommandsDone
-      case Nil => (this, AllCommandsDone)
-      case lastSubset :: Nil =>
-        val updatedSubset = lastSubset - command
-        // If the last subset is now empty, we're done
-        if (updatedSubset.isEmpty) (this.copy(commandsToWaitFor = List.empty), AllCommandsDone)
-        // otherwise update commandsToWaitFor and keep waiting
-        else (this.copy(commandsToWaitFor = List(updatedSubset)), StillWaiting)
-      case currentSubset :: otherSubsets =>
-        val updatedSubset = currentSubset - command
-        // This subset is done but there are other ones, remove it from commandsToWaitFor and return the next round of commands
-        if (updatedSubset.isEmpty) (this.copy(commandsToWaitFor = otherSubsets), NextSubSet(otherSubsets.head))
-        // otherwise update the head subset and keep waiting
-        else (this.copy(commandsToWaitFor = List(updatedSubset) ++ otherSubsets), StillWaiting)
-    }
+    def commandComplete(command: IoCommand[_]): (StandardCacheHitCopyingActorData, CommandSetState) =
+      commandsToWaitFor match {
+        // If everything was already done send back current data and AllCommandsDone
+        case Nil => (this, AllCommandsDone)
+        case lastSubset :: Nil =>
+          val updatedSubset = lastSubset - command
+          // If the last subset is now empty, we're done
+          if (updatedSubset.isEmpty) (this.copy(commandsToWaitFor = List.empty), AllCommandsDone)
+          // otherwise update commandsToWaitFor and keep waiting
+          else (this.copy(commandsToWaitFor = List(updatedSubset)), StillWaiting)
+        case currentSubset :: otherSubsets =>
+          val updatedSubset = currentSubset - command
+          // This subset is done but there are other ones, remove it from commandsToWaitFor and return the next round of commands
+          if (updatedSubset.isEmpty) (this.copy(commandsToWaitFor = otherSubsets), NextSubSet(otherSubsets.head))
+          // otherwise update the head subset and keep waiting
+          else (this.copy(commandsToWaitFor = List(updatedSubset) ++ otherSubsets), StillWaiting)
+      }
   }
 
   // Internal ADT to keep track of command set states
-  private[callcaching] sealed trait CommandSetState
+  sealed private[callcaching] trait CommandSetState
   private[callcaching] case object StillWaiting extends CommandSetState
   private[callcaching] case object AllCommandsDone extends CommandSetState
   private[callcaching] case class NextSubSet(commands: Set[IoCommand[_]]) extends CommandSetState
@@ -114,17 +119,23 @@ object StandardCacheHitCopyingActor {
   private val BucketRegex: Regex = "^gs://([^/]+).*".r
 }
 
-class DefaultStandardCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams) extends StandardCacheHitCopyingActor(standardParams)
+class DefaultStandardCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams)
+    extends StandardCacheHitCopyingActor(standardParams)
 
 /**
   * Standard implementation of a BackendCacheHitCopyingActor.
   */
 abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHitCopyingActorParams)
-  extends FSM[StandardCacheHitCopyingActorState, Option[StandardCacheHitCopyingActorData]]
-    with JobLogging with StandardCachingActorHelper with IoClientHelper with CromwellInstrumentationActor with CopyingActorBlacklistCacheSupport {
+    extends FSM[StandardCacheHitCopyingActorState, Option[StandardCacheHitCopyingActorData]]
+    with JobLogging
+    with StandardCachingActorHelper
+    with IoClientHelper
+    with CromwellInstrumentationActor
+    with CopyingActorBlacklistCacheSupport {
 
   override lazy val jobDescriptor: BackendJobDescriptor = standardParams.jobDescriptor
-  override lazy val backendInitializationDataOption: Option[BackendInitializationData] = standardParams.backendInitializationDataOption
+  override lazy val backendInitializationDataOption: Option[BackendInitializationData] =
+    standardParams.backendInitializationDataOption
   override lazy val serviceRegistryActor: ActorRef = standardParams.serviceRegistryActor
   override lazy val configurationDescriptor: BackendConfigurationDescriptor = standardParams.configurationDescriptor
   protected val commandBuilder: IoCommandBuilder = DefaultIoCommandBuilder
@@ -142,78 +153,78 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
   /** Override this method if you want to provide an alternative way to duplicate files than copying them. */
   protected def duplicate(copyPairs: Set[PathPair]): Option[Try[Unit]] = None
 
-  when(Idle) {
-    case Event(command @ CopyOutputsCommand(simpletons, jobDetritus, cacheHit, returnCode), None) =>
-      val (nextState, cacheReadType) =
-        if (isSourceBlacklisted(cacheHit)) {
-          // We don't want to log this because blacklisting is a common and expected occurrence.
-          (failAndStop(BlacklistSkip(MetricableCacheCopyErrorCategory.HitBlacklisted)), ReadHitOnly)
-        } else if (isSourceBlacklisted(command)) {
-          // We don't want to log this because blacklisting is a common and expected occurrence.
-          (failAndStop(BlacklistSkip(MetricableCacheCopyErrorCategory.BucketBlacklisted)), ReadHitAndBucket)
-        } else {
-          // Try to make a Path of the callRootPath from the detritus
-          val next = lookupSourceCallRootPath(jobDetritus) match {
-            case Success(sourceCallRootPath) =>
-
-              // process simpletons and detritus to get updated paths and corresponding IoCommands
-              val processed = for {
-                (destinationCallOutputs, simpletonIoCommands) <- processSimpletons(simpletons, sourceCallRootPath)
-                (destinationDetritus, detritusIoCommands) <- processDetritus(jobDetritus)
-              } yield (destinationCallOutputs, destinationDetritus, simpletonIoCommands ++ detritusIoCommands)
-
-              processed match {
-                case Success((destinationCallOutputs, destinationDetritus, detritusAndOutputsIoCommands)) =>
-                  duplicate(ioCommandsToCopyPairs(detritusAndOutputsIoCommands)) match {
-                    // Use the duplicate override if exists
-                    case Some(Success(_)) => succeedAndStop(returnCode, destinationCallOutputs, destinationDetritus)
-                    case Some(Failure(failure)) =>
-                      // Something went wrong in the custom duplication code. We consider this loggable because it's most likely a user-permission error:
-                      failAndStop(CopyAttemptError(failure))
-                    // Otherwise send the first round of IoCommands (file outputs and detritus) if any
-                    case None if detritusAndOutputsIoCommands.nonEmpty =>
-                      detritusAndOutputsIoCommands foreach sendIoCommand
-
-                      // Add potential additional commands to the list
-                      val additionalCommandsTry =
-                        additionalIoCommands(
-                          sourceCallRootPath = sourceCallRootPath,
-                          originalSimpletons = simpletons,
-                          newOutputs = destinationCallOutputs,
-                          originalDetritus = jobDetritus,
-                          newDetritus = destinationDetritus,
-                        )
-                      additionalCommandsTry match {
-                        case Success(additionalCommands) =>
-                          val allCommands = List(detritusAndOutputsIoCommands) ++ additionalCommands
-                          goto(WaitingForIoResponses) using
-                            Option(StandardCacheHitCopyingActorData(
+  when(Idle) { case Event(command @ CopyOutputsCommand(simpletons, jobDetritus, cacheHit, returnCode), None) =>
+    val (nextState, cacheReadType) =
+      if (isSourceBlacklisted(cacheHit)) {
+        // We don't want to log this because blacklisting is a common and expected occurrence.
+        (failAndStop(BlacklistSkip(MetricableCacheCopyErrorCategory.HitBlacklisted)), ReadHitOnly)
+      } else if (isSourceBlacklisted(command)) {
+        // We don't want to log this because blacklisting is a common and expected occurrence.
+        (failAndStop(BlacklistSkip(MetricableCacheCopyErrorCategory.BucketBlacklisted)), ReadHitAndBucket)
+      } else {
+        // Try to make a Path of the callRootPath from the detritus
+        val next = lookupSourceCallRootPath(jobDetritus) match {
+          case Success(sourceCallRootPath) =>
+            // process simpletons and detritus to get updated paths and corresponding IoCommands
+            val processed = for {
+              (destinationCallOutputs, simpletonIoCommands) <- processSimpletons(simpletons, sourceCallRootPath)
+              (destinationDetritus, detritusIoCommands) <- processDetritus(jobDetritus)
+            } yield (destinationCallOutputs, destinationDetritus, simpletonIoCommands ++ detritusIoCommands)
+
+            processed match {
+              case Success((destinationCallOutputs, destinationDetritus, detritusAndOutputsIoCommands)) =>
+                duplicate(ioCommandsToCopyPairs(detritusAndOutputsIoCommands)) match {
+                  // Use the duplicate override if exists
+                  case Some(Success(_)) => succeedAndStop(returnCode, destinationCallOutputs, destinationDetritus)
+                  case Some(Failure(failure)) =>
+                    // Something went wrong in the custom duplication code. We consider this loggable because it's most likely a user-permission error:
+                    failAndStop(CopyAttemptError(failure))
+                  // Otherwise send the first round of IoCommands (file outputs and detritus) if any
+                  case None if detritusAndOutputsIoCommands.nonEmpty =>
+                    detritusAndOutputsIoCommands foreach sendIoCommand
+
+                    // Add potential additional commands to the list
+                    val additionalCommandsTry =
+                      additionalIoCommands(
+                        sourceCallRootPath = sourceCallRootPath,
+                        originalSimpletons = simpletons,
+                        newOutputs = destinationCallOutputs,
+                        originalDetritus = jobDetritus,
+                        newDetritus = destinationDetritus
+                      )
+                    additionalCommandsTry match {
+                      case Success(additionalCommands) =>
+                        val allCommands = List(detritusAndOutputsIoCommands) ++ additionalCommands
+                        goto(WaitingForIoResponses) using
+                          Option(
+                            StandardCacheHitCopyingActorData(
                               commandsToWaitFor = allCommands,
                               newJobOutputs = destinationCallOutputs,
                               newDetritus = destinationDetritus,
                               cacheHit = cacheHit,
-                              returnCode = returnCode,
-                            ))
-                        // Something went wrong in generating duplication commands.
-                        // We consider this a loggable error because we don't expect this to happen:
-                        case Failure(failure) => failAndStop(CopyAttemptError(failure))
-                      }
-                    case _ => succeedAndStop(returnCode, destinationCallOutputs, destinationDetritus)
-                  }
-
-                // Something went wrong in generating duplication commands. We consider this loggable error because we don't expect this to happen:
-                case Failure(failure) => failAndStop(CopyAttemptError(failure))
-              }
-
-            // Something went wrong in looking up the call root... loggable because we don't expect this to happen:
-            case Failure(failure) => failAndStop(CopyAttemptError(failure))
-          }
-          (next, ReadHitAndBucket)
+                              returnCode = returnCode
+                            )
+                          )
+                      // Something went wrong in generating duplication commands.
+                      // We consider this a loggable error because we don't expect this to happen:
+                      case Failure(failure) => failAndStop(CopyAttemptError(failure))
+                    }
+                  case _ => succeedAndStop(returnCode, destinationCallOutputs, destinationDetritus)
+                }
+
+              // Something went wrong in generating duplication commands. We consider this loggable error because we don't expect this to happen:
+              case Failure(failure) => failAndStop(CopyAttemptError(failure))
+            }
+
+          // Something went wrong in looking up the call root... loggable because we don't expect this to happen:
+          case Failure(failure) => failAndStop(CopyAttemptError(failure))
         }
+        (next, ReadHitAndBucket)
+      }
 
-      publishBlacklistReadMetrics(command, cacheHit, cacheReadType)
+    publishBlacklistReadMetrics(command, cacheHit, cacheReadType)
 
-      nextState
+    nextState
   }
 
   when(WaitingForIoResponses) {
@@ -293,7 +304,7 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
       _ = blacklistAndMetricHit(cache, data.cacheHit)
       prefix <- extractBlacklistPrefix(path)
       _ = blacklistAndMetricBucket(cache, prefix)
-    } yield()
+    } yield ()
     andThen
   }
 
@@ -309,8 +320,18 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
 
   def succeedAndStop(returnCode: Option[Int], copiedJobOutputs: CallOutputs, detritusMap: DetritusMap): State = {
     import cromwell.services.metadata.MetadataService.implicits.MetadataAutoPutter
-    serviceRegistryActor.putMetadata(jobDescriptor.workflowDescriptor.id, Option(jobDescriptor.key), startMetadataKeyValues)
-    context.parent ! JobSucceededResponse(jobDescriptor.key, returnCode, copiedJobOutputs, Option(detritusMap), Seq.empty, None, resultGenerationMode = CallCached)
+    serviceRegistryActor.putMetadata(jobDescriptor.workflowDescriptor.id,
+                                     Option(jobDescriptor.key),
+                                     startMetadataKeyValues
+    )
+    context.parent ! JobSucceededResponse(jobDescriptor.key,
+                                          returnCode,
+                                          copiedJobOutputs,
+                                          Option(detritusMap),
+                                          Seq.empty,
+                                          None,
+                                          resultGenerationMode = CallCached
+    )
     context stop self
     stay()
   }
@@ -323,7 +344,10 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
 
   /** If there are no responses pending this behaves like `failAndStop`, otherwise this goes to `FailedState` and waits
     * for all the pending responses to come back before stopping. */
-  def failAndAwaitPendingResponses(failure: CacheCopyFailure, command: IoCommand[_], data: StandardCacheHitCopyingActorData): State = {
+  def failAndAwaitPendingResponses(failure: CacheCopyFailure,
+                                   command: IoCommand[_],
+                                   data: StandardCacheHitCopyingActorData
+  ): State = {
     context.parent ! CopyingOutputsFailedResponse(jobDescriptor.key, standardParams.cacheCopyAttempt, failure)
 
     val (newData, commandState) = data.commandComplete(command)
@@ -344,12 +368,16 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
     stay()
   }
 
-  protected def lookupSourceCallRootPath(sourceJobDetritusFiles: Map[String, String]): Try[Path] = {
+  protected def lookupSourceCallRootPath(sourceJobDetritusFiles: Map[String, String]): Try[Path] =
     sourceJobDetritusFiles.get(JobPaths.CallRootPathKey) match {
       case Some(source) => getPath(source)
-      case None => Failure(new RuntimeException(s"${JobPaths.CallRootPathKey} wasn't found for call ${jobDescriptor.taskCall.fullyQualifiedName}"))
+      case None =>
+        Failure(
+          new RuntimeException(
+            s"${JobPaths.CallRootPathKey} wasn't found for call ${jobDescriptor.taskCall.fullyQualifiedName}"
+          )
+        )
     }
-  }
 
   private def ioCommandsToCopyPairs(commands: Set[IoCommand[_]]): Set[PathPair] = commands collect {
     case copyCommand: IoCopyCommand => copyCommand.source -> copyCommand.destination
@@ -358,18 +386,22 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
   /**
     * Returns a pair of the list of simpletons with copied paths, and copy commands necessary to perform those copies.
     */
-  protected def processSimpletons(womValueSimpletons: Seq[WomValueSimpleton], sourceCallRootPath: Path): Try[(CallOutputs, Set[IoCommand[_]])] = Try {
-    val (destinationSimpletons, ioCommands): (List[WomValueSimpleton], Set[IoCommand[_]]) = womValueSimpletons.toList.foldMap({
-      case WomValueSimpleton(key, wdlFile: WomSingleFile) =>
-        val sourcePath = getPath(wdlFile.value).get
-        val destinationPath = PathCopier.getDestinationFilePath(sourceCallRootPath, sourcePath, destinationCallRootPath)
-
-        val destinationSimpleton = WomValueSimpleton(key, WomSingleFile(destinationPath.pathAsString))
-
-        // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
-        List(destinationSimpleton) -> Set(commandBuilder.copyCommand(sourcePath, destinationPath).get)
-      case nonFileSimpleton => (List(nonFileSimpleton), Set.empty[IoCommand[_]])
-    })
+  protected def processSimpletons(womValueSimpletons: Seq[WomValueSimpleton],
+                                  sourceCallRootPath: Path
+  ): Try[(CallOutputs, Set[IoCommand[_]])] = Try {
+    val (destinationSimpletons, ioCommands): (List[WomValueSimpleton], Set[IoCommand[_]]) =
+      womValueSimpletons.toList.foldMap {
+        case WomValueSimpleton(key, wdlFile: WomSingleFile) =>
+          val sourcePath = getPath(wdlFile.value).get
+          val destinationPath =
+            PathCopier.getDestinationFilePath(sourceCallRootPath, sourcePath, destinationCallRootPath)
+
+          val destinationSimpleton = WomValueSimpleton(key, WomSingleFile(destinationPath.pathAsString))
+
+          // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
+          List(destinationSimpleton) -> Set(commandBuilder.copyCommand(sourcePath, destinationPath).get)
+        case nonFileSimpleton => (List(nonFileSimpleton), Set.empty[IoCommand[_]])
+      }
 
     (WomValueBuilder.toJobOutputs(jobDescriptor.taskCall.outputPorts, destinationSimpletons), ioCommands)
   }
@@ -377,7 +409,7 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
   /**
     * Returns the file (and ONLY the file detritus) intersection between the cache hit and this call.
     */
-  protected final def detritusFileKeys(sourceJobDetritusFiles: Map[String, String]): Set[String] = {
+  final protected def detritusFileKeys(sourceJobDetritusFiles: Map[String, String]): Set[String] = {
     val sourceKeys = sourceJobDetritusFiles.keySet
     val destinationKeys = destinationJobDetritusPaths.keySet
     sourceKeys.intersect(destinationKeys).filterNot(_ == JobPaths.CallRootPathKey)
@@ -386,21 +418,22 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
   /**
     * Returns a pair of the detritus with copied paths, and copy commands necessary to perform those copies.
     */
-  protected def processDetritus(sourceJobDetritusFiles: Map[String, String]): Try[(Map[String, Path], Set[IoCommand[_]])] = Try {
+  protected def processDetritus(
+    sourceJobDetritusFiles: Map[String, String]
+  ): Try[(Map[String, Path], Set[IoCommand[_]])] = Try {
     val fileKeys = detritusFileKeys(sourceJobDetritusFiles)
 
     val zero = (Map.empty[String, Path], Set.empty[IoCommand[_]])
 
-    val (destinationDetritus, ioCommands) = fileKeys.foldLeft(zero)({
-      case ((detrituses, commands), detritus) =>
-        val sourcePath = getPath(sourceJobDetritusFiles(detritus)).get
-        val destinationPath = destinationJobDetritusPaths(detritus)
+    val (destinationDetritus, ioCommands) = fileKeys.foldLeft(zero) { case ((detrituses, commands), detritus) =>
+      val sourcePath = getPath(sourceJobDetritusFiles(detritus)).get
+      val destinationPath = destinationJobDetritusPaths(detritus)
 
-        val newDetrituses = detrituses + (detritus -> destinationPath)
+      val newDetrituses = detrituses + (detritus -> destinationPath)
 
       // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
       (newDetrituses, commands + commandBuilder.copyCommand(sourcePath, destinationPath).get)
-    })
+    }
 
     (destinationDetritus + (JobPaths.CallRootPathKey -> destinationCallRootPath), ioCommands)
   }
@@ -412,13 +445,16 @@ abstract class StandardCacheHitCopyingActor(val standardParams: StandardCacheHit
   protected def additionalIoCommands(sourceCallRootPath: Path,
                                      originalSimpletons: Seq[WomValueSimpleton],
                                      newOutputs: CallOutputs,
-                                     originalDetritus:  Map[String, String],
-                                     newDetritus: Map[String, Path]): Try[List[Set[IoCommand[_]]]] = Success(Nil)
+                                     originalDetritus: Map[String, String],
+                                     newDetritus: Map[String, Path]
+  ): Try[List[Set[IoCommand[_]]]] = Success(Nil)
 
   override protected def onTimeout(message: Any, to: ActorRef): Unit = {
     val exceptionMessage = message match {
-      case copyCommand: IoCopyCommand => s"The Cache hit copying actor timed out waiting for a response to copy ${copyCommand.source.pathAsString} to ${copyCommand.destination.pathAsString}"
-      case touchCommand: IoTouchCommand => s"The Cache hit copying actor timed out waiting for a response to touch ${touchCommand.file.pathAsString}"
+      case copyCommand: IoCopyCommand =>
+        s"The Cache hit copying actor timed out waiting for a response to copy ${copyCommand.source.pathAsString} to ${copyCommand.destination.pathAsString}"
+      case touchCommand: IoTouchCommand =>
+        s"The Cache hit copying actor timed out waiting for a response to touch ${touchCommand.file.pathAsString}"
       case other => s"The Cache hit copying actor timed out waiting for an unknown I/O operation: $other"
     }
 
diff --git a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardFileHashingActor.scala b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardFileHashingActor.scala
index 78fdc078cb9..67199a7a062 100644
--- a/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardFileHashingActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/callcaching/StandardFileHashingActor.scala
@@ -34,8 +34,7 @@ trait StandardFileHashingActorParams {
 }
 
 /** A default implementation of the cache hit copying params. */
-case class DefaultStandardFileHashingActorParams
-(
+case class DefaultStandardFileHashingActorParams(
   override val jobDescriptor: BackendJobDescriptor,
   override val backendInitializationDataOption: Option[BackendInitializationData],
   override val serviceRegistryActor: ActorRef,
@@ -46,7 +45,8 @@ case class DefaultStandardFileHashingActorParams
 
 case class FileHashContext(hashKey: HashKey, file: String)
 
-class DefaultStandardFileHashingActor(standardParams: StandardFileHashingActorParams) extends StandardFileHashingActor(standardParams) {
+class DefaultStandardFileHashingActor(standardParams: StandardFileHashingActorParams)
+    extends StandardFileHashingActor(standardParams) {
   override val ioCommandBuilder: IoCommandBuilder = DefaultIoCommandBuilder
 }
 
@@ -54,14 +54,20 @@ object StandardFileHashingActor {
   case class FileHashingFunction(work: (SingleFileHashRequest, LoggingAdapter) => Try[String])
 
   sealed trait BackendSpecificHasherCommand { def jobKey: JobKey }
-  final case class SingleFileHashRequest(jobKey: JobKey, hashKey: HashKey, file: WomFile, initializationData: Option[BackendInitializationData]) extends BackendSpecificHasherCommand
+  final case class SingleFileHashRequest(jobKey: JobKey,
+                                         hashKey: HashKey,
+                                         file: WomFile,
+                                         initializationData: Option[BackendInitializationData]
+  ) extends BackendSpecificHasherCommand
 
   sealed trait BackendSpecificHasherResponse extends SuccessfulHashResultMessage
-  case class FileHashResponse(hashResult: HashResult) extends BackendSpecificHasherResponse { override def hashes = Set(hashResult) }
+  case class FileHashResponse(hashResult: HashResult) extends BackendSpecificHasherResponse {
+    override def hashes = Set(hashResult)
+  }
 }
 
 abstract class StandardFileHashingActor(standardParams: StandardFileHashingActorParams)
-  extends Actor
+    extends Actor
     with ActorLogging
     with JobLogging
     with IoClientHelper
@@ -69,19 +75,21 @@ abstract class StandardFileHashingActor(standardParams: StandardFileHashingActor
     with Timers {
   override lazy val ioActor: ActorRef = standardParams.ioActor
   override lazy val jobDescriptor: BackendJobDescriptor = standardParams.jobDescriptor
-  override lazy val backendInitializationDataOption: Option[BackendInitializationData] = standardParams.backendInitializationDataOption
+  override lazy val backendInitializationDataOption: Option[BackendInitializationData] =
+    standardParams.backendInitializationDataOption
   override lazy val serviceRegistryActor: ActorRef = standardParams.serviceRegistryActor
   override lazy val configurationDescriptor: BackendConfigurationDescriptor = standardParams.configurationDescriptor
 
   protected def ioCommandBuilder: IoCommandBuilder = DefaultIoCommandBuilder
 
   def customHashStrategy(fileRequest: SingleFileHashRequest): Option[Try[String]] = None
-  
+
   def fileHashingReceive: Receive = {
     // Hash Request
     case fileRequest: SingleFileHashRequest =>
       customHashStrategy(fileRequest) match {
-        case Some(Success(result)) => context.parent ! FileHashResponse(HashResult(fileRequest.hashKey, HashValue(result)))
+        case Some(Success(result)) =>
+          context.parent ! FileHashResponse(HashResult(fileRequest.hashKey, HashValue(result)))
         case Some(Failure(failure)) => context.parent ! HashingFailedMessage(fileRequest.file.value, failure)
         case None => asyncHashing(fileRequest, context.parent)
       }
@@ -93,7 +101,7 @@ abstract class StandardFileHashingActor(standardParams: StandardFileHashingActor
     case (fileHashRequest: FileHashContext, IoSuccess(_, other)) =>
       context.parent ! HashingFailedMessage(
         fileHashRequest.file,
-        new Exception(s"Hash function supposedly succeeded but responded with '$other' instead of a string hash"),
+        new Exception(s"Hash function supposedly succeeded but responded with '$other' instead of a string hash")
       )
 
     // Hash Failure
@@ -124,9 +132,9 @@ abstract class StandardFileHashingActor(standardParams: StandardFileHashingActor
     }
   }
 
-  override def receive: Receive = ioReceive orElse fileHashingReceive 
+  override def receive: Receive = ioReceive orElse fileHashingReceive
 
-  override protected def onTimeout(message: Any, to: ActorRef): Unit = {
+  override protected def onTimeout(message: Any, to: ActorRef): Unit =
     message match {
       case (_, ioHashCommand: IoHashCommand) =>
         val fileAsString = ioHashCommand.file.pathAsString
@@ -137,5 +145,4 @@ abstract class StandardFileHashingActor(standardParams: StandardFileHashingActor
         log.warning(s"Async File hashing actor received unexpected timeout message: $other")
         context.parent ! HashingServiceUnvailable
     }
-  }
 }
diff --git a/backend/src/main/scala/cromwell/backend/standard/package.scala b/backend/src/main/scala/cromwell/backend/standard/package.scala
index 089efd4f614..b25d74ec8e7 100644
--- a/backend/src/main/scala/cromwell/backend/standard/package.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/package.scala
@@ -12,7 +12,7 @@ package object standard {
       def unapply(arg: StandardAdHocValue): Option[LocalizedAdHocValue] = arg.select[LocalizedAdHocValue]
     }
   }
-  
+
   // This is used to represent an AdHocValue that might have been localized
   type StandardAdHocValue = AdHocValue :+: LocalizedAdHocValue :+: CNil
 }
diff --git a/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCode.scala b/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCode.scala
index 06bc3d56c0a..c314a660122 100644
--- a/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCode.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCode.scala
@@ -10,18 +10,18 @@ object ContinueOnReturnCode {
   * Decides if a call/job continues upon a specific return code.
   */
 sealed trait ContinueOnReturnCode {
+
   /**
     * Returns true if the call is a success based on the return code.
     *
     * @param returnCode Return code from the process / script.
     * @return True if the call is a success.
     */
-  final def continueFor(returnCode: Int): Boolean = {
+  final def continueFor(returnCode: Int): Boolean =
     this match {
       case ContinueOnReturnCodeFlag(continue) => continue || returnCode == 0
       case ContinueOnReturnCodeSet(returnCodes) => returnCodes.contains(returnCode)
     }
-  }
 }
 
 /**
diff --git a/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala b/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala
index aaa2754f3e1..14dfb369d77 100644
--- a/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala
@@ -24,9 +24,10 @@ import scala.util.Try
   */
 object ContinueOnReturnCodeValidation {
   lazy val instance: RuntimeAttributesValidation[ContinueOnReturnCode] = new ContinueOnReturnCodeValidation
-  def default(runtimeConfig: Option[Config]): RuntimeAttributesValidation[ContinueOnReturnCode] = instance.withDefault(
-    configDefaultWdlValue(runtimeConfig) getOrElse WomInteger(0))
-  def configDefaultWdlValue(runtimeConfig: Option[Config]): Option[WomValue] = instance.configDefaultWomValue(runtimeConfig)
+  def default(runtimeConfig: Option[Config]): RuntimeAttributesValidation[ContinueOnReturnCode] =
+    instance.withDefault(configDefaultWdlValue(runtimeConfig) getOrElse WomInteger(0))
+  def configDefaultWdlValue(runtimeConfig: Option[Config]): Option[WomValue] =
+    instance.configDefaultWomValue(runtimeConfig)
 }
 
 class ContinueOnReturnCodeValidation extends RuntimeAttributesValidation[ContinueOnReturnCode] {
@@ -40,7 +41,7 @@ class ContinueOnReturnCodeValidation extends RuntimeAttributesValidation[Continu
     case WomString(value) if Try(value.toBoolean).isSuccess => ContinueOnReturnCodeFlag(value.toBoolean).validNel
     case WomString(value) if Try(value.toInt).isSuccess => ContinueOnReturnCodeSet(Set(value.toInt)).validNel
     case WomInteger(value) => ContinueOnReturnCodeSet(Set(value)).validNel
-    case value@WomArray(_, seq) =>
+    case value @ WomArray(_, seq) =>
       val errorOrInts: ErrorOr[List[Int]] = (seq.toList map validateInt).sequence[ErrorOr, Int]
       errorOrInts match {
         case Valid(ints) => ContinueOnReturnCodeSet(ints.toSet).validNel
@@ -54,8 +55,8 @@ class ContinueOnReturnCodeValidation extends RuntimeAttributesValidation[Continu
     case WomString(value) if Try(value.toBoolean).isSuccess => true
     case WomInteger(_) => true
     case WomArray(WomArrayType(WomStringType), elements) =>
-      elements forall {
-        value => Try(value.valueString.toInt).isSuccess
+      elements forall { value =>
+        Try(value.valueString.toInt).isSuccess
       }
     case WomArray(WomArrayType(WomIntegerType), _) => true
   }
diff --git a/backend/src/main/scala/cromwell/backend/validation/DockerValidation.scala b/backend/src/main/scala/cromwell/backend/validation/DockerValidation.scala
index b6c3fe0112b..eb8afc17c12 100644
--- a/backend/src/main/scala/cromwell/backend/validation/DockerValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/DockerValidation.scala
@@ -26,7 +26,7 @@ class DockerValidation extends StringRuntimeAttributesValidation(RuntimeAttribut
   override protected def invalidValueMessage(value: WomValue): String = super.missingValueMessage
 
   // NOTE: Docker's current test specs don't like WdlInteger, etc. auto converted to WdlString.
-  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = {
-    case WomString(value) => value.validNel
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = { case WomString(value) =>
+    value.validNel
   }
 }
diff --git a/backend/src/main/scala/cromwell/backend/validation/FailOnStderrValidation.scala b/backend/src/main/scala/cromwell/backend/validation/FailOnStderrValidation.scala
index 8ac39e50d16..7b55f9657fa 100644
--- a/backend/src/main/scala/cromwell/backend/validation/FailOnStderrValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/FailOnStderrValidation.scala
@@ -18,9 +18,10 @@ import wom.values._
 
 object FailOnStderrValidation {
   lazy val instance: RuntimeAttributesValidation[Boolean] = new FailOnStderrValidation
-  def default(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = instance.withDefault(
-    configDefaultWdlValue(runtimeConfig) getOrElse WomBoolean(false))
-  def configDefaultWdlValue(runtimeConfig: Option[Config]): Option[WomValue] = instance.configDefaultWomValue(runtimeConfig)
+  def default(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] =
+    instance.withDefault(configDefaultWdlValue(runtimeConfig) getOrElse WomBoolean(false))
+  def configDefaultWdlValue(runtimeConfig: Option[Config]): Option[WomValue] =
+    instance.configDefaultWomValue(runtimeConfig)
 }
 
 class FailOnStderrValidation extends BooleanRuntimeAttributesValidation(RuntimeAttributesKeys.FailOnStderrKey) {
diff --git a/backend/src/main/scala/cromwell/backend/validation/InformationValidation.scala b/backend/src/main/scala/cromwell/backend/validation/InformationValidation.scala
index 39b9f0b3031..e8c9dd1d7b3 100644
--- a/backend/src/main/scala/cromwell/backend/validation/InformationValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/InformationValidation.scala
@@ -25,18 +25,32 @@ import scala.util.{Failure, Success}
   * `withDefault` can be used to create a validation that defaults to a particular size.
   */
 object InformationValidation {
-  def instance(attributeName: String = RuntimeAttributesKeys.MemoryKey, defaultUnit: MemoryUnit, allowZero: Boolean = false): RuntimeAttributesValidation[MemorySize] =
+  def instance(attributeName: String = RuntimeAttributesKeys.MemoryKey,
+               defaultUnit: MemoryUnit,
+               allowZero: Boolean = false
+  ): RuntimeAttributesValidation[MemorySize] =
     new InformationValidation(attributeName, defaultUnit, allowZero)
-  def optional(attributeName: String = RuntimeAttributesKeys.MemoryKey, defaultUnit: MemoryUnit, allowZero: Boolean = false): OptionalRuntimeAttributesValidation[MemorySize] =
+  def optional(attributeName: String = RuntimeAttributesKeys.MemoryKey,
+               defaultUnit: MemoryUnit,
+               allowZero: Boolean = false
+  ): OptionalRuntimeAttributesValidation[MemorySize] =
     instance(attributeName, defaultUnit, allowZero).optional
-  def configDefaultString(attributeName: String = RuntimeAttributesKeys.MemoryKey, config: Option[Config], defaultUnit: MemoryUnit, allowZero: Boolean = false): Option[String] =
+  def configDefaultString(attributeName: String = RuntimeAttributesKeys.MemoryKey,
+                          config: Option[Config],
+                          defaultUnit: MemoryUnit,
+                          allowZero: Boolean = false
+  ): Option[String] =
     instance(attributeName, defaultUnit, allowZero).configDefaultValue(config)
-  def withDefaultMemory(attributeName: String = RuntimeAttributesKeys.MemoryKey, memorySize: String, defaultUnit: MemoryUnit, allowZero: Boolean = false): RuntimeAttributesValidation[MemorySize] = {
+  def withDefaultMemory(attributeName: String = RuntimeAttributesKeys.MemoryKey,
+                        memorySize: String,
+                        defaultUnit: MemoryUnit,
+                        allowZero: Boolean = false
+  ): RuntimeAttributesValidation[MemorySize] =
     MemorySize.parse(memorySize) match {
       case Success(memory) => instance(attributeName, defaultUnit, allowZero).withDefault(WomLong(memory.bytes.toLong))
-      case Failure(_) => instance(attributeName, defaultUnit, allowZero).withDefault(BadDefaultAttribute(WomString(memorySize.toString)))
+      case Failure(_) =>
+        instance(attributeName, defaultUnit, allowZero).withDefault(BadDefaultAttribute(WomString(memorySize.toString)))
     }
-  }
 
   private[validation] val wrongAmountFormat =
     "Expecting %s runtime attribute value greater than 0 but got %s"
@@ -44,39 +58,56 @@ object InformationValidation {
     "Expecting %s runtime attribute to be an Integer or String with format '8 GB'." +
       " Exception: %s"
 
-  private[validation] def validateString(attributeName: String, wdlString: WomString, allowZero: Boolean): ErrorOr[MemorySize] =
+  private[validation] def validateString(attributeName: String,
+                                         wdlString: WomString,
+                                         allowZero: Boolean
+  ): ErrorOr[MemorySize] =
     validateString(attributeName, wdlString.value, allowZero)
 
-  private[validation] def validateString(attributeName: String, value: String, allowZero: Boolean): ErrorOr[MemorySize] = {
+  private[validation] def validateString(attributeName: String,
+                                         value: String,
+                                         allowZero: Boolean
+  ): ErrorOr[MemorySize] =
     MemorySize.parse(value) match {
-      case scala.util.Success(memorySize: MemorySize) if memorySize.amount > 0 || (memorySize.amount == 0 && allowZero) =>
+      case scala.util.Success(memorySize: MemorySize)
+          if memorySize.amount > 0 || (memorySize.amount == 0 && allowZero) =>
         memorySize.to(MemoryUnit.GB).validNel
       case scala.util.Success(memorySize: MemorySize) =>
         wrongAmountFormat.format(attributeName, memorySize.amount).invalidNel
       case scala.util.Failure(throwable) =>
         wrongTypeFormat.format(attributeName, throwable.getMessage).invalidNel
     }
-  }
 
-  private[validation] def validateInteger(attributeName: String, wdlInteger: WomInteger, defaultUnit: MemoryUnit, allowZero: Boolean): ErrorOr[MemorySize] =
+  private[validation] def validateInteger(attributeName: String,
+                                          wdlInteger: WomInteger,
+                                          defaultUnit: MemoryUnit,
+                                          allowZero: Boolean
+  ): ErrorOr[MemorySize] =
     validateInteger(attributeName, wdlInteger.value, defaultUnit, allowZero)
 
-  private[validation] def validateInteger(attributeName: String, value: Int, defaultUnit: MemoryUnit, allowZero: Boolean): ErrorOr[MemorySize] = {
+  private[validation] def validateInteger(attributeName: String,
+                                          value: Int,
+                                          defaultUnit: MemoryUnit,
+                                          allowZero: Boolean
+  ): ErrorOr[MemorySize] =
     if (value < 0 || (value == 0 && !allowZero))
       wrongAmountFormat.format(attributeName, value).invalidNel
     else
       MemorySize(value.toDouble, defaultUnit).to(MemoryUnit.GB).validNel
-  }
 
-  def validateLong(attributeName: String, value: Long, defaultUnit: MemoryUnit, allowZero: Boolean): ErrorOr[MemorySize] = {
+  def validateLong(attributeName: String,
+                   value: Long,
+                   defaultUnit: MemoryUnit,
+                   allowZero: Boolean
+  ): ErrorOr[MemorySize] =
     if (value < 0 || (value == 0 && !allowZero))
       wrongAmountFormat.format(attributeName, value).invalidNel
     else
       MemorySize(value.toDouble, defaultUnit).to(MemoryUnit.GB).validNel
-  }
 }
 
-class InformationValidation(attributeName: String, defaultUnit: MemoryUnit, allowZero: Boolean = false) extends RuntimeAttributesValidation[MemorySize] {
+class InformationValidation(attributeName: String, defaultUnit: MemoryUnit, allowZero: Boolean = false)
+    extends RuntimeAttributesValidation[MemorySize] {
 
   import InformationValidation._
 
diff --git a/backend/src/main/scala/cromwell/backend/validation/MaxRetriesValidation.scala b/backend/src/main/scala/cromwell/backend/validation/MaxRetriesValidation.scala
index fdfd6467a85..f2c9ba9522e 100644
--- a/backend/src/main/scala/cromwell/backend/validation/MaxRetriesValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/MaxRetriesValidation.scala
@@ -21,8 +21,8 @@ object MaxRetriesValidation {
   lazy val instance: RuntimeAttributesValidation[Int] = new MaxRetriesValidation(MaxRetriesKey)
   lazy val optional: OptionalRuntimeAttributesValidation[Int] = instance.optional
 
-  def default(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = instance.withDefault(
-    configDefaultWomValue(runtimeConfig) getOrElse WomInteger(0))
+  def default(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] =
+    instance.withDefault(configDefaultWomValue(runtimeConfig) getOrElse WomInteger(0))
   def configDefaultWomValue(config: Option[Config]): Option[WomValue] = instance.configDefaultWomValue(config)
 }
 
diff --git a/backend/src/main/scala/cromwell/backend/validation/MemoryValidation.scala b/backend/src/main/scala/cromwell/backend/validation/MemoryValidation.scala
index 32be28026f0..299e043ec8f 100644
--- a/backend/src/main/scala/cromwell/backend/validation/MemoryValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/MemoryValidation.scala
@@ -25,16 +25,22 @@ import scala.util.{Failure, Success}
 object MemoryValidation {
   def instance(attributeName: String = RuntimeAttributesKeys.MemoryKey): RuntimeAttributesValidation[MemorySize] =
     new MemoryValidation(attributeName)
-  def optional(attributeName: String = RuntimeAttributesKeys.MemoryKey): OptionalRuntimeAttributesValidation[MemorySize] =
+  def optional(
+    attributeName: String = RuntimeAttributesKeys.MemoryKey
+  ): OptionalRuntimeAttributesValidation[MemorySize] =
     instance(attributeName).optional
-  def configDefaultString(attributeName: String = RuntimeAttributesKeys.MemoryKey, config: Option[Config]): Option[String] =
+  def configDefaultString(attributeName: String = RuntimeAttributesKeys.MemoryKey,
+                          config: Option[Config]
+  ): Option[String] =
     instance(attributeName).configDefaultValue(config)
-  def withDefaultMemory(attributeName: String = RuntimeAttributesKeys.MemoryKey, memorySize: String): RuntimeAttributesValidation[MemorySize] = {
+  def withDefaultMemory(attributeName: String = RuntimeAttributesKeys.MemoryKey,
+                        memorySize: String
+  ): RuntimeAttributesValidation[MemorySize] =
     MemorySize.parse(memorySize) match {
       case Success(memory) => instance(attributeName).withDefault(WomLong(memory.bytes.toLong))
       case Failure(_) => instance(attributeName).withDefault(BadDefaultAttribute(WomString(memorySize.toString)))
     }
-  }
 }
 
-class MemoryValidation(attributeName: String = RuntimeAttributesKeys.MemoryKey) extends InformationValidation(attributeName, MemoryUnit.Bytes)
+class MemoryValidation(attributeName: String = RuntimeAttributesKeys.MemoryKey)
+    extends InformationValidation(attributeName, MemoryUnit.Bytes)
diff --git a/backend/src/main/scala/cromwell/backend/validation/PrimitiveRuntimeAttributesValidation.scala b/backend/src/main/scala/cromwell/backend/validation/PrimitiveRuntimeAttributesValidation.scala
index d4dc78f83b2..af41bf8ad52 100644
--- a/backend/src/main/scala/cromwell/backend/validation/PrimitiveRuntimeAttributesValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/PrimitiveRuntimeAttributesValidation.scala
@@ -44,24 +44,24 @@ sealed trait PrimitiveRuntimeAttributesValidation[A, B <: WomPrimitive] extends
   protected def validateCoercedValue(womValue: B): ErrorOr[A]
 }
 
-class BooleanRuntimeAttributesValidation(override val key: String) extends
-  PrimitiveRuntimeAttributesValidation[Boolean, WomBoolean] {
+class BooleanRuntimeAttributesValidation(override val key: String)
+    extends PrimitiveRuntimeAttributesValidation[Boolean, WomBoolean] {
 
   override val womType = WomBooleanType
 
   override protected def validateCoercedValue(womValue: WomBoolean): ErrorOr[Boolean] = womValue.value.validNel
 }
 
-class FloatRuntimeAttributesValidation(override val key: String) extends
-  PrimitiveRuntimeAttributesValidation[Double, WomFloat] {
+class FloatRuntimeAttributesValidation(override val key: String)
+    extends PrimitiveRuntimeAttributesValidation[Double, WomFloat] {
 
   override val womType = WomFloatType
 
   override protected def validateCoercedValue(womValue: WomFloat): ErrorOr[Double] = womValue.value.validNel
 }
 
-class IntRuntimeAttributesValidation(override val key: String) extends
-  PrimitiveRuntimeAttributesValidation[Int, WomInteger] {
+class IntRuntimeAttributesValidation(override val key: String)
+    extends PrimitiveRuntimeAttributesValidation[Int, WomInteger] {
 
   override val womType = WomIntegerType
 
@@ -70,18 +70,19 @@ class IntRuntimeAttributesValidation(override val key: String) extends
   override protected def typeString: String = "an Integer"
 }
 
-class PositiveIntRuntimeAttributesValidation(override val key: String) extends
-  PrimitiveRuntimeAttributesValidation[Int Refined Positive, WomInteger] {
+class PositiveIntRuntimeAttributesValidation(override val key: String)
+    extends PrimitiveRuntimeAttributesValidation[Int Refined Positive, WomInteger] {
 
   override val womType = WomIntegerType
 
-  override protected def validateCoercedValue(womValue: WomInteger): ErrorOr[Int Refined Positive] = refineV[Positive](womValue.value).leftMap(NonEmptyList.one).toValidated
+  override protected def validateCoercedValue(womValue: WomInteger): ErrorOr[Int Refined Positive] =
+    refineV[Positive](womValue.value).leftMap(NonEmptyList.one).toValidated
 
   override protected def typeString: String = "an Integer"
 }
 
-class StringRuntimeAttributesValidation(override val key: String) extends
-  PrimitiveRuntimeAttributesValidation[String, WomString] {
+class StringRuntimeAttributesValidation(override val key: String)
+    extends PrimitiveRuntimeAttributesValidation[String, WomString] {
 
   override val womType = WomStringType
 
diff --git a/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesDefault.scala b/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesDefault.scala
index d46bc7a66d5..706cc1336e8 100644
--- a/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesDefault.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesDefault.scala
@@ -12,29 +12,32 @@ import scala.util.{Failure, Try}
 
 object RuntimeAttributesDefault {
 
-  def workflowOptionsDefault(options: WorkflowOptions, mapping: Map[String, Iterable[WomType]]):
-  Try[Map[String, WomValue]] = {
+  def workflowOptionsDefault(options: WorkflowOptions,
+                             mapping: Map[String, Iterable[WomType]]
+  ): Try[Map[String, WomValue]] =
     options.defaultRuntimeOptions flatMap { attrs =>
-      TryUtil.sequenceMap(attrs collect {
-        case (k, v) if mapping.contains(k) =>
-          val maybeTriedValue = mapping(k) map {  _.coerceRawValue(v) } find { _.isSuccess } getOrElse {
-            Failure(new RuntimeException(s"Could not parse JsonValue $v to valid WomValue for runtime attribute $k"))
-          }
-          k -> maybeTriedValue
-      }, "Failed to coerce default runtime options")
-    } recover {
-      case _: OptionNotFoundException => Map.empty[String, WomValue]
+      TryUtil.sequenceMap(
+        attrs collect {
+          case (k, v) if mapping.contains(k) =>
+            val maybeTriedValue = mapping(k) map { _.coerceRawValue(v) } find { _.isSuccess } getOrElse {
+              Failure(new RuntimeException(s"Could not parse JsonValue $v to valid WomValue for runtime attribute $k"))
+            }
+            k -> maybeTriedValue
+        },
+        "Failed to coerce default runtime options"
+      )
+    } recover { case _: OptionNotFoundException =>
+      Map.empty[String, WomValue]
     }
-  }
 
   /**
     * Traverse defaultsList in order, and for each of them add the missing (and only missing) runtime attributes.
    */
-  def withDefaults(attrs: EvaluatedRuntimeAttributes, defaultsList: List[EvaluatedRuntimeAttributes]): EvaluatedRuntimeAttributes = {
-    defaultsList.foldLeft(attrs)((acc, default) => {
-      acc ++ default.view.filterKeys(!acc.keySet.contains(_))
-    })
-  }
+  def withDefaults(attrs: EvaluatedRuntimeAttributes,
+                   defaultsList: List[EvaluatedRuntimeAttributes]
+  ): EvaluatedRuntimeAttributes =
+    defaultsList.foldLeft(attrs)((acc, default) => acc ++ default.view.filterKeys(!acc.keySet.contains(_)))
 
-  def noValueFoundFor[A](attribute: String): ValidatedNel[String, A] = s"Can't find an attribute value for key $attribute".invalidNel
+  def noValueFoundFor[A](attribute: String): ValidatedNel[String, A] =
+    s"Can't find an attribute value for key $attribute".invalidNel
 }
diff --git a/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala b/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala
index 65f2119a64b..5fa52dac53a 100644
--- a/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala
@@ -26,61 +26,56 @@ object RuntimeAttributesValidation {
     if (unrecognized.nonEmpty) logger.warn(s"Unrecognized runtime attribute keys: $unrecognized")
   }
 
-  def validateDocker(docker: Option[WomValue], onMissingKey: => ErrorOr[Option[String]]): ErrorOr[Option[String]] = {
+  def validateDocker(docker: Option[WomValue], onMissingKey: => ErrorOr[Option[String]]): ErrorOr[Option[String]] =
     validateWithValidation(docker, DockerValidation.instance.optional, onMissingKey)
-  }
 
-  def validateFailOnStderr(value: Option[WomValue], onMissingKey: => ErrorOr[Boolean]): ErrorOr[Boolean] = {
+  def validateFailOnStderr(value: Option[WomValue], onMissingKey: => ErrorOr[Boolean]): ErrorOr[Boolean] =
     validateWithValidation(value, FailOnStderrValidation.instance, onMissingKey)
-  }
 
   def validateContinueOnReturnCode(value: Option[WomValue],
-                                   onMissingKey: => ErrorOr[ContinueOnReturnCode]): ErrorOr[ContinueOnReturnCode] = {
+                                   onMissingKey: => ErrorOr[ContinueOnReturnCode]
+  ): ErrorOr[ContinueOnReturnCode] =
     validateWithValidation(value, ContinueOnReturnCodeValidation.instance, onMissingKey)
-  }
 
-  def validateMemory(value: Option[WomValue], onMissingKey: => ErrorOr[MemorySize]): ErrorOr[MemorySize] = {
+  def validateMemory(value: Option[WomValue], onMissingKey: => ErrorOr[MemorySize]): ErrorOr[MemorySize] =
     validateWithValidation(value, MemoryValidation.instance(), onMissingKey)
-  }
 
-  def validateCpu(cpu: Option[WomValue], onMissingKey: => ErrorOr[Int Refined Positive]): ErrorOr[Int Refined Positive] = {
+  def validateCpu(cpu: Option[WomValue],
+                  onMissingKey: => ErrorOr[Int Refined Positive]
+  ): ErrorOr[Int Refined Positive] =
     validateWithValidation(cpu, CpuValidation.instance, onMissingKey)
-  }
 
-  def validateMaxRetries(maxRetries: Option[WomValue], onMissingKey: => ErrorOr[Int]): ErrorOr[Int] = {
+  def validateMaxRetries(maxRetries: Option[WomValue], onMissingKey: => ErrorOr[Int]): ErrorOr[Int] =
     validateWithValidation(maxRetries, MaxRetriesValidation.instance, onMissingKey)
-  }
 
   private def validateWithValidation[T](valueOption: Option[WomValue],
                                         validation: RuntimeAttributesValidation[T],
-                                        onMissingValue: => ErrorOr[T]): ErrorOr[T] = {
+                                        onMissingValue: => ErrorOr[T]
+  ): ErrorOr[T] =
     valueOption match {
       case Some(value) =>
         validation.validateValue.applyOrElse(value, (_: Any) => validation.invalidValueFailure(value))
       case None => onMissingValue
     }
-  }
 
-  def validateInt(value: WomValue): ErrorOr[Int] = {
+  def validateInt(value: WomValue): ErrorOr[Int] =
     WomIntegerType.coerceRawValue(value) match {
       case scala.util.Success(WomInteger(i)) => i.intValue.validNel
       case _ => s"Could not coerce ${value.valueString} into an integer".invalidNel
     }
-  }
 
-  def validateBoolean(value: WomValue): ErrorOr[Boolean] = {
+  def validateBoolean(value: WomValue): ErrorOr[Boolean] =
     WomBooleanType.coerceRawValue(value) match {
       case scala.util.Success(WomBoolean(b)) => b.booleanValue.validNel
       case _ => s"Could not coerce ${value.valueString} into a boolean".invalidNel
     }
-  }
 
-  def parseMemoryString(k: String, s: WomString): ErrorOr[MemorySize] = {
+  def parseMemoryString(k: String, s: WomString): ErrorOr[MemorySize] =
     InformationValidation.validateString(k, s, allowZero = false)
-  }
 
   def withDefault[ValidatedType](validation: RuntimeAttributesValidation[ValidatedType],
-                                 default: WomValue): RuntimeAttributesValidation[ValidatedType] = {
+                                 default: WomValue
+  ): RuntimeAttributesValidation[ValidatedType] =
     new RuntimeAttributesValidation[ValidatedType] {
       override def key: String = validation.key
 
@@ -101,10 +96,10 @@ object RuntimeAttributesValidation {
 
       override protected def staticDefaultOption = Option(default)
     }
-  }
 
   def withUsedInCallCaching[ValidatedType](validation: RuntimeAttributesValidation[ValidatedType],
-                                           usedInCallCachingValue: Boolean): RuntimeAttributesValidation[ValidatedType] = {
+                                           usedInCallCachingValue: Boolean
+  ): RuntimeAttributesValidation[ValidatedType] =
     new RuntimeAttributesValidation[ValidatedType] {
       override def key: String = validation.key
 
@@ -125,10 +120,10 @@ object RuntimeAttributesValidation {
 
       override protected def staticDefaultOption = validation.staticDefaultOption
     }
-  }
 
-  def optional[ValidatedType](validation: RuntimeAttributesValidation[ValidatedType]):
-  OptionalRuntimeAttributesValidation[ValidatedType] = {
+  def optional[ValidatedType](
+    validation: RuntimeAttributesValidation[ValidatedType]
+  ): OptionalRuntimeAttributesValidation[ValidatedType] =
     new OptionalRuntimeAttributesValidation[ValidatedType] {
       override def key: String = validation.key
 
@@ -149,7 +144,6 @@ object RuntimeAttributesValidation {
 
       override protected def staticDefaultOption = validation.staticDefaultOption
     }
-  }
 
   /**
     * Returns the value from the attributes, unpacking options, and converting them to string values suitable for
@@ -181,9 +175,9 @@ object RuntimeAttributesValidation {
     * @throws ClassCastException if the validation is called on an optional validation.
     */
   def extract[A](runtimeAttributesValidation: RuntimeAttributesValidation[A],
-                 validatedRuntimeAttributes: ValidatedRuntimeAttributes): A = {
+                 validatedRuntimeAttributes: ValidatedRuntimeAttributes
+  ): A =
     extract(runtimeAttributesValidation.key, validatedRuntimeAttributes)
-  }
 
   /**
     * Returns the value from the attributes matching the key.
@@ -192,14 +186,15 @@ object RuntimeAttributesValidation {
     * @param validatedRuntimeAttributes The values to search.
     * @return The value matching the key.
     */
-  def extract[A](key: String,
-                 validatedRuntimeAttributes: ValidatedRuntimeAttributes): A = {
+  def extract[A](key: String, validatedRuntimeAttributes: ValidatedRuntimeAttributes): A = {
     val value = extractOption(key, validatedRuntimeAttributes)
     value match {
       // NOTE: Some(innerValue) aka Some.unapply() throws a `ClassCastException` to `Nothing$` as it can't tell the type
       case some: Some[_] => some.get.asInstanceOf[A]
-      case None => throw new RuntimeException(
-        s"$key not found in runtime attributes ${validatedRuntimeAttributes.attributes.keys}")
+      case None =>
+        throw new RuntimeException(
+          s"$key not found in runtime attributes ${validatedRuntimeAttributes.attributes.keys}"
+        )
     }
   }
 
@@ -211,9 +206,9 @@ object RuntimeAttributesValidation {
     * @return The Some(value) matching the key or None.
     */
   def extractOption[A](runtimeAttributesValidation: RuntimeAttributesValidation[A],
-                       validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[A] = {
+                       validatedRuntimeAttributes: ValidatedRuntimeAttributes
+  ): Option[A] =
     extractOption(runtimeAttributesValidation.key, validatedRuntimeAttributes)
-  }
 
   /**
     * Returns Some(value) from the attributes matching the key, or None.
@@ -234,13 +229,12 @@ object RuntimeAttributesValidation {
     * @tparam A The type to cast the unpacked value.
     * @return The Some(value) matching the key or None.
     */
-  final def unpackOption[A](value: Any): Option[A] = {
+  final def unpackOption[A](value: Any): Option[A] =
     value match {
       case None => None
       case Some(innerValue) => unpackOption(innerValue)
       case _ => Option(value.asInstanceOf[A])
     }
-  }
 }
 
 /**
@@ -251,13 +245,13 @@ case class BadDefaultAttribute(badDefaultValue: WomValue) extends WomValue {
   val womType = WomStringType
 }
 
-
 /**
   * Performs a validation on a runtime attribute and returns some value.
   *
   * @tparam ValidatedType The type of the validated value.
   */
 trait RuntimeAttributesValidation[ValidatedType] {
+
   /**
     * Returns the key of the runtime attribute.
     *
@@ -297,8 +291,8 @@ trait RuntimeAttributesValidation[ValidatedType] {
     *
     * @return true if the value can be validated.
     */
-  protected def validateExpression: PartialFunction[WomValue, Boolean] = {
-    case womValue => coercion.exists(_ == womValue.womType)
+  protected def validateExpression: PartialFunction[WomValue, Boolean] = { case womValue =>
+    coercion.exists(_ == womValue.womType)
   }
 
   /**
@@ -322,7 +316,7 @@ trait RuntimeAttributesValidation[ValidatedType] {
     *
     * @return Wrapped invalidValueMessage.
     */
-  protected final def invalidValueFailure(value: WomValue): ErrorOr[ValidatedType] =
+  final protected def invalidValueFailure(value: WomValue): ErrorOr[ValidatedType] =
     invalidValueMessage(value).invalidNel
 
   /**
@@ -337,7 +331,7 @@ trait RuntimeAttributesValidation[ValidatedType] {
     *
     * @return Wrapped missingValueMessage.
     */
-  protected final lazy val missingValueFailure: ErrorOr[ValidatedType] = missingValueMessage.invalidNel
+  final protected lazy val missingValueFailure: ErrorOr[ValidatedType] = missingValueMessage.invalidNel
 
   /**
     * Runs this validation on the value matching key.
@@ -347,12 +341,11 @@ trait RuntimeAttributesValidation[ValidatedType] {
     * @param values The full set of values.
     * @return The error or valid value for this key.
     */
-  def validate(values: Map[String, WomValue]): ErrorOr[ValidatedType] = {
+  def validate(values: Map[String, WomValue]): ErrorOr[ValidatedType] =
     values.get(key) match {
       case Some(value) => validateValue.applyOrElse(value, (_: Any) => invalidValueFailure(value))
       case None => validateNone
     }
-  }
 
   /**
     * Used during initialization, returning true if the expression __may be__ valid.
@@ -371,7 +364,7 @@ trait RuntimeAttributesValidation[ValidatedType] {
     * @param wdlExpressionMaybe The optional expression.
     * @return True if the expression may be evaluated.
     */
-  def validateOptionalWomValue(wdlExpressionMaybe: Option[WomValue]): Boolean = {
+  def validateOptionalWomValue(wdlExpressionMaybe: Option[WomValue]): Boolean =
     wdlExpressionMaybe match {
       case None => staticDefaultOption.isDefined || validateNone.isValid
       case Some(wdlExpression: WdlExpression) =>
@@ -381,9 +374,8 @@ trait RuntimeAttributesValidation[ValidatedType] {
         }
       case Some(womValue) => validateExpression.applyOrElse(womValue, (_: Any) => false)
     }
-  }
 
-  def validateOptionalWomExpression(womExpressionMaybe: Option[WomExpression]): Boolean = {
+  def validateOptionalWomExpression(womExpressionMaybe: Option[WomExpression]): Boolean =
     womExpressionMaybe match {
       case None => staticDefaultOption.isDefined || validateNone.isValid
       case Some(womExpression) =>
@@ -392,7 +384,7 @@ trait RuntimeAttributesValidation[ValidatedType] {
           case Invalid(_) => true // If we can't evaluate it, we'll let it pass for now...
         }
     }
-  }
+
   /**
     * Indicates whether this runtime attribute should be used in call caching calculations.
     *
@@ -410,7 +402,7 @@ trait RuntimeAttributesValidation[ValidatedType] {
     * Returns an optional version of this validation.
     */
   final lazy val optional: OptionalRuntimeAttributesValidation[ValidatedType] =
-  RuntimeAttributesValidation.optional(this)
+    RuntimeAttributesValidation.optional(this)
 
   /**
     * Returns a version of this validation with the default value.
@@ -432,7 +424,7 @@ trait RuntimeAttributesValidation[ValidatedType] {
     * @param optionalRuntimeConfig Optional default runtime attributes config of a particular backend.
     * @return The new version of this validation.
     */
-  final def configDefaultWomValue(optionalRuntimeConfig: Option[Config]): Option[WomValue] = {
+  final def configDefaultWomValue(optionalRuntimeConfig: Option[Config]): Option[WomValue] =
     optionalRuntimeConfig collect {
       case config if config.hasPath(key) =>
         val value = config.getValue(key).unwrapped()
@@ -442,13 +434,11 @@ trait RuntimeAttributesValidation[ValidatedType] {
           BadDefaultAttribute(WomString(value.toString))
         }
     }
-  }
 
-  final def configDefaultValue(optionalRuntimeConfig: Option[Config]): Option[String] = {
+  final def configDefaultValue(optionalRuntimeConfig: Option[Config]): Option[String] =
     optionalRuntimeConfig collect {
       case config if config.hasPath(key) => config.getValue(key).unwrapped().toString
     }
-  }
 
   /*
   Methods below provide aliases to expose protected methods to the package.
@@ -457,15 +447,15 @@ trait RuntimeAttributesValidation[ValidatedType] {
   access the protected values, except the `validation` package that uses these back doors.
    */
 
-  private[validation] final lazy val validateValuePackagePrivate = validateValue
+  final private[validation] lazy val validateValuePackagePrivate = validateValue
 
-  private[validation] final lazy val validateExpressionPackagePrivate = validateExpression
+  final private[validation] lazy val validateExpressionPackagePrivate = validateExpression
 
-  private[validation] final def invalidValueMessagePackagePrivate(value: WomValue) = invalidValueMessage(value)
+  final private[validation] def invalidValueMessagePackagePrivate(value: WomValue) = invalidValueMessage(value)
 
-  private[validation] final lazy val missingValueMessagePackagePrivate = missingValueMessage
+  final private[validation] lazy val missingValueMessagePackagePrivate = missingValueMessage
 
-  private[validation] final lazy val usedInCallCachingPackagePrivate = usedInCallCaching
+  final private[validation] lazy val usedInCallCachingPackagePrivate = usedInCallCaching
 }
 
 /**
@@ -474,6 +464,7 @@ trait RuntimeAttributesValidation[ValidatedType] {
   * @tparam ValidatedType The type of the validated value.
   */
 trait OptionalRuntimeAttributesValidation[ValidatedType] extends RuntimeAttributesValidation[Option[ValidatedType]] {
+
   /**
     * Validates the wdl value.
     *
@@ -484,13 +475,12 @@ trait OptionalRuntimeAttributesValidation[ValidatedType] extends RuntimeAttribut
     */
   protected def validateOption: PartialFunction[WomValue, ErrorOr[ValidatedType]]
 
-  override final protected lazy val validateValue = new PartialFunction[WomValue, ErrorOr[Option[ValidatedType]]] {
+  final override protected lazy val validateValue = new PartialFunction[WomValue, ErrorOr[Option[ValidatedType]]] {
     override def isDefinedAt(womValue: WomValue): Boolean = validateOption.isDefinedAt(womValue)
 
-    override def apply(womValue: WomValue): Validated[NonEmptyList[String], Option[ValidatedType]] = {
+    override def apply(womValue: WomValue): Validated[NonEmptyList[String], Option[ValidatedType]] =
       validateOption.apply(womValue).map(Option.apply)
-    }
   }
 
-  override final protected lazy val validateNone: ErrorOr[None.type] = None.validNel[String]
+  final override protected lazy val validateNone: ErrorOr[None.type] = None.validNel[String]
 }
diff --git a/backend/src/main/scala/cromwell/backend/validation/ValidatedRuntimeAttributesBuilder.scala b/backend/src/main/scala/cromwell/backend/validation/ValidatedRuntimeAttributesBuilder.scala
index 6e199c4c4fe..d1a6af6f58d 100644
--- a/backend/src/main/scala/cromwell/backend/validation/ValidatedRuntimeAttributesBuilder.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/ValidatedRuntimeAttributesBuilder.scala
@@ -38,18 +38,14 @@ trait ValidatedRuntimeAttributesBuilder {
   /**
     * Returns validators suitable for BackendWorkflowInitializationActor.runtimeAttributeValidators.
     */
-  final lazy val validatorMap: Map[String, Option[WomExpression] => Boolean] = {
-    validations.map(validation =>
-      validation.key -> validation.validateOptionalWomExpression _
-    ).toMap
-  }
+  final lazy val validatorMap: Map[String, Option[WomExpression] => Boolean] =
+    validations.map(validation => validation.key -> validation.validateOptionalWomExpression _).toMap
 
   /**
     * Returns a map of coercions suitable for RuntimeAttributesDefault.workflowOptionsDefault.
     */
-  final lazy val coercionMap: Map[String, Iterable[WomType]] = {
+  final lazy val coercionMap: Map[String, Iterable[WomType]] =
     validations.map(validation => validation.key -> validation.coercion).toMap
-  }
 
   def unsupportedKeys(keys: Seq[String]): Seq[String] = keys.diff(validationKeys)
 
@@ -61,11 +57,12 @@ trait ValidatedRuntimeAttributesBuilder {
     val runtimeAttributesErrorOr: ErrorOr[ValidatedRuntimeAttributes] = validate(attrs)
     runtimeAttributesErrorOr match {
       case Valid(runtimeAttributes) => runtimeAttributes
-      case Invalid(nel) => throw new RuntimeException with MessageAggregation with NoStackTrace {
-        override def exceptionContext: String = "Runtime attribute validation failed"
+      case Invalid(nel) =>
+        throw new RuntimeException with MessageAggregation with NoStackTrace {
+          override def exceptionContext: String = "Runtime attribute validation failed"
 
-        override def errorMessages: Iterable[String] = nel.toList
-      }
+          override def errorMessages: Iterable[String] = nel.toList
+        }
     }
   }
 
@@ -73,8 +70,8 @@ trait ValidatedRuntimeAttributesBuilder {
     val listOfKeysToErrorOrAnys: List[(String, ErrorOr[Any])] =
       validations.map(validation => validation.key -> validation.validate(values)).toList
 
-    val listOfErrorOrKeysToAnys: List[ErrorOr[(String, Any)]] = listOfKeysToErrorOrAnys map {
-      case (key, errorOrAny) => errorOrAny map { any => (key, any) }
+    val listOfErrorOrKeysToAnys: List[ErrorOr[(String, Any)]] = listOfKeysToErrorOrAnys map { case (key, errorOrAny) =>
+      errorOrAny map { any => (key, any) }
     }
 
     import cats.syntax.traverse._
diff --git a/backend/src/main/scala/cromwell/backend/validation/exception/ValidationAggregatedException.scala b/backend/src/main/scala/cromwell/backend/validation/exception/ValidationAggregatedException.scala
index ec3644674bb..325060aa4f6 100644
--- a/backend/src/main/scala/cromwell/backend/validation/exception/ValidationAggregatedException.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/exception/ValidationAggregatedException.scala
@@ -3,4 +3,5 @@ package cromwell.backend.validation.exception
 import common.exception.MessageAggregation
 
 case class ValidationAggregatedException(override val exceptionContext: String,
-                                         override val errorMessages: Iterable[String]) extends MessageAggregation
+                                         override val errorMessages: Iterable[String]
+) extends MessageAggregation
diff --git a/backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowPathBuilder.scala b/backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowPathBuilder.scala
index 43af11d8732..c112b8d5b6b 100644
--- a/backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowPathBuilder.scala
+++ b/backend/src/main/scala/cromwell/backend/wfs/DefaultWorkflowPathBuilder.scala
@@ -2,7 +2,6 @@ package cromwell.backend.wfs
 
 import cromwell.core.path.DefaultPathBuilder
 
-
 object DefaultWorkflowPathBuilder extends WorkflowPathBuilder {
   override def pathBuilderOption(params: WorkflowFileSystemProviderParams) = Option(DefaultPathBuilder)
 }
diff --git a/backend/src/main/scala/cromwell/backend/wfs/WorkflowPathBuilder.scala b/backend/src/main/scala/cromwell/backend/wfs/WorkflowPathBuilder.scala
index bd39ae2c911..c15ac945c12 100644
--- a/backend/src/main/scala/cromwell/backend/wfs/WorkflowPathBuilder.scala
+++ b/backend/src/main/scala/cromwell/backend/wfs/WorkflowPathBuilder.scala
@@ -1,7 +1,7 @@
 package cromwell.backend.wfs
 
 import com.typesafe.config.Config
-import cromwell.backend.io.{WorkflowPathsWithDocker, WorkflowPaths}
+import cromwell.backend.io.{WorkflowPaths, WorkflowPathsWithDocker}
 import cromwell.backend.{BackendConfigurationDescriptor, BackendWorkflowDescriptor}
 import cromwell.core.WorkflowOptions
 import cromwell.core.path.PathBuilder
@@ -11,14 +11,16 @@ import scala.concurrent.ExecutionContext
 object WorkflowPathBuilder {
   def workflowPaths(configurationDescriptor: BackendConfigurationDescriptor,
                     workflowDescriptor: BackendWorkflowDescriptor,
-                    pathBuilders: List[PathBuilder]): WorkflowPaths = {
+                    pathBuilders: List[PathBuilder]
+  ): WorkflowPaths =
     new WorkflowPathsWithDocker(workflowDescriptor, configurationDescriptor.backendConfig, pathBuilders)
-  }
 }
 
-final case class WorkflowFileSystemProviderParams(fileSystemConfig: Config, globalConfig: Config,
+final case class WorkflowFileSystemProviderParams(fileSystemConfig: Config,
+                                                  globalConfig: Config,
                                                   workflowOptions: WorkflowOptions,
-                                                  fileSystemExecutionContext: ExecutionContext)
+                                                  fileSystemExecutionContext: ExecutionContext
+)
 
 trait WorkflowPathBuilder {
   def pathBuilderOption(params: WorkflowFileSystemProviderParams): Option[PathBuilder]
diff --git a/backend/src/test/scala/cromwell/backend/BackendSpec.scala b/backend/src/test/scala/cromwell/backend/BackendSpec.scala
index 6c4c7a654e5..835abec8eb3 100644
--- a/backend/src/test/scala/cromwell/backend/BackendSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/BackendSpec.scala
@@ -3,7 +3,12 @@ package cromwell.backend
 import _root_.wdl.draft2.model._
 import _root_.wdl.transforms.draft2.wdlom2wom.WdlDraft2WomExecutableMakers._
 import common.exception.AggregatedException
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, JobFailedNonRetryableResponse, JobFailedRetryableResponse, JobSucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{
+  BackendJobExecutionResponse,
+  JobFailedNonRetryableResponse,
+  JobFailedRetryableResponse,
+  JobSucceededResponse
+}
 import cromwell.backend.io.TestWorkflows._
 import cromwell.core.callcaching.NoDocker
 import cromwell.core.labels.Labels
@@ -25,18 +30,17 @@ trait BackendSpec extends ScalaFutures with Matchers with ScaledTimeSpans {
   implicit val defaultPatience: PatienceConfig =
     PatienceConfig(timeout = scaled(Span(10, Seconds)), interval = Span(500, Millis))
 
-  def testWorkflow(workflow: TestWorkflow,
-                   backend: BackendJobExecutionActor): Unit = {
+  def testWorkflow(workflow: TestWorkflow, backend: BackendJobExecutionActor): Unit =
     executeJobAndAssertOutputs(backend, workflow.expectedResponse)
-  }
 
   def buildWorkflowDescriptor(workflowSource: WorkflowSource,
                               inputFileAsJson: Option[String],
                               options: WorkflowOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue])),
                               runtime: String = "",
-                              labels: Labels = Labels.empty): BackendWorkflowDescriptor = {
-    val wdlNamespace = WdlNamespaceWithWorkflow.load(workflowSource.replaceAll("RUNTIME", runtime),
-      Seq.empty[Draft2ImportResolver]).get
+                              labels: Labels = Labels.empty
+  ): BackendWorkflowDescriptor = {
+    val wdlNamespace =
+      WdlNamespaceWithWorkflow.load(workflowSource.replaceAll("RUNTIME", runtime), Seq.empty[Draft2ImportResolver]).get
     val executable = wdlNamespace.toWomExecutable(inputFileAsJson, NoIoFunctionSet, strictValidation = true) match {
       case Left(errors) => fail(s"Fail to build wom executable: ${errors.toList.mkString(", ")}")
       case Right(e) => e
@@ -45,7 +49,7 @@ trait BackendSpec extends ScalaFutures with Matchers with ScaledTimeSpans {
     BackendWorkflowDescriptor(
       WorkflowId.randomId(),
       executable.entryPoint,
-      executable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }}),
+      executable.resolvedExecutableInputs.flatMap { case (port, v) => v.select[WomValue] map { port -> _ } },
       options,
       labels,
       HogGroup("foo"),
@@ -55,68 +59,84 @@ trait BackendSpec extends ScalaFutures with Matchers with ScaledTimeSpans {
   }
 
   def buildWdlWorkflowDescriptor(workflowSource: WorkflowSource,
-                              inputFileAsJson: Option[String] = None,
-                              options: WorkflowOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue])),
-                              runtime: String = "",
-                              labels: Labels = Labels.empty): BackendWorkflowDescriptor = {
-
+                                 inputFileAsJson: Option[String] = None,
+                                 options: WorkflowOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue])),
+                                 runtime: String = "",
+                                 labels: Labels = Labels.empty
+  ): BackendWorkflowDescriptor =
     buildWorkflowDescriptor(workflowSource, inputFileAsJson, options, runtime, labels)
-  }
 
-  def fqnWdlMapToDeclarationMap(m: Map[String, WomValue]): Map[InputDefinition, WomValue] = {
-    m map {
-      case (fqn, v) =>
-        val mockDeclaration = RequiredInputDefinition(fqn, v.womType)
-        mockDeclaration -> v
+  def fqnWdlMapToDeclarationMap(m: Map[String, WomValue]): Map[InputDefinition, WomValue] =
+    m map { case (fqn, v) =>
+      val mockDeclaration = RequiredInputDefinition(fqn, v.womType)
+      mockDeclaration -> v
     }
-  }
 
-  def fqnMapToDeclarationMap(m: Map[OutputPort, WomValue]): Map[InputDefinition, WomValue] = {
-    m map {
-      case (outputPort, womValue) => RequiredInputDefinition(outputPort.name, womValue.womType) -> womValue
+  def fqnMapToDeclarationMap(m: Map[OutputPort, WomValue]): Map[InputDefinition, WomValue] =
+    m map { case (outputPort, womValue) =>
+      RequiredInputDefinition(outputPort.name, womValue.womType) -> womValue
     }
-  }
 
   def jobDescriptorFromSingleCallWorkflow(workflowDescriptor: BackendWorkflowDescriptor,
                                           inputs: Map[String, WomValue],
                                           options: WorkflowOptions,
-                                          runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition]): BackendJobDescriptor = {
-    val call = workflowDescriptor.callable.graph.nodes.collectFirst({ case t: CommandCallNode => t}).get
+                                          runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition]
+  ): BackendJobDescriptor = {
+    val call = workflowDescriptor.callable.graph.nodes.collectFirst { case t: CommandCallNode => t }.get
     val jobKey = BackendJobDescriptorKey(call, None, 1)
 
     val inputDeclarations: Map[InputDefinition, WomValue] = call.inputDefinitionMappings.map {
-      case (inputDef, resolved) => inputDef ->
-        resolved.select[WomValue].orElse(
-          resolved.select[WomExpression]
-            .map(
-              _.evaluateValue(inputs, NoIoFunctionSet).getOrElse(fail("Can't evaluate input"))
+      case (inputDef, resolved) =>
+        inputDef ->
+          resolved
+            .select[WomValue]
+            .orElse(
+              resolved
+                .select[WomExpression]
+                .map(
+                  _.evaluateValue(inputs, NoIoFunctionSet).getOrElse(fail("Can't evaluate input"))
+                )
             )
-        ).orElse(
-          resolved.select[OutputPort] flatMap {
-            case known if workflowDescriptor.knownValues.contains(known) => Option(workflowDescriptor.knownValues(known))
-            case hasDefault if hasDefault.graphNode.isInstanceOf[OptionalGraphInputNodeWithDefault] =>
-              Option(hasDefault.graphNode.asInstanceOf[OptionalGraphInputNodeWithDefault].default
-                .evaluateValue(inputs, NoIoFunctionSet).getOrElse(fail("Can't evaluate input")))
-            case _ => None
-          }
-        ).getOrElse {
-          inputs(inputDef.name)
-        }
+            .orElse(
+              resolved.select[OutputPort] flatMap {
+                case known if workflowDescriptor.knownValues.contains(known) =>
+                  Option(workflowDescriptor.knownValues(known))
+                case hasDefault if hasDefault.graphNode.isInstanceOf[OptionalGraphInputNodeWithDefault] =>
+                  Option(
+                    hasDefault.graphNode
+                      .asInstanceOf[OptionalGraphInputNodeWithDefault]
+                      .default
+                      .evaluateValue(inputs, NoIoFunctionSet)
+                      .getOrElse(fail("Can't evaluate input"))
+                  )
+                case _ => None
+              }
+            )
+            .getOrElse {
+              inputs(inputDef.name)
+            }
     }.toMap
-    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(call.callable.runtimeAttributes, NoIoFunctionSet, Map.empty).getOrElse(fail("Failed to evaluate runtime attributes")) // .get is OK here because this is a test
-    val runtimeAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, options)(evaluatedAttributes)
+    val evaluatedAttributes = RuntimeAttributeDefinition
+      .evaluateRuntimeAttributes(call.callable.runtimeAttributes, NoIoFunctionSet, Map.empty)
+      .getOrElse(fail("Failed to evaluate runtime attributes")) // .get is OK here because this is a test
+    val runtimeAttributes =
+      RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, options)(evaluatedAttributes)
     BackendJobDescriptor(workflowDescriptor, jobKey, runtimeAttributes, inputDeclarations, NoDocker, None, Map.empty)
   }
 
   def jobDescriptorFromSingleCallWorkflow(wdl: WorkflowSource,
                                           options: WorkflowOptions,
-                                          runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition]): BackendJobDescriptor = {
+                                          runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition]
+  ): BackendJobDescriptor = {
     val workflowDescriptor = buildWdlWorkflowDescriptor(wdl)
-    val call = workflowDescriptor.callable.graph.nodes.collectFirst({ case t: CommandCallNode => t}).get
+    val call = workflowDescriptor.callable.graph.nodes.collectFirst { case t: CommandCallNode => t }.get
     val jobKey = BackendJobDescriptorKey(call, None, 1)
     val inputDeclarations = fqnMapToDeclarationMap(workflowDescriptor.knownValues)
-    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(call.callable.runtimeAttributes, NoIoFunctionSet, inputDeclarations).getOrElse(fail("Failed to evaluate runtime attributes")) // .get is OK here because this is a test
-    val runtimeAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, options)(evaluatedAttributes)
+    val evaluatedAttributes = RuntimeAttributeDefinition
+      .evaluateRuntimeAttributes(call.callable.runtimeAttributes, NoIoFunctionSet, inputDeclarations)
+      .getOrElse(fail("Failed to evaluate runtime attributes")) // .get is OK here because this is a test
+    val runtimeAttributes =
+      RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, options)(evaluatedAttributes)
     BackendJobDescriptor(workflowDescriptor, jobKey, runtimeAttributes, inputDeclarations, NoDocker, None, Map.empty)
   }
 
@@ -124,25 +144,33 @@ trait BackendSpec extends ScalaFutures with Matchers with ScaledTimeSpans {
                                           runtime: String,
                                           attempt: Int,
                                           options: WorkflowOptions,
-                                          runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition]): BackendJobDescriptor = {
+                                          runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition]
+  ): BackendJobDescriptor = {
     val workflowDescriptor = buildWdlWorkflowDescriptor(wdl, runtime = runtime)
-    val call = workflowDescriptor.callable.graph.nodes.collectFirst({ case t: CommandCallNode => t}).get
+    val call = workflowDescriptor.callable.graph.nodes.collectFirst { case t: CommandCallNode => t }.get
     val jobKey = BackendJobDescriptorKey(call, None, attempt)
     val inputDeclarations = fqnMapToDeclarationMap(workflowDescriptor.knownValues)
-    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(call.callable.runtimeAttributes, NoIoFunctionSet, inputDeclarations).getOrElse(fail("Failed to evaluate runtime attributes")) // .get is OK here because this is a test
-    val runtimeAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, options)(evaluatedAttributes)
+    val evaluatedAttributes = RuntimeAttributeDefinition
+      .evaluateRuntimeAttributes(call.callable.runtimeAttributes, NoIoFunctionSet, inputDeclarations)
+      .getOrElse(fail("Failed to evaluate runtime attributes")) // .get is OK here because this is a test
+    val runtimeAttributes =
+      RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, options)(evaluatedAttributes)
     BackendJobDescriptor(workflowDescriptor, jobKey, runtimeAttributes, inputDeclarations, NoDocker, None, Map.empty)
   }
 
   def assertResponse(executionResponse: BackendJobExecutionResponse,
-                     expectedResponse: BackendJobExecutionResponse): Unit = {
+                     expectedResponse: BackendJobExecutionResponse
+  ): Unit = {
     (executionResponse, expectedResponse) match {
-      case (JobSucceededResponse(_, _, responseOutputs, _, _, _, _), JobSucceededResponse(_, _, expectedOutputs, _, _, _, _)) =>
+      case (JobSucceededResponse(_, _, responseOutputs, _, _, _, _),
+            JobSucceededResponse(_, _, expectedOutputs, _, _, _, _)
+          ) =>
         responseOutputs.outputs.size shouldBe expectedOutputs.outputs.size
-        responseOutputs.outputs foreach {
-          case (fqn, out) =>
-            val expectedOut = expectedOutputs.outputs.collectFirst({case (p, v) if p.name == fqn.name => v})
-            expectedOut.getOrElse(fail(s"Output ${fqn.name} not found in ${expectedOutputs.outputs.map(_._1.name)}")).valueString shouldBe out.valueString
+        responseOutputs.outputs foreach { case (fqn, out) =>
+          val expectedOut = expectedOutputs.outputs.collectFirst { case (p, v) if p.name == fqn.name => v }
+          expectedOut
+            .getOrElse(fail(s"Output ${fqn.name} not found in ${expectedOutputs.outputs.map(_._1.name)}"))
+            .valueString shouldBe out.valueString
         }
       case (JobFailedNonRetryableResponse(_, failure, _), JobFailedNonRetryableResponse(_, expectedFailure, _)) =>
         failure.getClass shouldBe expectedFailure.getClass
@@ -157,19 +185,20 @@ trait BackendSpec extends ScalaFutures with Matchers with ScaledTimeSpans {
 
   private def concatenateCauseMessages(t: Throwable): String = t match {
     case null => ""
-    case ae: AggregatedException => ae.getMessage + " " + ae.throwables.map(innerT => concatenateCauseMessages(innerT.getCause)).mkString("\n")
+    case ae: AggregatedException =>
+      ae.getMessage + " " + ae.throwables.map(innerT => concatenateCauseMessages(innerT.getCause)).mkString("\n")
     case other: Throwable => other.getMessage + concatenateCauseMessages(t.getCause)
   }
 
   def executeJobAndAssertOutputs(backend: BackendJobExecutionActor,
-                                 expectedResponse: BackendJobExecutionResponse): Unit = {
+                                 expectedResponse: BackendJobExecutionResponse
+  ): Unit =
     whenReady(backend.execute) { executionResponse =>
       assertResponse(executionResponse, expectedResponse)
     }
-  }
 
   def firstJobDescriptorKey(workflowDescriptor: BackendWorkflowDescriptor): BackendJobDescriptorKey = {
-    val call = workflowDescriptor.callable.graph.nodes.collectFirst({ case t: CommandCallNode => t}).get
+    val call = workflowDescriptor.callable.graph.nodes.collectFirst { case t: CommandCallNode => t }.get
     BackendJobDescriptorKey(call, None, 1)
   }
 }
diff --git a/backend/src/test/scala/cromwell/backend/BackendWorkflowInitializationActorSpec.scala b/backend/src/test/scala/cromwell/backend/BackendWorkflowInitializationActorSpec.scala
index 55772d1de90..4fc1efd7381 100644
--- a/backend/src/test/scala/cromwell/backend/BackendWorkflowInitializationActorSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/BackendWorkflowInitializationActorSpec.scala
@@ -19,23 +19,23 @@ import wom.values._
 import scala.concurrent.Future
 import scala.util.Try
 
-
-class BackendWorkflowInitializationActorSpec extends TestKitSuite
-  with AnyFlatSpecLike with Matchers with TableDrivenPropertyChecks {
+class BackendWorkflowInitializationActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with TableDrivenPropertyChecks {
 
   behavior of "BackendWorkflowInitializationActorSpec"
 
-  val testPredicateBackendWorkflowInitializationActorRef:
-    TestActorRef[TestPredicateBackendWorkflowInitializationActor] =
+  val testPredicateBackendWorkflowInitializationActorRef
+    : TestActorRef[TestPredicateBackendWorkflowInitializationActor] =
     TestActorRef[TestPredicateBackendWorkflowInitializationActor]
 
-  val testPredicateBackendWorkflowInitializationActor:
-    TestPredicateBackendWorkflowInitializationActor =
+  val testPredicateBackendWorkflowInitializationActor: TestPredicateBackendWorkflowInitializationActor =
     testPredicateBackendWorkflowInitializationActorRef.underlyingActor
 
-  val testContinueOnReturnCode: Option[WomValue] => Boolean = {
+  val testContinueOnReturnCode: Option[WomValue] => Boolean =
     testPredicateBackendWorkflowInitializationActor.continueOnReturnCodePredicate(valueRequired = false)
-  }
 
   val optionalConfig: Option[Config] = Option(TestConfig.optionalRuntimeConfig)
 
@@ -66,18 +66,22 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       "womValue",
       WomString(""),
       WomString("z"),
-      WomFloat(0.0D),
+      WomFloat(0.0d),
       WomArray(WomArrayType(WomBooleanType), Seq(WomBoolean(true))),
-      WomArray(WomArrayType(WomFloatType), Seq(WomFloat(0.0D)))
+      WomArray(WomArrayType(WomFloatType), Seq(WomFloat(0.0d)))
     )
 
     forAll(booleanRows) { value =>
       val womValue = WomBoolean(value)
       val result = true
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       val valid =
-        ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
+        ContinueOnReturnCodeValidation
+          .default(optionalConfig)
+          .validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
       valid.toEither.toOption.get should be(ContinueOnReturnCodeFlag(value))
     }
@@ -86,9 +90,13 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val womValue = WomString(value.toString)
       val result = true
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       val valid =
-        ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
+        ContinueOnReturnCodeValidation
+          .default(optionalConfig)
+          .validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
       valid.toEither.toOption.get should be(ContinueOnReturnCodeFlag(value))
     }
@@ -97,7 +105,9 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val womValue = WdlExpression.fromString(value.toString)
       val result = true
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       // NOTE: expressions are never valid to validate
     }
 
@@ -105,9 +115,13 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val womValue = WomInteger(value)
       val result = true
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       val valid =
-        ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
+        ContinueOnReturnCodeValidation
+          .default(optionalConfig)
+          .validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
       valid.toEither.toOption.get should be(ContinueOnReturnCodeSet(Set(value)))
     }
@@ -116,9 +130,13 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val womValue = WomString(value.toString)
       val result = true
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       val valid =
-        ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
+        ContinueOnReturnCodeValidation
+          .default(optionalConfig)
+          .validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
       valid.toEither.toOption.get should be(ContinueOnReturnCodeSet(Set(value)))
     }
@@ -127,7 +145,9 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val womValue = WdlExpression.fromString(value.toString)
       val result = true
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       // NOTE: expressions are never valid to validate
     }
 
@@ -135,9 +155,13 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val womValue = WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(value)))
       val result = true
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       val valid =
-        ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
+        ContinueOnReturnCodeValidation
+          .default(optionalConfig)
+          .validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
       valid.toEither.toOption.get should be(ContinueOnReturnCodeSet(Set(value)))
     }
@@ -146,9 +170,13 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val womValue = WomArray(WomArrayType(WomStringType), Seq(WomString(value.toString)))
       val result = true
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       val valid =
-        ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
+        ContinueOnReturnCodeValidation
+          .default(optionalConfig)
+          .validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
       valid.toEither.toOption.get should be(ContinueOnReturnCodeSet(Set(value)))
     }
@@ -157,7 +185,9 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val womValue = WomArray(WomArrayType(WdlExpressionType), Seq(WdlExpression.fromString(value.toString)))
       val result = false
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       // NOTE: expressions are never valid to validate
     }
 
@@ -165,16 +195,22 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val womValue = WdlExpression.fromString(expression)
       val result = true
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       // NOTE: expressions are never valid to validate
     }
 
     forAll(invalidWdlValueRows) { womValue =>
       val result = false
       testContinueOnReturnCode(Option(womValue)) should be(result)
-      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
       val valid =
-        ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
+        ContinueOnReturnCodeValidation
+          .default(optionalConfig)
+          .validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
       valid.toEither.swap.toOption.get.toList should contain theSameElementsAs List(
         "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
@@ -197,17 +233,18 @@ class TestPredicateBackendWorkflowInitializationActor extends BackendWorkflowIni
   override protected def coerceDefaultRuntimeAttributes(options: WorkflowOptions): Try[Map[String, WomValue]] =
     throw new UnsupportedOperationException("coerceDefaultRuntimeAttributes")
 
-  override def beforeAll(): Future[Option[BackendInitializationData]] = throw new UnsupportedOperationException("beforeAll")
+  override def beforeAll(): Future[Option[BackendInitializationData]] = throw new UnsupportedOperationException(
+    "beforeAll"
+  )
 
   override def validate(): Future[Unit] = throw new UnsupportedOperationException("validate")
 
   override protected def workflowDescriptor: BackendWorkflowDescriptor =
     throw new UnsupportedOperationException("workflowDescriptor")
 
-  override protected def configurationDescriptor: BackendConfigurationDescriptor = BackendConfigurationDescriptor(TestConfig.sampleBackendRuntimeConfig, ConfigFactory.empty())
+  override protected def configurationDescriptor: BackendConfigurationDescriptor =
+    BackendConfigurationDescriptor(TestConfig.sampleBackendRuntimeConfig, ConfigFactory.empty())
 
-  override def continueOnReturnCodePredicate(valueRequired: Boolean)
-                                            (wdlExpressionMaybe: Option[WomValue]): Boolean = {
+  override def continueOnReturnCodePredicate(valueRequired: Boolean)(wdlExpressionMaybe: Option[WomValue]): Boolean =
     super.continueOnReturnCodePredicate(valueRequired)(wdlExpressionMaybe)
-  }
 }
diff --git a/backend/src/test/scala/cromwell/backend/MemorySizeSpec.scala b/backend/src/test/scala/cromwell/backend/MemorySizeSpec.scala
index ac3c591f5df..57acada06d3 100644
--- a/backend/src/test/scala/cromwell/backend/MemorySizeSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/MemorySizeSpec.scala
@@ -66,7 +66,7 @@ class MemorySizeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
       memorySize.to(newUnit) shouldEqual result
     }
   }
-  
+
   it should "round trip" in {
     List(
       "2 GB"
diff --git a/backend/src/test/scala/cromwell/backend/OutputEvaluatorSpec.scala b/backend/src/test/scala/cromwell/backend/OutputEvaluatorSpec.scala
index 0959f92577b..997fd6f5df5 100644
--- a/backend/src/test/scala/cromwell/backend/OutputEvaluatorSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/OutputEvaluatorSpec.scala
@@ -24,7 +24,7 @@ class OutputEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   behavior of "OutputEvaluator"
 
   private val FutureTimeout = 20.seconds
-  final implicit val blockingEc: ExecutionContextExecutor = ExecutionContext.fromExecutor(
+  implicit final val blockingEc: ExecutionContextExecutor = ExecutionContext.fromExecutor(
     Executors.newCachedThreadPool()
   )
 
@@ -32,50 +32,56 @@ class OutputEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   private def o1Expression = new WomExpression {
     override def sourceString: String = "o1"
     override def inputs: Set[String] = Set("input")
-    override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
+    override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] =
       Validated.fromOption(inputValues.get("input"), NonEmptyList.one("Can't find a value for 'input'"))
-    }
-    override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] = throw new UnsupportedOperationException
-    override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = throw new UnsupportedOperationException
+    override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] =
+      throw new UnsupportedOperationException
+    override def evaluateFiles(inputTypes: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               coerceTo: WomType
+    ): ErrorOr[Set[FileEvaluation]] = throw new UnsupportedOperationException
   }
 
   // Depends on a previous output
   private def o2Expression = new WomExpression {
     override def sourceString: String = "o2"
     override def inputs: Set[String] = Set("o1")
-    override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
+    override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] =
       Validated.fromOption(inputValues.get("o1"), NonEmptyList.one("Can't find a value for 'o1'"))
-    }
-    override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] = throw new UnsupportedOperationException
-    override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = throw new UnsupportedOperationException
+    override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] =
+      throw new UnsupportedOperationException
+    override def evaluateFiles(inputTypes: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               coerceTo: WomType
+    ): ErrorOr[Set[FileEvaluation]] = throw new UnsupportedOperationException
   }
 
   private def invalidWomExpression1 = new WomExpression {
     override def sourceString: String = "invalid1"
     override def inputs: Set[String] = Set.empty
-    override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
+    override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] =
       "Invalid expression 1".invalidNel
-    }
-    override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] = {
+    override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] =
       "Invalid expression 1".invalidNel
-    }
-    override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
+    override def evaluateFiles(inputTypes: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               coerceTo: WomType
+    ): ErrorOr[Set[FileEvaluation]] =
       "Invalid expression 1".invalidNel
-    }
   }
 
   private def invalidWomExpression2 = new WomExpression {
     override def sourceString: String = "invalid2"
     override def inputs: Set[String] = Set.empty
-    override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
+    override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] =
       "Invalid expression 2".invalidNel
-    }
-    override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] = {
+    override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] =
       "Invalid expression 2".invalidNel
-    }
-    override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
+    override def evaluateFiles(inputTypes: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               coerceTo: WomType
+    ): ErrorOr[Set[FileEvaluation]] =
       "Invalid expression 2".invalidNel
-    }
   }
 
   val exception = new Exception("Expression evaluation exception")
@@ -83,15 +89,15 @@ class OutputEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   private def throwingWomExpression = new WomExpression {
     override def sourceString: String = "throwing"
     override def inputs: Set[String] = Set.empty
-    override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
+    override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] =
       throw exception
-    }
-    override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] = {
+    override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] =
       throw exception
-    }
-    override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
+    override def evaluateFiles(inputTypes: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               coerceTo: WomType
+    ): ErrorOr[Set[FileEvaluation]] =
       throw exception
-    }
   }
 
   val mockInputs: Map[InputDefinition, WomValue] = Map(
@@ -99,7 +105,7 @@ class OutputEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   )
 
   it should "evaluate valid jobs outputs" in {
-    val mockOutputs = List (
+    val mockOutputs = List(
       OutputDefinition("o1", WomIntegerType, o1Expression),
       OutputDefinition("o2", WomIntegerType, o2Expression)
     )
@@ -109,16 +115,19 @@ class OutputEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     val jobDescriptor = BackendJobDescriptor(null, key, null, mockInputs, null, None, null)
 
     Await.result(OutputEvaluator.evaluateOutputs(jobDescriptor, NoIoFunctionSet), FutureTimeout) match {
-      case ValidJobOutputs(outputs) => outputs shouldBe CallOutputs(Map(
-        jobDescriptor.taskCall.outputPorts.find(_.name == "o1").get -> WomInteger(5),
-        jobDescriptor.taskCall.outputPorts.find(_.name == "o2").get -> WomInteger(5)
-      ))
+      case ValidJobOutputs(outputs) =>
+        outputs shouldBe CallOutputs(
+          Map(
+            jobDescriptor.taskCall.outputPorts.find(_.name == "o1").get -> WomInteger(5),
+            jobDescriptor.taskCall.outputPorts.find(_.name == "o2").get -> WomInteger(5)
+          )
+        )
       case _ => fail("Failed to evaluate outputs")
     }
   }
 
   it should "return an InvalidJobOutputs if the evaluation returns ErrorOrs" in {
-    val mockOutputs = List (
+    val mockOutputs = List(
       OutputDefinition("o1", WomIntegerType, o1Expression),
       OutputDefinition("invalid1", WomIntegerType, invalidWomExpression1),
       OutputDefinition("invalid2", WomIntegerType, invalidWomExpression2)
@@ -129,15 +138,17 @@ class OutputEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     val jobDescriptor = BackendJobDescriptor(null, key, null, mockInputs, null, None, null)
 
     Await.result(OutputEvaluator.evaluateOutputs(jobDescriptor, NoIoFunctionSet), FutureTimeout) match {
-      case InvalidJobOutputs(errors) => errors shouldBe NonEmptyList.of(
-        "Bad output 'invalid1': Invalid expression 1", "Bad output 'invalid2': Invalid expression 2"
-      )
+      case InvalidJobOutputs(errors) =>
+        errors shouldBe NonEmptyList.of(
+          "Bad output 'invalid1': Invalid expression 1",
+          "Bad output 'invalid2': Invalid expression 2"
+        )
       case _ => fail("Output evaluation should have failed")
     }
   }
 
   it should "return an JobOutputsEvaluationException if the evaluation throws an exception" in {
-    val mockOutputs = List (
+    val mockOutputs = List(
       OutputDefinition("o1", WomIntegerType, o1Expression),
       OutputDefinition("invalid1", WomIntegerType, throwingWomExpression)
     )
diff --git a/backend/src/test/scala/cromwell/backend/RuntimeAttributeValidationSpec.scala b/backend/src/test/scala/cromwell/backend/RuntimeAttributeValidationSpec.scala
index 99bec0baebd..91b6ab06617 100644
--- a/backend/src/test/scala/cromwell/backend/RuntimeAttributeValidationSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/RuntimeAttributeValidationSpec.scala
@@ -19,12 +19,14 @@ class RuntimeAttributeValidationSpec extends AnyFlatSpec with Matchers with Scal
       val defaultValue = womValue.asWomExpression
       val validator: Option[WomExpression] => Boolean = _.contains(defaultValue)
       assert(
-        BackendWorkflowInitializationActor.validateRuntimeAttributes(
-          taskName = taskName,
-          defaultRuntimeAttributes = defaultRuntimeAttributes,
-          runtimeAttributes = Map.empty,
-          runtimeAttributeValidators = Map((attributeName, validator)),
-        ).isValid
+        BackendWorkflowInitializationActor
+          .validateRuntimeAttributes(
+            taskName = taskName,
+            defaultRuntimeAttributes = defaultRuntimeAttributes,
+            runtimeAttributes = Map.empty,
+            runtimeAttributeValidators = Map((attributeName, validator))
+          )
+          .isValid
       )
   }
 
@@ -33,12 +35,14 @@ class RuntimeAttributeValidationSpec extends AnyFlatSpec with Matchers with Scal
       val defaultRuntimeAttributes = Map(attributeName -> womValue)
 
       assert(
-        BackendWorkflowInitializationActor.validateRuntimeAttributes(
-          taskName = taskName,
-          defaultRuntimeAttributes = defaultRuntimeAttributes,
-          runtimeAttributes = Map.empty,
-          runtimeAttributeValidators = Map((attributeName, (_: Option[WomExpression]) => false)),
-        ).isInvalid
+        BackendWorkflowInitializationActor
+          .validateRuntimeAttributes(
+            taskName = taskName,
+            defaultRuntimeAttributes = defaultRuntimeAttributes,
+            runtimeAttributes = Map.empty,
+            runtimeAttributeValidators = Map((attributeName, (_: Option[WomExpression]) => false))
+          )
+          .isInvalid
       )
   }
 
@@ -49,47 +53,51 @@ class RuntimeAttributeValidationSpec extends AnyFlatSpec with Matchers with Scal
 
       val validator: Option[WomExpression] => Boolean = _.contains(runtimeWomExpression)
       assert(
-        BackendWorkflowInitializationActor.validateRuntimeAttributes(
-          taskName = taskName,
-          defaultRuntimeAttributes = defaultRuntimeAttributes,
-          runtimeAttributes = runtimeAttributes,
-          runtimeAttributeValidators = Map((attributeName, validator)),
-        ).isValid
+        BackendWorkflowInitializationActor
+          .validateRuntimeAttributes(
+            taskName = taskName,
+            defaultRuntimeAttributes = defaultRuntimeAttributes,
+            runtimeAttributes = runtimeAttributes,
+            runtimeAttributeValidators = Map((attributeName, validator))
+          )
+          .isValid
       )
   }
 
   it should "fail validation if no setting is present but it should be" in forAll {
     (taskName: String, attributeName: String) =>
-
       val validator: Option[WomExpression] => Boolean = {
         case None => false
         case Some(x) => throw new RuntimeException(s"expecting the runtime validator to receive a None but got $x")
       }
       assert(
-       BackendWorkflowInitializationActor.validateRuntimeAttributes(
-         taskName = taskName,
-         defaultRuntimeAttributes = Map.empty,
-         runtimeAttributes = Map.empty,
-         runtimeAttributeValidators = Map((attributeName, validator)),
-       ).isInvalid
+        BackendWorkflowInitializationActor
+          .validateRuntimeAttributes(
+            taskName = taskName,
+            defaultRuntimeAttributes = Map.empty,
+            runtimeAttributes = Map.empty,
+            runtimeAttributeValidators = Map((attributeName, validator))
+          )
+          .isInvalid
       )
   }
 
   it should "use the taskName and attribute name in correct places for failures" in forAll {
     (taskName: String, attributeName: String) =>
-
       val validator: Option[WomExpression] => Boolean = {
         case None => false
         case Some(x) => throw new RuntimeException(s"expecting the runtime validator to receive a None but got $x")
       }
-      BackendWorkflowInitializationActor.validateRuntimeAttributes(taskName, Map.empty, Map.empty, Map((attributeName,validator))).fold(
-        { errors =>
-          val error = errors.toList.head
-          withClue("attribute name should be set correctly")(error.runtimeAttributeName shouldBe attributeName)
-          withClue("task name should be set correctly")(error.jobTag shouldBe taskName)
-        },
-        _ => fail("expecting validation to fail!")
-      )
+      BackendWorkflowInitializationActor
+        .validateRuntimeAttributes(taskName, Map.empty, Map.empty, Map((attributeName, validator)))
+        .fold(
+          { errors =>
+            val error = errors.toList.head
+            withClue("attribute name should be set correctly")(error.runtimeAttributeName shouldBe attributeName)
+            withClue("task name should be set correctly")(error.jobTag shouldBe taskName)
+          },
+          _ => fail("expecting validation to fail!")
+        )
   }
 }
 
diff --git a/backend/src/test/scala/cromwell/backend/TestConfig.scala b/backend/src/test/scala/cromwell/backend/TestConfig.scala
index 42050dbe323..82e81818d13 100644
--- a/backend/src/test/scala/cromwell/backend/TestConfig.scala
+++ b/backend/src/test/scala/cromwell/backend/TestConfig.scala
@@ -30,7 +30,8 @@ object TestConfig {
 
   lazy val sampleBackendRuntimeConfig = ConfigFactory.parseString(sampleBackendRuntimeConfigString)
 
-  lazy val allRuntimeAttrsConfig = ConfigFactory.parseString(allBackendRuntimeAttrsString).getConfig("default-runtime-attributes")
+  lazy val allRuntimeAttrsConfig =
+    ConfigFactory.parseString(allBackendRuntimeAttrsString).getConfig("default-runtime-attributes")
 
   lazy val optionalRuntimeConfig = sampleBackendRuntimeConfig.getConfig("default-runtime-attributes")
 
diff --git a/backend/src/test/scala/cromwell/backend/io/DirectoryFunctionsSpec.scala b/backend/src/test/scala/cromwell/backend/io/DirectoryFunctionsSpec.scala
index 1a8a101acf8..94a5b00627c 100644
--- a/backend/src/test/scala/cromwell/backend/io/DirectoryFunctionsSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/io/DirectoryFunctionsSpec.scala
@@ -18,10 +18,11 @@ class DirectoryFunctionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
     override def copyFile(source: String, destination: String) = throw new UnsupportedOperationException()
     override def glob(pattern: String) = throw new UnsupportedOperationException()
     override def size(path: String) = throw new UnsupportedOperationException()
-    override def readFile(path: String, maxBytes: Option[Int], failOnOverflow: Boolean)  = throw new UnsupportedOperationException()
+    override def readFile(path: String, maxBytes: Option[Int], failOnOverflow: Boolean) =
+      throw new UnsupportedOperationException()
     override def pathFunctions = throw new UnsupportedOperationException()
     override def writeFile(path: String, content: String) = throw new UnsupportedOperationException()
-    override implicit def ec = throw new UnsupportedOperationException()
+    implicit override def ec = throw new UnsupportedOperationException()
     override def createTemporaryDirectory(name: Option[String]) = throw new UnsupportedOperationException()
     override def asyncIo = throw new UnsupportedOperationException()
   }
@@ -32,13 +33,12 @@ class DirectoryFunctionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
     val innerDir = (rootDir / "innerDir").createDirectories()
     val link = innerDir / "linkToRootDirInInnerDir"
     link.symbolicLinkTo(rootDir)
-    
-    def listRecursively(path: String)(visited: Vector[String] = Vector.empty): Iterator[String] = {
+
+    def listRecursively(path: String)(visited: Vector[String] = Vector.empty): Iterator[String] =
       Await.result(functions.listDirectory(path)(visited), Duration.Inf) flatMap {
         case IoFile(v) => List(v)
         case IoDirectory(v) => List(v) ++ listRecursively(v)(visited :+ path)
       }
-    }
 
     listRecursively(rootDir.pathAsString)().toList shouldBe List(innerDir, link).map(_.pathAsString)
   }
diff --git a/backend/src/test/scala/cromwell/backend/io/JobPathsSpec.scala b/backend/src/test/scala/cromwell/backend/io/JobPathsSpec.scala
index 286ed796311..21709bfda58 100644
--- a/backend/src/test/scala/cromwell/backend/io/JobPathsSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/io/JobPathsSpec.scala
@@ -26,7 +26,7 @@ class JobPathsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wi
       |        }
     """.stripMargin
 
-  val backendConfig =  ConfigFactory.parseString(configString)
+  val backendConfig = ConfigFactory.parseString(configString)
   val defaultBackendConfigDescriptor = BackendConfigurationDescriptor(backendConfig, TestConfig.globalConfig)
 
   "JobPaths" should "provide correct paths for a job" in {
@@ -55,8 +55,9 @@ class JobPathsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wi
       fullPath(s"/cromwell-executions/wf_hello/$id/call-hello")
     jobPaths.callExecutionDockerRoot.pathAsString shouldBe
       fullPath(s"/cromwell-executions/wf_hello/$id/call-hello/execution")
-    jobPaths.toDockerPath(DefaultPathBuilder.get(
-      s"local-cromwell-executions/wf_hello/$id/call-hello/execution/stdout")).pathAsString shouldBe
+    jobPaths
+      .toDockerPath(DefaultPathBuilder.get(s"local-cromwell-executions/wf_hello/$id/call-hello/execution/stdout"))
+      .pathAsString shouldBe
       fullPath(s"/cromwell-executions/wf_hello/$id/call-hello/execution/stdout")
     jobPaths.toDockerPath(DefaultPathBuilder.get("/cromwell-executions/dock/path")).pathAsString shouldBe
       fullPath("/cromwell-executions/dock/path")
diff --git a/backend/src/test/scala/cromwell/backend/io/TestWorkflows.scala b/backend/src/test/scala/cromwell/backend/io/TestWorkflows.scala
index 8e280eadf4e..f956607a573 100644
--- a/backend/src/test/scala/cromwell/backend/io/TestWorkflows.scala
+++ b/backend/src/test/scala/cromwell/backend/io/TestWorkflows.scala
@@ -7,25 +7,26 @@ object TestWorkflows {
 
   case class TestWorkflow(workflowDescriptor: BackendWorkflowDescriptor,
                           config: BackendConfigurationDescriptor,
-                          expectedResponse: BackendJobExecutionResponse)
+                          expectedResponse: BackendJobExecutionResponse
+  )
 
   val HelloWorld =
     s"""
-      |task hello {
-      |  String addressee = "you "
-      |  command {
-      |    echo "Hello $${addressee}!"
-      |  }
-      |  output {
-      |    String salutation = read_string(stdout())
-      |  }
-      |
-      |  RUNTIME
-      |}
-      |
-      |workflow wf_hello {
-      |  call hello
-      |}
+       |task hello {
+       |  String addressee = "you "
+       |  command {
+       |    echo "Hello $${addressee}!"
+       |  }
+       |  output {
+       |    String salutation = read_string(stdout())
+       |  }
+       |
+       |  RUNTIME
+       |}
+       |
+       |workflow wf_hello {
+       |  call hello
+       |}
     """.stripMargin
 
   val GoodbyeWorld =
@@ -46,25 +47,25 @@ object TestWorkflows {
 
   val InputFiles =
     s"""
-      |task localize {
-      |  File inputFileFromJson
-      |  File inputFileFromCallInputs
-      |  command {
-      |    cat $${inputFileFromJson}
-      |    echo ""
-      |    cat $${inputFileFromCallInputs}
-      |  }
-      |  output {
-      |    Array[String] out = read_lines(stdout())
-      |  }
-      |
-      |  RUNTIME
-      |}
-      |
-      |workflow wf_localize {
-      |  File workflowFile
-      |  call localize { input: inputFileFromCallInputs = workflowFile }
-      |}
+       |task localize {
+       |  File inputFileFromJson
+       |  File inputFileFromCallInputs
+       |  command {
+       |    cat $${inputFileFromJson}
+       |    echo ""
+       |    cat $${inputFileFromCallInputs}
+       |  }
+       |  output {
+       |    Array[String] out = read_lines(stdout())
+       |  }
+       |
+       |  RUNTIME
+       |}
+       |
+       |workflow wf_localize {
+       |  File workflowFile
+       |  call localize { input: inputFileFromCallInputs = workflowFile }
+       |}
     """.stripMargin
 
   val Sleep20 =
@@ -83,25 +84,25 @@ object TestWorkflows {
 
   val Scatter =
     s"""
-      |task scattering {
-      |  Int intNumber
-      |  command {
-      |    echo $${intNumber}
-      |  }
-      |  output {
-      |    Int out = read_string(stdout())
-      |  }
-      |}
-      |
-      |workflow wf_scattering {
-      |  Array[Int] numbers = [1, 2, 3]
-      |  scatter (i in numbers) {
-      |     call scattering { input: intNumber = i }
-      |  }
-      |}
+       |task scattering {
+       |  Int intNumber
+       |  command {
+       |    echo $${intNumber}
+       |  }
+       |  output {
+       |    Int out = read_string(stdout())
+       |  }
+       |}
+       |
+       |workflow wf_scattering {
+       |  Array[Int] numbers = [1, 2, 3]
+       |  scatter (i in numbers) {
+       |     call scattering { input: intNumber = i }
+       |  }
+       |}
     """.stripMargin
 
-  val OutputProcess = {
+  val OutputProcess =
     """
       |task localize {
       |  File inputFile
@@ -121,9 +122,8 @@ object TestWorkflows {
       |  call localize
       |}
     """.stripMargin
-  }
 
-  val MissingOutputProcess = {
+  val MissingOutputProcess =
     """
       |task localize {
       |  command {
@@ -137,5 +137,4 @@ object TestWorkflows {
       |  call localize
       |}
     """.stripMargin
-  }
 }
diff --git a/backend/src/test/scala/cromwell/backend/io/WorkflowPathsSpec.scala b/backend/src/test/scala/cromwell/backend/io/WorkflowPathsSpec.scala
index cb53276f499..790d42a7887 100644
--- a/backend/src/test/scala/cromwell/backend/io/WorkflowPathsSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/io/WorkflowPathsSpec.scala
@@ -16,16 +16,15 @@ class WorkflowPathsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
 
   def createConfig(values: Map[String, String]): Config = {
     val config = mock[Config]
-    values.foreach {
-      case (key: String, value: String) =>
-        when(config.hasPath(key)).thenReturn(true)
-        when(config.getString(key)).thenReturn(value)
+    values.foreach { case (key: String, value: String) =>
+      when(config.hasPath(key)).thenReturn(true)
+      when(config.getString(key)).thenReturn(value)
     }
     config
   }
 
   def rootConfig(root: Option[String], dockerRoot: Option[String]): Config = {
-    val values: Map[String,String] = root.map("root" -> _).toMap ++ dockerRoot.map("dockerRoot" -> _).toMap
+    val values: Map[String, String] = root.map("root" -> _).toMap ++ dockerRoot.map("dockerRoot" -> _).toMap
     createConfig(values)
   }
 
@@ -82,9 +81,12 @@ class WorkflowPathsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     val expectedDockerRoot = dockerRoot.getOrElse(WorkflowPathsWithDocker.DefaultDockerRoot)
 
     workflowPaths.workflowRoot.pathAsString shouldBe
-      DefaultPathBuilder.get(
-        s"$expectedRoot/rootWorkflow/$rootWorkflowId/call-call1/shard-1/attempt-2/subWorkflow/$subWorkflowId"
-      ).toAbsolutePath.pathAsString
+      DefaultPathBuilder
+        .get(
+          s"$expectedRoot/rootWorkflow/$rootWorkflowId/call-call1/shard-1/attempt-2/subWorkflow/$subWorkflowId"
+        )
+        .toAbsolutePath
+        .pathAsString
     workflowPaths.dockerWorkflowRoot.pathAsString shouldBe s"$expectedDockerRoot/rootWorkflow/$rootWorkflowId/call-call1/shard-1/attempt-2/subWorkflow/$subWorkflowId"
     ()
   }
diff --git a/backend/src/test/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilderSpec.scala b/backend/src/test/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilderSpec.scala
index 0497c8a1ba1..bd3024eda9a 100644
--- a/backend/src/test/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilderSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilderSpec.scala
@@ -14,37 +14,36 @@ import spray.json.{JsArray, JsBoolean, JsNumber, JsObject, JsValue}
 import wom.RuntimeAttributesKeys._
 import wom.values._
 
-class StandardValidatedRuntimeAttributesBuilderSpec extends AnyWordSpecLike with CromwellTimeoutSpec with Matchers
-  with MockSugar {
+class StandardValidatedRuntimeAttributesBuilderSpec
+    extends AnyWordSpecLike
+    with CromwellTimeoutSpec
+    with Matchers
+    with MockSugar {
 
   val HelloWorld: String =
     s"""
-      |task hello {
-      |  String addressee = "you"
-      |  command {
-      |    echo "Hello $${addressee}!"
-      |  }
-      |  output {
-      |    String salutation = read_string(stdout())
-      |  }
-      |
-      |  RUNTIME
-      |}
-      |
-      |workflow hello {
-      |  call hello
-      |}
+       |task hello {
+       |  String addressee = "you"
+       |  command {
+       |    echo "Hello $${addressee}!"
+       |  }
+       |  output {
+       |    String salutation = read_string(stdout())
+       |  }
+       |
+       |  RUNTIME
+       |}
+       |
+       |workflow hello {
+       |  call hello
+       |}
     """.stripMargin
 
+  val defaultRuntimeAttributes: Map[String, Any] =
+    Map(DockerKey -> None, FailOnStderrKey -> false, ContinueOnReturnCodeKey -> ContinueOnReturnCodeSet(Set(0)))
 
-  val defaultRuntimeAttributes: Map[String, Any] = Map(
-    DockerKey -> None,
-    FailOnStderrKey -> false,
-    ContinueOnReturnCodeKey -> ContinueOnReturnCodeSet(Set(0)))
-
-  def workflowOptionsWithDefaultRuntimeAttributes(defaults: Map[String, JsValue]): WorkflowOptions = {
+  def workflowOptionsWithDefaultRuntimeAttributes(defaults: Map[String, JsValue]): WorkflowOptions =
     WorkflowOptions(JsObject(Map("default_runtime_attributes" -> JsObject(defaults))))
-  }
 
   "SharedFileSystemValidatedRuntimeAttributesBuilder" should {
     "validate when there are no runtime attributes defined" in {
@@ -75,8 +74,11 @@ class StandardValidatedRuntimeAttributesBuilderSpec extends AnyWordSpecLike with
       var warnings = List.empty[Any]
       val mockLogger = mock[Logger]
       mockLogger.warn(anyString).answers((warnings :+= _): Any => Unit)
-      assertRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes,
-        includeDockerSupport = false, logger = mockLogger)
+      assertRuntimeAttributesSuccessfulCreation(runtimeAttributes,
+                                                expectedRuntimeAttributes,
+                                                includeDockerSupport = false,
+                                                logger = mockLogger
+      )
       warnings should contain theSameElementsAs List("Unrecognized runtime attribute keys: docker")
     }
 
@@ -97,44 +99,58 @@ class StandardValidatedRuntimeAttributesBuilderSpec extends AnyWordSpecLike with
       var warnings = List.empty[Any]
       val mockLogger = mock[Logger]
       mockLogger.warn(anyString).answers((warnings :+= _): Any => Unit)
-      assertRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes,
-        includeDockerSupport = false, logger = mockLogger)
+      assertRuntimeAttributesSuccessfulCreation(runtimeAttributes,
+                                                expectedRuntimeAttributes,
+                                                includeDockerSupport = false,
+                                                logger = mockLogger
+      )
       warnings should contain theSameElementsAs List("Unrecognized runtime attribute keys: docker")
     }
 
     "fail to validate an invalid failOnStderr entry" in {
       val runtimeAttributes = Map("failOnStderr" -> WomString("yes"))
-      assertRuntimeAttributesFailedCreation(runtimeAttributes,
-        "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'")
+      assertRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'"
+      )
     }
 
     "use workflow options as default if failOnStdErr key is missing" in {
       val expectedRuntimeAttributes = defaultRuntimeAttributes + (FailOnStderrKey -> true)
       val workflowOptions = workflowOptionsWithDefaultRuntimeAttributes(Map(FailOnStderrKey -> JsBoolean(true)))
       val runtimeAttributes = Map.empty[String, WomValue]
-      assertRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes,
-        workflowOptions = workflowOptions)
+      assertRuntimeAttributesSuccessfulCreation(runtimeAttributes,
+                                                expectedRuntimeAttributes,
+                                                workflowOptions = workflowOptions
+      )
     }
 
     "validate a valid continueOnReturnCode entry" in {
       val runtimeAttributes = Map("continueOnReturnCode" -> WomInteger(1))
-      val expectedRuntimeAttributes = defaultRuntimeAttributes + (ContinueOnReturnCodeKey -> ContinueOnReturnCodeSet(Set(1)))
+      val expectedRuntimeAttributes =
+        defaultRuntimeAttributes + (ContinueOnReturnCodeKey -> ContinueOnReturnCodeSet(Set(1)))
       assertRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid continueOnReturnCode entry" in {
       val runtimeAttributes = Map("continueOnReturnCode" -> WomString("value"))
-      assertRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]")
+      assertRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+      )
     }
 
     "use workflow options as default if continueOnReturnCode key is missing" in {
       val expectedRuntimeAttributes = defaultRuntimeAttributes +
         (ContinueOnReturnCodeKey -> ContinueOnReturnCodeSet(Set(1, 2)))
       val workflowOptions = workflowOptionsWithDefaultRuntimeAttributes(
-        Map(ContinueOnReturnCodeKey -> JsArray(Vector(JsNumber(1), JsNumber(2)))))
+        Map(ContinueOnReturnCodeKey -> JsArray(Vector(JsNumber(1), JsNumber(2))))
+      )
       val runtimeAttributes = Map.empty[String, WomValue]
-      assertRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes,
-        workflowOptions = workflowOptions)
+      assertRuntimeAttributesSuccessfulCreation(runtimeAttributes,
+                                                expectedRuntimeAttributes,
+                                                workflowOptions = workflowOptions
+      )
     }
 
   }
@@ -148,44 +164,52 @@ class StandardValidatedRuntimeAttributesBuilderSpec extends AnyWordSpecLike with
                                                         expectedRuntimeAttributes: Map[String, Any],
                                                         includeDockerSupport: Boolean = true,
                                                         workflowOptions: WorkflowOptions = emptyWorkflowOptions,
-                                                        logger: Logger = defaultLogger): Unit = {
+                                                        logger: Logger = defaultLogger
+  ): Unit = {
 
     val builder = if (includeDockerSupport) {
-      StandardValidatedRuntimeAttributesBuilder.default(mockBackendRuntimeConfig).withValidation(DockerValidation.optional)
+      StandardValidatedRuntimeAttributesBuilder
+        .default(mockBackendRuntimeConfig)
+        .withValidation(DockerValidation.optional)
     } else {
       StandardValidatedRuntimeAttributesBuilder.default(mockBackendRuntimeConfig)
     }
     val runtimeAttributeDefinitions = builder.definitions.toSet
-    val addDefaultsToAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, workflowOptions) _
+    val addDefaultsToAttributes =
+      RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, workflowOptions) _
 
     val validatedRuntimeAttributes = builder.build(addDefaultsToAttributes(runtimeAttributes), logger)
 
-    val docker = RuntimeAttributesValidation.extractOption(
-      DockerValidation.instance, validatedRuntimeAttributes)
-    val failOnStderr = RuntimeAttributesValidation.extract(
-      FailOnStderrValidation.instance, validatedRuntimeAttributes)
-    val continueOnReturnCode = RuntimeAttributesValidation.extract(
-      ContinueOnReturnCodeValidation.instance, validatedRuntimeAttributes)
+    val docker = RuntimeAttributesValidation.extractOption(DockerValidation.instance, validatedRuntimeAttributes)
+    val failOnStderr = RuntimeAttributesValidation.extract(FailOnStderrValidation.instance, validatedRuntimeAttributes)
+    val continueOnReturnCode =
+      RuntimeAttributesValidation.extract(ContinueOnReturnCodeValidation.instance, validatedRuntimeAttributes)
 
     docker should be(expectedRuntimeAttributes(DockerKey).asInstanceOf[Option[String]])
     failOnStderr should be(expectedRuntimeAttributes(FailOnStderrKey).asInstanceOf[Boolean])
     continueOnReturnCode should be(
-      expectedRuntimeAttributes(ContinueOnReturnCodeKey).asInstanceOf[ContinueOnReturnCode])
+      expectedRuntimeAttributes(ContinueOnReturnCodeKey).asInstanceOf[ContinueOnReturnCode]
+    )
     ()
   }
 
-  private def assertRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue], exMsg: String,
+  private def assertRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue],
+                                                    exMsg: String,
                                                     supportsDocker: Boolean = true,
                                                     workflowOptions: WorkflowOptions = emptyWorkflowOptions,
-                                                    logger: Logger = defaultLogger): Unit = {
+                                                    logger: Logger = defaultLogger
+  ): Unit = {
     val thrown = the[RuntimeException] thrownBy {
       val builder = if (supportsDocker) {
-        StandardValidatedRuntimeAttributesBuilder.default(mockBackendRuntimeConfig).withValidation(DockerValidation.optional)
+        StandardValidatedRuntimeAttributesBuilder
+          .default(mockBackendRuntimeConfig)
+          .withValidation(DockerValidation.optional)
       } else {
         StandardValidatedRuntimeAttributesBuilder.default(mockBackendRuntimeConfig)
       }
       val runtimeAttributeDefinitions = builder.definitions.toSet
-      val addDefaultsToAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, workflowOptions) _
+      val addDefaultsToAttributes =
+        RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, workflowOptions) _
 
       builder.build(addDefaultsToAttributes(runtimeAttributes), logger)
     }
diff --git a/backend/src/test/scala/cromwell/backend/standard/callcaching/CallCachingBlacklistManagerSpec.scala b/backend/src/test/scala/cromwell/backend/standard/callcaching/CallCachingBlacklistManagerSpec.scala
index fdfa7f97e04..f50cba5834c 100644
--- a/backend/src/test/scala/cromwell/backend/standard/callcaching/CallCachingBlacklistManagerSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/standard/callcaching/CallCachingBlacklistManagerSpec.scala
@@ -8,11 +8,10 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import spray.json._
 
-
 class CallCachingBlacklistManagerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "CallCachingBlacklistManager"
 
-  //noinspection RedundantDefaultArgument
+  // noinspection RedundantDefaultArgument
   val workflowSourcesNoGrouping = WorkflowSourceFilesWithoutImports(
     workflowSource = None,
     workflowUrl = None,
diff --git a/backend/src/test/scala/cromwell/backend/standard/callcaching/RootWorkflowHashCacheActorSpec.scala b/backend/src/test/scala/cromwell/backend/standard/callcaching/RootWorkflowHashCacheActorSpec.scala
index f546dd63630..0b462c74b81 100644
--- a/backend/src/test/scala/cromwell/backend/standard/callcaching/RootWorkflowHashCacheActorSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/standard/callcaching/RootWorkflowHashCacheActorSpec.scala
@@ -13,8 +13,7 @@ import org.scalatest.flatspec.AnyFlatSpecLike
 
 import scala.concurrent.duration._
 
-class RootWorkflowHashCacheActorSpec extends TestKitSuite with ImplicitSender
-  with AnyFlatSpecLike {
+class RootWorkflowHashCacheActorSpec extends TestKitSuite with ImplicitSender with AnyFlatSpecLike {
 
   private val fakeWorkflowId = WorkflowId.randomId()
   private val fakeFileName = "fakeFileName"
@@ -25,17 +24,24 @@ class RootWorkflowHashCacheActorSpec extends TestKitSuite with ImplicitSender
       props = Props(new RootWorkflowFileHashCacheActor(ioActorProbe.ref, fakeWorkflowId) {
         override lazy val defaultIoTimeout: FiniteDuration = 1.second
       }),
-      name = "rootWorkflowFileHashCacheActor-without-timer",
+      name = "rootWorkflowFileHashCacheActor-without-timer"
     )
 
-    val ioHashCommandWithContext = IoHashCommandWithContext(DefaultIoHashCommand(DefaultPathBuilder.build("").get), FileHashContext(HashKey(checkForHitOrMiss = false, List.empty), fakeFileName))
+    val ioHashCommandWithContext =
+      IoHashCommandWithContext(DefaultIoHashCommand(DefaultPathBuilder.build("").get),
+                               FileHashContext(HashKey(checkForHitOrMiss = false, List.empty), fakeFileName)
+      )
     rootWorkflowFileHashCacheActor ! ioHashCommandWithContext
 
-    //wait for timeout
+    // wait for timeout
     Thread.sleep(2000)
 
     EventFilter.info(msgIoAckWithNoRequesters.format(fakeFileName), occurrences = 1).intercept {
-      ioActorProbe.send(rootWorkflowFileHashCacheActor, ioHashCommandWithContext.fileHashContext -> IoSuccess(ioHashCommandWithContext.ioHashCommand, "Successful result"))
+      ioActorProbe.send(rootWorkflowFileHashCacheActor,
+                        ioHashCommandWithContext.fileHashContext -> IoSuccess(ioHashCommandWithContext.ioHashCommand,
+                                                                              "Successful result"
+                        )
+      )
     }
   }
 
@@ -46,17 +52,32 @@ class RootWorkflowHashCacheActorSpec extends TestKitSuite with ImplicitSender
         // Effectively disabling automatic timeout firing here. We'll send RequestTimeout ourselves
         override lazy val defaultIoTimeout: FiniteDuration = 1.hour
       }),
-      "rootWorkflowFileHashCacheActor-with-timer",
+      "rootWorkflowFileHashCacheActor-with-timer"
     )
 
-    val ioHashCommandWithContext = IoHashCommandWithContext(DefaultIoHashCommand(DefaultPathBuilder.build("").get), FileHashContext(HashKey(checkForHitOrMiss = false, List.empty), fakeFileName))
+    val ioHashCommandWithContext =
+      IoHashCommandWithContext(DefaultIoHashCommand(DefaultPathBuilder.build("").get),
+                               FileHashContext(HashKey(checkForHitOrMiss = false, List.empty), fakeFileName)
+      )
     rootWorkflowFileHashCacheActor ! ioHashCommandWithContext
 
     val hashVal = "Success"
-    EventFilter.info(msgTimeoutAfterIoAck.format(s"FileHashSuccess($hashVal)", ioHashCommandWithContext.fileHashContext.file), occurrences = 1).intercept {
-      ioActorProbe.send(rootWorkflowFileHashCacheActor, (ioHashCommandWithContext.fileHashContext, IoSuccess(ioHashCommandWithContext.ioHashCommand, hashVal)))
-      Thread.sleep(2000) // wait for actor to put value into cache
-      ioActorProbe.send(rootWorkflowFileHashCacheActor, RequestTimeout(ioHashCommandWithContext.fileHashContext -> ioHashCommandWithContext.ioHashCommand, rootWorkflowFileHashCacheActor))
-    }
+    EventFilter
+      .info(msgTimeoutAfterIoAck.format(s"FileHashSuccess($hashVal)", ioHashCommandWithContext.fileHashContext.file),
+            occurrences = 1
+      )
+      .intercept {
+        ioActorProbe.send(
+          rootWorkflowFileHashCacheActor,
+          (ioHashCommandWithContext.fileHashContext, IoSuccess(ioHashCommandWithContext.ioHashCommand, hashVal))
+        )
+        Thread.sleep(2000) // wait for actor to put value into cache
+        ioActorProbe.send(
+          rootWorkflowFileHashCacheActor,
+          RequestTimeout(ioHashCommandWithContext.fileHashContext -> ioHashCommandWithContext.ioHashCommand,
+                         rootWorkflowFileHashCacheActor
+          )
+        )
+      }
   }
 }
diff --git a/backend/src/test/scala/cromwell/backend/standard/callcaching/StandardFileHashingActorSpec.scala b/backend/src/test/scala/cromwell/backend/standard/callcaching/StandardFileHashingActorSpec.scala
index c7463cc50a0..2c7ec3ba726 100644
--- a/backend/src/test/scala/cromwell/backend/standard/callcaching/StandardFileHashingActorSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/standard/callcaching/StandardFileHashingActorSpec.scala
@@ -18,8 +18,12 @@ import scala.concurrent.duration._
 import scala.util.control.NoStackTrace
 import scala.util.{Failure, Try}
 
-class StandardFileHashingActorSpec extends TestKitSuite with ImplicitSender
-  with AnyFlatSpecLike with Matchers with MockSugar {
+class StandardFileHashingActorSpec
+    extends TestKitSuite
+    with ImplicitSender
+    with AnyFlatSpecLike
+    with Matchers
+    with MockSugar {
 
   behavior of "StandardFileHashingActor"
 
@@ -127,20 +131,21 @@ object StandardFileHashingActorSpec {
 
   def defaultParams(): StandardFileHashingActorParams = defaultParams(testing, testing, testing, testing, testing)
 
-  def ioActorParams(ioActor: ActorRef): StandardFileHashingActorParams = {
-    defaultParams(withJobDescriptor = testing,
+  def ioActorParams(ioActor: ActorRef): StandardFileHashingActorParams =
+    defaultParams(
+      withJobDescriptor = testing,
       withConfigurationDescriptor = testing,
       withIoActor = ioActor,
       withServiceRegistryActor = testing,
-      withBackendInitializationDataOption = testing)
-  }
+      withBackendInitializationDataOption = testing
+    )
 
   def defaultParams(withJobDescriptor: => BackendJobDescriptor,
                     withConfigurationDescriptor: => BackendConfigurationDescriptor,
                     withIoActor: => ActorRef,
                     withServiceRegistryActor: => ActorRef,
                     withBackendInitializationDataOption: => Option[BackendInitializationData]
-                   ): StandardFileHashingActorParams = new StandardFileHashingActorParams {
+  ): StandardFileHashingActorParams = new StandardFileHashingActorParams {
 
     override def jobDescriptor: BackendJobDescriptor = withJobDescriptor
 
@@ -150,10 +155,10 @@ object StandardFileHashingActorSpec {
 
     override def serviceRegistryActor: ActorRef = withServiceRegistryActor
 
-    override def backendInitializationDataOption: Option[BackendInitializationData] = withBackendInitializationDataOption
+    override def backendInitializationDataOption: Option[BackendInitializationData] =
+      withBackendInitializationDataOption
 
     override def fileHashCachingActor: Option[ActorRef] = None
   }
 
 }
-
diff --git a/backend/src/test/scala/cromwell/backend/validation/ContinueOnReturnCodeSpec.scala b/backend/src/test/scala/cromwell/backend/validation/ContinueOnReturnCodeSpec.scala
index faf835c6343..e0ff75d3176 100644
--- a/backend/src/test/scala/cromwell/backend/validation/ContinueOnReturnCodeSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/validation/ContinueOnReturnCodeSpec.scala
@@ -9,12 +9,12 @@ import org.scalatest.wordspec.AnyWordSpecLike
 class ContinueOnReturnCodeSpec extends AnyWordSpecLike with CromwellTimeoutSpec with Matchers with BeforeAndAfterAll {
   "Checking for return codes" should {
     "continue on expected return code flags" in {
-      val flagTests = Table(
-        ("flag", "returnCode", "expectedContinue"),
-        (true, 0, true),
-        (true, 1, true),
-        (false, 0, true),
-        (false, 1, false))
+      val flagTests = Table(("flag", "returnCode", "expectedContinue"),
+                            (true, 0, true),
+                            (true, 1, true),
+                            (false, 0, true),
+                            (false, 1, false)
+      )
 
       forAll(flagTests) { (flag, returnCode, expectedContinue) =>
         ContinueOnReturnCodeFlag(flag).continueFor(returnCode) should be(expectedContinue)
@@ -30,7 +30,8 @@ class ContinueOnReturnCodeSpec extends AnyWordSpecLike with CromwellTimeoutSpec
         (Set(1), 1, true),
         (Set(0, 1), 0, true),
         (Set(0, 1), 1, true),
-        (Set(0, 1), 2, false))
+        (Set(0, 1), 2, false)
+      )
 
       forAll(setTests) { (set, returnCode, expectedContinue) =>
         ContinueOnReturnCodeSet(set).continueFor(returnCode) should be(expectedContinue)
diff --git a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesDefaultSpec.scala b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesDefaultSpec.scala
index 766384b46fd..6123ecfe53b 100644
--- a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesDefaultSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesDefaultSpec.scala
@@ -21,9 +21,7 @@ class RuntimeAttributesDefaultSpec extends AnyFlatSpec with CromwellTimeoutSpec
   )
 
   it should "coerce workflow options from Json to WdlValues" in {
-    val workflowOptions = WorkflowOptions(JsObject(
-      "default_runtime_attributes" -> JsObject(map))
-    )
+    val workflowOptions = WorkflowOptions(JsObject("default_runtime_attributes" -> JsObject(map)))
 
     val coercionMap: Map[String, Set[WomType]] = Map(
       "str" -> Set(WomStringType),
@@ -43,9 +41,7 @@ class RuntimeAttributesDefaultSpec extends AnyFlatSpec with CromwellTimeoutSpec
   }
 
   it should "only return default values if they're in the coercionMap" in {
-    val workflowOptions = WorkflowOptions(JsObject(
-      "default_runtime_attributes" -> JsObject(map))
-    )
+    val workflowOptions = WorkflowOptions(JsObject("default_runtime_attributes" -> JsObject(map)))
 
     val coercionMap: Map[String, Set[WomType]] = Map(
       "str" -> Set(WomStringType),
@@ -69,9 +65,7 @@ class RuntimeAttributesDefaultSpec extends AnyFlatSpec with CromwellTimeoutSpec
   }
 
   it should "throw an exception if a value can't be coerced" in {
-    val workflowOptions = WorkflowOptions(JsObject(
-      "default_runtime_attributes" -> JsObject(map))
-    )
+    val workflowOptions = WorkflowOptions(JsObject("default_runtime_attributes" -> JsObject(map)))
 
     val coercionMap: Map[String, Set[WomType]] = Map(
       "str" -> Set(WomBooleanType),
diff --git a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala
index 1752da9014b..6d3bcb6bafa 100644
--- a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala
@@ -12,15 +12,21 @@ import wom.RuntimeAttributesKeys
 import wom.types._
 import wom.values._
 
-class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeoutSpec with Matchers with BeforeAndAfterAll {
+class RuntimeAttributesValidationSpec
+    extends AnyWordSpecLike
+    with CromwellTimeoutSpec
+    with Matchers
+    with BeforeAndAfterAll {
 
   val mockBackendRuntimeConfig = TestConfig.allRuntimeAttrsConfig
 
   "RuntimeAttributesValidation" should {
     "return success when tries to validate a valid Docker entry" in {
       val dockerValue = Some(WomString("someImage"))
-      val result = RuntimeAttributesValidation.validateDocker(dockerValue,
-        "Failed to get Docker mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateDocker(
+        dockerValue,
+        "Failed to get Docker mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(x.get == "someImage")
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -38,8 +44,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return failure (based on defined HoF) when tries to validate a docker entry but it does not contain a value" in {
       val dockerValue = None
-      val result = RuntimeAttributesValidation.validateDocker(dockerValue,
-        "Failed to get Docker mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateDocker(
+        dockerValue,
+        "Failed to get Docker mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Failed to get Docker mandatory key from runtime attributes")
@@ -48,8 +56,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return failure when there is an invalid docker runtime attribute defined" in {
       val dockerValue = Some(WomInteger(1))
-      val result = RuntimeAttributesValidation.validateDocker(dockerValue,
-        "Failed to get Docker mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateDocker(
+        dockerValue,
+        "Failed to get Docker mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting docker runtime attribute to be a String")
@@ -58,8 +68,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return success when tries to validate a failOnStderr boolean entry" in {
       val failOnStderrValue = Some(WomBoolean(true))
-      val result = RuntimeAttributesValidation.validateFailOnStderr(failOnStderrValue,
-        "Failed to get failOnStderr mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateFailOnStderr(
+        failOnStderrValue,
+        "Failed to get failOnStderr mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(x)
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -68,8 +80,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return success when tries to validate a failOnStderr 'true' string entry" in {
       val failOnStderrValue = Some(WomString("true"))
-      val result = RuntimeAttributesValidation.validateFailOnStderr(failOnStderrValue,
-        "Failed to get failOnStderr mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateFailOnStderr(
+        failOnStderrValue,
+        "Failed to get failOnStderr mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(x)
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -78,8 +92,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return success when tries to validate a failOnStderr 'false' string entry" in {
       val failOnStderrValue = Some(WomString("false"))
-      val result = RuntimeAttributesValidation.validateFailOnStderr(failOnStderrValue,
-        "Failed to get failOnStderr mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateFailOnStderr(
+        failOnStderrValue,
+        "Failed to get failOnStderr mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(!x)
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -88,11 +104,16 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return failure when there is an invalid failOnStderr runtime attribute defined" in {
       val failOnStderrValue = Some(WomInteger(1))
-      val result = RuntimeAttributesValidation.validateFailOnStderr(failOnStderrValue,
-        "Failed to get failOnStderr mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateFailOnStderr(
+        failOnStderrValue,
+        "Failed to get failOnStderr mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(_) => fail("A failure was expected.")
-        case Invalid(e) => assert(e.head == "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'")
+        case Invalid(e) =>
+          assert(
+            e.head == "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'"
+          )
       }
     }
 
@@ -107,8 +128,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return success when tries to validate a continueOnReturnCode boolean entry" in {
       val continueOnReturnCodeValue = Some(WomBoolean(true))
-      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue,
-        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(
+        continueOnReturnCodeValue,
+        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(x == ContinueOnReturnCodeFlag(true))
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -117,8 +140,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return success when tries to validate a continueOnReturnCode 'true' string entry" in {
       val continueOnReturnCodeValue = Some(WomString("true"))
-      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue,
-        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(
+        continueOnReturnCodeValue,
+        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(x == ContinueOnReturnCodeFlag(true))
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -127,8 +152,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return success when tries to validate a continueOnReturnCode 'false' string entry" in {
       val continueOnReturnCodeValue = Some(WomString("false"))
-      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue,
-        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(
+        continueOnReturnCodeValue,
+        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(x == ContinueOnReturnCodeFlag(false))
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -137,8 +164,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return success when tries to validate a continueOnReturnCode int entry" in {
       val continueOnReturnCodeValue = Some(WomInteger(12))
-      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue,
-        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(
+        continueOnReturnCodeValue,
+        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(x == ContinueOnReturnCodeSet(Set(12)))
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -147,19 +176,25 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return failure when there is an invalid continueOnReturnCode runtime attribute defined" in {
       val continueOnReturnCodeValue = Some(WomString("yes"))
-      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue,
-        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(
+        continueOnReturnCodeValue,
+        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) =>
-          assert(e.head == "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]")
+          assert(
+            e.head == "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+          )
       }
     }
 
     "return success when there is a valid integer array in continueOnReturnCode runtime attribute" in {
       val continueOnReturnCodeValue = Some(WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(1), WomInteger(2))))
-      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue,
-        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(
+        continueOnReturnCodeValue,
+        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(x == ContinueOnReturnCodeSet(Set(1, 2)))
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -167,18 +202,26 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
     }
 
     "return failure when there is an invalid array in continueOnReturnCode runtime attribute" in {
-      val continueOnReturnCodeValue = Some(WomArray(WomArrayType(WomStringType), Seq(WomString("one"), WomString("two"))))
-      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue,
-        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel)
+      val continueOnReturnCodeValue =
+        Some(WomArray(WomArrayType(WomStringType), Seq(WomString("one"), WomString("two"))))
+      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(
+        continueOnReturnCodeValue,
+        "Failed to get continueOnReturnCode mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(_) => fail("A failure was expected.")
-        case Invalid(e) => assert(e.head == "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]")
+        case Invalid(e) =>
+          assert(
+            e.head == "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+          )
       }
     }
 
     "return success (based on defined HoF) when tries to validate a continueOnReturnCode entry but it does not contain a value" in {
       val continueOnReturnCodeValue = None
-      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue, ContinueOnReturnCodeFlag(false).validNel)
+      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(continueOnReturnCodeValue,
+                                                                            ContinueOnReturnCodeFlag(false).validNel
+      )
       result match {
         case Valid(x) => assert(x == ContinueOnReturnCodeFlag(false))
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -188,8 +231,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
     "return success when tries to validate a valid Integer memory entry" in {
       val expectedGb = 1
       val memoryValue = Some(WomInteger(1 << 30))
-      val result = RuntimeAttributesValidation.validateMemory(memoryValue,
-        "Failed to get memory mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateMemory(
+        memoryValue,
+        "Failed to get memory mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(x.amount == expectedGb)
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -198,8 +243,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return failure when tries to validate an invalid Integer memory entry" in {
       val memoryValue = Some(WomInteger(-1))
-      val result = RuntimeAttributesValidation.validateMemory(memoryValue,
-        "Failed to get memory mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateMemory(
+        memoryValue,
+        "Failed to get memory mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting memory runtime attribute value greater than 0 but got -1")
@@ -209,8 +256,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
     "return success when tries to validate a valid String memory entry" in {
       val expectedGb = 2
       val memoryValue = Some(WomString("2 GB"))
-      val result = RuntimeAttributesValidation.validateMemory(memoryValue,
-        "Failed to get memory mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateMemory(
+        memoryValue,
+        "Failed to get memory mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(x) => assert(x.amount == expectedGb)
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -219,8 +268,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return failure when tries to validate an invalid size in String memory entry" in {
       val memoryValue = Some(WomString("0 GB"))
-      val result = RuntimeAttributesValidation.validateMemory(memoryValue,
-        "Failed to get memory mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateMemory(
+        memoryValue,
+        "Failed to get memory mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting memory runtime attribute value greater than 0 but got 0.0")
@@ -229,28 +280,40 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return failure when tries to validate an invalid String memory entry" in {
       val memoryValue = Some(WomString("value"))
-      val result = RuntimeAttributesValidation.validateMemory(memoryValue,
-        "Failed to get memory mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateMemory(
+        memoryValue,
+        "Failed to get memory mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(_) => fail("A failure was expected.")
-        case Invalid(e) => assert(e.head == "Expecting memory runtime attribute to be an Integer or String with format '8 GB'. Exception: value should be of the form 'X Unit' where X is a number, e.g. 8 GB")
+        case Invalid(e) =>
+          assert(
+            e.head == "Expecting memory runtime attribute to be an Integer or String with format '8 GB'. Exception: value should be of the form 'X Unit' where X is a number, e.g. 8 GB"
+          )
       }
     }
 
     "return failure when tries to validate an invalid memory entry" in {
       val memoryValue = Some(WomBoolean(true))
-      val result = RuntimeAttributesValidation.validateMemory(memoryValue,
-        "Failed to get memory mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateMemory(
+        memoryValue,
+        "Failed to get memory mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(_) => fail("A failure was expected.")
-        case Invalid(e) => assert(e.head == "Expecting memory runtime attribute to be an Integer or String with format '8 GB'. Exception: Not supported WDL type value")
+        case Invalid(e) =>
+          assert(
+            e.head == "Expecting memory runtime attribute to be an Integer or String with format '8 GB'. Exception: Not supported WDL type value"
+          )
       }
     }
 
     "return failure when tries to validate a non-provided memory entry" in {
       val memoryValue = None
-      val result = RuntimeAttributesValidation.validateMemory(memoryValue,
-        "Failed to get memory mandatory key from runtime attributes".invalidNel)
+      val result = RuntimeAttributesValidation.validateMemory(
+        memoryValue,
+        "Failed to get memory mandatory key from runtime attributes".invalidNel
+      )
       result match {
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Failed to get memory mandatory key from runtime attributes")
@@ -259,8 +322,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return success when tries to validate a valid cpu entry" in {
       val cpuValue = Some(WomInteger(1))
-      val result = RuntimeAttributesValidation.validateCpu(cpuValue,
-        "Failed to get cpu mandatory key from runtime attributes".invalidNel)
+      val result =
+        RuntimeAttributesValidation.validateCpu(cpuValue,
+                                                "Failed to get cpu mandatory key from runtime attributes".invalidNel
+        )
       result match {
         case Valid(x) => assert(x.value == 1)
         case Invalid(e) => fail(e.toList.mkString(" "))
@@ -269,8 +334,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return failure when tries to validate an invalid cpu entry" in {
       val cpuValue = Some(WomInteger(-1))
-      val result = RuntimeAttributesValidation.validateCpu(cpuValue,
-        "Failed to get cpu mandatory key from runtime attributes".invalidNel)
+      val result =
+        RuntimeAttributesValidation.validateCpu(cpuValue,
+                                                "Failed to get cpu mandatory key from runtime attributes".invalidNel
+        )
       result match {
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting cpu runtime attribute value greater than 0")
@@ -279,8 +346,10 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
 
     "return failure when tries to validate a non-provided cpu entry" in {
       val cpuValue = None
-      val result = RuntimeAttributesValidation.validateCpu(cpuValue,
-        "Failed to get cpu mandatory key from runtime attributes".invalidNel)
+      val result =
+        RuntimeAttributesValidation.validateCpu(cpuValue,
+                                                "Failed to get cpu mandatory key from runtime attributes".invalidNel
+        )
       result match {
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Failed to get cpu mandatory key from runtime attributes")
@@ -306,26 +375,25 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
     }
 
     "return default values as BadDefaultAttribute when they can't be coerced to expected WdlTypes" in {
-     val optionalInvalidAttrsConfig = Option(ConfigFactory.parseString(
-       """
-         |cpu = 1.4
-         |failOnStderr = "notReal"
-         |continueOnReturnCode = 0
+      val optionalInvalidAttrsConfig = Option(ConfigFactory.parseString("""
+                                                                          |cpu = 1.4
+                                                                          |failOnStderr = "notReal"
+                                                                          |continueOnReturnCode = 0
        """.stripMargin))
 
-     val defaultVals = Map(
-       "cpu" -> CpuValidation.configDefaultWomValue(optionalInvalidAttrsConfig).get,
-       "failOnStderr" -> FailOnStderrValidation.configDefaultWdlValue(optionalInvalidAttrsConfig).get,
-       "continueOnReturnCode" -> ContinueOnReturnCodeValidation.configDefaultWdlValue(optionalInvalidAttrsConfig).get
-     )
+      val defaultVals = Map(
+        "cpu" -> CpuValidation.configDefaultWomValue(optionalInvalidAttrsConfig).get,
+        "failOnStderr" -> FailOnStderrValidation.configDefaultWdlValue(optionalInvalidAttrsConfig).get,
+        "continueOnReturnCode" -> ContinueOnReturnCodeValidation.configDefaultWdlValue(optionalInvalidAttrsConfig).get
+      )
 
-     val expectedDefaultVals = Map(
-       "cpu" -> BadDefaultAttribute(WomString("1.4")),
-       "failOnStderr" -> BadDefaultAttribute(WomString("notReal")),
-       "continueOnReturnCode" -> WomInteger(0)
-     )
+      val expectedDefaultVals = Map(
+        "cpu" -> BadDefaultAttribute(WomString("1.4")),
+        "failOnStderr" -> BadDefaultAttribute(WomString("notReal")),
+        "continueOnReturnCode" -> WomInteger(0)
+      )
 
-     defaultVals shouldBe expectedDefaultVals
+      defaultVals shouldBe expectedDefaultVals
     }
 
     "should parse memory successfully" in {
@@ -338,14 +406,24 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
            |  }
            |""".stripMargin
 
-      val backendConfig: Config = ConfigFactory.parseString(backendConfigTemplate).getConfig("default-runtime-attributes")
+      val backendConfig: Config =
+        ConfigFactory.parseString(backendConfigTemplate).getConfig("default-runtime-attributes")
 
       val memoryVal = MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, Some(backendConfig))
       val memoryMinVal = MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMinKey, Some(backendConfig))
       val memoryMaxVal = MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMaxKey, Some(backendConfig))
-      MemoryValidation.withDefaultMemory(RuntimeAttributesKeys.MemoryKey, memoryVal.get).runtimeAttributeDefinition.factoryDefault shouldBe Some((WomLong(2147483648L)))
-      MemoryValidation.withDefaultMemory(RuntimeAttributesKeys.MemoryMinKey, memoryMinVal.get).runtimeAttributeDefinition.factoryDefault shouldBe Some((WomLong(322122547L)))
-      MemoryValidation.withDefaultMemory(RuntimeAttributesKeys.MemoryMaxKey, memoryMaxVal.get).runtimeAttributeDefinition.factoryDefault shouldBe Some((WomLong(429496729L)))
+      MemoryValidation
+        .withDefaultMemory(RuntimeAttributesKeys.MemoryKey, memoryVal.get)
+        .runtimeAttributeDefinition
+        .factoryDefault shouldBe Some(WomLong(2147483648L))
+      MemoryValidation
+        .withDefaultMemory(RuntimeAttributesKeys.MemoryMinKey, memoryMinVal.get)
+        .runtimeAttributeDefinition
+        .factoryDefault shouldBe Some(WomLong(322122547L))
+      MemoryValidation
+        .withDefaultMemory(RuntimeAttributesKeys.MemoryMaxKey, memoryMaxVal.get)
+        .runtimeAttributeDefinition
+        .factoryDefault shouldBe Some(WomLong(429496729L))
     }
 
     "shouldn't throw up if the value for a default-runtime-attribute key cannot be coerced into an expected WomType" in {
@@ -356,25 +434,33 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
            |  }
            |""".stripMargin
 
-      val backendConfig: Config = ConfigFactory.parseString(backendConfigTemplate).getConfig("default-runtime-attributes")
+      val backendConfig: Config =
+        ConfigFactory.parseString(backendConfigTemplate).getConfig("default-runtime-attributes")
 
       val memoryVal = MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, Some(backendConfig))
-      MemoryValidation.withDefaultMemory(RuntimeAttributesKeys.MemoryKey, memoryVal.get).runtimeAttributeDefinition.factoryDefault shouldBe Some(BadDefaultAttribute(WomString("blahblah")))
+      MemoryValidation
+        .withDefaultMemory(RuntimeAttributesKeys.MemoryKey, memoryVal.get)
+        .runtimeAttributeDefinition
+        .factoryDefault shouldBe Some(BadDefaultAttribute(WomString("blahblah")))
     }
 
     "should be able to coerce a list of return codes into an WdlArray" in {
-      val optinalBackendConfig = Option(ConfigFactory.parseString(
-        s"""
-           |continueOnReturnCode = [0,1,2]
-           |""".stripMargin))
+      val optinalBackendConfig = Option(ConfigFactory.parseString(s"""
+                                                                     |continueOnReturnCode = [0,1,2]
+                                                                     |""".stripMargin))
 
-      ContinueOnReturnCodeValidation.configDefaultWdlValue(optinalBackendConfig).get shouldBe WomArray(WomArrayType(WomIntegerType), List(WomInteger(0), WomInteger(1), WomInteger(2)))
+      ContinueOnReturnCodeValidation.configDefaultWdlValue(optinalBackendConfig).get shouldBe WomArray(
+        WomArrayType(WomIntegerType),
+        List(WomInteger(0), WomInteger(1), WomInteger(2))
+      )
     }
 
     "return failure when tries to validate an invalid maxRetries entry" in {
       val maxRetries = Option(WomInteger(-1))
-      val result = RuntimeAttributesValidation.validateMaxRetries(maxRetries,
-        "Failed to get maxRetries key from runtime attributes".invalidNel)
+      val result =
+        RuntimeAttributesValidation.validateMaxRetries(maxRetries,
+                                                       "Failed to get maxRetries key from runtime attributes".invalidNel
+        )
       result match {
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) => assert(e.head == "Expecting maxRetries runtime attribute value greater than or equal to 0")
diff --git a/centaur/src/it/scala/centaur/AbstractCentaurTestCaseSpec.scala b/centaur/src/it/scala/centaur/AbstractCentaurTestCaseSpec.scala
index 1ddebb6a09a..5a6606bce68 100644
--- a/centaur/src/it/scala/centaur/AbstractCentaurTestCaseSpec.scala
+++ b/centaur/src/it/scala/centaur/AbstractCentaurTestCaseSpec.scala
@@ -20,7 +20,10 @@ import org.scalatest.matchers.should.Matchers
 import scala.concurrent.Future
 
 @DoNotDiscover
-abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String], cromwellTracker: Option[CromwellTracker] = None) extends AsyncFlatSpec with Matchers {
+abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String],
+                                           cromwellTracker: Option[CromwellTracker] = None
+) extends AsyncFlatSpec
+    with Matchers {
 
   /*
   NOTE: We need to statically initialize the object so that the exceptions appear here in the class constructor.
@@ -47,10 +50,12 @@ abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String], cromw
     val duplicateTestNames = allTestsCases
       .map(_.workflow.testName)
       .groupBy(identity)
-      .collect({ case (key, values) if values.lengthCompare(1) > 0 => key })
+      .collect { case (key, values) if values.lengthCompare(1) > 0 => key }
     if (duplicateTestNames.nonEmpty) {
-      throw new RuntimeException("The following test names are duplicated in more than one test file: " +
-        duplicateTestNames.mkString(", "))
+      throw new RuntimeException(
+        "The following test names are duplicated in more than one test file: " +
+          duplicateTestNames.mkString(", ")
+      )
     }
     allTestsCases
   }
@@ -62,7 +67,9 @@ abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String], cromw
     } yield submitResponse
 
     // Make tags, but enforce lowercase:
-    val tags = (testCase.testOptions.tags :+ testCase.workflow.testName :+ testCase.testFormat.name) map { x => Tag(x.toLowerCase) }
+    val tags = (testCase.testOptions.tags :+ testCase.workflow.testName :+ testCase.testFormat.name) map { x =>
+      Tag(x.toLowerCase)
+    }
     val isIgnored = testCase.isIgnored(cromwellBackends)
     val retries = if (testCase.workflow.retryTestFailures) ErrorReporters.retryAttempts else 0
 
@@ -110,7 +117,10 @@ abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String], cromw
         testName = testCase.workflow.testName + " (draft-2 to 1.0 upgrade)",
         data = testCase.workflow.data.copy(
           workflowContent = Option(upgradeResult.stdout.get), // this '.get' catches an error if upgrade fails
-          zippedImports = Option(upgradedImportsDir.zip()))))(cromwellTracker) // An empty zip appears to be completely harmless, so no special handling
+          zippedImports = Option(upgradedImportsDir.zip())
+        )
+      )
+    )(cromwellTracker) // An empty zip appears to be completely harmless, so no special handling
 
     rootWorkflowFile.delete(swallowIOExceptions = true)
     upgradedImportsDir.delete(swallowIOExceptions = true)
@@ -123,14 +133,15 @@ abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String], cromw
                         tags: List[Tag],
                         ignore: Boolean,
                         retries: Int,
-                        runTest: => IO[SubmitResponse]): Unit = {
+                        runTest: => IO[SubmitResponse]
+  ): Unit = {
 
     val itShould: ItVerbString = it should testCase.name
 
     tags match {
       case Nil => runOrDont(itShould, ignore, testCase, retries, runTest)
       case head :: Nil => runOrDont(itShould taggedAs head, ignore, testCase, retries, runTest)
-      case head :: tail => runOrDont(itShould taggedAs(head, tail: _*), ignore, testCase, retries, runTest)
+      case head :: tail => runOrDont(itShould taggedAs (head, tail: _*), ignore, testCase, retries, runTest)
     }
   }
 
@@ -138,26 +149,26 @@ abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String], cromw
                         ignore: Boolean,
                         testCase: CentaurTestCase,
                         retries: Int,
-                        runTest: => IO[SubmitResponse]): Unit = {
+                        runTest: => IO[SubmitResponse]
+  ): Unit =
     if (ignore) {
       itVerbString ignore Future.successful(succeed)
     } else {
       itVerbString in tryTryAgain(testCase, runTest, retries).unsafeToFuture().map(_ => succeed)
     }
-  }
 
   private def runOrDont(itVerbStringTaggedAs: ItVerbStringTaggedAs,
                         ignore: Boolean,
                         testCase: CentaurTestCase,
                         retries: Int,
-                        runTest: => IO[SubmitResponse]): Unit = {
+                        runTest: => IO[SubmitResponse]
+  ): Unit =
     if (ignore) {
       itVerbStringTaggedAs ignore Future.successful(succeed)
     } else {
       itVerbStringTaggedAs in
         tryTryAgain(testCase, runTest, retries).unsafeToFuture().map(_ => succeed)
     }
-  }
 
   /**
     * Returns an IO effect that will recursively try to run a test.
@@ -168,21 +179,27 @@ abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String], cromw
     * @param attempt Current zero based attempt.
     * @return IO effect that will run the test, possibly retrying.
     */
-  private def tryTryAgain(testCase: CentaurTestCase, runTest: => IO[SubmitResponse], retries: Int, attempt: Int = 0): IO[SubmitResponse] = {
+  private def tryTryAgain(testCase: CentaurTestCase,
+                          runTest: => IO[SubmitResponse],
+                          retries: Int,
+                          attempt: Int = 0
+  ): IO[SubmitResponse] = {
 
     def maybeRetry(centaurTestException: CentaurTestException): IO[SubmitResponse] = {
 
-      def clearCachedResults(workflowId: WorkflowId): IO[Unit] = CromwellDatabaseCallCaching.clearCachedResults(workflowId.toString)
+      def clearCachedResults(workflowId: WorkflowId): IO[Unit] =
+        CromwellDatabaseCallCaching.clearCachedResults(workflowId.toString)
 
       val testEnvironment = TestEnvironment(testCase, retries, attempt)
       for {
         _ <- ErrorReporters.logFailure(testEnvironment, centaurTestException)
-        r <- if (attempt < retries) {
-          testCase.submittedWorkflowTracker.cleanUpBeforeRetry(clearCachedResults) *>
-            tryTryAgain(testCase, runTest, retries, attempt + 1)
-        } else {
-          IO.raiseError(centaurTestException)
-        }
+        r <-
+          if (attempt < retries) {
+            testCase.submittedWorkflowTracker.cleanUpBeforeRetry(clearCachedResults) *>
+              tryTryAgain(testCase, runTest, retries, attempt + 1)
+          } else {
+            IO.raiseError(centaurTestException)
+          }
       } yield r
     }
 
@@ -207,11 +224,10 @@ abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String], cromw
   /**
    * Clean up temporary zip files created for Imports testing.
    */
-  private def cleanUpImports(wfData: WorkflowData) = {
+  private def cleanUpImports(wfData: WorkflowData) =
     wfData.zippedImports match {
       case Some(zipFile) => zipFile.delete(swallowIOExceptions = true)
       case None => //
     }
-  }
 
 }
diff --git a/centaur/src/it/scala/centaur/AbstractCromwellEngineOrBackendUpgradeTestCaseSpec.scala b/centaur/src/it/scala/centaur/AbstractCromwellEngineOrBackendUpgradeTestCaseSpec.scala
index c55c0c5b17a..04f03d1eacf 100644
--- a/centaur/src/it/scala/centaur/AbstractCromwellEngineOrBackendUpgradeTestCaseSpec.scala
+++ b/centaur/src/it/scala/centaur/AbstractCromwellEngineOrBackendUpgradeTestCaseSpec.scala
@@ -13,7 +13,7 @@ import scala.concurrent.Future
 
 @DoNotDiscover
 abstract class AbstractCromwellEngineOrBackendUpgradeTestCaseSpec(cromwellBackends: List[String])
-  extends AbstractCentaurTestCaseSpec(cromwellBackends)
+    extends AbstractCentaurTestCaseSpec(cromwellBackends)
     with CentaurTestSuiteShutdown
     with BeforeAndAfter {
 
@@ -27,15 +27,20 @@ abstract class AbstractCromwellEngineOrBackendUpgradeTestCaseSpec(cromwellBacken
   override protected def beforeAll(): Unit = {
     super.beforeAll()
     val beforeAllIo = for {
-      _ <- checkIsEmpty(cromwellDatabase.engineDatabase, cromwellDatabase.engineDatabase.existsJobKeyValueEntries(), testType)
-      _ <- checkIsEmpty(cromwellDatabase.metadataDatabase, cromwellDatabase.metadataDatabase.existsMetadataEntries(), testType)
+      _ <- checkIsEmpty(cromwellDatabase.engineDatabase,
+                        cromwellDatabase.engineDatabase.existsJobKeyValueEntries(),
+                        testType
+      )
+      _ <- checkIsEmpty(cromwellDatabase.metadataDatabase,
+                        cromwellDatabase.metadataDatabase.existsMetadataEntries(),
+                        testType
+      )
     } yield ()
     beforeAllIo.unsafeRunSync()
   }
 
-  private def failNotSlick(database: SqlDatabase): IO[Unit] = {
+  private def failNotSlick(database: SqlDatabase): IO[Unit] =
     IO.raiseError(new RuntimeException(s"Expected a slick database for ${database.connectionDescription}."))
-  }
 
   after {
     val afterIo = for {
@@ -54,26 +59,29 @@ abstract class AbstractCromwellEngineOrBackendUpgradeTestCaseSpec(cromwellBacken
   def isMatchingUpgradeTest(testCase: CentaurTestCase): Boolean
 }
 
-
 object AbstractCromwellEngineOrBackendUpgradeTestCaseSpec {
-  private def checkIsEmpty(database: SqlDatabase, lookup: => Future[Boolean], testType: => String)(implicit cs: ContextShift[IO]): IO[Unit] = {
-    IO.fromFuture(IO(lookup)).flatMap(exists =>
-      if (exists) {
-        IO(Assertions.fail(
-          s"Database ${database.connectionDescription} contains data. " +
-            s"$testType tests should only be run on a completely empty database. " +
-            "You may need to manually drop and recreate the database to continue."
-        ))
-      } else {
-        IO.unit
-      }
-    )
-  }
+  private def checkIsEmpty(database: SqlDatabase, lookup: => Future[Boolean], testType: => String)(implicit
+    cs: ContextShift[IO]
+  ): IO[Unit] =
+    IO.fromFuture(IO(lookup))
+      .flatMap(exists =>
+        if (exists) {
+          IO(
+            Assertions.fail(
+              s"Database ${database.connectionDescription} contains data. " +
+                s"$testType tests should only be run on a completely empty database. " +
+                "You may need to manually drop and recreate the database to continue."
+            )
+          )
+        } else {
+          IO.unit
+        }
+      )
 
   private def recreateDatabase(slickDatabase: SlickDatabase)(implicit cs: ContextShift[IO]): IO[Unit] = {
     import slickDatabase.dataAccess.driver.api._
     val schemaName = slickDatabase.databaseConfig.getOrElse("db.cromwell-database-name", "cromwell_test")
-    //noinspection SqlDialectInspection
+    // noinspection SqlDialectInspection
     for {
       _ <- IO.fromFuture(IO(slickDatabase.database.run(sqlu"""DROP SCHEMA IF EXISTS #$schemaName""")))
       _ <- IO.fromFuture(IO(slickDatabase.database.run(sqlu"""CREATE SCHEMA #$schemaName""")))
diff --git a/centaur/src/it/scala/centaur/CentaurTestSuite.scala b/centaur/src/it/scala/centaur/CentaurTestSuite.scala
index 1746caee32b..27cb3e0d01b 100644
--- a/centaur/src/it/scala/centaur/CentaurTestSuite.scala
+++ b/centaur/src/it/scala/centaur/CentaurTestSuite.scala
@@ -16,13 +16,12 @@ object CentaurTestSuite extends StrictLogging {
   // before we can generate the tests.
   startCromwell()
 
-  def startCromwell(): Unit = {
+  def startCromwell(): Unit =
     CentaurConfig.runMode match {
       case ManagedCromwellServer(preRestart, _, _) =>
         CromwellManager.startCromwell(preRestart)
       case _ =>
     }
-  }
 
   val cromwellBackends = CentaurCromwellClient.backends.unsafeRunSync().supportedBackends.map(_.toLowerCase)
 
@@ -63,9 +62,8 @@ object CentaurTestSuite extends StrictLogging {
 trait CentaurTestSuiteShutdown extends Suite with BeforeAndAfterAll {
   private var shutdownHook: Option[ShutdownHookThread] = _
 
-  override protected def beforeAll() = {
-    shutdownHook = Option(sys.addShutdownHook { CromwellManager.stopCromwell("JVM Shutdown Hook") })
-  }
+  override protected def beforeAll() =
+    shutdownHook = Option(sys.addShutdownHook(CromwellManager.stopCromwell("JVM Shutdown Hook")))
 
   override protected def afterAll() = {
     CromwellManager.stopCromwell("ScalaTest AfterAll")
@@ -78,6 +76,6 @@ trait CentaurTestSuiteShutdown extends Suite with BeforeAndAfterAll {
   * The main centaur test suites, runs sub suites in parallel, but allows better control over the way each nested suite runs.
   */
 class CentaurTestSuite
-  extends Suites(new SequentialTestCaseSpec(), new ParallelTestCaseSpec())
+    extends Suites(new SequentialTestCaseSpec(), new ParallelTestCaseSpec())
     with ParallelTestExecution
     with CentaurTestSuiteShutdown
diff --git a/centaur/src/it/scala/centaur/EngineUpgradeTestCaseSpec.scala b/centaur/src/it/scala/centaur/EngineUpgradeTestCaseSpec.scala
index a16dda39b49..7a386f9d642 100644
--- a/centaur/src/it/scala/centaur/EngineUpgradeTestCaseSpec.scala
+++ b/centaur/src/it/scala/centaur/EngineUpgradeTestCaseSpec.scala
@@ -4,12 +4,13 @@ import centaur.test.standard.CentaurTestCase
 import org.scalatest.DoNotDiscover
 
 @DoNotDiscover
-class EngineUpgradeTestCaseSpec(cromwellBackends: List[String]) extends
-  AbstractCromwellEngineOrBackendUpgradeTestCaseSpec(cromwellBackends) {
+class EngineUpgradeTestCaseSpec(cromwellBackends: List[String])
+    extends AbstractCromwellEngineOrBackendUpgradeTestCaseSpec(cromwellBackends) {
 
   def this() = this(CentaurTestSuite.cromwellBackends)
 
   override def testType: String = "Engine upgrade"
 
-  override def isMatchingUpgradeTest(testCase: CentaurTestCase): Boolean = CentaurTestSuite.isEngineUpgradeTest(testCase)
+  override def isMatchingUpgradeTest(testCase: CentaurTestCase): Boolean =
+    CentaurTestSuite.isEngineUpgradeTest(testCase)
 }
diff --git a/centaur/src/it/scala/centaur/ExternalTestCaseSpec.scala b/centaur/src/it/scala/centaur/ExternalTestCaseSpec.scala
index 529a507301a..84ab3e14d9d 100644
--- a/centaur/src/it/scala/centaur/ExternalTestCaseSpec.scala
+++ b/centaur/src/it/scala/centaur/ExternalTestCaseSpec.scala
@@ -5,7 +5,9 @@ import cats.data.Validated.{Invalid, Valid}
 import centaur.test.standard.CentaurTestCase
 import com.typesafe.scalalogging.StrictLogging
 
-class ExternalTestCaseSpec(cromwellBackends: List[String]) extends AbstractCentaurTestCaseSpec(cromwellBackends) with StrictLogging {
+class ExternalTestCaseSpec(cromwellBackends: List[String])
+    extends AbstractCentaurTestCaseSpec(cromwellBackends)
+    with StrictLogging {
 
   def this() = this(CentaurTestSuite.cromwellBackends)
 
@@ -15,11 +17,10 @@ class ExternalTestCaseSpec(cromwellBackends: List[String]) extends AbstractCenta
       logger.info("No external test to run")
   }
 
-  def runTestFile(testFile: String) = {
+  def runTestFile(testFile: String) =
     CentaurTestCase.fromFile(cromwellTracker = None)(File(testFile)) match {
       case Valid(testCase) => executeStandardTest(testCase)
       case Invalid(error) =>
         fail(s"Invalid test case: ${error.toList.mkString(", ")}")
     }
-  }
 }
diff --git a/centaur/src/it/scala/centaur/PapiUpgradeTestCaseSpec.scala b/centaur/src/it/scala/centaur/PapiUpgradeTestCaseSpec.scala
index 300e50d937c..a63030ba40a 100644
--- a/centaur/src/it/scala/centaur/PapiUpgradeTestCaseSpec.scala
+++ b/centaur/src/it/scala/centaur/PapiUpgradeTestCaseSpec.scala
@@ -5,7 +5,7 @@ import org.scalatest.DoNotDiscover
 
 @DoNotDiscover
 class PapiUpgradeTestCaseSpec(cromwellBackends: List[String])
-  extends AbstractCromwellEngineOrBackendUpgradeTestCaseSpec(cromwellBackends) {
+    extends AbstractCromwellEngineOrBackendUpgradeTestCaseSpec(cromwellBackends) {
 
   def this() = this(CentaurTestSuite.cromwellBackends)
 
diff --git a/centaur/src/it/scala/centaur/ParallelTestCaseSpec.scala b/centaur/src/it/scala/centaur/ParallelTestCaseSpec.scala
index 456c974537a..a498807b14f 100644
--- a/centaur/src/it/scala/centaur/ParallelTestCaseSpec.scala
+++ b/centaur/src/it/scala/centaur/ParallelTestCaseSpec.scala
@@ -3,15 +3,15 @@ package centaur
 import centaur.CentaurTestSuite.cromwellTracker
 import org.scalatest._
 
-
 /**
   * Runs test cases in parallel, this should be the default type for tests unless they would otherwise crosstalk in undesirable
   * ways with other tests and must be made sequential.
   */
 @DoNotDiscover
 class ParallelTestCaseSpec(cromwellBackends: List[String])
-  extends AbstractCentaurTestCaseSpec(cromwellBackends, cromwellTracker = cromwellTracker) with ParallelTestExecution {
-  
+    extends AbstractCentaurTestCaseSpec(cromwellBackends, cromwellTracker = cromwellTracker)
+    with ParallelTestExecution {
+
   def this() = this(CentaurTestSuite.cromwellBackends)
 
   allTestCases.filter(_.testFormat.isParallel) foreach executeStandardTest
diff --git a/centaur/src/it/scala/centaur/SequentialTestCaseSpec.scala b/centaur/src/it/scala/centaur/SequentialTestCaseSpec.scala
index ab350f89fc1..12287d4686c 100644
--- a/centaur/src/it/scala/centaur/SequentialTestCaseSpec.scala
+++ b/centaur/src/it/scala/centaur/SequentialTestCaseSpec.scala
@@ -8,7 +8,9 @@ import org.scalatest.matchers.should.Matchers
   * such that the restarting tests execute sequentially to avoid a mayhem of Cromwell restarts
  */
 @DoNotDiscover
-class SequentialTestCaseSpec(cromwellBackends: List[String]) extends AbstractCentaurTestCaseSpec(cromwellBackends) with Matchers {
+class SequentialTestCaseSpec(cromwellBackends: List[String])
+    extends AbstractCentaurTestCaseSpec(cromwellBackends)
+    with Matchers {
 
   def this() = this(CentaurTestSuite.cromwellBackends)
 
diff --git a/centaur/src/it/scala/centaur/WdlUpgradeTestCaseSpec.scala b/centaur/src/it/scala/centaur/WdlUpgradeTestCaseSpec.scala
index 474bf0a7327..93f4457d050 100644
--- a/centaur/src/it/scala/centaur/WdlUpgradeTestCaseSpec.scala
+++ b/centaur/src/it/scala/centaur/WdlUpgradeTestCaseSpec.scala
@@ -4,7 +4,9 @@ import org.scalatest.{DoNotDiscover, ParallelTestExecution}
 
 @DoNotDiscover
 class WdlUpgradeTestCaseSpec(cromwellBackends: List[String])
-  extends AbstractCentaurTestCaseSpec(cromwellBackends) with ParallelTestExecution with CentaurTestSuiteShutdown {
+    extends AbstractCentaurTestCaseSpec(cromwellBackends)
+    with ParallelTestExecution
+    with CentaurTestSuiteShutdown {
 
   def this() = this(CentaurTestSuite.cromwellBackends)
 
diff --git a/centaur/src/it/scala/centaur/callcaching/CromwellDatabaseCallCaching.scala b/centaur/src/it/scala/centaur/callcaching/CromwellDatabaseCallCaching.scala
index b7976e64d97..6d3888767b9 100644
--- a/centaur/src/it/scala/centaur/callcaching/CromwellDatabaseCallCaching.scala
+++ b/centaur/src/it/scala/centaur/callcaching/CromwellDatabaseCallCaching.scala
@@ -11,7 +11,6 @@ object CromwellDatabaseCallCaching extends StrictLogging {
 
   private val cromwellDatabase = CromwellDatabase.instance
 
-  def clearCachedResults(workflowId: String)(implicit executionContext: ExecutionContext): IO[Unit] = {
+  def clearCachedResults(workflowId: String)(implicit executionContext: ExecutionContext): IO[Unit] =
     IO.fromFuture(IO(cromwellDatabase.engineDatabase.invalidateCallCacheEntryIdsForWorkflowId(workflowId)))
-  }
 }
diff --git a/centaur/src/it/scala/centaur/reporting/AggregatedIo.scala b/centaur/src/it/scala/centaur/reporting/AggregatedIo.scala
index e9dacd18987..5b8affee887 100644
--- a/centaur/src/it/scala/centaur/reporting/AggregatedIo.scala
+++ b/centaur/src/it/scala/centaur/reporting/AggregatedIo.scala
@@ -11,6 +11,7 @@ import cats.syntax.traverse._
   * Validation that aggregates multiple throwable errors.
   */
 object AggregatedIo {
+
   /**
     * Similar to common.validation.ErrorOr#ErrorOr, but retains the stack traces.
     */
@@ -39,16 +40,16 @@ object AggregatedIo {
   /**
     * Creates an aggregated exception for multiple exceptions.
     */
-  class AggregatedException private[reporting](exceptionContext: String, suppressed: List[Throwable])
-    extends RuntimeException(
-      {
-        val suppressedZipped = suppressed.zipWithIndex
-        val messages = suppressedZipped map {
-          case (throwable, index) => s"\n  ${index+1}: ${throwable.getMessage}"
+  class AggregatedException private[reporting] (exceptionContext: String, suppressed: List[Throwable])
+      extends RuntimeException(
+        {
+          val suppressedZipped = suppressed.zipWithIndex
+          val messages = suppressedZipped map { case (throwable, index) =>
+            s"\n  ${index + 1}: ${throwable.getMessage}"
+          }
+          s"$exceptionContext:$messages"
         }
-        s"$exceptionContext:$messages"
-      }
-    ) {
+      ) {
     suppressed foreach addSuppressed
   }
 
diff --git a/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala b/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
index 9a88a9ac109..b2335e4a794 100644
--- a/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
+++ b/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
@@ -14,7 +14,14 @@ import com.google.api.gax.retrying.RetrySettings
 import com.google.api.services.bigquery.BigqueryScopes
 import com.google.auth.Credentials
 import com.google.cloud.bigquery.InsertAllRequest.RowToInsert
-import com.google.cloud.bigquery.{BigQuery, BigQueryError, BigQueryOptions, InsertAllRequest, InsertAllResponse, TableId}
+import com.google.cloud.bigquery.{
+  BigQuery,
+  BigQueryError,
+  BigQueryOptions,
+  InsertAllRequest,
+  InsertAllResponse,
+  TableId
+}
 import common.util.TimeUtil._
 import common.validation.Validation._
 import cromwell.cloudsupport.gcp.GoogleConfiguration
@@ -35,8 +42,9 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
 
   override lazy val destination: String = bigQueryProjectOption.map(_ + "/").getOrElse("") + bigQueryDataset
 
-  private val retrySettings: RetrySettings = {
-    RetrySettings.newBuilder()
+  private val retrySettings: RetrySettings =
+    RetrySettings
+      .newBuilder()
       .setMaxAttempts(3)
       .setTotalTimeout(Duration.ofSeconds(30))
       .setInitialRetryDelay(Duration.ofMillis(100))
@@ -46,7 +54,6 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
       .setRpcTimeoutMultiplier(1.1)
       .setMaxRpcTimeout(Duration.ofSeconds(5))
       .build()
-  }
 
   private val bigQueryCredentials: Credentials = GoogleConfiguration
     .apply(params.rootConfig)
@@ -54,7 +61,8 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
     .unsafe
     .credentials(Set(BigqueryScopes.BIGQUERY_INSERTDATA))
 
-  private val bigQuery: BigQuery = BigQueryOptions.newBuilder()
+  private val bigQuery: BigQuery = BigQueryOptions
+    .newBuilder()
     .setRetrySettings(retrySettings)
     .setCredentials(bigQueryCredentials)
     .build()
@@ -65,21 +73,19 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
   private val jobKeyValueTableId = bigQueryTable("job_key_value")
   private val metadataTableId = bigQueryTable("metadata")
 
-  def bigQueryTable(table: String): TableId = {
+  def bigQueryTable(table: String): TableId =
     bigQueryProjectOption match {
       case Some(project) => TableId.of(project, bigQueryDataset, table)
       case None => TableId.of(bigQueryDataset, table)
     }
-  }
 
   /**
     * In this ErrorReporter implementation this method will send information about exceptions of type
     * CentaurTestException to BigQuery. Exceptions of other types will be ignored.
     */
-  override def logFailure(testEnvironment: TestEnvironment,
-                          ciEnvironment: CiEnvironment,
-                          throwable: Throwable)
-                         (implicit executionContext: ExecutionContext): IO[Unit] = {
+  override def logFailure(testEnvironment: TestEnvironment, ciEnvironment: CiEnvironment, throwable: Throwable)(implicit
+    executionContext: ExecutionContext
+  ): IO[Unit] =
     throwable match {
       case centaurTestException: CentaurTestException =>
         for {
@@ -98,57 +104,62 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
       case _ =>
         IO.unit // this ErrorReporter only supports exceptions of CentaurTestException type
     }
-  }
 
   private def sendBigQueryFailure(testEnvironment: TestEnvironment,
                                   ciEnvironment: CiEnvironment,
                                   centaurTestException: CentaurTestException,
                                   callAttemptFailures: Vector[CallAttemptFailure],
                                   jobKeyValueEntries: Seq[JobKeyValueEntry],
-                                  metadataEntries: Seq[MetadataEntry]): IO[Unit] = {
+                                  metadataEntries: Seq[MetadataEntry]
+  ): IO[Unit] = {
 
     val metadata: IO[List[BigQueryError]] = {
-      val metadataRows: List[util.List[RowToInsert]] = metadataEntries.map(toMetadataRow).grouped(10000).map(_.asJava).toList
+      val metadataRows: List[util.List[RowToInsert]] =
+        metadataEntries.map(toMetadataRow).grouped(10000).map(_.asJava).toList
       val metadataRequest: List[InsertAllRequest] = metadataRows.map(InsertAllRequest.of(metadataTableId, _))
 
       if (metadataEntries.nonEmpty)
-        metadataRequest.traverse[IO, List[BigQueryError]](req => IO(bigQuery.insertAll(req)).map(_.getErrors)).map(_.flatten)
+        metadataRequest
+          .traverse[IO, List[BigQueryError]](req => IO(bigQuery.insertAll(req)).map(_.getErrors))
+          .map(_.flatten)
       else
-        IO{Nil}
+        IO(Nil)
     }
     (IO {
-      val testFailureRow = toTestFailureRow(testEnvironment, ciEnvironment, centaurTestException)
-      val callAttemptFailureRows = callAttemptFailures.map(toCallAttemptFailureRow).asJava
-      val jobKeyValueRows = jobKeyValueEntries.map(toJobKeyValueRow).asJava
-
-      val testFailureRequest = InsertAllRequest.of(testFailureTableId, testFailureRow)
-      val callAttemptFailuresRequest = InsertAllRequest.of(callAttemptFailureTableId, callAttemptFailureRows)
-      val jobKeyValuesRequest = InsertAllRequest.of(jobKeyValueTableId, jobKeyValueRows)
-      val testFailureErrors = bigQuery.insertAll(testFailureRequest).getErrors
-      val callAttemptFailuresErrors =
-        if (callAttemptFailures.nonEmpty) bigQuery.insertAll(callAttemptFailuresRequest).getErrors else Nil
-      val jobKeyValuesErrors =
-        if (jobKeyValueEntries.nonEmpty) bigQuery.insertAll(jobKeyValuesRequest).getErrors else Nil
-
-      testFailureErrors ++ callAttemptFailuresErrors ++ jobKeyValuesErrors
-    }, metadata).mapN(_ ++ _).flatMap {
+       val testFailureRow = toTestFailureRow(testEnvironment, ciEnvironment, centaurTestException)
+       val callAttemptFailureRows = callAttemptFailures.map(toCallAttemptFailureRow).asJava
+       val jobKeyValueRows = jobKeyValueEntries.map(toJobKeyValueRow).asJava
+
+       val testFailureRequest = InsertAllRequest.of(testFailureTableId, testFailureRow)
+       val callAttemptFailuresRequest = InsertAllRequest.of(callAttemptFailureTableId, callAttemptFailureRows)
+       val jobKeyValuesRequest = InsertAllRequest.of(jobKeyValueTableId, jobKeyValueRows)
+       val testFailureErrors = bigQuery.insertAll(testFailureRequest).getErrors
+       val callAttemptFailuresErrors =
+         if (callAttemptFailures.nonEmpty) bigQuery.insertAll(callAttemptFailuresRequest).getErrors else Nil
+       val jobKeyValuesErrors =
+         if (jobKeyValueEntries.nonEmpty) bigQuery.insertAll(jobKeyValuesRequest).getErrors else Nil
+
+       testFailureErrors ++ callAttemptFailuresErrors ++ jobKeyValuesErrors
+     },
+     metadata
+    ).mapN(_ ++ _).flatMap {
       case errors if errors.isEmpty => IO.unit
-      case errors => IO.raiseError {
-        val errorCount = errors.size
-        val threeErrors = errors.map(String.valueOf).distinct.sorted.take(3)
-        val continued = if (errorCount > 3) "\n..." else ""
-        val message = threeErrors.mkString(
-          s"$errorCount error(s) occurred uploading to BigQuery: \n",
-          "\n",
-          continued)
-        new RuntimeException(message)
-      }
+      case errors =>
+        IO.raiseError {
+          val errorCount = errors.size
+          val threeErrors = errors.map(String.valueOf).distinct.sorted.take(3)
+          val continued = if (errorCount > 3) "\n..." else ""
+          val message =
+            threeErrors.mkString(s"$errorCount error(s) occurred uploading to BigQuery: \n", "\n", continued)
+          new RuntimeException(message)
+        }
     }
   }
 
   private def toTestFailureRow(testEnvironment: TestEnvironment,
                                ciEnvironment: CiEnvironment,
-                               centaurTestException: CentaurTestException): RowToInsert = {
+                               centaurTestException: CentaurTestException
+  ): RowToInsert =
     RowToInsert of Map(
       "ci_env_branch" -> ciEnvironment.branch,
       "ci_env_event" -> ciEnvironment.event,
@@ -165,13 +176,12 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
       "test_name" -> Option(testEnvironment.testCase.name),
       "test_stack_trace" -> Option(ExceptionUtils.getStackTrace(centaurTestException)),
       "test_timestamp" -> Option(OffsetDateTime.now.toUtcMilliString),
-      "test_workflow_id" -> centaurTestException.workflowIdOption,
-    ).collect {
-      case (key, Some(value)) => (key, value)
+      "test_workflow_id" -> centaurTestException.workflowIdOption
+    ).collect { case (key, Some(value)) =>
+      (key, value)
     }.asJava
-  }
 
-  private def toCallAttemptFailureRow(callAttemptFailure: CallAttemptFailure): RowToInsert = {
+  private def toCallAttemptFailureRow(callAttemptFailure: CallAttemptFailure): RowToInsert =
     RowToInsert of Map(
       "call_fully_qualified_name" -> Option(callAttemptFailure.callFullyQualifiedName),
       "call_root" -> callAttemptFailure.callRootOption,
@@ -182,24 +192,22 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
       "start" -> callAttemptFailure.startOption.map(_.toUtcMilliString),
       "stderr" -> callAttemptFailure.stderrOption,
       "stdout" -> callAttemptFailure.stdoutOption,
-      "workflow_id" -> Option(callAttemptFailure.workflowId),
-    ).collect {
-      case (key, Some(value)) => (key, value)
+      "workflow_id" -> Option(callAttemptFailure.workflowId)
+    ).collect { case (key, Some(value)) =>
+      (key, value)
     }.asJava
-  }
 
-  private def toJobKeyValueRow(jobKeyValueEntry: JobKeyValueEntry): RowToInsert = {
+  private def toJobKeyValueRow(jobKeyValueEntry: JobKeyValueEntry): RowToInsert =
     RowToInsert of Map[String, Any](
       "call_fully_qualified_name" -> jobKeyValueEntry.callFullyQualifiedName,
       "job_attempt" -> jobKeyValueEntry.jobAttempt,
       "job_index" -> jobKeyValueEntry.jobIndex,
       "store_key" -> jobKeyValueEntry.storeKey,
       "store_value" -> jobKeyValueEntry.storeValue,
-      "workflow_execution_uuid" -> jobKeyValueEntry.workflowExecutionUuid,
+      "workflow_execution_uuid" -> jobKeyValueEntry.workflowExecutionUuid
     ).asJava
-  }
 
-  private def toMetadataRow(metadataEntry: MetadataEntry): RowToInsert = {
+  private def toMetadataRow(metadataEntry: MetadataEntry): RowToInsert =
     RowToInsert of Map(
       "call_fully_qualified_name" -> metadataEntry.callFullyQualifiedName,
       "job_attempt" -> metadataEntry.jobAttempt,
@@ -208,11 +216,10 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
       "metadata_timestamp" -> Option(metadataEntry.metadataTimestamp.toSystemOffsetDateTime.toUtcMilliString),
       "metadata_value" -> metadataEntry.metadataValue.map(_.toRawString),
       "metadata_value_type" -> metadataEntry.metadataValueType,
-      "workflow_execution_uuid" -> Option(metadataEntry.workflowExecutionUuid),
-    ).collect {
-      case (key, Some(value)) => (key, value)
+      "workflow_execution_uuid" -> Option(metadataEntry.workflowExecutionUuid)
+    ).collect { case (key, Some(value)) =>
+      (key, value)
     }.asJava
-  }
 }
 
 object BigQueryReporter {
diff --git a/centaur/src/it/scala/centaur/reporting/CiEnvironment.scala b/centaur/src/it/scala/centaur/reporting/CiEnvironment.scala
index 6750925ca64..0845d8b8c94 100644
--- a/centaur/src/it/scala/centaur/reporting/CiEnvironment.scala
+++ b/centaur/src/it/scala/centaur/reporting/CiEnvironment.scala
@@ -5,8 +5,7 @@ import scala.util.Try
 /**
   * Scala representation of the CI environment values defined in `test.inc.sh`.
   */
-case class CiEnvironment
-(
+case class CiEnvironment(
   isCi: Option[Boolean],
   `type`: Option[String],
   branch: Option[String],
@@ -20,7 +19,7 @@ case class CiEnvironment
 )
 
 object CiEnvironment {
-  def apply(): CiEnvironment = {
+  def apply(): CiEnvironment =
     new CiEnvironment(
       isCi = sys.env.get("CROMWELL_BUILD_IS_CI").flatMap(tryToBoolean),
       `type` = sys.env.get("CROMWELL_BUILD_TYPE"),
@@ -31,9 +30,8 @@ object CiEnvironment {
       provider = sys.env.get("CROMWELL_BUILD_PROVIDER"),
       os = sys.env.get("CROMWELL_BUILD_OS"),
       url = sys.env.get("CROMWELL_BUILD_URL"),
-      centaurType = sys.env.get("CROMWELL_BUILD_CENTAUR_TYPE"),
+      centaurType = sys.env.get("CROMWELL_BUILD_CENTAUR_TYPE")
     )
-  }
 
   /** Try converting the value to a boolean, or return None. */
   private def tryToBoolean(string: String): Option[Boolean] = Try(string.toBoolean).toOption
diff --git a/centaur/src/it/scala/centaur/reporting/ErrorReporter.scala b/centaur/src/it/scala/centaur/reporting/ErrorReporter.scala
index 8481bf94c51..c654ad3cfc0 100644
--- a/centaur/src/it/scala/centaur/reporting/ErrorReporter.scala
+++ b/centaur/src/it/scala/centaur/reporting/ErrorReporter.scala
@@ -8,6 +8,7 @@ import scala.concurrent.ExecutionContext
   * Reports errors during testing.
   */
 trait ErrorReporter {
+
   /** The various parameters for this reporter. */
   def params: ErrorReporterParams
 
@@ -15,8 +16,7 @@ trait ErrorReporter {
   def destination: String
 
   /** Send a report of a failure. */
-  def logFailure(testEnvironment: TestEnvironment,
-                 ciEnvironment: CiEnvironment,
-                 throwable: Throwable)
-                (implicit executionContext: ExecutionContext): IO[Unit]
+  def logFailure(testEnvironment: TestEnvironment, ciEnvironment: CiEnvironment, throwable: Throwable)(implicit
+    executionContext: ExecutionContext
+  ): IO[Unit]
 }
diff --git a/centaur/src/it/scala/centaur/reporting/ErrorReporterCromwellDatabase.scala b/centaur/src/it/scala/centaur/reporting/ErrorReporterCromwellDatabase.scala
index 89a3e5210b8..79e13c47700 100644
--- a/centaur/src/it/scala/centaur/reporting/ErrorReporterCromwellDatabase.scala
+++ b/centaur/src/it/scala/centaur/reporting/ErrorReporterCromwellDatabase.scala
@@ -11,25 +11,25 @@ class ErrorReporterCromwellDatabase(cromwellDatabase: CromwellDatabase) {
 
   import centaur.TestContext._
 
-  def jobKeyValueEntriesIo(workflowExecutionUuidOption: Option[String])
-                          (implicit executionContext: ExecutionContext): IO[Seq[JobKeyValueEntry]] = {
+  def jobKeyValueEntriesIo(workflowExecutionUuidOption: Option[String])(implicit
+    executionContext: ExecutionContext
+  ): IO[Seq[JobKeyValueEntry]] =
     workflowExecutionUuidOption.map(jobKeyValueEntriesIo).getOrElse(IO.pure(Seq.empty))
-  }
 
-  def jobKeyValueEntriesIo(workflowExecutionUuid: String)
-                          (implicit executionContext: ExecutionContext): IO[Seq[JobKeyValueEntry]] = {
+  def jobKeyValueEntriesIo(workflowExecutionUuid: String)(implicit
+    executionContext: ExecutionContext
+  ): IO[Seq[JobKeyValueEntry]] =
     IO.fromFuture(IO(cromwellDatabase.engineDatabase.queryJobKeyValueEntries(workflowExecutionUuid)))
-  }
 
-  def metadataEntriesIo(workflowExecutionUuidOption: Option[String])
-                       (implicit executionContext: ExecutionContext): IO[Seq[MetadataEntry]] = {
+  def metadataEntriesIo(workflowExecutionUuidOption: Option[String])(implicit
+    executionContext: ExecutionContext
+  ): IO[Seq[MetadataEntry]] =
     workflowExecutionUuidOption.map(metadataEntriesIo).getOrElse(IO.pure(Seq.empty))
-  }
 
-  def metadataEntriesIo(workflowExecutionUuid: String)
-                       (implicit executionContext: ExecutionContext): IO[Seq[MetadataEntry]] = {
+  def metadataEntriesIo(workflowExecutionUuid: String)(implicit
+    executionContext: ExecutionContext
+  ): IO[Seq[MetadataEntry]] =
     // 30 seconds is less than production (60s as of 2018-08) but hopefully high enough to work on a CI machine with contended resources
     IO.fromFuture(IO(cromwellDatabase.metadataDatabase.queryMetadataEntries(workflowExecutionUuid, 30.seconds)))
-  }
 
 }
diff --git a/centaur/src/it/scala/centaur/reporting/ErrorReporterParams.scala b/centaur/src/it/scala/centaur/reporting/ErrorReporterParams.scala
index 6e716b82942..9a403e88138 100644
--- a/centaur/src/it/scala/centaur/reporting/ErrorReporterParams.scala
+++ b/centaur/src/it/scala/centaur/reporting/ErrorReporterParams.scala
@@ -5,8 +5,7 @@ import com.typesafe.config.Config
 /**
   * Collects all of the parameters to pass to a new ErrorReporter.
   */
-case class ErrorReporterParams
-(
+case class ErrorReporterParams(
   name: String,
   rootConfig: Config,
   reporterConfig: Config,
diff --git a/centaur/src/it/scala/centaur/reporting/ErrorReporters.scala b/centaur/src/it/scala/centaur/reporting/ErrorReporters.scala
index 8f989e3bd1b..2058264db29 100644
--- a/centaur/src/it/scala/centaur/reporting/ErrorReporters.scala
+++ b/centaur/src/it/scala/centaur/reporting/ErrorReporters.scala
@@ -25,9 +25,8 @@ class ErrorReporters(rootConfig: Config) {
     providersConfig.entrySet.asScala.map(_.getKey.split("\\.").toList.head).toList
   }
 
-  private val errorReportersIo: IO[List[ErrorReporter]] = {
+  private val errorReportersIo: IO[List[ErrorReporter]] =
     AggregatedIo.aggregateExceptions("Errors while creating ErrorReporters", errorReporterNames.map(getErrorReporter))
-  }
 
   val errorReporters: List[ErrorReporter] = errorReportersIo.unsafeRunSync()
 
@@ -42,26 +41,27 @@ class ErrorReporters(rootConfig: Config) {
     * @param throwable            The exception that occurred while running the test.
     * @return An IO effect that will log the failure.
     */
-  def logFailure(testEnvironment: TestEnvironment,
-                 ciEnvironment: CiEnvironment,
-                 throwable: Throwable)
-                (implicit executionContext: ExecutionContext): IO[Unit] = {
+  def logFailure(testEnvironment: TestEnvironment, ciEnvironment: CiEnvironment, throwable: Throwable)(implicit
+    executionContext: ExecutionContext
+  ): IO[Unit] =
     if (errorReporters.isEmpty) {
       // If the there are no reporters, then just "throw" the exception. Do not retry to run the test.
       IO.raiseError(throwable)
     } else {
       val listIo = errorReporters.map(_.logFailure(testEnvironment, ciEnvironment, throwable))
-      AggregatedIo.aggregateExceptions("Errors while reporting a failure", listIo).handleErrorWith(err => {
-        err.addSuppressed(throwable)
-        IO.raiseError(err)
-      }).void
+      AggregatedIo
+        .aggregateExceptions("Errors while reporting a failure", listIo)
+        .handleErrorWith { err =>
+          err.addSuppressed(throwable)
+          IO.raiseError(err)
+        }
+        .void
     }
-  }
 
   /**
     * Constructs the IO reporter by name.
     */
-  private def getErrorReporter(errorReporterName: String): IO[ErrorReporter] = {
+  private def getErrorReporter(errorReporterName: String): IO[ErrorReporter] =
     IO {
       val clazz = errorReporterConfig.getString(s"providers.$errorReporterName.class")
       val reporterConfig = errorReporterConfig.getOrElse(s"providers.$errorReporterName.config", ConfigFactory.empty)
@@ -69,7 +69,6 @@ class ErrorReporters(rootConfig: Config) {
       val params = ErrorReporterParams(errorReporterName, rootConfig, reporterConfig, errorReporterCromwellDatabase)
       constructor.newInstance(params).asInstanceOf[ErrorReporter]
     }
-  }
 }
 
 object ErrorReporters extends StrictLogging {
@@ -84,9 +83,8 @@ object ErrorReporters extends StrictLogging {
   if (retryAttempts > 0)
     logger.info("Error retry count: {}", retryAttempts)
 
-  def logFailure(testEnvironment: TestEnvironment,
-                 throwable: Throwable)
-                (implicit executionContext: ExecutionContext): IO[Unit] = {
+  def logFailure(testEnvironment: TestEnvironment, throwable: Throwable)(implicit
+    executionContext: ExecutionContext
+  ): IO[Unit] =
     errorReporters.logFailure(testEnvironment, ciEnvironment, throwable)
-  }
 }
diff --git a/centaur/src/it/scala/centaur/reporting/GcsReporter.scala b/centaur/src/it/scala/centaur/reporting/GcsReporter.scala
index 41e15d80b3b..55b5be270f4 100644
--- a/centaur/src/it/scala/centaur/reporting/GcsReporter.scala
+++ b/centaur/src/it/scala/centaur/reporting/GcsReporter.scala
@@ -9,7 +9,10 @@ import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.ExecutionContext
 
-class GcsReporter(override val params: ErrorReporterParams) extends ErrorReporter with SuccessReporter with StrictLogging {
+class GcsReporter(override val params: ErrorReporterParams)
+    extends ErrorReporter
+    with SuccessReporter
+    with StrictLogging {
   val storage = StorageOptions.getDefaultInstance.getService
   val reportBucket = params.reporterConfig.as[String]("report-bucket")
   val reportPath = params.reporterConfig.as[String]("report-path")
@@ -21,10 +24,9 @@ class GcsReporter(override val params: ErrorReporterParams) extends ErrorReporte
     * In this ErrorReporter implementation this method will save information about exceptions of type
     * CentaurTestException to GCS. Exceptions of other types will be ignored.
     */
-  override def logFailure(testEnvironment: TestEnvironment,
-                          ciEnvironment: CiEnvironment,
-                          throwable: Throwable)
-                         (implicit executionContext: ExecutionContext): IO[Unit] = {
+  override def logFailure(testEnvironment: TestEnvironment, ciEnvironment: CiEnvironment, throwable: Throwable)(implicit
+    executionContext: ExecutionContext
+  ): IO[Unit] =
     throwable match {
       case centaurTestException: CentaurTestException =>
         logger.info(s"Reporting failed metadata to gs://$reportBucket/$reportPath")
@@ -32,7 +34,6 @@ class GcsReporter(override val params: ErrorReporterParams) extends ErrorReporte
       case _ =>
         IO.unit // this ErrorReporter only supports exceptions of CentaurTestException type
     }
-  }
 
   override def logSuccessfulRun(submitResponse: SubmitWorkflowResponse): IO[Unit] = {
     logger.info(s"Reporting successful metadata to gs://$reportBucket/$reportPath")
@@ -44,7 +45,8 @@ class GcsReporter(override val params: ErrorReporterParams) extends ErrorReporte
 
   private def pushJsonToGcs(json: String) = IO {
     storage.create(
-      BlobInfo.newBuilder(reportBucket, reportPath)
+      BlobInfo
+        .newBuilder(reportBucket, reportPath)
         .setContentType("application/json")
         .build(),
       json.toArray.map(_.toByte)
diff --git a/centaur/src/it/scala/centaur/reporting/Slf4jReporter.scala b/centaur/src/it/scala/centaur/reporting/Slf4jReporter.scala
index 4332e01db24..ff5aeb5f7d5 100644
--- a/centaur/src/it/scala/centaur/reporting/Slf4jReporter.scala
+++ b/centaur/src/it/scala/centaur/reporting/Slf4jReporter.scala
@@ -13,15 +13,13 @@ import scala.concurrent.ExecutionContext
   * Useful as a backup in cases where another reporter is not available, for example in external PRs where secure
   * environment variables are not available.
   */
-class Slf4jReporter(override val params: ErrorReporterParams)
-  extends ErrorReporter with StrictLogging {
+class Slf4jReporter(override val params: ErrorReporterParams) extends ErrorReporter with StrictLogging {
 
   override lazy val destination: String = "error"
 
-  override def logFailure(testEnvironment: TestEnvironment,
-                          ciEnvironment: CiEnvironment,
-                          throwable: Throwable)
-                         (implicit executionContext: ExecutionContext): IO[Unit] = {
+  override def logFailure(testEnvironment: TestEnvironment, ciEnvironment: CiEnvironment, throwable: Throwable)(implicit
+    executionContext: ExecutionContext
+  ): IO[Unit] =
     IO {
 
       val errorMessage = throwable match {
@@ -41,9 +39,9 @@ class Slf4jReporter(override val params: ErrorReporterParams)
       if (testEnvironment.attempt >= testEnvironment.retries) {
         logger.error(message, throwable)
       } else {
-        val messageWithShortExceptionContext = message + " (" + ExceptionUtils.getMessage(throwable).replace("\n", " ").take(150) + "[...])"
+        val messageWithShortExceptionContext =
+          message + " (" + ExceptionUtils.getMessage(throwable).replace("\n", " ").take(150) + "[...])"
         logger.warn(messageWithShortExceptionContext)
       }
     }
-  }
 }
diff --git a/centaur/src/it/scala/centaur/reporting/SuccessReporter.scala b/centaur/src/it/scala/centaur/reporting/SuccessReporter.scala
index 2453ca71898..fb0c6a389e9 100644
--- a/centaur/src/it/scala/centaur/reporting/SuccessReporter.scala
+++ b/centaur/src/it/scala/centaur/reporting/SuccessReporter.scala
@@ -12,13 +12,13 @@ object SuccessReporters {
    * This is gross and piggy backs on the error reporting code but achieves what we need for now without a refactoring
    * of the error reporting code to handle both success and error reporting
    */
-  private val successReporters: List[ErrorReporter with SuccessReporter] = ErrorReporters.errorReporters.errorReporters.collect({case s: SuccessReporter => s })
+  private val successReporters: List[ErrorReporter with SuccessReporter] =
+    ErrorReporters.errorReporters.errorReporters.collect { case s: SuccessReporter => s }
 
-  def logSuccessfulRun(submitResponse: SubmitWorkflowResponse): IO[SubmitResponse] = {
-    if (successReporters.isEmpty) IO.pure(submitResponse) 
+  def logSuccessfulRun(submitResponse: SubmitWorkflowResponse): IO[SubmitResponse] =
+    if (successReporters.isEmpty) IO.pure(submitResponse)
     else {
       val listIo = successReporters.map(_.logSuccessfulRun(submitResponse))
       AggregatedIo.aggregateExceptions("Errors while reporting centaur success", listIo).map(_ => submitResponse)
     }
-  }
 }
diff --git a/centaur/src/main/scala/centaur/CentaurConfig.scala b/centaur/src/main/scala/centaur/CentaurConfig.scala
index f17c288283a..c15ae31f453 100644
--- a/centaur/src/main/scala/centaur/CentaurConfig.scala
+++ b/centaur/src/main/scala/centaur/CentaurConfig.scala
@@ -41,16 +41,19 @@ sealed trait CentaurRunMode {
   def cromwellUrl: URL
 }
 
-case class UnmanagedCromwellServer(cromwellUrl : URL) extends CentaurRunMode
-case class ManagedCromwellServer(preRestart: CromwellConfiguration, postRestart: CromwellConfiguration, withRestart: Boolean) extends CentaurRunMode {
+case class UnmanagedCromwellServer(cromwellUrl: URL) extends CentaurRunMode
+case class ManagedCromwellServer(preRestart: CromwellConfiguration,
+                                 postRestart: CromwellConfiguration,
+                                 withRestart: Boolean
+) extends CentaurRunMode {
   override val cromwellUrl = new URL(s"http://localhost:${CromwellManager.ManagedCromwellPort}")
 }
 
 object CentaurConfig {
   lazy val conf: Config = ConfigFactory.load().getConfig("centaur")
-  
+
   lazy val runMode: CentaurRunMode = CentaurRunMode(conf)
-  
+
   lazy val cromwellUrl: URL = runMode.cromwellUrl
   lazy val workflowProgressTimeout: FiniteDuration = conf.getDuration("workflow-progress-timeout").toScala
   lazy val sendReceiveTimeout: FiniteDuration = conf.getDuration("sendReceiveTimeout").toScala
diff --git a/centaur/src/main/scala/centaur/CromwellManager.scala b/centaur/src/main/scala/centaur/CromwellManager.scala
index a53416a0ded..55c317b41b3 100644
--- a/centaur/src/main/scala/centaur/CromwellManager.scala
+++ b/centaur/src/main/scala/centaur/CromwellManager.scala
@@ -18,15 +18,15 @@ object CromwellManager extends StrictLogging {
   private var cromwellProcess: Option[CromwellProcess] = None
   private var _ready: Boolean = false
   private var _isManaged: Boolean = false
-  
+
   /**
     * Returns true if Cromwell is ready to be queried, false otherwise
     * In Unmanaged mode, this is irrelevant so always return true.
     * In managed mode return the value of _ready
     */
   def isReady: Boolean = !_isManaged || _ready
-  
-  // Check that we have a cromwellProcess, that this process is alive, and that cromwell is ready to accept requests 
+
+  // Check that we have a cromwellProcess, that this process is alive, and that cromwell is ready to accept requests
   private def isAlive(checkType: String): Boolean = {
     val processAlive = cromwellProcess.exists(_.isAlive)
     logger.info(s"Cromwell process alive $checkType = $processAlive")
@@ -76,14 +76,14 @@ object CromwellManager extends StrictLogging {
   def stopCromwell(reason: String) = {
     _ready = false
     logger.info(s"Stopping Cromwell... ($reason)")
-    try {
+    try
       cromwellProcess foreach { _.stop() }
-    } catch {
-      case e: Exception => 
+    catch {
+      case e: Exception =>
         logger.error("Caught exception while stopping Cromwell")
         e.printStackTrace()
     }
-    
+
     cromwellProcess = None
   }
 }
diff --git a/centaur/src/main/scala/centaur/CromwellTracker.scala b/centaur/src/main/scala/centaur/CromwellTracker.scala
index 4a89dea302d..1ec6fefe54c 100644
--- a/centaur/src/main/scala/centaur/CromwellTracker.scala
+++ b/centaur/src/main/scala/centaur/CromwellTracker.scala
@@ -14,7 +14,6 @@ import org.apache.commons.math3.stat.inference.ChiSquareTest
 
 import scala.language.postfixOps
 
-
 case class CromwellTracker(backendCount: Int, configuredSignificance: Double) extends StrictLogging {
   var counts: Map[String, Int] = Map()
   def track(metadata: WorkflowMetadata): Unit = {
@@ -45,10 +44,15 @@ case class CromwellTracker(backendCount: Int, configuredSignificance: Double) ex
     val actual: Array[Long] = counts.values map { _.toLong } toArray
 
     val observedSignificance = new ChiSquareTest().chiSquareTest(expected, actual)
-    logger.info(f"configured/observed horicromtal significance levels: $configuredSignificance%.4f/$observedSignificance%.4f", configuredSignificance, observedSignificance)
+    logger.info(
+      f"configured/observed horicromtal significance levels: $configuredSignificance%.4f/$observedSignificance%.4f",
+      configuredSignificance,
+      observedSignificance
+    )
 
     if (observedSignificance < configuredSignificance) {
-      val message = f"Failed horicromtal check: observed significance level $observedSignificance%.4f, minimum of $configuredSignificance%.4f was required"
+      val message =
+        f"Failed horicromtal check: observed significance level $observedSignificance%.4f, minimum of $configuredSignificance%.4f was required"
       throw new RuntimeException(message)
     }
   }
diff --git a/centaur/src/main/scala/centaur/DockerComposeCromwellConfiguration.scala b/centaur/src/main/scala/centaur/DockerComposeCromwellConfiguration.scala
index 6fab385537b..eeb1df1557f 100644
--- a/centaur/src/main/scala/centaur/DockerComposeCromwellConfiguration.scala
+++ b/centaur/src/main/scala/centaur/DockerComposeCromwellConfiguration.scala
@@ -14,13 +14,17 @@ object DockerComposeCromwellConfiguration {
   }
 }
 
-case class DockerComposeCromwellConfiguration(dockerTag: String, dockerComposeFile: String, conf: String, logFile: String) extends CromwellConfiguration {
+case class DockerComposeCromwellConfiguration(dockerTag: String,
+                                              dockerComposeFile: String,
+                                              conf: String,
+                                              logFile: String
+) extends CromwellConfiguration {
   override def createProcess: CromwellProcess = {
-    case class DockerComposeCromwellProcess(override val cromwellConfiguration: DockerComposeCromwellConfiguration) extends CromwellProcess {
+    case class DockerComposeCromwellProcess(override val cromwellConfiguration: DockerComposeCromwellConfiguration)
+        extends CromwellProcess {
 
-      private def composeCommand(command: String*): Array[String] = {
+      private def composeCommand(command: String*): Array[String] =
         Array("docker-compose", "-f", dockerComposeFile) ++ command
-      }
 
       private val startCommand = composeCommand("up", "--abort-on-container-exit")
       private val logsCommand = composeCommand("logs")
@@ -29,14 +33,13 @@ case class DockerComposeCromwellConfiguration(dockerTag: String, dockerComposeFi
       private val envVariables = Map[String, String](
         "CROMWELL_BUILD_CENTAUR_MANAGED_PORT" -> ManagedCromwellPort.toString,
         "CROMWELL_BUILD_CENTAUR_MANAGED_TAG" -> dockerTag,
-        "CROMWELL_BUILD_CENTAUR_MANAGED_CONFIG" -> conf,
+        "CROMWELL_BUILD_CENTAUR_MANAGED_CONFIG" -> conf
       )
 
       private var process: Option[Process] = None
 
-      override def start(): Unit = {
+      override def start(): Unit =
         process = Option(runProcess(startCommand, envVariables))
-      }
 
       override def stop(): Unit = {
         if (!isAlive) {
diff --git a/centaur/src/main/scala/centaur/JarCromwellConfiguration.scala b/centaur/src/main/scala/centaur/JarCromwellConfiguration.scala
index c95316d1a32..1bf83b16ee1 100644
--- a/centaur/src/main/scala/centaur/JarCromwellConfiguration.scala
+++ b/centaur/src/main/scala/centaur/JarCromwellConfiguration.scala
@@ -15,20 +15,15 @@ object JarCromwellConfiguration {
 
 case class JarCromwellConfiguration(jar: String, conf: String, logFile: String) extends CromwellConfiguration {
   override def createProcess: CromwellProcess = {
-    case class JarCromwellProcess(override val cromwellConfiguration: JarCromwellConfiguration) extends CromwellProcess {
-      private val command = Array(
-        "java",
-        s"-Dconfig.file=$conf",
-        s"-Dwebservice.port=$ManagedCromwellPort",
-        "-jar",
-        jar,
-        "server")
+    case class JarCromwellProcess(override val cromwellConfiguration: JarCromwellConfiguration)
+        extends CromwellProcess {
+      private val command =
+        Array("java", s"-Dconfig.file=$conf", s"-Dwebservice.port=$ManagedCromwellPort", "-jar", jar, "server")
 
       private var process: Option[Process] = None
 
-      override def start(): Unit = {
+      override def start(): Unit =
         process = Option(runProcess(command, Map.empty))
-      }
 
       override def stop(): Unit = {
         process foreach {
@@ -37,7 +32,7 @@ case class JarCromwellConfiguration(jar: String, conf: String, logFile: String)
         process = None
       }
 
-      override def isAlive: Boolean = process.exists { _.isAlive }
+      override def isAlive: Boolean = process.exists(_.isAlive)
 
       override def logFile: String = cromwellConfiguration.logFile
     }
diff --git a/centaur/src/main/scala/centaur/api/CentaurCromwellClient.scala b/centaur/src/main/scala/centaur/api/CentaurCromwellClient.scala
index 33f96974b42..defc30bc108 100644
--- a/centaur/src/main/scala/centaur/api/CentaurCromwellClient.scala
+++ b/centaur/src/main/scala/centaur/api/CentaurCromwellClient.scala
@@ -30,20 +30,20 @@ object CentaurCromwellClient extends StrictLogging {
   // Do not use scala.concurrent.ExecutionContext.Implicits.global as long as this is using Await.result
   // See https://github.com/akka/akka-http/issues/602
   // And https://github.com/viktorklang/blog/blob/master/Futures-in-Scala-2.12-part-7.md
-  final implicit val blockingEc: ExecutionContextExecutor = ExecutionContext.fromExecutor(
-    Executors.newFixedThreadPool(100, DaemonizedDefaultThreadFactory))
+  implicit final val blockingEc: ExecutionContextExecutor =
+    ExecutionContext.fromExecutor(Executors.newFixedThreadPool(100, DaemonizedDefaultThreadFactory))
 
   // Akka HTTP needs both the actor system and a materializer
-  final implicit val system: ActorSystem = ActorSystem("centaur-acting-like-a-system")
-  final implicit val materializer: ActorMaterializer = ActorMaterializer(ActorMaterializerSettings(system))
+  implicit final val system: ActorSystem = ActorSystem("centaur-acting-like-a-system")
+  implicit final val materializer: ActorMaterializer = ActorMaterializer(ActorMaterializerSettings(system))
   final val apiVersion = "v1"
   val cromwellClient = new CromwellClient(CentaurConfig.cromwellUrl, apiVersion)
 
   val defaultMetadataArgs: Option[Map[String, List[String]]] =
     config.getAs[Map[String, List[String]]]("centaur.metadata-args")
 
-  def submit(workflow: Workflow): IO[SubmittedWorkflow] = {
-    sendReceiveFutureCompletion(() => {
+  def submit(workflow: Workflow): IO[SubmittedWorkflow] =
+    sendReceiveFutureCompletion { () =>
       val submitted = cromwellClient.submit(workflow.toWorkflowSubmission)
       submitted.biSemiflatMap(
         httpResponse =>
@@ -59,44 +59,40 @@ object CentaurCromwellClient extends StrictLogging {
             _ = workflow.submittedWorkflowTracker.add(submittedWorkflow)
           } yield submittedWorkflow
       )
-    })
-  }
+    }
 
-  def describe(workflow: Workflow): IO[WaasDescription] = {
+  def describe(workflow: Workflow): IO[WaasDescription] =
     sendReceiveFutureCompletion(() => cromwellClient.describe(workflow.toWorkflowDescribeRequest))
-  }
 
-  def status(workflow: SubmittedWorkflow): IO[WorkflowStatus] = {
+  def status(workflow: SubmittedWorkflow): IO[WorkflowStatus] =
     sendReceiveFutureCompletion(() => cromwellClient.status(workflow.id))
-  }
 
-  def abort(workflow: SubmittedWorkflow): IO[WorkflowStatus] = {
+  def abort(workflow: SubmittedWorkflow): IO[WorkflowStatus] =
     sendReceiveFutureCompletion(() => cromwellClient.abort(workflow.id))
-  }
 
-  def outputs(workflow: SubmittedWorkflow): IO[WorkflowOutputs] = {
+  def outputs(workflow: SubmittedWorkflow): IO[WorkflowOutputs] =
     sendReceiveFutureCompletion(() => cromwellClient.outputs(workflow.id))
-  }
 
-  def callCacheDiff(workflowA: SubmittedWorkflow, callA: String, workflowB: SubmittedWorkflow, callB: String): IO[CallCacheDiff] = {
-    sendReceiveFutureCompletion(() => cromwellClient.callCacheDiff(workflowA.id, callA, ShardIndex(None), workflowB.id, callB, ShardIndex(None)))
-  }
+  def callCacheDiff(workflowA: SubmittedWorkflow,
+                    callA: String,
+                    workflowB: SubmittedWorkflow,
+                    callB: String
+  ): IO[CallCacheDiff] =
+    sendReceiveFutureCompletion(() =>
+      cromwellClient.callCacheDiff(workflowA.id, callA, ShardIndex(None), workflowB.id, callB, ShardIndex(None))
+    )
 
-  def logs(workflow: SubmittedWorkflow): IO[WorkflowMetadata] = {
+  def logs(workflow: SubmittedWorkflow): IO[WorkflowMetadata] =
     sendReceiveFutureCompletion(() => cromwellClient.logs(workflow.id))
-  }
 
-  def labels(workflow: SubmittedWorkflow): IO[WorkflowLabels] = {
+  def labels(workflow: SubmittedWorkflow): IO[WorkflowLabels] =
     sendReceiveFutureCompletion(() => cromwellClient.labels(workflow.id))
-  }
 
-  def addLabels(workflow: SubmittedWorkflow, newLabels: List[Label]): IO[WorkflowLabels] = {
+  def addLabels(workflow: SubmittedWorkflow, newLabels: List[Label]): IO[WorkflowLabels] =
     sendReceiveFutureCompletion(() => cromwellClient.addLabels(workflow.id, newLabels))
-  }
 
-  def version: IO[CromwellVersion] = {
+  def version: IO[CromwellVersion] =
     sendReceiveFutureCompletion(() => cromwellClient.version)
-  }
 
   /*
     Sends a quick ping to the Cromwell query endpoint. The query endpoint is the only one which both hits the
@@ -104,7 +100,9 @@ object CentaurCromwellClient extends StrictLogging {
     currently does not support query.
    */
   def isAlive: Boolean = {
-    val response = Http().singleRequest(HttpRequest(uri=s"${CentaurConfig.cromwellUrl}/api/workflows/$apiVersion/query?status=Succeeded"))
+    val response = Http().singleRequest(
+      HttpRequest(uri = s"${CentaurConfig.cromwellUrl}/api/workflows/$apiVersion/query?status=Succeeded")
+    )
     // Silence the following warning by discarding the result of a successful query:
     // Response entity was not subscribed after 1 second. Make sure to read the response entity body or call `discardBytes()` on it.
     val successOrFailure = response map { _.entity.discardBytes() }
@@ -113,18 +111,19 @@ object CentaurCromwellClient extends StrictLogging {
 
   def metadata(workflow: SubmittedWorkflow,
                args: Option[Map[String, List[String]]] = defaultMetadataArgs,
-               expandSubworkflows: Boolean = false): IO[WorkflowMetadata] = {
+               expandSubworkflows: Boolean = false
+  ): IO[WorkflowMetadata] = {
     val mandatoryArgs = Map("expandSubWorkflows" -> List(expandSubworkflows.toString))
     metadataWithId(workflow.id, Option(args.getOrElse(Map.empty) ++ mandatoryArgs))
   }
 
-  def metadataWithId(id: WorkflowId, args: Option[Map[String, List[String]]] = defaultMetadataArgs): IO[WorkflowMetadata] = {
+  def metadataWithId(id: WorkflowId,
+                     args: Option[Map[String, List[String]]] = defaultMetadataArgs
+  ): IO[WorkflowMetadata] =
     sendReceiveFutureCompletion(() => cromwellClient.metadata(id, args))
-  }
 
-  def archiveStatus(id: WorkflowId): IO[String] = {
+  def archiveStatus(id: WorkflowId): IO[String] =
     sendReceiveFutureCompletion(() => cromwellClient.query(id)).map(_.results.head.metadataArchiveStatus)
-  }
 
   implicit private val timer: Timer[IO] = IO.timer(blockingEc)
   implicit private val contextShift: ContextShift[IO] = IO.contextShift(blockingEc)
@@ -137,42 +136,43 @@ object CentaurCromwellClient extends StrictLogging {
 
     val stackTraceString = ExceptionUtils.getStackTrace(new Exception)
 
-    ioDelay.flatMap( _ =>
+    ioDelay.flatMap(_ =>
       // Could probably use IO to do the retrying too. For now use a copyport of Retry from cromwell core. Retry 5 times,
       // wait 5 seconds between retries. Timeout the whole thing using the IO timeout.
       // https://github.com/cb372/cats-retry
       // https://typelevel.org/cats-effect/datatypes/io.html#example-retrying-with-exponential-backoff
-      IO.fromFuture(IO(Retry.withRetry(
-        () => func().asIo.unsafeToFuture(),
-        Option(5),
-        5.seconds,
-        isTransient = isTransient,
-        isFatal = isFatal
-      )).timeoutTo(timeout,
-        {
+      IO.fromFuture(
+        IO(
+          Retry.withRetry(
+            () => func().asIo.unsafeToFuture(),
+            Option(5),
+            5.seconds,
+            isTransient = isTransient,
+            isFatal = isFatal
+          )
+        ).timeoutTo(
+          timeout,
           IO.raiseError(new TimeoutException("Timeout from retryRequest " + timeout.toString + ": " + stackTraceString))
-        }
-    )))
+        )
+      )
+    )
   }
 
-  def sendReceiveFutureCompletion[T](x: () => FailureResponseOrT[T]): IO[T] = {
+  def sendReceiveFutureCompletion[T](x: () => FailureResponseOrT[T]): IO[T] =
     retryRequest(x, CentaurConfig.sendReceiveTimeout)
-  }
 
   private def isFatal(f: Throwable) = f match {
     case _: DeserializationException => true
     case _ => false
   }
 
-  private def isTransient(f: Throwable) = {
+  private def isTransient(f: Throwable) =
     f match {
-      case _: StreamTcpException |
-           _: IOException |
-           _: UnsupportedContentTypeException => true
+      case _: StreamTcpException | _: IOException | _: UnsupportedContentTypeException => true
       case BufferOverflowException(message) => message.contains("Please retry the request later.")
       case unsuccessful: UnsuccessfulRequestException => unsuccessful.httpResponse.status == StatusCodes.NotFound
-      case unexpected: RuntimeException => unexpected.getMessage.contains("The http server closed the connection unexpectedly")
+      case unexpected: RuntimeException =>
+        unexpected.getMessage.contains("The http server closed the connection unexpectedly")
       case _ => false
     }
-  }
 }
diff --git a/centaur/src/main/scala/centaur/api/Retry.scala b/centaur/src/main/scala/centaur/api/Retry.scala
index f384bc37684..1cbee9a1901 100644
--- a/centaur/src/main/scala/centaur/api/Retry.scala
+++ b/centaur/src/main/scala/centaur/api/Retry.scala
@@ -7,6 +7,7 @@ import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future}
 
 object Retry {
+
   /**
     * Copied from cromwell.core
     * Replaced the backoff with a fixed retry delay
@@ -16,8 +17,8 @@ object Retry {
                    delay: FiniteDuration,
                    isTransient: Throwable => Boolean = throwableToFalse,
                    isFatal: Throwable => Boolean = throwableToFalse,
-                   onRetry: Throwable => Unit = noopOnRetry)
-                   (implicit actorSystem: ActorSystem): Future[A] = {
+                   onRetry: Throwable => Unit = noopOnRetry
+  )(implicit actorSystem: ActorSystem): Future[A] = {
     // In the future we might want EC passed in separately but at the moment it caused more issues than it solved to do so
     implicit val ec: ExecutionContext = actorSystem.dispatcher
 
@@ -25,10 +26,18 @@ object Retry {
       case throwable if isFatal(throwable) => Future.failed(throwable)
       case throwable if !isFatal(throwable) =>
         val retriesLeft = if (isTransient(throwable)) maxRetries else maxRetries map { _ - 1 }
-        
+
         if (retriesLeft.forall(_ > 0)) {
           onRetry(throwable)
-          after(delay, actorSystem.scheduler)(withRetry(f, delay = delay, maxRetries = retriesLeft, isTransient = isTransient, isFatal = isFatal, onRetry = onRetry))
+          after(delay, actorSystem.scheduler)(
+            withRetry(f,
+                      delay = delay,
+                      maxRetries = retriesLeft,
+                      isTransient = isTransient,
+                      isFatal = isFatal,
+                      onRetry = onRetry
+            )
+          )
         } else {
           Future.failed(throwable)
         }
@@ -38,4 +47,3 @@ object Retry {
   def throwableToFalse(t: Throwable) = false
   def noopOnRetry(t: Throwable) = {}
 }
-
diff --git a/centaur/src/main/scala/centaur/json/JsonUtils.scala b/centaur/src/main/scala/centaur/json/JsonUtils.scala
index 1af725d595b..90e3bd91a98 100644
--- a/centaur/src/main/scala/centaur/json/JsonUtils.scala
+++ b/centaur/src/main/scala/centaur/json/JsonUtils.scala
@@ -8,6 +8,7 @@ object JsonUtils {
   val attemptNumber = "attempt"
 
   implicit class EnhancedJsValue(val jsValue: JsValue) extends AnyVal {
+
     /**
       * Modified from http://stackoverflow.com/a/31592156 - changes were made both to port from using
       * Play-JSON to Spray-JSON as well as to handle some cases specific to Cromwell's metadata response
@@ -32,9 +33,8 @@ object JsonUtils {
       */
     def flatten(prefix: String = ""): JsObject = {
 
-      def flattenShardAndAttempt(k:String, v: JsArray, f: JsObject => String): JsObject = {
-        v.elements.map(_.asJsObject).fold(JsObject.empty) { (x, y) => x ++ y.flatten(s"$k.${f(y)}") }
-      }
+      def flattenShardAndAttempt(k: String, v: JsArray, f: JsObject => String): JsObject =
+        v.elements.map(_.asJsObject).fold(JsObject.empty)((x, y) => x ++ y.flatten(s"$k.${f(y)}"))
 
       jsValue.asJsObject.fields.foldLeft(JsObject.empty) {
         case (acc, (k, v: JsArray)) if v.isSingleCallArray => acc ++ JsObject(k -> v.elements.head).flatten(prefix)
@@ -44,10 +44,13 @@ object JsonUtils {
              to avoid lossy conversion for multiple attempts of the same shard. The older way of flattening shards
              with only shard index in the flattened structure is also kept so that the new structure doesn't fail tests
              that rely on the older flattened structure. This should be cleaned up in https://broadworkbench.atlassian.net/browse/BW-483
-          */
+           */
           acc ++
             flattenShardAndAttempt(k, v, (y: JsObject) => y.getField(shardIndex).get) ++
-            flattenShardAndAttempt(k, v, (y: JsObject) => s"${y.getField(shardIndex).get}.${y.getField(attemptNumber).get}")
+            flattenShardAndAttempt(k,
+                                   v,
+                                   (y: JsObject) => s"${y.getField(shardIndex).get}.${y.getField(attemptNumber).get}"
+            )
         case (acc, (k, v: JsArray)) =>
           v.elements.zipWithIndex.foldLeft(acc) { case (accumulator, (element, idx)) =>
             val maybePrefix = if (prefix.isEmpty) "" else s"$prefix."
@@ -76,7 +79,7 @@ object JsonUtils {
     // A couple of helper functions to assist with flattening Cromwell metadata responses
     def hasField(fieldName: String): Boolean = jsObject.fields.keySet contains fieldName
     def getField(fieldName: String): Option[String] = jsObject.fields.get(fieldName) map { _.toString() }
-    def flattenToMap: Map [String, JsValue] = jsObject.flatten().fields map { case (k, v: JsValue) => k -> v}
+    def flattenToMap: Map[String, JsValue] = jsObject.flatten().fields map { case (k, v: JsValue) => k -> v }
   }
 
   /**
@@ -89,9 +92,8 @@ object JsonUtils {
     def nonEmptyObjectArray = jsArray.isObjectArray && jsArray.nonEmpty
     def isSingleCallArray = jsArray.hasField(shardIndex) && jsArray.size == 1
 
-    def hasField(fieldName: String): Boolean = {
+    def hasField(fieldName: String): Boolean =
       if (jsArray.nonEmptyObjectArray) jsArray.elements.map(_.asJsObject) forall { _.hasField(fieldName) }
       else false
-    }
   }
 }
diff --git a/centaur/src/main/scala/centaur/test/CentaurTestException.scala b/centaur/src/main/scala/centaur/test/CentaurTestException.scala
index fa83a3afb1a..ffc50a8dfdb 100644
--- a/centaur/src/main/scala/centaur/test/CentaurTestException.scala
+++ b/centaur/src/main/scala/centaur/test/CentaurTestException.scala
@@ -12,12 +12,12 @@ import cromwell.api.model.{SubmittedWorkflow, WorkflowMetadata}
   * @param metadataJsonOption The optional metadata.
   * @param causeOption The optional underlying cause.
   */
-case class CentaurTestException private(message: String,
-                                        testName: String,
-                                        workflowIdOption: Option[String],
-                                        metadataJsonOption: Option[String],
-                                        causeOption: Option[Exception])
-  extends RuntimeException(message, causeOption.orNull)
+case class CentaurTestException private (message: String,
+                                         testName: String,
+                                         workflowIdOption: Option[String],
+                                         metadataJsonOption: Option[String],
+                                         causeOption: Option[Exception]
+) extends RuntimeException(message, causeOption.orNull)
 
 object CentaurTestException {
 
@@ -25,7 +25,8 @@ object CentaurTestException {
   def apply(message: String,
             workflowDefinition: Workflow,
             submittedWorkflow: SubmittedWorkflow,
-            actualMetadata: WorkflowMetadata): CentaurTestException = {
+            actualMetadata: WorkflowMetadata
+  ): CentaurTestException =
     new CentaurTestException(
       message,
       workflowDefinition.testName,
@@ -33,12 +34,9 @@ object CentaurTestException {
       Option(actualMetadata.value),
       None
     )
-  }
 
   /** Create a new CentaurTestException for a submitted workflow. */
-  def apply(message: String,
-            workflowDefinition: Workflow,
-            submittedWorkflow: SubmittedWorkflow): CentaurTestException = {
+  def apply(message: String, workflowDefinition: Workflow, submittedWorkflow: SubmittedWorkflow): CentaurTestException =
     new CentaurTestException(
       message,
       workflowDefinition.testName,
@@ -46,10 +44,9 @@ object CentaurTestException {
       None,
       None
     )
-  }
 
   /** Create a new CentaurTestException for only a workflow definition. */
-  def apply(message: String, workflowDefinition: Workflow): CentaurTestException = {
+  def apply(message: String, workflowDefinition: Workflow): CentaurTestException =
     new CentaurTestException(
       message,
       workflowDefinition.testName,
@@ -57,10 +54,9 @@ object CentaurTestException {
       None,
       None
     )
-  }
 
   /** Create a new CentaurTestException for only a workflow definition, including a root cause. */
-  def apply(message: String, workflowDefinition: Workflow, cause: Exception): CentaurTestException = {
+  def apply(message: String, workflowDefinition: Workflow, cause: Exception): CentaurTestException =
     new CentaurTestException(
       message,
       workflowDefinition.testName,
@@ -68,5 +64,4 @@ object CentaurTestException {
       None,
       Option(cause)
     )
-  }
 }
diff --git a/centaur/src/main/scala/centaur/test/ObjectCounter.scala b/centaur/src/main/scala/centaur/test/ObjectCounter.scala
index 124f78e1dc8..a5cb51ea190 100644
--- a/centaur/src/main/scala/centaur/test/ObjectCounter.scala
+++ b/centaur/src/main/scala/centaur/test/ObjectCounter.scala
@@ -40,20 +40,19 @@ object ObjectCounterInstances {
     listObjectsAtPath(_).size
   }
 
-  implicit val blobObjectCounter: ObjectCounter[BlobContainerClient] = (containerClient : BlobContainerClient) => {
+  implicit val blobObjectCounter: ObjectCounter[BlobContainerClient] = (containerClient: BlobContainerClient) => {
     val pathToInt: Path => Int = providedPath => {
-      //Our path parsing is somewhat GCP centric. Convert to a blob path starting from the container root.
-      def pathToBlobPath(parsedPath : Path) : String = {
+      // Our path parsing is somewhat GCP centric. Convert to a blob path starting from the container root.
+      def pathToBlobPath(parsedPath: Path): String =
         (Option(parsedPath.bucket), Option(parsedPath.directory)) match {
           case (None, _) => ""
           case (Some(_), None) => parsedPath.bucket
           case (Some(_), Some(_)) => parsedPath.bucket + "/" + parsedPath.directory
         }
-      }
 
       val fullPath = pathToBlobPath(providedPath)
-      val blobsInFolder =  containerClient.listBlobsByHierarchy(fullPath)
-      //if something "isPrefix", it's a directory. Otherwise, its a file. We just want to count files.
+      val blobsInFolder = containerClient.listBlobsByHierarchy(fullPath)
+      // if something "isPrefix", it's a directory. Otherwise, its a file. We just want to count files.
       blobsInFolder.asScala.count(!_.isPrefix)
     }
     pathToInt(_)
@@ -63,7 +62,8 @@ object ObjectCounterInstances {
 object ObjectCounterSyntax {
 
   implicit class ObjectCounterSyntax[A](client: A) {
-    def countObjects(regex: String)(implicit c: ObjectCounter[A]): String => Int = c.parsePath(regex) andThen c.countObjectsAtPath(client)
+    def countObjects(regex: String)(implicit c: ObjectCounter[A]): String => Int =
+      c.parsePath(regex) andThen c.countObjectsAtPath(client)
   }
 
 }
diff --git a/centaur/src/main/scala/centaur/test/Test.scala b/centaur/src/main/scala/centaur/test/Test.scala
index d0a56a2cbf5..66a4655a107 100644
--- a/centaur/src/main/scala/centaur/test/Test.scala
+++ b/centaur/src/main/scala/centaur/test/Test.scala
@@ -22,9 +22,20 @@ import com.typesafe.scalalogging.StrictLogging
 import common.validation.Validation._
 import configs.syntax._
 import cromwell.api.CromwellClient.UnsuccessfulRequestException
-import cromwell.api.model.{CallCacheDiff, Failed, HashDifference, SubmittedWorkflow, Succeeded, TerminalStatus, WaasDescription, WorkflowId, WorkflowMetadata, WorkflowStatus}
+import cromwell.api.model.{
+  CallCacheDiff,
+  Failed,
+  HashDifference,
+  SubmittedWorkflow,
+  Succeeded,
+  TerminalStatus,
+  WaasDescription,
+  WorkflowId,
+  WorkflowMetadata,
+  WorkflowStatus
+}
 import cromwell.cloudsupport.aws.AwsConfiguration
-import cromwell.cloudsupport.azure.{AzureUtils}
+import cromwell.cloudsupport.azure.AzureUtils
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
 import io.circe.parser._
@@ -53,32 +64,28 @@ sealed abstract class Test[A] {
 object Test {
   def successful[A](value: A): Test[A] = testMonad.pure(value)
 
-  def invalidTestDefinition[A](message: String, workflowDefinition: Workflow): Test[A] = {
+  def invalidTestDefinition[A](message: String, workflowDefinition: Workflow): Test[A] =
     new Test[A] {
       override def run: IO[Nothing] = IO.raiseError(CentaurTestException(message, workflowDefinition))
     }
-  }
 
   implicit val testMonad: Monad[Test] = new Monad[Test] {
-    override def flatMap[A, B](fa: Test[A])(f: A => Test[B]): Test[B] = {
+    override def flatMap[A, B](fa: Test[A])(f: A => Test[B]): Test[B] =
       new Test[B] {
         override def run: IO[B] = fa.run flatMap { f(_).run }
       }
-    }
 
-    override def pure[A](x: A): Test[A] = {
+    override def pure[A](x: A): Test[A] =
       new Test[A] {
         override def run: IO[A] = IO.pure(x)
       }
-    }
 
     /** Call the default non-stack-safe but correct version of this method. */
-    override def tailRecM[A, B](a: A)(f: A => Test[Either[A, B]]): Test[B] = {
+    override def tailRecM[A, B](a: A)(f: A => Test[Either[A, B]]): Test[B] =
       flatMap(f(a)) {
         case Right(b) => pure(b)
         case Left(nextA) => tailRecM(nextA)(f)
       }
-    }
   }
 
   implicit class TestableIO[A](a: IO[A]) {
@@ -103,14 +110,14 @@ object Operations extends StrictLogging {
   lazy val authName: String = googleConf.getString("auth")
   lazy val genomicsEndpointUrl: String = googleConf.getString("genomics.endpoint-url")
   lazy val genomicsAndStorageScopes = List(StorageScopes.CLOUD_PLATFORM_READ_ONLY, GenomicsScopes.GENOMICS)
-  lazy val credentials: Credentials = configuration.auth(authName)
+  lazy val credentials: Credentials = configuration
+    .auth(authName)
     .unsafe
     .credentials(genomicsAndStorageScopes)
-  lazy val credentialsProjectOption: Option[String] = {
-    Option(credentials) collect {
-      case serviceAccountCredentials: ServiceAccountCredentials => serviceAccountCredentials.getProjectId
+  lazy val credentialsProjectOption: Option[String] =
+    Option(credentials) collect { case serviceAccountCredentials: ServiceAccountCredentials =>
+      serviceAccountCredentials.getProjectId
     }
-  }
   lazy val confProjectOption: Option[String] = googleConf.get[Option[String]]("project") valueOrElse None
   // The project from the config or from the credentials. By default the project is read from the system environment.
   lazy val projectOption: Option[String] = confProjectOption orElse credentialsProjectOption
@@ -140,13 +147,14 @@ object Operations extends StrictLogging {
   lazy val awsConfiguration: AwsConfiguration = AwsConfiguration(CentaurConfig.conf)
   lazy val awsConf: Config = CentaurConfig.conf.getConfig("aws")
   lazy val awsAuthName: String = awsConf.getString("auths")
-  lazy val region: String  = awsConf.getString("region")
-  lazy val accessKeyId: String  = awsConf.getString("access-key")
+  lazy val region: String = awsConf.getString("region")
+  lazy val accessKeyId: String = awsConf.getString("access-key")
   lazy val secretAccessKey: String = awsConf.getString("secret-key")
 
   def buildAmazonS3Client: S3Client = {
     val basicAWSCredentials = AwsBasicCredentials.create(accessKeyId, secretAccessKey)
-    S3Client.builder()
+    S3Client
+      .builder()
       .region(Region.of(region))
       .credentialsProvider(StaticCredentialsProvider.create(basicAWSCredentials))
       .build()
@@ -156,16 +164,16 @@ object Operations extends StrictLogging {
   val azureSubscription = azureConfig.getString("subscription")
   val blobContainer = azureConfig.getString("container")
   val azureEndpoint = azureConfig.getString("endpoint")
-  //NB: Centaur will throw an exception if it isn't able to authenticate with Azure blob storage via the local environment.
-  lazy val blobContainerClient: BlobContainerClient = AzureUtils.buildContainerClientFromLocalEnvironment(blobContainer, azureEndpoint, Option(azureSubscription)).get
+  // NB: Centaur will throw an exception if it isn't able to authenticate with Azure blob storage via the local environment.
+  lazy val blobContainerClient: BlobContainerClient =
+    AzureUtils.buildContainerClientFromLocalEnvironment(blobContainer, azureEndpoint, Option(azureSubscription)).get
 
-  def submitWorkflow(workflow: Workflow): Test[SubmittedWorkflow] = {
+  def submitWorkflow(workflow: Workflow): Test[SubmittedWorkflow] =
     new Test[SubmittedWorkflow] {
       override def run: IO[SubmittedWorkflow] = for {
         id <- CentaurCromwellClient.submit(workflow)
       } yield id
     }
-  }
 
   /**
     * A smoke test of the version endpoint, this confirms that a) nothing explodes and b) the result must be a JSON object
@@ -180,15 +188,15 @@ object Operations extends StrictLogging {
   def checkTimingRequirement(timeRequirement: Option[FiniteDuration]): Test[FiniteDuration] = new Test[FiniteDuration] {
     override def run: IO[FiniteDuration] = timeRequirement match {
       case Some(duration) => IO.pure(duration)
-      case None => IO.raiseError(new Exception("Duration value for 'maximumTime' required but not supplied in test config"))
+      case None =>
+        IO.raiseError(new Exception("Duration value for 'maximumTime' required but not supplied in test config"))
     }
   }
 
   def checkFastEnough(before: Long, after: Long, allowance: FiniteDuration): Test[Unit] = new Test[Unit] {
-    override def run: IO[Unit] = {
+    override def run: IO[Unit] =
       if (after - before < allowance.toSeconds) IO.pure(())
       else IO.raiseError(new Exception(s"Test took too long. Allowance was $allowance. Actual time: ${after - before}"))
-    }
   }
 
   def timingVerificationNotSupported(timingRequirement: Option[FiniteDuration]): Test[Unit] = new Test[Unit] {
@@ -198,7 +206,7 @@ object Operations extends StrictLogging {
 
   }
 
-  def checkDescription(workflow: Workflow, validityExpectation: Option[Boolean], retries: Int = 3): Test[Unit] = {
+  def checkDescription(workflow: Workflow, validityExpectation: Option[Boolean], retries: Int = 3): Test[Unit] =
     new Test[Unit] {
 
       private val timeout = 60.seconds
@@ -210,77 +218,79 @@ object Operations extends StrictLogging {
             case None => IO.pure(())
             case Some(d.valid) => IO.pure(())
             case Some(otherExpectation) =>
-              logger.error(s"Unexpected 'valid=${d.valid}' response when expecting $otherExpectation. Full unexpected description:${System.lineSeparator()}$d")
-              IO.raiseError(new Exception(s"Expected this workflow's /describe validity to be '$otherExpectation' but got: '${d.valid}' (errors: ${d.errors.mkString(", ")})"))
+              logger.error(
+                s"Unexpected 'valid=${d.valid}' response when expecting $otherExpectation. Full unexpected description:${System
+                    .lineSeparator()}$d"
+              )
+              IO.raiseError(
+                new Exception(
+                  s"Expected this workflow's /describe validity to be '$otherExpectation' but got: '${d.valid}' (errors: ${d.errors
+                      .mkString(", ")})"
+                )
+              )
           }
-        }).timeoutTo(timeout, IO {
-          if (alreadyTried + 1 >= retries) {
-            throw new TimeoutException("Timeout from checkDescription 60 seconds: " + timeoutStackTraceString)
-          } else {
-            logger.warn(s"checkDescription timeout on attempt ${alreadyTried + 1}. ")
-            checkDescriptionInner(alreadyTried + 1)
-            ()
+        }).timeoutTo(
+          timeout,
+          IO {
+            if (alreadyTried + 1 >= retries) {
+              throw new TimeoutException("Timeout from checkDescription 60 seconds: " + timeoutStackTraceString)
+            } else {
+              logger.warn(s"checkDescription timeout on attempt ${alreadyTried + 1}. ")
+              checkDescriptionInner(alreadyTried + 1)
+              ()
+            }
           }
-        })
+        )
       }
 
-
-      override def run: IO[Unit] = {
-
-
+      override def run: IO[Unit] =
         // We can't describe workflows based on zipped imports, so don't try:
         if (workflow.skipDescribeEndpointValidation || workflow.data.zippedImports.nonEmpty) {
           IO.pure(())
         } else {
           checkDescriptionInner(0)
         }
-      }
     }
-  }
 
-  def submitInvalidWorkflow(workflow: Workflow): Test[SubmitHttpResponse] = {
+  def submitInvalidWorkflow(workflow: Workflow): Test[SubmitHttpResponse] =
     new Test[SubmitHttpResponse] {
-      override def run: IO[SubmitHttpResponse] = {
-        CentaurCromwellClient.submit(workflow).redeemWith(
-          {
-            case unsuccessfulRequestException: UnsuccessfulRequestException =>
-              val httpResponse = unsuccessfulRequestException.httpResponse
-              val statusCode = httpResponse.status.intValue()
-              httpResponse.entity match {
-                case akka.http.scaladsl.model.HttpEntity.Strict(_, data) =>
-                  IO.pure(SubmitHttpResponse(statusCode, data.utf8String))
-                case _ =>
-                  val message = s"Expected a strict http response entity but got ${httpResponse.entity}"
-                  IO.raiseError(CentaurTestException(message, workflow, unsuccessfulRequestException))
-              }
-            case unexpected: Exception =>
-              val message = s"Unexpected error: ${unexpected.getMessage}"
-              IO.raiseError(CentaurTestException(message, workflow, unexpected))
-            case throwable: Throwable => throw throwable
-          },
-          {
-            submittedWorkflow => {
+      override def run: IO[SubmitHttpResponse] =
+        CentaurCromwellClient
+          .submit(workflow)
+          .redeemWith(
+            {
+              case unsuccessfulRequestException: UnsuccessfulRequestException =>
+                val httpResponse = unsuccessfulRequestException.httpResponse
+                val statusCode = httpResponse.status.intValue()
+                httpResponse.entity match {
+                  case akka.http.scaladsl.model.HttpEntity.Strict(_, data) =>
+                    IO.pure(SubmitHttpResponse(statusCode, data.utf8String))
+                  case _ =>
+                    val message = s"Expected a strict http response entity but got ${httpResponse.entity}"
+                    IO.raiseError(CentaurTestException(message, workflow, unsuccessfulRequestException))
+                }
+              case unexpected: Exception =>
+                val message = s"Unexpected error: ${unexpected.getMessage}"
+                IO.raiseError(CentaurTestException(message, workflow, unexpected))
+              case throwable: Throwable => throw throwable
+            },
+            { submittedWorkflow =>
               val message =
                 s"Expected a failure but got a successfully submitted workflow with id ${submittedWorkflow.id}"
               IO.raiseError(CentaurTestException(message, workflow))
             }
-          }
-        )
-      }
+          )
     }
-  }
 
-  def abortWorkflow(workflow: SubmittedWorkflow): Test[WorkflowStatus] = {
+  def abortWorkflow(workflow: SubmittedWorkflow): Test[WorkflowStatus] =
     new Test[WorkflowStatus] {
       override def run: IO[WorkflowStatus] = CentaurCromwellClient.abort(workflow)
     }
-  }
 
-  def waitFor(duration: FiniteDuration): Test[Unit] = {
+  def waitFor(duration: FiniteDuration): Test[Unit] =
     new Test[Unit] {
       override def run: IO[Unit] = IO.sleep(duration)
     }
-  }
 
   /**
     * Polls until a valid status is reached.
@@ -290,16 +300,18 @@ object Operations extends StrictLogging {
   def expectSomeProgress(workflow: SubmittedWorkflow,
                          testDefinition: Workflow,
                          expectedStatuses: Set[WorkflowStatus],
-                         timeout: FiniteDuration): Test[SubmittedWorkflow] = {
+                         timeout: FiniteDuration
+  ): Test[SubmittedWorkflow] =
     new Test[SubmittedWorkflow] {
-      def status(remainingTimeout: FiniteDuration): IO[SubmittedWorkflow] = {
+      def status(remainingTimeout: FiniteDuration): IO[SubmittedWorkflow] =
         for {
           workflowStatus <- CentaurCromwellClient.status(workflow)
           mappedStatus <- workflowStatus match {
             case s if expectedStatuses.contains(s) => IO.pure(workflow)
             case s: TerminalStatus =>
               CentaurCromwellClient.metadata(workflow) flatMap { metadata =>
-                val message = s"Unexpected terminal status $s while waiting for one of [${expectedStatuses.mkString(", ")}] (workflow ID: ${workflow.id})"
+                val message =
+                  s"Unexpected terminal status $s while waiting for one of [${expectedStatuses.mkString(", ")}] (workflow ID: ${workflow.id})"
                 IO.raiseError(CentaurTestException(message, testDefinition, workflow, metadata))
               }
             case _ if remainingTimeout > 0.seconds =>
@@ -308,16 +320,15 @@ object Operations extends StrictLogging {
                 s <- status(remainingTimeout - 10.seconds)
               } yield s
             case other =>
-              val message = s"Cromwell failed to progress into any of the statuses [${expectedStatuses.mkString(", ")}]. Was still '$other' after $timeout (workflow ID: ${workflow.id})"
+              val message =
+                s"Cromwell failed to progress into any of the statuses [${expectedStatuses.mkString(", ")}]. Was still '$other' after $timeout (workflow ID: ${workflow.id})"
               IO.raiseError(CentaurTestException(message, testDefinition, workflow))
           }
         } yield mappedStatus
-      }
 
       override def run: IO[SubmittedWorkflow] = status(timeout).timeout(CentaurConfig.maxWorkflowLength)
 
     }
-  }
 
   /**
     * Polls until a specific status is reached.
@@ -326,9 +337,10 @@ object Operations extends StrictLogging {
     */
   def pollUntilStatus(workflow: SubmittedWorkflow,
                       testDefinition: Workflow,
-                      expectedStatus: WorkflowStatus): Test[SubmittedWorkflow] = {
+                      expectedStatus: WorkflowStatus
+  ): Test[SubmittedWorkflow] =
     new Test[SubmittedWorkflow] {
-      def status: IO[SubmittedWorkflow] = {
+      def status: IO[SubmittedWorkflow] =
         for {
           workflowStatus <- CentaurCromwellClient.status(workflow)
           mappedStatus <- workflowStatus match {
@@ -336,35 +348,38 @@ object Operations extends StrictLogging {
             case s: TerminalStatus =>
               val reducedMetadataOptions: Map[String, List[String]] =
                 CentaurCromwellClient.defaultMetadataArgs.getOrElse(Map.empty) ++ Map(
-                  "includeKey" -> (List("status") ++ (if (expectedStatus == Succeeded) List("failures") else List.empty)),
+                  "includeKey" -> (List("status") ++ (if (expectedStatus == Succeeded) List("failures")
+                                                      else List.empty)),
                   "expandSubWorkflows" -> List("false")
                 )
 
-              CentaurCromwellClient.metadata(workflow = workflow, args = Option(reducedMetadataOptions)) flatMap { metadata =>
-                val failuresString = if (expectedStatus == Succeeded) {
-                  (for {
-                    metadataJson <- parse(metadata.value).toOption
-                    asObject <- metadataJson.asObject
-                    failures <- asObject.toMap.get("failures")
-                  } yield s" Metadata 'failures' content: ${failures.spaces2}").getOrElse("No additional failure information found in metadata.")
-                } else {
-                  ""
-                }
-
-                val message = s"Unexpected terminal status $s but was waiting for $expectedStatus (workflow ID: ${workflow.id}).$failuresString"
-                IO.raiseError(CentaurTestException(message, testDefinition, workflow, metadata))
+              CentaurCromwellClient.metadata(workflow = workflow, args = Option(reducedMetadataOptions)) flatMap {
+                metadata =>
+                  val failuresString = if (expectedStatus == Succeeded) {
+                    (for {
+                      metadataJson <- parse(metadata.value).toOption
+                      asObject <- metadataJson.asObject
+                      failures <- asObject.toMap.get("failures")
+                    } yield s" Metadata 'failures' content: ${failures.spaces2}")
+                      .getOrElse("No additional failure information found in metadata.")
+                  } else {
+                    ""
+                  }
+
+                  val message =
+                    s"Unexpected terminal status $s but was waiting for $expectedStatus (workflow ID: ${workflow.id}).$failuresString"
+                  IO.raiseError(CentaurTestException(message, testDefinition, workflow, metadata))
               }
-            case _ => for {
-              _ <- IO.sleep(10.seconds)
-              s <- status
-            } yield s
+            case _ =>
+              for {
+                _ <- IO.sleep(10.seconds)
+                s <- status
+              } yield s
           }
         } yield mappedStatus
-      }
 
       override def run: IO[SubmittedWorkflow] = status.timeout(CentaurConfig.maxWorkflowLength)
     }
-  }
 
   /**
     * Validate that the given jobId matches the one in the metadata
@@ -373,7 +388,8 @@ object Operations extends StrictLogging {
                         workflow: SubmittedWorkflow,
                         metadata: WorkflowMetadata,
                         callFqn: String,
-                        formerJobId: String): Test[Unit] = {
+                        formerJobId: String
+  ): Test[Unit] =
     new Test[Unit] {
       override def run: IO[Unit] = CentaurCromwellClient.metadata(workflow) flatMap { s =>
         s.asFlat.value.get(s"calls.$callFqn.jobId") match {
@@ -387,56 +403,58 @@ object Operations extends StrictLogging {
         }
       }
     }
-  }
 
-  def validatePAPIAborted(workflowDefinition: Workflow, workflow: SubmittedWorkflow, jobId: String): Test[Unit] = {
+  def validatePAPIAborted(workflowDefinition: Workflow, workflow: SubmittedWorkflow, jobId: String): Test[Unit] =
     new Test[Unit] {
-      def checkPAPIAborted(): IO[Unit] = {
+      def checkPAPIAborted(): IO[Unit] =
         for {
-          operation <- IO { genomics.projects().operations().get(jobId).execute() }
+          operation <- IO(genomics.projects().operations().get(jobId).execute())
           done = operation.getDone
           operationError = Option(operation.getError)
-          aborted = operationError.exists(_.getCode == 1) && operationError.exists(_.getMessage.startsWith("Operation canceled"))
-          result <- if (!(done && aborted)) {
-            CentaurCromwellClient.metadata(workflow) flatMap { metadata =>
-              val message = s"Underlying JES job was not aborted properly. " +
-                s"Done = $done. Error = ${operationError.map(_.getMessage).getOrElse("N/A")} (workflow ID: ${workflow.id})"
-              IO.raiseError(CentaurTestException(message, workflowDefinition, workflow, metadata))
-            }
-          } else IO.unit
+          aborted = operationError.exists(_.getCode == 1) && operationError.exists(
+            _.getMessage.startsWith("Operation canceled")
+          )
+          result <-
+            if (!(done && aborted)) {
+              CentaurCromwellClient.metadata(workflow) flatMap { metadata =>
+                val message = s"Underlying JES job was not aborted properly. " +
+                  s"Done = $done. Error = ${operationError.map(_.getMessage).getOrElse("N/A")} (workflow ID: ${workflow.id})"
+                IO.raiseError(CentaurTestException(message, workflowDefinition, workflow, metadata))
+              }
+            } else IO.unit
         } yield result
-      }
 
       override def run: IO[Unit] = if (jobId.startsWith("operations/")) {
         checkPAPIAborted()
       } else IO.unit
     }
-  }
 
   /**
     * Polls until a specific call is in Running state. Returns the job id.
     */
-  def pollUntilCallIsRunning(workflowDefinition: Workflow, workflow: SubmittedWorkflow, callFqn: String): Test[String] = {
+  def pollUntilCallIsRunning(workflowDefinition: Workflow,
+                             workflow: SubmittedWorkflow,
+                             callFqn: String
+  ): Test[String] = {
     // Special case for sub workflow testing
-    def findJobIdInSubWorkflow(subWorkflowId: String): IO[Option[String]] = {
+    def findJobIdInSubWorkflow(subWorkflowId: String): IO[Option[String]] =
       for {
         metadata <- CentaurCromwellClient
           .metadataWithId(WorkflowId.fromString(subWorkflowId))
           .redeem(_ => None, Option.apply)
         jobId <- IO.pure(metadata.flatMap(_.asFlat.value.get("calls.inner_abort.aborted.jobId")))
       } yield jobId.map(_.asInstanceOf[JsString].value)
-    }
 
-    def valueAsString(key: String, metadata: WorkflowMetadata) = {
+    def valueAsString(key: String, metadata: WorkflowMetadata) =
       metadata.asFlat.value.get(key).map(_.asInstanceOf[JsString].value)
-    }
 
     def findCallStatus(metadata: WorkflowMetadata): IO[Option[(String, String)]] = {
       val status = metadata.asFlat.value.get(s"calls.$callFqn.executionStatus")
       val statusString = status.map(_.asInstanceOf[JsString].value)
 
       for {
-        jobId <- valueAsString(s"calls.$callFqn.jobId", metadata).map(jobId => IO.pure(Option(jobId)))
+        jobId <- valueAsString(s"calls.$callFqn.jobId", metadata)
+          .map(jobId => IO.pure(Option(jobId)))
           .orElse(valueAsString(s"calls.$callFqn.subWorkflowId", metadata).map(findJobIdInSubWorkflow))
           .getOrElse(IO.pure(None))
         pair = (statusString, jobId) match {
@@ -447,7 +465,7 @@ object Operations extends StrictLogging {
     }
 
     new Test[String] {
-      def doPerform(): IO[String] = {
+      def doPerform(): IO[String] =
         for {
           // We don't want to keep going forever if the workflow failed
           status <- CentaurCromwellClient.status(workflow)
@@ -464,13 +482,13 @@ object Operations extends StrictLogging {
             case Some(("Failed", _)) =>
               val message = s"$callFqn failed"
               IO.raiseError(CentaurTestException(message, workflowDefinition, workflow, metadata))
-            case _ => for {
-              _ <- IO.sleep(5.seconds)
-              recurse <- doPerform()
-            } yield recurse
+            case _ =>
+              for {
+                _ <- IO.sleep(5.seconds)
+                recurse <- doPerform()
+              } yield recurse
           }
         } yield result
-      }
 
       override def run: IO[String] = doPerform().timeout(CentaurConfig.maxWorkflowLength)
     }
@@ -483,34 +501,40 @@ object Operations extends StrictLogging {
 
       for {
         md <- CentaurCromwellClient.metadata(workflowB)
-        calls = md.asFlat.value.keySet.flatMap({
+        calls = md.asFlat.value.keySet.flatMap {
           case callNameRegexp(name) => Option(name)
           case _ => None
-        })
-        diffs <- calls.toList.traverse[IO, CallCacheDiff]({ callName =>
+        }
+        diffs <- calls.toList.traverse[IO, CallCacheDiff] { callName =>
           CentaurCromwellClient.callCacheDiff(workflowA, callName, workflowB, callName)
-        })
+        }
       } yield diffs.flatMap(_.hashDifferential)
     }
 
-    override def run: IO[Unit] = {
+    override def run: IO[Unit] =
       hashDiffOfAllCalls map {
         case diffs if diffs.nonEmpty && CentaurCromwellClient.LogFailures =>
           Console.err.println(s"Hash differential for ${workflowA.id} and ${workflowB.id}")
-          diffs.map({ diff =>
-            s"For key ${diff.hashKey}:\nCall A: ${diff.callA.getOrElse("N/A")}\nCall B: ${diff.callB.getOrElse("N/A")}"
-          }).foreach(Console.err.println)
+          diffs
+            .map { diff =>
+              s"For key ${diff.hashKey}:\nCall A: ${diff.callA.getOrElse("N/A")}\nCall B: ${diff.callB.getOrElse("N/A")}"
+            }
+            .foreach(Console.err.println)
         case _ =>
       }
-    }
   }
 
   /* Select only those flat metadata items whose keys begin with the specified prefix, removing the prefix from the keys. Also
    * perform variable substitutions for UUID and WORKFLOW_ROOT and remove any ~> Centaur metadata expectation metacharacters. */
-  private def selectMetadataExpectationSubsetByPrefix(workflow: Workflow, prefix: String, workflowId: WorkflowId, workflowRoot: String): List[(String, JsValue)] = {
+  private def selectMetadataExpectationSubsetByPrefix(workflow: Workflow,
+                                                      prefix: String,
+                                                      workflowId: WorkflowId,
+                                                      workflowRoot: String
+  ): List[(String, JsValue)] = {
     import WorkflowFlatMetadata._
     def replaceVariables(value: JsValue): JsValue = value match {
-      case s: JsString => JsString(s.value.replaceExpectationVariables(workflowId, workflowRoot).replaceFirst("^~>", ""))
+      case s: JsString =>
+        JsString(s.value.replaceExpectationVariables(workflowId, workflowRoot).replaceFirst("^~>", ""))
       case o => o
     }
     val filterLabels: PartialFunction[(String, JsValue), (String, JsValue)] = {
@@ -525,7 +549,8 @@ object Operations extends StrictLogging {
 
   def fetchAndValidateOutputs(submittedWorkflow: SubmittedWorkflow,
                               workflow: Workflow,
-                              workflowRoot: String): Test[JsObject] = new Test[JsObject] {
+                              workflowRoot: String
+  ): Test[JsObject] = new Test[JsObject] {
 
     def checkOutputs(expectedOutputs: List[(String, JsValue)])(actualOutputs: Map[String, JsValue]): IO[Unit] = {
       val expected = expectedOutputs.toSet
@@ -535,11 +560,13 @@ object Operations extends StrictLogging {
       lazy val inExpectedButNotInActual = expected.diff(actual)
 
       if (!workflow.allowOtherOutputs && inActualButNotInExpected.nonEmpty) {
-        val message = s"In actual outputs but not in expected and other outputs not allowed: ${inActualButNotInExpected.mkString(", ")}"
+        val message =
+          s"In actual outputs but not in expected and other outputs not allowed: ${inActualButNotInExpected.mkString(", ")}"
         IO.raiseError(CentaurTestException(message, workflow, submittedWorkflow))
       } else if (inExpectedButNotInActual.nonEmpty) {
-        val message = s"In actual outputs but not in expected: ${inExpectedButNotInActual.mkString(", ")}" + System.lineSeparator +
-          s"In expected outputs but not in actual: ${inExpectedButNotInActual.mkString(", ")}"
+        val message =
+          s"In actual outputs but not in expected: ${inExpectedButNotInActual.mkString(", ")}" + System.lineSeparator +
+            s"In expected outputs but not in actual: ${inExpectedButNotInActual.mkString(", ")}"
         IO.raiseError(CentaurTestException(message, workflow, submittedWorkflow))
       } else {
         IO.unit
@@ -549,7 +576,8 @@ object Operations extends StrictLogging {
     override def run: IO[JsObject] = {
       import centaur.test.metadata.WorkflowFlatOutputs._
 
-      val expectedOutputs: List[(String, JsValue)] = selectMetadataExpectationSubsetByPrefix(workflow, "outputs.", submittedWorkflow.id, workflowRoot)
+      val expectedOutputs: List[(String, JsValue)] =
+        selectMetadataExpectationSubsetByPrefix(workflow, "outputs.", submittedWorkflow.id, workflowRoot)
 
       for {
         outputs <- CentaurCromwellClient.outputs(submittedWorkflow)
@@ -562,7 +590,8 @@ object Operations extends StrictLogging {
 
   def fetchAndValidateLabels(submittedWorkflow: SubmittedWorkflow,
                              workflow: Workflow,
-                             workflowRoot: String): Test[Unit] = new Test[Unit] {
+                             workflowRoot: String
+  ): Test[Unit] = new Test[Unit] {
     override def run: IO[Unit] = {
       import centaur.test.metadata.WorkflowFlatLabels._
 
@@ -570,17 +599,18 @@ object Operations extends StrictLogging {
       val expectedLabels: List[(String, JsValue)] = workflowIdLabel ::
         selectMetadataExpectationSubsetByPrefix(workflow, "labels.", submittedWorkflow.id, workflowRoot)
 
-
       def validateLabels(actualLabels: Map[String, JsValue]) = {
         val diff = expectedLabels.toSet.diff(actualLabels.toSet)
         if (diff.isEmpty) {
           IO.unit
         } else {
-          IO.raiseError(CentaurTestException(
-            s"In expected labels but not in actual: ${diff.mkString(", ")}",
-            workflow,
-            submittedWorkflow
-          ))
+          IO.raiseError(
+            CentaurTestException(
+              s"In expected labels but not in actual: ${diff.mkString(", ")}",
+              workflow,
+              submittedWorkflow
+            )
+          )
         }
       }
 
@@ -593,75 +623,77 @@ object Operations extends StrictLogging {
   }
 
   /** Compares logs filtered from the raw `metadata` endpoint with the `logs` endpoint. */
-  def validateLogs(metadata: WorkflowMetadata,
-                   submittedWorkflow: SubmittedWorkflow,
-                   workflow: Workflow): Test[Unit] = new Test[Unit] {
-    val suffixes = Set("stdout", "shardIndex", "stderr", "attempt", "backendLogs.log")
-
-    def removeSubworkflowKeys(flattened: Map[String, JsValue]): Map[String, JsValue] = {
-      val subWorkflowIdPrefixes = flattened.keys.filter(_.endsWith(".subWorkflowId")).map(s => s.substring(0, s.lastIndexOf('.')))
-      flattened filter { case (k, _) => !subWorkflowIdPrefixes.exists(k.startsWith) }
-    }
-
-    // Filter to only include the fields in the flattened metadata that should appear in the logs endpoint.
-    def filterForLogsFields(flattened: Map[String, JsValue]): Map[String, JsValue] = removeSubworkflowKeys(flattened).filter {
-      case (k, _) => k == "id" || suffixes.exists(s => k.endsWith("." + s) && !k.contains(".outputs.") && !k.startsWith("outputs."))
-    }
+  def validateLogs(metadata: WorkflowMetadata, submittedWorkflow: SubmittedWorkflow, workflow: Workflow): Test[Unit] =
+    new Test[Unit] {
+      val suffixes = Set("stdout", "shardIndex", "stderr", "attempt", "backendLogs.log")
 
-    override def run: IO[Unit] = {
+      def removeSubworkflowKeys(flattened: Map[String, JsValue]): Map[String, JsValue] = {
+        val subWorkflowIdPrefixes =
+          flattened.keys.filter(_.endsWith(".subWorkflowId")).map(s => s.substring(0, s.lastIndexOf('.')))
+        flattened filter { case (k, _) => !subWorkflowIdPrefixes.exists(k.startsWith) }
+      }
 
-      def validateLogsMetadata(flatLogs: Map[String, JsValue], flatFilteredMetadata: Map[String, JsValue]): IO[Unit] =
-        if (flatLogs.equals(flatFilteredMetadata)) {
-          IO.unit
-        } else {
-          val message = (List("actual logs endpoint output did not equal filtered metadata", "flat logs: ") ++
-            flatLogs.toList ++ List("flat filtered metadata: ") ++ flatFilteredMetadata.toList).mkString("\n")
-          IO.raiseError(CentaurTestException(message, workflow, submittedWorkflow))
+      // Filter to only include the fields in the flattened metadata that should appear in the logs endpoint.
+      def filterForLogsFields(flattened: Map[String, JsValue]): Map[String, JsValue] =
+        removeSubworkflowKeys(flattened).filter { case (k, _) =>
+          k == "id" || suffixes.exists(s =>
+            k.endsWith("." + s) && !k.contains(".outputs.") && !k.startsWith("outputs.")
+          )
         }
 
-      for {
-        logs <- CentaurCromwellClient.logs(submittedWorkflow)
-        flatLogs = logs.asFlat.value
-        flatFilteredMetadata = metadata.asFlat.value |> filterForLogsFields
-        _ <- validateLogsMetadata(flatLogs, flatFilteredMetadata)
-      } yield ()
+      override def run: IO[Unit] = {
+
+        def validateLogsMetadata(flatLogs: Map[String, JsValue], flatFilteredMetadata: Map[String, JsValue]): IO[Unit] =
+          if (flatLogs.equals(flatFilteredMetadata)) {
+            IO.unit
+          } else {
+            val message = (List("actual logs endpoint output did not equal filtered metadata", "flat logs: ") ++
+              flatLogs.toList ++ List("flat filtered metadata: ") ++ flatFilteredMetadata.toList).mkString("\n")
+            IO.raiseError(CentaurTestException(message, workflow, submittedWorkflow))
+          }
+
+        for {
+          logs <- CentaurCromwellClient.logs(submittedWorkflow)
+          flatLogs = logs.asFlat.value
+          flatFilteredMetadata = metadata.asFlat.value |> filterForLogsFields
+          _ <- validateLogsMetadata(flatLogs, flatFilteredMetadata)
+        } yield ()
+      }
     }
-  }
 
-  def fetchMetadata(submittedWorkflow: SubmittedWorkflow,
-                    expandSubworkflows: Boolean): IO[WorkflowMetadata] = {
+  def fetchMetadata(submittedWorkflow: SubmittedWorkflow, expandSubworkflows: Boolean): IO[WorkflowMetadata] =
     CentaurCromwellClient.metadata(submittedWorkflow, expandSubworkflows = expandSubworkflows)
-  }
 
   def fetchAndValidateNonSubworkflowMetadata(submittedWorkflow: SubmittedWorkflow,
                                              workflowSpec: Workflow,
-                                             cacheHitUUID: Option[UUID] = None): Test[WorkflowMetadata] = {
+                                             cacheHitUUID: Option[UUID] = None
+  ): Test[WorkflowMetadata] =
     new Test[WorkflowMetadata] {
 
       def fetchOnce(): IO[WorkflowMetadata] = fetchMetadata(submittedWorkflow, expandSubworkflows = false)
 
       def eventuallyMetadata(workflow: SubmittedWorkflow,
-                             expectedMetadata: WorkflowFlatMetadata): IO[WorkflowMetadata] = {
-        validateMetadata(workflow, expectedMetadata).handleErrorWith({ _ =>
+                             expectedMetadata: WorkflowFlatMetadata
+      ): IO[WorkflowMetadata] =
+        validateMetadata(workflow, expectedMetadata).handleErrorWith { _ =>
           for {
             _ <- IO.sleep(2.seconds)
             recurse <- eventuallyMetadata(workflow, expectedMetadata)
           } yield recurse
-        })
-      }
+        }
 
       def validateMetadata(workflow: SubmittedWorkflow,
-                           expectedMetadata: WorkflowFlatMetadata): IO[WorkflowMetadata] = {
-        def checkDiff(diffs: Iterable[String], actualMetadata: WorkflowMetadata): IO[Unit] = {
+                           expectedMetadata: WorkflowFlatMetadata
+      ): IO[WorkflowMetadata] = {
+        def checkDiff(diffs: Iterable[String], actualMetadata: WorkflowMetadata): IO[Unit] =
           if (diffs.nonEmpty) {
             val message = s"Invalid metadata response:\n -${diffs.mkString("\n -")}\n"
             IO.raiseError(CentaurTestException(message, workflowSpec, workflow, actualMetadata))
           } else {
             IO.unit
           }
-        }
 
-        def validateUnwantedMetadata(actualMetadata: WorkflowMetadata): IO[Unit] = {
+        def validateUnwantedMetadata(actualMetadata: WorkflowMetadata): IO[Unit] =
           if (workflowSpec.notInMetadata.nonEmpty) {
             // Check that none of the "notInMetadata" keys are in the actual metadata
             val absentMdIntersect = workflowSpec.notInMetadata.toSet.intersect(actualMetadata.asFlat.value.keySet)
@@ -674,23 +706,23 @@ object Operations extends StrictLogging {
           } else {
             IO.unit
           }
-        }
 
-        def validateAllowOtherOutputs(actualMetadata: WorkflowMetadata): IO[Unit] = {
+        def validateAllowOtherOutputs(actualMetadata: WorkflowMetadata): IO[Unit] =
           if (workflowSpec.allowOtherOutputs) IO.unit
           else {
             val flat = actualMetadata.asFlat.value
             val actualOutputs: Iterable[String] = flat.keys.filter(_.startsWith("outputs."))
-            val expectedOutputs: Iterable[String] = workflowSpec.metadata.map(w => w.value.keys.filter(_.startsWith("outputs."))).getOrElse(List.empty)
+            val expectedOutputs: Iterable[String] =
+              workflowSpec.metadata.map(w => w.value.keys.filter(_.startsWith("outputs."))).getOrElse(List.empty)
             val diff = actualOutputs.toSet.diff(expectedOutputs.toSet)
             if (diff.nonEmpty) {
-              val message = s"Found unwanted keys in metadata with `allow-other-outputs` = false: ${diff.mkString(", ")}"
+              val message =
+                s"Found unwanted keys in metadata with `allow-other-outputs` = false: ${diff.mkString(", ")}"
               IO.raiseError(CentaurTestException(message, workflowSpec, workflow, actualMetadata))
             } else {
               IO.unit
             }
           }
-        }
 
         for {
           actualMetadata <- fetchOnce()
@@ -709,14 +741,14 @@ object Operations extends StrictLogging {
         case None => fetchOnce()
       }
     }
-  }
 
   def validateMetadataJson(testType: String,
                            expected: JsObject,
                            actual: JsObject,
                            submittedWorkflow: SubmittedWorkflow,
                            workflow: Workflow,
-                           allowableAddedOneWordFields: List[String]): IO[Unit] = {
+                           allowableAddedOneWordFields: List[String]
+  ): IO[Unit] =
     if (actual.equals(expected)) {
       IO.unit
     } else {
@@ -748,46 +780,66 @@ object Operations extends StrictLogging {
       } else {
         val writer: JsonWriter[Vector[Operation[JsValue]]] = new JsonWriter[Vector[Operation[JsValue]]] {
           def processOperation(op: Operation[JsValue]): JsValue = op match {
-            case Add(path, value) => JsObject(Map[String, JsValue](
-              "description" -> JsString("Unexpected value found"),
-              "path" -> JsString(path.toString),
-              "value" -> value))
-            case Copy(from, path) => JsObject(Map[String, JsValue](
-              "description" -> JsString("Value(s) unexpectedly copied"),
-              "expected_at" -> JsString(from.toString),
-              "also_at" -> JsString(path.toString)))
-            case Move(from, path) => JsObject(Map[String, JsValue](
-              "description" -> JsString("Value(s) unexpectedly moved"),
-              "expected_location" -> JsString(from.toString),
-              "actual_location" -> JsString(path.toString)))
-            case Remove(path, old) => JsObject(Map[String, JsValue](
-              "description" -> JsString("Value missing"),
-              "expected_location" -> JsString(path.toString)) ++
-              old.map(o => "expected_value" -> o))
-            case Replace(path, value, old) => JsObject(Map[String, JsValue](
-              "description" -> JsString("Incorrect value found"),
-              "path" -> JsString(path.toString),
-              "found_value" -> value) ++ old.map(o => "expected_value" -> o))
-            case diffson.jsonpatch.Test(path, value) => JsObject(Map[String, JsValue](
-              "op" -> JsString("test"),
-              "path" -> JsString(path.toString),
-              "value" -> value))
+            case Add(path, value) =>
+              JsObject(
+                Map[String, JsValue]("description" -> JsString("Unexpected value found"),
+                                     "path" -> JsString(path.toString),
+                                     "value" -> value
+                )
+              )
+            case Copy(from, path) =>
+              JsObject(
+                Map[String, JsValue]("description" -> JsString("Value(s) unexpectedly copied"),
+                                     "expected_at" -> JsString(from.toString),
+                                     "also_at" -> JsString(path.toString)
+                )
+              )
+            case Move(from, path) =>
+              JsObject(
+                Map[String, JsValue]("description" -> JsString("Value(s) unexpectedly moved"),
+                                     "expected_location" -> JsString(from.toString),
+                                     "actual_location" -> JsString(path.toString)
+                )
+              )
+            case Remove(path, old) =>
+              JsObject(
+                Map[String, JsValue]("description" -> JsString("Value missing"),
+                                     "expected_location" -> JsString(path.toString)
+                ) ++
+                  old.map(o => "expected_value" -> o)
+              )
+            case Replace(path, value, old) =>
+              JsObject(
+                Map[String, JsValue]("description" -> JsString("Incorrect value found"),
+                                     "path" -> JsString(path.toString),
+                                     "found_value" -> value
+                ) ++ old.map(o => "expected_value" -> o)
+              )
+            case diffson.jsonpatch.Test(path, value) =>
+              JsObject(
+                Map[String, JsValue]("op" -> JsString("test"), "path" -> JsString(path.toString), "value" -> value)
+              )
           }
 
-          override def write(vector: Vector[Operation[JsValue]]): JsValue = {
+          override def write(vector: Vector[Operation[JsValue]]): JsValue =
             JsArray(vector.map(processOperation))
-          }
         }
 
         val jsonDiff = filteredDifferences.toJson(writer).prettyPrint
-        IO.raiseError(CentaurTestException(s"Error during $testType metadata comparison. Diff: $jsonDiff Expected: $expected Actual: $actual", workflow, submittedWorkflow))
+        IO.raiseError(
+          CentaurTestException(
+            s"Error during $testType metadata comparison. Diff: $jsonDiff Expected: $expected Actual: $actual",
+            workflow,
+            submittedWorkflow
+          )
+        )
       }
     }
-  }
 
   def fetchAndValidateJobManagerStyleMetadata(submittedWorkflow: SubmittedWorkflow,
                                               workflow: Workflow,
-                                              prefetchedOriginalNonSubWorkflowMetadata: Option[String]): Test[WorkflowMetadata] = new Test[WorkflowMetadata] {
+                                              prefetchedOriginalNonSubWorkflowMetadata: Option[String]
+  ): Test[WorkflowMetadata] = new Test[WorkflowMetadata] {
 
     // If the non-subworkflow metadata was already fetched, there's no need to fetch it again.
     def originalMetadataStringIO: IO[String] = prefetchedOriginalNonSubWorkflowMetadata match {
@@ -799,19 +851,43 @@ object Operations extends StrictLogging {
       originalMetadata <- originalMetadataStringIO
       jmMetadata <- CentaurCromwellClient.metadata(
         workflow = submittedWorkflow,
-        Option(CentaurCromwellClient.defaultMetadataArgs.getOrElse(Map.empty) ++ jmArgs))
+        Option(CentaurCromwellClient.defaultMetadataArgs.getOrElse(Map.empty) ++ jmArgs)
+      )
       jmMetadataObject <- IO.fromTry(Try(jmMetadata.value.parseJson.asJsObject))
       expectation <- IO.fromTry(Try(extractJmStyleMetadataFields(originalMetadata.parseJson.asJsObject)))
-      _ <- validateMetadataJson(testType = s"fetchAndValidateJobManagerStyleMetadata", expectation, jmMetadataObject, submittedWorkflow, workflow, allowableOneWordAdditionsInJmMetadata)
+      _ <- validateMetadataJson(testType = s"fetchAndValidateJobManagerStyleMetadata",
+                                expectation,
+                                jmMetadataObject,
+                                submittedWorkflow,
+                                workflow,
+                                allowableOneWordAdditionsInJmMetadata
+      )
     } yield jmMetadata
   }
 
   val oneWordJmIncludeKeys = List(
-    "attempt", "callRoot", "end",
-    "executionStatus", "failures", "inputs", "jobId",
-    "calls", "outputs", "shardIndex", "start", "stderr", "stdout",
-    "description", "executionEvents", "labels", "parentWorkflowId",
-    "returnCode", "status", "submission", "subWorkflowId", "workflowName"
+    "attempt",
+    "callRoot",
+    "end",
+    "executionStatus",
+    "failures",
+    "inputs",
+    "jobId",
+    "calls",
+    "outputs",
+    "shardIndex",
+    "start",
+    "stderr",
+    "stdout",
+    "description",
+    "executionEvents",
+    "labels",
+    "parentWorkflowId",
+    "returnCode",
+    "status",
+    "submission",
+    "subWorkflowId",
+    "workflowName"
   )
 
   // Our Job Manager metadata validation works by comparing the first pull of metadata which satisfies all test requirements
@@ -839,12 +915,13 @@ object Operations extends StrictLogging {
 
     // NB: this filter to remove "calls" is because - although it is a single word in the JM request,
     // it gets treated specially by the API (so has to be treated specially here too)
-    def processOneWordIncludes(json: JsObject) = (oneWordJmIncludeKeys.filterNot(_ == "calls") :+ "id").foldRight(JsObject.empty) { (toInclude, current) =>
-      json.fields.get(toInclude) match {
-        case Some(jsonToInclude) => JsObject(current.fields + (toInclude -> jsonToInclude))
-        case None => current
+    def processOneWordIncludes(json: JsObject) =
+      (oneWordJmIncludeKeys.filterNot(_ == "calls") :+ "id").foldRight(JsObject.empty) { (toInclude, current) =>
+        json.fields.get(toInclude) match {
+          case Some(jsonToInclude) => JsObject(current.fields + (toInclude -> jsonToInclude))
+          case None => current
+        }
       }
-    }
 
     def processCallCacheField(callJson: JsObject) = for {
       originalCallCachingField <- callJson.fields.get("callCaching")
@@ -864,7 +941,9 @@ object Operations extends StrictLogging {
     }
 
     val workflowLevelWithOneWordIncludes = processOneWordIncludes(originalWorkflowMetadataJson)
-    val callsField = originalCallMetadataJson map { calls => Map("calls" -> processCallsSection(calls)) } getOrElse Map.empty
+    val callsField = originalCallMetadataJson map { calls =>
+      Map("calls" -> processCallsSection(calls))
+    } getOrElse Map.empty
 
     JsObject(workflowLevelWithOneWordIncludes.fields ++ callsField)
   }
@@ -875,7 +954,8 @@ object Operations extends StrictLogging {
   def validateCacheResultField(workflowDefinition: Workflow,
                                submittedWorkflow: SubmittedWorkflow,
                                metadata: WorkflowMetadata,
-                               blacklistedValue: String): Test[Unit] = {
+                               blacklistedValue: String
+  ): Test[Unit] =
     new Test[Unit] {
       override def run: IO[Unit] = {
         val badCacheResults = metadata.asFlat.value collect {
@@ -891,24 +971,24 @@ object Operations extends StrictLogging {
         }
       }
     }
-  }
 
   def validateDirectoryContentsCounts(workflowDefinition: Workflow,
                                       submittedWorkflow: SubmittedWorkflow,
-                                      metadata: WorkflowMetadata): Test[Unit] = new Test[Unit] {
+                                      metadata: WorkflowMetadata
+  ): Test[Unit] = new Test[Unit] {
     private val workflowId = submittedWorkflow.id.id.toString
 
     override def run: IO[Unit] = workflowDefinition.directoryContentCounts match {
       case None => IO.unit
       case Some(directoryContentCountCheck) =>
-        val counts = directoryContentCountCheck.expectedDirectoryContentsCounts map {
-          case (directory, count) =>
-            val substitutedDir = directory.replaceAll("<<UUID>>", workflowId)
-            (substitutedDir, count, directoryContentCountCheck.checkFiles.countObjectsAtPath(substitutedDir))
+        val counts = directoryContentCountCheck.expectedDirectoryContentsCounts map { case (directory, count) =>
+          val substitutedDir = directory.replaceAll("<<UUID>>", workflowId)
+          (substitutedDir, count, directoryContentCountCheck.checkFiles.countObjectsAtPath(substitutedDir))
         }
 
         val badCounts = counts collect {
-          case (directory, expectedCount, actualCount) if expectedCount != actualCount => s"Expected to find $expectedCount item(s) at $directory but got $actualCount"
+          case (directory, expectedCount, actualCount) if expectedCount != actualCount =>
+            s"Expected to find $expectedCount item(s) at $directory but got $actualCount"
         }
         if (badCounts.isEmpty) {
           IO.unit
@@ -921,21 +1001,22 @@ object Operations extends StrictLogging {
 
   def validateNoCacheHits(submittedWorkflow: SubmittedWorkflow,
                           metadata: WorkflowMetadata,
-                          workflowDefinition: Workflow): Test[Unit] = {
+                          workflowDefinition: Workflow
+  ): Test[Unit] =
     validateCacheResultField(workflowDefinition, submittedWorkflow, metadata, "Cache Hit")
-  }
 
   def validateNoCacheMisses(submittedWorkflow: SubmittedWorkflow,
                             metadata: WorkflowMetadata,
-                            workflowDefinition: Workflow): Test[Unit] = {
+                            workflowDefinition: Workflow
+  ): Test[Unit] =
     validateCacheResultField(workflowDefinition, submittedWorkflow, metadata, "Cache Miss")
-  }
 
   def validateSubmitFailure(workflow: Workflow,
                             expectedSubmitResponse: SubmitHttpResponse,
-                            actualSubmitResponse: SubmitHttpResponse): Test[Unit] = {
+                            actualSubmitResponse: SubmitHttpResponse
+  ): Test[Unit] =
     new Test[Unit] {
-      override def run: IO[Unit] = {
+      override def run: IO[Unit] =
         if (expectedSubmitResponse == actualSubmitResponse) {
           IO.unit
         } else {
@@ -949,7 +1030,5 @@ object Operations extends StrictLogging {
                 |""".stripMargin
           IO.raiseError(CentaurTestException(message, workflow))
         }
-      }
     }
-  }
 }
diff --git a/centaur/src/main/scala/centaur/test/TestOptions.scala b/centaur/src/main/scala/centaur/test/TestOptions.scala
index 10354c756bb..ceba238a4da 100644
--- a/centaur/src/main/scala/centaur/test/TestOptions.scala
+++ b/centaur/src/main/scala/centaur/test/TestOptions.scala
@@ -18,15 +18,13 @@ object TestOptions {
     Apply[ErrorOr].map2(tags, ignore)((t, i) => TestOptions(t, i))
   }
 
-  def tagsFromConfig(conf: Config): ErrorOr[List[String]] = {
+  def tagsFromConfig(conf: Config): ErrorOr[List[String]] =
     conf.get[List[String]]("tags") match {
       case Success(tagStrings) => Valid(tagStrings.map(_.toLowerCase).distinct)
       case Failure(_) => Valid(List.empty[String])
     }
-  }
-
-  def ignoreFromConfig(conf: Config): ErrorOr[Boolean] = {
 
+  def ignoreFromConfig(conf: Config): ErrorOr[Boolean] =
     if (conf.hasPath("ignore")) {
       conf.get[Boolean]("ignore") match {
         case Success(ignore) => Valid(ignore)
@@ -35,6 +33,4 @@ object TestOptions {
     } else {
       Valid(false)
     }
-  }
 }
-
diff --git a/centaur/src/main/scala/centaur/test/formulas/TestFormulas.scala b/centaur/src/main/scala/centaur/test/formulas/TestFormulas.scala
index 774f852237d..6c006283894 100644
--- a/centaur/src/main/scala/centaur/test/formulas/TestFormulas.scala
+++ b/centaur/src/main/scala/centaur/test/formulas/TestFormulas.scala
@@ -12,11 +12,21 @@ import centaur.test.workflow.Workflow
 import centaur.test.{Operations, Test}
 import centaur.{CentaurConfig, CromwellManager, CromwellTracker, ManagedCromwellServer}
 import com.typesafe.scalalogging.StrictLogging
-import cromwell.api.model.{Aborted, Aborting, Failed, Running, SubmittedWorkflow, Succeeded, TerminalStatus, WorkflowMetadata}
+import cromwell.api.model.{
+  Aborted,
+  Aborting,
+  Failed,
+  Running,
+  SubmittedWorkflow,
+  Succeeded,
+  TerminalStatus,
+  WorkflowMetadata
+}
 
 import scala.concurrent.duration._
 import centaur.test.metadata.WorkflowFlatMetadata._
 import spray.json.JsString
+
 /**
   * A collection of test formulas which can be used, building upon operations by chaining them together via a
   * for comprehension. These assembled formulas can then be run by a client
@@ -33,7 +43,7 @@ object TestFormulas extends StrictLogging {
        |""".stripMargin.trim
   )
 
-  private def runWorkflowUntilTerminalStatus(workflow: Workflow, status: TerminalStatus): Test[SubmittedWorkflow] = {
+  private def runWorkflowUntilTerminalStatus(workflow: Workflow, status: TerminalStatus): Test[SubmittedWorkflow] =
     for {
       _ <- checkVersion()
       s <- submitWorkflow(workflow)
@@ -41,14 +51,15 @@ object TestFormulas extends StrictLogging {
         workflow = s,
         testDefinition = workflow,
         expectedStatuses = Set(Running, status),
-        timeout = CentaurConfig.workflowProgressTimeout,
+        timeout = CentaurConfig.workflowProgressTimeout
       )
       _ <- pollUntilStatus(s, workflow, status)
     } yield s
-  }
 
-  private def runSuccessfulWorkflow(workflow: Workflow): Test[SubmittedWorkflow] = runWorkflowUntilTerminalStatus(workflow, Succeeded)
-  private def runFailingWorkflow(workflow: Workflow): Test[SubmittedWorkflow] = runWorkflowUntilTerminalStatus(workflow, Failed)
+  private def runSuccessfulWorkflow(workflow: Workflow): Test[SubmittedWorkflow] =
+    runWorkflowUntilTerminalStatus(workflow, Succeeded)
+  private def runFailingWorkflow(workflow: Workflow): Test[SubmittedWorkflow] =
+    runWorkflowUntilTerminalStatus(workflow, Failed)
 
   def runSuccessfulWorkflowAndVerifyTimeAndOutputs(workflowDefinition: Workflow): Test[SubmitResponse] = for {
     _ <- checkDescription(workflowDefinition, validityExpectation = Option(true))
@@ -56,18 +67,28 @@ object TestFormulas extends StrictLogging {
     beforeTimestamp = OffsetDateTime.now().toInstant.getEpochSecond
     submittedWorkflow <- runSuccessfulWorkflow(workflowDefinition)
     afterTimestamp = OffsetDateTime.now().toInstant.getEpochSecond
-    _ <- fetchAndValidateOutputs(submittedWorkflow, workflowDefinition, "ROOT NOT SUPPORTED IN TIMING/OUTPUT ONLY TESTS")
+    _ <- fetchAndValidateOutputs(submittedWorkflow,
+                                 workflowDefinition,
+                                 "ROOT NOT SUPPORTED IN TIMING/OUTPUT ONLY TESTS"
+    )
     _ <- checkFastEnough(beforeTimestamp, afterTimestamp, timeAllowance)
   } yield SubmitResponse(submittedWorkflow)
 
-  def runSuccessfulWorkflowAndVerifyMetadata(workflowDefinition: Workflow)(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = for {
+  def runSuccessfulWorkflowAndVerifyMetadata(
+    workflowDefinition: Workflow
+  )(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = for {
     _ <- checkDescription(workflowDefinition, validityExpectation = Option(true))
     _ <- timingVerificationNotSupported(workflowDefinition.maximumAllowedTime)
     submittedWorkflow <- runSuccessfulWorkflow(workflowDefinition)
     metadata <- fetchAndValidateNonSubworkflowMetadata(submittedWorkflow, workflowDefinition)
-    _ <- fetchAndValidateJobManagerStyleMetadata(submittedWorkflow, workflowDefinition, prefetchedOriginalNonSubWorkflowMetadata = Option(metadata.value))
+    _ <- fetchAndValidateJobManagerStyleMetadata(submittedWorkflow,
+                                                 workflowDefinition,
+                                                 prefetchedOriginalNonSubWorkflowMetadata = Option(metadata.value)
+    )
     notArchivedFlatMetadata = metadata.asFlat
-    workflowRoot = notArchivedFlatMetadata.value.get("workflowRoot").collectFirst { case JsString(r) => r } getOrElse "No Workflow Root"
+    workflowRoot = notArchivedFlatMetadata.value.get("workflowRoot").collectFirst { case JsString(r) =>
+      r
+    } getOrElse "No Workflow Root"
     _ <- fetchAndValidateOutputs(submittedWorkflow, workflowDefinition, workflowRoot)
     _ <- fetchAndValidateLabels(submittedWorkflow, workflowDefinition, workflowRoot)
     _ <- validateLogs(metadata, submittedWorkflow, workflowDefinition)
@@ -75,17 +96,24 @@ object TestFormulas extends StrictLogging {
     _ <- validateDirectoryContentsCounts(workflowDefinition, submittedWorkflow, metadata)
   } yield SubmitResponse(submittedWorkflow)
 
-  def runFailingWorkflowAndVerifyMetadata(workflowDefinition: Workflow)(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = for {
+  def runFailingWorkflowAndVerifyMetadata(
+    workflowDefinition: Workflow
+  )(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = for {
     _ <- checkDescription(workflowDefinition, validityExpectation = None)
     _ <- timingVerificationNotSupported(workflowDefinition.maximumAllowedTime)
     submittedWorkflow <- runFailingWorkflow(workflowDefinition)
     metadata <- fetchAndValidateNonSubworkflowMetadata(submittedWorkflow, workflowDefinition)
-    _ <- fetchAndValidateJobManagerStyleMetadata(submittedWorkflow, workflowDefinition, prefetchedOriginalNonSubWorkflowMetadata = Option(metadata.value))
+    _ <- fetchAndValidateJobManagerStyleMetadata(submittedWorkflow,
+                                                 workflowDefinition,
+                                                 prefetchedOriginalNonSubWorkflowMetadata = Option(metadata.value)
+    )
     _ = cromwellTracker.track(metadata)
     _ <- validateDirectoryContentsCounts(workflowDefinition, submittedWorkflow, metadata)
   } yield SubmitResponse(submittedWorkflow)
 
-  def runWorkflowTwiceExpectingCaching(workflowDefinition: Workflow)(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = {
+  def runWorkflowTwiceExpectingCaching(
+    workflowDefinition: Workflow
+  )(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] =
     for {
       _ <- checkDescription(workflowDefinition, validityExpectation = Option(true))
       _ <- timingVerificationNotSupported(workflowDefinition.maximumAllowedTime)
@@ -93,14 +121,18 @@ object TestFormulas extends StrictLogging {
       secondWf <- runSuccessfulWorkflow(workflowDefinition.secondRun)
       _ <- printHashDifferential(firstWF, secondWf)
       metadata <- fetchAndValidateNonSubworkflowMetadata(secondWf, workflowDefinition, Option(firstWF.id.id))
-      _ <- fetchAndValidateJobManagerStyleMetadata(secondWf, workflowDefinition, prefetchedOriginalNonSubWorkflowMetadata = None)
+      _ <- fetchAndValidateJobManagerStyleMetadata(secondWf,
+                                                   workflowDefinition,
+                                                   prefetchedOriginalNonSubWorkflowMetadata = None
+      )
       _ = cromwellTracker.track(metadata)
       _ <- validateNoCacheMisses(secondWf, metadata, workflowDefinition)
       _ <- validateDirectoryContentsCounts(workflowDefinition, secondWf, metadata)
     } yield SubmitResponse(secondWf)
-  }
 
-  def runWorkflowThriceExpectingCaching(workflowDefinition: Workflow)(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = {
+  def runWorkflowThriceExpectingCaching(
+    workflowDefinition: Workflow
+  )(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] =
     for {
       _ <- checkDescription(workflowDefinition, validityExpectation = Option(true))
       _ <- timingVerificationNotSupported(workflowDefinition.maximumAllowedTime)
@@ -115,41 +147,48 @@ object TestFormulas extends StrictLogging {
       _ <- validateNoCacheMisses(thirdWf, metadataThree, workflowDefinition)
       _ <- validateDirectoryContentsCounts(workflowDefinition, thirdWf, metadataThree)
     } yield SubmitResponse(thirdWf)
-  }
 
-  def runWorkflowTwiceExpectingNoCaching(workflowDefinition: Workflow)(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = {
+  def runWorkflowTwiceExpectingNoCaching(
+    workflowDefinition: Workflow
+  )(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] =
     for {
       _ <- checkDescription(workflowDefinition, validityExpectation = Option(true))
       _ <- timingVerificationNotSupported(workflowDefinition.maximumAllowedTime)
       _ <- runSuccessfulWorkflow(workflowDefinition) // Build caches
       testWf <- runSuccessfulWorkflow(workflowDefinition.secondRun)
       metadata <- fetchAndValidateNonSubworkflowMetadata(testWf, workflowDefinition)
-      _ <- fetchAndValidateJobManagerStyleMetadata(testWf, workflowDefinition, prefetchedOriginalNonSubWorkflowMetadata = None)
+      _ <- fetchAndValidateJobManagerStyleMetadata(testWf,
+                                                   workflowDefinition,
+                                                   prefetchedOriginalNonSubWorkflowMetadata = None
+      )
       _ = cromwellTracker.track(metadata)
       _ <- validateNoCacheHits(testWf, metadata, workflowDefinition)
       _ <- validateDirectoryContentsCounts(workflowDefinition, testWf, metadata)
     } yield SubmitResponse(testWf)
-  }
 
-  def runFailingWorkflowTwiceExpectingNoCaching(workflowDefinition: Workflow)(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = {
+  def runFailingWorkflowTwiceExpectingNoCaching(
+    workflowDefinition: Workflow
+  )(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] =
     for {
       _ <- checkDescription(workflowDefinition, validityExpectation = None)
       _ <- timingVerificationNotSupported(workflowDefinition.maximumAllowedTime)
       _ <- runFailingWorkflow(workflowDefinition) // Build caches
       testWf <- runFailingWorkflow(workflowDefinition)
       metadata <- fetchAndValidateNonSubworkflowMetadata(testWf, workflowDefinition)
-      _ <- fetchAndValidateJobManagerStyleMetadata(testWf, workflowDefinition, prefetchedOriginalNonSubWorkflowMetadata = None)
+      _ <- fetchAndValidateJobManagerStyleMetadata(testWf,
+                                                   workflowDefinition,
+                                                   prefetchedOriginalNonSubWorkflowMetadata = None
+      )
       _ = cromwellTracker.track(metadata)
       _ <- validateNoCacheHits(testWf, metadata, workflowDefinition)
       _ <- validateDirectoryContentsCounts(workflowDefinition, testWf, metadata)
     } yield SubmitResponse(testWf)
-  }
 
   private def cromwellRestart(workflowDefinition: Workflow,
                               callMarker: CallMarker,
                               testRecover: Boolean,
-                              finalStatus: TerminalStatus)(
-                              implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = {
+                              finalStatus: TerminalStatus
+  )(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] =
     CentaurConfig.runMode match {
       case ManagedCromwellServer(_, postRestart, withRestart) if withRestart =>
         for {
@@ -163,27 +202,31 @@ object TestFormulas extends StrictLogging {
             workflow = submittedWorkflow,
             testDefinition = workflowDefinition,
             expectedStatuses = Set(Running, finalStatus),
-            timeout = CentaurConfig.workflowProgressTimeout,
+            timeout = CentaurConfig.workflowProgressTimeout
           )
           _ <- pollUntilStatus(submittedWorkflow, workflowDefinition, finalStatus)
           metadata <- fetchAndValidateNonSubworkflowMetadata(submittedWorkflow, workflowDefinition)
-          _ <- fetchAndValidateJobManagerStyleMetadata(submittedWorkflow, workflowDefinition, prefetchedOriginalNonSubWorkflowMetadata = None)
+          _ <- fetchAndValidateJobManagerStyleMetadata(submittedWorkflow,
+                                                       workflowDefinition,
+                                                       prefetchedOriginalNonSubWorkflowMetadata = None
+          )
           _ = cromwellTracker.track(metadata)
-          _ <- if (testRecover) {
-            validateRecovered(workflowDefinition, submittedWorkflow, metadata, callMarker.callKey, jobId)
-          }
-          else {
-            Test.successful(())
-          }
+          _ <-
+            if (testRecover) {
+              validateRecovered(workflowDefinition, submittedWorkflow, metadata, callMarker.callKey, jobId)
+            } else {
+              Test.successful(())
+            }
           _ <- validateDirectoryContentsCounts(workflowDefinition, submittedWorkflow, metadata)
         } yield SubmitResponse(submittedWorkflow)
       case _ if finalStatus == Succeeded => runSuccessfulWorkflowAndVerifyMetadata(workflowDefinition)
       case _ if finalStatus == Failed => runFailingWorkflowAndVerifyMetadata(workflowDefinition)
       case _ => Test.invalidTestDefinition("This test can only run successful or failed workflow", workflowDefinition)
     }
-  }
 
-  def instantAbort(workflowDefinition: Workflow)(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = for {
+  def instantAbort(
+    workflowDefinition: Workflow
+  )(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = for {
     _ <- checkDescription(workflowDefinition, validityExpectation = Option(true))
     _ <- timingVerificationNotSupported(workflowDefinition.maximumAllowedTime)
     submittedWorkflow <- submitWorkflow(workflowDefinition)
@@ -192,16 +235,21 @@ object TestFormulas extends StrictLogging {
       workflow = submittedWorkflow,
       testDefinition = workflowDefinition,
       expectedStatuses = Set(Running, Aborting, Aborted),
-      timeout = CentaurConfig.workflowProgressTimeout,
+      timeout = CentaurConfig.workflowProgressTimeout
     )
     _ <- pollUntilStatus(submittedWorkflow, workflowDefinition, Aborted)
     metadata <- fetchAndValidateNonSubworkflowMetadata(submittedWorkflow, workflowDefinition)
-    _ <- fetchAndValidateJobManagerStyleMetadata(submittedWorkflow, workflowDefinition, prefetchedOriginalNonSubWorkflowMetadata = None)
+    _ <- fetchAndValidateJobManagerStyleMetadata(submittedWorkflow,
+                                                 workflowDefinition,
+                                                 prefetchedOriginalNonSubWorkflowMetadata = None
+    )
     _ = cromwellTracker.track(metadata)
     _ <- validateDirectoryContentsCounts(workflowDefinition, submittedWorkflow, metadata)
   } yield SubmitResponse(submittedWorkflow)
 
-  def scheduledAbort(workflowDefinition: Workflow, callMarker: CallMarker, restart: Boolean)(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = {
+  def scheduledAbort(workflowDefinition: Workflow, callMarker: CallMarker, restart: Boolean)(implicit
+    cromwellTracker: Option[CromwellTracker]
+  ): Test[SubmitResponse] = {
     def withRestart(): Unit = CentaurConfig.runMode match {
       case ManagedCromwellServer(_, postRestart, withRestart) if withRestart =>
         CromwellManager.stopCromwell(s"Scheduled restart from ${workflowDefinition.testName}")
@@ -217,42 +265,45 @@ object TestFormulas extends StrictLogging {
       // The Cromwell call status could be running but the backend job might not have started yet, give it some time
       _ <- waitFor(30.seconds)
       _ <- abortWorkflow(submittedWorkflow)
-      _ = if(restart) withRestart()
+      _ = if (restart) withRestart()
       _ <- expectSomeProgress(
         workflow = submittedWorkflow,
         testDefinition = workflowDefinition,
         expectedStatuses = Set(Running, Aborting, Aborted),
-        timeout = CentaurConfig.workflowProgressTimeout,
+        timeout = CentaurConfig.workflowProgressTimeout
       )
       _ <- pollUntilStatus(submittedWorkflow, workflowDefinition, Aborted)
       _ <- validatePAPIAborted(workflowDefinition, submittedWorkflow, jobId)
       // Wait a little to make sure that if the abort didn't work and calls start running we see them in the metadata
       _ <- waitFor(30.seconds)
       metadata <- fetchAndValidateNonSubworkflowMetadata(submittedWorkflow, workflowDefinition)
-      _ <- fetchAndValidateJobManagerStyleMetadata(submittedWorkflow, workflowDefinition, prefetchedOriginalNonSubWorkflowMetadata = None)
+      _ <- fetchAndValidateJobManagerStyleMetadata(submittedWorkflow,
+                                                   workflowDefinition,
+                                                   prefetchedOriginalNonSubWorkflowMetadata = None
+      )
       _ = cromwellTracker.track(metadata)
       _ <- validateDirectoryContentsCounts(workflowDefinition, submittedWorkflow, metadata)
     } yield SubmitResponse(submittedWorkflow)
   }
 
   def workflowRestart(workflowDefinition: Workflow,
-                             callMarker: CallMarker,
-                             recover: Boolean,
-                             finalStatus: TerminalStatus)(
-                             implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = {
+                      callMarker: CallMarker,
+                      recover: Boolean,
+                      finalStatus: TerminalStatus
+  )(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] =
     cromwellRestart(workflowDefinition, callMarker, testRecover = recover, finalStatus = finalStatus)
-  }
 
-  def submitInvalidWorkflow(workflow: Workflow, expectedSubmitResponse: SubmitHttpResponse): Test[SubmitResponse] = {
+  def submitInvalidWorkflow(workflow: Workflow, expectedSubmitResponse: SubmitHttpResponse): Test[SubmitResponse] =
     for {
       _ <- checkDescription(workflow, validityExpectation = None)
       _ <- timingVerificationNotSupported(workflow.maximumAllowedTime)
       actualSubmitResponse <- Operations.submitInvalidWorkflow(workflow)
       _ <- validateSubmitFailure(workflow, expectedSubmitResponse, actualSubmitResponse)
     } yield actualSubmitResponse
-  }
 
-  def papiUpgrade(workflowDefinition: Workflow, callMarker: CallMarker)(implicit cromwellTracker: Option[CromwellTracker]): Test[SubmitResponse] = {
+  def papiUpgrade(workflowDefinition: Workflow, callMarker: CallMarker)(implicit
+    cromwellTracker: Option[CromwellTracker]
+  ): Test[SubmitResponse] =
     CentaurConfig.runMode match {
       case ManagedCromwellServer(_, postRestart, withRestart) if withRestart =>
         for {
@@ -266,21 +317,25 @@ object TestFormulas extends StrictLogging {
             workflow = first,
             testDefinition = workflowDefinition,
             expectedStatuses = Set(Running, Succeeded),
-            timeout = CentaurConfig.workflowProgressTimeout,
+            timeout = CentaurConfig.workflowProgressTimeout
           )
           _ <- pollUntilStatus(first, workflowDefinition, Succeeded)
           _ <- checkDescription(workflowDefinition.secondRun, validityExpectation = Option(true))
-          second <- runSuccessfulWorkflow(workflowDefinition.secondRun) // Same WDL and config but a "backend" runtime option targeting PAPI v2.
+          second <- runSuccessfulWorkflow(
+            workflowDefinition.secondRun
+          ) // Same WDL and config but a "backend" runtime option targeting PAPI v2.
           _ <- printHashDifferential(first, second)
           metadata <- fetchAndValidateNonSubworkflowMetadata(second, workflowDefinition, Option(first.id.id))
-          _ <- fetchAndValidateJobManagerStyleMetadata(second, workflowDefinition, prefetchedOriginalNonSubWorkflowMetadata = None)
+          _ <- fetchAndValidateJobManagerStyleMetadata(second,
+                                                       workflowDefinition,
+                                                       prefetchedOriginalNonSubWorkflowMetadata = None
+          )
           _ = cromwellTracker.track(metadata)
           _ <- validateNoCacheMisses(second, metadata, workflowDefinition)
           _ <- validateDirectoryContentsCounts(workflowDefinition, second, metadata)
         } yield SubmitResponse(second)
       case _ => Test.invalidTestDefinition("Configuration not supported by PapiUpgradeTest", workflowDefinition)
     }
-  }
 
   implicit class EnhancedCromwellTracker(val tracker: Option[CromwellTracker]) extends AnyVal {
     def track(metadata: WorkflowMetadata): Unit = tracker foreach { _.track(metadata) }
diff --git a/centaur/src/main/scala/centaur/test/markers/CallMarker.scala b/centaur/src/main/scala/centaur/test/markers/CallMarker.scala
index 08eafc09213..56274a07ed4 100644
--- a/centaur/src/main/scala/centaur/test/markers/CallMarker.scala
+++ b/centaur/src/main/scala/centaur/test/markers/CallMarker.scala
@@ -7,12 +7,11 @@ import configs.Result.{Failure, Success}
 import configs.syntax._
 
 object CallMarker {
-  def fromConfig(config: Config): ErrorOr[Option[CallMarker]] = {
+  def fromConfig(config: Config): ErrorOr[Option[CallMarker]] =
     config.get[Option[String]]("callMark") match {
       case Success(marker) => (marker map CallMarker.apply).validNel
       case Failure(f) => s"Invalid restart marker $f".invalidNel
     }
-  }
 }
 
 /**
diff --git a/centaur/src/main/scala/centaur/test/metadata/CallAttemptFailure.scala b/centaur/src/main/scala/centaur/test/metadata/CallAttemptFailure.scala
index 098328d0d41..f79aaca6826 100644
--- a/centaur/src/main/scala/centaur/test/metadata/CallAttemptFailure.scala
+++ b/centaur/src/main/scala/centaur/test/metadata/CallAttemptFailure.scala
@@ -12,8 +12,7 @@ import io.circe.parser._
   *
   * https://github.com/DataBiosphere/job-manager/blob/f83e4284e2419389b7e515720c9d960d2eb81a29/servers/cromwell/jobs/controllers/jobs_controller.py#L155-L162
   */
-case class CallAttemptFailure
-(
+case class CallAttemptFailure(
   workflowId: String,
   callFullyQualifiedName: String,
   jobIndex: Int,
@@ -27,29 +26,25 @@ case class CallAttemptFailure
 )
 
 object CallAttemptFailure {
-  def buildFailures(jsonOption: Option[String]): IO[Vector[CallAttemptFailure]] = {
+  def buildFailures(jsonOption: Option[String]): IO[Vector[CallAttemptFailure]] =
     jsonOption.map(buildFailures).getOrElse(IO.pure(Vector.empty))
-  }
 
-  def buildFailures(json: String): IO[Vector[CallAttemptFailure]] = {
+  def buildFailures(json: String): IO[Vector[CallAttemptFailure]] =
     IO.fromEither(decode[Vector[CallAttemptFailure]](json))
-  }
 
-  private implicit val decodeFailures: Decoder[Vector[CallAttemptFailure]] = {
+  implicit private val decodeFailures: Decoder[Vector[CallAttemptFailure]] =
     Decoder.instance { c =>
       for {
         workflowId <- c.get[String]("id")
         calls <- c.get[Map[String, Json]]("calls").map(_.toVector)
-        callAttemptFailures <- calls.flatTraverse[Decoder.Result, CallAttemptFailure] {
-          case (callName, callJson) =>
-            val decoderCallAttempt = decodeFromCallAttempt(workflowId, callName)
-            callJson.as[Vector[Option[CallAttemptFailure]]](Decoder.decodeVector(decoderCallAttempt)).map(_.flatten)
+        callAttemptFailures <- calls.flatTraverse[Decoder.Result, CallAttemptFailure] { case (callName, callJson) =>
+          val decoderCallAttempt = decodeFromCallAttempt(workflowId, callName)
+          callJson.as[Vector[Option[CallAttemptFailure]]](Decoder.decodeVector(decoderCallAttempt)).map(_.flatten)
         }
       } yield callAttemptFailures
     } or Decoder.const(Vector.empty)
-  }
 
-  private def decodeFromCallAttempt(workflowId: String, callName: String): Decoder[Option[CallAttemptFailure]] = {
+  private def decodeFromCallAttempt(workflowId: String, callName: String): Decoder[Option[CallAttemptFailure]] =
     Decoder.instance { c =>
       for {
         shardIndexOption <- c.get[Option[Int]]("shardIndex")
@@ -77,5 +72,4 @@ object CallAttemptFailure {
         }
       } yield callAttemptFailureOption
     } or Decoder.const(None)
-  }
 }
diff --git a/centaur/src/main/scala/centaur/test/metadata/WorkflowFlatMetadata.scala b/centaur/src/main/scala/centaur/test/metadata/WorkflowFlatMetadata.scala
index 182d1fad58f..5054105c154 100644
--- a/centaur/src/main/scala/centaur/test/metadata/WorkflowFlatMetadata.scala
+++ b/centaur/src/main/scala/centaur/test/metadata/WorkflowFlatMetadata.scala
@@ -17,7 +17,6 @@ import spray.json._
 import scala.language.postfixOps
 import scala.util.{Failure, Success, Try}
 
-
 /**
   * Workflow metadata that has been flattened for Centaur test purposes. The keys are similar to the simpleton-syntax
   * stored in the Cromwell database, and values are primitive types, not nested JSON objects or arrays.
@@ -27,15 +26,23 @@ case class WorkflowFlatMetadata(value: Map[String, JsValue]) extends AnyVal {
   def diff(actual: WorkflowFlatMetadata, workflowID: UUID, cacheHitUUID: Option[UUID] = None): Iterable[String] = {
     // If the test fails in initialization there wouldn't be workflow root metadata, and if that's the expectation
     // then that's ok.
-    val workflowRoot = actual.value.get("workflowRoot").collectFirst { case JsString(r) => r } getOrElse "No Workflow Root"
+    val workflowRoot =
+      actual.value.get("workflowRoot").collectFirst { case JsString(r) => r } getOrElse "No Workflow Root"
     val missingErrors = value.keySet.diff(actual.value.keySet) map { k => s"Missing key: $k" }
-    val mismatchErrors = value.keySet.intersect(actual.value.keySet) flatMap { k => diffValues(k, value(k), actual.value(k),
-      workflowID, workflowRoot, cacheHitUUID)}
+    val mismatchErrors = value.keySet.intersect(actual.value.keySet) flatMap { k =>
+      diffValues(k, value(k), actual.value(k), workflowID, workflowRoot, cacheHitUUID)
+    }
 
     mismatchErrors ++ missingErrors
   }
 
-  private def diffValues(key: String, expected: JsValue, actual: JsValue, workflowID: UUID, workflowRoot: String, cacheHitUUID: Option[UUID]): Option[String] = {
+  private def diffValues(key: String,
+                         expected: JsValue,
+                         actual: JsValue,
+                         workflowID: UUID,
+                         workflowRoot: String,
+                         cacheHitUUID: Option[UUID]
+  ): Option[String] = {
     /*
       FIXME/TODO:
 
@@ -59,8 +66,10 @@ case class WorkflowFlatMetadata(value: Map[String, JsValue]) extends AnyVal {
         val stripped = stripQuotes(cacheSubstitutions).stripPrefix("~~")
         (!stripQuotes(o.toString).contains(stripped)).option(s"Actual value ${o.toString()} does not contain $stripped")
       case o: JsString => (cacheSubstitutions != o.toString).option(s"expected: $cacheSubstitutions but got: $actual")
-      case o: JsNumber => (expected != JsString(o.value.toString)).option(s"expected: $cacheSubstitutions but got: $actual")
-      case o: JsBoolean => (expected != JsString(o.value.toString)).option(s"expected: $cacheSubstitutions but got: $actual")
+      case o: JsNumber =>
+        (expected != JsString(o.value.toString)).option(s"expected: $cacheSubstitutions but got: $actual")
+      case o: JsBoolean =>
+        (expected != JsString(o.value.toString)).option(s"expected: $cacheSubstitutions but got: $actual")
       case o: JsArray if stripQuotes(cacheSubstitutions).startsWith("~>") =>
         val stripped = stripQuotes(cacheSubstitutions).stripPrefix("~>")
         val replaced = stripped.replaceAll("\\\\\"", "\"")
@@ -76,12 +85,11 @@ case class WorkflowFlatMetadata(value: Map[String, JsValue]) extends AnyVal {
 
 object WorkflowFlatMetadata {
 
-  def fromConfig(config: Config): ErrorOr[WorkflowFlatMetadata] = {
+  def fromConfig(config: Config): ErrorOr[WorkflowFlatMetadata] =
     config.extract[Map[String, Option[String]]] match {
       case Result.Success(m) => Valid(WorkflowFlatMetadata(m safeMapValues { _.map(JsString.apply).getOrElse(JsNull) }))
       case Result.Failure(_) => invalidNel(s"Metadata block can not be converted to a Map: $config")
     }
-  }
 
   def fromWorkflowMetadata(workflowMetadata: WorkflowMetadata): ErrorOr[WorkflowFlatMetadata] = {
     val jsValue: ErrorOr[JsValue] = Try(workflowMetadata.value.parseJson) match {
@@ -96,9 +104,8 @@ object WorkflowFlatMetadata {
   }
 
   implicit class EnhancedWorkflowMetadata(val workflowMetadata: WorkflowMetadata) {
-    def asFlat: WorkflowFlatMetadata = {
+    def asFlat: WorkflowFlatMetadata =
       WorkflowFlatMetadata.fromWorkflowMetadata(workflowMetadata).unsafe
-    }
   }
 
   implicit class EnhancedWorkflowFlatMetadata(val workflowFlatMetadata: WorkflowFlatMetadata) {
@@ -113,25 +120,22 @@ object WorkflowFlatMetadata {
   }
 
   implicit class EnhancedExpectation(val expectation: String) extends AnyVal {
-    def replaceExpectationVariables(workflowId: WorkflowId, workflowRoot: String): String = {
+    def replaceExpectationVariables(workflowId: WorkflowId, workflowRoot: String): String =
       expectation.replaceAll("<<UUID>>", workflowId.toString).replaceAll("<<WORKFLOW_ROOT>>", workflowRoot)
-    }
   }
 }
 
 object WorkflowFlatOutputs {
   implicit class EnhancedWorkflowOutputs(val workflowOutputs: WorkflowOutputs) extends AnyVal {
-    def asFlat: WorkflowFlatMetadata = {
+    def asFlat: WorkflowFlatMetadata =
       workflowOutputs.outputs.asMap map WorkflowFlatMetadata.apply unsafe
-    }
   }
 }
 
 object WorkflowFlatLabels {
   implicit class EnhancedWorkflowLabels(val workflowLabels: WorkflowLabels) extends AnyVal {
-    def asFlat: WorkflowFlatMetadata = {
+    def asFlat: WorkflowFlatMetadata =
       workflowLabels.labels.asMap map WorkflowFlatMetadata.apply unsafe
-    }
   }
 }
 
@@ -140,11 +144,10 @@ object JsValueEnhancer {
     import DefaultJsonProtocol._
     import centaur.json.JsonUtils._
 
-    def asMap: ErrorOr[Map[String, JsValue]] = {
+    def asMap: ErrorOr[Map[String, JsValue]] =
       Try(jsValue.asJsObject.flatten().convertTo[Map[String, JsValue]]) match {
         case Success(m) => Valid(m)
         case Failure(e) => invalidNel(s"Unable to convert JsValue to JsObject: ${e.getMessage}")
       }
-    }
   }
 }
diff --git a/centaur/src/main/scala/centaur/test/standard/CentaurTestCase.scala b/centaur/src/main/scala/centaur/test/standard/CentaurTestCase.scala
index 258c211c900..f4ed8a57589 100644
--- a/centaur/src/main/scala/centaur/test/standard/CentaurTestCase.scala
+++ b/centaur/src/main/scala/centaur/test/standard/CentaurTestCase.scala
@@ -19,8 +19,8 @@ case class CentaurTestCase(workflow: Workflow,
                            testFormat: CentaurTestFormat,
                            testOptions: TestOptions,
                            submittedWorkflowTracker: SubmittedWorkflowTracker,
-                           submitResponseOption: Option[SubmitHttpResponse])(
-                           implicit cromwellTracker: Option[CromwellTracker]) {
+                           submitResponseOption: Option[SubmitHttpResponse]
+)(implicit cromwellTracker: Option[CromwellTracker]) {
 
   def testFunction: Test[SubmitResponse] = this.testFormat match {
     case WorkflowSuccessTest => TestFormulas.runSuccessfulWorkflowAndVerifyMetadata(workflow)
@@ -32,10 +32,14 @@ case class CentaurTestCase(workflow: Workflow,
     case RunFailingTwiceExpectingNoCallCachingTest => TestFormulas.runFailingWorkflowTwiceExpectingNoCaching(workflow)
     case SubmitFailureTest => TestFormulas.submitInvalidWorkflow(workflow, submitResponseOption.get)
     case InstantAbort => TestFormulas.instantAbort(workflow)
-    case CromwellRestartWithRecover(callMarker)=> TestFormulas.workflowRestart(workflow, callMarker, recover = true, finalStatus = Succeeded)
-    case WorkflowFailureRestartWithRecover(callMarker)=> TestFormulas.workflowRestart(workflow, callMarker, recover = true, finalStatus = Failed)
-    case WorkflowFailureRestartWithoutRecover(callMarker)=> TestFormulas.workflowRestart(workflow, callMarker, recover = false, finalStatus = Failed)
-    case CromwellRestartWithoutRecover(callMarker) => TestFormulas.workflowRestart(workflow, callMarker, recover = false, finalStatus = Succeeded)
+    case CromwellRestartWithRecover(callMarker) =>
+      TestFormulas.workflowRestart(workflow, callMarker, recover = true, finalStatus = Succeeded)
+    case WorkflowFailureRestartWithRecover(callMarker) =>
+      TestFormulas.workflowRestart(workflow, callMarker, recover = true, finalStatus = Failed)
+    case WorkflowFailureRestartWithoutRecover(callMarker) =>
+      TestFormulas.workflowRestart(workflow, callMarker, recover = false, finalStatus = Failed)
+    case CromwellRestartWithoutRecover(callMarker) =>
+      TestFormulas.workflowRestart(workflow, callMarker, recover = false, finalStatus = Succeeded)
     case ScheduledAbort(callMarker) => TestFormulas.scheduledAbort(workflow, callMarker, restart = false)
     case ScheduledAbortWithRestart(callMarker) => TestFormulas.scheduledAbort(workflow, callMarker, restart = true)
     case PapiUpgradeTest(callMarker) => TestFormulas.papiUpgrade(workflow, callMarker)
@@ -58,13 +62,14 @@ case class CentaurTestCase(workflow: Workflow,
 }
 
 object CentaurTestCase {
-  def fromFile(cromwellTracker: Option[CromwellTracker])(file: File): ErrorOr[CentaurTestCase] = {
+  def fromFile(cromwellTracker: Option[CromwellTracker])(file: File): ErrorOr[CentaurTestCase] =
     Try(ConfigFactory.parseFile(file.toJava).resolve()) match {
       case Success(c) =>
-        CentaurTestCase.fromConfig(c, file.parent, cromwellTracker) flatMap validateTestCase leftMap { s"Error in test file '$file'." :: _ }
+        CentaurTestCase.fromConfig(c, file.parent, cromwellTracker) flatMap validateTestCase leftMap {
+          s"Error in test file '$file'." :: _
+        }
       case Failure(f) => invalidNel(s"Invalid test config: $file (${f.getMessage})")
     }
-  }
 
   def fromConfig(conf: Config, configFile: File, cromwellTracker: Option[CromwellTracker]): ErrorOr[CentaurTestCase] = {
     val submittedWorkflowTracker = new SubmittedWorkflowTracker()
@@ -77,18 +82,18 @@ object CentaurTestCase {
     }
   }
 
-  private def validateTestCase(testCase: CentaurTestCase): ErrorOr[CentaurTestCase] = {
+  private def validateTestCase(testCase: CentaurTestCase): ErrorOr[CentaurTestCase] =
     testCase.testFormat match {
-      case SubmitFailureTest => validateSubmitFailure(testCase.workflow, testCase.submitResponseOption).map(_ => testCase)
+      case SubmitFailureTest =>
+        validateSubmitFailure(testCase.workflow, testCase.submitResponseOption).map(_ => testCase)
       case _ => Valid(testCase)
     }
-  }
 
   private def validateSubmitFailure(workflow: Workflow,
-                                    submitResponseOption: Option[SubmitHttpResponse]): ErrorOr[SubmitResponse] = {
+                                    submitResponseOption: Option[SubmitHttpResponse]
+  ): ErrorOr[SubmitResponse] =
     submitResponseOption match {
       case None => invalidNel("No submit stanza included in test config")
       case Some(response) => Valid(response)
     }
-  }
 }
diff --git a/centaur/src/main/scala/centaur/test/standard/CentaurTestFormat.scala b/centaur/src/main/scala/centaur/test/standard/CentaurTestFormat.scala
index 1cb2345f25c..eae961d6e5f 100644
--- a/centaur/src/main/scala/centaur/test/standard/CentaurTestFormat.scala
+++ b/centaur/src/main/scala/centaur/test/standard/CentaurTestFormat.scala
@@ -9,7 +9,7 @@ import configs.syntax._
 
 sealed abstract class CentaurTestFormat(val name: String) {
   val lowerCaseName = name.toLowerCase
-  
+
   def testSpecString: String = this match {
     case WorkflowSuccessTest => "successfully run"
     case WorkflowSuccessAndTimedOutputsTest => "successfully run"
@@ -20,12 +20,14 @@ sealed abstract class CentaurTestFormat(val name: String) {
     case RunFailingTwiceExpectingNoCallCachingTest => "Fail the first run and NOT call cache the second run of"
     case SubmitFailureTest => "fail to submit"
     case InstantAbort => "abort a workflow immediately after submission"
-    case _: PapiUpgradeTest => "make sure a PAPI upgrade preserves call caching when the `name-for-call-caching-purposes` attribute is used"
+    case _: PapiUpgradeTest =>
+      "make sure a PAPI upgrade preserves call caching when the `name-for-call-caching-purposes` attribute is used"
     case _: CromwellRestartWithRecover => "survive a Cromwell restart and recover jobs"
     case _: CromwellRestartWithoutRecover => "survive a Cromwell restart"
     case _: ScheduledAbort => "abort a workflow mid run"
     case _: ScheduledAbortWithRestart => "abort a workflow mid run and restart immediately"
-    case _: WorkflowFailureRestartWithRecover => "survive a Cromwell restart when a workflow was failing and recover jobs"
+    case _: WorkflowFailureRestartWithRecover =>
+      "survive a Cromwell restart when a workflow was failing and recover jobs"
     case _: WorkflowFailureRestartWithoutRecover => "survive a Cromwell restart when a workflow was failing"
     case other => s"unrecognized format $other"
   }
@@ -39,71 +41,89 @@ object CentaurTestFormat {
   sealed trait SequentialTestFormat extends CentaurTestFormat {
     override def isParallel: Boolean = false
   }
- 
+
   sealed trait RestartFormat extends SequentialTestFormat
-  sealed trait WithCallMarker { this: CentaurTestFormat => val build: CallMarker => CentaurTestFormat }
-  
+  sealed trait WithCallMarker { this: CentaurTestFormat =>
+    val build: CallMarker => CentaurTestFormat
+  }
+
   case object WorkflowSuccessTest extends CentaurTestFormat("WorkflowSuccess")
   case object WorkflowSuccessAndTimedOutputsTest extends CentaurTestFormat("WorkflowSuccessAndTimedOutputs")
   case object WorkflowFailureTest extends CentaurTestFormat("WorkflowFailure")
   case object RunTwiceExpectingCallCachingTest extends CentaurTestFormat("RunTwiceExpectingCallCaching")
   case object RunThriceExpectingCallCachingTest extends CentaurTestFormat(name = "RunThriceExpectingCallCaching")
   case object RunTwiceExpectingNoCallCachingTest extends CentaurTestFormat("RunTwiceExpectingNoCallCaching")
-  case object RunFailingTwiceExpectingNoCallCachingTest extends CentaurTestFormat("RunFailingTwiceExpectingNoCallCaching")
+  case object RunFailingTwiceExpectingNoCallCachingTest
+      extends CentaurTestFormat("RunFailingTwiceExpectingNoCallCaching")
   case object SubmitFailureTest extends CentaurTestFormat("SubmitFailure")
   case object InstantAbort extends CentaurTestFormat("InstantAbort") with SequentialTestFormat
 
   object CromwellRestartWithRecover extends CentaurTestFormat("CromwellRestartWithRecover") with WithCallMarker {
     val build = CromwellRestartWithRecover.apply _
   }
-  case class CromwellRestartWithRecover(callMarker: CallMarker) extends CentaurTestFormat(CromwellRestartWithRecover.name) with RestartFormat
-  
+  case class CromwellRestartWithRecover(callMarker: CallMarker)
+      extends CentaurTestFormat(CromwellRestartWithRecover.name)
+      with RestartFormat
+
   object CromwellRestartWithoutRecover extends CentaurTestFormat("CromwellRestartWithoutRecover") with WithCallMarker {
     val build = CromwellRestartWithoutRecover.apply _
   }
-  case class CromwellRestartWithoutRecover(callMarker: CallMarker) extends CentaurTestFormat(CromwellRestartWithoutRecover.name) with RestartFormat
+  case class CromwellRestartWithoutRecover(callMarker: CallMarker)
+      extends CentaurTestFormat(CromwellRestartWithoutRecover.name)
+      with RestartFormat
 
   object ScheduledAbort extends CentaurTestFormat("ScheduledAbort") with WithCallMarker {
     val build = ScheduledAbort.apply _
   }
-  case class ScheduledAbort(callMarker: CallMarker) extends CentaurTestFormat(ScheduledAbort.name) with SequentialTestFormat
+  case class ScheduledAbort(callMarker: CallMarker)
+      extends CentaurTestFormat(ScheduledAbort.name)
+      with SequentialTestFormat
 
   object ScheduledAbortWithRestart extends CentaurTestFormat("ScheduledAbortWithRestart") with WithCallMarker {
     val build = ScheduledAbortWithRestart.apply _
   }
-  case class ScheduledAbortWithRestart(callMarker: CallMarker) extends CentaurTestFormat(ScheduledAbortWithRestart.name) with RestartFormat
+  case class ScheduledAbortWithRestart(callMarker: CallMarker)
+      extends CentaurTestFormat(ScheduledAbortWithRestart.name)
+      with RestartFormat
 
-  object WorkflowFailureRestartWithRecover extends CentaurTestFormat("WorkflowFailureRestartWithRecover") with WithCallMarker {
+  object WorkflowFailureRestartWithRecover
+      extends CentaurTestFormat("WorkflowFailureRestartWithRecover")
+      with WithCallMarker {
     val build = WorkflowFailureRestartWithRecover.apply _
   }
-  case class WorkflowFailureRestartWithRecover(callMarker: CallMarker) extends CentaurTestFormat(WorkflowFailureRestartWithRecover.name) with RestartFormat
+  case class WorkflowFailureRestartWithRecover(callMarker: CallMarker)
+      extends CentaurTestFormat(WorkflowFailureRestartWithRecover.name)
+      with RestartFormat
 
-  object WorkflowFailureRestartWithoutRecover extends CentaurTestFormat("WorkflowFailureRestartWithoutRecover") with WithCallMarker {
+  object WorkflowFailureRestartWithoutRecover
+      extends CentaurTestFormat("WorkflowFailureRestartWithoutRecover")
+      with WithCallMarker {
     val build = WorkflowFailureRestartWithoutRecover.apply _
   }
-  case class WorkflowFailureRestartWithoutRecover(callMarker: CallMarker) extends CentaurTestFormat(WorkflowFailureRestartWithoutRecover.name) with RestartFormat
+  case class WorkflowFailureRestartWithoutRecover(callMarker: CallMarker)
+      extends CentaurTestFormat(WorkflowFailureRestartWithoutRecover.name)
+      with RestartFormat
 
   object PapiUpgradeTest extends CentaurTestFormat("PapiUpgrade") with WithCallMarker {
     val build = PapiUpgradeTest.apply _
   }
   case class PapiUpgradeTest(callMarker: CallMarker) extends CentaurTestFormat(PapiUpgradeTest.name) with RestartFormat
 
-  def fromConfig(conf: Config): Checked[CentaurTestFormat] = {
-    
+  def fromConfig(conf: Config): Checked[CentaurTestFormat] =
     CallMarker.fromConfig(conf).toEither flatMap { callMarker =>
       conf.get[String]("testFormat") match {
         case Success(f) => CentaurTestFormat.fromString(f, callMarker)
         case Failure(_) => "No testFormat string provided".invalidNelCheck[CentaurTestFormat]
       }
     }
-  }
 
   private def fromString(testFormat: String, callMarker: Option[CallMarker]): Checked[CentaurTestFormat] = {
     def withCallMarker(name: String, constructor: CallMarker => CentaurTestFormat) = callMarker match {
       case Some(marker) => constructor(marker).validNelCheck
-      case None => s"$name needs a callMarker to know on which call to trigger the restart".invalidNelCheck[CentaurTestFormat]
+      case None =>
+        s"$name needs a callMarker to know on which call to trigger the restart".invalidNelCheck[CentaurTestFormat]
     }
-    
+
     List(
       WorkflowSuccessTest,
       WorkflowSuccessAndTimedOutputsTest,
@@ -121,9 +141,10 @@ object CentaurTestFormat {
       WorkflowFailureRestartWithRecover,
       WorkflowFailureRestartWithoutRecover,
       PapiUpgradeTest
-    ).collectFirst({
-      case format: WithCallMarker if format.name.equalsIgnoreCase(testFormat) => withCallMarker(format.name, format.build)
+    ).collectFirst {
+      case format: WithCallMarker if format.name.equalsIgnoreCase(testFormat) =>
+        withCallMarker(format.name, format.build)
       case format if format.name.equalsIgnoreCase(testFormat) => format.validNelCheck
-    }).getOrElse(s"No such test format: $testFormat".invalidNelCheck[CentaurTestFormat])
+    }.getOrElse(s"No such test format: $testFormat".invalidNelCheck[CentaurTestFormat])
   }
 }
diff --git a/centaur/src/main/scala/centaur/test/submit/SubmitResponse.scala b/centaur/src/main/scala/centaur/test/submit/SubmitResponse.scala
index ed160482bef..faed88cc8cd 100644
--- a/centaur/src/main/scala/centaur/test/submit/SubmitResponse.scala
+++ b/centaur/src/main/scala/centaur/test/submit/SubmitResponse.scala
@@ -14,13 +14,11 @@ import cromwell.api.model.SubmittedWorkflow
 sealed trait SubmitResponse
 
 object SubmitResponse {
-  def apply(submittedWorkflow: SubmittedWorkflow): SubmitResponse = {
+  def apply(submittedWorkflow: SubmittedWorkflow): SubmitResponse =
     SubmitWorkflowResponse(submittedWorkflow)
-  }
 
-  def apply(statusCode: Int, message: String): SubmitResponse = {
+  def apply(statusCode: Int, message: String): SubmitResponse =
     SubmitHttpResponse(statusCode, message)
-  }
 }
 
 case class SubmitWorkflowResponse(submittedWorkflow: SubmittedWorkflow) extends SubmitResponse
@@ -29,7 +27,7 @@ case class SubmitHttpResponse(statusCode: Int, message: String) extends SubmitRe
 
 object SubmitHttpResponse {
 
-  def fromConfig(conf: Config): ErrorOr[Option[SubmitHttpResponse]] = {
+  def fromConfig(conf: Config): ErrorOr[Option[SubmitHttpResponse]] =
     conf.get[Config]("submit") match {
       case Result.Failure(_) => Valid(None)
       case Result.Success(submitConf) =>
@@ -41,17 +39,13 @@ object SubmitHttpResponse {
           Option(_)
         }
     }
-  }
 
-  private def toErrorOr[A](result: Result[A]): ErrorOr[A] = {
+  private def toErrorOr[A](result: Result[A]): ErrorOr[A] =
     result match {
       case Result.Success(value) => Valid(value)
       case Result.Failure(error) =>
-        error.messages
-          .toList
-          .toNel
+        error.messages.toList.toNel
           .getOrElse(throw new RuntimeException("Paranoia... error.messages is a Nel exposed as a Seq."))
           .invalid
     }
-  }
 }
diff --git a/centaur/src/main/scala/centaur/test/workflow/DirectoryContentCountCheck.scala b/centaur/src/main/scala/centaur/test/workflow/DirectoryContentCountCheck.scala
index 2bf90619dab..4d064455f8c 100644
--- a/centaur/src/main/scala/centaur/test/workflow/DirectoryContentCountCheck.scala
+++ b/centaur/src/main/scala/centaur/test/workflow/DirectoryContentCountCheck.scala
@@ -2,7 +2,7 @@ package centaur.test.workflow
 
 import cats.data.Validated._
 import cats.syntax.all._
-import centaur.test.{AWSFilesChecker, FilesChecker, LocalFilesChecker, PipelinesFilesChecker, BlobFilesChecker}
+import centaur.test.{AWSFilesChecker, BlobFilesChecker, FilesChecker, LocalFilesChecker, PipelinesFilesChecker}
 import com.typesafe.config.Config
 import common.validation.ErrorOr.ErrorOr
 import configs.Result
@@ -16,18 +16,23 @@ object DirectoryContentCountCheck {
     if (!keepGoing) {
       valid(None)
     } else {
-      val directoryContentCountsValidation: ErrorOr[Map[String, Int]] = conf.get[Map[String, Int]]("outputExpectations") match {
-        case Result.Success(a) => valid(a)
-        case Result.Failure(_) => invalidNel(s"Test '$name': Unable to read outputExpectations as a Map[String, Int]")
-      }
+      val directoryContentCountsValidation: ErrorOr[Map[String, Int]] =
+        conf.get[Map[String, Int]]("outputExpectations") match {
+          case Result.Success(a) => valid(a)
+          case Result.Failure(_) => invalidNel(s"Test '$name': Unable to read outputExpectations as a Map[String, Int]")
+        }
 
       val fileSystemChecker: ErrorOr[FilesChecker] = conf.get[String]("fileSystemCheck") match {
         case Result.Success("gcs") => valid(PipelinesFilesChecker)
         case Result.Success("local") => valid(LocalFilesChecker)
         case Result.Success("aws") => valid(AWSFilesChecker)
         case Result.Success("blob") => valid(BlobFilesChecker)
-        case Result.Success(_) => invalidNel(s"Test '$name': Invalid 'fileSystemCheck' value (must be either 'local', 'gcs', 'blob', or 'aws'")
-        case Result.Failure(_) => invalidNel(s"Test '$name': Must specify a 'fileSystemCheck' value (must be either 'local', 'gcs', 'blob', or 'aws'")
+        case Result.Success(_) =>
+          invalidNel(s"Test '$name': Invalid 'fileSystemCheck' value (must be either 'local', 'gcs', 'blob', or 'aws'")
+        case Result.Failure(_) =>
+          invalidNel(
+            s"Test '$name': Must specify a 'fileSystemCheck' value (must be either 'local', 'gcs', 'blob', or 'aws'"
+          )
       }
 
       (directoryContentCountsValidation, fileSystemChecker) mapN { (d, f) => Option(DirectoryContentCountCheck(d, f)) }
diff --git a/centaur/src/main/scala/centaur/test/workflow/SubmittedWorkflowTracker.scala b/centaur/src/main/scala/centaur/test/workflow/SubmittedWorkflowTracker.scala
index dc3f0355f80..718db740dab 100644
--- a/centaur/src/main/scala/centaur/test/workflow/SubmittedWorkflowTracker.scala
+++ b/centaur/src/main/scala/centaur/test/workflow/SubmittedWorkflowTracker.scala
@@ -25,7 +25,6 @@ class SubmittedWorkflowTracker {
    * object require a retry. Prevents unwanted cache hits from partially successful attempts when retrying a call
    * caching test case.
    */
-  def add(submittedWorkflow: SubmittedWorkflow): Unit = {
+  def add(submittedWorkflow: SubmittedWorkflow): Unit =
     submittedWorkflowIds = submittedWorkflow.id :: submittedWorkflowIds
-  }
 }
diff --git a/centaur/src/main/scala/centaur/test/workflow/Workflow.scala b/centaur/src/main/scala/centaur/test/workflow/Workflow.scala
index 743924bb9c6..212064acfe1 100644
--- a/centaur/src/main/scala/centaur/test/workflow/Workflow.scala
+++ b/centaur/src/main/scala/centaur/test/workflow/Workflow.scala
@@ -15,17 +15,18 @@ import cromwell.api.model.{WorkflowDescribeRequest, WorkflowSingleSubmission}
 import java.nio.file.Path
 import scala.concurrent.duration.FiniteDuration
 
-final case class Workflow private(testName: String,
-                                  data: WorkflowData,
-                                  metadata: Option[WorkflowFlatMetadata],
-                                  notInMetadata: List[String],
-                                  directoryContentCounts: Option[DirectoryContentCountCheck],
-                                  backends: BackendsRequirement,
-                                  retryTestFailures: Boolean,
-                                  allowOtherOutputs: Boolean,
-                                  skipDescribeEndpointValidation: Boolean,
-                                  submittedWorkflowTracker: SubmittedWorkflowTracker,
-                                  maximumAllowedTime: Option[FiniteDuration]) {
+final case class Workflow private (testName: String,
+                                   data: WorkflowData,
+                                   metadata: Option[WorkflowFlatMetadata],
+                                   notInMetadata: List[String],
+                                   directoryContentCounts: Option[DirectoryContentCountCheck],
+                                   backends: BackendsRequirement,
+                                   retryTestFailures: Boolean,
+                                   allowOtherOutputs: Boolean,
+                                   skipDescribeEndpointValidation: Boolean,
+                                   submittedWorkflowTracker: SubmittedWorkflowTracker,
+                                   maximumAllowedTime: Option[FiniteDuration]
+) {
 
   def toWorkflowSubmission: WorkflowSingleSubmission = WorkflowSingleSubmission(
     workflowSource = data.workflowContent,
@@ -36,7 +37,8 @@ final case class Workflow private(testName: String,
     inputsJson = data.inputs.map(_.unsafeRunSync()),
     options = data.options.map(_.unsafeRunSync()),
     labels = Option(data.labels),
-    zippedImports = data.zippedImports)
+    zippedImports = data.zippedImports
+  )
 
   def toWorkflowDescribeRequest: WorkflowDescribeRequest = WorkflowDescribeRequest(
     workflowSource = data.workflowContent,
@@ -46,22 +48,26 @@ final case class Workflow private(testName: String,
     inputsJson = data.inputs.map(_.unsafeRunSync())
   )
 
-  def secondRun: Workflow = {
+  def secondRun: Workflow =
     copy(data = data.copy(options = data.secondOptions))
-  }
 
-  def thirdRun: Workflow = {
+  def thirdRun: Workflow =
     copy(data = data.copy(options = data.thirdOptions))
-  }
 }
 
 object Workflow {
 
-  def fromConfig(conf: Config, configFile: File, submittedWorkflowTracker: SubmittedWorkflowTracker): ErrorOr[Workflow] = {
+  def fromConfig(conf: Config,
+                 configFile: File,
+                 submittedWorkflowTracker: SubmittedWorkflowTracker
+  ): ErrorOr[Workflow] =
     conf.get[String]("name") match {
       case Result.Success(n) =>
         // If backend is provided, Centaur will only run this test if that backend is available on Cromwell
-        val backendsRequirement = BackendsRequirement.fromConfig(conf.get[String]("backendsMode").map(_.toLowerCase).valueOrElse("all"), conf.get[List[String]]("backends").valueOrElse(List.empty[String]).map(_.toLowerCase))
+        val backendsRequirement = BackendsRequirement.fromConfig(
+          conf.get[String]("backendsMode").map(_.toLowerCase).valueOrElse("all"),
+          conf.get[List[String]]("backends").valueOrElse(List.empty[String]).map(_.toLowerCase)
+        )
         // If basePath is provided it'll be used as basis for finding other files, otherwise use the dir the config was in
         val basePath = conf.get[Option[Path]]("basePath") valueOrElse None map (File(_)) getOrElse configFile
         val metadata: ErrorOr[Option[WorkflowFlatMetadata]] = conf.get[Config]("metadata") match {
@@ -73,7 +79,8 @@ object Workflow {
           case Result.Failure(_) => List.empty
         }
 
-        val directoryContentCheckValidation: ErrorOr[Option[DirectoryContentCountCheck]] = DirectoryContentCountCheck.forConfig(n, conf)
+        val directoryContentCheckValidation: ErrorOr[Option[DirectoryContentCountCheck]] =
+          DirectoryContentCountCheck.forConfig(n, conf)
         val files = conf.get[Config]("files") match {
           case Result.Success(f) => WorkflowData.fromConfig(filesConfig = f, fullConfig = conf, basePath = basePath)
           case Result.Failure(_) => invalidNel(s"No 'files' block in $configFile")
@@ -89,10 +96,21 @@ object Workflow {
         val maximumTime: Option[FiniteDuration] = conf.get[Option[FiniteDuration]]("maximumTime").value
 
         (files, directoryContentCheckValidation, metadata, retryTestFailuresErrorOr) mapN {
-          (f, d, m, retryTestFailures) => Workflow(n, f, m, absentMetadata, d, backendsRequirement, retryTestFailures, allowOtherOutputs, validateDescription, submittedWorkflowTracker, maximumTime)
+          (f, d, m, retryTestFailures) =>
+            Workflow(n,
+                     f,
+                     m,
+                     absentMetadata,
+                     d,
+                     backendsRequirement,
+                     retryTestFailures,
+                     allowOtherOutputs,
+                     validateDescription,
+                     submittedWorkflowTracker,
+                     maximumTime
+            )
         }
 
       case Result.Failure(_) => invalidNel(s"No test 'name' for: $configFile")
     }
-  }
 }
diff --git a/centaur/src/main/scala/centaur/test/workflow/WorkflowData.scala b/centaur/src/main/scala/centaur/test/workflow/WorkflowData.scala
index 72e66b31e18..2096a5f88d7 100644
--- a/centaur/src/main/scala/centaur/test/workflow/WorkflowData.scala
+++ b/centaur/src/main/scala/centaur/test/workflow/WorkflowData.scala
@@ -34,7 +34,8 @@ case class WorkflowData(workflowContent: Option[String],
                         labels: List[Label],
                         zippedImports: Option[File],
                         secondOptions: Option[IO[String]] = None,
-                        thirdOptions: Option[IO[String]] = None)
+                        thirdOptions: Option[IO[String]] = None
+)
 
 object WorkflowData {
   val blockingEC = ExecutionContext.fromExecutorService(Executors.newFixedThreadPool(5))
@@ -47,55 +48,64 @@ object WorkflowData {
     val workflowSourcePath = filesConfig.as[Option[String]]("workflow")
 
     (workflowSourcePath, workflowUrl) match {
-      case (Some(workflowPath), None) => Valid(WorkflowData(
-        workflowPath = Option(workflowPath),
-        workflowUrl = None,
-        filesConfig = filesConfig,
-        fullConfig = fullConfig,
-        basePath = basePath))
-      case (None, Some(_)) => Valid(WorkflowData(
-        workflowPath = None,
-        workflowUrl = workflowUrl,
-        filesConfig = filesConfig,
-        fullConfig = fullConfig,
-        basePath = basePath))
+      case (Some(workflowPath), None) =>
+        Valid(
+          WorkflowData(workflowPath = Option(workflowPath),
+                       workflowUrl = None,
+                       filesConfig = filesConfig,
+                       fullConfig = fullConfig,
+                       basePath = basePath
+          )
+        )
+      case (None, Some(_)) =>
+        Valid(
+          WorkflowData(workflowPath = None,
+                       workflowUrl = workflowUrl,
+                       filesConfig = filesConfig,
+                       fullConfig = fullConfig,
+                       basePath = basePath
+          )
+        )
       case (Some(_), Some(_)) => invalidNel(s"Both 'workflow' path or 'workflowUrl' can't be provided.")
       case (None, None) => invalidNel(s"No 'workflow' path or 'workflowUrl' provided.")
     }
   }
 
-  def apply(workflowPath: Option[String], workflowUrl: Option[String], filesConfig: Config, fullConfig: Config, basePath: File): WorkflowData = {
+  def apply(workflowPath: Option[String],
+            workflowUrl: Option[String],
+            filesConfig: Config,
+            fullConfig: Config,
+            basePath: File
+  ): WorkflowData = {
     def slurp(file: String): IO[String] = file match {
-      case http if http.startsWith("http://") || http.startsWith("https://") => 
+      case http if http.startsWith("http://") || http.startsWith("https://") =>
         httpClient.expect[String](http)
       case gcs if gcs.startsWith("gs://") =>
         val noScheme = gcs.stripPrefix("gs://")
         val firstSlashPosition = noScheme.indexOf("/")
         val blob = BlobId.of(noScheme.substring(0, firstSlashPosition), noScheme.substring(firstSlashPosition + 1))
-        IO { gcsStorage.readAllBytes(blob).map(_.toChar).mkString }
+        IO(gcsStorage.readAllBytes(blob).map(_.toChar).mkString)
       case local =>
-        IO { basePath./(local).contentAsString }
+        IO(basePath./(local).contentAsString)
     }
-    
-    def getOptionalFileContent(name: String): Option[IO[String]] = {
+
+    def getOptionalFileContent(name: String): Option[IO[String]] =
       filesConfig.getAs[String](name).map(slurp)
-    }
 
     def getImports = filesConfig.get[List[String]]("imports") match {
       case Success(paths) => zipImports(paths map basePath./)
       case Failure(_) => None
     }
 
-    def getImportsDirName(workflowPath: Option[File], workflowUrl: Option[String]): String = {
+    def getImportsDirName(workflowPath: Option[File], workflowUrl: Option[String]): String =
       workflowPath match {
         case Some(file) => file.name.replaceAll("\\.[^.]*$", "")
         case None => // workflow url is defined
           val fileName = workflowUrl.get.split("/").last
           fileName.replaceAll("\\.[^.]*$", "")
       }
-    }
 
-    def zipImports(imports: List[File]): Option[File] = {
+    def zipImports(imports: List[File]): Option[File] =
       imports match {
         case Nil => None
         case _ =>
@@ -109,7 +119,6 @@ object WorkflowData {
 
           Option(importsDir.zip())
       }
-    }
 
     def getLabels: List[Label] = {
       import cromwell.api.model.LabelsJsonFormatter._
diff --git a/centaur/src/test/scala/centaur/api/DaemonizedDefaultThreadFactorySpec.scala b/centaur/src/test/scala/centaur/api/DaemonizedDefaultThreadFactorySpec.scala
index afd3918d738..7069cee9c40 100644
--- a/centaur/src/test/scala/centaur/api/DaemonizedDefaultThreadFactorySpec.scala
+++ b/centaur/src/test/scala/centaur/api/DaemonizedDefaultThreadFactorySpec.scala
@@ -9,7 +9,7 @@ class DaemonizedDefaultThreadFactorySpec extends AnyFlatSpec with CromwellTimeou
   behavior of "DaemonizedDefaultThreadFactory"
 
   it should "create a non-blocking execution context" in {
-    val thread = DaemonizedDefaultThreadFactory.newThread(() => {})
+    val thread = DaemonizedDefaultThreadFactory.newThread { () => }
     thread.getName should startWith("daemonpool-thread-")
     thread.isDaemon should be(true)
   }
diff --git a/centaur/src/test/scala/centaur/json/JsonUtilsSpec.scala b/centaur/src/test/scala/centaur/json/JsonUtilsSpec.scala
index 1f89477d388..91fe7123ed8 100644
--- a/centaur/src/test/scala/centaur/json/JsonUtilsSpec.scala
+++ b/centaur/src/test/scala/centaur/json/JsonUtilsSpec.scala
@@ -111,7 +111,7 @@ class JsonUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       "calls.wf_hello.hello.outputs.salutation" -> "Hello Mr. Bean!",
       "calls.wf_hello.hello.runtimeAttributes.bootDiskSizeGb" -> "10",
       "calls.wf_hello.hello.runtimeAttributes.continueOnReturnCode" -> "0",
-      "calls.wf_hello.hello.runtimeAttributes.maxRetries" -> "0",
+      "calls.wf_hello.hello.runtimeAttributes.maxRetries" -> "0"
     ).map(x => (x._1, JsString(x._2)))
 
     val actualFlattenedMetadata: Map[String, JsValue] = metadata.parseJson.asJsObject.flatten().fields
@@ -169,7 +169,7 @@ class JsonUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       "calls.wf_hello.task1.executionEvents.0.description" -> "task 1 step 1",
       "calls.wf_hello.task2.executionEvents.0.description" -> "task 2 step 1",
       "calls.wf_hello.task1.runtimeAttributes.bootDiskSizeGb" -> "10",
-      "calls.wf_hello.task2.runtimeAttributes.bootDiskSizeGb" -> "10",
+      "calls.wf_hello.task2.runtimeAttributes.bootDiskSizeGb" -> "10"
     ).map(x => (x._1, JsString(x._2)))
 
     val actualFlattenedMetadata: Map[String, JsValue] = metadata.parseJson.asJsObject.flatten().fields
@@ -249,7 +249,7 @@ class JsonUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       "wf_hello.hello.0.2.shardIndex" -> 0,
       "wf_hello.hello.1.shardIndex" -> 1,
       "wf_hello.hello.1.1.shardIndex" -> 1,
-      "wf_hello.hello.1.2.shardIndex" -> 1,
+      "wf_hello.hello.1.2.shardIndex" -> 1
     ).map(x => (x._1, JsNumber(x._2))) ++ Map(
       "id" -> "5abfaa90-570f-48d4-a35b-81d5ad4ea0f7",
       "status" -> "Succeeded",
@@ -265,7 +265,7 @@ class JsonUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       "wf_hello.hello.0.2.runtimeAttributes.memory" -> "1.1 GB",
       "wf_hello.hello.1.runtimeAttributes.memory" -> "1.1 GB",
       "wf_hello.hello.1.1.runtimeAttributes.memory" -> "1 GB",
-      "wf_hello.hello.1.2.runtimeAttributes.memory" -> "1.1 GB",
+      "wf_hello.hello.1.2.runtimeAttributes.memory" -> "1.1 GB"
     ).map(x => (x._1, JsString(x._2)))
 
     val actualFlattenedMetadata: Map[String, JsValue] = metadata.parseJson.asJsObject.flatten().fields
diff --git a/centaur/src/test/scala/centaur/test/CentaurOperationsSpec.scala b/centaur/src/test/scala/centaur/test/CentaurOperationsSpec.scala
index 9d09827027a..28a74274192 100644
--- a/centaur/src/test/scala/centaur/test/CentaurOperationsSpec.scala
+++ b/centaur/src/test/scala/centaur/test/CentaurOperationsSpec.scala
@@ -15,23 +15,29 @@ import scala.concurrent.duration._
 class CentaurOperationsSpec extends AnyFlatSpec with Matchers {
   behavior of "validateMetadataJson"
 
-  val placeholderSubmittedWorkflow: SubmittedWorkflow = SubmittedWorkflow(id = WorkflowId(UUID.randomUUID()), null, null)
-  val placeholderWorkflow: Workflow = Workflow(testName = "", null, null, null, null, null, false, false, false, null, null)
+  val placeholderSubmittedWorkflow: SubmittedWorkflow =
+    SubmittedWorkflow(id = WorkflowId(UUID.randomUUID()), null, null)
+  val placeholderWorkflow: Workflow =
+    Workflow(testName = "", null, null, null, null, null, false, false, false, null, null)
 
   val allowableOneWordAdditions = List("farmer")
 
   def runTest(json1: String, json2: String, expectMatching: Boolean): Unit = {
-    val validation = Operations.validateMetadataJson("",
-      json1.parseJson.asJsObject,
-      json2.parseJson.asJsObject,
-      placeholderSubmittedWorkflow,
-      placeholderWorkflow,
-      allowableAddedOneWordFields = allowableOneWordAdditions).unsafeToFuture()
+    val validation = Operations
+      .validateMetadataJson(
+        "",
+        json1.parseJson.asJsObject,
+        json2.parseJson.asJsObject,
+        placeholderSubmittedWorkflow,
+        placeholderWorkflow,
+        allowableAddedOneWordFields = allowableOneWordAdditions
+      )
+      .unsafeToFuture()
     Await.ready(validation, atMost = 10.seconds)
     validation.value.get match {
       case Success(()) if expectMatching => // great
       case Success(_) if !expectMatching => fail("Metadata unexpectedly matches")
-      case Failure(e) if expectMatching  => fail("Metadata unexpectedly mismatches", e)
+      case Failure(e) if expectMatching => fail("Metadata unexpectedly mismatches", e)
       case Failure(_) if !expectMatching => // great
       case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
     }
diff --git a/centaur/src/test/scala/centaur/test/metadata/CallAttemptFailureSpec.scala b/centaur/src/test/scala/centaur/test/metadata/CallAttemptFailureSpec.scala
index 2476bb4b231..0be16d9a57a 100644
--- a/centaur/src/test/scala/centaur/test/metadata/CallAttemptFailureSpec.scala
+++ b/centaur/src/test/scala/centaur/test/metadata/CallAttemptFailureSpec.scala
@@ -6,7 +6,6 @@ import io.circe.ParsingFailure
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class CallAttemptFailureSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "CallAttemptFailure"
diff --git a/centaur/src/test/scala/centaur/test/metadata/ExtractJobManagerStyleMetadataFieldsSpec.scala b/centaur/src/test/scala/centaur/test/metadata/ExtractJobManagerStyleMetadataFieldsSpec.scala
index 2b9cb409352..f4ce7300385 100644
--- a/centaur/src/test/scala/centaur/test/metadata/ExtractJobManagerStyleMetadataFieldsSpec.scala
+++ b/centaur/src/test/scala/centaur/test/metadata/ExtractJobManagerStyleMetadataFieldsSpec.scala
@@ -6,7 +6,6 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import spray.json._
 
-
 class ExtractJobManagerStyleMetadataFieldsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "extracting Job Manager style metadata fields"
 
@@ -45,6 +44,8 @@ class ExtractJobManagerStyleMetadataFieldsSpec extends AnyFlatSpec with Cromwell
         |	}
         |}""".stripMargin
 
-    Operations.extractJmStyleMetadataFields(originalMetadata.parseJson.asJsObject) should be(expectedExpectedMetadata.parseJson.asJsObject)
+    Operations.extractJmStyleMetadataFields(originalMetadata.parseJson.asJsObject) should be(
+      expectedExpectedMetadata.parseJson.asJsObject
+    )
   }
 }
diff --git a/centaur/src/test/scala/centaur/testfilecheck/FileCheckerSpec.scala b/centaur/src/test/scala/centaur/testfilecheck/FileCheckerSpec.scala
index f389192aa7f..0f9984d882e 100644
--- a/centaur/src/test/scala/centaur/testfilecheck/FileCheckerSpec.scala
+++ b/centaur/src/test/scala/centaur/testfilecheck/FileCheckerSpec.scala
@@ -11,7 +11,6 @@ import software.amazon.awssdk.services.s3.S3Client
 import software.amazon.awssdk.services.s3.model.{ListObjectsRequest, ListObjectsResponse, S3Object}
 import org.scalatest.flatspec.AnyFlatSpec
 
-
 class FileCheckerSpec extends AnyFlatSpec with CromwellTimeoutSpec with MockSugar {
 
   import centaur.test.ObjectCounterInstances._
@@ -26,24 +25,29 @@ class FileCheckerSpec extends AnyFlatSpec with CromwellTimeoutSpec with MockSuga
   private val wrongBucketPrefix = "s3Bucket://my-not-so-cool-bucket/somelogs/empty"
   private val EmptyTestPath = ""
   private val testGsPath = "gs://my-cool-bucket/path/to/file"
-  private val objResponse = ListObjectsResponse.builder()
-    .contents(util.Arrays.asList(S3Object.builder()
-      .build()))
+  private val objResponse = ListObjectsResponse
+    .builder()
+    .contents(
+      util.Arrays.asList(
+        S3Object
+          .builder()
+          .build()
+      )
+    )
     .build()
   private val objRequest = ListObjectsRequest.builder().bucket(bucketName).prefix(dirName).build()
   private val awsS3Path = awsS3ObjectCounter.parsePath(s3PrefixRegex)(testPath)
   private val gsPath = gcsObjectCounter.parsePath(gsPrefixRegex)(testGsPath)
 
-
   "parsePath" should "return a bucket and directories" in {
     assert(awsS3Path.bucket == bucketName)
     assert(awsS3Path.directory == dirName)
   }
 
   "parsePath" should "throw Exception for wrong path" in {
-    assertThrows[centaur.test.IllegalPathException] {awsS3ObjectCounter.parsePath(s3PrefixRegex)(wrongBucketPrefix)}
-    assertThrows[centaur.test.IllegalPathException] {awsS3ObjectCounter.parsePath(s3PrefixRegex)(testGsPath)}
-    assertThrows[centaur.test.IllegalPathException] {awsS3ObjectCounter.parsePath(s3PrefixRegex)(EmptyTestPath)}
+    assertThrows[centaur.test.IllegalPathException](awsS3ObjectCounter.parsePath(s3PrefixRegex)(wrongBucketPrefix))
+    assertThrows[centaur.test.IllegalPathException](awsS3ObjectCounter.parsePath(s3PrefixRegex)(testGsPath))
+    assertThrows[centaur.test.IllegalPathException](awsS3ObjectCounter.parsePath(s3PrefixRegex)(EmptyTestPath))
   }
 
   "countObjectAtPath" should "should return 1 if the file exist" in {
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
index 93f4cf77d34..2d3cba53bfc 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
@@ -11,11 +11,10 @@ import common.exception._
 import org.apache.commons.lang3.exception.ExceptionUtils
 import org.apache.http.HttpStatus
 
+class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver, drsReadInterpreter: DrsReadInterpreter)
+    extends CloudNioFileProvider {
 
-class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
-                              drsReadInterpreter: DrsReadInterpreter) extends CloudNioFileProvider {
-
-  private def checkIfPathExistsThroughDrsResolver(drsPath: String): IO[Boolean] = {
+  private def checkIfPathExistsThroughDrsResolver(drsPath: String): IO[Boolean] =
     /*
      * Unlike other cloud providers where directories are identified with a trailing slash at the end like `gs://bucket/dir/`,
      * DRS has a concept of bundles for directories (not supported yet). Hence for method `checkDirectoryExists` which appends a trailing '/'
@@ -23,12 +22,14 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
      */
     if (drsPath.endsWith("/")) IO(false)
     else {
-      drsPathResolver.rawDrsResolverResponse(drsPath, NonEmptyList.one(DrsResolverField.GsUri)).use { drsResolverResponse =>
-        val errorMsg = s"Status line was null for DRS Resolver response $drsResolverResponse."
-        toIO(Option(drsResolverResponse.getStatusLine), errorMsg)
-      }.map(_.getStatusCode == HttpStatus.SC_OK)
+      drsPathResolver
+        .rawDrsResolverResponse(drsPath, NonEmptyList.one(DrsResolverField.GsUri))
+        .use { drsResolverResponse =>
+          val errorMsg = s"Status line was null for DRS Resolver response $drsResolverResponse."
+          toIO(Option(drsResolverResponse.getStatusLine), errorMsg)
+        }
+        .map(_.getStatusCode == HttpStatus.SC_OK)
     }
-  }
 
   override def existsPath(drsPath: String, unused: String): Boolean =
     checkIfPathExistsThroughDrsResolver(drsPath).unsafeRunSync()
@@ -36,34 +37,46 @@ class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver,
   override def existsPaths(cloudHost: String, cloudPathPrefix: String): Boolean =
     existsPath(cloudHost, cloudPathPrefix)
 
-  override def listObjects(drsPath: String, unused: String, markerOption: Option[String]): CloudNioFileList = {
+  override def listObjects(drsPath: String, unused: String, markerOption: Option[String]): CloudNioFileList =
     throw new UnsupportedOperationException("DRS currently doesn't support list.")
-  }
 
-  override def copy(sourceCloudHost: String, sourceCloudPath: String, targetCloudHost: String, targetCloudPath: String): Unit =
+  override def copy(sourceCloudHost: String,
+                    sourceCloudPath: String,
+                    targetCloudHost: String,
+                    targetCloudPath: String
+  ): Unit =
     throw new UnsupportedOperationException("DRS currently doesn't support copy.")
 
   override def deleteIfExists(cloudHost: String, cloudPath: String): Boolean =
     throw new UnsupportedOperationException("DRS currently doesn't support delete.")
 
   override def read(drsPath: String, unused: String, offset: Long): ReadableByteChannel = {
-    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl)
+    val fields =
+      NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl)
 
     val byteChannelIO = for {
       drsResolverResponse <- drsPathResolver.resolveDrs(drsPath, fields)
       byteChannel <- drsReadInterpreter(drsPathResolver, drsResolverResponse)
     } yield byteChannel
 
-    byteChannelIO.handleErrorWith {
-        e => IO.raiseError(new RuntimeException(s"Error while reading from DRS path: $drsPath. Error: ${ExceptionUtils.getMessage(e)}"))
-    }.unsafeRunSync()
+    byteChannelIO
+      .handleErrorWith { e =>
+        IO.raiseError(
+          new RuntimeException(s"Error while reading from DRS path: $drsPath. Error: ${ExceptionUtils.getMessage(e)}")
+        )
+      }
+      .unsafeRunSync()
   }
 
   override def write(cloudHost: String, cloudPath: String): WritableByteChannel =
     throw new UnsupportedOperationException("DRS currently doesn't support write.")
 
   override def fileAttributes(drsPath: String, unused: String): Option[CloudNioRegularFileAttributes] = {
-    val fields = NonEmptyList.of(DrsResolverField.Size, DrsResolverField.TimeCreated, DrsResolverField.TimeUpdated, DrsResolverField.Hashes)
+    val fields = NonEmptyList.of(DrsResolverField.Size,
+                                 DrsResolverField.TimeCreated,
+                                 DrsResolverField.TimeUpdated,
+                                 DrsResolverField.Hashes
+    )
 
     val fileAttributesIO = for {
       drsResolverResponse <- drsPathResolver.resolveDrs(drsPath, fields)
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
index 884072e4a31..ff614646b13 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
@@ -8,10 +8,11 @@ import com.typesafe.config.Config
 
 class DrsCloudNioFileSystemProvider(rootConfig: Config,
                                     val drsCredentials: DrsCredentials,
-                                    drsReadInterpreter: DrsReadInterpreter,
-                                   ) extends CloudNioFileSystemProvider {
+                                    drsReadInterpreter: DrsReadInterpreter
+) extends CloudNioFileSystemProvider {
 
-  lazy val drsResolverConfig = if (rootConfig.hasPath("resolver")) rootConfig.getConfig("resolver") else rootConfig.getConfig("martha")
+  lazy val drsResolverConfig =
+    if (rootConfig.hasPath("resolver")) rootConfig.getConfig("resolver") else rootConfig.getConfig("martha")
   lazy val drsConfig: DrsConfig = DrsConfig.fromConfig(drsResolverConfig)
 
   lazy val drsPathResolver: EngineDrsPathResolver =
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
index 778d9b8380e..b09606294c6 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioRegularFileAttributes.scala
@@ -11,8 +11,8 @@ class DrsCloudNioRegularFileAttributes(drsPath: String,
                                        sizeOption: Option[Long],
                                        hashOption: Option[FileHash],
                                        timeCreatedOption: Option[FileTime],
-                                       timeUpdatedOption: Option[FileTime],
-                                      ) extends CloudNioRegularFileAttributes{
+                                       timeUpdatedOption: Option[FileTime]
+) extends CloudNioRegularFileAttributes {
 
   override def fileKey(): String = drsPath
 
@@ -33,50 +33,47 @@ object DrsCloudNioRegularFileAttributes {
     ("etag", HashType.S3Etag)
   )
 
-  def getPreferredHash(hashesOption: Option[Map[String, String]]): Option[FileHash] = {
+  def getPreferredHash(hashesOption: Option[Map[String, String]]): Option[FileHash] =
     hashesOption match {
       case Some(hashes: Map[String, String]) if hashes.nonEmpty =>
         priorityHashList collectFirst {
           case (key, hashType) if hashes.contains(key) => FileHash(hashType, hashes(key))
         }
-        // if no preferred hash was found, go ahead and return none because we don't support anything that the DRS object is offering
+      // if no preferred hash was found, go ahead and return none because we don't support anything that the DRS object is offering
       case _ => None
     }
-  }
 
-  private def convertToOffsetDateTime(timeInString: String): IO[OffsetDateTime] = {
+  private def convertToOffsetDateTime(timeInString: String): IO[OffsetDateTime] =
     // Here timeInString is assumed to be a ISO-8601 DateTime with timezone
     IO(OffsetDateTime.parse(timeInString))
-      .handleErrorWith(
-        offsetDateTimeException =>
-          // As a fallback timeInString is assumed to be a ISO-8601 DateTime without timezone
-          IO(LocalDateTime.parse(timeInString).atOffset(ZoneOffset.UTC))
-            .handleErrorWith(_ => IO.raiseError(offsetDateTimeException))
+      .handleErrorWith(offsetDateTimeException =>
+        // As a fallback timeInString is assumed to be a ISO-8601 DateTime without timezone
+        IO(LocalDateTime.parse(timeInString).atOffset(ZoneOffset.UTC))
+          .handleErrorWith(_ => IO.raiseError(offsetDateTimeException))
       )
-  }
 
-  private def convertToFileTime(timeInString: String): IO[FileTime] = {
+  private def convertToFileTime(timeInString: String): IO[FileTime] =
     convertToOffsetDateTime(timeInString)
       .map(_.toInstant)
       .map(FileTime.from)
-  }
 
-  def convertToFileTime(drsPath: String, key: DrsResolverField.Value, timeInStringOption: Option[String]): IO[Option[FileTime]] = {
+  def convertToFileTime(drsPath: String,
+                        key: DrsResolverField.Value,
+                        timeInStringOption: Option[String]
+  ): IO[Option[FileTime]] =
     timeInStringOption match {
       case None => IO.pure(None)
       case Some(timeInString) =>
         convertToFileTime(timeInString)
           .map(Option(_))
-          .handleErrorWith(
-            throwable =>
-              IO.raiseError(
-                new RuntimeException(
-                  s"Error while parsing '$key' value from DRS Resolver to FileTime for DRS path $drsPath. " +
-                    s"Reason: ${ExceptionUtils.getMessage(throwable)}.",
-                  throwable,
-                )
+          .handleErrorWith(throwable =>
+            IO.raiseError(
+              new RuntimeException(
+                s"Error while parsing '$key' value from DRS Resolver to FileTime for DRS path $drsPath. " +
+                  s"Reason: ${ExceptionUtils.getMessage(throwable)}.",
+                throwable
               )
+            )
           )
     }
-  }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
index a2b0a385680..28b1ee57b7a 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsConfig.scala
@@ -11,8 +11,8 @@ final case class DrsConfig(drsResolverUrl: String,
                            waitInitial: FiniteDuration,
                            waitMaximum: FiniteDuration,
                            waitMultiplier: Double,
-                           waitRandomizationFactor: Double,
-                          )
+                           waitRandomizationFactor: Double
+)
 
 object DrsConfig {
   // If you update these values also update Filesystems.md!
@@ -29,20 +29,17 @@ object DrsConfig {
   private val EnvDrsResolverWaitMultiplier = "DRS_RESOLVER_WAIT_MULTIPLIER"
   private val EnvDrsResolverWaitRandomizationFactor = "DRS_RESOLVER_WAIT_RANDOMIZATION_FACTOR"
 
-
-  def fromConfig(drsResolverConfig: Config): DrsConfig = {
+  def fromConfig(drsResolverConfig: Config): DrsConfig =
     DrsConfig(
       drsResolverUrl = drsResolverConfig.getString("url"),
       numRetries = drsResolverConfig.getOrElse("num-retries", DefaultNumRetries),
       waitInitial = drsResolverConfig.getOrElse("wait-initial", DefaultWaitInitial),
       waitMaximum = drsResolverConfig.getOrElse("wait-maximum", DefaultWaitMaximum),
       waitMultiplier = drsResolverConfig.getOrElse("wait-multiplier", DefaultWaitMultiplier),
-      waitRandomizationFactor =
-        drsResolverConfig.getOrElse("wait-randomization-factor", DefaultWaitRandomizationFactor),
+      waitRandomizationFactor = drsResolverConfig.getOrElse("wait-randomization-factor", DefaultWaitRandomizationFactor)
     )
-  }
 
-  def fromEnv(env: Map[String, String]): DrsConfig = {
+  def fromEnv(env: Map[String, String]): DrsConfig =
     DrsConfig(
       drsResolverUrl = env(EnvDrsResolverUrl),
       numRetries = env.get(EnvDrsResolverNumRetries).map(_.toInt).getOrElse(DefaultNumRetries),
@@ -50,18 +47,16 @@ object DrsConfig {
       waitMaximum = env.get(EnvDrsResolverWaitMaximumSeconds).map(_.toLong.seconds).getOrElse(DefaultWaitMaximum),
       waitMultiplier = env.get(EnvDrsResolverWaitMultiplier).map(_.toDouble).getOrElse(DefaultWaitMultiplier),
       waitRandomizationFactor =
-        env.get(EnvDrsResolverWaitRandomizationFactor).map(_.toDouble).getOrElse(DefaultWaitRandomizationFactor),
+        env.get(EnvDrsResolverWaitRandomizationFactor).map(_.toDouble).getOrElse(DefaultWaitRandomizationFactor)
     )
-  }
 
-  def toEnv(drsConfig: DrsConfig): Map[String, String] = {
+  def toEnv(drsConfig: DrsConfig): Map[String, String] =
     Map(
       EnvDrsResolverUrl -> drsConfig.drsResolverUrl,
       EnvDrsResolverNumRetries -> s"${drsConfig.numRetries}",
       EnvDrsResolverWaitInitialSeconds -> s"${drsConfig.waitInitial.toSeconds}",
       EnvDrsResolverWaitMaximumSeconds -> s"${drsConfig.waitMaximum.toSeconds}",
       EnvDrsResolverWaitMultiplier -> s"${drsConfig.waitMultiplier}",
-      EnvDrsResolverWaitRandomizationFactor -> s"${drsConfig.waitRandomizationFactor}",
+      EnvDrsResolverWaitRandomizationFactor -> s"${drsConfig.waitRandomizationFactor}"
     )
-  }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
index 2d3e972508a..78b2e9f3503 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
@@ -27,11 +27,10 @@ trait DrsCredentials {
   * is designed for use within the Cromwell engine.
   */
 case class GoogleOauthDrsCredentials(credentials: OAuth2Credentials, acceptableTTL: Duration) extends DrsCredentials {
-  //Based on method from GoogleRegistry
+  // Based on method from GoogleRegistry
   def getAccessToken: ErrorOr[String] = {
-    def accessTokenTTLIsAcceptable(accessToken: AccessToken): Boolean = {
+    def accessTokenTTLIsAcceptable(accessToken: AccessToken): Boolean =
       (accessToken.getExpirationTime.getTime - System.currentTimeMillis()).millis.gteq(acceptableTTL)
-    }
 
     Option(credentials.getAccessToken) match {
       case Some(accessToken) if accessTokenTTLIsAcceptable(accessToken) =>
@@ -51,26 +50,25 @@ object GoogleOauthDrsCredentials {
     GoogleOauthDrsCredentials(credentials, config.as[FiniteDuration]("access-token-acceptable-ttl"))
 }
 
-
 /**
   * Strategy for obtaining an access token from Google Application Default credentials that are assumed to already exist
   * in the environment. This class is designed for use by standalone executables running in environments
   * that have direct access to a Google identity (ex. CromwellDrsLocalizer).
   */
 case object GoogleAppDefaultTokenStrategy extends DrsCredentials {
-  private final val UserInfoEmailScope = "https://www.googleapis.com/auth/userinfo.email"
-  private final val UserInfoProfileScope = "https://www.googleapis.com/auth/userinfo.profile"
+  final private val UserInfoEmailScope = "https://www.googleapis.com/auth/userinfo.email"
+  final private val UserInfoProfileScope = "https://www.googleapis.com/auth/userinfo.profile"
 
-  def getAccessToken: ErrorOr[String] = {
+  def getAccessToken: ErrorOr[String] =
     Try {
-      val scopedCredentials = GoogleCredentials.getApplicationDefault().createScoped(UserInfoEmailScope, UserInfoProfileScope)
+      val scopedCredentials =
+        GoogleCredentials.getApplicationDefault().createScoped(UserInfoEmailScope, UserInfoProfileScope)
       scopedCredentials.refreshAccessToken().getTokenValue
     } match {
       case Success(null) => "null token value attempting to refresh access token".invalidNel
       case Success(value) => value.validNel
       case Failure(e) => s"Failed to refresh access token: ${e.getMessage}".invalidNel
     }
-  }
 }
 
 /**
@@ -96,9 +94,11 @@ case class AzureDrsCredentials(identityClientId: Option[String]) extends DrsCred
       .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
 
   def getAccessToken: ErrorOr[String] = {
-    val credentials = identityClientId.foldLeft(defaultCredentialBuilder) {
-      (builder, clientId) => builder.managedIdentityClientId(clientId)
-    }.build()
+    val credentials = identityClientId
+      .foldLeft(defaultCredentialBuilder) { (builder, clientId) =>
+        builder.managedIdentityClientId(clientId)
+      }
+      .build()
 
     Try(
       credentials
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
index 22d86c31726..f8d898a0bcf 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
@@ -6,7 +6,7 @@ import cats.effect.{IO, Resource}
 import cats.implicits._
 import cloud.nio.impl.drs.DrsPathResolver.{FatalRetryDisposition, RegularRetryDisposition}
 import cloud.nio.impl.drs.DrsResolverResponseSupport._
-import common.exception.{AggregatedMessageException, toIO}
+import common.exception.{toIO, AggregatedMessageException}
 import common.validation.ErrorOr.ErrorOr
 import io.circe._
 import io.circe.generic.semiauto._
@@ -40,22 +40,27 @@ abstract class DrsPathResolver(drsConfig: DrsConfig) {
 
   def getAccessToken: ErrorOr[String]
 
-  private def makeHttpRequestToDrsResolver(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): Resource[IO, HttpPost] = {
+  private def makeHttpRequestToDrsResolver(drsPath: String,
+                                           fields: NonEmptyList[DrsResolverField.Value]
+  ): Resource[IO, HttpPost] = {
     val io = getAccessToken match {
-      case Valid(token) => IO {
-        val postRequest = new HttpPost(drsConfig.drsResolverUrl)
-        val requestJson = DrsResolverRequest(drsPath, fields).asJson.noSpaces
-        postRequest.setEntity(new StringEntity(requestJson, ContentType.APPLICATION_JSON))
-        postRequest.setHeader("Authorization", s"Bearer $token")
-        postRequest
-      }
+      case Valid(token) =>
+        IO {
+          val postRequest = new HttpPost(drsConfig.drsResolverUrl)
+          val requestJson = DrsResolverRequest(drsPath, fields).asJson.noSpaces
+          postRequest.setEntity(new StringEntity(requestJson, ContentType.APPLICATION_JSON))
+          postRequest.setHeader("Authorization", s"Bearer $token")
+          postRequest
+        }
       case Invalid(errors) =>
         IO.raiseError(AggregatedMessageException("Error getting access token", errors.toList))
     }
     Resource.eval(io)
   }
 
-  private def httpResponseToDrsResolverResponse(drsPathForDebugging: String)(httpResponse: HttpResponse): IO[DrsResolverResponse] = {
+  private def httpResponseToDrsResolverResponse(
+    drsPathForDebugging: String
+  )(httpResponse: HttpResponse): IO[DrsResolverResponse] = {
     val responseStatusLine = httpResponse.getStatusLine
     val status = responseStatusLine.getStatusCode
 
@@ -73,45 +78,53 @@ abstract class DrsPathResolver(drsConfig: DrsConfig) {
         IO.raiseError(new RuntimeException(retryMessage) with RegularRetryDisposition)
       case _ =>
         val drsResolverResponseEntityOption = Option(httpResponse.getEntity).map(EntityUtils.toString)
-        val exceptionMsg = errorMessageFromResponse(drsPathForDebugging, drsResolverResponseEntityOption, responseStatusLine, drsConfig.drsResolverUrl)
-        val responseEntityOption = (responseStatusLine.getStatusCode == HttpStatus.SC_OK).valueOrZero(drsResolverResponseEntityOption)
+        val exceptionMsg = errorMessageFromResponse(drsPathForDebugging,
+                                                    drsResolverResponseEntityOption,
+                                                    responseStatusLine,
+                                                    drsConfig.drsResolverUrl
+        )
+        val responseEntityOption =
+          (responseStatusLine.getStatusCode == HttpStatus.SC_OK).valueOrZero(drsResolverResponseEntityOption)
         val responseContentIO = toIO(responseEntityOption, exceptionMsg)
 
-        responseContentIO.flatMap { responseContent =>
-          IO.fromEither(decode[DrsResolverResponse](responseContent))
-        }.handleErrorWith {
-          e => IO.raiseError(new RuntimeException(s"Unexpected response during DRS resolution: ${ExceptionUtils.getMessage(e)}"))
-        }
+        responseContentIO
+          .flatMap { responseContent =>
+            IO.fromEither(decode[DrsResolverResponse](responseContent))
+          }
+          .handleErrorWith { e =>
+            IO.raiseError(
+              new RuntimeException(s"Unexpected response during DRS resolution: ${ExceptionUtils.getMessage(e)}")
+            )
+          }
     }
   }
 
-  private def executeDrsResolverRequest(httpPost: HttpPost): Resource[IO, HttpResponse]= {
+  private def executeDrsResolverRequest(httpPost: HttpPost): Resource[IO, HttpResponse] =
     for {
       httpClient <- Resource.fromAutoCloseable(IO(httpClientBuilder.build()))
       httpResponse <- Resource.fromAutoCloseable(IO(httpClient.execute(httpPost)))
     } yield httpResponse
-  }
 
-  def rawDrsResolverResponse(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): Resource[IO, HttpResponse] = {
+  def rawDrsResolverResponse(drsPath: String,
+                             fields: NonEmptyList[DrsResolverField.Value]
+  ): Resource[IO, HttpResponse] =
     for {
       httpPost <- makeHttpRequestToDrsResolver(drsPath, fields)
       response <- executeDrsResolverRequest(httpPost)
     } yield response
-  }
 
   /** *
     * Resolves the DRS path through DRS Resolver url provided in the config.
     * Please note, this method returns an IO that would make a synchronous HTTP request to DRS Resolver when run.
     */
-  def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
+  def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] =
     rawDrsResolverResponse(drsPath, fields).use(httpResponseToDrsResolverResponse(drsPathForDebugging = drsPath))
-  }
 
-  def openChannel(accessUrl: AccessUrl): IO[ReadableByteChannel] = {
+  def openChannel(accessUrl: AccessUrl): IO[ReadableByteChannel] =
     IO {
       val httpGet = new HttpGet(accessUrl.url)
-      accessUrl.headers.getOrElse(Map.empty).toList foreach {
-        case (name, value) => httpGet.addHeader(name, value)
+      accessUrl.headers.getOrElse(Map.empty).toList foreach { case (name, value) =>
+        httpGet.addHeader(name, value)
       }
       val client = httpClientBuilder.build()
       val response = client.execute(httpGet)
@@ -130,7 +143,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig) {
 
         override def isOpen: Boolean = inner.isOpen
 
-        //noinspection ScalaUnusedExpression
+        // noinspection ScalaUnusedExpression
         override def close(): Unit = {
           val innerTry = Try(inner.close())
           val responseTry = Try(response.close())
@@ -141,7 +154,6 @@ abstract class DrsPathResolver(drsConfig: DrsConfig) {
         }
       }
     }
-  }
 }
 
 object DrsPathResolver {
@@ -198,14 +210,15 @@ final case class DrsResolverResponse(size: Option[Long] = None,
                                      hashes: Option[Map[String, String]] = None,
                                      accessUrl: Option[AccessUrl] = None,
                                      localizationPath: Option[String] = None
-                               )
+)
 
 final case class DrsResolverFailureResponse(response: DrsResolverFailureResponsePayload)
 final case class DrsResolverFailureResponsePayload(text: String)
 
 object DrsResolverResponseSupport {
 
-  implicit lazy val drsResolverFieldEncoder: Encoder[DrsResolverField.Value] = Encoder.encodeEnumeration(DrsResolverField)
+  implicit lazy val drsResolverFieldEncoder: Encoder[DrsResolverField.Value] =
+    Encoder.encodeEnumeration(DrsResolverField)
   implicit lazy val drsResolverRequestEncoder: Encoder[DrsResolverRequest] = deriveEncoder
 
   implicit lazy val saDataObjectDecoder: Decoder[SADataObject] = deriveDecoder
@@ -219,12 +232,17 @@ object DrsResolverResponseSupport {
   private val GcsScheme = "gs://"
 
   def getGcsBucketAndName(gcsUrl: String): (String, String) = {
-     val array = gcsUrl.substring(GcsScheme.length).split("/", 2)
-      (array(0), array(1))
+    val array = gcsUrl.substring(GcsScheme.length).split("/", 2)
+    (array(0), array(1))
   }
 
-  def errorMessageFromResponse(drsPathForDebugging: String, drsResolverResponseEntityOption: Option[String], responseStatusLine: StatusLine, drsResolverUri: String): String = {
-    val baseMessage = s"Could not access object \'$drsPathForDebugging\'. Status: ${responseStatusLine.getStatusCode}, reason: \'${responseStatusLine.getReasonPhrase}\', DRS Resolver location: \'$drsResolverUri\', message: "
+  def errorMessageFromResponse(drsPathForDebugging: String,
+                               drsResolverResponseEntityOption: Option[String],
+                               responseStatusLine: StatusLine,
+                               drsResolverUri: String
+  ): String = {
+    val baseMessage =
+      s"Could not access object \'$drsPathForDebugging\'. Status: ${responseStatusLine.getStatusCode}, reason: \'${responseStatusLine.getReasonPhrase}\', DRS Resolver location: \'$drsResolverUri\', message: "
 
     drsResolverResponseEntityOption match {
       case Some(entity) =>
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
index 39020f5a684..e39e7b49c81 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategy.scala
@@ -8,7 +8,8 @@ import org.apache.http.client.{HttpRequestRetryHandler, ServiceUnavailableRetryS
 import org.apache.http.protocol.HttpContext
 
 class DrsResolverHttpRequestRetryStrategy(drsConfig: DrsConfig)
-  extends ServiceUnavailableRetryStrategy with HttpRequestRetryHandler {
+    extends ServiceUnavailableRetryStrategy
+    with HttpRequestRetryHandler {
 
   // We can execute a total of one time, plus the number of retries
   private val executionMax: Int = drsConfig.numRetries + 1
@@ -17,23 +18,21 @@ class DrsResolverHttpRequestRetryStrategy(drsConfig: DrsConfig)
       initialInterval = drsConfig.waitInitial,
       maxInterval = drsConfig.waitMaximum,
       multiplier = drsConfig.waitMultiplier,
-      randomizationFactor = drsConfig.waitRandomizationFactor,
+      randomizationFactor = drsConfig.waitRandomizationFactor
     )
   private var transientFailures: Int = 0
 
   /** Returns true if an IOException should be immediately retried. */
-  override def retryRequest(exception: IOException, executionCount: Int, context: HttpContext): Boolean = {
+  override def retryRequest(exception: IOException, executionCount: Int, context: HttpContext): Boolean =
     retryRequest(executionCount)
-  }
 
   /** Returns true if HttpResponse should be retried after getRetryInterval. */
-  override def retryRequest(response: HttpResponse, executionCount: Int, context: HttpContext): Boolean = {
+  override def retryRequest(response: HttpResponse, executionCount: Int, context: HttpContext): Boolean =
     response.getStatusLine.getStatusCode match {
       case code if code == 408 || code == 429 => retryRequestTransient(executionCount)
       case code if 500 <= code && code <= 599 => retryRequest(executionCount)
       case _ => false
     }
-  }
 
   /** Returns the number of milliseconds to wait before retrying an HttpResponse. */
   override def getRetryInterval: Long = {
@@ -47,8 +46,7 @@ class DrsResolverHttpRequestRetryStrategy(drsConfig: DrsConfig)
     retryRequest(executionCount)
   }
 
-  private def retryRequest(executionCount: Int): Boolean = {
+  private def retryRequest(executionCount: Int): Boolean =
     // The first execution is executionCount == 1
     executionCount - transientFailures <= executionMax
-  }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala
index 01f7a488eb3..b53ba2cc7d8 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala
@@ -2,10 +2,8 @@ package cloud.nio.impl.drs
 
 import common.validation.ErrorOr.ErrorOr
 
-case class EngineDrsPathResolver(drsConfig: DrsConfig,
-                                 drsCredentials: DrsCredentials,
-                                )
-  extends DrsPathResolver(drsConfig) {
+case class EngineDrsPathResolver(drsConfig: DrsConfig, drsCredentials: DrsCredentials)
+    extends DrsPathResolver(drsConfig) {
 
   override def getAccessToken: ErrorOr[String] = drsCredentials.getAccessToken
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
index f61c608bd71..5edb8fd6a8b 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
@@ -52,11 +52,10 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
       "drs://dg.4DFC:0027045b-9ed6-45af-a68e-f55037b5184c",
       "drs://dg.4503:dg.4503/fc046e84-6cf9-43a3-99cc-ffa2964b88cb",
       "drs://dg.ANV0:dg.ANV0/0db6577e-57bd-48a1-93c6-327c292bcb6b",
-      "drs://dg.F82A1A:ed6be7ab-068e-46c8-824a-f39cfbb885cc",
+      "drs://dg.F82A1A:ed6be7ab-068e-46c8-824a-f39cfbb885cc"
     )
-    for (exampleUri <- exampleUris) {
+    for (exampleUri <- exampleUris)
       fileSystemProvider.getHost(exampleUri) should be(exampleUri)
-    }
   }
 
   it should "check existing drs objects" in {
@@ -79,52 +78,44 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
 
   it should "return a file provider that can read bytes from gcs" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrs(drsPath: String,
-                              fields: NonEmptyList[DrsResolverField.Value],
-                                          ): IO[DrsResolverResponse] = {
+      override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] =
         IO(DrsResolverResponse(gsUri = Option("gs://bucket/object/path")))
-      }
     }
 
     val readChannel = mock[ReadableByteChannel]
-    val drsReadInterpreter: DrsReadInterpreter = (_, drsResolverResponse) => {
+    val drsReadInterpreter: DrsReadInterpreter = (_, drsResolverResponse) =>
       IO(
         (drsResolverResponse.gsUri, drsResolverResponse.googleServiceAccount) match {
           case (Some("gs://bucket/object/path"), None) => readChannel
           case _ => fail(s"Unexpected parameters passed: $drsResolverResponse")
         }
       )
-    }
 
     val fileSystemProvider = new MockDrsCloudNioFileSystemProvider(
       mockResolver = Option(drsPathResolver),
-      drsReadInterpreter = drsReadInterpreter,
+      drsReadInterpreter = drsReadInterpreter
     )
     fileSystemProvider.fileProvider.read("dg.123", "abc", 0) should be(readChannel)
   }
 
   it should "return a file provider that can read bytes from an access url" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
-      override def resolveDrs(drsPath: String,
-                              fields: NonEmptyList[DrsResolverField.Value],
-                                          ): IO[DrsResolverResponse] = {
+      override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] =
         IO(DrsResolverResponse(accessUrl = Option(AccessUrl("https://host/object/path", None))))
-      }
     }
 
     val readChannel = mock[ReadableByteChannel]
-    val drsReadInterpreter: DrsReadInterpreter = (_, drsResolverResponse) => {
+    val drsReadInterpreter: DrsReadInterpreter = (_, drsResolverResponse) =>
       IO(
         drsResolverResponse.accessUrl match {
           case Some(AccessUrl("https://host/object/path", None)) => readChannel
           case _ => fail(s"Unexpected parameters passed: $drsResolverResponse")
         }
       )
-    }
 
     val fileSystemProvider = new MockDrsCloudNioFileSystemProvider(
       mockResolver = Option(drsPathResolver),
-      drsReadInterpreter = drsReadInterpreter,
+      drsReadInterpreter = drsReadInterpreter
     )
     fileSystemProvider.fileProvider.read("dg.123", "abc", 0) should be(readChannel)
   }
@@ -132,8 +123,8 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
   it should "return a file provider that can return file attributes" in {
     val drsPathResolver = new MockEngineDrsPathResolver() {
       override def resolveDrs(drsPath: String,
-                              fields: NonEmptyList[DrsResolverField.Value],
-                                          ): IO[DrsResolverResponse] = {
+                              fields: NonEmptyList[DrsResolverField.Value]
+      ): IO[DrsResolverResponse] = {
         val instantCreated = Instant.ofEpochMilli(123L)
         val instantUpdated = Instant.ofEpochMilli(456L)
         IO(
@@ -141,7 +132,7 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
             size = Option(789L),
             timeCreated = Option(OffsetDateTime.ofInstant(instantCreated, ZoneOffset.UTC).toString),
             timeUpdated = Option(OffsetDateTime.ofInstant(instantUpdated, ZoneOffset.UTC).toString),
-            hashes = Option(Map("md5" -> "gg0217869")),
+            hashes = Option(Map("md5" -> "gg0217869"))
           )
         )
       }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProviderSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProviderSpec.scala
index 88b95dc76e8..13df061d7a6 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProviderSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProviderSpec.scala
@@ -17,6 +17,6 @@ class DrsCloudNioFileSystemProviderSpec extends org.scalatest.flatspec.AnyFlatSp
     val path = fileSystemProvider.getCloudNioPath("drs://foo/bar/")
     the[UnsupportedOperationException] thrownBy {
       fileSystemProvider.deleteIfExists(path)
-    } should have message("DRS currently doesn't support delete.")
+    } should have message "DRS currently doesn't support delete."
   }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
index b4e5968e048..9c6cecd73f1 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
@@ -12,7 +12,7 @@ import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 
 class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matchers {
-  private val mockGSA = SADataObject(data = Json.fromJsonObject(JsonObject("key"-> Json.fromString("value"))))
+  private val mockGSA = SADataObject(data = Json.fromJsonObject(JsonObject("key" -> Json.fromString("value"))))
   private val crcHashValue = "8a366443"
   private val md5HashValue = "336ea55913bc261b72875bd259753046"
   private val shaHashValue = "f76877f8e86ec3932fd2ae04239fbabb8c90199dab0019ae55fa42b31c314c44"
@@ -40,54 +40,70 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
       .copy(timeUpdated = fullDrsResolverResponse.timeUpdated.map(_.stripSuffix("Z") + "BADTZ"))
 
   private val etagHashValue = "something"
-  private val completeHashesMap = Option(Map(
-    "betty" -> "abc123",
-    "charles" -> "456",
-    "alfred" -> "xrd",
-    "sha256" -> shaHashValue,
-    "crc32c" -> crcHashValue,
-    "md5" -> md5HashValue,
-    "etag" -> etagHashValue,
-  ))
-
-  private val missingCRCHashesMap = Option(Map(
-    "alfred" -> "xrd",
-    "sha256" -> shaHashValue,
-    "betty" -> "abc123",
-    "md5" -> md5HashValue,
-    "charles" -> "456",
-  ))
-
-  private val onlySHAHashesMap = Option(Map(
-    "betty" -> "abc123",
-    "charles" -> "456",
-    "alfred" -> "xrd",
-    "sha256" -> shaHashValue,
-  ))
-
-  private val onlyEtagHashesMap = Option(Map(
-    "alfred" -> "xrd",
-    "betty" -> "abc123",
-    "charles" -> "456",
-    "etag" -> etagHashValue,
-  ))
+  private val completeHashesMap = Option(
+    Map(
+      "betty" -> "abc123",
+      "charles" -> "456",
+      "alfred" -> "xrd",
+      "sha256" -> shaHashValue,
+      "crc32c" -> crcHashValue,
+      "md5" -> md5HashValue,
+      "etag" -> etagHashValue
+    )
+  )
+
+  private val missingCRCHashesMap = Option(
+    Map(
+      "alfred" -> "xrd",
+      "sha256" -> shaHashValue,
+      "betty" -> "abc123",
+      "md5" -> md5HashValue,
+      "charles" -> "456"
+    )
+  )
+
+  private val onlySHAHashesMap = Option(
+    Map(
+      "betty" -> "abc123",
+      "charles" -> "456",
+      "alfred" -> "xrd",
+      "sha256" -> shaHashValue
+    )
+  )
+
+  private val onlyEtagHashesMap = Option(
+    Map(
+      "alfred" -> "xrd",
+      "betty" -> "abc123",
+      "charles" -> "456",
+      "etag" -> etagHashValue
+    )
+  )
 
   behavior of "fileHash()"
 
   it should "return crc32c hash from `hashes` in DRS Resolver response when there is a crc32c" in {
-    DrsCloudNioRegularFileAttributes.getPreferredHash(completeHashesMap) shouldBe Option(FileHash(HashType.Crc32c, crcHashValue))
+    DrsCloudNioRegularFileAttributes.getPreferredHash(completeHashesMap) shouldBe Option(
+      FileHash(HashType.Crc32c, crcHashValue)
+    )
   }
 
   it should "return md5 hash from `hashes` in DRS Resolver response when there is no crc32c" in {
-    DrsCloudNioRegularFileAttributes.getPreferredHash(missingCRCHashesMap) shouldBe Option(FileHash(HashType.Md5, md5HashValue))
+    DrsCloudNioRegularFileAttributes.getPreferredHash(missingCRCHashesMap) shouldBe Option(
+      FileHash(HashType.Md5, md5HashValue)
+    )
   }
 
   it should "return sha256 hash from `hashes` in DRS Resolver response when there is only a sha256" in {
-    DrsCloudNioRegularFileAttributes.getPreferredHash(onlySHAHashesMap) shouldBe Option(FileHash(HashType.Sha256, shaHashValue))
+    DrsCloudNioRegularFileAttributes.getPreferredHash(onlySHAHashesMap) shouldBe Option(
+      FileHash(HashType.Sha256, shaHashValue)
+    )
   }
 
   it should "return etag hash from `hashes` in DRS Resolver response when there is only an etag" in {
-    DrsCloudNioRegularFileAttributes.getPreferredHash(onlyEtagHashesMap) shouldBe Option(FileHash(HashType.S3Etag, etagHashValue))
+    DrsCloudNioRegularFileAttributes.getPreferredHash(onlyEtagHashesMap) shouldBe Option(
+      FileHash(HashType.S3Etag, etagHashValue)
+    )
   }
 
   it should "return None when no hashes object is returned" in {
@@ -138,19 +154,27 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   import org.apache.http.message.BasicStatusLine
 
   val drsPathForDebugging = "drs://my_awesome_drs"
-  val responseStatusLine = new BasicStatusLine(new ProtocolVersion("http", 1, 2) , 345, "test-reason")
+  val responseStatusLine = new BasicStatusLine(new ProtocolVersion("http", 1, 2), 345, "test-reason")
   val testDrsResolverUri = "www.drshub_v4.com"
 
   it should "construct an error message from a populated, well-formed failure response" in {
     val failureResponse = Option(failureResponseJson)
 
-    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, failureResponse, responseStatusLine, testDrsResolverUri) shouldBe {
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging,
+                                                        failureResponse,
+                                                        responseStatusLine,
+                                                        testDrsResolverUri
+    ) shouldBe {
       "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: '{\"msg\":\"User 'null' does not have required action: read_data\",\"status_code\":500}'"
     }
   }
 
   it should "construct an error message from an empty failure response" in {
-    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, None, responseStatusLine, testDrsResolverUri) shouldBe {
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging,
+                                                        None,
+                                                        responseStatusLine,
+                                                        testDrsResolverUri
+    ) shouldBe {
       "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: (empty response)"
     }
   }
@@ -160,7 +184,11 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   it should "construct an error message from a malformed failure response" in {
     val unparsableFailureResponse = Option("something went horribly wrong")
 
-    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging, unparsableFailureResponse, responseStatusLine, testDrsResolverUri) shouldBe {
+    DrsResolverResponseSupport.errorMessageFromResponse(drsPathForDebugging,
+                                                        unparsableFailureResponse,
+                                                        responseStatusLine,
+                                                        testDrsResolverUri
+    ) shouldBe {
       "Could not access object 'drs://my_awesome_drs'. Status: 345, reason: 'test-reason', DRS Resolver location: 'www.drshub_v4.com', message: 'something went horribly wrong'"
     }
   }
@@ -169,7 +197,7 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
       DrsResolverField.TimeUpdated,
-      fullDrsResolverResponse.timeUpdated,
+      fullDrsResolverResponse.timeUpdated
     )
     lastModifiedTimeIO.unsafeRunSync() should
       be(Option(FileTime.from(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toInstant)))
@@ -179,7 +207,7 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
       DrsResolverField.TimeUpdated,
-      fullDrsResolverResponseNoTz.timeUpdated,
+      fullDrsResolverResponseNoTz.timeUpdated
     )
     lastModifiedTimeIO.unsafeRunSync() should
       be(Option(FileTime.from(OffsetDateTime.parse("2020-04-27T15:56:09.696Z").toInstant)))
@@ -189,7 +217,7 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
       DrsResolverField.TimeUpdated,
-      fullDrsResolverResponseNoTime.timeUpdated,
+      fullDrsResolverResponseNoTime.timeUpdated
     )
     lastModifiedTimeIO.unsafeRunSync() should be(None)
   }
@@ -198,10 +226,10 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
     val lastModifiedTimeIO = convertToFileTime(
       "drs://my_awesome_drs",
       DrsResolverField.TimeUpdated,
-      fullDrsResolverResponseBadTz.timeUpdated,
+      fullDrsResolverResponseBadTz.timeUpdated
     )
     the[RuntimeException] thrownBy lastModifiedTimeIO.unsafeRunSync() should have message
       "Error while parsing 'timeUpdated' value from DRS Resolver to FileTime for DRS path drs://my_awesome_drs. " +
-        "Reason: DateTimeParseException: Text '2020-04-27T15:56:09.696BADTZ' could not be parsed at index 23."
+      "Reason: DateTimeParseException: Text '2020-04-27T15:56:09.696BADTZ' could not be parsed at index 23."
   }
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
index b221038bedb..5be2b155391 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsResolverHttpRequestRetryStrategySpec.scala
@@ -93,7 +93,7 @@ class DrsResolverHttpRequestRetryStrategySpec extends AnyFlatSpec with Matchers
         waitInitial = 10.seconds,
         waitMultiplier = 2.0d,
         waitMaximum = 1.minute,
-        waitRandomizationFactor = 0d,
+        waitRandomizationFactor = 0d
       )
     val retryStrategy = new DrsResolverHttpRequestRetryStrategy(drsConfig)
 
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
index 07a02e096dc..2d0afd33336 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
@@ -15,18 +15,19 @@ class MockDrsCloudNioFileSystemProvider(config: Config = mockConfig,
                                           IO.raiseError(
                                             new UnsupportedOperationException("mock did not specify a read interpreter")
                                           ),
-                                        mockResolver: Option[EngineDrsPathResolver] = None,
-                                       )
-  extends DrsCloudNioFileSystemProvider(config, GoogleOauthDrsCredentials(NoCredentials.getInstance, config), drsReadInterpreter) {
+                                        mockResolver: Option[EngineDrsPathResolver] = None
+) extends DrsCloudNioFileSystemProvider(config,
+                                        GoogleOauthDrsCredentials(NoCredentials.getInstance, config),
+                                        drsReadInterpreter
+    ) {
 
-  override lazy val drsPathResolver: EngineDrsPathResolver = {
+  override lazy val drsPathResolver: EngineDrsPathResolver =
     mockResolver getOrElse
       new MockEngineDrsPathResolver(
         drsConfig = drsConfig,
         httpClientBuilderOverride = httpClientBuilder,
-        accessTokenAcceptableTTL = Duration.Inf,
+        accessTokenAcceptableTTL = Duration.Inf
       )
-  }
 }
 
 object MockDrsCloudNioFileSystemProvider {
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
index 9e22544c38b..1aff2f13470 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
@@ -12,9 +12,10 @@ import scala.concurrent.duration.Duration
 
 class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfig,
                                 httpClientBuilderOverride: Option[HttpClientBuilder] = None,
-                                accessTokenAcceptableTTL: Duration = Duration.Inf,
-                               )
-  extends EngineDrsPathResolver(drsConfig, GoogleOauthDrsCredentials(NoCredentials.getInstance, accessTokenAcceptableTTL)) {
+                                accessTokenAcceptableTTL: Duration = Duration.Inf
+) extends EngineDrsPathResolver(drsConfig,
+                                GoogleOauthDrsCredentials(NoCredentials.getInstance, accessTokenAcceptableTTL)
+    ) {
 
   override protected lazy val httpClientBuilder: HttpClientBuilder =
     httpClientBuilderOverride getOrElse MockSugar.mock[HttpClientBuilder]
@@ -38,13 +39,15 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
 
   private val drsResolverObjWithFileName = drsResolverObjWithGcsPath.copy(fileName = Option("file.txt"))
 
-  private val drsResolverObjWithLocalizationPath = drsResolverObjWithGcsPath.copy(localizationPath = Option("/dir/subdir/file.txt"))
+  private val drsResolverObjWithLocalizationPath =
+    drsResolverObjWithGcsPath.copy(localizationPath = Option("/dir/subdir/file.txt"))
 
-  private val drsResolverObjWithAllThePaths = drsResolverObjWithLocalizationPath.copy(fileName = drsResolverObjWithFileName.fileName)
+  private val drsResolverObjWithAllThePaths =
+    drsResolverObjWithLocalizationPath.copy(fileName = drsResolverObjWithFileName.fileName)
 
   private val drsResolverObjWithNoGcsPath = drsResolverObjWithGcsPath.copy(gsUri = None)
 
-  override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
+  override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] =
     drsPath match {
       case MockDrsPaths.drsPathResolvingGcsPath => IO(drsResolverObjWithGcsPath)
       case MockDrsPaths.drsPathWithNonPathChars => IO(drsResolverObjWithGcsPath)
@@ -60,7 +63,6 @@ class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfi
           )
         )
     }
-  }
 
   override lazy val getAccessToken: ErrorOr[String] = MockDrsPaths.mockToken.validNel
 }
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpClientPool.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpClientPool.scala
index d93b0aa6f82..b13eb844a24 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpClientPool.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpClientPool.scala
@@ -7,25 +7,26 @@ import org.apache.commons.net.ftp.FTPClient
 import scala.concurrent.duration._
 
 object FtpClientPool extends StrictLogging {
-  def dispose(ftpClient: FTPClient) = try {
+  def dispose(ftpClient: FTPClient) = try
     if (ftpClient.isConnected) {
       ftpClient.logout()
       ftpClient.disconnect()
     }
-  } catch {
+  catch {
     case e: Exception => logger.debug("Failed to disconnect ftp client", e)
   }
 }
 
-class FtpClientPool(capacity: Int, maxIdleTime: FiniteDuration, factory: () => FTPClient) extends ExpiringPool[FTPClient](
-  capacity = capacity,
-  maxIdleTime = maxIdleTime,
-  referenceType = ReferenceType.Strong,
-  _factory = factory,
-  // Reset is called every time a client is added or released back to the pool. We don't want to actually reset the connection here
-  // otherwise we'd need to login again and reconfigure the connection every time
-  _reset = Function.const(()),
-  _dispose = FtpClientPool.dispose,
-  // Could not find a good health check at the moment (isAvailable and isConnected on the socket seem to both return false sometimes even if the client is fine)
-  _healthCheck = Function.const(true)
-)
+class FtpClientPool(capacity: Int, maxIdleTime: FiniteDuration, factory: () => FTPClient)
+    extends ExpiringPool[FTPClient](
+      capacity = capacity,
+      maxIdleTime = maxIdleTime,
+      referenceType = ReferenceType.Strong,
+      _factory = factory,
+      // Reset is called every time a client is added or released back to the pool. We don't want to actually reset the connection here
+      // otherwise we'd need to login again and reconfigure the connection every time
+      _reset = Function.const(()),
+      _dispose = FtpClientPool.dispose,
+      // Could not find a good health check at the moment (isAvailable and isConnected on the socket seem to both return false sometimes even if the client is fine)
+      _healthCheck = Function.const(true)
+    )
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileProvider.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileProvider.scala
index 96e05702034..37ace6c250b 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileProvider.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileProvider.scala
@@ -37,17 +37,25 @@ class FtpCloudNioFileProvider(fsProvider: FtpCloudNioFileSystemProvider) extends
     * Returns a listing of keys within a bucket starting with prefix. The returned keys should include the prefix. The
     * paths must be absolute, but the key should not begin with a slash.
     */
-  override def listObjects(cloudHost: String, cloudPathPrefix: String, markerOption: Option[String]): CloudNioFileList = withAutoRelease(cloudHost) { client =>
-    FtpListFiles(cloudHost, cloudPathPrefix, "list objects")
-      .run(client)
-      .map({ files =>
-        val cleanFiles = files.map(_.getName).map(cloudPathPrefix.stripPrefix("/").ensureSlashed + _)
-        CloudNioFileList(cleanFiles, markerOption)
-      })
-  }.unsafeRunSync()
-
-  override def copy(sourceCloudHost: String, sourceCloudPath: String, targetCloudHost: String, targetCloudPath: String): Unit = {
-    if (sourceCloudHost != targetCloudHost) throw new UnsupportedOperationException(s"Cannot copy files across different ftp servers: Source host: $sourceCloudHost, Target host: $targetCloudHost")
+  override def listObjects(cloudHost: String, cloudPathPrefix: String, markerOption: Option[String]): CloudNioFileList =
+    withAutoRelease(cloudHost) { client =>
+      FtpListFiles(cloudHost, cloudPathPrefix, "list objects")
+        .run(client)
+        .map { files =>
+          val cleanFiles = files.map(_.getName).map(cloudPathPrefix.stripPrefix("/").ensureSlashed + _)
+          CloudNioFileList(cleanFiles, markerOption)
+        }
+    }.unsafeRunSync()
+
+  override def copy(sourceCloudHost: String,
+                    sourceCloudPath: String,
+                    targetCloudHost: String,
+                    targetCloudPath: String
+  ): Unit = {
+    if (sourceCloudHost != targetCloudHost)
+      throw new UnsupportedOperationException(
+        s"Cannot copy files across different ftp servers: Source host: $sourceCloudHost, Target host: $targetCloudHost"
+      )
 
     val fileSystem = findFileSystem(sourceCloudHost)
 
@@ -63,7 +71,11 @@ class FtpCloudNioFileProvider(fsProvider: FtpCloudNioFileSystemProvider) extends
       Util.copyStream(ios.inputStream, ios.outputStream)
     } match {
       case Success(_) =>
-      case Failure(failure) => throw new IOException(s"Failed to copy ftp://$sourceCloudHost/$sourceCloudPath to ftp://$targetCloudHost/$targetCloudPath", failure)
+      case Failure(failure) =>
+        throw new IOException(
+          s"Failed to copy ftp://$sourceCloudHost/$sourceCloudPath to ftp://$targetCloudHost/$targetCloudPath",
+          failure
+        )
     }
   }
 
@@ -71,12 +83,15 @@ class FtpCloudNioFileProvider(fsProvider: FtpCloudNioFileSystemProvider) extends
     FtpDeleteFile(cloudHost, cloudPath, "delete").run(client)
   }.unsafeRunSync()
 
-  private def inputStream(cloudHost: String, cloudPath: String, offset: Long, lease: Lease[FTPClient]): IO[LeasedInputStream] = {
+  private def inputStream(cloudHost: String,
+                          cloudPath: String,
+                          offset: Long,
+                          lease: Lease[FTPClient]
+  ): IO[LeasedInputStream] =
     FtpInputStream(cloudHost, cloudPath, offset)
       .run(lease.get())
       // Wrap the input stream in a LeasedInputStream so that the lease can be released when the stream is closed
       .map(new LeasedInputStream(cloudHost, cloudPath, _, lease))
-  }
 
   override def read(cloudHost: String, cloudPath: String, offset: Long): ReadableByteChannel = {
     for {
@@ -85,11 +100,10 @@ class FtpCloudNioFileProvider(fsProvider: FtpCloudNioFileSystemProvider) extends
     } yield Channels.newChannel(is)
   }.unsafeRunSync()
 
-  private def outputStream(cloudHost: String, cloudPath: String, lease: Lease[FTPClient]): IO[LeasedOutputStream] = {
+  private def outputStream(cloudHost: String, cloudPath: String, lease: Lease[FTPClient]): IO[LeasedOutputStream] =
     FtpOutputStream(cloudHost, cloudPath)
       .run(lease.get())
       .map(new LeasedOutputStream(cloudHost, cloudPath, _, lease))
-  }
 
   override def write(cloudHost: String, cloudPath: String): WritableByteChannel = {
     for {
@@ -98,15 +112,16 @@ class FtpCloudNioFileProvider(fsProvider: FtpCloudNioFileSystemProvider) extends
     } yield Channels.newChannel(os)
   }.unsafeRunSync()
 
-  override def fileAttributes(cloudHost: String, cloudPath: String): Option[CloudNioRegularFileAttributes] = withAutoRelease(cloudHost) { client =>
-    FtpListFiles(cloudHost, cloudPath, "get file attributes")
-      .run(client)
-      .map(
-        _.headOption map { file =>
-          new FtpCloudNioRegularFileAttributes(file, cloudHost + cloudPath)
-        }
-      )
-  }.unsafeRunSync()
+  override def fileAttributes(cloudHost: String, cloudPath: String): Option[CloudNioRegularFileAttributes] =
+    withAutoRelease(cloudHost) { client =>
+      FtpListFiles(cloudHost, cloudPath, "get file attributes")
+        .run(client)
+        .map(
+          _.headOption map { file =>
+            new FtpCloudNioRegularFileAttributes(file, cloudHost + cloudPath)
+          }
+        )
+    }.unsafeRunSync()
 
   override def createDirectory(cloudHost: String, cloudPath: String) = withAutoRelease(cloudHost) { client =>
     val operation = FtpCreateDirectory(cloudHost, cloudPath)
@@ -129,7 +144,8 @@ class FtpCloudNioFileProvider(fsProvider: FtpCloudNioFileSystemProvider) extends
 
   private def findFileSystem(host: String): FtpCloudNioFileSystem = fsProvider.newCloudNioFileSystemFromHost(host)
 
-  private def acquireLease[A](host: String): IO[Lease[FTPClient]] = IO { findFileSystem(host).leaseClient }
+  private def acquireLease[A](host: String): IO[Lease[FTPClient]] = IO(findFileSystem(host).leaseClient)
 
-  private def withAutoRelease[A](cloudHost: String): (FTPClient => IO[A]) => IO[A] = autoRelease[A](acquireLease(cloudHost))
+  private def withAutoRelease[A](cloudHost: String): (FTPClient => IO[A]) => IO[A] =
+    autoRelease[A](acquireLease(cloudHost))
 }
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystem.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystem.scala
index 91a26bc8f8e..dd0bb79cfa7 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystem.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystem.scala
@@ -12,7 +12,9 @@ object FtpCloudNioFileSystem {
   val logger = LoggerFactory.getLogger("FtpFileSystem")
 }
 
-class FtpCloudNioFileSystem(provider: FtpCloudNioFileSystemProvider, host: String) extends CloudNioFileSystem(provider, host) with StrictLogging {
+class FtpCloudNioFileSystem(provider: FtpCloudNioFileSystemProvider, host: String)
+    extends CloudNioFileSystem(provider, host)
+    with StrictLogging {
   private val credentials = provider.credentials
   private val ftpConfig = provider.ftpConfig
   private val connectionModeFunction: FTPClient => Unit = ftpConfig.connectionMode match {
@@ -20,7 +22,7 @@ class FtpCloudNioFileSystem(provider: FtpCloudNioFileSystemProvider, host: Strin
     case Active => client: FTPClient => client.enterLocalActiveMode()
   }
 
-  private [ftp] lazy val clientFactory = () => {
+  private[ftp] lazy val clientFactory = () => {
     val client = new FTPClient()
     client.setDefaultPort(ftpConfig.connectionPort)
     client.connect(host)
@@ -33,7 +35,10 @@ class FtpCloudNioFileSystem(provider: FtpCloudNioFileSystemProvider, host: Strin
   private val clientPool = new FtpClientPool(ftpConfig.capacity, ftpConfig.idleConnectionTimeout, clientFactory)
 
   def leaseClient = ftpConfig.leaseTimeout match {
-    case Some(timeout) => clientPool.tryAcquire(timeout).getOrElse(throw new TimeoutException("Timed out waiting for an available connection, try again later."))
+    case Some(timeout) =>
+      clientPool
+        .tryAcquire(timeout)
+        .getOrElse(throw new TimeoutException("Timed out waiting for an available connection, try again later."))
     case _ => clientPool.acquire()
   }
 
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemProvider.scala
index e20edfc76ff..bb2faaa5ccd 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemProvider.scala
@@ -11,7 +11,11 @@ import com.typesafe.scalalogging.StrictLogging
 
 import scala.util.{Failure, Success, Try}
 
-class FtpCloudNioFileSystemProvider(override val config: Config, val credentials: FtpCredentials, ftpFileSystems: FtpFileSystems) extends CloudNioFileSystemProvider with StrictLogging {
+class FtpCloudNioFileSystemProvider(override val config: Config,
+                                    val credentials: FtpCredentials,
+                                    ftpFileSystems: FtpFileSystems
+) extends CloudNioFileSystemProvider
+    with StrictLogging {
   val ftpConfig = ftpFileSystems.config
 
   override def fileProvider = new FtpCloudNioFileProvider(this)
@@ -29,18 +33,19 @@ class FtpCloudNioFileSystemProvider(override val config: Config, val credentials
      * will try to get it using the fileProvider which will require a new client lease and can result in a  deadlock of the client pool, since
      * the read channel holds on to its lease until its closed.
      */
-    val preComputedFileSize = retry.from(() => fileProvider.fileAttributes(cloudNioPath.cloudHost, cloudNioPath.cloudPath).map(_.size()))
+    val preComputedFileSize =
+      retry.from(() => fileProvider.fileAttributes(cloudNioPath.cloudHost, cloudNioPath.cloudPath).map(_.size()))
     new CloudNioReadChannel(fileProvider, retry, cloudNioPath) {
       override def fileSize = preComputedFileSize
     }
   }
 
-  override def createDirectory(dir: Path, attrs: FileAttribute[_]*): Unit = {
+  override def createDirectory(dir: Path, attrs: FileAttribute[_]*): Unit =
     Try {
-      retry.from(() => {
+      retry.from { () =>
         val cloudNioPath = CloudNioPath.checkPath(dir)
         fileProvider.createDirectory(cloudNioPath.cloudHost, cloudNioPath.cloudPath)
-      })
+      }
     } match {
       case Success(_) =>
       case Failure(f: FileAlreadyExistsException) => throw f
@@ -51,15 +56,12 @@ class FtpCloudNioFileSystemProvider(override val config: Config, val credentials
         throw f
       case Failure(f) => throw f
     }
-  }
 
   override def usePseudoDirectories = false
 
-  override def newCloudNioFileSystem(uriAsString: String, config: Config) = {
+  override def newCloudNioFileSystem(uriAsString: String, config: Config) =
     newCloudNioFileSystemFromHost(getHost(uriAsString))
-  }
-  
-  def newCloudNioFileSystemFromHost(host: String) = {
+
+  def newCloudNioFileSystemFromHost(host: String) =
     ftpFileSystems.getFileSystem(host, this)
-  }
 }
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCredentials.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCredentials.scala
index 2e553a5f66b..c63efad1de7 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCredentials.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpCredentials.scala
@@ -11,7 +11,8 @@ sealed trait FtpCredentials {
 }
 
 // Yes, FTP uses plain text username / password
-case class FtpAuthenticatedCredentials(username: String, password: String, account: Option[String]) extends FtpCredentials {
+case class FtpAuthenticatedCredentials(username: String, password: String, account: Option[String])
+    extends FtpCredentials {
   override def login(ftpClient: FTPClient) = {
     lazy val replyString = Option(ftpClient.getReplyString).getOrElse("N/A")
 
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpFileSystems.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpFileSystems.scala
index 006e19982ff..63f0c10f655 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpFileSystems.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpFileSystems.scala
@@ -9,7 +9,7 @@ import scala.concurrent.duration._
 object FtpFileSystems {
   val DefaultConfig = FtpFileSystemsConfiguration(1.day, Option(1.hour), 5, 1.hour, 21, Passive)
   val Default = new FtpFileSystems(DefaultConfig)
-  private [ftp] case class FtpCacheKey(host: String, ftpProvider: FtpCloudNioFileSystemProvider)
+  private[ftp] case class FtpCacheKey(host: String, ftpProvider: FtpCloudNioFileSystemProvider)
 }
 
 /**
@@ -21,18 +21,18 @@ class FtpFileSystems(val config: FtpFileSystemsConfiguration) {
 
   private val fileSystemTTL = config.cacheTTL
 
-  private val fileSystemsCache: LoadingCache[FtpCacheKey, FtpCloudNioFileSystem] = CacheBuilder.newBuilder()
+  private val fileSystemsCache: LoadingCache[FtpCacheKey, FtpCloudNioFileSystem] = CacheBuilder
+    .newBuilder()
     .expireAfterAccess(fileSystemTTL.length, fileSystemTTL.unit)
-    .removalListener((notification: RemovalNotification[FtpCacheKey, FtpCloudNioFileSystem]) => {
+    .removalListener { (notification: RemovalNotification[FtpCacheKey, FtpCloudNioFileSystem]) =>
       notification.getValue.close()
-    })
+    }
     .build[FtpCacheKey, FtpCloudNioFileSystem](new CacheLoader[FtpCacheKey, FtpCloudNioFileSystem] {
       override def load(key: FtpCacheKey) = createFileSystem(key)
     })
-  
-  private [ftp] def createFileSystem(key: FtpCacheKey) = new FtpCloudNioFileSystem(key.ftpProvider, key.host)
 
-  def getFileSystem(host: String, ftpCloudNioFileProvider: FtpCloudNioFileSystemProvider) = {
+  private[ftp] def createFileSystem(key: FtpCacheKey) = new FtpCloudNioFileSystem(key.ftpProvider, key.host)
+
+  def getFileSystem(host: String, ftpCloudNioFileProvider: FtpCloudNioFileSystemProvider) =
     fileSystemsCache.get(FtpCacheKey(host, ftpCloudNioFileProvider))
-  }
 }
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpFileSystemsConfiguration.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpFileSystemsConfiguration.scala
index 2c305f82edf..8e5071f604a 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpFileSystemsConfiguration.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpFileSystemsConfiguration.scala
@@ -9,7 +9,8 @@ case class FtpFileSystemsConfiguration(cacheTTL: FiniteDuration,
                                        capacity: Int,
                                        idleConnectionTimeout: FiniteDuration,
                                        connectionPort: Int,
-                                       connectionMode: ConnectionMode)
+                                       connectionMode: ConnectionMode
+)
 
 object FtpFileSystemsConfiguration {
   sealed trait ConnectionMode
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpUtil.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpUtil.scala
index 9138401f803..049c54d9d89 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpUtil.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/FtpUtil.scala
@@ -12,16 +12,16 @@ object FtpUtil {
     def ensureSlashed = if (cloudPath.endsWith("/")) cloudPath else s"$cloudPath/"
   }
 
-  case class FtpIoException(message: String, code: Int, replyString: String, cause: Option[Throwable] = None) extends IOException(s"$message: $replyString", cause.orNull) {
+  case class FtpIoException(message: String, code: Int, replyString: String, cause: Option[Throwable] = None)
+      extends IOException(s"$message: $replyString", cause.orNull) {
     def isTransient = FTPReply.isNegativeTransient(code)
     def isFatal = FTPReply.isNegativePermanent(code)
   }
 
-  def autoRelease[A](acquire: IO[Lease[FTPClient]])(action: FTPClient => IO[A]): IO[A] = {
-    acquire.bracketCase(lease => action(lease.get()))({
-      // If there's a cause, the call to the FTP client threw an exception, assume the connection is compromised and invalidate the lease  
-      case (lease, ExitCase.Error(FtpIoException(_, _, _, Some(_)))) => IO { lease.invalidate() }
-      case (lease, _) => IO { lease.release() }
-    })
-  }
+  def autoRelease[A](acquire: IO[Lease[FTPClient]])(action: FTPClient => IO[A]): IO[A] =
+    acquire.bracketCase(lease => action(lease.get())) {
+      // If there's a cause, the call to the FTP client threw an exception, assume the connection is compromised and invalidate the lease
+      case (lease, ExitCase.Error(FtpIoException(_, _, _, Some(_)))) => IO(lease.invalidate())
+      case (lease, _) => IO(lease.release())
+    }
 }
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/InputOutputStreams.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/InputOutputStreams.scala
index 2455fa2b86a..a1a8b158ec7 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/InputOutputStreams.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/InputOutputStreams.scala
@@ -3,11 +3,9 @@ package cloud.nio.impl.ftp
 import java.io.{InputStream, OutputStream}
 
 class InputOutputStreams(val inputStream: InputStream, val outputStream: OutputStream) extends AutoCloseable {
-  override def close() = {
-    try {
+  override def close() =
+    try
       inputStream.close()
-    } finally {
+    finally
       outputStream.close()
-    }
-  }
 }
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/LeasedInputStream.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/LeasedInputStream.scala
index 29d0b7c6bf7..2e794a96791 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/LeasedInputStream.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/LeasedInputStream.scala
@@ -8,7 +8,8 @@ import cloud.nio.impl.ftp.operations.FtpCompletePendingCommand
 import io.github.andrebeat.pool.Lease
 import org.apache.commons.net.ftp.FTPClient
 
-class LeasedInputStream(cloudHost: String, cloudPath: String, inputStream: InputStream, lease: Lease[FTPClient]) extends InputStream {
+class LeasedInputStream(cloudHost: String, cloudPath: String, inputStream: InputStream, lease: Lease[FTPClient])
+    extends InputStream {
   override def read() = inputStream.read()
   override def read(b: Array[Byte]) = inputStream.read(b)
   override def read(b: Array[Byte], off: Int, len: Int): Int = inputStream.read(b, off, len)
@@ -16,7 +17,8 @@ class LeasedInputStream(cloudHost: String, cloudPath: String, inputStream: Input
   override def available = inputStream.available()
   override def close() = {
     inputStream.close()
-    autoRelease(IO.pure(lease))(FtpCompletePendingCommand(cloudHost, cloudPath, "close input steam").run).void.unsafeRunSync()
+    autoRelease(IO.pure(lease))(FtpCompletePendingCommand(cloudHost, cloudPath, "close input steam").run).void
+      .unsafeRunSync()
   }
   override def mark(readlimit: Int) = inputStream.mark(readlimit)
   override def reset() = inputStream.reset()
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/LeasedOutputStream.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/LeasedOutputStream.scala
index 5a4f43acabb..7fe09f3fbf1 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/LeasedOutputStream.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/LeasedOutputStream.scala
@@ -8,13 +8,15 @@ import cloud.nio.impl.ftp.operations.FtpCompletePendingCommand
 import io.github.andrebeat.pool.Lease
 import org.apache.commons.net.ftp.FTPClient
 
-class LeasedOutputStream(cloudHost: String, cloudPath: String, outputStream: OutputStream, lease: Lease[FTPClient]) extends OutputStream {
+class LeasedOutputStream(cloudHost: String, cloudPath: String, outputStream: OutputStream, lease: Lease[FTPClient])
+    extends OutputStream {
   override def write(b: Int) = outputStream.write(b)
   override def write(b: Array[Byte]) = outputStream.write(b)
   override def write(b: Array[Byte], off: Int, len: Int): Unit = outputStream.write(b, off, len)
   override def flush() = outputStream.flush()
   override def close() = {
     outputStream.close()
-    autoRelease(IO.pure(lease))(FtpCompletePendingCommand(cloudHost, cloudPath, "close input steam").run).void.unsafeRunSync()
+    autoRelease(IO.pure(lease))(FtpCompletePendingCommand(cloudHost, cloudPath, "close input steam").run).void
+      .unsafeRunSync()
   }
 }
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/operations/FtpOperation.scala b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/operations/FtpOperation.scala
index 400b0b26740..dee465cff4c 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/operations/FtpOperation.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/main/scala/cloud/nio/impl/ftp/operations/FtpOperation.scala
@@ -14,93 +14,101 @@ sealed trait FtpOperation[A] {
   def description: String
   def action: FTPClient => A
   def run(client: FTPClient): IO[A]
-  
+
   def fullPath = s"ftp://$cloudHost/$cloudPath"
   protected def errorMessage = s"Failed to $description at $fullPath"
 
-  protected def fail(client: FTPClient, cause: Option[Throwable] = None) = {
+  protected def fail(client: FTPClient, cause: Option[Throwable] = None) =
     IO.raiseError[A](generateException(client, cause))
-  }
 
-  private [operations] def generateException(client: FTPClient, cause: Option[Throwable]) = cause match {
-    case None if client.getReplyCode == FTPReply.FILE_UNAVAILABLE && client.getReplyString.toLowerCase.contains("exists") =>
+  private[operations] def generateException(client: FTPClient, cause: Option[Throwable]) = cause match {
+    case None
+        if client.getReplyCode == FTPReply.FILE_UNAVAILABLE && client.getReplyString.toLowerCase.contains("exists") =>
       new FileAlreadyExistsException(fullPath)
-    case None if client.getReplyCode == FTPReply.FILE_UNAVAILABLE && client.getReplyString.toLowerCase.contains("no such file") =>
+    case None
+        if client.getReplyCode == FTPReply.FILE_UNAVAILABLE && client.getReplyString.toLowerCase.contains(
+          "no such file"
+        ) =>
       new NoSuchFileException(fullPath)
     case None =>
       FtpIoException(errorMessage, client.getReplyCode, Option(client.getReplyString).getOrElse("N/A"))
     case Some(c) =>
       FtpIoException(errorMessage, client.getReplyCode, Option(client.getReplyString).getOrElse("N/A"), Option(c))
   }
-  
+
   protected def handleError(client: FTPClient)(failure: Throwable) = fail(client, Option(failure))
 
-  protected def commonRun(client: FTPClient, bind: A => IO[A]): IO[A] = {
-    IO { action(client) } redeemWith (handleError(client), bind)
-  }
-  
+  protected def commonRun(client: FTPClient, bind: A => IO[A]): IO[A] =
+    IO(action(client)) redeemWith (handleError(client), bind)
+
   override def toString = s"$description at $fullPath"
 }
 
 sealed trait FtpBooleanOperation extends FtpOperation[Boolean] {
   protected def failOnFalse: Boolean = true
-  
-  def run(client: FTPClient): IO[Boolean] = {
+
+  def run(client: FTPClient): IO[Boolean] =
     commonRun(client,
-      {
-        // Operation didn't throw but the result is false which means it failed
-        case false if failOnFalse => fail(client)
-        case result => IO.pure(result)
-      }
+              {
+                // Operation didn't throw but the result is false which means it failed
+                case false if failOnFalse => fail(client)
+                case result => IO.pure(result)
+              }
     )
-  }
 }
 
 sealed trait FtpValueOperation[A <: AnyRef] extends FtpOperation[A] {
-  def run(client: FTPClient): IO[A] = {
-    commonRun(client, 
-      {
-        // Operation didn't throw but the result is null which means it failed
-        case null => fail(client)
-        case result => IO.pure(result)
-      }
+  def run(client: FTPClient): IO[A] =
+    commonRun(client,
+              {
+                // Operation didn't throw but the result is null which means it failed
+                case null => fail(client)
+                case result => IO.pure(result)
+              }
     )
-  }
 }
 
-case class FtpListFiles(cloudHost: String, cloudPath: String, description: String = "List files") extends FtpValueOperation[Array[FTPFile]] {
+case class FtpListFiles(cloudHost: String, cloudPath: String, description: String = "List files")
+    extends FtpValueOperation[Array[FTPFile]] {
   override val action = _.listFiles(cloudPath.ensureSlashedPrefix)
 }
 
-case class FtpListDirectories(cloudHost: String, cloudPath: String, description: String = "List files") extends FtpValueOperation[Array[FTPFile]] {
+case class FtpListDirectories(cloudHost: String, cloudPath: String, description: String = "List files")
+    extends FtpValueOperation[Array[FTPFile]] {
   // We need to list the directories in the parent and see if any matches the name, hence the string manipulations
-  lazy val parts = cloudPath.ensureSlashedPrefix.stripSuffix(CloudNioFileSystem.Separator).split(CloudNioFileSystem.Separator)
+  lazy val parts =
+    cloudPath.ensureSlashedPrefix.stripSuffix(CloudNioFileSystem.Separator).split(CloudNioFileSystem.Separator)
   lazy val parent = parts.init.mkString(CloudNioFileSystem.Separator)
   lazy val directoryName = parts.last
 
   override val action = _.listDirectories(parent)
 }
 
-case class FtpDeleteFile(cloudHost: String, cloudPath: String, description: String = "delete file") extends FtpBooleanOperation {
+case class FtpDeleteFile(cloudHost: String, cloudPath: String, description: String = "delete file")
+    extends FtpBooleanOperation {
   override val action = _.deleteFile(cloudPath.ensureSlashedPrefix)
   override val failOnFalse = false
 }
 
-case class FtpInputStream(cloudHost: String, cloudPath: String, offset: Long, description: String = "read") extends FtpValueOperation[InputStream] {
+case class FtpInputStream(cloudHost: String, cloudPath: String, offset: Long, description: String = "read")
+    extends FtpValueOperation[InputStream] {
   override val action = { client =>
     client.setRestartOffset(offset)
     client.retrieveFileStream(cloudPath.ensureSlashedPrefix)
   }
 }
 
-case class FtpOutputStream(cloudHost: String, cloudPath: String, description: String = "write") extends FtpValueOperation[OutputStream] {
+case class FtpOutputStream(cloudHost: String, cloudPath: String, description: String = "write")
+    extends FtpValueOperation[OutputStream] {
   override val action = _.storeFileStream(cloudPath.ensureSlashedPrefix)
 }
 
-case class FtpCreateDirectory(cloudHost: String, cloudPath: String, description: String = "create directory") extends FtpBooleanOperation {
+case class FtpCreateDirectory(cloudHost: String, cloudPath: String, description: String = "create directory")
+    extends FtpBooleanOperation {
   override val action = _.makeDirectory(cloudPath.ensureSlashedPrefix)
 }
 
-case class FtpCompletePendingCommand(cloudHost: String, cloudPath: String, description: String = "close stream") extends FtpBooleanOperation {
+case class FtpCompletePendingCommand(cloudHost: String, cloudPath: String, description: String = "close stream")
+    extends FtpBooleanOperation {
   override val action = _.completePendingCommand()
 }
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpClientPoolSpec.scala b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpClientPoolSpec.scala
index 91b69bf7e94..1837ee27139 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpClientPoolSpec.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpClientPoolSpec.scala
@@ -17,15 +17,13 @@ class FtpClientPoolSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     var loggedOut: Boolean = false
     var disconnected: Boolean = false
     client.isConnected.returns(true)
-    client.logout().responds(_ => {
+    client.logout().responds { _ =>
       loggedOut = true
       true
-    })
-    client.disconnect().responds(_ => {
-      disconnected = true
-    })
+    }
+    client.disconnect().responds(_ => disconnected = true)
 
-    val clientPool = new FtpClientPool(1, 10.minutes, () => { client })
+    val clientPool = new FtpClientPool(1, 10.minutes, () => client)
     clientPool.acquire().invalidate()
 
     loggedOut shouldBe true
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileProviderSpec.scala b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileProviderSpec.scala
index f68f67cbf67..f1ca24c847a 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileProviderSpec.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileProviderSpec.scala
@@ -46,7 +46,8 @@ class FtpCloudNioFileProviderSpec extends AnyFlatSpec with CromwellTimeoutSpec w
     fakeUnixFileSystem.add(new DirectoryEntry(directory))
 
     fileProvider.listObjects("localhost", root, None).paths should contain theSameElementsAs List(
-      file.stripPrefix("/"), directory.stripPrefix("/")
+      file.stripPrefix("/"),
+      directory.stripPrefix("/")
     )
   }
 
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemProviderSpec.scala b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemProviderSpec.scala
index e23e8ba450e..952e171f9ec 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemProviderSpec.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemProviderSpec.scala
@@ -13,8 +13,12 @@ import org.mockito.Mockito._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-class FtpCloudNioFileSystemProviderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with MockSugar
-  with MockFtpFileSystem {
+class FtpCloudNioFileSystemProviderSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with MockSugar
+    with MockFtpFileSystem {
 
   behavior of "FtpCloudNioFileSystemProviderSpec"
 
@@ -45,7 +49,9 @@ class FtpCloudNioFileSystemProviderSpec extends AnyFlatSpec with CromwellTimeout
   it should "pre compute the size before opening a read channel to avoid deadlocks" in {
     val mockSizeFunction = mock[() => Long]
     val provider: FtpCloudNioFileSystemProvider = new FtpCloudNioFileSystemProvider(
-      ConfigFactory.empty, FtpAnonymousCredentials, ftpFileSystems
+      ConfigFactory.empty,
+      FtpAnonymousCredentials,
+      ftpFileSystems
     ) {
 
       override def fileProvider: FtpCloudNioFileProvider = new FtpCloudNioFileProvider(this) {
@@ -59,9 +65,8 @@ class FtpCloudNioFileSystemProviderSpec extends AnyFlatSpec with CromwellTimeout
             }
           )
 
-        override def read(cloudHost: String, cloudPath: String, offset: Long): ReadableByteChannel = {
+        override def read(cloudHost: String, cloudPath: String, offset: Long): ReadableByteChannel =
           mock[ReadableByteChannel]
-        }
       }
     }
 
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemSpec.scala b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemSpec.scala
index d12db7ec612..f2b86fbd621 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemSpec.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCloudNioFileSystemSpec.scala
@@ -11,7 +11,6 @@ import org.scalatest.matchers.should.Matchers
 import scala.concurrent.TimeoutException
 import scala.concurrent.duration._
 
-
 class FtpCloudNioFileSystemSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with Eventually {
 
   behavior of "FtpCloudNioFileSystemSpec"
@@ -20,11 +19,12 @@ class FtpCloudNioFileSystemSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
   implicit val patience = patienceConfig
 
   it should "lease the number of clients configured, not more, not less" in {
-    val fileSystems = new FtpFileSystems(FtpFileSystems.DefaultConfig.copy(leaseTimeout = Option(1.second), capacity = 3))
+    val fileSystems =
+      new FtpFileSystems(FtpFileSystems.DefaultConfig.copy(leaseTimeout = Option(1.second), capacity = 3))
     val provider = new FtpCloudNioFileSystemProvider(ConfigFactory.empty, FtpAnonymousCredentials, fileSystems)
     val fileSystem = new FtpCloudNioFileSystem(provider, "ftp.example.com") {
       // Override so we don't try to connect to anything
-      override private[ftp] lazy val clientFactory = () => { new FTPClient() }
+      override private[ftp] lazy val clientFactory = () => new FTPClient()
     }
 
     val client1 = fileSystem.leaseClient
@@ -46,7 +46,7 @@ class FtpCloudNioFileSystemSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val provider = new FtpCloudNioFileSystemProvider(ConfigFactory.empty, FtpAnonymousCredentials, fileSystems)
     val fileSystem = new FtpCloudNioFileSystem(provider, "ftp.example.com") {
       // Override so we don't try to connect to anything
-      override private[ftp] lazy val clientFactory = () => { new FTPClient() }
+      override private[ftp] lazy val clientFactory = () => new FTPClient()
 
       override def leaseClient = {
         val lease = super.leaseClient
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCredentialsSpec.scala b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCredentialsSpec.scala
index 0ba19060ab2..b4262452e35 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCredentialsSpec.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpCredentialsSpec.scala
@@ -17,21 +17,21 @@ class FtpCredentialsSpec extends AnyFlatSpec with Matchers with MockSugar with C
     var loggedInWithAccount: Boolean = false
     var loggedInWithoutAccount: Boolean = false
     val client = mock[FTPClient]
-    client.login(anyString, anyString).responds(_ => {
+    client.login(anyString, anyString).responds { _ =>
       loggedInWithoutAccount = true
       true
-    })
-    client.login(anyString, anyString, anyString).responds(_ => {
+    }
+    client.login(anyString, anyString, anyString).responds { _ =>
       loggedInWithAccount = true
       true
-    })
+    }
 
     FtpAuthenticatedCredentials("user", "password", None).login(client)
     loggedInWithoutAccount shouldBe true
     loggedInWithAccount shouldBe false
 
     // reset
-    loggedInWithoutAccount= false
+    loggedInWithoutAccount = false
 
     FtpAuthenticatedCredentials("user", "password", Option("account")).login(client)
     loggedInWithAccount shouldBe true
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpFileSystemsSpec.scala b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpFileSystemsSpec.scala
index 86f86914103..6a186a0d5f2 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpFileSystemsSpec.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpFileSystemsSpec.scala
@@ -35,8 +35,8 @@ class FtpFileSystemsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     verify(mockCreateFunction).apply(ftpCacheKey)
   }
 
-  class MockFtpFileSystems(conf: FtpFileSystemsConfiguration,
-                           mockCreateFunction: FtpCacheKey => FtpCloudNioFileSystem) extends FtpFileSystems(conf) {
+  class MockFtpFileSystems(conf: FtpFileSystemsConfiguration, mockCreateFunction: FtpCacheKey => FtpCloudNioFileSystem)
+      extends FtpFileSystems(conf) {
     override private[ftp] def createFileSystem(key: FtpCacheKey) = mockCreateFunction(key)
   }
 }
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpUtilSpec.scala b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpUtilSpec.scala
index 0e86194ecbd..1796cef16b9 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpUtilSpec.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/FtpUtilSpec.scala
@@ -16,7 +16,7 @@ class FtpUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "autoRelease"
 
   it should "release the lease when the client fails the operation without throwing" in {
-    val clientPool = new FtpClientPool(1, 10.minutes, () => { new FTPClient })
+    val clientPool = new FtpClientPool(1, 10.minutes, () => new FTPClient)
     val lease = clientPool.acquire()
 
     val action = autoRelease(IO.pure(lease)) { _ =>
@@ -28,7 +28,7 @@ class FtpUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "invalidate the lease when the client fails the operation by throwing" in {
-    val clientPool = new FtpClientPool(1, 10.minutes, () => { new FTPClient })
+    val clientPool = new FtpClientPool(1, 10.minutes, () => new FTPClient)
     val lease = clientPool.acquire()
 
     val action = autoRelease(IO.pure(lease)) { _ =>
@@ -40,7 +40,7 @@ class FtpUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "release the lease when the operation succeeds" in {
-    val clientPool = new FtpClientPool(1, 10.minutes, () => { new FTPClient })
+    val clientPool = new FtpClientPool(1, 10.minutes, () => new FTPClient)
     val lease = clientPool.acquire()
 
     val action = autoRelease(IO.pure(lease)) { _ =>
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/LeaseInputStreamSpec.scala b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/LeaseInputStreamSpec.scala
index 6b70679a239..7042571b993 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/LeaseInputStreamSpec.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/LeaseInputStreamSpec.scala
@@ -22,11 +22,11 @@ class LeaseInputStreamSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     }
     val mockClient = mock[FTPClient]
     var completed: Boolean = false
-    mockClient.completePendingCommand().returns({
+    mockClient.completePendingCommand().returns {
       completed = true
       true
-    })
-    val clientPool = new FtpClientPool(1, 10.minutes, () => { mockClient })
+    }
+    val clientPool = new FtpClientPool(1, 10.minutes, () => mockClient)
     val lease = clientPool.acquire()
     val leasedInputStream = new LeasedInputStream("host", "path", is, lease)
 
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/LeaseOutputStreamSpec.scala b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/LeaseOutputStreamSpec.scala
index ee82de6ffea..5c5bef9b9f4 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/LeaseOutputStreamSpec.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/LeaseOutputStreamSpec.scala
@@ -17,11 +17,11 @@ class LeaseOutputStreamSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     val os = new TestOutputStream
     val mockClient = mock[FTPClient]
     var completed: Boolean = false
-    mockClient.completePendingCommand().returns({
+    mockClient.completePendingCommand().returns {
       completed = true
       true
-    })
-    val clientPool = new FtpClientPool(1, 10.minutes, () => { mockClient })
+    }
+    val clientPool = new FtpClientPool(1, 10.minutes, () => mockClient)
     val lease = clientPool.acquire()
     val leasedOutputStream = new LeasedOutputStream("host", "path", os, lease)
 
diff --git a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/MockFtpFileSystem.scala b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/MockFtpFileSystem.scala
index e3c954c8d24..42716da92cd 100644
--- a/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/MockFtpFileSystem.scala
+++ b/cloud-nio/cloud-nio-impl-ftp/src/test/scala/cloud/nio/impl/ftp/MockFtpFileSystem.scala
@@ -22,15 +22,18 @@ trait MockFtpFileSystem extends BeforeAndAfterAll { this: Suite =>
     connectionPort = Option(fakeFtpServer.getServerControlPort)
   }
 
-  override def afterAll() = {
+  override def afterAll() =
     fakeFtpServer.stop()
-  }
 
-  lazy val ftpFileSystemsConfiguration = FtpFileSystems.DefaultConfig.copy(connectionPort = connectionPort.getOrElse(throw new RuntimeException("Fake FTP server has not been started")))
+  lazy val ftpFileSystemsConfiguration = FtpFileSystems.DefaultConfig.copy(connectionPort =
+    connectionPort.getOrElse(throw new RuntimeException("Fake FTP server has not been started"))
+  )
   lazy val ftpFileSystems = new FtpFileSystems(ftpFileSystemsConfiguration)
 
   // Do not call this before starting the server
-  lazy val mockProvider = {
-    new FtpCloudNioFileSystemProvider(ConfigFactory.empty, FtpAuthenticatedCredentials("test_user", "test_password", None), ftpFileSystems)
-  }
+  lazy val mockProvider =
+    new FtpCloudNioFileSystemProvider(ConfigFactory.empty,
+                                      FtpAuthenticatedCredentials("test_user", "test_password", None),
+                                      ftpFileSystems
+    )
 }
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioBackoff.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioBackoff.scala
index e55031f5caa..eb0ae65df29 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioBackoff.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioBackoff.scala
@@ -6,8 +6,10 @@ import com.google.api.client.util.ExponentialBackOff
 import scala.concurrent.duration.{Duration, FiniteDuration}
 
 trait CloudNioBackoff {
+
   /** Next interval in millis */
   def backoffMillis: Long
+
   /** Get the next instance of backoff. This should be called after every call to backoffMillis */
   def next: CloudNioBackoff
 }
@@ -16,8 +18,8 @@ object CloudNioBackoff {
   private[spi] def newExponentialBackOff(initialInterval: FiniteDuration,
                                          maxInterval: FiniteDuration,
                                          multiplier: Double,
-                                         randomizationFactor: Double,
-                                        ): ExponentialBackOff = {
+                                         randomizationFactor: Double
+  ): ExponentialBackOff =
     new ExponentialBackOff.Builder()
       .setInitialIntervalMillis(initialInterval.toMillis.toInt)
       .setMaxIntervalMillis(maxInterval.toMillis.toInt)
@@ -25,7 +27,6 @@ object CloudNioBackoff {
       .setRandomizationFactor(randomizationFactor)
       .setMaxElapsedTimeMillis(Int.MaxValue)
       .build()
-  }
 }
 
 object CloudNioInitialGapBackoff {
@@ -33,24 +34,25 @@ object CloudNioInitialGapBackoff {
             initialInterval: FiniteDuration,
             maxInterval: FiniteDuration,
             multiplier: Double,
-            randomizationFactor: Double = ExponentialBackOff.DEFAULT_RANDOMIZATION_FACTOR,
-           ): CloudNioInitialGapBackoff = {
+            randomizationFactor: Double = ExponentialBackOff.DEFAULT_RANDOMIZATION_FACTOR
+  ): CloudNioInitialGapBackoff =
     new CloudNioInitialGapBackoff(
       initialGap,
       newExponentialBackOff(
         initialInterval = initialInterval,
         maxInterval = maxInterval,
         multiplier = multiplier,
-        randomizationFactor = randomizationFactor,
+        randomizationFactor = randomizationFactor
       )
     )
-  }
 }
 
-case class CloudNioInitialGapBackoff(initialGapMillis: FiniteDuration, googleBackoff: ExponentialBackOff) extends CloudNioBackoff {
+case class CloudNioInitialGapBackoff(initialGapMillis: FiniteDuration, googleBackoff: ExponentialBackOff)
+    extends CloudNioBackoff {
   assert(initialGapMillis.compareTo(Duration.Zero) != 0, "Initial gap cannot be null, use SimpleBackoff instead.")
 
   override val backoffMillis: Long = initialGapMillis.toMillis
+
   /** Switch to a SimpleExponentialBackoff after the initial gap has been used */
   override def next = new CloudNioSimpleExponentialBackoff(googleBackoff)
 }
@@ -59,21 +61,21 @@ object CloudNioSimpleExponentialBackoff {
   def apply(initialInterval: FiniteDuration,
             maxInterval: FiniteDuration,
             multiplier: Double,
-            randomizationFactor: Double = ExponentialBackOff.DEFAULT_RANDOMIZATION_FACTOR,
-           ): CloudNioSimpleExponentialBackoff = {
+            randomizationFactor: Double = ExponentialBackOff.DEFAULT_RANDOMIZATION_FACTOR
+  ): CloudNioSimpleExponentialBackoff =
     new CloudNioSimpleExponentialBackoff(
       newExponentialBackOff(
         initialInterval = initialInterval,
         maxInterval = maxInterval,
         multiplier = multiplier,
-        randomizationFactor = randomizationFactor,
+        randomizationFactor = randomizationFactor
       )
     )
-  }
 }
 
 case class CloudNioSimpleExponentialBackoff(googleBackoff: ExponentialBackOff) extends CloudNioBackoff {
   override def backoffMillis: Long = googleBackoff.nextBackOffMillis()
+
   /** google ExponentialBackOff is mutable so we can keep returning the same instance */
   override def next: CloudNioBackoff = this
 }
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioDirectoryStream.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioDirectoryStream.scala
index 909c1fc54db..25d0f34e7dc 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioDirectoryStream.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioDirectoryStream.scala
@@ -13,24 +13,19 @@ class CloudNioDirectoryStream(
 
   override def iterator(): java.util.Iterator[Path] = pathStream().filterNot(_ == prefix).iterator.asJava
 
-  private[this] def pathStream(markerOption: Option[String] = None): LazyList[Path] = {
+  private[this] def pathStream(markerOption: Option[String] = None): LazyList[Path] =
     listNext(markerOption) match {
       case CloudNioFileList(keys, Some(marker)) =>
         keys.to(LazyList).map(toPath) ++ pathStream(Option(marker))
       case CloudNioFileList(keys, None) =>
         keys.to(LazyList).map(toPath)
     }
-  }
 
-  private[this] def toPath(key: String): Path = {
+  private[this] def toPath(key: String): Path =
     prefix.getFileSystem.getPath("/" + key)
-  }
 
-  private[this] def listNext(markerOption: Option[String]): CloudNioFileList = {
-    retry.from(
-      () => fileProvider.listObjects(prefix.cloudHost, prefix.cloudPath, markerOption)
-    )
-  }
+  private[this] def listNext(markerOption: Option[String]): CloudNioFileList =
+    retry.from(() => fileProvider.listObjects(prefix.cloudHost, prefix.cloudPath, markerOption))
 
   override def close(): Unit = {}
 
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileAttributeView.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileAttributeView.scala
index 7cc34400676..852951784ac 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileAttributeView.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileAttributeView.scala
@@ -11,21 +11,17 @@ final case class CloudNioFileAttributeView(
 ) extends BasicFileAttributeView {
   override def name(): String = CloudNioFileAttributeView.Name
 
-  override def readAttributes(): CloudNioFileAttributes = {
+  override def readAttributes(): CloudNioFileAttributes =
     if (isDirectory) {
       CloudNioDirectoryAttributes(cloudNioPath)
     } else {
       retry
-        .from(
-          () => fileProvider.fileAttributes(cloudNioPath.cloudHost, cloudNioPath.cloudPath)
-        )
+        .from(() => fileProvider.fileAttributes(cloudNioPath.cloudHost, cloudNioPath.cloudPath))
         .getOrElse(throw new FileNotFoundException(cloudNioPath.uriAsString))
     }
-  }
 
-  override def setTimes(lastModifiedTime: FileTime, lastAccessTime: FileTime, createTime: FileTime): Unit = {
+  override def setTimes(lastModifiedTime: FileTime, lastAccessTime: FileTime, createTime: FileTime): Unit =
     throw new UnsupportedOperationException
-  }
 }
 
 object CloudNioFileAttributeView {
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystem.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystem.scala
index 8b93419f350..43384330388 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystem.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystem.scala
@@ -20,49 +20,40 @@ class CloudNioFileSystem(override val provider: CloudNioFileSystemProvider, val
     // do nothing currently.
   }
 
-  override def isOpen: Boolean = {
+  override def isOpen: Boolean =
     true
-  }
 
-  override def isReadOnly: Boolean = {
+  override def isReadOnly: Boolean =
     false
-  }
 
-  override def getSeparator: String = {
+  override def getSeparator: String =
     CloudNioFileSystem.Separator
-  }
 
-  override def getRootDirectories: java.lang.Iterable[Path] = {
+  override def getRootDirectories: java.lang.Iterable[Path] =
     Set[Path](getPath(UnixPath.Root)).asJava
-  }
 
-  override def getFileStores: java.lang.Iterable[FileStore] = {
+  override def getFileStores: java.lang.Iterable[FileStore] =
     Set.empty[FileStore].asJava
-  }
 
-  override def getPathMatcher(syntaxAndPattern: String): PathMatcher = {
+  override def getPathMatcher(syntaxAndPattern: String): PathMatcher =
     FileSystems.getDefault.getPathMatcher(syntaxAndPattern)
-  }
 
-  override def getUserPrincipalLookupService: UserPrincipalLookupService = {
+  override def getUserPrincipalLookupService: UserPrincipalLookupService =
     throw new UnsupportedOperationException
-  }
 
-  override def newWatchService(): WatchService = {
+  override def newWatchService(): WatchService =
     throw new UnsupportedOperationException
-  }
 
-  override def supportedFileAttributeViews(): java.util.Set[String] = {
+  override def supportedFileAttributeViews(): java.util.Set[String] =
     Set("basic", CloudNioFileAttributeView.Name).asJava
-  }
 
   def canEqual(other: Any): Boolean = other.isInstanceOf[CloudNioFileSystem]
 
   override def equals(other: Any): Boolean = other match {
     case that: CloudNioFileSystem =>
       (that canEqual this) &&
-        provider == that.provider &&
-        host == that.host
+      provider == that.provider &&
+      host == that.host
     case _ => false
   }
 
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystemProvider.scala
index 9b79e308afd..c78d30d2dce 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioFileSystemProvider.scala
@@ -3,7 +3,7 @@ package cloud.nio.spi
 import java.net.URI
 import java.nio.channels.SeekableByteChannel
 import java.nio.file._
-import java.nio.file.attribute.{BasicFileAttributeView, BasicFileAttributes, FileAttribute, FileAttributeView}
+import java.nio.file.attribute.{BasicFileAttributes, BasicFileAttributeView, FileAttribute, FileAttributeView}
 import java.nio.file.spi.FileSystemProvider
 
 import com.typesafe.config.{Config, ConfigFactory}
@@ -64,9 +64,8 @@ abstract class CloudNioFileSystemProvider extends FileSystemProvider {
     newCloudNioFileSystem(uri.toString, config)
   }
 
-  override def getPath(uri: URI): CloudNioPath = {
+  override def getPath(uri: URI): CloudNioPath =
     getFileSystem(uri).getPath(uri.getPath)
-  }
 
   override def newByteChannel(
     path: Path,
@@ -75,7 +74,7 @@ abstract class CloudNioFileSystemProvider extends FileSystemProvider {
   ): SeekableByteChannel = {
     val cloudNioPath = CloudNioPath.checkPath(path)
 
-    for (opt <- options.asScala) {
+    for (opt <- options.asScala)
       opt match {
         case StandardOpenOption.READ | StandardOpenOption.WRITE | StandardOpenOption.SPARSE |
             StandardOpenOption.TRUNCATE_EXISTING | StandardOpenOption.CREATE | StandardOpenOption.CREATE_NEW =>
@@ -84,7 +83,6 @@ abstract class CloudNioFileSystemProvider extends FileSystemProvider {
             StandardOpenOption.SYNC =>
           throw new UnsupportedOperationException(opt.toString)
       }
-    }
 
     if (options.contains(StandardOpenOption.READ) && options.contains(StandardOpenOption.WRITE)) {
       throw new UnsupportedOperationException("Cannot open a READ+WRITE channel")
@@ -95,70 +93,64 @@ abstract class CloudNioFileSystemProvider extends FileSystemProvider {
     }
   }
 
-  protected def cloudNioReadChannel(retry: CloudNioRetry, cloudNioPath: CloudNioPath): CloudNioReadChannel = new CloudNioReadChannel(fileProvider, retry, cloudNioPath)
-  protected def cloudNioWriteChannel(retry: CloudNioRetry, cloudNioPath: CloudNioPath): CloudNioWriteChannel = new CloudNioWriteChannel(fileProvider, retry, cloudNioPath)
+  protected def cloudNioReadChannel(retry: CloudNioRetry, cloudNioPath: CloudNioPath): CloudNioReadChannel =
+    new CloudNioReadChannel(fileProvider, retry, cloudNioPath)
+  protected def cloudNioWriteChannel(retry: CloudNioRetry, cloudNioPath: CloudNioPath): CloudNioWriteChannel =
+    new CloudNioWriteChannel(fileProvider, retry, cloudNioPath)
 
-  override def createDirectory(dir: Path, attrs: FileAttribute[_]*): Unit = retry.from(() => {
+  override def createDirectory(dir: Path, attrs: FileAttribute[_]*): Unit = retry.from { () =>
     val cloudNioPath = CloudNioPath.checkPath(dir)
     fileProvider.createDirectory(cloudNioPath.cloudHost, cloudNioPath.cloudPath)
-  })
+  }
 
   override def deleteIfExists(path: Path): Boolean = {
     val cloudNioPath = CloudNioPath.checkPath(path)
 
     if (checkDirectoryExists(cloudNioPath)) {
-      val hasObjects = retry.from(
-        () => fileProvider.existsPaths(cloudNioPath.cloudHost, cloudNioPath.cloudPath)
-      )
+      val hasObjects = retry.from(() => fileProvider.existsPaths(cloudNioPath.cloudHost, cloudNioPath.cloudPath))
       if (hasObjects) {
         throw new UnsupportedOperationException("Can not delete a non-empty directory")
       } else {
         true
       }
     } else {
-      retry.from(
-        () => fileProvider.deleteIfExists(cloudNioPath.cloudHost, cloudNioPath.cloudPath)
-      )
+      retry.from(() => fileProvider.deleteIfExists(cloudNioPath.cloudHost, cloudNioPath.cloudPath))
     }
   }
 
-  override def delete(path: Path): Unit = {
+  override def delete(path: Path): Unit =
     if (!deleteIfExists(path)) {
       val cloudNioPath = CloudNioPath.checkPath(path)
       throw new NoSuchFileException(cloudNioPath.uriAsString)
     }
-  }
 
   override def copy(source: Path, target: Path, options: CopyOption*): Unit = {
     val sourceCloudNioPath = CloudNioPath.checkPath(source)
     val targetCloudNioPath = CloudNioPath.checkPath(target)
 
     if (sourceCloudNioPath != targetCloudNioPath) {
-      retry.from(
-        () =>
-          fileProvider.copy(
-            sourceCloudNioPath.cloudHost,
-            sourceCloudNioPath.cloudPath,
-            targetCloudNioPath.cloudHost,
-            targetCloudNioPath.cloudPath
-          )
+      retry.from(() =>
+        fileProvider.copy(
+          sourceCloudNioPath.cloudHost,
+          sourceCloudNioPath.cloudPath,
+          targetCloudNioPath.cloudHost,
+          targetCloudNioPath.cloudPath
+        )
       )
     }
   }
 
   override def move(source: Path, target: Path, options: CopyOption*): Unit = {
-    for (option <- options) {
+    for (option <- options)
       if (option == StandardCopyOption.ATOMIC_MOVE)
         throw new AtomicMoveNotSupportedException(null, null, "Atomic move unsupported")
-    }
     copy(source, target, options: _*)
     delete(source)
     ()
   }
 
-  override def isSameFile(path: Path, path2: Path): Boolean = {
+  override def isSameFile(path: Path, path2: Path): Boolean =
     CloudNioPath.checkPath(path).equals(CloudNioPath.checkPath(path2))
-  }
 
   override def isHidden(path: Path): Boolean = {
     CloudNioPath.checkPath(path)
@@ -174,8 +166,8 @@ abstract class CloudNioFileSystemProvider extends FileSystemProvider {
 
     val cloudNioPath = CloudNioPath.checkPath(path)
 
-    val exists = checkDirectoryExists(cloudNioPath) || retry.from(
-      () => fileProvider.existsPath(cloudNioPath.cloudHost, cloudNioPath.cloudPath)
+    val exists = checkDirectoryExists(cloudNioPath) || retry.from(() =>
+      fileProvider.existsPath(cloudNioPath.cloudHost, cloudNioPath.cloudPath)
     )
 
     if (!exists) {
@@ -183,12 +175,11 @@ abstract class CloudNioFileSystemProvider extends FileSystemProvider {
     }
   }
 
-  def checkDirectoryExists(cloudNioPath: CloudNioPath): Boolean = {
+  def checkDirectoryExists(cloudNioPath: CloudNioPath): Boolean =
     // Anything that "seems" like a directory exists. Otherwise see if the path with a "/" contains files on the cloud.
-    (usePseudoDirectories && cloudNioPath.seemsLikeDirectory) || retry.from(
-      () => fileProvider.existsPaths(cloudNioPath.cloudHost, cloudNioPath.cloudPath + "/")
+    (usePseudoDirectories && cloudNioPath.seemsLikeDirectory) || retry.from(() =>
+      fileProvider.existsPaths(cloudNioPath.cloudHost, cloudNioPath.cloudPath + "/")
     )
-  }
 
   override def getFileAttributeView[V <: FileAttributeView](
     path: Path,
@@ -205,9 +196,8 @@ abstract class CloudNioFileSystemProvider extends FileSystemProvider {
     CloudNioFileAttributeView(fileProvider, retry, cloudNioPath, isDirectory).asInstanceOf[V]
   }
 
-  override def readAttributes(path: Path, attributes: String, options: LinkOption*): java.util.Map[String, AnyRef] = {
+  override def readAttributes(path: Path, attributes: String, options: LinkOption*): java.util.Map[String, AnyRef] =
     throw new UnsupportedOperationException
-  }
 
   override def readAttributes[A <: BasicFileAttributes](
     path: Path,
@@ -224,9 +214,7 @@ abstract class CloudNioFileSystemProvider extends FileSystemProvider {
       CloudNioDirectoryAttributes(cloudNioPath).asInstanceOf[A]
     } else {
       retry
-        .from(
-          () => fileProvider.fileAttributes(cloudNioPath.cloudHost, cloudNioPath.cloudPath)
-        )
+        .from(() => fileProvider.fileAttributes(cloudNioPath.cloudHost, cloudNioPath.cloudPath))
         .map(_.asInstanceOf[A])
         .getOrElse(throw new NoSuchFileException(cloudNioPath.uriAsString))
     }
@@ -237,16 +225,15 @@ abstract class CloudNioFileSystemProvider extends FileSystemProvider {
     new CloudNioDirectoryStream(fileProvider, retry, cloudNioPath, filter)
   }
 
-  override def setAttribute(path: Path, attribute: String, value: scala.Any, options: LinkOption*): Unit = {
+  override def setAttribute(path: Path, attribute: String, value: scala.Any, options: LinkOption*): Unit =
     throw new UnsupportedOperationException
-  }
 
   def canEqual(other: Any): Boolean = other.isInstanceOf[CloudNioFileSystemProvider]
 
   override def equals(other: Any): Boolean = other match {
     case that: CloudNioFileSystemProvider =>
       (that canEqual this) &&
-        config == that.config
+      config == that.config
     case _ => false
   }
 
@@ -258,7 +245,6 @@ abstract class CloudNioFileSystemProvider extends FileSystemProvider {
 
 object CloudNioFileSystemProvider {
 
-  def defaultConfig(scheme: String): Config = {
+  def defaultConfig(scheme: String): Config =
     ConfigFactory.load.getOrElse(s"cloud.nio.default.$scheme", ConfigFactory.empty)
-  }
 }
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
index ec0c701a9b9..b6803670d39 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
@@ -9,12 +9,11 @@ import scala.jdk.CollectionConverters._
 
 object CloudNioPath {
 
-  def checkPath(path: Path): CloudNioPath = {
+  def checkPath(path: Path): CloudNioPath =
     path match {
       case cloudNioPath: CloudNioPath => cloudNioPath
-      case _                          => throw new ProviderMismatchException(s"Not a CloudNioPath: $path")
+      case _ => throw new ProviderMismatchException(s"Not a CloudNioPath: $path")
     }
-  }
 }
 
 class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: UnixPath) extends Path {
@@ -65,13 +64,12 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
   /**
     * If is relative, returns just the normalized path. If is absolute, return the host + the absolute path.
     */
-  def relativeDependentPath: String = {
+  def relativeDependentPath: String =
     if (unixPath.isAbsolute) {
       cloudHost + "/" + unixPath.toString.stripPrefix("/")
     } else {
       unixPath.normalize().toString
     }
-  }
 
   /**
     * Returns true if the path probably represents a directory, but won't be known until contacting the host.
@@ -84,30 +82,25 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
 
   override def isAbsolute: Boolean = unixPath.isAbsolute
 
-  override def getRoot: CloudNioPath = {
+  override def getRoot: CloudNioPath =
     unixPath.getRoot.map(newPath).orNull
-  }
 
-  override def getFileName: CloudNioPath = {
+  override def getFileName: CloudNioPath =
     unixPath.getFileName.map(newPath).orNull
-  }
 
-  override def getParent: CloudNioPath = {
+  override def getParent: CloudNioPath =
     unixPath.getParent.map(newPath).orNull
-  }
 
   override def getNameCount: Int = unixPath.getNameCount
 
-  override def getName(index: Int): CloudNioPath = {
+  override def getName(index: Int): CloudNioPath =
     unixPath.getName(index).map(newPath).getOrElse(throw new IllegalArgumentException(s"Bad index $index"))
-  }
 
-  override def subpath(beginIndex: Int, endIndex: Int): CloudNioPath = {
+  override def subpath(beginIndex: Int, endIndex: Int): CloudNioPath =
     unixPath
       .subPath(beginIndex, endIndex)
       .map(newPath)
       .getOrElse(throw new IllegalArgumentException(s"Bad range $beginIndex-$endIndex"))
-  }
 
   override def startsWith(other: Path): Boolean = {
     if (!other.isInstanceOf[CloudNioPath]) {
@@ -122,9 +115,8 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
     unixPath.startsWith(that.unixPath)
   }
 
-  override def startsWith(other: String): Boolean = {
+  override def startsWith(other: String): Boolean =
     unixPath.startsWith(UnixPath.getPath(other))
-  }
 
   override def endsWith(other: Path): Boolean = {
     if (!other.isInstanceOf[CloudNioPath]) {
@@ -138,9 +130,8 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
     unixPath.endsWith(that.unixPath)
   }
 
-  override def endsWith(other: String): Boolean = {
+  override def endsWith(other: String): Boolean =
     unixPath.endsWith(UnixPath.getPath(other))
-  }
 
   override def normalize(): CloudNioPath = newPath(unixPath.normalize())
 
@@ -150,9 +141,8 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
     newPath(unixPath.resolve(that.unixPath))
   }
 
-  override def resolve(other: String): CloudNioPath = {
+  override def resolve(other: String): CloudNioPath =
     newPath(unixPath.resolve(UnixPath.getPath(other)))
-  }
 
   override def resolveSibling(other: Path): CloudNioPath = {
     val that = CloudNioPath.checkPath(other)
@@ -160,9 +150,8 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
     newPath(unixPath.resolveSibling(that.unixPath))
   }
 
-  override def resolveSibling(other: String): CloudNioPath = {
+  override def resolveSibling(other: String): CloudNioPath =
     newPath(unixPath.resolveSibling(UnixPath.getPath(other)))
-  }
 
   override def relativize(other: Path): CloudNioPath = {
     val that = CloudNioPath.checkPath(other)
@@ -170,9 +159,8 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
     newPath(unixPath.relativize(that.unixPath))
   }
 
-  override def toAbsolutePath: CloudNioPath = {
+  override def toAbsolutePath: CloudNioPath =
     newPath(unixPath.toAbsolutePath)
-  }
 
   override def toRealPath(options: LinkOption*): CloudNioPath = toAbsolutePath
 
@@ -187,13 +175,12 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
     modifiers: WatchEvent.Modifier*
   ): WatchKey = throw new UnsupportedOperationException
 
-  override def iterator(): java.util.Iterator[Path] = {
+  override def iterator(): java.util.Iterator[Path] =
     if (unixPath.isEmpty || unixPath.isRoot) {
       java.util.Collections.emptyIterator()
     } else {
       unixPath.split().to(LazyList).map(part => newPath(UnixPath.getPath(part)).asInstanceOf[Path]).iterator.asJava
     }
-  }
 
   override def compareTo(other: Path): Int = {
     if (other.isInstanceOf[CloudNioPath]) {
@@ -209,22 +196,19 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
     unixPath.compareTo(that.unixPath)
   }
 
-  override def equals(obj: scala.Any): Boolean = {
+  override def equals(obj: scala.Any): Boolean =
     (this eq obj.asInstanceOf[AnyRef]) ||
-    obj.isInstanceOf[CloudNioPath] &&
-    obj.asInstanceOf[CloudNioPath].cloudHost.equals(cloudHost) &&
-    obj.asInstanceOf[CloudNioPath].unixPath.equals(unixPath)
-  }
+      obj.isInstanceOf[CloudNioPath] &&
+      obj.asInstanceOf[CloudNioPath].cloudHost.equals(cloudHost) &&
+      obj.asInstanceOf[CloudNioPath].unixPath.equals(unixPath)
 
-  override def hashCode(): Int = {
+  override def hashCode(): Int =
     Objects.hash(cloudHost, unixPath)
-  }
 
-  protected def newPath(unixPath: UnixPath): CloudNioPath = {
+  protected def newPath(unixPath: UnixPath): CloudNioPath =
     if (this.unixPath == unixPath) {
       this
     } else {
       new CloudNioPath(filesystem, unixPath)
     }
-  }
 }
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioReadChannel.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioReadChannel.scala
index 1e6020307fa..b8260b9a599 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioReadChannel.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioReadChannel.scala
@@ -2,35 +2,28 @@ package cloud.nio.spi
 
 import java.io.FileNotFoundException
 import java.nio.ByteBuffer
-import java.nio.channels.{
-  ClosedChannelException,
-  NonWritableChannelException,
-  ReadableByteChannel,
-  SeekableByteChannel
-}
+import java.nio.channels.{ClosedChannelException, NonWritableChannelException, ReadableByteChannel, SeekableByteChannel}
 
 class CloudNioReadChannel(fileProvider: CloudNioFileProvider, retry: CloudNioRetry, cloudNioPath: CloudNioPath)
-  extends SeekableByteChannel {
+    extends SeekableByteChannel {
   private var internalPosition: Long = 0
   private var channel: ReadableByteChannel = channelPosition(0)
 
   override def read(dst: ByteBuffer): Int = {
     var resetConnection = false
-    val count = retry.from(
-      () => {
-        try {
-          if (resetConnection) {
-            if (channel.isOpen) channel.close()
-            channel = fileProvider.read(cloudNioPath.cloudHost, cloudNioPath.cloudPath, internalPosition)
-          }
-          channel.read(dst)
-        } catch {
-          case exception: Exception =>
-            resetConnection = true
-            throw exception
+    val count = retry.from { () =>
+      try {
+        if (resetConnection) {
+          if (channel.isOpen) channel.close()
+          channel = fileProvider.read(cloudNioPath.cloudHost, cloudNioPath.cloudPath, internalPosition)
         }
+        channel.read(dst)
+      } catch {
+        case exception: Exception =>
+          resetConnection = true
+          throw exception
       }
-    )
+    }
     if (count > 0)
       internalPosition += count
     count
@@ -50,25 +43,19 @@ class CloudNioReadChannel(fileProvider: CloudNioFileProvider, retry: CloudNioRet
     this
   }
 
-  private def channelPosition(newPosition: Long): ReadableByteChannel = {
-    retry.from(
-      () => fileProvider.read(cloudNioPath.cloudHost, cloudNioPath.cloudPath, newPosition)
-    )
-  }
+  private def channelPosition(newPosition: Long): ReadableByteChannel =
+    retry.from(() => fileProvider.read(cloudNioPath.cloudHost, cloudNioPath.cloudPath, newPosition))
 
-  override def size(): Long = {
+  override def size(): Long =
     retry
-      .from(
-        () => fileSize
-      )
+      .from(() => fileSize)
       .getOrElse(throw new FileNotFoundException(cloudNioPath.uriAsString))
-  }
 
   override def truncate(size: Long): SeekableByteChannel = throw new NonWritableChannelException
 
   override def isOpen: Boolean = channel.isOpen
 
   override def close(): Unit = channel.close()
-  
+
   protected def fileSize = fileProvider.fileAttributes(cloudNioPath.cloudHost, cloudNioPath.cloudPath).map(_.size())
 }
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioRetry.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioRetry.scala
index 9a4028ed859..40c8cba7377 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioRetry.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioRetry.scala
@@ -24,7 +24,7 @@ class CloudNioRetry(config: Config) {
     val delay = backoff.backoffMillis
 
     f() match {
-      case Success(ret)                                        => ret
+      case Success(ret) => ret
       case Failure(exception: Exception) if isFatal(exception) => throw exception
       case Failure(exception: Exception) if !isFatal(exception) =>
         val retriesLeft = if (isTransient(exception)) maxRetries else maxRetries map { _ - 1 }
@@ -38,11 +38,13 @@ class CloudNioRetry(config: Config) {
     }
   }
 
-  def from[A](f: () => A, maxRetries: Option[Int] = Option(defaultMaxRetries), backoff: CloudNioBackoff = defaultBackOff): A = {
+  def from[A](f: () => A,
+              maxRetries: Option[Int] = Option(defaultMaxRetries),
+              backoff: CloudNioBackoff = defaultBackOff
+  ): A =
     fromTry[A](
       () => Try(f()),
       maxRetries,
       backoff
     )
-  }
 }
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioWriteChannel.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioWriteChannel.scala
index 15a9d97213b..232cc25297b 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioWriteChannel.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioWriteChannel.scala
@@ -6,11 +6,8 @@ import java.nio.channels._
 class CloudNioWriteChannel(fileProvider: CloudNioFileProvider, retry: CloudNioRetry, cloudNioPath: CloudNioPath)
     extends SeekableByteChannel {
   private var internalPosition: Long = 0
-  private val channel: WritableByteChannel = {
-    retry.from(
-      () => fileProvider.write(cloudNioPath.cloudHost, cloudNioPath.cloudPath)
-    )
-  }
+  private val channel: WritableByteChannel =
+    retry.from(() => fileProvider.write(cloudNioPath.cloudHost, cloudNioPath.cloudPath))
 
   override def read(dst: ByteBuffer): Int = throw new NonReadableChannelException
 
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
index fb3a2bf8f50..b7d9ed02035 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
@@ -24,7 +24,7 @@ private[spi] object UnixPath {
 
   private def hasTrailingSeparator(path: String): Boolean = !path.isEmpty && path.charAt(path.length - 1) == Separator
 
-  def getPath(path: String): UnixPath = {
+  def getPath(path: String): UnixPath =
     if (path.isEmpty) {
       EmptyPath
     } else if (isRoot(path)) {
@@ -32,7 +32,6 @@ private[spi] object UnixPath {
     } else {
       UnixPath(path)
     }
-  }
 
   def getPath(first: String, more: String*): UnixPath = {
     if (more.isEmpty) {
@@ -40,7 +39,7 @@ private[spi] object UnixPath {
     }
 
     val builder = new StringBuilder(first)
-    for ((part, index) <- more.view.zipWithIndex) {
+    for ((part, index) <- more.view.zipWithIndex)
       if (part.isEmpty) {
         // do nothing
       } else if (isAbsolute(part)) {
@@ -55,7 +54,6 @@ private[spi] object UnixPath {
         builder.append(Separator)
         builder.append(part)
       }
-    }
 
     UnixPath(builder.toString)
   }
@@ -73,14 +71,13 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
 
   def hasTrailingSeparator: Boolean = UnixPath.hasTrailingSeparator(path)
 
-  def seemsLikeDirectory(): Boolean = {
+  def seemsLikeDirectory(): Boolean =
     path.isEmpty ||
-    hasTrailingSeparator ||
-    path.endsWith(".") && (length == 1 || path.charAt(length - 2) == UnixPath.Separator) ||
-    path.endsWith("..") && (length == 2 || path.charAt(length - 3) == UnixPath.Separator)
-  }
+      hasTrailingSeparator ||
+      path.endsWith(".") && (length == 1 || path.charAt(length - 2) == UnixPath.Separator) ||
+      path.endsWith("..") && (length == 2 || path.charAt(length - 3) == UnixPath.Separator)
 
-  def getFileName: Option[UnixPath] = {
+  def getFileName: Option[UnixPath] =
     if (path.isEmpty || isRoot) {
       None
     } else {
@@ -90,7 +87,6 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
         Some(UnixPath(parts.last))
       }
     }
-  }
 
   def getParent: Option[UnixPath] = {
     if (path.isEmpty || isRoot) {
@@ -103,7 +99,7 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
       else
         path.lastIndexOf(UnixPath.Separator.toInt)
     index match {
-      case -1  => if (isAbsolute) Some(UnixPath.RootPath) else None
+      case -1 => if (isAbsolute) Some(UnixPath.RootPath) else None
       case pos => Some(UnixPath(path.substring(0, pos + 1)))
     }
   }
@@ -122,7 +118,7 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
     Try(UnixPath(parts.slice(beginIndex, endIndex).mkString(UnixPath.Separator.toString)))
   }
 
-  def getNameCount: Int = {
+  def getNameCount: Int =
     if (path.isEmpty) {
       1
     } else if (isRoot) {
@@ -130,7 +126,6 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
     } else {
       parts.length
     }
-  }
 
   def getName(index: Int): Try[UnixPath] = {
     if (path.isEmpty) {
@@ -144,7 +139,7 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
     Success(UnixPath(parts(2)))
   }
 
-  def resolve(other: UnixPath): UnixPath = {
+  def resolve(other: UnixPath): UnixPath =
     if (other.path.isEmpty) {
       this
     } else if (other.isAbsolute) {
@@ -154,15 +149,13 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
     } else {
       new UnixPath(path + UnixPath.Separator.toString + other.path)
     }
-  }
 
-  def resolveSibling(other: UnixPath): UnixPath = {
+  def resolveSibling(other: UnixPath): UnixPath =
     getParent match {
       case Some(parent: UnixPath) =>
         parent.resolve(other)
       case None => other
     }
-  }
 
   def relativize(other: UnixPath): UnixPath = {
     if (path.isEmpty) {
@@ -247,21 +240,18 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
 
   def splitReverse(): Iterator[String] = parts.reverseIterator
 
-  def removeBeginningSeparator(): UnixPath = {
+  def removeBeginningSeparator(): UnixPath =
     if (isAbsolute) new UnixPath(path.substring(1)) else this
-  }
 
-  def addTrailingSeparator(): UnixPath = {
+  def addTrailingSeparator(): UnixPath =
     if (hasTrailingSeparator) this else new UnixPath(path + UnixPath.Separator)
-  }
 
-  def removeTrailingSeparator(): UnixPath = {
+  def removeTrailingSeparator(): UnixPath =
     if (!isRoot && hasTrailingSeparator) {
       new UnixPath(path.substring(0, length - 1))
     } else {
       this
     }
-  }
 
   def startsWith(other: UnixPath): Boolean = {
     val me = removeTrailingSeparator()
@@ -279,11 +269,10 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
   }
 
   def startsWith(left: Iterator[String], right: Iterator[String]): Boolean = {
-    while (right.hasNext) {
+    while (right.hasNext)
       if (!left.hasNext || right.next() != left.next()) {
         return false
       }
-    }
     true
   }
 
@@ -310,9 +299,8 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
     if (isAbsolute) Success(this) else Success(currentWorkingDirectory.resolve(this))
   }
 
-  def toAbsolutePath: UnixPath = {
+  def toAbsolutePath: UnixPath =
     if (isAbsolute) this else UnixPath.RootPath.resolve(this)
-  }
 
   def compareTo(other: UnixPath): Int = {
     val me = parts.toList
@@ -327,29 +315,24 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
     }
   }
 
-  override def equals(obj: scala.Any): Boolean = {
+  override def equals(obj: scala.Any): Boolean =
     (this eq obj.asInstanceOf[AnyRef]) || {
       obj.isInstanceOf[UnixPath] && obj.asInstanceOf[UnixPath].path.equals(path)
     }
-  }
 
-  override def length(): Int = {
+  override def length(): Int =
     path.length
-  }
 
-  override def charAt(index: Int): Char = {
+  override def charAt(index: Int): Char =
     path.charAt(index)
-  }
 
-  override def subSequence(start: Int, end: Int): CharSequence = {
+  override def subSequence(start: Int, end: Int): CharSequence =
     path.subSequence(start, end)
-  }
 
-  override def toString: String = {
+  override def toString: String =
     path
-  }
 
-  def initParts(): Array[String] = {
+  def initParts(): Array[String] =
     if (path.isEmpty) {
       Array.empty[String]
     } else {
@@ -359,5 +342,4 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
         path.split(UnixPath.Separator)
       }
     }
-  }
 }
diff --git a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/ChannelUtil.scala b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/ChannelUtil.scala
index 04c9d4cdd3f..bbd1cbaf4db 100644
--- a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/ChannelUtil.scala
+++ b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/ChannelUtil.scala
@@ -26,13 +26,12 @@ object ChannelUtil {
   def pipedStreamWriter(threadName: String)(consumer: InputStream => Unit): WritableByteChannel = {
     val pipe = Pipe.open()
     var threadResult: Option[Try[Unit]] = None
-    val runnable: Runnable = () => {
+    val runnable: Runnable = () =>
       threadResult = Option(
         Try(
           consumer(Channels.newInputStream(pipe.source))
         )
       )
-    }
     val thread = new Thread(runnable, threadName)
     thread.setDaemon(true)
     thread.start()
diff --git a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/CloudNioFiles.scala b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/CloudNioFiles.scala
index 162d47d08db..e15cb574031 100644
--- a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/CloudNioFiles.scala
+++ b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/CloudNioFiles.scala
@@ -12,13 +12,12 @@ object CloudNioFiles {
   /**
     * Lists all files under a path.
     */
-  def listRegularFiles(path: Path): Iterator[Path] = {
+  def listRegularFiles(path: Path): Iterator[Path] =
     Files
       .walk(path, Int.MaxValue)
       .iterator
       .asScala
       .filter(Files.isRegularFile(_))
-  }
 
   /**
     * Returns an iterator of all regular files under sourcePath mapped relatively to targetPath.
diff --git a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/CloudNioPaths.scala b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/CloudNioPaths.scala
index 7448b272426..66ab48100c6 100644
--- a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/CloudNioPaths.scala
+++ b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/CloudNioPaths.scala
@@ -21,15 +21,14 @@ object CloudNioPaths {
     * @see [[cloud.nio.util.CloudNioPaths#showAbsolute(java.nio.file.Path)]]
     * @see [[cloud.nio.spi.CloudNioPath#uriAsString()]]
     */
-  def get(filePath: String): Path = {
-    try {
+  def get(filePath: String): Path =
+    try
       // TODO: softer parsing using Guava UrlEscapers. May also be better to list the providers ourselves if possible.
       Paths.get(new URI(filePath))
-    } catch {
-      case _: URISyntaxException                                               => Paths.get(filePath)
+    catch {
+      case _: URISyntaxException => Paths.get(filePath)
       case iae: IllegalArgumentException if iae.getMessage == "Missing scheme" => Paths.get(filePath)
     }
-  }
 
   /**
     * Return a path in a way reciprocal with [[cloud.nio.util.CloudNioPaths#get]].
@@ -38,12 +37,11 @@ object CloudNioPaths {
     * @see [[cloud.nio.util.CloudNioPaths#showRelative(java.nio.file.Path)]]
     * @see [[cloud.nio.spi.CloudNioPath#uriAsString()]]
     */
-  def showAbsolute(path: Path): String = {
+  def showAbsolute(path: Path): String =
     path match {
       case cloudNioPath: CloudNioPath => cloudNioPath.uriAsString
-      case _                          => path.toAbsolutePath.toString
+      case _ => path.toAbsolutePath.toString
     }
-  }
 
   /**
     * When the path is relative returns a relative path in a way reciprocal with resolve.
@@ -53,11 +51,10 @@ object CloudNioPaths {
     * @see [[java.nio.file.Path#resolve(java.nio.file.Path)]]
     * @see [[cloud.nio.spi.CloudNioPath#uriAsString()]]
     */
-  def showRelative(path: Path): String = {
+  def showRelative(path: Path): String =
     path match {
       case cloudNioPath: CloudNioPath => cloudNioPath.relativeDependentPath
-      case _ if !path.isAbsolute      => path.normalize().toString
-      case _                          => path.getRoot.relativize(path).normalize().toString
+      case _ if !path.isAbsolute => path.normalize().toString
+      case _ => path.getRoot.relativize(path).normalize().toString
     }
-  }
 }
diff --git a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/IoUtil.scala b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/IoUtil.scala
index 0ff44ce2dd0..f8c7921d0d8 100644
--- a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/IoUtil.scala
+++ b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/IoUtil.scala
@@ -11,24 +11,21 @@ object IoUtil {
 
       type ACC = IO[Either[NonEmptyList[Exception], A]]
 
-      def attemptHead(headIo: IO[A]): ACC = {
+      def attemptHead(headIo: IO[A]): ACC =
         attemptIo(NonEmptyList.one)(headIo)
-      }
 
-      def attemptAcc(accIo: ACC, nextIo: IO[A]): ACC = {
+      def attemptAcc(accIo: ACC, nextIo: IO[A]): ACC =
         accIo flatMap {
-          case Right(previousSuccess)   => IO.pure(Right(previousSuccess))
+          case Right(previousSuccess) => IO.pure(Right(previousSuccess))
           case Left(previousExceptions) => attemptIo(_ :: previousExceptions)(nextIo)
         }
-      }
 
-      def attemptIo(f: Exception => NonEmptyList[Exception])(io: IO[A]): ACC = {
+      def attemptIo(f: Exception => NonEmptyList[Exception])(io: IO[A]): ACC =
         io.attempt flatMap {
-          case Right(success)             => IO.pure(Right(success))
+          case Right(success) => IO.pure(Right(success))
           case Left(exception: Exception) => IO.pure(Left(f(exception)))
-          case Left(throwable)            => throw throwable
+          case Left(throwable) => throw throwable
         }
-      }
 
       val res: ACC = tries.tail.foldLeft(attemptHead(tries.head))(attemptAcc)
 
diff --git a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/TryWithResource.scala b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/TryWithResource.scala
index 326a1821d84..f43ad24cb1f 100644
--- a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/TryWithResource.scala
+++ b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/TryWithResource.scala
@@ -20,17 +20,17 @@ object TryWithResource {
       case x: Throwable =>
         t = Option(x)
         throw x
-    } finally {
+    } finally
       resource foreach { r =>
-        try {
+        try
           r.close()
-        } catch {
-          case y: Throwable => t match {
-            case Some(_t) => _t.addSuppressed(y)
-            case None => throw y
-          }
+        catch {
+          case y: Throwable =>
+            t match {
+              case Some(_t) => _t.addSuppressed(y)
+              case None => throw y
+            }
         }
       }
-    }
   }
 }
diff --git a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/VersionUtil.scala b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/VersionUtil.scala
index 019dbe81caf..c11651879fa 100644
--- a/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/VersionUtil.scala
+++ b/cloud-nio/cloud-nio-util/src/main/scala/cloud/nio/util/VersionUtil.scala
@@ -35,19 +35,17 @@ object VersionUtil {
     * @param default     What to return when the version cannot be found. The parameter passed is the `projectName`.
     * @return The version from the conf or the default
     */
-  def getVersion(projectName: String, default: String => String = defaultMessage): String = {
+  def getVersion(projectName: String, default: String => String = defaultMessage): String =
     ConfigFactory
       .load(versionConf(projectName))
       .as[Option[String]](versionProperty(projectName))
       .getOrElse(default(projectName))
-  }
 
   /**
     * Instead of returning a version, states that the version conf will be generated by sbt.
     */
-  def defaultMessage(projectName: String): String = {
+  def defaultMessage(projectName: String): String =
     s"${versionConf(projectName)}-to-be-generated-by-sbt"
-  }
 
   /**
     * A regex compatible with the dependency constants in project/Dependencies.scala.
@@ -62,7 +60,7 @@ object VersionUtil {
     * @return The dependency version from project/Dependencies.scala
     * @throws RuntimeException If the dependency cannot be found
     */
-  def sbtDependencyVersion(dependencyName: String)(projectName: String): String = {
+  def sbtDependencyVersion(dependencyName: String)(projectName: String): String =
     try {
       val dependencies = Paths.get("project/Dependencies.scala").toAbsolutePath
       val lines = Files.readAllLines(dependencies).asScala
@@ -79,6 +77,5 @@ object VersionUtil {
           e
         )
     }
-  }
 
 }
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/AwsConfiguration.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/AwsConfiguration.scala
index 1aca98c9efd..df2cef13bde 100644
--- a/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/AwsConfiguration.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/AwsConfiguration.scala
@@ -46,16 +46,16 @@ import software.amazon.awssdk.regions.Region
 
 final case class AwsConfiguration private (applicationName: String,
                                            authsByName: Map[String, AwsAuthMode],
-                                           strRegion: Option[String]) {
+                                           strRegion: Option[String]
+) {
 
-  def auth(name: String): ErrorOr[AwsAuthMode] = {
+  def auth(name: String): ErrorOr[AwsAuthMode] =
     authsByName.get(name) match {
       case None =>
         val knownAuthNames = authsByName.keys.mkString(", ")
         s"`aws` configuration stanza does not contain an auth named '$name'.  Known auth names: $knownAuthNames".invalidNel
       case Some(a) => a.validNel
     }
-  }
 
   def region: Option[Region] = strRegion.map(Region.of)
 }
@@ -77,7 +77,7 @@ object AwsConfiguration {
 
     val awsConfig = config.getConfig("aws")
 
-    val appName = validate { awsConfig.as[String]("application-name") }
+    val appName = validate(awsConfig.as[String]("application-name"))
 
     val region: Option[String] =
       awsConfig.getAs[String]("region")
@@ -88,13 +88,16 @@ object AwsConfiguration {
         (authConfig.getAs[String]("access-key"), authConfig.getAs[String]("secret-key")) match {
           case (Some(accessKey), Some(secretKey)) =>
             CustomKeyMode(name, accessKey, secretKey, region)
-          case _ => throw new ConfigException.Generic(s"""Access key and/or secret """ +
-            s"""key missing for service account "$name". See reference.conf under the aws.auth, """ +
-            s"""custom key section for details of required configuration.""")
+          case _ =>
+            throw new ConfigException.Generic(
+              s"""Access key and/or secret """ +
+                s"""key missing for service account "$name". See reference.conf under the aws.auth, """ +
+                s"""custom key section for details of required configuration."""
+            )
         }
       }
 
-      def defaultAuth(authConfig: Config, name: String, region: Option[String]): ErrorOr[AwsAuthMode] =  validate {
+      def defaultAuth(authConfig: Config, name: String, region: Option[String]): ErrorOr[AwsAuthMode] = validate {
         DefaultMode(name, region)
       }
 
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/auth/AwsAuthMode.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/auth/AwsAuthMode.scala
index b8c351c4185..7335441ea80 100644
--- a/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/auth/AwsAuthMode.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/auth/AwsAuthMode.scala
@@ -52,9 +52,8 @@ sealed trait AwsAuthMode {
   /**
     * Validate the auth mode against provided options
     */
-  def validate(options: OptionLookup): Unit = {
+  def validate(options: OptionLookup): Unit =
     ()
-  }
 
   /**
    * The name of the auth mode
@@ -72,27 +71,30 @@ sealed trait AwsAuthMode {
     * All traits in this file are sealed, all classes final, meaning things
     * like Mockito or other java/scala overrides cannot work.
     */
-   private[auth] var credentialValidation: (AwsCredentialsProvider, Option[String]) => Unit =
-     (provider: AwsCredentialsProvider, region: Option[String]) => {
-       val builder = StsClient.builder
-
-       //If the region argument exists in config, set it in the builder.
-       //Otherwise it is left unset and the AwsCredentialsProvider will be responsible for sourcing a region
-       region.map(Region.of).foreach(builder.region)
-
-       // make an essentially no-op call just to assure ourselves the credentials from our provider are valid
-       builder.credentialsProvider(provider)
-         .build
-         .getCallerIdentity(GetCallerIdentityRequest.builder.build)
-       ()
-     }
-
-  protected def validateCredential(provider: AwsCredentialsProvider, region: Option[String]) = {
+  private[auth] var credentialValidation: (AwsCredentialsProvider, Option[String]) => Unit =
+    (provider: AwsCredentialsProvider, region: Option[String]) => {
+      val builder = StsClient.builder
+
+      // If the region argument exists in config, set it in the builder.
+      // Otherwise it is left unset and the AwsCredentialsProvider will be responsible for sourcing a region
+      region.map(Region.of).foreach(builder.region)
+
+      // make an essentially no-op call just to assure ourselves the credentials from our provider are valid
+      builder
+        .credentialsProvider(provider)
+        .build
+        .getCallerIdentity(GetCallerIdentityRequest.builder.build)
+      ()
+    }
+
+  protected def validateCredential(provider: AwsCredentialsProvider, region: Option[String]) =
     Try(credentialValidation(provider, region)) match {
-      case Failure(ex) => throw new RuntimeException(s"Credentials produced by the AWS provider ${name} are invalid: ${ex.getMessage}", ex)
+      case Failure(ex) =>
+        throw new RuntimeException(s"Credentials produced by the AWS provider ${name} are invalid: ${ex.getMessage}",
+                                   ex
+        )
       case Success(_) => provider
     }
-  }
 }
 
 /**
@@ -114,11 +116,8 @@ object CustomKeyMode
  * @param secretKey static AWS secret key
  * @param region an optional AWS region
  */
-final case class CustomKeyMode(override val name: String,
-                                    accessKey: String,
-                                    secretKey: String,
-                                    region: Option[String]
-                                    ) extends AwsAuthMode {
+final case class CustomKeyMode(override val name: String, accessKey: String, secretKey: String, region: Option[String])
+    extends AwsAuthMode {
   private lazy val _provider: AwsCredentialsProvider = {
     // make a provider locked to the given access and secret
     val p = StaticCredentialsProvider.create(AwsBasicCredentials.create(accessKey, secretKey))
@@ -159,17 +158,17 @@ final case class DefaultMode(override val name: String, region: Option[String])
  * @param region an optional AWS region
  */
 final case class AssumeRoleMode(override val name: String,
-                          baseAuthName: String,
-                          roleArn: String,
-                          externalId: String,
-                          region: Option[String]
-                          ) extends AwsAuthMode {
+                                baseAuthName: String,
+                                roleArn: String,
+                                externalId: String,
+                                region: Option[String]
+) extends AwsAuthMode {
 
   private lazy val _provider: AwsCredentialsProvider = {
     // we need to perform operations on STS using the credentials provided from the baseAuthName
     val stsBuilder = StsClient.builder
     region.foreach(str => stsBuilder.region(Region.of(str)))
-    baseAuthObj match{
+    baseAuthObj match {
       case Some(auth) => stsBuilder.credentialsProvider(auth.provider())
       case _ => throw new RuntimeException(s"Base auth configuration required for assume role")
     }
@@ -179,7 +178,7 @@ final case class AssumeRoleMode(override val name: String,
       .roleArn(roleArn)
       .durationSeconds(3600)
       .roleSessionName("cromwell")
-    if (! externalId.isEmpty) assumeRoleBuilder.externalId(externalId)
+    if (!externalId.isEmpty) assumeRoleBuilder.externalId(externalId)
 
     // this provider is one that will handle refreshing the assume-role creds when needed
     val p = StsAssumeRoleCredentialsProvider.builder
@@ -195,23 +194,21 @@ final case class AssumeRoleMode(override val name: String,
   // start a background thread to perform the refresh
   override def provider(): AwsCredentialsProvider = _provider
 
-  private var baseAuthObj : Option[AwsAuthMode] = None
+  private var baseAuthObj: Option[AwsAuthMode] = None
 
-  def assign(baseAuth: AwsAuthMode) : Unit = {
+  def assign(baseAuth: AwsAuthMode): Unit =
     baseAuthObj match {
       case None => baseAuthObj = Some(baseAuth)
       case _ => throw new RuntimeException(s"Base auth object has already been assigned")
     }
-  }
 
   // We want to allow our tests access to the value
   // of the baseAuthObj
-  def baseAuthentication() : AwsAuthMode = {
+  def baseAuthentication(): AwsAuthMode =
     baseAuthObj match {
       case Some(o) => o
       case _ => throw new RuntimeException(s"Base auth object has not been set")
     }
-  }
 }
 
 class OptionLookupException(val key: String, cause: Throwable) extends RuntimeException(key, cause)
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/s3/S3Storage.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/s3/S3Storage.scala
index 8ab07f37064..8caf8aa3fb1 100644
--- a/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/s3/S3Storage.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/aws/s3/S3Storage.scala
@@ -60,13 +60,13 @@ object S3Storage {
     builder.build
   }
 
-  def s3Client(provider: AwsCredentialsProvider, region: Option[Region]): S3Client = {
+  def s3Client(provider: AwsCredentialsProvider, region: Option[Region]): S3Client =
     s3Client(s3Configuration(), provider, region)
-  }
 
   def s3Configuration(accelerateModeEnabled: Boolean = false,
                       dualstackEnabled: Boolean = false,
-                      pathStyleAccessEnabled: Boolean = false): S3Configuration = {
+                      pathStyleAccessEnabled: Boolean = false
+  ): S3Configuration = {
 
     @nowarn("msg=method dualstackEnabled in trait Builder is deprecated")
     val builder = S3Configuration.builder
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala
index 200b162c614..d3d66e1bafc 100644
--- a/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureCredentials.scala
@@ -34,9 +34,11 @@ case object AzureCredentials {
       .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
 
   def getAccessToken(identityClientId: Option[String] = None): ErrorOr[String] = {
-    val credentials = identityClientId.foldLeft(defaultCredentialBuilder) {
-      (builder, clientId) => builder.managedIdentityClientId(clientId)
-    }.build()
+    val credentials = identityClientId
+      .foldLeft(defaultCredentialBuilder) { (builder, clientId) =>
+        builder.managedIdentityClientId(clientId)
+      }
+      .build()
 
     Try(
       credentials
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureUtils.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureUtils.scala
index 09cf5f3869d..dd379ed3564 100644
--- a/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureUtils.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/azure/AzureUtils.scala
@@ -14,6 +14,7 @@ import scala.jdk.CollectionConverters.IterableHasAsScala
 import scala.util.{Failure, Success, Try}
 
 object AzureUtils {
+
   /**
     * Generates a BlobContainerClient that can interact with the specified container. Authenticates using the local azure client running on the same machine.
     * @param blobContainer     Name of the blob container. Looks something like "my-blob-container".
@@ -21,10 +22,16 @@ object AzureUtils {
     * @param subscription      Azure subscription. A globally unique identifier. If not provided, a default subscription will be used.
     * @return A blob container client capable of interacting with the specified container.
     */
-  def buildContainerClientFromLocalEnvironment(blobContainer: String, azureEndpoint: String, subscription : Option[String]): Try[BlobContainerClient] = {
+  def buildContainerClientFromLocalEnvironment(blobContainer: String,
+                                               azureEndpoint: String,
+                                               subscription: Option[String]
+  ): Try[BlobContainerClient] = {
     def parseURI(string: String): Try[URI] = Try(URI.create(UrlEscapers.urlFragmentEscaper().escape(string)))
-    def parseStorageAccount(uri: URI): Try[String] = uri.getHost.split("\\.").find(_.nonEmpty)
-      .map(Success(_)).getOrElse(Failure(new Exception("Could not parse storage account")))
+    def parseStorageAccount(uri: URI): Try[String] = uri.getHost
+      .split("\\.")
+      .find(_.nonEmpty)
+      .map(Success(_))
+      .getOrElse(Failure(new Exception("Could not parse storage account")))
 
     val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
 
@@ -32,29 +39,37 @@ object AzureUtils {
       .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
       .build
 
-    def authenticateWithSubscription(sub: String) = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub)
+    def authenticateWithSubscription(sub: String) =
+      AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withSubscription(sub)
 
-    def authenticateWithDefaultSubscription = AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withDefaultSubscription()
+    def authenticateWithDefaultSubscription =
+      AzureResourceManager.authenticate(azureCredentialBuilder, azureProfile).withDefaultSubscription()
 
     def azure = subscription.map(authenticateWithSubscription(_)).getOrElse(authenticateWithDefaultSubscription)
 
-    def findAzureStorageAccount(storageAccountName: String) = azure.storageAccounts.list.asScala.find(_.name.equals(storageAccountName))
-      .map(Success(_)).getOrElse(Failure(new Exception("Azure Storage Account not found.")))
+    def findAzureStorageAccount(storageAccountName: String) = azure.storageAccounts.list.asScala
+      .find(_.name.equals(storageAccountName))
+      .map(Success(_))
+      .getOrElse(Failure(new Exception("Azure Storage Account not found.")))
 
-    def buildBlobContainerClient(credential: StorageSharedKeyCredential, endpointURL: String, blobContainerName: String): BlobContainerClient = {
+    def buildBlobContainerClient(credential: StorageSharedKeyCredential,
+                                 endpointURL: String,
+                                 blobContainerName: String
+    ): BlobContainerClient =
       new BlobContainerClientBuilder()
         .credential(credential)
         .endpoint(endpointURL)
         .containerName(blobContainerName)
         .buildClient()
-    }
 
     def generateBlobContainerClient: Try[BlobContainerClient] = for {
       uri <- parseURI(azureEndpoint)
       configuredAccount <- parseStorageAccount(uri)
       azureAccount <- findAzureStorageAccount(configuredAccount)
       keys = azureAccount.getKeys.asScala
-      key <- keys.headOption.fold[Try[StorageAccountKey]](Failure(new Exception("Storage account has no keys")))(Success(_))
+      key <- keys.headOption.fold[Try[StorageAccountKey]](Failure(new Exception("Storage account has no keys")))(
+        Success(_)
+      )
       first = key.value
       sskc = new StorageSharedKeyCredential(configuredAccount, first)
       bcc = buildBlobContainerClient(sskc, azureEndpoint, blobContainer)
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/GoogleConfiguration.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/GoogleConfiguration.scala
index 2b4a183c121..999a9c2867a 100644
--- a/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/GoogleConfiguration.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/GoogleConfiguration.scala
@@ -18,14 +18,13 @@ import org.slf4j.LoggerFactory
 
 final case class GoogleConfiguration private (applicationName: String, authsByName: Map[String, GoogleAuthMode]) {
 
-  def auth(name: String): ErrorOr[GoogleAuthMode] = {
+  def auth(name: String): ErrorOr[GoogleAuthMode] =
     authsByName.get(name) match {
       case None =>
         val knownAuthNames = authsByName.keys.mkString(", ")
         s"`google` configuration stanza does not contain an auth named '$name'.  Known auth names: $knownAuthNames".invalidNel
       case Some(a) => a.validNel
     }
-  }
 }
 
 object GoogleConfiguration {
@@ -37,7 +36,8 @@ object GoogleConfiguration {
 
   def withCustomTimeouts(httpRequestInitializer: HttpRequestInitializer,
                          connectionTimeout: FiniteDuration = DefaultConnectionTimeout,
-                         readTimeout: FiniteDuration = DefaultReadTimeout): HttpRequestInitializer = {
+                         readTimeout: FiniteDuration = DefaultReadTimeout
+  ): HttpRequestInitializer =
     new HttpRequestInitializer() {
       @throws[IOException]
       override def initialize(httpRequest: HttpRequest): Unit = {
@@ -47,7 +47,6 @@ object GoogleConfiguration {
         ()
       }
     }
-  }
 
   private val log = LoggerFactory.getLogger("GoogleConfiguration")
 
@@ -59,20 +58,27 @@ object GoogleConfiguration {
 
     val googleConfig = config.getConfig("google")
 
-    val appName = validate { googleConfig.as[String]("application-name") }
+    val appName = validate(googleConfig.as[String]("application-name"))
 
     def buildAuth(authConfig: Config): ErrorOr[GoogleAuthMode] = {
 
       def serviceAccountAuth(authConfig: Config, name: String): ErrorOr[GoogleAuthMode] = validate {
         (authConfig.getAs[String]("pem-file"), authConfig.getAs[String]("json-file")) match {
-          case (Some(pem), None) => ServiceAccountMode(name, PemFileFormat(authConfig.as[String]("service-account-id"), pem))
+          case (Some(pem), None) =>
+            ServiceAccountMode(name, PemFileFormat(authConfig.as[String]("service-account-id"), pem))
           case (None, Some(json)) => ServiceAccountMode(name, JsonFileFormat(json))
-          case (None, None) => throw new ConfigException.Generic(s"""No credential configuration was found for service account "$name". See reference.conf under the google.auth, service-account section for supported credential formats.""")
-          case (Some(_), Some(_)) => throw new ConfigException.Generic(s"""Both a pem file and a json file were supplied for service account "$name" in the configuration file. Only one credential file can be supplied for the same service account. Please choose between the two.""")
+          case (None, None) =>
+            throw new ConfigException.Generic(
+              s"""No credential configuration was found for service account "$name". See reference.conf under the google.auth, service-account section for supported credential formats."""
+            )
+          case (Some(_), Some(_)) =>
+            throw new ConfigException.Generic(
+              s"""Both a pem file and a json file were supplied for service account "$name" in the configuration file. Only one credential file can be supplied for the same service account. Please choose between the two."""
+            )
         }
       }
 
-      def userAccountAuth(authConfig: Config, name: String): ErrorOr[GoogleAuthMode] =  validate {
+      def userAccountAuth(authConfig: Config, name: String): ErrorOr[GoogleAuthMode] = validate {
         UserMode(name, authConfig.as[String]("secrets-file"))
       }
 
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/auth/GoogleAuthMode.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/auth/GoogleAuthMode.scala
index e850b53807a..52118303262 100644
--- a/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/auth/GoogleAuthMode.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/auth/GoogleAuthMode.scala
@@ -34,9 +34,8 @@ object GoogleAuthMode {
   type CredentialsValidation = Credentials => Unit
   private[auth] val NoCredentialsValidation = mouse.ignore _
 
-  private def noOptionLookup(string: String): Nothing = {
+  private def noOptionLookup(string: String): Nothing =
     throw new UnsupportedOperationException(s"cannot lookup $string")
-  }
 
   lazy val jsonFactory: GsonFactory = GsonFactory.getDefaultInstance
   lazy val httpTransport: HttpTransport = GoogleNetHttpTransport.newTrustedTransport
@@ -46,33 +45,29 @@ object GoogleAuthMode {
   val DockerCredentialsEncryptionKeyNameKey = "docker_credentials_key_name"
   val DockerCredentialsTokenKey = "docker_credentials_token"
 
-  def checkReadable(file: File): Unit = {
+  def checkReadable(file: File): Unit =
     if (!file.isReadable) throw new FileNotFoundException(s"File $file does not exist or is not readable")
-  }
 
-  def isFatal(ex: Throwable): Boolean = {
+  def isFatal(ex: Throwable): Boolean =
     ex match {
       case http: HttpResponseException =>
         // Using HttpURLConnection fields as com.google.api.client.http.HttpStatusCodes doesn't have Bad Request (400)
         http.getStatusCode == HTTP_UNAUTHORIZED ||
-          http.getStatusCode == HTTP_FORBIDDEN ||
-          http.getStatusCode == HTTP_BAD_REQUEST
+        http.getStatusCode == HTTP_FORBIDDEN ||
+        http.getStatusCode == HTTP_BAD_REQUEST
       case _: OptionLookupException => true
       case _ => false
     }
-  }
 
-  def extract(options: OptionLookup, key: String): String = {
+  def extract(options: OptionLookup, key: String): String =
     Try(options(key)) match {
       case Success(result) => result
       case Failure(throwable) => throw new OptionLookupException(key, throwable)
     }
-  }
 
   /** Used for both checking that the credential is valid and creating a fresh credential. */
-  private def refreshCredentials(credentials: Credentials): Unit = {
+  private def refreshCredentials(credentials: Credentials): Unit =
     credentials.refresh()
-  }
 }
 
 sealed trait GoogleAuthMode extends LazyLogging {
@@ -87,25 +82,22 @@ sealed trait GoogleAuthMode extends LazyLogging {
     * Alias for credentials(GoogleAuthMode.NoOptionLookup, scopes).
     * Only valid for credentials that are NOT externally provided, such as ApplicationDefault.
     */
-  def credentials(scopes: Iterable[String]): OAuth2Credentials = {
+  def credentials(scopes: Iterable[String]): OAuth2Credentials =
     credentials(GoogleAuthMode.NoOptionLookup, scopes)
-  }
 
   /**
     * Alias for credentials(GoogleAuthMode.NoOptionLookup, Nil).
     * Only valid for credentials that are NOT externally provided and do not need scopes, such as ApplicationDefault.
     */
-  private[auth] def credentials(): OAuth2Credentials = {
+  private[auth] def credentials(): OAuth2Credentials =
     credentials(GoogleAuthMode.NoOptionLookup, Nil)
-  }
 
   /**
     * Alias for credentials(options, Nil).
     * Only valid for credentials that are NOT externally provided and do not need scopes, such as ApplicationDefault.
     */
-  private[auth] def credentials(options: OptionLookup): OAuth2Credentials = {
+  private[auth] def credentials(options: OptionLookup): OAuth2Credentials =
     credentials(options, Nil)
-  }
 
   /**
     * Enables swapping out credential validation for various testing purposes ONLY.
@@ -116,7 +108,8 @@ sealed trait GoogleAuthMode extends LazyLogging {
   private[auth] var credentialsValidation: CredentialsValidation = refreshCredentials
 
   protected def validateCredentials[A <: GoogleCredentials](credential: A,
-                                                            scopes: Iterable[String]): GoogleCredentials = {
+                                                            scopes: Iterable[String]
+  ): GoogleCredentials = {
     val scopedCredentials = credential.createScoped(scopes.asJavaCollection)
     Try(credentialsValidation(scopedCredentials)) match {
       case Failure(ex) => throw new RuntimeException(s"Google credentials are invalid: ${ex.getMessage}", ex)
@@ -126,9 +119,8 @@ sealed trait GoogleAuthMode extends LazyLogging {
 }
 
 case class MockAuthMode(override val name: String) extends GoogleAuthMode {
-  override def credentials(unusedOptions: OptionLookup, unusedScopes: Iterable[String]): NoCredentials = {
+  override def credentials(unusedOptions: OptionLookup, unusedScopes: Iterable[String]): NoCredentials =
     NoCredentials.getInstance
-  }
 }
 
 object ServiceAccountMode {
@@ -143,35 +135,29 @@ object ServiceAccountMode {
 
 }
 
-final case class ServiceAccountMode(override val name: String,
-                                    fileFormat: CredentialFileFormat)
-  extends GoogleAuthMode {
+final case class ServiceAccountMode(override val name: String, fileFormat: CredentialFileFormat)
+    extends GoogleAuthMode {
   private val credentialsFile = File(fileFormat.file)
   checkReadable(credentialsFile)
 
-  private lazy val serviceAccountCredentials: ServiceAccountCredentials = {
+  private lazy val serviceAccountCredentials: ServiceAccountCredentials =
     fileFormat match {
       case PemFileFormat(accountId, _) =>
         logger.warn("The PEM file format will be deprecated in the upcoming Cromwell version. Please use JSON instead.")
         ServiceAccountCredentials.fromPkcs8(accountId, accountId, credentialsFile.contentAsString, null, null)
       case _: JsonFileFormat => ServiceAccountCredentials.fromStream(credentialsFile.newInputStream)
     }
-  }
 
-  override def credentials(unusedOptions: OptionLookup,
-                           scopes: Iterable[String]): GoogleCredentials = {
+  override def credentials(unusedOptions: OptionLookup, scopes: Iterable[String]): GoogleCredentials =
     validateCredentials(serviceAccountCredentials, scopes)
-  }
 }
 
 final case class UserServiceAccountMode(override val name: String) extends GoogleAuthMode {
-  private def extractServiceAccount(options: OptionLookup): String = {
+  private def extractServiceAccount(options: OptionLookup): String =
     extract(options, UserServiceAccountKey)
-  }
 
-  private def credentialStream(options: OptionLookup): InputStream = {
+  private def credentialStream(options: OptionLookup): InputStream =
     new ByteArrayInputStream(extractServiceAccount(options).getBytes(StandardCharsets.UTF_8))
-  }
 
   override def credentials(options: OptionLookup, scopes: Iterable[String]): GoogleCredentials = {
     val newCredentials = ServiceAccountCredentials.fromStream(credentialStream(options))
@@ -179,7 +165,6 @@ final case class UserServiceAccountMode(override val name: String) extends Googl
   }
 }
 
-
 final case class UserMode(override val name: String, secretsPath: String) extends GoogleAuthMode {
 
   private lazy val secretsStream = {
@@ -190,9 +175,8 @@ final case class UserMode(override val name: String, secretsPath: String) extend
 
   private lazy val userCredentials: UserCredentials = UserCredentials.fromStream(secretsStream)
 
-  override def credentials(unusedOptions: OptionLookup, scopes: Iterable[String]): GoogleCredentials = {
+  override def credentials(unusedOptions: OptionLookup, scopes: Iterable[String]): GoogleCredentials =
     validateCredentials(userCredentials, scopes)
-  }
 }
 
 object ApplicationDefaultMode {
@@ -200,10 +184,8 @@ object ApplicationDefaultMode {
 }
 
 final case class ApplicationDefaultMode(name: String) extends GoogleAuthMode {
-  override def credentials(unusedOptions: OptionLookup,
-                           scopes: Iterable[String]): GoogleCredentials = {
+  override def credentials(unusedOptions: OptionLookup, scopes: Iterable[String]): GoogleCredentials =
     validateCredentials(applicationDefaultCredentials, scopes)
-  }
 }
 
 sealed trait ClientSecrets {
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/gcs/GcsStorage.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/gcs/GcsStorage.scala
index 29ed842377d..6ae6e88542c 100644
--- a/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/gcs/GcsStorage.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/gcs/GcsStorage.scala
@@ -18,9 +18,11 @@ object GcsStorage {
   val HttpTransport = GoogleNetHttpTransport.newTrustedTransport
 
   val DefaultCloudStorageConfiguration = {
-    val UploadBufferBytes = ConfigFactory.load().as[Option[Int]]("google.upload-buffer-bytes").getOrElse(MediaHttpUploader.MINIMUM_CHUNK_SIZE)
+    val UploadBufferBytes =
+      ConfigFactory.load().as[Option[Int]]("google.upload-buffer-bytes").getOrElse(MediaHttpUploader.MINIMUM_CHUNK_SIZE)
 
-    CloudStorageConfiguration.builder()
+    CloudStorageConfiguration
+      .builder()
       .blockSize(UploadBufferBytes)
       .permitEmptyPathComponents(true)
       .stripPrefixSlash(true)
@@ -28,23 +30,24 @@ object GcsStorage {
       .build()
   }
 
-  def gcsStorage(applicationName: String,
-                 storageOptions: StorageOptions): Storage = {
-    new Storage.Builder(HttpTransport,
+  def gcsStorage(applicationName: String, storageOptions: StorageOptions): Storage =
+    new Storage.Builder(
+      HttpTransport,
       JsonFactory,
-      GoogleConfiguration.withCustomTimeouts(TransportOptions.getHttpRequestInitializer(storageOptions)))
+      GoogleConfiguration.withCustomTimeouts(TransportOptions.getHttpRequestInitializer(storageOptions))
+    )
       .setApplicationName(applicationName)
       .build()
-  }
 
-  def gcsStorage(applicationName: String, credentials: Credentials, retrySettings: RetrySettings): Storage = {
+  def gcsStorage(applicationName: String, credentials: Credentials, retrySettings: RetrySettings): Storage =
     gcsStorage(applicationName, gcsStorageOptions(credentials, retrySettings))
-  }
 
   def gcsStorageOptions(credentials: Credentials,
                         retrySettings: RetrySettings,
-                        project: Option[String] = None): StorageOptions = {
-    val storageOptionsBuilder = StorageOptions.newBuilder()
+                        project: Option[String] = None
+  ): StorageOptions = {
+    val storageOptionsBuilder = StorageOptions
+      .newBuilder()
       .setTransportOptions(TransportOptions)
       .setCredentials(credentials)
 
diff --git a/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/http/GoogleHttpTransportOptions.scala b/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/http/GoogleHttpTransportOptions.scala
index 13faef01e0c..f328756cf67 100644
--- a/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/http/GoogleHttpTransportOptions.scala
+++ b/cloudSupport/src/main/scala/cromwell/cloudsupport/gcp/http/GoogleHttpTransportOptions.scala
@@ -4,7 +4,8 @@ import com.google.cloud.http.HttpTransportOptions
 import scala.concurrent.duration._
 
 object GoogleHttpTransportOptions {
-  val TransportOptions = HttpTransportOptions.newBuilder()
+  val TransportOptions = HttpTransportOptions
+    .newBuilder()
     .setReadTimeout(3.minutes.toMillis.toInt)
     .build()
 }
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/aws/AwsConfigurationSpec.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/aws/AwsConfigurationSpec.scala
index 6ead310c925..27c66305466 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/aws/AwsConfigurationSpec.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/aws/AwsConfigurationSpec.scala
@@ -39,7 +39,6 @@ import cromwell.cloudsupport.aws.auth.{AssumeRoleMode, CustomKeyMode, DefaultMod
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class AwsConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "AwsConfiguration"
@@ -47,38 +46,38 @@ class AwsConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
   it should "parse all manner of well-formed auths" in {
     val righteousAwsConfig =
       s"""
-        |aws {
-        |  application-name = "cromwell"
-        |
-        |  auths = [
-        |    {
-        |      name = "default"
-        |      scheme = "default"
-        |    },
-        |    {
-        |      name = "custom-keys"
-        |      scheme = "custom_keys"
-        |      access-key = "access_key_id"
-        |      secret-key = "secret_key"
-        |    },
-        |    {
-        |      name = "assume-role-based-on-another-with-external"
-        |      scheme = "assume_role"
-        |      base-auth = "default"
-        |      role-arn = "my-role-arn"
-        |      external-id = "my-external-id"
-        |    },
-        |    {
-        |      name = "assume-role-based-on-another"
-        |      scheme = "assume_role"
-        |      base-auth = "default"
-        |      role-arn = "my-role-arn"
-        |    }
-        |  ]
-        |
-        |  region = "region"
-        |}
-        |
+         |aws {
+         |  application-name = "cromwell"
+         |
+         |  auths = [
+         |    {
+         |      name = "default"
+         |      scheme = "default"
+         |    },
+         |    {
+         |      name = "custom-keys"
+         |      scheme = "custom_keys"
+         |      access-key = "access_key_id"
+         |      secret-key = "secret_key"
+         |    },
+         |    {
+         |      name = "assume-role-based-on-another-with-external"
+         |      scheme = "assume_role"
+         |      base-auth = "default"
+         |      role-arn = "my-role-arn"
+         |      external-id = "my-external-id"
+         |    },
+         |    {
+         |      name = "assume-role-based-on-another"
+         |      scheme = "assume_role"
+         |      base-auth = "default"
+         |      role-arn = "my-role-arn"
+         |    }
+         |  ]
+         |
+         |  region = "region"
+         |}
+         |
       """.stripMargin
 
     val conf = AwsConfiguration(ConfigFactory.parseString(righteousAwsConfig))
@@ -146,8 +145,8 @@ class AwsConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
 
     val conf = AwsConfiguration(ConfigFactory.parseString(config))
     conf.auth("name-botched") should be(
-      "`aws` configuration stanza does not contain an auth named 'name-botched'.  Known auth names: name-default"
-        .invalidNel)
+      "`aws` configuration stanza does not contain an auth named 'name-botched'.  Known auth names: name-default".invalidNel
+    )
   }
 
   it should "not parse a configuration stanza without applicationName" in {
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/aws/s3/S3StorageSpec.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/aws/s3/S3StorageSpec.scala
index 5311714e89c..e50b24d928f 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/aws/s3/S3StorageSpec.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/aws/s3/S3StorageSpec.scala
@@ -36,7 +36,6 @@ import org.scalatest.matchers.should.Matchers
 import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider
 import software.amazon.awssdk.regions.Region
 
-
 class S3StorageSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "S3Storage"
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/GoogleConfigurationSpec.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/GoogleConfigurationSpec.scala
index 95a2380034a..7ed9162a6d1 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/GoogleConfigurationSpec.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/GoogleConfigurationSpec.scala
@@ -14,7 +14,6 @@ import cromwell.cloudsupport.gcp.auth._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class GoogleConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "GoogleConfiguration"
@@ -25,39 +24,39 @@ class GoogleConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec with
 
     val righteousGoogleConfig =
       s"""
-        |google {
-        |  application-name = "cromwell"
-        |
-        |  auths = [
-        |    {
-        |      name = "name-default"
-        |      scheme = "application_default"
-        |    },
-        |    {
-        |      name = "name-user"
-        |      scheme = "user_account"
-        |      user = "me"
-        |      secrets-file = "${pemMockFile.pathAsString}"
-        |      data-store-dir = "/where/the/data/at"
-        |    },
-        |    {
-        |      name = "name-pem-service"
-        |      scheme = "service_account"
-        |      service-account-id = "my-google-account"
-        |      pem-file = "${pemMockFile.pathAsString}"
-        |    },
-        |    {
-        |      name = "name-json-service"
-        |      scheme = "service_account"
-        |      json-file = "${jsonMockFile.pathAsString}"
-        |    },
-        |    {
-        |      name = "name-user-service-account"
-        |      scheme = "user_service_account"
-        |    }
-        |  ]
-        |}
-        |
+         |google {
+         |  application-name = "cromwell"
+         |
+         |  auths = [
+         |    {
+         |      name = "name-default"
+         |      scheme = "application_default"
+         |    },
+         |    {
+         |      name = "name-user"
+         |      scheme = "user_account"
+         |      user = "me"
+         |      secrets-file = "${pemMockFile.pathAsString}"
+         |      data-store-dir = "/where/the/data/at"
+         |    },
+         |    {
+         |      name = "name-pem-service"
+         |      scheme = "service_account"
+         |      service-account-id = "my-google-account"
+         |      pem-file = "${pemMockFile.pathAsString}"
+         |    },
+         |    {
+         |      name = "name-json-service"
+         |      scheme = "service_account"
+         |      json-file = "${jsonMockFile.pathAsString}"
+         |    },
+         |    {
+         |      name = "name-user-service-account"
+         |      scheme = "user_service_account"
+         |    }
+         |  ]
+         |}
+         |
       """.stripMargin
 
     val gconf = GoogleConfiguration(ConfigFactory.parseString(righteousGoogleConfig))
@@ -125,16 +124,16 @@ class GoogleConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec with
 
     val googleConfiguration = GoogleConfiguration(ConfigFactory.parseString(config))
     googleConfiguration.auth("name-botched") should be(
-      "`google` configuration stanza does not contain an auth named 'name-botched'.  Known auth names: name-default"
-        .invalidNel)
+      "`google` configuration stanza does not contain an auth named 'name-botched'.  Known auth names: name-default".invalidNel
+    )
   }
 
   it should "create an initializer with custom timeouts" in {
     val transport = new MockHttpTransport()
-    val initializer = GoogleConfiguration.withCustomTimeouts(request => {
+    val initializer = GoogleConfiguration.withCustomTimeouts { request =>
       request.getHeaders.set("custom_init", "ok")
       ()
-    })
+    }
     val factory = transport.createRequestFactory(initializer)
     val request = factory.buildGetRequest(new GenericUrl(new URL("http://example.com")))
     request.getConnectTimeout should be(180000)
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ApplicationDefaultModeSpec.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ApplicationDefaultModeSpec.scala
index bb661ce9742..dde1f82a3a5 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ApplicationDefaultModeSpec.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ApplicationDefaultModeSpec.scala
@@ -4,7 +4,6 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class ApplicationDefaultModeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "ApplicationDefaultMode"
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/GoogleAuthModeSpec.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/GoogleAuthModeSpec.scala
index 368ce5d2472..bf77f65850d 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/GoogleAuthModeSpec.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/GoogleAuthModeSpec.scala
@@ -10,14 +10,12 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 
 import scala.util.{Failure, Try}
 
-
 class GoogleAuthModeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
 
   behavior of "GoogleAuthMode"
 
-  private def mockHttpResponseException(statusCode: Int): HttpResponseException = {
+  private def mockHttpResponseException(statusCode: Int): HttpResponseException =
     new HttpResponseException.Builder(statusCode, "mock message", new HttpHeaders).build()
-  }
 
   private val testedExceptions = Table(
     ("description", "exception", "isFatal"),
@@ -55,14 +53,13 @@ object GoogleAuthModeSpec extends ServiceAccountTestSupport {
     ()
   }
 
-  lazy val userCredentialsContents: String = {
+  lazy val userCredentialsContents: String =
     toJson(
       "type" -> "authorized_user",
       "client_id" -> "the_id",
       "client_secret" -> "the_secret",
       "refresh_token" -> "the_token"
     )
-  }
 
   lazy val refreshTokenOptions: OptionLookup = Map("refresh_token" -> "the_refresh_token")
   lazy val userServiceAccountOptions: OptionLookup = Map("user_service_account_json" -> serviceAccountJsonContents)
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/MockAuthModeSpec.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/MockAuthModeSpec.scala
index 591da3354a7..b0c89e368c5 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/MockAuthModeSpec.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/MockAuthModeSpec.scala
@@ -4,7 +4,6 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class MockAuthModeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "MockAuthMode"
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ServiceAccountModeSpec.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ServiceAccountModeSpec.scala
index 94831b1410b..b10a823a6ca 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ServiceAccountModeSpec.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ServiceAccountModeSpec.scala
@@ -30,7 +30,7 @@ class ServiceAccountModeSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
       .write(serviceAccountPemContents)
     val serviceAccountMode = ServiceAccountMode(
       "service-account",
-      ServiceAccountMode.PemFileFormat("the_account_id", pemMockFile.pathAsString),
+      ServiceAccountMode.PemFileFormat("the_account_id", pemMockFile.pathAsString)
     )
     val exception = intercept[RuntimeException](serviceAccountMode.credentials())
     exception.getMessage should startWith("Google credentials are invalid: ")
@@ -53,7 +53,7 @@ class ServiceAccountModeSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
     val exception = intercept[FileNotFoundException] {
       ServiceAccountMode(
         "service-account",
-        ServiceAccountMode.PemFileFormat("the_account_id", pemMockFile.pathAsString),
+        ServiceAccountMode.PemFileFormat("the_account_id", pemMockFile.pathAsString)
       )
     }
     exception.getMessage should fullyMatch regex "File .*/service-account..*.pem does not exist or is not readable"
@@ -79,7 +79,7 @@ class ServiceAccountModeSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
       .write(serviceAccountPemContents)
     val serviceAccountMode = ServiceAccountMode(
       "service-account",
-      ServiceAccountMode.PemFileFormat("the_account_id", pemMockFile.pathAsString),
+      ServiceAccountMode.PemFileFormat("the_account_id", pemMockFile.pathAsString)
     )
     serviceAccountMode.credentialsValidation = GoogleAuthMode.NoCredentialsValidation
     val credentials = serviceAccountMode.credentials()
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ServiceAccountTestSupport.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ServiceAccountTestSupport.scala
index 1624674b875..a87df58e21d 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ServiceAccountTestSupport.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/ServiceAccountTestSupport.scala
@@ -23,7 +23,7 @@ trait ServiceAccountTestSupport {
   // Hide me from git secrets false positives
   private val theStringThatShallNotBeNamed = List("private", "key").mkString("_")
 
-  def serviceAccountJsonContents: String = {
+  def serviceAccountJsonContents: String =
     toJson(
       "type" -> "service_account",
       "client_id" -> "the_account_id",
@@ -31,7 +31,6 @@ trait ServiceAccountTestSupport {
       theStringThatShallNotBeNamed -> serviceAccountPemContents,
       s"${theStringThatShallNotBeNamed}_id" -> "the_key_id"
     )
-  }
 
   def toJson(contents: (String, String)*): String = {
     // Generator doesn't matter as long as it generates JSON. Using `jsonFactory` to get an extra line hit of coverage.
@@ -40,10 +39,9 @@ trait ServiceAccountTestSupport {
     val generator = factory.createJsonGenerator(writer)
     generator.enablePrettyPrint()
     generator.writeStartObject()
-    contents foreach {
-      case (key, value) =>
-        generator.writeFieldName(key)
-        generator.writeString(value)
+    contents foreach { case (key, value) =>
+      generator.writeFieldName(key)
+      generator.writeString(value)
     }
     generator.writeEndObject()
     generator.close()
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/UserModeSpec.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/UserModeSpec.scala
index cfc22b0ca9b..95a64ee1e6c 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/UserModeSpec.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/UserModeSpec.scala
@@ -7,7 +7,6 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class UserModeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "UserMode"
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/UserServiceAccountModeSpec.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/UserServiceAccountModeSpec.scala
index 70a1f470d32..092072f7511 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/UserServiceAccountModeSpec.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/auth/UserServiceAccountModeSpec.scala
@@ -4,7 +4,6 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class UserServiceAccountModeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "UserServiceAccountMode"
diff --git a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/gcs/GcsStorageSpec.scala b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/gcs/GcsStorageSpec.scala
index 558c9b74c4a..1f673acec67 100644
--- a/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/gcs/GcsStorageSpec.scala
+++ b/cloudSupport/src/test/scala/cromwell/cloudsupport/gcp/gcs/GcsStorageSpec.scala
@@ -6,7 +6,6 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class GcsStorageSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "GcsStorage"
@@ -19,7 +18,8 @@ class GcsStorageSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   }
 
   it should "build gcs storage" in {
-    val configuration = GcsStorage.gcsStorage("gcs-storage-spec", NoCredentials.getInstance(), RetrySettings.newBuilder().build())
+    val configuration =
+      GcsStorage.gcsStorage("gcs-storage-spec", NoCredentials.getInstance(), RetrySettings.newBuilder().build())
     configuration.getApplicationName should be("gcs-storage-spec")
   }
 
diff --git a/codegen_java/project/Artifactory.scala b/codegen_java/project/Artifactory.scala
index a13c9cc8c21..6d385ffbbc7 100644
--- a/codegen_java/project/Artifactory.scala
+++ b/codegen_java/project/Artifactory.scala
@@ -1,4 +1,4 @@
 object Artifactory {
   val artifactoryHost = "broadinstitute.jfrog.io"
   val artifactory = s"https://$artifactoryHost/broadinstitute/"
-}
\ No newline at end of file
+}
diff --git a/codegen_java/project/Publishing.scala b/codegen_java/project/Publishing.scala
index 6c3de9881fc..880cf40f1ff 100644
--- a/codegen_java/project/Publishing.scala
+++ b/codegen_java/project/Publishing.scala
@@ -2,10 +2,10 @@ import sbt.Keys._
 import sbt._
 import Artifactory._
 
- object Publishing {
+object Publishing {
   private val buildTimestamp = System.currentTimeMillis() / 1000
 
-   private def artifactoryResolver(isSnapshot: Boolean): Resolver = {
+  private def artifactoryResolver(isSnapshot: Boolean): Resolver = {
     val repoType = if (isSnapshot) "snapshot" else "release"
     val repoUrl =
       s"${artifactory}libs-$repoType-local;build.timestamp=$buildTimestamp"
@@ -13,15 +13,15 @@ import Artifactory._
     repoName at repoUrl
   }
 
-   private val artifactoryCredentials: Credentials = {
+  private val artifactoryCredentials: Credentials = {
     val username = sys.env.getOrElse("ARTIFACTORY_USERNAME", "")
     val password = sys.env.getOrElse("ARTIFACTORY_PASSWORD", "")
     Credentials("Artifactory Realm", artifactoryHost, username, password)
   }
 
-   val publishSettings: Seq[Setting[_]] =
-  //we only publish to libs-release-local because of a bug in sbt that makes snapshots take
-  //priority over the local package cache. see here: https://github.com/sbt/sbt/issues/2687#issuecomment-236586241
+  val publishSettings: Seq[Setting[_]] =
+    // we only publish to libs-release-local because of a bug in sbt that makes snapshots take
+    // priority over the local package cache. see here: https://github.com/sbt/sbt/issues/2687#issuecomment-236586241
     Seq(
       publishTo := Option(artifactoryResolver(false)),
       Compile / publishArtifact := true,
@@ -29,9 +29,9 @@ import Artifactory._
       credentials += artifactoryCredentials
     )
 
-   val noPublishSettings: Seq[Setting[_]] =
+  val noPublishSettings: Seq[Setting[_]] =
     Seq(
       publish := {},
       publishLocal := {}
     )
-}
\ No newline at end of file
+}
diff --git a/codegen_java/project/Version.scala b/codegen_java/project/Version.scala
index 875a80e2e10..be7c57bc527 100644
--- a/codegen_java/project/Version.scala
+++ b/codegen_java/project/Version.scala
@@ -1,20 +1,20 @@
 import scala.sys.process._
 
- object Version {
+object Version {
 
-   def createVersion(baseVersion: String) = {
-    def getLastCommitFromGit = { s"""git rev-parse --short HEAD""" !! }
+  def createVersion(baseVersion: String) = {
+    def getLastCommitFromGit = s"""git rev-parse --short HEAD""" !!
 
-     // either specify git hash as an env var or derive it
+    // either specify git hash as an env var or derive it
     // if building from the broadinstitute/scala-baseimage docker image use env var
     // (scala-baseimage doesn't have git in it)
-    val lastCommit = sys.env.getOrElse("GIT_HASH", getLastCommitFromGit ).trim()
+    val lastCommit = sys.env.getOrElse("GIT_HASH", getLastCommitFromGit).trim()
     val version = baseVersion + "-" + lastCommit
 
-     // The project isSnapshot string passed in via command line settings, if desired.
+    // The project isSnapshot string passed in via command line settings, if desired.
     val isSnapshot = sys.props.getOrElse("project.isSnapshot", "true").toBoolean
 
-     // For now, obfuscate SNAPSHOTs from sbt's developers: https://github.com/sbt/sbt/issues/2687#issuecomment-236586241
+    // For now, obfuscate SNAPSHOTs from sbt's developers: https://github.com/sbt/sbt/issues/2687#issuecomment-236586241
     if (isSnapshot) s"$version-SNAP" else version
   }
-}
\ No newline at end of file
+}
diff --git a/common/src/main/scala/common/collections/EnhancedCollections.scala b/common/src/main/scala/common/collections/EnhancedCollections.scala
index beede1f9510..e1eb983029c 100644
--- a/common/src/main/scala/common/collections/EnhancedCollections.scala
+++ b/common/src/main/scala/common/collections/EnhancedCollections.scala
@@ -15,7 +15,10 @@ object EnhancedCollections {
     * After trying and failing to do this myself, I got this to work by copying the answer from here:
     * https://stackoverflow.com/questions/29886246/scala-filter-by-type
     */
-  implicit class EnhancedIterableOps[T2, Repr[x] <: IterableOps[x, Repr, Repr[x]]](val iterableOps: IterableOps[T2, Repr, Repr[T2]]) extends AnyVal {
+  implicit class EnhancedIterableOps[T2, Repr[x] <: IterableOps[x, Repr, Repr[x]]](
+    val iterableOps: IterableOps[T2, Repr, Repr[T2]]
+  ) extends AnyVal {
+
     /**
       * Lets you filter a collection by type.
       *
@@ -58,27 +61,29 @@ object EnhancedCollections {
     def takeWhileWeighted[W](maxWeight: W,
                              weightFunction: A => W,
                              maxHeadLength: Option[Int],
-                             strict: Boolean = false)
-                            (implicit n: Numeric[W], c: Ordering[W]): DeQueued[A] = {
+                             strict: Boolean = false
+    )(implicit n: Numeric[W], c: Ordering[W]): DeQueued[A] = {
       import n._
 
       @tailrec
-      def takeWhileWeightedRec(tail: Queue[A], head: Vector[A], weight: W): (Vector[A], Queue[A]) = {
+      def takeWhileWeightedRec(tail: Queue[A], head: Vector[A], weight: W): (Vector[A], Queue[A]) =
         // Stay under maxHeadLength if it's specified
         if (maxHeadLength.exists(head.size >= _)) head -> tail
-        else tail.dequeueOption
-          .map({
-            // Compute the dequeued element's weight
-            case (element, dequeued) => (element, weightFunction(element), dequeued)
-          }) match {
-          // If the element's weight is > maxWeight and strict is true, drop the element
-          case Some((_, elementWeight, dequeued)) if c.gteq(elementWeight, maxWeight) && strict => takeWhileWeightedRec(dequeued, head, weight)
-          // If we're under the max weight, add the element to the head and recurse
-          case Some((element, elementWeight, dequeued)) if c.lteq(elementWeight + weight, maxWeight) => takeWhileWeightedRec(dequeued, head :+ element, weight + elementWeight)
-          // Otherwise stop here (make sure to return the original queue so we don't lose the last dequeued element)
-          case _ => head -> tail
-        }
-      }
+        else
+          tail.dequeueOption
+            .map {
+              // Compute the dequeued element's weight
+              case (element, dequeued) => (element, weightFunction(element), dequeued)
+            } match {
+            // If the element's weight is > maxWeight and strict is true, drop the element
+            case Some((_, elementWeight, dequeued)) if c.gteq(elementWeight, maxWeight) && strict =>
+              takeWhileWeightedRec(dequeued, head, weight)
+            // If we're under the max weight, add the element to the head and recurse
+            case Some((element, elementWeight, dequeued)) if c.lteq(elementWeight + weight, maxWeight) =>
+              takeWhileWeightedRec(dequeued, head :+ element, weight + elementWeight)
+            // Otherwise stop here (make sure to return the original queue so we don't lose the last dequeued element)
+            case _ => head -> tail
+          }
 
       if (queue.isEmpty || maxHeadLength.contains(0)) DeQueued(Vector.empty, queue)
       // If strict is enabled, we should never return a head with a weight > maxWeight. So start from the original queue and drop elements over maxWeight if necessary
@@ -88,13 +93,17 @@ object EnhancedCollections {
       }
       // Otherwise to ensure we don't deadlock, start the recursion with the head of the queue, this way even if it's over maxWeight it'll return a single element head
       else {
-        val (head, tail) = takeWhileWeightedRec(queue.tail, queue.headOption.toVector, queue.headOption.map(weightFunction).getOrElse(n.zero))
+        val (head, tail) = takeWhileWeightedRec(queue.tail,
+                                                queue.headOption.toVector,
+                                                queue.headOption.map(weightFunction).getOrElse(n.zero)
+        )
         DeQueued(head, tail)
       }
     }
   }
 
   implicit class EnhancedMapLike[A, +B, +This <: Map[A, B]](val mapLike: Map[A, B]) {
+
     /**
       * 'safe' in that unlike the implementation hiding behind `MapLike#mapValues` this is strict. i.e. this will only
       * evaluate the supplied function once on each value and at the time this method is called.
@@ -104,17 +113,15 @@ object EnhancedCollections {
     /**
       * Based on scalaz's intersectWith, applies `f` to values of keys found in this `mapLike` and map
       */
-    def intersectWith[C, D](map: Map[A, C])(f: (B, C) => D): Map[A, D] = {
+    def intersectWith[C, D](map: Map[A, C])(f: (B, C) => D): Map[A, D] =
       mapLike collect {
         case (mapLikeKey, mapLikeValue) if map.contains(mapLikeKey) =>
           mapLikeKey -> f(mapLikeValue, map(mapLikeKey))
       }
-    }
   }
 
   implicit class EnhancedNonEmptyList[A](val nel: NonEmptyList[A]) extends AnyVal {
-    def foreach(f: A => Unit): Unit = {
+    def foreach(f: A => Unit): Unit =
       nel.toList foreach f
-    }
   }
 }
diff --git a/common/src/main/scala/common/collections/Table.scala b/common/src/main/scala/common/collections/Table.scala
index 57c1b3f4a57..3f8b262bfb1 100644
--- a/common/src/main/scala/common/collections/Table.scala
+++ b/common/src/main/scala/common/collections/Table.scala
@@ -3,6 +3,7 @@ package common.collections
 import scala.collection.immutable
 
 object Table {
+
   /**
     * Instantiates an empty table
     */
@@ -22,7 +23,7 @@ object Table {
   * @tparam V type of the value
   */
 case class Table[R, C, V](table: Map[R, Map[C, V]]) {
-  
+
   /**
     * Returns true if the table contains a value at row / column
     */
@@ -51,18 +52,16 @@ case class Table[R, C, V](table: Map[R, Map[C, V]]) {
   /**
     * Add a value at row / column
     */
-  def add(row: R, column: C, value: V): Table[R, C, V] = {
+  def add(row: R, column: C, value: V): Table[R, C, V] =
     this.copy(
       table = table.updated(row, table.getOrElse(row, Map.empty).updated(column, value))
     )
-  }
 
   /**
     * Add all values
     */
-  def addAll(values: Iterable[(R, C, V)]): Table[R, C, V] = {
+  def addAll(values: Iterable[(R, C, V)]): Table[R, C, V] =
     values.foldLeft(this)(_.addTriplet(_))
-  }
 
   /**
     * Add a value as a triplet
diff --git a/common/src/main/scala/common/collections/WeightedQueue.scala b/common/src/main/scala/common/collections/WeightedQueue.scala
index 1ba5d869a64..fecb857db9b 100644
--- a/common/src/main/scala/common/collections/WeightedQueue.scala
+++ b/common/src/main/scala/common/collections/WeightedQueue.scala
@@ -4,9 +4,8 @@ import common.collections.EnhancedCollections._
 import scala.collection.immutable.Queue
 
 object WeightedQueue {
-  def empty[T, W](weightFunction: T => W)(implicit n: Numeric[W]) = {
+  def empty[T, W](weightFunction: T => W)(implicit n: Numeric[W]) =
     WeightedQueue(Queue.empty[T], weightFunction, n.zero)
-  }
 }
 
 /**
@@ -14,27 +13,24 @@ object WeightedQueue {
   * In addition to the queue, a weight function is provided that provides the weight W of an element T.
   * The total weight of the queue is accessible, as well as a method to take the head of the queue based on a max weight value.
   */
-final case class WeightedQueue[T, W](innerQueue: Queue[T],
-                                     private val weightFunction: T => W,
-                                     weight: W)(implicit n: Numeric[W]) {
+final case class WeightedQueue[T, W](innerQueue: Queue[T], private val weightFunction: T => W, weight: W)(implicit
+  n: Numeric[W]
+) {
   import n._
 
-  def enqueue(element: T): WeightedQueue[T, W] = {
+  def enqueue(element: T): WeightedQueue[T, W] =
     this.copy(innerQueue = innerQueue.enqueue(element), weight = weight + weightFunction(element))
-  }
 
   def dequeue: (T, WeightedQueue[T, W]) = {
     val (element, tail) = innerQueue.dequeue
     element -> this.copy(innerQueue = tail, weight = weight - weightFunction(element))
   }
 
-  def dequeueOption: Option[(T, WeightedQueue[T, W])] = {
-    innerQueue.dequeueOption map {
-      case (element, tail) =>
-        element -> this.copy(innerQueue = tail, weight = weight - weightFunction(element))
+  def dequeueOption: Option[(T, WeightedQueue[T, W])] =
+    innerQueue.dequeueOption map { case (element, tail) =>
+      element -> this.copy(innerQueue = tail, weight = weight - weightFunction(element))
     }
-  }
-  
+
   def behead(maxWeight: W, maxLength: Option[Int] = None, strict: Boolean = false): (Vector[T], WeightedQueue[T, W]) = {
     val DeQueued(head, tail) = innerQueue.takeWhileWeighted(maxWeight, weightFunction, maxLength, strict)
     head -> this.copy(innerQueue = tail, weight = weight - head.map(weightFunction).sum)
diff --git a/common/src/main/scala/common/exception/ExceptionAggregation.scala b/common/src/main/scala/common/exception/ExceptionAggregation.scala
index bd7f030331c..94059e94f50 100644
--- a/common/src/main/scala/common/exception/ExceptionAggregation.scala
+++ b/common/src/main/scala/common/exception/ExceptionAggregation.scala
@@ -8,12 +8,11 @@ import common.exception.Aggregation._
 import scala.annotation.tailrec
 
 object Aggregation {
-  def formatMessageWithList(message: String, list: Iterable[String]) = {
+  def formatMessageWithList(message: String, list: Iterable[String]) =
     if (list.nonEmpty) {
       val messages = s"\n${list.mkString("\n")}"
       s"$message:$messages"
     } else message
-  }
 
   def flattenThrowable(throwable: Throwable) = {
     @tailrec
@@ -57,12 +56,12 @@ trait ThrowableAggregation extends MessageAggregation {
   override def errorMessages = throwables map buildMessage
 
   private def buildMessage(t: Throwable): String = t match {
-      // The message for file not found exception only contains the file name, so add the actual reason
+    // The message for file not found exception only contains the file name, so add the actual reason
     case _: FileNotFoundException | _: NoSuchFileException => s"File not found ${t.getMessage}"
     case aggregation: ThrowableAggregation =>
       formatMessageWithList(aggregation.exceptionContext, aggregation.throwables.map(buildMessage).map("\t" + _))
     case other =>
-      val cause = Option(other.getCause) map { c => s"\n\t${buildMessage(c)}" }  getOrElse ""
+      val cause = Option(other.getCause) map { c => s"\n\t${buildMessage(c)}" } getOrElse ""
       s"${other.getMessage}$cause"
   }
 }
@@ -70,6 +69,14 @@ trait ThrowableAggregation extends MessageAggregation {
 /**
   * Generic convenience case class for aggregated exceptions.
   */
-case class AggregatedException(exceptionContext: String, throwables: Iterable[Throwable]) extends Exception with ThrowableAggregation
-case class AggregatedMessageException(exceptionContext: String, errorMessages: Iterable[String]) extends Exception with MessageAggregation
-case class CompositeException(exceptionContext: String, throwables: Iterable[Throwable], override val errorMessages: Iterable[String]) extends Exception with ThrowableAggregation
+case class AggregatedException(exceptionContext: String, throwables: Iterable[Throwable])
+    extends Exception
+    with ThrowableAggregation
+case class AggregatedMessageException(exceptionContext: String, errorMessages: Iterable[String])
+    extends Exception
+    with MessageAggregation
+case class CompositeException(exceptionContext: String,
+                              throwables: Iterable[Throwable],
+                              override val errorMessages: Iterable[String]
+) extends Exception
+    with ThrowableAggregation
diff --git a/common/src/main/scala/common/exception/package.scala b/common/src/main/scala/common/exception/package.scala
index dccd49f2643..48d3dd43fb3 100644
--- a/common/src/main/scala/common/exception/package.scala
+++ b/common/src/main/scala/common/exception/package.scala
@@ -4,7 +4,6 @@ import cats.effect.IO
 
 package object exception {
 
-  def toIO[A](option: Option[A], errorMsg: String): IO[A] = {
+  def toIO[A](option: Option[A], errorMsg: String): IO[A] =
     IO.fromEither(option.toRight(new RuntimeException(errorMsg)))
-  }
 }
diff --git a/common/src/main/scala/common/numeric/IntegerUtil.scala b/common/src/main/scala/common/numeric/IntegerUtil.scala
index 4c33c5ace64..e24e478d400 100644
--- a/common/src/main/scala/common/numeric/IntegerUtil.scala
+++ b/common/src/main/scala/common/numeric/IntegerUtil.scala
@@ -2,14 +2,13 @@ package common.numeric
 
 object IntegerUtil {
 
-  private def ordinal(int: Int): String = {
+  private def ordinal(int: Int): String =
     int match {
       case 1 => "st"
       case 2 => "nd"
       case 3 => "rd"
       case _ => "th"
     }
-  }
 
   implicit class IntEnhanced(val value: Int) extends AnyVal {
     def toOrdinal: String = value match {
@@ -19,9 +18,8 @@ object IntegerUtil {
         s"$v$suffix"
     }
 
-    def isBetweenInclusive(min: Int, max: Int): Boolean = {
+    def isBetweenInclusive(min: Int, max: Int): Boolean =
       min <= value && value <= max
-    }
   }
 
 }
diff --git a/common/src/main/scala/common/transforms/package.scala b/common/src/main/scala/common/transforms/package.scala
index 028f426d54a..112fb22d682 100644
--- a/common/src/main/scala/common/transforms/package.scala
+++ b/common/src/main/scala/common/transforms/package.scala
@@ -12,30 +12,42 @@ package object transforms {
   object CheckedAtoB {
     def apply[A, B](implicit runner: CheckedAtoB[A, B]): CheckedAtoB[A, B] = runner
     def fromCheck[A, B](run: A => Checked[B]): CheckedAtoB[A, B] = Kleisli(run)
-    def fromCheck[A, B](context: String)(run: A => Checked[B]): CheckedAtoB[A, B] = Kleisli(runCheckWithContext(run, _ => context))
-    def fromCheck[A, B](context: A => String)(run: A => Checked[B]): CheckedAtoB[A, B] = Kleisli(runCheckWithContext(run, context))
+    def fromCheck[A, B](context: String)(run: A => Checked[B]): CheckedAtoB[A, B] = Kleisli(
+      runCheckWithContext(run, _ => context)
+    )
+    def fromCheck[A, B](context: A => String)(run: A => Checked[B]): CheckedAtoB[A, B] = Kleisli(
+      runCheckWithContext(run, context)
+    )
     def fromErrorOr[A, B](run: A => ErrorOr[B]): CheckedAtoB[A, B] = Kleisli(runThenCheck(run))
-    def fromErrorOr[A, B](context: String)(run: A => ErrorOr[B]): CheckedAtoB[A, B] = Kleisli(runErrorOrWithContext(run, _ => context))
-    def fromErrorOr[A, B](context: A => String)(run: A => ErrorOr[B]): CheckedAtoB[A, B] = Kleisli(runErrorOrWithContext(run, context))
-    private def runThenCheck[A, B](run: A => ErrorOr[B]): A => Checked[B] = (a: A) => { run(a).toEither }
-    private def runErrorOrWithContext[A, B](run: A => ErrorOr[B], context: A => String): A => Checked[B] = (a: A) => { run(a).toEither.contextualizeErrors(context(a)) }
-    private def runCheckWithContext[A, B](run: A => Checked[B], context: A => String): A => Checked[B] = (a: A) => { run(a).contextualizeErrors(context(a)) }
+    def fromErrorOr[A, B](context: String)(run: A => ErrorOr[B]): CheckedAtoB[A, B] = Kleisli(
+      runErrorOrWithContext(run, _ => context)
+    )
+    def fromErrorOr[A, B](context: A => String)(run: A => ErrorOr[B]): CheckedAtoB[A, B] = Kleisli(
+      runErrorOrWithContext(run, context)
+    )
+    private def runThenCheck[A, B](run: A => ErrorOr[B]): A => Checked[B] = (a: A) => run(a).toEither
+    private def runErrorOrWithContext[A, B](run: A => ErrorOr[B], context: A => String): A => Checked[B] = (a: A) =>
+      run(a).toEither.contextualizeErrors(context(a))
+    private def runCheckWithContext[A, B](run: A => Checked[B], context: A => String): A => Checked[B] = (a: A) =>
+      run(a).contextualizeErrors(context(a))
 
-    def firstSuccess[A, B](options: List[CheckedAtoB[A, B]], operationName: String): CheckedAtoB[A, B] = Kleisli[Checked, A, B] { a =>
-      if (options.isEmpty) {
-        s"Unable to $operationName: No import resolvers provided".invalidNelCheck
-      } else {
-        val firstAttempt = options.head.run(a)
-        options.tail.foldLeft[Checked[B]](firstAttempt) { (currentResult, nextOption) =>
-          currentResult match {
-            case v: Right[_, _] => v
-            case Left(currentErrors) => nextOption.run(a) match {
+    def firstSuccess[A, B](options: List[CheckedAtoB[A, B]], operationName: String): CheckedAtoB[A, B] =
+      Kleisli[Checked, A, B] { a =>
+        if (options.isEmpty) {
+          s"Unable to $operationName: No import resolvers provided".invalidNelCheck
+        } else {
+          val firstAttempt = options.head.run(a)
+          options.tail.foldLeft[Checked[B]](firstAttempt) { (currentResult, nextOption) =>
+            currentResult match {
               case v: Right[_, _] => v
-              case Left(newErrors) => Left(currentErrors ++ newErrors.toList)
+              case Left(currentErrors) =>
+                nextOption.run(a) match {
+                  case v: Right[_, _] => v
+                  case Left(newErrors) => Left(currentErrors ++ newErrors.toList)
+                }
             }
           }
         }
       }
-    }
   }
 }
diff --git a/common/src/main/scala/common/util/Backoff.scala b/common/src/main/scala/common/util/Backoff.scala
index f748785eb10..747508083aa 100644
--- a/common/src/main/scala/common/util/Backoff.scala
+++ b/common/src/main/scala/common/util/Backoff.scala
@@ -3,8 +3,10 @@ package common.util
 import scala.concurrent.duration.FiniteDuration
 
 trait Backoff {
+
   /** Next interval in millis */
   def backoffMillis: Long
+
   /** Get the next instance of backoff. This should be called after every call to backoffMillis */
   def next: Backoff
 }
diff --git a/common/src/main/scala/common/util/IORetry.scala b/common/src/main/scala/common/util/IORetry.scala
index a8a7a63a209..db983fa7711 100644
--- a/common/src/main/scala/common/util/IORetry.scala
+++ b/common/src/main/scala/common/util/IORetry.scala
@@ -7,7 +7,7 @@ import scala.util.control.NonFatal
 
 object IORetry {
   def noOpOnRetry[S]: (Throwable, S) => S = (_, s) => s
-  
+
   object StatefulIoError {
     def noop[S] = new StatefulIoError[S] {
       override def toThrowable(state: S, throwable: Throwable) = throwable
@@ -35,8 +35,8 @@ object IORetry {
                       backoff: Backoff,
                       isRetryable: Throwable => Boolean = throwableToTrue,
                       isInfinitelyRetryable: Throwable => Boolean = throwableToFalse,
-                      onRetry: (Throwable, S) => S = noOpOnRetry[S])
-                     (implicit timer: Timer[IO], statefulIoException: StatefulIoError[S]): IO[A] = {
+                      onRetry: (Throwable, S) => S = noOpOnRetry[S]
+  )(implicit timer: Timer[IO], statefulIoException: StatefulIoError[S]): IO[A] = {
     lazy val delay = backoff.backoffMillis.millis
 
     def fail(throwable: Throwable) = IO.raiseError(statefulIoException.toThrowable(state, throwable))
@@ -49,10 +49,16 @@ object IORetry {
         if (retriesLeft.forall(_ > 0)) {
           for {
             _ <- IO.sleep(delay)
-            retried <- withRetry(io, onRetry(throwable, state), retriesLeft, backoff.next, isRetryable, isInfinitelyRetryable, onRetry)
+            retried <- withRetry(io,
+                                 onRetry(throwable, state),
+                                 retriesLeft,
+                                 backoff.next,
+                                 isRetryable,
+                                 isInfinitelyRetryable,
+                                 onRetry
+            )
           } yield retried
-        }
-        else fail(throwable)
+        } else fail(throwable)
       case fatal => throw fatal
     }
 
diff --git a/common/src/main/scala/common/util/IntrospectableLazy.scala b/common/src/main/scala/common/util/IntrospectableLazy.scala
index e578f49c1a1..7fe05dd1f4c 100644
--- a/common/src/main/scala/common/util/IntrospectableLazy.scala
+++ b/common/src/main/scala/common/util/IntrospectableLazy.scala
@@ -21,20 +21,21 @@ object IntrospectableLazy {
 
 }
 
-class IntrospectableLazy[A] private(f: => A) {
+class IntrospectableLazy[A] private (f: => A) {
 
   private var option: Option[A] = None
 
-  def apply(): A = {
+  def apply(): A =
     option match {
       case Some(a) => a
       case None =>
-        synchronized { option match {
-          case Some(a) => a
-          case None => val a = f; option = Some(a); a
-        }}
+        synchronized {
+          option match {
+            case Some(a) => a
+            case None => val a = f; option = Some(a); a
+          }
+        }
     }
-  }
 
   def exists: Boolean = option.isDefined
 
diff --git a/common/src/main/scala/common/util/StringUtil.scala b/common/src/main/scala/common/util/StringUtil.scala
index 044ef890dea..2ddce884112 100644
--- a/common/src/main/scala/common/util/StringUtil.scala
+++ b/common/src/main/scala/common/util/StringUtil.scala
@@ -64,11 +64,10 @@ object StringUtil {
       */
     def relativeDirectory: String = string.ensureNoLeadingSlash.ensureSlashed
 
-    def elided(limit: Int): String = {
+    def elided(limit: Int): String =
       if (string.length > limit) {
         s"(elided) ${string.take(limit)}..."
       } else string
-    }
 
     /**
       * Removes userInfo and sensitive query parts from strings that are RFC 2396 URIs.
@@ -84,10 +83,9 @@ object StringUtil {
       * - the StringUtilSpec for current expectations
       * - https://stackoverflow.com/questions/4571346/how-to-encode-url-to-avoid-special-characters-in-java#answer-4571518
       */
-    def maskSensitiveUri: String = {
+    def maskSensitiveUri: String =
       Try(new URI(string))
         .map(_.maskSensitive.toASCIIString)
         .getOrElse(string)
-    }
   }
 }
diff --git a/common/src/main/scala/common/util/TerminalUtil.scala b/common/src/main/scala/common/util/TerminalUtil.scala
index cb7c980aecb..33e30f612df 100644
--- a/common/src/main/scala/common/util/TerminalUtil.scala
+++ b/common/src/main/scala/common/util/TerminalUtil.scala
@@ -1,15 +1,15 @@
 package common.util
 
 object TerminalUtil {
-  def highlight(colorCode:Int, string:String) = s"\u001B[38;5;${colorCode}m$string\u001B[0m"
+  def highlight(colorCode: Int, string: String) = s"\u001B[38;5;${colorCode}m$string\u001B[0m"
   def mdTable(rows: Seq[Seq[String]], header: Seq[String]): String = {
-    def maxWidth(lengths: Seq[Seq[Int]], column: Int) = lengths.map { length => length(column) }.max
-    val widths = (rows :+ header).map { row => row.map { s => s.length } }
-    val maxWidths = widths.head.indices.map { column => maxWidth(widths, column) }
-    val tableHeader = header.indices.map { i => header(i).padTo(maxWidths(i), ' ').mkString("") }.mkString("|")
-    val tableDivider = header.indices.map { i => "-" * maxWidths(i) }.mkString("|")
+    def maxWidth(lengths: Seq[Seq[Int]], column: Int) = lengths.map(length => length(column)).max
+    val widths = (rows :+ header).map(row => row.map(s => s.length))
+    val maxWidths = widths.head.indices.map(column => maxWidth(widths, column))
+    val tableHeader = header.indices.map(i => header(i).padTo(maxWidths(i), ' ').mkString("")).mkString("|")
+    val tableDivider = header.indices.map(i => "-" * maxWidths(i)).mkString("|")
     val tableRows = rows.map { row =>
-      val mdRow = row.indices.map { i => row(i).padTo(maxWidths(i), ' ').mkString("") }.mkString("|")
+      val mdRow = row.indices.map(i => row(i).padTo(maxWidths(i), ' ').mkString("")).mkString("|")
       s"|$mdRow|"
     }
     s"|$tableHeader|\n|$tableDivider|\n${tableRows.mkString("\n")}\n"
diff --git a/common/src/main/scala/common/util/TimeUtil.scala b/common/src/main/scala/common/util/TimeUtil.scala
index dbd94c99b80..8c64dd341ce 100644
--- a/common/src/main/scala/common/util/TimeUtil.scala
+++ b/common/src/main/scala/common/util/TimeUtil.scala
@@ -4,6 +4,7 @@ import java.time.format.DateTimeFormatter
 import java.time.{OffsetDateTime, ZoneOffset}
 
 object TimeUtil {
+
   /**
     * Instead of "one of" the valid ISO-8601 formats, standardize on this one:
     * https://github.com/openjdk/jdk/blob/jdk8-b120/jdk/src/share/classes/java/time/OffsetDateTime.java#L1886
@@ -11,12 +12,15 @@ object TimeUtil {
   private val Iso8601MillisecondsFormat = DateTimeFormatter.ofPattern("uuuu-MM-dd'T'HH:mm:ss.SSSXXXXX")
 
   implicit class EnhancedOffsetDateTime(val offsetDateTime: OffsetDateTime) extends AnyVal {
+
     /**
       * Discards the original timezone and shifts the time to UTC, then returns the ISO-8601 formatted string with
       * exactly three digits of milliseconds.
       */
-    def toUtcMilliString: String = Option(offsetDateTime).map(
-      _.atZoneSameInstant(ZoneOffset.UTC).format(Iso8601MillisecondsFormat)
-    ).orNull
+    def toUtcMilliString: String = Option(offsetDateTime)
+      .map(
+        _.atZoneSameInstant(ZoneOffset.UTC).format(Iso8601MillisecondsFormat)
+      )
+      .orNull
   }
 }
diff --git a/common/src/main/scala/common/util/TryUtil.scala b/common/src/main/scala/common/util/TryUtil.scala
index e8edf01f8e5..02a90a5e983 100644
--- a/common/src/main/scala/common/util/TryUtil.scala
+++ b/common/src/main/scala/common/util/TryUtil.scala
@@ -22,14 +22,13 @@ object TryUtil {
   def stringifyFailures[T](possibleFailures: Iterable[Try[T]]): Iterable[String] =
     possibleFailures.collect { case failure: Failure[T] => stringifyFailure(failure) }
 
-  private def sequenceIterable[T](tries: Iterable[Try[_]], unbox: () => T, prefixErrorMessage: String): Try[T] = {
+  private def sequenceIterable[T](tries: Iterable[Try[_]], unbox: () => T, prefixErrorMessage: String): Try[T] =
     tries collect { case f: Failure[_] => f } match {
       case failures if failures.nonEmpty =>
         val exceptions = failures.toSeq.map(_.exception)
         Failure(AggregatedException(prefixErrorMessage, exceptions.toList))
       case _ => Success(unbox())
     }
-  }
 
   def sequence[T](tries: Seq[Try[T]], prefixErrorMessage: String = ""): Try[Seq[T]] = {
     def unbox = tries map { _.get }
diff --git a/common/src/main/scala/common/util/UriUtil.scala b/common/src/main/scala/common/util/UriUtil.scala
index eb8c125768c..24625be1edb 100644
--- a/common/src/main/scala/common/util/UriUtil.scala
+++ b/common/src/main/scala/common/util/UriUtil.scala
@@ -15,20 +15,19 @@ object UriUtil {
       * - the StringUtilSpec for current expectations
       * - https://stackoverflow.com/questions/4571346/how-to-encode-url-to-avoid-special-characters-in-java#answer-4571518
       */
-    def maskSensitive: URI = {
+    def maskSensitive: URI =
       Try {
-          new URI(
-            uri.getScheme,
-            null, // Remove all userInfo
-            uri.getHost,
-            uri.getPort,
-            uri.getPath,
-            Option(uri.getQuery).map(maskSensitiveQuery).orNull,
-            uri.getFragment,
-          )
+        new URI(
+          uri.getScheme,
+          null, // Remove all userInfo
+          uri.getHost,
+          uri.getPort,
+          uri.getPath,
+          Option(uri.getQuery).map(maskSensitiveQuery).orNull,
+          uri.getFragment
+        )
       }
-      .getOrElse(uri)
-    }
+        .getOrElse(uri)
   }
 
   private def maskSensitiveQuery(query: String): String = {
@@ -85,7 +84,7 @@ object UriUtil {
   private val SensitiveKeyParts =
     List(
       "credential",
-      "signature",
+      "signature"
     )
 
   private def isSensitiveKey(name: String): Boolean = {
diff --git a/common/src/main/scala/common/util/VersionUtil.scala b/common/src/main/scala/common/util/VersionUtil.scala
index 3ddea0750d5..fcbffca77a4 100644
--- a/common/src/main/scala/common/util/VersionUtil.scala
+++ b/common/src/main/scala/common/util/VersionUtil.scala
@@ -35,19 +35,17 @@ object VersionUtil {
     * @param default     What to return when the version cannot be found. The parameter passed is the `projectName`.
     * @return The version from the conf or the default
     */
-  def getVersion(projectName: String, default: String => String = defaultMessage): String = {
+  def getVersion(projectName: String, default: String => String = defaultMessage): String =
     ConfigFactory
       .load(versionConf(projectName))
       .as[Option[String]](versionProperty(projectName))
       .getOrElse(default(projectName))
-  }
 
   /**
     * Instead of returning a version, states that the version conf will be generated by sbt.
     */
-  def defaultMessage(projectName: String): String = {
+  def defaultMessage(projectName: String): String =
     s"${versionConf(projectName)}-to-be-generated-by-sbt"
-  }
 
   /**
     * A regex compatible with the dependency constants in project/Dependencies.scala.
@@ -62,7 +60,7 @@ object VersionUtil {
     * @return The dependency version from project/Dependencies.scala
     * @throws RuntimeException If the dependency cannot be found
     */
-  def sbtDependencyVersion(dependencyName: String)(projectName: String): String = {
+  def sbtDependencyVersion(dependencyName: String)(projectName: String): String =
     try {
       val dependencies = Paths.get("project/Dependencies.scala").toAbsolutePath
       val lines = Files.readAllLines(dependencies).asScala
@@ -79,6 +77,5 @@ object VersionUtil {
           e
         )
     }
-  }
 
 }
diff --git a/common/src/main/scala/common/validation/ErrorOr.scala b/common/src/main/scala/common/validation/ErrorOr.scala
index 4be2aa633c9..3afdfcc5fb7 100644
--- a/common/src/main/scala/common/validation/ErrorOr.scala
+++ b/common/src/main/scala/common/validation/ErrorOr.scala
@@ -12,9 +12,8 @@ import scala.util.Try
 object ErrorOr {
   type ErrorOr[+A] = Validated[NonEmptyList[String], A]
 
-  def apply[A](f: => A): ErrorOr[A] = {
+  def apply[A](f: => A): ErrorOr[A] =
     Try(f).toErrorOr
-  }
 
   implicit class EnhancedErrorOr[A](val eoa: ErrorOr[A]) extends AnyVal {
     def contextualizeErrors(s: => String): ErrorOr[A] = eoa.leftMap { errors =>
@@ -31,17 +30,17 @@ object ErrorOr {
   }
 
   implicit class ShortCircuitingFlatMap[A](val fa: ErrorOr[A]) extends AnyVal {
+
     /**
       * Not consistent with `Applicative#ap` but useful in for comprehensions.
       *
       * @see http://typelevel.org/cats/tut/validated.html#of-flatmaps-and-xors
       */
-    def flatMap[B](f: A => ErrorOr[B]): ErrorOr[B] = {
+    def flatMap[B](f: A => ErrorOr[B]): ErrorOr[B] =
       fa match {
         case Valid(v) => ErrorOr(f(v)).flatten
         case i @ Invalid(_) => i
       }
-    }
   }
 
   implicit class MapErrorOrRhs[A, B](val m: Map[A, ErrorOr[B]]) extends AnyVal {
@@ -49,8 +48,8 @@ object ErrorOr {
   }
 
   implicit class MapTraversal[A, B](val m: Map[A, B]) extends AnyVal {
-    def traverse[C,D](f: ((A,B)) => ErrorOr[(C,D)]): ErrorOr[Map[C,D]] = m.toList.traverse(f).map(_.toMap)
-    def traverseValues[C](f: B => ErrorOr[C]): ErrorOr[Map[A,C]] = m.traverse { case (a, b) => f(b).map(c => (a,c)) }
+    def traverse[C, D](f: ((A, B)) => ErrorOr[(C, D)]): ErrorOr[Map[C, D]] = m.toList.traverse(f).map(_.toMap)
+    def traverseValues[C](f: B => ErrorOr[C]): ErrorOr[Map[A, C]] = m.traverse { case (a, b) => f(b).map(c => (a, c)) }
   }
 
   // Note! See the bottom of this file for a generator function for 2 through 22 of these near-identical ShortCircuitingFlatMapTupleNs...
@@ -67,83 +66,346 @@ object ErrorOr {
     def flatMapN[T_OUT](f3: (A, B, C) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t3.tupled flatMap f3.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple4[A, B, C, D](val t4: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D])) extends AnyVal {
+  implicit class ShortCircuitingFlatMapTuple4[A, B, C, D](val t4: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D]))
+      extends AnyVal {
     def flatMapN[T_OUT](f4: (A, B, C, D) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t4.tupled flatMap f4.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple5[A, B, C, D, E](val t5: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E])) extends AnyVal {
+  implicit class ShortCircuitingFlatMapTuple5[A, B, C, D, E](
+    val t5: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E])
+  ) extends AnyVal {
     def flatMapN[T_OUT](f5: (A, B, C, D, E) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t5.tupled flatMap f5.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple6[A, B, C, D, E, F](val t6: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F])) extends AnyVal {
+  implicit class ShortCircuitingFlatMapTuple6[A, B, C, D, E, F](
+    val t6: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F])
+  ) extends AnyVal {
     def flatMapN[T_OUT](f6: (A, B, C, D, E, F) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t6.tupled flatMap f6.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple7[A, B, C, D, E, F, G](val t7: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G])) extends AnyVal {
+  implicit class ShortCircuitingFlatMapTuple7[A, B, C, D, E, F, G](
+    val t7: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G])
+  ) extends AnyVal {
     def flatMapN[T_OUT](f7: (A, B, C, D, E, F, G) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t7.tupled flatMap f7.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple8[A, B, C, D, E, F, G, H](val t8: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H])) extends AnyVal {
+  implicit class ShortCircuitingFlatMapTuple8[A, B, C, D, E, F, G, H](
+    val t8: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H])
+  ) extends AnyVal {
     def flatMapN[T_OUT](f8: (A, B, C, D, E, F, G, H) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t8.tupled flatMap f8.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple9[A, B, C, D, E, F, G, H, I](val t9: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I])) extends AnyVal {
+  implicit class ShortCircuitingFlatMapTuple9[A, B, C, D, E, F, G, H, I](
+    val t9: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I])
+  ) extends AnyVal {
     def flatMapN[T_OUT](f9: (A, B, C, D, E, F, G, H, I) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t9.tupled flatMap f9.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple10[A, B, C, D, E, F, G, H, I, J](val t10: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J])) extends AnyVal {
-    def flatMapN[T_OUT](f10: (A, B, C, D, E, F, G, H, I, J) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t10.tupled flatMap f10.tupled
+  implicit class ShortCircuitingFlatMapTuple10[A, B, C, D, E, F, G, H, I, J](
+    val t10: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](f10: (A, B, C, D, E, F, G, H, I, J) => ErrorOr[T_OUT]): ErrorOr[T_OUT] =
+      t10.tupled flatMap f10.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple11[A, B, C, D, E, F, G, H, I, J, K](val t11: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K])) extends AnyVal {
-    def flatMapN[T_OUT](f11: (A, B, C, D, E, F, G, H, I, J, K) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t11.tupled flatMap f11.tupled
+  implicit class ShortCircuitingFlatMapTuple11[A, B, C, D, E, F, G, H, I, J, K](
+    val t11: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](f11: (A, B, C, D, E, F, G, H, I, J, K) => ErrorOr[T_OUT]): ErrorOr[T_OUT] =
+      t11.tupled flatMap f11.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple12[A, B, C, D, E, F, G, H, I, J, K, L](val t12: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L])) extends AnyVal {
-    def flatMapN[T_OUT](f12: (A, B, C, D, E, F, G, H, I, J, K, L) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t12.tupled flatMap f12.tupled
+  implicit class ShortCircuitingFlatMapTuple12[A, B, C, D, E, F, G, H, I, J, K, L](
+    val t12: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](f12: (A, B, C, D, E, F, G, H, I, J, K, L) => ErrorOr[T_OUT]): ErrorOr[T_OUT] =
+      t12.tupled flatMap f12.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple13[A, B, C, D, E, F, G, H, I, J, K, L, M](val t13: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L], ErrorOr[M])) extends AnyVal {
-    def flatMapN[T_OUT](f13: (A, B, C, D, E, F, G, H, I, J, K, L, M) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t13.tupled flatMap f13.tupled
+  implicit class ShortCircuitingFlatMapTuple13[A, B, C, D, E, F, G, H, I, J, K, L, M](
+    val t13: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L],
+              ErrorOr[M]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](f13: (A, B, C, D, E, F, G, H, I, J, K, L, M) => ErrorOr[T_OUT]): ErrorOr[T_OUT] =
+      t13.tupled flatMap f13.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple14[A, B, C, D, E, F, G, H, I, J, K, L, M, N](val t14: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L], ErrorOr[M], ErrorOr[N])) extends AnyVal {
-    def flatMapN[T_OUT](f14: (A, B, C, D, E, F, G, H, I, J, K, L, M, N) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t14.tupled flatMap f14.tupled
+  implicit class ShortCircuitingFlatMapTuple14[A, B, C, D, E, F, G, H, I, J, K, L, M, N](
+    val t14: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L],
+              ErrorOr[M],
+              ErrorOr[N]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](f14: (A, B, C, D, E, F, G, H, I, J, K, L, M, N) => ErrorOr[T_OUT]): ErrorOr[T_OUT] =
+      t14.tupled flatMap f14.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple15[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O](val t15: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L], ErrorOr[M], ErrorOr[N], ErrorOr[O])) extends AnyVal {
-    def flatMapN[T_OUT](f15: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t15.tupled flatMap f15.tupled
+  implicit class ShortCircuitingFlatMapTuple15[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O](
+    val t15: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L],
+              ErrorOr[M],
+              ErrorOr[N],
+              ErrorOr[O]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](f15: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O) => ErrorOr[T_OUT]): ErrorOr[T_OUT] =
+      t15.tupled flatMap f15.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple16[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P](val t16: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L], ErrorOr[M], ErrorOr[N], ErrorOr[O], ErrorOr[P])) extends AnyVal {
-    def flatMapN[T_OUT](f16: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t16.tupled flatMap f16.tupled
+  implicit class ShortCircuitingFlatMapTuple16[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P](
+    val t16: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L],
+              ErrorOr[M],
+              ErrorOr[N],
+              ErrorOr[O],
+              ErrorOr[P]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](f16: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P) => ErrorOr[T_OUT]): ErrorOr[T_OUT] =
+      t16.tupled flatMap f16.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple17[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q](val t17: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L], ErrorOr[M], ErrorOr[N], ErrorOr[O], ErrorOr[P], ErrorOr[Q])) extends AnyVal {
-    def flatMapN[T_OUT](f17: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t17.tupled flatMap f17.tupled
+  implicit class ShortCircuitingFlatMapTuple17[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q](
+    val t17: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L],
+              ErrorOr[M],
+              ErrorOr[N],
+              ErrorOr[O],
+              ErrorOr[P],
+              ErrorOr[Q]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](f17: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q) => ErrorOr[T_OUT]): ErrorOr[T_OUT] =
+      t17.tupled flatMap f17.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple18[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R](val t18: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L], ErrorOr[M], ErrorOr[N], ErrorOr[O], ErrorOr[P], ErrorOr[Q], ErrorOr[R])) extends AnyVal {
-    def flatMapN[T_OUT](f18: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t18.tupled flatMap f18.tupled
+  implicit class ShortCircuitingFlatMapTuple18[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R](
+    val t18: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L],
+              ErrorOr[M],
+              ErrorOr[N],
+              ErrorOr[O],
+              ErrorOr[P],
+              ErrorOr[Q],
+              ErrorOr[R]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](f18: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R) => ErrorOr[T_OUT]): ErrorOr[T_OUT] =
+      t18.tupled flatMap f18.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple19[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S](val t19: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L], ErrorOr[M], ErrorOr[N], ErrorOr[O], ErrorOr[P], ErrorOr[Q], ErrorOr[R], ErrorOr[S])) extends AnyVal {
-    def flatMapN[T_OUT](f19: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t19.tupled flatMap f19.tupled
+  implicit class ShortCircuitingFlatMapTuple19[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S](
+    val t19: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L],
+              ErrorOr[M],
+              ErrorOr[N],
+              ErrorOr[O],
+              ErrorOr[P],
+              ErrorOr[Q],
+              ErrorOr[R],
+              ErrorOr[S]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](
+      f19: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S) => ErrorOr[T_OUT]
+    ): ErrorOr[T_OUT] = t19.tupled flatMap f19.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple20[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T](val t20: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L], ErrorOr[M], ErrorOr[N], ErrorOr[O], ErrorOr[P], ErrorOr[Q], ErrorOr[R], ErrorOr[S], ErrorOr[T])) extends AnyVal {
-    def flatMapN[T_OUT](f20: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t20.tupled flatMap f20.tupled
+  implicit class ShortCircuitingFlatMapTuple20[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T](
+    val t20: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L],
+              ErrorOr[M],
+              ErrorOr[N],
+              ErrorOr[O],
+              ErrorOr[P],
+              ErrorOr[Q],
+              ErrorOr[R],
+              ErrorOr[S],
+              ErrorOr[T]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](
+      f20: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T) => ErrorOr[T_OUT]
+    ): ErrorOr[T_OUT] = t20.tupled flatMap f20.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple21[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U](val t21: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L], ErrorOr[M], ErrorOr[N], ErrorOr[O], ErrorOr[P], ErrorOr[Q], ErrorOr[R], ErrorOr[S], ErrorOr[T], ErrorOr[U])) extends AnyVal {
-    def flatMapN[T_OUT](f21: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t21.tupled flatMap f21.tupled
+  implicit class ShortCircuitingFlatMapTuple21[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U](
+    val t21: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L],
+              ErrorOr[M],
+              ErrorOr[N],
+              ErrorOr[O],
+              ErrorOr[P],
+              ErrorOr[Q],
+              ErrorOr[R],
+              ErrorOr[S],
+              ErrorOr[T],
+              ErrorOr[U]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](
+      f21: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U) => ErrorOr[T_OUT]
+    ): ErrorOr[T_OUT] = t21.tupled flatMap f21.tupled
   }
 
-  implicit class ShortCircuitingFlatMapTuple22[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V](val t22: (ErrorOr[A], ErrorOr[B], ErrorOr[C], ErrorOr[D], ErrorOr[E], ErrorOr[F], ErrorOr[G], ErrorOr[H], ErrorOr[I], ErrorOr[J], ErrorOr[K], ErrorOr[L], ErrorOr[M], ErrorOr[N], ErrorOr[O], ErrorOr[P], ErrorOr[Q], ErrorOr[R], ErrorOr[S], ErrorOr[T], ErrorOr[U], ErrorOr[V])) extends AnyVal {
-    def flatMapN[T_OUT](f22: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t22.tupled flatMap f22.tupled
+  implicit class ShortCircuitingFlatMapTuple22[A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V](
+    val t22: (ErrorOr[A],
+              ErrorOr[B],
+              ErrorOr[C],
+              ErrorOr[D],
+              ErrorOr[E],
+              ErrorOr[F],
+              ErrorOr[G],
+              ErrorOr[H],
+              ErrorOr[I],
+              ErrorOr[J],
+              ErrorOr[K],
+              ErrorOr[L],
+              ErrorOr[M],
+              ErrorOr[N],
+              ErrorOr[O],
+              ErrorOr[P],
+              ErrorOr[Q],
+              ErrorOr[R],
+              ErrorOr[S],
+              ErrorOr[T],
+              ErrorOr[U],
+              ErrorOr[V]
+    )
+  ) extends AnyVal {
+    def flatMapN[T_OUT](
+      f22: (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V) => ErrorOr[T_OUT]
+    ): ErrorOr[T_OUT] = t22.tupled flatMap f22.tupled
   }
 
   object ErrorOrGen {
+
     /**
       * Because maintaining 22 near-identical functions is a bore...
       * This function can regenerate them if we need to make changes.
@@ -168,8 +430,7 @@ object ErrorOr {
          |  ${line2(n)}
          |}
          |
-       |""".stripMargin
+         |""".stripMargin
     }
   }
 }
-
diff --git a/common/src/main/scala/common/validation/IOChecked.scala b/common/src/main/scala/common/validation/IOChecked.scala
index f838e5ceb32..62e61f87eb4 100644
--- a/common/src/main/scala/common/validation/IOChecked.scala
+++ b/common/src/main/scala/common/validation/IOChecked.scala
@@ -1,6 +1,5 @@
 package common.validation
 
-
 import cats.arrow.FunctionK
 import cats.data.EitherT.fromEither
 import cats.data.{EitherT, NonEmptyList, ValidatedNel}
@@ -22,6 +21,7 @@ object IOChecked {
     * The monad transformer allows to flatMap over the value while keeping the IO effect as well as the list of potential errors
     */
   type IOChecked[A] = EitherT[IO, NonEmptyList[String], A]
+
   /**
     * Fixes the left type of Either to Throwable
     * This is useful when calling on IO[A].attempt, transforming it to IO[ Either[Throwable, A] ] == IO[ Attempt[A] ]
@@ -40,22 +40,22 @@ object IOChecked {
     */
   implicit val eitherThrowableApplicative = new Applicative[Attempt] {
     override def pure[A](x: A) = Right(x)
-    override def ap[A, B](ff: Attempt[A => B])(fa: Attempt[A]): Attempt[B] = {
+    override def ap[A, B](ff: Attempt[A => B])(fa: Attempt[A]): Attempt[B] =
       (fa, ff) match {
-          // Both have a list or error messages, combine them in a single one
-        case (Left(t1: MessageAggregation), Left(t2: MessageAggregation)) => Left(AggregatedMessageException("", t1.errorMessages ++ t2.errorMessages))
-          // Only one of them is a MessageAggregation, combined the errors and the other exception in a CompositeException
+        // Both have a list or error messages, combine them in a single one
+        case (Left(t1: MessageAggregation), Left(t2: MessageAggregation)) =>
+          Left(AggregatedMessageException("", t1.errorMessages ++ t2.errorMessages))
+        // Only one of them is a MessageAggregation, combined the errors and the other exception in a CompositeException
         case (Left(t1: MessageAggregation), Left(t2)) => Left(CompositeException("", List(t2), t1.errorMessages))
         case (Left(t2), Left(t1: MessageAggregation)) => Left(CompositeException("", List(t2), t1.errorMessages))
-          // None of them is a MessageAggregation, combine the 2 throwables in an AggregatedException
+        // None of them is a MessageAggregation, combine the 2 throwables in an AggregatedException
         case (Left(t1), Left(t2)) => Left(AggregatedException("", List(t1, t2)))
-          // Success case, apply f on v
+        // Success case, apply f on v
         case (Right(v), Right(f)) => Right(f(v))
-          // Default failure case, just keep the failure
+        // Default failure case, just keep the failure
         case (Left(t1), _) => Left(t1)
         case (_, Left(t1)) => Left(t1)
       }
-    }
   }
 
   /**
@@ -100,7 +100,7 @@ object IOChecked {
       * We now have an IO[ Either[NonEmptyList[String], A] ] which we can wrap into an IOChecked with EitherT.apply
       */
     override def sequential: FunctionK[IOCheckedPar, IOChecked] =
-      new FunctionK[IOCheckedPar, IOChecked] { 
+      new FunctionK[IOCheckedPar, IOChecked] {
         def apply[A](fa: IOCheckedPar[A]): IOChecked[A] = EitherT {
           IO.Par.unwrap(fa: IO.Par[Attempt[A]]) flatMap {
             case Left(t: MessageAggregation) => IO.pure(Left(NonEmptyList.fromListUnsafe(t.errorMessages.toList)))
@@ -138,7 +138,7 @@ object IOChecked {
   def error[A](error: String, tail: String*): IOChecked[A] = EitherT.leftT {
     NonEmptyList.of(error, tail: _*)
   }
-  
+
   def pure[A](value: A): IOChecked[A] = EitherT.pure(value)
 
   def goIOChecked[A](f: => A): IOChecked[A] = Try(f).toIOChecked
@@ -150,12 +150,11 @@ object IOChecked {
   implicit class EnhancedIOChecked[A](val p: IOChecked[A]) extends AnyVal {
     import cats.syntax.either._
 
-    def toChecked: Checked[A] = {
+    def toChecked: Checked[A] =
       Try(p.value.unsafeRunSync()) match {
         case Success(r) => r
         case Failure(f) => NonEmptyList.one(f.getMessage).asLeft
       }
-    }
 
     def toErrorOr: ErrorOr[A] = toChecked.toValidated
 
@@ -163,12 +162,11 @@ object IOChecked {
 
     def unsafe(context: String) = unsafeToEither().unsafe(context)
 
-    def contextualizeErrors(context: String): IOChecked[A] = {
-      p.leftMap({ errors =>
+    def contextualizeErrors(context: String): IOChecked[A] =
+      p.leftMap { errors =>
         val total = errors.size
         errors.zipWithIndex map { case (e, i) => s"Failed to $context (reason ${i + 1} of $total): $e" }
-      })
-    }
+      }
   }
 
   implicit class TryIOChecked[A](val t: Try[A]) extends AnyVal {
@@ -176,9 +174,8 @@ object IOChecked {
   }
 
   implicit class FutureIOChecked[A](val future: Future[A]) extends AnyVal {
-    def toIOChecked(implicit cs: ContextShift[IO]): IOChecked[A] = {
+    def toIOChecked(implicit cs: ContextShift[IO]): IOChecked[A] =
       IO.fromFuture(IO(future)).to[IOChecked]
-    }
   }
 
   implicit class ErrorOrIOChecked[A](val e: ErrorOr[A]) extends AnyVal {
@@ -198,9 +195,8 @@ object IOChecked {
   }
 
   implicit class OptionIOChecked[A](val o: Option[A]) extends AnyVal {
-    def toIOChecked(errorMessage: String): IOChecked[A] = {
+    def toIOChecked(errorMessage: String): IOChecked[A] =
       EitherT.fromOption(o, NonEmptyList.of(errorMessage))
-    }
   }
 
   type IOCheckedValidated[A] = IO[ValidatedNel[String, A]]
diff --git a/common/src/main/scala/common/validation/Validation.scala b/common/src/main/scala/common/validation/Validation.scala
index 4099eff8ac6..af568909b5b 100644
--- a/common/src/main/scala/common/validation/Validation.scala
+++ b/common/src/main/scala/common/validation/Validation.scala
@@ -46,12 +46,12 @@ object Validation {
     case Failure(f) => defaultThrowableToString(f).invalidNel
   }
 
-  implicit class ValidationOps[B,A](val v: ValidatedNel[B, A]) {
-    //Convert this into a future by folding over the state and returning the corresponding Future terminal state.
+  implicit class ValidationOps[B, A](val v: ValidatedNel[B, A]) {
+    // Convert this into a future by folding over the state and returning the corresponding Future terminal state.
     def toFuture(f: NonEmptyList[B] => Throwable) =
-      v fold(
-        //Use f to turn the failure list into a Throwable, then fail a future with it.
-        //Function composition lets us ignore the actual argument of the error list
+      v fold (
+        // Use f to turn the failure list into a Throwable, then fail a future with it.
+        // Function composition lets us ignore the actual argument of the error list
         Future.failed _ compose f,
         Future.successful
       )
@@ -59,31 +59,30 @@ object Validation {
 
   implicit class TryValidation[A](val t: Try[A]) extends AnyVal {
     def toErrorOr: ErrorOr[A] = toErrorOr(defaultThrowableToString)
-    def toErrorOr(throwableToStringFunction: ThrowableToStringFunction): ErrorOr[A] = {
+    def toErrorOr(throwableToStringFunction: ThrowableToStringFunction): ErrorOr[A] =
       Validated.fromTry(t).leftMap(throwableToStringFunction).toValidatedNel[String, A]
-    }
 
     def toErrorOrWithContext(context: String): ErrorOr[A] = toErrorOrWithContext(context, defaultThrowableToString)
-    def toErrorOrWithContext(context: String,
-                            throwableToStringFunction: ThrowableToStringFunction): ErrorOr[A] = toChecked(throwableToStringFunction)
-      .contextualizeErrors(context)
-      .leftMap({contextualizedErrors =>
-        if (t.failed.isFailure) {
-          val errors = new StringWriter
-          t.failed.get.printStackTrace(new PrintWriter(errors))
-          contextualizedErrors.::(s"Stacktrace: ${errors.toString}")
-        } else contextualizedErrors
-      })
-      .toValidated
+    def toErrorOrWithContext(context: String, throwableToStringFunction: ThrowableToStringFunction): ErrorOr[A] =
+      toChecked(throwableToStringFunction)
+        .contextualizeErrors(context)
+        .leftMap { contextualizedErrors =>
+          if (t.failed.isFailure) {
+            val errors = new StringWriter
+            t.failed.get.printStackTrace(new PrintWriter(errors))
+            contextualizedErrors.::(s"Stacktrace: ${errors.toString}")
+          } else contextualizedErrors
+        }
+        .toValidated
 
     def toChecked: Checked[A] = toChecked(defaultThrowableToString)
-    def toChecked(throwableToStringFunction: ThrowableToStringFunction): Checked[A] = {
-      Either.fromTry(t).leftMap { ex => NonEmptyList.one(throwableToStringFunction(ex)) }
-    }
+    def toChecked(throwableToStringFunction: ThrowableToStringFunction): Checked[A] =
+      Either.fromTry(t).leftMap(ex => NonEmptyList.one(throwableToStringFunction(ex)))
 
-    def toCheckedWithContext(context: String): Checked[A] = toErrorOrWithContext(context, defaultThrowableToString).toEither
-    def toCheckedWithContext(context: String,
-                             throwableToStringFunction: ThrowableToStringFunction): Checked[A] = toErrorOrWithContext(context, throwableToStringFunction).toEither
+    def toCheckedWithContext(context: String): Checked[A] =
+      toErrorOrWithContext(context, defaultThrowableToString).toEither
+    def toCheckedWithContext(context: String, throwableToStringFunction: ThrowableToStringFunction): Checked[A] =
+      toErrorOrWithContext(context, throwableToStringFunction).toEither
   }
 
   implicit class ValidationTry[A](val e: ErrorOr[A]) extends AnyVal {
@@ -109,12 +108,10 @@ object Validation {
   }
 
   implicit class OptionValidation[A](val o: Option[A]) extends AnyVal {
-    def toErrorOr(errorMessage: => String): ErrorOr[A] = {
+    def toErrorOr(errorMessage: => String): ErrorOr[A] =
       Validated.fromOption(o, NonEmptyList.of(errorMessage))
-    }
 
-    def toChecked(errorMessage: => String): Checked[A] = {
+    def toChecked(errorMessage: => String): Checked[A] =
       Either.fromOption(o, NonEmptyList.of(errorMessage))
-    }
   }
 }
diff --git a/common/src/test/scala/common/assertion/CaseClassAssertions.scala b/common/src/test/scala/common/assertion/CaseClassAssertions.scala
index 4cc191df2f6..f273898de1c 100644
--- a/common/src/test/scala/common/assertion/CaseClassAssertions.scala
+++ b/common/src/test/scala/common/assertion/CaseClassAssertions.scala
@@ -5,10 +5,9 @@ import org.scalatest.matchers.should.Matchers
 object CaseClassAssertions extends Matchers {
   implicit class ComparableCaseClass[A <: Product](actualA: A) {
     // Assumes that expectedA and actualA are the same type. If we don't subtype case classes, that should hold...
-    def shouldEqualFieldwise(expectedA: A): Unit = {
+    def shouldEqualFieldwise(expectedA: A): Unit =
       (0 until actualA.productArity) foreach { i =>
         actualA.productElement(i) should be(expectedA.productElement(i))
       }
-    }
   }
 }
diff --git a/common/src/test/scala/common/assertion/ErrorOrAssertions.scala b/common/src/test/scala/common/assertion/ErrorOrAssertions.scala
index 02a5e594bb4..00c3ab4fcfc 100644
--- a/common/src/test/scala/common/assertion/ErrorOrAssertions.scala
+++ b/common/src/test/scala/common/assertion/ErrorOrAssertions.scala
@@ -6,7 +6,6 @@ import common.validation.ErrorOr.ErrorOr
 import org.scalatest.Assertion
 import org.scalatest.matchers.should.Matchers
 
-
 object ErrorOrAssertions {
   implicit class ErrorOrWithAssertions[A](errorOr: ErrorOr[A]) extends Matchers {
     def shouldBeValid(other: A): Assertion = errorOr match {
diff --git a/common/src/test/scala/common/collections/TableSpec.scala b/common/src/test/scala/common/collections/TableSpec.scala
index 7000e151df4..581fcf466e8 100644
--- a/common/src/test/scala/common/collections/TableSpec.scala
+++ b/common/src/test/scala/common/collections/TableSpec.scala
@@ -4,7 +4,6 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class TableSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "Table"
@@ -21,10 +20,14 @@ class TableSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "fill a table" in {
-    Table.fill(List(
-      ("a", "b", "c"),
-      ("d", "e", "f")
-    )).table shouldBe Map(
+    Table
+      .fill(
+        List(
+          ("a", "b", "c"),
+          ("d", "e", "f")
+        )
+      )
+      .table shouldBe Map(
       "a" -> Map("b" -> "c"),
       "d" -> Map("e" -> "f")
     )
@@ -48,7 +51,7 @@ class TableSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     someTable.rowOptional("a") shouldBe Some(Map("b" -> "c"))
     someTable.rowOptional("b") shouldBe None
   }
-  
+
   it should "implement row" in {
     someTable.row("a") shouldBe Map("b" -> "c")
     someTable.row("b") shouldBe empty
@@ -87,7 +90,7 @@ class TableSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   it should "implement addTriplet" in {
     someTable.addTriplet(
-        ("0", "1", "2")
+      ("0", "1", "2")
     ) shouldBe Table(
       Map(
         "a" -> Map("b" -> "c"),
diff --git a/common/src/test/scala/common/collections/WeightedQueueSpec.scala b/common/src/test/scala/common/collections/WeightedQueueSpec.scala
index 5d29b54949e..ba9cd81d908 100644
--- a/common/src/test/scala/common/collections/WeightedQueueSpec.scala
+++ b/common/src/test/scala/common/collections/WeightedQueueSpec.scala
@@ -4,7 +4,6 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class WeightedQueueSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "WeightedQueue"
@@ -39,7 +38,8 @@ class WeightedQueueSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
   it should "behead the queue" in {
     // A queue of strings for which the weight is the number of char in the string
     val q = WeightedQueue.empty[String, Int](_.length)
-    val q2 = q.enqueue("hello")
+    val q2 = q
+      .enqueue("hello")
       .enqueue("hola")
       .enqueue("bonjour")
     val (head, q3) = q2.behead(10)
diff --git a/common/src/test/scala/common/exception/ExceptionAggregationSpec.scala b/common/src/test/scala/common/exception/ExceptionAggregationSpec.scala
index cd425b626f0..071b7836ceb 100644
--- a/common/src/test/scala/common/exception/ExceptionAggregationSpec.scala
+++ b/common/src/test/scala/common/exception/ExceptionAggregationSpec.scala
@@ -7,7 +7,6 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 
-
 class ExceptionAggregationSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matchers {
 
   "MessageAggregation" should "aggregate messages" in {
diff --git a/common/src/test/scala/common/mock/MockImplicits.scala b/common/src/test/scala/common/mock/MockImplicits.scala
index 3e90e183d8e..424dbfbdfde 100644
--- a/common/src/test/scala/common/mock/MockImplicits.scala
+++ b/common/src/test/scala/common/mock/MockImplicits.scala
@@ -11,31 +11,27 @@ trait MockImplicits {
     * https://github.com/etorreborre/specs2/commit/6d56660e70980b5958e6c4ed8fd4158bf1cecf70#diff-a2627f56c432e4bc37f36bc56e13852225813aa604918471b61ec2080462d722
     */
   implicit class MockEnhanced[A](methodCall: A) {
-    def returns(result: A): OngoingStubbing[A] = {
+    def returns(result: A): OngoingStubbing[A] =
       Mockito.when(methodCall).thenReturn(result)
-    }
 
-    def answers(function: Any => A): OngoingStubbing[A] = {
-      Mockito.when(methodCall) thenAnswer {
-        invocationOnMock => {
-          val args = invocationOnMock.getArguments
-          // The DSL behavior of the below is directly taken with thanks from the link above.
-          args.size match {
-            case 0 =>
-              function match {
-                case function0: Function0[_] =>
-                  function0.apply().asInstanceOf[A]
-                case _ =>
-                  function.apply(invocationOnMock.getMock)
-              }
-            case 1 =>
-              function(args(0))
-            case _ =>
-              function(args)
-          }
+    def answers(function: Any => A): OngoingStubbing[A] =
+      Mockito.when(methodCall) thenAnswer { invocationOnMock =>
+        val args = invocationOnMock.getArguments
+        // The DSL behavior of the below is directly taken with thanks from the link above.
+        args.size match {
+          case 0 =>
+            function match {
+              case function0: Function0[_] =>
+                function0.apply().asInstanceOf[A]
+              case _ =>
+                function.apply(invocationOnMock.getMock)
+            }
+          case 1 =>
+            function(args(0))
+          case _ =>
+            function(args)
         }
       }
-    }
 
     def responds(f: Any => A): OngoingStubbing[A] = answers(f)
   }
diff --git a/common/src/test/scala/common/mock/MockSugar.scala b/common/src/test/scala/common/mock/MockSugar.scala
index 27a4ae87b55..6a92bd2fd47 100644
--- a/common/src/test/scala/common/mock/MockSugar.scala
+++ b/common/src/test/scala/common/mock/MockSugar.scala
@@ -2,7 +2,7 @@ package common.mock
 
 import org.mockito.{ArgumentCaptor, Mockito}
 
-import scala.reflect.{ClassTag, classTag}
+import scala.reflect.{classTag, ClassTag}
 
 /**
   * Yet another scala wrapper around Mockito.
@@ -37,12 +37,11 @@ trait MockSugar extends MockImplicits {
     *
     * Note: if you run into issues with `mock` then try [[mockWithDefaults]].
     */
-  def mock[A: ClassTag]: A = {
+  def mock[A: ClassTag]: A =
     Mockito.mock(
       classTag[A].runtimeClass.asInstanceOf[Class[A]],
-      Mockito.withSettings().defaultAnswer(Mockito.RETURNS_SMART_NULLS),
+      Mockito.withSettings().defaultAnswer(Mockito.RETURNS_SMART_NULLS)
     )
-  }
 
   /**
     * Creates a mock returning default values instead of Smart Nulls.
@@ -56,16 +55,14 @@ trait MockSugar extends MockImplicits {
     *
     * An alternative workaround was to use `Mockito.doReturn(retVal).when(mockObj).someMethod`.
     */
-  def mockWithDefaults[A: ClassTag]: A = {
+  def mockWithDefaults[A: ClassTag]: A =
     Mockito.mock(
       classTag[A].runtimeClass.asInstanceOf[Class[A]],
-      Mockito.withSettings().defaultAnswer(Mockito.RETURNS_DEFAULTS),
+      Mockito.withSettings().defaultAnswer(Mockito.RETURNS_DEFAULTS)
     )
-  }
 
-  def capture[A: ClassTag]: ArgumentCaptor[A] = {
+  def capture[A: ClassTag]: ArgumentCaptor[A] =
     ArgumentCaptor.forClass(classTag[A].runtimeClass.asInstanceOf[Class[A]])
-  }
 }
 
 object MockSugar extends MockSugar
diff --git a/common/src/test/scala/common/numeric/IntegerUtilSpec.scala b/common/src/test/scala/common/numeric/IntegerUtilSpec.scala
index b06af539626..48fc9ed3b3b 100644
--- a/common/src/test/scala/common/numeric/IntegerUtilSpec.scala
+++ b/common/src/test/scala/common/numeric/IntegerUtilSpec.scala
@@ -5,18 +5,33 @@ import common.numeric.IntegerUtil.IntEnhanced
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class IntegerUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   it should "return ordinal String for any Int" in {
-    val numbers = List(0, 1, 2, 3, 4,
-        10, 11, 12, 13, 14,
-        20, 21, 22, 23, 24,
-        100, 101, 102, 103, 104) map { _.toOrdinal }
+    val numbers = List(0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 100, 101, 102, 103, 104) map {
+      _.toOrdinal
+    }
 
-    val expected = List("0th", "1st", "2nd", "3rd", "4th",
-    "10th", "11th", "12th", "13th", "14th",
-    "20th", "21st", "22nd", "23rd", "24th",
-    "100th", "101st", "102nd", "103rd", "104th")
+    val expected = List("0th",
+                        "1st",
+                        "2nd",
+                        "3rd",
+                        "4th",
+                        "10th",
+                        "11th",
+                        "12th",
+                        "13th",
+                        "14th",
+                        "20th",
+                        "21st",
+                        "22nd",
+                        "23rd",
+                        "24th",
+                        "100th",
+                        "101st",
+                        "102nd",
+                        "103rd",
+                        "104th"
+    )
 
     numbers should contain theSameElementsInOrderAs expected
   }
diff --git a/common/src/test/scala/common/util/IntrospectableLazySpec.scala b/common/src/test/scala/common/util/IntrospectableLazySpec.scala
index 337e193ab8f..91243135ab6 100644
--- a/common/src/test/scala/common/util/IntrospectableLazySpec.scala
+++ b/common/src/test/scala/common/util/IntrospectableLazySpec.scala
@@ -22,17 +22,19 @@ class IntrospectableLazySpec extends AnyFlatSpec with CromwellTimeoutSpec with M
       4
     }
 
-    val myLazy = lazily { lazyContents }
+    val myLazy = lazily(lazyContents)
 
     assert(lazyInstantiations == 0)
     assert(!myLazy.exists)
 
     // Fails without `synchronized { ... }`
     Await.result(Future.sequence(
-      Seq.fill(100)(Future {
-        myLazy() shouldBe 4
-      })
-    ), 1.seconds)
+                   Seq.fill(100)(Future {
+                     myLazy() shouldBe 4
+                   })
+                 ),
+                 1.seconds
+    )
 
     assert(lazyInstantiations == 1)
     assert(myLazy.exists)
diff --git a/common/src/test/scala/common/util/IoRetrySpec.scala b/common/src/test/scala/common/util/IoRetrySpec.scala
index 4a5fc582eac..2ec5c56aba4 100644
--- a/common/src/test/scala/common/util/IoRetrySpec.scala
+++ b/common/src/test/scala/common/util/IoRetrySpec.scala
@@ -9,7 +9,6 @@ import org.scalatest.matchers.should.Matchers
 import scala.concurrent.ExecutionContext
 import scala.concurrent.duration._
 
-
 class IoRetrySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   implicit val timer = IO.timer(ExecutionContext.global)
   implicit val ioError = new StatefulIoError[Int] {
@@ -28,7 +27,8 @@ class IoRetrySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     }
 
     val incrementOnRetry: (Throwable, Int) => Int = (_, s) => s + 1
-    val io = IORetry.withRetry(work, 1, Option(3), backoff = Backoff.staticBackoff(10.millis), onRetry = incrementOnRetry)
+    val io =
+      IORetry.withRetry(work, 1, Option(3), backoff = Backoff.staticBackoff(10.millis), onRetry = incrementOnRetry)
     val statefulException = the[Exception] thrownBy io.unsafeRunSync()
     statefulException.getCause shouldBe exception
     statefulException.getMessage shouldBe "Attempted 3 times"
diff --git a/common/src/test/scala/common/util/StringUtilSpec.scala b/common/src/test/scala/common/util/StringUtilSpec.scala
index 3d7b8db92d1..f71d79819cb 100644
--- a/common/src/test/scala/common/util/StringUtilSpec.scala
+++ b/common/src/test/scala/common/util/StringUtilSpec.scala
@@ -17,11 +17,13 @@ class StringUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
     // With the elided string, we stop processing early and are able to produce a nice, short string without ever
     // touching the later elements:
-    fooOfBars.toPrettyElidedString(1000) should be("""Foo(
-                                                    |  bar = "long long list",
-                                                    |  list = List(
-                                                    |    "blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0",
-                                                    |    "blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah...""".stripMargin)
+    fooOfBars.toPrettyElidedString(1000) should be(
+      """Foo(
+        |  bar = "long long list",
+        |  list = List(
+        |    "blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0blah0",
+        |    "blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah1blah...""".stripMargin
+    )
 
   }
 
@@ -36,84 +38,84 @@ class StringUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     (
       "mask user info",
       "https://user:pass@example.com/path/to/file",
-      "https://example.com/path/to/file",
+      "https://example.com/path/to/file"
     ),
     (
       "mask the entire query if no known sensitive query params are found",
       s"https://example.com/path/to/file?my_new_hidden_param=$InputToBeMasked",
-      "https://example.com/path/to/file?masked",
+      "https://example.com/path/to/file?masked"
     ),
     (
       "mask credential params",
       s"https://example.com/path/to/file?my_credential_param=$InputToBeMasked&my_other_param=ok",
-      s"https://example.com/path/to/file?my_credential_param=$OutputMasked&my_other_param=ok",
+      s"https://example.com/path/to/file?my_credential_param=$OutputMasked&my_other_param=ok"
     ),
     (
       "mask signature params",
       s"https://example.com/path/to/file?my_signature_param=$InputToBeMasked&my_other_param=ok",
-      s"https://example.com/path/to/file?my_signature_param=$OutputMasked&my_other_param=ok",
+      s"https://example.com/path/to/file?my_signature_param=$OutputMasked&my_other_param=ok"
     ),
     (
       "mask encoded signature params",
       s"https://example.com/path/to/file?my_sign%61ture_param=$InputToBeMasked&my_other_param=ok",
-      s"https://example.com/path/to/file?my_signature_param=$OutputMasked&my_other_param=ok",
+      s"https://example.com/path/to/file?my_signature_param=$OutputMasked&my_other_param=ok"
     ),
     (
       // There is a note in the docs for common.util.StringUtil.EnhancedString.maskSensitiveUri about this behavior
       "mask uris with encoded parameters",
       s"https://example.com/path/to/file?my_signature_param=$InputToBeMasked&my_other_param=%26%2F%3F",
-      s"https://example.com/path/to/file?my_signature_param=$OutputMasked&my_other_param=&/?",
+      s"https://example.com/path/to/file?my_signature_param=$OutputMasked&my_other_param=&/?"
     ),
     (
       "mask uris with parameters without values",
       s"https://example.com/path/to/file?my_signature_param=$InputToBeMasked&my_other_param",
-      s"https://example.com/path/to/file?my_signature_param=$OutputMasked&my_other_param",
+      s"https://example.com/path/to/file?my_signature_param=$OutputMasked&my_other_param"
     ),
     (
       "mask uris with parameters values containing equal signs",
       s"https://example.com/path/to/file?my_signature_param=$InputToBeMasked&my_other_param=with=equal",
-      s"https://example.com/path/to/file?my_signature_param=$OutputMasked&my_other_param=with=equal",
+      s"https://example.com/path/to/file?my_signature_param=$OutputMasked&my_other_param=with=equal"
     ),
     (
       "not mask the fragment",
       s"https://example.com?my_signature_param=$InputToBeMasked#nofilter",
-      s"https://example.com?my_signature_param=$OutputMasked#nofilter",
+      s"https://example.com?my_signature_param=$OutputMasked#nofilter"
     ),
     (
       "not mask the port number",
       s"https://example.com:1234?my_signature_param=$InputToBeMasked",
-      s"https://example.com:1234?my_signature_param=$OutputMasked",
+      s"https://example.com:1234?my_signature_param=$OutputMasked"
     ),
     (
       // via: https://cr.openjdk.java.net/~dfuchs/writeups/updating-uri/
       "not mask a RFC 3986 specific uri",
       s"urn:isbn:096139210?my_credential_param=$InputToBeMasked",
-      s"urn:isbn:096139210?my_credential_param=$InputToBeMasked",
+      s"urn:isbn:096139210?my_credential_param=$InputToBeMasked"
     ),
     (
       // via: https://bvdp-saturn-dev.appspot.com/#workspaces/general-dev-billing-account/DRS%20and%20Signed%20URL%20Development%20-%20Dev/notebooks/launch/drs_signed_url_flow_kids_dev.ipynb
       "not mask a DRS CIB URI",
       "drs://dg.F82A1A:371b834f-a896-42e6-b1d1-9fad96891f33",
-      "drs://dg.F82A1A:371b834f-a896-42e6-b1d1-9fad96891f33",
+      "drs://dg.F82A1A:371b834f-a896-42e6-b1d1-9fad96891f33"
     ),
     (
       // via: https://bvdp-saturn-dev.appspot.com/#workspaces/general-dev-billing-account/DRS%20and%20Signed%20URL%20Development%20-%20Dev/notebooks/launch/drs_signed_url_flow_kids_dev.ipynb
       "mask an AWS Signed URL",
       s"https://example-redacted-but-not-masked.s3.amazonaws.com/$InputRedacted.CNVs.p.value.txt?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=$InputToBeMasked&X-Amz-Date=20210504T200819Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&user_id=122&username=$InputRedacted&X-Amz-Signature=$InputToBeMasked",
-      s"https://example-redacted-but-not-masked.s3.amazonaws.com/$InputRedacted.CNVs.p.value.txt?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=$OutputMasked&X-Amz-Date=20210504T200819Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&user_id=122&username=$InputRedacted&X-Amz-Signature=$OutputMasked",
+      s"https://example-redacted-but-not-masked.s3.amazonaws.com/$InputRedacted.CNVs.p.value.txt?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=$OutputMasked&X-Amz-Date=20210504T200819Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&user_id=122&username=$InputRedacted&X-Amz-Signature=$OutputMasked"
     ),
     (
       // via: https://bvdp-saturn-dev.appspot.com/#workspaces/general-dev-billing-account/DRS%20and%20Signed%20URL%20Development%20-%20Dev/notebooks/launch/drs_signed_url_flow_bdcat_dev.ipynb
       "mask a GCS V2 Signed URL",
       s"https://storage.googleapis.com/$InputRedacted/testfile.txt?GoogleAccessId=$InputRedacted&Expires=1614119022&Signature=$InputToBeMasked&userProject=$InputRedacted",
-      s"https://storage.googleapis.com/$InputRedacted/testfile.txt?GoogleAccessId=$InputRedacted&Expires=1614119022&Signature=$OutputMasked&userProject=$InputRedacted",
+      s"https://storage.googleapis.com/$InputRedacted/testfile.txt?GoogleAccessId=$InputRedacted&Expires=1614119022&Signature=$OutputMasked&userProject=$InputRedacted"
     ),
     (
       // via: gsutil signurl $HOME/.config/gcloud/legacy_credentials/cromwell@broad-dsde-cromwell-dev.iam.gserviceaccount.com/adc.json gs://cloud-cromwell-dev/some/gumby.png
       "mask a GCS V4 Signed URL",
       s"https://storage.googleapis.com/cloud-cromwell-dev/some/gumby.png?x-goog-signature=$InputToBeMasked&x-goog-algorithm=GOOG4-RSA-SHA256&x-goog-credential=$InputToBeMasked&x-goog-date=20210505T042119Z&x-goog-expires=3600&x-goog-signedheaders=host",
-      s"https://storage.googleapis.com/cloud-cromwell-dev/some/gumby.png?x-goog-signature=$OutputMasked&x-goog-algorithm=GOOG4-RSA-SHA256&x-goog-credential=$OutputMasked&x-goog-date=20210505T042119Z&x-goog-expires=3600&x-goog-signedheaders=host",
-    ),
+      s"https://storage.googleapis.com/cloud-cromwell-dev/some/gumby.png?x-goog-signature=$OutputMasked&x-goog-algorithm=GOOG4-RSA-SHA256&x-goog-credential=$OutputMasked&x-goog-date=20210505T042119Z&x-goog-expires=3600&x-goog-signedheaders=host"
+    )
   )
 
   forAll(maskSensitiveUriTests) { (description, input, expected) =>
@@ -128,7 +130,7 @@ object StringUtilSpec {
   final case class Foo(bar: String, list: List[Bar])
 
   final class Bar(index: Int) {
-    private def longLine(i: Int) = "\"" +  s"blah$i" * 100 + "\""
+    private def longLine(i: Int) = "\"" + s"blah$i" * 100 + "\""
     override def toString: String = if (index < 2) {
       longLine(index)
     } else {
diff --git a/common/src/test/scala/common/util/TerminalUtilSpec.scala b/common/src/test/scala/common/util/TerminalUtilSpec.scala
index c8fda6627e4..1c68b9f17fc 100644
--- a/common/src/test/scala/common/util/TerminalUtilSpec.scala
+++ b/common/src/test/scala/common/util/TerminalUtilSpec.scala
@@ -5,7 +5,6 @@ import common.util.TerminalUtil._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class TerminalUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "TerminalUtil"
diff --git a/common/src/test/scala/common/util/TryUtilSpec.scala b/common/src/test/scala/common/util/TryUtilSpec.scala
index d7b8739337b..0bb62f9ed33 100644
--- a/common/src/test/scala/common/util/TryUtilSpec.scala
+++ b/common/src/test/scala/common/util/TryUtilSpec.scala
@@ -9,7 +9,6 @@ import org.scalatest.matchers.should.Matchers
 import scala.util.{Failure, Success, Try}
 import org.scalatest.enablers.Emptiness._
 
-
 class TryUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "TryUtil"
@@ -80,15 +79,15 @@ class TryUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "sequence successful keys and successful values" in {
-    val result: Try[Map[String, String]] = sequenceKeyValues(
-      Map(Success("success key") -> Success("success value")), "prefix")
+    val result: Try[Map[String, String]] =
+      sequenceKeyValues(Map(Success("success key") -> Success("success value")), "prefix")
     result.isSuccess should be(true)
     result.get.toList should contain theSameElementsAs Map("success key" -> "success value")
   }
 
   it should "sequence successful keys and failed values" in {
-    val result: Try[Map[String, String]] = sequenceKeyValues(
-      Map(Success("success key") -> Failure(new RuntimeException("failed value"))), "prefix")
+    val result: Try[Map[String, String]] =
+      sequenceKeyValues(Map(Success("success key") -> Failure(new RuntimeException("failed value"))), "prefix")
     result.isFailure should be(true)
     result.failed.get should be(an[AggregatedException])
     val exception = result.failed.get.asInstanceOf[AggregatedException]
@@ -98,8 +97,8 @@ class TryUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "sequence failed keys and successful values" in {
-    val result: Try[Map[String, String]] = sequenceKeyValues(
-      Map(Failure(new RuntimeException("failed key")) -> Success("success value")), "prefix")
+    val result: Try[Map[String, String]] =
+      sequenceKeyValues(Map(Failure(new RuntimeException("failed key")) -> Success("success value")), "prefix")
     result.isFailure should be(true)
     result.failed.get should be(an[AggregatedException])
     val exception = result.failed.get.asInstanceOf[AggregatedException]
@@ -110,7 +109,9 @@ class TryUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   it should "sequence failed keys and failed values" in {
     val result: Try[Map[String, String]] = sequenceKeyValues(
-      Map(Failure(new RuntimeException("failed key")) -> Failure(new RuntimeException("failed value"))), "prefix")
+      Map(Failure(new RuntimeException("failed key")) -> Failure(new RuntimeException("failed value"))),
+      "prefix"
+    )
     result.isFailure should be(true)
     result.failed.get should be(an[AggregatedException])
     val exception = result.failed.get.asInstanceOf[AggregatedException]
@@ -127,8 +128,8 @@ class TryUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "sequence a successful key with a failed value" in {
-    val result: Try[(String, String)] = sequenceTuple(
-      (Success("success key"), Failure(new RuntimeException("failed value"))), "prefix")
+    val result: Try[(String, String)] =
+      sequenceTuple((Success("success key"), Failure(new RuntimeException("failed value"))), "prefix")
     result.isFailure should be(true)
     result.failed.get should be(an[AggregatedException])
     val exception = result.failed.get.asInstanceOf[AggregatedException]
@@ -138,8 +139,8 @@ class TryUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "sequence a failed key with a successful value" in {
-    val result: Try[(String, String)] = sequenceTuple(
-      (Failure(new RuntimeException("failed key")), Success("success value")), "prefix")
+    val result: Try[(String, String)] =
+      sequenceTuple((Failure(new RuntimeException("failed key")), Success("success value")), "prefix")
     result.isFailure should be(true)
     result.failed.get should be(an[AggregatedException])
     val exception = result.failed.get.asInstanceOf[AggregatedException]
@@ -149,8 +150,10 @@ class TryUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "sequence a failed key with a failed value" in {
-    val result: Try[(String, String)] = sequenceTuple(
-      (Failure(new RuntimeException("failed key")), Failure(new RuntimeException("failed value"))), "prefix")
+    val result: Try[(String, String)] =
+      sequenceTuple((Failure(new RuntimeException("failed key")), Failure(new RuntimeException("failed value"))),
+                    "prefix"
+      )
     result.isFailure should be(true)
     result.failed.get should be(an[AggregatedException])
     val exception = result.failed.get.asInstanceOf[AggregatedException]
diff --git a/common/src/test/scala/common/util/VersionUtilSpec.scala b/common/src/test/scala/common/util/VersionUtilSpec.scala
index 50aab84bad6..5d58d2f0852 100644
--- a/common/src/test/scala/common/util/VersionUtilSpec.scala
+++ b/common/src/test/scala/common/util/VersionUtilSpec.scala
@@ -4,7 +4,6 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class VersionUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "VersionUtil"
@@ -22,12 +21,12 @@ class VersionUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
   it should "getVersion with the default" in {
     val version = VersionUtil.getVersion("made-up-artifact")
-    version should be ("made-up-artifact-version.conf-to-be-generated-by-sbt")
+    version should be("made-up-artifact-version.conf-to-be-generated-by-sbt")
   }
 
   it should "getVersion with a default override" in {
     val version = VersionUtil.getVersion("made-up-artifact", _ => "default override")
-    version should be ("default override")
+    version should be("default override")
   }
 
   it should "defaultMessage" in {
@@ -38,7 +37,7 @@ class VersionUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     val expected = intercept[RuntimeException](VersionUtil.sbtDependencyVersion("madeUp")("made-up-project"))
     expected.getMessage should fullyMatch regex
       "Did not parse a version for 'madeUpV' from .*/project/Dependencies.scala " +
-        "\\(This occurred after made-up-project-version.conf was not found.\\)"
+      "\\(This occurred after made-up-project-version.conf was not found.\\)"
   }
 
   it should "pass sbtDependencyVersion check for typesafeConfig" in {
diff --git a/common/src/test/scala/common/validation/CheckedSpec.scala b/common/src/test/scala/common/validation/CheckedSpec.scala
index c9b5a387666..23281fccc0b 100644
--- a/common/src/test/scala/common/validation/CheckedSpec.scala
+++ b/common/src/test/scala/common/validation/CheckedSpec.scala
@@ -6,10 +6,9 @@ import common.validation.Checked._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class CheckedSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "Checked"
-  
+
   it should "provide helper methods" in {
     5.validNelCheck shouldBe Right(5)
     "argh".invalidNelCheck[Int] shouldBe Left(NonEmptyList.one("argh"))
diff --git a/common/src/test/scala/common/validation/ErrorOrSpec.scala b/common/src/test/scala/common/validation/ErrorOrSpec.scala
index ac0ebfd957b..55a7d004cc3 100644
--- a/common/src/test/scala/common/validation/ErrorOrSpec.scala
+++ b/common/src/test/scala/common/validation/ErrorOrSpec.scala
@@ -8,7 +8,6 @@ import common.validation.ErrorOr._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class ErrorOrSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "ErrorOr"
@@ -44,11 +43,33 @@ class ErrorOrSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   val DivBy0Error: String = "Divide by 0!"
-  def errorOrDiv(v1: Int, v2: Int): ErrorOr[Double] = if (v2 != 0) { Valid(v1.toDouble / v2.toDouble) } else { DivBy0Error.invalidNel }
-  def errorOrDiv(v1: Double, v2: Int): ErrorOr[Double] = if (v2 != 0) { Valid(v1.toDouble / v2.toDouble) } else { DivBy0Error.invalidNel }
-  def errorOrSelect(v1: Int, v2: Int, v3: Int, v4: Int, v5: Int, v6: Int, v7: Int,
-                    v8: Int, v9: Int, v10: Int, v11: Int, v12: Int, v13: Int, v14: Int,
-                    v15: Int, v16: Int, v17: Int, v18: Int, v19: Int, v20: Int, v21: Int, v22: Int): ErrorOr[Int] = Valid(v4 + v6 + v22)
+  def errorOrDiv(v1: Int, v2: Int): ErrorOr[Double] = if (v2 != 0) { Valid(v1.toDouble / v2.toDouble) }
+  else { DivBy0Error.invalidNel }
+  def errorOrDiv(v1: Double, v2: Int): ErrorOr[Double] = if (v2 != 0) { Valid(v1.toDouble / v2.toDouble) }
+  else { DivBy0Error.invalidNel }
+  def errorOrSelect(v1: Int,
+                    v2: Int,
+                    v3: Int,
+                    v4: Int,
+                    v5: Int,
+                    v6: Int,
+                    v7: Int,
+                    v8: Int,
+                    v9: Int,
+                    v10: Int,
+                    v11: Int,
+                    v12: Int,
+                    v13: Int,
+                    v14: Int,
+                    v15: Int,
+                    v16: Int,
+                    v17: Int,
+                    v18: Int,
+                    v19: Int,
+                    v20: Int,
+                    v21: Int,
+                    v22: Int
+  ): ErrorOr[Int] = Valid(v4 + v6 + v22)
 
   val valid0 = Valid(0)
   val valid1 = Valid(1)
@@ -63,13 +84,29 @@ class ErrorOrSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "flatMapN 22-tuples into a Valid" in {
-    (valid0, valid1, valid2,
-      valid0, valid1, valid2,
-      valid0, valid1, valid2,
-      valid0, valid1, valid2,
-      valid0, valid1, valid2,
-      valid0, valid1, valid2,
-      valid0, valid1, valid2, valid0) flatMapN errorOrSelect should be(Valid(0 + 2 + 0))
+    (valid0,
+     valid1,
+     valid2,
+     valid0,
+     valid1,
+     valid2,
+     valid0,
+     valid1,
+     valid2,
+     valid0,
+     valid1,
+     valid2,
+     valid0,
+     valid1,
+     valid2,
+     valid0,
+     valid1,
+     valid2,
+     valid0,
+     valid1,
+     valid2,
+     valid0
+    ) flatMapN errorOrSelect should be(Valid(0 + 2 + 0))
   }
 
   it should "flatMapN 1-tuples into a Valid string" in {
@@ -139,82 +176,211 @@ class ErrorOrSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "flatMapN 13-tuples into a Valid string" in {
-    val result = (
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2,
-      valid0)
-      .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
+    val result =
+      (valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0)
+        .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
     result should be(Valid("0120120120120"))
   }
 
   it should "flatMapN 14-tuples into a Valid string" in {
-    val result = (
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2,
-      valid0, valid1)
-      .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
+    val result =
+      (valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1)
+        .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
     result should be(Valid("01201201201201"))
   }
 
   it should "flatMapN 15-tuples into a Valid string" in {
-    val result = (
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2,
-      valid0, valid1, valid2)
+    val result = (valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2
+    )
       .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
     result should be(Valid("012012012012012"))
   }
 
   it should "flatMapN 16-tuples into a Valid string" in {
-    val result = (
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2,
-      valid0, valid1, valid2, valid0)
+    val result = (valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0
+    )
       .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
     result should be(Valid("0120120120120120"))
   }
 
   it should "flatMapN 17-tuples into a Valid string" in {
-    val result = (
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2,
-      valid0, valid1, valid2, valid0, valid1)
+    val result = (valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1
+    )
       .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
     result should be(Valid("01201201201201201"))
   }
 
   it should "flatMapN 18-tuples into a Valid string" in {
-    val result = (
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2,
-      valid0, valid1, valid2, valid0, valid1, valid2)
+    val result = (valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2
+    )
       .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
     result should be(Valid("012012012012012012"))
   }
 
   it should "flatMapN 19-tuples into a Valid string" in {
-    val result = (
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2,
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0)
+    val result = (valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0
+    )
       .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
     result should be(Valid("0120120120120120120"))
   }
 
   it should "flatMapN 20-tuples into a Valid string" in {
-    val result = (
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2,
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1)
+    val result = (valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1
+    )
       .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
     result should be(Valid("01201201201201201201"))
   }
 
   it should "flatMapN 21-tuples into a Valid string" in {
-    val result = (
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2,
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2)
+    val result = (valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2
+    )
       .flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
     result should be(Valid("012012012012012012012"))
   }
 
   it should "flatMapN 22-tuples into a Valid string" in {
-    val result = (
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2,
-      valid0, valid1, valid2, valid0, valid1, valid2, valid0, valid1, valid2, valid0).flatMapN(
-      Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
+    val result = (valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0,
+                  valid1,
+                  valid2,
+                  valid0
+    ).flatMapN(Array(_, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _).mkString.valid)
     result should be(Valid("0120120120120120120120"))
   }
 
@@ -228,7 +394,8 @@ class ErrorOrSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
          |    def flatMapN[T_OUT](f1: (A) => ErrorOr[T_OUT]): ErrorOr[T_OUT] = t1.tupled flatMap f1.tupled
          |}
          |
-         |""".stripMargin)
+         |""".stripMargin
+    )
     result
   }
 
diff --git a/common/src/test/scala/common/validation/ValidationSpec.scala b/common/src/test/scala/common/validation/ValidationSpec.scala
index 543e33d7573..8a1c72a922e 100644
--- a/common/src/test/scala/common/validation/ValidationSpec.scala
+++ b/common/src/test/scala/common/validation/ValidationSpec.scala
@@ -14,7 +14,6 @@ import common.mock.MockSugar
 
 import scala.util.{Failure, Success}
 
-
 class ValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with MockSugar {
 
   behavior of "Validation"
diff --git a/core/src/main/scala/cromwell/core/BackendDockerConfiguration.scala b/core/src/main/scala/cromwell/core/BackendDockerConfiguration.scala
index 3000b30e8df..8c53b38c36d 100644
--- a/core/src/main/scala/cromwell/core/BackendDockerConfiguration.scala
+++ b/core/src/main/scala/cromwell/core/BackendDockerConfiguration.scala
@@ -14,7 +14,9 @@ object DockerCredentials {
 object DockerCredentialUsernameAndPassword {
   private val tokenStringFormat = raw"([^:]*):(.*)".r
 
-  def unapply(arg: DockerCredentials): Option[(String, String)] = Try(new String(Base64.getDecoder.decode(arg.token))).toOption match {
+  def unapply(arg: DockerCredentials): Option[(String, String)] = Try(
+    new String(Base64.getDecoder.decode(arg.token))
+  ).toOption match {
     case Some(tokenStringFormat(username, password)) => Some((username, password))
     case _ => None
   }
diff --git a/core/src/main/scala/cromwell/core/ConfigUtil.scala b/core/src/main/scala/cromwell/core/ConfigUtil.scala
index 0fd5002ffa8..5adf56ec0a4 100644
--- a/core/src/main/scala/cromwell/core/ConfigUtil.scala
+++ b/core/src/main/scala/cromwell/core/ConfigUtil.scala
@@ -8,7 +8,7 @@ import com.typesafe.config.{Config, ConfigException, ConfigValue}
 import org.slf4j.LoggerFactory
 
 import scala.jdk.CollectionConverters._
-import scala.reflect.{ClassTag, classTag}
+import scala.reflect.{classTag, ClassTag}
 
 object ConfigUtil {
 
@@ -20,12 +20,12 @@ object ConfigUtil {
     /**
      * For keys that are in the configuration but not in the reference keySet, log a warning.
      */
-    def warnNotRecognized(keySet: Set[String], context: String) = {
+    def warnNotRecognized(keySet: Set[String], context: String) =
       keys.diff(keySet) match {
-        case warnings if warnings.nonEmpty => validationLogger.warn(s"Unrecognized configuration key(s) for $context: ${warnings.mkString(", ")}")
+        case warnings if warnings.nonEmpty =>
+          validationLogger.warn(s"Unrecognized configuration key(s) for $context: ${warnings.mkString(", ")}")
         case _ =>
       }
-    }
 
     /**
      * Validates that the value for this key is a well formed URL.
@@ -34,15 +34,15 @@ object ConfigUtil {
       new URL(config.getString(url))
     }
 
-    def validateString(key: String): ValidatedNel[String, String] = try {
+    def validateString(key: String): ValidatedNel[String, String] = try
       config.getString(key).validNel
-    } catch {
+    catch {
       case _: ConfigException.Missing => s"Could not find key: $key".invalidNel
     }
 
-    def validateConfig(key: String): ValidatedNel[String, Config] = try {
+    def validateConfig(key: String): ValidatedNel[String, Config] = try
       config.getConfig(key).validNel
-    } catch {
+    catch {
       case _: ConfigException.Missing => s"Could not find key: $key".invalidNel
       case _: ConfigException.WrongType => s"key $key cannot be parsed to a Config".invalidNel
     }
@@ -50,6 +50,7 @@ object ConfigUtil {
   }
 
   implicit class EnhancedValidation[I <: AnyRef](val value: I) extends AnyVal {
+
     /**
      * Validates this value by applying validationFunction to it and returning a Validation:
      * Returns successNel upon success.
@@ -58,9 +59,9 @@ object ConfigUtil {
      * @tparam O return type of validationFunction
      * @tparam E Restricts the subtype of Exception that should be caught during validation
      */
-    def validateAny[O, E <: Exception: ClassTag](validationFunction: I => O): ValidatedNel[String, O] = try {
+    def validateAny[O, E <: Exception: ClassTag](validationFunction: I => O): ValidatedNel[String, O] = try
       validationFunction(value).validNel
-    } catch {
+    catch {
       case e if classTag[E].runtimeClass.isInstance(e) => e.getMessage.invalidNel
     }
   }
diff --git a/core/src/main/scala/cromwell/core/DockerConfiguration.scala b/core/src/main/scala/cromwell/core/DockerConfiguration.scala
index e765eec80fe..3f2dfa5c6f8 100644
--- a/core/src/main/scala/cromwell/core/DockerConfiguration.scala
+++ b/core/src/main/scala/cromwell/core/DockerConfiguration.scala
@@ -18,23 +18,30 @@ object DockerConfiguration {
 
   lazy val instance: DockerConfiguration = {
     if (dockerHashLookupConfig.hasPath("gcr-api-queries-per-100-seconds")) {
-      logger.warn("'docker.hash-lookup.gcr-api-queries-per-100-seconds' is no longer supported, use 'docker.hash-lookup.google.throttle' instead (see reference.conf)")
+      logger.warn(
+        "'docker.hash-lookup.gcr-api-queries-per-100-seconds' is no longer supported, use 'docker.hash-lookup.google.throttle' instead (see reference.conf)"
+      )
     }
-    val enabled = validate { dockerHashLookupConfig.as[Boolean]("enabled") }
-    val cacheEntryTtl = validate { dockerHashLookupConfig.as[FiniteDuration]("cache-entry-ttl") }
-    val cacheSize = validate { dockerHashLookupConfig.as[Long]("cache-size") }
-    val method: ErrorOr[DockerHashLookupMethod] = validate { dockerHashLookupConfig.as[String]("method") } map {
+    val enabled = validate(dockerHashLookupConfig.as[Boolean]("enabled"))
+    val cacheEntryTtl = validate(dockerHashLookupConfig.as[FiniteDuration]("cache-entry-ttl"))
+    val cacheSize = validate(dockerHashLookupConfig.as[Long]("cache-size"))
+    val method: ErrorOr[DockerHashLookupMethod] = validate(dockerHashLookupConfig.as[String]("method")) map {
       case "local" => DockerLocalLookup
       case "remote" => DockerRemoteLookup
       case other => throw new IllegalArgumentException(s"Unrecognized docker hash lookup method: $other")
     }
-    val sizeCompressionFactor = validate { dockerHashLookupConfig.as[Double]("size-compression-factor") }
-    val maxTimeBetweenRetries = validate { dockerHashLookupConfig.as[FiniteDuration]("max-time-between-retries") }
-    val maxRetries = validate { dockerHashLookupConfig.as[Int]("max-retries") }
+    val sizeCompressionFactor = validate(dockerHashLookupConfig.as[Double]("size-compression-factor"))
+    val maxTimeBetweenRetries = validate(dockerHashLookupConfig.as[FiniteDuration]("max-time-between-retries"))
+    val maxRetries = validate(dockerHashLookupConfig.as[Int]("max-retries"))
 
     val dockerConfiguration = (enabled,
-      cacheEntryTtl, cacheSize, method,
-      sizeCompressionFactor, maxTimeBetweenRetries, maxRetries) mapN DockerConfiguration.apply
+                               cacheEntryTtl,
+                               cacheSize,
+                               method,
+                               sizeCompressionFactor,
+                               maxTimeBetweenRetries,
+                               maxRetries
+    ) mapN DockerConfiguration.apply
 
     dockerConfiguration match {
       case Valid(conf) => conf
@@ -44,14 +51,14 @@ object DockerConfiguration {
 }
 
 case class DockerConfiguration(
-                                enabled: Boolean,
-                                cacheEntryTtl: FiniteDuration,
-                                cacheSize: Long,
-                                method: DockerHashLookupMethod,
-                                sizeCompressionFactor: Double,
-                                maxTimeBetweenRetries: FiniteDuration,
-                                maxRetries: Int
-                              )
+  enabled: Boolean,
+  cacheEntryTtl: FiniteDuration,
+  cacheSize: Long,
+  method: DockerHashLookupMethod,
+  sizeCompressionFactor: Double,
+  maxTimeBetweenRetries: FiniteDuration,
+  maxRetries: Int
+)
 
 sealed trait DockerHashLookupMethod
 
diff --git a/core/src/main/scala/cromwell/core/Encryption.scala b/core/src/main/scala/cromwell/core/Encryption.scala
index 0258d4511e3..4e05693b003 100644
--- a/core/src/main/scala/cromwell/core/Encryption.scala
+++ b/core/src/main/scala/cromwell/core/Encryption.scala
@@ -31,15 +31,18 @@ case object Aes256Cbc {
     cipher
   }
 
-  final def validateLength(arrayName: String, array: Array[Byte], expectedBitLength: Int): Try[Unit] = {
+  final def validateLength(arrayName: String, array: Array[Byte], expectedBitLength: Int): Try[Unit] =
     if (array.length * 8 == expectedBitLength) {
       Success(())
     } else {
-      Failure(new IllegalArgumentException(s"$arrayName size (${array.length * 8} bits) did not match the required length $expectedBitLength"))
+      Failure(
+        new IllegalArgumentException(
+          s"$arrayName size (${array.length * 8} bits) did not match the required length $expectedBitLength"
+        )
+      )
     }
-  }
 
-  final def encrypt(plainText: Array[Byte], secretKey: SecretKey): Try[EncryptedBytes] = {
+  final def encrypt(plainText: Array[Byte], secretKey: SecretKey): Try[EncryptedBytes] =
     validateLength("Secret key", secretKey.key, keySize) map { _ =>
       val iv = new Array[Byte](blockSize / 8)
       ranGen.nextBytes(iv)
@@ -47,15 +50,15 @@ case object Aes256Cbc {
       val cipher = init(Cipher.ENCRYPT_MODE, secretKey.key, iv)
       EncryptedBytes(cipher.doFinal(plainText), iv)
     }
-  }
 
-  final def decrypt(encryptedBytes: EncryptedBytes, secretKey: SecretKey): Try[Array[Byte]] = {
+  final def decrypt(encryptedBytes: EncryptedBytes, secretKey: SecretKey): Try[Array[Byte]] =
     for {
       _ <- validateLength("Secret key", secretKey.key, keySize)
       _ <- validateLength("Initialization vector", encryptedBytes.initializationVector, blockSize)
-      bytes = init(Cipher.DECRYPT_MODE, secretKey.key, encryptedBytes.initializationVector).doFinal(encryptedBytes.cipherText)
+      bytes = init(Cipher.DECRYPT_MODE, secretKey.key, encryptedBytes.initializationVector).doFinal(
+        encryptedBytes.cipherText
+      )
     } yield bytes
-  }
 }
 
 final case class EncryptedBytes(cipherText: Array[Byte], initializationVector: Array[Byte]) {
@@ -71,4 +74,4 @@ object EncryptedBytes {
 final case class SecretKey(key: Array[Byte])
 object SecretKey {
   def apply(base64KeyString: String): SecretKey = SecretKey(Base64.decodeBase64(base64KeyString))
-}
\ No newline at end of file
+}
diff --git a/core/src/main/scala/cromwell/core/ExecutionIndex.scala b/core/src/main/scala/cromwell/core/ExecutionIndex.scala
index 4f04179db0c..926fad13c11 100644
--- a/core/src/main/scala/cromwell/core/ExecutionIndex.scala
+++ b/core/src/main/scala/cromwell/core/ExecutionIndex.scala
@@ -23,8 +23,7 @@ object ExecutionIndex {
   }
 
   implicit val ExecutionIndexOrdering = new Ordering[ExecutionIndex] {
-    override def compare(x: ExecutionIndex, y: ExecutionIndex): Int = {
+    override def compare(x: ExecutionIndex, y: ExecutionIndex): Int =
       x.fromIndex.compareTo(y.fromIndex)
-    }
   }
 }
diff --git a/core/src/main/scala/cromwell/core/ExecutionStatus.scala b/core/src/main/scala/cromwell/core/ExecutionStatus.scala
index 3d4016d90a5..fa2ece67ab5 100644
--- a/core/src/main/scala/cromwell/core/ExecutionStatus.scala
+++ b/core/src/main/scala/cromwell/core/ExecutionStatus.scala
@@ -2,7 +2,8 @@ package cromwell.core
 
 object ExecutionStatus extends Enumeration {
   type ExecutionStatus = Value
-  val NotStarted, WaitingForQueueSpace, QueuedInCromwell, Starting, Running, Aborting, Failed, RetryableFailure, Done, Bypassed, Aborted, Unstartable = Value
+  val NotStarted, WaitingForQueueSpace, QueuedInCromwell, Starting, Running, Aborting, Failed, RetryableFailure, Done,
+    Bypassed, Aborted, Unstartable = Value
   val TerminalStatuses = Set(Failed, Done, Aborted, Bypassed, Unstartable)
   val TerminalOrRetryableStatuses = TerminalStatuses + RetryableFailure
   val NonTerminalStatuses = values.diff(TerminalOrRetryableStatuses)
@@ -24,7 +25,7 @@ object ExecutionStatus extends Enumeration {
       case Done => 11
     }
   }
-  
+
   implicit class EnhancedExecutionStatus(val status: ExecutionStatus) extends AnyVal {
     def isTerminal: Boolean = TerminalStatuses contains status
 
diff --git a/core/src/main/scala/cromwell/core/HogGroup.scala b/core/src/main/scala/cromwell/core/HogGroup.scala
index 87bcad5d0c9..c49b84a9ecc 100644
--- a/core/src/main/scala/cromwell/core/HogGroup.scala
+++ b/core/src/main/scala/cromwell/core/HogGroup.scala
@@ -17,16 +17,16 @@ object HogGroup {
     if (config.hasPath("system.hog-safety.workflow-option")) {
       val hogGroupField = config.getString("system.hog-safety.workflow-option")
 
-      (options, workflowId) => {
+      (options, workflowId) =>
         options.get(hogGroupField) match {
           case Success(hg) => HogGroup(hg)
           case Failure(_) => HogGroup(workflowId.shortString)
         }
-      }
-    } else {
-      (_, workflowId) => HogGroup(workflowId.shortString)
+    } else { (_, workflowId) =>
+      HogGroup(workflowId.shortString)
     }
   }
 
-  def decide(workflowOptions: WorkflowOptions, workflowId: WorkflowId): HogGroup = HogGroupDeciderFunction.apply(workflowOptions, workflowId)
+  def decide(workflowOptions: WorkflowOptions, workflowId: WorkflowId): HogGroup =
+    HogGroupDeciderFunction.apply(workflowOptions, workflowId)
 }
diff --git a/core/src/main/scala/cromwell/core/JobKey.scala b/core/src/main/scala/cromwell/core/JobKey.scala
index e5f990aa433..99118dc2235 100644
--- a/core/src/main/scala/cromwell/core/JobKey.scala
+++ b/core/src/main/scala/cromwell/core/JobKey.scala
@@ -13,6 +13,6 @@ trait JobKey {
     import ExecutionIndex.IndexEnhancedIndex
     s"${getClass.getSimpleName}_${node.getClass.getSimpleName}_${node.fullyQualifiedName}:${index.fromIndex}:$attempt"
   }
-  
- def isShard = index.isDefined
+
+  def isShard = index.isDefined
 }
diff --git a/core/src/main/scala/cromwell/core/MonitoringCompanionActor.scala b/core/src/main/scala/cromwell/core/MonitoringCompanionActor.scala
index 53f0e4de6fc..8932b3f6836 100644
--- a/core/src/main/scala/cromwell/core/MonitoringCompanionActor.scala
+++ b/core/src/main/scala/cromwell/core/MonitoringCompanionActor.scala
@@ -9,21 +9,21 @@ import scala.language.postfixOps
 
 object MonitoringCompanionActor {
   sealed trait MonitoringCompanionCommand
-  private [core] case object AddWork extends MonitoringCompanionCommand
-  private [core] case object RemoveWork extends MonitoringCompanionCommand
-  private [core] def props(actorToMonitor: ActorRef) = Props(new MonitoringCompanionActor(actorToMonitor))
+  private[core] case object AddWork extends MonitoringCompanionCommand
+  private[core] case object RemoveWork extends MonitoringCompanionCommand
+  private[core] def props(actorToMonitor: ActorRef) = Props(new MonitoringCompanionActor(actorToMonitor))
 }
 
-private [core] class MonitoringCompanionActor(actorToMonitor: ActorRef) extends Actor with ActorLogging {
+private[core] class MonitoringCompanionActor(actorToMonitor: ActorRef) extends Actor with ActorLogging {
   private var workCount: Int = 0
-  
+
   override def receive = {
     case AddWork => workCount += 1
     case RemoveWork => workCount -= 1
     case ShutdownCommand if workCount <= 0 =>
       context stop actorToMonitor
       context stop self
-    case ShutdownCommand => 
+    case ShutdownCommand =>
       log.info(s"{} is still processing {} messages", actorToMonitor.path.name, workCount)
       context.system.scheduler.scheduleOnce(1 second, self, ShutdownCommand)(context.dispatcher)
       ()
@@ -33,12 +33,12 @@ private [core] class MonitoringCompanionActor(actorToMonitor: ActorRef) extends
 trait MonitoringCompanionHelper { this: Actor =>
   private val monitoringActor = context.actorOf(MonitoringCompanionActor.props(self))
   private var shuttingDown: Boolean = false
-  
+
   def addWork() = monitoringActor ! AddWork
   def removeWork() = monitoringActor ! RemoveWork
 
   val monitoringReceive: Receive = {
-    case ShutdownCommand if !shuttingDown => 
+    case ShutdownCommand if !shuttingDown =>
       shuttingDown = true
       monitoringActor ! ShutdownCommand
     case ShutdownCommand => // Ignore if we're already shutting down
diff --git a/core/src/main/scala/cromwell/core/WorkflowId.scala b/core/src/main/scala/cromwell/core/WorkflowId.scala
index feb0ee601a9..f2444738fed 100644
--- a/core/src/main/scala/cromwell/core/WorkflowId.scala
+++ b/core/src/main/scala/cromwell/core/WorkflowId.scala
@@ -8,19 +8,17 @@ sealed trait WorkflowId {
   override def toString = id.toString
   def shortString = id.toString.split("-")(0)
 
-  def toRoot: RootWorkflowId = {
+  def toRoot: RootWorkflowId =
     this match {
       case root: RootWorkflowId => root
       case _ => RootWorkflowId(id)
     }
-  }
 
-  def toPossiblyNotRoot: PossiblyNotRootWorkflowId = {
+  def toPossiblyNotRoot: PossiblyNotRootWorkflowId =
     this match {
       case possiblyNotRoot: PossiblyNotRootWorkflowId => possiblyNotRoot
       case _ => PossiblyNotRootWorkflowId(id)
     }
-  }
 }
 
 object WorkflowId {
diff --git a/core/src/main/scala/cromwell/core/WorkflowOptions.scala b/core/src/main/scala/cromwell/core/WorkflowOptions.scala
index 91a7c30bbfe..cbdb1201986 100644
--- a/core/src/main/scala/cromwell/core/WorkflowOptions.scala
+++ b/core/src/main/scala/cromwell/core/WorkflowOptions.scala
@@ -55,7 +55,7 @@ object WorkflowOptions {
   case object FinalWorkflowLogDir extends WorkflowOption("final_workflow_log_dir")
   case object FinalCallLogsDir extends WorkflowOption("final_call_logs_dir")
   case object FinalWorkflowOutputsDir extends WorkflowOption("final_workflow_outputs_dir")
-  case object UseRelativeOutputPaths extends WorkflowOption(name="use_relative_output_paths")
+  case object UseRelativeOutputPaths extends WorkflowOption(name = "use_relative_output_paths")
 
   // Misc.
   case object DefaultRuntimeOptions extends WorkflowOption("default_runtime_attributes")
@@ -70,23 +70,28 @@ object WorkflowOptions {
   private lazy val defaultRuntimeOptionKey: String = DefaultRuntimeOptions.name
   private lazy val validObjectKeys: Set[String] = Set(DefaultRuntimeOptions.name, "google_labels")
 
-  def encryptField(value: JsString): Try[JsObject] = {
+  def encryptField(value: JsString): Try[JsObject] =
     Aes256Cbc.encrypt(value.value.getBytes("utf-8"), SecretKey(EncryptionKey)) match {
-      case Success(encryptedValue) => Success(JsObject(Map(
-        "iv" -> JsString(encryptedValue.base64Iv),
-        "ciphertext" -> JsString(encryptedValue.base64CipherText)
-      )))
+      case Success(encryptedValue) =>
+        Success(
+          JsObject(
+            Map(
+              "iv" -> JsString(encryptedValue.base64Iv),
+              "ciphertext" -> JsString(encryptedValue.base64CipherText)
+            )
+          )
+        )
       case Failure(ex) => Failure(ex)
     }
-  }
 
-  def decryptField(obj: JsObject): Try[String] = {
+  def decryptField(obj: JsObject): Try[String] =
     (obj.fields.get("iv"), obj.fields.get("ciphertext")) match {
       case (Some(iv: JsString), Some(ciphertext: JsString)) =>
-        Aes256Cbc.decrypt(EncryptedBytes(ciphertext.value, iv.value), SecretKey(WorkflowOptions.EncryptionKey)).map(new String(_, "utf-8"))
+        Aes256Cbc
+          .decrypt(EncryptedBytes(ciphertext.value, iv.value), SecretKey(WorkflowOptions.EncryptionKey))
+          .map(new String(_, "utf-8"))
       case _ => Failure(new RuntimeException(s"JsObject must have 'iv' and 'ciphertext' fields to decrypt: $obj"))
     }
-  }
 
   def isEncryptedField(jsValue: JsValue): Boolean = jsValue match {
     case obj: JsObject if obj.fields.keys.exists(_ == "iv") && obj.fields.keys.exists(_ == "ciphertext") => true
@@ -102,7 +107,8 @@ object WorkflowOptions {
       case (k, v: JsNumber) => k -> Success(v)
       case (k, v) if isEncryptedField(v) => k -> Success(v)
       case (k, v: JsArray) => k -> Success(v)
-      case (k, v) => k -> Failure(new UnsupportedOperationException(s"Unsupported key/value pair in WorkflowOptions: $k -> $v"))
+      case (k, v) =>
+        k -> Failure(new UnsupportedOperationException(s"Unsupported key/value pair in WorkflowOptions: $k -> $v"))
     }
 
     encrypted.values collect { case f: Failure[_] => f } match {
@@ -117,7 +123,7 @@ object WorkflowOptions {
     case Success(x) => Failure(new UnsupportedOperationException(s"Expecting JSON object, got $x"))
   }
 
-  def fromMap(m: Map[String, String]) = fromJsonObject(JsObject(m map { case (k, v) => k -> JsString(v)}))
+  def fromMap(m: Map[String, String]) = fromJsonObject(JsObject(m map { case (k, v) => k -> JsString(v) }))
 
   private def getAsJson(key: String, jsObject: JsObject) = jsObject.fields.get(key) match {
     case Some(jsStr: JsString) => Success(jsStr)
@@ -157,7 +163,7 @@ case class WorkflowOptions(jsObject: JsObject) {
   }
 
   def getVectorOfStrings(key: String): ErrorOr[Option[Vector[String]]] = jsObject.fields.get(key) match {
-    case Some(jsArr: JsArray) => Option(jsArr.elements collect { case e: JsString => e.value } ).validNel
+    case Some(jsArr: JsArray) => Option(jsArr.elements collect { case e: JsString => e.value }).validNel
     case Some(jsVal: JsValue) => s"Unsupported JsValue as JsArray: $jsVal".invalidNel
     case _ => None.validNel
   }
@@ -167,8 +173,14 @@ case class WorkflowOptions(jsObject: JsObject) {
   }
 
   lazy val defaultRuntimeOptions = jsObject.fields.get(defaultRuntimeOptionKey) match {
-    case Some(jsObj: JsObject) => TryUtil.sequenceMap(jsObj.fields map { case (k, _) => k -> WorkflowOptions.getAsJson(k, jsObj) })
-    case Some(jsVal) => Failure(new IllegalArgumentException(s"Unsupported JsValue for $defaultRuntimeOptionKey: $jsVal. Expected a JSON object."))
+    case Some(jsObj: JsObject) =>
+      TryUtil.sequenceMap(jsObj.fields map { case (k, _) => k -> WorkflowOptions.getAsJson(k, jsObj) })
+    case Some(jsVal) =>
+      Failure(
+        new IllegalArgumentException(
+          s"Unsupported JsValue for $defaultRuntimeOptionKey: $jsVal. Expected a JSON object."
+        )
+      )
     case None => Failure(OptionNotFoundException(s"Cannot find definition for default runtime attributes"))
   }
 
diff --git a/core/src/main/scala/cromwell/core/WorkflowProcessingEvents.scala b/core/src/main/scala/cromwell/core/WorkflowProcessingEvents.scala
index ab80bf78724..e2db6df75c8 100644
--- a/core/src/main/scala/cromwell/core/WorkflowProcessingEvents.scala
+++ b/core/src/main/scala/cromwell/core/WorkflowProcessingEvents.scala
@@ -36,4 +36,8 @@ object WorkflowProcessingEvents {
   val ProcessingEventsKey = "workflowProcessingEvents"
 }
 
-case class WorkflowProcessingEvent(cromwellId: String, description: String, timestamp: OffsetDateTime, cromwellVersion: String)
+case class WorkflowProcessingEvent(cromwellId: String,
+                                   description: String,
+                                   timestamp: OffsetDateTime,
+                                   cromwellVersion: String
+)
diff --git a/core/src/main/scala/cromwell/core/WorkflowSourceFilesCollection.scala b/core/src/main/scala/cromwell/core/WorkflowSourceFilesCollection.scala
index ee936b86819..aa1faf89542 100644
--- a/core/src/main/scala/cromwell/core/WorkflowSourceFilesCollection.scala
+++ b/core/src/main/scala/cromwell/core/WorkflowSourceFilesCollection.scala
@@ -22,16 +22,15 @@ sealed trait WorkflowSourceFilesCollection {
 
   def importsZipFileOption: Option[Array[Byte]] = this match {
     case _: WorkflowSourceFilesWithoutImports => None
-    case w: WorkflowSourceFilesWithDependenciesZip => Option(w.importsZip) // i.e. Some(importsZip) if our wiring is correct
+    case w: WorkflowSourceFilesWithDependenciesZip =>
+      Option(w.importsZip) // i.e. Some(importsZip) if our wiring is correct
   }
 
-  def setOptions(workflowOptions: WorkflowOptions) = {
-
+  def setOptions(workflowOptions: WorkflowOptions) =
     this match {
       case w: WorkflowSourceFilesWithoutImports => w.copy(workflowOptions = workflowOptions)
       case w: WorkflowSourceFilesWithDependenciesZip => w.copy(workflowOptions = workflowOptions)
     }
-  }
 }
 
 trait HasWorkflowIdAndSources {
@@ -51,7 +50,8 @@ object WorkflowSourceFilesCollection {
             importsFile: Option[Array[Byte]],
             workflowOnHold: Boolean,
             warnings: Seq[String],
-            requestedWorkflowId: Option[WorkflowId]): WorkflowSourceFilesCollection = importsFile match {
+            requestedWorkflowId: Option[WorkflowId]
+  ): WorkflowSourceFilesCollection = importsFile match {
     case Some(imports) =>
       WorkflowSourceFilesWithDependenciesZip(
         workflowSource = workflowSource,
@@ -65,7 +65,8 @@ object WorkflowSourceFilesCollection {
         importsZip = imports,
         workflowOnHold = workflowOnHold,
         warnings = warnings,
-        requestedWorkflowId = requestedWorkflowId)
+        requestedWorkflowId = requestedWorkflowId
+      )
     case None =>
       WorkflowSourceFilesWithoutImports(
         workflowSource = workflowSource,
@@ -78,7 +79,8 @@ object WorkflowSourceFilesCollection {
         labelsJson = labelsJson,
         workflowOnHold = workflowOnHold,
         warnings = warnings,
-        requestedWorkflowId = requestedWorkflowId)
+        requestedWorkflowId = requestedWorkflowId
+      )
   }
 }
 
@@ -92,7 +94,8 @@ final case class WorkflowSourceFilesWithoutImports(workflowSource: Option[Workfl
                                                    labelsJson: WorkflowJson,
                                                    workflowOnHold: Boolean = false,
                                                    warnings: Seq[String],
-                                                   requestedWorkflowId: Option[WorkflowId]) extends WorkflowSourceFilesCollection
+                                                   requestedWorkflowId: Option[WorkflowId]
+) extends WorkflowSourceFilesCollection
 
 final case class WorkflowSourceFilesWithDependenciesZip(workflowSource: Option[WorkflowSource],
                                                         workflowUrl: Option[WorkflowUrl],
@@ -105,9 +108,9 @@ final case class WorkflowSourceFilesWithDependenciesZip(workflowSource: Option[W
                                                         importsZip: Array[Byte],
                                                         workflowOnHold: Boolean = false,
                                                         warnings: Seq[String],
-                                                        requestedWorkflowId: Option[WorkflowId]) extends WorkflowSourceFilesCollection {
-  override def toString = {
+                                                        requestedWorkflowId: Option[WorkflowId]
+) extends WorkflowSourceFilesCollection {
+  override def toString =
     s"WorkflowSourceFilesWithDependenciesZip($workflowSource, $workflowUrl, $workflowType, $workflowTypeVersion," +
       s""" $inputsJson, ${workflowOptions.asPrettyJson}, $labelsJson, <<ZIP BINARY CONTENT>>, $warnings)"""
-  }
 }
diff --git a/core/src/main/scala/cromwell/core/WorkflowState.scala b/core/src/main/scala/cromwell/core/WorkflowState.scala
index db4bddfedc5..26294ff648b 100644
--- a/core/src/main/scala/cromwell/core/WorkflowState.scala
+++ b/core/src/main/scala/cromwell/core/WorkflowState.scala
@@ -2,7 +2,6 @@ package cromwell.core
 
 import cats.Semigroup
 
-
 sealed trait WorkflowState {
   def isTerminal: Boolean
   protected def ordinal: Int
@@ -10,10 +9,18 @@ sealed trait WorkflowState {
 }
 
 object WorkflowState {
-  lazy val WorkflowStateValues = Seq(WorkflowOnHold, WorkflowSubmitted, WorkflowRunning, WorkflowFailed, WorkflowSucceeded, WorkflowAborting, WorkflowAborted)
+  lazy val WorkflowStateValues = Seq(WorkflowOnHold,
+                                     WorkflowSubmitted,
+                                     WorkflowRunning,
+                                     WorkflowFailed,
+                                     WorkflowSucceeded,
+                                     WorkflowAborting,
+                                     WorkflowAborted
+  )
 
-  def withName(str: String): WorkflowState = WorkflowStateValues.find(_.toString.equalsIgnoreCase(str)).getOrElse(
-    throw new NoSuchElementException(s"No such WorkflowState: $str"))
+  def withName(str: String): WorkflowState = WorkflowStateValues
+    .find(_.toString.equalsIgnoreCase(str))
+    .getOrElse(throw new NoSuchElementException(s"No such WorkflowState: $str"))
 
   implicit val WorkflowStateSemigroup = new Semigroup[WorkflowState] {
     override def combine(f1: WorkflowState, f2: WorkflowState): WorkflowState = f1.combine(f2)
@@ -22,7 +29,7 @@ object WorkflowState {
   implicit val WorkflowStateOrdering = Ordering.by { self: WorkflowState => self.ordinal }
 }
 
-case object WorkflowOnHold extends WorkflowState{
+case object WorkflowOnHold extends WorkflowState {
   override val toString: String = "On Hold"
   override val isTerminal = false
   override val ordinal = 0
diff --git a/core/src/main/scala/cromwell/core/actor/BatchActor.scala b/core/src/main/scala/cromwell/core/actor/BatchActor.scala
index 5988dd822d2..9b002f4fcf5 100644
--- a/core/src/main/scala/cromwell/core/actor/BatchActor.scala
+++ b/core/src/main/scala/cromwell/core/actor/BatchActor.scala
@@ -14,7 +14,6 @@ import scala.concurrent.Future
 import scala.concurrent.duration.{Duration, FiniteDuration}
 import scala.util.{Failure, Success}
 
-
 /** A collection of state, data, and message types to support BatchActor. */
 object BatchActor {
   type BatchData[C] = WeightedQueue[C, Int]
@@ -45,8 +44,9 @@ object BatchActor {
   * It is backed by a WeightedQueue which makes it possible to decouple the number of messages received from
   * the effective "weight" of the queue.
   */
-abstract class BatchActor[C](val flushRate: FiniteDuration,
-                             val batchSize: Int) extends FSM[BatchActorState, BatchData[C]] with Timers {
+abstract class BatchActor[C](val flushRate: FiniteDuration, val batchSize: Int)
+    extends FSM[BatchActorState, BatchData[C]]
+    with Timers {
   private var shuttingDown: Boolean = false
 
   implicit val ec = context.dispatcher
@@ -63,7 +63,8 @@ abstract class BatchActor[C](val flushRate: FiniteDuration,
   protected def routed: Boolean = false
 
   override def preStart(): Unit = {
-    if (logOnStartUp) log.info("{} configured to flush with batch size {} and process rate {}.", name, batchSize, flushRate)
+    if (logOnStartUp)
+      log.info("{} configured to flush with batch size {} and process rate {}.", name, batchSize, flushRate)
     if (flushRate != Duration.Zero) {
       timers.startPeriodicTimer(ScheduledFlushKey, ScheduledProcessAction, flushRate)
     }
@@ -133,10 +134,9 @@ abstract class BatchActor[C](val flushRate: FiniteDuration,
     */
   protected def process(data: NonEmptyVector[C]): Future[Int]
 
-  private def processIfBatchSizeReached(data: BatchData[C]) = {
+  private def processIfBatchSizeReached(data: BatchData[C]) =
     if (data.weight >= batchSize) processHead(data)
     else goto(WaitingToProcess) using data
-  }
 
   private def processHead(data: BatchData[C]) = if (data.innerQueue.nonEmpty) {
     val (head, newQueue) = data.behead(batchSize)
@@ -159,8 +159,8 @@ abstract class BatchActor[C](val flushRate: FiniteDuration,
 
     goto(Processing) using newQueue
   } else
-  // This goto is important, even if we're already in WaitingToProcess we want to trigger the onTransition below
-  // to check if it's time to shutdown
+    // This goto is important, even if we're already in WaitingToProcess we want to trigger the onTransition below
+    // to check if it's time to shutdown
     goto(WaitingToProcess) using data
 
   onTransition {
diff --git a/core/src/main/scala/cromwell/core/actor/RobustClientHelper.scala b/core/src/main/scala/cromwell/core/actor/RobustClientHelper.scala
index d8b0cbe0716..85376bedb37 100644
--- a/core/src/main/scala/cromwell/core/actor/RobustClientHelper.scala
+++ b/core/src/main/scala/cromwell/core/actor/RobustClientHelper.scala
@@ -15,14 +15,14 @@ object RobustClientHelper {
 }
 
 trait RobustClientHelper { this: Actor with ActorLogging =>
-  private [actor] implicit val robustActorHelperEc = context.dispatcher
+  implicit private[actor] val robustActorHelperEc = context.dispatcher
 
   private var backoff: Option[Backoff] = None
 
   // package private for testing
-  private [core] var timeouts = Map.empty[Any, (Cancellable, FiniteDuration)]
+  private[core] var timeouts = Map.empty[Any, (Cancellable, FiniteDuration)]
 
-  protected def initialBackoff(): Backoff = SimpleExponentialBackoff(5.seconds, 20.minutes, 2D)
+  protected def initialBackoff(): Backoff = SimpleExponentialBackoff(5.seconds, 20.minutes, 2d)
 
   def robustReceive: Receive = {
     case BackPressure(request) =>
@@ -33,39 +33,38 @@ trait RobustClientHelper { this: Actor with ActorLogging =>
     case RequestTimeout(request, to) => onTimeout(request, to)
   }
 
-  private final def newTimer(msg: Any, to: ActorRef, in: FiniteDuration) = {
+  final private def newTimer(msg: Any, to: ActorRef, in: FiniteDuration) =
     context.system.scheduler.scheduleOnce(in, to, msg)(robustActorHelperEc, self)
-  }
 
   def robustSend(msg: Any, to: ActorRef, timeout: FiniteDuration = DefaultRequestLostTimeout): Unit = {
     to ! msg
     addTimeout(msg, to, timeout)
   }
 
-  private final def addTimeout(command: Any, to: ActorRef, timeout: FiniteDuration) = {
+  final private def addTimeout(command: Any, to: ActorRef, timeout: FiniteDuration) = {
     val cancellable = newTimer(RequestTimeout(command, to), self, timeout)
     timeouts = timeouts + (command -> (cancellable -> timeout))
   }
 
-  protected final def hasTimeout(command: Any) = timeouts.get(command).isDefined
+  final protected def hasTimeout(command: Any) = timeouts.get(command).isDefined
 
-  protected final def cancelTimeout(command: Any) = {
+  final protected def cancelTimeout(command: Any) = {
     timeouts.get(command) foreach { case (cancellable, _) => cancellable.cancel() }
     timeouts = timeouts - command
   }
 
-  private final def resetTimeout(command: Any, to: ActorRef) = {
+  final private def resetTimeout(command: Any, to: ActorRef) = {
     val timeout = timeouts.get(command) map { _._2 }
     cancelTimeout(command)
     timeout foreach { addTimeout(command, to, _) }
   }
 
-  private [actor] final def generateBackpressureTime: FiniteDuration = {
-    val effectiveBackoff = backoff.getOrElse({
+  final private[actor] def generateBackpressureTime: FiniteDuration = {
+    val effectiveBackoff = backoff.getOrElse {
       val firstBackoff = initialBackoff()
       backoff = Option(firstBackoff)
       firstBackoff
-    })
+    }
     val backoffTime = effectiveBackoff.backoffMillis
     backoff = Option(effectiveBackoff.next)
     backoffTime.millis
diff --git a/core/src/main/scala/cromwell/core/actor/StreamActorHelper.scala b/core/src/main/scala/cromwell/core/actor/StreamActorHelper.scala
index d03853e5585..023a01dc450 100644
--- a/core/src/main/scala/cromwell/core/actor/StreamActorHelper.scala
+++ b/core/src/main/scala/cromwell/core/actor/StreamActorHelper.scala
@@ -13,8 +13,8 @@ import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success}
 
 object StreamActorHelper {
-  private [actor] case class StreamFailed(failure: Throwable)
-  private [actor] case object StreamCompleted
+  private[actor] case class StreamFailed(failure: Throwable)
+  private[actor] case object StreamCompleted
   class ActorRestartException(throwable: Throwable) extends RuntimeException(throwable)
 }
 
@@ -25,71 +25,68 @@ trait StreamActorHelper[T <: StreamContext] { this: Actor with ActorLogging =>
   implicit def materializer: ActorMaterializer
 
   private val decider: Supervision.Decider = _ => Supervision.Resume
-  
-  private val replySink = Sink.foreach[(Any, T)] {
-    case (response, commandContext) =>
-      val reply = commandContext.clientContext map { (_, response) } getOrElse response
-      commandContext.replyTo ! reply
+
+  private val replySink = Sink.foreach[(Any, T)] { case (response, commandContext) =>
+    val reply = commandContext.clientContext map { (_, response) } getOrElse response
+    commandContext.replyTo ! reply
   }
 
   protected def actorReceive: Receive
-  
+
   protected def streamSource: Source[(Any, T), SourceQueueWithComplete[T]]
 
   override def receive = streamReceive.orElse(actorReceive)
-  
+
   protected def onBackpressure(scale: Option[Double] = None): Unit = {}
 
-  private [actor] lazy val stream = {
+  private[actor] lazy val stream =
     streamSource
       .to(replySink)
       .withAttributes(ActorAttributes.supervisionStrategy(decider))
       .run()
-  }
 
-  override def preStart(): Unit = {
+  override def preStart(): Unit =
     stream.watchCompletion() onComplete {
       case Success(_) => self ! StreamCompleted
       case Failure(failure) => self ! StreamFailed(failure)
     }
-  }
 
   def sendToStream(commandContext: T) = {
     val enqueue = stream offer commandContext map {
       case Enqueued => EnqueueResponse(Enqueued, commandContext)
       case other => EnqueueResponse(other, commandContext)
-    } recoverWith {
-      case t => Future.successful(FailedToEnqueue(t, commandContext))
+    } recoverWith { case t =>
+      Future.successful(FailedToEnqueue(t, commandContext))
     }
 
     pipe(enqueue) to self
     ()
   }
-  
+
   private def backpressure(commandContext: StreamContext) = {
-    val originalRequest = commandContext.clientContext map { _ -> commandContext.request } getOrElse commandContext.request
+    val originalRequest = commandContext.clientContext map {
+      _ -> commandContext.request
+    } getOrElse commandContext.request
     commandContext.replyTo ! BackPressure(originalRequest)
     onBackpressure()
   }
 
   private def streamReceive: Receive = {
-    case ShutdownCommand => 
+    case ShutdownCommand =>
       stream.complete()
     case EnqueueResponse(Enqueued, _: T @unchecked) => // Good !
-
     case EnqueueResponse(_, commandContext) => backpressure(commandContext)
     case FailedToEnqueue(_, commandContext) => backpressure(commandContext)
-      
-    case StreamCompleted => 
+
+    case StreamCompleted =>
       context stop self
-    case StreamFailed(failure) => 
+    case StreamFailed(failure) =>
       restart(failure)
   }
 
   /** Throw the exception to force the actor to restart so it can be back in business
     * IMPORTANT: Make sure the supervision strategy for this actor is Restart
     */
-  private def restart(throwable: Throwable) = {
+  private def restart(throwable: Throwable) =
     throw new ActorRestartException(throwable)
-  }
 }
diff --git a/core/src/main/scala/cromwell/core/actor/ThrottlerActor.scala b/core/src/main/scala/cromwell/core/actor/ThrottlerActor.scala
index c1128897445..6ddbb5f8b18 100644
--- a/core/src/main/scala/cromwell/core/actor/ThrottlerActor.scala
+++ b/core/src/main/scala/cromwell/core/actor/ThrottlerActor.scala
@@ -15,7 +15,7 @@ import scala.concurrent.duration._
 abstract class ThrottlerActor[C] extends BatchActor[C](Duration.Zero, 1) {
   override protected def logOnStartUp = false
   override def weightFunction(command: C) = 1
-  override final def process(data: NonEmptyVector[C]): Future[Int] = {
+  final override def process(data: NonEmptyVector[C]): Future[Int] =
     // This ShouldNotBePossible™ but in case it happens, instead of dropping elements process them all anyway
     // Explanation: batch size is 1 which means as soon as we receive 1 element, the process method should be called.
     // Because the BatchActor calls the process method with vector of elements which total weight is batch size, and because
@@ -25,6 +25,5 @@ abstract class ThrottlerActor[C] extends BatchActor[C](Duration.Zero, 1) {
       log.error("{} is throttled and is not supposed to process more than one element at a time !", self.path.name)
       data.toVector.traverse(processHead).map(_.length)
     } else processHead(data.head).map(_ => 1)
-  }
   def processHead(head: C): Future[Int]
 }
diff --git a/core/src/main/scala/cromwell/core/callcaching/CallCachingMode.scala b/core/src/main/scala/cromwell/core/callcaching/CallCachingMode.scala
index 23d4f396a2c..08527dbcf1d 100644
--- a/core/src/main/scala/cromwell/core/callcaching/CallCachingMode.scala
+++ b/core/src/main/scala/cromwell/core/callcaching/CallCachingMode.scala
@@ -1,6 +1,7 @@
 package cromwell.core.callcaching
 
 sealed trait CallCachingMode {
+
   /**
     * Return an equivalent of this call caching mode with READ disabled.
     */
@@ -19,11 +20,14 @@ case object CallCachingOff extends CallCachingMode {
   override val withoutWrite = this
 }
 
-case class CallCachingActivity(readWriteMode: ReadWriteMode, options: CallCachingOptions = CallCachingOptions()) extends CallCachingMode {
+case class CallCachingActivity(readWriteMode: ReadWriteMode, options: CallCachingOptions = CallCachingOptions())
+    extends CallCachingMode {
   override val readFromCache = readWriteMode.r
   override val writeToCache = readWriteMode.w
-  override lazy val withoutRead: CallCachingMode = if (!writeToCache) CallCachingOff else this.copy(readWriteMode = WriteCache)
-  override lazy val withoutWrite: CallCachingMode = if (!readFromCache) CallCachingOff else this.copy(readWriteMode = ReadCache)
+  override lazy val withoutRead: CallCachingMode =
+    if (!writeToCache) CallCachingOff else this.copy(readWriteMode = WriteCache)
+  override lazy val withoutWrite: CallCachingMode =
+    if (!readFromCache) CallCachingOff else this.copy(readWriteMode = ReadCache)
   override val toString = readWriteMode.toString
 }
 
@@ -35,4 +39,6 @@ case object ReadCache extends ReadWriteMode { override val w = false }
 case object WriteCache extends ReadWriteMode { override val r = false }
 case object ReadAndWriteCache extends ReadWriteMode
 
-final case class CallCachingOptions(invalidateBadCacheResults: Boolean = true, workflowOptionCallCachePrefixes: Option[Vector[String]] = None)
+final case class CallCachingOptions(invalidateBadCacheResults: Boolean = true,
+                                    workflowOptionCallCachePrefixes: Option[Vector[String]] = None
+)
diff --git a/core/src/main/scala/cromwell/core/callcaching/HashResultMessage.scala b/core/src/main/scala/cromwell/core/callcaching/HashResultMessage.scala
index 920702280b0..a78c7f20b6a 100644
--- a/core/src/main/scala/cromwell/core/callcaching/HashResultMessage.scala
+++ b/core/src/main/scala/cromwell/core/callcaching/HashResultMessage.scala
@@ -2,7 +2,6 @@ package cromwell.core.callcaching
 
 import cromwell.core.callcaching.HashKey.KeySeparator
 
-
 object HashKey {
   private val KeySeparator = ": "
   def apply(keyComponents: String*) = new HashKey(true, keyComponents.toList)
diff --git a/core/src/main/scala/cromwell/core/core.scala b/core/src/main/scala/cromwell/core/core.scala
index 68edbaacbe7..2535a58f5c6 100644
--- a/core/src/main/scala/cromwell/core/core.scala
+++ b/core/src/main/scala/cromwell/core/core.scala
@@ -7,7 +7,6 @@ import mouse.boolean._
 
 import scala.concurrent.duration.FiniteDuration
 
-
 case class StandardPaths(output: Path, error: Path)
 
 case class CallContext(root: Path, standardPaths: StandardPaths, isDocker: Boolean)
@@ -27,26 +26,35 @@ object CromwellFatalException {
 class CromwellFatalException(val exception: Throwable) extends Exception(exception) with CromwellFatalExceptionMarker
 
 case class CromwellAggregatedException(throwables: Seq[Throwable], exceptionContext: String = "")
-  extends Exception with ThrowableAggregation
+    extends Exception
+    with ThrowableAggregation
 
 case class CacheConfig(concurrency: Int, size: Long, ttl: FiniteDuration)
 
 import net.ceedubs.ficus.Ficus._
 object CacheConfig {
+
   /**
     * From an optional `Config` entry and specified defaults, always return a `CacheConfig` object.
     */
-  def config(caching: Option[Config], defaultConcurrency: Int, defaultSize: Long, defaultTtl: FiniteDuration): CacheConfig = {
+  def config(caching: Option[Config],
+             defaultConcurrency: Int,
+             defaultSize: Long,
+             defaultTtl: FiniteDuration
+  ): CacheConfig =
     caching flatMap { c =>
       optionalConfig(c, defaultConcurrency = defaultConcurrency, defaultSize = defaultSize, defaultTtl = defaultTtl)
     } getOrElse CacheConfig(concurrency = defaultConcurrency, size = defaultSize, ttl = defaultTtl)
-  }
 
   /**
     * From a non-optional `Config` and specified defaults, if caching is enabled return a `CacheConfig` object wrapped in a `Some`,
     * otherwise return `None`.
     */
-  def optionalConfig(caching: Config, defaultConcurrency: Int, defaultSize: Long, defaultTtl: FiniteDuration): Option[CacheConfig] = {
+  def optionalConfig(caching: Config,
+                     defaultConcurrency: Int,
+                     defaultSize: Long,
+                     defaultTtl: FiniteDuration
+  ): Option[CacheConfig] = {
     val cachingEnabled = caching.getOrElse("enabled", false)
 
     cachingEnabled.option(
diff --git a/core/src/main/scala/cromwell/core/filesystem/CromwellFileSystems.scala b/core/src/main/scala/cromwell/core/filesystem/CromwellFileSystems.scala
index caeb56509fd..ac2fe473572 100644
--- a/core/src/main/scala/cromwell/core/filesystem/CromwellFileSystems.scala
+++ b/core/src/main/scala/cromwell/core/filesystem/CromwellFileSystems.scala
@@ -24,23 +24,29 @@ import scala.util.{Failure, Try}
   */
 class CromwellFileSystems(globalConfig: Config) {
   // Validate the configuration and creates a Map of PathBuilderFactory constructors, along with their optional singleton config
-  private [filesystem] val factoryBuilders: Map[String, (Constructor[_], Option[AnyRef])] = if (globalConfig.hasPath("filesystems")) {
-    val rawConfigSet = globalConfig.getObject("filesystems").entrySet.asScala
-    val configMap = rawConfigSet.toList.map({ entry => entry.getKey -> entry.getValue })
-    val constructorMap = configMap.traverse[ErrorOr, (String, (Constructor[_], Option[AnyRef]))]({
-      case (key, fsConfig: ConfigObject) => processFileSystem(key, fsConfig)
-      case (key, _) => s"Invalid filesystem configuration for $key".invalidNel
-    }).map(_.toMap)
-
-    constructorMap.unsafe("Failed to initialize Cromwell filesystems")
-  } else Map.empty
+  private[filesystem] val factoryBuilders: Map[String, (Constructor[_], Option[AnyRef])] =
+    if (globalConfig.hasPath("filesystems")) {
+      val rawConfigSet = globalConfig.getObject("filesystems").entrySet.asScala
+      val configMap = rawConfigSet.toList.map(entry => entry.getKey -> entry.getValue)
+      val constructorMap = configMap
+        .traverse[ErrorOr, (String, (Constructor[_], Option[AnyRef]))] {
+          case (key, fsConfig: ConfigObject) => processFileSystem(key, fsConfig)
+          case (key, _) => s"Invalid filesystem configuration for $key".invalidNel
+        }
+        .map(_.toMap)
+
+      constructorMap.unsafe("Failed to initialize Cromwell filesystems")
+    } else Map.empty
 
   val supportedFileSystems: Iterable[String] = factoryBuilders.keys
 
   // Generate the appropriate constructor and optional singleton instance for a filesystem
-  private def processFileSystem(key: String, fsConfig: ConfigObject): ErrorOr[(String, (Constructor[_], Option[AnyRef]))] = {
+  private def processFileSystem(key: String,
+                                fsConfig: ConfigObject
+  ): ErrorOr[(String, (Constructor[_], Option[AnyRef]))] = {
     // This is the (optional) singleton instance shared by all factory instances
-    val singletonInstance: Checked[Option[AnyRef]] = fsConfig.toConfig.getAs[Config]("global")
+    val singletonInstance: Checked[Option[AnyRef]] = fsConfig.toConfig
+      .getAs[Config]("global")
       .map(c => instantiateSingletonConfig(key, c).toValidated)
       .sequence[ErrorOr, AnyRef]
       .toEither
@@ -57,70 +63,88 @@ class CromwellFileSystems(globalConfig: Config) {
   }
 
   // Instantiates the singleton config for a filesystem
-  private def instantiateSingletonConfig(filesystem: String, config: Config): Checked[AnyRef] = {
+  private def instantiateSingletonConfig(filesystem: String, config: Config): Checked[AnyRef] =
     for {
       constructor <- createConstructor(filesystem, config, List(classOf[Config]))
       instanceConfig = config.getAs[Config]("config").getOrElse(ConfigFactory.empty)
       instance <- Try(constructor.newInstance(instanceConfig)).toChecked
-      cast <- instance.cast[AnyRef].toChecked(s"The filesystem global configuration class for $filesystem is not a Java Object")
+      cast <- instance
+        .cast[AnyRef]
+        .toChecked(s"The filesystem global configuration class for $filesystem is not a Java Object")
     } yield cast
-  }
 
   // Create a constructor from a configuration object
-  private def createConstructor(key: String, config: Config, parameterTypes: List[Class[_]]): Checked[Constructor[_]] = for {
-    clazz <- config.as[Option[String]]("class").toChecked(s"Filesystem configuration $key doesn't have a class field")
-    constructor <- createConstructor(key, clazz, parameterTypes)
-  } yield constructor
+  private def createConstructor(key: String, config: Config, parameterTypes: List[Class[_]]): Checked[Constructor[_]] =
+    for {
+      clazz <- config.as[Option[String]]("class").toChecked(s"Filesystem configuration $key doesn't have a class field")
+      constructor <- createConstructor(key, clazz, parameterTypes)
+    } yield constructor
 
   // Getting a constructor from a class name
-  private def createConstructor(filesystem: String, className: String, parameterTypes: List[Class[_]]): Checked[Constructor[_]] = Try (
+  private def createConstructor(filesystem: String,
+                                className: String,
+                                parameterTypes: List[Class[_]]
+  ): Checked[Constructor[_]] = Try(
     Class.forName(className).getConstructor(parameterTypes: _*)
-  ).recoverWith({
-    case e: ClassNotFoundException => Failure(
-      new RuntimeException(s"Class $className for filesystem $filesystem cannot be found in the class path.", e)
-    )
-    case e: NoSuchMethodException => Failure(
-      new RuntimeException(s"Class $className for filesystem $filesystem does not have the required constructor signature: (${parameterTypes.map(_.getCanonicalName).mkString(", ")})", e)
-    )
-  }).toChecked
+  ).recoverWith {
+    case e: ClassNotFoundException =>
+      Failure(
+        new RuntimeException(s"Class $className for filesystem $filesystem cannot be found in the class path.", e)
+      )
+    case e: NoSuchMethodException =>
+      Failure(
+        new RuntimeException(
+          s"Class $className for filesystem $filesystem does not have the required constructor signature: (${parameterTypes.map(_.getCanonicalName).mkString(", ")})",
+          e
+        )
+      )
+  }.toChecked
 
   // Instantiate a PathBuilderFactory from its constructor and instance config
-  private def instantiate(name: String, constructor: Constructor[_], instanceConfig: Config, global: Option[AnyRef]): Checked[PathBuilderFactory] = {
+  private def instantiate(name: String,
+                          constructor: Constructor[_],
+                          instanceConfig: Config,
+                          global: Option[AnyRef]
+  ): Checked[PathBuilderFactory] =
     for {
       instance <- global match {
         case Some(g) => Try(constructor.newInstance(globalConfig, instanceConfig, g)).toChecked
         case None => Try(constructor.newInstance(globalConfig, instanceConfig)).toChecked
       }
-      cast <- instance.cast[PathBuilderFactory].toChecked(s"The filesystem class for $name is not an instance of PathBuilderFactory")
+      cast <- instance
+        .cast[PathBuilderFactory]
+        .toChecked(s"The filesystem class for $name is not an instance of PathBuilderFactory")
     } yield cast
-  }
 
   // Look for a constructor in the map of known filesystems
   private def getConstructor(fileSystemName: String): Checked[(Constructor[_], Option[AnyRef])] = factoryBuilders
     .get(fileSystemName)
-    .toChecked(s"Cannot find a filesystem with name $fileSystemName in the configuration. Available filesystems: ${factoryBuilders.keySet.mkString(", ")}")
+    .toChecked(
+      s"Cannot find a filesystem with name $fileSystemName in the configuration. Available filesystems: ${factoryBuilders.keySet
+          .mkString(", ")}"
+    )
 
   /**
     * Try to find a configured filesystem with the given name and build a PathFactory for it
     * @param name name of the filesystem
     * @param instanceConfig filesystem specific configuration for this instance of the factory to build
     */
-  def buildFactory(name: String, instanceConfig: Config): Checked[PathBuilderFactory] = {
+  def buildFactory(name: String, instanceConfig: Config): Checked[PathBuilderFactory] =
     if (DefaultPathBuilderFactory.name.equalsIgnoreCase(name)) DefaultPathBuilderFactory.validNelCheck
-    else for {
-      constructorAndGlobal <- getConstructor(name)
-      factory <- instantiate(name, constructorAndGlobal._1, instanceConfig, constructorAndGlobal._2)
-    } yield factory
-  }
+    else
+      for {
+        constructorAndGlobal <- getConstructor(name)
+        factory <- instantiate(name, constructorAndGlobal._1, instanceConfig, constructorAndGlobal._2)
+      } yield factory
 
   /**
     * Given a filesystems config, build the PathBuilderFactories
     */
-  def factoriesFromConfig(filesystemsConfig: Config): Checked[Map[String, PathBuilderFactory]] = {
+  def factoriesFromConfig(filesystemsConfig: Config): Checked[Map[String, PathBuilderFactory]] =
     if (filesystemsConfig.hasPath("filesystems")) {
       // Iterate over the config entries under the "filesystems" config
       val rawConfigSet = filesystemsConfig.getObject("filesystems").entrySet().asScala
-      val configMap = rawConfigSet.toList.map({ entry => entry.getKey -> entry.getValue })
+      val configMap = rawConfigSet.toList.map(entry => entry.getKey -> entry.getValue)
       import net.ceedubs.ficus.Ficus._
 
       def isFilesystemEnabled(configObject: ConfigObject): Boolean = {
@@ -141,7 +165,6 @@ class CromwellFileSystems(globalConfig: Config) {
         case (key, _) => s"Invalid filesystem backend configuration for $key".invalidNel
       } map { _.toMap } toEither
     } else Map.empty[String, PathBuilderFactory].validNelCheck
-  }
 }
 
 object CromwellFileSystems {
diff --git a/core/src/main/scala/cromwell/core/io/AsyncIo.scala b/core/src/main/scala/cromwell/core/io/AsyncIo.scala
index 435058d942c..535c7e1a8a4 100644
--- a/core/src/main/scala/cromwell/core/io/AsyncIo.scala
+++ b/core/src/main/scala/cromwell/core/io/AsyncIo.scala
@@ -23,7 +23,8 @@ object AsyncIo {
   */
 class AsyncIo(ioEndpoint: ActorRef, ioCommandBuilder: IoCommandBuilder) {
   private def asyncCommand[A](commandTry: Try[IoCommand[A]],
-                              timeout: FiniteDuration = AsyncIo.defaultTimeout): Future[A] = {
+                              timeout: FiniteDuration = AsyncIo.defaultTimeout
+  ): Future[A] =
     commandTry match {
       case Failure(throwable) =>
         Future.failed(throwable)
@@ -32,46 +33,36 @@ class AsyncIo(ioEndpoint: ActorRef, ioCommandBuilder: IoCommandBuilder) {
         ioEndpoint ! commandWithPromise
         commandWithPromise.promise.future
     }
-  }
 
   /**
     * IMPORTANT: This loads the entire content of the file into memory !
     * Only use for small files !
     */
-  def contentAsStringAsync(path: Path, maxBytes: Option[Int], failOnOverflow: Boolean): Future[String] = {
+  def contentAsStringAsync(path: Path, maxBytes: Option[Int], failOnOverflow: Boolean): Future[String] =
     asyncCommand(ioCommandBuilder.contentAsStringCommand(path, maxBytes, failOnOverflow))
-  }
 
-  def writeAsync(path: Path, content: String, options: OpenOptions, compressPayload: Boolean = false): Future[Unit] = {
+  def writeAsync(path: Path, content: String, options: OpenOptions, compressPayload: Boolean = false): Future[Unit] =
     asyncCommand(ioCommandBuilder.writeCommand(path, content, options, compressPayload))
-  }
 
-  def sizeAsync(path: Path): Future[Long] = {
+  def sizeAsync(path: Path): Future[Long] =
     asyncCommand(ioCommandBuilder.sizeCommand(path))
-  }
 
-  def hashAsync(path: Path): Future[String] = {
+  def hashAsync(path: Path): Future[String] =
     asyncCommand(ioCommandBuilder.hashCommand(path))
-  }
 
-  def deleteAsync(path: Path, swallowIoExceptions: Boolean = false): Future[Unit] = {
+  def deleteAsync(path: Path, swallowIoExceptions: Boolean = false): Future[Unit] =
     asyncCommand(ioCommandBuilder.deleteCommand(path, swallowIoExceptions))
-  }
 
-  def existsAsync(path: Path): Future[Boolean] = {
+  def existsAsync(path: Path): Future[Boolean] =
     asyncCommand(ioCommandBuilder.existsCommand(path))
-  }
 
-  def readLinesAsync(path: Path): Future[Iterable[String]] = {
+  def readLinesAsync(path: Path): Future[Iterable[String]] =
     asyncCommand(ioCommandBuilder.readLines(path))
-  }
 
-  def isDirectory(path: Path): Future[Boolean] = {
+  def isDirectory(path: Path): Future[Boolean] =
     asyncCommand(ioCommandBuilder.isDirectoryCommand(path))
-  }
 
-  def copyAsync(src: Path, dest: Path): Future[Unit] = {
+  def copyAsync(src: Path, dest: Path): Future[Unit] =
     // Allow for a much larger timeout for copies, as large files can take a while (even on gcs, if they are in different locations...)
     asyncCommand(ioCommandBuilder.copyCommand(src, dest), AsyncIo.copyTimeout)
-  }
 }
diff --git a/core/src/main/scala/cromwell/core/io/AsyncIoFunctions.scala b/core/src/main/scala/cromwell/core/io/AsyncIoFunctions.scala
index 6b4a7763d2a..c7bb7927a00 100644
--- a/core/src/main/scala/cromwell/core/io/AsyncIoFunctions.scala
+++ b/core/src/main/scala/cromwell/core/io/AsyncIoFunctions.scala
@@ -3,6 +3,7 @@ package cromwell.core.io
 import wom.expression.IoFunctionSet
 
 trait AsyncIoFunctions { this: IoFunctionSet =>
+
   /**
     * Used to perform io functions asynchronously through the ioActorProxy
     */
diff --git a/core/src/main/scala/cromwell/core/io/CorePathFunctionSet.scala b/core/src/main/scala/cromwell/core/io/CorePathFunctionSet.scala
index cf79d06cd2b..59eed184e45 100644
--- a/core/src/main/scala/cromwell/core/io/CorePathFunctionSet.scala
+++ b/core/src/main/scala/cromwell/core/io/CorePathFunctionSet.scala
@@ -8,7 +8,9 @@ import wom.expression.{IoFunctionSet, PathFunctionSet}
 import scala.util.Try
 
 class WorkflowCorePathFunctionSet(override val pathBuilders: PathBuilders) extends PathFunctionSet with PathFactory {
-  private def fail(name: String) = throw new UnsupportedOperationException(s"$name is not implemented at the workflow level")
+  private def fail(name: String) = throw new UnsupportedOperationException(
+    s"$name is not implemented at the workflow level"
+  )
   override def sibling(of: String, path: String): String = buildPath(of).sibling(path).pathAsString
   override def isAbsolute(path: String): Boolean = Try(buildPath(path)).map(_.isAbsolute).toOption.contains(true)
   override def name(path: String) = buildPath(path).name
@@ -19,8 +21,10 @@ class WorkflowCorePathFunctionSet(override val pathBuilders: PathBuilders) exten
   override def stderr: String = fail("stderr")
 }
 
-class CallCorePathFunctionSet(pathBuilders: PathBuilders, callContext: CallContext) extends WorkflowCorePathFunctionSet(pathBuilders) {
-  override def relativeToHostCallRoot(path: String) = if (isAbsolute(path)) path else callContext.root.resolve(path).pathAsString
+class CallCorePathFunctionSet(pathBuilders: PathBuilders, callContext: CallContext)
+    extends WorkflowCorePathFunctionSet(pathBuilders) {
+  override def relativeToHostCallRoot(path: String) =
+    if (isAbsolute(path)) path else callContext.root.resolve(path).pathAsString
   override def stdout = callContext.standardPaths.output.pathAsString
   override def stderr = callContext.standardPaths.error.pathAsString
 }
@@ -29,7 +33,6 @@ trait WorkflowCorePathFunctions extends { this: IoFunctionSet with PathFactory =
   override lazy val pathFunctions = new WorkflowCorePathFunctionSet(pathBuilders)
 }
 
-
 trait CallCorePathFunctions extends { this: IoFunctionSet with PathFactory =>
   def callContext: CallContext
   override lazy val pathFunctions = new CallCorePathFunctionSet(pathBuilders, callContext)
diff --git a/core/src/main/scala/cromwell/core/io/DefaultIoCommand.scala b/core/src/main/scala/cromwell/core/io/DefaultIoCommand.scala
index bb5e5eec973..2faf49696ac 100644
--- a/core/src/main/scala/cromwell/core/io/DefaultIoCommand.scala
+++ b/core/src/main/scala/cromwell/core/io/DefaultIoCommand.scala
@@ -5,13 +5,13 @@ import cromwell.core.io.IoContentAsStringCommand.IoReadOptions
 import cromwell.core.path.Path
 
 object DefaultIoCommand {
-  case class DefaultIoCopyCommand(override val source: Path,
-                                  override val destination: Path,
-                                 ) extends IoCopyCommand(source, destination) {
+  case class DefaultIoCopyCommand(override val source: Path, override val destination: Path)
+      extends IoCopyCommand(source, destination) {
     override def commandDescription: String = s"DefaultIoCopyCommand source '$source' destination '$destination'"
   }
 
-  case class DefaultIoContentAsStringCommand(override val file: Path, override val options: IoReadOptions) extends IoContentAsStringCommand(file, options) {
+  case class DefaultIoContentAsStringCommand(override val file: Path, override val options: IoReadOptions)
+      extends IoContentAsStringCommand(file, options) {
     override def commandDescription: String = s"DefaultIoContentAsStringCommand file '$file' options '$options'"
   }
 
@@ -22,18 +22,24 @@ object DefaultIoCommand {
   case class DefaultIoWriteCommand(override val file: Path,
                                    override val content: String,
                                    override val openOptions: OpenOptions,
-                                   override val compressPayload: Boolean) extends IoWriteCommand(
-    file, content, openOptions, compressPayload
-  ) {
+                                   override val compressPayload: Boolean
+  ) extends IoWriteCommand(
+        file,
+        content,
+        openOptions,
+        compressPayload
+      ) {
     override def commandDescription: String = s"DefaultIoWriteCommand file '$file' content length " +
       s"'${content.length}' openOptions '$openOptions' compressPayload '$compressPayload'"
   }
 
-  case class DefaultIoDeleteCommand(override val file: Path,
-                                    override val swallowIOExceptions: Boolean) extends IoDeleteCommand(
-    file, swallowIOExceptions
-  ) {
-    override def commandDescription: String = s"DefaultIoDeleteCommand file '$file' swallowIOExceptions '$swallowIOExceptions'"
+  case class DefaultIoDeleteCommand(override val file: Path, override val swallowIOExceptions: Boolean)
+      extends IoDeleteCommand(
+        file,
+        swallowIOExceptions
+      ) {
+    override def commandDescription: String =
+      s"DefaultIoDeleteCommand file '$file' swallowIOExceptions '$swallowIOExceptions'"
   }
 
   case class DefaultIoHashCommand(override val file: Path) extends IoHashCommand(file) {
diff --git a/core/src/main/scala/cromwell/core/io/IoAck.scala b/core/src/main/scala/cromwell/core/io/IoAck.scala
index 430b30db792..41066791fe3 100644
--- a/core/src/main/scala/cromwell/core/io/IoAck.scala
+++ b/core/src/main/scala/cromwell/core/io/IoAck.scala
@@ -8,6 +8,7 @@ import scala.util.{Failure, Success, Try}
   * @tparam T type of the returned value if success
   */
 sealed trait IoAck[T] {
+
   /**
     * Original command
     */
@@ -20,13 +21,12 @@ case class IoSuccess[T](command: IoCommand[T], result: T) extends IoAck[T] {
 }
 
 object IoFailAck {
-  def unapply(any: Any): Option[(IoCommand[_], Throwable)] = {
+  def unapply(any: Any): Option[(IoCommand[_], Throwable)] =
     any match {
       case f: IoFailAck[_] =>
         Option((f.command, f.failure))
       case _ => None
     }
-  }
 }
 
 trait IoFailAck[T] extends IoAck[T] {
@@ -36,5 +36,7 @@ trait IoFailAck[T] extends IoAck[T] {
 
 /** Failure of an unspecified variety. */
 case class IoFailure[T](command: IoCommand[T], override val failure: Throwable) extends IoFailAck[T]
+
 /** Specifically read forbidden failure. */
-case class IoReadForbiddenFailure[T](command: IoCommand[T], override val failure: Throwable, forbiddenPath: String) extends IoFailAck[T]
+case class IoReadForbiddenFailure[T](command: IoCommand[T], override val failure: Throwable, forbiddenPath: String)
+    extends IoFailAck[T]
diff --git a/core/src/main/scala/cromwell/core/io/IoClientHelper.scala b/core/src/main/scala/cromwell/core/io/IoClientHelper.scala
index 26dd0732d33..169e55a496d 100644
--- a/core/src/main/scala/cromwell/core/io/IoClientHelper.scala
+++ b/core/src/main/scala/cromwell/core/io/IoClientHelper.scala
@@ -13,9 +13,9 @@ trait IoClientHelper extends RobustClientHelper { this: Actor with ActorLogging
   def ioActor: ActorRef
 
   lazy val defaultIoTimeout = RobustClientHelper.DefaultRequestLostTimeout
-  
+
   protected def config = ConfigFactory.load().as[Config]("system.io.backpressure-backoff")
-  
+
   override protected def initialBackoff(): Backoff = SimpleExponentialBackoff(config)
 
   protected def ioResponseReceive: Receive = {
@@ -26,19 +26,16 @@ trait IoClientHelper extends RobustClientHelper { this: Actor with ActorLogging
       cancelTimeout(context -> ack.command)
       receive.apply(context -> ack)
   }
-  
+
   def ioReceive = robustReceive orElse ioResponseReceive
-  
-  def sendIoCommand(ioCommand: IoCommand[_]) = {
+
+  def sendIoCommand(ioCommand: IoCommand[_]) =
     sendIoCommandWithCustomTimeout(ioCommand, defaultIoTimeout)
-  }
 
-  def sendIoCommandWithCustomTimeout(ioCommand: IoCommand[_], timeout: FiniteDuration) = {
+  def sendIoCommandWithCustomTimeout(ioCommand: IoCommand[_], timeout: FiniteDuration) =
     robustSend(ioCommand, ioActor, timeout)
-  }
 
-  def sendIoCommandWithContext[T](ioCommand: IoCommand[_], context: T, timeout: FiniteDuration = defaultIoTimeout) = {
+  def sendIoCommandWithContext[T](ioCommand: IoCommand[_], context: T, timeout: FiniteDuration = defaultIoTimeout) =
     robustSend(context -> ioCommand, ioActor, timeout)
-  }
 
 }
diff --git a/core/src/main/scala/cromwell/core/io/IoCommand.scala b/core/src/main/scala/cromwell/core/io/IoCommand.scala
index 7d71f9bd307..9db50bc2c87 100644
--- a/core/src/main/scala/cromwell/core/io/IoCommand.scala
+++ b/core/src/main/scala/cromwell/core/io/IoCommand.scala
@@ -23,7 +23,7 @@ object IoCommand {
     .setInitialIntervalMillis((1 second).toMillis.toInt)
     .setMaxIntervalMillis((5 minutes).toMillis.toInt)
     .setMultiplier(3L)
-    .setRandomizationFactor(0.2D)
+    .setRandomizationFactor(0.2d)
     .setMaxElapsedTimeMillis((10 minutes).toMillis.toInt)
     .build()
 
@@ -47,7 +47,7 @@ trait IoCommand[+T] {
   def logIOMsgOverLimit(message: => String): Unit = {
     val millis: Long = java.time.Duration.between(creation, OffsetDateTime.now).toMillis
     if (millis > IoCommand.IOCommandWarnLimit.toMillis) {
-      val seconds = millis / 1000D
+      val seconds = millis / 1000d
 
       /*
         For now we decided to log this as INFO. In future if needed, we can update this to WARN.
@@ -59,8 +59,10 @@ trait IoCommand[+T] {
                 (https://github.com/broadinstitute/firecloud-develop/blob/c77e0f371be0aac545e204f1a134cc6f8ef3c301/run-context/live/configs/cromwell/app.env.ctmpl#L42-L51)
               - Logback manual (http://logback.qos.ch/manual/index.html)
        */
-      IoCommand.logger.info(f"(IO-$uuid) '$message' is over 5 minutes. It was running for " +
-        f"$seconds%,.3f seconds. IO command description: '$commandDescription'")
+      IoCommand.logger.info(
+        f"(IO-$uuid) '$message' is over 5 minutes. It was running for " +
+          f"$seconds%,.3f seconds. IO command description: '$commandDescription'"
+      )
     }
   }
 
@@ -82,7 +84,9 @@ trait IoCommand[+T] {
   }
 
   def failReadForbidden[S >: T](failure: Throwable, forbiddenPath: String): IoReadForbiddenFailure[S] = {
-    logIOMsgOverLimit(s"IOCommand.failReadForbidden '${failure.toPrettyElidedString(limit = 1000)}' path '$forbiddenPath'")
+    logIOMsgOverLimit(
+      s"IOCommand.failReadForbidden '${failure.toPrettyElidedString(limit = 1000)}' path '$forbiddenPath'"
+    )
     IoReadForbiddenFailure(this, failure, forbiddenPath)
   }
 
@@ -118,7 +122,9 @@ object IoContentAsStringCommand {
 /**
   * Read file as a string (load the entire content in memory)
   */
-abstract class IoContentAsStringCommand(val file: Path, val options: IoReadOptions = IoReadOptions(None, failOnOverflow = false)) extends SingleFileIoCommand[String] {
+abstract class IoContentAsStringCommand(val file: Path,
+                                        val options: IoReadOptions = IoReadOptions(None, failOnOverflow = false)
+) extends SingleFileIoCommand[String] {
   override def toString = s"read content of ${file.pathAsString}"
   override lazy val name = "read"
 }
@@ -138,7 +144,8 @@ abstract class IoSizeCommand(val file: Path) extends SingleFileIoCommand[Long] {
 abstract class IoWriteCommand(val file: Path,
                               val content: String,
                               val openOptions: OpenOptions,
-                              val compressPayload: Boolean) extends SingleFileIoCommand[Unit] {
+                              val compressPayload: Boolean
+) extends SingleFileIoCommand[Unit] {
   override def toString = s"write to ${file.pathAsString}"
   override lazy val name = "write"
 }
diff --git a/core/src/main/scala/cromwell/core/io/IoCommandBuilder.scala b/core/src/main/scala/cromwell/core/io/IoCommandBuilder.scala
index 43a6f5864b0..c4f5da49959 100644
--- a/core/src/main/scala/cromwell/core/io/IoCommandBuilder.scala
+++ b/core/src/main/scala/cromwell/core/io/IoCommandBuilder.scala
@@ -26,13 +26,11 @@ abstract class PartialIoCommandBuilder {
 }
 
 object IoCommandBuilder {
-  def apply(partialBuilders: PartialIoCommandBuilder*): IoCommandBuilder = {
+  def apply(partialBuilders: PartialIoCommandBuilder*): IoCommandBuilder =
     new IoCommandBuilder(partialBuilders.toList)
-  }
 
-  def apply: IoCommandBuilder = {
+  def apply: IoCommandBuilder =
     new IoCommandBuilder(List.empty)
-  }
 }
 
 /**
@@ -49,56 +47,58 @@ class IoCommandBuilder(partialBuilders: List[PartialIoCommandBuilder] = List.emp
   // Find the first partialBuilder for which the partial function is defined, or use the default
   private def buildOrDefault[A, B](builder: PartialIoCommandBuilder => PartialFunction[A, Try[B]],
                                    params: A,
-                                   default: => B): Try[B] = {
-    partialBuilders.to(LazyList).map(builder(_).lift(params)).collectFirst({
-      case Some(command) => command
-    }).getOrElse(Try(default))
-  }
+                                   default: => B
+  ): Try[B] =
+    partialBuilders
+      .to(LazyList)
+      .map(builder(_).lift(params))
+      .collectFirst { case Some(command) =>
+        command
+      }
+      .getOrElse(Try(default))
 
   def contentAsStringCommand(path: Path,
                              maxBytes: Option[Int],
-                             failOnOverflow: Boolean): Try[IoContentAsStringCommand] = {
-    buildOrDefault(_.contentAsStringCommand, (path, maxBytes, failOnOverflow), DefaultIoContentAsStringCommand(path, IoReadOptions(maxBytes, failOnOverflow)))
-  }
+                             failOnOverflow: Boolean
+  ): Try[IoContentAsStringCommand] =
+    buildOrDefault(_.contentAsStringCommand,
+                   (path, maxBytes, failOnOverflow),
+                   DefaultIoContentAsStringCommand(path, IoReadOptions(maxBytes, failOnOverflow))
+    )
 
   def writeCommand(path: Path,
                    content: String,
                    options: OpenOptions,
-                   compressPayload: Boolean = false): Try[IoWriteCommand] = {
-    buildOrDefault(_.writeCommand, (path, content, options, compressPayload), DefaultIoWriteCommand(path, content, options, compressPayload))
-  }
-
-  def sizeCommand(path: Path): Try[IoSizeCommand] = {
+                   compressPayload: Boolean = false
+  ): Try[IoWriteCommand] =
+    buildOrDefault(_.writeCommand,
+                   (path, content, options, compressPayload),
+                   DefaultIoWriteCommand(path, content, options, compressPayload)
+    )
+
+  def sizeCommand(path: Path): Try[IoSizeCommand] =
     buildOrDefault(_.sizeCommand, path, DefaultIoSizeCommand(path))
-  }
 
-  def deleteCommand(path: Path, swallowIoExceptions: Boolean = true): Try[IoDeleteCommand] = {
+  def deleteCommand(path: Path, swallowIoExceptions: Boolean = true): Try[IoDeleteCommand] =
     buildOrDefault(_.deleteCommand, (path, swallowIoExceptions), DefaultIoDeleteCommand(path, swallowIoExceptions))
-  }
 
-  def copyCommand(src: Path, dest: Path): Try[IoCopyCommand] = {
+  def copyCommand(src: Path, dest: Path): Try[IoCopyCommand] =
     buildOrDefault(_.copyCommand, (src, dest), DefaultIoCopyCommand(src, dest))
-  }
 
-  def hashCommand(file: Path): Try[IoHashCommand] = {
+  def hashCommand(file: Path): Try[IoHashCommand] =
     buildOrDefault(_.hashCommand, file, DefaultIoHashCommand(file))
-  }
 
-  def touchCommand(file: Path): Try[IoTouchCommand] = {
+  def touchCommand(file: Path): Try[IoTouchCommand] =
     buildOrDefault(_.touchCommand, file, DefaultIoTouchCommand(file))
-  }
 
-  def existsCommand(file: Path): Try[IoExistsCommand] = {
+  def existsCommand(file: Path): Try[IoExistsCommand] =
     buildOrDefault(_.existsCommand, file, DefaultIoExistsCommand(file))
-  }
 
-  def isDirectoryCommand(file: Path): Try[IoIsDirectoryCommand] = {
+  def isDirectoryCommand(file: Path): Try[IoIsDirectoryCommand] =
     buildOrDefault(_.isDirectoryCommand, file, DefaultIoIsDirectoryCommand(file))
-  }
 
-  def readLines(file: Path): Try[IoReadLinesCommand] = {
+  def readLines(file: Path): Try[IoReadLinesCommand] =
     buildOrDefault(_.readLinesCommand, file, DefaultIoReadLinesCommand(file))
-  }
 }
 
 /**
diff --git a/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala b/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
index dd8f44464f3..e9a8a8934bc 100644
--- a/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
+++ b/core/src/main/scala/cromwell/core/io/IoPromiseProxyActor.scala
@@ -25,17 +25,15 @@ object IoPromiseProxyActor {
 class IoPromiseProxyActor(override val ioActor: ActorRef) extends Actor with ActorLogging with IoClientHelper {
   override def receive = ioReceive orElse actorReceive
 
-  def actorReceive: Receive = {
-    case withPromise: IoCommandWithPromise[_] =>
-      sendIoCommandWithContext(withPromise.ioCommand, withPromise.promise, withPromise.timeout)
+  def actorReceive: Receive = { case withPromise: IoCommandWithPromise[_] =>
+    sendIoCommandWithContext(withPromise.ioCommand, withPromise.promise, withPromise.timeout)
   }
 
-  override protected def ioResponseReceive: Receive = {
-    case (promise: Promise[_], ack: IoAck[Any] @unchecked) =>
-      cancelTimeout(promise -> ack.command)
-      // This is not typesafe and assumes the Promise context is of the same type as the IoAck response.
-      promise.asInstanceOf[Promise[Any]].complete(ack.toTry)
-      ()
+  override protected def ioResponseReceive: Receive = { case (promise: Promise[_], ack: IoAck[Any] @unchecked) =>
+    cancelTimeout(promise -> ack.command)
+    // This is not typesafe and assumes the Promise context is of the same type as the IoAck response.
+    promise.asInstanceOf[Promise[Any]].complete(ack.toTry)
+    ()
   }
 
   override def onTimeout(message: Any, to: ActorRef): Unit = message match {
diff --git a/core/src/main/scala/cromwell/core/io/Throttle.scala b/core/src/main/scala/cromwell/core/io/Throttle.scala
index 88246f1d88f..aaa5b5d30f5 100644
--- a/core/src/main/scala/cromwell/core/io/Throttle.scala
+++ b/core/src/main/scala/cromwell/core/io/Throttle.scala
@@ -11,11 +11,10 @@ case class Throttle(elements: Int, per: FiniteDuration, maximumBurst: Int) {
 }
 
 object Throttle {
-  implicit val throttleOptionValueReader: ValueReader[Option[Throttle]] = (config: Config, path: String) => {
+  implicit val throttleOptionValueReader: ValueReader[Option[Throttle]] = (config: Config, path: String) =>
     config.getAs[Config](path) map { throttleConfig =>
       val elements = throttleConfig.as[Int]("number-of-requests")
       val per = throttleConfig.as[FiniteDuration]("per")
       Throttle(elements, per, elements)
     }
-  }
 }
diff --git a/core/src/main/scala/cromwell/core/labels/Label.scala b/core/src/main/scala/cromwell/core/labels/Label.scala
index 759300da5b1..616298840b7 100644
--- a/core/src/main/scala/cromwell/core/labels/Label.scala
+++ b/core/src/main/scala/cromwell/core/labels/Label.scala
@@ -12,21 +12,19 @@ object Label {
   val MaxLabelLength = 255
   val LabelExpectationsMessage = s"A Label key must be non-empty."
 
-  def validateLabelKey(s: String): ErrorOr[String] = {
+  def validateLabelKey(s: String): ErrorOr[String] =
     (s.length >= 1, s.length <= MaxLabelLength) match {
       case (true, true) => s.validNel
       case (false, _) => s"Invalid label: `$s` can't be empty".invalidNel
       case (_, false) => s"Invalid label: `$s` is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
     }
-  }
 
-  def validateLabelValue(s: String): ErrorOr[String] = {
+  def validateLabelValue(s: String): ErrorOr[String] =
     if (s.length <= MaxLabelLength) {
       s.validNel
     } else {
       s"Invalid label: `$s` is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
     }
-  }
 
   def validateLabel(key: String, value: String): ErrorOr[Label] = {
     val validatedKey = validateLabelKey(key)
@@ -35,7 +33,6 @@ object Label {
     (validatedKey, validatedValue) mapN Label.apply
   }
 
-  def apply(key: String, value: String) = {
+  def apply(key: String, value: String) =
     new Label(key, value) {}
-  }
 }
diff --git a/core/src/main/scala/cromwell/core/labels/Labels.scala b/core/src/main/scala/cromwell/core/labels/Labels.scala
index 5499fa5b2e8..148a0a7926d 100644
--- a/core/src/main/scala/cromwell/core/labels/Labels.scala
+++ b/core/src/main/scala/cromwell/core/labels/Labels.scala
@@ -19,13 +19,11 @@ case class Labels(value: Vector[Label]) {
 }
 
 object Labels {
-  def apply(values: (String, String)*): Labels = {
+  def apply(values: (String, String)*): Labels =
     Labels(values.toVector map (Label.apply _).tupled)
-  }
 
-  def validateMapOfLabels(labels: Map[String, String]): ErrorOr[Labels] = {
+  def validateMapOfLabels(labels: Map[String, String]): ErrorOr[Labels] =
     labels.toVector traverse { Label.validateLabel _ }.tupled map Labels.apply
-  }
 
   def empty = Labels(Vector.empty)
 }
diff --git a/core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala b/core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala
index dcf62bc0b28..47eb951199a 100644
--- a/core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala
+++ b/core/src/main/scala/cromwell/core/logging/EnhancedDateConverter.scala
@@ -25,9 +25,9 @@ class EnhancedDateConverter extends DateConverter {
     cachingDateFormatterProtected = Option(getFirstOption) match {
       case Some(CoreConstants.ISO8601_STR) | None => new CachingDateFormatter(CoreConstants.ISO8601_PATTERN)
       case Some(datePattern) =>
-        try {
+        try
           new CachingDateFormatter(datePattern)
-        } catch {
+        catch {
           case e: IllegalArgumentException =>
             addWarn("Could not instantiate SimpleDateFormat with pattern " + datePattern, e)
             // default to the ISO8601 format
@@ -35,8 +35,7 @@ class EnhancedDateConverter extends DateConverter {
         }
     }
     // if the option list contains a TZ option, then set it.
-    Option(getOptionList)
-      .toList
+    Option(getOptionList).toList
       .flatMap(_.asScala)
       .drop(1)
       .headOption
diff --git a/core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala b/core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala
index 0999ec18055..6f9e5f2fdfb 100644
--- a/core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala
+++ b/core/src/main/scala/cromwell/core/logging/EnhancedSlf4jLogger.scala
@@ -3,6 +3,7 @@ package cromwell.core.logging
 import akka.event.slf4j.Slf4jLogger
 
 class EnhancedSlf4jLogger extends Slf4jLogger {
+
   /**
     * Format the timestamp as a simple long. Allows the akkaTimestamp to be retrieved later from the MDC by custom
     * converters.
diff --git a/core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala b/core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala
index 1dc10fab46d..beff484f941 100644
--- a/core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala
+++ b/core/src/main/scala/cromwell/core/logging/JavaLoggingBridge.scala
@@ -8,6 +8,7 @@ import org.slf4j.bridge.SLF4JBridgeHandler
 import scala.jdk.CollectionConverters._
 
 object JavaLoggingBridge {
+
   /**
     * Replace java.util.logging with SLF4J while ensuring Logback is configured with a LevelChangePropogator.
     *
diff --git a/core/src/main/scala/cromwell/core/logging/JobLogger.scala b/core/src/main/scala/cromwell/core/logging/JobLogger.scala
index 37ab6cfa2da..4af851124cb 100644
--- a/core/src/main/scala/cromwell/core/logging/JobLogger.scala
+++ b/core/src/main/scala/cromwell/core/logging/JobLogger.scala
@@ -28,14 +28,14 @@ class JobLogger(loggerName: String,
                 rootWorkflowIdForLogging: RootWorkflowId,
                 jobTag: String,
                 akkaLogger: Option[LoggingAdapter] = None,
-                otherLoggers: Set[Logger] = Set.empty[Logger])
-  extends WorkflowLogger(
-    loggerName = loggerName,
-    workflowId = workflowIdForLogging,
-    rootWorkflowId = rootWorkflowIdForLogging,
-    akkaLogger = akkaLogger,
-    otherLoggers = otherLoggers
-  ) {
+                otherLoggers: Set[Logger] = Set.empty[Logger]
+) extends WorkflowLogger(
+      loggerName = loggerName,
+      workflowId = workflowIdForLogging,
+      rootWorkflowId = rootWorkflowIdForLogging,
+      akkaLogger = akkaLogger,
+      otherLoggers = otherLoggers
+    ) {
 
   override def tag = s"$loggerName [UUID(${workflowIdForLogging.shortString})$jobTag]"
 }
diff --git a/core/src/main/scala/cromwell/core/logging/LoggerWrapper.scala b/core/src/main/scala/cromwell/core/logging/LoggerWrapper.scala
index 5af71c7099c..3f9044aeaa3 100644
--- a/core/src/main/scala/cromwell/core/logging/LoggerWrapper.scala
+++ b/core/src/main/scala/cromwell/core/logging/LoggerWrapper.scala
@@ -23,9 +23,8 @@ abstract class LoggerWrapper extends MarkerIgnoringBase {
     *
     * https://github.com/qos-ch/slf4j/blob/v_1.7.30/slf4j-simple/src/main/java/org/slf4j/impl/SimpleLogger.java#L293-L295
     */
-  private def format(msg: String, throwable: Throwable): String = {
+  private def format(msg: String, throwable: Throwable): String =
     format(msg) + "\n" + ExceptionUtils.getStackTrace(throwable)
-  }
 
   /**
     * Passes a formatted string to akka similar to slf4j's SimpleLogger
@@ -113,7 +112,7 @@ abstract class LoggerWrapper extends MarkerIgnoringBase {
     lazy val formatted: String = format(pattern)
 
     varargsAkkaLog(Logging.ErrorLevel, pattern, arguments)
-    slf4jLoggers.foreach(_.error(formatted, arguments:_*))
+    slf4jLoggers.foreach(_.error(formatted, arguments: _*))
   }
 
   override def error(pattern: String, arg: Any): Unit = {
@@ -130,10 +129,9 @@ abstract class LoggerWrapper extends MarkerIgnoringBase {
     slf4jLoggers.foreach(_.error(formatted, arg1, arg2: Any))
   }
 
-  def error(t: Throwable, pattern: String, arguments: Any*): Unit = {
+  def error(t: Throwable, pattern: String, arguments: Any*): Unit =
     // slf4j extracts the last variable argument as a throwable.
     error(pattern, (arguments :+ t).map(_.asInstanceOf[AnyRef]): _*)
-  }
 
   override def debug(msg: String): Unit = {
     lazy val formatted: String = format(msg)
@@ -153,7 +151,7 @@ abstract class LoggerWrapper extends MarkerIgnoringBase {
     lazy val formatted: String = format(pattern)
 
     varargsAkkaLog(Logging.DebugLevel, pattern, arguments)
-    slf4jLoggers.foreach(_.debug(formatted, arguments:_*))
+    slf4jLoggers.foreach(_.debug(formatted, arguments: _*))
   }
 
   override def debug(pattern: String, argument: Any): Unit = {
@@ -170,25 +168,20 @@ abstract class LoggerWrapper extends MarkerIgnoringBase {
     slf4jLoggers.foreach(_.debug(formatted, arg1, arg2: Any))
   }
 
-  override def trace(msg: String): Unit = {
+  override def trace(msg: String): Unit =
     slf4jLoggers.foreach(_.trace(format(msg)))
-  }
 
-  override def trace(msg: String, t: Throwable): Unit = {
+  override def trace(msg: String, t: Throwable): Unit =
     slf4jLoggers.foreach(_.trace(format(msg), t))
-  }
 
-  override def trace(pattern: String, arguments: AnyRef*): Unit = {
-    slf4jLoggers.foreach(_.trace(format(pattern), arguments:_*))
-  }
+  override def trace(pattern: String, arguments: AnyRef*): Unit =
+    slf4jLoggers.foreach(_.trace(format(pattern), arguments: _*))
 
-  override def trace(pattern: String, arg: Any): Unit = {
+  override def trace(pattern: String, arg: Any): Unit =
     slf4jLoggers.foreach(_.trace(format(pattern), arg))
-  }
 
-  override def trace(pattern: String, arg1: Any, arg2: Any): Unit = {
+  override def trace(pattern: String, arg1: Any, arg2: Any): Unit =
     slf4jLoggers.foreach(_.trace(format(pattern), arg1, arg2: Any))
-  }
 
   override def info(msg: String): Unit = {
     lazy val formatted: String = format(msg)
@@ -208,7 +201,7 @@ abstract class LoggerWrapper extends MarkerIgnoringBase {
     lazy val formatted: String = format(pattern)
 
     varargsAkkaLog(Logging.InfoLevel, pattern, arguments)
-    slf4jLoggers.foreach(_.info(formatted, arguments:_*))
+    slf4jLoggers.foreach(_.info(formatted, arguments: _*))
   }
 
   override def info(pattern: String, arg: Any): Unit = {
@@ -225,14 +218,24 @@ abstract class LoggerWrapper extends MarkerIgnoringBase {
     slf4jLoggers.foreach(_.info(formatted, arg1, arg2: Any))
   }
 
-  override def isErrorEnabled: Boolean = throw new UnsupportedOperationException("This logger wraps an arbitrary set of loggers that can each have a different level enabled.")
+  override def isErrorEnabled: Boolean = throw new UnsupportedOperationException(
+    "This logger wraps an arbitrary set of loggers that can each have a different level enabled."
+  )
 
-  override def isInfoEnabled: Boolean = throw new UnsupportedOperationException("This logger wraps an arbitrary set of loggers that can each have a different level enabled.")
+  override def isInfoEnabled: Boolean = throw new UnsupportedOperationException(
+    "This logger wraps an arbitrary set of loggers that can each have a different level enabled."
+  )
 
-  override def isDebugEnabled: Boolean = throw new UnsupportedOperationException("This logger wraps an arbitrary set of loggers that can each have a different level enabled.")
+  override def isDebugEnabled: Boolean = throw new UnsupportedOperationException(
+    "This logger wraps an arbitrary set of loggers that can each have a different level enabled."
+  )
 
-  override def isTraceEnabled: Boolean = throw new UnsupportedOperationException("This logger wraps an arbitrary set of loggers that can each have a different level enabled.")
+  override def isTraceEnabled: Boolean = throw new UnsupportedOperationException(
+    "This logger wraps an arbitrary set of loggers that can each have a different level enabled."
+  )
 
-  override def isWarnEnabled: Boolean = throw new UnsupportedOperationException("This logger wraps an arbitrary set of loggers that can each have a different level enabled.")
+  override def isWarnEnabled: Boolean = throw new UnsupportedOperationException(
+    "This logger wraps an arbitrary set of loggers that can each have a different level enabled."
+  )
 
 }
diff --git a/core/src/main/scala/cromwell/core/logging/WorkflowLogger.scala b/core/src/main/scala/cromwell/core/logging/WorkflowLogger.scala
index 94028b39407..d404cb36336 100644
--- a/core/src/main/scala/cromwell/core/logging/WorkflowLogger.scala
+++ b/core/src/main/scala/cromwell/core/logging/WorkflowLogger.scala
@@ -49,41 +49,40 @@ object WorkflowLogger {
   https://github.com/qos-ch/logback/commit/77128a003a7fd7e8bd7a6ddb12da7a65cf296593#diff-f8cd32379a53986c2e70e2abe86fa0faR145
    */
   private def makeSynchronizedFileLogger(path: Path, level: Level, ctx: LoggerContext, name: String): Logger =
-  ctx.synchronized {
-    Option(ctx.exists(name)) match {
-      case Some(existingLogger) => existingLogger
-      case None =>
-        val encoder = new PatternLayoutEncoder()
-        encoder.setPattern("%date %-5level - %msg%n")
-        encoder.setContext(ctx)
-        encoder.start()
-
-        val appender = new FileAppender[ILoggingEvent]()
-        appender.setFile(path.pathAsString)
-        appender.setEncoder(encoder)
-        appender.setName(name)
-        appender.setContext(ctx)
-        appender.start()
-
-        val fileLogger = ctx.getLogger(name)
-        fileLogger.addAppender(appender)
-        fileLogger.setAdditive(false)
-        fileLogger.setLevel(level)
-        fileLogger
+    ctx.synchronized {
+      Option(ctx.exists(name)) match {
+        case Some(existingLogger) => existingLogger
+        case None =>
+          val encoder = new PatternLayoutEncoder()
+          encoder.setPattern("%date %-5level - %msg%n")
+          encoder.setContext(ctx)
+          encoder.start()
+
+          val appender = new FileAppender[ILoggingEvent]()
+          appender.setFile(path.pathAsString)
+          appender.setEncoder(encoder)
+          appender.setName(name)
+          appender.setContext(ctx)
+          appender.start()
+
+          val fileLogger = ctx.getLogger(name)
+          fileLogger.addAppender(appender)
+          fileLogger.setAdditive(false)
+          fileLogger.setLevel(level)
+          fileLogger
+      }
     }
-  }
 
   case class WorkflowLogConfiguration(dir: Path, temporary: Boolean)
 
   private val conf = ConfigFactory.load()
 
-  val workflowLogConfiguration: Option[WorkflowLogConfiguration] = {
+  val workflowLogConfiguration: Option[WorkflowLogConfiguration] =
     for {
       workflowConfig <- conf.as[Option[Config]]("workflow-options")
       dir <- workflowConfig.as[Option[String]]("workflow-log-dir") if !dir.isEmpty
       temporary <- workflowConfig.as[Option[Boolean]]("workflow-log-temporary") orElse Option(true)
     } yield WorkflowLogConfiguration(DefaultPathBuilder.get(dir).toAbsolutePath, temporary)
-  }
 
   val isEnabled = workflowLogConfiguration.isDefined
   val isTemporary = workflowLogConfiguration exists {
@@ -111,8 +110,8 @@ class WorkflowLogger(loggerName: String,
                      workflowId: PossiblyNotRootWorkflowId,
                      rootWorkflowId: RootWorkflowId,
                      override val akkaLogger: Option[LoggingAdapter],
-                     otherLoggers: Set[Logger] = Set.empty[Logger])
-  extends LoggerWrapper {
+                     otherLoggers: Set[Logger] = Set.empty[Logger]
+) extends LoggerWrapper {
 
   override def getName = loggerName
 
@@ -137,7 +136,8 @@ class WorkflowLogger(loggerName: String,
   import WorkflowLogger._
 
   lazy val workflowLogPath = workflowLogConfiguration.map(workflowLogConfigurationActual =>
-    workflowLogConfigurationActual.dir.createPermissionedDirectories() / s"workflow.$rootWorkflowId.log")
+    workflowLogConfigurationActual.dir.createPermissionedDirectories() / s"workflow.$rootWorkflowId.log"
+  )
 
   lazy val fileLogger = workflowLogPath match {
     case Some(path) => makeFileLogger(path, Level.toLevel(sys.props.getOrElse("LOG_LEVEL", "debug")))
diff --git a/core/src/main/scala/cromwell/core/path/BetterFileMethods.scala b/core/src/main/scala/cromwell/core/path/BetterFileMethods.scala
index f0a6464f12e..ba300da9b83 100644
--- a/core/src/main/scala/cromwell/core/path/BetterFileMethods.scala
+++ b/core/src/main/scala/cromwell/core/path/BetterFileMethods.scala
@@ -27,9 +27,9 @@ trait BetterFileMethods {
 
   import BetterFileMethods._
 
-  private final def newPath(file: better.files.File): Path = newPath(file.path)
+  final private def newPath(file: better.files.File): Path = newPath(file.path)
 
-  private final def newPathOrNull(file: better.files.File): Path = Option(file).map(newPath).orNull
+  final private def newPathOrNull(file: better.files.File): Path = Option(file).map(newPath).orNull
 
   final def toJava: JFile = betterFile.toJava
 
@@ -44,8 +44,10 @@ trait BetterFileMethods {
 
   final def extension: Option[String] = betterFile.extension
 
-  final def extension(includeDot: Boolean = true, includeAll: Boolean = false,
-                      toLowerCase: Boolean = true): Option[String] =
+  final def extension(includeDot: Boolean = true,
+                      includeAll: Boolean = false,
+                      toLowerCase: Boolean = true
+  ): Option[String] =
     betterFile.extension(includeDot, includeAll, toLowerCase)
 
   final def hasExtension: Boolean = betterFile.hasExtension
@@ -60,16 +62,17 @@ trait BetterFileMethods {
 
   final def /(child: String): Path = newPath(betterFile./(child))
 
-  final def createChild(child: String, asDirectory: Boolean = false)
-                       (implicit attributes: Attributes = Attributes.default,
-                        linkOptions: LinkOptions = LinkOptions.default): Path =
+  final def createChild(child: String, asDirectory: Boolean = false)(implicit
+    attributes: Attributes = Attributes.default,
+    linkOptions: LinkOptions = LinkOptions.default
+  ): Path =
     newPath(betterFile.createChild(child, asDirectory)(attributes, linkOptions))
 
-  final def createIfNotExists(asDirectory: Boolean = false, createParents: Boolean = false)
-                             (implicit attributes: Attributes = Attributes.default,
-                              linkOptions: LinkOptions = LinkOptions.default): Path = {
+  final def createIfNotExists(asDirectory: Boolean = false, createParents: Boolean = false)(implicit
+    attributes: Attributes = Attributes.default,
+    linkOptions: LinkOptions = LinkOptions.default
+  ): Path =
     newPath(betterFile.createIfNotExists(asDirectory, createParents)(attributes, linkOptions))
-  }
 
   final def exists(implicit linkOptions: LinkOptions = LinkOptions.default): Boolean = betterFile.exists(linkOptions)
 
@@ -108,15 +111,17 @@ trait BetterFileMethods {
 
   final def lines(implicit charset: Charset = DefaultCharset): Iterable[String] = betterFile.lines(charset)
 
-  final def lineIterator(implicit charset: Charset= DefaultCharset): Iterator[String] = betterFile.lineIterator(charset)
+  final def lineIterator(implicit charset: Charset = DefaultCharset): Iterator[String] =
+    betterFile.lineIterator(charset)
 
-  final def tokens(splitter: StringSplitter = StringSplitter.Default)
-                  (implicit charset: Charset = DefaultCharset): Iterator[String] =
+  final def tokens(splitter: StringSplitter = StringSplitter.Default)(implicit
+    charset: Charset = DefaultCharset
+  ): Iterator[String] =
     betterFile.tokens(splitter)(charset)
 
   final def contentAsString(implicit charset: Charset = DefaultCharset): String = betterFile.contentAsString(charset)
 
-  final def `!`(implicit charset: Charset= DefaultCharset): String = betterFile.contentAsString(charset)
+  final def `!`(implicit charset: Charset = DefaultCharset): String = betterFile.contentAsString(charset)
 
   final def printLines(lines: Iterator[Any])(implicit openOptions: OpenOptions = OpenOptions.append): this.type = {
     betterFile.printLines(lines)(openOptions)
@@ -173,33 +178,37 @@ trait BetterFileMethods {
     this
   }
 
-  final def writeText(text: String)(implicit openOptions: OpenOptions = OpenOptions.default,
-                                    charset: Charset = DefaultCharset): this.type = {
+  final def writeText(
+    text: String
+  )(implicit openOptions: OpenOptions = OpenOptions.default, charset: Charset = DefaultCharset): this.type = {
     betterFile.writeText(text)(openOptions, charset)
     this
   }
 
-  final def write(text: String)
-                 (implicit openOptions: OpenOptions = OpenOptions.default,
-                  charset: Charset = DefaultCharset): this.type = {
+  final def write(
+    text: String
+  )(implicit openOptions: OpenOptions = OpenOptions.default, charset: Charset = DefaultCharset): this.type = {
     betterFile.write(text)(openOptions, charset)
     this
   }
 
-  final def overwrite(text: String)(implicit openOptions: OpenOptions = OpenOptions.default,
-                                    charset: Charset = DefaultCharset): this.type = {
+  final def overwrite(
+    text: String
+  )(implicit openOptions: OpenOptions = OpenOptions.default, charset: Charset = DefaultCharset): this.type = {
     betterFile.overwrite(text)(openOptions, charset)
     this
   }
 
-  final def <(text: String)(implicit openOptions: OpenOptions = OpenOptions.default,
-                            charset: Charset = DefaultCharset): this.type = {
+  final def <(
+    text: String
+  )(implicit openOptions: OpenOptions = OpenOptions.default, charset: Charset = DefaultCharset): this.type = {
     betterFile.write(text)(openOptions, charset)
     this
   }
 
-  final def `>:`(text: String)(implicit openOptions: OpenOptions = OpenOptions.default,
-                               charset: Charset = DefaultCharset): this.type = {
+  final def `>:`(
+    text: String
+  )(implicit openOptions: OpenOptions = OpenOptions.default, charset: Charset = DefaultCharset): this.type = {
     betterFile.write(text)(openOptions, charset)
     this
   }
@@ -221,12 +230,16 @@ trait BetterFileMethods {
   final def bufferedReader(implicit charset: Charset = DefaultCharset): Dispose[BufferedReader] =
     betterFile.bufferedReader(charset)
 
-  final def newBufferedWriter(implicit charset: Charset = DefaultCharset,
-                              openOptions: OpenOptions = OpenOptions.default): BufferedWriter =
+  final def newBufferedWriter(implicit
+    charset: Charset = DefaultCharset,
+    openOptions: OpenOptions = OpenOptions.default
+  ): BufferedWriter =
     betterFile.newBufferedWriter(charset, openOptions)
 
-  final def bufferedWriter(implicit charset: Charset = DefaultCharset,
-                           openOptions: OpenOptions = OpenOptions.default): Dispose[BufferedWriter] =
+  final def bufferedWriter(implicit
+    charset: Charset = DefaultCharset,
+    openOptions: OpenOptions = OpenOptions.default
+  ): Dispose[BufferedWriter] =
     betterFile.bufferedWriter(charset, openOptions)
 
   final def newFileReader: FileReader = betterFile.newFileReader
@@ -237,12 +250,14 @@ trait BetterFileMethods {
 
   final def fileWriter(append: Boolean = false): Dispose[FileWriter] = betterFile.fileWriter(append)
 
-  final def newPrintWriter(autoFlush: Boolean = false)
-                          (implicit openOptions: OpenOptions = OpenOptions.default): PrintWriter =
+  final def newPrintWriter(autoFlush: Boolean = false)(implicit
+    openOptions: OpenOptions = OpenOptions.default
+  ): PrintWriter =
     betterFile.newPrintWriter(autoFlush)
 
-  final def printWriter(autoFlush: Boolean = false)
-                       (implicit openOptions: OpenOptions = OpenOptions.default): Dispose[PrintWriter] =
+  final def printWriter(autoFlush: Boolean = false)(implicit
+    openOptions: OpenOptions = OpenOptions.default
+  ): Dispose[PrintWriter] =
     betterFile.printWriter(autoFlush)
 
   final def newInputStream(implicit openOptions: OpenOptions = OpenOptions.default): InputStream =
@@ -251,12 +266,14 @@ trait BetterFileMethods {
   final def inputStream(implicit openOptions: OpenOptions = OpenOptions.default): Dispose[InputStream] =
     betterFile.inputStream(openOptions)
 
-  final def newScanner(splitter: StringSplitter = StringSplitter.Default)
-                      (implicit charset: Charset = DefaultCharset): Scanner =
+  final def newScanner(splitter: StringSplitter = StringSplitter.Default)(implicit
+    charset: Charset = DefaultCharset
+  ): Scanner =
     betterFile.newScanner(splitter)(charset)
 
-  final def scanner(splitter: StringSplitter = StringSplitter.Default)
-                   (implicit charset: Charset = DefaultCharset): Dispose[Scanner] =
+  final def scanner(splitter: StringSplitter = StringSplitter.Default)(implicit
+    charset: Charset = DefaultCharset
+  ): Dispose[Scanner] =
     betterFile.scanner(splitter)(charset)
 
   final def newOutputStream(implicit openOptions: OpenOptions = OpenOptions.default): OutputStream =
@@ -265,19 +282,25 @@ trait BetterFileMethods {
   final def outputStream(implicit openOptions: OpenOptions = OpenOptions.default): Dispose[OutputStream] =
     betterFile.outputStream(openOptions)
 
-  final def newFileChannel(implicit openOptions: OpenOptions = OpenOptions.default,
-                           attributes: Attributes = Attributes.default): FileChannel =
+  final def newFileChannel(implicit
+    openOptions: OpenOptions = OpenOptions.default,
+    attributes: Attributes = Attributes.default
+  ): FileChannel =
     betterFile.newFileChannel(openOptions, attributes)
 
-  final def fileChannel(implicit openOptions: OpenOptions = OpenOptions.default,
-                        attributes: Attributes = Attributes.default): Dispose[FileChannel] =
+  final def fileChannel(implicit
+    openOptions: OpenOptions = OpenOptions.default,
+    attributes: Attributes = Attributes.default
+  ): Dispose[FileChannel] =
     betterFile.fileChannel(openOptions, attributes)
 
-  final def newAsynchronousFileChannel(implicit openOptions: OpenOptions = OpenOptions.default):
-  AsynchronousFileChannel = betterFile.newAsynchronousFileChannel(openOptions)
+  final def newAsynchronousFileChannel(implicit
+    openOptions: OpenOptions = OpenOptions.default
+  ): AsynchronousFileChannel = betterFile.newAsynchronousFileChannel(openOptions)
 
-  final def asynchronousFileChannel(implicit openOptions: OpenOptions = OpenOptions.default):
-  Dispose[AsynchronousFileChannel] = betterFile.asynchronousFileChannel(openOptions)
+  final def asynchronousFileChannel(implicit
+    openOptions: OpenOptions = OpenOptions.default
+  ): Dispose[AsynchronousFileChannel] = betterFile.asynchronousFileChannel(openOptions)
 
   final def digest(algorithmName: String): Array[Byte] = {
     val messageDigest = MessageDigest.getInstance(algorithmName)
@@ -307,8 +330,11 @@ trait BetterFileMethods {
 
   final def isHidden: Boolean = betterFile.isHidden
 
-  final def isLocked(mode: RandomAccessMode, position: Long = 0L, size: Long = Long.MaxValue,
-                     isShared: Boolean = false): Boolean = betterFile.isLocked(mode, position, size, isShared)
+  final def isLocked(mode: RandomAccessMode,
+                     position: Long = 0L,
+                     size: Long = Long.MaxValue,
+                     isShared: Boolean = false
+  ): Boolean = betterFile.isLocked(mode, position, size, isShared)
 
   final def isReadLocked(position: Long = 0L, size: Long = Long.MaxValue, isShared: Boolean = false): Boolean =
     betterFile.isReadLocked(position, size, isShared)
@@ -359,7 +385,7 @@ trait BetterFileMethods {
   }
 
   // Conflicts with the legacy cromwell.core.path.Obsolete.PathMethodAliases.getFileName(). Uncomment when that's gone.
-  //final def apply(permission: PosixFilePermission): Boolean = betterFile.apply(permission)
+  // final def apply(permission: PosixFilePermission): Boolean = betterFile.apply(permission)
 
   final def isOwnerReadable: Boolean = betterFile.isOwnerReadable
 
@@ -416,9 +442,9 @@ trait BetterFileMethods {
     this
   }
 
-  final def touch(time: Instant = Instant.now())
-                 (implicit attributes: Attributes = Attributes.default,
-                  linkOptions: LinkOptions = LinkOptions.default): this.type = {
+  final def touch(
+    time: Instant = Instant.now()
+  )(implicit attributes: Attributes = Attributes.default, linkOptions: LinkOptions = LinkOptions.default): this.type = {
     betterFile.touch(time)(attributes, linkOptions)
     this
   }
@@ -443,14 +469,16 @@ trait BetterFileMethods {
     destination
   }
 
-  final def symbolicLinkTo(destination: Path)
-                          (implicit attributes: Attributes = Attributes.default): destination.type = {
+  final def symbolicLinkTo(
+    destination: Path
+  )(implicit attributes: Attributes = Attributes.default): destination.type = {
     betterFile.symbolicLinkTo(destination.betterFile)(attributes)
     destination
   }
 
-  final def linkTo(destination: Path, symbolic: Boolean = false)
-                  (implicit attributes: Attributes = Attributes.default): destination.type = {
+  final def linkTo(destination: Path, symbolic: Boolean = false)(implicit
+    attributes: Attributes = Attributes.default
+  ): destination.type = {
     betterFile.linkTo(destination.betterFile, symbolic)(attributes)
     destination
   }
@@ -477,13 +505,16 @@ trait BetterFileMethods {
     this
   }
 
-  final def zipTo(destination: Path, compressionLevel: Int = Deflater.DEFAULT_COMPRESSION)
-                 (implicit charset: Charset = DefaultCharset): destination.type = {
+  final def zipTo(destination: Path, compressionLevel: Int = Deflater.DEFAULT_COMPRESSION)(implicit
+    charset: Charset = DefaultCharset
+  ): destination.type = {
     betterFile.zipTo(destination.betterFile, compressionLevel)(charset)
     destination
   }
 
-  final def zip(compressionLevel: Int = Deflater.DEFAULT_COMPRESSION)(implicit charset: Charset = DefaultCharset): Path =
+  final def zip(compressionLevel: Int = Deflater.DEFAULT_COMPRESSION)(implicit
+    charset: Charset = DefaultCharset
+  ): Path =
     newPath(betterFile.zip(compressionLevel)(charset))
 
   final def unzipTo(destination: Path)(implicit charset: Charset = DefaultCharset): destination.type = {
@@ -515,9 +546,9 @@ object BetterFileMethods {
 
     def cwd: Path = pwd
 
-    val `..`: Path => Path = _.parent
+    val `..` : Path => Path = _.parent
 
-    val `.`: Path => Path = identity
+    val `.` : Path => Path = identity
 
     implicit class FileDsl(file: Path) {
       def /(f: Path => Path): Path = f(file)
@@ -561,7 +592,8 @@ object BetterFileMethods {
 
     def chgrp(group: String, file: Path): Path = file.setGroup(group)
 
-    def chmod(permissions: String, file: Path): Path = file.setPermissions(PosixFilePermissions.fromString(permissions).asScala.toSet)
+    def chmod(permissions: String, file: Path): Path =
+      file.setPermissions(PosixFilePermissions.fromString(permissions).asScala.toSet)
 
     def chmod_+(permission: PosixFilePermission, file: Path): Path = file.addPermission(permission)
 
@@ -572,10 +604,12 @@ object BetterFileMethods {
     def unzip(zipFile: Path)(destination: Path)(implicit charset: Charset = DefaultCharset): destination.type =
       zipFile.unzipTo(destination)(charset)
 
-    def zip(files: better.files.File*)(destination: better.files.File, compressionLevel: Int = Deflater.DEFAULT_COMPRESSION)
-           (implicit charset: Charset = DefaultCharset): destination.type = {
+    def zip(
+      files: better.files.File*
+    )(destination: better.files.File, compressionLevel: Int = Deflater.DEFAULT_COMPRESSION)(implicit
+      charset: Charset = DefaultCharset
+    ): destination.type =
       destination.zipIn(files.iterator, compressionLevel)(charset)
-    }
   }
 
   type PathMatcherSyntax = better.files.File.PathMatcherSyntax
diff --git a/core/src/main/scala/cromwell/core/path/CustomRetryParams.scala b/core/src/main/scala/cromwell/core/path/CustomRetryParams.scala
index 13f577a1718..5136d7baa20 100644
--- a/core/src/main/scala/cromwell/core/path/CustomRetryParams.scala
+++ b/core/src/main/scala/cromwell/core/path/CustomRetryParams.scala
@@ -11,7 +11,7 @@ object CustomRetryParams {
   val Default = CustomRetryParams(
     timeout = Duration.Inf,
     maxRetries = Option(3),
-    backoff = SimpleExponentialBackoff(1 seconds, 3 seconds, 1.5D),
+    backoff = SimpleExponentialBackoff(1 seconds, 3 seconds, 1.5d),
     isTransient = throwableToFalse,
     isFatal = throwableToFalse
   )
@@ -23,4 +23,5 @@ case class CustomRetryParams(timeout: Duration,
                              maxRetries: Option[Int],
                              backoff: Backoff,
                              isTransient: Throwable => Boolean,
-                             isFatal: Throwable => Boolean)
+                             isFatal: Throwable => Boolean
+)
diff --git a/core/src/main/scala/cromwell/core/path/DefaultPathBuilder.scala b/core/src/main/scala/cromwell/core/path/DefaultPathBuilder.scala
index 4bbefe71d0a..f478d04aa67 100644
--- a/core/src/main/scala/cromwell/core/path/DefaultPathBuilder.scala
+++ b/core/src/main/scala/cromwell/core/path/DefaultPathBuilder.scala
@@ -19,7 +19,6 @@ case object DefaultPathBuilder extends PathBuilder {
     val uri = URI.create(UrlEscapers.urlFragmentEscaper().escape(pathAsString))
     Option(uri.getScheme) match {
       case Some("file") | None =>
-
         if (pathAsString.startsWith("file://")) {
           // NOTE: Legacy support for old paths generated as URIs by the old .toRealString
           val host = Option(uri.getHost) getOrElse ""
@@ -44,15 +43,14 @@ case object DefaultPathBuilder extends PathBuilder {
 
   def createTempDirectory(prefix: String): DefaultPath = DefaultPath(java.nio.file.Files.createTempDirectory(prefix))
 
-  def createTempFile(prefix: String = "", suffix: String = "", parent: Option[Path] = None): Path = {
+  def createTempFile(prefix: String = "", suffix: String = "", parent: Option[Path] = None): Path =
     parent match {
       case Some(dir) => dir.createTempFile(prefix, suffix)
       case _ => DefaultPath(java.nio.file.Files.createTempFile(prefix, suffix))
     }
-  }
 }
 
-case class DefaultPath private[path](nioPath: NioPath) extends Path {
+case class DefaultPath private[path] (nioPath: NioPath) extends Path {
   override protected def newPath(nioPath: NioPath): DefaultPath = DefaultPath(nioPath)
 
   override def pathAsString: String = nioPath.toString
diff --git a/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala b/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
index 20a2afdd5ce..f986dcfa1a5 100644
--- a/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
+++ b/core/src/main/scala/cromwell/core/path/DefaultPathBuilderFactory.scala
@@ -7,7 +7,8 @@ import cromwell.core.path.PathBuilderFactory.PriorityDefault
 import scala.concurrent.{ExecutionContext, Future}
 
 case object DefaultPathBuilderFactory extends PathBuilderFactory {
-  override def withOptions(options: WorkflowOptions)(implicit actorSystem: ActorSystem, ec: ExecutionContext) = Future.successful(DefaultPathBuilder)
+  override def withOptions(options: WorkflowOptions)(implicit actorSystem: ActorSystem, ec: ExecutionContext) =
+    Future.successful(DefaultPathBuilder)
   val name = "local"
   val tuple = name -> this
 
diff --git a/core/src/main/scala/cromwell/core/path/EvenBetterPathMethods.scala b/core/src/main/scala/cromwell/core/path/EvenBetterPathMethods.scala
index ffe862c2df3..e455867e5e6 100644
--- a/core/src/main/scala/cromwell/core/path/EvenBetterPathMethods.scala
+++ b/core/src/main/scala/cromwell/core/path/EvenBetterPathMethods.scala
@@ -1,6 +1,6 @@
 package cromwell.core.path
 
-import java.io.{BufferedInputStream, BufferedReader, ByteArrayOutputStream, IOException, InputStream, InputStreamReader}
+import java.io.{BufferedInputStream, BufferedReader, ByteArrayOutputStream, InputStream, InputStreamReader, IOException}
 import java.nio.file.{FileAlreadyExistsException, Files}
 import java.nio.file.attribute.{PosixFilePermission, PosixFilePermissions}
 import java.util.zip.GZIPOutputStream
@@ -33,13 +33,11 @@ trait EvenBetterPathMethods {
 
   final def plusSuffix(suffix: String): Path = swapSuffix("", suffix)
 
-  final def swapSuffix(oldSuffix: String, newSuffix: String): Path = {
+  final def swapSuffix(oldSuffix: String, newSuffix: String): Path =
     sibling(s"${name.stripSuffix(oldSuffix)}$newSuffix")
-  }
 
-  final def createTempFile(prefix: String = "", suffix: String = ""): Path = {
+  final def createTempFile(prefix: String = "", suffix: String = ""): Path =
     newPath(java.nio.file.Files.createTempFile(nioPathPrivate, prefix, suffix))
-  }
 
   def chmod(permissions: String): this.type = {
     setPermissions(PosixFilePermissions.fromString(permissions).asScala.toSet)
@@ -49,18 +47,16 @@ trait EvenBetterPathMethods {
   // betterFile.symbolicLink calls Files.readSymbolicLink, but then implicitly converts the java.nio.Path returned to a better.File
   // which calls toAbsolutePath. Consequently, if the path was relative, the current directory is used to make it absolute.
   // This is not the desired behavior to be able to follow relative symbolic links, so bypass better files method and directly use the java one.
-  final def symbolicLinkRelative: Option[Path] = {
+  final def symbolicLinkRelative: Option[Path] =
     if (betterFile.isSymbolicLink) {
       Option(newPath(Files.readSymbolicLink(betterFile.path)))
     } else None
-  }
 
-  final def followSymbolicLinks: Path = {
+  final def followSymbolicLinks: Path =
     symbolicLinkRelative match {
       case Some(target) => parent.resolve(target.followSymbolicLinks)
       case None => this
     }
-  }
 
   final def createPermissionedDirectories(): this.type = {
     if (!exists) {
@@ -73,8 +69,7 @@ trait EvenBetterPathMethods {
         addPermission(PosixFilePermission.OTHERS_READ)
         addPermission(PosixFilePermission.OTHERS_WRITE)
         addPermission(PosixFilePermission.OTHERS_EXECUTE)
-      }
-      catch {
+      } catch {
         // Race condition that's particularly likely with scatters.  Ignore.
         case _: FileAlreadyExistsException =>
         // The GCS filesystem does not support setting permissions and will throw an `UnsupportedOperationException`.
@@ -105,7 +100,9 @@ trait EvenBetterPathMethods {
     byteStream.toByteArray
   }
 
-  def writeContent(content: String)(openOptions: OpenOptions, codec: Codec, compressPayload: Boolean)(implicit ec: ExecutionContext): this.type = {
+  def writeContent(
+    content: String
+  )(openOptions: OpenOptions, codec: Codec, compressPayload: Boolean)(implicit ec: ExecutionContext): this.type = {
     locally(ec)
     val contentByteArray = content.getBytes(codec.charSet)
     writeByteArray {
@@ -113,8 +110,8 @@ trait EvenBetterPathMethods {
     }(openOptions)
   }
 
-  private def fileIoErrorPf[A]: PartialFunction[Throwable, Try[A]] = {
-    case ex: Throwable => Failure(new IOException(s"Could not read from ${this.pathAsString}: ${ex.getMessage}", ex))
+  private def fileIoErrorPf[A]: PartialFunction[Throwable, Try[A]] = { case ex: Throwable =>
+    Failure(new IOException(s"Could not read from ${this.pathAsString}: ${ex.getMessage}", ex))
   }
 
   /**
@@ -122,35 +119,36 @@ trait EvenBetterPathMethods {
     * The input stream will be closed when this method returns, which means the f function
     * cannot leak an open stream.
     */
-  def withReader[A](f: BufferedReader => A)(implicit ec: ExecutionContext): A = {
+  def withReader[A](f: BufferedReader => A)(implicit ec: ExecutionContext): A =
     // Use an input reader to convert the byte stream to character stream. Buffered reader for efficiency.
-    tryWithResource(() => new BufferedReader(new InputStreamReader(this.mediaInputStream, Codec.UTF8.name)))(f).recoverWith(fileIoErrorPf).get
-  }
+    tryWithResource(() => new BufferedReader(new InputStreamReader(this.mediaInputStream, Codec.UTF8.name)))(f)
+      .recoverWith(fileIoErrorPf)
+      .get
 
   /**
     * InputStream's read method reads bytes, whereas InputStreamReader's read method reads characters.
     * BufferedInputStream can be used to read bytes directly from input stream, without conversion to characters.
     */
-  def withBufferedStream[A](f: BufferedInputStream => A)(implicit ec: ExecutionContext): A = {
+  def withBufferedStream[A](f: BufferedInputStream => A)(implicit ec: ExecutionContext): A =
     tryWithResource(() => new BufferedInputStream(this.mediaInputStream))(f).recoverWith(fileIoErrorPf).get
-  }
 
   /**
     * Returns an Array[Byte] from a Path. Limit the array size to "limit" byte if defined.
     * @throws IOException if failOnOverflow is true and the file is larger than limit
     */
-  def limitFileContent(limit: Option[Int], failOnOverflow: Boolean)(implicit ec: ExecutionContext): Array[Byte] = withBufferedStream { bufferedStream =>
-    val bytesIterator = Iterator.continually(bufferedStream.read).takeWhile(_ != -1).map(_.toByte)
-    // Take 1 more than the limit so that we can look at the size and know if it's overflowing
-    val bytesArray = limit.map(l => bytesIterator.take(l + 1)).getOrElse(bytesIterator).toArray
-
-    limit match {
-      case Some(l) if failOnOverflow && bytesArray.length > l =>
-        throw new IOException(s"File $this is larger than requested maximum of $l Bytes.")
-      case Some(l) => bytesArray.take(l)
-      case _ => bytesArray
+  def limitFileContent(limit: Option[Int], failOnOverflow: Boolean)(implicit ec: ExecutionContext): Array[Byte] =
+    withBufferedStream { bufferedStream =>
+      val bytesIterator = Iterator.continually(bufferedStream.read).takeWhile(_ != -1).map(_.toByte)
+      // Take 1 more than the limit so that we can look at the size and know if it's overflowing
+      val bytesArray = limit.map(l => bytesIterator.take(l + 1)).getOrElse(bytesIterator).toArray
+
+      limit match {
+        case Some(l) if failOnOverflow && bytesArray.length > l =>
+          throw new IOException(s"File $this is larger than requested maximum of $l Bytes.")
+        case Some(l) => bytesArray.take(l)
+        case _ => bytesArray
+      }
     }
-  }
 
   /**
     * Reads the first limitBytes of a file and makes a String. Prepend with an annotation at the start (to say that this is the
diff --git a/core/src/main/scala/cromwell/core/path/JavaWriterImplicits.scala b/core/src/main/scala/cromwell/core/path/JavaWriterImplicits.scala
index cc1b7f40dde..2b5e36f2086 100644
--- a/core/src/main/scala/cromwell/core/path/JavaWriterImplicits.scala
+++ b/core/src/main/scala/cromwell/core/path/JavaWriterImplicits.scala
@@ -4,6 +4,7 @@ import java.io.Writer
 
 object JavaWriterImplicits {
   implicit class FlushingAndClosingWriter(writer: Writer) {
+
     /** Convenience method to flush and close in one shot. */
     def flushAndClose() = {
       writer.flush()
diff --git a/core/src/main/scala/cromwell/core/path/NioPathMethods.scala b/core/src/main/scala/cromwell/core/path/NioPathMethods.scala
index 42c17ca3222..3ce92dddd93 100644
--- a/core/src/main/scala/cromwell/core/path/NioPathMethods.scala
+++ b/core/src/main/scala/cromwell/core/path/NioPathMethods.scala
@@ -35,9 +35,9 @@ trait NioPathMethods {
   final def getNameCount: Int = nioPathPrivate.getNameCount
 
   /* This method cannot be used safely because it could fail for valid GcsPaths that are not valid URIs
-    * See https://github.com/GoogleCloudPlatform/google-cloud-java/issues/1343
+   * See https://github.com/GoogleCloudPlatform/google-cloud-java/issues/1343
    */
-  //final def toUri: URI = nioPathPrivate.toUri
+  // final def toUri: URI = nioPathPrivate.toUri
 
   final def compareTo(other: Path): Int = nioPathPrivate.compareTo(other.nioPathPrivate)
 
@@ -73,5 +73,5 @@ trait NioPathMethods {
     * Default implementation assumes symlinks are supported, and that toRealPath may return a valid path.
     * This implementation may be overridden for NIO implementations that do not support symbolic links (For example the Azure NIO library)
     */
-  def getSymlinkSafePath(options: LinkOption*): Path  = toRealPath(options: _*)
+  def getSymlinkSafePath(options: LinkOption*): Path = toRealPath(options: _*)
 }
diff --git a/core/src/main/scala/cromwell/core/path/Obsolete.scala b/core/src/main/scala/cromwell/core/path/Obsolete.scala
index 77fd32b54a7..78c346ce09d 100644
--- a/core/src/main/scala/cromwell/core/path/Obsolete.scala
+++ b/core/src/main/scala/cromwell/core/path/Obsolete.scala
@@ -47,16 +47,14 @@ object Obsolete {
   val File = ObsoleteFile
 
   object ObsoleteFile {
-    def newTemporaryDirectory(prefix: String = ""): DefaultPath = {
+    def newTemporaryDirectory(prefix: String = ""): DefaultPath =
       DefaultPath(better.files.File.newTemporaryDirectory(prefix).path)
-    }
 
-    def newTemporaryFile(prefix: String = "", suffix: String = "", parent: Option[Path] = None): Path = {
+    def newTemporaryFile(prefix: String = "", suffix: String = "", parent: Option[Path] = None): Path =
       parent match {
         case Some(dir) => dir.createTempFile(prefix, suffix)
         case _ => DefaultPathBuilder.createTempFile(prefix, suffix)
       }
-    }
 
     def apply(path: String, fragments: String*) = DefaultPath(better.files.File(path, fragments: _*).path)
 
diff --git a/core/src/main/scala/cromwell/core/path/PathBuilder.scala b/core/src/main/scala/cromwell/core/path/PathBuilder.scala
index 371c9e98157..fecfaebd507 100644
--- a/core/src/main/scala/cromwell/core/path/PathBuilder.scala
+++ b/core/src/main/scala/cromwell/core/path/PathBuilder.scala
@@ -40,6 +40,7 @@ trait PreResolvePathBuilder extends PathBuilder {
   * @see [[cromwell.core.path.EvenBetterPathMethods]]
   */
 trait Path extends PathObjectMethods with NioPathMethods with BetterFileMethods with EvenBetterPathMethods {
+
   /**
     * A reference to the underlying nioPath, used to create new java.nio.Path's that will then be sent to newPath
     * for wrapping.
@@ -132,11 +133,11 @@ trait Path extends PathObjectMethods with NioPathMethods with BetterFileMethods
   def pathWithoutScheme: String
 
   // Used by various extension traits within this scala package
-  private[path] final def nioPathPrivate: NioPath = nioPath
+  final private[path] def nioPathPrivate: NioPath = nioPath
 
   // Used within BetterFileMethods
-  private[path] final def betterFile: better.files.File = nioPathPrivate
+  final private[path] def betterFile: better.files.File = nioPathPrivate
 
   // Some Path methods return null.
-  private[path] final def newPathOrNull(nioPath: NioPath) = Option(nioPath).map(newPath).orNull
+  final private[path] def newPathOrNull(nioPath: NioPath) = Option(nioPath).map(newPath).orNull
 }
diff --git a/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala b/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
index 79adaae4d6b..cbc750f9f6f 100644
--- a/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
+++ b/core/src/main/scala/cromwell/core/path/PathBuilderFactory.scala
@@ -11,15 +11,18 @@ import scala.concurrent.{ExecutionContext, Future}
 
 object PathBuilderFactory {
   // Given a list of factories, instantiates the corresponding path builders
-  def instantiatePathBuilders(factories: List[PathBuilderFactory], workflowOptions: WorkflowOptions)(implicit as: ActorSystem): Future[List[PathBuilder]] = {
+  def instantiatePathBuilders(factories: List[PathBuilderFactory], workflowOptions: WorkflowOptions)(implicit
+    as: ActorSystem
+  ): Future[List[PathBuilder]] = {
     implicit val ec: ExecutionContext = as.dispatchers.lookup(Dispatcher.IoDispatcher)
     val sortedFactories = factories.sortBy(_.priority)
     sortedFactories.traverse(_.withOptions(workflowOptions))
   }
 
-  val PriorityBlob     = 100   // High priority to evaluate first, because blob files may inadvertently match other filesystems
+  val PriorityBlob =
+    100 // High priority to evaluate first, because blob files may inadvertently match other filesystems
   val PriorityStandard = 1000
-  val PriorityDefault  = 10000 // "Default" is a fallback, evaluate last
+  val PriorityDefault = 10000 // "Default" is a fallback, evaluate last
 }
 
 /**
diff --git a/core/src/main/scala/cromwell/core/path/PathCopier.scala b/core/src/main/scala/cromwell/core/path/PathCopier.scala
index b9352cb2082..6848ab3d24b 100644
--- a/core/src/main/scala/cromwell/core/path/PathCopier.scala
+++ b/core/src/main/scala/cromwell/core/path/PathCopier.scala
@@ -18,7 +18,7 @@ object PathCopier {
     val tokens2 = string2.split(regexIncludingSlashes)
 
     val matchingTokens: Array[(String, String)] = tokens1.zip(tokens2).takeWhile(Function.tupled(_ == _))
-    val matchingPrefix = matchingTokens.map({ case (str, _) => str }).mkString
+    val matchingPrefix = matchingTokens.map { case (str, _) => str }.mkString
 
     string2.stripPrefix(matchingPrefix).replaceAll("^/+", "")
   }
@@ -39,13 +39,12 @@ object PathCopier {
   /**
     * Copies from source to destination. NOTE: Copies are not atomic, and may create a partial copy.
     */
-  def copy(sourceFilePath: Path, destinationFilePath: Path): Try[Unit] = {
+  def copy(sourceFilePath: Path, destinationFilePath: Path): Try[Unit] =
     Try {
       Option(destinationFilePath.parent).foreach(_.createDirectories())
       sourceFilePath.copyTo(destinationFilePath, overwrite = true)
       ()
-    } recoverWith {
-      case ex => Failure(new IOException(s"Failed to copy $sourceFilePath to $destinationFilePath", ex))
+    } recoverWith { case ex =>
+      Failure(new IOException(s"Failed to copy $sourceFilePath to $destinationFilePath", ex))
     }
-  }
 }
diff --git a/core/src/main/scala/cromwell/core/path/PathFactory.scala b/core/src/main/scala/cromwell/core/path/PathFactory.scala
index a9e074afcc7..b2777b0fc83 100644
--- a/core/src/main/scala/cromwell/core/path/PathFactory.scala
+++ b/core/src/main/scala/cromwell/core/path/PathFactory.scala
@@ -15,6 +15,7 @@ import scala.util.{Failure, Success, Try}
   * Convenience trait delegating to the PathFactory singleton
   */
 trait PathFactory {
+
   /**
     * Path builders to be applied (in order) to attempt to build a Path from a string.
     */
@@ -43,11 +44,13 @@ object PathFactory {
   private def findFirstSuccess(string: String,
                                allPathBuilders: PathBuilders,
                                restPathBuilders: PathBuilders,
-                               failures: Vector[String]): ErrorOr[Path] = restPathBuilders match {
-    case Nil => NonEmptyList.fromList(failures.toList) match {
-      case Some(errors) => Invalid(errors)
-      case None => s"Could not parse '$string' to path. No PathBuilders were provided".invalidNel
-    }
+                               failures: Vector[String]
+  ): ErrorOr[Path] = restPathBuilders match {
+    case Nil =>
+      NonEmptyList.fromList(failures.toList) match {
+        case Some(errors) => Invalid(errors)
+        case None => s"Could not parse '$string' to path. No PathBuilders were provided".invalidNel
+      }
     case pb :: rest =>
       pb.build(string, allPathBuilders) match {
         case Success(path) =>
@@ -64,7 +67,8 @@ object PathFactory {
   def buildPath(string: String,
                 pathBuilders: PathBuilders,
                 preMapping: String => String = identity[String],
-                postMapping: Path => Path = identity[Path]): Path = {
+                postMapping: Path => Path = identity[Path]
+  ): Path = {
 
     lazy val pathBuilderNames: String = pathBuilders map { _.name } mkString ", "
 
@@ -77,12 +81,12 @@ object PathFactory {
     path match {
       case Valid(v) => v
       case Invalid(errors) =>
-      throw PathParsingException(
-        s"""Could not build the path "$string". It may refer to a filesystem not supported by this instance of Cromwell.""" +
-          s" Supported filesystems are: $pathBuilderNames." +
-          s" Failures: ${errors.toList.mkString(System.lineSeparator, System.lineSeparator, System.lineSeparator)}" +
-          s" Please refer to the documentation for more information on how to configure filesystems: http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems"
-      )
+        throw PathParsingException(
+          s"""Could not build the path "$string". It may refer to a filesystem not supported by this instance of Cromwell.""" +
+            s" Supported filesystems are: $pathBuilderNames." +
+            s" Failures: ${errors.toList.mkString(System.lineSeparator, System.lineSeparator, System.lineSeparator)}" +
+            s" Please refer to the documentation for more information on how to configure filesystems: http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems"
+        )
     }
   }
 }
diff --git a/core/src/main/scala/cromwell/core/path/PathObjectMethods.scala b/core/src/main/scala/cromwell/core/path/PathObjectMethods.scala
index d109faa797c..ab3d981316c 100644
--- a/core/src/main/scala/cromwell/core/path/PathObjectMethods.scala
+++ b/core/src/main/scala/cromwell/core/path/PathObjectMethods.scala
@@ -8,12 +8,11 @@ trait PathObjectMethods {
 
   override def toString: String = pathAsString
 
-  override def equals(obj: Any) = {
+  override def equals(obj: Any) =
     obj match {
       case other: Path => nioPathPrivate == other.nioPathPrivate
       case _ => false
     }
-  }
 
   override def hashCode = nioPathPrivate.hashCode()
 }
diff --git a/core/src/main/scala/cromwell/core/path/PathWriter.scala b/core/src/main/scala/cromwell/core/path/PathWriter.scala
index 5a602810183..ee7717b6765 100644
--- a/core/src/main/scala/cromwell/core/path/PathWriter.scala
+++ b/core/src/main/scala/cromwell/core/path/PathWriter.scala
@@ -59,7 +59,7 @@ case class TailedWriter(path: Path, tailedSize: Int) extends PathWriter {
     *
     * @return a descriptive tail of the `path` and the last `tailedLines` written.
     */
-  def tailString: String = {
+  def tailString: String =
     if (tailedLines.isEmpty) {
       s"Contents of $path were empty."
     } else if (isTailed) {
@@ -67,5 +67,4 @@ case class TailedWriter(path: Path, tailedSize: Int) extends PathWriter {
     } else {
       s"Contents of $path:\n${tailedLines.mkString("\n")}"
     }
-  }
 }
diff --git a/core/src/main/scala/cromwell/core/retry/GoogleBackoff.scala b/core/src/main/scala/cromwell/core/retry/GoogleBackoff.scala
index 0a50b79e091..c901bc0d1ec 100644
--- a/core/src/main/scala/cromwell/core/retry/GoogleBackoff.scala
+++ b/core/src/main/scala/cromwell/core/retry/GoogleBackoff.scala
@@ -8,47 +8,59 @@ import net.ceedubs.ficus.Ficus._
 import scala.concurrent.duration.{Duration, FiniteDuration}
 
 object InitialGapBackoff {
-  def apply(initialGap: FiniteDuration, initialInterval: FiniteDuration, maxInterval: FiniteDuration, multiplier: Double) = {
-    new InitialGapBackoff(initialGap, new ExponentialBackOff.Builder()
-      .setInitialIntervalMillis(initialInterval.toMillis.toInt)
-      .setMaxIntervalMillis(maxInterval.toMillis.toInt)
-      .setMultiplier(multiplier)
-      .setMaxElapsedTimeMillis(Int.MaxValue)
-      .build())
-  }
+  def apply(initialGap: FiniteDuration,
+            initialInterval: FiniteDuration,
+            maxInterval: FiniteDuration,
+            multiplier: Double
+  ) =
+    new InitialGapBackoff(
+      initialGap,
+      new ExponentialBackOff.Builder()
+        .setInitialIntervalMillis(initialInterval.toMillis.toInt)
+        .setMaxIntervalMillis(maxInterval.toMillis.toInt)
+        .setMultiplier(multiplier)
+        .setMaxElapsedTimeMillis(Int.MaxValue)
+        .build()
+    )
 }
 
 case class InitialGapBackoff(initialGapMillis: FiniteDuration, googleBackoff: ExponentialBackOff) extends Backoff {
   assert(initialGapMillis.compareTo(Duration.Zero) != 0, "Initial gap cannot be null, use SimpleBackoff instead.")
 
   override val backoffMillis = initialGapMillis.toMillis
+
   /** Switch to a SimpleExponentialBackoff after the initial gap has been used */
   override def next = new SimpleExponentialBackoff(googleBackoff)
 }
 
 object SimpleExponentialBackoff {
-  def apply(initialInterval: FiniteDuration, maxInterval: FiniteDuration, multiplier: Double, randomizationFactor: Double = ExponentialBackOff.DEFAULT_RANDOMIZATION_FACTOR) = {
-    new SimpleExponentialBackoff(new ExponentialBackOff.Builder()
-      .setInitialIntervalMillis(initialInterval.toMillis.toInt)
-      .setMaxIntervalMillis(maxInterval.toMillis.toInt)
-      .setMultiplier(multiplier)
-      .setMaxElapsedTimeMillis(Int.MaxValue)
-      .setRandomizationFactor(randomizationFactor)
-      .build())
-  }
-  
-  def apply(config: Config): SimpleExponentialBackoff = {
+  def apply(initialInterval: FiniteDuration,
+            maxInterval: FiniteDuration,
+            multiplier: Double,
+            randomizationFactor: Double = ExponentialBackOff.DEFAULT_RANDOMIZATION_FACTOR
+  ) =
+    new SimpleExponentialBackoff(
+      new ExponentialBackOff.Builder()
+        .setInitialIntervalMillis(initialInterval.toMillis.toInt)
+        .setMaxIntervalMillis(maxInterval.toMillis.toInt)
+        .setMultiplier(multiplier)
+        .setMaxElapsedTimeMillis(Int.MaxValue)
+        .setRandomizationFactor(randomizationFactor)
+        .build()
+    )
+
+  def apply(config: Config): SimpleExponentialBackoff =
     SimpleExponentialBackoff(
       config.as[FiniteDuration]("min"),
       config.as[FiniteDuration]("max"),
       config.as[Double]("multiplier"),
       config.as[Double]("randomization-factor")
     )
-  }
 }
 
 case class SimpleExponentialBackoff(googleBackoff: ExponentialBackOff) extends Backoff {
   override def backoffMillis = googleBackoff.nextBackOffMillis()
+
   /** google ExponentialBackOff is mutable so we can keep returning the same instance */
   override def next = this
 }
diff --git a/core/src/main/scala/cromwell/core/retry/Retry.scala b/core/src/main/scala/cromwell/core/retry/Retry.scala
index 5e5ba4fe6b1..a7c10cd48dd 100644
--- a/core/src/main/scala/cromwell/core/retry/Retry.scala
+++ b/core/src/main/scala/cromwell/core/retry/Retry.scala
@@ -34,11 +34,11 @@ object Retry extends StrictLogging {
     */
   def withRetry[A](f: () => Future[A],
                    maxRetries: Option[Int] = Option(10),
-                   backoff: Backoff = SimpleExponentialBackoff(5 seconds, 10 seconds, 1.1D),
+                   backoff: Backoff = SimpleExponentialBackoff(5 seconds, 10 seconds, 1.1d),
                    isTransient: Throwable => Boolean = throwableToFalse,
                    isFatal: Throwable => Boolean = throwableToFalse,
-                   onRetry: Throwable => Unit = noopOnRetry)
-                   (implicit actorSystem: ActorSystem): Future[A] = {
+                   onRetry: Throwable => Unit = noopOnRetry
+  )(implicit actorSystem: ActorSystem): Future[A] = {
     // In the future we might want EC passed in separately but at the moment it caused more issues than it solved to do so
     implicit val ec: ExecutionContext = actorSystem.dispatcher
     val delay = backoff.backoffMillis.millis
@@ -47,10 +47,18 @@ object Retry extends StrictLogging {
       case throwable if isFatal(throwable) => Future.failed(CromwellFatalException(throwable))
       case throwable if !isFatal(throwable) =>
         val retriesLeft = if (isTransient(throwable)) maxRetries else maxRetries map { _ - 1 }
-        
+
         if (retriesLeft.forall(_ > 0)) {
           onRetry(throwable)
-          after(delay, actorSystem.scheduler)(withRetry(f, backoff = backoff.next, maxRetries = retriesLeft, isTransient = isTransient, isFatal = isFatal, onRetry = onRetry))
+          after(delay, actorSystem.scheduler)(
+            withRetry(f,
+                      backoff = backoff.next,
+                      maxRetries = retriesLeft,
+                      isTransient = isTransient,
+                      isFatal = isFatal,
+                      onRetry = onRetry
+            )
+          )
         } else {
           Future.failed(new CromwellFatalException(throwable))
         }
@@ -69,8 +77,8 @@ object Retry extends StrictLogging {
    */
   def withRetryForTransactionRollback[A](f: () => Future[A],
                                          maxRetries: Int = 5,
-                                         backoff: Backoff = SimpleExponentialBackoff(5 seconds, 10 seconds, 1.1D))
-                                        (implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[A] = {
+                                         backoff: Backoff = SimpleExponentialBackoff(5 seconds, 10 seconds, 1.1d)
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[A] = {
     val delay = backoff.backoffMillis.millis
 
     f() recoverWith {
@@ -85,4 +93,3 @@ object Retry extends StrictLogging {
     }
   }
 }
-
diff --git a/core/src/main/scala/cromwell/core/simpleton/WomValueBuilder.scala b/core/src/main/scala/cromwell/core/simpleton/WomValueBuilder.scala
index bfae7232d64..d2387b5062a 100644
--- a/core/src/main/scala/cromwell/core/simpleton/WomValueBuilder.scala
+++ b/core/src/main/scala/cromwell/core/simpleton/WomValueBuilder.scala
@@ -8,7 +8,6 @@ import wom.values._
 
 import scala.language.postfixOps
 
-
 /**
   * Builds arbitrary `WomValues` from `WomValueSimpletons`.
   **/
@@ -63,28 +62,26 @@ object WomValueBuilder {
   private val MapElementPattern = raw"^:((?:\\[]\[:]|[^]\[:])+)(.*)".r
 
   // Group tuples by key using a Map with key type `K`.
-  private def group[K](tuples: Iterable[(K, SimpletonComponent)]): Map[K, Iterable[SimpletonComponent]] = {
-    tuples groupBy { case (i, _) => i } map { case (k, v) => k -> (v map { case (_, s) => s}) }
-  }
+  private def group[K](tuples: Iterable[(K, SimpletonComponent)]): Map[K, Iterable[SimpletonComponent]] =
+    tuples groupBy { case (i, _) => i } map { case (k, v) => k -> (v map { case (_, s) => s }) }
 
   // Returns a tuple of the index into the outermost array and a `SimpletonComponent` whose path reflects the "descent"
   // into the array.  e.g. for a component
   // SimpletonComponent("[0][1]", v) this would return (0 -> SimpletonComponent("[1]", v)).
-  private def descendIntoArray(component: SimpletonComponent): (Int, SimpletonComponent) = {
-    component.path match { case ArrayElementPattern(index, more) => index.toInt -> component.copy(path = more)}
-  }
+  private def descendIntoArray(component: SimpletonComponent): (Int, SimpletonComponent) =
+    component.path match { case ArrayElementPattern(index, more) => index.toInt -> component.copy(path = more) }
 
   // Returns a tuple of the key into the outermost map and a `SimpletonComponent` whose path reflects the "descent"
   // into the map.  e.g. for a component
   // SimpletonComponent(":bar:baz", v) this would return ("bar" -> SimpletonComponent(":baz", v)).
   // Map keys are treated as Strings by this method, the caller must ultimately do the appropriate coercion to the
   // actual map key type.
-  private def descendIntoMap(component: SimpletonComponent): (String, SimpletonComponent) = {
-    component.path match { case MapElementPattern(key, more) => key.unescapeMeta -> component.copy(path = more)}
-  }
+  private def descendIntoMap(component: SimpletonComponent): (String, SimpletonComponent) =
+    component.path match { case MapElementPattern(key, more) => key.unescapeMeta -> component.copy(path = more) }
 
-  private implicit class EnhancedSimpletonComponents(val components: Iterable[SimpletonComponent]) extends AnyVal {
-    def asArray: List[Iterable[SimpletonComponent]] = group(components map descendIntoArray).toList.sortBy(_._1).map(_._2)
+  implicit private class EnhancedSimpletonComponents(val components: Iterable[SimpletonComponent]) extends AnyVal {
+    def asArray: List[Iterable[SimpletonComponent]] =
+      group(components map descendIntoArray).toList.sortBy(_._1).map(_._2)
     def asMap: Map[String, Iterable[SimpletonComponent]] = group(components map descendIntoMap)
     def asPrimitive: WomValue = components.head.value
     def asString: String = asPrimitive.valueString
@@ -92,51 +89,50 @@ object WomValueBuilder {
 
   private def toWomValue(outputType: WomType, components: Iterable[SimpletonComponent]): WomValue = {
 
-
-
     // Returns a tuple of the key into the pair (i.e. left or right) and a `SimpletonComponent` whose path reflects the "descent"
     // into the pair.  e.g. for a component
     // SimpletonComponent(":left:foo", someValue) this would return (PairLeft -> SimpletonComponent(":baz", someValue)).
     sealed trait PairLeftOrRight
     case object PairLeft extends PairLeftOrRight
     case object PairRight extends PairLeftOrRight
-    def descendIntoPair(component: SimpletonComponent): (PairLeftOrRight, SimpletonComponent) = {
+    def descendIntoPair(component: SimpletonComponent): (PairLeftOrRight, SimpletonComponent) =
       component.path match {
         case MapElementPattern("left", more) => PairLeft -> component.copy(path = more)
         case MapElementPattern("right", more) => PairRight -> component.copy(path = more)
       }
-    }
 
-    def toWomFile(components: Iterable[SimpletonComponent]) = {
+    def toWomFile(components: Iterable[SimpletonComponent]) =
       // If there's just one simpleton, it's a primitive (file or directory)
       if (components.size == 1) components.asPrimitive
       else {
         // Otherwise make a map of the components and detect the type of file from the class field
         val groupedListing = components.asMap
 
-        def isClass(className: String) = {
-          groupedListing.get(ClassKey)
-          /* If the class field is in an array it will be prefixed with a ':', so check for that as well.
-           * e.g: secondaryFiles[0]:class -> "File"
-           *      secondaryFiles[0]:value -> "file/path"
-           * would produce a Map(
-           *  ":class" -> List(Simpleton("File")),
-           *  ":value" -> List(Simpleton("file/path"))
-           * )
-           */
-          .orElse(groupedListing.get(s":$ClassKey"))
-          .map(_.asPrimitive.valueString)
-          .contains(className)
-        }
+        def isClass(className: String) =
+          groupedListing
+            .get(ClassKey)
+            /* If the class field is in an array it will be prefixed with a ':', so check for that as well.
+             * e.g: secondaryFiles[0]:class -> "File"
+             *      secondaryFiles[0]:value -> "file/path"
+             * would produce a Map(
+             *  ":class" -> List(Simpleton("File")),
+             *  ":value" -> List(Simpleton("file/path"))
+             * )
+             */
+            .orElse(groupedListing.get(s":$ClassKey"))
+            .map(_.asPrimitive.valueString)
+            .contains(className)
 
         def isDirectory = isClass(WomValueSimpleton.DirectoryClass)
         def isFile = isClass(WomValueSimpleton.FileClass)
 
         if (isDirectory) toWomValue(WomMaybeListedDirectoryType, components)
         else if (isFile) toWomValue(WomMaybePopulatedFileType, components)
-        else throw new IllegalArgumentException(s"There is no WomFile that can be built from simpletons: ${groupedListing.toList.mkString(", ")}")
+        else
+          throw new IllegalArgumentException(
+            s"There is no WomFile that can be built from simpletons: ${groupedListing.toList.mkString(", ")}"
+          )
       }
-    }
 
     outputType match {
       case _: WomPrimitiveType =>
@@ -151,19 +147,31 @@ object WomValueBuilder {
         WomArray(arrayType, components.asArray map { toWomValue(arrayType.memberType, _) })
       case mapType: WomMapType =>
         // map keys are guaranteed by WOM to be primitives, so the "coerceRawValue(..).get" is safe.
-        WomMap(mapType, components.asMap map { case (k, ss) => mapType.keyType.coerceRawValue(k).get -> toWomValue(mapType.valueType, ss) })
+        WomMap(mapType,
+               components.asMap map { case (k, ss) =>
+                 mapType.keyType.coerceRawValue(k).get -> toWomValue(mapType.valueType, ss)
+               }
+        )
       case pairType: WomPairType =>
-        val groupedByLeftOrRight: Map[PairLeftOrRight, Iterable[SimpletonComponent]] = group(components map descendIntoPair)
-        WomPair(toWomValue(pairType.leftType, groupedByLeftOrRight(PairLeft)), toWomValue(pairType.rightType, groupedByLeftOrRight(PairRight)))
+        val groupedByLeftOrRight: Map[PairLeftOrRight, Iterable[SimpletonComponent]] = group(
+          components map descendIntoPair
+        )
+        WomPair(toWomValue(pairType.leftType, groupedByLeftOrRight(PairLeft)),
+                toWomValue(pairType.rightType, groupedByLeftOrRight(PairRight))
+        )
       case WomObjectType =>
         // map keys are guaranteed by WOM to be primitives, so the "coerceRawValue(..).get" is safe.
         val map: Map[String, WomValue] = components.asMap map { case (k, ss) => k -> toWomValue(WomAnyType, ss) }
         WomObject(map)
       case composite: WomCompositeType =>
         val map: Map[String, WomValue] = components.asMap map { case (k, ss) =>
-          val valueType = composite
-            .typeMap
-            .getOrElse(k, throw new RuntimeException(s"Field $k is not a declared field of composite type $composite. Cannot build a WomValue from the simpletons."))
+          val valueType = composite.typeMap
+            .getOrElse(
+              k,
+              throw new RuntimeException(
+                s"Field $k is not a declared field of composite type $composite. Cannot build a WomValue from the simpletons."
+              )
+            )
           k -> toWomValue(valueType, ss)
         }
         WomObject.withTypeUnsafe(map, composite)
@@ -171,8 +179,9 @@ object WomValueBuilder {
         val directoryValues = components.asMap
 
         val value = directoryValues.get("value").map(_.asString)
-        val listing = directoryValues.get("listing")
-          .map({ _.asArray.map(toWomFile).collect({ case womFile: WomFile => womFile }) })
+        val listing = directoryValues
+          .get("listing")
+          .map(_.asArray.map(toWomFile).collect { case womFile: WomFile => womFile })
 
         WomMaybeListedDirectory(value, listing)
       case WomMaybePopulatedFileType =>
@@ -183,9 +192,9 @@ object WomValueBuilder {
         val size = populatedValues.get("size").map(_.asString.toLong)
         val format = populatedValues.get("format").map(_.asString)
         val contents = populatedValues.get("contents").map(_.asString)
-        val secondaryFiles = populatedValues.get("secondaryFiles").toList.flatMap({
-          _.asArray.map(toWomFile).collect({ case womFile: WomFile => womFile })
-        })
+        val secondaryFiles = populatedValues.get("secondaryFiles").toList.flatMap {
+          _.asArray.map(toWomFile).collect { case womFile: WomFile => womFile }
+        }
 
         WomMaybePopulatedFile(
           valueOption = value,
@@ -234,23 +243,28 @@ object WomValueBuilder {
     */
   private case class SimpletonComponent(path: String, value: WomValue)
 
-  def toJobOutputs(taskOutputs: Iterable[OutputPort], simpletons: Iterable[WomValueSimpleton]): CallOutputs = {
+  def toJobOutputs(taskOutputs: Iterable[OutputPort], simpletons: Iterable[WomValueSimpleton]): CallOutputs =
     CallOutputs(toWomValues(taskOutputs, simpletons))
-  }
 
-  def toWomValues(taskOutputs: Iterable[OutputPort], simpletons: Iterable[WomValueSimpleton]): Map[OutputPort, WomValue] = {
+  def toWomValues(taskOutputs: Iterable[OutputPort],
+                  simpletons: Iterable[WomValueSimpleton]
+  ): Map[OutputPort, WomValue] = {
 
-    def simpletonToComponent(name: String)(simpleton: WomValueSimpleton): SimpletonComponent = {
+    def simpletonToComponent(name: String)(simpleton: WomValueSimpleton): SimpletonComponent =
       SimpletonComponent(simpleton.simpletonKey.drop(name.length), simpleton.simpletonValue)
-    }
 
     // This is meant to "rehydrate" simpletonized WomValues back to WomValues.  It is assumed that these WomValues were
     // "dehydrated" to WomValueSimpletons correctly. This code is not robust to corrupt input whatsoever.
     val types = taskOutputs map { o => o -> o.womType } toMap
-    val simpletonsByOutputName = simpletons groupBy { _.simpletonKey match { case IdentifierAndPathPattern(i, _) => i } }
+    val simpletonsByOutputName = simpletons groupBy {
+      _.simpletonKey match { case IdentifierAndPathPattern(i, _) => i }
+    }
     val simpletonComponentsByOutputName: Map[String, Iterable[SimpletonComponent]] =
       simpletonsByOutputName map { case (name, ss) => name -> (ss map simpletonToComponent(name)) }
-    types map { case (outputPort, outputType) => outputPort -> toWomValue(outputType, simpletonComponentsByOutputName.getOrElse(outputPort.internalName, Seq.empty))}
+    types map { case (outputPort, outputType) =>
+      outputPort -> toWomValue(outputType,
+                               simpletonComponentsByOutputName.getOrElse(outputPort.internalName, Seq.empty)
+      )
+    }
   }
 }
-
diff --git a/core/src/main/scala/cromwell/core/simpleton/WomValueSimpleton.scala b/core/src/main/scala/cromwell/core/simpleton/WomValueSimpleton.scala
index 01ec7ddf8c8..35e7accdf07 100644
--- a/core/src/main/scala/cromwell/core/simpleton/WomValueSimpleton.scala
+++ b/core/src/main/scala/cromwell/core/simpleton/WomValueSimpleton.scala
@@ -15,7 +15,7 @@ case class WomValueSimpleton(simpletonKey: String, simpletonValue: WomPrimitive)
   * `WomValueSimpleton`s are transformed back to `WomValue`s.
   */
 object WomValueSimpleton {
-  
+
   val ClassKey = "class"
   val DirectoryClass = "Directory"
   val FileClass = "File"
@@ -35,23 +35,30 @@ object WomValueSimpleton {
     private def toNumberSimpleton(key: String)(value: Long) = WomValueSimpleton(key, WomInteger(value.toInt))
 
     // Pass the simplifyMode down to recursive calls without having to sling the parameter around explicitly.
-    def simplify(name: String)(implicit simplifyMode: SimplifyMode = SimplifyMode(forCaching = false)): Iterable[WomValueSimpleton] = {
+    def simplify(
+      name: String
+    )(implicit simplifyMode: SimplifyMode = SimplifyMode(forCaching = false)): Iterable[WomValueSimpleton] = {
       def suffix(suffix: String) = s"$name:$suffix"
       val fileValueSimplifier: String => String => WomValueSimpleton =
         if (simplifyMode.forCaching) key => value => WomValueSimpleton(key, WomSingleFile(value)) else toStringSimpleton
       // What should this even do? Maybe just pick out the last bit of the path and store that as a String?
       val directoryValueSimplifier: String => String => WomValueSimpleton =
-        if (simplifyMode.forCaching) key => value => WomValueSimpleton(key, WomString(value.substring(value.lastIndexOf("/") + 1))) else toStringSimpleton
+        if (simplifyMode.forCaching)
+          key => value => WomValueSimpleton(key, WomString(value.substring(value.lastIndexOf("/") + 1)))
+        else toStringSimpleton
 
       womValue match {
         case prim: WomPrimitive => List(WomValueSimpleton(name, prim))
         case opt: WomOptionalValue => opt.value.map(_.simplify(name)).getOrElse(Seq.empty)
-        case WomArray(_, arrayValue) => arrayValue.zipWithIndex flatMap { case (arrayItem, index) => arrayItem.simplify(s"$name[$index]") }
-        case WomMap(_, mapValue) => mapValue flatMap { case (key, value) => value.simplify(s"$name:${key.valueString.escapeMeta}") }
+        case WomArray(_, arrayValue) =>
+          arrayValue.zipWithIndex flatMap { case (arrayItem, index) => arrayItem.simplify(s"$name[$index]") }
+        case WomMap(_, mapValue) =>
+          mapValue flatMap { case (key, value) => value.simplify(s"$name:${key.valueString.escapeMeta}") }
         case WomPair(left, right) => left.simplify(s"$name:left") ++ right.simplify(s"$name:right")
-        case womObjectLike: WomObjectLike => womObjectLike.values flatMap {
-          case (key, value) => value.simplify(s"$name:${key.escapeMeta}")
-        }
+        case womObjectLike: WomObjectLike =>
+          womObjectLike.values flatMap { case (key, value) =>
+            value.simplify(s"$name:${key.escapeMeta}")
+          }
         case WomMaybeListedDirectory(valueOption, listingOption, _, _) =>
           // This simpleton is not strictly part of the WomFile but is used to record the type of this WomValue so it can
           // be re-built appropriately in the WomValueBuilder
@@ -82,10 +89,14 @@ object WomValueSimpleton {
   }
 
   implicit class WomValuesSimplifier(womValues: Map[String, WomValue]) {
-    def simplifyForCaching: Iterable[WomValueSimpleton] = womValues flatMap { case (name, value) => value.simplify(name)(simplifyMode = SimplifyMode(forCaching = true)) }
+    def simplifyForCaching: Iterable[WomValueSimpleton] = womValues flatMap { case (name, value) =>
+      value.simplify(name)(simplifyMode = SimplifyMode(forCaching = true))
+    }
   }
 
   implicit class WomValuesSimplifierPort(womValues: Map[OutputPort, WomValue]) {
-    def simplify: Iterable[WomValueSimpleton] = womValues flatMap { case (port, value) => value.simplify(port.internalName) }
+    def simplify: Iterable[WomValueSimpleton] = womValues flatMap { case (port, value) =>
+      value.simplify(port.internalName)
+    }
   }
 }
diff --git a/core/src/main/scala/cromwell/util/DatabaseUtil.scala b/core/src/main/scala/cromwell/util/DatabaseUtil.scala
index d5033415df1..af1b7c176d2 100644
--- a/core/src/main/scala/cromwell/util/DatabaseUtil.scala
+++ b/core/src/main/scala/cromwell/util/DatabaseUtil.scala
@@ -16,7 +16,7 @@ object DatabaseUtil {
   }
 
   def withRetry[A](f: () => Future[A])(implicit actorSystem: ActorSystem): Future[A] = {
-    val RetryBackoff = SimpleExponentialBackoff(50 millis, 1 seconds, 1D)
+    val RetryBackoff = SimpleExponentialBackoff(50 millis, 1 seconds, 1d)
     Retry.withRetry(f, maxRetries = Option(10), backoff = RetryBackoff, isTransient = isTransient)
   }
 }
diff --git a/core/src/main/scala/cromwell/util/GracefulShutdownHelper.scala b/core/src/main/scala/cromwell/util/GracefulShutdownHelper.scala
index 5ed66fb5e9c..5a1ea5ef2d9 100644
--- a/core/src/main/scala/cromwell/util/GracefulShutdownHelper.scala
+++ b/core/src/main/scala/cromwell/util/GracefulShutdownHelper.scala
@@ -12,10 +12,10 @@ object GracefulShutdownHelper {
 trait GracefulShutdownHelper extends GracefulStopSupport { this: Actor with ActorLogging =>
   private var shuttingDown: Boolean = false
   private var shutdownList: Set[ActorRef] = Set.empty
-  
+
   def isShuttingDown: Boolean = shuttingDown
 
-  def waitForActorsAndShutdown(actorsLists: NonEmptyList[ActorRef]): Unit = {
+  def waitForActorsAndShutdown(actorsLists: NonEmptyList[ActorRef]): Unit =
     if (shuttingDown) {
       log.error("Programmer error, this actor has already initiated its shutdown. Only call this once per actor !")
     } else {
@@ -23,12 +23,11 @@ trait GracefulShutdownHelper extends GracefulStopSupport { this: Actor with Acto
       shutdownList = actorsLists.toList.toSet
       shutdownList foreach context.watch
       shutdownList foreach { _ ! ShutdownCommand }
-      
+
       context become {
         case Terminated(actor) if shuttingDown && shutdownList.contains(actor) =>
           shutdownList = shutdownList - actor
           if (shutdownList.isEmpty) context stop self
       }
     }
-  }
 }
diff --git a/core/src/main/scala/cromwell/util/JsonFormatting/WomValueJsonFormatter.scala b/core/src/main/scala/cromwell/util/JsonFormatting/WomValueJsonFormatter.scala
index 811f9dce61f..1de0da45989 100644
--- a/core/src/main/scala/cromwell/util/JsonFormatting/WomValueJsonFormatter.scala
+++ b/core/src/main/scala/cromwell/util/JsonFormatting/WomValueJsonFormatter.scala
@@ -12,15 +12,15 @@ object WomValueJsonFormatter extends DefaultJsonProtocol {
       case f: WomFloat => JsNumber(f.value)
       case b: WomBoolean => JsBoolean(b.value)
       case f: WomSingleFile => JsString(f.value)
-      case o: WomObjectLike => new JsObject(o.values map {case(k, v) => k -> write(v)})
+      case o: WomObjectLike => new JsObject(o.values map { case (k, v) => k -> write(v) })
       case a: WomArray => new JsArray(a.value.map(write).toVector)
-      case m: WomMap => new JsObject(m.value map {case(k,v) => k.valueString -> write(v)})
+      case m: WomMap => new JsObject(m.value map { case (k, v) => k.valueString -> write(v) })
       case q: WomPair => new JsObject(Map("left" -> write(q.left), "right" -> write(q.right)))
       case WomOptionalValue(_, Some(innerValue)) => write(innerValue)
       case WomOptionalValue(_, None) => JsNull
       case WomCoproductValue(_, innerValue) => write(innerValue)
       case WomEnumerationValue(_, innerValue) => JsString(innerValue)
-        // handles WdlExpression
+      // handles WdlExpression
       case v: WomValue => JsString(v.toWomString)
 
     }
@@ -31,7 +31,7 @@ object WomValueJsonFormatter extends DefaultJsonProtocol {
     // In addition, we make a lot of assumptions about what type of WomValue to create. Oh well... it should all fall out in the coercion (fingercrossed)!
     def read(value: JsValue): WomValue = value match {
       case JsObject(fields) =>
-        val wdlFields: Map[WomValue, WomValue] = fields map {case (k, v) => WomString(k) -> read(v)}
+        val wdlFields: Map[WomValue, WomValue] = fields map { case (k, v) => WomString(k) -> read(v) }
         if (fields.isEmpty) WomMap(WomMapType(WomStringType, WomStringType), Map.empty[WomValue, WomValue])
         else WomMap(WomMapType(wdlFields.head._1.womType, wdlFields.head._2.womType), wdlFields)
       case JsArray(vector) if vector.nonEmpty => WomArray(WomArrayType(read(vector.head).womType), vector map read)
@@ -53,4 +53,3 @@ object WomSingleFileJsonFormatter extends DefaultJsonProtocol {
     }
   }
 }
-
diff --git a/core/src/main/scala/cromwell/util/PromiseActor.scala b/core/src/main/scala/cromwell/util/PromiseActor.scala
index bd5efa5b0c4..efe3f0cb217 100644
--- a/core/src/main/scala/cromwell/util/PromiseActor.scala
+++ b/core/src/main/scala/cromwell/util/PromiseActor.scala
@@ -17,7 +17,10 @@ private class PromiseActor(promise: Promise[Any], sendTo: ActorRef, msg: Any) ex
       if (actorRef == sendTo) {
         promise.tryFailure(new RuntimeException("Promise-watched actor completed before sending back a message"))
       } else {
-        log.error("Spooky happenstances! A Terminated({}) message  was sent to a private Promise actor which wasn't watching it!?", actorRef)
+        log.error(
+          "Spooky happenstances! A Terminated({}) message  was sent to a private Promise actor which wasn't watching it!?",
+          actorRef
+        )
       }
       context.stop(self)
     case success =>
@@ -27,6 +30,7 @@ private class PromiseActor(promise: Promise[Any], sendTo: ActorRef, msg: Any) ex
 }
 
 object PromiseActor {
+
   /**
     * Sends a message to an actor and returns the future associated with the fullfilment of the reply
     * Can be used instead of the akka `ask` semantics, without any timeout
@@ -42,11 +46,11 @@ object PromiseActor {
     promise.future
   }
 
-  def props(promise: Promise[Any], sendTo: ActorRef, msg: Any): Props = Props(new PromiseActor(promise, sendTo, msg)).withDispatcher(EngineDispatcher)
+  def props(promise: Promise[Any], sendTo: ActorRef, msg: Any): Props =
+    Props(new PromiseActor(promise, sendTo, msg)).withDispatcher(EngineDispatcher)
 
   implicit class EnhancedActorRef(val actorRef: ActorRef) extends AnyVal {
-    def askNoTimeout(message: Any)(implicit actorRefFactory: ActorRefFactory): Future[Any] = {
+    def askNoTimeout(message: Any)(implicit actorRefFactory: ActorRefFactory): Future[Any] =
       PromiseActor.askNoTimeout(message, actorRef)
-    }
   }
 }
diff --git a/core/src/main/scala/cromwell/util/StopAndLogSupervisor.scala b/core/src/main/scala/cromwell/util/StopAndLogSupervisor.scala
index 238cdd70573..50a43cf2987 100644
--- a/core/src/main/scala/cromwell/util/StopAndLogSupervisor.scala
+++ b/core/src/main/scala/cromwell/util/StopAndLogSupervisor.scala
@@ -8,13 +8,12 @@ trait StopAndLogSupervisor { this: Actor =>
   protected def onFailure(actorRef: ActorRef, throwable: => Throwable): Unit
 
   final val stopAndLogStrategy: SupervisorStrategy = {
-    def stoppingDecider: Decider = {
-      case e: Exception =>
-        onFailure(sender(), e)
-        Stop
+    def stoppingDecider: Decider = { case e: Exception =>
+      onFailure(sender(), e)
+      Stop
     }
     OneForOneStrategy(loggingEnabled = false)(stoppingDecider)
   }
 
-  override final val supervisorStrategy = stopAndLogStrategy
+  final override val supervisorStrategy = stopAndLogStrategy
 }
diff --git a/core/src/main/scala/cromwell/util/TryWithResource.scala b/core/src/main/scala/cromwell/util/TryWithResource.scala
index fdbfbda1882..6909232150d 100644
--- a/core/src/main/scala/cromwell/util/TryWithResource.scala
+++ b/core/src/main/scala/cromwell/util/TryWithResource.scala
@@ -20,17 +20,17 @@ object TryWithResource {
       case x: Throwable =>
         t = Option(x)
         throw x
-    } finally {
+    } finally
       resource foreach { r =>
-        try {
+        try
           r.close()
-        } catch {
-          case y: Throwable => t match {
-            case Some(_t) => _t.addSuppressed(y)
-            case None => throw y
-          }
+        catch {
+          case y: Throwable =>
+            t match {
+              case Some(_t) => _t.addSuppressed(y)
+              case None => throw y
+            }
         }
       }
-    }
   }
 }
diff --git a/core/src/test/scala/cromwell/core/DockerCredentialsSpec.scala b/core/src/test/scala/cromwell/core/DockerCredentialsSpec.scala
index 25418a88fa3..4a3dc8c4929 100644
--- a/core/src/test/scala/cromwell/core/DockerCredentialsSpec.scala
+++ b/core/src/test/scala/cromwell/core/DockerCredentialsSpec.scala
@@ -18,11 +18,11 @@ class DockerCredentialsSpec extends AnyFlatSpec with Matchers {
       val credentials: Any = new DockerCredentials(Base64.getEncoder.encodeToString(tokenString.getBytes()), None, None)
 
       credentials match {
-        case DockerCredentialUsernameAndPassword(u, p) => {
+        case DockerCredentialUsernameAndPassword(u, p) =>
           u should be(expectedUsername)
           p should be(expectedPassword)
-        }
-        case _ => fail(s"Expected to decompose ${tokenString} into username=$expectedPassword and password=$expectedPassword")
+        case _ =>
+          fail(s"Expected to decompose ${tokenString} into username=$expectedPassword and password=$expectedPassword")
       }
     }
   }
diff --git a/core/src/test/scala/cromwell/core/LoadConfigSpec.scala b/core/src/test/scala/cromwell/core/LoadConfigSpec.scala
index 0ac4947aa1c..b2008ef3aa0 100644
--- a/core/src/test/scala/cromwell/core/LoadConfigSpec.scala
+++ b/core/src/test/scala/cromwell/core/LoadConfigSpec.scala
@@ -8,7 +8,7 @@ import scala.concurrent.duration._
 
 class LoadConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "LoadConfig"
-  
+
   it should "parse load config" in {
     LoadConfig.JobStoreReadThreshold shouldBe 10000
     LoadConfig.JobStoreWriteThreshold shouldBe 10000
diff --git a/core/src/test/scala/cromwell/core/MockIoActor.scala b/core/src/test/scala/cromwell/core/MockIoActor.scala
index 3c1831ae8d3..dd2e8d114ac 100644
--- a/core/src/test/scala/cromwell/core/MockIoActor.scala
+++ b/core/src/test/scala/cromwell/core/MockIoActor.scala
@@ -18,13 +18,14 @@ class MockIoActor(returnCode: String, stderrSize: Long) extends Actor {
     case command: IoSizeCommand => sender() ! IoSuccess(command, 0L)
     case command: IoContentAsStringCommand => sender() ! IoSuccess(command, "0")
     case command: IoExistsCommand => sender() ! IoSuccess(command, false)
-      
-      // With context
+
+    // With context
     case (requestContext: Any, command: IoCopyCommand) => sender() ! (requestContext -> IoSuccess(command, ()))
     case (requestContext: Any, command: IoWriteCommand) => sender() ! (requestContext -> IoSuccess(command, ()))
     case (requestContext: Any, command: IoDeleteCommand) => sender() ! (requestContext -> IoSuccess(command, ()))
     case (requestContext: Any, command: IoSizeCommand) => sender() ! (requestContext -> IoSuccess(command, stderrSize))
-    case (requestContext: Any, command: IoContentAsStringCommand) => sender() ! (requestContext -> IoSuccess(command, returnCode))
+    case (requestContext: Any, command: IoContentAsStringCommand) =>
+      sender() ! (requestContext -> IoSuccess(command, returnCode))
     case (requestContext: Any, command: IoExistsCommand) => sender() ! (requestContext -> IoSuccess(command, false))
 
     case withPromise: IoCommandWithPromise[_] => self ! ((withPromise.promise, withPromise.ioCommand))
diff --git a/core/src/test/scala/cromwell/core/SimpleIoActor.scala b/core/src/test/scala/cromwell/core/SimpleIoActor.scala
index 589065758c5..4ca3d3c1bdf 100644
--- a/core/src/test/scala/cromwell/core/SimpleIoActor.scala
+++ b/core/src/test/scala/cromwell/core/SimpleIoActor.scala
@@ -14,49 +14,44 @@ object SimpleIoActor {
 }
 
 class SimpleIoActor extends Actor {
-  
+
   override def receive: Receive = {
     case command: IoCopyCommand =>
-      
       Try(command.source.copyTo(command.destination)) match {
         case Success(_) => sender() ! IoSuccess(command, ())
         case Failure(failure) => sender() ! IoFailure(command, failure)
       }
-      
+
     case command: IoWriteCommand =>
-      
       Try(command.file.write(command.content)(command.openOptions, StandardCharsets.UTF_8)) match {
         case Success(_) => sender() ! IoSuccess(command, ())
         case Failure(failure) => sender() ! IoFailure(command, failure)
       }
-      
+
     case command: IoDeleteCommand =>
-      
       Try(command.file.delete(command.swallowIOExceptions)) match {
         case Success(_) => sender() ! IoSuccess(command, ())
         case Failure(failure) => sender() ! IoFailure(command, failure)
       }
-      
+
     case command: IoSizeCommand =>
-      
       Try(command.file.size) match {
         case Success(size) => sender() ! IoSuccess(command, size)
         case Failure(failure) => sender() ! IoFailure(command, failure)
       }
-      
+
     case command: IoContentAsStringCommand =>
-      
       Try(command.file.contentAsString) match {
         case Success(content) => sender() ! IoSuccess(command, content)
         case Failure(failure) => sender() ! IoFailure(command, failure)
       }
-      
+
     case command: IoHashCommand =>
       Try(command.file.md5) match {
         case Success(hash) => sender() ! IoSuccess(command, hash)
         case Failure(failure) => sender() ! IoFailure(command, failure)
       }
-      
+
     case command: IoExistsCommand =>
       Try(command.file.exists) match {
         case Success(exists) => sender() ! IoSuccess(command, exists)
@@ -65,49 +60,42 @@ class SimpleIoActor extends Actor {
 
     // With context
     case (requestContext: Any, command: IoCopyCommand) =>
-      
       Try(command.source.copyTo(command.destination, overwrite = true)) match {
         case Success(_) => sender() ! (requestContext -> IoSuccess(command, ()))
         case Failure(failure) => sender() ! (requestContext -> IoFailure(command, failure))
       }
-      
-    case (requestContext: Any, command: IoWriteCommand) =>
 
+    case (requestContext: Any, command: IoWriteCommand) =>
       Try(command.file.write(command.content)) match {
         case Success(_) => sender() ! (requestContext -> IoSuccess(command, ()))
         case Failure(failure) => sender() ! (requestContext -> IoFailure(command, failure))
       }
-      
-    case (requestContext: Any, command: IoDeleteCommand) =>
 
+    case (requestContext: Any, command: IoDeleteCommand) =>
       Try(command.file.delete(command.swallowIOExceptions)) match {
         case Success(_) => sender() ! (requestContext -> IoSuccess(command, ()))
         case Failure(failure) => sender() ! (requestContext -> IoFailure(command, failure))
       }
-      
+
     case (requestContext: Any, command: IoSizeCommand) =>
-      
       Try(command.file.size) match {
         case Success(size) => sender() ! (requestContext -> IoSuccess(command, size))
         case Failure(failure) => sender() ! (requestContext -> IoFailure(command, failure))
       }
-      
-    case (requestContext: Any, command: IoContentAsStringCommand) =>
 
+    case (requestContext: Any, command: IoContentAsStringCommand) =>
       Try(command.file.contentAsString) match {
         case Success(content) => sender() ! (requestContext -> IoSuccess(command, content))
         case Failure(failure) => sender() ! (requestContext -> IoFailure(command, failure))
       }
-      
+
     case (requestContext: Any, command: IoHashCommand) =>
-      
       Try(command.file.md5) match {
         case Success(hash) => sender() ! (requestContext -> IoSuccess(command, hash))
         case Failure(failure) => sender() ! (requestContext -> IoFailure(command, failure))
       }
 
     case (requestContext: Any, command: IoExistsCommand) =>
-
       Try(command.file.exists) match {
         case Success(exists) => sender() ! (requestContext -> IoSuccess(command, exists))
         case Failure(failure) => sender() ! (requestContext -> IoFailure(command, failure))
diff --git a/core/src/test/scala/cromwell/core/TestKitSuite.scala b/core/src/test/scala/cromwell/core/TestKitSuite.scala
index d9fe5c3d56c..8febaa3edd8 100644
--- a/core/src/test/scala/cromwell/core/TestKitSuite.scala
+++ b/core/src/test/scala/cromwell/core/TestKitSuite.scala
@@ -18,9 +18,8 @@ abstract class TestKitSuite extends TestKitBase with Suite with BeforeAndAfterAl
 
   implicit lazy val system: ActorSystem = ActorSystem(actorSystemName, actorSystemConfig)
 
-  override protected def afterAll(): Unit = {
+  override protected def afterAll(): Unit =
     shutdown()
-  }
 
   // 'BlackHoleActor' swallows messages without logging them (thus reduces log file overhead):
   val emptyActor: ActorRef = system.actorOf(TestActors.blackholeProps, "TestKitSuiteEmptyActor")
diff --git a/core/src/test/scala/cromwell/core/WorkflowOptionsSpec.scala b/core/src/test/scala/cromwell/core/WorkflowOptionsSpec.scala
index 22aa4577c63..dd4de0a4773 100644
--- a/core/src/test/scala/cromwell/core/WorkflowOptionsSpec.scala
+++ b/core/src/test/scala/cromwell/core/WorkflowOptionsSpec.scala
@@ -21,11 +21,11 @@ class WorkflowOptionsSpec extends Matchers with AnyWordSpecLike {
       WorkflowOptions.fromJsonObject(workflowOptionsJson) match {
         case Success(options) =>
           options.get("key") shouldEqual Success("value")
-          options.get("bad_key") shouldBe a [Failure[_]]
+          options.get("bad_key") shouldBe a[Failure[_]]
 
           options.clearEncryptedValues.asPrettyJson shouldEqual """{
-                                                         |  "key": "value"
-                                                         |}""".stripMargin
+                                                                  |  "key": "value"
+                                                                  |}""".stripMargin
         case _ => fail("Expecting workflow options to be parseable")
       }
     }
diff --git a/core/src/test/scala/cromwell/core/actor/BatchActorSpec.scala b/core/src/test/scala/cromwell/core/actor/BatchActorSpec.scala
index e426a349448..1fe0ca6658b 100644
--- a/core/src/test/scala/cromwell/core/actor/BatchActorSpec.scala
+++ b/core/src/test/scala/cromwell/core/actor/BatchActorSpec.scala
@@ -189,24 +189,23 @@ class BatchActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wit
     }
   }
 
-  class BatchActorTest(processingTime: FiniteDuration = Duration.Zero, fail: Boolean = false) extends BatchActor[String](10.hours, 10) {
+  class BatchActorTest(processingTime: FiniteDuration = Duration.Zero, fail: Boolean = false)
+      extends BatchActor[String](10.hours, 10) {
     var processed: Vector[String] = Vector.empty
-    override def commandToData(snd: ActorRef) = {
-      case command: String => command
+    override def commandToData(snd: ActorRef) = { case command: String =>
+      command
     }
     override protected def weightFunction(command: String) = command.length
-    override protected def process(data: NonEmptyVector[String]) = {
+    override protected def process(data: NonEmptyVector[String]) =
       if (processingTime != Duration.Zero) {
         processed = processed ++ data.toVector
-       val promise = Promise[Int]()
-        system.scheduler.scheduleOnce(processingTime) { promise.success(data.map(weightFunction).toVector.sum) }
+        val promise = Promise[Int]()
+        system.scheduler.scheduleOnce(processingTime)(promise.success(data.map(weightFunction).toVector.sum))
         promise.future
       } else if (!fail) {
         processed = processed ++ data.toVector
         Future.successful(data.map(weightFunction).toVector.sum)
-      }
-      else Future.failed(new Exception("Oh nose ! (This is a test failure and is expected !)") with NoStackTrace)
-    }
+      } else Future.failed(new Exception("Oh nose ! (This is a test failure and is expected !)") with NoStackTrace)
   }
 
 }
diff --git a/core/src/test/scala/cromwell/core/actor/RobustClientHelperSpec.scala b/core/src/test/scala/cromwell/core/actor/RobustClientHelperSpec.scala
index 939a1aa1834..dc29807d061 100644
--- a/core/src/test/scala/cromwell/core/actor/RobustClientHelperSpec.scala
+++ b/core/src/test/scala/cromwell/core/actor/RobustClientHelperSpec.scala
@@ -14,39 +14,39 @@ import scala.language.postfixOps
 
 class RobustClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with ImplicitSender {
   behavior of "RobustClientHelper"
-  
+
   it should "handle Backpressure responses" in {
     val remoteActor = TestProbe()
     val delegateActor = TestProbe()
-    
+
     val margin = 2.second
-    val backoff = SimpleExponentialBackoff(1.second, 10.seconds, 2D, 0D)
+    val backoff = SimpleExponentialBackoff(1.second, 10.seconds, 2d, 0d)
     val noResponseTimeout = 10 seconds
     val testActor = TestActorRef(new TestActor(delegateActor.ref, backoff, noResponseTimeout))
-    
+
     val messageToSend = TestActor.TestMessage("hello")
-    
-    //send message
+
+    // send message
     testActor.underlyingActor.sendMessage(messageToSend, remoteActor.ref)
-    
+
     // remote actor receives message
     remoteActor.expectMsg(messageToSend)
-    
+
     // remote actor sends a backpressure message
     remoteActor.reply(BackPressure(messageToSend))
-    
+
     // remote actor expects request again after backpressureTimeout
     remoteActor.expectMsg(1.second + margin, messageToSend)
-    
+
     // remote actor replies
     remoteActor.reply("world")
-    
+
     // delegate actor receives response
     delegateActor.expectMsg("world")
-    
+
     // remote actor doesn't receives new messages
     remoteActor.expectNoMessage()
-    
+
     // Wait long enough that to make sure that we won't receive a ServiceUnreachable message, meaning the timeout timer
     // has been cancelled. Note that it is the responsibility of the actor to cancel it, the RobustClientHelper does not
     // handle that part.
@@ -57,7 +57,7 @@ class RobustClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     val remoteActor = TestProbe()
     val delegateActor = TestProbe()
 
-    val backoff = SimpleExponentialBackoff(1.second, 10.seconds, 2D, 0D)
+    val backoff = SimpleExponentialBackoff(1.second, 10.seconds, 2d, 0d)
     val noResponseTimeout = 20 seconds
     val testActor = TestActorRef(new TestActor(delegateActor.ref, backoff, noResponseTimeout))
 
@@ -68,13 +68,13 @@ class RobustClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matc
 
     // remote actor receives message
     remoteActor.expectMsg(messageToSend)
-    
+
     // remote actor replies
     remoteActor.reply("world")
-    
+
     // delegate receives response
     delegateActor.expectMsg("world")
-    
+
     // remote actor doesn't receives new messages
     remoteActor.expectNoMessage()
     delegateActor.expectNoMessage()
@@ -84,7 +84,7 @@ class RobustClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     val remoteActor = TestProbe()
     val delegateActor = TestProbe()
 
-    val backoff = SimpleExponentialBackoff(1.second, 10.seconds, 2D, 0D)
+    val backoff = SimpleExponentialBackoff(1.second, 10.seconds, 2d, 0d)
     val noResponseTimeout = 2 seconds
     val testActor = TestActorRef(new TestActor(delegateActor.ref, backoff, noResponseTimeout))
 
@@ -109,9 +109,9 @@ class RobustClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matc
   it should "reset timeout when backpressured is received" in {
     val remoteActor = TestProbe()
     val delegateActor = TestProbe()
-    
+
     val margin = 1 second
-    val backoff = SimpleExponentialBackoff(1.second, 10.seconds, 2D, 0D)
+    val backoff = SimpleExponentialBackoff(1.second, 10.seconds, 2d, 0d)
     val noResponseTimeout = 3 seconds
     val testActor = TestActorRef(new TestActor(delegateActor.ref, backoff, noResponseTimeout))
 
@@ -141,32 +141,31 @@ class RobustClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     delegateActor.expectNoMessage(4 seconds)
   }
 
-  private [actor] object TestActor {
+  private[actor] object TestActor {
     case class TestMessage(v: String)
     case object ServiceUnreachable
   }
-  private class TestActor(delegateTo: ActorRef,
-                          backoff: Backoff,
-                          noResponseTimeout: FiniteDuration) extends Actor with ActorLogging with RobustClientHelper {
+  private class TestActor(delegateTo: ActorRef, backoff: Backoff, noResponseTimeout: FiniteDuration)
+      extends Actor
+      with ActorLogging
+      with RobustClientHelper {
 
     override def initialBackoff(): Backoff = backoff
 
     context.become(robustReceive orElse receive)
     var messageSent: Any = _
-    
-    override def receive: Receive = {
-      case message =>
-        cancelTimeout(messageSent)
-        delegateTo ! message
+
+    override def receive: Receive = { case message =>
+      cancelTimeout(messageSent)
+      delegateTo ! message
     }
-    
+
     def sendMessage(message: Any, to: ActorRef) = {
       messageSent = message
       robustSend(message, to, noResponseTimeout)
     }
 
-    override protected def onTimeout(message: Any, to: ActorRef): Unit = {
+    override protected def onTimeout(message: Any, to: ActorRef): Unit =
       delegateTo ! TestActor.ServiceUnreachable
-    }
   }
 }
diff --git a/core/src/test/scala/cromwell/core/actor/StreamActorHelperSpec.scala b/core/src/test/scala/cromwell/core/actor/StreamActorHelperSpec.scala
index a7d42d7ffdd..b45a5e6fba7 100644
--- a/core/src/test/scala/cromwell/core/actor/StreamActorHelperSpec.scala
+++ b/core/src/test/scala/cromwell/core/actor/StreamActorHelperSpec.scala
@@ -13,10 +13,9 @@ import org.scalatest.matchers.should.Matchers
 
 import scala.concurrent.ExecutionContext
 
-
 class StreamActorHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with ImplicitSender {
   behavior of "StreamActorHelper"
-  
+
   implicit val materializer = ActorMaterializer()
 
   it should "catch EnqueueResponse message" in {
@@ -26,7 +25,7 @@ class StreamActorHelperSpec extends TestKitSuite with AnyFlatSpecLike with Match
     expectMsg("hello")
     system stop actor
   }
-  
+
   it should "send a backpressure message when messages are dropped by the queue" in {
     val actor = TestActorRef(new TestStreamActor(1))
     val command = new TestStreamActorCommand
@@ -50,14 +49,19 @@ class StreamActorHelperSpec extends TestKitSuite with AnyFlatSpecLike with Match
   }
 }
 
-
 private object TestStreamActor {
   class TestStreamActorCommand
-  case class TestStreamActorContext(request: TestStreamActorCommand, replyTo: ActorRef, override val clientContext: Option[Any]) extends StreamContext
+  case class TestStreamActorContext(request: TestStreamActorCommand,
+                                    replyTo: ActorRef,
+                                    override val clientContext: Option[Any]
+  ) extends StreamContext
 }
 
-private class TestStreamActor(queueSize: Int)(implicit override val materializer: ActorMaterializer) extends Actor with ActorLogging with StreamActorHelper[TestStreamActorContext] {
-  
+private class TestStreamActor(queueSize: Int)(implicit override val materializer: ActorMaterializer)
+    extends Actor
+    with ActorLogging
+    with StreamActorHelper[TestStreamActorContext] {
+
   override protected def actorReceive: Receive = {
     case command: TestStreamActorCommand =>
       val replyTo = sender()
@@ -69,8 +73,9 @@ private class TestStreamActor(queueSize: Int)(implicit override val materializer
       sendToStream(commandContext)
   }
 
-  override protected val streamSource = Source.queue[TestStreamActorContext](queueSize, OverflowStrategy.dropNew)
-    .map{ ("hello", _) }
+  override protected val streamSource = Source
+    .queue[TestStreamActorContext](queueSize, OverflowStrategy.dropNew)
+    .map(("hello", _))
 
-  override implicit def ec: ExecutionContext = context.dispatcher
+  implicit override def ec: ExecutionContext = context.dispatcher
 }
diff --git a/core/src/test/scala/cromwell/core/callcaching/HashKeySpec.scala b/core/src/test/scala/cromwell/core/callcaching/HashKeySpec.scala
index 82bc6bacb25..dbd8bd4b82c 100644
--- a/core/src/test/scala/cromwell/core/callcaching/HashKeySpec.scala
+++ b/core/src/test/scala/cromwell/core/callcaching/HashKeySpec.scala
@@ -4,7 +4,6 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class HashKeySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   "HashKey" should "produce consistent key value" in {
@@ -20,7 +19,7 @@ class HashKeySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       HashKey("output", "String myOutput"),
       HashKey("runtime attribute", "docker")
     )
-    
+
     keys map { _.key } should contain theSameElementsAs Set(
       "command template",
       "backend name",
@@ -34,5 +33,5 @@ class HashKeySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       "runtime attribute: docker"
     )
   }
-  
+
 }
diff --git a/core/src/test/scala/cromwell/core/filesystem/CromwellFileSystemsSpec.scala b/core/src/test/scala/cromwell/core/filesystem/CromwellFileSystemsSpec.scala
index 8e958cce518..caacfd54ed8 100644
--- a/core/src/test/scala/cromwell/core/filesystem/CromwellFileSystemsSpec.scala
+++ b/core/src/test/scala/cromwell/core/filesystem/CromwellFileSystemsSpec.scala
@@ -15,13 +15,12 @@ import scala.concurrent.ExecutionContext
 class CromwellFileSystemsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "CromwellFileSystems"
 
-  val globalConfig = ConfigFactory.parseString(
-    """
-      |filesystems {
-      |  fs1.class = "cromwell.core.path.MockPathBuilderFactory"
-      |  fs2.class = "cromwell.core.path.MockPathBuilderFactory"
-      |  fs3.class = "cromwell.core.filesystem.MockNotPathBuilderFactory"
-      |}
+  val globalConfig = ConfigFactory.parseString("""
+                                                 |filesystems {
+                                                 |  fs1.class = "cromwell.core.path.MockPathBuilderFactory"
+                                                 |  fs2.class = "cromwell.core.path.MockPathBuilderFactory"
+                                                 |  fs3.class = "cromwell.core.filesystem.MockNotPathBuilderFactory"
+                                                 |}
     """.stripMargin)
 
   val cromwellFileSystems = new CromwellFileSystems(globalConfig)
@@ -29,12 +28,11 @@ class CromwellFileSystemsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   it should "build factory builders and factories for valid configuration" in {
     cromwellFileSystems.factoryBuilders.keySet shouldBe Set("fs1", "fs2", "fs3")
 
-    val factoriesConfig = ConfigFactory.parseString(
-      """
-        |filesystems {
-        | fs1.somekey = "somevalue"
-        | fs2.someotherkey = "someothervalue"
-        |}
+    val factoriesConfig = ConfigFactory.parseString("""
+                                                      |filesystems {
+                                                      | fs1.somekey = "somevalue"
+                                                      | fs2.someotherkey = "someothervalue"
+                                                      |}
       """.stripMargin)
 
     val pathFactories = cromwellFileSystems.factoriesFromConfig(factoriesConfig)
@@ -48,16 +46,16 @@ class CromwellFileSystemsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   }
 
   it should "build singleton instance if specified" in {
-    val rootConf = ConfigFactory.parseString(
-      """
-        |filesystems {
-        |  fs1 {
-        |    class = "cromwell.core.filesystem.MockPathBuilderFactoryCustomSingletonConfig"
-        |    global {
-        |      class = "cromwell.core.filesystem.MockSingletonConfig"
-        |    }
-        |  }
-        |}
+    val rootConf =
+      ConfigFactory.parseString("""
+                                  |filesystems {
+                                  |  fs1 {
+                                  |    class = "cromwell.core.filesystem.MockPathBuilderFactoryCustomSingletonConfig"
+                                  |    global {
+                                  |      class = "cromwell.core.filesystem.MockSingletonConfig"
+                                  |    }
+                                  |  }
+                                  |}
       """.stripMargin)
 
     val cromwellFileSystems = new CromwellFileSystems(rootConf)
@@ -69,21 +67,33 @@ class CromwellFileSystemsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     val factory2 = cromwellFileSystems.buildFactory("fs1", ConfigFactory.empty)
 
     // The singleton configs should be the same for different factories
-    assert(factory1.toOption.get.asInstanceOf[MockPathBuilderFactoryCustomSingletonConfig].singletonConfig ==
-      factory2.toOption.get.asInstanceOf[MockPathBuilderFactoryCustomSingletonConfig].singletonConfig)
+    assert(
+      factory1.toOption.get.asInstanceOf[MockPathBuilderFactoryCustomSingletonConfig].singletonConfig ==
+        factory2.toOption.get.asInstanceOf[MockPathBuilderFactoryCustomSingletonConfig].singletonConfig
+    )
   }
 
   List(
-    ("if the filesystem does not exist", "filesystems.fs4.key = value", NonEmptyList.one("Cannot find a filesystem with name fs4 in the configuration. Available filesystems: fs1, fs2, fs3")),
-    ("if the config is invalid", "filesystems.fs1 = true", NonEmptyList.one("Invalid filesystem backend configuration for fs1")),
-    ("the class is not a PathBuilderFactory", "filesystems.fs3.key = value", NonEmptyList.one("The filesystem class for fs3 is not an instance of PathBuilderFactory"))
-  ) foreach {
-    case (description, config, expected) =>
-      it should s"fail to build factories $description" in {
-        val result = cromwellFileSystems.factoriesFromConfig(ConfigFactory.parseString(config))
-          result.isLeft shouldBe true
-        result.swap.toOption.get shouldBe expected
-      }
+    ("if the filesystem does not exist",
+     "filesystems.fs4.key = value",
+     NonEmptyList.one(
+       "Cannot find a filesystem with name fs4 in the configuration. Available filesystems: fs1, fs2, fs3"
+     )
+    ),
+    ("if the config is invalid",
+     "filesystems.fs1 = true",
+     NonEmptyList.one("Invalid filesystem backend configuration for fs1")
+    ),
+    ("the class is not a PathBuilderFactory",
+     "filesystems.fs3.key = value",
+     NonEmptyList.one("The filesystem class for fs3 is not an instance of PathBuilderFactory")
+    )
+  ) foreach { case (description, config, expected) =>
+    it should s"fail to build factories $description" in {
+      val result = cromwellFileSystems.factoriesFromConfig(ConfigFactory.parseString(config))
+      result.isLeft shouldBe true
+      result.swap.toOption.get shouldBe expected
+    }
   }
 
   val classNotFoundException = AggregatedMessageException(
@@ -93,7 +103,9 @@ class CromwellFileSystemsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
 
   val wrongSignatureException = AggregatedMessageException(
     "Failed to initialize Cromwell filesystems",
-    List("Class cromwell.core.filesystem.MockPathBuilderFactoryWrongSignature for filesystem fs1 does not have the required constructor signature: (com.typesafe.config.Config, com.typesafe.config.Config)")
+    List(
+      "Class cromwell.core.filesystem.MockPathBuilderFactoryWrongSignature for filesystem fs1 does not have the required constructor signature: (com.typesafe.config.Config, com.typesafe.config.Config)"
+    )
   )
 
   val invalidConfigException = AggregatedMessageException(
@@ -110,13 +122,15 @@ class CromwellFileSystemsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     ("is invalid", "filesystems.gcs = true", invalidConfigException),
     ("is missing class fields", "filesystems.fs1.notclass = hello", missingClassFieldException),
     ("can't find class", "filesystems.fs1.class = do.not.exists", classNotFoundException),
-    ("has invalid class signature", "filesystems.fs1.class = cromwell.core.filesystem.MockPathBuilderFactoryWrongSignature", wrongSignatureException)
-  ) foreach {
-    case (description, config, expected) =>
-      it should s"fail if global filesystems config $description" in {
-        val ex = the[Exception] thrownBy { new CromwellFileSystems(ConfigFactory.parseString(config)) }
-        ex shouldBe expected
-      }
+    ("has invalid class signature",
+     "filesystems.fs1.class = cromwell.core.filesystem.MockPathBuilderFactoryWrongSignature",
+     wrongSignatureException
+    )
+  ) foreach { case (description, config, expected) =>
+    it should s"fail if global filesystems config $description" in {
+      val ex = the[Exception] thrownBy new CromwellFileSystems(ConfigFactory.parseString(config))
+      ex shouldBe expected
+    }
   }
 }
 
@@ -124,6 +138,10 @@ class MockPathBuilderFactoryWrongSignature()
 class MockNotPathBuilderFactory(globalConfig: Config, val instanceConfig: Config)
 
 class MockSingletonConfig(config: Config)
-class MockPathBuilderFactoryCustomSingletonConfig(globalConfig: Config, val instanceConfig: Config, val singletonConfig: MockSingletonConfig) extends cromwell.core.path.PathBuilderFactory {
-  override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext) = throw new UnsupportedOperationException
+class MockPathBuilderFactoryCustomSingletonConfig(globalConfig: Config,
+                                                  val instanceConfig: Config,
+                                                  val singletonConfig: MockSingletonConfig
+) extends cromwell.core.path.PathBuilderFactory {
+  override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext) =
+    throw new UnsupportedOperationException
 }
diff --git a/core/src/test/scala/cromwell/core/io/AsyncIoSpec.scala b/core/src/test/scala/cromwell/core/io/AsyncIoSpec.scala
index 83521ea3432..07ad722ead2 100644
--- a/core/src/test/scala/cromwell/core/io/AsyncIoSpec.scala
+++ b/core/src/test/scala/cromwell/core/io/AsyncIoSpec.scala
@@ -95,7 +95,7 @@ class AsyncIoSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers {
     }
 
     // Honor swallow exception false
-    //noinspection RedundantDefaultArgument
+    // noinspection RedundantDefaultArgument
     recoverToSucceededIf[NoSuchFileException] {
       testActor.underlyingActor.asyncIo.deleteAsync(testPath, swallowIoExceptions = false)
     }
@@ -103,8 +103,8 @@ class AsyncIoSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers {
 
   it should "handle command creation errors asynchronously" in {
     val partialIoCommandBuilder = new PartialIoCommandBuilder {
-      override def existsCommand: PartialFunction[Path, Try[IoExistsCommand]] = {
-        case _ => Failure(new Exception("everything's fine, I am an expected exists fail") with NoStackTrace)
+      override def existsCommand: PartialFunction[Path, Try[IoExistsCommand]] = { case _ =>
+        Failure(new Exception("everything's fine, I am an expected exists fail") with NoStackTrace)
       }
     }
     val testActor =
@@ -120,10 +120,11 @@ class AsyncIoSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers {
 
   private class AsyncIoTestActor(override val ioActor: ActorRef,
                                  override val ioCommandBuilder: IoCommandBuilder = DefaultIoCommandBuilder
-                                ) extends Actor with ActorLogging with AsyncIoActorClient {
+  ) extends Actor
+      with ActorLogging
+      with AsyncIoActorClient {
 
-    override def receive: Receive = {
-      case _ =>
+    override def receive: Receive = { case _ =>
     }
   }
 
diff --git a/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala b/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
index 06132ba152b..ed07aeb3fc5 100644
--- a/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
+++ b/core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala
@@ -21,10 +21,11 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   it should "intercept IoAcks and cancel timers" in {
     val ioActorProbe = TestProbe()
     val delegateProbe = TestProbe()
-    val backoff = SimpleExponentialBackoff(100 seconds, 10.hours, 2D, 0D)
+    val backoff = SimpleExponentialBackoff(100 seconds, 10.hours, 2d, 0d)
     val noResponseTimeout = 3 seconds
 
-    val testActor = TestActorRef(new IoClientHelperTestActor(ioActorProbe.ref, delegateProbe.ref, backoff, noResponseTimeout))
+    val testActor =
+      TestActorRef(new IoClientHelperTestActor(ioActorProbe.ref, delegateProbe.ref, backoff, noResponseTimeout))
 
     val command = DefaultIoSizeCommand(mock[Path])
     val response = IoSuccess(command, 5L)
@@ -51,10 +52,11 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   it should "intercept IoAcks and cancel timers for a command with context" in {
     val ioActorProbe = TestProbe()
     val delegateProbe = TestProbe()
-    val backoff = SimpleExponentialBackoff(100 seconds, 10.hours, 2D, 0D)
+    val backoff = SimpleExponentialBackoff(100 seconds, 10.hours, 2d, 0d)
     val noResponseTimeout = 3 seconds
 
-    val testActor = TestActorRef(new IoClientHelperTestActor(ioActorProbe.ref, delegateProbe.ref, backoff, noResponseTimeout))
+    val testActor =
+      TestActorRef(new IoClientHelperTestActor(ioActorProbe.ref, delegateProbe.ref, backoff, noResponseTimeout))
 
     val commandContext = "context"
     val command = DefaultIoSizeCommand(mock[Path])
@@ -71,7 +73,7 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
 
     // delegate should receive the response
     delegateProbe.expectMsgPF(1 second) {
-      case (contextReceived,  responseReceived) if contextReceived == "context" && responseReceived == response =>
+      case (contextReceived, responseReceived) if contextReceived == "context" && responseReceived == response =>
     }
 
     // And nothing else, meaning the timeout timer has been cancelled
@@ -84,9 +86,12 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   private case object ServiceUnreachable
 
   private class IoClientHelperTestActor(override val ioActor: ActorRef,
-                                delegateTo: ActorRef,
-                                backoff: Backoff,
-                                noResponseTimeout: FiniteDuration) extends Actor with ActorLogging with IoClientHelper {
+                                        delegateTo: ActorRef,
+                                        backoff: Backoff,
+                                        noResponseTimeout: FiniteDuration
+  ) extends Actor
+      with ActorLogging
+      with IoClientHelper {
 
     implicit val ioCommandBuilder: DefaultIoCommandBuilder.type = DefaultIoCommandBuilder
 
@@ -94,21 +99,18 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
 
     context.become(ioReceive orElse receive)
 
-    override def receive: Receive = {
-      case message => delegateTo ! message
+    override def receive: Receive = { case message =>
+      delegateTo ! message
     }
 
-    def sendMessage(command: IoCommand[_]): Unit = {
+    def sendMessage(command: IoCommand[_]): Unit =
       sendIoCommandWithCustomTimeout(command, noResponseTimeout)
-    }
 
-    def sendMessageWithContext(context: Any, command: IoCommand[_]): Unit = {
+    def sendMessageWithContext(context: Any, command: IoCommand[_]): Unit =
       sendIoCommandWithContext(command, context, noResponseTimeout)
-    }
 
-    override protected def onTimeout(message: Any, to: ActorRef): Unit = {
+    override protected def onTimeout(message: Any, to: ActorRef): Unit =
       delegateTo ! ServiceUnreachable
-    }
   }
 
 }
diff --git a/core/src/test/scala/cromwell/core/labels/LabelSpec.scala b/core/src/test/scala/cromwell/core/labels/LabelSpec.scala
index 6bf4e046ed2..bdb443a91ac 100644
--- a/core/src/test/scala/cromwell/core/labels/LabelSpec.scala
+++ b/core/src/test/scala/cromwell/core/labels/LabelSpec.scala
@@ -29,7 +29,7 @@ class LabelSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     "11f2468c-39d6-4be3-85c8-32735c01e66b",
     "",
     "!@#$%^&*()_+={}[]:;'<>?,./`~",
-    "now valid 255 character value-at vero eosd accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpa",
+    "now valid 255 character value-at vero eosd accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpa"
   )
 
   val badLabelKeys = List(
diff --git a/core/src/test/scala/cromwell/core/logging/LoggerWrapperSpec.scala b/core/src/test/scala/cromwell/core/logging/LoggerWrapperSpec.scala
index d40456e0128..d3d99289a35 100644
--- a/core/src/test/scala/cromwell/core/logging/LoggerWrapperSpec.scala
+++ b/core/src/test/scala/cromwell/core/logging/LoggerWrapperSpec.scala
@@ -13,8 +13,12 @@ import org.slf4j.Logger
 import org.slf4j.event.Level
 import common.mock.MockSugar
 
-class LoggerWrapperSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with MockSugar
-  with TableDrivenPropertyChecks {
+class LoggerWrapperSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with MockSugar
+    with TableDrivenPropertyChecks {
 
   behavior of "LoggerWrapper"
 
@@ -25,7 +29,6 @@ class LoggerWrapperSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
       "slf4jMessages",
       "akkaMessages"
     ),
-
     (
       "log error with no args",
       _.error("Hello {} {} {} {}"),
@@ -80,7 +83,6 @@ class LoggerWrapperSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
       List(Slf4jMessage(Level.ERROR, List("tag: Hello {} {} {} {}", "arg1", exception))),
       List(AkkaMessage(Logging.ErrorLevel, s"tag: Hello arg1 {} {} {}", Option(exception)))
     ),
-
     (
       "log warn with no args",
       _.warn("Hello {} {} {} {}"),
@@ -123,7 +125,6 @@ class LoggerWrapperSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
       List(Slf4jMessage(Level.WARN, List("tag: Hello {} {} {} {}", exception))),
       List(AkkaMessage(Logging.WarningLevel, s"tag: Hello {} {} {} {}\n$exceptionMessage"))
     ),
-
     (
       "log info with no args",
       _.info("Hello {} {} {} {}"),
@@ -138,7 +139,7 @@ class LoggerWrapperSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     ),
     (
       "log info with one arg",
-      _.info("Hello {} {} {} {}", arg ="arg1"),
+      _.info("Hello {} {} {} {}", arg = "arg1"),
       List(Slf4jMessage(Level.INFO, List("tag: Hello {} {} {} {}", "arg1"))),
       List(AkkaMessage(Logging.InfoLevel, "tag: Hello arg1 {} {} {}"))
     ),
@@ -166,7 +167,6 @@ class LoggerWrapperSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
       List(Slf4jMessage(Level.INFO, List("tag: Hello {} {} {} {}", exception))),
       List(AkkaMessage(Logging.InfoLevel, s"tag: Hello {} {} {} {}\n$exceptionMessage"))
     ),
-
     (
       "log debug with no args",
       _.debug("Hello {} {} {} {}"),
@@ -181,7 +181,7 @@ class LoggerWrapperSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     ),
     (
       "log debug with one arg",
-      _.debug("Hello {} {} {} {}", argument ="arg1"),
+      _.debug("Hello {} {} {} {}", argument = "arg1"),
       List(Slf4jMessage(Level.DEBUG, List("tag: Hello {} {} {} {}", "arg1"))),
       List(AkkaMessage(Logging.DebugLevel, "tag: Hello arg1 {} {} {}"))
     ),
@@ -209,7 +209,6 @@ class LoggerWrapperSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
       List(Slf4jMessage(Level.DEBUG, List("tag: Hello {} {} {} {}", exception))),
       List(AkkaMessage(Logging.DebugLevel, s"tag: Hello {} {} {} {}\n$exceptionMessage"))
     ),
-
     (
       "log trace with no args",
       _.trace("Hello {} {} {} {}"),
@@ -260,40 +259,36 @@ class LoggerWrapperSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
 
       var actualAkkaMessages = List.empty[AkkaMessage]
 
-      def toList(arguments: Any): List[Any] = {
+      def toList(arguments: Any): List[Any] =
         arguments match {
           case array: Array[_] => toLastFlattened(array)
           case seq: Seq[_] => seq.toList
           case any => List(any)
         }
-      }
 
       /*
-        * Flatten the last element of the array if the last element is itself an array.
-        *
-        * org.mockito.ArgumentMatchers#anyVararg() is deprecated, but works, sending in an empty array in the tail
-        * position. If we tried to use org.mockito.ArgumentMatchers#any(), it ends up mocking the wrong overloaded
-        * method. At each logging level there are two methods with very similar signatures:
-        *
-        * cromwell.core.logging.LoggerWrapper.error(pattern: String, arguments: AnyRef*)
-        * cromwell.core.logging.LoggerWrapper.error(pattern: String, arg: Any)
-        *
-        * As is, the Any vs. AnyRef overloads are barely dodging the issue https://issues.scala-lang.org/browse/SI-2991.
-        */
-      def toLastFlattened(array: Array[_]): List[Any] = {
+       * Flatten the last element of the array if the last element is itself an array.
+       *
+       * org.mockito.ArgumentMatchers#anyVararg() is deprecated, but works, sending in an empty array in the tail
+       * position. If we tried to use org.mockito.ArgumentMatchers#any(), it ends up mocking the wrong overloaded
+       * method. At each logging level there are two methods with very similar signatures:
+       *
+       * cromwell.core.logging.LoggerWrapper.error(pattern: String, arguments: AnyRef*)
+       * cromwell.core.logging.LoggerWrapper.error(pattern: String, arg: Any)
+       *
+       * As is, the Any vs. AnyRef overloads are barely dodging the issue https://issues.scala-lang.org/browse/SI-2991.
+       */
+      def toLastFlattened(array: Array[_]): List[Any] =
         array.toList.reverse match {
           case (array: Array[_]) :: tail => tail.reverse ++ array.toList
           case other => other.reverse
         }
-      }
 
-      def updateSlf4jMessages(level: Level, arguments: Any): Unit = {
+      def updateSlf4jMessages(level: Level, arguments: Any): Unit =
         actualSlf4jMessages :+= Slf4jMessage(level, toList(arguments))
-      }
 
-      def updateAkkaMessages(logLevel: LogLevel, message: String, causeOption: Option[Throwable] = None): Unit = {
+      def updateAkkaMessages(logLevel: LogLevel, message: String, causeOption: Option[Throwable] = None): Unit =
         actualAkkaMessages :+= AkkaMessage(logLevel, message, causeOption)
-      }
 
       val mockLogger = mock[Logger]
 
@@ -333,25 +328,20 @@ class LoggerWrapperSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
         override val isInfoEnabled: Boolean = true
         override val isDebugEnabled: Boolean = true
 
-        override protected def notifyError(message: String): Unit = {
+        override protected def notifyError(message: String): Unit =
           updateAkkaMessages(Logging.ErrorLevel, message)
-        }
 
-        override protected def notifyError(cause: Throwable, message: String): Unit = {
+        override protected def notifyError(cause: Throwable, message: String): Unit =
           updateAkkaMessages(Logging.ErrorLevel, message, Option(cause))
-        }
 
-        override protected def notifyWarning(message: String): Unit = {
+        override protected def notifyWarning(message: String): Unit =
           updateAkkaMessages(Logging.WarningLevel, message)
-        }
 
-        override protected def notifyInfo(message: String): Unit = {
+        override protected def notifyInfo(message: String): Unit =
           updateAkkaMessages(Logging.InfoLevel, message)
-        }
 
-        override protected def notifyDebug(message: String): Unit = {
+        override protected def notifyDebug(message: String): Unit =
           updateAkkaMessages(Logging.DebugLevel, message)
-        }
       }
 
       val wrapper = new LoggerWrapper {
diff --git a/core/src/test/scala/cromwell/core/path/DefaultPathBuilderSpec.scala b/core/src/test/scala/cromwell/core/path/DefaultPathBuilderSpec.scala
index 63a5a8604cf..5235f711063 100644
--- a/core/src/test/scala/cromwell/core/path/DefaultPathBuilderSpec.scala
+++ b/core/src/test/scala/cromwell/core/path/DefaultPathBuilderSpec.scala
@@ -6,7 +6,12 @@ import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.Tables.Table
 
-class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers with PathBuilderSpecUtils with TestFileUtil {
+class DefaultPathBuilderSpec
+    extends Suite
+    with AnyFlatSpecLike
+    with Matchers
+    with PathBuilderSpecUtils
+    with TestFileUtil {
 
   private val pwd = BetterFileMethods.Cmds.pwd
   private val parentOption = Option(pwd.parent)
@@ -57,7 +62,6 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
   )
 
   private def goodPaths = Seq(
-
     // Normal paths, not normalized
 
     GoodPath(
@@ -72,8 +76,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "world",
       getFileName = "world",
       getNameCount = 2,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a relative path",
       path = "hello/world",
@@ -86,8 +90,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "world",
       getFileName = "world",
       getNameCount = 2,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a path with spaces",
       path = "/hello/world/with spaces",
@@ -100,8 +104,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "with spaces",
       getFileName = "with spaces",
       getNameCount = 3,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path with encode spaces",
       path = "/hello/world/encoded%20spaces",
@@ -114,8 +118,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "encoded%20spaces",
       getFileName = "encoded%20spaces",
       getNameCount = 3,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path with non-ascii characters",
       path = "/hello/world/with non ascii £€",
@@ -128,7 +132,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "with non ascii £€",
       getFileName = "with non ascii £€",
       getNameCount = 3,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // Special paths
 
@@ -144,8 +149,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = pwdName,
       getFileName = "",
       getNameCount = 1,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a path from /",
       path = "/",
@@ -158,8 +163,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "",
       getFileName = null,
       getNameCount = 0,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path from .",
       path = ".",
@@ -172,8 +177,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = pwdName,
       getFileName = ".",
       getNameCount = 1,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a path from ..",
       path = "..",
@@ -186,8 +191,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = parentName,
       getFileName = "..",
       getNameCount = 1,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a path including .",
       path = "/hello/world/with/./dots",
@@ -200,8 +205,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "dots",
       getFileName = "dots",
       getNameCount = 5,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path including ..",
       path = "/hello/world/with/../dots",
@@ -214,7 +219,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "dots",
       getFileName = "dots",
       getNameCount = 5,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // Normalized
 
@@ -230,8 +236,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = pwdName,
       getFileName = "",
       getNameCount = 1,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a normalized path from /",
       path = "/",
@@ -244,8 +250,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "",
       getFileName = null,
       getNameCount = 0,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a normalized path from .",
       path = ".",
@@ -258,8 +264,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = pwdName,
       getFileName = "",
       getNameCount = 1,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a normalized path from ..",
       path = "..",
@@ -272,8 +278,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = parentName,
       getFileName = "..",
       getNameCount = 1,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a normalized path including a .",
       path = "/hello/world/with/./dots",
@@ -286,8 +292,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "dots",
       getFileName = "dots",
       getNameCount = 4,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a normalized path including ..",
       path = "/hello/world/with/../dots",
@@ -300,7 +306,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "dots",
       getFileName = "dots",
       getNameCount = 3,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // URI
 
@@ -316,8 +323,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "world",
       getFileName = "world",
       getNameCount = 2,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path from a file uri with encoded spaces",
       path = "file:///hello/world/encoded%20spaces",
@@ -330,7 +337,8 @@ class DefaultPathBuilderSpec extends Suite with AnyFlatSpecLike with Matchers wi
       name = "encoded%20spaces",
       getFileName = "encoded%20spaces",
       getNameCount = 3,
-      isAbsolute = true)
+      isAbsolute = true
+    )
   )
 
   private def badPaths = Seq(
diff --git a/core/src/test/scala/cromwell/core/path/PathBuilderFactorySpec.scala b/core/src/test/scala/cromwell/core/path/PathBuilderFactorySpec.scala
index 7fea4f7b9f3..7119a62b1f6 100644
--- a/core/src/test/scala/cromwell/core/path/PathBuilderFactorySpec.scala
+++ b/core/src/test/scala/cromwell/core/path/PathBuilderFactorySpec.scala
@@ -12,24 +12,28 @@ import scala.concurrent.{ExecutionContext, Future}
 class PathBuilderFactorySpec extends TestKitSuite with AnyFlatSpecLike with ScalaFutures with Matchers {
   behavior of "PathBuilderFactory"
   implicit val ec = system.dispatcher
-  
+
   it should "sort factories when instantiating path builders" in {
     val factory1 = new MockPathBuilderFactory(ConfigFactory.empty(), ConfigFactory.parseString("name=factory1"))
     val factory2 = new MockPathBuilderFactory(ConfigFactory.empty(), ConfigFactory.parseString("name=factory2"))
     PathBuilderFactory
-      .instantiatePathBuilders(List(DefaultPathBuilderFactory, factory1, factory2), WorkflowOptions.empty).map({ pathBuilders =>
-      pathBuilders.last shouldBe DefaultPathBuilder
-      // check that the order of the other factories has not been changed
-      pathBuilders.map(_.name) shouldBe List("factory1", "factory2", DefaultPathBuilder.name)
-    }).futureValue
+      .instantiatePathBuilders(List(DefaultPathBuilderFactory, factory1, factory2), WorkflowOptions.empty)
+      .map { pathBuilders =>
+        pathBuilders.last shouldBe DefaultPathBuilder
+        // check that the order of the other factories has not been changed
+        pathBuilders.map(_.name) shouldBe List("factory1", "factory2", DefaultPathBuilder.name)
+      }
+      .futureValue
   }
 }
 
-class MockPathBuilderFactory(globalConfig: Config, val instanceConfig: Config) extends cromwell.core.path.PathBuilderFactory {
-  override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext) = Future.successful(
-    new PathBuilder {
-      override def name = instanceConfig.getString("name")
-      override def build(pathAsString: String) = throw new UnsupportedOperationException
-    }
-  )
+class MockPathBuilderFactory(globalConfig: Config, val instanceConfig: Config)
+    extends cromwell.core.path.PathBuilderFactory {
+  override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext) =
+    Future.successful(
+      new PathBuilder {
+        override def name = instanceConfig.getString("name")
+        override def build(pathAsString: String) = throw new UnsupportedOperationException
+      }
+    )
 }
diff --git a/core/src/test/scala/cromwell/core/path/PathBuilderSpecUtils.scala b/core/src/test/scala/cromwell/core/path/PathBuilderSpecUtils.scala
index 92bfd77233f..324928d2cb4 100644
--- a/core/src/test/scala/cromwell/core/path/PathBuilderSpecUtils.scala
+++ b/core/src/test/scala/cromwell/core/path/PathBuilderSpecUtils.scala
@@ -17,7 +17,8 @@ case class GoodPath(description: String,
                     name: String,
                     getFileName: String,
                     getNameCount: Int,
-                    isAbsolute: Boolean)
+                    isAbsolute: Boolean
+)
 
 case class BadPath(description: String, path: String, exceptionMessage: String)
 
@@ -29,7 +30,8 @@ trait PathBuilderSpecUtils {
 
   def truncateCommonRoots(builder: => PathBuilder,
                           pathsToTruncate: TableFor3[String, String, String],
-                          tag: Tag = PathBuilderSpecUtils.PathTest): Unit = {
+                          tag: Tag = PathBuilderSpecUtils.PathTest
+  ): Unit = {
     behavior of s"PathCopier"
 
     it should "truncate common roots" taggedAs tag in {
diff --git a/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala b/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
index c6a008feb02..e5d947da83d 100644
--- a/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
+++ b/core/src/test/scala/cromwell/core/retry/BackoffSpec.scala
@@ -18,11 +18,10 @@ class BackoffSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
         .setInitialIntervalMillis(1.second.toMillis.toInt)
         .setMaxIntervalMillis(2.seconds.toMillis.toInt)
         .setMaxElapsedTimeMillis(Integer.MAX_VALUE)
-        .setRandomizationFactor(0D)
+        .setRandomizationFactor(0d)
         .build()
     )
 
-
     exponentialBackoff.backoffMillis shouldBe 3.seconds.toMillis
     exponentialBackoff.next.backoffMillis shouldBe 1.second.toMillis
   }
@@ -33,7 +32,7 @@ class BackoffSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
         .setInitialIntervalMillis(1.second.toMillis.toInt)
         .setMaxIntervalMillis(2.seconds.toMillis.toInt)
         .setMaxElapsedTimeMillis(Integer.MAX_VALUE)
-        .setRandomizationFactor(0D)
+        .setRandomizationFactor(0d)
         .build()
     ).backoffMillis shouldBe 1.second.toMillis
   }
@@ -46,7 +45,7 @@ class BackoffSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
           .setInitialIntervalMillis(1.second.toMillis.toInt)
           .setMaxIntervalMillis(2.seconds.toMillis.toInt)
           .setMaxElapsedTimeMillis(Integer.MAX_VALUE)
-          .setRandomizationFactor(0D)
+          .setRandomizationFactor(0d)
           .build()
       )
     }
@@ -57,16 +56,16 @@ class BackoffSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       Map[String, Any](
         "min" -> "5 seconds",
         "max" -> "30 seconds",
-        "multiplier" -> 6D,
-        "randomization-factor" -> 0D
+        "multiplier" -> 6d,
+        "randomization-factor" -> 0d
       ).asJava
     )
 
     val backoff = SimpleExponentialBackoff(config)
     backoff.googleBackoff.getCurrentIntervalMillis shouldBe 5.seconds.toMillis.toInt
     backoff.googleBackoff.getMaxIntervalMillis shouldBe 30.seconds.toMillis.toInt
-    backoff.googleBackoff.getMultiplier shouldBe 6D
-    backoff.googleBackoff.getRandomizationFactor shouldBe 0D
+    backoff.googleBackoff.getMultiplier shouldBe 6d
+    backoff.googleBackoff.getRandomizationFactor shouldBe 0d
   }
 
 }
diff --git a/core/src/test/scala/cromwell/core/retry/RetrySpec.scala b/core/src/test/scala/cromwell/core/retry/RetrySpec.scala
index 83516f3328b..134b1c1db25 100644
--- a/core/src/test/scala/cromwell/core/retry/RetrySpec.scala
+++ b/core/src/test/scala/cromwell/core/retry/RetrySpec.scala
@@ -16,7 +16,7 @@ class RetrySpec extends TestKitSuite with AnyFlatSpecLike with Matchers with Sca
 
     var counter: Int = n
 
-    def doIt(): Future[Int] = {
+    def doIt(): Future[Int] =
       if (counter == 0)
         Future.successful(9)
       else {
@@ -24,23 +24,22 @@ class RetrySpec extends TestKitSuite with AnyFlatSpecLike with Matchers with Sca
         val ex = if (counter <= transients) new TransientException else new IllegalArgumentException("Failed")
         Future.failed(ex)
       }
-    }
   }
 
-  implicit val defaultPatience: PatienceConfig = PatienceConfig(timeout = Span(30, Seconds), interval = Span(100, Millis))
+  implicit val defaultPatience: PatienceConfig =
+    PatienceConfig(timeout = Span(30, Seconds), interval = Span(100, Millis))
 
   private def runRetry(retries: Int,
                        work: MockWork,
                        isTransient: Throwable => Boolean = Retry.throwableToFalse,
-                       isFatal: Throwable => Boolean = Retry.throwableToFalse): Future[Int] = {
-
+                       isFatal: Throwable => Boolean = Retry.throwableToFalse
+  ): Future[Int] =
     withRetry(
       f = () => work.doIt(),
       maxRetries = Option(retries),
       isTransient = isTransient,
       isFatal = isFatal
     )
-  }
 
   "Retry" should "retry a function until it works" in {
     val work = new MockWork(2)
@@ -53,7 +52,7 @@ class RetrySpec extends TestKitSuite with AnyFlatSpecLike with Matchers with Sca
 
   it should "fail if it hits the max retry count" in {
     whenReady(runRetry(1, new MockWork(3)).failed) { x =>
-      x shouldBe an [CromwellFatalException]
+      x shouldBe an[CromwellFatalException]
     }
   }
 
@@ -61,18 +60,19 @@ class RetrySpec extends TestKitSuite with AnyFlatSpecLike with Matchers with Sca
     val work = new MockWork(3)
 
     whenReady(runRetry(3, work, isFatal = (t: Throwable) => t.isInstanceOf[IllegalArgumentException]).failed) { x =>
-      x shouldBe an [CromwellFatalException]
+      x shouldBe an[CromwellFatalException]
       work.counter shouldBe 2
     }
 
     val work2 = new MockWork(4, 2)
     val retry = runRetry(4,
-      work2,
-      isFatal = (t: Throwable) => t.isInstanceOf[IllegalArgumentException],
-      isTransient = (t: Throwable) => t.isInstanceOf[TransientException])
+                         work2,
+                         isFatal = (t: Throwable) => t.isInstanceOf[IllegalArgumentException],
+                         isTransient = (t: Throwable) => t.isInstanceOf[TransientException]
+    )
 
     whenReady(retry.failed) { x =>
-      x shouldBe an [CromwellFatalException]
+      x shouldBe an[CromwellFatalException]
       work2.counter shouldBe 3
     }
   }
diff --git a/core/src/test/scala/cromwell/core/simpleton/WomValueBuilderSpec.scala b/core/src/test/scala/cromwell/core/simpleton/WomValueBuilderSpec.scala
index 8db76caab1d..fb347e43441 100644
--- a/core/src/test/scala/cromwell/core/simpleton/WomValueBuilderSpec.scala
+++ b/core/src/test/scala/cromwell/core/simpleton/WomValueBuilderSpec.scala
@@ -23,110 +23,165 @@ class WomValueBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   case class SimpletonConversion(name: String, womValue: WomValue, simpletons: Seq[WomValueSimpleton])
   val simpletonConversions = List(
     SimpletonConversion("foo", WomString("none"), List(WomValueSimpleton("foo", WomString("none")))),
-    SimpletonConversion("bar", WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2))), List(WomValueSimpleton("bar[0]", WomInteger(1)), WomValueSimpleton("bar[1]", WomInteger(2)))),
+    SimpletonConversion(
+      "bar",
+      WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2))),
+      List(WomValueSimpleton("bar[0]", WomInteger(1)), WomValueSimpleton("bar[1]", WomInteger(2)))
+    ),
     SimpletonConversion("empty_array", WomArray(WomArrayType(WomIntegerType), List.empty), List()),
     SimpletonConversion(
       "baz",
-      WomArray(WomArrayType(WomArrayType(WomIntegerType)), List(
-        WomArray(WomArrayType(WomIntegerType), List(WomInteger(0), WomInteger(1))),
-        WomArray(WomArrayType(WomIntegerType), List(WomInteger(2), WomInteger(3))))),
-      List(WomValueSimpleton("baz[0][0]", WomInteger(0)), WomValueSimpleton("baz[0][1]", WomInteger(1)), WomValueSimpleton("baz[1][0]", WomInteger(2)), WomValueSimpleton("baz[1][1]", WomInteger(3)))
+      WomArray(
+        WomArrayType(WomArrayType(WomIntegerType)),
+        List(WomArray(WomArrayType(WomIntegerType), List(WomInteger(0), WomInteger(1))),
+             WomArray(WomArrayType(WomIntegerType), List(WomInteger(2), WomInteger(3)))
+        )
+      ),
+      List(
+        WomValueSimpleton("baz[0][0]", WomInteger(0)),
+        WomValueSimpleton("baz[0][1]", WomInteger(1)),
+        WomValueSimpleton("baz[1][0]", WomInteger(2)),
+        WomValueSimpleton("baz[1][1]", WomInteger(3))
+      )
     ),
     SimpletonConversion(
       "map",
-      WomMap(WomMapType(WomStringType, WomStringType), Map(
-        WomString("foo") -> WomString("foo"),
-        WomString("bar") -> WomString("bar"))),
+      WomMap(WomMapType(WomStringType, WomStringType),
+             Map(WomString("foo") -> WomString("foo"), WomString("bar") -> WomString("bar"))
+      ),
       List(WomValueSimpleton("map:foo", WomString("foo")), WomValueSimpleton("map:bar", WomString("bar")))
     ),
     SimpletonConversion(
       "mapOfMaps",
-      WomMap(WomMapType(WomStringType, WomMapType(WomStringType, WomStringType)), Map(
-        WomString("foo") -> WomMap(WomMapType(WomStringType, WomStringType), Map(WomString("foo2") -> WomString("foo"))),
-        WomString("bar") ->WomMap(WomMapType(WomStringType, WomStringType), Map(WomString("bar2") -> WomString("bar"))))),
-      List(WomValueSimpleton("mapOfMaps:foo:foo2", WomString("foo")), WomValueSimpleton("mapOfMaps:bar:bar2", WomString("bar")))
+      WomMap(
+        WomMapType(WomStringType, WomMapType(WomStringType, WomStringType)),
+        Map(
+          WomString("foo") -> WomMap(WomMapType(WomStringType, WomStringType),
+                                     Map(WomString("foo2") -> WomString("foo"))
+          ),
+          WomString("bar") -> WomMap(WomMapType(WomStringType, WomStringType),
+                                     Map(WomString("bar2") -> WomString("bar"))
+          )
+        )
+      ),
+      List(WomValueSimpleton("mapOfMaps:foo:foo2", WomString("foo")),
+           WomValueSimpleton("mapOfMaps:bar:bar2", WomString("bar"))
+      )
     ),
     SimpletonConversion(
       "simplePair1",
       WomPair(WomInteger(1), WomString("hello")),
-      List(WomValueSimpleton("simplePair1:left", WomInteger(1)), WomValueSimpleton("simplePair1:right", WomString("hello")))
+      List(WomValueSimpleton("simplePair1:left", WomInteger(1)),
+           WomValueSimpleton("simplePair1:right", WomString("hello"))
+      )
     ),
     SimpletonConversion(
       "simplePair2",
       WomPair(WomString("left"), WomInteger(5)),
-      List(WomValueSimpleton("simplePair2:left", WomString("left")), WomValueSimpleton("simplePair2:right", WomInteger(5)))
+      List(WomValueSimpleton("simplePair2:left", WomString("left")),
+           WomValueSimpleton("simplePair2:right", WomInteger(5))
+      )
     ),
     SimpletonConversion(
       "pairOfPairs",
-      WomPair(
-        WomPair(WomInteger(1), WomString("one")),
-        WomPair(WomString("two"), WomInteger(2))),
+      WomPair(WomPair(WomInteger(1), WomString("one")), WomPair(WomString("two"), WomInteger(2))),
       List(
         WomValueSimpleton("pairOfPairs:left:left", WomInteger(1)),
         WomValueSimpleton("pairOfPairs:left:right", WomString("one")),
         WomValueSimpleton("pairOfPairs:right:left", WomString("two")),
-        WomValueSimpleton("pairOfPairs:right:right", WomInteger(2)))
+        WomValueSimpleton("pairOfPairs:right:right", WomInteger(2))
+      )
     ),
     SimpletonConversion(
       "pairOfArrayAndMap",
       WomPair(
         WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2))),
-        WomMap(WomMapType(WomStringType, WomIntegerType), Map(WomString("left") -> WomInteger(100), WomString("right") -> WomInteger(200)))),
+        WomMap(WomMapType(WomStringType, WomIntegerType),
+               Map(WomString("left") -> WomInteger(100), WomString("right") -> WomInteger(200))
+        )
+      ),
       List(
         WomValueSimpleton("pairOfArrayAndMap:left[0]", WomInteger(1)),
         WomValueSimpleton("pairOfArrayAndMap:left[1]", WomInteger(2)),
         WomValueSimpleton("pairOfArrayAndMap:right:left", WomInteger(100)),
-        WomValueSimpleton("pairOfArrayAndMap:right:right", WomInteger(200)))
+        WomValueSimpleton("pairOfArrayAndMap:right:right", WomInteger(200))
+      )
     ),
     SimpletonConversion(
       "mapOfArrays",
-      WomMap(WomMapType(WomStringType, WomArrayType(WomIntegerType)), Map(
-        WomString("foo") -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(0), WomInteger(1))),
-        WomString("bar") -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(2), WomInteger(3))))),
-      List(WomValueSimpleton("mapOfArrays:foo[0]", WomInteger(0)), WomValueSimpleton("mapOfArrays:foo[1]", WomInteger(1)),
-        WomValueSimpleton("mapOfArrays:bar[0]", WomInteger(2)), WomValueSimpleton("mapOfArrays:bar[1]", WomInteger(3)))
+      WomMap(
+        WomMapType(WomStringType, WomArrayType(WomIntegerType)),
+        Map(
+          WomString("foo") -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(0), WomInteger(1))),
+          WomString("bar") -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(2), WomInteger(3)))
+        )
+      ),
+      List(
+        WomValueSimpleton("mapOfArrays:foo[0]", WomInteger(0)),
+        WomValueSimpleton("mapOfArrays:foo[1]", WomInteger(1)),
+        WomValueSimpleton("mapOfArrays:bar[0]", WomInteger(2)),
+        WomValueSimpleton("mapOfArrays:bar[1]", WomInteger(3))
+      )
     ),
     SimpletonConversion(
       "escapology",
-      WomMap(WomMapType(WomStringType, WomStringType), Map(
-        WomString("foo[1]") -> WomString("foo"),
-        WomString("bar[[") -> WomString("bar"),
-        WomString("baz:qux") -> WomString("baz:qux"))),
-      List(WomValueSimpleton("escapology:foo\\[1\\]", WomString("foo")),
+      WomMap(
+        WomMapType(WomStringType, WomStringType),
+        Map(WomString("foo[1]") -> WomString("foo"),
+            WomString("bar[[") -> WomString("bar"),
+            WomString("baz:qux") -> WomString("baz:qux")
+        )
+      ),
+      List(
+        WomValueSimpleton("escapology:foo\\[1\\]", WomString("foo")),
         WomValueSimpleton("escapology:bar\\[\\[", WomString("bar")),
-        WomValueSimpleton("escapology:baz\\:qux", WomString("baz:qux")))
+        WomValueSimpleton("escapology:baz\\:qux", WomString("baz:qux"))
+      )
     ),
     SimpletonConversion(
       "flat_object",
-      WomObject(Map(
-        "a" -> WomString("aardvark"),
-        "b" -> WomInteger(25),
-        "c" -> WomBoolean(false)
-      )),
-      List(WomValueSimpleton("flat_object:a", WomString("aardvark")),
+      WomObject(
+        Map(
+          "a" -> WomString("aardvark"),
+          "b" -> WomInteger(25),
+          "c" -> WomBoolean(false)
+        )
+      ),
+      List(
+        WomValueSimpleton("flat_object:a", WomString("aardvark")),
         WomValueSimpleton("flat_object:b", WomInteger(25)),
-        WomValueSimpleton("flat_object:c", WomBoolean(false)))
+        WomValueSimpleton("flat_object:c", WomBoolean(false))
+      )
     ),
     SimpletonConversion(
       "object_with_array",
-      WomObject(Map(
-        "a" -> WomArray(WomArrayType(WomStringType), Seq(WomString("aardvark"), WomString("beetle")))
-      )),
+      WomObject(
+        Map(
+          "a" -> WomArray(WomArrayType(WomStringType), Seq(WomString("aardvark"), WomString("beetle")))
+        )
+      ),
       List(WomValueSimpleton("object_with_array:a[0]", WomString("aardvark")),
-        WomValueSimpleton("object_with_array:a[1]", WomString("beetle")))
+           WomValueSimpleton("object_with_array:a[1]", WomString("beetle"))
+      )
     ),
     SimpletonConversion(
       "object_with_object",
-      WomObject(Map(
-        "a" -> WomObject(Map(
-          "aa" -> WomArray(WomArrayType(WomStringType), Seq(WomString("aardvark"), WomString("aaron"))),
-          "ab" -> WomArray(WomArrayType(WomStringType), Seq(WomString("abacus"), WomString("a bee")))
-        )),
-        "b" -> WomObject(Map(
-          "ba" -> WomArray(WomArrayType(WomStringType), Seq(WomString("baa"), WomString("battle"))),
-          "bb" -> WomArray(WomArrayType(WomStringType), Seq(WomString("bbrrrr"), WomString("bb gun")))
-        ))
-      )),
+      WomObject(
+        Map(
+          "a" -> WomObject(
+            Map(
+              "aa" -> WomArray(WomArrayType(WomStringType), Seq(WomString("aardvark"), WomString("aaron"))),
+              "ab" -> WomArray(WomArrayType(WomStringType), Seq(WomString("abacus"), WomString("a bee")))
+            )
+          ),
+          "b" -> WomObject(
+            Map(
+              "ba" -> WomArray(WomArrayType(WomStringType), Seq(WomString("baa"), WomString("battle"))),
+              "bb" -> WomArray(WomArrayType(WomStringType), Seq(WomString("bbrrrr"), WomString("bb gun")))
+            )
+          )
+        )
+      ),
       List(
         WomValueSimpleton("object_with_object:a:aa[0]", WomString("aardvark")),
         WomValueSimpleton("object_with_object:a:aa[1]", WomString("aaron")),
@@ -135,58 +190,59 @@ class WomValueBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
         WomValueSimpleton("object_with_object:b:ba[0]", WomString("baa")),
         WomValueSimpleton("object_with_object:b:ba[1]", WomString("battle")),
         WomValueSimpleton("object_with_object:b:bb[0]", WomString("bbrrrr")),
-        WomValueSimpleton("object_with_object:b:bb[1]", WomString("bb gun")),
+        WomValueSimpleton("object_with_object:b:bb[1]", WomString("bb gun"))
       )
     ),
     /*
-      * Wom object representing a directory listing
-      *  - a single file
-      *  - a "maybe populated file" with some properties (checksum etc..) and secondary files:
-      *         - another single file
-      *         - a directory listing a single file
-      *         - an unlisted directory
-      *         - a glob file
-      *  - an unlisted directory
-      *  - a glob file
-      *
-      *  Note: glob files technically are never simpletonized but as WomFiles they *can* be
+     * Wom object representing a directory listing
+     *  - a single file
+     *  - a "maybe populated file" with some properties (checksum etc..) and secondary files:
+     *         - another single file
+     *         - a directory listing a single file
+     *         - an unlisted directory
+     *         - a glob file
+     *  - an unlisted directory
+     *  - a glob file
+     *
+     *  Note: glob files technically are never simpletonized but as WomFiles they *can* be
      */
     SimpletonConversion(
       "directory",
       WomMaybeListedDirectory(
         Option("outerValueName"),
-        Option(List(
-          WomSingleFile("outerSingleFile"),
-          WomMaybeListedDirectory(Option("innerValueName"), Option(List(WomSingleFile("innerSingleFile")))),
-          WomMaybePopulatedFile(
-            Option("populatedInnerValueName"),
-            Option("innerChecksum"),
-            Option(10L),
-            Option("innerFormat"),
-            Option("innerContents"),
-            List(
-              WomSingleFile("populatedInnerSingleFile"),
-              WomMaybeListedDirectory(Option("innerDirectoryValueName"), Option(List(WomSingleFile("innerDirectorySingleFile")))),
-              WomUnlistedDirectory("innerUnlistedDirectory"),
-              WomGlobFile("innerGlobFile")
-            )
-          ),
-          WomUnlistedDirectory("outerUnlistedDirectory"),
-          WomGlobFile("outerGlobFile")
-      ))),
+        Option(
+          List(
+            WomSingleFile("outerSingleFile"),
+            WomMaybeListedDirectory(Option("innerValueName"), Option(List(WomSingleFile("innerSingleFile")))),
+            WomMaybePopulatedFile(
+              Option("populatedInnerValueName"),
+              Option("innerChecksum"),
+              Option(10L),
+              Option("innerFormat"),
+              Option("innerContents"),
+              List(
+                WomSingleFile("populatedInnerSingleFile"),
+                WomMaybeListedDirectory(Option("innerDirectoryValueName"),
+                                        Option(List(WomSingleFile("innerDirectorySingleFile")))
+                ),
+                WomUnlistedDirectory("innerUnlistedDirectory"),
+                WomGlobFile("innerGlobFile")
+              )
+            ),
+            WomUnlistedDirectory("outerUnlistedDirectory"),
+            WomGlobFile("outerGlobFile")
+          )
+        )
+      ),
       List(
         WomValueSimpleton("directory:class", WomString("Directory")),
         WomValueSimpleton("directory:value", WomString("outerValueName")),
-
         WomValueSimpleton("directory:listing[0]", WomSingleFile("outerSingleFile")),
-
         WomValueSimpleton("directory:listing[1]:class", WomString("Directory")),
         WomValueSimpleton("directory:listing[1]:value", WomString("innerValueName")),
         WomValueSimpleton("directory:listing[1]:listing[0]", WomSingleFile("innerSingleFile")),
-
         WomValueSimpleton("directory:listing[2]:class", WomString("File")),
         WomValueSimpleton("directory:listing[2]:value", WomString("populatedInnerValueName")),
-
         WomValueSimpleton("directory:listing[2]:checksum", WomString("innerChecksum")),
         WomValueSimpleton("directory:listing[2]:size", WomInteger(10)),
         WomValueSimpleton("directory:listing[2]:format", WomString("innerFormat")),
@@ -194,10 +250,11 @@ class WomValueBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
         WomValueSimpleton("directory:listing[2]:secondaryFiles[0]", WomSingleFile("populatedInnerSingleFile")),
         WomValueSimpleton("directory:listing[2]:secondaryFiles[1]:class", WomString("Directory")),
         WomValueSimpleton("directory:listing[2]:secondaryFiles[1]:value", WomString("innerDirectoryValueName")),
-        WomValueSimpleton("directory:listing[2]:secondaryFiles[1]:listing[0]", WomSingleFile("innerDirectorySingleFile")),
+        WomValueSimpleton("directory:listing[2]:secondaryFiles[1]:listing[0]",
+                          WomSingleFile("innerDirectorySingleFile")
+        ),
         WomValueSimpleton("directory:listing[2]:secondaryFiles[2]", WomUnlistedDirectory("innerUnlistedDirectory")),
         WomValueSimpleton("directory:listing[2]:secondaryFiles[3]", WomGlobFile("innerGlobFile")),
-
         WomValueSimpleton("directory:listing[3]", WomUnlistedDirectory("outerUnlistedDirectory")),
         WomValueSimpleton("directory:listing[4]", WomGlobFile("outerGlobFile"))
       )
@@ -225,7 +282,9 @@ class WomValueBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
 
   it should "round trip everything together with no losses" in {
 
-    val wdlValues = (simpletonConversions map { case SimpletonConversion(name, womValue, _) => WomMocks.mockOutputPort(name, womValue.womType) -> womValue }).toMap
+    val wdlValues = (simpletonConversions map { case SimpletonConversion(name, womValue, _) =>
+      WomMocks.mockOutputPort(name, womValue.womType) -> womValue
+    }).toMap
     val allSimpletons = simpletonConversions flatMap { case SimpletonConversion(_, _, simpletons) => simpletons }
 
     val actualSimpletons = wdlValues.simplify
@@ -239,17 +298,23 @@ class WomValueBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   // coerceable back into the original type:
   it should "decompose then reconstruct a map in an object into a coerceable value" in {
 
-    val aMap = WomMap(WomMapType(WomStringType, WomArrayType(WomStringType)), Map(
-      WomString("aa") -> WomArray(WomArrayType(WomStringType), Seq(WomString("aardvark"), WomString("aaron"))),
-      WomString("ab") -> WomArray(WomArrayType(WomStringType), Seq(WomString("abacus"), WomString("a bee")))
-    ))
+    val aMap = WomMap(
+      WomMapType(WomStringType, WomArrayType(WomStringType)),
+      Map(
+        WomString("aa") -> WomArray(WomArrayType(WomStringType), Seq(WomString("aardvark"), WomString("aaron"))),
+        WomString("ab") -> WomArray(WomArrayType(WomStringType), Seq(WomString("abacus"), WomString("a bee")))
+      )
+    )
 
-    val bMap = WomMap(WomMapType(WomStringType, WomArrayType(WomStringType)), Map(
-      WomString("ba") -> WomArray(WomArrayType(WomStringType), Seq(WomString("baa"), WomString("battle"))),
-      WomString("bb") -> WomArray(WomArrayType(WomStringType), Seq(WomString("bbrrrr"), WomString("bb gun")))
-    ))
+    val bMap = WomMap(
+      WomMapType(WomStringType, WomArrayType(WomStringType)),
+      Map(
+        WomString("ba") -> WomArray(WomArrayType(WomStringType), Seq(WomString("baa"), WomString("battle"))),
+        WomString("bb") -> WomArray(WomArrayType(WomStringType), Seq(WomString("bbrrrr"), WomString("bb gun")))
+      )
+    )
 
-    val initial = WomObject(Map("a" -> aMap, "b" -> bMap ))
+    val initial = WomObject(Map("a" -> aMap, "b" -> bMap))
 
     val map = Map(WomMocks.mockOutputPort("map_in_object") -> initial)
 
@@ -263,9 +328,10 @@ class WomValueBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
         WomValueSimpleton("map_in_object:b:ba[0]", WomString("baa")),
         WomValueSimpleton("map_in_object:b:ba[1]", WomString("battle")),
         WomValueSimpleton("map_in_object:b:bb[0]", WomString("bbrrrr")),
-        WomValueSimpleton("map_in_object:b:bb[1]", WomString("bb gun")),
+        WomValueSimpleton("map_in_object:b:bb[1]", WomString("bb gun"))
       ),
-      actualSimpletons)
+      actualSimpletons
+    )
 
     // Reconstruct:
     val outputPort = WomMocks.mockOutputPort(OutputDefinition("map_in_object", initial.womType, IgnoredExpression))
@@ -283,7 +349,8 @@ class WomValueBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   }
 
   private def assertSimpletonsEqual(expectedSimpletons: Iterable[WomValueSimpleton],
-                                    actualSimpletons: Iterable[WomValueSimpleton]): Unit = {
+                                    actualSimpletons: Iterable[WomValueSimpleton]
+  ): Unit = {
 
     // Sanity check, make sure we don't lose anything when we "toSet":
     actualSimpletons.toSet should contain theSameElementsAs actualSimpletons
diff --git a/core/src/test/scala/cromwell/util/AkkaTestUtil.scala b/core/src/test/scala/cromwell/util/AkkaTestUtil.scala
index ef1183e9a07..c237ee8c127 100644
--- a/core/src/test/scala/cromwell/util/AkkaTestUtil.scala
+++ b/core/src/test/scala/cromwell/util/AkkaTestUtil.scala
@@ -39,7 +39,9 @@ object AkkaTestUtil {
   class DeathTestActor extends Actor {
     protected def stoppingReceive: Actor.Receive = {
       case InternalStop => context.stop(self)
-      case ThrowException => throw new Exception("Don't panic, dear debugger! This was a deliberate exception for the test case.") with NoStackTrace
+      case ThrowException =>
+        throw new Exception("Don't panic, dear debugger! This was a deliberate exception for the test case.")
+          with NoStackTrace
     }
     override def receive = stoppingReceive orElse Actor.ignoringBehavior
   }
@@ -55,6 +57,6 @@ object AkkaTestUtil {
 
     def loggedReceive: Receive
 
-    override final def receive: Receive = logMessage orElse loggedReceive
+    final override def receive: Receive = logMessage orElse loggedReceive
   }
 }
diff --git a/core/src/test/scala/cromwell/util/EncryptionSpec.scala b/core/src/test/scala/cromwell/util/EncryptionSpec.scala
index d1d64f3725d..f9b91107c96 100644
--- a/core/src/test/scala/cromwell/util/EncryptionSpec.scala
+++ b/core/src/test/scala/cromwell/util/EncryptionSpec.scala
@@ -14,7 +14,8 @@ object EncryptionSpec {
     """|
        |Did you install the Java Cryptography Extension (JCE) Unlimited Strength Jurisdiction Policy Files?
        |http://www.oracle.com/technetwork/java/javase/downloads/jce8-download-2133166.html
-       |""".stripMargin)
+       |""".stripMargin
+  )
 }
 
 class EncryptionSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
diff --git a/core/src/test/scala/cromwell/util/GracefulShutdownHelperSpec.scala b/core/src/test/scala/cromwell/util/GracefulShutdownHelperSpec.scala
index 875ffd48e3d..214ca6c8454 100644
--- a/core/src/test/scala/cromwell/util/GracefulShutdownHelperSpec.scala
+++ b/core/src/test/scala/cromwell/util/GracefulShutdownHelperSpec.scala
@@ -10,17 +10,17 @@ import org.scalatest.matchers.should.Matchers
 
 class GracefulShutdownHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers {
   behavior of "GracefulShutdownHelper"
-  
+
   it should "send ShutdownCommand to actors, wait for them to shutdown, then shut itself down" in {
     val testProbeA = TestProbe()
     val testProbeB = TestProbe()
-    
+
     val testActor = system.actorOf(Props(new Actor with GracefulShutdownHelper with ActorLogging {
-      override def receive: Receive = {
-        case ShutdownCommand => waitForActorsAndShutdown(NonEmptyList.of(testProbeA.ref, testProbeB.ref))
+      override def receive: Receive = { case ShutdownCommand =>
+        waitForActorsAndShutdown(NonEmptyList.of(testProbeA.ref, testProbeB.ref))
       }
     }))
-    
+
     watch(testActor)
 
     testActor ! ShutdownCommand
@@ -37,7 +37,7 @@ class GracefulShutdownHelperSpec extends TestKitSuite with AnyFlatSpecLike with
     expectNoMessage()
 
     system stop testProbeB.ref
-    
+
     expectTerminated(testActor)
   }
 }
diff --git a/core/src/test/scala/cromwell/util/SampleWdl.scala b/core/src/test/scala/cromwell/util/SampleWdl.scala
index 6e790ca67be..8180049fc73 100644
--- a/core/src/test/scala/cromwell/util/SampleWdl.scala
+++ b/core/src/test/scala/cromwell/util/SampleWdl.scala
@@ -2,7 +2,12 @@ package cromwell.util
 
 import java.util.UUID
 import cromwell.core.path.{DefaultPath, DefaultPathBuilder, Path}
-import cromwell.core.{WorkflowOptions, WorkflowSourceFilesCollection, WorkflowSourceFilesWithDependenciesZip, WorkflowSourceFilesWithoutImports}
+import cromwell.core.{
+  WorkflowOptions,
+  WorkflowSourceFilesCollection,
+  WorkflowSourceFilesWithDependenciesZip,
+  WorkflowSourceFilesWithoutImports
+}
 import spray.json._
 import wom.core.{ExecutableInputMap, WorkflowJson, WorkflowSource}
 import wom.values._
@@ -30,7 +35,8 @@ trait SampleWdl extends TestFileUtil {
                         labels: String = "{}",
                         workflowType: Option[String] = Option("WDL"),
                         workflowTypeVersion: Option[String] = None,
-                        workflowOnHold: Boolean = false): WorkflowSourceFilesCollection = {
+                        workflowOnHold: Boolean = false
+  ): WorkflowSourceFilesCollection =
     importsZip match {
       case Some(zip) =>
         WorkflowSourceFilesWithDependenciesZip(
@@ -45,7 +51,8 @@ trait SampleWdl extends TestFileUtil {
           warnings = Vector.empty,
           workflowOnHold = workflowOnHold,
           importsZip = zip,
-          requestedWorkflowId = None)
+          requestedWorkflowId = None
+        )
       case None =>
         WorkflowSourceFilesWithoutImports(
           workflowSource = Option(workflowSource(runtime)),
@@ -58,9 +65,9 @@ trait SampleWdl extends TestFileUtil {
           workflowTypeVersion = workflowTypeVersion,
           warnings = Vector.empty,
           workflowOnHold = workflowOnHold,
-          requestedWorkflowId = None)
+          requestedWorkflowId = None
+        )
     }
-  }
 
   val rawInputs: ExecutableInputMap
 
@@ -84,8 +91,8 @@ trait SampleWdl extends TestFileUtil {
     def write(x: Any): JsValue = x match {
       case n: Int => JsNumber(n)
       case s: String => JsString(s)
-      case b: Boolean => if(b) JsTrue else JsFalse
-      case s: Seq[Any] => JsArray(s map {_.toJson} toVector)
+      case b: Boolean => if (b) JsTrue else JsFalse
+      case s: Seq[Any] => JsArray(s map { _.toJson } toVector)
       case a: WomArray => write(a.value)
       case s: WomString => JsString(s.value)
       case i: WomInteger => JsNumber(i.value)
@@ -111,20 +118,20 @@ object SampleWdl {
   object HelloWorld extends SampleWdl {
     override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""
-        |task hello {
-        |  String addressee
-        |  command {
-        |    echo "Hello $${addressee}!"
-        |  }
-        |  output {
-        |    String salutation = read_string(stdout())
-        |  }
-        |  RUNTIME
-        |}
-        |
-        |workflow wf_hello {
-        |  call hello
-        |}
+         |task hello {
+         |  String addressee
+         |  command {
+         |    echo "Hello $${addressee}!"
+         |  }
+         |  output {
+         |    String salutation = read_string(stdout())
+         |  }
+         |  RUNTIME
+         |}
+         |
+         |workflow wf_hello {
+         |  call hello
+         |}
       """.stripMargin.replace("RUNTIME", runtime)
 
     val Addressee = "wf_hello.hello.addressee"
@@ -157,35 +164,35 @@ object SampleWdl {
   object EmptyString extends SampleWdl {
     override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""
-        |task hello {
-        |  command {
-        |    echo "Hello!"
-        |  }
-        |  output {
-        |    String empty = ""
-        |  }
-        |  RUNTIME
-        |}
-        |
-        |task goodbye {
-        |  String emptyInputString
-        |  command {
-        |    echo "$${emptyInputString}"
-        |  }
-        |  output {
-        |    String empty = read_string(stdout())
-        |  }
-        |  RUNTIME
-        |}
-        |
-        |workflow wf_hello {
-        |  call hello
-        |  call goodbye {input: emptyInputString=hello.empty }
-        |  output {
-        |   hello.empty
-        |   goodbye.empty
-        |  }
-        |}
+         |task hello {
+         |  command {
+         |    echo "Hello!"
+         |  }
+         |  output {
+         |    String empty = ""
+         |  }
+         |  RUNTIME
+         |}
+         |
+         |task goodbye {
+         |  String emptyInputString
+         |  command {
+         |    echo "$${emptyInputString}"
+         |  }
+         |  output {
+         |    String empty = read_string(stdout())
+         |  }
+         |  RUNTIME
+         |}
+         |
+         |workflow wf_hello {
+         |  call hello
+         |  call goodbye {input: emptyInputString=hello.empty }
+         |  output {
+         |   hello.empty
+         |   goodbye.empty
+         |  }
+         |}
       """.stripMargin.replace("RUNTIME", runtime)
 
     val rawInputs = Map.empty[String, Any]
@@ -196,32 +203,31 @@ object SampleWdl {
   }
 
   object CoercionNotDefined extends SampleWdl {
-    override def workflowSource(runtime: String = ""): WorkflowSource = {
+    override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""
-        |task summary {
-        |  String bfile
-        |  command {
-        |    ~/plink --bfile $${bfile} --missing --hardy --out foo --allow-no-sex
-        |  }
-        |  output {
-        |    File hwe = "foo.hwe"
-        |    File log = "foo.log"
-        |    File imiss = "foo.imiss"
-        |    File lmiss = "foo.lmiss"
-        |  }
-        |  meta {
-        |    author: "Jackie Goldstein"
-        |    email: "jigold@broadinstitute.org"
-        |  }
-        |}
-        |
-        |workflow test1 {
-        |  call summary {
-        |     input: bfile = bfile
-        |  }
-        |}
+         |task summary {
+         |  String bfile
+         |  command {
+         |    ~/plink --bfile $${bfile} --missing --hardy --out foo --allow-no-sex
+         |  }
+         |  output {
+         |    File hwe = "foo.hwe"
+         |    File log = "foo.log"
+         |    File imiss = "foo.imiss"
+         |    File lmiss = "foo.lmiss"
+         |  }
+         |  meta {
+         |    author: "Jackie Goldstein"
+         |    email: "jigold@broadinstitute.org"
+         |  }
+         |}
+         |
+         |workflow test1 {
+         |  call summary {
+         |     input: bfile = bfile
+         |  }
+         |}
       """.stripMargin
-    }
 
     override val rawInputs: ExecutableInputMap = Map("test1.bfile" -> "data/example1")
   }
@@ -281,67 +287,66 @@ object SampleWdl {
       withPlaceholders.stripMargin.replace(outputSectionPlaceholder, outputsSection)
     }
 
-    val PatternKey ="three_step.cgrep.pattern"
+    val PatternKey = "three_step.cgrep.pattern"
     override lazy val rawInputs = Map(PatternKey -> "...")
   }
 
   object ThreeStep extends ThreeStepTemplate
 
   object ThreeStepWithOutputsSection extends ThreeStepTemplate {
-    override def workflowSource(runtime: String = ""): WorkflowJson = sourceString(outputsSection =
-      """
-        |output {
-        | cgrep.count
-        | wc.count
-        |}
+    override def workflowSource(runtime: String = ""): WorkflowJson = sourceString(outputsSection = """
+                                                                                                      |output {
+                                                                                                      | cgrep.count
+                                                                                                      | wc.count
+                                                                                                      |}
       """.stripMargin).replaceAll("RUNTIME", runtime)
   }
 
   object DeclarationsWorkflow extends SampleWdl {
     override def workflowSource(runtime: String): WorkflowSource =
       s"""
-        |task cat {
-        |  File file
-        |  String? flags
-        |  String? flags2 # This should be a workflow input
-        |  command {
-        |    cat $${flags} $${flags2} $${file}
-        |  }
-        |  output {
-        |    File procs = stdout()
-        |  }
-        |}
-        |
-        |task cgrep {
-        |  String str_decl
-        |  String pattern
-        |  File in_file
-        |  command {
-        |    grep '$${pattern}' $${in_file} | wc -l
-        |  }
-        |  output {
-        |    Int count = read_int(stdout())
-        |    String str = str_decl
-        |  }
-        |}
-        |
-        |workflow two_step {
-        |  String flags_suffix
-        |  String flags = "-" + flags_suffix
-        |  String static_string = "foobarbaz"
-        |  call cat {
-        |    input: flags = flags
-        |  }
-        |  call cgrep {
-        |    input: in_file = cat.procs
-        |  }
-        |}
+         |task cat {
+         |  File file
+         |  String? flags
+         |  String? flags2 # This should be a workflow input
+         |  command {
+         |    cat $${flags} $${flags2} $${file}
+         |  }
+         |  output {
+         |    File procs = stdout()
+         |  }
+         |}
+         |
+         |task cgrep {
+         |  String str_decl
+         |  String pattern
+         |  File in_file
+         |  command {
+         |    grep '$${pattern}' $${in_file} | wc -l
+         |  }
+         |  output {
+         |    Int count = read_int(stdout())
+         |    String str = str_decl
+         |  }
+         |}
+         |
+         |workflow two_step {
+         |  String flags_suffix
+         |  String flags = "-" + flags_suffix
+         |  String static_string = "foobarbaz"
+         |  call cat {
+         |    input: flags = flags
+         |  }
+         |  call cgrep {
+         |    input: in_file = cat.procs
+         |  }
+         |}
       """.stripMargin
 
     private val fileContents =
       s"""first line
-          |second line
-          |third line
+         |second line
+         |third line
        """.stripMargin
 
     override val rawInputs: ExecutableInputMap = Map(
@@ -446,94 +451,94 @@ object SampleWdl {
   object ArrayIO extends SampleWdl {
     override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""
-        |task serialize {
-        |  Array[String] strs
-        |  command {
-        |    cat $${write_lines(strs)}
-        |  }
-        |  output {
-        |    String contents = read_string(stdout())
-        |  }
-        |  RUNTIME
-        |}
-        |
-        |workflow wf {
-        |  Array[String] strings = ["str1", "str2", "str3"]
-        |  call serialize {
-        |    input: strs = strings
-        |  }
-        |}
+         |task serialize {
+         |  Array[String] strs
+         |  command {
+         |    cat $${write_lines(strs)}
+         |  }
+         |  output {
+         |    String contents = read_string(stdout())
+         |  }
+         |  RUNTIME
+         |}
+         |
+         |workflow wf {
+         |  Array[String] strings = ["str1", "str2", "str3"]
+         |  call serialize {
+         |    input: strs = strings
+         |  }
+         |}
       """.stripMargin.replace("RUNTIME", runtime)
     override val rawInputs: Map[String, Any] = Map.empty
   }
 
   class ScatterWdl extends SampleWdl {
     val tasks: String = s"""task A {
-      |  command {
-      |    echo -n -e "jeff\nchris\nmiguel\nthibault\nkhalid\nruchi"
-      |  }
-      |  RUNTIME
-      |  output {
-      |    Array[String] A_out = read_lines(stdout())
-      |  }
-      |}
-      |
-      |task B {
-      |  String B_in
-      |  command {
-      |    python -c "print(len('$${B_in}'))"
-      |  }
-      |  RUNTIME
-      |  output {
-      |    Int B_out = read_int(stdout())
-      |  }
-      |}
-      |
-      |task C {
-      |  Int C_in
-      |  command {
-      |    python -c "print($${C_in}*100)"
-      |  }
-      |  RUNTIME
-      |  output {
-      |    Int C_out = read_int(stdout())
-      |  }
-      |}
-      |
-      |task D {
-      |  Array[Int] D_in
-      |  command {
-      |    python -c "print($${sep = '+' D_in})"
-      |  }
-      |  RUNTIME
-      |  output {
-      |    Int D_out = read_int(stdout())
-      |  }
-      |}
-      |
-      |task E {
-      |  command {
-      |    python -c "print(9)"
-      |  }
-      |  RUNTIME
-      |  output {
-      |    Int E_out = read_int(stdout())
-      |  }
-      |}
+                           |  command {
+                           |    echo -n -e "jeff\nchris\nmiguel\nthibault\nkhalid\nruchi"
+                           |  }
+                           |  RUNTIME
+                           |  output {
+                           |    Array[String] A_out = read_lines(stdout())
+                           |  }
+                           |}
+                           |
+                           |task B {
+                           |  String B_in
+                           |  command {
+                           |    python -c "print(len('$${B_in}'))"
+                           |  }
+                           |  RUNTIME
+                           |  output {
+                           |    Int B_out = read_int(stdout())
+                           |  }
+                           |}
+                           |
+                           |task C {
+                           |  Int C_in
+                           |  command {
+                           |    python -c "print($${C_in}*100)"
+                           |  }
+                           |  RUNTIME
+                           |  output {
+                           |    Int C_out = read_int(stdout())
+                           |  }
+                           |}
+                           |
+                           |task D {
+                           |  Array[Int] D_in
+                           |  command {
+                           |    python -c "print($${sep = '+' D_in})"
+                           |  }
+                           |  RUNTIME
+                           |  output {
+                           |    Int D_out = read_int(stdout())
+                           |  }
+                           |}
+                           |
+                           |task E {
+                           |  command {
+                           |    python -c "print(9)"
+                           |  }
+                           |  RUNTIME
+                           |  output {
+                           |    Int E_out = read_int(stdout())
+                           |  }
+                           |}
     """.stripMargin
 
     override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""$tasks
-        |
-        |workflow w {
-        |  call A
-        |  scatter (item in A.A_out) {
-        |    call B {input: B_in = item}
-        |    call C {input: C_in = B.B_out}
-        |    call E
-        |  }
-        |  call D {input: D_in = B.B_out}
-        |}
+         |
+         |workflow w {
+         |  call A
+         |  scatter (item in A.A_out) {
+         |    call B {input: B_in = item}
+         |    call C {input: C_in = B.B_out}
+         |    call E
+         |  }
+         |  call D {input: D_in = B.B_out}
+         |}
       """.stripMargin.replace("RUNTIME", runtime)
 
     override lazy val rawInputs = Map.empty[String, String]
@@ -542,21 +547,21 @@ object SampleWdl {
   object SimpleScatterWdl extends SampleWdl {
     override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""task echo_int {
-        |  Int int
-        |  command {echo $${int}}
-        |  output {Int out = read_int(stdout())}
-        |  RUNTIME_PLACEHOLDER
-        |}
-        |
-        |workflow scatter0 {
-        |  Array[Int] ints = [1,2,3,4,5]
-        |  call echo_int as outside_scatter {input: int = 8000}
-        |  scatter(i in ints) {
-        |    call echo_int as inside_scatter {
-        |      input: int = i
-        |    }
-        |  }
-        |}
+         |  Int int
+         |  command {echo $${int}}
+         |  output {Int out = read_int(stdout())}
+         |  RUNTIME_PLACEHOLDER
+         |}
+         |
+         |workflow scatter0 {
+         |  Array[Int] ints = [1,2,3,4,5]
+         |  call echo_int as outside_scatter {input: int = 8000}
+         |  scatter(i in ints) {
+         |    call echo_int as inside_scatter {
+         |      input: int = i
+         |    }
+         |  }
+         |}
       """.stripMargin.replace("RUNTIME_PLACEHOLDER", runtime)
 
     override lazy val rawInputs = Map.empty[String, String]
@@ -565,108 +570,108 @@ object SampleWdl {
   object SimpleScatterWdlWithOutputs extends SampleWdl {
     override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""task echo_int {
-        |  Int int
-        |  command {echo $${int}}
-        |  output {Int out = read_int(stdout())}
-        |}
-        |
-        |workflow scatter0 {
-        |  Array[Int] ints = [1,2,3,4,5]
-        |  call echo_int as outside_scatter {input: int = 8000}
-        |  scatter(i in ints) {
-        |    call echo_int as inside_scatter {
-        |      input: int = i
-        |    }
-        |  }
-        |  output {
-        |    inside_scatter.*
-        |  }
-        |}
+         |  Int int
+         |  command {echo $${int}}
+         |  output {Int out = read_int(stdout())}
+         |}
+         |
+         |workflow scatter0 {
+         |  Array[Int] ints = [1,2,3,4,5]
+         |  call echo_int as outside_scatter {input: int = 8000}
+         |  scatter(i in ints) {
+         |    call echo_int as inside_scatter {
+         |      input: int = i
+         |    }
+         |  }
+         |  output {
+         |    inside_scatter.*
+         |  }
+         |}
       """.stripMargin
 
     override lazy val rawInputs = Map.empty[String, String]
   }
 
   case class PrepareScatterGatherWdl(salt: String = UUID.randomUUID().toString) extends SampleWdl {
-    override def workflowSource(runtime: String = ""): WorkflowSource = {
+    override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""
-        |#
-        |# Goal here is to split up the input file into files of 1 line each (in the prepare) then in parallel call wc -w on each newly created file and count the words into another file then in the gather, sum the results of each parallel call to come up with
-        |# the word-count for the fil
-        |#
-        |# splits each line into a file with the name temp_?? (shuffle)
-        |task do_prepare {
-        |    File input_file
-        |    command {
-        |        split -l 1 $${input_file} temp_ && ls -1 temp_?? > files.list
-        |    }
-        |    output {
-        |        Array[File] split_files = read_lines("files.list")
-        |    }
-        |    RUNTIME
-        |}
-        |# count the number of words in the input file, writing the count to an output file overkill in this case, but simulates a real scatter-gather that would just return an Int (map)
-        |task do_scatter {
-        |    String salt
-        |    File input_file
-        |    command {
-        |        # $${salt}
-        |        wc -w $${input_file} > output.txt
-        |    }
-        |    output {
-        |        File count_file = "output.txt"
-        |    }
-        |    RUNTIME
-        |}
-        |# aggregate the results back together (reduce)
-        |task do_gather {
-        |    Array[File] input_files
-        |    command <<<
-        |        cat $${sep = ' ' input_files} | awk '{s+=$$1} END {print s}'
-        |    >>>
-        |    output {
-        |        Int sum = read_int(stdout())
-        |    }
-        |    RUNTIME
-        |}
-        |workflow sc_test {
-        |    call do_prepare
-        |    scatter(f in do_prepare.split_files) {
-        |        call do_scatter {
-        |            input: input_file = f
-        |        }
-        |    }
-        |    call do_gather {
-        |        input: input_files = do_scatter.count_file
-        |    }
-        |}
+         |#
+         |# Goal here is to split up the input file into files of 1 line each (in the prepare) then in parallel call wc -w on each newly created file and count the words into another file then in the gather, sum the results of each parallel call to come up with
+         |# the word-count for the fil
+         |#
+         |# splits each line into a file with the name temp_?? (shuffle)
+         |task do_prepare {
+         |    File input_file
+         |    command {
+         |        split -l 1 $${input_file} temp_ && ls -1 temp_?? > files.list
+         |    }
+         |    output {
+         |        Array[File] split_files = read_lines("files.list")
+         |    }
+         |    RUNTIME
+         |}
+         |# count the number of words in the input file, writing the count to an output file overkill in this case, but simulates a real scatter-gather that would just return an Int (map)
+         |task do_scatter {
+         |    String salt
+         |    File input_file
+         |    command {
+         |        # $${salt}
+         |        wc -w $${input_file} > output.txt
+         |    }
+         |    output {
+         |        File count_file = "output.txt"
+         |    }
+         |    RUNTIME
+         |}
+         |# aggregate the results back together (reduce)
+         |task do_gather {
+         |    Array[File] input_files
+         |    command <<<
+         |        cat $${sep = ' ' input_files} | awk '{s+=$$1} END {print s}'
+         |    >>>
+         |    output {
+         |        Int sum = read_int(stdout())
+         |    }
+         |    RUNTIME
+         |}
+         |workflow sc_test {
+         |    call do_prepare
+         |    scatter(f in do_prepare.split_files) {
+         |        call do_scatter {
+         |            input: input_file = f
+         |        }
+         |    }
+         |    call do_gather {
+         |        input: input_files = do_scatter.count_file
+         |    }
+         |}
       """.stripMargin.replace("RUNTIME", runtime)
-    }
 
     val contents: String =
-        """|the
-           |total number
-           |of words in this
-           |text file is 11
-           |""".stripMargin
+      """|the
+         |total number
+         |of words in this
+         |text file is 11
+         |""".stripMargin
 
     override lazy val rawInputs = Map(
       "sc_test.do_prepare.input_file" -> createCannedFile("scatter", contents).pathAsString,
-      "sc_test.do_scatter.salt" -> salt)
+      "sc_test.do_scatter.salt" -> salt
+    )
   }
 
   object FileClobber extends SampleWdl {
     override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""task read_line {
-        |  File in
-        |  command { cat $${in} }
-        |  output { String out = read_string(stdout()) }
-        |}
-        |
-        |workflow two {
-        |  call read_line as x
-        |  call read_line as y
-        |}
+         |  File in
+         |  command { cat $${in} }
+         |  output { String out = read_string(stdout()) }
+         |}
+         |
+         |workflow two {
+         |  call read_line as x
+         |  call read_line as y
+         |}
       """.stripMargin
 
     val tempDir1: DefaultPath = DefaultPathBuilder.createTempDirectory("FileClobber1")
@@ -683,26 +688,26 @@ object SampleWdl {
   object FilePassingWorkflow extends SampleWdl {
     override def workflowSource(runtime: String): WorkflowSource =
       s"""task a {
-        |  File in
-        |  String out_name = "out"
-        |
-        |  command {
-        |    cat $${in} > $${out_name}
-        |  }
-        |  RUNTIME
-        |  output {
-        |    File out = "out"
-        |    File out_interpolation = "$${out_name}"
-        |    String contents = read_string("$${out_name}")
-        |  }
-        |}
-        |
-        |workflow file_passing {
-        |  File f
-        |
-        |  call a {input: in = f}
-        |  call a as b {input: in = a.out}
-        |}
+         |  File in
+         |  String out_name = "out"
+         |
+         |  command {
+         |    cat $${in} > $${out_name}
+         |  }
+         |  RUNTIME
+         |  output {
+         |    File out = "out"
+         |    File out_interpolation = "$${out_name}"
+         |    String contents = read_string("$${out_name}")
+         |  }
+         |}
+         |
+         |workflow file_passing {
+         |  File f
+         |
+         |  call a {input: in = f}
+         |  call a as b {input: in = a.out}
+         |}
       """.stripMargin.replace("RUNTIME", runtime)
 
     private val fileContents = s"foo bar baz"
@@ -723,30 +728,30 @@ object SampleWdl {
   case class CallCachingWorkflow(salt: String) extends SampleWdl {
     override def workflowSource(runtime: String): WorkflowSource =
       s"""task a {
-        |  File in
-        |  String out_name = "out"
-        |  String salt
-        |
-        |  command {
-        |    # $${salt}
-        |    echo "Something"
-        |    cat $${in} > $${out_name}
-        |  }
-        |  RUNTIME
-        |  output {
-        |    File out = "out"
-        |    File out_interpolation = "$${out_name}"
-        |    String contents = read_string("$${out_name}")
-        |    Array[String] stdoutContent = read_lines(stdout())
-        |  }
-        |}
-        |
-        |workflow file_passing {
-        |  File f
-        |
-        |  call a {input: in = f}
-        |  call a as b {input: in = a.out}
-        |}
+         |  File in
+         |  String out_name = "out"
+         |  String salt
+         |
+         |  command {
+         |    # $${salt}
+         |    echo "Something"
+         |    cat $${in} > $${out_name}
+         |  }
+         |  RUNTIME
+         |  output {
+         |    File out = "out"
+         |    File out_interpolation = "$${out_name}"
+         |    String contents = read_string("$${out_name}")
+         |    Array[String] stdoutContent = read_lines(stdout())
+         |  }
+         |}
+         |
+         |workflow file_passing {
+         |  File f
+         |
+         |  call a {input: in = f}
+         |  call a as b {input: in = a.out}
+         |}
       """.stripMargin.replace("RUNTIME", runtime)
 
     private val fileContents = s"foo bar baz"
@@ -761,29 +766,29 @@ object SampleWdl {
   object CallCachingHashingWdl extends SampleWdl {
     override def workflowSource(runtime: String): WorkflowSource =
       s"""task t {
-        |  Int a
-        |  Float b
-        |  String c
-        |  File d
-        |
-        |  command {
-        |    echo "$${a}" > a
-        |    echo "$${b}" > b
-        |    echo "$${c}" > c
-        |    cat $${d} > d
-        |  }
-        |  output {
-        |    Int w = read_int("a") + 2
-        |    Float x = read_float("b")
-        |    String y = read_string("c")
-        |    File z = "d"
-        |  }
-        |  RUNTIME
-        |}
-        |
-        |workflow w {
-        |  call t
-        |}
+         |  Int a
+         |  Float b
+         |  String c
+         |  File d
+         |
+         |  command {
+         |    echo "$${a}" > a
+         |    echo "$${b}" > b
+         |    echo "$${c}" > c
+         |    cat $${d} > d
+         |  }
+         |  output {
+         |    Int w = read_int("a") + 2
+         |    Float x = read_float("b")
+         |    String y = read_string("c")
+         |    File z = "d"
+         |  }
+         |  RUNTIME
+         |}
+         |
+         |workflow w {
+         |  call t
+         |}
       """.stripMargin.replace("RUNTIME", runtime)
 
     val tempDir: DefaultPath = DefaultPathBuilder.createTempDirectory("CallCachingHashingWdl")
@@ -799,26 +804,26 @@ object SampleWdl {
   object ExpressionsInInputs extends SampleWdl {
     override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""task echo {
-        |  String inString
-        |  command {
-        |    echo $${inString}
-        |  }
-        |
-        |  output {
-        |    String outString = read_string(stdout())
-        |  }
-        |}
-        |
-        |workflow wf {
-        |  String a1
-        |  String a2
-        |  call echo {
-        |   input: inString = a1 + " " + a2
-        |  }
-        |  call echo as echo2 {
-        |    input: inString = a1 + " " + echo.outString + " " + a2
-        |  }
-        |}
+         |  String inString
+         |  command {
+         |    echo $${inString}
+         |  }
+         |
+         |  output {
+         |    String outString = read_string(stdout())
+         |  }
+         |}
+         |
+         |workflow wf {
+         |  String a1
+         |  String a2
+         |  call echo {
+         |   input: inString = a1 + " " + a2
+         |  }
+         |  call echo as echo2 {
+         |    input: inString = a1 + " " + echo.outString + " " + a2
+         |  }
+         |}
       """.stripMargin
     override val rawInputs = Map(
       "wf.a1" -> WomString("hello"),
@@ -830,61 +835,61 @@ object SampleWdl {
     override def workflowSource(runtime: String = ""): WorkflowSource =
       s"""
 task shouldCompleteFast {
-        |    Int a
-        |    command {
-        |        echo "The number was: $${a}"
-        |    }
-        |    output {
-        |        Int echo = a
-        |    }
-        |}
-        |
-        |task shouldCompleteSlow {
-        |    Int a
-        |    command {
-        |        echo "The number was: $${a}"
-        |        # More than 1 so this should finish second
-        |        sleep 2
-        |    }
-        |    output {
-        |        Int echo = a
-        |    }
-        |}
-        |
-        |task failMeSlowly {
-        |    Int a
-        |    command {
-        |        echo "The number was: $${a}"
-        |        # Less than 2 so this should finish first
-        |        sleep 1
-        |        ./NOOOOOO
-        |    }
-        |    output {
-        |        Int echo = a
-        |    }
-        |}
-        |
-        |task shouldNeverRun {
-        |    Int a
-        |    Int b
-        |    command {
-        |        echo "You can't fight in here - this is the war room $${a + b}"
-        |    }
-        |    output {
-        |        Int echo = a
-        |    }
-        |}
-        |
-        |workflow wf {
-        |    call shouldCompleteFast as A { input: a = 5 }
-        |    call shouldCompleteFast as B { input: a = 5 }
-        |
-        |    call failMeSlowly as ohNOOOOOOOO { input: a = A.echo }
-        |    call shouldCompleteSlow as C { input: a = B.echo }
-        |
-        |    call shouldNeverRun as D { input: a = ohNOOOOOOOO.echo, b = C.echo }
-        |    call shouldCompleteSlow as E { input: a = C.echo }
-        |}
+         |    Int a
+         |    command {
+         |        echo "The number was: $${a}"
+         |    }
+         |    output {
+         |        Int echo = a
+         |    }
+         |}
+         |
+         |task shouldCompleteSlow {
+         |    Int a
+         |    command {
+         |        echo "The number was: $${a}"
+         |        # More than 1 so this should finish second
+         |        sleep 2
+         |    }
+         |    output {
+         |        Int echo = a
+         |    }
+         |}
+         |
+         |task failMeSlowly {
+         |    Int a
+         |    command {
+         |        echo "The number was: $${a}"
+         |        # Less than 2 so this should finish first
+         |        sleep 1
+         |        ./NOOOOOO
+         |    }
+         |    output {
+         |        Int echo = a
+         |    }
+         |}
+         |
+         |task shouldNeverRun {
+         |    Int a
+         |    Int b
+         |    command {
+         |        echo "You can't fight in here - this is the war room $${a + b}"
+         |    }
+         |    output {
+         |        Int echo = a
+         |    }
+         |}
+         |
+         |workflow wf {
+         |    call shouldCompleteFast as A { input: a = 5 }
+         |    call shouldCompleteFast as B { input: a = 5 }
+         |
+         |    call failMeSlowly as ohNOOOOOOOO { input: a = A.echo }
+         |    call shouldCompleteSlow as C { input: a = B.echo }
+         |
+         |    call shouldNeverRun as D { input: a = ohNOOOOOOOO.echo, b = C.echo }
+         |    call shouldCompleteSlow as E { input: a = C.echo }
+         |}
       """.stripMargin
 
     val rawInputs = Map(
diff --git a/core/src/test/scala/cromwell/util/TestFileUtil.scala b/core/src/test/scala/cromwell/util/TestFileUtil.scala
index dbdad8a47ed..f13fb57891b 100644
--- a/core/src/test/scala/cromwell/util/TestFileUtil.scala
+++ b/core/src/test/scala/cromwell/util/TestFileUtil.scala
@@ -17,9 +17,8 @@ trait TestFileUtil {
     tempFile.write(contents)
   }
 
-  def createFile(name: String, dir: Path, contents: String): Path = {
+  def createFile(name: String, dir: Path, contents: String): Path =
     dir.createPermissionedDirectories()./(name).write(contents)
-  }
 }
 
 trait HashUtil extends TestFileUtil {
@@ -36,6 +35,7 @@ trait HashUtil extends TestFileUtil {
 
 object ErrorOrUtil {
   implicit class EnhancedErrorOr[A](val value: ErrorOr[A]) extends AnyVal {
+
     /** Extract a value from an `ErrorOr` box if the box is `Valid`, throw an exception if the box is `Invalid`.
       * For test code only. */
     def get: A = value match {
diff --git a/core/src/test/scala/cromwell/util/TryWithResourceSpec.scala b/core/src/test/scala/cromwell/util/TryWithResourceSpec.scala
index 0764bdd9826..b15cdcebec7 100644
--- a/core/src/test/scala/cromwell/util/TryWithResourceSpec.scala
+++ b/core/src/test/scala/cromwell/util/TryWithResourceSpec.scala
@@ -11,31 +11,34 @@ class TryWithResourceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   behavior of "tryWithResource"
 
   it should "catch instantiation errors" in {
-    val triedMyBest = tryWithResource(() => if (1 == 1) throw InstantiationException else null) { _ => 5 }
+    val triedMyBest = tryWithResource(() => if (1 == 1) throw InstantiationException else null)(_ => 5)
     triedMyBest should be(Failure(InstantiationException))
   }
 
   it should "close the closeable" in {
     val myCloseable = new MyCloseable
-    val triedMyBest = tryWithResource(() => myCloseable) { _.value } // Nothing special about 5... Just need to return something!
+    val triedMyBest = tryWithResource(() => myCloseable) {
+      _.value
+    } // Nothing special about 5... Just need to return something!
     triedMyBest should be(Success(5))
     myCloseable.isClosed should be(true)
   }
 
   it should "catch errors and still close the closeable" in {
     val myCloseable = new MyCloseable
-    val triedMyBest = tryWithResource(() => myCloseable) { _.badValue }
+    val triedMyBest = tryWithResource(() => myCloseable)(_.badValue)
     triedMyBest should be(Failure(ReadValueException))
     myCloseable.isClosed should be(true)
   }
 
   it should "be robust to failures in close methods" in {
     val myCloseable = new FailingCloseable
-    val triedMyBest = tryWithResource(() => myCloseable) { _.value }
+    val triedMyBest = tryWithResource(() => myCloseable)(_.value)
     triedMyBest should be(Failure(CloseCloseableException))
-    val triedMyBest2 = tryWithResource(() => myCloseable) { _.badValue }
+    val triedMyBest2 = tryWithResource(() => myCloseable)(_.badValue)
     triedMyBest2 match {
-      case Failure(ReadValueException) => ReadValueException.getSuppressed.headOption should be(Some(CloseCloseableException))
+      case Failure(ReadValueException) =>
+        ReadValueException.getSuppressed.headOption should be(Some(CloseCloseableException))
       case x => fail(s"$x was not equal to $ReadValueException")
     }
   }
@@ -47,9 +50,8 @@ class MyCloseable extends AutoCloseable {
   val value = if (isClosed) throw ReadValueException else 5 // Ensures we aren't closed when .value is called
   def badValue = throw ReadValueException
 
-  override def close() = {
+  override def close() =
     isClosed = true
-  }
 }
 
 class FailingCloseable extends MyCloseable {
diff --git a/core/src/test/scala/cromwell/util/WomMocks.scala b/core/src/test/scala/cromwell/util/WomMocks.scala
index 2dc75385658..07111be17ce 100644
--- a/core/src/test/scala/cromwell/util/WomMocks.scala
+++ b/core/src/test/scala/cromwell/util/WomMocks.scala
@@ -6,44 +6,71 @@ import wom.RuntimeAttributes
 import wom.callable.Callable.OutputDefinition
 import wom.callable.{CallableTaskDefinition, CommandTaskDefinition, WorkflowDefinition}
 import wom.graph.GraphNodePort.{GraphNodeOutputPort, OutputPort}
-import wom.graph.{Graph, CommandCallNode, WomIdentifier, WorkflowCallNode}
+import wom.graph.{CommandCallNode, Graph, WomIdentifier, WorkflowCallNode}
 import wom.types.{WomStringType, WomType}
 import wom.values.WomValue
 
 object WomMocks {
-  val EmptyTaskDefinition = CallableTaskDefinition("emptyTask", Function.const(List.empty.validNel), RuntimeAttributes(Map.empty),
-    Map.empty, Map.empty, List.empty, List.empty, Set.empty, Map.empty, sourceLocation = None)
+  val EmptyTaskDefinition = CallableTaskDefinition(
+    "emptyTask",
+    Function.const(List.empty.validNel),
+    RuntimeAttributes(Map.empty),
+    Map.empty,
+    Map.empty,
+    List.empty,
+    List.empty,
+    Set.empty,
+    Map.empty,
+    sourceLocation = None
+  )
 
   val EmptyWorkflowDefinition = mockWorkflowDefinition("emptyWorkflow")
 
-  def mockTaskCall(identifier: WomIdentifier, definition: CommandTaskDefinition = EmptyTaskDefinition) = {
-    CommandCallNode(identifier, definition, Set.empty, List.empty, Set.empty, (_, localName) => WomIdentifier(localName = localName), None)
-  }
+  def mockTaskCall(identifier: WomIdentifier, definition: CommandTaskDefinition = EmptyTaskDefinition) =
+    CommandCallNode(identifier,
+                    definition,
+                    Set.empty,
+                    List.empty,
+                    Set.empty,
+                    (_, localName) => WomIdentifier(localName = localName),
+                    None
+    )
 
-  def mockWorkflowCall(identifier: WomIdentifier, definition: WorkflowDefinition = EmptyWorkflowDefinition) = {
-    WorkflowCallNode(identifier, definition, Set.empty, List.empty, Set.empty, (_, localName) => identifier.combine(localName), None)
-  }
+  def mockWorkflowCall(identifier: WomIdentifier, definition: WorkflowDefinition = EmptyWorkflowDefinition) =
+    WorkflowCallNode(identifier,
+                     definition,
+                     Set.empty,
+                     List.empty,
+                     Set.empty,
+                     (_, localName) => identifier.combine(localName),
+                     None
+    )
 
-  def mockWorkflowDefinition(name: String) = {
+  def mockWorkflowDefinition(name: String) =
     WorkflowDefinition(name, Graph(Set.empty), Map.empty, Map.empty, None)
-  }
 
-  def mockTaskDefinition(name: String) = {
-    CallableTaskDefinition(name, Function.const(List.empty.validNel), RuntimeAttributes(Map.empty),
-      Map.empty, Map.empty, List.empty, List.empty, Set.empty, Map.empty, sourceLocation = None)
-  }
+  def mockTaskDefinition(name: String) =
+    CallableTaskDefinition(
+      name,
+      Function.const(List.empty.validNel),
+      RuntimeAttributes(Map.empty),
+      Map.empty,
+      Map.empty,
+      List.empty,
+      List.empty,
+      Set.empty,
+      Map.empty,
+      sourceLocation = None
+    )
 
-  def mockOutputPort(name: String, womType: WomType = WomStringType): OutputPort = {
+  def mockOutputPort(name: String, womType: WomType = WomStringType): OutputPort =
     GraphNodeOutputPort(WomIdentifier(name, name), womType, null)
-  }
 
-  def mockOutputPort(outputDefinition: OutputDefinition): OutputPort = {
+  def mockOutputPort(outputDefinition: OutputDefinition): OutputPort =
     GraphNodeOutputPort(WomIdentifier(outputDefinition.name, outputDefinition.name), outputDefinition.womType, null)
-  }
 
-  def mockOutputExpectations(outputs: Map[String, WomValue]): CallOutputs = {
-    CallOutputs(outputs.map {
-      case (key, value) => WomMocks.mockOutputPort(key, value.womType) -> value
+  def mockOutputExpectations(outputs: Map[String, WomValue]): CallOutputs =
+    CallOutputs(outputs.map { case (key, value) =>
+      WomMocks.mockOutputPort(key, value.womType) -> value
     })
-  }
 }
diff --git a/core/src/test/scala/cromwell/util/WomValueJsonFormatterSpec.scala b/core/src/test/scala/cromwell/util/WomValueJsonFormatterSpec.scala
index 1c4cc15dfdd..69739d9868f 100644
--- a/core/src/test/scala/cromwell/util/WomValueJsonFormatterSpec.scala
+++ b/core/src/test/scala/cromwell/util/WomValueJsonFormatterSpec.scala
@@ -4,7 +4,7 @@ import common.assertion.CromwellTimeoutSpec
 import cromwell.util.JsonFormatting.WomValueJsonFormatter.WomValueJsonFormat
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
-import spray.json.{JsObject, enrichString}
+import spray.json.{enrichString, JsObject}
 import wom.types._
 import wom.values._
 
@@ -15,7 +15,7 @@ class WomValueJsonFormatterSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
   it should "write WdlPair to left/right structured JsObject" in {
     val left = "sanders"
     val right = Vector("rubio", "carson", "cruz")
-    val wdlPair = WomPair(WomString(left), WomArray(WomArrayType(WomStringType), right.map { WomString(_) }))
+    val wdlPair = WomPair(WomString(left), WomArray(WomArrayType(WomStringType), right.map(WomString(_))))
     val ExpectedJson: JsObject =
       """|{
          |  "left": "sanders",
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
index 3b7be2b38bd..2dbe3fa6c27 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
@@ -4,7 +4,6 @@ import common.util.VersionUtil
 import drs.localizer.CommandLineParser.AccessTokenStrategy._
 import drs.localizer.CommandLineParser.Usage
 
-
 class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage) {
   lazy val localizerVersion: String = VersionUtil.getVersion("cromwell-drs-localizer")
 
@@ -14,31 +13,30 @@ class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage)
 
   head("cromwell-drs-localizer", localizerVersion)
 
-  arg[String]("drs-object-id").text("DRS object ID").optional().
-    action((s, c) =>
-      c.copy(drsObject = Option(s)))
-  arg[String]("container-path").text("Container path").optional().
-    action((s, c) =>
-      c.copy(containerPath = Option(s)))
-  arg[String]("requester-pays-project").text(s"Requester pays project (only valid with '$Google' auth strategy)").optional().
-    action((s, c) =>
-      c.copy(googleRequesterPaysProject = Option(s)))
-  opt[String]('m', "manifest-path").text("File path of manifest containing multiple files to localize").
-    action((s, c) =>
-      c.copy(manifestPath = Option(s)))
-  opt[String]('r', "requester-pays-project").text(s"Requester pays project (only valid with '$Google' auth strategy)").optional().
-    action((s, c) => {
+  arg[String]("drs-object-id").text("DRS object ID").optional().action((s, c) => c.copy(drsObject = Option(s)))
+  arg[String]("container-path").text("Container path").optional().action((s, c) => c.copy(containerPath = Option(s)))
+  arg[String]("requester-pays-project")
+    .text(s"Requester pays project (only valid with '$Google' auth strategy)")
+    .optional()
+    .action((s, c) => c.copy(googleRequesterPaysProject = Option(s)))
+  opt[String]('m', "manifest-path")
+    .text("File path of manifest containing multiple files to localize")
+    .action((s, c) => c.copy(manifestPath = Option(s)))
+  opt[String]('r', "requester-pays-project")
+    .text(s"Requester pays project (only valid with '$Google' auth strategy)")
+    .optional()
+    .action { (s, c) =>
       c.copy(
         googleRequesterPaysProject = Option(s),
         googleRequesterPaysProjectConflict = c.googleRequesterPaysProject.exists(_ != s)
       )
-    })
-  opt[String]('t', "access-token-strategy").text(s"Access token strategy, must be one of '$Azure' or '$Google' (default '$Google')").
-    action((s, c) =>
-      c.copy(accessTokenStrategy = Option(s.toLowerCase())))
-  opt[String]('i', "identity-client-id").text("Azure identity client id").
-    action((s, c) =>
-      c.copy(azureIdentityClientId = Option(s)))
+    }
+  opt[String]('t', "access-token-strategy")
+    .text(s"Access token strategy, must be one of '$Azure' or '$Google' (default '$Google')")
+    .action((s, c) => c.copy(accessTokenStrategy = Option(s.toLowerCase())))
+  opt[String]('i', "identity-client-id")
+    .text("Azure identity client id")
+    .action((s, c) => c.copy(azureIdentityClientId = Option(s)))
   checkConfig(c =>
     if (c.googleRequesterPaysProjectConflict)
       failure("Requester pays project differs between positional argument and option flag")
@@ -66,6 +64,7 @@ class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage)
 }
 
 object CommandLineParser {
+
   /**
    * These access token strategies are named simplistically as there is currently only one access token strategy being
    * used for each of these cloud vendors. But it is certainly possible that multiple strategies could come into use
@@ -95,4 +94,5 @@ case class CommandLineArguments(accessTokenStrategy: Option[String] = Option(Goo
                                 googleRequesterPaysProject: Option[String] = None,
                                 azureIdentityClientId: Option[String] = None,
                                 manifestPath: Option[String] = None,
-                                googleRequesterPaysProjectConflict: Boolean = false)
+                                googleRequesterPaysProjectConflict: Boolean = false
+)
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
index 944d418acbb..94cc30e103c 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
@@ -3,7 +3,7 @@ package drs.localizer
 import cloud.nio.impl.drs.{DrsConfig, DrsCredentials, DrsPathResolver}
 import common.validation.ErrorOr.ErrorOr
 
-
-class DrsLocalizerDrsPathResolver(drsConfig: DrsConfig, drsCredentials: DrsCredentials) extends DrsPathResolver(drsConfig) {
+class DrsLocalizerDrsPathResolver(drsConfig: DrsConfig, drsCredentials: DrsCredentials)
+    extends DrsPathResolver(drsConfig) {
   override def getAccessToken: ErrorOr[String] = drsCredentials.getAccessToken
 }
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
index 3d99538f614..29ad9d25bd1 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
@@ -43,16 +43,19 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
 
   // Default retry parameters for resolving a DRS url
   val defaultNumRetries: Int = 5
-  val defaultBackoff: CloudNioBackoff = CloudNioSimpleExponentialBackoff(
-    initialInterval = 1 seconds, maxInterval = 60 seconds, multiplier = 2)
+  val defaultBackoff: CloudNioBackoff =
+    CloudNioSimpleExponentialBackoff(initialInterval = 1 seconds, maxInterval = 60 seconds, multiplier = 2)
 
   val defaultDownloaderFactory: DownloaderFactory = new DownloaderFactory {
-    override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader =
+    override def buildGcsUriDownloader(gcsPath: String,
+                                       serviceAccountJsonOption: Option[String],
+                                       downloadLoc: String,
+                                       requesterPaysProjectOption: Option[String]
+    ): Downloader =
       GcsUriDownloader(gcsPath, serviceAccountJsonOption, downloadLoc, requesterPaysProjectOption)
 
-    override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+    override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader =
       BulkAccessUrlDownloader(urlsToDownload)
-    }
   }
 
   private def printUsage: IO[ExitCode] = {
@@ -64,52 +67,55 @@ object DrsLocalizerMain extends IOApp with StrictLogging {
     * Helper function to read a CSV file as pairs of drsURL -> local download destination.
     * @param csvManifestPath Path to a CSV file where each row is something like: drs://asdf.ghj, path/to/my/directory
     */
-  def loadCSVManifest(csvManifestPath: String): IO[List[UnresolvedDrsUrl]] = {
+  def loadCSVManifest(csvManifestPath: String): IO[List[UnresolvedDrsUrl]] =
     IO {
       val openFile = new File(csvManifestPath)
       val csvParser = CSVParser.parse(openFile, Charset.defaultCharset(), CSVFormat.DEFAULT)
-      try{
+      try
         csvParser.getRecords.asScala.map(record => UnresolvedDrsUrl(record.get(0), record.get(1))).toList
-      } finally {
+      finally
         csvParser.close()
-      }
     }
-  }
 
-  def runLocalizer(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials) : IO[ExitCode] = {
-    val urlList = (commandLineArguments.manifestPath, commandLineArguments.drsObject, commandLineArguments.containerPath) match {
-      case (Some(manifestPath), _, _) => {
-        loadCSVManifest(manifestPath)
-      }
-      case (_, Some(drsObject), Some(containerPath)) => {
-        IO.pure(List(UnresolvedDrsUrl(drsObject, containerPath)))
-      }
-      case(_,_,_) => {
-        throw new RuntimeException("Illegal command line arguments supplied to drs localizer.")
+  def runLocalizer(commandLineArguments: CommandLineArguments, drsCredentials: DrsCredentials): IO[ExitCode] = {
+    val urlList =
+      (commandLineArguments.manifestPath, commandLineArguments.drsObject, commandLineArguments.containerPath) match {
+        case (Some(manifestPath), _, _) =>
+          loadCSVManifest(manifestPath)
+        case (_, Some(drsObject), Some(containerPath)) =>
+          IO.pure(List(UnresolvedDrsUrl(drsObject, containerPath)))
+        case (_, _, _) =>
+          throw new RuntimeException("Illegal command line arguments supplied to drs localizer.")
       }
-    }
-    val main = new DrsLocalizerMain(urlList, defaultDownloaderFactory, drsCredentials, commandLineArguments.googleRequesterPaysProject)
+    val main = new DrsLocalizerMain(urlList,
+                                    defaultDownloaderFactory,
+                                    drsCredentials,
+                                    commandLineArguments.googleRequesterPaysProject
+    )
     main.resolveAndDownload().map(_.exitCode)
-    }
+  }
 
   /**
     * Helper function to decide which downloader to use based on data from the DRS response.
     * Throws a runtime exception if the DRS response is invalid.
     */
-  def toValidatedUriType(accessUrl: Option[AccessUrl], gsUri: Option[String]): URIType = {
+  def toValidatedUriType(accessUrl: Option[AccessUrl], gsUri: Option[String]): URIType =
     // if both are provided, prefer using access urls
     (accessUrl, gsUri) match {
       case (Some(_), _) =>
-        if(!accessUrl.get.url.startsWith("https://")) { throw new RuntimeException("Resolved Access URL does not start with https://")}
+        if (!accessUrl.get.url.startsWith("https://")) {
+          throw new RuntimeException("Resolved Access URL does not start with https://")
+        }
         URIType.ACCESS
       case (_, Some(_)) =>
-        if(!gsUri.get.startsWith("gs://")) { throw new RuntimeException("Resolved Google URL does not start with gs://")}
+        if (!gsUri.get.startsWith("gs://")) {
+          throw new RuntimeException("Resolved Google URL does not start with gs://")
+        }
         URIType.GCS
       case (_, _) =>
         throw new RuntimeException("DRS response did not contain any URLs")
     }
-  }
-  }
+}
 
 object URIType extends Enumeration {
   type URIType = Value
@@ -119,7 +125,8 @@ object URIType extends Enumeration {
 class DrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
                        downloaderFactory: DownloaderFactory,
                        drsCredentials: DrsCredentials,
-                       requesterPaysProjectIdOption: Option[String]) extends StrictLogging {
+                       requesterPaysProjectIdOption: Option[String]
+) extends StrictLogging {
 
   /**
     * This will:
@@ -132,18 +139,17 @@ class DrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
     val downloadResults = buildDownloaders().flatMap { downloaderList =>
       downloaderList.map(downloader => downloader.download).traverse(identity)
     }
-    downloadResults.map{list =>
+    downloadResults.map { list =>
       list.find(result => result != DownloadSuccess).getOrElse(DownloadSuccess)
     }
   }
 
-  def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] = {
+  def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] =
     IO {
       val drsConfig = DrsConfig.fromEnv(sys.env)
       logger.info(s"Using ${drsConfig.drsResolverUrl} to resolve DRS Objects")
       new DrsLocalizerDrsPathResolver(drsConfig, drsCredentials)
     }
-  }
 
   /**
     * After resolving all of the URLs, this sorts them into an "Access" or "GCS" bucket.
@@ -151,80 +157,97 @@ class DrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
     * All google URLs will be downloaded individually in their own google downloader.
     * @return List of all downloaders required to fulfill the request.
     */
-  def buildDownloaders() : IO[List[Downloader]] = {
+  def buildDownloaders(): IO[List[Downloader]] =
     resolveUrls(toResolveAndDownload).map { pendingDownloads =>
       val accessUrls = pendingDownloads.filter(url => url.uriType == URIType.ACCESS)
       val googleUrls = pendingDownloads.filter(url => url.uriType == URIType.GCS)
-      val bulkDownloader: List[Downloader] = if (accessUrls.isEmpty) List() else List(buildBulkAccessUrlDownloader(accessUrls))
+      val bulkDownloader: List[Downloader] =
+        if (accessUrls.isEmpty) List() else List(buildBulkAccessUrlDownloader(accessUrls))
       val googleDownloaders: List[Downloader] = if (googleUrls.isEmpty) List() else buildGoogleDownloaders(googleUrls)
       bulkDownloader ++ googleDownloaders
     }
-  }
 
-  def buildGoogleDownloaders(resolvedGoogleUrls: List[ResolvedDrsUrl]) : List[Downloader] = {
-    resolvedGoogleUrls.map{url=>
+  def buildGoogleDownloaders(resolvedGoogleUrls: List[ResolvedDrsUrl]): List[Downloader] =
+    resolvedGoogleUrls.map { url =>
       downloaderFactory.buildGcsUriDownloader(
         gcsPath = url.drsResponse.gsUri.get,
         serviceAccountJsonOption = url.drsResponse.googleServiceAccount.map(_.data.spaces2),
         downloadLoc = url.downloadDestinationPath,
-        requesterPaysProjectOption = requesterPaysProjectIdOption)
+        requesterPaysProjectOption = requesterPaysProjectIdOption
+      )
     }
-  }
-  def buildBulkAccessUrlDownloader(resolvedUrls: List[ResolvedDrsUrl]) : Downloader = {
+  def buildBulkAccessUrlDownloader(resolvedUrls: List[ResolvedDrsUrl]): Downloader =
     downloaderFactory.buildBulkAccessUrlDownloader(resolvedUrls)
-  }
 
   /**
     * Runs a synchronous HTTP request to resolve the provided DRS URL with the provided resolver.
     */
-  def resolveSingleUrl(resolverObject: DrsLocalizerDrsPathResolver, drsUrlToResolve: UnresolvedDrsUrl): IO[ResolvedDrsUrl] = {
-    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.GoogleServiceAccount, DrsResolverField.AccessUrl, DrsResolverField.Hashes)
+  def resolveSingleUrl(resolverObject: DrsLocalizerDrsPathResolver,
+                       drsUrlToResolve: UnresolvedDrsUrl
+  ): IO[ResolvedDrsUrl] = {
+    val fields = NonEmptyList.of(DrsResolverField.GsUri,
+                                 DrsResolverField.GoogleServiceAccount,
+                                 DrsResolverField.AccessUrl,
+                                 DrsResolverField.Hashes
+    )
     val drsResponse = resolverObject.resolveDrs(drsUrlToResolve.drsUrl, fields)
-    drsResponse.map(resp => ResolvedDrsUrl(resp, drsUrlToResolve.downloadDestinationPath, toValidatedUriType(resp.accessUrl, resp.gsUri)))
+    drsResponse.map(resp =>
+      ResolvedDrsUrl(resp, drsUrlToResolve.downloadDestinationPath, toValidatedUriType(resp.accessUrl, resp.gsUri))
+    )
   }
 
-
-  val defaultBackoff: CloudNioBackoff = CloudNioSimpleExponentialBackoff(
-    initialInterval = 10 seconds, maxInterval = 60 seconds, multiplier = 2)
+  val defaultBackoff: CloudNioBackoff =
+    CloudNioSimpleExponentialBackoff(initialInterval = 10 seconds, maxInterval = 60 seconds, multiplier = 2)
 
   /**
     * Runs synchronous HTTP requests to resolve all the DRS urls.
     */
-  def resolveUrls(unresolvedUrls: IO[List[UnresolvedDrsUrl]]): IO[List[ResolvedDrsUrl]] = {
+  def resolveUrls(unresolvedUrls: IO[List[UnresolvedDrsUrl]]): IO[List[ResolvedDrsUrl]] =
     unresolvedUrls.flatMap { unresolvedList =>
       getDrsPathResolver.flatMap { resolver =>
-        unresolvedList.map { unresolvedUrl =>
-          resolveWithRetries(resolver, unresolvedUrl, defaultNumRetries, Option(defaultBackoff))
-        }.traverse(identity)
+        unresolvedList
+          .map { unresolvedUrl =>
+            resolveWithRetries(resolver, unresolvedUrl, defaultNumRetries, Option(defaultBackoff))
+          }
+          .traverse(identity)
       }
     }
-  }
 
   def resolveWithRetries(resolverObject: DrsLocalizerDrsPathResolver,
                          drsUrlToResolve: UnresolvedDrsUrl,
                          resolutionRetries: Int,
                          backoff: Option[CloudNioBackoff],
-                        resolutionAttempt: Int = 0) : IO[ResolvedDrsUrl] = {
+                         resolutionAttempt: Int = 0
+  ): IO[ResolvedDrsUrl] = {
 
-    def maybeRetryForResolutionFailure(t: Throwable): IO[ResolvedDrsUrl] = {
+    def maybeRetryForResolutionFailure(t: Throwable): IO[ResolvedDrsUrl] =
       if (resolutionAttempt < resolutionRetries) {
         backoff foreach { b => Thread.sleep(b.backoffMillis) }
-        logger.warn(s"Attempting retry $resolutionAttempt of $resolutionRetries drs resolution retries to resolve ${drsUrlToResolve.drsUrl}", t)
-        resolveWithRetries(resolverObject, drsUrlToResolve, resolutionRetries, backoff map { _.next }, resolutionAttempt+1)
+        logger.warn(
+          s"Attempting retry $resolutionAttempt of $resolutionRetries drs resolution retries to resolve ${drsUrlToResolve.drsUrl}",
+          t
+        )
+        resolveWithRetries(resolverObject,
+                           drsUrlToResolve,
+                           resolutionRetries,
+                           backoff map { _.next },
+                           resolutionAttempt + 1
+        )
       } else {
-        IO.raiseError(new RuntimeException(s"Exhausted $resolutionRetries resolution retries to resolve $drsUrlToResolve.drsUrl", t))
+        IO.raiseError(
+          new RuntimeException(s"Exhausted $resolutionRetries resolution retries to resolve $drsUrlToResolve.drsUrl", t)
+        )
       }
-    }
 
     resolveSingleUrl(resolverObject, drsUrlToResolve).redeemWith(
       recover = maybeRetryForResolutionFailure,
       bind = {
-      case f: FatalRetryDisposition =>
-        IO.raiseError(new RuntimeException(s"Fatal error resolving DRS URL: $f"))
-      case _: RegularRetryDisposition =>
-        resolveWithRetries(resolverObject, drsUrlToResolve, resolutionRetries, backoff, resolutionAttempt+1)
-      case o => IO.pure(o)
-    })
+        case f: FatalRetryDisposition =>
+          IO.raiseError(new RuntimeException(s"Fatal error resolving DRS URL: $f"))
+        case _: RegularRetryDisposition =>
+          resolveWithRetries(resolverObject, drsUrlToResolve, resolutionRetries, backoff, resolutionAttempt + 1)
+        case o => IO.pure(o)
+      }
+    )
   }
 }
-
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
index f47265d7730..00957083bc9 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
@@ -1,7 +1,7 @@
 package drs.localizer.downloaders
 
 import cats.effect.{ExitCode, IO}
-import cloud.nio.impl.drs.{AccessUrl}
+import cloud.nio.impl.drs.AccessUrl
 import com.typesafe.scalalogging.StrictLogging
 
 import java.nio.charset.StandardCharsets
@@ -9,19 +9,21 @@ import java.nio.file.{Files, Path, Paths}
 import scala.sys.process.{Process, ProcessLogger}
 import scala.util.matching.Regex
 import drs.localizer.ResolvedDrsUrl
-import spray.json.DefaultJsonProtocol.{StringJsonFormat, listFormat, mapFormat}
+import spray.json.DefaultJsonProtocol.{listFormat, mapFormat, StringJsonFormat}
 import spray.json._
 
 case class GetmResult(returnCode: Int, stderr: String)
+
 /**
   * Getm is a python tool that is used to download resolved DRS uris quickly and in parallel.
   * This class builds a getm-manifest.json file that it uses for input, and builds/executes a shell command
   * to invoke the Getm tool, which is expected to already be installed in the local environment.
   * @param resolvedUrls
   */
-case class BulkAccessUrlDownloader(resolvedUrls : List[ResolvedDrsUrl]) extends Downloader with StrictLogging {
+case class BulkAccessUrlDownloader(resolvedUrls: List[ResolvedDrsUrl]) extends Downloader with StrictLogging {
 
   val getmManifestPath: Path = Paths.get("getm-manifest.json")
+
   /**
     * Write a json manifest to disk that looks like:
     * // [
@@ -42,39 +44,42 @@ case class BulkAccessUrlDownloader(resolvedUrls : List[ResolvedDrsUrl]) extends
     * @param resolvedUrls
     * @return Filepath of a getm-manifest.json that Getm can use to download multiple files in parallel.
     */
-  def generateJsonManifest(resolvedUrls : List[ResolvedDrsUrl]): IO[Path] = {
-    def resolvedUrlToJsonMap(resolvedUrl: ResolvedDrsUrl): Map[String,String] = {
+  def generateJsonManifest(resolvedUrls: List[ResolvedDrsUrl]): IO[Path] = {
+    def resolvedUrlToJsonMap(resolvedUrl: ResolvedDrsUrl): Map[String, String] = {
       val accessUrl: AccessUrl = resolvedUrl.drsResponse.accessUrl.getOrElse(AccessUrl("missing", None))
-      resolvedUrl.drsResponse.hashes.map{_ =>
-        val checksum = GetmChecksum(resolvedUrl.drsResponse.hashes, accessUrl).value.getOrElse("error_calculating_checksum")
-        val checksumAlgorithm = GetmChecksum(resolvedUrl.drsResponse.hashes, accessUrl).getmAlgorithm
-        Map(
-          ("url", accessUrl.url),
-          ("filepath", resolvedUrl.downloadDestinationPath),
-          ("checksum", checksum),
-          ("checksum-algorithm", checksumAlgorithm)
+      resolvedUrl.drsResponse.hashes
+        .map { _ =>
+          val checksum =
+            GetmChecksum(resolvedUrl.drsResponse.hashes, accessUrl).value.getOrElse("error_calculating_checksum")
+          val checksumAlgorithm = GetmChecksum(resolvedUrl.drsResponse.hashes, accessUrl).getmAlgorithm
+          Map(
+            ("url", accessUrl.url),
+            ("filepath", resolvedUrl.downloadDestinationPath),
+            ("checksum", checksum),
+            ("checksum-algorithm", checksumAlgorithm)
+          )
+        }
+        .getOrElse(
+          Map(
+            ("url", accessUrl.url),
+            ("filepath", resolvedUrl.downloadDestinationPath)
+          )
         )
-      }.getOrElse(Map(
-        ("url", accessUrl.url),
-        ("filepath", resolvedUrl.downloadDestinationPath)
-      ))
     }
 
     val jsonArray: String = resolvedUrls.map(resolved => resolvedUrlToJsonMap(resolved)).toJson.prettyPrint
     IO(Files.write(getmManifestPath, jsonArray.getBytes(StandardCharsets.UTF_8)))
   }
 
-  def deleteJsonManifest() = {
+  def deleteJsonManifest() =
     Files.deleteIfExists(getmManifestPath)
-  }
 
-  def generateGetmCommand(pathToMainfestJson : Path) : String = {
+  def generateGetmCommand(pathToMainfestJson: Path): String =
     s"""getm --manifest ${pathToMainfestJson.toString}"""
-  }
-  def runGetm: IO[GetmResult] = {
-    generateJsonManifest(resolvedUrls).flatMap{ manifestPath =>
+  def runGetm: IO[GetmResult] =
+    generateJsonManifest(resolvedUrls).flatMap { manifestPath =>
       val script = generateGetmCommand(manifestPath)
-      val copyCommand : Seq[String] = Seq("bash", "-c", script)
+      val copyCommand: Seq[String] = Seq("bash", "-c", script)
       logger.info(script)
       val copyProcess = Process(copyCommand)
       val stderr = new StringBuilder()
@@ -84,7 +89,6 @@ case class BulkAccessUrlDownloader(resolvedUrls : List[ResolvedDrsUrl]) extends
       logger.info(stderr.toString().trim())
       IO(GetmResult(returnCode, stderr.toString().trim()))
     }
-  }
 
   override def download: IO[DownloadResult] = {
     // We don't want to log the unmasked signed URL here. On a PAPI backend this log will end up under the user's
@@ -94,7 +98,7 @@ case class BulkAccessUrlDownloader(resolvedUrls : List[ResolvedDrsUrl]) extends
     runGetm map toDownloadResult
   }
 
-  def toDownloadResult(getmResult: GetmResult): DownloadResult = {
+  def toDownloadResult(getmResult: GetmResult): DownloadResult =
     getmResult match {
       case GetmResult(0, stderr) if stderr.isEmpty =>
         DownloadSuccess
@@ -122,10 +126,9 @@ case class BulkAccessUrlDownloader(resolvedUrls : List[ResolvedDrsUrl]) extends
             UnrecognizedRetryableDownloadFailure(ExitCode(rc))
         }
     }
-  }
 }
 
-object BulkAccessUrlDownloader{
+object BulkAccessUrlDownloader {
   type Hashes = Option[Map[String, String]]
 
   val ChecksumFailureMessage: Regex = raw""".*AssertionError: Checksum failed!.*""".r
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/DownloaderFactory.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/DownloaderFactory.scala
index 6c7f27e8a6e..c35a2b1634e 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/DownloaderFactory.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/DownloaderFactory.scala
@@ -3,10 +3,11 @@ package drs.localizer.downloaders
 import drs.localizer.ResolvedDrsUrl
 
 trait DownloaderFactory {
-  def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]) : Downloader
+  def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader
 
   def buildGcsUriDownloader(gcsPath: String,
                             serviceAccountJsonOption: Option[String],
                             downloadLoc: String,
-                            requesterPaysProjectOption: Option[String]): Downloader
+                            requesterPaysProjectOption: Option[String]
+  ): Downloader
 }
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
index 8991e79f5fd..74f5bc64621 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GcsUriDownloader.scala
@@ -12,15 +12,16 @@ import scala.sys.process.{Process, ProcessLogger}
 case class GcsUriDownloader(gcsUrl: String,
                             serviceAccountJson: Option[String],
                             downloadLoc: String,
-                            requesterPaysProjectIdOption: Option[String]) extends Downloader with StrictLogging {
+                            requesterPaysProjectIdOption: Option[String]
+) extends Downloader
+    with StrictLogging {
 
   val defaultNumRetries: Int = 5
-  val defaultBackoff: CloudNioBackoff = CloudNioSimpleExponentialBackoff(
-    initialInterval = 1 seconds, maxInterval = 60 seconds, multiplier = 2)
+  val defaultBackoff: CloudNioBackoff =
+    CloudNioSimpleExponentialBackoff(initialInterval = 1 seconds, maxInterval = 60 seconds, multiplier = 2)
 
-  override def download: IO[DownloadResult] = {
+  override def download: IO[DownloadResult] =
     downloadWithRetries(defaultNumRetries, Option(defaultBackoff))
-  }
 
   def runDownloadCommand: IO[DownloadResult] = {
 
@@ -45,27 +46,30 @@ case class GcsUriDownloader(gcsUrl: String,
     // run the multiple bash script to download file and log stream sent to stdout and stderr using ProcessLogger
     val returnCode = copyProcess ! ProcessLogger(logger.underlying.info, logger.underlying.error)
 
-    val result = if (returnCode == 0) DownloadSuccess else RecognizedRetryableDownloadFailure(exitCode = ExitCode(returnCode))
+    val result =
+      if (returnCode == 0) DownloadSuccess else RecognizedRetryableDownloadFailure(exitCode = ExitCode(returnCode))
 
     IO.pure(result)
   }
 
   def downloadWithRetries(downloadRetries: Int,
                           backoff: Option[CloudNioBackoff],
-                          downloadAttempt: Int = 0): IO[DownloadResult] =
-  {
+                          downloadAttempt: Int = 0
+  ): IO[DownloadResult] = {
 
-    def maybeRetryForDownloadFailure(t: Throwable): IO[DownloadResult] = {
+    def maybeRetryForDownloadFailure(t: Throwable): IO[DownloadResult] =
       if (downloadAttempt < downloadRetries) {
         backoff foreach { b => Thread.sleep(b.backoffMillis) }
         logger.warn(s"Attempting download retry $downloadAttempt of $downloadRetries for a GCS url", t)
-        downloadWithRetries(downloadRetries, backoff map {
-          _.next
-        }, downloadAttempt + 1)
+        downloadWithRetries(downloadRetries,
+                            backoff map {
+                              _.next
+                            },
+                            downloadAttempt + 1
+        )
       } else {
         IO.raiseError(new RuntimeException(s"Exhausted $downloadRetries resolution retries to download GCS file", t))
       }
-    }
 
     runDownloadCommand.redeemWith(
       recover = maybeRetryForDownloadFailure,
@@ -73,12 +77,13 @@ case class GcsUriDownloader(gcsUrl: String,
         case s: DownloadSuccess.type =>
           IO.pure(s)
         case _: RecognizedRetryableDownloadFailure =>
-          downloadWithRetries(downloadRetries, backoff, downloadAttempt+1)
+          downloadWithRetries(downloadRetries, backoff, downloadAttempt + 1)
         case _: UnrecognizedRetryableDownloadFailure =>
-          downloadWithRetries(downloadRetries, backoff, downloadAttempt+1)
+          downloadWithRetries(downloadRetries, backoff, downloadAttempt + 1)
         case _ =>
-          downloadWithRetries(downloadRetries, backoff, downloadAttempt+1)
-      })
+          downloadWithRetries(downloadRetries, backoff, downloadAttempt + 1)
+      }
+    )
   }
 
   /**
@@ -88,7 +93,7 @@ case class GcsUriDownloader(gcsUrl: String,
 
     def gcsCopyCommand(flag: String = ""): String = s"gsutil $flag cp $gcsUrl $downloadLoc"
 
-    def setServiceAccount(): String = {
+    def setServiceAccount(): String =
       saJsonPathOption match {
         case Some(saJsonPath) =>
           s"""# Set gsutil to use the service account returned from the DRS Resolver
@@ -103,9 +108,8 @@ case class GcsUriDownloader(gcsUrl: String,
              |""".stripMargin
         case None => ""
       }
-    }
 
-    def recoverWithRequesterPays(): String = {
+    def recoverWithRequesterPays(): String =
       requesterPaysProjectIdOption match {
         case Some(userProject) =>
           s"""if [ "$$RC_GSUTIL" != "0" ]; then
@@ -119,7 +123,6 @@ case class GcsUriDownloader(gcsUrl: String,
              |""".stripMargin
         case None => ""
       }
-    }
 
     // bash to download the GCS file using gsutil
     s"""set -euo pipefail
@@ -145,5 +148,5 @@ case class GcsUriDownloader(gcsUrl: String,
 }
 
 object GcsUriDownloader {
-  private final val RequesterPaysErrorMsg = "requester pays bucket but no user project"
+  final private val RequesterPaysErrorMsg = "requester pays bucket but no user project"
 }
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
index 2ca1bd3d2e3..a72459cdb7b 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/GetmChecksum.scala
@@ -8,12 +8,11 @@ import org.apache.commons.codec.binary.Base64.encodeBase64String
 import org.apache.commons.codec.binary.Hex.decodeHex
 import org.apache.commons.text.StringEscapeUtils
 
-
 sealed trait GetmChecksum {
   def getmAlgorithm: String
   def rawValue: String
   def value: ErrorOr[String] = rawValue.validNel
-  def args: ErrorOr[String] = {
+  def args: ErrorOr[String] =
     // The value for `--checksum-algorithm` is constrained by the algorithm names in the `sealed` hierarchy of
     // `GetmChecksum`, but the value for `--checksum` is largely a function of data returned by the DRS server.
     // Shell escape this to avoid injection.
@@ -21,7 +20,6 @@ sealed trait GetmChecksum {
       val escapedValue = StringEscapeUtils.escapeXSI(v)
       s"--checksum-algorithm '$getmAlgorithm' --checksum $escapedValue"
     }
-  }
 }
 
 case class Md5(override val rawValue: String) extends GetmChecksum {
@@ -33,7 +31,8 @@ case class Crc32c(override val rawValue: String) extends GetmChecksum {
   // The DRS spec says that all hash values should be hex strings,
   // but getm expects crc32c values to be base64.
   override def value: ErrorOr[String] =
-    GetmChecksum.validateHex(rawValue)
+    GetmChecksum
+      .validateHex(rawValue)
       .map(decodeHex)
       .map(encodeBase64String)
 
@@ -52,7 +51,7 @@ case class Unsupported(override val rawValue: String) extends GetmChecksum {
 }
 
 object GetmChecksum {
-  def apply(hashes: Hashes, accessUrl: AccessUrl): GetmChecksum = {
+  def apply(hashes: Hashes, accessUrl: AccessUrl): GetmChecksum =
     hashes match {
       case Some(hashes) if hashes.nonEmpty =>
         // `hashes` is keyed by the DRS Resolver names for these hash algorithms, which in turn are the forwarded DRS
@@ -61,8 +60,7 @@ object GetmChecksum {
         // but all of the other algorithm names currently differ between DRS providers and `getm`.
         if (hashes.contains("md5")) {
           Md5(hashes("md5"))
-        }
-        else if (hashes.contains("crc32c")) {
+        } else if (hashes.contains("crc32c")) {
           Crc32c(hashes("crc32c"))
         }
         // etags could be anything; only ask `getm` to check s3 etags if this actually looks like an s3 signed url.
@@ -81,7 +79,6 @@ object GetmChecksum {
         }
       case _ => Null // None or an empty hashes map.
     }
-  }
 
   def validateHex(s: String): ErrorOr[String] = {
     val trimmed = s.trim
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
index 7be30be8ac0..6658428e650 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/CommandLineParserSpec.scala
@@ -63,7 +63,9 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "successfully parse with three arguments and requester pays project" in {
-    val args = parser.parse(Array(drsObject, containerPath, requesterPaysProject, "-r", requesterPaysProject), CommandLineArguments()).get
+    val args = parser
+      .parse(Array(drsObject, containerPath, requesterPaysProject, "-r", requesterPaysProject), CommandLineArguments())
+      .get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
@@ -74,7 +76,9 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "fail if requester pays argument and flag specify different projects" in {
-    parser.parse(Array(drsObject, containerPath, requesterPaysProject, "-r", "boom!"), CommandLineArguments()) shouldBe None
+    parser.parse(Array(drsObject, containerPath, requesterPaysProject, "-r", "boom!"),
+                 CommandLineArguments()
+    ) shouldBe None
   }
 
   it should "successfully parse args with a manifest file" in {
@@ -99,12 +103,18 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "successfully parse an explicit Google access token strategy invocation" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", "google",
-      drsObject,
-      containerPath,
-      "--requester-pays-project", requesterPaysProject
-    ), CommandLineArguments()).get
+    val args = parser
+      .parse(Array(
+               "--access-token-strategy",
+               "google",
+               drsObject,
+               containerPath,
+               "--requester-pays-project",
+               requesterPaysProject
+             ),
+             CommandLineArguments()
+      )
+      .get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
@@ -115,19 +125,26 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "fail to parse an Azure invocation that specifies requester pays" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      drsObject,
-      containerPath,
-      "--requester-pays-project", requesterPaysProject), CommandLineArguments())
+    val args = parser.parse(
+      Array("--access-token-strategy",
+            AccessTokenStrategy.Azure,
+            drsObject,
+            containerPath,
+            "--requester-pays-project",
+            requesterPaysProject
+      ),
+      CommandLineArguments()
+    )
 
     args shouldBe None
   }
 
   it should "successfully parse an Azure invocation" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      drsObject, containerPath), CommandLineArguments()).get
+    val args = parser
+      .parse(Array("--access-token-strategy", AccessTokenStrategy.Azure, drsObject, containerPath),
+             CommandLineArguments()
+      )
+      .get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
@@ -138,10 +155,18 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "successfully parse an Azure invocation with identity" in {
-    val args = parser.parse(Array(
-      "--access-token-strategy", AccessTokenStrategy.Azure,
-      "--identity-client-id", azureIdentityClientId,
-      drsObject, containerPath), CommandLineArguments()).get
+    val args = parser
+      .parse(
+        Array("--access-token-strategy",
+              AccessTokenStrategy.Azure,
+              "--identity-client-id",
+              azureIdentityClientId,
+              drsObject,
+              containerPath
+        ),
+        CommandLineArguments()
+      )
+      .get
 
     args.drsObject.get shouldBe drsObject
     args.containerPath.get shouldBe containerPath
@@ -152,7 +177,8 @@ class CommandLineParserSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   }
 
   it should "fail to parse with an unrecognized access token strategy" in {
-    val args = parser.parse(Array("--access-token-strategy", "nebulous", drsObject, containerPath), CommandLineArguments())
+    val args =
+      parser.parse(Array("--access-token-strategy", "nebulous", drsObject, containerPath), CommandLineArguments())
     args shouldBe None
   }
 }
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
index 52fa4c99330..1f3bfcfc623 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
@@ -12,33 +12,40 @@ import drs.localizer.downloaders._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   val fakeDownloadLocation = "/root/foo/foo-123.bam"
   val fakeRequesterPaysId = "fake-billing-project"
 
-  val fakeGoogleInput : IO[List[UnresolvedDrsUrl]] = IO(List(
-    UnresolvedDrsUrl(fakeDrsUrlWithGcsResolutionOnly, "/path/to/nowhere")
-  ))
+  val fakeGoogleInput: IO[List[UnresolvedDrsUrl]] = IO(
+    List(
+      UnresolvedDrsUrl(fakeDrsUrlWithGcsResolutionOnly, "/path/to/nowhere")
+    )
+  )
 
-  val fakeAccessInput: IO[List[UnresolvedDrsUrl]] = IO(List(
-    UnresolvedDrsUrl("https://my-fake-access-url.com", "/path/to/somewhereelse")
-  ))
+  val fakeAccessInput: IO[List[UnresolvedDrsUrl]] = IO(
+    List(
+      UnresolvedDrsUrl("https://my-fake-access-url.com", "/path/to/somewhereelse")
+    )
+  )
 
-  val fakeBulkGoogleInput: IO[List[UnresolvedDrsUrl]] = IO(List(
-    UnresolvedDrsUrl("drs://my-fake-google-url.com", "/path/to/nowhere"),
-    UnresolvedDrsUrl("drs://my-fake-google-url.com2", "/path/to/nowhere2"),
-    UnresolvedDrsUrl("drs://my-fake-google-url.com3", "/path/to/nowhere3"),
-    UnresolvedDrsUrl("drs://my-fake-google-url.com4", "/path/to/nowhere4")
-  ))
+  val fakeBulkGoogleInput: IO[List[UnresolvedDrsUrl]] = IO(
+    List(
+      UnresolvedDrsUrl("drs://my-fake-google-url.com", "/path/to/nowhere"),
+      UnresolvedDrsUrl("drs://my-fake-google-url.com2", "/path/to/nowhere2"),
+      UnresolvedDrsUrl("drs://my-fake-google-url.com3", "/path/to/nowhere3"),
+      UnresolvedDrsUrl("drs://my-fake-google-url.com4", "/path/to/nowhere4")
+    )
+  )
 
-  val fakeBulkAccessInput: IO[List[UnresolvedDrsUrl]] = IO(List(
-    UnresolvedDrsUrl("drs://my-fake-access-url.com", "/path/to/somewhereelse"),
-    UnresolvedDrsUrl("drs://my-fake-access-url2.com", "/path/to/somewhereelse2"),
-    UnresolvedDrsUrl("drs://my-fake-access-url3.com", "/path/to/somewhereelse3"),
-    UnresolvedDrsUrl("drs://my-fake-access-url4.com", "/path/to/somewhereelse4")
-  ))
+  val fakeBulkAccessInput: IO[List[UnresolvedDrsUrl]] = IO(
+    List(
+      UnresolvedDrsUrl("drs://my-fake-access-url.com", "/path/to/somewhereelse"),
+      UnresolvedDrsUrl("drs://my-fake-access-url2.com", "/path/to/somewhereelse2"),
+      UnresolvedDrsUrl("drs://my-fake-access-url3.com", "/path/to/somewhereelse3"),
+      UnresolvedDrsUrl("drs://my-fake-access-url4.com", "/path/to/somewhereelse4")
+    )
+  )
 
   behavior of "DrsLocalizerMain"
 
@@ -52,34 +59,43 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
 
   it should "tolerate no URLs being provided" in {
     val mockDownloadFactory = new DownloaderFactory {
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader = {
+      override def buildGcsUriDownloader(gcsPath: String,
+                                         serviceAccountJsonOption: Option[String],
+                                         downloadLoc: String,
+                                         requesterPaysProjectOption: Option[String]
+      ): Downloader =
         // This test path should never ask for the Google downloader
         throw new RuntimeException("test failure111")
-      }
 
-      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader =
         // This test path should never ask for the Bulk downloader
         throw new RuntimeException("test failure111")
-      }
     }
-    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(List()), mockDownloadFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val mockdrsLocalizer =
+      new MockDrsLocalizerMain(IO(List()), mockDownloadFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
     val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
     downloaders.length shouldBe 0
   }
 
   it should "build correct downloader(s) for a single google URL" in {
     val mockDownloadFactory = new DownloaderFactory {
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader = {
+      override def buildGcsUriDownloader(gcsPath: String,
+                                         serviceAccountJsonOption: Option[String],
+                                         downloadLoc: String,
+                                         requesterPaysProjectOption: Option[String]
+      ): Downloader =
         GcsUriDownloader(gcsPath, serviceAccountJsonOption, downloadLoc, requesterPaysProjectOption)
-      }
 
-      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader =
         // This test path should never ask for the Bulk downloader
         throw new RuntimeException("test failure111")
-      }
     }
 
-    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(List(fakeGoogleUrls.head._1)), mockDownloadFactory,FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(List(fakeGoogleUrls.head._1)),
+                                                    mockDownloadFactory,
+                                                    FakeAccessTokenStrategy,
+                                                    Option(fakeRequesterPaysId)
+    )
     val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
     downloaders.length shouldBe 1
 
@@ -92,17 +108,23 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
 
   it should "build correct downloader(s) for a single access URL" in {
     val mockDownloadFactory = new DownloaderFactory {
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader = {
+      override def buildGcsUriDownloader(gcsPath: String,
+                                         serviceAccountJsonOption: Option[String],
+                                         downloadLoc: String,
+                                         requesterPaysProjectOption: Option[String]
+      ): Downloader =
         // This test path should never ask for the GCS downloader
         throw new RuntimeException("test failure")
-      }
 
-      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader =
         BulkAccessUrlDownloader(urlsToDownload)
-      }
     }
 
-    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(List(fakeAccessUrls.head._1)), mockDownloadFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(List(fakeAccessUrls.head._1)),
+                                                    mockDownloadFactory,
+                                                    FakeAccessTokenStrategy,
+                                                    Option(fakeRequesterPaysId)
+    )
     val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
     downloaders.length shouldBe 1
 
@@ -114,48 +136,64 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
 
   it should "build correct downloader(s) for multiple google URLs" in {
     val mockDownloadFactory = new DownloaderFactory {
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader = {
+      override def buildGcsUriDownloader(gcsPath: String,
+                                         serviceAccountJsonOption: Option[String],
+                                         downloadLoc: String,
+                                         requesterPaysProjectOption: Option[String]
+      ): Downloader =
         GcsUriDownloader(gcsPath, serviceAccountJsonOption, downloadLoc, requesterPaysProjectOption)
-      }
 
-      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader =
         // This test path should never ask for the GCS downloader
         throw new RuntimeException("test failure")
-      }
     }
-    val unresolvedUrls : List[UnresolvedDrsUrl] = fakeGoogleUrls.map(pair => pair._1).toList
-    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(unresolvedUrls), mockDownloadFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val unresolvedUrls: List[UnresolvedDrsUrl] = fakeGoogleUrls.map(pair => pair._1).toList
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(unresolvedUrls),
+                                                    mockDownloadFactory,
+                                                    FakeAccessTokenStrategy,
+                                                    Option(fakeRequesterPaysId)
+    )
     val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
     downloaders.length shouldBe unresolvedUrls.length
 
-    val countGoogleDownloaders = downloaders.count(downloader => downloader match {
-      case _: GcsUriDownloader => true
-      case _ => false
-    })
+    val countGoogleDownloaders = downloaders.count(downloader =>
+      downloader match {
+        case _: GcsUriDownloader => true
+        case _ => false
+      }
+    )
     // We expect one GCS downloader for each GCS uri provided
     countGoogleDownloaders shouldBe downloaders.length
   }
 
   it should "build a single bulk downloader for multiple access URLs" in {
     val mockDownloadFactory = new DownloaderFactory {
-      override def buildGcsUriDownloader(gcsPath: String, serviceAccountJsonOption: Option[String], downloadLoc: String, requesterPaysProjectOption: Option[String]): Downloader = {
+      override def buildGcsUriDownloader(gcsPath: String,
+                                         serviceAccountJsonOption: Option[String],
+                                         downloadLoc: String,
+                                         requesterPaysProjectOption: Option[String]
+      ): Downloader =
         // This test path should never ask for the GCS downloader
         throw new RuntimeException("test failure")
-      }
 
-      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader = {
+      override def buildBulkAccessUrlDownloader(urlsToDownload: List[ResolvedDrsUrl]): Downloader =
         BulkAccessUrlDownloader(urlsToDownload)
-      }
     }
     val unresolvedUrls: List[UnresolvedDrsUrl] = fakeAccessUrls.map(pair => pair._1).toList
-    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(unresolvedUrls), mockDownloadFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(unresolvedUrls),
+                                                    mockDownloadFactory,
+                                                    FakeAccessTokenStrategy,
+                                                    Option(fakeRequesterPaysId)
+    )
     val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
     downloaders.length shouldBe 1
 
-    val countBulkDownloaders = downloaders.count(downloader => downloader match {
-      case _: BulkAccessUrlDownloader => true
-      case _ => false
-    })
+    val countBulkDownloaders = downloaders.count(downloader =>
+      downloader match {
+        case _: BulkAccessUrlDownloader => true
+        case _ => false
+      }
+    )
     // We expect one total Bulk downloader for all access URIs to share
     countBulkDownloaders shouldBe 1
     val expected = BulkAccessUrlDownloader(
@@ -165,23 +203,32 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
   }
 
   it should "build 1 bulk downloader and 5 google downloaders for a mix of URLs" in {
-    val unresolvedUrls: List[UnresolvedDrsUrl] = fakeAccessUrls.map(pair => pair._1).toList ++ fakeGoogleUrls.map(pair => pair._1).toList
-    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(unresolvedUrls), DrsLocalizerMain.defaultDownloaderFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val unresolvedUrls: List[UnresolvedDrsUrl] =
+      fakeAccessUrls.map(pair => pair._1).toList ++ fakeGoogleUrls.map(pair => pair._1).toList
+    val mockdrsLocalizer = new MockDrsLocalizerMain(IO(unresolvedUrls),
+                                                    DrsLocalizerMain.defaultDownloaderFactory,
+                                                    FakeAccessTokenStrategy,
+                                                    Option(fakeRequesterPaysId)
+    )
     val downloaders: List[Downloader] = mockdrsLocalizer.buildDownloaders().unsafeRunSync()
 
     downloaders.length shouldBe 6
 
-    //we expect a single bulk downloader despite 5 access URLs being provided
-    val countBulkDownloaders = downloaders.count(downloader => downloader match {
-      case _: BulkAccessUrlDownloader => true
-      case _ => false
-    })
+    // we expect a single bulk downloader despite 5 access URLs being provided
+    val countBulkDownloaders = downloaders.count(downloader =>
+      downloader match {
+        case _: BulkAccessUrlDownloader => true
+        case _ => false
+      }
+    )
     // We expect one GCS downloader for each GCS uri provided
     countBulkDownloaders shouldBe 1
-    val countGoogleDownloaders = downloaders.count(downloader => downloader match {
-      case _: GcsUriDownloader => true
-      case _ => false
-    })
+    val countGoogleDownloaders = downloaders.count(downloader =>
+      downloader match {
+        case _: GcsUriDownloader => true
+        case _ => false
+      }
+    )
     // We expect one GCS downloader for each GCS uri provided
     countBulkDownloaders shouldBe 1
     countGoogleDownloaders shouldBe 5
@@ -189,24 +236,34 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
 
   it should "accept arguments and run successfully without Requester Pays ID" in {
     val unresolved = fakeGoogleUrls.head._1
-    val mockDrsLocalizer = new MockDrsLocalizerMain(IO(List(unresolved)), DrsLocalizerMain.defaultDownloaderFactory, FakeAccessTokenStrategy, None)
+    val mockDrsLocalizer = new MockDrsLocalizerMain(IO(List(unresolved)),
+                                                    DrsLocalizerMain.defaultDownloaderFactory,
+                                                    FakeAccessTokenStrategy,
+                                                    None
+    )
     val expected = GcsUriDownloader(
       gcsUrl = fakeGoogleUrls.get(unresolved).get.drsResponse.gsUri.get,
       serviceAccountJson = None,
       downloadLoc = unresolved.downloadDestinationPath,
-      requesterPaysProjectIdOption = None)
+      requesterPaysProjectIdOption = None
+    )
     val downloader: Downloader = mockDrsLocalizer.buildDownloaders().unsafeRunSync().head
     downloader shouldBe expected
   }
 
   it should "run successfully with all 3 arguments" in {
     val unresolved = fakeGoogleUrls.head._1
-    val mockDrsLocalizer = new MockDrsLocalizerMain(IO(List(unresolved)), DrsLocalizerMain.defaultDownloaderFactory, FakeAccessTokenStrategy, Option(fakeRequesterPaysId))
+    val mockDrsLocalizer = new MockDrsLocalizerMain(IO(List(unresolved)),
+                                                    DrsLocalizerMain.defaultDownloaderFactory,
+                                                    FakeAccessTokenStrategy,
+                                                    Option(fakeRequesterPaysId)
+    )
     val expected = GcsUriDownloader(
       gcsUrl = fakeGoogleUrls.get(unresolved).get.drsResponse.gsUri.get,
       serviceAccountJson = None,
       downloadLoc = unresolved.downloadDestinationPath,
-      requesterPaysProjectIdOption = Option(fakeRequesterPaysId))
+      requesterPaysProjectIdOption = Option(fakeRequesterPaysId)
+    )
     val downloader: Downloader = mockDrsLocalizer.buildDownloaders().unsafeRunSync().head
     downloader shouldBe expected
   }
@@ -214,10 +271,18 @@ class DrsLocalizerMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
   it should "successfully identify uri types, preferring access" in {
     val exampleAccessResponse = DrsResolverResponse(accessUrl = Option(AccessUrl("https://something.com", FakeHashes)))
     val exampleGoogleResponse = DrsResolverResponse(gsUri = Option("gs://something"))
-    val exampleMixedResponse = DrsResolverResponse(accessUrl = Option(AccessUrl("https://something.com", FakeHashes)), gsUri = Option("gs://something"))
-    DrsLocalizerMain.toValidatedUriType(exampleAccessResponse.accessUrl, exampleAccessResponse.gsUri) shouldBe URIType.ACCESS
-    DrsLocalizerMain.toValidatedUriType(exampleGoogleResponse.accessUrl, exampleGoogleResponse.gsUri) shouldBe URIType.GCS
-    DrsLocalizerMain.toValidatedUriType(exampleMixedResponse.accessUrl, exampleMixedResponse.gsUri) shouldBe URIType.ACCESS
+    val exampleMixedResponse = DrsResolverResponse(accessUrl = Option(AccessUrl("https://something.com", FakeHashes)),
+                                                   gsUri = Option("gs://something")
+    )
+    DrsLocalizerMain.toValidatedUriType(exampleAccessResponse.accessUrl,
+                                        exampleAccessResponse.gsUri
+    ) shouldBe URIType.ACCESS
+    DrsLocalizerMain.toValidatedUriType(exampleGoogleResponse.accessUrl,
+                                        exampleGoogleResponse.gsUri
+    ) shouldBe URIType.GCS
+    DrsLocalizerMain.toValidatedUriType(exampleMixedResponse.accessUrl,
+                                        exampleMixedResponse.gsUri
+    ) shouldBe URIType.ACCESS
   }
 
   it should "throw an exception if the DRS Resolver response is invalid" in {
@@ -246,48 +311,87 @@ object MockDrsPaths {
   val fakeDrsUrlWithoutAnyResolution = "drs://foo/bar/no-gcs-path"
 
   val fakeGoogleUrls: Map[UnresolvedDrsUrl, ResolvedDrsUrl] = Map(
-    (UnresolvedDrsUrl("drs://abc/foo-123/google/0", "/path/to/google/local0"), ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri0")), "/path/to/google/local0", URIType.GCS)),
-    (UnresolvedDrsUrl("drs://abc/foo-123/google/1", "/path/to/google/local1"), ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri1")), "/path/to/google/local1", URIType.GCS)),
-    (UnresolvedDrsUrl("drs://abc/foo-123/google/2", "/path/to/google/local2"), ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri2")), "/path/to/google/local2", URIType.GCS)),
-    (UnresolvedDrsUrl("drs://abc/foo-123/google/3", "/path/to/google/local3"), ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri3")), "/path/to/google/local3", URIType.GCS)),
-    (UnresolvedDrsUrl("drs://abc/foo-123/google/4", "/path/to/google/local4"), ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri4")), "/path/to/google/local4", URIType.GCS))
+    (UnresolvedDrsUrl("drs://abc/foo-123/google/0", "/path/to/google/local0"),
+     ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri0")), "/path/to/google/local0", URIType.GCS)
+    ),
+    (UnresolvedDrsUrl("drs://abc/foo-123/google/1", "/path/to/google/local1"),
+     ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri1")), "/path/to/google/local1", URIType.GCS)
+    ),
+    (UnresolvedDrsUrl("drs://abc/foo-123/google/2", "/path/to/google/local2"),
+     ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri2")), "/path/to/google/local2", URIType.GCS)
+    ),
+    (UnresolvedDrsUrl("drs://abc/foo-123/google/3", "/path/to/google/local3"),
+     ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri3")), "/path/to/google/local3", URIType.GCS)
+    ),
+    (UnresolvedDrsUrl("drs://abc/foo-123/google/4", "/path/to/google/local4"),
+     ResolvedDrsUrl(DrsResolverResponse(gsUri = Option("gs://some/uri4")), "/path/to/google/local4", URIType.GCS)
+    )
   )
 
   val fakeAccessUrls: Map[UnresolvedDrsUrl, ResolvedDrsUrl] = Map(
-    (UnresolvedDrsUrl("drs://abc/foo-123/access/0", "/path/to/access/local0"), ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/0", FakeHashes))), "/path/to/access/local0", URIType.ACCESS)),
-    (UnresolvedDrsUrl("drs://abc/foo-123/access/1", "/path/to/access/local1"), ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/1", FakeHashes))), "/path/to/access/local1", URIType.ACCESS)),
-    (UnresolvedDrsUrl("drs://abc/foo-123/access/2", "/path/to/access/local2"), ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/2", FakeHashes))), "/path/to/access/local2", URIType.ACCESS)),
-    (UnresolvedDrsUrl("drs://abc/foo-123/access/3", "/path/to/access/local3"), ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/3", FakeHashes))), "/path/to/access/local3", URIType.ACCESS)),
-    (UnresolvedDrsUrl("drs://abc/foo-123/access/4", "/path/to/access/local4"), ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/4", FakeHashes))), "/path/to/access/local4", URIType.ACCESS))
+    (UnresolvedDrsUrl("drs://abc/foo-123/access/0", "/path/to/access/local0"),
+     ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/0", FakeHashes))),
+                    "/path/to/access/local0",
+                    URIType.ACCESS
+     )
+    ),
+    (UnresolvedDrsUrl("drs://abc/foo-123/access/1", "/path/to/access/local1"),
+     ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/1", FakeHashes))),
+                    "/path/to/access/local1",
+                    URIType.ACCESS
+     )
+    ),
+    (UnresolvedDrsUrl("drs://abc/foo-123/access/2", "/path/to/access/local2"),
+     ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/2", FakeHashes))),
+                    "/path/to/access/local2",
+                    URIType.ACCESS
+     )
+    ),
+    (UnresolvedDrsUrl("drs://abc/foo-123/access/3", "/path/to/access/local3"),
+     ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/3", FakeHashes))),
+                    "/path/to/access/local3",
+                    URIType.ACCESS
+     )
+    ),
+    (UnresolvedDrsUrl("drs://abc/foo-123/access/4", "/path/to/access/local4"),
+     ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://abc/foo-123/access/4", FakeHashes))),
+                    "/path/to/access/local4",
+                    URIType.ACCESS
+     )
+    )
   )
 }
 
-
 class MockDrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
                            downloaderFactory: DownloaderFactory,
                            drsCredentials: DrsCredentials,
                            requesterPaysProjectIdOption: Option[String]
-                          )
+) extends DrsLocalizerMain(toResolveAndDownload,
+                           downloaderFactory,
+                           FakeAccessTokenStrategy,
+                           requesterPaysProjectIdOption
+    ) {
 
-  extends DrsLocalizerMain(toResolveAndDownload, downloaderFactory, FakeAccessTokenStrategy, requesterPaysProjectIdOption) {
-
-  override def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] = {
+  override def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] =
     IO {
       new MockDrsLocalizerDrsPathResolver(cloud.nio.impl.drs.MockDrsPaths.mockDrsConfig)
     }
-  }
-  override def resolveSingleUrl(resolverObject: DrsLocalizerDrsPathResolver, drsUrlToResolve: UnresolvedDrsUrl): IO[ResolvedDrsUrl] = {
+  override def resolveSingleUrl(resolverObject: DrsLocalizerDrsPathResolver,
+                                drsUrlToResolve: UnresolvedDrsUrl
+  ): IO[ResolvedDrsUrl] =
     IO {
       if (!fakeAccessUrls.contains(drsUrlToResolve) && !fakeGoogleUrls.contains(drsUrlToResolve)) {
         throw new RuntimeException("Unexpected URI during testing")
       }
-      fakeAccessUrls.getOrElse(drsUrlToResolve, fakeGoogleUrls.getOrElse(drsUrlToResolve, ResolvedDrsUrl(DrsResolverResponse(),"/12/3/", URIType.UNKNOWN)))
+      fakeAccessUrls.getOrElse(
+        drsUrlToResolve,
+        fakeGoogleUrls.getOrElse(drsUrlToResolve, ResolvedDrsUrl(DrsResolverResponse(), "/12/3/", URIType.UNKNOWN))
+      )
     }
-  }
 }
 
-class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig) extends
-  DrsLocalizerDrsPathResolver(drsConfig, FakeAccessTokenStrategy) {
+class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig)
+    extends DrsLocalizerDrsPathResolver(drsConfig, FakeAccessTokenStrategy) {
 
   override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
 
@@ -298,17 +402,15 @@ class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig) extends
 
     IO.pure(drsPath) map {
       case MockDrsPaths.fakeDrsUrlWithGcsResolutionOnly =>
-        drsResolverResponse.copy(
-          gsUri = Option("gs://abc/foo-123/abc123"))
+        drsResolverResponse.copy(gsUri = Option("gs://abc/foo-123/abc123"))
       case MockDrsPaths.fakeDrsUrlWithoutAnyResolution =>
         drsResolverResponse
       case MockDrsPaths.fakeDrsUrlWithAccessUrlResolutionOnly =>
-        drsResolverResponse.copy(
-          accessUrl = Option(AccessUrl(url = "http://abc/def/ghi.bam", headers = None)))
+        drsResolverResponse.copy(accessUrl = Option(AccessUrl(url = "http://abc/def/ghi.bam", headers = None)))
       case MockDrsPaths.fakeDrsUrlWithAccessUrlAndGcsResolution =>
-        drsResolverResponse.copy(
-          accessUrl = Option(AccessUrl(url = "http://abc/def/ghi.bam", headers = None)),
-          gsUri = Option("gs://some/uri"))
+        drsResolverResponse.copy(accessUrl = Option(AccessUrl(url = "http://abc/def/ghi.bam", headers = None)),
+                                 gsUri = Option("gs://some/uri")
+        )
       case e => throw new RuntimeException(s"Unexpected exception in DRS localization test code: $e")
     }
   }
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
index 0e0714febb8..4255b407b1a 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
@@ -12,10 +12,19 @@ import org.scalatest.matchers.should.Matchers
 import java.nio.file.Path
 
 class BulkAccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  val ex1 = ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://my.fake/url123", None))), "path/to/local/download/dest", URIType.ACCESS)
-  val ex2 = ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://my.fake/url1234", None))), "path/to/local/download/dest2", URIType.ACCESS)
-  val ex3 = ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://my.fake/url1235", None))), "path/to/local/download/dest3", URIType.ACCESS)
-  val emptyList : List[ResolvedDrsUrl] = List()
+  val ex1 = ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://my.fake/url123", None))),
+                           "path/to/local/download/dest",
+                           URIType.ACCESS
+  )
+  val ex2 = ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://my.fake/url1234", None))),
+                           "path/to/local/download/dest2",
+                           URIType.ACCESS
+  )
+  val ex3 = ResolvedDrsUrl(DrsResolverResponse(accessUrl = Option(AccessUrl("https://my.fake/url1235", None))),
+                           "path/to/local/download/dest3",
+                           URIType.ACCESS
+  )
+  val emptyList: List[ResolvedDrsUrl] = List()
   val oneElement: List[ResolvedDrsUrl] = List(ex1)
   val threeElements: List[ResolvedDrsUrl] = List(ex1, ex2, ex3)
 
@@ -35,7 +44,9 @@ class BulkAccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec w
 
     val filepath: IO[Path] = downloader.generateJsonManifest(threeElements)
     val source = scala.io.Source.fromFile(filepath.unsafeRunSync().toString)
-    val lines = try source.mkString finally source.close()
+    val lines =
+      try source.mkString
+      finally source.close()
     lines shouldBe expected
   }
 
@@ -44,7 +55,9 @@ class BulkAccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec w
     val downloader = BulkAccessUrlDownloader(emptyList)
     val filepath: IO[Path] = downloader.generateJsonManifest(emptyList)
     val source = scala.io.Source.fromFile(filepath.unsafeRunSync().toString)
-    val lines = try source.mkString finally source.close()
+    val lines =
+      try source.mkString
+      finally source.close()
     lines shouldBe expected
   }
 
@@ -58,7 +71,9 @@ class BulkAccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec w
     val downloader = BulkAccessUrlDownloader(oneElement)
     val filepath: IO[Path] = downloader.generateJsonManifest(oneElement)
     val source = scala.io.Source.fromFile(filepath.unsafeRunSync().toString)
-    val lines = try source.mkString finally source.close()
+    val lines =
+      try source.mkString
+      finally source.close()
     lines shouldBe expected
   }
 
@@ -82,15 +97,30 @@ class BulkAccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec w
       // Unrecognized because of non-zero exit code without an HTTP status.
       (1, " foobar ", UnrecognizedRetryableDownloadFailure(ExitCode(1))),
       // Unrecognized because of zero exit status with stderr that does not look like a checksum failure.
-      (0, """ERROR:getm.cli possibly some words "status_code": 503 words""", UnrecognizedRetryableDownloadFailure(ExitCode(0))),
+      (0,
+       """ERROR:getm.cli possibly some words "status_code": 503 words""",
+       UnrecognizedRetryableDownloadFailure(ExitCode(0))
+      ),
       // Recognized because of non-zero exit status and an HTTP status.
-      (1, """ERROR:getm.cli possibly some words "status_code": 503 words""", RecognizedRetryableDownloadFailure(ExitCode(1))),
+      (1,
+       """ERROR:getm.cli possibly some words "status_code": 503 words""",
+       RecognizedRetryableDownloadFailure(ExitCode(1))
+      ),
       // Recognized because of non-zero exit status and an HTTP status.
-      (1, """ERROR:getm.cli possibly some words "status_code": 408 more words""", RecognizedRetryableDownloadFailure(ExitCode(1))),
+      (1,
+       """ERROR:getm.cli possibly some words "status_code": 408 more words""",
+       RecognizedRetryableDownloadFailure(ExitCode(1))
+      ),
       // Recognized and non-retryable because of non-zero exit status and 404 HTTP status.
-      (1, """ERROR:getm.cli possibly some words "status_code": 404 even more words""", FatalDownloadFailure(ExitCode(1))),
+      (1,
+       """ERROR:getm.cli possibly some words "status_code": 404 even more words""",
+       FatalDownloadFailure(ExitCode(1))
+      ),
       // Unrecognized because of zero exit status and 404 HTTP status.
-      (0, """ERROR:getm.cli possibly some words "status_code": 404 even more words""", UnrecognizedRetryableDownloadFailure(ExitCode(0))),
+      (0,
+       """ERROR:getm.cli possibly some words "status_code": 404 even more words""",
+       UnrecognizedRetryableDownloadFailure(ExitCode(0))
+      )
     )
     val bulkDownloader = BulkAccessUrlDownloader(null)
 
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
index 69c063ff616..a8ac76fa6c0 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/GetmChecksumSpec.scala
@@ -17,9 +17,15 @@ class GetmChecksumSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
       (Option(Map("something weird" -> "012345", "md5" -> "abcdefg")), "https://whatever", Md5("abcdefg")),
       (Option(Map("something weird" -> "abcdefg", "crc32c" -> "012345")), "https://whatever", Crc32c("012345")),
       (Option(Map("etag" -> "abcdefg", "crc32c" -> "012345")), "https://whatever", Crc32c("012345")),
-      (Option(Map("etag" -> "abcdefg", "something weird" -> "012345")), "https://whatever", Unsupported("etag, something weird")),
-      (Option(Map("etag" -> "abcdefg", "something weird" -> "012345")), "https://whatever.s3.amazonaws.com/foo", AwsEtag("abcdefg")),
-      (None, "https://whatever.s3.amazonaws.com/foo", Null),
+      (Option(Map("etag" -> "abcdefg", "something weird" -> "012345")),
+       "https://whatever",
+       Unsupported("etag, something weird")
+      ),
+      (Option(Map("etag" -> "abcdefg", "something weird" -> "012345")),
+       "https://whatever.s3.amazonaws.com/foo",
+       AwsEtag("abcdefg")
+      ),
+      (None, "https://whatever.s3.amazonaws.com/foo", Null)
     )
 
     forAll(results) { (hashes, url, expected) =>
@@ -31,14 +37,23 @@ class GetmChecksumSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     val results = Table(
       ("description", "algorithm", "expected"),
       ("md5 hex", Md5("abcdef"), "--checksum-algorithm 'md5' --checksum abcdef".validNel),
-      ("md5 base64", Md5("cR84lXY1y17c3q7/7riLEA=="), "Invalid checksum value, expected hex but got: cR84lXY1y17c3q7/7riLEA==".invalidNel),
-      ("md5 gibberish", Md5("what is this???"), "Invalid checksum value, expected hex but got: what is this???".invalidNel),
+      ("md5 base64",
+       Md5("cR84lXY1y17c3q7/7riLEA=="),
+       "Invalid checksum value, expected hex but got: cR84lXY1y17c3q7/7riLEA==".invalidNel
+      ),
+      ("md5 gibberish",
+       Md5("what is this???"),
+       "Invalid checksum value, expected hex but got: what is this???".invalidNel
+      ),
       ("crc32c", Crc32c("012345"), "--checksum-algorithm 'gs_crc32c' --checksum ASNF".validNel),
       ("crc32c gibberish", Crc32c("????"), "Invalid checksum value, expected hex but got: ????".invalidNel),
       ("AWS ETag", AwsEtag("012345"), "--checksum-algorithm 's3_etag' --checksum 012345".validNel),
       // Escape checksum values constructed from unvalidated data returned by DRS servers.
-      ("Unsupported", Unsupported("Robert'); DROP TABLE Students;\n --\\"), raw"--checksum-algorithm 'null' --checksum Robert\'\)\;\ DROP\ TABLE\ Students\;\ --\\".validNel),
-      ("Null", Null, "--checksum-algorithm 'null' --checksum null".validNel),
+      ("Unsupported",
+       Unsupported("Robert'); DROP TABLE Students;\n --\\"),
+       raw"--checksum-algorithm 'null' --checksum Robert\'\)\;\ DROP\ TABLE\ Students\;\ --\\".validNel
+      ),
+      ("Null", Null, "--checksum-algorithm 'null' --checksum null".validNel)
     )
 
     forAll(results) { (description, algorithm, expected) =>
@@ -55,7 +70,7 @@ class GetmChecksumSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
       (" ", "Invalid checksum value, expected hex but got: ".invalidNel),
       ("myfavoritestring", "Invalid checksum value, expected hex but got: myfavoritestring".invalidNel),
       (" AbC123 ", "AbC123".validNel),
-      ("456", "456".validNel),
+      ("456", "456".validNel)
     )
 
     forAll(results) { (testString, expected) =>
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/CromwellClient.scala b/cromwellApiClient/src/main/scala/cromwell/api/CromwellClient.scala
index b2a088e681b..18df2ff5244 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/CromwellClient.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/CromwellClient.scala
@@ -20,10 +20,10 @@ import scala.concurrent.ExecutionContext
 
 class CromwellClient(val cromwellUrl: URL,
                      val apiVersion: String,
-                     val defaultCredentials: Option[HttpCredentials]=None)
-                    (implicit actorSystem: ActorSystem, materializer: ActorMaterializer) {
+                     val defaultCredentials: Option[HttpCredentials] = None
+)(implicit actorSystem: ActorSystem, materializer: ActorMaterializer) {
 
-  lazy val defaultAuthorization: Option[Authorization] = defaultCredentials.map { Authorization(_) }
+  lazy val defaultAuthorization: Option[Authorization] = defaultCredentials.map(Authorization(_))
   lazy val defaultHeaders: List[HttpHeader] = defaultAuthorization.toList
 
   lazy val engineEndpoint = s"$cromwellUrl/engine/$apiVersion"
@@ -33,7 +33,7 @@ class CromwellClient(val cromwellUrl: URL,
 
   lazy val submitEndpoint = workflowsEndpoint
   lazy val batchSubmitEndpoint = s"$submitEndpoint/batch"
-  def describeEndpoint= s"$womtoolEndpoint/describe"
+  def describeEndpoint = s"$womtoolEndpoint/describe"
 
   def queryEndpoint(args: List[(String, String)]): Uri = {
     val base = s"$workflowsEndpoint/query"
@@ -49,11 +49,20 @@ class CromwellClient(val cromwellUrl: URL,
 
   def abortEndpoint(workflowId: WorkflowId): Uri = workflowSpecificGetEndpoint(workflowsEndpoint, workflowId, "abort")
   def statusEndpoint(workflowId: WorkflowId): Uri = workflowSpecificGetEndpoint(workflowsEndpoint, workflowId, "status")
-  def metadataEndpoint(workflowId: WorkflowId, args: Option[Map[String, List[String]]] = None): Uri = workflowSpecificGetEndpoint(workflowsEndpoint, workflowId, "metadata", args)
-  def outputsEndpoint(workflowId: WorkflowId, args: Option[Map[String, List[String]]] = None): Uri = workflowSpecificGetEndpoint(workflowsEndpoint, workflowId, "outputs", args)
+  def metadataEndpoint(workflowId: WorkflowId, args: Option[Map[String, List[String]]] = None): Uri =
+    workflowSpecificGetEndpoint(workflowsEndpoint, workflowId, "metadata", args)
+  def outputsEndpoint(workflowId: WorkflowId, args: Option[Map[String, List[String]]] = None): Uri =
+    workflowSpecificGetEndpoint(workflowsEndpoint, workflowId, "outputs", args)
   def labelsEndpoint(workflowId: WorkflowId): Uri = workflowSpecificGetEndpoint(workflowsEndpoint, workflowId, "labels")
-  def logsEndpoint(workflowId: WorkflowId, args: Option[Map[String, List[String]]] = None): Uri = workflowSpecificGetEndpoint(workflowsEndpoint, workflowId, "logs", args)
-  def diffEndpoint(workflowA: WorkflowId, callA: String, indexA: ShardIndex, workflowB: WorkflowId, callB: String, indexB: ShardIndex): String = {
+  def logsEndpoint(workflowId: WorkflowId, args: Option[Map[String, List[String]]] = None): Uri =
+    workflowSpecificGetEndpoint(workflowsEndpoint, workflowId, "logs", args)
+  def diffEndpoint(workflowA: WorkflowId,
+                   callA: String,
+                   indexA: ShardIndex,
+                   workflowB: WorkflowId,
+                   callB: String,
+                   indexB: ShardIndex
+  ): String = {
     def shardParam(aOrB: String, s: ShardIndex) = s.index.map(i => s"&index$aOrB=$i.toString").getOrElse("")
     s"$workflowsEndpoint/callcaching/diff?workflowA=$workflowA&callA=$callA&workflowB=$workflowB&callB=$callB${shardParam("A", indexA)}${shardParam("B", indexB)}"
   }
@@ -69,40 +78,48 @@ class CromwellClient(val cromwellUrl: URL,
   import model.WorkflowDescriptionJsonSupport._
   import model.CromwellQueryResultJsonSupport._
 
-  def submit(workflow: WorkflowSubmission)
-            (implicit ec: ExecutionContext): FailureResponseOrT[SubmittedWorkflow] = {
+  def submit(workflow: WorkflowSubmission)(implicit ec: ExecutionContext): FailureResponseOrT[SubmittedWorkflow] = {
     val requestEntity = requestEntityForSubmit(workflow)
 
-    makeRequest[CromwellStatus](HttpRequest(HttpMethods.POST, submitEndpoint, List.empty[HttpHeader], requestEntity)) map { status =>
+    makeRequest[CromwellStatus](
+      HttpRequest(HttpMethods.POST, submitEndpoint, List.empty[HttpHeader], requestEntity)
+    ) map { status =>
       SubmittedWorkflow(WorkflowId.fromString(status.id), cromwellUrl, workflow)
     }
   }
 
-  def describe(workflow: WorkflowDescribeRequest)
-              (implicit ec: ExecutionContext): FailureResponseOrT[WaasDescription] = {
+  def describe(
+    workflow: WorkflowDescribeRequest
+  )(implicit ec: ExecutionContext): FailureResponseOrT[WaasDescription] = {
     val requestEntity = requestEntityForDescribe(workflow)
     makeRequest[WaasDescription](HttpRequest(HttpMethods.POST, describeEndpoint, List.empty[HttpHeader], requestEntity))
   }
 
-  def submitBatch(workflow: WorkflowBatchSubmission)
-                 (implicit ec: ExecutionContext): FailureResponseOrT[List[SubmittedWorkflow]] = {
+  def submitBatch(
+    workflow: WorkflowBatchSubmission
+  )(implicit ec: ExecutionContext): FailureResponseOrT[List[SubmittedWorkflow]] = {
     import DefaultJsonProtocol._
 
     val requestEntity = requestEntityForSubmit(workflow)
 
     // Make a set of submissions that represent the batch (so we can zip with the results later):
-    val submissionSet = workflow.inputsBatch.map(inputs => WorkflowSingleSubmission(
-      workflowSource = workflow.workflowSource,
-      workflowUrl = workflow.workflowUrl,
-      workflowRoot = workflow.workflowRoot,
-      workflowType = workflow.workflowType,
-      workflowTypeVersion = workflow.workflowTypeVersion,
-      inputsJson = Option(inputs),
-      options = workflow.options,
-      labels = workflow.labels,
-      zippedImports = workflow.zippedImports))
-
-    makeRequest[List[CromwellStatus]](HttpRequest(HttpMethods.POST, batchSubmitEndpoint, List.empty[HttpHeader], requestEntity)) map { statuses =>
+    val submissionSet = workflow.inputsBatch.map(inputs =>
+      WorkflowSingleSubmission(
+        workflowSource = workflow.workflowSource,
+        workflowUrl = workflow.workflowUrl,
+        workflowRoot = workflow.workflowRoot,
+        workflowType = workflow.workflowType,
+        workflowTypeVersion = workflow.workflowTypeVersion,
+        inputsJson = Option(inputs),
+        options = workflow.options,
+        labels = workflow.labels,
+        zippedImports = workflow.zippedImports
+      )
+    )
+
+    makeRequest[List[CromwellStatus]](
+      HttpRequest(HttpMethods.POST, batchSubmitEndpoint, List.empty[HttpHeader], requestEntity)
+    ) map { statuses =>
       val zipped = submissionSet.zip(statuses)
       zipped map { case (submission, status) =>
         SubmittedWorkflow(WorkflowId.fromString(status.id), cromwellUrl, submission)
@@ -110,48 +127,42 @@ class CromwellClient(val cromwellUrl: URL,
     }
   }
 
-  def abort(workflowId: WorkflowId)(implicit ec: ExecutionContext): FailureResponseOrT[WorkflowStatus] = {
+  def abort(workflowId: WorkflowId)(implicit ec: ExecutionContext): FailureResponseOrT[WorkflowStatus] =
     simpleRequest[CromwellStatus](uri = abortEndpoint(workflowId), method = HttpMethods.POST) map WorkflowStatus.apply
-  }
 
-  def status(workflowId: WorkflowId)(implicit ec: ExecutionContext): FailureResponseOrT[WorkflowStatus] = {
+  def status(workflowId: WorkflowId)(implicit ec: ExecutionContext): FailureResponseOrT[WorkflowStatus] =
     simpleRequest[CromwellStatus](statusEndpoint(workflowId)) map WorkflowStatus.apply
-  }
 
   def metadata(workflowId: WorkflowId,
                args: Option[Map[String, List[String]]] = None,
                headers: List[HttpHeader] = defaultHeaders
-              )(implicit ec: ExecutionContext): FailureResponseOrT[WorkflowMetadata] = {
-    simpleRequest[String](metadataEndpoint(workflowId, args), headers=headers) map WorkflowMetadata
-  }
+  )(implicit ec: ExecutionContext): FailureResponseOrT[WorkflowMetadata] =
+    simpleRequest[String](metadataEndpoint(workflowId, args), headers = headers) map WorkflowMetadata
 
-  def outputs(workflowId: WorkflowId,
-              args: Option[Map[String, List[String]]] = None)(implicit ec: ExecutionContext): FailureResponseOrT[WorkflowOutputs] = {
+  def outputs(workflowId: WorkflowId, args: Option[Map[String, List[String]]] = None)(implicit
+    ec: ExecutionContext
+  ): FailureResponseOrT[WorkflowOutputs] =
     simpleRequest[WorkflowOutputs](outputsEndpoint(workflowId, args))
-  }
 
-  def labels(workflowId: WorkflowId,
-             headers: List[HttpHeader] = defaultHeaders)
-            (implicit ec: ExecutionContext): FailureResponseOrT[WorkflowLabels] = {
+  def labels(workflowId: WorkflowId, headers: List[HttpHeader] = defaultHeaders)(implicit
+    ec: ExecutionContext
+  ): FailureResponseOrT[WorkflowLabels] =
     simpleRequest[WorkflowLabels](labelsEndpoint(workflowId), headers = headers)
-  }
 
-  def addLabels(workflowId: WorkflowId,
-                newLabels: List[Label],
-                headers: List[HttpHeader] = defaultHeaders)
-               (implicit ec: ExecutionContext): FailureResponseOrT[WorkflowLabels] = {
+  def addLabels(workflowId: WorkflowId, newLabels: List[Label], headers: List[HttpHeader] = defaultHeaders)(implicit
+    ec: ExecutionContext
+  ): FailureResponseOrT[WorkflowLabels] = {
     val requestEntity = requestEntityForAddLabels(newLabels)
     makeRequest[WorkflowLabels](HttpRequest(HttpMethods.PATCH, labelsEndpoint(workflowId), headers, requestEntity))
   }
 
-  def logs(workflowId: WorkflowId,
-           args: Option[Map[String, List[String]]] = None)(implicit ec: ExecutionContext): FailureResponseOrT[WorkflowMetadata] = {
+  def logs(workflowId: WorkflowId, args: Option[Map[String, List[String]]] = None)(implicit
+    ec: ExecutionContext
+  ): FailureResponseOrT[WorkflowMetadata] =
     simpleRequest[String](logsEndpoint(workflowId, args)) map WorkflowMetadata
-  }
 
-  def query(workflowId: WorkflowId)(implicit ec: ExecutionContext): FailureResponseOrT[CromwellQueryResults] = {
+  def query(workflowId: WorkflowId)(implicit ec: ExecutionContext): FailureResponseOrT[CromwellQueryResults] =
     simpleRequest[CromwellQueryResults](queryEndpoint(List(("id", workflowId.id.toString))))
-  }
 
   def callCacheDiff(workflowA: WorkflowId,
                     callA: String,
@@ -159,27 +170,26 @@ class CromwellClient(val cromwellUrl: URL,
                     workflowB: WorkflowId,
                     callB: String,
                     shardIndexB: ShardIndex
-                   )(implicit ec: ExecutionContext): FailureResponseOrT[CallCacheDiff] = {
+  )(implicit ec: ExecutionContext): FailureResponseOrT[CallCacheDiff] =
     simpleRequest[CallCacheDiff](diffEndpoint(workflowA, callA, shardIndexA, workflowB, callB, shardIndexB))
-  }
 
-  def backends(implicit ec: ExecutionContext): FailureResponseOrT[CromwellBackends] = {
+  def backends(implicit ec: ExecutionContext): FailureResponseOrT[CromwellBackends] =
     simpleRequest[CromwellBackends](backendsEndpoint)
-  }
 
-  def version(implicit ec: ExecutionContext): FailureResponseOrT[CromwellVersion] = {
+  def version(implicit ec: ExecutionContext): FailureResponseOrT[CromwellVersion] =
     simpleRequest[CromwellVersion](versionEndpoint)
-  }
 
-  private [api] def executeRequest(request: HttpRequest, headers: List[HttpHeader]) = Http().singleRequest(request.withHeaders(headers))
+  private[api] def executeRequest(request: HttpRequest, headers: List[HttpHeader]) =
+    Http().singleRequest(request.withHeaders(headers))
 
   /**
     *
     * @tparam A The type of response expected. Must be supported by an implicit unmarshaller from ResponseEntity.
     */
-  private def makeRequest[A](request: HttpRequest, headers: List[HttpHeader] = defaultHeaders)
-                            (implicit um: Unmarshaller[ResponseEntity, A], ec: ExecutionContext):
-  FailureResponseOrT[A] = {
+  private def makeRequest[A](request: HttpRequest, headers: List[HttpHeader] = defaultHeaders)(implicit
+    um: Unmarshaller[ResponseEntity, A],
+    ec: ExecutionContext
+  ): FailureResponseOrT[A] = {
     implicit def cs = IO.contextShift(ec)
     for {
       response <- executeRequest(request, headers).asFailureResponseOrT
@@ -191,11 +201,9 @@ class CromwellClient(val cromwellUrl: URL,
 
   private def simpleRequest[A](uri: Uri,
                                method: HttpMethod = HttpMethods.GET,
-                               headers: List[HttpHeader] = defaultHeaders)
-                              (implicit um: Unmarshaller[ResponseEntity, A],
-                               ec: ExecutionContext): FailureResponseOrT[A] = {
+                               headers: List[HttpHeader] = defaultHeaders
+  )(implicit um: Unmarshaller[ResponseEntity, A], ec: ExecutionContext): FailureResponseOrT[A] =
     makeRequest[A](HttpRequest(uri = uri, method = method), headers)
-  }
 
   private val decoders = Map(
     HttpEncodings.gzip -> Gzip,
@@ -203,15 +211,14 @@ class CromwellClient(val cromwellUrl: URL,
     HttpEncodings.identity -> NoCoding
   )
 
-  private def decodeResponse(response: HttpResponse): IO[HttpResponse] = {
+  private def decodeResponse(response: HttpResponse): IO[HttpResponse] =
     decoders.get(response.encoding) map { decoder =>
       IO(decoder.decodeMessage(response))
     } getOrElse IO.raiseError(UnsuccessfulRequestException(s"No decoder for ${response.encoding}", response))
-  }
 }
 
 object CromwellClient {
-  final implicit class EnhancedHttpResponse(val response: HttpResponse) extends AnyVal {
+  implicit final class EnhancedHttpResponse(val response: HttpResponse) extends AnyVal {
 
     def toEntity: IO[Unmarshal[ResponseEntity]] = response match {
       case HttpResponse(_: StatusCodes.Success, _, entity, _) => IO(Unmarshal(entity))
@@ -233,18 +240,17 @@ object CromwellClient {
       "workflowInputs" -> workflowSubmission.inputsJson,
       "workflowOptions" -> workflowSubmission.options,
       "labels" -> workflowSubmission.labels.map(_.toJson.toString)
-    ) collect {
-      case (name, Some(source: String)) =>
-        Multipart.FormData.BodyPart(name, HttpEntity(MediaTypes.`application/json`, ByteString(source)))
+    ) collect { case (name, Some(source: String)) =>
+      Multipart.FormData.BodyPart(name, HttpEntity(MediaTypes.`application/json`, ByteString(source)))
     }
 
     val zipBodyParts = Map(
       "workflowDependencies" -> workflowSubmission.zippedImports
-    ) collect {
-      case (name, Some(file)) => Multipart.FormData.BodyPart.fromPath(name, MediaTypes.`application/zip`, file.path)
+    ) collect { case (name, Some(file)) =>
+      Multipart.FormData.BodyPart.fromPath(name, MediaTypes.`application/zip`, file.path)
     }
 
-    val multipartFormData = Multipart.FormData((sourceBodyParts ++ zipBodyParts).toSeq : _*)
+    val multipartFormData = Multipart.FormData((sourceBodyParts ++ zipBodyParts).toSeq: _*)
     multipartFormData.toEntity()
   }
 
@@ -256,12 +262,11 @@ object CromwellClient {
       "workflowType" -> describeRequest.workflowType,
       "workflowTypeVersion" -> describeRequest.workflowTypeVersion,
       "workflowInputs" -> describeRequest.inputsJson
-    ) collect {
-      case (name, Some(source: String)) =>
-        Multipart.FormData.BodyPart(name, HttpEntity(MediaTypes.`application/json`, ByteString(source)))
+    ) collect { case (name, Some(source: String)) =>
+      Multipart.FormData.BodyPart(name, HttpEntity(MediaTypes.`application/json`, ByteString(source)))
     }
 
-    val multipartFormData = Multipart.FormData(sourceBodyParts.toSeq : _*)
+    val multipartFormData = Multipart.FormData(sourceBodyParts.toSeq: _*)
     multipartFormData.toEntity()
   }
 
@@ -273,12 +278,16 @@ object CromwellClient {
   /**
     * @param args an optional map of HTTP arguments which will be added to the URL
     */
-  private [api] def workflowSpecificGetEndpoint(submitEndpoint: String, workflowId: WorkflowId, endpoint: String, args: Option[Map[String, List[String]]] = None) = {
+  private[api] def workflowSpecificGetEndpoint(submitEndpoint: String,
+                                               workflowId: WorkflowId,
+                                               endpoint: String,
+                                               args: Option[Map[String, List[String]]] = None
+  ) = {
     val url = s"$submitEndpoint/$workflowId/$endpoint"
     val queryBuilder = Uri.Query.newBuilder
-    args.getOrElse(Map.empty).foreach({
-      case (key, l) => l.foreach(v => queryBuilder.+=(key -> v))
-    })
+    args.getOrElse(Map.empty).foreach { case (key, l) =>
+      l.foreach(v => queryBuilder.+=(key -> v))
+    }
     val queryResult = queryBuilder.result()
     Uri(url).withQuery(queryResult)
   }
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/model/CallCacheDiff.scala b/cromwellApiClient/src/main/scala/cromwell/api/model/CallCacheDiff.scala
index fa4e7fb9187..64cafc2b611 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/model/CallCacheDiff.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/model/CallCacheDiff.scala
@@ -4,9 +4,17 @@ import ShardIndexFormatter._
 import WorkflowIdJsonFormatter._
 import spray.json.DefaultJsonProtocol
 
-case class CallCacheDiffCallDescription(executionStatus: String, allowResultReuse: Boolean, callFqn: String, jobIndex: ShardIndex, workflowId: WorkflowId)
+case class CallCacheDiffCallDescription(executionStatus: String,
+                                        allowResultReuse: Boolean,
+                                        callFqn: String,
+                                        jobIndex: ShardIndex,
+                                        workflowId: WorkflowId
+)
 case class HashDifference(hashKey: String, callA: Option[String], callB: Option[String])
-case class CallCacheDiff(callA: CallCacheDiffCallDescription, callB: CallCacheDiffCallDescription, hashDifferential: List[HashDifference])
+case class CallCacheDiff(callA: CallCacheDiffCallDescription,
+                         callB: CallCacheDiffCallDescription,
+                         hashDifferential: List[HashDifference]
+)
 
 object CallCacheDiffJsonSupport extends DefaultJsonProtocol {
   implicit val CallCacheDiffCallDescriptionFormat = jsonFormat5(CallCacheDiffCallDescription)
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/model/CromwellQueryResult.scala b/cromwellApiClient/src/main/scala/cromwell/api/model/CromwellQueryResult.scala
index 4a54cb58469..658ea72489f 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/model/CromwellQueryResult.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/model/CromwellQueryResult.scala
@@ -7,7 +7,13 @@ import cromwell.api.model.WorkflowStatusJsonFormatter._
 
 case class CromwellQueryResults(results: Seq[CromwellQueryResult])
 
-case class CromwellQueryResult(name: Option[String], id: WorkflowId, status: WorkflowStatus, end: Option[OffsetDateTime], start: Option[OffsetDateTime], metadataArchiveStatus: String)
+case class CromwellQueryResult(name: Option[String],
+                               id: WorkflowId,
+                               status: WorkflowStatus,
+                               end: Option[OffsetDateTime],
+                               start: Option[OffsetDateTime],
+                               metadataArchiveStatus: String
+)
 
 object CromwellQueryResultJsonSupport extends DefaultJsonProtocol {
   implicit val CromwellQueryResultJsonFormat = jsonFormat6(CromwellQueryResult)
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/model/Label.scala b/cromwellApiClient/src/main/scala/cromwell/api/model/Label.scala
index fd9d88d2177..0d111626f84 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/model/Label.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/model/Label.scala
@@ -5,7 +5,7 @@ import scala.language.postfixOps
 
 object LabelsJsonFormatter extends DefaultJsonProtocol {
   implicit object LabelJsonFormat extends RootJsonFormat[List[Label]] {
-    def write(l: List[Label]) = JsObject(l map { label => label.key -> JsString(label.value)} :_* )
+    def write(l: List[Label]) = JsObject(l map { label => label.key -> JsString(label.value) }: _*)
     def read(value: JsValue) = value.asJsObject.fields map {
       case (k, JsString(v)) => Label(k, v)
       case other => throw new UnsupportedOperationException(s"Cannot deserialize $other to a Label")
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/model/TimeUtil.scala b/cromwellApiClient/src/main/scala/cromwell/api/model/TimeUtil.scala
index 1688da92ff7..0db0f1c8f66 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/model/TimeUtil.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/model/TimeUtil.scala
@@ -4,6 +4,7 @@ import java.time.format.DateTimeFormatter
 import java.time.{OffsetDateTime, ZoneOffset}
 
 object TimeUtil {
+
   /**
     * Instead of "one of" the valid ISO-8601 formats, standardize on this one:
     * https://github.com/openjdk/jdk/blob/jdk8-b120/jdk/src/share/classes/java/time/OffsetDateTime.java#L1886
@@ -11,12 +12,15 @@ object TimeUtil {
   private val Iso8601MillisecondsFormat = DateTimeFormatter.ofPattern("uuuu-MM-dd'T'HH:mm:ss.SSSXXXXX")
 
   implicit class EnhancedOffsetDateTime(val offsetDateTime: OffsetDateTime) extends AnyVal {
+
     /**
       * Discards the original timezone and shifts the time to UTC, then returns the ISO-8601 formatted string with
       * exactly three digits of milliseconds.
       */
-    def toUtcMilliString: String = Option(offsetDateTime).map(
-      _.atZoneSameInstant(ZoneOffset.UTC).format(Iso8601MillisecondsFormat)
-    ).orNull
+    def toUtcMilliString: String = Option(offsetDateTime)
+      .map(
+        _.atZoneSameInstant(ZoneOffset.UTC).format(Iso8601MillisecondsFormat)
+      )
+      .orNull
   }
 }
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/model/WaasDescription.scala b/cromwellApiClient/src/main/scala/cromwell/api/model/WaasDescription.scala
index e1f679a7b35..f83ca95fb9a 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/model/WaasDescription.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/model/WaasDescription.scala
@@ -22,17 +22,20 @@ final case class WaasDescription(valid: Boolean,
                                  importedDescriptorTypes: List[WaasWorkflowDescriptorType],
                                  meta: JsObject,
                                  parameterMeta: JsObject,
-                                 isRunnableWorkflow: Boolean)
+                                 isRunnableWorkflow: Boolean
+)
 
 final case class WaasDescriptionInputDefinition(name: String,
                                                 valueType: WaasDescriptionWomType,
                                                 optional: Option[Boolean],
                                                 default: Option[JsValue],
-                                                typeDisplayName: String)
+                                                typeDisplayName: String
+)
 
 final case class WaasDescriptionOutputDefinition(name: String,
                                                  valueType: WaasDescriptionWomType,
-                                                 typeDisplayName: String)
+                                                 typeDisplayName: String
+)
 
 final case class WaasDescriptionWomType(typeName: String)
 final case class WaasWorkflowDescriptorType(descriptorType: Option[String], descriptorTypeVersion: Option[String])
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowDescribeRequest.scala b/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowDescribeRequest.scala
index 9ab7ea45ec4..1a46e2117f9 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowDescribeRequest.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowDescribeRequest.scala
@@ -4,4 +4,5 @@ final case class WorkflowDescribeRequest(workflowSource: Option[String],
                                          workflowUrl: Option[String],
                                          workflowType: Option[String],
                                          workflowTypeVersion: Option[String],
-                                         inputsJson: Option[String])
+                                         inputsJson: Option[String]
+)
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowId.scala b/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowId.scala
index f52495136c3..20c3a558790 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowId.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowId.scala
@@ -30,4 +30,3 @@ object WorkflowIdJsonFormatter extends DefaultJsonProtocol {
     }
   }
 }
-
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowStatus.scala b/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowStatus.scala
index 6da1282d2da..70f9aa1efeb 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowStatus.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowStatus.scala
@@ -25,7 +25,7 @@ case object Running extends NonTerminalStatus
 case object Aborting extends NonTerminalStatus
 
 object WorkflowStatus {
-  def apply(status: String): WorkflowStatus = {
+  def apply(status: String): WorkflowStatus =
     status match {
       case "Submitted" => Submitted
       case "Running" => Running
@@ -35,7 +35,6 @@ object WorkflowStatus {
       case "Succeeded" => Succeeded
       case bad => throw new IllegalArgumentException(s"No such status: $bad")
     }
-  }
 
   def apply(workflowStatus: CromwellStatus): WorkflowStatus = apply(workflowStatus.status)
 }
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowSubmission.scala b/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowSubmission.scala
index 5f59368de13..e22d3e93e2e 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowSubmission.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/model/WorkflowSubmission.scala
@@ -22,7 +22,8 @@ final case class WorkflowSingleSubmission(workflowSource: Option[String],
                                           inputsJson: Option[String],
                                           options: Option[String],
                                           labels: Option[List[Label]],
-                                          zippedImports: Option[File]) extends WorkflowSubmission
+                                          zippedImports: Option[File]
+) extends WorkflowSubmission
 
 final case class WorkflowBatchSubmission(workflowSource: Option[String],
                                          workflowUrl: Option[String],
@@ -32,7 +33,8 @@ final case class WorkflowBatchSubmission(workflowSource: Option[String],
                                          inputsBatch: List[String],
                                          options: Option[String],
                                          labels: Option[List[Label]],
-                                         zippedImports: Option[File]) extends WorkflowSubmission {
+                                         zippedImports: Option[File]
+) extends WorkflowSubmission {
 
   override val inputsJson: Option[String] = Option(inputsBatch.mkString(start = "[", sep = ",", end = "]"))
 }
diff --git a/cromwellApiClient/src/main/scala/cromwell/api/model/package.scala b/cromwellApiClient/src/main/scala/cromwell/api/model/package.scala
index 9067ce7157a..ccd75efac1f 100644
--- a/cromwellApiClient/src/main/scala/cromwell/api/model/package.scala
+++ b/cromwellApiClient/src/main/scala/cromwell/api/model/package.scala
@@ -45,7 +45,7 @@ package object model {
   }
 
   implicit class EnhancedFailureResponseOrHttpResponseT(val responseIoT: FailureResponseOrT[HttpResponse])
-    extends AnyVal {
+      extends AnyVal {
     def asHttpResponse: Future[HttpResponse] = {
       val io = responseIoT.value map {
         case Left(response) => response
@@ -55,13 +55,14 @@ package object model {
     }
   }
 
-  implicit class EnhancedFailureResponseOrT[SuccessType](val responseIoT: FailureResponseOrT[SuccessType]) extends AnyVal {
-    final def timeout(duration: FiniteDuration)
-                     (implicit timer: Timer[IO], cs: ContextShift[IO]): FailureResponseOrT[SuccessType] = {
+  implicit class EnhancedFailureResponseOrT[SuccessType](val responseIoT: FailureResponseOrT[SuccessType])
+      extends AnyVal {
+    final def timeout(
+      duration: FiniteDuration
+    )(implicit timer: Timer[IO], cs: ContextShift[IO]): FailureResponseOrT[SuccessType] =
       EitherT(responseIoT.value.timeout(duration))
-    }
 
-    def asIo(implicit materializer: ActorMaterializer, executionContext: ExecutionContext): IO[SuccessType] = {
+    def asIo(implicit materializer: ActorMaterializer, executionContext: ExecutionContext): IO[SuccessType] =
       responseIoT.value flatMap {
         case Left(response) =>
           implicit def cs = IO.contextShift(executionContext)
@@ -72,15 +73,13 @@ package object model {
           })
         case Right(a) => IO.pure(a)
       }
-    }
 
     /**
       * Transforms the IO error from one type to another.
       */
     def mapErrorWith(mapper: Throwable => IO[Nothing]): FailureResponseOrT[SuccessType] = {
-      def handleErrorIo[A](ioIn: IO[A]): IO[A] = {
+      def handleErrorIo[A](ioIn: IO[A]): IO[A] =
         ioIn handleErrorWith mapper
-      }
 
       responseIoT.mapK(FunctionK.lift(handleErrorIo))
     }
diff --git a/cromwellApiClient/src/test/scala/cromwell/api/CromwellClientSpec.scala b/cromwellApiClient/src/test/scala/cromwell/api/CromwellClientSpec.scala
index 1bfecebc0d5..ab653523801 100644
--- a/cromwellApiClient/src/test/scala/cromwell/api/CromwellClientSpec.scala
+++ b/cromwellApiClient/src/test/scala/cromwell/api/CromwellClientSpec.scala
@@ -11,7 +11,6 @@ import org.scalatest.BeforeAndAfterAll
 import org.scalatest.flatspec.AsyncFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class CromwellClientSpec extends AsyncFlatSpec with BeforeAndAfterAll with Matchers with TableDrivenPropertyChecks {
   behavior of "CromwellClient"
 
@@ -40,86 +39,81 @@ class CromwellClientSpec extends AsyncFlatSpec with BeforeAndAfterAll with Match
 
   private val okRequestEntityTests = Table(
     ("description", "workflowSubmission", "expectedJsons", "expectedFiles"),
-
     ("submit a wdl",
-      WorkflowSingleSubmission(Option("wdl"), None, None, None, None, None, None, None, None),
-      Map("workflowSource" -> "wdl"),
-      Map()
+     WorkflowSingleSubmission(Option("wdl"), None, None, None, None, None, None, None, None),
+     Map("workflowSource" -> "wdl"),
+     Map()
     ),
-
     ("batch submit a wdl",
-      WorkflowBatchSubmission(Option("wdl"), None, None, None, None, List(), None, None, None),
-      Map("workflowSource" -> "wdl", "workflowInputs" -> "[]"),
-      Map()
+     WorkflowBatchSubmission(Option("wdl"), None, None, None, None, List(), None, None, None),
+     Map("workflowSource" -> "wdl", "workflowInputs" -> "[]"),
+     Map()
     ),
-
     ("submit a wdl with data",
-      WorkflowSingleSubmission(
-        Option("wdl"),
-        None,
-        None,
-        Option("wfType"),
-        Option("wfTypeVersion"),
-        Option("inputsJson"),
-        Option("optionsJson"),
-        Option(List(Label("labelKey", "labelValue"))),
-        Option(tempFile)
-      ),
-      Map(
-        "workflowSource" -> "wdl",
-        "workflowType" -> "wfType",
-        "workflowTypeVersion" -> "wfTypeVersion",
-        "workflowInputs" -> "inputsJson",
-        "workflowOptions" -> "optionsJson",
-        "labels" -> """{"labelKey":"labelValue"}"""
-      ),
-      Map("workflowDependencies" -> tempFile)
+     WorkflowSingleSubmission(
+       Option("wdl"),
+       None,
+       None,
+       Option("wfType"),
+       Option("wfTypeVersion"),
+       Option("inputsJson"),
+       Option("optionsJson"),
+       Option(List(Label("labelKey", "labelValue"))),
+       Option(tempFile)
+     ),
+     Map(
+       "workflowSource" -> "wdl",
+       "workflowType" -> "wfType",
+       "workflowTypeVersion" -> "wfTypeVersion",
+       "workflowInputs" -> "inputsJson",
+       "workflowOptions" -> "optionsJson",
+       "labels" -> """{"labelKey":"labelValue"}"""
+     ),
+     Map("workflowDependencies" -> tempFile)
     ),
-
     ("submit a wdl using workflow url",
-      WorkflowSingleSubmission(
-        None,
-        Option("https://link-to-url"),
-        None,
-        Option("wfType"),
-        Option("wfTypeVersion"),
-        Option("inputsJson"),
-        Option("optionsJson"),
-        Option(List(Label("labelKey", "labelValue"))),
-        Option(tempFile)
-      ),
-      Map(
-        "workflowUrl" -> "https://link-to-url",
-        "workflowType" -> "wfType",
-        "workflowTypeVersion" -> "wfTypeVersion",
-        "workflowInputs" -> "inputsJson",
-        "workflowOptions" -> "optionsJson",
-        "labels" -> """{"labelKey":"labelValue"}"""
-      ),
-      Map("workflowDependencies" -> tempFile)
+     WorkflowSingleSubmission(
+       None,
+       Option("https://link-to-url"),
+       None,
+       Option("wfType"),
+       Option("wfTypeVersion"),
+       Option("inputsJson"),
+       Option("optionsJson"),
+       Option(List(Label("labelKey", "labelValue"))),
+       Option(tempFile)
+     ),
+     Map(
+       "workflowUrl" -> "https://link-to-url",
+       "workflowType" -> "wfType",
+       "workflowTypeVersion" -> "wfTypeVersion",
+       "workflowInputs" -> "inputsJson",
+       "workflowOptions" -> "optionsJson",
+       "labels" -> """{"labelKey":"labelValue"}"""
+     ),
+     Map("workflowDependencies" -> tempFile)
     ),
-
     ("batch submit a wdl with data",
-      WorkflowBatchSubmission(
-        Option("wdl"),
-        None,
-        None,
-        Option("wfType"),
-        Option("wfTypeVersion"),
-        List("inputsJson1", "inputsJson2"),
-        Option("optionsJson"),
-        Option(List(Label("labelKey", "labelValue"))),
-        Option(tempFile)
-      ),
-      Map(
-        "workflowSource" -> "wdl",
-        "workflowType" -> "wfType",
-        "workflowTypeVersion" -> "wfTypeVersion",
-        "workflowInputs" -> "[inputsJson1,inputsJson2]",
-        "workflowOptions" -> "optionsJson",
-        "labels" -> """{"labelKey":"labelValue"}"""
-      ),
-      Map("workflowDependencies" -> tempFile)
+     WorkflowBatchSubmission(
+       Option("wdl"),
+       None,
+       None,
+       Option("wfType"),
+       Option("wfTypeVersion"),
+       List("inputsJson1", "inputsJson2"),
+       Option("optionsJson"),
+       Option(List(Label("labelKey", "labelValue"))),
+       Option(tempFile)
+     ),
+     Map(
+       "workflowSource" -> "wdl",
+       "workflowType" -> "wfType",
+       "workflowTypeVersion" -> "wfTypeVersion",
+       "workflowInputs" -> "[inputsJson1,inputsJson2]",
+       "workflowOptions" -> "optionsJson",
+       "labels" -> """{"labelKey":"labelValue"}"""
+     ),
+     Map("workflowDependencies" -> tempFile)
     )
   )
 
@@ -132,24 +126,22 @@ class CromwellClientSpec extends AsyncFlatSpec with BeforeAndAfterAll with Match
           contentType.mediaType.isMultipart should be(true)
           val boundary = contentType.mediaType.params("boundary")
 
-          val expectedJsonChunks = expectedJsons map {
-            case (chunkKey, chunkValue) =>
-              s"""|--$boundary
-                  |Content-Type: application/json
-                  |Content-Disposition: form-data; name="$chunkKey"
-                  |
-                  |$chunkValue
-                  |""".stripMargin.replace("\n", "\r\n").trim
+          val expectedJsonChunks = expectedJsons map { case (chunkKey, chunkValue) =>
+            s"""|--$boundary
+                |Content-Type: application/json
+                |Content-Disposition: form-data; name="$chunkKey"
+                |
+                |$chunkValue
+                |""".stripMargin.replace("\n", "\r\n").trim
           }
-          val expectedFileChunks = expectedFiles.iterator map {
-            case (chunkKey, chunkFile) =>
-              s"""|--$boundary
-                  |Content-Type: application/zip
-                  |Content-Disposition: form-data; filename="${chunkFile.name}"; name="$chunkKey"
-                  |""".stripMargin.replace("\n", "\r\n").trim
+          val expectedFileChunks = expectedFiles.iterator map { case (chunkKey, chunkFile) =>
+            s"""|--$boundary
+                |Content-Type: application/zip
+                |Content-Disposition: form-data; filename="${chunkFile.name}"; name="$chunkKey"
+                |""".stripMargin.replace("\n", "\r\n").trim
           }
-          val expectedFileContents = expectedFiles.iterator map {
-            case (_, chunkFile) => chunkFile.contentAsString
+          val expectedFileContents = expectedFiles.iterator map { case (_, chunkFile) =>
+            chunkFile.contentAsString
           }
           val boundaryEnd = s"--$boundary--"
 
diff --git a/cromwellApiClient/src/test/scala/cromwell/api/CromwellResponseFailedSpec.scala b/cromwellApiClient/src/test/scala/cromwell/api/CromwellResponseFailedSpec.scala
index 06841bfad71..34e901857b7 100644
--- a/cromwellApiClient/src/test/scala/cromwell/api/CromwellResponseFailedSpec.scala
+++ b/cromwellApiClient/src/test/scala/cromwell/api/CromwellResponseFailedSpec.scala
@@ -15,15 +15,18 @@ import org.scalatest.matchers.should.Matchers
 import scala.concurrent.duration._
 import scala.concurrent.{Await, Future}
 
-class CromwellResponseFailedSpec extends TestKit(ActorSystem("CromwellResponseFailedSpec"))
-  with AsyncFlatSpecLike with Matchers with BeforeAndAfterAll {
+class CromwellResponseFailedSpec
+    extends TestKit(ActorSystem("CromwellResponseFailedSpec"))
+    with AsyncFlatSpecLike
+    with Matchers
+    with BeforeAndAfterAll {
   override def afterAll(): Unit = {
     Await.ready(system.terminate(), 10.seconds.dilated)
     super.afterAll()
   }
-  
+
   implicit val materializer: ActorMaterializer = ActorMaterializer()
-  
+
   "CromwellAPIClient" should "fail the Future if the HttpResponse is unsuccessful" in {
     val errorMessage =
       """|{
@@ -32,14 +35,15 @@ class CromwellResponseFailedSpec extends TestKit(ActorSystem("CromwellResponseFa
          |}
          |""".stripMargin.trim
     val client = new CromwellClient(new URL("http://fakeurl"), "v1") {
-      override def executeRequest(request: HttpRequest, headers: List[HttpHeader]): Future[HttpResponse] = Future.successful(
-        new HttpResponse(
-          StatusCodes.ServiceUnavailable,
-          List.empty[HttpHeader],
-          HttpEntity(ContentTypes.`application/json`, errorMessage),
-          HttpProtocols.`HTTP/1.1`
+      override def executeRequest(request: HttpRequest, headers: List[HttpHeader]): Future[HttpResponse] =
+        Future.successful(
+          new HttpResponse(
+            StatusCodes.ServiceUnavailable,
+            List.empty[HttpHeader],
+            HttpEntity(ContentTypes.`application/json`, errorMessage),
+            HttpProtocols.`HTTP/1.1`
+          )
         )
-      )
     }
 
     for {
diff --git a/cromwellApiClient/src/test/scala/cromwell/api/model/CromwellQueryResultJsonFormatterSpec.scala b/cromwellApiClient/src/test/scala/cromwell/api/model/CromwellQueryResultJsonFormatterSpec.scala
index 9ac224970bf..4eb0a450aca 100644
--- a/cromwellApiClient/src/test/scala/cromwell/api/model/CromwellQueryResultJsonFormatterSpec.scala
+++ b/cromwellApiClient/src/test/scala/cromwell/api/model/CromwellQueryResultJsonFormatterSpec.scala
@@ -7,50 +7,51 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import spray.json._
 
-
 class CromwellQueryResultJsonFormatterSpec extends AnyFlatSpec with Matchers {
 
   behavior of "CromwellQueryResultJsonFormat"
 
-  val sampleQueryResult = CromwellQueryResults(results = List(
-    CromwellQueryResult(
-      Option("switcheroo"),
-      WorkflowId.fromString("bee51f36-396d-4e22-8a81-33dedff66bf6"),
-      Failed,
-      Option(OffsetDateTime.parse("2017-07-24T14:44:34.010Z")),
+  val sampleQueryResult = CromwellQueryResults(results =
+    List(
+      CromwellQueryResult(
+        Option("switcheroo"),
+        WorkflowId.fromString("bee51f36-396d-4e22-8a81-33dedff66bf6"),
+        Failed,
+        Option(OffsetDateTime.parse("2017-07-24T14:44:34.010Z")),
         Option(OffsetDateTime.parse("2017-07-24T14:44:33.227Z")),
-      "Archived"
-    ),
-    CromwellQueryResult(
-      Option("switcheroo"),
-      WorkflowId.fromString("0071495e-39eb-478e-bc98-8614b986c91e"),
-      Succeeded,
+        "Archived"
+      ),
+      CromwellQueryResult(
+        Option("switcheroo"),
+        WorkflowId.fromString("0071495e-39eb-478e-bc98-8614b986c91e"),
+        Succeeded,
         Option(OffsetDateTime.parse("2017-07-24T15:06:45.940Z")),
-          Option(OffsetDateTime.parse("2017-07-24T15:04:54.372Z")),
-      "Unarchived"
-    ),
-  ))
-
-  val sampleJson =  """|{
-                       |  "results": [
-                       |    {
-                       |      "name": "switcheroo",
-                       |      "id": "bee51f36-396d-4e22-8a81-33dedff66bf6",
-                       |      "status": "Failed",
-                       |      "end": "2017-07-24T14:44:34.010Z",
-                       |      "start": "2017-07-24T14:44:33.227Z",
-                       |      "metadataArchiveStatus": "Archived"
-                       |    },
-                       |    {
-                       |      "name": "switcheroo",
-                       |      "id": "0071495e-39eb-478e-bc98-8614b986c91e",
-                       |      "status": "Succeeded",
-                       |      "end": "2017-07-24T15:06:45.940Z",
-                       |      "start": "2017-07-24T15:04:54.372Z",
-                       |      "metadataArchiveStatus": "Unarchived"
-                       |    }
-                       |  ]
-                       |}""".stripMargin.parseJson.asJsObject
+        Option(OffsetDateTime.parse("2017-07-24T15:04:54.372Z")),
+        "Unarchived"
+      )
+    )
+  )
+
+  val sampleJson = """|{
+                      |  "results": [
+                      |    {
+                      |      "name": "switcheroo",
+                      |      "id": "bee51f36-396d-4e22-8a81-33dedff66bf6",
+                      |      "status": "Failed",
+                      |      "end": "2017-07-24T14:44:34.010Z",
+                      |      "start": "2017-07-24T14:44:33.227Z",
+                      |      "metadataArchiveStatus": "Archived"
+                      |    },
+                      |    {
+                      |      "name": "switcheroo",
+                      |      "id": "0071495e-39eb-478e-bc98-8614b986c91e",
+                      |      "status": "Succeeded",
+                      |      "end": "2017-07-24T15:06:45.940Z",
+                      |      "start": "2017-07-24T15:04:54.372Z",
+                      |      "metadataArchiveStatus": "Unarchived"
+                      |    }
+                      |  ]
+                      |}""".stripMargin.parseJson.asJsObject
 
   it should "write a query result as a structured JsObject" in {
     sampleQueryResult.toJson shouldEqual sampleJson
diff --git a/cromwellApiClient/src/test/scala/cromwell/api/model/LabelsJsonFormatterSpec.scala b/cromwellApiClient/src/test/scala/cromwell/api/model/LabelsJsonFormatterSpec.scala
index c1f1e89c08a..ab0c7e08cbc 100644
--- a/cromwellApiClient/src/test/scala/cromwell/api/model/LabelsJsonFormatterSpec.scala
+++ b/cromwellApiClient/src/test/scala/cromwell/api/model/LabelsJsonFormatterSpec.scala
@@ -4,18 +4,17 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import spray.json._
 
-
 class LabelsJsonFormatterSpec extends AnyFlatSpec with Matchers {
   import cromwell.api.model.LabelsJsonFormatter._
 
   behavior of "WdlValueJsonFormat"
 
   val sampleLabels = List(Label("key-1", "value-1"), Label("key-2", "value-2"), Label("key-3", "value-3"))
-  val sampleJson =  """|{
-                       |  "key-1":"value-1",
-                       |  "key-2":"value-2",
-                       |  "key-3":"value-3"
-                       |}""".stripMargin.parseJson.asJsObject
+  val sampleJson = """|{
+                      |  "key-1":"value-1",
+                      |  "key-2":"value-2",
+                      |  "key-3":"value-3"
+                      |}""".stripMargin.parseJson.asJsObject
 
   it should "write a Label as a structured JsObject" in {
     val label = List(Label("test-key", "test-value"))
diff --git a/cromwellApiClient/src/test/scala/cromwell/api/model/WaasDescriptionJsonSupportSpec.scala b/cromwellApiClient/src/test/scala/cromwell/api/model/WaasDescriptionJsonSupportSpec.scala
index 5bad5f8b21f..7e328ee4725 100644
--- a/cromwellApiClient/src/test/scala/cromwell/api/model/WaasDescriptionJsonSupportSpec.scala
+++ b/cromwellApiClient/src/test/scala/cromwell/api/model/WaasDescriptionJsonSupportSpec.scala
@@ -3,7 +3,6 @@ package cromwell.api.model
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class WaasDescriptionJsonSupportSpec extends AnyFlatSpec with Matchers {
 
   it should "deserialize invalid result JSON" in {
@@ -25,7 +24,6 @@ class WaasDescriptionJsonSupportSpec extends AnyFlatSpec with Matchers {
         |  "isRunnableWorkflow": false
         |}""".stripMargin
 
-
     import cromwell.api.model.WorkflowDescriptionJsonSupport._
     import spray.json._
 
@@ -33,7 +31,11 @@ class WaasDescriptionJsonSupportSpec extends AnyFlatSpec with Matchers {
     val deserialized = jsonAst.convertTo[WaasDescription]
 
     deserialized.valid should be(false)
-    deserialized.errors should be(List("""Failed to import workflow sub_workflow_aborted_import.wdl.:\nBad import sub_workflow_aborted_import.wdl: Failed to resolve 'sub_workflow_aborted_import.wdl' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path"""))
+    deserialized.errors should be(
+      List(
+        """Failed to import workflow sub_workflow_aborted_import.wdl.:\nBad import sub_workflow_aborted_import.wdl: Failed to resolve 'sub_workflow_aborted_import.wdl' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path"""
+      )
+    )
     deserialized.validWorkflow should be(false)
     deserialized.name should be("")
     deserialized.inputs should be(List.empty)
diff --git a/database/migration/src/main/scala/cromwell/database/migration/WdlTransformation.scala b/database/migration/src/main/scala/cromwell/database/migration/WdlTransformation.scala
index cea987fc89a..4f493492d7e 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/WdlTransformation.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/WdlTransformation.scala
@@ -11,15 +11,16 @@ import wom.types.{WomPrimitiveType, WomType}
 
 import scala.util.Try
 
-private [migration] object WdlTransformation {
+private[migration] object WdlTransformation {
 
   def inflate(value: String): Try[String] = Try {
     Option(value) match {
-      case Some(v) => IOUtils.toString(new GZIPInputStream(new ByteArrayInputStream(Base64.decodeBase64(v))), Charset.defaultCharset)
+      case Some(v) =>
+        IOUtils.toString(new GZIPInputStream(new ByteArrayInputStream(Base64.decodeBase64(v))), Charset.defaultCharset)
       case None => null
     }
-  } recover {
-    case _: IOException => value
+  } recover { case _: IOException =>
+    value
   }
 
   def coerceStringToWdl(wdlString: String, womType: WomType) = womType match {
diff --git a/database/migration/src/main/scala/cromwell/database/migration/custom/BatchedTaskChange.scala b/database/migration/src/main/scala/cromwell/database/migration/custom/BatchedTaskChange.scala
index 49db7e4446f..4d5eb16de18 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/custom/BatchedTaskChange.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/custom/BatchedTaskChange.scala
@@ -9,6 +9,7 @@ import liquibase.exception.CustomChangeException
   * Runs a migration as a series of batches.
   */
 trait BatchedTaskChange extends MigrationTaskChange {
+
   /**
     * Returns sql to retrieve the maximum primary key for the table.
     *
@@ -80,14 +81,16 @@ trait BatchedTaskChange extends MigrationTaskChange {
 
   override def migrate(connection: JdbcConnection): Unit = {
 
-    logger.info(s"Running migration $migrationName with a read batch size of " +
-      s"$readBatchSize and a write batch size of $writeBatchSize")
+    logger.info(
+      s"Running migration $migrationName with a read batch size of " +
+        s"$readBatchSize and a write batch size of $writeBatchSize"
+    )
 
     /*
-      * Keep count of the size of the batch.
-      *
-      * @see writeBatchSize
-      */
+     * Keep count of the size of the batch.
+     *
+     * @see writeBatchSize
+     */
     var batchMigrationCounter: Int = 0
 
     val readCount = getReadCount(connection)
@@ -101,25 +104,24 @@ trait BatchedTaskChange extends MigrationTaskChange {
     val paginator = new QueryPaginator(readBatchStatement, readBatchSize, readCount)
 
     // Loop over pages
-    paginator.zipWithIndex foreach {
-      case (resultBatch, page) =>
-        // Loop over rows in page
-        new ResultSetIterator(resultBatch) foreach { row =>
-            batchMigrationCounter += migrateBatchRow(row, migrateBatchStatements)
-            // batchMigrationCounter can actually be bigger than writeBatchSize as wdlValues are processed atomically,
-            // so this is a best effort
-            if (batchMigrationCounter >= writeBatchSize) {
-              migrateBatchStatements.foreach(_.executeBatch())
-              connection.commit()
-              batchMigrationCounter = 0
-            }
+    paginator.zipWithIndex foreach { case (resultBatch, page) =>
+      // Loop over rows in page
+      new ResultSetIterator(resultBatch) foreach { row =>
+        batchMigrationCounter += migrateBatchRow(row, migrateBatchStatements)
+        // batchMigrationCounter can actually be bigger than writeBatchSize as wdlValues are processed atomically,
+        // so this is a best effort
+        if (batchMigrationCounter >= writeBatchSize) {
+          migrateBatchStatements.foreach(_.executeBatch())
+          connection.commit()
+          batchMigrationCounter = 0
         }
+      }
 
-        resultBatch.close()
+      resultBatch.close()
 
-        val progress = Math.min((page + 1) * 100 / pageCount, 100)
-        val progressMessage = s"[$migrationName] $progress%"
-        logger.info(progressMessage)
+      val progress = Math.min((page + 1) * 100 / pageCount, 100)
+      val progressMessage = s"[$migrationName] $progress%"
+      logger.info(progressMessage)
     }
 
     if (batchMigrationCounter != 0) {
diff --git a/database/migration/src/main/scala/cromwell/database/migration/custom/MigrationTaskChange.scala b/database/migration/src/main/scala/cromwell/database/migration/custom/MigrationTaskChange.scala
index 4fa7935e632..f02d0c46d28 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/custom/MigrationTaskChange.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/custom/MigrationTaskChange.scala
@@ -24,7 +24,7 @@ trait MigrationTaskChange extends CustomTaskChange with LazyLogging {
     */
   def migrate(connection: JdbcConnection): Unit
 
-  override def execute(database: Database): Unit = {
+  override def execute(database: Database): Unit =
     try {
       val dbConn = database.getConnection.asInstanceOf[JdbcConnection]
       val autoCommit = dbConn.getAutoCommit
@@ -36,7 +36,6 @@ trait MigrationTaskChange extends CustomTaskChange with LazyLogging {
       case exception: Exception =>
         throw new CustomChangeException(s"Could not apply migration script for $migrationName", exception)
     }
-  }
 
   override def setUp() = {}
 
diff --git a/database/migration/src/main/scala/cromwell/database/migration/custom/QueryPaginator.scala b/database/migration/src/main/scala/cromwell/database/migration/custom/QueryPaginator.scala
index 0e6514043c3..cb85ffdbcac 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/custom/QueryPaginator.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/custom/QueryPaginator.scala
@@ -2,13 +2,10 @@ package cromwell.database.migration.custom
 
 import java.sql.{PreparedStatement, ResultSet}
 
-
-class QueryPaginator(statement: PreparedStatement,
-                     batchSize: Int,
-                     count: Int) extends Iterator[ResultSet] {
+class QueryPaginator(statement: PreparedStatement, batchSize: Int, count: Int) extends Iterator[ResultSet] {
   var cursor = 0
 
-  def next(): ResultSet =  {
+  def next(): ResultSet = {
     statement.setInt(1, cursor)
     statement.setInt(2, cursor + batchSize)
 
diff --git a/database/migration/src/main/scala/cromwell/database/migration/failuremetadata/DeduplicateFailureMessageIds.scala b/database/migration/src/main/scala/cromwell/database/migration/failuremetadata/DeduplicateFailureMessageIds.scala
index 74ab0769b34..9ffea901284 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/failuremetadata/DeduplicateFailureMessageIds.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/failuremetadata/DeduplicateFailureMessageIds.scala
@@ -17,8 +17,10 @@ class DeduplicateFailureMessageIds extends BatchedTaskChange {
   val callFqnColumn = "CALL_FQN"
   val jobScatterIndexColumn = "JOB_SCATTER_INDEX"
   val retryAttemptColumn = "JOB_RETRY_ATTEMPT"
-  val contentEqualityCheck = List(workflowIdColumn, metadataKeyColumn, callFqnColumn, jobScatterIndexColumn, retryAttemptColumn)
-    .map(s => s"(t2.$s = t1.$s OR (t2.$s IS NULL AND t1.$s IS NULL))").mkString(" AND ")
+  val contentEqualityCheck =
+    List(workflowIdColumn, metadataKeyColumn, callFqnColumn, jobScatterIndexColumn, retryAttemptColumn)
+      .map(s => s"(t2.$s = t1.$s OR (t2.$s IS NULL AND t1.$s IS NULL))")
+      .mkString(" AND ")
 
   val fixableFailureMessageFilter = "METADATA_KEY LIKE '%failures[%]%:message'"
 
diff --git a/database/migration/src/main/scala/cromwell/database/migration/liquibase/DiffResultFilter.scala b/database/migration/src/main/scala/cromwell/database/migration/liquibase/DiffResultFilter.scala
index 2365dcf1e4b..e56fa88bc36 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/liquibase/DiffResultFilter.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/liquibase/DiffResultFilter.scala
@@ -1,7 +1,7 @@
 package cromwell.database.migration.liquibase
 
 import liquibase.database.Database
-import liquibase.diff.{DiffResult, Difference, ObjectDifferences}
+import liquibase.diff.{Difference, DiffResult, ObjectDifferences}
 import liquibase.structure.DatabaseObject
 import liquibase.structure.core._
 
@@ -11,6 +11,7 @@ import scala.jdk.CollectionConverters._
   * Filters liquibase results.
   */
 object DiffResultFilter {
+
   /**
     * A filter for a database object.
     */
@@ -42,19 +43,16 @@ object DiffResultFilter {
     val unexpectedObjects = diffResult.getUnexpectedObjects.asScala
     val changedObjects = diffResult.getChangedObjects.asScala
 
-    val newDiffResult = new DiffResult(
-      diffResult.getReferenceSnapshot,
-      diffResult.getComparisonSnapshot,
-      diffResult.getCompareControl)
+    val newDiffResult =
+      new DiffResult(diffResult.getReferenceSnapshot, diffResult.getComparisonSnapshot, diffResult.getCompareControl)
 
     missingObjects.filterNot(unchangedFilter(referenceDatabase, _)).foreach(newDiffResult.addMissingObject)
     unexpectedObjects.filterNot(unchangedFilter(comparisonDatabase, _)).foreach(newDiffResult.addUnexpectedObject)
 
     val filteredChangedObjects =
       changedObjects.filterNot(isSameObject(referenceDatabase, comparisonDatabase, changedFilters))
-    for ((obj, difference) <- filteredChangedObjects) {
+    for ((obj, difference) <- filteredChangedObjects)
       newDiffResult.addChangedObject(obj, difference)
-    }
 
     newDiffResult
   }
@@ -71,12 +69,14 @@ object DiffResultFilter {
     * @param objectAndDiff A tuple of the object and the set of differences.
     * @return True if the object is actually the same.
     */
-  def isSameObject(referenceDatabase: Database, comparisonDatabase: Database, filters: Seq[DiffFilter])
-                  (objectAndDiff: (DatabaseObject, ObjectDifferences)): Boolean = {
+  def isSameObject(referenceDatabase: Database, comparisonDatabase: Database, filters: Seq[DiffFilter])(
+    objectAndDiff: (DatabaseObject, ObjectDifferences)
+  ): Boolean = {
     val (obj, objectDifferences) = objectAndDiff
     val differences = objectDifferences.getDifferences.asScala
     val filtered = filters.foldLeft(differences)((diffs, diffFilter) =>
-      diffs.filterNot(diffFilter(referenceDatabase, comparisonDatabase, obj, _)))
+      diffs.filterNot(diffFilter(referenceDatabase, comparisonDatabase, obj, _))
+    )
     filtered.isEmpty
   }
 
@@ -89,16 +89,19 @@ object DiffResultFilter {
     * @param difference         The difference reported.
     * @return True if the object is actually the same with slightly different column widths.
     */
-  def isVarchar255(referenceDatabase: Database, comparisonDatabase: Database,
-                   databaseObject: DatabaseObject, difference: Difference): Boolean = {
+  def isVarchar255(referenceDatabase: Database,
+                   comparisonDatabase: Database,
+                   databaseObject: DatabaseObject,
+                   difference: Difference
+  ): Boolean = {
     val compared = difference.getComparedValue
     val referenced = difference.getReferenceValue
     compared.isInstanceOf[DataType] && referenced.isInstanceOf[DataType] && {
       val comparedDataType = compared.asInstanceOf[DataType]
       val referencedDataType = referenced.asInstanceOf[DataType]
       comparedDataType.getTypeName == "VARCHAR" && referencedDataType.getTypeName == "VARCHAR" &&
-        // Our liquibase copypasta defaults VARCHAR to 255. Slick without a value defaults to 254
-        (comparedDataType.getColumnSize + referencedDataType.getColumnSize == 255 + 254)
+      // Our liquibase copypasta defaults VARCHAR to 255. Slick without a value defaults to 254
+      (comparedDataType.getColumnSize + referencedDataType.getColumnSize == 255 + 254)
     }
   }
 
@@ -114,9 +117,11 @@ object DiffResultFilter {
     * @param difference The difference reported.
     * @return True if the object is actually similar based on type.
     */
-  def isTypeSimilar(similarTypes: String*)
-                   (referenceDatabase: Database, comparisonDatabase: Database,
-                    databaseObject: DatabaseObject, difference: Difference): Boolean = {
+  def isTypeSimilar(similarTypes: String*)(referenceDatabase: Database,
+                                           comparisonDatabase: Database,
+                                           databaseObject: DatabaseObject,
+                                           difference: Difference
+  ): Boolean = {
     val compared = difference.getComparedValue
     val referenced = difference.getReferenceValue
     compared.isInstanceOf[DataType] && referenced.isInstanceOf[DataType] && {
@@ -137,10 +142,12 @@ object DiffResultFilter {
     * @param difference The difference reported.
     * @return True if the object is actually similar based on type.
     */
-  def isReordered(referenceDatabase: Database, comparisonDatabase: Database,
-                  databaseObject: DatabaseObject, difference: Difference): Boolean = {
+  def isReordered(referenceDatabase: Database,
+                  comparisonDatabase: Database,
+                  databaseObject: DatabaseObject,
+                  difference: Difference
+  ): Boolean =
     difference.getField == "order"
-  }
 
   /**
     * Returns true if the object is a change log object.
@@ -149,7 +156,7 @@ object DiffResultFilter {
     * @param databaseObject The database object.
     * @return True if the object is a change log object.
     */
-  def isChangeLog(database: Database, databaseObject: DatabaseObject): Boolean = {
+  def isChangeLog(database: Database, databaseObject: DatabaseObject): Boolean =
     databaseObject match {
       case table: Table => table.getName.contains("DATABASECHANGELOG")
       case column: Column => isChangeLog(database, column.getRelation)
@@ -157,7 +164,6 @@ object DiffResultFilter {
       case key: PrimaryKey => isChangeLog(database, key.getTable)
       case _ => false
     }
-  }
 
   /**
     * Returns true if the object is liquibase database object.
@@ -166,9 +172,8 @@ object DiffResultFilter {
     * @param databaseObject The database object.
     * @return True if the object is a liquibase database object.
     */
-  def isLiquibaseObject(database: Database, databaseObject: DatabaseObject): Boolean = {
+  def isLiquibaseObject(database: Database, databaseObject: DatabaseObject): Boolean =
     database.isLiquibaseObject(databaseObject)
-  }
 
   /**
     * Returns true if the object is a member of the excluded table.
@@ -178,23 +183,19 @@ object DiffResultFilter {
     * @param databaseObject The database object.
     * @return True if the object is a member of the tables.
     */
-  def isTableObject(tables: Seq[String])
-                   (database: Database, databaseObject: DatabaseObject): Boolean = {
+  def isTableObject(tables: Seq[String])(database: Database, databaseObject: DatabaseObject): Boolean =
     isTableObject(tables, databaseObject)
-  }
 
-  private def isTableObject(tables: Seq[String], databaseObject: DatabaseObject): Boolean = {
+  private def isTableObject(tables: Seq[String], databaseObject: DatabaseObject): Boolean =
     tables.exists(table =>
       databaseObject.getName.equalsIgnoreCase(table) ||
         getContainingObjects(databaseObject).exists(isTableObject(tables, _))
     )
-  }
 
   // getContainingObjects is ill-mannered and returns null when really it ought to return an empty array, so wrap
   // in an `Option` and `getOrElse`.
-  private def getContainingObjects(databaseObject: DatabaseObject): Array[DatabaseObject] = {
+  private def getContainingObjects(databaseObject: DatabaseObject): Array[DatabaseObject] =
     Option(databaseObject.getContainingObjects).getOrElse(Array.empty)
-  }
 
   /**
     * Adds utility methods to a liquibase diff result.
@@ -202,6 +203,7 @@ object DiffResultFilter {
     * @param diffResult The origin diff result.
     */
   implicit class EnhancedDiffResult(val diffResult: DiffResult) extends AnyVal {
+
     /**
       * Filters changelogs.
       *
diff --git a/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala b/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala
index e4823b8b0ac..d8c32f7b8fa 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/liquibase/LiquibaseUtils.scala
@@ -34,7 +34,7 @@ object LiquibaseUtils {
     * @param settings The liquibase settings.
     * @param jdbcConnection A jdbc connection to the database.
     */
-  def updateSchema(settings: LiquibaseSettings)(jdbcConnection: Connection): Unit = {
+  def updateSchema(settings: LiquibaseSettings)(jdbcConnection: Connection): Unit =
     mutex.synchronized {
       val liquibaseConnection = newConnection(jdbcConnection)
       try {
@@ -44,11 +44,9 @@ object LiquibaseUtils {
 
         val liquibase = new Liquibase(settings.changeLogResourcePath, new ClassLoaderResourceAccessor(), database)
         updateSchema(liquibase)
-      } finally {
+      } finally
         closeConnection(liquibaseConnection)
-      }
     }
-  }
 
   /**
     * Wraps a jdbc connection in the database with the appropriate liquibase connection.
@@ -58,21 +56,19 @@ object LiquibaseUtils {
     * @param jdbcConnection The liquibase connection.
     * @return
     */
-  private def newConnection(jdbcConnection: Connection): DatabaseConnection = {
+  private def newConnection(jdbcConnection: Connection): DatabaseConnection =
     jdbcConnection.getMetaData.getDatabaseProductName match {
       case HsqlDatabaseProperties.PRODUCT_NAME => new HsqlConnection(jdbcConnection)
       case _ => new JdbcConnection(jdbcConnection)
     }
-  }
 
   /**
     * Updates the liquibase database.
     *
     * @param liquibase The facade for interacting with liquibase.
     */
-  private def updateSchema(liquibase: Liquibase): Unit = {
+  private def updateSchema(liquibase: Liquibase): Unit =
     liquibase.update(DefaultContexts, DefaultLabelExpression)
-  }
 
   /**
     * Converts a liquibase connection to a liquibase database.
@@ -80,9 +76,8 @@ object LiquibaseUtils {
     * @param liquibaseConnection The liquibase connection.
     * @return The liquibase database.
     */
-  private def toDatabase(liquibaseConnection: DatabaseConnection): Database = {
+  private def toDatabase(liquibaseConnection: DatabaseConnection): Database =
     DatabaseFactory.getInstance().findCorrectDatabaseImplementation(liquibaseConnection)
-  }
 
   /**
     * Compares a reference to a comparison liquibase database.
@@ -91,9 +86,8 @@ object LiquibaseUtils {
     * @param comparisonDatabase The comparison liquibase database.
     * @return The complete diff results.
     */
-  private def compare(referenceDatabase: Database, comparisonDatabase: Database): DiffResult = {
+  private def compare(referenceDatabase: Database, comparisonDatabase: Database): DiffResult =
     DiffGeneratorFactory.getInstance().compare(referenceDatabase, comparisonDatabase, CompareControl.STANDARD)
-  }
 
   /**
     * Compares a reference to a comparison JDBC connection.
@@ -103,7 +97,7 @@ object LiquibaseUtils {
     * @param block          Block of code to run before closing the connections.
     * @return The complete diff results.
     */
-  def compare[T](referenceJdbc: Connection, comparisonJdbc: Connection)(block: DiffResult => T): T = {
+  def compare[T](referenceJdbc: Connection, comparisonJdbc: Connection)(block: DiffResult => T): T =
     mutex.synchronized {
       withConnection(referenceJdbc) { referenceLiquibase =>
         withConnection(comparisonJdbc) { comparisonLiquibase =>
@@ -112,7 +106,6 @@ object LiquibaseUtils {
         }
       }
     }
-  }
 
   /**
     * Provides a connection to a block of code, closing the connection afterwards.
@@ -124,11 +117,10 @@ object LiquibaseUtils {
     */
   private def withConnection[T](jdbcConnection: Connection)(block: DatabaseConnection => T): T = {
     val liquibaseConnection = newConnection(jdbcConnection)
-    try {
+    try
       block(liquibaseConnection)
-    } finally {
+    finally
       closeConnection(liquibaseConnection)
-    }
   }
 
   /**
@@ -136,13 +128,12 @@ object LiquibaseUtils {
     *
     * @param connection The liquibase connection.
     */
-  private def closeConnection(connection: DatabaseConnection): Unit = {
-    try {
+  private def closeConnection(connection: DatabaseConnection): Unit =
+    try
       connection.close()
-    } finally {
+    finally {
       /* ignore */
     }
-  }
 
   /**
     * Returns the changelog for a liquibase setting.
@@ -165,11 +156,10 @@ object LiquibaseUtils {
     * @param settings The liquibase settings.
     * @return The database change sets.
     */
-  def getChangeSets(settings: LiquibaseSettings): Seq[ChangeSet] = {
+  def getChangeSets(settings: LiquibaseSettings): Seq[ChangeSet] =
     mutex.synchronized {
       getChangeLog(settings).getChangeSets.asScala.toList
     }
-  }
 
   /**
     * Returns a schema snapshot.
@@ -177,7 +167,7 @@ object LiquibaseUtils {
     * @param jdbcConnection A jdbc connection to the database.
     * @return The database change sets.
     */
-  def getSnapshot(jdbcConnection: Connection): DatabaseSnapshot = {
+  def getSnapshot(jdbcConnection: Connection): DatabaseSnapshot =
     mutex.synchronized {
       withConnection(jdbcConnection) { referenceLiquibase =>
         val database = toDatabase(referenceLiquibase)
@@ -191,10 +181,8 @@ object LiquibaseUtils {
             database,
             new SnapshotControl(database)
           )
-        } finally {
+        } finally
           database.setObjectQuotingStrategy(objectQuotingStrategy)
-        }
       }
     }
-  }
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/MetadataCustomSql.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/MetadataCustomSql.scala
index 13515de2e8c..84734d37b5a 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/MetadataCustomSql.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/MetadataCustomSql.scala
@@ -17,15 +17,13 @@ abstract class MetadataCustomSql extends CustomSqlChange {
 
   def queries: Array[String]
 
-  override def generateStatements(database: Database): Array[SqlStatement] = {
-    queries map { query =>  new RawSqlStatement(query) }
-  }
+  override def generateStatements(database: Database): Array[SqlStatement] =
+    queries map { query => new RawSqlStatement(query) }
 
   override def setUp(): Unit = ()
 
-  override def validate(database: Database): ValidationErrors = {
+  override def validate(database: Database): ValidationErrors =
     new ValidationErrors()
-  }
 
   override def setFileOpener(resourceAccessor: ResourceAccessor): Unit = ()
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/ExecutionTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/ExecutionTableMigration.scala
index 2792c00ccf0..991bcacb0f0 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/ExecutionTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/ExecutionTableMigration.scala
@@ -32,9 +32,8 @@ class ExecutionTableMigration extends MetadataCustomSql {
     FROM TMP_EXECUTION_MIGRATION e
     JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID
     WHERE
-    e.START_DT IS NOT NULL;"""
-    ,
-    """INSERT INTO METADATA_JOURNAL (
+    e.START_DT IS NOT NULL;""",
+      """INSERT INTO METADATA_JOURNAL (
       WORKFLOW_EXECUTION_UUID,
       METADATA_KEY,
       CALL_FQN,
@@ -54,9 +53,8 @@ class ExecutionTableMigration extends MetadataCustomSql {
     'string',
     NOW()
     FROM TMP_EXECUTION_MIGRATION e
-    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;"""
-    ,
-    s"""INSERT INTO METADATA_JOURNAL (
+    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;""",
+      s"""INSERT INTO METADATA_JOURNAL (
       WORKFLOW_EXECUTION_UUID,
       METADATA_KEY,
       CALL_FQN,
@@ -78,9 +76,8 @@ class ExecutionTableMigration extends MetadataCustomSql {
     FROM TMP_EXECUTION_MIGRATION e
     JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID
     WHERE
-    e.END_DT IS NOT NULL;"""
-    ,
-    """INSERT INTO METADATA_JOURNAL (
+    e.END_DT IS NOT NULL;""",
+      """INSERT INTO METADATA_JOURNAL (
       WORKFLOW_EXECUTION_UUID,
       METADATA_KEY,
       CALL_FQN,
@@ -100,9 +97,8 @@ class ExecutionTableMigration extends MetadataCustomSql {
     'string',
     NOW()
     FROM TMP_EXECUTION_MIGRATION e
-    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;"""
-    ,
-    """INSERT INTO METADATA_JOURNAL (
+    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;""",
+      """INSERT INTO METADATA_JOURNAL (
       WORKFLOW_EXECUTION_UUID,
       METADATA_KEY,
       CALL_FQN,
@@ -123,9 +119,8 @@ class ExecutionTableMigration extends MetadataCustomSql {
     NOW()
     FROM TMP_EXECUTION_MIGRATION e
     JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID
-    WHERE e.RC IS NOT NULL;"""
-    ,
-    s"""INSERT INTO METADATA_JOURNAL (
+    WHERE e.RC IS NOT NULL;""",
+      s"""INSERT INTO METADATA_JOURNAL (
       WORKFLOW_EXECUTION_UUID,
       METADATA_KEY,
       CALL_FQN,
@@ -145,9 +140,8 @@ class ExecutionTableMigration extends MetadataCustomSql {
     'boolean',
     NOW()
     FROM TMP_EXECUTION_MIGRATION e
-    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;"""
-    ,
-    s"""INSERT INTO METADATA_JOURNAL (
+    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;""",
+      s"""INSERT INTO METADATA_JOURNAL (
       WORKFLOW_EXECUTION_UUID,
       METADATA_KEY,
       CALL_FQN,
@@ -169,9 +163,8 @@ class ExecutionTableMigration extends MetadataCustomSql {
     FROM TMP_EXECUTION_MIGRATION e
     JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID
     LEFT JOIN RUNTIME_ATTRIBUTES ra ON e.EXECUTION_ID = ra.EXECUTION_ID AND ra.ATTRIBUTE_NAME = 'preemptible'
-    WHERE ra.ATTRIBUTE_VALUE IS NOT NULL;"""
-    ,
-    """INSERT INTO METADATA_JOURNAL (
+    WHERE ra.ATTRIBUTE_VALUE IS NOT NULL;""",
+      """INSERT INTO METADATA_JOURNAL (
       WORKFLOW_EXECUTION_UUID,
       METADATA_KEY,
       CALL_FQN,
@@ -187,9 +180,8 @@ class ExecutionTableMigration extends MetadataCustomSql {
     ATTEMPT,
     '1900-01-01'
     FROM TMP_EXECUTION_MIGRATION e
-    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;"""
-    ,
-    """INSERT INTO METADATA_JOURNAL (
+    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;""",
+      """INSERT INTO METADATA_JOURNAL (
       WORKFLOW_EXECUTION_UUID,
       METADATA_KEY,
       CALL_FQN,
@@ -205,9 +197,8 @@ class ExecutionTableMigration extends MetadataCustomSql {
     ATTEMPT,
     '1900-01-01'
     FROM TMP_EXECUTION_MIGRATION e
-    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;"""
-    ,
-    """INSERT INTO METADATA_JOURNAL (
+    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;""",
+      """INSERT INTO METADATA_JOURNAL (
       WORKFLOW_EXECUTION_UUID,
       METADATA_KEY,
       CALL_FQN,
@@ -223,9 +214,8 @@ class ExecutionTableMigration extends MetadataCustomSql {
     ATTEMPT,
     '1900-01-01'
     FROM TMP_EXECUTION_MIGRATION e
-    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;"""
-    ,
-    """INSERT INTO METADATA_JOURNAL (
+    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;""",
+      """INSERT INTO METADATA_JOURNAL (
       WORKFLOW_EXECUTION_UUID,
       METADATA_KEY,
       CALL_FQN,
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/FailureEventTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/FailureEventTableMigration.scala
index 60d12342e77..01fa8de0bdf 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/FailureEventTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/FailureEventTableMigration.scala
@@ -5,7 +5,7 @@ import cromwell.database.migration.metadata.MetadataCustomSql
 class FailureEventTableMigration extends MetadataCustomSql {
   import MetadataCustomSql._
 
-  override def queries: Array[String] = {
+  override def queries: Array[String] =
     Array(
       """
         |INSERT INTO METADATA_JOURNAL (
@@ -32,31 +32,30 @@ class FailureEventTableMigration extends MetadataCustomSql {
         |  JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;
       """.stripMargin,
       s"""
-        |INSERT INTO METADATA_JOURNAL (
-        |  WORKFLOW_EXECUTION_UUID,
-        |  METADATA_KEY,
-        |  CALL_FQN,
-        |  JOB_SCATTER_INDEX,
-        |  JOB_RETRY_ATTEMPT,
-        |  METADATA_VALUE,
-        |  METADATA_VALUE_TYPE,
-        |  METADATA_TIMESTAMP
-        |)
-        |SELECT
-        |  WORKFLOW_EXECUTION_UUID,
-        |  CONCAT('failures[', fe.FAILURE_EVENT_ID ,']:timestamp'),
-        |  CALL_FQN,
-        |  IDX,
-        |  ATTEMPT,
-        |  DATE_FORMAT(fe.EVENT_TIMESTAMP, '%Y-%m-%dT%T.%f$Offset'),
-        |  'string',
-        |  NOW()
-        |FROM FAILURE_EVENT fe
-        |  LEFT JOIN EXECUTION e ON fe.EXECUTION_ID = e.EXECUTION_ID
-        |  JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;
+         |INSERT INTO METADATA_JOURNAL (
+         |  WORKFLOW_EXECUTION_UUID,
+         |  METADATA_KEY,
+         |  CALL_FQN,
+         |  JOB_SCATTER_INDEX,
+         |  JOB_RETRY_ATTEMPT,
+         |  METADATA_VALUE,
+         |  METADATA_VALUE_TYPE,
+         |  METADATA_TIMESTAMP
+         |)
+         |SELECT
+         |  WORKFLOW_EXECUTION_UUID,
+         |  CONCAT('failures[', fe.FAILURE_EVENT_ID ,']:timestamp'),
+         |  CALL_FQN,
+         |  IDX,
+         |  ATTEMPT,
+         |  DATE_FORMAT(fe.EVENT_TIMESTAMP, '%Y-%m-%dT%T.%f$Offset'),
+         |  'string',
+         |  NOW()
+         |FROM FAILURE_EVENT fe
+         |  LEFT JOIN EXECUTION e ON fe.EXECUTION_ID = e.EXECUTION_ID
+         |  JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;
       """.stripMargin
     )
-  }
 
   override def getConfirmationMessage: String = "Failure Table migration complete."
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableDescriptionMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableDescriptionMigration.scala
index 8ee97fcc90d..4181d369572 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableDescriptionMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableDescriptionMigration.scala
@@ -4,7 +4,7 @@ import cromwell.database.migration.metadata.MetadataCustomSql
 
 class ExecutionEventTableDescriptionMigration extends MetadataCustomSql {
 
-  override def queries: Array[String] = {
+  override def queries: Array[String] =
     Array(
       """
         |INSERT INTO METADATA_JOURNAL (
@@ -31,7 +31,6 @@ class ExecutionEventTableDescriptionMigration extends MetadataCustomSql {
         |    JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;
       """.stripMargin
     )
-  }
 
   override def getConfirmationMessage: String = "Execution Event Table (Description field) migration complete."
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableEndMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableEndMigration.scala
index d3d80e74f46..669bfd823bc 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableEndMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableEndMigration.scala
@@ -5,34 +5,33 @@ import MetadataCustomSql._
 
 class ExecutionEventTableEndMigration extends MetadataCustomSql {
 
-  override def queries: Array[String] = {
+  override def queries: Array[String] =
     Array(
       s"""
-        |INSERT INTO METADATA_JOURNAL (
-        |  WORKFLOW_EXECUTION_UUID,
-        |  METADATA_KEY,
-        |  CALL_FQN,
-        |  JOB_SCATTER_INDEX,
-        |  JOB_RETRY_ATTEMPT,
-        |  METADATA_VALUE,
-        |  METADATA_VALUE_TYPE,
-        |  METADATA_TIMESTAMP
-        |)
-        |SELECT
-        |  WORKFLOW_EXECUTION_UUID,
-        |  CONCAT('executionEvents[', ev.EVENT_ID ,']:endTime'),
-        |  CALL_FQN,
-        |  IDX,
-        |  ATTEMPT,
-        |  DATE_FORMAT(ev.END_DT, '%Y-%m-%dT%T.%f$Offset'),
-        |  'string',
-        |  NOW()
-        |FROM EXECUTION_EVENT ev
-        |  LEFT JOIN EXECUTION e ON ev.EXECUTION_ID = e.EXECUTION_ID
-        |  JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;
+         |INSERT INTO METADATA_JOURNAL (
+         |  WORKFLOW_EXECUTION_UUID,
+         |  METADATA_KEY,
+         |  CALL_FQN,
+         |  JOB_SCATTER_INDEX,
+         |  JOB_RETRY_ATTEMPT,
+         |  METADATA_VALUE,
+         |  METADATA_VALUE_TYPE,
+         |  METADATA_TIMESTAMP
+         |)
+         |SELECT
+         |  WORKFLOW_EXECUTION_UUID,
+         |  CONCAT('executionEvents[', ev.EVENT_ID ,']:endTime'),
+         |  CALL_FQN,
+         |  IDX,
+         |  ATTEMPT,
+         |  DATE_FORMAT(ev.END_DT, '%Y-%m-%dT%T.%f$Offset'),
+         |  'string',
+         |  NOW()
+         |FROM EXECUTION_EVENT ev
+         |  LEFT JOIN EXECUTION e ON ev.EXECUTION_ID = e.EXECUTION_ID
+         |  JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;
       """.stripMargin
     )
-  }
 
   override def getConfirmationMessage: String = "Execution Event Table (End field) migration complete."
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableStartMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableStartMigration.scala
index e0c9b418460..86168daddf9 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableStartMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/executionevent/ExecutionEventTableStartMigration.scala
@@ -5,33 +5,31 @@ import MetadataCustomSql._
 
 class ExecutionEventTableStartMigration extends MetadataCustomSql {
 
-  override def queries: Array[String] = {
-    Array(
-      s"""
-        |INSERT INTO METADATA_JOURNAL (
-        |  WORKFLOW_EXECUTION_UUID,
-        |  METADATA_KEY,
-        |  CALL_FQN,
-        |  JOB_SCATTER_INDEX,
-        |  JOB_RETRY_ATTEMPT,
-        |  METADATA_VALUE,
-        |  METADATA_VALUE_TYPE,
-        |  METADATA_TIMESTAMP
-        |)
-        |SELECT
-        |  WORKFLOW_EXECUTION_UUID,
-        |  CONCAT('executionEvents[', ev.EVENT_ID ,']:startTime'),
-        |  CALL_FQN,
-        |  IDX,
-        |  ATTEMPT,
-        |  DATE_FORMAT(ev.START_DT, '%Y-%m-%dT%T.%f$Offset'),
-        |  'string',
-        |  NOW()
-        |FROM EXECUTION_EVENT ev
-        |  LEFT JOIN EXECUTION e ON ev.EXECUTION_ID = e.EXECUTION_ID
-        |  JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;
+  override def queries: Array[String] =
+    Array(s"""
+             |INSERT INTO METADATA_JOURNAL (
+             |  WORKFLOW_EXECUTION_UUID,
+             |  METADATA_KEY,
+             |  CALL_FQN,
+             |  JOB_SCATTER_INDEX,
+             |  JOB_RETRY_ATTEMPT,
+             |  METADATA_VALUE,
+             |  METADATA_VALUE_TYPE,
+             |  METADATA_TIMESTAMP
+             |)
+             |SELECT
+             |  WORKFLOW_EXECUTION_UUID,
+             |  CONCAT('executionEvents[', ev.EVENT_ID ,']:startTime'),
+             |  CALL_FQN,
+             |  IDX,
+             |  ATTEMPT,
+             |  DATE_FORMAT(ev.START_DT, '%Y-%m-%dT%T.%f$Offset'),
+             |  'string',
+             |  NOW()
+             |FROM EXECUTION_EVENT ev
+             |  LEFT JOIN EXECUTION e ON ev.EXECUTION_ID = e.EXECUTION_ID
+             |  JOIN WORKFLOW_EXECUTION we ON we.WORKFLOW_EXECUTION_ID = e.WORKFLOW_EXECUTION_ID;
       """.stripMargin)
-  }
 
   override def getConfirmationMessage: String = "Execution Event Table (Start field) migration complete."
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/CallOutputSymbolTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/CallOutputSymbolTableMigration.scala
index 822e8e15fbe..c148fc2dce5 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/CallOutputSymbolTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/CallOutputSymbolTableMigration.scala
@@ -11,23 +11,20 @@ class CallOutputSymbolTableMigration extends SymbolTableMigration {
                              symbolScope: String,
                              symbolIndex: Option[Int],
                              symbolAttempt: Option[Int],
-                             womValue: WomValue): Int = {
-
+                             womValue: WomValue
+  ): Int =
     (symbolIndex, symbolAttempt) match {
       case (Some(index), Some(attempt)) =>
-        val metadataStatementForCall = new MetadataStatementForCall(statement,
-          workflowUuid,
-          symbolScope,
-          index,
-          attempt
-        )
+        val metadataStatementForCall =
+          new MetadataStatementForCall(statement, workflowUuid, symbolScope, index, attempt)
 
         addWdlValue(s"outputs:$symbolName", womValue, metadataStatementForCall)
       case _ =>
-        logger.warn(s"Found output without index or attempt: [$workflowUuid] $symbolScope - $symbolName:$symbolIndex:$symbolAttempt")
+        logger.warn(
+          s"Found output without index or attempt: [$workflowUuid] $symbolScope - $symbolName:$symbolIndex:$symbolAttempt"
+        )
         0
     }
-  }
 
   override def getConfirmationMessage: String = "Call outputs from Symbol Table migration complete."
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/InputSymbolTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/InputSymbolTableMigration.scala
index 13021ed9c72..6aed6fb870c 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/InputSymbolTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/InputSymbolTableMigration.scala
@@ -12,17 +12,13 @@ class InputSymbolTableMigration extends SymbolTableMigration {
                              symbolScope: String,
                              symbolIndex: Option[Int],
                              symbolAttempt: Option[Int],
-                             womValue: WomValue): Int = {
-
+                             womValue: WomValue
+  ): Int =
     (symbolIndex, symbolAttempt) match {
-      case (Some(index) , Some(attempt)) =>
+      case (Some(index), Some(attempt)) =>
         // Call scoped
-        val metadataStatementForCall = new MetadataStatementForCall(statement,
-          workflowUuid,
-          symbolScope,
-          index,
-          attempt
-        )
+        val metadataStatementForCall =
+          new MetadataStatementForCall(statement, workflowUuid, symbolScope, index, attempt)
 
         addWdlValue(s"inputs:$symbolName", womValue, metadataStatementForCall)
       case (None, None) if !symbolScope.contains('.') =>
@@ -31,7 +27,6 @@ class InputSymbolTableMigration extends SymbolTableMigration {
       case _ =>
         0
     }
-  }
 
   override def getConfirmationMessage: String = "Inputs from Symbol Table migration complete."
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/MetadataStatement.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/MetadataStatement.scala
index da3decae867..eb2d6b89e52 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/MetadataStatement.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/MetadataStatement.scala
@@ -42,7 +42,7 @@ class MetadataStatementForWorkflow(preparedStatement: PreparedStatement, workflo
   val dawn = OffsetDateTime.of(0, 1, 1, 0, 0, 0, 0, ZoneOffset.UTC).toSystemTimestamp
   var batchSizeCounter: Int = 0
 
-  private def metadataType(value: Any) = {
+  private def metadataType(value: Any) =
     value match {
       case WomInteger(_) => "int"
       case WomFloat(_) => "number"
@@ -51,16 +51,14 @@ class MetadataStatementForWorkflow(preparedStatement: PreparedStatement, workflo
       case _: Int | Long => "int"
       case _: Double | Float => "number"
       case _: Boolean => "boolean"
-      case _ =>"string"
+      case _ => "string"
     }
-  }
 
-  private def metadataValue(value: Any) = {
+  private def metadataValue(value: Any) =
     value match {
-      case v: WomValue  => v.valueString
+      case v: WomValue => v.valueString
       case v => v.toString
     }
-  }
 
   protected def setStatement() = {
     preparedStatement.setString(MetadataStatement.WorkflowIdIdx, workflowId)
@@ -93,12 +91,11 @@ class MetadataStatementForWorkflow(preparedStatement: PreparedStatement, workflo
   }
 
   /** Adds a non-null value to the metadata journal. */
-  override def addKeyValue(key: String, value: Any) = {
+  override def addKeyValue(key: String, value: Any) =
     if (value != null) {
       preparedStatement.setTimestamp(MetadataStatement.TimestampIdx, OffsetDateTime.now().toSystemTimestamp)
       add(key, value, s"Failed to migrate metadata value $value with key $key for workflow $workflowId")
     }
-  }
 
   override def addEmptyValue(key: String): Unit = {
     preparedStatement.setTimestamp(MetadataStatement.TimestampIdx, dawn)
@@ -106,11 +103,16 @@ class MetadataStatementForWorkflow(preparedStatement: PreparedStatement, workflo
   }
 }
 
-class MetadataStatementForCall(preparedStatement: PreparedStatement, workflowId: String, callFqn: String, index: Int, attempt: Int) extends MetadataStatementForWorkflow(preparedStatement, workflowId) {
+class MetadataStatementForCall(preparedStatement: PreparedStatement,
+                               workflowId: String,
+                               callFqn: String,
+                               index: Int,
+                               attempt: Int
+) extends MetadataStatementForWorkflow(preparedStatement, workflowId) {
   override def setStatement() = {
     preparedStatement.setString(MetadataStatement.WorkflowIdIdx, workflowId)
     preparedStatement.setString(MetadataStatement.CallFqnIdx, callFqn)
     preparedStatement.setInt(MetadataStatement.CallIndexIdx, index)
     preparedStatement.setInt(MetadataStatement.CallAttemptIdx, attempt)
   }
-}
\ No newline at end of file
+}
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/SymbolTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/SymbolTableMigration.scala
index f3d148ed0c5..4ca834535d7 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/SymbolTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/SymbolTableMigration.scala
@@ -25,16 +25,16 @@ trait SymbolTableMigration extends BatchedTaskChange {
   override val readCountQuery = SymbolTableMigration.NbRowsQuery
 
   override val readBatchQuery: String = """
-      |SELECT
-      |    WORKFLOW_EXECUTION_UUID,
-      |    SYMBOL_NAME,
-      |    SYMBOL_SCOPE,
-      |    SYMBOL_INDEX,
-      |    SYMBOL_ATTEMPT,
-      |    WDL_TYPE,
-      |    WDL_VALUE
-      |   FROM TMP_SYMBOL
-      |   WHERE TMP_SYMBOL_ID >= ? AND TMP_SYMBOL_ID < ?;
+                                          |SELECT
+                                          |    WORKFLOW_EXECUTION_UUID,
+                                          |    SYMBOL_NAME,
+                                          |    SYMBOL_SCOPE,
+                                          |    SYMBOL_INDEX,
+                                          |    SYMBOL_ATTEMPT,
+                                          |    WDL_TYPE,
+                                          |    WDL_VALUE
+                                          |   FROM TMP_SYMBOL
+                                          |   WHERE TMP_SYMBOL_ID >= ? AND TMP_SYMBOL_ID < ?;
     """.stripMargin
 
   override val migrateBatchQueries = List(MetadataStatement.InsertSql)
@@ -66,7 +66,9 @@ trait SymbolTableMigration extends BatchedTaskChange {
       case Failure(f) =>
         logger.error(
           s"""Could not parse symbol of type ${row.getString("WDL_TYPE")}
-              |for Workflow $workflowUuid - Call $symbolScope:$symbolIndex""".stripMargin, f)
+             |for Workflow $workflowUuid - Call $symbolScope:$symbolIndex""".stripMargin,
+          f
+        )
         0
     }
   }
@@ -77,14 +79,18 @@ trait SymbolTableMigration extends BatchedTaskChange {
                     symbolScope: String,
                     symbolIndex: Option[Int],
                     symbolAttempt: Option[Int],
-                    womValue: WomValue): Int
+                    womValue: WomValue
+  ): Int
 
   /**
     * Add all necessary statements to the batch for the provided WomValue.
     */
-  protected final def addWdlValue(metadataKey: String, womValue: WomValue, metadataStatementForCall: MetadataStatement): Int = {
+  final protected def addWdlValue(metadataKey: String,
+                                  womValue: WomValue,
+                                  metadataStatementForCall: MetadataStatement
+  ): Int =
     womValue match {
-        // simplify doesn't handle WdlExpression
+      // simplify doesn't handle WdlExpression
       case expr: WdlExpression =>
         metadataStatementForCall.addKeyValue(metadataKey, expr.valueString)
         1
@@ -95,5 +101,4 @@ trait SymbolTableMigration extends BatchedTaskChange {
         }
         simplified.size
     }
-  }
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/WorkflowOutputSymbolTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/WorkflowOutputSymbolTableMigration.scala
index 8902739666e..0e7562310c2 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/WorkflowOutputSymbolTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/symbol/WorkflowOutputSymbolTableMigration.scala
@@ -12,7 +12,8 @@ class WorkflowOutputSymbolTableMigration extends SymbolTableMigration {
                              symbolScope: String,
                              symbolIndex: Option[Int],
                              symbolAttempt: Option[Int],
-                             womValue: WomValue): Int = {
+                             womValue: WomValue
+  ): Int = {
     val metadataStatementForWorkflow = new MetadataStatementForWorkflow(statement, workflowUuid)
     addWdlValue(s"outputs:$symbolScope.$symbolName", womValue, metadataStatementForWorkflow)
   }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/workflowexecution/WorkflowExecutionTableMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/workflowexecution/WorkflowExecutionTableMigration.scala
index 411f596e962..6c343e2c420 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/metadata/table/workflowexecution/WorkflowExecutionTableMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/metadata/table/workflowexecution/WorkflowExecutionTableMigration.scala
@@ -5,108 +5,102 @@ import MetadataCustomSql._
 
 class WorkflowExecutionTableMigration extends MetadataCustomSql {
 
-  override def queries: Array[String] = {
+  override def queries: Array[String] =
     Array(
-    s"""
-      |INSERT INTO METADATA_JOURNAL (
-      |WORKFLOW_EXECUTION_UUID,
-      |METADATA_KEY,
-      |METADATA_VALUE,
-      |METADATA_VALUE_TYPE,
-      |METADATA_TIMESTAMP
-      |)
-      |SELECT
-      |  WORKFLOW_EXECUTION_UUID,
-      |  'submission',
-      |  DATE_FORMAT(START_DT, '%Y-%m-%dT%T.%f$Offset'),
-      |  'string',
-      |  NOW()
-      |FROM WORKFLOW_EXECUTION
-      |WHERE START_DT IS NOT NULL;""".stripMargin
-    ,
-    s"""
-      |INSERT INTO METADATA_JOURNAL (
-      |WORKFLOW_EXECUTION_UUID,
-      |METADATA_KEY,
-      |METADATA_VALUE,
-      |METADATA_VALUE_TYPE,
-      |METADATA_TIMESTAMP
-      |)
-      |SELECT
-      |  WORKFLOW_EXECUTION_UUID,
-      |  'start',
-      |  DATE_FORMAT(START_DT, '%Y-%m-%dT%T.%f$Offset'),
-      |  'string',
-      |  NOW()
-      |FROM WORKFLOW_EXECUTION
-      |WHERE START_DT IS NOT NULL;""".stripMargin
-    ,
-    s"""
-      |INSERT INTO METADATA_JOURNAL (
-      |WORKFLOW_EXECUTION_UUID,
-      |METADATA_KEY,
-      |METADATA_VALUE,
-      |METADATA_VALUE_TYPE,
-      |METADATA_TIMESTAMP
-      |)
-      |SELECT
-      |  WORKFLOW_EXECUTION_UUID,
-      |  'end',
-      |  DATE_FORMAT(END_DT, '%Y-%m-%dT%T.%f$Offset'),
-      |  'string',
-      |  NOW()
-      |FROM WORKFLOW_EXECUTION
-      |WHERE END_DT IS NOT NULL;""".stripMargin
-    ,
-    s"""
-      |INSERT INTO METADATA_JOURNAL (
-      |WORKFLOW_EXECUTION_UUID,
-      |METADATA_KEY,
-      |METADATA_VALUE,
-      |METADATA_VALUE_TYPE,
-      |METADATA_TIMESTAMP
-      |)
-      |SELECT
-      |  WORKFLOW_EXECUTION_UUID,
-      |  'status',
-      |  STATUS,
-      |  'string',
-      |  NOW()
-      |FROM WORKFLOW_EXECUTION;""".stripMargin
-    ,
-    """
-      |INSERT INTO METADATA_JOURNAL (
-      |WORKFLOW_EXECUTION_UUID,
-      |METADATA_KEY,
-      |METADATA_VALUE,
-      |METADATA_VALUE_TYPE,
-      |METADATA_TIMESTAMP
-      |)
-      |SELECT
-      |  WORKFLOW_EXECUTION_UUID,
-      |  'workflowName',
-      |  WORKFLOW_NAME,
-      |  'string',
-      |  NOW()
-      |FROM WORKFLOW_EXECUTION;""".stripMargin
-    ,
-    """
-      |INSERT INTO METADATA_JOURNAL (
-      |WORKFLOW_EXECUTION_UUID,
-      |METADATA_KEY,
-      |METADATA_VALUE,
-      |METADATA_VALUE_TYPE,
-      |METADATA_TIMESTAMP
-      |)
-      |SELECT
-      |  WORKFLOW_EXECUTION_UUID,
-      |  'outputs',
-      |  NULL,
-      |  NULL,
-      |  '1900-01-01 0.000000'
-      |FROM WORKFLOW_EXECUTION;""".stripMargin
+      s"""
+         |INSERT INTO METADATA_JOURNAL (
+         |WORKFLOW_EXECUTION_UUID,
+         |METADATA_KEY,
+         |METADATA_VALUE,
+         |METADATA_VALUE_TYPE,
+         |METADATA_TIMESTAMP
+         |)
+         |SELECT
+         |  WORKFLOW_EXECUTION_UUID,
+         |  'submission',
+         |  DATE_FORMAT(START_DT, '%Y-%m-%dT%T.%f$Offset'),
+         |  'string',
+         |  NOW()
+         |FROM WORKFLOW_EXECUTION
+         |WHERE START_DT IS NOT NULL;""".stripMargin,
+      s"""
+         |INSERT INTO METADATA_JOURNAL (
+         |WORKFLOW_EXECUTION_UUID,
+         |METADATA_KEY,
+         |METADATA_VALUE,
+         |METADATA_VALUE_TYPE,
+         |METADATA_TIMESTAMP
+         |)
+         |SELECT
+         |  WORKFLOW_EXECUTION_UUID,
+         |  'start',
+         |  DATE_FORMAT(START_DT, '%Y-%m-%dT%T.%f$Offset'),
+         |  'string',
+         |  NOW()
+         |FROM WORKFLOW_EXECUTION
+         |WHERE START_DT IS NOT NULL;""".stripMargin,
+      s"""
+         |INSERT INTO METADATA_JOURNAL (
+         |WORKFLOW_EXECUTION_UUID,
+         |METADATA_KEY,
+         |METADATA_VALUE,
+         |METADATA_VALUE_TYPE,
+         |METADATA_TIMESTAMP
+         |)
+         |SELECT
+         |  WORKFLOW_EXECUTION_UUID,
+         |  'end',
+         |  DATE_FORMAT(END_DT, '%Y-%m-%dT%T.%f$Offset'),
+         |  'string',
+         |  NOW()
+         |FROM WORKFLOW_EXECUTION
+         |WHERE END_DT IS NOT NULL;""".stripMargin,
+      s"""
+         |INSERT INTO METADATA_JOURNAL (
+         |WORKFLOW_EXECUTION_UUID,
+         |METADATA_KEY,
+         |METADATA_VALUE,
+         |METADATA_VALUE_TYPE,
+         |METADATA_TIMESTAMP
+         |)
+         |SELECT
+         |  WORKFLOW_EXECUTION_UUID,
+         |  'status',
+         |  STATUS,
+         |  'string',
+         |  NOW()
+         |FROM WORKFLOW_EXECUTION;""".stripMargin,
+      """
+        |INSERT INTO METADATA_JOURNAL (
+        |WORKFLOW_EXECUTION_UUID,
+        |METADATA_KEY,
+        |METADATA_VALUE,
+        |METADATA_VALUE_TYPE,
+        |METADATA_TIMESTAMP
+        |)
+        |SELECT
+        |  WORKFLOW_EXECUTION_UUID,
+        |  'workflowName',
+        |  WORKFLOW_NAME,
+        |  'string',
+        |  NOW()
+        |FROM WORKFLOW_EXECUTION;""".stripMargin,
+      """
+        |INSERT INTO METADATA_JOURNAL (
+        |WORKFLOW_EXECUTION_UUID,
+        |METADATA_KEY,
+        |METADATA_VALUE,
+        |METADATA_VALUE_TYPE,
+        |METADATA_TIMESTAMP
+        |)
+        |SELECT
+        |  WORKFLOW_EXECUTION_UUID,
+        |  'outputs',
+        |  NULL,
+        |  NULL,
+        |  '1900-01-01 0.000000'
+        |FROM WORKFLOW_EXECUTION;""".stripMargin
     )
-  }
 
   override def getConfirmationMessage: String = "Workflow Execution Table migration complete."
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/restart/table/JobStoreSimpletonMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/restart/table/JobStoreSimpletonMigration.scala
index a1857aae21e..13c2ba14e3e 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/restart/table/JobStoreSimpletonMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/restart/table/JobStoreSimpletonMigration.scala
@@ -12,7 +12,7 @@ class JobStoreSimpletonMigration extends AbstractRestartMigration {
 
   // GOTC (substituting COUNT(*) for the projection): 1 row in set (5.22 sec)
   private val QueryOutputsForDoneCallsInRunningWorkflows =
-  """
+    """
       SELECT
         js.JOB_STORE_ID,   -- 1
         s.NAME,            -- 2
@@ -51,9 +51,10 @@ class JobStoreSimpletonMigration extends AbstractRestartMigration {
 
     def buildJobStoreSimpletonEntries(name: String, womValue: WomValue, womType: WomType) = Option(womValue) match {
       case None => List(JobStoreSimpletonEntry(name, null, womType.stableName))
-      case Some(_) => womValue.simplify(name) map { s =>
-        JobStoreSimpletonEntry(s.simpletonKey, s.simpletonValue.valueString, s.simpletonValue.womType.stableName)
-      }
+      case Some(_) =>
+        womValue.simplify(name) map { s =>
+          JobStoreSimpletonEntry(s.simpletonKey, s.simpletonValue.valueString, s.simpletonValue.womType.stableName)
+        }
     }
 
     while (results.next()) {
@@ -73,5 +74,3 @@ class JobStoreSimpletonMigration extends AbstractRestartMigration {
     }
   }
 }
-
-
diff --git a/database/migration/src/main/scala/cromwell/database/migration/restart/table/RenameWorkflowOptionKeysMigration.scala b/database/migration/src/main/scala/cromwell/database/migration/restart/table/RenameWorkflowOptionKeysMigration.scala
index c0610ae368b..9019b95f1c0 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/restart/table/RenameWorkflowOptionKeysMigration.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/restart/table/RenameWorkflowOptionKeysMigration.scala
@@ -11,7 +11,6 @@ object RenameWorkflowOptionKeysMigration {
   private val UpdateWorkflowStore = " UPDATE WORKFLOW_STORE SET WORKFLOW_OPTIONS = ? WHERE WORKFLOW_STORE_ID = ? "
 }
 
-
 class RenameWorkflowOptionKeysMigration extends AbstractRestartMigration {
 
   override protected def description: String = "Workflow option renaming"
@@ -27,7 +26,8 @@ class RenameWorkflowOptionKeysMigration extends AbstractRestartMigration {
         val optionsJson = options.parseJson
         val newOptionsJson = optionsJson match {
           case JsObject(fields) => JsObject(fields map renameOptionKeys)
-          case other => other // There really shouldn't be workflow options of other types, but if there are pass them through.
+          case other =>
+            other // There really shouldn't be workflow options of other types, but if there are pass them through.
         }
 
         insert.setString(1, newOptionsJson.prettyPrint)
diff --git a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/ClearMetadataEntryWorkflowOptions.scala b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/ClearMetadataEntryWorkflowOptions.scala
index 2892e9bc830..d07e8be76ef 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/ClearMetadataEntryWorkflowOptions.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/ClearMetadataEntryWorkflowOptions.scala
@@ -11,5 +11,6 @@ class ClearMetadataEntryWorkflowOptions extends WorkflowOptionsChange {
   override val workflowOptionsColumn = "METADATA_VALUE"
   override val additionalReadBatchFilters = "AND METADATA_KEY = 'submittedFiles:options'"
 
-  override def migrateWorkflowOptions(workflowOptions: WorkflowOptions) = workflowOptions.clearEncryptedValues.asPrettyJson
+  override def migrateWorkflowOptions(workflowOptions: WorkflowOptions) =
+    workflowOptions.clearEncryptedValues.asPrettyJson
 }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/RenameWorkflowOptionsInMetadata.scala b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/RenameWorkflowOptionsInMetadata.scala
index 40dc4533b2d..5f0167b2ac1 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/RenameWorkflowOptionsInMetadata.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/RenameWorkflowOptionsInMetadata.scala
@@ -20,12 +20,14 @@ class RenameWorkflowOptionsInMetadata extends BatchedTaskChange {
         |  WHERE $primaryKeyColumn >= ? AND $primaryKeyColumn < ? $additionalReadBatchFilters;
         |""".stripMargin
 
-  override def migrateBatchQueries = List(s"UPDATE $tableName SET $workflowOptionsColumn = ? WHERE $primaryKeyColumn = ?;")
+  override def migrateBatchQueries = List(
+    s"UPDATE $tableName SET $workflowOptionsColumn = ? WHERE $primaryKeyColumn = ?;"
+  )
 
   override def migrateBatchRow(readRow: ResultSet, migrateStatements: List[PreparedStatement]): Int = {
     val migrateStatement = migrateStatements.head
     val rowId = readRow.getInt(1)
-    
+
     val migratedJson = readRow.getString(2).parseJson match {
       case JsObject(fields) => JsObject(fields map renameOptionKeys)
       case other => other
diff --git a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsChange.scala b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsChange.scala
index 1b519fb65fd..aa6e4ed0557 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsChange.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsChange.scala
@@ -12,6 +12,7 @@ import scala.util.{Failure, Success}
   * Edits the workflow options stored in a table.
   */
 trait WorkflowOptionsChange extends BatchedTaskChange {
+
   /** @return name of the table */
   def tableName: String
 
@@ -47,7 +48,9 @@ trait WorkflowOptionsChange extends BatchedTaskChange {
         |  WHERE $primaryKeyColumn >= ? AND $primaryKeyColumn < ? $additionalReadBatchFilters;
         |""".stripMargin
 
-  override def migrateBatchQueries = List(s"UPDATE $tableName SET $workflowOptionsColumn = ? WHERE $primaryKeyColumn = ?;")
+  override def migrateBatchQueries = List(
+    s"UPDATE $tableName SET $workflowOptionsColumn = ? WHERE $primaryKeyColumn = ?;"
+  )
 
   override def migrateBatchRow(readRow: ResultSet, migrateStatements: List[PreparedStatement]): Int = {
     val migrateStatement = migrateStatements.head
@@ -61,8 +64,7 @@ trait WorkflowOptionsChange extends BatchedTaskChange {
         migrateStatement.addBatch()
         1
       case Failure(exception) =>
-        logger.error(
-          s"Unable to process $tableName pk $rowId\njson:\n$workflowOptionsJson", exception)
+        logger.error(s"Unable to process $tableName pk $rowId\njson:\n$workflowOptionsJson", exception)
         0
     }
   }
diff --git a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsRenaming.scala b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsRenaming.scala
index d148a570fdf..aca4a9f6925 100644
--- a/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsRenaming.scala
+++ b/database/migration/src/main/scala/cromwell/database/migration/workflowoptions/WorkflowOptionsRenaming.scala
@@ -12,10 +12,9 @@ object WorkflowOptionsRenaming {
     "call_logs_dir" -> "final_call_logs_dir"
   )
 
-  def renameOptionKeys(field: JsField): JsField = {
+  def renameOptionKeys(field: JsField): JsField =
     field match {
       case (oldName, value) if RenamedOptionKeys.contains(oldName) => RenamedOptionKeys(oldName) -> value
       case noop => noop
     }
-  }
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/CallCachingSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/CallCachingSlickDatabase.scala
index 8e1b98a4a1c..f0968750cba 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/CallCachingSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/CallCachingSlickDatabase.scala
@@ -18,28 +18,38 @@ trait CallCachingSlickDatabase extends CallCachingSqlDatabase {
 
   import dataAccess.driver.api._
 
-  override def addCallCaching(joins: Seq[CallCachingJoin], batchSize: Int)
-                             (implicit ec: ExecutionContext): Future[Unit] = {
+  override def addCallCaching(joins: Seq[CallCachingJoin], batchSize: Int)(implicit
+    ec: ExecutionContext
+  ): Future[Unit] = {
 
     // Construct parallel lists of parent entries, hashes, simpletons, and detritus from `CallCachingJoin`s.
     val (entries, hashes, simpletons, detritus, aggregations) = joins.toList.foldMap { j =>
-      (List(j.callCachingEntry), List(j.callCachingHashEntries), List(j.callCachingSimpletonEntries), List(j.callCachingDetritusEntries), List(j.callCachingAggregationEntry.toList)) }
+      (List(j.callCachingEntry),
+       List(j.callCachingHashEntries),
+       List(j.callCachingSimpletonEntries),
+       List(j.callCachingDetritusEntries),
+       List(j.callCachingAggregationEntry.toList)
+      )
+    }
 
     // Use the supplied `assigner` function to assign parent entry row IDs into the parallel `Seq` of children entities.
-    def assignEntryIdsToChildren[C](ids: Seq[Long], groupingsOfChildren: Seq[Seq[C]], assigner: (Long, C) => C): Seq[C] = {
+    def assignEntryIdsToChildren[C](ids: Seq[Long],
+                                    groupingsOfChildren: Seq[Seq[C]],
+                                    assigner: (Long, C) => C
+    ): Seq[C] =
       (ids zip groupingsOfChildren) flatMap { case (id, children) => children.map(assigner(id, _)) }
-    }
 
     // Batch insert entities into the appropriate `Table`.
-    def batchInsert[E, T <: Table[E]](entries: Seq[E], tableQuery: TableQuery[T]): DBIO[_] = {
-      DBIO.sequence(entries.grouped(batchSize).map { tableQuery ++= _ })
-    }
+    def batchInsert[E, T <: Table[E]](entries: Seq[E], tableQuery: TableQuery[T]): DBIO[_] =
+      DBIO.sequence(entries.grouped(batchSize).map(tableQuery ++= _))
 
     // Functions to assign call cache entry IDs into child hash entry, simpleton, and detritus rows.
     def hashAssigner(id: Long, hash: CallCachingHashEntry) = hash.copy(callCachingEntryId = Option(id))
-    def simpletonAssigner(id: Long, simpleton: CallCachingSimpletonEntry) = simpleton.copy(callCachingEntryId = Option(id))
+    def simpletonAssigner(id: Long, simpleton: CallCachingSimpletonEntry) =
+      simpleton.copy(callCachingEntryId = Option(id))
     def detritusAssigner(id: Long, detritus: CallCachingDetritusEntry) = detritus.copy(callCachingEntryId = Option(id))
-    def aggregationAssigner(id: Long, aggregation: CallCachingAggregationEntry) = aggregation.copy(callCachingEntryId = Option(id))
+    def aggregationAssigner(id: Long, aggregation: CallCachingAggregationEntry) =
+      aggregation.copy(callCachingEntryId = Option(id))
 
     val action = for {
       entryIds <- dataAccess.callCachingEntryIdsAutoInc ++= entries
@@ -70,87 +80,114 @@ trait CallCachingSlickDatabase extends CallCachingSqlDatabase {
     (0 to 2).toList map { total(_) map { p => PrefixAndLength(p, p.length) } getOrElse doNotMatch }
   }
 
-  override def hasMatchingCallCachingEntriesForBaseAggregation(baseAggregationHash: String, callCachePrefixes: Option[List[String]] = None)
-                                                              (implicit ec: ExecutionContext): Future[Boolean] = {
+  override def hasMatchingCallCachingEntriesForBaseAggregation(baseAggregationHash: String,
+                                                               callCachePrefixes: Option[List[String]] = None
+  )(implicit ec: ExecutionContext): Future[Boolean] = {
     val action = callCachePrefixes match {
       case None => dataAccess.existsCallCachingEntriesForBaseAggregationHash(baseAggregationHash).result
       case Some(ps) =>
         val one :: two :: three :: _ = prefixesAndLengths(ps)
-        dataAccess.existsCallCachingEntriesForBaseAggregationHashWithCallCachePrefix(
-          (baseAggregationHash,
-            one.prefix, one.length,
-            two.prefix, two.length,
-            three.prefix, three.length)).result
+        dataAccess
+          .existsCallCachingEntriesForBaseAggregationHashWithCallCachePrefix(
+            (baseAggregationHash, one.prefix, one.length, two.prefix, two.length, three.prefix, three.length)
+          )
+          .result
     }
     runTransaction(action)
   }
 
-  override def findCacheHitForAggregation(baseAggregationHash: String, inputFilesAggregationHash: Option[String], callCachePathPrefixes: Option[List[String]], excludedIds: Set[Long])
-                                         (implicit ec: ExecutionContext): Future[Option[Long]] = {
+  override def findCacheHitForAggregation(baseAggregationHash: String,
+                                          inputFilesAggregationHash: Option[String],
+                                          callCachePathPrefixes: Option[List[String]],
+                                          excludedIds: Set[Long]
+  )(implicit ec: ExecutionContext): Future[Option[Long]] = {
 
     val action = callCachePathPrefixes match {
       case None =>
-        dataAccess.callCachingEntriesForAggregatedHashes(baseAggregationHash, inputFilesAggregationHash, excludedIds).result.headOption
+        dataAccess
+          .callCachingEntriesForAggregatedHashes(baseAggregationHash, inputFilesAggregationHash, excludedIds)
+          .result
+          .headOption
       case Some(ps) =>
         val one :: two :: three :: _ = prefixesAndLengths(ps)
-        dataAccess.callCachingEntriesForAggregatedHashesWithPrefixes(
-          baseAggregationHash, inputFilesAggregationHash,
-          one.prefix, one.length,
-          two.prefix, two.length,
-          three.prefix, three.length,
-          excludedIds).result.headOption
+        dataAccess
+          .callCachingEntriesForAggregatedHashesWithPrefixes(baseAggregationHash,
+                                                             inputFilesAggregationHash,
+                                                             one.prefix,
+                                                             one.length,
+                                                             two.prefix,
+                                                             two.length,
+                                                             three.prefix,
+                                                             three.length,
+                                                             excludedIds
+          )
+          .result
+          .headOption
     }
 
     runTransaction(action)
   }
 
-  override def queryResultsForCacheId(callCachingEntryId: Long)
-                                     (implicit ec: ExecutionContext): Future[Option[CallCachingJoin]] = {
+  override def queryResultsForCacheId(
+    callCachingEntryId: Long
+  )(implicit ec: ExecutionContext): Future[Option[CallCachingJoin]] = {
     val action = for {
-      callCachingEntryOption <- dataAccess.
-        callCachingEntriesForId(callCachingEntryId).result.headOption
-      callCachingSimpletonEntries <- dataAccess.
-        callCachingSimpletonEntriesForCallCachingEntryId(callCachingEntryId).result
-      callCachingDetritusEntries <- dataAccess.
-        callCachingDetritusEntriesForCallCachingEntryId(callCachingEntryId).result
+      callCachingEntryOption <- dataAccess.callCachingEntriesForId(callCachingEntryId).result.headOption
+      callCachingSimpletonEntries <- dataAccess
+        .callCachingSimpletonEntriesForCallCachingEntryId(callCachingEntryId)
+        .result
+      callCachingDetritusEntries <- dataAccess
+        .callCachingDetritusEntriesForCallCachingEntryId(callCachingEntryId)
+        .result
     } yield callCachingEntryOption.map(
-      CallCachingJoin(_, Seq.empty, None, callCachingSimpletonEntries, callCachingDetritusEntries))
+      CallCachingJoin(_, Seq.empty, None, callCachingSimpletonEntries, callCachingDetritusEntries)
+    )
 
     runTransaction(action)
   }
 
-  private def callCacheJoinFromEntryQuery(callCachingEntry: CallCachingEntry)
-                            (implicit ec: ExecutionContext): DBIO[CallCachingJoin] = {
+  private def callCacheJoinFromEntryQuery(
+    callCachingEntry: CallCachingEntry
+  )(implicit ec: ExecutionContext): DBIO[CallCachingJoin] = {
     val callCachingEntryId = callCachingEntry.callCachingEntryId.get
-    val callCachingSimpletonEntries: DBIO[Seq[CallCachingSimpletonEntry]] = dataAccess.
-      callCachingSimpletonEntriesForCallCachingEntryId(callCachingEntryId).result
-    val callCachingDetritusEntries: DBIO[Seq[CallCachingDetritusEntry]] = dataAccess.
-      callCachingDetritusEntriesForCallCachingEntryId(callCachingEntryId).result
-    val callCachingHashEntries: DBIO[Seq[CallCachingHashEntry]] = dataAccess.
-      callCachingHashEntriesForCallCachingEntryId(callCachingEntryId).result
-    val callCachingAggregationEntries: DBIO[Option[CallCachingAggregationEntry]] = dataAccess.
-      callCachingAggregationForCacheEntryId(callCachingEntryId).result.headOption
-    
-    (callCachingHashEntries, callCachingAggregationEntries, callCachingSimpletonEntries, callCachingDetritusEntries) mapN { 
-      case (hashes, aggregation, simpletons, detrituses) =>
-        CallCachingJoin(callCachingEntry, hashes, aggregation, simpletons, detrituses)
+    val callCachingSimpletonEntries: DBIO[Seq[CallCachingSimpletonEntry]] =
+      dataAccess.callCachingSimpletonEntriesForCallCachingEntryId(callCachingEntryId).result
+    val callCachingDetritusEntries: DBIO[Seq[CallCachingDetritusEntry]] =
+      dataAccess.callCachingDetritusEntriesForCallCachingEntryId(callCachingEntryId).result
+    val callCachingHashEntries: DBIO[Seq[CallCachingHashEntry]] =
+      dataAccess.callCachingHashEntriesForCallCachingEntryId(callCachingEntryId).result
+    val callCachingAggregationEntries: DBIO[Option[CallCachingAggregationEntry]] =
+      dataAccess.callCachingAggregationForCacheEntryId(callCachingEntryId).result.headOption
+
+    (callCachingHashEntries,
+     callCachingAggregationEntries,
+     callCachingSimpletonEntries,
+     callCachingDetritusEntries
+    ) mapN { case (hashes, aggregation, simpletons, detrituses) =>
+      CallCachingJoin(callCachingEntry, hashes, aggregation, simpletons, detrituses)
     }
   }
 
-  override def callCacheJoinForCall(workflowExecutionUuid: String, callFqn: String, index: Int)
-                                   (implicit ec: ExecutionContext): Future[Option[CallCachingJoin]] = {
+  override def callCacheJoinForCall(workflowExecutionUuid: String, callFqn: String, index: Int)(implicit
+    ec: ExecutionContext
+  ): Future[Option[CallCachingJoin]] = {
     val action = for {
-      callCachingEntryOption <- dataAccess.
-        callCachingEntriesForWorkflowFqnIndex((workflowExecutionUuid, callFqn, index)).result.headOption
+      callCachingEntryOption <- dataAccess
+        .callCachingEntriesForWorkflowFqnIndex((workflowExecutionUuid, callFqn, index))
+        .result
+        .headOption
       callCacheJoin <- callCachingEntryOption
-        .fold[DBIOAction[Option[CallCachingJoin], NoStream, Effect.All]](DBIO.successful(None))(callCacheJoinFromEntryQuery(_).map(Option.apply))
+        .fold[DBIOAction[Option[CallCachingJoin], NoStream, Effect.All]](DBIO.successful(None))(
+          callCacheJoinFromEntryQuery(_).map(Option.apply)
+        )
     } yield callCacheJoin
 
     runTransaction(action)
   }
 
-  override def invalidateCall(callCachingEntryId: Long)
-                             (implicit ec: ExecutionContext): Future[Option[CallCachingEntry]] = {
+  override def invalidateCall(
+    callCachingEntryId: Long
+  )(implicit ec: ExecutionContext): Future[Option[CallCachingEntry]] = {
     val action = for {
       _ <- dataAccess.allowResultReuseForCallCachingEntryId(callCachingEntryId).update(false)
       callCachingEntryOption <- dataAccess.callCachingEntriesForId(callCachingEntryId).result.headOption
@@ -159,13 +196,16 @@ trait CallCachingSlickDatabase extends CallCachingSqlDatabase {
     runTransaction(action)
   }
 
-  override def invalidateCallCacheEntryIdsForWorkflowId(workflowExecutionUuid: String)
-                                                       (implicit ec: ExecutionContext): Future[Unit] = {
+  override def invalidateCallCacheEntryIdsForWorkflowId(
+    workflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Unit] = {
     val action = dataAccess.allowResultReuseForWorkflowId(workflowExecutionUuid).update(false)
     runTransaction(action).void
   }
 
-  override def callCacheEntryIdsForWorkflowId(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Seq[Long]] = {
+  override def callCacheEntryIdsForWorkflowId(
+    workflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Seq[Long]] = {
     val action = dataAccess.callCachingEntryIdsForWorkflowId(workflowExecutionUuid).result
     runTransaction(action)
   }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/DockerHashStoreSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/DockerHashStoreSlickDatabase.scala
index 1b70e187083..5109ad17476 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/DockerHashStoreSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/DockerHashStoreSlickDatabase.scala
@@ -15,8 +15,9 @@ trait DockerHashStoreSlickDatabase extends DockerHashStoreSqlDatabase {
   /**
     * Adds a docker hash entry to the store.
     */
-  override def addDockerHashStoreEntry(dockerHashStoreEntry: DockerHashStoreEntry)
-                                      (implicit ec: ExecutionContext): Future[Unit] = {
+  override def addDockerHashStoreEntry(
+    dockerHashStoreEntry: DockerHashStoreEntry
+  )(implicit ec: ExecutionContext): Future[Unit] = {
     val action = dataAccess.dockerHashStoreEntries += dockerHashStoreEntry
     runTransaction(action) void
   }
@@ -25,8 +26,9 @@ trait DockerHashStoreSlickDatabase extends DockerHashStoreSqlDatabase {
     * Retrieves docker hash entries for a workflow.
     *
     */
-  override def queryDockerHashStoreEntries(workflowExecutionUuid: String)
-                                          (implicit ec: ExecutionContext): Future[Seq[DockerHashStoreEntry]] = {
+  override def queryDockerHashStoreEntries(
+    workflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Seq[DockerHashStoreEntry]] = {
     val action = dataAccess.dockerHashStoreEntriesForWorkflowExecutionUuid(workflowExecutionUuid).result
     runTransaction(action)
   }
@@ -34,7 +36,9 @@ trait DockerHashStoreSlickDatabase extends DockerHashStoreSqlDatabase {
   /**
     * Deletes docker hash entries related to a workflow, returning the number of rows affected.
     */
-  override def removeDockerHashStoreEntries(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Int] = {
+  override def removeDockerHashStoreEntries(
+    workflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Int] = {
     val action = dataAccess.dockerHashStoreEntriesForWorkflowExecutionUuid(workflowExecutionUuid).delete
     runTransaction(action)
   }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/EngineSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/EngineSlickDatabase.scala
index bacc10da1ee..fde45e29d6f 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/EngineSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/EngineSlickDatabase.scala
@@ -12,7 +12,7 @@ object EngineSlickDatabase {
 }
 
 class EngineSlickDatabase(originalDatabaseConfig: Config)
-  extends SlickDatabase(originalDatabaseConfig)
+    extends SlickDatabase(originalDatabaseConfig)
     with EngineSqlDatabase
     with WorkflowStoreSlickDatabase
     with JobKeyValueSlickDatabase
diff --git a/database/sql/src/main/scala/cromwell/database/slick/JobKeyValueSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/JobKeyValueSlickDatabase.scala
index 4e28cdb33d5..ec416791ad6 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/JobKeyValueSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/JobKeyValueSlickDatabase.scala
@@ -16,8 +16,7 @@ trait JobKeyValueSlickDatabase extends JobKeyValueSqlDatabase {
     runTransaction(action)
   }
 
-  override def addJobKeyValueEntry(jobKeyValueEntry: JobKeyValueEntry)
-                                  (implicit ec: ExecutionContext): Future[Unit] = {
+  override def addJobKeyValueEntry(jobKeyValueEntry: JobKeyValueEntry)(implicit ec: ExecutionContext): Future[Unit] = {
     val action = if (useSlickUpserts) {
       for {
         _ <- dataAccess.jobKeyValueEntryIdsAutoInc.insertOrUpdate(jobKeyValueEntry)
@@ -31,24 +30,26 @@ trait JobKeyValueSlickDatabase extends JobKeyValueSqlDatabase {
   // !!!!!!! updates running in a single transaction.            !!!!!!!!
   // !!!!!!! https://broadworkbench.atlassian.net/browse/BA-6262 !!!!!!!!
   // !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  private def manualUpsertQuery(jobKeyValueEntry: JobKeyValueEntry)
-                       (implicit ec: ExecutionContext) = for {
-    updateCount <- dataAccess.
-      storeValuesForJobKeyAndStoreKey((
-        jobKeyValueEntry.workflowExecutionUuid,
-        jobKeyValueEntry.callFullyQualifiedName,
-        jobKeyValueEntry.jobIndex,
-        jobKeyValueEntry.jobAttempt,
-        jobKeyValueEntry.storeKey)).
-      update(jobKeyValueEntry.storeValue)
+  private def manualUpsertQuery(jobKeyValueEntry: JobKeyValueEntry)(implicit ec: ExecutionContext) = for {
+    updateCount <- dataAccess
+      .storeValuesForJobKeyAndStoreKey(
+        (jobKeyValueEntry.workflowExecutionUuid,
+         jobKeyValueEntry.callFullyQualifiedName,
+         jobKeyValueEntry.jobIndex,
+         jobKeyValueEntry.jobAttempt,
+         jobKeyValueEntry.storeKey
+        )
+      )
+      .update(jobKeyValueEntry.storeValue)
     _ <- updateCount match {
       case 0 => dataAccess.jobKeyValueEntryIdsAutoInc += jobKeyValueEntry
       case _ => assertUpdateCount("addJobKeyValueEntry", updateCount, 1)
     }
   } yield ()
 
-  def addJobKeyValueEntries(jobKeyValueEntries: Iterable[JobKeyValueEntry])
-                           (implicit ec: ExecutionContext): Future[Unit] = {
+  def addJobKeyValueEntries(
+    jobKeyValueEntries: Iterable[JobKeyValueEntry]
+  )(implicit ec: ExecutionContext): Future[Unit] = {
     val action = if (useSlickUpserts) {
       createBatchUpsert("KeyValueStore", dataAccess.jobKeyValueTableQueryCompiled, jobKeyValueEntries)
     } else {
@@ -57,18 +58,23 @@ trait JobKeyValueSlickDatabase extends JobKeyValueSqlDatabase {
     runTransaction(action).void
   }
 
-  override def queryJobKeyValueEntries(workflowExecutionUuid: String)
-                                      (implicit ec: ExecutionContext): Future[Seq[JobKeyValueEntry]] = {
+  override def queryJobKeyValueEntries(
+    workflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Seq[JobKeyValueEntry]] = {
     val action = dataAccess.jobKeyValueEntriesForWorkflowExecutionUuid(workflowExecutionUuid).result
     runTransaction(action)
   }
 
-  override def queryStoreValue(workflowExecutionUuid: String, callFqn: String, jobScatterIndex: Int,
-                               jobRetryAttempt: Int, storeKey: String)
-                              (implicit ec: ExecutionContext): Future[Option[String]] = {
-    val action = dataAccess.
-      storeValuesForJobKeyAndStoreKey((workflowExecutionUuid, callFqn, jobScatterIndex, jobRetryAttempt, storeKey)).
-      result.headOption
+  override def queryStoreValue(workflowExecutionUuid: String,
+                               callFqn: String,
+                               jobScatterIndex: Int,
+                               jobRetryAttempt: Int,
+                               storeKey: String
+  )(implicit ec: ExecutionContext): Future[Option[String]] = {
+    val action = dataAccess
+      .storeValuesForJobKeyAndStoreKey((workflowExecutionUuid, callFqn, jobScatterIndex, jobRetryAttempt, storeKey))
+      .result
+      .headOption
     runTransaction(action)
   }
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/JobStoreSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/JobStoreSlickDatabase.scala
index 5c13de6dbe3..08c8e637908 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/JobStoreSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/JobStoreSlickDatabase.scala
@@ -11,8 +11,9 @@ trait JobStoreSlickDatabase extends JobStoreSqlDatabase {
 
   import dataAccess.driver.api._
 
-  override def addJobStores(jobStoreJoins: Seq[JobStoreJoin], batchSize: Int)
-                           (implicit ec: ExecutionContext): Future[Unit] = {
+  override def addJobStores(jobStoreJoins: Seq[JobStoreJoin], batchSize: Int)(implicit
+    ec: ExecutionContext
+  ): Future[Unit] = {
 
     def assignJobStoreIdsToSimpletons(jobStoreIds: Seq[Long]): Seq[JobStoreSimpletonEntry] = {
       val simpletonsByJobStoreEntry = jobStoreJoins map { _.jobStoreSimpletonEntries }
@@ -32,13 +33,17 @@ trait JobStoreSlickDatabase extends JobStoreSqlDatabase {
     runTransaction(action)
   }
 
-  override def queryJobStores(workflowExecutionUuid: String, callFqn: String, jobScatterIndex: Int,
-                              jobScatterAttempt: Int)(implicit ec: ExecutionContext):
-  Future[Option[JobStoreJoin]] = {
+  override def queryJobStores(workflowExecutionUuid: String,
+                              callFqn: String,
+                              jobScatterIndex: Int,
+                              jobScatterAttempt: Int
+  )(implicit ec: ExecutionContext): Future[Option[JobStoreJoin]] = {
 
     val action = for {
-      jobStoreEntryOption <- dataAccess.
-        jobStoreEntriesForJobKey((workflowExecutionUuid, callFqn, jobScatterIndex, jobScatterAttempt)).result.headOption
+      jobStoreEntryOption <- dataAccess
+        .jobStoreEntriesForJobKey((workflowExecutionUuid, callFqn, jobScatterIndex, jobScatterAttempt))
+        .result
+        .headOption
       jobStoreSimpletonEntries <- jobStoreEntryOption match {
         case Some(jobStoreEntry) =>
           dataAccess.jobStoreSimpletonEntriesForJobStoreEntryId(jobStoreEntry.jobStoreEntryId.get).result
@@ -49,10 +54,9 @@ trait JobStoreSlickDatabase extends JobStoreSqlDatabase {
     runTransaction(action)
   }
 
-  override def removeJobStores(workflowExecutionUuids: Seq[String])
-                              (implicit ec: ExecutionContext): Future[Seq[Int]] = {
-    val actions = workflowExecutionUuids map {
-      workflowExecutionUuid => dataAccess.jobStoreEntriesForWorkflowExecutionUuid(workflowExecutionUuid).delete
+  override def removeJobStores(workflowExecutionUuids: Seq[String])(implicit ec: ExecutionContext): Future[Seq[Int]] = {
+    val actions = workflowExecutionUuids map { workflowExecutionUuid =>
+      dataAccess.jobStoreEntriesForWorkflowExecutionUuid(workflowExecutionUuid).delete
     }
     runTransaction(DBIO.sequence(actions))
   }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
index eb87f88d101..c0723af6795 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
@@ -8,7 +8,12 @@ import cromwell.database.slick.tables.MetadataDataAccessComponent
 import cromwell.database.sql.MetadataSqlDatabase
 import cromwell.database.sql.SqlConverters._
 import cromwell.database.sql.joins.{CallOrWorkflowQuery, CallQuery, MetadataJobQueryValue, WorkflowQuery}
-import cromwell.database.sql.tables.{CustomLabelEntry, InformationSchemaEntry, MetadataEntry, WorkflowMetadataSummaryEntry}
+import cromwell.database.sql.tables.{
+  CustomLabelEntry,
+  InformationSchemaEntry,
+  MetadataEntry,
+  WorkflowMetadataSummaryEntry
+}
 import net.ceedubs.ficus.Ficus._
 import slick.basic.DatabasePublisher
 import slick.jdbc.{ResultSetConcurrency, ResultSetType}
@@ -23,7 +28,8 @@ object MetadataSlickDatabase {
   }
 
   case class SummarizationPartitionedMetadata(nonSummarizableMetadata: Seq[MetadataEntry],
-                                              summarizableMetadata: Seq[MetadataEntry])
+                                              summarizableMetadata: Seq[MetadataEntry]
+  )
 
   def partitionSummarizationMetadata(rawMetadataEntries: Seq[MetadataEntry],
                                      startMetadataKey: String,
@@ -33,14 +39,24 @@ object MetadataSlickDatabase {
                                      submissionMetadataKey: String,
                                      parentWorkflowIdKey: String,
                                      rootWorkflowIdKey: String,
-                                     labelMetadataKey: String): SummarizationPartitionedMetadata = {
-
-    val exactMatchMetadataKeys = Set(startMetadataKey, endMetadataKey, nameMetadataKey, statusMetadataKey, submissionMetadataKey, parentWorkflowIdKey, rootWorkflowIdKey)
+                                     labelMetadataKey: String
+  ): SummarizationPartitionedMetadata = {
+
+    val exactMatchMetadataKeys = Set(startMetadataKey,
+                                     endMetadataKey,
+                                     nameMetadataKey,
+                                     statusMetadataKey,
+                                     submissionMetadataKey,
+                                     parentWorkflowIdKey,
+                                     rootWorkflowIdKey
+    )
     val startsWithMetadataKeys = Set(labelMetadataKey)
 
     val (summarizable, nonSummarizable) = rawMetadataEntries partition { entry =>
       entry.callFullyQualifiedName.isEmpty && entry.jobIndex.isEmpty && entry.jobAttempt.isEmpty &&
-        (exactMatchMetadataKeys.contains(entry.metadataKey) || startsWithMetadataKeys.exists(entry.metadataKey.startsWith))
+      (exactMatchMetadataKeys.contains(entry.metadataKey) || startsWithMetadataKeys.exists(
+        entry.metadataKey.startsWith
+      ))
     }
 
     SummarizationPartitionedMetadata(
@@ -51,7 +67,7 @@ object MetadataSlickDatabase {
 }
 
 class MetadataSlickDatabase(originalDatabaseConfig: Config)
-  extends SlickDatabase(originalDatabaseConfig)
+    extends SlickDatabase(originalDatabaseConfig)
     with MetadataSqlDatabase
     with SummaryStatusSlickDatabase
     with SummaryQueueSlickDatabase {
@@ -75,24 +91,26 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
                                   submissionMetadataKey: String,
                                   parentWorkflowIdKey: String,
                                   rootWorkflowIdKey: String,
-                                  labelMetadataKey: String)
-                                 (implicit ec: ExecutionContext): Future[Unit] = {
+                                  labelMetadataKey: String
+  )(implicit ec: ExecutionContext): Future[Unit] = {
 
     val partitioned = partitionSummarizationMetadata(
-        rawMetadataEntries = metadataEntries.toSeq,
-        startMetadataKey,
-        endMetadataKey,
-        nameMetadataKey,
-        statusMetadataKey,
-        submissionMetadataKey,
-        parentWorkflowIdKey,
-        rootWorkflowIdKey,
-        labelMetadataKey)
+      rawMetadataEntries = metadataEntries.toSeq,
+      startMetadataKey,
+      endMetadataKey,
+      nameMetadataKey,
+      statusMetadataKey,
+      submissionMetadataKey,
+      parentWorkflowIdKey,
+      rootWorkflowIdKey,
+      labelMetadataKey
+    )
 
     val roleSet = pgLargeObjectWriteRole.map(role => sqlu"""SET ROLE TO "#$role"""")
 
     // These entries also require a write to the summary queue.
-    def writeSummarizable(): Future[Unit] = if (partitioned.summarizableMetadata.isEmpty) Future.successful(()) else {
+    def writeSummarizable(): Future[Unit] = if (partitioned.summarizableMetadata.isEmpty) Future.successful(())
+    else {
       val batchesToWrite = partitioned.summarizableMetadata.grouped(insertBatchSize).toList
       val insertActions = batchesToWrite.map { batch =>
         val insertMetadata = dataAccess.metadataEntryIdsAutoInc ++= batch
@@ -103,8 +121,11 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
 
     // Non-summarizable metadata that only needs to go to the metadata table can be written much more efficiently
     // than summarizable metadata.
-    def writeNonSummarizable(): Future[Unit] = if (partitioned.nonSummarizableMetadata.isEmpty) Future.successful(()) else {
-      val action = DBIO.sequence(roleSet ++ partitioned.nonSummarizableMetadata.grouped(insertBatchSize).map(dataAccess.metadataEntries ++= _))
+    def writeNonSummarizable(): Future[Unit] = if (partitioned.nonSummarizableMetadata.isEmpty) Future.successful(())
+    else {
+      val action = DBIO.sequence(
+        roleSet ++ partitioned.nonSummarizableMetadata.grouped(insertBatchSize).map(dataAccess.metadataEntries ++= _)
+      )
       runLobAction(action).void
     }
 
@@ -119,42 +140,45 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
     runTransaction(action)
   }
 
-  override def metadataSummaryEntryExists(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Boolean] = {
+  override def metadataSummaryEntryExists(
+    workflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Boolean] = {
     val action = dataAccess.workflowMetadataSummaryEntryExistsForWorkflowExecutionUuid(workflowExecutionUuid).result
     runTransaction(action)
   }
 
-  override def queryMetadataEntries(workflowExecutionUuid: String,
-                                    timeout: Duration)
-                                   (implicit ec: ExecutionContext): Future[Seq[MetadataEntry]] = {
+  override def queryMetadataEntries(workflowExecutionUuid: String, timeout: Duration)(implicit
+    ec: ExecutionContext
+  ): Future[Seq[MetadataEntry]] = {
     val action = dataAccess.metadataEntriesForWorkflowExecutionUuid(workflowExecutionUuid).result
     runTransaction(action, timeout = timeout)
   }
 
   override def streamMetadataEntries(workflowExecutionUuid: String): DatabasePublisher[MetadataEntry] = {
-    val action = dataAccess.metadataEntriesForWorkflowSortedById(workflowExecutionUuid)
+    val action = dataAccess
+      .metadataEntriesForWorkflowSortedById(workflowExecutionUuid)
       .result
       .withStatementParameters(
         rsType = ResultSetType.ForwardOnly,
         rsConcurrency = ResultSetConcurrency.ReadOnly,
         // Magic number alert: fetchSize is set to MIN_VALUE for MySQL to stream rather than cache in memory first.
         // Inspired by: https://github.com/slick/slick/issues/1218
-        fetchSize = Integer.MIN_VALUE)
+        fetchSize = Integer.MIN_VALUE
+      )
     database.stream(action)
   }
 
-  override def countMetadataEntries(workflowExecutionUuid: String,
-                                    expandSubWorkflows: Boolean,
-                                    timeout: Duration)
-                                   (implicit ec: ExecutionContext): Future[Int] = {
-    val action = dataAccess.countMetadataEntriesForWorkflowExecutionUuid((workflowExecutionUuid, expandSubWorkflows)).result
+  override def countMetadataEntries(workflowExecutionUuid: String, expandSubWorkflows: Boolean, timeout: Duration)(
+    implicit ec: ExecutionContext
+  ): Future[Int] = {
+    val action =
+      dataAccess.countMetadataEntriesForWorkflowExecutionUuid((workflowExecutionUuid, expandSubWorkflows)).result
     runTransaction(action, timeout = timeout)
   }
 
-  override def queryMetadataEntries(workflowExecutionUuid: String,
-                                    metadataKey: String,
-                                    timeout: Duration)
-                                   (implicit ec: ExecutionContext): Future[Seq[MetadataEntry]] = {
+  override def queryMetadataEntries(workflowExecutionUuid: String, metadataKey: String, timeout: Duration)(implicit
+    ec: ExecutionContext
+  ): Future[Seq[MetadataEntry]] = {
     val action =
       dataAccess.metadataEntriesForWorkflowExecutionUuidAndMetadataKey((workflowExecutionUuid, metadataKey)).result
     runTransaction(action, timeout = timeout)
@@ -163,10 +187,14 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
   override def countMetadataEntries(workflowExecutionUuid: String,
                                     metadataKey: String,
                                     expandSubWorkflows: Boolean,
-                                    timeout: Duration)
-                                   (implicit ec: ExecutionContext): Future[Int] = {
+                                    timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Int] = {
     val action =
-      dataAccess.countMetadataEntriesForWorkflowExecutionUuidAndMetadataKey((workflowExecutionUuid, metadataKey, expandSubWorkflows)).result
+      dataAccess
+        .countMetadataEntriesForWorkflowExecutionUuidAndMetadataKey(
+          (workflowExecutionUuid, metadataKey, expandSubWorkflows)
+        )
+        .result
     runTransaction(action, timeout = timeout)
   }
 
@@ -174,10 +202,10 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
                                     callFullyQualifiedName: String,
                                     jobIndex: Option[Int],
                                     jobAttempt: Option[Int],
-                                    timeout: Duration)
-                                   (implicit ec: ExecutionContext): Future[Seq[MetadataEntry]] = {
-    val action = dataAccess.
-      metadataEntriesForJobKey((workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt)).result
+                                    timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Seq[MetadataEntry]] = {
+    val action =
+      dataAccess.metadataEntriesForJobKey((workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt)).result
     runTransaction(action, timeout = timeout)
   }
 
@@ -186,10 +214,13 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
                                     jobIndex: Option[Int],
                                     jobAttempt: Option[Int],
                                     expandSubWorkflows: Boolean,
-                                    timeout: Duration)
-                                   (implicit ec: ExecutionContext): Future[Int] = {
-    val action = dataAccess.
-      countMetadataEntriesForJobKey((workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt, expandSubWorkflows)).result
+                                    timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Int] = {
+    val action = dataAccess
+      .countMetadataEntriesForJobKey(
+        (workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt, expandSubWorkflows)
+      )
+      .result
     runTransaction(action, timeout = timeout)
   }
 
@@ -198,10 +229,11 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
                                     callFullyQualifiedName: String,
                                     jobIndex: Option[Int],
                                     jobAttempt: Option[Int],
-                                    timeout: Duration)
-                                   (implicit ec: ExecutionContext): Future[Seq[MetadataEntry]] = {
-    val action = dataAccess.metadataEntriesForJobKeyAndMetadataKey((
-      workflowUuid, metadataKey, callFullyQualifiedName, jobIndex, jobAttempt)).result
+                                    timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Seq[MetadataEntry]] = {
+    val action = dataAccess
+      .metadataEntriesForJobKeyAndMetadataKey((workflowUuid, metadataKey, callFullyQualifiedName, jobIndex, jobAttempt))
+      .result
     runTransaction(action, timeout = timeout)
   }
 
@@ -211,10 +243,13 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
                                     jobIndex: Option[Int],
                                     jobAttempt: Option[Int],
                                     expandSubWorkflows: Boolean,
-                                    timeout: Duration)
-                                   (implicit ec: ExecutionContext): Future[Int] = {
-    val action = dataAccess.countMetadataEntriesForJobKeyAndMetadataKey((
-      workflowUuid, metadataKey, callFullyQualifiedName, jobIndex, jobAttempt, expandSubWorkflows)).result
+                                    timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Int] = {
+    val action = dataAccess
+      .countMetadataEntriesForJobKeyAndMetadataKey(
+        (workflowUuid, metadataKey, callFullyQualifiedName, jobIndex, jobAttempt, expandSubWorkflows)
+      )
+      .result
     runTransaction(action, timeout = timeout)
   }
 
@@ -222,15 +257,35 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
                                                     metadataKeysToFilterFor: List[String],
                                                     metadataKeysToFilterOut: List[String],
                                                     metadataJobQueryValue: MetadataJobQueryValue,
-                                                    timeout: Duration)
-                                                   (implicit ec: ExecutionContext): Future[Seq[MetadataEntry]] = {
+                                                    timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Seq[MetadataEntry]] = {
     val action = metadataJobQueryValue match {
       case CallQuery(callFqn, jobIndex, jobAttempt) =>
-        dataAccess.metadataEntriesForJobWithKeyConstraints(workflowExecutionUuid, metadataKeysToFilterFor, metadataKeysToFilterOut, callFqn, jobIndex, jobAttempt).result
+        dataAccess
+          .metadataEntriesForJobWithKeyConstraints(workflowExecutionUuid,
+                                                   metadataKeysToFilterFor,
+                                                   metadataKeysToFilterOut,
+                                                   callFqn,
+                                                   jobIndex,
+                                                   jobAttempt
+          )
+          .result
       case WorkflowQuery =>
-        dataAccess.metadataEntriesWithKeyConstraints(workflowExecutionUuid, metadataKeysToFilterFor, metadataKeysToFilterOut, requireEmptyJobKey = true).result
+        dataAccess
+          .metadataEntriesWithKeyConstraints(workflowExecutionUuid,
+                                             metadataKeysToFilterFor,
+                                             metadataKeysToFilterOut,
+                                             requireEmptyJobKey = true
+          )
+          .result
       case CallOrWorkflowQuery =>
-        dataAccess.metadataEntriesWithKeyConstraints(workflowExecutionUuid, metadataKeysToFilterFor, metadataKeysToFilterOut, requireEmptyJobKey = false).result
+        dataAccess
+          .metadataEntriesWithKeyConstraints(workflowExecutionUuid,
+                                             metadataKeysToFilterFor,
+                                             metadataKeysToFilterOut,
+                                             requireEmptyJobKey = false
+          )
+          .result
     }
     runTransaction(action, timeout = timeout)
   }
@@ -240,88 +295,115 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
                                                     metadataKeysToFilterOut: List[String],
                                                     metadataJobQueryValue: MetadataJobQueryValue,
                                                     expandSubWorkflows: Boolean,
-                                                    timeout: Duration)
-                                                   (implicit ec: ExecutionContext): Future[Int] = {
+                                                    timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Int] = {
     val action = metadataJobQueryValue match {
       case CallQuery(callFqn, jobIndex, jobAttempt) =>
-        dataAccess.countMetadataEntriesForJobWithKeyConstraints(workflowExecutionUuid, metadataKeysToFilterFor, metadataKeysToFilterOut, callFqn, jobIndex, jobAttempt, expandSubWorkflows).result
+        dataAccess
+          .countMetadataEntriesForJobWithKeyConstraints(workflowExecutionUuid,
+                                                        metadataKeysToFilterFor,
+                                                        metadataKeysToFilterOut,
+                                                        callFqn,
+                                                        jobIndex,
+                                                        jobAttempt,
+                                                        expandSubWorkflows
+          )
+          .result
       case WorkflowQuery =>
-        dataAccess.countMetadataEntriesWithKeyConstraints(workflowExecutionUuid, metadataKeysToFilterFor, metadataKeysToFilterOut, requireEmptyJobKey = true, expandSubWorkflows = expandSubWorkflows).result
+        dataAccess
+          .countMetadataEntriesWithKeyConstraints(workflowExecutionUuid,
+                                                  metadataKeysToFilterFor,
+                                                  metadataKeysToFilterOut,
+                                                  requireEmptyJobKey = true,
+                                                  expandSubWorkflows = expandSubWorkflows
+          )
+          .result
       case CallOrWorkflowQuery =>
-        dataAccess.countMetadataEntriesWithKeyConstraints(workflowExecutionUuid, metadataKeysToFilterFor, metadataKeysToFilterOut, requireEmptyJobKey = false, expandSubWorkflows = expandSubWorkflows).result
+        dataAccess
+          .countMetadataEntriesWithKeyConstraints(workflowExecutionUuid,
+                                                  metadataKeysToFilterFor,
+                                                  metadataKeysToFilterOut,
+                                                  requireEmptyJobKey = false,
+                                                  expandSubWorkflows = expandSubWorkflows
+          )
+          .result
     }
     runTransaction(action, timeout = timeout)
   }
 
-  private def updateWorkflowMetadataSummaryEntry(buildUpdatedWorkflowMetadataSummaryEntry:
-                                                 (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry]) =>
-                                                   WorkflowMetadataSummaryEntry)
-                                                (workflowExecutionUuuidAndMetadataEntries: (String, Seq[MetadataEntry]))
-                                                (implicit ec: ExecutionContext): DBIO[Unit] = {
+  private def updateWorkflowMetadataSummaryEntry(
+    buildUpdatedWorkflowMetadataSummaryEntry: (Option[WorkflowMetadataSummaryEntry],
+                                               Seq[MetadataEntry]
+    ) => WorkflowMetadataSummaryEntry
+  )(
+    workflowExecutionUuuidAndMetadataEntries: (String, Seq[MetadataEntry])
+  )(implicit ec: ExecutionContext): DBIO[Unit] = {
     val (workflowExecutionUuid, metadataEntries) = workflowExecutionUuuidAndMetadataEntries
     for {
-    // There might not be a preexisting summary for a given UUID, so `headOption` the result
-      existingWorkflowMetadataSummaryEntry <- dataAccess.
-        workflowMetadataSummaryEntriesForWorkflowExecutionUuid(workflowExecutionUuid).result.headOption
+      // There might not be a preexisting summary for a given UUID, so `headOption` the result
+      existingWorkflowMetadataSummaryEntry <- dataAccess
+        .workflowMetadataSummaryEntriesForWorkflowExecutionUuid(workflowExecutionUuid)
+        .result
+        .headOption
       updatedWorkflowMetadataSummaryEntry = buildUpdatedWorkflowMetadataSummaryEntry(
-        existingWorkflowMetadataSummaryEntry, metadataEntries)
+        existingWorkflowMetadataSummaryEntry,
+        metadataEntries
+      )
       _ <- upsertWorkflowMetadataSummaryEntry(updatedWorkflowMetadataSummaryEntry)
     } yield ()
   }
 
   private def toCustomLabelEntry(metadataEntry: MetadataEntry): CustomLabelEntry = {
-    //Extracting the label key from the MetadataEntry key
+    // Extracting the label key from the MetadataEntry key
     val labelKey = metadataEntry.metadataKey.split("\\:", 2)(1)
     val labelValue = metadataEntry.metadataValue.toRawString
     val customLabelEntry = CustomLabelEntry(labelKey, labelValue, metadataEntry.workflowExecutionUuid)
     customLabelEntry
   }
 
-  private def upsertCustomLabelEntry(customLabelEntry: CustomLabelEntry)
-                                    (implicit ec: ExecutionContext): DBIO[Unit] = {
+  private def upsertCustomLabelEntry(customLabelEntry: CustomLabelEntry)(implicit ec: ExecutionContext): DBIO[Unit] =
     if (useSlickUpserts) {
       for {
         _ <- dataAccess.customLabelEntryIdsAutoInc.insertOrUpdate(customLabelEntry)
       } yield ()
     } else {
       for {
-        updateCount <- dataAccess.
-          customLabelEntriesForWorkflowExecutionUuidAndLabelKey(
+        updateCount <- dataAccess
+          .customLabelEntriesForWorkflowExecutionUuidAndLabelKey(
             (customLabelEntry.workflowExecutionUuid, customLabelEntry.customLabelKey)
-          ).update(customLabelEntry)
+          )
+          .update(customLabelEntry)
         _ <- updateCount match {
           case 0 => dataAccess.customLabelEntryIdsAutoInc += customLabelEntry
           case _ => assertUpdateCount("upsertCustomLabelEntry", updateCount, 1)
         }
       } yield ()
     }
-  }
 
-  private def upsertWorkflowMetadataSummaryEntry(workflowMetadataSummaryEntry: WorkflowMetadataSummaryEntry)
-                                                (implicit ec: ExecutionContext): DBIO[Unit] = {
+  private def upsertWorkflowMetadataSummaryEntry(
+    workflowMetadataSummaryEntry: WorkflowMetadataSummaryEntry
+  )(implicit ec: ExecutionContext): DBIO[Unit] =
     if (useSlickUpserts) {
       for {
         _ <- dataAccess.workflowMetadataSummaryEntryIdsAutoInc.insertOrUpdate(workflowMetadataSummaryEntry)
       } yield ()
     } else {
       for {
-        updateCount <- dataAccess.
-          workflowMetadataSummaryEntriesForWorkflowExecutionUuid(workflowMetadataSummaryEntry.workflowExecutionUuid).
-          update(workflowMetadataSummaryEntry)
+        updateCount <- dataAccess
+          .workflowMetadataSummaryEntriesForWorkflowExecutionUuid(workflowMetadataSummaryEntry.workflowExecutionUuid)
+          .update(workflowMetadataSummaryEntry)
         _ <- updateCount match {
           case 0 => dataAccess.workflowMetadataSummaryEntryIdsAutoInc += workflowMetadataSummaryEntry
           case _ => assertUpdateCount("upsertWorkflowMetadataSummaryEntry", updateCount, 1)
         }
       } yield ()
     }
-  }
 
-  override def summarizeIncreasing(labelMetadataKey: String,
-                                   limit: Int,
-                                   buildUpdatedSummary:
-                                   (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry])
-                                     => WorkflowMetadataSummaryEntry)
-                                  (implicit ec: ExecutionContext): Future[Long] = {
+  override def summarizeIncreasing(
+    labelMetadataKey: String,
+    limit: Int,
+    buildUpdatedSummary: (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry]) => WorkflowMetadataSummaryEntry
+  )(implicit ec: ExecutionContext): Future[Long] = {
     val action = for {
       rawMetadataEntries <- dataAccess.metadataEntriesToSummarizeQuery(limit.toLong).result
       _ <-
@@ -337,14 +419,13 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
     runTransaction(action)
   }
 
-  override def summarizeDecreasing(summaryNameDecreasing: String,
-                                   summaryNameIncreasing: String,
-                                   labelMetadataKey: String,
-                                   limit: Int,
-                                   buildUpdatedSummary:
-                                   (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry])
-                                     => WorkflowMetadataSummaryEntry)
-                                  (implicit ec: ExecutionContext): Future[(Long, Long)] = {
+  override def summarizeDecreasing(
+    summaryNameDecreasing: String,
+    summaryNameIncreasing: String,
+    labelMetadataKey: String,
+    limit: Int,
+    buildUpdatedSummary: (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry]) => WorkflowMetadataSummaryEntry
+  )(implicit ec: ExecutionContext): Future[(Long, Long)] = {
     val action = for {
       previousExistingMetadataEntryIdOption <- getSummaryStatusEntrySummaryPosition(summaryNameDecreasing)
       previousInitializedMetadataEntryIdOption <- previousExistingMetadataEntryIdOption match {
@@ -372,13 +453,14 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
     runTransaction(action)
   }
 
-  private def buildMetadataSummaryFromRawMetadataAndWriteToDb(rawMetadataEntries: Seq[MetadataEntry],
-                                                              labelMetadataKey: String,
-                                                              buildUpdatedSummary:
-                                                              (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry]) => WorkflowMetadataSummaryEntry
-                                                             )(implicit ec: ExecutionContext): DBIO[Unit] = {
+  private def buildMetadataSummaryFromRawMetadataAndWriteToDb(
+    rawMetadataEntries: Seq[MetadataEntry],
+    labelMetadataKey: String,
+    buildUpdatedSummary: (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry]) => WorkflowMetadataSummaryEntry
+  )(implicit ec: ExecutionContext): DBIO[Unit] = {
 
-    val (summarizableLabelsMetadata, summarizableRegularMetadata) = rawMetadataEntries.partition(_.metadataKey.contains(labelMetadataKey))
+    val (summarizableLabelsMetadata, summarizableRegularMetadata) =
+      rawMetadataEntries.partition(_.metadataKey.contains(labelMetadataKey))
     val groupedSummarizableRegularMetadata = summarizableRegularMetadata.groupBy(_.workflowExecutionUuid)
 
     for {
@@ -387,25 +469,32 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
     } yield ()
   }
 
-  override def updateMetadataArchiveStatus(workflowExecutionUuid: String, newArchiveStatus: Option[String]): Future[Int] = {
+  override def updateMetadataArchiveStatus(workflowExecutionUuid: String,
+                                           newArchiveStatus: Option[String]
+  ): Future[Int] = {
     val action = dataAccess.metadataArchiveStatusByWorkflowId(workflowExecutionUuid).update(newArchiveStatus)
     runTransaction(action)
   }
 
-  override def getWorkflowStatus(workflowExecutionUuid: String)
-                                (implicit ec: ExecutionContext): Future[Option[String]] = {
+  override def getWorkflowStatus(
+    workflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Option[String]] = {
     val action = dataAccess.workflowStatusesForWorkflowExecutionUuid(workflowExecutionUuid).result.headOption
     // The workflow might not exist, so `headOption`.  But even if the workflow does exist, the status might be None.
     // So flatten the Option[Option[String]] to Option[String].
     runTransaction(action).map(_.flatten)
   }
 
-  override def getWorkflowLabels(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Map[String, String]] = {
+  override def getWorkflowLabels(
+    workflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Map[String, String]] = {
     val action = dataAccess.labelsForWorkflowExecutionUuid(workflowExecutionUuid).result
     runTransaction(action).map(_.toMap)
   }
 
-  override def getRootAndSubworkflowLabels(rootWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Map[String, Map[String, String]]] = {
+  override def getRootAndSubworkflowLabels(
+    rootWorkflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Map[String, Map[String, String]]] = {
     val action = dataAccess.labelsForWorkflowAndSubworkflows(rootWorkflowExecutionUuid).result
     // An empty Map of String workflow IDs to an inner Map of label keys to label values.
     // The outer Map has a default value so any request for a workflow ID not already present
@@ -424,10 +513,10 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
                                       workflowStatuses: Set[String],
                                       workflowNames: Set[String],
                                       workflowExecutionUuids: Set[String],
-                                      labelAndKeyLabelValues: Set[(String,String)],
-                                      labelOrKeyLabelValues: Set[(String,String)],
-                                      excludeLabelAndValues: Set[(String,String)],
-                                      excludeLabelOrValues: Set[(String,String)],
+                                      labelAndKeyLabelValues: Set[(String, String)],
+                                      labelOrKeyLabelValues: Set[(String, String)],
+                                      excludeLabelAndValues: Set[(String, String)],
+                                      excludeLabelOrValues: Set[(String, String)],
                                       submissionTimestampOption: Option[Timestamp],
                                       startTimestampOption: Option[Timestamp],
                                       endTimestampOption: Option[Timestamp],
@@ -435,12 +524,27 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
                                       includeSubworkflows: Boolean,
                                       page: Option[Int],
                                       pageSize: Option[Int],
-                                      newestFirst: Boolean)
-                                     (implicit ec: ExecutionContext): Future[Seq[WorkflowMetadataSummaryEntry]] = {
-
-    val action = dataAccess.queryWorkflowMetadataSummaryEntries(parentIdWorkflowMetadataKey, workflowStatuses, workflowNames, workflowExecutionUuids,
-      labelAndKeyLabelValues, labelOrKeyLabelValues, excludeLabelAndValues, excludeLabelOrValues, submissionTimestampOption, startTimestampOption,
-      endTimestampOption, metadataArchiveStatus, includeSubworkflows, page, pageSize, newestFirst)
+                                      newestFirst: Boolean
+  )(implicit ec: ExecutionContext): Future[Seq[WorkflowMetadataSummaryEntry]] = {
+
+    val action = dataAccess.queryWorkflowMetadataSummaryEntries(
+      parentIdWorkflowMetadataKey,
+      workflowStatuses,
+      workflowNames,
+      workflowExecutionUuids,
+      labelAndKeyLabelValues,
+      labelOrKeyLabelValues,
+      excludeLabelAndValues,
+      excludeLabelOrValues,
+      submissionTimestampOption,
+      startTimestampOption,
+      endTimestampOption,
+      metadataArchiveStatus,
+      includeSubworkflows,
+      page,
+      pageSize,
+      newestFirst
+    )
     runTransaction(action)
   }
 
@@ -448,79 +552,110 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
                                       workflowStatuses: Set[String],
                                       workflowNames: Set[String],
                                       workflowExecutionUuids: Set[String],
-                                      labelAndKeyLabelValues: Set[(String,String)],
-                                      labelOrKeyLabelValues: Set[(String,String)],
-                                      excludeLabelAndValues: Set[(String,String)],
-                                      excludeLabelOrValues: Set[(String,String)],
+                                      labelAndKeyLabelValues: Set[(String, String)],
+                                      labelOrKeyLabelValues: Set[(String, String)],
+                                      excludeLabelAndValues: Set[(String, String)],
+                                      excludeLabelOrValues: Set[(String, String)],
                                       submissionTimestampOption: Option[Timestamp],
                                       startTimestampOption: Option[Timestamp],
                                       endTimestampOption: Option[Timestamp],
                                       metadataArchiveStatus: Set[Option[String]],
-                                      includeSubworkflows: Boolean)
-                                     (implicit ec: ExecutionContext): Future[Int] = {
-    val action = dataAccess.countWorkflowMetadataSummaryEntries(parentIdWorkflowMetadataKey, workflowStatuses, workflowNames, workflowExecutionUuids,
-      labelAndKeyLabelValues, labelOrKeyLabelValues, excludeLabelAndValues, excludeLabelOrValues, submissionTimestampOption, startTimestampOption,
-      endTimestampOption, metadataArchiveStatus, includeSubworkflows)
+                                      includeSubworkflows: Boolean
+  )(implicit ec: ExecutionContext): Future[Int] = {
+    val action = dataAccess.countWorkflowMetadataSummaryEntries(
+      parentIdWorkflowMetadataKey,
+      workflowStatuses,
+      workflowNames,
+      workflowExecutionUuids,
+      labelAndKeyLabelValues,
+      labelOrKeyLabelValues,
+      excludeLabelAndValues,
+      excludeLabelOrValues,
+      submissionTimestampOption,
+      startTimestampOption,
+      endTimestampOption,
+      metadataArchiveStatus,
+      includeSubworkflows
+    )
     runTransaction(action)
   }
 
-  override def deleteAllMetadataForWorkflowAndUpdateArchiveStatus(workflowId: String, newArchiveStatus: Option[String])(implicit ec: ExecutionContext): Future[Int] = {
+  override def deleteAllMetadataForWorkflowAndUpdateArchiveStatus(workflowId: String, newArchiveStatus: Option[String])(
+    implicit ec: ExecutionContext
+  ): Future[Int] =
     runTransaction {
       for {
         numDeleted <- dataAccess.metadataEntriesForWorkflowSortedById(workflowId).delete
         _ <- dataAccess.metadataArchiveStatusByWorkflowId(workflowId).update(newArchiveStatus)
       } yield numDeleted
     }
-  }
 
-  override def getRootWorkflowId(workflowId: String)(implicit ec: ExecutionContext): Future[Option[String]] = {
+  override def getRootWorkflowId(workflowId: String)(implicit ec: ExecutionContext): Future[Option[String]] =
     runAction(
       dataAccess.rootWorkflowId(workflowId).result.headOption
     )
-  }
 
-  override def queryWorkflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp(archiveStatus: Option[String], thresholdTimestamp: Timestamp, batchSize: Long)(implicit ec: ExecutionContext): Future[Seq[String]] = {
+  override def queryWorkflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp(archiveStatus: Option[String],
+                                                                                   thresholdTimestamp: Timestamp,
+                                                                                   batchSize: Long
+  )(implicit ec: ExecutionContext): Future[Seq[String]] =
     runAction(
-      dataAccess.workflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp((archiveStatus, thresholdTimestamp, batchSize)).result
+      dataAccess
+        .workflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp((archiveStatus, thresholdTimestamp, batchSize))
+        .result
     )
-  }
 
   override def getSummaryQueueSize()(implicit ec: ExecutionContext): Future[Int] =
     runAction(
       countSummaryQueueEntries()
     )
 
-  override def getMetadataArchiveStatusAndEndTime(workflowId: String)(implicit ec: ExecutionContext):  Future[(Option[String], Option[Timestamp])] = {
+  override def getMetadataArchiveStatusAndEndTime(
+    workflowId: String
+  )(implicit ec: ExecutionContext): Future[(Option[String], Option[Timestamp])] = {
     val action = dataAccess.metadataArchiveStatusAndEndTimeByWorkflowId(workflowId).result.headOption
     runTransaction(action).map(_.getOrElse((None, None)))
   }
 
   override def queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String],
                                                                             workflowEndTimestampThreshold: Timestamp,
-                                                                            batchSize: Long)(implicit ec: ExecutionContext): Future[Seq[WorkflowMetadataSummaryEntry]] = {
+                                                                            batchSize: Long
+  )(implicit ec: ExecutionContext): Future[Seq[WorkflowMetadataSummaryEntry]] =
     runAction(
-      dataAccess.workflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses, workflowEndTimestampThreshold, batchSize).result
+      dataAccess
+        .workflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses,
+                                                                 workflowEndTimestampThreshold,
+                                                                 batchSize
+        )
+        .result
     )
-  }
 
   override def countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String],
-                                                                                workflowEndTimestampThreshold: Timestamp)(implicit ec: ExecutionContext): Future[Int] = {
+                                                                                workflowEndTimestampThreshold: Timestamp
+  )(implicit ec: ExecutionContext): Future[Int] =
     runAction(
-      dataAccess.countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses, workflowEndTimestampThreshold).result
+      dataAccess
+        .countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses,
+                                                                          workflowEndTimestampThreshold
+        )
+        .result
     )
-  }
 
-  override def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold: Timestamp)(implicit ec: ExecutionContext): Future[Int] = {
+  override def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(
+    workflowEndTimestampThreshold: Timestamp
+  )(implicit ec: ExecutionContext): Future[Int] =
     runAction(
       dataAccess.countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold).result
     )
-  }
 
-  override def getMetadataTableSizeInformation()(implicit ec: ExecutionContext): Future[Option[InformationSchemaEntry]] = {
+  override def getMetadataTableSizeInformation()(implicit
+    ec: ExecutionContext
+  ): Future[Option[InformationSchemaEntry]] =
     runAction(dataAccess.metadataTableSizeInformation())
-  }
 
-  override def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: String)(implicit ec: ExecutionContext): Future[Vector[MetadataEntry]] = {
+  override def getFailedJobsMetadataWithWorkflowId(
+    rootWorkflowId: String
+  )(implicit ec: ExecutionContext): Future[Vector[MetadataEntry]] = {
     val isPostgres = databaseConfig.getValue("db.driver").toString.toLowerCase().contains("postgres")
     runLobAction(dataAccess.failedJobsMetadataWithWorkflowId(rootWorkflowId, isPostgres))
   }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala
index 459c705480e..55c408f944f 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala
@@ -11,11 +11,12 @@ import slick.basic.DatabaseConfig
 import slick.jdbc.{JdbcCapabilities, JdbcProfile, PostgresProfile, TransactionIsolation}
 
 import java.sql.{Connection, PreparedStatement, Statement}
-import java.util.concurrent.{ExecutorService, Executors}
+import java.util.concurrent.{Executors, ExecutorService}
 import scala.concurrent.duration._
 import scala.concurrent.{Await, ExecutionContext, Future}
 
 object SlickDatabase {
+
   /**
     * Returns either the "url" or "properties.url"
     */
@@ -23,7 +24,7 @@ object SlickDatabase {
 
   lazy val log: Logger = LoggerFactory.getLogger("cromwell.database.slick")
 
-  def createSchema(slickDatabase: SlickDatabase): Unit = {
+  def createSchema(slickDatabase: SlickDatabase): Unit =
     // NOTE: Slick 3.0.0 schema creation, Clobs, and MySQL don't mix:  https://github.com/slick/slick/issues/637
     //
     // Not really an issue, since externally run liquibase is standard way of installing / upgrading MySQL.
@@ -43,7 +44,6 @@ object SlickDatabase {
       import slickDatabase.dataAccess.driver.api._
       Await.result(slickDatabase.database.run(slickDatabase.dataAccess.schema.create), Duration.Inf)
     }
-  }
 
   def getDatabaseConfig(name: String, parentConfig: Config): Config = {
     val rootDatabaseConfig = parentConfig.getConfig("database")
@@ -130,7 +130,8 @@ abstract class SlickDatabase(override val originalDatabaseConfig: Config) extend
   }
 
   private val actionExecutionContext: ExecutionContext = ExecutionContext.fromExecutor(
-    actionThreadPool, database.executor.executionContext.reportFailure
+    actionThreadPool,
+    database.executor.executionContext.reportFailure
   )
 
   protected[this] lazy val insertBatchSize: Int = databaseConfig.getOrElse("insert-batch-size", 2000)
@@ -138,23 +139,21 @@ abstract class SlickDatabase(override val originalDatabaseConfig: Config) extend
   protected[this] lazy val useSlickUpserts: Boolean =
     dataAccess.driver.capabilities.contains(JdbcCapabilities.insertOrUpdate)
 
-  //noinspection SameParameterValue
-  protected[this] def assertUpdateCount(description: String, updates: Int, expected: Int): DBIO[Unit] = {
+  // noinspection SameParameterValue
+  protected[this] def assertUpdateCount(description: String, updates: Int, expected: Int): DBIO[Unit] =
     if (updates == expected) {
       DBIO.successful(())
     } else {
       DBIO.failed(new RuntimeException(s"$description expected update count $expected, got $updates"))
     }
-  }
 
-  override def withConnection[A](block: Connection => A): A = {
+  override def withConnection[A](block: Connection => A): A =
     /*
      TODO: Should this withConnection() method have a (implicit?) timeout parameter, that it passes on to Await.result?
      If we run completely asynchronously, nest calls to withConnection, and then call flatMap, the outer connection may
      already be closed before an inner block finishes running.
      */
     Await.result(database.run(SimpleDBIO(context => block(context.connection))), Duration.Inf)
-  }
 
   override def close(): Unit = {
     actionThreadPool.shutdown()
@@ -166,40 +165,41 @@ abstract class SlickDatabase(override val originalDatabaseConfig: Config) extend
 
   protected[this] def runTransaction[R](action: DBIO[R],
                                         isolationLevel: TransactionIsolation = TransactionIsolation.RepeatableRead,
-                                        timeout: Duration = Duration.Inf): Future[R] = {
+                                        timeout: Duration = Duration.Inf
+  ): Future[R] =
     runActionInternal(action.transactionally.withTransactionIsolation(isolationLevel), timeout = timeout)
-  }
 
   /* Note that this is only appropriate for actions that do not involve Blob
    * or Clob fields in Postgres, since large object support requires running
    * transactionally.  Use runLobAction instead, which will still run in
    * auto-commit mode when using other database engines.
    */
-  protected[this] def runAction[R](action: DBIO[R]): Future[R] = {
+  protected[this] def runAction[R](action: DBIO[R]): Future[R] =
     runActionInternal(action.withPinnedSession)
-  }
 
   /* Wrapper for queries where Clob/Blob types are used
    * https://stackoverflow.com/questions/3164072/large-objects-may-not-be-used-in-auto-commit-mode#answer-3164352
    */
-  protected[this] def runLobAction[R](action: DBIO[R]): Future[R] = {
+  protected[this] def runLobAction[R](action: DBIO[R]): Future[R] =
     dataAccess.driver match {
       case PostgresProfile => runTransaction(action)
       case _ => runAction(action)
     }
-  }
 
-  private def runActionInternal[R](action: DBIO[R], timeout: Duration = Duration.Inf): Future[R] = {
-    //database.run(action) <-- See comment above private val actionThreadPool
+  private def runActionInternal[R](action: DBIO[R], timeout: Duration = Duration.Inf): Future[R] =
+    // database.run(action) <-- See comment above private val actionThreadPool
     Future {
-      try {
+      try
         if (timeout.isFinite) {
           // https://stackoverflow.com/a/52569275/818054
-          Await.result(database.run(action.withStatementParameters(statementInit = _.setQueryTimeout(timeout.toSeconds.toInt))), Duration.Inf)
+          Await.result(
+            database.run(action.withStatementParameters(statementInit = _.setQueryTimeout(timeout.toSeconds.toInt))),
+            Duration.Inf
+          )
         } else {
           Await.result(database.run(action), Duration.Inf)
         }
-      } catch {
+      catch {
         case rollbackException: MySQLTransactionRollbackException =>
           debugExitStatusCodeOption match {
             case Some(status) =>
@@ -229,17 +229,16 @@ abstract class SlickDatabase(override val originalDatabaseConfig: Config) extend
           }
       }
     }(actionExecutionContext)
-  }
 
   /*
-    * Upsert the provided values in batch.
-    * Fails the query if one or more upsert failed.
-    * Adapted from https://github.com/slick/slick/issues/1781
+   * Upsert the provided values in batch.
+   * Fails the query if one or more upsert failed.
+   * Adapted from https://github.com/slick/slick/issues/1781
    */
   protected[this] def createBatchUpsert[T](description: String,
                                            compiled: dataAccess.driver.JdbcCompiledInsert,
                                            values: Iterable[T]
-                                          )(implicit ec: ExecutionContext): DBIO[Unit] = {
+  )(implicit ec: ExecutionContext): DBIO[Unit] =
     SimpleDBIO { context =>
       context.session.withPreparedStatement[Array[Int]](compiled.upsert.sql) { st: PreparedStatement =>
         values.foreach { update =>
@@ -255,10 +254,11 @@ abstract class SlickDatabase(override val originalDatabaseConfig: Config) extend
       else {
         val valueList = values.toList
         val failedRequests = failures.toList.map(valueList(_))
-        DBIO.failed(new RuntimeException(
-          s"$description failed to upsert the following rows: ${failedRequests.mkString(", ")}"
-        ))
+        DBIO.failed(
+          new RuntimeException(
+            s"$description failed to upsert the following rows: ${failedRequests.mkString(", ")}"
+          )
+        )
       }
     }
-  }
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/SubWorkflowStoreSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/SubWorkflowStoreSlickDatabase.scala
index 21dd3ece7a0..973f18540fc 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/SubWorkflowStoreSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/SubWorkflowStoreSlickDatabase.scala
@@ -12,14 +12,18 @@ trait SubWorkflowStoreSlickDatabase extends SubWorkflowStoreSqlDatabase {
 
   import dataAccess.driver.api._
 
-  def addSubWorkflowStoreEntry(rootWorkflowExecutionUuid: String, 
+  def addSubWorkflowStoreEntry(rootWorkflowExecutionUuid: String,
                                parentWorkflowExecutionUuid: String,
                                callFullyQualifiedName: String,
                                jobIndex: Int,
                                jobAttempt: Int,
-                               subWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Unit] = {
+                               subWorkflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Unit] = {
     val action = for {
-      workflowStoreEntry <- dataAccess.workflowStoreEntriesForWorkflowExecutionUuid(rootWorkflowExecutionUuid).result.headOption
+      workflowStoreEntry <- dataAccess
+        .workflowStoreEntriesForWorkflowExecutionUuid(rootWorkflowExecutionUuid)
+        .result
+        .headOption
       _ <- workflowStoreEntry match {
         case Some(rootWorkflow) =>
           dataAccess.subWorkflowStoreEntryIdsAutoInc +=
@@ -31,28 +35,41 @@ trait SubWorkflowStoreSlickDatabase extends SubWorkflowStoreSqlDatabase {
               jobAttempt,
               subWorkflowExecutionUuid
             )
-        case None => DBIO.failed(new IllegalArgumentException(s"Could not find root workflow with UUID $rootWorkflowExecutionUuid"))
+        case None =>
+          DBIO.failed(
+            new IllegalArgumentException(s"Could not find root workflow with UUID $rootWorkflowExecutionUuid")
+          )
       }
     } yield ()
-    
+
     runTransaction(action) void
   }
 
-  override def querySubWorkflowStore(parentWorkflowExecutionUuid: String, callFqn: String, jobIndex: Int, jobAttempt: Int)
-                                    (implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]] = {
+  override def querySubWorkflowStore(parentWorkflowExecutionUuid: String,
+                                     callFqn: String,
+                                     jobIndex: Int,
+                                     jobAttempt: Int
+  )(implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]] = {
     val action = for {
-      subWorkflowStoreEntryOption <- dataAccess.subWorkflowStoreEntriesForJobKey(
-        (parentWorkflowExecutionUuid, callFqn, jobIndex, jobAttempt)
-      ).result.headOption
+      subWorkflowStoreEntryOption <- dataAccess
+        .subWorkflowStoreEntriesForJobKey(
+          (parentWorkflowExecutionUuid, callFqn, jobIndex, jobAttempt)
+        )
+        .result
+        .headOption
     } yield subWorkflowStoreEntryOption
 
     runTransaction(action)
   }
 
-  override def removeSubWorkflowStoreEntries(rootWorkflowExecutionUuid: String)
-                                            (implicit ec: ExecutionContext): Future[Int] = {
+  override def removeSubWorkflowStoreEntries(
+    rootWorkflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Int] = {
     val action = for {
-      workflowStoreEntry <- dataAccess.workflowStoreEntriesForWorkflowExecutionUuid(rootWorkflowExecutionUuid).result.headOption
+      workflowStoreEntry <- dataAccess
+        .workflowStoreEntriesForWorkflowExecutionUuid(rootWorkflowExecutionUuid)
+        .result
+        .headOption
       deleted <- workflowStoreEntry match {
         case Some(rootWorkflow) =>
           dataAccess.subWorkflowStoreEntriesForRootWorkflowId(rootWorkflow.workflowStoreEntryId.get).delete
@@ -60,7 +77,7 @@ trait SubWorkflowStoreSlickDatabase extends SubWorkflowStoreSqlDatabase {
           DBIO.successful(0)
       }
     } yield deleted
-    
+
     runTransaction(action)
   }
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/SummaryQueueSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/SummaryQueueSlickDatabase.scala
index af04939b99b..7f6365493d2 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/SummaryQueueSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/SummaryQueueSlickDatabase.scala
@@ -7,16 +7,13 @@ trait SummaryQueueSlickDatabase {
 
   import dataAccess.driver.api._
 
-  private[slick] def writeSummaryQueueEntries(metadataJournalIds: Seq[Long]) = {
+  private[slick] def writeSummaryQueueEntries(metadataJournalIds: Seq[Long]) =
     dataAccess.summaryQueueEntries ++= metadataJournalIds.map(id => SummaryQueueEntry(id))
-  }
 
-  private[slick] def deleteSummaryQueueEntriesByMetadataJournalIds(metadataJournalIds: Seq[Long]) = {
+  private[slick] def deleteSummaryQueueEntriesByMetadataJournalIds(metadataJournalIds: Seq[Long]) =
     dataAccess.summaryQueueEntries.filter(_.metadataJournalId.inSet(metadataJournalIds)).delete
-  }
 
-  private[slick] def countSummaryQueueEntries() = {
+  private[slick] def countSummaryQueueEntries() =
     dataAccess.summaryQueueEntries.length.result
-  }
 
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/SummaryStatusSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/SummaryStatusSlickDatabase.scala
index 43a3aff9273..a7fa1a57a62 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/SummaryStatusSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/SummaryStatusSlickDatabase.scala
@@ -9,17 +9,15 @@ trait SummaryStatusSlickDatabase {
 
   import dataAccess.driver.api._
 
-  private[slick] def getSummaryStatusEntrySummaryPosition(summaryName: String): DBIO[Option[Long]] = {
+  private[slick] def getSummaryStatusEntrySummaryPosition(summaryName: String): DBIO[Option[Long]] =
     dataAccess.summaryPositionForSummaryName(summaryName).result.headOption
-  }
 
-  private[slick] def upsertSummaryStatusEntrySummaryPosition(summaryName: String,
-                                                             summaryPosition: Long)
-                                                            (implicit ec: ExecutionContext): DBIO[Unit] = {
+  private[slick] def upsertSummaryStatusEntrySummaryPosition(summaryName: String, summaryPosition: Long)(implicit
+    ec: ExecutionContext
+  ): DBIO[Unit] =
     if (useSlickUpserts) {
       for {
-        _ <- dataAccess.summaryStatusEntryIdsAutoInc.
-          insertOrUpdate(SummaryStatusEntry(summaryName, summaryPosition))
+        _ <- dataAccess.summaryStatusEntryIdsAutoInc.insertOrUpdate(SummaryStatusEntry(summaryName, summaryPosition))
       } yield ()
     } else {
       for {
@@ -32,5 +30,4 @@ trait SummaryStatusSlickDatabase {
         }
       } yield ()
     }
-  }
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/WorkflowStoreSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/WorkflowStoreSlickDatabase.scala
index a39dcbf4195..d7d3e7bb6db 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/WorkflowStoreSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/WorkflowStoreSlickDatabase.scala
@@ -14,8 +14,9 @@ trait WorkflowStoreSlickDatabase extends WorkflowStoreSqlDatabase {
 
   import dataAccess.driver.api._
 
-  override def setStateToState(fromWorkflowState: String, toWorkflowState: String)
-                              (implicit ec: ExecutionContext): Future[Unit] = {
+  override def setStateToState(fromWorkflowState: String, toWorkflowState: String)(implicit
+    ec: ExecutionContext
+  ): Future[Unit] = {
     val action = dataAccess
       .workflowStateForWorkflowState(fromWorkflowState)
       .update(toWorkflowState)
@@ -26,8 +27,8 @@ trait WorkflowStoreSlickDatabase extends WorkflowStoreSqlDatabase {
   override def deleteOrUpdateWorkflowToState(workflowExecutionUuid: String,
                                              workflowStateToDelete1: String,
                                              workflowStateToDelete2: String,
-                                             workflowStateForUpdate: String)
-                                            (implicit ec: ExecutionContext): Future[Option[Boolean]] = {
+                                             workflowStateForUpdate: String
+  )(implicit ec: ExecutionContext): Future[Option[Boolean]] = {
     val action = for {
       // First, delete all rows in either of our states to be deleted.
       deleted <- dataAccess
@@ -44,11 +45,14 @@ trait WorkflowStoreSlickDatabase extends WorkflowStoreSqlDatabase {
         }
     } yield (deleted, updated)
 
-    runTransaction(action) map { case (deleted, updated) => if (deleted == 0 && updated == 0) None else Option(deleted > 0) }
+    runTransaction(action) map { case (deleted, updated) =>
+      if (deleted == 0 && updated == 0) None else Option(deleted > 0)
+    }
   }
 
-  override def addWorkflowStoreEntries(workflowStoreEntries: Iterable[WorkflowStoreEntry])
-                                      (implicit ec: ExecutionContext): Future[Unit] = {
+  override def addWorkflowStoreEntries(
+    workflowStoreEntries: Iterable[WorkflowStoreEntry]
+  )(implicit ec: ExecutionContext): Future[Unit] = {
     val action = dataAccess.workflowStoreEntryIdsAutoInc ++= workflowStoreEntries
     runTransaction(action).void
   }
@@ -60,15 +64,14 @@ trait WorkflowStoreSlickDatabase extends WorkflowStoreSqlDatabase {
                                      workflowStateFrom: String,
                                      workflowStateTo: String,
                                      workflowStateExcluded: String,
-                                     excludedGroups: Set[String])
-                                    (implicit ec: ExecutionContext): Future[Seq[WorkflowStoreEntry]] = {
+                                     excludedGroups: Set[String]
+  )(implicit ec: ExecutionContext): Future[Seq[WorkflowStoreEntry]] = {
 
     def updateForFetched(cromwellId: String,
                          heartbeatTimestampTo: Timestamp,
                          workflowStateFrom: String,
-                         workflowStateTo: String)
-                        (workflowStoreEntry: WorkflowStoreEntry)
-                        (implicit ec: ExecutionContext): DBIO[Unit] = {
+                         workflowStateTo: String
+    )(workflowStoreEntry: WorkflowStoreEntry)(implicit ec: ExecutionContext): DBIO[Unit] = {
       val workflowExecutionUuid = workflowStoreEntry.workflowExecutionUuid
       val updateState = workflowStoreEntry.workflowState match {
         case matched if matched == workflowStateFrom => workflowStateTo
@@ -88,20 +91,28 @@ trait WorkflowStoreSlickDatabase extends WorkflowStoreSqlDatabase {
       } yield ()
     }
 
-    def fetchAndUpdateStartableWfs(hogGroup: Option[String]) = {
+    def fetchAndUpdateStartableWfs(hogGroup: Option[String]) =
       for {
-        workflowStoreEntries <- dataAccess.fetchStartableWfsForHogGroup(
-          (limit.toLong, heartbeatTimestampTimedOut, workflowStateExcluded, hogGroup)
-        ).result
+        workflowStoreEntries <- dataAccess
+          .fetchStartableWfsForHogGroup(
+            (limit.toLong, heartbeatTimestampTimedOut, workflowStateExcluded, hogGroup)
+          )
+          .result
         _ <- DBIO.sequence(
-          workflowStoreEntries map updateForFetched(cromwellId, heartbeatTimestampTo, workflowStateFrom, workflowStateTo)
+          workflowStoreEntries map updateForFetched(cromwellId,
+                                                    heartbeatTimestampTo,
+                                                    workflowStateFrom,
+                                                    workflowStateTo
+          )
         )
       } yield workflowStoreEntries
-    }
 
     val action = for {
       // find hog group with lowest count of actively running workflows
-      hogGroupOption <- dataAccess.getHogGroupWithLowestRunningWfs(heartbeatTimestampTimedOut, workflowStateExcluded, excludedGroups).result.headOption
+      hogGroupOption <- dataAccess
+        .getHogGroupWithLowestRunningWfs(heartbeatTimestampTimedOut, workflowStateExcluded, excludedGroups)
+        .result
+        .headOption
       workflowStoreEntries <- hogGroupOption match {
         // if no such hog group was found, all hog groups have workflows that are either actively running or in "OnHold" status
         case None => DBIO.successful(Seq.empty[WorkflowStoreEntry])
@@ -118,9 +129,9 @@ trait WorkflowStoreSlickDatabase extends WorkflowStoreSqlDatabase {
     runTransaction(action, TransactionIsolation.ReadCommitted)
   }
 
-  override def writeWorkflowHeartbeats(workflowExecutionUuids: Seq[String],
-                                       heartbeatTimestamp: Timestamp)
-                                      (implicit ec: ExecutionContext): Future[Int] = {
+  override def writeWorkflowHeartbeats(workflowExecutionUuids: Seq[String], heartbeatTimestamp: Timestamp)(implicit
+    ec: ExecutionContext
+  ): Future[Int] = {
     // Return the count of heartbeats written. This could legitimately be less than the size of the `workflowExecutionUuids`
     // List if any of those workflows completed and their workflow store entries were removed.
     val action = for {
@@ -147,10 +158,9 @@ trait WorkflowStoreSlickDatabase extends WorkflowStoreSqlDatabase {
     runTransaction(action) map { _.toMap }
   }
 
-  override def updateWorkflowState(workflowExecutionUuid: String,
-                                   fromWorkflowState: String,
-                                   toWorkflowState: String)
-                                  (implicit ec: ExecutionContext): Future[Int] = {
+  override def updateWorkflowState(workflowExecutionUuid: String, fromWorkflowState: String, toWorkflowState: String)(
+    implicit ec: ExecutionContext
+  ): Future[Int] = {
     val action = for {
       updated <- dataAccess
         .workflowStateForWorkflowExecutionUUidAndWorkflowState((workflowExecutionUuid, fromWorkflowState))
@@ -160,15 +170,14 @@ trait WorkflowStoreSlickDatabase extends WorkflowStoreSqlDatabase {
     runTransaction(action)
   }
 
-  override def findWorkflowsWithAbortRequested(cromwellId: String)(implicit ec: ExecutionContext): Future[Iterable[String]] = {
+  override def findWorkflowsWithAbortRequested(cromwellId: String)(implicit
+    ec: ExecutionContext
+  ): Future[Iterable[String]] =
     runTransaction(dataAccess.findWorkflowsWithAbortRequested(cromwellId).result)
-  }
 
-  override def findWorkflows(cromwellId: String)(implicit ec: ExecutionContext): Future[Iterable[String]] = {
+  override def findWorkflows(cromwellId: String)(implicit ec: ExecutionContext): Future[Iterable[String]] =
     runTransaction(dataAccess.findWorkflows(cromwellId).result)
-  }
 
-  override def checkWhetherWorkflowExists(workflowId: String)(implicit ec: ExecutionContext): Future[Boolean] = {
+  override def checkWhetherWorkflowExists(workflowId: String)(implicit ec: ExecutionContext): Future[Boolean] =
     runTransaction(dataAccess.checkExists(workflowId).result.map(_.nonEmpty))
-  }
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingAggregationEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingAggregationEntryComponent.scala
index 139558aa7b8..1cbc705e019 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingAggregationEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingAggregationEntryComponent.scala
@@ -2,14 +2,14 @@ package cromwell.database.slick.tables
 
 import cromwell.database.sql.tables.CallCachingAggregationEntry
 
-
 trait CallCachingAggregationEntryComponent {
 
   this: DriverComponent with CallCachingEntryComponent with CallCachingDetritusEntryComponent =>
 
   import driver.api._
 
-  class CallCachingAggregationEntries(tag: Tag) extends Table[CallCachingAggregationEntry](tag, "CALL_CACHING_AGGREGATION_ENTRY") {
+  class CallCachingAggregationEntries(tag: Tag)
+      extends Table[CallCachingAggregationEntry](tag, "CALL_CACHING_AGGREGATION_ENTRY") {
     def callCachingAggregationEntryId = column[Long]("CALL_CACHING_AGGREGATION_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def baseAggregation = column[String]("BASE_AGGREGATION", O.Length(255))
@@ -21,8 +21,10 @@ trait CallCachingAggregationEntryComponent {
     override def * = (baseAggregation, inputFilesAggregation, callCachingEntryId.?, callCachingAggregationEntryId.?) <>
       (CallCachingAggregationEntry.tupled, CallCachingAggregationEntry.unapply)
 
-    def fkCallCachingAggregationEntryCallCachingEntryId = foreignKey("FK_CALL_CACHING_AGGREGATION_ENTRY_CALL_CACHING_ENTRY_ID",
-      callCachingEntryId, callCachingEntries)(_.callCachingEntryId)
+    def fkCallCachingAggregationEntryCallCachingEntryId =
+      foreignKey("FK_CALL_CACHING_AGGREGATION_ENTRY_CALL_CACHING_ENTRY_ID", callCachingEntryId, callCachingEntries)(
+        _.callCachingEntryId
+      )
 
     def ixCallCachingAggregationEntryBaIfa =
       index("IX_CALL_CACHING_AGGREGATION_ENTRY_BA_IFA", (baseAggregation, inputFilesAggregation), unique = false)
@@ -32,16 +34,16 @@ trait CallCachingAggregationEntryComponent {
 
   val callCachingAggregationEntryIdsAutoInc = callCachingAggregationEntries returning
     callCachingAggregationEntries.map(_.callCachingAggregationEntryId)
-  
-  val callCachingAggregationForCacheEntryId = Compiled(
-    (callCachingEntryId: Rep[Long]) => for {
-      callCachingAggregationEntry <- callCachingAggregationEntries 
+
+  val callCachingAggregationForCacheEntryId = Compiled((callCachingEntryId: Rep[Long]) =>
+    for {
+      callCachingAggregationEntry <- callCachingAggregationEntries
       if callCachingAggregationEntry.callCachingEntryId === callCachingEntryId
     } yield callCachingAggregationEntry
   )
 
-  val existsCallCachingEntriesForBaseAggregationHash = Compiled(
-    (baseAggregation: Rep[String]) => (for {
+  val existsCallCachingEntriesForBaseAggregationHash = Compiled((baseAggregation: Rep[String]) =>
+    (for {
       callCachingEntry <- callCachingEntries
       if callCachingEntry.allowResultReuse
       callCachingAggregationEntry <- callCachingAggregationEntries
@@ -52,24 +54,32 @@ trait CallCachingAggregationEntryComponent {
 
   val existsCallCachingEntriesForBaseAggregationHashWithCallCachePrefix = Compiled(
     (baseAggregation: Rep[String],
-     prefix1: Rep[String], prefix1Length: Rep[Int],
-     prefix2: Rep[String], prefix2Length: Rep[Int],
-     prefix3: Rep[String], prefix3Length: Rep[Int]
-    ) => (for {
-      callCachingEntry <- callCachingEntries
-      if callCachingEntry.allowResultReuse
-      callCachingAggregationEntry <- callCachingAggregationEntries
-      if callCachingEntry.callCachingEntryId === callCachingAggregationEntry.callCachingEntryId
-      if callCachingAggregationEntry.baseAggregation === baseAggregation
-      detritus <- callCachingDetritusEntries
-      if detritus.callCachingEntryId === callCachingEntry.callCachingEntryId
-      detritusPath = detritus.detritusValue.map(clobToString)
-      if (detritusPath.substring(0, prefix1Length) === prefix1) ||
-        (detritusPath.substring(0, prefix2Length) === prefix2) ||
-        (detritusPath.substring(0, prefix3Length) === prefix3)} yield ()).exists
+     prefix1: Rep[String],
+     prefix1Length: Rep[Int],
+     prefix2: Rep[String],
+     prefix2Length: Rep[Int],
+     prefix3: Rep[String],
+     prefix3Length: Rep[Int]
+    ) =>
+      (for {
+        callCachingEntry <- callCachingEntries
+        if callCachingEntry.allowResultReuse
+        callCachingAggregationEntry <- callCachingAggregationEntries
+        if callCachingEntry.callCachingEntryId === callCachingAggregationEntry.callCachingEntryId
+        if callCachingAggregationEntry.baseAggregation === baseAggregation
+        detritus <- callCachingDetritusEntries
+        if detritus.callCachingEntryId === callCachingEntry.callCachingEntryId
+        detritusPath = detritus.detritusValue.map(clobToString)
+        if (detritusPath.substring(0, prefix1Length) === prefix1) ||
+          (detritusPath.substring(0, prefix2Length) === prefix2) ||
+          (detritusPath.substring(0, prefix3Length) === prefix3)
+      } yield ()).exists
   )
 
-  def callCachingEntriesForAggregatedHashes(baseAggregation: Rep[String], inputFilesAggregation: Rep[Option[String]], excludedIds: Set[Long]) = {
+  def callCachingEntriesForAggregatedHashes(baseAggregation: Rep[String],
+                                            inputFilesAggregation: Rep[Option[String]],
+                                            excludedIds: Set[Long]
+  ) =
     (for {
       callCachingEntry <- callCachingEntries
       if callCachingEntry.allowResultReuse && !(callCachingEntry.callCachingEntryId inSet excludedIds)
@@ -79,13 +89,17 @@ trait CallCachingAggregationEntryComponent {
       if (callCachingAggregationEntry.inputFilesAggregation.isEmpty && inputFilesAggregation.isEmpty) ||
         (callCachingAggregationEntry.inputFilesAggregation === inputFilesAggregation)
     } yield callCachingAggregationEntry.callCachingEntryId).take(1)
-  }
 
-  def callCachingEntriesForAggregatedHashesWithPrefixes(baseAggregation: Rep[String], inputFilesAggregation: Rep[Option[String]],
-                                                        prefix1: Rep[String], prefix1Length: Rep[Int],
-                                                        prefix2: Rep[String], prefix2Length: Rep[Int],
-                                                        prefix3: Rep[String], prefix3Length: Rep[Int],
-                                                        excludedIds: Set[Long]) = {
+  def callCachingEntriesForAggregatedHashesWithPrefixes(baseAggregation: Rep[String],
+                                                        inputFilesAggregation: Rep[Option[String]],
+                                                        prefix1: Rep[String],
+                                                        prefix1Length: Rep[Int],
+                                                        prefix2: Rep[String],
+                                                        prefix2Length: Rep[Int],
+                                                        prefix3: Rep[String],
+                                                        prefix3Length: Rep[Int],
+                                                        excludedIds: Set[Long]
+  ) =
     (for {
       callCachingEntry <- callCachingEntries
       if callCachingEntry.allowResultReuse && !(callCachingEntry.callCachingEntryId inSet excludedIds)
@@ -104,5 +118,4 @@ trait CallCachingAggregationEntryComponent {
         (detritusPath.substring(0, prefix2Length) === prefix2) ||
         (detritusPath.substring(0, prefix3Length) === prefix3)
     } yield callCachingAggregationEntry.callCachingEntryId).take(1)
-  }
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingDetritusEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingDetritusEntryComponent.scala
index b668adb4940..cafaa91d9b0 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingDetritusEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingDetritusEntryComponent.scala
@@ -11,7 +11,7 @@ trait CallCachingDetritusEntryComponent {
   import driver.api._
 
   class CallCachingDetritusEntries(tag: Tag)
-    extends Table[CallCachingDetritusEntry](tag, "CALL_CACHING_DETRITUS_ENTRY") {
+      extends Table[CallCachingDetritusEntry](tag, "CALL_CACHING_DETRITUS_ENTRY") {
     def callCachingDetritusEntryId = column[Long]("CALL_CACHING_DETRITUS_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def detritusKey = column[String]("DETRITUS_KEY", O.Length(255))
@@ -23,9 +23,10 @@ trait CallCachingDetritusEntryComponent {
     override def * = (detritusKey, detritusValue, callCachingEntryId.?, callCachingDetritusEntryId.?) <>
       (CallCachingDetritusEntry.tupled, CallCachingDetritusEntry.unapply)
 
-    def fkCallCachingDetritusEntryCallCachingEntryId = foreignKey(
-      "FK_CALL_CACHING_DETRITUS_ENTRY_CALL_CACHING_ENTRY_ID",
-      callCachingEntryId, callCachingEntries)(_.callCachingEntryId)
+    def fkCallCachingDetritusEntryCallCachingEntryId =
+      foreignKey("FK_CALL_CACHING_DETRITUS_ENTRY_CALL_CACHING_ENTRY_ID", callCachingEntryId, callCachingEntries)(
+        _.callCachingEntryId
+      )
 
     def ucCallCachingDetritusEntryCceiDk =
       index("UC_CALL_CACHING_DETRITUS_ENTRY_CCEI_DK", (callCachingEntryId, detritusKey), unique = true)
@@ -36,8 +37,8 @@ trait CallCachingDetritusEntryComponent {
   val callCachingDetritusEntryIdsAutoInc =
     callCachingDetritusEntries returning callCachingDetritusEntries.map(_.callCachingDetritusEntryId)
 
-  val callCachingDetritusEntriesForCallCachingEntryId = Compiled(
-    (callCachingEntryId: Rep[Long]) => for {
+  val callCachingDetritusEntriesForCallCachingEntryId = Compiled((callCachingEntryId: Rep[Long]) =>
+    for {
       callCachingDetritusEntry <- callCachingDetritusEntries
       if callCachingDetritusEntry.callCachingEntryId === callCachingEntryId
     } yield callCachingDetritusEntry
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingEntryComponent.scala
index db9c5dc1654..b9a26585bec 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingEntryComponent.scala
@@ -22,51 +22,60 @@ trait CallCachingEntryComponent {
     def returnCode = column[Option[Int]]("RETURN_CODE")
 
     def allowResultReuse = column[Boolean]("ALLOW_RESULT_REUSE", O.Default(true))
-    
-    override def * = (workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt, returnCode, allowResultReuse,
-      callCachingEntryId.?) <> (CallCachingEntry.tupled, CallCachingEntry.unapply)
+
+    override def * = (workflowExecutionUuid,
+                      callFullyQualifiedName,
+                      jobIndex,
+                      jobAttempt,
+                      returnCode,
+                      allowResultReuse,
+                      callCachingEntryId.?
+    ) <> (CallCachingEntry.tupled, CallCachingEntry.unapply)
 
     def ucCallCachingEntryWeuCfqnJi =
-      index("UC_CALL_CACHING_ENTRY_WEU_CFQN_JI", (workflowExecutionUuid, callFullyQualifiedName, jobIndex),
-        unique = true)
+      index("UC_CALL_CACHING_ENTRY_WEU_CFQN_JI",
+            (workflowExecutionUuid, callFullyQualifiedName, jobIndex),
+            unique = true
+      )
   }
 
   protected val callCachingEntries = TableQuery[CallCachingEntries]
 
   val callCachingEntryIdsAutoInc = callCachingEntries returning callCachingEntries.map(_.callCachingEntryId)
 
-  val callCachingEntriesForId = Compiled(
-    (callCachingEntryId: Rep[Long]) => for {
+  val callCachingEntriesForId = Compiled((callCachingEntryId: Rep[Long]) =>
+    for {
       callCachingEntry <- callCachingEntries
       if callCachingEntry.callCachingEntryId === callCachingEntryId
     } yield callCachingEntry
   )
 
-  val allowResultReuseForCallCachingEntryId = Compiled(
-    (callCachingEntryId: Rep[Long]) => for {
+  val allowResultReuseForCallCachingEntryId = Compiled((callCachingEntryId: Rep[Long]) =>
+    for {
       callCachingEntry <- callCachingEntries
       if callCachingEntry.callCachingEntryId === callCachingEntryId
     } yield callCachingEntry.allowResultReuse
   )
 
-  val callCachingEntriesForWorkflowFqnIndex = Compiled(
-    (workflowId: Rep[String], callFqn: Rep[String], jobIndex: Rep[Int]) => for {
-      callCachingEntry <- callCachingEntries
-      if callCachingEntry.workflowExecutionUuid === workflowId
-      if callCachingEntry.callFullyQualifiedName === callFqn
-      if callCachingEntry.jobIndex === jobIndex
-    } yield callCachingEntry
-  )
-
-  val callCachingEntryIdsForWorkflowId = Compiled(
-    (workflowId: Rep[String]) => for {
+  val callCachingEntriesForWorkflowFqnIndex =
+    Compiled((workflowId: Rep[String], callFqn: Rep[String], jobIndex: Rep[Int]) =>
+      for {
+        callCachingEntry <- callCachingEntries
+        if callCachingEntry.workflowExecutionUuid === workflowId
+        if callCachingEntry.callFullyQualifiedName === callFqn
+        if callCachingEntry.jobIndex === jobIndex
+      } yield callCachingEntry
+    )
+
+  val callCachingEntryIdsForWorkflowId = Compiled((workflowId: Rep[String]) =>
+    for {
       callCachingEntry <- callCachingEntries
       if callCachingEntry.workflowExecutionUuid === workflowId
     } yield callCachingEntry.callCachingEntryId
   )
 
-  val allowResultReuseForWorkflowId = Compiled(
-    (workflowId: Rep[String]) => for {
+  val allowResultReuseForWorkflowId = Compiled((workflowId: Rep[String]) =>
+    for {
       callCachingEntry <- callCachingEntries
       if callCachingEntry.workflowExecutionUuid === workflowId
     } yield callCachingEntry.allowResultReuse
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingHashEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingHashEntryComponent.scala
index b556b3f22de..b89fe7f5cc8 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingHashEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingHashEntryComponent.scala
@@ -20,8 +20,10 @@ trait CallCachingHashEntryComponent {
     override def * = (hashKey, hashValue, callCachingEntryId.?, callCachingHashEntryId.?) <>
       (CallCachingHashEntry.tupled, CallCachingHashEntry.unapply)
 
-    def fkCallCachingHashEntryCallCachingEntryId = foreignKey("FK_CALL_CACHING_HASH_ENTRY_CALL_CACHING_ENTRY_ID",
-      callCachingEntryId, callCachingEntries)(_.callCachingEntryId)
+    def fkCallCachingHashEntryCallCachingEntryId =
+      foreignKey("FK_CALL_CACHING_HASH_ENTRY_CALL_CACHING_ENTRY_ID", callCachingEntryId, callCachingEntries)(
+        _.callCachingEntryId
+      )
 
     def ucCallCachingHashEntryCceiHk =
       index("UC_CALL_CACHING_HASH_ENTRY_CCEI_HK", (callCachingEntryId, hashKey), unique = true)
@@ -31,12 +33,12 @@ trait CallCachingHashEntryComponent {
 
   val callCachingHashEntryIdsAutoInc = callCachingHashEntries returning
     callCachingHashEntries.map(_.callCachingHashEntryId)
-  
+
   /**
     * Find all hashes for a CALL_CACHING_ENTRY_ID
     */
-  val callCachingHashEntriesForCallCachingEntryId = Compiled(
-    (callCachingEntryId: Rep[Long]) => for {
+  val callCachingHashEntriesForCallCachingEntryId = Compiled((callCachingEntryId: Rep[Long]) =>
+    for {
       callCachingHashEntry <- callCachingHashEntries
       if callCachingHashEntry.callCachingEntryId === callCachingEntryId
     } yield callCachingHashEntry
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingSimpletonEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingSimpletonEntryComponent.scala
index b2e6f02b5b9..8c624798ce4 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingSimpletonEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/CallCachingSimpletonEntryComponent.scala
@@ -11,7 +11,7 @@ trait CallCachingSimpletonEntryComponent {
   import driver.api._
 
   class CallCachingSimpletonEntries(tag: Tag)
-    extends Table[CallCachingSimpletonEntry](tag, "CALL_CACHING_SIMPLETON_ENTRY") {
+      extends Table[CallCachingSimpletonEntry](tag, "CALL_CACHING_SIMPLETON_ENTRY") {
     def callCachingSimpletonEntryId = column[Long]("CALL_CACHING_SIMPLETON_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def simpletonKey = column[String]("SIMPLETON_KEY", O.Length(255))
@@ -25,8 +25,10 @@ trait CallCachingSimpletonEntryComponent {
     override def * = (simpletonKey, simpletonValue, wdlType, callCachingEntryId.?, callCachingSimpletonEntryId.?) <>
       (CallCachingSimpletonEntry.tupled, CallCachingSimpletonEntry.unapply)
 
-    def fkCallCachingSimpletonEntryCallCachingEntryId = foreignKey(
-      "FK_CALL_CACHING_SIMPLETON_ENTRY_CALL_CACHING_ENTRY_ID", callCachingEntryId, callCachingEntries)(_.callCachingEntryId)
+    def fkCallCachingSimpletonEntryCallCachingEntryId =
+      foreignKey("FK_CALL_CACHING_SIMPLETON_ENTRY_CALL_CACHING_ENTRY_ID", callCachingEntryId, callCachingEntries)(
+        _.callCachingEntryId
+      )
 
     def ucCallCachingSimpletonEntryCceiSk =
       index("UC_CALL_CACHING_SIMPLETON_ENTRY_CCEI_SK", (callCachingEntryId, simpletonKey), unique = true)
@@ -40,8 +42,8 @@ trait CallCachingSimpletonEntryComponent {
   /**
     * Find all result simpletons which match a given CALL_CACHING_ENTRY_ID
     */
-  val callCachingSimpletonEntriesForCallCachingEntryId = Compiled(
-    (callCachingEntryId: Rep[Long]) => for {
+  val callCachingSimpletonEntriesForCallCachingEntryId = Compiled((callCachingEntryId: Rep[Long]) =>
+    for {
       callCachingSimpletonEntry <- callCachingSimpletonEntries
       if callCachingSimpletonEntry.callCachingEntryId === callCachingEntryId
     } yield callCachingSimpletonEntry
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/CustomLabelEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/CustomLabelEntryComponent.scala
index 36789edb696..de988ff2bb1 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/CustomLabelEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/CustomLabelEntryComponent.scala
@@ -11,8 +11,7 @@ trait CustomLabelEntryComponent {
   import driver.api.TupleMethods._
   import driver.api._
 
-  class CustomLabelEntries(tag: Tag)
-    extends Table[CustomLabelEntry](tag, "CUSTOM_LABEL_ENTRY") {
+  class CustomLabelEntries(tag: Tag) extends Table[CustomLabelEntry](tag, "CUSTOM_LABEL_ENTRY") {
     def customLabelEntryId = column[Long]("CUSTOM_LABEL_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def customLabelKey = column[String]("CUSTOM_LABEL_KEY", O.Length(255))
@@ -31,45 +30,52 @@ trait CustomLabelEntryComponent {
     )
 
     def fkCustomLabelEntryWorkflowExecutionUuid = foreignKey("FK_CUSTOM_LABEL_ENTRY_WORKFLOW_EXECUTION_UUID",
-      workflowExecutionUuid, workflowMetadataSummaryEntries)(_.workflowExecutionUuid, onDelete = Cascade)
+                                                             workflowExecutionUuid,
+                                                             workflowMetadataSummaryEntries
+    )(_.workflowExecutionUuid, onDelete = Cascade)
 
-    def ucCustomLabelEntryClkWeu = index("UC_CUSTOM_LABEL_ENTRY_CLK_WEU",
-      (customLabelKey, workflowExecutionUuid), unique = true)
+    def ucCustomLabelEntryClkWeu =
+      index("UC_CUSTOM_LABEL_ENTRY_CLK_WEU", (customLabelKey, workflowExecutionUuid), unique = true)
 
-    def ixCustomLabelEntryClkClv = index("IX_CUSTOM_LABEL_ENTRY_CLK_CLV", (customLabelKey, customLabelValue), unique = false)
-}
+    def ixCustomLabelEntryClkClv =
+      index("IX_CUSTOM_LABEL_ENTRY_CLK_CLV", (customLabelKey, customLabelValue), unique = false)
+  }
 
   val customLabelEntries = TableQuery[CustomLabelEntries]
 
   val customLabelEntryIdsAutoInc = customLabelEntries returning
     customLabelEntries.map(_.customLabelEntryId)
 
-  val customLabelEntriesForWorkflowExecutionUuidAndLabelKey = Compiled(
-    (workflowExecutionUuid: Rep[String], labelKey: Rep[String]) => for {
-      customLabelEntry <- customLabelEntries
-      if customLabelEntry.workflowExecutionUuid === workflowExecutionUuid &&
-        customLabelEntry.customLabelKey === labelKey
-    } yield customLabelEntry.forUpdate)
+  val customLabelEntriesForWorkflowExecutionUuidAndLabelKey =
+    Compiled((workflowExecutionUuid: Rep[String], labelKey: Rep[String]) =>
+      for {
+        customLabelEntry <- customLabelEntries
+        if customLabelEntry.workflowExecutionUuid === workflowExecutionUuid &&
+          customLabelEntry.customLabelKey === labelKey
+      } yield customLabelEntry.forUpdate
+    )
 
   def existsWorkflowIdLabelKeyAndValue(workflowId: Rep[String],
                                        labelKey: Rep[String],
-                                       labelValue: Rep[String]): Rep[Boolean] = {
-    customLabelEntries.filter(customLabelEntry =>
-      customLabelEntry.workflowExecutionUuid === workflowId &&
-        customLabelEntry.customLabelKey === labelKey &&
-        customLabelEntry.customLabelValue === labelValue
-    ).exists
-  }
-
-  val labelsForWorkflowExecutionUuid = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+                                       labelValue: Rep[String]
+  ): Rep[Boolean] =
+    customLabelEntries
+      .filter(customLabelEntry =>
+        customLabelEntry.workflowExecutionUuid === workflowId &&
+          customLabelEntry.customLabelKey === labelKey &&
+          customLabelEntry.customLabelValue === labelValue
+      )
+      .exists
+
+  val labelsForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       customLabelEntry <- customLabelEntries
       if customLabelEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield (customLabelEntry.customLabelKey, customLabelEntry.customLabelValue)
   )
 
-  val labelsForWorkflowAndSubworkflows = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+  val labelsForWorkflowAndSubworkflows = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       summary <- workflowMetadataSummaryEntries
       if summary.rootWorkflowExecutionUuid === workflowExecutionUuid || summary.workflowExecutionUuid === workflowExecutionUuid
       customLabelEntry <- customLabelEntries
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
index 5929b2e5a6a..be8bda6863b 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/DockerHashStoreEntryComponent.scala
@@ -19,20 +19,27 @@ trait DockerHashStoreEntryComponent {
 
     def dockerSize = column[Option[Long]]("DOCKER_SIZE", O.Default(None))
 
-    override def * = (workflowExecutionUuid, dockerTag, dockerHash, dockerSize, dockerHashStoreEntryId.?) <> (DockerHashStoreEntry.tupled, DockerHashStoreEntry.unapply)
-
-    def ucDockerHashStoreEntryWeuDt = index("UC_DOCKER_HASH_STORE_ENTRY_WEU_DT", (workflowExecutionUuid, dockerTag), unique = true)
+    override def * = (workflowExecutionUuid,
+                      dockerTag,
+                      dockerHash,
+                      dockerSize,
+                      dockerHashStoreEntryId.?
+    ) <> (DockerHashStoreEntry.tupled, DockerHashStoreEntry.unapply)
+
+    def ucDockerHashStoreEntryWeuDt =
+      index("UC_DOCKER_HASH_STORE_ENTRY_WEU_DT", (workflowExecutionUuid, dockerTag), unique = true)
   }
 
   val dockerHashStoreEntries = TableQuery[DockerHashStoreEntries]
 
-  val dockerHashStoreEntryIdsAutoInc = dockerHashStoreEntries returning dockerHashStoreEntries.map(_.dockerHashStoreEntryId)
+  val dockerHashStoreEntryIdsAutoInc =
+    dockerHashStoreEntries returning dockerHashStoreEntries.map(_.dockerHashStoreEntryId)
 
   /**
     * Useful for finding the docker hash store for a given workflow execution UUID
     */
-  val dockerHashStoreEntriesForWorkflowExecutionUuid = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+  val dockerHashStoreEntriesForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       dockerHashStoreEntry <- dockerHashStoreEntries
       if dockerHashStoreEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield dockerHashStoreEntry
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/DriverComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/DriverComponent.scala
index 7822e9896ff..fb5160ba69d 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/DriverComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/DriverComponent.scala
@@ -53,16 +53,15 @@ trait DriverComponent {
   /** Adds quotes around the string if required by the DBMS. */
   def quoted(string: String) = if (shouldQuote) s""""$string"""" else string
 
-  val clobToString: Rep[SerialClob] => Rep[String] = {
+  val clobToString: Rep[SerialClob] => Rep[String] =
     this.driver match {
-        /*
+      /*
         Workaround https://jira.mariadb.org/browse/CONJ-717
         Bypass Slick `asColumnOf[String]` calling the JDBC `{fn convert(Column, VARCHAR)}`.
         Instead directly call `concat(Column)` supported by both the MariaDB driver and the MySQL driver.
-         */
+       */
       case MySQLProfile => SimpleFunction.unary("concat")
       case _ => _.asColumnOf[String]
     }
-  }
 
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/EngineDataAccessComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/EngineDataAccessComponent.scala
index 6b1bda3d12d..cd2c16379ab 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/EngineDataAccessComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/EngineDataAccessComponent.scala
@@ -2,18 +2,19 @@ package cromwell.database.slick.tables
 
 import slick.jdbc.JdbcProfile
 
-class EngineDataAccessComponent(val driver: JdbcProfile) extends DataAccessComponent
-  with CallCachingDetritusEntryComponent
-  with CallCachingEntryComponent
-  with CallCachingHashEntryComponent
-  with CallCachingAggregationEntryComponent
-  with CallCachingSimpletonEntryComponent
-  with DockerHashStoreEntryComponent
-  with JobKeyValueEntryComponent
-  with JobStoreEntryComponent
-  with JobStoreSimpletonEntryComponent
-  with SubWorkflowStoreEntryComponent
-  with WorkflowStoreEntryComponent {
+class EngineDataAccessComponent(val driver: JdbcProfile)
+    extends DataAccessComponent
+    with CallCachingDetritusEntryComponent
+    with CallCachingEntryComponent
+    with CallCachingHashEntryComponent
+    with CallCachingAggregationEntryComponent
+    with CallCachingSimpletonEntryComponent
+    with DockerHashStoreEntryComponent
+    with JobKeyValueEntryComponent
+    with JobStoreEntryComponent
+    with JobStoreSimpletonEntryComponent
+    with SubWorkflowStoreEntryComponent
+    with WorkflowStoreEntryComponent {
 
   import driver.api._
 
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/JobKeyValueEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/JobKeyValueEntryComponent.scala
index ee75cda27c0..cd730a5c154 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/JobKeyValueEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/JobKeyValueEntryComponent.scala
@@ -23,11 +23,20 @@ trait JobKeyValueEntryComponent {
 
     def storeValue = column[String]("STORE_VALUE", O.Length(255))
 
-    override def * = (workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt, storeKey, storeValue,
-      jobKeyValueEntryId.?) <> (JobKeyValueEntry.tupled, JobKeyValueEntry.unapply)
-
-    def ucJobKeyValueEntryWeuCfqnJiJaSk = index("UC_JOB_KEY_VALUE_ENTRY_WEU_CFQN_JI_JA_SK",
-      (workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt, storeKey), unique = true)
+    override def * = (workflowExecutionUuid,
+                      callFullyQualifiedName,
+                      jobIndex,
+                      jobAttempt,
+                      storeKey,
+                      storeValue,
+                      jobKeyValueEntryId.?
+    ) <> (JobKeyValueEntry.tupled, JobKeyValueEntry.unapply)
+
+    def ucJobKeyValueEntryWeuCfqnJiJaSk = index(
+      "UC_JOB_KEY_VALUE_ENTRY_WEU_CFQN_JI_JA_SK",
+      (workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt, storeKey),
+      unique = true
+    )
   }
 
   protected val jobKeyValueEntries = TableQuery[JobKeyValueEntries]
@@ -37,21 +46,27 @@ trait JobKeyValueEntryComponent {
 
   val jobKeyValueEntriesExists = Compiled(jobKeyValueEntries.take(1).exists)
 
-  val jobKeyValueEntriesForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) => for {
+  val jobKeyValueEntriesForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       jobKeyValueEntry <- jobKeyValueEntries
       if jobKeyValueEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield jobKeyValueEntry
   )
 
   val storeValuesForJobKeyAndStoreKey = Compiled(
-    (workflowExecutionUuid: Rep[String], callFullyQualifiedName: Rep[String], jobIndex: Rep[Int], jobAttempt: Rep[Int],
-     storeKey: Rep[String]) => for {
-      jobKeyValueEntry <- jobKeyValueEntries
-      if jobKeyValueEntry.workflowExecutionUuid === workflowExecutionUuid
-      if jobKeyValueEntry.callFullyQualifiedName === callFullyQualifiedName
-      if jobKeyValueEntry.jobIndex === jobIndex
-      if jobKeyValueEntry.jobAttempt === jobAttempt
-      if jobKeyValueEntry.storeKey === storeKey
-    } yield jobKeyValueEntry.storeValue
+    (workflowExecutionUuid: Rep[String],
+     callFullyQualifiedName: Rep[String],
+     jobIndex: Rep[Int],
+     jobAttempt: Rep[Int],
+     storeKey: Rep[String]
+    ) =>
+      for {
+        jobKeyValueEntry <- jobKeyValueEntries
+        if jobKeyValueEntry.workflowExecutionUuid === workflowExecutionUuid
+        if jobKeyValueEntry.callFullyQualifiedName === callFullyQualifiedName
+        if jobKeyValueEntry.jobIndex === jobIndex
+        if jobKeyValueEntry.jobAttempt === jobAttempt
+        if jobKeyValueEntry.storeKey === storeKey
+      } yield jobKeyValueEntry.storeValue
   )
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/JobStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/JobStoreEntryComponent.scala
index 04c01ead0cb..acc9c6f12d3 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/JobStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/JobStoreEntryComponent.scala
@@ -30,11 +30,21 @@ trait JobStoreEntryComponent {
 
     def retryableFailure = column[Option[Boolean]]("RETRYABLE_FAILURE")
 
-    override def * = (workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt, jobSuccessful, returnCode,
-      exceptionMessage, retryableFailure, jobStoreEntryId.?) <> (JobStoreEntry.tupled, JobStoreEntry.unapply)
+    override def * = (workflowExecutionUuid,
+                      callFullyQualifiedName,
+                      jobIndex,
+                      jobAttempt,
+                      jobSuccessful,
+                      returnCode,
+                      exceptionMessage,
+                      retryableFailure,
+                      jobStoreEntryId.?
+    ) <> (JobStoreEntry.tupled, JobStoreEntry.unapply)
 
     def ucJobStoreEntryWeuCfqnJiJa = index("UC_JOB_STORE_ENTRY_WEU_CFQN_JI_JA",
-      (workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt), unique = true)
+                                           (workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt),
+                                           unique = true
+    )
 
     def ixJobStoreEntryWeu = index("IX_JOB_STORE_ENTRY_WEU", workflowExecutionUuid, unique = false)
   }
@@ -46,8 +56,8 @@ trait JobStoreEntryComponent {
   /**
     * Useful for finding all job stores for a given workflow execution UUID (e.g. so you can delete them! Bwahaha)
     */
-  val jobStoreEntriesForWorkflowExecutionUuid = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+  val jobStoreEntriesForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       jobStoreEntry <- jobStoreEntries
       if jobStoreEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield jobStoreEntry
@@ -57,8 +67,11 @@ trait JobStoreEntryComponent {
     * Useful for finding the unique job store for a given job key
     */
   val jobStoreEntriesForJobKey = Compiled(
-    (workflowExecutionUuid: Rep[String], callFullyQualifiedName: Rep[String], jobIndex: Rep[Int],
-     jobAttempt: Rep[Int]) =>
+    (workflowExecutionUuid: Rep[String],
+     callFullyQualifiedName: Rep[String],
+     jobIndex: Rep[Int],
+     jobAttempt: Rep[Int]
+    ) =>
       for {
         jobStoreEntry <- jobStoreEntries
         if jobStoreEntry.workflowExecutionUuid === workflowExecutionUuid &&
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/JobStoreSimpletonEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/JobStoreSimpletonEntryComponent.scala
index 285ccc93b82..da14cede6e8 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/JobStoreSimpletonEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/JobStoreSimpletonEntryComponent.scala
@@ -26,7 +26,9 @@ trait JobStoreSimpletonEntryComponent {
       (JobStoreSimpletonEntry.tupled, JobStoreSimpletonEntry.unapply)
 
     def fkJobStoreSimpletonEntryJobStoreEntryId = foreignKey("FK_JOB_STORE_SIMPLETON_ENTRY_JOB_STORE_ENTRY_ID",
-      jobStoreEntryId, jobStoreEntries)(_.jobStoreEntryId, onDelete = Cascade)
+                                                             jobStoreEntryId,
+                                                             jobStoreEntries
+    )(_.jobStoreEntryId, onDelete = Cascade)
 
     def ucJobStoreSimpletonEntryJseiSk =
       index("UC_JOB_STORE_SIMPLETON_ENTRY_JSEI_SK", (jobStoreEntryId, simpletonKey), unique = true)
@@ -40,8 +42,8 @@ trait JobStoreSimpletonEntryComponent {
   /**
     * Find all result simpletons which match a given JOB_STORE_ENTRY_ID
     */
-  val jobStoreSimpletonEntriesForJobStoreEntryId = Compiled(
-    (jobStoreEntryId: Rep[Long]) => for {
+  val jobStoreSimpletonEntriesForJobStoreEntryId = Compiled((jobStoreEntryId: Rep[Long]) =>
+    for {
       jobStoreSimpletonEntry <- jobStoreSimpletonEntries if jobStoreSimpletonEntry.jobStoreEntryId === jobStoreEntryId
     } yield jobStoreSimpletonEntry
   )
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataDataAccessComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataDataAccessComponent.scala
index f3acdd6736d..a8eb1e2c22e 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataDataAccessComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataDataAccessComponent.scala
@@ -2,17 +2,18 @@ package cromwell.database.slick.tables
 
 import slick.jdbc.JdbcProfile
 
-class MetadataDataAccessComponent(val driver: JdbcProfile) extends DataAccessComponent
-  with CustomLabelEntryComponent
-  with MetadataEntryComponent
-  with SummaryStatusEntryComponent
-  with SummaryQueueEntryComponent
-  with WorkflowMetadataSummaryEntryComponent {
+class MetadataDataAccessComponent(val driver: JdbcProfile)
+    extends DataAccessComponent
+    with CustomLabelEntryComponent
+    with MetadataEntryComponent
+    with SummaryStatusEntryComponent
+    with SummaryQueueEntryComponent
+    with WorkflowMetadataSummaryEntryComponent {
 
   import driver.api._
 
   override lazy val schema: driver.SchemaDescription =
-      customLabelEntries.schema ++
+    customLabelEntries.schema ++
       metadataEntries.schema ++
       summaryStatusEntries.schema ++
       workflowMetadataSummaryEntries.schema ++
@@ -20,12 +21,11 @@ class MetadataDataAccessComponent(val driver: JdbcProfile) extends DataAccessCom
 
   // Looks like here is the most appropriate place for this val since it doesn't fit neither in
   // SummaryQueueEntryComponent nor in MetadataEntryComponent
-  val metadataEntriesToSummarizeQuery = {
-    Compiled(
-      (limit: ConstColumn[Long]) => (for {
+  val metadataEntriesToSummarizeQuery =
+    Compiled((limit: ConstColumn[Long]) =>
+      (for {
         summaryEntry <- summaryQueueEntries.take(limit)
         metadataEntry <- metadataEntries if metadataEntry.metadataEntryId === summaryEntry.metadataJournalId
       } yield metadataEntry).sortBy(_.metadataEntryId)
     )
-  }
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
index 8c3c0aa27c9..3ba54ee2760 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/MetadataEntryComponent.scala
@@ -27,7 +27,8 @@ trait MetadataEntryComponent {
 
     def metadataEntryId = column[Long]("METADATA_JOURNAL_ID", O.PrimaryKey, O.AutoInc)
 
-    def workflowExecutionUuid = column[String]("WORKFLOW_EXECUTION_UUID", O.Length(255)) // TODO: rename column via liquibase
+    def workflowExecutionUuid =
+      column[String]("WORKFLOW_EXECUTION_UUID", O.Length(255)) // TODO: rename column via liquibase
 
     def callFullyQualifiedName = column[Option[String]]("CALL_FQN", O.Length(255)) // TODO: rename column via liquibase
 
@@ -43,8 +44,16 @@ trait MetadataEntryComponent {
 
     def metadataTimestamp = column[Timestamp]("METADATA_TIMESTAMP")
 
-    override def * = (workflowExecutionUuid, callFullyQualifiedName, jobIndex, jobAttempt, metadataKey, metadataValue,
-      metadataValueType, metadataTimestamp, metadataEntryId.?) <> (MetadataEntry.tupled, MetadataEntry.unapply)
+    override def * = (workflowExecutionUuid,
+                      callFullyQualifiedName,
+                      jobIndex,
+                      jobAttempt,
+                      metadataKey,
+                      metadataValue,
+                      metadataValueType,
+                      metadataTimestamp,
+                      metadataEntryId.?
+    ) <> (MetadataEntry.tupled, MetadataEntry.unapply)
 
     // TODO: rename index via liquibase
     def ixMetadataEntryWeu = index("METADATA_WORKFLOW_IDX", workflowExecutionUuid, unique = false)
@@ -56,151 +65,173 @@ trait MetadataEntryComponent {
 
   val metadataEntriesExists = Compiled(metadataEntries.take(1).exists)
 
-  val metadataEntriesForWorkflowExecutionUuid = Compiled(
-    (workflowExecutionUuid: Rep[String]) => (for {
+  val metadataEntriesForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) =>
+    (for {
       metadataEntry <- metadataEntries
       if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield metadataEntry).sortBy(_.metadataTimestamp)
   )
 
-  val metadataEntriesForWorkflowSortedById = Compiled(
-    (workflowExecutionUuid: Rep[String]) => (for {
+  val metadataEntriesForWorkflowSortedById = Compiled((workflowExecutionUuid: Rep[String]) =>
+    (for {
       metadataEntry <- metadataEntries
       if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield metadataEntry).sortBy(_.metadataEntryId)
   )
 
-  val countMetadataEntriesForWorkflowExecutionUuid = Compiled(
-    (rootWorkflowId: Rep[String], expandSubWorkflows: Rep[Boolean]) => {
-      val targetWorkflowIds = for {
-        summary <- workflowMetadataSummaryEntries
-        // Uses `IX_WORKFLOW_METADATA_SUMMARY_ENTRY_RWEU`, `UC_WORKFLOW_METADATA_SUMMARY_ENTRY_WEU`
-        if summary.workflowExecutionUuid === rootWorkflowId || ((summary.rootWorkflowExecutionUuid === rootWorkflowId) && expandSubWorkflows)
-      } yield summary.workflowExecutionUuid
-
-      for {
-        metadata <- metadataEntries
-        if metadata.workflowExecutionUuid in targetWorkflowIds // Uses `METADATA_WORKFLOW_IDX`
-      } yield metadata
-    }.size
-  )
-
-  val metadataEntryExistsForWorkflowExecutionUuid = Compiled(
-    (workflowExecutionUuid: Rep[String]) => (for {
+  val countMetadataEntriesForWorkflowExecutionUuid =
+    Compiled((rootWorkflowId: Rep[String], expandSubWorkflows: Rep[Boolean]) =>
+      {
+        val targetWorkflowIds = for {
+          summary <- workflowMetadataSummaryEntries
+          // Uses `IX_WORKFLOW_METADATA_SUMMARY_ENTRY_RWEU`, `UC_WORKFLOW_METADATA_SUMMARY_ENTRY_WEU`
+          if summary.workflowExecutionUuid === rootWorkflowId || ((summary.rootWorkflowExecutionUuid === rootWorkflowId) && expandSubWorkflows)
+        } yield summary.workflowExecutionUuid
+
+        for {
+          metadata <- metadataEntries
+          if metadata.workflowExecutionUuid in targetWorkflowIds // Uses `METADATA_WORKFLOW_IDX`
+        } yield metadata
+      }.size
+    )
+
+  val metadataEntryExistsForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) =>
+    (for {
       metadataEntry <- metadataEntries
       if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield metadataEntry).exists
   )
 
-  def metadataEntryExistsForWorkflowExecutionUuid(workflowId: Rep[String], key: Rep[String]): Rep[Boolean] = {
-    metadataEntries.filter( metadataEntry =>
-      metadataEntry.workflowExecutionUuid === workflowId &&
-      metadataEntry.metadataKey === key &&
-      metadataEntry.metadataValue.isDefined
-    ).exists
-  }
-
-  val metadataEntriesForWorkflowExecutionUuidAndMetadataKey = Compiled(
-    (workflowExecutionUuid: Rep[String], metadataKey: Rep[String]) => (for {
-      metadataEntry <- metadataEntries
-      if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
-      if metadataEntry.metadataKey === metadataKey
-      if metadataEntry.callFullyQualifiedName.isEmpty
-      if metadataEntry.jobIndex.isEmpty
-      if metadataEntry.jobAttempt.isEmpty
-    } yield metadataEntry).sortBy(_.metadataTimestamp)
-  )
+  def metadataEntryExistsForWorkflowExecutionUuid(workflowId: Rep[String], key: Rep[String]): Rep[Boolean] =
+    metadataEntries
+      .filter(metadataEntry =>
+        metadataEntry.workflowExecutionUuid === workflowId &&
+          metadataEntry.metadataKey === key &&
+          metadataEntry.metadataValue.isDefined
+      )
+      .exists
 
-  val countMetadataEntriesForWorkflowExecutionUuidAndMetadataKey = Compiled(
-    (rootWorkflowId: Rep[String], metadataKey: Rep[String], expandSubWorkflows: Rep[Boolean]) => {
-      val targetWorkflowIds = for {
-        summary <- workflowMetadataSummaryEntries
-        // Uses `IX_WORKFLOW_METADATA_SUMMARY_ENTRY_RWEU`, `UC_WORKFLOW_METADATA_SUMMARY_ENTRY_WEU`
-        if summary.workflowExecutionUuid === rootWorkflowId || ((summary.rootWorkflowExecutionUuid === rootWorkflowId) && expandSubWorkflows)
-      } yield summary.workflowExecutionUuid
-
-      for {
-        metadata <- metadataEntries
-        if metadata.workflowExecutionUuid in targetWorkflowIds // Uses `METADATA_WORKFLOW_IDX`
-        if metadata.metadataKey === metadataKey
-        if metadata.callFullyQualifiedName.isEmpty
-        if metadata.jobIndex.isEmpty
-        if metadata.jobAttempt.isEmpty
-      } yield metadata
-    }.size
-  )
+  val metadataEntriesForWorkflowExecutionUuidAndMetadataKey =
+    Compiled((workflowExecutionUuid: Rep[String], metadataKey: Rep[String]) =>
+      (for {
+        metadataEntry <- metadataEntries
+        if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
+        if metadataEntry.metadataKey === metadataKey
+        if metadataEntry.callFullyQualifiedName.isEmpty
+        if metadataEntry.jobIndex.isEmpty
+        if metadataEntry.jobAttempt.isEmpty
+      } yield metadataEntry).sortBy(_.metadataTimestamp)
+    )
+
+  val countMetadataEntriesForWorkflowExecutionUuidAndMetadataKey =
+    Compiled((rootWorkflowId: Rep[String], metadataKey: Rep[String], expandSubWorkflows: Rep[Boolean]) =>
+      {
+        val targetWorkflowIds = for {
+          summary <- workflowMetadataSummaryEntries
+          // Uses `IX_WORKFLOW_METADATA_SUMMARY_ENTRY_RWEU`, `UC_WORKFLOW_METADATA_SUMMARY_ENTRY_WEU`
+          if summary.workflowExecutionUuid === rootWorkflowId || ((summary.rootWorkflowExecutionUuid === rootWorkflowId) && expandSubWorkflows)
+        } yield summary.workflowExecutionUuid
+
+        for {
+          metadata <- metadataEntries
+          if metadata.workflowExecutionUuid in targetWorkflowIds // Uses `METADATA_WORKFLOW_IDX`
+          if metadata.metadataKey === metadataKey
+          if metadata.callFullyQualifiedName.isEmpty
+          if metadata.jobIndex.isEmpty
+          if metadata.jobAttempt.isEmpty
+        } yield metadata
+      }.size
+    )
 
   val metadataEntriesForJobKey = Compiled(
-    (workflowExecutionUuid: Rep[String], callFullyQualifiedName: Rep[String], jobIndex: Rep[Option[Int]],
-     jobAttempt: Rep[Option[Int]]) => (for {
-      metadataEntry <- metadataEntries
-      if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
-      if metadataEntry.callFullyQualifiedName === callFullyQualifiedName
-      if hasSameIndex(metadataEntry, jobIndex)
-      if hasSameAttempt(metadataEntry, jobAttempt)
-    } yield metadataEntry).sortBy(_.metadataTimestamp)
+    (workflowExecutionUuid: Rep[String],
+     callFullyQualifiedName: Rep[String],
+     jobIndex: Rep[Option[Int]],
+     jobAttempt: Rep[Option[Int]]
+    ) =>
+      (for {
+        metadataEntry <- metadataEntries
+        if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
+        if metadataEntry.callFullyQualifiedName === callFullyQualifiedName
+        if hasSameIndex(metadataEntry, jobIndex)
+        if hasSameAttempt(metadataEntry, jobAttempt)
+      } yield metadataEntry).sortBy(_.metadataTimestamp)
   )
 
   val countMetadataEntriesForJobKey = Compiled(
-    (rootWorkflowId: Rep[String], callFullyQualifiedName: Rep[String], jobIndex: Rep[Option[Int]],
-     jobAttempt: Rep[Option[Int]], expandSubWorkflows: Rep[Boolean]) => {
-      val targetWorkflowIds = for {
-        summary <- workflowMetadataSummaryEntries
-        // Uses `IX_WORKFLOW_METADATA_SUMMARY_ENTRY_RWEU`, `UC_WORKFLOW_METADATA_SUMMARY_ENTRY_WEU`
-        if summary.workflowExecutionUuid === rootWorkflowId || ((summary.rootWorkflowExecutionUuid === rootWorkflowId) && expandSubWorkflows)
-      } yield summary.workflowExecutionUuid
-
-      for {
-        metadata <- metadataEntries
-        if metadata.workflowExecutionUuid in targetWorkflowIds // Uses `METADATA_WORKFLOW_IDX`
-        if metadata.callFullyQualifiedName === callFullyQualifiedName
-        if hasSameIndex(metadata, jobIndex)
-        if hasSameAttempt(metadata, jobAttempt)
-      } yield metadata
-    }.size
+    (rootWorkflowId: Rep[String],
+     callFullyQualifiedName: Rep[String],
+     jobIndex: Rep[Option[Int]],
+     jobAttempt: Rep[Option[Int]],
+     expandSubWorkflows: Rep[Boolean]
+    ) =>
+      {
+        val targetWorkflowIds = for {
+          summary <- workflowMetadataSummaryEntries
+          // Uses `IX_WORKFLOW_METADATA_SUMMARY_ENTRY_RWEU`, `UC_WORKFLOW_METADATA_SUMMARY_ENTRY_WEU`
+          if summary.workflowExecutionUuid === rootWorkflowId || ((summary.rootWorkflowExecutionUuid === rootWorkflowId) && expandSubWorkflows)
+        } yield summary.workflowExecutionUuid
+
+        for {
+          metadata <- metadataEntries
+          if metadata.workflowExecutionUuid in targetWorkflowIds // Uses `METADATA_WORKFLOW_IDX`
+          if metadata.callFullyQualifiedName === callFullyQualifiedName
+          if hasSameIndex(metadata, jobIndex)
+          if hasSameAttempt(metadata, jobAttempt)
+        } yield metadata
+      }.size
   )
 
   val metadataEntriesForJobKeyAndMetadataKey = Compiled(
-    (workflowExecutionUuid: Rep[String], metadataKey: Rep[String], callFullyQualifiedName: Rep[String],
-     jobIndex: Rep[Option[Int]], jobAttempt: Rep[Option[Int]]) => (for {
-      metadataEntry <- metadataEntries
-      if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
-      if metadataEntry.metadataKey === metadataKey
-      if metadataEntry.callFullyQualifiedName === callFullyQualifiedName
-      if hasSameIndex(metadataEntry, jobIndex)
-      if hasSameAttempt(metadataEntry, jobAttempt)
-    } yield metadataEntry).sortBy(_.metadataTimestamp)
+    (workflowExecutionUuid: Rep[String],
+     metadataKey: Rep[String],
+     callFullyQualifiedName: Rep[String],
+     jobIndex: Rep[Option[Int]],
+     jobAttempt: Rep[Option[Int]]
+    ) =>
+      (for {
+        metadataEntry <- metadataEntries
+        if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
+        if metadataEntry.metadataKey === metadataKey
+        if metadataEntry.callFullyQualifiedName === callFullyQualifiedName
+        if hasSameIndex(metadataEntry, jobIndex)
+        if hasSameAttempt(metadataEntry, jobAttempt)
+      } yield metadataEntry).sortBy(_.metadataTimestamp)
   )
 
   val countMetadataEntriesForJobKeyAndMetadataKey = Compiled(
-    (rootWorkflowId: Rep[String], metadataKey: Rep[String], callFullyQualifiedName: Rep[String],
-     jobIndex: Rep[Option[Int]], jobAttempt: Rep[Option[Int]], expandSubWorkflows: Rep[Boolean]) => {
-      val targetWorkflowIds = for {
-        summary <- workflowMetadataSummaryEntries
-        // Uses `IX_WORKFLOW_METADATA_SUMMARY_ENTRY_RWEU`, `UC_WORKFLOW_METADATA_SUMMARY_ENTRY_WEU`
-        if summary.workflowExecutionUuid === rootWorkflowId || ((summary.rootWorkflowExecutionUuid === rootWorkflowId) && expandSubWorkflows)
-      } yield summary.workflowExecutionUuid
-
-      for {
-        metadata <- metadataEntries
-        if metadata.workflowExecutionUuid in targetWorkflowIds // Uses `METADATA_WORKFLOW_IDX`
-        if metadata.metadataKey === metadataKey
-        if metadata.callFullyQualifiedName === callFullyQualifiedName
-        if hasSameIndex(metadata, jobIndex)
-        if hasSameAttempt(metadata, jobAttempt)
-      } yield metadata
-    }.size
+    (rootWorkflowId: Rep[String],
+     metadataKey: Rep[String],
+     callFullyQualifiedName: Rep[String],
+     jobIndex: Rep[Option[Int]],
+     jobAttempt: Rep[Option[Int]],
+     expandSubWorkflows: Rep[Boolean]
+    ) =>
+      {
+        val targetWorkflowIds = for {
+          summary <- workflowMetadataSummaryEntries
+          // Uses `IX_WORKFLOW_METADATA_SUMMARY_ENTRY_RWEU`, `UC_WORKFLOW_METADATA_SUMMARY_ENTRY_WEU`
+          if summary.workflowExecutionUuid === rootWorkflowId || ((summary.rootWorkflowExecutionUuid === rootWorkflowId) && expandSubWorkflows)
+        } yield summary.workflowExecutionUuid
+
+        for {
+          metadata <- metadataEntries
+          if metadata.workflowExecutionUuid in targetWorkflowIds // Uses `METADATA_WORKFLOW_IDX`
+          if metadata.metadataKey === metadataKey
+          if metadata.callFullyQualifiedName === callFullyQualifiedName
+          if hasSameIndex(metadata, jobIndex)
+          if hasSameAttempt(metadata, jobAttempt)
+        } yield metadata
+      }.size
   )
 
-  val metadataEntriesForIdRange = Compiled(
-    (minMetadataEntryId: Rep[Long], maxMetadataEntryId: Rep[Long]) => {
-      for {
-        metadataEntry <- metadataEntries
-        if metadataEntry.metadataEntryId >= minMetadataEntryId
-        if metadataEntry.metadataEntryId <= maxMetadataEntryId
-      } yield metadataEntry
-    }
-  )
+  val metadataEntriesForIdRange = Compiled { (minMetadataEntryId: Rep[Long], maxMetadataEntryId: Rep[Long]) =>
+    for {
+      metadataEntry <- metadataEntries
+      if metadataEntry.metadataEntryId >= minMetadataEntryId
+      if metadataEntry.metadataEntryId <= maxMetadataEntryId
+    } yield metadataEntry
+  }
 
   /**
     * Returns metadata entries that are "like" metadataKeys for the specified workflow.
@@ -210,14 +241,14 @@ trait MetadataEntryComponent {
   def metadataEntriesWithKeyConstraints(workflowExecutionUuid: String,
                                         metadataKeysToFilterFor: List[String],
                                         metadataKeysToFilterOut: List[String],
-                                        requireEmptyJobKey: Boolean) = {
+                                        requireEmptyJobKey: Boolean
+  ) =
     (for {
       metadataEntry <- metadataEntries
       if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
       if metadataEntryHasMetadataKeysLike(metadataEntry, metadataKeysToFilterFor, metadataKeysToFilterOut)
       if metadataEntryHasEmptyJobKey(metadataEntry, requireEmptyJobKey)
     } yield metadataEntry).sortBy(_.metadataTimestamp)
-  }
 
   /**
     * Counts metadata entries that are "like" metadataKeys for the specified workflow.
@@ -228,7 +259,8 @@ trait MetadataEntryComponent {
                                              metadataKeysToFilterFor: List[String],
                                              metadataKeysToFilterOut: List[String],
                                              requireEmptyJobKey: Boolean,
-                                             expandSubWorkflows: Boolean) = {
+                                             expandSubWorkflows: Boolean
+  ) = {
 
     val targetWorkflowIds = for {
       summary <- workflowMetadataSummaryEntries
@@ -253,7 +285,8 @@ trait MetadataEntryComponent {
                                               metadataKeysToFilterOut: List[String],
                                               callFqn: String,
                                               jobIndex: Option[Int],
-                                              jobAttempt: Option[Int]) = {
+                                              jobAttempt: Option[Int]
+  ) =
     (for {
       metadataEntry <- metadataEntries
       if metadataEntry.workflowExecutionUuid === workflowExecutionUuid
@@ -265,7 +298,6 @@ trait MetadataEntryComponent {
       // regardless of the attempt
       if (metadataEntry.jobAttempt === jobAttempt) || jobAttempt.isEmpty
     } yield metadataEntry).sortBy(_.metadataTimestamp)
-  }
 
   /**
     * Counts metadata entries that are "like" metadataKeys for the specified call.
@@ -277,7 +309,8 @@ trait MetadataEntryComponent {
                                                    callFqn: String,
                                                    jobIndex: Option[Int],
                                                    jobAttempt: Option[Int],
-                                                   expandSubWorkflows: Boolean) = {
+                                                   expandSubWorkflows: Boolean
+  ) = {
 
     val targetWorkflowIds = for {
       summary <- workflowMetadataSummaryEntries
@@ -301,31 +334,43 @@ trait MetadataEntryComponent {
   def metadataTableSizeInformation() = {
     val query =
       sql"""
-          |SELECT DATA_LENGTH, INDEX_LENGTH, DATA_FREE
-          |FROM information_schema.tables
-          |WHERE TABLE_NAME = 'METADATA_ENTRY'
+           |SELECT DATA_LENGTH, INDEX_LENGTH, DATA_FREE
+           |FROM information_schema.tables
+           |WHERE TABLE_NAME = 'METADATA_ENTRY'
          """.stripMargin
-    query.as[InformationSchemaEntry](rconv = GetResult { r =>
-      InformationSchemaEntry(r.<<, r.<<, r.<<)
-    }).headOption
+    query
+      .as[InformationSchemaEntry](rconv = GetResult { r =>
+        InformationSchemaEntry(r.<<, r.<<, r.<<)
+      })
+      .headOption
   }
 
   def failedJobsMetadataWithWorkflowId(rootWorkflowId: String, isPostgres: Boolean) = {
-    val getMetadataEntryResult = GetResult(r => {
-      MetadataEntry(r.<<, r.<<, r.<<, r.<<, r.<<, r.nextClobOption().map(clob => new SerialClob(clob)), r.<<, r.<<, r.<<)
-    })
-
-    def dbIdentifierWrapper(identifier: String, isPostgres: Boolean) = {
-      if(isPostgres) s"${'"'}$identifier${'"'}" else identifier
+    val getMetadataEntryResult = GetResult { r =>
+      MetadataEntry(r.<<,
+                    r.<<,
+                    r.<<,
+                    r.<<,
+                    r.<<,
+                    r.nextClobOption().map(clob => new SerialClob(clob)),
+                    r.<<,
+                    r.<<,
+                    r.<<
+      )
     }
 
-    def evaluateMetadataValue(isPostgres: Boolean, colName: String): String = {
-      if(isPostgres) s"convert_from(lo_get(${colName}::oid), 'UTF8')" else colName
-    }
+    def dbIdentifierWrapper(identifier: String, isPostgres: Boolean) =
+      if (isPostgres) s"${'"'}$identifier${'"'}" else identifier
+
+    def evaluateMetadataValue(isPostgres: Boolean, colName: String): String =
+      if (isPostgres) s"convert_from(lo_get(${colName}::oid), 'UTF8')" else colName
 
-    def attemptAndIndexSelectStatement(callFqn: String, scatterIndex: String, retryAttempt: String, variablePrefix: String): String = {
+    def attemptAndIndexSelectStatement(callFqn: String,
+                                       scatterIndex: String,
+                                       retryAttempt: String,
+                                       variablePrefix: String
+    ): String =
       s"SELECT ${callFqn}, MAX(COALESCE(${scatterIndex}, 0)) as ${variablePrefix}Scatter, MAX(COALESCE(${retryAttempt}, 0)) AS ${variablePrefix}Retry"
-    }
 
     val workflowUuid = dbIdentifierWrapper("WORKFLOW_EXECUTION_UUID", isPostgres)
     val callFqn = dbIdentifierWrapper("CALL_FQN", isPostgres)
@@ -339,7 +384,8 @@ trait MetadataEntryComponent {
     val metadataValue = dbIdentifierWrapper("METADATA_VALUE", isPostgres)
     val metadataEntry = dbIdentifierWrapper("METADATA_ENTRY", isPostgres)
     val wmse = dbIdentifierWrapper("WORKFLOW_METADATA_SUMMARY_ENTRY", isPostgres)
-    val resultSetColumnNames = s"me.${workflowUuid}, me.${callFqn}, me.${scatterIndex}, me.${retryAttempt}, me.${metadataKey}, me.${metadataValue}, me.${metadataValueType}, me.${metadataTimestamp}, me.${metadataJournalId}"
+    val resultSetColumnNames =
+      s"me.${workflowUuid}, me.${callFqn}, me.${scatterIndex}, me.${retryAttempt}, me.${metadataKey}, me.${metadataValue}, me.${metadataValueType}, me.${metadataTimestamp}, me.${metadataJournalId}"
 
     val query =
       sql"""
@@ -351,7 +397,9 @@ trait MetadataEntryComponent {
         INNER JOIN #${wmse} wmse
         ON wmse.#${workflowUuid} = me.#${workflowUuid}
         WHERE (wmse.#${rootUuid} = $rootWorkflowId OR wmse.#${workflowUuid} = $rootWorkflowId)
-        AND (me.#${metadataKey} in ('executionStatus', 'backendStatus') AND #${evaluateMetadataValue(isPostgres, metadataValue)} = 'Failed')
+        AND (me.#${metadataKey} in ('executionStatus', 'backendStatus') AND #${evaluateMetadataValue(isPostgres,
+                                                                                                     metadataValue
+        )} = 'Failed')
         GROUP BY #${callFqn}, #${metadataValue} 
         HAVING #${evaluateMetadataValue(isPostgres, metadataValue)} = 'Failed'
       ) AS failedCalls
@@ -396,7 +444,8 @@ trait MetadataEntryComponent {
 
   private[this] def metadataEntryHasMetadataKeysLike(metadataEntry: MetadataEntries,
                                                      metadataKeysToFilterFor: List[String],
-                                                     metadataKeysToFilterOut: List[String]): Rep[Boolean] = {
+                                                     metadataKeysToFilterOut: List[String]
+  ): Rep[Boolean] = {
 
     def containsKey(key: String): Rep[Boolean] = metadataEntry.metadataKey like key
 
@@ -414,19 +463,17 @@ trait MetadataEntryComponent {
     }
   }
 
-  private[this] def hasSameIndex(metadataEntry: MetadataEntries, jobIndex: Rep[Option[Int]]) = {
+  private[this] def hasSameIndex(metadataEntry: MetadataEntries, jobIndex: Rep[Option[Int]]) =
     (metadataEntry.jobIndex.isEmpty && jobIndex.isEmpty) || (metadataEntry.jobIndex === jobIndex)
-  }
 
-  private[this] def hasSameAttempt(metadataEntry: MetadataEntries, jobAttempt: Rep[Option[Int]]) = {
+  private[this] def hasSameAttempt(metadataEntry: MetadataEntries, jobAttempt: Rep[Option[Int]]) =
     (metadataEntry.jobAttempt.isEmpty && jobAttempt.isEmpty) || (metadataEntry.jobAttempt === jobAttempt)
-  }
 
   private[this] def metadataEntryHasEmptyJobKey(metadataEntry: MetadataEntries,
-                                                requireEmptyJobKey: Rep[Boolean]): Rep[Boolean] = {
+                                                requireEmptyJobKey: Rep[Boolean]
+  ): Rep[Boolean] =
     !requireEmptyJobKey ||
       (metadataEntry.callFullyQualifiedName.isEmpty &&
         metadataEntry.jobIndex.isEmpty &&
         metadataEntry.jobAttempt.isEmpty)
-  }
 }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
index 11fa2191cb2..77e39b43816 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/SubWorkflowStoreEntryComponent.scala
@@ -13,7 +13,7 @@ trait SubWorkflowStoreEntryComponent {
     def subWorkflowStoreEntryId = column[Long]("SUB_WORKFLOW_STORE_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def rootWorkflowId = column[Long]("ROOT_WORKFLOW_ID")
-    
+
     def parentWorkflowExecutionUuid = column[String]("PARENT_WORKFLOW_EXECUTION_UUID", O.Length(255))
 
     def callFullyQualifiedName = column[String]("CALL_FULLY_QUALIFIED_NAME", O.Length(255))
@@ -24,23 +24,37 @@ trait SubWorkflowStoreEntryComponent {
 
     def subWorkflowExecutionUuid = column[String]("SUB_WORKFLOW_EXECUTION_UUID", O.Length(255))
 
-    override def * = (rootWorkflowId.?, parentWorkflowExecutionUuid, callFullyQualifiedName, callIndex, callAttempt, subWorkflowExecutionUuid, subWorkflowStoreEntryId.?) <> (SubWorkflowStoreEntry.tupled, SubWorkflowStoreEntry.unapply)
-
-    def ucSubWorkflowStoreEntryPweuCfqnCiCa = index("UC_SUB_WORKFLOW_STORE_ENTRY_PWEU_CFQN_CI_CA",
-      (parentWorkflowExecutionUuid, callFullyQualifiedName, callIndex, callAttempt), unique = true)
+    override def * = (rootWorkflowId.?,
+                      parentWorkflowExecutionUuid,
+                      callFullyQualifiedName,
+                      callIndex,
+                      callAttempt,
+                      subWorkflowExecutionUuid,
+                      subWorkflowStoreEntryId.?
+    ) <> (SubWorkflowStoreEntry.tupled, SubWorkflowStoreEntry.unapply)
+
+    def ucSubWorkflowStoreEntryPweuCfqnCiCa = index(
+      "UC_SUB_WORKFLOW_STORE_ENTRY_PWEU_CFQN_CI_CA",
+      (parentWorkflowExecutionUuid, callFullyQualifiedName, callIndex, callAttempt),
+      unique = true
+    )
 
     def fkSubWorkflowStoreEntryRootWorkflowId = foreignKey("FK_SUB_WORKFLOW_STORE_ENTRY_ROOT_WORKFLOW_ID",
-      rootWorkflowId, workflowStoreEntries)(_.workflowStoreEntryId, onDelete = Cascade)
+                                                           rootWorkflowId,
+                                                           workflowStoreEntries
+    )(_.workflowStoreEntryId, onDelete = Cascade)
 
-    def ixSubWorkflowStoreEntryPweu = index("IX_SUB_WORKFLOW_STORE_ENTRY_PWEU", parentWorkflowExecutionUuid, unique = false)
+    def ixSubWorkflowStoreEntryPweu =
+      index("IX_SUB_WORKFLOW_STORE_ENTRY_PWEU", parentWorkflowExecutionUuid, unique = false)
   }
 
   protected val subWorkflowStoreEntries = TableQuery[SubWorkflowStoreEntries]
 
-  val subWorkflowStoreEntryIdsAutoInc = subWorkflowStoreEntries returning subWorkflowStoreEntries.map(_.subWorkflowStoreEntryId)
+  val subWorkflowStoreEntryIdsAutoInc =
+    subWorkflowStoreEntries returning subWorkflowStoreEntries.map(_.subWorkflowStoreEntryId)
 
-  val subWorkflowStoreEntriesForRootWorkflowId = Compiled(
-    (rootWorkflowId: Rep[Long]) => for {
+  val subWorkflowStoreEntriesForRootWorkflowId = Compiled((rootWorkflowId: Rep[Long]) =>
+    for {
       subWorkflowStoreEntry <- subWorkflowStoreEntries
       if subWorkflowStoreEntry.rootWorkflowId === rootWorkflowId
     } yield subWorkflowStoreEntry
@@ -50,8 +64,11 @@ trait SubWorkflowStoreEntryComponent {
     * Useful for finding the unique sub workflow entry for a given job key
     */
   val subWorkflowStoreEntriesForJobKey = Compiled(
-    (parentWorkflowExecutionUuid: Rep[String], callFullyQualifiedName: Rep[String], jobIndex: Rep[Int],
-     jobAttempt: Rep[Int]) =>
+    (parentWorkflowExecutionUuid: Rep[String],
+     callFullyQualifiedName: Rep[String],
+     jobIndex: Rep[Int],
+     jobAttempt: Rep[Int]
+    ) =>
       for {
         subWorkflowStoreEntry <- subWorkflowStoreEntries
         if subWorkflowStoreEntry.parentWorkflowExecutionUuid === parentWorkflowExecutionUuid &&
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/SummaryStatusEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/SummaryStatusEntryComponent.scala
index 807cb0802f7..72d1ece4bb0 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/SummaryStatusEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/SummaryStatusEntryComponent.scala
@@ -24,8 +24,8 @@ trait SummaryStatusEntryComponent {
 
   val summaryStatusEntryIdsAutoInc = summaryStatusEntries returning summaryStatusEntries.map(_.summaryStatusEntryId)
 
-  val summaryPositionForSummaryName = Compiled(
-    (summaryName: Rep[String]) => for {
+  val summaryPositionForSummaryName = Compiled((summaryName: Rep[String]) =>
+    for {
       summaryStatusEntry <- summaryStatusEntries
       if summaryStatusEntry.summaryName === summaryName
     } yield summaryStatusEntry.summaryPosition
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowMetadataSummaryEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowMetadataSummaryEntryComponent.scala
index c3020790be3..82489d4ae28 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowMetadataSummaryEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowMetadataSummaryEntryComponent.scala
@@ -17,7 +17,7 @@ trait WorkflowMetadataSummaryEntryComponent {
   import driver.api._
 
   class WorkflowMetadataSummaryEntries(tag: Tag)
-    extends Table[WorkflowMetadataSummaryEntry](tag, "WORKFLOW_METADATA_SUMMARY_ENTRY") {
+      extends Table[WorkflowMetadataSummaryEntry](tag, "WORKFLOW_METADATA_SUMMARY_ENTRY") {
     def workflowMetadataSummaryEntryId = column[Long]("WORKFLOW_METADATA_SUMMARY_ENTRY_ID", O.PrimaryKey, O.AutoInc)
 
     def workflowExecutionUuid = column[String]("WORKFLOW_EXECUTION_UUID", O.Length(100))
@@ -38,10 +38,19 @@ trait WorkflowMetadataSummaryEntryComponent {
 
     def metadataArchiveStatus: Rep[Option[String]] = column[Option[String]]("METADATA_ARCHIVE_STATUS", O.Length(30))
 
-    def baseProjection = (workflowExecutionUuid, workflowName, workflowStatus, startTimestamp, endTimestamp,
-      submissionTimestamp, parentWorkflowExecutionUuid, rootWorkflowExecutionUuid, metadataArchiveStatus)
+    def baseProjection = (workflowExecutionUuid,
+                          workflowName,
+                          workflowStatus,
+                          startTimestamp,
+                          endTimestamp,
+                          submissionTimestamp,
+                          parentWorkflowExecutionUuid,
+                          rootWorkflowExecutionUuid,
+                          metadataArchiveStatus
+    )
 
-    override def * = baseProjection ~ workflowMetadataSummaryEntryId.? <> (WorkflowMetadataSummaryEntry.tupled, WorkflowMetadataSummaryEntry.unapply)
+    override def * =
+      baseProjection ~ workflowMetadataSummaryEntryId.? <> (WorkflowMetadataSummaryEntry.tupled, WorkflowMetadataSummaryEntry.unapply)
 
     def forUpdate = baseProjection.shaped <> (
       tuple => WorkflowMetadataSummaryEntry.tupled(tuple :+ None),
@@ -71,112 +80,123 @@ trait WorkflowMetadataSummaryEntryComponent {
   val workflowMetadataSummaryEntryIdsAutoInc = workflowMetadataSummaryEntries returning
     workflowMetadataSummaryEntries.map(_.workflowMetadataSummaryEntryId)
 
-  val workflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp = Compiled(
-    (metadataArchiveStatus: Rep[Option[String]], workflowEndTimestampThreshold: Rep[Timestamp], batchSize: ConstColumn[Long]) => {
+  val workflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp = Compiled {
+    (metadataArchiveStatus: Rep[Option[String]],
+     workflowEndTimestampThreshold: Rep[Timestamp],
+     batchSize: ConstColumn[Long]
+    ) =>
       (for {
         summary <- workflowMetadataSummaryEntries
         if summary.metadataArchiveStatus === metadataArchiveStatus
         if summary.endTimestamp <= workflowEndTimestampThreshold
       } yield summary.workflowExecutionUuid).take(batchSize)
-    })
+  }
 
-  val workflowMetadataSummaryEntriesForWorkflowExecutionUuid = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+  val workflowMetadataSummaryEntriesForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       workflowMetadataSummaryEntry <- workflowMetadataSummaryEntries
       if workflowMetadataSummaryEntry.workflowExecutionUuid === workflowExecutionUuid
-    } yield workflowMetadataSummaryEntry.forUpdate)
+    } yield workflowMetadataSummaryEntry.forUpdate
+  )
 
-  val workflowMetadataSummaryEntryExistsForWorkflowExecutionUuid = Compiled(
-    (workflowExecutionUuid: Rep[String]) => (for {
+  val workflowMetadataSummaryEntryExistsForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) =>
+    (for {
       summaryEntry <- workflowMetadataSummaryEntries
       if summaryEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield summaryEntry).exists
   )
 
-  val workflowStatusesForWorkflowExecutionUuid = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+  val workflowStatusesForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       workflowMetadataSummaryEntry <- workflowMetadataSummaryEntries
       if workflowMetadataSummaryEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield workflowMetadataSummaryEntry.workflowStatus
   )
 
-  val rootWorkflowId = Compiled(
-    (workflowId: Rep[String]) => for {
+  val rootWorkflowId = Compiled((workflowId: Rep[String]) =>
+    for {
       summary <- workflowMetadataSummaryEntries
       if summary.workflowExecutionUuid === workflowId
-    } yield {
-      summary.rootWorkflowExecutionUuid.getOrElse(summary.workflowExecutionUuid)
-    }
+    } yield summary.rootWorkflowExecutionUuid.getOrElse(summary.workflowExecutionUuid)
   )
 
-  val metadataArchiveStatusByWorkflowId = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+  val metadataArchiveStatusByWorkflowId = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       workflowMetadataSummaryEntry <- workflowMetadataSummaryEntries
       if workflowMetadataSummaryEntry.workflowExecutionUuid === workflowExecutionUuid
-    } yield workflowMetadataSummaryEntry.metadataArchiveStatus)
+    } yield workflowMetadataSummaryEntry.metadataArchiveStatus
+  )
 
-  val metadataArchiveStatusAndEndTimeByWorkflowId = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+  val metadataArchiveStatusAndEndTimeByWorkflowId = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       workflowMetadataSummaryEntry <- workflowMetadataSummaryEntries
       if workflowMetadataSummaryEntry.workflowExecutionUuid === workflowExecutionUuid
-    } yield (workflowMetadataSummaryEntry.metadataArchiveStatus, workflowMetadataSummaryEntry.endTimestamp))
+    } yield (workflowMetadataSummaryEntry.metadataArchiveStatus, workflowMetadataSummaryEntry.endTimestamp)
+  )
 
   private def fetchAllWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String],
-                                                                              workflowEndTimestampThreshold: Timestamp): Query[WorkflowMetadataSummaryEntries, WorkflowMetadataSummaryEntry, Seq] = {
+                                                                              workflowEndTimestampThreshold: Timestamp
+  ): Query[WorkflowMetadataSummaryEntries, WorkflowMetadataSummaryEntry, Seq] =
     for {
       summaryEntry <- workflowMetadataSummaryEntries
       if summaryEntry.workflowStatus.inSet(workflowStatuses)
       if summaryEntry.metadataArchiveStatus.isEmpty // get Unarchived workflows only
       if summaryEntry.endTimestamp <= workflowEndTimestampThreshold
     } yield summaryEntry
-  }
 
-  private def fetchAllWorkflowsToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold: Timestamp): Query[WorkflowMetadataSummaryEntries, WorkflowMetadataSummaryEntry, Seq] = {
+  private def fetchAllWorkflowsToDeleteThatEndedOnOrBeforeThresholdTimestamp(
+    workflowEndTimestampThreshold: Timestamp
+  ): Query[WorkflowMetadataSummaryEntries, WorkflowMetadataSummaryEntry, Seq] =
     for {
       summaryEntry <- workflowMetadataSummaryEntries
       if summaryEntry.metadataArchiveStatus === Option("Archived") // get archived but not deleted workflows only
       if summaryEntry.endTimestamp <= workflowEndTimestampThreshold
     } yield summaryEntry
-  }
 
   def workflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String],
                                                               workflowEndTimestampThreshold: Timestamp,
-                                                              batchSize: Long): Query[WorkflowMetadataSummaryEntries, WorkflowMetadataSummaryEntry, Seq] = {
+                                                              batchSize: Long
+  ): Query[WorkflowMetadataSummaryEntries, WorkflowMetadataSummaryEntry, Seq] =
     fetchAllWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(
       workflowStatuses,
       workflowEndTimestampThreshold
     ).sortBy(_.endTimestamp).take(batchSize)
-  }
 
   def countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String],
-                                                                       workflowEndTimestampThreshold: Timestamp): Rep[Int] = {
+                                                                       workflowEndTimestampThreshold: Timestamp
+  ): Rep[Int] =
     fetchAllWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(
       workflowStatuses,
       workflowEndTimestampThreshold
     ).length
-  }
 
-  def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold: Timestamp): Rep[Int] = {
+  def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(
+    workflowEndTimestampThreshold: Timestamp
+  ): Rep[Int] =
     fetchAllWorkflowsToDeleteThatEndedOnOrBeforeThresholdTimestamp(
       workflowEndTimestampThreshold
     ).length
-  }
 
-  def concat(a: SQLActionBuilder, b: SQLActionBuilder): SQLActionBuilder = {
-    SQLActionBuilder(a.queryParts ++ b.queryParts, (p: Unit, pp: PositionedParameters) => {
-      a.unitPConv.apply(p, pp)
-      b.unitPConv.apply(p, pp)
-    })
-  }
+  def concat(a: SQLActionBuilder, b: SQLActionBuilder): SQLActionBuilder =
+    SQLActionBuilder(a.queryParts ++ b.queryParts,
+                     (p: Unit, pp: PositionedParameters) => {
+                       a.unitPConv.apply(p, pp)
+                       b.unitPConv.apply(p, pp)
+                     }
+    )
 
-  def concatNel(nel: NonEmptyList[SQLActionBuilder]): SQLActionBuilder = nel.tail.foldLeft(nel.head) { (acc, next) => concat(acc, next) }
+  def concatNel(nel: NonEmptyList[SQLActionBuilder]): SQLActionBuilder = nel.tail.foldLeft(nel.head) { (acc, next) =>
+    concat(acc, next)
+  }
 
-  def and(list: NonEmptyList[SQLActionBuilder]): SQLActionBuilder = if (list.size == 1) list.head else {
+  def and(list: NonEmptyList[SQLActionBuilder]): SQLActionBuilder = if (list.size == 1) list.head
+  else {
     val fullList = data.NonEmptyList.of(sql"(") ++ list.init.flatMap(x => List(x, sql" AND ")) :+ list.last :+ sql")"
     concatNel(fullList)
   }
 
-  def or(list: NonEmptyList[SQLActionBuilder]): SQLActionBuilder = if (list.size == 1) list.head else {
+  def or(list: NonEmptyList[SQLActionBuilder]): SQLActionBuilder = if (list.size == 1) list.head
+  else {
     val fullList = data.NonEmptyList.of(sql"(") ++ list.init.flatMap(x => List(x, sql" OR ")) :+ list.last :+ sql")"
     concatNel(fullList)
   }
@@ -192,15 +212,16 @@ trait WorkflowMetadataSummaryEntryComponent {
                        workflowStatuses: Set[String],
                        workflowNames: Set[String],
                        workflowExecutionUuids: Set[String],
-                       labelAndKeyLabelValues: Set[(String,String)],
-                       labelOrKeyLabelValues: Set[(String,String)],
-                       excludeLabelAndValues: Set[(String,String)],
-                       excludeLabelOrValues: Set[(String,String)],
+                       labelAndKeyLabelValues: Set[(String, String)],
+                       labelOrKeyLabelValues: Set[(String, String)],
+                       excludeLabelAndValues: Set[(String, String)],
+                       excludeLabelOrValues: Set[(String, String)],
                        submissionTimestampOption: Option[Timestamp],
                        startTimestampOption: Option[Timestamp],
                        endTimestampOption: Option[Timestamp],
                        metadataArchiveStatus: Set[Option[String]],
-                       includeSubworkflows: Boolean): SQLActionBuilder = {
+                       includeSubworkflows: Boolean
+  ): SQLActionBuilder = {
 
     val customLabelEntryTable = quoted("CUSTOM_LABEL_ENTRY")
     val workflowMetadataSummaryEntryTable = quoted("WORKFLOW_METADATA_SUMMARY_ENTRY")
@@ -212,8 +233,8 @@ trait WorkflowMetadataSummaryEntryComponent {
 
     val summaryTableAlias = quoted("summaryTable")
     val labelsOrTableAlias = quoted("labelsOrMixin")
-    val labelsAndTableAliases = labelAndKeyLabelValues.zipWithIndex.map {
-      case (labelPair, i) => quoted(s"labelAndTable$i") -> labelPair
+    val labelsAndTableAliases = labelAndKeyLabelValues.zipWithIndex.map { case (labelPair, i) =>
+      quoted(s"labelAndTable$i") -> labelPair
     }.toMap
 
     val selectColumns = List(
@@ -226,7 +247,7 @@ trait WorkflowMetadataSummaryEntryComponent {
       "PARENT_WORKFLOW_EXECUTION_UUID",
       "ROOT_WORKFLOW_EXECUTION_UUID",
       "METADATA_ARCHIVE_STATUS",
-      "WORKFLOW_METADATA_SUMMARY_ENTRY_ID",
+      "WORKFLOW_METADATA_SUMMARY_ENTRY_ID"
     )
       .map(quoted)
       .mkString(s"$summaryTableAlias.", ", ", "")
@@ -241,11 +262,10 @@ trait WorkflowMetadataSummaryEntryComponent {
     }
 
     val labelOrJoin = if (labelOrKeyLabelValues.nonEmpty) {
-      Option(
-        sql"""|  JOIN #$customLabelEntryTable #$labelsOrTableAlias
-              |    ON #$summaryTableAlias.#$workflowExecutionUuidColumn
-              |      = #$labelsOrTableAlias.#$workflowExecutionUuidColumn
-              |""".stripMargin)
+      Option(sql"""|  JOIN #$customLabelEntryTable #$labelsOrTableAlias
+                   |    ON #$summaryTableAlias.#$workflowExecutionUuidColumn
+                   |      = #$labelsOrTableAlias.#$workflowExecutionUuidColumn
+                   |""".stripMargin)
     } else None
 
     val labelAndJoins = labelsAndTableAliases.toList.map { case (labelAndTableAlias, _) =>
@@ -255,9 +275,8 @@ trait WorkflowMetadataSummaryEntryComponent {
             |""".stripMargin
     }
 
-    val from = concatNel(NonEmptyList.of(
-      sql"""|FROM #$workflowMetadataSummaryEntryTable #$summaryTableAlias
-            |""".stripMargin) ++ labelOrJoin.toList ++ labelAndJoins)
+    val from = concatNel(NonEmptyList.of(sql"""|FROM #$workflowMetadataSummaryEntryTable #$summaryTableAlias
+                                               |""".stripMargin) ++ labelOrJoin.toList ++ labelAndJoins)
 
     def makeSetConstraint(column: String, elements: Set[String]) = {
       val list = elements.toList.map(element => sql"""#$summaryTableAlias.#${quoted(column)} = $element""")
@@ -272,9 +291,8 @@ trait WorkflowMetadataSummaryEntryComponent {
       NonEmptyList.fromList(list).map(or).toList
     }
 
-    def makeTimeConstraint(column: String, comparison: String, elementOption: Option[Timestamp]) = {
+    def makeTimeConstraint(column: String, comparison: String, elementOption: Option[Timestamp]) =
       elementOption.map(element => sql"""#$summaryTableAlias.#${quoted(column)} #$comparison $element""").toList
-    }
 
     val statusConstraint = makeSetConstraint("WORKFLOW_STATUS", workflowStatuses)
     val nameConstraint = makeSetConstraint("WORKFLOW_NAME", workflowNames)
@@ -287,23 +305,30 @@ trait WorkflowMetadataSummaryEntryComponent {
     val metadataArchiveStatusConstraint = makeSetConstraintWithNulls("METADATA_ARCHIVE_STATUS", metadataArchiveStatus)
 
     // *ALL* of the labelAnd list of KV pairs must exist:
-    val labelsAndConstraint = NonEmptyList.fromList(labelsAndTableAliases.toList.map {
-      case (labelsAndTableAlias, (labelKey, labelValue)) =>
-        and(NonEmptyList.of(
-          sql"""#$labelsAndTableAlias.#$customLabelKeyColumn = $labelKey""",
-          sql"""#$labelsAndTableAlias.#$customLabelValueColumn = $labelValue""",
-        ))
-    }).map(and).toList
+    val labelsAndConstraint = NonEmptyList
+      .fromList(labelsAndTableAliases.toList.map { case (labelsAndTableAlias, (labelKey, labelValue)) =>
+        and(
+          NonEmptyList.of(
+            sql"""#$labelsAndTableAlias.#$customLabelKeyColumn = $labelKey""",
+            sql"""#$labelsAndTableAlias.#$customLabelValueColumn = $labelValue"""
+          )
+        )
+      })
+      .map(and)
+      .toList
 
     // At least one of the labelOr list of KV pairs must exist:
-    val labelOrConstraint = NonEmptyList.fromList(labelOrKeyLabelValues.toList.map {
-      case (labelKey, labelValue) =>
-        and(NonEmptyList.of(
-          sql"""#$labelsOrTableAlias.#$customLabelKeyColumn = $labelKey""",
-          sql"""#$labelsOrTableAlias.#$customLabelValueColumn = $labelValue""",
-        ))
-    }).map(or).toList
-
+    val labelOrConstraint = NonEmptyList
+      .fromList(labelOrKeyLabelValues.toList.map { case (labelKey, labelValue) =>
+        and(
+          NonEmptyList.of(
+            sql"""#$labelsOrTableAlias.#$customLabelKeyColumn = $labelKey""",
+            sql"""#$labelsOrTableAlias.#$customLabelValueColumn = $labelValue"""
+          )
+        )
+      })
+      .map(or)
+      .toList
 
     var mixinTableCounter = 0
 
@@ -322,18 +347,26 @@ trait WorkflowMetadataSummaryEntryComponent {
     }
 
     // *ALL* of the excludeLabelOr list of KV pairs must *NOT* exist:
-    val excludeLabelsOrConstraint = NonEmptyList.fromList(excludeLabelOrValues.toList map {
-      case (labelKey, labelValue) => not(labelExists(labelKey, labelValue))
-    }).map(and).toList
+    val excludeLabelsOrConstraint = NonEmptyList
+      .fromList(excludeLabelOrValues.toList map { case (labelKey, labelValue) =>
+        not(labelExists(labelKey, labelValue))
+      })
+      .map(and)
+      .toList
 
     // At least one of the excludeLabelAnd list of KV pairs must *NOT* exist:
-    val excludeLabelsAndConstraint = NonEmptyList.fromList(excludeLabelAndValues.toList.map {
-      case (labelKey, labelValue) => not(labelExists(labelKey, labelValue))
-    }).map(or).toList
-
-    val includeSubworkflowsConstraint = if (includeSubworkflows) List.empty else {
-      List(sql"""#$summaryTableAlias.#$parentWorkflowExecutionUuidColumn IS NULL""".stripMargin)
-    }
+    val excludeLabelsAndConstraint = NonEmptyList
+      .fromList(excludeLabelAndValues.toList.map { case (labelKey, labelValue) =>
+        not(labelExists(labelKey, labelValue))
+      })
+      .map(or)
+      .toList
+
+    val includeSubworkflowsConstraint =
+      if (includeSubworkflows) List.empty
+      else {
+        List(sql"""#$summaryTableAlias.#$parentWorkflowExecutionUuidColumn IS NULL""".stripMargin)
+      }
 
     val constraintList =
       statusConstraint ++
@@ -359,19 +392,20 @@ trait WorkflowMetadataSummaryEntryComponent {
     concatNel((NonEmptyList.of(select) :+ from) ++ where)
   }
 
-
   def countWorkflowMetadataSummaryEntries(parentIdWorkflowMetadataKey: String,
-                                          workflowStatuses: Set[String], workflowNames: Set[String],
+                                          workflowStatuses: Set[String],
+                                          workflowNames: Set[String],
                                           workflowExecutionUuids: Set[String],
-                                          labelAndKeyLabelValues: Set[(String,String)],
-                                          labelOrKeyLabelValues: Set[(String,String)],
-                                          excludeLabelAndValues: Set[(String,String)],
-                                          excludeLabelOrValues: Set[(String,String)],
+                                          labelAndKeyLabelValues: Set[(String, String)],
+                                          labelOrKeyLabelValues: Set[(String, String)],
+                                          excludeLabelAndValues: Set[(String, String)],
+                                          excludeLabelOrValues: Set[(String, String)],
                                           submissionTimestampOption: Option[Timestamp],
                                           startTimestampOption: Option[Timestamp],
                                           endTimestampOption: Option[Timestamp],
                                           metadataArchiveStatus: Set[Option[String]],
-                                          includeSubworkflows: Boolean) = {
+                                          includeSubworkflows: Boolean
+  ) =
     buildQueryAction(
       selectOrCount = Count,
       parentIdWorkflowMetadataKey,
@@ -388,18 +422,18 @@ trait WorkflowMetadataSummaryEntryComponent {
       metadataArchiveStatus,
       includeSubworkflows = includeSubworkflows
     ).as[Int].head
-  }
 
   /**
     * Query workflow execution using the filter criteria encapsulated by the `WorkflowExecutionQueryParameters`.
     */
   def queryWorkflowMetadataSummaryEntries(parentIdWorkflowMetadataKey: String,
-                                          workflowStatuses: Set[String], workflowNames: Set[String],
+                                          workflowStatuses: Set[String],
+                                          workflowNames: Set[String],
                                           workflowExecutionUuids: Set[String],
-                                          labelAndKeyLabelValues: Set[(String,String)],
-                                          labelOrKeyLabelValues: Set[(String,String)],
-                                          excludeLabelAndValues: Set[(String,String)],
-                                          excludeLabelOrValues: Set[(String,String)],
+                                          labelAndKeyLabelValues: Set[(String, String)],
+                                          labelOrKeyLabelValues: Set[(String, String)],
+                                          excludeLabelAndValues: Set[(String, String)],
+                                          excludeLabelOrValues: Set[(String, String)],
                                           submissionTimestampOption: Option[Timestamp],
                                           startTimestampOption: Option[Timestamp],
                                           endTimestampOption: Option[Timestamp],
@@ -407,7 +441,8 @@ trait WorkflowMetadataSummaryEntryComponent {
                                           includeSubworkflows: Boolean,
                                           page: Option[Int],
                                           pageSize: Option[Int],
-                                          newestFirst: Boolean) = {
+                                          newestFirst: Boolean
+  ) = {
     val mainQuery = buildQueryAction(
       selectOrCount = Select,
       parentIdWorkflowMetadataKey,
@@ -433,13 +468,13 @@ trait WorkflowMetadataSummaryEntryComponent {
 
     // `true` for queries, newest workflows are the most relevant
     // `false` for archiving, going oldest-to-newest
-    val orderByAddendum = if (newestFirst)
-      sql"""|  ORDER BY #${quoted("WORKFLOW_METADATA_SUMMARY_ENTRY_ID")} DESC
-            |""".stripMargin
-    else
-      sql"""|  ORDER BY #${quoted("WORKFLOW_METADATA_SUMMARY_ENTRY_ID")} ASC
-            |""".stripMargin
-
+    val orderByAddendum =
+      if (newestFirst)
+        sql"""|  ORDER BY #${quoted("WORKFLOW_METADATA_SUMMARY_ENTRY_ID")} DESC
+              |""".stripMargin
+      else
+        sql"""|  ORDER BY #${quoted("WORKFLOW_METADATA_SUMMARY_ENTRY_ID")} ASC
+              |""".stripMargin
 
     // NB you can preview the prepared statement created here by using, for example: println(result.statements.head)
 
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
index 847fa862405..874fcbd0c0c 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
@@ -43,8 +43,23 @@ trait WorkflowStoreEntryComponent {
 
     def hogGroup = column[Option[String]]("HOG_GROUP", O.Length(100))
 
-    override def * = (workflowExecutionUuid, workflowDefinition, workflowUrl, workflowRoot, workflowType, workflowTypeVersion, workflowInputs, workflowOptions, workflowState,
-      submissionTime, importsZip, customLabels, cromwellId, heartbeatTimestamp, hogGroup, workflowStoreEntryId.?) <> ((WorkflowStoreEntry.apply _).tupled, WorkflowStoreEntry.unapply)
+    override def * = (workflowExecutionUuid,
+                      workflowDefinition,
+                      workflowUrl,
+                      workflowRoot,
+                      workflowType,
+                      workflowTypeVersion,
+                      workflowInputs,
+                      workflowOptions,
+                      workflowState,
+                      submissionTime,
+                      importsZip,
+                      customLabels,
+                      cromwellId,
+                      heartbeatTimestamp,
+                      hogGroup,
+                      workflowStoreEntryId.?
+    ) <> ((WorkflowStoreEntry.apply _).tupled, WorkflowStoreEntry.unapply)
 
     def ucWorkflowStoreEntryWeu = index("UC_WORKFLOW_STORE_ENTRY_WEU", workflowExecutionUuid, unique = true)
 
@@ -58,15 +73,15 @@ trait WorkflowStoreEntryComponent {
   /**
     * Useful for finding the workflow store for a given workflow execution UUID
     */
-  val workflowStoreEntriesForWorkflowExecutionUuid = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+  val workflowStoreEntriesForWorkflowExecutionUuid = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       workflowStoreEntry <- workflowStoreEntries
       if workflowStoreEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield workflowStoreEntry
   )
 
-  val heartbeatForWorkflowStoreEntry = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+  val heartbeatForWorkflowStoreEntry = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       workflowStoreEntry <- workflowStoreEntries
       if workflowStoreEntry.workflowExecutionUuid === workflowExecutionUuid
     } yield workflowStoreEntry.heartbeatTimestamp
@@ -77,7 +92,8 @@ trait WorkflowStoreEntryComponent {
    */
   def getHogGroupWithLowestRunningWfs(heartbeatTimestampTimedOut: Timestamp,
                                       excludeWorkflowState: String,
-                                      excludedGroups: Set[String]): Query[Rep[Option[String]], Option[String], Seq] = {
+                                      excludedGroups: Set[String]
+  ): Query[Rep[Option[String]], Option[String], Seq] = {
     val startableWorkflows = for {
       row <- workflowStoreEntries
       /*
@@ -86,7 +102,7 @@ trait WorkflowStoreEntryComponent {
         2) Workflows with old heartbeats, presumably abandoned by a defunct Cromwell.
         3) Workflows not in "OnHold" state
         4) Workflows that don't belong to hog groups in excludedGroups
-      */
+       */
       if (row.heartbeatTimestamp.isEmpty || row.heartbeatTimestamp < heartbeatTimestampTimedOut) &&
         (row.workflowState =!= excludeWorkflowState) &&
         !(row.hogGroup inSet excludedGroups)
@@ -109,7 +125,7 @@ trait WorkflowStoreEntryComponent {
         This looks for:
         1) Workflows not in "OnHold" state
         2) Workflows that don't belong to hog groups in excludedGroups
-      */
+       */
       if row.workflowState =!= excludeWorkflowState &&
         !(row.hogGroup inSet excludedGroups)
     } yield row
@@ -129,27 +145,31 @@ trait WorkflowStoreEntryComponent {
       Seq
     ] = for {
       (hog_group, workflows_ct) <- totalWorkflowsByHogGroup
-      (startable_hog_group, startable_workflows_ct, oldest_submission_time) <- numOfStartableWfsByHogGroup if hog_group === startable_hog_group
+      (startable_hog_group, startable_workflows_ct, oldest_submission_time) <- numOfStartableWfsByHogGroup
+      if hog_group === startable_hog_group
     } yield (hog_group, workflows_ct - startable_workflows_ct, oldest_submission_time)
 
     // sort the above calculated result set first by the count of actively running workflows, then by hog group with
     // oldest submission timestamp and then sort it alphabetically by hog group name. Then take the first row of
     // the result and return the hog group name.
-    wfsRunningPerHogGroup.sortBy {
-      case (hogGroupName, running_wf_ct, oldest_submission_time) => (running_wf_ct.asc, oldest_submission_time, hogGroupName)
-    }.take(1).map(_._1)
+    wfsRunningPerHogGroup
+      .sortBy { case (hogGroupName, running_wf_ct, oldest_submission_time) =>
+        (running_wf_ct.asc, oldest_submission_time, hogGroupName)
+      }
+      .take(1)
+      .map(_._1)
   }
 
   /**
    * Returns up to "limit" startable workflows, sorted by submission time, that belong to
    * given hog group and are not in "OnHold" status.
    */
-  val fetchStartableWfsForHogGroup = Compiled(
+  val fetchStartableWfsForHogGroup = Compiled {
     (limit: ConstColumn[Long],
      heartbeatTimestampTimedOut: ConstColumn[Timestamp],
      excludeWorkflowState: Rep[String],
-     hogGroup: Rep[Option[String]]) => {
-
+     hogGroup: Rep[Option[String]]
+    ) =>
       val workflowsToStart = for {
         row <- workflowStoreEntries
         /*
@@ -158,7 +178,7 @@ trait WorkflowStoreEntryComponent {
           2) Workflows with old heartbeats, presumably abandoned by a defunct Cromwell.
           3) Workflows not in "OnHold" state
           4) Workflows that belong to included hog group
-        */
+         */
         if (row.heartbeatTimestamp.isEmpty || row.heartbeatTimestamp < heartbeatTimestampTimedOut) &&
           (row.workflowState =!= excludeWorkflowState) &&
           (row.hogGroup === hogGroup)
@@ -169,8 +189,7 @@ trait WorkflowStoreEntryComponent {
         do an update subsequent to this select in the same transaction that we know will impact those readers.
        */
       workflowsToStart.forUpdate.sortBy(_.submissionTime.asc).take(limit)
-    }
-  )
+  }
 
   /**
     * Useful for counting workflows in a given state.
@@ -184,8 +203,8 @@ trait WorkflowStoreEntryComponent {
   /**
     * Useful for updating the relevant fields of a workflow store entry when a workflow is picked up for processing.
     */
-  val workflowStoreFieldsForPickup = Compiled(
-    (workflowExecutionUuid: Rep[String]) => for {
+  val workflowStoreFieldsForPickup = Compiled((workflowExecutionUuid: Rep[String]) =>
+    for {
       row <- workflowStoreEntries
       if row.workflowExecutionUuid === workflowExecutionUuid
     } yield (row.workflowState, row.cromwellId, row.heartbeatTimestamp)
@@ -194,8 +213,8 @@ trait WorkflowStoreEntryComponent {
   /**
     * Useful for clearing out cromwellId and heartbeatTimestamp on an orderly Cromwell shutdown.
     */
-  val releaseWorkflowStoreEntries = Compiled(
-    (cromwellId: Rep[String]) => for {
+  val releaseWorkflowStoreEntries = Compiled((cromwellId: Rep[String]) =>
+    for {
       row <- workflowStoreEntries
       if row.cromwellId === cromwellId
     } yield (row.cromwellId, row.heartbeatTimestamp)
@@ -204,8 +223,8 @@ trait WorkflowStoreEntryComponent {
   /**
     * Useful for updating state for all entries matching a given state
     */
-  val workflowStateForWorkflowState = Compiled(
-    (workflowState: Rep[String]) => for {
+  val workflowStateForWorkflowState = Compiled((workflowState: Rep[String]) =>
+    for {
       workflowStoreEntry <- workflowStoreEntries
       if workflowStoreEntry.workflowState === workflowState
     } yield workflowStoreEntry.workflowState
@@ -214,8 +233,8 @@ trait WorkflowStoreEntryComponent {
   /**
     * Useful for updating a given workflow to a new state
     */
-  val workflowStateForWorkflowExecutionUUid = Compiled(
-    (workflowId: Rep[String]) => for {
+  val workflowStateForWorkflowExecutionUUid = Compiled((workflowId: Rep[String]) =>
+    for {
       workflowStoreEntry <- workflowStoreEntries
       if workflowStoreEntry.workflowExecutionUuid === workflowId
     } yield workflowStoreEntry.workflowState
@@ -224,53 +243,48 @@ trait WorkflowStoreEntryComponent {
   /**
     * Useful for updating a given workflow to a 'Submitted' state when it's currently 'On Hold'
     */
-  val workflowStateForWorkflowExecutionUUidAndWorkflowState = Compiled(
-    (workflowId: Rep[String], workflowState: Rep[String]) => {
+  val workflowStateForWorkflowExecutionUUidAndWorkflowState = Compiled {
+    (workflowId: Rep[String], workflowState: Rep[String]) =>
       for {
         workflowStoreEntry <- workflowStoreEntries
         if workflowStoreEntry.workflowExecutionUuid === workflowId
         if workflowStoreEntry.workflowState === workflowState
       } yield workflowStoreEntry.workflowState
-    }
-  )
+  }
 
   /**
     * Useful for deleting a given workflow to a 'Submitted' state when it's currently 'On Hold' or 'Submitted'
     */
-  val workflowStoreEntryForWorkflowExecutionUUidAndWorkflowStates = Compiled(
-    (workflowId: Rep[String],
-     workflowStateOr1: Rep[String],
-     workflowStateOr2: Rep[String]
-    ) => {
+  val workflowStoreEntryForWorkflowExecutionUUidAndWorkflowStates = Compiled {
+    (workflowId: Rep[String], workflowStateOr1: Rep[String], workflowStateOr2: Rep[String]) =>
       for {
         workflowStoreEntry <- workflowStoreEntries
         if workflowStoreEntry.workflowExecutionUuid === workflowId
         if workflowStoreEntry.workflowState === workflowStateOr1 ||
           workflowStoreEntry.workflowState === workflowStateOr2
       } yield workflowStoreEntry
-    }
-  )
+  }
 
   // Find workflows running on a given Cromwell instance with abort requested:
-  val findWorkflowsWithAbortRequested = Compiled(
-    (cromwellId: Rep[String]) => for {
+  val findWorkflowsWithAbortRequested = Compiled((cromwellId: Rep[String]) =>
+    for {
       workflowStoreEntry <- workflowStoreEntries
       if workflowStoreEntry.workflowState === "Aborting" && workflowStoreEntry.cromwellId === cromwellId
     } yield workflowStoreEntry.workflowExecutionUuid
   )
 
   // Find workflows running on a given Cromwell instance:
-  val findWorkflows = Compiled(
-    (cromwellId: Rep[String]) => for {
+  val findWorkflows = Compiled((cromwellId: Rep[String]) =>
+    for {
       workflowStoreEntry <- workflowStoreEntries
       if workflowStoreEntry.cromwellId === cromwellId
     } yield workflowStoreEntry.workflowExecutionUuid
   )
 
-  val checkExists = Compiled(
-    (workflowId: Rep[String]) => (for {
+  val checkExists = Compiled((workflowId: Rep[String]) =>
+    for {
       workflowStoreEntry <- workflowStoreEntries
       if workflowStoreEntry.workflowExecutionUuid === workflowId
-    } yield 1)
+    } yield 1
   )
 }
diff --git a/database/sql/src/main/scala/cromwell/database/sql/CallCachingSqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/CallCachingSqlDatabase.scala
index 25380dc41b5..ef51b15b2ff 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/CallCachingSqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/CallCachingSqlDatabase.scala
@@ -8,23 +8,27 @@ import scala.concurrent.{ExecutionContext, Future}
 trait CallCachingSqlDatabase {
   def addCallCaching(joins: Seq[CallCachingJoin], batchSize: Int)(implicit ec: ExecutionContext): Future[Unit]
 
-  def hasMatchingCallCachingEntriesForBaseAggregation(baseAggregationHash: String, callCachePathPrefixes: Option[List[String]])
-                                                     (implicit ec: ExecutionContext): Future[Boolean]
+  def hasMatchingCallCachingEntriesForBaseAggregation(baseAggregationHash: String,
+                                                      callCachePathPrefixes: Option[List[String]]
+  )(implicit ec: ExecutionContext): Future[Boolean]
 
-  def findCacheHitForAggregation(baseAggregationHash: String, inputFilesAggregationHash: Option[String], callCachePathPrefixes: Option[List[String]], excludedIds: Set[Long])
-                                (implicit ec: ExecutionContext): Future[Option[Long]]
+  def findCacheHitForAggregation(baseAggregationHash: String,
+                                 inputFilesAggregationHash: Option[String],
+                                 callCachePathPrefixes: Option[List[String]],
+                                 excludedIds: Set[Long]
+  )(implicit ec: ExecutionContext): Future[Option[Long]]
 
-  def queryResultsForCacheId(callCachingEntryId: Long)
-                            (implicit ec: ExecutionContext): Future[Option[CallCachingJoin]]
-  
-  def callCacheJoinForCall(workflowExecutionUuid: String, callFqn: String, index: Int)
-                          (implicit ec: ExecutionContext): Future[Option[CallCachingJoin]]
+  def queryResultsForCacheId(callCachingEntryId: Long)(implicit ec: ExecutionContext): Future[Option[CallCachingJoin]]
 
-  def invalidateCall(callCachingEntryId: Long)
-                    (implicit ec: ExecutionContext): Future[Option[CallCachingEntry]]
+  def callCacheJoinForCall(workflowExecutionUuid: String, callFqn: String, index: Int)(implicit
+    ec: ExecutionContext
+  ): Future[Option[CallCachingJoin]]
 
-  def invalidateCallCacheEntryIdsForWorkflowId(workflowExecutionUuid: String)
-                                              (implicit ec: ExecutionContext): Future[Unit]
+  def invalidateCall(callCachingEntryId: Long)(implicit ec: ExecutionContext): Future[Option[CallCachingEntry]]
+
+  def invalidateCallCacheEntryIdsForWorkflowId(workflowExecutionUuid: String)(implicit
+    ec: ExecutionContext
+  ): Future[Unit]
 
   def callCacheEntryIdsForWorkflowId(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Seq[Long]]
 }
diff --git a/database/sql/src/main/scala/cromwell/database/sql/DockerHashStoreSqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/DockerHashStoreSqlDatabase.scala
index 8a719185c98..11c09154364 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/DockerHashStoreSqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/DockerHashStoreSqlDatabase.scala
@@ -11,15 +11,15 @@ trait DockerHashStoreSqlDatabase {
     * Adds a docker hash entry to the store.
     *
     */
-  def addDockerHashStoreEntry(dockerHashStoreEntry: DockerHashStoreEntry)
-                             (implicit ec: ExecutionContext): Future[Unit]
+  def addDockerHashStoreEntry(dockerHashStoreEntry: DockerHashStoreEntry)(implicit ec: ExecutionContext): Future[Unit]
 
   /**
     * Retrieves docker hash entries for a workflow.
     *
     */
-  def queryDockerHashStoreEntries(workflowExecutionUuid: String)
-                                 (implicit ec: ExecutionContext): Future[Seq[DockerHashStoreEntry]]
+  def queryDockerHashStoreEntries(workflowExecutionUuid: String)(implicit
+    ec: ExecutionContext
+  ): Future[Seq[DockerHashStoreEntry]]
 
   /**
     * Deletes docker hash entries related to a workflow, returning the number of rows affected.
diff --git a/database/sql/src/main/scala/cromwell/database/sql/EngineSqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/EngineSqlDatabase.scala
index 1062e18ed25..3e5e16f881c 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/EngineSqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/EngineSqlDatabase.scala
@@ -1,9 +1,10 @@
 package cromwell.database.sql
 
-trait EngineSqlDatabase extends SqlDatabase
-  with JobKeyValueSqlDatabase
-  with CallCachingSqlDatabase
-  with JobStoreSqlDatabase
-  with WorkflowStoreSqlDatabase
-  with SubWorkflowStoreSqlDatabase
-  with DockerHashStoreSqlDatabase
+trait EngineSqlDatabase
+    extends SqlDatabase
+    with JobKeyValueSqlDatabase
+    with CallCachingSqlDatabase
+    with JobStoreSqlDatabase
+    with WorkflowStoreSqlDatabase
+    with SubWorkflowStoreSqlDatabase
+    with DockerHashStoreSqlDatabase
diff --git a/database/sql/src/main/scala/cromwell/database/sql/JobKeyValueSqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/JobKeyValueSqlDatabase.scala
index 372c4907df0..efda8010eb0 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/JobKeyValueSqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/JobKeyValueSqlDatabase.scala
@@ -9,16 +9,18 @@ trait JobKeyValueSqlDatabase {
 
   def existsJobKeyValueEntries()(implicit ec: ExecutionContext): Future[Boolean]
 
-  def addJobKeyValueEntry(jobKeyValueEntry: JobKeyValueEntry)
-                         (implicit ec: ExecutionContext): Future[Unit]
+  def addJobKeyValueEntry(jobKeyValueEntry: JobKeyValueEntry)(implicit ec: ExecutionContext): Future[Unit]
 
-  def addJobKeyValueEntries(jobKeyValueEntries: Iterable[JobKeyValueEntry])
-                           (implicit ec: ExecutionContext): Future[Unit]
+  def addJobKeyValueEntries(jobKeyValueEntries: Iterable[JobKeyValueEntry])(implicit ec: ExecutionContext): Future[Unit]
 
-  def queryJobKeyValueEntries(workflowExecutionUuid: String)
-                             (implicit ec: ExecutionContext): Future[Seq[JobKeyValueEntry]]
+  def queryJobKeyValueEntries(workflowExecutionUuid: String)(implicit
+    ec: ExecutionContext
+  ): Future[Seq[JobKeyValueEntry]]
 
-  def queryStoreValue(workflowExecutionUuid: String, callFqn: String, jobScatterIndex: Int,
-                      jobRetryAttempt: Int, storeKey: String)
-                     (implicit ec: ExecutionContext): Future[Option[String]]
+  def queryStoreValue(workflowExecutionUuid: String,
+                      callFqn: String,
+                      jobScatterIndex: Int,
+                      jobRetryAttempt: Int,
+                      storeKey: String
+  )(implicit ec: ExecutionContext): Future[Option[String]]
 }
diff --git a/database/sql/src/main/scala/cromwell/database/sql/JobStoreSqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/JobStoreSqlDatabase.scala
index a5497ae49c2..769eac0a3b2 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/JobStoreSqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/JobStoreSqlDatabase.scala
@@ -9,8 +9,9 @@ trait JobStoreSqlDatabase {
 
   def addJobStores(jobStoreJoins: Seq[JobStoreJoin], batchSize: Int)(implicit ec: ExecutionContext): Future[Unit]
 
-  def queryJobStores(workflowExecutionUuid: String, callFqn: String, jobScatterIndex: Int, jobScatterAttempt: Int)
-                    (implicit ec: ExecutionContext): Future[Option[JobStoreJoin]]
+  def queryJobStores(workflowExecutionUuid: String, callFqn: String, jobScatterIndex: Int, jobScatterAttempt: Int)(
+    implicit ec: ExecutionContext
+  ): Future[Option[JobStoreJoin]]
 
   def removeJobStores(workflowExecutionUuids: Seq[String])(implicit ec: ExecutionContext): Future[Seq[Int]]
 }
diff --git a/database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala
index 9139c819999..5746af4f501 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/MetadataSqlDatabase.scala
@@ -34,56 +34,55 @@ trait MetadataSqlDatabase extends SqlDatabase {
                          submissionMetadataKey: String,
                          parentWorkflowIdKey: String,
                          rootWorkflowIdKey: String,
-                         labelMetadataKey: String)(implicit ec: ExecutionContext): Future[Unit]
+                         labelMetadataKey: String
+  )(implicit ec: ExecutionContext): Future[Unit]
 
   def metadataEntryExists(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Boolean]
 
   def metadataSummaryEntryExists(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Boolean]
 
-  def queryMetadataEntries(workflowExecutionUuid: String,
-                           timeout: Duration)
-                          (implicit ec: ExecutionContext): Future[Seq[MetadataEntry]]
+  def queryMetadataEntries(workflowExecutionUuid: String, timeout: Duration)(implicit
+    ec: ExecutionContext
+  ): Future[Seq[MetadataEntry]]
 
   def streamMetadataEntries(workflowExecutionUuid: String): DatabasePublisher[MetadataEntry]
 
-  def countMetadataEntries(workflowExecutionUuid: String,
-                           expandSubWorkflows: Boolean,
-                           timeout: Duration)
-                          (implicit ec: ExecutionContext): Future[Int]
+  def countMetadataEntries(workflowExecutionUuid: String, expandSubWorkflows: Boolean, timeout: Duration)(implicit
+    ec: ExecutionContext
+  ): Future[Int]
 
-  def queryMetadataEntries(workflowExecutionUuid: String,
-                           metadataKey: String,
-                           timeout: Duration)
-                          (implicit ec: ExecutionContext): Future[Seq[MetadataEntry]]
+  def queryMetadataEntries(workflowExecutionUuid: String, metadataKey: String, timeout: Duration)(implicit
+    ec: ExecutionContext
+  ): Future[Seq[MetadataEntry]]
 
   def countMetadataEntries(workflowExecutionUuid: String,
                            metadataKey: String,
                            expandSubWorkflows: Boolean,
-                           timeout: Duration)
-                          (implicit ec: ExecutionContext): Future[Int]
+                           timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Int]
 
   def queryMetadataEntries(workflowExecutionUuid: String,
                            callFullyQualifiedName: String,
                            jobIndex: Option[Int],
                            jobAttempt: Option[Int],
-                           timeout: Duration)
-                          (implicit ec: ExecutionContext): Future[Seq[MetadataEntry]]
+                           timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Seq[MetadataEntry]]
 
   def countMetadataEntries(workflowExecutionUuid: String,
                            callFullyQualifiedName: String,
                            jobIndex: Option[Int],
                            jobAttempt: Option[Int],
                            expandSubWorkflows: Boolean,
-                           timeout: Duration)
-                          (implicit ec: ExecutionContext): Future[Int]
+                           timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Int]
 
   def queryMetadataEntries(workflowUuid: String,
                            metadataKey: String,
                            callFullyQualifiedName: String,
                            jobIndex: Option[Int],
                            jobAttempt: Option[Int],
-                           timeout: Duration)
-                          (implicit ec: ExecutionContext): Future[Seq[MetadataEntry]]
+                           timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Seq[MetadataEntry]]
 
   def countMetadataEntries(workflowUuid: String,
                            metadataKey: String,
@@ -91,23 +90,23 @@ trait MetadataSqlDatabase extends SqlDatabase {
                            jobIndex: Option[Int],
                            jobAttempt: Option[Int],
                            expandSubWorkflows: Boolean,
-                           timeout: Duration)
-                          (implicit ec: ExecutionContext): Future[Int]
+                           timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Int]
 
   def queryMetadataEntryWithKeyConstraints(workflowExecutionUuid: String,
                                            metadataKeysToFilterFor: List[String],
                                            metadataKeysToFilterAgainst: List[String],
                                            metadataJobQueryValue: MetadataJobQueryValue,
-                                           timeout: Duration)
-                                          (implicit ec: ExecutionContext): Future[Seq[MetadataEntry]]
+                                           timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Seq[MetadataEntry]]
 
   def countMetadataEntryWithKeyConstraints(workflowExecutionUuid: String,
                                            metadataKeysToFilterFor: List[String],
                                            metadataKeysToFilterAgainst: List[String],
                                            metadataJobQueryValue: MetadataJobQueryValue,
                                            expandSubWorkflows: Boolean,
-                                           timeout: Duration)
-                                          (implicit ec: ExecutionContext): Future[Int]
+                                           timeout: Duration
+  )(implicit ec: ExecutionContext): Future[Int]
 
   /**
     * Retrieves next summarizable block of metadata satisfying the specified criteria.
@@ -115,12 +114,11 @@ trait MetadataSqlDatabase extends SqlDatabase {
     * @param buildUpdatedSummary Takes in the optional existing summary and the metadata, returns the new summary.
     * @return A `Future` with the number of rows summarized by the invocation, and the number of rows still to summarize.
     */
-  def summarizeIncreasing(labelMetadataKey: String,
-                          limit: Int,
-                          buildUpdatedSummary:
-                          (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry])
-                            => WorkflowMetadataSummaryEntry)
-                         (implicit ec: ExecutionContext): Future[Long]
+  def summarizeIncreasing(
+    labelMetadataKey: String,
+    limit: Int,
+    buildUpdatedSummary: (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry]) => WorkflowMetadataSummaryEntry
+  )(implicit ec: ExecutionContext): Future[Long]
 
   /**
     * Retrieves a window of summarizable metadata satisfying the specified criteria.
@@ -128,14 +126,13 @@ trait MetadataSqlDatabase extends SqlDatabase {
     * @param buildUpdatedSummary Takes in the optional existing summary and the metadata, returns the new summary.
     * @return A `Future` with the number of rows summarized by this invocation, and the number of rows still to summarize.
     */
-  def summarizeDecreasing(summaryNameDecreasing: String,
-                          summaryNameIncreasing: String,
-                          labelMetadataKey: String,
-                          limit: Int,
-                          buildUpdatedSummary:
-                          (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry])
-                            => WorkflowMetadataSummaryEntry)
-                         (implicit ec: ExecutionContext): Future[(Long, Long)]
+  def summarizeDecreasing(
+    summaryNameDecreasing: String,
+    summaryNameIncreasing: String,
+    labelMetadataKey: String,
+    limit: Int,
+    buildUpdatedSummary: (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry]) => WorkflowMetadataSummaryEntry
+  )(implicit ec: ExecutionContext): Future[(Long, Long)]
 
   def updateMetadataArchiveStatus(workflowExecutionUuid: String, newArchiveStatus: Option[String]): Future[Int]
 
@@ -143,16 +140,18 @@ trait MetadataSqlDatabase extends SqlDatabase {
 
   def getWorkflowLabels(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Map[String, String]]
 
-  def getRootAndSubworkflowLabels(rootWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Map[String, Map[String, String]]]
+  def getRootAndSubworkflowLabels(rootWorkflowExecutionUuid: String)(implicit
+    ec: ExecutionContext
+  ): Future[Map[String, Map[String, String]]]
 
   def queryWorkflowSummaries(parentIdWorkflowMetadataKey: String,
                              workflowStatuses: Set[String],
                              workflowNames: Set[String],
                              workflowExecutionUuids: Set[String],
-                             labelAndKeyLabelValues: Set[(String,String)],
-                             labelOrKeyLabelValues: Set[(String,String)],
-                             excludeLabelAndValues: Set[(String,String)],
-                             excludeLabelOrValues: Set[(String,String)],
+                             labelAndKeyLabelValues: Set[(String, String)],
+                             labelOrKeyLabelValues: Set[(String, String)],
+                             excludeLabelAndValues: Set[(String, String)],
+                             excludeLabelOrValues: Set[(String, String)],
                              submissionTimestamp: Option[Timestamp],
                              startTimestampOption: Option[Timestamp],
                              endTimestampOption: Option[Timestamp],
@@ -160,43 +159,57 @@ trait MetadataSqlDatabase extends SqlDatabase {
                              includeSubworkflows: Boolean,
                              page: Option[Int],
                              pageSize: Option[Int],
-                             newestFirst: Boolean)
-                             (implicit ec: ExecutionContext): Future[Iterable[WorkflowMetadataSummaryEntry]]
+                             newestFirst: Boolean
+  )(implicit ec: ExecutionContext): Future[Iterable[WorkflowMetadataSummaryEntry]]
 
   def countWorkflowSummaries(parentIdWorkflowMetadataKey: String,
-                             workflowStatuses: Set[String], workflowNames: Set[String],
+                             workflowStatuses: Set[String],
+                             workflowNames: Set[String],
                              workflowExecutionUuids: Set[String],
-                             labelAndKeyLabelValues: Set[(String,String)],
-                             labelOrKeyLabelValues: Set[(String,String)],
-                             excludeLabelAndValues: Set[(String,String)],
-                             excludeLabelOrValues: Set[(String,String)],
+                             labelAndKeyLabelValues: Set[(String, String)],
+                             labelOrKeyLabelValues: Set[(String, String)],
+                             excludeLabelAndValues: Set[(String, String)],
+                             excludeLabelOrValues: Set[(String, String)],
                              submissionTimestamp: Option[Timestamp],
                              startTimestampOption: Option[Timestamp],
                              endTimestampOption: Option[Timestamp],
                              metadataArchiveStatus: Set[Option[String]],
-                             includeSubworkflows: Boolean)
-                             (implicit ec: ExecutionContext): Future[Int]
+                             includeSubworkflows: Boolean
+  )(implicit ec: ExecutionContext): Future[Int]
 
-  def deleteAllMetadataForWorkflowAndUpdateArchiveStatus(rootWorkflowId: String, newArchiveStatus: Option[String])(implicit ec: ExecutionContext): Future[Int]
+  def deleteAllMetadataForWorkflowAndUpdateArchiveStatus(rootWorkflowId: String, newArchiveStatus: Option[String])(
+    implicit ec: ExecutionContext
+  ): Future[Int]
 
   def getRootWorkflowId(workflowId: String)(implicit ec: ExecutionContext): Future[Option[String]]
 
-  def queryWorkflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp(archiveStatus: Option[String], thresholdTimestamp: Timestamp, batchSizeOpt: Long)(implicit ec: ExecutionContext): Future[Seq[String]]
+  def queryWorkflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp(archiveStatus: Option[String],
+                                                                          thresholdTimestamp: Timestamp,
+                                                                          batchSizeOpt: Long
+  )(implicit ec: ExecutionContext): Future[Seq[String]]
 
   def getSummaryQueueSize()(implicit ec: ExecutionContext): Future[Int]
 
-  def getMetadataArchiveStatusAndEndTime(workflowId: String)(implicit ec: ExecutionContext): Future[(Option[String], Option[Timestamp])]
+  def getMetadataArchiveStatusAndEndTime(workflowId: String)(implicit
+    ec: ExecutionContext
+  ): Future[(Option[String], Option[Timestamp])]
 
   def queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String],
                                                                    workflowEndTimestampThreshold: Timestamp,
-                                                                   batchSize: Long)(implicit ec: ExecutionContext): Future[Seq[WorkflowMetadataSummaryEntry]]
+                                                                   batchSize: Long
+  )(implicit ec: ExecutionContext): Future[Seq[WorkflowMetadataSummaryEntry]]
 
   def countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String],
-                                                                       workflowEndTimestampThreshold: Timestamp)(implicit ec: ExecutionContext): Future[Int]
+                                                                       workflowEndTimestampThreshold: Timestamp
+  )(implicit ec: ExecutionContext): Future[Int]
 
-  def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold: Timestamp)(implicit ec: ExecutionContext): Future[Int]
+  def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold: Timestamp)(implicit
+    ec: ExecutionContext
+  ): Future[Int]
 
   def getMetadataTableSizeInformation()(implicit ec: ExecutionContext): Future[Option[InformationSchemaEntry]]
 
-  def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: String)(implicit ec: ExecutionContext): Future[Vector[MetadataEntry]]
+  def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: String)(implicit
+    ec: ExecutionContext
+  ): Future[Vector[MetadataEntry]]
 }
diff --git a/database/sql/src/main/scala/cromwell/database/sql/SqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/SqlDatabase.scala
index 842dcd775d4..64a4f2dd2a3 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/SqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/SqlDatabase.scala
@@ -16,6 +16,7 @@ trait SqlDatabase extends AutoCloseable {
 }
 
 object SqlDatabase {
+
   /**
     * Modifies config.getString("url") to return a unique schema, if the original url contains the text
     * "\${uniqueSchema}".
diff --git a/database/sql/src/main/scala/cromwell/database/sql/SubWorkflowStoreSqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/SubWorkflowStoreSqlDatabase.scala
index 10707dc9031..e6430730497 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/SubWorkflowStoreSqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/SubWorkflowStoreSqlDatabase.scala
@@ -12,10 +12,12 @@ trait SubWorkflowStoreSqlDatabase {
                                callFullyQualifiedName: String,
                                jobIndex: Int,
                                jobAttempt: Int,
-                               subWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Unit]
+                               subWorkflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Unit]
 
-  def querySubWorkflowStore(parentWorkflowExecutionUuid: String, callFqn: String, jobIndex: Int, jobAttempt: Int)
-                    (implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]]
+  def querySubWorkflowStore(parentWorkflowExecutionUuid: String, callFqn: String, jobIndex: Int, jobAttempt: Int)(
+    implicit ec: ExecutionContext
+  ): Future[Option[SubWorkflowStoreEntry]]
 
   def removeSubWorkflowStoreEntries(parentWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Int]
 }
diff --git a/database/sql/src/main/scala/cromwell/database/sql/WorkflowStoreSqlDatabase.scala b/database/sql/src/main/scala/cromwell/database/sql/WorkflowStoreSqlDatabase.scala
index 82dc51c875b..66dc97be3da 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/WorkflowStoreSqlDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/WorkflowStoreSqlDatabase.scala
@@ -29,8 +29,7 @@ ____    __    ____  ______   .______       __  ___  _______  __        ______
   /**
     * Set all running workflows to aborting state.
     */
-  def setStateToState(fromWorkflowState: String, toWorkflowState: String)
-                     (implicit ec: ExecutionContext): Future[Unit]
+  def setStateToState(fromWorkflowState: String, toWorkflowState: String)(implicit ec: ExecutionContext): Future[Unit]
 
   /**
     * Set the workflow Id from one state to another.
@@ -45,14 +44,15 @@ ____    __    ____  ______   .______       __  ___  _______  __        ______
   def deleteOrUpdateWorkflowToState(workflowExecutionUuid: String,
                                     workflowStateToDelete1: String,
                                     workflowStateToDelete2: String,
-                                    workflowStateForUpdate: String)
-                                   (implicit ec: ExecutionContext): Future[Option[Boolean]]
+                                    workflowStateForUpdate: String
+  )(implicit ec: ExecutionContext): Future[Option[Boolean]]
 
   /**
     * Adds the requested WorkflowSourceFiles to the store.
     */
-  def addWorkflowStoreEntries(workflowStoreEntries: Iterable[WorkflowStoreEntry])
-                             (implicit ec: ExecutionContext): Future[Unit]
+  def addWorkflowStoreEntries(workflowStoreEntries: Iterable[WorkflowStoreEntry])(implicit
+    ec: ExecutionContext
+  ): Future[Unit]
 
   /**
     * Retrieves a limited number of workflows which have not already been pulled into the engine and updates their
@@ -75,12 +75,12 @@ ____    __    ____  ______   .______       __  ___  _______  __        ______
                             workflowStateFrom: String,
                             workflowStateTo: String,
                             workflowStateExcluded: String,
-                            excludedGroups: Set[String])
-                           (implicit ec: ExecutionContext): Future[Seq[WorkflowStoreEntry]]
+                            excludedGroups: Set[String]
+  )(implicit ec: ExecutionContext): Future[Seq[WorkflowStoreEntry]]
 
-  def writeWorkflowHeartbeats(workflowExecutionUuids: Seq[String],
-                              heartbeatTimestamp: Timestamp)
-                             (implicit ec: ExecutionContext): Future[Int]
+  def writeWorkflowHeartbeats(workflowExecutionUuids: Seq[String], heartbeatTimestamp: Timestamp)(implicit
+    ec: ExecutionContext
+  ): Future[Int]
 
   /**
     * Clears out cromwellId and heartbeatTimestamp for all workflow store entries currently assigned
@@ -98,8 +98,9 @@ ____    __    ____  ______   .______       __  ___  _______  __        ______
   /**
     * Returns the number of rows updated from one state to another.
     */
-  def updateWorkflowState(workflowExecutionUuid: String, fromWorkflowState: String, toWorkflowState: String)
-                         (implicit ec: ExecutionContext): Future[Int]
+  def updateWorkflowState(workflowExecutionUuid: String, fromWorkflowState: String, toWorkflowState: String)(implicit
+    ec: ExecutionContext
+  ): Future[Int]
 
   def findWorkflowsWithAbortRequested(cromwellId: String)(implicit ec: ExecutionContext): Future[Iterable[String]]
 
diff --git a/database/sql/src/main/scala/cromwell/database/sql/joins/CallCachingDiffJoin.scala b/database/sql/src/main/scala/cromwell/database/sql/joins/CallCachingDiffJoin.scala
index 2b56e9f88d5..d45e7a72cf3 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/joins/CallCachingDiffJoin.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/joins/CallCachingDiffJoin.scala
@@ -2,4 +2,7 @@ package cromwell.database.sql.joins
 
 import cromwell.database.sql.tables.CallCachingEntry
 
-case class CallCachingDiffJoin(cacheEntryA: CallCachingEntry, cacheEntryB: CallCachingEntry, diff: Seq[(Option[(String, String)], Option[(String, String)])])
+case class CallCachingDiffJoin(cacheEntryA: CallCachingEntry,
+                               cacheEntryB: CallCachingEntry,
+                               diff: Seq[(Option[(String, String)], Option[(String, String)])]
+)
diff --git a/database/sql/src/main/scala/cromwell/database/sql/joins/CallCachingJoin.scala b/database/sql/src/main/scala/cromwell/database/sql/joins/CallCachingJoin.scala
index 07313980bc1..a9d32ee9115 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/joins/CallCachingJoin.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/joins/CallCachingJoin.scala
@@ -2,8 +2,7 @@ package cromwell.database.sql.joins
 
 import cromwell.database.sql.tables._
 
-case class CallCachingJoin
-(
+case class CallCachingJoin(
   callCachingEntry: CallCachingEntry,
   callCachingHashEntries: Seq[CallCachingHashEntry],
   callCachingAggregationEntry: Option[CallCachingAggregationEntry],
diff --git a/database/sql/src/main/scala/cromwell/database/sql/joins/JobStoreJoin.scala b/database/sql/src/main/scala/cromwell/database/sql/joins/JobStoreJoin.scala
index 3a2c19a0b81..d47ffd8f615 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/joins/JobStoreJoin.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/joins/JobStoreJoin.scala
@@ -2,8 +2,7 @@ package cromwell.database.sql.joins
 
 import cromwell.database.sql.tables.{JobStoreEntry, JobStoreSimpletonEntry}
 
-case class JobStoreJoin
-(
+case class JobStoreJoin(
   jobStoreEntry: JobStoreEntry,
   jobStoreSimpletonEntries: Seq[JobStoreSimpletonEntry]
 )
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingAggregationEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingAggregationEntry.scala
index 088c07bf3c7..c1f87bd1b02 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingAggregationEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingAggregationEntry.scala
@@ -1,7 +1,6 @@
 package cromwell.database.sql.tables
 
-case class CallCachingAggregationEntry
-(
+case class CallCachingAggregationEntry(
   baseAggregation: String,
   inputFilesAggregation: Option[String],
   callCachingEntryId: Option[Long] = None,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingDetritusEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingDetritusEntry.scala
index 36afadd4c8e..3462ad527cc 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingDetritusEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingDetritusEntry.scala
@@ -2,8 +2,7 @@ package cromwell.database.sql.tables
 
 import javax.sql.rowset.serial.SerialClob
 
-case class CallCachingDetritusEntry
-(
+case class CallCachingDetritusEntry(
   detritusKey: String,
   detritusValue: Option[SerialClob],
   callCachingEntryId: Option[Long] = None,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingEntry.scala
index 24263b0cb80..ba748261e82 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingEntry.scala
@@ -1,7 +1,6 @@
 package cromwell.database.sql.tables
 
-case class CallCachingEntry
-(
+case class CallCachingEntry(
   workflowExecutionUuid: String,
   callFullyQualifiedName: String,
   jobIndex: Int,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingHashEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingHashEntry.scala
index 5f2aff9fb14..580c5e5bb3f 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingHashEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingHashEntry.scala
@@ -1,7 +1,6 @@
 package cromwell.database.sql.tables
 
-case class CallCachingHashEntry
-(
+case class CallCachingHashEntry(
   hashKey: String,
   hashValue: String,
   callCachingEntryId: Option[Long] = None,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingSimpletonEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingSimpletonEntry.scala
index c4e6628ee81..36a39f7fd5f 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingSimpletonEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/CallCachingSimpletonEntry.scala
@@ -2,8 +2,7 @@ package cromwell.database.sql.tables
 
 import javax.sql.rowset.serial.SerialClob
 
-case class CallCachingSimpletonEntry
-(
+case class CallCachingSimpletonEntry(
   simpletonKey: String,
   simpletonValue: Option[SerialClob],
   wdlType: String,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/CustomLabelEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/CustomLabelEntry.scala
index 030a5e0bb25..19c959be929 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/CustomLabelEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/CustomLabelEntry.scala
@@ -1,7 +1,6 @@
 package cromwell.database.sql.tables
 
-case class CustomLabelEntry
-(
+case class CustomLabelEntry(
   customLabelKey: String,
   customLabelValue: String,
   workflowExecutionUuid: String,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
index 542558324f5..05fc6c4e7db 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/DockerHashStoreEntry.scala
@@ -1,7 +1,6 @@
 package cromwell.database.sql.tables
 
-case class DockerHashStoreEntry
-(
+case class DockerHashStoreEntry(
   workflowExecutionUuid: String,
   dockerTag: String,
   dockerHash: String,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/InformationSchemaEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/InformationSchemaEntry.scala
index 0cf05e0b5b5..b29bba61205 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/InformationSchemaEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/InformationSchemaEntry.scala
@@ -1,7 +1,6 @@
 package cromwell.database.sql.tables
 
-final case class InformationSchemaEntry
-(
+final case class InformationSchemaEntry(
   dataLength: Long,
   indexLength: Long,
   dataFree: Long
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/JobKeyValueEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/JobKeyValueEntry.scala
index 5f91bee2091..8b768ff66de 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/JobKeyValueEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/JobKeyValueEntry.scala
@@ -1,7 +1,6 @@
 package cromwell.database.sql.tables
 
-case class JobKeyValueEntry
-(
+case class JobKeyValueEntry(
   workflowExecutionUuid: String,
   callFullyQualifiedName: String,
   jobIndex: Int,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/JobStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/JobStoreEntry.scala
index 6f59a0c738c..a7be44561c4 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/JobStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/JobStoreEntry.scala
@@ -2,8 +2,7 @@ package cromwell.database.sql.tables
 
 import javax.sql.rowset.serial.SerialClob
 
-case class JobStoreEntry
-(
+case class JobStoreEntry(
   workflowExecutionUuid: String,
   callFullyQualifiedName: String,
   jobIndex: Int,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/JobStoreSimpletonEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/JobStoreSimpletonEntry.scala
index 4a6c19864dd..b0c3463625f 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/JobStoreSimpletonEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/JobStoreSimpletonEntry.scala
@@ -2,8 +2,7 @@ package cromwell.database.sql.tables
 
 import javax.sql.rowset.serial.SerialClob
 
-case class JobStoreSimpletonEntry
-(
+case class JobStoreSimpletonEntry(
   simpletonKey: String,
   simpletonValue: Option[SerialClob],
   wdlType: String,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/MetadataEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/MetadataEntry.scala
index c273c3e47e3..97c4cc9acf2 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/MetadataEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/MetadataEntry.scala
@@ -4,8 +4,7 @@ import java.sql.Timestamp
 
 import javax.sql.rowset.serial.SerialClob
 
-case class MetadataEntry
-(
+case class MetadataEntry(
   workflowExecutionUuid: String,
   callFullyQualifiedName: Option[String],
   jobIndex: Option[Int],
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
index 4cf89381ad0..6d081845a84 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/SubWorkflowStoreEntry.scala
@@ -1,7 +1,6 @@
 package cromwell.database.sql.tables
 
-case class SubWorkflowStoreEntry
-(
+case class SubWorkflowStoreEntry(
   rootWorkflowId: Option[Long],
   parentWorkflowExecutionUuid: String,
   callFullyQualifiedName: String,
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/SummaryStatusEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/SummaryStatusEntry.scala
index 6315295d478..8dfdeea1626 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/SummaryStatusEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/SummaryStatusEntry.scala
@@ -1,7 +1,6 @@
 package cromwell.database.sql.tables
 
-case class SummaryStatusEntry
-(
+case class SummaryStatusEntry(
   summaryName: String,
   summaryPosition: Long,
   summaryStatusEntryId: Option[Int] = None
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowMetadataSummaryEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowMetadataSummaryEntry.scala
index 19e553630e6..bd98d398d75 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowMetadataSummaryEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowMetadataSummaryEntry.scala
@@ -2,8 +2,7 @@ package cromwell.database.sql.tables
 
 import java.sql.Timestamp
 
-case class WorkflowMetadataSummaryEntry
-(
+case class WorkflowMetadataSummaryEntry(
   workflowExecutionUuid: String,
   workflowName: Option[String],
   workflowStatus: Option[String],
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
index efb594444d4..6017bb5d539 100644
--- a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
+++ b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
@@ -4,8 +4,7 @@ import java.sql.Timestamp
 
 import javax.sql.rowset.serial.{SerialBlob, SerialClob}
 
-case class WorkflowStoreEntry
-(
+case class WorkflowStoreEntry(
   workflowExecutionUuid: String,
   workflowDefinition: Option[SerialClob],
   workflowUrl: Option[String],
diff --git a/dockerHashing/src/main/scala/cromwell/docker/DockerClientHelper.scala b/dockerHashing/src/main/scala/cromwell/docker/DockerClientHelper.scala
index 706cbfef3d8..e034319033a 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/DockerClientHelper.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/DockerClientHelper.scala
@@ -7,10 +7,10 @@ import cromwell.docker.DockerInfoActor.DockerInfoResponse
 import scala.concurrent.duration.FiniteDuration
 
 trait DockerClientHelper extends RobustClientHelper { this: Actor with ActorLogging =>
-  
+
   protected def dockerHashingActor: ActorRef
-  
-  private [docker] def dockerResponseReceive: Receive = {
+
+  private[docker] def dockerResponseReceive: Receive = {
     case dockerResponse: DockerInfoResponse if hasTimeout(dockerResponse.request) =>
       cancelTimeout(dockerResponse.request)
       receive.apply(dockerResponse)
@@ -19,9 +19,10 @@ trait DockerClientHelper extends RobustClientHelper { this: Actor with ActorLogg
       receive.apply(context -> dockerResponse)
   }
 
-  def sendDockerCommand(dockerHashRequest: DockerInfoRequest, timeout: FiniteDuration = RobustClientHelper.DefaultRequestLostTimeout) = {
+  def sendDockerCommand(dockerHashRequest: DockerInfoRequest,
+                        timeout: FiniteDuration = RobustClientHelper.DefaultRequestLostTimeout
+  ) =
     robustSend(dockerHashRequest, dockerHashingActor, timeout)
-  }
 
   def dockerReceive = robustReceive orElse dockerResponseReceive
 }
diff --git a/dockerHashing/src/main/scala/cromwell/docker/DockerHashResult.scala b/dockerHashing/src/main/scala/cromwell/docker/DockerHashResult.scala
index e3120516a9a..771db6d6576 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/DockerHashResult.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/DockerHashResult.scala
@@ -5,13 +5,13 @@ import scala.util.{Failure, Success, Try}
 object DockerHashResult {
   // See https://docs.docker.com/registry/spec/api/#/content-digests
   val DigestRegex = """([a-zA-Z0-9_+.-]+):([a-zA-Z0-9]+)""".r
-  
-  def fromString(str: String): Try[DockerHashResult] = {
+
+  def fromString(str: String): Try[DockerHashResult] =
     str match {
       case DigestRegex(alg, hash) => Success(DockerHashResult(alg, hash))
-      case _ => Failure(new IllegalArgumentException(s"Hash value $str does not have the expected 'algorithm:hash' syntax"))
+      case _ =>
+        Failure(new IllegalArgumentException(s"Hash value $str does not have the expected 'algorithm:hash' syntax"))
     }
-  }
 }
 
 case class DockerHashResult(hashAlgorithm: String, hashValue: String) {
diff --git a/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala b/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala
index a798f351f17..f34702509db 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala
@@ -16,25 +16,33 @@ sealed trait DockerImageIdentifier {
   lazy val name = repository map { r => s"$r/$image" } getOrElse image
   // The name of the image with a repository prefix if a repository was specified, or with a default repository prefix of
   // "library" if no repository was specified.
-  lazy val nameWithDefaultRepository = {
+  lazy val nameWithDefaultRepository =
     // In ACR, the repository is part of the registry domain instead of the path
     // e.g. `terrabatchdev.azurecr.io`
     if (host.exists(_.contains(AzureContainerRegistry.domain)))
       image
     else
       repository.getOrElse("library") + s"/$image"
-  }
   lazy val hostAsString = host map { h => s"$h/" } getOrElse ""
   // The full name of this image, including a repository prefix only if a repository was explicitly specified.
   lazy val fullName = s"$hostAsString$name:$reference"
 }
 
-case class DockerImageIdentifierWithoutHash(host: Option[String], repository: Option[String], image: String, reference: String) extends DockerImageIdentifier {
+case class DockerImageIdentifierWithoutHash(host: Option[String],
+                                            repository: Option[String],
+                                            image: String,
+                                            reference: String
+) extends DockerImageIdentifier {
   def withHash(hash: DockerHashResult) = DockerImageIdentifierWithHash(host, repository, image, reference, hash)
   override def swapReference(newReference: String) = this.copy(reference = newReference)
 }
 
-case class DockerImageIdentifierWithHash(host: Option[String], repository: Option[String], image: String, reference: String, hash: DockerHashResult) extends DockerImageIdentifier {
+case class DockerImageIdentifierWithHash(host: Option[String],
+                                         repository: Option[String],
+                                         image: String,
+                                         reference: String,
+                                         hash: DockerHashResult
+) extends DockerImageIdentifier {
   override lazy val fullName: String = s"$hostAsString$name@${hash.algorithmAndHash}"
   override def swapReference(newReference: String) = this.copy(reference = newReference)
 }
@@ -68,12 +76,11 @@ object DockerImageIdentifier {
        )?
        """.trim.r
 
-  def fromString(dockerString: String): Try[DockerImageIdentifier] = {
+  def fromString(dockerString: String): Try[DockerImageIdentifier] =
     dockerString.trim match {
       case DockerStringRegex(name, tag, hash) => buildId(name, Option(tag), Option(hash))
       case _ => Failure(new IllegalArgumentException(s"Docker image $dockerString has an invalid syntax."))
     }
-  }
 
   private def isRegistryHostName(str: String) = str.contains('.') || str.startsWith("localhost")
 
@@ -97,10 +104,17 @@ object DockerImageIdentifier {
     }
 
     (tag, hash) match {
-      case (None, None) => Success(DockerImageIdentifierWithoutHash(dockerHost, dockerRepo, dockerImage, DefaultDockerTag))
+      case (None, None) =>
+        Success(DockerImageIdentifierWithoutHash(dockerHost, dockerRepo, dockerImage, DefaultDockerTag))
       case (Some(t), None) => Success(DockerImageIdentifierWithoutHash(dockerHost, dockerRepo, dockerImage, t))
-      case (None, Some(h)) => DockerHashResult.fromString(h) map { hash => DockerImageIdentifierWithHash(dockerHost, dockerRepo, dockerImage, h, hash) }
-      case (Some(t), Some(h)) => DockerHashResult.fromString(h) map { hash => DockerImageIdentifierWithHash(dockerHost, dockerRepo, dockerImage, s"$t@$h", hash) }
+      case (None, Some(h)) =>
+        DockerHashResult.fromString(h) map { hash =>
+          DockerImageIdentifierWithHash(dockerHost, dockerRepo, dockerImage, h, hash)
+        }
+      case (Some(t), Some(h)) =>
+        DockerHashResult.fromString(h) map { hash =>
+          DockerImageIdentifierWithHash(dockerHost, dockerRepo, dockerImage, s"$t@$h", hash)
+        }
     }
   }
 }
diff --git a/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala b/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala
index 3ebb8d98f39..3b3c0e5d7c5 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/DockerInfoActor.scala
@@ -30,16 +30,21 @@ import scala.concurrent.ExecutionContextExecutor
 import scala.concurrent.duration._
 
 final class DockerInfoActor(
-                             dockerRegistryFlows: Seq[DockerRegistry],
-                             queueBufferSize: Int,
-                             cacheEntryTTL: FiniteDuration,
-                             cacheSize: Long
-                           ) extends Actor with ActorLogging {
+  dockerRegistryFlows: Seq[DockerRegistry],
+  queueBufferSize: Int,
+  cacheEntryTTL: FiniteDuration,
+  cacheSize: Long
+) extends Actor
+    with ActorLogging {
 
   implicit val system: ActorSystem = context.system
   implicit val ec: ExecutionContextExecutor = context.dispatcher
   implicit val cs: ContextShift[IO] = IO.contextShift(ec)
-  val retryPolicy: RetryPolicy[IO] = RetryPolicy[IO](RetryPolicy.exponentialBackoff(DockerConfiguration.instance.maxTimeBetweenRetries, DockerConfiguration.instance.maxRetries))
+  val retryPolicy: RetryPolicy[IO] = RetryPolicy[IO](
+    RetryPolicy.exponentialBackoff(DockerConfiguration.instance.maxTimeBetweenRetries,
+                                   DockerConfiguration.instance.maxRetries
+    )
+  )
 
   /* Use the guava CacheBuilder class that implements a thread safe map with built in cache features.
    * https://google.github.io/guava/releases/20.0/api/docs/com/google/common/cache/CacheBuilder.html
@@ -47,29 +52,29 @@ final class DockerInfoActor(
    *  - Added to the cache by the streamSink, running on a thread from the stream thread pool
    *  - Accessed by this actor on its receive method thread, to check if an element is in the cache and use it
    *  - Automatically removed from the cache by the cache itself
-   *  
+   *
    *  + Concurrency level is the number of expected threads to modify the cache.
    *      Set to "2" because the stream will add elements, and the cache itself remove them.
-   *      This value has not a critical impact: 
+   *      This value has not a critical impact:
    *        https://google.github.io/guava/releases/20.0/api/docs/com/google/common/cache/CacheBuilder.html#concurrencyLevel-int-
-   *        
-   *  + expireAfterWrite sets the time after which cache entries must expire. 
+   *
+   *  + expireAfterWrite sets the time after which cache entries must expire.
    *      We use expireAfterWrite (as opposed to expireAfterAccess because we want to the entry to expire
-   *      even if it's accessed. The goal here is to force the actor to ask again for the hash after a certain 
+   *      even if it's accessed. The goal here is to force the actor to ask again for the hash after a certain
    *      amount of time to guarantee its relative accuracy.
-   *      
-   *  + maximumSize sets the maximum amount of entries the cache can contain. 
+   *
+   *  + maximumSize sets the maximum amount of entries the cache can contain.
    *    If/when this size is reached, least used entries will be expired
    */
-  private val cache = CacheBuilder.newBuilder()
+  private val cache = CacheBuilder
+    .newBuilder()
     .concurrencyLevel(2)
     .expireAfterWrite(cacheEntryTTL._1, cacheEntryTTL._2)
     .maximumSize(cacheSize)
     .build[DockerImageIdentifier, DockerInformation]()
 
-  private def checkCache(dockerHashRequest: DockerInfoRequest) = {
+  private def checkCache(dockerHashRequest: DockerInfoRequest) =
     Option(cache.getIfPresent(dockerHashRequest.dockerImageID))
-  }
 
   override def receive: Receive = receiveBehavior(Map.empty)
 
@@ -83,26 +88,24 @@ final class DockerInfoActor(
       }
     case ShutdownCommand =>
       // Shutdown all streams by sending None to the queue
-      registries
-        .values.toList
+      registries.values.toList
         .parTraverse[IO, Unit](_.enqueue1(None))
         .unsafeRunSync()
 
       context stop self
   }
 
-  def sendToStream(registries: Map[DockerRegistry, StreamQueue], context: DockerInfoActor.DockerInfoContext): Unit = {
+  def sendToStream(registries: Map[DockerRegistry, StreamQueue], context: DockerInfoActor.DockerInfoContext): Unit =
     registries collectFirst {
       case (registry, queue) if registry.accepts(context.dockerImageID) => queue
     } match {
       case Some(queue) => enqueue(context, queue)
       case None => context.replyTo ! DockerHashUnknownRegistry(context.request)
     }
-  }
 
   def enqueue(dockerInfoContext: DockerInfoContext, queue: StreamQueue): Unit = {
     val enqueueIO = queue.offer1(Option(dockerInfoContext)).runAsync {
-      case Right(true) => IO.unit// Good !
+      case Right(true) => IO.unit // Good !
       case _ => backpressure(dockerInfoContext)
     }
 
@@ -148,13 +151,13 @@ final class DockerInfoActor(
       // If the registry imposes throttling, debounce the stream to ensure the throttling rate is respected
       val throttledSource = registry.config.throttle.map(_.delay).map(source.metered[IO]).getOrElse(source)
 
-      val stream = clientStream.flatMap({ client =>
+      val stream = clientStream.flatMap { client =>
         throttledSource
           // Run requests in parallel - allow nbThreads max concurrent requests - order doesn't matter
-          .parEvalMapUnordered(registry.config.nbThreads)({ request => registry.run(request)(client) })
+          .parEvalMapUnordered(registry.config.nbThreads)(request => registry.run(request)(client))
           // Send to the sink for finalization of the result
           .through(streamSink)
-      })
+      }
 
       // Start the stream now asynchronously. It will keep running until we terminate the queue by sending None to it
       stream.compile.drain.unsafeRunAsyncAndForget()
@@ -166,7 +169,7 @@ final class DockerInfoActor(
   override def preStart(): Unit = {
     // Force initialization of the header constants to make sure they're valid
     locally(DockerRegistryV2Abstract)
-    
+
     val registries =
       dockerRegistryFlows.toList
         .parTraverse(startAndRegisterStream)
@@ -194,12 +197,14 @@ object DockerInfoActor {
   }
 
   case class DockerInformation(dockerHash: DockerHashResult, dockerCompressedSize: Option[DockerSize])
-  case class DockerInfoSuccessResponse(dockerInformation: DockerInformation, request: DockerInfoRequest) extends DockerInfoResponse
+  case class DockerInfoSuccessResponse(dockerInformation: DockerInformation, request: DockerInfoRequest)
+      extends DockerInfoResponse
 
   sealed trait DockerHashFailureResponse extends DockerInfoResponse {
     def reason: String
   }
-  case class DockerInfoFailedResponse(failure: Throwable, request: DockerInfoRequest) extends DockerHashFailureResponse {
+  case class DockerInfoFailedResponse(failure: Throwable, request: DockerInfoRequest)
+      extends DockerHashFailureResponse {
     override val reason = s"Failed to get docker hash for ${request.dockerImageID.fullName} ${failure.getMessage}"
   }
   case class DockerHashUnknownRegistry(request: DockerInfoRequest) extends DockerHashFailureResponse {
@@ -224,9 +229,10 @@ object DockerInfoActor {
   def props(dockerRegistryFlows: Seq[DockerRegistry],
             queueBufferSize: Int = 100,
             cacheEntryTTL: FiniteDuration,
-            cacheSize: Long): Props = {
-    Props(new DockerInfoActor(dockerRegistryFlows, queueBufferSize, cacheEntryTTL, cacheSize)).withDispatcher(Dispatcher.IoDispatcher)
-  }
+            cacheSize: Long
+  ): Props =
+    Props(new DockerInfoActor(dockerRegistryFlows, queueBufferSize, cacheEntryTTL, cacheSize))
+      .withDispatcher(Dispatcher.IoDispatcher)
 
   def remoteRegistriesFromConfig(config: Config): List[DockerRegistry] = {
     import cats.syntax.traverse._
@@ -237,8 +243,8 @@ object DockerInfoActor {
       ("dockerhub", { c: DockerRegistryConfig => new DockerHubRegistry(c) }),
       ("google", { c: DockerRegistryConfig => new GoogleRegistry(c) }),
       ("quay", { c: DockerRegistryConfig => new QuayRegistry(c) })
-    ).traverse[ErrorOr, DockerRegistry]({
-      case (configPath, constructor) => DockerRegistryConfig.fromConfig(config.as[Config](configPath)).map(constructor)
-    }).unsafe("Docker registry configuration")
+    ).traverse[ErrorOr, DockerRegistry] { case (configPath, constructor) =>
+      DockerRegistryConfig.fromConfig(config.as[Config](configPath)).map(constructor)
+    }.unsafe("Docker registry configuration")
   }
 }
diff --git a/dockerHashing/src/main/scala/cromwell/docker/DockerRegistry.scala b/dockerHashing/src/main/scala/cromwell/docker/DockerRegistry.scala
index d35e6e0c91b..fac486d114d 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/DockerRegistry.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/DockerRegistry.scala
@@ -8,7 +8,9 @@ import org.http4s.client.Client
   * Interface used by the docker hash actor to build a flow and validate whether or not it can accept an image.
   */
 trait DockerRegistry {
-  def run(dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]): IO[(DockerInfoResponse, DockerInfoContext)]
+  def run(dockerInfoContext: DockerInfoContext)(implicit
+    client: Client[IO]
+  ): IO[(DockerInfoResponse, DockerInfoContext)]
   def accepts(dockerImageIdentifier: DockerImageIdentifier): Boolean
   def config: DockerRegistryConfig
 }
diff --git a/dockerHashing/src/main/scala/cromwell/docker/DockerRegistryConfig.scala b/dockerHashing/src/main/scala/cromwell/docker/DockerRegistryConfig.scala
index a6e15846e5e..327d9e8038c 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/DockerRegistryConfig.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/DockerRegistryConfig.scala
@@ -19,9 +19,9 @@ object DockerRegistryConfig {
   lazy val default = DockerRegistryConfig(None, 5)
 
   def fromConfig(config: Config): ErrorOr[DockerRegistryConfig] = {
-    val throttle = validate { config.getAs[Throttle]("throttle") }
-    val threads = validate { config.as[Int]("num-threads") }
-   
+    val throttle = validate(config.getAs[Throttle]("throttle"))
+    val threads = validate(config.as[Int]("num-threads"))
+
     (throttle, threads) mapN DockerRegistryConfig.apply
   }
 }
diff --git a/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliClient.scala b/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliClient.scala
index e0e2a383d92..4f2e2b7e891 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliClient.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliClient.scala
@@ -11,13 +11,14 @@ import scala.util.Try
   * https://docs.docker.com/engine/api/v1.27/
   */
 trait DockerCliClient {
+
   /**
     * Looks up a docker hash.
     *
     * @param dockerCliKey The docker hash to lookup.
     * @return The hash if found, None if not found, and Failure if an error occurs.
     */
-  def lookupHash(dockerCliKey: DockerCliKey): Try[Option[String]] = {
+  def lookupHash(dockerCliKey: DockerCliKey): Try[Option[String]] =
     /*
     The stdout contains the tab separated repository/tag/digest for __all__ local images.
     Would be great to just get a single hash using the key... unfortunately
@@ -26,16 +27,14 @@ trait DockerCliClient {
     forRun("docker", "images", "--digests", "--format", """{{printf "%s\t%s\t%s" .Repository .Tag .Digest}}""") {
       _.flatMap(parseHashLine).find(_.key == dockerCliKey).map(_.digest)
     }
-  }
 
   /**
     * Pulls a docker image.
     * @param dockerCliKey The docker hash to lookup.
     * @return Failure if an error occurs.
     */
-  def pull(dockerCliKey: DockerCliKey): Try[Unit] = {
-    forRun("docker", "pull", dockerCliKey.fullName) { const(()) }
-  }
+  def pull(dockerCliKey: DockerCliKey): Try[Unit] =
+    forRun("docker", "pull", dockerCliKey.fullName)(const(()))
 
   /**
     * Tries to run the command, then feeds the stdout to `f`. If the exit code is non-zero, returns a `Failure` with
@@ -46,20 +45,18 @@ trait DockerCliClient {
     * @tparam A Return type.
     * @return An attempt to run A.
     */
-  private def forRun[A](cmd: String*)(f: Seq[String] => A): Try[A] = {
+  private def forRun[A](cmd: String*)(f: Seq[String] => A): Try[A] =
     Try {
       val dockerCliResult = run(cmd)
       if (dockerCliResult.exitCode == 0) {
         f(dockerCliResult.stdout)
       } else {
-        throw new RuntimeException(
-          s"""|Error running: ${cmd.mkString(" ")}
-              |Exit code: ${dockerCliResult.exitCode}
-              |${dockerCliResult.stderr.mkString("\n")}
-              |""".stripMargin)
+        throw new RuntimeException(s"""|Error running: ${cmd.mkString(" ")}
+                                       |Exit code: ${dockerCliResult.exitCode}
+                                       |${dockerCliResult.stderr.mkString("\n")}
+                                       |""".stripMargin)
       }
     }
-  }
 
   /**
     * Run a command and return the result. Overridable for testing.
diff --git a/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliFlow.scala b/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliFlow.scala
index f6bf6e96d4c..513d27bc001 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliFlow.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/local/DockerCliFlow.scala
@@ -28,20 +28,22 @@ class DockerCliFlow(implicit ec: ExecutionContext) extends DockerRegistry {
   override def run(dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]) = {
     implicit val timer = IO.timer(ec)
 
-    DockerCliFlow.lookupHashOrTimeout(firstLookupTimeout)(dockerInfoContext)
-      .flatMap({
+    DockerCliFlow
+      .lookupHashOrTimeout(firstLookupTimeout)(dockerInfoContext)
+      .flatMap {
         // If the image isn't there, pull it and try again
         case (_: DockerInfoNotFound, _) =>
           DockerCliFlow.pull(dockerInfoContext)
           DockerCliFlow.lookupHashOrTimeout(firstLookupTimeout)(dockerInfoContext)
         case other => IO.pure(other)
-      })
+      }
   }
 
   override def config = DockerRegistryConfig.default
 }
 
 object DockerCliFlow {
+
   /**
     * Lookup the hash for the image referenced in the context.
     *
@@ -53,10 +55,11 @@ object DockerCliFlow {
     DockerInfoActor.logger.debug("Looking up hash of {}", dockerCliKey.fullName)
     val result = DockerCliClient.lookupHash(dockerCliKey) match {
       case Success(None) => DockerInfoNotFound(context.request)
-      case Success(Some(hash)) => DockerHashResult.fromString(hash) match {
-        case Success(r) => DockerInfoSuccessResponse(DockerInformation(r, None), context.request)
-        case Failure(t) => DockerInfoFailedResponse(t, context.request)
-      }
+      case Success(Some(hash)) =>
+        DockerHashResult.fromString(hash) match {
+          case Success(r) => DockerInfoSuccessResponse(DockerInformation(r, None), context.request)
+          case Failure(t) => DockerInfoFailedResponse(t, context.request)
+        }
       case Failure(throwable) => DockerInfoFailedResponse(throwable, context.request)
     }
     // give the compiler a hint on the debug() override we're trying to use.
@@ -72,22 +75,22 @@ object DockerCliFlow {
     * @param context   The image to lookup.
     * @return The docker hash response plus the context of our flow.
     */
-  private def lookupHashOrTimeout(timeout: FiniteDuration)
-                                 (context: DockerInfoContext)
-                                 (implicit cs: ContextShift[IO], timer: Timer[IO]): IO[(DockerInfoResponse, DockerInfoContext)] = {
-    IO(lookupHash(context)).timeout(timeout)
-      .handleErrorWith({
-        case _: TimeoutException => IO.pure {
-          val dockerCliKey = cliKeyFromImageId(context)
-          val exception = new TimeoutException(
-            s"""|Timeout while looking up hash of ${dockerCliKey.fullName}.
-                |Ensure that docker is running correctly.
-                |""".stripMargin)
-          DockerInfoFailedResponse(exception, context.request) -> context
-        }
+  private def lookupHashOrTimeout(timeout: FiniteDuration)(
+    context: DockerInfoContext
+  )(implicit cs: ContextShift[IO], timer: Timer[IO]): IO[(DockerInfoResponse, DockerInfoContext)] =
+    IO(lookupHash(context))
+      .timeout(timeout)
+      .handleErrorWith {
+        case _: TimeoutException =>
+          IO.pure {
+            val dockerCliKey = cliKeyFromImageId(context)
+            val exception = new TimeoutException(s"""|Timeout while looking up hash of ${dockerCliKey.fullName}.
+                                                     |Ensure that docker is running correctly.
+                                                     |""".stripMargin)
+            DockerInfoFailedResponse(exception, context.request) -> context
+          }
         case other => IO.pure(DockerInfoFailedResponse(other, context.request) -> context)
-      })
-  }
+      }
 
   /**
     * Pull the docker image referenced in context.
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerManifest.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerManifest.scala
index a7990d3cb09..8f9a2743d20 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerManifest.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerManifest.scala
@@ -3,7 +3,7 @@ package cromwell.docker.registryv2
 // From https://docs.docker.com/registry/spec/manifest-v2-2/
 sealed trait DockerManifestResponse
 
-case class DockerManifest(layers: Array[DockerLayer]) extends DockerManifestResponse{
+case class DockerManifest(layers: Array[DockerLayer]) extends DockerManifestResponse {
   lazy val compressedSize: Long = layers.map(_.size).sum
 }
 case class DockerLayer(size: Long)
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
index bb25cb4bc3d..234b762429d 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/DockerRegistryV2Abstract.scala
@@ -34,16 +34,21 @@ object DockerRegistryV2Abstract {
   val OCIIndexV1MediaType = "application/vnd.oci.image.index.v1+json"
 
   // If one of those fails it means someone changed one of the strings above to an invalid one.
-  val DockerManifestV2MediaRange = MediaRange.parse(DockerManifestV2MediaType)
+  val DockerManifestV2MediaRange = MediaRange
+    .parse(DockerManifestV2MediaType)
     .unsafe("Cannot parse invalid manifest v2 content type. Please report this error.")
-  val DockerManifestListV2MediaRange = MediaRange.parse(DockerManifestListV2MediaType)
+  val DockerManifestListV2MediaRange = MediaRange
+    .parse(DockerManifestListV2MediaType)
     .unsafe("Cannot parse invalid manifest list v2 content type. Please report this error.")
-  val AcceptDockerManifestV2Header = Accept.parse(DockerManifestV2MediaType)
+  val AcceptDockerManifestV2Header = Accept
+    .parse(DockerManifestV2MediaType)
     .unsafe("Cannot parse invalid manifest v2 Accept header. Please report this error.")
 
-  val OCIIndexV1MediaRange = MediaRange.parse(OCIIndexV1MediaType)
+  val OCIIndexV1MediaRange = MediaRange
+    .parse(OCIIndexV1MediaType)
     .unsafe("Cannot parse invalid OCI index v1 content type. Please report this error.")
-  val AcceptOCIIndexV1Header = Accept.parse(OCIIndexV1MediaType)
+  val AcceptOCIIndexV1Header = Accept
+    .parse(OCIIndexV1MediaType)
     .unsafe("Cannot parse invalid OCI index v1 Accept header. Please report this error.")
 
   implicit val entityManifestDecoder = jsonEntityDecoder[DockerManifest](DockerManifestV2MediaRange)
@@ -55,19 +60,21 @@ object DockerRegistryV2Abstract {
     * This is necessary because the docker registry API responds with an "application/vnd.docker.distribution.manifest.v2+json"
     * and not the traditional "application/json". Adapted from CirceInstances.jsonOf
     */
-  private def jsonEntityDecoder[A](mediaRange: MediaRange)(implicit decoder: Decoder[A]): EntityDecoder[IO, A] = EntityDecoder.decodeBy[IO, A](mediaRange) { message =>
-    CirceInstances.builder.build.jsonDecoderByteBuffer[IO]
-      .decode(message, strict = false)
-      .flatMap({ json =>
-        decoder.decodeJson(json)
-          .fold(
-            failure =>
-              DecodeResult.failureT(
-                InvalidMessageBodyFailure(s"Could not decode JSON: $json", Some(failure))),
-            DecodeResult.successT(_)
-          )
-      })
-  }
+  private def jsonEntityDecoder[A](mediaRange: MediaRange)(implicit decoder: Decoder[A]): EntityDecoder[IO, A] =
+    EntityDecoder.decodeBy[IO, A](mediaRange) { message =>
+      CirceInstances.builder.build
+        .jsonDecoderByteBuffer[IO]
+        .decode(message, strict = false)
+        .flatMap { json =>
+          decoder
+            .decodeJson(json)
+            .fold(
+              failure =>
+                DecodeResult.failureT(InvalidMessageBodyFailure(s"Could not decode JSON: $json", Some(failure))),
+              DecodeResult.successT(_)
+            )
+        }
+    }
 
   // Placeholder exceptions that can be carried through IO before being converted to a DockerInfoFailedResponse
   private class Unauthorized(message: String) extends Exception(message)
@@ -88,7 +95,9 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
   /**
     * This is the main function. Given a docker context and an http client, retrieve information about the docker image.
     */
-  def run(dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]): IO[(DockerInfoResponse, DockerInfoContext)] = {
+  def run(
+    dockerInfoContext: DockerInfoContext
+  )(implicit client: Client[IO]): IO[(DockerInfoResponse, DockerInfoContext)] = {
     val dockerResponse = for {
       token <- getToken(dockerInfoContext)
       dockerSuccessResponse <- getDockerResponse(token, dockerInfoContext)
@@ -97,19 +106,20 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     // Always map failures to a DockerHashFailedResponse instead of letting the IO fail, this is important so that the stream
     // that is calling this function will not fail
     dockerResponse.attempt
-      .map({
+      .map {
         case Left(_: Unauthorized) => DockerInfoUnauthorized(dockerInfoContext.request)
         case Left(_: NotFound) => DockerInfoNotFound(dockerInfoContext.request)
         case Left(failure) => DockerInfoFailedResponse(failure, dockerInfoContext.request)
         case Right(value) => value
-      })
+      }
       .map(_ -> dockerInfoContext)
   }
 
   // Execute a request. No retries because they're expected to already be handled by the client
-  protected def executeRequest[A](request: IO[Request[IO]], handler: Response[IO] => IO[A])(implicit client: Client[IO]): IO[A] = {
+  protected def executeRequest[A](request: IO[Request[IO]], handler: Response[IO] => IO[A])(implicit
+    client: Client[IO]
+  ): IO[A] =
     request.flatMap(client.run(_).use[IO, A](handler))
-  }
 
   /**
     * Obtain an authorization token for the subsequent manifest request. Return IO.pure(None) if no token is needed
@@ -129,11 +139,16 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * @param client http client
     * @return docker info response
     */
-  protected def getDockerResponse(token: Option[String], dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]): IO[DockerInfoSuccessResponse] = {
+  protected def getDockerResponse(token: Option[String], dockerInfoContext: DockerInfoContext)(implicit
+    client: Client[IO]
+  ): IO[DockerInfoSuccessResponse] = {
     val requestDockerManifest = manifestRequest(token, dockerInfoContext.dockerImageID, AcceptDockerManifestV2Header)
     lazy val requestOCIManifest = manifestRequest(token, dockerInfoContext.dockerImageID, AcceptOCIIndexV1Header)
     def tryOCIManifest(err: Throwable) = {
-      logger.info(s"Manifest request failed for docker manifest V2, falling back to OCI manifest. Image: ${dockerInfoContext.dockerImageID}", err)
+      logger.info(
+        s"Manifest request failed for docker manifest V2, falling back to OCI manifest. Image: ${dockerInfoContext.dockerImageID}",
+        err
+      )
       executeRequest(requestOCIManifest, handleManifestResponse(dockerInfoContext, token))
     }
     // Try to execute a request using the Docker Manifest format, and if that fails, try using the newer OCI manifest format
@@ -145,7 +160,8 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * Returns true if this flow is able to process this docker image,
     * false otherwise
     */
-  def accepts(dockerImageIdentifier: DockerImageIdentifier) = dockerImageIdentifier.host.contains(registryHostName(dockerImageIdentifier))
+  def accepts(dockerImageIdentifier: DockerImageIdentifier) =
+    dockerImageIdentifier.host.contains(registryHostName(dockerImageIdentifier))
 
   /* Methods that must to be implemented by a subclass */
 
@@ -201,26 +217,30 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     */
   private def tokenResponseHandler(response: Response[IO]): IO[String] = response match {
     case Status.Successful(r) => r.as[DockerAccessToken].map(_.token)
-    case r => r.as[String]
-      .flatMap(b => IO.raiseError(new Exception(s"Request failed with status ${r.status.code} and body $b")))
+    case r =>
+      r.as[String]
+        .flatMap(b => IO.raiseError(new Exception(s"Request failed with status ${r.status.code} and body $b")))
   }
 
   /**
     * Builds the manifest URI to be queried based on a DockerImageID
     */
-  private def buildManifestUri(dockerImageID: DockerImageIdentifier): Uri = {
+  private def buildManifestUri(dockerImageID: DockerImageIdentifier): Uri =
     Uri.apply(
       scheme = Option(Scheme.https),
       authority = Option(Authority(host = Uri.RegName(registryHostName(dockerImageID)))),
       path = s"/v2/${dockerImageID.nameWithDefaultRepository}/manifests/${dockerImageID.reference}"
     )
-  }
 
   /**
     * Request to get the manifest, using the auth token if provided
     */
-  private def manifestRequest(token: Option[String], imageId: DockerImageIdentifier, manifestHeader: Accept): IO[Request[IO]] = {
-    val authorizationHeader: Option[Authorization] = token.map(t => Authorization(Credentials.Token(AuthScheme.Bearer, t)))
+  private def manifestRequest(token: Option[String],
+                              imageId: DockerImageIdentifier,
+                              manifestHeader: Accept
+  ): IO[Request[IO]] = {
+    val authorizationHeader: Option[Authorization] =
+      token.map(t => Authorization(Credentials.Token(AuthScheme.Bearer, t)))
     val request = Method.GET(
       buildManifestUri(imageId),
       List(
@@ -231,19 +251,26 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     request
   }
 
-  private def handleManifestResponse(dockerInfoContext: DockerInfoContext, token: Option[String])(response: Response[IO])(implicit client: Client[IO]): IO[DockerInfoSuccessResponse] = {
+  private def handleManifestResponse(dockerInfoContext: DockerInfoContext, token: Option[String])(
+    response: Response[IO]
+  )(implicit client: Client[IO]): IO[DockerInfoSuccessResponse] = {
     // Getting the manifest content is not strictly necessary but just a bonus to get the size. If it fails, log the error and return None
-    def handleManifestAttempt(attempt: Either[Throwable, Option[DockerManifest]]): Option[DockerManifest] = attempt match {
-      case Left(failure) =>
-        logger.warn(s"Could not get manifest for ${dockerInfoContext.dockerImageID.fullName}", failure)
-        None
-      case Right(manifest) => manifest
-    }
+    def handleManifestAttempt(attempt: Either[Throwable, Option[DockerManifest]]): Option[DockerManifest] =
+      attempt match {
+        case Left(failure) =>
+          logger.warn(s"Could not get manifest for ${dockerInfoContext.dockerImageID.fullName}", failure)
+          None
+        case Right(manifest) => manifest
+      }
 
     for {
       hashResult <- getDigestFromResponse(response)
-      maybeManifest <- parseManifest(dockerInfoContext.dockerImageID, token)(response).attempt.map(handleManifestAttempt)
-    } yield DockerInfoSuccessResponse(DockerInformation(hashResult, maybeManifest.map(_.compressedSize).map(DockerSize.apply)), dockerInfoContext.request)
+      maybeManifest <- parseManifest(dockerInfoContext.dockerImageID, token)(response).attempt
+        .map(handleManifestAttempt)
+    } yield DockerInfoSuccessResponse(
+      DockerInformation(hashResult, maybeManifest.map(_.compressedSize).map(DockerSize.apply)),
+      dockerInfoContext.request
+    )
   }
 
   /**
@@ -259,19 +286,22 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
     * between platforms.
     * If that assumption turns out to be incorrect, a smarter decision may need to be made to choose the manifest to lookup.
     */
-  private def parseManifest(dockerImageIdentifier: DockerImageIdentifier, token: Option[String])(response: Response[IO])(implicit client: Client[IO]): IO[Option[DockerManifest]] = response match {
+  private def parseManifest(dockerImageIdentifier: DockerImageIdentifier, token: Option[String])(
+    response: Response[IO]
+  )(implicit client: Client[IO]): IO[Option[DockerManifest]] = response match {
     case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(DockerManifestV2MediaType)) =>
       r.as[DockerManifest].map(Option.apply)
     case Status.Successful(r) if r.headers.exists(_.value.equalsIgnoreCase(DockerManifestListV2MediaType)) =>
-      r.as[DockerManifestList].flatMap({ dockerManifestList =>
+      r.as[DockerManifestList].flatMap { dockerManifestList =>
         obtainManifestFromList(dockerManifestList, dockerImageIdentifier, token)
-      })
+      }
     case _ => IO.pure(None)
   }
 
   private def obtainManifestFromList(dockerManifestList: DockerManifestList,
                                      dockerImageIdentifier: DockerImageIdentifier,
-                                     token: Option[String])(implicit client: Client[IO]): IO[Option[DockerManifest]] = {
+                                     token: Option[String]
+  )(implicit client: Client[IO]): IO[Option[DockerManifest]] =
     dockerManifestList.manifests.headOption
       .map(_.digest)
       .map(dockerImageIdentifier.swapReference) match {
@@ -279,23 +309,24 @@ abstract class DockerRegistryV2Abstract(override val config: DockerRegistryConfi
         val request = manifestRequest(token, identifierWithNewHash, AcceptDockerManifestV2Header)
         executeRequest(request, parseManifest(dockerImageIdentifier, token))
       case None =>
-        logger.error(s"The manifest list for ${dockerImageIdentifier.fullName} was empty. Cannot proceed to obtain the size of image")
+        logger.error(
+          s"The manifest list for ${dockerImageIdentifier.fullName} was empty. Cannot proceed to obtain the size of image"
+        )
         IO.pure(None)
     }
-  }
 
   private def getDigestFromResponse(response: Response[IO]): IO[DockerHashResult] = response match {
     case Status.Successful(r) => extractDigestFromHeaders(r.headers)
-    case Status.Unauthorized(r) => r.as[String].flatMap(body => IO.raiseError(new Unauthorized(r.status.toString + " " + body)))
+    case Status.Unauthorized(r) =>
+      r.as[String].flatMap(body => IO.raiseError(new Unauthorized(r.status.toString + " " + body)))
     case Status.NotFound(r) => r.as[String].flatMap(body => IO.raiseError(new NotFound(r.status.toString + " " + body)))
-    case failed => failed.as[String].flatMap(body => IO.raiseError(new UnknownError(failed.status.toString + " " + body))
-    )
+    case failed =>
+      failed.as[String].flatMap(body => IO.raiseError(new UnknownError(failed.status.toString + " " + body)))
   }
 
-  private def extractDigestFromHeaders(headers: Headers) = {
+  private def extractDigestFromHeaders(headers: Headers) =
     headers.find(a => a.toRaw.name.equals(DigestHeaderName)) match {
       case Some(digest) => IO.fromEither(DockerHashResult.fromString(digest.value).toEither)
       case None => IO.raiseError(new Exception(s"Manifest response did not have a digest header"))
     }
-  }
 }
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AzureContainerRegistry.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AzureContainerRegistry.scala
index 46dfd116bc6..ff251839ba9 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AzureContainerRegistry.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/azure/AzureContainerRegistry.scala
@@ -15,7 +15,6 @@ import org.http4s.client.Client
 import io.circe.generic.auto._
 import org.http4s._
 
-
 class AzureContainerRegistry(config: DockerRegistryConfig) extends DockerRegistryV2Abstract(config) with LazyLogging {
 
   /**
@@ -25,7 +24,7 @@ class AzureContainerRegistry(config: DockerRegistryConfig) extends DockerRegistr
     dockerImageIdentifier.host.getOrElse("")
 
   override def accepts(dockerImageIdentifier: DockerImageIdentifier): Boolean =
-    dockerImageIdentifier.hostAsString.contains(domain) 
+    dockerImageIdentifier.hostAsString.contains(domain)
 
   override protected def authorizationServerHostName(dockerImageIdentifier: DockerImageIdentifier): String =
     dockerImageIdentifier.host.getOrElse("")
@@ -35,13 +34,12 @@ class AzureContainerRegistry(config: DockerRegistryConfig) extends DockerRegistr
     */
   override def serviceName: Option[String] =
     throw new Exception("ACR service name is host of user-defined registry, must derive from `DockerImageIdentifier`")
-  
+
   /**
     * Builds the list of headers for the token request
     */
-  override protected def buildTokenRequestHeaders(dockerInfoContext: DockerInfoContext): List[Header] = {
+  override protected def buildTokenRequestHeaders(dockerInfoContext: DockerInfoContext): List[Header] =
     List(contentTypeHeader)
-  }
 
   private val contentTypeHeader: Header = {
     import org.http4s.headers.`Content-Type`
@@ -49,7 +47,7 @@ class AzureContainerRegistry(config: DockerRegistryConfig) extends DockerRegistr
 
     `Content-Type`(MediaType.application.`x-www-form-urlencoded`)
   }
-  
+
   private def getRefreshToken(authServerHostname: String, defaultAccessToken: String): IO[Request[IO]] = {
     import org.http4s.Uri.{Authority, Scheme}
     import org.http4s.client.dsl.io._
@@ -69,16 +67,16 @@ class AzureContainerRegistry(config: DockerRegistryConfig) extends DockerRegistr
         "grant_type" -> "access_token"
       ),
       uri,
-      List(contentTypeHeader): _* 
+      List(contentTypeHeader): _*
     )
   }
 
   /*
   Unlike other repositories, Azure reserves `GET /oauth2/token` for Basic Authentication [0]
   In order to use Oauth we must `POST /oauth2/token` [1]
-  
+
   [0] https://github.com/Azure/acr/blob/main/docs/Token-BasicAuth.md#using-the-token-api
-  [1] https://github.com/Azure/acr/blob/main/docs/AAD-OAuth.md#calling-post-oauth2token-to-get-an-acr-access-token 
+  [1] https://github.com/Azure/acr/blob/main/docs/AAD-OAuth.md#calling-post-oauth2token-to-get-an-acr-access-token
    */
   private def getDockerAccessToken(hostname: String, repository: String, refreshToken: String): IO[Request[IO]] = {
     import org.http4s.Uri.{Authority, Scheme}
@@ -102,14 +100,17 @@ class AzureContainerRegistry(config: DockerRegistryConfig) extends DockerRegistr
         "grant_type" -> "refresh_token"
       ),
       uri,
-      List(contentTypeHeader): _* 
+      List(contentTypeHeader): _*
     )
   }
 
-  override protected def getToken(dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]): IO[Option[String]] = {
+  override protected def getToken(
+    dockerInfoContext: DockerInfoContext
+  )(implicit client: Client[IO]): IO[Option[String]] = {
     val hostname = authorizationServerHostName(dockerInfoContext.dockerImageID)
-    val maybeAadAccessToken: ErrorOr[String] = AzureCredentials.getAccessToken(None) // AAD token suitable for get-refresh-token request
-    val repository = dockerInfoContext.dockerImageID.image // ACR uses what we think of image name, as the repository 
+    val maybeAadAccessToken: ErrorOr[String] =
+      AzureCredentials.getAccessToken(None) // AAD token suitable for get-refresh-token request
+    val repository = dockerInfoContext.dockerImageID.image // ACR uses what we think of image name, as the repository
 
     // Top-level flow: AAD access token -> refresh token -> ACR access token
     maybeAadAccessToken match {
@@ -131,19 +132,21 @@ class AzureContainerRegistry(config: DockerRegistryConfig) extends DockerRegistr
   private def parseRefreshToken(response: Response[IO]): IO[String] = response match {
     case Status.Successful(r) => r.as[AcrRefreshToken].map(_.refresh_token)
     case r =>
-      r.as[String].flatMap(b => IO.raiseError(new Exception(s"Request failed with status ${r.status.code} and body $b")))
+      r.as[String]
+        .flatMap(b => IO.raiseError(new Exception(s"Request failed with status ${r.status.code} and body $b")))
   }
 
   private def parseAccessToken(response: Response[IO]): IO[String] = response match {
     case Status.Successful(r) => r.as[AcrAccessToken].map(_.access_token)
     case r =>
-      r.as[String].flatMap(b => IO.raiseError(new Exception(s"Request failed with status ${r.status.code} and body $b")))
+      r.as[String]
+        .flatMap(b => IO.raiseError(new Exception(s"Request failed with status ${r.status.code} and body $b")))
   }
 
 }
 
 object AzureContainerRegistry {
-  
+
   def domain: String = "azurecr.io"
-  
+
 }
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/dockerhub/DockerHubRegistry.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/dockerhub/DockerHubRegistry.scala
index 33fb2dabfa9..c523fe71169 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/dockerhub/DockerHubRegistry.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/dockerhub/DockerHubRegistry.scala
@@ -17,12 +17,10 @@ class DockerHubRegistry(config: DockerRegistryConfig) extends DockerRegistryV2Ab
   /**
     * Builds the list of headers for the token request
     */
-   def buildTokenRequestHeaders(dockerInfoContext: DockerInfoContext) = {
-    dockerInfoContext.credentials collect {
-      case DockerCredentials(token) =>
-        Authorization(org.http4s.BasicCredentials(token))
+  def buildTokenRequestHeaders(dockerInfoContext: DockerInfoContext) =
+    dockerInfoContext.credentials collect { case DockerCredentials(token) =>
+      Authorization(org.http4s.BasicCredentials(token))
     }
-  }
 
   override def accepts(dockerImageIdentifier: DockerImageIdentifier): Boolean =
     dockerImageIdentifier.host |> isValidDockerHubHost
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/google/GoogleRegistry.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/google/GoogleRegistry.scala
index 4db74317e07..81bcb4dd4ec 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/google/GoogleRegistry.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/google/GoogleRegistry.scala
@@ -11,12 +11,17 @@ import scala.concurrent.duration._
 
 class GoogleRegistry(config: DockerRegistryConfig) extends DockerRegistryV2Abstract(config) {
   private val AccessTokenAcceptableTTL = 1.minute
-  
-  def googleRegion(dockerImageIdentifier: DockerImageIdentifier): String = dockerImageIdentifier.host.flatMap(_.split("/").headOption).getOrElse("")
 
-  override def registryHostName(dockerImageIdentifier: DockerImageIdentifier): String = googleRegion(dockerImageIdentifier)
-  override def authorizationServerHostName(dockerImageIdentifier: DockerImageIdentifier): String = googleRegion(dockerImageIdentifier)
-  
+  def googleRegion(dockerImageIdentifier: DockerImageIdentifier): String =
+    dockerImageIdentifier.host.flatMap(_.split("/").headOption).getOrElse("")
+
+  override def registryHostName(dockerImageIdentifier: DockerImageIdentifier): String = googleRegion(
+    dockerImageIdentifier
+  )
+  override def authorizationServerHostName(dockerImageIdentifier: DockerImageIdentifier): String = googleRegion(
+    dockerImageIdentifier
+  )
+
   override protected def buildTokenRequestUri(dockerImageID: DockerImageIdentifier): Uri = {
     val uri = super.buildTokenRequestUri(dockerImageID)
     uri.withPath(s"/v2${uri.path}")
@@ -25,17 +30,15 @@ class GoogleRegistry(config: DockerRegistryConfig) extends DockerRegistryV2Abstr
   /**
     * Builds the list of headers for the token request
     */
-   def buildTokenRequestHeaders(dockerInfoContext: DockerInfoContext): List[Authorization] = {
-    dockerInfoContext.credentials collect {
-      case credentials: OAuth2Credentials => Authorization(org.http4s.Credentials.Token(AuthScheme.Bearer, freshAccessToken(credentials)))
+  def buildTokenRequestHeaders(dockerInfoContext: DockerInfoContext): List[Authorization] =
+    dockerInfoContext.credentials collect { case credentials: OAuth2Credentials =>
+      Authorization(org.http4s.Credentials.Token(AuthScheme.Bearer, freshAccessToken(credentials)))
     }
-  }
-  
+
   private def freshAccessToken(credential: OAuth2Credentials) = {
-    def accessTokenTTLIsAcceptable(accessToken: AccessToken) = {
+    def accessTokenTTLIsAcceptable(accessToken: AccessToken) =
       (accessToken.getExpirationTime.getTime - System.currentTimeMillis()).millis.gteq(AccessTokenAcceptableTTL)
-    }
-    
+
     Option(credential.getAccessToken) match {
       case Some(accessToken) if accessTokenTTLIsAcceptable(accessToken) => accessToken.getTokenValue
       case _ =>
@@ -44,8 +47,9 @@ class GoogleRegistry(config: DockerRegistryConfig) extends DockerRegistryV2Abstr
     }
   }
 
-  override def accepts(dockerImageIdentifier: DockerImageIdentifier): Boolean = {
+  override def accepts(dockerImageIdentifier: DockerImageIdentifier): Boolean =
     // Supports both GCR (Google Container Registry) and GAR (Google Artifact Registry).
-    dockerImageIdentifier.hostAsString.contains("gcr.io") || dockerImageIdentifier.hostAsString.contains("-docker.pkg.dev")
-  }
+    dockerImageIdentifier.hostAsString.contains("gcr.io") || dockerImageIdentifier.hostAsString.contains(
+      "-docker.pkg.dev"
+    )
 }
diff --git a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/quay/QuayRegistry.scala b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/quay/QuayRegistry.scala
index d739eba2651..00ca2836636 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/quay/QuayRegistry.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/registryv2/flows/quay/QuayRegistry.scala
@@ -9,12 +9,13 @@ import org.http4s.client.Client
 
 class QuayRegistry(config: DockerRegistryConfig) extends DockerRegistryV2Abstract(config) {
   override protected def registryHostName(dockerImageIdentifier: DockerImageIdentifier): String = "quay.io"
-  // Not used for now because we bypass the token part as quay doesn't require one for public images 
+  // Not used for now because we bypass the token part as quay doesn't require one for public images
   override protected def authorizationServerHostName(dockerImageIdentifier: DockerImageIdentifier): String = "quay.io"
   // Not used for now, same reason as above
   override protected def buildTokenRequestHeaders(dockerInfoContext: DockerInfoContext): List[Header] = List.empty
 
-  override protected def getToken(dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]): IO[Option[String]] = {
+  override protected def getToken(dockerInfoContext: DockerInfoContext)(implicit
+    client: Client[IO]
+  ): IO[Option[String]] =
     IO.pure(None)
-  }
 }
diff --git a/dockerHashing/src/test/scala/cromwell/docker/DockerHashMocks.scala b/dockerHashing/src/test/scala/cromwell/docker/DockerHashMocks.scala
index 4c664912aeb..d39cd538d17 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/DockerHashMocks.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/DockerHashMocks.scala
@@ -11,26 +11,27 @@ class DockerRegistryMock(responses: MockHashResponse*) extends DockerRegistry {
   // Counts the number of elements going through this "flow"
   private var _count: Int = 0
 
-  private def nextResponse(context: DockerInfoContext): (DockerInfoResponse, DockerInfoContext) = 
-      responsesLeft.headOption match {
-        case Some(mockResponse) =>
-          _count += 1
-          if (mockResponse.nb > 1)
-            responsesLeft.update(0, mockResponse.copy(nb = mockResponse.nb - 1))
-          else
-            responsesLeft.remove(0)
-          (mockResponse.hashResponse, context)
-        // When we hit the end, loop
-        case None =>
-          responsesLeft = responses.toBuffer
-          nextResponse(context)
-  }
-  
+  private def nextResponse(context: DockerInfoContext): (DockerInfoResponse, DockerInfoContext) =
+    responsesLeft.headOption match {
+      case Some(mockResponse) =>
+        _count += 1
+        if (mockResponse.nb > 1)
+          responsesLeft.update(0, mockResponse.copy(nb = mockResponse.nb - 1))
+        else
+          responsesLeft.remove(0)
+        (mockResponse.hashResponse, context)
+      // When we hit the end, loop
+      case None =>
+        responsesLeft = responses.toBuffer
+        nextResponse(context)
+    }
+
   def count() = _count
 
   override def accepts(dockerImageIdentifier: DockerImageIdentifier): Boolean = true
 
-  override def run(dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]) = IO.pure(nextResponse(dockerInfoContext))
+  override def run(dockerInfoContext: DockerInfoContext)(implicit client: Client[IO]) =
+    IO.pure(nextResponse(dockerInfoContext))
 
   override def config = DockerRegistryConfig.default
 }
diff --git a/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala
index 41353934fc6..35fe341737b 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala
@@ -5,30 +5,49 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks
 
-class DockerImageIdentifierSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
+class DockerImageIdentifierSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks {
   behavior of "DockerImageID"
 
   it should "parse valid docker images" in {
     val valid = Table(
-      ("sourceString",                            "host",             "repo",                 "image",     "reference"),
+      ("sourceString", "host", "repo", "image", "reference"),
       // Without tags -> latest
-      ("ubuntu",                                  None,               None,                   "ubuntu",     "latest"),
-      ("broad/cromwell",                          None,               Option("broad"),          "cromwell",   "latest"),
-      ("index.docker.io/ubuntu",         Option("index.docker.io"),   None,                   "ubuntu",     "latest"),
-      ("broad/cromwell/submarine",                None,               Option("broad/cromwell"), "submarine",  "latest"),
-      ("gcr.io/google/slim",              Option("gcr.io"),         Option("google"),         "slim",     "latest"),
-      ("us-central1-docker.pkg.dev/google/slim", Option("us-central1-docker.pkg.dev"), Option("google"), "slim", "latest"),
-      ("terrabatchdev.azurecr.io/postgres",      Option("terrabatchdev.azurecr.io"),         None,     "postgres", "latest"),
+      ("ubuntu", None, None, "ubuntu", "latest"),
+      ("broad/cromwell", None, Option("broad"), "cromwell", "latest"),
+      ("index.docker.io/ubuntu", Option("index.docker.io"), None, "ubuntu", "latest"),
+      ("broad/cromwell/submarine", None, Option("broad/cromwell"), "submarine", "latest"),
+      ("gcr.io/google/slim", Option("gcr.io"), Option("google"), "slim", "latest"),
+      ("us-central1-docker.pkg.dev/google/slim",
+       Option("us-central1-docker.pkg.dev"),
+       Option("google"),
+       "slim",
+       "latest"
+      ),
+      ("terrabatchdev.azurecr.io/postgres", Option("terrabatchdev.azurecr.io"), None, "postgres", "latest"),
       // With tags
-      ("ubuntu:latest",                           None,               None,                   "ubuntu",     "latest"),
-      ("ubuntu:1235-SNAP",                        None,               None,                   "ubuntu",     "1235-SNAP"),
-      ("ubuntu:V3.8-5_1",                         None,               None,                   "ubuntu",     "V3.8-5_1"),
-      ("index.docker.io:9999/ubuntu:170904",  Option("index.docker.io:9999"), None,             "ubuntu",    "170904"),
-      ("localhost:5000/capture/transwf:170904", Option("localhost:5000"), Option("capture"),      "transwf",    "170904"),
-      ("quay.io/biocontainers/platypus-variant:0.8.1.1--htslib1.5_0", Option("quay.io"), Option("biocontainers"), "platypus-variant", "0.8.1.1--htslib1.5_0"),
+      ("ubuntu:latest", None, None, "ubuntu", "latest"),
+      ("ubuntu:1235-SNAP", None, None, "ubuntu", "1235-SNAP"),
+      ("ubuntu:V3.8-5_1", None, None, "ubuntu", "V3.8-5_1"),
+      ("index.docker.io:9999/ubuntu:170904", Option("index.docker.io:9999"), None, "ubuntu", "170904"),
+      ("localhost:5000/capture/transwf:170904", Option("localhost:5000"), Option("capture"), "transwf", "170904"),
+      ("quay.io/biocontainers/platypus-variant:0.8.1.1--htslib1.5_0",
+       Option("quay.io"),
+       Option("biocontainers"),
+       "platypus-variant",
+       "0.8.1.1--htslib1.5_0"
+      ),
       ("terrabatchdev.azurecr.io/postgres:latest", Option("terrabatchdev.azurecr.io"), None, "postgres", "latest"),
       // Very long tags with trailing spaces cause problems for the re engine
-      ("someuser/someimage:supercalifragilisticexpialidociouseventhoughthesoundofitissomethingquiteatrociousifyousayitloudenoughyoullalwayssoundprecocious ",              None,         Some("someuser"),         "someimage",     "supercalifragilisticexpialidociouseventhoughthesoundofitissomethingquiteatrociousifyousayitloudenoughyoullalwayssoundprecocious")
+      ("someuser/someimage:supercalifragilisticexpialidociouseventhoughthesoundofitissomethingquiteatrociousifyousayitloudenoughyoullalwayssoundprecocious ",
+       None,
+       Some("someuser"),
+       "someimage",
+       "supercalifragilisticexpialidociouseventhoughthesoundofitissomethingquiteatrociousifyousayitloudenoughyoullalwayssoundprecocious"
+      )
     )
 
     forAll(valid) { (dockerString, host, repo, image, reference) =>
diff --git a/dockerHashing/src/test/scala/cromwell/docker/DockerInfoActorSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/DockerInfoActorSpec.scala
index 72baec70825..ed48762c2cb 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/DockerInfoActorSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/DockerInfoActorSpec.scala
@@ -25,44 +25,40 @@ class DockerInfoActorSpec extends DockerRegistrySpec with AnyFlatSpecLike with M
 
   it should "retrieve a public docker hash" taggedAs IntegrationTest in {
     dockerActor ! makeRequest("ubuntu:latest")
-    
-    expectMsgPF(5 second) {
-      case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) => 
-        alg shouldBe "sha256"
-        hash should not be empty
+
+    expectMsgPF(5 second) { case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
+      alg shouldBe "sha256"
+      hash should not be empty
     }
   }
 
   it should "retrieve a public docker hash on gcr" taggedAs IntegrationTest in {
     dockerActor ! makeRequest("gcr.io/google-containers/alpine-with-bash:1.0")
 
-    expectMsgPF(5 second) {
-      case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
-        alg shouldBe "sha256"
-        hash should not be empty
+    expectMsgPF(5 second) { case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
+      alg shouldBe "sha256"
+      hash should not be empty
     }
   }
 
   it should "retrieve a public docker hash on gar" taggedAs IntegrationTest in {
     dockerActor ! makeRequest("us-central1-docker.pkg.dev/broad-dsde-cromwell-dev/bt-335/ubuntu:bt-335")
 
-    expectMsgPF(5 second) {
-      case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
-        alg shouldBe "sha256"
-        hash should not be empty
+    expectMsgPF(5 second) { case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
+      alg shouldBe "sha256"
+      hash should not be empty
     }
   }
 
   it should "retrieve a private docker hash on acr" taggedAs IntegrationTest in {
     dockerActor ! makeRequest("terrabatchdev.azurecr.io/postgres:latest")
 
-    expectMsgPF(15 second) {
-      case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
-        alg shouldBe "sha256"
-        hash should not be empty
+    expectMsgPF(15 second) { case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
+      alg shouldBe "sha256"
+      hash should not be empty
     }
   }
-  
+
   it should "send image not found message back if the image does not exist" taggedAs IntegrationTest in {
     val notFound = makeRequest("ubuntu:nonexistingtag")
     dockerActor ! notFound
@@ -76,38 +72,38 @@ class DockerInfoActorSpec extends DockerRegistrySpec with AnyFlatSpecLike with M
 
     expectMsgClass(5 seconds, classOf[DockerInfoUnauthorized])
   }
-  
+
   it should "send an unrecognized host message if no flow can process the docker string" taggedAs IntegrationTest in {
     val unauthorized = makeRequest("unknown.io/image:v1")
     dockerActor ! unauthorized
 
     expectMsgClass(5 seconds, classOf[DockerHashUnknownRegistry])
   }
-  
+
   it should "cache results" in {
-    
+
     val image1 = dockerImage("ubuntu:latest")
     val request = DockerInfoRequest(image1)
-    
+
     val hashSuccess = DockerHashResult("sha256", "hashvalue")
     val responseSuccess = DockerInfoSuccessResponse(DockerInformation(hashSuccess, None), request)
     val mockResponseSuccess = MockHashResponse(responseSuccess, 1)
-    
+
     val responseFailure = DockerInfoFailedResponse(new Exception("Docker hash failed - part of test flow"), request)
     val mockResponseFailure = MockHashResponse(responseFailure, 1)
-    
+
     // Send back success, failure, success, failure, ...
     val mockHttpFlow = new DockerRegistryMock(mockResponseSuccess, mockResponseFailure)
     val dockerActorWithCache = system.actorOf(
       props = DockerInfoActor.props(Seq(mockHttpFlow), 1000, 3 seconds, 10),
-      name = "dockerActorWithCache",
+      name = "dockerActorWithCache"
     )
-    
+
     dockerActorWithCache ! request
     expectMsg(DockerInfoSuccessResponse(DockerInformation(hashSuccess, None), request))
     // Necessary to give some time to the cache to be updated - as it's decoupled from sending back the response
     Thread.sleep(1000)
-    
+
     dockerActorWithCache ! request
     // Without caching, the second request would have yielded a Failure since the mock flow alternates between a success and a failure
     // Getting a success here means the request didn't make it to the stream
@@ -122,11 +118,10 @@ class DockerInfoActorSpec extends DockerRegistrySpec with AnyFlatSpecLike with M
     mockHttpFlow.count() shouldBe 2
   }
 
-
   it should "not deadlock" taggedAs IntegrationTest in {
     lazy val dockerActorScale = system.actorOf(
       props = DockerInfoActor.props(registryFlows, 1000, 20.minutes, 0),
-      name = "dockerActorScale",
+      name = "dockerActorScale"
     )
     0 until 400 foreach { _ =>
       dockerActorScale ! makeRequest("gcr.io/google-containers/alpine-with-bash:1.0")
diff --git a/dockerHashing/src/test/scala/cromwell/docker/DockerRegistrySpec.scala b/dockerHashing/src/test/scala/cromwell/docker/DockerRegistrySpec.scala
index ab35c216b51..5742f44bc2c 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/DockerRegistrySpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/DockerRegistrySpec.scala
@@ -18,14 +18,13 @@ abstract class DockerRegistrySpec extends TestKitSuite with ImplicitSender {
   // Disable cache by setting a cache size of 0 - A separate test tests the cache
   lazy val dockerActor: ActorRef = system.actorOf(
     props = DockerInfoActor.props(registryFlows, 1000, 20.minutes, 0),
-    name = "dockerActor",
+    name = "dockerActor"
   )
 
   def dockerImage(string: String): DockerImageIdentifier = DockerImageIdentifier.fromString(string).get
 
-  def makeRequest(string: String): DockerInfoRequest = {
+  def makeRequest(string: String): DockerInfoRequest =
     DockerInfoRequest(dockerImage(string))
-  }
 
   override protected def afterAll(): Unit = {
     system.stop(dockerActor)
diff --git a/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliClientSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliClientSpec.scala
index 6553979f9ff..14b9e4f3ba3 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliClientSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliClientSpec.scala
@@ -7,18 +7,24 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 
 import scala.util.{Failure, Success}
 
-class DockerCliClientSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
+class DockerCliClientSpec
+    extends AnyFlatSpecLike
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks {
   behavior of "DockerCliClient"
 
   private val lookupSuccessStdout = Seq(
     "<none>\t<none>\t<none>",
     "fauxbuntu\tlatest\tsha256:0123456789abcdef0123456789abcdef0123456789abcdef0123456789abcdef",
-    "fauxbuntu\tmytag\tsha256:00001111222233334444555566667777888899990000aaaabbbbccccddddeeee")
+    "fauxbuntu\tmytag\tsha256:00001111222233334444555566667777888899990000aaaabbbbccccddddeeee"
+  )
 
   private val lookupSuccessHashes = Table(
     ("dockerCliKey", "hashValue"),
     (DockerCliKey("fauxbuntu", "latest"), "0123456789abcdef0123456789abcdef0123456789abcdef0123456789abcdef"),
-    (DockerCliKey("fauxbuntu", "mytag"), "00001111222233334444555566667777888899990000aaaabbbbccccddddeeee"))
+    (DockerCliKey("fauxbuntu", "mytag"), "00001111222233334444555566667777888899990000aaaabbbbccccddddeeee")
+  )
 
   forAll(lookupSuccessHashes) { (dockerCliKey, hashValue) =>
     it should s"successfully lookup simulated hash for ${dockerCliKey.fullName}" in {
@@ -47,7 +53,8 @@ class DockerCliClientSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
       """|Error running: docker images --digests --format {{printf "%s\t%s\t%s" .Repository .Tag .Digest}}
          |Exit code: 1
          |Error response from daemon: Bad response from Docker engine
-         |""".stripMargin)
+         |""".stripMargin
+    )
   }
 }
 
diff --git a/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliSpec.scala
index 3a8d88cdb01..7565195f1d2 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliSpec.scala
@@ -1,7 +1,7 @@
 package cromwell.docker.local
 
 import cromwell.core.Tags.IntegrationTest
-import cromwell.docker.DockerInfoActor.{DockerInfoNotFound, DockerInfoSuccessResponse, DockerInformation}
+import cromwell.docker.DockerInfoActor.{DockerInfoNotFound, DockerInformation, DockerInfoSuccessResponse}
 import cromwell.docker.{DockerHashResult, DockerRegistry, DockerRegistrySpec}
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
@@ -16,30 +16,27 @@ class DockerCliSpec extends DockerRegistrySpec with AnyFlatSpecLike with Matcher
   it should "retrieve a public docker hash" taggedAs IntegrationTest in {
     dockerActor ! makeRequest("ubuntu:latest")
 
-    expectMsgPF(30.seconds) {
-      case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
-        alg shouldBe "sha256"
-        hash should not be empty
+    expectMsgPF(30.seconds) { case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
+      alg shouldBe "sha256"
+      hash should not be empty
     }
   }
 
   it should "retrieve a public docker hash on gcr" taggedAs IntegrationTest in {
     dockerActor ! makeRequest("gcr.io/google-containers/alpine-with-bash:1.0")
 
-    expectMsgPF(30.seconds) {
-      case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
-        alg shouldBe "sha256"
-        hash should not be empty
+    expectMsgPF(30.seconds) { case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
+      alg shouldBe "sha256"
+      hash should not be empty
     }
   }
 
   it should "retrieve a public docker hash on gar" taggedAs IntegrationTest in {
     dockerActor ! makeRequest("us-central1-docker.pkg.dev/broad-dsde-cromwell-dev/bt-335/ubuntu:bt-335")
 
-    expectMsgPF(30.seconds) {
-      case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
-        alg shouldBe "sha256"
-        hash should not be empty
+    expectMsgPF(30.seconds) { case DockerInfoSuccessResponse(DockerInformation(DockerHashResult(alg, hash), _), _) =>
+      alg shouldBe "sha256"
+      hash should not be empty
     }
   }
 
diff --git a/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliTimeoutSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliTimeoutSpec.scala
index 90b3a2fa0ca..445c4378dd1 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliTimeoutSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/local/DockerCliTimeoutSpec.scala
@@ -19,24 +19,20 @@ class DockerCliTimeoutSpec extends DockerRegistrySpec with AnyFlatSpecLike with
   it should "timeout retrieving a public docker hash" taggedAs IntegrationTest in {
     dockerActor ! makeRequest("ubuntu:latest")
 
-    expectMsgPF(5.seconds) {
-      case DockerInfoFailedResponse(exception: TimeoutException, _) =>
-        exception.getMessage should be(
-          """|Timeout while looking up hash of ubuntu:latest.
-             |Ensure that docker is running correctly.
-             |""".stripMargin)
+    expectMsgPF(5.seconds) { case DockerInfoFailedResponse(exception: TimeoutException, _) =>
+      exception.getMessage should be("""|Timeout while looking up hash of ubuntu:latest.
+                                        |Ensure that docker is running correctly.
+                                        |""".stripMargin)
     }
   }
 
   it should "timeout retrieving a public docker hash on gcr" taggedAs IntegrationTest in {
     dockerActor ! makeRequest("gcr.io/google-containers/alpine-with-bash:1.0")
 
-    expectMsgPF(5.seconds) {
-      case DockerInfoFailedResponse(exception: TimeoutException, _) =>
-        exception.getMessage should be(
-          """|Timeout while looking up hash of gcr.io/google-containers/alpine-with-bash:1.0.
-             |Ensure that docker is running correctly.
-             |""".stripMargin)
+    expectMsgPF(5.seconds) { case DockerInfoFailedResponse(exception: TimeoutException, _) =>
+      exception.getMessage should be("""|Timeout while looking up hash of gcr.io/google-containers/alpine-with-bash:1.0.
+                                        |Ensure that docker is running correctly.
+                                        |""".stripMargin)
     }
 
   }
@@ -44,12 +40,12 @@ class DockerCliTimeoutSpec extends DockerRegistrySpec with AnyFlatSpecLike with
   it should "timeout retrieving a public docker hash on gar" taggedAs IntegrationTest in {
     dockerActor ! makeRequest("us-central1-docker.pkg.dev/broad-dsde-cromwell-dev/bt-335/ubuntu:bt-335")
 
-    expectMsgPF(5.seconds) {
-      case DockerInfoFailedResponse(exception: TimeoutException, _) =>
-        exception.getMessage should be(
-          """|Timeout while looking up hash of us-central1-docker.pkg.dev/broad-dsde-cromwell-dev/bt-335/ubuntu:bt-335.
-             |Ensure that docker is running correctly.
-             |""".stripMargin)
+    expectMsgPF(5.seconds) { case DockerInfoFailedResponse(exception: TimeoutException, _) =>
+      exception.getMessage should be(
+        """|Timeout while looking up hash of us-central1-docker.pkg.dev/broad-dsde-cromwell-dev/bt-335/ubuntu:bt-335.
+           |Ensure that docker is running correctly.
+           |""".stripMargin
+      )
     }
 
   }
@@ -58,12 +54,10 @@ class DockerCliTimeoutSpec extends DockerRegistrySpec with AnyFlatSpecLike with
     val notFound = makeRequest("ubuntu:nonexistingtag")
     dockerActor ! notFound
 
-    expectMsgPF(5.seconds) {
-      case DockerInfoFailedResponse(exception: TimeoutException, _) =>
-        exception.getMessage should be(
-          """|Timeout while looking up hash of ubuntu:nonexistingtag.
-             |Ensure that docker is running correctly.
-             |""".stripMargin)
+    expectMsgPF(5.seconds) { case DockerInfoFailedResponse(exception: TimeoutException, _) =>
+      exception.getMessage should be("""|Timeout while looking up hash of ubuntu:nonexistingtag.
+                                        |Ensure that docker is running correctly.
+                                        |""".stripMargin)
     }
   }
 
@@ -71,12 +65,10 @@ class DockerCliTimeoutSpec extends DockerRegistrySpec with AnyFlatSpecLike with
     val unauthorized = makeRequest("tjeandet/sinatra:v1")
     dockerActor ! unauthorized
 
-    expectMsgPF(5.seconds) {
-      case DockerInfoFailedResponse(exception: TimeoutException, _) =>
-        exception.getMessage should be(
-          """|Timeout while looking up hash of tjeandet/sinatra:v1.
-             |Ensure that docker is running correctly.
-             |""".stripMargin)
+    expectMsgPF(5.seconds) { case DockerInfoFailedResponse(exception: TimeoutException, _) =>
+      exception.getMessage should be("""|Timeout while looking up hash of tjeandet/sinatra:v1.
+                                        |Ensure that docker is running correctly.
+                                        |""".stripMargin)
     }
   }
 
@@ -84,12 +76,10 @@ class DockerCliTimeoutSpec extends DockerRegistrySpec with AnyFlatSpecLike with
     val unauthorized = makeRequest("unknown.io/image:v1")
     dockerActor ! unauthorized
 
-    expectMsgPF(5.seconds) {
-      case DockerInfoFailedResponse(exception: TimeoutException, _) =>
-        exception.getMessage should be(
-          """|Timeout while looking up hash of unknown.io/library/image:v1.
-             |Ensure that docker is running correctly.
-             |""".stripMargin)
+    expectMsgPF(5.seconds) { case DockerInfoFailedResponse(exception: TimeoutException, _) =>
+      exception.getMessage should be("""|Timeout while looking up hash of unknown.io/library/image:v1.
+                                        |Ensure that docker is running correctly.
+                                        |""".stripMargin)
     }
   }
 }
diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
index e99383ac131..f084a85b035 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/DockerRegistryV2AbstractSpec.scala
@@ -23,15 +23,18 @@ class DockerRegistryV2AbstractSpec extends AnyFlatSpec with CromwellTimeoutSpec
     val mediaType = MediaType.parse(DockerRegistryV2Abstract.DockerManifestV2MediaType).toOption.get
     val contentType: Header = `Content-Type`(mediaType)
 
-    val mockClient = Client({ _: Request[IO] =>
+    val mockClient = Client { _: Request[IO] =>
       // This response will have an empty body, so we need to be explicit about the typing:
-      Resource.pure[IO, Response[IO]](Response(headers = Headers.of(contentType))) : Resource[IO, Response[IO]]
-    })
+      Resource.pure[IO, Response[IO]](Response(headers = Headers.of(contentType))): Resource[IO, Response[IO]]
+    }
 
     val dockerImageIdentifier = DockerImageIdentifier.fromString("ubuntu").get
     val dockerInfoRequest = DockerInfoRequest(dockerImageIdentifier)
     val context = DockerInfoContext(dockerInfoRequest, null)
     val result = registry.run(context)(mockClient).unsafeRunSync()
-    result.asInstanceOf[(DockerInfoFailedResponse, DockerInfoContext)]._1.reason shouldBe "Failed to get docker hash for ubuntu:latest Malformed message body: Invalid JSON: empty body"
+    result
+      .asInstanceOf[(DockerInfoFailedResponse, DockerInfoContext)]
+      ._1
+      .reason shouldBe "Failed to get docker hash for ubuntu:latest Malformed message body: Invalid JSON: empty body"
   }
 }
diff --git a/engine/src/main/scala/cromwell/Simpletons.scala b/engine/src/main/scala/cromwell/Simpletons.scala
index 259e57a62e8..6ef40548438 100644
--- a/engine/src/main/scala/cromwell/Simpletons.scala
+++ b/engine/src/main/scala/cromwell/Simpletons.scala
@@ -12,13 +12,11 @@ import scala.util.Try
   * to `WdlSingleFile` instances.
   */
 object Simpletons {
-  def toSimpleton(entry: CallCachingSimpletonEntry): WomValueSimpleton = {
+  def toSimpleton(entry: CallCachingSimpletonEntry): WomValueSimpleton =
     toSimpleton(entry.wdlType, entry.simpletonKey, entry.simpletonValue.toRawString)
-  }
 
-  def toSimpleton(entry: JobStoreSimpletonEntry): WomValueSimpleton = {
+  def toSimpleton(entry: JobStoreSimpletonEntry): WomValueSimpleton =
     toSimpleton(entry.wdlType, entry.simpletonKey, entry.simpletonValue.toRawString)
-  }
 
   private def toSimpleton(womType: String, simpletonKey: String, simpletonValue: String): WomValueSimpleton = {
     val womValue: String => Try[WomValue] = womType match {
diff --git a/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala b/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
index c648261a7f4..332664f1d56 100644
--- a/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
+++ b/engine/src/main/scala/cromwell/engine/EngineFilesystems.scala
@@ -19,17 +19,18 @@ object EngineFilesystems {
       .filter(_ => config.as[Boolean]("engine.filesystems.local.enabled"))
       .to(collection.immutable.SortedMap)
 
-  private val pathBuilderFactories: SortedMap[String, PathBuilderFactory] = {
+  private val pathBuilderFactories: SortedMap[String, PathBuilderFactory] =
     // Unordered maps are a classical source of randomness injection into a system
     (
-      CromwellFileSystems.instance.factoriesFromConfig(config.as[Config]("engine"))
+      CromwellFileSystems.instance
+        .factoriesFromConfig(config.as[Config]("engine"))
         .unsafe("Failed to instantiate engine filesystem") ++ defaultFileSystemFactory
     ).to(collection.immutable.SortedMap)
-  }
 
   def configuredPathBuilderFactories: List[PathBuilderFactory] = pathBuilderFactories.values.toList
 
-  def pathBuildersForWorkflow(workflowOptions: WorkflowOptions, factories: List[PathBuilderFactory])(implicit as: ActorSystem): Future[List[PathBuilder]] = {
+  def pathBuildersForWorkflow(workflowOptions: WorkflowOptions, factories: List[PathBuilderFactory])(implicit
+    as: ActorSystem
+  ): Future[List[PathBuilder]] =
     PathBuilderFactory.instantiatePathBuilders(factories, workflowOptions)
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/EngineIoFunctions.scala b/engine/src/main/scala/cromwell/engine/EngineIoFunctions.scala
index 6dcc487b8d6..d752c3b4d42 100644
--- a/engine/src/main/scala/cromwell/engine/EngineIoFunctions.scala
+++ b/engine/src/main/scala/cromwell/engine/EngineIoFunctions.scala
@@ -8,16 +8,23 @@ import better.files.File._
 
 import scala.concurrent.{ExecutionContext, Future}
 
-class EngineIoFunctions(val pathBuilders: List[PathBuilder], override val asyncIo: AsyncIo, override val ec: ExecutionContext) extends ReadLikeFunctions with WorkflowCorePathFunctions {
-  override def glob(pattern: String): Future[Seq[String]] = throw new UnsupportedOperationException(s"glob(path, pattern) not implemented yet")
+class EngineIoFunctions(val pathBuilders: List[PathBuilder],
+                        override val asyncIo: AsyncIo,
+                        override val ec: ExecutionContext
+) extends ReadLikeFunctions
+    with WorkflowCorePathFunctions {
+  override def glob(pattern: String): Future[Seq[String]] = throw new UnsupportedOperationException(
+    s"glob(path, pattern) not implemented yet"
+  )
 
   // TODO: This is not suited for multi backend / multi filesystem use. Keep local for now to not break local CWL conf tests
   override def writeFile(path: String, content: String): Future[WomSingleFile] = Future.successful {
     val cromwellPath = buildPath(path)
-    val string = if (cromwellPath.isAbsolute) 
-      cromwellPath.write(content).pathAsString
-    else 
-      (newTemporaryDirectory() / path).write(content).pathAsString
+    val string =
+      if (cromwellPath.isAbsolute)
+        cromwellPath.write(content).pathAsString
+      else
+        (newTemporaryDirectory() / path).write(content).pathAsString
     WomSingleFile(string)
   }
 
@@ -27,7 +34,9 @@ class EngineIoFunctions(val pathBuilders: List[PathBuilder], override val asyncI
   override def listAllFilesUnderDirectory(dirPath: String): Nothing =
     throw new UnsupportedOperationException(s"listAllFilesUnderDirectory not implemented yet")
 
-  override def listDirectory(path: String)(visited: Vector[String]) = throw new UnsupportedOperationException(s"listDirectory not implemented yet")
+  override def listDirectory(path: String)(visited: Vector[String]) = throw new UnsupportedOperationException(
+    s"listDirectory not implemented yet"
+  )
 
   override def isDirectory(path: String) = Future.successful(buildPath(path).isDirectory)
 
diff --git a/engine/src/main/scala/cromwell/engine/EngineWorkflowDescriptor.scala b/engine/src/main/scala/cromwell/engine/EngineWorkflowDescriptor.scala
index ab062853a2b..99c93ba330b 100644
--- a/engine/src/main/scala/cromwell/engine/EngineWorkflowDescriptor.scala
+++ b/engine/src/main/scala/cromwell/engine/EngineWorkflowDescriptor.scala
@@ -13,7 +13,8 @@ case class EngineWorkflowDescriptor(topLevelCallable: Callable,
                                     failureMode: WorkflowFailureMode,
                                     pathBuilders: List[PathBuilder],
                                     callCachingMode: CallCachingMode,
-                                    parentWorkflow: Option[EngineWorkflowDescriptor] = None) {
+                                    parentWorkflow: Option[EngineWorkflowDescriptor] = None
+) {
 
   val rootWorkflow: EngineWorkflowDescriptor = parentWorkflow match {
     case Some(parent) => parent.rootWorkflow
diff --git a/engine/src/main/scala/cromwell/engine/backend/BackendConfiguration.scala b/engine/src/main/scala/cromwell/engine/backend/BackendConfiguration.scala
index 410a6261b5c..74d652b741d 100644
--- a/engine/src/main/scala/cromwell/engine/backend/BackendConfiguration.scala
+++ b/engine/src/main/scala/cromwell/engine/backend/BackendConfiguration.scala
@@ -8,10 +8,11 @@ import scala.util.{Failure, Success, Try}
 
 case class BackendConfigurationEntry(name: String, lifecycleActorFactoryClass: String, config: Config) {
   def asBackendLifecycleActorFactory: Try[BackendLifecycleActorFactory] = Try {
-    Class.forName(lifecycleActorFactoryClass)
-         .getConstructor(classOf[String], classOf[BackendConfigurationDescriptor])
-         .newInstance(name, asBackendConfigurationDescriptor)
-         .asInstanceOf[BackendLifecycleActorFactory]
+    Class
+      .forName(lifecycleActorFactoryClass)
+      .getConstructor(classOf[String], classOf[BackendConfigurationDescriptor])
+      .newInstance(name, asBackendConfigurationDescriptor)
+      .asInstanceOf[BackendLifecycleActorFactory]
   }
 
   def asBackendConfigurationDescriptor = BackendConfigurationDescriptor(config, ConfigFactory.load)
@@ -21,7 +22,8 @@ object BackendConfiguration {
   private val BackendConfig = ConfigFactory.load.getConfig("backend")
   private val DefaultBackendName = BackendConfig.getString("default")
   private val BackendProviders = BackendConfig.getConfig("providers")
-  private val BackendNames: Set[String] = BackendProviders.entrySet().asScala.map(_.getKey.split("\\.").toSeq.head).toSet
+  private val BackendNames: Set[String] =
+    BackendProviders.entrySet().asScala.map(_.getKey.split("\\.").toSeq.head).toSet
 
   val AllBackendEntries: List[BackendConfigurationEntry] = BackendNames.toList map { backendName =>
     val entry = BackendProviders.getConfig(backendName)
@@ -33,14 +35,17 @@ object BackendConfiguration {
   }
 
   val DefaultBackendEntry: BackendConfigurationEntry = AllBackendEntries.find(_.name == DefaultBackendName) getOrElse {
-    throw new IllegalArgumentException(s"Could not find specified default backend name '$DefaultBackendName' " +
-      s"in '${BackendNames.mkString("', '")}'.")
+    throw new IllegalArgumentException(
+      s"Could not find specified default backend name '$DefaultBackendName' " +
+        s"in '${BackendNames.mkString("', '")}'."
+    )
   }
 
-  def backendConfigurationDescriptor(backendName: String): Try[BackendConfigurationDescriptor] = {
-    AllBackendEntries.collect({case entry if entry.name.equalsIgnoreCase(backendName) => entry.asBackendConfigurationDescriptor}).headOption match {
+  def backendConfigurationDescriptor(backendName: String): Try[BackendConfigurationDescriptor] =
+    AllBackendEntries.collect {
+      case entry if entry.name.equalsIgnoreCase(backendName) => entry.asBackendConfigurationDescriptor
+    }.headOption match {
       case Some(descriptor) => Success(descriptor)
       case None => Failure(new Exception(s"invalid backend: $backendName"))
     }
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/backend/CromwellBackends.scala b/engine/src/main/scala/cromwell/engine/backend/CromwellBackends.scala
index 24eb59d2d95..09acd74476a 100644
--- a/engine/src/main/scala/cromwell/engine/backend/CromwellBackends.scala
+++ b/engine/src/main/scala/cromwell/engine/backend/CromwellBackends.scala
@@ -11,11 +11,11 @@ import cromwell.backend.BackendLifecycleActorFactory
 case class CromwellBackends(backendEntries: List[BackendConfigurationEntry]) {
 
   // Raise the exception here if some backend factories failed to instantiate
-  val backendLifecycleActorFactories = TryUtil.sequenceMap(backendEntries.map(e => e.name -> e.asBackendLifecycleActorFactory).toMap).get
+  val backendLifecycleActorFactories =
+    TryUtil.sequenceMap(backendEntries.map(e => e.name -> e.asBackendLifecycleActorFactory).toMap).get
 
-  def backendLifecycleActorFactoryByName(backendName: String): ErrorOr[BackendLifecycleActorFactory] = {
+  def backendLifecycleActorFactoryByName(backendName: String): ErrorOr[BackendLifecycleActorFactory] =
     backendLifecycleActorFactories.get(backendName).toValidNel(s"Backend $backendName was not found")
-  }
 
   def isValidBackendName(name: String): Boolean = backendLifecycleActorFactories.contains(name)
 }
@@ -24,21 +24,17 @@ object CromwellBackends {
 
   var instance: Option[CromwellBackends] = None
 
-
   def isValidBackendName(name: String): Boolean = evaluateIfInitialized(_.isValidBackendName(name))
 
-  def backendLifecycleFactoryActorByName(backendName: String): ErrorOr[BackendLifecycleActorFactory] = {
+  def backendLifecycleFactoryActorByName(backendName: String): ErrorOr[BackendLifecycleActorFactory] =
     evaluateIfInitialized(_.backendLifecycleActorFactoryByName(backendName))
-  }
 
-  private def evaluateIfInitialized[A](func: CromwellBackends => A): A = {
+  private def evaluateIfInitialized[A](func: CromwellBackends => A): A =
     instance match {
       case Some(cromwellBackend) => func(cromwellBackend)
       case None => throw new Exception("Cannot use CromwellBackend until initBackends is called")
     }
-  }
 
-  def initBackends(backendEntries: List[BackendConfigurationEntry]): Unit = {
+  def initBackends(backendEntries: List[BackendConfigurationEntry]): Unit =
     instance = Option(CromwellBackends(backendEntries))
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/engine.scala b/engine/src/main/scala/cromwell/engine/engine.scala
index 1c282aab703..e5971622beb 100644
--- a/engine/src/main/scala/cromwell/engine/engine.scala
+++ b/engine/src/main/scala/cromwell/engine/engine.scala
@@ -13,7 +13,9 @@ final case class CallAttempt(fqn: FullyQualifiedName, attempt: Int)
 object WorkflowFailureMode {
   def tryParse(mode: String): Try[WorkflowFailureMode] = {
     val modes = Seq(ContinueWhilePossible, NoNewCalls)
-    modes find { _.toString.equalsIgnoreCase(mode) } map { Success(_) } getOrElse Failure(new Exception(s"Invalid workflow failure mode: $mode"))
+    modes find { _.toString.equalsIgnoreCase(mode) } map { Success(_) } getOrElse Failure(
+      new Exception(s"Invalid workflow failure mode: $mode")
+    )
   }
 }
 sealed trait WorkflowFailureMode {
diff --git a/engine/src/main/scala/cromwell/engine/instrumentation/HttpInstrumentation.scala b/engine/src/main/scala/cromwell/engine/instrumentation/HttpInstrumentation.scala
index 2c909e1f776..aa65d6506be 100644
--- a/engine/src/main/scala/cromwell/engine/instrumentation/HttpInstrumentation.scala
+++ b/engine/src/main/scala/cromwell/engine/instrumentation/HttpInstrumentation.scala
@@ -18,29 +18,31 @@ object HttpInstrumentation {
 }
 
 trait HttpInstrumentation extends CromwellInstrumentation {
-  
-  private def makeRequestPath(httpRequest: HttpRequest, httpResponse: HttpResponse): InstrumentationPath = NonEmptyList.of(
-    // Returns the path of the URI only, without query parameters (e.g: api/engine/workflows/metadata)
-    httpRequest.uri.path.toString().stripPrefix("/")
-      // Replace UUIDs with [id] to keep paths same regardless of the workflow
-      .replaceAll(HttpInstrumentation.UUIDRegex, "[id]"),
-    // Name of the method (e.g: GET)
-    httpRequest.method.value,
-    // Status code of the Response (e.g: 200)
-    httpResponse.status.intValue.toString
-  )
 
-  private def sendTimingApi(statsDPath: InstrumentationPath, timing: FiniteDuration) = {
+  private def makeRequestPath(httpRequest: HttpRequest, httpResponse: HttpResponse): InstrumentationPath =
+    NonEmptyList.of(
+      // Returns the path of the URI only, without query parameters (e.g: api/engine/workflows/metadata)
+      httpRequest.uri.path
+        .toString()
+        .stripPrefix("/")
+        // Replace UUIDs with [id] to keep paths same regardless of the workflow
+        .replaceAll(HttpInstrumentation.UUIDRegex, "[id]"),
+      // Name of the method (e.g: GET)
+      httpRequest.method.value,
+      // Status code of the Response (e.g: 200)
+      httpResponse.status.intValue.toString
+    )
+
+  private def sendTimingApi(statsDPath: InstrumentationPath, timing: FiniteDuration) =
     sendTiming(statsDPath, timing, ApiPrefix)
-  }
 
   def instrumentRequest: Directive0 = extractRequest flatMap { request =>
     val timeStamp = System.currentTimeMillis
     mapResponse { response =>
       /*
-        * Send a metric corresponding to the request response time.
-        * Note: The current StatsD implementation always pairs a timing metric with a counter metric
-        * So no need to explicitly send one
+       * Send a metric corresponding to the request response time.
+       * Note: The current StatsD implementation always pairs a timing metric with a counter metric
+       * So no need to explicitly send one
        */
       sendTimingApi(makeRequestPath(request, response), (System.currentTimeMillis - timeStamp).millis)
       response
diff --git a/engine/src/main/scala/cromwell/engine/instrumentation/IoInstrumentation.scala b/engine/src/main/scala/cromwell/engine/instrumentation/IoInstrumentation.scala
index 15d799d222b..ba0c4591c91 100644
--- a/engine/src/main/scala/cromwell/engine/instrumentation/IoInstrumentation.scala
+++ b/engine/src/main/scala/cromwell/engine/instrumentation/IoInstrumentation.scala
@@ -27,6 +27,7 @@ private object IoInstrumentationImplicits {
     * Augments IoResult to provide instrumentation conversion methods
     */
   implicit class InstrumentedIoResult(val ioResult: IoResult) extends AnyVal {
+
     /**
       * Returns the instrumentation path of this IoResult
       */
@@ -34,6 +35,7 @@ private object IoInstrumentationImplicits {
       case (_: IoSuccess[_], ioCommandContext) => ioCommandContext.request.successPath
       case (f: IoFailAck[_], ioCommandContext) => ioCommandContext.request.failedPath(f.failure)
     }
+
     /**
       * Returns the instrumentation path of this IoResult
       */
@@ -44,19 +46,22 @@ private object IoInstrumentationImplicits {
     * Augments IoCommand to provide instrumentation conversion methods
     */
   implicit class InstrumentedIoCommand(val ioCommand: IoCommand[_]) extends AnyVal {
+
     /**
       * Returns the instrumentation path of this IoCommand
       */
     def toPath: InstrumentationPath = {
       val path = ioCommand match {
-        case copy: IoCopyCommand => (copy.source, copy.destination) match {
-          case (_: GcsPath, _) | (_, _: GcsPath) => GcsPath
-          case _ => LocalPath
-        }
-        case singleFileCommand: SingleFileIoCommand[_] => singleFileCommand.file match {
-          case _: GcsPath => GcsPath
-          case _ => LocalPath
-        }
+        case copy: IoCopyCommand =>
+          (copy.source, copy.destination) match {
+            case (_: GcsPath, _) | (_, _: GcsPath) => GcsPath
+            case _ => LocalPath
+          }
+        case singleFileCommand: SingleFileIoCommand[_] =>
+          singleFileCommand.file match {
+            case _: GcsPath => GcsPath
+            case _ => LocalPath
+          }
         case _ => UnknownFileSystemPath
       }
 
@@ -71,16 +76,14 @@ private object IoInstrumentationImplicits {
     /**
       * Returns a failed instrumentation path for this IoCommand provided a throwable
       */
-    def failedPath(failure: Throwable): InstrumentationPath = {
+    def failedPath(failure: Throwable): InstrumentationPath =
       ioCommand.toPath.concatNel(FailureKey).withStatusCodeFailure(GoogleUtil.extractStatusCode(failure))
-    }
 
     /**
       * Returns a retried instrumentation path for this IoCommand provided a throwable
       */
-    def retriedPath(failure: Throwable): InstrumentationPath = {
+    def retriedPath(failure: Throwable): InstrumentationPath =
       ioCommand.toPath.concatNel(RetryKey).withStatusCodeFailure(GoogleUtil.extractStatusCode(failure))
-    }
   }
 }
 
@@ -100,7 +103,9 @@ trait IoInstrumentation extends CromwellInstrumentationActor { this: Actor =>
     */
   final def instrumentIoResult(ioResult: IoResult): Unit = {
     incrementIo(ioResult.toCounterPath)
-    sendTiming(ioResult.toDurationPath, (OffsetDateTime.now.toEpochSecond - ioResult._2.creationTime.toEpochSecond).seconds)
+    sendTiming(ioResult.toDurationPath,
+               (OffsetDateTime.now.toEpochSecond - ioResult._2.creationTime.toEpochSecond).seconds
+    )
   }
 
   final def incrementBackpressure(): Unit = incrementIo(backpressure)
@@ -108,5 +113,7 @@ trait IoInstrumentation extends CromwellInstrumentationActor { this: Actor =>
   /**
     * Increment an IoCommand to the proper bucket depending on the request type.
     */
-  final def incrementIoRetry(ioCommand: IoCommand[_], failure: Throwable): Unit = incrementIo(ioCommand.retriedPath(failure))
+  final def incrementIoRetry(ioCommand: IoCommand[_], failure: Throwable): Unit = incrementIo(
+    ioCommand.retriedPath(failure)
+  )
 }
diff --git a/engine/src/main/scala/cromwell/engine/instrumentation/JobInstrumentation.scala b/engine/src/main/scala/cromwell/engine/instrumentation/JobInstrumentation.scala
index 91613a7c2cb..49e479e7b3d 100644
--- a/engine/src/main/scala/cromwell/engine/instrumentation/JobInstrumentation.scala
+++ b/engine/src/main/scala/cromwell/engine/instrumentation/JobInstrumentation.scala
@@ -35,25 +35,21 @@ trait JobInstrumentation extends CromwellInstrumentationActor { this: Actor =>
   /**
     * Generic method to add a workflow related timing metric value
     */
-  def setTimingJob(statsDPath: InstrumentationPath, duration: FiniteDuration): Unit = {
+  def setTimingJob(statsDPath: InstrumentationPath, duration: FiniteDuration): Unit =
     sendTiming(statsDPath, duration, JobPrefix)
-  }
 
   /**
     * Generic method to update a job related gauge metric value
     */
-  def sendGaugeJob(statsDPath: InstrumentationPath, value: Long): Unit = {
+  def sendGaugeJob(statsDPath: InstrumentationPath, value: Long): Unit =
     sendGauge(statsDPath, value, JobPrefix)
-  }
 
   /**
     * Add a timing value for the run time of a job in a given state
     */
-  def setJobTimePerState(response: BackendJobExecutionResponse, duration: FiniteDuration): Unit = {
+  def setJobTimePerState(response: BackendJobExecutionResponse, duration: FiniteDuration): Unit =
     setTimingJob(backendJobExecutionResponsePaths(response), duration)
-  }
-  
-  def recordExecutionStepTiming(state: String, duration: FiniteDuration): Unit = {
+
+  def recordExecutionStepTiming(state: String, duration: FiniteDuration): Unit =
     sendTiming(jobTimingKey.concatNel("state").concatNel(state), duration, JobPrefix)
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/instrumentation/WorkflowInstrumentation.scala b/engine/src/main/scala/cromwell/engine/instrumentation/WorkflowInstrumentation.scala
index ac9d28a9eb6..a9272bcf7d3 100644
--- a/engine/src/main/scala/cromwell/engine/instrumentation/WorkflowInstrumentation.scala
+++ b/engine/src/main/scala/cromwell/engine/instrumentation/WorkflowInstrumentation.scala
@@ -13,8 +13,9 @@ import scala.concurrent.duration.FiniteDuration
 import scala.language.postfixOps
 
 object WorkflowInstrumentation {
-  private val WorkflowStatePaths: Map[WorkflowState, InstrumentationPath] = WorkflowState.WorkflowStateValues map { state =>
-    state -> NonEmptyList.of(state.toString)
+  private val WorkflowStatePaths: Map[WorkflowState, InstrumentationPath] = WorkflowState.WorkflowStateValues map {
+    state =>
+      state -> NonEmptyList.of(state.toString)
   } toMap
 
   // Use "Queued" instead of "Submitted" as it seems to reflect better the actual state
@@ -28,43 +29,39 @@ object WorkflowInstrumentation {
   * Provides helper methods for workflow instrumentation
   */
 trait WorkflowInstrumentation extends CromwellInstrumentationActor { this: Actor =>
-  private def workflowStatePath(workflowState: WorkflowState): InstrumentationPath = WorkflowInstrumentation.WorkflowStatePaths(workflowState)
+  private def workflowStatePath(workflowState: WorkflowState): InstrumentationPath =
+    WorkflowInstrumentation.WorkflowStatePaths(workflowState)
 
   /**
     * Generic method to increment a workflow related counter metric value
     */
-  def incrementWorkflow(statsDPath: InstrumentationPath): Unit = {
+  def incrementWorkflow(statsDPath: InstrumentationPath): Unit =
     increment(statsDPath, WorkflowPrefix)
-  }
 
   /**
     * Generic method to add a workflow related timing metric value
     */
-  def setTimingWorkflow(statsDPath: InstrumentationPath, duration: FiniteDuration): Unit = {
+  def setTimingWorkflow(statsDPath: InstrumentationPath, duration: FiniteDuration): Unit =
     sendTiming(statsDPath, duration, WorkflowPrefix)
-  }
 
   /**
     * Generic method to update a workflow related gauge metric value
     */
-  def sendGaugeWorkflow(statsDPath: InstrumentationPath, value: Long): Unit = {
+  def sendGaugeWorkflow(statsDPath: InstrumentationPath, value: Long): Unit =
     sendGauge(statsDPath, value, WorkflowPrefix)
-  }
 
   /**
     * Counts every time a workflow enters a given state
     */
-  def incrementWorkflowState(workflowState: WorkflowState): Unit = {
+  def incrementWorkflowState(workflowState: WorkflowState): Unit =
     incrementWorkflow(workflowStatePath(workflowState))
-  }
 
   /**
     * Add a timing value for the run time of a workflow in a given state
     */
-  //* TODO: enforce a terminal state ?
-  def setWorkflowTimePerState(workflowState: WorkflowState, duration: FiniteDuration): Unit = {
+  // * TODO: enforce a terminal state ?
+  def setWorkflowTimePerState(workflowState: WorkflowState, duration: FiniteDuration): Unit =
     setTimingWorkflow(workflowStatePath(workflowState), duration)
-  }
 
   /**
     * Set the current number of submitted workflows (queued but not running)
diff --git a/engine/src/main/scala/cromwell/engine/io/IoActor.scala b/engine/src/main/scala/cromwell/engine/io/IoActor.scala
index 80a362a7b78..5d69ba844a0 100644
--- a/engine/src/main/scala/cromwell/engine/io/IoActor.scala
+++ b/engine/src/main/scala/cromwell/engine/io/IoActor.scala
@@ -27,7 +27,6 @@ import java.time.temporal.ChronoUnit
 import scala.concurrent.ExecutionContext
 import scala.concurrent.duration._
 
-
 /**
   * Actor that performs IO operations asynchronously using akka streams
   * 
@@ -35,26 +34,28 @@ import scala.concurrent.duration._
   * @param materializer actor materializer to run the stream
   * @param serviceRegistryActor actorRef for the serviceRegistryActor
   */
-final class IoActor(ioConfig: IoConfig,
-                    override val serviceRegistryActor: ActorRef,
-                    applicationName: String)(implicit val materializer: ActorMaterializer)
-  extends Actor with ActorLogging with StreamActorHelper[IoCommandContext[_]] with IoInstrumentation with Timers {
+final class IoActor(ioConfig: IoConfig, override val serviceRegistryActor: ActorRef, applicationName: String)(implicit
+  val materializer: ActorMaterializer
+) extends Actor
+    with ActorLogging
+    with StreamActorHelper[IoCommandContext[_]]
+    with IoInstrumentation
+    with Timers {
   implicit val ec: ExecutionContext = context.dispatcher
   implicit val system: ActorSystem = context.system
 
   // IntelliJ disapproves of mutable state in Actors, but this should be safe as long as access occurs only in
   // the `receive` method. Alternatively IntelliJ does suggest a `become` workaround we might try in the future.
 
-  //noinspection ActorMutableStateInspection
+  // noinspection ActorMutableStateInspection
   private var backpressureExpiration: Option[OffsetDateTime] = None
 
   /**
     * Method for instrumentation to be executed when a IoCommand failed and is being retried.
     * Can be passed to flows so they can invoke it when necessary.
     */
-  private def onRetry(commandContext: IoCommandContext[_])(throwable: Throwable): Unit = {
+  private def onRetry(commandContext: IoCommandContext[_])(throwable: Throwable): Unit =
     incrementIoRetry(commandContext.request, throwable)
-  }
 
   override def preStart(): Unit = {
     // On start up, let the controller know that the load is normal
@@ -62,25 +63,25 @@ final class IoActor(ioConfig: IoConfig,
     super.preStart()
   }
 
-  private [io] lazy val defaultFlow =
+  private[io] lazy val defaultFlow =
     new NioFlow(
       parallelism = ioConfig.nio.parallelism,
       onRetryCallback = onRetry,
       onBackpressure = onBackpressure,
       numberOfAttempts = ioConfig.numberOfAttempts,
-      commandBackpressureStaleness = ioConfig.commandBackpressureStaleness)
-      .flow
+      commandBackpressureStaleness = ioConfig.commandBackpressureStaleness
+    ).flow
       .withAttributes(ActorAttributes.dispatcher(Dispatcher.IoDispatcher))
 
-  private [io] lazy val gcsBatchFlow =
+  private[io] lazy val gcsBatchFlow =
     new ParallelGcsBatchFlow(
       config = ioConfig.gcsBatch,
       scheduler = context.system.scheduler,
       onRetry = onRetry,
       onBackpressure = onBackpressure,
       applicationName = applicationName,
-      commandBackpressureStaleness = ioConfig.commandBackpressureStaleness)
-      .flow
+      commandBackpressureStaleness = ioConfig.commandBackpressureStaleness
+    ).flow
       .withAttributes(ActorAttributes.dispatcher(Dispatcher.IoDispatcher))
 
   private val source = Source.queue[IoCommandContext[_]](ioConfig.queueSize, OverflowStrategy.dropNew)
@@ -91,10 +92,14 @@ final class IoActor(ioConfig: IoConfig,
     val input = builder.add(Flow[IoCommandContext[_]])
 
     // Partitions requests between gcs batch, and single nio requests
-    val batchPartitioner = builder.add(Partition[IoCommandContext[_]](2, {
-      case _: GcsBatchCommandContext[_, _] => 0
-      case _ => 1
-    }))
+    val batchPartitioner = builder.add(
+      Partition[IoCommandContext[_]](2,
+                                     {
+                                       case _: GcsBatchCommandContext[_, _] => 0
+                                       case _ => 1
+                                     }
+      )
+    )
 
     // Sub flow for batched gcs requests
     val batches = batchPartitioner.out(0) collect { case batch: GcsBatchCommandContext[_, _] => batch }
@@ -112,8 +117,8 @@ final class IoActor(ioConfig: IoConfig,
     val batchFlowPorts = builder.add(gcsBatchFlow)
 
     input ~> batchPartitioner
-             defaults.outlet ~> defaultFlowPorts ~> merger
-             batches.outlet ~> batchFlowPorts ~> merger
+    defaults.outlet ~> defaultFlowPorts ~> merger
+    batches.outlet ~> batchFlowPorts ~> merger
 
     FlowShape[IoCommandContext[_], IoResult](input.in, merger.out)
   }
@@ -149,11 +154,11 @@ final class IoActor(ioConfig: IoConfig,
     /* GCS Batch command with context */
     case (clientContext: Any, gcsBatchCommand: GcsBatchIoCommand[_, _]) =>
       val replyTo = sender()
-      val commandContext = GcsBatchCommandContext(
-        request = gcsBatchCommand,
-        maxAttemptsNumber = ioConfig.numberOfAttempts,
-        replyTo = replyTo,
-        clientContext = Option(clientContext))
+      val commandContext = GcsBatchCommandContext(request = gcsBatchCommand,
+                                                  maxAttemptsNumber = ioConfig.numberOfAttempts,
+                                                  replyTo = replyTo,
+                                                  clientContext = Option(clientContext)
+      )
       sendToStream(commandContext)
 
     /* GCS Batch command without context */
@@ -202,7 +207,10 @@ final class IoActor(ioConfig: IoConfig,
           }
 
           val newExpiration = OffsetDateTime.now().until(proposedExpiry, ChronoUnit.MILLIS)
-          timers.startSingleTimer(BackPressureTimerResetKey, BackPressureTimerResetAction, FiniteDuration(newExpiration, MILLISECONDS))
+          timers.startSingleTimer(BackPressureTimerResetKey,
+                                  BackPressureTimerResetAction,
+                                  FiniteDuration(newExpiration, MILLISECONDS)
+          )
           backpressureExpiration = Option(proposedExpiry)
 
         case _ => // Ignore proposed expiries that would be before the current expiry
@@ -220,7 +228,8 @@ trait IoCommandContext[T] extends StreamContext {
   def request: IoCommand[T]
   def replyTo: ActorRef
   def fail(failure: Throwable): IoResult = (request.fail(failure), this)
-  def failReadForbidden(failure: Throwable, forbiddenPath: String): IoResult = (request.failReadForbidden(failure, forbiddenPath), this)
+  def failReadForbidden(failure: Throwable, forbiddenPath: String): IoResult =
+    (request.failReadForbidden(failure, forbiddenPath), this)
   def success(value: T): IoResult = (request.success(value), this)
 }
 
@@ -234,7 +243,10 @@ object IoActor {
   /** Result type of an IoFlow, contains the original command context and the final IoAck response. */
   type IoResult = (IoAck[_], IoCommandContext[_])
 
-  case class DefaultCommandContext[T](request: IoCommand[T], replyTo: ActorRef, override val clientContext: Option[Any] = None) extends IoCommandContext[T]
+  case class DefaultCommandContext[T](request: IoCommand[T],
+                                      replyTo: ActorRef,
+                                      override val clientContext: Option[Any] = None
+  ) extends IoCommandContext[T]
 
   case object BackPressureTimerResetKey
 
@@ -242,13 +254,10 @@ object IoActor {
 
   case class BackPressure(duration: FiniteDuration) extends ControlMessage
 
-  def props(ioConfig: IoConfig,
-            serviceRegistryActor: ActorRef,
-            applicationName: String,
-           )
-           (implicit materializer: ActorMaterializer): Props = {
+  def props(ioConfig: IoConfig, serviceRegistryActor: ActorRef, applicationName: String)(implicit
+    materializer: ActorMaterializer
+  ): Props =
     Props(new IoActor(ioConfig, serviceRegistryActor, applicationName)).withDispatcher(IoDispatcher)
-  }
 
   case class IoConfig(queueSize: Int,
                       numberOfAttempts: Int,
@@ -258,7 +267,8 @@ object IoActor {
                       ioNormalWindowMaximum: FiniteDuration,
                       nio: NioFlowConfig,
                       gcsBatch: GcsBatchFlowConfig,
-                      throttle: Option[Throttle])
+                      throttle: Option[Throttle]
+  )
 
   implicit val ioConfigReader: ValueReader[IoConfig] = (config: Config, _: String) => {
 
diff --git a/engine/src/main/scala/cromwell/engine/io/IoActorProxy.scala b/engine/src/main/scala/cromwell/engine/io/IoActorProxy.scala
index 5491440a979..c8ed10ca86b 100644
--- a/engine/src/main/scala/cromwell/engine/io/IoActorProxy.scala
+++ b/engine/src/main/scala/cromwell/engine/io/IoActorProxy.scala
@@ -14,7 +14,8 @@ object IoActorProxy {
 }
 
 class IoActorProxy(ioActor: ActorRef) extends Actor with ActorLogging with GracefulShutdownHelper {
-  private val cache = CacheBuilder.newBuilder()
+  private val cache = CacheBuilder
+    .newBuilder()
     .build[IoCommandWithPromise[_], IoResult]()
 
   private val ioPromiseProxyActor: ActorRef = context.actorOf(IoPromiseProxyActor.props(ioActor), "IoPromiseProxyActor")
@@ -31,7 +32,7 @@ class IoActorProxy(ioActor: ActorRef) extends Actor with ActorLogging with Grace
     case ioCommand: IoCommand[_] => ioActor forward ioCommand
     case withContext: (Any, IoCommand[_]) @unchecked => ioActor forward withContext
 
-    case ShutdownCommand => 
+    case ShutdownCommand =>
       context stop ioPromiseProxyActor
       waitForActorsAndShutdown(NonEmptyList.one(ioActor))
   }
diff --git a/engine/src/main/scala/cromwell/engine/io/IoAttempts.scala b/engine/src/main/scala/cromwell/engine/io/IoAttempts.scala
index d43e003ecb1..a51112029e9 100644
--- a/engine/src/main/scala/cromwell/engine/io/IoAttempts.scala
+++ b/engine/src/main/scala/cromwell/engine/io/IoAttempts.scala
@@ -7,18 +7,18 @@ import org.apache.commons.lang3.exception.ExceptionUtils
 
 object IoAttempts {
   object EnhancedCromwellIoException {
-    def apply[S](state: S, cause: Throwable)(implicit showState: Show[S]): EnhancedCromwellIoException = {
+    def apply[S](state: S, cause: Throwable)(implicit showState: Show[S]): EnhancedCromwellIoException =
       EnhancedCromwellIoException(s"[${showState.show(state)}] - ${ExceptionUtils.getMessage(cause)}", cause)
-    }
   }
-  
-  case class EnhancedCromwellIoException(message: String, cause: Throwable) 
-    extends Throwable(message, cause, true, false) with CromwellFatalExceptionMarker
-  
+
+  case class EnhancedCromwellIoException(message: String, cause: Throwable)
+      extends Throwable(message, cause, true, false)
+      with CromwellFatalExceptionMarker
+
   implicit val showState = new Show[IoAttempts] {
     override def show(t: IoAttempts) = s"Attempted ${t.attempts} time(s)"
   }
-  
+
   implicit val stateToThrowable = new StatefulIoError[IoAttempts] {
     override def toThrowable(state: IoAttempts, throwable: Throwable) = {
       state.throwables.foreach(throwable.addSuppressed)
@@ -26,9 +26,8 @@ object IoAttempts {
     }
   }
 
-  val updateState: (Throwable, IoAttempts) => IoAttempts = (throwable, state) => {
+  val updateState: (Throwable, IoAttempts) => IoAttempts = (throwable, state) =>
     state.copy(attempts = state.attempts + 1, throwables = state.throwables :+ throwable)
-  }
 }
 
 case class IoAttempts(attempts: Int, throwables: List[Throwable] = List.empty)
diff --git a/engine/src/main/scala/cromwell/engine/io/IoCommandStalenessBackpressuring.scala b/engine/src/main/scala/cromwell/engine/io/IoCommandStalenessBackpressuring.scala
index e8ceda43656..47591516d7b 100644
--- a/engine/src/main/scala/cromwell/engine/io/IoCommandStalenessBackpressuring.scala
+++ b/engine/src/main/scala/cromwell/engine/io/IoCommandStalenessBackpressuring.scala
@@ -19,17 +19,18 @@ trait IoCommandStalenessBackpressuring extends StrictLogging {
 
     val seconds = millis / 1000.0
     logger.info("I/O command {} seconds stale, applying I/O subsystem backpressure with scale {}",
-      f"$seconds%,.3f", f"$scale%.2f")
+                f"$seconds%,.3f",
+                f"$scale%.2f"
+    )
 
     onBackpressure(Option(scale))
   }
 
   /** Invokes `onBackpressure` if `ioCommand` is older than the staleness limit returned by `maxStaleness`. */
-  def backpressureIfStale(ioCommand: IoCommand[_], onBackpressure: Option[Double] => Unit): Unit = {
+  def backpressureIfStale(ioCommand: IoCommand[_], onBackpressure: Option[Double] => Unit): Unit =
     if (ioCommand.creation.isBefore(commandStalenessThreshold)) {
       logAndBackpressure(ioCommand, onBackpressure)
     }
-  }
 
   /** Invokes `onBackpressure` if at least one IoCommandContext in `contexts` is older than the
     * staleness limit returned by `maxStaleness`. */
diff --git a/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala b/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
index d2aa427a567..1a75bdd4c15 100644
--- a/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
+++ b/engine/src/main/scala/cromwell/engine/io/RetryableRequestSupport.scala
@@ -15,17 +15,19 @@ object RetryableRequestSupport {
     * The default count is `5` and may be customized with `system.io.number-of-attempts`.
     */
   def isRetryable(failure: Throwable): Boolean = failure match {
-    case gcs: StorageException => gcs.isRetryable ||
+    case gcs: StorageException =>
+      gcs.isRetryable ||
       isRetryable(gcs.getCause) ||
       AdditionalRetryableHttpCodes.contains(gcs.getCode) ||
-      Option(gcs.getMessage).exists(msg =>
-        AdditionalRetryableErrorMessages.contains(msg.toLowerCase))
+      Option(gcs.getMessage).exists(msg => AdditionalRetryableErrorMessages.contains(msg.toLowerCase))
     case _: SSLException => true
     case _: BatchFailedException => true
     case _: ChecksumFailedException => true
     case _: SocketException => true
     case _: SocketTimeoutException => true
-    case ioE: IOException if Option(ioE.getMessage).exists(_.contains("Error getting access token for service account")) => true
+    case ioE: IOException
+        if Option(ioE.getMessage).exists(_.contains("Error getting access token for service account")) =>
+      true
     case ioE: IOException => isGcs500(ioE) || isGcs503(ioE) || isGcs504(ioE)
     case other =>
       // Infinitely retryable is a subset of retryable
@@ -68,24 +70,21 @@ object RetryableRequestSupport {
     isGcsRateLimitException(failure)
   }
 
-  def isGcs500(failure: Throwable): Boolean = {
+  def isGcs500(failure: Throwable): Boolean =
     Option(failure.getMessage).exists(msg =>
       msg.contains("Could not read from gs") &&
-      msg.contains("500 Internal Server Error")
+        msg.contains("500 Internal Server Error")
     )
-  }
 
-  def isGcs503(failure: Throwable): Boolean = {
+  def isGcs503(failure: Throwable): Boolean =
     Option(failure.getMessage).exists(msg =>
       msg.contains("Could not read from gs") &&
-      msg.contains("503 Service Unavailable")
+        msg.contains("503 Service Unavailable")
     )
-  }
 
-  def isGcs504(failure: Throwable): Boolean = {
+  def isGcs504(failure: Throwable): Boolean =
     Option(failure.getMessage).exists(msg =>
       msg.contains("Could not read from gs") &&
-      msg.contains("504 Gateway Timeout")
+        msg.contains("504 Gateway Timeout")
     )
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/io/gcs/GcsBatchCommandContext.scala b/engine/src/main/scala/cromwell/engine/io/gcs/GcsBatchCommandContext.scala
index d41b0539dc6..27f6afe4299 100644
--- a/engine/src/main/scala/cromwell/engine/io/gcs/GcsBatchCommandContext.scala
+++ b/engine/src/main/scala/cromwell/engine/io/gcs/GcsBatchCommandContext.scala
@@ -34,7 +34,7 @@ object GcsBatchCommandContext {
       .setInitialIntervalMillis(1.second.toMillis.toInt)
       .setMultiplier(4)
       .setMaxIntervalMillis(30.seconds.toMillis.toInt)
-      .setRandomizationFactor(0.2D)
+      .setRandomizationFactor(0.2d)
       .setMaxElapsedTimeMillis(30.minutes.toMillis.toInt)
       .build()
   )
@@ -48,14 +48,14 @@ final case class GcsBatchCommandContext[T, U](request: GcsBatchIoCommand[T, U],
                                               backoff: Backoff = GcsBatchCommandContext.defaultBackoff,
                                               currentAttempt: Int = 1,
                                               promise: Promise[BatchResponse] = Promise[BatchResponse]()
-                                             )
-  extends IoCommandContext[T]
-  with StrictLogging {
+) extends IoCommandContext[T]
+    with StrictLogging {
 
   /**
     * None if no retry should be attempted, Some(timeToWaitBeforeNextAttempt) otherwise
     */
-  lazy val retryIn: Option[FiniteDuration] = if (currentAttempt >= maxAttemptsNumber) None else Option(backoff.backoffMillis milliseconds)
+  lazy val retryIn: Option[FiniteDuration] =
+    if (currentAttempt >= maxAttemptsNumber) None else Option(backoff.backoffMillis milliseconds)
 
   /**
     * Json batch call back for a batched request
@@ -63,19 +63,20 @@ final case class GcsBatchCommandContext[T, U](request: GcsBatchIoCommand[T, U],
   lazy val callback: JsonBatchCallback[U] = new JsonBatchCallback[U]() {
     // These callbacks are only called once, therefore it's imperative that they set the promise value before exiting.
     // This tryCallbackOrFail ensures that if the callback function itself errors, we get _some_ result back on the future.
-    def onSuccess(response: U, httpHeaders: HttpHeaders): Unit = tryCallbackOrFail("onSuccessCallback", onSuccessCallback(response, httpHeaders))
-    def onFailure(googleJsonError: GoogleJsonError, httpHeaders: HttpHeaders): Unit = tryCallbackOrFail(callbackName = "onFailureCallback", onFailureCallback(googleJsonError, httpHeaders))
+    def onSuccess(response: U, httpHeaders: HttpHeaders): Unit =
+      tryCallbackOrFail("onSuccessCallback", onSuccessCallback(response, httpHeaders))
+    def onFailure(googleJsonError: GoogleJsonError, httpHeaders: HttpHeaders): Unit =
+      tryCallbackOrFail(callbackName = "onFailureCallback", onFailureCallback(googleJsonError, httpHeaders))
   }
 
   def tryCallbackOrFail(callbackName: String, callback: () => Unit): Unit = {
     Try {
       callback.apply()
-    }.recover {
-      case t =>
-        // Ideally we would catch and handle the cases which might lead us here before they actually get this far:
-        logger.error(s"Programmer Error: Error processing IO response in $callbackName", t)
-        promise.tryFailure(new Exception(s"Error processing IO response in $callbackName: ${t.getMessage}"))
-        ()
+    }.recover { case t =>
+      // Ideally we would catch and handle the cases which might lead us here before they actually get this far:
+      logger.error(s"Programmer Error: Error processing IO response in $callbackName", t)
+      promise.tryFailure(new Exception(s"Error processing IO response in $callbackName: ${t.getMessage}"))
+      ()
     }
     ()
   }
@@ -83,16 +84,14 @@ final case class GcsBatchCommandContext[T, U](request: GcsBatchIoCommand[T, U],
   /**
     * Increment backoff time and attempt count
     */
-  lazy val next: GcsBatchCommandContext[T, U] = {
+  lazy val next: GcsBatchCommandContext[T, U] =
     this.copy(backoff = backoff.next, currentAttempt = currentAttempt + 1, promise = Promise[BatchResponse]())
-  }
 
   /**
     * Only increment backoff. To be used for failures that should be retried infinitely
     */
-  lazy val nextTransient: GcsBatchCommandContext[T, U] = {
+  lazy val nextTransient: GcsBatchCommandContext[T, U] =
     this.copy(backoff = backoff.next, promise = Promise[BatchResponse]())
-  }
 
   /**
     * Queue the request for batching
@@ -106,7 +105,9 @@ final case class GcsBatchCommandContext[T, U](request: GcsBatchIoCommand[T, U],
     * On success callback. Transform the request response to a stream-ready response that can complete the promise
     */
   private def onSuccessCallback(response: U, httpHeaders: HttpHeaders)(): Unit = {
-    request.logIOMsgOverLimit(s"GcsBatchCommandContext.onSuccessCallback '${response.toPrettyElidedString(limit = 1000)}'")
+    request.logIOMsgOverLimit(
+      s"GcsBatchCommandContext.onSuccessCallback '${response.toPrettyElidedString(limit = 1000)}'"
+    )
     handleSuccessOrNextRequest(request.onSuccess(response, httpHeaders))
   }
 
@@ -131,7 +132,9 @@ final case class GcsBatchCommandContext[T, U](request: GcsBatchIoCommand[T, U],
     * On failure callback. Fail the promise with a StorageException
     */
   private def onFailureCallback(googleJsonError: GoogleJsonError, httpHeaders: HttpHeaders)(): Unit = {
-    request.logIOMsgOverLimit(s"GcsBatchCommandContext.onFailureCallback '${googleJsonError.toPrettyElidedString(limit = 1000)}'")
+    request.logIOMsgOverLimit(
+      s"GcsBatchCommandContext.onFailureCallback '${googleJsonError.toPrettyElidedString(limit = 1000)}'"
+    )
     if (isProjectNotProvidedError(googleJsonError)) {
       // Returning an Either.Right here means that the operation is not complete and that we need to do another request
       handleSuccessOrNextRequest(Right(request.withUserProject).validNel)
diff --git a/engine/src/main/scala/cromwell/engine/io/gcs/GcsBatchFlow.scala b/engine/src/main/scala/cromwell/engine/io/gcs/GcsBatchFlow.scala
index 0007b77a42f..972a52530de 100644
--- a/engine/src/main/scala/cromwell/engine/io/gcs/GcsBatchFlow.scala
+++ b/engine/src/main/scala/cromwell/engine/io/gcs/GcsBatchFlow.scala
@@ -35,7 +35,8 @@ object GcsBatchFlow {
     */
   case class BatchFailedException(failure: Throwable) extends IOException(failure)
 
-  private val ReadForbiddenPattern = ".*does not have storage\\.objects\\.(?:get|list|copy) access to ([^/]+).*".r.pattern
+  private val ReadForbiddenPattern =
+    ".*does not have storage\\.objects\\.(?:get|list|copy) access to ([^/]+).*".r.pattern
 
   /* Returns `Some(bucket)` if the specified argument represents a forbidden attempt to read from `bucket`. */
   private[gcs] def getReadForbiddenBucket(errorMsg: String): Option[String] = {
@@ -60,8 +61,9 @@ class GcsBatchFlow(batchSize: Int,
                    onRetry: IoCommandContext[_] => Throwable => Unit,
                    onBackpressure: Option[Double] => Unit,
                    applicationName: String,
-                   backpressureStaleness: FiniteDuration)
-                  (implicit ec: ExecutionContext) extends IoCommandStalenessBackpressuring {
+                   backpressureStaleness: FiniteDuration
+)(implicit ec: ExecutionContext)
+    extends IoCommandStalenessBackpressuring {
 
   // Does not carry any authentication, assumes all underlying requests are properly authenticated
   private val httpRequestInitializer = new HttpRequestInitializer {
@@ -113,9 +115,9 @@ class GcsBatchFlow(batchSize: Int,
   val flow: Graph[
     FlowShape[
       GcsBatchCommandContext[_, _],
-      (IoAck[_], IoCommandContext[_]),
+      (IoAck[_], IoCommandContext[_])
     ],
-    NotUsed,
+    NotUsed
   ] = GraphDSL.create() { implicit builder =>
     import GraphDSL.Implicits._
 
@@ -129,21 +131,22 @@ class GcsBatchFlow(batchSize: Int,
     val batchProcessor = builder.add(
       Flow[GcsBatchCommandContext[_, _]]
         // Group commands together in batches so they can be processed as such
-      .groupedWithin(batchSize, batchTimespan)
+        .groupedWithin(batchSize, batchTimespan)
         // execute the batch and outputs each sub-response individually, as a Future
-      .mapConcat[Future[GcsBatchResponse[_]]](executeBatch)
+        .mapConcat[Future[GcsBatchResponse[_]]](executeBatch)
         // Wait for each Future to complete
-      .mapAsyncUnordered[GcsBatchResponse[_]](batchSize) { identity }
+        .mapAsyncUnordered[GcsBatchResponse[_]](batchSize)(identity)
     )
 
     // Partitions the responses: Terminal responses exit the flow, others go back to the sourceMerger
     val responseHandler = builder.add(responseHandlerFlow)
 
     // Buffer commands to be retried to avoid backpressuring too rapidly
-    val nextRequestBuffer = builder.add(Flow[GcsBatchCommandContext[_, _]].buffer(batchSize, OverflowStrategy.backpressure))
+    val nextRequestBuffer =
+      builder.add(Flow[GcsBatchCommandContext[_, _]].buffer(batchSize, OverflowStrategy.backpressure))
 
     source ~> sourceMerger ~> batchProcessor ~> responseHandler.in
-              sourceMerger.preferred <~ nextRequestBuffer <~ responseHandler.out1
+    sourceMerger.preferred <~ nextRequestBuffer <~ responseHandler.out1
 
     FlowShape[GcsBatchCommandContext[_, _], IoResult](source.in, responseHandler.out0)
   }
@@ -156,10 +159,14 @@ class GcsBatchFlow(batchSize: Int,
   private lazy val responseHandlerFlow = GraphDSL.create() { implicit builder =>
     import GraphDSL.Implicits._
 
-    val source = builder.add(Partition[GcsBatchResponse[_]](2, {
-      case _: GcsBatchTerminal[_] => 0
-      case _ => 1
-    }))
+    val source = builder.add(
+      Partition[GcsBatchResponse[_]](2,
+                                     {
+                                       case _: GcsBatchTerminal[_] => 0
+                                       case _ => 1
+                                     }
+      )
+    )
 
     // Terminal responses: output of this flow
     val terminals = source.out(0) collect { case terminal: GcsBatchTerminal[_] => terminal.ioResult }
@@ -170,7 +177,10 @@ class GcsBatchFlow(batchSize: Int,
       case nextRequest: GcsBatchNextRequest[_] => nextRequest.context
     }
 
-    new FanOutShape2[GcsBatchResponse[_], IoResult, GcsBatchCommandContext[_, _]](source.in, terminals.outlet, nextRequest.outlet)
+    new FanOutShape2[GcsBatchResponse[_], IoResult, GcsBatchCommandContext[_, _]](source.in,
+                                                                                  terminals.outlet,
+                                                                                  nextRequest.outlet
+    )
   }
 
   private def executeBatch(contexts: Seq[GcsBatchCommandContext[_, _]]): List[Future[GcsBatchResponse[_]]] = {
@@ -193,12 +203,16 @@ class GcsBatchFlow(batchSize: Int,
     // Otherwise fail with the original exception
     Try(batchRequest.execute()) match {
       case Failure(failure: IOException) =>
-        logger.info(s"Failed to execute GCS Batch request. Failed request belonged to batch of size ${batchRequest.size()} containing commands: " +
-          s"${batchCommandNamesList.mkString("\n")}.\n${failure.toPrettyElidedString(limit = 1000)}")
+        logger.info(
+          s"Failed to execute GCS Batch request. Failed request belonged to batch of size ${batchRequest.size()} containing commands: " +
+            s"${batchCommandNamesList.mkString("\n")}.\n${failure.toPrettyElidedString(limit = 1000)}"
+        )
         failAllPromisesWith(BatchFailedException(failure))
       case Failure(failure) =>
-        logger.info(s"Failed to execute GCS Batch request. Failed request belonged to batch of size ${batchRequest.size()} containing commands: " +
-          s"${batchCommandNamesList.mkString("\n")}.\n${failure.toPrettyElidedString(limit = 1000)}")
+        logger.info(
+          s"Failed to execute GCS Batch request. Failed request belonged to batch of size ${batchRequest.size()} containing commands: " +
+            s"${batchCommandNamesList.mkString("\n")}.\n${failure.toPrettyElidedString(limit = 1000)}"
+        )
         failAllPromisesWith(failure)
       case _ =>
     }
@@ -219,7 +233,9 @@ class GcsBatchFlow(batchSize: Int,
     *   Otherwise create a GcsBatchTerminal response with the IoFailure
     *   In both cases, returns a successful Future to avoid failing the stream or dropping elements
     */
-  private def recoverCommand(context: GcsBatchCommandContext[_, _]): PartialFunction[Throwable, Future[GcsBatchResponse[_]]] = {
+  private def recoverCommand(
+    context: GcsBatchCommandContext[_, _]
+  ): PartialFunction[Throwable, Future[GcsBatchResponse[_]]] = {
     // If the failure is retryable - recover with a GcsBatchRetry so it can be retried in the next batch
     case failure if isRetryable(failure) =>
       context.retryIn match {
@@ -246,22 +262,22 @@ class GcsBatchFlow(batchSize: Int,
   /**
     * Fail a command context with a failure.
     */
-  private def fail(context: GcsBatchCommandContext[_, _], failure: Throwable) = {
+  private def fail(context: GcsBatchCommandContext[_, _], failure: Throwable) =
     Future.successful(
       GcsBatchTerminal(
         context.fail(EnhancedCromwellIoException(IoAttempts(context.currentAttempt), failure))
       )
     )
-  }
 
   /**
     * Fail a command context with a forbidden failure.
     */
-  private def failReadForbidden(context: GcsBatchCommandContext[_, _], failure: Throwable, forbiddenPath: String) = {
+  private def failReadForbidden(context: GcsBatchCommandContext[_, _], failure: Throwable, forbiddenPath: String) =
     Future.successful(
       GcsBatchTerminal(
-        context.failReadForbidden(EnhancedCromwellIoException(IoAttempts(context.currentAttempt), failure), forbiddenPath)
+        context.failReadForbidden(EnhancedCromwellIoException(IoAttempts(context.currentAttempt), failure),
+                                  forbiddenPath
+        )
       )
     )
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/io/gcs/GcsResponse.scala b/engine/src/main/scala/cromwell/engine/io/gcs/GcsResponse.scala
index 937e2b66063..b8a4cb4a873 100644
--- a/engine/src/main/scala/cromwell/engine/io/gcs/GcsResponse.scala
+++ b/engine/src/main/scala/cromwell/engine/io/gcs/GcsResponse.scala
@@ -6,7 +6,8 @@ import cromwell.engine.io.IoActor._
   * ADT used only inside the batch stream
   * @tparam T final type of the result of the Command
   */
-private [gcs] sealed trait GcsBatchResponse[T]
-private [gcs] case class GcsBatchTerminal[T](ioResult: IoResult) extends GcsBatchResponse[T]
-private [gcs] case class GcsBatchRetry[T](context: GcsBatchCommandContext[T, _], failure: Throwable) extends GcsBatchResponse[T]
-private [gcs] case class GcsBatchNextRequest[T](context: GcsBatchCommandContext[T, _]) extends GcsBatchResponse[T]
+sealed private[gcs] trait GcsBatchResponse[T]
+private[gcs] case class GcsBatchTerminal[T](ioResult: IoResult) extends GcsBatchResponse[T]
+private[gcs] case class GcsBatchRetry[T](context: GcsBatchCommandContext[T, _], failure: Throwable)
+    extends GcsBatchResponse[T]
+private[gcs] case class GcsBatchNextRequest[T](context: GcsBatchCommandContext[T, _]) extends GcsBatchResponse[T]
diff --git a/engine/src/main/scala/cromwell/engine/io/gcs/ParallelGcsBatchFlow.scala b/engine/src/main/scala/cromwell/engine/io/gcs/ParallelGcsBatchFlow.scala
index 3ef3548bdec..9fc5c5fc7ea 100644
--- a/engine/src/main/scala/cromwell/engine/io/gcs/ParallelGcsBatchFlow.scala
+++ b/engine/src/main/scala/cromwell/engine/io/gcs/ParallelGcsBatchFlow.scala
@@ -18,10 +18,10 @@ class ParallelGcsBatchFlow(config: GcsBatchFlowConfig,
                            onRetry: IoCommandContext[_] => Throwable => Unit,
                            onBackpressure: Option[Double] => Unit,
                            applicationName: String,
-                           commandBackpressureStaleness: FiniteDuration)
-                          (implicit ec: ExecutionContext) {
+                           commandBackpressureStaleness: FiniteDuration
+)(implicit ec: ExecutionContext) {
 
-  //noinspection TypeAnnotation
+  // noinspection TypeAnnotation
   val flow = GraphDSL.create() { implicit builder =>
     import GraphDSL.Implicits._
     val balancer = builder.add(Balance[GcsBatchCommandContext[_, _]](config.parallelism, waitForAllDownstreams = false))
@@ -35,7 +35,8 @@ class ParallelGcsBatchFlow(config: GcsBatchFlowConfig,
         onRetry = onRetry,
         onBackpressure = onBackpressure,
         applicationName = applicationName,
-        backpressureStaleness = commandBackpressureStaleness).flow
+        backpressureStaleness = commandBackpressureStaleness
+      ).flow
       // for each worker, add an edge from the balancer to the worker, then wire
       // it to the merge element
       balancer ~> workerFlow.async ~> merge
diff --git a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
index 69e5551b8a9..b1fe8b05462 100644
--- a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
+++ b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
@@ -27,7 +27,6 @@ import java.nio.charset.StandardCharsets
 import scala.concurrent.ExecutionContext
 import scala.concurrent.duration.FiniteDuration
 
-
 /**
   * Flow that executes IO operations by calling java.nio.Path methods
   */
@@ -36,7 +35,8 @@ class NioFlow(parallelism: Int,
               onBackpressure: Option[Double] => Unit,
               numberOfAttempts: Int,
               commandBackpressureStaleness: FiniteDuration
-              )(implicit system: ActorSystem) extends IoCommandStalenessBackpressuring {
+)(implicit system: ActorSystem)
+    extends IoCommandStalenessBackpressuring {
 
   implicit private val ec: ExecutionContext = system.dispatcher
   implicit private val timer: Timer[IO] = IO.timer(ec)
@@ -66,18 +66,19 @@ class NioFlow(parallelism: Int,
       result <- operationResult
     } yield (result, commandContext)
 
-    io handleErrorWith {
-      failure => IO.pure(commandContext.fail(failure))
+    io handleErrorWith { failure =>
+      IO.pure(commandContext.fail(failure))
     }
   }
 
-  private [nio] def handleSingleCommand(ioSingleCommand: IoCommand[_]): IO[IoSuccess[_]] = {
+  private[nio] def handleSingleCommand(ioSingleCommand: IoCommand[_]): IO[IoSuccess[_]] = {
     val ret = ioSingleCommand match {
       case copyCommand: IoCopyCommand => copy(copyCommand) map copyCommand.success
       case writeCommand: IoWriteCommand => write(writeCommand) map writeCommand.success
       case deleteCommand: IoDeleteCommand => delete(deleteCommand) map deleteCommand.success
       case sizeCommand: IoSizeCommand => size(sizeCommand) map sizeCommand.success
-      case readAsStringCommand: IoContentAsStringCommand => readAsString(readAsStringCommand) map readAsStringCommand.success
+      case readAsStringCommand: IoContentAsStringCommand =>
+        readAsString(readAsStringCommand) map readAsStringCommand.success
       case hashCommand: IoHashCommand => hash(hashCommand) map hashCommand.success
       case touchCommand: IoTouchCommand => touch(touchCommand) map touchCommand.success
       case existsCommand: IoExistsCommand => exists(existsCommand) map existsCommand.success
@@ -131,7 +132,7 @@ class NioFlow(parallelism: Int,
       )
     }
 
-    def readFileAndChecksum: IO[String] = {
+    def readFileAndChecksum: IO[String] =
       for {
         fileHash <- getStoredHash(command.file)
         uncheckedValue <- readFile
@@ -145,23 +146,25 @@ class NioFlow(parallelism: Int,
         verifiedValue <- checksumResult match {
           case _: ChecksumSkipped => IO.pure(uncheckedValue)
           case _: ChecksumSuccess => IO.pure(uncheckedValue)
-          case failure: ChecksumFailure => IO.raiseError(
-            ChecksumFailedException(
-              fileHash match {
-                case Some(hash) => s"Failed checksum for '${command.file}'. Expected '${hash.hashType}' hash of '${hash.hash}'. Calculated hash '${failure.calculatedHash}'"
-                case None => s"Failed checksum for '${command.file}'. Couldn't find stored file hash." // This should never happen
-              }
+          case failure: ChecksumFailure =>
+            IO.raiseError(
+              ChecksumFailedException(
+                fileHash match {
+                  case Some(hash) =>
+                    s"Failed checksum for '${command.file}'. Expected '${hash.hashType}' hash of '${hash.hash}'. Calculated hash '${failure.calculatedHash}'"
+                  case None =>
+                    s"Failed checksum for '${command.file}'. Couldn't find stored file hash." // This should never happen
+                }
+              )
             )
-          )
         }
       } yield verifiedValue
-    }
 
     val fileContentIo = command.file match {
-      case _: DrsPath  => readFileAndChecksum
+      case _: DrsPath => readFileAndChecksum
       // Temporarily disable since our hashing algorithm doesn't match the stored hash
       // https://broadworkbench.atlassian.net/browse/WX-1257
-      case _: BlobPath => readFile//readFileAndChecksum
+      case _: BlobPath => readFile // readFileAndChecksum
       case _ => readFile
     }
     fileContentIo.map(_.replaceAll("\\r\\n", "\\\n"))
@@ -173,30 +176,32 @@ class NioFlow(parallelism: Int,
       case nioPath => IO(nioPath.size)
     }
 
-  private def hash(hash: IoHashCommand): IO[String] = {
+  private def hash(hash: IoHashCommand): IO[String] =
     // If there is no hash accessible from the file storage system,
     // we'll read the file and generate the hash ourselves.
-    getStoredHash(hash.file).flatMap {
-      case Some(storedHash) => IO.pure(storedHash)
-      case None => generateMd5FileHashForPath(hash.file)
-    }.map(_.hash)
-  }
+    getStoredHash(hash.file)
+      .flatMap {
+        case Some(storedHash) => IO.pure(storedHash)
+        case None => generateMd5FileHashForPath(hash.file)
+      }
+      .map(_.hash)
 
-  private def getStoredHash(file: Path): IO[Option[FileHash]] = {
+  private def getStoredHash(file: Path): IO[Option[FileHash]] =
     file match {
       case gcsPath: GcsPath => getFileHashForGcsPath(gcsPath).map(Option(_))
       case blobPath: BlobPath => getFileHashForBlobPath(blobPath)
-      case drsPath: DrsPath => IO {
-        // We assume all DRS files have a stored hash; this will throw
-        // if the file does not.
-        drsPath.getFileHash
-      }.map(Option(_))
-      case s3Path: S3Path => IO {
-        Option(FileHash(HashType.S3Etag, s3Path.eTag))
-      }
+      case drsPath: DrsPath =>
+        IO {
+          // We assume all DRS files have a stored hash; this will throw
+          // if the file does not.
+          drsPath.getFileHash
+        }.map(Option(_))
+      case s3Path: S3Path =>
+        IO {
+          Option(FileHash(HashType.S3Etag, s3Path.eTag))
+        }
       case _ => IO.pure(None)
     }
-  }
 
   private def touch(touch: IoTouchCommand) = IO {
     touch.file.touch()
@@ -224,7 +229,7 @@ class NioFlow(parallelism: Int,
     * IMPORTANT: Use this instead of IO.fromTry to make sure the Try will be reevaluated if the
     * IoCommand is retried.
     */
-  private def delayedIoFromTry[A](t: => Try[A]): IO[A] = IO[A] { t.get }
+  private def delayedIoFromTry[A](t: => Try[A]): IO[A] = IO[A](t.get)
 
   private def getFileHashForGcsPath(gcsPath: GcsPath): IO[FileHash] = delayedIoFromTry {
     gcsPath.objectBlobId.map(id => FileHash(HashType.GcsCrc32c, gcsPath.cloudStorage.get(id).getCrc32c))
diff --git a/engine/src/main/scala/cromwell/engine/package.scala b/engine/src/main/scala/cromwell/engine/package.scala
index f4083286612..1bd7a13a244 100644
--- a/engine/src/main/scala/cromwell/engine/package.scala
+++ b/engine/src/main/scala/cromwell/engine/package.scala
@@ -14,8 +14,8 @@ package object engine {
   }
 
   implicit class EnhancedCallOutputMap[A](val m: Map[A, JobOutput]) extends AnyVal {
-    def mapToValues: Map[A, WomValue] = m map {
-      case (k, JobOutput(womValue)) => (k, womValue)
+    def mapToValues: Map[A, WomValue] = m map { case (k, JobOutput(womValue)) =>
+      (k, womValue)
     }
   }
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala b/engine/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala
index 91be71fbf35..8b72d7eaaba 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/SingleWorkflowRunnerActor.scala
@@ -20,8 +20,13 @@ import cromwell.engine.workflow.workflowstore.WorkflowStoreActor.SubmitWorkflow
 import cromwell.engine.workflow.workflowstore.{InMemoryWorkflowStore, WorkflowStoreSubmitActor}
 import cromwell.jobstore.EmptyJobStoreActor
 import cromwell.server.CromwellRootActor
-import cromwell.services.{SuccessfulMetadataJsonResponse, FailedMetadataJsonResponse}
-import cromwell.services.metadata.MetadataService.{GetSingleWorkflowMetadataAction, GetStatus, ListenToMetadataWriteActor, WorkflowOutputs}
+import cromwell.services.{FailedMetadataJsonResponse, SuccessfulMetadataJsonResponse}
+import cromwell.services.metadata.MetadataService.{
+  GetSingleWorkflowMetadataAction,
+  GetStatus,
+  ListenToMetadataWriteActor,
+  WorkflowOutputs
+}
 import cromwell.subworkflowstore.EmptySubWorkflowStoreActor
 import spray.json._
 
@@ -40,8 +45,8 @@ class SingleWorkflowRunnerActor(source: WorkflowSourceFilesCollection,
                                 gracefulShutdown: Boolean,
                                 abortJobsOnTerminate: Boolean,
                                 config: Config
-                                )(implicit materializer: ActorMaterializer)
-  extends CromwellRootActor(terminator, gracefulShutdown, abortJobsOnTerminate, false, config)
+)(implicit materializer: ActorMaterializer)
+    extends CromwellRootActor(terminator, gracefulShutdown, abortJobsOnTerminate, false, config)
     with LoggingFSM[RunnerState, SwraData] {
 
   import SingleWorkflowRunnerActor._
@@ -54,14 +59,13 @@ class SingleWorkflowRunnerActor(source: WorkflowSourceFilesCollection,
   log.info("{}: Version {}", Tag, VersionUtil.getVersion("cromwell-engine"))
   startWith(NotStarted, EmptySwraData)
 
-  when (NotStarted) {
-    case Event(RunWorkflow, EmptySwraData) =>
-      log.info(s"$Tag: Submitting workflow")
-      workflowStoreActor ! SubmitWorkflow(source)
-      goto(SubmittedWorkflow) using SubmittedSwraData(sender())
+  when(NotStarted) { case Event(RunWorkflow, EmptySwraData) =>
+    log.info(s"$Tag: Submitting workflow")
+    workflowStoreActor ! SubmitWorkflow(source)
+    goto(SubmittedWorkflow) using SubmittedSwraData(sender())
   }
 
-  when (SubmittedWorkflow) {
+  when(SubmittedWorkflow) {
     case Event(WorkflowStoreSubmitActor.WorkflowSubmittedToStore(id, WorkflowSubmitted), SubmittedSwraData(replyTo)) =>
       log.info(s"$Tag: Workflow submitted UUID($id)")
       // Since we only have a single workflow, force the WorkflowManagerActor's hand in case the polling rate is long
@@ -72,51 +76,57 @@ class SingleWorkflowRunnerActor(source: WorkflowSourceFilesCollection,
       goto(RunningWorkflow) using RunningSwraData(replyTo, id)
   }
 
-  when (RunningWorkflow) {
+  when(RunningWorkflow) {
     case Event(IssuePollRequest, RunningSwraData(_, id)) =>
       requestStatus(id)
       stay()
-    case Event(SuccessfulMetadataJsonResponse(_, jsObject: JsObject), RunningSwraData(_, _)) if !jsObject.state.isTerminal =>
+    case Event(SuccessfulMetadataJsonResponse(_, jsObject: JsObject), RunningSwraData(_, _))
+        if !jsObject.state.isTerminal =>
       schedulePollRequest()
       stay()
-    case Event(SuccessfulMetadataJsonResponse(_, jsObject: JsObject), RunningSwraData(replyTo, id)) if jsObject.state == WorkflowSucceeded =>
+    case Event(SuccessfulMetadataJsonResponse(_, jsObject: JsObject), RunningSwraData(replyTo, id))
+        if jsObject.state == WorkflowSucceeded =>
       log.info(s"$Tag workflow finished with status '$WorkflowSucceeded'.")
       serviceRegistryActor ! ListenToMetadataWriteActor
       goto(WaitingForFlushedMetadata) using SucceededSwraData(replyTo, id)
-    case Event(SuccessfulMetadataJsonResponse(_, jsObject: JsObject), RunningSwraData(replyTo, id)) if jsObject.state == WorkflowFailed =>
+    case Event(SuccessfulMetadataJsonResponse(_, jsObject: JsObject), RunningSwraData(replyTo, id))
+        if jsObject.state == WorkflowFailed =>
       log.info(s"$Tag workflow finished with status '$WorkflowFailed'.")
       serviceRegistryActor ! ListenToMetadataWriteActor
-      goto(WaitingForFlushedMetadata) using FailedSwraData(replyTo, id, new RuntimeException(s"Workflow $id transitioned to state $WorkflowFailed"))
-    case Event(SuccessfulMetadataJsonResponse(_, jsObject: JsObject), RunningSwraData(replyTo, id)) if jsObject.state == WorkflowAborted =>
+      goto(WaitingForFlushedMetadata) using FailedSwraData(
+        replyTo,
+        id,
+        new RuntimeException(s"Workflow $id transitioned to state $WorkflowFailed")
+      )
+    case Event(SuccessfulMetadataJsonResponse(_, jsObject: JsObject), RunningSwraData(replyTo, id))
+        if jsObject.state == WorkflowAborted =>
       log.info(s"$Tag workflow finished with status '$WorkflowAborted'.")
       serviceRegistryActor ! ListenToMetadataWriteActor
       goto(WaitingForFlushedMetadata) using AbortedSwraData(replyTo, id)
   }
-  
-  when (WaitingForFlushedMetadata) {
+
+  when(WaitingForFlushedMetadata) {
     case Event(QueueWeight(weight), _) if weight > 0 => stay()
     case Event(QueueWeight(_), data: SucceededSwraData) =>
-
       serviceRegistryActor ! WorkflowOutputs(data.id)
       goto(RequestingOutputs)
-    case Event(QueueWeight(_), data : TerminalSwraData) =>
+    case Event(QueueWeight(_), data: TerminalSwraData) =>
       requestMetadataOrIssueReply(data)
   }
 
-  when (RequestingOutputs) {
-    case Event(SuccessfulMetadataJsonResponse(_, outputs: JsObject), data: TerminalSwraData) =>
-      outputOutputs(outputs)
-      requestMetadataOrIssueReply(data)
+  when(RequestingOutputs) { case Event(SuccessfulMetadataJsonResponse(_, outputs: JsObject), data: TerminalSwraData) =>
+    outputOutputs(outputs)
+    requestMetadataOrIssueReply(data)
   }
 
-  when (RequestingMetadata) {
+  when(RequestingMetadata) {
     case Event(SuccessfulMetadataJsonResponse(_, metadata: JsObject), data: TerminalSwraData) =>
       outputMetadata(metadata)
       issueReply(data)
   }
 
-  onTransition {
-    case NotStarted -> RunningWorkflow => schedulePollRequest()
+  onTransition { case NotStarted -> RunningWorkflow =>
+    schedulePollRequest()
   }
 
   whenUnhandled {
@@ -137,11 +147,12 @@ class SingleWorkflowRunnerActor(source: WorkflowSourceFilesCollection,
       stay()
   }
 
-  private def requestMetadataOrIssueReply(newData: TerminalSwraData) = if (metadataOutputPath.isDefined) requestMetadata(newData) else issueReply(newData)
-  
+  private def requestMetadataOrIssueReply(newData: TerminalSwraData) =
+    if (metadataOutputPath.isDefined) requestMetadata(newData) else issueReply(newData)
+
   private def requestMetadata(newData: TerminalSwraData): State = {
     serviceRegistryActor ! GetSingleWorkflowMetadataAction(newData.id, None, None, expandSubWorkflows = true)
-    goto (RequestingMetadata) using newData
+    goto(RequestingMetadata) using newData
   }
 
   private def schedulePollRequest(): Unit = {
@@ -150,12 +161,11 @@ class SingleWorkflowRunnerActor(source: WorkflowSourceFilesCollection,
     ()
   }
 
-  private def requestStatus(id: WorkflowId): Unit = {
+  private def requestStatus(id: WorkflowId): Unit =
     // This requests status via the metadata service rather than instituting an FSM watch on the underlying workflow actor.
     // Cromwell's eventual consistency means it isn't safe to use an FSM transition to a terminal state as the signal for
     // when outputs or metadata have stabilized.
     serviceRegistryActor ! GetStatus(id)
-  }
 
   private def issueSuccessReply(replyTo: ActorRef): State = {
     replyTo.tell(msg = (), sender = self) // Because replyTo ! () is the parameterless call replyTo.!()
@@ -168,17 +178,16 @@ class SingleWorkflowRunnerActor(source: WorkflowSourceFilesCollection,
     done()
     stay()
   }
-  
-  private [workflow] def done() = {}
 
-  private def issueReply(data: TerminalSwraData) = {
+  private[workflow] def done() = {}
+
+  private def issueReply(data: TerminalSwraData) =
     data match {
       case s: SucceededSwraData => issueSuccessReply(s.replyTo)
       case f: FailedSwraData => issueFailureReply(f.replyTo, f.failure)
       case a: AbortedSwraData => issueSuccessReply(a.replyTo)
 
     }
-  }
 
   private def failAndFinish(e: Throwable, data: SwraData): State = {
     log.error(e, s"$Tag received Failure message: ${e.getMessage}")
@@ -199,11 +208,10 @@ class SingleWorkflowRunnerActor(source: WorkflowSourceFilesCollection,
   /**
     * Outputs the outputs to stdout, and then requests the metadata.
     */
-  private def outputOutputs(outputs: JsObject): Unit = {
+  private def outputOutputs(outputs: JsObject): Unit =
     println(outputs.prettyPrint)
-  }
 
-  private def outputMetadata(metadata: JsObject): Try[Unit] = {
+  private def outputMetadata(metadata: JsObject): Try[Unit] =
     Try {
       val path = metadataOutputPath.get
       if (path.isDirectory) {
@@ -213,7 +221,6 @@ class SingleWorkflowRunnerActor(source: WorkflowSourceFilesCollection,
         path.createIfNotExists(createParents = true).write(metadata.prettyPrint)
       }
     } void
-  }
 }
 
 object SingleWorkflowRunnerActor {
@@ -222,8 +229,8 @@ object SingleWorkflowRunnerActor {
             terminator: CromwellTerminator,
             gracefulShutdown: Boolean,
             abortJobsOnTerminate: Boolean,
-            config: Config)
-           (implicit materializer: ActorMaterializer): Props = {
+            config: Config
+  )(implicit materializer: ActorMaterializer): Props =
     Props(
       new SingleWorkflowRunnerActor(
         source = source,
@@ -234,7 +241,6 @@ object SingleWorkflowRunnerActor {
         config = config
       )
     ).withDispatcher(EngineDispatcher)
-  }
 
   sealed trait RunnerMessage
   // The message to actually run the workflow is made explicit so the non-actor Main can `ask` this actor to do the
@@ -255,16 +261,20 @@ object SingleWorkflowRunnerActor {
   final case class SubmittedSwraData(replyTo: ActorRef) extends SwraData
   final case class RunningSwraData(replyTo: ActorRef, id: WorkflowId) extends SwraData
 
-  sealed trait TerminalSwraData extends SwraData { def replyTo: ActorRef; def terminalState: WorkflowState; def id: WorkflowId }
-  final case class SucceededSwraData(replyTo: ActorRef,
-                                     id: WorkflowId) extends TerminalSwraData { override val terminalState = WorkflowSucceeded }
+  sealed trait TerminalSwraData extends SwraData {
+    def replyTo: ActorRef; def terminalState: WorkflowState; def id: WorkflowId
+  }
+  final case class SucceededSwraData(replyTo: ActorRef, id: WorkflowId) extends TerminalSwraData {
+    override val terminalState = WorkflowSucceeded
+  }
 
-  final case class FailedSwraData(replyTo: ActorRef,
-                                  id: WorkflowId,
-                                  failure: Throwable) extends TerminalSwraData { override val terminalState = WorkflowFailed }
+  final case class FailedSwraData(replyTo: ActorRef, id: WorkflowId, failure: Throwable) extends TerminalSwraData {
+    override val terminalState = WorkflowFailed
+  }
 
-  final case class AbortedSwraData(replyTo: ActorRef,
-                                   id: WorkflowId) extends TerminalSwraData { override val terminalState = WorkflowAborted }
+  final case class AbortedSwraData(replyTo: ActorRef, id: WorkflowId) extends TerminalSwraData {
+    override val terminalState = WorkflowAborted
+  }
 
   implicit class EnhancedJsObject(val jsObject: JsObject) extends AnyVal {
     def state: WorkflowState = WorkflowState.withName(jsObject.fields("status").asInstanceOf[JsString].value)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
index 3061e2e8a74..8bf936fa88b 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowActor.scala
@@ -19,19 +19,49 @@ import cromwell.engine.workflow.WorkflowActor._
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowActorWorkComplete
 import cromwell.engine.workflow.lifecycle._
 import cromwell.engine.workflow.lifecycle.deletion.DeleteWorkflowFilesActor
-import cromwell.engine.workflow.lifecycle.deletion.DeleteWorkflowFilesActor.{DeleteWorkflowFilesFailedResponse, DeleteWorkflowFilesSucceededResponse, StartWorkflowFilesDeletion}
+import cromwell.engine.workflow.lifecycle.deletion.DeleteWorkflowFilesActor.{
+  DeleteWorkflowFilesFailedResponse,
+  DeleteWorkflowFilesSucceededResponse,
+  StartWorkflowFilesDeletion
+}
 import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor
 import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor._
 import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackActor.PerformCallbackCommand
-import cromwell.engine.workflow.lifecycle.finalization.WorkflowFinalizationActor.{StartFinalizationCommand, WorkflowFinalizationFailedResponse, WorkflowFinalizationSucceededResponse}
-import cromwell.engine.workflow.lifecycle.finalization.{CopyWorkflowLogsActor, CopyWorkflowOutputsActor, WorkflowFinalizationActor}
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowFinalizationActor.{
+  StartFinalizationCommand,
+  WorkflowFinalizationFailedResponse,
+  WorkflowFinalizationSucceededResponse
+}
+import cromwell.engine.workflow.lifecycle.finalization.{
+  CopyWorkflowLogsActor,
+  CopyWorkflowOutputsActor,
+  WorkflowFinalizationActor
+}
 import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor
-import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{StartInitializationCommand, WorkflowInitializationFailedResponse, WorkflowInitializationResponse, WorkflowInitializationSucceededResponse}
+import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{
+  StartInitializationCommand,
+  WorkflowInitializationFailedResponse,
+  WorkflowInitializationResponse,
+  WorkflowInitializationSucceededResponse
+}
 import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor
-import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.{MaterializeWorkflowDescriptorCommand, MaterializeWorkflowDescriptorFailureResponse, MaterializeWorkflowDescriptorSuccessResponse}
+import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.{
+  MaterializeWorkflowDescriptorCommand,
+  MaterializeWorkflowDescriptorFailureResponse,
+  MaterializeWorkflowDescriptorSuccessResponse
+}
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor.WorkflowStoreWriteHeartbeatCommand
-import cromwell.engine.workflow.workflowstore.{RestartableAborting, StartableState, WorkflowHeartbeatConfig, WorkflowToStart}
-import cromwell.services.metadata.MetadataService.{MetadataWriteFailure, MetadataWriteSuccess, PutMetadataActionAndRespond}
+import cromwell.engine.workflow.workflowstore.{
+  RestartableAborting,
+  StartableState,
+  WorkflowHeartbeatConfig,
+  WorkflowToStart
+}
+import cromwell.services.metadata.MetadataService.{
+  MetadataWriteFailure,
+  MetadataWriteSuccess,
+  PutMetadataActionAndRespond
+}
 import cromwell.subworkflowstore.SubWorkflowStoreActor.WorkflowComplete
 import cromwell.webservice.EngineStatsActor
 import org.apache.commons.lang3.exception.ExceptionUtils
@@ -152,14 +182,16 @@ object WorkflowActor {
                                workflowFinalOutputs: Option[CallOutputs] = None,
                                workflowAllOutputs: Set[WomValue] = Set.empty,
                                rootAndSubworkflowIds: Set[WorkflowId] = Set.empty,
-                               failedInitializationAttempts: Int = 0)
+                               failedInitializationAttempts: Int = 0
+  )
   object WorkflowActorData {
     def apply(startableState: StartableState): WorkflowActorData = WorkflowActorData(
       currentLifecycleStateActor = None,
       workflowDescriptor = None,
       initializationData = AllBackendInitializationData.empty,
       lastStateReached = StateCheckpoint(WorkflowUnstartedState),
-      effectiveStartableState = startableState)
+      effectiveStartableState = startableState
+    )
   }
 
   /**
@@ -190,7 +222,8 @@ object WorkflowActor {
             workflowHeartbeatConfig: WorkflowHeartbeatConfig,
             totalJobsByRootWf: AtomicInteger,
             fileHashCacheActorProps: Option[Props],
-            blacklistCache: Option[BlacklistCache]): Props = {
+            blacklistCache: Option[BlacklistCache]
+  ): Props =
     Props(
       new WorkflowActor(
         workflowToStart = workflowToStart,
@@ -214,8 +247,9 @@ object WorkflowActor {
         workflowHeartbeatConfig = workflowHeartbeatConfig,
         totalJobsByRootWf = totalJobsByRootWf,
         fileHashCacheActorProps = fileHashCacheActorProps,
-        blacklistCache = blacklistCache)).withDispatcher(EngineDispatcher)
-  }
+        blacklistCache = blacklistCache
+      )
+    ).withDispatcher(EngineDispatcher)
 }
 
 /**
@@ -224,7 +258,7 @@ object WorkflowActor {
 class WorkflowActor(workflowToStart: WorkflowToStart,
                     conf: Config,
                     callCachingEnabled: Boolean,
-                    invalidateBadCacheResults:Boolean,
+                    invalidateBadCacheResults: Boolean,
                     ioActor: ActorRef,
                     override val serviceRegistryActor: ActorRef,
                     workflowLogCopyRouter: ActorRef,
@@ -245,9 +279,12 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
                     // child of this actor. The sbt subproject of `RootWorkflowFileHashCacheActor` is not visible from
                     // the subproject this class belongs to so the `Props` are passed in.
                     fileHashCacheActorProps: Option[Props],
-                    blacklistCache: Option[BlacklistCache])
-  extends LoggingFSM[WorkflowActorState, WorkflowActorData] with WorkflowLogging with WorkflowMetadataHelper
-  with WorkflowInstrumentation with Timers {
+                    blacklistCache: Option[BlacklistCache]
+) extends LoggingFSM[WorkflowActorState, WorkflowActorData]
+    with WorkflowLogging
+    with WorkflowMetadataHelper
+    with WorkflowInstrumentation
+    with Timers {
 
   implicit val ec = context.dispatcher
   private val WorkflowToStart(workflowId, submissionTime, sources, initialStartableState, hogGroup) = workflowToStart
@@ -261,7 +298,9 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   private val deleteWorkflowFiles = conf.getBoolean("system.delete-workflow-files")
 
   private val workflowDockerLookupActor = context.actorOf(
-    WorkflowDockerLookupActor.props(workflowId, dockerHashActor, initialStartableState.restarted), s"WorkflowDockerLookupActor-$workflowId")
+    WorkflowDockerLookupActor.props(workflowId, dockerHashActor, initialStartableState.restarted),
+    s"WorkflowDockerLookupActor-$workflowId"
+  )
 
   protected val pathBuilderFactories: List[PathBuilderFactory] = EngineFilesystems.configuredPathBuilderFactories
 
@@ -297,8 +336,15 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
 
   when(WorkflowUnstartedState) {
     case Event(StartWorkflowCommand, _) =>
-      val actor = context.actorOf(MaterializeWorkflowDescriptorActor.props(serviceRegistryActor, workflowId, importLocalFilesystem = !serverMode, ioActorProxy = ioActor, hogGroup = hogGroup),
-        "MaterializeWorkflowDescriptorActor")
+      val actor = context.actorOf(
+        MaterializeWorkflowDescriptorActor.props(serviceRegistryActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = !serverMode,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = hogGroup
+        ),
+        "MaterializeWorkflowDescriptorActor"
+      )
       pushWorkflowStart(workflowId)
       actor ! MaterializeWorkflowDescriptorCommand(sources, conf, callCachingEnabled, invalidateBadCacheResults)
       goto(MaterializingWorkflowDescriptorState) using stateData.copy(currentLifecycleStateActor = Option(actor))
@@ -315,7 +361,9 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
       self ! StartInitializing
       goto(InitializingWorkflowState) using data.copy(workflowDescriptor = Option(workflowDescriptor))
     case Event(MaterializeWorkflowDescriptorFailureResponse(reason: Throwable), data) =>
-      goto(WorkflowFailedState) using data.copy(lastStateReached = StateCheckpoint(MaterializingWorkflowDescriptorState, Option(List(reason))))
+      goto(WorkflowFailedState) using data.copy(lastStateReached =
+        StateCheckpoint(MaterializingWorkflowDescriptorState, Option(List(reason)))
+      )
     // If the workflow is not being restarted then we can abort it immediately as nothing happened yet
     case Event(AbortWorkflowCommand, _) if !restarting => goto(WorkflowAbortedState)
   }
@@ -323,25 +371,31 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   /* ************************** */
   /* ****** Initializing ****** */
   /* ************************** */
-  protected def createInitializationActor(workflowDescriptor: EngineWorkflowDescriptor, name: String): ActorRef = {
-    context.actorOf(
-      WorkflowInitializationActor.props(
-        workflowIdForLogging,
-        rootWorkflowIdForLogging,
-        workflowDescriptor,
-        ioActor,
-        serviceRegistryActor,
-        restarting
-      ),
-      name)
-  }
+  protected def createInitializationActor(workflowDescriptor: EngineWorkflowDescriptor, name: String): ActorRef =
+    context.actorOf(WorkflowInitializationActor.props(
+                      workflowIdForLogging,
+                      rootWorkflowIdForLogging,
+                      workflowDescriptor,
+                      ioActor,
+                      serviceRegistryActor,
+                      restarting
+                    ),
+                    name
+    )
 
   when(InitializingWorkflowState) {
     case Event(StartInitializing, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
-      val initializerActor = createInitializationActor(workflowDescriptor, s"WorkflowInitializationActor-$workflowId-${data.failedInitializationAttempts + 1}")
+      val initializerActor =
+        createInitializationActor(workflowDescriptor,
+                                  s"WorkflowInitializationActor-$workflowId-${data.failedInitializationAttempts + 1}"
+        )
       initializerActor ! StartInitializationCommand
-      goto(InitializingWorkflowState) using data.copy(currentLifecycleStateActor = Option(initializerActor), workflowDescriptor = Option(workflowDescriptor))
-    case Event(WorkflowInitializationSucceededResponse(initializationData), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+      goto(InitializingWorkflowState) using data.copy(currentLifecycleStateActor = Option(initializerActor),
+                                                      workflowDescriptor = Option(workflowDescriptor)
+      )
+    case Event(WorkflowInitializationSucceededResponse(initializationData),
+               data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)
+        ) =>
       val dataWithInitializationData = data.copy(initializationData = initializationData)
       val executionActor = createWorkflowExecutionActor(workflowDescriptor, dataWithInitializationData)
       executionActor ! ExecuteWorkflowCommand
@@ -350,18 +404,26 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
         case _ => ExecutingWorkflowState
       }
       goto(nextState) using dataWithInitializationData.copy(currentLifecycleStateActor = Option(executionActor))
-    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+    case Event(WorkflowInitializationFailedResponse(reason),
+               data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)
+        ) =>
       val failedInitializationAttempts = data.failedInitializationAttempts + 1
       if (failedInitializationAttempts < maxInitializationAttempts) {
-        workflowLogger.info(s"Initialization failed on attempt $failedInitializationAttempts. Will retry up to $maxInitializationAttempts times. Next retry is in $initializationRetryInterval", CromwellAggregatedException(reason, "Initialization Failure"))
-        context.system.scheduler.scheduleOnce(initializationRetryInterval) { self ! StartInitializing}
-        stay() using data.copy(currentLifecycleStateActor = None, failedInitializationAttempts = failedInitializationAttempts)
+        workflowLogger.info(
+          s"Initialization failed on attempt $failedInitializationAttempts. Will retry up to $maxInitializationAttempts times. Next retry is in $initializationRetryInterval",
+          CromwellAggregatedException(reason, "Initialization Failure")
+        )
+        context.system.scheduler.scheduleOnce(initializationRetryInterval)(self ! StartInitializing)
+        stay() using data.copy(currentLifecycleStateActor = None,
+                               failedInitializationAttempts = failedInitializationAttempts
+        )
       } else {
         finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
       }
 
     // If the workflow is not restarting, handle the Abort command normally and send an abort message to the init actor
-    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) if !restarting =>
+    case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _))
+        if !restarting =>
       handleAbortCommand(data, workflowDescriptor)
   }
 
@@ -369,43 +431,51 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   /* ****** Running ****** */
   /* ********************* */
 
-  def createWorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor, data: WorkflowActorData): ActorRef = {
-    context.actorOf(WorkflowExecutionActor.props(
-      workflowDescriptor,
-      ioActor = ioActor,
-      serviceRegistryActor = serviceRegistryActor,
-      jobStoreActor = jobStoreActor,
-      subWorkflowStoreActor = subWorkflowStoreActor,
-      callCacheReadActor = callCacheReadActor,
-      callCacheWriteActor = callCacheWriteActor,
-      workflowDockerLookupActor = workflowDockerLookupActor,
-      jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
-      jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
-      backendSingletonCollection,
-      data.initializationData,
-      startState = data.effectiveStartableState,
-      rootConfig = conf,
-      totalJobsByRootWf = totalJobsByRootWf,
-      fileHashCacheActor = fileHashCacheActorProps map context.system.actorOf,
-      blacklistCache = blacklistCache), name = s"WorkflowExecutionActor-$workflowId")
-  }
+  def createWorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor, data: WorkflowActorData): ActorRef =
+    context.actorOf(
+      WorkflowExecutionActor.props(
+        workflowDescriptor,
+        ioActor = ioActor,
+        serviceRegistryActor = serviceRegistryActor,
+        jobStoreActor = jobStoreActor,
+        subWorkflowStoreActor = subWorkflowStoreActor,
+        callCacheReadActor = callCacheReadActor,
+        callCacheWriteActor = callCacheWriteActor,
+        workflowDockerLookupActor = workflowDockerLookupActor,
+        jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
+        jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
+        backendSingletonCollection,
+        data.initializationData,
+        startState = data.effectiveStartableState,
+        rootConfig = conf,
+        totalJobsByRootWf = totalJobsByRootWf,
+        fileHashCacheActor = fileHashCacheActorProps map context.system.actorOf,
+        blacklistCache = blacklistCache
+      ),
+      name = s"WorkflowExecutionActor-$workflowId"
+    )
 
   // Handles workflow completion events from the WEA and abort command
   val executionResponseHandler: StateFunction = {
     // Workflow responses
     case Event(WorkflowExecutionSucceededResponse(jobKeys, rootAndSubworklowIds, finalOutputs, allOutputs),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+               data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)
+        ) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, finalOutputs, None, allOutputs, rootAndSubworklowIds)
     case Event(WorkflowExecutionFailedResponse(jobKeys, failures),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+               data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)
+        ) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, CallOutputs.empty, Option(List(failures)))
     case Event(WorkflowExecutionAbortedResponse(jobKeys),
-    data @ WorkflowActorData(_, Some(workflowDescriptor), _, StateCheckpoint(_, failures), _, _, _, _, _)) =>
+               data @ WorkflowActorData(_, Some(workflowDescriptor), _, StateCheckpoint(_, failures), _, _, _, _, _)
+        ) =>
       finalizeWorkflow(data, workflowDescriptor, jobKeys, CallOutputs.empty, failures)
 
     // Whether we're running or aborting, restarting or not, pass along the abort command.
     // Note that aborting a workflow multiple times will result in as many abort commands sent to the execution actor
-    case Event(AbortWorkflowWithExceptionCommand(ex), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+    case Event(AbortWorkflowWithExceptionCommand(ex),
+               data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)
+        ) =>
       handleAbortCommand(data, workflowDescriptor, Option(ex))
     case Event(AbortWorkflowCommand, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
       handleAbortCommand(data, workflowDescriptor)
@@ -420,11 +490,15 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   // Handles initialization responses we can get if the abort came in when we were initializing the workflow
   val abortHandler: StateFunction = {
     // If the initialization failed, record the failure in the data and finalize the workflow
-    case Event(WorkflowInitializationFailedResponse(reason), data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+    case Event(WorkflowInitializationFailedResponse(reason),
+               data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)
+        ) =>
       finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, Option(reason.toList))
 
     // Otherwise (success or abort), finalize the workflow without failures
-    case Event(_: WorkflowInitializationResponse, data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)) =>
+    case Event(_: WorkflowInitializationResponse,
+               data @ WorkflowActorData(_, Some(workflowDescriptor), _, _, _, _, _, _, _)
+        ) =>
       finalizeWorkflow(data, workflowDescriptor, Map.empty, CallOutputs.empty, failures = None)
 
     case Event(StartInitializing, _) =>
@@ -444,7 +518,9 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
     case Event(WorkflowFinalizationSucceededResponse, data) => finalizationSucceeded(data)
     case Event(WorkflowFinalizationFailedResponse(finalizationFailures), data) =>
       val failures = data.lastStateReached.failures.getOrElse(List.empty) ++ finalizationFailures
-      goto(WorkflowFailedState) using data.copy(lastStateReached = StateCheckpoint(FinalizingWorkflowState, Option(failures)))
+      goto(WorkflowFailedState) using data.copy(lastStateReached =
+        StateCheckpoint(FinalizingWorkflowState, Option(failures))
+      )
     case Event(AbortWorkflowCommand, _) => stay()
     case Event(StartInitializing, _) =>
       // An initialization trigger we no longer need to action. Ignore:
@@ -461,12 +537,18 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
       // better luck. If we continue to be unable to write the completion message to the DB it's better to leave the
       // workflow in its current state in the DB than to let the WMA delete it
       // Note: this is an infinite retry right now, but it doesn't consume much in terms of resources and could help us successfully weather maintenance downtime on the DB
-      workflowLogger.error(reason, "Unable to complete workflow due to inability to write concluding metadata status. Retrying...")
+      workflowLogger.error(
+        reason,
+        "Unable to complete workflow due to inability to write concluding metadata status. Retrying..."
+      )
       PutMetadataActionAndRespond(msgs, self)
       stay()
   }
 
-  def handleAbortCommand(data: WorkflowActorData, workflowDescriptor: EngineWorkflowDescriptor, exceptionCausedAbortOpt: Option[Throwable] = None) = {
+  def handleAbortCommand(data: WorkflowActorData,
+                         workflowDescriptor: EngineWorkflowDescriptor,
+                         exceptionCausedAbortOpt: Option[Throwable] = None
+  ) = {
     val updatedData = data.copy(lastStateReached = StateCheckpoint(stateName, exceptionCausedAbortOpt.map(List(_))))
     data.currentLifecycleStateActor match {
       case Some(currentActor) =>
@@ -474,11 +556,21 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
         goto(WorkflowAbortingState) using updatedData
       case None =>
         if (stateName == InitializingWorkflowState) {
-          workflowLogger.info(s"Received an abort command in state $stateName (while awaiting an initialization retry). Finalizing the workflow.")
+          workflowLogger.info(
+            s"Received an abort command in state $stateName (while awaiting an initialization retry). Finalizing the workflow."
+          )
         } else {
-          workflowLogger.warn(s"Received an abort command in state $stateName but there's no lifecycle actor associated. This is an abnormal state, finalizing the workflow anyway.")
+          workflowLogger.warn(
+            s"Received an abort command in state $stateName but there's no lifecycle actor associated. This is an abnormal state, finalizing the workflow anyway."
+          )
         }
-        finalizeWorkflow(updatedData, workflowDescriptor, Map.empty, CallOutputs.empty, failures = None, lastStateOverride = Option(WorkflowAbortingState))
+        finalizeWorkflow(updatedData,
+                         workflowDescriptor,
+                         Map.empty,
+                         CallOutputs.empty,
+                         failures = None,
+                         lastStateOverride = Option(WorkflowAbortingState)
+        )
     }
   }
 
@@ -490,19 +582,23 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
   // since deletion happens only if the workflow and finalization succeeded we can directly goto Succeeded state
   when(DeletingFilesState) {
     case Event(DeleteWorkflowFilesSucceededResponse(filesNotFound, callCacheInvalidationErrors), data) =>
-      workflowLogger.info(s"Successfully deleted intermediate output file(s) for root workflow $rootWorkflowIdForLogging." +
-        deleteFilesAdditionalError(filesNotFound, callCacheInvalidationErrors))
+      workflowLogger.info(
+        s"Successfully deleted intermediate output file(s) for root workflow $rootWorkflowIdForLogging." +
+          deleteFilesAdditionalError(filesNotFound, callCacheInvalidationErrors)
+      )
       goto(WorkflowSucceededState) using data.copy(currentLifecycleStateActor = None)
     case Event(DeleteWorkflowFilesFailedResponse(errors, filesNotFound, callCacheInvalidationErrors), data) =>
-      workflowLogger.info(s"Failed to delete ${errors.size} intermediate output file(s) for root workflow $rootWorkflowIdForLogging." +
-        deleteFilesAdditionalError(filesNotFound, callCacheInvalidationErrors) + s" Errors: ${errors.map(ExceptionUtils.getMessage)}")
+      workflowLogger.info(
+        s"Failed to delete ${errors.size} intermediate output file(s) for root workflow $rootWorkflowIdForLogging." +
+          deleteFilesAdditionalError(filesNotFound, callCacheInvalidationErrors) + s" Errors: ${errors.map(ExceptionUtils.getMessage)}"
+      )
       goto(WorkflowSucceededState) using data.copy(currentLifecycleStateActor = None)
   }
 
   // Let these messages fall through to the whenUnhandled handler:
-  when(WorkflowAbortedState) { FSM.NullFunction }
-  when(WorkflowFailedState) { FSM.NullFunction }
-  when(WorkflowSucceededState) { FSM.NullFunction }
+  when(WorkflowAbortedState)(FSM.NullFunction)
+  when(WorkflowFailedState)(FSM.NullFunction)
+  when(WorkflowSucceededState)(FSM.NullFunction)
 
   whenUnhandled {
     case Event(SendWorkflowHeartbeatCommand, _) =>
@@ -514,11 +610,14 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
     case Event(msg @ EngineStatsActor.JobCountQuery, data) =>
       data.currentLifecycleStateActor match {
         case Some(a) => a forward msg
-        case None => sender() ! EngineStatsActor.NoJobs // This should be impossible, but if somehow here it's technically correct
+        case None =>
+          sender() ! EngineStatsActor.NoJobs // This should be impossible, but if somehow here it's technically correct
       }
       stay()
     case Event(AwaitMetadataIntegrity, data) =>
-      goto(MetadataIntegrityValidationState) using data.copy(lastStateReached = data.lastStateReached.copy(state = stateName))
+      goto(MetadataIntegrityValidationState) using data.copy(lastStateReached =
+        data.lastStateReached.copy(state = stateName)
+      )
   }
 
   onTransition {
@@ -527,7 +626,11 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
       setWorkflowTimePerState(terminalState.workflowState, (System.currentTimeMillis() - startTime).millis)
       workflowLogger.debug(s"transition from {} to {}. Stopping self.", arg1 = oldState, arg2 = terminalState)
       pushWorkflowEnd(workflowId)
-      WorkflowProcessingEventPublishing.publish(workflowId, workflowHeartbeatConfig.cromwellId, Finished, serviceRegistryActor)
+      WorkflowProcessingEventPublishing.publish(workflowId,
+                                                workflowHeartbeatConfig.cromwellId,
+                                                Finished,
+                                                serviceRegistryActor
+      )
       subWorkflowStoreActor ! WorkflowComplete(workflowId)
       terminalState match {
         case WorkflowFailedState =>
@@ -546,10 +649,11 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
 
       val system = context.system
       val ec = context.system.dispatcher
-      def bruteForcePathBuilders: Future[List[PathBuilder]] = {
+      def bruteForcePathBuilders: Future[List[PathBuilder]] =
         // Protect against path builders that may throw an exception instead of returning a failed future
-        Future(EngineFilesystems.pathBuildersForWorkflow(bruteForceWorkflowOptions, pathBuilderFactories)(system))(ec).flatten
-      }
+        Future(EngineFilesystems.pathBuildersForWorkflow(bruteForceWorkflowOptions, pathBuilderFactories)(system))(
+          ec
+        ).flatten
 
       val (workflowOptions, pathBuilders) = stateData.workflowDescriptor match {
         case Some(wd) => (wd.backendDescriptor.workflowOptions, Future.successful(wd.pathBuilders))
@@ -561,12 +665,17 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
         workflowOptions.get(FinalWorkflowLogDir).toOption match {
           case Some(destinationDir) =>
             pathBuilders
-              .map(pb => workflowLogCopyRouter ! CopyWorkflowLogsActor.Copy(workflowId, PathFactory.buildPath(destinationDir, pb)))(ec)
+              .map(pb =>
+                workflowLogCopyRouter ! CopyWorkflowLogsActor.Copy(workflowId,
+                                                                   PathFactory.buildPath(destinationDir, pb)
+                )
+              )(ec)
               .recover { case e => log.error(e, "Failed to copy workflow log") }(ec)
-          case None => workflowLogger.close(andDelete = WorkflowLogger.isTemporary) match {
-            case Failure(f) => log.error(f, "Failed to delete workflow log")
-            case _ =>
-          }
+          case None =>
+            workflowLogger.close(andDelete = WorkflowLogger.isTemporary) match {
+              case Failure(f) => log.error(f, "Failed to delete workflow log")
+              case _ =>
+            }
         }
       }
 
@@ -598,7 +707,9 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
       }
   }
 
-  private def deleteFilesAdditionalError(filesNotFound: List[Path], callCacheInvalidationErrors: List[Throwable]): String = {
+  private def deleteFilesAdditionalError(filesNotFound: List[Path],
+                                         callCacheInvalidationErrors: List[Throwable]
+  ): String = {
     val filesNotFoundMsg =
       if (filesNotFound.nonEmpty) {
         s" File(s) not found during deletion: ${filesNotFound.mkString(",")}"
@@ -634,30 +745,35 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
     it instantiates the DeleteWorkflowFilesActor and waits for it to respond.
     Note: We can't start deleting files before finalization succeeds as we don't want to start deleting
     them as they are being copied to another location.
-  */
+   */
   private def deleteFilesOrGotoFinalState(data: WorkflowActorData) = {
 
     def deleteFiles() = {
       val rootWorkflowId = data.workflowDescriptor.get.rootWorkflowId
-      val deleteActor = context.actorOf(DeleteWorkflowFilesActor.props(
-        rootWorkflowId = rootWorkflowId,
-        rootWorkflowRootPaths = data.initializationData.getWorkflowRoots(),
-        rootAndSubworkflowIds = data.rootAndSubworkflowIds,
-        workflowFinalOutputs = data.workflowFinalOutputs.map(out => out.outputs.values.toSet).getOrElse(Set.empty),
-        workflowAllOutputs = data.workflowAllOutputs,
-        pathBuilders = data.workflowDescriptor.get.pathBuilders,
-        serviceRegistryActor = serviceRegistryActor,
-        ioActor = ioActor),
-        name = s"DeleteWorkflowFilesActor-${rootWorkflowId.id}")
+      val deleteActor = context.actorOf(
+        DeleteWorkflowFilesActor.props(
+          rootWorkflowId = rootWorkflowId,
+          rootWorkflowRootPaths = data.initializationData.getWorkflowRoots(),
+          rootAndSubworkflowIds = data.rootAndSubworkflowIds,
+          workflowFinalOutputs = data.workflowFinalOutputs.map(out => out.outputs.values.toSet).getOrElse(Set.empty),
+          workflowAllOutputs = data.workflowAllOutputs,
+          pathBuilders = data.workflowDescriptor.get.pathBuilders,
+          serviceRegistryActor = serviceRegistryActor,
+          ioActor = ioActor
+        ),
+        name = s"DeleteWorkflowFilesActor-${rootWorkflowId.id}"
+      )
 
       deleteActor ! StartWorkflowFilesDeletion
 
       goto(DeletingFilesState) using data
     }
 
-    val userDeleteFileWfOption = data.workflowDescriptor.flatMap(
-      _.backendDescriptor.workflowOptions.getBoolean("delete_intermediate_output_files").toOption
-    ).getOrElse(false)
+    val userDeleteFileWfOption = data.workflowDescriptor
+      .flatMap(
+        _.backendDescriptor.workflowOptions.getBoolean("delete_intermediate_output_files").toOption
+      )
+      .getOrElse(false)
 
     (deleteWorkflowFiles, userDeleteFileWfOption, data.workflowAllOutputs.nonEmpty) match {
       case (true, true, true) => deleteFiles()
@@ -668,26 +784,42 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
         // user has not enabled delete intermediate outputs option, so go to succeeded status
         goto(WorkflowSucceededState) using data.copy(currentLifecycleStateActor = None)
       case (false, true, _) =>
-        log.info(s"User wants to delete intermediate files but it is not enabled in Cromwell config. To use it system.delete-workflow-files to true.")
+        log.info(
+          s"User wants to delete intermediate files but it is not enabled in Cromwell config. To use it system.delete-workflow-files to true."
+        )
         goto(WorkflowSucceededState) using data.copy(currentLifecycleStateActor = None)
       case (false, false, _) => goto(WorkflowSucceededState) using data.copy(currentLifecycleStateActor = None)
     }
   }
 
-  private[workflow] def makeFinalizationActor(workflowDescriptor: EngineWorkflowDescriptor, jobExecutionMap: JobExecutionMap, workflowOutputs: CallOutputs) = {
+  private[workflow] def makeFinalizationActor(workflowDescriptor: EngineWorkflowDescriptor,
+                                              jobExecutionMap: JobExecutionMap,
+                                              workflowOutputs: CallOutputs
+  ) = {
     val copyWorkflowOutputsActorProps = stateName match {
       case InitializingWorkflowState => None
-      case _ => Option(CopyWorkflowOutputsActor.props(workflowIdForLogging, ioActor, workflowDescriptor, workflowOutputs, stateData.initializationData))
+      case _ =>
+        Option(
+          CopyWorkflowOutputsActor.props(workflowIdForLogging,
+                                         ioActor,
+                                         workflowDescriptor,
+                                         workflowOutputs,
+                                         stateData.initializationData
+          )
+        )
     }
 
-    context.actorOf(WorkflowFinalizationActor.props(
-      workflowDescriptor = workflowDescriptor,
-      ioActor = ioActor,
-      jobExecutionMap = jobExecutionMap,
-      workflowOutputs = workflowOutputs,
-      initializationData = stateData.initializationData,
-      copyWorkflowOutputsActor = copyWorkflowOutputsActorProps
-    ), name = s"WorkflowFinalizationActor")
+    context.actorOf(
+      WorkflowFinalizationActor.props(
+        workflowDescriptor = workflowDescriptor,
+        ioActor = ioActor,
+        jobExecutionMap = jobExecutionMap,
+        workflowOutputs = workflowOutputs,
+        initializationData = stateData.initializationData,
+        copyWorkflowOutputsActor = copyWorkflowOutputsActorProps
+      ),
+      name = s"WorkflowFinalizationActor"
+    )
   }
 
   /**
@@ -700,17 +832,19 @@ class WorkflowActor(workflowToStart: WorkflowToStart,
                                failures: Option[List[Throwable]],
                                workflowAllOutputs: Set[WomValue] = Set.empty,
                                rootAndSubworkflowIds: Set[WorkflowId] = Set.empty,
-                               lastStateOverride: Option[WorkflowActorState] = None) = {
+                               lastStateOverride: Option[WorkflowActorState] = None
+  ) = {
     val finalizationActor = makeFinalizationActor(workflowDescriptor, jobExecutionMap, workflowFinalOutputs)
     finalizationActor ! StartFinalizationCommand
     goto(FinalizingWorkflowState) using data.copy(
-      lastStateReached = StateCheckpoint (lastStateOverride.getOrElse(stateName), failures),
+      lastStateReached = StateCheckpoint(lastStateOverride.getOrElse(stateName), failures),
       workflowFinalOutputs = Option(workflowFinalOutputs),
       workflowAllOutputs = workflowAllOutputs,
       rootAndSubworkflowIds = rootAndSubworkflowIds
     )
   }
 
-  private def sendHeartbeat(): Unit = workflowStoreActor ! WorkflowStoreWriteHeartbeatCommand(workflowId, submissionTime)
+  private def sendHeartbeat(): Unit =
+    workflowStoreActor ! WorkflowStoreWriteHeartbeatCommand(workflowId, submissionTime)
 
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowDockerLookupActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowDockerLookupActor.scala
index 32889f7f849..8c3afe375a1 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowDockerLookupActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowDockerLookupActor.scala
@@ -8,7 +8,12 @@ import cromwell.core.Dispatcher.EngineDispatcher
 import cromwell.core.{Dispatcher, WorkflowId}
 import cromwell.database.sql.EngineSqlDatabase
 import cromwell.database.sql.tables.DockerHashStoreEntry
-import cromwell.docker.DockerInfoActor.{DockerHashFailureResponse, DockerInfoSuccessResponse, DockerInformation, DockerSize}
+import cromwell.docker.DockerInfoActor.{
+  DockerHashFailureResponse,
+  DockerInformation,
+  DockerInfoSuccessResponse,
+  DockerSize
+}
 import cromwell.docker.{DockerClientHelper, DockerHashResult, DockerImageIdentifier, DockerInfoRequest}
 import cromwell.engine.workflow.WorkflowDockerLookupActor._
 import cromwell.services.EngineServicesStore
@@ -37,11 +42,12 @@ import scala.util.{Failure, Success}
   *      for this tag will be attempted again.
   */
 
-class WorkflowDockerLookupActor private[workflow](workflowId: WorkflowId,
-                                                  val dockerHashingActor: ActorRef,
-                                                  isRestart: Boolean,
-                                                  databaseInterface: EngineSqlDatabase)
-  extends LoggingFSM[WorkflowDockerLookupActorState, WorkflowDockerLookupActorData] with DockerClientHelper {
+class WorkflowDockerLookupActor private[workflow] (workflowId: WorkflowId,
+                                                   val dockerHashingActor: ActorRef,
+                                                   isRestart: Boolean,
+                                                   databaseInterface: EngineSqlDatabase
+) extends LoggingFSM[WorkflowDockerLookupActorState, WorkflowDockerLookupActorData]
+    with DockerClientHelper {
 
   implicit val ec = context.system.dispatchers.lookup(Dispatcher.EngineDispatcher)
 
@@ -55,10 +61,9 @@ class WorkflowDockerLookupActor private[workflow](workflowId: WorkflowId,
   // `AwaitingFirstRequestOnRestart` is only used in restart scenarios.  This state waits until there's at least one hash
   // request before trying to load the docker hash mappings.  This is so we'll have at least one `JobPreparationActor`
   // reference available to message with a terminal failure in case the reading or parsing of these mappings fails.
-  when(AwaitingFirstRequestOnRestart) {
-    case Event(request: DockerInfoRequest, data) =>
-      loadDockerHashStoreEntries()
-      goto(LoadingCache) using data.addHashRequest(request, sender())
+  when(AwaitingFirstRequestOnRestart) { case Event(request: DockerInfoRequest, data) =>
+    loadDockerHashStoreEntries()
+    goto(LoadingCache) using data.addHashRequest(request, sender())
   }
 
   // Waiting for a response from the database with the hash mapping for this workflow.
@@ -89,7 +94,10 @@ class WorkflowDockerLookupActor private[workflow](workflowId: WorkflowId,
     case Event(DockerHashStoreSuccess(response), data) =>
       recordMappingAndRespond(response, data)
     case Event(DockerHashStoreFailure(request, e), data) =>
-      handleStoreFailure(request, new Exception(s"Failure storing docker hash for ${request.dockerImageID.fullName}", e), data)
+      handleStoreFailure(request,
+                         new Exception(s"Failure storing docker hash for ${request.dockerImageID.fullName}", e),
+                         data
+      )
   }
 
   when(Terminal) {
@@ -97,7 +105,10 @@ class WorkflowDockerLookupActor private[workflow](workflowId: WorkflowId,
       // In the Terminal state we reject all requests with the cause set in the state data.
       sender() ! WorkflowDockerLookupFailure(data.failureCause.orNull, request)
       stay()
-    case Event(_ @ (_: DockerInfoSuccessResponse | _: DockerHashFailureResponse | _: DockerHashStoreSuccess | _: DockerHashStoreFailure), _) =>
+    case Event(_ @(_: DockerInfoSuccessResponse | _: DockerHashFailureResponse | _: DockerHashStoreSuccess |
+               _: DockerHashStoreFailure),
+               _
+        ) =>
       // Other expected message types are unsurprising in the Terminal state and can be swallowed. Unexpected message
       // types will be handled by `whenUnhandled`.
       stay()
@@ -110,7 +121,8 @@ class WorkflowDockerLookupActor private[workflow](workflowId: WorkflowId,
 
   whenUnhandled {
     case Event(DockerHashActorTimeout(request), data) =>
-      val reason = new Exception(s"Timeout looking up hash for Docker image ${request.dockerImageID} in state $stateName")
+      val reason =
+        new Exception(s"Timeout looking up hash for Docker image ${request.dockerImageID} in state $stateName")
       data.hashRequests.get(request.dockerImageID) match {
         case Some(requestsAndReplyTos) =>
           requestsAndReplyTos foreach { case RequestAndReplyTo(_, replyTo) =>
@@ -119,9 +131,16 @@ class WorkflowDockerLookupActor private[workflow](workflowId: WorkflowId,
           val updatedData = data.copy(hashRequests = data.hashRequests - request.dockerImageID)
           stay() using updatedData
         case None =>
-          val headline = s"Unable to find requesters for timed out lookup of Docker image '${request.dockerImageID}' in state $stateName"
-          val pendingImageIdsAndCounts = stateData.hashRequests.toList map { case (imageId, requestAndReplyTos) => s"$imageId -> ${requestAndReplyTos.size}" }
-          val message = pendingImageIdsAndCounts.mkString(headline + "\n" + "Pending image ID requests with requester counts: ", ", ", "")
+          val headline =
+            s"Unable to find requesters for timed out lookup of Docker image '${request.dockerImageID}' in state $stateName"
+          val pendingImageIdsAndCounts = stateData.hashRequests.toList map { case (imageId, requestAndReplyTos) =>
+            s"$imageId -> ${requestAndReplyTos.size}"
+          }
+          val message =
+            pendingImageIdsAndCounts.mkString(headline + "\n" + "Pending image ID requests with requester counts: ",
+                                              ", ",
+                                              ""
+            )
           fail(new RuntimeException(message) with NoStackTrace)
       }
     case Event(TransitionToFailed(cause), data) =>
@@ -137,27 +156,37 @@ class WorkflowDockerLookupActor private[workflow](workflowId: WorkflowId,
     * Load mappings from the database into the state data, reply to queued requests which have mappings, and initiate
     * hash lookups for requests which don't have mappings.
     */
-  private def loadCacheAndHandleHashRequests(hashEntries: Map[String, DockerHashStoreEntry], data: WorkflowDockerLookupActorData): State = {
-    val dockerMappingsTry = hashEntries map {
-      case (dockerTag, entry) => (
+  private def loadCacheAndHandleHashRequests(hashEntries: Map[String, DockerHashStoreEntry],
+                                             data: WorkflowDockerLookupActorData
+  ): State = {
+    val dockerMappingsTry = hashEntries map { case (dockerTag, entry) =>
+      (
         DockerImageIdentifier.fromString(dockerTag),
-        DockerHashResult.fromString(entry.dockerHash) map { hash => DockerInformation(hash, entry.dockerSize.map(DockerSize.apply)) }
+        DockerHashResult.fromString(entry.dockerHash) map { hash =>
+          DockerInformation(hash, entry.dockerSize.map(DockerSize.apply))
+        }
       )
     }
 
     TryUtil.sequenceKeyValues(dockerMappingsTry) match {
       case Success(dockerMappings) =>
         // Figure out which of the queued requests already have established mappings.
-        val (hasMappings, doesNotHaveMappings) = data.hashRequests.partition { case (dockerImageId, _) => dockerMappings.contains(dockerImageId) }
+        val (hasMappings, doesNotHaveMappings) = data.hashRequests.partition { case (dockerImageId, _) =>
+          dockerMappings.contains(dockerImageId)
+        }
 
         // The requests which have mappings receive success responses.
         hasMappings foreach { case (dockerImageId, requestAndReplyTos) =>
           val result = dockerMappings(dockerImageId)
-          requestAndReplyTos foreach { case RequestAndReplyTo(request, replyTo) => replyTo ! DockerInfoSuccessResponse(result, request)}
+          requestAndReplyTos foreach { case RequestAndReplyTo(request, replyTo) =>
+            replyTo ! DockerInfoSuccessResponse(result, request)
+          }
         }
 
         // The requests without mappings need to be looked up.
-        doesNotHaveMappings foreach { case (_, requestAndReplyTos) => sendDockerCommand(requestAndReplyTos.head.request) }
+        doesNotHaveMappings foreach { case (_, requestAndReplyTos) =>
+          sendDockerCommand(requestAndReplyTos.head.request)
+        }
 
         // Update state data accordingly.
         val newData = data.copy(hashRequests = doesNotHaveMappings, mappings = dockerMappings, failureCause = None)
@@ -171,55 +200,83 @@ class WorkflowDockerLookupActor private[workflow](workflowId: WorkflowId,
   private def requestDockerHash(request: DockerInfoRequest, data: WorkflowDockerLookupActorData): State = {
     sendDockerCommand(request)
     val replyTo = sender()
-    val updatedData = data.copy(hashRequests = data.hashRequests + (request.dockerImageID -> NonEmptyList.of(RequestAndReplyTo(request, replyTo))))
+    val updatedData = data.copy(hashRequests =
+      data.hashRequests + (request.dockerImageID -> NonEmptyList.of(RequestAndReplyTo(request, replyTo)))
+    )
     stay() using updatedData
   }
 
-  private def recordMappingAndRespond(response: DockerInfoSuccessResponse, data: WorkflowDockerLookupActorData): State = {
+  private def recordMappingAndRespond(response: DockerInfoSuccessResponse,
+                                      data: WorkflowDockerLookupActorData
+  ): State = {
     // Add the new label to hash mapping to the current set of mappings.
     val request = response.request
     data.hashRequests.get(request.dockerImageID) match {
-      case Some(actors) => actors foreach { case RequestAndReplyTo(_, replyTo) => replyTo ! DockerInfoSuccessResponse(response.dockerInformation, request) }
-      case None => fail(new Exception(s"Could not find the actors associated with $request. Available requests are ${data.hashRequests.keys.mkString(", ")}") with NoStackTrace)
+      case Some(actors) =>
+        actors foreach { case RequestAndReplyTo(_, replyTo) =>
+          replyTo ! DockerInfoSuccessResponse(response.dockerInformation, request)
+        }
+      case None =>
+        fail(
+          new Exception(
+            s"Could not find the actors associated with $request. Available requests are ${data.hashRequests.keys.mkString(", ")}"
+          ) with NoStackTrace
+        )
     }
-    val updatedData = data.copy(hashRequests = data.hashRequests - request.dockerImageID, mappings = data.mappings + (request.dockerImageID -> response.dockerInformation))
+    val updatedData = data.copy(hashRequests = data.hashRequests - request.dockerImageID,
+                                mappings = data.mappings + (request.dockerImageID -> response.dockerInformation)
+    )
     stay() using updatedData
   }
 
   private def respondToAllRequests(reason: Throwable,
                                    data: WorkflowDockerLookupActorData,
-                                   messageBuilder: (Throwable, DockerInfoRequest) => WorkflowDockerLookupResponse): WorkflowDockerLookupActorData = {
+                                   messageBuilder: (Throwable, DockerInfoRequest) => WorkflowDockerLookupResponse
+  ): WorkflowDockerLookupActorData = {
     data.hashRequests foreach { case (_, replyTos) =>
       replyTos foreach { case RequestAndReplyTo(request, replyTo) => replyTo ! messageBuilder(reason, request) }
     }
     data.clearHashRequests
   }
 
-  private def respondToAllRequestsWithTerminalFailure(reason: Throwable, data: WorkflowDockerLookupActorData): WorkflowDockerLookupActorData = {
+  private def respondToAllRequestsWithTerminalFailure(reason: Throwable,
+                                                      data: WorkflowDockerLookupActorData
+  ): WorkflowDockerLookupActorData =
     respondToAllRequests(reason, data, WorkflowDockerTerminalFailure.apply)
-  }
 
   private def persistDockerHash(response: DockerInfoSuccessResponse, data: WorkflowDockerLookupActorData): State = {
     // BA-6495 if there are actors awaiting for this data, then proceed, otherwise - don't bother to persist
     if (data.hashRequests.contains(response.request.dockerImageID)) {
-      val dockerHashStoreEntry = DockerHashStoreEntry(workflowId.toString, response.request.dockerImageID.fullName, response.dockerInformation.dockerHash.algorithmAndHash, response.dockerInformation.dockerCompressedSize.map(_.compressedSize))
+      val dockerHashStoreEntry = DockerHashStoreEntry(
+        workflowId.toString,
+        response.request.dockerImageID.fullName,
+        response.dockerInformation.dockerHash.algorithmAndHash,
+        response.dockerInformation.dockerCompressedSize.map(_.compressedSize)
+      )
       databaseInterface.addDockerHashStoreEntry(dockerHashStoreEntry) onComplete {
         case Success(_) => self ! DockerHashStoreSuccess(response)
         case Failure(ex) => self ! DockerHashStoreFailure(response.request, ex)
       }
     } else {
-      log.debug(s"Unable to find requesters for succeeded lookup of Docker image " +
-        s"'${response.request.dockerImageID}'. Most likely reason is that requesters have already been cleaned out " +
-        s"earlier by the timeout.")
+      log.debug(
+        s"Unable to find requesters for succeeded lookup of Docker image " +
+          s"'${response.request.dockerImageID}'. Most likely reason is that requesters have already been cleaned out " +
+          s"earlier by the timeout."
+      )
     }
     stay()
   }
 
-  private def handleLookupFailure(dockerResponse: DockerHashFailureResponse, data: WorkflowDockerLookupActorData): State = {
+  private def handleLookupFailure(dockerResponse: DockerHashFailureResponse,
+                                  data: WorkflowDockerLookupActorData
+  ): State = {
     // Fail all pending requests.  This logic does not blacklist the tag, which will allow lookups to be attempted
     // again in the future.
-    val exceptionMessage = s"Failed Docker lookup '${dockerResponse.request.dockerImageID}' '${dockerResponse.request.credentialDetails.mkString("[", ", ", "]")}'"
-    val failureResponse = WorkflowDockerLookupFailure(new Exception(dockerResponse.reason), dockerResponse.request, exceptionMessage)
+    val exceptionMessage =
+      s"Failed Docker lookup '${dockerResponse.request.dockerImageID}' '${dockerResponse.request.credentialDetails
+          .mkString("[", ", ", "]")}'"
+    val failureResponse =
+      WorkflowDockerLookupFailure(new Exception(dockerResponse.reason), dockerResponse.request, exceptionMessage)
     val request = dockerResponse.request
     data.hashRequests.get(request.dockerImageID) match {
       case Some(requestAndReplyTos) =>
@@ -227,27 +284,35 @@ class WorkflowDockerLookupActor private[workflow](workflowId: WorkflowId,
         val updatedData = data.copy(hashRequests = data.hashRequests - request.dockerImageID)
         stay() using updatedData
       case None =>
-        log.debug(s"Unable to find requesters for failed lookup of Docker image '${request.dockerImageID}'. " +
-          s"Most likely reason is that requesters have already been cleaned out earlier by the timeout.")
+        log.debug(
+          s"Unable to find requesters for failed lookup of Docker image '${request.dockerImageID}'. " +
+            s"Most likely reason is that requesters have already been cleaned out earlier by the timeout."
+        )
         stay()
     }
   }
 
-  private def handleStoreFailure(dockerHashRequest: DockerInfoRequest, reason: Throwable, data: WorkflowDockerLookupActorData): State = {
+  private def handleStoreFailure(dockerHashRequest: DockerInfoRequest,
+                                 reason: Throwable,
+                                 data: WorkflowDockerLookupActorData
+  ): State =
     data.hashRequests.get(dockerHashRequest.dockerImageID) match {
       case Some(requestAndReplyTos) =>
-        requestAndReplyTos foreach { case RequestAndReplyTo(_, replyTo) => replyTo ! WorkflowDockerLookupFailure(reason, dockerHashRequest) }
+        requestAndReplyTos foreach { case RequestAndReplyTo(_, replyTo) =>
+          replyTo ! WorkflowDockerLookupFailure(reason, dockerHashRequest)
+        }
         // Remove these requesters from the collection of those awaiting hashes.
         stay() using data.copy(hashRequests = data.hashRequests - dockerHashRequest.dockerImageID)
       case None =>
-        log.debug(s"Unable to find requesters for failed store of hash for Docker image " +
-          s"'${dockerHashRequest.dockerImageID}'. Most likely reason is that requesters have already been cleaned " +
-          s"out earlier by the timeout.")
+        log.debug(
+          s"Unable to find requesters for failed store of hash for Docker image " +
+            s"'${dockerHashRequest.dockerImageID}'. Most likely reason is that requesters have already been cleaned " +
+            s"out earlier by the timeout."
+        )
         stay()
     }
-  }
 
-  def loadDockerHashStoreEntries(): Unit = {
+  def loadDockerHashStoreEntries(): Unit =
     databaseInterface.queryDockerHashStoreEntries(workflowId.toString) onComplete {
       case Success(dockerHashEntries) =>
         val dockerMappings = dockerHashEntries.map(entry => entry.dockerTag -> entry).toMap
@@ -255,13 +320,11 @@ class WorkflowDockerLookupActor private[workflow](workflowId: WorkflowId,
       case Failure(ex) =>
         fail(new RuntimeException("Failed to load docker tag -> hash mappings from DB", ex))
     }
-  }
 
-  override protected def onTimeout(message: Any, to: ActorRef): Unit = {
+  override protected def onTimeout(message: Any, to: ActorRef): Unit =
     message match {
       case r: DockerInfoRequest => self ! DockerHashActorTimeout(r)
     }
-  }
 }
 
 object WorkflowDockerLookupActor {
@@ -272,41 +335,52 @@ object WorkflowDockerLookupActor {
   case object Running extends WorkflowDockerLookupActorState
   case object Terminal extends WorkflowDockerLookupActorState
   private val FailedException =
-    new Exception(s"The WorkflowDockerLookupActor has failed. Subsequent docker tags for this workflow will not be resolved.")
+    new Exception(
+      s"The WorkflowDockerLookupActor has failed. Subsequent docker tags for this workflow will not be resolved."
+    )
 
   /* Internal ADTs */
   final case class DockerRequestContext(dockerHashRequest: DockerInfoRequest, replyTo: ActorRef)
   sealed trait DockerHashStoreResponse
   final case class DockerHashStoreSuccess(successResponse: DockerInfoSuccessResponse) extends DockerHashStoreResponse
-  final case class DockerHashStoreFailure(dockerHashRequest: DockerInfoRequest, reason: Throwable) extends DockerHashStoreResponse
+  final case class DockerHashStoreFailure(dockerHashRequest: DockerInfoRequest, reason: Throwable)
+      extends DockerHashStoreResponse
   final case class DockerHashStoreLoadingSuccess(dockerMappings: Map[String, DockerHashStoreEntry])
   final case class DockerHashActorTimeout(request: DockerInfoRequest)
 
   /* Messages */
   sealed trait WorkflowDockerLookupActorMessage
-  private final case class TransitionToFailed(cause: Throwable) extends WorkflowDockerLookupActorMessage
+  final private case class TransitionToFailed(cause: Throwable) extends WorkflowDockerLookupActorMessage
 
   /* Responses */
   sealed trait WorkflowDockerLookupResponse
-  final case class WorkflowDockerLookupFailure(reason: Throwable, request: DockerInfoRequest, additionalLoggingMessage: String = "") extends WorkflowDockerLookupResponse
-  final case class WorkflowDockerTerminalFailure(reason: Throwable, request: DockerInfoRequest) extends WorkflowDockerLookupResponse
+  final case class WorkflowDockerLookupFailure(reason: Throwable,
+                                               request: DockerInfoRequest,
+                                               additionalLoggingMessage: String = ""
+  ) extends WorkflowDockerLookupResponse
+  final case class WorkflowDockerTerminalFailure(reason: Throwable, request: DockerInfoRequest)
+      extends WorkflowDockerLookupResponse
 
   case class RequestAndReplyTo(request: DockerInfoRequest, replyTo: ActorRef)
 
   def props(workflowId: WorkflowId,
             dockerHashingActor: ActorRef,
             isRestart: Boolean,
-            databaseInterface: EngineSqlDatabase = EngineServicesStore.engineDatabaseInterface): Props = {
-    Props(new WorkflowDockerLookupActor(workflowId, dockerHashingActor, isRestart, databaseInterface)).withDispatcher(EngineDispatcher)
-  }
+            databaseInterface: EngineSqlDatabase = EngineServicesStore.engineDatabaseInterface
+  ): Props =
+    Props(new WorkflowDockerLookupActor(workflowId, dockerHashingActor, isRestart, databaseInterface))
+      .withDispatcher(EngineDispatcher)
 
   object WorkflowDockerLookupActorData {
     def empty = WorkflowDockerLookupActorData(hashRequests = Map.empty, mappings = Map.empty, failureCause = None)
   }
 
-  final case class WorkflowDockerLookupActorData(hashRequests: Map[DockerImageIdentifier, NonEmptyList[RequestAndReplyTo]],
-                                                 mappings: Map[DockerImageIdentifier, DockerInformation],
-                                                 failureCause: Option[Throwable]) {
+  final case class WorkflowDockerLookupActorData(
+    hashRequests: Map[DockerImageIdentifier, NonEmptyList[RequestAndReplyTo]],
+    mappings: Map[DockerImageIdentifier, DockerInformation],
+    failureCause: Option[Throwable]
+  ) {
+
     /**
       * Add the specified request and replyTo to this state data.
       *
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
index c3b1b998a94..abad4961211 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowManagerActor.scala
@@ -37,6 +37,7 @@ object WorkflowManagerActor {
   class WorkflowNotFoundException(s: String) extends Exception(s)
 
   sealed trait WorkflowManagerActorMessage
+
   /**
     * Commands
     */
@@ -48,7 +49,8 @@ object WorkflowManagerActor {
   final case class SubscribeToWorkflowCommand(id: WorkflowId) extends WorkflowManagerActorCommand
   case object EngineStatsCommand extends WorkflowManagerActorCommand
   case class AbortWorkflowsCommand(ids: Set[WorkflowId]) extends WorkflowManagerActorCommand
-  final case class WorkflowActorWorkComplete(id: WorkflowId, actor: ActorRef, finalState: WorkflowState) extends WorkflowManagerActorCommand
+  final case class WorkflowActorWorkComplete(id: WorkflowId, actor: ActorRef, finalState: WorkflowState)
+      extends WorkflowManagerActorCommand
 
   def props(config: Config,
             callCachingEnabled: Boolean,
@@ -67,7 +69,8 @@ object WorkflowManagerActor {
             jobExecutionTokenDispenserActor: ActorRef,
             backendSingletonCollection: BackendSingletonCollection,
             serverMode: Boolean,
-            workflowHeartbeatConfig: WorkflowHeartbeatConfig): Props = {
+            workflowHeartbeatConfig: WorkflowHeartbeatConfig
+  ): Props = {
     val params = WorkflowManagerActorParams(
       config = config,
       callCachingEnabled = callCachingEnabled,
@@ -86,7 +89,8 @@ object WorkflowManagerActor {
       jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
       backendSingletonCollection = backendSingletonCollection,
       serverMode = serverMode,
-      workflowHeartbeatConfig = workflowHeartbeatConfig)
+      workflowHeartbeatConfig = workflowHeartbeatConfig
+    )
     Props(new WorkflowManagerActor(params)).withDispatcher(EngineDispatcher)
   }
 
@@ -111,11 +115,10 @@ object WorkflowManagerActor {
     }
 
     def without(id: WorkflowId): WorkflowManagerData = this.copy(workflows = workflows - id)
-    def without(actor: ActorRef): WorkflowManagerData = {
+    def without(actor: ActorRef): WorkflowManagerData =
       // If the ID was found in the lookup return a modified copy of the state data, otherwise just return
       // the same state data.
       idFromActor(actor) map without getOrElse this
-    }
   }
 }
 
@@ -136,25 +139,30 @@ case class WorkflowManagerActorParams(config: Config,
                                       jobExecutionTokenDispenserActor: ActorRef,
                                       backendSingletonCollection: BackendSingletonCollection,
                                       serverMode: Boolean,
-                                      workflowHeartbeatConfig: WorkflowHeartbeatConfig)
+                                      workflowHeartbeatConfig: WorkflowHeartbeatConfig
+)
 
 class WorkflowManagerActor(params: WorkflowManagerActorParams)
-  extends LoggingFSM[WorkflowManagerState, WorkflowManagerData] with WorkflowMetadataHelper with Timers {
+    extends LoggingFSM[WorkflowManagerState, WorkflowManagerData]
+    with WorkflowMetadataHelper
+    with Timers {
 
   private val config = params.config
   private val callCachingEnabled: Boolean = params.callCachingEnabled
   private val invalidateBadCacheResults = params.invalidateBadCacheResults
   override val serviceRegistryActor = params.serviceRegistryActor
 
-  private val maxWorkflowsRunning = config.getConfig("system").as[Option[Int]]("max-concurrent-workflows").getOrElse(DefaultMaxWorkflowsToRun)
-  private val maxWorkflowsToLaunch = config.getConfig("system").as[Option[Int]]("max-workflow-launch-count").getOrElse(DefaultMaxWorkflowsToLaunch)
-  private val newWorkflowPollRate = config.getConfig("system").as[Option[Int]]("new-workflow-poll-rate").getOrElse(DefaultNewWorkflowPollRate).seconds
+  private val maxWorkflowsRunning =
+    config.getConfig("system").as[Option[Int]]("max-concurrent-workflows").getOrElse(DefaultMaxWorkflowsToRun)
+  private val maxWorkflowsToLaunch =
+    config.getConfig("system").as[Option[Int]]("max-workflow-launch-count").getOrElse(DefaultMaxWorkflowsToLaunch)
+  private val newWorkflowPollRate =
+    config.getConfig("system").as[Option[Int]]("new-workflow-poll-rate").getOrElse(DefaultNewWorkflowPollRate).seconds
   private val fileHashCacheEnabled = config.as[Option[Boolean]]("system.file-hash-cache").getOrElse(false)
 
   private val logger = Logging(context.system, this)
   private val tag = self.path.name
 
-
   override def preStart(): Unit = {
     // Starts the workflow polling cycle
     timers.startSingleTimer(RetrieveNewWorkflowsKey, RetrieveNewWorkflows, Duration.Zero)
@@ -182,7 +190,8 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
       val wfCount = stateData.workflows.size
       val swfCount = stateData.subWorkflows.size
       val maxNewWorkflows = maxWorkflowsToLaunch min (maxWorkflowsRunning - wfCount - swfCount)
-      val fetchCountLog = s"Fetching $maxNewWorkflows new workflows ($wfCount workflows and $swfCount subworkflows in flight)"
+      val fetchCountLog =
+        s"Fetching $maxNewWorkflows new workflows ($wfCount workflows and $swfCount subworkflows in flight)"
       if (groups.nonEmpty)
         log.info(s"${fetchCountLog}, excluding groups: ${groups.mkString(", ")}")
       else if (maxNewWorkflows < 1)
@@ -199,13 +208,13 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
       log.info("Retrieved {} workflows from the WorkflowStoreActor", newSubmissions.toList.size)
       stay() using stateData.withAddition(newSubmissions)
     case Event(SubscribeToWorkflowCommand(id), data) =>
-      data.workflows.get(id) foreach {_ ! SubscribeTransitionCallBack(sender())}
+      data.workflows.get(id) foreach { _ ! SubscribeTransitionCallBack(sender()) }
       stay()
     case Event(AbortAllWorkflowsCommand, data) if data.workflows.isEmpty =>
       goto(Done)
     case Event(AbortAllWorkflowsCommand, data) =>
       log.info(s"$tag: Aborting all workflows")
-      data.workflows.values.foreach { _ ! WorkflowActor.AbortWorkflowCommand }
+      data.workflows.values.foreach(_ ! WorkflowActor.AbortWorkflowCommand)
       goto(Aborting)
     /*
      Responses from services
@@ -214,7 +223,9 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
       log.info(s"$tag: Workflow $workflowId failed (during $inState): ${expandFailureReasons(reasons)}")
       stay()
     case Event(WorkflowActorWorkComplete(id: WorkflowId, workflowActor: ActorRef, finalState: WorkflowState), data) =>
-      log.info(s"$tag: Workflow actor for $id completed with status '$finalState'. The workflow will be removed from the workflow store.")
+      log.info(
+        s"$tag: Workflow actor for $id completed with status '$finalState'. The workflow will be removed from the workflow store."
+      )
       // This silently fails if idFromActor is None, but data.without call right below will as well
       data.idFromActor(workflowActor) foreach { workflowId =>
         params.jobStoreActor ! RegisterWorkflowCompleted(workflowId)
@@ -223,16 +234,18 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
   }
 
   val scheduleNextNewWorkflowPollStateFunction: StateFunction = {
-    case event @ Event(WorkflowStoreEngineActor.NoNewWorkflowsToStart | _: WorkflowStoreEngineActor.NewWorkflowsToStart, _) =>
+    case event @ Event(WorkflowStoreEngineActor.NoNewWorkflowsToStart | _: WorkflowStoreEngineActor.NewWorkflowsToStart,
+                       _
+        ) =>
       scheduleNextNewWorkflowPoll()
       runningAndNotStartingNewWorkflowsStateFunction(event)
   }
 
-  when (Running) (scheduleNextNewWorkflowPollStateFunction.orElse(runningAndNotStartingNewWorkflowsStateFunction))
+  when(Running)(scheduleNextNewWorkflowPollStateFunction.orElse(runningAndNotStartingNewWorkflowsStateFunction))
 
-  when (RunningAndNotStartingNewWorkflows) (runningAndNotStartingNewWorkflowsStateFunction)
+  when(RunningAndNotStartingNewWorkflows)(runningAndNotStartingNewWorkflowsStateFunction)
 
-  when (Aborting) {
+  when(Aborting) {
     case Event(Transition(workflowActor, _, _: WorkflowActorTerminalState), data) =>
       // Remove this terminal actor from the workflowStore and log a progress message.
       val updatedData = data.without(workflowActor)
@@ -249,7 +262,7 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
     case Event(_, _) => stay()
   }
 
-  when (Done) { FSM.NullFunction }
+  when(Done)(FSM.NullFunction)
 
   whenUnhandled {
     case Event(AbortWorkflowsCommand(ids), stateData) =>
@@ -280,7 +293,9 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
       stay()
     case Event(EngineStatsCommand, data) =>
       val sndr = sender()
-      context.actorOf(EngineStatsActor.props(data.workflows.values.toList, sndr), s"EngineStatsActor-${sndr.hashCode()}")
+      context.actorOf(EngineStatsActor.props(data.workflows.values.toList, sndr),
+                      s"EngineStatsActor-${sndr.hashCode()}"
+      )
       stay()
     // Anything else certainly IS interesting:
     case Event(unhandled, _) =>
@@ -311,12 +326,13 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
       logger.info(s"$tag: Starting workflow UUID($workflowId)")
     }
 
-    val fileHashCacheActorProps: Option[Props] = fileHashCacheEnabled.option(RootWorkflowFileHashCacheActor.props(params.ioActor, workflowId))
+    val fileHashCacheActorProps: Option[Props] =
+      fileHashCacheEnabled.option(RootWorkflowFileHashCacheActor.props(params.ioActor, workflowId))
 
     val wfProps = WorkflowActor.props(
       workflowToStart = workflow,
       conf = config,
-      callCachingEnabled = callCachingEnabled ,
+      callCachingEnabled = callCachingEnabled,
       invalidateBadCacheResults = invalidateBadCacheResults,
       ioActor = params.ioActor,
       serviceRegistryActor = params.serviceRegistryActor,
@@ -335,7 +351,8 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
       workflowHeartbeatConfig = params.workflowHeartbeatConfig,
       totalJobsByRootWf = new AtomicInteger(),
       fileHashCacheActorProps = fileHashCacheActorProps,
-      blacklistCache = callCachingBlacklistManager.blacklistCacheFor(workflow))
+      blacklistCache = callCachingBlacklistManager.blacklistCacheFor(workflow)
+    )
     val wfActor = context.actorOf(wfProps, name = s"WorkflowActor-$workflowId")
 
     wfActor ! SubscribeTransitionCallBack(self)
@@ -344,9 +361,8 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
     WorkflowIdToActorRef(workflowId, wfActor)
   }
 
-  private def scheduleNextNewWorkflowPoll() = {
+  private def scheduleNextNewWorkflowPoll() =
     timers.startSingleTimer(RetrieveNewWorkflowsKey, RetrieveNewWorkflows, newWorkflowPollRate)
-  }
 
   private def expandFailureReasons(reasons: Seq[Throwable]): String = {
 
@@ -356,9 +372,9 @@ class WorkflowManagerActor(params: WorkflowManagerActorParams)
       case reason: ThrowableAggregation => expandFailureReasons(reason.throwables.toSeq)
       case reason: KnownJobFailureException =>
         val stderrMessage = reason.stderrPath map { path =>
-          val content = Try(path.annotatedContentAsStringWithLimit(3000)).recover({
-            case e => s"Could not retrieve content: ${e.getMessage}"
-          }).get
+          val content = Try(path.annotatedContentAsStringWithLimit(3000)).recover { case e =>
+            s"Could not retrieve content: ${e.getMessage}"
+          }.get
           s"\nCheck the content of stderr for potential additional information: ${path.pathAsString}.\n $content"
         } getOrElse ""
         reason.getMessage + stderrMessage
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowMetadataHelper.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowMetadataHelper.scala
index e26dfaf4eea..784604be614 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowMetadataHelper.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowMetadataHelper.scala
@@ -10,7 +10,7 @@ import cromwell.services.metadata.MetadataService._
 trait WorkflowMetadataHelper {
 
   def serviceRegistryActor: ActorRef
-  
+
   def pushWorkflowStart(workflowId: WorkflowId) = {
     val startEvent = MetadataEvent(
       MetadataKey(workflowId, None, WorkflowMetadataKeys.StartTime),
@@ -18,7 +18,7 @@ trait WorkflowMetadataHelper {
     )
     serviceRegistryActor ! PutMetadataAction(startEvent)
   }
-  
+
   def pushWorkflowEnd(workflowId: WorkflowId) = {
     val metadataEventMsg = MetadataEvent(
       MetadataKey(workflowId, None, WorkflowMetadataKeys.EndTime),
@@ -26,19 +26,25 @@ trait WorkflowMetadataHelper {
     )
     serviceRegistryActor ! PutMetadataAction(metadataEventMsg)
   }
-  
+
   def pushWorkflowFailures(workflowId: WorkflowId, failures: List[Throwable]) = {
-    val failureEvents = failures flatMap { r => throwableToMetadataEvents(MetadataKey(workflowId, None, s"${WorkflowMetadataKeys.Failures}"), r) }
+    val failureEvents = failures flatMap { r =>
+      throwableToMetadataEvents(MetadataKey(workflowId, None, s"${WorkflowMetadataKeys.Failures}"), r)
+    }
     serviceRegistryActor ! PutMetadataAction(failureEvents)
   }
-  
-  def pushCurrentStateToMetadataService(workflowId: WorkflowId, workflowState: WorkflowState, confirmTo: Option[ActorRef] = None): Unit = {
-    val metadataEventMsg = MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.Status), MetadataValue(workflowState))
+
+  def pushCurrentStateToMetadataService(workflowId: WorkflowId,
+                                        workflowState: WorkflowState,
+                                        confirmTo: Option[ActorRef] = None
+  ): Unit = {
+    val metadataEventMsg =
+      MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.Status), MetadataValue(workflowState))
 
     confirmTo match {
       case None => serviceRegistryActor ! PutMetadataAction(metadataEventMsg)
       case Some(actorRef) => serviceRegistryActor ! PutMetadataActionAndRespond(List(metadataEventMsg), actorRef)
     }
   }
-  
+
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/WorkflowProcessingEventPublishing.scala b/engine/src/main/scala/cromwell/engine/workflow/WorkflowProcessingEventPublishing.scala
index 67b5626f018..83bac473d26 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/WorkflowProcessingEventPublishing.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/WorkflowProcessingEventPublishing.scala
@@ -17,7 +17,11 @@ import scala.util.Random
 object WorkflowProcessingEventPublishing {
   private lazy val cromwellVersion = VersionUtil.getVersion("cromwell")
 
-  def publish(workflowId: WorkflowId, cromwellId: String, descriptionValue: DescriptionEventValue.Value, serviceRegistry: ActorRef): Unit = {
+  def publish(workflowId: WorkflowId,
+              cromwellId: String,
+              descriptionValue: DescriptionEventValue.Value,
+              serviceRegistry: ActorRef
+  ): Unit = {
     def randomNumberString: String = Random.nextInt(Int.MaxValue).toString
 
     def metadataKey(workflowId: WorkflowId, randomNumberString: String, key: String) =
@@ -41,18 +45,16 @@ object WorkflowProcessingEventPublishing {
 
   def publishLabelsToMetadata(workflowId: WorkflowId,
                               labels: Map[String, String],
-                              serviceRegistry: ActorRef): IOChecked[Unit] = {
+                              serviceRegistry: ActorRef
+  ): IOChecked[Unit] = {
     val defaultLabel = "cromwell-workflow-id" -> s"cromwell-$workflowId"
     Monad[IOChecked].pure(labelsToMetadata(workflowId, labels + defaultLabel, serviceRegistry))
   }
 
-  private def labelsToMetadata(workflowId: WorkflowId,
-                               labels: Map[String, String],
-                               serviceRegistry: ActorRef): Unit = {
+  private def labelsToMetadata(workflowId: WorkflowId, labels: Map[String, String], serviceRegistry: ActorRef): Unit =
     labels foreach { case (labelKey, labelValue) =>
       val metadataKey = MetadataKey(workflowId, None, s"${WorkflowMetadataKeys.Labels}:$labelKey")
       val metadataValue = MetadataValue(labelValue)
       serviceRegistry ! PutMetadataAction(MetadataEvent(metadataKey, metadataValue))
     }
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/TimedFSM.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/TimedFSM.scala
index 8b29fe561c5..9367ba6e3cc 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/TimedFSM.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/TimedFSM.scala
@@ -11,10 +11,9 @@ trait TimedFSM[S] { this: FSM[S, _] =>
 
   def currentStateDuration: FiniteDuration = (System.currentTimeMillis() - lastTransitionTime).milliseconds
 
-  onTransition {
-    case from -> to =>
-      val now = System.currentTimeMillis()
-      onTimedTransition(from, to, (now - lastTransitionTime).milliseconds)
-      lastTransitionTime = now
+  onTransition { case from -> to =>
+    val now = System.currentTimeMillis()
+    onTimedTransition(from, to, (now - lastTransitionTime).milliseconds)
+    lastTransitionTime = now
   }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowLifecycleActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowLifecycleActor.scala
index c5657e9a60a..0e76c4fb900 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowLifecycleActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/WorkflowLifecycleActor.scala
@@ -27,17 +27,18 @@ object WorkflowLifecycleActor {
   case class WorkflowLifecycleActorData(actors: Set[ActorRef],
                                         successes: Seq[BackendActorAndInitializationData],
                                         failures: Map[ActorRef, Throwable],
-                                        aborted: Seq[ActorRef]) {
+                                        aborted: Seq[ActorRef]
+  ) {
 
     def withActors(actors: Set[ActorRef]) = this.copy(
       actors = this.actors ++ actors
     )
     def withSuccess(successfulActor: ActorRef, data: Option[BackendInitializationData] = None) = this.copy(
       actors = this.actors - successfulActor,
-      successes = successes :+ BackendActorAndInitializationData(successfulActor, data))
-    def withFailure(failedActor: ActorRef, reason: Throwable) = this.copy(
-      actors = this.actors - failedActor,
-      failures = failures + (failedActor -> reason))
+      successes = successes :+ BackendActorAndInitializationData(successfulActor, data)
+    )
+    def withFailure(failedActor: ActorRef, reason: Throwable) =
+      this.copy(actors = this.actors - failedActor, failures = failures + (failedActor -> reason))
     def withAborted(abortedActor: ActorRef) = this.copy(
       actors = this.actors - abortedActor,
       aborted = aborted :+ abortedActor
@@ -51,7 +52,7 @@ trait AbortableWorkflowLifecycleActor[S <: WorkflowLifecycleActorState] extends
 
   def abortedResponse: EngineLifecycleActorAbortedResponse
 
-  override protected def checkForDoneAndTransition(newData: WorkflowLifecycleActorData): State = {
+  override protected def checkForDoneAndTransition(newData: WorkflowLifecycleActorData): State =
     if (checkForDone(newData)) {
       if (stateName == abortingState) {
         context.parent ! abortedResponse
@@ -60,10 +61,11 @@ trait AbortableWorkflowLifecycleActor[S <: WorkflowLifecycleActorState] extends
     } else {
       stay() using newData
     }
-  }
 }
 
-trait WorkflowLifecycleActor[S <: WorkflowLifecycleActorState] extends LoggingFSM[S, WorkflowLifecycleActorData] with WorkflowLogging {
+trait WorkflowLifecycleActor[S <: WorkflowLifecycleActorState]
+    extends LoggingFSM[S, WorkflowLifecycleActorData]
+    with WorkflowLogging {
   val successState: S
   val failureState: S
 
@@ -78,10 +80,9 @@ trait WorkflowLifecycleActor[S <: WorkflowLifecycleActorState] extends LoggingFS
     case t => super.supervisorStrategy.decider.applyOrElse(t, (_: Any) => Escalate)
   }
 
-  whenUnhandled {
-    case unhandledMessage =>
-      workflowLogger.warn(s"received an unhandled message: $unhandledMessage")
-      stay()
+  whenUnhandled { case unhandledMessage =>
+    workflowLogger.warn(s"received an unhandled message: $unhandledMessage")
+    stay()
   }
 
   onTransition {
@@ -92,7 +93,7 @@ trait WorkflowLifecycleActor[S <: WorkflowLifecycleActorState] extends LoggingFS
       workflowLogger.debug(s"State is transitioning from $fromState to $toState.")
   }
 
-  protected def checkForDoneAndTransition(newData: WorkflowLifecycleActorData): State = {
+  protected def checkForDoneAndTransition(newData: WorkflowLifecycleActorData): State =
     if (checkForDone(newData)) {
       if (newData.failures.isEmpty) {
         context.parent ! successResponse(newData)
@@ -104,7 +105,6 @@ trait WorkflowLifecycleActor[S <: WorkflowLifecycleActorState] extends LoggingFS
     } else {
       stay() using newData
     }
-  }
 
-  protected final def checkForDone(stateData: WorkflowLifecycleActorData) = stateData.actors.isEmpty
+  final protected def checkForDone(stateData: WorkflowLifecycleActorData) = stateData.actors.isEmpty
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/deletion/DeleteWorkflowFilesActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/deletion/DeleteWorkflowFilesActor.scala
index 56d6012125d..3b32aa1feaf 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/deletion/DeleteWorkflowFilesActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/deletion/DeleteWorkflowFilesActor.scala
@@ -34,16 +34,15 @@ class DeleteWorkflowFilesActor(rootWorkflowId: RootWorkflowId,
                                pathBuilders: List[PathBuilder],
                                serviceRegistryActor: ActorRef,
                                ioActorRef: ActorRef,
-                               gcsCommandBuilder: IoCommandBuilder,
-                              )
-  extends LoggingFSM[DeleteWorkflowFilesActorState, DeleteWorkflowFilesActorStateData] with IoClientHelper {
+                               gcsCommandBuilder: IoCommandBuilder
+) extends LoggingFSM[DeleteWorkflowFilesActorState, DeleteWorkflowFilesActorStateData]
+    with IoClientHelper {
 
   implicit val ec: ExecutionContext = context.dispatcher
 
   val asyncIO = new AsyncIo(ioActorRef, gcsCommandBuilder)
   val callCache = new CallCache(EngineServicesStore.engineDatabaseInterface)
 
-
   startWith(Pending, NoData)
 
   when(Pending) {
@@ -55,8 +54,7 @@ class DeleteWorkflowFilesActor(rootWorkflowId: RootWorkflowId,
       if (intermediateOutputs.nonEmpty) {
         self ! DeleteFiles
         goto(DeleteIntermediateFiles) using DeletingIntermediateFilesData(intermediateOutputs)
-      }
-      else {
+      } else {
         log.info(s"Root workflow ${rootWorkflowId.id} does not have any intermediate output files to delete.")
         respondAndStop(Nil, Nil, Nil)
       }
@@ -112,7 +110,8 @@ class DeleteWorkflowFilesActor(rootWorkflowId: RootWorkflowId,
          In both these cases, we consider the deletion process a success, but warn the users of such files not found.
        */
       val newDataWithErrorUpdates = error match {
-        case EnhancedCromwellIoException(_, _: FileNotFoundException) => newData.copy(filesNotFound = newData.filesNotFound :+ command.file)
+        case EnhancedCromwellIoException(_, _: FileNotFoundException) =>
+          newData.copy(filesNotFound = newData.filesNotFound :+ command.file)
         case _ => newData.copy(deleteErrors = newData.deleteErrors :+ error)
       }
       commandState match {
@@ -120,7 +119,9 @@ class DeleteWorkflowFilesActor(rootWorkflowId: RootWorkflowId,
         case AllCommandsDone =>
           // once deletion is complete, invalidate call cache entries
           self ! InvalidateCallCache
-          goto(InvalidatingCallCache) using InvalidateCallCacheData(newDataWithErrorUpdates.deleteErrors, newDataWithErrorUpdates.filesNotFound)
+          goto(InvalidatingCallCache) using InvalidateCallCacheData(newDataWithErrorUpdates.deleteErrors,
+                                                                    newDataWithErrorUpdates.filesNotFound
+          )
       }
   }
 
@@ -159,14 +160,17 @@ class DeleteWorkflowFilesActor(rootWorkflowId: RootWorkflowId,
       val (newData: WaitingForInvalidateCCResponsesData, invalidateState) = data.commandComplete(cacheId.id)
       invalidateState match {
         case StillWaiting => stay() using newData
-        case AllCommandsDone => respondAndStop(newData.deleteErrors, newData.filesNotFound, newData.callCacheInvalidationErrors)
+        case AllCommandsDone =>
+          respondAndStop(newData.deleteErrors, newData.filesNotFound, newData.callCacheInvalidationErrors)
       }
     case Event(CallCacheInvalidatedFailure(cacheId, error), data: WaitingForInvalidateCCResponsesData) =>
       val (newData: WaitingForInvalidateCCResponsesData, invalidateState) = data.commandComplete(cacheId.id)
-      val updatedDataWithError = newData.copy(callCacheInvalidationErrors = newData.callCacheInvalidationErrors :+ error)
+      val updatedDataWithError =
+        newData.copy(callCacheInvalidationErrors = newData.callCacheInvalidationErrors :+ error)
       invalidateState match {
         case StillWaiting => stay() using updatedDataWithError
-        case AllCommandsDone => respondAndStop(newData.deleteErrors, newData.filesNotFound, updatedDataWithError.callCacheInvalidationErrors)
+        case AllCommandsDone =>
+          respondAndStop(newData.deleteErrors, newData.filesNotFound, updatedDataWithError.callCacheInvalidationErrors)
       }
   }
 
@@ -176,28 +180,37 @@ class DeleteWorkflowFilesActor(rootWorkflowId: RootWorkflowId,
       stay()
     case Event(ShutdownCommand, _) => stopSelf()
     case other =>
-      log.error(s"Programmer Error: Unexpected message to ${getClass.getSimpleName} ${self.path.name} in state $stateName with $stateData: ${other.toPrettyElidedString(1000)}")
+      log.error(
+        s"Programmer Error: Unexpected message to ${getClass.getSimpleName} ${self.path.name} in state $stateName with $stateData: ${other
+            .toPrettyElidedString(1000)}"
+      )
       stay()
   }
 
-
   private def stopSelf() = {
     context stop self
     stay()
   }
 
-
-  private def respondAndStop(errors: List[Throwable], filesNotFound: List[Path], callCacheInvalidationErrors: List[Throwable]) = {
+  private def respondAndStop(errors: List[Throwable],
+                             filesNotFound: List[Path],
+                             callCacheInvalidationErrors: List[Throwable]
+  ) = {
     val (metadataEvent, response) =
-      if (errors.isEmpty) (metadataEventForDeletionStatus(Succeeded), DeleteWorkflowFilesSucceededResponse(filesNotFound, callCacheInvalidationErrors))
-      else (metadataEventForDeletionStatus(Failed), DeleteWorkflowFilesFailedResponse(errors, filesNotFound, callCacheInvalidationErrors))
+      if (errors.isEmpty)
+        (metadataEventForDeletionStatus(Succeeded),
+         DeleteWorkflowFilesSucceededResponse(filesNotFound, callCacheInvalidationErrors)
+        )
+      else
+        (metadataEventForDeletionStatus(Failed),
+         DeleteWorkflowFilesFailedResponse(errors, filesNotFound, callCacheInvalidationErrors)
+        )
 
     serviceRegistryActor ! PutMetadataAction(metadataEvent)
     context.parent ! response
     stopSelf()
   }
 
-
   private def metadataEventForDeletionStatus(status: FileDeletionStatus): MetadataEvent = {
     val key = MetadataKey(rootWorkflowId, None, WorkflowMetadataKeys.FileDeletionStatus)
     val value = MetadataValue(FileDeletionStatus.toDatabaseValue(status))
@@ -205,27 +218,28 @@ class DeleteWorkflowFilesActor(rootWorkflowId: RootWorkflowId,
     MetadataEvent(key, value)
   }
 
-
   private def fetchCallCacheEntries(callCache: CallCache): Future[Set[Long]] = {
-    val callCacheEntryIdsFuture = rootAndSubworkflowIds.map(x => callCache.callCacheEntryIdsForWorkflowId(x.toString)).map { f =>
-      f.map { Success(_) }.recover { case t => Failure(t) }}
-
-    Future.sequence(callCacheEntryIdsFuture).map { _.flatMap {
-      case Success(callCacheEntryIds) =>
-        Option(callCacheEntryIds)
-      case Failure(e) =>
-        log.error(s"Failed to fetch call cache entry ids for workflow. Error: ${ExceptionUtils.getMessage(e)}")
-        None
-    }.flatten}
+    val callCacheEntryIdsFuture =
+      rootAndSubworkflowIds.map(x => callCache.callCacheEntryIdsForWorkflowId(x.toString)).map { f =>
+        f.map(Success(_)).recover { case t => Failure(t) }
+      }
+
+    Future.sequence(callCacheEntryIdsFuture).map {
+      _.flatMap {
+        case Success(callCacheEntryIds) =>
+          Option(callCacheEntryIds)
+        case Failure(e) =>
+          log.error(s"Failed to fetch call cache entry ids for workflow. Error: ${ExceptionUtils.getMessage(e)}")
+          None
+      }.flatten
+    }
   }
 
-  private def toPath(womSingleFile: WomSingleFile): Option[Path] = {
+  private def toPath(womSingleFile: WomSingleFile): Option[Path] =
     Try(PathFactory.buildPath(womSingleFile.valueString, pathBuilders)).toOption
-  }
 
-  private def getWomSingleFiles(womValue: WomValue): Seq[WomSingleFile] = {
-    womValue.collectAsSeq({ case womSingleFile: WomSingleFile => womSingleFile })
-  }
+  private def getWomSingleFiles(womValue: WomValue): Seq[WomSingleFile] =
+    womValue.collectAsSeq { case womSingleFile: WomSingleFile => womSingleFile }
 
   /**
     * Returns Paths for WomSingleFiles in allOutputs that are not in finalOutputs, verifying that the Paths are contained
@@ -236,27 +250,33 @@ class DeleteWorkflowFilesActor(rootWorkflowId: RootWorkflowId,
     val allOutputFiles = allOutputs.flatMap(getWomSingleFiles)
     val finalOutputFiles = finalOutputs.flatMap(getWomSingleFiles)
     val potentialIntermediaries = allOutputFiles.diff(finalOutputFiles).flatMap(toPath)
-    val checkedIntermediaries = potentialIntermediaries.filter(p => rootWorkflowRootPaths.exists(r => p.toAbsolutePath.startsWith(r.toAbsolutePath)))
-    for ( path <- potentialIntermediaries.diff(checkedIntermediaries) ) {
-      log.info(s"Did not delete $path because it is not contained within a workflow root directory for $rootWorkflowId.")
-    }
+    val checkedIntermediaries = potentialIntermediaries.filter(p =>
+      rootWorkflowRootPaths.exists(r => p.toAbsolutePath.startsWith(r.toAbsolutePath))
+    )
+    for (path <- potentialIntermediaries.diff(checkedIntermediaries))
+      log.info(
+        s"Did not delete $path because it is not contained within a workflow root directory for $rootWorkflowId."
+      )
     checkedIntermediaries
   }
 
   override def ioActor: ActorRef = ioActorRef
 
-
-  override protected def onTimeout(message: Any, to: ActorRef): Unit = {
+  override protected def onTimeout(message: Any, to: ActorRef): Unit =
     message match {
-      case delete: IoDeleteCommand => log.error(s"The DeleteWorkflowFilesActor for root workflow $rootWorkflowId timed out " +
-        s"waiting for a response for deleting file ${delete.file}.")
-      case other => log.error(s"The DeleteWorkflowFilesActor for root workflow $rootWorkflowId timed out " +
-        s"waiting for a response for unknown operation: $other.")
+      case delete: IoDeleteCommand =>
+        log.error(
+          s"The DeleteWorkflowFilesActor for root workflow $rootWorkflowId timed out " +
+            s"waiting for a response for deleting file ${delete.file}."
+        )
+      case other =>
+        log.error(
+          s"The DeleteWorkflowFilesActor for root workflow $rootWorkflowId timed out " +
+            s"waiting for a response for unknown operation: $other."
+        )
     }
-  }
 }
 
-
 object DeleteWorkflowFilesActor {
 
   //@formatter:off
@@ -289,63 +309,68 @@ object DeleteWorkflowFilesActor {
 
     def setCommandsToWaitFor(updatedCommandsToWaitFor: Set[A]): WaitingForResponseFromActorData[A]
 
-    def commandComplete(command: A): (WaitingForResponseFromActorData[A], WaitingForResponseState) = {
+    def commandComplete(command: A): (WaitingForResponseFromActorData[A], WaitingForResponseState) =
       if (commandsToWaitFor.isEmpty) (this, AllCommandsDone)
       else {
         val updatedCommandsSet = commandsToWaitFor - command
 
         val expectedCommandSetSize = updatedCommandsSet.size
         val requiredCommandSetSize = commandsToWaitFor.size - 1
-        require(expectedCommandSetSize == requiredCommandSetSize, assertionFailureMsg(expectedCommandSetSize, requiredCommandSetSize))
+        require(expectedCommandSetSize == requiredCommandSetSize,
+                assertionFailureMsg(expectedCommandSetSize, requiredCommandSetSize)
+        )
 
         if (updatedCommandsSet.isEmpty) (setCommandsToWaitFor(Set.empty), AllCommandsDone)
         else (setCommandsToWaitFor(updatedCommandsSet), StillWaiting)
       }
-    }
   }
 
   case class WaitingForIoResponsesData(commandsToWaitFor: Set[IoDeleteCommand],
                                        deleteErrors: List[Throwable] = List.empty,
-                                       filesNotFound: List[Path] = List.empty)
-    extends WaitingForResponseFromActorData[IoDeleteCommand](commandsToWaitFor) with DeleteWorkflowFilesActorStateData {
+                                       filesNotFound: List[Path] = List.empty
+  ) extends WaitingForResponseFromActorData[IoDeleteCommand](commandsToWaitFor)
+      with DeleteWorkflowFilesActorStateData {
 
-    override def assertionFailureMsg(expectedSize: Int, requiredSize: Int): String = {
+    override def assertionFailureMsg(expectedSize: Int, requiredSize: Int): String =
       s"Found updated command set size as $expectedSize instead of $requiredSize. The updated set of commands that " +
         s"DeleteWorkflowFilesActor has to wait for should be 1 less after removing a completed command."
-    }
 
-    override def setCommandsToWaitFor(updatedCommandsToWaitFor: Set[IoDeleteCommand]): WaitingForResponseFromActorData[IoDeleteCommand] = {
+    override def setCommandsToWaitFor(
+      updatedCommandsToWaitFor: Set[IoDeleteCommand]
+    ): WaitingForResponseFromActorData[IoDeleteCommand] =
       this.copy(commandsToWaitFor = updatedCommandsToWaitFor)
-    }
   }
 
   case class WaitingForInvalidateCCResponsesData(commandsToWaitFor: Set[Long],
                                                  deleteErrors: List[Throwable],
                                                  filesNotFound: List[Path],
-                                                 callCacheInvalidationErrors: List[Throwable] = List.empty)
-    extends WaitingForResponseFromActorData[Long](commandsToWaitFor) with DeleteWorkflowFilesActorStateData {
+                                                 callCacheInvalidationErrors: List[Throwable] = List.empty
+  ) extends WaitingForResponseFromActorData[Long](commandsToWaitFor)
+      with DeleteWorkflowFilesActorStateData {
 
-    override def assertionFailureMsg(expectedSize: Int, requiredSize: Int): String = {
+    override def assertionFailureMsg(expectedSize: Int, requiredSize: Int): String =
       s"Found updated call cache entries set size as $expectedSize instead of $requiredSize. The updated set of call cache entries" +
         s" that DeleteWorkflowFilesActor has to wait for should be 1 less after a call cache entry is invalidated."
-    }
 
-    override def setCommandsToWaitFor(updatedCommandsToWaitFor: Set[Long]): WaitingForResponseFromActorData[Long] = {
+    override def setCommandsToWaitFor(updatedCommandsToWaitFor: Set[Long]): WaitingForResponseFromActorData[Long] =
       this.copy(commandsToWaitFor = updatedCommandsToWaitFor)
-    }
   }
 
   // Responses
   sealed trait DeleteWorkflowFilesResponse
-  case class DeleteWorkflowFilesSucceededResponse(filesNotFound: List[Path], callCacheInvalidationErrors: List[Throwable]) extends DeleteWorkflowFilesResponse
-  case class DeleteWorkflowFilesFailedResponse(errors: List[Throwable], filesNotFound: List[Path], callCacheInvalidationErrors: List[Throwable]) extends DeleteWorkflowFilesResponse
+  case class DeleteWorkflowFilesSucceededResponse(filesNotFound: List[Path],
+                                                  callCacheInvalidationErrors: List[Throwable]
+  ) extends DeleteWorkflowFilesResponse
+  case class DeleteWorkflowFilesFailedResponse(errors: List[Throwable],
+                                               filesNotFound: List[Path],
+                                               callCacheInvalidationErrors: List[Throwable]
+  ) extends DeleteWorkflowFilesResponse
 
   // internal state to keep track of deletion of files and call cache invalidation
   sealed trait WaitingForResponseState
   private[deletion] case object StillWaiting extends WaitingForResponseState
   private[deletion] case object AllCommandsDone extends WaitingForResponseState
 
-
   def props(rootWorkflowId: RootWorkflowId,
             rootAndSubworkflowIds: Set[WorkflowId],
             rootWorkflowRootPaths: Set[Path],
@@ -354,18 +379,19 @@ object DeleteWorkflowFilesActor {
             pathBuilders: List[PathBuilder],
             serviceRegistryActor: ActorRef,
             ioActor: ActorRef,
-            gcsCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder,
-           ): Props = {
-    Props(new DeleteWorkflowFilesActor(
-      rootWorkflowId = rootWorkflowId,
-      rootAndSubworkflowIds = rootAndSubworkflowIds,
-      rootWorkflowRootPaths = rootWorkflowRootPaths,
-      workflowFinalOutputs = workflowFinalOutputs,
-      workflowAllOutputs = workflowAllOutputs,
-      pathBuilders = pathBuilders,
-      serviceRegistryActor = serviceRegistryActor,
-      ioActorRef = ioActor,
-      gcsCommandBuilder = gcsCommandBuilder,
-    ))
-  }
+            gcsCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder
+  ): Props =
+    Props(
+      new DeleteWorkflowFilesActor(
+        rootWorkflowId = rootWorkflowId,
+        rootAndSubworkflowIds = rootAndSubworkflowIds,
+        rootWorkflowRootPaths = rootWorkflowRootPaths,
+        workflowFinalOutputs = workflowFinalOutputs,
+        workflowAllOutputs = workflowAllOutputs,
+        pathBuilders = pathBuilders,
+        serviceRegistryActor = serviceRegistryActor,
+        ioActorRef = ioActor,
+        gcsCommandBuilder = gcsCommandBuilder
+      )
+    )
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/CallMetadataHelper.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/CallMetadataHelper.scala
index 0a7e3760a67..7df49b106e3 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/CallMetadataHelper.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/CallMetadataHelper.scala
@@ -21,15 +21,23 @@ trait CallMetadataHelper {
   def pushNewCallMetadata(callKey: CallKey, backendName: Option[String], serviceRegistryActor: ActorRef) = {
     val startEvents = List(
       Option(MetadataEvent(metadataKeyForCall(callKey, CallMetadataKeys.Start), MetadataValue(OffsetDateTime.now))),
-      Option(MetadataEvent(metadataKeyForCall(callKey, CallMetadataKeys.ExecutionStatus), MetadataValue(ExecutionStatus.QueuedInCromwell))),
-      backendName map { name => MetadataEvent(metadataKeyForCall(callKey, CallMetadataKeys.Backend), MetadataValue(name)) }
+      Option(
+        MetadataEvent(metadataKeyForCall(callKey, CallMetadataKeys.ExecutionStatus),
+                      MetadataValue(ExecutionStatus.QueuedInCromwell)
+        )
+      ),
+      backendName map { name =>
+        MetadataEvent(metadataKeyForCall(callKey, CallMetadataKeys.Backend), MetadataValue(name))
+      }
     ).flatten
 
     serviceRegistryActor ! PutMetadataAction(startEvents)
   }
 
   def pushStartingCallMetadata(callKey: CallKey) = {
-    val statusChange = MetadataEvent(metadataKeyForCall(callKey, CallMetadataKeys.ExecutionStatus), MetadataValue(ExecutionStatus.Starting))
+    val statusChange = MetadataEvent(metadataKeyForCall(callKey, CallMetadataKeys.ExecutionStatus),
+                                     MetadataValue(ExecutionStatus.Starting)
+    )
     serviceRegistryActor ! PutMetadataAction(statusChange)
   }
 
@@ -42,13 +50,16 @@ trait CallMetadataHelper {
         case empty if empty.isEmpty =>
           List(MetadataEvent.empty(metadataKeyForCall(key, s"${CallMetadataKeys.Inputs}")))
         case inputs =>
-          inputs flatMap {
-            case (inputName, inputValue) =>
-              womValueToMetadataEvents(metadataKeyForCall(key, s"${CallMetadataKeys.Inputs}:${inputName.name}"), inputValue)
+          inputs flatMap { case (inputName, inputValue) =>
+            womValueToMetadataEvents(metadataKeyForCall(key, s"${CallMetadataKeys.Inputs}:${inputName.name}"),
+                                     inputValue
+            )
           }
       }
 
-      val runningEvent = List(MetadataEvent(metadataKeyForCall(key, CallMetadataKeys.ExecutionStatus), MetadataValue(ExecutionStatus.Running)))
+      val runningEvent = List(
+        MetadataEvent(metadataKeyForCall(key, CallMetadataKeys.ExecutionStatus), MetadataValue(ExecutionStatus.Running))
+      )
       serviceRegistryActor ! PutMetadataAction(runningEvent ++ inputEvents)
       alreadyPushedRunningCallMetadata += metadataKeyForUniqueness
     }
@@ -59,7 +70,10 @@ trait CallMetadataHelper {
       List(MetadataEvent.empty(MetadataKey(workflowIdForCallMetadata, None, WorkflowMetadataKeys.Outputs)))
     } else {
       outputs flatMap { case (outputName, outputValue) =>
-        womValueToMetadataEvents(MetadataKey(workflowIdForCallMetadata, None, s"${WorkflowMetadataKeys.Outputs}:$outputName"), outputValue)
+        womValueToMetadataEvents(
+          MetadataKey(workflowIdForCallMetadata, None, s"${WorkflowMetadataKeys.Outputs}:$outputName"),
+          outputValue
+        )
       }
     }
 
@@ -74,7 +88,10 @@ trait CallMetadataHelper {
         List(MetadataEvent.empty(metadataKeyForCall(jobKey, s"${CallMetadataKeys.Outputs}")))
       case _ =>
         outputs.outputs flatMap { case (outputPort, outputValue) =>
-          womValueToMetadataEvents(metadataKeyForCall(jobKey, s"${CallMetadataKeys.Outputs}:${outputPort.internalName}"), outputValue)
+          womValueToMetadataEvents(
+            metadataKeyForCall(jobKey, s"${CallMetadataKeys.Outputs}:${outputPort.internalName}"),
+            outputValue
+          )
         }
     }
 
@@ -84,13 +101,15 @@ trait CallMetadataHelper {
   def pushFailedCallMetadata(jobKey: JobKey, returnCode: Option[Int], failure: Throwable, retryableFailure: Boolean) = {
     val failedState = if (retryableFailure) ExecutionStatus.RetryableFailure else ExecutionStatus.Failed
     val completionEvents = completedCallMetadataEvents(jobKey, failedState, returnCode)
-    val retryableFailureEvent = MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.RetryableFailure), MetadataValue(retryableFailure))
+    val retryableFailureEvent =
+      MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.RetryableFailure), MetadataValue(retryableFailure))
 
     val failureEvents = failure match {
       // If the job was already failed, don't republish the failure reasons, they're already there
       case _: JobAlreadyFailedInJobStore => List.empty
       case _ =>
-        throwableToMetadataEvents(metadataKeyForCall(jobKey, s"${CallMetadataKeys.Failures}"), failure).+:(retryableFailureEvent)
+        throwableToMetadataEvents(metadataKeyForCall(jobKey, s"${CallMetadataKeys.Failures}"), failure)
+          .+:(retryableFailureEvent)
     }
 
     serviceRegistryActor ! PutMetadataAction(completionEvents ++ failureEvents)
@@ -117,14 +136,13 @@ trait CallMetadataHelper {
       val now = OffsetDateTime.now.withOffsetSameInstant(offset)
       val lastEvent = ExecutionEvent("!!Bring Back the Monarchy!!", now)
       val tailedEventList = sortedEvents :+ lastEvent
-      val events = tailedEventList.sliding(2) flatMap {
-        case Seq(eventCurrent, eventNext) =>
-          val eventKey = s"${CallMetadataKeys.ExecutionEvents}[$randomNumberString]"
-          List(
-            metadataEvent(s"$eventKey:description", eventCurrent.name),
-            metadataEvent(s"$eventKey:startTime", eventCurrent.offsetDateTime),
-            metadataEvent(s"$eventKey:endTime", eventNext.offsetDateTime)
-          ) ++ (eventCurrent.grouping map { g => metadataEvent(s"$eventKey:grouping", g) })
+      val events = tailedEventList.sliding(2) flatMap { case Seq(eventCurrent, eventNext) =>
+        val eventKey = s"${CallMetadataKeys.ExecutionEvents}[$randomNumberString]"
+        List(
+          metadataEvent(s"$eventKey:description", eventCurrent.name),
+          metadataEvent(s"$eventKey:startTime", eventCurrent.offsetDateTime),
+          metadataEvent(s"$eventKey:endTime", eventNext.offsetDateTime)
+        ) ++ (eventCurrent.grouping map { g => metadataEvent(s"$eventKey:grouping", g) })
       }
 
       serviceRegistryActor ! PutMetadataAction(events.toList)
@@ -144,5 +162,9 @@ trait CallMetadataHelper {
 
   private def randomNumberString: String = Random.nextInt().toString.stripPrefix("-")
 
-  def metadataKeyForCall(jobKey: JobKey, myKey: String) = MetadataKey(workflowIdForCallMetadata, Option(MetadataJobKey(jobKey.node.fullyQualifiedName, jobKey.index, jobKey.attempt)), myKey)
+  def metadataKeyForCall(jobKey: JobKey, myKey: String) = MetadataKey(
+    workflowIdForCallMetadata,
+    Option(MetadataJobKey(jobKey.node.fullyQualifiedName, jobKey.index, jobKey.attempt)),
+    myKey
+  )
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala
index 1cd48695ba2..861989de5f6 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala
@@ -48,7 +48,11 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
                                 rootConfig: Config,
                                 totalJobsByRootWf: AtomicInteger,
                                 fileHashCacheActor: Option[ActorRef],
-                                blacklistCache: Option[BlacklistCache]) extends LoggingFSM[SubWorkflowExecutionActorState, SubWorkflowExecutionActorData] with JobLogging with WorkflowMetadataHelper with CallMetadataHelper {
+                                blacklistCache: Option[BlacklistCache]
+) extends LoggingFSM[SubWorkflowExecutionActorState, SubWorkflowExecutionActorData]
+    with JobLogging
+    with WorkflowMetadataHelper
+    with CallMetadataHelper {
 
   override def supervisorStrategy: SupervisorStrategy = OneForOneStrategy() { case _ => Escalate }
 
@@ -66,14 +70,13 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
 
   private var eventList: Seq[ExecutionEvent] = Seq(ExecutionEvent(stateName.toString))
 
-  when(SubWorkflowPendingState) {
-    case Event(Execute, _) =>
-      if (startState.restarted) {
-        subWorkflowStoreActor ! QuerySubWorkflow(parentWorkflow.id, key)
-        goto(SubWorkflowCheckingStoreState)
-      } else {
-        requestValueStore(createSubWorkflowId())
-      }
+  when(SubWorkflowPendingState) { case Event(Execute, _) =>
+    if (startState.restarted) {
+      subWorkflowStoreActor ! QuerySubWorkflow(parentWorkflow.id, key)
+      goto(SubWorkflowCheckingStoreState)
+    } else {
+      requestValueStore(createSubWorkflowId())
+    }
   }
 
   when(SubWorkflowCheckingStoreState) {
@@ -87,18 +90,23 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
   }
 
   /*
-    * ! Hot Potato Warning !
-    * We ask explicitly for the `ValueStore` so we can use it on the fly and more importantly not store it as a
-    * variable in this actor, which would prevent it from being garbage collected for the duration of the
-    * subworkflow and would lead to memory leaks.
-    */
+   * ! Hot Potato Warning !
+   * We ask explicitly for the `ValueStore` so we can use it on the fly and more importantly not store it as a
+   * variable in this actor, which would prevent it from being garbage collected for the duration of the
+   * subworkflow and would lead to memory leaks.
+   */
   when(WaitingForValueStore) {
     case Event(valueStore: ValueStore, SubWorkflowExecutionActorLiveData(Some(subWorkflowId), _)) =>
       prepareSubWorkflow(subWorkflowId, valueStore)
     case Event(_: ValueStore, _) =>
-      context.parent ! SubWorkflowFailedResponse(key, Map.empty, new IllegalStateException(
-        "This is a programmer error, we're ready to prepare the job and should have" +
-          " a SubWorkflowId to use by now but somehow haven't. Failing the workflow."))
+      context.parent ! SubWorkflowFailedResponse(
+        key,
+        Map.empty,
+        new IllegalStateException(
+          "This is a programmer error, we're ready to prepare the job and should have" +
+            " a SubWorkflowId to use by now but somehow haven't. Failing the workflow."
+        )
+      )
       context stop self
       stay()
   }
@@ -108,16 +116,36 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
       startSubWorkflow(subWorkflowEngineDescriptor, inputs, data)
     case Event(failure: CallPreparationFailed, data) =>
       // No subworkflow ID yet, so no need to record the status. Fail here and let the parent handle the fallout:
-      recordTerminalState(SubWorkflowFailedState, SubWorkflowExecutionActorTerminalData(data.subWorkflowId, SubWorkflowFailedResponse(key, Map.empty, failure.throwable)))
+      recordTerminalState(
+        SubWorkflowFailedState,
+        SubWorkflowExecutionActorTerminalData(data.subWorkflowId,
+                                              SubWorkflowFailedResponse(key, Map.empty, failure.throwable)
+        )
+      )
   }
 
   when(SubWorkflowRunningState) {
-    case Event(WorkflowExecutionSucceededResponse(executedJobKeys, rootAndSubworklowIds, outputs, cumulativeOutputs), data) =>
-      recordTerminalState(SubWorkflowSucceededState, SubWorkflowExecutionActorTerminalData(data.subWorkflowId, SubWorkflowSucceededResponse(key, executedJobKeys, rootAndSubworklowIds, outputs, cumulativeOutputs)))
+    case Event(WorkflowExecutionSucceededResponse(executedJobKeys, rootAndSubworklowIds, outputs, cumulativeOutputs),
+               data
+        ) =>
+      recordTerminalState(
+        SubWorkflowSucceededState,
+        SubWorkflowExecutionActorTerminalData(
+          data.subWorkflowId,
+          SubWorkflowSucceededResponse(key, executedJobKeys, rootAndSubworklowIds, outputs, cumulativeOutputs)
+        )
+      )
     case Event(WorkflowExecutionFailedResponse(executedJobKeys, reason), data) =>
-      recordTerminalState(SubWorkflowFailedState, SubWorkflowExecutionActorTerminalData(data.subWorkflowId, SubWorkflowFailedResponse(key, executedJobKeys, reason)))
+      recordTerminalState(SubWorkflowFailedState,
+                          SubWorkflowExecutionActorTerminalData(data.subWorkflowId,
+                                                                SubWorkflowFailedResponse(key, executedJobKeys, reason)
+                          )
+      )
     case Event(WorkflowExecutionAbortedResponse(executedJobKeys), data) =>
-      recordTerminalState(SubWorkflowAbortedState, SubWorkflowExecutionActorTerminalData(data.subWorkflowId, SubWorkflowAbortedResponse(key, executedJobKeys)))
+      recordTerminalState(
+        SubWorkflowAbortedState,
+        SubWorkflowExecutionActorTerminalData(data.subWorkflowId, SubWorkflowAbortedResponse(key, executedJobKeys))
+      )
     case Event(EngineLifecycleActorAbortCommand, SubWorkflowExecutionActorLiveData(_, Some(actorRef))) =>
       actorRef ! EngineLifecycleActorAbortCommand
       stay()
@@ -134,14 +162,22 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
       // If the final state can't be written, it's fairly likely that other metadata has also been lost, so
       // the best answer may unfortunately be to fail the workflow rather than retry. Assuming the call cache is working
       // correctly, a retry of the workflow should at least cache-hit instead of having to re-run the work:
-      recordTerminalState(SubWorkflowFailedState, terminalData.copy(terminalStateResponse = SubWorkflowFailedResponse(key,
-        terminalData.terminalStateResponse.jobExecutionMap,
-        new Exception("Sub workflow execution actor unable to write final state to metadata", reason) with NoStackTrace)))
+      recordTerminalState(
+        SubWorkflowFailedState,
+        terminalData.copy(terminalStateResponse =
+          SubWorkflowFailedResponse(
+            key,
+            terminalData.terminalStateResponse.jobExecutionMap,
+            new Exception("Sub workflow execution actor unable to write final state to metadata", reason)
+              with NoStackTrace
+          )
+        )
+      )
   }
 
-  when(SubWorkflowSucceededState) { terminalMetadataWriteResponseHandler }
-  when(SubWorkflowFailedState) { terminalMetadataWriteResponseHandler }
-  when(SubWorkflowAbortedState) { terminalMetadataWriteResponseHandler }
+  when(SubWorkflowSucceededState)(terminalMetadataWriteResponseHandler)
+  when(SubWorkflowFailedState)(terminalMetadataWriteResponseHandler)
+  when(SubWorkflowAbortedState)(terminalMetadataWriteResponseHandler)
 
   whenUnhandled {
     case Event(SubWorkflowStoreRegisterSuccess(_), _) =>
@@ -151,10 +187,15 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
       jobLogger.error(reason, s"SubWorkflowStore failure for command $command")
       stay()
     case Event(EngineLifecycleActorAbortCommand, data) =>
-      recordTerminalState(SubWorkflowAbortedState, SubWorkflowExecutionActorTerminalData(data.subWorkflowId, SubWorkflowAbortedResponse(key, Map.empty)))
+      recordTerminalState(
+        SubWorkflowAbortedState,
+        SubWorkflowExecutionActorTerminalData(data.subWorkflowId, SubWorkflowAbortedResponse(key, Map.empty))
+      )
   }
 
-  def recordTerminalState(terminalState: SubWorkflowTerminalState, newStateData: SubWorkflowExecutionActorTerminalData): State = {
+  def recordTerminalState(terminalState: SubWorkflowTerminalState,
+                          newStateData: SubWorkflowExecutionActorTerminalData
+  ): State =
     newStateData.subWorkflowId match {
       case Some(id) =>
         pushWorkflowEnd(id)
@@ -165,23 +206,27 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
         jobLogger.error("Programmer Error: Sub workflow completed without ever having a Sub Workflow UUID.")
         // Same situation as if we fail to write the final state metadata. Bail out and hope the workflow is more
         // successful next time:
-        context.parent ! SubWorkflowFailedResponse(key,
+        context.parent ! SubWorkflowFailedResponse(
+          key,
           Map.empty,
-          new Exception("Programmer Error: Sub workflow completed without ever having a Sub Workflow UUID") with NoStackTrace)
+          new Exception("Programmer Error: Sub workflow completed without ever having a Sub Workflow UUID")
+            with NoStackTrace
+        )
         context.stop(self)
         stay()
     }
-  }
 
-  onTransition {
-    case (_, toState) =>
-      eventList :+= ExecutionEvent(toState.toString)
-      if (!toState.isInstanceOf[SubWorkflowTerminalState]) {
-        stateData.subWorkflowId foreach { id => pushCurrentStateToMetadataService(id, toState.workflowState) }
-      }
+  onTransition { case (_, toState) =>
+    eventList :+= ExecutionEvent(toState.toString)
+    if (!toState.isInstanceOf[SubWorkflowTerminalState]) {
+      stateData.subWorkflowId foreach { id => pushCurrentStateToMetadataService(id, toState.workflowState) }
+    }
   }
 
-  private def startSubWorkflow(subWorkflowEngineDescriptor: EngineWorkflowDescriptor, inputs: WomEvaluatedCallInputs, data: SubWorkflowExecutionActorData) = {
+  private def startSubWorkflow(subWorkflowEngineDescriptor: EngineWorkflowDescriptor,
+                               inputs: WomEvaluatedCallInputs,
+                               data: SubWorkflowExecutionActorData
+  ) = {
     val subWorkflowActor = createSubWorkflowActor(subWorkflowEngineDescriptor)
 
     subWorkflowActor ! WorkflowExecutionActor.ExecuteWorkflowCommand
@@ -204,14 +249,13 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
     goto(WaitingForValueStore) using SubWorkflowExecutionActorLiveData(Option(workflowId), None)
   }
 
-  def createSubWorkflowPreparationActor(subWorkflowId: WorkflowId) = {
+  def createSubWorkflowPreparationActor(subWorkflowId: WorkflowId) =
     context.actorOf(
       SubWorkflowPreparationActor.props(parentWorkflow, expressionLanguageFunctions, key, subWorkflowId),
       s"$subWorkflowId-SubWorkflowPreparationActor-${key.tag}"
     )
-  }
 
-  def createSubWorkflowActor(subWorkflowEngineDescriptor: EngineWorkflowDescriptor) = {
+  def createSubWorkflowActor(subWorkflowEngineDescriptor: EngineWorkflowDescriptor) =
     context.actorOf(
       WorkflowExecutionActor.props(
         subWorkflowEngineDescriptor,
@@ -234,25 +278,37 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
       ),
       s"${subWorkflowEngineDescriptor.id}-SubWorkflowActor-${key.tag}"
     )
-  }
 
-  private def pushWorkflowRunningMetadata(subWorkflowDescriptor: BackendWorkflowDescriptor, workflowInputs: WomEvaluatedCallInputs) = {
+  private def pushWorkflowRunningMetadata(subWorkflowDescriptor: BackendWorkflowDescriptor,
+                                          workflowInputs: WomEvaluatedCallInputs
+  ) = {
     val subWorkflowId = subWorkflowDescriptor.id
-    val parentWorkflowMetadataKey = MetadataKey(parentWorkflow.id, Option(MetadataJobKey(key.node.fullyQualifiedName, key.index, key.attempt)), CallMetadataKeys.SubWorkflowId)
+    val parentWorkflowMetadataKey = MetadataKey(
+      parentWorkflow.id,
+      Option(MetadataJobKey(key.node.fullyQualifiedName, key.index, key.attempt)),
+      CallMetadataKeys.SubWorkflowId
+    )
 
     val events = List(
       MetadataEvent(parentWorkflowMetadataKey, MetadataValue(subWorkflowId)),
       MetadataEvent(MetadataKey(subWorkflowId, None, WorkflowMetadataKeys.Name), MetadataValue(key.node.localName)),
-      MetadataEvent(MetadataKey(subWorkflowId, None, WorkflowMetadataKeys.ParentWorkflowId), MetadataValue(parentWorkflow.id)),
-      MetadataEvent(MetadataKey(subWorkflowId, None, WorkflowMetadataKeys.RootWorkflowId), MetadataValue(parentWorkflow.rootWorkflow.id))
+      MetadataEvent(MetadataKey(subWorkflowId, None, WorkflowMetadataKeys.ParentWorkflowId),
+                    MetadataValue(parentWorkflow.id)
+      ),
+      MetadataEvent(MetadataKey(subWorkflowId, None, WorkflowMetadataKeys.RootWorkflowId),
+                    MetadataValue(parentWorkflow.rootWorkflow.id)
+      )
     )
 
     val inputEvents = workflowInputs match {
       case empty if empty.isEmpty =>
-        List(MetadataEvent.empty(MetadataKey(subWorkflowId, None,WorkflowMetadataKeys.Inputs)))
+        List(MetadataEvent.empty(MetadataKey(subWorkflowId, None, WorkflowMetadataKeys.Inputs)))
       case inputs =>
         inputs flatMap { case (inputName, womValue) =>
-          womValueToMetadataEvents(MetadataKey(subWorkflowId, None, s"${WorkflowMetadataKeys.Inputs}:${inputName.name}"), womValue)
+          womValueToMetadataEvents(
+            MetadataKey(subWorkflowId, None, s"${WorkflowMetadataKeys.Inputs}:${inputName.name}"),
+            womValue
+          )
         }
     }
 
@@ -264,14 +320,17 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
   private def buildWorkflowRootMetadataEvents(subWorkflowDescriptor: BackendWorkflowDescriptor) = {
     val subWorkflowId = subWorkflowDescriptor.id
 
-    factories flatMap {
-      case (backendName, factory) =>
-        BackendConfiguration.backendConfigurationDescriptor(backendName).toOption map { config =>
-          backendName -> factory.getWorkflowExecutionRootPath(subWorkflowDescriptor, config.backendConfig, initializationData.get(backendName))
-        }
-    } map {
-      case (backend, wfRoot) =>
-        MetadataEvent(MetadataKey(subWorkflowId, None, s"${WorkflowMetadataKeys.WorkflowRoot}[$backend]"), MetadataValue(wfRoot.toAbsolutePath))
+    factories flatMap { case (backendName, factory) =>
+      BackendConfiguration.backendConfigurationDescriptor(backendName).toOption map { config =>
+        backendName -> factory.getWorkflowExecutionRootPath(subWorkflowDescriptor,
+                                                            config.backendConfig,
+                                                            initializationData.get(backendName)
+        )
+      }
+    } map { case (backend, wfRoot) =>
+      MetadataEvent(MetadataKey(subWorkflowId, None, s"${WorkflowMetadataKeys.WorkflowRoot}[$backend]"),
+                    MetadataValue(wfRoot.toAbsolutePath)
+      )
     }
   }
 
@@ -324,8 +383,12 @@ object SubWorkflowExecutionActor {
   sealed trait SubWorkflowExecutionActorData {
     def subWorkflowId: Option[WorkflowId]
   }
-  final case class SubWorkflowExecutionActorLiveData(subWorkflowId: Option[WorkflowId], subWorkflowActor: Option[ActorRef]) extends SubWorkflowExecutionActorData
-  final case class SubWorkflowExecutionActorTerminalData(subWorkflowId: Option[WorkflowId], terminalStateResponse: SubWorkflowTerminalStateResponse) extends SubWorkflowExecutionActorData
+  final case class SubWorkflowExecutionActorLiveData(subWorkflowId: Option[WorkflowId],
+                                                     subWorkflowActor: Option[ActorRef]
+  ) extends SubWorkflowExecutionActorData
+  final case class SubWorkflowExecutionActorTerminalData(subWorkflowId: Option[WorkflowId],
+                                                         terminalStateResponse: SubWorkflowTerminalStateResponse
+  ) extends SubWorkflowExecutionActorData
 
   sealed trait EngineWorkflowExecutionActorCommand
   case object Execute
@@ -349,28 +412,30 @@ object SubWorkflowExecutionActor {
             rootConfig: Config,
             totalJobsByRootWf: AtomicInteger,
             fileHashCacheActor: Option[ActorRef],
-            blacklistCache: Option[BlacklistCache]) = {
-    Props(new SubWorkflowExecutionActor(
-      key,
-      parentWorkflow,
-      expressionLanguageFunctions,
-      factories,
-      ioActor = ioActor,
-      serviceRegistryActor = serviceRegistryActor,
-      jobStoreActor = jobStoreActor,
-      subWorkflowStoreActor = subWorkflowStoreActor,
-      callCacheReadActor = callCacheReadActor,
-      callCacheWriteActor = callCacheWriteActor,
-      workflowDockerLookupActor = workflowDockerLookupActor,
-      jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
-      jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
-      backendSingletonCollection,
-      initializationData,
-      startState,
-      rootConfig,
-      totalJobsByRootWf,
-      fileHashCacheActor = fileHashCacheActor,
-      blacklistCache = blacklistCache)
+            blacklistCache: Option[BlacklistCache]
+  ) =
+    Props(
+      new SubWorkflowExecutionActor(
+        key,
+        parentWorkflow,
+        expressionLanguageFunctions,
+        factories,
+        ioActor = ioActor,
+        serviceRegistryActor = serviceRegistryActor,
+        jobStoreActor = jobStoreActor,
+        subWorkflowStoreActor = subWorkflowStoreActor,
+        callCacheReadActor = callCacheReadActor,
+        callCacheWriteActor = callCacheWriteActor,
+        workflowDockerLookupActor = workflowDockerLookupActor,
+        jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
+        jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
+        backendSingletonCollection,
+        initializationData,
+        startState,
+        rootConfig,
+        totalJobsByRootWf,
+        fileHashCacheActor = fileHashCacheActor,
+        blacklistCache = blacklistCache
+      )
     ).withDispatcher(EngineDispatcher)
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala
index dd6f0a42835..106b14a9a0c 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActor.scala
@@ -28,7 +28,10 @@ import cromwell.engine.backend.{BackendSingletonCollection, CromwellBackends}
 import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor._
 import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActorData.DataStoreUpdate
 import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor
-import cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.{ExpressionEvaluationFailedResponse, ExpressionEvaluationSucceededResponse}
+import cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.{
+  ExpressionEvaluationFailedResponse,
+  ExpressionEvaluationSucceededResponse
+}
 import cromwell.engine.workflow.lifecycle.execution.keys._
 import cromwell.engine.workflow.lifecycle.execution.stores.{ActiveExecutionStore, ExecutionStore}
 import cromwell.engine.workflow.lifecycle.{EngineLifecycleActorAbortCommand, EngineLifecycleActorAbortedResponse}
@@ -52,7 +55,7 @@ import scala.language.postfixOps
 import scala.util.control.NoStackTrace
 
 case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
-  extends LoggingFSM[WorkflowExecutionActorState, WorkflowExecutionActorData]
+    extends LoggingFSM[WorkflowExecutionActorState, WorkflowExecutionActorData]
     with WorkflowLogging
     with CallMetadataHelper
     with StopAndLogSupervisor
@@ -71,23 +74,25 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
 
   private val DefaultTotalMaxJobsPerRootWf = 1000000
   private val DefaultMaxScatterSize = 1000000
-  private val TotalMaxJobsPerRootWf = params.rootConfig.getOrElse("system.total-max-jobs-per-root-workflow", DefaultTotalMaxJobsPerRootWf)
-  private val MaxScatterWidth = params.rootConfig.getOrElse("system.max-scatter-width-per-scatter", DefaultMaxScatterSize)
+  private val TotalMaxJobsPerRootWf =
+    params.rootConfig.getOrElse("system.total-max-jobs-per-root-workflow", DefaultTotalMaxJobsPerRootWf)
+  private val MaxScatterWidth =
+    params.rootConfig.getOrElse("system.max-scatter-width-per-scatter", DefaultMaxScatterSize)
   private val FileHashBatchSize: Int = params.rootConfig.as[Int]("system.file-hash-batch-size")
 
   private val backendFactories: Map[String, BackendLifecycleActorFactory] = {
     val factoriesValidation = workflowDescriptor.backendAssignments.values.toList
-      .traverse[ErrorOr, (String, BackendLifecycleActorFactory)] {
-      backendName => CromwellBackends.backendLifecycleFactoryActorByName(backendName) map { backendName -> _ }
-    }
+      .traverse[ErrorOr, (String, BackendLifecycleActorFactory)] { backendName =>
+        CromwellBackends.backendLifecycleFactoryActorByName(backendName) map { backendName -> _ }
+      }
 
     factoriesValidation
       .map(_.toMap)
       .valueOr(errors => throw AggregatedMessageException("Could not instantiate backend factories", errors.toList))
   }
 
-
-  val executionStore: ErrorOr[ActiveExecutionStore] = ExecutionStore(workflowDescriptor.callable, params.totalJobsByRootWf, TotalMaxJobsPerRootWf)
+  val executionStore: ErrorOr[ActiveExecutionStore] =
+    ExecutionStore(workflowDescriptor.callable, params.totalJobsByRootWf, TotalMaxJobsPerRootWf)
 
   // If executionStore returns a Failure about root workflow creating jobs more than total jobs per root workflow limit,
   // the WEA will fail by sending WorkflowExecutionFailedResponse to its parent and kill itself
@@ -95,7 +100,12 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
     case Valid(validExecutionStore) =>
       startWith(
         WorkflowExecutionPendingState,
-        WorkflowExecutionActorData(workflowDescriptor, ioEc, new AsyncIo(params.ioActor, GcsBatchCommandBuilder), params.totalJobsByRootWf, validExecutionStore)
+        WorkflowExecutionActorData(workflowDescriptor,
+                                   ioEc,
+                                   new AsyncIo(params.ioActor, GcsBatchCommandBuilder),
+                                   params.totalJobsByRootWf,
+                                   validExecutionStore
+        )
       )
     case Invalid(e) =>
       val errorMsg = s"Failed to initialize WorkflowExecutionActor. Error: $e"
@@ -106,7 +116,12 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
       // it throws NullPointerException as FSM.goto can't find the currentState
       startWith(
         WorkflowExecutionFailedState,
-        WorkflowExecutionActorData(workflowDescriptor, ioEc, new AsyncIo(params.ioActor, GcsBatchCommandBuilder), params.totalJobsByRootWf, ExecutionStore.empty)
+        WorkflowExecutionActorData(workflowDescriptor,
+                                   ioEc,
+                                   new AsyncIo(params.ioActor, GcsBatchCommandBuilder),
+                                   params.totalJobsByRootWf,
+                                   ExecutionStore.empty
+        )
       )
 
       workflowLogger.debug("Actor failed to initialize. Stopping self.")
@@ -124,14 +139,14 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
       sendHeartBeat()
 
       /*
-        * Note that we don't record the fact that a workflow was failing, therefore we either restart in running or aborting state.
-        * If the workflow was failing, it means at least one job failed in which case it'll still be failed when we get to it.
-        * When that happens, we'll go to failing state.
-        *
-        * An effect of that is that up until the moment when we come across the failed job,
-        * all backend jobs will be restarted with a Recover command which could potentially re-execute the job if the backend doesn't support
-        * job recovery. A better way would be to record that the workflow was failing an restart in failing mode. However there will always be a gap
-        * between when a job has failed and Cromwell is aware of it, or has time to persist that information.
+       * Note that we don't record the fact that a workflow was failing, therefore we either restart in running or aborting state.
+       * If the workflow was failing, it means at least one job failed in which case it'll still be failed when we get to it.
+       * When that happens, we'll go to failing state.
+       *
+       * An effect of that is that up until the moment when we come across the failed job,
+       * all backend jobs will be restarted with a Recover command which could potentially re-execute the job if the backend doesn't support
+       * job recovery. A better way would be to record that the workflow was failing an restart in failing mode. However there will always be a gap
+       * between when a job has failed and Cromwell is aware of it, or has time to persist that information.
        */
       params.startState match {
         case RestartableAborting => goto(WorkflowExecutionAbortingState)
@@ -165,8 +180,9 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
     // A job not found here means we were trying to reconnect to a job that was likely never started. Indicate this in the message.
     case Event(JobFailedNonRetryableResponse(jobKey, _: JobNotFoundException, _), _) if restarting =>
       val benignException =
-        new Exception("Cromwell server was restarted while this workflow was running. As part of the restart process, Cromwell attempted to reconnect to this job, however it was never started in the first place. This is a benign failure and not the cause of failure for this workflow, it can be safely ignored.")
-          with NoStackTrace
+        new Exception(
+          "Cromwell server was restarted while this workflow was running. As part of the restart process, Cromwell attempted to reconnect to this job, however it was never started in the first place. This is a benign failure and not the cause of failure for this workflow, it can be safely ignored."
+        ) with NoStackTrace
       handleNonRetryableFailure(stateData, jobKey, benignException)
   }
 
@@ -187,20 +203,28 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
       handleCallAborted(stateData, jobKey, executedKeys)
 
     // Here we can't really know what the status of the job is. For now declare it aborted anyway but add some info in the metadata
-    case Event(JobFailedNonRetryableResponse(jobKey: BackendJobDescriptorKey, failure: JobReconnectionNotSupportedException, _), _) if restarting =>
+    case Event(JobFailedNonRetryableResponse(jobKey: BackendJobDescriptorKey,
+                                             failure: JobReconnectionNotSupportedException,
+                                             _
+               ),
+               _
+        ) if restarting =>
       pushBackendStatusUnknown(jobKey)
       handleNonRetryableFailure(stateData, jobKey, failure, None)
   }
 
-  when(WorkflowExecutionSuccessfulState) { FSM.NullFunction }
-  when(WorkflowExecutionFailedState) { FSM.NullFunction }
-  when(WorkflowExecutionAbortedState) { FSM.NullFunction }
+  when(WorkflowExecutionSuccessfulState)(FSM.NullFunction)
+  when(WorkflowExecutionFailedState)(FSM.NullFunction)
+  when(WorkflowExecutionAbortedState)(FSM.NullFunction)
 
   var previousHeartbeatTime: Option[OffsetDateTime] = None
   def measureTimeBetweenHeartbeats(): Unit = {
     val now = OffsetDateTime.now
     previousHeartbeatTime foreach { previous =>
-      sendGauge(NonEmptyList("workflows", List("workflowexecutionactor", "heartbeat", "interval_millis", "set")), now.toInstant.toEpochMilli - previous.toInstant.toEpochMilli)
+      sendGauge(
+        NonEmptyList("workflows", List("workflowexecutionactor", "heartbeat", "interval_millis", "set")),
+        now.toInstant.toEpochMilli - previous.toInstant.toEpochMilli
+      )
     }
     previousHeartbeatTime = Option(now)
   }
@@ -225,15 +249,20 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
       stay() using stateData
         .mergeExecutionDiff(WorkflowExecutionDiff(Map(key -> ExecutionStatus.Running)))
 
-    //Success
+    // Success
     // Job
     case Event(r: JobSucceededResponse, stateData) =>
       if (r.resultGenerationMode != RunOnBackend) {
-        workflowLogger.info(s"Job results retrieved (${r.resultGenerationMode}): '${r.jobKey.call.fullyQualifiedName}' (scatter index: ${r.jobKey.index}, attempt ${r.jobKey.attempt})")
+        workflowLogger.info(
+          s"Job results retrieved (${r.resultGenerationMode}): '${r.jobKey.call.fullyQualifiedName}' (scatter index: ${r.jobKey.index}, attempt ${r.jobKey.attempt})"
+        )
       }
       handleCallSuccessful(r.jobKey, r.jobOutputs, r.returnCode, stateData, Map.empty, Set(workflowDescriptor.id))
     // Sub Workflow
-    case Event(SubWorkflowSucceededResponse(jobKey, descendantJobKeys, rootAndSubworklowIds, callOutputs, cumulativeOutputs), currentStateData) =>
+    case Event(
+          SubWorkflowSucceededResponse(jobKey, descendantJobKeys, rootAndSubworklowIds, callOutputs, cumulativeOutputs),
+          currentStateData
+        ) =>
       // Update call outputs to come from sub-workflow output ports:
       val subworkflowOutputs: Map[OutputPort, WomValue] = callOutputs.outputs flatMap { case (port, value) =>
         jobKey.node.subworkflowCallOutputPorts collectFirst {
@@ -241,16 +270,30 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
         }
       }
 
-      if(subworkflowOutputs.size == callOutputs.outputs.size) {
-        handleCallSuccessful(jobKey, CallOutputs(subworkflowOutputs), None, currentStateData, descendantJobKeys, rootAndSubworklowIds, cumulativeOutputs)
+      if (subworkflowOutputs.size == callOutputs.outputs.size) {
+        handleCallSuccessful(jobKey,
+                             CallOutputs(subworkflowOutputs),
+                             None,
+                             currentStateData,
+                             descendantJobKeys,
+                             rootAndSubworklowIds,
+                             cumulativeOutputs
+        )
       } else {
-        handleNonRetryableFailure(currentStateData, jobKey, new Exception(s"Subworkflow produced outputs: [${callOutputs.outputs.keys.mkString(", ")}], but we expected all of [${jobKey.node.subworkflowCallOutputPorts.map(_.internalName)}]"))
+        handleNonRetryableFailure(
+          currentStateData,
+          jobKey,
+          new Exception(s"Subworkflow produced outputs: [${callOutputs.outputs.keys
+              .mkString(", ")}], but we expected all of [${jobKey.node.subworkflowCallOutputPorts.map(_.internalName)}]")
+        )
       }
     // Expression
     case Event(ExpressionEvaluationSucceededResponse(expressionKey, callOutputs), stateData) =>
       expressionKey.node match {
         case _: ExposedExpressionNode | _: ExpressionBasedGraphOutputNode =>
-          workflowLogger.debug(s"Expression evaluation succeeded: '${expressionKey.node.fullyQualifiedName}' (scatter index: ${expressionKey.index}, attempt: ${expressionKey.attempt})")
+          workflowLogger.debug(
+            s"Expression evaluation succeeded: '${expressionKey.node.fullyQualifiedName}' (scatter index: ${expressionKey.index}, attempt: ${expressionKey.attempt})"
+          )
         case _ => // No logging; anonymous node
       }
 
@@ -314,11 +357,23 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
   override protected def onFailure(actorRef: ActorRef, throwable: => Throwable) = {
     // Both of these Should Never Happen (tm), assuming the state data is set correctly on EJEA creation.
     // If they do, it's a big programmer error and the workflow execution fails.
-    val jobKey = stateData.jobKeyActorMappings.getOrElse(actorRef, throw new RuntimeException("Programmer Error: A job or sub workflow actor has terminated but was not assigned a jobKey"))
-    val jobStatus = stateData.executionStore.jobStatus(jobKey).getOrElse(throw new RuntimeException(s"Programmer Error: An actor representing ${jobKey.tag} which this workflow is not running has sent up a terminated message."))
+    val jobKey = stateData.jobKeyActorMappings.getOrElse(
+      actorRef,
+      throw new RuntimeException(
+        "Programmer Error: A job or sub workflow actor has terminated but was not assigned a jobKey"
+      )
+    )
+    val jobStatus = stateData.executionStore
+      .jobStatus(jobKey)
+      .getOrElse(
+        throw new RuntimeException(
+          s"Programmer Error: An actor representing ${jobKey.tag} which this workflow is not running has sent up a terminated message."
+        )
+      )
 
     if (!jobStatus.isTerminalOrRetryable) {
-      val terminationException = new RuntimeException(s"Unexpected failure or termination of the actor monitoring ${jobKey.tag}", throwable)
+      val terminationException =
+        new RuntimeException(s"Unexpected failure or termination of the actor monitoring ${jobKey.tag}", throwable)
       self ! JobFailedNonRetryableResponse(jobKey, terminationException, None)
     }
   }
@@ -328,7 +383,9 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
     // Send the abort to all children
     context.children foreach { _ ! EngineLifecycleActorAbortCommand }
     // As well as all backend singleton actors
-    params.backendSingletonCollection.backendSingletonActors.values.flatten.foreach { _ ! BackendSingletonActorAbortWorkflow(workflowIdForLogging) }
+    params.backendSingletonCollection.backendSingletonActors.values.flatten.foreach {
+      _ ! BackendSingletonActorAbortWorkflow(workflowIdForLogging)
+    }
 
     // Only seal the execution store if we're not restarting, otherwise we could miss some jobs that have been started before the
     // restart but are not started yet at this point
@@ -344,8 +401,8 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
     import spray.json._
 
     def handleSuccessfulWorkflowOutputs(outputs: Map[GraphOutputNode, WomValue]) = {
-      val fullyQualifiedOutputs = outputs map {
-        case (outputNode, value) => outputNode.identifier.fullyQualifiedName.value -> value
+      val fullyQualifiedOutputs = outputs map { case (outputNode, value) =>
+        outputNode.identifier.fullyQualifiedName.value -> value
       }
       // Publish fully qualified workflow outputs to log and metadata
       workflowLogger.info(
@@ -354,15 +411,19 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
       )
       pushWorkflowOutputMetadata(fullyQualifiedOutputs)
 
-      val localOutputs = CallOutputs(outputs map {
-        case (outputNode, value) => outputNode.graphOutputPort -> value
+      val localOutputs = CallOutputs(outputs map { case (outputNode, value) =>
+        outputNode.graphOutputPort -> value
       })
 
       val currentCumulativeOutputs = data.cumulativeOutputs ++ localOutputs.outputs.values
 
       val currentRootAndSubworkflowIds = data.rootAndSubworkflowIds + workflowDescriptor.id
 
-      context.parent ! WorkflowExecutionSucceededResponse(data.jobExecutionMap, currentRootAndSubworkflowIds, localOutputs, currentCumulativeOutputs)
+      context.parent ! WorkflowExecutionSucceededResponse(data.jobExecutionMap,
+                                                          currentRootAndSubworkflowIds,
+                                                          localOutputs,
+                                                          currentCumulativeOutputs
+      )
       goto(WorkflowExecutionSuccessfulState) using data
     }
 
@@ -380,14 +441,13 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
 
     val workflowOutputValuesValidation = workflowOutputNodes
       // Try to find a value for each port in the value store
-      .map(outputNode =>
-      outputNode -> data.valueStore.get(outputNode.graphOutputPort, None)
-    )
-      .toList.traverse[IOChecked, (GraphOutputNode, WomValue)]({
-      case (name, Some(value)) => value.initialize(data.expressionLanguageFunctions).map(name -> _)
-      case (name, None) =>
-        s"Cannot find an output value for ${name.identifier.fullyQualifiedName.value}".invalidIOChecked
-    })
+      .map(outputNode => outputNode -> data.valueStore.get(outputNode.graphOutputPort, None))
+      .toList
+      .traverse[IOChecked, (GraphOutputNode, WomValue)] {
+        case (name, Some(value)) => value.initialize(data.expressionLanguageFunctions).map(name -> _)
+        case (name, None) =>
+          s"Cannot find an output value for ${name.identifier.fullyQualifiedName.value}".invalidIOChecked
+      }
       // Convert the list of tuples to a Map
       .map(_.toMap)
 
@@ -410,7 +470,8 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
                                         failedJobKey: JobKey,
                                         reason: Throwable,
                                         returnCode: Option[Int] = None,
-                                        jobExecutionMap: JobExecutionMap = Map.empty) = {
+                                        jobExecutionMap: JobExecutionMap = Map.empty
+  ) = {
     pushFailedCallMetadata(failedJobKey, returnCode, reason, retryableFailure = false)
 
     val dataWithFailure = stateData.executionFailure(failedJobKey, reason, jobExecutionMap)
@@ -442,7 +503,7 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
      * and for which reconnection will fail. When that happens we'll fail the job (see failing state).
      *
      * This guarantees that we'll try to reconnect to all potentially running jobs on restart.
-    */
+     */
     val newData = if (workflowDescriptor.failureMode.allowNewCallsAfterFailure || restarting) {
       dataWithFailure
     } else {
@@ -458,7 +519,10 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
     goto(nextState) using newData
   }
 
-  private def handleCallAborted(data: WorkflowExecutionActorData, jobKey: JobKey, jobExecutionMap: JobExecutionMap = Map.empty) = {
+  private def handleCallAborted(data: WorkflowExecutionActorData,
+                                jobKey: JobKey,
+                                jobExecutionMap: JobExecutionMap = Map.empty
+  ) = {
     pushAbortedCallMetadata(jobKey)
     workflowLogger.info(s"$tag aborted: ${jobKey.tag}")
     val newStateData = data
@@ -469,19 +533,20 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
   }
 
   private def pushBackendStatusUnknown(jobKey: BackendJobDescriptorKey): Unit = {
-    val unknownBackendStatus = MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.BackendStatus), MetadataValue("Unknown"))
+    val unknownBackendStatus =
+      MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.BackendStatus), MetadataValue("Unknown"))
     serviceRegistryActor ! PutMetadataAction(unknownBackendStatus)
   }
 
-  private def handleRetryableFailure(jobKey: BackendJobDescriptorKey,
-                                     reason: Throwable,
-                                     returnCode: Option[Int]) = {
+  private def handleRetryableFailure(jobKey: BackendJobDescriptorKey, reason: Throwable, returnCode: Option[Int]) = {
     pushFailedCallMetadata(jobKey, returnCode, reason, retryableFailure = true)
     val newJobKey = jobKey.copy(attempt = jobKey.attempt + 1)
     workflowLogger.info(s"Retrying job execution for ${newJobKey.tag}")
 
     // Update current key to RetryableFailure status and add new key with attempt incremented and NotStarted status
-    val executionDiff = WorkflowExecutionDiff(Map(jobKey -> ExecutionStatus.RetryableFailure, newJobKey -> ExecutionStatus.NotStarted))
+    val executionDiff = WorkflowExecutionDiff(
+      Map(jobKey -> ExecutionStatus.RetryableFailure, newJobKey -> ExecutionStatus.NotStarted)
+    )
 
     stay() using stateData.mergeExecutionDiff(executionDiff)
   }
@@ -492,20 +557,30 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
                                    data: WorkflowExecutionActorData,
                                    jobExecutionMap: JobExecutionMap,
                                    rootAndSubworkflowIds: Set[WorkflowId],
-                                   cumulativeOutputs: Set[WomValue] = Set.empty) = {
+                                   cumulativeOutputs: Set[WomValue] = Set.empty
+  ) = {
     pushSuccessfulCallMetadata(jobKey, returnCode, outputs)
-    stay() using data.callExecutionSuccess(jobKey, outputs, cumulativeOutputs, rootAndSubworkflowIds).addExecutions(jobExecutionMap)
+    stay() using data
+      .callExecutionSuccess(jobKey, outputs, cumulativeOutputs, rootAndSubworkflowIds)
+      .addExecutions(jobExecutionMap)
   }
 
-  private def handleDeclarationEvaluationSuccessful(key: ExpressionKey, values: Map[OutputPort, WomValue], data: WorkflowExecutionActorData) = {
+  private def handleDeclarationEvaluationSuccessful(key: ExpressionKey,
+                                                    values: Map[OutputPort, WomValue],
+                                                    data: WorkflowExecutionActorData
+  ) =
     stay() using data.expressionEvaluationSuccess(key, values)
-  }
 
-  override def receive: Receive = {
-    case msg =>
-      val starttime = OffsetDateTime.now
-      super[LoggingFSM].receive(msg)
-      sendGauge(NonEmptyList("workflows", List("workflowexecutionactor", this.stateName.toString, msg.getClass.getSimpleName , "processing_millis", "set")), OffsetDateTime.now.toInstant.toEpochMilli - starttime.toInstant.toEpochMilli)
+  override def receive: Receive = { case msg =>
+    val starttime = OffsetDateTime.now
+    super[LoggingFSM].receive(msg)
+    sendGauge(
+      NonEmptyList(
+        "workflows",
+        List("workflowexecutionactor", this.stateName.toString, msg.getClass.getSimpleName, "processing_millis", "set")
+      ),
+      OffsetDateTime.now.toInstant.toEpochMilli - starttime.toInstant.toEpochMilli
+    )
   }
 
   /**
@@ -517,10 +592,14 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
 
     val startRunnableStartTimestamp = OffsetDateTime.now
 
-    def updateExecutionStore(diffs: List[WorkflowExecutionDiff], updatedData: WorkflowExecutionActorData): WorkflowExecutionActorData = {
-      val notStartedBackendJobs = diffs.flatMap(d => d.executionStoreChanges.collect{
-        case (key: BackendJobDescriptorKey, status: ExecutionStatus.NotStarted.type) => (key, status)
-      }.keys)
+    def updateExecutionStore(diffs: List[WorkflowExecutionDiff],
+                             updatedData: WorkflowExecutionActorData
+    ): WorkflowExecutionActorData = {
+      val notStartedBackendJobs = diffs.flatMap(d =>
+        d.executionStoreChanges.collect {
+          case (key: BackendJobDescriptorKey, status: ExecutionStatus.NotStarted.type) => (key, status)
+        }.keys
+      )
       val notStartedBackendJobsCt = notStartedBackendJobs.size
 
       // this limits the total max jobs that can be created by a root workflow
@@ -528,56 +607,66 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
         // Since the root workflow tried creating jobs more than the total max jobs allowed per root workflow
         // we fail all the BackendJobDescriptorKey which are in 'Not Started' state, and update the execution
         // store with the status update of remaining keys
-        val updatedDiffs = diffs.map(d => d.copy(executionStoreChanges = d.executionStoreChanges -- notStartedBackendJobs))
+        val updatedDiffs =
+          diffs.map(d => d.copy(executionStoreChanges = d.executionStoreChanges -- notStartedBackendJobs))
 
-        notStartedBackendJobs.foreach(key => {
-          val errorMsg = s"Job $key failed to be created! Error: Root workflow tried creating ${data.totalJobsByRootWf.get} jobs, which is more than $TotalMaxJobsPerRootWf, the max cumulative jobs allowed per root workflow"
+        notStartedBackendJobs.foreach { key =>
+          val errorMsg =
+            s"Job $key failed to be created! Error: Root workflow tried creating ${data.totalJobsByRootWf.get} jobs, which is more than $TotalMaxJobsPerRootWf, the max cumulative jobs allowed per root workflow"
           workflowLogger.error(errorMsg)
           self ! JobFailedNonRetryableResponse(key, new Exception(errorMsg), None)
-        })
+        }
         updatedData.mergeExecutionDiffs(updatedDiffs)
-      }
-      else updatedData.mergeExecutionDiffs(diffs)
+      } else updatedData.mergeExecutionDiffs(diffs)
     }
 
     val DataStoreUpdate(runnableKeys, _, updatedData) = data.executionStoreUpdate
     val runnableCalls = runnableKeys.view
-      .collect({ case k: BackendJobDescriptorKey => k })
+      .collect { case k: BackendJobDescriptorKey => k }
       .groupBy(_.node)
-      .map({
-        case (node, keys) =>
-          val tag = node.fullyQualifiedName
-          val shardCount = keys.map(_.index).toList.distinct.size
-          if (shardCount == 1) tag
-          else s"$tag ($shardCount shards)"
-      })
+      .map { case (node, keys) =>
+        val tag = node.fullyQualifiedName
+        val shardCount = keys.map(_.index).toList.distinct.size
+        if (shardCount == 1) tag
+        else s"$tag ($shardCount shards)"
+      }
     val mode = if (restarting) "Restarting" else "Starting"
     if (runnableCalls.nonEmpty) workflowLogger.info(s"$mode " + runnableCalls.mkString(", "))
 
-    val keyStartDiffs: List[WorkflowExecutionDiff] = runnableKeys map { k => k -> (k match {
-      case key: BackendJobDescriptorKey => processRunnableJob(key, data)
-      case key: SubWorkflowKey => processRunnableSubWorkflow(key, data)
-      case key: ConditionalCollectorKey => key.processRunnable(data)
-      case key: ConditionalKey => key.processRunnable(data, workflowLogger)
-      case key @ ExpressionKey(expr: TaskCallInputExpressionNode, _) => processRunnableTaskCallInputExpression(key, data, expr)
-      case key: ExpressionKey => key.processRunnable(data.expressionLanguageFunctions, data.valueStore, self)
-      case key: ScatterCollectorKey => key.processRunnable(data)
-      case key: ScatteredCallCompletionKey => key.processRunnable(data)
-      case key: ScatterKey => key.processRunnable(data, self, MaxScatterWidth)
-      case other =>
-        workflowLogger.error(s"${other.tag} is not a runnable key")
-        WorkflowExecutionDiff.empty.validNel
-    })} map {
-      case (key: JobKey, value: ErrorOr[WorkflowExecutionDiff]) => value.valueOr(errors => {
-        self ! JobFailedNonRetryableResponse(key, new Exception(errors.toList.mkString(System.lineSeparator)) with NoStackTrace, None)
+    val keyStartDiffs: List[WorkflowExecutionDiff] = runnableKeys map { k =>
+      k -> (k match {
+        case key: BackendJobDescriptorKey => processRunnableJob(key, data)
+        case key: SubWorkflowKey => processRunnableSubWorkflow(key, data)
+        case key: ConditionalCollectorKey => key.processRunnable(data)
+        case key: ConditionalKey => key.processRunnable(data, workflowLogger)
+        case key @ ExpressionKey(expr: TaskCallInputExpressionNode, _) =>
+          processRunnableTaskCallInputExpression(key, data, expr)
+        case key: ExpressionKey => key.processRunnable(data.expressionLanguageFunctions, data.valueStore, self)
+        case key: ScatterCollectorKey => key.processRunnable(data)
+        case key: ScatteredCallCompletionKey => key.processRunnable(data)
+        case key: ScatterKey => key.processRunnable(data, self, MaxScatterWidth)
+        case other =>
+          workflowLogger.error(s"${other.tag} is not a runnable key")
+          WorkflowExecutionDiff.empty.validNel
+      })
+    } map { case (key: JobKey, value: ErrorOr[WorkflowExecutionDiff]) =>
+      value.valueOr { errors =>
+        self ! JobFailedNonRetryableResponse(key,
+                                             new Exception(errors.toList.mkString(System.lineSeparator))
+                                               with NoStackTrace,
+                                             None
+        )
         // Don't update the execution store now - the failure message we just sent to ourselves will take care of that:
         WorkflowExecutionDiff.empty
-      })
+      }
     }
 
     // Merge the execution diffs upon success
     val result = updateExecutionStore(keyStartDiffs, updatedData)
-    sendGauge(NonEmptyList("workflows", List("workflowexecutionactor", "startRunnableNodes", "duration_millis", "set")), OffsetDateTime.now.toInstant.toEpochMilli - startRunnableStartTimestamp.toInstant.toEpochMilli)
+    sendGauge(
+      NonEmptyList("workflows", List("workflowexecutionactor", "startRunnableNodes", "duration_millis", "set")),
+      OffsetDateTime.now.toInstant.toEpochMilli - startRunnableStartTimestamp.toInstant.toEpochMilli
+    )
     result
   }
 
@@ -587,35 +676,45 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
    */
   private def processRunnableTaskCallInputExpression(key: ExpressionKey,
                                                      data: WorkflowExecutionActorData,
-                                                     expressionNode: TaskCallInputExpressionNode): ErrorOr[WorkflowExecutionDiff] = {
+                                                     expressionNode: TaskCallInputExpressionNode
+  ): ErrorOr[WorkflowExecutionDiff] = {
     import cats.syntax.either._
     val taskCallNode: CommandCallNode = expressionNode.taskCallNodeReceivingInput.get(())
 
     (for {
-      backendJobDescriptorKey <- data.executionStore.backendJobDescriptorKeyForNode(taskCallNode) toChecked s"No BackendJobDescriptorKey found for call node ${taskCallNode.identifier.fullyQualifiedName}"
+      backendJobDescriptorKey <- data.executionStore.backendJobDescriptorKeyForNode(
+        taskCallNode
+      ) toChecked s"No BackendJobDescriptorKey found for call node ${taskCallNode.identifier.fullyQualifiedName}"
       factory <- backendFactoryForTaskCallNode(taskCallNode)
       backendInitializationData = params.initializationData.get(factory.name)
-      functions = factory.expressionLanguageFunctions(workflowDescriptor.backendDescriptor, backendJobDescriptorKey, backendInitializationData, params.ioActor, ioEc)
+      functions = factory.expressionLanguageFunctions(workflowDescriptor.backendDescriptor,
+                                                      backendJobDescriptorKey,
+                                                      backendInitializationData,
+                                                      params.ioActor,
+                                                      ioEc
+      )
       diff <- key.processRunnable(functions, data.valueStore, self).toEither
     } yield diff).toValidated
   }
 
-  private def backendFactoryForTaskCallNode(taskCallNode: CommandCallNode): Checked[BackendLifecycleActorFactory] = {
+  private def backendFactoryForTaskCallNode(taskCallNode: CommandCallNode): Checked[BackendLifecycleActorFactory] =
     for {
-      name <- workflowDescriptor
-        .backendAssignments.get(taskCallNode).toChecked(s"Cannot find an assigned backend for call ${taskCallNode.fullyQualifiedName}")
+      name <- workflowDescriptor.backendAssignments
+        .get(taskCallNode)
+        .toChecked(s"Cannot find an assigned backend for call ${taskCallNode.fullyQualifiedName}")
       factory <- backendFactories.get(name).toChecked(s"Cannot find a backend factory for backend $name")
     } yield factory
-  }
 
   /*
-    * Job and Sub Workflow processing
-    *
-    * Unlike other job keys, those methods are not embedded in the key class itself because they require creating a child actor.
-    * While it would be possible to extract those methods from the WEA as well and provide them with an actor factory, the majority of the objects needed to create
-    * the children actors are attributes of this class, so it makes more sense to keep the functions here.
+   * Job and Sub Workflow processing
+   *
+   * Unlike other job keys, those methods are not embedded in the key class itself because they require creating a child actor.
+   * While it would be possible to extract those methods from the WEA as well and provide them with an actor factory, the majority of the objects needed to create
+   * the children actors are attributes of this class, so it makes more sense to keep the functions here.
    */
-  private def processRunnableJob(key: BackendJobDescriptorKey, data: WorkflowExecutionActorData): ErrorOr[WorkflowExecutionDiff] = {
+  private def processRunnableJob(key: BackendJobDescriptorKey,
+                                 data: WorkflowExecutionActorData
+  ): ErrorOr[WorkflowExecutionDiff] = {
     import cats.syntax.either._
     import common.validation.Checked._
 
@@ -650,7 +749,8 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
 
   private def startEJEA(jobKey: BackendJobDescriptorKey,
                         backendLifecycleActorFactory: BackendLifecycleActorFactory,
-                        command: BackendJobExecutionActorCommand): WorkflowExecutionDiff = {
+                        command: BackendJobExecutionActorCommand
+  ): WorkflowExecutionDiff = {
     val ejeaName = s"${workflowDescriptor.id}-EngineJobExecutionActor-${jobKey.tag}"
     val backendName = backendLifecycleActorFactory.name
     val backendSingleton = params.backendSingletonCollection.backendSingletonActors(backendName)
@@ -695,9 +795,11 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
   }
 
   /*
-    * Creates another WEA to process the SubWorkflowKey
+   * Creates another WEA to process the SubWorkflowKey
    */
-  private def processRunnableSubWorkflow(key:SubWorkflowKey, data: WorkflowExecutionActorData): ErrorOr[WorkflowExecutionDiff] = {
+  private def processRunnableSubWorkflow(key: SubWorkflowKey,
+                                         data: WorkflowExecutionActorData
+  ): ErrorOr[WorkflowExecutionDiff] = {
     val sweaRef = context.actorOf(
       SubWorkflowExecutionActor.props(
         key,
@@ -719,7 +821,9 @@ case class WorkflowExecutionActor(params: WorkflowExecutionActorParams)
         params.rootConfig,
         params.totalJobsByRootWf,
         fileHashCacheActor = params.fileHashCacheActor,
-        blacklistCache = params.blacklistCache), s"$workflowIdForLogging-SubWorkflowExecutionActor-${key.tag}"
+        blacklistCache = params.blacklistCache
+      ),
+      s"$workflowIdForLogging-SubWorkflowExecutionActor-${key.tag}"
     )
 
     context watch sweaRef
@@ -784,17 +888,19 @@ object WorkflowExecutionActor {
   case class WorkflowExecutionSucceededResponse(jobExecutionMap: JobExecutionMap,
                                                 rootAndSubworklowIds: Set[WorkflowId],
                                                 outputs: CallOutputs,
-                                                cumulativeOutputs: Set[WomValue] = Set.empty)
-    extends WorkflowExecutionActorResponse {
+                                                cumulativeOutputs: Set[WomValue] = Set.empty
+  ) extends WorkflowExecutionActorResponse {
     override def toString = "WorkflowExecutionSucceededResponse"
   }
 
   case class WorkflowExecutionAbortedResponse(jobExecutionMap: JobExecutionMap)
-    extends WorkflowExecutionActorResponse with EngineLifecycleActorAbortedResponse {
+      extends WorkflowExecutionActorResponse
+      with EngineLifecycleActorAbortedResponse {
     override def toString = "WorkflowExecutionAbortedResponse"
   }
 
-  final case class WorkflowExecutionFailedResponse(jobExecutionMap: JobExecutionMap, reason: Throwable) extends WorkflowExecutionActorResponse {
+  final case class WorkflowExecutionFailedResponse(jobExecutionMap: JobExecutionMap, reason: Throwable)
+      extends WorkflowExecutionActorResponse {
     override def toString = "WorkflowExecutionFailedResponse"
   }
 
@@ -822,31 +928,34 @@ object WorkflowExecutionActor {
                                           jobExecutionMap: JobExecutionMap,
                                           rootAndSubworklowIds: Set[WorkflowId],
                                           outputs: CallOutputs,
-                                          cumulativeOutputs: Set[WomValue] = Set.empty) extends SubWorkflowTerminalStateResponse
+                                          cumulativeOutputs: Set[WomValue] = Set.empty
+  ) extends SubWorkflowTerminalStateResponse
 
-  case class SubWorkflowFailedResponse(key: SubWorkflowKey, jobExecutionMap: JobExecutionMap, reason: Throwable) extends SubWorkflowTerminalStateResponse
+  case class SubWorkflowFailedResponse(key: SubWorkflowKey, jobExecutionMap: JobExecutionMap, reason: Throwable)
+      extends SubWorkflowTerminalStateResponse
 
-  case class SubWorkflowAbortedResponse(key: SubWorkflowKey, jobExecutionMap: JobExecutionMap) extends SubWorkflowTerminalStateResponse
+  case class SubWorkflowAbortedResponse(key: SubWorkflowKey, jobExecutionMap: JobExecutionMap)
+      extends SubWorkflowTerminalStateResponse
 
   case class WorkflowExecutionActorParams(
-                                           workflowDescriptor: EngineWorkflowDescriptor,
-                                           ioActor: ActorRef,
-                                           serviceRegistryActor: ActorRef,
-                                           jobStoreActor: ActorRef,
-                                           subWorkflowStoreActor: ActorRef,
-                                           callCacheReadActor: ActorRef,
-                                           callCacheWriteActor: ActorRef,
-                                           workflowDockerLookupActor: ActorRef,
-                                           jobRestartCheckTokenDispenserActor: ActorRef,
-                                           jobExecutionTokenDispenserActor: ActorRef,
-                                           backendSingletonCollection: BackendSingletonCollection,
-                                           initializationData: AllBackendInitializationData,
-                                           startState: StartableState,
-                                           rootConfig: Config,
-                                           totalJobsByRootWf: AtomicInteger,
-                                           fileHashCacheActor: Option[ActorRef],
-                                           blacklistCache: Option[BlacklistCache]
-                                         )
+    workflowDescriptor: EngineWorkflowDescriptor,
+    ioActor: ActorRef,
+    serviceRegistryActor: ActorRef,
+    jobStoreActor: ActorRef,
+    subWorkflowStoreActor: ActorRef,
+    callCacheReadActor: ActorRef,
+    callCacheWriteActor: ActorRef,
+    workflowDockerLookupActor: ActorRef,
+    jobRestartCheckTokenDispenserActor: ActorRef,
+    jobExecutionTokenDispenserActor: ActorRef,
+    backendSingletonCollection: BackendSingletonCollection,
+    initializationData: AllBackendInitializationData,
+    startState: StartableState,
+    rootConfig: Config,
+    totalJobsByRootWf: AtomicInteger,
+    fileHashCacheActor: Option[ActorRef],
+    blacklistCache: Option[BlacklistCache]
+  )
 
   def props(workflowDescriptor: EngineWorkflowDescriptor,
             ioActor: ActorRef,
@@ -864,7 +973,8 @@ object WorkflowExecutionActor {
             rootConfig: Config,
             totalJobsByRootWf: AtomicInteger,
             fileHashCacheActor: Option[ActorRef],
-            blacklistCache: Option[BlacklistCache]): Props = {
+            blacklistCache: Option[BlacklistCache]
+  ): Props =
     Props(
       WorkflowExecutionActor(
         WorkflowExecutionActorParams(
@@ -888,7 +998,6 @@ object WorkflowExecutionActor {
         )
       )
     ).withDispatcher(EngineDispatcher)
-  }
 
   implicit class EnhancedWorkflowOutputs(val outputs: Map[LocallyQualifiedName, WomValue]) extends AnyVal {
     def maxStringLength = 1000
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorData.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorData.scala
index ce00523a6e9..75e29db9c2f 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorData.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorData.scala
@@ -20,15 +20,16 @@ import scala.concurrent.ExecutionContext
 object WorkflowExecutionDiff {
   def empty = WorkflowExecutionDiff(Map.empty)
 }
+
 /** Data differential between current execution data, and updates performed in a method that needs to be merged. */
 final case class WorkflowExecutionDiff(executionStoreChanges: Map[JobKey, ExecutionStatus],
                                        jobKeyActorMappings: Map[ActorRef, JobKey] = Map.empty,
                                        valueStoreAdditions: Map[ValueKey, WomValue] = Map.empty,
                                        cumulativeOutputsChanges: Set[WomValue] = Set.empty,
-                                       rootAndSubworkflowIds: Set[WorkflowId] = Set.empty) {
-  def containsNewEntry: Boolean = {
+                                       rootAndSubworkflowIds: Set[WorkflowId] = Set.empty
+) {
+  def containsNewEntry: Boolean =
     executionStoreChanges.exists(esc => esc._2 == NotStarted) || valueStoreAdditions.nonEmpty
-  }
 }
 
 object WorkflowExecutionActorData {
@@ -36,7 +37,8 @@ object WorkflowExecutionActorData {
             ec: ExecutionContext,
             asyncIo: AsyncIo,
             totalJobsByRootWf: AtomicInteger,
-            executionStore: ExecutionStore): WorkflowExecutionActorData = {
+            executionStore: ExecutionStore
+  ): WorkflowExecutionActorData =
     WorkflowExecutionActorData(
       workflowDescriptor,
       executionStore,
@@ -46,9 +48,11 @@ object WorkflowExecutionActorData {
       totalJobsByRootWf = totalJobsByRootWf,
       rootAndSubworkflowIds = Set(workflowDescriptor.id)
     )
-  }
 
-  final case class DataStoreUpdate(runnableKeys: List[JobKey], statusChanges: Map[JobKey, ExecutionStatus], newData: WorkflowExecutionActorData)
+  final case class DataStoreUpdate(runnableKeys: List[JobKey],
+                                   statusChanges: Map[JobKey, ExecutionStatus],
+                                   newData: WorkflowExecutionActorData
+  )
 }
 
 case class WorkflowExecutionActorData(workflowDescriptor: EngineWorkflowDescriptor,
@@ -61,7 +65,8 @@ case class WorkflowExecutionActorData(workflowDescriptor: EngineWorkflowDescript
                                       downstreamExecutionMap: JobExecutionMap = Map.empty,
                                       totalJobsByRootWf: AtomicInteger,
                                       cumulativeOutputs: Set[WomValue] = Set.empty,
-                                      rootAndSubworkflowIds: Set[WorkflowId]) {
+                                      rootAndSubworkflowIds: Set[WorkflowId]
+) {
 
   val expressionLanguageFunctions = new EngineIoFunctions(workflowDescriptor.pathBuilders, asyncIo, ec)
 
@@ -69,54 +74,63 @@ case class WorkflowExecutionActorData(workflowDescriptor: EngineWorkflowDescript
     executionStore = executionStore.seal
   )
 
-  def callExecutionSuccess(jobKey: JobKey, outputs: CallOutputs, cumulativeOutputs: Set[WomValue], rootAndSubworkflowIds: Set[WorkflowId]): WorkflowExecutionActorData = {
-    mergeExecutionDiff(WorkflowExecutionDiff(
-      executionStoreChanges = Map(jobKey -> Done),
-      valueStoreAdditions = toValuesMap(jobKey, outputs),
-      cumulativeOutputsChanges = cumulativeOutputs ++ outputs.outputs.values,
-      rootAndSubworkflowIds = rootAndSubworkflowIds
-    ))
-  }
-
-  final def expressionEvaluationSuccess(expressionKey: ExpressionKey, values: Map[OutputPort, WomValue]): WorkflowExecutionActorData = {
-    val valueStoreAdditions = values.map({
-      case (outputPort, value) => ValueKey(outputPort, expressionKey.index) -> value
-    })
-    mergeExecutionDiff(WorkflowExecutionDiff(
-      executionStoreChanges = Map(expressionKey -> Done),
-      valueStoreAdditions =valueStoreAdditions
-    ))
-  }
+  def callExecutionSuccess(jobKey: JobKey,
+                           outputs: CallOutputs,
+                           cumulativeOutputs: Set[WomValue],
+                           rootAndSubworkflowIds: Set[WorkflowId]
+  ): WorkflowExecutionActorData =
+    mergeExecutionDiff(
+      WorkflowExecutionDiff(
+        executionStoreChanges = Map(jobKey -> Done),
+        valueStoreAdditions = toValuesMap(jobKey, outputs),
+        cumulativeOutputsChanges = cumulativeOutputs ++ outputs.outputs.values,
+        rootAndSubworkflowIds = rootAndSubworkflowIds
+      )
+    )
 
-  def executionFailure(failedJobKey: JobKey, reason: Throwable, jobExecutionMap: JobExecutionMap): WorkflowExecutionActorData = {
-    mergeExecutionDiff(WorkflowExecutionDiff(
-      executionStoreChanges = Map(failedJobKey -> ExecutionStatus.Failed))
-    ).addExecutions(jobExecutionMap)
-    .copy(
-      jobFailures = jobFailures + (failedJobKey -> reason)
+  final def expressionEvaluationSuccess(expressionKey: ExpressionKey,
+                                        values: Map[OutputPort, WomValue]
+  ): WorkflowExecutionActorData = {
+    val valueStoreAdditions = values.map { case (outputPort, value) =>
+      ValueKey(outputPort, expressionKey.index) -> value
+    }
+    mergeExecutionDiff(
+      WorkflowExecutionDiff(
+        executionStoreChanges = Map(expressionKey -> Done),
+        valueStoreAdditions = valueStoreAdditions
+      )
     )
   }
 
-  def executionFailed(jobKey: JobKey): WorkflowExecutionActorData = mergeExecutionDiff(WorkflowExecutionDiff(Map(jobKey -> ExecutionStatus.Failed)))
+  def executionFailure(failedJobKey: JobKey,
+                       reason: Throwable,
+                       jobExecutionMap: JobExecutionMap
+  ): WorkflowExecutionActorData =
+    mergeExecutionDiff(WorkflowExecutionDiff(executionStoreChanges = Map(failedJobKey -> ExecutionStatus.Failed)))
+      .addExecutions(jobExecutionMap)
+      .copy(
+        jobFailures = jobFailures + (failedJobKey -> reason)
+      )
+
+  def executionFailed(jobKey: JobKey): WorkflowExecutionActorData = mergeExecutionDiff(
+    WorkflowExecutionDiff(Map(jobKey -> ExecutionStatus.Failed))
+  )
 
   /** Converts call outputs to a ValueStore entries */
-  private def toValuesMap(jobKey: JobKey, outputs: CallOutputs): Map[ValueKey, WomValue] = {
-    outputs.outputs.map({
-      case (outputPort, jobOutput) => ValueKey(outputPort, jobKey.index) -> jobOutput
-    })
-  }
+  private def toValuesMap(jobKey: JobKey, outputs: CallOutputs): Map[ValueKey, WomValue] =
+    outputs.outputs.map { case (outputPort, jobOutput) =>
+      ValueKey(outputPort, jobKey.index) -> jobOutput
+    }
 
-  def addExecutions(jobExecutionMap: JobExecutionMap): WorkflowExecutionActorData = {
+  def addExecutions(jobExecutionMap: JobExecutionMap): WorkflowExecutionActorData =
     this.copy(downstreamExecutionMap = downstreamExecutionMap ++ jobExecutionMap)
-  }
 
-  def removeJobKeyActor(actorRef: ActorRef): WorkflowExecutionActorData = {
+  def removeJobKeyActor(actorRef: ActorRef): WorkflowExecutionActorData =
     this.copy(
       jobKeyActorMappings = jobKeyActorMappings - actorRef
     )
-  }
 
-  def mergeExecutionDiff(diff: WorkflowExecutionDiff): WorkflowExecutionActorData = {
+  def mergeExecutionDiff(diff: WorkflowExecutionDiff): WorkflowExecutionActorData =
     this.copy(
       executionStore = executionStore.updateKeys(diff.executionStoreChanges),
       valueStore = valueStore.add(diff.valueStoreAdditions),
@@ -124,15 +138,12 @@ case class WorkflowExecutionActorData(workflowDescriptor: EngineWorkflowDescript
       cumulativeOutputs = cumulativeOutputs ++ diff.cumulativeOutputsChanges,
       rootAndSubworkflowIds = rootAndSubworkflowIds ++ diff.rootAndSubworkflowIds
     )
-  }
 
-  def mergeExecutionDiffs(diffs: Iterable[WorkflowExecutionDiff]): WorkflowExecutionActorData = {
+  def mergeExecutionDiffs(diffs: Iterable[WorkflowExecutionDiff]): WorkflowExecutionActorData =
     diffs.foldLeft(this)((newData, diff) => newData.mergeExecutionDiff(diff))
-  }
 
-  def jobExecutionMap: JobExecutionMap = {
+  def jobExecutionMap: JobExecutionMap =
     downstreamExecutionMap updated (workflowDescriptor.backendDescriptor, executionStore.startedJobs)
-  }
 
   def executionStoreUpdate: DataStoreUpdate = {
     val update = executionStore.update
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCache.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCache.scala
index 5e23a69d0c7..d904333bc22 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCache.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCache.scala
@@ -33,7 +33,8 @@ class CallCache(database: CallCachingSqlDatabase) {
         jobIndex = b.jobIndex.fromIndex,
         jobAttempt = b.jobAttempt,
         returnCode = b.returnCode,
-        allowResultReuse = b.allowResultReuse)
+        allowResultReuse = b.allowResultReuse
+      )
       val result = b.callOutputs.outputs.simplify
       val jobDetritus = b.jobDetritusFiles.getOrElse(Map.empty)
       buildCallCachingJoin(metaInfo, b.callCacheHashes, result, jobDetritus)
@@ -42,70 +43,81 @@ class CallCache(database: CallCachingSqlDatabase) {
     database.addCallCaching(joins, batchSize)
   }
 
-  private def buildCallCachingJoin(callCachingEntry: CallCachingEntry, callCacheHashes: CallCacheHashes,
-                                   result: Iterable[WomValueSimpleton], jobDetritus: Map[String, Path]): CallCachingJoin = {
+  private def buildCallCachingJoin(callCachingEntry: CallCachingEntry,
+                                   callCacheHashes: CallCacheHashes,
+                                   result: Iterable[WomValueSimpleton],
+                                   jobDetritus: Map[String, Path]
+  ): CallCachingJoin = {
 
-    val hashesToInsert: Iterable[CallCachingHashEntry] = {
+    val hashesToInsert: Iterable[CallCachingHashEntry] =
       callCacheHashes.hashes map { hash => CallCachingHashEntry(hash.hashKey.key, hash.hashValue.value) }
-    }
 
-    val aggregatedHashesToInsert: Option[CallCachingAggregationEntry] = {
-      Option(CallCachingAggregationEntry(
-        baseAggregation = callCacheHashes.aggregatedInitialHash,
-        inputFilesAggregation = callCacheHashes.fileHashes.map(_.aggregatedHash)
-      ))
-    }
+    val aggregatedHashesToInsert: Option[CallCachingAggregationEntry] =
+      Option(
+        CallCachingAggregationEntry(
+          baseAggregation = callCacheHashes.aggregatedInitialHash,
+          inputFilesAggregation = callCacheHashes.fileHashes.map(_.aggregatedHash)
+        )
+      )
 
-    val resultToInsert: Iterable[CallCachingSimpletonEntry] = {
-      result map {
-        case WomValueSimpleton(simpletonKey, wdlPrimitive) =>
-          CallCachingSimpletonEntry(simpletonKey, wdlPrimitive.valueString.toClobOption, wdlPrimitive.womType.stableName)
+    val resultToInsert: Iterable[CallCachingSimpletonEntry] =
+      result map { case WomValueSimpleton(simpletonKey, wdlPrimitive) =>
+        CallCachingSimpletonEntry(simpletonKey, wdlPrimitive.valueString.toClobOption, wdlPrimitive.womType.stableName)
       }
-    }
 
-    val jobDetritusToInsert: Iterable[CallCachingDetritusEntry] = {
-      jobDetritus map {
-        case (fileName, filePath) => CallCachingDetritusEntry(fileName, filePath.pathAsString.toClobOption)
+    val jobDetritusToInsert: Iterable[CallCachingDetritusEntry] =
+      jobDetritus map { case (fileName, filePath) =>
+        CallCachingDetritusEntry(fileName, filePath.pathAsString.toClobOption)
       }
-    }
 
-    CallCachingJoin(callCachingEntry, hashesToInsert.toSeq, aggregatedHashesToInsert, resultToInsert.toSeq, jobDetritusToInsert.toSeq)
+    CallCachingJoin(callCachingEntry,
+                    hashesToInsert.toSeq,
+                    aggregatedHashesToInsert,
+                    resultToInsert.toSeq,
+                    jobDetritusToInsert.toSeq
+    )
   }
 
-  def hasBaseAggregatedHashMatch(baseAggregatedHash: String, hints: List[CacheHitHint])(implicit ec: ExecutionContext): Future[Boolean] = {
+  def hasBaseAggregatedHashMatch(baseAggregatedHash: String, hints: List[CacheHitHint])(implicit
+    ec: ExecutionContext
+  ): Future[Boolean] = {
     val ccpp = hints collectFirst { case h: CallCachePathPrefixes => h.prefixes }
     database.hasMatchingCallCachingEntriesForBaseAggregation(baseAggregatedHash, ccpp)
   }
 
-  def callCachingHitForAggregatedHashes(aggregatedCallHashes: AggregatedCallHashes, prefixesHint: Option[CallCachePathPrefixes], excludedIds: Set[CallCachingEntryId])
-                                       (implicit ec: ExecutionContext): Future[Option[CallCachingEntryId]] = {
-    database.findCacheHitForAggregation(
-      baseAggregationHash = aggregatedCallHashes.baseAggregatedHash,
-      inputFilesAggregationHash = aggregatedCallHashes.inputFilesAggregatedHash,
-      callCachePathPrefixes = prefixesHint.map(_.prefixes),
-      excludedIds.map(_.id)).map(_ map CallCachingEntryId.apply)
-  }
+  def callCachingHitForAggregatedHashes(aggregatedCallHashes: AggregatedCallHashes,
+                                        prefixesHint: Option[CallCachePathPrefixes],
+                                        excludedIds: Set[CallCachingEntryId]
+  )(implicit ec: ExecutionContext): Future[Option[CallCachingEntryId]] =
+    database
+      .findCacheHitForAggregation(
+        baseAggregationHash = aggregatedCallHashes.baseAggregatedHash,
+        inputFilesAggregationHash = aggregatedCallHashes.inputFilesAggregatedHash,
+        callCachePathPrefixes = prefixesHint.map(_.prefixes),
+        excludedIds.map(_.id)
+      )
+      .map(_ map CallCachingEntryId.apply)
 
-  def fetchCachedResult(callCachingEntryId: CallCachingEntryId)(implicit ec: ExecutionContext): Future[Option[CallCachingJoin]] = {
+  def fetchCachedResult(callCachingEntryId: CallCachingEntryId)(implicit
+    ec: ExecutionContext
+  ): Future[Option[CallCachingJoin]] =
     database.queryResultsForCacheId(callCachingEntryId.id)
-  }
 
-  def callCachingJoinForCall(workflowUuid: String, callFqn: String, index: Int)(implicit ec: ExecutionContext): Future[Option[CallCachingJoin]] = {
+  def callCachingJoinForCall(workflowUuid: String, callFqn: String, index: Int)(implicit
+    ec: ExecutionContext
+  ): Future[Option[CallCachingJoin]] =
     database.callCacheJoinForCall(workflowUuid, callFqn, index)
-  }
 
-  def invalidate(callCachingEntryId: CallCachingEntryId)(implicit ec: ExecutionContext) = {
+  def invalidate(callCachingEntryId: CallCachingEntryId)(implicit ec: ExecutionContext) =
     database.invalidateCall(callCachingEntryId.id)
-  }
 
-  def callCacheEntryIdsForWorkflowId(workflowId: String)(implicit ec: ExecutionContext) = {
+  def callCacheEntryIdsForWorkflowId(workflowId: String)(implicit ec: ExecutionContext) =
     database.callCacheEntryIdsForWorkflowId(workflowId)
-  }
 }
 
 object CallCache {
   object CallCacheHashBundle {
-    def apply(workflowId: WorkflowId, callCacheHashes: CallCacheHashes, jobSucceededResponse: JobSucceededResponse) = {
+    def apply(workflowId: WorkflowId, callCacheHashes: CallCacheHashes, jobSucceededResponse: JobSucceededResponse) =
       new CallCacheHashBundle(
         workflowId = workflowId,
         callCacheHashes = callCacheHashes,
@@ -117,9 +129,11 @@ object CallCache {
         callOutputs = jobSucceededResponse.jobOutputs,
         jobDetritusFiles = jobSucceededResponse.jobDetritusFiles
       )
-    }
 
-    def apply(workflowId: WorkflowId, callCacheHashes: CallCacheHashes, jobFailedNonRetryableResponse: JobFailedNonRetryableResponse) = {
+    def apply(workflowId: WorkflowId,
+              callCacheHashes: CallCacheHashes,
+              jobFailedNonRetryableResponse: JobFailedNonRetryableResponse
+    ) =
       new CallCacheHashBundle(
         workflowId = workflowId,
         callCacheHashes = callCacheHashes,
@@ -131,47 +145,58 @@ object CallCache {
         callOutputs = CallOutputs.empty,
         jobDetritusFiles = None
       )
-    }
   }
   case class CallCacheHashBundle private (
-                                           workflowId: WorkflowId,
-                                           callCacheHashes: CallCacheHashes,
-                                           fullyQualifiedName: FullyQualifiedName,
-                                           jobIndex: ExecutionIndex,
-                                           jobAttempt: Option[Int],
-                                           returnCode: Option[Int],
-                                           allowResultReuse: Boolean,
-                                           callOutputs: CallOutputs,
-                                           jobDetritusFiles: Option[Map[String, Path]]
-                                         )
+    workflowId: WorkflowId,
+    callCacheHashes: CallCacheHashes,
+    fullyQualifiedName: FullyQualifiedName,
+    jobIndex: ExecutionIndex,
+    jobAttempt: Option[Int],
+    returnCode: Option[Int],
+    allowResultReuse: Boolean,
+    callOutputs: CallOutputs,
+    jobDetritusFiles: Option[Map[String, Path]]
+  )
 
   implicit class EnhancedCallCachingJoin(val callCachingJoin: CallCachingJoin) extends AnyVal {
     def toJobSuccess(key: BackendJobDescriptorKey, pathBuilders: List[PathBuilder]): JobSucceededResponse = {
       import cromwell.Simpletons._
       import cromwell.core.path.PathFactory._
-      val detritus = callCachingJoin.callCachingDetritusEntries.map({ jobDetritusEntry =>
+      val detritus = callCachingJoin.callCachingDetritusEntries.map { jobDetritusEntry =>
         jobDetritusEntry.detritusKey -> buildPath(jobDetritusEntry.detritusValue.toRawString, pathBuilders)
-      }).toMap
-
-      val outputs = if (callCachingJoin.callCachingSimpletonEntries.isEmpty) CallOutputs(Map.empty)
-      else WomValueBuilder.toJobOutputs(key.call.outputPorts, callCachingJoin.callCachingSimpletonEntries map toSimpleton)
-
-      JobSucceededResponse(key, callCachingJoin.callCachingEntry.returnCode,outputs, Option(detritus), Seq.empty, None, resultGenerationMode = CallCached)
+      }.toMap
+
+      val outputs =
+        if (callCachingJoin.callCachingSimpletonEntries.isEmpty) CallOutputs(Map.empty)
+        else
+          WomValueBuilder.toJobOutputs(key.call.outputPorts,
+                                       callCachingJoin.callCachingSimpletonEntries map toSimpleton
+          )
+
+      JobSucceededResponse(key,
+                           callCachingJoin.callCachingEntry.returnCode,
+                           outputs,
+                           Option(detritus),
+                           Seq.empty,
+                           None,
+                           resultGenerationMode = CallCached
+      )
     }
 
     def callCacheHashes: Set[HashResult] = {
-      val hashResults = callCachingJoin.callCachingHashEntries.map({
-        case CallCachingHashEntry(k, v, _, _) => HashResult(HashKey.deserialize(k), HashValue(v))
-      }) ++ callCachingJoin.callCachingAggregationEntry.collect({
-        case CallCachingAggregationEntry(k, Some(v), _, _) => HashResult(HashKey.deserialize(k), HashValue(v))
-      })
+      val hashResults = callCachingJoin.callCachingHashEntries.map { case CallCachingHashEntry(k, v, _, _) =>
+        HashResult(HashKey.deserialize(k), HashValue(v))
+      } ++ callCachingJoin.callCachingAggregationEntry.collect { case CallCachingAggregationEntry(k, Some(v), _, _) =>
+        HashResult(HashKey.deserialize(k), HashValue(v))
+      }
 
       hashResults.toSet
     }
   }
 
   sealed trait CacheHitHint
-  case class CallCachePathPrefixes(callCacheRootPrefix: Option[String], workflowOptionPrefixes: List[String]) extends CacheHitHint {
+  case class CallCachePathPrefixes(callCacheRootPrefix: Option[String], workflowOptionPrefixes: List[String])
+      extends CacheHitHint {
     lazy val prefixes: List[String] = (callCacheRootPrefix.toList ++ workflowOptionPrefixes) map { _.ensureSlashed }
   }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActor.scala
index 22a1612c672..f99ff6ee675 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActor.scala
@@ -14,35 +14,43 @@ import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheDiffAct
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheDiffQueryParameter.CallCacheDiffQueryCall
 import cromwell.services.metadata.MetadataService.GetMetadataAction
 import cromwell.services.metadata._
-import cromwell.services.{SuccessfulMetadataJsonResponse, FailedMetadataJsonResponse}
+import cromwell.services.{FailedMetadataJsonResponse, SuccessfulMetadataJsonResponse}
 import spray.json.{JsArray, JsBoolean, JsNumber, JsObject, JsString, JsValue}
 
-class CallCacheDiffActor(serviceRegistryActor: ActorRef) extends LoggingFSM[CallCacheDiffActorState, CallCacheDiffActorData] {
+class CallCacheDiffActor(serviceRegistryActor: ActorRef)
+    extends LoggingFSM[CallCacheDiffActorState, CallCacheDiffActorData] {
   startWith(Idle, CallCacheDiffNoData)
 
-  when(Idle) {
-    case Event(CallCacheDiffQueryParameter(callA, callB), CallCacheDiffNoData) =>
-      val queryA = makeMetadataQuery(callA)
-      val queryB = makeMetadataQuery(callB)
-      serviceRegistryActor ! GetMetadataAction(queryA)
-      serviceRegistryActor ! GetMetadataAction(queryB)
-      goto(WaitingForMetadata) using CallCacheDiffWithRequest(queryA, queryB, None, None, sender())
+  when(Idle) { case Event(CallCacheDiffQueryParameter(callA, callB), CallCacheDiffNoData) =>
+    val queryA = makeMetadataQuery(callA)
+    val queryB = makeMetadataQuery(callB)
+    serviceRegistryActor ! GetMetadataAction(queryA)
+    serviceRegistryActor ! GetMetadataAction(queryB)
+    goto(WaitingForMetadata) using CallCacheDiffWithRequest(queryA, queryB, None, None, sender())
   }
 
   when(WaitingForMetadata) {
     // First Response
     // Response A
-    case Event(SuccessfulMetadataJsonResponse(GetMetadataAction(originalQuery, _), responseJson), data@CallCacheDiffWithRequest(queryA, _, None, None, _)) if queryA == originalQuery =>
+    case Event(SuccessfulMetadataJsonResponse(GetMetadataAction(originalQuery, _), responseJson),
+               data @ CallCacheDiffWithRequest(queryA, _, None, None, _)
+        ) if queryA == originalQuery =>
       stay() using data.copy(responseA = Option(WorkflowMetadataJson(responseJson)))
     // Response B
-    case Event(SuccessfulMetadataJsonResponse(GetMetadataAction(originalQuery, _), responseJson), data@CallCacheDiffWithRequest(_, queryB, None, None, _)) if queryB == originalQuery =>
+    case Event(SuccessfulMetadataJsonResponse(GetMetadataAction(originalQuery, _), responseJson),
+               data @ CallCacheDiffWithRequest(_, queryB, None, None, _)
+        ) if queryB == originalQuery =>
       stay() using data.copy(responseB = Option(WorkflowMetadataJson(responseJson)))
     // Second Response
     // Response A
-    case Event(SuccessfulMetadataJsonResponse(GetMetadataAction(originalQuery, _), responseJson), CallCacheDiffWithRequest(queryA, queryB, None, Some(responseB), replyTo)) if queryA == originalQuery =>
+    case Event(SuccessfulMetadataJsonResponse(GetMetadataAction(originalQuery, _), responseJson),
+               CallCacheDiffWithRequest(queryA, queryB, None, Some(responseB), replyTo)
+        ) if queryA == originalQuery =>
       buildDiffAndRespond(queryA, queryB, WorkflowMetadataJson(responseJson), responseB, replyTo)
     // Response B
-    case Event(SuccessfulMetadataJsonResponse(GetMetadataAction(originalQuery, _), responseJson), CallCacheDiffWithRequest(queryA, queryB, Some(responseA), None, replyTo)) if queryB == originalQuery =>
+    case Event(SuccessfulMetadataJsonResponse(GetMetadataAction(originalQuery, _), responseJson),
+               CallCacheDiffWithRequest(queryA, queryB, Some(responseA), None, replyTo)
+        ) if queryB == originalQuery =>
       buildDiffAndRespond(queryA, queryB, responseA, WorkflowMetadataJson(responseJson), replyTo)
     case Event(FailedMetadataJsonResponse(_, failure), data: CallCacheDiffWithRequest) =>
       data.replyTo ! FailedCallCacheDiffResponse(failure)
@@ -50,10 +58,11 @@ class CallCacheDiffActor(serviceRegistryActor: ActorRef) extends LoggingFSM[Call
       stay()
   }
 
-  whenUnhandled {
-    case Event(oops, oopsData) =>
-      log.error(s"Programmer Error: Unexpected event received by ${this.getClass.getSimpleName}: $oops / $oopsData (in state $stateName)")
-      stay()
+  whenUnhandled { case Event(oops, oopsData) =>
+    log.error(
+      s"Programmer Error: Unexpected event received by ${this.getClass.getSimpleName}: $oops / $oopsData (in state $stateName)"
+    )
+    stay()
 
   }
 
@@ -61,17 +70,22 @@ class CallCacheDiffActor(serviceRegistryActor: ActorRef) extends LoggingFSM[Call
                                   queryB: MetadataQuery,
                                   responseA: WorkflowMetadataJson,
                                   responseB: WorkflowMetadataJson,
-                                  replyTo: ActorRef) = {
+                                  replyTo: ActorRef
+  ) = {
 
-    def describeCallFromQuery(query: MetadataQuery): String = s"${query.workflowId} / ${query.jobKey.map(_.callFqn).getOrElse("<<CallMissing>>")}:${query.jobKey.map(_.index.getOrElse(-1)).getOrElse("<<CallMissing>>")}"
+    def describeCallFromQuery(query: MetadataQuery): String =
+      s"${query.workflowId} / ${query.jobKey.map(_.callFqn).getOrElse("<<CallMissing>>")}:${query.jobKey.map(_.index.getOrElse(-1)).getOrElse("<<CallMissing>>")}"
 
-    val callACachingMetadata = extractCallMetadata(queryA, responseA).contextualizeErrors(s"extract relevant metadata for call A (${describeCallFromQuery(queryA)})")
-    val callBCachingMetadata = extractCallMetadata(queryB, responseB).contextualizeErrors(s"extract relevant metadata for call B (${describeCallFromQuery(queryB)})")
+    val callACachingMetadata = extractCallMetadata(queryA, responseA).contextualizeErrors(
+      s"extract relevant metadata for call A (${describeCallFromQuery(queryA)})"
+    )
+    val callBCachingMetadata = extractCallMetadata(queryB, responseB).contextualizeErrors(
+      s"extract relevant metadata for call B (${describeCallFromQuery(queryB)})"
+    )
 
     val response = (callACachingMetadata, callBCachingMetadata) flatMapN { case (callA, callB) =>
-
-        val callADetails = extractCallDetails(queryA, callA)
-        val callBDetails = extractCallDetails(queryB, callB)
+      val callADetails = extractCallDetails(queryA, callA)
+      val callBDetails = extractCallDetails(queryB, callB)
 
       (callADetails, callBDetails) mapN { (cad, cbd) =>
         val callAHashes = callA.callCachingMetadataJson.hashes
@@ -79,8 +93,10 @@ class CallCacheDiffActor(serviceRegistryActor: ActorRef) extends LoggingFSM[Call
 
         SuccessfulCallCacheDiffResponse(cad, cbd, calculateHashDifferential(callAHashes, callBHashes))
       }
-    } valueOr {
-      e => FailedCallCacheDiffResponse(AggregatedMessageException("Failed to calculate diff for call A and call B", e.toList))
+    } valueOr { e =>
+      FailedCallCacheDiffResponse(
+        AggregatedMessageException("Failed to calculate diff for call A and call B", e.toList)
+      )
     }
 
     replyTo ! response
@@ -90,7 +106,6 @@ class CallCacheDiffActor(serviceRegistryActor: ActorRef) extends LoggingFSM[Call
   }
 }
 
-
 object CallCacheDiffActor {
 
   final case class CachedCallNotFoundException(message: String) extends Exception {
@@ -108,18 +123,26 @@ object CallCacheDiffActor {
                                       responseA: Option[WorkflowMetadataJson],
                                       responseB: Option[WorkflowMetadataJson],
                                       replyTo: ActorRef
-                                     ) extends CallCacheDiffActorData
+  ) extends CallCacheDiffActorData
 
   sealed abstract class CallCacheDiffActorResponse
 
   case class FailedCallCacheDiffResponse(reason: Throwable) extends CallCacheDiffActorResponse
-  final case class SuccessfulCallCacheDiffResponse(callA: CallDetails, callB: CallDetails, hashDifferential: List[HashDifference]) extends CallCacheDiffActorResponse
-  def props(serviceRegistryActor: ActorRef) = Props(new CallCacheDiffActor(serviceRegistryActor)).withDispatcher(EngineDispatcher)
-
-  final case class CallDetails(executionStatus: String, allowResultReuse: Boolean, callFqn: String, jobIndex: Int, workflowId: String)
+  final case class SuccessfulCallCacheDiffResponse(callA: CallDetails,
+                                                   callB: CallDetails,
+                                                   hashDifferential: List[HashDifference]
+  ) extends CallCacheDiffActorResponse
+  def props(serviceRegistryActor: ActorRef) =
+    Props(new CallCacheDiffActor(serviceRegistryActor)).withDispatcher(EngineDispatcher)
+
+  final case class CallDetails(executionStatus: String,
+                               allowResultReuse: Boolean,
+                               callFqn: String,
+                               jobIndex: Int,
+                               workflowId: String
+  )
   final case class HashDifference(hashKey: String, callA: Option[String], callB: Option[String])
 
-
   /**
     * Create a Metadata query from a CallCacheDiffQueryCall
     */
@@ -135,15 +158,16 @@ object CallCacheDiffActor {
 
   // These simple case classes are just to help apply a little type safety to input and output types:
   final case class WorkflowMetadataJson(value: JsObject) extends AnyVal
-  final case class CallMetadataJson(rawValue: JsObject, jobKey: MetadataQueryJobKey, callCachingMetadataJson: CallCachingMetadataJson)
+  final case class CallMetadataJson(rawValue: JsObject,
+                                    jobKey: MetadataQueryJobKey,
+                                    callCachingMetadataJson: CallCachingMetadataJson
+  )
   final case class CallCachingMetadataJson(rawValue: JsObject, hashes: Map[String, String])
 
-
   /*
    * Takes in the JsObject returned from a metadata query and filters out only the appropriate call's callCaching section
    */
-  def extractCallMetadata(query: MetadataQuery, response: WorkflowMetadataJson): ErrorOr[CallMetadataJson] = {
-
+  def extractCallMetadata(query: MetadataQuery, response: WorkflowMetadataJson): ErrorOr[CallMetadataJson] =
     for {
       // Sanity Checks:
       _ <- response.value.validateNonEmptyResponse()
@@ -158,17 +182,18 @@ object CallCacheDiffActor {
       callCachingElement <- onlyShardElement.fieldAsObject(CallMetadataKeys.CallCaching)
       hashes <- extractHashes(callCachingElement)
     } yield CallMetadataJson(onlyShardElement, jobKey, CallCachingMetadataJson(callCachingElement, hashes))
-  }
 
   def extractHashes(callCachingMetadataJson: JsObject): ErrorOr[Map[String, String]] = {
-    def processField(keyPrefix: String)(fieldValue: (String, JsValue)): ErrorOr[Map[String, String]] = fieldValue match {
-      case (key, hashString: JsString) => Map(keyPrefix + key -> hashString.value).validNel
-      case (key, subObject: JsObject) => extractHashEntries(s"$keyPrefix$key:", subObject)
-      case (key, jsArray: JsArray) =>
-        val subObjectElements = jsArray.elements.zipWithIndex.map { case (element, index) => (s"[$index]", element) }
-        extractHashEntries(keyPrefix + key, JsObject(subObjectElements: _*))
-      case (key, otherValue) => s"Cannot extract hashes for $key. Expected JsString, JsObject, or JsArray but got ${otherValue.getClass.getSimpleName} $otherValue".invalidNel
-    }
+    def processField(keyPrefix: String)(fieldValue: (String, JsValue)): ErrorOr[Map[String, String]] =
+      fieldValue match {
+        case (key, hashString: JsString) => Map(keyPrefix + key -> hashString.value).validNel
+        case (key, subObject: JsObject) => extractHashEntries(s"$keyPrefix$key:", subObject)
+        case (key, jsArray: JsArray) =>
+          val subObjectElements = jsArray.elements.zipWithIndex.map { case (element, index) => (s"[$index]", element) }
+          extractHashEntries(keyPrefix + key, JsObject(subObjectElements: _*))
+        case (key, otherValue) =>
+          s"Cannot extract hashes for $key. Expected JsString, JsObject, or JsArray but got ${otherValue.getClass.getSimpleName} $otherValue".invalidNel
+      }
 
     def extractHashEntries(keyPrefix: String, jsObject: JsObject): ErrorOr[Map[String, String]] = {
       val traversed = jsObject.fields.toList.traverse(processField(keyPrefix))
@@ -215,10 +240,12 @@ object CallCacheDiffActor {
     def fieldAsBoolean(field: String): ErrorOr[JsBoolean] = jsObject.getField(field) flatMap { _.mapToJsBoolean }
     def checkFieldValue(field: String, expectation: String): ErrorOr[Unit] = jsObject.getField(field) flatMap {
       case v: JsValue if v.toString == expectation => ().validNel
-      case other => s"Unexpected value '${other.toString}' for metadata field '$field', should have been '$expectation'".invalidNel
+      case other =>
+        s"Unexpected value '${other.toString}' for metadata field '$field', should have been '$expectation'".invalidNel
     }
 
-    def validateNonEmptyResponse(): ErrorOr[Unit] = if (jsObject.fields.nonEmpty) { ().validNel } else {
+    def validateNonEmptyResponse(): ErrorOr[Unit] = if (jsObject.fields.nonEmpty) { ().validNel }
+    else {
       "No metadata was found for that workflow/call/index combination. Check that the workflow ID is correct, that the call name is formatted like 'workflowname.callname' and that an index is provided if this was a scattered task. (NOTE: the default index is -1, i.e. non-scattered)".invalidNel
     }
   }
@@ -231,18 +258,20 @@ object CallCacheDiffActor {
         attempt <- asObject.fieldAsNumber("attempt")
       } yield (attempt.value.intValue, asObject)
 
-      def foldFunction(accumulator: ErrorOr[(Int, JsObject)], nextElement: JsValue): ErrorOr[(Int, JsObject)] = {
-        (accumulator, extractAttemptAndObject(nextElement)) mapN { case ((previousHighestAttempt, previousJsObject), (nextAttempt, nextJsObject)) =>
-          if (previousHighestAttempt > nextAttempt) {
-            (previousHighestAttempt, previousJsObject)
-          } else {
-            (nextAttempt, nextJsObject)
-          }
+      def foldFunction(accumulator: ErrorOr[(Int, JsObject)], nextElement: JsValue): ErrorOr[(Int, JsObject)] =
+        (accumulator, extractAttemptAndObject(nextElement)) mapN {
+          case ((previousHighestAttempt, previousJsObject), (nextAttempt, nextJsObject)) =>
+            if (previousHighestAttempt > nextAttempt) {
+              (previousHighestAttempt, previousJsObject)
+            } else {
+              (nextAttempt, nextJsObject)
+            }
         }
-      }
 
       for {
-        attemptListNel <- NonEmptyList.fromList(jsArray.elements.toList).toErrorOr("Expected at least one attempt but found 0")
+        attemptListNel <- NonEmptyList
+          .fromList(jsArray.elements.toList)
+          .toErrorOr("Expected at least one attempt but found 0")
         highestAttempt <- attemptListNel.toList.foldLeft(extractAttemptAndObject(attemptListNel.head))(foldFunction)
       } yield highestAttempt._2
     }
@@ -251,23 +280,28 @@ object CallCacheDiffActor {
   implicit class EnhancedJsValue(val jsValue: JsValue) extends AnyVal {
     def mapToJsObject: ErrorOr[JsObject] = jsValue match {
       case obj: JsObject => obj.validNel
-      case other => s"Invalid value type. Expected JsObject but got ${other.getClass.getSimpleName}: ${other.prettyPrint}".invalidNel
+      case other =>
+        s"Invalid value type. Expected JsObject but got ${other.getClass.getSimpleName}: ${other.prettyPrint}".invalidNel
     }
     def mapToJsArray: ErrorOr[JsArray] = jsValue match {
       case arr: JsArray => arr.validNel
-      case other => s"Invalid value type. Expected JsArray but got ${other.getClass.getSimpleName}: ${other.prettyPrint}".invalidNel
+      case other =>
+        s"Invalid value type. Expected JsArray but got ${other.getClass.getSimpleName}: ${other.prettyPrint}".invalidNel
     }
     def mapToJsString: ErrorOr[JsString] = jsValue match {
       case str: JsString => str.validNel
-      case other => s"Invalid value type. Expected JsString but got ${other.getClass.getSimpleName}: ${other.prettyPrint}".invalidNel
+      case other =>
+        s"Invalid value type. Expected JsString but got ${other.getClass.getSimpleName}: ${other.prettyPrint}".invalidNel
     }
     def mapToJsBoolean: ErrorOr[JsBoolean] = jsValue match {
       case boo: JsBoolean => boo.validNel
-      case other => s"Invalid value type. Expected JsBoolean but got ${other.getClass.getSimpleName}: ${other.prettyPrint}".invalidNel
+      case other =>
+        s"Invalid value type. Expected JsBoolean but got ${other.getClass.getSimpleName}: ${other.prettyPrint}".invalidNel
     }
     def mapToJsNumber: ErrorOr[JsNumber] = jsValue match {
       case boo: JsNumber => boo.validNel
-      case other => s"Invalid value type. Expected JsNumber but got ${other.getClass.getSimpleName}: ${other.prettyPrint}".invalidNel
+      case other =>
+        s"Invalid value type. Expected JsNumber but got ${other.getClass.getSimpleName}: ${other.prettyPrint}".invalidNel
     }
   }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActorJsonFormatting.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActorJsonFormatting.scala
index 11ba8bfc3a4..8012c8951d8 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActorJsonFormatting.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActorJsonFormatting.scala
@@ -1,6 +1,10 @@
 package cromwell.engine.workflow.lifecycle.execution.callcaching
 
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheDiffActor.{CallDetails, HashDifference, SuccessfulCallCacheDiffResponse}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheDiffActor.{
+  CallDetails,
+  HashDifference,
+  SuccessfulCallCacheDiffResponse
+}
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport
 import org.apache.commons.lang3.NotImplementedException
 import spray.json._
@@ -13,14 +17,18 @@ object CallCacheDiffActorJsonFormatting extends SprayJsonSupport with DefaultJso
   implicit val hashDifferenceJsonFormatter = new RootJsonFormat[HashDifference] {
     override def write(hashDifference: HashDifference): JsValue = {
       def fromOption(opt: Option[String]) = opt.map(JsString.apply).getOrElse(JsNull)
-      JsObject(Map(
-        "hashKey" -> JsString(hashDifference.hashKey),
-        "callA" -> fromOption(hashDifference.callA),
-        "callB" -> fromOption(hashDifference.callB)
-      ))
+      JsObject(
+        Map(
+          "hashKey" -> JsString(hashDifference.hashKey),
+          "callA" -> fromOption(hashDifference.callA),
+          "callB" -> fromOption(hashDifference.callB)
+        )
+      )
     }
     override def read(json: JsValue): HashDifference =
-      throw new NotImplementedException("Programmer Error: No reader for HashDifferentials written. It was not expected to be required")
+      throw new NotImplementedException(
+        "Programmer Error: No reader for HashDifferentials written. It was not expected to be required"
+      )
   }
 
   implicit val successfulResponseJsonFormatter = jsonFormat3(SuccessfulCallCacheDiffResponse)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffQueryParameter.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffQueryParameter.scala
index ca094105988..6b32632a5a9 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffQueryParameter.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffQueryParameter.scala
@@ -15,30 +15,29 @@ object CallCacheDiffQueryParameter {
   private def missingWorkflowError(attribute: String) = s"missing $attribute query parameter".invalidNel
 
   def fromParameters(parameters: Seq[(String, String)]): ErrorOr[CallCacheDiffQueryParameter] = {
-    def extractIndex(parameter: String): ErrorOr[Option[Int]] = {
+    def extractIndex(parameter: String): ErrorOr[Option[Int]] =
       parameters.find(_._1 == parameter) match {
-        case Some((_, value)) => Try(value.trim.toInt) match {
-          case Success(index) => Option(index).validNel
-          case Failure(f) => f.getMessage.invalidNel
-        }
+        case Some((_, value)) =>
+          Try(value.trim.toInt) match {
+            case Success(index) => Option(index).validNel
+            case Failure(f) => f.getMessage.invalidNel
+          }
         case None => None.validNel
       }
-    }
 
-    def extractAttribute(parameter: String): ErrorOr[String] = {
+    def extractAttribute(parameter: String): ErrorOr[String] =
       parameters.find(_._1 == parameter) match {
         case Some((_, value)) => value.validNel
         case None => missingWorkflowError(parameter)
       }
-    }
-    
+
     def validateWorkflowId(parameter: String): ErrorOr[WorkflowId] = for {
       workflowIdString <- extractAttribute(parameter)
       workflowId <- fromTry(Try(WorkflowId.fromString(workflowIdString.trim)))
         .leftMap(_.getMessage)
         .toValidatedNel[String, WorkflowId]
     } yield workflowId
-    
+
     val workflowAValidation = validateWorkflowId("workflowA")
     val workflowBValidation = validateWorkflowId("workflowB")
 
@@ -49,15 +48,16 @@ object CallCacheDiffQueryParameter {
     val indexBValidation: ErrorOr[Option[Int]] = extractIndex("indexB")
 
     (workflowAValidation,
-      callAValidation,
-      indexAValidation,
-      workflowBValidation,
-      callBValidation,
-      indexBValidation) mapN { (workflowA, callA, indexA, workflowB, callB, indexB) =>
-        CallCacheDiffQueryParameter(
-          CallCacheDiffQueryCall(workflowA, callA, indexA),
-          CallCacheDiffQueryCall(workflowB, callB, indexB)
-        )
+     callAValidation,
+     indexAValidation,
+     workflowBValidation,
+     callBValidation,
+     indexBValidation
+    ) mapN { (workflowA, callA, indexA, workflowB, callB, indexB) =>
+      CallCacheDiffQueryParameter(
+        CallCacheDiffQueryCall(workflowA, callA, indexA),
+        CallCacheDiffQueryCall(workflowB, callB, indexB)
+      )
     }
   }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActor.scala
index 2329ad1331b..ff36d6deb2f 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActor.scala
@@ -17,7 +17,6 @@ import wom.values._
 import java.security.MessageDigest
 import javax.xml.bind.DatatypeConverter
 
-
 /**
   * Actor responsible for calculating individual as well as aggregated hashes for a job.
   * First calculate the initial hashes (individual and aggregated), and send them to its parent
@@ -42,7 +41,7 @@ class CallCacheHashingJobActor(jobDescriptor: BackendJobDescriptor,
                                callCachingActivity: CallCachingActivity,
                                callCachePathPrefixes: Option[CallCachePathPrefixes],
                                fileHashBatchSize: Int
-                              ) extends LoggingFSM[CallCacheHashingJobActorState, CallCacheHashingJobActorData] {
+) extends LoggingFSM[CallCacheHashingJobActorState, CallCacheHashingJobActorData] {
 
   val fileHashingActor: ActorRef = makeFileHashingActor()
 
@@ -103,9 +102,8 @@ class CallCacheHashingJobActor(jobDescriptor: BackendJobDescriptor,
   }
 
   // In its own function so it can be overridden in the test
-  private [callcaching] def addFileHash(hashResult: HashResult, data: CallCacheHashingJobActorData) = {
+  private[callcaching] def addFileHash(hashResult: HashResult, data: CallCacheHashingJobActorData) =
     data.withFileHash(hashResult)
-  }
 
   private def stopAndStay(fileHashResult: Option[FinalFileHashingResult]) = {
     fileHashResult foreach { context.parent ! _ }
@@ -114,14 +112,15 @@ class CallCacheHashingJobActor(jobDescriptor: BackendJobDescriptor,
     stay()
   }
 
-  private def sendToCallCacheReadingJobActor(message: Any, data: CallCacheHashingJobActorData): Unit = {
+  private def sendToCallCacheReadingJobActor(message: Any, data: CallCacheHashingJobActorData): Unit =
     data.callCacheReadingJobActor foreach { _ ! message }
-  }
 
   private def initializeCCHJA(): Unit = {
     import cromwell.core.simpleton.WomValueSimpleton._
 
-    val unqualifiedInputs = jobDescriptor.evaluatedTaskInputs map { case (declaration, value) => declaration.name -> value }
+    val unqualifiedInputs = jobDescriptor.evaluatedTaskInputs map { case (declaration, value) =>
+      declaration.name -> value
+    }
 
     val inputSimpletons = unqualifiedInputs.simplifyForCaching
     val (fileInputSimpletons, nonFileInputSimpletons) = inputSimpletons partition {
@@ -131,11 +130,12 @@ class CallCacheHashingJobActor(jobDescriptor: BackendJobDescriptor,
 
     val initialHashes = calculateInitialHashes(nonFileInputSimpletons, fileInputSimpletons)
 
-    val fileHashRequests = fileInputSimpletons collect {
-      case WomValueSimpleton(name, x: WomFile) => SingleFileHashRequest(jobDescriptor.key, HashKey(true, "input", s"File $name"), x, initializationData)
+    val fileHashRequests = fileInputSimpletons collect { case WomValueSimpleton(name, x: WomFile) =>
+      SingleFileHashRequest(jobDescriptor.key, HashKey(true, "input", s"File $name"), x, initializationData)
     }
 
-    val hashingJobActorData = CallCacheHashingJobActorData(fileHashRequests.toList, callCacheReadingJobActor, fileHashBatchSize)
+    val hashingJobActorData =
+      CallCacheHashingJobActorData(fileHashRequests.toList, callCacheReadingJobActor, fileHashBatchSize)
     startWith(WaitingForHashFileRequest, hashingJobActorData)
 
     val aggregatedBaseHash = calculateHashAggregation(initialHashes, MessageDigest.getInstance("MD5"))
@@ -149,39 +149,65 @@ class CallCacheHashingJobActor(jobDescriptor: BackendJobDescriptor,
     if (hashingJobActorData.callCacheReadingJobActor.isEmpty) self ! NextBatchOfFileHashesRequest
   }
 
-  private def calculateInitialHashes(nonFileInputs: Iterable[WomValueSimpleton], fileInputs: Iterable[WomValueSimpleton]): Set[HashResult] = {
+  private def calculateInitialHashes(nonFileInputs: Iterable[WomValueSimpleton],
+                                     fileInputs: Iterable[WomValueSimpleton]
+  ): Set[HashResult] = {
 
-    val commandTemplateHash = HashResult(HashKey("command template"), jobDescriptor.taskCall.callable.commandTemplateString(jobDescriptor.evaluatedTaskInputs).md5HashValue)
+    val commandTemplateHash = HashResult(
+      HashKey("command template"),
+      jobDescriptor.taskCall.callable.commandTemplateString(jobDescriptor.evaluatedTaskInputs).md5HashValue
+    )
     val backendNameHash = HashResult(HashKey("backend name"), backendNameForCallCachingPurposes.md5HashValue)
-    val inputCountHash = HashResult(HashKey("input count"), (nonFileInputs.size + fileInputs.size).toString.md5HashValue)
-    val outputCountHash = HashResult(HashKey("output count"), jobDescriptor.taskCall.callable.outputs.size.toString.md5HashValue)
-
-    val runtimeAttributeHashes = runtimeAttributeDefinitions map { definition => jobDescriptor.runtimeAttributes.get(definition.name) match {
-      case Some(_) if definition.name == RuntimeAttributesKeys.DockerKey && callCachingEligible.dockerHash.isDefined =>
-        HashResult(HashKey(definition.usedInCallCaching, "runtime attribute", definition.name), callCachingEligible.dockerHash.get.md5HashValue)
-      case Some(womValue) => HashResult(HashKey(definition.usedInCallCaching, "runtime attribute", definition.name), womValue.valueString.md5HashValue)
-      case None => HashResult(HashKey(definition.usedInCallCaching, "runtime attribute", definition.name), UnspecifiedRuntimeAttributeHashValue)
-    }}
-
-    val inputHashResults = nonFileInputs map {
-      case WomValueSimpleton(name, value) =>
-        val womTypeHashKeyString = value.womType.toHashKeyString
-        log.debug("Hashing input expression as {} {}", womTypeHashKeyString, name)
-        HashResult(HashKey("input", s"$womTypeHashKeyString $name"),  value.toWomString.md5HashValue)
+    val inputCountHash =
+      HashResult(HashKey("input count"), (nonFileInputs.size + fileInputs.size).toString.md5HashValue)
+    val outputCountHash =
+      HashResult(HashKey("output count"), jobDescriptor.taskCall.callable.outputs.size.toString.md5HashValue)
+
+    val runtimeAttributeHashes = runtimeAttributeDefinitions map { definition =>
+      jobDescriptor.runtimeAttributes.get(definition.name) match {
+        case Some(_)
+            if definition.name == RuntimeAttributesKeys.DockerKey && callCachingEligible.dockerHash.isDefined =>
+          HashResult(HashKey(definition.usedInCallCaching, "runtime attribute", definition.name),
+                     callCachingEligible.dockerHash.get.md5HashValue
+          )
+        case Some(womValue) =>
+          HashResult(HashKey(definition.usedInCallCaching, "runtime attribute", definition.name),
+                     womValue.valueString.md5HashValue
+          )
+        case None =>
+          HashResult(HashKey(definition.usedInCallCaching, "runtime attribute", definition.name),
+                     UnspecifiedRuntimeAttributeHashValue
+          )
+      }
+    }
+
+    val inputHashResults = nonFileInputs map { case WomValueSimpleton(name, value) =>
+      val womTypeHashKeyString = value.womType.toHashKeyString
+      log.debug("Hashing input expression as {} {}", womTypeHashKeyString, name)
+      HashResult(HashKey("input", s"$womTypeHashKeyString $name"), value.toWomString.md5HashValue)
     }
 
     val outputExpressionHashResults = jobDescriptor.taskCall.callable.outputs map { output =>
       val womTypeHashKeyString = output.womType.toHashKeyString
       val outputExpressionCacheString = output.expression.cacheString
-      log.debug("Hashing output expression type as '{}' and value as '{}'", womTypeHashKeyString, outputExpressionCacheString)
-      HashResult(HashKey("output expression", s"$womTypeHashKeyString ${output.name}"), outputExpressionCacheString.md5HashValue)
+      log.debug("Hashing output expression type as '{}' and value as '{}'",
+                womTypeHashKeyString,
+                outputExpressionCacheString
+      )
+      HashResult(HashKey("output expression", s"$womTypeHashKeyString ${output.name}"),
+                 outputExpressionCacheString.md5HashValue
+      )
     }
 
     // Build these all together for the final set of initial hashes:
-    Set(commandTemplateHash, backendNameHash, inputCountHash, outputCountHash) ++ runtimeAttributeHashes ++ inputHashResults ++ outputExpressionHashResults
+    Set(commandTemplateHash,
+        backendNameHash,
+        inputCountHash,
+        outputCountHash
+    ) ++ runtimeAttributeHashes ++ inputHashResults ++ outputExpressionHashResults
   }
 
-  private [callcaching] def makeFileHashingActor() = {
+  private[callcaching] def makeFileHashingActor() = {
     val fileHashingActorName = s"FileHashingActor_for_${jobDescriptor.key.tag}"
     context.actorOf(fileHashingActorProps, fileHashingActorName)
   }
@@ -199,18 +225,20 @@ object CallCacheHashingJobActor {
             callCachingActivity: CallCachingActivity,
             callCachePathPrefixes: Option[CallCachePathPrefixes],
             fileHashBatchSize: Int
-           ): Props = Props(new CallCacheHashingJobActor(
-    jobDescriptor,
-    callCacheReadingJobActor,
-    initializationData,
-    runtimeAttributeDefinitions,
-    backendNameForCallCachingPurposes,
-    fileHashingActorProps,
-    callCachingEligible,
-    callCachingActivity,
-    callCachePathPrefixes,
-    fileHashBatchSize
-  )).withDispatcher(EngineDispatcher)
+  ): Props = Props(
+    new CallCacheHashingJobActor(
+      jobDescriptor,
+      callCacheReadingJobActor,
+      initializationData,
+      runtimeAttributeDefinitions,
+      backendNameForCallCachingPurposes,
+      fileHashingActorProps,
+      callCachingEligible,
+      callCachingActivity,
+      callCachePathPrefixes,
+      fileHashBatchSize
+    )
+  ).withDispatcher(EngineDispatcher)
 
   sealed trait CallCacheHashingJobActorState
   case object WaitingForHashFileRequest extends CallCacheHashingJobActorState
@@ -227,22 +255,29 @@ object CallCacheHashingJobActor {
     val sortedHashes = hashes.toList
       .filter(_.hashKey.checkForHitOrMiss)
       .sortBy(_.hashKey.key)
-      .map({ case HashResult(hashKey, HashValue(hashValue)) => hashKey.key + hashValue })
+      .map { case HashResult(hashKey, HashValue(hashValue)) => hashKey.key + hashValue }
       .map(_.getBytes)
     sortedHashes foreach messageDigest.update
     DatatypeConverter.printHexBinary(messageDigest.digest())
   }
 
   object CallCacheHashingJobActorData {
-    def apply(fileHashRequestsRemaining: List[SingleFileHashRequest], callCacheReadingJobActor: Option[ActorRef], batchSize: Int): CallCacheHashingJobActorData = {
-      new CallCacheHashingJobActorData(fileHashRequestsRemaining.grouped(batchSize).toList, List.empty, callCacheReadingJobActor, batchSize)
-    }
+    def apply(fileHashRequestsRemaining: List[SingleFileHashRequest],
+              callCacheReadingJobActor: Option[ActorRef],
+              batchSize: Int
+    ): CallCacheHashingJobActorData =
+      new CallCacheHashingJobActorData(fileHashRequestsRemaining.grouped(batchSize).toList,
+                                       List.empty,
+                                       callCacheReadingJobActor,
+                                       batchSize
+      )
   }
 
   final case class CallCacheHashingJobActorData(fileHashRequestsRemaining: List[List[SingleFileHashRequest]],
                                                 fileHashResults: List[HashResult],
                                                 callCacheReadingJobActor: Option[ActorRef],
-                                                batchSize: Int) {
+                                                batchSize: Int
+  ) {
     private val md5Digest = MessageDigest.getInstance("MD5")
 
     /**
@@ -259,7 +294,14 @@ object CallCacheHashingJobActor {
           val updatedBatch = lastBatch.filterNot(_.hashKey == hashResult.hashKey)
           // If we're processing the last batch, and it's now empty, then we're done
           // In that case compute the aggregated hash and send that
-          if (updatedBatch.isEmpty) (List.empty, Option(CompleteFileHashingResult(newFileHashResults.toSet, calculateHashAggregation(newFileHashResults, md5Digest))))
+          if (updatedBatch.isEmpty)
+            (List.empty,
+             Option(
+               CompleteFileHashingResult(newFileHashResults.toSet,
+                                         calculateHashAggregation(newFileHashResults, md5Digest)
+               )
+             )
+            )
           // Otherwise just return the updated batch and no message
           else (List(updatedBatch), None)
         case currentBatch :: otherBatches =>
@@ -275,7 +317,9 @@ object CallCacheHashingJobActor {
           else (updatedBatch :: otherBatches, None)
       }
 
-      (this.copy(fileHashRequestsRemaining = updatedRequestsList, fileHashResults = newFileHashResults), responseMessage)
+      (this.copy(fileHashRequestsRemaining = updatedRequestsList, fileHashResults = newFileHashResults),
+       responseMessage
+      )
     }
   }
 
@@ -285,14 +329,18 @@ object CallCacheHashingJobActor {
   case object NextBatchOfFileHashesRequest extends CCHJARequest
 
   sealed trait CCHJAResponse
-  case class InitialHashingResult(initialHashes: Set[HashResult], aggregatedBaseHash: String, cacheHitHints: List[CacheHitHint] = List.empty) extends CCHJAResponse
+  case class InitialHashingResult(initialHashes: Set[HashResult],
+                                  aggregatedBaseHash: String,
+                                  cacheHitHints: List[CacheHitHint] = List.empty
+  ) extends CCHJAResponse
 
   // File Hashing responses
   sealed trait CCHJAFileHashResponse extends CCHJAResponse
   case class PartialFileHashingResult(initialHashes: NonEmptyList[HashResult]) extends CCHJAFileHashResponse
 
   sealed trait FinalFileHashingResult extends CCHJAFileHashResponse
-  case class CompleteFileHashingResult(fileHashes: Set[HashResult], aggregatedFileHash: String) extends FinalFileHashingResult
+  case class CompleteFileHashingResult(fileHashes: Set[HashResult], aggregatedFileHash: String)
+      extends FinalFileHashingResult
   case object NoFileHashesResult extends FinalFileHashingResult
 
   implicit class StringMd5er(val unhashedString: String) extends AnyVal {
@@ -303,11 +351,11 @@ object CallCacheHashingJobActor {
   }
 
   implicit class WomTypeHashString(val womType: WomType) extends AnyVal {
-    def toHashKeyString: String = {
+    def toHashKeyString: String =
       womType match {
         case c: WomCompositeType =>
-          val fieldTypes = c.typeMap map {
-            case (key, value) => s"$key -> ${value.stableName}"
+          val fieldTypes = c.typeMap map { case (key, value) =>
+            s"$key -> ${value.stableName}"
           }
           "CompositeType_digest_" + fieldTypes.mkString("\n").md5Sum
         case a: WomArrayType =>
@@ -321,6 +369,5 @@ object CallCacheHashingJobActor {
           s"Coproduct($hashStrings)"
         case o => o.stableName
       }
-    }
   }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheInvalidateActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheInvalidateActor.scala
index 16bb0fb9caa..f61a15cf3de 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheInvalidateActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheInvalidateActor.scala
@@ -23,18 +23,19 @@ class CallCacheInvalidateActor(callCache: CallCache, cacheId: CallCachingEntryId
       context.stop(self)
   }
 
-  override def receive: Receive = {
-    case any => log.error("Unexpected message to InvalidateCallCacheActor: " + any)
+  override def receive: Receive = { case any =>
+    log.error("Unexpected message to InvalidateCallCacheActor: " + any)
   }
 }
 
 object CallCacheInvalidateActor {
-  def props(callCache: CallCache, cacheId: CallCachingEntryId) = {
-    Props(new CallCacheInvalidateActor(callCache: CallCache, cacheId: CallCachingEntryId)).withDispatcher(EngineDispatcher)
-  }
+  def props(callCache: CallCache, cacheId: CallCachingEntryId) =
+    Props(new CallCacheInvalidateActor(callCache: CallCache, cacheId: CallCachingEntryId))
+      .withDispatcher(EngineDispatcher)
 }
 
 sealed trait CallCacheInvalidatedResponse
-case class CallCacheInvalidatedSuccess(cacheId: CallCachingEntryId, maybeEntry: Option[CallCachingEntry]) extends CallCacheInvalidatedResponse
+case class CallCacheInvalidatedSuccess(cacheId: CallCachingEntryId, maybeEntry: Option[CallCachingEntry])
+    extends CallCacheInvalidatedResponse
 case object CallCacheInvalidationUnnecessary extends CallCacheInvalidatedResponse
 case class CallCacheInvalidatedFailure(cacheId: CallCachingEntryId, t: Throwable) extends CallCacheInvalidatedResponse
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadActor.scala
index 16c4ce39ed7..63cc33d76b5 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadActor.scala
@@ -20,10 +20,8 @@ import cromwell.services.CallCaching.CallCachingEntryId
   *
   * Would be nice if instead there was a pull- rather than push-based mailbox but I can't find one...
   */
-class CallCacheReadActor(cache: CallCache,
-                         override val serviceRegistryActor: ActorRef,
-                         override val threshold: Int)
-  extends EnhancedThrottlerActor[CommandAndReplyTo[CallCacheReadActorRequest]]
+class CallCacheReadActor(cache: CallCache, override val serviceRegistryActor: ActorRef, override val threshold: Int)
+    extends EnhancedThrottlerActor[CommandAndReplyTo[CallCacheReadActorRequest]]
     with ActorLogging {
   override def routed = true
   override def processHead(request: CommandAndReplyTo[CallCacheReadActorRequest]): Future[Int] = instrumentedProcess {
@@ -58,29 +56,34 @@ class CallCacheReadActor(cache: CallCache,
   override def receive: Receive = enhancedReceive.orElse(super.receive)
   override protected def instrumentationPath = NonEmptyList.of("callcaching", "read")
   override protected def instrumentationPrefix = InstrumentationPrefixes.JobPrefix
-  override def commandToData(snd: ActorRef) = {
-    case request: CallCacheReadActorRequest => CommandAndReplyTo(request, snd)
+  override def commandToData(snd: ActorRef) = { case request: CallCacheReadActorRequest =>
+    CommandAndReplyTo(request, snd)
   }
 }
 
 object CallCacheReadActor {
-  def props(callCache: CallCache, serviceRegistryActor: ActorRef): Props = {
-    Props(new CallCacheReadActor(callCache, serviceRegistryActor, LoadConfig.CallCacheReadThreshold)).withDispatcher(EngineDispatcher)
-  }
+  def props(callCache: CallCache, serviceRegistryActor: ActorRef): Props =
+    Props(new CallCacheReadActor(callCache, serviceRegistryActor, LoadConfig.CallCacheReadThreshold))
+      .withDispatcher(EngineDispatcher)
 
   private[CallCacheReadActor] case class RequestTuple(requester: ActorRef, request: CallCacheReadActorRequest)
 
   object AggregatedCallHashes {
-    def apply(baseAggregatedHash: String, inputFilesAggregatedHash: String) = {
+    def apply(baseAggregatedHash: String, inputFilesAggregatedHash: String) =
       new AggregatedCallHashes(baseAggregatedHash, Option(inputFilesAggregatedHash))
-    }
   }
   case class AggregatedCallHashes(baseAggregatedHash: String, inputFilesAggregatedHash: Option[String])
 
   sealed trait CallCacheReadActorRequest
-  final case class CacheLookupRequest(aggregatedCallHashes: AggregatedCallHashes, excludedIds: Set[CallCachingEntryId], prefixesHint: Option[CallCachePathPrefixes]) extends CallCacheReadActorRequest
-  final case class HasMatchingInitialHashLookup(aggregatedTaskHash: String, cacheHitHints: List[CacheHitHint] = List.empty) extends CallCacheReadActorRequest
-  final case class CallCacheEntryForCall(workflowId: WorkflowId, jobKey: BackendJobDescriptorKey) extends CallCacheReadActorRequest
+  final case class CacheLookupRequest(aggregatedCallHashes: AggregatedCallHashes,
+                                      excludedIds: Set[CallCachingEntryId],
+                                      prefixesHint: Option[CallCachePathPrefixes]
+  ) extends CallCacheReadActorRequest
+  final case class HasMatchingInitialHashLookup(aggregatedTaskHash: String,
+                                                cacheHitHints: List[CacheHitHint] = List.empty
+  ) extends CallCacheReadActorRequest
+  final case class CallCacheEntryForCall(workflowId: WorkflowId, jobKey: BackendJobDescriptorKey)
+      extends CallCacheReadActorRequest
 
   sealed trait CallCacheReadActorResponse
   // Responses on whether or not there is at least one matching entry (can for initial matches of file matches)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadingJobActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadingJobActor.scala
index 953da95042f..dee9dd2aeea 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadingJobActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadingJobActor.scala
@@ -4,7 +4,12 @@ import akka.actor.{ActorRef, LoggingFSM, Props}
 import cromwell.core.Dispatcher.EngineDispatcher
 import cromwell.core.callcaching.HashingFailedMessage
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCache.CallCachePathPrefixes
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{CompleteFileHashingResult, InitialHashingResult, NextBatchOfFileHashesRequest, NoFileHashesResult}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{
+  CompleteFileHashingResult,
+  InitialHashingResult,
+  NextBatchOfFileHashesRequest,
+  NoFileHashesResult
+}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadActor._
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadingJobActor._
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.{CacheHit, CacheMiss, HashError}
@@ -24,16 +29,16 @@ import cromwell.services.CallCaching.CallCachingEntryId
   * Sends the response to its parent.
   * In case of a CacheHit, stays alive in case using the hit fails and it needs to fetch the next one. Otherwise just dies.
   */
-class CallCacheReadingJobActor(callCacheReadActor: ActorRef, prefixesHint: Option[CallCachePathPrefixes]) extends LoggingFSM[CallCacheReadingJobActorState, CCRJAData] {
-  
+class CallCacheReadingJobActor(callCacheReadActor: ActorRef, prefixesHint: Option[CallCachePathPrefixes])
+    extends LoggingFSM[CallCacheReadingJobActorState, CCRJAData] {
+
   startWith(WaitingForInitialHash, CCRJANoData)
-  
-  when(WaitingForInitialHash) {
-    case Event(InitialHashingResult(_, aggregatedBaseHash, hints), CCRJANoData) =>
-      callCacheReadActor ! HasMatchingInitialHashLookup(aggregatedBaseHash, hints)
-      goto(WaitingForHashCheck) using CCRJAWithData(sender(), aggregatedBaseHash, fileHash = None, seenCaches = Set.empty)
+
+  when(WaitingForInitialHash) { case Event(InitialHashingResult(_, aggregatedBaseHash, hints), CCRJANoData) =>
+    callCacheReadActor ! HasMatchingInitialHashLookup(aggregatedBaseHash, hints)
+    goto(WaitingForHashCheck) using CCRJAWithData(sender(), aggregatedBaseHash, fileHash = None, seenCaches = Set.empty)
   }
-  
+
   when(WaitingForHashCheck) {
     case Event(HasMatchingEntries, CCRJAWithData(hashingActor, _, _, _)) =>
       hashingActor ! NextBatchOfFileHashesRequest
@@ -41,16 +46,22 @@ class CallCacheReadingJobActor(callCacheReadActor: ActorRef, prefixesHint: Optio
     case Event(NoMatchingEntries, _) =>
       cacheMiss
   }
-  
+
   when(WaitingForFileHashes) {
     case Event(CompleteFileHashingResult(_, aggregatedFileHash), data: CCRJAWithData) =>
-      callCacheReadActor ! CacheLookupRequest(AggregatedCallHashes(data.initialHash, aggregatedFileHash), data.seenCaches, prefixesHint)
+      callCacheReadActor ! CacheLookupRequest(AggregatedCallHashes(data.initialHash, aggregatedFileHash),
+                                              data.seenCaches,
+                                              prefixesHint
+      )
       goto(WaitingForCacheHitOrMiss) using data.withFileHash(aggregatedFileHash)
     case Event(NoFileHashesResult, data: CCRJAWithData) =>
-      callCacheReadActor ! CacheLookupRequest(AggregatedCallHashes(data.initialHash, None), data.seenCaches, prefixesHint)
+      callCacheReadActor ! CacheLookupRequest(AggregatedCallHashes(data.initialHash, None),
+                                              data.seenCaches,
+                                              prefixesHint
+      )
       goto(WaitingForCacheHitOrMiss)
   }
-  
+
   when(WaitingForCacheHitOrMiss) {
     case Event(CacheLookupNextHit(hit), data: CCRJAWithData) =>
       context.parent ! CacheHit(hit)
@@ -58,7 +69,10 @@ class CallCacheReadingJobActor(callCacheReadActor: ActorRef, prefixesHint: Optio
     case Event(CacheLookupNoHit, _) =>
       cacheMiss
     case Event(NextHit, CCRJAWithData(_, aggregatedInitialHash, aggregatedFileHash, seenCaches)) =>
-      callCacheReadActor ! CacheLookupRequest(AggregatedCallHashes(aggregatedInitialHash, aggregatedFileHash), seenCaches, prefixesHint)
+      callCacheReadActor ! CacheLookupRequest(AggregatedCallHashes(aggregatedInitialHash, aggregatedFileHash),
+                                              seenCaches,
+                                              prefixesHint
+      )
       stay()
   }
 
@@ -80,9 +94,8 @@ class CallCacheReadingJobActor(callCacheReadActor: ActorRef, prefixesHint: Optio
 
 object CallCacheReadingJobActor {
 
-  def props(callCacheReadActor: ActorRef, prefixesHint: Option[CallCachePathPrefixes]) = {
+  def props(callCacheReadActor: ActorRef, prefixesHint: Option[CallCachePathPrefixes]) =
     Props(new CallCacheReadingJobActor(callCacheReadActor, prefixesHint)).withDispatcher(EngineDispatcher)
-  }
 
   sealed trait CallCacheReadingJobActorState
   case object WaitingForInitialHash extends CallCacheReadingJobActorState
@@ -92,7 +105,11 @@ object CallCacheReadingJobActor {
 
   sealed trait CCRJAData
   case object CCRJANoData extends CCRJAData
-  case class CCRJAWithData(hashingActor: ActorRef, initialHash: String, fileHash: Option[String], seenCaches: Set[CallCachingEntryId]) extends CCRJAData {
+  case class CCRJAWithData(hashingActor: ActorRef,
+                           initialHash: String,
+                           fileHash: Option[String],
+                           seenCaches: Set[CallCachingEntryId]
+  ) extends CCRJAData {
     def withSeenCache(id: CallCachingEntryId): CCRJAWithData = this.copy(seenCaches = seenCaches + id)
     def withFileHash(aggregatedFileHash: String): CCRJAWithData = this.copy(fileHash = Option(aggregatedFileHash))
   }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheWriteActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheWriteActor.scala
index 06d48fcdea0..012f2b0a7c0 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheWriteActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheWriteActor.scala
@@ -16,18 +16,22 @@ import scala.concurrent.duration._
 import scala.language.postfixOps
 
 case class CallCacheWriteActor(callCache: CallCache, serviceRegistryActor: ActorRef, threshold: Int)
-  extends EnhancedBatchActor[CommandAndReplyTo[SaveCallCacheHashes]](
-    CallCacheWriteActor.dbFlushRate,
-    CallCacheWriteActor.dbBatchSize) {
+    extends EnhancedBatchActor[CommandAndReplyTo[SaveCallCacheHashes]](CallCacheWriteActor.dbFlushRate,
+                                                                       CallCacheWriteActor.dbBatchSize
+    ) {
 
   override protected def process(data: NonEmptyVector[CommandAndReplyTo[SaveCallCacheHashes]]) = instrumentedProcess {
     log.debug("Flushing {} call cache hashes sets to the DB", data.length)
 
     //     Collect all the bundles of hashes that should be written and all the senders which should be informed of
     //     success or failure.
-    val (bundles, replyTos) = data.toList.foldMap { case CommandAndReplyTo(s: SaveCallCacheHashes, r: ActorRef) => (List(s.bundle), List(r)) }
+    val (bundles, replyTos) = data.toList.foldMap { case CommandAndReplyTo(s: SaveCallCacheHashes, r: ActorRef) =>
+      (List(s.bundle), List(r))
+    }
     if (bundles.nonEmpty) {
-      val futureMessage = callCache.addToCache(bundles, batchSize) map { _ => CallCacheWriteSuccess } recover { case t => CallCacheWriteFailure(t) }
+      val futureMessage = callCache.addToCache(bundles, batchSize) map { _ => CallCacheWriteSuccess } recover {
+        case t => CallCacheWriteFailure(t)
+      }
       futureMessage map { message =>
         replyTos foreach { _ ! message }
       }
@@ -46,9 +50,9 @@ case class CallCacheWriteActor(callCache: CallCache, serviceRegistryActor: Actor
 }
 
 object CallCacheWriteActor {
-  def props(callCache: CallCache, registryActor: ActorRef): Props = {
-    Props(CallCacheWriteActor(callCache, registryActor, LoadConfig.CallCacheWriteThreshold)).withDispatcher(EngineDispatcher)
-  }
+  def props(callCache: CallCache, registryActor: ActorRef): Props =
+    Props(CallCacheWriteActor(callCache, registryActor, LoadConfig.CallCacheWriteThreshold))
+      .withDispatcher(EngineDispatcher)
 
   case class SaveCallCacheHashes(bundle: CallCacheHashBundle)
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActor.scala
index 698f1d20d4d..d1d5a9a6db0 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActor.scala
@@ -8,7 +8,12 @@ import cromwell.core.callcaching._
 import cromwell.core.logging.JobLogging
 import cromwell.engine.workflow.lifecycle.execution.CallMetadataHelper
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCache.CallCachePathPrefixes
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{CompleteFileHashingResult, FinalFileHashingResult, InitialHashingResult, NoFileHashesResult}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{
+  CompleteFileHashingResult,
+  FinalFileHashingResult,
+  InitialHashingResult,
+  NoFileHashesResult
+}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadingJobActor.NextHit
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor._
 import cromwell.services.CallCaching.CallCachingEntryId
@@ -31,7 +36,11 @@ class EngineJobHashingActor(receiver: ActorRef,
                             activity: CallCachingActivity,
                             callCachingEligible: CallCachingEligible,
                             callCachePathPrefixes: Option[CallCachePathPrefixes],
-                            fileHashBatchSize: Int) extends Actor with ActorLogging with JobLogging with CallMetadataHelper {
+                            fileHashBatchSize: Int
+) extends Actor
+    with ActorLogging
+    with JobLogging
+    with CallMetadataHelper {
 
   override val jobTag = jobDescriptor.key.tag
   val workflowId = jobDescriptor.workflowDescriptor.id
@@ -39,25 +48,28 @@ class EngineJobHashingActor(receiver: ActorRef,
   override val rootWorkflowIdForLogging = jobDescriptor.workflowDescriptor.rootWorkflowId
   override val workflowIdForCallMetadata: WorkflowId = workflowId
 
-  private [callcaching] var initialHash: Option[InitialHashingResult] = None
+  private[callcaching] var initialHash: Option[InitialHashingResult] = None
 
-  private [callcaching] val callCacheReadingJobActor = if (activity.readFromCache) {
+  private[callcaching] val callCacheReadingJobActor = if (activity.readFromCache) {
     Option(context.actorOf(callCacheReadingJobActorProps, s"CCReadingJobActor-${workflowId.shortString}-$jobTag"))
   } else None
 
   override def preStart(): Unit = {
-    context.actorOf(CallCacheHashingJobActor.props(
-      jobDescriptor,
-      callCacheReadingJobActor,
-      initializationData,
-      runtimeAttributeDefinitions,
-      backendNameForCallCachingPurposes,
-      fileHashingActorProps,
-      callCachingEligible,
-      activity,
-      callCachePathPrefixes,
-      fileHashBatchSize
-    ), s"CCHashingJobActor-${workflowId.shortString}-$jobTag")
+    context.actorOf(
+      CallCacheHashingJobActor.props(
+        jobDescriptor,
+        callCacheReadingJobActor,
+        initializationData,
+        runtimeAttributeDefinitions,
+        backendNameForCallCachingPurposes,
+        fileHashingActorProps,
+        callCachingEligible,
+        activity,
+        callCachePathPrefixes,
+        fileHashBatchSize
+      ),
+      s"CCHashingJobActor-${workflowId.shortString}-$jobTag"
+    )
     super.preStart()
   }
 
@@ -81,7 +93,10 @@ class EngineJobHashingActor(receiver: ActorRef,
 
   private def publishHashFailure(failure: Throwable) = {
     import cromwell.services.metadata.MetadataService._
-    val failureAsEvents = throwableToMetadataEvents(metadataKeyForCall(jobDescriptor.key, CallMetadataKeys.CallCachingKeys.HashFailuresKey), failure)
+    val failureAsEvents = throwableToMetadataEvents(
+      metadataKeyForCall(jobDescriptor.key, CallMetadataKeys.CallCachingKeys.HashFailuresKey),
+      failure
+    )
     serviceRegistryActor ! PutMetadataAction(failureAsEvents)
   }
 
@@ -125,7 +140,10 @@ object EngineJobHashingActor {
   case class CacheHit(cacheResultId: CallCachingEntryId) extends EJHAResponse
   case class HashError(reason: Throwable) extends EJHAResponse
   case class FileHashes(hashes: Set[HashResult], aggregatedHash: String)
-  case class CallCacheHashes(initialHashes: Set[HashResult], aggregatedInitialHash: String, fileHashes: Option[FileHashes]) extends EJHAResponse {
+  case class CallCacheHashes(initialHashes: Set[HashResult],
+                             aggregatedInitialHash: String,
+                             fileHashes: Option[FileHashes]
+  ) extends EJHAResponse {
     val hashes = initialHashes ++ fileHashes.map(_.hashes).getOrElse(Set.empty)
     def aggregatedHashString: String = {
       val file = fileHashes match {
@@ -147,17 +165,21 @@ object EngineJobHashingActor {
             activity: CallCachingActivity,
             callCachingEligible: CallCachingEligible,
             callCachePathPrefixes: Option[CallCachePathPrefixes],
-            fileHashBatchSize: Int): Props = Props(new EngineJobHashingActor(
-    receiver = receiver,
-    serviceRegistryActor = serviceRegistryActor,
-    jobDescriptor = jobDescriptor,
-    initializationData = initializationData,
-    fileHashingActorProps = fileHashingActorProps,
-    callCacheReadingJobActorProps = callCacheReadingJobActorProps,
-    runtimeAttributeDefinitions = runtimeAttributeDefinitions,
-    backendNameForCallCachingPurposes = backendNameForCallCachingPurposes,
-    activity = activity,
-    callCachingEligible = callCachingEligible,
-    callCachePathPrefixes = callCachePathPrefixes,
-    fileHashBatchSize = fileHashBatchSize)).withDispatcher(EngineDispatcher)
+            fileHashBatchSize: Int
+  ): Props = Props(
+    new EngineJobHashingActor(
+      receiver = receiver,
+      serviceRegistryActor = serviceRegistryActor,
+      jobDescriptor = jobDescriptor,
+      initializationData = initializationData,
+      fileHashingActorProps = fileHashingActorProps,
+      callCacheReadingJobActorProps = callCacheReadingJobActorProps,
+      runtimeAttributeDefinitions = runtimeAttributeDefinitions,
+      backendNameForCallCachingPurposes = backendNameForCallCachingPurposes,
+      activity = activity,
+      callCachingEligible = callCachingEligible,
+      callCachePathPrefixes = callCachePathPrefixes,
+      fileHashBatchSize = fileHashBatchSize
+    )
+  ).withDispatcher(EngineDispatcher)
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
index 89745e6523d..5d30adf9ce0 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala
@@ -5,7 +5,10 @@ import cromwell.Simpletons._
 import cromwell.core.Dispatcher.EngineDispatcher
 import cromwell.core.simpleton.WomValueSimpleton
 import cromwell.database.sql.SqlConverters._
-import cromwell.engine.workflow.lifecycle.execution.callcaching.FetchCachedResultsActor.{CachedOutputLookupFailed, CachedOutputLookupSucceeded}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.FetchCachedResultsActor.{
+  CachedOutputLookupFailed,
+  CachedOutputLookupSucceeded
+}
 import cromwell.services.CallCaching.CallCachingEntryId
 
 import scala.concurrent.ExecutionContext
@@ -16,14 +19,19 @@ object FetchCachedResultsActor {
     Props(new FetchCachedResultsActor(callCachingEntryId, replyTo, callCache)).withDispatcher(EngineDispatcher)
 
   sealed trait CachedResultResponse
-  case class CachedOutputLookupFailed(callCachingEntryId: CallCachingEntryId, failure: Throwable) extends CachedResultResponse
-  case class CachedOutputLookupSucceeded(simpletons: Seq[WomValueSimpleton], callOutputFiles: Map[String,String],
-                                         returnCode: Option[Int], cacheHit: CallCachingEntryId, cacheHitDetails: String) extends CachedResultResponse
+  case class CachedOutputLookupFailed(callCachingEntryId: CallCachingEntryId, failure: Throwable)
+      extends CachedResultResponse
+  case class CachedOutputLookupSucceeded(simpletons: Seq[WomValueSimpleton],
+                                         callOutputFiles: Map[String, String],
+                                         returnCode: Option[Int],
+                                         cacheHit: CallCachingEntryId,
+                                         cacheHitDetails: String
+  ) extends CachedResultResponse
 }
 
-
 class FetchCachedResultsActor(cacheResultId: CallCachingEntryId, replyTo: ActorRef, callCache: CallCache)
-  extends Actor with ActorLogging {
+    extends Actor
+    with ActorLogging {
 
   {
     implicit val ec: ExecutionContext = context.dispatcher
@@ -36,12 +44,16 @@ class FetchCachedResultsActor(cacheResultId: CallCachingEntryId, replyTo: ActorR
         }
 
         val sourceCacheDetails = Seq(result.callCachingEntry.workflowExecutionUuid,
-          result.callCachingEntry.callFullyQualifiedName,
-          result.callCachingEntry.jobIndex.toString).mkString(":")
+                                     result.callCachingEntry.callFullyQualifiedName,
+                                     result.callCachingEntry.jobIndex.toString
+        ).mkString(":")
 
-        CachedOutputLookupSucceeded(simpletons, jobDetritusFiles.toMap,
-          result.callCachingEntry.returnCode,
-          cacheResultId, sourceCacheDetails)
+        CachedOutputLookupSucceeded(simpletons,
+                                    jobDetritusFiles.toMap,
+                                    result.callCachingEntry.returnCode,
+                                    cacheResultId,
+                                    sourceCacheDetails
+        )
       case None =>
         val reason = new RuntimeException(s"Cache hit vanished between discovery and retrieval: $cacheResultId")
         CachedOutputLookupFailed(cacheResultId, reason)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/package.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/package.scala
index 1913e64c9a9..917b559693f 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/package.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/package.scala
@@ -1,6 +1,3 @@
 package cromwell.engine.workflow.lifecycle.execution
 
-package object callcaching {
-
-
-}
+package object callcaching {}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
index 4423de202cc..b6db1f05fcd 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala
@@ -3,7 +3,13 @@ package cromwell.engine.workflow.lifecycle.execution.job
 import akka.actor.SupervisorStrategy.{Escalate, Stop}
 import akka.actor.{ActorInitializationException, ActorRef, LoggingFSM, OneForOneStrategy, Props}
 import cats.data.NonEmptyList
-import cromwell.backend.BackendCacheHitCopyingActor.{CacheCopyFailure, CopyOutputsCommand, CopyingOutputsFailedResponse, CopyAttemptError, BlacklistSkip}
+import cromwell.backend.BackendCacheHitCopyingActor.{
+  BlacklistSkip,
+  CacheCopyFailure,
+  CopyAttemptError,
+  CopyingOutputsFailedResponse,
+  CopyOutputsCommand
+}
 import cromwell.backend.BackendJobExecutionActor._
 import cromwell.backend.BackendLifecycleActor.AbortJobCommand
 import cromwell.backend.MetricableCacheCopyErrorCategory.MetricableCacheCopyErrorCategory
@@ -27,10 +33,16 @@ import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadAct
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadingJobActor.NextHit
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheWriteActor._
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor._
-import cromwell.engine.workflow.lifecycle.execution.callcaching.FetchCachedResultsActor.{CachedOutputLookupFailed, CachedOutputLookupSucceeded}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.FetchCachedResultsActor.{
+  CachedOutputLookupFailed,
+  CachedOutputLookupSucceeded
+}
 import cromwell.engine.workflow.lifecycle.execution.callcaching._
 import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor._
-import cromwell.engine.workflow.lifecycle.execution.job.preparation.CallPreparation.{BackendJobPreparationSucceeded, CallPreparationFailed}
+import cromwell.engine.workflow.lifecycle.execution.job.preparation.CallPreparation.{
+  BackendJobPreparationSucceeded,
+  CallPreparationFailed
+}
 import cromwell.engine.workflow.lifecycle.execution.job.preparation.{CallPreparation, JobPreparationActor}
 import cromwell.engine.workflow.lifecycle.execution.stores.ValueStore
 import cromwell.engine.workflow.lifecycle.{EngineLifecycleActorAbortCommand, TimedFSM}
@@ -63,12 +75,13 @@ class EngineJobExecutionActor(replyTo: ActorRef,
                               jobExecutionTokenDispenserActor: ActorRef,
                               backendSingletonActor: Option[ActorRef],
                               command: BackendJobExecutionActorCommand,
-                              callCachingParameters: CallCachingParameters) extends LoggingFSM[EngineJobExecutionActorState, EJEAData]
-  with WorkflowLogging
-  with CallMetadataHelper
-  with JobInstrumentation
-  with CromwellInstrumentation
-  with TimedFSM[EngineJobExecutionActorState] {
+                              callCachingParameters: CallCachingParameters
+) extends LoggingFSM[EngineJobExecutionActorState, EJEAData]
+    with WorkflowLogging
+    with CallMetadataHelper
+    with JobInstrumentation
+    with CromwellInstrumentation
+    with TimedFSM[EngineJobExecutionActorState] {
 
   override val workflowIdForLogging = workflowDescriptor.possiblyNotRootWorkflowId
   override val rootWorkflowIdForLogging = workflowDescriptor.rootWorkflowId
@@ -85,21 +98,21 @@ class EngineJobExecutionActor(replyTo: ActorRef,
       super.supervisorStrategy.decider.applyOrElse(t, (_: Any) => Escalate)
   }
 
-  val jobTag = s"${workflowIdForLogging.shortString}:${jobDescriptorKey.call.fullyQualifiedName}:${jobDescriptorKey.index.fromIndex}:${jobDescriptorKey.attempt}"
+  val jobTag =
+    s"${workflowIdForLogging.shortString}:${jobDescriptorKey.call.fullyQualifiedName}:${jobDescriptorKey.index.fromIndex}:${jobDescriptorKey.attempt}"
   val tag = s"EJEA_$jobTag"
 
-  //noinspection ActorMutableStateInspection
+  // noinspection ActorMutableStateInspection
   // There's no need to check for a cache hit again if we got preempted, or if there's no result copying actor defined
   // NB: this can also change (e.g. if we have a HashError we just force this to CallCachingOff)
-  private[execution] var effectiveCallCachingMode = {
+  private[execution] var effectiveCallCachingMode =
     if (backendLifecycleActorFactory.fileHashingActorProps.isEmpty) CallCachingOff
     else if (jobDescriptorKey.node.callable.meta.get("volatile").contains(MetaValueElementBoolean(true))) CallCachingOff
     else if (backendLifecycleActorFactory.cacheHitCopyingActorProps.isEmpty || jobDescriptorKey.attempt > 1) {
       callCachingParameters.mode.withoutRead
     } else callCachingParameters.mode
-  }
 
-  //noinspection ActorMutableStateInspection
+  // noinspection ActorMutableStateInspection
   // If this actor is currently holding a job token, the token dispenser to which the token should be returned.
   private var currentTokenDispenser: Option[ActorRef] = None
 
@@ -128,48 +141,46 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
   implicit val ec: ExecutionContext = context.dispatcher
 
-  override def preStart() = {
+  override def preStart() =
     log.debug(s"$tag: $effectiveCallCachingKey: $effectiveCallCachingMode")
-  }
 
   startWith(Pending, NoData)
-  //noinspection ActorMutableStateInspection
+  // noinspection ActorMutableStateInspection
   private var eventList: Seq[ExecutionEvent] = Seq(ExecutionEvent(stateName.toString))
 
-  override def onTimedTransition(from: EngineJobExecutionActorState, to: EngineJobExecutionActorState, duration: FiniteDuration) = {
+  override def onTimedTransition(from: EngineJobExecutionActorState,
+                                 to: EngineJobExecutionActorState,
+                                 duration: FiniteDuration
+  ) =
     // Send to StatsD
     recordExecutionStepTiming(from.toString, duration)
-  }
 
   // When Pending, the FSM always has NoData
-  when(Pending) {
-    case Event(Execute, NoData) =>
-      increment(NonEmptyList("jobs", List("ejea", "executing", "starting")))
-      if (restarting) {
-        requestRestartCheckToken()
-        goto(RequestingRestartCheckToken)
-      } else {
-        requestExecutionToken()
-        goto(RequestingExecutionToken)
-      }
+  when(Pending) { case Event(Execute, NoData) =>
+    increment(NonEmptyList("jobs", List("ejea", "executing", "starting")))
+    if (restarting) {
+      requestRestartCheckToken()
+      goto(RequestingRestartCheckToken)
+    } else {
+      requestExecutionToken()
+      goto(RequestingExecutionToken)
+    }
   }
 
   // This condition only applies for restarts
-  when(RequestingRestartCheckToken) {
-    case Event(JobTokenDispensed, NoData) =>
-      currentTokenDispenser = Option(jobRestartCheckTokenDispenserActor)
-      replyTo ! JobStarting(jobDescriptorKey)
-      val jobStoreKey = jobDescriptorKey.toJobStoreKey(workflowIdForLogging)
-      jobStoreActor ! QueryJobCompletion(jobStoreKey, jobDescriptorKey.call.outputPorts.toSeq)
-      goto(CheckingJobStore)
+  when(RequestingRestartCheckToken) { case Event(JobTokenDispensed, NoData) =>
+    currentTokenDispenser = Option(jobRestartCheckTokenDispenserActor)
+    replyTo ! JobStarting(jobDescriptorKey)
+    val jobStoreKey = jobDescriptorKey.toJobStoreKey(workflowIdForLogging)
+    jobStoreActor ! QueryJobCompletion(jobStoreKey, jobDescriptorKey.call.outputPorts.toSeq)
+    goto(CheckingJobStore)
   }
 
-  when(RequestingExecutionToken) {
-    case Event(JobTokenDispensed, NoData) =>
-      currentTokenDispenser = Option(jobExecutionTokenDispenserActor)
-      if (!restarting)
-        replyTo ! JobStarting(jobDescriptorKey)
-      requestValueStore()
+  when(RequestingExecutionToken) { case Event(JobTokenDispensed, NoData) =>
+    currentTokenDispenser = Option(jobExecutionTokenDispenserActor)
+    if (!restarting)
+      replyTo ! JobStarting(jobDescriptorKey)
+    requestValueStore()
   }
 
   // When CheckingJobStore, the FSM always has NoData
@@ -196,37 +207,45 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   when(CheckingCacheEntryExistence) {
     // There was already a cache entry for this job
     case Event(join: CallCachingJoin, NoData) =>
-      Try(join.toJobSuccess(jobDescriptorKey, backendLifecycleActorFactory.pathBuilders(initializationData))).map({ jobSuccess =>
-        // We can't create a CallCacheHashes to give to the SucceededResponseData here because it involves knowledge of
-        // which hashes are file hashes and which are not. We can't know that (nor do we care) when pulling them from the
-        // database. So instead manually publish the hashes here.
-        publishHashResultsToMetadata(Option(Success(join.callCacheHashes)))
-        saveJobCompletionToJobStore(SucceededResponseData(jobSuccess, None))
-      }).recover({
-        case f =>
+      Try(join.toJobSuccess(jobDescriptorKey, backendLifecycleActorFactory.pathBuilders(initializationData)))
+        .map { jobSuccess =>
+          // We can't create a CallCacheHashes to give to the SucceededResponseData here because it involves knowledge of
+          // which hashes are file hashes and which are not. We can't know that (nor do we care) when pulling them from the
+          // database. So instead manually publish the hashes here.
+          publishHashResultsToMetadata(Option(Success(join.callCacheHashes)))
+          saveJobCompletionToJobStore(SucceededResponseData(jobSuccess, None))
+        }
+        .recover { case f =>
           // If for some reason the above fails, fail the job cleanly
-          saveJobCompletionToJobStore(FailedResponseData(JobFailedNonRetryableResponse(jobDescriptorKey, f, None), None))
-      }).get
+          saveJobCompletionToJobStore(
+            FailedResponseData(JobFailedNonRetryableResponse(jobDescriptorKey, f, None), None)
+          )
+        }
+        .get
     // No cache entry for this job - keep going
     case Event(NoCallCacheEntry(_), NoData) =>
       returnCurrentToken()
       requestExecutionToken()
       goto(RequestingExecutionToken)
     case Event(CacheResultLookupFailure(reason), NoData) =>
-      log.error(reason, "{}: Failure checking for cache entry existence: {}. Attempting to resume job anyway.", jobTag, reason.getMessage)
+      log.error(reason,
+                "{}: Failure checking for cache entry existence: {}. Attempting to resume job anyway.",
+                jobTag,
+                reason.getMessage
+      )
       returnCurrentToken()
       requestExecutionToken()
       goto(RequestingExecutionToken)
   }
 
   /*
-  * ! Hot Potato Warning !
-  * We ask explicitly for the output store so we can use it on the fly and more importantly not store it as a
-  * variable in this actor, which would prevent it from being garbage collected for the duration of the
-  * job and would lead to memory leaks.
-  */
-  when(WaitingForValueStore) {
-    case Event(valueStore: ValueStore, NoData) => prepareJob(valueStore)
+   * ! Hot Potato Warning !
+   * We ask explicitly for the output store so we can use it on the fly and more importantly not store it as a
+   * variable in this actor, which would prevent it from being garbage collected for the duration of the
+   * job and would lead to memory leaks.
+   */
+  when(WaitingForValueStore) { case Event(valueStore: ValueStore, NoData) =>
+    prepareJob(valueStore)
   }
 
   // When PreparingJob, the FSM always has NoData
@@ -234,7 +253,8 @@ class EngineJobExecutionActor(replyTo: ActorRef,
     case Event(BackendJobPreparationSucceeded(jobDescriptor, bjeaProps), NoData) =>
       val updatedData = ResponsePendingData(jobDescriptor, bjeaProps)
       effectiveCallCachingMode match {
-        case activity: CallCachingActivity if activity.readFromCache => handleReadFromCacheOn(jobDescriptor, activity, updatedData)
+        case activity: CallCachingActivity if activity.readFromCache =>
+          handleReadFromCacheOn(jobDescriptor, activity, updatedData)
         case activity: CallCachingActivity => handleReadFromCacheOff(jobDescriptor, activity, updatedData)
         case CallCachingOff => runJob(updatedData)
       }
@@ -244,9 +264,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
   when(CheckingCallCache) {
     case Event(CacheMiss, data: ResponsePendingData) =>
-      writeToMetadata(Map(
-        callCachingHitResultMetadataKey -> false,
-        callCachingReadResultMetadataKey -> "Cache Miss"))
+      writeToMetadata(Map(callCachingHitResultMetadataKey -> false, callCachingReadResultMetadataKey -> "Cache Miss"))
 
       if (data.cacheHitFailureCount > 0) {
         val totalHits = data.cacheHitFailureCount
@@ -259,7 +277,12 @@ class EngineJobExecutionActor(replyTo: ActorRef,
             s"Falling back to running job."
         )
         val template = s"BT-322 {} cache hit copying failure: {} failed copy attempts of maximum {} with {}."
-        log.info(template, jobTag, data.failedCopyAttempts, callCachingParameters.maxFailedCopyAttempts, data.aggregatedHashString)
+        log.info(template,
+                 jobTag,
+                 data.failedCopyAttempts,
+                 callCachingParameters.maxFailedCopyAttempts,
+                 data.aggregatedHashString
+        )
       } else {
         log.info(s"BT-322 {} cache hit copying nomatch: could not find a suitable cache hit.", jobTag)
         workflowLogger.info("Could not copy a suitable cache hit for {}. No copy attempts were made.", arg = jobTag)
@@ -280,17 +303,25 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
   when(FetchingCachedOutputsFromDatabase) {
     case Event(
-    CachedOutputLookupSucceeded(womValueSimpletons, jobDetritus, returnCode, cacheResultId, cacheHitDetails),
-    data@ResponsePendingData(_, _, _, _, Some(ejeaCacheHit), _, _, _),
-    ) =>
+          CachedOutputLookupSucceeded(womValueSimpletons, jobDetritus, returnCode, cacheResultId, cacheHitDetails),
+          data @ ResponsePendingData(_, _, _, _, Some(ejeaCacheHit), _, _, _)
+        ) =>
       if (cacheResultId != ejeaCacheHit.hit.cacheResultId) {
         // Sanity check: was this the right set of results (a false here is a BAD thing!):
-        log.error(s"Received incorrect call cache results from FetchCachedResultsActor. Expected ${ejeaCacheHit.hit} but got $cacheResultId. Running job")
+        log.error(
+          s"Received incorrect call cache results from FetchCachedResultsActor. Expected ${ejeaCacheHit.hit} but got $cacheResultId. Running job"
+        )
         // Treat this like the "CachedOutputLookupFailed" event:
         runJob(data)
       } else {
         log.debug("Cache hit for {}! Fetching cached result {}", jobTag, cacheResultId)
-        makeBackendCopyCacheHit(womValueSimpletons, jobDetritus, returnCode, data, cacheResultId, ejeaCacheHit.hitNumber) using data.withCacheDetails(cacheHitDetails)
+        makeBackendCopyCacheHit(womValueSimpletons,
+                                jobDetritus,
+                                returnCode,
+                                data,
+                                cacheResultId,
+                                ejeaCacheHit.hitNumber
+        ) using data.withCacheDetails(cacheHitDetails)
       }
     case Event(CachedOutputLookupFailed(_, error), data: ResponsePendingData) =>
       log.warning("Can't fetch a list of cached outputs to copy for {} due to {}. Running job.", jobTag, error)
@@ -306,12 +337,13 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   when(BackendIsCopyingCachedOutputs) {
     // Backend copying response:
     case Event(
-    response: JobSucceededResponse,
-    data@ResponsePendingData(_, _, Some(Success(hashes)), _, _, _, _, _),
-    ) =>
+          response: JobSucceededResponse,
+          data @ ResponsePendingData(_, _, Some(Success(hashes)), _, _, _, _, _)
+        ) =>
       logCacheHitSuccessAndNotifyMetadata(data)
       saveCacheResults(hashes, data.withSuccessResponse(response))
-    case Event(response: JobSucceededResponse, data: ResponsePendingData) if effectiveCallCachingMode.writeToCache && data.hashes.isEmpty =>
+    case Event(response: JobSucceededResponse, data: ResponsePendingData)
+        if effectiveCallCachingMode.writeToCache && data.hashes.isEmpty =>
       logCacheHitSuccessAndNotifyMetadata(data)
       // Wait for the CallCacheHashes
       stay() using data.withSuccessResponse(response)
@@ -319,9 +351,9 @@ class EngineJobExecutionActor(replyTo: ActorRef,
       logCacheHitSuccessAndNotifyMetadata(data)
       saveJobCompletionToJobStore(data.withSuccessResponse(response))
     case Event(
-    CopyingOutputsFailedResponse(_, cacheCopyAttempt, reason),
-    data@ResponsePendingData(_, _, _, _, Some(cacheHit), _, _, _)
-    ) if cacheCopyAttempt == cacheHit.hitNumber =>
+          CopyingOutputsFailedResponse(_, cacheCopyAttempt, reason),
+          data @ ResponsePendingData(_, _, _, _, Some(cacheHit), _, _, _)
+        ) if cacheCopyAttempt == cacheHit.hitNumber =>
       invalidateCacheHitAndTransition(cacheHit, data, reason)
 
     // Hashes arrive:
@@ -359,16 +391,17 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   val jobSuccessHandler: StateFunction = {
     // writeToCache is true and all hashes have already been retrieved - save to the cache
     case Event(
-    response: JobSucceededResponse,
-    data@ResponsePendingData(_, _, Some(Success(hashes)), _, _, _, _, _)
-    ) if effectiveCallCachingMode.writeToCache =>
+          response: JobSucceededResponse,
+          data @ ResponsePendingData(_, _, Some(Success(hashes)), _, _, _, _, _)
+        ) if effectiveCallCachingMode.writeToCache =>
       eventList ++= response.executionEvents
       // Publish the image used now that we have it as we might lose the information if Cromwell is restarted
       // in between writing to the cache and writing to the job store
       response.dockerImageUsed foreach publishDockerImageUsed
       saveCacheResults(hashes, data.withSuccessResponse(response))
     // Hashes are still missing and we want them (writeToCache is true) - wait for them
-    case Event(response: JobSucceededResponse, data: ResponsePendingData) if effectiveCallCachingMode.writeToCache && data.hashes.isEmpty =>
+    case Event(response: JobSucceededResponse, data: ResponsePendingData)
+        if effectiveCallCachingMode.writeToCache && data.hashes.isEmpty =>
       eventList ++= response.executionEvents
       stay() using data.withSuccessResponse(response)
     // Hashes are missing but writeToCache is OFF - complete the job
@@ -381,12 +414,13 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   val jobFailedHandler: StateFunction = {
     // writeToCache is true and all hashes already retrieved - save to job store
     case Event(
-    response: BackendJobFailedResponse,
-    data@ResponsePendingData(_, _, Some(Success(_)), _, _, _, _, _)
-    ) if effectiveCallCachingMode.writeToCache =>
+          response: BackendJobFailedResponse,
+          data @ ResponsePendingData(_, _, Some(Success(_)), _, _, _, _, _)
+        ) if effectiveCallCachingMode.writeToCache =>
       saveJobCompletionToJobStore(data.withFailedResponse(response))
     // Hashes are still missing and we want them (writeToCache is true) - wait for them
-    case Event(response: BackendJobFailedResponse, data: ResponsePendingData) if effectiveCallCachingMode.writeToCache && data.hashes.isEmpty =>
+    case Event(response: BackendJobFailedResponse, data: ResponsePendingData)
+        if effectiveCallCachingMode.writeToCache && data.hashes.isEmpty =>
       stay() using data.withFailedResponse(response)
     // Hashes are missing but writeToCache is OFF - complete the job
     case Event(response: BackendJobFailedResponse, data: ResponsePendingData) =>
@@ -448,7 +482,13 @@ class EngineJobExecutionActor(replyTo: ActorRef,
       stay() using data.copy(hashes = Option(Failure(t)))
   }
 
-  when(RunningJob)(jobSuccessHandler.orElse(jobFailedHandler).orElse(jobAbortedHandler).orElse(hashSuccessResponseHandler).orElse(hashFailureResponseHandler))
+  when(RunningJob)(
+    jobSuccessHandler
+      .orElse(jobFailedHandler)
+      .orElse(jobAbortedHandler)
+      .orElse(hashSuccessResponseHandler)
+      .orElse(hashFailureResponseHandler)
+  )
 
   // When UpdatingCallCache, the FSM always has SucceededResponseData.
   when(UpdatingCallCache) {
@@ -464,16 +504,20 @@ class EngineJobExecutionActor(replyTo: ActorRef,
     case Event(JobStoreWriteSuccess(_), data: ResponseData) =>
       forwardAndStop(data.response)
     case Event(JobStoreWriteFailure(t), _: ResponseData) =>
-      respondAndStop(JobFailedNonRetryableResponse(jobDescriptorKey, new Exception(s"JobStore write failure: ${t.getMessage}", t), None))
+      respondAndStop(
+        JobFailedNonRetryableResponse(jobDescriptorKey,
+                                      new Exception(s"JobStore write failure: ${t.getMessage}", t),
+                                      None
+        )
+      )
   }
 
-  onTransition {
-    case fromState -> toState =>
-      log.debug("Transitioning from {}({}) to {}({})", fromState, stateData, toState, nextStateData)
+  onTransition { case fromState -> toState =>
+    log.debug("Transitioning from {}({}) to {}({})", fromState, stateData, toState, nextStateData)
 
-      EngineJobExecutionActorState.transitionEventString(fromState, toState) foreach {
-        eventList :+= ExecutionEvent(_)
-      }
+    EngineJobExecutionActorState.transitionEventString(fromState, toState) foreach {
+      eventList :+= ExecutionEvent(_)
+    }
 
   }
 
@@ -502,23 +546,35 @@ class EngineJobExecutionActor(replyTo: ActorRef,
       // due to timeouts). That's ok, we just ignore this message in any other situation:
       stay()
     case Event(msg, _) =>
-      log.error("Bad message from {} to EngineJobExecutionActor in state {}(with data {}): {}", sender(), stateName, stateData, msg)
+      log.error("Bad message from {} to EngineJobExecutionActor in state {}(with data {}): {}",
+                sender(),
+                stateName,
+                stateData,
+                msg
+      )
       stay()
   }
 
-  private def publishHashesToMetadata(maybeHashes: Option[Try[CallCacheHashes]]) = publishHashResultsToMetadata(maybeHashes.map(_.map(_.hashes)))
+  private def publishHashesToMetadata(maybeHashes: Option[Try[CallCacheHashes]]) = publishHashResultsToMetadata(
+    maybeHashes.map(_.map(_.hashes))
+  )
   private def publishDockerImageUsed(image: String) = writeToMetadata(Map("dockerImageUsed" -> image))
   private def publishHashResultsToMetadata(maybeHashes: Option[Try[Set[HashResult]]]) = maybeHashes match {
     case Some(Success(hashes)) =>
-      val hashMap = hashes.collect({
+      val hashMap = hashes.collect {
         case HashResult(HashKey(useInCallCaching, keyComponents), HashValue(value)) if useInCallCaching =>
-          (callCachingHashes + MetadataKey.KeySeparator + keyComponents.mkString(MetadataKey.KeySeparator.toString)) -> value
-      }).toMap
+          (callCachingHashes + MetadataKey.KeySeparator + keyComponents.mkString(
+            MetadataKey.KeySeparator.toString
+          )) -> value
+      }.toMap
       writeToMetadata(hashMap)
     case _ =>
   }
 
-  private def handleReadFromCacheOn(jobDescriptor: BackendJobDescriptor, activity: CallCachingActivity, updatedData: ResponsePendingData) = {
+  private def handleReadFromCacheOn(jobDescriptor: BackendJobDescriptor,
+                                    activity: CallCachingActivity,
+                                    updatedData: ResponsePendingData
+  ) =
     jobDescriptor.maybeCallCachingEligible match {
       // If the job is eligible, initialize job hashing and go to CheckingCallCache state
       case eligible: CallCachingEligible =>
@@ -538,21 +594,24 @@ class EngineJobExecutionActor(replyTo: ActorRef,
         disableCallCaching()
         runJob(updatedData)
     }
-  }
 
-  private def handleReadFromCacheOff(jobDescriptor: BackendJobDescriptor, activity: CallCachingActivity, updatedData: ResponsePendingData) = {
+  private def handleReadFromCacheOff(jobDescriptor: BackendJobDescriptor,
+                                     activity: CallCachingActivity,
+                                     updatedData: ResponsePendingData
+  ) = {
     jobDescriptor.maybeCallCachingEligible match {
       // If the job is eligible, initialize job hashing so it can be written to the cache
-      case eligible: CallCachingEligible => initializeJobHashing(jobDescriptor, activity, eligible) match {
-        case Failure(failure) =>
-          log.warning(s"BT-322 {} failed to initialize job hashing", jobTag)
-          // This condition in `handleReadFromCacheOn` ends in a `respondAndStop(JobFailedNonRetryableResponse(...))`,
-          // but with cache reading off Cromwell instead logs this condition and runs the job.
-          log.error(failure, "Failed to initialize job hashing. The job will not be written to the cache")
-        case _ =>
-          val template = s"BT-322 {} is eligible for call caching with read = {} and write = {}"
-          log.info(template, jobTag, activity.readFromCache, activity.writeToCache)
-      }
+      case eligible: CallCachingEligible =>
+        initializeJobHashing(jobDescriptor, activity, eligible) match {
+          case Failure(failure) =>
+            log.warning(s"BT-322 {} failed to initialize job hashing", jobTag)
+            // This condition in `handleReadFromCacheOn` ends in a `respondAndStop(JobFailedNonRetryableResponse(...))`,
+            // but with cache reading off Cromwell instead logs this condition and runs the job.
+            log.error(failure, "Failed to initialize job hashing. The job will not be written to the cache")
+          case _ =>
+            val template = s"BT-322 {} is eligible for call caching with read = {} and write = {}"
+            log.info(template, jobTag, activity.readFromCache, activity.writeToCache)
+        }
       // Don't even initialize hashing to write to the cache if the job is ineligible
       case _ =>
         log.info(s"BT-322 {} is not eligible for call caching", jobTag)
@@ -562,16 +621,20 @@ class EngineJobExecutionActor(replyTo: ActorRef,
     runJob(updatedData)
   }
 
-  private def requestRestartCheckToken(): Unit = {
-    jobRestartCheckTokenDispenserActor ! JobTokenRequest(workflowDescriptor.backendDescriptor.hogGroup, backendLifecycleActorFactory.jobRestartCheckTokenType)
-  }
+  private def requestRestartCheckToken(): Unit =
+    jobRestartCheckTokenDispenserActor ! JobTokenRequest(workflowDescriptor.backendDescriptor.hogGroup,
+                                                         backendLifecycleActorFactory.jobRestartCheckTokenType
+    )
 
-  private def requestExecutionToken(): Unit = {
-    jobExecutionTokenDispenserActor ! JobTokenRequest(workflowDescriptor.backendDescriptor.hogGroup, backendLifecycleActorFactory.jobExecutionTokenType)
-  }
+  private def requestExecutionToken(): Unit =
+    jobExecutionTokenDispenserActor ! JobTokenRequest(workflowDescriptor.backendDescriptor.hogGroup,
+                                                      backendLifecycleActorFactory.jobExecutionTokenType
+    )
 
   // Return any currently held job restart check or execution token.
-  private def returnCurrentToken(): Unit = if (stateName != Pending && stateName != RequestingRestartCheckToken && stateName != RequestingExecutionToken) {
+  private def returnCurrentToken(): Unit = if (
+    stateName != Pending && stateName != RequestingRestartCheckToken && stateName != RequestingExecutionToken
+  ) {
     currentTokenDispenser foreach { _ ! JobTokenReturn }
     currentTokenDispenser = None
   }
@@ -597,9 +660,8 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   }
 
   // Note: StatsD will automatically add a counter value so ne need to separately increment a counter.
-  private def instrumentJobComplete(response: BackendJobExecutionResponse) = {
+  private def instrumentJobComplete(response: BackendJobExecutionResponse) =
     setJobTimePerState(response, (System.currentTimeMillis() - jobStartTime).millis)
-  }
 
   private def disableCallCaching(reason: Option[Throwable] = None) = {
     log.warning(s"BT-322 {} disabling call caching due to error", jobTag)
@@ -626,8 +688,16 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   def prepareJob(valueStore: ValueStore) = {
     writeCallCachingModeToMetadata()
     val jobPreparationActorName = s"BackendPreparationActor_for_$jobTag"
-    val jobPrepProps = JobPreparationActor.props(workflowDescriptor, jobDescriptorKey, backendLifecycleActorFactory, workflowDockerLookupActor = workflowDockerLookupActor,
-      initializationData, serviceRegistryActor = serviceRegistryActor, ioActor = ioActor, backendSingletonActor = backendSingletonActor)
+    val jobPrepProps = JobPreparationActor.props(
+      workflowDescriptor,
+      jobDescriptorKey,
+      backendLifecycleActorFactory,
+      workflowDockerLookupActor = workflowDockerLookupActor,
+      initializationData,
+      serviceRegistryActor = serviceRegistryActor,
+      ioActor = ioActor,
+      backendSingletonActor = backendSingletonActor
+    )
     val jobPreparationActor = createJobPreparationActor(jobPrepProps, jobPreparationActorName)
     jobPreparationActor ! CallPreparation.Start(valueStore)
     goto(PreparingJob)
@@ -638,9 +708,17 @@ class EngineJobExecutionActor(replyTo: ActorRef,
     goto(WaitingForValueStore)
   }
 
-  def initializeJobHashing(jobDescriptor: BackendJobDescriptor, activity: CallCachingActivity, callCachingEligible: CallCachingEligible): Try[ActorRef] = {
+  def initializeJobHashing(jobDescriptor: BackendJobDescriptor,
+                           activity: CallCachingActivity,
+                           callCachingEligible: CallCachingEligible
+  ): Try[ActorRef] = {
     val maybeFileHashingActorProps = backendLifecycleActorFactory.fileHashingActorProps map {
-      _.apply(jobDescriptor, initializationData, serviceRegistryActor, ioActor, callCachingParameters.fileHashCacheActor)
+      _.apply(jobDescriptor,
+              initializationData,
+              serviceRegistryActor,
+              ioActor,
+              callCachingParameters.fileHashCacheActor
+      )
     }
 
     maybeFileHashingActorProps match {
@@ -667,41 +745,55 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   }
 
   def makeFetchCachedResultsActor(callCachingEntryId: CallCachingEntryId): Unit = {
-    context.actorOf(FetchCachedResultsActor.props(callCachingEntryId, self,
-      new CallCache(EngineServicesStore.engineDatabaseInterface)))
+    context.actorOf(
+      FetchCachedResultsActor.props(callCachingEntryId,
+                                    self,
+                                    new CallCache(EngineServicesStore.engineDatabaseInterface)
+      )
+    )
     ()
   }
 
-  private def fetchCachedResults( callCachingEntryId: CallCachingEntryId, data: ResponsePendingData) = {
+  private def fetchCachedResults(callCachingEntryId: CallCachingEntryId, data: ResponsePendingData) = {
     makeFetchCachedResultsActor(callCachingEntryId)
     goto(FetchingCachedOutputsFromDatabase) using data
   }
 
   private def makeBackendCopyCacheHit(womValueSimpletons: Seq[WomValueSimpleton],
-                                      jobDetritusFiles: Map[String,String],
+                                      jobDetritusFiles: Map[String, String],
                                       returnCode: Option[Int],
                                       data: ResponsePendingData,
                                       cacheResultId: CallCachingEntryId,
-                                      cacheCopyAttempt: Int) = {
+                                      cacheCopyAttempt: Int
+  ) =
     backendLifecycleActorFactory.cacheHitCopyingActorProps match {
       case Some(propsMaker) =>
-        val backendCacheHitCopyingActorProps = propsMaker(data.jobDescriptor, initializationData, serviceRegistryActor, ioActor, cacheCopyAttempt, callCachingParameters.blacklistCache)
-        val cacheHitCopyActor = context.actorOf(backendCacheHitCopyingActorProps, buildCacheHitCopyingActorName(data.jobDescriptor, cacheResultId))
+        val backendCacheHitCopyingActorProps = propsMaker(data.jobDescriptor,
+                                                          initializationData,
+                                                          serviceRegistryActor,
+                                                          ioActor,
+                                                          cacheCopyAttempt,
+                                                          callCachingParameters.blacklistCache
+        )
+        val cacheHitCopyActor = context.actorOf(backendCacheHitCopyingActorProps,
+                                                buildCacheHitCopyingActorName(data.jobDescriptor, cacheResultId)
+        )
         cacheHitCopyActor ! CopyOutputsCommand(womValueSimpletons, jobDetritusFiles, cacheResultId, returnCode)
         replyTo ! JobRunning(data.jobDescriptor.key, data.jobDescriptor.evaluatedTaskInputs)
         goto(BackendIsCopyingCachedOutputs)
       case None =>
         // This should be impossible with the FSM, but luckily, we CAN recover if some foolish future programmer makes this happen:
-        val errorMessage = "Call caching copying should never have even been attempted with no copy actor props! (Programmer error!)"
+        val errorMessage =
+          "Call caching copying should never have even been attempted with no copy actor props! (Programmer error!)"
         log.error(errorMessage)
         self ! JobFailedNonRetryableResponse(data.jobDescriptor.key, new RuntimeException(errorMessage), None)
         goto(BackendIsCopyingCachedOutputs)
     }
-  }
 
-  private [job] def createBackendJobExecutionActor(data: ResponsePendingData) = {
-    context.actorOf(data.bjeaProps, BackendJobExecutionActor.buildJobExecutionActorName(workflowIdForLogging, data.jobDescriptor.key))
-  }
+  private[job] def createBackendJobExecutionActor(data: ResponsePendingData) =
+    context.actorOf(data.bjeaProps,
+                    BackendJobExecutionActor.buildJobExecutionActorName(workflowIdForLogging, data.jobDescriptor.key)
+    )
 
   private def runJob(data: ResponsePendingData) = {
     val backendJobExecutionActor = createBackendJobExecutionActor(data)
@@ -724,7 +816,8 @@ class EngineJobExecutionActor(replyTo: ActorRef,
     }
 
     response match {
-      case CallCacheInvalidatedFailure(_, failure) => log.error(failure, "Failed to invalidate cache entry for job: {}", jobDescriptorKey)
+      case CallCacheInvalidatedFailure(_, failure) =>
+        log.error(failure, "Failed to invalidate cache entry for job: {}", jobDescriptorKey)
       case CallCacheInvalidatedSuccess(_, Some(entry)) => updateMetadataForInvalidatedEntry(entry)
       case _ =>
     }
@@ -735,25 +828,36 @@ class EngineJobExecutionActor(replyTo: ActorRef,
         ejha ! NextHit
         goto(CheckingCallCache) using data
       case Some(_) =>
-        writeToMetadata(Map(
-          callCachingHitResultMetadataKey -> false,
-          callCachingReadResultMetadataKey -> s"Cache Miss (${callCachingParameters.maxFailedCopyAttempts} failed copy attempts)"))
-        log.warning("BT-322 {} cache hit copying maxfail: Cache miss due to exceeding the maximum of {} failed copy attempts.", jobTag, callCachingParameters.maxFailedCopyAttempts)
+        writeToMetadata(
+          Map(
+            callCachingHitResultMetadataKey -> false,
+            callCachingReadResultMetadataKey -> s"Cache Miss (${callCachingParameters.maxFailedCopyAttempts} failed copy attempts)"
+          )
+        )
+        log.warning(
+          "BT-322 {} cache hit copying maxfail: Cache miss due to exceeding the maximum of {} failed copy attempts.",
+          jobTag,
+          callCachingParameters.maxFailedCopyAttempts
+        )
         publishCopyAttemptAbandonedMetrics(data)
         runJob(data)
       case _ =>
-        workflowLogger.error("Programmer error: We got a cache failure but there was no hashing actor scanning for hits. Falling back to running job")
+        workflowLogger.error(
+          "Programmer error: We got a cache failure but there was no hashing actor scanning for hits. Falling back to running job"
+        )
         runJob(data)
     }
   }
 
-  private def buildCacheHitCopyingActorName(jobDescriptor: BackendJobDescriptor, cacheResultId: CallCachingEntryId) = {
+  private def buildCacheHitCopyingActorName(jobDescriptor: BackendJobDescriptor, cacheResultId: CallCachingEntryId) =
     s"$workflowIdForLogging-BackendCacheHitCopyingActor-$jobTag-${cacheResultId.id}"
-  }
 
   private def logCacheHitSuccessAndNotifyMetadata(data: ResponsePendingData): Unit = {
 
-    val metadataMap = Map[String, Any](callCachingHitResultMetadataKey -> true) ++ data.ejeaCacheHit.flatMap(_.details).map(details => callCachingReadResultMetadataKey -> s"Cache Hit: $details").toMap
+    val metadataMap = Map[String, Any](callCachingHitResultMetadataKey -> true) ++ data.ejeaCacheHit
+      .flatMap(_.details)
+      .map(details => callCachingReadResultMetadataKey -> s"Cache Hit: $details")
+      .toMap
 
     writeToMetadata(metadataMap)
 
@@ -786,19 +890,15 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
     workflowLogger.info(
       s"Failure copying cache results for job $jobDescriptorKey (${reason.getClass.getSimpleName}: ${reason.getMessage})"
-      + multipleFailuresContext
+        + multipleFailuresContext
     )
   }
 
   private def publishCopyAttemptFailuresMetrics(data: ResponsePendingData): Unit = {
     val copyErrorsPerHitPath: NonEmptyList[String] =
-      NonEmptyList.of(
-        "job",
-        "callcaching", "read", "error", "invalidhits", "copyerrors")
+      NonEmptyList.of("job", "callcaching", "read", "error", "invalidhits", "copyerrors")
     val copyBlacklistsPerHitPath: NonEmptyList[String] =
-      NonEmptyList.of(
-        "job",
-        "callcaching", "read", "error", "invalidhits", "blacklisted")
+      NonEmptyList.of("job", "callcaching", "read", "error", "invalidhits", "blacklisted")
 
     sendGauge(copyErrorsPerHitPath, data.failedCopyAttempts.longValue)
     sendGauge(copyBlacklistsPerHitPath, data.cacheHitFailureCount - data.failedCopyAttempts.longValue)
@@ -806,24 +906,33 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
   private def publishCopyAttemptAbandonedMetrics(data: ResponsePendingData): Unit = {
     val cacheCopyAttemptAbandonedPath: NonEmptyList[String] =
-      NonEmptyList.of(
-        "job",
-        "callcaching", "read", "error", "invalidhits", "abandonments")
+      NonEmptyList.of("job", "callcaching", "read", "error", "invalidhits", "abandonments")
     increment(cacheCopyAttemptAbandonedPath)
 
     // Also publish the attempt failure metrics
     publishCopyAttemptFailuresMetrics(data)
   }
 
-  private def publishBlacklistReadMetrics(data: ResponsePendingData, failureCategory: MetricableCacheCopyErrorCategory): Unit = {
+  private def publishBlacklistReadMetrics(data: ResponsePendingData,
+                                          failureCategory: MetricableCacheCopyErrorCategory
+  ): Unit = {
     val callCachingErrorsMetricPath: NonEmptyList[String] =
       NonEmptyList.of(
         "job",
-        "callcaching", "read", "error", failureCategory.toString, data.jobDescriptor.taskCall.localName, data.jobDescriptor.workflowDescriptor.hogGroup.value)
+        "callcaching",
+        "read",
+        "error",
+        failureCategory.toString,
+        data.jobDescriptor.taskCall.localName,
+        data.jobDescriptor.workflowDescriptor.hogGroup.value
+      )
     increment(callCachingErrorsMetricPath)
   }
 
-  private def invalidateCacheHitAndTransition(ejeaCacheHit: EJEACacheHit, data: ResponsePendingData, reason: CacheCopyFailure) = {
+  private def invalidateCacheHitAndTransition(ejeaCacheHit: EJEACacheHit,
+                                              data: ResponsePendingData,
+                                              reason: CacheCopyFailure
+  ) = {
     val copyAttemptIncrement = reason match {
       case CopyAttemptError(failure) =>
         logCacheHitFailure(data, failure)
@@ -837,10 +946,13 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
     // Increment the total failure count and actual copy failure count as appropriate.
     val updatedData = data.copy(cacheHitFailureCount = data.cacheHitFailureCount + 1,
-                                failedCopyAttempts = data.failedCopyAttempts + copyAttemptIncrement)
+                                failedCopyAttempts = data.failedCopyAttempts + copyAttemptIncrement
+    )
 
     if (invalidationRequired) {
-      workflowLogger.warn(s"Invalidating cache entry ${ejeaCacheHit.hit.cacheResultId} (Cache entry details: ${ejeaCacheHit.details})")
+      workflowLogger.warn(
+        s"Invalidating cache entry ${ejeaCacheHit.hit.cacheResultId} (Cache entry details: ${ejeaCacheHit.details})"
+      )
       invalidateCacheHit(ejeaCacheHit.hit.cacheResultId)
       goto(InvalidatingCacheEntry) using updatedData
     } else {
@@ -860,7 +972,9 @@ class EngineJobExecutionActor(replyTo: ActorRef,
   }
 
   private def saveCacheResults(hashes: CallCacheHashes, data: SucceededResponseData) = {
-    callCachingParameters.writeActor ! SaveCallCacheHashes(CallCacheHashBundle(workflowIdForLogging, hashes, data.response))
+    callCachingParameters.writeActor ! SaveCallCacheHashes(
+      CallCacheHashBundle(workflowIdForLogging, hashes, data.response)
+    )
     val updatedData = data.copy(hashes = Option(Success(hashes)))
     goto(UpdatingCallCache) using updatedData
   }
@@ -890,7 +1004,11 @@ class EngineJobExecutionActor(replyTo: ActorRef,
     jobStoreActor ! RegisterJobCompleted(jobStoreKey, jobStoreResult)
   }
 
-  private def saveUnsuccessfulJobResults(jobKey: JobKey, returnCode: Option[Int], reason: Throwable, retryable: Boolean) = {
+  private def saveUnsuccessfulJobResults(jobKey: JobKey,
+                                         returnCode: Option[Int],
+                                         reason: Throwable,
+                                         retryable: Boolean
+  ) = {
     val jobStoreKey = jobKey.toJobStoreKey(workflowIdForLogging)
     val jobStoreResult = JobResultFailure(returnCode, reason, retryable)
     jobStoreActor ! RegisterJobCompleted(jobStoreKey, jobStoreResult)
@@ -912,6 +1030,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 }
 
 object EngineJobExecutionActor {
+
   /** States */
   sealed trait EngineJobExecutionActorState
   case object Pending extends EngineJobExecutionActorState
@@ -930,7 +1049,9 @@ object EngineJobExecutionActor {
   case object InvalidatingCacheEntry extends EngineJobExecutionActorState
 
   object EngineJobExecutionActorState {
-    def transitionEventString(fromState: EngineJobExecutionActorState, toState: EngineJobExecutionActorState): Option[String] = {
+    def transitionEventString(fromState: EngineJobExecutionActorState,
+                              toState: EngineJobExecutionActorState
+    ): Option[String] = {
 
       def callCacheStateGroup: Set[EngineJobExecutionActorState] = Set(
         CheckingCallCache,
@@ -948,14 +1069,14 @@ object EngineJobExecutionActor {
   }
 
   case class CallCachingParameters(
-                                  mode: CallCachingMode,
-                                  readActor: ActorRef,
-                                  writeActor: ActorRef,
-                                  fileHashCacheActor: Option[ActorRef],
-                                  maxFailedCopyAttempts: Int,
-                                  blacklistCache: Option[BlacklistCache],
-                                  fileHashBatchSize: Int
-                                  )
+    mode: CallCachingMode,
+    readActor: ActorRef,
+    writeActor: ActorRef,
+    fileHashCacheActor: Option[ActorRef],
+    maxFailedCopyAttempts: Int,
+    blacklistCache: Option[BlacklistCache],
+    fileHashBatchSize: Int
+  )
 
   /** Commands */
   sealed trait EngineJobExecutionActorCommand
@@ -977,29 +1098,31 @@ object EngineJobExecutionActor {
             jobExecutionTokenDispenserActor: ActorRef,
             backendSingletonActor: Option[ActorRef],
             command: BackendJobExecutionActorCommand,
-            callCachingParameters: EngineJobExecutionActor.CallCachingParameters) = {
-
-    Props(new EngineJobExecutionActor(
-      replyTo = replyTo,
-      jobDescriptorKey = jobDescriptorKey,
-      workflowDescriptor = workflowDescriptor,
-      backendLifecycleActorFactory = backendLifecycleActorFactory,
-      initializationData = initializationData,
-      restarting = restarting,
-      serviceRegistryActor = serviceRegistryActor,
-      ioActor = ioActor,
-      jobStoreActor = jobStoreActor,
-      workflowDockerLookupActor = workflowDockerLookupActor,
-      jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
-      jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
-      backendSingletonActor = backendSingletonActor,
-      command = command,
-      callCachingParameters = callCachingParameters)).withDispatcher(EngineDispatcher)
-  }
+            callCachingParameters: EngineJobExecutionActor.CallCachingParameters
+  ) =
+    Props(
+      new EngineJobExecutionActor(
+        replyTo = replyTo,
+        jobDescriptorKey = jobDescriptorKey,
+        workflowDescriptor = workflowDescriptor,
+        backendLifecycleActorFactory = backendLifecycleActorFactory,
+        initializationData = initializationData,
+        restarting = restarting,
+        serviceRegistryActor = serviceRegistryActor,
+        ioActor = ioActor,
+        jobStoreActor = jobStoreActor,
+        workflowDockerLookupActor = workflowDockerLookupActor,
+        jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
+        jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
+        backendSingletonActor = backendSingletonActor,
+        command = command,
+        callCachingParameters = callCachingParameters
+      )
+    ).withDispatcher(EngineDispatcher)
 
   case class EJEACacheHit(hit: CacheHit, hitNumber: Int, details: Option[String])
 
-  private[execution] sealed trait EJEAData {
+  sealed private[execution] trait EJEAData {
     override def toString = getClass.getSimpleName
   }
 
@@ -1013,13 +1136,14 @@ object EngineJobExecutionActor {
                                                     backendJobActor: Option[ActorRef] = None,
                                                     cacheHitFailureCount: Int = 0,
                                                     failedCopyAttempts: Int = 0
-                                                   ) extends EJEAData {
+  ) extends EJEAData {
 
     def withEJHA(ejha: ActorRef): EJEAData = this.copy(ejha = Option(ejha))
 
     def withBackendActor(actorRef: ActorRef) = this.copy(backendJobActor = Option(actorRef))
 
-    def withSuccessResponse(success: JobSucceededResponse): SucceededResponseData = SucceededResponseData(success, hashes)
+    def withSuccessResponse(success: JobSucceededResponse): SucceededResponseData =
+      SucceededResponseData(success, hashes)
     def withFailedResponse(failed: BackendJobFailedResponse): FailedResponseData = FailedResponseData(failed, hashes)
     def withAbortedResponse(aborted: JobAbortedResponse): AbortedResponseData = AbortedResponseData(aborted, hashes)
 
@@ -1031,7 +1155,8 @@ object EngineJobExecutionActor {
       this.copy(ejeaCacheHit = Option(newEjeaCacheHit))
     }
 
-    def withCacheDetails(details: String) = this.copy(ejeaCacheHit = ejeaCacheHit.map(_.copy(details = Option(details))))
+    def withCacheDetails(details: String) =
+      this.copy(ejeaCacheHit = ejeaCacheHit.map(_.copy(details = Option(details))))
 
     def aggregatedHashString: String = hashes match {
       case Some(Success(hashes)) => hashes.aggregatedHashString
@@ -1051,14 +1176,16 @@ object EngineJobExecutionActor {
   private[execution] trait ShouldBeSavedToJobStoreResponseData extends ResponseData
 
   private[execution] case class SucceededResponseData(successResponse: JobSucceededResponse,
-                                                       hashes: Option[Try[CallCacheHashes]] = None) extends ShouldBeSavedToJobStoreResponseData {
+                                                      hashes: Option[Try[CallCacheHashes]] = None
+  ) extends ShouldBeSavedToJobStoreResponseData {
     override def response = successResponse
     override def dockerImageUsed = successResponse.dockerImageUsed
     override def withHashes(hashes: Option[Try[CallCacheHashes]]) = copy(hashes = hashes)
   }
 
   private[execution] case class FailedResponseData(failedResponse: BackendJobFailedResponse,
-                                                      hashes: Option[Try[CallCacheHashes]] = None) extends ShouldBeSavedToJobStoreResponseData {
+                                                   hashes: Option[Try[CallCacheHashes]] = None
+  ) extends ShouldBeSavedToJobStoreResponseData {
     override def response = failedResponse
     // Seems like we should be able to get the docker image used even if the job failed
     override def dockerImageUsed = None
@@ -1066,7 +1193,8 @@ object EngineJobExecutionActor {
   }
 
   private[execution] case class AbortedResponseData(abortedResponse: JobAbortedResponse,
-                                                   hashes: Option[Try[CallCacheHashes]] = None) extends ResponseData {
+                                                    hashes: Option[Try[CallCacheHashes]] = None
+  ) extends ResponseData {
     override def response = abortedResponse
     override def dockerImageUsed = None
     override def withHashes(hashes: Option[Try[CallCacheHashes]]) = copy(hashes = hashes)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/CallPreparation.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/CallPreparation.scala
index e9665aa01b6..efdee8df7a0 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/CallPreparation.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/CallPreparation.scala
@@ -15,15 +15,15 @@ object CallPreparation {
 
   trait CallPreparationActorResponse
 
-  case class BackendJobPreparationSucceeded(jobDescriptor: BackendJobDescriptor, bjeaProps: Props) extends CallPreparationActorResponse
+  case class BackendJobPreparationSucceeded(jobDescriptor: BackendJobDescriptor, bjeaProps: Props)
+      extends CallPreparationActorResponse
 
   case class JobCallPreparationFailed(jobKey: JobKey, throwable: Throwable) extends CallPreparationActorResponse
   case class CallPreparationFailed(jobKey: JobKey, throwable: Throwable) extends CallPreparationActorResponse
 
   def resolveAndEvaluateInputs(callKey: CallKey,
                                expressionLanguageFunctions: IoFunctionSet,
-                               valueStore: ValueStore): ErrorOr[WomEvaluatedCallInputs] = {
-
+                               valueStore: ValueStore
+  ): ErrorOr[WomEvaluatedCallInputs] =
     CallNode.resolveAndEvaluateInputs(callKey.node, expressionLanguageFunctions, valueStore.resolve(callKey.index))
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActor.scala
index 8540717a073..b621c26ed4d 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActor.scala
@@ -13,7 +13,7 @@ import cromwell.core.Dispatcher.EngineDispatcher
 import cromwell.core.callcaching._
 import cromwell.core.logging.WorkflowLogging
 import cromwell.core.{Dispatcher, DockerConfiguration}
-import cromwell.docker.DockerInfoActor.{DockerInfoSuccessResponse, DockerInformation, DockerSize}
+import cromwell.docker.DockerInfoActor.{DockerInformation, DockerInfoSuccessResponse, DockerSize}
 import cromwell.docker._
 import cromwell.engine.EngineWorkflowDescriptor
 import cromwell.engine.workflow.WorkflowDockerLookupActor.{WorkflowDockerLookupFailure, WorkflowDockerTerminalFailure}
@@ -51,8 +51,10 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
                           initializationData: Option[BackendInitializationData],
                           val serviceRegistryActor: ActorRef,
                           ioActor: ActorRef,
-                          backendSingletonActor: Option[ActorRef])
-  extends FSM[JobPreparationActorState, JobPreparationActorData] with WorkflowLogging with CallMetadataHelper {
+                          backendSingletonActor: Option[ActorRef]
+) extends FSM[JobPreparationActorState, JobPreparationActorData]
+    with WorkflowLogging
+    with CallMetadataHelper {
 
   override lazy val workflowIdForLogging = workflowDescriptor.possiblyNotRootWorkflowId
   override lazy val workflowIdForCallMetadata = workflowDescriptor.possiblyNotRootWorkflowId
@@ -62,29 +64,39 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
   private[preparation] val ioEc = context.system.dispatchers.lookup(Dispatcher.IoDispatcher)
 
   private[preparation] lazy val expressionLanguageFunctions = {
-    val ioFunctionSet: IoFunctionSet = factory.expressionLanguageFunctions(workflowDescriptor.backendDescriptor, jobKey, initializationData, ioActor, ioEc)
+    val ioFunctionSet: IoFunctionSet = factory.expressionLanguageFunctions(workflowDescriptor.backendDescriptor,
+                                                                           jobKey,
+                                                                           initializationData,
+                                                                           ioActor,
+                                                                           ioEc
+    )
     ioFunctionSet.makeInputSpecificFunctions()
   }
 
-  private[preparation] lazy val dockerHashCredentials = factory.dockerHashCredentials(workflowDescriptor.backendDescriptor, initializationData)
+  private[preparation] lazy val dockerHashCredentials =
+    factory.dockerHashCredentials(workflowDescriptor.backendDescriptor, initializationData)
   private[preparation] lazy val runtimeAttributeDefinitions = factory.runtimeAttributeDefinitions(initializationData)
-  private[preparation] lazy val hasDockerDefinition = runtimeAttributeDefinitions.exists(_.name == DockerValidation.instance.key)
+  private[preparation] lazy val hasDockerDefinition =
+    runtimeAttributeDefinitions.exists(_.name == DockerValidation.instance.key)
 
   startWith(Idle, JobPreparationActorNoData)
 
-  when(Idle) {
-    case Event(Start(valueStore), JobPreparationActorNoData) =>
-      evaluateInputsAndAttributes(valueStore) match {
-        case Valid((inputs, attributes)) => fetchDockerHashesIfNecessary(inputs, attributes)
-        case Invalid(failure) => sendFailureAndStop(new MessageAggregation with NoStackTrace {
-          override def exceptionContext: String = s"Call input and runtime attributes evaluation failed for ${jobKey.call.localName}"
+  when(Idle) { case Event(Start(valueStore), JobPreparationActorNoData) =>
+    evaluateInputsAndAttributes(valueStore) match {
+      case Valid((inputs, attributes)) => fetchDockerHashesIfNecessary(inputs, attributes)
+      case Invalid(failure) =>
+        sendFailureAndStop(new MessageAggregation with NoStackTrace {
+          override def exceptionContext: String =
+            s"Call input and runtime attributes evaluation failed for ${jobKey.call.localName}"
           override def errorMessages: Iterable[String] = failure.toList
         })
-      }
+    }
   }
 
   when(WaitingForDockerHash) {
-    case Event(DockerInfoSuccessResponse(DockerInformation(dockerHash, dockerSize), _), data: JobPreparationDockerLookupData) =>
+    case Event(DockerInfoSuccessResponse(DockerInformation(dockerHash, dockerSize), _),
+               data: JobPreparationDockerLookupData
+        ) =>
       handleDockerHashSuccess(dockerHash, dockerSize, data)
     case Event(WorkflowDockerLookupFailure(reason, _, _), data: JobPreparationDockerLookupData) =>
       workflowLogger.warn("Docker lookup failed", reason)
@@ -94,32 +106,45 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
   }
 
   when(FetchingKeyValueStoreEntries) {
-    case Event(kvResponse: KvResponse, data @ JobPreparationKeyLookupData(keyLookups, maybeCallCachingEligible, dockerSize, inputs, attributes)) =>
+    case Event(kvResponse: KvResponse,
+               data @ JobPreparationKeyLookupData(keyLookups, maybeCallCachingEligible, dockerSize, inputs, attributes)
+        ) =>
       keyLookups.withResponse(kvResponse.key, kvResponse) match {
         case newPartialLookup: PartialKeyValueLookups => stay() using data.copy(keyLookups = newPartialLookup)
         case finished: KeyValueLookupResults =>
-          sendResponseAndStop(prepareBackendDescriptor(inputs, attributes, maybeCallCachingEligible, finished.unscoped, dockerSize))
+          sendResponseAndStop(
+            prepareBackendDescriptor(inputs, attributes, maybeCallCachingEligible, finished.unscoped, dockerSize)
+          )
       }
   }
 
-  whenUnhandled {
-    case Event(unexpectedMessage, _) =>
-      workflowLogger.warn(s"JobPreparation actor received an unexpected message in state $stateName: $unexpectedMessage")
-      stay()
+  whenUnhandled { case Event(unexpectedMessage, _) =>
+    workflowLogger.warn(s"JobPreparation actor received an unexpected message in state $stateName: $unexpectedMessage")
+    stay()
   }
 
-  private[preparation] lazy val kvStoreKeysToPrefetch: Seq[String] = factory.requestedKeyValueStoreKeys ++ factory.defaultKeyValueStoreKeys
+  private[preparation] lazy val kvStoreKeysToPrefetch: Seq[String] =
+    factory.requestedKeyValueStoreKeys ++ factory.defaultKeyValueStoreKeys
   private[preparation] def scopedKey(key: String) = ScopedKey(workflowDescriptor.id, KvJobKey(jobKey), key)
   private[preparation] def lookupKeyValueEntries(inputs: WomEvaluatedCallInputs,
                                                  attributes: Map[LocallyQualifiedName, WomValue],
                                                  maybeCallCachingEligible: MaybeCallCachingEligible,
-                                                 dockerSize: Option[DockerSize]) = {
+                                                 dockerSize: Option[DockerSize]
+  ) = {
     val keysToLookup = kvStoreKeysToPrefetch map scopedKey
     keysToLookup foreach { serviceRegistryActor ! KvGet(_) }
-    goto(FetchingKeyValueStoreEntries) using JobPreparationKeyLookupData(PartialKeyValueLookups(Map.empty, keysToLookup), maybeCallCachingEligible, dockerSize, inputs, attributes)
+    goto(FetchingKeyValueStoreEntries) using JobPreparationKeyLookupData(
+      PartialKeyValueLookups(Map.empty, keysToLookup),
+      maybeCallCachingEligible,
+      dockerSize,
+      inputs,
+      attributes
+    )
   }
 
-  private [preparation] def evaluateInputsAndAttributes(valueStore: ValueStore): ErrorOr[(WomEvaluatedCallInputs, Map[LocallyQualifiedName, WomValue])] = {
+  private[preparation] def evaluateInputsAndAttributes(
+    valueStore: ValueStore
+  ): ErrorOr[(WomEvaluatedCallInputs, Map[LocallyQualifiedName, WomValue])] = {
     import common.validation.ErrorOr.{ShortCircuitingFlatMap, NestedErrorOr}
     for {
       evaluatedInputs <- ErrorOr(resolveAndEvaluateInputs(jobKey, expressionLanguageFunctions, valueStore)).flatten
@@ -127,7 +152,9 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
     } yield (evaluatedInputs, runtimeAttributes)
   }
 
-  private def fetchDockerHashesIfNecessary(inputs: WomEvaluatedCallInputs, attributes: Map[LocallyQualifiedName, WomValue]) = {
+  private def fetchDockerHashesIfNecessary(inputs: WomEvaluatedCallInputs,
+                                           attributes: Map[LocallyQualifiedName, WomValue]
+  ) = {
     def sendDockerRequest(dockerImageId: DockerImageIdentifier) = {
       val dockerHashRequest = DockerInfoRequest(dockerImageId, dockerHashCredentials)
       val newData = JobPreparationDockerLookupData(dockerHashRequest, inputs, attributes)
@@ -136,12 +163,17 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
     }
 
     def handleDockerValue(value: String) = DockerImageIdentifier.fromString(value) match {
-        // If the backend supports docker, lookup is enabled, and we got a tag - we need to lookup the hash
-      case Success(dockerImageId: DockerImageIdentifierWithoutHash) if hasDockerDefinition && DockerConfiguration.instance.enabled =>
+      // If the backend supports docker, lookup is enabled, and we got a tag - we need to lookup the hash
+      case Success(dockerImageId: DockerImageIdentifierWithoutHash)
+          if hasDockerDefinition && DockerConfiguration.instance.enabled =>
         sendDockerRequest(dockerImageId)
-        // If the backend supports docker, we got a tag but lookup is disabled, continue with no call caching and no hash
+      // If the backend supports docker, we got a tag but lookup is disabled, continue with no call caching and no hash
       case Success(dockerImageId: DockerImageIdentifierWithoutHash) if hasDockerDefinition =>
-        lookupKvsOrBuildDescriptorAndStop(inputs, attributes, FloatingDockerTagWithoutHash(dockerImageId.fullName), None)
+        lookupKvsOrBuildDescriptorAndStop(inputs,
+                                          attributes,
+                                          FloatingDockerTagWithoutHash(dockerImageId.fullName),
+                                          None
+        )
 
       // If the backend doesn't support docker - no need to lookup and we're ok for call caching
       case Success(_: DockerImageIdentifierWithoutHash) if !hasDockerDefinition =>
@@ -165,8 +197,9 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
   }
 
   private def updateRuntimeMemory(runtimeAttributes: Map[LocallyQualifiedName, WomValue],
-                                  memoryMultiplierOption: Option[Double]): Map[LocallyQualifiedName, WomValue] = {
-    def multiplyRuntimeMemory(multiplier: Double): Map[LocallyQualifiedName, WomValue] = {
+                                  memoryMultiplierOption: Option[Double]
+  ): Map[LocallyQualifiedName, WomValue] = {
+    def multiplyRuntimeMemory(multiplier: Double): Map[LocallyQualifiedName, WomValue] =
       runtimeAttributes.get(RuntimeAttributesKeys.MemoryKey) match {
         case Some(WomString(memory)) =>
           MemorySize.parse(memory) match {
@@ -177,7 +210,6 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
           }
         case _ => runtimeAttributes
       }
-    }
 
     memoryMultiplierOption match {
       case None => runtimeAttributes
@@ -192,12 +224,16 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
   private def lookupKvsOrBuildDescriptorAndStop(inputs: WomEvaluatedCallInputs,
                                                 attributes: Map[LocallyQualifiedName, WomValue],
                                                 maybeCallCachingEligible: MaybeCallCachingEligible,
-                                                dockerSize: Option[DockerSize]) = {
+                                                dockerSize: Option[DockerSize]
+  ) =
     if (kvStoreKeysToPrefetch.nonEmpty) lookupKeyValueEntries(inputs, attributes, maybeCallCachingEligible, dockerSize)
-    else sendResponseAndStop(prepareBackendDescriptor(inputs, attributes, maybeCallCachingEligible, Map.empty, dockerSize))
-  }
+    else
+      sendResponseAndStop(prepareBackendDescriptor(inputs, attributes, maybeCallCachingEligible, Map.empty, dockerSize))
 
-  private def handleDockerHashSuccess(dockerHashResult: DockerHashResult, dockerSize: Option[DockerSize], data: JobPreparationDockerLookupData) = {
+  private def handleDockerHashSuccess(dockerHashResult: DockerHashResult,
+                                      dockerSize: Option[DockerSize],
+                                      data: JobPreparationDockerLookupData
+  ) = {
     val hashValue = data.dockerHashRequest.dockerImageID match {
       case withoutHash: DockerImageIdentifierWithoutHash => withoutHash.withHash(dockerHashResult)
       case withHash => withHash
@@ -207,13 +243,19 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
   }
 
   private def sendCompressedDockerSizeToMetadata(dockerSize: DockerSize) = {
-    val event = MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.CompressedDockerSize), MetadataValue(dockerSize.compressedSize))
+    val event = MetadataEvent(metadataKeyForCall(jobKey, CallMetadataKeys.CompressedDockerSize),
+                              MetadataValue(dockerSize.compressedSize)
+    )
     serviceRegistryActor ! PutMetadataAction(event)
   }
 
   private def handleDockerHashFailed(data: JobPreparationDockerLookupData) = {
     val floatingDockerTag = data.dockerHashRequest.dockerImageID.fullName
-    lookupKvsOrBuildDescriptorAndStop(data.inputs, data.attributes, FloatingDockerTagWithoutHash(floatingDockerTag), None)
+    lookupKvsOrBuildDescriptorAndStop(data.inputs,
+                                      data.attributes,
+                                      FloatingDockerTagWithoutHash(floatingDockerTag),
+                                      None
+    )
   }
 
   private def sendResponseAndStop(response: CallPreparationActorResponse) = {
@@ -221,44 +263,70 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
     stay()
   }
 
-  private def sendFailureAndStop(failure: Throwable) = {
+  private def sendFailureAndStop(failure: Throwable) =
     sendResponseAndStop(CallPreparationFailed(jobKey, failure))
-  }
 
   // 'jobExecutionProps' is broken into a separate function for TestJobPreparationActor to override:
   private[preparation] def jobExecutionProps(jobDescriptor: BackendJobDescriptor,
                                              initializationData: Option[BackendInitializationData],
                                              serviceRegistryActor: ActorRef,
                                              ioActor: ActorRef,
-                                             backendSingletonActor: Option[ActorRef]) = factory.jobExecutionActorProps(jobDescriptor, initializationData, serviceRegistryActor, ioActor, backendSingletonActor)
+                                             backendSingletonActor: Option[ActorRef]
+  ) = factory.jobExecutionActorProps(jobDescriptor,
+                                     initializationData,
+                                     serviceRegistryActor,
+                                     ioActor,
+                                     backendSingletonActor
+  )
 
   private[preparation] def prepareBackendDescriptor(inputEvaluation: WomEvaluatedCallInputs,
                                                     runtimeAttributes: Map[LocallyQualifiedName, WomValue],
                                                     maybeCallCachingEligible: MaybeCallCachingEligible,
                                                     prefetchedJobStoreEntries: Map[String, KvResponse],
-                                                    dockerSize: Option[DockerSize]): BackendJobPreparationSucceeded = {
+                                                    dockerSize: Option[DockerSize]
+  ): BackendJobPreparationSucceeded = {
     val memoryMultiplier: Option[Double] = prefetchedJobStoreEntries.get(MemoryMultiplierKey) match {
-      case Some(KvPair(_,v)) => Try(v.toDouble) match {
-        case Success(m) => Option(m)
-        case Failure(e) =>
-          // should not happen as we are converting a value that Cromwell put in DB after validation
-          log.error(e, s"Programmer error: unexpected failure attempting to convert value of MemoryMultiplierKey from JOB_KEY_VALUE_ENTRY table to Double.")
-          None
-      }
+      case Some(KvPair(_, v)) =>
+        Try(v.toDouble) match {
+          case Success(m) => Option(m)
+          case Failure(e) =>
+            // should not happen as we are converting a value that Cromwell put in DB after validation
+            log.error(
+              e,
+              s"Programmer error: unexpected failure attempting to convert value of MemoryMultiplierKey from JOB_KEY_VALUE_ENTRY table to Double."
+            )
+            None
+        }
       case _ => None
     }
 
     val updatedRuntimeAttributes = updateRuntimeMemory(runtimeAttributes, memoryMultiplier)
 
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor.backendDescriptor, jobKey, updatedRuntimeAttributes, inputEvaluation, maybeCallCachingEligible, dockerSize, prefetchedJobStoreEntries)
-    BackendJobPreparationSucceeded(jobDescriptor, jobExecutionProps(jobDescriptor, initializationData, serviceRegistryActor, ioActor, backendSingletonActor))
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor.backendDescriptor,
+                                             jobKey,
+                                             updatedRuntimeAttributes,
+                                             inputEvaluation,
+                                             maybeCallCachingEligible,
+                                             dockerSize,
+                                             prefetchedJobStoreEntries
+    )
+    BackendJobPreparationSucceeded(
+      jobDescriptor,
+      jobExecutionProps(jobDescriptor, initializationData, serviceRegistryActor, ioActor, backendSingletonActor)
+    )
   }
 
-  private [preparation] def prepareRuntimeAttributes(inputEvaluation: Map[InputDefinition, WomValue]): ErrorOr[Map[LocallyQualifiedName, WomValue]] = {
+  private[preparation] def prepareRuntimeAttributes(
+    inputEvaluation: Map[InputDefinition, WomValue]
+  ): ErrorOr[Map[LocallyQualifiedName, WomValue]] = {
     import RuntimeAttributeDefinition.{addDefaultsToAttributes, evaluateRuntimeAttributes}
-    val curriedAddDefaultsToAttributes = addDefaultsToAttributes(runtimeAttributeDefinitions, workflowDescriptor.backendDescriptor.workflowOptions) _
+    val curriedAddDefaultsToAttributes =
+      addDefaultsToAttributes(runtimeAttributeDefinitions, workflowDescriptor.backendDescriptor.workflowOptions) _
     val unevaluatedRuntimeAttributes = jobKey.call.callable.runtimeAttributes
-    evaluateRuntimeAttributes(unevaluatedRuntimeAttributes, expressionLanguageFunctions, inputEvaluation) map curriedAddDefaultsToAttributes
+    evaluateRuntimeAttributes(unevaluatedRuntimeAttributes,
+                              expressionLanguageFunctions,
+                              inputEvaluation
+    ) map curriedAddDefaultsToAttributes
   }
 }
 
@@ -266,14 +334,16 @@ object JobPreparationActor {
 
   sealed trait JobPreparationActorData
   case object JobPreparationActorNoData extends JobPreparationActorData
-  private final case class JobPreparationKeyLookupData(keyLookups: PartialKeyValueLookups,
+  final private case class JobPreparationKeyLookupData(keyLookups: PartialKeyValueLookups,
                                                        maybeCallCachingEligible: MaybeCallCachingEligible,
                                                        dockerSize: Option[DockerSize],
                                                        inputs: WomEvaluatedCallInputs,
-                                                       attributes: Map[LocallyQualifiedName, WomValue]) extends JobPreparationActorData
-  private final case class JobPreparationDockerLookupData(dockerHashRequest: DockerInfoRequest,
+                                                       attributes: Map[LocallyQualifiedName, WomValue]
+  ) extends JobPreparationActorData
+  final private case class JobPreparationDockerLookupData(dockerHashRequest: DockerInfoRequest,
                                                           inputs: WomEvaluatedCallInputs,
-                                                          attributes: Map[LocallyQualifiedName, WomValue]) extends JobPreparationActorData
+                                                          attributes: Map[LocallyQualifiedName, WomValue]
+  ) extends JobPreparationActorData
 
   sealed trait JobPreparationActorState
   case object Idle extends JobPreparationActorState
@@ -287,16 +357,20 @@ object JobPreparationActor {
             initializationData: Option[BackendInitializationData],
             serviceRegistryActor: ActorRef,
             ioActor: ActorRef,
-            backendSingletonActor: Option[ActorRef]) = {
+            backendSingletonActor: Option[ActorRef]
+  ) =
     // Note that JobPreparationActor doesn't run on the engine dispatcher as it mostly executes backend-side code
     // (WDL expression evaluation using Backend's expressionLanguageFunctions)
-    Props(new JobPreparationActor(workflowDescriptor,
-      jobKey,
-      factory,
-      workflowDockerLookupActor = workflowDockerLookupActor,
-      initializationData,
-      serviceRegistryActor = serviceRegistryActor,
-      ioActor = ioActor,
-      backendSingletonActor = backendSingletonActor)).withDispatcher(EngineDispatcher)
-  }
+    Props(
+      new JobPreparationActor(
+        workflowDescriptor,
+        jobKey,
+        factory,
+        workflowDockerLookupActor = workflowDockerLookupActor,
+        initializationData,
+        serviceRegistryActor = serviceRegistryActor,
+        ioActor = ioActor,
+        backendSingletonActor = backendSingletonActor
+      )
+    ).withDispatcher(EngineDispatcher)
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/KeyValueLookups.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/KeyValueLookups.scala
index f4d5786223b..73014807d26 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/KeyValueLookups.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/KeyValueLookups.scala
@@ -5,9 +5,11 @@ import cromwell.services.keyvalue.KeyValueServiceActor.{KvResponse, ScopedKey}
 /**
   * Handles the determination of when we know key lookups are successful.
   */
-private sealed trait KeyValueLookups
+sealed private trait KeyValueLookups
 
-private[preparation] final case class PartialKeyValueLookups(responses: Map[ScopedKey, KvResponse], awaiting: Seq[ScopedKey]) {
+final private[preparation] case class PartialKeyValueLookups(responses: Map[ScopedKey, KvResponse],
+                                                             awaiting: Seq[ScopedKey]
+) {
   def withResponse(key: ScopedKey, response: KvResponse) = {
     val newResponses = responses + (key -> response)
     val newAwaiting = awaiting diff List(key)
@@ -19,6 +21,6 @@ private[preparation] final case class PartialKeyValueLookups(responses: Map[Scop
   }
 }
 
-private final case class KeyValueLookupResults(values: Map[ScopedKey, KvResponse]) {
+final private case class KeyValueLookupResults(values: Map[ScopedKey, KvResponse]) {
   def unscoped: Map[String, KvResponse] = values map { case (k, v) => k.key -> v }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/SubWorkflowPreparationActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/SubWorkflowPreparationActor.scala
index f14c00965d7..8165b13128b 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/SubWorkflowPreparationActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/SubWorkflowPreparationActor.scala
@@ -20,7 +20,9 @@ import wom.values.{WomEvaluatedCallInputs, WomValue}
 class SubWorkflowPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
                                   expressionLanguageFunctions: EngineIoFunctions,
                                   callKey: SubWorkflowKey,
-                                  subWorkflowId: WorkflowId) extends Actor with WorkflowLogging {
+                                  subWorkflowId: WorkflowId
+) extends Actor
+    with WorkflowLogging {
 
   override lazy val workflowIdForLogging = workflowDescriptor.possiblyNotRootWorkflowId
   override lazy val rootWorkflowIdForLogging = workflowDescriptor.rootWorkflowId
@@ -33,9 +35,13 @@ class SubWorkflowPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
         id = subWorkflowId,
         callable = callKey.node.callable,
         knownValues = startingValues,
-        breadCrumbs = oldBackendDescriptor.breadCrumbs :+ BackendJobBreadCrumb(workflowDescriptor.callable, workflowDescriptor.id, callKey)
+        breadCrumbs = oldBackendDescriptor.breadCrumbs :+ BackendJobBreadCrumb(workflowDescriptor.callable,
+                                                                               workflowDescriptor.id,
+                                                                               callKey
+        )
       )
-      val engineDescriptor = workflowDescriptor.copy(backendDescriptor = newBackendDescriptor, parentWorkflow = Option(workflowDescriptor))
+      val engineDescriptor =
+        workflowDescriptor.copy(backendDescriptor = newBackendDescriptor, parentWorkflow = Option(workflowDescriptor))
       SubWorkflowPreparationSucceeded(engineDescriptor, inputEvaluation)
     }
   }
@@ -43,7 +49,9 @@ class SubWorkflowPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
   /**
     * Work out a set of  "workflow inputs" to pass to this subworkflow as though it were a top-level workflow receiving inputs
     */
-  private def evaluateStartingKnownValues(inputEvaluation: WomEvaluatedCallInputs, workflowInputs: Set[GraphInputNode]): ErrorOr[Map[OutputPort, WomValue]] = {
+  private def evaluateStartingKnownValues(inputEvaluation: WomEvaluatedCallInputs,
+                                          workflowInputs: Set[GraphInputNode]
+  ): ErrorOr[Map[OutputPort, WomValue]] = {
 
     // Find the values in the provided inputs that match up with subworkflow inputs. Silently drop the rest on the floor.
     val providedInputs: Map[OutputPort, WomValue] = inputEvaluation.toList.flatMap { case (name, value) =>
@@ -59,9 +67,14 @@ class SubWorkflowPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
     }
 
     // Make sure the subworkflow will be getting a value for every required input:
-    NonEmptyList.fromList((workflowInputs.toSet[GraphNode] diff providedInputs.keySet.map(_.graphNode) diff optionalsAndDefaults).toList) match {
+    NonEmptyList.fromList(
+      (workflowInputs.toSet[GraphNode] diff providedInputs.keySet.map(_.graphNode) diff optionalsAndDefaults).toList
+    ) match {
       case None => Valid(providedInputs)
-      case Some(missingNodeNel) => Invalid(missingNodeNel map (n => s"Couldn't find starting value for subworkflow input: ${n.identifier.localName}"))
+      case Some(missingNodeNel) =>
+        Invalid(
+          missingNodeNel map (n => s"Couldn't find starting value for subworkflow input: ${n.identifier.localName}")
+        )
     }
   }
 
@@ -71,10 +84,14 @@ class SubWorkflowPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
       import common.validation.ErrorOr._
       evaluatedInputs.flatMap(prepareExecutionActor) match {
         case Valid(response) => context.parent ! response
-        case Invalid(f) => context.parent ! CallPreparationFailed(callKey, new MessageAggregation {
-          override def exceptionContext: String = "Failed to evaluate inputs for sub workflow"
-          override def errorMessages: Iterable[String] = f.toList
-        })
+        case Invalid(f) =>
+          context.parent ! CallPreparationFailed(
+            callKey,
+            new MessageAggregation {
+              override def exceptionContext: String = "Failed to evaluate inputs for sub workflow"
+              override def errorMessages: Iterable[String] = f.toList
+            }
+          )
       }
       context stop self
 
@@ -83,14 +100,17 @@ class SubWorkflowPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
 }
 
 object SubWorkflowPreparationActor {
-  case class SubWorkflowPreparationSucceeded(workflowDescriptor: EngineWorkflowDescriptor, inputs: WomEvaluatedCallInputs) extends CallPreparationActorResponse
+  case class SubWorkflowPreparationSucceeded(workflowDescriptor: EngineWorkflowDescriptor,
+                                             inputs: WomEvaluatedCallInputs
+  ) extends CallPreparationActorResponse
 
   def props(workflowDescriptor: EngineWorkflowDescriptor,
             expressionLanguageFunctions: EngineIoFunctions,
             key: SubWorkflowKey,
-            subWorkflowId: WorkflowId) = {
+            subWorkflowId: WorkflowId
+  ) =
     // Note that JobPreparationActor doesn't run on the engine dispatcher as it mostly executes backend-side code
     // (WDL expression evaluation using Backend's expressionLanguageFunctions)
-    Props(new SubWorkflowPreparationActor(workflowDescriptor, expressionLanguageFunctions, key, subWorkflowId)).withDispatcher(EngineDispatcher)
-  }
+    Props(new SubWorkflowPreparationActor(workflowDescriptor, expressionLanguageFunctions, key, subWorkflowId))
+      .withDispatcher(EngineDispatcher)
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ConditionalCollectorKey.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ConditionalCollectorKey.scala
index 8645ce0f6a5..244c1dba99b 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ConditionalCollectorKey.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ConditionalCollectorKey.scala
@@ -11,19 +11,19 @@ import wom.graph.GraphNodePort.ConditionalOutputPort
   * Key that becomes runnable when a node inside a conditional node is complete.
   * This is needed so that the ConditionalOutputPort of the conditional can be given a value.
   */
-private [execution] case class ConditionalCollectorKey(conditionalOutputPort: ConditionalOutputPort,
-                                                       index: ExecutionIndex) extends JobKey {
+private[execution] case class ConditionalCollectorKey(conditionalOutputPort: ConditionalOutputPort,
+                                                      index: ExecutionIndex
+) extends JobKey {
   val outputNodeToCollect: PortBasedGraphOutputNode = conditionalOutputPort.outputToExpose
   override val node: GraphNode = conditionalOutputPort.outputToExpose
   override val attempt = 1
   override val tag = s"Collector-${node.localName}"
 
-  def processRunnable(data: WorkflowExecutionActorData): ErrorOr[WorkflowExecutionDiff] = {
+  def processRunnable(data: WorkflowExecutionActorData): ErrorOr[WorkflowExecutionDiff] =
     data.valueStore.collectConditional(this) map { outputs =>
       WorkflowExecutionDiff(
         executionStoreChanges = Map(this -> ExecutionStatus.Done),
         valueStoreAdditions = outputs
       )
     }
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ConditionalKey.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ConditionalKey.scala
index a263601f488..7cc18c3b964 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ConditionalKey.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ConditionalKey.scala
@@ -16,7 +16,7 @@ import wom.values.{WomBoolean, WomValue}
   * Represents a conditional node in the execution store.
   * Runnable when the associated expression (represented by an expression node in the graph) is done.
   */
-private [execution] case class ConditionalKey(node: ConditionalNode, index: ExecutionIndex) extends JobKey {
+private[execution] case class ConditionalKey(node: ConditionalNode, index: ExecutionIndex) extends JobKey {
   override val tag = node.localName
   override val attempt = 1
 
@@ -30,10 +30,10 @@ private [execution] case class ConditionalKey(node: ConditionalNode, index: Exec
     * @return ExecutionStore of scattered children.
     */
   def populate(bypassed: Boolean): Map[JobKey, ExecutionStatus.Value] = {
-    val conditionalKeys = node.innerGraph.nodes.flatMap({ node => keyify(node) })
+    val conditionalKeys = node.innerGraph.nodes.flatMap(node => keyify(node))
 
     val finalStatus = if (bypassed) ExecutionStatus.NotStarted else ExecutionStatus.Bypassed
-    (conditionalKeys ++ collectors).map({ _ -> finalStatus }).toMap
+    (conditionalKeys ++ collectors).map(_ -> finalStatus).toMap
   }
 
   /**
@@ -48,12 +48,16 @@ private [execution] case class ConditionalKey(node: ConditionalNode, index: Exec
     case _: GraphInputNode => None
     case _: PortBasedGraphOutputNode => None
     case _: ScatterNode =>
-      throw new UnsupportedOperationException("Nested Scatters are not supported (yet) ... but you might try a sub workflow to achieve the same effect!")
+      throw new UnsupportedOperationException(
+        "Nested Scatters are not supported (yet) ... but you might try a sub workflow to achieve the same effect!"
+      )
     case e =>
       throw new UnsupportedOperationException(s"Scope ${e.getClass.getName} is not supported in an If block.")
   }
 
-  def processRunnable(data: WorkflowExecutionActorData, workflowLogger: WorkflowLogger): ErrorOr[WorkflowExecutionDiff] = {
+  def processRunnable(data: WorkflowExecutionActorData,
+                      workflowLogger: WorkflowLogger
+  ): ErrorOr[WorkflowExecutionDiff] = {
     // This is the output port from the conditional's 'condition' input:
     val conditionOutputPort = node.conditionExpression.singleOutputPort
     data.valueStore.get(conditionOutputPort, index) match {
@@ -64,9 +68,9 @@ private [execution] case class ConditionalKey(node: ConditionalNode, index: Exec
           node.conditionalOutputPorts.map(op => ValueKey(op, index) -> op.womType.none).toMap
         } else Map.empty
 
-        WorkflowExecutionDiff(
-          executionStoreChanges = populate(b.value) + (this -> conditionalStatus),
-          valueStoreAdditions = valueStoreAdditions).validNel
+        WorkflowExecutionDiff(executionStoreChanges = populate(b.value) + (this -> conditionalStatus),
+                              valueStoreAdditions = valueStoreAdditions
+        ).validNel
       case Some(v: WomValue) =>
         s"'if' condition ${node.conditionExpression.womExpression.sourceString} must evaluate to a boolean but instead got ${v.womType.stableName}".invalidNel
       case None =>
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ExpressionKey.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ExpressionKey.scala
index 5978ec8c254..5fd8e36cac5 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ExpressionKey.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ExpressionKey.scala
@@ -7,7 +7,10 @@ import common.validation.Validation._
 import cromwell.core.ExecutionIndex._
 import cromwell.core.{ExecutionStatus, JobKey}
 import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionDiff
-import cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.{ExpressionEvaluationFailedResponse, ExpressionEvaluationSucceededResponse}
+import cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.{
+  ExpressionEvaluationFailedResponse,
+  ExpressionEvaluationSucceededResponse
+}
 import cromwell.engine.workflow.lifecycle.execution.stores.ValueStore
 import wom.expression.IoFunctionSet
 import wom.graph.GraphNodePort.OutputPort
@@ -18,14 +21,17 @@ final case class ExpressionKey(node: ExpressionNodeLike, index: ExecutionIndex)
   override val attempt = 1
   override lazy val tag = s"Expression-${node.localName}:${index.fromIndex}:$attempt"
 
-  def processRunnable(ioFunctionSet: IoFunctionSet, valueStore: ValueStore, workflowExecutionActor: ActorRef): ErrorOr[WorkflowExecutionDiff] = {
+  def processRunnable(ioFunctionSet: IoFunctionSet,
+                      valueStore: ValueStore,
+                      workflowExecutionActor: ActorRef
+  ): ErrorOr[WorkflowExecutionDiff] = {
     // Send a message to self in case we decide to change evaluate to return asynchronously, if we don't we could
     // directly add the value to the value store in the execution diff
     node
       .evaluate(valueStore.resolve(index), ioFunctionSet)
       .contextualizeErrors(s"evaluate '${node.fullyQualifiedName}'") match {
       case Right(result) => workflowExecutionActor ! ExpressionEvaluationSucceededResponse(this, result)
-      case Left(f) => 
+      case Left(f) =>
         workflowExecutionActor ! ExpressionEvaluationFailedResponse(this, new RuntimeException(f.toList.mkString(", ")))
     }
 
@@ -34,6 +40,8 @@ final case class ExpressionKey(node: ExpressionNodeLike, index: ExecutionIndex)
 }
 
 object ExpressionKey {
-  private [execution] case class ExpressionEvaluationSucceededResponse(expressionKey: ExpressionKey, values: Map[OutputPort, WomValue])
-  private [execution] case class ExpressionEvaluationFailedResponse(expressionKey: ExpressionKey, reason: Throwable)
+  private[execution] case class ExpressionEvaluationSucceededResponse(expressionKey: ExpressionKey,
+                                                                      values: Map[OutputPort, WomValue]
+  )
+  private[execution] case class ExpressionEvaluationFailedResponse(expressionKey: ExpressionKey, reason: Throwable)
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterCollectorKey.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterCollectorKey.scala
index 353971bd652..aa50be93144 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterCollectorKey.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterCollectorKey.scala
@@ -11,21 +11,21 @@ import wom.graph.{GraphNode, PortBasedGraphOutputNode}
   * Key that becomes runnable when all shards of a collectible node are complete and need to be collected to form the output of this
   * call outside the scatter block.
   */
-private [execution] case class ScatterCollectorKey(scatterGatherPort: ScatterGathererPort,
-                                                   scatterWidth: Int,
-                                                   scatterCollectionFunction: ScatterCollectionFunction) extends JobKey {
+private[execution] case class ScatterCollectorKey(scatterGatherPort: ScatterGathererPort,
+                                                  scatterWidth: Int,
+                                                  scatterCollectionFunction: ScatterCollectionFunction
+) extends JobKey {
   val outputNodeToGather: PortBasedGraphOutputNode = scatterGatherPort.outputToGather
   override val node: GraphNode = outputNodeToGather
   override val index = None
   override val attempt = 1
   override val tag = s"Collector-${node.localName}"
 
-  def processRunnable(data: WorkflowExecutionActorData): ErrorOr[WorkflowExecutionDiff] = {
+  def processRunnable(data: WorkflowExecutionActorData): ErrorOr[WorkflowExecutionDiff] =
     data.valueStore.collectShards(this) map { outputs =>
       WorkflowExecutionDiff(
         executionStoreChanges = Map(this -> ExecutionStatus.Done),
         valueStoreAdditions = outputs
       )
     }
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterKey.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterKey.scala
index b3e4529b9d3..0bd8a14f3a3 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterKey.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterKey.scala
@@ -20,18 +20,19 @@ import wom.values.WomValue
 
 import scala.language.postfixOps
 
-private [execution] case class ScatterKey(node: ScatterNode) extends JobKey {
+private[execution] case class ScatterKey(node: ScatterNode) extends JobKey {
 
   // When scatters are nested, this might become Some(_)
   override val index = None
   override val attempt = 1
   override val tag = node.localName
 
-  def makeCollectors(count: Int, scatterCollectionFunction: ScatterCollectionFunction): Set[ScatterCollectorKey] = (node.outputMapping.groupBy(_.outputToGather.source.graphNode) flatMap {
-    case (_: CallNode | _: ExposedExpressionNode | _: ConditionalNode, scatterGatherPorts) =>
-      scatterGatherPorts.map(sgp => ScatterCollectorKey(sgp, count, scatterCollectionFunction))
-    case _ => Set.empty[ScatterCollectorKey]
-  }).toSet
+  def makeCollectors(count: Int, scatterCollectionFunction: ScatterCollectionFunction): Set[ScatterCollectorKey] =
+    (node.outputMapping.groupBy(_.outputToGather.source.graphNode) flatMap {
+      case (_: CallNode | _: ExposedExpressionNode | _: ConditionalNode, scatterGatherPorts) =>
+        scatterGatherPorts.map(sgp => ScatterCollectorKey(sgp, count, scatterCollectionFunction))
+      case _ => Set.empty[ScatterCollectorKey]
+    }).toSet
 
   /**
     * Creates a sub-ExecutionStore with Starting entries for each of the scoped children.
@@ -54,12 +55,17 @@ private [execution] case class ScatterKey(node: ScatterNode) extends JobKey {
     case _: GraphInputNode => List.empty
     case _: PortBasedGraphOutputNode => List.empty
     case _: ScatterNode =>
-      throw new UnsupportedOperationException("Nested Scatters are not supported (yet) ... but you might try a sub workflow to achieve the same effect!")
+      throw new UnsupportedOperationException(
+        "Nested Scatters are not supported (yet) ... but you might try a sub workflow to achieve the same effect!"
+      )
     case e =>
       throw new UnsupportedOperationException(s"Scope ${e.getClass.getName} is not supported.")
   }
 
-  def processRunnable(data: WorkflowExecutionActorData, workflowExecutionActor: ActorRef, maxScatterWidth: Int): ErrorOr[WorkflowExecutionDiff] = {
+  def processRunnable(data: WorkflowExecutionActorData,
+                      workflowExecutionActor: ActorRef,
+                      maxScatterWidth: Int
+  ): ErrorOr[WorkflowExecutionDiff] = {
     import cats.syntax.traverse._
 
     def getScatterArray(scatterVariableNode: ScatterVariableNode): ErrorOr[ScatterVariableAndValue] = {
@@ -84,26 +90,29 @@ private [execution] case class ScatterKey(node: ScatterNode) extends JobKey {
 
     // Execution changes (for execution store and value store) generated by the scatter iteration nodes
     def buildExecutionChanges(scatterVariableAndValues: List[ScatterVariableAndValue]) = {
-      val (executionStoreChanges, valueStoreChanges) = scatterVariableAndValues.map({
+      val (executionStoreChanges, valueStoreChanges) = scatterVariableAndValues.map {
         case ScatterVariableAndValue(scatterVariableNode, arrayValue) =>
           val executionStoreChange = ScatterVariableInputKey(scatterVariableNode, arrayValue) -> ExecutionStatus.Done
           val valueStoreChange = ValueKey(scatterVariableNode.singleOutputPort, None) -> arrayValue
 
           executionStoreChange -> valueStoreChange
-      }).unzip
+      }.unzip
 
       executionStoreChanges.toMap -> valueStoreChanges.toMap
     }
 
     // Checks the scatter width of a scatter node and builds WorkflowExecutionDiff accordingly
     // If scatter width is more than max allowed limit, it fails the ScatterNode key
-    def buildExecutionDiff(scatterSize: Int, arrays: List[ScatterVariableAndValue]): WorkflowExecutionDiff = {
-      if(scatterSize > maxScatterWidth) {
-        workflowExecutionActor ! JobFailedNonRetryableResponse(this, new Exception(s"Workflow scatter width of $scatterSize exceeds configured limit of $maxScatterWidth."), None)
+    def buildExecutionDiff(scatterSize: Int, arrays: List[ScatterVariableAndValue]): WorkflowExecutionDiff =
+      if (scatterSize > maxScatterWidth) {
+        workflowExecutionActor ! JobFailedNonRetryableResponse(
+          this,
+          new Exception(s"Workflow scatter width of $scatterSize exceeds configured limit of $maxScatterWidth."),
+          None
+        )
 
         WorkflowExecutionDiff(Map(this -> ExecutionStatus.Failed))
-      }
-      else {
+      } else {
         val (scatterVariablesExecutionChanges, valueStoreChanges) = buildExecutionChanges(arrays)
         val executionStoreChanges = populate(
           scatterSize,
@@ -115,8 +124,6 @@ private [execution] case class ScatterKey(node: ScatterNode) extends JobKey {
           valueStoreAdditions = valueStoreChanges
         )
       }
-    }
-
 
     (for {
       arrays <- scatterArraysValuesCheck
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterVariableInputKey.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterVariableInputKey.scala
index 202e1e2db7b..6480c643ea0 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterVariableInputKey.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatterVariableInputKey.scala
@@ -4,7 +4,7 @@ import cromwell.core.JobKey
 import wom.graph.GraphInputNode
 import wom.values.WomArray.WomArrayLike
 
-private [execution] case class ScatterVariableInputKey(node: GraphInputNode, womArrayLike: WomArrayLike) extends JobKey {
+private[execution] case class ScatterVariableInputKey(node: GraphInputNode, womArrayLike: WomArrayLike) extends JobKey {
   override def index: Option[Int] = None
   override def attempt: Int = 1
   override def tag: String = node.localName
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatteredCallCompletionKey.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatteredCallCompletionKey.scala
index c58982e807c..e418cbe1d43 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatteredCallCompletionKey.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ScatteredCallCompletionKey.scala
@@ -9,15 +9,13 @@ import wom.graph.{CallNode, GraphNode}
 /**
   * Key that should become runnable when all shards of a scattered call are complete.
   */
-private [execution] case class ScatteredCallCompletionKey(call: CallNode,
-                                                          scatterWidth: Int) extends JobKey {
+private[execution] case class ScatteredCallCompletionKey(call: CallNode, scatterWidth: Int) extends JobKey {
   override val node: GraphNode = call
   override val index = None
   override val attempt = 1
   override val totalIndices = scatterWidth
   override val tag = s"CallCompletion-${node.localName}"
 
-  def processRunnable(data: WorkflowExecutionActorData): ErrorOr[WorkflowExecutionDiff] = {
+  def processRunnable(data: WorkflowExecutionActorData): ErrorOr[WorkflowExecutionDiff] =
     WorkflowExecutionDiff(executionStoreChanges = Map(this -> ExecutionStatus.Done)).validNel
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/SubWorkflowKey.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/SubWorkflowKey.scala
index 44c2f0a57e2..f66f7f2fade 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/SubWorkflowKey.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/SubWorkflowKey.scala
@@ -4,6 +4,7 @@ import cromwell.core.CallKey
 import cromwell.core.ExecutionIndex._
 import wom.graph.WorkflowCallNode
 
-private [execution] case class SubWorkflowKey(node: WorkflowCallNode, index: ExecutionIndex, attempt: Int) extends CallKey {
+private[execution] case class SubWorkflowKey(node: WorkflowCallNode, index: ExecutionIndex, attempt: Int)
+    extends CallKey {
   override val tag = s"SubWorkflow-${node.localName}:${index.fromIndex}:$attempt"
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/package.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/package.scala
index 95d00892c4a..4ddef0c980d 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/package.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/package.scala
@@ -15,9 +15,8 @@ package object keys {
     ).validNel
   }
 
-  private def bypassedScopeResults(jobKey: JobKey): Map[ValueKey, WomOptionalValue] = {
-    jobKey.node.outputPorts.map({ outputPort =>
-      ValueKey(outputPort, jobKey.index) ->  WomOptionalValue.none(outputPort.womType)
-    }).toMap
-  }
+  private def bypassedScopeResults(jobKey: JobKey): Map[ValueKey, WomOptionalValue] =
+    jobKey.node.outputPorts.map { outputPort =>
+      ValueKey(outputPort, jobKey.index) -> WomOptionalValue.none(outputPort.womType)
+    }.toMap
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ExecutionStore.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ExecutionStore.scala
index 32d9aa2ca4c..e6445ffda23 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ExecutionStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ExecutionStore.scala
@@ -25,6 +25,7 @@ object ExecutionStore {
   val MaxJobsToStartPerTick = 1000
 
   implicit class EnhancedJobKey(val key: JobKey) extends AnyVal {
+
     /**
       * Given a StatusStable, return true if all dependencies of this key are in the table (and therefore are in this status),
       * false otherwise.
@@ -42,26 +43,30 @@ object ExecutionStore {
         case scatterCollector: ScatterCollectorKey =>
           // The outputToGather is the PortBasedGraphOutputNode of the inner graph that we're collecting. Go one step upstream and then
           // find the node which will have entries in the execution store. If that has 'n' entries, then we're good to start collecting,
-          statusTable.row(scatterCollector.outputNodeToGather.singleUpstreamPort.executionNode).size == scatterCollector.scatterWidth
+          statusTable
+            .row(scatterCollector.outputNodeToGather.singleUpstreamPort.executionNode)
+            .size == scatterCollector.scatterWidth
         case conditionalCollector: ConditionalCollectorKey =>
           val upstreamPort = conditionalCollector.outputNodeToCollect.singleUpstreamPort
           upstreamPort.executionNode.isInStatus(chooseIndex(upstreamPort), statusTable)
         // In the general case, the dependencies are held by the upstreamPorts
         case _ =>
           key.node.upstreamPorts forall { p =>
-              p.executionNode.isInStatus(chooseIndex(p), statusTable)
+            p.executionNode.isInStatus(chooseIndex(p), statusTable)
           }
       }
     }
 
     def nonStartableOutputKeys: Set[JobKey] = key match {
-      case scatterKey: ScatterKey => scatterKey.makeCollectors(0, scatterKey.node.scatterCollectionFunctionBuilder(List.empty)).toSet[JobKey]
+      case scatterKey: ScatterKey =>
+        scatterKey.makeCollectors(0, scatterKey.node.scatterCollectionFunctionBuilder(List.empty)).toSet[JobKey]
       case conditionalKey: ConditionalKey => conditionalKey.collectors.toSet[JobKey]
       case _ => Set.empty[JobKey]
     }
   }
 
   implicit class EnhancedOutputPort(val outputPort: OutputPort) extends AnyVal {
+
     /**
       * Node that should be considered to determine upstream dependencies
       */
@@ -78,18 +83,25 @@ object ExecutionStore {
       case svn: ScatterVariableNode => table.contains(svn.linkToOuterGraph.graphNode, None)
       // OuterGraphInputNodes signal that an input comes from outside the graph.
       // Depending on whether or not this input is outside of a scatter graph will change the index which we need to look at
-      case ogin: OuterGraphInputNode if !ogin.preserveScatterIndex => ogin.linkToOuterGraph.executionNode.isInStatus(None, table)
+      case ogin: OuterGraphInputNode if !ogin.preserveScatterIndex =>
+        ogin.linkToOuterGraph.executionNode.isInStatus(None, table)
       case ogin: OuterGraphInputNode => ogin.linkToOuterGraph.executionNode.isInStatus(index, table)
       case _: GraphInputNode => true
       case _ => table.contains(graphNode, index)
     }
   }
 
-  case class ExecutionStoreUpdate(runnableKeys: List[JobKey], updatedStore: ExecutionStore, statusChanges: Map[JobKey, ExecutionStatus])
+  case class ExecutionStoreUpdate(runnableKeys: List[JobKey],
+                                  updatedStore: ExecutionStore,
+                                  statusChanges: Map[JobKey, ExecutionStatus]
+  )
 
   def empty = ActiveExecutionStore(Map.empty[JobKey, ExecutionStatus], needsUpdate = false)
 
-  def apply(callable: ExecutableCallable, totalJobsByRootWf: AtomicInteger, totalMaxJobsPerRootWf: Int): ErrorOr[ActiveExecutionStore] = {
+  def apply(callable: ExecutableCallable,
+            totalJobsByRootWf: AtomicInteger,
+            totalMaxJobsPerRootWf: Int
+  ): ErrorOr[ActiveExecutionStore] = {
     // Keys that are added in a NotStarted Status
     val notStartedKeys = callable.graph.nodes collect {
       case call: CommandCallNode => BackendJobDescriptorKey(call, None, attempt = 1)
@@ -118,21 +130,25 @@ object ExecutionStore {
 /**
   * Execution store in its nominal state
   */
-final case class ActiveExecutionStore private[stores](private val statusStore: Map[JobKey, ExecutionStatus], override val needsUpdate: Boolean) extends ExecutionStore(statusStore, needsUpdate) {
+final case class ActiveExecutionStore private[stores] (private val statusStore: Map[JobKey, ExecutionStatus],
+                                                       override val needsUpdate: Boolean
+) extends ExecutionStore(statusStore, needsUpdate) {
 
   override def toString: String = {
     import io.circe.syntax._
     import io.circe.Printer
 
-    statusStore.map {
-      case (k, v) if k.isShard => s"${k.node.fullyQualifiedName}:${k.index.get}" -> v.toString
-      case (k, v) => k.node.fullyQualifiedName -> v.toString
-    }.asJson.printWith(Printer.spaces2.copy(dropNullValues = true, colonLeft = ""))
+    statusStore
+      .map {
+        case (k, v) if k.isShard => s"${k.node.fullyQualifiedName}:${k.index.get}" -> v.toString
+        case (k, v) => k.node.fullyQualifiedName -> v.toString
+      }
+      .asJson
+      .printWith(Printer.spaces2.copy(dropNullValues = true, colonLeft = ""))
   }
 
-  override def updateKeys(values: Map[JobKey, ExecutionStatus], needsUpdate: Boolean): ActiveExecutionStore = {
+  override def updateKeys(values: Map[JobKey, ExecutionStatus], needsUpdate: Boolean): ActiveExecutionStore =
     this.copy(statusStore = statusStore ++ values, needsUpdate = needsUpdate)
-  }
   override def seal: SealedExecutionStore = SealedExecutionStore(statusStore.filterNot(_._2 == NotStarted), needsUpdate)
   override def withNeedsUpdateFalse: ExecutionStore = if (!needsUpdate) this else this.copy(needsUpdate = false)
   override def withNeedsUpdateTrue: ExecutionStore = if (needsUpdate) this else this.copy(needsUpdate = true)
@@ -142,12 +158,13 @@ final case class ActiveExecutionStore private[stores](private val statusStore: M
   * Execution store when the workflow is in either Failing or Aborting state. Keys in NotStarted state have been removed and
   * no new NotStarted key can be added. Other statuses can still be updated.
   */
-final case class SealedExecutionStore private[stores](private val statusStore: Map[JobKey, ExecutionStatus], override val needsUpdate: Boolean) extends ExecutionStore(statusStore, false) {
+final case class SealedExecutionStore private[stores] (private val statusStore: Map[JobKey, ExecutionStatus],
+                                                       override val needsUpdate: Boolean
+) extends ExecutionStore(statusStore, false) {
 
-  override def updateKeys(values: Map[JobKey, ExecutionStatus], needsUpdate: Boolean): SealedExecutionStore = {
+  override def updateKeys(values: Map[JobKey, ExecutionStatus], needsUpdate: Boolean): SealedExecutionStore =
     // Don't allow NotStarted keys in sealed mode
     this.copy(statusStore = statusStore ++ values.filterNot(_._2 == NotStarted), needsUpdate = needsUpdate)
-  }
   override def seal: SealedExecutionStore = this
   override def withNeedsUpdateFalse: ExecutionStore = this.copy(needsUpdate = false)
   override def withNeedsUpdateTrue: ExecutionStore = this.copy(needsUpdate = true)
@@ -162,13 +179,14 @@ final case class SealedExecutionStore private[stores](private val statusStore: M
   *                    when true, something happened since the last update that could yield new runnable keys, so update should be called
   *                    when false, nothing happened between the last update and now that will yield different results so no need to call the update method
   */
-sealed abstract class ExecutionStore private[stores](statusStore: Map[JobKey, ExecutionStatus], val needsUpdate: Boolean) {
+sealed abstract class ExecutionStore private[stores] (statusStore: Map[JobKey, ExecutionStatus],
+                                                      val needsUpdate: Boolean
+) {
   // View of the statusStore more suited for lookup based on status
   lazy val store: Map[ExecutionStatus, List[JobKey]] = statusStore.groupBy(_._2).safeMapValues(_.keys.toList)
 
-  def backendJobDescriptorKeyForNode(node: GraphNode): Option[BackendJobDescriptorKey] = {
+  def backendJobDescriptorKeyForNode(node: GraphNode): Option[BackendJobDescriptorKey] =
     statusStore.keys collectFirst { case k: BackendJobDescriptorKey if k.node eq node => k }
-  }
 
   /**
     * Number of queued jobs
@@ -183,10 +201,9 @@ sealed abstract class ExecutionStore private[stores](statusStore: Map[JobKey, Ex
   /**
     * Update key statuses
     */
-  def updateKeys(values: Map[JobKey, ExecutionStatus]): ExecutionStore = {
+  def updateKeys(values: Map[JobKey, ExecutionStatus]): ExecutionStore =
     // The store might newly need updating now if a job has completed because downstream jobs might now be runnable
     updateKeys(values, needsUpdate || values.values.exists(_.isTerminalOrRetryable))
-  }
 
   /**
     * Returns a SealedExecutionStore: all NotStarted keys will be removed and no new NotStarted keys can be added after that
@@ -204,23 +221,23 @@ sealed abstract class ExecutionStore private[stores](statusStore: Map[JobKey, Ex
   protected def withNeedsUpdateFalse: ExecutionStore
 
   /*
-    * Create 2 Tables, one for keys in done status and one for keys in terminal status.
-    * A Table is nothing more than a Map[R, Map[C, V]], see Table trait for more details
-    * In this case, rows are GraphNodes, columns are ExecutionIndexes, and values are JobKeys
-    * This allows for quick lookup of all shards for a node, as well as accessing a specific key with a
-    * (node, index) pair
+   * Create 2 Tables, one for keys in done status and one for keys in terminal status.
+   * A Table is nothing more than a Map[R, Map[C, V]], see Table trait for more details
+   * In this case, rows are GraphNodes, columns are ExecutionIndexes, and values are JobKeys
+   * This allows for quick lookup of all shards for a node, as well as accessing a specific key with a
+   * (node, index) pair
    */
   lazy val (doneStatus, terminalStatus) = {
     def toTableEntry(key: JobKey) = (key.node, key.index, key)
 
-    store.foldLeft((Table.empty[GraphNode, ExecutionIndex, JobKey], Table.empty[GraphNode, ExecutionIndex, JobKey]))({
-      case ((done, terminal), (status, keys))  =>
+    store.foldLeft((Table.empty[GraphNode, ExecutionIndex, JobKey], Table.empty[GraphNode, ExecutionIndex, JobKey])) {
+      case ((done, terminal), (status, keys)) =>
         lazy val newMapEntries = keys map toTableEntry
         val newDone = if (status.isDoneOrBypassed) done.addAll(newMapEntries) else done
         val newTerminal = if (status.isTerminal) terminal.addAll(newMapEntries) else terminal
 
         newDone -> newTerminal
-    })
+    }
   }
 
   private def keysWithStatus(status: ExecutionStatus) = store.getOrElse(status, List.empty)
@@ -229,29 +246,28 @@ sealed abstract class ExecutionStore private[stores](statusStore: Map[JobKey, Ex
     * We're done when all the keys have a terminal status,
     * which is equivalent to non of them being in a non-terminal status and faster to verify
     */
-  def isDone: Boolean = {
+  def isDone: Boolean =
     NonTerminalStatuses.toList.map(keysWithStatus).forall(_.isEmpty)
-  }
 
-  def isStalled: Boolean = {
+  def isStalled: Boolean =
     !isDone && !needsUpdate && ActiveStatuses.map(keysWithStatus).forall(_.isEmpty)
-  }
 
   def unstarted = keysWithStatus(NotStarted)
 
   def jobStatus(jobKey: JobKey): Option[ExecutionStatus] = statusStore.get(jobKey)
 
-  def startedJobs: List[BackendJobDescriptorKey] = {
-    store.filterNot({ case (s, _) => s == NotStarted}).values.toList.flatten collect {
+  def startedJobs: List[BackendJobDescriptorKey] =
+    store.filterNot { case (s, _) => s == NotStarted }.values.toList.flatten collect {
       case k: BackendJobDescriptorKey => k
     }
-  }
 
   override def toString: String =
     s"""
        |ExecutionStore(
        |  statusStore = {
-       |    ${store.map { case (j, s) => s"$j -> ${s.mkString(System.lineSeparator + "      ", ", " + System.lineSeparator + "      ", "")}" } mkString("," + System.lineSeparator + "    ")}
+       |    ${store.map { case (j, s) =>
+        s"$j -> ${s.mkString(System.lineSeparator + "      ", ", " + System.lineSeparator + "      ", "")}"
+      } mkString ("," + System.lineSeparator + "    ")}
        |  },
        |  needsUpdate = $needsUpdate
        |)""".stripMargin
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
index a5c1d6fc995..778e434f634 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/stores/ValueStore.scala
@@ -39,9 +39,8 @@ case class ValueStore(store: Table[OutputPort, ExecutionIndex, WomValue]) {
     values.asJson.printWith(Printer.spaces2.copy(dropNullValues = true, colonLeft = ""))
   }
 
-  final def add(values: Map[ValueKey, WomValue]): ValueStore = {
-    this.copy(store = store.addAll(values.map({ case (key, value) => (key.port, key.index, value) })))
-  }
+  final def add(values: Map[ValueKey, WomValue]): ValueStore =
+    this.copy(store = store.addAll(values.map { case (key, value) => (key.port, key.index, value) }))
 
   final def get(outputKey: ValueKey): Option[WomValue] = store.getValue(outputKey.port, outputKey.index)
 
@@ -76,7 +75,8 @@ case class ValueStore(store: Table[OutputPort, ExecutionIndex, WomValue]) {
           }
         } else {
           // If we don't find enough shards, this collector was found "runnable" when it shouldn't have
-          s"Some shards are missing from the value store for node ${collector.node.fullyQualifiedName}, expected ${collector.scatterWidth} shards but only got ${collectedValue.size}: ${collectedValue.mkString(", ")}".invalidNel
+          s"Some shards are missing from the value store for node ${collector.node.fullyQualifiedName}, expected ${collector.scatterWidth} shards but only got ${collectedValue.size}: ${collectedValue
+              .mkString(", ")}".invalidNel
         }
       case None if collector.scatterWidth == 0 =>
         // If there's nothing, the scatter was empty, let the scatterCollectionFunction deal with it and just pass it an empty shard list
@@ -92,8 +92,10 @@ case class ValueStore(store: Table[OutputPort, ExecutionIndex, WomValue]) {
     val conditionalPort = collector.conditionalOutputPort
     val sourcePort = conditionalPort.outputToExpose.source
     store.getValue(sourcePort, collector.index) match {
-      case Some(womValue) => Map(ValueKey(conditionalPort, collector.index) -> WomOptionalValue(womValue).flattenOptional).validNel
-      case None => s"Conditional collector cannot find a value for output port ${sourcePort.identifier.fullyQualifiedName.value} in value store: $this".invalidNel
+      case Some(womValue) =>
+        Map(ValueKey(conditionalPort, collector.index) -> WomOptionalValue(womValue).flattenOptional).validNel
+      case None =>
+        s"Conditional collector cannot find a value for output port ${sourcePort.identifier.fullyQualifiedName.value} in value store: $this".invalidNel
     }
   }
 
@@ -107,12 +109,16 @@ case class ValueStore(store: Table[OutputPort, ExecutionIndex, WomValue]) {
         case Some(womValue: WomArrayLike) =>
           index match {
             case Some(jobIndex) =>
-              womValue.asArray.value.lift(svn.indexForShard(jobIndex, womValue.asArray.value.size))
+              womValue.asArray.value
+                .lift(svn.indexForShard(jobIndex, womValue.asArray.value.size))
                 .toValidNel(s"Shard index $jobIndex exceeds scatter array length: ${womValue.asArray.value.size}")
-            case None => s"Unsharded execution key references a scatter variable: ${p.identifier.fullyQualifiedName}".invalidNel
+            case None =>
+              s"Unsharded execution key references a scatter variable: ${p.identifier.fullyQualifiedName}".invalidNel
           }
-        case Some(other) => s"Value for scatter collection ${p.identifier.fullyQualifiedName} is not an array: ${other.womType.stableName}".invalidNel
-        case None => s"Can't find a value for scatter collection ${p.identifier.fullyQualifiedName} (looking for index $index)".invalidNel
+        case Some(other) =>
+          s"Value for scatter collection ${p.identifier.fullyQualifiedName} is not an array: ${other.womType.stableName}".invalidNel
+        case None =>
+          s"Can't find a value for scatter collection ${p.identifier.fullyQualifiedName} (looking for index $index)".invalidNel
       }
     }
 
@@ -123,7 +129,7 @@ case class ValueStore(store: Table[OutputPort, ExecutionIndex, WomValue]) {
         s"Can't find a ValueStore value for $p at index $index in $this".invalidNel
     }
 
-    def findValueStorePort(p: OutputPort, index: ExecutionIndex): ErrorOr[WomValue] = {
+    def findValueStorePort(p: OutputPort, index: ExecutionIndex): ErrorOr[WomValue] =
       p.graphNode match {
         case svn: ScatterVariableNode => forScatterVariable(svn)
         case ogin: OuterGraphInputNode if ogin.preserveScatterIndex => findValueStorePort(ogin.linkToOuterGraph, index)
@@ -131,7 +137,6 @@ case class ValueStore(store: Table[OutputPort, ExecutionIndex, WomValue]) {
         case _: GraphInputNode => forGraphNodePort(p, None) // Must be a workflow input, which never have indices
         case _ => forGraphNodePort(p, index)
       }
-    }
 
     findValueStorePort(outputPort, index)
   }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowLogsActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowLogsActor.scala
index 467cc1c2586..f29482cb75e 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowLogsActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowLogsActor.scala
@@ -22,14 +22,13 @@ object CopyWorkflowLogsActor {
   // Commands
   case class Copy(workflowId: WorkflowId, destinationDirPath: Path)
 
-  val strategy: OneForOneStrategy = OneForOneStrategy(maxNrOfRetries = 3) {
-    case _: IOException => Restart
+  val strategy: OneForOneStrategy = OneForOneStrategy(maxNrOfRetries = 3) { case _: IOException =>
+    Restart
   }
 
   def props(serviceRegistryActor: ActorRef,
             ioActor: ActorRef,
-            workflowLogConfigurationOption: Option[WorkflowLogConfiguration] =
-            WorkflowLogger.workflowLogConfiguration,
+            workflowLogConfigurationOption: Option[WorkflowLogConfiguration] = WorkflowLogger.workflowLogConfiguration,
             /*
             The theory is that the `GcsBatchCommandBuilder` copies the temporary workflow logs from the local disk to
             GCS. Then later, the separate `DefaultIOCommandBuilder` deletes files from the local disk.
@@ -47,16 +46,17 @@ object CopyWorkflowLogsActor {
             implemented, It Works (TM), and I'm not changing it for now.
              */
             copyCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder,
-            deleteCommandBuilder: IoCommandBuilder = DefaultIoCommandBuilder,
-           ): Props = {
-    Props(new CopyWorkflowLogsActor(
-      serviceRegistryActor = serviceRegistryActor,
-      ioActor = ioActor,
-      workflowLogConfigurationOption = workflowLogConfigurationOption,
-      copyCommandBuilder = copyCommandBuilder,
-      deleteCommandBuilder = deleteCommandBuilder,
-    )).withDispatcher(IoDispatcher)
-  }
+            deleteCommandBuilder: IoCommandBuilder = DefaultIoCommandBuilder
+  ): Props =
+    Props(
+      new CopyWorkflowLogsActor(
+        serviceRegistryActor = serviceRegistryActor,
+        ioActor = ioActor,
+        workflowLogConfigurationOption = workflowLogConfigurationOption,
+        copyCommandBuilder = copyCommandBuilder,
+        deleteCommandBuilder = deleteCommandBuilder
+      )
+    ).withDispatcher(IoDispatcher)
 }
 
 // This could potentially be turned into a more generic "Copy/Move something from A to B"
@@ -65,9 +65,12 @@ class CopyWorkflowLogsActor(override val serviceRegistryActor: ActorRef,
                             override val ioActor: ActorRef,
                             workflowLogConfigurationOption: Option[WorkflowLogConfiguration],
                             copyCommandBuilder: IoCommandBuilder,
-                            deleteCommandBuilder: IoCommandBuilder,
-                           ) extends Actor
-  with ActorLogging with IoClientHelper with WorkflowMetadataHelper with MonitoringCompanionHelper {
+                            deleteCommandBuilder: IoCommandBuilder
+) extends Actor
+    with ActorLogging
+    with IoClientHelper
+    with WorkflowMetadataHelper
+    with MonitoringCompanionHelper {
 
   implicit val ec: ExecutionContext = context.dispatcher
 
@@ -87,9 +90,10 @@ class CopyWorkflowLogsActor(override val serviceRegistryActor: ActorRef,
         removeWork()
     }
   } else removeWork()
-  
+
   private def updateLogsPathInMetadata(workflowId: WorkflowId, path: Path): Unit = {
-    val metadataEventMsg = MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.WorkflowLog), MetadataValue(path.pathAsString))
+    val metadataEventMsg =
+      MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.WorkflowLog), MetadataValue(path.pathAsString))
     serviceRegistryActor ! PutMetadataAction(metadataEventMsg)
   }
 
@@ -111,30 +115,31 @@ class CopyWorkflowLogsActor(override val serviceRegistryActor: ActorRef,
             case Failure(failure) =>
               log.error(
                 cause = failure,
-                message =
-                  s"Failed to copy workflow logs from ${src.pathAsString} to ${destPath.pathAsString}: " +
-                    s"${failure.getMessage}",
+                message = s"Failed to copy workflow logs from ${src.pathAsString} to ${destPath.pathAsString}: " +
+                  s"${failure.getMessage}"
               )
               deleteLog(src)
             case Success(_) =>
-              // Deliberately not deleting the file here, that will be done in batch in `deleteLog`
-              // after the copy is terminal.
+            // Deliberately not deleting the file here, that will be done in batch in `deleteLog`
+            // after the copy is terminal.
           }
           workflowLogger.close()
         }
       }
-      
+
     case (workflowId: WorkflowId, IoSuccess(copy: IoCopyCommand, _)) =>
       updateLogsPathInMetadata(workflowId, copy.destination)
       deleteLog(copy.source)
-      
+
     case (workflowId: WorkflowId, IoFailAck(copy: IoCopyCommand, failure)) =>
       pushWorkflowFailures(workflowId, List(new IOException("Could not copy workflow logs", failure)))
-      log.error(failure, s"Failed to copy workflow logs from ${copy.source.pathAsString} to ${copy.destination.pathAsString}")
+      log.error(failure,
+                s"Failed to copy workflow logs from ${copy.source.pathAsString} to ${copy.destination.pathAsString}"
+      )
       deleteLog(copy.source)
-      
+
     case IoSuccess(_: IoDeleteCommand, _) => removeWork()
-      
+
     case IoFailAck(delete: IoDeleteCommand, failure) =>
       removeWork()
       log.error(failure, s"Failed to delete workflow logs from ${delete.file.pathAsString}")
@@ -148,13 +153,14 @@ class CopyWorkflowLogsActor(override val serviceRegistryActor: ActorRef,
   override def receive: Receive = monitoringReceive orElse ioReceive orElse copyLogsReceive
   /*_*/
 
-  override def preRestart(t: Throwable, message: Option[Any]): Unit = {
+  override def preRestart(t: Throwable, message: Option[Any]): Unit =
     message foreach self.forward
-  }
 
   override protected def onTimeout(message: Any, to: ActorRef): Unit = message match {
     case copy: IoCopyCommand =>
-      log.error(s"Failed to copy workflow logs from ${copy.source.pathAsString} to ${copy.destination.pathAsString}: Timeout")
+      log.error(
+        s"Failed to copy workflow logs from ${copy.source.pathAsString} to ${copy.destination.pathAsString}: Timeout"
+      )
       deleteLog(copy.source)
     case delete: IoDeleteCommand =>
       log.error(s"Failed to delete workflow logs from ${delete.file.pathAsString}: Timeout")
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowOutputsActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowOutputsActor.scala
index b6fa6b285a6..142a6623fcd 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowOutputsActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowOutputsActor.scala
@@ -3,8 +3,18 @@ package cromwell.engine.workflow.lifecycle.finalization
 import akka.actor.{Actor, ActorLogging, ActorRef, Props}
 import akka.event.LoggingReceive
 import cromwell.backend.BackendLifecycleActor.BackendWorkflowLifecycleActorResponse
-import cromwell.backend.BackendWorkflowFinalizationActor.{FinalizationFailed, FinalizationResponse, FinalizationSuccess, Finalize}
-import cromwell.backend.{AllBackendInitializationData, BackendConfigurationDescriptor, BackendInitializationData, BackendLifecycleActorFactory}
+import cromwell.backend.BackendWorkflowFinalizationActor.{
+  FinalizationFailed,
+  FinalizationResponse,
+  FinalizationSuccess,
+  Finalize
+}
+import cromwell.backend.{
+  AllBackendInitializationData,
+  BackendConfigurationDescriptor,
+  BackendInitializationData,
+  BackendLifecycleActorFactory
+}
 import cromwell.core.Dispatcher.IoDispatcher
 import cromwell.core.WorkflowOptions._
 import cromwell.core._
@@ -19,26 +29,36 @@ import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success}
 
 object CopyWorkflowOutputsActor {
-  def props(workflowId: WorkflowId, ioActor: ActorRef, workflowDescriptor: EngineWorkflowDescriptor, workflowOutputs: CallOutputs,
-            initializationData: AllBackendInitializationData) = Props(
+  def props(workflowId: WorkflowId,
+            ioActor: ActorRef,
+            workflowDescriptor: EngineWorkflowDescriptor,
+            workflowOutputs: CallOutputs,
+            initializationData: AllBackendInitializationData
+  ) = Props(
     new CopyWorkflowOutputsActor(workflowId, ioActor, workflowDescriptor, workflowOutputs, initializationData)
   ).withDispatcher(IoDispatcher)
 }
 
-class CopyWorkflowOutputsActor(workflowId: WorkflowId, override val ioActor: ActorRef, val workflowDescriptor: EngineWorkflowDescriptor, workflowOutputs: CallOutputs,
-                               initializationData: AllBackendInitializationData)
-  extends Actor with ActorLogging with PathFactory with AsyncIoActorClient {
+class CopyWorkflowOutputsActor(workflowId: WorkflowId,
+                               override val ioActor: ActorRef,
+                               val workflowDescriptor: EngineWorkflowDescriptor,
+                               workflowOutputs: CallOutputs,
+                               initializationData: AllBackendInitializationData
+) extends Actor
+    with ActorLogging
+    with PathFactory
+    with AsyncIoActorClient {
   override lazy val ioCommandBuilder = GcsBatchCommandBuilder
   implicit val ec = context.dispatcher
   override val pathBuilders = workflowDescriptor.pathBuilders
 
-  override def receive = LoggingReceive {
-    case Finalize => performActionThenRespond(afterAll()(context.dispatcher), FinalizationFailed)(context.dispatcher)
+  override def receive = LoggingReceive { case Finalize =>
+    performActionThenRespond(afterAll()(context.dispatcher), FinalizationFailed)(context.dispatcher)
   }
 
   private def performActionThenRespond(operation: => Future[BackendWorkflowLifecycleActorResponse],
-                                       onFailure: (Throwable) => BackendWorkflowLifecycleActorResponse)
-                                      (implicit ec: ExecutionContext) = {
+                                       onFailure: (Throwable) => BackendWorkflowLifecycleActorResponse
+  )(implicit ec: ExecutionContext) = {
     val respondTo: ActorRef = sender()
     operation onComplete {
       case Success(r) => respondTo ! r
@@ -53,34 +73,36 @@ class CopyWorkflowOutputsActor(workflowId: WorkflowId, override val ioActor: Act
     // Check if there are duplicated destination paths and throw an exception if that is the case.
     // This creates a map of destinations and source paths which point to them in cases where there are multiple
     // source paths that point to the same destination.
-    val duplicatedDestPaths: Map[Path, List[Path]] = outputFilePaths.groupBy{ case (_, destPath) => destPath}.collect {
-      case (destPath, list) if list.size > 1 => destPath -> list.map {case (source, _) => source}
-    }
+    val duplicatedDestPaths: Map[Path, List[Path]] =
+      outputFilePaths.groupBy { case (_, destPath) => destPath }.collect {
+        case (destPath, list) if list.size > 1 => destPath -> list.map { case (source, _) => source }
+      }
     if (duplicatedDestPaths.nonEmpty) {
       val formattedCollidingCopyOptions = duplicatedDestPaths.toList
-        .sortBy{case(dest, _) => dest.pathAsString} // Sort by destination path
+        .sortBy { case (dest, _) => dest.pathAsString } // Sort by destination path
         // Make a '/my/src -> /my/dest' copy tape string for each source and destination. Use flat map to get a single list
         // srcList is also sorted to get a deterministic output order. This is necessary for making sure the tests
         // for the error always succeed.
-        .flatMap{ case (dest, srcList) => srcList.sortBy(_.pathAsString).map(_.pathAsString + s" -> $dest")}
+        .flatMap { case (dest, srcList) => srcList.sortBy(_.pathAsString).map(_.pathAsString + s" -> $dest") }
       throw new IllegalStateException(
         "Cannot copy output files to given final_workflow_outputs_dir" +
-          s" as multiple files will be copied to the same path: \n${formattedCollidingCopyOptions.mkString("\n")}")}
+          s" as multiple files will be copied to the same path: \n${formattedCollidingCopyOptions.mkString("\n")}"
+      )
+    }
 
-    val copies = outputFilePaths map {
-      case (srcPath, dstPath) => asyncIo.copyAsync(srcPath, dstPath)
+    val copies = outputFilePaths map { case (srcPath, dstPath) =>
+      asyncIo.copyAsync(srcPath, dstPath)
     }
 
     Future.sequence(copies)
   }
 
-  private def findFiles(values: Seq[WomValue]): Seq[WomSingleFile] = {
+  private def findFiles(values: Seq[WomValue]): Seq[WomSingleFile] =
     values flatMap {
-      _.collectAsSeq {
-        case file: WomSingleFile => file
+      _.collectAsSeq { case file: WomSingleFile =>
+        file
       }
     }
-  }
 
   private def getOutputFilePaths(workflowOutputsPath: Path): List[(Path, Path)] = {
 
@@ -100,42 +122,37 @@ class CopyWorkflowOutputsActor(workflowId: WorkflowId, override val ioActor: Act
     // "execution" should be optional, because its not created on AWS.
     // Also cacheCopy or attempt-<int> folders are optional.
     lazy val truncateRegex = ".*/call-[^/]*/(shard-[0-9]+/)?(cacheCopy/)?(attempt-[0-9]+/)?(execution/)?".r
-    val outputFileDestinations = rootAndFiles flatMap {
-      case (workflowRoot, outputs) =>
-        outputs map { output =>
-          val outputPath = PathFactory.buildPath(output, pathBuilders)
-          outputPath -> {
-            if (useRelativeOutputPaths) {
-              val pathRelativeToExecDir = truncateRegex.replaceFirstIn(outputPath.pathAsString, "")
-              workflowOutputsPath.resolve(pathRelativeToExecDir)
-            }
-            else PathCopier.getDestinationFilePath(workflowRoot, outputPath, workflowOutputsPath)
-          }
+    val outputFileDestinations = rootAndFiles flatMap { case (workflowRoot, outputs) =>
+      outputs map { output =>
+        val outputPath = PathFactory.buildPath(output, pathBuilders)
+        outputPath -> {
+          if (useRelativeOutputPaths) {
+            val pathRelativeToExecDir = truncateRegex.replaceFirstIn(outputPath.pathAsString, "")
+            workflowOutputsPath.resolve(pathRelativeToExecDir)
+          } else PathCopier.getDestinationFilePath(workflowRoot, outputPath, workflowOutputsPath)
         }
+      }
     }
     outputFileDestinations.distinct.toList
   }
 
-  private def getBackendRootPath(backend: String, config: BackendConfigurationDescriptor): Option[Path] = {
+  private def getBackendRootPath(backend: String, config: BackendConfigurationDescriptor): Option[Path] =
     getBackendFactory(backend) map getRootPath(config, initializationData.get(backend))
-  }
 
-  private def getBackendFactory(backend: String): Option[BackendLifecycleActorFactory] = {
+  private def getBackendFactory(backend: String): Option[BackendLifecycleActorFactory] =
     CromwellBackends.backendLifecycleFactoryActorByName(backend).toOption
-  }
 
-  private def getRootPath(config: BackendConfigurationDescriptor, initializationData: Option[BackendInitializationData])
-                         (backendFactory: BackendLifecycleActorFactory): Path = {
+  private def getRootPath(config: BackendConfigurationDescriptor,
+                          initializationData: Option[BackendInitializationData]
+  )(backendFactory: BackendLifecycleActorFactory): Path =
     backendFactory.getExecutionRootPath(workflowDescriptor.backendDescriptor, config.backendConfig, initializationData)
-  }
 
   /**
     * Happens after everything else runs
     */
-  final def afterAll()(implicit ec: ExecutionContext): Future[FinalizationResponse] = {
+  final def afterAll()(implicit ec: ExecutionContext): Future[FinalizationResponse] =
     workflowDescriptor.getWorkflowOption(FinalWorkflowOutputsDir) match {
       case Some(outputs) => copyWorkflowOutputs(outputs) map { _ => FinalizationSuccess }
       case None => Future.successful(FinalizationSuccess)
     }
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
index c8eb1790365..bd5547e0252 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
@@ -36,16 +36,16 @@ import java.time.Instant
 import java.util.concurrent.Executors
 import scala.util.{Failure, Success}
 
-
 case class WorkflowCallbackConfig(enabled: Boolean,
                                   numThreads: Int,
                                   retryBackoff: SimpleExponentialBackoff,
                                   maxRetries: Int,
                                   defaultUri: Option[URI], // May be overridden by workflow options
-                                  authMethod: Option[WorkflowCallbackConfig.AuthMethod])
+                                  authMethod: Option[WorkflowCallbackConfig.AuthMethod]
+)
 
 object WorkflowCallbackConfig extends LazyLogging {
-  sealed trait AuthMethod { def getAccessToken:  ErrorOr.ErrorOr[String]  }
+  sealed trait AuthMethod { def getAccessToken: ErrorOr.ErrorOr[String] }
   case object AzureAuth extends AuthMethod {
     override def getAccessToken: ErrorOr.ErrorOr[String] = AzureCredentials.getAccessToken()
   }
@@ -55,13 +55,19 @@ object WorkflowCallbackConfig extends LazyLogging {
   private lazy val defaultMaxRetries = 10
 
   def empty: WorkflowCallbackConfig = WorkflowCallbackConfig(
-    false, defaultNumThreads, defaultRetryBackoff, defaultMaxRetries, None, None
+    false,
+    defaultNumThreads,
+    defaultRetryBackoff,
+    defaultMaxRetries,
+    None,
+    None
   )
 
   def apply(config: Config): WorkflowCallbackConfig = {
     val enabled = config.as[Boolean]("enabled")
     val numThreads = config.as[Option[Int]]("num-threads").getOrElse(defaultNumThreads)
-    val backoff = config.as[Option[Config]]("request-backoff").map(SimpleExponentialBackoff(_)).getOrElse(defaultRetryBackoff)
+    val backoff =
+      config.as[Option[Config]]("request-backoff").map(SimpleExponentialBackoff(_)).getOrElse(defaultRetryBackoff)
     val maxRetries = config.as[Option[Int]]("max-retries").getOrElse(defaultMaxRetries)
     val uri = config.as[Option[String]]("endpoint").flatMap(createAndValidateUri)
 
@@ -79,14 +85,13 @@ object WorkflowCallbackConfig extends LazyLogging {
     )
   }
 
-  def createAndValidateUri(uriString: String): Option[URI] = {
+  def createAndValidateUri(uriString: String): Option[URI] =
     Try(new URI(uriString)) match {
       case Success(uri) => Option(uri)
       case Failure(err) =>
         logger.warn(s"Failed to parse provided workflow callback URI (${uriString}): $err")
         None
     }
-  }
 }
 
 /**
@@ -100,23 +105,22 @@ object WorkflowCallbackActor {
                                           uri: Option[String],
                                           terminalState: WorkflowState,
                                           workflowOutputs: CallOutputs,
-                                          failureMessage: List[String])
+                                          failureMessage: List[String]
+  )
 
   def props(serviceRegistryActor: ActorRef,
             callbackConfig: WorkflowCallbackConfig,
             httpClient: CallbackHttpHandler = CallbackHttpHandlerImpl
-           ) = Props(
-    new WorkflowCallbackActor(
-      serviceRegistryActor,
-      callbackConfig,
-      httpClient)
+  ) = Props(
+    new WorkflowCallbackActor(serviceRegistryActor, callbackConfig, httpClient)
   ).withDispatcher(IoDispatcher)
 }
 
 class WorkflowCallbackActor(serviceRegistryActor: ActorRef,
                             config: WorkflowCallbackConfig,
-                            httpClient: CallbackHttpHandler)
-  extends Actor with ActorLogging {
+                            httpClient: CallbackHttpHandler
+) extends Actor
+    with ActorLogging {
 
   // Create a dedicated thread pool for this actor so its damage is limited if we end up with
   // too many threads all taking a long time to do callbacks. If we're frequently saturating
@@ -130,32 +134,50 @@ class WorkflowCallbackActor(serviceRegistryActor: ActorRef,
     case PerformCallbackCommand(workflowId, requestedCallbackUri, terminalState, outputs, failures) =>
       // If no uri was provided to us here, fall back to the one in config. If there isn't
       // one there, do not perform a callback.
-      val callbackUri: Option[URI] = requestedCallbackUri.map(WorkflowCallbackConfig.createAndValidateUri).getOrElse(config.defaultUri)
-      callbackUri.map { uri =>
-        performCallback(workflowId, uri, terminalState, outputs, failures) onComplete {
-          case Success(_) =>
-            log.info(s"Successfully sent callback for workflow for workflow $workflowId in state $terminalState to $uri")
-            sendMetadata(workflowId, successful = true, uri)
-          case Failure(t) =>
-            log.warning(s"Permanently failed to send callback for workflow $workflowId in state $terminalState to $uri: ${t.getMessage}")
-            sendMetadata(workflowId, successful = false, uri)
+      val callbackUri: Option[URI] =
+        requestedCallbackUri.map(WorkflowCallbackConfig.createAndValidateUri).getOrElse(config.defaultUri)
+      callbackUri
+        .map { uri =>
+          performCallback(workflowId, uri, terminalState, outputs, failures) onComplete {
+            case Success(_) =>
+              log.info(
+                s"Successfully sent callback for workflow for workflow $workflowId in state $terminalState to $uri"
+              )
+              sendMetadata(workflowId, successful = true, uri)
+            case Failure(t) =>
+              log.warning(
+                s"Permanently failed to send callback for workflow $workflowId in state $terminalState to $uri: ${t.getMessage}"
+              )
+              sendMetadata(workflowId, successful = false, uri)
+          }
         }
-      }.getOrElse(())
+        .getOrElse(())
     case Broadcast(ShutdownCommand) | ShutdownCommand => context stop self
     case other => log.warning(s"WorkflowCallbackActor received an unexpected message: $other")
   }
 
-  private def makeHeaders: Future[List[HttpHeader]] = {
-    config.authMethod.toList.map(_.getAccessToken).map {
-      case Valid(header) => Future.successful(header)
-      case Invalid(err) => Future.failed(new RuntimeException(err.toString))
-    }
+  private def makeHeaders: Future[List[HttpHeader]] =
+    config.authMethod.toList
+      .map(_.getAccessToken)
+      .map {
+        case Valid(header) => Future.successful(header)
+        case Invalid(err) => Future.failed(new RuntimeException(err.toString))
+      }
       .map(t => t.map(t => RawHeader("Authorization", s"Bearer $t")))
       .traverse(identity)
-  }
 
-  private def performCallback(workflowId: WorkflowId, callbackUri: URI, terminalState: WorkflowState, outputs: CallOutputs, failures: List[String]): Future[Done] = {
-    val callbackPostBody = CallbackMessage(workflowId.toString, terminalState.toString, outputs.outputs.map(entry => (entry._1.identifier.fullyQualifiedName.value, entry._2)), failures)
+  private def performCallback(workflowId: WorkflowId,
+                              callbackUri: URI,
+                              terminalState: WorkflowState,
+                              outputs: CallOutputs,
+                              failures: List[String]
+  ): Future[Done] = {
+    val callbackPostBody = CallbackMessage(
+      workflowId.toString,
+      terminalState.toString,
+      outputs.outputs.map(entry => (entry._1.identifier.fullyQualifiedName.value, entry._2)),
+      failures
+    )
     for {
       entity <- Marshal(callbackPostBody).to[RequestEntity]
       headers <- makeHeaders
@@ -164,7 +186,10 @@ class WorkflowCallbackActor(serviceRegistryActor: ActorRef,
         () => sendRequestOrFail(request),
         backoff = config.retryBackoff,
         maxRetries = Option(config.maxRetries),
-        onRetry = err => log.warning(s"Will retry after failure to send workflow callback for workflow $workflowId in state $terminalState to $callbackUri : $err")
+        onRetry = err =>
+          log.warning(
+            s"Will retry after failure to send workflow callback for workflow $workflowId in state $terminalState to $callbackUri : $err"
+          )
       )
       result <-
         // Akka will get upset if we have a response body and leave it totally unread.
@@ -174,15 +199,17 @@ class WorkflowCallbackActor(serviceRegistryActor: ActorRef,
   }
 
   private def sendRequestOrFail(request: HttpRequest): Future[HttpResponse] =
-    httpClient.sendRequest(request).flatMap(response =>
-      if (response.status.isFailure()) {
-        response.entity.dataBytes.runFold(ByteString(""))(_ ++ _).map(_.utf8String) flatMap { errorBody =>
-          Future.failed(
-            new RuntimeException(s"HTTP ${response.status.value}: $errorBody")
-          )
-        }
-      } else Future.successful(response)
-    )
+    httpClient
+      .sendRequest(request)
+      .flatMap(response =>
+        if (response.status.isFailure()) {
+          response.entity.dataBytes.runFold(ByteString(""))(_ ++ _).map(_.utf8String) flatMap { errorBody =>
+            Future.failed(
+              new RuntimeException(s"HTTP ${response.status.value}: $errorBody")
+            )
+          }
+        } else Future.successful(response)
+      )
 
   private def sendMetadata(workflowId: WorkflowId, successful: Boolean, uri: URI): Unit = {
     val events = List(
@@ -210,7 +237,6 @@ trait CallbackHttpHandler {
 }
 
 object CallbackHttpHandlerImpl extends CallbackHttpHandler {
-  override def sendRequest(httpRequest: HttpRequest)(implicit actorSystem: ActorSystem): Future[HttpResponse] = {
+  override def sendRequest(httpRequest: HttpRequest)(implicit actorSystem: ActorSystem): Future[HttpResponse] =
     Http().singleRequest(httpRequest)
-  }
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackJsonSupport.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackJsonSupport.scala
index eb9b1c7ea9e..42eb4991c47 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackJsonSupport.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackJsonSupport.scala
@@ -7,7 +7,8 @@ import wom.values.WomValue
 final case class CallbackMessage(workflowId: String,
                                  state: String,
                                  outputs: Map[String, WomValue],
-                                 failures: List[String])
+                                 failures: List[String]
+)
 
 object WorkflowCallbackJsonSupport extends DefaultJsonProtocol {
   implicit val callbackMessageFormat = jsonFormat4(CallbackMessage)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowFinalizationActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowFinalizationActor.scala
index 8731367cfb7..d94c8033584 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowFinalizationActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowFinalizationActor.scala
@@ -46,16 +46,18 @@ object WorkflowFinalizationActor {
             jobExecutionMap: JobExecutionMap,
             workflowOutputs: CallOutputs,
             initializationData: AllBackendInitializationData,
-            copyWorkflowOutputsActor: Option[Props]): Props = {
-    Props(new WorkflowFinalizationActor(
-      workflowDescriptor,
-      ioActor,
-      jobExecutionMap,
-      workflowOutputs,
-      initializationData,
-      copyWorkflowOutputsActor
-    )).withDispatcher(EngineDispatcher)
-  }
+            copyWorkflowOutputsActor: Option[Props]
+  ): Props =
+    Props(
+      new WorkflowFinalizationActor(
+        workflowDescriptor,
+        ioActor,
+        jobExecutionMap,
+        workflowOutputs,
+        initializationData,
+        copyWorkflowOutputsActor
+      )
+    ).withDispatcher(EngineDispatcher)
 }
 
 case class WorkflowFinalizationActor(workflowDescriptor: EngineWorkflowDescriptor,
@@ -63,8 +65,8 @@ case class WorkflowFinalizationActor(workflowDescriptor: EngineWorkflowDescripto
                                      jobExecutionMap: JobExecutionMap,
                                      workflowOutputs: CallOutputs,
                                      initializationData: AllBackendInitializationData,
-                                     copyWorkflowOutputsActorProps: Option[Props])
-  extends WorkflowLifecycleActor[WorkflowFinalizationActorState] {
+                                     copyWorkflowOutputsActorProps: Option[Props]
+) extends WorkflowLifecycleActor[WorkflowFinalizationActorState] {
 
   override lazy val workflowIdForLogging = workflowDescriptor.possiblyNotRootWorkflowId
   override lazy val rootWorkflowIdForLogging = workflowDescriptor.rootWorkflowId
@@ -79,63 +81,72 @@ case class WorkflowFinalizationActor(workflowDescriptor: EngineWorkflowDescripto
   override def failureResponse(reasons: Seq[Throwable]) = WorkflowFinalizationFailedResponse(reasons)
 
   // If an engine or backend finalization actor (children of this actor) dies, send ourselves the failure and stop the child actor
-  override def supervisorStrategy = OneForOneStrategy() {
-    case failure =>
-      self.tell(FinalizationFailed(failure), sender())
-      Stop
+  override def supervisorStrategy = OneForOneStrategy() { case failure =>
+    self.tell(FinalizationFailed(failure), sender())
+    Stop
   }
 
   startWith(FinalizationPendingState, WorkflowLifecycleActorData.empty)
 
-  when(FinalizationPendingState) {
-    case Event(StartFinalizationCommand, _) =>
-      val backendFinalizationActors = Try {
-        for {
-          (backend, calls) <- workflowDescriptor.backendAssignments.groupBy(_._2).safeMapValues(_.keySet)
-          props <- CromwellBackends.backendLifecycleFactoryActorByName(backend).map(
-            _.workflowFinalizationActorProps(workflowDescriptor.backendDescriptor, ioActor, calls, filterJobExecutionsForBackend(calls), workflowOutputs, initializationData.get(backend))
-          ).valueOr(errors => throw AggregatedMessageException("Cannot validate backend factories", errors.toList))
-          actor = context.actorOf(props, backend)
-        } yield actor
-      }
-
-      val engineFinalizationActor = Try { copyWorkflowOutputsActorProps.map(context.actorOf(_, "CopyWorkflowOutputsActor")).toList }
-
-      val allActors = for {
-        backendFinalizationActorsFromTry <- backendFinalizationActors
-        engineFinalizationActorFromTry <- engineFinalizationActor
-      } yield backendFinalizationActorsFromTry.toList ++ engineFinalizationActorFromTry
-
-      allActors match {
-        case Failure(ex) =>
-          sender() ! WorkflowFinalizationFailedResponse(Seq(ex))
-          goto(WorkflowFinalizationFailedState)
-        case Success(actors) if actors.isEmpty =>
-          sender() ! WorkflowFinalizationSucceededResponse
-          goto(FinalizationSucceededState)
-        case Success(actors) =>
-          val actorSet = actors.toSet
-          actorSet.foreach(_ ! Finalize)
-          goto(FinalizationInProgressState) using stateData.withActors(actorSet)
-        case _ =>
-          goto(WorkflowFinalizationFailedState)
-      }
+  when(FinalizationPendingState) { case Event(StartFinalizationCommand, _) =>
+    val backendFinalizationActors = Try {
+      for {
+        (backend, calls) <- workflowDescriptor.backendAssignments.groupBy(_._2).safeMapValues(_.keySet)
+        props <- CromwellBackends
+          .backendLifecycleFactoryActorByName(backend)
+          .map(
+            _.workflowFinalizationActorProps(workflowDescriptor.backendDescriptor,
+                                             ioActor,
+                                             calls,
+                                             filterJobExecutionsForBackend(calls),
+                                             workflowOutputs,
+                                             initializationData.get(backend)
+            )
+          )
+          .valueOr(errors => throw AggregatedMessageException("Cannot validate backend factories", errors.toList))
+        actor = context.actorOf(props, backend)
+      } yield actor
+    }
+
+    val engineFinalizationActor = Try {
+      copyWorkflowOutputsActorProps.map(context.actorOf(_, "CopyWorkflowOutputsActor")).toList
+    }
+
+    val allActors = for {
+      backendFinalizationActorsFromTry <- backendFinalizationActors
+      engineFinalizationActorFromTry <- engineFinalizationActor
+    } yield backendFinalizationActorsFromTry.toList ++ engineFinalizationActorFromTry
+
+    allActors match {
+      case Failure(ex) =>
+        sender() ! WorkflowFinalizationFailedResponse(Seq(ex))
+        goto(WorkflowFinalizationFailedState)
+      case Success(actors) if actors.isEmpty =>
+        sender() ! WorkflowFinalizationSucceededResponse
+        goto(FinalizationSucceededState)
+      case Success(actors) =>
+        val actorSet = actors.toSet
+        actorSet.foreach(_ ! Finalize)
+        goto(FinalizationInProgressState) using stateData.withActors(actorSet)
+      case _ =>
+        goto(WorkflowFinalizationFailedState)
+    }
   }
 
   // Only send to each backend the jobs that it executed
-  private def filterJobExecutionsForBackend(calls: Set[CommandCallNode]): JobExecutionMap = {
-    jobExecutionMap map {
-      case (wd, executedKeys) => wd -> (executedKeys filter { jobKey => calls.contains(jobKey.call) })
-    } filter {
-      case (_, keys) => keys.nonEmpty
+  private def filterJobExecutionsForBackend(calls: Set[CommandCallNode]): JobExecutionMap =
+    jobExecutionMap map { case (wd, executedKeys) =>
+      wd -> (executedKeys filter { jobKey => calls.contains(jobKey.call) })
+    } filter { case (_, keys) =>
+      keys.nonEmpty
     }
-  }
 
   when(FinalizationInProgressState) {
     case Event(FinalizationSuccess, stateData) => checkForDoneAndTransition(stateData.withSuccess(sender()))
-    case Event(FinalizationFailed(reason), stateData) => checkForDoneAndTransition(stateData.withFailure(sender(), reason))
+    case Event(FinalizationFailed(reason), stateData) =>
+      checkForDoneAndTransition(stateData.withFailure(sender(), reason))
   }
 
-  when(FinalizationSucceededState) { FSM.NullFunction }
-  when(WorkflowFinalizationFailedState) { FSM.NullFunction }
+  when(FinalizationSucceededState)(FSM.NullFunction)
+  when(WorkflowFinalizationFailedState)(FSM.NullFunction)
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/initialization/WorkflowInitializationActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/initialization/WorkflowInitializationActor.scala
index 2c0e8cb5fd3..6af8d7e6116 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/initialization/WorkflowInitializationActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/initialization/WorkflowInitializationActor.scala
@@ -12,7 +12,11 @@ import cromwell.engine.EngineWorkflowDescriptor
 import cromwell.engine.backend.CromwellBackends
 import cromwell.engine.workflow.lifecycle.WorkflowLifecycleActor._
 import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor._
-import cromwell.engine.workflow.lifecycle.{AbortableWorkflowLifecycleActor, EngineLifecycleActorAbortCommand, EngineLifecycleActorAbortedResponse}
+import cromwell.engine.workflow.lifecycle.{
+  AbortableWorkflowLifecycleActor,
+  EngineLifecycleActorAbortCommand,
+  EngineLifecycleActorAbortedResponse
+}
 
 import scala.util.{Failure, Success, Try}
 
@@ -22,7 +26,9 @@ object WorkflowInitializationActor {
     * States
     */
   sealed trait WorkflowInitializationActorState extends WorkflowLifecycleActorState
-  sealed trait WorkflowInitializationActorTerminalState extends WorkflowInitializationActorState with WorkflowLifecycleActorTerminalState
+  sealed trait WorkflowInitializationActorTerminalState
+      extends WorkflowInitializationActorState
+      with WorkflowLifecycleActorTerminalState
 
   case object InitializationPendingState extends WorkflowInitializationActorState
   case object InitializationInProgressState extends WorkflowInitializationActorState
@@ -41,25 +47,33 @@ object WorkflowInitializationActor {
     * Responses
     */
   sealed trait WorkflowInitializationResponse
-  final case class WorkflowInitializationSucceededResponse(initializationData: AllBackendInitializationData) extends WorkflowLifecycleSuccessResponse with WorkflowInitializationResponse
-  case object WorkflowInitializationAbortedResponse extends EngineLifecycleActorAbortedResponse with WorkflowInitializationResponse
-  final case class WorkflowInitializationFailedResponse(reasons: Seq[Throwable]) extends WorkflowLifecycleFailureResponse with WorkflowInitializationResponse
+  final case class WorkflowInitializationSucceededResponse(initializationData: AllBackendInitializationData)
+      extends WorkflowLifecycleSuccessResponse
+      with WorkflowInitializationResponse
+  case object WorkflowInitializationAbortedResponse
+      extends EngineLifecycleActorAbortedResponse
+      with WorkflowInitializationResponse
+  final case class WorkflowInitializationFailedResponse(reasons: Seq[Throwable])
+      extends WorkflowLifecycleFailureResponse
+      with WorkflowInitializationResponse
 
   def props(workflowIdForLogging: PossiblyNotRootWorkflowId,
             rootWorkflowIdForLogging: RootWorkflowId,
             workflowDescriptor: EngineWorkflowDescriptor,
             ioActor: ActorRef,
             serviceRegistryActor: ActorRef,
-            restarting: Boolean): Props = {
-    Props(new WorkflowInitializationActor(
-      workflowIdForLogging = workflowIdForLogging,
-      rootWorkflowIdForLogging = rootWorkflowIdForLogging,
-      workflowDescriptor = workflowDescriptor,
-      ioActor = ioActor,
-      serviceRegistryActor = serviceRegistryActor,
-      restarting = restarting
-    )).withDispatcher(EngineDispatcher)
-  }
+            restarting: Boolean
+  ): Props =
+    Props(
+      new WorkflowInitializationActor(
+        workflowIdForLogging = workflowIdForLogging,
+        rootWorkflowIdForLogging = rootWorkflowIdForLogging,
+        workflowDescriptor = workflowDescriptor,
+        ioActor = ioActor,
+        serviceRegistryActor = serviceRegistryActor,
+        restarting = restarting
+      )
+    ).withDispatcher(EngineDispatcher)
 
   case class BackendActorAndBackend(actor: ActorRef, backend: String)
 }
@@ -69,8 +83,8 @@ case class WorkflowInitializationActor(workflowIdForLogging: PossiblyNotRootWork
                                        workflowDescriptor: EngineWorkflowDescriptor,
                                        ioActor: ActorRef,
                                        serviceRegistryActor: ActorRef,
-                                       restarting: Boolean)
-  extends AbortableWorkflowLifecycleActor[WorkflowInitializationActorState] {
+                                       restarting: Boolean
+) extends AbortableWorkflowLifecycleActor[WorkflowInitializationActorState] {
 
   startWith(InitializationPendingState, WorkflowLifecycleActorData.empty)
   val tag = self.path.name
@@ -83,7 +97,9 @@ case class WorkflowInitializationActor(workflowIdForLogging: PossiblyNotRootWork
   override def successResponse(data: WorkflowLifecycleActorData) = {
     val actorsToBackends = backendActorsAndBackends.map(ab => ab.actor -> ab.backend).toMap
     val actorsToData = data.successes.map(ad => ad.actor -> ad.data).toMap
-    val allBackendInitializationData = AllBackendInitializationData(actorsToBackends collect { case (a, b) => b -> actorsToData(a) })
+    val allBackendInitializationData = AllBackendInitializationData(actorsToBackends collect { case (a, b) =>
+      b -> actorsToData(a)
+    })
     WorkflowInitializationSucceededResponse(allBackendInitializationData)
   }
   override def failureResponse(reasons: Seq[Throwable]) = WorkflowInitializationFailedResponse(reasons)
@@ -96,9 +112,17 @@ case class WorkflowInitializationActor(workflowIdForLogging: PossiblyNotRootWork
       val backendInitializationActors = Try {
         for {
           (backend, calls) <- workflowDescriptor.backendAssignments.groupBy(_._2).safeMapValues(_.keySet)
-          props <- CromwellBackends.backendLifecycleFactoryActorByName(backend).map(factory =>
-            factory.workflowInitializationActorProps(workflowDescriptor.backendDescriptor, ioActor, calls, serviceRegistryActor, restarting)
-          ).valueOr(errors => throw AggregatedMessageException("Cannot validate backend factories", errors.toList))
+          props <- CromwellBackends
+            .backendLifecycleFactoryActorByName(backend)
+            .map(factory =>
+              factory.workflowInitializationActorProps(workflowDescriptor.backendDescriptor,
+                                                       ioActor,
+                                                       calls,
+                                                       serviceRegistryActor,
+                                                       restarting
+              )
+            )
+            .valueOr(errors => throw AggregatedMessageException("Cannot validate backend factories", errors.toList))
           actor = context.actorOf(props, backend)
         } yield BackendActorAndBackend(actor, backend)
       }
@@ -124,20 +148,24 @@ case class WorkflowInitializationActor(workflowIdForLogging: PossiblyNotRootWork
   }
 
   when(InitializationInProgressState) {
-    case Event(InitializationSuccess(initData), stateData) => checkForDoneAndTransition(stateData.withSuccess(sender(), initData))
-    case Event(InitializationFailed(reason), stateData) => checkForDoneAndTransition(stateData.withFailure(sender(), reason))
+    case Event(InitializationSuccess(initData), stateData) =>
+      checkForDoneAndTransition(stateData.withSuccess(sender(), initData))
+    case Event(InitializationFailed(reason), stateData) =>
+      checkForDoneAndTransition(stateData.withFailure(sender(), reason))
     case Event(EngineLifecycleActorAbortCommand, stateData) =>
       stateData.actors foreach { _ ! BackendWorkflowInitializationActor.Abort }
       goto(InitializationAbortingState)
   }
 
   when(InitializationAbortingState) {
-    case Event(InitializationSuccess(initData), stateData) => checkForDoneAndTransition(stateData.withSuccess(sender(), initData))
-    case Event(InitializationFailed(reason), stateData) => checkForDoneAndTransition(stateData.withFailure(sender(), reason))
+    case Event(InitializationSuccess(initData), stateData) =>
+      checkForDoneAndTransition(stateData.withSuccess(sender(), initData))
+    case Event(InitializationFailed(reason), stateData) =>
+      checkForDoneAndTransition(stateData.withFailure(sender(), reason))
     case Event(BackendActorAbortedResponse, stateData) => checkForDoneAndTransition(stateData.withAborted(sender()))
   }
 
-  when(InitializationSucceededState) { FSM.NullFunction }
-  when(InitializationFailedState) { FSM.NullFunction }
-  when(InitializationsAbortedState) { FSM.NullFunction }
+  when(InitializationSucceededState)(FSM.NullFunction)
+  when(InitializationFailedState)(FSM.NullFunction)
+  when(InitializationsAbortedState)(FSM.NullFunction)
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala
index 70365819fe5..6b515114149 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala
@@ -63,10 +63,22 @@ object MaterializeWorkflowDescriptorActor {
   // exception if not initialized yet.
   private def cromwellBackends = CromwellBackends.instance.get
 
-  def props(serviceRegistryActor: ActorRef, workflowId: WorkflowId, cromwellBackends: => CromwellBackends = cromwellBackends,
-            importLocalFilesystem: Boolean, ioActorProxy: ActorRef, hogGroup: HogGroup): Props = {
-    Props(new MaterializeWorkflowDescriptorActor(serviceRegistryActor, workflowId, cromwellBackends, importLocalFilesystem, ioActorProxy, hogGroup)).withDispatcher(EngineDispatcher)
-  }
+  def props(serviceRegistryActor: ActorRef,
+            workflowId: WorkflowId,
+            cromwellBackends: => CromwellBackends = cromwellBackends,
+            importLocalFilesystem: Boolean,
+            ioActorProxy: ActorRef,
+            hogGroup: HogGroup
+  ): Props =
+    Props(
+      new MaterializeWorkflowDescriptorActor(serviceRegistryActor,
+                                             workflowId,
+                                             cromwellBackends,
+                                             importLocalFilesystem,
+                                             ioActorProxy,
+                                             hogGroup
+      )
+    ).withDispatcher(EngineDispatcher)
 
   /*
   Commands
@@ -75,15 +87,19 @@ object MaterializeWorkflowDescriptorActor {
   case class MaterializeWorkflowDescriptorCommand(workflowSourceFiles: WorkflowSourceFilesCollection,
                                                   conf: Config,
                                                   callCachingEnabled: Boolean,
-                                                  invalidateBadCacheResults: Boolean) extends MaterializeWorkflowDescriptorActorMessage
+                                                  invalidateBadCacheResults: Boolean
+  ) extends MaterializeWorkflowDescriptorActorMessage
   case object MaterializeWorkflowDescriptorAbortCommand
 
   /*
   Responses
    */
   sealed trait WorkflowDescriptorMaterializationResult extends MaterializeWorkflowDescriptorActorMessage
-  case class MaterializeWorkflowDescriptorSuccessResponse(workflowDescriptor: EngineWorkflowDescriptor) extends WorkflowDescriptorMaterializationResult
-  case class MaterializeWorkflowDescriptorFailureResponse(reason: Throwable) extends Exception with WorkflowDescriptorMaterializationResult
+  case class MaterializeWorkflowDescriptorSuccessResponse(workflowDescriptor: EngineWorkflowDescriptor)
+      extends WorkflowDescriptorMaterializationResult
+  case class MaterializeWorkflowDescriptorFailureResponse(reason: Throwable)
+      extends Exception
+      with WorkflowDescriptorMaterializationResult
 
   /*
   States
@@ -102,30 +118,30 @@ object MaterializeWorkflowDescriptorActor {
 
   private[lifecycle] def validateCallCachingMode(workflowOptions: WorkflowOptions,
                                                  callCachingEnabled: Boolean,
-                                                 invalidateBadCacheResults: Boolean): ErrorOr[CallCachingMode] = {
+                                                 invalidateBadCacheResults: Boolean
+  ): ErrorOr[CallCachingMode] = {
 
-    def readOptionalOption(option: WorkflowOption): ErrorOr[Boolean] = {
+    def readOptionalOption(option: WorkflowOption): ErrorOr[Boolean] =
       workflowOptions.getBoolean(option.name) match {
         case Success(x) => x.validNel
         case Failure(_: OptionNotFoundException) => true.validNel
         case Failure(t) => t.getMessage.invalidNel
       }
-    }
 
     if (callCachingEnabled) {
       val readFromCache = readOptionalOption(ReadFromCache)
       val writeToCache = readOptionalOption(WriteToCache)
 
-      def errorOrCallCachingMode(callCachingOptions: CallCachingOptions): ErrorOr[CallCachingMode] = {
+      def errorOrCallCachingMode(callCachingOptions: CallCachingOptions): ErrorOr[CallCachingMode] =
         (readFromCache, writeToCache) mapN {
           case (false, false) => CallCachingOff
           case (true, false) => CallCachingActivity(ReadCache, callCachingOptions)
           case (false, true) => CallCachingActivity(WriteCache, callCachingOptions)
           case (true, true) => CallCachingActivity(ReadAndWriteCache, callCachingOptions)
         }
-      }
 
-      val errorOrMaybePrefixes: ErrorOr[Option[Vector[String]]] = workflowOptions.getVectorOfStrings("call_cache_hit_path_prefixes")
+      val errorOrMaybePrefixes: ErrorOr[Option[Vector[String]]] =
+        workflowOptions.getVectorOfStrings("call_cache_hit_path_prefixes")
 
       val errorOrCallCachingOptions: ErrorOr[CallCachingOptions] = errorOrMaybePrefixes.map { maybePrefixes =>
         CallCachingOptions(invalidateBadCacheResults, maybePrefixes)
@@ -134,8 +150,7 @@ object MaterializeWorkflowDescriptorActor {
         options <- errorOrCallCachingOptions
         mode <- errorOrCallCachingMode(options)
       } yield mode
-    }
-    else {
+    } else {
       CallCachingOff.validNel
     }
   }
@@ -144,23 +159,25 @@ object MaterializeWorkflowDescriptorActor {
   def validateMemoryRetryMultiplier(workflowOptions: WorkflowOptions): ErrorOr[Unit] = {
     val optionName = WorkflowOptions.MemoryRetryMultiplier.name
 
-    def refineMultiplier(value: Double): ErrorOr[Unit] = {
+    def refineMultiplier(value: Double): ErrorOr[Unit] =
       refineV[MemoryRetryMultiplier](value.toDouble) match {
         case Left(_) => s"Workflow option '$optionName' is invalid. It should be in the range 1.0 ≤ n ≤ 99.0".invalidNel
         case Right(_) => ().validNel
       }
-    }
 
     workflowOptions.get(optionName) match {
-      case Success(value) => Try(value.toDouble) match {
-        case Success(v) => refineMultiplier(v)
-        case Failure(e) => (s"Workflow option '$optionName' is invalid. It should be of type Double and in the range " +
-          s"1.0 ≤ n ≤ 99.0. Error: ${ExceptionUtils.getMessage(e)}").invalidNel
-      }
+      case Success(value) =>
+        Try(value.toDouble) match {
+          case Success(v) => refineMultiplier(v)
+          case Failure(e) =>
+            (s"Workflow option '$optionName' is invalid. It should be of type Double and in the range " +
+              s"1.0 ≤ n ≤ 99.0. Error: ${ExceptionUtils.getMessage(e)}").invalidNel
+        }
       case Failure(OptionNotFoundException(_)) =>
         // This is an optional... option, so "not found" is fine
         ().validNel
-      case Failure(e) => s"'$optionName' is specified in workflow options but value is not of expected Double type: ${e.getMessage}".invalidNel
+      case Failure(e) =>
+        s"'$optionName' is specified in workflow options but value is not of expected Double type: ${e.getMessage}".invalidNel
     }
   }
 }
@@ -171,7 +188,10 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
                                          cromwellBackends: => CromwellBackends,
                                          importLocalFilesystem: Boolean,
                                          ioActorProxy: ActorRef,
-                                         hogGroup: HogGroup) extends LoggingFSM[MaterializeWorkflowDescriptorActorState, Unit] with StrictLogging with WorkflowLogging {
+                                         hogGroup: HogGroup
+) extends LoggingFSM[MaterializeWorkflowDescriptorActorState, Unit]
+    with StrictLogging
+    with WorkflowLogging {
 
   import MaterializeWorkflowDescriptorActor._
   val tag = self.path.name
@@ -186,27 +206,32 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
 
   startWith(ReadyToMaterializeState, ())
 
-
   when(ReadyToMaterializeState) {
 
-    case Event(MaterializeWorkflowDescriptorCommand(workflowSourceFiles, conf, callCachingEnabled, invalidateBadCacheResults), _) =>
+    case Event(MaterializeWorkflowDescriptorCommand(workflowSourceFiles,
+                                                    conf,
+                                                    callCachingEnabled,
+                                                    invalidateBadCacheResults
+               ),
+               _
+        ) =>
       val replyTo = sender()
       workflowOptionsAndPathBuilders(workflowSourceFiles) match {
         case (workflowOptions, pathBuilders) =>
           val futureDescriptor: Future[ErrorOr[EngineWorkflowDescriptor]] = pathBuilders flatMap { pb =>
-            val engineIoFunctions = new EngineIoFunctions(pb, new AsyncIo(ioActorProxy, GcsBatchCommandBuilder), iOExecutionContext)
-            buildWorkflowDescriptor(
-              workflowId,
-              workflowSourceFiles,
-              conf,
-              callCachingEnabled,
-              invalidateBadCacheResults,
-              workflowOptions,
-              pb,
-              engineIoFunctions)
-              .value
-              .unsafeToFuture().
-              map(_.toValidated)
+            val engineIoFunctions =
+              new EngineIoFunctions(pb, new AsyncIo(ioActorProxy, GcsBatchCommandBuilder), iOExecutionContext)
+            buildWorkflowDescriptor(workflowId,
+                                    workflowSourceFiles,
+                                    conf,
+                                    callCachingEnabled,
+                                    invalidateBadCacheResults,
+                                    workflowOptions,
+                                    pb,
+                                    engineIoFunctions
+            ).value
+              .unsafeToFuture()
+              .map(_.toValidated)
           }
 
           // Pipe the response to self, but make it look like it comes from the sender of the command
@@ -223,18 +248,21 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
     case Event(Valid(descriptor: EngineWorkflowDescriptor), _) =>
       sender() ! MaterializeWorkflowDescriptorSuccessResponse(descriptor)
       goto(MaterializationSuccessfulState)
-    case Event(Invalid(error: NonEmptyList[String]@unchecked), _) =>
+    case Event(Invalid(error: NonEmptyList[String] @unchecked), _) =>
       workflowInitializationFailed(error, sender())
       goto(MaterializationFailedState)
     case Event(Status.Failure(failure), _) =>
-      workflowInitializationFailed(NonEmptyList.of(failure.getMessage, failure.getStackTrace.toList.map(_.toString):_*), sender())
+      workflowInitializationFailed(
+        NonEmptyList.of(failure.getMessage, failure.getStackTrace.toList.map(_.toString): _*),
+        sender()
+      )
       goto(MaterializationFailedState)
   }
 
   // Let these fall through to the whenUnhandled handler:
-  when(MaterializationSuccessfulState) { FSM.NullFunction }
-  when(MaterializationFailedState) { FSM.NullFunction }
-  when(MaterializationAbortedState) { FSM.NullFunction }
+  when(MaterializationSuccessfulState)(FSM.NullFunction)
+  when(MaterializationFailedState)(FSM.NullFunction)
+  when(MaterializationAbortedState)(FSM.NullFunction)
 
   onTransition {
     case oldState -> terminalState if terminalState.terminal =>
@@ -252,17 +280,18 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
       stay()
   }
 
-  private def workflowInitializationFailed(errors: NonEmptyList[String], replyTo: ActorRef) = {
-    sender() ! MaterializeWorkflowDescriptorFailureResponse(
-      new IllegalArgumentException with MessageAggregation {
-        val exceptionContext = "Workflow input processing failed"
-        val errorMessages = errors.toList
-      })
-  }
+  private def workflowInitializationFailed(errors: NonEmptyList[String], replyTo: ActorRef) =
+    sender() ! MaterializeWorkflowDescriptorFailureResponse(new IllegalArgumentException with MessageAggregation {
+      val exceptionContext = "Workflow input processing failed"
+      val errorMessages = errors.toList
+    })
 
-  private def workflowOptionsAndPathBuilders(sourceFiles: WorkflowSourceFilesCollection): (WorkflowOptions, Future[List[PathBuilder]]) = {
+  private def workflowOptionsAndPathBuilders(
+    sourceFiles: WorkflowSourceFilesCollection
+  ): (WorkflowOptions, Future[List[PathBuilder]]) = {
     sourceFiles.workflowOptions
-    val pathBuilders = EngineFilesystems.pathBuildersForWorkflow(sourceFiles.workflowOptions, pathBuilderFactories)(context.system)
+    val pathBuilders =
+      EngineFilesystems.pathBuildersForWorkflow(sourceFiles.workflowOptions, pathBuilderFactories)(context.system)
     (sourceFiles.workflowOptions, pathBuilders)
   }
 
@@ -273,7 +302,8 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
                                       invalidateBadCacheResults: Boolean,
                                       workflowOptions: WorkflowOptions,
                                       pathBuilders: List[PathBuilder],
-                                      engineIoFunctions: EngineIoFunctions): IOChecked[EngineWorkflowDescriptor] = {
+                                      engineIoFunctions: EngineIoFunctions
+  ): IOChecked[EngineWorkflowDescriptor] = {
 
     def findFactory(workflowSource: WorkflowSource): ErrorOr[LanguageFactory] = {
 
@@ -287,7 +317,10 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
       factory
     }
 
-    def buildValidatedNamespace(factory: LanguageFactory, workflowSource: WorkflowSource, importResolvers: List[ImportResolver]): IOChecked[ValidatedWomNamespace] = {
+    def buildValidatedNamespace(factory: LanguageFactory,
+                                workflowSource: WorkflowSource,
+                                importResolvers: List[ImportResolver]
+    ): IOChecked[ValidatedWomNamespace] =
       factory.validateNamespace(
         sourceFiles,
         workflowSource,
@@ -297,16 +330,16 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
         engineIoFunctions,
         importResolvers
       )
-    }
 
     val localFilesystemResolvers =
       if (importLocalFilesystem) DirectoryResolver.localFilesystemResolvers(None)
       else List.empty
 
-    val zippedResolverCheck: IOChecked[Option[DirectoryResolver]] = fromEither[IO](sourceFiles.importsZipFileOption match {
-      case None => None.validNelCheck
-      case Some(zipContent) => zippedImportResolver(zipContent, workflowId).toEither.map(Option.apply)
-    })
+    val zippedResolverCheck: IOChecked[Option[DirectoryResolver]] =
+      fromEither[IO](sourceFiles.importsZipFileOption match {
+        case None => None.validNelCheck
+        case Some(zipContent) => zippedImportResolver(zipContent, workflowId).toEither.map(Option.apply)
+      })
 
     val labels = convertJsonToLabels(sourceFiles.labelsJson)
 
@@ -314,15 +347,25 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
       _ <- publishLabelsToMetadata(id, labels.asMap, serviceRegistryActor)
       zippedImportResolver <- zippedResolverCheck
       importResolvers = zippedImportResolver.toList ++ localFilesystemResolvers :+ HttpResolver(None, Map.empty)
-      sourceAndResolvers <- fromEither[IO](LanguageFactoryUtil.findWorkflowSource(sourceFiles.workflowSource, sourceFiles.workflowUrl, importResolvers))
-      _ = if(sourceFiles.workflowUrl.isDefined) publishWorkflowSourceToMetadata(id, sourceAndResolvers._1)
+      sourceAndResolvers <- fromEither[IO](
+        LanguageFactoryUtil.findWorkflowSource(sourceFiles.workflowSource, sourceFiles.workflowUrl, importResolvers)
+      )
+      _ = if (sourceFiles.workflowUrl.isDefined) publishWorkflowSourceToMetadata(id, sourceAndResolvers._1)
       factory <- findFactory(sourceAndResolvers._1).toIOChecked
       outputRuntimeExtractor <- factory.womOutputRuntimeExtractor.toValidated.toIOChecked
       validatedNamespace <- buildValidatedNamespace(factory, sourceAndResolvers._1, sourceAndResolvers._2)
       closeResult = sourceAndResolvers._2.traverse(_.cleanupIfNecessary())
       _ = pushNamespaceMetadata(validatedNamespace)
-      ewd <- buildWorkflowDescriptor(id, validatedNamespace, workflowOptions, labels, conf, callCachingEnabled,
-        invalidateBadCacheResults, pathBuilders, outputRuntimeExtractor).toIOChecked
+      ewd <- buildWorkflowDescriptor(id,
+                                     validatedNamespace,
+                                     workflowOptions,
+                                     labels,
+                                     conf,
+                                     callCachingEnabled,
+                                     invalidateBadCacheResults,
+                                     pathBuilders,
+                                     outputRuntimeExtractor
+      ).toIOChecked
     } yield {
       closeResult match {
         case Valid(_) => ()
@@ -335,7 +378,10 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
   }
 
   private def publishWorkflowSourceToMetadata(id: WorkflowId, workflowSource: WorkflowSource): Unit = {
-    val event = MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Workflow), MetadataValue(workflowSource))
+    val event = MetadataEvent(
+      MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Workflow),
+      MetadataValue(workflowSource)
+    )
     serviceRegistryActor ! PutMetadataAction(event)
   }
 
@@ -347,7 +393,7 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
   }
 
   private def pushLanguageToMetadata(languageName: String, languageVersion: String): Unit = {
-    val events = List (
+    val events = List(
       MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.LanguageName), MetadataValue(languageName)),
       MetadataEvent(
         MetadataKey(workflowId, None, WorkflowMetadataKeys.LanguageVersionName),
@@ -366,7 +412,9 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
       case inputs =>
         inputs flatMap { case (outputPort, womValue) =>
           val inputName = outputPort.fullyQualifiedName
-          womValueToMetadataEvents(MetadataKey(workflowId, None, s"${WorkflowMetadataKeys.Inputs}:$inputName"), womValue)
+          womValueToMetadataEvents(MetadataKey(workflowId, None, s"${WorkflowMetadataKeys.Inputs}:$inputName"),
+                                   womValue
+          )
         }
     }
   }
@@ -385,28 +433,27 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
     imported map { case (uri, value) => metadataEventForImportedFile(uri, value) }
   }
 
-  private def wfNameMetadata(name: String): MetadataEvent = {
+  private def wfNameMetadata(name: String): MetadataEvent =
     // Workflow name:
     MetadataEvent(MetadataKey(workflowId, None, WorkflowMetadataKeys.Name), MetadataValue(name))
-  }
 
-  private def convertJsonToLabels(json: String): Labels = {
+  private def convertJsonToLabels(json: String): Labels =
     json.parseJson match {
-      case JsObject(inputs) => Labels(inputs.toVector.collect({
-        case (key, JsString(value)) => Label(key, value)
-      }))
+      case JsObject(inputs) =>
+        Labels(inputs.toVector.collect { case (key, JsString(value)) =>
+          Label(key, value)
+        })
       case _ => Labels(Vector.empty)
     }
-  }
 
   // Perform a fail-fast validation that the `use_reference_disks` workflow option is boolean if present.
-  private def validateUseReferenceDisks(workflowOptions: WorkflowOptions) : ErrorOr[Unit] = {
+  private def validateUseReferenceDisks(workflowOptions: WorkflowOptions): ErrorOr[Unit] = {
     val optionName = WorkflowOptions.UseReferenceDisks.name
     workflowOptions.getBoolean(optionName) match {
       case Success(_) =>
         // If present must be boolean
         ().validNel
-      case Failure (OptionNotFoundException(_)) =>
+      case Failure(OptionNotFoundException(_)) =>
         // This is an optional... option, so "not found" is fine
         ().validNel
       case Failure(e) =>
@@ -423,29 +470,51 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
                                       callCachingEnabled: Boolean,
                                       invalidateBadCacheResults: Boolean,
                                       pathBuilders: List[PathBuilder],
-                                      outputRuntimeExtractor: Option[WomOutputRuntimeExtractor]): ErrorOr[EngineWorkflowDescriptor] = {
+                                      outputRuntimeExtractor: Option[WomOutputRuntimeExtractor]
+  ): ErrorOr[EngineWorkflowDescriptor] = {
     val taskCalls = womNamespace.executable.graph.allNodes collect { case taskNode: CommandCallNode => taskNode }
     val defaultBackendName = conf.as[Option[String]]("backend.default")
 
     val failureModeValidation = validateWorkflowFailureMode(workflowOptions, conf)
     val backendAssignmentsValidation = validateBackendAssignments(taskCalls, workflowOptions, defaultBackendName)
 
-    val callCachingModeValidation = validateCallCachingMode(workflowOptions, callCachingEnabled,
-      invalidateBadCacheResults)
+    val callCachingModeValidation =
+      validateCallCachingMode(workflowOptions, callCachingEnabled, invalidateBadCacheResults)
 
     val useReferenceDisksValidation: ErrorOr[Unit] = validateUseReferenceDisks(workflowOptions)
 
     val memoryRetryMultiplierValidation: ErrorOr[Unit] = validateMemoryRetryMultiplier(workflowOptions)
 
-    (failureModeValidation, backendAssignmentsValidation, callCachingModeValidation, useReferenceDisksValidation, memoryRetryMultiplierValidation) mapN {
-      case (failureMode, backendAssignments, callCachingMode, _, _) =>
-        val callable = womNamespace.executable.entryPoint
-        val backendDescriptor = BackendWorkflowDescriptor(id, callable, womNamespace.womValueInputs, workflowOptions, labels, hogGroup, List.empty, outputRuntimeExtractor)
-        EngineWorkflowDescriptor(callable, backendDescriptor, backendAssignments, failureMode, pathBuilders, callCachingMode)
+    (failureModeValidation,
+     backendAssignmentsValidation,
+     callCachingModeValidation,
+     useReferenceDisksValidation,
+     memoryRetryMultiplierValidation
+    ) mapN { case (failureMode, backendAssignments, callCachingMode, _, _) =>
+      val callable = womNamespace.executable.entryPoint
+      val backendDescriptor = BackendWorkflowDescriptor(id,
+                                                        callable,
+                                                        womNamespace.womValueInputs,
+                                                        workflowOptions,
+                                                        labels,
+                                                        hogGroup,
+                                                        List.empty,
+                                                        outputRuntimeExtractor
+      )
+      EngineWorkflowDescriptor(callable,
+                               backendDescriptor,
+                               backendAssignments,
+                               failureMode,
+                               pathBuilders,
+                               callCachingMode
+      )
     }
   }
 
-  private def validateBackendAssignments(calls: Set[CommandCallNode], workflowOptions: WorkflowOptions, defaultBackendName: Option[String]): ErrorOr[Map[CommandCallNode, String]] = {
+  private def validateBackendAssignments(calls: Set[CommandCallNode],
+                                         workflowOptions: WorkflowOptions,
+                                         defaultBackendName: Option[String]
+  ): ErrorOr[Map[CommandCallNode, String]] = {
     val callToBackendMap = Try {
       calls map { call =>
         val backendPriorities = Seq(
@@ -456,7 +525,10 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
 
         backendPriorities.flatten.headOption match {
           case Some(backendName) if cromwellBackends.isValidBackendName(backendName) => call -> backendName
-          case Some(backendName) => throw new Exception(s"Backend for call ${call.fullyQualifiedName} ('$backendName') not registered in configuration file")
+          case Some(backendName) =>
+            throw new Exception(
+              s"Backend for call ${call.fullyQualifiedName} ('$backendName') not registered in configuration file"
+            )
           case None => throw new Exception(s"No backend could be found for call ${call.fullyQualifiedName}")
         }
       } toMap
@@ -464,7 +536,7 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
 
     callToBackendMap match {
       case Success(backendMap) =>
-        val backendMapAsString = backendMap.map({case (k, v) => s"${k.fullyQualifiedName} -> $v"}).mkString(", ")
+        val backendMapAsString = backendMap.map { case (k, v) => s"${k.fullyQualifiedName} -> $v" }.mkString(", ")
         workflowLogger.info(s"Call-to-Backend assignments: $backendMapAsString")
         backendMap.validNel
       case Failure(t) => t.getMessage.invalidNel
@@ -476,25 +548,34 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
     */
   private def assignBackendUsingRuntimeAttrs(call: CommandCallNode): Option[String] = {
     val runtimeAttributesMap = call.callable.runtimeAttributes.attributes
-    runtimeAttributesMap.get(RuntimeBackendKey) map { wdlExpr => evaluateBackendNameExpression(call.fullyQualifiedName, wdlExpr) }
+    runtimeAttributesMap.get(RuntimeBackendKey) map { wdlExpr =>
+      evaluateBackendNameExpression(call.fullyQualifiedName, wdlExpr)
+    }
   }
 
-  private def evaluateBackendNameExpression(callName: String, backendNameAsExp: WomExpression): String = {
+  private def evaluateBackendNameExpression(callName: String, backendNameAsExp: WomExpression): String =
     backendNameAsExp.evaluateValue(Map.empty, NoIoFunctionSet) match {
       case Valid(runtimeString: WomString) => runtimeString.valueString
       case Valid(x: WomValue) =>
-        throw new Exception(s"Non-string values are not currently supported for backends! Cannot use backend '${x.valueString}' to backend to Call: $callName")
+        throw new Exception(
+          s"Non-string values are not currently supported for backends! Cannot use backend '${x.valueString}' to backend to Call: $callName"
+        )
       case Invalid(errors) =>
         // TODO WOM: need access to a "source string" for WomExpressions
         // TODO WOM: ErrorOrify this ?
-        throw AggregatedMessageException(s"Dynamic backends are not currently supported! Cannot assign backend '$backendNameAsExp' for Call: $callName", errors.toList)
+        throw AggregatedMessageException(
+          s"Dynamic backends are not currently supported! Cannot assign backend '$backendNameAsExp' for Call: $callName",
+          errors.toList
+        )
     }
-  }
 
-  private def validateWorkflowFailureMode(workflowOptions: WorkflowOptions, conf: Config): ErrorOr[WorkflowFailureMode] = {
+  private def validateWorkflowFailureMode(workflowOptions: WorkflowOptions,
+                                          conf: Config
+  ): ErrorOr[WorkflowFailureMode] = {
     val modeString: Try[String] = workflowOptions.get(WorkflowOptions.WorkflowFailureMode) match {
       case Success(x) => Success(x)
-      case Failure(_: OptionNotFoundException) => Success(conf.as[Option[String]]("workflow-options.workflow-failure-mode") getOrElse DefaultWorkflowFailureMode)
+      case Failure(_: OptionNotFoundException) =>
+        Success(conf.as[Option[String]]("workflow-options.workflow-failure-mode") getOrElse DefaultWorkflowFailureMode)
       case Failure(t) => Failure(t)
     }
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/tokens/DynamicRateLimiter.scala b/engine/src/main/scala/cromwell/engine/workflow/tokens/DynamicRateLimiter.scala
index 6f1c068af5a..16b3026fc16 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/tokens/DynamicRateLimiter.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/tokens/DynamicRateLimiter.scala
@@ -28,9 +28,8 @@ trait DynamicRateLimiter { this: Actor with Timers with ActorLogging =>
     timers.startPeriodicTimer(ResetKey, ResetAction, dispensingRate.per)
   }
 
-  private def releaseTokens() = {
+  private def releaseTokens() =
     self ! TokensAvailable(dispensingRate.n)
-  }
 
   // When load is high, freeze token distribution
   private def highLoad(doLogging: Boolean = true) = {
diff --git a/engine/src/main/scala/cromwell/engine/workflow/tokens/JobTokenDispenserActor.scala b/engine/src/main/scala/cromwell/engine/workflow/tokens/JobTokenDispenserActor.scala
index e97ae9974f4..e201d0917ba 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/tokens/JobTokenDispenserActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/tokens/JobTokenDispenserActor.scala
@@ -29,23 +29,25 @@ class JobTokenDispenserActor(override val serviceRegistryActor: ActorRef,
                              override val dispensingRate: DynamicRateLimiter.Rate,
                              logInterval: Option[FiniteDuration],
                              dispenserType: String,
-                             tokenAllocatedDescription: String)
-  extends Actor
+                             tokenAllocatedDescription: String
+) extends Actor
     with ActorLogging
     with JobInstrumentation
     with CromwellInstrumentationScheduler
     with Timers
     with DynamicRateLimiter
-    with CromwellInstrumentation
-{
+    with CromwellInstrumentation {
 
   // Metrics paths are based on the dispenser type
   private val tokenDispenserMetricsBasePath: NonEmptyList[String] = NonEmptyList.of("token_dispenser", dispenserType)
 
-  private val tokenLeaseDurationMetricPath: NonEmptyList[String] = tokenDispenserMetricsBasePath :+ "token_hold_duration"
+  private val tokenLeaseDurationMetricPath: NonEmptyList[String] =
+    tokenDispenserMetricsBasePath :+ "token_hold_duration"
 
-  private val tokenDispenserMetricsActivityRates: NonEmptyList[String] = tokenDispenserMetricsBasePath :+ "activity_rate"
-  private val requestsEnqueuedMetricPath: NonEmptyList[String] = tokenDispenserMetricsActivityRates :+ "requests_enqueued"
+  private val tokenDispenserMetricsActivityRates: NonEmptyList[String] =
+    tokenDispenserMetricsBasePath :+ "activity_rate"
+  private val requestsEnqueuedMetricPath: NonEmptyList[String] =
+    tokenDispenserMetricsActivityRates :+ "requests_enqueued"
   private val tokensLeasedMetricPath: NonEmptyList[String] = tokenDispenserMetricsActivityRates :+ "tokens_dispensed"
   private val tokensReturnedMetricPath: NonEmptyList[String] = tokenDispenserMetricsActivityRates :+ "tokens_returned"
 
@@ -90,7 +92,8 @@ class JobTokenDispenserActor(override val serviceRegistryActor: ActorRef,
     super.preStart()
   }
 
-  override def receive: Actor.Receive = tokenDispensingReceive.orElse(rateReceive).orElse(instrumentationReceive(instrumentationAction))
+  override def receive: Actor.Receive =
+    tokenDispensingReceive.orElse(rateReceive).orElse(instrumentationReceive(instrumentationAction))
 
   private def tokenDispensingReceive: Receive = {
     case JobTokenRequest(hogGroup, tokenType) => enqueue(sender(), hogGroup.value, tokenType)
@@ -111,7 +114,7 @@ class JobTokenDispenserActor(override val serviceRegistryActor: ActorRef,
     count(tokensReturnedMetricPath, 0L, ServicesPrefix)
   }
 
-  private def enqueue(sndr: ActorRef, hogGroup: String, tokenType: JobTokenType): Unit = {
+  private def enqueue(sndr: ActorRef, hogGroup: String, tokenType: JobTokenType): Unit =
     if (tokenAssignments.contains(sndr)) {
       sndr ! JobTokenDispensed
     } else {
@@ -121,12 +124,12 @@ class JobTokenDispenserActor(override val serviceRegistryActor: ActorRef,
       increment(requestsEnqueuedMetricPath, ServicesPrefix)
       ()
     }
-  }
 
   private def dispense(n: Int) = if (tokenQueues.nonEmpty) {
 
     // Sort by backend name to avoid re-ordering across iterations:
-    val iterator = new RoundRobinQueueIterator(tokenQueues.toList.sortBy(_._1.backend).map(_._2), currentTokenQueuePointer)
+    val iterator =
+      new RoundRobinQueueIterator(tokenQueues.toList.sortBy(_._1.backend).map(_._2), currentTokenQueuePointer)
 
     // In rare cases, an abort might empty an inner queue between "available" and "dequeue", which could cause an
     // exception.
@@ -139,11 +142,12 @@ class JobTokenDispenserActor(override val serviceRegistryActor: ActorRef,
     }
 
     if (nextTokens.nonEmpty) {
-      val hogGroupCounts = nextTokens.groupBy(t => t.queuePlaceholder.hogGroup).map { case (hogGroup, list) => s"$hogGroup: ${list.size}" }
+      val hogGroupCounts =
+        nextTokens.groupBy(t => t.queuePlaceholder.hogGroup).map { case (hogGroup, list) => s"$hogGroup: ${list.size}" }
       log.info(s"Assigned new job $dispenserType tokens to the following groups: ${hogGroupCounts.mkString(", ")}")
     }
 
-    nextTokens.foreach({
+    nextTokens.foreach {
       case LeasedActor(queuePlaceholder, lease) if !tokenAssignments.contains(queuePlaceholder.actor) =>
         tokenAssignments = tokenAssignments + (queuePlaceholder.actor -> TokenLeaseRecord(lease, OffsetDateTime.now()))
         incrementJob("Started")
@@ -151,19 +155,21 @@ class JobTokenDispenserActor(override val serviceRegistryActor: ActorRef,
         queuePlaceholder.actor ! JobTokenDispensed
       // Only one token per actor, so if you've already got one, we don't need to use this new one:
       case LeasedActor(queuePlaceholder, lease) =>
-        log.error(s"Programmer Error: Actor ${queuePlaceholder.actor.path} requested a job $dispenserType token more than once.")
+        log.error(
+          s"Programmer Error: Actor ${queuePlaceholder.actor.path} requested a job $dispenserType token more than once."
+        )
         // Because this actor already has a lease assigned to it:
         // a) tell the actor that it has a lease
         // b) don't hold onto this new lease - release it and let some other actor take it instead
         queuePlaceholder.actor ! JobTokenDispensed
         lease.release()
-    })
+    }
 
     tokenQueues = iterator.updatedQueues.map(queue => queue.tokenType -> queue).toMap
     currentTokenQueuePointer = iterator.updatedPointer
   }
 
-  private def release(actor: ActorRef): Unit = {
+  private def release(actor: ActorRef): Unit =
     tokenAssignments.get(actor) match {
       case Some(TokenLeaseRecord(leasedToken, timestamp)) =>
         tokenAssignments -= actor
@@ -175,7 +181,6 @@ class JobTokenDispenserActor(override val serviceRegistryActor: ActorRef,
       case None =>
         log.error(s"Job {} token returned from incorrect actor: {}", dispenserType, actor.path.name)
     }
-  }
 
   private def onTerminate(terminee: ActorRef): Unit = {
     tokenAssignments.get(terminee) match {
@@ -185,8 +190,8 @@ class JobTokenDispenserActor(override val serviceRegistryActor: ActorRef,
       case None =>
         log.debug("Actor {} stopped before receiving a token, removing it from any queues if necessary", terminee)
         // This is a very inefficient way to remove the actor from the queue and can lead to very poor performance for a large queue and a large number of actors to remove
-        tokenQueues = tokenQueues map {
-          case (tokenType, tokenQueue) => tokenType -> tokenQueue.removeTokenlessActor(terminee)
+        tokenQueues = tokenQueues map { case (tokenType, tokenQueue) =>
+          tokenType -> tokenQueue.removeTokenlessActor(terminee)
         }
     }
     context.unwatch(terminee)
@@ -214,7 +219,9 @@ class JobTokenDispenserActor(override val serviceRegistryActor: ActorRef,
     }
 
     // Schedule the next log event:
-    context.system.scheduler.scheduleOnce(someInterval) { self ! LogJobTokenAllocation(someInterval) }(context.dispatcher)
+    context.system.scheduler.scheduleOnce(someInterval)(self ! LogJobTokenAllocation(someInterval))(
+      context.dispatcher
+    )
     ()
   }
 
@@ -225,19 +232,23 @@ class JobTokenDispenserActor(override val serviceRegistryActor: ActorRef,
           so it's desirable that a group submitting to two or more backends pause workflow
           pickup globally when it exhausts tokens in one of the backends
    */
-  private def tokenExhaustedGroups: ReplyLimitedGroups = {
+  private def tokenExhaustedGroups: ReplyLimitedGroups =
     ReplyLimitedGroups(
       tokenQueues.values.flatMap(_.eventLogger.tokenExhaustedGroups).toSet
     )
-  }
 }
 
 object JobTokenDispenserActor {
   case object TokensTimerKey
 
-  def props(serviceRegistryActor: ActorRef, rate: DynamicRateLimiter.Rate, logInterval: Option[FiniteDuration],
-            dispenserType: String, tokenAllocatedDescription: String): Props =
-    Props(new JobTokenDispenserActor(serviceRegistryActor, rate, logInterval, dispenserType, tokenAllocatedDescription)).withDispatcher(EngineDispatcher)
+  def props(serviceRegistryActor: ActorRef,
+            rate: DynamicRateLimiter.Rate,
+            logInterval: Option[FiniteDuration],
+            dispenserType: String,
+            tokenAllocatedDescription: String
+  ): Props =
+    Props(new JobTokenDispenserActor(serviceRegistryActor, rate, logInterval, dispenserType, tokenAllocatedDescription))
+      .withDispatcher(EngineDispatcher)
 
   case class JobTokenRequest(hogGroup: HogGroup, jobTokenType: JobTokenType)
 
@@ -250,7 +261,11 @@ object JobTokenDispenserActor {
   implicit val tokenEncoder = deriveEncoder[JobTokenType]
 
   @JsonCodec(encodeOnly = true)
-  final case class TokenDispenserState(dispenserType: String, tokenTypes: Vector[TokenTypeState], pointer: Int, leased: Int)
+  final case class TokenDispenserState(dispenserType: String,
+                                       tokenTypes: Vector[TokenTypeState],
+                                       pointer: Int,
+                                       leased: Int
+  )
 
   @JsonCodec(encodeOnly = true)
   final case class TokenTypeState(tokenType: JobTokenType, queue: TokenQueueState)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/tokens/RoundRobinQueueIterator.scala b/engine/src/main/scala/cromwell/engine/workflow/tokens/RoundRobinQueueIterator.scala
index 36e555be98b..472ca190912 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/tokens/RoundRobinQueueIterator.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/tokens/RoundRobinQueueIterator.scala
@@ -7,7 +7,8 @@ import cromwell.engine.workflow.tokens.TokenQueue.{DequeueResult, LeasedActor}
   * It will keep rotating the list until it finds a queue with an element that can be dequeued.
   * If no queue can be dequeued, the iterator is empty.
   */
-final class RoundRobinQueueIterator(initialTokenQueue: List[TokenQueue], initialPointer: Int) extends Iterator[LeasedActor] {
+final class RoundRobinQueueIterator(initialTokenQueue: List[TokenQueue], initialPointer: Int)
+    extends Iterator[LeasedActor] {
   // Assumes the number of queues won't change during iteration (it really shouldn't !)
   private val numberOfQueues = initialTokenQueue.size
   // Indicate the index of next queue to try to dequeue from.
@@ -45,14 +46,14 @@ final class RoundRobinQueueIterator(initialTokenQueue: List[TokenQueue], initial
     val indexStream = ((pointer until numberOfQueues) ++ (0 until pointer)).to(LazyList)
     val dequeuedTokenStream = indexStream.map(index => tokenQueues(index).dequeue -> index)
 
-    val firstLeasedActor = dequeuedTokenStream.collectFirst({
+    val firstLeasedActor = dequeuedTokenStream.collectFirst {
       case (DequeueResult(Some(dequeuedActor), newTokenQueue), index) =>
         // Update the tokenQueues with the new queue
         tokenQueues = tokenQueues.updated(index, newTokenQueue)
         // Update the index. Add 1 to force trying all the queues as we call next, even if the first one is available
         pointer = (index + 1) % numberOfQueues
         dequeuedActor
-    })
+    }
 
     firstLeasedActor
   }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/tokens/TokenEventLogger.scala b/engine/src/main/scala/cromwell/engine/workflow/tokens/TokenEventLogger.scala
index 7ee35f86cd5..e61c17c1949 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/tokens/TokenEventLogger.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/tokens/TokenEventLogger.scala
@@ -22,29 +22,28 @@ case object NullTokenEventLogger extends TokenEventLogger {
 
 class CachingTokenEventLogger(cacheEntryTTL: FiniteDuration) extends TokenEventLogger {
 
-  private val groupCache = CacheBuilder.newBuilder()
+  private val groupCache = CacheBuilder
+    .newBuilder()
     .expireAfterWrite(cacheEntryTTL._1, cacheEntryTTL._2)
     .maximumSize(10000)
     .build[String, Object]()
 
-  override def flagTokenHog(hogGroup: String): Unit = {
+  override def flagTokenHog(hogGroup: String): Unit =
     groupCache.put(hogGroup, new Object())
-  }
 
   override def tokenExhaustedGroups: Set[String] = {
     import scala.jdk.CollectionConverters._
     groupCache.asMap().keySet().asScala.toSet
   }
 
-
-  private val backendCache = CacheBuilder.newBuilder()
+  private val backendCache = CacheBuilder
+    .newBuilder()
     .expireAfterWrite(cacheEntryTTL._1, cacheEntryTTL._2)
     .maximumSize(10000)
     .build[String, Object]()
 
-  override def outOfTokens(backend: String): Unit = {
+  override def outOfTokens(backend: String): Unit =
     backendCache.put(backend, new Object())
-  }
 
   override def tokenExhaustedBackends: Set[String] = {
     import scala.jdk.CollectionConverters._
diff --git a/engine/src/main/scala/cromwell/engine/workflow/tokens/TokenQueue.scala b/engine/src/main/scala/cromwell/engine/workflow/tokens/TokenQueue.scala
index af31384f415..c16ae9dad91 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/tokens/TokenQueue.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/tokens/TokenQueue.scala
@@ -18,7 +18,8 @@ import scala.collection.immutable.Queue
 final case class TokenQueue(queues: Map[String, Queue[TokenQueuePlaceholder]],
                             queueOrder: Vector[String],
                             eventLogger: TokenEventLogger,
-                            private [tokens] val pool: UnhoggableTokenPool) extends StrictLogging {
+                            private[tokens] val pool: UnhoggableTokenPool
+) extends StrictLogging {
   val tokenType = pool.tokenType
 
   /**
@@ -31,7 +32,7 @@ final case class TokenQueue(queues: Map[String, Queue[TokenQueuePlaceholder]],
     *
     * @return the new token queue
     */
-  def enqueue(placeholder: TokenQueuePlaceholder): TokenQueue = {
+  def enqueue(placeholder: TokenQueuePlaceholder): TokenQueue =
     if (queues.contains(placeholder.hogGroup)) {
       this.copy(
         queues = queues + (placeholder.hogGroup -> queues(placeholder.hogGroup).enqueue(placeholder))
@@ -42,7 +43,6 @@ final case class TokenQueue(queues: Map[String, Queue[TokenQueuePlaceholder]],
         queueOrder = queueOrder :+ placeholder.hogGroup
       )
     }
-  }
 
   /**
     * Returns a dequeue'd actor if one exists and there's a token available for it
@@ -57,7 +57,10 @@ final case class TokenQueue(queues: Map[String, Queue[TokenQueuePlaceholder]],
     recursingDequeue(guaranteedNonEmptyQueues, Vector.empty, queueOrder)
   }
 
-  private def recursingDequeue(queues: Map[String, Queue[TokenQueuePlaceholder]], queuesTried: Vector[String], queuesRemaining: Vector[String]): DequeueResult = {
+  private def recursingDequeue(queues: Map[String, Queue[TokenQueuePlaceholder]],
+                               queuesTried: Vector[String],
+                               queuesRemaining: Vector[String]
+  ): DequeueResult =
     if (queuesRemaining.isEmpty) {
       DequeueResult(None, this)
     } else {
@@ -69,7 +72,9 @@ final case class TokenQueue(queues: Map[String, Queue[TokenQueuePlaceholder]],
 
       if (oldQueue.isEmpty) {
         // We should have caught this above. But just in case:
-        logger.warn(s"Programmer error: Empty token queue value still present in TokenQueue: $hogGroup *and* made it through into recursiveDequeue(!): $hogGroup")
+        logger.warn(
+          s"Programmer error: Empty token queue value still present in TokenQueue: $hogGroup *and* made it through into recursiveDequeue(!): $hogGroup"
+        )
         recursingDequeue(queues, queuesTried :+ hogGroup, remainingHogGroups)
       } else {
         leaseTry match {
@@ -80,7 +85,9 @@ final case class TokenQueue(queues: Map[String, Queue[TokenQueuePlaceholder]],
             } else {
               (queues + (hogGroup -> newQueue), remainingHogGroups ++ queuesTried :+ hogGroup)
             }
-            DequeueResult(Option(LeasedActor(placeholder, thl)), TokenQueue(newQueues, newQueueOrder, eventLogger, pool))
+            DequeueResult(Option(LeasedActor(placeholder, thl)),
+                          TokenQueue(newQueues, newQueueOrder, eventLogger, pool)
+            )
           case TokenTypeExhausted =>
             // The pool is completely full right now, so there's no benefit trying the other hog groups:
             eventLogger.outOfTokens(tokenType.backend)
@@ -91,7 +98,6 @@ final case class TokenQueue(queues: Map[String, Queue[TokenQueuePlaceholder]],
         }
       }
     }
-  }
 
   def removeTokenlessActor(actor: ActorRef): TokenQueue = {
     val actorRemovedQueues = queues.map { case (hogGroup, queue) =>
@@ -139,7 +145,8 @@ object TokenQueue {
   case class LeasedActor(queuePlaceholder: TokenQueuePlaceholder, lease: Lease[JobToken]) {
     def actor: ActorRef = queuePlaceholder.actor
   }
-  def apply(tokenType: JobTokenType, logger: TokenEventLogger) = new TokenQueue(Map.empty, Vector.empty, logger, new UnhoggableTokenPool(tokenType))
+  def apply(tokenType: JobTokenType, logger: TokenEventLogger) =
+    new TokenQueue(Map.empty, Vector.empty, logger, new UnhoggableTokenPool(tokenType))
   final case class TokenQueuePlaceholder(actor: ActorRef, hogGroup: String)
 
   @JsonCodec
diff --git a/engine/src/main/scala/cromwell/engine/workflow/tokens/UnhoggableTokenPool.scala b/engine/src/main/scala/cromwell/engine/workflow/tokens/UnhoggableTokenPool.scala
index 761748abb49..e4c3885b60c 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/tokens/UnhoggableTokenPool.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/tokens/UnhoggableTokenPool.scala
@@ -12,13 +12,15 @@ import io.github.andrebeat.pool._
 import scala.collection.immutable.HashSet
 import scala.collection.mutable
 
-final class UnhoggableTokenPool(val tokenType: JobTokenType) extends SimplePool[JobToken](
-  capacity = tokenType.maxPoolSize.getOrElse(UnhoggableTokenPool.MaxCapacity),
-  referenceType = ReferenceType.Strong,
-  _factory = () => JobToken(tokenType, UUID.randomUUID()),
-  _reset = Function.const(()),
-  _dispose = Function.const(()),
-  _healthCheck = Function.const(true)) {
+final class UnhoggableTokenPool(val tokenType: JobTokenType)
+    extends SimplePool[JobToken](
+      capacity = tokenType.maxPoolSize.getOrElse(UnhoggableTokenPool.MaxCapacity),
+      referenceType = ReferenceType.Strong,
+      _factory = () => JobToken(tokenType, UUID.randomUUID()),
+      _reset = Function.const(()),
+      _dispose = Function.const(()),
+      _healthCheck = Function.const(true)
+    ) {
 
   lazy val hogLimitOption: Option[Int] = tokenType match {
     case JobTokenType(_, Some(limit), hogFactor) if hogFactor > 1 =>
@@ -28,10 +30,11 @@ final class UnhoggableTokenPool(val tokenType: JobTokenType) extends SimplePool[
 
   private[this] val hogGroupAssignments: mutable.Map[String, HashSet[JobToken]] = mutable.Map.empty
 
-  override def tryAcquire(): Option[Lease[JobToken]] = throw new UnsupportedOperationException("Use tryAcquire(hogGroup)")
-
-  def available(hogGroup: String): UnhoggableTokenPoolAvailability = {
+  override def tryAcquire(): Option[Lease[JobToken]] = throw new UnsupportedOperationException(
+    "Use tryAcquire(hogGroup)"
+  )
 
+  def available(hogGroup: String): UnhoggableTokenPoolAvailability =
     hogLimitOption match {
       case None if leased() < capacity => TokensAvailable
       case None => TokenTypeExhausted
@@ -46,10 +49,8 @@ final class UnhoggableTokenPool(val tokenType: JobTokenType) extends SimplePool[
           }
         } else TokenTypeExhausted
     }
-  }
-
-  def tryAcquire(hogGroup: String): UnhoggableTokenPoolResult = {
 
+  def tryAcquire(hogGroup: String): UnhoggableTokenPoolResult =
     hogLimitOption match {
       case Some(hogLimit) =>
         synchronized {
@@ -75,9 +76,8 @@ final class UnhoggableTokenPool(val tokenType: JobTokenType) extends SimplePool[
           case None => TokenTypeExhausted
         }
     }
-  }
 
-  def unhog(hogGroup: String, lease: Lease[JobToken]): Unit = {
+  def unhog(hogGroup: String, lease: Lease[JobToken]): Unit =
     hogLimitOption foreach { _ =>
       synchronized {
         val newAssignment = hogGroupAssignments.getOrElse(hogGroup, HashSet.empty) - lease.get()
@@ -89,15 +89,15 @@ final class UnhoggableTokenPool(val tokenType: JobTokenType) extends SimplePool[
         }
       }
     }
-  }
 
   def poolState: TokenPoolState = {
     val (hogGroupUsages, hogLimitValue): (Option[Set[HogGroupState]], Option[Int]) = hogLimitOption match {
       case Some(hogLimit) =>
         synchronized {
-          val entries: Set[HogGroupState] = hogGroupAssignments.toSet[(String, HashSet[JobToken])].map { case (hogGroup, set) =>
-            HogGroupState(hogGroup, set.size, !hogGroupAssignments.get(hogGroup).forall(_.size < hogLimit))
-          }
+          val entries: Set[HogGroupState] =
+            hogGroupAssignments.toSet[(String, HashSet[JobToken])].map { case (hogGroup, set) =>
+              HogGroupState(hogGroup, set.size, !hogGroupAssignments.get(hogGroup).forall(_.size < hogLimit))
+            }
           (Option(entries), Option(hogLimit))
         }
       case None => (None, None)
@@ -113,7 +113,9 @@ object UnhoggableTokenPool {
 
   sealed trait UnhoggableTokenPoolResult
 
-  final class TokenHoggingLease(lease: Lease[JobToken], hogGroup: String, pool: UnhoggableTokenPool) extends Lease[JobToken] with UnhoggableTokenPoolResult {
+  final class TokenHoggingLease(lease: Lease[JobToken], hogGroup: String, pool: UnhoggableTokenPool)
+      extends Lease[JobToken]
+      with UnhoggableTokenPoolResult {
     private[this] val dirty = new AtomicBoolean(false)
     override protected[this] def a: JobToken = lease.get()
 
@@ -153,6 +155,11 @@ object UnhoggableTokenPool {
   final case class HogGroupState(hogGroup: String, used: Int, atLimit: Boolean)
 
   @JsonCodec
-  final case class TokenPoolState(hogGroups: Option[Set[HogGroupState]], hogLimit: Option[Int], capacity: Int, leased: Int, available: Boolean)
+  final case class TokenPoolState(hogGroups: Option[Set[HogGroupState]],
+                                  hogLimit: Option[Int],
+                                  capacity: Int,
+                                  leased: Int,
+                                  available: Boolean
+  )
 
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/AbortRequestScanningActor.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/AbortRequestScanningActor.scala
index 1e565886941..6e8a8f96ea3 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/AbortRequestScanningActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/AbortRequestScanningActor.scala
@@ -5,19 +5,26 @@ import com.google.common.cache.CacheBuilder
 import cromwell.core.{CacheConfig, WorkflowId}
 import cromwell.engine.workflow.WorkflowManagerActor
 import cromwell.engine.workflow.workflowstore.AbortRequestScanningActor.{AbortConfig, RunScan}
-import cromwell.engine.workflow.workflowstore.WorkflowStoreActor.{FindWorkflowsWithAbortRequested, FindWorkflowsWithAbortRequestedFailure, FindWorkflowsWithAbortRequestedSuccess}
+import cromwell.engine.workflow.workflowstore.WorkflowStoreActor.{
+  FindWorkflowsWithAbortRequested,
+  FindWorkflowsWithAbortRequestedFailure,
+  FindWorkflowsWithAbortRequestedSuccess
+}
 
 import scala.jdk.CollectionConverters._
 import scala.concurrent.duration._
 
-
 class AbortRequestScanningActor(workflowStoreActor: ActorRef,
                                 workflowManagerActor: ActorRef,
                                 abortConfig: AbortConfig,
-                                workflowHeartbeatConfig: WorkflowHeartbeatConfig) extends Actor with Timers with ActorLogging {
+                                workflowHeartbeatConfig: WorkflowHeartbeatConfig
+) extends Actor
+    with Timers
+    with ActorLogging {
   private val cache = {
     val cacheConfig = abortConfig.cacheConfig
-    CacheBuilder.newBuilder()
+    CacheBuilder
+      .newBuilder()
       .concurrencyLevel(cacheConfig.concurrency)
       .expireAfterWrite(cacheConfig.ttl.length, cacheConfig.ttl.unit)
       .build[WorkflowId, java.lang.Boolean]()
@@ -52,6 +59,10 @@ object AbortRequestScanningActor {
 
   case object RunScan
 
-  def props(workflowStoreActor: ActorRef, workflowManagerActor: ActorRef, abortConfig: AbortConfig, workflowHeartbeatConfig: WorkflowHeartbeatConfig): Props =
+  def props(workflowStoreActor: ActorRef,
+            workflowManagerActor: ActorRef,
+            abortConfig: AbortConfig,
+            workflowHeartbeatConfig: WorkflowHeartbeatConfig
+  ): Props =
     Props(new AbortRequestScanningActor(workflowStoreActor, workflowManagerActor, abortConfig, workflowHeartbeatConfig))
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemorySubWorkflowStore.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemorySubWorkflowStore.scala
index c17a38b36fc..16557207b1b 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemorySubWorkflowStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemorySubWorkflowStore.scala
@@ -14,7 +14,8 @@ class InMemorySubWorkflowStore(workflowStore: InMemoryWorkflowStore) extends Sub
                                         callFullyQualifiedName: String,
                                         jobIndex: Int,
                                         jobAttempt: Int,
-                                        subWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Unit] = {
+                                        subWorkflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Unit] =
     if (workflowStore.workflowStore.exists { case (wf, _) => wf.id.toString == rootWorkflowExecutionUuid }) {
       subWorkflowStore = subWorkflowStore +
         SubWorkflowStoreEntry(
@@ -27,24 +28,24 @@ class InMemorySubWorkflowStore(workflowStore: InMemoryWorkflowStore) extends Sub
         )
       Future.successful(())
     } else Future.failed(new Throwable(s"No such root workflow: $rootWorkflowExecutionUuid"))
-  }
 
   override def querySubWorkflowStore(parentWorkflowExecutionUuid: String,
                                      callFqn: String,
                                      jobIndex: Int,
-                                     jobAttempt: Int)(implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]] = {
+                                     jobAttempt: Int
+  )(implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]] =
     Future.successful(
-      subWorkflowStore.find(
-        k =>
-          k.parentWorkflowExecutionUuid == parentWorkflowExecutionUuid &&
-            k.callFullyQualifiedName == callFqn &&
-            k.callIndex == jobIndex &&
-            k.callAttempt == jobAttempt
+      subWorkflowStore.find(k =>
+        k.parentWorkflowExecutionUuid == parentWorkflowExecutionUuid &&
+          k.callFullyQualifiedName == callFqn &&
+          k.callIndex == jobIndex &&
+          k.callAttempt == jobAttempt
       )
     )
-  }
 
-  override def removeSubWorkflowStoreEntries(parentWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Int] = {
+  override def removeSubWorkflowStoreEntries(
+    parentWorkflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Int] = {
     val toRemove = subWorkflowStore.filter(k => k.parentWorkflowExecutionUuid == parentWorkflowExecutionUuid)
     subWorkflowStore = subWorkflowStore -- toRemove
     Future.successful(toRemove.size)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala
index b6913f6172c..ebce8c92720 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/InMemoryWorkflowStore.scala
@@ -5,7 +5,11 @@ import cats.data.NonEmptyList
 import cromwell.core.{HogGroup, WorkflowId, WorkflowSourceFilesCollection}
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.WorkflowStoreAbortResponse.WorkflowStoreAbortResponse
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.WorkflowStoreState.WorkflowStoreState
-import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.{WorkflowStoreAbortResponse, WorkflowStoreState, WorkflowSubmissionResponse}
+import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.{
+  WorkflowStoreAbortResponse,
+  WorkflowStoreState,
+  WorkflowSubmissionResponse
+}
 
 import scala.concurrent.duration.FiniteDuration
 import scala.concurrent.{ExecutionContext, Future}
@@ -18,12 +22,15 @@ class InMemoryWorkflowStore extends WorkflowStore {
     * Adds the requested WorkflowSourceFiles to the store and returns a WorkflowId for each one (in order)
     * for tracking purposes.
     */
-  override def add(sources: NonEmptyList[WorkflowSourceFilesCollection])(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowSubmissionResponse]] = {
-    val actualWorkflowState = if (sources.head.workflowOnHold) WorkflowStoreState.OnHold else WorkflowStoreState.Submitted
+  override def add(
+    sources: NonEmptyList[WorkflowSourceFilesCollection]
+  )(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowSubmissionResponse]] = {
+    val actualWorkflowState =
+      if (sources.head.workflowOnHold) WorkflowStoreState.OnHold else WorkflowStoreState.Submitted
     val addedWorkflows = sources map { WorkflowIdAndSources(WorkflowId.randomId(), _) -> actualWorkflowState }
     workflowStore ++= addedWorkflows.toList.toMap
-    Future.successful(addedWorkflows map {
-      case (WorkflowIdAndSources(id, _), _) => WorkflowSubmissionResponse(actualWorkflowState, id)
+    Future.successful(addedWorkflows map { case (WorkflowIdAndSources(id, _), _) =>
+      WorkflowSubmissionResponse(actualWorkflowState, id)
     })
   }
 
@@ -31,9 +38,15 @@ class InMemoryWorkflowStore extends WorkflowStore {
     * Retrieves up to n workflows which have not already been pulled into the engine and sets their pickedUp
     * flag to true
     */
-  override def fetchStartableWorkflows(n: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])(implicit ec: ExecutionContext): Future[List[WorkflowToStart]] = {
+  override def fetchStartableWorkflows(n: Int,
+                                       cromwellId: String,
+                                       heartbeatTtl: FiniteDuration,
+                                       excludedGroups: Set[String]
+  )(implicit ec: ExecutionContext): Future[List[WorkflowToStart]] = {
     if (excludedGroups.nonEmpty)
-      throw new UnsupportedOperationException("Programmer Error: group filtering not supported for single-tenant/in-memory workflow store")
+      throw new UnsupportedOperationException(
+        "Programmer Error: group filtering not supported for single-tenant/in-memory workflow store"
+      )
 
     val startableWorkflows = workflowStore filter { _._2 == WorkflowStoreState.Submitted } take n
     val updatedWorkflows = startableWorkflows map { _._1 -> WorkflowStoreState.Running }
@@ -51,17 +64,18 @@ class InMemoryWorkflowStore extends WorkflowStore {
 
   override def initialize(implicit ec: ExecutionContext): Future[Unit] = Future.successful(())
 
-  override def stats(implicit ec: ExecutionContext): Future[Map[WorkflowStoreState, Int]] = Future.successful(Map(WorkflowStoreState.Submitted -> workflowStore.size))
+  override def stats(implicit ec: ExecutionContext): Future[Map[WorkflowStoreState, Int]] =
+    Future.successful(Map(WorkflowStoreState.Submitted -> workflowStore.size))
 
   override def abortAllRunning()(implicit ec: ExecutionContext): Future[Unit] = {
-    workflowStore = workflowStore.map({
+    workflowStore = workflowStore.map {
       case (workflow, WorkflowStoreState.Running) => workflow -> WorkflowStoreState.Aborting
       case (workflow, state) => workflow -> state
-    })
+    }
     Future.successful(())
   }
 
-  override def abort(id: WorkflowId)(implicit ec: ExecutionContext): Future[WorkflowStoreAbortResponse] = {
+  override def abort(id: WorkflowId)(implicit ec: ExecutionContext): Future[WorkflowStoreAbortResponse] =
     workflowStore collectFirst {
       case (workflowIdAndSources, workflowStoreState) if workflowIdAndSources.id == id =>
         (workflowIdAndSources, workflowStoreState)
@@ -76,21 +90,24 @@ class InMemoryWorkflowStore extends WorkflowStore {
       case None =>
         Future.successful(WorkflowStoreAbortResponse.NotFound)
     }
-  }
 
   override def writeWorkflowHeartbeats(workflowIds: Set[(WorkflowId, OffsetDateTime)],
-                                       heartbeatDateTime: OffsetDateTime)
-                                      (implicit ec: ExecutionContext): Future[Int] = {
+                                       heartbeatDateTime: OffsetDateTime
+  )(implicit ec: ExecutionContext): Future[Int] =
     Future.successful(workflowIds.size)
-  }
 
-  override def switchOnHoldToSubmitted(id: WorkflowId)(implicit ec: ExecutionContext): Future[Unit] = Future.successful(())
+  override def switchOnHoldToSubmitted(id: WorkflowId)(implicit ec: ExecutionContext): Future[Unit] =
+    Future.successful(())
 
-  override def findWorkflowsWithAbortRequested(cromwellId: String)(implicit ec: ExecutionContext): Future[Iterable[WorkflowId]] = Future.successful(List.empty)
+  override def findWorkflowsWithAbortRequested(cromwellId: String)(implicit
+    ec: ExecutionContext
+  ): Future[Iterable[WorkflowId]] = Future.successful(List.empty)
 
-  override def findWorkflows(cromwellId: String)(implicit ec: ExecutionContext): Future[Iterable[WorkflowId]] = Future.successful(workflowStore.keys.map(_.id))
+  override def findWorkflows(cromwellId: String)(implicit ec: ExecutionContext): Future[Iterable[WorkflowId]] =
+    Future.successful(workflowStore.keys.map(_.id))
 
-  override def deleteFromStore(workflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Int] = Future.successful(0)
+  override def deleteFromStore(workflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Int] =
+    Future.successful(0)
 }
 
 final case class WorkflowIdAndSources(id: WorkflowId, sources: WorkflowSourceFilesCollection)
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStore.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStore.scala
index b36cb008933..2243ff32573 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStore.scala
@@ -13,7 +13,14 @@ import cromwell.database.sql.{MetadataSqlDatabase, WorkflowStoreSqlDatabase}
 import cromwell.database.sql.tables.WorkflowStoreEntry
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.WorkflowStoreAbortResponse.WorkflowStoreAbortResponse
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.WorkflowStoreState.WorkflowStoreState
-import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.{DuplicateWorkflowIdsRequested, NotInOnHoldStateException, WorkflowIdsAlreadyInUseException, WorkflowStoreAbortResponse, WorkflowStoreState, WorkflowSubmissionResponse}
+import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.{
+  DuplicateWorkflowIdsRequested,
+  NotInOnHoldStateException,
+  WorkflowIdsAlreadyInUseException,
+  WorkflowStoreAbortResponse,
+  WorkflowStoreState,
+  WorkflowSubmissionResponse
+}
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.collection._
 
@@ -23,17 +30,17 @@ import scala.concurrent.{ExecutionContext, Future}
 object SqlWorkflowStore {
   case class WorkflowSubmissionResponse(state: WorkflowStoreState, id: WorkflowId)
 
-  case class DuplicateWorkflowIdsRequested(workflowIds: Seq[WorkflowId]) extends
-    Exception (s"Requested workflow IDs are duplicated: ${workflowIds.mkString(", ")}")
+  case class DuplicateWorkflowIdsRequested(workflowIds: Seq[WorkflowId])
+      extends Exception(s"Requested workflow IDs are duplicated: ${workflowIds.mkString(", ")}")
 
-  case class WorkflowIdsAlreadyInUseException(workflowIds: Seq[WorkflowId]) extends
-    Exception (s"Requested workflow IDs are already in use: ${workflowIds.mkString(", ")}")
+  case class WorkflowIdsAlreadyInUseException(workflowIds: Seq[WorkflowId])
+      extends Exception(s"Requested workflow IDs are already in use: ${workflowIds.mkString(", ")}")
 
-  case class NotInOnHoldStateException(workflowId: WorkflowId) extends
-    Exception(
-      s"Couldn't change status of workflow $workflowId to " +
-        "'Submitted' because the workflow is not in 'On Hold' state"
-    )
+  case class NotInOnHoldStateException(workflowId: WorkflowId)
+      extends Exception(
+        s"Couldn't change status of workflow $workflowId to " +
+          "'Submitted' because the workflow is not in 'On Hold' state"
+      )
 
   object WorkflowStoreState extends Enumeration {
     type WorkflowStoreState = Value
@@ -51,12 +58,14 @@ object SqlWorkflowStore {
   }
 }
 
-case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase, metadataSqlDatabase: MetadataSqlDatabase) extends WorkflowStore {
+case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase, metadataSqlDatabase: MetadataSqlDatabase)
+    extends WorkflowStore {
+
   /** This is currently hardcoded to success but used to do stuff, left in place for now as a useful
     *  startup initialization hook. */
   override def initialize(implicit ec: ExecutionContext): Future[Unit] = Future.successful(())
 
-  override def abort(id: WorkflowId)(implicit ec: ExecutionContext): Future[WorkflowStoreAbortResponse] = {
+  override def abort(id: WorkflowId)(implicit ec: ExecutionContext): Future[WorkflowStoreAbortResponse] =
     sqlDatabase.deleteOrUpdateWorkflowToState(
       workflowExecutionUuid = id.toString,
       workflowStateToDelete1 = WorkflowStoreState.OnHold.toString,
@@ -70,33 +79,34 @@ case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase, metadataSqlDa
       case None =>
         WorkflowStoreAbortResponse.NotFound
     }
-  }
 
-  override def findWorkflows(cromwellId: String)(implicit ec: ExecutionContext): Future[Iterable[WorkflowId]] = {
+  override def findWorkflows(cromwellId: String)(implicit ec: ExecutionContext): Future[Iterable[WorkflowId]] =
     sqlDatabase.findWorkflows(cromwellId) map { _ map WorkflowId.fromString }
-  }
 
-  override def findWorkflowsWithAbortRequested(cromwellId: String)(implicit ec: ExecutionContext): Future[Iterable[WorkflowId]] = {
+  override def findWorkflowsWithAbortRequested(cromwellId: String)(implicit
+    ec: ExecutionContext
+  ): Future[Iterable[WorkflowId]] =
     sqlDatabase.findWorkflowsWithAbortRequested(cromwellId) map { _ map WorkflowId.fromString }
-  }
 
-  override def abortAllRunning()(implicit ec: ExecutionContext): Future[Unit] = {
+  override def abortAllRunning()(implicit ec: ExecutionContext): Future[Unit] =
     sqlDatabase.setStateToState(WorkflowStoreState.Running.toString, WorkflowStoreState.Aborting.toString)
-  }
 
-  override def stats(implicit ec: ExecutionContext): Future[Map[WorkflowStoreState, Int]] = {
+  override def stats(implicit ec: ExecutionContext): Future[Map[WorkflowStoreState, Int]] =
     sqlDatabase.workflowStateCounts.map {
-      _ map {
-        case (key, value) => WorkflowStoreState.withName(key) -> value
+      _ map { case (key, value) =>
+        WorkflowStoreState.withName(key) -> value
       }
     }
-  }
 
   /**
     * Retrieves up to n workflows which have not already been pulled into the engine and sets their pickedUp
     * flag to true
     */
-  override def fetchStartableWorkflows(n: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])(implicit ec: ExecutionContext): Future[List[WorkflowToStart]] = {
+  override def fetchStartableWorkflows(n: Int,
+                                       cromwellId: String,
+                                       heartbeatTtl: FiniteDuration,
+                                       excludedGroups: Set[String]
+  )(implicit ec: ExecutionContext): Future[List[WorkflowToStart]] = {
     import cats.syntax.traverse._
     import common.validation.Validation._
     sqlDatabase.fetchWorkflowsInState(
@@ -115,38 +125,44 @@ case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase, metadataSqlDa
   }
 
   override def writeWorkflowHeartbeats(workflowIds: Set[(WorkflowId, OffsetDateTime)],
-                                       heartbeatDateTime: OffsetDateTime)
-                                      (implicit ec: ExecutionContext): Future[Int] = {
-    val sortedWorkflowIds = workflowIds.toList sortBy(_._2) map (_._1.toString)
+                                       heartbeatDateTime: OffsetDateTime
+  )(implicit ec: ExecutionContext): Future[Int] = {
+    val sortedWorkflowIds = workflowIds.toList sortBy (_._2) map (_._1.toString)
     sqlDatabase.writeWorkflowHeartbeats(sortedWorkflowIds, heartbeatDateTime.toSystemTimestamp)
   }
 
-  def workflowAlreadyExists(workflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Boolean] = {
-    Future.sequence(Seq(
-      sqlDatabase.checkWhetherWorkflowExists(workflowId.id.toString),
-      metadataSqlDatabase.getWorkflowStatus(workflowId.id.toString).map(_.nonEmpty)
-    )).map(_.exists(_ == true))
-  }
-
-  def findPreexistingWorkflowIds(workflowIds: Seq[WorkflowId])(implicit ec: ExecutionContext): Future[Seq[WorkflowId]] = {
-    Future.sequence(workflowIds.map(wfid => {
-      workflowAlreadyExists(wfid).map {
-        case true => Option(wfid)
-        case false => None
-      }
-    })).map { _.collect { case Some(existingId) => existingId } }
-  }
+  def workflowAlreadyExists(workflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Boolean] =
+    Future
+      .sequence(
+        Seq(
+          sqlDatabase.checkWhetherWorkflowExists(workflowId.id.toString),
+          metadataSqlDatabase.getWorkflowStatus(workflowId.id.toString).map(_.nonEmpty)
+        )
+      )
+      .map(_.exists(_ == true))
+
+  def findPreexistingWorkflowIds(workflowIds: Seq[WorkflowId])(implicit ec: ExecutionContext): Future[Seq[WorkflowId]] =
+    Future
+      .sequence(workflowIds.map { wfid =>
+        workflowAlreadyExists(wfid).map {
+          case true => Option(wfid)
+          case false => None
+        }
+      })
+      .map(_.collect { case Some(existingId) => existingId })
 
   /**
     * Adds the requested WorkflowSourceFiles to the store and returns a WorkflowId for each one (in order)
     * for tracking purposes.
     */
-  override def add(sources: NonEmptyList[WorkflowSourceFilesCollection])(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowSubmissionResponse]] = {
+  override def add(
+    sources: NonEmptyList[WorkflowSourceFilesCollection]
+  )(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowSubmissionResponse]] = {
 
     val requestedWorkflowIds = sources.map(_.requestedWorkflowId).collect { case Some(id) => id }
     val duplicatedIds = requestedWorkflowIds.diff(requestedWorkflowIds.toSet.toSeq)
 
-    if(duplicatedIds.nonEmpty) {
+    if (duplicatedIds.nonEmpty) {
       Future.failed(DuplicateWorkflowIdsRequested(duplicatedIds))
     } else {
       findPreexistingWorkflowIds(requestedWorkflowIds) flatMap { preexistingIds =>
@@ -168,7 +184,7 @@ case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase, metadataSqlDa
     }
   }
 
-  override def switchOnHoldToSubmitted(id: WorkflowId)(implicit ec: ExecutionContext): Future[Unit] = {
+  override def switchOnHoldToSubmitted(id: WorkflowId)(implicit ec: ExecutionContext): Future[Unit] =
     for {
       updated <- sqlDatabase.updateWorkflowState(
         id.toString,
@@ -177,19 +193,17 @@ case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase, metadataSqlDa
       )
       _ <- if (updated == 0) Future.failed(NotInOnHoldStateException(id)) else Future.successful(())
     } yield ()
-  }
 
-  override def deleteFromStore(workflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Int] = {
+  override def deleteFromStore(workflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Int] =
     sqlDatabase.removeWorkflowStoreEntry(workflowId.toString)
-  }
 
   private def fromWorkflowStoreEntry(workflowStoreEntry: WorkflowStoreEntry): ErrorOr[WorkflowToStart] = {
 
-    val workflowOptionsValidation: ErrorOr[WorkflowOptions] = WorkflowOptions.fromJsonString(workflowStoreEntry.workflowOptions.toRawString).toErrorOr
+    val workflowOptionsValidation: ErrorOr[WorkflowOptions] =
+      WorkflowOptions.fromJsonString(workflowStoreEntry.workflowOptions.toRawString).toErrorOr
     val startableStateValidation = workflowStoreStateToStartableState(workflowStoreEntry)
 
     (startableStateValidation, workflowOptionsValidation) mapN { (startableState, workflowOptions) =>
-
       val id = WorkflowId.fromString(workflowStoreEntry.workflowExecutionUuid)
 
       val sources = WorkflowSourceFilesCollection(
@@ -207,7 +221,8 @@ case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase, metadataSqlDa
         requestedWorkflowId = Option(id)
       )
 
-      val hogGroup: HogGroup = workflowStoreEntry.hogGroup.map(HogGroup(_)).getOrElse(HogGroup.decide(workflowOptions, id))
+      val hogGroup: HogGroup =
+        workflowStoreEntry.hogGroup.map(HogGroup(_)).getOrElse(HogGroup.decide(workflowOptions, id))
 
       WorkflowToStart(
         id = id,
@@ -219,16 +234,15 @@ case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase, metadataSqlDa
     }
   }
 
-  private def workflowSubmissionState(workflowSourceFiles: WorkflowSourceFilesCollection) = {
+  private def workflowSubmissionState(workflowSourceFiles: WorkflowSourceFilesCollection) =
     if (workflowSourceFiles.workflowOnHold)
       WorkflowStoreState.OnHold
     else
       WorkflowStoreState.Submitted
-  }
 
   private def toWorkflowStoreEntry(workflowSourceFiles: WorkflowSourceFilesCollection): WorkflowStoreEntry = {
     import eu.timepit.refined._
-    val nonEmptyJsonString: String Refined NonEmpty  = refineMV[NonEmpty]("{}")
+    val nonEmptyJsonString: String Refined NonEmpty = refineMV[NonEmpty]("{}")
 
     val actualWorkflowState = workflowSubmissionState(workflowSourceFiles)
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowHeartbeatConfig.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowHeartbeatConfig.scala
index d27d6d5b1f6..99d35c8a02d 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowHeartbeatConfig.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowHeartbeatConfig.scala
@@ -25,13 +25,13 @@ import scala.concurrent.duration._
   * @param writeBatchSize     The maximum size of a write batch.
   * @param writeThreshold     The threshold of heartbeat writes above which load is considered high.
   */
-case class WorkflowHeartbeatConfig(
-                                    cromwellId: String,
-                                    heartbeatInterval: FiniteDuration,
-                                    ttl: FiniteDuration,
-                                    failureShutdownDuration: FiniteDuration,
-                                    writeBatchSize: Int,
-                                    writeThreshold: Int) {
+case class WorkflowHeartbeatConfig(cromwellId: String,
+                                   heartbeatInterval: FiniteDuration,
+                                   ttl: FiniteDuration,
+                                   failureShutdownDuration: FiniteDuration,
+                                   writeBatchSize: Int,
+                                   writeThreshold: Int
+) {
   override def toString: String = this.asInstanceOf[WorkflowHeartbeatConfig].asJson.spaces2
 }
 
@@ -41,14 +41,12 @@ object WorkflowHeartbeatConfig {
   // compiler flag settings then promote to an error.
 
   // NOTE: This is a different encoding than circe's finiteDurationEncoder: https://github.com/circe/circe/pull/978
-  private[engine] implicit lazy val encodeFiniteDuration: Encoder[FiniteDuration] = {
+  implicit private[engine] lazy val encodeFiniteDuration: Encoder[FiniteDuration] =
     Encoder.encodeString.contramap(_.toString)
-  }
-  private[engine] implicit lazy val encodeWorkflowHeartbeatConfig: Encoder[WorkflowHeartbeatConfig] = deriveEncoder
+  implicit private[engine] lazy val encodeWorkflowHeartbeatConfig: Encoder[WorkflowHeartbeatConfig] = deriveEncoder
 
-  def apply(config: Config): WorkflowHeartbeatConfig = {
+  def apply(config: Config): WorkflowHeartbeatConfig =
     validate(config).toTry("Errors parsing WorkflowHeartbeatConfig").get
-  }
 
   private def validate(config: Config): ErrorOr[WorkflowHeartbeatConfig] = {
     val randomSuffix = config
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStore.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStore.scala
index 375a24db8b3..8ca4d5314ef 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStore.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStore.scala
@@ -32,17 +32,21 @@ trait WorkflowStore {
     * Adds the requested WorkflowSourceFiles to the store and returns a WorkflowId for each one (in order)
     * for tracking purposes.
     */
-  def add(sources: NonEmptyList[WorkflowSourceFilesCollection])(implicit ec: ExecutionContext): Future[NonEmptyList[WorkflowSubmissionResponse]]
+  def add(sources: NonEmptyList[WorkflowSourceFilesCollection])(implicit
+    ec: ExecutionContext
+  ): Future[NonEmptyList[WorkflowSubmissionResponse]]
 
   /**
     * Retrieves up to n workflows which have not already been pulled into the engine and sets their pickedUp
     * flag to true
     */
-  def fetchStartableWorkflows(n: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])(implicit ec: ExecutionContext): Future[List[WorkflowToStart]]
+  def fetchStartableWorkflows(n: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])(
+    implicit ec: ExecutionContext
+  ): Future[List[WorkflowToStart]]
 
-  def writeWorkflowHeartbeats(workflowIds: Set[(WorkflowId, OffsetDateTime)],
-                              heartbeatDateTime: OffsetDateTime)
-                             (implicit ec: ExecutionContext): Future[Int]
+  def writeWorkflowHeartbeats(workflowIds: Set[(WorkflowId, OffsetDateTime)], heartbeatDateTime: OffsetDateTime)(
+    implicit ec: ExecutionContext
+  ): Future[Int]
 
   def switchOnHoldToSubmitted(id: WorkflowId)(implicit ec: ExecutionContext): Future[Unit]
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreAccess.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreAccess.scala
index 2086cd34256..16ad4ee669c 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreAccess.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreAccess.scala
@@ -24,17 +24,20 @@ import scala.concurrent.{ExecutionContext, Future}
   */
 sealed trait WorkflowStoreAccess {
   def writeWorkflowHeartbeats(workflowIds: NonEmptyVector[(WorkflowId, OffsetDateTime)],
-                              heartbeatDateTime: OffsetDateTime)
-                             (implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int]
+                              heartbeatDateTime: OffsetDateTime
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int]
 
-  def fetchStartableWorkflows(maxWorkflows: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])
-                             (implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[List[WorkflowToStart]]
+  def fetchStartableWorkflows(maxWorkflows: Int,
+                              cromwellId: String,
+                              heartbeatTtl: FiniteDuration,
+                              excludedGroups: Set[String]
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[List[WorkflowToStart]]
 
-  def abort(workflowId: WorkflowId)
-           (implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[WorkflowStoreAbortResponse]
+  def abort(
+    workflowId: WorkflowId
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[WorkflowStoreAbortResponse]
 
-  def deleteFromStore(workflowId: WorkflowId)
-                     (implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int]
+  def deleteFromStore(workflowId: WorkflowId)(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int]
 
 }
 
@@ -45,23 +48,26 @@ sealed trait WorkflowStoreAccess {
 case class UncoordinatedWorkflowStoreAccess(store: WorkflowStore) extends WorkflowStoreAccess {
 
   override def writeWorkflowHeartbeats(workflowIds: NonEmptyVector[(WorkflowId, OffsetDateTime)],
-                                       heartbeatDateTime: OffsetDateTime)
-                                      (implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int] = {
+                                       heartbeatDateTime: OffsetDateTime
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int] =
     store.writeWorkflowHeartbeats(workflowIds.toVector.toSet, heartbeatDateTime)
-  }
 
-  override def fetchStartableWorkflows(maxWorkflows: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])
-                                      (implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[List[WorkflowToStart]] = {
+  override def fetchStartableWorkflows(maxWorkflows: Int,
+                                       cromwellId: String,
+                                       heartbeatTtl: FiniteDuration,
+                                       excludedGroups: Set[String]
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[List[WorkflowToStart]] =
     store.fetchStartableWorkflows(maxWorkflows, cromwellId, heartbeatTtl, excludedGroups)
-  }
 
-  override def deleteFromStore(workflowId: WorkflowId)(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int] = {
+  override def deleteFromStore(
+    workflowId: WorkflowId
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int] =
     store.deleteFromStore(workflowId)
-  }
 
-  override def abort(workflowId: WorkflowId)(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[WorkflowStoreAbortResponse] = {
+  override def abort(
+    workflowId: WorkflowId
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[WorkflowStoreAbortResponse] =
     store.abort(workflowId)
-  }
 }
 
 /**
@@ -72,31 +78,42 @@ case class CoordinatedWorkflowStoreAccess(coordinatedWorkflowStoreAccessActor: A
   implicit val timeout = Timeout(WorkflowStoreCoordinatedAccessActor.Timeout)
 
   override def writeWorkflowHeartbeats(workflowIds: NonEmptyVector[(WorkflowId, OffsetDateTime)],
-                                       heartbeatDateTime: OffsetDateTime)
-                                      (implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int] = {
-    withRetryForTransactionRollback(
-      () => coordinatedWorkflowStoreAccessActor.ask(WorkflowStoreCoordinatedAccessActor.WriteHeartbeats(workflowIds, heartbeatDateTime)).mapTo[Int]
+                                       heartbeatDateTime: OffsetDateTime
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int] =
+    withRetryForTransactionRollback(() =>
+      coordinatedWorkflowStoreAccessActor
+        .ask(WorkflowStoreCoordinatedAccessActor.WriteHeartbeats(workflowIds, heartbeatDateTime))
+        .mapTo[Int]
     )
-  }
 
-  override def fetchStartableWorkflows(maxWorkflows: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])
-                                      (implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[List[WorkflowToStart]] = {
-    val message = WorkflowStoreCoordinatedAccessActor.FetchStartableWorkflows(maxWorkflows, cromwellId, heartbeatTtl, excludedGroups)
-    withRetryForTransactionRollback(
-      () => coordinatedWorkflowStoreAccessActor.ask(message).mapTo[List[WorkflowToStart]]
+  override def fetchStartableWorkflows(maxWorkflows: Int,
+                                       cromwellId: String,
+                                       heartbeatTtl: FiniteDuration,
+                                       excludedGroups: Set[String]
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[List[WorkflowToStart]] = {
+    val message = WorkflowStoreCoordinatedAccessActor.FetchStartableWorkflows(maxWorkflows,
+                                                                              cromwellId,
+                                                                              heartbeatTtl,
+                                                                              excludedGroups
     )
+    withRetryForTransactionRollback(() => coordinatedWorkflowStoreAccessActor.ask(message).mapTo[List[WorkflowToStart]])
   }
 
-  override def deleteFromStore(workflowId: WorkflowId)(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int] = {
-    withRetryForTransactionRollback(
-      () => coordinatedWorkflowStoreAccessActor.ask(WorkflowStoreCoordinatedAccessActor.DeleteFromStore(workflowId)).mapTo[Int]
+  override def deleteFromStore(
+    workflowId: WorkflowId
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[Int] =
+    withRetryForTransactionRollback(() =>
+      coordinatedWorkflowStoreAccessActor
+        .ask(WorkflowStoreCoordinatedAccessActor.DeleteFromStore(workflowId))
+        .mapTo[Int]
     )
-  }
 
-  override def abort(workflowId: WorkflowId)(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[WorkflowStoreAbortResponse] = {
-    withRetryForTransactionRollback(
-      () => coordinatedWorkflowStoreAccessActor.ask(WorkflowStoreCoordinatedAccessActor.Abort(workflowId)).mapTo[WorkflowStoreAbortResponse]
+  override def abort(
+    workflowId: WorkflowId
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[WorkflowStoreAbortResponse] =
+    withRetryForTransactionRollback(() =>
+      coordinatedWorkflowStoreAccessActor
+        .ask(WorkflowStoreCoordinatedAccessActor.Abort(workflowId))
+        .mapTo[WorkflowStoreAbortResponse]
     )
-  }
 }
-
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreActor.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreActor.scala
index 4bb31db4a6d..2d309f369c2 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreActor.scala
@@ -11,23 +11,23 @@ import cromwell.engine.CromwellTerminator
 import cromwell.util.GracefulShutdownHelper
 import cromwell.util.GracefulShutdownHelper.ShutdownCommand
 
-final case class WorkflowStoreActor private(
-                                             workflowStore: WorkflowStore,
+final case class WorkflowStoreActor private (workflowStore: WorkflowStore,
                                              workflowStoreAccess: WorkflowStoreAccess,
                                              serviceRegistryActor: ActorRef,
                                              terminator: CromwellTerminator,
                                              abortAllJobsOnTerminate: Boolean,
-                                             workflowHeartbeatConfig: WorkflowHeartbeatConfig)
-  extends Actor with ActorLogging with GracefulShutdownHelper {
+                                             workflowHeartbeatConfig: WorkflowHeartbeatConfig
+) extends Actor
+    with ActorLogging
+    with GracefulShutdownHelper {
   import WorkflowStoreActor._
 
   implicit val ec = context.dispatcher
 
   lazy val workflowStoreSubmitActor: ActorRef = context.actorOf(
-    WorkflowStoreSubmitActor.props(
-      workflowStoreDatabase = workflowStore,
-      serviceRegistryActor = serviceRegistryActor),
-    "WorkflowStoreSubmitActor")
+    WorkflowStoreSubmitActor.props(workflowStoreDatabase = workflowStore, serviceRegistryActor = serviceRegistryActor),
+    "WorkflowStoreSubmitActor"
+  )
 
   lazy val workflowStoreEngineActor: ActorRef = context.actorOf(
     WorkflowStoreEngineActor.props(
@@ -35,19 +35,24 @@ final case class WorkflowStoreActor private(
       workflowStoreAccess = workflowStoreAccess,
       serviceRegistryActor = serviceRegistryActor,
       abortAllJobsOnTerminate = abortAllJobsOnTerminate,
-      workflowHeartbeatConfig = workflowHeartbeatConfig),
-    "WorkflowStoreEngineActor")
+      workflowHeartbeatConfig = workflowHeartbeatConfig
+    ),
+    "WorkflowStoreEngineActor"
+  )
 
   lazy val workflowStoreHeartbeatWriteActor: ActorRef = context.actorOf(
     WorkflowStoreHeartbeatWriteActor.props(
       workflowStoreAccess = workflowStoreAccess,
       workflowHeartbeatConfig = workflowHeartbeatConfig,
       terminator = terminator,
-      serviceRegistryActor = serviceRegistryActor),
-    "WorkflowStoreHeartbeatWriteActor")
+      serviceRegistryActor = serviceRegistryActor
+    ),
+    "WorkflowStoreHeartbeatWriteActor"
+  )
 
   override def receive = {
-    case ShutdownCommand => waitForActorsAndShutdown(NonEmptyList.of(workflowStoreSubmitActor, workflowStoreEngineActor))
+    case ShutdownCommand =>
+      waitForActorsAndShutdown(NonEmptyList.of(workflowStoreSubmitActor, workflowStoreEngineActor))
     case cmd: WorkflowStoreActorSubmitCommand => workflowStoreSubmitActor forward cmd
     case cmd: WorkflowStoreActorEngineCommand => workflowStoreEngineActor forward cmd
     case cmd: WorkflowStoreWriteHeartbeatCommand => workflowStoreHeartbeatWriteActor forward cmd
@@ -75,26 +80,32 @@ object WorkflowStoreActor {
 
   sealed trait WorkflowStoreActorSubmitCommand
   final case class SubmitWorkflow(source: WorkflowSourceFilesCollection) extends WorkflowStoreActorSubmitCommand
-  final case class BatchSubmitWorkflows(sources: NonEmptyList[WorkflowSourceFilesCollection]) extends WorkflowStoreActorSubmitCommand
+  final case class BatchSubmitWorkflows(sources: NonEmptyList[WorkflowSourceFilesCollection])
+      extends WorkflowStoreActorSubmitCommand
 
   final case object GetWorkflowStoreStats
 
-  case class WorkflowStoreWriteHeartbeatCommand(workflowId: WorkflowId, submissionTime: OffsetDateTime, heartbeatTime: OffsetDateTime = OffsetDateTime.now())
+  case class WorkflowStoreWriteHeartbeatCommand(workflowId: WorkflowId,
+                                                submissionTime: OffsetDateTime,
+                                                heartbeatTime: OffsetDateTime = OffsetDateTime.now()
+  )
 
   def props(
-             workflowStoreDatabase: WorkflowStore,
-             workflowStoreAccess: WorkflowStoreAccess,
-             serviceRegistryActor: ActorRef,
-             terminator: CromwellTerminator,
-             abortAllJobsOnTerminate: Boolean,
-             workflowHeartbeatConfig: WorkflowHeartbeatConfig
-      ) = {
-    Props(WorkflowStoreActor(
-      workflowStore = workflowStoreDatabase,
-      workflowStoreAccess = workflowStoreAccess,
-      serviceRegistryActor = serviceRegistryActor,
-      terminator = terminator,
-      abortAllJobsOnTerminate = abortAllJobsOnTerminate,
-      workflowHeartbeatConfig = workflowHeartbeatConfig)).withDispatcher(EngineDispatcher)
-  }
+    workflowStoreDatabase: WorkflowStore,
+    workflowStoreAccess: WorkflowStoreAccess,
+    serviceRegistryActor: ActorRef,
+    terminator: CromwellTerminator,
+    abortAllJobsOnTerminate: Boolean,
+    workflowHeartbeatConfig: WorkflowHeartbeatConfig
+  ) =
+    Props(
+      WorkflowStoreActor(
+        workflowStore = workflowStoreDatabase,
+        workflowStoreAccess = workflowStoreAccess,
+        serviceRegistryActor = serviceRegistryActor,
+        terminator = terminator,
+        abortAllJobsOnTerminate = abortAllJobsOnTerminate,
+        workflowHeartbeatConfig = workflowHeartbeatConfig
+      )
+    ).withDispatcher(EngineDispatcher)
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreCoordinatedAccessActor.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreCoordinatedAccessActor.scala
index 3d36a5a8062..2adbfe25da5 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreCoordinatedAccessActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreCoordinatedAccessActor.scala
@@ -13,7 +13,6 @@ import scala.concurrent.{Await, ExecutionContext, Future}
 import scala.language.postfixOps
 import scala.util.{Failure, Success, Try}
 
-
 /**
   * Serializes access to the workflow store for workflow store writers that acquire locks to multiple rows inside a single
   * transaction and otherwise are prone to deadlock.
@@ -44,12 +43,18 @@ class WorkflowStoreCoordinatedAccessActor(workflowStore: WorkflowStore) extends
 
 object WorkflowStoreCoordinatedAccessActor {
   final case class WriteHeartbeats(workflowIds: NonEmptyVector[(WorkflowId, OffsetDateTime)],
-                                   heartbeatDateTime: OffsetDateTime)
-  final case class FetchStartableWorkflows(count: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])
+                                   heartbeatDateTime: OffsetDateTime
+  )
+  final case class FetchStartableWorkflows(count: Int,
+                                           cromwellId: String,
+                                           heartbeatTtl: FiniteDuration,
+                                           excludedGroups: Set[String]
+  )
   final case class DeleteFromStore(workflowId: WorkflowId)
   final case class Abort(workflowId: WorkflowId)
 
   val Timeout = 1 minute
 
-  def props(workflowStore: WorkflowStore): Props = Props(new WorkflowStoreCoordinatedAccessActor(workflowStore)).withDispatcher(Dispatcher.IoDispatcher)
+  def props(workflowStore: WorkflowStore): Props =
+    Props(new WorkflowStoreCoordinatedAccessActor(workflowStore)).withDispatcher(Dispatcher.IoDispatcher)
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreEngineActor.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreEngineActor.scala
index 44ecc09f1c8..a2fec62eda9 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreEngineActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreEngineActor.scala
@@ -5,7 +5,7 @@ import cats.data.NonEmptyList
 import cromwell.core.Dispatcher._
 import cromwell.core.WorkflowProcessingEvents.DescriptionEventValue.PickedUp
 import cromwell.core._
-import cromwell.core.abort.{WorkflowAbortFailureResponse, WorkflowAbortRequestedResponse, WorkflowAbortedResponse}
+import cromwell.core.abort.{WorkflowAbortedResponse, WorkflowAbortFailureResponse, WorkflowAbortRequestedResponse}
 import cromwell.engine.instrumentation.WorkflowInstrumentation
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
 import cromwell.engine.workflow.{WorkflowMetadataHelper, WorkflowProcessingEventPublishing}
@@ -20,12 +20,17 @@ import org.apache.commons.lang3.exception.ExceptionUtils
 import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success}
 
-final case class WorkflowStoreEngineActor private(store: WorkflowStore,
-                                                  workflowStoreAccess: WorkflowStoreAccess,
-                                                  serviceRegistryActor: ActorRef,
-                                                  abortAllJobsOnTerminate: Boolean,
-                                                  workflowHeartbeatConfig: WorkflowHeartbeatConfig)
-  extends LoggingFSM[WorkflowStoreActorState, WorkflowStoreActorData] with ActorLogging with WorkflowInstrumentation with CromwellInstrumentationScheduler with WorkflowMetadataHelper with Timers {
+final case class WorkflowStoreEngineActor private (store: WorkflowStore,
+                                                   workflowStoreAccess: WorkflowStoreAccess,
+                                                   serviceRegistryActor: ActorRef,
+                                                   abortAllJobsOnTerminate: Boolean,
+                                                   workflowHeartbeatConfig: WorkflowHeartbeatConfig
+) extends LoggingFSM[WorkflowStoreActorState, WorkflowStoreActorData]
+    with ActorLogging
+    with WorkflowInstrumentation
+    with CromwellInstrumentationScheduler
+    with WorkflowMetadataHelper
+    with Timers {
 
   implicit val actorSystem: ActorSystem = context.system
   implicit val ec: ExecutionContext = context.dispatcher
@@ -63,12 +68,11 @@ final case class WorkflowStoreEngineActor private(store: WorkflowStore,
       stay() using stateData.withPendingCommand(x, sender())
   }
 
-  when(Idle) {
-    case Event(cmd: WorkflowStoreActorEngineCommand, _) =>
-      if (stateData.currentOperation.nonEmpty || stateData.pendingOperations.nonEmpty) {
-        log.error("Non-empty WorkflowStoreActorData when in Idle state: {}", stateData)
-      }
-      startNewWork(cmd, sender(), stateData.withCurrentCommand(cmd, sender()))
+  when(Idle) { case Event(cmd: WorkflowStoreActorEngineCommand, _) =>
+    if (stateData.currentOperation.nonEmpty || stateData.pendingOperations.nonEmpty) {
+      log.error("Non-empty WorkflowStoreActorData when in Idle state: {}", stateData)
+    }
+    startNewWork(cmd, sender(), stateData.withCurrentCommand(cmd, sender()))
   }
 
   when(Working) {
@@ -93,12 +97,14 @@ final case class WorkflowStoreEngineActor private(store: WorkflowStore,
       stay()
   }
 
-  onTransition {
-    case fromState -> toState =>
-      log.debug("WorkflowStore moving from {} (using {}) to {} (using {})", fromState, stateData, toState, nextStateData)
+  onTransition { case fromState -> toState =>
+    log.debug("WorkflowStore moving from {} (using {}) to {} (using {})", fromState, stateData, toState, nextStateData)
   }
 
-  private def startNewWork(command: WorkflowStoreActorEngineCommand, sndr: ActorRef, nextData: WorkflowStoreActorData) = {
+  private def startNewWork(command: WorkflowStoreActorEngineCommand,
+                           sndr: ActorRef,
+                           nextData: WorkflowStoreActorData
+  ) = {
     val work: Future[Any] = command match {
       case FetchRunnableWorkflows(count, excludedGroups) =>
         newWorkflowMessage(count, excludedGroups) map { response =>
@@ -113,7 +119,11 @@ final case class WorkflowStoreEngineActor private(store: WorkflowStore,
               )
 
               workflowsIds foreach { w =>
-                WorkflowProcessingEventPublishing.publish(w, workflowHeartbeatConfig.cromwellId, PickedUp, serviceRegistryActor)
+                WorkflowProcessingEventPublishing.publish(w,
+                                                          workflowHeartbeatConfig.cromwellId,
+                                                          PickedUp,
+                                                          serviceRegistryActor
+                )
               }
 
             case NoNewWorkflowsToStart => log.debug("No workflows fetched by {}", workflowHeartbeatConfig.cromwellId)
@@ -122,10 +132,10 @@ final case class WorkflowStoreEngineActor private(store: WorkflowStore,
           sndr ! response
         }
       case FindWorkflowsWithAbortRequested(cromwellId) =>
-        store.findWorkflowsWithAbortRequested(cromwellId) map {
-          ids => sndr ! FindWorkflowsWithAbortRequestedSuccess(ids)
-        } recover {
-          case t => sndr ! FindWorkflowsWithAbortRequestedFailure(t)
+        store.findWorkflowsWithAbortRequested(cromwellId) map { ids =>
+          sndr ! FindWorkflowsWithAbortRequestedSuccess(ids)
+        } recover { case t =>
+          sndr ! FindWorkflowsWithAbortRequestedFailure(t)
         }
       case AbortWorkflowCommand(id) =>
         workflowStoreAccess.abort(id) map { workflowStoreAbortResponse =>
@@ -139,14 +149,16 @@ final case class WorkflowStoreEngineActor private(store: WorkflowStore,
             pushCurrentStateToMetadataService(id, WorkflowAborting)
             sndr ! WorkflowAbortRequestedResponse(id)
           case WorkflowStoreAbortResponse.NotFound =>
-            sndr ! WorkflowAbortFailureResponse(id, new WorkflowNotFoundException(s"Couldn't abort $id because no workflow with that ID is in progress"))
-        } recover {
-          case t =>
-            val message = s"Unable to update workflow store to abort $id"
-            log.error(t, message)
-            // A generic exception type like RuntimeException will produce a 500 at the API layer, which seems appropriate
-            // given we don't know much about what went wrong here.  `t.getMessage` so the cause propagates to the client.
-            sndr ! WorkflowAbortFailureResponse(id, new RuntimeException(s"$message: ${t.getMessage}", t))
+            sndr ! WorkflowAbortFailureResponse(
+              id,
+              new WorkflowNotFoundException(s"Couldn't abort $id because no workflow with that ID is in progress")
+            )
+        } recover { case t =>
+          val message = s"Unable to update workflow store to abort $id"
+          log.error(t, message)
+          // A generic exception type like RuntimeException will produce a 500 at the API layer, which seems appropriate
+          // given we don't know much about what went wrong here.  `t.getMessage` so the cause propagates to the client.
+          sndr ! WorkflowAbortFailureResponse(id, new RuntimeException(s"$message: ${t.getMessage}", t))
         }
       case AbortAllRunningWorkflowsCommandAndStop =>
         store.abortAllRunning() map { _ =>
@@ -158,11 +170,10 @@ final case class WorkflowStoreEngineActor private(store: WorkflowStore,
           sndr ! WorkflowOnHoldToSubmittedSuccess(id)
           pushCurrentStateToMetadataService(id, WorkflowSubmitted)
           log.info(s"Status changed to 'Submitted' for $id")
-        } recover {
-          case t =>
-            val message = s"Couldn't change the status to 'Submitted' from 'On Hold' for workflow $id"
-            log.error(message)
-            sndr ! WorkflowOnHoldToSubmittedFailure(id, t)
+        } recover { case t =>
+          val message = s"Couldn't change the status to 'Submitted' from 'On Hold' for workflow $id"
+          log.error(message)
+          sndr ! WorkflowOnHoldToSubmittedFailure(id, t)
         }
       case oops =>
         log.error("Unexpected type of start work command: {}", oops.getClass.getSimpleName)
@@ -172,64 +183,81 @@ final case class WorkflowStoreEngineActor private(store: WorkflowStore,
     goto(Working) using nextData
   }
 
-  private def addWorkCompletionHooks[A](command: WorkflowStoreActorEngineCommand, work: Future[A]) = {
+  private def addWorkCompletionHooks[A](command: WorkflowStoreActorEngineCommand, work: Future[A]) =
     work.onComplete {
       case Success(_) =>
         self ! WorkDone
       case Failure(t) =>
-        log.error("Error occurred during {}: {} because {}", command.getClass.getSimpleName, t.toString, ExceptionUtils.getStackTrace(t))
+        log.error("Error occurred during {}: {} because {}",
+                  command.getClass.getSimpleName,
+                  t.toString,
+                  ExceptionUtils.getStackTrace(t)
+        )
         self ! WorkDone
     }
-  }
 
   /**
     * Fetches at most n workflows, and builds the correct response message based on if there were any workflows or not
     */
-  private def newWorkflowMessage(maxWorkflows: Int, excludedGroups: Set[String]): Future[WorkflowStoreEngineActorResponse] = {
-    def fetchStartableWorkflowsIfNeeded = {
+  private def newWorkflowMessage(maxWorkflows: Int,
+                                 excludedGroups: Set[String]
+  ): Future[WorkflowStoreEngineActorResponse] = {
+    def fetchStartableWorkflowsIfNeeded =
       if (maxWorkflows > 0) {
-        workflowStoreAccess.fetchStartableWorkflows(maxWorkflows, workflowHeartbeatConfig.cromwellId, workflowHeartbeatConfig.ttl, excludedGroups)
+        workflowStoreAccess.fetchStartableWorkflows(maxWorkflows,
+                                                    workflowHeartbeatConfig.cromwellId,
+                                                    workflowHeartbeatConfig.ttl,
+                                                    excludedGroups
+        )
       } else {
         Future.successful(List.empty[WorkflowToStart])
       }
-    }
 
     fetchStartableWorkflowsIfNeeded map {
       case x :: xs => NewWorkflowsToStart(NonEmptyList.of(x, xs: _*))
       case _ => NoNewWorkflowsToStart
-    } recover {
-      case e =>
-        // Log the error but return a successful Future so as not to hang future workflow store polls.
-        log.error(e, "Error trying to fetch new workflows")
-        NoNewWorkflowsToStart
+    } recover { case e =>
+      // Log the error but return a successful Future so as not to hang future workflow store polls.
+      log.error(e, "Error trying to fetch new workflows")
+      NoNewWorkflowsToStart
     }
   }
 }
 
 object WorkflowStoreEngineActor {
   def props(
-             workflowStore: WorkflowStore,
-             workflowStoreAccess: WorkflowStoreAccess,
-             serviceRegistryActor: ActorRef,
-             abortAllJobsOnTerminate: Boolean,
-             workflowHeartbeatConfig: WorkflowHeartbeatConfig
-             ) = {
-    Props(WorkflowStoreEngineActor(workflowStore, workflowStoreAccess, serviceRegistryActor, abortAllJobsOnTerminate, workflowHeartbeatConfig)).withDispatcher(EngineDispatcher)
-  }
+    workflowStore: WorkflowStore,
+    workflowStoreAccess: WorkflowStoreAccess,
+    serviceRegistryActor: ActorRef,
+    abortAllJobsOnTerminate: Boolean,
+    workflowHeartbeatConfig: WorkflowHeartbeatConfig
+  ) =
+    Props(
+      WorkflowStoreEngineActor(workflowStore,
+                               workflowStoreAccess,
+                               serviceRegistryActor,
+                               abortAllJobsOnTerminate,
+                               workflowHeartbeatConfig
+      )
+    ).withDispatcher(EngineDispatcher)
 
   sealed trait WorkflowStoreEngineActorResponse
   case object NoNewWorkflowsToStart extends WorkflowStoreEngineActorResponse
-  final case class NewWorkflowsToStart(workflows: NonEmptyList[WorkflowToStart]) extends WorkflowStoreEngineActorResponse
+  final case class NewWorkflowsToStart(workflows: NonEmptyList[WorkflowToStart])
+      extends WorkflowStoreEngineActorResponse
 
   final case class WorkflowStoreActorCommandWithSender(command: WorkflowStoreActorEngineCommand, sender: ActorRef)
 
-  final case class WorkflowStoreActorData(currentOperation: Option[WorkflowStoreActorCommandWithSender], pendingOperations: List[WorkflowStoreActorCommandWithSender]) {
-    def withCurrentCommand(command: WorkflowStoreActorEngineCommand, sender: ActorRef) = this.copy(currentOperation = Option(WorkflowStoreActorCommandWithSender(command, sender)))
-    def withPendingCommand(newCommand: WorkflowStoreActorEngineCommand, sender: ActorRef) = this.copy(pendingOperations = this.pendingOperations :+ WorkflowStoreActorCommandWithSender(newCommand, sender))
-    def pop = {
+  final case class WorkflowStoreActorData(currentOperation: Option[WorkflowStoreActorCommandWithSender],
+                                          pendingOperations: List[WorkflowStoreActorCommandWithSender]
+  ) {
+    def withCurrentCommand(command: WorkflowStoreActorEngineCommand, sender: ActorRef) =
+      this.copy(currentOperation = Option(WorkflowStoreActorCommandWithSender(command, sender)))
+    def withPendingCommand(newCommand: WorkflowStoreActorEngineCommand, sender: ActorRef) =
+      this.copy(pendingOperations = this.pendingOperations :+ WorkflowStoreActorCommandWithSender(newCommand, sender))
+    def pop =
       if (pendingOperations.isEmpty) { WorkflowStoreActorData(None, List.empty) }
       else { WorkflowStoreActorData(Option(pendingOperations.head), pendingOperations.tail) }
-    }
   }
 
   sealed trait WorkflowStoreActorState
@@ -239,5 +267,6 @@ object WorkflowStoreEngineActor {
 
   sealed trait WorkflowOnHoldToSubmittedResponse
   case class WorkflowOnHoldToSubmittedSuccess(workflowId: WorkflowId) extends WorkflowOnHoldToSubmittedResponse
-  case class WorkflowOnHoldToSubmittedFailure(workflowId: WorkflowId, failure: Throwable) extends WorkflowOnHoldToSubmittedResponse
+  case class WorkflowOnHoldToSubmittedFailure(workflowId: WorkflowId, failure: Throwable)
+      extends WorkflowOnHoldToSubmittedResponse
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreHeartbeatWriteActor.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreHeartbeatWriteActor.scala
index ee88627cdfe..2cefd06ad7f 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreHeartbeatWriteActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreHeartbeatWriteActor.scala
@@ -1,6 +1,6 @@
 package cromwell.engine.workflow.workflowstore
 
-import java.time.{OffsetDateTime, Duration => JDuration}
+import java.time.{Duration => JDuration, OffsetDateTime}
 import java.util.concurrent.TimeUnit
 
 import akka.actor.{ActorRef, ActorSystem, CoordinatedShutdown, Props}
@@ -20,11 +20,10 @@ import scala.util.{Failure, Success, Try}
 case class WorkflowStoreHeartbeatWriteActor(workflowStoreAccess: WorkflowStoreAccess,
                                             workflowHeartbeatConfig: WorkflowHeartbeatConfig,
                                             terminator: CromwellTerminator,
-                                            override val serviceRegistryActor: ActorRef)
-
-  extends EnhancedBatchActor[WorkflowStoreWriteHeartbeatCommand](
-    flushRate = workflowHeartbeatConfig.heartbeatInterval,
-    batchSize = workflowHeartbeatConfig.writeBatchSize) {
+                                            override val serviceRegistryActor: ActorRef
+) extends EnhancedBatchActor[WorkflowStoreWriteHeartbeatCommand](flushRate = workflowHeartbeatConfig.heartbeatInterval,
+                                                                 batchSize = workflowHeartbeatConfig.writeBatchSize
+    ) {
 
   implicit val actorSystem: ActorSystem = context.system
 
@@ -32,7 +31,7 @@ case class WorkflowStoreHeartbeatWriteActor(workflowStoreAccess: WorkflowStoreAc
 
   private val failureShutdownDuration = workflowHeartbeatConfig.failureShutdownDuration
 
-  //noinspection ActorMutableStateInspection
+  // noinspection ActorMutableStateInspection
   private var lastSuccessOption: Option[OffsetDateTime] = None
 
   /**
@@ -40,50 +39,52 @@ case class WorkflowStoreHeartbeatWriteActor(workflowStoreAccess: WorkflowStoreAc
     *
     * @return the number of elements processed
     */
-  override protected def process(data: NonEmptyVector[WorkflowStoreWriteHeartbeatCommand]): Future[Int] = instrumentedProcess {
-    val now = OffsetDateTime.now()
-
-    val warnDuration = (failureShutdownDuration + workflowHeartbeatConfig.heartbeatInterval) / 2
-    val warnThreshold = warnDuration.toNanos
-    val errorThreshold = failureShutdownDuration.toNanos
-
-    // Traverse these heartbeats looking for staleness of warning or error severity.
-    val (warningIds, errorIds) = data.foldLeft((Seq.empty[WorkflowId], Seq.empty[WorkflowId])) { case ((w, e), h) =>
-      val staleness = JDuration.between(h.heartbeatTime, now).toNanos
-
-      // w = warning ids, e = error ids, h = heartbeat datum
-      if (staleness > errorThreshold) (w, e :+ h.workflowId)
-      else if (staleness > warnThreshold) (w :+ h.workflowId, e)
-      else (w, e)
-    }
+  override protected def process(data: NonEmptyVector[WorkflowStoreWriteHeartbeatCommand]): Future[Int] =
+    instrumentedProcess {
+      val now = OffsetDateTime.now()
+
+      val warnDuration = (failureShutdownDuration + workflowHeartbeatConfig.heartbeatInterval) / 2
+      val warnThreshold = warnDuration.toNanos
+      val errorThreshold = failureShutdownDuration.toNanos
+
+      // Traverse these heartbeats looking for staleness of warning or error severity.
+      val (warningIds, errorIds) = data.foldLeft((Seq.empty[WorkflowId], Seq.empty[WorkflowId])) { case ((w, e), h) =>
+        val staleness = JDuration.between(h.heartbeatTime, now).toNanos
+
+        // w = warning ids, e = error ids, h = heartbeat datum
+        if (staleness > errorThreshold) (w, e :+ h.workflowId)
+        else if (staleness > warnThreshold) (w :+ h.workflowId, e)
+        else (w, e)
+      }
 
-    if (warningIds.nonEmpty) {
-      log.warning(
-        "Found {} stale workflow heartbeats (more than {} old): {}",
-        warningIds.size.toString,
-        warnDuration.toString(),
-        warningIds.mkString(", ")
-      )
-    }
+      if (warningIds.nonEmpty) {
+        log.warning(
+          "Found {} stale workflow heartbeats (more than {} old): {}",
+          warningIds.size.toString,
+          warnDuration.toString(),
+          warningIds.mkString(", ")
+        )
+      }
 
-    if (errorIds.isEmpty) {
-      val processFuture = workflowStoreAccess.writeWorkflowHeartbeats(data.map { h => (h.workflowId, h.submissionTime) }, now)
-      processFuture transform {
-        // Track the `Try`, and then return the original `Try`. Similar to `andThen` but doesn't swallow exceptions.
-        _ <| trackRepeatedFailures(now, data.length)
+      if (errorIds.isEmpty) {
+        val processFuture =
+          workflowStoreAccess.writeWorkflowHeartbeats(data.map(h => (h.workflowId, h.submissionTime)), now)
+        processFuture transform {
+          // Track the `Try`, and then return the original `Try`. Similar to `andThen` but doesn't swallow exceptions.
+          _ <| trackRepeatedFailures(now, data.length)
+        }
+      } else {
+        log.error(
+          "Shutting down Cromwell instance {} as {} stale workflow heartbeats (more than {} old) were found: {}",
+          workflowHeartbeatConfig.cromwellId,
+          errorIds.size.toString,
+          failureShutdownDuration.toString(),
+          errorIds.mkString(", ")
+        )
+        terminator.beginCromwellShutdown(WorkflowStoreHeartbeatWriteActor.Shutdown)
+        Future.successful(0)
       }
-    } else {
-      log.error(
-        "Shutting down Cromwell instance {} as {} stale workflow heartbeats (more than {} old) were found: {}",
-        workflowHeartbeatConfig.cromwellId,
-        errorIds.size.toString,
-        failureShutdownDuration.toString(),
-        errorIds.mkString(", ")
-      )
-      terminator.beginCromwellShutdown(WorkflowStoreHeartbeatWriteActor.Shutdown)
-      Future.successful(0)
     }
-  }
 
   override def receive: Receive = enhancedReceive.orElse(super.receive)
   override protected def weightFunction(command: WorkflowStoreWriteHeartbeatCommand) = 1
@@ -100,7 +101,7 @@ case class WorkflowStoreHeartbeatWriteActor(workflowStoreAccess: WorkflowStoreAc
   We are expecting the underlying FSM to ensure that the call to this method does NOT occur in parallel, waiting for
   the call to `process` to complete.
    */
-  private def trackRepeatedFailures(heartbeatDateTime: OffsetDateTime, workflowCount: Int)(processTry: Try[Int]): Unit = {
+  private def trackRepeatedFailures(heartbeatDateTime: OffsetDateTime, workflowCount: Int)(processTry: Try[Int]): Unit =
     processTry match {
       case Success(_) =>
         lastSuccessOption = Option(heartbeatDateTime)
@@ -118,15 +119,17 @@ case class WorkflowStoreHeartbeatWriteActor(workflowStoreAccess: WorkflowStoreAc
         if (failureJDuration.toNanos >= failureShutdownDuration.toNanos) {
           val failureUnits = failureShutdownDuration.unit
           val failureLength = FiniteDuration(failureJDuration.toNanos, TimeUnit.NANOSECONDS).toUnit(failureUnits)
-          log.error(String.format(
-            "Shutting down %s as at least %d heartbeat write errors have occurred between %s and %s (%s %s)",
-            workflowHeartbeatConfig.cromwellId,
-            Integer.valueOf(workflowCount),
-            lastSuccess,
-            now,
-            failureLength.toString,
-            failureUnits.toString.toLowerCase
-          ))
+          log.error(
+            String.format(
+              "Shutting down %s as at least %d heartbeat write errors have occurred between %s and %s (%s %s)",
+              workflowHeartbeatConfig.cromwellId,
+              Integer.valueOf(workflowCount),
+              lastSuccess,
+              now,
+              failureLength.toString,
+              failureUnits.toString.toLowerCase
+            )
+          )
           terminator.beginCromwellShutdown(WorkflowStoreHeartbeatWriteActor.Shutdown)
         }
         ()
@@ -135,7 +138,6 @@ case class WorkflowStoreHeartbeatWriteActor(workflowStoreAccess: WorkflowStoreAc
         terminator.beginCromwellShutdown(WorkflowStoreHeartbeatWriteActor.Shutdown)
         ()
     }
-  }
 
 }
 
@@ -143,16 +145,17 @@ object WorkflowStoreHeartbeatWriteActor {
   object Shutdown extends CoordinatedShutdown.Reason
 
   def props(
-             workflowStoreAccess: WorkflowStoreAccess,
-             workflowHeartbeatConfig: WorkflowHeartbeatConfig,
-             terminator: CromwellTerminator,
-             serviceRegistryActor: ActorRef
-           ): Props =
+    workflowStoreAccess: WorkflowStoreAccess,
+    workflowHeartbeatConfig: WorkflowHeartbeatConfig,
+    terminator: CromwellTerminator,
+    serviceRegistryActor: ActorRef
+  ): Props =
     Props(
       WorkflowStoreHeartbeatWriteActor(
         workflowStoreAccess = workflowStoreAccess,
         workflowHeartbeatConfig = workflowHeartbeatConfig,
         terminator = terminator,
         serviceRegistryActor = serviceRegistryActor
-      )).withDispatcher(EngineDispatcher)
+      )
+    ).withDispatcher(EngineDispatcher)
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreSubmitActor.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreSubmitActor.scala
index 5ba36f8befe..6920e1a40be 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreSubmitActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreSubmitActor.scala
@@ -14,7 +14,11 @@ import cromwell.engine.workflow.WorkflowProcessingEventPublishing._
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.WorkflowStoreState.WorkflowStoreState
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.{WorkflowStoreState, WorkflowSubmissionResponse}
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor._
-import cromwell.engine.workflow.workflowstore.WorkflowStoreSubmitActor.{WorkflowSubmitFailed, WorkflowSubmittedToStore, WorkflowsBatchSubmittedToStore}
+import cromwell.engine.workflow.workflowstore.WorkflowStoreSubmitActor.{
+  WorkflowsBatchSubmittedToStore,
+  WorkflowSubmitFailed,
+  WorkflowSubmittedToStore
+}
 import cromwell.services.metadata.MetadataService.PutMetadataAction
 import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
 import spray.json._
@@ -22,8 +26,12 @@ import spray.json._
 import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success}
 
-final case class WorkflowStoreSubmitActor(store: WorkflowStore, serviceRegistryActor: ActorRef) extends Actor 
-  with ActorLogging with WorkflowMetadataHelper with MonitoringCompanionHelper with WorkflowInstrumentation {
+final case class WorkflowStoreSubmitActor(store: WorkflowStore, serviceRegistryActor: ActorRef)
+    extends Actor
+    with ActorLogging
+    with WorkflowMetadataHelper
+    with MonitoringCompanionHelper
+    with WorkflowInstrumentation {
   implicit val ec: ExecutionContext = context.dispatcher
 
   val workflowStoreReceive: Receive = {
@@ -80,32 +88,32 @@ final case class WorkflowStoreSubmitActor(store: WorkflowStore, serviceRegistryA
           removeWork()
       }
   }
-  
+
   override def receive = workflowStoreReceive.orElse(monitoringReceive)
 
-  private def convertDatabaseStateToApiState(workflowStoreState: WorkflowStoreState): WorkflowState ={
+  private def convertDatabaseStateToApiState(workflowStoreState: WorkflowStoreState): WorkflowState =
     workflowStoreState match {
       case WorkflowStoreState.Submitted => WorkflowSubmitted
       case WorkflowStoreState.OnHold => WorkflowOnHold
       case WorkflowStoreState.Aborting => WorkflowAborting
       case WorkflowStoreState.Running => WorkflowRunning
     }
-  }
 
-  private def storeWorkflowSources(sources: NonEmptyList[WorkflowSourceFilesCollection]): Future[NonEmptyList[WorkflowSubmissionResponse]] = {
+  private def storeWorkflowSources(
+    sources: NonEmptyList[WorkflowSourceFilesCollection]
+  ): Future[NonEmptyList[WorkflowSubmissionResponse]] =
     for {
       workflowSubmissionResponses <- store.add(sources)
     } yield workflowSubmissionResponses
-  }
 
-  private def convertJsonToLabelsMap(json: String): Map[String, String] = {
+  private def convertJsonToLabelsMap(json: String): Map[String, String] =
     json.parseJson match {
-      case JsObject(inputs) => inputs.collect({
-        case (key, JsString(value)) => key -> value
-      })
+      case JsObject(inputs) =>
+        inputs.collect { case (key, JsString(value)) =>
+          key -> value
+        }
       case _ => Map.empty
     }
-  }
 
   /**
     * Runs processing on workflow source files before they are stored.
@@ -114,61 +122,97 @@ final case class WorkflowStoreSubmitActor(store: WorkflowStore, serviceRegistryA
     * @param source         Original workflow source
     * @return Attempted updated workflow source
     */
-  private def processSource(processOptions: WorkflowOptions => WorkflowOptions)
-                           (source: WorkflowSourceFilesCollection): WorkflowSourceFilesCollection = {
-
+  private def processSource(processOptions: WorkflowOptions => WorkflowOptions)(
+    source: WorkflowSourceFilesCollection
+  ): WorkflowSourceFilesCollection =
     source.setOptions(processOptions(source.workflowOptions))
-  }
 
   /**
     * Takes the workflow id and sends it over to the metadata service w/ default empty values for inputs/outputs
     */
-  private def registerSubmission(
-      id: WorkflowId,
-      originalSourceFiles: WorkflowSourceFilesCollection): Unit = {
+  private def registerSubmission(id: WorkflowId, originalSourceFiles: WorkflowSourceFilesCollection): Unit = {
     // Increment the workflow submitted count
     incrementWorkflowState(WorkflowSubmitted)
 
-    val actualWorkflowState = if(originalSourceFiles.workflowOnHold)
-      WorkflowOnHold
-    else
-      WorkflowSubmitted
+    val actualWorkflowState =
+      if (originalSourceFiles.workflowOnHold)
+        WorkflowOnHold
+      else
+        WorkflowSubmitted
 
     val sourceFiles = processSource(_.clearEncryptedValues)(originalSourceFiles)
 
-      val submissionEvents: List[MetadataEvent] = List(
-        MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionTime), MetadataValue(OffsetDateTime.now)),
-        MetadataEvent.empty(MetadataKey(id, None, WorkflowMetadataKeys.Inputs)),
-        MetadataEvent.empty(MetadataKey(id, None, WorkflowMetadataKeys.Outputs)),
-        MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.Status), MetadataValue(actualWorkflowState)),
-
-        MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Workflow), MetadataValue(sourceFiles.workflowSource.orNull)),
-        MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_WorkflowUrl), MetadataValue(sourceFiles.workflowUrl.orNull)),
-        MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Root), MetadataValue(sourceFiles.workflowRoot.orNull)),
-        MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Inputs), MetadataValue(sourceFiles.inputsJson)),
-        MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Options), MetadataValue(sourceFiles.workflowOptions.asPrettyJson)),
-        MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Labels), MetadataValue(sourceFiles.labelsJson))
-      )
-
-      // Don't publish metadata for either workflow type or workflow type version if not defined.
-      val workflowTypeAndVersionEvents: List[Option[MetadataEvent]] = List(
-        sourceFiles.workflowType map { wt => MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_WorkflowType), MetadataValue(wt)) },
-        sourceFiles.workflowTypeVersion map { wtv => MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_WorkflowTypeVersion), MetadataValue(wtv)) }
+    val submissionEvents: List[MetadataEvent] = List(
+      MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.SubmissionTime), MetadataValue(OffsetDateTime.now)),
+      MetadataEvent.empty(MetadataKey(id, None, WorkflowMetadataKeys.Inputs)),
+      MetadataEvent.empty(MetadataKey(id, None, WorkflowMetadataKeys.Outputs)),
+      MetadataEvent(MetadataKey(id, None, WorkflowMetadataKeys.Status), MetadataValue(actualWorkflowState)),
+      MetadataEvent(
+        MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Workflow),
+        MetadataValue(sourceFiles.workflowSource.orNull)
+      ),
+      MetadataEvent(
+        MetadataKey(id,
+                    None,
+                    WorkflowMetadataKeys.SubmissionSection,
+                    WorkflowMetadataKeys.SubmissionSection_WorkflowUrl
+        ),
+        MetadataValue(sourceFiles.workflowUrl.orNull)
+      ),
+      MetadataEvent(
+        MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Root),
+        MetadataValue(sourceFiles.workflowRoot.orNull)
+      ),
+      MetadataEvent(
+        MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Inputs),
+        MetadataValue(sourceFiles.inputsJson)
+      ),
+      MetadataEvent(
+        MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Options),
+        MetadataValue(sourceFiles.workflowOptions.asPrettyJson)
+      ),
+      MetadataEvent(
+        MetadataKey(id, None, WorkflowMetadataKeys.SubmissionSection, WorkflowMetadataKeys.SubmissionSection_Labels),
+        MetadataValue(sourceFiles.labelsJson)
       )
+    )
+
+    // Don't publish metadata for either workflow type or workflow type version if not defined.
+    val workflowTypeAndVersionEvents: List[Option[MetadataEvent]] = List(
+      sourceFiles.workflowType map { wt =>
+        MetadataEvent(MetadataKey(id,
+                                  None,
+                                  WorkflowMetadataKeys.SubmissionSection,
+                                  WorkflowMetadataKeys.SubmissionSection_WorkflowType
+                      ),
+                      MetadataValue(wt)
+        )
+      },
+      sourceFiles.workflowTypeVersion map { wtv =>
+        MetadataEvent(MetadataKey(id,
+                                  None,
+                                  WorkflowMetadataKeys.SubmissionSection,
+                                  WorkflowMetadataKeys.SubmissionSection_WorkflowTypeVersion
+                      ),
+                      MetadataValue(wtv)
+        )
+      }
+    )
 
-      serviceRegistryActor ! PutMetadataAction(submissionEvents ++ workflowTypeAndVersionEvents.flatten)
-      ()
+    serviceRegistryActor ! PutMetadataAction(submissionEvents ++ workflowTypeAndVersionEvents.flatten)
+    ()
   }
 }
 
 object WorkflowStoreSubmitActor {
-  def props(workflowStoreDatabase: WorkflowStore, serviceRegistryActor: ActorRef) = {
+  def props(workflowStoreDatabase: WorkflowStore, serviceRegistryActor: ActorRef) =
     Props(WorkflowStoreSubmitActor(workflowStoreDatabase, serviceRegistryActor)).withDispatcher(ApiDispatcher)
-  }
 
   sealed trait WorkflowStoreSubmitActorResponse
-  final case class WorkflowSubmittedToStore(workflowId: WorkflowId, state: WorkflowState) extends WorkflowStoreSubmitActorResponse
-  final case class WorkflowsBatchSubmittedToStore(workflowIds: NonEmptyList[WorkflowId], state: WorkflowState) extends WorkflowStoreSubmitActorResponse
+  final case class WorkflowSubmittedToStore(workflowId: WorkflowId, state: WorkflowState)
+      extends WorkflowStoreSubmitActorResponse
+  final case class WorkflowsBatchSubmittedToStore(workflowIds: NonEmptyList[WorkflowId], state: WorkflowState)
+      extends WorkflowStoreSubmitActorResponse
 
   final case class WorkflowSubmitFailed(throwable: Throwable) extends WorkflowStoreSubmitActorResponse
 }
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/workflowstore_.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/workflowstore_.scala
index 382b963670d..c8e9a19ac78 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/workflowstore_.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/workflowstore_.scala
@@ -27,4 +27,5 @@ final case class WorkflowToStart(id: WorkflowId,
                                  submissionTime: OffsetDateTime,
                                  sources: WorkflowSourceFilesCollection,
                                  state: StartableState,
-                                 hogGroup: HogGroup) extends HasWorkflowIdAndSources
+                                 hogGroup: HogGroup
+) extends HasWorkflowIdAndSources
diff --git a/engine/src/main/scala/cromwell/jobstore/JobResultJsonFormatter.scala b/engine/src/main/scala/cromwell/jobstore/JobResultJsonFormatter.scala
index 204998d115d..92c8dd407cb 100644
--- a/engine/src/main/scala/cromwell/jobstore/JobResultJsonFormatter.scala
+++ b/engine/src/main/scala/cromwell/jobstore/JobResultJsonFormatter.scala
@@ -17,8 +17,12 @@ object JobResultJsonFormatter extends DefaultJsonProtocol {
   }
 
   implicit object CallOutputsFormat extends RootJsonFormat[CallOutputs] {
-    def write(value: CallOutputs) = value.outputs.map({case (port, v) => port.identifier.fullyQualifiedName.value -> v }).toJson
-    def read(value: JsValue): CallOutputs = throw new UnsupportedOperationException("Cannot deserialize outputs to output ports")
+    def write(value: CallOutputs) = value.outputs.map { case (port, v) =>
+      port.identifier.fullyQualifiedName.value -> v
+    }.toJson
+    def read(value: JsValue): CallOutputs = throw new UnsupportedOperationException(
+      "Cannot deserialize outputs to output ports"
+    )
   }
 
   implicit val JobResultSuccessFormat = jsonFormat2(JobResultSuccess)
diff --git a/engine/src/main/scala/cromwell/jobstore/JobStore.scala b/engine/src/main/scala/cromwell/jobstore/JobStore.scala
index abc5e8765b4..a98928686fe 100644
--- a/engine/src/main/scala/cromwell/jobstore/JobStore.scala
+++ b/engine/src/main/scala/cromwell/jobstore/JobStore.scala
@@ -7,8 +7,12 @@ import wom.graph.GraphNodePort.OutputPort
 import scala.concurrent.{ExecutionContext, Future}
 
 trait JobStore {
-  def writeToDatabase(workflowCompletions: Seq[WorkflowCompletion], jobCompletions: Seq[JobCompletion], batchSize: Int)(implicit ec: ExecutionContext): Future[Unit]
-  def readJobResult(jobStoreKey: JobStoreKey, taskOutputs: Seq[OutputPort])(implicit ec: ExecutionContext): Future[Option[JobResult]]
+  def writeToDatabase(workflowCompletions: Seq[WorkflowCompletion], jobCompletions: Seq[JobCompletion], batchSize: Int)(
+    implicit ec: ExecutionContext
+  ): Future[Unit]
+  def readJobResult(jobStoreKey: JobStoreKey, taskOutputs: Seq[OutputPort])(implicit
+    ec: ExecutionContext
+  ): Future[Option[JobResult]]
 }
 
 object JobStore {
diff --git a/engine/src/main/scala/cromwell/jobstore/JobStoreActor.scala b/engine/src/main/scala/cromwell/jobstore/JobStoreActor.scala
index 6e14f6b8682..fd86080bc0d 100644
--- a/engine/src/main/scala/cromwell/jobstore/JobStoreActor.scala
+++ b/engine/src/main/scala/cromwell/jobstore/JobStoreActor.scala
@@ -12,14 +12,25 @@ import wom.graph.GraphNodePort.OutputPort
 
 import scala.concurrent.duration._
 import scala.language.postfixOps
+
 /**
   * Joins the service registry API to the JobStoreReaderActor and JobStoreWriterActor.
   *
   * This level of indirection is a tiny bit awkward but allows the database to be injected.
   */
-class JobStoreActor(jobStore: JobStore, dbBatchSize: Int, dbFlushRate: FiniteDuration, registryActor: ActorRef, workflowStoreAccess: WorkflowStoreAccess) extends Actor with ActorLogging with GracefulShutdownHelper {
+class JobStoreActor(jobStore: JobStore,
+                    dbBatchSize: Int,
+                    dbFlushRate: FiniteDuration,
+                    registryActor: ActorRef,
+                    workflowStoreAccess: WorkflowStoreAccess
+) extends Actor
+    with ActorLogging
+    with GracefulShutdownHelper {
   import JobStoreActor._
-  val jobStoreWriterActor = context.actorOf(JobStoreWriterActor.props(jobStore, dbBatchSize, dbFlushRate, registryActor, workflowStoreAccess), "JobStoreWriterActor")
+  val jobStoreWriterActor = context.actorOf(
+    JobStoreWriterActor.props(jobStore, dbBatchSize, dbFlushRate, registryActor, workflowStoreAccess),
+    "JobStoreWriterActor"
+  )
   val jobStoreReaderActor = context.actorOf(JobStoreReaderActor.props(jobStore, registryActor), "JobStoreReaderActor")
 
   override def receive: Receive = {
@@ -47,16 +58,19 @@ object JobStoreActor {
   case class JobStoreWriteFailure(reason: Throwable) extends JobStoreWriterResponse
 
   sealed trait JobStoreReaderCommand extends JobStoreCommand
+
   /**
     * Message to query the JobStoreReaderActor, asks whether the specified job has already been completed.
     */
   case class QueryJobCompletion(jobKey: JobStoreKey, taskOutputs: Seq[OutputPort]) extends JobStoreReaderCommand
 
   sealed trait JobStoreReaderResponse
+
   /**
     * Message which indicates that a job has already completed, and contains the results of the job
     */
   case class JobComplete(jobResult: JobResult) extends JobStoreReaderResponse
+
   /**
     * Indicates that the job has not been completed yet. Makes no statement about whether the job is
     * running versus unstarted or (maybe?) doesn't even exist!
@@ -65,7 +79,9 @@ object JobStoreActor {
 
   case class JobStoreReadFailure(reason: Throwable) extends JobStoreReaderResponse
 
-  def props(database: JobStore, registryActor: ActorRef, workflowStoreAccess: WorkflowStoreAccess) = Props(new JobStoreActor(database, dbBatchSize, dbFlushRate, registryActor, workflowStoreAccess)).withDispatcher(EngineDispatcher)
+  def props(database: JobStore, registryActor: ActorRef, workflowStoreAccess: WorkflowStoreAccess) = Props(
+    new JobStoreActor(database, dbBatchSize, dbFlushRate, registryActor, workflowStoreAccess)
+  ).withDispatcher(EngineDispatcher)
 
   val dbFlushRate = 1 second
 
diff --git a/engine/src/main/scala/cromwell/jobstore/JobStoreReaderActor.scala b/engine/src/main/scala/cromwell/jobstore/JobStoreReaderActor.scala
index ba8d1665aa3..341c757fdb8 100644
--- a/engine/src/main/scala/cromwell/jobstore/JobStoreReaderActor.scala
+++ b/engine/src/main/scala/cromwell/jobstore/JobStoreReaderActor.scala
@@ -12,11 +12,13 @@ import cromwell.services.EnhancedThrottlerActor
 import scala.util.{Failure, Success}
 
 object JobStoreReaderActor {
-  def props(database: JobStore, registryActor: ActorRef) = Props(new JobStoreReaderActor(database, registryActor, LoadConfig.JobStoreReadThreshold)).withDispatcher(EngineDispatcher)
+  def props(database: JobStore, registryActor: ActorRef) = Props(
+    new JobStoreReaderActor(database, registryActor, LoadConfig.JobStoreReadThreshold)
+  ).withDispatcher(EngineDispatcher)
 }
 
 class JobStoreReaderActor(database: JobStore, override val serviceRegistryActor: ActorRef, override val threshold: Int)
-  extends EnhancedThrottlerActor[CommandAndReplyTo[QueryJobCompletion]]
+    extends EnhancedThrottlerActor[CommandAndReplyTo[QueryJobCompletion]]
     with ActorLogging {
 
   override def processHead(head: CommandAndReplyTo[QueryJobCompletion]) = instrumentedProcess {
@@ -35,7 +37,7 @@ class JobStoreReaderActor(database: JobStore, override val serviceRegistryActor:
   override def receive = enhancedReceive.orElse(super.receive)
   override protected def instrumentationPath = NonEmptyList.of("store", "read")
   override protected def instrumentationPrefix = InstrumentationPrefixes.JobPrefix
-  override def commandToData(snd: ActorRef) = {
-    case query: QueryJobCompletion => CommandAndReplyTo(query, sender())
+  override def commandToData(snd: ActorRef) = { case query: QueryJobCompletion =>
+    CommandAndReplyTo(query, sender())
   }
 }
diff --git a/engine/src/main/scala/cromwell/jobstore/JobStoreWriterActor.scala b/engine/src/main/scala/cromwell/jobstore/JobStoreWriterActor.scala
index f00693d1daf..ea9113bd101 100644
--- a/engine/src/main/scala/cromwell/jobstore/JobStoreWriterActor.scala
+++ b/engine/src/main/scala/cromwell/jobstore/JobStoreWriterActor.scala
@@ -16,50 +16,51 @@ import scala.concurrent.duration._
 import scala.language.postfixOps
 import scala.util.{Failure, Success}
 
-
 case class JobStoreWriterActor(jsd: JobStore,
                                override val batchSize: Int,
                                override val flushRate: FiniteDuration,
                                serviceRegistryActor: ActorRef,
                                threshold: Int,
                                workflowStoreAccess: WorkflowStoreAccess
-                              )
-  extends EnhancedBatchActor[CommandAndReplyTo[JobStoreWriterCommand]](flushRate, batchSize) {
+) extends EnhancedBatchActor[CommandAndReplyTo[JobStoreWriterCommand]](flushRate, batchSize) {
 
-  override protected def process(nonEmptyData: NonEmptyVector[CommandAndReplyTo[JobStoreWriterCommand]]): Future[Int] = instrumentedProcess {
-    implicit val actorSystem: ActorSystem = context.system
+  override protected def process(nonEmptyData: NonEmptyVector[CommandAndReplyTo[JobStoreWriterCommand]]): Future[Int] =
+    instrumentedProcess {
+      implicit val actorSystem: ActorSystem = context.system
 
-    val data = nonEmptyData.toVector
-    log.debug("Flushing {} job store commands to the DB", data.length)
-    val completions = data.collect({ case CommandAndReplyTo(c: JobStoreWriterCommand, _) => c.completion })
+      val data = nonEmptyData.toVector
+      log.debug("Flushing {} job store commands to the DB", data.length)
+      val completions = data.collect { case CommandAndReplyTo(c: JobStoreWriterCommand, _) => c.completion }
 
-    if (completions.nonEmpty) {
-      val workflowCompletions = completions collect { case w: WorkflowCompletion => w }
-      val completedWorkflowIds = workflowCompletions map { _.workflowId } toSet
-      // Filter job completions that also have a corresponding workflow completion; these would just be
-      // immediately deleted anyway.
-      val jobCompletions = completions.toList collect { case j: JobCompletion if !completedWorkflowIds.contains(j.key.workflowId) => j }
-      val jobStoreAction: Future[Unit] = jsd.writeToDatabase(workflowCompletions, jobCompletions, batchSize)
-      val workflowStoreAction: Future[List[Int]] = Future.sequence {
-        completedWorkflowIds.map(workflowStoreAccess.deleteFromStore(_)).toList
-      }
+      if (completions.nonEmpty) {
+        val workflowCompletions = completions collect { case w: WorkflowCompletion => w }
+        val completedWorkflowIds = workflowCompletions map { _.workflowId } toSet
+        // Filter job completions that also have a corresponding workflow completion; these would just be
+        // immediately deleted anyway.
+        val jobCompletions = completions.toList collect {
+          case j: JobCompletion if !completedWorkflowIds.contains(j.key.workflowId) => j
+        }
+        val jobStoreAction: Future[Unit] = jsd.writeToDatabase(workflowCompletions, jobCompletions, batchSize)
+        val workflowStoreAction: Future[List[Int]] = Future.sequence {
+          completedWorkflowIds.map(workflowStoreAccess.deleteFromStore(_)).toList
+        }
 
-      val combinedAction: Future[Unit] = for {
-        _ <- jobStoreAction
-        _ <- workflowStoreAction
-      } yield ()
+        val combinedAction: Future[Unit] = for {
+          _ <- jobStoreAction
+          _ <- workflowStoreAction
+        } yield ()
 
-      combinedAction onComplete {
-        case Success(_) =>
-          data foreach { case CommandAndReplyTo(c: JobStoreWriterCommand, r) => r ! JobStoreWriteSuccess(c) }
-        case Failure(error) =>
-          log.error(error, "Failed to write job store entries to database")
-          data foreach { case CommandAndReplyTo(_, r) => r ! JobStoreWriteFailure(error) }
-      }
+        combinedAction onComplete {
+          case Success(_) =>
+            data foreach { case CommandAndReplyTo(c: JobStoreWriterCommand, r) => r ! JobStoreWriteSuccess(c) }
+          case Failure(error) =>
+            log.error(error, "Failed to write job store entries to database")
+            data foreach { case CommandAndReplyTo(_, r) => r ! JobStoreWriteFailure(error) }
+        }
 
-      combinedAction.map(_ => 1)
-    } else Future.successful(0)
-  }
+        combinedAction.map(_ => 1)
+      } else Future.successful(0)
+    }
 
   // EnhancedBatchActor overrides
   override def receive = enhancedReceive.orElse(super.receive)
@@ -76,7 +77,15 @@ object JobStoreWriterActor {
             dbBatchSize: Int,
             dbFlushRate: FiniteDuration,
             registryActor: ActorRef,
-            workflowStoreAccess: WorkflowStoreAccess): Props = {
-    Props(new JobStoreWriterActor(jobStoreDatabase, dbBatchSize, dbFlushRate, registryActor, LoadConfig.JobStoreWriteThreshold, workflowStoreAccess)).withDispatcher(EngineDispatcher)
-  }
+            workflowStoreAccess: WorkflowStoreAccess
+  ): Props =
+    Props(
+      new JobStoreWriterActor(jobStoreDatabase,
+                              dbBatchSize,
+                              dbFlushRate,
+                              registryActor,
+                              LoadConfig.JobStoreWriteThreshold,
+                              workflowStoreAccess
+      )
+    ).withDispatcher(EngineDispatcher)
 }
diff --git a/engine/src/main/scala/cromwell/jobstore/SqlJobStore.scala b/engine/src/main/scala/cromwell/jobstore/SqlJobStore.scala
index baeaa79221d..b6f28a8a24d 100644
--- a/engine/src/main/scala/cromwell/jobstore/SqlJobStore.scala
+++ b/engine/src/main/scala/cromwell/jobstore/SqlJobStore.scala
@@ -19,7 +19,10 @@ import scala.concurrent.{ExecutionContext, Future}
 class SqlJobStore(sqlDatabase: EngineSqlDatabase) extends JobStore {
   val log = LoggerFactory.getLogger(classOf[SqlJobStore])
 
-  override def writeToDatabase(workflowCompletions: Seq[WorkflowCompletion], jobCompletions: Seq[JobCompletion], batchSize: Int)(implicit ec: ExecutionContext): Future[Unit] = {
+  override def writeToDatabase(workflowCompletions: Seq[WorkflowCompletion],
+                               jobCompletions: Seq[JobCompletion],
+                               batchSize: Int
+  )(implicit ec: ExecutionContext): Future[Unit] = {
     val completedWorkflowIds = workflowCompletions.toList.map(_.workflowId.toString)
     for {
       _ <- sqlDatabase.addJobStores(jobCompletions map toDatabase, batchSize)
@@ -28,23 +31,24 @@ class SqlJobStore(sqlDatabase: EngineSqlDatabase) extends JobStore {
     } yield ()
   }
 
-  private def toDatabase(jobCompletion: JobCompletion): JobStoreJoin = {
+  private def toDatabase(jobCompletion: JobCompletion): JobStoreJoin =
     jobCompletion match {
       case JobCompletion(key, JobResultSuccess(returnCode, jobOutputs)) =>
-        val entry = JobStoreEntry(
-          key.workflowId.toString,
-          key.callFqn,
-          key.index.fromIndex,
-          key.attempt,
-          jobSuccessful = true,
-          returnCode,
-          None,
-          None)
+        val entry = JobStoreEntry(key.workflowId.toString,
+                                  key.callFqn,
+                                  key.index.fromIndex,
+                                  key.attempt,
+                                  jobSuccessful = true,
+                                  returnCode,
+                                  None,
+                                  None
+        )
         val jobStoreResultSimpletons =
-          jobOutputs.outputs.simplify.map {
-            womValueSimpleton => JobStoreSimpletonEntry(
-              womValueSimpleton.simpletonKey, womValueSimpleton.simpletonValue.valueString.toClobOption,
-              womValueSimpleton.simpletonValue.womType.stableName)
+          jobOutputs.outputs.simplify.map { womValueSimpleton =>
+            JobStoreSimpletonEntry(womValueSimpleton.simpletonKey,
+                                   womValueSimpleton.simpletonValue.valueString.toClobOption,
+                                   womValueSimpleton.simpletonValue.womType.stableName
+            )
           }
         JobStoreJoin(entry, jobStoreResultSimpletons.toSeq)
       case JobCompletion(key, JobResultFailure(returnCode, throwable, retryable)) =>
@@ -56,14 +60,19 @@ class SqlJobStore(sqlDatabase: EngineSqlDatabase) extends JobStore {
           jobSuccessful = false,
           returnCode,
           Option(throwable.getMessage).toClobOption,
-          Option(retryable))
+          Option(retryable)
+        )
         JobStoreJoin(entry, Seq.empty)
     }
-  }
 
-  override def readJobResult(jobStoreKey: JobStoreKey, taskOutputs: Seq[OutputPort])(implicit ec: ExecutionContext): Future[Option[JobResult]] = {
-    sqlDatabase.queryJobStores(jobStoreKey.workflowId.toString, jobStoreKey.callFqn, jobStoreKey.index.fromIndex,
-      jobStoreKey.attempt) map {
+  override def readJobResult(jobStoreKey: JobStoreKey, taskOutputs: Seq[OutputPort])(implicit
+    ec: ExecutionContext
+  ): Future[Option[JobResult]] =
+    sqlDatabase.queryJobStores(jobStoreKey.workflowId.toString,
+                               jobStoreKey.callFqn,
+                               jobStoreKey.index.fromIndex,
+                               jobStoreKey.attempt
+    ) map {
       _ map { case JobStoreJoin(entry, simpletonEntries) =>
         entry match {
           case JobStoreEntry(_, _, _, _, true, returnCode, None, None, _) =>
@@ -72,12 +81,12 @@ class SqlJobStore(sqlDatabase: EngineSqlDatabase) extends JobStore {
             JobResultSuccess(returnCode, jobOutputs)
           case JobStoreEntry(_, _, _, _, false, returnCode, Some(_), Some(retryable), _) =>
             JobResultFailure(returnCode,
-              JobAlreadyFailedInJobStore(jobStoreKey.tag, entry.exceptionMessage.toRawString),
-              retryable)
+                             JobAlreadyFailedInJobStore(jobStoreKey.tag, entry.exceptionMessage.toRawString),
+                             retryable
+            )
           case bad =>
             throw new Exception(s"Invalid contents of JobStore table: $bad")
         }
       }
     }
-  }
 }
diff --git a/engine/src/main/scala/cromwell/jobstore/jobstore_.scala b/engine/src/main/scala/cromwell/jobstore/jobstore_.scala
index 886de33ebdb..9bcd641330e 100644
--- a/engine/src/main/scala/cromwell/jobstore/jobstore_.scala
+++ b/engine/src/main/scala/cromwell/jobstore/jobstore_.scala
@@ -1,7 +1,12 @@
 package cromwell.jobstore
 
 import cromwell.backend.BackendJobDescriptorKey
-import cromwell.backend.BackendJobExecutionActor.{FetchedFromJobStore, JobFailedNonRetryableResponse, JobFailedRetryableResponse, JobSucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{
+  FetchedFromJobStore,
+  JobFailedNonRetryableResponse,
+  JobFailedRetryableResponse,
+  JobSucceededResponse
+}
 import cromwell.core.{CallOutputs, WorkflowId}
 
 case class JobStoreKey(workflowId: WorkflowId, callFqn: String, index: Option[Int], attempt: Int) {
@@ -13,7 +18,15 @@ sealed trait JobResult {
   def toBackendJobResponse(key: BackendJobDescriptorKey) = this match {
     // Always puts `None` for `dockerImageUsed` for a successfully completed job on restart. This shouldn't be a
     // problem since `saveJobCompletionToJobStore` in EJEA will already have sent this to metadata.
-    case JobResultSuccess(returnCode, jobOutputs) => JobSucceededResponse(key, returnCode, jobOutputs, None, Seq.empty, None, resultGenerationMode = FetchedFromJobStore)
+    case JobResultSuccess(returnCode, jobOutputs) =>
+      JobSucceededResponse(key,
+                           returnCode,
+                           jobOutputs,
+                           None,
+                           Seq.empty,
+                           None,
+                           resultGenerationMode = FetchedFromJobStore
+      )
     case JobResultFailure(returnCode, reason, false) => JobFailedNonRetryableResponse(key, reason, returnCode)
     case JobResultFailure(returnCode, reason, true) => JobFailedRetryableResponse(key, reason, returnCode)
   }
diff --git a/engine/src/main/scala/cromwell/jobstore/package.scala b/engine/src/main/scala/cromwell/jobstore/package.scala
index 1e4dbaecbbb..6d5bdb834e1 100644
--- a/engine/src/main/scala/cromwell/jobstore/package.scala
+++ b/engine/src/main/scala/cromwell/jobstore/package.scala
@@ -4,6 +4,7 @@ import cromwell.core.{JobKey, WorkflowId}
 
 package object jobstore {
   implicit class EnhancedJobKey(val jobKey: JobKey) extends AnyVal {
-    def toJobStoreKey(workflowId: WorkflowId): JobStoreKey = JobStoreKey(workflowId, jobKey.node.fullyQualifiedName, jobKey.index, jobKey.attempt)
+    def toJobStoreKey(workflowId: WorkflowId): JobStoreKey =
+      JobStoreKey(workflowId, jobKey.node.fullyQualifiedName, jobKey.index, jobKey.attempt)
   }
 }
diff --git a/engine/src/main/scala/cromwell/logging/TerminalLayout.scala b/engine/src/main/scala/cromwell/logging/TerminalLayout.scala
index 8871341f976..6bb67e5a1af 100644
--- a/engine/src/main/scala/cromwell/logging/TerminalLayout.scala
+++ b/engine/src/main/scala/cromwell/logging/TerminalLayout.scala
@@ -20,15 +20,14 @@ object TerminalLayout {
   }
 
   implicit class ColorString(msg: String) {
-    def colorizeUuids: String = {
-      "UUID\\((.*?)\\)".r.findAllMatchIn(msg).foldLeft(msg) {
-        case (l, r) =>
-          val color = if (Option(System.getProperty("RAINBOW_UUID")).isDefined)
-            Math.abs(17 * r.group(1).substring(0,8).map(_.toInt).product) % 209 + 22
+    def colorizeUuids: String =
+      "UUID\\((.*?)\\)".r.findAllMatchIn(msg).foldLeft(msg) { case (l, r) =>
+        val color =
+          if (Option(System.getProperty("RAINBOW_UUID")).isDefined)
+            Math.abs(17 * r.group(1).substring(0, 8).map(_.toInt).product) % 209 + 22
           else 2
-          l.replace(r.group(0), TerminalUtil.highlight(color, r.group(1)))
+        l.replace(r.group(0), TerminalUtil.highlight(color, r.group(1)))
       }
-    }
     def colorizeCommand: String = msg.replaceAll("`([^`]*?)`", TerminalUtil.highlight(5, "$1"))
   }
 }
diff --git a/engine/src/main/scala/cromwell/server/CromwellAkkaLogFilter.scala b/engine/src/main/scala/cromwell/server/CromwellAkkaLogFilter.scala
index 31dc6408b77..9789b354f37 100644
--- a/engine/src/main/scala/cromwell/server/CromwellAkkaLogFilter.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellAkkaLogFilter.scala
@@ -4,17 +4,19 @@ import akka.actor.ActorSystem
 import akka.event.EventStream
 import akka.event.slf4j.Slf4jLoggingFilter
 
-class CromwellAkkaLogFilter(settings: ActorSystem.Settings, eventStream: EventStream) extends Slf4jLoggingFilter(settings, eventStream) {
-  override def isErrorEnabled(logClass: Class[_], logSource: String) = {
+class CromwellAkkaLogFilter(settings: ActorSystem.Settings, eventStream: EventStream)
+    extends Slf4jLoggingFilter(settings, eventStream) {
+  override def isErrorEnabled(logClass: Class[_], logSource: String) =
     /*
      * This might filter out too much but it's the finest granularity we have here
-     * The goal is to not log the 
-     * "Outgoing request stream error akka.stream.AbruptTerminationException: 
+     * The goal is to not log the
+     * "Outgoing request stream error akka.stream.AbruptTerminationException:
      *  Processor actor [Actor[akka://cromwell-system/user/StreamSupervisor-1/flow-6-0-mergePreferred#1200284127]] terminated abruptly"
      * type of message
-     * 
+     *
      * See https://github.com/akka/akka-http/issues/907 and https://github.com/akka/akka/issues/18747
      */
-    super.isErrorEnabled(logClass, logSource) && !(logSource.startsWith("akka.actor.ActorSystemImpl") && CromwellShutdown.shutdownInProgress())
-  }
+    super.isErrorEnabled(logClass, logSource) && !(logSource.startsWith(
+      "akka.actor.ActorSystemImpl"
+    ) && CromwellShutdown.shutdownInProgress())
 }
diff --git a/engine/src/main/scala/cromwell/server/CromwellDeadLetterListener.scala b/engine/src/main/scala/cromwell/server/CromwellDeadLetterListener.scala
index 5cea81c37d2..c7af7991b6c 100644
--- a/engine/src/main/scala/cromwell/server/CromwellDeadLetterListener.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellDeadLetterListener.scala
@@ -6,14 +6,15 @@ import cats.Show
 import cats.syntax.show._
 
 class CromwellDeadLetterListener extends DeadLetterListener with ActorLogging {
-  implicit val showActor: Show[ActorRef]  = Show.show(actor =>
-   s"Actor of path ${actor.path} toString ${actor.toString()}"
-  )
-  
+  implicit val showActor: Show[ActorRef] =
+    Show.show(actor => s"Actor of path ${actor.path} toString ${actor.toString()}")
+
   def shutdownReceive: Receive = {
     // This silences the dead letter messages when Cromwell is shutting down
     case DeadLetter(msg, from, to) if CromwellShutdown.shutdownInProgress() =>
-      log.debug(s"Got a dead letter during Cromwell shutdown. Sent by\n${from.show}\nto ${to.show}\n consisting of message: $msg\n ")
+      log.debug(
+        s"Got a dead letter during Cromwell shutdown. Sent by\n${from.show}\nto ${to.show}\n consisting of message: $msg\n "
+      )
   }
   override def receive = shutdownReceive.orElse(super.receive)
 }
diff --git a/engine/src/main/scala/cromwell/server/CromwellRootActor.scala b/engine/src/main/scala/cromwell/server/CromwellRootActor.scala
index c37d6466fcc..b4cdbef735b 100644
--- a/engine/src/main/scala/cromwell/server/CromwellRootActor.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellRootActor.scala
@@ -20,7 +20,11 @@ import cromwell.engine.io.{IoActor, IoActorProxy}
 import cromwell.engine.workflow.WorkflowManagerActor
 import cromwell.engine.workflow.WorkflowManagerActor.AbortAllWorkflowsCommand
 import cromwell.engine.workflow.lifecycle.execution.callcaching.{CallCache, CallCacheReadActor, CallCacheWriteActor}
-import cromwell.engine.workflow.lifecycle.finalization.{CopyWorkflowLogsActor, WorkflowCallbackActor, WorkflowCallbackConfig}
+import cromwell.engine.workflow.lifecycle.finalization.{
+  CopyWorkflowLogsActor,
+  WorkflowCallbackActor,
+  WorkflowCallbackConfig
+}
 import cromwell.engine.workflow.tokens.{DynamicRateLimiter, JobTokenDispenserActor}
 import cromwell.engine.workflow.workflowstore.AbortRequestScanningActor.AbortConfig
 import cromwell.engine.workflow.workflowstore._
@@ -54,9 +58,11 @@ abstract class CromwellRootActor(terminator: CromwellTerminator,
                                  gracefulShutdown: Boolean,
                                  abortJobsOnTerminate: Boolean,
                                  val serverMode: Boolean,
-                                 protected val config: Config)
-                                (implicit materializer: ActorMaterializer)
-  extends Actor with ActorLogging with GracefulShutdownHelper {
+                                 protected val config: Config
+)(implicit materializer: ActorMaterializer)
+    extends Actor
+    with ActorLogging
+    with GracefulShutdownHelper {
 
   import CromwellRootActor._
 
@@ -72,9 +78,11 @@ abstract class CromwellRootActor(terminator: CromwellTerminator,
 
   lazy val systemConfig = config.getConfig("system")
   lazy val serviceRegistryActor: ActorRef = context.actorOf(ServiceRegistryActor.props(config), "ServiceRegistryActor")
-  lazy val numberOfWorkflowLogCopyWorkers = systemConfig.as[Option[Int]]("number-of-workflow-log-copy-workers").getOrElse(DefaultNumberOfWorkflowLogCopyWorkers)
+  lazy val numberOfWorkflowLogCopyWorkers =
+    systemConfig.as[Option[Int]]("number-of-workflow-log-copy-workers").getOrElse(DefaultNumberOfWorkflowLogCopyWorkers)
 
-  lazy val workflowStore: WorkflowStore = SqlWorkflowStore(EngineServicesStore.engineDatabaseInterface, MetadataServicesStore.metadataDatabaseInterface)
+  lazy val workflowStore: WorkflowStore =
+    SqlWorkflowStore(EngineServicesStore.engineDatabaseInterface, MetadataServicesStore.metadataDatabaseInterface)
 
   val workflowStoreAccess: WorkflowStoreAccess = {
     val coordinatedWorkflowStoreAccess = config.as[Option[Boolean]]("system.coordinated-workflow-store-access")
@@ -90,41 +98,49 @@ abstract class CromwellRootActor(terminator: CromwellTerminator,
   }
 
   lazy val workflowStoreActor =
-    context.actorOf(WorkflowStoreActor.props(
-      workflowStoreDatabase = workflowStore,
-      workflowStoreAccess = workflowStoreAccess,
-      serviceRegistryActor = serviceRegistryActor,
-      terminator = terminator,
-      abortAllJobsOnTerminate = abortJobsOnTerminate,
-      workflowHeartbeatConfig = workflowHeartbeatConfig),
-      "WorkflowStoreActor")
+    context.actorOf(
+      WorkflowStoreActor.props(
+        workflowStoreDatabase = workflowStore,
+        workflowStoreAccess = workflowStoreAccess,
+        serviceRegistryActor = serviceRegistryActor,
+        terminator = terminator,
+        abortAllJobsOnTerminate = abortJobsOnTerminate,
+        workflowHeartbeatConfig = workflowHeartbeatConfig
+      ),
+      "WorkflowStoreActor"
+    )
 
   lazy val jobStore: JobStore = new SqlJobStore(EngineServicesStore.engineDatabaseInterface)
-  lazy val jobStoreActor: ActorRef = context.actorOf(JobStoreActor.props(jobStore, serviceRegistryActor, workflowStoreAccess), "JobStoreActor")
+  lazy val jobStoreActor: ActorRef =
+    context.actorOf(JobStoreActor.props(jobStore, serviceRegistryActor, workflowStoreAccess), "JobStoreActor")
 
   lazy val subWorkflowStore: SubWorkflowStore = new SqlSubWorkflowStore(EngineServicesStore.engineDatabaseInterface)
-  lazy val subWorkflowStoreActor: ActorRef = context.actorOf(SubWorkflowStoreActor.props(subWorkflowStore), "SubWorkflowStoreActor")
+  lazy val subWorkflowStoreActor: ActorRef =
+    context.actorOf(SubWorkflowStoreActor.props(subWorkflowStore), "SubWorkflowStoreActor")
 
   lazy val ioConfig: IoConfig = config.as[IoConfig]
-  lazy val ioActor: ActorRef = context.actorOf(
-    IoActor.props(
-      ioConfig = ioConfig,
-      serviceRegistryActor = serviceRegistryActor,
-      applicationName = GoogleConfiguration(config).applicationName),
-    "IoActor")
+  lazy val ioActor: ActorRef = context.actorOf(IoActor.props(ioConfig = ioConfig,
+                                                             serviceRegistryActor = serviceRegistryActor,
+                                                             applicationName =
+                                                               GoogleConfiguration(config).applicationName
+                                               ),
+                                               "IoActor"
+  )
   lazy val ioActorProxy: ActorRef = context.actorOf(IoActorProxy.props(ioActor), "IoProxy")
 
   // Register the IoActor with the service registry:
   serviceRegistryActor ! IoActorRef(ioActorProxy)
 
-  lazy val workflowLogCopyRouter: ActorRef = context.actorOf(RoundRobinPool(numberOfWorkflowLogCopyWorkers)
-    .withSupervisorStrategy(CopyWorkflowLogsActor.strategy)
-    .props(CopyWorkflowLogsActor.props(serviceRegistryActor, ioActor)),
-    "WorkflowLogCopyRouter")
+  lazy val workflowLogCopyRouter: ActorRef = context.actorOf(
+    RoundRobinPool(numberOfWorkflowLogCopyWorkers)
+      .withSupervisorStrategy(CopyWorkflowLogsActor.strategy)
+      .props(CopyWorkflowLogsActor.props(serviceRegistryActor, ioActor)),
+    "WorkflowLogCopyRouter"
+  )
 
   private val workflowCallbackConfig = WorkflowCallbackConfig(config.getConfig("workflow-state-callback"))
 
-  lazy val workflowCallbackActor: Option[ActorRef] = {
+  lazy val workflowCallbackActor: Option[ActorRef] =
     if (workflowCallbackConfig.enabled) {
       val props = WorkflowCallbackActor.props(
         serviceRegistryActor,
@@ -132,21 +148,25 @@ abstract class CromwellRootActor(terminator: CromwellTerminator,
       )
       Option(context.actorOf(props, "WorkflowCallbackActor"))
     } else None
-  }
 
-  //Call-caching config validation
+  // Call-caching config validation
   lazy val callCachingConfig = config.getConfig("call-caching")
   lazy val callCachingEnabled = callCachingConfig.getBoolean("enabled")
   lazy val callInvalidateBadCacheResults = callCachingConfig.getBoolean("invalidate-bad-cache-results")
 
   lazy val callCache: CallCache = new CallCache(EngineServicesStore.engineDatabaseInterface)
 
-  lazy val numberOfCacheReadWorkers = config.getConfig("system").as[Option[Int]]("number-of-cache-read-workers").getOrElse(DefaultNumberOfCacheReadWorkers)
+  lazy val numberOfCacheReadWorkers = config
+    .getConfig("system")
+    .as[Option[Int]]("number-of-cache-read-workers")
+    .getOrElse(DefaultNumberOfCacheReadWorkers)
   lazy val callCacheReadActor = context.actorOf(RoundRobinPool(numberOfCacheReadWorkers)
-    .props(CallCacheReadActor.props(callCache, serviceRegistryActor)),
-    "CallCacheReadActor")
+                                                  .props(CallCacheReadActor.props(callCache, serviceRegistryActor)),
+                                                "CallCacheReadActor"
+  )
 
-  lazy val callCacheWriteActor = context.actorOf(CallCacheWriteActor.props(callCache, serviceRegistryActor), "CallCacheWriteActor")
+  lazy val callCacheWriteActor =
+    context.actorOf(CallCacheWriteActor.props(callCache, serviceRegistryActor), "CallCacheWriteActor")
 
   // Docker Actor
   lazy val ioEc = context.system.dispatchers.lookup(Dispatcher.IoDispatcher)
@@ -160,22 +180,49 @@ abstract class CromwellRootActor(terminator: CromwellTerminator,
     case DockerRemoteLookup => DockerInfoActor.remoteRegistriesFromConfig(DockerConfiguration.dockerHashLookupConfig)
   }
 
-  lazy val dockerHashActor = context.actorOf(DockerInfoActor.props(dockerFlows, dockerActorQueueSize,
-    dockerConf.cacheEntryTtl, dockerConf.cacheSize), "DockerHashActor")
+  lazy val dockerHashActor = context.actorOf(
+    DockerInfoActor.props(dockerFlows, dockerActorQueueSize, dockerConf.cacheEntryTtl, dockerConf.cacheSize),
+    "DockerHashActor"
+  )
 
   lazy val backendSingletons = CromwellBackends.instance.get.backendLifecycleActorFactories map {
-    case (name, factory) => name -> (factory.backendSingletonActorProps(serviceRegistryActor) map { context.actorOf(_, s"$name-Singleton") })
+    case (name, factory) =>
+      name -> (factory.backendSingletonActorProps(serviceRegistryActor) map { context.actorOf(_, s"$name-Singleton") })
   }
   lazy val backendSingletonCollection = BackendSingletonCollection(backendSingletons)
 
-  lazy val jobRestartCheckRate: DynamicRateLimiter.Rate = DynamicRateLimiter.Rate(systemConfig.as[Int]("job-restart-check-rate-control.jobs"), systemConfig.as[FiniteDuration]("job-restart-check-rate-control.per"))
-  lazy val jobExecutionRate: DynamicRateLimiter.Rate = DynamicRateLimiter.Rate(systemConfig.as[Int]("job-rate-control.jobs"), systemConfig.as[FiniteDuration]("job-rate-control.per"))
-
-  lazy val restartCheckTokenLogInterval: Option[FiniteDuration] = systemConfig.as[Option[Int]]("job-restart-check-rate-control.token-log-interval-seconds").map(_.seconds)
-  lazy val executionTokenLogInterval: Option[FiniteDuration] = systemConfig.as[Option[Int]]("hog-safety.token-log-interval-seconds").map(_.seconds)
-
-  lazy val jobRestartCheckTokenDispenserActor: ActorRef = context.actorOf(JobTokenDispenserActor.props(serviceRegistryActor, jobRestartCheckRate, restartCheckTokenLogInterval, "restart checking", "CheckingRestart"), "JobRestartCheckTokenDispenser")
-  lazy val jobExecutionTokenDispenserActor: ActorRef = context.actorOf(JobTokenDispenserActor.props(serviceRegistryActor, jobExecutionRate, executionTokenLogInterval, "execution", ExecutionStatus.Running.toString), "JobExecutionTokenDispenser")
+  lazy val jobRestartCheckRate: DynamicRateLimiter.Rate = DynamicRateLimiter.Rate(
+    systemConfig.as[Int]("job-restart-check-rate-control.jobs"),
+    systemConfig.as[FiniteDuration]("job-restart-check-rate-control.per")
+  )
+  lazy val jobExecutionRate: DynamicRateLimiter.Rate = DynamicRateLimiter.Rate(
+    systemConfig.as[Int]("job-rate-control.jobs"),
+    systemConfig.as[FiniteDuration]("job-rate-control.per")
+  )
+
+  lazy val restartCheckTokenLogInterval: Option[FiniteDuration] =
+    systemConfig.as[Option[Int]]("job-restart-check-rate-control.token-log-interval-seconds").map(_.seconds)
+  lazy val executionTokenLogInterval: Option[FiniteDuration] =
+    systemConfig.as[Option[Int]]("hog-safety.token-log-interval-seconds").map(_.seconds)
+
+  lazy val jobRestartCheckTokenDispenserActor: ActorRef = context.actorOf(
+    JobTokenDispenserActor.props(serviceRegistryActor,
+                                 jobRestartCheckRate,
+                                 restartCheckTokenLogInterval,
+                                 "restart checking",
+                                 "CheckingRestart"
+    ),
+    "JobRestartCheckTokenDispenser"
+  )
+  lazy val jobExecutionTokenDispenserActor: ActorRef = context.actorOf(
+    JobTokenDispenserActor.props(serviceRegistryActor,
+                                 jobExecutionRate,
+                                 executionTokenLogInterval,
+                                 "execution",
+                                 ExecutionStatus.Running.toString
+    ),
+    "JobExecutionTokenDispenser"
+  )
 
   lazy val workflowManagerActor = context.actorOf(
     WorkflowManagerActor.props(
@@ -196,19 +243,24 @@ abstract class CromwellRootActor(terminator: CromwellTerminator,
       jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
       backendSingletonCollection = backendSingletonCollection,
       serverMode = serverMode,
-      workflowHeartbeatConfig = workflowHeartbeatConfig),
-    "WorkflowManagerActor")
+      workflowHeartbeatConfig = workflowHeartbeatConfig
+    ),
+    "WorkflowManagerActor"
+  )
 
   val abortRequestScanningActor = {
     val abortConfigBlock = config.as[Option[Config]]("system.abort")
 
-    val abortCacheConfig = CacheConfig.config(caching = abortConfigBlock.flatMap { _.as[Option[Config]]("cache") },
+    val abortCacheConfig = CacheConfig.config(caching = abortConfigBlock.flatMap(_.as[Option[Config]]("cache")),
                                               defaultConcurrency = 1,
                                               defaultSize = 100000L,
-                                              defaultTtl = 20 minutes)
+                                              defaultTtl = 20 minutes
+    )
 
     val abortConfig = AbortConfig(
-      scanFrequency = abortConfigBlock.flatMap { _.as[Option[FiniteDuration]]("scan-frequency") } getOrElse (30 seconds),
+      scanFrequency = abortConfigBlock.flatMap {
+        _.as[Option[FiniteDuration]]("scan-frequency")
+      } getOrElse (30 seconds),
       cacheConfig = abortCacheConfig
     )
 
@@ -262,8 +314,8 @@ abstract class CromwellRootActor(terminator: CromwellTerminator,
     }
   }
 
-  override def receive = {
-    case message => logger.error(s"Unknown message received by CromwellRootActor: $message")
+  override def receive = { case message =>
+    logger.error(s"Unknown message received by CromwellRootActor: $message")
   }
 
   /**
diff --git a/engine/src/main/scala/cromwell/server/CromwellServer.scala b/engine/src/main/scala/cromwell/server/CromwellServer.scala
index 76f784875fc..cc2a1d409e9 100644
--- a/engine/src/main/scala/cromwell/server/CromwellServer.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellServer.scala
@@ -20,26 +20,29 @@ object CromwellServer {
   def run(gracefulShutdown: Boolean, abortJobsOnTerminate: Boolean)(cromwellSystem: CromwellSystem): Future[Any] = {
     implicit val actorSystem = cromwellSystem.actorSystem
     implicit val materializer = cromwellSystem.materializer
-    actorSystem.actorOf(CromwellServerActor.props(cromwellSystem, gracefulShutdown, abortJobsOnTerminate), "cromwell-service")
+    actorSystem.actorOf(CromwellServerActor.props(cromwellSystem, gracefulShutdown, abortJobsOnTerminate),
+                        "cromwell-service"
+    )
     actorSystem.whenTerminated
   }
 }
 
-class CromwellServerActor(cromwellSystem: CromwellSystem, gracefulShutdown: Boolean, abortJobsOnTerminate: Boolean)(override implicit val materializer: ActorMaterializer)
-  extends CromwellRootActor(
-    terminator = cromwellSystem,
-    gracefulShutdown = gracefulShutdown,
-    abortJobsOnTerminate = abortJobsOnTerminate,
-    serverMode = true,
-    config = cromwellSystem.config
-  )
+class CromwellServerActor(cromwellSystem: CromwellSystem, gracefulShutdown: Boolean, abortJobsOnTerminate: Boolean)(
+  implicit override val materializer: ActorMaterializer
+) extends CromwellRootActor(
+      terminator = cromwellSystem,
+      gracefulShutdown = gracefulShutdown,
+      abortJobsOnTerminate = abortJobsOnTerminate,
+      serverMode = true,
+      config = cromwellSystem.config
+    )
     with CromwellApiService
     with CromwellInstrumentationActor
     with WesRouteSupport
     with SwaggerService
     with ActorLogging {
   implicit val actorSystem = context.system
-  override implicit val ec = context.dispatcher
+  implicit override val ec = context.dispatcher
   override def actorRefFactory: ActorContext = context
 
   val webserviceConf = cromwellSystem.config.getConfig("webservice")
@@ -71,7 +74,7 @@ class CromwellServerActor(cromwellSystem: CromwellSystem, gracefulShutdown: Bool
         If/when CromwellServer behaves like a better async citizen, we may be less paranoid about our async log messages
         not appearing due to the actor system shutdown. For now, synchronously print to the stderr so that the user has
         some idea of why the server failed to start up.
-      */
+       */
       Console.err.println(s"Binding failed interface $interface port $port")
       e.printStackTrace(Console.err)
       cromwellSystem.shutdownActorSystem()
@@ -85,7 +88,9 @@ class CromwellServerActor(cromwellSystem: CromwellSystem, gracefulShutdown: Bool
 }
 
 object CromwellServerActor {
-  def props(cromwellSystem: CromwellSystem, gracefulShutdown: Boolean, abortJobsOnTerminate: Boolean)(implicit materializer: ActorMaterializer): Props = {
-    Props(new CromwellServerActor(cromwellSystem, gracefulShutdown, abortJobsOnTerminate)).withDispatcher(EngineDispatcher)
-  }
+  def props(cromwellSystem: CromwellSystem, gracefulShutdown: Boolean, abortJobsOnTerminate: Boolean)(implicit
+    materializer: ActorMaterializer
+  ): Props =
+    Props(new CromwellServerActor(cromwellSystem, gracefulShutdown, abortJobsOnTerminate))
+      .withDispatcher(EngineDispatcher)
 }
diff --git a/engine/src/main/scala/cromwell/server/CromwellShutdown.scala b/engine/src/main/scala/cromwell/server/CromwellShutdown.scala
index ce204249b1e..991d8dfabb6 100644
--- a/engine/src/main/scala/cromwell/server/CromwellShutdown.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellShutdown.scala
@@ -59,17 +59,16 @@ object CromwellShutdown extends GracefulStopSupport {
   /**
     * Register a task to unbind from the port during the ServiceUnbind phase.
     */
-  def registerUnbindTask(actorSystem: ActorSystem, serverBinding: Future[Http.ServerBinding]) = {
+  def registerUnbindTask(actorSystem: ActorSystem, serverBinding: Future[Http.ServerBinding]) =
     instance(actorSystem).addTask(CoordinatedShutdown.PhaseServiceUnbind, "UnbindingServerPort") { () =>
       // At this point it's still safe to schedule work on the actor system's dispatcher
       implicit val ec = actorSystem.dispatcher
       for {
         binding <- serverBinding
         _ <- binding.unbind()
-        _ = logger.info("Http server unbound.") 
+        _ = logger.info("Http server unbound.")
       } yield Done
     }
-  }
 
   /**
     * Register tasks on the coordinated shutdown instance allowing a controlled, ordered shutdown process
@@ -77,29 +76,28 @@ object CromwellShutdown extends GracefulStopSupport {
     * Calling this method will add a JVM shutdown hook.
     */
   def registerShutdownTasks(
-                             cromwellId: String,
-                             abortJobsOnTerminate: Boolean,
-                             actorSystem: ActorSystem,
-                             workflowManagerActor: ActorRef,
-                             logCopyRouter: ActorRef,
-                             workflowCallbackActor: Option[ActorRef],
-                             jobTokenDispenser: ActorRef,
-                             jobStoreActor: ActorRef,
-                             workflowStoreActor: ActorRef,
-                             subWorkflowStoreActor: ActorRef,
-                             callCacheWriteActor: ActorRef,
-                             ioActor: ActorRef,
-                             dockerHashActor: ActorRef,
-                             serviceRegistryActor: ActorRef,
-                             materializer: ActorMaterializer
-                           ): Unit = {
+    cromwellId: String,
+    abortJobsOnTerminate: Boolean,
+    actorSystem: ActorSystem,
+    workflowManagerActor: ActorRef,
+    logCopyRouter: ActorRef,
+    workflowCallbackActor: Option[ActorRef],
+    jobTokenDispenser: ActorRef,
+    jobStoreActor: ActorRef,
+    workflowStoreActor: ActorRef,
+    subWorkflowStoreActor: ActorRef,
+    callCacheWriteActor: ActorRef,
+    ioActor: ActorRef,
+    dockerHashActor: ActorRef,
+    serviceRegistryActor: ActorRef,
+    materializer: ActorMaterializer
+  ): Unit = {
 
     val coordinatedShutdown = this.instance(actorSystem)
 
-    def shutdownActor(actor: ActorRef,
-                      phase: String,
-                      message: AnyRef,
-                      customTimeout: Option[FiniteDuration] = None)(implicit executionContext: ExecutionContext) = {
+    def shutdownActor(actor: ActorRef, phase: String, message: AnyRef, customTimeout: Option[FiniteDuration] = None)(
+      implicit executionContext: ExecutionContext
+    ) =
       coordinatedShutdown.addTask(phase, s"stop${actor.path.name.capitalize}") { () =>
         val timeout = coordinatedShutdown.timeout(phase)
         logger.info(s"Shutting down ${actor.path.name} - Timeout = ${timeout.toSeconds} seconds")
@@ -115,7 +113,6 @@ object CromwellShutdown extends GracefulStopSupport {
 
         action map { _ => Done }
       }
-    }
 
     implicit val ec = actorSystem.dispatcher
 
@@ -131,61 +128,70 @@ object CromwellShutdown extends GracefulStopSupport {
     }
 
     /* 2) The socket is unbound from the port in the CoordinatedShutdown.PhaseServiceUnbind
-      * See cromwell.engine.server.CromwellServer
+     * See cromwell.engine.server.CromwellServer
      */
 
     /* 3) Finish processing all requests:
-      *  - Release any WorkflowStore entries held by this Cromwell instance.
-      *  - Publish workflow processing event metadata for the released workflows.
-      *  - Stop the WorkflowStore: The port is not bound anymore so we can't have new submissions.
-      *   Process what's left in the message queue and stop. 
-      *   Note that it's possible that some submissions are still asynchronously being prepared at the 
-      *   akka http API layer (CromwellApiService) to be sent to the WorkflowStore.
-      *   Those submissions might be lost if the WorkflowStore shuts itself down when it's finished processing its current work.
-      *   In that case the "ask" over in the CromwellAPIService will fail with a AskTimeoutException and should be handled appropriately.
-      *   This process still ensures that no submission can make it to the database without a response being sent back to the client.
-      *   
-      *  - Stop WorkflowManagerActor: We've already stopped starting new workflows but the Running workflows are still
-      *   going. This is tricky because all the actor hierarchy under the WMA can be in a variety of state combinations.
-      *   Specifically there is an asynchronous gap in several cases between emission of messages towards engine level
-      *   actors (job store, cache store, etc...) and emission of messages towards the metadata service for the same logical
-      *   event (e.g: job complete).
-      *   The current behavior upon restart however is to re-play the graph, skipping execution of completed jobs (determined by
-      *   engine job store) but still re-submitting all related metadata events. This is likely sub-optimal, but is used here
-      *   to simply stop the WMA (which will trigger all its descendants to be stopped recursively) without more coordination.
-      *   Indeed even if the actor is stopped in between the above mentioned gap, metadata will be re-submitted anyway on restart,
-      *   even for completed jobs.
-      *   
-      *  - Stop the LogCopyRouter: it can generate metadata events and must therefore be stopped before the service registry.
-      *   Wrap the ShutdownCommand in a Broadcast message so the router forwards it to all its routees
-      *   Use the ShutdownCommand because a PoisonPill could stop the routees in the middle of "transaction"
-      *   with the IoActor. The routees handle the ShutdownCommand properly and shutdown only when they have
-      *   no outstanding requests to the IoActor. When all routees are dead the router automatically stops itself.
-      *   
-      *  - Stop the job token dispenser: stop it before stopping WMA and its EJEA descendants because
-      *  the dispenser is watching all EJEAs and would be flooded by Terminated messages otherwise  
-    */
+     *  - Release any WorkflowStore entries held by this Cromwell instance.
+     *  - Publish workflow processing event metadata for the released workflows.
+     *  - Stop the WorkflowStore: The port is not bound anymore so we can't have new submissions.
+     *   Process what's left in the message queue and stop.
+     *   Note that it's possible that some submissions are still asynchronously being prepared at the
+     *   akka http API layer (CromwellApiService) to be sent to the WorkflowStore.
+     *   Those submissions might be lost if the WorkflowStore shuts itself down when it's finished processing its current work.
+     *   In that case the "ask" over in the CromwellAPIService will fail with a AskTimeoutException and should be handled appropriately.
+     *   This process still ensures that no submission can make it to the database without a response being sent back to the client.
+     *
+     *  - Stop WorkflowManagerActor: We've already stopped starting new workflows but the Running workflows are still
+     *   going. This is tricky because all the actor hierarchy under the WMA can be in a variety of state combinations.
+     *   Specifically there is an asynchronous gap in several cases between emission of messages towards engine level
+     *   actors (job store, cache store, etc...) and emission of messages towards the metadata service for the same logical
+     *   event (e.g: job complete).
+     *   The current behavior upon restart however is to re-play the graph, skipping execution of completed jobs (determined by
+     *   engine job store) but still re-submitting all related metadata events. This is likely sub-optimal, but is used here
+     *   to simply stop the WMA (which will trigger all its descendants to be stopped recursively) without more coordination.
+     *   Indeed even if the actor is stopped in between the above mentioned gap, metadata will be re-submitted anyway on restart,
+     *   even for completed jobs.
+     *
+     *  - Stop the LogCopyRouter: it can generate metadata events and must therefore be stopped before the service registry.
+     *   Wrap the ShutdownCommand in a Broadcast message so the router forwards it to all its routees
+     *   Use the ShutdownCommand because a PoisonPill could stop the routees in the middle of "transaction"
+     *   with the IoActor. The routees handle the ShutdownCommand properly and shutdown only when they have
+     *   no outstanding requests to the IoActor. When all routees are dead the router automatically stops itself.
+     *
+     *  - Stop the job token dispenser: stop it before stopping WMA and its EJEA descendants because
+     *  the dispenser is watching all EJEAs and would be flooded by Terminated messages otherwise
+     */
     coordinatedShutdown.addTask(CoordinatedShutdown.PhaseServiceRequestsDone, "releaseWorkflowStoreEntries") { () =>
-      EngineServicesStore.engineDatabaseInterface.releaseWorkflowStoreEntries(cromwellId).map(count => {
-        logger.info("{} workflows released by {}", count, cromwellId)
-      }).as(Done)
+      EngineServicesStore.engineDatabaseInterface
+        .releaseWorkflowStoreEntries(cromwellId)
+        .map(count => logger.info("{} workflows released by {}", count, cromwellId))
+        .as(Done)
     }
-    coordinatedShutdown.addTask(CoordinatedShutdown.PhaseServiceRequestsDone, "publishMetadataForReleasedWorkflowStoreEntries") { () =>
-      EngineServicesStore.engineDatabaseInterface.findWorkflows(cromwellId).map(ids =>
-        ids foreach { id =>
-          WorkflowProcessingEventPublishing.publish(WorkflowId.fromString(id), cromwellId, Released, serviceRegistryActor)
-        }
-      ).as(Done)
+    coordinatedShutdown.addTask(CoordinatedShutdown.PhaseServiceRequestsDone,
+                                "publishMetadataForReleasedWorkflowStoreEntries"
+    ) { () =>
+      EngineServicesStore.engineDatabaseInterface
+        .findWorkflows(cromwellId)
+        .map(ids =>
+          ids foreach { id =>
+            WorkflowProcessingEventPublishing
+              .publish(WorkflowId.fromString(id), cromwellId, Released, serviceRegistryActor)
+          }
+        )
+        .as(Done)
     }
 
     shutdownActor(workflowStoreActor, CoordinatedShutdown.PhaseServiceRequestsDone, ShutdownCommand)
     shutdownActor(logCopyRouter, CoordinatedShutdown.PhaseServiceRequestsDone, Broadcast(ShutdownCommand))
-    workflowCallbackActor.foreach(wca => shutdownActor(wca, CoordinatedShutdown.PhaseServiceRequestsDone, Broadcast(ShutdownCommand)))
+    workflowCallbackActor.foreach(wca =>
+      shutdownActor(wca, CoordinatedShutdown.PhaseServiceRequestsDone, Broadcast(ShutdownCommand))
+    )
     shutdownActor(jobTokenDispenser, CoordinatedShutdown.PhaseServiceRequestsDone, ShutdownCommand)
-    
+
     /*
-      * Aborting is only a special case of shutdown. Instead of sending a PoisonPill, send a AbortAllWorkflowsCommand
-      * Also attach this task to a special shutdown phase allowing for a longer timeout.
+     * Aborting is only a special case of shutdown. Instead of sending a PoisonPill, send a AbortAllWorkflowsCommand
+     * Also attach this task to a special shutdown phase allowing for a longer timeout.
      */
     if (abortJobsOnTerminate) {
       val abortTimeout = coordinatedShutdown.timeout(PhaseAbortAllWorkflows)
@@ -197,10 +203,10 @@ object CromwellShutdown extends GracefulStopSupport {
     }
 
     /* 4) Shutdown connection pools
-      * This will close all akka http opened connection pools tied to the actor system.
-      * The pools stop accepting new work but are given a chance to execute the work submitted prior to the shutdown call.
-      * When this future returns, all outstanding connections to client will be terminated.
-      * Note that this also includes connection pools like the one used to lookup docker hashes.
+     * This will close all akka http opened connection pools tied to the actor system.
+     * The pools stop accepting new work but are given a chance to execute the work submitted prior to the shutdown call.
+     * When this future returns, all outstanding connections to client will be terminated.
+     * Note that this also includes connection pools like the one used to lookup docker hashes.
      */
     coordinatedShutdown.addTask(CoordinatedShutdown.PhaseServiceStop, "TerminatingConnections") { () =>
       Http(actorSystem).shutdownAllConnectionPools() as {
@@ -210,14 +216,20 @@ object CromwellShutdown extends GracefulStopSupport {
     }
 
     /* 5) Stop system level actors that require writing to the database or I/O
-      * - SubWorkflowStoreActor
-      * - JobStoreActor
-      * - CallCacheWriteActor
-      * - ServiceRegistryActor
-      * - DockerHashActor
-      * - IoActor
-    */
-    List(subWorkflowStoreActor, jobStoreActor, callCacheWriteActor, serviceRegistryActor, dockerHashActor, ioActor) foreach {
+     * - SubWorkflowStoreActor
+     * - JobStoreActor
+     * - CallCacheWriteActor
+     * - ServiceRegistryActor
+     * - DockerHashActor
+     * - IoActor
+     */
+    List(subWorkflowStoreActor,
+         jobStoreActor,
+         callCacheWriteActor,
+         serviceRegistryActor,
+         dockerHashActor,
+         ioActor
+    ) foreach {
       shutdownActor(_, PhaseStopIoActivity, ShutdownCommand)
     }
 
@@ -236,12 +248,13 @@ object CromwellShutdown extends GracefulStopSupport {
 
     // 7) Close out the backend used for WDL HTTP import resolution
     // http://sttp.readthedocs.io/en/latest/backends/start_stop.html
-    coordinatedShutdown.addTask(CoordinatedShutdown.PhaseBeforeActorSystemTerminate, "wdlHttpImportResolverBackend") { () =>
-      Future {
-        HttpResolver.closeBackendIfNecessary()
-        logger.info("WDL HTTP import resolver closed")
-        Done
-      }
+    coordinatedShutdown.addTask(CoordinatedShutdown.PhaseBeforeActorSystemTerminate, "wdlHttpImportResolverBackend") {
+      () =>
+        Future {
+          HttpResolver.closeBackendIfNecessary()
+          logger.info("WDL HTTP import resolver closed")
+          Done
+        }
     }
   }
 }
diff --git a/engine/src/main/scala/cromwell/server/CromwellSystem.scala b/engine/src/main/scala/cromwell/server/CromwellSystem.scala
index 1a6a709c8f3..ec9b95999d0 100644
--- a/engine/src/main/scala/cromwell/server/CromwellSystem.scala
+++ b/engine/src/main/scala/cromwell/server/CromwellSystem.scala
@@ -40,26 +40,23 @@ trait CromwellSystem extends CromwellTerminator {
 
   implicit final lazy val actorSystem = newActorSystem()
   implicit final lazy val materializer = ActorMaterializer()
-  implicit private final lazy val ec = actorSystem.dispatcher
+  implicit final private lazy val ec = actorSystem.dispatcher
 
-  override def beginCromwellShutdown(reason: CoordinatedShutdown.Reason): Future[Done] = {
+  override def beginCromwellShutdown(reason: CoordinatedShutdown.Reason): Future[Done] =
     CromwellShutdown.instance(actorSystem).run(reason)
-  }
 
-  def shutdownActorSystem(): Future[Terminated] = {
+  def shutdownActorSystem(): Future[Terminated] =
     // If the actor system is already terminated it's already too late for a clean shutdown
     // Note: This does not protect again starting 2 shutdowns concurrently
     if (!actorSystem.whenTerminated.isCompleted) {
       Http().shutdownAllConnectionPools() flatMap { _ =>
         shutdownMaterializerAndActorSystem()
-      } recoverWith {
-        case _ =>
-          // we still want to shutdown the materializer and actor system if shutdownAllConnectionPools failed
-          shutdownMaterializerAndActorSystem()
+      } recoverWith { case _ =>
+        // we still want to shutdown the materializer and actor system if shutdownAllConnectionPools failed
+        shutdownMaterializerAndActorSystem()
       }
     } else actorSystem.whenTerminated
-  }
-  
+
   private def shutdownMaterializerAndActorSystem() = {
     materializer.shutdown()
     actorSystem.terminate()
diff --git a/engine/src/main/scala/cromwell/subworkflowstore/EmptySubWorkflowStoreActor.scala b/engine/src/main/scala/cromwell/subworkflowstore/EmptySubWorkflowStoreActor.scala
index cbbae2410c3..82e7a733817 100644
--- a/engine/src/main/scala/cromwell/subworkflowstore/EmptySubWorkflowStoreActor.scala
+++ b/engine/src/main/scala/cromwell/subworkflowstore/EmptySubWorkflowStoreActor.scala
@@ -7,7 +7,7 @@ import cromwell.util.GracefulShutdownHelper.ShutdownCommand
 
 class EmptySubWorkflowStoreActor extends Actor with ActorLogging {
   override def receive: Receive = {
-    case register: RegisterSubWorkflow => sender() ! SubWorkflowStoreRegisterSuccess(register) 
+    case register: RegisterSubWorkflow => sender() ! SubWorkflowStoreRegisterSuccess(register)
     case query: QuerySubWorkflow => sender() ! SubWorkflowNotFound(query)
     case _: WorkflowComplete => // No-op!
     case ShutdownCommand => context stop self
diff --git a/engine/src/main/scala/cromwell/subworkflowstore/SqlSubWorkflowStore.scala b/engine/src/main/scala/cromwell/subworkflowstore/SqlSubWorkflowStore.scala
index 64f21275ff4..acf760c8143 100644
--- a/engine/src/main/scala/cromwell/subworkflowstore/SqlSubWorkflowStore.scala
+++ b/engine/src/main/scala/cromwell/subworkflowstore/SqlSubWorkflowStore.scala
@@ -10,7 +10,8 @@ class SqlSubWorkflowStore(subWorkflowStoreSqlDatabase: SubWorkflowStoreSqlDataba
                                         callFullyQualifiedName: String,
                                         jobIndex: Int,
                                         jobAttempt: Int,
-                                        subWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Unit] = {
+                                        subWorkflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Unit] =
     subWorkflowStoreSqlDatabase.addSubWorkflowStoreEntry(
       rootWorkflowExecutionUuid,
       parentWorkflowExecutionUuid,
@@ -19,13 +20,16 @@ class SqlSubWorkflowStore(subWorkflowStoreSqlDatabase: SubWorkflowStoreSqlDataba
       jobAttempt,
       subWorkflowExecutionUuid
     )
-  }
 
-  override def querySubWorkflowStore(parentWorkflowExecutionUuid: String, callFqn: String, jobIndex: Int, jobAttempt: Int)(implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]] = {
+  override def querySubWorkflowStore(parentWorkflowExecutionUuid: String,
+                                     callFqn: String,
+                                     jobIndex: Int,
+                                     jobAttempt: Int
+  )(implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]] =
     subWorkflowStoreSqlDatabase.querySubWorkflowStore(parentWorkflowExecutionUuid, callFqn, jobIndex, jobAttempt)
-  }
 
-  override def removeSubWorkflowStoreEntries(parentWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Int] = {
+  override def removeSubWorkflowStoreEntries(parentWorkflowExecutionUuid: String)(implicit
+    ec: ExecutionContext
+  ): Future[Int] =
     subWorkflowStoreSqlDatabase.removeSubWorkflowStoreEntries(parentWorkflowExecutionUuid)
-  }
 }
diff --git a/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStore.scala b/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStore.scala
index 8ad92fa9bae..ef303be8e0e 100644
--- a/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStore.scala
+++ b/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStore.scala
@@ -10,10 +10,12 @@ trait SubWorkflowStore {
                                callFullyQualifiedName: String,
                                jobIndex: Int,
                                jobAttempt: Int,
-                               subWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Unit]
+                               subWorkflowExecutionUuid: String
+  )(implicit ec: ExecutionContext): Future[Unit]
 
-  def querySubWorkflowStore(parentWorkflowExecutionUuid: String, callFqn: String, jobIndex: Int, jobAttempt: Int)
-                           (implicit ec: ExecutionContext): Future[Option[SubWorkflowStoreEntry]]
+  def querySubWorkflowStore(parentWorkflowExecutionUuid: String, callFqn: String, jobIndex: Int, jobAttempt: Int)(
+    implicit ec: ExecutionContext
+  ): Future[Option[SubWorkflowStoreEntry]]
 
   def removeSubWorkflowStoreEntries(parentWorkflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Int]
 }
diff --git a/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStoreActor.scala b/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStoreActor.scala
index 22ec0476220..a3540c3497a 100644
--- a/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStoreActor.scala
+++ b/engine/src/main/scala/cromwell/subworkflowstore/SubWorkflowStoreActor.scala
@@ -11,7 +11,7 @@ import scala.concurrent.ExecutionContext
 import scala.util.{Failure, Success}
 
 class SubWorkflowStoreActor(database: SubWorkflowStore) extends Actor with ActorLogging with MonitoringCompanionHelper {
-  
+
   implicit val ec: ExecutionContext = context.dispatcher
 
   val subWorkflowStoreReceive: Receive = {
@@ -19,9 +19,9 @@ class SubWorkflowStoreActor(database: SubWorkflowStore) extends Actor with Actor
     case query: QuerySubWorkflow => querySubWorkflow(sender(), query)
     case complete: WorkflowComplete => workflowComplete(sender(), complete)
   }
-  
+
   override def receive = subWorkflowStoreReceive.orElse(monitoringReceive)
-  
+
   private def registerSubWorkflow(replyTo: ActorRef, command: RegisterSubWorkflow) = {
     addWork()
     database.addSubWorkflowStoreEntry(
@@ -31,9 +31,9 @@ class SubWorkflowStoreActor(database: SubWorkflowStore) extends Actor with Actor
       command.jobKey.index.fromIndex,
       command.jobKey.attempt,
       command.subWorkflowExecutionUuid.toString
-    ) onComplete { 
+    ) onComplete {
       case Success(_) =>
-        replyTo ! SubWorkflowStoreRegisterSuccess(command) 
+        replyTo ! SubWorkflowStoreRegisterSuccess(command)
         removeWork()
       case Failure(ex) =>
         replyTo ! SubWorkflowStoreFailure(command, ex)
@@ -43,7 +43,11 @@ class SubWorkflowStoreActor(database: SubWorkflowStore) extends Actor with Actor
 
   private def querySubWorkflow(replyTo: ActorRef, command: QuerySubWorkflow) = {
     val jobKey = command.jobKey
-    database.querySubWorkflowStore(command.parentWorkflowExecutionUuid.toString, jobKey.node.fullyQualifiedName, jobKey.index.fromIndex, jobKey.attempt) onComplete {
+    database.querySubWorkflowStore(command.parentWorkflowExecutionUuid.toString,
+                                   jobKey.node.fullyQualifiedName,
+                                   jobKey.index.fromIndex,
+                                   jobKey.attempt
+    ) onComplete {
       case Success(Some(result)) => replyTo ! SubWorkflowFound(result)
       case Success(None) => replyTo ! SubWorkflowNotFound(command)
       case Failure(ex) => replyTo ! SubWorkflowStoreFailure(command, ex)
@@ -54,27 +58,33 @@ class SubWorkflowStoreActor(database: SubWorkflowStore) extends Actor with Actor
     addWork()
     database.removeSubWorkflowStoreEntries(command.workflowExecutionUuid.toString) onComplete {
       case Success(_) => removeWork()
-      case Failure(ex) => 
+      case Failure(ex) =>
         replyTo ! SubWorkflowStoreFailure(command, ex)
         removeWork()
     }
   }
-  
+
 }
 
 object SubWorkflowStoreActor {
   sealed trait SubWorkflowStoreActorCommand
-  case class RegisterSubWorkflow(rootWorkflowExecutionUuid: WorkflowId, parentWorkflowExecutionUuid: WorkflowId, jobKey: JobKey, subWorkflowExecutionUuid: WorkflowId) extends SubWorkflowStoreActorCommand
-  case class QuerySubWorkflow(parentWorkflowExecutionUuid: WorkflowId, jobKey: JobKey) extends SubWorkflowStoreActorCommand
+  case class RegisterSubWorkflow(rootWorkflowExecutionUuid: WorkflowId,
+                                 parentWorkflowExecutionUuid: WorkflowId,
+                                 jobKey: JobKey,
+                                 subWorkflowExecutionUuid: WorkflowId
+  ) extends SubWorkflowStoreActorCommand
+  case class QuerySubWorkflow(parentWorkflowExecutionUuid: WorkflowId, jobKey: JobKey)
+      extends SubWorkflowStoreActorCommand
   case class WorkflowComplete(workflowExecutionUuid: WorkflowId) extends SubWorkflowStoreActorCommand
 
   sealed trait SubWorkflowStoreActorResponse
   case class SubWorkflowStoreRegisterSuccess(command: RegisterSubWorkflow) extends SubWorkflowStoreActorResponse
   case class SubWorkflowFound(subWorkflowStoreEntry: SubWorkflowStoreEntry) extends SubWorkflowStoreActorResponse
   case class SubWorkflowNotFound(command: QuerySubWorkflow) extends SubWorkflowStoreActorResponse
-  
-  case class SubWorkflowStoreFailure(command: SubWorkflowStoreActorCommand, failure: Throwable) extends SubWorkflowStoreActorResponse
-  
+
+  case class SubWorkflowStoreFailure(command: SubWorkflowStoreActorCommand, failure: Throwable)
+      extends SubWorkflowStoreActorResponse
+
   def props(database: SubWorkflowStore) = Props(
     new SubWorkflowStoreActor(database)
   ).withDispatcher(EngineDispatcher)
diff --git a/engine/src/main/scala/cromwell/webservice/ApiDataModels.scala b/engine/src/main/scala/cromwell/webservice/ApiDataModels.scala
index 61bd2ee7d01..ceb4c1b67e7 100644
--- a/engine/src/main/scala/cromwell/webservice/ApiDataModels.scala
+++ b/engine/src/main/scala/cromwell/webservice/ApiDataModels.scala
@@ -6,7 +6,6 @@ import spray.json._
 import wdl.draft2.model.FullyQualifiedName
 import wom.values.WomValue
 
-
 case class WorkflowStatusResponse(id: String, status: String)
 
 case class WorkflowSubmitResponse(id: String, status: String)
@@ -21,16 +20,16 @@ case class WorkflowMetadataQueryParameters(outputs: Boolean = true, timings: Boo
 
 object APIResponse {
 
-  private def constructFailureResponse(status: String, ex: Throwable) = {
+  private def constructFailureResponse(status: String, ex: Throwable) =
     ex match {
       case exceptionWithErrors: MessageAggregation =>
-        FailureResponse(
-          status,
-          exceptionWithErrors.exceptionContext,
-          Option(exceptionWithErrors.errorMessages.toVector))
-      case e: Throwable => FailureResponse(status, e.getMessage, Option(e.getCause).map(c => Vector(ExceptionUtils.getMessage(c))))
+        FailureResponse(status,
+                        exceptionWithErrors.exceptionContext,
+                        Option(exceptionWithErrors.errorMessages.toVector)
+        )
+      case e: Throwable =>
+        FailureResponse(status, e.getMessage, Option(e.getCause).map(c => Vector(ExceptionUtils.getMessage(c))))
     }
-  }
 
   /** When the data submitted in the request is incorrect. */
   def fail(ex: Throwable) = constructFailureResponse("fail", ex)
diff --git a/engine/src/main/scala/cromwell/webservice/EngineStatsActor.scala b/engine/src/main/scala/cromwell/webservice/EngineStatsActor.scala
index ce123db4d20..6aa5edc94fb 100644
--- a/engine/src/main/scala/cromwell/webservice/EngineStatsActor.scala
+++ b/engine/src/main/scala/cromwell/webservice/EngineStatsActor.scala
@@ -13,7 +13,9 @@ import scala.concurrent.duration._
   * Because of the vagaries of timing, etc this is intended to give a rough idea of what's going on instead of
   * being a ground truth.
   */
-final case class EngineStatsActor(workflowActors: List[ActorRef], replyTo: ActorRef, timeout: FiniteDuration) extends Actor with ActorLogging {
+final case class EngineStatsActor(workflowActors: List[ActorRef], replyTo: ActorRef, timeout: FiniteDuration)
+    extends Actor
+    with ActorLogging {
   implicit val ec = context.dispatcher
 
   private var jobCounts = Map.empty[ActorRef, Int]
@@ -23,7 +25,7 @@ final case class EngineStatsActor(workflowActors: List[ActorRef], replyTo: Actor
    * Because of sub workflows there is currently no reliable way to know if we received responses from all running WEAs.
    * For now, we always wait for the timeout duration before responding to give a chance to all WEAs to respond (even nested ones).
    * This could be improved by having WEAs wait for their sub WEAs before sending back the response.
-  */
+   */
   val scheduledMsg = context.system.scheduler.scheduleOnce(timeout, self, ShutItDown)
 
   if (workflowActors.isEmpty) reportStats()
@@ -47,9 +49,8 @@ final case class EngineStatsActor(workflowActors: List[ActorRef], replyTo: Actor
 object EngineStatsActor {
   import scala.language.postfixOps
 
-  def props(workflowActors: List[ActorRef], replyTo: ActorRef, timeout: FiniteDuration = MaxTimeToWait) = {
+  def props(workflowActors: List[ActorRef], replyTo: ActorRef, timeout: FiniteDuration = MaxTimeToWait) =
     Props(EngineStatsActor(workflowActors, replyTo, timeout)).withDispatcher(Dispatcher.ApiDispatcher)
-  }
 
   sealed abstract class EngineStatsActorMessage
   private case object ShutItDown extends EngineStatsActorMessage
diff --git a/engine/src/main/scala/cromwell/webservice/LabelsManagerActor.scala b/engine/src/main/scala/cromwell/webservice/LabelsManagerActor.scala
index ca85c8de694..9d317152ba9 100644
--- a/engine/src/main/scala/cromwell/webservice/LabelsManagerActor.scala
+++ b/engine/src/main/scala/cromwell/webservice/LabelsManagerActor.scala
@@ -11,7 +11,8 @@ import spray.json.{DefaultJsonProtocol, JsObject, JsString}
 
 object LabelsManagerActor {
 
-  def props(serviceRegistryActor: ActorRef): Props = Props(new LabelsManagerActor(serviceRegistryActor)).withDispatcher(Dispatcher.ApiDispatcher)
+  def props(serviceRegistryActor: ActorRef): Props =
+    Props(new LabelsManagerActor(serviceRegistryActor)).withDispatcher(Dispatcher.ApiDispatcher)
 
   final case class LabelsData(workflowId: WorkflowId, labels: Labels)
 
@@ -49,7 +50,7 @@ class LabelsManagerActor(serviceRegistryActor: ActorRef) extends Actor with Acto
       /*
         Ask the metadata store for the current set of labels, so we can return the full label set to the user.
         At this point in the actor lifecycle, wfId has already been filled out so the .get is safe
-      */
+       */
       serviceRegistryActor ! GetLabels(wfId.get)
     case SuccessfulMetadataJsonResponse(_, jsObject) =>
       /*
@@ -64,7 +65,7 @@ class LabelsManagerActor(serviceRegistryActor: ActorRef) extends Actor with Acto
         the return packet, this is a likely cause.
 
         At this point in the actor lifecycle, newLabels will have been filled in so the .get is safe
-      */
+       */
 
       def replaceOrAddLabel(originalJson: JsObject, label: Label): JsObject = {
         val labels = originalJson.fields.get("labels").map(_.asJsObject.fields).getOrElse(Map.empty)
@@ -83,7 +84,9 @@ class LabelsManagerActor(serviceRegistryActor: ActorRef) extends Actor with Acto
 
         At this point in the actor lifecycle, wfId has already been filled out so the .get is safe
        */
-      target ! FailedLabelsManagerResponse(new RuntimeException(s"Unable to update labels for ${wfId.get} due to ${f.reason.getMessage}"))
+      target ! FailedLabelsManagerResponse(
+        new RuntimeException(s"Unable to update labels for ${wfId.get} due to ${f.reason.getMessage}")
+      )
       context stop self
   }
 }
diff --git a/engine/src/main/scala/cromwell/webservice/PartialWorkflowSources.scala b/engine/src/main/scala/cromwell/webservice/PartialWorkflowSources.scala
index 9862dc01151..22adbe6e0f8 100644
--- a/engine/src/main/scala/cromwell/webservice/PartialWorkflowSources.scala
+++ b/engine/src/main/scala/cromwell/webservice/PartialWorkflowSources.scala
@@ -36,7 +36,8 @@ final case class PartialWorkflowSources(workflowSource: Option[WorkflowSource] =
                                         zippedImports: Option[Array[Byte]] = None,
                                         warnings: Seq[String] = List.empty,
                                         workflowOnHold: Boolean,
-                                        requestedWorkflowIds: Vector[WorkflowId])
+                                        requestedWorkflowIds: Vector[WorkflowId]
+)
 
 object PartialWorkflowSources {
   val log = LoggerFactory.getLogger(classOf[PartialWorkflowSources])
@@ -56,15 +57,29 @@ object PartialWorkflowSources {
   val workflowOnHoldKey = "workflowOnHold"
   val RequestedWorkflowIdKey = "requestedWorkflowId"
 
-  val allKeys = List(WdlSourceKey, WorkflowUrlKey, WorkflowRootKey, WorkflowSourceKey, WorkflowTypeKey, WorkflowTypeVersionKey, WorkflowInputsKey,
-    WorkflowOptionsKey, labelsKey, WdlDependenciesKey, WorkflowDependenciesKey, workflowOnHoldKey, RequestedWorkflowIdKey)
+  val allKeys = List(
+    WdlSourceKey,
+    WorkflowUrlKey,
+    WorkflowRootKey,
+    WorkflowSourceKey,
+    WorkflowTypeKey,
+    WorkflowTypeVersionKey,
+    WorkflowInputsKey,
+    WorkflowOptionsKey,
+    labelsKey,
+    WdlDependenciesKey,
+    WorkflowDependenciesKey,
+    workflowOnHoldKey,
+    RequestedWorkflowIdKey
+  )
 
   val allPrefixes = List(WorkflowInputsAuxPrefix)
 
   val MaxWorkflowUrlLength = 2000
 
   def fromSubmitRoute(formData: Map[String, ByteString],
-                      allowNoInputs: Boolean): Try[Seq[WorkflowSourceFilesCollection]] = {
+                      allowNoInputs: Boolean
+  ): Try[Seq[WorkflowSourceFilesCollection]] = {
     import cats.syntax.apply._
     import cats.syntax.traverse._
     import cats.syntax.validated._
@@ -78,7 +93,7 @@ object PartialWorkflowSources {
       val unrecognized: ErrorOr[Unit] = formData.keySet
         .filterNot(name => allKeys.contains(name) || allPrefixes.exists(name.startsWith))
         .toList
-        .map(name => s"Unexpected body part name: $name")  match {
+        .map(name => s"Unexpected body part name: $name") match {
         case Nil => ().validNel
         case head :: tail => NonEmptyList.of(head, tail: _*).invalid
       }
@@ -88,17 +103,17 @@ object PartialWorkflowSources {
       val workflowSource = getStringValue(WorkflowSourceKey)
       val workflowUrl = getStringValue(WorkflowUrlKey)
 
-      def deprecationWarning(out: String, in: String)(actual: String): String = {
+      def deprecationWarning(out: String, in: String)(actual: String): String =
         if (actual == out) {
           val warning =
             Array(
               s"The '$out' parameter name has been deprecated in favor of '$in'.",
               s"Support for '$out' will be removed from future versions of Cromwell.",
-              s"Please switch to using '$in' in future submissions.").mkString(" ")
+              s"Please switch to using '$in' in future submissions."
+            ).mkString(" ")
           log.warn(warning)
           warning
         } else ""
-      }
 
       val wdlSourceDeprecationWarning: String => String = deprecationWarning(out = WdlSourceKey, in = WorkflowSourceKey)
       val wdlSourceWarning = wdlSource.as(WdlSourceKey) map wdlSourceDeprecationWarning
@@ -110,7 +125,8 @@ object PartialWorkflowSources {
         case (Some(_), Some(_), None) => s"$WdlSourceKey and $WorkflowSourceKey can't both be supplied".invalidNel
         case (None, Some(_), Some(_)) => s"$WorkflowSourceKey and $WorkflowUrlKey can't both be supplied".invalidNel
         case (Some(_), None, Some(_)) => s"$WdlSourceKey and $WorkflowUrlKey can't both be supplied".invalidNel
-        case (Some(_), Some(_), Some(_)) => s"$WdlSourceKey, $WorkflowSourceKey and $WorkflowUrlKey all 3 can't be supplied".invalidNel
+        case (Some(_), Some(_), Some(_)) =>
+          s"$WdlSourceKey, $WorkflowSourceKey and $WorkflowUrlKey all 3 can't be supplied".invalidNel
         case (None, None, None) => s"$WorkflowSourceKey or $WorkflowUrlKey needs to be supplied".invalidNel
       }
 
@@ -124,17 +140,20 @@ object PartialWorkflowSources {
         case None => Vector.empty.validNel
       }
 
-      val workflowInputsAux: ErrorOr[Map[Int, String]] = formData.toList.flatTraverse[ErrorOr, (Int, String)]({
-        case (name, value) if name.startsWith(WorkflowInputsAuxPrefix) =>
-          Try(name.stripPrefix(WorkflowInputsAuxPrefix).toInt).toErrorOr.map(index => List((index, value.utf8String)))
-        case _ => List.empty.validNel
-      }).map(_.toMap)
+      val workflowInputsAux: ErrorOr[Map[Int, String]] = formData.toList
+        .flatTraverse[ErrorOr, (Int, String)] {
+          case (name, value) if name.startsWith(WorkflowInputsAuxPrefix) =>
+            Try(name.stripPrefix(WorkflowInputsAuxPrefix).toInt).toErrorOr.map(index => List((index, value.utf8String)))
+          case _ => List.empty.validNel
+        }
+        .map(_.toMap)
 
       // dependencies
       val wdlDependencies = getArrayValue(WdlDependenciesKey)
       val workflowDependencies = getArrayValue(WorkflowDependenciesKey)
 
-      val wdlDependenciesDeprecationWarning: String => String = deprecationWarning(out = "wdlDependencies", in = "workflowDependencies")
+      val wdlDependenciesDeprecationWarning: String => String =
+        deprecationWarning(out = "wdlDependencies", in = "workflowDependencies")
       val wdlDependenciesWarning = wdlDependencies.as(WdlDependenciesKey) map wdlDependenciesDeprecationWarning
 
       val workflowDependenciesFinal: ErrorOr[Option[Array[Byte]]] = (wdlDependencies, workflowDependencies) match {
@@ -146,15 +165,22 @@ object PartialWorkflowSources {
 
       val onHold: ErrorOr[Boolean] = getBooleanValue(workflowOnHoldKey).getOrElse(false.validNel)
 
-      (unrecognized, workflowSourceFinal, requestedIds, workflowInputs, workflowInputsAux, workflowDependenciesFinal, onHold) mapN {
-        case (_, source, ids, inputs, aux, dep, onHoldActual) => PartialWorkflowSources(
+      (unrecognized,
+       workflowSourceFinal,
+       requestedIds,
+       workflowInputs,
+       workflowInputsAux,
+       workflowDependenciesFinal,
+       onHold
+      ) mapN { case (_, source, ids, inputs, aux, dep, onHoldActual) =>
+        PartialWorkflowSources(
           workflowSource = source,
           workflowUrl = workflowUrl,
           workflowRoot = getStringValue(WorkflowRootKey),
           workflowType = getStringValue(WorkflowTypeKey),
           workflowTypeVersion = getStringValue(WorkflowTypeVersionKey),
           workflowInputs = inputs,
-          workflowInputsAux= aux,
+          workflowInputsAux = aux,
           workflowOptions = getStringValue(WorkflowOptionsKey),
           customLabels = getStringValue(labelsKey),
           zippedImports = dep,
@@ -171,20 +197,28 @@ object PartialWorkflowSources {
     }
   }
 
-  private def arrayTypeElementValidation[A](data: String, interpretElementFunction: _root_.io.circe.Json => ErrorOr[A]) = {
+  private def arrayTypeElementValidation[A](data: String,
+                                            interpretElementFunction: _root_.io.circe.Json => ErrorOr[A]
+  ) = {
     import cats.syntax.validated._
 
     val parseInputsTry = Try {
       YamlUtils.parse(data) match {
         // If it's an array, treat each element as an individual input object, otherwise simply toString the whole thing
-        case Right(json) => json.asArray.map(_.traverse(interpretElementFunction)).getOrElse(interpretElementFunction(json).map(Vector(_))).validNel
-        case Left(error) => s"Input file is not a valid yaml or json. Inputs data: '$data'. Error: ${ExceptionUtils.getMessage(error)}.".invalidNel
+        case Right(json) =>
+          json.asArray
+            .map(_.traverse(interpretElementFunction))
+            .getOrElse(interpretElementFunction(json).map(Vector(_)))
+            .validNel
+        case Left(error) =>
+          s"Input file is not a valid yaml or json. Inputs data: '$data'. Error: ${ExceptionUtils.getMessage(error)}.".invalidNel
       }
     }
 
     parseInputsTry match {
       case Success(v) => v.flatten
-      case Failure(error) => s"Input file is not a valid yaml or json. Inputs data: '$data'. Error: ${ExceptionUtils.getMessage(error)}.".invalidNel
+      case Failure(error) =>
+        s"Input file is not a valid yaml or json. Inputs data: '$data'. Error: ${ExceptionUtils.getMessage(error)}.".invalidNel
     }
   }
 
@@ -203,17 +237,17 @@ object PartialWorkflowSources {
     import _root_.io.circe.Printer
     import cats.syntax.validated._
 
-    def interpretEachElement(json: Json): ErrorOr[WorkflowId] = {
+    def interpretEachElement(json: Json): ErrorOr[WorkflowId] =
       if (json.isString) {
         Try(WorkflowId.fromString(json.asString.get)).toErrorOrWithContext("parse requested workflow ID as UUID")
       } else s"Requested workflow IDs must be strings but got: '${json.printWith(Printer.noSpaces)}'".invalidNel
-    }
 
     arrayTypeElementValidation(data, interpretEachElement)
   }
 
   private def partialSourcesToSourceCollections(partialSources: ErrorOr[PartialWorkflowSources],
-                                                allowNoInputs: Boolean): ErrorOr[Seq[WorkflowSourceFilesCollection]] = {
+                                                allowNoInputs: Boolean
+  ): ErrorOr[Seq[WorkflowSourceFilesCollection]] = {
     case class RequestedIdAndInputs(requestedId: Option[WorkflowId], inputs: WorkflowJson)
 
     def validateInputsAndRequestedIds(pws: PartialWorkflowSources): ErrorOr[Seq[RequestedIdAndInputs]] = {
@@ -221,7 +255,9 @@ object PartialWorkflowSources {
         case (true, true) => Vector("{}").validNel
         case (true, false) => "No inputs were provided".invalidNel
         case _ =>
-          val sortedInputAuxes = pws.workflowInputsAux.toSeq.sortBy { case (index, _) => index } map { case(_, inputJson) => Option(inputJson) }
+          val sortedInputAuxes = pws.workflowInputsAux.toSeq.sortBy { case (index, _) => index } map {
+            case (_, inputJson) => Option(inputJson)
+          }
           pws.workflowInputs.toList.traverse[ErrorOr, String] { workflowInputSet: WorkflowJson =>
             mergeMaps(Seq(Option(workflowInputSet)) ++ sortedInputAuxes).map(_.toString)
           }
@@ -231,7 +267,10 @@ object PartialWorkflowSources {
         if (pws.requestedWorkflowIds.isEmpty) {
           (workflowInputs map { i => RequestedIdAndInputs(None, i) }).validNel
         } else if (pws.requestedWorkflowIds.size == workflowInputs.size) {
-          (pws.requestedWorkflowIds.zip(workflowInputs).map { case (id, inputs) => RequestedIdAndInputs(Option(id), inputs) }).validNel
+          pws.requestedWorkflowIds
+            .zip(workflowInputs)
+            .map { case (id, inputs) => RequestedIdAndInputs(Option(id), inputs) }
+            .validNel
         } else {
           s"Mismatch between requested IDs count (${pws.requestedWorkflowIds.size}) and workflow inputs counts (${workflowInputs.size})".invalidNel
         }
@@ -239,18 +278,23 @@ object PartialWorkflowSources {
     }
 
     def validateOptions(options: Option[WorkflowOptionsJson]): ErrorOr[WorkflowOptions] =
-      WorkflowOptions.fromJsonString(options.getOrElse("{}")).toErrorOr leftMap { _ map { i => s"Invalid workflow options provided: $i" } }
+      WorkflowOptions.fromJsonString(options.getOrElse("{}")).toErrorOr leftMap {
+        _ map { i => s"Invalid workflow options provided: $i" }
+      }
 
-    def validateLabels(labels: WorkflowJson) : ErrorOr[WorkflowJson] = {
+    def validateLabels(labels: WorkflowJson): ErrorOr[WorkflowJson] = {
 
-      def validateKeyValuePair(key: String, value: String): ErrorOr[Unit] = (Label.validateLabelKey(key), Label.validateLabelValue(value)).tupled.void
+      def validateKeyValuePair(key: String, value: String): ErrorOr[Unit] =
+        (Label.validateLabelKey(key), Label.validateLabelValue(value)).tupled.void
 
-      def validateLabelRestrictions(inputs: Map[String, JsValue]): ErrorOr[Unit] = {
-        inputs.toList.traverse[ErrorOr, Unit]({
-          case (key, JsString(s)) => validateKeyValuePair(key, s)
-          case (key, other) => s"Invalid label $key: $other : Labels must be strings. ${Label.LabelExpectationsMessage}".invalidNel
-        }).void
-      }
+      def validateLabelRestrictions(inputs: Map[String, JsValue]): ErrorOr[Unit] =
+        inputs.toList
+          .traverse[ErrorOr, Unit] {
+            case (key, JsString(s)) => validateKeyValuePair(key, s)
+            case (key, other) =>
+              s"Invalid label $key: $other : Labels must be strings. ${Label.LabelExpectationsMessage}".invalidNel
+          }
+          .void
 
       Try(labels.parseJson) match {
         case Success(JsObject(inputs)) => validateLabelRestrictions(inputs).map(_ => labels)
@@ -262,11 +306,12 @@ object PartialWorkflowSources {
     partialSources match {
       case Valid(partialSource) =>
         (validateInputsAndRequestedIds(partialSource),
-          validateOptions(partialSource.workflowOptions),
-          validateLabels(partialSource.customLabels.getOrElse("{}")),
-          partialSource.workflowUrl.traverse(validateWorkflowUrl)) mapN {
-          case (wfInputsAndIds, wfOptions, workflowLabels, wfUrl) =>
-            wfInputsAndIds.map { case RequestedIdAndInputs(id, inputsJson) => WorkflowSourceFilesCollection(
+         validateOptions(partialSource.workflowOptions),
+         validateLabels(partialSource.customLabels.getOrElse("{}")),
+         partialSource.workflowUrl.traverse(validateWorkflowUrl)
+        ) mapN { case (wfInputsAndIds, wfOptions, workflowLabels, wfUrl) =>
+          wfInputsAndIds.map { case RequestedIdAndInputs(id, inputsJson) =>
+            WorkflowSourceFilesCollection(
               workflowSource = partialSource.workflowSource,
               workflowUrl = wfUrl,
               workflowRoot = partialSource.workflowRoot,
@@ -278,7 +323,9 @@ object PartialWorkflowSources {
               importsFile = partialSource.zippedImports,
               warnings = partialSource.warnings,
               workflowOnHold = partialSource.workflowOnHold,
-              requestedWorkflowId = id) }
+              requestedWorkflowId = id
+            )
+          }
         }
       case Invalid(err) => err.invalid
     }
@@ -294,27 +341,28 @@ object PartialWorkflowSources {
   }
 
   def validateWorkflowUrl(workflowUrl: String): ErrorOr[WorkflowUrl] = {
-    def convertStringToUrl(workflowUrl: String): ErrorOr[WorkflowUrl] = {
+    def convertStringToUrl(workflowUrl: String): ErrorOr[WorkflowUrl] =
       Try(new URL(workflowUrl)) match {
         case Success(_) => workflowUrl.validNel
         case Failure(e) => s"Error while validating workflow url: ${e.getMessage}".invalidNel
       }
-    }
 
     val len = workflowUrl.length
-    if (len > MaxWorkflowUrlLength) s"Invalid workflow url: url has length $len, longer than the maximum allowed $MaxWorkflowUrlLength characters".invalidNel
+    if (len > MaxWorkflowUrlLength)
+      s"Invalid workflow url: url has length $len, longer than the maximum allowed $MaxWorkflowUrlLength characters".invalidNel
     else convertStringToUrl(workflowUrl)
   }
 
-  private def toMap(someInput: Option[String]): ErrorOr[Map[String, JsValue]] = {
+  private def toMap(someInput: Option[String]): ErrorOr[Map[String, JsValue]] =
     someInput match {
       case Some(input: String) =>
-        Try(input.parseJson).toErrorOrWithContext(s"parse input: '$input', which is not a valid json. Please check for syntactical errors.") flatMap {
+        Try(input.parseJson).toErrorOrWithContext(
+          s"parse input: '$input', which is not a valid json. Please check for syntactical errors."
+        ) flatMap {
           case JsObject(inputMap) => inputMap.validNel
-          case j: JsValue => s"Submitted input '$input' of type ${j.getClass.getSimpleName} is not a valid JSON object.".invalidNel
+          case j: JsValue =>
+            s"Submitted input '$input' of type ${j.getClass.getSimpleName} is not a valid JSON object.".invalidNel
         }
       case None => Map.empty[String, JsValue].validNel
     }
-  }
 }
-
diff --git a/engine/src/main/scala/cromwell/webservice/SwaggerUiHttpService.scala b/engine/src/main/scala/cromwell/webservice/SwaggerUiHttpService.scala
index d63ab3bcb51..dd1d88d5f5d 100644
--- a/engine/src/main/scala/cromwell/webservice/SwaggerUiHttpService.scala
+++ b/engine/src/main/scala/cromwell/webservice/SwaggerUiHttpService.scala
@@ -41,7 +41,7 @@ trait SwaggerUiHttpService {
    *
    * @return Route serving the swagger UI.
    */
-  final def swaggerUiRoute: Route = {
+  final def swaggerUiRoute: Route =
     pathEndOrSingleSlash {
       get {
         serveIndex
@@ -61,13 +61,13 @@ trait SwaggerUiHttpService {
       // the subject of the CVE linked below while preserving any fragment identifiers to scroll to the right spot in
       // the Swagger UI.
       // https://github.com/swagger-api/swagger-ui/security/advisories/GHSA-qrmm-w75w-3wpx
-      (path("swagger" / "index.html") | path ("swagger")) {
+      (path("swagger" / "index.html") | path("swagger")) {
         get {
           redirect("/", StatusCodes.MovedPermanently)
         }
       }
-  }
 }
+
 /**
  * An extension of HttpService to serve up a resource containing the swagger api as yaml or json. The resource
  * directory and path on the classpath must match the path for route. The resource can be any file type supported by the
@@ -75,9 +75,8 @@ trait SwaggerUiHttpService {
  */
 trait SwaggerResourceHttpService {
 
-  def getBasePathOverride(): Option[String] = {
+  def getBasePathOverride(): Option[String] =
     Option(System.getenv("SWAGGER_BASE_PATH"))
-  }
 
   /**
    * @return The directory for the resource under the classpath, and in the url
@@ -104,18 +103,21 @@ trait SwaggerResourceHttpService {
    */
   final def swaggerResourceRoute: Route = {
     // Serve Cromwell API docs from either `/swagger/cromwell.yaml` or just `cromwell.yaml`.
-    val swaggerDocsDirective = path(separateOnSlashes(swaggerDocsPath)) | path(s"$swaggerServiceName.$swaggerResourceType")
+    val swaggerDocsDirective =
+      path(separateOnSlashes(swaggerDocsPath)) | path(s"$swaggerServiceName.$swaggerResourceType")
 
-    def injectBasePath(basePath: Option[String])(response: HttpResponse): HttpResponse = {
+    def injectBasePath(basePath: Option[String])(response: HttpResponse): HttpResponse =
       basePath match {
         case _ if response.status != StatusCodes.OK => response
         case None => response
-        case Some(base_path) => response.mapEntity { entity =>
-          val swapperFlow: Flow[ByteString, ByteString, Any] = Flow[ByteString].map(byteString => ByteString.apply(byteString.utf8String.replace("#basePath: ...", "basePath: " + base_path)))
-          entity.transformDataBytes(swapperFlow)
-        }
+        case Some(base_path) =>
+          response.mapEntity { entity =>
+            val swapperFlow: Flow[ByteString, ByteString, Any] = Flow[ByteString].map(byteString =>
+              ByteString.apply(byteString.utf8String.replace("#basePath: ...", "basePath: " + base_path))
+            )
+            entity.transformDataBytes(swapperFlow)
+          }
       }
-    }
 
     val route = get {
       swaggerDocsDirective {
@@ -135,6 +137,7 @@ trait SwaggerResourceHttpService {
  * Extends the SwaggerUiHttpService and SwaggerResourceHttpService to serve up both.
  */
 trait SwaggerUiResourceHttpService extends SwaggerUiHttpService with SwaggerResourceHttpService {
+
   /**
    * @return A route that redirects to the swagger UI and returns the swagger resource.
    */
diff --git a/engine/src/main/scala/cromwell/webservice/WebServiceUtils.scala b/engine/src/main/scala/cromwell/webservice/WebServiceUtils.scala
index 7483b300f2b..ab5f26caa37 100644
--- a/engine/src/main/scala/cromwell/webservice/WebServiceUtils.scala
+++ b/engine/src/main/scala/cromwell/webservice/WebServiceUtils.scala
@@ -18,28 +18,35 @@ trait WebServiceUtils {
 
   type MaterializedFormData = Map[String, ByteString]
 
-  def materializeFormData(formData: Multipart.FormData)(implicit timeout: Timeout, materializer: Materializer, executionContext: ExecutionContext): Future[MaterializedFormData] = {
-    formData.parts.mapAsync[(String, ByteString)](1) {
-      bodyPart => bodyPart.toStrict(timeout.duration)(materializer).map(strict => bodyPart.name -> strict.entity.data)(executionContext)
-    }.runFold(Map.empty[String, ByteString])((map, tuple) => map + tuple)(materializer)
-  }
+  def materializeFormData(formData: Multipart.FormData)(implicit
+    timeout: Timeout,
+    materializer: Materializer,
+    executionContext: ExecutionContext
+  ): Future[MaterializedFormData] =
+    formData.parts
+      .mapAsync[(String, ByteString)](1) { bodyPart =>
+        bodyPart
+          .toStrict(timeout.duration)(materializer)
+          .map(strict => bodyPart.name -> strict.entity.data)(executionContext)
+      }
+      .runFold(Map.empty[String, ByteString])((map, tuple) => map + tuple)(materializer)
 
   /**
     * Completes a response of a Product, probably a case class, using an implicit marshaller, probably a json encoder.
     */
-  def completeResponse[A <: Product](statusCode: StatusCode, value: A, warnings: Seq[String])
-                                    (implicit mt: ToEntityMarshaller[A]): Route = {
+  def completeResponse[A <: Product](statusCode: StatusCode, value: A, warnings: Seq[String])(implicit
+    mt: ToEntityMarshaller[A]
+  ): Route =
     complete((statusCode, warningHeaders(warnings), value))
-  }
 
   // 2.13 added this, not sure why the baseline version was compiling actually.
   /**
    * Completes a response of a List of Product (probably a case class), using an implicit marshaller, probably a json encoder.
    */
-  def completeResponse[A <: Product](statusCode: StatusCode, values: List[A], warnings: Seq[String])
-                                    (implicit mt: ToEntityMarshaller[List[A]]): Route = {
+  def completeResponse[A <: Product](statusCode: StatusCode, values: List[A], warnings: Seq[String])(implicit
+    mt: ToEntityMarshaller[List[A]]
+  ): Route =
     complete((statusCode, warningHeaders(warnings), values))
-  }
 
   /**
     * Completes a response of string with the supplied content type.
@@ -52,11 +59,11 @@ trait WebServiceUtils {
   def completeResponse(statusCode: StatusCode,
                        contentType: ContentType.NonBinary,
                        value: String,
-                       warnings: Seq[String]): Route = {
+                       warnings: Seq[String]
+  ): Route =
     complete((statusCode, warningHeaders(warnings), HttpEntity(contentType, value)))
-  }
 
-  def warningHeaders(warnings: Seq[String]): List[HttpHeader] = {
+  def warningHeaders(warnings: Seq[String]): List[HttpHeader] =
     warnings.toList map { warning =>
       /*
       Need a quoted string.
@@ -65,12 +72,11 @@ trait WebServiceUtils {
       Using a poor version of ~~#!
       https://github.com/akka/akka-http/blob/v10.0.9/akka-http-core/src/main/scala/akka/http/impl/util/Rendering.scala#L206
        */
-      val quotedString = "\"" + warning.replaceAll("\"","\\\\\"").replaceAll("[\\r\\n]+", " ").trim + "\""
+      val quotedString = "\"" + warning.replaceAll("\"", "\\\\\"").replaceAll("[\\r\\n]+", " ").trim + "\""
 
       // https://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html#sec14.46
       RawHeader("Warning", s"299 cromwell/$cromwellVersion $quotedString")
     }
-  }
 }
 
 object WebServiceUtils extends WebServiceUtils {
@@ -79,17 +85,14 @@ object WebServiceUtils extends WebServiceUtils {
   // A: There are customers who rely on the pretty printing to display the error directly in a terminal or GUI.
   // AEN 2018-12-05
   implicit class EnhancedThrowable(val e: Throwable) extends AnyVal {
-    def failRequest(statusCode: StatusCode, warnings: Seq[String] = Vector.empty): Route = {
+    def failRequest(statusCode: StatusCode, warnings: Seq[String] = Vector.empty): Route =
       completeResponse(statusCode, ContentTypes.`application/json`, prettyPrint(APIResponse.fail(e)), warnings)
-    }
-    def errorRequest(statusCode: StatusCode, warnings: Seq[String] = Vector.empty): Route = {
+    def errorRequest(statusCode: StatusCode, warnings: Seq[String] = Vector.empty): Route =
       completeResponse(statusCode, ContentTypes.`application/json`, prettyPrint(APIResponse.error(e)), warnings)
-    }
   }
 
-  private def prettyPrint(failureResponse: FailureResponse): String ={
+  private def prettyPrint(failureResponse: FailureResponse): String =
     // .asJson cannot live inside a value class like `EnhancedThrowable`, hence the object method
     failureResponse.asJson.printWith(Printer.spaces2.copy(dropNullValues = true, colonLeft = ""))
-  }
 
 }
diff --git a/engine/src/main/scala/cromwell/webservice/WorkflowJsonSupport.scala b/engine/src/main/scala/cromwell/webservice/WorkflowJsonSupport.scala
index 0bb398f67af..b504818c1a4 100644
--- a/engine/src/main/scala/cromwell/webservice/WorkflowJsonSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/WorkflowJsonSupport.scala
@@ -13,7 +13,7 @@ import cromwell.services.metadata.MetadataArchiveStatus
 import cromwell.services.metadata.MetadataService._
 import cromwell.util.JsonFormatting.WomValueJsonFormatter._
 import cromwell.webservice.routes.CromwellApiService.BackendResponse
-import spray.json.{DefaultJsonProtocol, JsString, JsValue, JsonFormat, RootJsonFormat}
+import spray.json.{DefaultJsonProtocol, JsonFormat, JsString, JsValue, RootJsonFormat}
 
 object WorkflowJsonSupport extends DefaultJsonProtocol {
   implicit val workflowStatusResponseProtocol = jsonFormat2(WorkflowStatusResponse)
@@ -25,18 +25,24 @@ object WorkflowJsonSupport extends DefaultJsonProtocol {
   implicit val BackendResponseFormat = jsonFormat2(BackendResponse)
   implicit val callAttempt = jsonFormat2(CallAttempt)
 
-  implicit val workflowOptionsFormatter: JsonFormat[WorkflowOptions] = new JsonFormat[WorkflowOptions]  {
+  implicit val workflowOptionsFormatter: JsonFormat[WorkflowOptions] = new JsonFormat[WorkflowOptions] {
     override def read(json: JsValue): WorkflowOptions = json match {
       case str: JsString => WorkflowOptions.fromJsonString(str.value).get
-      case other => throw new UnsupportedOperationException(s"Cannot use ${other.getClass.getSimpleName} value. Expected a workflow options String")
+      case other =>
+        throw new UnsupportedOperationException(
+          s"Cannot use ${other.getClass.getSimpleName} value. Expected a workflow options String"
+        )
     }
     override def write(obj: WorkflowOptions): JsValue = JsString(obj.asPrettyJson)
   }
 
-  implicit val workflowIdFormatter: JsonFormat[WorkflowId] = new JsonFormat[WorkflowId]  {
+  implicit val workflowIdFormatter: JsonFormat[WorkflowId] = new JsonFormat[WorkflowId] {
     override def read(json: JsValue): WorkflowId = json match {
       case str: JsString => WorkflowId.fromString(str.value)
-      case other => throw new UnsupportedOperationException(s"Cannot use ${other.getClass.getSimpleName} value. Expected a workflow ID String")
+      case other =>
+        throw new UnsupportedOperationException(
+          s"Cannot use ${other.getClass.getSimpleName} value. Expected a workflow ID String"
+        )
     }
     override def write(obj: WorkflowId): JsValue = JsString(obj.id.toString)
   }
@@ -58,7 +64,7 @@ object WorkflowJsonSupport extends DefaultJsonProtocol {
 
   // By default the formatter for JsValues prints them out ADT-style.
   // In the case of SuccessResponses, we just want raw JsValues to be included in our output verbatim.
-  private implicit val identityJsValueFormatter = new RootJsonFormat[JsValue] {
+  implicit private val identityJsValueFormatter = new RootJsonFormat[JsValue] {
     override def read(json: JsValue): JsValue = json
     override def write(obj: JsValue): JsValue = obj
   }
diff --git a/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala b/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
index a1c4f023135..d75eed4ccd8 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/CromwellApiService.scala
@@ -10,7 +10,7 @@ import akka.http.scaladsl.model._
 import akka.http.scaladsl.model.ContentTypes._
 import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server.{ExceptionHandler, Route}
-import akka.pattern.{AskTimeoutException, ask}
+import akka.pattern.{ask, AskTimeoutException}
 import akka.stream.ActorMaterializer
 import akka.util.Timeout
 import cats.data.NonEmptyList
@@ -23,7 +23,12 @@ import cromwell.core.{path => _, _}
 import cromwell.engine.backend.BackendConfiguration
 import cromwell.engine.instrumentation.HttpInstrumentation
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheDiffActor.{CachedCallNotFoundException, CallCacheDiffActorResponse, FailedCallCacheDiffResponse, SuccessfulCallCacheDiffResponse}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheDiffActor.{
+  CachedCallNotFoundException,
+  CallCacheDiffActorResponse,
+  FailedCallCacheDiffResponse,
+  SuccessfulCallCacheDiffResponse
+}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.{CallCacheDiffActor, CallCacheDiffQueryParameter}
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.NotInOnHoldStateException
 import cromwell.engine.workflow.workflowstore.{WorkflowStoreActor, WorkflowStoreEngineActor, WorkflowStoreSubmitActor}
@@ -42,7 +47,11 @@ import scala.concurrent.{ExecutionContext, Future, TimeoutException}
 import scala.io.Source
 import scala.util.{Failure, Success, Try}
 
-trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport with WomtoolRouteSupport with WebServiceUtils {
+trait CromwellApiService
+    extends HttpInstrumentation
+    with MetadataRouteSupport
+    with WomtoolRouteSupport
+    with WebServiceUtils {
   import CromwellApiService._
 
   implicit def actorRefFactory: ActorRefFactory
@@ -60,11 +69,14 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
   val engineRoutes = concat(
     path("engine" / Segment / "stats") { _ =>
       get {
-        completeResponse(StatusCodes.Forbidden, APIResponse.fail(new RuntimeException("The /stats endpoint is currently disabled.")), warnings = Seq.empty)
+        completeResponse(StatusCodes.Forbidden,
+                         APIResponse.fail(new RuntimeException("The /stats endpoint is currently disabled.")),
+                         warnings = Seq.empty
+        )
       }
     },
     path("engine" / Segment / "version") { _ =>
-      get { complete(versionResponse) }
+      get(complete(versionResponse))
     },
     path("engine" / Segment / "status") { _ =>
       onComplete(serviceRegistryActor.ask(GetCurrentStatus).mapTo[StatusCheckResponse]) {
@@ -72,14 +84,15 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
           val httpCode = if (status.ok) StatusCodes.OK else StatusCodes.InternalServerError
           complete(ToResponseMarshallable((httpCode, status.systems)))
         case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
-        case Failure(_) => new RuntimeException("Unable to gather engine status").failRequest(StatusCodes.InternalServerError)
+        case Failure(_) =>
+          new RuntimeException("Unable to gather engine status").failRequest(StatusCodes.InternalServerError)
       }
     }
   )
 
   val workflowRoutes =
     path("workflows" / Segment / "backends") { _ =>
-      get { instrumentRequest { complete(ToResponseMarshallable(backendResponse)) } }
+      get(instrumentRequest(complete(ToResponseMarshallable(backendResponse))))
     } ~
       path("workflows" / Segment / "callcaching" / "diff") { _ =>
         parameterSeq { parameters =>
@@ -87,11 +100,15 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
             instrumentRequest {
               CallCacheDiffQueryParameter.fromParameters(parameters) match {
                 case Valid(queryParameter) =>
-                  val diffActor = actorRefFactory.actorOf(CallCacheDiffActor.props(serviceRegistryActor), "CallCacheDiffActor-" + UUID.randomUUID())
+                  val diffActor = actorRefFactory.actorOf(CallCacheDiffActor.props(serviceRegistryActor),
+                                                          "CallCacheDiffActor-" + UUID.randomUUID()
+                  )
                   onComplete(diffActor.ask(queryParameter).mapTo[CallCacheDiffActorResponse]) {
                     case Success(r: SuccessfulCallCacheDiffResponse) => complete(r)
-                    case Success(r: FailedCallCacheDiffResponse) => r.reason.errorRequest(StatusCodes.InternalServerError)
-                    case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
+                    case Success(r: FailedCallCacheDiffResponse) =>
+                      r.reason.errorRequest(StatusCodes.InternalServerError)
+                    case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() =>
+                      serviceShuttingDownResponse
                     case Failure(e: CachedCallNotFoundException) => e.errorRequest(StatusCodes.NotFound)
                     case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
                     case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
@@ -142,13 +159,21 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
       path("workflows" / Segment / Segment / "releaseHold") { (_, possibleWorkflowId) =>
         post {
           instrumentRequest {
-            val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor) flatMap { workflowId =>
-              workflowStoreActor.ask(WorkflowStoreActor.WorkflowOnHoldToSubmittedCommand(workflowId)).mapTo[WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedResponse]
+            val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor) flatMap {
+              workflowId =>
+                workflowStoreActor
+                  .ask(WorkflowStoreActor.WorkflowOnHoldToSubmittedCommand(workflowId))
+                  .mapTo[WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedResponse]
             }
-            onComplete(response){
-              case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e: NotInOnHoldStateException)) => e.errorRequest(StatusCodes.Forbidden)
-              case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e)) => e.errorRequest(StatusCodes.InternalServerError)
-              case Success(r: WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedSuccess) => completeResponse(StatusCodes.OK, toResponse(r.workflowId, WorkflowSubmitted), Seq.empty)
+            onComplete(response) {
+              case Success(
+                    WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e: NotInOnHoldStateException)
+                  ) =>
+                e.errorRequest(StatusCodes.Forbidden)
+              case Success(WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedFailure(_, e)) =>
+                e.errorRequest(StatusCodes.InternalServerError)
+              case Success(r: WorkflowStoreEngineActor.WorkflowOnHoldToSubmittedSuccess) =>
+                completeResponse(StatusCodes.OK, toResponse(r.workflowId, WorkflowSubmitted), Seq.empty)
               case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
               case Failure(e: InvalidWorkflowException) => e.failRequest(StatusCodes.BadRequest)
               case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
@@ -157,44 +182,49 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
         }
       } ~ metadataRoutes
 
-
   private def metadataLookupForTimingRoute(workflowId: WorkflowId): Future[MetadataJsonResponse] = {
     val includeKeys = NonEmptyList.of("start", "end", "executionStatus", "executionEvents", "subWorkflowMetadata")
-    val readMetadataRequest = (w: WorkflowId) => GetSingleWorkflowMetadataAction(w, Option(includeKeys), None, expandSubWorkflows = true)
+    val readMetadataRequest = (w: WorkflowId) =>
+      GetSingleWorkflowMetadataAction(w, Option(includeKeys), None, expandSubWorkflows = true)
 
     serviceRegistryActor.ask(readMetadataRequest(workflowId)).mapTo[MetadataJsonResponse]
   }
 
-  private def completeTimingRouteResponse(metadataResponse: Future[MetadataJsonResponse]) = {
+  private def completeTimingRouteResponse(metadataResponse: Future[MetadataJsonResponse]) =
     onComplete(metadataResponse) {
       case Success(r: SuccessfulMetadataJsonResponse) =>
-
         Try(Source.fromResource("workflowTimings/workflowTimings.html").mkString) match {
           case Success(wfTimingsContent) =>
-            val response = HttpResponse(entity = wfTimingsContent.replace("\"{{REPLACE_THIS_WITH_METADATA}}\"", r.responseJson.toString))
+            val response = HttpResponse(entity =
+              wfTimingsContent.replace("\"{{REPLACE_THIS_WITH_METADATA}}\"", r.responseJson.toString)
+            )
             complete(response.withEntity(response.entity.withContentType(`text/html(UTF-8)`)))
-          case Failure(e) => completeResponse(StatusCodes.InternalServerError, APIResponse.fail(new RuntimeException("Error while loading workflowTimings.html", e)), Seq.empty)
+          case Failure(e) =>
+            completeResponse(StatusCodes.InternalServerError,
+                             APIResponse.fail(new RuntimeException("Error while loading workflowTimings.html", e)),
+                             Seq.empty
+            )
         }
       case Success(r: FailedMetadataJsonResponse) => r.reason.errorRequest(StatusCodes.InternalServerError)
       case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
       case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
       case Failure(e) => e.failRequest(StatusCodes.InternalServerError)
     }
-  }
 
-  private def toResponse(workflowId: WorkflowId, workflowState: WorkflowState): WorkflowSubmitResponse = {
+  private def toResponse(workflowId: WorkflowId, workflowState: WorkflowState): WorkflowSubmitResponse =
     WorkflowSubmitResponse(workflowId.toString, workflowState.toString)
-  }
 
   private def submitRequest(formData: Multipart.FormData, isSingleSubmission: Boolean): Route = {
 
-    def getWorkflowState(workflowOnHold: Boolean): WorkflowState = {
+    def getWorkflowState(workflowOnHold: Boolean): WorkflowState =
       if (workflowOnHold)
         WorkflowOnHold
       else WorkflowSubmitted
-    }
 
-    def askSubmit(command: WorkflowStoreActor.WorkflowStoreActorSubmitCommand, warnings: Seq[String], workflowState: WorkflowState): Route = {
+    def askSubmit(command: WorkflowStoreActor.WorkflowStoreActorSubmitCommand,
+                  warnings: Seq[String],
+                  workflowState: WorkflowState
+    ): Route =
       // NOTE: Do not blindly copy the akka-http -to- ask-actor pattern below without knowing the pros and cons.
       onComplete(workflowStoreActor.ask(command).mapTo[WorkflowStoreSubmitActor.WorkflowStoreSubmitActorResponse]) {
         case Success(w) =>
@@ -210,14 +240,16 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
         case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
         case Failure(e) => e.failRequest(StatusCodes.InternalServerError, warnings)
       }
-    }
 
     onComplete(materializeFormData(formData)) {
       case Success(data) =>
         PartialWorkflowSources.fromSubmitRoute(data, allowNoInputs = isSingleSubmission) match {
           case Success(workflowSourceFiles) if isSingleSubmission && workflowSourceFiles.size == 1 =>
             val warnings = workflowSourceFiles.flatMap(_.warnings)
-            askSubmit(WorkflowStoreActor.SubmitWorkflow(workflowSourceFiles.head), warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+            askSubmit(WorkflowStoreActor.SubmitWorkflow(workflowSourceFiles.head),
+                      warnings,
+                      getWorkflowState(workflowSourceFiles.head.workflowOnHold)
+            )
           // Catches the case where someone has gone through the single submission endpoint w/ more than one workflow
           case Success(workflowSourceFiles) if isSingleSubmission =>
             val warnings = workflowSourceFiles.flatMap(_.warnings)
@@ -227,7 +259,9 @@ trait CromwellApiService extends HttpInstrumentation with MetadataRouteSupport w
             val warnings = workflowSourceFiles.flatMap(_.warnings)
             askSubmit(
               WorkflowStoreActor.BatchSubmitWorkflows(NonEmptyList.fromListUnsafe(workflowSourceFiles.toList)),
-              warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+              warnings,
+              getWorkflowState(workflowSourceFiles.head.workflowOnHold)
+            )
           case Failure(t) => t.failRequest(StatusCodes.BadRequest)
         }
       case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
@@ -248,12 +282,13 @@ object CromwellApiService {
                     workflowStoreActor: ActorRef,
                     workflowManagerActor: ActorRef,
                     successHandler: PartialFunction[SuccessfulAbortResponse, Route] = standardAbortSuccessHandler,
-                    errorHandler: PartialFunction[Throwable, Route] = standardAbortErrorHandler)
-                   (implicit timeout: Timeout): Route = {
+                    errorHandler: PartialFunction[Throwable, Route] = standardAbortErrorHandler
+  )(implicit timeout: Timeout): Route =
     handleExceptions(ExceptionHandler(errorHandler)) {
       Try(WorkflowId.fromString(possibleWorkflowId)) match {
         case Success(workflowId) =>
-          val response = workflowStoreActor.ask(WorkflowStoreActor.AbortWorkflowCommand(workflowId)).mapTo[AbortResponse]
+          val response =
+            workflowStoreActor.ask(WorkflowStoreActor.AbortWorkflowCommand(workflowId)).mapTo[AbortResponse]
           onComplete(response) {
             case Success(x: SuccessfulAbortResponse) => successHandler(x)
             case Success(x: WorkflowAbortFailureResponse) => throw x.failure
@@ -262,14 +297,15 @@ object CromwellApiService {
         case Failure(_) => throw InvalidWorkflowException(possibleWorkflowId)
       }
     }
-  }
 
   /**
     * The abort success handler for typical cases, i.e. cromwell's API.
     */
   private def standardAbortSuccessHandler: PartialFunction[SuccessfulAbortResponse, Route] = {
-    case WorkflowAbortedResponse(id) => complete(ToResponseMarshallable(WorkflowAbortResponse(id.toString, WorkflowAborted.toString)))
-    case WorkflowAbortRequestedResponse(id) => complete(ToResponseMarshallable(WorkflowAbortResponse(id.toString, WorkflowAborting.toString)))
+    case WorkflowAbortedResponse(id) =>
+      complete(ToResponseMarshallable(WorkflowAbortResponse(id.toString, WorkflowAborted.toString)))
+    case WorkflowAbortRequestedResponse(id) =>
+      complete(ToResponseMarshallable(WorkflowAbortResponse(id.toString, WorkflowAborting.toString)))
   }
 
   /**
@@ -283,9 +319,10 @@ object CromwellApiService {
     case e: Exception => e.errorRequest(StatusCodes.InternalServerError)
   }
 
-  def validateWorkflowIdInMetadata(possibleWorkflowId: String,
-                                   serviceRegistryActor: ActorRef)
-                                  (implicit timeout: Timeout, executor: ExecutionContext): Future[WorkflowId] = {
+  def validateWorkflowIdInMetadata(possibleWorkflowId: String, serviceRegistryActor: ActorRef)(implicit
+    timeout: Timeout,
+    executor: ExecutionContext
+  ): Future[WorkflowId] =
     Try(WorkflowId.fromString(possibleWorkflowId)) match {
       case Success(w) =>
         serviceRegistryActor.ask(ValidateWorkflowIdInMetadata(w)).mapTo[WorkflowValidationResponse] flatMap {
@@ -295,11 +332,11 @@ object CromwellApiService {
         }
       case Failure(_) => Future.failed(InvalidWorkflowException(possibleWorkflowId))
     }
-  }
 
-  def validateWorkflowIdInMetadataSummaries(possibleWorkflowId: String,
-                                            serviceRegistryActor: ActorRef)
-                                           (implicit timeout: Timeout, executor: ExecutionContext): Future[WorkflowId] = {
+  def validateWorkflowIdInMetadataSummaries(possibleWorkflowId: String, serviceRegistryActor: ActorRef)(implicit
+    timeout: Timeout,
+    executor: ExecutionContext
+  ): Future[WorkflowId] =
     Try(WorkflowId.fromString(possibleWorkflowId)) match {
       case Success(w) =>
         serviceRegistryActor.ask(ValidateWorkflowIdInMetadataSummaries(w)).mapTo[WorkflowValidationResponse] map {
@@ -309,17 +346,20 @@ object CromwellApiService {
         }
       case Failure(_) => Future.failed(InvalidWorkflowException(possibleWorkflowId))
     }
-  }
 
   final case class BackendResponse(supportedBackends: List[String], defaultBackend: String)
 
   final case class UnrecognizedWorkflowException(id: WorkflowId) extends Exception(s"Unrecognized workflow ID: $id")
 
-  final case class InvalidWorkflowException(possibleWorkflowId: String) extends Exception(s"Invalid workflow ID: '$possibleWorkflowId'.")
+  final case class InvalidWorkflowException(possibleWorkflowId: String)
+      extends Exception(s"Invalid workflow ID: '$possibleWorkflowId'.")
 
   val cromwellVersion = VersionUtil.getVersion("cromwell-engine")
   val swaggerUiVersion = VersionUtil.getVersion("swagger-ui", VersionUtil.sbtDependencyVersion("swaggerUi"))
-  val backendResponse = BackendResponse(BackendConfiguration.AllBackendEntries.map(_.name).sorted, BackendConfiguration.DefaultBackendEntry.name)
+  val backendResponse = BackendResponse(BackendConfiguration.AllBackendEntries.map(_.name).sorted,
+                                        BackendConfiguration.DefaultBackendEntry.name
+  )
   val versionResponse = JsObject(Map("cromwell" -> cromwellVersion.toJson))
-  val serviceShuttingDownResponse = new Exception("Cromwell service is shutting down.").failRequest(StatusCodes.ServiceUnavailable)
+  val serviceShuttingDownResponse =
+    new Exception("Cromwell service is shutting down.").failRequest(StatusCodes.ServiceUnavailable)
 }
diff --git a/engine/src/main/scala/cromwell/webservice/routes/MetadataRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/MetadataRouteSupport.scala
index b84ff59d5a3..4ec1d0babc7 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/MetadataRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/MetadataRouteSupport.scala
@@ -1,6 +1,6 @@
 package cromwell.webservice.routes
 
-import java.time.{OffsetDateTime, Duration => JDuration}
+import java.time.{Duration => JDuration, OffsetDateTime}
 import java.util.concurrent.TimeUnit
 
 import akka.actor.{ActorRef, ActorRefFactory}
@@ -9,14 +9,14 @@ import akka.http.scaladsl.marshalling.ToResponseMarshallable
 import akka.http.scaladsl.model.StatusCodes
 import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server.Route
-import akka.pattern.{AskTimeoutException, ask}
+import akka.pattern.{ask, AskTimeoutException}
 import akka.util.Timeout
 import cats.data.NonEmptyList
 import cats.data.Validated.{Invalid, Valid}
 import cromwell.core.Dispatcher.ApiDispatcher
 import cromwell.core.instrumentation.InstrumentationPrefixes.ServicesPrefix
 import cromwell.core.labels.Labels
-import cromwell.core.{WorkflowId, WorkflowMetadataKeys, path => _}
+import cromwell.core.{path => _, WorkflowId, WorkflowMetadataKeys}
 import cromwell.engine.instrumentation.HttpInstrumentation
 import cromwell.server.CromwellShutdown
 import cromwell.services._
@@ -38,7 +38,6 @@ import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future, TimeoutException}
 import scala.util.{Failure, Success}
 
-
 trait MetadataRouteSupport extends HttpInstrumentation {
   implicit def actorRefFactory: ActorRefFactory
   implicit val ec: ExecutionContext
@@ -83,15 +82,21 @@ trait MetadataRouteSupport extends HttpInstrumentation {
     encodeResponse {
       path("workflows" / Segment / Segment / "metadata") { (_, possibleWorkflowId) =>
         instrumentRequest {
-          parameters((Symbol("includeKey").*, Symbol("excludeKey").*, Symbol("expandSubWorkflows").as[Boolean].?)) { (includeKeys, excludeKeys, expandSubWorkflowsOption) =>
-            val includeKeysOption = NonEmptyList.fromList(includeKeys.toList)
-            val excludeKeysOption = NonEmptyList.fromList(excludeKeys.toList)
-            val expandSubWorkflows = expandSubWorkflowsOption.getOrElse(false)
+          parameters((Symbol("includeKey").*, Symbol("excludeKey").*, Symbol("expandSubWorkflows").as[Boolean].?)) {
+            (includeKeys, excludeKeys, expandSubWorkflowsOption) =>
+              val includeKeysOption = NonEmptyList.fromList(includeKeys.toList)
+              val excludeKeysOption = NonEmptyList.fromList(excludeKeys.toList)
+              val expandSubWorkflows = expandSubWorkflowsOption.getOrElse(false)
 
-            metadataLookup(
-              possibleWorkflowId,
-              (w: WorkflowId) => GetSingleWorkflowMetadataAction(w, includeKeysOption, excludeKeysOption, expandSubWorkflows),
-              serviceRegistryActor)
+              metadataLookup(possibleWorkflowId,
+                             (w: WorkflowId) =>
+                               GetSingleWorkflowMetadataAction(w,
+                                                               includeKeysOption,
+                                                               excludeKeysOption,
+                                                               expandSubWorkflows
+                               ),
+                             serviceRegistryActor
+              )
           }
         }
       }
@@ -107,7 +112,8 @@ trait MetadataRouteSupport extends HttpInstrumentation {
           entity(as[Map[String, String]]) { parameterMap =>
             instrumentRequest {
               Labels.validateMapOfLabels(parameterMap) match {
-                case Valid(labels) => patchLabelsRequest(possibleWorkflowId, labels, serviceRegistryActor, actorRefFactory)
+                case Valid(labels) =>
+                  patchLabelsRequest(possibleWorkflowId, labels, serviceRegistryActor, actorRefFactory)
                 case Invalid(e) =>
                   val iae = new IllegalArgumentException(e.toList.mkString(","))
                   iae.failRequest(StatusCodes.BadRequest)
@@ -141,41 +147,42 @@ object MetadataRouteSupport {
   private def processMetadataArchivedResponse(workflowId: WorkflowId,
                                               archiveStatus: MetadataArchiveStatus,
                                               endTime: Option[OffsetDateTime],
-                                              additionalMsg: String = ""): JsObject = {
+                                              additionalMsg: String = ""
+  ): JsObject = {
     val baseMessage = "Cromwell has archived this workflow's metadata according to the lifecycle policy."
     val timeSinceMessage = endTime map { timestamp =>
       val duration = FiniteDuration(JDuration.between(timestamp, OffsetDateTime.now()).toMillis, TimeUnit.MILLISECONDS)
       s" The workflow completed at $timestamp, which was ${duration} ago."
-    } getOrElse("")
-    val additionalDetails = if (archiveStatus == MetadataArchiveStatus.ArchivedAndDeleted)
-      " It is available in the archive bucket, or via a support request in the case of a managed instance."
-    else ""
+    } getOrElse ""
+    val additionalDetails =
+      if (archiveStatus == MetadataArchiveStatus.ArchivedAndDeleted)
+        " It is available in the archive bucket, or via a support request in the case of a managed instance."
+      else ""
 
-    JsObject(Map(
-      WorkflowMetadataKeys.Id -> JsString(workflowId.toString),
-      WorkflowMetadataKeys.MetadataArchiveStatus -> JsString(archiveStatus.toString),
-      WorkflowMetadataKeys.Message -> JsString(baseMessage + timeSinceMessage + additionalDetails + additionalMsg)
-    ))
+    JsObject(
+      Map(
+        WorkflowMetadataKeys.Id -> JsString(workflowId.toString),
+        WorkflowMetadataKeys.MetadataArchiveStatus -> JsString(archiveStatus.toString),
+        WorkflowMetadataKeys.Message -> JsString(baseMessage + timeSinceMessage + additionalDetails + additionalMsg)
+      )
+    )
   }
 
   def metadataLookup(possibleWorkflowId: String,
                      request: WorkflowId => BuildMetadataJsonAction,
-                     serviceRegistryActor: ActorRef)
-                    (implicit timeout: Timeout,
-                     ec: ExecutionContext): Route = {
+                     serviceRegistryActor: ActorRef
+  )(implicit timeout: Timeout, ec: ExecutionContext): Route =
     completeMetadataBuilderResponse(metadataBuilderActorRequest(possibleWorkflowId, request, serviceRegistryActor))
-  }
 
-  def queryMetadata(parameters: Seq[(String, String)],
-                    serviceRegistryActor: ActorRef)(implicit timeout: Timeout): Route = {
+  def queryMetadata(parameters: Seq[(String, String)], serviceRegistryActor: ActorRef)(implicit
+    timeout: Timeout
+  ): Route =
     completeMetadataQueryResponse(metadataQueryRequest(parameters, serviceRegistryActor))
-  }
 
   def metadataBuilderActorRequest(possibleWorkflowId: String,
                                   request: WorkflowId => BuildMetadataJsonAction,
-                                  serviceRegistryActor: ActorRef)
-                                 (implicit timeout: Timeout,
-                                  ec: ExecutionContext): Future[MetadataJsonResponse] = {
+                                  serviceRegistryActor: ActorRef
+  )(implicit timeout: Timeout, ec: ExecutionContext): Future[MetadataJsonResponse] = {
 
     def recordHistoricalMetadataLookupMetrics(endTime: Option[OffsetDateTime]): Unit = {
       val timeSinceEndTime = endTime match {
@@ -183,8 +190,11 @@ object MetadataRouteSupport {
         case None => 0.seconds
       }
 
-      val lagInstrumentationPath = MetadataServiceActor.MetadataInstrumentationPrefix :+ "archiver" :+ "historical_metadata_lookup" :+ "lag"
-      val lagMessage = InstrumentationServiceMessage(CromwellTiming(CromwellBucket(ServicesPrefix.toList, lagInstrumentationPath), timeSinceEndTime))
+      val lagInstrumentationPath =
+        MetadataServiceActor.MetadataInstrumentationPrefix :+ "archiver" :+ "historical_metadata_lookup" :+ "lag"
+      val lagMessage = InstrumentationServiceMessage(
+        CromwellTiming(CromwellBucket(ServicesPrefix.toList, lagInstrumentationPath), timeSinceEndTime)
+      )
       serviceRegistryActor ! lagMessage
 
       val interestingDayMarks = (5.to(55, step = 5) ++ 0.to(4)).map(d => (d.days, s"${d}_day_old"))
@@ -192,29 +202,39 @@ object MetadataRouteSupport {
 
       (interestingDayMarks ++ interestingMonthMarks) foreach {
         case (timeSpan, metricName) if timeSinceEndTime >= timeSpan =>
-          val oldMetadataCounterPath = MetadataServiceActor.MetadataInstrumentationPrefix :+ "archiver" :+ "historical_metadata_lookup" :+ "lookup_age_counts" :+ metricName
-          val oldMetadataCounterMessage = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(ServicesPrefix.toList, oldMetadataCounterPath)))
+          val oldMetadataCounterPath =
+            MetadataServiceActor.MetadataInstrumentationPrefix :+ "archiver" :+ "historical_metadata_lookup" :+ "lookup_age_counts" :+ metricName
+          val oldMetadataCounterMessage = InstrumentationServiceMessage(
+            CromwellIncrement(CromwellBucket(ServicesPrefix.toList, oldMetadataCounterPath))
+          )
           serviceRegistryActor ! oldMetadataCounterMessage
         case _ => // Do nothing
       }
     }
 
     def checkIfMetadataDeletedAndRespond(id: WorkflowId,
-                                         metadataRequest: BuildWorkflowMetadataJsonWithOverridableSourceAction): Future[MetadataJsonResponse] = {
-      serviceRegistryActor.ask(FetchWorkflowMetadataArchiveStatusAndEndTime(id)).mapTo[FetchWorkflowArchiveStatusAndEndTimeResponse] flatMap {
+                                         metadataRequest: BuildWorkflowMetadataJsonWithOverridableSourceAction
+    ): Future[MetadataJsonResponse] =
+      serviceRegistryActor
+        .ask(FetchWorkflowMetadataArchiveStatusAndEndTime(id))
+        .mapTo[FetchWorkflowArchiveStatusAndEndTimeResponse] flatMap {
         case WorkflowMetadataArchivedStatusAndEndTime(archiveStatus, endTime) =>
           recordHistoricalMetadataLookupMetrics(endTime)
-          if (archiveStatus.isDeleted) Future.successful(SuccessfulMetadataJsonResponse(metadataRequest, processMetadataArchivedResponse(id, archiveStatus, endTime)))
+          if (archiveStatus.isDeleted)
+            Future.successful(
+              SuccessfulMetadataJsonResponse(metadataRequest,
+                                             processMetadataArchivedResponse(id, archiveStatus, endTime)
+              )
+            )
           else serviceRegistryActor.ask(request(id)).mapTo[MetadataJsonResponse]
         case FailedToGetArchiveStatusAndEndTime(e) => Future.failed(e)
       }
-    }
 
     validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor) flatMap { id =>
       /*
         for requests made to one of /metadata, /logs or /outputs endpoints, perform an additional check to see
         if metadata for the workflow has been archived and deleted or not (as they interact with metadata table)
-      */
+       */
       request(id) match {
         case m: BuildWorkflowMetadataJsonWithOverridableSourceAction => checkIfMetadataDeletedAndRespond(id, m)
         case _ => serviceRegistryActor.ask(request(id)).mapTo[MetadataJsonResponse]
@@ -222,8 +242,9 @@ object MetadataRouteSupport {
     }
   }
 
-  def completeMetadataBuilderResponse(response: Future[MetadataJsonResponse]): Route = {
-    onComplete(response) { case Success(r: SuccessfulMetadataJsonResponse) => complete(r.responseJson)
+  def completeMetadataBuilderResponse(response: Future[MetadataJsonResponse]): Route =
+    onComplete(response) {
+      case Success(r: SuccessfulMetadataJsonResponse) => complete(r.responseJson)
       case Success(r: FailedMetadataJsonResponse) => r.reason.errorRequest(StatusCodes.InternalServerError)
       case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => serviceShuttingDownResponse
       case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
@@ -231,12 +252,11 @@ object MetadataRouteSupport {
       case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
       case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
     }
-  }
 
-  def metadataQueryRequest(parameters: Seq[(String, String)],
-                           serviceRegistryActor: ActorRef)(implicit timeout: Timeout): Future[MetadataQueryResponse] = {
+  def metadataQueryRequest(parameters: Seq[(String, String)], serviceRegistryActor: ActorRef)(implicit
+    timeout: Timeout
+  ): Future[MetadataQueryResponse] =
     serviceRegistryActor.ask(QueryForWorkflowsMatchingParameters(parameters)).mapTo[MetadataQueryResponse]
-  }
 
   def completeMetadataQueryResponse(response: Future[MetadataQueryResponse]): Route = {
     import cromwell.webservice.WorkflowJsonSupport.workflowQueryResponse
@@ -250,41 +270,49 @@ object MetadataRouteSupport {
     }
   }
 
-  def completePatchLabelsResponse(response: Future[LabelsManagerActorResponse]): Route = {
+  def completePatchLabelsResponse(response: Future[LabelsManagerActorResponse]): Route =
     onComplete(response) {
       case Success(r: BuiltLabelsManagerResponse) => complete(r.response)
-      case Success(r: WorkflowArchivedLabelsManagerResponse) => completeResponse(StatusCodes.BadRequest, r.response, Seq.empty)
+      case Success(r: WorkflowArchivedLabelsManagerResponse) =>
+        completeResponse(StatusCodes.BadRequest, r.response, Seq.empty)
       case Success(e: FailedLabelsManagerResponse) => e.reason.failRequest(StatusCodes.InternalServerError)
       case Failure(e: UnrecognizedWorkflowException) => e.failRequest(StatusCodes.NotFound)
       case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
       case Failure(e) => e.errorRequest(StatusCodes.InternalServerError)
     }
-  }
 
   def patchLabelsRequest(possibleWorkflowId: String,
                          labels: Labels,
                          serviceRegistryActor: ActorRef,
-                         actorRefFactory: ActorRefFactory)
-                        (implicit timeout: Timeout, ec: ExecutionContext): Route = {
+                         actorRefFactory: ActorRefFactory
+  )(implicit timeout: Timeout, ec: ExecutionContext): Route = {
 
-    def checkIfMetadataArchivedAndRespond(id: WorkflowId, archiveStatusResponse: FetchWorkflowArchiveStatusAndEndTimeResponse): Future[LabelsManagerActorResponse] = {
+    def checkIfMetadataArchivedAndRespond(id: WorkflowId,
+                                          archiveStatusResponse: FetchWorkflowArchiveStatusAndEndTimeResponse
+    ): Future[LabelsManagerActorResponse] =
       archiveStatusResponse match {
         case WorkflowMetadataArchivedStatusAndEndTime(archiveStatus, endTime) =>
           if (archiveStatus.isArchived) {
-            val message = " As a result, new labels can't be added or existing labels can't be updated for this workflow."
-            Future.successful(WorkflowArchivedLabelsManagerResponse(processMetadataArchivedResponse(id, archiveStatus, endTime, message)))
-          }
-          else {
-            val lma = actorRefFactory.actorOf(LabelsManagerActor.props(serviceRegistryActor).withDispatcher(ApiDispatcher))
+            val message =
+              " As a result, new labels can't be added or existing labels can't be updated for this workflow."
+            Future.successful(
+              WorkflowArchivedLabelsManagerResponse(
+                processMetadataArchivedResponse(id, archiveStatus, endTime, message)
+              )
+            )
+          } else {
+            val lma =
+              actorRefFactory.actorOf(LabelsManagerActor.props(serviceRegistryActor).withDispatcher(ApiDispatcher))
             lma.ask(LabelsAddition(LabelsData(id, labels))).mapTo[LabelsManagerActorResponse]
           }
         case FailedToGetArchiveStatusAndEndTime(e) => Future.failed(e)
       }
-    }
 
     val response = for {
       id <- validateWorkflowIdInMetadataSummaries(possibleWorkflowId, serviceRegistryActor)
-      archiveStatusResponse <- serviceRegistryActor.ask(FetchWorkflowMetadataArchiveStatusAndEndTime(id)).mapTo[FetchWorkflowArchiveStatusAndEndTimeResponse]
+      archiveStatusResponse <- serviceRegistryActor
+        .ask(FetchWorkflowMetadataArchiveStatusAndEndTime(id))
+        .mapTo[FetchWorkflowArchiveStatusAndEndTimeResponse]
       response <- checkIfMetadataArchivedAndRespond(id, archiveStatusResponse)
     } yield response
 
diff --git a/engine/src/main/scala/cromwell/webservice/routes/WomtoolRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/WomtoolRouteSupport.scala
index 0690c11dcb5..dec26a63dbf 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/WomtoolRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/WomtoolRouteSupport.scala
@@ -8,7 +8,12 @@ import akka.pattern.ask
 import akka.stream.ActorMaterializer
 import akka.util.Timeout
 import cromwell.core.{WorkflowOptions, WorkflowSourceFilesCollection}
-import cromwell.services.womtool.WomtoolServiceMessages.{DescribeFailure, DescribeRequest, DescribeResult, DescribeSuccess}
+import cromwell.services.womtool.WomtoolServiceMessages.{
+  DescribeFailure,
+  DescribeRequest,
+  DescribeResult,
+  DescribeSuccess
+}
 import cromwell.webservice.WebServiceUtils
 import cromwell.webservice.WebServiceUtils.EnhancedThrowable
 
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/CromwellMetadata.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/CromwellMetadata.scala
index d8c38de8dc9..0ff96489169 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/CromwellMetadata.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/CromwellMetadata.scala
@@ -8,7 +8,7 @@ final case class CromwellSubmittedFiles(workflow: Option[String],
                                         options: Option[String],
                                         inputs: Option[String],
                                         labels: Option[String]
-                                       )
+)
 
 final case class CromwellCallsMetadata(shardIndex: Option[Int],
                                        commandLine: Option[String],
@@ -17,7 +17,7 @@ final case class CromwellCallsMetadata(shardIndex: Option[Int],
                                        end: Option[String],
                                        stdout: Option[String],
                                        stderr: Option[String]
-                                      )
+)
 
 final case class CromwellMetadata(workflowName: Option[String],
                                   id: String,
@@ -27,7 +27,7 @@ final case class CromwellMetadata(workflowName: Option[String],
                                   submittedFiles: CromwellSubmittedFiles,
                                   outputs: Option[JsObject],
                                   calls: Option[Map[String, Seq[CromwellCallsMetadata]]]
-                                 ) {
+) {
   import CromwellMetadata._
 
   def wesRunLog: WesRunLog = {
@@ -35,7 +35,8 @@ final case class CromwellMetadata(workflowName: Option[String],
     val workflowTags = submittedFiles.labels.map(JsonParser(_).asJsObject)
     val workflowEngineParams = submittedFiles.options.map(JsonParser(_).asJsObject)
 
-    val workflowRequest = WesRunRequest(workflow_params = workflowParams,
+    val workflowRequest = WesRunRequest(
+      workflow_params = workflowParams,
       workflow_type = submittedFiles.workflowType.getOrElse("None supplied"),
       workflow_type_version = submittedFiles.workflowTypeVersion.getOrElse("None supplied"),
       tags = workflowTags,
@@ -44,12 +45,12 @@ final case class CromwellMetadata(workflowName: Option[String],
     )
 
     val workflowLogData = WesLog(name = workflowName,
-      cmd = None,
-      start_time = start,
-      end_time = end,
-      stdout = None,
-      stderr = None,
-      exit_code = None
+                                 cmd = None,
+                                 start_time = start,
+                                 end_time = end,
+                                 stdout = None,
+                                 stderr = None,
+                                 exit_code = None
     )
 
     val taskLogs = for {
@@ -74,7 +75,9 @@ object CromwellMetadata {
   import spray.json.DefaultJsonProtocol._
 
   implicit val cromwellCallsMetadataFormat: JsonFormat[CromwellCallsMetadata] = jsonFormat7(CromwellCallsMetadata.apply)
-  implicit val cromwellSubmittedFilesFormat: JsonFormat[CromwellSubmittedFiles] = jsonFormat6(CromwellSubmittedFiles.apply)
+  implicit val cromwellSubmittedFilesFormat: JsonFormat[CromwellSubmittedFiles] = jsonFormat6(
+    CromwellSubmittedFiles.apply
+  )
   implicit val cromwellMetadataFormat: JsonFormat[CromwellMetadata] = jsonFormat8(CromwellMetadata.apply)
 
   def fromJson(json: String): CromwellMetadata = {
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/RunListResponse.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/RunListResponse.scala
index b9bea188061..11ca85082ac 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/RunListResponse.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/RunListResponse.scala
@@ -8,13 +8,11 @@ import cromwell.webservice.routes.wes.WesState.fromStatusString
 case class RunListResponse(runs: List[WesRunStatus], next_page_token: String)
 
 object RunListResponse {
-  def fromMetadataQueryResponse(response: MetadataService.MetadataQueryResponse): WesResponse = {
-
-      response match {
+  def fromMetadataQueryResponse(response: MetadataService.MetadataQueryResponse): WesResponse =
+    response match {
       case w: WorkflowQuerySuccess =>
         val runs = w.response.results.toList.map(x => WesRunStatus(x.id, fromStatusString(x.status)))
         WesResponseRunList(runs)
       case f: WorkflowQueryFailure => WesErrorResponse(f.reason.getMessage, StatusCodes.BadRequest.intValue)
     }
-  }
 }
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/ServiceInfo.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/ServiceInfo.scala
index 02710a5c7e1..c6a3a8401cd 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/ServiceInfo.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/ServiceInfo.scala
@@ -49,9 +49,12 @@ object ServiceInfo {
   /**
     * Generate any runtime level information and create a response to the client
     */
-  def toWesResponse(workflowStoreActor: ActorRef)(implicit ec: ExecutionContext, timeout: Timeout): Future[WesStatusInfoResponse] = {
+  def toWesResponse(
+    workflowStoreActor: ActorRef
+  )(implicit ec: ExecutionContext, timeout: Timeout): Future[WesStatusInfoResponse] =
     workflowStats(workflowStoreActor).map(stats =>
-      WesStatusInfoResponse(WorkflowTypeVersion,
+      WesStatusInfoResponse(
+        WorkflowTypeVersion,
         SupportedWesVersions,
         SupportedFilesystemProtocols,
         WorkflowEngineVerisons,
@@ -59,18 +62,20 @@ object ServiceInfo {
         stats,
         AuthInstructionsUrl.toString,
         ContactInfoUrl.toString,
-        Tags)
+        Tags
+      )
     )
-  }
 
   /**
     * Retrieve a map from state to count for all represented non-terminal workflow states
     */
-  private def workflowStats(workflowStoreActor: ActorRef)(implicit ec: ExecutionContext, timeout: Timeout): Future[Map[WesState, Int]] = {
-    workflowStoreActor.ask(GetWorkflowStoreStats)
+  private def workflowStats(
+    workflowStoreActor: ActorRef
+  )(implicit ec: ExecutionContext, timeout: Timeout): Future[Map[WesState, Int]] =
+    workflowStoreActor
+      .ask(GetWorkflowStoreStats)
       .mapTo[Map[WorkflowState, Int]]
       .map(m => m.map(e => WesState.fromCromwellStatus(e._1) -> e._2)) // Convert WorkflowState -> WesState
-  }
 }
 
 /*
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
index 58313cb5946..9d2ca2a5e82 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesResponse.scala
@@ -17,22 +17,22 @@ final case class WesRunLog(run_id: String,
                            run_log: Option[WesLog],
                            task_logs: Option[List[WesLog]],
                            outputs: Option[JsObject]
-                          ) extends WesResponse
+) extends WesResponse
 
 object WesRunLog {
   def fromJson(json: String): WesRunLog = CromwellMetadata.fromJson(json).wesRunLog
 }
 
-
 final case class WesStatusInfoResponse(workflow_type_version: Map[String, Iterable[String]],
-                                    supported_wes_versions: Iterable[String],
-                                    supported_filesystem_protocols: Iterable[String],
-                                    workflow_engine_versions: Map[String, String],
-                                    default_workflow_engine_parameters: Iterable[DefaultWorkflowEngineParameter],
-                                    system_state_counts: Map[WesState, Int],
-                                    auth_instructions_url: String,
-                                    contact_info_url: String,
-                                    tags: Map[String, String]) extends WesResponse
+                                       supported_wes_versions: Iterable[String],
+                                       supported_filesystem_protocols: Iterable[String],
+                                       workflow_engine_versions: Map[String, String],
+                                       default_workflow_engine_parameters: Iterable[DefaultWorkflowEngineParameter],
+                                       system_state_counts: Map[WesState, Int],
+                                       auth_instructions_url: String,
+                                       contact_info_url: String,
+                                       tags: Map[String, String]
+) extends WesResponse
 
 object WesResponseJsonSupport extends SprayJsonSupport with DefaultJsonProtocol {
   import WesStateJsonSupport._
@@ -51,7 +51,7 @@ object WesResponseJsonSupport extends SprayJsonSupport with DefaultJsonProtocol
   implicit object WesResponseFormat extends RootJsonFormat[WesResponse] {
     import spray.json._
 
-    def write(r: WesResponse) = {
+    def write(r: WesResponse) =
       r match {
         case r: WesRunId => r.toJson
         case s: WesRunStatus => s.toJson
@@ -61,8 +61,9 @@ object WesResponseJsonSupport extends SprayJsonSupport with DefaultJsonProtocol
         case m: WesResponseWorkflowMetadata => m.toJson
         case w: WesRunLog => w.toJson
       }
-    }
 
-    def read(value: JsValue) = throw new UnsupportedOperationException("Reading WesResponse objects from JSON is not supported")
+    def read(value: JsValue) = throw new UnsupportedOperationException(
+      "Reading WesResponse objects from JSON is not supported"
+    )
   }
 }
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
index 41973bb8981..bd5977ae853 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRouteSupport.scala
@@ -5,7 +5,7 @@ import akka.http.scaladsl.model.{Multipart, StatusCode, StatusCodes}
 import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server.directives.RouteDirectives.complete
 import akka.http.scaladsl.server.{Directive1, Route}
-import akka.pattern.{AskTimeoutException, ask}
+import akka.pattern.{ask, AskTimeoutException}
 import akka.stream.ActorMaterializer
 import akka.util.Timeout
 import cats.data.NonEmptyList
@@ -16,12 +16,18 @@ import cromwell.engine.instrumentation.HttpInstrumentation
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
 import cromwell.engine.workflow.workflowstore.{WorkflowStoreActor, WorkflowStoreSubmitActor}
 import cromwell.server.CromwellShutdown
-import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, GetSingleWorkflowMetadataAction, GetStatus, MetadataServiceResponse, StatusLookupFailed}
+import cromwell.services.metadata.MetadataService.{
+  BuildMetadataJsonAction,
+  GetSingleWorkflowMetadataAction,
+  GetStatus,
+  MetadataServiceResponse,
+  StatusLookupFailed
+}
 import cromwell.services.{FailedMetadataJsonResponse, SuccessfulMetadataJsonResponse}
 import cromwell.webservice.PartialWorkflowSources
-import cromwell.webservice.WebServiceUtils.{EnhancedThrowable, completeResponse, materializeFormData}
+import cromwell.webservice.WebServiceUtils.{completeResponse, materializeFormData, EnhancedThrowable}
 import cromwell.webservice.routes.CromwellApiService
-import cromwell.webservice.routes.CromwellApiService.{UnrecognizedWorkflowException, validateWorkflowIdInMetadata}
+import cromwell.webservice.routes.CromwellApiService.{validateWorkflowIdInMetadata, UnrecognizedWorkflowException}
 import cromwell.webservice.routes.MetadataRouteSupport.{metadataBuilderActorRequest, metadataQueryRequest}
 import cromwell.webservice.routes.wes.WesResponseJsonSupport._
 import cromwell.webservice.routes.wes.WesRouteSupport.{respondWithWesError, _}
@@ -31,8 +37,6 @@ import scala.concurrent.duration.FiniteDuration
 import scala.concurrent.{ExecutionContext, Future, TimeoutException}
 import scala.util.{Failure, Success}
 
-
-
 trait WesRouteSupport extends HttpInstrumentation {
 
   val serviceRegistryActor: ActorRef
@@ -55,7 +59,7 @@ trait WesRouteSupport extends HttpInstrumentation {
       - It'd require a fairly substantial refactor of the MetadataBuilderActor to be more general
       - It's expected that for now the usage of these endpoints will not be extensive, so the protections of the regulator
          should not be necessary
-    */
+   */
   val wesRoutes: Route =
     instrumentRequest {
       concat(
@@ -74,19 +78,25 @@ trait WesRouteSupport extends HttpInstrumentation {
               } ~
                 post {
                   extractSubmission() { submission =>
-                    wesSubmitRequest(submission.entity,
-                      isSingleSubmission = true)
+                    wesSubmitRequest(submission.entity, isSingleSubmission = true)
                   }
                 }
             },
             path("runs" / Segment) { workflowId =>
               get {
                 // this is what it was like in code found in the project… it perhaps isn’t ideal but doesn’t seem to hurt, so leaving it like this for now.
-                completeCromwellResponse(runLog(workflowId, (w: WorkflowId) => GetSingleWorkflowMetadataAction(w, None, None, expandSubWorkflows = false), serviceRegistryActor))
+                completeCromwellResponse(
+                  runLog(workflowId,
+                         (w: WorkflowId) => GetSingleWorkflowMetadataAction(w, None, None, expandSubWorkflows = false),
+                         serviceRegistryActor
+                  )
+                )
               }
             },
             path("runs" / Segment / "status") { possibleWorkflowId =>
-              val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor).flatMap(w => serviceRegistryActor.ask(GetStatus(w)).mapTo[MetadataServiceResponse])
+              val response = validateWorkflowIdInMetadata(possibleWorkflowId, serviceRegistryActor).flatMap(w =>
+                serviceRegistryActor.ask(GetStatus(w)).mapTo[MetadataServiceResponse]
+              )
               // WES can also return a 401 or a 403 but that requires user auth knowledge which Cromwell doesn't currently have
               onComplete(response) {
                 case Success(SuccessfulMetadataJsonResponse(_, jsObject)) =>
@@ -104,10 +114,11 @@ trait WesRouteSupport extends HttpInstrumentation {
             path("runs" / Segment / "cancel") { possibleWorkflowId =>
               post {
                 CromwellApiService.abortWorkflow(possibleWorkflowId,
-                  workflowStoreActor,
-                  workflowManagerActor,
-                  successHandler = WesAbortSuccessHandler,
-                  errorHandler = WesAbortErrorHandler)
+                                                 workflowStoreActor,
+                                                 workflowManagerActor,
+                                                 successHandler = WesAbortSuccessHandler,
+                                                 errorHandler = WesAbortErrorHandler
+                )
               }
             }
           )
@@ -115,22 +126,22 @@ trait WesRouteSupport extends HttpInstrumentation {
       )
     }
 
-  def toWesResponse(workflowId: WorkflowId, workflowState: WorkflowState):  WesRunStatus = {
+  def toWesResponse(workflowId: WorkflowId, workflowState: WorkflowState): WesRunStatus =
     WesRunStatus(workflowId.toString, WesState.fromCromwellStatus(workflowState))
-  }
 
-  def toWesResponseId(workflowId: WorkflowId): WesRunId ={
+  def toWesResponseId(workflowId: WorkflowId): WesRunId =
     WesRunId(workflowId.toString)
-  }
 
   def wesSubmitRequest(formData: Multipart.FormData, isSingleSubmission: Boolean): Route = {
-    def getWorkflowState(workflowOnHold: Boolean): WorkflowState = {
+    def getWorkflowState(workflowOnHold: Boolean): WorkflowState =
       if (workflowOnHold)
         WorkflowOnHold
       else WorkflowSubmitted
-    }
 
-    def sendToWorkflowStore(command: WorkflowStoreActor.WorkflowStoreActorSubmitCommand, warnings: Seq[String], workflowState: WorkflowState): Route = {
+    def sendToWorkflowStore(command: WorkflowStoreActor.WorkflowStoreActorSubmitCommand,
+                            warnings: Seq[String],
+                            workflowState: WorkflowState
+    ): Route =
       // NOTE: Do not blindly copy the akka-http -to- ask-actor pattern below without knowing the pros and cons.
       onComplete(workflowStoreActor.ask(command).mapTo[WorkflowStoreSubmitActor.WorkflowStoreSubmitActorResponse]) {
         case Success(w) =>
@@ -142,18 +153,21 @@ trait WesRouteSupport extends HttpInstrumentation {
             case WorkflowStoreSubmitActor.WorkflowSubmitFailed(throwable) =>
               respondWithWesError(throwable.getLocalizedMessage, StatusCodes.BadRequest)
           }
-        case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() => respondWithWesError("Cromwell service is shutting down", StatusCodes.InternalServerError)
+        case Failure(_: AskTimeoutException) if CromwellShutdown.shutdownInProgress() =>
+          respondWithWesError("Cromwell service is shutting down", StatusCodes.InternalServerError)
         case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
         case Failure(e) => e.failRequest(StatusCodes.InternalServerError, warnings)
       }
-    }
 
     onComplete(materializeFormData(formData)) {
       case Success(data) =>
         PartialWorkflowSources.fromSubmitRoute(data, allowNoInputs = isSingleSubmission) match {
           case Success(workflowSourceFiles) if isSingleSubmission && workflowSourceFiles.size == 1 =>
             val warnings = workflowSourceFiles.flatMap(_.warnings)
-            sendToWorkflowStore(WorkflowStoreActor.SubmitWorkflow(workflowSourceFiles.head), warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+            sendToWorkflowStore(WorkflowStoreActor.SubmitWorkflow(workflowSourceFiles.head),
+                                warnings,
+                                getWorkflowState(workflowSourceFiles.head.workflowOnHold)
+            )
           // Catches the case where someone has gone through the single submission endpoint w/ more than one workflow
           case Success(workflowSourceFiles) if isSingleSubmission =>
             val warnings = workflowSourceFiles.flatMap(_.warnings)
@@ -163,7 +177,9 @@ trait WesRouteSupport extends HttpInstrumentation {
             val warnings = workflowSourceFiles.flatMap(_.warnings)
             sendToWorkflowStore(
               WorkflowStoreActor.BatchSubmitWorkflows(NonEmptyList.fromListUnsafe(workflowSourceFiles.toList)),
-              warnings, getWorkflowState(workflowSourceFiles.head.workflowOnHold))
+              warnings,
+              getWorkflowState(workflowSourceFiles.head.workflowOnHold)
+            )
           case Failure(t) => t.failRequest(StatusCodes.BadRequest)
         }
       case Failure(e: TimeoutException) => e.failRequest(StatusCodes.ServiceUnavailable)
@@ -172,64 +188,67 @@ trait WesRouteSupport extends HttpInstrumentation {
   }
 }
 
-
-
 object WesRouteSupport {
   import WesResponseJsonSupport._
 
-  implicit lazy val duration: FiniteDuration = ConfigFactory.load().as[FiniteDuration]("akka.http.server.request-timeout")
+  implicit lazy val duration: FiniteDuration =
+    ConfigFactory.load().as[FiniteDuration]("akka.http.server.request-timeout")
   implicit lazy val timeout: Timeout = duration
   import scala.concurrent.ExecutionContext.Implicits.global
 
   val NotFoundError = WesErrorResponse("The requested workflow run wasn't found", StatusCodes.NotFound.intValue)
 
-  def WesAbortSuccessHandler: PartialFunction[SuccessfulAbortResponse, Route] = {
-    case response => complete(WesRunId(response.workflowId.toString))
+  def WesAbortSuccessHandler: PartialFunction[SuccessfulAbortResponse, Route] = { case response =>
+    complete(WesRunId(response.workflowId.toString))
   }
 
   def WesAbortErrorHandler: PartialFunction[Throwable, Route] = {
     // There are also some auth situations which should be handled, but at the moment Cromwell doesn't allow for those
     case e: IllegalStateException => respondWithWesError(e.getLocalizedMessage, StatusCodes.Forbidden)
     case e: WorkflowNotFoundException => respondWithWesError(e.getLocalizedMessage, StatusCodes.NotFound)
-    case _: AskTimeoutException if CromwellShutdown.shutdownInProgress() => respondWithWesError("Cromwell service is shutting down", StatusCodes.InternalServerError)
+    case _: AskTimeoutException if CromwellShutdown.shutdownInProgress() =>
+      respondWithWesError("Cromwell service is shutting down", StatusCodes.InternalServerError)
     case e: Exception => respondWithWesError(e.getLocalizedMessage, StatusCodes.InternalServerError)
   }
 
-  private def respondWithWesError(errorMsg: String, status: StatusCode): Route = {
+  private def respondWithWesError(errorMsg: String, status: StatusCode): Route =
     complete((status, WesErrorResponse(errorMsg, status.intValue)))
-  }
 
-  def extractSubmission(): Directive1[WesSubmission] = {
-    formFields((
-      "workflow_params".?,
-      "workflow_type".?,
-      "workflow_type_version".?,
-      "tags".?,
-      "workflow_engine_parameters".?,
-      "workflow_url".?,
-      "workflow_attachment".as[String].*
-    )).as(WesSubmission)
-  }
+  def extractSubmission(): Directive1[WesSubmission] =
+    formFields(
+      (
+        "workflow_params".?,
+        "workflow_type".?,
+        "workflow_type_version".?,
+        "tags".?,
+        "workflow_engine_parameters".?,
+        "workflow_url".?,
+        "workflow_attachment".as[String].*
+      )
+    ).as(WesSubmission)
 
-  def completeCromwellResponse(future: => Future[WesResponse]): Route = {
+  def completeCromwellResponse(future: => Future[WesResponse]): Route =
     onComplete(future) {
       case Success(response: WesResponse) => complete(response)
       case Failure(e) => complete(WesErrorResponse(e.getMessage, StatusCodes.InternalServerError.intValue))
     }
-  }
 
-  def listRuns(pageSize: Option[Int], pageToken: Option[String], serviceRegistryActor: ActorRef): Future[WesResponse] = {
+  def listRuns(pageSize: Option[Int], pageToken: Option[String], serviceRegistryActor: ActorRef): Future[WesResponse] =
     // FIXME: to handle - page_size, page_token
     // FIXME: How to handle next_page_token in response?
-    metadataQueryRequest(Seq.empty[(String, String)], serviceRegistryActor).map(RunListResponse.fromMetadataQueryResponse)
-  }
+    metadataQueryRequest(Seq.empty[(String, String)], serviceRegistryActor)
+      .map(RunListResponse.fromMetadataQueryResponse)
 
-  def runLog(workflowId: String, request: WorkflowId => BuildMetadataJsonAction, serviceRegistryActor: ActorRef): Future[WesResponse] = {
+  def runLog(workflowId: String,
+             request: WorkflowId => BuildMetadataJsonAction,
+             serviceRegistryActor: ActorRef
+  ): Future[WesResponse] = {
     val metadataJsonResponse = metadataBuilderActorRequest(workflowId, request, serviceRegistryActor)
 
     metadataJsonResponse.map {
       case SuccessfulMetadataJsonResponse(_, responseJson) => WesRunLog.fromJson(responseJson.toString())
-      case FailedMetadataJsonResponse(_, reason) => WesErrorResponse(reason.getMessage, StatusCodes.InternalServerError.intValue)
+      case FailedMetadataJsonResponse(_, reason) =>
+        WesErrorResponse(reason.getMessage, StatusCodes.InternalServerError.intValue)
     }
   }
-}
\ No newline at end of file
+}
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
index c882ebf4f8b..240fce01341 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesRunLog.scala
@@ -2,7 +2,6 @@ package cromwell.webservice.routes.wes
 
 import spray.json.JsObject
 
-
 final case class WesLog(name: Option[String],
                         cmd: Option[Seq[String]],
                         start_time: Option[String],
@@ -10,7 +9,7 @@ final case class WesLog(name: Option[String],
                         stdout: Option[String],
                         stderr: Option[String],
                         exit_code: Option[Int]
-                       )
+)
 
 final case class WesRunRequest(workflow_params: Option[JsObject],
                                workflow_type: String,
@@ -18,4 +17,4 @@ final case class WesRunRequest(workflow_params: Option[JsObject],
                                tags: Option[JsObject],
                                workflow_engine_parameters: Option[JsObject],
                                workflow_url: Option[String]
-                              )
+)
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesState.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesState.scala
index f7feee727b8..58cf69e6a08 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesState.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesState.scala
@@ -6,24 +6,23 @@ import spray.json.{DefaultJsonProtocol, JsObject, JsString, JsValue, RootJsonFor
 
 object WesState {
   sealed trait WesState extends Product with Serializable { val name: String }
-  case object Unknown extends WesState { override val name = "UNKNOWN"}
-  case object Queued extends WesState { override val name = "QUEUED"}
-  case object Initializing extends WesState { override val name = "INITIALIZING"}
-  case object Running extends WesState { override val name = "RUNNING"}
-  case object Paused extends WesState { override val name = "PAUSED"}
-  case object Complete extends WesState { override val name = "COMPLETE"}
-  case object ExecutorError extends WesState { override val name = "EXECUTOR_ERROR"}
-  case object SystemError extends WesState { override val name = "SYSTEM_ERROR"}
-  case object Canceled extends WesState { override val name = "CANCELED"}
-  case object Canceling extends WesState { override val name = "CANCELING"}
+  case object Unknown extends WesState { override val name = "UNKNOWN" }
+  case object Queued extends WesState { override val name = "QUEUED" }
+  case object Initializing extends WesState { override val name = "INITIALIZING" }
+  case object Running extends WesState { override val name = "RUNNING" }
+  case object Paused extends WesState { override val name = "PAUSED" }
+  case object Complete extends WesState { override val name = "COMPLETE" }
+  case object ExecutorError extends WesState { override val name = "EXECUTOR_ERROR" }
+  case object SystemError extends WesState { override val name = "SYSTEM_ERROR" }
+  case object Canceled extends WesState { override val name = "CANCELED" }
+  case object Canceling extends WesState { override val name = "CANCELING" }
 
-  def fromStatusString(status: Option[String]): WesState = {
+  def fromStatusString(status: Option[String]): WesState =
     status match {
       case Some(status) => fromCromwellStatus(WorkflowState.withName(status))
       case None => Unknown
     }
-  }
-  def fromCromwellStatus(cromwellStatus: WorkflowState): WesState = {
+  def fromCromwellStatus(cromwellStatus: WorkflowState): WesState =
     cromwellStatus match {
       case WorkflowOnHold => Paused
       case WorkflowSubmitted => Queued
@@ -34,18 +33,24 @@ object WesState {
       case WorkflowFailed => ExecutorError
       case _ => Unknown
     }
-  }
 
   def fromCromwellStatusJson(jsonResponse: JsObject): WesState = {
 
-    val statusString = jsonResponse.fields.get("status").collect {
-      case str: JsString => str.value
-    }.getOrElse(throw new IllegalArgumentException(s"Could not coerce Cromwell status response ${jsonResponse.compactPrint} into a valid WES status"))
+    val statusString = jsonResponse.fields
+      .get("status")
+      .collect { case str: JsString =>
+        str.value
+      }
+      .getOrElse(
+        throw new IllegalArgumentException(
+          s"Could not coerce Cromwell status response ${jsonResponse.compactPrint} into a valid WES status"
+        )
+      )
 
     fromCromwellStatus(WorkflowState.withName(statusString))
   }
 
-  def fromString(status: String): WesState = {
+  def fromString(status: String): WesState =
     status match {
       case Unknown.name => Unknown
       case Queued.name => Queued
@@ -59,7 +64,6 @@ object WesState {
       case Canceling.name => Canceling
       case doh => throw new IllegalArgumentException(s"Invalid status attempting to be coerced to WesState: $doh")
     }
-  }
 }
 
 object WesStateJsonSupport extends SprayJsonSupport with DefaultJsonProtocol {
@@ -70,8 +74,8 @@ object WesStateJsonSupport extends SprayJsonSupport with DefaultJsonProtocol {
 
     def read(json: JsValue): WesState =
       json match {
-      case JsString(string) => WesState.fromString(string)
-      case other => throw new UnsupportedOperationException(s"Cannot deserialize $other into a WesState")
-    }
+        case JsString(string) => WesState.fromString(string)
+        case other => throw new UnsupportedOperationException(s"Cannot deserialize $other into a WesState")
+      }
   }
 }
diff --git a/engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala b/engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala
index 1db2cd801b8..a3de8bbb24a 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/wes/WesSubmission.scala
@@ -10,7 +10,7 @@ final case class WesSubmission(workflowParams: Option[String],
                                workflowEngineParameters: Option[String],
                                workflowUrl: Option[String],
                                workflowAttachment: Iterable[String]
-                              ) {
+) {
   val entity: Multipart.FormData = {
     /*
       FIXME:
@@ -27,15 +27,29 @@ final case class WesSubmission(workflowParams: Option[String],
       Content-Disposition headers on each of these files which can be used to describe directory structure and such
       for relative import resolution
      */
-    val sourcePart = workflowAttachment.headOption map { a => Multipart.FormData.BodyPart(WorkflowSourceKey, HttpEntity(MediaTypes.`application/json`, a)) }
-
-    val urlPart = workflowUrl map { u => Multipart.FormData.BodyPart(WorkflowUrlKey, HttpEntity(MediaTypes.`application/json`, u)) }
-
-    val typePart = workflowType map { w => Multipart.FormData.BodyPart(WorkflowTypeKey, HttpEntity(MediaTypes.`application/json`, w)) }
-    val typeVersionPart = workflowTypeVersion map { v => Multipart.FormData.BodyPart(WorkflowTypeVersionKey, HttpEntity(MediaTypes.`application/json`, v)) }
-    val inputsPart = workflowParams map { p => Multipart.FormData.BodyPart(WorkflowInputsKey, HttpEntity(MediaTypes.`application/json`, p)) }
-    val optionsPart = workflowEngineParameters map { o => Multipart.FormData.BodyPart(WorkflowOptionsKey, HttpEntity(MediaTypes.`application/json`, o)) }
-    val labelsPart = tags map { t => Multipart.FormData.BodyPart(labelsKey, HttpEntity(MediaTypes.`application/json`, t)) }
+    val sourcePart = workflowAttachment.headOption map { a =>
+      Multipart.FormData.BodyPart(WorkflowSourceKey, HttpEntity(MediaTypes.`application/json`, a))
+    }
+
+    val urlPart = workflowUrl map { u =>
+      Multipart.FormData.BodyPart(WorkflowUrlKey, HttpEntity(MediaTypes.`application/json`, u))
+    }
+
+    val typePart = workflowType map { w =>
+      Multipart.FormData.BodyPart(WorkflowTypeKey, HttpEntity(MediaTypes.`application/json`, w))
+    }
+    val typeVersionPart = workflowTypeVersion map { v =>
+      Multipart.FormData.BodyPart(WorkflowTypeVersionKey, HttpEntity(MediaTypes.`application/json`, v))
+    }
+    val inputsPart = workflowParams map { p =>
+      Multipart.FormData.BodyPart(WorkflowInputsKey, HttpEntity(MediaTypes.`application/json`, p))
+    }
+    val optionsPart = workflowEngineParameters map { o =>
+      Multipart.FormData.BodyPart(WorkflowOptionsKey, HttpEntity(MediaTypes.`application/json`, o))
+    }
+    val labelsPart = tags map { t =>
+      Multipart.FormData.BodyPart(labelsKey, HttpEntity(MediaTypes.`application/json`, t))
+    }
 
     val parts = List(sourcePart, urlPart, typePart, typeVersionPart, inputsPart, optionsPart, labelsPart).flatten
 
diff --git a/engine/src/main/scala/cromwell/webservice/webservice_.scala b/engine/src/main/scala/cromwell/webservice/webservice_.scala
index d68ba0bdb1f..08b57cfc378 100644
--- a/engine/src/main/scala/cromwell/webservice/webservice_.scala
+++ b/engine/src/main/scala/cromwell/webservice/webservice_.scala
@@ -35,5 +35,5 @@ object Patterns {
         \.                               #   Literal dot.
         (\d+)                            #   Captured shard digits.
       )?                                 # End outer optional noncapturing group for shard.
-                               """.trim.r                         // The trim is necessary as (?x) must be at the beginning of the regex.
+                               """.trim.r // The trim is necessary as (?x) must be at the beginning of the regex.
 }
diff --git a/engine/src/test/scala/cromwell/MetadataWatchActor.scala b/engine/src/test/scala/cromwell/MetadataWatchActor.scala
index 2c43ff74463..e9c7710d79f 100644
--- a/engine/src/test/scala/cromwell/MetadataWatchActor.scala
+++ b/engine/src/test/scala/cromwell/MetadataWatchActor.scala
@@ -18,7 +18,7 @@ final case class MetadataWatchActor(promise: Promise[Unit], matchers: Matcher*)
   var unsatisfiedMatchers = matchers
 
   def tryMatchingEvents(events: Iterable[MetadataEvent]) = {
-    unsatisfiedMatchers = unsatisfiedMatchers.filterNot { m => m.matches(events) }
+    unsatisfiedMatchers = unsatisfiedMatchers.filterNot(m => m.matches(events))
     if (unsatisfiedMatchers.isEmpty) {
       promise.trySuccess(())
       ()
@@ -41,7 +41,8 @@ final case class MetadataWatchActor(promise: Promise[Unit], matchers: Matcher*)
 
 object MetadataWatchActor {
 
-  def props(promise: Promise[Unit], matchers: Matcher*): Props = Props(MetadataWatchActor(promise, matchers: _*)).withDispatcher(EngineDispatcher)
+  def props(promise: Promise[Unit], matchers: Matcher*): Props =
+    Props(MetadataWatchActor(promise, matchers: _*)).withDispatcher(EngineDispatcher)
 
   trait Matcher {
     private var _fullEventList: List[MetadataEvent] = List.empty
@@ -57,7 +58,8 @@ object MetadataWatchActor {
 
     def checkMetadataValueContains(key: String, actual: MetadataValue, expected: String): Boolean = {
       val result = actual.value.contains(expected)
-      if (!result) addNearMissInfo(s"Key $key had unexpected value.\nActual value: ${actual.value}\n\nDid not contain: $expected")
+      if (!result)
+        addNearMissInfo(s"Key $key had unexpected value.\nActual value: ${actual.value}\n\nDid not contain: $expected")
       result
     }
   }
@@ -67,20 +69,28 @@ object MetadataWatchActor {
     case None => false
   }
 
-  final case class JobKeyMetadataKeyAndValueContainStringMatcher(jobKeyCheck: Option[MetadataJobKey] => Boolean, key: String, value: String) extends Matcher {
-    def _matches(events: Iterable[MetadataEvent]): Boolean = {
-      events.exists(e => e.key.key.contains(key) && jobKeyCheck(e.key.jobKey) && e.value.exists { v => v.valueType == MetadataString && checkMetadataValueContains(e.key.key, v, value) })
-    }
+  final case class JobKeyMetadataKeyAndValueContainStringMatcher(jobKeyCheck: Option[MetadataJobKey] => Boolean,
+                                                                 key: String,
+                                                                 value: String
+  ) extends Matcher {
+    def _matches(events: Iterable[MetadataEvent]): Boolean =
+      events.exists(e =>
+        e.key.key.contains(key) && jobKeyCheck(e.key.jobKey) && e.value.exists { v =>
+          v.valueType == MetadataString && checkMetadataValueContains(e.key.key, v, value)
+        }
+      )
   }
 
   abstract class KeyMatchesRegexAndValueContainsStringMatcher(keyTemplate: String, value: String) extends Matcher {
     val templateRegex = keyTemplate.r
-    def _matches(events: Iterable[MetadataEvent]): Boolean = {
-      events.exists(e => templateRegex.findFirstIn(e.key.key).isDefined &&
-        e.value.exists { v => checkMetadataValueContains(e.key.key, v, value) })
-    }
+    def _matches(events: Iterable[MetadataEvent]): Boolean =
+      events.exists(e =>
+        templateRegex.findFirstIn(e.key.key).isDefined &&
+          e.value.exists(v => checkMetadataValueContains(e.key.key, v, value))
+      )
   }
 
   val failurePattern = """failures\[\d*\].*\:message"""
-  final case class FailureMatcher(value: String) extends KeyMatchesRegexAndValueContainsStringMatcher(failurePattern, value) { }
+  final case class FailureMatcher(value: String)
+      extends KeyMatchesRegexAndValueContainsStringMatcher(failurePattern, value) {}
 }
diff --git a/engine/src/test/scala/cromwell/engine/MockCromwellTerminator.scala b/engine/src/test/scala/cromwell/engine/MockCromwellTerminator.scala
index 1ef165ce14b..24b21541a1a 100644
--- a/engine/src/test/scala/cromwell/engine/MockCromwellTerminator.scala
+++ b/engine/src/test/scala/cromwell/engine/MockCromwellTerminator.scala
@@ -6,7 +6,6 @@ import akka.actor.CoordinatedShutdown
 import scala.concurrent.Future
 
 object MockCromwellTerminator extends CromwellTerminator {
-  override def beginCromwellShutdown(notUsed: CoordinatedShutdown.Reason): Future[Done] = {
+  override def beginCromwellShutdown(notUsed: CoordinatedShutdown.Reason): Future[Done] =
     Future.successful(Done)
-  }
 }
diff --git a/engine/src/test/scala/cromwell/engine/backend/mock/DefaultBackendJobExecutionActor.scala b/engine/src/test/scala/cromwell/engine/backend/mock/DefaultBackendJobExecutionActor.scala
index f31e4d72002..6fc7ed0fbd5 100644
--- a/engine/src/test/scala/cromwell/engine/backend/mock/DefaultBackendJobExecutionActor.scala
+++ b/engine/src/test/scala/cromwell/engine/backend/mock/DefaultBackendJobExecutionActor.scala
@@ -10,13 +10,26 @@ import wom.graph.CommandCallNode
 import scala.concurrent.{ExecutionContext, Future}
 
 object DefaultBackendJobExecutionActor {
-  def props(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor) = Props(DefaultBackendJobExecutionActor(jobDescriptor, configurationDescriptor))
+  def props(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor) = Props(
+    DefaultBackendJobExecutionActor(jobDescriptor, configurationDescriptor)
+  )
 }
 
-case class DefaultBackendJobExecutionActor(override val jobDescriptor: BackendJobDescriptor, override val configurationDescriptor: BackendConfigurationDescriptor) extends BackendJobExecutionActor {
-  override def execute: Future[BackendJobExecutionResponse] = {
-    Future.successful(JobSucceededResponse(jobDescriptor.key, Some(0), CallOutputs((jobDescriptor.taskCall.outputPorts map taskOutputToJobOutput).toMap), None, Seq.empty, dockerImageUsed = None, resultGenerationMode = RunOnBackend))
-  }
+case class DefaultBackendJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
+                                           override val configurationDescriptor: BackendConfigurationDescriptor
+) extends BackendJobExecutionActor {
+  override def execute: Future[BackendJobExecutionResponse] =
+    Future.successful(
+      JobSucceededResponse(
+        jobDescriptor.key,
+        Some(0),
+        CallOutputs((jobDescriptor.taskCall.outputPorts map taskOutputToJobOutput).toMap),
+        None,
+        Seq.empty,
+        dockerImageUsed = None,
+        resultGenerationMode = RunOnBackend
+      )
+    )
 
   override def recover = execute
 
@@ -24,25 +37,26 @@ case class DefaultBackendJobExecutionActor(override val jobDescriptor: BackendJo
 }
 
 class DefaultBackendLifecycleActorFactory(val name: String, val configurationDescriptor: BackendConfigurationDescriptor)
-  extends BackendLifecycleActorFactory {
+    extends BackendLifecycleActorFactory {
   override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
                                                 ioActor: ActorRef,
                                                 calls: Set[CommandCallNode],
                                                 serviceRegistryActor: ActorRef,
-                                                restarting: Boolean): Option[Props] = None
+                                                restarting: Boolean
+  ): Option[Props] = None
 
   override def jobExecutionActorProps(jobDescriptor: BackendJobDescriptor,
                                       initializationData: Option[BackendInitializationData],
                                       serviceRegistryActor: ActorRef,
                                       ioActor: ActorRef,
-                                      backendSingletonActor: Option[ActorRef]): Props = {
+                                      backendSingletonActor: Option[ActorRef]
+  ): Props =
     DefaultBackendJobExecutionActor.props(jobDescriptor, configurationDescriptor)
-  }
 
   override def expressionLanguageFunctions(workflowDescriptor: BackendWorkflowDescriptor,
                                            jobKey: BackendJobDescriptorKey,
                                            initializationData: Option[BackendInitializationData],
                                            ioActorProxy: ActorRef,
-                                           ec: ExecutionContext): IoFunctionSet = NoIoFunctionSet
+                                           ec: ExecutionContext
+  ): IoFunctionSet = NoIoFunctionSet
 }
-
diff --git a/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendJobExecutionActor.scala b/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendJobExecutionActor.scala
index 6bc7b04adce..69685d58176 100644
--- a/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendJobExecutionActor.scala
+++ b/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendJobExecutionActor.scala
@@ -2,26 +2,39 @@ package cromwell.engine.backend.mock
 
 import akka.actor.Props
 import cromwell.backend.{BackendConfigurationDescriptor, BackendJobDescriptor, BackendJobExecutionActor}
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, JobFailedNonRetryableResponse, JobFailedRetryableResponse}
+import cromwell.backend.BackendJobExecutionActor.{
+  BackendJobExecutionResponse,
+  JobFailedNonRetryableResponse,
+  JobFailedRetryableResponse
+}
 
 import scala.concurrent.Future
 
 object RetryableBackendJobExecutionActor {
-  def props(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor) = Props(RetryableBackendJobExecutionActor(jobDescriptor, configurationDescriptor))
+  def props(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor) = Props(
+    RetryableBackendJobExecutionActor(jobDescriptor, configurationDescriptor)
+  )
 }
 
-final case class RetryableBackendJobExecutionActor(override val jobDescriptor: BackendJobDescriptor, override val configurationDescriptor: BackendConfigurationDescriptor) extends BackendJobExecutionActor {
+final case class RetryableBackendJobExecutionActor(override val jobDescriptor: BackendJobDescriptor,
+                                                   override val configurationDescriptor: BackendConfigurationDescriptor
+) extends BackendJobExecutionActor {
 
   val attempts = 3
 
-  override def execute: Future[BackendJobExecutionResponse] = {
+  override def execute: Future[BackendJobExecutionResponse] =
     if (jobDescriptor.key.attempt < attempts) {
-      Future.successful(JobFailedRetryableResponse(jobDescriptor.key, new RuntimeException("An apparent transient Exception!"), None))
-    }
-    else {
-      Future.successful(JobFailedNonRetryableResponse(jobDescriptor.key, new RuntimeException("A permanent Exception! Yikes, what a pickle!"), None))
+      Future.successful(
+        JobFailedRetryableResponse(jobDescriptor.key, new RuntimeException("An apparent transient Exception!"), None)
+      )
+    } else {
+      Future.successful(
+        JobFailedNonRetryableResponse(jobDescriptor.key,
+                                      new RuntimeException("A permanent Exception! Yikes, what a pickle!"),
+                                      None
+        )
+      )
     }
-  }
 
   override def recover = execute
 
diff --git a/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendLifecycleActorFactory.scala b/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendLifecycleActorFactory.scala
index 3ee7afc8767..23ea949f9d6 100644
--- a/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendLifecycleActorFactory.scala
+++ b/engine/src/test/scala/cromwell/engine/backend/mock/RetryableBackendLifecycleActorFactory.scala
@@ -8,25 +8,27 @@ import wom.graph.CommandCallNode
 import scala.concurrent.ExecutionContext
 
 class RetryableBackendLifecycleActorFactory(val name: String,
-                                            val configurationDescriptor: BackendConfigurationDescriptor)
-  extends BackendLifecycleActorFactory {
+                                            val configurationDescriptor: BackendConfigurationDescriptor
+) extends BackendLifecycleActorFactory {
   override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
                                                 ioActor: ActorRef,
                                                 calls: Set[CommandCallNode],
                                                 serviceRegistryActor: ActorRef,
-                                                restarting: Boolean): Option[Props] = None
+                                                restarting: Boolean
+  ): Option[Props] = None
 
   override def jobExecutionActorProps(jobDescriptor: BackendJobDescriptor,
                                       initializationData: Option[BackendInitializationData],
                                       serviceRegistryActor: ActorRef,
                                       ioActor: ActorRef,
-                                      backendSingletonActor: Option[ActorRef]): Props = {
+                                      backendSingletonActor: Option[ActorRef]
+  ): Props =
     RetryableBackendJobExecutionActor.props(jobDescriptor, configurationDescriptor)
-  }
 
   override def expressionLanguageFunctions(workflowDescriptor: BackendWorkflowDescriptor,
                                            jobKey: BackendJobDescriptorKey,
                                            initializationData: Option[BackendInitializationData],
                                            ioActorProxy: ActorRef,
-                                           ec: ExecutionContext): IoFunctionSet = NoIoFunctionSet
+                                           ec: ExecutionContext
+  ): IoFunctionSet = NoIoFunctionSet
 }
diff --git a/engine/src/test/scala/cromwell/engine/backend/mock/package.scala b/engine/src/test/scala/cromwell/engine/backend/mock/package.scala
index 4de47444c64..ef75c0df703 100644
--- a/engine/src/test/scala/cromwell/engine/backend/mock/package.scala
+++ b/engine/src/test/scala/cromwell/engine/backend/mock/package.scala
@@ -17,6 +17,7 @@ package object mock {
     case WomSingleFileType => WomSingleFile("/root/of/all/evil")
     case WomArrayType(memberType) => WomArray(WomArrayType(memberType), List(sampleValue(memberType)))
     case WomObjectType => WomObject(Map("a" -> WomString("1"), "b" -> WomString("2")))
-    case WomMapType(keyType, valueType) => WomMap(WomMapType(keyType, valueType), Map(sampleValue(keyType) -> sampleValue(valueType)))
+    case WomMapType(keyType, valueType) =>
+      WomMap(WomMapType(keyType, valueType), Map(sampleValue(keyType) -> sampleValue(valueType)))
   }
 }
diff --git a/engine/src/test/scala/cromwell/engine/io/IoActorProxyGcsBatchSpec.scala b/engine/src/test/scala/cromwell/engine/io/IoActorProxyGcsBatchSpec.scala
index 6c69fe98af6..57b85dd2a3b 100644
--- a/engine/src/test/scala/cromwell/engine/io/IoActorProxyGcsBatchSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/io/IoActorProxyGcsBatchSpec.scala
@@ -21,7 +21,12 @@ import scala.concurrent.duration._
 import scala.concurrent.{Await, ExecutionContext}
 import scala.language.postfixOps
 
-class IoActorProxyGcsBatchSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with ImplicitSender with Eventually {
+class IoActorProxyGcsBatchSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with ImplicitSender
+    with Eventually {
   behavior of "IoActor [GCS Batch]"
 
   implicit val ec: ExecutionContext = system.dispatcher
@@ -74,10 +79,11 @@ class IoActorProxyGcsBatchSpec extends TestKitSuite with AnyFlatSpecLike with Ma
                        dst: GcsPath,
                        directory: GcsPath,
                        testActorName: String,
-                       serviceRegistryActorName: String) = {
+                       serviceRegistryActorName: String
+  ) = {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe(serviceRegistryActorName).ref, "cromwell test"),
-      name = testActorName,
+      name = testActorName
     )
 
     val copyCommand = GcsBatchCopyCommand.forPaths(src, dst).get
@@ -102,20 +108,24 @@ class IoActorProxyGcsBatchSpec extends TestKitSuite with AnyFlatSpecLike with Ma
     received1.size shouldBe 5
     received1 forall { _.isInstanceOf[IoSuccess[_]] } shouldBe true
 
-    received1 collect {
-      case IoSuccess(_: GcsBatchSizeCommand, fileSize: Long) => fileSize shouldBe 5
+    received1 collect { case IoSuccess(_: GcsBatchSizeCommand, fileSize: Long) =>
+      fileSize shouldBe 5
     }
 
-    received1 collect {
-      case IoSuccess(_: GcsBatchCrc32Command, hash: String) => hash shouldBe "mnG7TA=="
+    received1 collect { case IoSuccess(_: GcsBatchCrc32Command, hash: String) =>
+      hash shouldBe "mnG7TA=="
     }
 
     received1 collect {
-      case IoSuccess(command: GcsBatchIsDirectoryCommand, isDirectory: Boolean) if command.file.pathAsString == directory.pathAsString => isDirectory shouldBe true
+      case IoSuccess(command: GcsBatchIsDirectoryCommand, isDirectory: Boolean)
+          if command.file.pathAsString == directory.pathAsString =>
+        isDirectory shouldBe true
     }
 
     received1 collect {
-      case IoSuccess(command: GcsBatchIsDirectoryCommand, isDirectory: Boolean) if command.file.pathAsString == src.pathAsString => isDirectory shouldBe false
+      case IoSuccess(command: GcsBatchIsDirectoryCommand, isDirectory: Boolean)
+          if command.file.pathAsString == src.pathAsString =>
+        isDirectory shouldBe false
     }
 
     testActor ! deleteSrcCommand
@@ -136,7 +146,7 @@ class IoActorProxyGcsBatchSpec extends TestKitSuite with AnyFlatSpecLike with Ma
       dst = dst,
       directory = directory,
       testActorName = "testActor-batch",
-      serviceRegistryActorName = "serviceRegistryActor-batch",
+      serviceRegistryActorName = "serviceRegistryActor-batch"
     )
   }
 
@@ -146,14 +156,14 @@ class IoActorProxyGcsBatchSpec extends TestKitSuite with AnyFlatSpecLike with Ma
       dst = dstRequesterPays,
       directory = directoryRequesterPays,
       testActorName = "testActor-batch-rp",
-      serviceRegistryActorName = "serviceRegistryActor-batch-rp",
+      serviceRegistryActorName = "serviceRegistryActor-batch-rp"
     )
   }
 
   it should "copy files across GCS storage classes" taggedAs IntegrationTest in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActor").ref, "cromwell test"),
-      name = "testActor",
+      name = "testActor"
     )
 
     val copyCommand = GcsBatchCopyCommand.forPaths(srcRegional, dstMultiRegional).get
diff --git a/engine/src/test/scala/cromwell/engine/io/IoActorSpec.scala b/engine/src/test/scala/cromwell/engine/io/IoActorSpec.scala
index e6209ff5958..880e9028282 100644
--- a/engine/src/test/scala/cromwell/engine/io/IoActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/io/IoActorSpec.scala
@@ -37,7 +37,7 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
   it should "copy a file" in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActorCopy").ref, "cromwell test"),
-      name = "testActorCopy",
+      name = "testActorCopy"
     )
 
     val src = DefaultPathBuilder.createTempFile()
@@ -59,7 +59,7 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
   it should "write to a file" in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActorWrite").ref, "cromwell test"),
-      name = "testActorWrite",
+      name = "testActorWrite"
     )
 
     val src = DefaultPathBuilder.createTempFile()
@@ -79,7 +79,7 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
   it should "delete a file" in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActorDelete").ref, "cromwell test"),
-      name = "testActorDelete",
+      name = "testActorDelete"
     )
 
     val src = DefaultPathBuilder.createTempFile()
@@ -98,7 +98,7 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
   it should "read a file" in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActorRead").ref, "cromwell test"),
-      name = "testActorRead",
+      name = "testActorRead"
     )
 
     val src = DefaultPathBuilder.createTempFile()
@@ -120,7 +120,7 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
   it should "read only the first bytes of file" in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActorFirstBytes").ref, "cromwell test"),
-      name = "testActorFirstBytes",
+      name = "testActorFirstBytes"
     )
 
     val src = DefaultPathBuilder.createTempFile()
@@ -142,7 +142,7 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
   it should "read the file if it's under the byte limit" in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActorByteLimit").ref, "cromwell test"),
-      name = "testActorByteLimit",
+      name = "testActorByteLimit"
     )
 
     val src = DefaultPathBuilder.createTempFile()
@@ -164,7 +164,7 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
   it should "fail if the file is larger than the read limit" in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActorReadLimit").ref, "cromwell test"),
-      name = "testActorReadLimit",
+      name = "testActorReadLimit"
     )
 
     val src = DefaultPathBuilder.createTempFile()
@@ -174,8 +174,10 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
 
     testActor ! readCommand
     expectMsgPF(5 seconds) {
-      case _: IoSuccess[_] => fail("Command should have failed because the read limit was < file size and failOnOverflow was true")
-      case response: IoFailure[_] => response.failure.getMessage shouldBe s"[Attempted 1 time(s)] - IOException: Could not read from ${src.pathAsString}: File ${src.pathAsString} is larger than requested maximum of 2 Bytes."
+      case _: IoSuccess[_] =>
+        fail("Command should have failed because the read limit was < file size and failOnOverflow was true")
+      case response: IoFailure[_] =>
+        response.failure.getMessage shouldBe s"[Attempted 1 time(s)] - IOException: Could not read from ${src.pathAsString}: File ${src.pathAsString} is larger than requested maximum of 2 Bytes."
     }
 
     src.delete()
@@ -184,7 +186,7 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
   it should "return a file size" in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActorSize").ref, "cromwell test"),
-      name = "testActorSize",
+      name = "testActorSize"
     )
 
     val src = DefaultPathBuilder.createTempFile()
@@ -206,7 +208,7 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
   it should "return a file md5 hash (local)" in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActorHash").ref, "cromwell test"),
-      name = "testActorHash",
+      name = "testActorHash"
     )
 
     val src = DefaultPathBuilder.createTempFile()
@@ -228,7 +230,7 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
   it should "touch a file (local)" in {
     val testActor = TestActorRef(
       factory = new IoActor(IoActorConfig, TestProbe("serviceRegistryActorTouch").ref, "cromwell test"),
-      name = "testActorTouch",
+      name = "testActorTouch"
     )
 
     val src = DefaultPathBuilder.createTempFile()
@@ -259,25 +261,45 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
       new SocketException(),
       new SocketTimeoutException(),
       new IOException("text Error getting access token for service account some other text"),
-
-      new IOException("Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 500 Internal Server Error\nBackend Error"),
-      new IOException("Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 500 Internal Server Error Backend Error"),
-
-      new IOException("Could not read from gs://broad-epi-cromwell/workflows/ChipSeq/ce6a5671-baf6-4734-a32b-abf3d9138e9b/call-epitope_classifier/memory_retry_rc: 503 Service Unavailable\nBackend Error"),
-      new IOException("Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 503 Service Unavailable Backend Error"),
-
-      new IOException("Could not read from gs://mccarroll-mocha/cromwell/cromwell-executions/mocha/86d47e9a-5745-4ec0-b4eb-0164f073e5f4/call-idat2gtc/shard-73/rc: 504 Gateway Timeout\nGET https://storage.googleapis.com/download/storage/v1/b/mccarroll-mocha/o/cromwell%2Fcromwell-executions%2Fmocha%2F86d47e9a-5745-4ec0-b4eb-0164f073e5f4%2Fcall-idat2gtc%2Fshard-73%2Frc?alt=media"),
+      new IOException(
+        "Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 500 Internal Server Error\nBackend Error"
+      ),
+      new IOException(
+        "Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 500 Internal Server Error Backend Error"
+      ),
+      new IOException(
+        "Could not read from gs://broad-epi-cromwell/workflows/ChipSeq/ce6a5671-baf6-4734-a32b-abf3d9138e9b/call-epitope_classifier/memory_retry_rc: 503 Service Unavailable\nBackend Error"
+      ),
+      new IOException(
+        "Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 503 Service Unavailable Backend Error"
+      ),
+      new IOException(
+        "Could not read from gs://mccarroll-mocha/cromwell/cromwell-executions/mocha/86d47e9a-5745-4ec0-b4eb-0164f073e5f4/call-idat2gtc/shard-73/rc: 504 Gateway Timeout\nGET https://storage.googleapis.com/download/storage/v1/b/mccarroll-mocha/o/cromwell%2Fcromwell-executions%2Fmocha%2F86d47e9a-5745-4ec0-b4eb-0164f073e5f4%2Fcall-idat2gtc%2Fshard-73%2Frc?alt=media"
+      ),
 
       // Prove that `isRetryable` successfully recurses to unwrap the lowest-level Throwable
-      new IOException(new Throwable("Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 500 Internal Server Error Backend Error")),
-      new IOException(new Throwable("Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 503 Service Unavailable Backend Error")),
-
-      new IOException("Some other text. Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 503 Service Unavailable"),
-      new IOException("Some other text. Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 504 Gateway Timeout"),
+      new IOException(
+        new Throwable(
+          "Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 500 Internal Server Error Backend Error"
+        )
+      ),
+      new IOException(
+        new Throwable(
+          "Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 503 Service Unavailable Backend Error"
+        )
+      ),
+      new IOException(
+        "Some other text. Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 503 Service Unavailable"
+      ),
+      new IOException(
+        "Some other text. Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-4688/rc: 504 Gateway Timeout"
+      )
     )
 
-    retryables foreach { e => withClue(e) {
-      RetryableRequestSupport.isRetryable(e) shouldBe true }
+    retryables foreach { e =>
+      withClue(e) {
+        RetryableRequestSupport.isRetryable(e) shouldBe true
+      }
     }
   }
 
@@ -288,7 +310,9 @@ class IoActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with I
       new IOException("502 HTTP Status Code"),
       new Exception("502 HTTP Status Code"),
       new Exception("5xx HTTP Status Code"),
-      new IOException("Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-500/rc: 404 File Not Found")
+      new IOException(
+        "Could not read from gs://fc-secure-<snip>/JointGenotyping/<snip>/call-HardFilterAndMakeSitesOnlyVcf/shard-500/rc: 404 File Not Found"
+      )
     )
 
     nonRetryables foreach { RetryableRequestSupport.isRetryable(_) shouldBe false }
diff --git a/engine/src/test/scala/cromwell/engine/io/gcs/GcsBatchCommandContextSpec.scala b/engine/src/test/scala/cromwell/engine/io/gcs/GcsBatchCommandContextSpec.scala
index a7bf613efa1..ac19b4d8ad1 100644
--- a/engine/src/test/scala/cromwell/engine/io/gcs/GcsBatchCommandContextSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/io/gcs/GcsBatchCommandContextSpec.scala
@@ -13,7 +13,11 @@ import org.scalatest.matchers.should.Matchers
 import scala.util.{Failure, Success}
 
 class GcsBatchCommandContextSpec
-  extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with Eventually with BeforeAndAfter {
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with Eventually
+    with BeforeAndAfter {
   behavior of "GcsBatchCommandContext"
 
   it should "handle exceptions in success handlers" in {
@@ -34,7 +38,10 @@ class GcsBatchCommandContextSpec
 
     exceptionSpewingCommandContext.promise.future.value.get match {
       case Success(oops) => fail(s"Should not have produced a success: $oops")
-      case Failure(error) => error.getMessage should be("Error processing IO response in onSuccessCallback: Ill behaved code that throws in mapGoogleResponse")
+      case Failure(error) =>
+        error.getMessage should be(
+          "Error processing IO response in onSuccessCallback: Ill behaved code that throws in mapGoogleResponse"
+        )
     }
   }
 
@@ -48,7 +55,7 @@ class GcsBatchCommandContextSpec
     exceptionSpewingCommandContext.promise.isCompleted should be(false)
 
     // Simulate a failure response from an underlying IO operation:
-    exceptionSpewingCommandContext.callback.onFailure(new GoogleJsonError { }, new HttpHeaders())
+    exceptionSpewingCommandContext.callback.onFailure(new GoogleJsonError {}, new HttpHeaders())
 
     eventually {
       exceptionSpewingCommandContext.promise.isCompleted should be(true)
@@ -56,7 +63,10 @@ class GcsBatchCommandContextSpec
 
     exceptionSpewingCommandContext.promise.future.value.get match {
       case Success(oops) => fail(s"Should not have produced a success: $oops")
-      case Failure(error) => error.getMessage should be("Error processing IO response in onFailureCallback: Ill behaved code that throws in onFailure")
+      case Failure(error) =>
+        error.getMessage should be(
+          "Error processing IO response in onFailureCallback: Ill behaved code that throws in onFailure"
+        )
     }
   }
 
@@ -78,7 +88,10 @@ class GcsBatchCommandContextSpec
 
     errorReturningCommandContext.promise.future.value.get match {
       case Success(oops) => fail(s"Should not have produced a success: $oops")
-      case Failure(error) => error.getMessage should be("Unexpected result in successful Google API call:\nWell behaved code that returns an error in mapGoogleResponse")
+      case Failure(error) =>
+        error.getMessage should be(
+          "Unexpected result in successful Google API call:\nWell behaved code that returns an error in mapGoogleResponse"
+        )
     }
   }
 }
diff --git a/engine/src/test/scala/cromwell/engine/io/gcs/GcsBatchFlowSpec.scala b/engine/src/test/scala/cromwell/engine/io/gcs/GcsBatchFlowSpec.scala
index c133e7618c0..9b0a99752fe 100644
--- a/engine/src/test/scala/cromwell/engine/io/gcs/GcsBatchFlowSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/io/gcs/GcsBatchFlowSpec.scala
@@ -17,14 +17,20 @@ import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContextExecutor, Future}
 import scala.language.postfixOps
 
-class GcsBatchFlowSpec extends TestKitSuite with AnyFlatSpecLike with CromwellTimeoutSpec with Matchers
-  with PrivateMethodTester with MockSugar {
+class GcsBatchFlowSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with CromwellTimeoutSpec
+    with Matchers
+    with PrivateMethodTester
+    with MockSugar {
 
   private val NoopOnRetry: IoCommandContext[_] => Throwable => Unit = _ => _ => ()
   private val NoopOnBackpressure: Option[Double] => Unit = _ => ()
 
   "GcsBatchFlow" should "know what read forbidden bucket failures look like" in {
-    val ErrorTemplate = "foo@bar.iam.gserviceaccount.com does not have storage.objects.%s access to %s/three_step/f0000000-baaa-f000-baaa-f00000000000/call-foo/foo.log"
+    val ErrorTemplate =
+      "foo@bar.iam.gserviceaccount.com does not have storage.objects.%s access to %s/three_step/f0000000-baaa-f000-baaa-f00000000000/call-foo/foo.log"
     val UnreadableBucketName = "unreadable-bucket"
 
     val objectReadOperationNames = Set(
@@ -41,7 +47,9 @@ class GcsBatchFlowSpec extends TestKitSuite with AnyFlatSpecLike with CromwellTi
       } yield new StorageException(code, String.format(ErrorTemplate, op, UnreadableBucketName))
     }
     // Can't flatMap this since any Nones would just be squashed out.
-    storageExceptions(objectReadOperationNames) map (_.getMessage) map GcsBatchFlow.getReadForbiddenBucket map { _.get } shouldBe Set(UnreadableBucketName)
+    storageExceptions(objectReadOperationNames) map (_.getMessage) map GcsBatchFlow.getReadForbiddenBucket map {
+      _.get
+    } shouldBe Set(UnreadableBucketName)
 
     // A sampling of write operations, not an exhaustive list.
     val objectWriteOperationNames = Set(
@@ -49,9 +57,13 @@ class GcsBatchFlowSpec extends TestKitSuite with AnyFlatSpecLike with CromwellTi
       "delete",
       "insert"
     )
-    storageExceptions(objectWriteOperationNames) map (_.getMessage) flatMap GcsBatchFlow.getReadForbiddenBucket shouldBe Set.empty
+    storageExceptions(
+      objectWriteOperationNames
+    ) map (_.getMessage) flatMap GcsBatchFlow.getReadForbiddenBucket shouldBe Set.empty
 
-    Set(new RuntimeException("random exception")) map (_.getMessage) flatMap GcsBatchFlow.getReadForbiddenBucket shouldBe Set.empty
+    Set(
+      new RuntimeException("random exception")
+    ) map (_.getMessage) flatMap GcsBatchFlow.getReadForbiddenBucket shouldBe Set.empty
   }
 
   "GcsBatchFlow" should "not throw unhandled exception and kill the thread when trying to recover from unretryable exception with null error message" in {
@@ -63,19 +75,23 @@ class GcsBatchFlowSpec extends TestKitSuite with AnyFlatSpecLike with CromwellTi
       onRetry = NoopOnRetry,
       onBackpressure = NoopOnBackpressure,
       applicationName = "testAppName",
-      backpressureStaleness = 5 seconds)
+      backpressureStaleness = 5 seconds
+    )
 
     val mockGcsPath = GcsPath(
       nioPath = CloudStorageFileSystem.forBucket("bucket").getPath("test"),
       apiStorage = mock[com.google.api.services.storage.Storage],
       cloudStorage = mock[com.google.cloud.storage.Storage],
-      projectId = "GcsBatchFlowSpec-project",
+      projectId = "GcsBatchFlowSpec-project"
     )
-    val gcsBatchCommandContext = GcsBatchCommandContext(GcsBatchCrc32Command.forPath(mockGcsPath).get, TestProbe().ref, 5)
-    val recoverCommandPrivateMethod = PrivateMethod[PartialFunction[Throwable, Future[GcsBatchResponse[_]]]](Symbol("recoverCommand"))
+    val gcsBatchCommandContext =
+      GcsBatchCommandContext(GcsBatchCrc32Command.forPath(mockGcsPath).get, TestProbe().ref, 5)
+    val recoverCommandPrivateMethod =
+      PrivateMethod[PartialFunction[Throwable, Future[GcsBatchResponse[_]]]](Symbol("recoverCommand"))
     val partialFuncAcceptingThrowable = gcsBatchFlow invokePrivate recoverCommandPrivateMethod(gcsBatchCommandContext)
 
-    val futureRes = partialFuncAcceptingThrowable(new NullPointerException(null)) // no unhandled exceptions should be thrown here
+    val futureRes =
+      partialFuncAcceptingThrowable(new NullPointerException(null)) // no unhandled exceptions should be thrown here
     futureRes.isCompleted shouldBe true
   }
 }
diff --git a/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala b/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
index 41c121da0cc..5859684e756 100644
--- a/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/io/nio/NioFlowSpec.scala
@@ -38,12 +38,12 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
   private val NoopOnRetry: IoCommandContext[_] => Throwable => Unit = _ => _ => ()
   private val NoopOnBackpressure: Option[Double] => Unit = _ => ()
 
-  private val flow = new NioFlow(
-    parallelism = 1,
-    onRetryCallback = NoopOnRetry,
-    onBackpressure = NoopOnBackpressure,
-    numberOfAttempts = 3,
-    commandBackpressureStaleness = 5 seconds)(system).flow
+  private val flow = new NioFlow(parallelism = 1,
+                                 onRetryCallback = NoopOnRetry,
+                                 onBackpressure = NoopOnBackpressure,
+                                 numberOfAttempts = 3,
+                                 commandBackpressureStaleness = 5 seconds
+  )(system).flow
 
   implicit val materializer: ActorMaterializer = ActorMaterializer()
   private val replyTo = mock[ActorRef]
@@ -106,7 +106,7 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     val stream = testSource.via(flow).toMat(readSink)(Keep.right)
     stream.run() map {
       case (IoFailure(_, EnhancedCromwellIoException(_, receivedException)), _) =>
-        receivedException.getMessage should include ("UnknownHost")
+        receivedException.getMessage should include("UnknownHost")
       case (ack, _) => fail(s"size should have failed with UnknownHost but didn't:\n$ack\n\n")
     }
   }
@@ -120,7 +120,7 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     val stream = testSource.via(flow).toMat(readSink)(Keep.right)
     stream.run() map {
       case (IoFailure(_, EnhancedCromwellIoException(_, receivedException)), _) =>
-        receivedException.getMessage should include ("Couldn't fetch size")
+        receivedException.getMessage should include("Couldn't fetch size")
       case (ack, _) => fail(s"size should have failed but didn't:\n$ack\n\n")
     }
   }
@@ -135,7 +135,8 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     val stream = testSource.via(flow).toMat(readSink)(Keep.right)
 
     stream.run() map {
-      case (success: IoSuccess[_], _) => assert(success.result.asInstanceOf[String] == "5d41402abc4b2a76b9719d911017c592")
+      case (success: IoSuccess[_], _) =>
+        assert(success.result.asInstanceOf[String] == "5d41402abc4b2a76b9719d911017c592")
       case _ => fail("hash returned an unexpected message")
     }
   }
@@ -177,16 +178,19 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
   it should "fail if DrsPath hash doesn't match checksum" in {
     val testPath = mock[DrsPath]
     when(testPath.limitFileContent(any[Option[Int]], any[Boolean])(any[ExecutionContext])).thenReturn("hello".getBytes)
-    when(testPath.getFileHash).thenReturn(FileHash(HashType.Crc32c, "boom")) // correct Base64-encoded crc32c checksum is "9a71bb4c"
+    when(testPath.getFileHash).thenReturn(
+      FileHash(HashType.Crc32c, "boom")
+    ) // correct Base64-encoded crc32c checksum is "9a71bb4c"
 
-    val context = DefaultCommandContext(contentAsStringCommand(testPath, Option(100), failOnOverflow = true).get, replyTo)
+    val context =
+      DefaultCommandContext(contentAsStringCommand(testPath, Option(100), failOnOverflow = true).get, replyTo)
     val testSource = Source.single(context)
 
     val stream = testSource.via(flow).toMat(readSink)(Keep.right)
 
     stream.run() map {
       case (IoFailure(_, EnhancedCromwellIoException(_, receivedException)), _) =>
-        receivedException.getMessage should include ("Failed checksum")
+        receivedException.getMessage should include("Failed checksum")
       case (ack, _) => fail(s"read returned an unexpected message:\n$ack\n\n")
     }
   }
@@ -202,7 +206,8 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
       .thenReturn(FileHash(HashType.Crc32c, "boom"))
       .thenReturn(FileHash(HashType.Crc32c, "9a71bb4c"))
 
-    val context = DefaultCommandContext(contentAsStringCommand(testPath, Option(100), failOnOverflow = true).get, replyTo)
+    val context =
+      DefaultCommandContext(contentAsStringCommand(testPath, Option(100), failOnOverflow = true).get, replyTo)
     val testSource = Source.single(context)
 
     val stream = testSource.via(flow).toMat(readSink)(Keep.right)
@@ -225,7 +230,8 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
     when(testPath.md5HexString)
       .thenReturn(Success(None))
 
-    val context = DefaultCommandContext(contentAsStringCommand(testPath, Option(100), failOnOverflow = true).get, replyTo)
+    val context =
+      DefaultCommandContext(contentAsStringCommand(testPath, Option(100), failOnOverflow = true).get, replyTo)
     val testSource = Source.single(context)
 
     val stream = testSource.via(flow).toMat(readSink)(Keep.right)
@@ -290,7 +296,7 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
   it should "delete a Nio path with swallowIoExceptions true" in {
     val testPath = DefaultPathBuilder.build("/this/does/not/exist").get
 
-    //noinspection RedundantDefaultArgument
+    // noinspection RedundantDefaultArgument
     val context = DefaultCommandContext(deleteCommand(testPath, swallowIoExceptions = true).get, replyTo)
 
     val testSource = Source.single(context)
@@ -328,21 +334,20 @@ class NioFlowSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers with
 
     val testSource = Source.single(context)
 
-    val customFlow = new NioFlow(
-      parallelism = 1,
-      onRetryCallback = NoopOnRetry,
-      onBackpressure = NoopOnBackpressure,
-      numberOfAttempts = 3,
-      commandBackpressureStaleness = 5 seconds)(system) {
+    val customFlow = new NioFlow(parallelism = 1,
+                                 onRetryCallback = NoopOnRetry,
+                                 onBackpressure = NoopOnBackpressure,
+                                 numberOfAttempts = 3,
+                                 commandBackpressureStaleness = 5 seconds
+    )(system) {
 
       private var tries = 0
-      override def handleSingleCommand(ioSingleCommand: IoCommand[_]): IO[IoSuccess[_]] = {
+      override def handleSingleCommand(ioSingleCommand: IoCommand[_]): IO[IoSuccess[_]] =
         IO {
           tries += 1
           if (tries < 3) throw new StorageException(500, "message")
           else IoSuccess(ioSingleCommand, "content")
         }
-       }
     }.flow
 
     val stream = testSource.via(customFlow).toMat(readSink)(Keep.right)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/WorkflowDockerLookupActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/WorkflowDockerLookupActorSpec.scala
index 1d2652b83f1..667861801a4 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/WorkflowDockerLookupActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/WorkflowDockerLookupActorSpec.scala
@@ -9,9 +9,14 @@ import cromwell.core.retry.SimpleExponentialBackoff
 import cromwell.core.{TestKitSuite, WorkflowId}
 import cromwell.database.slick.EngineSlickDatabase
 import cromwell.database.sql.tables.DockerHashStoreEntry
-import cromwell.docker.DockerInfoActor.{DockerInfoFailedResponse, DockerInfoSuccessResponse, DockerInformation}
+import cromwell.docker.DockerInfoActor.{DockerInfoFailedResponse, DockerInformation, DockerInfoSuccessResponse}
 import cromwell.docker.{DockerHashResult, DockerImageIdentifier, DockerImageIdentifierWithoutHash, DockerInfoRequest}
-import cromwell.engine.workflow.WorkflowDockerLookupActor.{DockerHashActorTimeout, Running, WorkflowDockerLookupFailure, WorkflowDockerTerminalFailure}
+import cromwell.engine.workflow.WorkflowDockerLookupActor.{
+  DockerHashActorTimeout,
+  Running,
+  WorkflowDockerLookupFailure,
+  WorkflowDockerTerminalFailure
+}
 import cromwell.engine.workflow.WorkflowDockerLookupActorSpec._
 import cromwell.engine.workflow.workflowstore.{StartableState, Submitted}
 import cromwell.services.EngineServicesStore
@@ -25,9 +30,8 @@ import scala.concurrent.{ExecutionContext, Future}
 import scala.language.postfixOps
 import scala.util.control.NoStackTrace
 
-
 class WorkflowDockerLookupActorSpec
-  extends TestKitSuite
+    extends TestKitSuite
     with AnyFlatSpecLike
     with Matchers
     with ImplicitSender
@@ -55,11 +59,11 @@ class WorkflowDockerLookupActorSpec
   }
 
   it should "wait and resubmit the docker request when it gets a backpressure message" in {
-    val backoff = SimpleExponentialBackoff(2.seconds, 10.minutes, 2D)
+    val backoff = SimpleExponentialBackoff(2.seconds, 10.minutes, 2d)
 
     val lookupActor = TestActorRef(
       Props(new TestWorkflowDockerLookupActor(workflowId, dockerHashingActor.ref, Submitted, backoff)),
-      dockerSendingActor.ref,
+      dockerSendingActor.ref
     )
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
 
@@ -75,7 +79,8 @@ class WorkflowDockerLookupActorSpec
       Future.successful(())
     }
 
-    val lookupActor = TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = false, db))
+    val lookupActor =
+      TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = false, db))
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
 
     // The WorkflowDockerLookupActor should not have the hash for this tag yet and will need to query the dockerHashingActor.
@@ -94,7 +99,8 @@ class WorkflowDockerLookupActorSpec
   }
 
   it should "soldier on after docker hashing actor timeouts" in {
-    val lookupActor = TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = false))
+    val lookupActor =
+      TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = false))
 
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
     lookupActor.tell(OlderRequest, dockerSendingActor.ref)
@@ -131,7 +137,13 @@ class WorkflowDockerLookupActorSpec
 
   // BA-6495
   it should "not fail and enter terminal state when response for certain image id from DockerHashingActor arrived after the self-imposed timeout" in {
-    val lookupActor = TestFSMRef(new WorkflowDockerLookupActor(workflowId, dockerHashingActor.ref, isRestart = false, EngineServicesStore.engineDatabaseInterface))
+    val lookupActor = TestFSMRef(
+      new WorkflowDockerLookupActor(workflowId,
+                                    dockerHashingActor.ref,
+                                    isRestart = false,
+                                    EngineServicesStore.engineDatabaseInterface
+      )
+    )
 
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
 
@@ -142,7 +154,8 @@ class WorkflowDockerLookupActorSpec
     // WorkflowDockerLookupActor actually sends DockerHashActorTimeout to itself
     lookupActor.tell(timeout, lookupActor)
 
-    val failedRequest: WorkflowDockerLookupFailure = dockerSendingActor.receiveOne(2 seconds).asInstanceOf[WorkflowDockerLookupFailure]
+    val failedRequest: WorkflowDockerLookupFailure =
+      dockerSendingActor.receiveOne(2 seconds).asInstanceOf[WorkflowDockerLookupFailure]
     failedRequest.request shouldBe LatestRequest
 
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
@@ -160,7 +173,8 @@ class WorkflowDockerLookupActorSpec
   }
 
   it should "respond appropriately to docker hash lookup failures" in {
-    val lookupActor = TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = false))
+    val lookupActor =
+      TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = false))
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
     lookupActor.tell(OlderRequest, dockerSendingActor.ref)
 
@@ -176,7 +190,9 @@ class WorkflowDockerLookupActorSpec
     val mixedResponses = results collect {
       case msg: DockerInfoSuccessResponse => msg
       // Scoop out the request here since we can't match the exception on the whole message.
-      case msg: WorkflowDockerLookupFailure if msg.reason.getMessage == "Failed to get docker hash for ubuntu:older Lookup failed" => msg.request
+      case msg: WorkflowDockerLookupFailure
+          if msg.reason.getMessage == "Failed to get docker hash for ubuntu:older Lookup failed" =>
+        msg.request
     }
 
     Set(LatestSuccessResponse, OlderRequest) should equal(mixedResponses)
@@ -190,11 +206,11 @@ class WorkflowDockerLookupActorSpec
 
   it should "reuse previously looked up hashes following a restart" in {
     val db = dbWithQuery {
-      Future.successful(
-        Seq(LatestStoreEntry(workflowId), OlderStoreEntry(workflowId)))
+      Future.successful(Seq(LatestStoreEntry(workflowId), OlderStoreEntry(workflowId)))
     }
 
-    val lookupActor = TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = true, db))
+    val lookupActor =
+      TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = true, db))
 
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
     lookupActor.tell(OlderRequest, dockerSendingActor.ref)
@@ -209,7 +225,8 @@ class WorkflowDockerLookupActorSpec
 
   it should "not try to look up hashes if not restarting" in {
     val db = dbWithWrite(Future.successful(()))
-    val lookupActor = TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = false, db))
+    val lookupActor =
+      TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = false, db))
 
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
     lookupActor.tell(OlderRequest, dockerSendingActor.ref)
@@ -231,7 +248,8 @@ class WorkflowDockerLookupActorSpec
       if (numWrites == 1) Future.failed(new RuntimeException("Fake exception from a test.")) else Future.successful(())
     }
 
-    val lookupActor = TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = false, db))
+    val lookupActor =
+      TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = false, db))
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
 
     // The WorkflowDockerLookupActor should not have the hash for this tag yet and will need to query the dockerHashingActor.
@@ -256,7 +274,8 @@ class WorkflowDockerLookupActorSpec
       Future.failed(new Exception("Don't worry this is just a dummy failure in a test") with NoStackTrace)
     }
 
-    val lookupActor = TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = true, db))
+    val lookupActor =
+      TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = true, db))
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
 
     dockerHashingActor.expectNoMessage()
@@ -267,14 +286,17 @@ class WorkflowDockerLookupActorSpec
   it should "emit a terminal failure message if unable to parse hashes read from the database on restart" in {
     val db = dbWithQuery {
       numReads = numReads + 1
-      Future.successful(Seq(
-        DockerHashStoreEntry(workflowId.toString, Latest, "md5:AAAAA", None),
-        // missing the "algorithm:" preceding the hash value so this should fail parsing.
-        DockerHashStoreEntry(workflowId.toString, Older, "BBBBB", None)
-      ))
+      Future.successful(
+        Seq(
+          DockerHashStoreEntry(workflowId.toString, Latest, "md5:AAAAA", None),
+          // missing the "algorithm:" preceding the hash value so this should fail parsing.
+          DockerHashStoreEntry(workflowId.toString, Older, "BBBBB", None)
+        )
+      )
     }
 
-    val lookupActor = TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = true, db))
+    val lookupActor =
+      TestActorRef(WorkflowDockerLookupActor.props(workflowId, dockerHashingActor.ref, isRestart = true, db))
     lookupActor.tell(LatestRequest, dockerSendingActor.ref)
 
     dockerHashingActor.expectNoMessage()
@@ -282,25 +304,26 @@ class WorkflowDockerLookupActorSpec
     numReads should equal(1)
   }
 
-  def dbWithWrite(writeFn: => Future[Unit]): EngineSlickDatabase = {
+  def dbWithWrite(writeFn: => Future[Unit]): EngineSlickDatabase =
     databaseInterface(write = _ => writeFn)
-  }
 
-  def dbWithQuery(queryFn: => Future[Seq[DockerHashStoreEntry]]): EngineSlickDatabase = {
+  def dbWithQuery(queryFn: => Future[Seq[DockerHashStoreEntry]]): EngineSlickDatabase =
     databaseInterface(query = _ => queryFn)
-  }
 
   def databaseInterface(query: String => Future[Seq[DockerHashStoreEntry]] = abjectFailure,
-                        write: DockerHashStoreEntry => Future[Unit] = abjectFailure): EngineSlickDatabase = {
+                        write: DockerHashStoreEntry => Future[Unit] = abjectFailure
+  ): EngineSlickDatabase =
     new EngineSlickDatabase(DatabaseConfig) {
-      override def queryDockerHashStoreEntries(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Future[Seq[DockerHashStoreEntry]] = query(workflowExecutionUuid)
+      override def queryDockerHashStoreEntries(workflowExecutionUuid: String)(implicit
+        ec: ExecutionContext
+      ): Future[Seq[DockerHashStoreEntry]] = query(workflowExecutionUuid)
 
-      override def addDockerHashStoreEntry(dockerHashStoreEntry: DockerHashStoreEntry)(implicit ec: ExecutionContext): Future[Unit] = write(dockerHashStoreEntry)
+      override def addDockerHashStoreEntry(dockerHashStoreEntry: DockerHashStoreEntry)(implicit
+        ec: ExecutionContext
+      ): Future[Unit] = write(dockerHashStoreEntry)
     }.initialized(EngineServicesStore.EngineLiquibaseSettings)
-  }
 }
 
-
 object WorkflowDockerLookupActorSpec {
   val Latest = "ubuntu:latest"
   val Older = "ubuntu:older"
@@ -313,8 +336,10 @@ object WorkflowDockerLookupActorSpec {
   val LatestRequest: DockerInfoRequest = DockerInfoRequest(LatestImageId)
   val OlderRequest: DockerInfoRequest = DockerInfoRequest(OlderImageId)
 
-  def LatestStoreEntry(workflowId: WorkflowId): DockerHashStoreEntry = DockerHashStoreEntry(workflowId.toString, Latest, "md5:AAAAAAAA", None)
-  def OlderStoreEntry(workflowId: WorkflowId): DockerHashStoreEntry = DockerHashStoreEntry(workflowId.toString, Older, "md5:BBBBBBBB", None)
+  def LatestStoreEntry(workflowId: WorkflowId): DockerHashStoreEntry =
+    DockerHashStoreEntry(workflowId.toString, Latest, "md5:AAAAAAAA", None)
+  def OlderStoreEntry(workflowId: WorkflowId): DockerHashStoreEntry =
+    DockerHashStoreEntry(workflowId.toString, Older, "md5:BBBBBBBB", None)
 
   val LatestSuccessResponse: DockerInfoSuccessResponse =
     DockerInfoSuccessResponse(DockerInformation(DockerHashResult("md5", "AAAAAAAA"), None), LatestRequest)
@@ -325,12 +350,15 @@ object WorkflowDockerLookupActorSpec {
 
   def abjectFailure[A, B]: A => Future[B] = _ => Future.failed(new RuntimeException("Should not be called!"))
 
-  class TestWorkflowDockerLookupActor(workflowId: WorkflowId, dockerHashingActor: ActorRef, startState: StartableState, backoff: Backoff)
-    extends WorkflowDockerLookupActor(
-      workflowId,
-      dockerHashingActor,
-      startState.restarted,
-      EngineServicesStore.engineDatabaseInterface) {
+  class TestWorkflowDockerLookupActor(workflowId: WorkflowId,
+                                      dockerHashingActor: ActorRef,
+                                      startState: StartableState,
+                                      backoff: Backoff
+  ) extends WorkflowDockerLookupActor(workflowId,
+                                      dockerHashingActor,
+                                      startState.restarted,
+                                      EngineServicesStore.engineDatabaseInterface
+      ) {
     override protected def initialBackoff(): Backoff = backoff
   }
 }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
index 095721569e7..b5a46729b24 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala
@@ -8,26 +8,28 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 
 import scala.util.{Failure, Success, Try}
 
-class ValidatingCachingConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
+class ValidatingCachingConfigSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks {
 
-    it should "run config tests" in {
-      val cases = Table[String, Any](
-        ("config"                 , "exceptionMessage"                                                              ),
-        ("enabled = not-a-boolean", "String: 1: enabled has type STRING rather than BOOLEAN"                        ),
-        ("enabled = true"         , true                                                                            ),
-        ("enabled = false"        , false                                                                           ),
-        ("enabled = 1"            , "String: 1: enabled has type NUMBER rather than BOOLEAN"                        ),
-        (""                       , "String: 1: No configuration setting found for key 'enabled'"                   )
-      )
+  it should "run config tests" in {
+    val cases = Table[String, Any](
+      ("config", "exceptionMessage"),
+      ("enabled = not-a-boolean", "String: 1: enabled has type STRING rather than BOOLEAN"),
+      ("enabled = true", true),
+      ("enabled = false", false),
+      ("enabled = 1", "String: 1: enabled has type NUMBER rather than BOOLEAN"),
+      ("", "String: 1: No configuration setting found for key 'enabled'")
+    )
 
-      forEvery(cases) { (config, expected) =>
-        val rootConfig = ConfigFactory.parseString(config)
-        Try(rootConfig.getBoolean("enabled")) match {
-          case Success(what) => what shouldBe a [java.lang.Boolean]
-          case Failure(exception) => exception.getMessage should be (expected)
-        }
+    forEvery(cases) { (config, expected) =>
+      val rootConfig = ConfigFactory.parseString(config)
+      Try(rootConfig.getBoolean("enabled")) match {
+        case Success(what) => what shouldBe a[java.lang.Boolean]
+        case Failure(exception) => exception.getMessage should be(expected)
       }
     }
   }
-
-
+}
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCallCachingModeSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCallCachingModeSpec.scala
index e7dc1aeaa4f..f2a4aafa6c7 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCallCachingModeSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCallCachingModeSpec.scala
@@ -12,7 +12,11 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 
 import scala.util.{Success, Try}
 
-class ValidatingCallCachingModeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
+class ValidatingCallCachingModeSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks {
 
   def makeOptions(writeOpt: Option[Boolean], readOpt: Option[Boolean]) = {
     val writeValue = writeOpt map { v => s""""write_to_cache": $v""" }
@@ -29,54 +33,54 @@ class ValidatingCallCachingModeSpec extends AnyFlatSpec with CromwellTimeoutSpec
   val allCombinations = (for {
     writeOption <- options
     readOption <- options
-  } yield (makeOptions(writeOption, readOption))).toSet
+  } yield makeOptions(writeOption, readOption)).toSet
 
   // writeCache is ON when config is ON and write_to_cache is None or true
   val writeCacheOnCombinations = (for {
     writeOption <- options if writeOption.isEmpty || writeOption.get
     readOption <- options
-  } yield (makeOptions(writeOption, readOption))).toSet
+  } yield makeOptions(writeOption, readOption)).toSet
 
   // readCache is ON when config is ON and read_from_cache is None or true
   val readCacheOnCombinations = (for {
     writeOption <- options
     readOption <- options if readOption.isEmpty || readOption.get
-  } yield (makeOptions(writeOption, readOption))).toSet
+  } yield makeOptions(writeOption, readOption)).toSet
 
   val writeCacheOffCombinations = allCombinations -- writeCacheOnCombinations
   val readCacheOffCombinations = allCombinations -- readCacheOnCombinations
 
-  validateCallCachingMode(
-    "write cache on options",
-    writeCacheOnCombinations,
-    callCachingEnabled,
-    invalidBadCaсheResults) { _.writeToCache should be(true) }
-  validateCallCachingMode(
-    "read cache on options",
-    readCacheOnCombinations,
-    callCachingEnabled,
-    invalidBadCaсheResults) { _.readFromCache should be(true) }
-  validateCallCachingMode(
-    "write cache off options",
-    writeCacheOffCombinations,
-    callCachingEnabled,
-    invalidBadCaсheResults) { _.writeToCache should be(false) }
-  validateCallCachingMode(
-    "read cache off options",
-    readCacheOffCombinations,
-    callCachingEnabled,
-    invalidBadCaсheResults) { _.readFromCache should be(false) }
+  validateCallCachingMode("write cache on options",
+                          writeCacheOnCombinations,
+                          callCachingEnabled,
+                          invalidBadCaсheResults
+  )(_.writeToCache should be(true))
+  validateCallCachingMode("read cache on options", readCacheOnCombinations, callCachingEnabled, invalidBadCaсheResults)(
+    _.readFromCache should be(true)
+  )
+  validateCallCachingMode("write cache off options",
+                          writeCacheOffCombinations,
+                          callCachingEnabled,
+                          invalidBadCaсheResults
+  )(_.writeToCache should be(false))
+  validateCallCachingMode("read cache off options",
+                          readCacheOffCombinations,
+                          callCachingEnabled,
+                          invalidBadCaсheResults
+  )(_.readFromCache should be(false))
 
   private def validateCallCachingMode(testName: String,
                                       wfOptions: Set[Try[WorkflowOptions]],
                                       callCachingEnabled: Boolean,
-                                      invalidBadCacheResults: Boolean)
-                                      (verificationFunction: CallCachingMode => Assertion): Unit = {
+                                      invalidBadCacheResults: Boolean
+  )(verificationFunction: CallCachingMode => Assertion): Unit =
     it should s"correctly identify $testName" in {
-      wfOptions foreach  {
+      wfOptions foreach {
         case Success(wfOptions) =>
           MaterializeWorkflowDescriptorActor.validateCallCachingMode(wfOptions,
-            callCachingEnabled, invalidBadCacheResults) match {
+                                                                     callCachingEnabled,
+                                                                     invalidBadCacheResults
+          ) match {
             case Valid(activity) => verificationFunction(activity)
             case Invalid(errors) =>
               val errorsList = errors.toList.mkString(", ")
@@ -85,5 +89,4 @@ class ValidatingCallCachingModeSpec extends AnyFlatSpec with CromwellTimeoutSpec
         case x => fail(s"Unexpected test tuple: $x")
       }
     }
-  }
 }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/deletion/DeleteWorkflowFilesActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/deletion/DeleteWorkflowFilesActorSpec.scala
index 1d117e0a8bc..d1759afef9d 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/deletion/DeleteWorkflowFilesActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/deletion/DeleteWorkflowFilesActorSpec.scala
@@ -12,7 +12,10 @@ import cromwell.core.path.Path
 import cromwell.core.path.PathFactory.PathBuilders
 import cromwell.core.retry.SimpleExponentialBackoff
 import cromwell.engine.io.IoAttempts.EnhancedCromwellIoException
-import cromwell.engine.workflow.lifecycle.deletion.DeleteWorkflowFilesActor.{StartWorkflowFilesDeletion, WaitingForIoResponses}
+import cromwell.engine.workflow.lifecycle.deletion.DeleteWorkflowFilesActor.{
+  StartWorkflowFilesDeletion,
+  WaitingForIoResponses
+}
 import cromwell.filesystems.gcs.batch.{GcsBatchCommandBuilder, GcsBatchDeleteCommand}
 import cromwell.filesystems.gcs.{GcsPath, GcsPathBuilder, MockGcsPathBuilder}
 import cromwell.services.metadata.MetadataService.PutMetadataAction
@@ -31,10 +34,7 @@ import scala.concurrent.duration._
 import scala.util.control.NoStackTrace
 import scala.util.{Failure, Try}
 
-class DeleteWorkflowFilesActorSpec extends TestKitSuite
-  with AnyFlatSpecLike
-  with Matchers
-  with BeforeAndAfter {
+class DeleteWorkflowFilesActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with BeforeAndAfter {
 
   val mockPathBuilder: GcsPathBuilder = MockGcsPathBuilder.instance
   val mockPathBuilders = List(mockPathBuilder)
@@ -50,7 +50,10 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
   var rootWorkflowRoots: Set[Path] = _
   var allOutputs: CallOutputs = _
   var finalOutputs: CallOutputs = _
-  var testDeleteWorkflowFilesActor: TestFSMRef[DeleteWorkflowFilesActor.DeleteWorkflowFilesActorState, DeleteWorkflowFilesActor.DeleteWorkflowFilesActorStateData, MockDeleteWorkflowFilesActor] = _
+  var testDeleteWorkflowFilesActor: TestFSMRef[DeleteWorkflowFilesActor.DeleteWorkflowFilesActorState,
+                                               DeleteWorkflowFilesActor.DeleteWorkflowFilesActorStateData,
+                                               MockDeleteWorkflowFilesActor
+  ] = _
   var gcsFilePath: GcsPath = _
 
   before {
@@ -60,44 +63,103 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
     rootWorkflowRoots = Set[Path](mockPathBuilder.build(rootWorkflowExecutionDir).get)
     testProbe = TestProbe(s"test-probe-$rootWorkflowId")
 
-    allOutputs = CallOutputs(Map(
-      GraphNodeOutputPort(WomIdentifier(LocalName("main_output"),FullyQualifiedName("main_workflow.main_output")), WomSingleFileType, null)
-        -> WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"),
-      ExpressionBasedOutputPort(WomIdentifier(LocalName("first_task.first_task_output_2"),FullyQualifiedName("first_sub_workflow.first_task.first_task_output_2")), WomSingleFileType, null, null)
-        -> WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file2.txt"),
-      GraphNodeOutputPort(WomIdentifier(LocalName("first_output_file"),FullyQualifiedName("first_sub_workflow.first_output_file")), WomSingleFileType, null)
-        -> WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"),
-      ExpressionBasedOutputPort(WomIdentifier(LocalName("first_task.first_task_output_1"),FullyQualifiedName("first_sub_workflow.first_task.first_task_output_1")), WomSingleFileType, null, null)
-        -> WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"),
-      GraphNodeOutputPort(WomIdentifier(LocalName("second_output_file"),FullyQualifiedName("first_sub_workflow.second_output_file")), WomSingleFileType, null)
-        -> WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file2.txt")
-    ))
-    finalOutputs = CallOutputs(Map(
-      GraphNodeOutputPort(WomIdentifier(LocalName("main_output"),FullyQualifiedName("main_workflow.main_output")), WomSingleFileType, null)
-        -> WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file2.txt")
-    ))
-
-    testDeleteWorkflowFilesActor = TestFSMRef(new MockDeleteWorkflowFilesActor(rootWorkflowId, emptyWorkflowIdSet, rootWorkflowRoots, finalOutputs, allOutputs, mockPathBuilders, serviceRegistryActor.ref, ioActor.ref))
+    allOutputs = CallOutputs(
+      Map(
+        GraphNodeOutputPort(WomIdentifier(LocalName("main_output"), FullyQualifiedName("main_workflow.main_output")),
+                            WomSingleFileType,
+                            null
+        )
+          -> WomSingleFile(
+            s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"
+          ),
+        ExpressionBasedOutputPort(
+          WomIdentifier(LocalName("first_task.first_task_output_2"),
+                        FullyQualifiedName("first_sub_workflow.first_task.first_task_output_2")
+          ),
+          WomSingleFileType,
+          null,
+          null
+        )
+          -> WomSingleFile(
+            s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file2.txt"
+          ),
+        GraphNodeOutputPort(WomIdentifier(LocalName("first_output_file"),
+                                          FullyQualifiedName("first_sub_workflow.first_output_file")
+                            ),
+                            WomSingleFileType,
+                            null
+        )
+          -> WomSingleFile(
+            s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"
+          ),
+        ExpressionBasedOutputPort(
+          WomIdentifier(LocalName("first_task.first_task_output_1"),
+                        FullyQualifiedName("first_sub_workflow.first_task.first_task_output_1")
+          ),
+          WomSingleFileType,
+          null,
+          null
+        )
+          -> WomSingleFile(
+            s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"
+          ),
+        GraphNodeOutputPort(WomIdentifier(LocalName("second_output_file"),
+                                          FullyQualifiedName("first_sub_workflow.second_output_file")
+                            ),
+                            WomSingleFileType,
+                            null
+        )
+          -> WomSingleFile(
+            s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file2.txt"
+          )
+      )
+    )
+    finalOutputs = CallOutputs(
+      Map(
+        GraphNodeOutputPort(WomIdentifier(LocalName("main_output"), FullyQualifiedName("main_workflow.main_output")),
+                            WomSingleFileType,
+                            null
+        )
+          -> WomSingleFile(
+            s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file2.txt"
+          )
+      )
+    )
+
+    testDeleteWorkflowFilesActor = TestFSMRef(
+      new MockDeleteWorkflowFilesActor(rootWorkflowId,
+                                       emptyWorkflowIdSet,
+                                       rootWorkflowRoots,
+                                       finalOutputs,
+                                       allOutputs,
+                                       mockPathBuilders,
+                                       serviceRegistryActor.ref,
+                                       ioActor.ref
+      )
+    )
     testProbe watch testDeleteWorkflowFilesActor
 
-    gcsFilePath = mockPathBuilder.build(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt").get
+    gcsFilePath = mockPathBuilder
+      .build(
+        s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"
+      )
+      .get
   }
 
   it should "follow the expected golden-path lifecycle" in {
 
     testDeleteWorkflowFilesActor ! StartWorkflowFilesDeletion
 
-    serviceRegistryActor.expectMsgPF(10.seconds) {
-      case m: PutMetadataAction =>
-        val event = m.events.head
-        m.events.size shouldBe 1
-        event.key.workflowId shouldBe rootWorkflowId
-        event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
-        event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(InProgress)
+    serviceRegistryActor.expectMsgPF(10.seconds) { case m: PutMetadataAction =>
+      val event = m.events.head
+      m.events.size shouldBe 1
+      event.key.workflowId shouldBe rootWorkflowId
+      event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
+      event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(InProgress)
     }
 
-    ioActor.expectMsgPF(10.seconds) {
-      case cmd: IoDeleteCommand => cmd.file shouldBe gcsFilePath
+    ioActor.expectMsgPF(10.seconds) { case cmd: IoDeleteCommand =>
+      cmd.file shouldBe gcsFilePath
     }
 
     eventually {
@@ -107,13 +169,12 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
     testDeleteWorkflowFilesActor !
       IoSuccess(GcsBatchDeleteCommand.forPath(gcsFilePath, swallowIOExceptions = false).get, ())
 
-    serviceRegistryActor.expectMsgPF(10.seconds) {
-      case m: PutMetadataAction =>
-        val event = m.events.head
-        m.events.size shouldBe 1
-        event.key.workflowId shouldBe rootWorkflowId
-        event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
-        event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(Succeeded)
+    serviceRegistryActor.expectMsgPF(10.seconds) { case m: PutMetadataAction =>
+      val event = m.events.head
+      m.events.size shouldBe 1
+      event.key.workflowId shouldBe rootWorkflowId
+      event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
+      event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(Succeeded)
     }
 
     testProbe.expectTerminated(testDeleteWorkflowFilesActor, 10.seconds)
@@ -123,19 +184,17 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
 
     testDeleteWorkflowFilesActor ! StartWorkflowFilesDeletion
 
-    serviceRegistryActor.expectMsgPF(10.seconds) {
-      case m: PutMetadataAction =>
-        val event = m.events.head
-        m.events.size shouldBe 1
-        event.key.workflowId shouldBe rootWorkflowId
-        event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
-        event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(InProgress)
+    serviceRegistryActor.expectMsgPF(10.seconds) { case m: PutMetadataAction =>
+      val event = m.events.head
+      m.events.size shouldBe 1
+      event.key.workflowId shouldBe rootWorkflowId
+      event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
+      event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(InProgress)
     }
 
     val expectedDeleteCommand = GcsBatchDeleteCommand.forPath(gcsFilePath, swallowIOExceptions = false).get
 
-    ioActor.expectMsgPF(10.seconds) {
-      case `expectedDeleteCommand` => // woohoo!
+    ioActor.expectMsgPF(10.seconds) { case `expectedDeleteCommand` => // woohoo!
     }
 
     eventually {
@@ -153,13 +212,12 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
 
     ioActor.send(testDeleteWorkflowFilesActor, IoSuccess(expectedDeleteCommand, ()))
 
-    serviceRegistryActor.expectMsgPF(10.seconds) {
-      case m: PutMetadataAction =>
-        val event = m.events.head
-        m.events.size shouldBe 1
-        event.key.workflowId shouldBe rootWorkflowId
-        event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
-        event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(Succeeded)
+    serviceRegistryActor.expectMsgPF(10.seconds) { case m: PutMetadataAction =>
+      val event = m.events.head
+      m.events.size shouldBe 1
+      event.key.workflowId shouldBe rootWorkflowId
+      event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
+      event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(Succeeded)
     }
 
     testProbe.expectTerminated(testDeleteWorkflowFilesActor, 10.seconds)
@@ -169,17 +227,16 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
 
     testDeleteWorkflowFilesActor ! StartWorkflowFilesDeletion
 
-    serviceRegistryActor.expectMsgPF(10.seconds) {
-      case m: PutMetadataAction =>
-        val event = m.events.head
-        m.events.size shouldBe 1
-        event.key.workflowId shouldBe rootWorkflowId
-        event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
-        event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(InProgress)
+    serviceRegistryActor.expectMsgPF(10.seconds) { case m: PutMetadataAction =>
+      val event = m.events.head
+      m.events.size shouldBe 1
+      event.key.workflowId shouldBe rootWorkflowId
+      event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
+      event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(InProgress)
     }
 
-    ioActor.expectMsgPF(10.seconds) {
-      case cmd: IoDeleteCommand => cmd.file shouldBe gcsFilePath
+    ioActor.expectMsgPF(10.seconds) { case cmd: IoDeleteCommand =>
+      cmd.file shouldBe gcsFilePath
     }
 
     eventually {
@@ -189,63 +246,59 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
     testDeleteWorkflowFilesActor !
       IoFailure(
         command = GcsBatchDeleteCommand.forPath(gcsFilePath, swallowIOExceptions = false).get,
-        failure = new Exception(s"Something is fishy!"),
+        failure = new Exception(s"Something is fishy!")
       )
 
-    serviceRegistryActor.expectMsgPF(10.seconds) {
-      case m: PutMetadataAction =>
-        val event = m.events.head
-        m.events.size shouldBe 1
-        event.key.workflowId shouldBe rootWorkflowId
-        event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
-        event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(Failed)
+    serviceRegistryActor.expectMsgPF(10.seconds) { case m: PutMetadataAction =>
+      val event = m.events.head
+      m.events.size shouldBe 1
+      event.key.workflowId shouldBe rootWorkflowId
+      event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
+      event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(Failed)
     }
 
     testProbe.expectTerminated(testDeleteWorkflowFilesActor, 10.seconds)
   }
 
-
   it should "send success when the failure is FileNotFound" in {
 
     testDeleteWorkflowFilesActor ! StartWorkflowFilesDeletion
 
-    serviceRegistryActor.expectMsgPF(10.seconds) {
-      case m: PutMetadataAction =>
-        val event = m.events.head
-        m.events.size shouldBe 1
-        event.key.workflowId shouldBe rootWorkflowId
-        event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
-        event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(InProgress)
+    serviceRegistryActor.expectMsgPF(10.seconds) { case m: PutMetadataAction =>
+      val event = m.events.head
+      m.events.size shouldBe 1
+      event.key.workflowId shouldBe rootWorkflowId
+      event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
+      event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(InProgress)
     }
 
-    ioActor.expectMsgPF(10.seconds) {
-      case cmd: IoDeleteCommand => cmd.file shouldBe gcsFilePath
+    ioActor.expectMsgPF(10.seconds) { case cmd: IoDeleteCommand =>
+      cmd.file shouldBe gcsFilePath
     }
 
     eventually {
       testDeleteWorkflowFilesActor.stateName shouldBe WaitingForIoResponses
     }
 
-    val fileNotFoundException = EnhancedCromwellIoException(s"File not found", new FileNotFoundException(gcsFilePath.pathAsString))
+    val fileNotFoundException =
+      EnhancedCromwellIoException(s"File not found", new FileNotFoundException(gcsFilePath.pathAsString))
     testDeleteWorkflowFilesActor !
       IoFailure(
         command = GcsBatchDeleteCommand.forPath(gcsFilePath, swallowIOExceptions = false).get,
-        failure = fileNotFoundException,
+        failure = fileNotFoundException
       )
 
-    serviceRegistryActor.expectMsgPF(10.seconds) {
-      case m: PutMetadataAction =>
-        val event = m.events.head
-        m.events.size shouldBe 1
-        event.key.workflowId shouldBe rootWorkflowId
-        event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
-        event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(Succeeded)
+    serviceRegistryActor.expectMsgPF(10.seconds) { case m: PutMetadataAction =>
+      val event = m.events.head
+      m.events.size shouldBe 1
+      event.key.workflowId shouldBe rootWorkflowId
+      event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
+      event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(Succeeded)
     }
 
     testProbe.expectTerminated(testDeleteWorkflowFilesActor, 10.seconds)
   }
 
-
   it should "remove any non-file intermediate outputs" in {
 
     val expectedIntermediateFiles = Set(gcsFilePath)
@@ -258,16 +311,33 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
     actualIntermediateFiles shouldBe expectedIntermediateFiles
   }
 
-
   it should "delete all file outputs if there are no final outputs" in {
 
     finalOutputs = CallOutputs.empty
 
-    val gcsFilePath1: Path = mockPathBuilder.build(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt").get
-    val gcsFilePath2: Path = mockPathBuilder.build(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file2.txt").get
+    val gcsFilePath1: Path = mockPathBuilder
+      .build(
+        s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"
+      )
+      .get
+    val gcsFilePath2: Path = mockPathBuilder
+      .build(
+        s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file2.txt"
+      )
+      .get
     val expectedIntermediateFiles = Set(gcsFilePath1, gcsFilePath2)
 
-    testDeleteWorkflowFilesActor = TestFSMRef(new MockDeleteWorkflowFilesActor(rootWorkflowId, emptyWorkflowIdSet, rootWorkflowRoots, finalOutputs, allOutputs, mockPathBuilders, serviceRegistryActor.ref, ioActor.ref))
+    testDeleteWorkflowFilesActor = TestFSMRef(
+      new MockDeleteWorkflowFilesActor(rootWorkflowId,
+                                       emptyWorkflowIdSet,
+                                       rootWorkflowRoots,
+                                       finalOutputs,
+                                       allOutputs,
+                                       mockPathBuilders,
+                                       serviceRegistryActor.ref,
+                                       ioActor.ref
+      )
+    )
 
     val actualIntermediateFiles = testDeleteWorkflowFilesActor.underlyingActor.gatherIntermediateOutputFiles(
       allOutputs.outputs.values.toSet,
@@ -280,14 +350,15 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
   it should "send failure when delete command creation is unsuccessful for a file" in {
 
     val partialIoCommandBuilder = new PartialIoCommandBuilder {
-      override def deleteCommand: PartialFunction[(Path, Boolean), Try[IoDeleteCommand]] = {
-        case _ => Failure(new Exception("everything's fine, I am an expected delete fail") with NoStackTrace)
+      override def deleteCommand: PartialFunction[(Path, Boolean), Try[IoDeleteCommand]] = { case _ =>
+        Failure(new Exception("everything's fine, I am an expected delete fail") with NoStackTrace)
       }
     }
     val ioCommandBuilder = new IoCommandBuilder(List(partialIoCommandBuilder))
 
-    testDeleteWorkflowFilesActor =
-      TestFSMRef(new MockDeleteWorkflowFilesActor(rootWorkflowId,
+    testDeleteWorkflowFilesActor = TestFSMRef(
+      new MockDeleteWorkflowFilesActor(
+        rootWorkflowId,
         rootAndSubworkflowIds = emptyWorkflowIdSet,
         rootWorkflowRoots = rootWorkflowRoots,
         workflowFinalOutputs = finalOutputs,
@@ -295,19 +366,19 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
         pathBuilders = mockPathBuilders,
         serviceRegistryActor = serviceRegistryActor.ref,
         ioActor = ioActor.ref,
-        gcsCommandBuilder = ioCommandBuilder,
-      ))
+        gcsCommandBuilder = ioCommandBuilder
+      )
+    )
     testProbe.watch(testDeleteWorkflowFilesActor)
 
     testDeleteWorkflowFilesActor ! StartWorkflowFilesDeletion
 
-    serviceRegistryActor.expectMsgPF(10.seconds) {
-      case m: PutMetadataAction =>
-        val event = m.events.head
-        m.events.size shouldBe 1
-        event.key.workflowId shouldBe rootWorkflowId
-        event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
-        event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(InProgress)
+    serviceRegistryActor.expectMsgPF(10.seconds) { case m: PutMetadataAction =>
+      val event = m.events.head
+      m.events.size shouldBe 1
+      event.key.workflowId shouldBe rootWorkflowId
+      event.key.key shouldBe WorkflowMetadataKeys.FileDeletionStatus
+      event.value.get.value shouldBe FileDeletionStatus.toDatabaseValue(InProgress)
     }
 
     testProbe.expectTerminated(testDeleteWorkflowFilesActor, 10.seconds)
@@ -316,14 +387,40 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
 
   it should "terminate if root workflow has no intermediate outputs to delete" in {
 
-    finalOutputs = CallOutputs(Map(
-      GraphNodeOutputPort(WomIdentifier(LocalName("main_output_1"),FullyQualifiedName("main_workflow.main_output_1")), WomSingleFileType, null)
-        -> WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt") ,
-      GraphNodeOutputPort(WomIdentifier(LocalName("main_output_2"),FullyQualifiedName("main_workflow.main_output_2")), WomSingleFileType, null)
-        -> WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file2.txt")
-    ))
+    finalOutputs = CallOutputs(
+      Map(
+        GraphNodeOutputPort(WomIdentifier(LocalName("main_output_1"),
+                                          FullyQualifiedName("main_workflow.main_output_1")
+                            ),
+                            WomSingleFileType,
+                            null
+        )
+          -> WomSingleFile(
+            s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"
+          ),
+        GraphNodeOutputPort(WomIdentifier(LocalName("main_output_2"),
+                                          FullyQualifiedName("main_workflow.main_output_2")
+                            ),
+                            WomSingleFileType,
+                            null
+        )
+          -> WomSingleFile(
+            s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file2.txt"
+          )
+      )
+    )
 
-    val testDeleteWorkflowFilesActor = TestFSMRef(new MockDeleteWorkflowFilesActor(rootWorkflowId, emptyWorkflowIdSet, rootWorkflowRoots, finalOutputs, allOutputs, mockPathBuilders, serviceRegistryActor.ref, ioActor.ref))
+    val testDeleteWorkflowFilesActor = TestFSMRef(
+      new MockDeleteWorkflowFilesActor(rootWorkflowId,
+                                       emptyWorkflowIdSet,
+                                       rootWorkflowRoots,
+                                       finalOutputs,
+                                       allOutputs,
+                                       mockPathBuilders,
+                                       serviceRegistryActor.ref,
+                                       ioActor.ref
+      )
+    )
 
     testProbe watch testDeleteWorkflowFilesActor
 
@@ -332,21 +429,56 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
     testProbe.expectTerminated(testDeleteWorkflowFilesActor, 10.seconds)
   }
 
-
   it should "remove values that are file names in form of string" in {
 
-    allOutputs = allOutputs.copy(outputs = allOutputs.outputs ++ Map(
-      GraphNodeOutputPort(WomIdentifier(LocalName("file_with_file_path_string_output"),FullyQualifiedName("first_sub_workflow.file_with_file_path_string_output")), WomStringType, null)
-        -> WomString(s"gs://my_bucket/non_existent_file.txt"),
-      ExpressionBasedOutputPort(WomIdentifier(LocalName("first_task.first_task_file_with_file_path_output"),FullyQualifiedName("first_sub_workflow.first_task.first_task_file_with_file_path_output")), WomSingleFileType, null, null)
-        -> WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/file_with_file_path.txt")
-    ))
+    allOutputs = allOutputs.copy(outputs =
+      allOutputs.outputs ++ Map(
+        GraphNodeOutputPort(
+          WomIdentifier(LocalName("file_with_file_path_string_output"),
+                        FullyQualifiedName("first_sub_workflow.file_with_file_path_string_output")
+          ),
+          WomStringType,
+          null
+        )
+          -> WomString(s"gs://my_bucket/non_existent_file.txt"),
+        ExpressionBasedOutputPort(
+          WomIdentifier(
+            LocalName("first_task.first_task_file_with_file_path_output"),
+            FullyQualifiedName("first_sub_workflow.first_task.first_task_file_with_file_path_output")
+          ),
+          WomSingleFileType,
+          null,
+          null
+        )
+          -> WomSingleFile(
+            s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/file_with_file_path.txt"
+          )
+      )
+    )
 
-    val gcsFilePath1: Path = mockPathBuilder.build(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt").get
-    val gcsFilePath2: Path = mockPathBuilder.build(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/file_with_file_path.txt").get
+    val gcsFilePath1: Path = mockPathBuilder
+      .build(
+        s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"
+      )
+      .get
+    val gcsFilePath2: Path = mockPathBuilder
+      .build(
+        s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/file_with_file_path.txt"
+      )
+      .get
     val expectedIntermediateFiles = Set(gcsFilePath1, gcsFilePath2)
 
-    val testDeleteWorkflowFilesActor = TestFSMRef(new MockDeleteWorkflowFilesActor(rootWorkflowId, emptyWorkflowIdSet, rootWorkflowRoots, finalOutputs, allOutputs, mockPathBuilders, serviceRegistryActor.ref, ioActor.ref))
+    val testDeleteWorkflowFilesActor = TestFSMRef(
+      new MockDeleteWorkflowFilesActor(rootWorkflowId,
+                                       emptyWorkflowIdSet,
+                                       rootWorkflowRoots,
+                                       finalOutputs,
+                                       allOutputs,
+                                       mockPathBuilders,
+                                       serviceRegistryActor.ref,
+                                       ioActor.ref
+      )
+    )
 
     val actualIntermediateFiles = testDeleteWorkflowFilesActor.underlyingActor.gatherIntermediateOutputFiles(
       allOutputs.outputs.values.toSet,
@@ -356,25 +488,76 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
     actualIntermediateFiles shouldBe expectedIntermediateFiles
   }
 
-
   it should "identify and gather glob files" in {
 
-    allOutputs = allOutputs.copy(outputs = allOutputs.outputs ++ Map(
-      GraphNodeOutputPort(WomIdentifier(LocalName("glob_output"),FullyQualifiedName("first_sub_workflow.glob_output")), WomMaybeEmptyArrayType(WomSingleFileType), null)
-        -> WomArray(Seq(WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file1.txt"),
-        WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file2.txt"))),
-      ExpressionBasedOutputPort(WomIdentifier(LocalName("first_task.first_task_glob"),FullyQualifiedName("first_sub_workflow.first_task.first_task_glob")), WomMaybeEmptyArrayType(WomSingleFileType), null, null)
-        -> WomArray(Seq(WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file1.txt"),
-        WomSingleFile(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file2.txt")))
-    ))
+    allOutputs = allOutputs.copy(outputs =
+      allOutputs.outputs ++ Map(
+        GraphNodeOutputPort(WomIdentifier(LocalName("glob_output"),
+                                          FullyQualifiedName("first_sub_workflow.glob_output")
+                            ),
+                            WomMaybeEmptyArrayType(WomSingleFileType),
+                            null
+        )
+          -> WomArray(
+            Seq(
+              WomSingleFile(
+                s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file1.txt"
+              ),
+              WomSingleFile(
+                s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file2.txt"
+              )
+            )
+          ),
+        ExpressionBasedOutputPort(
+          WomIdentifier(LocalName("first_task.first_task_glob"),
+                        FullyQualifiedName("first_sub_workflow.first_task.first_task_glob")
+          ),
+          WomMaybeEmptyArrayType(WomSingleFileType),
+          null,
+          null
+        )
+          -> WomArray(
+            Seq(
+              WomSingleFile(
+                s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file1.txt"
+              ),
+              WomSingleFile(
+                s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file2.txt"
+              )
+            )
+          )
+      )
+    )
 
-    val gcsFilePath1: Path = mockPathBuilder.build(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt").get
-    val gcsGlobFilePath1: Path = mockPathBuilder.build(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file1.txt").get
-    val gcsGlobFilePath2: Path = mockPathBuilder.build(s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file2.txt").get
+    val gcsFilePath1: Path = mockPathBuilder
+      .build(
+        s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/intermediate_file1.txt"
+      )
+      .get
+    val gcsGlobFilePath1: Path = mockPathBuilder
+      .build(
+        s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file1.txt"
+      )
+      .get
+    val gcsGlobFilePath2: Path = mockPathBuilder
+      .build(
+        s"$rootWorkflowExecutionDir/call-first_sub_workflow/firstSubWf.first_sub_workflow/$subworkflowId/call-first_task/glob-random_id/intermediate_file2.txt"
+      )
+      .get
 
     val expectedIntermediateFiles = Set(gcsFilePath1, gcsGlobFilePath1, gcsGlobFilePath2)
 
-    val testDeleteWorkflowFilesActor = TestFSMRef(new MockDeleteWorkflowFilesActor(rootWorkflowId, emptyWorkflowIdSet, rootWorkflowRoots, finalOutputs, allOutputs, mockPathBuilders, serviceRegistryActor.ref, ioActor.ref))
+    val testDeleteWorkflowFilesActor = TestFSMRef(
+      new MockDeleteWorkflowFilesActor(rootWorkflowId,
+                                       emptyWorkflowIdSet,
+                                       rootWorkflowRoots,
+                                       finalOutputs,
+                                       allOutputs,
+                                       mockPathBuilders,
+                                       serviceRegistryActor.ref,
+                                       ioActor.ref
+      )
+    )
 
     val actualIntermediateFiles = testDeleteWorkflowFilesActor.underlyingActor.gatherIntermediateOutputFiles(
       allOutputs.outputs.values.toSet,
@@ -384,7 +567,6 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
     actualIntermediateFiles shouldBe expectedIntermediateFiles
   }
 
-
   it should "sanity check in multiple rootWorkflowRoots" in {
     val expectedIntermediateFiles = Set(gcsFilePath)
 
@@ -393,7 +575,17 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
       mockPathBuilder.build(s"gs://my_bucket/main_workflow/yyyy").get,
       mockPathBuilder.build(rootWorkflowExecutionDir).get
     )
-    val testDeleteWorkflowFilesActor = TestFSMRef(new MockDeleteWorkflowFilesActor(rootWorkflowId, emptyWorkflowIdSet, rootWorkflowRoots, finalOutputs, allOutputs, mockPathBuilders, serviceRegistryActor.ref, ioActor.ref))
+    val testDeleteWorkflowFilesActor = TestFSMRef(
+      new MockDeleteWorkflowFilesActor(rootWorkflowId,
+                                       emptyWorkflowIdSet,
+                                       rootWorkflowRoots,
+                                       finalOutputs,
+                                       allOutputs,
+                                       mockPathBuilders,
+                                       serviceRegistryActor.ref,
+                                       ioActor.ref
+      )
+    )
 
     val actualIntermediateFiles = testDeleteWorkflowFilesActor.underlyingActor.gatherIntermediateOutputFiles(
       allOutputs.outputs.values.toSet,
@@ -403,10 +595,19 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
     actualIntermediateFiles shouldBe expectedIntermediateFiles
   }
 
-
   it should "not delete outputs if they are outside the root workflow execution directory" in {
     val rootWorkflowRoots = Set[Path](mockPathBuilder.build(s"gs://my_bucket/main_workflow/xxxx").get)
-    val testDeleteWorkflowFilesActor = TestFSMRef(new MockDeleteWorkflowFilesActor(rootWorkflowId, emptyWorkflowIdSet, rootWorkflowRoots, finalOutputs, allOutputs, mockPathBuilders, serviceRegistryActor.ref, ioActor.ref))
+    val testDeleteWorkflowFilesActor = TestFSMRef(
+      new MockDeleteWorkflowFilesActor(rootWorkflowId,
+                                       emptyWorkflowIdSet,
+                                       rootWorkflowRoots,
+                                       finalOutputs,
+                                       allOutputs,
+                                       mockPathBuilders,
+                                       serviceRegistryActor.ref,
+                                       ioActor.ref
+      )
+    )
 
     val actualIntermediateFiles = testDeleteWorkflowFilesActor.underlyingActor.gatherIntermediateOutputFiles(
       allOutputs.outputs.values.toSet,
@@ -417,9 +618,6 @@ class DeleteWorkflowFilesActorSpec extends TestKitSuite
   }
 }
 
-
-
-
 class MockDeleteWorkflowFilesActor(rootWorkflowId: RootWorkflowId,
                                    rootAndSubworkflowIds: Set[WorkflowId],
                                    rootWorkflowRoots: Set[Path],
@@ -428,19 +626,18 @@ class MockDeleteWorkflowFilesActor(rootWorkflowId: RootWorkflowId,
                                    pathBuilders: PathBuilders,
                                    serviceRegistryActor: ActorRef,
                                    ioActor: ActorRef,
-                                   gcsCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder,
-                                  ) extends
-  DeleteWorkflowFilesActor(
-    rootWorkflowId,
-    rootAndSubworkflowIds,
-    rootWorkflowRoots,
-    workflowFinalOutputs.outputs.values.toSet,
-    workflowAllOutputs.outputs.values.toSet,
-    pathBuilders,
-    serviceRegistryActor,
-    ioActor,
-    gcsCommandBuilder,
-  ) {
+                                   gcsCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder
+) extends DeleteWorkflowFilesActor(
+      rootWorkflowId,
+      rootAndSubworkflowIds,
+      rootWorkflowRoots,
+      workflowFinalOutputs.outputs.values.toSet,
+      workflowAllOutputs.outputs.values.toSet,
+      pathBuilders,
+      serviceRegistryActor,
+      ioActor,
+      gcsCommandBuilder
+    ) {
   // Override the IO actor backoff for the benefit of the backpressure tests:
-  override def initialBackoff(): Backoff = SimpleExponentialBackoff(100.millis, 1.second, 1.2D)
+  override def initialBackoff(): Backoff = SimpleExponentialBackoff(100.millis, 1.second, 1.2d)
 }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ExecutionStoreBenchmark.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ExecutionStoreBenchmark.scala
index 6feb8338bab..797321d7ba9 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ExecutionStoreBenchmark.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ExecutionStoreBenchmark.scala
@@ -34,28 +34,33 @@ object ExecutionStoreBenchmark extends Bench[Double] with DefaultJsonProtocol {
 
   val inputJson = Option(SampleWdl.PrepareScatterGatherWdl().rawInputs.toJson.compactPrint)
   val namespace = WdlNamespaceWithWorkflow.load(SampleWdl.PrepareScatterGatherWdl().workflowSource(), Seq.empty).get
-  val graph = namespace.toWomExecutable(inputJson, NoIoFunctionSet, strictValidation = true).getOrElse(throw new Exception("Failed to build womExecutable")).graph
+  val graph = namespace
+    .toWomExecutable(inputJson, NoIoFunctionSet, strictValidation = true)
+    .getOrElse(throw new Exception("Failed to build womExecutable"))
+    .graph
   val prepareCall: CommandCallNode = graph.calls.find(_.localName == "do_prepare").get.asInstanceOf[CommandCallNode]
   val scatterCall: CommandCallNode = graph.allNodes.find(_.localName == "do_scatter").get.asInstanceOf[CommandCallNode]
   val scatter: ScatterNode = graph.scatters.head
 
-  private def makeKey(call: CommandCallNode, executionStatus: ExecutionStatus)(index: Int) = {
+  private def makeKey(call: CommandCallNode, executionStatus: ExecutionStatus)(index: Int) =
     BackendJobDescriptorKey(call, Option(index), 1) -> executionStatus
-  }
 
   // Generates executionStores using the given above sizes
   // Each execution store contains X simulated shards of "prepareCall" in status Done and X simulated shards of "scatterCall" in status NotStarted
   // This provides a good starting point to evaluate the speed of "runnableCalls", as it needs to iterate over all "NotStarted" keys, and for each one
   // look for their upstreams keys in status "Done"
-  private def stores(sizes: Gen[Int]): Gen[ActiveExecutionStore] = {
+  private def stores(sizes: Gen[Int]): Gen[ActiveExecutionStore] =
     for {
       size <- sizes
       doneMap = (0 until size map makeKey(prepareCall, ExecutionStatus.Done)).toMap
-      collectorKeys = scatter.outputMapping.map(om => ScatterCollectorKey(om, size, ScatterNode.DefaultScatterCollectionFunction) -> ExecutionStatus.NotStarted).toMap
+      collectorKeys = scatter.outputMapping
+        .map(om =>
+          ScatterCollectorKey(om, size, ScatterNode.DefaultScatterCollectionFunction) -> ExecutionStatus.NotStarted
+        )
+        .toMap
       notStartedMap = (0 until size map makeKey(scatterCall, ExecutionStatus.NotStarted)).toMap ++ collectorKeys
       finalMap = doneMap ++ notStartedMap
     } yield ActiveExecutionStore(finalMap.toMap, needsUpdate = true)
-  }
 
   performance of "ExecutionStore" in {
     // Measures how fast the execution store can find runnable calls with lots of "Done" calls and "NotStarted" calls.
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActorSpec.scala
index fa90e796d95..ebd76a8e5fb 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActorSpec.scala
@@ -23,7 +23,11 @@ import cromwell.engine.workflow.lifecycle.execution.keys.SubWorkflowKey
 import cromwell.engine.workflow.lifecycle.execution.stores.ValueStore
 import cromwell.engine.workflow.workflowstore.{RestartableRunning, StartableState, Submitted}
 import cromwell.engine.{ContinueWhilePossible, EngineIoFunctions, EngineWorkflowDescriptor}
-import cromwell.services.metadata.MetadataService.{MetadataWriteFailure, MetadataWriteSuccess, PutMetadataActionAndRespond}
+import cromwell.services.metadata.MetadataService.{
+  MetadataWriteFailure,
+  MetadataWriteSuccess,
+  PutMetadataActionAndRespond
+}
 import cromwell.subworkflowstore.SubWorkflowStoreActor.{QuerySubWorkflow, SubWorkflowFound, SubWorkflowNotFound}
 import cromwell.util.WomMocks
 import org.scalatest.BeforeAndAfterAll
@@ -37,8 +41,13 @@ import scala.concurrent.duration._
 import scala.language.postfixOps
 import scala.util.control.NoStackTrace
 
-class SubWorkflowExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with MockSugar
-  with Eventually with BeforeAndAfterAll {
+class SubWorkflowExecutionActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with MockSugar
+    with Eventually
+    with BeforeAndAfterAll {
 
   behavior of "SubWorkflowExecutionActor"
 
@@ -90,35 +99,40 @@ class SubWorkflowExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
     parentProbe = TestProbe()
   }
 
-  private def buildSWEA(startState: StartableState = Submitted) = {
-    new TestFSMRef[SubWorkflowExecutionActorState, SubWorkflowExecutionActorData, SubWorkflowExecutionActor](system, Props(
-      new SubWorkflowExecutionActor(
-        subKey,
-        parentWorkflowDescriptor,
-        new EngineIoFunctions(List.empty, new AsyncIo(simpleIoActor, DefaultIoCommandBuilder), system.dispatcher),
-        Map.empty,
-        ioActorProbe.ref,
-        serviceRegistryProbe.ref,
-        jobStoreProbe.ref,
-        subWorkflowStoreProbe.ref,
-        callCacheReadActorProbe.ref,
-        callCacheWriteActorProbe.ref,
-        dockerHashActorProbe.ref,
-        jobRestartCheckTokenDispenserProbe.ref,
-        jobExecutionTokenDispenserProbe.ref,
-        BackendSingletonCollection(Map.empty),
-        AllBackendInitializationData(Map.empty),
-        startState,
-        rootConfig,
-        new AtomicInteger(),
-        fileHashCacheActor = None,
-        blacklistCache = None
-      ) {
-        override def createSubWorkflowPreparationActor(subWorkflowId: WorkflowId): ActorRef = preparationActor.ref
-        override def createSubWorkflowActor(createSubWorkflowActor: EngineWorkflowDescriptor): ActorRef =
-          subWorkflowActor.ref
-      }), parentProbe.ref, s"SubWorkflowExecutionActorSpec-${UUID.randomUUID()}")
-  }
+  private def buildSWEA(startState: StartableState = Submitted) =
+    new TestFSMRef[SubWorkflowExecutionActorState, SubWorkflowExecutionActorData, SubWorkflowExecutionActor](
+      system,
+      Props(
+        new SubWorkflowExecutionActor(
+          subKey,
+          parentWorkflowDescriptor,
+          new EngineIoFunctions(List.empty, new AsyncIo(simpleIoActor, DefaultIoCommandBuilder), system.dispatcher),
+          Map.empty,
+          ioActorProbe.ref,
+          serviceRegistryProbe.ref,
+          jobStoreProbe.ref,
+          subWorkflowStoreProbe.ref,
+          callCacheReadActorProbe.ref,
+          callCacheWriteActorProbe.ref,
+          dockerHashActorProbe.ref,
+          jobRestartCheckTokenDispenserProbe.ref,
+          jobExecutionTokenDispenserProbe.ref,
+          BackendSingletonCollection(Map.empty),
+          AllBackendInitializationData(Map.empty),
+          startState,
+          rootConfig,
+          new AtomicInteger(),
+          fileHashCacheActor = None,
+          blacklistCache = None
+        ) {
+          override def createSubWorkflowPreparationActor(subWorkflowId: WorkflowId): ActorRef = preparationActor.ref
+          override def createSubWorkflowActor(createSubWorkflowActor: EngineWorkflowDescriptor): ActorRef =
+            subWorkflowActor.ref
+        }
+      ),
+      parentProbe.ref,
+      s"SubWorkflowExecutionActorSpec-${UUID.randomUUID()}"
+    )
 
   it should "Check the sub workflow store when restarting" in {
     val swea = buildSWEA(startState = RestartableRunning)
@@ -138,7 +152,16 @@ class SubWorkflowExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
     swea.setState(SubWorkflowCheckingStoreState)
 
     val subWorkflowUuid = WorkflowId.randomId()
-    swea ! SubWorkflowFound(SubWorkflowStoreEntry(Option(0), parentWorkflowId.toString, subKey.node.fullyQualifiedName, subKey.index.fromIndex, subKey.attempt, subWorkflowUuid.toString, None))
+    swea ! SubWorkflowFound(
+      SubWorkflowStoreEntry(Option(0),
+                            parentWorkflowId.toString,
+                            subKey.node.fullyQualifiedName,
+                            subKey.index.fromIndex,
+                            subKey.attempt,
+                            subWorkflowUuid.toString,
+                            None
+      )
+    )
     parentProbe.expectMsg(RequestValueStore)
 
     eventually {
@@ -210,8 +233,8 @@ class SubWorkflowExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
     val preparationFailedMessage: CallPreparationFailed = CallPreparationFailed(subWorkflowKey, throwable)
     swea ! preparationFailedMessage
 
-    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) {
-      case PutMetadataActionAndRespond(events, _, _) => swea ! MetadataWriteSuccess(events)
+    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) { case PutMetadataActionAndRespond(events, _, _) =>
+      swea ! MetadataWriteSuccess(events)
     }
     parentProbe.expectMsg(SubWorkflowFailedResponse(subKey, Map.empty, throwable))
     deathWatch.expectTerminated(swea, awaitTimeout)
@@ -228,8 +251,8 @@ class SubWorkflowExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
     val outputs: CallOutputs = CallOutputs.empty
     val workflowSuccessfulMessage = WorkflowExecutionSucceededResponse(jobExecutionMap, Set.empty[WorkflowId], outputs)
     swea ! workflowSuccessfulMessage
-    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) {
-      case PutMetadataActionAndRespond(events, _, _) => swea ! MetadataWriteSuccess(events)
+    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) { case PutMetadataActionAndRespond(events, _, _) =>
+      swea ! MetadataWriteSuccess(events)
     }
     parentProbe.expectMsg(SubWorkflowSucceededResponse(subKey, jobExecutionMap, Set.empty[WorkflowId], outputs))
     deathWatch.expectTerminated(swea, awaitTimeout)
@@ -246,8 +269,8 @@ class SubWorkflowExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
 
     val workflowFailedMessage = WorkflowExecutionFailedResponse(jobExecutionMap, expectedException)
     swea ! workflowFailedMessage
-    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) {
-      case PutMetadataActionAndRespond(events, _, _) => swea ! MetadataWriteSuccess(events)
+    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) { case PutMetadataActionAndRespond(events, _, _) =>
+      swea ! MetadataWriteSuccess(events)
     }
     parentProbe.expectMsg(SubWorkflowFailedResponse(subKey, jobExecutionMap, expectedException))
     deathWatch.expectTerminated(swea, awaitTimeout)
@@ -265,33 +288,31 @@ class SubWorkflowExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
     val outputs: CallOutputs = CallOutputs.empty
     val workflowSuccessfulMessage = WorkflowExecutionSucceededResponse(jobExecutionMap, Set.empty[WorkflowId], outputs)
     swea ! workflowSuccessfulMessage
-    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) {
-      case PutMetadataActionAndRespond(events, _, _) => swea ! MetadataWriteFailure(expectedException, events)
+    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) { case PutMetadataActionAndRespond(events, _, _) =>
+      swea ! MetadataWriteFailure(expectedException, events)
     }
 
     import ManyTimes.intWithTimes
     10.times {
-      serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) {
-        case PutMetadataActionAndRespond(events, _, _) =>
-          events.size should be(1)
-          events.head.key.key should be("status")
-          events.head.value.get.value should be("Failed")
-          swea ! MetadataWriteFailure(expectedException, events)
+      serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) { case PutMetadataActionAndRespond(events, _, _) =>
+        events.size should be(1)
+        events.head.key.key should be("status")
+        events.head.value.get.value should be("Failed")
+        swea ! MetadataWriteFailure(expectedException, events)
       }
       // Check there are no messages going to the parent yet:
       parentProbe.expectNoMessage(10.millis)
     }
 
     // Now let's say eventually the write does somehow get through.
-    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) {
-      case PutMetadataActionAndRespond(events, _, _) => swea ! MetadataWriteSuccess(events)
+    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) { case PutMetadataActionAndRespond(events, _, _) =>
+      swea ! MetadataWriteSuccess(events)
     }
 
     // The workflow is now considered failed since lots of metadata is probably lost:
-    parentProbe.expectMsgPF(awaitTimeout) {
-      case SubWorkflowFailedResponse(`subKey`, `jobExecutionMap`, reason) =>
-        reason.getMessage should be("Sub workflow execution actor unable to write final state to metadata")
-        reason.getCause should be(expectedException)
+    parentProbe.expectMsgPF(awaitTimeout) { case SubWorkflowFailedResponse(`subKey`, `jobExecutionMap`, reason) =>
+      reason.getMessage should be("Sub workflow execution actor unable to write final state to metadata")
+      reason.getCause should be(expectedException)
     }
     deathWatch.expectTerminated(swea, awaitTimeout)
   }
@@ -305,8 +326,8 @@ class SubWorkflowExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
     val jobExecutionMap: JobExecutionMap = Map.empty
     val workflowAbortedMessage = WorkflowExecutionAbortedResponse(jobExecutionMap)
     swea ! workflowAbortedMessage
-    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) {
-      case PutMetadataActionAndRespond(events, _, _) => swea ! MetadataWriteSuccess(events)
+    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) { case PutMetadataActionAndRespond(events, _, _) =>
+      swea ! MetadataWriteSuccess(events)
     }
     parentProbe.expectMsg(SubWorkflowAbortedResponse(subKey, jobExecutionMap))
     deathWatch.expectTerminated(swea, awaitTimeout)
@@ -316,7 +337,7 @@ class SubWorkflowExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
     val swea = buildSWEA()
     swea.setState(
       SubWorkflowRunningState,
-      SubWorkflowExecutionActorLiveData(Option(WorkflowId.randomId()), Option(subWorkflowActor.ref)),
+      SubWorkflowExecutionActorLiveData(Option(WorkflowId.randomId()), Option(subWorkflowActor.ref))
     )
 
     deathWatch watch swea
@@ -325,8 +346,8 @@ class SubWorkflowExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
     swea ! EngineLifecycleActorAbortCommand
     subWorkflowActor.expectMsg(EngineLifecycleActorAbortCommand)
     subWorkflowActor.reply(WorkflowExecutionAbortedResponse(jobExecutionMap))
-    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) {
-      case PutMetadataActionAndRespond(events, _, _) => swea ! MetadataWriteSuccess(events)
+    serviceRegistryProbe.fishForSpecificMessage(awaitTimeout) { case PutMetadataActionAndRespond(events, _, _) =>
+      swea ! MetadataWriteSuccess(events)
     }
     parentProbe.expectMsg(SubWorkflowAbortedResponse(subKey, jobExecutionMap))
     deathWatch.expectTerminated(swea, awaitTimeout)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActorSpec.scala
index 61877de8a1a..094a41c78a5 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheDiffActorSpec.scala
@@ -15,7 +15,12 @@ import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import spray.json.{JsArray, JsField, JsObject, JsString, JsValue}
 
-class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with ImplicitSender with Eventually {
+class CallCacheDiffActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with ImplicitSender
+    with Eventually {
 
   behavior of "CallCacheDiffActor"
 
@@ -50,23 +55,37 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
   )
 
   val eventsA = List(
-      MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "executionStatus"), MetadataValue("Done")),
-      MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:allowResultReuse"), MetadataValue(true)),
-      MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in only in A"), MetadataValue("hello from A")),
-      MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in A and B with same value"), MetadataValue("we are thinking the same thought")),
-      MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in A and B with different value"), MetadataValue("I'm the hash for A !"))
+    MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "executionStatus"), MetadataValue("Done")),
+    MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:allowResultReuse"), MetadataValue(true)),
+    MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in only in A"),
+                  MetadataValue("hello from A")
+    ),
+    MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in A and B with same value"),
+                  MetadataValue("we are thinking the same thought")
+    ),
+    MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in A and B with different value"),
+                  MetadataValue("I'm the hash for A !")
+    )
   )
-  val workflowMetadataA: JsObject = MetadataBuilderActor.workflowMetadataResponse(workflowIdA, eventsA, includeCallsIfEmpty = false, Map.empty)
+  val workflowMetadataA: JsObject =
+    MetadataBuilderActor.workflowMetadataResponse(workflowIdA, eventsA, includeCallsIfEmpty = false, Map.empty)
   val responseForA = SuccessfulMetadataJsonResponse(MetadataService.GetMetadataAction(queryA), workflowMetadataA)
 
   val eventsB = List(
     MetadataEvent(MetadataKey(workflowIdB, metadataJobKeyB, "executionStatus"), MetadataValue("Failed")),
     MetadataEvent(MetadataKey(workflowIdB, metadataJobKeyB, "callCaching:allowResultReuse"), MetadataValue(false)),
-    MetadataEvent(MetadataKey(workflowIdB, metadataJobKeyB, "callCaching:hashes:hash in only in B"), MetadataValue("hello from B")),
-    MetadataEvent(MetadataKey(workflowIdB, metadataJobKeyB, "callCaching:hashes:hash in A and B with same value"), MetadataValue("we are thinking the same thought")),
-    MetadataEvent(MetadataKey(workflowIdB, metadataJobKeyB, "callCaching:hashes:hash in A and B with different value"), MetadataValue("I'm the hash for B !"))
+    MetadataEvent(MetadataKey(workflowIdB, metadataJobKeyB, "callCaching:hashes:hash in only in B"),
+                  MetadataValue("hello from B")
+    ),
+    MetadataEvent(MetadataKey(workflowIdB, metadataJobKeyB, "callCaching:hashes:hash in A and B with same value"),
+                  MetadataValue("we are thinking the same thought")
+    ),
+    MetadataEvent(MetadataKey(workflowIdB, metadataJobKeyB, "callCaching:hashes:hash in A and B with different value"),
+                  MetadataValue("I'm the hash for B !")
+    )
   )
-  val workflowMetadataB: JsObject = MetadataBuilderActor.workflowMetadataResponse(workflowIdB, eventsB, includeCallsIfEmpty = false, Map.empty)
+  val workflowMetadataB: JsObject =
+    MetadataBuilderActor.workflowMetadataResponse(workflowIdB, eventsB, includeCallsIfEmpty = false, Map.empty)
   val responseForB = SuccessfulMetadataJsonResponse(MetadataService.GetMetadataAction(queryB), workflowMetadataB)
 
   it should "send correct queries to MetadataService when receiving a CallCacheDiffRequest" in {
@@ -90,7 +109,12 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     actor ! responseForA
 
     eventually {
-      actor.stateData shouldBe CallCacheDiffWithRequest(queryA, queryB, Some(WorkflowMetadataJson(workflowMetadataA)), None, self)
+      actor.stateData shouldBe CallCacheDiffWithRequest(queryA,
+                                                        queryB,
+                                                        Some(WorkflowMetadataJson(workflowMetadataA)),
+                                                        None,
+                                                        self
+      )
       actor.stateName shouldBe WaitingForMetadata
     }
 
@@ -106,7 +130,12 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     actor ! responseForB
 
     eventually {
-      actor.stateData shouldBe CallCacheDiffWithRequest(queryA, queryB, None, Some(WorkflowMetadataJson(workflowMetadataB)), self)
+      actor.stateData shouldBe CallCacheDiffWithRequest(queryA,
+                                                        queryB,
+                                                        None,
+                                                        Some(WorkflowMetadataJson(workflowMetadataB)),
+                                                        self
+      )
       actor.stateName shouldBe WaitingForMetadata
     }
 
@@ -118,7 +147,9 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     val actor = TestFSMRef(new CallCacheDiffActor(mockServiceRegistryActor.ref))
     watch(actor)
 
-    actor.setState(WaitingForMetadata, CallCacheDiffWithRequest(queryA, queryB, None, Some(WorkflowMetadataJson(workflowMetadataB)), self))
+    actor.setState(WaitingForMetadata,
+                   CallCacheDiffWithRequest(queryA, queryB, None, Some(WorkflowMetadataJson(workflowMetadataB)), self)
+    )
 
     actor ! responseForA
 
@@ -131,7 +162,9 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     val actor = TestFSMRef(new CallCacheDiffActor(mockServiceRegistryActor.ref))
     watch(actor)
 
-    actor.setState(WaitingForMetadata, CallCacheDiffWithRequest(queryA, queryB, Some(WorkflowMetadataJson(workflowMetadataA)), None, self))
+    actor.setState(WaitingForMetadata,
+                   CallCacheDiffWithRequest(queryA, queryB, Some(WorkflowMetadataJson(workflowMetadataA)), None, self)
+    )
 
     actor ! responseForB
 
@@ -194,11 +227,11 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     expectMsgPF() {
       case r: SuccessfulCallCacheDiffResponse =>
         withClue(s"""
-             |Expected:
-             |${correctCallCacheDiff.prettyPrint}
-             |
-             |Actual:
-             |${r.toJson.prettyPrint}""".stripMargin) {
+                    |Expected:
+                    |${correctCallCacheDiff.prettyPrint}
+                    |
+                    |Actual:
+                    |${r.toJson.prettyPrint}""".stripMargin) {
           r.toJson should be(correctCallCacheDiff)
         }
       case other => fail(s"Expected SuccessfulCallCacheDiffResponse but got $other")
@@ -219,19 +252,30 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     val eventsAAttempt1 = List(
       MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "executionStatus"), MetadataValue("Failed")),
       MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:allowResultReuse"), MetadataValue(false)),
-      MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in only in A"), MetadataValue("ouch!")),
-      MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in A and B with same value"), MetadataValue("ouch!")),
-      MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in A and B with different value"), MetadataValue("ouch!"))
+      MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in only in A"),
+                    MetadataValue("ouch!")
+      ),
+      MetadataEvent(MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in A and B with same value"),
+                    MetadataValue("ouch!")
+      ),
+      MetadataEvent(
+        MetadataKey(workflowIdA, metadataJobKeyA, "callCaching:hashes:hash in A and B with different value"),
+        MetadataValue("ouch!")
+      )
     )
     // And update the old "eventsA" to represent attempt 2:
-    val eventsAAttempt2 = eventsA.map(event => event.copy(key = event.key.copy(jobKey = event.key.jobKey.map(_.copy(attempt = 2)))))
+    val eventsAAttempt2 =
+      eventsA.map(event => event.copy(key = event.key.copy(jobKey = event.key.jobKey.map(_.copy(attempt = 2)))))
 
     val modifiedEventsA = eventsAAttempt1 ++ eventsAAttempt2
 
-    val workflowMetadataA: JsObject = MetadataBuilderActor.workflowMetadataResponse(workflowIdA, modifiedEventsA, includeCallsIfEmpty = false, Map.empty)
+    val workflowMetadataA: JsObject = MetadataBuilderActor.workflowMetadataResponse(workflowIdA,
+                                                                                    modifiedEventsA,
+                                                                                    includeCallsIfEmpty = false,
+                                                                                    Map.empty
+    )
     val responseForA = SuccessfulMetadataJsonResponse(MetadataService.GetMetadataAction(queryA), workflowMetadataA)
 
-
     actor ! responseForB
     actor ! responseForA
 
@@ -267,9 +311,8 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
 
     actor ! responseA
 
-    expectMsgPF(1 second) {
-      case FailedCallCacheDiffResponse(e: Throwable) =>
-        e.getMessage shouldBe "Query lookup failed - but it's ok ! this is a test !"
+    expectMsgPF(1 second) { case FailedCallCacheDiffResponse(e: Throwable) =>
+      e.getMessage shouldBe "Query lookup failed - but it's ok ! this is a test !"
     }
 
     expectTerminated(actor)
@@ -278,18 +321,20 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
   it should "respond with an appropriate error if calls' hashes are missing" in {
     testExpectedErrorForModifiedMetadata(
       metadataFilter = _.key.key.contains("hashes"),
-      error = s"""Failed to calculate diff for call A and call B:
-                 |Failed to extract relevant metadata for call A (971652a6-139c-4ef3-96b5-aeb611a40dbf / callFqnA:1) (reason 1 of 1): No 'hashes' field found
-                 |Failed to extract relevant metadata for call B (bb85b3ec-e179-4f12-b90f-5191216da598 / callFqnB:-1) (reason 1 of 1): No 'hashes' field found""".stripMargin
+      error =
+        s"""Failed to calculate diff for call A and call B:
+           |Failed to extract relevant metadata for call A (971652a6-139c-4ef3-96b5-aeb611a40dbf / callFqnA:1) (reason 1 of 1): No 'hashes' field found
+           |Failed to extract relevant metadata for call B (bb85b3ec-e179-4f12-b90f-5191216da598 / callFqnB:-1) (reason 1 of 1): No 'hashes' field found""".stripMargin
     )
   }
 
   it should "respond with an appropriate error if both calls are missing" in {
     testExpectedErrorForModifiedMetadata(
       metadataFilter = _.key.jobKey.nonEmpty,
-      error = s"""Failed to calculate diff for call A and call B:
-                 |Failed to extract relevant metadata for call A (971652a6-139c-4ef3-96b5-aeb611a40dbf / callFqnA:1) (reason 1 of 1): No 'calls' field found
-                 |Failed to extract relevant metadata for call B (bb85b3ec-e179-4f12-b90f-5191216da598 / callFqnB:-1) (reason 1 of 1): No 'calls' field found""".stripMargin
+      error =
+        s"""Failed to calculate diff for call A and call B:
+           |Failed to extract relevant metadata for call A (971652a6-139c-4ef3-96b5-aeb611a40dbf / callFqnA:1) (reason 1 of 1): No 'calls' field found
+           |Failed to extract relevant metadata for call B (bb85b3ec-e179-4f12-b90f-5191216da598 / callFqnB:-1) (reason 1 of 1): No 'calls' field found""".stripMargin
     )
   }
 
@@ -301,7 +346,9 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     def str(s: String): JsString = JsString(s)
 
     it should "handle nested JsObjects if field names collide" in {
-      val objectToParse = obj("hashes" -> obj("subObj" -> obj("field" -> str("fieldValue1"), "subObj" -> obj("field" -> str("fieldValue2")))))
+      val objectToParse = obj(
+        "hashes" -> obj("subObj" -> obj("field" -> str("fieldValue1"), "subObj" -> obj("field" -> str("fieldValue2"))))
+      )
       val res = CallCacheDiffActor.extractHashes(objectToParse).toOption
 
       res should be(defined)
@@ -324,9 +371,16 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     val actor = TestFSMRef(new CallCacheDiffActor(mockServiceRegistryActor.ref))
     watch(actor)
 
-    def getModifiedResponse(workflowId: WorkflowId, query: MetadataQuery, events: Seq[MetadataEvent]): SuccessfulMetadataJsonResponse = {
+    def getModifiedResponse(workflowId: WorkflowId,
+                            query: MetadataQuery,
+                            events: Seq[MetadataEvent]
+    ): SuccessfulMetadataJsonResponse = {
       val modifiedEvents = events.filterNot(metadataFilter) // filters out any "call" level metadata
-      val modifiedWorkflowMetadata = MetadataBuilderActor.workflowMetadataResponse(workflowId, modifiedEvents, includeCallsIfEmpty = false, Map.empty)
+      val modifiedWorkflowMetadata = MetadataBuilderActor.workflowMetadataResponse(workflowId,
+                                                                                   modifiedEvents,
+                                                                                   includeCallsIfEmpty = false,
+                                                                                   Map.empty
+      )
       SuccessfulMetadataJsonResponse(MetadataService.GetMetadataAction(query), modifiedWorkflowMetadata)
     }
 
@@ -335,8 +389,8 @@ class CallCacheDiffActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     actor ! getModifiedResponse(workflowIdA, queryA, eventsA)
     actor ! getModifiedResponse(workflowIdB, queryB, eventsB)
 
-    expectMsgPF(1 second) {
-      case FailedCallCacheDiffResponse(e) => e.getMessage shouldBe error
+    expectMsgPF(1 second) { case FailedCallCacheDiffResponse(e) =>
+      e.getMessage shouldBe error
     }
     expectTerminated(actor)
   }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActorDataSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActorDataSpec.scala
index 4cb279602c2..13b1a2205de 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActorDataSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActorDataSpec.scala
@@ -5,13 +5,24 @@ import cromwell.backend._
 import cromwell.backend.standard.callcaching.StandardFileHashingActor.SingleFileHashRequest
 import cromwell.core.TestKitSuite
 import cromwell.core.callcaching._
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{CallCacheHashingJobActorData, CompleteFileHashingResult, NoFileHashesResult, PartialFileHashingResult}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{
+  CallCacheHashingJobActorData,
+  CompleteFileHashingResult,
+  NoFileHashesResult,
+  PartialFileHashingResult
+}
 import org.scalatest.concurrent.Eventually
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks
 
-class CallCacheHashingJobActorDataSpec extends TestKitSuite with AnyFlatSpecLike with BackendSpec with Matchers with Eventually with TableDrivenPropertyChecks {
+class CallCacheHashingJobActorDataSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with BackendSpec
+    with Matchers
+    with Eventually
+    with TableDrivenPropertyChecks {
   behavior of "CallCacheReadingJobActorData"
 
   private val fileHash1 = HashResult(HashKey("key"), HashValue("value"))
@@ -20,71 +31,107 @@ class CallCacheHashingJobActorDataSpec extends TestKitSuite with AnyFlatSpecLike
   private val fileHashRequest1 = SingleFileHashRequest(null, fileHash1.hashKey, null, null)
   private val fileHashRequest2 = SingleFileHashRequest(null, fileHash2.hashKey, null, null)
   private val fileHashRequest3 = SingleFileHashRequest(null, fileHash3.hashKey, null, null)
-  
+
   private val testCases = Table(
     ("dataBefore", "dataAfter", "result"),
     // No fileHashRequestsRemaining
     (
       CallCacheHashingJobActorData(
-        List.empty, List.empty, None, 50
+        List.empty,
+        List.empty,
+        None,
+        50
       ),
       CallCacheHashingJobActorData(
-        List.empty, List(fileHash1), None, 50
+        List.empty,
+        List(fileHash1),
+        None,
+        50
       ),
       Option(NoFileHashesResult)
     ),
     // Last fileHashRequestsRemaining
     (
       CallCacheHashingJobActorData(
-        List(List(fileHashRequest1)), List.empty, None, 50
+        List(List(fileHashRequest1)),
+        List.empty,
+        None,
+        50
       ),
       CallCacheHashingJobActorData(
-        List.empty, List(fileHash1), None, 50
+        List.empty,
+        List(fileHash1),
+        None,
+        50
       ),
       Option(CompleteFileHashingResult(Set(fileHash1), "6A02F950958AEDA3DBBF83FBB306A030"))
     ),
     // Last batch and not last value
     (
       CallCacheHashingJobActorData(
-        List(List(fileHashRequest1, fileHashRequest2)), List.empty, None, 50
+        List(List(fileHashRequest1, fileHashRequest2)),
+        List.empty,
+        None,
+        50
       ),
       CallCacheHashingJobActorData(
-        List(List(fileHashRequest2)), List(fileHash1), None, 50
+        List(List(fileHashRequest2)),
+        List(fileHash1),
+        None,
+        50
       ),
       None
     ),
     // Not last batch but last value of this batch
     (
       CallCacheHashingJobActorData(
-        List(List(fileHashRequest1), List(fileHashRequest2)), List.empty, None, 50
+        List(List(fileHashRequest1), List(fileHashRequest2)),
+        List.empty,
+        None,
+        50
       ),
       CallCacheHashingJobActorData(
-        List(List(fileHashRequest2)), List(fileHash1), None, 50
+        List(List(fileHashRequest2)),
+        List(fileHash1),
+        None,
+        50
       ),
       Option(PartialFileHashingResult(NonEmptyList.of(fileHash1)))
     ),
     // Not last batch and not last value of this batch
     (
       CallCacheHashingJobActorData(
-        List(List(fileHashRequest1, fileHashRequest2), List(fileHashRequest3)), List.empty, None, 50
+        List(List(fileHashRequest1, fileHashRequest2), List(fileHashRequest3)),
+        List.empty,
+        None,
+        50
       ),
       CallCacheHashingJobActorData(
-        List(List(fileHashRequest2), List(fileHashRequest3)), List(fileHash1), None, 50
+        List(List(fileHashRequest2), List(fileHashRequest3)),
+        List(fileHash1),
+        None,
+        50
       ),
       None
     ),
     // Makes sure new hash is added at the front of the list
     (
       CallCacheHashingJobActorData(
-        List(List(fileHashRequest1, fileHashRequest2), List(fileHashRequest3)), List(fileHash2), None, 50
+        List(List(fileHashRequest1, fileHashRequest2), List(fileHashRequest3)),
+        List(fileHash2),
+        None,
+        50
       ),
       CallCacheHashingJobActorData(
-        List(List(fileHashRequest2), List(fileHashRequest3)), List(fileHash1, fileHash2), None, 50
+        List(List(fileHashRequest2), List(fileHashRequest3)),
+        List(fileHash1, fileHash2),
+        None,
+        50
       ),
       None
     )
   )
-  
+
   it should "process new file hashes" in {
     forAll(testCases) { case (oldData, newData, result) =>
       oldData.withFileHash(fileHash1) shouldBe (newData -> result)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActorSpec.scala
index 602d04c145d..b70722c4200 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheHashingJobActorSpec.scala
@@ -10,7 +10,17 @@ import cromwell.backend._
 import cromwell.backend.standard.callcaching.StandardFileHashingActor.{FileHashResponse, SingleFileHashRequest}
 import cromwell.core.TestKitSuite
 import cromwell.core.callcaching.{HashingFailedMessage, _}
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{CCHJAFileHashResponse, CallCacheHashingJobActorData, CompleteFileHashingResult, HashingFiles, InitialHashingResult, NextBatchOfFileHashesRequest, NoFileHashesResult, PartialFileHashingResult, WaitingForHashFileRequest}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{
+  CallCacheHashingJobActorData,
+  CCHJAFileHashResponse,
+  CompleteFileHashingResult,
+  HashingFiles,
+  InitialHashingResult,
+  NextBatchOfFileHashesRequest,
+  NoFileHashesResult,
+  PartialFileHashingResult,
+  WaitingForHashFileRequest
+}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.CacheMiss
 import cromwell.util.WomMocks
 import org.scalatest.Assertion
@@ -24,12 +34,20 @@ import wom.values.{WomInteger, WomSingleFile, WomString, WomValue}
 
 import scala.util.control.NoStackTrace
 
-class CallCacheHashingJobActorSpec extends TestKitSuite with AnyFlatSpecLike with BackendSpec with Matchers
-  with Eventually with TableDrivenPropertyChecks with MockSugar {
+class CallCacheHashingJobActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with BackendSpec
+    with Matchers
+    with Eventually
+    with TableDrivenPropertyChecks
+    with MockSugar {
   behavior of "CallCacheReadingJobActor"
 
   def templateJobDescriptor(inputs: Map[LocallyQualifiedName, WomValue] = Map.empty): BackendJobDescriptor = {
-    val task = WomMocks.mockTaskDefinition("task").copy(commandTemplateBuilder = Function.const(List(StringCommandPart("Do the stuff... now!!")).validNel))
+    val task = WomMocks
+      .mockTaskDefinition("task")
+      .copy(commandTemplateBuilder = Function.const(List(StringCommandPart("Do the stuff... now!!")).validNel))
     val call = WomMocks.mockTaskCall(WomIdentifier("call"), definition = task)
     val workflowDescriptor = mock[BackendWorkflowDescriptor]
     val runtimeAttributes = Map(
@@ -38,24 +56,34 @@ class CallCacheHashingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
       "continueOnReturnCode" -> WomInteger(0),
       "docker" -> WomString("ubuntu:latest")
     )
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, BackendJobDescriptorKey(call, None, 1), runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                             BackendJobDescriptorKey(call, None, 1),
+                                             runtimeAttributes,
+                                             fqnWdlMapToDeclarationMap(inputs),
+                                             NoDocker,
+                                             None,
+                                             Map.empty
+    )
     jobDescriptor
   }
 
   it should "die immediately if created without cache read actor and write to cache turned off" in {
     val parent = TestProbe()
-    val testActor = TestFSMRef(new CallCacheHashingJobActor(
-      templateJobDescriptor(),
-      None,
-      None,
-      Set.empty,
-      "backedName",
-      Props.empty,
-      DockerWithHash("ubuntu@sha256:blablablba"),
-      CallCachingActivity(readWriteMode = ReadCache),
-      callCachePathPrefixes = None,
-      fileHashBatchSize = 100
-    ), parent.ref)
+    val testActor = TestFSMRef(
+      new CallCacheHashingJobActor(
+        templateJobDescriptor(),
+        None,
+        None,
+        Set.empty,
+        "backedName",
+        Props.empty,
+        DockerWithHash("ubuntu@sha256:blablablba"),
+        CallCachingActivity(readWriteMode = ReadCache),
+        callCachePathPrefixes = None,
+        fileHashBatchSize = 100
+      ),
+      parent.ref
+    )
     watch(testActor)
     expectTerminated(testActor)
     parent.expectMsgClass(classOf[InitialHashingResult])
@@ -80,18 +108,21 @@ class CallCacheHashingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     )
     val callCacheRead = TestProbe()
     val jobDescriptor: BackendJobDescriptor = templateJobDescriptor(inputs)
-    val actorUnderTest = TestFSMRef(new CallCacheHashingJobActor(
-      jobDescriptor,
-      Option(callCacheRead.ref),
-      None,
-      runtimeAttributeDefinitions,
-      "backedName",
-      Props.empty,
-      DockerWithHash("ubuntu@sha256:blablablba"),
-      CallCachingActivity(readWriteMode = ReadAndWriteCache),
-      callCachePathPrefixes = None,
-      fileHashBatchSize = 100
-    ), parent.ref)
+    val actorUnderTest = TestFSMRef(
+      new CallCacheHashingJobActor(
+        jobDescriptor,
+        Option(callCacheRead.ref),
+        None,
+        runtimeAttributeDefinitions,
+        "backedName",
+        Props.empty,
+        DockerWithHash("ubuntu@sha256:blablablba"),
+        CallCachingActivity(readWriteMode = ReadAndWriteCache),
+        callCachePathPrefixes = None,
+        fileHashBatchSize = 100
+      ),
+      parent.ref
+    )
 
     val expectedInitialHashes = Set(
       // md5 of Do the stuff... now
@@ -104,7 +135,9 @@ class CallCacheHashingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
       HashResult(HashKey("output count"), HashValue("CFCD208495D565EF66E7DFF9F98764DA")),
       HashResult(HashKey("runtime attribute", "failOnStderr"), HashValue("N/A")),
       // md5 of 1
-      HashResult(HashKey(checkForHitOrMiss = false, "runtime attribute", "cpu"), HashValue("C4CA4238A0B923820DCC509A6F75849B")),
+      HashResult(HashKey(checkForHitOrMiss = false, "runtime attribute", "cpu"),
+                 HashValue("C4CA4238A0B923820DCC509A6F75849B")
+      ),
       // md5 of 0
       HashResult(HashKey("runtime attribute", "continueOnReturnCode"), HashValue("CFCD208495D565EF66E7DFF9F98764DA")),
       // md5 of "hello" (with quotes)
@@ -128,25 +161,32 @@ class CallCacheHashingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
                 testFileHashingActor: ActorRef,
                 parent: ActorRef,
                 writeToCache: Boolean = true,
-                addFileHashMockResult: Option[(CallCacheHashingJobActorData, Option[CCHJAFileHashResponse])] = None): TestFSMRef[CallCacheHashingJobActor.CallCacheHashingJobActorState, CallCacheHashingJobActorData, CallCacheHashingJobActor] = {
-    TestFSMRef(new CallCacheHashingJobActor(
-      templateJobDescriptor(),
-      callCacheReader,
-      None,
-      Set.empty,
-      "backend",
-      Props.empty,
-      DockerWithHash("ubuntu@256:blablabla"),
-      CallCachingActivity(readWriteMode = if (writeToCache) ReadAndWriteCache else ReadCache),
-      callCachePathPrefixes = None,
-      fileHashBatchSize = 100
-    ) {
-      override def makeFileHashingActor(): ActorRef = testFileHashingActor
-      override def addFileHash(hashResult: HashResult, data: CallCacheHashingJobActorData): (CallCacheHashingJobActorData, Option[CCHJAFileHashResponse]) = {
-        addFileHashMockResult.getOrElse(super.addFileHash(hashResult, data))
-      }
-    }, parent)
-  }
+                addFileHashMockResult: Option[(CallCacheHashingJobActorData, Option[CCHJAFileHashResponse])] = None
+  ): TestFSMRef[CallCacheHashingJobActor.CallCacheHashingJobActorState,
+                CallCacheHashingJobActorData,
+                CallCacheHashingJobActor
+  ] =
+    TestFSMRef(
+      new CallCacheHashingJobActor(
+        templateJobDescriptor(),
+        callCacheReader,
+        None,
+        Set.empty,
+        "backend",
+        Props.empty,
+        DockerWithHash("ubuntu@256:blablabla"),
+        CallCachingActivity(readWriteMode = if (writeToCache) ReadAndWriteCache else ReadCache),
+        callCachePathPrefixes = None,
+        fileHashBatchSize = 100
+      ) {
+        override def makeFileHashingActor(): ActorRef = testFileHashingActor
+        override def addFileHash(hashResult: HashResult,
+                                 data: CallCacheHashingJobActorData
+        ): (CallCacheHashingJobActorData, Option[CCHJAFileHashResponse]) =
+          addFileHashMockResult.getOrElse(super.addFileHash(hashResult, data))
+      },
+      parent
+    )
 
   it should "send hash file requests when receiving a NextBatchOfFileHashesRequest" in {
     val callCacheReadProbe = TestProbe()
@@ -198,7 +238,12 @@ class CallCacheHashingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     // still gives a CCReader when instantiating the actor, but not in the data (above)
     // This ensures the check is done with the data and not the actor attribute, as the data will change if the ccreader dies but the actor attribute
     // will stay Some(...)
-    val cchja = makeCCHJA(Option(TestProbe().ref), fileHashingActor.ref, TestProbe().ref, writeToCache = true, Option(newData -> Option(result)))
+    val cchja = makeCCHJA(Option(TestProbe().ref),
+                          fileHashingActor.ref,
+                          TestProbe().ref,
+                          writeToCache = true,
+                          Option(newData -> Option(result))
+    )
     watch(cchja)
     cchja.setState(HashingFiles)
 
@@ -211,19 +256,24 @@ class CallCacheHashingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
 
   List(
     ("send itself a NextBatchOfFileHashesRequest when a batch is complete and there is no CC Reader", None),
-    ("send itself a NextBatchOfFileHashesRequest when a batch is complete and there is a CC Reader", Option(TestProbe().ref))
-  ) foreach {
-    case (description, ccReader) =>
-      it should description in selfSendNextBatchRequest(ccReader)
+    ("send itself a NextBatchOfFileHashesRequest when a batch is complete and there is a CC Reader",
+     Option(TestProbe().ref)
+    )
+  ) foreach { case (description, ccReader) =>
+    it should description in selfSendNextBatchRequest(ccReader)
   }
 
   it should "send FinalFileHashingResult to parent and CCReader and die" in {
     val parent = TestProbe()
     val callCacheReadProbe = TestProbe()
-    List(CompleteFileHashingResult(Set(mock[HashResult]), "AggregatedFileHash"), NoFileHashesResult) foreach
-      { result =>
+    List(CompleteFileHashingResult(Set(mock[HashResult]), "AggregatedFileHash"), NoFileHashesResult) foreach { result =>
       val newData = CallCacheHashingJobActorData(List.empty, List.empty, Option(callCacheReadProbe.ref), 50)
-      val cchja = makeCCHJA(Option(callCacheReadProbe.ref), TestProbe().ref, parent.ref, writeToCache = true, Option(newData -> Option(result)))
+      val cchja = makeCCHJA(Option(callCacheReadProbe.ref),
+                            TestProbe().ref,
+                            parent.ref,
+                            writeToCache = true,
+                            Option(newData -> Option(result))
+      )
 
       parent.expectMsgClass(classOf[InitialHashingResult])
       callCacheReadProbe.expectMsgClass(classOf[InitialHashingResult])
@@ -242,8 +292,14 @@ class CallCacheHashingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
   it should "wait for next file hash if the batch is not complete yet" in {
     val callCacheReadProbe = TestProbe()
     val parent = TestProbe()
-    val newData: CallCacheHashingJobActorData = CallCacheHashingJobActorData(List.empty, List.empty, Option(callCacheReadProbe.ref), 50)
-    val cchja = makeCCHJA(Option(callCacheReadProbe.ref), TestProbe().ref, parent.ref, writeToCache = true, Option(newData -> None))
+    val newData: CallCacheHashingJobActorData =
+      CallCacheHashingJobActorData(List.empty, List.empty, Option(callCacheReadProbe.ref), 50)
+    val cchja = makeCCHJA(Option(callCacheReadProbe.ref),
+                          TestProbe().ref,
+                          parent.ref,
+                          writeToCache = true,
+                          Option(newData -> None)
+    )
 
     parent.expectMsgClass(classOf[InitialHashingResult])
     callCacheReadProbe.expectMsgClass(classOf[InitialHashingResult])
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadingJobActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadingJobActorSpec.scala
index a39597fa347..78106628ca3 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadingJobActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCacheReadingJobActorSpec.scala
@@ -2,10 +2,19 @@ package cromwell.engine.workflow.lifecycle.execution.callcaching
 
 import akka.testkit.{TestFSMRef, TestProbe}
 import cromwell.core.TestKitSuite
-import cromwell.core.callcaching.{HashKey, HashResult, HashValue, HashingFailedMessage}
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{CompleteFileHashingResult, InitialHashingResult, NextBatchOfFileHashesRequest, NoFileHashesResult}
+import cromwell.core.callcaching.{HashingFailedMessage, HashKey, HashResult, HashValue}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{
+  CompleteFileHashingResult,
+  InitialHashingResult,
+  NextBatchOfFileHashesRequest,
+  NoFileHashesResult
+}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadActor._
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadingJobActor.{CCRJAWithData, WaitingForCacheHitOrMiss, _}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadingJobActor.{
+  CCRJAWithData,
+  WaitingForCacheHitOrMiss,
+  _
+}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.{CacheHit, CacheMiss, HashError}
 import cromwell.services.CallCaching.CallCachingEntryId
 import org.scalatest.concurrent.Eventually
@@ -35,7 +44,9 @@ class CallCacheReadingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     val callCacheReadProbe = TestProbe()
     val callCacheHashingActor = TestProbe()
     val actorUnderTest = TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None))
-    actorUnderTest.setState(WaitingForHashCheck, CCRJAWithData(callCacheHashingActor.ref, "AggregatedInitialHash", None, Set.empty))
+    actorUnderTest.setState(WaitingForHashCheck,
+                            CCRJAWithData(callCacheHashingActor.ref, "AggregatedInitialHash", None, Set.empty)
+    )
 
     callCacheReadProbe.send(actorUnderTest, HasMatchingEntries)
     callCacheHashingActor.expectMsg(NextBatchOfFileHashesRequest)
@@ -49,10 +60,13 @@ class CallCacheReadingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     val callCacheHashingActor = TestProbe()
     val parent = TestProbe()
 
-    val actorUnderTest = TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), parent.ref)
+    val actorUnderTest =
+      TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), parent.ref)
     parent.watch(actorUnderTest)
 
-    actorUnderTest.setState(WaitingForHashCheck, CCRJAWithData(callCacheHashingActor.ref, "AggregatedInitialHash", None, Set.empty))
+    actorUnderTest.setState(WaitingForHashCheck,
+                            CCRJAWithData(callCacheHashingActor.ref, "AggregatedInitialHash", None, Set.empty)
+    )
 
     callCacheReadProbe.send(actorUnderTest, NoMatchingEntries)
     parent.expectMsg(CacheMiss)
@@ -63,19 +77,31 @@ class CallCacheReadingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     val callCacheReadProbe = TestProbe()
     val callCacheHashingActor = TestProbe()
 
-    val actorUnderTest = TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), TestProbe().ref)
+    val actorUnderTest =
+      TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), TestProbe().ref)
 
     val aggregatedInitialHash: String = "AggregatedInitialHash"
     val aggregatedFileHash: String = "AggregatedFileHash"
-    actorUnderTest.setState(WaitingForFileHashes, CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty))
+    actorUnderTest.setState(WaitingForFileHashes,
+                            CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty)
+    )
 
     val fileHashes = Set(HashResult(HashKey("f1"), HashValue("h1")), HashResult(HashKey("f2"), HashValue("h2")))
     callCacheHashingActor.send(actorUnderTest, CompleteFileHashingResult(fileHashes, aggregatedFileHash))
-    callCacheReadProbe.expectMsg(CacheLookupRequest(AggregatedCallHashes(aggregatedInitialHash, aggregatedFileHash), Set.empty, prefixesHint = None))
+    callCacheReadProbe.expectMsg(
+      CacheLookupRequest(AggregatedCallHashes(aggregatedInitialHash, aggregatedFileHash),
+                         Set.empty,
+                         prefixesHint = None
+      )
+    )
 
     eventually {
       actorUnderTest.stateName shouldBe WaitingForCacheHitOrMiss
-      actorUnderTest.stateData shouldBe CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, Some(aggregatedFileHash), Set.empty)
+      actorUnderTest.stateData shouldBe CCRJAWithData(callCacheHashingActor.ref,
+                                                      aggregatedInitialHash,
+                                                      Some(aggregatedFileHash),
+                                                      Set.empty
+      )
     }
   }
 
@@ -83,13 +109,18 @@ class CallCacheReadingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     val callCacheReadProbe = TestProbe()
     val callCacheHashingActor = TestProbe()
 
-    val actorUnderTest = TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), TestProbe().ref)
+    val actorUnderTest =
+      TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), TestProbe().ref)
 
     val aggregatedInitialHash: String = "AggregatedInitialHash"
-    actorUnderTest.setState(WaitingForFileHashes, CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty))
+    actorUnderTest.setState(WaitingForFileHashes,
+                            CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty)
+    )
 
     callCacheHashingActor.send(actorUnderTest, NoFileHashesResult)
-    callCacheReadProbe.expectMsg(CacheLookupRequest(AggregatedCallHashes(aggregatedInitialHash, None), Set.empty, prefixesHint = None))
+    callCacheReadProbe.expectMsg(
+      CacheLookupRequest(AggregatedCallHashes(aggregatedInitialHash, None), Set.empty, prefixesHint = None)
+    )
 
     eventually {
       actorUnderTest.stateName shouldBe WaitingForCacheHitOrMiss
@@ -102,10 +133,13 @@ class CallCacheReadingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     val callCacheHashingActor = TestProbe()
     val parent = TestProbe()
 
-    val actorUnderTest = TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), parent.ref)
+    val actorUnderTest =
+      TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), parent.ref)
 
     val aggregatedInitialHash: String = "AggregatedInitialHash"
-    actorUnderTest.setState(WaitingForCacheHitOrMiss, CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty))
+    actorUnderTest.setState(WaitingForCacheHitOrMiss,
+                            CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty)
+    )
 
     val id: CallCachingEntryId = CallCachingEntryId(8)
     callCacheReadProbe.send(actorUnderTest, CacheLookupNextHit(id))
@@ -122,11 +156,14 @@ class CallCacheReadingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     val callCacheHashingActor = TestProbe()
     val parent = TestProbe()
 
-    val actorUnderTest = TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), parent.ref)
+    val actorUnderTest =
+      TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), parent.ref)
     parent.watch(actorUnderTest)
 
     val aggregatedInitialHash: String = "AggregatedInitialHash"
-    actorUnderTest.setState(WaitingForCacheHitOrMiss, CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty))
+    actorUnderTest.setState(WaitingForCacheHitOrMiss,
+                            CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty)
+    )
 
     callCacheReadProbe.send(actorUnderTest, CacheLookupNoHit)
     parent.expectMsg(CacheMiss)
@@ -138,14 +175,19 @@ class CallCacheReadingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     val callCacheReadProbe = TestProbe()
     val callCacheHashingActor = TestProbe()
 
-    val actorUnderTest = TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), TestProbe().ref)
+    val actorUnderTest =
+      TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), TestProbe().ref)
 
     val aggregatedInitialHash: String = "AggregatedInitialHash"
     val seenCaches: Set[CallCachingEntryId] = Set(CallCachingEntryId(0))
-    actorUnderTest.setState(WaitingForCacheHitOrMiss, CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, seenCaches))
+    actorUnderTest.setState(WaitingForCacheHitOrMiss,
+                            CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, seenCaches)
+    )
 
     actorUnderTest ! NextHit
-    callCacheReadProbe.expectMsg(CacheLookupRequest(AggregatedCallHashes(aggregatedInitialHash, None), seenCaches, prefixesHint = None))
+    callCacheReadProbe.expectMsg(
+      CacheLookupRequest(AggregatedCallHashes(aggregatedInitialHash, None), seenCaches, prefixesHint = None)
+    )
 
     actorUnderTest.stateName shouldBe WaitingForCacheHitOrMiss
   }
@@ -154,15 +196,24 @@ class CallCacheReadingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     val callCacheReadProbe = TestProbe()
     val callCacheHashingActor = TestProbe()
 
-    val actorUnderTest = TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), TestProbe().ref)
+    val actorUnderTest =
+      TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), TestProbe().ref)
 
     val aggregatedInitialHash: String = "AggregatedInitialHash"
     val aggregatedFileHash: String = "AggregatedFileHash"
     val seenCaches: Set[CallCachingEntryId] = Set(CallCachingEntryId(0))
-    actorUnderTest.setState(WaitingForCacheHitOrMiss, CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, Option(aggregatedFileHash), seenCaches))
+    actorUnderTest.setState(
+      WaitingForCacheHitOrMiss,
+      CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, Option(aggregatedFileHash), seenCaches)
+    )
 
     actorUnderTest ! NextHit
-    callCacheReadProbe.expectMsg(CacheLookupRequest(AggregatedCallHashes(aggregatedInitialHash, Option(aggregatedFileHash)), seenCaches, prefixesHint = None))
+    callCacheReadProbe.expectMsg(
+      CacheLookupRequest(AggregatedCallHashes(aggregatedInitialHash, Option(aggregatedFileHash)),
+                         seenCaches,
+                         prefixesHint = None
+      )
+    )
 
     actorUnderTest.stateName shouldBe WaitingForCacheHitOrMiss
   }
@@ -172,11 +223,14 @@ class CallCacheReadingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     val callCacheHashingActor = TestProbe()
     val parent = TestProbe()
 
-    val actorUnderTest = TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), parent.ref)
+    val actorUnderTest =
+      TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), parent.ref)
     parent.watch(actorUnderTest)
 
     val aggregatedInitialHash: String = "AggregatedInitialHash"
-    actorUnderTest.setState(WaitingForCacheHitOrMiss, CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty))
+    actorUnderTest.setState(WaitingForCacheHitOrMiss,
+                            CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty)
+    )
 
     callCacheHashingActor.send(actorUnderTest, HashingFailedMessage("file", new Exception("Hashing failed")))
     parent.expectMsg(CacheMiss)
@@ -189,11 +243,14 @@ class CallCacheReadingJobActorSpec extends TestKitSuite with AnyFlatSpecLike wit
     val callCacheHashingActor = TestProbe()
     val parent = TestProbe()
 
-    val actorUnderTest = TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), parent.ref)
+    val actorUnderTest =
+      TestFSMRef(new CallCacheReadingJobActor(callCacheReadProbe.ref, prefixesHint = None), parent.ref)
     parent.watch(actorUnderTest)
 
     val aggregatedInitialHash: String = "AggregatedInitialHash"
-    actorUnderTest.setState(WaitingForCacheHitOrMiss, CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty))
+    actorUnderTest.setState(WaitingForCacheHitOrMiss,
+                            CCRJAWithData(callCacheHashingActor.ref, aggregatedInitialHash, None, Set.empty)
+    )
 
     val reason: Exception = new Exception("Lookup failed")
     callCacheHashingActor.send(actorUnderTest, CacheResultLookupFailure(reason))
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCachingSlickDatabaseSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCachingSlickDatabaseSpec.scala
index 279ee80681c..d3dcf58e3d3 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCachingSlickDatabaseSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/CallCachingSlickDatabaseSpec.scala
@@ -18,7 +18,11 @@ import org.scalatest.time.{Millis, Seconds, Span}
 import scala.concurrent.ExecutionContext
 
 class CallCachingSlickDatabaseSpec
-  extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalaFutures with BeforeAndAfterAll
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalaFutures
+    with BeforeAndAfterAll
     with TableDrivenPropertyChecks {
 
   implicit val ec: ExecutionContext = ExecutionContext.global
@@ -30,7 +34,7 @@ class CallCachingSlickDatabaseSpec
     ("description", "prefixOption"),
     ("without prefixes", None),
     ("with some prefixes", Option(List("prefix1", "prefix2", "prefix3", "prefix4"))),
-    ("with thousands of prefixes", Option((1 to 10000).map("prefix" + _).toList)),
+    ("with thousands of prefixes", Option((1 to 10000).map("prefix" + _).toList))
   )
 
   DatabaseSystem.All foreach { databaseSystem =>
@@ -38,14 +42,14 @@ class CallCachingSlickDatabaseSpec
 
     val containerOpt: Option[Container] = DatabaseTestKit.getDatabaseTestContainer(databaseSystem)
 
-    lazy val dataAccess = DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, EngineDatabaseType, databaseSystem)
+    lazy val dataAccess =
+      DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, EngineDatabaseType, databaseSystem)
 
     it should "start container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.start }
+      containerOpt.foreach(_.start)
     }
 
     forAll(allowResultReuseTests) { (description, prefixOption) =>
-
       val idA = WorkflowId.randomId().toString
       val callA = "AwesomeWorkflow.GoodJob"
       val callCachingEntryA = CallCachingEntry(
@@ -85,14 +89,15 @@ class CallCachingSlickDatabaseSpec
       it should s"honor allowResultReuse $description" taggedAs DbmsTest in {
         (for {
           _ <- dataAccess.addCallCaching(Seq(
-            CallCachingJoin(
-              callCachingEntryA,
-              callCachingHashEntriesA,
-              aggregation,
-              callCachingSimpletonsA, callCachingDetritusesA
-            )
-          ),
-            100
+                                           CallCachingJoin(
+                                             callCachingEntryA,
+                                             callCachingHashEntriesA,
+                                             aggregation,
+                                             callCachingSimpletonsA,
+                                             callCachingDetritusesA
+                                           )
+                                         ),
+                                         100
           )
           hasBaseAggregation <- dataAccess.hasMatchingCallCachingEntriesForBaseAggregation(
             "BASE_AGGREGATION",
@@ -115,20 +120,16 @@ class CallCachingSlickDatabaseSpec
           _ = join shouldBe defined
           getJoin = join.get
           // We can't compare directly because the ones out from the DB have IDs filled in, so just compare the relevant values
-          _ = getJoin
-            .callCachingHashEntries
+          _ = getJoin.callCachingHashEntries
             .map(e => (e.hashKey, e.hashValue)) should contain theSameElementsAs
             callCachingHashEntriesA.map(e => (e.hashKey, e.hashValue))
-          _ = getJoin
-            .callCachingSimpletonEntries
+          _ = getJoin.callCachingSimpletonEntries
             .map(e => (e.simpletonKey, e.simpletonValue.map(_.toRawString))) should contain theSameElementsAs
             callCachingSimpletonsA.map(e => (e.simpletonKey, e.simpletonValue.map(_.toRawString)))
-          _ = getJoin
-            .callCachingAggregationEntry
+          _ = getJoin.callCachingAggregationEntry
             .map(e => (e.baseAggregation, e.inputFilesAggregation)) shouldBe
             aggregation.map(e => (e.baseAggregation, e.inputFilesAggregation))
-          _ = getJoin
-            .callCachingDetritusEntries
+          _ = getJoin.callCachingDetritusEntries
             .map(e => (e.detritusKey, e.detritusValue.map(_.toRawString))) should contain theSameElementsAs
             callCachingDetritusesA.map(e => (e.detritusKey, e.detritusValue.map(_.toRawString)))
         } yield ()).futureValue
@@ -141,7 +142,7 @@ class CallCachingSlickDatabaseSpec
     }
 
     it should "stop container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.stop() }
+      containerOpt.foreach(_.stop())
     }
   }
 }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActorSpec.scala
index 1d78da0e37b..5e3bff33671 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/EngineJobHashingActorSpec.scala
@@ -6,7 +6,11 @@ import cats.syntax.validated._
 import cromwell.backend._
 import cromwell.core._
 import cromwell.core.callcaching._
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{CompleteFileHashingResult, InitialHashingResult, NoFileHashesResult}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheHashingJobActor.{
+  CompleteFileHashingResult,
+  InitialHashingResult,
+  NoFileHashesResult
+}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadingJobActor.NextHit
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor._
 import cromwell.services.metadata.MetadataService.PutMetadataAction
@@ -21,24 +25,42 @@ import wom.graph.WomIdentifier
 import wom.values.WomValue
 import common.mock.MockSugar
 
-class EngineJobHashingActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with BackendSpec
-  with MockSugar with TableDrivenPropertyChecks with Eventually {
+class EngineJobHashingActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with BackendSpec
+    with MockSugar
+    with TableDrivenPropertyChecks
+    with Eventually {
   behavior of "EngineJobHashingActor"
 
   def templateJobDescriptor(inputs: Map[LocallyQualifiedName, WomValue] = Map.empty): BackendJobDescriptor = {
-    val task = WomMocks.mockTaskDefinition("hello").copy(
-      commandTemplateBuilder = Function.const(List(StringCommandPart("Do the stuff... now!!")).validNel)
-    )
+    val task = WomMocks
+      .mockTaskDefinition("hello")
+      .copy(
+        commandTemplateBuilder = Function.const(List(StringCommandPart("Do the stuff... now!!")).validNel)
+      )
     val call = WomMocks.mockTaskCall(WomIdentifier("hello", "workflow.hello")).copy(callable = task)
     val workflowDescriptor = mock[BackendWorkflowDescriptor]
     workflowDescriptor.id returns WorkflowId.randomId()
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, BackendJobDescriptorKey(call, None, 1), Map.empty, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+    val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                             BackendJobDescriptorKey(call, None, 1),
+                                             Map.empty,
+                                             fqnWdlMapToDeclarationMap(inputs),
+                                             NoDocker,
+                                             None,
+                                             Map.empty
+    )
     jobDescriptor
   }
 
   val serviceRegistryActorProbe: TestProbe = TestProbe()
 
-  def makeEJHA(receiver: ActorRef, activity: CallCachingActivity, ccReaderProps: Props = Props.empty): TestActorRef[EngineJobHashingActor] = {
+  def makeEJHA(receiver: ActorRef,
+               activity: CallCachingActivity,
+               ccReaderProps: Props = Props.empty
+  ): TestActorRef[EngineJobHashingActor] =
     TestActorRef[EngineJobHashingActor](
       EngineJobHashingActorTest.props(
         receiver,
@@ -54,7 +76,6 @@ class EngineJobHashingActorSpec extends TestKitSuite with AnyFlatSpecLike with M
         fileHashBatchSize = 100
       )
     )
-  }
 
   it should "record initial hashes" in {
     val receiver = TestProbe()
@@ -106,7 +127,9 @@ class EngineJobHashingActorSpec extends TestKitSuite with AnyFlatSpecLike with M
 
     actorUnderTest ! initialResult
     actorUnderTest ! fileResult
-    receiver.expectMsg(CallCacheHashes(initialHashes, initialAggregatedHash, Option(FileHashes(fileHashes, fileAggregatedHash))))
+    receiver.expectMsg(
+      CallCacheHashes(initialHashes, initialAggregatedHash, Option(FileHashes(fileHashes, fileAggregatedHash)))
+    )
   }
 
   it should "forward CacheMiss to receiver" in {
@@ -133,8 +156,8 @@ class EngineJobHashingActorSpec extends TestKitSuite with AnyFlatSpecLike with M
     val activity = CallCachingActivity(ReadAndWriteCache)
     val monitorProbe = TestProbe()
     val ccReadActorProps = Props(new Actor {
-      override def receive: Receive = {
-        case NextHit => monitorProbe.ref forward NextHit
+      override def receive: Receive = { case NextHit =>
+        monitorProbe.ref forward NextHit
       }
     })
 
@@ -188,18 +211,22 @@ class EngineJobHashingActorSpec extends TestKitSuite with AnyFlatSpecLike with M
               backendName: String,
               activity: CallCachingActivity,
               callCachingEligible: CallCachingEligible,
-              fileHashBatchSize: Int): Props = Props(new EngineJobHashingActorTest(
-      receiver = receiver,
-      serviceRegistryActor = serviceRegistryActor,
-      jobDescriptor = jobDescriptor,
-      initializationData = initializationData,
-      fileHashingActorProps = fileHashingActorProps,
-      callCacheReadingJobActorProps = callCacheReadingJobActorProps,
-      runtimeAttributeDefinitions = runtimeAttributeDefinitions,
-      backendName = backendName,
-      activity = activity,
-      callCachingEligible = callCachingEligible,
-      fileHashBatchSize = fileHashBatchSize))
+              fileHashBatchSize: Int
+    ): Props = Props(
+      new EngineJobHashingActorTest(
+        receiver = receiver,
+        serviceRegistryActor = serviceRegistryActor,
+        jobDescriptor = jobDescriptor,
+        initializationData = initializationData,
+        fileHashingActorProps = fileHashingActorProps,
+        callCacheReadingJobActorProps = callCacheReadingJobActorProps,
+        runtimeAttributeDefinitions = runtimeAttributeDefinitions,
+        backendName = backendName,
+        activity = activity,
+        callCachingEligible = callCachingEligible,
+        fileHashBatchSize = fileHashBatchSize
+      )
+    )
   }
 
   class EngineJobHashingActorTest(receiver: ActorRef,
@@ -212,19 +239,21 @@ class EngineJobHashingActorSpec extends TestKitSuite with AnyFlatSpecLike with M
                                   backendName: String,
                                   activity: CallCachingActivity,
                                   callCachingEligible: CallCachingEligible,
-                                  fileHashBatchSize: Int) extends EngineJobHashingActor(
-    receiver = receiver,
-    serviceRegistryActor = serviceRegistryActor,
-    jobDescriptor = jobDescriptor,
-    initializationData = initializationData,
-    fileHashingActorProps = fileHashingActorProps,
-    callCacheReadingJobActorProps = callCacheReadingJobActorProps,
-    runtimeAttributeDefinitions = runtimeAttributeDefinitions,
-    backendNameForCallCachingPurposes = backendName,
-    activity = activity,
-    callCachingEligible = callCachingEligible,
-    callCachePathPrefixes = None,
-    fileHashBatchSize = fileHashBatchSize) {
+                                  fileHashBatchSize: Int
+  ) extends EngineJobHashingActor(
+        receiver = receiver,
+        serviceRegistryActor = serviceRegistryActor,
+        jobDescriptor = jobDescriptor,
+        initializationData = initializationData,
+        fileHashingActorProps = fileHashingActorProps,
+        callCacheReadingJobActorProps = callCacheReadingJobActorProps,
+        runtimeAttributeDefinitions = runtimeAttributeDefinitions,
+        backendNameForCallCachingPurposes = backendName,
+        activity = activity,
+        callCachingEligible = callCachingEligible,
+        callCachePathPrefixes = None,
+        fileHashBatchSize = fileHashBatchSize
+      ) {
     // override preStart to nothing to prevent the creation of the CCHJA.
     // This way it doesn't interfere with the tests and we can manually inject the messages we want
     override def preStart(): Unit = ()
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/CallPreparationSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/CallPreparationSpec.scala
index 7d0d40fd6f7..5b876319a8e 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/CallPreparationSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/CallPreparationSpec.scala
@@ -19,7 +19,8 @@ class CallPreparationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   it should "disallow empty Strings being input as Files" in {
     val callKey = mock[CallKey]
 
-    val inputExpressionPointer: InputDefinitionPointer = Coproduct[InputDefinitionPointer](WomString("").asWomExpression: WomExpression)
+    val inputExpressionPointer: InputDefinitionPointer =
+      Coproduct[InputDefinitionPointer](WomString("").asWomExpression: WomExpression)
     val inputs: InputDefinitionMappings = List(
       (RequiredInputDefinition("inputVal", WomSingleFileType), inputExpressionPointer)
     )
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActorSpec.scala
index 3744ea9e3cd..23e44e32900 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActorSpec.scala
@@ -4,10 +4,14 @@ import akka.testkit.{ImplicitSender, TestActorRef}
 import cats.syntax.validated._
 import cromwell.core.TestKitSuite
 import cromwell.core.callcaching.{DockerWithHash, FloatingDockerTagWithoutHash}
-import cromwell.docker.DockerInfoActor.{DockerInfoSuccessResponse, DockerInformation, DockerSize}
+import cromwell.docker.DockerInfoActor.{DockerInformation, DockerInfoSuccessResponse, DockerSize}
 import cromwell.docker.{DockerHashResult, DockerImageIdentifier, DockerImageIdentifierWithoutHash, DockerInfoRequest}
 import cromwell.engine.workflow.WorkflowDockerLookupActor.WorkflowDockerLookupFailure
-import cromwell.engine.workflow.lifecycle.execution.job.preparation.CallPreparation.{BackendJobPreparationSucceeded, CallPreparationFailed, Start}
+import cromwell.engine.workflow.lifecycle.execution.job.preparation.CallPreparation.{
+  BackendJobPreparationSucceeded,
+  CallPreparationFailed,
+  Start
+}
 import cromwell.engine.workflow.lifecycle.execution.stores.ValueStore
 import cromwell.services.keyvalue.KeyValueServiceActor.{KvGet, KvKeyLookupFailed, KvPair}
 import org.scalatest.BeforeAndAfter
@@ -24,7 +28,12 @@ import scala.language.postfixOps
 import scala.util.control.NoStackTrace
 
 class JobPreparationActorSpec
-  extends TestKitSuite with AnyFlatSpecLike with Matchers with ImplicitSender with BeforeAndAfter with MockSugar {
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with ImplicitSender
+    with BeforeAndAfter
+    with MockSugar {
 
   behavior of "JobPreparationActor"
 
@@ -41,8 +50,8 @@ class JobPreparationActorSpec
     val error = "Failed to prepare inputs/attributes - part of test flow"
     val actor = TestActorRef(helper.buildTestJobPreparationActor(null, null, null, error.invalidNel, List.empty), self)
     actor ! Start(ValueStore.empty)
-    expectMsgPF(1.second) {
-      case CallPreparationFailed(_, ex) => ex.getMessage shouldBe "Call input and runtime attributes evaluation failed for JobPreparationSpec_call:\nFailed to prepare inputs/attributes - part of test flow"
+    expectMsgPF(1.second) { case CallPreparationFailed(_, ex) =>
+      ex.getMessage shouldBe "Call input and runtime attributes evaluation failed for JobPreparationSpec_call:\nFailed to prepare inputs/attributes - part of test flow"
     }
     helper.workflowDockerLookupActor.expectNoMessage(100 millis)
   }
@@ -50,11 +59,11 @@ class JobPreparationActorSpec
   it should "prepare successfully a job without docker attribute" in {
     val attributes = Map.empty[LocallyQualifiedName, WomValue]
     val inputsAndAttributes = (inputs, attributes).validNel
-    val actor = TestActorRef(helper.buildTestJobPreparationActor(null, null, null, inputsAndAttributes, List.empty), self)
+    val actor =
+      TestActorRef(helper.buildTestJobPreparationActor(null, null, null, inputsAndAttributes, List.empty), self)
     actor ! Start(ValueStore.empty)
-    expectMsgPF(5 seconds) {
-      case success: BackendJobPreparationSucceeded =>
-        success.jobDescriptor.maybeCallCachingEligible.dockerHash shouldBe None
+    expectMsgPF(5 seconds) { case success: BackendJobPreparationSucceeded =>
+      success.jobDescriptor.maybeCallCachingEligible.dockerHash shouldBe None
     }
     helper.workflowDockerLookupActor.expectNoMessage(1 second)
   }
@@ -65,7 +74,8 @@ class JobPreparationActorSpec
       "docker" -> WomString(dockerValue)
     )
     val inputsAndAttributes = (inputs, attributes).validNel
-    val actor = TestActorRef(helper.buildTestJobPreparationActor(null, null, null, inputsAndAttributes, List.empty), self)
+    val actor =
+      TestActorRef(helper.buildTestJobPreparationActor(null, null, null, inputsAndAttributes, List.empty), self)
     actor ! Start(ValueStore.empty)
     helper.workflowDockerLookupActor.expectMsgClass(classOf[DockerInfoRequest])
     actor ! DockerInfoSuccessResponse(
@@ -75,17 +85,18 @@ class JobPreparationActorSpec
       ),
       null
     )
-    expectMsgPF(5 seconds) {
-      case success: BackendJobPreparationSucceeded =>
-        success.jobDescriptor.runtimeAttributes("docker").valueString shouldBe dockerValue
-        success.jobDescriptor.maybeCallCachingEligible shouldBe DockerWithHash("ubuntu@sha256:71cd81252a3563a03ad8daee81047b62ab5d892ebbfbf71cf53415f29c130950")
-        success.jobDescriptor.dockerSize shouldBe Option(DockerSize(100))
+    expectMsgPF(5 seconds) { case success: BackendJobPreparationSucceeded =>
+      success.jobDescriptor.runtimeAttributes("docker").valueString shouldBe dockerValue
+      success.jobDescriptor.maybeCallCachingEligible shouldBe DockerWithHash(
+        "ubuntu@sha256:71cd81252a3563a03ad8daee81047b62ab5d892ebbfbf71cf53415f29c130950"
+      )
+      success.jobDescriptor.dockerSize shouldBe Option(DockerSize(100))
     }
   }
 
   it should "lookup any requested key/value prefetches after (not) performing a docker hash lookup" in {
     val dockerValue = "ubuntu:latest"
-    val attributes = Map (
+    val attributes = Map(
       "docker" -> WomString(dockerValue)
     )
     val hashResult = DockerHashResult("sha256", "71cd81252a3563a03ad8daee81047b62ab5d892ebbfbf71cf53415f29c130950")
@@ -96,73 +107,88 @@ class JobPreparationActorSpec
     val prefetchedVal2 = KvKeyLookupFailed(KvGet(helper.scopedKeyMaker(prefetchedKey2)))
     val prefetchedValues = Map(prefetchedKey1 -> prefetchedVal1, prefetchedKey2 -> prefetchedVal2)
     var keysToPrefetch = List(prefetchedKey1, prefetchedKey2)
-    val actor = TestActorRef(helper.buildTestJobPreparationActor(1 minute, 1 minutes, List.empty, inputsAndAttributes, List(prefetchedKey1, prefetchedKey2)), self)
+    val actor = TestActorRef(helper.buildTestJobPreparationActor(1 minute,
+                                                                 1 minutes,
+                                                                 List.empty,
+                                                                 inputsAndAttributes,
+                                                                 List(prefetchedKey1, prefetchedKey2)
+                             ),
+                             self
+    )
     actor ! Start(ValueStore.empty)
 
     val req = helper.workflowDockerLookupActor.expectMsgClass(classOf[DockerInfoRequest])
     helper.workflowDockerLookupActor.reply(DockerInfoSuccessResponse(DockerInformation(hashResult, None), req))
 
-    def respondFromKv(): Unit = {
+    def respondFromKv(): Unit =
       helper.serviceRegistryProbe.expectMsgPF(max = 100 milliseconds) {
         case KvGet(k) if keysToPrefetch.contains(k.key) =>
           actor.tell(msg = prefetchedValues(k.key), sender = helper.serviceRegistryProbe.ref)
           keysToPrefetch = keysToPrefetch diff List(k.key)
       }
-    }
     respondFromKv()
     helper.workflowDockerLookupActor.expectNoMessage(max = 100 milliseconds)
     respondFromKv()
 
-    expectMsgPF(5 seconds) {
-      case success: BackendJobPreparationSucceeded =>
-        success.jobDescriptor.prefetchedKvStoreEntries should be(Map(prefetchedKey1 -> prefetchedVal1, prefetchedKey2 -> prefetchedVal2))
+    expectMsgPF(5 seconds) { case success: BackendJobPreparationSucceeded =>
+      success.jobDescriptor.prefetchedKvStoreEntries should be(
+        Map(prefetchedKey1 -> prefetchedVal1, prefetchedKey2 -> prefetchedVal2)
+      )
     }
   }
 
   it should "leave the docker attribute as is and provide a DockerWithHash value" in {
     val dockerValue = "ubuntu:latest"
-    val attributes = Map (
+    val attributes = Map(
       "docker" -> WomString(dockerValue)
     )
     val hashResult = DockerHashResult("sha256", "71cd81252a3563a03ad8daee81047b62ab5d892ebbfbf71cf53415f29c130950")
     val inputsAndAttributes = (inputs, attributes).validNel
     val finalValue = "ubuntu@sha256:71cd81252a3563a03ad8daee81047b62ab5d892ebbfbf71cf53415f29c130950"
-    val actor = TestActorRef(helper.buildTestJobPreparationActor(1 minute, 1 minutes, List.empty, inputsAndAttributes, List.empty), self)
+    val actor = TestActorRef(
+      helper.buildTestJobPreparationActor(1 minute, 1 minutes, List.empty, inputsAndAttributes, List.empty),
+      self
+    )
     actor ! Start(ValueStore.empty)
     helper.workflowDockerLookupActor.expectMsgClass(classOf[DockerInfoRequest])
     helper.workflowDockerLookupActor.reply(
       DockerInfoSuccessResponse(DockerInformation(hashResult, None), mock[DockerInfoRequest])
     )
-    expectMsgPF(5 seconds) {
-      case success: BackendJobPreparationSucceeded =>
-        success.jobDescriptor.runtimeAttributes("docker").valueString shouldBe dockerValue
-        success.jobDescriptor.maybeCallCachingEligible shouldBe DockerWithHash(finalValue)
+    expectMsgPF(5 seconds) { case success: BackendJobPreparationSucceeded =>
+      success.jobDescriptor.runtimeAttributes("docker").valueString shouldBe dockerValue
+      success.jobDescriptor.maybeCallCachingEligible shouldBe DockerWithHash(finalValue)
     }
   }
 
   it should "not provide a DockerWithHash value if it can't get the docker hash" in {
     val dockerValue = "ubuntu:latest"
-    val request = DockerInfoRequest(DockerImageIdentifier.fromString(dockerValue).get.asInstanceOf[DockerImageIdentifierWithoutHash])
-    val attributes = Map (
+    val request = DockerInfoRequest(
+      DockerImageIdentifier.fromString(dockerValue).get.asInstanceOf[DockerImageIdentifierWithoutHash]
+    )
+    val attributes = Map(
       "docker" -> WomString(dockerValue)
     )
     val inputsAndAttributes = (inputs, attributes).validNel
-    val actor = TestActorRef(helper.buildTestJobPreparationActor(1 minute, 1 minutes, List.empty, inputsAndAttributes, List.empty), self)
+    val actor = TestActorRef(
+      helper.buildTestJobPreparationActor(1 minute, 1 minutes, List.empty, inputsAndAttributes, List.empty),
+      self
+    )
     actor ! Start(ValueStore.empty)
     helper.workflowDockerLookupActor.expectMsgClass(classOf[DockerInfoRequest])
-    helper.workflowDockerLookupActor.reply(WorkflowDockerLookupFailure(
-      new Exception("Failed to get docker hash - part of test flow") with NoStackTrace,
-      request
-    ))
-    expectMsgPF(5 seconds) {
-      case success: BackendJobPreparationSucceeded =>
-        success.jobDescriptor.runtimeAttributes("docker").valueString shouldBe dockerValue
-        success.jobDescriptor.maybeCallCachingEligible shouldBe FloatingDockerTagWithoutHash("ubuntu:latest")
+    helper.workflowDockerLookupActor.reply(
+      WorkflowDockerLookupFailure(
+        new Exception("Failed to get docker hash - part of test flow") with NoStackTrace,
+        request
+      )
+    )
+    expectMsgPF(5 seconds) { case success: BackendJobPreparationSucceeded =>
+      success.jobDescriptor.runtimeAttributes("docker").valueString shouldBe dockerValue
+      success.jobDescriptor.maybeCallCachingEligible shouldBe FloatingDockerTagWithoutHash("ubuntu:latest")
     }
   }
 
   it should "lookup MemoryMultiplier key/value if available and accordingly update runtime attributes" in {
-    val attributes = Map (
+    val attributes = Map(
       "memory" -> WomString("1.1 GB")
     )
     val inputsAndAttributes = (inputs, attributes).validNel
@@ -170,7 +196,10 @@ class JobPreparationActorSpec
     val prefetchedVal = KvPair(helper.scopedKeyMaker(prefetchedKey), "1.1")
     val prefetchedValues = Map(prefetchedKey -> prefetchedVal)
     var keysToPrefetch = List(prefetchedKey)
-    val actor = TestActorRef(helper.buildTestJobPreparationActor(1 minute, 1 minutes, List.empty, inputsAndAttributes, List(prefetchedKey)), self)
+    val actor = TestActorRef(
+      helper.buildTestJobPreparationActor(1 minute, 1 minutes, List.empty, inputsAndAttributes, List(prefetchedKey)),
+      self
+    )
     actor ! Start(ValueStore.empty)
 
     helper.serviceRegistryProbe.expectMsgPF(max = 100 milliseconds) {
@@ -179,10 +208,11 @@ class JobPreparationActorSpec
         keysToPrefetch = keysToPrefetch diff List(k.key)
     }
 
-    expectMsgPF(5 seconds) {
-      case success: BackendJobPreparationSucceeded =>
-        success.jobDescriptor.prefetchedKvStoreEntries should be(Map(prefetchedKey -> prefetchedVal))
-        success.jobDescriptor.runtimeAttributes(RuntimeAttributesKeys.MemoryKey) shouldBe WomString("1.2100000000000002 GB")
+    expectMsgPF(5 seconds) { case success: BackendJobPreparationSucceeded =>
+      success.jobDescriptor.prefetchedKvStoreEntries should be(Map(prefetchedKey -> prefetchedVal))
+      success.jobDescriptor.runtimeAttributes(RuntimeAttributesKeys.MemoryKey) shouldBe WomString(
+        "1.2100000000000002 GB"
+      )
     }
   }
 
@@ -190,7 +220,7 @@ class JobPreparationActorSpec
     val prefetchedKey = "MemoryMultiplier"
     val retryFactor = 1.1
     val taskMemory = 1.0
-    val attributes = Map ("memory" -> WomString(s"$taskMemory GB"))
+    val attributes = Map("memory" -> WomString(s"$taskMemory GB"))
     val inputsAndAttributes = (inputs, attributes).validNel
 
     var previousMultiplier = 1.0
@@ -207,7 +237,10 @@ class JobPreparationActorSpec
       val prefetchedValues = Map(prefetchedKey -> prefetchedVal)
       var keysToPrefetch = List(prefetchedKey)
 
-      val actor = TestActorRef(helper.buildTestJobPreparationActor(1 minute, 1 minutes, List.empty, inputsAndAttributes, List(prefetchedKey)), self)
+      val actor = TestActorRef(
+        helper.buildTestJobPreparationActor(1 minute, 1 minutes, List.empty, inputsAndAttributes, List(prefetchedKey)),
+        self
+      )
       actor ! Start(ValueStore.empty)
 
       helper.serviceRegistryProbe.expectMsgPF(max = 100 milliseconds) {
@@ -216,10 +249,11 @@ class JobPreparationActorSpec
           keysToPrefetch = keysToPrefetch diff List(k.key)
       }
 
-      expectMsgPF(5 seconds) {
-        case success: BackendJobPreparationSucceeded =>
-          success.jobDescriptor.prefetchedKvStoreEntries should be(Map(prefetchedKey -> prefetchedVal))
-          success.jobDescriptor.runtimeAttributes(RuntimeAttributesKeys.MemoryKey) shouldBe WomString(s"${taskMemory * nextMultiplier} GB")
+      expectMsgPF(5 seconds) { case success: BackendJobPreparationSucceeded =>
+        success.jobDescriptor.prefetchedKvStoreEntries should be(Map(prefetchedKey -> prefetchedVal))
+        success.jobDescriptor.runtimeAttributes(RuntimeAttributesKeys.MemoryKey) shouldBe WomString(
+          s"${taskMemory * nextMultiplier} GB"
+        )
       }
     }
   }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationTestHelper.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationTestHelper.scala
index d4e62c262f6..58498d5ca4c 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationTestHelper.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationTestHelper.scala
@@ -36,48 +36,56 @@ class JobPreparationTestHelper(implicit val system: ActorSystem) extends MockSug
   val ioActor: TestProbe = TestProbe()
   val workflowDockerLookupActor: TestProbe = TestProbe()
 
-  val scopedKeyMaker: ScopedKeyMaker = key => ScopedKey(workflowId, KvJobKey("correct.horse.battery.staple", None, 1), key)
+  val scopedKeyMaker: ScopedKeyMaker = key =>
+    ScopedKey(workflowId, KvJobKey("correct.horse.battery.staple", None, 1), key)
 
-  def buildTestJobPreparationActor(backpressureTimeout: FiniteDuration,
-                                   noResponseTimeout: FiniteDuration,
-                                   dockerHashCredentials: List[Any],
-                                   inputsAndAttributes: ErrorOr[(WomEvaluatedCallInputs, Map[LocallyQualifiedName, WomValue])],
-                                   kvStoreKeysForPrefetch: List[String],
-                                   jobKey: BackendJobDescriptorKey = mockJobKey): Props = {
+  def buildTestJobPreparationActor(
+    backpressureTimeout: FiniteDuration,
+    noResponseTimeout: FiniteDuration,
+    dockerHashCredentials: List[Any],
+    inputsAndAttributes: ErrorOr[(WomEvaluatedCallInputs, Map[LocallyQualifiedName, WomValue])],
+    kvStoreKeysForPrefetch: List[String],
+    jobKey: BackendJobDescriptorKey = mockJobKey
+  ): Props =
+    Props(
+      new TestJobPreparationActor(
+        kvStoreKeysForPrefetch = kvStoreKeysForPrefetch,
+        dockerHashCredentialsInput = dockerHashCredentials,
+        backpressureWaitTimeInput = backpressureTimeout,
+        dockerNoResponseTimeoutInput = noResponseTimeout,
+        inputsAndAttributes = inputsAndAttributes,
+        workflowDescriptor = workflowDescriptor,
+        jobKey = jobKey,
+        workflowDockerLookupActor = workflowDockerLookupActor.ref,
+        serviceRegistryActor = serviceRegistryProbe.ref,
+        ioActor = ioActor.ref,
+        scopedKeyMaker
+      )
+    )
+}
 
-    Props(new TestJobPreparationActor(
-      kvStoreKeysForPrefetch = kvStoreKeysForPrefetch,
-      dockerHashCredentialsInput = dockerHashCredentials,
-      backpressureWaitTimeInput = backpressureTimeout,
-      dockerNoResponseTimeoutInput = noResponseTimeout,
-      inputsAndAttributes = inputsAndAttributes,
+private[preparation] class TestJobPreparationActor(
+  kvStoreKeysForPrefetch: List[String],
+  dockerHashCredentialsInput: List[Any],
+  backpressureWaitTimeInput: FiniteDuration,
+  dockerNoResponseTimeoutInput: FiniteDuration,
+  inputsAndAttributes: ErrorOr[(WomEvaluatedCallInputs, Map[LocallyQualifiedName, WomValue])],
+  workflowDescriptor: EngineWorkflowDescriptor,
+  jobKey: BackendJobDescriptorKey,
+  workflowDockerLookupActor: ActorRef,
+  serviceRegistryActor: ActorRef,
+  ioActor: ActorRef,
+  scopedKeyMaker: ScopedKeyMaker
+) extends JobPreparationActor(
       workflowDescriptor = workflowDescriptor,
       jobKey = jobKey,
-      workflowDockerLookupActor = workflowDockerLookupActor.ref,
-      serviceRegistryActor = serviceRegistryProbe.ref,
-      ioActor = ioActor.ref,
-      scopedKeyMaker))
-  }
-}
-
-private[preparation] class TestJobPreparationActor(kvStoreKeysForPrefetch: List[String],
-                                                   dockerHashCredentialsInput: List[Any],
-                                                   backpressureWaitTimeInput: FiniteDuration,
-                                                   dockerNoResponseTimeoutInput: FiniteDuration,
-                                                   inputsAndAttributes: ErrorOr[(WomEvaluatedCallInputs, Map[LocallyQualifiedName, WomValue])],
-                                                   workflowDescriptor: EngineWorkflowDescriptor,
-                                                   jobKey: BackendJobDescriptorKey,
-                                                   workflowDockerLookupActor: ActorRef,
-                                                   serviceRegistryActor: ActorRef,
-                                                   ioActor: ActorRef,
-                                                   scopedKeyMaker: ScopedKeyMaker) extends JobPreparationActor(workflowDescriptor = workflowDescriptor,
-                                                                                                  jobKey = jobKey,
-                                                                                                  factory = null,
-                                                                                                  workflowDockerLookupActor = workflowDockerLookupActor,
-                                                                                                  initializationData = None,
-                                                                                                  serviceRegistryActor = serviceRegistryActor,
-                                                                                                  ioActor = ioActor,
-                                                                                                  backendSingletonActor = None) {
+      factory = null,
+      workflowDockerLookupActor = workflowDockerLookupActor,
+      initializationData = None,
+      serviceRegistryActor = serviceRegistryActor,
+      ioActor = ioActor,
+      backendSingletonActor = None
+    ) {
 
   override private[preparation] lazy val kvStoreKeysToPrefetch = kvStoreKeysForPrefetch
 
@@ -93,7 +101,8 @@ private[preparation] class TestJobPreparationActor(kvStoreKeysForPrefetch: List[
                                                       initializationData: Option[BackendInitializationData],
                                                       serviceRegistryActor: ActorRef,
                                                       ioActor: ActorRef,
-                                                      backendSingletonActor: Option[ActorRef]) = Props.empty
+                                                      backendSingletonActor: Option[ActorRef]
+  ) = Props.empty
 }
 
 object JobPreparationTestHelper {
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/stores/ExecutionStoreSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/stores/ExecutionStoreSpec.scala
index 20b1ae40c0a..a1a741c27ff 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/stores/ExecutionStoreSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/execution/stores/ExecutionStoreSpec.scala
@@ -13,20 +13,23 @@ import scala.util.Random
 
 class ExecutionStoreSpec extends AnyFlatSpec with Matchers with BeforeAndAfter {
 
-
   it should "allow 10000 unconnected call keys to be enqueued and started in small batches" in {
 
-    def jobKeys: Map[JobKey, ExecutionStatus] = (0.until(10000).toList map {
-      i => BackendJobDescriptorKey(noConnectionsGraphNode, Option(i), 1) -> NotStarted })
-      .toMap
+    def jobKeys: Map[JobKey, ExecutionStatus] = (0.until(10000).toList map { i =>
+      BackendJobDescriptorKey(noConnectionsGraphNode, Option(i), 1) -> NotStarted
+    }).toMap
 
     var store: ExecutionStore = ActiveExecutionStore(jobKeys, needsUpdate = true)
 
     var iterationNumber = 0
     while (store.needsUpdate) {
       // Assert that we're increasing the queue size by 1000 each time
-      store.store.getOrElse(NotStarted, List.empty).size should be(10000 - iterationNumber * ExecutionStore.MaxJobsToStartPerTick)
-      store.store.getOrElse(QueuedInCromwell, List.empty).size should be(iterationNumber * ExecutionStore.MaxJobsToStartPerTick)
+      store.store.getOrElse(NotStarted, List.empty).size should be(
+        10000 - iterationNumber * ExecutionStore.MaxJobsToStartPerTick
+      )
+      store.store.getOrElse(QueuedInCromwell, List.empty).size should be(
+        iterationNumber * ExecutionStore.MaxJobsToStartPerTick
+      )
       val update = store.update
       store = update.updatedStore.updateKeys(update.runnableKeys.map(_ -> QueuedInCromwell).toMap)
       iterationNumber = iterationNumber + 1
@@ -36,7 +39,7 @@ class ExecutionStoreSpec extends AnyFlatSpec with Matchers with BeforeAndAfter {
     var previouslyRunning = store.store.getOrElse(Running, List.empty).size
     previouslyRunning should be(0)
 
-    while(store.store.getOrElse(Running, List.empty).size < 10000) {
+    while (store.store.getOrElse(Running, List.empty).size < 10000) {
       val toStartRunning = store.store(QueuedInCromwell).take(Random.nextInt(1000))
       store = store.updateKeys(toStartRunning.map(j => j -> Running).toMap)
       val nowRunning = store.store.getOrElse(Running, List.empty).size
@@ -60,7 +63,7 @@ object ExecutionStoreSpec {
   val noConnectionsGraphNode: CommandCallNode = CommandCallNode(
     identifier = WomIdentifier("mock_task", "mock_wf.mock_task"),
     callable = null,
-    inputPorts =  Set.empty[GraphNodePort.InputPort],
+    inputPorts = Set.empty[GraphNodePort.InputPort],
     inputDefinitionMappings = List.empty,
     nonInputBasedPrerequisites = Set.empty[GraphNode],
     outputIdentifierCompoundingFunction = (wi, _) => wi,
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowLogsActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowLogsActorSpec.scala
index 554ad52abd0..f2b2a615e58 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowLogsActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/CopyWorkflowLogsActorSpec.scala
@@ -14,8 +14,7 @@ import scala.concurrent.duration._
 import scala.util.control.NoStackTrace
 import scala.util.{Failure, Try}
 
-class CopyWorkflowLogsActorSpec
-  extends TestKitSuite with AnyFlatSpecLike with Matchers {
+class CopyWorkflowLogsActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers {
 
   behavior of "CopyWorkflowLogsActor"
 
@@ -25,9 +24,8 @@ class CopyWorkflowLogsActorSpec
   private val deathWatch = TestProbe("deathWatch")
   private val tempDir = DefaultPathBuilder.createTempDirectory("tempDir.")
 
-  override protected def beforeAll(): Unit = {
+  override protected def beforeAll(): Unit =
     super.beforeAll()
-  }
 
   override protected def afterAll(): Unit = {
     super.afterAll()
@@ -43,7 +41,7 @@ class CopyWorkflowLogsActorSpec
         ioActor = ioActor.ref,
         workflowLogConfigurationOption = WorkflowLogger.workflowLogConfiguration,
         copyCommandBuilder = DefaultIoCommandBuilder,
-        deleteCommandBuilder = DefaultIoCommandBuilder,
+        deleteCommandBuilder = DefaultIoCommandBuilder
       )
     val copyWorkflowLogsActor = system.actorOf(props, "testCopyWorkflowLogsActor")
 
@@ -60,7 +58,7 @@ class CopyWorkflowLogsActorSpec
     copyWorkflowLogsActor !
       ((
         workflowId,
-        IoFailure(copyCommand, new Exception("everything's fine, I am an expected copy fail") with NoStackTrace),
+        IoFailure(copyCommand, new Exception("everything's fine, I am an expected copy fail") with NoStackTrace)
       ))
 
     // There should now be a delete command sent to the ioActor
@@ -83,8 +81,8 @@ class CopyWorkflowLogsActorSpec
     val workflowId = WorkflowId.randomId()
     val destinationPath = DefaultPathBuilder.createTempFile(s"test_file_$workflowId.", ".file", Option(tempDir))
     val partialIoCommandBuilder = new PartialIoCommandBuilder {
-      override def copyCommand: PartialFunction[(Path, Path), Try[IoCopyCommand]] = {
-        case _ => Failure(new Exception("everything's fine, I am an expected copy fail") with NoStackTrace)
+      override def copyCommand: PartialFunction[(Path, Path), Try[IoCopyCommand]] = { case _ =>
+        Failure(new Exception("everything's fine, I am an expected copy fail") with NoStackTrace)
       }
     }
     val ioCommandBuilder = new IoCommandBuilder(List(partialIoCommandBuilder))
@@ -93,7 +91,7 @@ class CopyWorkflowLogsActorSpec
         serviceRegistryActor = serviceRegistryActor.ref,
         ioActor = ioActor.ref,
         workflowLogConfigurationOption = WorkflowLogger.workflowLogConfiguration,
-        copyCommandBuilder = ioCommandBuilder,
+        copyCommandBuilder = ioCommandBuilder
       )
     val copyWorkflowLogsActor = system.actorOf(props, "testCopyWorkflowLogsActorFailCopy")
 
@@ -105,7 +103,9 @@ class CopyWorkflowLogsActorSpec
     val deleteCommand = DefaultIoDeleteCommand(workflowLogPath, swallowIOExceptions = true)
     ioActor.expectMsg(msgWait, deleteCommand)
 
-    copyWorkflowLogsActor ! IoFailure(deleteCommand, new Exception("everything's fine, I am an expected delete fail") with NoStackTrace)
+    copyWorkflowLogsActor ! IoFailure(deleteCommand,
+                                      new Exception("everything's fine, I am an expected delete fail") with NoStackTrace
+    )
 
     // Send a shutdown after the delete
     deathWatch.watch(copyWorkflowLogsActor)
@@ -119,8 +119,8 @@ class CopyWorkflowLogsActorSpec
     val workflowId = WorkflowId.randomId()
     val destinationPath = DefaultPathBuilder.createTempFile(s"test_file_$workflowId.", ".file", Option(tempDir))
     val partialIoCommandBuilder = new PartialIoCommandBuilder {
-      override def copyCommand: PartialFunction[(Path, Path), Try[IoCopyCommand]] = {
-        case _ => Failure(new Exception("everything's fine, I am an expected copy fail") with NoStackTrace)
+      override def copyCommand: PartialFunction[(Path, Path), Try[IoCopyCommand]] = { case _ =>
+        Failure(new Exception("everything's fine, I am an expected copy fail") with NoStackTrace)
       }
     }
     val ioCommandBuilder = new IoCommandBuilder(List(partialIoCommandBuilder))
@@ -128,7 +128,7 @@ class CopyWorkflowLogsActorSpec
       serviceRegistryActor = serviceRegistryActor.ref,
       ioActor = ioActor.ref,
       workflowLogConfigurationOption = WorkflowLogger.workflowLogConfiguration,
-      copyCommandBuilder = ioCommandBuilder,
+      copyCommandBuilder = ioCommandBuilder
     )
     val copyWorkflowLogsActor = system.actorOf(props, "testCopyWorkflowLogsActorFailCopyShutdown")
 
@@ -146,7 +146,10 @@ class CopyWorkflowLogsActorSpec
 
     // Test that the actor is still alive and receiving messages even after a shutdown was requested
     EventFilter.error(pattern = "Failed to delete workflow logs", occurrences = 1).intercept {
-      copyWorkflowLogsActor ! IoFailure(deleteCommand, new Exception("everything's fine, I am an expected delete fail") with NoStackTrace)
+      copyWorkflowLogsActor ! IoFailure(deleteCommand,
+                                        new Exception("everything's fine, I am an expected delete fail")
+                                          with NoStackTrace
+      )
     }
 
     // Then the actor should shutdown
@@ -157,12 +160,12 @@ class CopyWorkflowLogsActorSpec
     val workflowId = WorkflowId.randomId()
     val destinationPath = DefaultPathBuilder.createTempFile(s"test_file_$workflowId.", ".file", Option(tempDir))
     val partialIoCommandBuilder = new PartialIoCommandBuilder {
-      override def copyCommand: PartialFunction[(Path, Path), Try[IoCopyCommand]] = {
-        case _ => Failure(new Exception("everything's fine, I am an expected copy fail") with NoStackTrace)
+      override def copyCommand: PartialFunction[(Path, Path), Try[IoCopyCommand]] = { case _ =>
+        Failure(new Exception("everything's fine, I am an expected copy fail") with NoStackTrace)
       }
 
-      override def deleteCommand: PartialFunction[(Path, Boolean), Try[IoDeleteCommand]] = {
-        case _ => Failure(new Exception("everything's fine, I am an expected delete fail") with NoStackTrace)
+      override def deleteCommand: PartialFunction[(Path, Boolean), Try[IoDeleteCommand]] = { case _ =>
+        Failure(new Exception("everything's fine, I am an expected delete fail") with NoStackTrace)
       }
     }
     val ioCommandBuilder = new IoCommandBuilder(List(partialIoCommandBuilder))
@@ -172,7 +175,7 @@ class CopyWorkflowLogsActorSpec
         ioActor = ioActor.ref,
         workflowLogConfigurationOption = WorkflowLogger.workflowLogConfiguration,
         copyCommandBuilder = ioCommandBuilder,
-        deleteCommandBuilder = ioCommandBuilder,
+        deleteCommandBuilder = ioCommandBuilder
       )
     val copyWorkflowLogsActor = system.actorOf(props, "testCopyWorkflowLogsActorFailDelete")
 
diff --git a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
index 383e75458ff..976a8994c9e 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActorSpec.scala
@@ -25,22 +25,25 @@ import java.time.Instant
 import scala.concurrent.Future
 import scala.concurrent.duration._
 
-class WorkflowCallbackActorSpec
-  extends TestKitSuite with AnyFlatSpecLike with Matchers with MockSugar {
+class WorkflowCallbackActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with MockSugar {
 
   behavior of "WorkflowCallbackActor"
 
-  private implicit val ec = system.dispatcher
+  implicit private val ec = system.dispatcher
 
   private val msgWait = 10.second.dilated
   private val awaitAlmostNothing = 1.second
   private val serviceRegistryActor = TestProbe("testServiceRegistryActor")
   private val deathWatch = TestProbe("deathWatch")
   private val mockUri = new URI("http://example.com")
-  private val basicConfig = WorkflowCallbackConfig.empty.copy(enabled = true).copy(retryBackoff = SimpleExponentialBackoff(100.millis, 200.millis, 1.1))
-  private val basicOutputs = CallOutputs(Map(
-    GraphNodeOutputPort(WomIdentifier("foo", "wf.foo"), WomStringType, null) -> WomString("bar")
-  ))
+  private val basicConfig = WorkflowCallbackConfig.empty
+    .copy(enabled = true)
+    .copy(retryBackoff = SimpleExponentialBackoff(100.millis, 200.millis, 1.1))
+  private val basicOutputs = CallOutputs(
+    Map(
+      GraphNodeOutputPort(WomIdentifier("foo", "wf.foo"), WomStringType, null) -> WomString("bar")
+    )
+  )
 
   private val httpSuccess = Future.successful(HttpResponse.apply(StatusCodes.OK))
   private val httpFailure = Future.successful(HttpResponse.apply(StatusCodes.GatewayTimeout))
@@ -85,7 +88,11 @@ class WorkflowCallbackActorSpec
 
     // Do the thing
     val cmd = PerformCallbackCommand(
-      workflowId = workflowId, uri = None, terminalState = WorkflowSucceeded, workflowOutputs = basicOutputs, List.empty
+      workflowId = workflowId,
+      uri = None,
+      terminalState = WorkflowSucceeded,
+      workflowOutputs = basicOutputs,
+      List.empty
     )
     workflowCallbackActor ! cmd
 
@@ -97,7 +104,7 @@ class WorkflowCallbackActorSpec
         uriEvent.key shouldBe expectedUriMetadata.key
         uriEvent.value shouldBe expectedUriMetadata.value
         timestampEvent.key shouldBe expectedTimestampMetadata.key
-        // Not checking timestamp value because it won't match
+      // Not checking timestamp value because it won't match
       case _ =>
     }
 
@@ -136,7 +143,11 @@ class WorkflowCallbackActorSpec
 
     // Do the thing
     val cmd = PerformCallbackCommand(
-      workflowId = workflowId, uri = None, terminalState = WorkflowSucceeded, workflowOutputs = basicOutputs, List.empty
+      workflowId = workflowId,
+      uri = None,
+      terminalState = WorkflowSucceeded,
+      workflowOutputs = basicOutputs,
+      List.empty
     )
     workflowCallbackActor ! cmd
 
@@ -183,7 +194,7 @@ class WorkflowCallbackActorSpec
       serviceRegistryActor.ref,
       basicConfig.copy(
         retryBackoff = SimpleExponentialBackoff(500.millis, 1.minute, 1.1),
-        maxRetries = 5,
+        maxRetries = 5
       ),
       httpClient = mockHttpClient
     )
@@ -234,7 +245,11 @@ class WorkflowCallbackActorSpec
 
     // Do the thing
     val cmd = PerformCallbackCommand(
-      workflowId = workflowId, uri = None, terminalState = WorkflowSucceeded, workflowOutputs = basicOutputs, List.empty
+      workflowId = workflowId,
+      uri = None,
+      terminalState = WorkflowSucceeded,
+      workflowOutputs = basicOutputs,
+      List.empty
     )
     workflowCallbackActor ! cmd
 
diff --git a/engine/src/test/scala/cromwell/engine/workflow/mocks/DeclarationMock.scala b/engine/src/test/scala/cromwell/engine/workflow/mocks/DeclarationMock.scala
index be7b0d741a3..5f8f846d7d4 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/mocks/DeclarationMock.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/mocks/DeclarationMock.scala
@@ -9,9 +9,7 @@ object DeclarationMock {
 }
 
 trait DeclarationMock extends MockSugar {
-  def mockDeclaration(name: String,
-                      womType: WomType,
-                      expression: WdlExpression): Declaration = {
+  def mockDeclaration(name: String, womType: WomType, expression: WdlExpression): Declaration = {
     val declaration = mock[Declaration]
     declaration.unqualifiedName returns name
     declaration.expression returns Option(expression)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/mocks/TaskMock.scala b/engine/src/test/scala/cromwell/engine/workflow/mocks/TaskMock.scala
index 7ce565a4b6c..77aaa449c3b 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/mocks/TaskMock.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/mocks/TaskMock.scala
@@ -12,15 +12,15 @@ trait TaskMock extends MockSugar {
                runtimeAttributes: WdlRuntimeAttributes = new WdlRuntimeAttributes(Map.empty),
                commandTemplateString: String = "!!shazam!!",
                outputs: Seq[DeclarationMockType] = Seq.empty
-              ): WdlTask = {
+  ): WdlTask = {
     val task = mock[WdlTask]
     task.declarations returns declarations
     task.runtimeAttributes returns runtimeAttributes
     task.commandTemplateString returns commandTemplateString
     task.name returns name
     task.unqualifiedName returns name
-    task.outputs returns (outputs map {
-      case (outputName, womType, expression) => TaskOutput(outputName, womType, expression, mock[Ast], Option(task))
+    task.outputs returns (outputs map { case (outputName, womType, expression) =>
+      TaskOutput(outputName, womType, expression, mock[Ast], Option(task))
     })
     task
   }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/tokens/JobTokenDispenserActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/tokens/JobTokenDispenserActorSpec.scala
index adaadb0fef7..ca2409b4931 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/tokens/JobTokenDispenserActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/tokens/JobTokenDispenserActorSpec.scala
@@ -18,8 +18,14 @@ import org.scalatest.matchers.should.Matchers
 import scala.concurrent.duration._
 import scala.util.Random
 
-class JobTokenDispenserActorSpec extends TestKitSuite
-  with ImplicitSender with AnyFlatSpecLike with Matchers with BeforeAndAfter with BeforeAndAfterAll with Eventually {
+class JobTokenDispenserActorSpec
+    extends TestKitSuite
+    with ImplicitSender
+    with AnyFlatSpecLike
+    with Matchers
+    with BeforeAndAfter
+    with BeforeAndAfterAll
+    with Eventually {
 
   val MaxWaitTime: FiniteDuration = 10.seconds
   implicit val pc: PatienceConfig = PatienceConfig(MaxWaitTime)
@@ -30,43 +36,49 @@ class JobTokenDispenserActorSpec extends TestKitSuite
   val hogGroupB: HogGroup = HogGroup("hogGroupB")
 
   private def getActorRefUnderTest(serviceRegistryActorName: String,
-                                   jobExecutionTokenDispenserActorName: String,
-                                  ): TestActorRef[JobTokenDispenserActor] = {
+                                   jobExecutionTokenDispenserActorName: String
+  ): TestActorRef[JobTokenDispenserActor] =
     TestActorRef(
-      factory =
-        new JobTokenDispenserActor(
-          serviceRegistryActor = TestProbe(serviceRegistryActorName).ref,
-          dispensingRate = Rate(10, 100.millis),
-          logInterval = None,
-          dispenserType = "execution",
-          tokenAllocatedDescription = "Running"
-        ),
-      name = jobExecutionTokenDispenserActorName,
+      factory = new JobTokenDispenserActor(
+        serviceRegistryActor = TestProbe(serviceRegistryActorName).ref,
+        dispensingRate = Rate(10, 100.millis),
+        logInterval = None,
+        dispenserType = "execution",
+        tokenAllocatedDescription = "Running"
+      ),
+      name = jobExecutionTokenDispenserActorName
     )
-  }
 
   it should "dispense an infinite token correctly" in {
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-dispense-infinite",
-        jobExecutionTokenDispenserActorName = "dispense-infinite",
+        jobExecutionTokenDispenserActorName = "dispense-infinite"
       )
     actorRefUnderTest ! JobTokenRequest(hogGroupA, TestInfiniteTokenType)
     expectMsg(max = MaxWaitTime, JobTokenDispensed)
     actorRefUnderTest.underlyingActor.tokenAssignments.contains(self) shouldBe true
-    actorRefUnderTest.underlyingActor.tokenAssignments(self).tokenLease.get().jobTokenType shouldBe TestInfiniteTokenType
+    actorRefUnderTest.underlyingActor
+      .tokenAssignments(self)
+      .tokenLease
+      .get()
+      .jobTokenType shouldBe TestInfiniteTokenType
   }
 
   it should "accept return of an infinite token correctly" in {
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-accept-return",
-        jobExecutionTokenDispenserActorName = "accept-return",
+        jobExecutionTokenDispenserActorName = "accept-return"
       )
     actorRefUnderTest ! JobTokenRequest(hogGroupA, TestInfiniteTokenType)
     expectMsg(max = MaxWaitTime, JobTokenDispensed)
     actorRefUnderTest.underlyingActor.tokenAssignments.contains(self) shouldBe true
-    actorRefUnderTest.underlyingActor.tokenAssignments(self).tokenLease.get().jobTokenType shouldBe TestInfiniteTokenType
+    actorRefUnderTest.underlyingActor
+      .tokenAssignments(self)
+      .tokenLease
+      .get()
+      .jobTokenType shouldBe TestInfiniteTokenType
     actorRefUnderTest ! JobTokenReturn
     actorRefUnderTest.underlyingActor.tokenAssignments.contains(self) shouldBe false
   }
@@ -75,10 +87,12 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-dispense-indefinitely",
-        jobExecutionTokenDispenserActorName = "dispense-indefinitely",
+        jobExecutionTokenDispenserActorName = "dispense-indefinitely"
       )
     val senders = (1 to 20).map(index => TestProbe(s"sender-dispense-indefinitely-$index"))
-    senders.foreach(sender => actorRefUnderTest.tell(msg = JobTokenRequest(hogGroupA, TestInfiniteTokenType), sender = sender.ref))
+    senders.foreach(sender =>
+      actorRefUnderTest.tell(msg = JobTokenRequest(hogGroupA, TestInfiniteTokenType), sender = sender.ref)
+    )
     senders.foreach(_.expectMsg(max = MaxWaitTime, JobTokenDispensed))
     actorRefUnderTest.underlyingActor.tokenAssignments.size shouldBe 20
   }
@@ -87,19 +101,20 @@ class JobTokenDispenserActorSpec extends TestKitSuite
 
     // Override with a slower distribution rate for this one test:
     val actorRefUnderTest = TestActorRef(
-      factory =
-        new JobTokenDispenserActor(
-          serviceRegistryActor = TestProbe("serviceRegistryActor-dispense-correct-amount").ref,
-          dispensingRate = Rate(10, 4.seconds),
-          logInterval = None,
-          dispenserType = "execution",
-          tokenAllocatedDescription = "Running"
-        ),
-      name = "dispense-correct-amount",
+      factory = new JobTokenDispenserActor(
+        serviceRegistryActor = TestProbe("serviceRegistryActor-dispense-correct-amount").ref,
+        dispensingRate = Rate(10, 4.seconds),
+        logInterval = None,
+        dispenserType = "execution",
+        tokenAllocatedDescription = "Running"
+      ),
+      name = "dispense-correct-amount"
     )
 
     val senders = (1 to 20).map(index => TestProbe(s"sender-dispense-correct-amount-$index"))
-    senders.foreach(sender => actorRefUnderTest.tell(msg = JobTokenRequest(hogGroupA, TestInfiniteTokenType), sender = sender.ref))
+    senders.foreach(sender =>
+      actorRefUnderTest.tell(msg = JobTokenRequest(hogGroupA, TestInfiniteTokenType), sender = sender.ref)
+    )
     // The first 10 should get their token
     senders.take(10).foreach(_.expectMsg(max = MaxWaitTime, JobTokenDispensed))
     // Couldn't figure out a cleaner way to "verify that none of this probes gets a message in the next X seconds"
@@ -113,7 +128,7 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-dispense-limited",
-        jobExecutionTokenDispenserActorName = "dispense-limited",
+        jobExecutionTokenDispenserActorName = "dispense-limited"
       )
     actorRefUnderTest ! JobTokenRequest(hogGroupA, LimitedTo5Tokens)
     expectMsg(max = MaxWaitTime, JobTokenDispensed)
@@ -125,7 +140,7 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-accept-return-limited",
-        jobExecutionTokenDispenserActorName = "accept-return-limited",
+        jobExecutionTokenDispenserActorName = "accept-return-limited"
       )
     actorRefUnderTest ! JobTokenRequest(hogGroupA, LimitedTo5Tokens)
     expectMsg(max = MaxWaitTime, JobTokenDispensed)
@@ -142,23 +157,32 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-limit-dispensing-limited",
-        jobExecutionTokenDispenserActorName = "limit-dispensing-limited",
+        jobExecutionTokenDispenserActorName = "limit-dispensing-limited"
       )
     val senders = (1 to 15).map(index => TestProbe(s"sender-limit-dispensing-limited-$index"))
     // Ask for 20 tokens
-    senders.foreach(sender => actorRefUnderTest.tell(msg = JobTokenRequest(hogGroupA, LimitedTo5Tokens), sender = sender.ref))
+    senders.foreach(sender =>
+      actorRefUnderTest.tell(msg = JobTokenRequest(hogGroupA, LimitedTo5Tokens), sender = sender.ref)
+    )
 
     // Force token distribution
     actorRefUnderTest ! TokensAvailable(100)
     senders.take(5).foreach(_.expectMsg(JobTokenDispensed))
 
     actorRefUnderTest.underlyingActor.tokenAssignments.size shouldBe 5
-    actorRefUnderTest.underlyingActor.tokenAssignments.keySet should contain theSameElementsAs senders.map(_.ref).take(5).toSet
+    actorRefUnderTest.underlyingActor.tokenAssignments.keySet should contain theSameElementsAs senders
+      .map(_.ref)
+      .take(5)
+      .toSet
 
     // The last 10 should be queued
     // At this point [0, 1, 2, 3, 4] are the ones with tokens, and [5, 14] are still queued
     actorRefUnderTest.underlyingActor.tokenQueues(LimitedTo5Tokens).size shouldBe 10
-    actorRefUnderTest.underlyingActor.tokenQueues(LimitedTo5Tokens).queues.flatMap(_._2).toList should contain theSameElementsInOrderAs senders.drop(5).map(asHogGroupAPlaceholder)
+    actorRefUnderTest.underlyingActor
+      .tokenQueues(LimitedTo5Tokens)
+      .queues
+      .flatMap(_._2)
+      .toList should contain theSameElementsInOrderAs senders.drop(5).map(asHogGroupAPlaceholder)
 
     // Force token distribution
     actorRefUnderTest ! TokensAvailable(100)
@@ -174,7 +198,11 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     senders.slice(5, 8).foreach(_.expectMsg(JobTokenDispensed))
 
     // At this point [3, 4, 5, 6, 7] are the ones with tokens, and [8, 19] are still queued
-    actorRefUnderTest.underlyingActor.tokenQueues(LimitedTo5Tokens).queues.flatMap(_._2).toList should contain theSameElementsInOrderAs senders.slice(8, 20).map(asHogGroupAPlaceholder)
+    actorRefUnderTest.underlyingActor
+      .tokenQueues(LimitedTo5Tokens)
+      .queues
+      .flatMap(_._2)
+      .toList should contain theSameElementsInOrderAs senders.slice(8, 20).map(asHogGroupAPlaceholder)
 
     // Double-check the queue state: when we request a token now, we should still be denied:
     actorRefUnderTest ! JobTokenRequest(hogGroupA, LimitedTo5Tokens)
@@ -182,13 +210,19 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     actorRefUnderTest ! TokensAvailable(100)
     expectNoMessage()
     // We should be enqueued and the last in the queue though
-    actorRefUnderTest.underlyingActor.tokenQueues(LimitedTo5Tokens).queues.flatMap(_._2).last shouldBe TokenQueuePlaceholder(self, "hogGroupA")
+    actorRefUnderTest.underlyingActor
+      .tokenQueues(LimitedTo5Tokens)
+      .queues
+      .flatMap(_._2)
+      .last shouldBe TokenQueuePlaceholder(self, "hogGroupA")
 
     // Release all currently owned tokens
     senders.slice(3, 8).foreach(_.send(actorRefUnderTest, JobTokenReturn))
     // Force token distribution
     actorRefUnderTest ! TokensAvailable(100)
-    actorRefUnderTest.underlyingActor.tokenAssignments.keySet should contain theSameElementsAs senders.map(_.ref).slice(8, 13)
+    actorRefUnderTest.underlyingActor.tokenAssignments.keySet should contain theSameElementsAs senders
+      .map(_.ref)
+      .slice(8, 13)
     // Keep accepting and returning tokens immediately
     senders.slice(8, 13).foreach(_.expectMsg(JobTokenDispensed))
     senders.slice(8, 13).foreach(_.reply(JobTokenReturn))
@@ -203,14 +237,16 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     actorRefUnderTest.underlyingActor.tokenQueues(LimitedTo5Tokens).size shouldBe 0
 
     // There should be 3 assigned tokens: index 18, 19, and this test actor
-    actorRefUnderTest.underlyingActor.tokenAssignments.keySet should contain theSameElementsAs senders.map(_.ref).slice(13, 15) :+ self
+    actorRefUnderTest.underlyingActor.tokenAssignments.keySet should contain theSameElementsAs senders
+      .map(_.ref)
+      .slice(13, 15) :+ self
   }
 
   it should "resend the same token to an actor which already has one" in {
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-resend-same",
-        jobExecutionTokenDispenserActorName = "resend-same",
+        jobExecutionTokenDispenserActorName = "resend-same"
       )
     5 indexedTimes { _ =>
       actorRefUnderTest ! JobTokenRequest(hogGroupA, LimitedTo5Tokens)
@@ -225,17 +261,18 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     actorRefUnderTest.underlyingActor.tokenQueues(LimitedTo5Tokens).pool.leased() shouldBe 1
   }
 
-
-  //Incidentally, also covers: it should "not be fooled if the wrong actor returns a token"
+  // Incidentally, also covers: it should "not be fooled if the wrong actor returns a token"
   it should "not be fooled by a doubly-returned token" in {
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-not-fooled",
-        jobExecutionTokenDispenserActorName = "not-fooled",
+        jobExecutionTokenDispenserActorName = "not-fooled"
       )
     val senders = (1 to 7).map(index => TestProbe(s"sender-not-fooled-$index"))
     // Ask for 7 tokens
-    senders.foreach(sender => actorRefUnderTest.tell(msg = JobTokenRequest(hogGroupA, LimitedTo5Tokens), sender = sender.ref))
+    senders.foreach(sender =>
+      actorRefUnderTest.tell(msg = JobTokenRequest(hogGroupA, LimitedTo5Tokens), sender = sender.ref)
+    )
 
     // Force token distribution
     actorRefUnderTest ! TokensAvailable(5)
@@ -261,16 +298,21 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     it should s"recover tokens lost to actors which are $name before they hand back their token" in {
       val actorRefUnderTest =
         TestActorRef(
-          new JobTokenDispenserActor(TestProbe(s"serviceRegistryActor-$name").ref, Rate(10, 100.millis), None,
-            dispenserType = "execution",
-            tokenAllocatedDescription = "Running"
+          new JobTokenDispenserActor(TestProbe(s"serviceRegistryActor-$name").ref,
+                                     Rate(10, 100.millis),
+                                     None,
+                                     dispenserType = "execution",
+                                     tokenAllocatedDescription = "Running"
           ),
-          s"lost-to-$name",
+          s"lost-to-$name"
         )
       val grabberSupervisor = TestActorRef(new StoppingSupervisor(), s"lost-to-$name-supervisor")
       // The first 5 get a token and the 6th one is queued
       val tokenGrabbingActors = (1 to 6).map { i =>
-        TestActorRef[TestTokenGrabbingActor](TestTokenGrabbingActor.props(actorRefUnderTest, LimitedTo5Tokens), grabberSupervisor, s"grabber_${name}_" + i)
+        TestActorRef[TestTokenGrabbingActor](TestTokenGrabbingActor.props(actorRefUnderTest, LimitedTo5Tokens),
+                                             grabberSupervisor,
+                                             s"grabber_${name}_" + i
+        )
       }
 
       // Force token distribution
@@ -289,7 +331,7 @@ class JobTokenDispenserActorSpec extends TestKitSuite
       deathwatch watch actorToStop
       stopMethod(actorToStop)
       deathwatch.expectTerminated(actorToStop)
-      eventually { nextInLine.underlyingActor.hasToken shouldBe true }
+      eventually(nextInLine.underlyingActor.hasToken shouldBe true)
     }
   }
 
@@ -297,12 +339,15 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-skip-dead",
-        jobExecutionTokenDispenserActorName = "skip-dead",
+        jobExecutionTokenDispenserActorName = "skip-dead"
       )
     val grabberSupervisor = TestActorRef(new StoppingSupervisor(), "skip-dead-supervisor")
     // The first 5 get a token and the 6th and 7h one are queued
     val tokenGrabbingActors = (1 to 7).map { i =>
-      TestActorRef[TestTokenGrabbingActor](TestTokenGrabbingActor.props(actorRefUnderTest, LimitedTo5Tokens), grabberSupervisor, s"grabber_" + i)
+      TestActorRef[TestTokenGrabbingActor](TestTokenGrabbingActor.props(actorRefUnderTest, LimitedTo5Tokens),
+                                           grabberSupervisor,
+                                           s"grabber_" + i
+      )
     }
 
     // Force token distribution
@@ -315,7 +360,11 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     // Check that the next in lines have no tokens and are indeed in the queue
     nextInLine1.underlyingActor.hasToken shouldBe false
     nextInLine2.underlyingActor.hasToken shouldBe false
-    actorRefUnderTest.underlyingActor.tokenQueues(LimitedTo5Tokens).queues.flatMap(_._2).toList should contain theSameElementsInOrderAs List(nextInLine1, nextInLine2).map(asHogGroupAPlaceholder)
+    actorRefUnderTest.underlyingActor
+      .tokenQueues(LimitedTo5Tokens)
+      .queues
+      .flatMap(_._2)
+      .toList should contain theSameElementsInOrderAs List(nextInLine1, nextInLine2).map(asHogGroupAPlaceholder)
 
     // First, kill off the actor which would otherwise be first in line:
     val deathwatch = TestProbe("death-watch-skip-dead")
@@ -327,19 +376,22 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     actorRefUnderTest.tell(msg = JobTokenReturn, sender = tokenGrabbingActors.head)
     // Force token distribution
     actorRefUnderTest ! TokensAvailable(1)
-    eventually { nextInLine2.underlyingActor.hasToken shouldBe true }
+    eventually(nextInLine2.underlyingActor.hasToken shouldBe true)
   }
 
   it should "skip over dead actors repeatedly when assigning tokens to the actor queue" in {
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-skip-dead-repeatedly",
-        jobExecutionTokenDispenserActorName = "skip-dead-repeatedly",
+        jobExecutionTokenDispenserActorName = "skip-dead-repeatedly"
       )
     val grabberSupervisor = TestActorRef(new StoppingSupervisor(), "skip-dead-repeatedly-supervisor")
     // The first 5 get a token and the 6th and 7th one are queued
     val tokenGrabbingActors = (0 until 1000).toVector.map { i =>
-      TestActorRef[TestTokenGrabbingActor](TestTokenGrabbingActor.props(actorRefUnderTest, LimitedTo5Tokens), grabberSupervisor, s"grabber_" + i)
+      TestActorRef[TestTokenGrabbingActor](TestTokenGrabbingActor.props(actorRefUnderTest, LimitedTo5Tokens),
+                                           grabberSupervisor,
+                                           s"grabber_" + i
+      )
     }
 
     // Create a sliding window of 10 actors, skipping by 10 so the windows do not overlap.
@@ -374,7 +426,7 @@ class JobTokenDispenserActorSpec extends TestKitSuite
       actorRefUnderTest.tell(msg = JobTokenReturn, sender = withTokens(3))
 
       actorRefUnderTest ! TokensAvailable(100)
-      eventually { nextInLine(3).underlyingActor.hasToken shouldBe true }
+      eventually(nextInLine(3).underlyingActor.hasToken shouldBe true)
 
       // And kill off the rest of the actors:
       (withTokens :+ nextInLine(3)) foreach { actor => actor ! PoisonPill }
@@ -387,7 +439,7 @@ class JobTokenDispenserActorSpec extends TestKitSuite
     val actorRefUnderTest =
       getActorRefUnderTest(
         serviceRegistryActorName = "serviceRegistryActor-resilient-last-request",
-        jobExecutionTokenDispenserActorName = "resilient-last-request",
+        jobExecutionTokenDispenserActorName = "resilient-last-request"
       )
     val tokenType = JobTokenType(s"mini", maxPoolSize = Option(6), hogFactor = 2)
 
@@ -404,7 +456,9 @@ class JobTokenDispenserActorSpec extends TestKitSuite
         actorRefUnderTest.underlyingActor.tokenAssignments.keys should contain(probe.ref)
       }
       // And both groups should have one item in the queue:
-      actorRefUnderTest.underlyingActor.tokenQueues(tokenType).queues.values.foreach { queue => queue.size should be(1) }
+      actorRefUnderTest.underlyingActor.tokenQueues(tokenType).queues.values.foreach { queue =>
+        queue.size should be(1)
+      }
     }
 
     // Group B gets bored and aborts all jobs (in reverse order to make sure ):
@@ -430,6 +484,7 @@ object JobTokenDispenserActorSpec {
   }
 
   val TestInfiniteTokenType: JobTokenType = JobTokenType("infinite", maxPoolSize = None, hogFactor = 1)
-  def limitedTokenType(limit: Int): JobTokenType = JobTokenType(s"$limit-limit", maxPoolSize = Option(limit), hogFactor = 1)
+  def limitedTokenType(limit: Int): JobTokenType =
+    JobTokenType(s"$limit-limit", maxPoolSize = Option(limit), hogFactor = 1)
   val LimitedTo5Tokens: JobTokenType = limitedTokenType(5)
 }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/tokens/RoundRobinQueueIteratorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/tokens/RoundRobinQueueIteratorSpec.scala
index b2c22f3bebc..d26cde04faf 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/tokens/RoundRobinQueueIteratorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/tokens/RoundRobinQueueIteratorSpec.scala
@@ -40,7 +40,9 @@ class RoundRobinQueueIteratorSpec extends TestKitSuite with AnyFlatSpecLike with
     val probe2 = TestProbe("probe-2").ref
     val probe3 = TestProbe("probe-3").ref
     val queues = List(
-      TokenQueue(InfiniteTokenType, tokenEventLogger).enqueue(TokenQueuePlaceholder(probe1, "hogGroupA")).enqueue(TokenQueuePlaceholder(probe3, "hogGroupA")),
+      TokenQueue(InfiniteTokenType, tokenEventLogger)
+        .enqueue(TokenQueuePlaceholder(probe1, "hogGroupA"))
+        .enqueue(TokenQueuePlaceholder(probe3, "hogGroupA")),
       TokenQueue(Pool2, tokenEventLogger).enqueue(TokenQueuePlaceholder(probe2, "hogGroupA"))
     )
     val iterator = new RoundRobinQueueIterator(queues, 0)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/tokens/TestTokenGrabbingActor.scala b/engine/src/test/scala/cromwell/engine/workflow/tokens/TestTokenGrabbingActor.scala
index caaef991994..2fe028910ef 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/tokens/TestTokenGrabbingActor.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/tokens/TestTokenGrabbingActor.scala
@@ -13,8 +13,8 @@ class TestTokenGrabbingActor(tokenDispenser: ActorRef, tokenType: JobTokenType)
 
   var hasToken: Boolean = false
 
-  override def receive = stoppingReceive orElse {
-    case JobTokenDispensed => hasToken = true
+  override def receive = stoppingReceive orElse { case JobTokenDispensed =>
+    hasToken = true
   }
 
   tokenDispenser ! JobTokenRequest(HogGroup("hogGroupA"), tokenType)
@@ -22,7 +22,9 @@ class TestTokenGrabbingActor(tokenDispenser: ActorRef, tokenType: JobTokenType)
 
 object TestTokenGrabbingActor {
 
-  def props(tokenDispenserActor: ActorRef, tokenType: JobTokenType) = Props(new TestTokenGrabbingActor(tokenDispenserActor, tokenType))
+  def props(tokenDispenserActor: ActorRef, tokenType: JobTokenType) = Props(
+    new TestTokenGrabbingActor(tokenDispenserActor, tokenType)
+  )
 
   class StoppingSupervisor extends Actor {
     override val supervisorStrategy = SupervisorStrategy.stoppingStrategy
diff --git a/engine/src/test/scala/cromwell/engine/workflow/tokens/TokenQueueSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/tokens/TokenQueueSpec.scala
index 6786c02ae83..306e589a241 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/tokens/TokenQueueSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/tokens/TokenQueueSpec.scala
@@ -156,7 +156,7 @@ class TokenQueueSpec extends TestKitSuite with AnyFlatSpecLike with Matchers {
     val expectedOrder = (0 until 23).toVector.map(i => s"hogGroup${i + 2}") ++ Vector("hogGroup0", "hogGroup1")
     usedQueue.queueOrder should be(expectedOrder)
 
-      usedQueue.size should be(jobCount - poolSize)
+    usedQueue.size should be(jobCount - poolSize)
 
   }
 
diff --git a/engine/src/test/scala/cromwell/engine/workflow/tokens/UnhoggableTokenPoolSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/tokens/UnhoggableTokenPoolSpec.scala
index f9bbd73fd34..d120b87b605 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/tokens/UnhoggableTokenPoolSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/tokens/UnhoggableTokenPoolSpec.scala
@@ -2,7 +2,12 @@ package cromwell.engine.workflow.tokens
 
 import common.assertion.CromwellTimeoutSpec
 import cromwell.core.JobToken.JobTokenType
-import cromwell.engine.workflow.tokens.UnhoggableTokenPool.{HogLimitExceeded, TokenHoggingLease, TokenTypeExhausted, TokensAvailable}
+import cromwell.engine.workflow.tokens.UnhoggableTokenPool.{
+  HogLimitExceeded,
+  TokenHoggingLease,
+  TokensAvailable,
+  TokenTypeExhausted
+}
 import org.scalatest.concurrent.Eventually
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
@@ -25,7 +30,7 @@ class UnhoggableTokenPoolSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     JobTokenType("backend", Some(150), 200) -> Some(1),
     JobTokenType("backend", None, 1) -> None,
     JobTokenType("backend", None, 150) -> None
-  ) ++ (hogLimitingTokenTypeToHogLimit map { case (k,v) => (k, Some(v)) })
+  ) ++ (hogLimitingTokenTypeToHogLimit map { case (k, v) => (k, Some(v)) })
 
   tokenTypeToHogLimit foreach { case (tokenType, expectedHogLimit) =>
     it should s"correctly calculate hogLimit for $tokenType as $expectedHogLimit" in {
@@ -44,8 +49,12 @@ class UnhoggableTokenPoolSpec extends AnyFlatSpec with CromwellTimeoutSpec with
         (0 until hogLimit) foreach { index =>
           pool.tryAcquire(hogGroup) match {
             case _: TokenHoggingLease => // great!
-            case TokenTypeExhausted => fail(s"Unhoggable token pool ran out after $index tokens distributed to $hogGroupNumber")
-            case HogLimitExceeded => fail(s"Unhoggable token pool making unfounded accusations of hogging after $index tokens distributed to $hogGroupNumber")
+            case TokenTypeExhausted =>
+              fail(s"Unhoggable token pool ran out after $index tokens distributed to $hogGroupNumber")
+            case HogLimitExceeded =>
+              fail(
+                s"Unhoggable token pool making unfounded accusations of hogging after $index tokens distributed to $hogGroupNumber"
+              )
           }
 
           val acquiredTokensForGroup = index + 1
@@ -89,7 +98,7 @@ class UnhoggableTokenPoolSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     hogLimitPool.tryAcquire("group1") should be(HogLimitExceeded)
 
     lease1.release()
-    eventually { hogLimitPool.available("group1") shouldBe TokensAvailable }
+    eventually(hogLimitPool.available("group1") shouldBe TokensAvailable)
     hogLimitPool.tryAcquire("group1") match {
       case _: TokenHoggingLease => // Great!
       case other => fail(s"expected lease but got $other")
@@ -97,7 +106,7 @@ class UnhoggableTokenPoolSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     hogLimitPool.tryAcquire("group1") should be(HogLimitExceeded)
 
     lease2.release()
-    eventually { hogLimitPool.available("group1") shouldBe TokensAvailable }
+    eventually(hogLimitPool.available("group1") shouldBe TokensAvailable)
     hogLimitPool.tryAcquire("group1") match {
       case _: TokenHoggingLease => // Great!
       case other => fail(s"expected lease but got $other")
diff --git a/engine/src/test/scala/cromwell/engine/workflow/tokens/large/LargeScaleJobTokenDispenserActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/tokens/large/LargeScaleJobTokenDispenserActorSpec.scala
index af93aaaa73e..779dd98065a 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/tokens/large/LargeScaleJobTokenDispenserActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/tokens/large/LargeScaleJobTokenDispenserActorSpec.scala
@@ -17,7 +17,14 @@ import org.scalatest.matchers.should.Matchers
 
 import scala.concurrent.duration._
 
-class LargeScaleJobTokenDispenserActorSpec extends TestKit(ActorSystem("LSJETDASpec")) with ImplicitSender with AnyFlatSpecLike with Matchers with BeforeAndAfter with BeforeAndAfterAll with Eventually {
+class LargeScaleJobTokenDispenserActorSpec
+    extends TestKit(ActorSystem("LSJETDASpec"))
+    with ImplicitSender
+    with AnyFlatSpecLike
+    with Matchers
+    with BeforeAndAfter
+    with BeforeAndAfterAll
+    with Eventually {
 
   val multipleTokenUsingActorIndex: AtomicInteger = new AtomicInteger(0)
   def multipleTokenUsingActorName() = s"multipleTokenUsingActor${multipleTokenUsingActorIndex.getAndIncrement()}"
@@ -32,14 +39,35 @@ class LargeScaleJobTokenDispenserActorSpec extends TestKit(ActorSystem("LSJETDAS
     val totalJobsPerWorkflow = maxConcurrencyToTest + 1
     val tokenType = JobTokenType(backendName, Some(maxConcurrencyToTest), hogFactor)
 
-    val tokenDispenserUnderTest = TestActorRef(new JobTokenDispenserActor(TestProbe().ref, Rate(maxConcurrencyToTest + 1, 100.millis), None,
-      dispenserType = "execution",
-      tokenAllocatedDescription = "Running"
-    ), "tokenDispenserUnderTest1")
+    val tokenDispenserUnderTest = TestActorRef(
+      new JobTokenDispenserActor(TestProbe().ref,
+                                 Rate(maxConcurrencyToTest + 1, 100.millis),
+                                 None,
+                                 dispenserType = "execution",
+                                 tokenAllocatedDescription = "Running"
+      ),
+      "tokenDispenserUnderTest1"
+    )
 
     val globalRunningJobsCounter = new RunningJobCounter()
-    val bigWorkflow1 = TestActorRef(new MultipleTokenUsingActor(tokenDispenserUnderTest, tokenType, totalJobsPerWorkflow, hogGroup = "hogGroupA", globalRunningJobsCounter), multipleTokenUsingActorName())
-    val bigWorkflow2 = TestActorRef(new MultipleTokenUsingActor(tokenDispenserUnderTest, tokenType, totalJobsPerWorkflow, hogGroup = "hogGroupA", globalRunningJobsCounter), multipleTokenUsingActorName())
+    val bigWorkflow1 = TestActorRef(
+      new MultipleTokenUsingActor(tokenDispenserUnderTest,
+                                  tokenType,
+                                  totalJobsPerWorkflow,
+                                  hogGroup = "hogGroupA",
+                                  globalRunningJobsCounter
+      ),
+      multipleTokenUsingActorName()
+    )
+    val bigWorkflow2 = TestActorRef(
+      new MultipleTokenUsingActor(tokenDispenserUnderTest,
+                                  tokenType,
+                                  totalJobsPerWorkflow,
+                                  hogGroup = "hogGroupA",
+                                  globalRunningJobsCounter
+      ),
+      multipleTokenUsingActorName()
+    )
 
     val parentProbe = new TestProbe(system, "parent")
 
@@ -47,11 +75,12 @@ class LargeScaleJobTokenDispenserActorSpec extends TestKit(ActorSystem("LSJETDAS
     parentProbe.send(bigWorkflow2, Begin)
 
     (0 until 2) foreach { _ =>
-      parentProbe.expectMsgPF(100.seconds) {
-        case TokenUsingActorCompletion(queueWaits, maximumConcurrency, errors) =>
-          Assertions.assert(maximumConcurrency <= maxConcurrencyToTest, "(asserting maxActualConcurrency <= maxRequestedConcurrency)")
-          queueWaits.size should be(totalJobsPerWorkflow)
-          errors shouldBe List.empty
+      parentProbe.expectMsgPF(100.seconds) { case TokenUsingActorCompletion(queueWaits, maximumConcurrency, errors) =>
+        Assertions.assert(maximumConcurrency <= maxConcurrencyToTest,
+                          "(asserting maxActualConcurrency <= maxRequestedConcurrency)"
+        )
+        queueWaits.size should be(totalJobsPerWorkflow)
+        errors shouldBe List.empty
       }
     }
 
@@ -69,14 +98,35 @@ class LargeScaleJobTokenDispenserActorSpec extends TestKit(ActorSystem("LSJETDAS
     val totalJobsPerWorkflow = maxConcurrencyExpected + 1
     val tokenType = JobTokenType(backendName, Some(totalTokensAvailable), hogFactor)
 
-    val tokenDispenserUnderTest = TestActorRef(new JobTokenDispenserActor(TestProbe().ref, Rate(maxConcurrencyExpected + 1, 100.millis), None,
-      dispenserType = "execution",
-      tokenAllocatedDescription = "Running"
-    ), "tokenDispenserUnderTest2")
+    val tokenDispenserUnderTest = TestActorRef(
+      new JobTokenDispenserActor(TestProbe().ref,
+                                 Rate(maxConcurrencyExpected + 1, 100.millis),
+                                 None,
+                                 dispenserType = "execution",
+                                 tokenAllocatedDescription = "Running"
+      ),
+      "tokenDispenserUnderTest2"
+    )
 
     val globalRunningJobsCounter = new RunningJobCounter()
-    val bigWorkflow1 = TestActorRef(new MultipleTokenUsingActor(tokenDispenserUnderTest, tokenType, totalJobsPerWorkflow, hogGroup = "hogGroupA", globalRunningJobsCounter), multipleTokenUsingActorName())
-    val bigWorkflow2 = TestActorRef(new MultipleTokenUsingActor(tokenDispenserUnderTest, tokenType, totalJobsPerWorkflow, hogGroup = "hogGroupA", globalRunningJobsCounter), multipleTokenUsingActorName())
+    val bigWorkflow1 = TestActorRef(
+      new MultipleTokenUsingActor(tokenDispenserUnderTest,
+                                  tokenType,
+                                  totalJobsPerWorkflow,
+                                  hogGroup = "hogGroupA",
+                                  globalRunningJobsCounter
+      ),
+      multipleTokenUsingActorName()
+    )
+    val bigWorkflow2 = TestActorRef(
+      new MultipleTokenUsingActor(tokenDispenserUnderTest,
+                                  tokenType,
+                                  totalJobsPerWorkflow,
+                                  hogGroup = "hogGroupA",
+                                  globalRunningJobsCounter
+      ),
+      multipleTokenUsingActorName()
+    )
 
     val parentProbe = new TestProbe(system, "parent")
 
@@ -84,11 +134,12 @@ class LargeScaleJobTokenDispenserActorSpec extends TestKit(ActorSystem("LSJETDAS
     parentProbe.send(bigWorkflow2, Begin)
 
     (0 until 2) foreach { _ =>
-      parentProbe.expectMsgPF(100.seconds) {
-        case TokenUsingActorCompletion(queueWaits, maximumConcurrency, errors) =>
-          Assertions.assert(maximumConcurrency <= maxConcurrencyExpected, "(asserting maxActualConcurrency <= maxRequestedConcurrency)")
-          queueWaits.size should be(totalJobsPerWorkflow)
-          errors shouldBe List.empty
+      parentProbe.expectMsgPF(100.seconds) { case TokenUsingActorCompletion(queueWaits, maximumConcurrency, errors) =>
+        Assertions.assert(maximumConcurrency <= maxConcurrencyExpected,
+                          "(asserting maxActualConcurrency <= maxRequestedConcurrency)"
+        )
+        queueWaits.size should be(totalJobsPerWorkflow)
+        errors shouldBe List.empty
       }
     }
 
@@ -106,14 +157,35 @@ class LargeScaleJobTokenDispenserActorSpec extends TestKit(ActorSystem("LSJETDAS
     val totalJobsPerWorkflow = maxConcurrencyPerWorkflow + 1
     val tokenType = JobTokenType(backendName, Some(totalTokensAvailable), hogFactor)
 
-    val tokenDispenserUnderTest = TestActorRef(new JobTokenDispenserActor(TestProbe().ref, Rate(maxConcurrencyOverall + 1, 100.millis), None,
-      dispenserType = "execution",
-      tokenAllocatedDescription = "Running"
-    ), "tokenDispenserUnderTest3")
+    val tokenDispenserUnderTest = TestActorRef(
+      new JobTokenDispenserActor(TestProbe().ref,
+                                 Rate(maxConcurrencyOverall + 1, 100.millis),
+                                 None,
+                                 dispenserType = "execution",
+                                 tokenAllocatedDescription = "Running"
+      ),
+      "tokenDispenserUnderTest3"
+    )
 
     val globalRunningJobsCounter = new RunningJobCounter()
-    val bigWorkflow1 = TestActorRef(new MultipleTokenUsingActor(tokenDispenserUnderTest, tokenType, totalJobsPerWorkflow, hogGroup = "hogGroupA", globalRunningJobsCounter), multipleTokenUsingActorName())
-    val bigWorkflow2 = TestActorRef(new MultipleTokenUsingActor(tokenDispenserUnderTest, tokenType, totalJobsPerWorkflow, hogGroup = "hogGroupB", globalRunningJobsCounter), multipleTokenUsingActorName())
+    val bigWorkflow1 = TestActorRef(
+      new MultipleTokenUsingActor(tokenDispenserUnderTest,
+                                  tokenType,
+                                  totalJobsPerWorkflow,
+                                  hogGroup = "hogGroupA",
+                                  globalRunningJobsCounter
+      ),
+      multipleTokenUsingActorName()
+    )
+    val bigWorkflow2 = TestActorRef(
+      new MultipleTokenUsingActor(tokenDispenserUnderTest,
+                                  tokenType,
+                                  totalJobsPerWorkflow,
+                                  hogGroup = "hogGroupB",
+                                  globalRunningJobsCounter
+      ),
+      multipleTokenUsingActorName()
+    )
 
     val parentProbe = new TestProbe(system, "parent")
 
@@ -121,11 +193,12 @@ class LargeScaleJobTokenDispenserActorSpec extends TestKit(ActorSystem("LSJETDAS
     parentProbe.send(bigWorkflow2, Begin)
 
     (0 until 2) foreach { _ =>
-      parentProbe.expectMsgPF(100.seconds) {
-        case TokenUsingActorCompletion(queueWaits, maximumConcurrency, errors) =>
-          Assertions.assert(maximumConcurrency == maxConcurrencyPerWorkflow, "(asserting maxActualConcurrency <= maxRequestedConcurrency)")
-          queueWaits.size should be(totalJobsPerWorkflow)
-          errors shouldBe List.empty
+      parentProbe.expectMsgPF(100.seconds) { case TokenUsingActorCompletion(queueWaits, maximumConcurrency, errors) =>
+        Assertions.assert(maximumConcurrency == maxConcurrencyPerWorkflow,
+                          "(asserting maxActualConcurrency <= maxRequestedConcurrency)"
+        )
+        queueWaits.size should be(totalJobsPerWorkflow)
+        errors shouldBe List.empty
       }
     }
 
@@ -143,27 +216,41 @@ class LargeScaleJobTokenDispenserActorSpec extends TestKit(ActorSystem("LSJETDAS
     val totalJobsPerWorkflow = maxConcurrencyPerWorkflow * 2
     val tokenType = JobTokenType(backendName, Some(totalTokensAvailable), hogFactor)
 
-    val tokenDispenserUnderTest = TestActorRef(new JobTokenDispenserActor(TestProbe().ref, Rate(maxConcurrencyOverall + 1, 100.millis), None,
-      dispenserType = "execution",
-      tokenAllocatedDescription = "Running"
-    ), "tokenDispenserUnderTest4")
+    val tokenDispenserUnderTest = TestActorRef(
+      new JobTokenDispenserActor(TestProbe().ref,
+                                 Rate(maxConcurrencyOverall + 1, 100.millis),
+                                 None,
+                                 dispenserType = "execution",
+                                 tokenAllocatedDescription = "Running"
+      ),
+      "tokenDispenserUnderTest4"
+    )
 
     val globalRunningJobsCounter = new RunningJobCounter()
 
     val workflows = (0 until 100) map { i =>
-      TestActorRef(new MultipleTokenUsingActor(tokenDispenserUnderTest, tokenType, totalJobsPerWorkflow, hogGroup = s"hogGroup$i", globalRunningJobsCounter), multipleTokenUsingActorName())
+      TestActorRef(
+        new MultipleTokenUsingActor(tokenDispenserUnderTest,
+                                    tokenType,
+                                    totalJobsPerWorkflow,
+                                    hogGroup = s"hogGroup$i",
+                                    globalRunningJobsCounter
+        ),
+        multipleTokenUsingActorName()
+      )
     }
 
     val parentProbe = new TestProbe(system, "parent")
 
-    workflows foreach { parentProbe.send(_, Begin)}
+    workflows foreach { parentProbe.send(_, Begin) }
 
     workflows.indices foreach { _ =>
-      parentProbe.expectMsgPF(100.seconds) {
-        case TokenUsingActorCompletion(queueWaits, maximumConcurrency, errors) =>
-          Assertions.assert(maximumConcurrency == maxConcurrencyPerWorkflow, "(asserting maxActualConcurrency <= maxRequestedConcurrency)")
-          queueWaits.size should be(totalJobsPerWorkflow)
-          errors shouldBe List.empty
+      parentProbe.expectMsgPF(100.seconds) { case TokenUsingActorCompletion(queueWaits, maximumConcurrency, errors) =>
+        Assertions.assert(maximumConcurrency == maxConcurrencyPerWorkflow,
+                          "(asserting maxActualConcurrency <= maxRequestedConcurrency)"
+        )
+        queueWaits.size should be(totalJobsPerWorkflow)
+        errors shouldBe List.empty
       }
     }
 
@@ -182,28 +269,42 @@ class LargeScaleJobTokenDispenserActorSpec extends TestKit(ActorSystem("LSJETDAS
     val totalJobsPerWorkflow = maxConcurrencyPerHogGroup * 2
     val tokenType = JobTokenType(backendName, Some(totalTokensAvailable), hogFactor)
 
-    val tokenDispenserUnderTest = TestActorRef(new JobTokenDispenserActor(TestProbe().ref, Rate(maxConcurrencyOverall + 1, 100.millis), None,
-      dispenserType = "execution",
-      tokenAllocatedDescription = "Running"
-    ), "tokenDispenserUnderTest5")
+    val tokenDispenserUnderTest = TestActorRef(
+      new JobTokenDispenserActor(TestProbe().ref,
+                                 Rate(maxConcurrencyOverall + 1, 100.millis),
+                                 None,
+                                 dispenserType = "execution",
+                                 tokenAllocatedDescription = "Running"
+      ),
+      "tokenDispenserUnderTest5"
+    )
 
     val hogGroupConcurrencyCounters = (0 until totalHogGroups).toVector map { _ => new RunningJobCounter() }
 
     val workflows = (0 until totalWorkflows) map { i =>
       val hogGroupNumber = i % totalHogGroups
-      TestActorRef(new MultipleTokenUsingActor(tokenDispenserUnderTest, tokenType, totalJobsPerWorkflow, hogGroup = s"hogGroup$hogGroupNumber", hogGroupConcurrencyCounters(hogGroupNumber)), multipleTokenUsingActorName())
+      TestActorRef(
+        new MultipleTokenUsingActor(tokenDispenserUnderTest,
+                                    tokenType,
+                                    totalJobsPerWorkflow,
+                                    hogGroup = s"hogGroup$hogGroupNumber",
+                                    hogGroupConcurrencyCounters(hogGroupNumber)
+        ),
+        multipleTokenUsingActorName()
+      )
     }
 
     val parentProbe = new TestProbe(system, "parent")
 
-    workflows foreach { parentProbe.send(_, Begin)}
+    workflows foreach { parentProbe.send(_, Begin) }
 
     workflows.indices foreach { _ =>
-      parentProbe.expectMsgPF(100.seconds) {
-        case TokenUsingActorCompletion(queueWaits, maximumConcurrency, errors) =>
-          Assertions.assert(maximumConcurrency <= maxConcurrencyPerHogGroup, "(asserting maxActualConcurrency per workflow <= maxRequestedConcurrency per hog group)")
-          queueWaits.size should be(totalJobsPerWorkflow)
-          errors shouldBe List.empty
+      parentProbe.expectMsgPF(100.seconds) { case TokenUsingActorCompletion(queueWaits, maximumConcurrency, errors) =>
+        Assertions.assert(maximumConcurrency <= maxConcurrencyPerHogGroup,
+                          "(asserting maxActualConcurrency per workflow <= maxRequestedConcurrency per hog group)"
+        )
+        queueWaits.size should be(totalJobsPerWorkflow)
+        errors shouldBe List.empty
       }
     }
 
@@ -219,12 +320,21 @@ class LargeScaleJobTokenDispenserActorSpec extends TestKit(ActorSystem("LSJETDAS
     (0 until totalHogGroups).toVector foreach { hogGroupNumber =>
       val c: RunningJobCounter = hogGroupConcurrencyCounters(hogGroupNumber)
 
-      if (c.getMax == maxConcurrencyPerHogGroup) { exactlyAtLimit += 1 } else {
-        Assertions.assert(c.getMax <= maxConcurrencyPerHogGroup, s"(asserting maxActualConcurrency for each hog group <= maxRequestedConcurrency per hog group)")
-        Assertions.assert(c.getMax >= maxConcurrencyPerHogGroup * 0.95, s"(asserting maxActualConcurrency for each hog group >= (95% of maxRequestedConcurrency per hog group))")
+      if (c.getMax == maxConcurrencyPerHogGroup) { exactlyAtLimit += 1 }
+      else {
+        Assertions.assert(
+          c.getMax <= maxConcurrencyPerHogGroup,
+          s"(asserting maxActualConcurrency for each hog group <= maxRequestedConcurrency per hog group)"
+        )
+        Assertions.assert(
+          c.getMax >= maxConcurrencyPerHogGroup * 0.95,
+          s"(asserting maxActualConcurrency for each hog group >= (95% of maxRequestedConcurrency per hog group))"
+        )
       }
     }
-    Assertions.assert(exactlyAtLimit >= (totalHogGroups * 0.95), "(at least 95% of the hog groups reached the full concurrency limit)")
+    Assertions.assert(exactlyAtLimit >= (totalHogGroups * 0.95),
+                      "(at least 95% of the hog groups reached the full concurrency limit)"
+    )
 
     workflows foreach { system.stop(_) }
     system.stop(tokenDispenserUnderTest)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/tokens/large/MultipleTokenUsingActor.scala b/engine/src/test/scala/cromwell/engine/workflow/tokens/large/MultipleTokenUsingActor.scala
index 79bf6951948..c35315c19ca 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/tokens/large/MultipleTokenUsingActor.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/tokens/large/MultipleTokenUsingActor.scala
@@ -1,6 +1,5 @@
 package cromwell.engine.workflow.tokens.large
 
-
 import akka.actor.{Actor, ActorRef}
 import cromwell.core.JobToken.JobTokenType
 import cromwell.engine.workflow.tokens.large.LargeScaleJobTokenDispenserActorSpec.RunningJobCounter
@@ -15,7 +14,12 @@ import cromwell.engine.workflow.tokens.large.PatientTokenNeedingActor.{AllDone,
   *
   * Because I'm a good citizen, I'm going to record and return a value representing my "peak concurrent tokens distributed"
   */
-class MultipleTokenUsingActor(tokenDispenser: ActorRef, tokenType: JobTokenType, totalJobs: Int, hogGroup: String, globalRunningJobCounter: RunningJobCounter) extends Actor {
+class MultipleTokenUsingActor(tokenDispenser: ActorRef,
+                              tokenType: JobTokenType,
+                              totalJobs: Int,
+                              hogGroup: String,
+                              globalRunningJobCounter: RunningJobCounter
+) extends Actor {
 
   var hasToken: Boolean = false
 
@@ -32,7 +36,9 @@ class MultipleTokenUsingActor(tokenDispenser: ActorRef, tokenType: JobTokenType,
     case Begin =>
       starter = sender()
       (0 until totalJobs) foreach { i =>
-        val jobActor = context.actorOf(PatientTokenNeedingActor.props(tokenDispenser, tokenType, hogGroup), name = self.path.name + s"job$i")
+        val jobActor = context.actorOf(PatientTokenNeedingActor.props(tokenDispenser, tokenType, hogGroup),
+                                       name = self.path.name + s"job$i"
+        )
         jobActor ! Begin
       }
       startedJobs = totalJobs
@@ -55,7 +61,6 @@ class MultipleTokenUsingActor(tokenDispenser: ActorRef, tokenType: JobTokenType,
   }
 }
 
-
 object MultipleTokenUsingActor {
   final case class TokenUsingActorCompletion(queueWaits: Seq[Long], maximumConcurrency: Int, errors: List[String])
 }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/tokens/large/PatientTokenNeedingActor.scala b/engine/src/test/scala/cromwell/engine/workflow/tokens/large/PatientTokenNeedingActor.scala
index debe5fe2537..817fa46934e 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/tokens/large/PatientTokenNeedingActor.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/tokens/large/PatientTokenNeedingActor.scala
@@ -60,5 +60,7 @@ object PatientTokenNeedingActor {
   // Indicate to myself that I'm done (and gets forwarded to my parent)
   case object AllDone
 
-  def props(tokenDispenser: ActorRef, tokenType: JobTokenType, hogGroup: String): Props = Props(new PatientTokenNeedingActor(tokenDispenser, tokenType, hogGroup))
+  def props(tokenDispenser: ActorRef, tokenType: JobTokenType, hogGroup: String): Props = Props(
+    new PatientTokenNeedingActor(tokenDispenser, tokenType, hogGroup)
+  )
 }
diff --git a/engine/src/test/scala/cromwell/engine/workflow/tokens/large/TokenDispenserBenchmark.scala b/engine/src/test/scala/cromwell/engine/workflow/tokens/large/TokenDispenserBenchmark.scala
index 8a5cbe6729f..590b5624b20 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/tokens/large/TokenDispenserBenchmark.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/tokens/large/TokenDispenserBenchmark.scala
@@ -38,7 +38,7 @@ object TokenDispenserBenchmark extends Bench[Double] with DefaultJsonProtocol {
   def fillQueue(tokenQueueIn: TokenQueue, jobsPerGroup: Int, hogGroups: List[String]): TokenQueue = {
     var tokenQueue = tokenQueueIn
     hogGroups foreach { hogGroup =>
-    (0 until jobsPerGroup) foreach { _ =>
+      (0 until jobsPerGroup) foreach { _ =>
         tokenQueue = tokenQueue.enqueue(TokenQueuePlaceholder(actorToQueue, hogGroup))
       }
     }
@@ -71,7 +71,8 @@ object TokenDispenserBenchmark extends Bench[Double] with DefaultJsonProtocol {
 
     measure method "enqueuing and dequeuing with multiple hog groups" in {
       val poolSize = 5 * ScaleFactor
-      val jobCounts: Gen[Int] = Gen.range("initialJobsInQueue")(from = 1 * ScaleFactor, upto = 15 * ScaleFactor, hop = 3 * ScaleFactor)
+      val jobCounts: Gen[Int] =
+        Gen.range("initialJobsInQueue")(from = 1 * ScaleFactor, upto = 15 * ScaleFactor, hop = 3 * ScaleFactor)
       val jobsAtATime = 50
 
       val queues = for {
diff --git a/engine/src/test/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStoreSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStoreSpec.scala
index fe51c9b065b..497482ddcc2 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStoreSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStoreSpec.scala
@@ -20,9 +20,12 @@ import spray.json.{JsObject, JsString}
 import scala.concurrent.duration._
 import scala.concurrent.{Await, ExecutionContext, Future}
 
-
-class SqlWorkflowStoreSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalaFutures
-  with BeforeAndAfterAll {
+class SqlWorkflowStoreSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalaFutures
+    with BeforeAndAfterAll {
   implicit val ec: ExecutionContextExecutor = ExecutionContext.global
   implicit val defaultPatience: PatienceConfig = PatienceConfig(scaled(Span(20, Seconds)), scaled(Span(100, Millis)))
 
@@ -112,25 +115,27 @@ class SqlWorkflowStoreSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
   )
 
   DatabaseSystem.All foreach { databaseSystem =>
-
     behavior of s"SqlWorkflowStore on ${databaseSystem.name}"
 
     val containerOpt: Option[Container] = DatabaseTestKit.getDatabaseTestContainer(databaseSystem)
 
-    lazy val dataAccess = DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, EngineDatabaseType, databaseSystem)
-    lazy val metadataDataAccess = DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, MetadataDatabaseType, databaseSystem)
+    lazy val dataAccess =
+      DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, EngineDatabaseType, databaseSystem)
+    lazy val metadataDataAccess =
+      DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, MetadataDatabaseType, databaseSystem)
 
     lazy val workflowStore = SqlWorkflowStore(dataAccess, metadataDataAccess)
 
-    def updateWfToRunning(startableWorkflows: List[WorkflowToStart]): Unit = {
+    def updateWfToRunning(startableWorkflows: List[WorkflowToStart]): Unit =
       startableWorkflows.foreach { wf =>
         Await.result(workflowStore.sqlDatabase.updateWorkflowState(
-          wf.id.toString,
-          WorkflowStoreState.Submitted.toString,
-          WorkflowStoreState.Running.toString
-        ), 5.seconds)
+                       wf.id.toString,
+                       WorkflowStoreState.Submitted.toString,
+                       WorkflowStoreState.Running.toString
+                     ),
+                     5.seconds
+        )
       }
-    }
 
     it should "start container if required" taggedAs DbmsTest in {
       containerOpt.foreach {
@@ -257,52 +262,72 @@ class SqlWorkflowStoreSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
 
     it should "start workflows from hog group with lowest count of running workflows" taggedAs DbmsTest in {
       // first submission of 50 workflows for hogGroup "Goldfinger"
-      val goldFingerWorkflowIds = (for (_ <- 1 to 50) yield Await.result(workflowStore.add(includedGroupSourceFilesCollection1), 5.seconds)).flatMap(_.map(_.id).toList)
+      val goldFingerWorkflowIds =
+        (for (_ <- 1 to 50) yield Await.result(workflowStore.add(includedGroupSourceFilesCollection1), 5.seconds))
+          .flatMap(_.map(_.id).toList)
 
       // second submission of 50 workflows for hogGroup "Highlander"
-      val highlanderWorkflowIds = (for (_ <- 1 to 50) yield Await.result(workflowStore.add(includedGroupSourceFilesCollection2), 5.seconds)).flatMap(_.map(_.id).toList)
-
-      for (_ <- 1 to 10) yield {
-        (for {
-          // since both hog groups have 0 workflows running, the hog group with oldest submission time is picked first
-          startableWorkflows1 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, Set.empty[String])
-          _ = startableWorkflows1.map(_.hogGroup.value).toSet.head should be("Goldfinger")
-          _ = startableWorkflows1.map(_.id).foreach(x => goldFingerWorkflowIds.toList should contain(x))
-          _ = updateWfToRunning(startableWorkflows1)
-
-          startableWorkflows2 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, Set.empty[String])
-          _ = startableWorkflows2.map(_.hogGroup.value).toSet.head should be("Highlander")
-          _ = startableWorkflows2.map(_.id).foreach(x => highlanderWorkflowIds.toList should contain(x))
-          _ = updateWfToRunning(startableWorkflows2)
-        } yield ()).futureValue
-      }
+      val highlanderWorkflowIds =
+        (for (_ <- 1 to 50) yield Await.result(workflowStore.add(includedGroupSourceFilesCollection2), 5.seconds))
+          .flatMap(_.map(_.id).toList)
+
+      for (_ <- 1 to 10) yield (for {
+        // since both hog groups have 0 workflows running, the hog group with oldest submission time is picked first
+        startableWorkflows1 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, Set.empty[String])
+        _ = startableWorkflows1.map(_.hogGroup.value).toSet.head should be("Goldfinger")
+        _ = startableWorkflows1.map(_.id).foreach(x => goldFingerWorkflowIds.toList should contain(x))
+        _ = updateWfToRunning(startableWorkflows1)
+
+        startableWorkflows2 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, Set.empty[String])
+        _ = startableWorkflows2.map(_.hogGroup.value).toSet.head should be("Highlander")
+        _ = startableWorkflows2.map(_.id).foreach(x => highlanderWorkflowIds.toList should contain(x))
+        _ = updateWfToRunning(startableWorkflows2)
+      } yield ()).futureValue
 
       // remove entries from WorkflowStore
-      (goldFingerWorkflowIds ++ highlanderWorkflowIds).foreach(id => Await.result(workflowStore.deleteFromStore(id), 5.seconds))
+      (goldFingerWorkflowIds ++ highlanderWorkflowIds).foreach(id =>
+        Await.result(workflowStore.deleteFromStore(id), 5.seconds)
+      )
     }
 
     it should "respect excludedHogGroups and start workflows from hog group with lowest count of running workflows" taggedAs DbmsTest in {
       (for {
         // first submission of 10 workflows for hogGroup "Goldfinger"
-        goldFingerSubmissions <- Future.sequence(for (_ <- 1 to 10) yield workflowStore.add(includedGroupSourceFilesCollection1))
+        goldFingerSubmissions <- Future.sequence(
+          for (_ <- 1 to 10) yield workflowStore.add(includedGroupSourceFilesCollection1)
+        )
         goldFingerWorkflowIds = goldFingerSubmissions.flatMap(_.map(_.id).toList)
 
         // second submission of 10 workflows for hogGroup "Zardoz"
-        zardozSubmissions <- Future.sequence(for (_ <- 1 to 10) yield workflowStore.add(excludedGroupSourceFilesCollection))
+        zardozSubmissions <- Future.sequence(
+          for (_ <- 1 to 10) yield workflowStore.add(excludedGroupSourceFilesCollection)
+        )
         zardozWorkflowIds = zardozSubmissions.flatMap(_.map(_.id).toList)
 
-        startableWorkflows1 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, excludedGroups = Set("Zardoz"))
+        startableWorkflows1 <- workflowStore.fetchStartableWorkflows(5,
+                                                                     "A08",
+                                                                     5.minutes,
+                                                                     excludedGroups = Set("Zardoz")
+        )
         _ = startableWorkflows1.map(_.hogGroup.value).toSet.head should be("Goldfinger")
         _ = startableWorkflows1.map(_.id).foreach(x => goldFingerWorkflowIds.toList should contain(x))
         _ = updateWfToRunning(startableWorkflows1)
 
-        startableWorkflows2 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, excludedGroups = Set("Zardoz"))
+        startableWorkflows2 <- workflowStore.fetchStartableWorkflows(5,
+                                                                     "A08",
+                                                                     5.minutes,
+                                                                     excludedGroups = Set("Zardoz")
+        )
         _ = startableWorkflows2.map(_.hogGroup.value).toSet.head should be("Goldfinger")
         _ = startableWorkflows2.map(_.id).foreach(x => goldFingerWorkflowIds.toList should contain(x))
         _ = updateWfToRunning(startableWorkflows2)
 
         // there are 10 workflows from hog group "Zardoz" in the store, but since the group is excluded, 0 workflows are returned here
-        startableWorkflows3 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, excludedGroups = Set("Zardoz"))
+        startableWorkflows3 <- workflowStore.fetchStartableWorkflows(5,
+                                                                     "A08",
+                                                                     5.minutes,
+                                                                     excludedGroups = Set("Zardoz")
+        )
         _ = startableWorkflows3.size should be(0)
 
         // hog group "Zardoz" has tokens to run workflows, hence don't exclude it
@@ -319,59 +344,93 @@ class SqlWorkflowStoreSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
         // remove entries from WorkflowStore
         workflowsList = goldFingerWorkflowIds ++ zardozWorkflowIds
         _ = workflowsList.foreach(id => Await.result(workflowStore.deleteFromStore(id), 5.seconds))
-      } yield()).futureValue
+      } yield ()).futureValue
     }
 
     it should "start workflows from hog group with lowest count of running workflows for multiple hog groups" taggedAs DbmsTest in {
       (for {
         // first submission of 10 workflows for hogGroup "Goldfinger"
-        goldFingerSubmissions <- Future.sequence(for (_ <- 1 to 10) yield workflowStore.add(includedGroupSourceFilesCollection1))
+        goldFingerSubmissions <- Future.sequence(
+          for (_ <- 1 to 10) yield workflowStore.add(includedGroupSourceFilesCollection1)
+        )
         goldFingerWorkflowIds = goldFingerSubmissions.flatMap(_.map(_.id).toList)
 
         // second submission of 10 workflows for hogGroup "Highlander"
-        highlanderSubmissions <- Future.sequence(for (_ <- 1 to 15) yield workflowStore.add(includedGroupSourceFilesCollection2))
+        highlanderSubmissions <- Future.sequence(
+          for (_ <- 1 to 15) yield workflowStore.add(includedGroupSourceFilesCollection2)
+        )
         highlanderWorkflowIds = highlanderSubmissions.flatMap(_.map(_.id).toList)
 
         // since both hog groups have 0 workflows running, the hog group with oldest submission time is picked first
-        startableWorkflows1 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, excludedGroups = Set.empty[String])
+        startableWorkflows1 <- workflowStore.fetchStartableWorkflows(5,
+                                                                     "A08",
+                                                                     5.minutes,
+                                                                     excludedGroups = Set.empty[String]
+        )
         _ = startableWorkflows1.map(_.hogGroup.value).toSet.head should be("Goldfinger")
         _ = startableWorkflows1.map(_.id).foreach(x => goldFingerWorkflowIds.toList should contain(x))
         _ = updateWfToRunning(startableWorkflows1)
 
-        startableWorkflows2 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, excludedGroups = Set.empty[String])
+        startableWorkflows2 <- workflowStore.fetchStartableWorkflows(5,
+                                                                     "A08",
+                                                                     5.minutes,
+                                                                     excludedGroups = Set.empty[String]
+        )
         _ = startableWorkflows2.map(_.hogGroup.value).toSet.head should be("Highlander")
         _ = startableWorkflows2.map(_.id).foreach(x => highlanderWorkflowIds.toList should contain(x))
         _ = updateWfToRunning(startableWorkflows2)
 
         // new submission for hog group "Finding Forrester"
-        foresterSubmissions <- Future.sequence(for (_ <- 1 to 10) yield workflowStore.add(includedGroupSourceFilesCollection3))
+        foresterSubmissions <- Future.sequence(
+          for (_ <- 1 to 10) yield workflowStore.add(includedGroupSourceFilesCollection3)
+        )
         foresterWorkflowIds = foresterSubmissions.flatMap(_.map(_.id).toList)
 
         // now hog group "Finding Forrester" has 0 workflows running, hence it is picked to run
-        startableWorkflows3 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, excludedGroups = Set.empty[String])
+        startableWorkflows3 <- workflowStore.fetchStartableWorkflows(5,
+                                                                     "A08",
+                                                                     5.minutes,
+                                                                     excludedGroups = Set.empty[String]
+        )
         _ = startableWorkflows3.map(_.hogGroup.value).toSet.head should be("Finding Forrester")
         _ = startableWorkflows3.map(_.id).foreach(x => foresterWorkflowIds.toList should contain(x))
         _ = updateWfToRunning(startableWorkflows3)
 
         // since all 3 hog groups have 5 workflows running each, the hog group with oldest submission time is picked first
-        startableWorkflows5 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, excludedGroups = Set.empty[String])
+        startableWorkflows5 <- workflowStore.fetchStartableWorkflows(5,
+                                                                     "A08",
+                                                                     5.minutes,
+                                                                     excludedGroups = Set.empty[String]
+        )
         _ = startableWorkflows5.map(_.hogGroup.value).toSet.head should be("Goldfinger")
         _ = startableWorkflows5.map(_.id).foreach(x => goldFingerWorkflowIds.toList should contain(x))
         _ = updateWfToRunning(startableWorkflows5)
 
         // since both "Highlander" and "Finding Forrester" have 5 workflows in Running state, the hog group with oldest submission time is picked first
-        startableWorkflows6 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, excludedGroups = Set.empty[String])
+        startableWorkflows6 <- workflowStore.fetchStartableWorkflows(5,
+                                                                     "A08",
+                                                                     5.minutes,
+                                                                     excludedGroups = Set.empty[String]
+        )
         _ = startableWorkflows6.map(_.hogGroup.value).toSet.head should be("Highlander")
         _ = startableWorkflows6.map(_.id).foreach(x => highlanderWorkflowIds.toList should contain(x))
         _ = updateWfToRunning(startableWorkflows6)
 
         // "Finding Forrester" is now the hog group with least running workflows and has 5 more workflows to run, hence it is picked to run
-        startableWorkflows4 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, excludedGroups = Set.empty[String])
+        startableWorkflows4 <- workflowStore.fetchStartableWorkflows(5,
+                                                                     "A08",
+                                                                     5.minutes,
+                                                                     excludedGroups = Set.empty[String]
+        )
         _ = startableWorkflows4.map(_.hogGroup.value).toSet.head should be("Finding Forrester")
         _ = startableWorkflows4.map(_.id).foreach(x => foresterWorkflowIds.toList should contain(x))
         _ = updateWfToRunning(startableWorkflows4)
 
-        startableWorkflows7 <- workflowStore.fetchStartableWorkflows(5, "A08", 5.minutes, excludedGroups = Set.empty[String])
+        startableWorkflows7 <- workflowStore.fetchStartableWorkflows(5,
+                                                                     "A08",
+                                                                     5.minutes,
+                                                                     excludedGroups = Set.empty[String]
+        )
         _ = startableWorkflows7.map(_.hogGroup.value).toSet.head should be("Highlander")
         _ = startableWorkflows7.map(_.id).foreach(x => highlanderWorkflowIds.toList should contain(x))
         _ = updateWfToRunning(startableWorkflows7)
@@ -385,10 +444,13 @@ class SqlWorkflowStoreSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     it should "accept and honor a requested workflow ID" taggedAs DbmsTest in {
       val requestedId = WorkflowId.randomId()
 
-      val sourcesToSubmit = onHoldSourceFilesCollection.map(c => c.asInstanceOf[WorkflowSourceFilesWithoutImports].copy(
-        requestedWorkflowId = Option(requestedId),
-        workflowOnHold = false
-      ))
+      val sourcesToSubmit = onHoldSourceFilesCollection.map(c =>
+        c.asInstanceOf[WorkflowSourceFilesWithoutImports]
+          .copy(
+            requestedWorkflowId = Option(requestedId),
+            workflowOnHold = false
+          )
+      )
 
       (for {
         submissionResponses <- workflowStore.add(sourcesToSubmit)
@@ -402,9 +464,11 @@ class SqlWorkflowStoreSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     it should "not accept a duplicate workflow ID" taggedAs DbmsTest in {
       val requestedId = WorkflowId.randomId()
 
-      val workflowSourceFilesTemplate = onHoldSourceFilesCollection.head.asInstanceOf[WorkflowSourceFilesWithoutImports].copy(
-        requestedWorkflowId = Option(requestedId)
-      )
+      val workflowSourceFilesTemplate = onHoldSourceFilesCollection.head
+        .asInstanceOf[WorkflowSourceFilesWithoutImports]
+        .copy(
+          requestedWorkflowId = Option(requestedId)
+        )
 
       val sourcesToSubmit1 = NonEmptyList.of(workflowSourceFilesTemplate)
       val sourcesToSubmit2 = NonEmptyList.of(workflowSourceFilesTemplate.copy(workflowOnHold = false))
@@ -412,14 +476,16 @@ class SqlWorkflowStoreSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
       ((for {
         _ <- workflowStore.add(sourcesToSubmit1)
         _ <- workflowStore.add(sourcesToSubmit2)
-      } yield "incorrectly accepted") recoverWith {
-        case error => for {
+      } yield "incorrectly accepted") recoverWith { case error =>
+        for {
           message <- Future {
             error.getMessage should be(s"Requested workflow IDs are already in use: $requestedId")
             "duplicate ID correctly detected"
           }
           stats <- workflowStore.stats
-          _ = stats should be(Map(WorkflowStoreState.OnHold -> 1)) // Only the original (on-hold) version of requested ID 1 should be in the store
+          _ = stats should be(
+            Map(WorkflowStoreState.OnHold -> 1)
+          ) // Only the original (on-hold) version of requested ID 1 should be in the store
           _ <- workflowStore.deleteFromStore(requestedId) // tidy up
         } yield message
       }).futureValue should be("duplicate ID correctly detected")
@@ -430,29 +496,35 @@ class SqlWorkflowStoreSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
       val requestedId2 = WorkflowId.randomId()
       val requestedId3 = WorkflowId.randomId()
 
-      val workflowSourceFilesTemplate = onHoldSourceFilesCollection.head.asInstanceOf[WorkflowSourceFilesWithoutImports].copy(
-        requestedWorkflowId = Option(requestedId1)
-      )
+      val workflowSourceFilesTemplate = onHoldSourceFilesCollection.head
+        .asInstanceOf[WorkflowSourceFilesWithoutImports]
+        .copy(
+          requestedWorkflowId = Option(requestedId1)
+        )
 
       val sourcesToSubmit1 = NonEmptyList.of(workflowSourceFilesTemplate)
 
       val sourcesToSubmit2 = NonEmptyList.of(
         workflowSourceFilesTemplate.copy(requestedWorkflowId = Option(requestedId2), workflowOnHold = false),
         workflowSourceFilesTemplate.copy(requestedWorkflowId = Option(requestedId3), workflowOnHold = false),
-        workflowSourceFilesTemplate.copy(requestedWorkflowId = Option(requestedId1), workflowOnHold = false) // duplicates the existing ID.
+        workflowSourceFilesTemplate.copy(requestedWorkflowId = Option(requestedId1),
+                                         workflowOnHold = false
+        ) // duplicates the existing ID.
       )
 
       ((for {
         _ <- workflowStore.add(sourcesToSubmit1)
         _ <- workflowStore.add(sourcesToSubmit2)
-      } yield "incorrectly accepted") recoverWith {
-        case error => for {
+      } yield "incorrectly accepted") recoverWith { case error =>
+        for {
           message <- Future {
             error.getMessage should be(s"Requested workflow IDs are already in use: $requestedId1")
             "duplicate ID correctly detected"
           }
           stats <- workflowStore.stats
-          _ = stats should be(Map(WorkflowStoreState.OnHold -> 1)) // Only the original (on-hold) version of requested ID 1 should be in the store
+          _ = stats should be(
+            Map(WorkflowStoreState.OnHold -> 1)
+          ) // Only the original (on-hold) version of requested ID 1 should be in the store
           _ <- workflowStore.deleteFromStore(requestedId1)
 
         } yield message
@@ -470,13 +542,15 @@ class SqlWorkflowStoreSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
         workflowSourceFilesTemplate.copy(requestedWorkflowId = Option(requestedId1), workflowOnHold = false),
         workflowSourceFilesTemplate.copy(requestedWorkflowId = Option(requestedId2), workflowOnHold = false),
         workflowSourceFilesTemplate.copy(requestedWorkflowId = Option(requestedId3), workflowOnHold = false),
-        workflowSourceFilesTemplate.copy(requestedWorkflowId = Option(requestedId1), workflowOnHold = false) // duplicates an ID already in the set
+        workflowSourceFilesTemplate.copy(requestedWorkflowId = Option(requestedId1),
+                                         workflowOnHold = false
+        ) // duplicates an ID already in the set
       )
 
       ((for {
         _ <- workflowStore.add(sourcesToSubmit)
-      } yield "incorrectly accepted") recoverWith {
-        case error => for {
+      } yield "incorrectly accepted") recoverWith { case error =>
+        for {
           message <- Future {
             error.getMessage should be(s"Requested workflow IDs are duplicated: $requestedId1")
             "duplicate ID correctly detected"
diff --git a/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowHeartbeatConfigSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowHeartbeatConfigSpec.scala
index fe4b951ec06..768731b815c 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowHeartbeatConfigSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowHeartbeatConfigSpec.scala
@@ -9,7 +9,11 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 
 import scala.concurrent.duration._
 
-class WorkflowHeartbeatConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
+class WorkflowHeartbeatConfigSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks {
 
   behavior of "WorkflowHeartbeatConfig"
 
@@ -17,7 +21,7 @@ class WorkflowHeartbeatConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec w
     val workflowHeartbeatConfig = WorkflowHeartbeatConfig(WorkflowHeartbeatConfigSpec.DefaultConfig)
     workflowHeartbeatConfig.cromwellId should startWith("cromid-")
     workflowHeartbeatConfig.cromwellId should have length 14
-    workflowHeartbeatConfig.heartbeatInterval should be (2.minutes)
+    workflowHeartbeatConfig.heartbeatInterval should be(2.minutes)
     workflowHeartbeatConfig.ttl should be(10.minutes)
     workflowHeartbeatConfig.failureShutdownDuration should be(5.minutes)
     workflowHeartbeatConfig.writeBatchSize should be(10000)
@@ -29,22 +33,22 @@ class WorkflowHeartbeatConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec w
     (
       "from an empty config",
       "system.cromwell_id_random_suffix = false",
-      WorkflowHeartbeatConfig("cromid", 2.minutes, 10.minutes, 5.minutes, 10000, 10000),
+      WorkflowHeartbeatConfig("cromid", 2.minutes, 10.minutes, 5.minutes, 10000, 10000)
     ),
     (
       "with a specified cromid",
       """system.cromwell_id = "new_crom_name"""",
-      WorkflowHeartbeatConfig("new_crom_name", 2.minutes, 10.minutes, 5.minutes, 10000, 10000),
+      WorkflowHeartbeatConfig("new_crom_name", 2.minutes, 10.minutes, 5.minutes, 10000, 10000)
     ),
     (
       "with a specified heartbeat interval",
       "system.workflow-heartbeats.heartbeat-interval = 3 minutes",
-      WorkflowHeartbeatConfig("cromid", 3.minutes, 10.minutes, 5.minutes, 10000, 10000),
+      WorkflowHeartbeatConfig("cromid", 3.minutes, 10.minutes, 5.minutes, 10000, 10000)
     ),
     (
       "with a specified ttl",
       "system.workflow-heartbeats.ttl = 5 minutes",
-      WorkflowHeartbeatConfig("cromid", 2.minutes, 5.minutes, 5.minutes, 10000, 10000),
+      WorkflowHeartbeatConfig("cromid", 2.minutes, 5.minutes, 5.minutes, 10000, 10000)
     ),
     (
       "with a ttl less than the default heartbeat interval",
@@ -52,22 +56,22 @@ class WorkflowHeartbeatConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec w
          |system.workflow-heartbeats.heartbeat-interval = 59 seconds
          |system.workflow-heartbeats.write-failure-shutdown-duration = 0 minutes
          |""".stripMargin,
-      WorkflowHeartbeatConfig("cromid", 59.seconds, 1.minutes, 0.minutes, 10000, 10000),
+      WorkflowHeartbeatConfig("cromid", 59.seconds, 1.minutes, 0.minutes, 10000, 10000)
     ),
     (
       "with a specified shutdown duration",
       "system.workflow-heartbeats.write-failure-shutdown-duration = 1 minute",
-      WorkflowHeartbeatConfig("cromid", 2.minutes, 10.minutes, 1.minute, 10000, 10000),
+      WorkflowHeartbeatConfig("cromid", 2.minutes, 10.minutes, 1.minute, 10000, 10000)
     ),
     (
       "with a specified batch size",
       "system.workflow-heartbeats.write-batch-size = 2000",
-      WorkflowHeartbeatConfig("cromid", 2.minutes, 10.minutes, 5.minutes, 2000, 10000),
+      WorkflowHeartbeatConfig("cromid", 2.minutes, 10.minutes, 5.minutes, 2000, 10000)
     ),
     (
       "with a specified threshold",
       "system.workflow-heartbeats.write-threshold = 5000",
-      WorkflowHeartbeatConfig("cromid", 2.minutes, 10.minutes, 5.minutes, 10000, 5000),
+      WorkflowHeartbeatConfig("cromid", 2.minutes, 10.minutes, 5.minutes, 10000, 5000)
     ),
     (
       "when trying to set the ttl below the minimum",
@@ -75,28 +79,30 @@ class WorkflowHeartbeatConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec w
          |system.workflow-heartbeats.heartbeat-interval = 8 seconds
          |system.workflow-heartbeats.write-failure-shutdown-duration = 0 minutes
          |""".stripMargin,
-      WorkflowHeartbeatConfig("cromid", 8.seconds, 10.seconds, 0.minutes, 10000, 10000),
+      WorkflowHeartbeatConfig("cromid", 8.seconds, 10.seconds, 0.minutes, 10000, 10000)
     ),
     (
       "when trying to set the interval below the minimum",
       "system.workflow-heartbeats.heartbeat-interval = 3 seconds",
-      WorkflowHeartbeatConfig("cromid", 10.seconds / 3, 10.minutes, 5.minutes, 10000, 10000),
+      WorkflowHeartbeatConfig("cromid", 10.seconds / 3, 10.minutes, 5.minutes, 10000, 10000)
     ),
     (
       "when trying to set a negative shutdown duration",
       "system.workflow-heartbeats.write-failure-shutdown-duration = -1 seconds",
-      WorkflowHeartbeatConfig("cromid", 2.minutes, 10.minutes, 0.minutes, 10000, 10000),
-    ),
+      WorkflowHeartbeatConfig("cromid", 2.minutes, 10.minutes, 0.minutes, 10000, 10000)
+    )
   )
 
   forAll(validConfigTests) { (description, configString, expected) =>
     it should s"create an instance $description" in {
-      val config = ConfigFactory.parseString(
-        // Remove the randomness from the cromid
-        s"""|system.cromwell_id_random_suffix = false
-            |$configString
-            |""".stripMargin
-      ).withFallback(WorkflowHeartbeatConfigSpec.DefaultConfig)
+      val config = ConfigFactory
+        .parseString(
+          // Remove the randomness from the cromid
+          s"""|system.cromwell_id_random_suffix = false
+              |$configString
+              |""".stripMargin
+        )
+        .withFallback(WorkflowHeartbeatConfigSpec.DefaultConfig)
       WorkflowHeartbeatConfig(config) should be(expected)
     }
   }
@@ -114,7 +120,7 @@ class WorkflowHeartbeatConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec w
         "Errors parsing WorkflowHeartbeatConfig",
         List(
           "The system.workflow-heartbeats.heartbeat-interval (2 minutes)" +
-            " is not less than the system.workflow-heartbeats.ttl (2 minutes).",
+            " is not less than the system.workflow-heartbeats.ttl (2 minutes)."
         )
       )
     ),
@@ -129,7 +135,7 @@ class WorkflowHeartbeatConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec w
         "Errors parsing WorkflowHeartbeatConfig",
         List(
           "The system.workflow-heartbeats.heartbeat-interval (2 minutes)" +
-            " is not less than the system.workflow-heartbeats.ttl (1 minute).",
+            " is not less than the system.workflow-heartbeats.ttl (1 minute)."
         )
       )
     ),
@@ -144,10 +150,10 @@ class WorkflowHeartbeatConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec w
         "Errors parsing WorkflowHeartbeatConfig",
         List(
           "The system.workflow-heartbeats.write-failure-shutdown-duration (301 seconds)" +
-            " is greater than the system.workflow-heartbeats.ttl (5 minutes).",
+            " is greater than the system.workflow-heartbeats.ttl (5 minutes)."
         )
       )
-    ),
+    )
   )
 
   forAll(invalidConfigTests) { (description, configString, expected: AggregatedMessageException) =>
diff --git a/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreCoordinatedAccessActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreCoordinatedAccessActorSpec.scala
index b68a7f9e64b..dcc4f87f897 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreCoordinatedAccessActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreCoordinatedAccessActorSpec.scala
@@ -10,7 +10,12 @@ import cats.data.NonEmptyVector
 import cromwell.core._
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.WorkflowStoreAbortResponse
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.WorkflowStoreAbortResponse.WorkflowStoreAbortResponse
-import cromwell.engine.workflow.workflowstore.WorkflowStoreCoordinatedAccessActor.{Abort, DeleteFromStore, FetchStartableWorkflows, WriteHeartbeats}
+import cromwell.engine.workflow.workflowstore.WorkflowStoreCoordinatedAccessActor.{
+  Abort,
+  DeleteFromStore,
+  FetchStartableWorkflows,
+  WriteHeartbeats
+}
 import org.scalatest.flatspec.AsyncFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks
@@ -18,13 +23,16 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future}
 
-class WorkflowStoreCoordinatedAccessActorSpec extends TestKitSuite
-  with AsyncFlatSpecLike with Matchers with TableDrivenPropertyChecks {
+class WorkflowStoreCoordinatedAccessActorSpec
+    extends TestKitSuite
+    with AsyncFlatSpecLike
+    with Matchers
+    with TableDrivenPropertyChecks {
 
   behavior of "WorkflowStoreCoordinatedWriteActor"
 
   // So that we can timeout the asks below, change from the serial execution context to a parallel one
-  override implicit def executionContext: ExecutionContext = scala.concurrent.ExecutionContext.Implicits.global
+  implicit override def executionContext: ExecutionContext = scala.concurrent.ExecutionContext.Implicits.global
 
   def sleepAndThrow: Nothing = {
     Thread.sleep(30.seconds.dilated.toMillis)
@@ -35,10 +43,9 @@ class WorkflowStoreCoordinatedAccessActorSpec extends TestKitSuite
     val expected = 12345
     val workflowStore = new InMemoryWorkflowStore {
       override def writeWorkflowHeartbeats(workflowIds: Set[(WorkflowId, OffsetDateTime)],
-                                           heartbeatDateTime: OffsetDateTime)
-                                          (implicit ec: ExecutionContext): Future[Int] = {
+                                           heartbeatDateTime: OffsetDateTime
+      )(implicit ec: ExecutionContext): Future[Int] =
         Future.successful(expected)
-      }
     }
     val actor = TestActorRef(new WorkflowStoreCoordinatedAccessActor(workflowStore))
     val request = WriteHeartbeats(NonEmptyVector.of((WorkflowId.randomId(), OffsetDateTime.now)), OffsetDateTime.now)
@@ -64,12 +71,15 @@ class WorkflowStoreCoordinatedAccessActorSpec extends TestKitSuite
       requestedWorkflowId = None
     )
     val now = OffsetDateTime.now()
-    val expected: List[WorkflowToStart] = List(WorkflowToStart(WorkflowId.randomId(), now, collection, Submitted, HogGroup("foo")))
+    val expected: List[WorkflowToStart] =
+      List(WorkflowToStart(WorkflowId.randomId(), now, collection, Submitted, HogGroup("foo")))
     val workflowStore = new InMemoryWorkflowStore {
-      override def fetchStartableWorkflows(n: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])
-                                          (implicit ec: ExecutionContext): Future[List[WorkflowToStart]] = {
+      override def fetchStartableWorkflows(n: Int,
+                                           cromwellId: String,
+                                           heartbeatTtl: FiniteDuration,
+                                           excludedGroups: Set[String]
+      )(implicit ec: ExecutionContext): Future[List[WorkflowToStart]] =
         Future.successful(expected)
-      }
     }
     val actor = TestActorRef(new WorkflowStoreCoordinatedAccessActor(workflowStore))
     val request = FetchStartableWorkflows(1, "test fetchStartableWorkflows success", 1.second, Set.empty)
@@ -95,15 +105,19 @@ class WorkflowStoreCoordinatedAccessActorSpec extends TestKitSuite
       requestedWorkflowId = None
     )
     val now = OffsetDateTime.now()
-    val expected: List[WorkflowToStart] = List(WorkflowToStart(WorkflowId.randomId(), now, collection, Submitted, HogGroup("foo")))
+    val expected: List[WorkflowToStart] =
+      List(WorkflowToStart(WorkflowId.randomId(), now, collection, Submitted, HogGroup("foo")))
     val workflowStore = new InMemoryWorkflowStore {
-      override def fetchStartableWorkflows(n: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])
-                                          (implicit ec: ExecutionContext): Future[List[WorkflowToStart]] = {
+      override def fetchStartableWorkflows(n: Int,
+                                           cromwellId: String,
+                                           heartbeatTtl: FiniteDuration,
+                                           excludedGroups: Set[String]
+      )(implicit ec: ExecutionContext): Future[List[WorkflowToStart]] =
         Future.successful(expected)
-      }
     }
     val actor = TestActorRef(new WorkflowStoreCoordinatedAccessActor(workflowStore))
-    val request = FetchStartableWorkflows(1, "test fetchStartableWorkflows with workflow url success", 1.second, Set.empty)
+    val request =
+      FetchStartableWorkflows(1, "test fetchStartableWorkflows with workflow url success", 1.second, Set.empty)
     implicit val timeout: Timeout = Timeout(2.seconds.dilated)
     actor.ask(request).mapTo[List[WorkflowToStart]] map { actual =>
       actual should be(expected)
@@ -113,9 +127,8 @@ class WorkflowStoreCoordinatedAccessActorSpec extends TestKitSuite
   it should "abort workflows" in {
     val expected = WorkflowStoreAbortResponse.AbortRequested
     val workflowStore = new InMemoryWorkflowStore {
-      override def abort(id: WorkflowId)(implicit ec: ExecutionContext): Future[WorkflowStoreAbortResponse] = {
+      override def abort(id: WorkflowId)(implicit ec: ExecutionContext): Future[WorkflowStoreAbortResponse] =
         Future.successful(WorkflowStoreAbortResponse.AbortRequested)
-      }
     }
     val actor = TestActorRef(new WorkflowStoreCoordinatedAccessActor(workflowStore))
     val request = Abort(WorkflowId.fromString("00001111-2222-3333-aaaa-bbbbccccdddd"))
@@ -128,9 +141,8 @@ class WorkflowStoreCoordinatedAccessActorSpec extends TestKitSuite
   it should "delete workflow store entries" in {
     val expected = 1 // 1 row deleted
     val workflowStore = new InMemoryWorkflowStore {
-      override def deleteFromStore(workflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Int] = {
+      override def deleteFromStore(workflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Int] =
         Future.successful(1)
-      }
     }
     val actor = TestActorRef(new WorkflowStoreCoordinatedAccessActor(workflowStore))
     val request = DeleteFromStore(WorkflowId.fromString("00001111-2222-3333-aaaa-bbbbccccdddd"))
@@ -143,17 +155,16 @@ class WorkflowStoreCoordinatedAccessActorSpec extends TestKitSuite
   val failureResponses = Table(
     ("description", "result", "expectedException", "expectedMessagePrefix"),
     ("a failure", () => Future.failed(new IOException("expected")), classOf[IOException], "expected"),
-    ("a timeout", () => Future(sleepAndThrow), classOf[AskTimeoutException], "Ask timed out"),
+    ("a timeout", () => Future(sleepAndThrow), classOf[AskTimeoutException], "Ask timed out")
   )
 
   forAll(failureResponses) { (description, result, expectedException, expectedMessagePrefix) =>
     it should s"fail to writeHeartBeats due to $description" in {
       val workflowStore = new InMemoryWorkflowStore {
         override def writeWorkflowHeartbeats(workflowIds: Set[(WorkflowId, OffsetDateTime)],
-                                             heartbeatDateTime: OffsetDateTime)
-                                            (implicit ec: ExecutionContext): Future[Nothing] = {
+                                             heartbeatDateTime: OffsetDateTime
+        )(implicit ec: ExecutionContext): Future[Nothing] =
           result()
-        }
       }
       val actor = TestActorRef(new WorkflowStoreCoordinatedAccessActor(workflowStore))
       val request = WriteHeartbeats(NonEmptyVector.of((WorkflowId.randomId(), OffsetDateTime.now)), OffsetDateTime.now)
@@ -166,14 +177,17 @@ class WorkflowStoreCoordinatedAccessActorSpec extends TestKitSuite
 
     it should s"fail to fetchStartableWorkflows due to $description" in {
       val workflowStore = new InMemoryWorkflowStore {
-        override def fetchStartableWorkflows(n: Int, cromwellId: String, heartbeatTtl: FiniteDuration, excludedGroups: Set[String])
-                                            (implicit ec: ExecutionContext): Future[Nothing] = {
+        override def fetchStartableWorkflows(n: Int,
+                                             cromwellId: String,
+                                             heartbeatTtl: FiniteDuration,
+                                             excludedGroups: Set[String]
+        )(implicit ec: ExecutionContext): Future[Nothing] =
           result()
-        }
       }
       val actor = TestActorRef(new WorkflowStoreCoordinatedAccessActor(workflowStore))
       val heartbeatTtlNotReallyUsed = 1.second
-      val request = FetchStartableWorkflows(1, s"test $description fetchStartableWorkflows", heartbeatTtlNotReallyUsed, Set.empty)
+      val request =
+        FetchStartableWorkflows(1, s"test $description fetchStartableWorkflows", heartbeatTtlNotReallyUsed, Set.empty)
       implicit val timeout: Timeout = Timeout(2.seconds.dilated)
       actor.ask(request).failed map { actual =>
         actual.getMessage should startWith(expectedMessagePrefix)
diff --git a/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreHeartbeatWriteActorSpec.scala b/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreHeartbeatWriteActorSpec.scala
index 6749f53931c..71b6e440470 100644
--- a/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreHeartbeatWriteActorSpec.scala
+++ b/engine/src/test/scala/cromwell/engine/workflow/workflowstore/WorkflowStoreHeartbeatWriteActorSpec.scala
@@ -16,8 +16,7 @@ import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future}
 import scala.util.control.NoStackTrace
 
-class WorkflowStoreHeartbeatWriteActorSpec extends TestKitSuite
-  with AnyFlatSpecLike with Matchers with Eventually {
+class WorkflowStoreHeartbeatWriteActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with Eventually {
 
   behavior of "WorkflowStoreHeartbeatWriteActor"
 
@@ -27,22 +26,23 @@ class WorkflowStoreHeartbeatWriteActorSpec extends TestKitSuite
 
     val workflowStore = new InMemoryWorkflowStore {
       override def writeWorkflowHeartbeats(workflowIds: Set[(WorkflowId, OffsetDateTime)],
-                                           heartbeatDateTime: OffsetDateTime)
-                                          (implicit ec: ExecutionContext): Future[Int] = {
+                                           heartbeatDateTime: OffsetDateTime
+      )(implicit ec: ExecutionContext): Future[Int] =
         Future.failed(new RuntimeException("this is expected") with NoStackTrace)
-      }
     }
 
     val workflowStoreAccess = UncoordinatedWorkflowStoreAccess(workflowStore)
-    val workflowHeartbeatTypesafeConfig = ConfigFactory.parseString(
-      """|danger.debug.only.minimum-heartbeat-ttl = 10 ms
-         |system.workflow-heartbeats {
-         |  heartbeat-interval = 500 ms
-         |  write-batch-size = 1
-         |  write-failure-shutdown-duration = 1 s
-         |}
-         |""".stripMargin
-    ).withFallback(ConfigFactory.load())
+    val workflowHeartbeatTypesafeConfig = ConfigFactory
+      .parseString(
+        """|danger.debug.only.minimum-heartbeat-ttl = 10 ms
+           |system.workflow-heartbeats {
+           |  heartbeat-interval = 500 ms
+           |  write-batch-size = 1
+           |  write-failure-shutdown-duration = 1 s
+           |}
+           |""".stripMargin
+      )
+      .withFallback(ConfigFactory.load())
     val workflowHeartbeatConfig = WorkflowHeartbeatConfig(workflowHeartbeatTypesafeConfig)
     val terminator = new CromwellTerminator {
       override def beginCromwellShutdown(reason: CoordinatedShutdown.Reason): Future[Done] = {
diff --git a/engine/src/test/scala/cromwell/jobstore/JobResultSpec.scala b/engine/src/test/scala/cromwell/jobstore/JobResultSpec.scala
index d623e9eee23..a951c479449 100644
--- a/engine/src/test/scala/cromwell/jobstore/JobResultSpec.scala
+++ b/engine/src/test/scala/cromwell/jobstore/JobResultSpec.scala
@@ -23,7 +23,16 @@ class JobResultSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "write more complicated WdlValues" in {
-    val success = JobResultSuccess(Some(0), WomMocks.mockOutputExpectations(Map("abc" -> WomMap(WomMapType(WomStringType, WomIntegerType), Map(WomString("hello") -> WomInteger(4), WomString("goodbye") -> WomInteger(6))))))
+    val success = JobResultSuccess(
+      Some(0),
+      WomMocks.mockOutputExpectations(
+        Map(
+          "abc" -> WomMap(WomMapType(WomStringType, WomIntegerType),
+                          Map(WomString("hello") -> WomInteger(4), WomString("goodbye") -> WomInteger(6))
+          )
+        )
+      )
+    )
     val asJson = success.toJson
 
     val jsonString = asJson.toString()
diff --git a/engine/src/test/scala/cromwell/webservice/EngineStatsActorSpec.scala b/engine/src/test/scala/cromwell/webservice/EngineStatsActorSpec.scala
index 9f7567e8eee..08e5125e55c 100644
--- a/engine/src/test/scala/cromwell/webservice/EngineStatsActorSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/EngineStatsActorSpec.scala
@@ -49,8 +49,8 @@ class EngineStatsActorSpec extends TestKitSuite with AnyFlatSpecLike with Matche
 
 object EngineStatsActorSpec {
   final case class FakeWorkflowActor(jobs: Int) extends Actor {
-    override def receive = {
-      case JobCountQuery => sender() ! JobCount(jobs)
+    override def receive = { case JobCountQuery =>
+      sender() ! JobCount(jobs)
     }
   }
 }
diff --git a/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala b/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala
index 700c0274026..b0669721518 100644
--- a/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/MetadataBuilderActorSpec.scala
@@ -22,8 +22,12 @@ import scala.concurrent.Future
 import scala.concurrent.duration._
 import scala.util.Random
 
-class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with Matchers
-  with TableDrivenPropertyChecks with ImplicitSender {
+class MetadataBuilderActorSpec
+    extends TestKitSuite
+    with AsyncFlatSpecLike
+    with Matchers
+    with TableDrivenPropertyChecks
+    with ImplicitSender {
 
   behavior of "MetadataBuilderActor"
 
@@ -37,42 +41,40 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
                              expectedRes: String,
                              metadataBuilderActorName: String,
                              failedTasks: Boolean = false
-                            ): Future[Assertion] = {
+  ): Future[Assertion] = {
     val mockReadMetadataWorkerActor = TestProbe("mockReadMetadataWorkerActor")
     def readMetadataWorkerMaker = () => mockReadMetadataWorkerActor.props
 
-
     val mba = system.actorOf(
       props = MetadataBuilderActor.props(readMetadataWorkerMaker, 1000000),
-      name = metadataBuilderActorName,
+      name = metadataBuilderActorName
     )
 
     val response = mba.ask(action).mapTo[MetadataJsonResponse]
     mockReadMetadataWorkerActor.expectMsg(defaultTimeout, action)
     mockReadMetadataWorkerActor.reply(
-      if(failedTasks) FetchFailedJobsMetadataLookupResponse(events) else MetadataLookupResponse(queryReply, events)
+      if (failedTasks) FetchFailedJobsMetadataLookupResponse(events) else MetadataLookupResponse(queryReply, events)
     )
-    response map { r => r shouldBe a [SuccessfulMetadataJsonResponse] }
-    response.mapTo[SuccessfulMetadataJsonResponse] map { b => b.responseJson shouldBe expectedRes.parseJson}
+    response map { r => r shouldBe a[SuccessfulMetadataJsonResponse] }
+    response.mapTo[SuccessfulMetadataJsonResponse] map { b => b.responseJson shouldBe expectedRes.parseJson }
   }
 
-
   def assertMetadataFailureResponse(action: MetadataServiceAction,
                                     metadataServiceResponse: MetadataServiceResponse,
                                     expectedException: Exception,
-                                    metadataBuilderActorName: String,
-                                   ): Future[Assertion] = {
+                                    metadataBuilderActorName: String
+  ): Future[Assertion] = {
     val mockReadMetadataWorkerActor = TestProbe("mockReadMetadataWorkerActor")
     val mba = system.actorOf(
       props = MetadataBuilderActor.props(() => mockReadMetadataWorkerActor.props, defaultSafetyRowNumberThreshold),
-      name = metadataBuilderActorName,
+      name = metadataBuilderActorName
     )
     val response = mba.ask(action).mapTo[MetadataServiceResponse]
 
     mockReadMetadataWorkerActor.expectMsg(defaultTimeout, action)
     mockReadMetadataWorkerActor.reply(metadataServiceResponse)
 
-    response map { r => r shouldBe a [FailedMetadataJsonResponse] }
+    response map { r => r shouldBe a[FailedMetadataJsonResponse] }
     response.mapTo[FailedMetadataJsonResponse] map { b =>
       b.reason.getClass shouldBe expectedException.getClass
       b.reason.getMessage shouldBe expectedException.getMessage
@@ -80,9 +82,8 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
   }
 
   it should "build workflow scope tree from metadata events" in {
-    def makeEvent(workflow: WorkflowId, key: Option[MetadataJobKey]) = {
+    def makeEvent(workflow: WorkflowId, key: Option[MetadataJobKey]) =
       MetadataEvent(MetadataKey(workflow, key, "NOT_CHECKED"), MetadataValue("NOT_CHECKED"))
-    }
 
     val workflowA = WorkflowId.randomId()
 
@@ -145,30 +146,32 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
 
   type EventBuilder = (String, String, OffsetDateTime)
 
-  def makeEvent(workflow: WorkflowId)(key: String, value: MetadataValue, offsetDateTime: OffsetDateTime): MetadataEvent = {
+  def makeEvent(
+    workflow: WorkflowId
+  )(key: String, value: MetadataValue, offsetDateTime: OffsetDateTime): MetadataEvent =
     MetadataEvent(MetadataKey(workflow, None, key), Option(value), offsetDateTime)
-  }
 
-  def makeCallEvent(workflow: WorkflowId)
-                   (key: String, value: MetadataValue, offsetDateTime: OffsetDateTime): MetadataEvent = {
+  def makeCallEvent(
+    workflow: WorkflowId
+  )(key: String, value: MetadataValue, offsetDateTime: OffsetDateTime): MetadataEvent = {
     val jobKey = MetadataJobKey("fqn", None, 1)
     MetadataEvent(MetadataKey(workflow, Option(jobKey), key), Option(value), offsetDateTime)
   }
 
-  //noinspection ScalaUnusedSymbol
-  def makeEmptyValue(workflow: WorkflowId)
-                    (key: String, value: MetadataValue, offsetDateTime: OffsetDateTime): MetadataEvent = {
+  // noinspection ScalaUnusedSymbol
+  def makeEmptyValue(
+    workflow: WorkflowId
+  )(key: String, value: MetadataValue, offsetDateTime: OffsetDateTime): MetadataEvent =
     MetadataEvent(MetadataKey(workflow, None, key), None, offsetDateTime)
-  }
 
   def assertMetadataKeyStructure(eventList: List[EventBuilder],
                                  expectedJson: String,
                                  workflow: WorkflowId = WorkflowId.randomId(),
                                  eventMaker: WorkflowId => (String, MetadataValue, OffsetDateTime) => MetadataEvent =
-                                 makeEvent,
+                                   makeEvent,
                                  metadataBuilderActorName: String,
                                  isFailedTaskFetch: Boolean = false
-                                ): Future[Assertion] = {
+  ): Future[Assertion] = {
 
     val events = eventList map { e => (e._1, MetadataValue(e._2), e._3) } map Function.tupled(eventMaker(workflow))
     val expectedRes = s"""{ "calls": {}, $expectedJson, "id":"$workflow" }"""
@@ -180,9 +183,8 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
 
   it should "build the call list for failed tasks when prompted" in {
 
-    def makeEvent(workflow: WorkflowId, key: Option[MetadataJobKey]) = {
+    def makeEvent(workflow: WorkflowId, key: Option[MetadataJobKey]) =
       MetadataEvent(MetadataKey(workflow, key, "NOT_CHECKED"), MetadataValue("NOT_CHECKED"))
-    }
 
     val workflowA = WorkflowId.randomId()
 
@@ -242,7 +244,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       events = workflowAEvents,
       expectedRes = expectedRes,
       failedTasks = true,
-      metadataBuilderActorName = "mba-failed-tasks",
+      metadataBuilderActorName = "mba-failed-tasks"
     )
   }
 
@@ -257,7 +259,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     assertMetadataKeyStructure(
       eventList = eventBuilderList,
       expectedJson = expectedRes,
-      metadataBuilderActorName = "mba-same-key",
+      metadataBuilderActorName = "mba-same-key"
     )
   }
 
@@ -272,7 +274,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     assertMetadataKeyStructure(
       eventList = eventBuilderList,
       expectedJson = expectedRes,
-      metadataBuilderActorName = "mba-not-workflow-state",
+      metadataBuilderActorName = "mba-not-workflow-state"
     )
   }
 
@@ -284,30 +286,29 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     val workflowId = WorkflowId.randomId()
     val expectedRes =
       s""""calls": {
-        |    "fqn": [{
-        |      "attempt": 1,
-        |      "executionStatus": "Done",
-        |      "shardIndex": -1
-        |    }]
-        |  },
-        |  "id": "$workflowId"""".stripMargin
+         |    "fqn": [{
+         |      "attempt": 1,
+         |      "executionStatus": "Done",
+         |      "shardIndex": -1
+         |    }]
+         |  },
+         |  "id": "$workflowId"""".stripMargin
 
     assertMetadataKeyStructure(
       eventList = eventBuilderList,
       expectedJson = expectedRes,
       workflow = workflowId,
       eventMaker = makeCallEvent,
-      metadataBuilderActorName = "mba-not-execution-status",
+      metadataBuilderActorName = "mba-not-execution-status"
     )
   }
 
-
   it should "use reverse date ordering (oldest first) for event start and stop values" in {
     val eventBuilderList = List(
       ("start", "1990-12-20T12:30:00.000Z", OffsetDateTime.now),
       ("start", "1990-12-20T12:30:01.000Z", OffsetDateTime.now.plusSeconds(1)),
       ("end", "2018-06-02T12:30:00.000Z", OffsetDateTime.now.plusSeconds(2)),
-      ("end", "2018-06-02T12:30:01.000Z", OffsetDateTime.now.plusSeconds(3)),
+      ("end", "2018-06-02T12:30:01.000Z", OffsetDateTime.now.plusSeconds(3))
     )
     val workflowId = WorkflowId.randomId()
     val expectedRes =
@@ -326,11 +327,10 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       expectedJson = expectedRes,
       workflow = workflowId,
       eventMaker = makeCallEvent,
-      metadataBuilderActorName = "mba-start-end-values",
+      metadataBuilderActorName = "mba-start-end-values"
     )
   }
 
-
   it should "build JSON object structure from dotted key syntax" in {
     val eventBuilderList = List(
       ("a:b:c", "abc", OffsetDateTime.now),
@@ -352,11 +352,10 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     assertMetadataKeyStructure(
       eventList = eventBuilderList,
       expectedJson = expectedRes,
-      metadataBuilderActorName = "mba-object-key",
+      metadataBuilderActorName = "mba-object-key"
     )
   }
 
-
   it should "build numerically sorted JSON list structure from dotted key syntax" in {
     val eventBuilderList = List(
       ("l[1]", "l1", OffsetDateTime.now),
@@ -375,7 +374,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     assertMetadataKeyStructure(
       eventList = eventBuilderList,
       expectedJson = expectedRes,
-      metadataBuilderActorName = "mba-list-key",
+      metadataBuilderActorName = "mba-list-key"
     )
   }
 
@@ -397,7 +396,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     assertMetadataKeyStructure(
       eventList = eventBuilderList,
       expectedJson = expectedRes,
-      metadataBuilderActorName = "mba-same-index",
+      metadataBuilderActorName = "mba-same-index"
     )
   }
 
@@ -442,7 +441,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     assertMetadataKeyStructure(
       eventList = eventBuilderList,
       expectedJson = expectedRes,
-      metadataBuilderActorName = "mba-nest-objects",
+      metadataBuilderActorName = "mba-nest-objects"
     )
   }
 
@@ -467,7 +466,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     assertMetadataKeyStructure(
       eventList = eventBuilderList,
       expectedJson = expectedRes,
-      metadataBuilderActorName = "mba-nest-lists",
+      metadataBuilderActorName = "mba-nest-lists"
     )
   }
 
@@ -486,7 +485,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       eventList = eventBuilderList,
       expectedJson = expectedRes,
       eventMaker = makeEmptyValue,
-      metadataBuilderActorName = "mba-nest-empty",
+      metadataBuilderActorName = "mba-nest-empty"
     )
   }
 
@@ -497,19 +496,18 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     val kiv4 = ("key[0]", "value4", OffsetDateTime.now.plusSeconds(3))
 
     val tuples = List(
-      ("mba-json-1", List(kv),  """"key": "value""""),
-      ("mba-json-2", List(kv, ksv2),  """"key": { "subkey": "value2" }"""),
-      ("mba-json-3", List(kv, ksv2, kisv3),  """"key": [ { "subkey": "value3" } ]"""),
-      ("mba-json-4", List(kv, ksv2, kisv3, kiv4),  """"key": [ "value4" ]""")
-    )
-
-    Future.sequence(tuples map {
-      case (metadataBuilderActorName, eventList, expectedJson) =>
-        assertMetadataKeyStructure(
-          eventList = eventList,
-          expectedJson = expectedJson,
-          metadataBuilderActorName = metadataBuilderActorName,
-        )
+      ("mba-json-1", List(kv), """"key": "value""""),
+      ("mba-json-2", List(kv, ksv2), """"key": { "subkey": "value2" }"""),
+      ("mba-json-3", List(kv, ksv2, kisv3), """"key": [ { "subkey": "value3" } ]"""),
+      ("mba-json-4", List(kv, ksv2, kisv3, kiv4), """"key": [ "value4" ]""")
+    )
+
+    Future.sequence(tuples map { case (metadataBuilderActorName, eventList, expectedJson) =>
+      assertMetadataKeyStructure(
+        eventList = eventList,
+        expectedJson = expectedJson,
+        metadataBuilderActorName = metadataBuilderActorName
+      )
     }) map { assertions =>
       assertions should contain only Succeeded
     }
@@ -530,17 +528,17 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
 
     val expectedResponse =
       s"""{
-          | "calls": {},
-          | "a": 2,
-          | "b": 2,
-          | "c": 2,
-          | "d": 2.9,
-          | "e": 2.9,
-          | "f": true,
-          | "g": false,
-          | "h": "false",
-          | "id":"$workflowId"
-          | }
+         | "calls": {},
+         | "a": 2,
+         | "b": 2,
+         | "c": 2,
+         | "d": 2.9,
+         | "e": 2.9,
+         | "f": true,
+         | "g": false,
+         | "h": "false",
+         | "id":"$workflowId"
+         | }
       """.stripMargin
 
     val mdQuery = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
@@ -550,7 +548,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       queryReply = mdQuery,
       events = events,
       expectedRes = expectedResponse,
-      metadataBuilderActorName = "mba-coerce-type",
+      metadataBuilderActorName = "mba-coerce-type"
     )
   }
 
@@ -564,10 +562,10 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
 
     val expectedResponse =
       s"""{
-          | "calls": {},
-          | "i": "UnknownClass(50)",
-          | "id":"$workflowId"
-          |}
+         | "calls": {},
+         | "i": "UnknownClass(50)",
+         | "id":"$workflowId"
+         |}
       """.stripMargin
 
     val mdQuery = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
@@ -577,7 +575,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       queryReply = mdQuery,
       events = events,
       expectedRes = expectedResponse,
-      metadataBuilderActorName = "mba-unknown-type",
+      metadataBuilderActorName = "mba-unknown-type"
     )
   }
 
@@ -590,10 +588,10 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
 
     val expectedResponse =
       s"""{
-          | "calls": {},
-          | "i": "notAnInt",
-          | "id":"$workflowId"
-          |}
+         | "calls": {},
+         | "i": "notAnInt",
+         | "id":"$workflowId"
+         |}
       """.stripMargin
 
     val mdQuery = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
@@ -603,7 +601,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       queryReply = mdQuery,
       events = events,
       expectedRes = expectedResponse,
-      metadataBuilderActorName = "mba-coerce-fails",
+      metadataBuilderActorName = "mba-coerce-fails"
     )
   }
 
@@ -624,11 +622,11 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
 
     val expectedEmptyResponse =
       s"""{
-          | "calls": {},
-          | "hey": {},
-          | "emptyList": [],
-          | "id":"$workflowId"
-          |}
+         | "calls": {},
+         | "hey": {},
+         | "emptyList": [],
+         | "id":"$workflowId"
+         |}
       """.stripMargin
 
     val mdQuery = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
@@ -638,16 +636,16 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       queryReply = mdQuery,
       events = emptyEvents,
       expectedRes = expectedEmptyResponse,
-      metadataBuilderActorName = "mba-empty-values",
+      metadataBuilderActorName = "mba-empty-values"
     )
 
     val expectedNonEmptyResponse =
       s"""{
-          | "calls": {},
-          | "hey": "something",
-          | "emptyList": ["something", "something"],
-          | "id":"$workflowId"
-          |}
+         | "calls": {},
+         | "hey": "something",
+         | "emptyList": ["something", "something"],
+         | "id":"$workflowId"
+         |}
       """.stripMargin
 
     assertMetadataResponse(
@@ -655,7 +653,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       queryReply = mdQuery,
       events = valueEvents,
       expectedRes = expectedNonEmptyResponse,
-      metadataBuilderActorName = "mba-non-empty-values",
+      metadataBuilderActorName = "mba-non-empty-values"
     )
   }
 
@@ -664,7 +662,9 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     val subWorkflowId = WorkflowId.randomId()
 
     val mainEvents = List(
-      MetadataEvent(MetadataKey(mainWorkflowId, Option(MetadataJobKey("callA", None, 1)), "subWorkflowId"), MetadataValue(subWorkflowId))
+      MetadataEvent(MetadataKey(mainWorkflowId, Option(MetadataJobKey("callA", None, 1)), "subWorkflowId"),
+                    MetadataValue(subWorkflowId)
+      )
     )
 
     val subEvents = List(
@@ -686,7 +686,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       TestActorRef(
         props = MetadataBuilderActor.props(readMetadataWorkerMaker, 1000000),
         supervisor = parentProbe.ref,
-        name = s"MetadataActor-$mainWorkflowId",
+        name = s"MetadataActor-$mainWorkflowId"
       )
     val response = metadataBuilder.ask(mainQueryAction).mapTo[MetadataJsonResponse]
     mockReadMetadataWorkerActor.expectMsg(defaultTimeout, mainQueryAction)
@@ -714,9 +714,9 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
          |}
        """.stripMargin
 
-    response map { r => r shouldBe a [SuccessfulMetadataJsonResponse] }
+    response map { r => r shouldBe a[SuccessfulMetadataJsonResponse] }
     val bmr = response.mapTo[SuccessfulMetadataJsonResponse]
-    bmr map { b => b.responseJson shouldBe expandedRes.parseJson}
+    bmr map { b => b.responseJson shouldBe expandedRes.parseJson }
   }
 
   it should "NOT expand sub workflow metadata when NOT asked for" in {
@@ -724,7 +724,9 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     val subWorkflowId = WorkflowId.randomId()
 
     val mainEvents = List(
-      MetadataEvent(MetadataKey(mainWorkflowId, Option(MetadataJobKey("callA", None, 1)), "subWorkflowId"), MetadataValue(subWorkflowId))
+      MetadataEvent(MetadataKey(mainWorkflowId, Option(MetadataJobKey("callA", None, 1)), "subWorkflowId"),
+                    MetadataValue(subWorkflowId)
+      )
     )
 
     val queryNoExpand = MetadataQuery(mainWorkflowId, None, None, None, None, expandSubWorkflows = false)
@@ -733,18 +735,17 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     val parentProbe = TestProbe("parentProbe")
 
     val mockReadMetadataWorkerActor = TestProbe("mockReadMetadataWorkerActor")
-    def readMetadataWorkerMaker= () => mockReadMetadataWorkerActor.props
+    def readMetadataWorkerMaker = () => mockReadMetadataWorkerActor.props
 
     val metadataBuilder = TestActorRef(
       props = MetadataBuilderActor.props(readMetadataWorkerMaker, 1000000),
       supervisor = parentProbe.ref,
-      name = s"MetadataActor-$mainWorkflowId",
+      name = s"MetadataActor-$mainWorkflowId"
     )
     val response = metadataBuilder.ask(queryNoExpandAction).mapTo[MetadataJsonResponse]
     mockReadMetadataWorkerActor.expectMsg(defaultTimeout, queryNoExpandAction)
     mockReadMetadataWorkerActor.reply(MetadataLookupResponse(queryNoExpand, mainEvents))
 
-
     val nonExpandedRes =
       s"""
          |{
@@ -761,9 +762,9 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
          |}
        """.stripMargin
 
-    response map { r => r shouldBe a [SuccessfulMetadataJsonResponse] }
+    response map { r => r shouldBe a[SuccessfulMetadataJsonResponse] }
     val bmr = response.mapTo[SuccessfulMetadataJsonResponse]
-    bmr map { b => b.responseJson shouldBe nonExpandedRes.parseJson}
+    bmr map { b => b.responseJson shouldBe nonExpandedRes.parseJson }
 
   }
 
@@ -788,7 +789,6 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       ee(workflowId, Bar, eventIndex = 5, StartTime, Interval4.start),
       ee(workflowId, Bar, eventIndex = 5, EndTime, Interval4.end),
       ee(workflowId, Bar, eventIndex = 5, Grouping, Delocalizing),
-
       ee(workflowId, Baz, eventIndex = 6, StartTime, Interval2.start),
       ee(workflowId, Baz, eventIndex = 6, EndTime, Interval2.end),
       ee(workflowId, Baz, eventIndex = 6, Grouping, Localizing),
@@ -804,7 +804,6 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       // cause problems.
       pe(workflowId, Quux, StartTime, Interval8.start),
       pe(workflowId, Quux, EndTime, Interval8.end),
-
       pe(workflowId, Corge, StartTime, Interval9.start),
       pe(workflowId, Corge, EndTime, Interval9.end)
     )
@@ -817,36 +816,32 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       ee(workflowId, Foo, eventIndex = 1, StartTime, Interval1.start),
       ee(workflowId, Foo, eventIndex = 1, EndTime, Interval2.end),
       ee(workflowId, Foo, eventIndex = 1, Description, Localizing.name),
-
       ee(workflowId, Bar, eventIndex = 3, StartTime, Interval3.start),
       ee(workflowId, Bar, eventIndex = 3, Description, Delocalizing.name),
-
       ee(workflowId, Baz, eventIndex = 6, StartTime, Interval1.start),
       ee(workflowId, Baz, eventIndex = 6, EndTime, Interval2.end),
       ee(workflowId, Baz, eventIndex = 6, Description, Localizing.name),
-
       ee(workflowId, Qux, eventIndex = 8, StartTime, Interval7.start),
       ee(workflowId, Qux, eventIndex = 8, EndTime, Interval7.end),
-
       pe(workflowId, Quux, StartTime, Interval8.start),
       pe(workflowId, Quux, EndTime, Interval8.end),
-
       pe(workflowId, Corge, StartTime, Interval9.start),
       pe(workflowId, Corge, EndTime, Interval9.end)
     )
 
     val actual = MetadataBuilderActor.groupEvents(events).toSet
 
-    def filterEventsByCall(events: Iterable[MetadataEvent])(call: Call): Iterable[MetadataEvent] = {
-      events collect { case e@MetadataEvent(MetadataKey(_, Some(MetadataJobKey(n, _, _)), _), _, _) if call.name == n => e}
-    }
+    def filterEventsByCall(events: Iterable[MetadataEvent])(call: Call): Iterable[MetadataEvent] =
+      events collect {
+        case e @ MetadataEvent(MetadataKey(_, Some(MetadataJobKey(n, _, _)), _), _, _) if call.name == n => e
+      }
 
     val calls = List(Foo, Bar, Baz, Qux, Quux, Corge)
     val actuals = calls map filterEventsByCall(actual)
     val expecteds = calls map filterEventsByCall(expectations)
 
-    val matchesExpectations = (actuals zip expecteds) map {
-      case (as, es) => as.toList.map(_.toString).sorted == es.toList.map(_.toString).sorted
+    val matchesExpectations = (actuals zip expecteds) map { case (as, es) =>
+      as.toList.map(_.toString).sorted == es.toList.map(_.toString).sorted
     }
     matchesExpectations.reduceLeft(_ && _) shouldBe true
   }
@@ -854,9 +849,10 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
   it should "correctly order statuses (even unused ones)" in {
     val workflowId = WorkflowId.randomId()
 
-    def statusEvent(callName: String, status: String) = {
-      MetadataEvent(MetadataKey(workflowId, Option(MetadataJobKey(callName, None, 1)), "executionStatus"), MetadataValue(status))
-    }
+    def statusEvent(callName: String, status: String) =
+      MetadataEvent(MetadataKey(workflowId, Option(MetadataJobKey(callName, None, 1)), "executionStatus"),
+                    MetadataValue(status)
+      )
 
     // Combines standard "setup" statuses plus the conclusion status(es).
     def setupStatusesPlusConclusion(callName: String, conclusionStatuses: String*): Vector[MetadataEvent] = Vector(
@@ -874,11 +870,11 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
 
     val events =
       setupStatusesPlusConclusion("Foo", "Done") ++
-      setupStatusesPlusConclusion("Bar", "Aborting", "Aborted") ++
-      setupStatusesPlusConclusion("Baz", "Failed") ++
-      setupStatusesPlusConclusion("Qux", "RetryableFailure") ++
-      setupStatusesPlusConclusion("Quux", "Bypassed") ++
-      setupStatusesPlusConclusion("Quuux", "Unstartable")
+        setupStatusesPlusConclusion("Bar", "Aborting", "Aborted") ++
+        setupStatusesPlusConclusion("Baz", "Failed") ++
+        setupStatusesPlusConclusion("Qux", "RetryableFailure") ++
+        setupStatusesPlusConclusion("Quux", "Bypassed") ++
+        setupStatusesPlusConclusion("Quuux", "Unstartable")
 
     val expectedRes =
       s"""{
@@ -909,12 +905,13 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
     val action = GetMetadataAction(mdQuery)
 
     val metadataRowNumber = 100500
-    val expectedException = new MetadataTooLargeNumberOfRowsException(workflowId, metadataRowNumber, defaultSafetyRowNumberThreshold)
+    val expectedException =
+      new MetadataTooLargeNumberOfRowsException(workflowId, metadataRowNumber, defaultSafetyRowNumberThreshold)
     assertMetadataFailureResponse(
       action = action,
       metadataServiceResponse = MetadataLookupFailedTooLargeResponse(mdQuery, metadataRowNumber),
       expectedException = expectedException,
-      metadataBuilderActorName = "mba-too-large",
+      metadataBuilderActorName = "mba-too-large"
     )
   }
 
@@ -929,7 +926,7 @@ class MetadataBuilderActorSpec extends TestKitSuite with AsyncFlatSpecLike with
       action = action,
       metadataServiceResponse = MetadataLookupFailedTimeoutResponse(mdQuery),
       expectedException = expectedException,
-      metadataBuilderActorName = "mba-read-timeout",
+      metadataBuilderActorName = "mba-read-timeout"
     )
   }
 }
@@ -990,8 +987,8 @@ object MetadataBuilderActorSpec {
 
   def executionEventName(i: Int, a: Attr): String = s"executionEvents[$i]:${a.name}"
 
-  def executionEventKey(workflowId: WorkflowId, call: Call, eventIndex: Int, attr: Attr): MetadataKey = MetadataKey(workflowId, Option(MetadataJobKey(call.name, None, 1)), executionEventName(eventIndex, attr))
-
+  def executionEventKey(workflowId: WorkflowId, call: Call, eventIndex: Int, attr: Attr): MetadataKey =
+    MetadataKey(workflowId, Option(MetadataJobKey(call.name, None, 1)), executionEventName(eventIndex, attr))
 
   def ee(workflowId: WorkflowId, call: Call, eventIndex: Int, attr: Attr, value: Any): MetadataEvent = {
     val metadataValue = value match {
@@ -1001,7 +998,9 @@ object MetadataBuilderActorSpec {
     new MetadataEvent(executionEventKey(workflowId, call, eventIndex, attr), Option(MetadataValue(metadataValue)), y2k)
   }
 
-  def eventKey(workflowId: WorkflowId, call: Call, attr: Attr): MetadataKey = MetadataKey(workflowId, Option(MetadataJobKey(call.name, None, 1)), attr.name)
+  def eventKey(workflowId: WorkflowId, call: Call, attr: Attr): MetadataKey =
+    MetadataKey(workflowId, Option(MetadataJobKey(call.name, None, 1)), attr.name)
 
-  def pe(workflowId: WorkflowId, call: Call, attr: Attr, value: Any): MetadataEvent = new MetadataEvent(eventKey(workflowId, call, attr), Option(MetadataValue(value)), y2k)
+  def pe(workflowId: WorkflowId, call: Call, attr: Attr, value: Any): MetadataEvent =
+    new MetadataEvent(eventKey(workflowId, call, attr), Option(MetadataValue(value)), y2k)
 }
diff --git a/engine/src/test/scala/cromwell/webservice/PartialWorkflowSourcesSpec.scala b/engine/src/test/scala/cromwell/webservice/PartialWorkflowSourcesSpec.scala
index f19e3c667ab..d1b86bfa216 100644
--- a/engine/src/test/scala/cromwell/webservice/PartialWorkflowSourcesSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/PartialWorkflowSourcesSpec.scala
@@ -16,13 +16,13 @@ class PartialWorkflowSourcesSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     val input1 = Map("wf.a1" -> "hello", "wf.a2" -> "world").toJson.toString
     val input2 = Map.empty[String, String].toJson.toString
     val overrideInput1 = Map("wf.a2" -> "universe").toJson.toString
-    val mergedMapsErrorOr = PartialWorkflowSources.mergeMaps(Seq(Option(input1), Option(input2), Option(overrideInput1)))
+    val mergedMapsErrorOr =
+      PartialWorkflowSources.mergeMaps(Seq(Option(input1), Option(input2), Option(overrideInput1)))
 
     mergedMapsErrorOr match {
-      case Valid(inputs) => {
-        inputs.fields.keys should contain allOf("wf.a1", "wf.a2")
+      case Valid(inputs) =>
+        inputs.fields.keys should contain allOf ("wf.a1", "wf.a2")
         inputs.fields("wf.a2") should be(JsString("universe"))
-      }
       case Invalid(error) => fail(s"This is unexpected! This test should pass! Error: $error")
     }
   }
@@ -33,7 +33,8 @@ class PartialWorkflowSourcesSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
 
     mergedMapsErrorOr match {
       case Valid(_) => fail("This is unexpected! This test is designed to fail!")
-      case Invalid(error) => error.head shouldBe "Submitted input '\"invalidInput\"' of type JsString is not a valid JSON object."
+      case Invalid(error) =>
+        error.head shouldBe "Submitted input '\"invalidInput\"' of type JsString is not a valid JSON object."
     }
   }
 
@@ -44,7 +45,8 @@ class PartialWorkflowSourcesSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
 
     mergedMapsErrorOr match {
       case Valid(_) => fail("This is unexpected! This test is designed to fail!")
-      case Invalid(error) => error.head shouldBe "Failed to parse input: 'invalidInput', which is not a valid json. Please check for syntactical errors. (reason 1 of 1): Unexpected character 'i' at input index 0 (line 1, position 1), expected JSON Value:\ninvalidInput\n^\n"
+      case Invalid(error) =>
+        error.head shouldBe "Failed to parse input: 'invalidInput', which is not a valid json. Please check for syntactical errors. (reason 1 of 1): Unexpected character 'i' at input index 0 (line 1, position 1), expected JSON Value:\ninvalidInput\n^\n"
     }
   }
 
@@ -76,9 +78,8 @@ class PartialWorkflowSourcesSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         |}]
         |""".stripMargin
 
-    val expected = Vector(
-    """{"mywf.inInt":1,"mywf.inString":"one"}""",
-    """{"mywf.inInt":2,"mywf.inString":"two"}""").validNel
+    val expected =
+      Vector("""{"mywf.inInt":1,"mywf.inString":"one"}""", """{"mywf.inInt":2,"mywf.inString":"two"}""").validNel
 
     val actual = PartialWorkflowSources.workflowInputsValidation(input)
 
diff --git a/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
index 24cce8ae932..897e4beeec0 100644
--- a/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/SwaggerServiceSpec.scala
@@ -15,8 +15,13 @@ import org.yaml.snakeyaml.{LoaderOptions, Yaml => SnakeYaml}
 
 import scala.jdk.CollectionConverters._
 
-class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with SwaggerService with ScalatestRouteTest with Matchers
-  with TableDrivenPropertyChecks {
+class SwaggerServiceSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with SwaggerService
+    with ScalatestRouteTest
+    with Matchers
+    with TableDrivenPropertyChecks {
   def actorRefFactory = system
 
   behavior of "SwaggerService"
@@ -28,7 +33,8 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
         status should be(StatusCodes.OK)
 
         val body = responseAs[String]
-        val yaml = new SnakeYaml(new UniqueKeyConstructor(new LoaderOptions)).loadAs(body, classOf[java.util.Map[String, AnyRef]])
+        val yaml = new SnakeYaml(new UniqueKeyConstructor(new LoaderOptions))
+          .loadAs(body, classOf[java.util.Map[String, AnyRef]])
 
         yaml.get("swagger") should be("2.0")
       }
@@ -53,27 +59,42 @@ class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Swagg
 
         resultWithInfo.getSwagger.getDefinitions.asScala foreach {
           // If no properties, `getProperties` returns `null` instead of an empty map
-          case (defKey, defVal) => Option(defVal.getProperties).map(_.asScala).getOrElse(Map.empty) foreach {
-            /*
+          case (defKey, defVal) =>
+            Option(defVal.getProperties).map(_.asScala).getOrElse(Map.empty) foreach {
+              /*
             Two against one.
             Swagger parser implementation lets a RefProperty have descriptions.
             http://swagger.io/specification/#referenceObject & http://editor.swagger.io both say it's ref ONLY!
-             */
-            case (propKey, propVal: RefProperty) =>
-              withClue(s"RefProperty $defKey.$propKey has a description: ") {
-                propVal.getDescription should be(null)
-              }
-            case _ => /* ignore */
-          }
+               */
+              case (propKey, propVal: RefProperty) =>
+                withClue(s"RefProperty $defKey.$propKey has a description: ") {
+                  propVal.getDescription should be(null)
+                }
+              case _ => /* ignore */
+            }
         }
       }
   }
 
   it should "return status OK when getting OPTIONS on paths" in {
-    val pathExamples = Table("path", "/", "/swagger", "/swagger/cromwell.yaml", "/swagger/index.html", "/api",
-      "/api/workflows/", "/api/workflows/v1", "/workflows/v1/outputs", "/workflows/v1/status",
-      "/api/workflows/v1/validate", "/workflows", "/workflows/v1", "/workflows/v1/outputs", "/workflows/v1/status",
-      "/workflows/v1/validate")
+    val pathExamples = Table(
+      "path",
+      "/",
+      "/swagger",
+      "/swagger/cromwell.yaml",
+      "/swagger/index.html",
+      "/api",
+      "/api/workflows/",
+      "/api/workflows/v1",
+      "/workflows/v1/outputs",
+      "/workflows/v1/status",
+      "/api/workflows/v1/validate",
+      "/workflows",
+      "/workflows/v1",
+      "/workflows/v1/outputs",
+      "/workflows/v1/status",
+      "/workflows/v1/validate"
+    )
 
     forAll(pathExamples) { path =>
       Options(path) ~>
diff --git a/engine/src/test/scala/cromwell/webservice/SwaggerUiHttpServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/SwaggerUiHttpServiceSpec.scala
index 6afcf12bac8..e574f93dd0a 100644
--- a/engine/src/test/scala/cromwell/webservice/SwaggerUiHttpServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/SwaggerUiHttpServiceSpec.scala
@@ -11,18 +11,37 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 
 import scala.concurrent.duration._
 
-trait SwaggerUiHttpServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalatestRouteTest with SwaggerUiHttpService
-
-trait SwaggerResourceHttpServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalatestRouteTest with
-TableDrivenPropertyChecks with SwaggerResourceHttpService {
-  val testPathsForOptions = Table("endpoint", "/", "/swagger", "/swagger/index.html", "/api", "/api/example",
-    "/api/example?with=param", "/api/example/path")
+trait SwaggerUiHttpServiceSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalatestRouteTest
+    with SwaggerUiHttpService
+
+trait SwaggerResourceHttpServiceSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalatestRouteTest
+    with TableDrivenPropertyChecks
+    with SwaggerResourceHttpService {
+  val testPathsForOptions = Table("endpoint",
+                                  "/",
+                                  "/swagger",
+                                  "/swagger/index.html",
+                                  "/api",
+                                  "/api/example",
+                                  "/api/example?with=param",
+                                  "/api/example/path"
+  )
 
   implicit val timeout: RouteTestTimeout = RouteTestTimeout(5.seconds)
 }
 
-trait SwaggerUiResourceHttpServiceSpec extends SwaggerUiHttpServiceSpec with SwaggerResourceHttpServiceSpec with
-SwaggerUiResourceHttpService
+trait SwaggerUiResourceHttpServiceSpec
+    extends SwaggerUiHttpServiceSpec
+    with SwaggerResourceHttpServiceSpec
+    with SwaggerUiResourceHttpService
 
 object SwaggerUiHttpServiceSpec {
   val SwaggerIndexPreamble =
@@ -95,7 +114,6 @@ class OverrideBasePathSwaggerUiHttpServiceSpec extends SwaggerResourceHttpServic
   }
 }
 
-
 class YamlSwaggerResourceHttpServiceSpec extends SwaggerResourceHttpServiceSpec {
   override def swaggerServiceName = "testservice"
 
@@ -194,7 +212,6 @@ class YamlSwaggerUiResourceHttpServiceSpec extends SwaggerUiResourceHttpServiceS
   }
 }
 
-
 class JsonSwaggerUiResourceHttpServiceSpec extends SwaggerUiResourceHttpServiceSpec {
   override def swaggerServiceName = "testservice"
 
diff --git a/engine/src/test/scala/cromwell/webservice/WorkflowJsonSupportSpec.scala b/engine/src/test/scala/cromwell/webservice/WorkflowJsonSupportSpec.scala
index fc25bd3cd2f..c6d944c3285 100644
--- a/engine/src/test/scala/cromwell/webservice/WorkflowJsonSupportSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/WorkflowJsonSupportSpec.scala
@@ -8,7 +8,8 @@ import spray.json._
 
 class WorkflowJsonSupportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
-  val sampleSuccessResponse1 = SuccessResponse("good", "msg", Option(JsArray(Vector(JsString("data1"), JsString("data2")))))
+  val sampleSuccessResponse1 =
+    SuccessResponse("good", "msg", Option(JsArray(Vector(JsString("data1"), JsString("data2")))))
   val sampleSuccessResponse2 = SuccessResponse("good", "msg", None)
   val sampleSuccessResponseJson1 =
     """{
diff --git a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
index 4e7caf932ef..b7440bbe31c 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
@@ -9,14 +9,24 @@ import akka.stream.ActorMaterializer
 import com.typesafe.scalalogging.StrictLogging
 import common.util.VersionUtil
 import cromwell.core._
-import cromwell.core.abort.{WorkflowAbortFailureResponse, WorkflowAbortRequestedResponse, WorkflowAbortedResponse}
+import cromwell.core.abort.{WorkflowAbortedResponse, WorkflowAbortFailureResponse, WorkflowAbortRequestedResponse}
 import cromwell.engine.workflow.WorkflowManagerActor
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor._
-import cromwell.engine.workflow.workflowstore.WorkflowStoreEngineActor.{WorkflowOnHoldToSubmittedFailure, WorkflowOnHoldToSubmittedSuccess}
-import cromwell.engine.workflow.workflowstore.WorkflowStoreSubmitActor.{WorkflowSubmittedToStore, WorkflowsBatchSubmittedToStore}
+import cromwell.engine.workflow.workflowstore.WorkflowStoreEngineActor.{
+  WorkflowOnHoldToSubmittedFailure,
+  WorkflowOnHoldToSubmittedSuccess
+}
+import cromwell.engine.workflow.workflowstore.WorkflowStoreSubmitActor.{
+  WorkflowsBatchSubmittedToStore,
+  WorkflowSubmittedToStore
+}
 import cromwell.services._
-import cromwell.services.healthmonitor.ProtoHealthMonitorServiceActor.{GetCurrentStatus, StatusCheckResponse, SubsystemStatus}
+import cromwell.services.healthmonitor.ProtoHealthMonitorServiceActor.{
+  GetCurrentStatus,
+  StatusCheckResponse,
+  SubsystemStatus
+}
 import cromwell.services.instrumentation.InstrumentationService.InstrumentationServiceMessage
 import cromwell.services.metadata.MetadataArchiveStatus._
 import cromwell.services.metadata.MetadataService._
@@ -71,64 +81,62 @@ class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with
   "REST ENGINE /status endpoint" should "return 200 for status when all is well" in {
     Get(s"/engine/$version/status") ~>
       akkaHttpService.engineRoutes ~>
-        check {
-          status should be(StatusCodes.OK)
-          contentType should be(ContentTypes.`application/json`)
-          val resp = responseAs[JsObject]
-          val db = resp.fields("Engine Database").asJsObject
-          db.fields("ok").asInstanceOf[JsBoolean].value should be(true)
-        }
+      check {
+        status should be(StatusCodes.OK)
+        contentType should be(ContentTypes.`application/json`)
+        val resp = responseAs[JsObject]
+        val db = resp.fields("Engine Database").asJsObject
+        db.fields("ok").asInstanceOf[JsBoolean].value should be(true)
+      }
   }
 
+  behavior of "REST API /abort endpoint"
+  it should "return 404 for abort of unknown workflow" in {
+    val workflowId = CromwellApiServiceSpec.UnrecognizedWorkflowId
 
-    behavior of "REST API /abort endpoint"
-    it should "return 404 for abort of unknown workflow" in {
-      val workflowId = CromwellApiServiceSpec.UnrecognizedWorkflowId
-
-      Post(s"/workflows/$version/$workflowId/abort") ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(StatusCodes.NotFound) {
-            status
-          }
-          assertResult {
-            s"""|{
-                |  "status": "error",
-                |  "message": "Couldn't abort $workflowId because no workflow with that ID is in progress"
-                |}
-                |""".stripMargin.trim
-          } {
-            responseAs[String]
-          }
-          assertResult(ContentTypes.`application/json`)(contentType)
+    Post(s"/workflows/$version/$workflowId/abort") ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(StatusCodes.NotFound) {
+          status
         }
-    }
-
-    it should "return 400 for abort of a malformed workflow id" in {
-      Post(s"/workflows/$version/foobar/abort") ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(StatusCodes.BadRequest) {
-            status
-          }
-          assertResult(
-            """{
-              |  "status": "fail",
-              |  "message": "Invalid workflow ID: 'foobar'."
-              |}""".stripMargin
-          ) {
-            responseAs[String]
-          }
-          assertResult(ContentTypes.`application/json`)(contentType)
+        assertResult {
+          s"""|{
+              |  "status": "error",
+              |  "message": "Couldn't abort $workflowId because no workflow with that ID is in progress"
+              |}
+              |""".stripMargin.trim
+        } {
+          responseAs[String]
         }
-    }
+        assertResult(ContentTypes.`application/json`)(contentType)
+      }
+  }
 
-    it should "return 200 Aborted for abort of a workflow which a workflow is in OnHold state" in {
-      Post(s"/workflows/$version/${CromwellApiServiceSpec.OnHoldWorkflowId}/abort") ~>
-        akkaHttpService.workflowRoutes ~>
+  it should "return 400 for abort of a malformed workflow id" in {
+    Post(s"/workflows/$version/foobar/abort") ~>
+      akkaHttpService.workflowRoutes ~>
       check {
+        assertResult(StatusCodes.BadRequest) {
+          status
+        }
         assertResult(
-          s"""{"id":"${CromwellApiServiceSpec.OnHoldWorkflowId.toString}","status":"Aborted"}""") {
+          """{
+            |  "status": "fail",
+            |  "message": "Invalid workflow ID: 'foobar'."
+            |}""".stripMargin
+        ) {
+          responseAs[String]
+        }
+        assertResult(ContentTypes.`application/json`)(contentType)
+      }
+  }
+
+  it should "return 200 Aborted for abort of a workflow which a workflow is in OnHold state" in {
+    Post(s"/workflows/$version/${CromwellApiServiceSpec.OnHoldWorkflowId}/abort") ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(s"""{"id":"${CromwellApiServiceSpec.OnHoldWorkflowId.toString}","status":"Aborted"}""") {
           responseAs[String]
         }
         assertResult(StatusCodes.OK) {
@@ -136,14 +144,13 @@ class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with
         }
         assertResult(ContentTypes.`application/json`)(contentType)
       }
-    }
+  }
 
   it should "return 200 Aborted for abort of a workflow which a workflow is in Submitted state" in {
     Post(s"/workflows/$version/${CromwellApiServiceSpec.SubmittedWorkflowId}/abort") ~>
       akkaHttpService.workflowRoutes ~>
       check {
-        assertResult(
-          s"""{"id":"${CromwellApiServiceSpec.SubmittedWorkflowId.toString}","status":"Aborted"}""") {
+        assertResult(s"""{"id":"${CromwellApiServiceSpec.SubmittedWorkflowId.toString}","status":"Aborted"}""") {
           responseAs[String]
         }
         assertResult(StatusCodes.OK) {
@@ -153,55 +160,63 @@ class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with
       }
   }
 
-    it should "return 200 Aborting for abort of a known workflow id which is currently running" in {
-      Post(s"/workflows/$version/${CromwellApiServiceSpec.AbortingWorkflowId}/abort") ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(
-            s"""{"id":"${CromwellApiServiceSpec.AbortingWorkflowId.toString}","status":"Aborting"}""") {
-            responseAs[String]
-          }
-          assertResult(StatusCodes.OK) {
-            status
-          }
-          assertResult(ContentTypes.`application/json`)(contentType)
+  it should "return 200 Aborting for abort of a known workflow id which is currently running" in {
+    Post(s"/workflows/$version/${CromwellApiServiceSpec.AbortingWorkflowId}/abort") ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(s"""{"id":"${CromwellApiServiceSpec.AbortingWorkflowId.toString}","status":"Aborting"}""") {
+          responseAs[String]
         }
-    }
+        assertResult(StatusCodes.OK) {
+          status
+        }
+        assertResult(ContentTypes.`application/json`)(contentType)
+      }
+  }
 
-    behavior of "REST API submission endpoint"
-    it should "return 201 for a successful workflow submission " in {
-      val workflowSource = Multipart.FormData.BodyPart("workflowSource", HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()))
-      val workflowInputs = Multipart.FormData.BodyPart("workflowInputs", HttpEntity(MediaTypes.`application/json`, HelloWorld.rawInputs.toJson.toString()))
-      val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
-      Post(s"/workflows/$version", formData) ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(
-            s"""{
-                |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
-                |  "status": "Submitted"
-                |}""".stripMargin) {
-            responseAs[String].parseJson.prettyPrint
-          }
-          assertResult(StatusCodes.Created) {
-            status
-          }
-          headers should be(Seq.empty)
+  behavior of "REST API submission endpoint"
+  it should "return 201 for a successful workflow submission " in {
+    val workflowSource =
+      Multipart.FormData.BodyPart("workflowSource",
+                                  HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource())
+      )
+    val workflowInputs =
+      Multipart.FormData.BodyPart("workflowInputs",
+                                  HttpEntity(MediaTypes.`application/json`, HelloWorld.rawInputs.toJson.toString())
+      )
+    val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
+    Post(s"/workflows/$version", formData) ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(s"""{
+                        |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
+                        |  "status": "Submitted"
+                        |}""".stripMargin) {
+          responseAs[String].parseJson.prettyPrint
         }
-    }
+        assertResult(StatusCodes.Created) {
+          status
+        }
+        headers should be(Seq.empty)
+      }
+  }
 
   it should "return 201 for a successful workflow submission using workflowUrl" in {
-    val workflowUrl = Multipart.FormData.BodyPart("workflowUrl", HttpEntity("https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"))
+    val workflowUrl = Multipart.FormData.BodyPart(
+      "workflowUrl",
+      HttpEntity(
+        "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"
+      )
+    )
     val formData = Multipart.FormData(workflowUrl).toEntity()
 
     Post(s"/workflows/$version", formData) ~>
       akkaHttpService.workflowRoutes ~>
       check {
-        assertResult(
-          s"""{
-             |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
-             |  "status": "Submitted"
-             |}""".stripMargin) {
+        assertResult(s"""{
+                        |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
+                        |  "status": "Submitted"
+                        |}""".stripMargin) {
           responseAs[String].parseJson.prettyPrint
         }
         assertResult(StatusCodes.Created) {
@@ -212,17 +227,21 @@ class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with
   }
 
   it should "return 400 for a workflow submission using workflowUrl with invalid protocol" in {
-    val workflowUrl = Multipart.FormData.BodyPart("workflowUrl", HttpEntity("htpps://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"))
+    val workflowUrl = Multipart.FormData.BodyPart(
+      "workflowUrl",
+      HttpEntity(
+        "htpps://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"
+      )
+    )
     val formData = Multipart.FormData(workflowUrl).toEntity()
 
     Post(s"/workflows/$version", formData) ~>
       akkaHttpService.workflowRoutes ~>
       check {
-        assertResult(
-          s"""{
-             |  "message": "Error(s): Error while validating workflow url: unknown protocol: htpps",
-             |  "status": "fail"
-             |}""".stripMargin) {
+        assertResult(s"""{
+                        |  "message": "Error(s): Error while validating workflow url: unknown protocol: htpps",
+                        |  "status": "fail"
+                        |}""".stripMargin) {
           responseAs[String].parseJson.prettyPrint
         }
         assertResult(StatusCodes.BadRequest) {
@@ -233,18 +252,23 @@ class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with
   }
 
   it should "return 201 for a successful workflow submission with onHold = true" in {
-    val workflowSource = Multipart.FormData.BodyPart("workflowSource", HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()))
-    val workflowInputs = Multipart.FormData.BodyPart("workflowInputs", HttpEntity(MediaTypes.`application/json`, HelloWorld.rawInputs.toJson.toString()))
-    val onHold =  Multipart.FormData.BodyPart("workflowOnHold", HttpEntity("true"))
+    val workflowSource =
+      Multipart.FormData.BodyPart("workflowSource",
+                                  HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource())
+      )
+    val workflowInputs =
+      Multipart.FormData.BodyPart("workflowInputs",
+                                  HttpEntity(MediaTypes.`application/json`, HelloWorld.rawInputs.toJson.toString())
+      )
+    val onHold = Multipart.FormData.BodyPart("workflowOnHold", HttpEntity("true"))
     val formData = Multipart.FormData(workflowSource, workflowInputs, onHold).toEntity()
     Post(s"/workflows/$version", formData) ~>
       akkaHttpService.workflowRoutes ~>
       check {
-        assertResult(
-          s"""{
-             |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
-             |  "status": "On Hold"
-             |}""".stripMargin) {
+        assertResult(s"""{
+                        |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
+                        |  "status": "On Hold"
+                        |}""".stripMargin) {
           responseAs[String].parseJson.prettyPrint
         }
         assertResult(StatusCodes.Created) {
@@ -259,11 +283,10 @@ class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with
     Post(s"/workflows/$version/$id/releaseHold") ~>
       akkaHttpService.workflowRoutes ~>
       check {
-        assertResult(
-          s"""{
-             |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
-             |  "status": "Submitted"
-             |}""".stripMargin) {
+        assertResult(s"""{
+                        |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
+                        |  "status": "Submitted"
+                        |}""".stripMargin) {
           responseAs[String].parseJson.prettyPrint
         }
         assertResult(StatusCodes.OK) {
@@ -282,7 +305,8 @@ class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with
           s"""{
              |  "message": "Unrecognized workflow ID: ${CromwellApiServiceSpec.UnrecognizedWorkflowId.toString}",
              |  "status": "fail"
-             |}""".stripMargin) {
+             |}""".stripMargin
+        ) {
           responseAs[String].parseJson.prettyPrint
         }
         assertResult(StatusCodes.NotFound) {
@@ -293,8 +317,8 @@ class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with
   }
 
   it should "return 201 with warnings for a successful v1 workflow submission still using wdlSource" in {
-    val workflowSource = Multipart.FormData.BodyPart("wdlSource",
-      HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()))
+    val workflowSource =
+      Multipart.FormData.BodyPart("wdlSource", HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()))
     val formData = Multipart.FormData(workflowSource).toEntity()
     Post(s"/workflows/v1", formData) ~>
       akkaHttpService.workflowRoutes ~>
@@ -313,205 +337,230 @@ class CromwellApiServiceSpec extends AsyncFlatSpec with ScalatestRouteTest with
         warningHeader shouldNot be(empty)
         warningHeader.get.value should fullyMatch regex
           s"""299 cromwell/(\\d+-([0-9a-f]){7}(-SNAP)?|${VersionUtil.defaultMessage("cromwell-engine")}) """ +
-            "\"The 'wdlSource' parameter name has been deprecated in favor of 'workflowSource'. " +
-            "Support for 'wdlSource' will be removed from future versions of Cromwell. " +
-            "Please switch to using 'workflowSource' in future submissions.\""
+          "\"The 'wdlSource' parameter name has been deprecated in favor of 'workflowSource'. " +
+          "Support for 'wdlSource' will be removed from future versions of Cromwell. " +
+          "Please switch to using 'workflowSource' in future submissions.\""
       }
   }
 
-    it should "return 400 for an unrecognized form data request parameter " in {
-      val formData = Multipart.FormData(Map(
-        "incorrectParameter" -> HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()),
-        "incorrectParameter2" -> HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource())
-      )).toEntity
-
-      Post(s"/workflows/$version", formData) ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(
-            s"""{
-                |  "status": "fail",
-                |  "message": "Error(s): Unexpected body part name: incorrectParameter\\nUnexpected body part name: incorrectParameter2\\nworkflowSource or workflowUrl needs to be supplied"
-                |}""".stripMargin) {
-            responseAs[String]
-          }
-          assertResult(StatusCodes.BadRequest) {
-            status
-          }
-          assertResult(ContentTypes.`application/json`)(contentType)
+  it should "return 400 for an unrecognized form data request parameter " in {
+    val formData = Multipart
+      .FormData(
+        Map(
+          "incorrectParameter" -> HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()),
+          "incorrectParameter2" -> HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource())
+        )
+      )
+      .toEntity
+
+    Post(s"/workflows/$version", formData) ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(
+          s"""{
+             |  "status": "fail",
+             |  "message": "Error(s): Unexpected body part name: incorrectParameter\\nUnexpected body part name: incorrectParameter2\\nworkflowSource or workflowUrl needs to be supplied"
+             |}""".stripMargin
+        ) {
+          responseAs[String]
         }
-    }
+        assertResult(StatusCodes.BadRequest) {
+          status
+        }
+        assertResult(ContentTypes.`application/json`)(contentType)
+      }
+  }
 
-    it should "return 400 for a workflow submission with unsupported workflow option keys" in {
-      val options = """
-                      |{
-                      |  "defaultRuntimeOptions": {
-                      |  "cpu":1
-                      |  }
-                      |}
-                      |""".stripMargin
-
-      val workflowSource = Multipart.FormData.BodyPart("workflowSource", HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()))
-      val workflowInputs = Multipart.FormData.BodyPart("workflowOptions", HttpEntity(MediaTypes.`application/json`, options))
-      val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
-
-      Post(s"/workflows/$version", formData) ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(StatusCodes.BadRequest) {
-            status
-          }
-          assertResult {
-            """|{
-               |  "status": "fail",
-               |  "message": "Error(s): Invalid workflow options provided: Unsupported key/value pair in WorkflowOptions: defaultRuntimeOptions -> {\"cpu\":1}"
-               |}
-               |""".stripMargin.trim
-          } {
-            responseAs[String]
-          }
-          assertResult(ContentTypes.`application/json`)(contentType)
+  it should "return 400 for a workflow submission with unsupported workflow option keys" in {
+    val options = """
+                    |{
+                    |  "defaultRuntimeOptions": {
+                    |  "cpu":1
+                    |  }
+                    |}
+                    |""".stripMargin
+
+    val workflowSource =
+      Multipart.FormData.BodyPart("workflowSource",
+                                  HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource())
+      )
+    val workflowInputs =
+      Multipart.FormData.BodyPart("workflowOptions", HttpEntity(MediaTypes.`application/json`, options))
+    val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
+
+    Post(s"/workflows/$version", formData) ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(StatusCodes.BadRequest) {
+          status
         }
-    }
+        assertResult {
+          """|{
+             |  "status": "fail",
+             |  "message": "Error(s): Invalid workflow options provided: Unsupported key/value pair in WorkflowOptions: defaultRuntimeOptions -> {\"cpu\":1}"
+             |}
+             |""".stripMargin.trim
+        } {
+          responseAs[String]
+        }
+        assertResult(ContentTypes.`application/json`)(contentType)
+      }
+  }
+
+  it should "return 400 for a workflow submission with malformed workflow options json" in {
+    val options = s"""
+                     |{"read_from_cache": "true"
+                     |""".stripMargin
+
+    val workflowSource =
+      Multipart.FormData.BodyPart("workflowSource",
+                                  HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource())
+      )
+    val workflowInputs =
+      Multipart.FormData.BodyPart("workflowOptions", HttpEntity(MediaTypes.`application/json`, options))
+    val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
 
-    it should "return 400 for a workflow submission with malformed workflow options json" in {
-      val options = s"""
-                       |{"read_from_cache": "true"
-                       |""".stripMargin
-
-      val workflowSource = Multipart.FormData.BodyPart("workflowSource", HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()))
-      val workflowInputs = Multipart.FormData.BodyPart("workflowOptions", HttpEntity(MediaTypes.`application/json`, options))
-      val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
-
-      Post(s"/workflows/$version", formData) ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(StatusCodes.BadRequest) {
-            status
-          }
-          assertResult {
-            """|{
-               |  "status": "fail",
-               |  "message": "Error(s): Invalid workflow options provided: Unexpected end-of-input at input index 28 (line 3, position 1), expected '}':\n\n^\n"
-               |}
-               |""".stripMargin.trim
-          } {
-            responseAs[String]
-          }
-          assertResult(ContentTypes.`application/json`)(contentType)
+    Post(s"/workflows/$version", formData) ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(StatusCodes.BadRequest) {
+          status
         }
-    }
+        assertResult {
+          """|{
+             |  "status": "fail",
+             |  "message": "Error(s): Invalid workflow options provided: Unexpected end-of-input at input index 28 (line 3, position 1), expected '}':\n\n^\n"
+             |}
+             |""".stripMargin.trim
+        } {
+          responseAs[String]
+        }
+        assertResult(ContentTypes.`application/json`)(contentType)
+      }
+  }
 
-    it should "return 400 for a workflow submission with invalid workflow custom labels" in {
-      val labels = s"""
-                      |{"key with more than 255 characters-at vero eos et accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpas":"value with more than 255 characters-at vero eos et accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpa"}
-                      |""".stripMargin
+  it should "return 400 for a workflow submission with invalid workflow custom labels" in {
+    val labels =
+      s"""
+         |{"key with more than 255 characters-at vero eos et accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpas":"value with more than 255 characters-at vero eos et accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpa"}
+         |""".stripMargin
 
-      val workflowSource = Multipart.FormData.BodyPart("workflowSource", HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()))
-      val customLabels =  Multipart.FormData.BodyPart("labels", HttpEntity(MediaTypes.`application/json`, labels))
-      val onHold =  Multipart.FormData.BodyPart("workflowOnHold", HttpEntity("true"))
-      val formData = Multipart.FormData(workflowSource, customLabels, onHold).toEntity()
+    val workflowSource =
+      Multipart.FormData.BodyPart("workflowSource",
+                                  HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource())
+      )
+    val customLabels = Multipart.FormData.BodyPart("labels", HttpEntity(MediaTypes.`application/json`, labels))
+    val onHold = Multipart.FormData.BodyPart("workflowOnHold", HttpEntity("true"))
+    val formData = Multipart.FormData(workflowSource, customLabels, onHold).toEntity()
 
-      Post(s"/workflows/$version", formData) ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(StatusCodes.BadRequest) {
-            status
-          }
-          assertResult(ContentTypes.`application/json`)(contentType)
+    Post(s"/workflows/$version", formData) ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(StatusCodes.BadRequest) {
+          status
         }
-    }
+        assertResult(ContentTypes.`application/json`)(contentType)
+      }
+  }
+
+  behavior of "REST API batch submission endpoint"
+  it should "return 200 for a successful workflow submission " in {
+    val inputs = HelloWorld.rawInputs.toJson
+    val workflowSource =
+      Multipart.FormData.BodyPart("workflowSource",
+                                  HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource())
+      )
+    val workflowInputs =
+      Multipart.FormData.BodyPart("workflowInputs", HttpEntity(MediaTypes.`application/json`, s"[$inputs, $inputs]"))
+    val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
 
-    behavior of "REST API batch submission endpoint"
-    it should "return 200 for a successful workflow submission " in {
-      val inputs = HelloWorld.rawInputs.toJson
-      val workflowSource = Multipart.FormData.BodyPart("workflowSource", HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()))
-      val workflowInputs = Multipart.FormData.BodyPart("workflowInputs", HttpEntity(MediaTypes.`application/json`, s"[$inputs, $inputs]"))
-      val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
-
-      Post(s"/workflows/$version/batch", formData) ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(
-            s"""[{
-                |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
-                |  "status": "Submitted"
-                |}, {
-                |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
-                |  "status": "Submitted"
-                |}]""".stripMargin) {
-            responseAs[String].parseJson.prettyPrint
-          }
-          assertResult(StatusCodes.Created) {
-            status
-          }
-          assertResult(ContentTypes.`application/json`)(contentType)
+    Post(s"/workflows/$version/batch", formData) ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(s"""[{
+                        |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
+                        |  "status": "Submitted"
+                        |}, {
+                        |  "id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}",
+                        |  "status": "Submitted"
+                        |}]""".stripMargin) {
+          responseAs[String].parseJson.prettyPrint
         }
-    }
+        assertResult(StatusCodes.Created) {
+          status
+        }
+        assertResult(ContentTypes.`application/json`)(contentType)
+      }
+  }
+
+  it should "return 400 for an submission with no inputs" in {
+    val formData = Multipart
+      .FormData(
+        Multipart.FormData.BodyPart("workflowSource",
+                                    HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource())
+        )
+      )
+      .toEntity()
 
-    it should "return 400 for an submission with no inputs" in {
-      val formData = Multipart.FormData(Multipart.FormData.BodyPart("workflowSource", HttpEntity(MediaTypes.`application/json`, HelloWorld.workflowSource()))).toEntity()
-
-      Post(s"/workflows/$version/batch", formData) ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(
-            s"""{
-                |  "status": "fail",
-                |  "message": "Error(s): No inputs were provided"
-                |}""".stripMargin) {
-            responseAs[String]
-          }
-          assertResult(StatusCodes.BadRequest) {
-            status
-          }
-          assertResult(ContentTypes.`application/json`)(contentType)
+    Post(s"/workflows/$version/batch", formData) ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(s"""{
+                        |  "status": "fail",
+                        |  "message": "Error(s): No inputs were provided"
+                        |}""".stripMargin) {
+          responseAs[String]
         }
-    }
+        assertResult(StatusCodes.BadRequest) {
+          status
+        }
+        assertResult(ContentTypes.`application/json`)(contentType)
+      }
+  }
 
-    behavior of "REST API /timing endpoint"
-    it should "return 200 with an HTML document for the timings route" in {
-      Get(s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/timing") ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(StatusCodes.OK) { status }
-          assertResult(`text/html(UTF-8)`) { contentType }
-          assertResult("<html>") {
-            responseAs[String].substring(0, 6)
-          }
+  behavior of "REST API /timing endpoint"
+  it should "return 200 with an HTML document for the timings route" in {
+    Get(s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/timing") ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(StatusCodes.OK)(status)
+        assertResult(`text/html(UTF-8)`)(contentType)
+        assertResult("<html>") {
+          responseAs[String].substring(0, 6)
         }
-    }
+      }
+  }
 
-    it should "return 404 when unrecognized workflow id is submitted" in {
-      Get(s"/workflows/$version/${CromwellApiServiceSpec.UnrecognizedWorkflowId}/timing") ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(StatusCodes.NotFound) { status }
-          assertResult(
-            s"""{
-               |  "message": "Unrecognized workflow ID: ${CromwellApiServiceSpec.UnrecognizedWorkflowId.toString}",
-               |  "status": "fail"
-               |}""".stripMargin) {
-            responseAs[String].parseJson.prettyPrint
-          }
+  it should "return 404 when unrecognized workflow id is submitted" in {
+    Get(s"/workflows/$version/${CromwellApiServiceSpec.UnrecognizedWorkflowId}/timing") ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(StatusCodes.NotFound)(status)
+        assertResult(
+          s"""{
+             |  "message": "Unrecognized workflow ID: ${CromwellApiServiceSpec.UnrecognizedWorkflowId.toString}",
+             |  "status": "fail"
+             |}""".stripMargin
+        ) {
+          responseAs[String].parseJson.prettyPrint
         }
-    }
+      }
+  }
 
-    it should "return 400 when invalid workflow id is submitted" in {
-      Get(s"/workflows/$version/foo/timing") ~>
-        akkaHttpService.workflowRoutes ~>
-        check {
-          assertResult(StatusCodes.BadRequest) { status }
-          assertResult(
-            s"""{
-               |  "message": "Invalid workflow ID: 'foo'.",
-               |  "status": "fail"
-               |}""".stripMargin) {
-            responseAs[String].parseJson.prettyPrint
-          }
-          assertResult(ContentTypes.`application/json`)(contentType)
+  it should "return 400 when invalid workflow id is submitted" in {
+    Get(s"/workflows/$version/foo/timing") ~>
+      akkaHttpService.workflowRoutes ~>
+      check {
+        assertResult(StatusCodes.BadRequest)(status)
+        assertResult(s"""{
+                        |  "message": "Invalid workflow ID: 'foo'.",
+                        |  "status": "fail"
+                        |}""".stripMargin) {
+          responseAs[String].parseJson.prettyPrint
         }
-    }
+        assertResult(ContentTypes.`application/json`)(contentType)
+      }
+  }
 }
 
 object CromwellApiServiceSpec {
@@ -561,26 +610,25 @@ object CromwellApiServiceSpec {
 
   object MockServiceRegistryActor {
 
-    private def fullMetadataResponse(workflowId: WorkflowId) = {
+    private def fullMetadataResponse(workflowId: WorkflowId) =
       List(
         MetadataEvent(MetadataKey(workflowId, None, "testKey1a"), MetadataValue("myValue1a", MetadataString)),
         MetadataEvent(MetadataKey(workflowId, None, "testKey1b"), MetadataValue("myValue1b", MetadataString)),
-        MetadataEvent(MetadataKey(workflowId, None, "testKey2a"), MetadataValue("myValue2a", MetadataString)),
+        MetadataEvent(MetadataKey(workflowId, None, "testKey2a"), MetadataValue("myValue2a", MetadataString))
       )
-    }
 
-    private def wesFullMetadataResponse(workflowId: WorkflowId) = {
+    private def wesFullMetadataResponse(workflowId: WorkflowId) =
       List(
         MetadataEvent(MetadataKey(workflowId, None, "status"), MetadataValue("Running", MetadataString)),
-        MetadataEvent(MetadataKey(workflowId, None, "submittedFiles:workflow"), MetadataValue("myValue2a", MetadataString)),
-
+        MetadataEvent(MetadataKey(workflowId, None, "submittedFiles:workflow"),
+                      MetadataValue("myValue2a", MetadataString)
+        )
       )
-    }
-
 
     def responseMetadataValues(workflowId: WorkflowId, withKeys: List[String], withoutKeys: List[String]): JsObject = {
       def keyFilter(keys: List[String])(m: MetadataEvent) = keys.exists(k => m.key.key.startsWith(k))
-      val metadataEvents = if (workflowId == wesWorkflowId) wesFullMetadataResponse(workflowId) else fullMetadataResponse(workflowId)
+      val metadataEvents =
+        if (workflowId == wesWorkflowId) wesFullMetadataResponse(workflowId) else fullMetadataResponse(workflowId)
       val events = metadataEvents
         .filter(m => withKeys.isEmpty || keyFilter(withKeys)(m))
         .filter(m => withoutKeys.isEmpty || !keyFilter(withoutKeys)(m))
@@ -592,9 +640,16 @@ object CromwellApiServiceSpec {
       MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
 
     def logsEvents(id: WorkflowId) = {
-      val stdout = MetadataEvent(MetadataKey(id, Some(MetadataJobKey("mycall", None, 1)), CallMetadataKeys.Stdout), MetadataValue("stdout.txt", MetadataString))
-      val stderr = MetadataEvent(MetadataKey(id, Some(MetadataJobKey("mycall", None, 1)), CallMetadataKeys.Stderr), MetadataValue("stderr.txt", MetadataString))
-      val backend = MetadataEvent(MetadataKey(id, Some(MetadataJobKey("mycall", None, 1)), s"${CallMetadataKeys.BackendLogsPrefix}:log"), MetadataValue("backend.log", MetadataString))
+      val stdout = MetadataEvent(MetadataKey(id, Some(MetadataJobKey("mycall", None, 1)), CallMetadataKeys.Stdout),
+                                 MetadataValue("stdout.txt", MetadataString)
+      )
+      val stderr = MetadataEvent(MetadataKey(id, Some(MetadataJobKey("mycall", None, 1)), CallMetadataKeys.Stderr),
+                                 MetadataValue("stderr.txt", MetadataString)
+      )
+      val backend = MetadataEvent(
+        MetadataKey(id, Some(MetadataJobKey("mycall", None, 1)), s"${CallMetadataKeys.BackendLogsPrefix}:log"),
+        MetadataValue("backend.log", MetadataString)
+      )
       Vector(stdout, stderr, backend)
     }
   }
@@ -604,13 +659,30 @@ object CromwellApiServiceSpec {
 
     override def receive = {
       case QueryForWorkflowsMatchingParameters(parameters) =>
-        val labels: Option[Map[String, String]] = {
-          parameters.contains(("additionalQueryResultFields", "labels")).option(
-            Map("key1" -> "label1", "key2" -> "label2"))
-        }
-
-        val response = WorkflowQuerySuccess(WorkflowQueryResponse(List(WorkflowQueryResult(ExistingWorkflowId.toString,
-          None, Some(WorkflowSucceeded.toString), None, None, None, labels, Option("pid"), Option("rid"), Unarchived)), 1), None)
+        val labels: Option[Map[String, String]] =
+          parameters
+            .contains(("additionalQueryResultFields", "labels"))
+            .option(Map("key1" -> "label1", "key2" -> "label2"))
+
+        val response = WorkflowQuerySuccess(
+          WorkflowQueryResponse(
+            List(
+              WorkflowQueryResult(ExistingWorkflowId.toString,
+                                  None,
+                                  Some(WorkflowSucceeded.toString),
+                                  None,
+                                  None,
+                                  None,
+                                  labels,
+                                  Option("pid"),
+                                  Option("rid"),
+                                  Unarchived
+              )
+            ),
+            1
+          ),
+          None
+        )
         sender() ! response
       case ValidateWorkflowIdInMetadata(id) =>
         if (RecognizedWorkflowIds.contains(id)) sender() ! MetadataService.RecognizedWorkflowId
@@ -620,15 +692,16 @@ object CromwellApiServiceSpec {
         else sender() ! MetadataService.UnrecognizedWorkflowId
       case FetchWorkflowMetadataArchiveStatusAndEndTime(id) =>
         id match {
-          case ArchivedAndDeletedWorkflowId => sender() ! WorkflowMetadataArchivedStatusAndEndTime(ArchivedAndDeleted, Option(OffsetDateTime.now))
-          case ArchivedWorkflowId => sender() ! WorkflowMetadataArchivedStatusAndEndTime(Archived, Option(OffsetDateTime.now))
+          case ArchivedAndDeletedWorkflowId =>
+            sender() ! WorkflowMetadataArchivedStatusAndEndTime(ArchivedAndDeleted, Option(OffsetDateTime.now))
+          case ArchivedWorkflowId =>
+            sender() ! WorkflowMetadataArchivedStatusAndEndTime(Archived, Option(OffsetDateTime.now))
           case _ => sender() ! WorkflowMetadataArchivedStatusAndEndTime(Unarchived, Option(OffsetDateTime.now))
         }
       case GetCurrentStatus =>
-        sender() ! StatusCheckResponse(
-          ok = true,
-          systems = Map(
-            "Engine Database" -> SubsystemStatus(ok = true, messages = None)))
+        sender() ! StatusCheckResponse(ok = true,
+                                       systems = Map("Engine Database" -> SubsystemStatus(ok = true, messages = None))
+        )
       case request @ GetStatus(id) =>
         val status = id match {
           case OnHoldWorkflowId => WorkflowOnHold
@@ -641,12 +714,22 @@ object CromwellApiServiceSpec {
         }
         sender() ! SuccessfulMetadataJsonResponse(request, MetadataBuilderActor.processStatusResponse(id, status))
       case request @ GetLabels(id) =>
-        sender() ! SuccessfulMetadataJsonResponse(request, MetadataBuilderActor.processLabelsResponse(id, Map("key1" -> "label1", "key2" -> "label2")))
+        sender() ! SuccessfulMetadataJsonResponse(
+          request,
+          MetadataBuilderActor.processLabelsResponse(id, Map("key1" -> "label1", "key2" -> "label2"))
+        )
       case request @ WorkflowOutputs(id) =>
-        val event = Vector(MetadataEvent(MetadataKey(id, None, "outputs:test.hello.salutation"), MetadataValue("Hello foo!", MetadataString)))
+        val event = Vector(
+          MetadataEvent(MetadataKey(id, None, "outputs:test.hello.salutation"),
+                        MetadataValue("Hello foo!", MetadataString)
+          )
+        )
         sender() ! SuccessfulMetadataJsonResponse(request, MetadataBuilderActor.processOutputsResponse(id, event))
       case request @ GetLogs(id) =>
-        sender() ! SuccessfulMetadataJsonResponse(request, MetadataBuilderActor.workflowMetadataResponse(id, logsEvents(id), includeCallsIfEmpty = false, Map.empty))
+        sender() ! SuccessfulMetadataJsonResponse(
+          request,
+          MetadataBuilderActor.workflowMetadataResponse(id, logsEvents(id), includeCallsIfEmpty = false, Map.empty)
+        )
       case request @ FetchFailedJobsMetadataWithWorkflowId(id) =>
         sender() ! SuccessfulMetadataJsonResponse(request, responseMetadataValues(id, List.empty, List.empty))
       case request @ GetMetadataAction(MetadataQuery(id, _, _, withKeys, withoutKeys, _), _) =>
@@ -657,8 +740,12 @@ object CromwellApiServiceSpec {
         events.head.key.workflowId match {
           case CromwellApiServiceSpec.ExistingWorkflowId => sender() ! MetadataWriteSuccess(events)
           case CromwellApiServiceSpec.SummarizedWorkflowId => sender() ! MetadataWriteSuccess(events)
-          case CromwellApiServiceSpec.AbortedWorkflowId => sender() ! MetadataWriteFailure(new Exception("mock exception of db failure"), events)
-          case WorkflowId(_) => throw new Exception("Something untoward happened, this situation is not believed to be possible at this time")
+          case CromwellApiServiceSpec.AbortedWorkflowId =>
+            sender() ! MetadataWriteFailure(new Exception("mock exception of db failure"), events)
+          case WorkflowId(_) =>
+            throw new Exception(
+              "Something untoward happened, this situation is not believed to be possible at this time"
+            )
           case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
         }
       case DescribeRequest(sourceFiles) =>
@@ -677,7 +764,9 @@ object CromwellApiServiceSpec {
               s"[reading back DescribeRequest contents] version: ${sourceFiles.workflowTypeVersion}"
             )
 
-            sender() ! DescribeSuccess(description = WorkflowDescription(valid = true, errors = readBack, validWorkflow = true))
+            sender() ! DescribeSuccess(description =
+              WorkflowDescription(valid = true, errors = readBack, validWorkflow = true)
+            )
         }
       case _: InstrumentationServiceMessage => // Do nothing.
       case m => logger.error("Unexpected message received by MockServiceRegistryActor: {}", m)
@@ -698,7 +787,11 @@ object CromwellApiServiceSpec {
         val message = id match {
           case AbortingWorkflowId => WorkflowAbortRequestedResponse(id)
           case OnHoldWorkflowId | SubmittedWorkflowId => WorkflowAbortedResponse(id)
-          case UnrecognizedWorkflowId => WorkflowAbortFailureResponse(id, new WorkflowNotFoundException(s"Couldn't abort $id because no workflow with that ID is in progress"))
+          case UnrecognizedWorkflowId =>
+            WorkflowAbortFailureResponse(
+              id,
+              new WorkflowNotFoundException(s"Couldn't abort $id because no workflow with that ID is in progress")
+            )
           case WorkflowId(_) => throw new Exception("Something untoward happened")
           case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
         }
diff --git a/engine/src/test/scala/cromwell/webservice/routes/MetadataRouteSupportSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/MetadataRouteSupportSpec.scala
index 73cc257e828..64d5ae24376 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/MetadataRouteSupportSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/MetadataRouteSupportSpec.scala
@@ -2,7 +2,7 @@ package cromwell.webservice.routes
 
 import akka.actor.{ActorSystem, Props}
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
-import akka.http.scaladsl.model.headers.{HttpEncodings, `Accept-Encoding`}
+import akka.http.scaladsl.model.headers.{`Accept-Encoding`, HttpEncodings}
 import akka.http.scaladsl.model.{ContentTypes, HttpEntity, StatusCodes}
 import akka.http.scaladsl.server.Route
 import akka.http.scaladsl.testkit.{RouteTestTimeout, ScalatestRouteTest}
@@ -83,7 +83,7 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       akkaHttpService.metadataRoutes ~>
       check {
         status should be(StatusCodes.OK)
-        responseAs[JsObject].fields.keys should contain allOf(WorkflowMetadataKeys.Id, WorkflowMetadataKeys.Outputs)
+        responseAs[JsObject].fields.keys should contain allOf (WorkflowMetadataKeys.Id, WorkflowMetadataKeys.Outputs)
         contentType should be(ContentTypes.`application/json`)
       }
   }
@@ -116,19 +116,28 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       akkaHttpService.metadataRoutes ~>
       check {
         status should be(StatusCodes.OK)
-        responseAs[JsObject].fields.keys should contain allOf(WorkflowMetadataKeys.Id, WorkflowMetadataKeys.Outputs)
+        responseAs[JsObject].fields.keys should contain allOf (WorkflowMetadataKeys.Id, WorkflowMetadataKeys.Outputs)
         contentType should be(ContentTypes.`application/json`)
       }
   }
 
-  def validateArchivedMetadataResponseMessage(responseJson: JsObject, includeAvailabilityMessage: Boolean, includeLabelsMessage: Boolean) = {
+  def validateArchivedMetadataResponseMessage(responseJson: JsObject,
+                                              includeAvailabilityMessage: Boolean,
+                                              includeLabelsMessage: Boolean
+  ) = {
     val responseMessage = responseJson.fields("message").asInstanceOf[JsString].value
     val expectedSuffix =
-      (if (includeAvailabilityMessage) " It is available in the archive bucket, or via a support request in the case of a managed instance." else "") +
-        (if (includeLabelsMessage) " As a result, new labels can't be added or existing labels can't be updated for this workflow." else "")
-
-    responseMessage should startWith("Cromwell has archived this workflow's metadata " +
-      "according to the lifecycle policy. The workflow completed at ")
+      (if (includeAvailabilityMessage)
+         " It is available in the archive bucket, or via a support request in the case of a managed instance."
+       else "") +
+        (if (includeLabelsMessage)
+           " As a result, new labels can't be added or existing labels can't be updated for this workflow."
+         else "")
+
+    responseMessage should startWith(
+      "Cromwell has archived this workflow's metadata " +
+        "according to the lifecycle policy. The workflow completed at "
+    )
     // The missing middle of the message looks like "The workflow completed at x timestamp, which was y milliseconds ago."
     responseMessage should endWith(s"ago.${expectedSuffix}")
   }
@@ -139,10 +148,13 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status should be(StatusCodes.OK)
 
-        val responseJson =  responseAs[JsObject]
-        responseJson.fields.keys should contain allOf(WorkflowMetadataKeys.Id, WorkflowMetadataKeys.MetadataArchiveStatus, WorkflowMetadataKeys.Message)
+        val responseJson = responseAs[JsObject]
+        responseJson.fields.keys should contain allOf (WorkflowMetadataKeys.Id, WorkflowMetadataKeys.MetadataArchiveStatus, WorkflowMetadataKeys.Message)
         responseJson.fields("metadataArchiveStatus").asInstanceOf[JsString].value shouldBe "ArchivedAndDeleted"
-        validateArchivedMetadataResponseMessage(responseJson, includeAvailabilityMessage = true, includeLabelsMessage = false)
+        validateArchivedMetadataResponseMessage(responseJson,
+                                                includeAvailabilityMessage = true,
+                                                includeLabelsMessage = false
+        )
         contentType should be(ContentTypes.`application/json`)
       }
   }
@@ -154,11 +166,12 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status should be(StatusCodes.OK)
 
-        val call = responseAs[JsObject].fields("calls").convertTo[JsObject].fields("mycall").convertTo[Seq[JsObject]].head
+        val call =
+          responseAs[JsObject].fields("calls").convertTo[JsObject].fields("mycall").convertTo[Seq[JsObject]].head
         call.fields("stdout") should be(JsString("stdout.txt"))
         call.fields("stderr") should be(JsString("stderr.txt"))
         call.fields("stdout") should be(JsString("stdout.txt"))
-        call.fields("backendLogs").convertTo[JsObject].fields("log") should be (JsString("backend.log"))
+        call.fields("backendLogs").convertTo[JsObject].fields("log") should be(JsString("backend.log"))
       }
   }
 
@@ -178,11 +191,12 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status should be(StatusCodes.OK)
 
-        val call = responseAs[JsObject].fields("calls").convertTo[JsObject].fields("mycall").convertTo[Seq[JsObject]].head
+        val call =
+          responseAs[JsObject].fields("calls").convertTo[JsObject].fields("mycall").convertTo[Seq[JsObject]].head
         call.fields("stdout") should be(JsString("stdout.txt"))
         call.fields("stderr") should be(JsString("stderr.txt"))
         call.fields("stdout") should be(JsString("stdout.txt"))
-        call.fields("backendLogs").convertTo[JsObject].fields("log") should be (JsString("backend.log"))
+        call.fields("backendLogs").convertTo[JsObject].fields("log") should be(JsString("backend.log"))
       }
   }
 
@@ -192,11 +206,14 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status should be(StatusCodes.OK)
 
-        val responseJson =  responseAs[JsObject]
-        responseJson.fields.keys should contain allOf(WorkflowMetadataKeys.Id, WorkflowMetadataKeys.MetadataArchiveStatus, WorkflowMetadataKeys.Message)
+        val responseJson = responseAs[JsObject]
+        responseJson.fields.keys should contain allOf (WorkflowMetadataKeys.Id, WorkflowMetadataKeys.MetadataArchiveStatus, WorkflowMetadataKeys.Message)
         responseJson.fields("metadataArchiveStatus").asInstanceOf[JsString].value shouldBe "ArchivedAndDeleted"
-        validateArchivedMetadataResponseMessage(responseJson, includeAvailabilityMessage = true, includeLabelsMessage = false)
-       }
+        validateArchivedMetadataResponseMessage(responseJson,
+                                                includeAvailabilityMessage = true,
+                                                includeLabelsMessage = false
+        )
+      }
   }
 
   behavior of "REST API /metadata endpoint"
@@ -206,7 +223,7 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status should be(StatusCodes.OK)
         val result = responseAs[JsObject]
-        result.fields.keys should contain allOf("testKey1a", "testKey1b", "testKey2a")
+        result.fields.keys should contain allOf ("testKey1a", "testKey1b", "testKey2a")
         result.fields.keys shouldNot contain("testKey3")
         result.fields("testKey1a") should be(JsString("myValue1a"))
         result.fields("testKey1b") should be(JsString("myValue1b"))
@@ -220,7 +237,7 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status should be(StatusCodes.OK)
         val result = responseAs[JsObject]
-        result.fields.keys should contain allOf("testKey1a", "testKey1b", "testKey2a")
+        result.fields.keys should contain allOf ("testKey1a", "testKey1b", "testKey2a")
         result.fields.keys shouldNot contain("testKey3")
         result.fields("testKey1a") should be(JsString("myValue1a"))
         result.fields("testKey1b") should be(JsString("myValue1b"))
@@ -229,7 +246,8 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
   }
 
   it should "return with gzip encoding when requested" in {
-    Get(s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/metadata").addHeader(`Accept-Encoding`(HttpEncodings.gzip)) ~>
+    Get(s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/metadata")
+      .addHeader(`Accept-Encoding`(HttpEncodings.gzip)) ~>
       akkaHttpService.metadataRoutes ~>
       check {
         response.headers.find(_.name == "Content-Encoding").get.value should be("gzip")
@@ -245,13 +263,15 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
   }
 
   it should "return with included metadata from the metadata route" in {
-    Get(s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/metadata?includeKey=testKey1&includeKey=testKey2a") ~>
+    Get(
+      s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/metadata?includeKey=testKey1&includeKey=testKey2a"
+    ) ~>
       akkaHttpService.metadataRoutes ~>
       check {
         status should be(StatusCodes.OK)
         val result = responseAs[JsObject]
-        result.fields.keys should contain allOf("testKey1a", "testKey1b", "testKey2a")
-        result.fields.keys should contain noneOf("testKey2b", "testKey3")
+        result.fields.keys should contain allOf ("testKey1a", "testKey1b", "testKey2a")
+        result.fields.keys should contain noneOf ("testKey2b", "testKey3")
         result.fields("testKey1a") should be(JsString("myValue1a"))
         result.fields("testKey1b") should be(JsString("myValue1b"))
         result.fields("testKey2a") should be(JsString("myValue2a"))
@@ -259,28 +279,32 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
   }
 
   it should "return with excluded metadata from the metadata route" in {
-    Get(s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/metadata?excludeKey=testKey2&excludeKey=testKey3") ~>
+    Get(
+      s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/metadata?excludeKey=testKey2&excludeKey=testKey3"
+    ) ~>
       akkaHttpService.metadataRoutes ~>
       check {
         status should be(StatusCodes.OK)
         val result = responseAs[JsObject]
-        result.fields.keys should contain allOf("testKey1a", "testKey1b")
-        result.fields.keys should contain noneOf("testKey2a", "testKey3")
+        result.fields.keys should contain allOf ("testKey1a", "testKey1b")
+        result.fields.keys should contain noneOf ("testKey2a", "testKey3")
         result.fields("testKey1a") should be(JsString("myValue1a"))
         result.fields("testKey1b") should be(JsString("myValue1b"))
       }
   }
 
   it should "correctly include and exclude metadata keys in workflow details requests" in {
-    Get(s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/metadata?includeKey=testKey1&excludeKey=testKey1a") ~>
+    Get(
+      s"/workflows/$version/${CromwellApiServiceSpec.ExistingWorkflowId}/metadata?includeKey=testKey1&excludeKey=testKey1a"
+    ) ~>
       akkaHttpService.metadataRoutes ~>
       check {
         val r = responseAs[String]
         withClue(s"From response $r") {
           status should be(StatusCodes.OK)
           val result = responseAs[JsObject]
-          result.fields.keys should contain allElementsOf(List("testKey1b"))
-          result.fields.keys should contain noneOf("testKey1a", "testKey2")
+          result.fields.keys should contain allElementsOf (List("testKey1b"))
+          result.fields.keys should contain noneOf ("testKey1a", "testKey2")
           result.fields("testKey1b") should be(JsString("myValue1b"))
         }
       }
@@ -292,7 +316,7 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status should be(StatusCodes.OK)
         val result = responseAs[JsObject]
-        result.fields.keys should contain allOf("testKey1a", "testKey1b", "testKey2a")
+        result.fields.keys should contain allOf ("testKey1a", "testKey1b", "testKey2a")
         result.fields.keys shouldNot contain("testKey3")
         result.fields("testKey1a") should be(JsString("myValue1a"))
         result.fields("testKey1b") should be(JsString("myValue1b"))
@@ -306,10 +330,13 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status should be(StatusCodes.OK)
 
-        val responseJson =  responseAs[JsObject]
-        responseJson.fields.keys should contain allOf(WorkflowMetadataKeys.Id, WorkflowMetadataKeys.MetadataArchiveStatus, WorkflowMetadataKeys.Message)
+        val responseJson = responseAs[JsObject]
+        responseJson.fields.keys should contain allOf (WorkflowMetadataKeys.Id, WorkflowMetadataKeys.MetadataArchiveStatus, WorkflowMetadataKeys.Message)
         responseJson.fields("metadataArchiveStatus").asInstanceOf[JsString].value shouldBe "ArchivedAndDeleted"
-        validateArchivedMetadataResponseMessage(responseJson, includeAvailabilityMessage = true, includeLabelsMessage = false)
+        validateArchivedMetadataResponseMessage(responseJson,
+                                                includeAvailabilityMessage = true,
+                                                includeLabelsMessage = false
+        )
       }
   }
 
@@ -319,7 +346,7 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status should be(StatusCodes.OK)
         val result = responseAs[JsObject]
-        result.fields.keys should contain allOf("testKey1a", "testKey1b", "testKey2a")
+        result.fields.keys should contain allOf ("testKey1a", "testKey1b", "testKey2a")
         result.fields.keys shouldNot contain("testKey3")
         result.fields("testKey1a") should be(JsString("myValue1a"))
         result.fields("testKey1b") should be(JsString("myValue1b"))
@@ -341,7 +368,9 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
   }
 
   it should "return labels if specified in additionalQueryResultFields param" in {
-    Get(s"/workflows/$version/query?additionalQueryResultFields=labels&id=${CromwellApiServiceSpec.ExistingWorkflowId}") ~>
+    Get(
+      s"/workflows/$version/query?additionalQueryResultFields=labels&id=${CromwellApiServiceSpec.ExistingWorkflowId}"
+    ) ~>
       akkaHttpService.metadataRoutes ~>
       check {
         status should be(StatusCodes.OK)
@@ -355,7 +384,9 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
   }
 
   it should "return parentWorkflowId if specified in additionalQueryResultFields param" in {
-    Get(s"/workflows/$version/query?additionalQueryResultFields=parentWorkflowId&id=${CromwellApiServiceSpec.ExistingWorkflowId}") ~>
+    Get(
+      s"/workflows/$version/query?additionalQueryResultFields=parentWorkflowId&id=${CromwellApiServiceSpec.ExistingWorkflowId}"
+    ) ~>
       akkaHttpService.metadataRoutes ~>
       check {
         status should be(StatusCodes.OK)
@@ -382,7 +413,9 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
   }
 
   it should "return labels if specified in additionalQueryResultFields param" in {
-    Post(s"/workflows/$version/query", HttpEntity(ContentTypes.`application/json`, """[{"additionalQueryResultFields":"labels"}]""")) ~>
+    Post(s"/workflows/$version/query",
+         HttpEntity(ContentTypes.`application/json`, """[{"additionalQueryResultFields":"labels"}]""")
+    ) ~>
       akkaHttpService.metadataRoutes ~>
       check {
         assertResult(StatusCodes.OK) {
@@ -396,7 +429,9 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
   }
 
   it should "return parentWorkflowId if specified in additionalQueryResultFields param" in {
-    Post(s"/workflows/$version/query", HttpEntity(ContentTypes.`application/json`, """[{"additionalQueryResultFields":"parentWorkflowId"}]""")) ~>
+    Post(s"/workflows/$version/query",
+         HttpEntity(ContentTypes.`application/json`, """[{"additionalQueryResultFields":"parentWorkflowId"}]""")
+    ) ~>
       akkaHttpService.metadataRoutes ~>
       check {
         assertResult(StatusCodes.OK) {
@@ -480,9 +515,12 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status shouldBe StatusCodes.BadRequest
         val actualResult = responseAs[JsObject]
-        actualResult.fields.keys should contain allOf(WorkflowMetadataKeys.Id, WorkflowMetadataKeys.MetadataArchiveStatus, WorkflowMetadataKeys.Message)
+        actualResult.fields.keys should contain allOf (WorkflowMetadataKeys.Id, WorkflowMetadataKeys.MetadataArchiveStatus, WorkflowMetadataKeys.Message)
         actualResult.fields("metadataArchiveStatus").asInstanceOf[JsString].value shouldBe "Archived"
-        validateArchivedMetadataResponseMessage(actualResult, includeAvailabilityMessage = false, includeLabelsMessage = true)
+        validateArchivedMetadataResponseMessage(actualResult,
+                                                includeAvailabilityMessage = false,
+                                                includeLabelsMessage = true
+        )
       }
   }
 
@@ -502,9 +540,12 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       check {
         status shouldBe StatusCodes.BadRequest
         val actualResult = responseAs[JsObject]
-        actualResult.fields.keys should contain allOf(WorkflowMetadataKeys.Id, WorkflowMetadataKeys.MetadataArchiveStatus, WorkflowMetadataKeys.Message)
+        actualResult.fields.keys should contain allOf (WorkflowMetadataKeys.Id, WorkflowMetadataKeys.MetadataArchiveStatus, WorkflowMetadataKeys.Message)
         actualResult.fields("metadataArchiveStatus").asInstanceOf[JsString].value shouldBe "ArchivedAndDeleted"
-        validateArchivedMetadataResponseMessage(actualResult, includeAvailabilityMessage = true, includeLabelsMessage = true)
+        validateArchivedMetadataResponseMessage(actualResult,
+                                                includeAvailabilityMessage = true,
+                                                includeLabelsMessage = true
+        )
       }
   }
 
@@ -518,7 +559,9 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
       """.stripMargin
 
     val unsummarizedId = CromwellApiServiceSpec.ExistingWorkflowId
-    Patch(s"/workflows/$version/$unsummarizedId/labels", HttpEntity(ContentTypes.`application/json`, validLabelsJson)) ~>
+    Patch(s"/workflows/$version/$unsummarizedId/labels",
+          HttpEntity(ContentTypes.`application/json`, validLabelsJson)
+    ) ~>
       akkaHttpService.metadataRoutes ~>
       check {
         status shouldBe StatusCodes.NotFound
@@ -528,7 +571,8 @@ class MetadataRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest wit
 }
 
 object MetadataRouteSupportSpec {
-  class MockMetadataRouteSupport()(implicit val system: ActorSystem, routeTestTimeout: RouteTestTimeout) extends MetadataRouteSupport {
+  class MockMetadataRouteSupport()(implicit val system: ActorSystem, routeTestTimeout: RouteTestTimeout)
+      extends MetadataRouteSupport {
     override def actorRefFactory = system
     override val ec = system.dispatcher
     override val timeout = routeTestTimeout.duration
diff --git a/engine/src/test/scala/cromwell/webservice/routes/WomtoolRouteSupportSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/WomtoolRouteSupportSpec.scala
index 24f8ce18ee7..06c48a42b77 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/WomtoolRouteSupportSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/WomtoolRouteSupportSpec.scala
@@ -16,7 +16,6 @@ import org.scalatest.matchers.should.Matchers
 
 import scala.concurrent.duration._
 
-
 // N.B. this suite only tests the routing and creation of the WorkflowSourceFilesCollection, it uses the MockServiceRegistryActor
 // to return fake results instead of going to a real WomtoolServiceActor
 class WomtoolRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Matchers {
@@ -29,12 +28,24 @@ class WomtoolRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with
   behavior of "/describe endpoint"
 
   object BodyParts {
-    val workflowSource  = Multipart.FormData.BodyPart("workflowSource", HttpEntity(ContentTypes.`text/plain(UTF-8)`, "This is not a WDL, but that's OK for this test of request routing."))
-    val workflowUrl     = Multipart.FormData.BodyPart("workflowUrl", HttpEntity(MediaTypes.`application/json`,
-      "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"))
-    val workflowInputs = Multipart.FormData.BodyPart("workflowInputs", HttpEntity(MediaTypes.`application/json`, "{\"a\":\"is for apple\"}"))
+    val workflowSource = Multipart.FormData.BodyPart(
+      "workflowSource",
+      HttpEntity(ContentTypes.`text/plain(UTF-8)`, "This is not a WDL, but that's OK for this test of request routing.")
+    )
+    val workflowUrl = Multipart.FormData.BodyPart(
+      "workflowUrl",
+      HttpEntity(
+        MediaTypes.`application/json`,
+        "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"
+      )
+    )
+    val workflowInputs = Multipart.FormData.BodyPart(
+      "workflowInputs",
+      HttpEntity(MediaTypes.`application/json`, "{\"a\":\"is for apple\"}")
+    )
     val workflowType = Multipart.FormData.BodyPart("workflowType", HttpEntity(ContentTypes.`text/plain(UTF-8)`, "WDL"))
-    val workflowVersion = Multipart.FormData.BodyPart("workflowTypeVersion", HttpEntity(ContentTypes.`text/plain(UTF-8)`, "1.0"))
+    val workflowVersion =
+      Multipart.FormData.BodyPart("workflowTypeVersion", HttpEntity(ContentTypes.`text/plain(UTF-8)`, "1.0"))
 
     val workflowSourceTriggerDescribeFailure =
       Multipart.FormData.BodyPart("workflowSource", HttpEntity(ContentTypes.`text/plain(UTF-8)`, "fail to describe"))
@@ -43,16 +54,17 @@ class WomtoolRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with
   }
 
   it should "return Bad Request if the actor returns DescribeFailure" in {
-    Post(s"/womtool/$version/describe", Multipart.FormData(BodyParts.workflowSourceTriggerDescribeFailure).toEntity()) ~>
+    Post(s"/womtool/$version/describe",
+         Multipart.FormData(BodyParts.workflowSourceTriggerDescribeFailure).toEntity()
+    ) ~>
       akkaHttpService.womtoolRoutes ~>
       check {
         status should be(StatusCodes.BadRequest)
 
-        assertResult(
-          s"""{
-             |  "status": "fail",
-             |  "message": "as requested, failing to describe"
-             |}""".stripMargin) {
+        assertResult(s"""{
+                        |  "status": "fail",
+                        |  "message": "as requested, failing to describe"
+                        |}""".stripMargin) {
           responseAs[String]
         }
       }
@@ -75,7 +87,8 @@ class WomtoolRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with
         status should be(StatusCodes.OK)
 
         assertResult {
-          WorkflowDescription(valid = true,
+          WorkflowDescription(
+            valid = true,
             errors = List(
               "this is fake data from the mock SR actor",
               "[reading back DescribeRequest contents] workflow hashcode: Some(580529622)",
@@ -86,7 +99,7 @@ class WomtoolRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with
             ),
             validWorkflow = true
           )
-        } { responseAs[WorkflowDescription] }
+        }(responseAs[WorkflowDescription])
       }
   }
 
@@ -97,7 +110,8 @@ class WomtoolRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with
         status should be(StatusCodes.OK)
 
         assertResult {
-          WorkflowDescription(valid = true,
+          WorkflowDescription(
+            valid = true,
             errors = List(
               "this is fake data from the mock SR actor",
               "[reading back DescribeRequest contents] workflow hashcode: None",
@@ -108,18 +122,24 @@ class WomtoolRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with
             ),
             validWorkflow = true
           )
-        } { responseAs[WorkflowDescription] }
+        }(responseAs[WorkflowDescription])
       }
   }
 
   it should "include inputs, workflow type, and workflow version in the WorkflowSourceFilesCollection" in {
-    Post(s"/womtool/$version/describe", Multipart.FormData(BodyParts.workflowSource, BodyParts.workflowInputs, BodyParts.workflowType, BodyParts.workflowVersion).toEntity()) ~>
+    Post(
+      s"/womtool/$version/describe",
+      Multipart
+        .FormData(BodyParts.workflowSource, BodyParts.workflowInputs, BodyParts.workflowType, BodyParts.workflowVersion)
+        .toEntity()
+    ) ~>
       akkaHttpService.womtoolRoutes ~>
       check {
         status should be(StatusCodes.OK)
 
         assertResult {
-          WorkflowDescription(valid = true,
+          WorkflowDescription(
+            valid = true,
             errors = List(
               "this is fake data from the mock SR actor",
               "[reading back DescribeRequest contents] workflow hashcode: Some(580529622)",
@@ -130,17 +150,18 @@ class WomtoolRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with
             ),
             validWorkflow = true
           )
-        } { responseAs[WorkflowDescription] }
+        }(responseAs[WorkflowDescription])
       }
   }
 }
 
 object WomtoolRouteSupportSpec {
-  class MockWomtoolRouteSupport()(implicit val system: ActorSystem, routeTestTimeout: RouteTestTimeout) extends WomtoolRouteSupport {
+  class MockWomtoolRouteSupport()(implicit val system: ActorSystem, routeTestTimeout: RouteTestTimeout)
+      extends WomtoolRouteSupport {
     override def actorRefFactory = system
     override val ec = system.dispatcher
     override val timeout = routeTestTimeout.duration
     override val serviceRegistryActor = actorRefFactory.actorOf(Props(new MockServiceRegistryActor()))
-    override implicit val materializer = ActorMaterializer()
+    implicit override val materializer = ActorMaterializer()
   }
 }
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
index ba60258476c..e75e3236254 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/ServiceInfoSpec.scala
@@ -22,7 +22,8 @@ class ServiceInfoSpec extends AsyncFlatSpec with ScalatestRouteTest with Matcher
 
   behavior of "ServiceInfo"
 
-  val expectedResponse = WesStatusInfoResponse(Map("WDL" -> Set("draft-2", "1.0", "biscayne", "cascades")),
+  val expectedResponse = WesStatusInfoResponse(
+    Map("WDL" -> Set("draft-2", "1.0", "biscayne", "cascades")),
     List("1.0"),
     Set("ftp", "s3", "drs", "gcs", "http"),
     Map("Cromwell" -> CromwellApiService.cromwellVersion),
@@ -30,8 +31,8 @@ class ServiceInfoSpec extends AsyncFlatSpec with ScalatestRouteTest with Matcher
     Map(WesState.Running -> 5, WesState.Queued -> 3, WesState.Canceling -> 2),
     "https://cromwell.readthedocs.io/en/stable/",
     "https://cromwell.readthedocs.io/en/stable/",
-    Map())
-
+    Map()
+  )
 
   it should "should eventually build the right WesResponse" in {
     ServiceInfo.toWesResponse(workflowStoreActor) map { r =>
diff --git a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
index 00a361a3174..80d4ec23f6a 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/wes/WesRouteSupportSpec.scala
@@ -7,7 +7,11 @@ import akka.http.scaladsl.server.MethodRejection
 import akka.http.scaladsl.testkit.{RouteTestTimeout, ScalatestRouteTest}
 import cromwell.util.SampleWdl.HelloWorld
 import cromwell.webservice.routes.CromwellApiServiceSpec
-import cromwell.webservice.routes.CromwellApiServiceSpec.{MockServiceRegistryActor, MockWorkflowManagerActor, MockWorkflowStoreActor}
+import cromwell.webservice.routes.CromwellApiServiceSpec.{
+  MockServiceRegistryActor,
+  MockWorkflowManagerActor,
+  MockWorkflowStoreActor
+}
 import cromwell.webservice.routes.wes.WesResponseJsonSupport._
 import org.scalatest.flatspec.AsyncFlatSpec
 import org.scalatest.matchers.should.Matchers
@@ -18,11 +22,10 @@ import scala.concurrent.duration._
 class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Matchers with WesRouteSupport {
 
   val actorRefFactory = system
-  override implicit val ec = system.dispatcher
+  implicit override val ec = system.dispatcher
   override val timeout = routeTestTimeout.duration
   implicit def routeTestTimeout = RouteTestTimeout(5.seconds)
 
-
   override val workflowStoreActor = actorRefFactory.actorOf(Props(new MockWorkflowStoreActor()))
   override val serviceRegistryActor = actorRefFactory.actorOf(Props(new MockServiceRegistryActor()))
   override val workflowManagerActor = actorRefFactory.actorOf(Props(new MockWorkflowManagerActor()))
@@ -33,16 +36,20 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
   it should "return PAUSED when on hold" in {
     Get(s"/ga4gh/wes/$version/runs/${CromwellApiServiceSpec.OnHoldWorkflowId}/status") ~>
       wesRoutes ~>
-        check {
-          responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.OnHoldWorkflowId.toString, WesState.Paused)
-        }
+      check {
+        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.OnHoldWorkflowId.toString,
+                                                          WesState.Paused
+        )
+      }
   }
 
   it should "return QUEUED when submitted" in {
     Get(s"/ga4gh/wes/$version/runs/${CromwellApiServiceSpec.ExistingWorkflowId}/status") ~>
       wesRoutes ~>
       check {
-        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.ExistingWorkflowId.toString, WesState.Queued)
+        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.ExistingWorkflowId.toString,
+                                                          WesState.Queued
+        )
       }
   }
 
@@ -50,7 +57,9 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
     Get(s"/ga4gh/wes/$version/runs/${CromwellApiServiceSpec.RunningWorkflowId}/status") ~>
       wesRoutes ~>
       check {
-        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.RunningWorkflowId.toString, WesState.Running)
+        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.RunningWorkflowId.toString,
+                                                          WesState.Running
+        )
       }
   }
 
@@ -58,7 +67,9 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
     Get(s"/ga4gh/wes/$version/runs/${CromwellApiServiceSpec.AbortingWorkflowId}/status") ~>
       wesRoutes ~>
       check {
-        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.AbortingWorkflowId.toString, WesState.Canceling)
+        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.AbortingWorkflowId.toString,
+                                                          WesState.Canceling
+        )
       }
   }
 
@@ -66,7 +77,9 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
     Get(s"/ga4gh/wes/$version/runs/${CromwellApiServiceSpec.AbortedWorkflowId}/status") ~>
       wesRoutes ~>
       check {
-        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.AbortedWorkflowId.toString, WesState.Canceled)
+        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.AbortedWorkflowId.toString,
+                                                          WesState.Canceled
+        )
       }
   }
 
@@ -74,7 +87,9 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
     Get(s"/ga4gh/wes/$version/runs/${CromwellApiServiceSpec.SucceededWorkflowId}/status") ~>
       wesRoutes ~>
       check {
-        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.SucceededWorkflowId.toString, WesState.Complete)
+        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.SucceededWorkflowId.toString,
+                                                          WesState.Complete
+        )
       }
   }
 
@@ -82,7 +97,9 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
     Get(s"/ga4gh/wes/$version/runs/${CromwellApiServiceSpec.FailedWorkflowId}/status") ~>
       wesRoutes ~>
       check {
-        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.FailedWorkflowId.toString, WesState.ExecutorError)
+        responseAs[WesRunStatus] shouldEqual WesRunStatus(CromwellApiServiceSpec.FailedWorkflowId.toString,
+                                                          WesState.ExecutorError
+        )
       }
   }
 
@@ -107,7 +124,9 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
           status
         }
 
-        responseAs[WesErrorResponse] shouldEqual WesErrorResponse("Invalid workflow ID: 'foobar'.", StatusCodes.InternalServerError.intValue)
+        responseAs[WesErrorResponse] shouldEqual WesErrorResponse("Invalid workflow ID: 'foobar'.",
+                                                                  StatusCodes.InternalServerError.intValue
+        )
       }
   }
 
@@ -157,16 +176,24 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
 
   behavior of "WES API /runs POST endpoint"
   it should "return 201 for a successful workflow submission" in {
-    val workflowSource = Multipart.FormData.BodyPart("workflow_url", HttpEntity(MediaTypes.`application/json`, "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"))
-    val workflowInputs = Multipart.FormData.BodyPart("workflow_params", HttpEntity(MediaTypes.`application/json`, HelloWorld.rawInputs.toJson.toString()))
+    val workflowSource = Multipart.FormData.BodyPart(
+      "workflow_url",
+      HttpEntity(
+        MediaTypes.`application/json`,
+        "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"
+      )
+    )
+    val workflowInputs =
+      Multipart.FormData.BodyPart("workflow_params",
+                                  HttpEntity(MediaTypes.`application/json`, HelloWorld.rawInputs.toJson.toString())
+      )
     val formData = Multipart.FormData(workflowSource, workflowInputs).toEntity()
     Post(s"/ga4gh/wes/$version/runs", formData) ~>
       wesRoutes ~>
       check {
-        assertResult(
-          s"""{
-             |  "run_id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}"
-             |}""".stripMargin) {
+        assertResult(s"""{
+                        |  "run_id": "${CromwellApiServiceSpec.ExistingWorkflowId.toString}"
+                        |}""".stripMargin) {
           responseAs[String].parseJson.prettyPrint
         }
         assertResult(StatusCodes.Created) {
@@ -176,7 +203,6 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
       }
   }
 
-
   behavior of "WES API /runs GET endpoint"
   it should "return results for a good query" in {
     Get(s"/ga4gh/wes/v1/runs") ~>
@@ -197,9 +223,9 @@ class WesRouteSupportSpec extends AsyncFlatSpec with ScalatestRouteTest with Mat
       check {
         status should be(StatusCodes.OK)
         val result = responseAs[JsObject]
-        result.fields.keys should contain allOf("request", "run_id", "state")
+        result.fields.keys should contain allOf ("request", "run_id", "state")
         result.fields("state") should be(JsString("RUNNING"))
         result.fields("run_id") should be(JsString(CromwellApiServiceSpec.wesWorkflowId.toString))
       }
   }
-}
\ No newline at end of file
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
index c5467c78ffe..172b3e8a9d0 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemConfig.scala
@@ -10,12 +10,12 @@ import java.util.UUID
 
 // WSM config is needed for accessing WSM-managed blob containers created in Terra workspaces.
 // If the identity executing Cromwell has native access to the blob container, this can be ignored.
-final case class WorkspaceManagerConfig(url: WorkspaceManagerURL,
-                                        overrideWsmAuthToken: Option[String]) // dev-only
+final case class WorkspaceManagerConfig(url: WorkspaceManagerURL, overrideWsmAuthToken: Option[String]) // dev-only
 
 final case class BlobFileSystemConfig(subscriptionId: Option[SubscriptionId],
                                       expiryBufferMinutes: Long,
-                                      workspaceManagerConfig: Option[WorkspaceManagerConfig])
+                                      workspaceManagerConfig: Option[WorkspaceManagerConfig]
+)
 
 object BlobFileSystemConfig {
 
@@ -36,8 +36,7 @@ object BlobFileSystemConfig {
         (wsmURL, overrideWsmAuthToken)
           .mapN(WorkspaceManagerConfig)
           .map(Option(_))
-      }
-      else None.validNel
+      } else None.validNel
 
     (subscriptionId, expiryBufferMinutes, wsmConfig)
       .mapN(BlobFileSystemConfig.apply)
@@ -45,16 +44,16 @@ object BlobFileSystemConfig {
   }
 
   private def parseString(config: Config, path: String) =
-    validate[String] { config.as[String](path) }
+    validate[String](config.as[String](path))
 
   private def parseStringOpt(config: Config, path: String) =
-    validate[Option[String]] { config.as[Option[String]](path) }
+    validate[Option[String]](config.as[Option[String]](path))
 
   private def parseUUIDOpt(config: Config, path: String) =
-    validate[Option[UUID]] { config.as[Option[String]](path).map(UUID.fromString) }
+    validate[Option[UUID]](config.as[Option[String]](path).map(UUID.fromString))
 
   private def parseLongOpt(config: Config, path: String) =
-    validate[Option[Long]] { config.as[Option[Long]](path) }
+    validate[Option[Long]](config.as[Option[Long]](path))
 }
 
 // Our filesystem setup magic can't use BlobFileSystemConfig.apply directly, so we need this
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
index 8f03dbe7e33..21316250146 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala
@@ -23,9 +23,12 @@ import scala.util.{Failure, Success, Try}
 // actually connecting to Blob storage.
 case class AzureFileSystemAPI(private val provider: FileSystemProvider = new AzureFileSystemProvider()) {
   def getFileSystem(uri: URI): Try[AzureFileSystem] = Try(provider.getFileSystem(uri).asInstanceOf[AzureFileSystem])
-  def newFileSystem(uri: URI, config: Map[String, Object]): Try[AzureFileSystem] = Try(provider.newFileSystem(uri, config.asJava).asInstanceOf[AzureFileSystem])
+  def newFileSystem(uri: URI, config: Map[String, Object]): Try[AzureFileSystem] = Try(
+    provider.newFileSystem(uri, config.asJava).asInstanceOf[AzureFileSystem]
+  )
   def closeFileSystem(uri: URI): Option[Unit] = getFileSystem(uri).toOption.map(_.close)
 }
+
 /**
   * The BlobFileSystemManager is an object that is responsible for managing the open filesystem,
   * and refreshing the SAS token that is used to access the blob container containing that filesystem.
@@ -37,27 +40,33 @@ object BlobFileSystemManager {
   def buildConfigMap(credential: AzureSasCredential, container: BlobContainerName): Map[String, Object] = {
     // Special handling is done here to provide a special key value pair if the placeholder token is provided
     // This is due to the BlobClient requiring an auth token even for public blob paths.
-    val sasTuple = if (credential == PLACEHOLDER_TOKEN) (AzureFileSystem.AZURE_STORAGE_PUBLIC_ACCESS_CREDENTIAL, PLACEHOLDER_TOKEN)
-    else (AzureFileSystem.AZURE_STORAGE_SAS_TOKEN_CREDENTIAL, credential)
+    val sasTuple =
+      if (credential == PLACEHOLDER_TOKEN) (AzureFileSystem.AZURE_STORAGE_PUBLIC_ACCESS_CREDENTIAL, PLACEHOLDER_TOKEN)
+      else (AzureFileSystem.AZURE_STORAGE_SAS_TOKEN_CREDENTIAL, credential)
 
-    Map(sasTuple, (AzureFileSystem.AZURE_STORAGE_FILE_STORES, container.value),
-        (AzureFileSystem.AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK, java.lang.Boolean.TRUE))
+    Map(
+      sasTuple,
+      (AzureFileSystem.AZURE_STORAGE_FILE_STORES, container.value),
+      (AzureFileSystem.AZURE_STORAGE_SKIP_INITIAL_CONTAINER_CHECK, java.lang.Boolean.TRUE)
+    )
   }
-  def combinedEnpointContainerUri(endpoint: EndpointURL, container: BlobContainerName) = new URI("azb://?endpoint=" + endpoint + "/" + container.value)
+  def combinedEnpointContainerUri(endpoint: EndpointURL, container: BlobContainerName) = new URI(
+    "azb://?endpoint=" + endpoint + "/" + container.value
+  )
 
   val PLACEHOLDER_TOKEN = new AzureSasCredential("this-is-a-public-sas")
 }
 
 class BlobFileSystemManager(val expiryBufferMinutes: Long,
                             val blobTokenGenerator: BlobSasTokenGenerator,
-                            val fileSystemAPI: AzureFileSystemAPI = AzureFileSystemAPI()) extends LazyLogging {
+                            val fileSystemAPI: AzureFileSystemAPI = AzureFileSystemAPI()
+) extends LazyLogging {
 
-  def this(config: BlobFileSystemConfig) = {
+  def this(config: BlobFileSystemConfig) =
     this(
       config.expiryBufferMinutes,
       BlobSasTokenGenerator.createBlobTokenGeneratorFromConfig(config)
     )
-  }
 
   def this(rawConfig: Config) = this(BlobFileSystemConfig(rawConfig))
 
@@ -68,18 +77,16 @@ class BlobFileSystemManager(val expiryBufferMinutes: Long,
     synchronized {
       fileSystemAPI.getFileSystem(uri).filter(!_.isExpired(buffer)).recoverWith {
         // If no filesystem already exists, this will create a new connection, with the provided configs
-        case _: FileSystemNotFoundException => {
+        case _: FileSystemNotFoundException =>
           logger.info(s"Creating new blob filesystem for URI $uri")
           generateFilesystem(uri, container, endpoint)
-        }
-        case _ : NoSuchElementException => {
+        case _: NoSuchElementException =>
           // When the filesystem expires, the above filter results in a
           // NoSuchElementException. If expired, close the filesystem
           // and reopen the filesystem with the fresh token
           logger.info(s"Closing & regenerating token for existing blob filesystem at URI $uri")
           fileSystemAPI.closeFileSystem(uri)
           generateFilesystem(uri, container, endpoint)
-        }
       }
     }
   }
@@ -93,15 +100,17 @@ class BlobFileSystemManager(val expiryBufferMinutes: Long,
     * @param endpoint the endpoint containing the storage account for the container to open
     * @return a try with either the successfully created filesystem, or a failure containing the exception
     */
-  private def generateFilesystem(uri: URI, container: BlobContainerName, endpoint: EndpointURL): Try[AzureFileSystem] = {
-    blobTokenGenerator.generateBlobSasToken(endpoint, container)
-      .flatMap((token: AzureSasCredential) => {
+  private def generateFilesystem(uri: URI, container: BlobContainerName, endpoint: EndpointURL): Try[AzureFileSystem] =
+    blobTokenGenerator
+      .generateBlobSasToken(endpoint, container)
+      .flatMap { (token: AzureSasCredential) =>
         fileSystemAPI.newFileSystem(uri, BlobFileSystemManager.buildConfigMap(token, container))
-      })
-  }
+      }
 }
 
-sealed trait BlobSasTokenGenerator { def generateBlobSasToken(endpoint: EndpointURL, container: BlobContainerName): Try[AzureSasCredential] }
+sealed trait BlobSasTokenGenerator {
+  def generateBlobSasToken(endpoint: EndpointURL, container: BlobContainerName): Try[AzureSasCredential]
+}
 object BlobSasTokenGenerator {
 
   /**
@@ -123,16 +132,18 @@ object BlobSasTokenGenerator {
     * @return An appropriate BlobSasTokenGenerator
     */
   def createBlobTokenGeneratorFromConfig(config: BlobFileSystemConfig): BlobSasTokenGenerator =
-    config.workspaceManagerConfig.map { wsmConfig =>
-      val wsmClient: WorkspaceManagerApiClientProvider = new HttpWorkspaceManagerClientProvider(wsmConfig.url)
+    config.workspaceManagerConfig
+      .map { wsmConfig =>
+        val wsmClient: WorkspaceManagerApiClientProvider = new HttpWorkspaceManagerClientProvider(wsmConfig.url)
 
-      // WSM-mediated mediated SAS token generator
-      // parameterizing client instead of URL to make injecting mock client possible
-      BlobSasTokenGenerator.createBlobTokenGenerator(wsmClient, wsmConfig.overrideWsmAuthToken)
-    }.getOrElse(
-      // Native SAS token generator
-      BlobSasTokenGenerator.createBlobTokenGenerator(config.subscriptionId)
-    )
+        // WSM-mediated mediated SAS token generator
+        // parameterizing client instead of URL to make injecting mock client possible
+        BlobSasTokenGenerator.createBlobTokenGenerator(wsmClient, wsmConfig.overrideWsmAuthToken)
+      }
+      .getOrElse(
+        // Native SAS token generator
+        BlobSasTokenGenerator.createBlobTokenGenerator(config.subscriptionId)
+      )
 
   /**
     * Native SAS token generator, uses the DefaultAzureCredentialBuilder in the local environment
@@ -143,9 +154,8 @@ object BlobSasTokenGenerator {
     * @return A NativeBlobTokenGenerator, able to produce a valid SAS token for accessing the provided blob
     * container and endpoint locally
     */
-  def createBlobTokenGenerator(subscription: Option[SubscriptionId]): BlobSasTokenGenerator = {
+  def createBlobTokenGenerator(subscription: Option[SubscriptionId]): BlobSasTokenGenerator =
     NativeBlobSasTokenGenerator(subscription)
-  }
 
   /**
     * WSM-mediated SAS token generator, uses the DefaultAzureCredentialBuilder in the cloud environment
@@ -160,16 +170,17 @@ object BlobSasTokenGenerator {
     * container and endpoint that is managed by WSM
     */
   def createBlobTokenGenerator(workspaceManagerClient: WorkspaceManagerApiClientProvider,
-                               overrideWsmAuthToken: Option[String]): BlobSasTokenGenerator = {
+                               overrideWsmAuthToken: Option[String]
+  ): BlobSasTokenGenerator =
     new WSMBlobSasTokenGenerator(workspaceManagerClient, overrideWsmAuthToken)
-  }
 
 }
 
 case class WSMTerraCoordinates(wsmEndpoint: String, workspaceId: UUID, containerResourceId: UUID)
 
 class WSMBlobSasTokenGenerator(wsmClientProvider: WorkspaceManagerApiClientProvider,
-                                    overrideWsmAuthToken: Option[String]) extends BlobSasTokenGenerator {
+                               overrideWsmAuthToken: Option[String]
+) extends BlobSasTokenGenerator {
 
   /**
     * Generate a BlobSasToken by using the available authorization information
@@ -184,7 +195,7 @@ class WSMBlobSasTokenGenerator(wsmClientProvider: WorkspaceManagerApiClientProvi
     val wsmAuthToken: Try[String] = getWsmAuth
     container.workspaceId match {
       // If this is a Terra workspace, request a token from WSM
-      case Success(workspaceId) => {
+      case Success(workspaceId) =>
         (for {
           wsmAuth <- wsmAuthToken
           wsmAzureResourceClient = wsmClientProvider.getControlledAzureResourceApi(wsmAuth)
@@ -194,7 +205,6 @@ class WSMBlobSasTokenGenerator(wsmClientProvider: WorkspaceManagerApiClientProvi
           // If the storage account was still not found in WSM, this may be a public filesystem
           case exception: ApiException if exception.getCode == 404 => Try(BlobFileSystemManager.PLACEHOLDER_TOKEN)
         }
-      }
       // Otherwise assume that the container is public and use a placeholder
       // SAS token to bypass the BlobClient authentication requirement
       case Failure(_) => Try(BlobFileSystemManager.PLACEHOLDER_TOKEN)
@@ -205,36 +215,40 @@ class WSMBlobSasTokenGenerator(wsmClientProvider: WorkspaceManagerApiClientProvi
 
   // Optionally provide wsmAuth to avoid acquiring it twice in generateBlobSasToken.
   // In the case that the resourceId is not cached and no auth is provided, this function will acquire a new auth as necessary.
-  private def getContainerResourceId(workspaceId: UUID, container: BlobContainerName, precomputedWsmAuth: Option[String]): Try[UUID] = {
+  private def getContainerResourceId(workspaceId: UUID,
+                                     container: BlobContainerName,
+                                     precomputedWsmAuth: Option[String]
+  ): Try[UUID] =
     cachedContainerResourceIds.get(container) match {
-      case Some(id) => Try(id) //cache hit
-      case _ => { //cache miss
+      case Some(id) => Try(id) // cache hit
+      case _ => // cache miss
         val auth: Try[String] = precomputedWsmAuth.map(auth => Try(auth)).getOrElse(getWsmAuth)
         val resourceId = for {
           wsmAuth <- auth
           wsmResourceApi = wsmClientProvider.getResourceApi(wsmAuth)
           resourceId <- wsmResourceApi.findContainerResourceId(workspaceId, container)
         } yield resourceId
-        resourceId.map(id => cachedContainerResourceIds.put(container, id)) //NB: Modifying cache state here.
+        resourceId.map(id => cachedContainerResourceIds.put(container, id)) // NB: Modifying cache state here.
         cachedContainerResourceIds.get(container) match {
           case Some(uuid) => Try(uuid)
           case _ => Failure(new NoSuchElementException("Could not retrieve container resource ID from WSM"))
         }
-      }
     }
-  }
 
-  private def getWsmAuth: Try[String] = {
+  private def getWsmAuth: Try[String] =
     overrideWsmAuthToken match {
       case Some(t) => Success(t)
       case None => AzureCredentials.getAccessToken(None).toTry
     }
-  }
 
-  private def parseTerraWorkspaceIdFromPath(blobPath: BlobPath): Try[UUID] = {
+  private def parseTerraWorkspaceIdFromPath(blobPath: BlobPath): Try[UUID] =
     if (blobPath.container.value.startsWith("sc-")) Try(UUID.fromString(blobPath.container.value.substring(3)))
-    else Failure(new Exception("Could not parse workspace ID from storage container. Are you sure this is a file in a Terra Workspace?"))
-  }
+    else
+      Failure(
+        new Exception(
+          "Could not parse workspace ID from storage container. Are you sure this is a file in a Terra Workspace?"
+        )
+      )
 
   /**
    * Return a REST endpoint that will reply with a sas token for the blob storage container associated with the provided blob path.
@@ -245,13 +259,14 @@ class WSMBlobSasTokenGenerator(wsmClientProvider: WorkspaceManagerApiClientProvi
    */
   def getWSMSasFetchEndpoint(blobPath: BlobPath, tokenDuration: Option[Duration] = None): Try[String] = {
     val wsmEndpoint = wsmClientProvider.getBaseWorkspaceManagerUrl
-    val lifetimeQueryParameters: String = tokenDuration.map(d => s"?sasExpirationDuration=${d.toSeconds.intValue}").getOrElse("")
+    val lifetimeQueryParameters: String =
+      tokenDuration.map(d => s"?sasExpirationDuration=${d.toSeconds.intValue}").getOrElse("")
     val terraInfo: Try[WSMTerraCoordinates] = for {
       workspaceId <- parseTerraWorkspaceIdFromPath(blobPath)
       containerResourceId <- getContainerResourceId(workspaceId, blobPath.container, None)
       coordinates = WSMTerraCoordinates(wsmEndpoint, workspaceId, containerResourceId)
     } yield coordinates
-    terraInfo.map{terraCoordinates =>
+    terraInfo.map { terraCoordinates =>
       s"${terraCoordinates.wsmEndpoint}/api/workspaces/v1/${terraCoordinates.workspaceId.toString}/resources/controlled/azure/storageContainer/${terraCoordinates.containerResourceId.toString}/getSasToken${lifetimeQueryParameters}"
     }
   }
@@ -273,11 +288,14 @@ case class NativeBlobSasTokenGenerator(subscription: Option[SubscriptionId] = No
     * @return an AzureSasCredential for accessing a blob container
     */
   def generateBlobSasToken(endpoint: EndpointURL, container: BlobContainerName): Try[AzureSasCredential] = {
-    val c = AzureUtils.buildContainerClientFromLocalEnvironment(container.toString, endpoint.toString, subscription.map(_.toString))
+    val c = AzureUtils.buildContainerClientFromLocalEnvironment(container.toString,
+                                                                endpoint.toString,
+                                                                subscription.map(_.toString)
+    )
 
     c.map { bcc =>
-        val bsssv = new BlobServiceSasSignatureValues(OffsetDateTime.now.plusDays(1), bcsp)
-        new AzureSasCredential(bcc.generateSas(bsssv))
-      }.orElse(Try(BlobFileSystemManager.PLACEHOLDER_TOKEN))
+      val bsssv = new BlobServiceSasSignatureValues(OffsetDateTime.now.plusDays(1), bcsp)
+      new AzureSasCredential(bcc.generateSas(bsssv))
+    }.orElse(Try(BlobFileSystemManager.PLACEHOLDER_TOKEN))
   }
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 3acb99857e0..22bf6b44742 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -17,11 +17,17 @@ object BlobPathBuilder {
   case class ValidBlobPath(path: String, container: BlobContainerName, endpoint: EndpointURL) extends BlobPathValidation
   case class UnparsableBlobPath(errorMessage: Throwable) extends BlobPathValidation
 
-  def invalidBlobHostMessage(endpoint: EndpointURL) = s"Malformed Blob URL for this builder: The endpoint $endpoint doesn't contain the expected host string '{SA}.blob.core.windows.net/'"
-  def invalidBlobContainerMessage(endpoint: EndpointURL) = s"Malformed Blob URL for this builder: Could not parse container"
+  def invalidBlobHostMessage(endpoint: EndpointURL) =
+    s"Malformed Blob URL for this builder: The endpoint $endpoint doesn't contain the expected host string '{SA}.blob.core.windows.net/'"
+  def invalidBlobContainerMessage(endpoint: EndpointURL) =
+    s"Malformed Blob URL for this builder: Could not parse container"
   def parseURI(string: String): Try[URI] = Try(URI.create(UrlEscapers.urlFragmentEscaper().escape(string)))
-  def parseStorageAccount(uri: URI): Try[StorageAccountName] = uri.getHost.split("\\.").find(_.nonEmpty).map(StorageAccountName(_))
-      .map(Success(_)).getOrElse(Failure(new Exception("Could not parse storage account")))
+  def parseStorageAccount(uri: URI): Try[StorageAccountName] = uri.getHost
+    .split("\\.")
+    .find(_.nonEmpty)
+    .map(StorageAccountName(_))
+    .map(Success(_))
+    .getOrElse(Failure(new Exception("Could not parse storage account")))
 
   /**
     * Validates a that a path from a string is a valid BlobPath of the format:
@@ -41,7 +47,7 @@ object BlobPathBuilder {
     *
     * If the configured container and storage account do not match, the string is considered unparsable
     */
- def validateBlobPath(string: String): BlobPathValidation = {
+  def validateBlobPath(string: String): BlobPathValidation = {
     val blobValidation = for {
       testUri <- parseURI(string)
       testEndpoint = EndpointURL(testUri.getScheme + "://" + testUri.getHost())
@@ -49,10 +55,8 @@ object BlobPathBuilder {
       testContainer = testUri.getPath.split("/").find(_.nonEmpty)
       isBlobHost = testUri.getHost().contains(blobHostnameSuffix) && testUri.getScheme().contains("https")
       blobPathValidation = (isBlobHost, testContainer) match {
-        case (true, Some(container)) => ValidBlobPath(
-            testUri.getPath.replaceFirst("/" + container, ""),
-            BlobContainerName(container),
-            testEndpoint)
+        case (true, Some(container)) =>
+          ValidBlobPath(testUri.getPath.replaceFirst("/" + container, ""), BlobContainerName(container), testEndpoint)
         case (false, _) => UnparsableBlobPath(new MalformedURLException(invalidBlobHostMessage(testEndpoint)))
         case (true, None) => UnparsableBlobPath(new MalformedURLException(invalidBlobContainerMessage(testEndpoint)))
       }
@@ -63,12 +67,11 @@ object BlobPathBuilder {
 
 class BlobPathBuilder()(private val fsm: BlobFileSystemManager) extends PathBuilder {
 
-  def build(string: String): Try[BlobPath] = {
+  def build(string: String): Try[BlobPath] =
     validateBlobPath(string) match {
       case ValidBlobPath(path, container, endpoint) => Try(BlobPath(path, endpoint, container)(fsm))
       case UnparsableBlobPath(errorMessage: Throwable) => Failure(errorMessage)
     }
-  }
   override def name: String = "Azure Blob Storage"
 }
 
@@ -103,33 +106,36 @@ object BlobPath {
         s"${containerName}:/${pathInContainer}"
       case _ => nioString
     }
-    pathStr.substring(pathStr.indexOf(":")+1)
+    pathStr.substring(pathStr.indexOf(":") + 1)
   }
 
   def apply(nioPath: NioPath,
             endpoint: EndpointURL,
             container: BlobContainerName,
-            fsm: BlobFileSystemManager): BlobPath = {
+            fsm: BlobFileSystemManager
+  ): BlobPath =
     BlobPath(cleanedNioPathString(nioPath.toString), endpoint, container)(fsm)
-  }
 }
 
-case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, container: BlobContainerName)(private val fsm: BlobFileSystemManager) extends Path {
+case class BlobPath private[blob] (pathString: String, endpoint: EndpointURL, container: BlobContainerName)(
+  private val fsm: BlobFileSystemManager
+) extends Path {
   override def nioPath: NioPath = findNioPath(pathString)
 
   override protected def newPath(nioPath: NioPath): Path = BlobPath(nioPath, endpoint, container, fsm)
 
   override def pathAsString: String = List(endpoint, container, pathString.stripPrefix("/")).mkString("/")
 
-  //This is purposefully an unprotected get because if the endpoint cannot be parsed this should fail loudly rather than quietly
-  override def pathWithoutScheme: String = parseURI(endpoint.value).map(u => List(u.getHost, container, pathString.stripPrefix("/")).mkString("/")).get
+  // This is purposefully an unprotected get because if the endpoint cannot be parsed this should fail loudly rather than quietly
+  override def pathWithoutScheme: String =
+    parseURI(endpoint.value).map(u => List(u.getHost, container, pathString.stripPrefix("/")).mkString("/")).get
 
   private def findNioPath(path: String): NioPath = (for {
     fileSystem <- fsm.retrieveFilesystem(endpoint, container)
     // The Azure NIO library uses `{container}:` to represent the root of the path
     nioPath = fileSystem.getPath(s"${container.value}:", path)
-  // This is purposefully an unprotected get because the NIO API needing an unwrapped path object.
-  // If an error occurs the api expects a thrown exception
+    // This is purposefully an unprotected get because the NIO API needing an unwrapped path object.
+    // If an error occurs the api expects a thrown exception
   } yield nioPath).get
 
   def blobFileAttributes: Try[AzureBlobFileAttributes] =
@@ -168,15 +174,13 @@ case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, con
     * Return the pathString of this BlobPath, with the given prefix removed if this path shares that
     * prefix.
     */
-  def pathStringWithoutPrefix(prefix: Path): String = {
+  def pathStringWithoutPrefix(prefix: Path): String =
     if (this.startsWith(prefix)) {
       prefix.relativize(this) match {
         case b: BlobPath => b.pathString // path inside the blob container
         case p: Path => p.pathAsString // full path
       }
-    }
-    else pathString
-  }
+    } else pathString
 
   /**
     * Returns the path relative to the container root.
@@ -184,10 +188,10 @@ case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, con
     * will be returned as path/to/my/file.
     * @return Path string relative to the container root.
     */
-  def pathWithoutContainer : String = pathString
+  def pathWithoutContainer: String = pathString
 
   def getFilesystemManager: BlobFileSystemManager = fsm
 
-  override def getSymlinkSafePath(options: LinkOption*): Path  = toAbsolutePath
+  override def getSymlinkSafePath(options: LinkOption*): Path = toAbsolutePath
 
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index 47245552dc2..2dafa6ab5d2 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -10,17 +10,16 @@ import java.util.UUID
 import scala.concurrent.{ExecutionContext, Future}
 import scala.util.Try
 
-final case class SubscriptionId(value: UUID) {override def toString: String = value.toString}
+final case class SubscriptionId(value: UUID) { override def toString: String = value.toString }
 final case class BlobContainerName(value: String) {
   override def toString: String = value
-  lazy val workspaceId: Try[UUID] = {
-    Try(UUID.fromString(value.replaceFirst("sc-","")))
-  }
+  lazy val workspaceId: Try[UUID] =
+    Try(UUID.fromString(value.replaceFirst("sc-", "")))
 }
-final case class StorageAccountName(value: String) {override def toString: String = value}
+final case class StorageAccountName(value: String) { override def toString: String = value }
 final case class EndpointURL(value: String) {
   override def toString: String = value
-  lazy val storageAccountName : Try[StorageAccountName] = {
+  lazy val storageAccountName: Try[StorageAccountName] = {
     val sa = for {
       host <- value.split("//").findLast(_.nonEmpty)
       storageAccountName <- host.split("\\.").find(_.nonEmpty)
@@ -28,17 +27,19 @@ final case class EndpointURL(value: String) {
     sa.toRight(new Exception(s"Storage account name could not be parsed from $value")).toTry
   }
 }
-final case class WorkspaceId(value: UUID) {override def toString: String = value.toString}
-final case class ContainerResourceId(value: UUID) {override def toString: String = value.toString}
-final case class WorkspaceManagerURL(value: String) {override def toString: String = value}
+final case class WorkspaceId(value: UUID) { override def toString: String = value.toString }
+final case class ContainerResourceId(value: UUID) { override def toString: String = value.toString }
+final case class WorkspaceManagerURL(value: String) { override def toString: String = value }
 
-final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, fsm: BlobFileSystemManager) extends PathBuilderFactory {
+final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, fsm: BlobFileSystemManager)
+    extends PathBuilderFactory {
 
-  override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[BlobPathBuilder] = {
+  override def withOptions(
+    options: WorkflowOptions
+  )(implicit as: ActorSystem, ec: ExecutionContext): Future[BlobPathBuilder] =
     Future {
       new BlobPathBuilder()(fsm)
     }
-  }
 
   override def priority: Int = PriorityBlob
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
index 490d0fcc704..8698dc7f859 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/WorkspaceManagerApiClientProvider.scala
@@ -23,7 +23,8 @@ trait WorkspaceManagerApiClientProvider {
   def getBaseWorkspaceManagerUrl: String
 }
 
-class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManagerURL) extends WorkspaceManagerApiClientProvider {
+class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManagerURL)
+    extends WorkspaceManagerApiClientProvider {
   private def getApiClient: ApiClient = {
     val client: ApiClient = new ApiClient()
     client.setBasePath(baseWorkspaceManagerUrl.value)
@@ -44,27 +45,37 @@ class HttpWorkspaceManagerClientProvider(baseWorkspaceManagerUrl: WorkspaceManag
   def getBaseWorkspaceManagerUrl: String = baseWorkspaceManagerUrl.value
 }
 
-case class WsmResourceApi(resourcesApi : ResourceApi) {
-  def findContainerResourceId(workspaceId : UUID, container: BlobContainerName): Try[UUID] = {
+case class WsmResourceApi(resourcesApi: ResourceApi) {
+  def findContainerResourceId(workspaceId: UUID, container: BlobContainerName): Try[UUID] =
     for {
-      workspaceResources <- Try(resourcesApi.enumerateResources(workspaceId, 0, 10, ResourceType.AZURE_STORAGE_CONTAINER, StewardshipType.CONTROLLED).getResources())
-      workspaceStorageContainerOption = workspaceResources.asScala.find(r => r.getMetadata().getName() == container.value)
-      workspaceStorageContainer <- workspaceStorageContainerOption.toRight(new Exception("No storage container found for this workspace")).toTry
+      workspaceResources <- Try(
+        resourcesApi
+          .enumerateResources(workspaceId, 0, 10, ResourceType.AZURE_STORAGE_CONTAINER, StewardshipType.CONTROLLED)
+          .getResources()
+      )
+      workspaceStorageContainerOption = workspaceResources.asScala.find(r =>
+        r.getMetadata().getName() == container.value
+      )
+      workspaceStorageContainer <- workspaceStorageContainerOption
+        .toRight(new Exception("No storage container found for this workspace"))
+        .toTry
       resourceId = workspaceStorageContainer.getMetadata().getResourceId()
     } yield resourceId
-  }
 }
-case class WsmControlledAzureResourceApi(controlledAzureResourceApi : ControlledAzureResourceApi) {
-  def createAzureStorageContainerSasToken(workspaceId: UUID, resourceId: UUID): Try[AzureSasCredential] = {
+case class WsmControlledAzureResourceApi(controlledAzureResourceApi: ControlledAzureResourceApi) {
+  def createAzureStorageContainerSasToken(workspaceId: UUID, resourceId: UUID): Try[AzureSasCredential] =
     for {
-      sas <- Try(controlledAzureResourceApi.createAzureStorageContainerSasToken(
-        workspaceId,
-        resourceId,
-        null,
-        null,
-        null,
-        null
-      ).getToken)
+      sas <- Try(
+        controlledAzureResourceApi
+          .createAzureStorageContainerSasToken(
+            workspaceId,
+            resourceId,
+            null,
+            null,
+            null,
+            null
+          )
+          .getToken
+      )
     } yield new AzureSasCredential(sas)
-  }
 }
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala
index 9b8362ced80..0626a008de0 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/AzureFileSystemSpec.scala
@@ -23,34 +23,36 @@ class AzureFileSystemSpec extends AnyFlatSpec with Matchers {
     val combinedEndpoint = BlobFileSystemManager.combinedEnpointContainerUri(storageEndpoint, container)
 
     val provider = new AzureFileSystemProvider()
-    provider.newFileSystem(
-      combinedEndpoint,
-      BlobFileSystemManager.buildConfigMap(creds, container).asJava
-    ).asInstanceOf[AzureFileSystem]
+    provider
+      .newFileSystem(
+        combinedEndpoint,
+        BlobFileSystemManager.buildConfigMap(creds, container).asJava
+      )
+      .asInstanceOf[AzureFileSystem]
   }
 
   it should "parse an expiration from a sas token" in {
     val now = Instant.now()
-    val filesystem : AzureFileSystem = makeFilesystemWithExpiration(now)
+    val filesystem: AzureFileSystem = makeFilesystemWithExpiration(now)
     filesystem.getExpiry.asScala shouldBe Some(now)
     filesystem.getFileStores.asScala.map(_.name()).exists(_ == "testContainer") shouldBe true
   }
 
   it should "not be expired when the token is fresh" in {
     val anHourFromNow = Instant.now().plusSeconds(3600)
-    val filesystem : AzureFileSystem = makeFilesystemWithExpiration(anHourFromNow)
+    val filesystem: AzureFileSystem = makeFilesystemWithExpiration(anHourFromNow)
     filesystem.isExpired(fiveMinutes) shouldBe false
   }
 
   it should "be expired when we're within the buffer" in {
     val threeMinutesFromNow = Instant.now().plusSeconds(180)
-    val filesystem : AzureFileSystem = makeFilesystemWithExpiration(threeMinutesFromNow)
+    val filesystem: AzureFileSystem = makeFilesystemWithExpiration(threeMinutesFromNow)
     filesystem.isExpired(fiveMinutes) shouldBe true
   }
 
   it should "be expired when the token is stale" in {
     val anHourAgo = Instant.now().minusSeconds(3600)
-    val filesystem : AzureFileSystem = makeFilesystemWithExpiration(anHourAgo)
+    val filesystem: AzureFileSystem = makeFilesystemWithExpiration(anHourAgo)
     filesystem.isExpired(fiveMinutes) shouldBe true
   }
 
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
index 68804113763..30d580a6e49 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobFileSystemConfigSpec.scala
@@ -12,8 +12,7 @@ class BlobFileSystemConfigSpec extends AnyFlatSpec with Matchers {
 
   it should "parse configs for a minimal functioning factory with native blob access" in {
     val config = BlobFileSystemConfig(
-      ConfigFactory.parseString(
-      s"""
+      ConfigFactory.parseString(s"""
       """.stripMargin)
     )
     config.expiryBufferMinutes should equal(BlobFileSystemConfig.defaultExpiryBufferMinutes)
@@ -21,14 +20,13 @@ class BlobFileSystemConfigSpec extends AnyFlatSpec with Matchers {
 
   it should "parse configs for a functioning factory with WSM-mediated blob access" in {
     val config = BlobFileSystemConfig(
-      ConfigFactory.parseString(
-        s"""
-           |expiry-buffer-minutes = "20"
-           |workspace-manager {
-           |  url = "$workspaceManagerURL"
-           |  b2cToken = "$b2cToken"
-           |}
-           |
+      ConfigFactory.parseString(s"""
+                                   |expiry-buffer-minutes = "20"
+                                   |workspace-manager {
+                                   |  url = "$workspaceManagerURL"
+                                   |  b2cToken = "$b2cToken"
+                                   |}
+                                   |
         """.stripMargin)
     )
     config.expiryBufferMinutes should equal(20L)
@@ -39,13 +37,12 @@ class BlobFileSystemConfigSpec extends AnyFlatSpec with Matchers {
 
   it should "fail when partial WSM config is supplied" in {
     val rawConfig =
-      ConfigFactory.parseString(
-        s"""
-         |expiry-buffer-minutes = "10"
-         |workspace-manager {
-         |  b2cToken = "$b2cToken"
-         |}
-         |
+      ConfigFactory.parseString(s"""
+                                   |expiry-buffer-minutes = "10"
+                                   |workspace-manager {
+                                   |  b2cToken = "$b2cToken"
+                                   |}
+                                   |
         """.stripMargin)
 
     val error = intercept[AggregatedMessageException](BlobFileSystemConfig(rawConfig))
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
index 24783c15780..2b46a8b80b8 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderFactorySpec.scala
@@ -14,12 +14,11 @@ import java.time.{Duration, Instant, ZoneId}
 import java.util.UUID
 import scala.util.{Failure, Success, Try}
 
-
 object BlobPathBuilderFactorySpec {
   def buildExampleSasToken(expiry: Instant): AzureSasCredential = {
     val formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd").withZone(ZoneId.systemDefault())
     val sv = formatter.format(expiry)
-    val se = expiry.toString().replace(":","%3A")
+    val se = expiry.toString().replace(":", "%3A")
     new AzureSasCredential(s"sv=$sv&se=$se&sr=c&sp=rcl")
   }
 }
@@ -47,15 +46,15 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
 
   it should "test retrieveFileSystem with expired Terra filesystem" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    //val expiredToken = generateTokenExpiration(9L)
+    // val expiredToken = generateTokenExpiration(9L)
     val refreshedToken = generateTokenExpiration(69L)
     val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
     val container = BlobContainerName("sc-" + UUID.randomUUID().toString())
     val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
     val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
 
-    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
-    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    // Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    // at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
     val azureFileSystem = mock[AzureFileSystem]
     when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(true)
     val fileSystems = mock[AzureFileSystemAPI]
@@ -73,15 +72,15 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
 
   it should "test retrieveFileSystem with an unexpired Terra fileSystem" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
-    //val initialToken = generateTokenExpiration(11L)
+    // val initialToken = generateTokenExpiration(11L)
     val refreshedToken = generateTokenExpiration(71L)
     val sasToken = BlobPathBuilderFactorySpec.buildExampleSasToken(refreshedToken)
     val container = BlobContainerName("sc-" + UUID.randomUUID().toString())
     val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
-    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint,container)
+    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
 
-    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
-    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    // Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    // at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
     val azureFileSystem = mock[AzureFileSystem]
     when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(false)
     val fileSystems = mock[AzureFileSystemAPI]
@@ -106,8 +105,8 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
     val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
 
-    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
-    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    // Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    // at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
     val azureFileSystem = mock[AzureFileSystem]
     when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(false)
     val fileSystems = mock[AzureFileSystemAPI]
@@ -131,8 +130,8 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
     val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
 
-    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
-    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    // Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    // at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
     val azureFileSystem = mock[AzureFileSystem]
     when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(true)
     val fileSystems = mock[AzureFileSystemAPI]
@@ -153,10 +152,10 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val sasToken = BlobFileSystemManager.PLACEHOLDER_TOKEN
     val container = BlobContainerName("sc-" + UUID.randomUUID().toString())
     val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
-    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint,container)
+    val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
 
-    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
-    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    // Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    // at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
     val azureFileSystem = mock[AzureFileSystem]
     when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(false)
     val fileSystems = mock[AzureFileSystemAPI]
@@ -180,8 +179,8 @@ class BlobPathBuilderFactorySpec extends AnyFlatSpec with Matchers with MockSuga
     val configMap = BlobFileSystemManager.buildConfigMap(sasToken, container)
     val azureUri = BlobFileSystemManager.combinedEnpointContainerUri(endpoint, container)
 
-    //Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
-    //at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
+    // Mocking this final class requires the plugin Mock Maker Inline plugin, configured here
+    // at filesystems/blob/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker
     val azureFileSystem = mock[AzureFileSystem]
     when(azureFileSystem.isExpired(Duration.ofMinutes(10L))).thenReturn(false)
     val fileSystems = mock[AzureFileSystemAPI]
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index a8ca7d58d6f..fbff8e47431 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -19,11 +19,10 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val evalPath = "/path/to/file"
     val testString = endpoint.value + "/" + container + evalPath
     BlobPathBuilder.validateBlobPath(testString) match {
-      case BlobPathBuilder.ValidBlobPath(path, parsedContainer, parsedEndpoint) => {
+      case BlobPathBuilder.ValidBlobPath(path, parsedContainer, parsedEndpoint) =>
         path should equal(evalPath)
         parsedContainer should equal(container)
         parsedEndpoint should equal(endpoint)
-      }
       case BlobPathBuilder.UnparsableBlobPath(errorMessage) => fail(errorMessage)
     }
   }
@@ -119,9 +118,14 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val builder = makeBlobPathBuilder()
     val rootString = s"${endpoint.value}/${container.value}/cromwell-execution"
     val blobRoot: BlobPath = builder build rootString getOrElse fail()
-    blobRoot.toAbsolutePath.pathAsString should equal ("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution")
-    val otherFile = blobRoot.resolve("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution/test/inputFile.txt")
-    otherFile.toAbsolutePath.pathAsString should equal ("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution/test/inputFile.txt")
+    blobRoot.toAbsolutePath.pathAsString should equal(
+      "https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution"
+    )
+    val otherFile =
+      blobRoot.resolve("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution/test/inputFile.txt")
+    otherFile.toAbsolutePath.pathAsString should equal(
+      "https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution/test/inputFile.txt"
+    )
   }
 
   it should "build a blob path from a test string and read a file" in {
@@ -136,8 +140,8 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     blobPath.pathAsString should equal(testString)
     blobPath.pathWithoutScheme should equal(endpointHost + "/" + container + evalPath)
     val is = blobPath.newInputStream()
-    val fileText = (is.readAllBytes.map(_.toChar)).mkString
-    fileText should include ("This is my test file!!!! Did it work?")
+    val fileText = is.readAllBytes.map(_.toChar).mkString
+    fileText should include("This is my test file!!!! Did it work?")
   }
 
   it should "build duplicate blob paths in the same filesystem" in {
@@ -149,38 +153,47 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     val blobPath2: BlobPath = builder build testString getOrElse fail()
     blobPath1 should equal(blobPath2)
     val is = blobPath1.newInputStream()
-    val fileText = (is.readAllBytes.map(_.toChar)).mkString
-    fileText should include ("This is my test file!!!! Did it work?")
+    val fileText = is.readAllBytes.map(_.toChar).mkString
+    fileText should include("This is my test file!!!! Did it work?")
   }
 
   it should "resolve a path without duplicating container name" in {
     val builder = makeBlobPathBuilder()
     val rootString = s"${endpoint.value}/${container.value}/cromwell-execution"
     val blobRoot: BlobPath = builder build rootString getOrElse fail()
-    blobRoot.toAbsolutePath.pathAsString should equal ("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution")
+    blobRoot.toAbsolutePath.pathAsString should equal(
+      "https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution"
+    )
     val otherFile = blobRoot.resolve("test/inputFile.txt")
-    otherFile.toAbsolutePath.pathAsString should equal ("https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution/test/inputFile.txt")
+    otherFile.toAbsolutePath.pathAsString should equal(
+      "https://centaurtesting.blob.core.windows.net/test-blob/cromwell-execution/test/inputFile.txt"
+    )
   }
 
   it should "correctly remove a prefix from the blob path" in {
     val builder = makeBlobPathBuilder()
     val rootString = s"${endpoint.value}/${container.value}/cromwell-execution/"
-    val execDirString = s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/"
-    val fileString = s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
+    val execDirString =
+      s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/"
+    val fileString =
+      s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
     val blobRoot: BlobPath = builder build rootString getOrElse fail()
     val execDir: BlobPath = builder build execDirString getOrElse fail()
     val blobFile: BlobPath = builder build fileString getOrElse fail()
-    blobFile.pathStringWithoutPrefix(blobRoot) should equal ("abc123/myworkflow/task1/def4356/execution/stdout")
-    blobFile.pathStringWithoutPrefix(execDir) should equal ("stdout")
-    blobFile.pathStringWithoutPrefix(blobFile) should equal ("")
+    blobFile.pathStringWithoutPrefix(blobRoot) should equal("abc123/myworkflow/task1/def4356/execution/stdout")
+    blobFile.pathStringWithoutPrefix(execDir) should equal("stdout")
+    blobFile.pathStringWithoutPrefix(blobFile) should equal("")
   }
 
   it should "not change a path if it doesn't start with a prefix" in {
     val builder = makeBlobPathBuilder()
     val otherRootString = s"${endpoint.value}/${container.value}/foobar/"
-    val fileString = s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
+    val fileString =
+      s"${endpoint.value}/${container.value}/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
     val otherBlobRoot: BlobPath = builder build otherRootString getOrElse fail()
     val blobFile: BlobPath = builder build fileString getOrElse fail()
-    blobFile.pathStringWithoutPrefix(otherBlobRoot) should equal ("/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout")
+    blobFile.pathStringWithoutPrefix(otherBlobRoot) should equal(
+      "/cromwell-execution/abc123/myworkflow/task1/def4356/execution/stdout"
+    )
   }
 }
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
index 5856e41f97b..59b056f7247 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPath.scala
@@ -6,14 +6,12 @@ import cromwell.core.path.{NioPath, Path}
 
 import java.io.IOException
 
-
 case class DrsPath(drsPath: CloudNioPath, requesterPaysProjectIdOption: Option[String]) extends Path {
 
   override def nioPath: NioPath = drsPath
 
-  override protected def newPath(nioPath: NioPath): Path = {
+  override protected def newPath(nioPath: NioPath): Path =
     DrsPath(nioPath.asInstanceOf[CloudNioPath], requesterPaysProjectIdOption)
-  }
 
   override def pathAsString: String = drsPath.cloudHost
 
@@ -28,9 +26,15 @@ case class DrsPath(drsPath: CloudNioPath, requesterPaysProjectIdOption: Option[S
       case Some(fileAttributes) =>
         fileAttributes.fileHash match {
           case Some(fileHash) => fileHash
-          case None => throw new IOException(s"Error while resolving DRS path $this. The response from DRS Resolver doesn't contain the 'md5' hash for the file.")
+          case None =>
+            throw new IOException(
+              s"Error while resolving DRS path $this. The response from DRS Resolver doesn't contain the 'md5' hash for the file."
+            )
         }
-      case None => throw new IOException(s"Error getting file hash of DRS path $this. Reason: File attributes class DrsCloudNioRegularFileAttributes wasn't defined in DrsCloudNioFileProvider.")
+      case None =>
+        throw new IOException(
+          s"Error getting file hash of DRS path $this. Reason: File attributes class DrsCloudNioRegularFileAttributes wasn't defined in DrsCloudNioFileProvider."
+        )
     }
   }
 }
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
index b464772eec8..4b0b6c9758f 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilder.scala
@@ -9,20 +9,20 @@ import scala.util.{Failure, Success, Try}
 
 case class DrsPathBuilder(fileSystemProvider: DrsCloudNioFileSystemProvider,
                           requesterPaysProjectIdOption: Option[String],
-                          preResolve: Boolean = false,
-                         ) extends PreResolvePathBuilder with StrictLogging {
+                          preResolve: Boolean = false
+) extends PreResolvePathBuilder
+    with StrictLogging {
 
   private val drsScheme: String = fileSystemProvider.getScheme
 
   override def name: String = "DRS"
 
-  override def build(pathAsString: String, pathBuilders: PathBuilders): Try[Path] = {
+  override def build(pathAsString: String, pathBuilders: PathBuilders): Try[Path] =
     if (pathAsString.startsWith(s"$drsScheme://")) {
       Try(createDrsOrOtherPath(pathAsString, pathBuilders))
     } else {
       Failure(new IllegalArgumentException(s"$pathAsString does not have a $drsScheme scheme."))
     }
-  }
 
   private def createDrsOrOtherPath(pathAsString: String, pathBuilders: PathBuilders): Path = {
     def drsPath = DrsPath(fileSystemProvider.getCloudNioPath(pathAsString), requesterPaysProjectIdOption)
@@ -35,17 +35,15 @@ case class DrsPathBuilder(fileSystemProvider: DrsCloudNioFileSystemProvider,
 
   private def maybeCreateOtherPath(pathAsString: String, pathBuilders: PathBuilders): Option[Path] = {
 
-    def logAttempt[A](description: String, attempt: => A): Option[A] = {
+    def logAttempt[A](description: String, attempt: => A): Option[A] =
       logTry(description, Try(attempt))
-    }
 
-    def logTry[A](description: String, tried: Try[A]): Option[A] = {
+    def logTry[A](description: String, tried: Try[A]): Option[A] =
       tried match {
         case Success(result) => Option(result)
         case Failure(exception) =>
           logFailure(description, exception)
       }
-    }
 
     def logFailure(description: String, reason: Any): None.type = {
       logger.debug(s"Unable to $description, will use a DrsPath to access '$pathAsString': $reason")
@@ -66,7 +64,7 @@ case class DrsPathBuilder(fileSystemProvider: DrsCloudNioFileSystemProvider,
       gcsUrlWithNoCreds <- gsUriOption
       gcsPath <- logAttempt(
         s"create a GcsPath for '$gcsUrlWithNoCreds'",
-        PathFactory.buildPath(gcsUrlWithNoCreds, pathBuilders),
+        PathFactory.buildPath(gcsUrlWithNoCreds, pathBuilders)
       )
       // Extra: Make sure the GcsPath _actually_ has permission to access the path
       _ <- logAttempt(s"access '$gcsPath' with GCS credentials", gcsPath.size)
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
index 873874912a0..b39dde25358 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsPathBuilderFactory.scala
@@ -17,8 +17,8 @@ import scala.concurrent.{ExecutionContext, Future}
   */
 class DrsFileSystemConfig(val config: Config)
 
-
-class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, singletonConfig: DrsFileSystemConfig) extends PathBuilderFactory {
+class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, singletonConfig: DrsFileSystemConfig)
+    extends PathBuilderFactory {
 
   private lazy val googleConfiguration: GoogleConfiguration = GoogleConfiguration(globalConfig)
   private lazy val scheme = instanceConfig.getString("auth")
@@ -26,7 +26,9 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
   // For Azure support - this should be the UAMI client id
   private val dataAccessIdentityKey = "data_access_identity"
 
-  override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] = {
+  override def withOptions(
+    options: WorkflowOptions
+  )(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] =
     Future {
       val drsResolverScopes = List(
         // Profile and Email scopes are requirements for interacting with DRS Resolvers
@@ -36,13 +38,20 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
 
       val (googleAuthMode, drsCredentials) = scheme match {
         case "azure" => (None, AzureDrsCredentials(options.get(dataAccessIdentityKey).toOption))
-        case googleAuthScheme => googleConfiguration.auth(googleAuthScheme) match {
-          case Valid(auth) => (
-            Option(auth),
-            GoogleOauthDrsCredentials(auth.credentials(options.get(_).get, drsResolverScopes), singletonConfig.config)
-          )
-          case Invalid(error) => throw new RuntimeException(s"Error while instantiating DRS path builder factory. Errors: ${error.toString}")
-        }
+        case googleAuthScheme =>
+          googleConfiguration.auth(googleAuthScheme) match {
+            case Valid(auth) =>
+              (
+                Option(auth),
+                GoogleOauthDrsCredentials(auth.credentials(options.get(_).get, drsResolverScopes),
+                                          singletonConfig.config
+                )
+              )
+            case Invalid(error) =>
+              throw new RuntimeException(
+                s"Error while instantiating DRS path builder factory. Errors: ${error.toString}"
+              )
+          }
       }
 
       // Unlike PAPI we're not going to fall back to a "default" project from the backend config.
@@ -58,8 +67,7 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
           .getBoolean("override_preresolve_for_test")
           .toOption
           .getOrElse(
-            singletonConfig
-              .config
+            singletonConfig.config
               .getBoolean("resolver.preresolve")
           )
 
@@ -67,15 +75,15 @@ class DrsPathBuilderFactory(globalConfig: Config, instanceConfig: Config, single
         new DrsCloudNioFileSystemProvider(
           singletonConfig.config,
           drsCredentials,
-          DrsReader.readInterpreter(googleAuthMode, options, requesterPaysProjectIdOption),
+          DrsReader.readInterpreter(googleAuthMode, options, requesterPaysProjectIdOption)
         ),
         requesterPaysProjectIdOption,
-        preResolve,
+        preResolve
       )
     }
-  }
 }
 
 case class UrlNotFoundException(scheme: String) extends Exception(s"No $scheme url associated with given DRS path.")
 
-case class DrsResolverResponseMissingKeyException(missingKey: String) extends Exception(s"The response from the DRS Resolver doesn't contain the key '$missingKey'.")
+case class DrsResolverResponseMissingKeyException(missingKey: String)
+    extends Exception(s"The response from the DRS Resolver doesn't contain the key '$missingKey'.")
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
index 3256d6da248..e82790b454c 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsReader.scala
@@ -21,49 +21,48 @@ object DrsReader {
              options: WorkflowOptions,
              requesterPaysProjectIdOption: Option[String],
              drsPathResolver: DrsPathResolver,
-             drsResolverResponse: DrsResolverResponse): IO[DrsReader] = {
+             drsResolverResponse: DrsResolverResponse
+  ): IO[DrsReader] =
     (drsResolverResponse.accessUrl, drsResolverResponse.gsUri, googleAuthMode) match {
       case (Some(accessUrl), _, _) =>
         IO.pure(AccessUrlReader(drsPathResolver, accessUrl))
       case (_, Some(gcsPath), Some(authMode)) =>
-        IO.pure(GcsReader(
-          authMode,
-          options,
-          requesterPaysProjectIdOption,
-          gcsPath,
-          drsResolverResponse.googleServiceAccount,
-        ))
+        IO.pure(
+          GcsReader(
+            authMode,
+            options,
+            requesterPaysProjectIdOption,
+            gcsPath,
+            drsResolverResponse.googleServiceAccount
+          )
+        )
       case (_, Some(_), _) =>
         IO.raiseError(new RuntimeException("GCS URI found in the DRS Resolver response, but no Google auth found!"))
       case _ =>
         IO.raiseError(new RuntimeException(DrsPathResolver.ExtractUriErrorMsg))
     }
-  }
 
   def readInterpreter(googleAuthMode: Option[GoogleAuthMode],
                       options: WorkflowOptions,
-                      requesterPaysProjectIdOption: Option[String])
-                     (drsPathResolver: DrsPathResolver,
-                      drsResolverResponse: DrsResolverResponse): IO[ReadableByteChannel] = {
+                      requesterPaysProjectIdOption: Option[String]
+  )(drsPathResolver: DrsPathResolver, drsResolverResponse: DrsResolverResponse): IO[ReadableByteChannel] =
     for {
       reader <- reader(googleAuthMode, options, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
       channel <- reader.read()
     } yield channel
-  }
 }
 
 case class AccessUrlReader(drsPathResolver: DrsPathResolver, accessUrl: AccessUrl) extends DrsReader {
-  override def read(): IO[ReadableByteChannel] = {
+  override def read(): IO[ReadableByteChannel] =
     drsPathResolver.openChannel(accessUrl)
-  }
 }
 
 case class GcsReader(googleAuthMode: GoogleAuthMode,
                      options: WorkflowOptions,
                      requesterPaysProjectIdOption: Option[String],
                      gsUri: String,
-                     googleServiceAccount: Option[SADataObject],
-                    ) extends DrsReader {
+                     googleServiceAccount: Option[SADataObject]
+) extends DrsReader {
   override def read(): IO[ReadableByteChannel] = {
     val readScopes = List(StorageScopes.DEVSTORAGE_READ_ONLY)
     val credentialsIo = googleServiceAccount match {
@@ -71,7 +70,7 @@ case class GcsReader(googleAuthMode: GoogleAuthMode,
         IO(
           UserServiceAccountMode("drs_resolver_service_account").credentials(
             Map(GoogleAuthMode.UserServiceAccountKey -> googleSA.data.noSpaces),
-            readScopes,
+            readScopes
           )
         )
       case None =>
@@ -86,25 +85,23 @@ case class GcsReader(googleAuthMode: GoogleAuthMode,
 
   private def gcsInputStream(gcsFile: String,
                              credentials: OAuth2Credentials,
-                             requesterPaysProjectIdOption: Option[String],
-                            ): IO[ReadableByteChannel] = {
+                             requesterPaysProjectIdOption: Option[String]
+  ): IO[ReadableByteChannel] =
     for {
       storage <- IO(StorageOptions.newBuilder().setCredentials(credentials).build().getService)
       gcsBucketAndName <- IO(getGcsBucketAndName(gcsFile))
       (bucketName, objectName) = gcsBucketAndName
-      readChannel <- IO(storage.get(bucketName, objectName).reader()) handleErrorWith {
-        throwable =>
-          (requesterPaysProjectIdOption, throwable) match {
-            case (Some(requesterPaysProjectId), storageException: StorageException)
+      readChannel <- IO(storage.get(bucketName, objectName).reader()) handleErrorWith { throwable =>
+        (requesterPaysProjectIdOption, throwable) match {
+          case (Some(requesterPaysProjectId), storageException: StorageException)
               if storageException.getMessage.contains("requester pays bucket but no user project") =>
-              IO(
-                storage
-                  .get(bucketName, objectName, BlobGetOption.userProject(requesterPaysProjectId))
-                  .reader(Blob.BlobSourceOption.userProject(requesterPaysProjectId))
-              )
-            case _ => IO.raiseError(throwable)
-          }
+            IO(
+              storage
+                .get(bucketName, objectName, BlobGetOption.userProject(requesterPaysProjectId))
+                .reader(Blob.BlobSourceOption.userProject(requesterPaysProjectId))
+            )
+          case _ => IO.raiseError(throwable)
+        }
       }
     } yield readChannel
-  }
 }
diff --git a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
index 4aa760f17e1..39115e1633e 100644
--- a/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
+++ b/filesystems/drs/src/main/scala/cromwell/filesystems/drs/DrsResolver.scala
@@ -8,7 +8,6 @@ import cromwell.core.path.{DefaultPathBuilder, Path}
 import org.apache.commons.lang3.exception.ExceptionUtils
 import shapeless.syntax.typeable._
 
-
 object DrsResolver {
   private val GcsScheme: String = "gs"
 
@@ -16,18 +15,18 @@ object DrsResolver {
 
   private val DrsLocalizationPathsContainer = "drs_localization_paths"
 
-  private def resolveError[A](pathAsString: String)(throwable: Throwable): IO[A] = {
+  private def resolveError[A](pathAsString: String)(throwable: Throwable): IO[A] =
     IO.raiseError(
       new RuntimeException(
         s"Error while resolving DRS path: $pathAsString. Error: ${ExceptionUtils.getMessage(throwable)}"
       )
     )
-  }
 
   private def getDrsPathResolver(drsPath: DrsPath): IO[DrsPathResolver] = {
     val drsFileSystemProviderOption = drsPath.drsPath.getFileSystem.provider.cast[DrsCloudNioFileSystemProvider]
 
-    val noFileSystemForDrsError = s"Unable to cast file system provider to DrsCloudNioFileSystemProvider for DRS path $drsPath."
+    val noFileSystemForDrsError =
+      s"Unable to cast file system provider to DrsCloudNioFileSystemProvider for DRS path $drsPath."
 
     for {
       drsFileSystemProvider <- toIO(drsFileSystemProviderOption, noFileSystemForDrsError)
@@ -37,11 +36,17 @@ object DrsResolver {
   case class DrsResolverLocalizationData(gsUri: Option[String],
                                          fileName: Option[String],
                                          bondProvider: Option[String],
-                                         localizationPath: Option[String])
+                                         localizationPath: Option[String]
+  )
 
   private def getDrsResolverLocalizationData(pathAsString: String,
-                                        drsPathResolver: DrsPathResolver): IO[DrsResolverLocalizationData] = {
-    val fields = NonEmptyList.of(DrsResolverField.GsUri, DrsResolverField.FileName, DrsResolverField.BondProvider, DrsResolverField.LocalizationPath)
+                                             drsPathResolver: DrsPathResolver
+  ): IO[DrsResolverLocalizationData] = {
+    val fields = NonEmptyList.of(DrsResolverField.GsUri,
+                                 DrsResolverField.FileName,
+                                 DrsResolverField.BondProvider,
+                                 DrsResolverField.LocalizationPath
+    )
 
     drsPathResolver.resolveDrs(pathAsString, fields) map { r =>
       DrsResolverLocalizationData(r.gsUri, r.fileName, r.bondProvider, r.localizationPath)
@@ -49,7 +54,7 @@ object DrsResolver {
   }
 
   /** Returns the `gsUri` if it ends in the `fileName` and the `bondProvider` is empty. */
-  private def getSimpleGsUri(localizationData: DrsResolverLocalizationData): Option[String] = {
+  private def getSimpleGsUri(localizationData: DrsResolverLocalizationData): Option[String] =
     localizationData match {
       // `gsUri` not defined so no gsUri can be returned.
       case DrsResolverLocalizationData(None, _, _, _) => None
@@ -60,11 +65,9 @@ object DrsResolver {
       // Barring any of the situations above return the `gsUri`.
       case DrsResolverLocalizationData(Some(gsUri), _, _, _) => Option(gsUri)
     }
-  }
 
   /** Returns the `gsUri` if it ends in the `fileName` and the `bondProvider` is empty. */
-  def getSimpleGsUri(pathAsString: String,
-                     drsPathResolver: DrsPathResolver): IO[Option[String]] = {
+  def getSimpleGsUri(pathAsString: String, drsPathResolver: DrsPathResolver): IO[Option[String]] = {
 
     val gsUriIO = getDrsResolverLocalizationData(pathAsString, drsPathResolver) map getSimpleGsUri
 
@@ -72,12 +75,11 @@ object DrsResolver {
   }
 
   /** Returns the `gsUri` if it ends in the `fileName` and the `bondProvider` is empty. */
-  def getSimpleGsUri(drsPath: DrsPath): IO[Option[String]] = {
+  def getSimpleGsUri(drsPath: DrsPath): IO[Option[String]] =
     for {
       drsPathResolver <- getDrsPathResolver(drsPath)
       gsUri <- getSimpleGsUri(drsPath.pathAsString, drsPathResolver)
     } yield gsUri
-  }
 
   def getContainerRelativePath(drsPath: DrsPath): IO[String] = {
     val pathIO = for {
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
index d207bba8d86..5fc3257ed9d 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderFactorySpec.scala
@@ -6,7 +6,7 @@ import cromwell.core.filesystem.CromwellFileSystems
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-class DrsPathBuilderFactorySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers{
+class DrsPathBuilderFactorySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "DrsPathBuilderFactory"
 
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
index 315e51b5d04..65f71e029c7 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsPathBuilderSpec.scala
@@ -51,9 +51,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a path with non-ascii",
       path = s"drs://$bucket/hello/world/with non ascii £€",
@@ -66,9 +65,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a gs uri path with encoded characters",
       path = s"drs://$bucket/hello/world/encoded%20spaces",
@@ -81,9 +79,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a file at the top of the bucket",
       path = s"drs://$bucket/hello",
@@ -96,9 +93,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a path ending in /",
       path = s"drs://$bucket/hello/world/",
@@ -111,7 +107,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
 
     // Special paths
@@ -128,9 +124,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a bucket with a path ..",
       path = s"drs://$bucket/..",
@@ -143,9 +138,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a bucket including . in the path",
       path = s"drs://$bucket/hello/./world",
@@ -158,9 +152,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a bucket including .. in the path",
       path = s"drs://$bucket/hello/../world",
@@ -173,7 +166,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
 
     // Normalized
@@ -190,9 +183,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a bucket with a normalized path ..",
       path = s"drs://$bucket/..",
@@ -205,9 +197,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a bucket including . in the normalized path",
       path = s"drs://$bucket/hello/./world",
@@ -220,9 +211,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a bucket including .. in the normalized path",
       path = s"drs://$bucket/hello/../world",
@@ -235,9 +225,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a bucket with an underscore",
       path = s"drs://hello_underscore/world",
@@ -250,9 +239,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a bucket named .",
       path = s"drs://./hello/world",
@@ -265,9 +253,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "a non ascii bucket name",
       path = s"drs://nonasciibucket£€/hello/world",
@@ -280,9 +267,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "an non-absolute path without a host",
       path = s"drs://blah/",
@@ -295,9 +281,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
-
     GoodPath(
       description = "an absolute path without a host",
       path = s"drs://blah",
@@ -310,7 +295,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
 
     // No spec says this is illegal... so pass it to the DRS Resolver's various GCFs JIC
@@ -326,7 +311,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
 
     // Sample via: https://docs.google.com/document/d/1Wf4enSGOEXD5_AE-uzLoYqjIp5MnePbZ6kYTVFp1WoM/edit
@@ -340,12 +325,11 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
         "drs.data.humancellatlas.org/8aca942c-17f7-4e34-b8fd-3c12e50f9291?version=2019-07-04T151444.185805Z",
       parent = null,
       getParent = null,
-      root =
-        "drs://drs.data.humancellatlas.org/8aca942c-17f7-4e34-b8fd-3c12e50f9291?version=2019-07-04T151444.185805Z",
+      root = "drs://drs.data.humancellatlas.org/8aca942c-17f7-4e34-b8fd-3c12e50f9291?version=2019-07-04T151444.185805Z",
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
+      isAbsolute = false
     ),
 
     // Sample via: https://docs.google.com/document/d/1Wf4enSGOEXD5_AE-uzLoYqjIp5MnePbZ6kYTVFp1WoM/edit
@@ -361,8 +345,8 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false,
-    ),
+      isAbsolute = false
+    )
   )
 
   private def badPaths = Seq(
@@ -371,7 +355,7 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
     BadPath("a https path", "https://hello/world", "https://hello/world does not have a drs scheme."),
     BadPath("a file uri path", "file:///hello/world", "file:///hello/world does not have a drs scheme."),
     BadPath("a relative file path", "hello/world", "hello/world does not have a drs scheme."),
-    BadPath("an absolute file path", "/hello/world", "/hello/world does not have a drs scheme."),
+    BadPath("an absolute file path", "/hello/world", "/hello/world does not have a drs scheme.")
   )
 
   private val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
@@ -387,7 +371,10 @@ class DrsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
   private lazy val fakeCredentials = NoCredentials.getInstance
 
   private lazy val drsPathBuilder = DrsPathBuilder(
-    new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
-    None,
+    new DrsCloudNioFileSystemProvider(drsResolverConfig,
+                                      GoogleOauthDrsCredentials(fakeCredentials, 1.minutes),
+                                      drsReadInterpreter
+    ),
+    None
   )
 }
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
index b5bee55b301..2cee6c49b12 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
@@ -31,7 +31,12 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val googleServiceAccount = None
     val drsResolverResponse = DrsResolverResponse(gsUri = Option(gsUri), googleServiceAccount = googleServiceAccount)
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
+      DrsReader.reader(Option(googleAuthMode),
+                       workflowOptions,
+                       requesterPaysProjectIdOption,
+                       drsPathResolver,
+                       drsResolverResponse
+      )
     readerIo.unsafeRunSync() should be(
       GcsReader(googleAuthMode, workflowOptions, requesterPaysProjectIdOption, gsUri, googleServiceAccount)
     )
@@ -45,7 +50,12 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val accessUrl = AccessUrl("https://host/object/path", Option(Map("hello" -> "world")))
     val drsResolverResponse = DrsResolverResponse(accessUrl = Option(accessUrl))
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
+      DrsReader.reader(Option(googleAuthMode),
+                       workflowOptions,
+                       requesterPaysProjectIdOption,
+                       drsPathResolver,
+                       drsResolverResponse
+      )
     readerIo.unsafeRunSync() should be(
       AccessUrlReader(drsPathResolver, accessUrl)
     )
@@ -58,7 +68,12 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val drsPathResolver = new MockEngineDrsPathResolver()
     val drsResolverResponse = DrsResolverResponse()
     val readerIo =
-      DrsReader.reader(Option(googleAuthMode), workflowOptions, requesterPaysProjectIdOption, drsPathResolver, drsResolverResponse)
+      DrsReader.reader(Option(googleAuthMode),
+                       workflowOptions,
+                       requesterPaysProjectIdOption,
+                       drsPathResolver,
+                       drsResolverResponse
+      )
     the[RuntimeException] thrownBy {
       readerIo.unsafeRunSync()
     } should have message DrsPathResolver.ExtractUriErrorMsg
@@ -80,16 +95,18 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val accessUrl = AccessUrl("https://host/object/path", Option(Map("hello" -> "world")))
     val drsResolverResponse = DrsResolverResponse(accessUrl = Option(accessUrl))
     val channelIo =
-      DrsReader.readInterpreter(Option(MockAuthMode("unused")), WorkflowOptions.empty, None)(drsPathResolver, drsResolverResponse)
+      DrsReader.readInterpreter(Option(MockAuthMode("unused")), WorkflowOptions.empty, None)(drsPathResolver,
+                                                                                             drsResolverResponse
+      )
     val channel = channelIo.unsafeRunSync()
 
     val buffer = ByteBuffer.allocate(exampleBytes.length)
-    channel.isOpen should be (true)
+    channel.isOpen should be(true)
     DrsReaderSpec.readToBuffer(channel, buffer)
     channel.close()
 
     val httpGetCapture = capture[HttpGet]
-    channel.isOpen should be (false)
+    channel.isOpen should be(false)
     buffer.array() should be(exampleBytes)
     verify(httpClient).execute(httpGetCapture.capture)
     verify(httpClient).close()
@@ -104,7 +121,7 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
 
 object DrsReaderSpec {
   @tailrec
-  def readToBuffer(input: ReadableByteChannel, buffer: ByteBuffer): Unit = {
+  def readToBuffer(input: ReadableByteChannel, buffer: ByteBuffer): Unit =
     if (buffer.remaining() > 0) {
       if (input.read(buffer) >= 0) {
         readToBuffer(input, buffer)
@@ -112,5 +129,4 @@ object DrsReaderSpec {
         throw new EOFException(s"input exhausted with ${buffer.remaining()} expected bytes")
       }
     }
-  }
 }
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
index 23dcb1bcd66..ac37fe26f59 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsResolverSpec.scala
@@ -8,7 +8,6 @@ import org.scalatest.matchers.should.Matchers
 
 import scala.jdk.CollectionConverters._
 
-
 class DrsResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   private val drsResolverConfig: Config = ConfigFactory.parseMap(
@@ -21,37 +20,40 @@ class DrsResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   private val mockFileSystemProvider = new MockDrsCloudNioFileSystemProvider(config = drsResolverConfig)
   private val drsPathBuilder = DrsPathBuilder(mockFileSystemProvider, None)
 
-
   behavior of "DrsResolver"
 
   it should "find DRS path from a GCS path" in {
     val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathResolvingGcsPath).get.asInstanceOf[DrsPath]
 
-    DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync() should be (MockDrsPaths.drsRelativePath)
+    DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync() should be(MockDrsPaths.drsRelativePath)
   }
 
   it should "find DRS path from a path replacing characters" in {
     val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathWithNonPathChars).get.asInstanceOf[DrsPath]
 
-    DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync() should be (MockDrsPaths.drsReplacedChar)
+    DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync() should be(MockDrsPaths.drsReplacedChar)
   }
 
   it should "find DRS path from a file name" in {
     val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathResolvingWithFileName).get.asInstanceOf[DrsPath]
 
-    DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync() should be (MockDrsPaths.gcsRelativePathWithFileName)
+    DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync() should be(MockDrsPaths.gcsRelativePathWithFileName)
   }
 
   it should "find DRS path from a localization path" in {
     val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathResolvingWithLocalizationPath).get.asInstanceOf[DrsPath]
 
-    DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync() should be (MockDrsPaths.gcsRelativePathWithFileNameFromLocalizationPath)
+    DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync() should be(
+      MockDrsPaths.gcsRelativePathWithFileNameFromLocalizationPath
+    )
   }
 
   it should "find DRS path from all the paths" in {
     val drsPath = drsPathBuilder.build(MockDrsPaths.drsPathResolvingWithAllThePaths).get.asInstanceOf[DrsPath]
 
-    DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync() should be (MockDrsPaths.gcsRelativePathWithFileNameFromAllThePaths)
+    DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync() should be(
+      MockDrsPaths.gcsRelativePathWithFileNameFromAllThePaths
+    )
   }
 
   it should "throw GcsUrlNotFoundException when DRS path doesn't resolve to at least one GCS url" in {
@@ -69,7 +71,7 @@ class DrsResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
       DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
     } should have message
       s"Error while resolving DRS path: ${drsPath.pathAsString}. " +
-        s"Error: RuntimeException: Unexpected response resolving ${drsPath.pathAsString} " +
-        s"through DRS Resolver url https://drshub-url/drshub_v4. Error: 404 Not Found."
+      s"Error: RuntimeException: Unexpected response resolving ${drsPath.pathAsString} " +
+      s"through DRS Resolver url https://drshub-url/drshub_v4. Error: 404 Not Found."
   }
 }
diff --git a/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/CromwellFtpFileSystems.scala b/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/CromwellFtpFileSystems.scala
index 70593c41e68..27fb1698fd7 100644
--- a/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/CromwellFtpFileSystems.scala
+++ b/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/CromwellFtpFileSystems.scala
@@ -25,19 +25,21 @@ object CromwellFtpFileSystems {
   }
 
   def parseConfig(config: Config): FtpFileSystemsConfiguration = {
-    val cacheTTL = validate[FiniteDuration] { config.as[FiniteDuration]("cache-ttl") }
-    val leaseTimeout = validate[Option[FiniteDuration]] { config.getAs[FiniteDuration]("obtain-connection-timeout") }
+    val cacheTTL = validate[FiniteDuration](config.as[FiniteDuration]("cache-ttl"))
+    val leaseTimeout = validate[Option[FiniteDuration]](config.getAs[FiniteDuration]("obtain-connection-timeout"))
     // Cannot be less than 2, otherwise we can't copy files as we need 2 connections to copy a file (one for downstream and one for upstream)
-    val capacity: ErrorOr[Int] = validate[Int] { config.as[Int]("max-connection-per-server-per-user") } map { c => Math.max(2, c) }
-    val idleConnectionTimeout = validate[FiniteDuration] { config.as[FiniteDuration]("idle-connection-timeout") }
-    val connectionPort = validate[Int] { config.as[Int]("connection-port") }
-    val connectionMode = validate[ConnectionMode] { config.as[ConnectionMode]("connection-mode") }
+    val capacity: ErrorOr[Int] = validate[Int](config.as[Int]("max-connection-per-server-per-user")) map { c =>
+      Math.max(2, c)
+    }
+    val idleConnectionTimeout = validate[FiniteDuration](config.as[FiniteDuration]("idle-connection-timeout"))
+    val connectionPort = validate[Int](config.as[Int]("connection-port"))
+    val connectionMode = validate[ConnectionMode](config.as[ConnectionMode]("connection-mode"))
 
     (cacheTTL, leaseTimeout, capacity, idleConnectionTimeout, connectionPort, connectionMode)
       .mapN(FtpFileSystemsConfiguration.apply)
       .unsafe("Failed to parse FTP configuration")
   }
-  
+
   val Default = new CromwellFtpFileSystems(FtpFileSystems.Default)
 }
 
diff --git a/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpInstanceConfiguration.scala b/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpInstanceConfiguration.scala
index 6af3c8863c5..23c8504872f 100644
--- a/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpInstanceConfiguration.scala
+++ b/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpInstanceConfiguration.scala
@@ -25,12 +25,12 @@ case class FtpInstanceConfiguration(ftpCredentials: FtpCredentials)
 
 object FtpInstanceConfiguration {
   lazy val Default = FtpInstanceConfiguration(FtpAnonymousCredentials)
-  
+
   def apply(conf: Config): FtpInstanceConfiguration = {
     val credentials: ErrorOr[FtpCredentials] = conf.getAs[Config]("auth") map { authConfig =>
-      val username = validate { authConfig.as[String]("username") }
-      val password = validate { authConfig.as[String]("password") }
-      val account = validate { authConfig.getAs[String]("account") }
+      val username = validate(authConfig.as[String]("username"))
+      val password = validate(authConfig.as[String]("password"))
+      val account = validate(authConfig.getAs[String]("account"))
       (username, password, account) mapN FtpAuthenticatedCredentials.apply
     } getOrElse Default.ftpCredentials.validNel
 
diff --git a/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpPathBuilder.scala b/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpPathBuilder.scala
index 409a4027437..ed708ef41e0 100644
--- a/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpPathBuilder.scala
+++ b/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpPathBuilder.scala
@@ -16,7 +16,7 @@ object FtpPathBuilder {
 case class FtpPathBuilder(fileSystemProvider: CloudNioFileSystemProvider) extends PathBuilder {
   override def name = "FTP"
 
-  override def build(string: String) = {
+  override def build(string: String) =
     if (string == "ftp://") Failure(new IllegalArgumentException(s"$string does not have a valid host"))
     else {
       Try(URI.create(UrlEscapers.urlFragmentEscaper().escape(string))) flatMap { uri =>
@@ -31,5 +31,4 @@ case class FtpPathBuilder(fileSystemProvider: CloudNioFileSystemProvider) extend
         }
       }
     }
-  }
 }
diff --git a/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpPathBuilderFactory.scala b/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpPathBuilderFactory.scala
index cd599349d27..da55640d4e1 100644
--- a/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpPathBuilderFactory.scala
+++ b/filesystems/ftp/src/main/scala/cromwell/filesystems/ftp/FtpPathBuilderFactory.scala
@@ -19,24 +19,37 @@ object FtpPathBuilderFactory {
   def credentialsFromWorkflowOptions(workflowOptions: WorkflowOptions) = {
     def getValue(key: String) = workflowOptions.get(key).toOption
 
-    (getValue(WorkflowOptions.FtpUsername), getValue(WorkflowOptions.FtpPassword), getValue(WorkflowOptions.FtpAccount)) match {
+    (getValue(WorkflowOptions.FtpUsername),
+     getValue(WorkflowOptions.FtpPassword),
+     getValue(WorkflowOptions.FtpAccount)
+    ) match {
       case (Some(username), Some(password), account) => Option(FtpAuthenticatedCredentials(username, password, account))
       case _ => None
     }
   }
 }
 
-class FtpPathBuilderFactory(globalConfig: Config, instanceConfig: Config, cromwellFtpFileSystems: CromwellFtpFileSystems) extends PathBuilderFactory {
-  private [ftp] lazy val configFtpConfiguration = FtpInstanceConfiguration(instanceConfig)
-  private lazy val defaultFtpProvider = new FtpCloudNioFileSystemProvider(instanceConfig, configFtpConfiguration.ftpCredentials, cromwellFtpFileSystems.ftpFileSystems)
-
-  override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext) = Future.successful {
-    val provider = credentialsFromWorkflowOptions(options) match {
-      case Some(overriddenCredentials) =>
-        new FtpCloudNioFileSystemProvider(instanceConfig, overriddenCredentials, cromwellFtpFileSystems.ftpFileSystems)
-      case _ => defaultFtpProvider
+class FtpPathBuilderFactory(globalConfig: Config,
+                            instanceConfig: Config,
+                            cromwellFtpFileSystems: CromwellFtpFileSystems
+) extends PathBuilderFactory {
+  private[ftp] lazy val configFtpConfiguration = FtpInstanceConfiguration(instanceConfig)
+  private lazy val defaultFtpProvider = new FtpCloudNioFileSystemProvider(instanceConfig,
+                                                                          configFtpConfiguration.ftpCredentials,
+                                                                          cromwellFtpFileSystems.ftpFileSystems
+  )
+
+  override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext) =
+    Future.successful {
+      val provider = credentialsFromWorkflowOptions(options) match {
+        case Some(overriddenCredentials) =>
+          new FtpCloudNioFileSystemProvider(instanceConfig,
+                                            overriddenCredentials,
+                                            cromwellFtpFileSystems.ftpFileSystems
+          )
+        case _ => defaultFtpProvider
+      }
+
+      FtpPathBuilder(provider)
     }
-
-    FtpPathBuilder(provider)
-  }
 }
diff --git a/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/CromwellFtpFileSystemsSpec.scala b/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/CromwellFtpFileSystemsSpec.scala
index 90229c30cc2..ea1985797e3 100644
--- a/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/CromwellFtpFileSystemsSpec.scala
+++ b/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/CromwellFtpFileSystemsSpec.scala
@@ -13,14 +13,13 @@ class CromwellFtpFileSystemsSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
   behavior of "CromwellFtpFileSystemsSpec"
 
   it should "parse configuration" in {
-    val config = ConfigFactory.parseString(
-      """cache-ttl = 10 days
-        |obtain-connection-timeout = 12 hours
-        |max-connection-per-server-per-user = 1
-        |idle-connection-timeout = 14 hours
-        |connection-port: 212
-        |connection-mode = "active" """.stripMargin)
-    
+    val config = ConfigFactory.parseString("""cache-ttl = 10 days
+                                             |obtain-connection-timeout = 12 hours
+                                             |max-connection-per-server-per-user = 1
+                                             |idle-connection-timeout = 14 hours
+                                             |connection-port: 212
+                                             |connection-mode = "active" """.stripMargin)
+
     val fs = new CromwellFtpFileSystems(config)
     fs.ftpFileSystems.config.cacheTTL shouldBe 10.days
     fs.ftpFileSystems.config.leaseTimeout shouldBe Some(12.hours)
diff --git a/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/FtpInstanceConfigurationSpec.scala b/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/FtpInstanceConfigurationSpec.scala
index 5fa5de22ea2..09ce6ec863c 100644
--- a/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/FtpInstanceConfigurationSpec.scala
+++ b/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/FtpInstanceConfigurationSpec.scala
@@ -15,21 +15,19 @@ class FtpInstanceConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec
   }
 
   it should "parse authenticated credentials" in {
-    FtpInstanceConfiguration(ConfigFactory.parseString(
-      """
-        |auth {
-        |  username = "me"
-        |  password = "mot de passe"
-        |}
+    FtpInstanceConfiguration(ConfigFactory.parseString("""
+                                                         |auth {
+                                                         |  username = "me"
+                                                         |  password = "mot de passe"
+                                                         |}
       """.stripMargin)).ftpCredentials shouldBe FtpAuthenticatedCredentials("me", "mot de passe", None)
 
-    FtpInstanceConfiguration(ConfigFactory.parseString(
-      """
-        |auth {
-        |  username = "me"
-        |  password = "mot de passe"
-        |  account = "account"
-        |}
+    FtpInstanceConfiguration(ConfigFactory.parseString("""
+                                                         |auth {
+                                                         |  username = "me"
+                                                         |  password = "mot de passe"
+                                                         |  account = "account"
+                                                         |}
       """.stripMargin)).ftpCredentials shouldBe FtpAuthenticatedCredentials("me", "mot de passe", Option("account"))
   }
 
diff --git a/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/FtpPathSpec.scala b/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/FtpPathSpec.scala
index 9224b4f4124..0c164127514 100644
--- a/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/FtpPathSpec.scala
+++ b/filesystems/ftp/src/test/scala/cromwell/filesystems/ftp/FtpPathSpec.scala
@@ -16,9 +16,10 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
 
   behavior of "FtpPathSpec"
 
-  val pathBuilderFactory = new FtpPathBuilderFactory(ConfigFactory.empty(), ConfigFactory.empty(), CromwellFtpFileSystems.Default) {
-    override private [ftp] lazy val configFtpConfiguration = new FtpInstanceConfiguration(FtpAnonymousCredentials)
-  }
+  val pathBuilderFactory =
+    new FtpPathBuilderFactory(ConfigFactory.empty(), ConfigFactory.empty(), CromwellFtpFileSystems.Default) {
+      override private[ftp] lazy val configFtpConfiguration = new FtpInstanceConfiguration(FtpAnonymousCredentials)
+    }
 
   val pathBuilder =
     Await.result(pathBuilderFactory.withOptions(WorkflowOptions.empty)(null, null), 1.second)
@@ -41,7 +42,10 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
     ("ftp://ftp-server.com/path/to/my//dir", "ftp://ftp-server.com/path/to/my/dir/file", "dir/file"),
     ("ftp://ftp-server.com/path/to/my//dir", "ftp://ftp-server.com/path/to/my/dir//file", "dir//file"),
     ("ftp://ftp-server.com/path/to/my/dir", "ftp://ftp-server.com/path/./to/my/dir/file", "./to/my/dir/file"),
-    ("ftp://ftp-server.com/path/to/my/dir/with/file", "ftp://ftp-server.com/path/to/other/dir/with/file", "other/dir/with/file")
+    ("ftp://ftp-server.com/path/to/my/dir/with/file",
+     "ftp://ftp-server.com/path/to/other/dir/with/file",
+     "other/dir/with/file"
+    )
   )
 
   private def goodPaths = Seq(
@@ -57,8 +61,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "with spaces",
       getFileName = s"ftp://ftp-server.com/with spaces",
       getNameCount = 3,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path with non-ascii",
       path = s"ftp://ftp-server.com/hello/world/with non ascii £€",
@@ -71,8 +75,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "with non ascii £€",
       getFileName = s"ftp://ftp-server.com/with non ascii £€",
       getNameCount = 3,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "an ftp uri path with encoded characters",
       path = s"ftp://ftp-server.com/hello/world/encoded%20spaces",
@@ -85,8 +89,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "encoded%20spaces",
       getFileName = s"ftp://ftp-server.com/encoded%20spaces",
       getNameCount = 3,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a hostname only path (root path)",
       path = s"ftp://ftp-server.com",
@@ -99,8 +103,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a hostname only path ending in a /",
       path = s"ftp://ftp-server.com/",
@@ -113,8 +117,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "",
       getFileName = null,
       getNameCount = 0,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a file at the top of the hostname",
       path = s"ftp://ftp-server.com/hello",
@@ -127,8 +131,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "hello",
       getFileName = s"ftp://ftp-server.com/hello",
       getNameCount = 1,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path ending in /",
       path = s"ftp://ftp-server.com/hello/world/",
@@ -141,7 +145,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "world",
       getFileName = s"ftp://ftp-server.com/world",
       getNameCount = 2,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // Special paths
 
@@ -157,8 +162,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "",
       getFileName = s"ftp://ftp-server.com/.",
       getNameCount = 1,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a hostname with a path ..",
       path = s"ftp://ftp-server.com/..",
@@ -171,8 +176,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "",
       getFileName = s"ftp://ftp-server.com/..",
       getNameCount = 1,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a bucket including . in the path",
       path = s"ftp://ftp-server.com/hello/./world",
@@ -185,8 +190,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "world",
       getFileName = s"ftp://ftp-server.com/world",
       getNameCount = 3,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path including .. in the path",
       path = s"ftp://ftp-server.com/hello/../world",
@@ -199,7 +204,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "world",
       getFileName = s"ftp://ftp-server.com/world",
       getNameCount = 3,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // Normalized
 
@@ -215,8 +221,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "",
       getFileName = null,
       getNameCount = 0,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path with a normalized path ..",
       path = s"ftp://ftp-server.com/..",
@@ -229,8 +235,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "",
       getFileName = null,
       getNameCount = 1,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a path including . in the normalized path",
       path = s"ftp://ftp-server.com/hello/./world",
@@ -243,8 +249,8 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "world",
       getFileName = s"ftp://ftp-server.com/world",
       getNameCount = 2,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path including .. in the normalized path",
       path = s"ftp://ftp-server.com/hello/../world",
@@ -257,14 +263,18 @@ class FtpPathSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       name = "world",
       getFileName = s"ftp://ftp-server.com/world",
       getNameCount = 1,
-      isAbsolute = true),
+      isAbsolute = true
+    )
   )
 
   private def badPaths = Seq(
     BadPath("an empty path", "", " does not have an ftp scheme"),
     BadPath("a hostless path", "ftp://", "ftp:// does not have a valid host"),
     BadPath("a bucket named .", "ftp://./hello/world", "ftp://./hello/world does not have a valid host"),
-    BadPath("a non ascii bucket name", "ftp://nonasciibucket£€/hello/world", "ftp://nonasciibucket£€/hello/world does not have a valid host"),
+    BadPath("a non ascii bucket name",
+            "ftp://nonasciibucket£€/hello/world",
+            "ftp://nonasciibucket£€/hello/world does not have a valid host"
+    ),
     BadPath("a https path", "https://hello/world", "https://hello/world does not have an ftp scheme"),
     BadPath("a file uri path", "file:///hello/world", "file:///hello/world does not have an ftp scheme"),
     BadPath("a relative file path", "hello/world", "hello/world does not have an ftp scheme"),
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsEnhancedRequest.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsEnhancedRequest.scala
index 76887905387..638d23e50ec 100644
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsEnhancedRequest.scala
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsEnhancedRequest.scala
@@ -11,20 +11,19 @@ import java.io.FileNotFoundException
 object GcsEnhancedRequest {
 
   // If the request fails because no project was passed, recover the request, this time setting the project
-  def recoverFromProjectNotProvided[A](path: GcsPath, f: Boolean => A) = {
-    IO(f(false)).handleErrorWith({
-        // Only retry with the the project if the error is right
-        case error: StorageException if isProjectNotProvidedError(error) =>
-          IO(f(true))
-        // Use NoSuchFileException for better error reporting
-        case e: StorageException if e.getCode == StatusCodes.NotFound.intValue =>
-          IO.raiseError(new FileNotFoundException(s"File not found: ${path.pathAsString}"))
-        case e: GoogleJsonResponseException if isProjectNotProvidedError(e) =>
-          IO(f(true))
-        case e: GoogleJsonResponseException if e.getStatusCode == StatusCodes.NotFound.intValue =>
-          IO.raiseError(new FileNotFoundException(s"File not found: ${path.pathAsString}"))
-        case e =>
-          IO.raiseError(e)
-      })
-  }
+  def recoverFromProjectNotProvided[A](path: GcsPath, f: Boolean => A) =
+    IO(f(false)).handleErrorWith {
+      // Only retry with the the project if the error is right
+      case error: StorageException if isProjectNotProvidedError(error) =>
+        IO(f(true))
+      // Use NoSuchFileException for better error reporting
+      case e: StorageException if e.getCode == StatusCodes.NotFound.intValue =>
+        IO.raiseError(new FileNotFoundException(s"File not found: ${path.pathAsString}"))
+      case e: GoogleJsonResponseException if isProjectNotProvidedError(e) =>
+        IO(f(true))
+      case e: GoogleJsonResponseException if e.getStatusCode == StatusCodes.NotFound.intValue =>
+        IO.raiseError(new FileNotFoundException(s"File not found: ${path.pathAsString}"))
+      case e =>
+        IO.raiseError(e)
+    }
 }
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilder.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilder.scala
index 00aee93e537..2a618e48aa0 100644
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilder.scala
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilder.scala
@@ -29,11 +29,11 @@ import scala.language.postfixOps
 import scala.util.{Failure, Try}
 object GcsPathBuilder {
   /*
-    * Provides some level of validation of GCS bucket names
-    * This is meant to alert the user early if they mistyped a gcs path in their workflow / inputs and not to validate
-    * exact bucket syntax, which is done by GCS.
-    * See https://cloud.google.com/storage/docs/naming for full spec
-  */
+   * Provides some level of validation of GCS bucket names
+   * This is meant to alert the user early if they mistyped a gcs path in their workflow / inputs and not to validate
+   * exact bucket syntax, which is done by GCS.
+   * See https://cloud.google.com/storage/docs/naming for full spec
+   */
   private val GcsBucketPattern =
     """
       (?x)                                      # Turn on comments and whitespace insensitivity
@@ -57,13 +57,12 @@ object GcsPathBuilder {
     override def errorMessage = s"Cloud Storage URIs must have 'gs' scheme: $pathString"
   }
   final case class InvalidFullGcsPath(pathString: String) extends InvalidGcsPath {
-    override def errorMessage: String = {
+    override def errorMessage: String =
       s"""
          |The path '$pathString' does not seem to be a valid GCS path.
          |Please check that it starts with gs:// and that the bucket and object follow GCS naming guidelines at
          |https://cloud.google.com/storage/docs/naming.
       """.stripMargin.replace("\n", " ").trim
-    }
   }
   final case class UnparseableGcsPath(pathString: String, throwable: Throwable) extends InvalidGcsPath {
     override def errorMessage: String =
@@ -79,7 +78,7 @@ object GcsPathBuilder {
     case _ => None
   }
 
-  def validateGcsPath(string: String): GcsPathValidation = {
+  def validateGcsPath(string: String): GcsPathValidation =
     Try {
       val uri = URI.create(UrlEscapers.urlFragmentEscaper().escape(string))
       if (uri.getScheme == null) PossiblyValidRelativeGcsPath
@@ -89,39 +88,32 @@ object GcsPathBuilder {
         } else ValidFullGcsPath(uri.getHost, uri.getPath)
       } else InvalidScheme(string)
     } recover { case t => UnparseableGcsPath(string, t) } get
-  }
 
-  def isGcsPath(nioPath: NioPath): Boolean = {
+  def isGcsPath(nioPath: NioPath): Boolean =
     nioPath.getFileSystem.provider().getScheme.equalsIgnoreCase(CloudStorageFileSystem.URI_SCHEME)
-  }
 
   def fromAuthMode(authMode: GoogleAuthMode,
                    applicationName: String,
                    retrySettings: RetrySettings,
                    cloudStorageConfiguration: CloudStorageConfiguration,
                    options: WorkflowOptions,
-                   defaultProject: Option[String])(implicit as: ActorSystem, ec: ExecutionContext): Future[GcsPathBuilder] = {
+                   defaultProject: Option[String]
+  )(implicit as: ActorSystem, ec: ExecutionContext): Future[GcsPathBuilder] =
     authMode.retryCredentials(options, List(StorageScopes.DEVSTORAGE_FULL_CONTROL)) map { credentials =>
-      fromCredentials(credentials,
-        applicationName,
-        retrySettings,
-        cloudStorageConfiguration,
-        options,
-        defaultProject
-      )
+      fromCredentials(credentials, applicationName, retrySettings, cloudStorageConfiguration, options, defaultProject)
     }
-  }
 
   def fromCredentials(credentials: Credentials,
                       applicationName: String,
                       retrySettings: RetrySettings,
                       cloudStorageConfiguration: CloudStorageConfiguration,
                       options: WorkflowOptions,
-                      defaultProject: Option[String]): GcsPathBuilder = {
+                      defaultProject: Option[String]
+  ): GcsPathBuilder = {
     // Grab the google project from Workflow Options if specified and set
     // that to be the project used by the StorageOptions Builder. If it's not
     // specified use the default project mentioned in config file
-    val project: Option[String] =  options.get("google_project").toOption match {
+    val project: Option[String] = options.get("google_project").toOption match {
       case Some(googleProject) => Option(googleProject)
       case None => defaultProject
     }
@@ -139,8 +131,9 @@ object GcsPathBuilder {
 
 class GcsPathBuilder(apiStorage: com.google.api.services.storage.Storage,
                      cloudStorageConfiguration: CloudStorageConfiguration,
-                     storageOptions: StorageOptions) extends PathBuilder {
-  private [gcs] val projectId = storageOptions.getProjectId
+                     storageOptions: StorageOptions
+) extends PathBuilder {
+  private[gcs] val projectId = storageOptions.getProjectId
   private lazy val cloudStorage = storageOptions.getService
 
   /**
@@ -153,7 +146,7 @@ class GcsPathBuilder(apiStorage: com.google.api.services.storage.Storage,
     *
     * Also see https://github.com/GoogleCloudPlatform/google-cloud-java/issues/1343
     */
-  def build(string: String): Try[GcsPath] = {
+  def build(string: String): Try[GcsPath] =
     validateGcsPath(string) match {
       case ValidFullGcsPath(bucket, path) =>
         Try {
@@ -161,18 +154,19 @@ class GcsPathBuilder(apiStorage: com.google.api.services.storage.Storage,
           val cloudStoragePath = fileSystem.getPath(path)
           GcsPath(cloudStoragePath, apiStorage, cloudStorage, projectId)
         }
-      case PossiblyValidRelativeGcsPath => Failure(new IllegalArgumentException(s"""Path "$string" does not have a gcs scheme"""))
+      case PossiblyValidRelativeGcsPath =>
+        Failure(new IllegalArgumentException(s"""Path "$string" does not have a gcs scheme"""))
       case invalid: InvalidGcsPath => Failure(new IllegalArgumentException(invalid.errorMessage))
     }
-  }
 
   override def name: String = "Google Cloud Storage"
 }
 
-case class GcsPath private[gcs](nioPath: NioPath,
-                                apiStorage: com.google.api.services.storage.Storage,
-                                cloudStorage: com.google.cloud.storage.Storage,
-                                projectId: String) extends Path {
+case class GcsPath private[gcs] (nioPath: NioPath,
+                                 apiStorage: com.google.api.services.storage.Storage,
+                                 cloudStorage: com.google.cloud.storage.Storage,
+                                 projectId: String
+) extends Path {
   lazy val objectBlobId: Try[BlobId] = Try {
     val bucketName = cloudStoragePath.bucket
     val objectName = cloudStoragePath.toRealPath().toString
@@ -202,13 +196,12 @@ case class GcsPath private[gcs](nioPath: NioPath,
     BlobId.of(bucketName, objectName)
   }
 
-  lazy val bucketOrObjectBlobId: Try[BlobId] = {
+  lazy val bucketOrObjectBlobId: Try[BlobId] =
     Try {
       val bucketName = cloudStoragePath.bucket
       val objectName = cloudStoragePath.toRealPath().toString
       BlobId.of(bucketName, objectName)
     }
-  }
 
   override protected def newPath(nioPath: NioPath): GcsPath = GcsPath(nioPath, apiStorage, cloudStorage, projectId)
 
@@ -218,9 +211,9 @@ case class GcsPath private[gcs](nioPath: NioPath,
     s"${CloudStorageFileSystem.URI_SCHEME}://$host/$path"
   }
 
-  override def writeContent(content: String)
-                           (openOptions: OpenOptions, codec: Codec, compressPayload: Boolean)
-                           (implicit ec: ExecutionContext): GcsPath.this.type = {
+  override def writeContent(content: String)(openOptions: OpenOptions, codec: Codec, compressPayload: Boolean)(implicit
+    ec: ExecutionContext
+  ): GcsPath.this.type = {
     def request(withProject: Boolean) = {
       val builder = BlobInfo.newBuilder(objectBlobId.get).setContentType(ContentTypes.`text/plain(UTF-8)`.value)
       if (compressPayload) {
@@ -243,14 +236,14 @@ case class GcsPath private[gcs](nioPath: NioPath,
   }
 
   override def mediaInputStream(implicit ec: ExecutionContext): InputStream = {
-    def request(withProject: Boolean) = {
+    def request(withProject: Boolean) =
       // Use apiStorage here instead of cloudStorage, because apiStorage throws now if the bucket has requester pays,
       // whereas cloudStorage creates the input stream anyway and only throws one `read` is called (which only happens in NioFlow)
-      apiStorage.objects()
+      apiStorage
+        .objects()
         .get(objectBlobId.get.getBucket, objectBlobId.get.getName)
         .setUserProject(withProject.option(projectId).orNull)
         .executeMediaAsInputStream()
-    }
     // Since the NIO interface is synchronous we need to run this synchronously here. It is however wrapped in a Future
     // in the NioFlow so we don't need to worry about exceptions
     runOnEc(recoverFromProjectNotProvided(this, request)).unsafeRunSync()
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilderFactory.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilderFactory.scala
index 74d88b05476..f63ef73b4dd 100644
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilderFactory.scala
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GcsPathBuilderFactory.scala
@@ -14,8 +14,7 @@ import org.threeten.bp.Duration
 
 import scala.concurrent.{ExecutionContext, Future}
 
-final case class GcsPathBuilderFactory(globalConfig: Config, instanceConfig: Config)
-  extends PathBuilderFactory {
+final case class GcsPathBuilderFactory(globalConfig: Config, instanceConfig: Config) extends PathBuilderFactory {
   import net.ceedubs.ficus.Ficus._
   // Parse the configuration and create a GoogleConfiguration
   val googleConf: GoogleConfiguration = GoogleConfiguration(globalConfig)
@@ -30,8 +29,9 @@ final case class GcsPathBuilderFactory(globalConfig: Config, instanceConfig: Con
 
   val defaultProject = instanceConfig.as[Option[String]]("project")
 
-  lazy val defaultRetrySettings: RetrySettings = {
-    RetrySettings.newBuilder()
+  lazy val defaultRetrySettings: RetrySettings =
+    RetrySettings
+      .newBuilder()
       .setMaxAttempts(maxAttempts)
       .setTotalTimeout(Duration.ofSeconds(30))
       .setInitialRetryDelay(Duration.ofMillis(100))
@@ -41,9 +41,8 @@ final case class GcsPathBuilderFactory(globalConfig: Config, instanceConfig: Con
       .setRpcTimeoutMultiplier(1.1)
       .setMaxRpcTimeout(Duration.ofSeconds(5))
       .build()
-  }
 
-  def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[GcsPathBuilder] = {
+  def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[GcsPathBuilder] =
     GcsPathBuilder.fromAuthMode(
       authMode,
       applicationName,
@@ -52,7 +51,6 @@ final case class GcsPathBuilderFactory(globalConfig: Config, instanceConfig: Con
       options,
       defaultProject
     )
-  }
 }
 
 object GcsPathBuilderFactory {
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleUtil.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleUtil.scala
index 481a3f36d10..8149c822670 100644
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleUtil.scala
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/GoogleUtil.scala
@@ -11,43 +11,43 @@ import cromwell.core.{CromwellFatalExceptionMarker, WorkflowOptions}
 import scala.concurrent.{ExecutionContext, Future}
 
 object GoogleUtil {
+
   /**
     * Extract status code from an exception if it's a com.google.api.client.http.HttpResponseException
     */
-  def extractStatusCode(exception: Throwable): Option[Int] = {
+  def extractStatusCode(exception: Throwable): Option[Int] =
     exception match {
       case t: HttpResponseException => Option(t.getStatusCode)
       case t: BaseServiceException => Option(t.getCode)
       case _ => None
     }
-  }
 
   implicit class EnhancedGoogleAuthMode(val googleAuthMode: GoogleAuthMode) extends AnyVal {
+
     /**
       * Retries getting the credentials three times.
       *
       * There is nothing GCS specific about this method. This package just happens to be the lowest level with access
       * to core's version of Retry + cloudSupport's implementation of GoogleAuthMode.
       */
-    def retryCredentials(options: WorkflowOptions, scopes: Iterable[String])
-                        (implicit actorSystem: ActorSystem, executionContext: ExecutionContext): Future[Credentials] = {
-      def credential(): Credentials = {
-
-        try {
+    def retryCredentials(options: WorkflowOptions, scopes: Iterable[String])(implicit
+      actorSystem: ActorSystem,
+      executionContext: ExecutionContext
+    ): Future[Credentials] = {
+      def credential(): Credentials =
+        try
           googleAuthMode.credentials(options.get(_).get, scopes)
-        } catch {
+        catch {
           case exception: OptionLookupException =>
             throw new IllegalArgumentException(s"Missing parameters in workflow options: ${exception.key}", exception)
               with CromwellFatalExceptionMarker
         }
-      }
 
-      def isFatal(throwable: Throwable): Boolean = {
+      def isFatal(throwable: Throwable): Boolean =
         throwable match {
           case _: IllegalArgumentException => Option(throwable.getCause).exists(isFatal)
           case _ => GoogleAuthMode.isFatal(throwable)
         }
-      }
 
       Retry.withRetry(
         () => Future(credential()),
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/RequesterPaysErrors.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/RequesterPaysErrors.scala
index 26ee0868c65..cf693698d18 100644
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/RequesterPaysErrors.scala
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/RequesterPaysErrors.scala
@@ -12,7 +12,7 @@ object RequesterPaysErrors {
 
   def isProjectNotProvidedError(storageException: StorageException) =
     storageException.getCode == BucketIsRequesterPaysErrorCode &&
-    StringUtils.contains(storageException.getMessage, BucketIsRequesterPaysErrorMessage)
+      StringUtils.contains(storageException.getMessage, BucketIsRequesterPaysErrorMessage)
 
   def isProjectNotProvidedError(googleJsonError: GoogleJsonError) =
     googleJsonError.getCode == BucketIsRequesterPaysErrorCode &&
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/batch/GcsBatchCommandBuilder.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/batch/GcsBatchCommandBuilder.scala
index 5c7b2b724d3..77c15d09a84 100644
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/batch/GcsBatchCommandBuilder.scala
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/batch/GcsBatchCommandBuilder.scala
@@ -7,32 +7,32 @@ import cromwell.filesystems.gcs.GcsPath
 import scala.util.Try
 
 private case object PartialGcsBatchCommandBuilder extends PartialIoCommandBuilder {
-  override def sizeCommand: PartialFunction[Path, Try[GcsBatchSizeCommand]] = {
-    case gcsPath: GcsPath => GcsBatchSizeCommand.forPath(gcsPath)
+  override def sizeCommand: PartialFunction[Path, Try[GcsBatchSizeCommand]] = { case gcsPath: GcsPath =>
+    GcsBatchSizeCommand.forPath(gcsPath)
   }
-  
+
   override def deleteCommand: PartialFunction[(Path, Boolean), Try[GcsBatchDeleteCommand]] = {
     case (gcsPath: GcsPath, swallowIoExceptions) => GcsBatchDeleteCommand.forPath(gcsPath, swallowIoExceptions)
   }
-  
+
   override def copyCommand: PartialFunction[(Path, Path), Try[GcsBatchCopyCommand]] = {
     case (gcsSrc: GcsPath, gcsDest: GcsPath) => GcsBatchCopyCommand.forPaths(gcsSrc, gcsDest)
   }
-  
-  override def hashCommand: PartialFunction[Path, Try[GcsBatchCrc32Command]] = {
-    case gcsPath: GcsPath => GcsBatchCrc32Command.forPath(gcsPath)
+
+  override def hashCommand: PartialFunction[Path, Try[GcsBatchCrc32Command]] = { case gcsPath: GcsPath =>
+    GcsBatchCrc32Command.forPath(gcsPath)
   }
 
-  override def touchCommand: PartialFunction[Path, Try[GcsBatchTouchCommand]] = {
-    case gcsPath: GcsPath => GcsBatchTouchCommand.forPath(gcsPath)
+  override def touchCommand: PartialFunction[Path, Try[GcsBatchTouchCommand]] = { case gcsPath: GcsPath =>
+    GcsBatchTouchCommand.forPath(gcsPath)
   }
 
-  override def existsCommand: PartialFunction[Path, Try[GcsBatchExistsCommand]] = {
-    case gcsPath: GcsPath => GcsBatchExistsCommand.forPath(gcsPath)
+  override def existsCommand: PartialFunction[Path, Try[GcsBatchExistsCommand]] = { case gcsPath: GcsPath =>
+    GcsBatchExistsCommand.forPath(gcsPath)
   }
 
-  override def isDirectoryCommand: PartialFunction[Path, Try[GcsBatchIsDirectoryCommand]] = {
-    case gcsPath: GcsPath => GcsBatchIsDirectoryCommand.forPath(gcsPath)
+  override def isDirectoryCommand: PartialFunction[Path, Try[GcsBatchIsDirectoryCommand]] = { case gcsPath: GcsPath =>
+    GcsBatchIsDirectoryCommand.forPath(gcsPath)
   }
 }
 
diff --git a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/batch/GcsBatchIoCommand.scala b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/batch/GcsBatchIoCommand.scala
index ed07fdb3605..f8d1239992a 100644
--- a/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/batch/GcsBatchIoCommand.scala
+++ b/filesystems/gcs/src/main/scala/cromwell/filesystems/gcs/batch/GcsBatchIoCommand.scala
@@ -24,6 +24,7 @@ import scala.util.Try
   * @tparam U Return type of the Google response
   */
 sealed trait GcsBatchIoCommand[T, U] extends IoCommand[T] {
+
   /**
     * StorageRequest operation to be executed by this command
     */
@@ -50,7 +51,9 @@ sealed trait GcsBatchIoCommand[T, U] extends IoCommand[T] {
   /**
     * Override to handle a failure differently and potentially return a successful response.
     */
-  def onFailure(googleJsonError: GoogleJsonError, httpHeaders: HttpHeaders): Option[Either[T, GcsBatchIoCommand[T, U]]] = None
+  def onFailure(googleJsonError: GoogleJsonError,
+                httpHeaders: HttpHeaders
+  ): Option[Either[T, GcsBatchIoCommand[T, U]]] = None
 
   /**
     * Use to signal that the request has failed because the user project was not set and that it can be retried with it.
@@ -60,25 +63,26 @@ sealed trait GcsBatchIoCommand[T, U] extends IoCommand[T] {
 
 sealed trait SingleFileGcsBatchIoCommand[T, U] extends GcsBatchIoCommand[T, U] with SingleFileIoCommand[T] {
   override def file: GcsPath
-  //noinspection MutatorLikeMethodIsParameterless
+  // noinspection MutatorLikeMethodIsParameterless
   def setUserProject: Boolean
   def userProject: String = setUserProject.option(file.projectId).orNull
 }
 
 case class GcsBatchCopyCommand(
-                                override val source: GcsPath,
-                                sourceBlob: BlobId,
-                                override val destination: GcsPath,
-                                destinationBlob: BlobId,
-                                rewriteToken: Option[String] = None,
-                                setUserProject: Boolean = false
-                              )
-  extends IoCopyCommand(source, destination) with GcsBatchIoCommand[Unit, RewriteResponse] {
+  override val source: GcsPath,
+  sourceBlob: BlobId,
+  override val destination: GcsPath,
+  destinationBlob: BlobId,
+  rewriteToken: Option[String] = None,
+  setUserProject: Boolean = false
+) extends IoCopyCommand(source, destination)
+    with GcsBatchIoCommand[Unit, RewriteResponse] {
   override def commandDescription: String = s"GcsBatchCopyCommand source '$source' destination '$destination' " +
     s"setUserProject '$setUserProject' rewriteToken '$rewriteToken'"
 
   override def operation: StorageRequest[RewriteResponse] = {
-    val rewriteOperation = source.apiStorage.objects()
+    val rewriteOperation = source.apiStorage
+      .objects()
       .rewrite(sourceBlob.getBucket, sourceBlob.getName, destinationBlob.getBucket, destinationBlob.getName, null)
       .setUserProject(setUserProject.option(source.projectId).orNull)
 
@@ -92,13 +96,14 @@ case class GcsBatchCopyCommand(
     */
   def withRewriteToken(rewriteToken: String): GcsBatchCopyCommand = copy(rewriteToken = Option(rewriteToken))
 
-  override def onSuccess(response: RewriteResponse, httpHeaders: HttpHeaders): ErrorOr[Either[Unit, GcsBatchCopyCommand]] = {
+  override def onSuccess(response: RewriteResponse,
+                         httpHeaders: HttpHeaders
+  ): ErrorOr[Either[Unit, GcsBatchCopyCommand]] =
     if (response.getDone) {
       mapGoogleResponse(response) map Left.apply
     } else {
       Right(withRewriteToken(response.getRewriteToken)).validNel
     }
-  }
 
   override def mapGoogleResponse(response: RewriteResponse): ErrorOr[Unit] = ().validNel
 
@@ -106,31 +111,29 @@ case class GcsBatchCopyCommand(
 }
 
 object GcsBatchCopyCommand {
-  def forPaths(source: GcsPath, destination: GcsPath): Try[GcsBatchCopyCommand] = {
+  def forPaths(source: GcsPath, destination: GcsPath): Try[GcsBatchCopyCommand] =
     for {
       sourceBlob <- source.objectBlobId
       destinationBlob <- destination.objectBlobId
     } yield GcsBatchCopyCommand(source, sourceBlob, destination, destinationBlob)
-  }
 }
 
 case class GcsBatchDeleteCommand(
-                                  override val file: GcsPath,
-                                  blob: BlobId,
-                                  override val swallowIOExceptions: Boolean,
-                                  setUserProject: Boolean = false
-                                ) extends IoDeleteCommand(file, swallowIOExceptions) with SingleFileGcsBatchIoCommand[Unit, Void] {
-  override def operation: StorageRequest[Void] = {
+  override val file: GcsPath,
+  blob: BlobId,
+  override val swallowIOExceptions: Boolean,
+  setUserProject: Boolean = false
+) extends IoDeleteCommand(file, swallowIOExceptions)
+    with SingleFileGcsBatchIoCommand[Unit, Void] {
+  override def operation: StorageRequest[Void] =
     file.apiStorage.objects().delete(blob.getBucket, blob.getName).setUserProject(userProject)
-  }
 
   override def mapGoogleResponse(response: Void): ErrorOr[Unit] = ().validNel
 
   override def onFailure(googleJsonError: GoogleJsonError,
-                         httpHeaders: HttpHeaders,
-                        ): Option[Either[Unit, GcsBatchDeleteCommand]] = {
+                         httpHeaders: HttpHeaders
+  ): Option[Either[Unit, GcsBatchDeleteCommand]] =
     if (swallowIOExceptions) Option(Left(())) else None
-  }
   override def withUserProject: GcsBatchDeleteCommand = this.copy(setUserProject = true)
 
   override def commandDescription: String = s"GcsBatchDeleteCommand file '$file' swallowIOExceptions " +
@@ -138,9 +141,8 @@ case class GcsBatchDeleteCommand(
 }
 
 object GcsBatchDeleteCommand {
-  def forPath(file: GcsPath, swallowIOExceptions: Boolean): Try[GcsBatchDeleteCommand] = {
+  def forPath(file: GcsPath, swallowIOExceptions: Boolean): Try[GcsBatchDeleteCommand] =
     file.objectBlobId.map(GcsBatchDeleteCommand(file, _, swallowIOExceptions))
-  }
 }
 
 /**
@@ -149,21 +151,18 @@ object GcsBatchDeleteCommand {
 sealed trait GcsBatchGetCommand[T] extends SingleFileGcsBatchIoCommand[T, StorageObject] {
   def file: GcsPath
   def blob: BlobId
-  override def operation: StorageRequest[StorageObject] = {
+  override def operation: StorageRequest[StorageObject] =
     file.apiStorage.objects().get(blob.getBucket, blob.getName).setUserProject(userProject)
-  }
 }
 
-case class GcsBatchSizeCommand(override val file: GcsPath,
-                               override val blob: BlobId,
-                               setUserProject: Boolean = false,
-                              ) extends IoSizeCommand(file) with GcsBatchGetCommand[Long] {
-  override def mapGoogleResponse(response: StorageObject): ErrorOr[Long] = {
+case class GcsBatchSizeCommand(override val file: GcsPath, override val blob: BlobId, setUserProject: Boolean = false)
+    extends IoSizeCommand(file)
+    with GcsBatchGetCommand[Long] {
+  override def mapGoogleResponse(response: StorageObject): ErrorOr[Long] =
     Option(response.getSize) match {
       case None => s"'${file.pathAsString}' in project '${file.projectId}' returned null size".invalidNel
       case Some(size) => size.longValue().validNel
     }
-  }
 
   override def withUserProject: GcsBatchSizeCommand = this.copy(setUserProject = true)
 
@@ -171,21 +170,18 @@ case class GcsBatchSizeCommand(override val file: GcsPath,
 }
 
 object GcsBatchSizeCommand {
-  def forPath(file: GcsPath): Try[GcsBatchSizeCommand] = {
+  def forPath(file: GcsPath): Try[GcsBatchSizeCommand] =
     file.objectBlobId.map(GcsBatchSizeCommand(file, _))
-  }
 }
 
-case class GcsBatchCrc32Command(override val file: GcsPath,
-                                override val blob: BlobId,
-                                setUserProject: Boolean = false,
-                               ) extends IoHashCommand(file) with GcsBatchGetCommand[String] {
-  override def mapGoogleResponse(response: StorageObject): ErrorOr[String] = {
+case class GcsBatchCrc32Command(override val file: GcsPath, override val blob: BlobId, setUserProject: Boolean = false)
+    extends IoHashCommand(file)
+    with GcsBatchGetCommand[String] {
+  override def mapGoogleResponse(response: StorageObject): ErrorOr[String] =
     Option(response.getCrc32c) match {
       case None => s"'${file.pathAsString}' in project '${file.projectId}' returned null CRC32C checksum".invalidNel
       case Some(crc32c) => crc32c.validNel
     }
-  }
 
   override def withUserProject: GcsBatchCrc32Command = this.copy(setUserProject = true)
 
@@ -193,15 +189,13 @@ case class GcsBatchCrc32Command(override val file: GcsPath,
 }
 
 object GcsBatchCrc32Command {
-  def forPath(file: GcsPath): Try[GcsBatchCrc32Command] = {
+  def forPath(file: GcsPath): Try[GcsBatchCrc32Command] =
     file.objectBlobId.map(GcsBatchCrc32Command(file, _))
-  }
 }
 
-case class GcsBatchTouchCommand(override val file: GcsPath,
-                                override val blob: BlobId,
-                                setUserProject: Boolean = false,
-                               ) extends IoTouchCommand(file) with GcsBatchGetCommand[Unit] {
+case class GcsBatchTouchCommand(override val file: GcsPath, override val blob: BlobId, setUserProject: Boolean = false)
+    extends IoTouchCommand(file)
+    with GcsBatchGetCommand[Unit] {
   override def mapGoogleResponse(response: StorageObject): ErrorOr[Unit] = ().validNel
 
   override def withUserProject: GcsBatchTouchCommand = this.copy(setUserProject = true)
@@ -210,9 +204,8 @@ case class GcsBatchTouchCommand(override val file: GcsPath,
 }
 
 object GcsBatchTouchCommand {
-  def forPath(file: GcsPath): Try[GcsBatchTouchCommand] = {
+  def forPath(file: GcsPath): Try[GcsBatchTouchCommand] =
     file.objectBlobId.map(GcsBatchTouchCommand(file, _))
-  }
 }
 
 /*
@@ -220,47 +213,46 @@ object GcsBatchTouchCommand {
  * Specifically, list objects that have this path as a prefix. Since we don't really care about what's inside here,
  * set max results to 1 to avoid unnecessary payload.
  */
-case class GcsBatchIsDirectoryCommand(override val file: GcsPath,
-                                      blob: BlobId,
-                                      setUserProject: Boolean = false,
-                                     )
-  extends IoIsDirectoryCommand(file) with SingleFileGcsBatchIoCommand[Boolean, Objects] {
-  override def operation: StorageRequest[Objects] = {
-    file.apiStorage.objects().list(blob.getBucket).setPrefix(blob.getName.ensureSlashed).setMaxResults(1L).setUserProject(userProject)
-  }
-
-  override def mapGoogleResponse(response: Objects): ErrorOr[Boolean] = {
+case class GcsBatchIsDirectoryCommand(override val file: GcsPath, blob: BlobId, setUserProject: Boolean = false)
+    extends IoIsDirectoryCommand(file)
+    with SingleFileGcsBatchIoCommand[Boolean, Objects] {
+  override def operation: StorageRequest[Objects] =
+    file.apiStorage
+      .objects()
+      .list(blob.getBucket)
+      .setPrefix(blob.getName.ensureSlashed)
+      .setMaxResults(1L)
+      .setUserProject(userProject)
+
+  override def mapGoogleResponse(response: Objects): ErrorOr[Boolean] =
     // Wrap in an Option because getItems can (always ?) return null if there are no objects
     Option(response.getItems).map(_.asScala).exists(_.nonEmpty).validNel
-  }
   override def withUserProject: GcsBatchIsDirectoryCommand = this.copy(setUserProject = true)
   override def commandDescription: String = s"GcsBatchIsDirectoryCommand file '$file' setUserProject '$setUserProject'"
 }
 
 object GcsBatchIsDirectoryCommand {
-  def forPath(file: GcsPath): Try[GcsBatchIsDirectoryCommand] = {
+  def forPath(file: GcsPath): Try[GcsBatchIsDirectoryCommand] =
     file.bucketOrObjectBlobId.map(GcsBatchIsDirectoryCommand(file, _))
-  }
 }
 
-case class GcsBatchExistsCommand(override val file: GcsPath,
-                                 override val blob: BlobId,
-                                 setUserProject: Boolean = false,
-                                ) extends IoExistsCommand(file) with GcsBatchGetCommand[Boolean] {
+case class GcsBatchExistsCommand(override val file: GcsPath, override val blob: BlobId, setUserProject: Boolean = false)
+    extends IoExistsCommand(file)
+    with GcsBatchGetCommand[Boolean] {
   override def mapGoogleResponse(response: StorageObject): ErrorOr[Boolean] = true.validNel
 
-  override def onFailure(googleJsonError: GoogleJsonError, httpHeaders: HttpHeaders): Option[Either[Boolean, GcsBatchIoCommand[Boolean, StorageObject]]] = {
+  override def onFailure(googleJsonError: GoogleJsonError,
+                         httpHeaders: HttpHeaders
+  ): Option[Either[Boolean, GcsBatchIoCommand[Boolean, StorageObject]]] =
     // If the object can't be found, don't fail the request but just return false as we were testing for existence
     if (googleJsonError.getCode == 404) Option(Left(false)) else None
-  }
   override def withUserProject: GcsBatchExistsCommand = this.copy(setUserProject = true)
   override def commandDescription: String = s"GcsBatchExistsCommand file '$file' setUserProject '$setUserProject'"
 }
 
 object GcsBatchExistsCommand {
-  def forPath(file: GcsPath): Try[GcsBatchExistsCommand] = {
+  def forPath(file: GcsPath): Try[GcsBatchExistsCommand] =
     file.objectBlobId.map(GcsBatchExistsCommand(file, _))
-  }
 }
 
 /** A GcsBatchIoCommand for use in tests. */
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsEnhancedRequestSpec.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsEnhancedRequestSpec.scala
index 01a75e21ee5..be91888a610 100644
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsEnhancedRequestSpec.scala
+++ b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsEnhancedRequestSpec.scala
@@ -22,9 +22,11 @@ class GcsEnhancedRequestSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
       CloudStorageFileSystem.forBucket("bucket").getPath("test"),
       mock[com.google.api.services.storage.Storage],
       mock[com.google.cloud.storage.Storage],
-      "GcsEnhancedRequest-project",
+      "GcsEnhancedRequest-project"
     )
-  val requesterPaysException = new StorageException(BucketIsRequesterPaysErrorCode, "Bucket is a requester pays bucket but no user project provided.")
+  val requesterPaysException = new StorageException(BucketIsRequesterPaysErrorCode,
+                                                    "Bucket is a requester pays bucket but no user project provided."
+  )
 
   it should "attempt first without project, and not retry if the requests succeeds" in {
     val testFunction = mock[Boolean => String]
@@ -54,7 +56,9 @@ class GcsEnhancedRequestSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
     when(testFunction.apply(false)).thenThrow(requesterPaysException)
     // We expect it to be called a second time with withProject = true this time, and fail for another reason
     when(testFunction.apply(true)).thenThrow(new RuntimeException("it really doesn't work"))
-    a[RuntimeException] should be thrownBy GcsEnhancedRequest.recoverFromProjectNotProvided(path, testFunction).unsafeRunSync()
+    a[RuntimeException] should be thrownBy GcsEnhancedRequest
+      .recoverFromProjectNotProvided(path, testFunction)
+      .unsafeRunSync()
   }
 
   it should "not retry requests if the error does not match" in {
@@ -62,7 +66,9 @@ class GcsEnhancedRequestSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
     // Throw an unrelated exception, should only be called once
     when(testFunction.apply(false)).thenThrow(new RuntimeException("it really doesn't work"))
-    a[RuntimeException] should be thrownBy GcsEnhancedRequest.recoverFromProjectNotProvided(path, testFunction).unsafeRunSync()
+    a[RuntimeException] should be thrownBy GcsEnhancedRequest
+      .recoverFromProjectNotProvided(path, testFunction)
+      .unsafeRunSync()
     verify(testFunction).apply(false)
     verify(testFunction).apply(anyBoolean)
   }
@@ -72,7 +78,9 @@ class GcsEnhancedRequestSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
     // Throw an unrelated exception, should only be called once
     when(testFunction.apply(false)).thenThrow(new StorageException(404, "gs://does/not/exist"))
-    a[FileNotFoundException] should be thrownBy GcsEnhancedRequest.recoverFromProjectNotProvided(path, testFunction).unsafeRunSync()
+    a[FileNotFoundException] should be thrownBy GcsEnhancedRequest
+      .recoverFromProjectNotProvided(path, testFunction)
+      .unsafeRunSync()
     verify(testFunction).apply(false)
     verify(testFunction).apply(anyBoolean)
   }
@@ -86,7 +94,9 @@ class GcsEnhancedRequestSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
     // Throw an unrelated exception, should only be called once
     when(testFunction.apply(false)).thenAnswer(_ => throw new GoogleJsonResponseException(builder, error))
-    a[FileNotFoundException] should be thrownBy GcsEnhancedRequest.recoverFromProjectNotProvided(path, testFunction).unsafeRunSync()
+    a[FileNotFoundException] should be thrownBy GcsEnhancedRequest
+      .recoverFromProjectNotProvided(path, testFunction)
+      .unsafeRunSync()
     verify(testFunction).apply(false)
     verify(testFunction).apply(anyBoolean)
   }
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala
index 22e63ea0f32..a275d163e4a 100644
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala
+++ b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/GcsPathBuilderSpec.scala
@@ -15,7 +15,12 @@ import org.scalatest.prop.Tables.Table
 
 import java.io.ByteArrayInputStream
 
-class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with PathBuilderSpecUtils with ServiceAccountTestSupport {
+class GcsPathBuilderSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with PathBuilderSpecUtils
+    with ServiceAccountTestSupport {
 
   behavior of "GcsPathBuilder"
 
@@ -64,8 +69,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "with spaces",
       getFileName = s"gs://$bucket/with spaces",
       getNameCount = 3,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path with non-ascii",
       path = s"gs://$bucket/hello/world/with non ascii £€",
@@ -78,8 +83,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "with non ascii £€",
       getFileName = s"gs://$bucket/with non ascii £€",
       getNameCount = 3,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a gs uri path with encoded characters",
       path = s"gs://$bucket/hello/world/encoded%20spaces",
@@ -92,8 +97,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "encoded%20spaces",
       getFileName = s"gs://$bucket/encoded%20spaces",
       getNameCount = 3,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a bucket only path",
       path = s"gs://$bucket",
@@ -106,8 +111,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = s"gs://$bucket/",
       getNameCount = 1,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a bucket only path ending in a /",
       path = s"gs://$bucket/",
@@ -120,8 +125,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 0,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a file at the top of the bucket",
       path = s"gs://$bucket/hello",
@@ -134,8 +139,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "hello",
       getFileName = s"gs://$bucket/hello",
       getNameCount = 1,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a path ending in /",
       path = s"gs://$bucket/hello/world/",
@@ -148,7 +153,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "world",
       getFileName = s"gs://$bucket/world",
       getNameCount = 2,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // Special paths
 
@@ -164,8 +170,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = s"gs://$bucket/.",
       getNameCount = 1,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a bucket with a path ..",
       path = s"gs://$bucket/..",
@@ -178,8 +184,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = s"gs://$bucket/..",
       getNameCount = 1,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a bucket including . in the path",
       path = s"gs://$bucket/hello/./world",
@@ -192,8 +198,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "world",
       getFileName = s"gs://$bucket/world",
       getNameCount = 3,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a bucket including .. in the path",
       path = s"gs://$bucket/hello/../world",
@@ -206,7 +212,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "world",
       getFileName = s"gs://$bucket/world",
       getNameCount = 3,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // Normalized
 
@@ -222,8 +229,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 0,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a bucket with a normalized path ..",
       path = s"gs://$bucket/..",
@@ -236,8 +243,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = s"gs://$bucket/",
       getNameCount = 1,
-      isAbsolute = false),
-
+      isAbsolute = false
+    ),
     GoodPath(
       description = "a bucket including . in the normalized path",
       path = s"gs://$bucket/hello/./world",
@@ -250,8 +257,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "world",
       getFileName = s"gs://$bucket/world",
       getNameCount = 2,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a bucket including .. in the normalized path",
       path = s"gs://$bucket/hello/../world",
@@ -264,8 +271,8 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "world",
       getFileName = s"gs://$bucket/world",
       getNameCount = 1,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a bucket with an underscore",
       path = s"gs://hello_underscore/world",
@@ -278,24 +285,34 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "world",
       getFileName = s"gs://hello_underscore/world",
       getNameCount = 1,
-      isAbsolute = true)
+      isAbsolute = true
+    )
   )
 
   private def badPaths = Seq(
     BadPath("an empty path", "", "Path \"\" does not have a gcs scheme"),
-    BadPath("an bucketless path", "gs://", "The specified GCS path 'gs://' does not parse as a URI.\nExpected authority at index 5: gs://"),
-    BadPath("a bucket named .", "gs://./hello/world", "The path 'gs://./hello/world' does not seem to be a valid GCS path. Please check that it starts with gs:// and that the bucket and object follow GCS naming guidelines at https://cloud.google.com/storage/docs/naming."),
-    BadPath("a non ascii bucket name", "gs://nonasciibucket£€/hello/world",
-      "The path 'gs://nonasciibucket£€/hello/world' does not seem to be a valid GCS path. Please check that it starts with gs:// and that the bucket and object follow GCS naming guidelines at https://cloud.google.com/storage/docs/naming."),
+    BadPath("an bucketless path",
+            "gs://",
+            "The specified GCS path 'gs://' does not parse as a URI.\nExpected authority at index 5: gs://"
+    ),
+    BadPath(
+      "a bucket named .",
+      "gs://./hello/world",
+      "The path 'gs://./hello/world' does not seem to be a valid GCS path. Please check that it starts with gs:// and that the bucket and object follow GCS naming guidelines at https://cloud.google.com/storage/docs/naming."
+    ),
+    BadPath(
+      "a non ascii bucket name",
+      "gs://nonasciibucket£€/hello/world",
+      "The path 'gs://nonasciibucket£€/hello/world' does not seem to be a valid GCS path. Please check that it starts with gs:// and that the bucket and object follow GCS naming guidelines at https://cloud.google.com/storage/docs/naming."
+    ),
     BadPath("a https path", "https://hello/world", "Cloud Storage URIs must have 'gs' scheme: https://hello/world"),
     BadPath("a file uri path", "file:///hello/world", "Cloud Storage URIs must have 'gs' scheme: file:///hello/world"),
     BadPath("a relative file path", "hello/world", "Path \"hello/world\" does not have a gcs scheme"),
     BadPath("an absolute file path", "/hello/world", "Path \"/hello/world\" does not have a gcs scheme")
   )
 
-  private lazy val pathBuilder = {
+  private lazy val pathBuilder =
     MockGcsPathBuilder.instance
-  }
 
   it should "not mix up credentials" in {
     def retrySettings: RetrySettings = RetrySettings.newBuilder().build()
@@ -304,22 +321,25 @@ class GcsPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
     val noCredentials = NoCredentials.getInstance()
     val noCredentialsPathBuilder: GcsPathBuilder = {
       val noCredentialsStorage = GcsStorage.gcsStorage("no-credentials", noCredentials, retrySettings)
-      val noCredentialsStorageOptions = GcsStorage.gcsStorageOptions(noCredentials, retrySettings, Option("proj-no-credentials"))
+      val noCredentialsStorageOptions =
+        GcsStorage.gcsStorageOptions(noCredentials, retrySettings, Option("proj-no-credentials"))
 
       new GcsPathBuilder(noCredentialsStorage, cloudStorageConfig, noCredentialsStorageOptions)
     }
 
-    val serviceAccountCredentials = ServiceAccountCredentials.fromStream(
-      new ByteArrayInputStream(serviceAccountJsonContents.getBytes))
+    val serviceAccountCredentials =
+      ServiceAccountCredentials.fromStream(new ByteArrayInputStream(serviceAccountJsonContents.getBytes))
     val serviceAccountPathBuilder: GcsPathBuilder = {
       val serviceAccountStorage = GcsStorage.gcsStorage("service-account", serviceAccountCredentials, retrySettings)
-      val serviceAccountStorageOptions = GcsStorage.gcsStorageOptions(serviceAccountCredentials, retrySettings, Option("proj-service-account"))
+      val serviceAccountStorageOptions =
+        GcsStorage.gcsStorageOptions(serviceAccountCredentials, retrySettings, Option("proj-service-account"))
 
       new GcsPathBuilder(serviceAccountStorage, cloudStorageConfig, serviceAccountStorageOptions)
     }
 
     def credentialsForPath(gcsPath: GcsPath): Credentials = {
-      val cloudFilesystemProvider = gcsPath.nioPath.getFileSystem.provider().asInstanceOf[CloudStorageFileSystemProvider]
+      val cloudFilesystemProvider =
+        gcsPath.nioPath.getFileSystem.provider().asInstanceOf[CloudStorageFileSystemProvider]
       val storageOptionsField = cloudFilesystemProvider.getClass.getDeclaredField("storageOptions")
       storageOptionsField.setAccessible(true)
       val storageOptions = storageOptionsField.get(cloudFilesystemProvider)
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/MockGcsPathBuilder.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/MockGcsPathBuilder.scala
index c42b7b324d0..8834d4c6476 100644
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/MockGcsPathBuilder.scala
+++ b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/MockGcsPathBuilder.scala
@@ -12,12 +12,13 @@ import scala.concurrent.ExecutionContext
 
 object MockGcsPathBuilder {
   implicit val ec = ExecutionContext.fromExecutor(Executors.newSingleThreadExecutor())
-  private def makeStorageOptions(project: Option[String] = Option("cromwell-test")) = GcsStorage.gcsStorageOptions(NoCredentials.getInstance(), RetrySettings.newBuilder().build(), project)
+  private def makeStorageOptions(project: Option[String] = Option("cromwell-test")) =
+    GcsStorage.gcsStorageOptions(NoCredentials.getInstance(), RetrySettings.newBuilder().build(), project)
   private val storageOptions = makeStorageOptions()
   private val apiStorage = GcsStorage.gcsStorage("cromwell-test-app", storageOptions)
 
   lazy val instance = new GcsPathBuilder(apiStorage, CloudStorageConfiguration.DEFAULT, storageOptions)
-  
+
   def withOptions(workflowOptions: WorkflowOptions) = {
     val customStorageOptions = makeStorageOptions(workflowOptions.get("google_project").toOption)
     new GcsPathBuilder(apiStorage, GcsStorage.DefaultCloudStorageConfiguration, customStorageOptions)
diff --git a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/batch/GcsBatchIoCommandSpec.scala b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/batch/GcsBatchIoCommandSpec.scala
index d54662f3535..a4c936a463d 100644
--- a/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/batch/GcsBatchIoCommandSpec.scala
+++ b/filesystems/gcs/src/test/scala/cromwell/filesystems/gcs/batch/GcsBatchIoCommandSpec.scala
@@ -182,7 +182,9 @@ class GcsBatchIoCommandSpec extends AnyFlatSpec with Matchers with BeforeAndAfte
 
     response.setDone(false)
     response.setRewriteToken("token")
-    command.onSuccess(response, new HttpHeaders()).toEither.toOption.get.toOption.get.rewriteToken should be(Option("token"))
+    command.onSuccess(response, new HttpHeaders()).toEither.toOption.get.toOption.get.rewriteToken should be(
+      Option("token")
+    )
 
     command.onFailure(new GoogleJsonError(), new HttpHeaders()) should be(None)
   }
diff --git a/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala b/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala
index 89bb22021df..fa1861dd81a 100644
--- a/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala
+++ b/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala
@@ -16,19 +16,20 @@ object HttpPathBuilder {
   def accepts(url: String): Boolean = url.matches("^http[s]?://.*")
 }
 
-
 class HttpPathBuilder extends PathBuilder {
   override def name: String = "HTTP"
 
-  override def build(pathAsString: String): Try[Path] = {
+  override def build(pathAsString: String): Try[Path] =
     if (HttpPathBuilder.accepts(pathAsString)) Try {
       HttpPath(Paths.get(pathAsString))
-    } else {
+    }
+    else {
       Failure(new IllegalArgumentException(s"$pathAsString does not have an http or https scheme"))
     }
-  }
 
-  def content(url: String)(implicit actorContext: ActorContext, actorMaterializer: ActorMaterializer): Future[NioPath] = {
+  def content(
+    url: String
+  )(implicit actorContext: ActorContext, actorMaterializer: ActorMaterializer): Future[NioPath] = {
     implicit val actorSystem: ActorSystem = actorContext.system
     implicit val executionContext: ExecutionContext = actorContext.dispatcher
 
@@ -54,19 +55,19 @@ case class HttpPath(nioPath: NioPath) extends Path {
 
   override def pathWithoutScheme: String = pathAsString.replaceFirst("http[s]?://", "")
 
-  def fetchSize(implicit executionContext: ExecutionContext, actorSystem: ActorSystem): Future[Long] = {
+  def fetchSize(implicit executionContext: ExecutionContext, actorSystem: ActorSystem): Future[Long] =
     Http().singleRequest(HttpRequest(uri = pathAsString, method = HttpMethods.HEAD)).map { response =>
       response.discardEntityBytes()
-      val length = if (response.status.isSuccess())
-        response.entity.contentLengthOption
-      else
-        None
+      val length =
+        if (response.status.isSuccess())
+          response.entity.contentLengthOption
+        else
+          None
       length.getOrElse(
         throw new RuntimeException(
           s"Couldn't fetch size for $pathAsString, missing Content-Length header or path doesn't exist (HTTP ${response.status.toString()})."
         )
       )
     }
-  }
 
 }
diff --git a/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilderFactory.scala b/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilderFactory.scala
index 7a42c113921..bf65ed34a31 100644
--- a/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilderFactory.scala
+++ b/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilderFactory.scala
@@ -8,10 +8,10 @@ import cromwell.core.path.{PathBuilder, PathBuilderFactory}
 import scala.concurrent.{ExecutionContext, Future}
 
 class HttpPathBuilderFactory(globalConfig: Config, instanceConfig: Config) extends PathBuilderFactory {
-  override def withOptions(options: WorkflowOptions)
-                          (implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] = {
+  override def withOptions(
+    options: WorkflowOptions
+  )(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] =
     Future {
       new HttpPathBuilder
     }
-  }
 }
diff --git a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/S3PathBuilder.scala b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/S3PathBuilder.scala
index 0713afa1a71..4de28288cd6 100644
--- a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/S3PathBuilder.scala
+++ b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/S3PathBuilder.scala
@@ -76,13 +76,12 @@ object S3PathBuilder {
     override def errorMessage: String = s"S3 URIs must have 's3' scheme: $pathString"
   }
   final case class InvalidFullS3Path(pathString: String) extends InvalidS3Path {
-    override def errorMessage: String = {
+    override def errorMessage: String =
       s"""
          |The path '$pathString' does not seem to be a valid S3 path.
          |Please check that it starts with s3:// and that the bucket and object follow S3 naming guidelines at
          |https://docs.aws.amazon.com/AmazonS3/latest/dev/BucketRestrictions.html
       """.stripMargin.replace("\n", " ").trim
-    }
   }
   final case class UnparseableS3Path(pathString: String, throwable: Throwable) extends InvalidS3Path {
     override def errorMessage: String =
@@ -98,7 +97,7 @@ object S3PathBuilder {
   def pathToUri(string: String): URI =
     URI.create(UrlEscapers.urlFragmentEscaper.escape(string))
 
-  def validatePath(string: String): S3PathValidation = {
+  def validatePath(string: String): S3PathValidation =
     Try {
       val uri = pathToUri(string)
       if (uri.getScheme == null) { PossiblyValidRelativeS3Path }
@@ -108,56 +107,46 @@ object S3PathBuilder {
         } else { ValidFullS3Path(uri.getHost, uri.getPath) }
       } else { InvalidScheme(string) }
     } recover { case t => UnparseableS3Path(string, t) } get
-  }
 
   def fromAuthMode(authMode: AwsAuthMode,
                    configuration: S3Configuration,
                    options: WorkflowOptions,
-                   storageRegion: Option[Region])(implicit ec: ExecutionContext): Future[S3PathBuilder] = {
+                   storageRegion: Option[Region]
+  )(implicit ec: ExecutionContext): Future[S3PathBuilder] = {
     val provider = authMode.provider()
 
     // Other backends needed retry here. In case we need retry, we'll return
     // a future. This will allow us to add capability without changing signature
-    Future(fromProvider(provider,
-      configuration,
-      options,
-      storageRegion
-    ))
+    Future(fromProvider(provider, configuration, options, storageRegion))
   }
 
   def fromProvider(provider: AwsCredentialsProvider,
                    configuration: S3Configuration,
                    options: WorkflowOptions,
-                   storageRegion: Option[Region]): S3PathBuilder = {
+                   storageRegion: Option[Region]
+  ): S3PathBuilder =
     new S3PathBuilder(configuration)
-  }
 }
 
-class S3PathBuilder(configuration: S3Configuration
-                     ) extends PathBuilder {
+class S3PathBuilder(configuration: S3Configuration) extends PathBuilder {
   // Tries to create a new S3Path from a String representing an absolute s3 path: s3://<bucket>[/<key>].
-  def build(string: String): Try[S3Path] = {
+  def build(string: String): Try[S3Path] =
     validatePath(string) match {
       case ValidFullS3Path(bucket, path) =>
         Try {
           val s3Path = new S3FileSystemProvider()
             .getFileSystem(URI.create("s3:////"), System.getenv)
             .getPath(s"""/$bucket/$path""")
-          S3Path(s3Path, bucket,
-            new AmazonS3ClientFactory().getS3Client(URI.create("s3:////"), System.getProperties))
+          S3Path(s3Path, bucket, new AmazonS3ClientFactory().getS3Client(URI.create("s3:////"), System.getProperties))
         }
       case PossiblyValidRelativeS3Path => Failure(new IllegalArgumentException(s"$string does not have a s3 scheme"))
       case invalid: InvalidS3Path => Failure(new IllegalArgumentException(invalid.errorMessage))
     }
-  }
 
   override def name: String = "s3"
 }
 
-case class S3Path private[s3](nioPath: NioPath,
-                               bucket: String,
-                               client: S3Client
-                               ) extends Path {
+case class S3Path private[s3] (nioPath: NioPath, bucket: String, client: S3Client) extends Path {
   override protected def newPath(nioPath: NioPath): S3Path = S3Path(nioPath, bucket, client)
 
   override def pathAsString: String = s"s3://$pathWithoutScheme"
@@ -188,7 +177,7 @@ case class S3Path private[s3](nioPath: NioPath,
     val originalPath = s3Path.toString
     if (originalPath.startsWith("s3")) return s3Path.toAbsolutePath.toString
     originalPath.charAt(0) match {
-      case '/' =>  s3Path.toAbsolutePath.toString
+      case '/' => s3Path.toAbsolutePath.toString
       case _ => s3Path.resolve(s"/$bucket/$originalPath").toAbsolutePath.toString
     }
   }
diff --git a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/S3PathBuilderFactory.scala b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/S3PathBuilderFactory.scala
index 880b0b984c1..ad505a35929 100644
--- a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/S3PathBuilderFactory.scala
+++ b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/S3PathBuilderFactory.scala
@@ -46,8 +46,8 @@ import scala.concurrent.{ExecutionContext, Future}
 
 // The constructor of this class is required to be Config, Config by cromwell
 // So, we need to take this config and get the AuthMode out of it
-final case class S3PathBuilderFactory private(globalConfig: Config, instanceConfig: Config)
-  extends PathBuilderFactory {
+final case class S3PathBuilderFactory private (globalConfig: Config, instanceConfig: Config)
+    extends PathBuilderFactory {
 
   // Grab the authMode out of configuration
   val conf: AwsConfiguration = AwsConfiguration(globalConfig)
@@ -55,19 +55,16 @@ final case class S3PathBuilderFactory private(globalConfig: Config, instanceConf
   val authModeValidation: ErrorOr[AwsAuthMode] = conf.auth(authModeAsString)
   val authMode = authModeValidation.unsafe(s"Failed to get authentication mode for $authModeAsString")
 
-  def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[S3PathBuilder] = {
-    S3PathBuilder.fromAuthMode(authMode, S3Storage.DefaultConfiguration,  options, conf.region)
-  }
+  def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[S3PathBuilder] =
+    S3PathBuilder.fromAuthMode(authMode, S3Storage.DefaultConfiguration, options, conf.region)
 
   // Ignores the authMode and creates an S3PathBuilder using the passed credentials directly.
   // Can be used when the Credentials are already available.
-  def fromProvider(options: WorkflowOptions, provider: AwsCredentialsProvider): S3PathBuilder = {
+  def fromProvider(options: WorkflowOptions, provider: AwsCredentialsProvider): S3PathBuilder =
     S3PathBuilder.fromProvider(provider, S3Storage.DefaultConfiguration, options, conf.region)
-  }
 }
 
 object S3PathBuilderFactory {
-  def apply(globalConfig: Config, instanceConfig: Config): S3PathBuilderFactory = {
+  def apply(globalConfig: Config, instanceConfig: Config): S3PathBuilderFactory =
     new S3PathBuilderFactory(globalConfig, instanceConfig)
-  }
 }
diff --git a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
index 8058d897975..74ec4e1b6b6 100644
--- a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
+++ b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
@@ -40,8 +40,8 @@ import scala.util.Try
   * Generates commands for IO operations on S3
   */
 private case object PartialS3BatchCommandBuilder extends PartialIoCommandBuilder {
-  override def sizeCommand: PartialFunction[Path, Try[S3BatchSizeCommand]] = {
-    case path: S3Path => Try(S3BatchSizeCommand(path))
+  override def sizeCommand: PartialFunction[Path, Try[S3BatchSizeCommand]] = { case path: S3Path =>
+    Try(S3BatchSizeCommand(path))
   }
 
   override def deleteCommand: PartialFunction[(Path, Boolean), Try[S3BatchDeleteCommand]] = {
@@ -52,16 +52,16 @@ private case object PartialS3BatchCommandBuilder extends PartialIoCommandBuilder
     case (src: S3Path, dest: S3Path) => Try(S3BatchCopyCommand(src, dest))
   }
 
-  override def hashCommand: PartialFunction[Path, Try[S3BatchEtagCommand]] = {
-    case path: S3Path => Try(S3BatchEtagCommand(path))
+  override def hashCommand: PartialFunction[Path, Try[S3BatchEtagCommand]] = { case path: S3Path =>
+    Try(S3BatchEtagCommand(path))
   }
 
-  override def touchCommand: PartialFunction[Path, Try[S3BatchTouchCommand]] = {
-    case path: S3Path => Try(S3BatchTouchCommand(path))
+  override def touchCommand: PartialFunction[Path, Try[S3BatchTouchCommand]] = { case path: S3Path =>
+    Try(S3BatchTouchCommand(path))
   }
 
-  override def existsCommand: PartialFunction[Path, Try[S3BatchExistsCommand]] = {
-    case path: S3Path => Try(S3BatchExistsCommand(path))
+  override def existsCommand: PartialFunction[Path, Try[S3BatchExistsCommand]] = { case path: S3Path =>
+    Try(S3BatchExistsCommand(path))
   }
 }
 
diff --git a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchIoCommand.scala b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchIoCommand.scala
index 75c224f6418..696c4d0240c 100644
--- a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchIoCommand.scala
+++ b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchIoCommand.scala
@@ -32,14 +32,16 @@ package cromwell.filesystems.s3.batch
 
 import software.amazon.awssdk.core.exception.SdkException
 
-import software.amazon.awssdk.services.s3.model.{HeadObjectResponse, CopyObjectResponse, NoSuchKeyException}
-import cromwell.core.io.{IoCommand,
-                         IoDeleteCommand,
-                         IoSizeCommand,
-                         IoHashCommand,
-                         IoTouchCommand,
-                         IoExistsCommand,
-                         IoCopyCommand}
+import software.amazon.awssdk.services.s3.model.{CopyObjectResponse, HeadObjectResponse, NoSuchKeyException}
+import cromwell.core.io.{
+  IoCommand,
+  IoCopyCommand,
+  IoDeleteCommand,
+  IoExistsCommand,
+  IoHashCommand,
+  IoSizeCommand,
+  IoTouchCommand
+}
 
 import cromwell.filesystems.s3.S3Path
 
@@ -49,6 +51,7 @@ import cromwell.filesystems.s3.S3Path
   * @tparam U Return type of the response
   */
 sealed trait S3BatchIoCommand[T, U] extends IoCommand[T] {
+
   /**
     * Maps the response of type U to the Cromwell Io response of type T
     */
@@ -61,9 +64,8 @@ sealed trait S3BatchIoCommand[T, U] extends IoCommand[T] {
     *   Right(newCommand) means the command is not complete and needs another request to be executed.
     * Most commands will reply with Left(value).
     */
-  def onSuccess(response: U): Either[T, S3BatchIoCommand[T, U]] = {
+  def onSuccess(response: U): Either[T, S3BatchIoCommand[T, U]] =
     Left(mapResponse(response))
-  }
 
   /**
     * Override to handle a failure differently and potentially return a successful response.
@@ -72,19 +74,22 @@ sealed trait S3BatchIoCommand[T, U] extends IoCommand[T] {
 }
 
 case class S3BatchCopyCommand(
-                           override val source: S3Path,
-                           override val destination: S3Path,
-                         ) extends IoCopyCommand(source, destination) with S3BatchIoCommand[Unit, CopyObjectResponse] {
+  override val source: S3Path,
+  override val destination: S3Path
+) extends IoCopyCommand(source, destination)
+    with S3BatchIoCommand[Unit, CopyObjectResponse] {
   override def mapResponse(response: CopyObjectResponse): Unit = ()
   override def commandDescription: String = s"S3BatchCopyCommand source '$source' destination '$destination'"
 }
 
 case class S3BatchDeleteCommand(
-                                  override val file: S3Path,
-                                  override val swallowIOExceptions: Boolean
-                                ) extends IoDeleteCommand(file, swallowIOExceptions) with S3BatchIoCommand[Unit, Void] {
+  override val file: S3Path,
+  override val swallowIOExceptions: Boolean
+) extends IoDeleteCommand(file, swallowIOExceptions)
+    with S3BatchIoCommand[Unit, Void] {
   override protected def mapResponse(response: Void): Unit = ()
-  override def commandDescription: String = s"S3BatchDeleteCommand file '$file' swallowIOExceptions '$swallowIOExceptions'"
+  override def commandDescription: String =
+    s"S3BatchDeleteCommand file '$file' swallowIOExceptions '$swallowIOExceptions'"
 }
 
 /**
@@ -126,14 +131,15 @@ case class S3BatchTouchCommand(override val file: S3Path) extends IoTouchCommand
   * `IoCommand` to determine the existence of an object in S3
   * @param file the path to the object
   */
-case class S3BatchExistsCommand(override val file: S3Path) extends IoExistsCommand(file) with S3BatchHeadCommand[Boolean] {
+case class S3BatchExistsCommand(override val file: S3Path)
+    extends IoExistsCommand(file)
+    with S3BatchHeadCommand[Boolean] {
   override def mapResponse(response: HeadObjectResponse): Boolean = true
-  override def onFailure(error: SdkException): Option[Left[Boolean, Nothing]] = {
+  override def onFailure(error: SdkException): Option[Left[Boolean, Nothing]] =
     // If the object can't be found, don't fail the request but just return false as we were testing for existence
     error match {
-      case _ : NoSuchKeyException => Option(Left(false))
+      case _: NoSuchKeyException => Option(Left(false))
       case _ => None
     }
-  }
   override def commandDescription: String = s"S3BatchExistsCommand file '$file'"
 }
diff --git a/filesystems/s3/src/test/scala/cromwell/filesystems/s3/S3PathBuilderSpec.scala b/filesystems/s3/src/test/scala/cromwell/filesystems/s3/S3PathBuilderSpec.scala
index 262ad2cc7de..05703f548d2 100644
--- a/filesystems/s3/src/test/scala/cromwell/filesystems/s3/S3PathBuilderSpec.scala
+++ b/filesystems/s3/src/test/scala/cromwell/filesystems/s3/S3PathBuilderSpec.scala
@@ -107,7 +107,8 @@ class S3PathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "with spaces",
       getFileName = s"s3://$bucket/with spaces",
       getNameCount = 3,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // GoodPath(
     //   description = "a path with non-ascii",
@@ -134,7 +135,8 @@ class S3PathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "with non ascii £€",
       getFileName = s"s3://$bucket/with non ascii £€",
       getNameCount = 3,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // GoodPath(
     //   description = "a s3 uri path with encoded characters",
@@ -162,7 +164,8 @@ class S3PathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "encoded                    paces",
       getFileName = s"s3://$bucket/encoded                    paces",
       getNameCount = 3,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // TODO: In order for this to pass tests, S3Path needs to implement the
     //       Path trait directly and cannot inherit. We will work on this later
@@ -192,8 +195,8 @@ class S3PathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = null,
       getNameCount = 0,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a file at the top of the bucket",
       path = s"s3://$bucket/hello",
@@ -206,7 +209,8 @@ class S3PathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "hello",
       getFileName = s"s3://$bucket/hello",
       getNameCount = 1,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // parent/getParent do not end in a "/".
     // TODO: Determine if this is critcal. Note
@@ -236,7 +240,8 @@ class S3PathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "world",
       getFileName = s"s3://$bucket/world",
       getNameCount = 2,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // Special paths
 
@@ -252,7 +257,8 @@ class S3PathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "",
       getFileName = s"s3://$bucket/.",
       getNameCount = 1,
-      isAbsolute = true),
+      isAbsolute = true
+    ),
 
     // GoodPath(
     //   description = "a bucket with a path ..",
@@ -352,8 +358,8 @@ class S3PathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "world",
       getFileName = s"s3://$bucket/world",
       getNameCount = 1,
-      isAbsolute = true),
-
+      isAbsolute = true
+    ),
     GoodPath(
       description = "a bucket with an underscore",
       path = s"s3://hello_underscore/world",
@@ -366,27 +372,37 @@ class S3PathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
       name = "world",
       getFileName = s"s3://hello_underscore/world",
       getNameCount = 1,
-      isAbsolute = true)
+      isAbsolute = true
+    )
   )
 
   private def badPaths = Seq(
     BadPath("an empty path", "", " does not have a s3 scheme"),
-    BadPath("a bucketless path", "s3://", "The specified S3 path 's3://' does not parse as a URI.\nExpected authority at index 5: s3://"),
-    BadPath("a bucket named .", "s3://./hello/world", "The path 's3://./hello/world' does not seem to be a valid S3 path. Please check that it starts with s3:// and that the bucket and object follow S3 naming guidelines at https://docs.aws.amazon.com/AmazonS3/latest/dev/BucketRestrictions.html"),
-    BadPath("a non ascii bucket name", "s3://nonasciibucket£€/hello/world",
-      "The path 's3://nonasciibucket£€/hello/world' does not seem to be a valid S3 path. Please check that it starts with s3:// and that the bucket and object follow S3 naming guidelines at https://docs.aws.amazon.com/AmazonS3/latest/dev/BucketRestrictions.html"),
+    BadPath("a bucketless path",
+            "s3://",
+            "The specified S3 path 's3://' does not parse as a URI.\nExpected authority at index 5: s3://"
+    ),
+    BadPath(
+      "a bucket named .",
+      "s3://./hello/world",
+      "The path 's3://./hello/world' does not seem to be a valid S3 path. Please check that it starts with s3:// and that the bucket and object follow S3 naming guidelines at https://docs.aws.amazon.com/AmazonS3/latest/dev/BucketRestrictions.html"
+    ),
+    BadPath(
+      "a non ascii bucket name",
+      "s3://nonasciibucket£€/hello/world",
+      "The path 's3://nonasciibucket£€/hello/world' does not seem to be a valid S3 path. Please check that it starts with s3:// and that the bucket and object follow S3 naming guidelines at https://docs.aws.amazon.com/AmazonS3/latest/dev/BucketRestrictions.html"
+    ),
     BadPath("a https path", "https://hello/world", "S3 URIs must have 's3' scheme: https://hello/world"),
     BadPath("a file uri path", "file:///hello/world", "S3 URIs must have 's3' scheme: file:///hello/world"),
     BadPath("a relative file path", "hello/world", "hello/world does not have a s3 scheme"),
     BadPath("an absolute file path", "/hello/world", "/hello/world does not have a s3 scheme")
   )
 
-  private lazy val pathBuilder = {
+  private lazy val pathBuilder =
     S3PathBuilder.fromProvider(
       AnonymousCredentialsProvider.create,
       S3Storage.s3Configuration(),
       WorkflowOptions.empty,
       Option(Region.US_EAST_1)
     )
-  }
 }
diff --git a/filesystems/sra/src/main/scala/cromwell/filesystems/sra/SraPathBuilder.scala b/filesystems/sra/src/main/scala/cromwell/filesystems/sra/SraPathBuilder.scala
index 7b539709079..1455a8898ea 100644
--- a/filesystems/sra/src/main/scala/cromwell/filesystems/sra/SraPathBuilder.scala
+++ b/filesystems/sra/src/main/scala/cromwell/filesystems/sra/SraPathBuilder.scala
@@ -27,6 +27,8 @@ case class SraPath(accession: String, path: String) extends Path {
   override def pathAsString: String = SraPath.Scheme + pathWithoutScheme
   override def pathWithoutScheme: String = accession + "/" + path
 
-  protected def newPath(nioPath: NioPath): Path = throw new UnsupportedOperationException("'newPath' not implemented for SraPath")
+  protected def newPath(nioPath: NioPath): Path = throw new UnsupportedOperationException(
+    "'newPath' not implemented for SraPath"
+  )
   def nioPath: NioPath = throw new UnsupportedOperationException("'nioPath' not implemented for SraPath")
 }
diff --git a/filesystems/sra/src/main/scala/cromwell/filesystems/sra/SraPathBuilderFactory.scala b/filesystems/sra/src/main/scala/cromwell/filesystems/sra/SraPathBuilderFactory.scala
index bc487f1dd73..c3855aa4635 100644
--- a/filesystems/sra/src/main/scala/cromwell/filesystems/sra/SraPathBuilderFactory.scala
+++ b/filesystems/sra/src/main/scala/cromwell/filesystems/sra/SraPathBuilderFactory.scala
@@ -7,9 +7,9 @@ import cromwell.core.path.PathBuilderFactory
 
 import scala.concurrent.{ExecutionContext, Future}
 
-final case class SraPathBuilderFactory(globalConfig: Config, instanceConfig: Config)
-  extends PathBuilderFactory {
-  def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[SraPathBuilder] = Future.successful(SraPathBuilderFactory.pathBuilder)
+final case class SraPathBuilderFactory(globalConfig: Config, instanceConfig: Config) extends PathBuilderFactory {
+  def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[SraPathBuilder] =
+    Future.successful(SraPathBuilderFactory.pathBuilder)
 }
 
 object SraPathBuilderFactory {
diff --git a/filesystems/sra/src/test/scala/cromwell/filesystems/sra/SraPathBuilderSpec.scala b/filesystems/sra/src/test/scala/cromwell/filesystems/sra/SraPathBuilderSpec.scala
index bbc44b55793..193e684c0ae 100644
--- a/filesystems/sra/src/test/scala/cromwell/filesystems/sra/SraPathBuilderSpec.scala
+++ b/filesystems/sra/src/test/scala/cromwell/filesystems/sra/SraPathBuilderSpec.scala
@@ -8,12 +8,12 @@ import org.scalatest.matchers.should.Matchers
 class SraPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with PathBuilderSpecUtils {
   behavior of "SraPathBuilder"
 
-  goodPaths foreach {
-    good => it should behave like buildGood(good)
+  goodPaths foreach { good =>
+    it should behave like buildGood(good)
   }
 
-  badPaths foreach {
-    bad => it should behave like buildBad(bad)
+  badPaths foreach { bad =>
+    it should behave like buildBad(bad)
   }
 
   private def buildGood(good: Good): Unit = {
@@ -28,11 +28,11 @@ class SraPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
     val sraPath = path.asInstanceOf[SraPath]
 
     it should "match expected accession" in {
-      sraPath.accession should be (good.accession)
+      sraPath.accession should be(good.accession)
     }
 
     it should "match expected path" in {
-      sraPath.path should be (good.path)
+      sraPath.path should be(good.path)
     }
   }
 
@@ -40,50 +40,47 @@ class SraPathBuilderSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
     behavior of s"Building ${bad.description}"
 
     it should "fail to build an SraPath" in {
-      pathBuilder.build(bad.in).isSuccess should be (false)
+      pathBuilder.build(bad.in).isSuccess should be(false)
     }
   }
 
   private lazy val pathBuilder = new SraPathBuilder
 
-  private case class Good(description: String,
-                          in: String,
-                          accession: String,
-                          path: String)
+  private case class Good(description: String, in: String, accession: String, path: String)
   private def goodPaths = Seq(
     Good(
       description = "well-formed path",
       in = "sra://SXP000001/asdf.bam",
       accession = "SXP000001",
-      path = "asdf.bam",
+      path = "asdf.bam"
     ),
     Good(
       description = "nested path",
       in = "sra://SRA42424242/first/second/third.bam.bai",
       accession = "SRA42424242",
-      path = "first/second/third.bam.bai",
+      path = "first/second/third.bam.bai"
     ),
     Good(
       description = "path with spaces",
       in = "sra://SXP111111/top level/nested level/file name.bz2",
       accession = "SXP111111",
-      path = "top level/nested level/file name.bz2",
-    ),
+      path = "top level/nested level/file name.bz2"
+    )
   )
 
   private case class Bad(description: String, in: String)
   private def badPaths = Seq(
     Bad(
       description = "not an SRA path",
-      in = "gcs://some/gcs/path/thing.txt",
+      in = "gcs://some/gcs/path/thing.txt"
     ),
     Bad(
       description = "missing accession",
-      in = "sra://",
+      in = "sra://"
     ),
     Bad(
       description = "missing path within accession",
-      in = "sra://SRA00001",
-    ),
+      in = "sra://SRA00001"
+    )
   )
 }
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/LanguageFactory.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/LanguageFactory.scala
index f16054f15a7..e2f1d48e9f4 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/LanguageFactory.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/LanguageFactory.scala
@@ -23,27 +23,31 @@ trait LanguageFactory {
   import net.ceedubs.ficus.Ficus._
 
   lazy val enabled = !config.as[Option[Boolean]]("enabled").contains(false)
-  lazy val enabledCheck: Checked[Unit] = if (enabled) ().validNelCheck else
-    s"The language factory for $languageName ($languageVersionName) is not currently enabled in this Cromwell".invalidNelCheck
-
+  lazy val enabledCheck: Checked[Unit] =
+    if (enabled) ().validNelCheck
+    else
+      s"The language factory for $languageName ($languageVersionName) is not currently enabled in this Cromwell".invalidNelCheck
 
   lazy val strictValidation: Boolean = !config.as[Option[Boolean]]("strict-validation").contains(false)
 
-  lazy val womOutputRuntimeExtractor: Checked[Option[WomOutputRuntimeExtractor]] = config.getAs[Config]("output-runtime-extractor") match {
-    case Some(c) => WomOutputRuntimeExtractor.fromConfig(c).map(Option.apply).toEither
-    case _ => None.validNelCheck
-  }
+  lazy val womOutputRuntimeExtractor: Checked[Option[WomOutputRuntimeExtractor]] =
+    config.getAs[Config]("output-runtime-extractor") match {
+      case Some(c) => WomOutputRuntimeExtractor.fromConfig(c).map(Option.apply).toEither
+      case _ => None.validNelCheck
+    }
 
   def getWomBundle(workflowSource: WorkflowSource,
                    workflowSourceOrigin: Option[ResolvedImportRecord],
                    workflowOptionsJson: WorkflowOptionsJson,
                    importResolvers: List[ImportResolver],
                    languageFactories: List[LanguageFactory],
-                   convertNestedScatterToSubworkflow : Boolean = true): Checked[WomBundle]
+                   convertNestedScatterToSubworkflow: Boolean = true
+  ): Checked[WomBundle]
 
   def createExecutable(womBundle: WomBundle,
                        inputs: WorkflowJson,
-                       ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace]
+                       ioFunctions: IoFunctionSet
+  ): Checked[ValidatedWomNamespace]
 
   def validateNamespace(source: WorkflowSourceFilesCollection,
                         workflowSource: WorkflowSource,
@@ -51,7 +55,8 @@ trait LanguageFactory {
                         importLocalFilesystem: Boolean,
                         workflowIdForLogging: WorkflowId,
                         ioFunctions: IoFunctionSet,
-                        importResolvers: List[ImportResolver]): IOChecked[ValidatedWomNamespace]
+                        importResolvers: List[ImportResolver]
+  ): IOChecked[ValidatedWomNamespace]
 
   /**
     * In case no version is specified: does this language factory feel like it might be suitable for this file?
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/ValidatedWomNamespace.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/ValidatedWomNamespace.scala
index 306a442672b..828b9c2bbc0 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/ValidatedWomNamespace.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/ValidatedWomNamespace.scala
@@ -11,4 +11,5 @@ import wom.values.WomValue
   */
 final case class ValidatedWomNamespace(executable: Executable,
                                        womValueInputs: Map[OutputPort, WomValue],
-                                       importedFileContent: Map[String, String])
+                                       importedFileContent: Map[String, String]
+)
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/config/CromwellLanguages.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/config/CromwellLanguages.scala
index b7c4460df98..e05b48d991b 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/config/CromwellLanguages.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/config/CromwellLanguages.scala
@@ -5,10 +5,11 @@ import cromwell.languages.config.CromwellLanguages.{CromwellLanguageName, Cromwe
 import cromwell.languages.LanguageFactory
 
 // Construct a singleton instance of this class using 'initLanguages' below.
-final case class CromwellLanguages private(languageConfig: LanguagesConfiguration) {
+final case class CromwellLanguages private (languageConfig: LanguagesConfiguration) {
 
   val languages: Map[CromwellLanguageName, LanguageVersions] = makeLanguages
-  val default: LanguageVersions = languages.find(lang => languageConfig.default.contains(lang._1)).getOrElse(languages.head)._2
+  val default: LanguageVersions =
+    languages.find(lang => languageConfig.default.contains(lang._1)).getOrElse(languages.head)._2
 
   private def makeLanguages: Map[CromwellLanguageName, LanguageVersions] = (languageConfig.languages map { lc =>
     val versions = lc.versions map { case (languageVersion, languageConfigEntryFields) =>
@@ -19,18 +20,20 @@ final case class CromwellLanguages private(languageConfig: LanguagesConfiguratio
     lc.name.toUpperCase -> LanguageVersions(versions, default)
   }).toMap
 
-  private def makeLanguageFactory(className: String, config: Config) = {
-    Class.forName(className)
+  private def makeLanguageFactory(className: String, config: Config) =
+    Class
+      .forName(className)
       .getConstructor(classOf[Config])
       .newInstance(config)
       .asInstanceOf[LanguageFactory]
-  }
 }
 
 /**
   * Holds all the registered versions of a language.
   */
-final case class LanguageVersions private(allVersions: Map[CromwellLanguageVersion, LanguageFactory], default: LanguageFactory)
+final case class LanguageVersions private (allVersions: Map[CromwellLanguageVersion, LanguageFactory],
+                                           default: LanguageFactory
+)
 
 object CromwellLanguages {
   type CromwellLanguageName = String
@@ -39,7 +42,6 @@ object CromwellLanguages {
   private var _instance: CromwellLanguages = _
   lazy val instance: CromwellLanguages = _instance
 
-  def initLanguages(backendEntries: LanguagesConfiguration): Unit = {
+  def initLanguages(backendEntries: LanguagesConfiguration): Unit =
     _instance = CromwellLanguages(backendEntries)
-  }
 }
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/config/LanguageConfiguration.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/config/LanguageConfiguration.scala
index 2cb09dd8a3d..153bdfd029c 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/config/LanguageConfiguration.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/config/LanguageConfiguration.scala
@@ -8,18 +8,22 @@ import cromwell.languages.config.CromwellLanguages.{CromwellLanguageName, Cromwe
 import scala.jdk.CollectionConverters._
 
 final case class LanguagesConfiguration(languages: List[LanguageVersionConfigurationEntry], default: Option[String])
-final case class LanguageVersionConfigurationEntry(name: CromwellLanguageName, versions: Map[CromwellLanguageVersion, LanguageVersionConfig], default: Option[String])
+final case class LanguageVersionConfigurationEntry(name: CromwellLanguageName,
+                                                   versions: Map[CromwellLanguageVersion, LanguageVersionConfig],
+                                                   default: Option[String]
+)
 final case class LanguageVersionConfig(className: String, config: Config)
 
 object LanguageConfiguration {
   private val LanguagesConfig = ConfigFactory.load.getConfig("languages")
-  private val DefaultLanguageName: Option[String] = if (LanguagesConfig.hasPath("default")) Option(LanguagesConfig.getString("default")) else None
+  private val DefaultLanguageName: Option[String] =
+    if (LanguagesConfig.hasPath("default")) Option(LanguagesConfig.getString("default")) else None
 
-  private val LanguageNames: Set[String] = LanguagesConfig.entrySet().asScala.map(findFirstKey).filterNot(_ == "default").toSet
+  private val LanguageNames: Set[String] =
+    LanguagesConfig.entrySet().asScala.map(findFirstKey).filterNot(_ == "default").toSet
 
   val AllLanguageEntries: LanguagesConfiguration = {
     val languages = LanguageNames.toList map { languageName =>
-
       val languageConfig = LanguagesConfig.getConfig(languageName)
       val versionSet = languageConfig.getConfig("versions")
       val allLanguageVersionNames: Set[String] = versionSet.entrySet().asScala.map(findFirstKey).toSet
@@ -29,7 +33,8 @@ object LanguageConfiguration {
       val versions = (languageVersionNames.toList map { languageVersionName =>
         val configEntry = versionSet.getConfig(s""""$languageVersionName"""")
         val className: String = configEntry.getString("language-factory")
-        val factoryConfig: Config = if (configEntry.hasPath("config")) configEntry.getConfig("config") else ConfigFactory.empty()
+        val factoryConfig: Config =
+          if (configEntry.hasPath("config")) configEntry.getConfig("config") else ConfigFactory.empty()
         val fields = LanguageVersionConfig(className, factoryConfig)
         languageVersionName -> fields
       }).toMap
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
index f7fd70cfc56..e3690248b09 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
@@ -32,13 +32,18 @@ import scala.util.{Failure, Success, Try}
 object ImportResolver {
 
   case class ImportResolutionRequest(toResolve: String, currentResolvers: List[ImportResolver])
-  case class ResolvedImportBundle(source: WorkflowSource, newResolvers: List[ImportResolver], resolvedImportRecord: ResolvedImportRecord)
+  case class ResolvedImportBundle(source: WorkflowSource,
+                                  newResolvers: List[ImportResolver],
+                                  resolvedImportRecord: ResolvedImportRecord
+  )
 
   trait ImportResolver {
     def name: String
     protected def innerResolver(path: String, currentResolvers: List[ImportResolver]): Checked[ResolvedImportBundle]
     def resolver: CheckedAtoB[ImportResolutionRequest, ResolvedImportBundle] = CheckedAtoB.fromCheck { request =>
-      innerResolver(request.toResolve, request.currentResolvers).contextualizeErrors(s"resolve '${request.toResolve}' using resolver: '$name'")
+      innerResolver(request.toResolve, request.currentResolvers).contextualizeErrors(
+        s"resolve '${request.toResolve}' using resolver: '$name'"
+      )
     }
     def cleanupIfNecessary(): ErrorOr[Unit]
 
@@ -48,7 +53,10 @@ object ImportResolver {
   }
 
   object DirectoryResolver {
-    private def apply(directory: Path, allowEscapingDirectory: Boolean, customName: Option[String]): DirectoryResolver = {
+    private def apply(directory: Path,
+                      allowEscapingDirectory: Boolean,
+                      customName: Option[String]
+    ): DirectoryResolver = {
       val dontEscapeFrom = if (allowEscapingDirectory) None else Option(directory.toJava.getCanonicalPath)
       DirectoryResolver(directory, dontEscapeFrom, customName, deleteOnClose = false, directoryHash = None)
     }
@@ -77,19 +85,23 @@ object ImportResolver {
                                dontEscapeFrom: Option[String] = None,
                                customName: Option[String],
                                deleteOnClose: Boolean,
-                               directoryHash: Option[String]) extends ImportResolver {
+                               directoryHash: Option[String]
+  ) extends ImportResolver {
     lazy val absolutePathToDirectory: String = directory.toJava.getCanonicalPath
 
     override def innerResolver(path: String, currentResolvers: List[ImportResolver]): Checked[ResolvedImportBundle] = {
 
-      def updatedResolverSet(oldRootDirectory: Path, newRootDirectory: Path, current: List[ImportResolver]): List[ImportResolver] = {
+      def updatedResolverSet(oldRootDirectory: Path,
+                             newRootDirectory: Path,
+                             current: List[ImportResolver]
+      ): List[ImportResolver] =
         current map {
-          case d if d == this => DirectoryResolver(newRootDirectory, dontEscapeFrom, customName, deleteOnClose = false, directoryHash = None)
+          case d if d == this =>
+            DirectoryResolver(newRootDirectory, dontEscapeFrom, customName, deleteOnClose = false, directoryHash = None)
           case other => other
         }
-      }
 
-      def fetchContentFromAbsolutePath(absolutePathToFile: NioPath): ErrorOr[String] = {
+      def fetchContentFromAbsolutePath(absolutePathToFile: NioPath): ErrorOr[String] =
         checkLocation(absolutePathToFile, path) flatMap { _ =>
           val file = File(absolutePathToFile)
           if (file.exists) {
@@ -98,7 +110,6 @@ object ImportResolver {
             s"File not found: $path".invalidNel
           }
         }
-      }
 
       val errorOr = for {
         resolvedPath <- resolvePath(path)
@@ -111,7 +122,9 @@ object ImportResolver {
     }
 
     private def resolvePath(path: String): ErrorOr[Path] = Try(directory.resolve(path)).toErrorOr
-    private def makeAbsolute(resolvedPath: Path): ErrorOr[NioPath] = Try(Paths.get(resolvedPath.toFile.getCanonicalPath)).toErrorOr
+    private def makeAbsolute(resolvedPath: Path): ErrorOr[NioPath] = Try(
+      Paths.get(resolvedPath.toFile.getCanonicalPath)
+    ).toErrorOr
     private def checkLocation(absoluteNioPath: NioPath, reportedPathIfBad: String): ErrorOr[Unit] =
       if (dontEscapeFrom.forall(absoluteNioPath.startsWith))
         ().validNel
@@ -135,7 +148,8 @@ object ImportResolver {
 
         s"relative to directory $relativePathToDirectory (without escaping $relativePathToDontEscapeFrom)"
       case (None, None) =>
-        val shortPathToDirectory = Paths.get(absolutePathToDirectory).toFile.getCanonicalFile.toPath.getFileName.toString
+        val shortPathToDirectory =
+          Paths.get(absolutePathToDirectory).toFile.getCanonicalFile.toPath.getFileName.toString
         s"relative to directory [...]/$shortPathToDirectory (escaping allowed)"
     }
 
@@ -148,20 +162,25 @@ object ImportResolver {
       else
         ().validNel
 
-    override def hashKey: ErrorOr[String] = directoryHash.map(_.validNel).getOrElse("No hashKey available for directory importer".invalidNel)
+    override def hashKey: ErrorOr[String] =
+      directoryHash.map(_.validNel).getOrElse("No hashKey available for directory importer".invalidNel)
   }
 
   def zippedImportResolver(zippedImports: Array[Byte], workflowId: WorkflowId): ErrorOr[DirectoryResolver] = {
 
     val zipHash = new String(MessageDigest.getInstance("MD5").digest(zippedImports))
     LanguageFactoryUtil.createImportsDirectory(zippedImports, workflowId) map { dir =>
-      DirectoryResolver(dir, Option(dir.toJava.getCanonicalPath), None, deleteOnClose = true, directoryHash = Option(zipHash))
+      DirectoryResolver(dir,
+                        Option(dir.toJava.getCanonicalPath),
+                        None,
+                        deleteOnClose = true,
+                        directoryHash = Option(zipHash)
+      )
     }
   }
 
-  case class HttpResolver(relativeTo: Option[String],
-                          headers: Map[String, String],
-                          hostAllowlist: Option[List[String]]) extends ImportResolver {
+  case class HttpResolver(relativeTo: Option[String], headers: Map[String, String], hostAllowlist: Option[List[String]])
+      extends ImportResolver {
     import HttpResolver._
 
     override def name: String = relativeTo match {
@@ -192,7 +211,7 @@ object ImportResolver {
       case None => true
     }
 
-    override def innerResolver(str: String, currentResolvers: List[ImportResolver]): Checked[ResolvedImportBundle] = {
+    override def innerResolver(str: String, currentResolvers: List[ImportResolver]): Checked[ResolvedImportBundle] =
       pathToLookup(str) flatMap { toLookup: WorkflowSource =>
         (Try {
           val uri: Uri = uri"$toLookup"
@@ -207,7 +226,6 @@ object ImportResolver {
           case Failure(e) => s"HTTP resolver with headers had an unexpected error (${e.getMessage})".invalidNelCheck
         }).contextualizeErrors(s"download $toLookup")
       }
-    }
 
     private def getUri(toLookup: WorkflowSource): Either[NonEmptyList[WorkflowSource], ResolvedImportBundle] = {
       implicit val sttpBackend = HttpResolver.sttpBackend()
@@ -215,7 +233,9 @@ object ImportResolver {
 
       // temporary situation to get functionality working before
       // starting in on async-ifying the entire WdlNamespace flow
-      val result: Checked[WorkflowSource] = Await.result(responseIO.unsafeToFuture(), 15.seconds).body.leftMap { e => NonEmptyList(e.toString.trim, List.empty) }
+      val result: Checked[WorkflowSource] = Await.result(responseIO.unsafeToFuture(), 15.seconds).body.leftMap { e =>
+        NonEmptyList(e.toString.trim, List.empty)
+      }
 
       result map {
         ResolvedImportBundle(_, newResolverList(toLookup), ResolvedImportRecord(toLookup))
@@ -232,8 +252,7 @@ object ImportResolver {
     import common.util.IntrospectableLazy
     import common.util.IntrospectableLazy._
 
-    def apply(relativeTo: Option[String] = None,
-              headers: Map[String, String] = Map.empty): HttpResolver = {
+    def apply(relativeTo: Option[String] = None, headers: Map[String, String] = Map.empty): HttpResolver = {
       val config = ConfigFactory.load().getConfig("languages.WDL.http-allow-list")
       val allowListEnabled = config.as[Option[Boolean]]("enabled").getOrElse(false)
       val allowList: Option[List[String]] =
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala
index da0860c3a86..8fabb445bac 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/LanguageFactoryUtil.scala
@@ -32,7 +32,9 @@ object LanguageFactoryUtil {
   def createImportsDirectory(zipContents: Array[Byte], workflowId: WorkflowId): ErrorOr[Path] = {
 
     def makeZipFile: Try[Path] = Try {
-      DefaultPathBuilder.createTempFile(s"imports_workflow_${workflowId}_", ".zip").writeByteArray(zipContents)(OpenOptions.default)
+      DefaultPathBuilder
+        .createTempFile(s"imports_workflow_${workflowId}_", ".zip")
+        .writeByteArray(zipContents)(OpenOptions.default)
     }
 
     def unZipFile(f: Path) = Try(f.unzip())
@@ -49,25 +51,28 @@ object LanguageFactoryUtil {
     }
   }
 
-  def validateWomNamespace(womExecutable: Executable, ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace] = for {
-    evaluatedInputs <- validateExecutableInputs(womExecutable.resolvedExecutableInputs, ioFunctions).toEither
-    validatedWomNamespace = ValidatedWomNamespace(womExecutable, evaluatedInputs, Map.empty)
-    _ <- validateWdlFiles(validatedWomNamespace.womValueInputs)
-  } yield validatedWomNamespace
+  def validateWomNamespace(womExecutable: Executable, ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace] =
+    for {
+      evaluatedInputs <- validateExecutableInputs(womExecutable.resolvedExecutableInputs, ioFunctions).toEither
+      validatedWomNamespace = ValidatedWomNamespace(womExecutable, evaluatedInputs, Map.empty)
+      _ <- validateWdlFiles(validatedWomNamespace.womValueInputs)
+    } yield validatedWomNamespace
 
   /*
-    * At this point input values are either a WomValue (if it was provided through the input file)
-    * or a WomExpression (if we fell back to the default).
-    * We assume that default expressions do NOT reference any "variables" (other inputs, call outputs ...)
-    * Should this assumption prove not sufficient InstantiatedExpressions or ExpressionNodes would need to be provided
-    * instead so that they can be evaluated JIT.
-    * Note that the ioFunctions use engine level pathBuilders. This means that their credentials come from the engine section
-    * of the configuration, and are not backend specific.
+   * At this point input values are either a WomValue (if it was provided through the input file)
+   * or a WomExpression (if we fell back to the default).
+   * We assume that default expressions do NOT reference any "variables" (other inputs, call outputs ...)
+   * Should this assumption prove not sufficient InstantiatedExpressions or ExpressionNodes would need to be provided
+   * instead so that they can be evaluated JIT.
+   * Note that the ioFunctions use engine level pathBuilders. This means that their credentials come from the engine section
+   * of the configuration, and are not backend specific.
    */
-  private def validateExecutableInputs(inputs: ResolvedExecutableInputs, ioFunctions: IoFunctionSet): ErrorOr[Map[OutputPort, WomValue]] = {
+  private def validateExecutableInputs(inputs: ResolvedExecutableInputs,
+                                       ioFunctions: IoFunctionSet
+  ): ErrorOr[Map[OutputPort, WomValue]] = {
     import common.validation.ErrorOr.MapTraversal
-    inputs.traverse {
-      case (key, value) => value.fold(ResolvedExecutableInputsPoly).apply(ioFunctions) map { key -> _ }
+    inputs.traverse { case (key, value) =>
+      value.fold(ResolvedExecutableInputsPoly).apply(ioFunctions) map { key -> _ }
     }
   }
 
@@ -88,16 +93,18 @@ object LanguageFactoryUtil {
     }
   }
 
-  def simpleLooksParseable(startsWithOptions: List[String], commentIndicators: List[String])(content: String): Boolean = {
+  def simpleLooksParseable(startsWithOptions: List[String], commentIndicators: List[String])(
+    content: String
+  ): Boolean = {
     val fileWithoutInitialWhitespace = content.linesIterator.toList.dropWhile { l =>
       l.forall(_.isWhitespace) || commentIndicators.exists(l.dropWhile(_.isWhitespace).startsWith(_))
     }
 
     val firstCodeLine = fileWithoutInitialWhitespace.headOption.map(_.dropWhile(_.isWhitespace))
-    firstCodeLine.exists { line => startsWithOptions.contains(line.trim) }
+    firstCodeLine.exists(line => startsWithOptions.contains(line.trim))
   }
 
-  def chooseFactory(workflowSource: WorkflowSource, wsfc: WorkflowSourceFilesCollection): ErrorOr[LanguageFactory] = {
+  def chooseFactory(workflowSource: WorkflowSource, wsfc: WorkflowSourceFilesCollection): ErrorOr[LanguageFactory] =
     wsfc.workflowType match {
       case Some(languageName) if CromwellLanguages.instance.languages.contains(languageName.toUpperCase) =>
         val language = CromwellLanguages.instance.languages(languageName.toUpperCase)
@@ -110,21 +117,25 @@ object LanguageFactoryUtil {
       case Some(other) => s"Unknown workflow type: $other".invalidNel[LanguageFactory]
       case None =>
         val allFactories = CromwellLanguages.instance.languages.values.flatMap(_.allVersions.values)
-        allFactories.find(_.looksParsable(workflowSource)).getOrElse(CromwellLanguages.instance.default.default).validNel
+        allFactories
+          .find(_.looksParsable(workflowSource))
+          .getOrElse(CromwellLanguages.instance.default.default)
+          .validNel
     }
-  }
 
   def findWorkflowSource(workflowSource: Option[WorkflowSource],
                          workflowUrl: Option[WorkflowUrl],
-                         resolvers: List[ImportResolver]): Checked[(WorkflowSource, List[ImportResolver])] = {
+                         resolvers: List[ImportResolver]
+  ): Checked[(WorkflowSource, List[ImportResolver])] =
     (workflowSource, workflowUrl) match {
       case (Some(source), None) => (source, resolvers).validNelCheck
       case (None, Some(url)) =>
-        val compoundImportResolver: CheckedAtoB[ImportResolutionRequest, ResolvedImportBundle] = CheckedAtoB.firstSuccess(resolvers.map(_.resolver), s"resolve workflowUrl '$url'")
-        val wfSourceAndResolvers: Checked[ResolvedImportBundle] = compoundImportResolver.run(ImportResolutionRequest(url, resolvers))
+        val compoundImportResolver: CheckedAtoB[ImportResolutionRequest, ResolvedImportBundle] =
+          CheckedAtoB.firstSuccess(resolvers.map(_.resolver), s"resolve workflowUrl '$url'")
+        val wfSourceAndResolvers: Checked[ResolvedImportBundle] =
+          compoundImportResolver.run(ImportResolutionRequest(url, resolvers))
         wfSourceAndResolvers map { v => (v.source, v.newResolvers) }
       case (Some(_), Some(_)) => "Both workflow source and url can't be supplied".invalidNelCheck
       case (None, None) => "Either workflow source or url has to be supplied".invalidNelCheck
     }
-  }
 }
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ParserCache.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ParserCache.scala
index 5d6feda9882..839c4e855f8 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ParserCache.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ParserCache.scala
@@ -22,23 +22,27 @@ import scala.concurrent.duration._
 
 trait ParserCache[A] extends StrictLogging { this: LanguageFactory =>
 
-  def retrieveOrCalculate(cacheInputs: ParserCacheInputs,
-                          calculationCallable: Callable[ErrorOr[A]]): ErrorOr[A] = {
-
+  def retrieveOrCalculate(cacheInputs: ParserCacheInputs, calculationCallable: Callable[ErrorOr[A]]): ErrorOr[A] =
     (cache map { c: Cache[String, ErrorOr[A]] =>
-      workflowHashKey(cacheInputs.workflowSource, cacheInputs.workflowUrl, cacheInputs.workflowRoot, cacheInputs.importResolvers) match {
+      workflowHashKey(cacheInputs.workflowSource,
+                      cacheInputs.workflowUrl,
+                      cacheInputs.workflowRoot,
+                      cacheInputs.importResolvers
+      ) match {
         case Valid(hashKey) => c.get(hashKey, calculationCallable)
         case Invalid(errors) =>
-          logger.info(s"Failed to calculate hash key for 'workflow source to WOM' cache: {}", errors.toList.mkString(", "))
+          logger.info(s"Failed to calculate hash key for 'workflow source to WOM' cache: {}",
+                      errors.toList.mkString(", ")
+          )
           calculationCallable.call
       }
     }).getOrElse(calculationCallable.call())
-  }
 
   private[this] def workflowHashKey(workflowSource: Option[WorkflowSource],
                                     workflowUrl: Option[WorkflowUrl],
                                     workflowRoot: Option[String],
-                                    importResolvers: List[ImportResolver]): ErrorOr[String] = {
+                                    importResolvers: List[ImportResolver]
+  ): ErrorOr[String] = {
     def stringOptionToHash(opt: Option[String]): String = opt map { _.md5Sum } getOrElse ""
 
     val importResolversToHash: ErrorOr[String] = importResolvers.traverse(_.hashKey).map(_.mkString(":"))
@@ -48,17 +52,21 @@ trait ParserCache[A] extends StrictLogging { this: LanguageFactory =>
     }
   }
 
-  private[this] lazy val cacheConfig: Option[CacheConfig] = {
+  private[this] lazy val cacheConfig: Option[CacheConfig] =
     // Caching is an opt-in activity:
     for {
       _ <- enabled.option(())
       cachingConfigSection <- config.as[Option[Config]]("caching")
-      cc <- CacheConfig.optionalConfig(cachingConfigSection, defaultConcurrency = 2, defaultSize = 1000L, defaultTtl = 20.minutes)
+      cc <- CacheConfig.optionalConfig(cachingConfigSection,
+                                       defaultConcurrency = 2,
+                                       defaultSize = 1000L,
+                                       defaultTtl = 20.minutes
+      )
     } yield cc
-  }
 
   private[this] lazy val cache: Option[Cache[String, ErrorOr[A]]] = cacheConfig map { c =>
-    CacheBuilder.newBuilder()
+    CacheBuilder
+      .newBuilder()
       .concurrencyLevel(c.concurrency)
       .expireAfterAccess(c.ttl.length, c.ttl.unit)
       .maximumSize(c.size)
@@ -70,5 +78,6 @@ object ParserCache {
   final case class ParserCacheInputs(workflowSource: Option[WorkflowSource],
                                      workflowUrl: Option[WorkflowUrl],
                                      workflowRoot: Option[String],
-                                     importResolvers: List[ImportResolver])
+                                     importResolvers: List[ImportResolver]
+  )
 }
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ResolvedExecutableInputsPoly.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ResolvedExecutableInputsPoly.scala
index dce4da0df38..888be25cfb5 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ResolvedExecutableInputsPoly.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ResolvedExecutableInputsPoly.scala
@@ -8,10 +8,13 @@ import wom.expression.{IoFunctionSet, WomExpression}
 import wom.values.WomValue
 
 object ResolvedExecutableInputsPoly extends Poly1 {
-  implicit def fromWdlValue: Case.Aux[WomValue, IoFunctionSet => ErrorOr[WomValue]] = at[WomValue] { wdlValue =>
-    _: IoFunctionSet => wdlValue.validNel 
+  implicit def fromWdlValue: Case.Aux[WomValue, IoFunctionSet => ErrorOr[WomValue]] = at[WomValue] {
+    wdlValue => _: IoFunctionSet => wdlValue.validNel
   }
-  implicit def fromWomExpression: Case.Aux[WomExpression, IoFunctionSet => ErrorOr[WomValue]] = at[WomExpression] { womExpression =>
-    ioFunctions: IoFunctionSet => womExpression.evaluateValue(Map.empty, ioFunctions).contextualizeErrors(s"evaluate expression '${womExpression.sourceString}'")
+  implicit def fromWomExpression: Case.Aux[WomExpression, IoFunctionSet => ErrorOr[WomValue]] = at[WomExpression] {
+    womExpression => ioFunctions: IoFunctionSet =>
+      womExpression
+        .evaluateValue(Map.empty, ioFunctions)
+        .contextualizeErrors(s"evaluate expression '${womExpression.sourceString}'")
   }
 }
diff --git a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
index 813a688a573..720a7f279af 100644
--- a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
+++ b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
@@ -11,7 +11,6 @@ import cromwell.languages.util.ImportResolver.{DirectoryResolver, HttpResolver}
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "HttpResolver"
 
@@ -49,7 +48,8 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
 
   it should "resolve a path and store the import in ResolvedImportRecord" in {
     val resolver = HttpResolver(None, Map.empty, None)
-    val importUri = "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.wdl"
+    val importUri =
+      "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.wdl"
     val resolvedBundle = resolver.innerResolver(importUri, List(resolver))
 
     resolvedBundle.map(_.resolvedImportRecord) match {
@@ -158,7 +158,8 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   behavior of "directory resolver from root"
 
   val workingDirectory = sys.props("user.dir")
-  val rootDirectoryResolver = DirectoryResolver(DefaultPath(Paths.get("/")), customName = None, deleteOnClose = false, directoryHash = None)
+  val rootDirectoryResolver =
+    DirectoryResolver(DefaultPath(Paths.get("/")), customName = None, deleteOnClose = false, directoryHash = None)
 
   it should "resolve a random path" in {
     val pathToLookup = rootDirectoryResolver.resolveAndMakeAbsolute("/path/to/file.wdl")
@@ -177,10 +178,18 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
 
   behavior of "unprotected relative directory resolver"
 
-  val relativeDirectoryResolver = DirectoryResolver(DefaultPath(Paths.get("/path/to/imports/")), customName = None, deleteOnClose = false, directoryHash = None)
+  val relativeDirectoryResolver = DirectoryResolver(DefaultPath(Paths.get("/path/to/imports/")),
+                                                    customName = None,
+                                                    deleteOnClose = false,
+                                                    directoryHash = None
+  )
 
   val relativeDirForSampleWf = s"$workingDirectory/languageFactories/language-factory-core/src/test/"
-  val relativeDirResolverForSampleWf = DirectoryResolver(DefaultPath(Paths.get(relativeDirForSampleWf)), customName = None, deleteOnClose = false, directoryHash = None)
+  val relativeDirResolverForSampleWf = DirectoryResolver(DefaultPath(Paths.get(relativeDirForSampleWf)),
+                                                         customName = None,
+                                                         deleteOnClose = false,
+                                                         directoryHash = None
+  )
 
   it should "resolve an absolute path" in {
     val pathToLookup = relativeDirectoryResolver.resolveAndMakeAbsolute("/path/to/file.wdl")
@@ -208,14 +217,24 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
 
     resolvedBundle.map(_.resolvedImportRecord) match {
       case Left(e) => fail(s"Expected ResolvedImportBundle but got $e")
-      case Right(resolvedImport) => resolvedImport.importPath shouldBe(relativeDirForSampleWf + path)
+      case Right(resolvedImport) => resolvedImport.importPath shouldBe (relativeDirForSampleWf + path)
     }
   }
 
   behavior of "protected relative directory resolver"
 
-  val protectedRelativeDirectoryResolver = DirectoryResolver(DefaultPath(Paths.get("/path/to/imports/")), Some("/path/to/imports/"), customName = None, deleteOnClose = false, directoryHash = None)
-  val protectedRelativeDirResolverForSampleWf = DirectoryResolver(DefaultPath(Paths.get(relativeDirForSampleWf)), Some(relativeDirForSampleWf), customName = None, deleteOnClose = false, directoryHash = None)
+  val protectedRelativeDirectoryResolver = DirectoryResolver(DefaultPath(Paths.get("/path/to/imports/")),
+                                                             Some("/path/to/imports/"),
+                                                             customName = None,
+                                                             deleteOnClose = false,
+                                                             directoryHash = None
+  )
+  val protectedRelativeDirResolverForSampleWf = DirectoryResolver(DefaultPath(Paths.get(relativeDirForSampleWf)),
+                                                                  Some(relativeDirForSampleWf),
+                                                                  customName = None,
+                                                                  deleteOnClose = false,
+                                                                  directoryHash = None
+  )
 
   it should "resolve a good relative path" in {
     val pathToLookup = protectedRelativeDirectoryResolver.resolveAndMakeAbsolute("path/to/file.wdl")
@@ -224,11 +243,12 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
 
   it should "resolve a good relative path to sampleWorkflow" in {
     val path = "resources/sampleWorkflow.wdl"
-    val resolvedBundle = protectedRelativeDirResolverForSampleWf.innerResolver(path, List(protectedRelativeDirResolverForSampleWf))
+    val resolvedBundle =
+      protectedRelativeDirResolverForSampleWf.innerResolver(path, List(protectedRelativeDirResolverForSampleWf))
 
     resolvedBundle.map(_.resolvedImportRecord) match {
       case Left(e) => fail(s"Expected ResolvedImportBundle but got $e")
-      case Right(resolvedImport) => resolvedImport.importPath shouldBe(relativeDirForSampleWf + path)
+      case Right(resolvedImport) => resolvedImport.importPath shouldBe (relativeDirForSampleWf + path)
     }
   }
 
@@ -252,7 +272,7 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     resolver.resolveAndMakeAbsolute("QC.wdl").map(Files.exists(_)).toOption shouldBe Some(true)
     resolver.resolveAndMakeAbsolute("tasks/cutadapt.wdl").map(Files.exists(_)).toOption shouldBe Some(true)
     resolver.resolveAndMakeAbsolute("tasks/fastqc.wdl").map(Files.exists(_)).toOption shouldBe Some(true)
-      // Make sure above testing is correct by testing for a non-existent wdl.
+    // Make sure above testing is correct by testing for a non-existent wdl.
     resolver.resolveAndMakeAbsolute("machine_learning_skynet.wdl").map(Files.exists(_)).toOption shouldBe Some(false)
   }
 
diff --git a/languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala b/languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala
index 355a637439b..eace0c91f9b 100644
--- a/languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala
+++ b/languageFactories/wdl-biscayne/src/main/scala/languages/wdl/biscayne/WdlBiscayneLanguageFactory.scala
@@ -38,13 +38,19 @@ class WdlBiscayneLanguageFactory(override val config: Config) extends LanguageFa
                                  importLocalFilesystem: Boolean,
                                  workflowIdForLogging: WorkflowId,
                                  ioFunctions: IoFunctionSet,
-                                 importResolvers: List[ImportResolver]): IOChecked[ValidatedWomNamespace] = {
+                                 importResolvers: List[ImportResolver]
+  ): IOChecked[ValidatedWomNamespace] = {
 
     val factories: List[LanguageFactory] = List(this)
 
     val checked: Checked[ValidatedWomNamespace] = for {
       _ <- enabledCheck
-      bundle <- getWomBundle(workflowSource, workflowSourceOrigin = None, source.workflowOptions.asPrettyJson, importResolvers, factories)
+      bundle <- getWomBundle(workflowSource,
+                             workflowSourceOrigin = None,
+                             source.workflowOptions.asPrettyJson,
+                             importResolvers,
+                             factories
+      )
       executable <- createExecutable(bundle, source.inputsJson, ioFunctions)
     } yield executable
 
@@ -57,17 +63,31 @@ class WdlBiscayneLanguageFactory(override val config: Config) extends LanguageFa
                             workflowOptionsJson: WorkflowOptionsJson,
                             importResolvers: List[ImportResolver],
                             languageFactories: List[LanguageFactory],
-                            convertNestedScatterToSubworkflow : Boolean = true): Checked[WomBundle] = {
-
-    val converter: CheckedAtoB[FileStringParserInput, WomBundle] = stringToAst andThen wrapAst andThen astToFileElement.map(FileElementToWomBundleInputs(_, workflowOptionsJson, convertNestedScatterToSubworkflow, importResolvers, languageFactories, workflowDefinitionElementToWomWorkflowDefinition, taskDefinitionElementToWomTaskDefinition)) andThen fileElementToWomBundle
+                            convertNestedScatterToSubworkflow: Boolean = true
+  ): Checked[WomBundle] = {
+
+    val converter: CheckedAtoB[FileStringParserInput, WomBundle] =
+      stringToAst andThen wrapAst andThen astToFileElement.map(
+        FileElementToWomBundleInputs(
+          _,
+          workflowOptionsJson,
+          convertNestedScatterToSubworkflow,
+          importResolvers,
+          languageFactories,
+          workflowDefinitionElementToWomWorkflowDefinition,
+          taskDefinitionElementToWomTaskDefinition
+        )
+      ) andThen fileElementToWomBundle
 
     lazy val validationCallable = new Callable[ErrorOr[WomBundle]] {
       def call: ErrorOr[WomBundle] = converter
         .run(FileStringParserInput(workflowSource, workflowSourceOrigin.map(_.importPath).getOrElse("input.wdl")))
-        .map(b => b.copyResolvedImportRecord(b, workflowSourceOrigin)).toValidated
+        .map(b => b.copyResolvedImportRecord(b, workflowSourceOrigin))
+        .toValidated
     }
 
-    lazy val parserCacheInputs = ParserCacheInputs(Option(workflowSource), workflowSourceOrigin.map(_.importPath), None, importResolvers)
+    lazy val parserCacheInputs =
+      ParserCacheInputs(Option(workflowSource), workflowSourceOrigin.map(_.importPath), None, importResolvers)
 
     for {
       _ <- enabledCheck
@@ -75,13 +95,16 @@ class WdlBiscayneLanguageFactory(override val config: Config) extends LanguageFa
     } yield womBundle
   }
 
-  override def createExecutable(womBundle: WomBundle, inputsJson: WorkflowJson, ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace] = {
+  override def createExecutable(womBundle: WomBundle,
+                                inputsJson: WorkflowJson,
+                                ioFunctions: IoFunctionSet
+  ): Checked[ValidatedWomNamespace] =
     for {
       _ <- enabledCheck
       executable <- womBundle.toWomExecutable(Option(inputsJson), ioFunctions, strictValidation)
       validated <- LanguageFactoryUtil.validateWomNamespace(executable, ioFunctions)
     } yield validated
-  }
 
-  override def looksParsable(content: String): Boolean = LanguageFactoryUtil.simpleLooksParseable(List("version development-1.1"), List("#"))(content)
+  override def looksParsable(content: String): Boolean =
+    LanguageFactoryUtil.simpleLooksParseable(List("version development-1.1"), List("#"))(content)
 }
diff --git a/languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala b/languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala
index d7757e83e71..5954f964fc5 100644
--- a/languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala
+++ b/languageFactories/wdl-cascades/src/main/scala/languages/wdl/cascades/WdlCascadesLanguageFactory.scala
@@ -38,13 +38,19 @@ class WdlCascadesLanguageFactory(override val config: Config) extends LanguageFa
                                  importLocalFilesystem: Boolean,
                                  workflowIdForLogging: WorkflowId,
                                  ioFunctions: IoFunctionSet,
-                                 importResolvers: List[ImportResolver]): IOChecked[ValidatedWomNamespace] = {
+                                 importResolvers: List[ImportResolver]
+  ): IOChecked[ValidatedWomNamespace] = {
 
     val factories: List[LanguageFactory] = List(this)
 
     val checked: Checked[ValidatedWomNamespace] = for {
       _ <- enabledCheck
-      bundle <- getWomBundle(workflowSource, workflowSourceOrigin = None, source.workflowOptions.asPrettyJson, importResolvers, factories)
+      bundle <- getWomBundle(workflowSource,
+                             workflowSourceOrigin = None,
+                             source.workflowOptions.asPrettyJson,
+                             importResolvers,
+                             factories
+      )
       executable <- createExecutable(bundle, source.inputsJson, ioFunctions)
     } yield executable
 
@@ -57,17 +63,31 @@ class WdlCascadesLanguageFactory(override val config: Config) extends LanguageFa
                             workflowOptionsJson: WorkflowOptionsJson,
                             importResolvers: List[ImportResolver],
                             languageFactories: List[LanguageFactory],
-                            convertNestedScatterToSubworkflow : Boolean = true): Checked[WomBundle] = {
-
-    val converter: CheckedAtoB[FileStringParserInput, WomBundle] = stringToAst andThen wrapAst andThen astToFileElement.map(FileElementToWomBundleInputs(_, workflowOptionsJson, convertNestedScatterToSubworkflow, importResolvers, languageFactories, workflowDefinitionElementToWomWorkflowDefinition, taskDefinitionElementToWomTaskDefinition)) andThen fileElementToWomBundle
+                            convertNestedScatterToSubworkflow: Boolean = true
+  ): Checked[WomBundle] = {
+
+    val converter: CheckedAtoB[FileStringParserInput, WomBundle] =
+      stringToAst andThen wrapAst andThen astToFileElement.map(
+        FileElementToWomBundleInputs(
+          _,
+          workflowOptionsJson,
+          convertNestedScatterToSubworkflow,
+          importResolvers,
+          languageFactories,
+          workflowDefinitionElementToWomWorkflowDefinition,
+          taskDefinitionElementToWomTaskDefinition
+        )
+      ) andThen fileElementToWomBundle
 
     lazy val validationCallable = new Callable[ErrorOr[WomBundle]] {
       def call: ErrorOr[WomBundle] = converter
         .run(FileStringParserInput(workflowSource, workflowSourceOrigin.map(_.importPath).getOrElse("input.wdl")))
-        .map(b => b.copyResolvedImportRecord(b, workflowSourceOrigin)).toValidated
+        .map(b => b.copyResolvedImportRecord(b, workflowSourceOrigin))
+        .toValidated
     }
 
-    lazy val parserCacheInputs = ParserCacheInputs(Option(workflowSource), workflowSourceOrigin.map(_.importPath), None, importResolvers)
+    lazy val parserCacheInputs =
+      ParserCacheInputs(Option(workflowSource), workflowSourceOrigin.map(_.importPath), None, importResolvers)
 
     for {
       _ <- enabledCheck
@@ -75,13 +95,16 @@ class WdlCascadesLanguageFactory(override val config: Config) extends LanguageFa
     } yield womBundle
   }
 
-  override def createExecutable(womBundle: WomBundle, inputsJson: WorkflowJson, ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace] = {
+  override def createExecutable(womBundle: WomBundle,
+                                inputsJson: WorkflowJson,
+                                ioFunctions: IoFunctionSet
+  ): Checked[ValidatedWomNamespace] =
     for {
       _ <- enabledCheck
       executable <- womBundle.toWomExecutable(Option(inputsJson), ioFunctions, strictValidation)
       validated <- LanguageFactoryUtil.validateWomNamespace(executable, ioFunctions)
     } yield validated
-  }
 
-  override def looksParsable(content: String): Boolean = LanguageFactoryUtil.simpleLooksParseable(List("version development"), List("#"))(content)
+  override def looksParsable(content: String): Boolean =
+    LanguageFactoryUtil.simpleLooksParseable(List("version development"), List("#"))(content)
 }
diff --git a/languageFactories/wdl-draft2/src/main/scala/languages/wdl/draft2/WdlDraft2LanguageFactory.scala b/languageFactories/wdl-draft2/src/main/scala/languages/wdl/draft2/WdlDraft2LanguageFactory.scala
index a2cbc5e90f4..a1b4927517a 100644
--- a/languageFactories/wdl-draft2/src/main/scala/languages/wdl/draft2/WdlDraft2LanguageFactory.scala
+++ b/languageFactories/wdl-draft2/src/main/scala/languages/wdl/draft2/WdlDraft2LanguageFactory.scala
@@ -24,7 +24,7 @@ import languages.wdl.draft2.WdlDraft2LanguageFactory._
 import mouse.all._
 import net.ceedubs.ficus.Ficus._
 import wdl.draft2.Draft2ResolvedImportBundle
-import wdl.draft2.model.{Draft2ImportResolver, WdlNamespace, WdlNamespaceWithWorkflow, WdlNamespaceWithoutWorkflow}
+import wdl.draft2.model.{Draft2ImportResolver, WdlNamespace, WdlNamespaceWithoutWorkflow, WdlNamespaceWithWorkflow}
 import wdl.shared.transforms.wdlom2wom.WdlSharedInputParsing
 import wdl.transforms.draft2.wdlom2wom.WdlDraft2WomBundleMakers._
 import wdl.transforms.draft2.wdlom2wom.WdlDraft2WomExecutableMakers._
@@ -40,7 +40,10 @@ import wom.values._
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-class WdlDraft2LanguageFactory(override val config: Config) extends LanguageFactory with ParserCache[WdlNamespace] with StrictLogging {
+class WdlDraft2LanguageFactory(override val config: Config)
+    extends LanguageFactory
+    with ParserCache[WdlNamespace]
+    with StrictLogging {
 
   override val languageName: String = "WDL"
   override val languageVersionName: String = "draft-2"
@@ -51,19 +54,22 @@ class WdlDraft2LanguageFactory(override val config: Config) extends LanguageFact
                                  importLocalFilesystem: Boolean,
                                  workflowIdForLogging: WorkflowId,
                                  ioFunctions: IoFunctionSet,
-                                 importResolvers: List[ImportResolver]): IOChecked[ValidatedWomNamespace] = {
+                                 importResolvers: List[ImportResolver]
+  ): IOChecked[ValidatedWomNamespace] = {
 
     def checkTypes(namespace: WdlNamespace, inputs: Map[OutputPort, WomValue]): Checked[Unit] = namespace match {
 
       case namespaceWithWorkflow: WdlNamespaceWithWorkflow =>
-        val allDeclarations = namespaceWithWorkflow.workflow.declarations ++ namespaceWithWorkflow.workflow.calls.flatMap(_.declarations)
-        val list: List[Checked[Unit]] = inputs.map({ case (k, v) =>
+        val allDeclarations =
+          namespaceWithWorkflow.workflow.declarations ++ namespaceWithWorkflow.workflow.calls.flatMap(_.declarations)
+        val list: List[Checked[Unit]] = inputs.map { case (k, v) =>
           allDeclarations.find(_.fullyQualifiedName == k) match {
             case Some(decl) if decl.womType.coerceRawValue(v).isFailure =>
-              s"Invalid right-side type of '$k'.  Expecting ${decl.womType.stableName}, got ${v.womType.stableName}".invalidNelCheck[Unit]
+              s"Invalid right-side type of '$k'.  Expecting ${decl.womType.stableName}, got ${v.womType.stableName}"
+                .invalidNelCheck[Unit]
             case _ => ().validNelCheck
           }
-        }).toList
+        }.toList
 
         list.sequence[Checked, Unit].void
 
@@ -73,14 +79,16 @@ class WdlDraft2LanguageFactory(override val config: Config) extends LanguageFact
     }
 
     def validationCallable = new Callable[ErrorOr[WdlNamespace]] {
-      def call: ErrorOr[WdlNamespace] = WdlNamespaceWithWorkflow.load(workflowSource, importResolvers map resolverConverter).toErrorOr
+      def call: ErrorOr[WdlNamespace] =
+        WdlNamespaceWithWorkflow.load(workflowSource, importResolvers map resolverConverter).toErrorOr
     }
 
-    lazy val wdlNamespaceValidation: ErrorOr[WdlNamespace] = retrieveOrCalculate(ParserCacheInputs(Option(workflowSource), None, None, importResolvers), validationCallable)
+    lazy val wdlNamespaceValidation: ErrorOr[WdlNamespace] =
+      retrieveOrCalculate(ParserCacheInputs(Option(workflowSource), None, None, importResolvers), validationCallable)
 
     def evaluateImports(wdlNamespace: WdlNamespace): Map[String, String] = {
       // Descend the namespace looking for imports and construct `MetadataEvent`s for them.
-      def collectImportEvents: Map[String, String] = {
+      def collectImportEvents: Map[String, String] =
         (wdlNamespace.allNamespacesRecursively flatMap { ns =>
           ns.importUri.toList collect {
             // Do not publish import events for URIs which correspond to literal strings as these are the top-level
@@ -88,7 +96,6 @@ class WdlDraft2LanguageFactory(override val config: Config) extends LanguageFact
             case uri if uri != WdlNamespace.WorkflowResourceString => uri -> ns.sourceString
           }
         }).toMap
-      }
 
       collectImportEvents
     }
@@ -108,7 +115,8 @@ class WdlDraft2LanguageFactory(override val config: Config) extends LanguageFact
 
   private def validateWorkflowNameLengths(namespace: WdlNamespace): Checked[Unit] = {
     import common.validation.Checked._
-    def allWorkflowNames(n: WdlNamespace): Seq[String] = n.workflows.map(_.unqualifiedName) ++ n.namespaces.flatMap(allWorkflowNames)
+    def allWorkflowNames(n: WdlNamespace): Seq[String] =
+      n.workflows.map(_.unqualifiedName) ++ n.namespaces.flatMap(allWorkflowNames)
     val tooLong = allWorkflowNames(namespace).filter(_.length >= 100)
     if (tooLong.nonEmpty) {
       ("Workflow names must be shorter than 100 characters: " + tooLong.mkString(" ")).invalidNelCheck
@@ -122,12 +130,15 @@ class WdlDraft2LanguageFactory(override val config: Config) extends LanguageFact
                             workflowOptionsJson: WorkflowOptionsJson,
                             importResolvers: List[ImportResolver],
                             languageFactories: List[LanguageFactory],
-                            convertNestedScatterToSubworkflow : Boolean = true): Checked[WomBundle] = {
+                            convertNestedScatterToSubworkflow: Boolean = true
+  ): Checked[WomBundle] = {
     lazy val validationCallable = new Callable[ErrorOr[WdlNamespace]] {
-      def call: ErrorOr[WdlNamespace] = WdlNamespace.loadUsingSource(workflowSource, None, Some(importResolvers map resolverConverter)).toErrorOr
+      def call: ErrorOr[WdlNamespace] =
+        WdlNamespace.loadUsingSource(workflowSource, None, Some(importResolvers map resolverConverter)).toErrorOr
     }
 
-    lazy val parserCacheInputs = ParserCacheInputs(Option(workflowSource), workflowSourceOrigin.map(_.importPath), None, importResolvers)
+    lazy val parserCacheInputs =
+      ParserCacheInputs(Option(workflowSource), workflowSourceOrigin.map(_.importPath), None, importResolvers)
 
     for {
       _ <- enabledCheck
@@ -136,7 +147,10 @@ class WdlDraft2LanguageFactory(override val config: Config) extends LanguageFact
     } yield womBundle.copyResolvedImportRecord(womBundle, workflowSourceOrigin)
   }
 
-  override def createExecutable(womBundle: WomBundle, inputs: WorkflowJson, ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace] = for {
+  override def createExecutable(womBundle: WomBundle,
+                                inputs: WorkflowJson,
+                                ioFunctions: IoFunctionSet
+  ): Checked[ValidatedWomNamespace] = for {
     _ <- enabledCheck
     executable <- WdlSharedInputParsing.buildWomExecutable(womBundle, Option(inputs), ioFunctions, strictValidation)
     validatedNamespace <- LanguageFactoryUtil.validateWomNamespace(executable, ioFunctions)
@@ -145,22 +159,25 @@ class WdlDraft2LanguageFactory(override val config: Config) extends LanguageFact
   // Commentary: we'll set this as the default in the reference.conf, so most people will get WDL draft 2 if nothing else looks parsable.
   override def looksParsable(content: String): Boolean = false
 
-  private[draft2] lazy val cacheConfig: Option[CacheConfig] = {
+  private[draft2] lazy val cacheConfig: Option[CacheConfig] =
     // WDL version 2 namespace caching is now opt-in.
     for {
       _ <- enabled.option(())
       caching <- config.as[Option[Config]]("caching")
       cc <- CacheConfig.optionalConfig(caching, defaultConcurrency = 2, defaultSize = 1000L, defaultTtl = 20 minutes)
     } yield cc
-  }
 }
 
 object WdlDraft2LanguageFactory {
-  private def resolverConverter(importResolver: ImportResolver): Draft2ImportResolver = str => importResolver.resolver.run(ImportResolutionRequest(str, List.empty)) match {
-    case Right(imported) => Draft2ResolvedImportBundle(imported.source, imported.resolvedImportRecord)
-    case Left(errors) => throw new RuntimeException(s"Bad import $str: ${errors.toList.mkString(System.lineSeparator)}")
-  }
+  private def resolverConverter(importResolver: ImportResolver): Draft2ImportResolver = str =>
+    importResolver.resolver.run(ImportResolutionRequest(str, List.empty)) match {
+      case Right(imported) => Draft2ResolvedImportBundle(imported.source, imported.resolvedImportRecord)
+      case Left(errors) =>
+        throw new RuntimeException(s"Bad import $str: ${errors.toList.mkString(System.lineSeparator)}")
+    }
 
   val httpResolver = resolverConverter(ImportResolver.HttpResolver())
-  def httpResolverWithHeaders(headers: Map[String, String]) = resolverConverter(ImportResolver.HttpResolver(headers = headers))
+  def httpResolverWithHeaders(headers: Map[String, String]) = resolverConverter(
+    ImportResolver.HttpResolver(headers = headers)
+  )
 }
diff --git a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/ArrayCoercionsSpec.scala b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/ArrayCoercionsSpec.scala
index 08cd91f3432..a44f34f5af1 100644
--- a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/ArrayCoercionsSpec.scala
+++ b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/ArrayCoercionsSpec.scala
@@ -14,22 +14,25 @@ import wom.expression.EmptyIoFunctionSet
 import wom.types.{WomArrayType, WomSingleFileType, WomStringType}
 import wom.values.{WomArray, WomSingleFile, WomString}
 
-
 class ArrayCoercionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   var factory: WdlDraft2LanguageFactory = new WdlDraft2LanguageFactory(ConfigFactory.parseString(ConfigString))
-  val arrayLiteralNamespace: WdlNamespaceWithWorkflow = WdlNamespaceWithWorkflow.load(ArrayDeclarationWorkflow, List.empty).get
+  val arrayLiteralNamespace: WdlNamespaceWithWorkflow =
+    WdlNamespaceWithWorkflow.load(ArrayDeclarationWorkflow, List.empty).get
 
   "A static Array[File] declaration" should "be a valid declaration" in {
-    val declaration = arrayLiteralNamespace.workflow.declarations.find {_.unqualifiedName == "arr"}.getOrElse {
+    val declaration = arrayLiteralNamespace.workflow.declarations.find(_.unqualifiedName == "arr").getOrElse {
       fail("Expected declaration 'arr' to be found")
     }
     val expression = declaration.expression.getOrElse {
       fail("Expected an expression for declaration 'arr'")
     }
-    expression.evaluate((_: String) => fail("No lookups"), NoFunctions).toChecked.shouldBeValid(
-      WomArray(WomArrayType(WomStringType), Seq(WomString("f1"), WomString("f2"), WomString("f3")))
-    )
+    expression
+      .evaluate((_: String) => fail("No lookups"), NoFunctions)
+      .toChecked
+      .shouldBeValid(
+        WomArray(WomArrayType(WomStringType), Seq(WomString("f1"), WomString("f2"), WomString("f3")))
+      )
   }
 
   "An Array[File]" should "be usable as an input" in {
@@ -40,9 +43,10 @@ class ArrayCoercionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     val catTask = arrayLiteralNamespace.findTask("cat").getOrElse {
       fail("Expected to find task 'cat'")
     }
-    val command = catTask.instantiateCommand(catTask.inputsFromMap(Map("cat.files" -> expectedArray)), NoFunctions).getOrElse {
-      fail("Expected instantiation to work")
-    }
+    val command =
+      catTask.instantiateCommand(catTask.inputsFromMap(Map("cat.files" -> expectedArray)), NoFunctions).getOrElse {
+        fail("Expected instantiation to work")
+      }
     command.head.commandString shouldEqual "cat -s f1 f2 f3"
   }
 
diff --git a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/MapWorkflowSpec.scala b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/MapWorkflowSpec.scala
index 981ad1380c4..dbba026fcbb 100644
--- a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/MapWorkflowSpec.scala
+++ b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/MapWorkflowSpec.scala
@@ -11,21 +11,25 @@ import wom.values.{WomMap, WomSingleFile, WomString, WomValue}
 
 import scala.util.{Success, Try}
 
-
 class MapWorkflowSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   val namespace = WdlNamespaceWithWorkflow.load(WorkflowSource, Seq.empty[Draft2ImportResolver]).get
-  val expectedMap = WomMap(WomMapType(WomSingleFileType, WomStringType), Map(
-    WomSingleFile("f1") -> WomString("alice"),
-    WomSingleFile("f2") -> WomString("bob"),
-    WomSingleFile("f3") -> WomString("chuck")
-  ))
+  val expectedMap = WomMap(
+    WomMapType(WomSingleFileType, WomStringType),
+    Map(
+      WomSingleFile("f1") -> WomString("alice"),
+      WomSingleFile("f2") -> WomString("bob"),
+      WomSingleFile("f3") -> WomString("chuck")
+    )
+  )
 
   "A static Map[File, String] declaration" should "be a valid declaration" in {
-    val declaration = namespace.workflow.declarations.find {
-      _.unqualifiedName == "map"
-    }.getOrElse {
-      fail("Expected declaration 'map' to be found")
-    }
+    val declaration = namespace.workflow.declarations
+      .find {
+        _.unqualifiedName == "map"
+      }
+      .getOrElse {
+        fail("Expected declaration 'map' to be found")
+      }
     val expression = declaration.expression.getOrElse {
       fail("Expected an expression for declaration 'map'")
     }
@@ -47,9 +51,11 @@ class MapWorkflowSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
         case _ => throw new UnsupportedOperationException("Only write_map should be called")
       }
     }
-    val command = writeMapTask.instantiateCommand(writeMapTask.inputsFromMap(Map("file_to_name" -> expectedMap)), new CannedFunctions).getOrElse {
-      fail("Expected instantiation to work")
-    }
+    val command = writeMapTask
+      .instantiateCommand(writeMapTask.inputsFromMap(Map("file_to_name" -> expectedMap)), new CannedFunctions)
+      .getOrElse {
+        fail("Expected instantiation to work")
+      }
     command.head.commandString shouldEqual "cat /test/map/path"
   }
 }
diff --git a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
index b96cfa5c2f6..eab4163410d 100644
--- a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
+++ b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
@@ -69,14 +69,18 @@ class NamespaceCacheSpec extends AnyFlatSpec with CromwellTimeoutSpec with Befor
     }
 
     def validate = {
-      val futureNamespace = factory.validateNamespace(
-        source = collection,
-        workflowSource = ThreeStep,
-        workflowOptions = WorkflowOptions(new spray.json.JsObject(Map.empty)),
-        importLocalFilesystem = false,
-        workflowIdForLogging = WorkflowId.randomId(),
-        ioFunctions = NoIoFunctionSet,
-        importResolvers = List(countingResolver)).value.unsafeToFuture()
+      val futureNamespace = factory
+        .validateNamespace(
+          source = collection,
+          workflowSource = ThreeStep,
+          workflowOptions = WorkflowOptions(new spray.json.JsObject(Map.empty)),
+          importLocalFilesystem = false,
+          workflowIdForLogging = WorkflowId.randomId(),
+          ioFunctions = NoIoFunctionSet,
+          importResolvers = List(countingResolver)
+        )
+        .value
+        .unsafeToFuture()
       Await.result(futureNamespace, Duration.Inf).toOption.get
     }
 
diff --git a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/WdlWorkflowHttpImportSpec.scala b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/WdlWorkflowHttpImportSpec.scala
index a31df438f3a..1d1d96c07e8 100644
--- a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/WdlWorkflowHttpImportSpec.scala
+++ b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/WdlWorkflowHttpImportSpec.scala
@@ -11,8 +11,7 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import wdl.draft2.model._
 
-
-class WdlWorkflowHttpImportSpec extends AnyFlatSpec with CromwellTimeoutSpec with BeforeAndAfterAll with Matchers  {
+class WdlWorkflowHttpImportSpec extends AnyFlatSpec with CromwellTimeoutSpec with BeforeAndAfterAll with Matchers {
   val tinyImport =
     s"""
        |task hello {
@@ -27,7 +26,7 @@ class WdlWorkflowHttpImportSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
        |
      """.stripMargin
 
-  def tinyWorkflow(imp:String) =
+  def tinyWorkflow(imp: String) =
     s"""
        | import "$imp" as imp
        |
@@ -45,29 +44,35 @@ class WdlWorkflowHttpImportSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     mockServer = startClientAndServer(PortFactory.findFreePort())
     host = "http://localhost:" + mockServer.getLocalPort
 
-    mockServer.when(
-      request().withPath("/hello.wdl")
-    ).respond(
-      response().withStatusCode(200).withBody(tinyImport)
-    )
-
-    mockServer.when(
-      request().withPath("/protected.wdl").withHeader("Authorization", "Bearer my-token-value")
-    ).
-      respond(
-      response().withStatusCode(200).withBody(tinyImport)
-    )
-
-    mockServer.when(
-      request().withPath("/redirect.wdl")
-    ).respond(
-      response().withStatusCode(301).withHeader("Location","/hello.wdl"))
-
-    mockServer.when(
-      request().withPath("/none.wdl")
-    ).respond(
-      response().withStatusCode(404)
-    )
+    mockServer
+      .when(
+        request().withPath("/hello.wdl")
+      )
+      .respond(
+        response().withStatusCode(200).withBody(tinyImport)
+      )
+
+    mockServer
+      .when(
+        request().withPath("/protected.wdl").withHeader("Authorization", "Bearer my-token-value")
+      )
+      .respond(
+        response().withStatusCode(200).withBody(tinyImport)
+      )
+
+    mockServer
+      .when(
+        request().withPath("/redirect.wdl")
+      )
+      .respond(response().withStatusCode(301).withHeader("Location", "/hello.wdl"))
+
+    mockServer
+      .when(
+        request().withPath("/none.wdl")
+      )
+      .respond(
+        response().withStatusCode(404)
+      )
 
     () // explicitly return unit
   }
@@ -84,28 +89,28 @@ class WdlWorkflowHttpImportSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
   }
 
   it should "resolve an http URL" in {
-    val wf = tinyWorkflow( s"$host/hello.wdl")
+    val wf = tinyWorkflow(s"$host/hello.wdl")
     val ns = WdlNamespaceWithWorkflow.load(wf, httpResolver)
     ns.isFailure shouldBe false
   }
 
   it should "fail with a 404" in {
-    val wf = tinyWorkflow( s"$host/none.wdl")
+    val wf = tinyWorkflow(s"$host/none.wdl")
     val ns = WdlNamespaceWithWorkflow.load(wf, httpResolver)
     ns.isFailure shouldBe true
   }
 
   it should "follow a redirect" in {
-    val wf = tinyWorkflow( s"$host/redirect.wdl")
+    val wf = tinyWorkflow(s"$host/redirect.wdl")
     val ns = WdlNamespaceWithWorkflow.load(wf, httpResolver)
     ns.isFailure shouldBe false
   }
 
   it should "be able to supply a bearer token to a protected resource" in {
     val auth = Map("Authorization" -> "Bearer my-token-value")
-    val authHttpResolver : Seq[Draft2ImportResolver] = Seq(WdlDraft2LanguageFactory.httpResolverWithHeaders(auth))
+    val authHttpResolver: Seq[Draft2ImportResolver] = Seq(WdlDraft2LanguageFactory.httpResolverWithHeaders(auth))
 
-    val wf = tinyWorkflow( s"$host/protected.wdl")
+    val wf = tinyWorkflow(s"$host/protected.wdl")
     val ns = WdlNamespaceWithWorkflow.load(wf, authHttpResolver)
     ns.isFailure shouldBe false
   }
diff --git a/languageFactories/wdl-draft3/src/main/scala/languages/wdl/draft3/WdlDraft3LanguageFactory.scala b/languageFactories/wdl-draft3/src/main/scala/languages/wdl/draft3/WdlDraft3LanguageFactory.scala
index 56337b0010e..d6eb4ab056d 100644
--- a/languageFactories/wdl-draft3/src/main/scala/languages/wdl/draft3/WdlDraft3LanguageFactory.scala
+++ b/languageFactories/wdl-draft3/src/main/scala/languages/wdl/draft3/WdlDraft3LanguageFactory.scala
@@ -32,40 +32,57 @@ class WdlDraft3LanguageFactory(override val config: Config) extends LanguageFact
   override val languageName: String = "WDL"
   override val languageVersionName: String = "1.0"
 
-
   override def validateNamespace(source: WorkflowSourceFilesCollection,
                                  workflowSource: WorkflowSource,
                                  workflowOptions: WorkflowOptions,
                                  importLocalFilesystem: Boolean,
                                  workflowIdForLogging: WorkflowId,
                                  ioFunctions: IoFunctionSet,
-                                 importResolvers: List[ImportResolver]): IOChecked[ValidatedWomNamespace] = {
+                                 importResolvers: List[ImportResolver]
+  ): IOChecked[ValidatedWomNamespace] = {
 
     val factories: List[LanguageFactory] = List(this)
 
     val checked: Checked[ValidatedWomNamespace] = for {
       _ <- enabledCheck
-      bundle <- getWomBundle(workflowSource, workflowSourceOrigin = None, source.workflowOptions.asPrettyJson, importResolvers, factories)
+      bundle <- getWomBundle(workflowSource,
+                             workflowSourceOrigin = None,
+                             source.workflowOptions.asPrettyJson,
+                             importResolvers,
+                             factories
+      )
       executable <- createExecutable(bundle, source.inputsJson, ioFunctions)
     } yield executable
 
     fromEither[IO](checked)
   }
 
-
   // The only reason this isn't a sub-def inside 'getWomBundle' is that it gets overridden in test cases:
   protected def makeWomBundle(workflowSource: WorkflowSource,
-                            workflowSourceOrigin: Option[ResolvedImportRecord],
-                            workflowOptionsJson: WorkflowOptionsJson,
-                            importResolvers: List[ImportResolver],
-                            languageFactories: List[LanguageFactory],
-                            convertNestedScatterToSubworkflow : Boolean = true): ErrorOr[WomBundle] = {
-
-    val converter: CheckedAtoB[FileStringParserInput, WomBundle] = stringToAst andThen wrapAst andThen astToFileElement.map(FileElementToWomBundleInputs(_, workflowOptionsJson, convertNestedScatterToSubworkflow, importResolvers, languageFactories, workflowDefinitionElementToWomWorkflowDefinition, taskDefinitionElementToWomTaskDefinition)) andThen fileElementToWomBundle
+                              workflowSourceOrigin: Option[ResolvedImportRecord],
+                              workflowOptionsJson: WorkflowOptionsJson,
+                              importResolvers: List[ImportResolver],
+                              languageFactories: List[LanguageFactory],
+                              convertNestedScatterToSubworkflow: Boolean = true
+  ): ErrorOr[WomBundle] = {
+
+    val converter: CheckedAtoB[FileStringParserInput, WomBundle] =
+      stringToAst andThen wrapAst andThen astToFileElement.map(
+        FileElementToWomBundleInputs(
+          _,
+          workflowOptionsJson,
+          convertNestedScatterToSubworkflow,
+          importResolvers,
+          languageFactories,
+          workflowDefinitionElementToWomWorkflowDefinition,
+          taskDefinitionElementToWomTaskDefinition
+        )
+      ) andThen fileElementToWomBundle
 
     converter
       .run(FileStringParserInput(workflowSource, workflowSourceOrigin.map(_.importPath).getOrElse("input.wdl")))
-      .map(b => b.copyResolvedImportRecord(b, workflowSourceOrigin)).toValidated
+      .map(b => b.copyResolvedImportRecord(b, workflowSourceOrigin))
+      .toValidated
   }
 
   override def getWomBundle(workflowSource: WorkflowSource,
@@ -73,13 +90,21 @@ class WdlDraft3LanguageFactory(override val config: Config) extends LanguageFact
                             workflowOptionsJson: WorkflowOptionsJson,
                             importResolvers: List[ImportResolver],
                             languageFactories: List[LanguageFactory],
-                            convertNestedScatterToSubworkflow : Boolean = true): Checked[WomBundle] = {
+                            convertNestedScatterToSubworkflow: Boolean = true
+  ): Checked[WomBundle] = {
 
     lazy val validationCallable = new Callable[ErrorOr[WomBundle]] {
-      def call: ErrorOr[WomBundle] = makeWomBundle(workflowSource, workflowSourceOrigin, workflowOptionsJson, importResolvers, languageFactories, convertNestedScatterToSubworkflow)
+      def call: ErrorOr[WomBundle] = makeWomBundle(workflowSource,
+                                                   workflowSourceOrigin,
+                                                   workflowOptionsJson,
+                                                   importResolvers,
+                                                   languageFactories,
+                                                   convertNestedScatterToSubworkflow
+      )
     }
 
-    lazy val parserCacheInputs = ParserCacheInputs(Option(workflowSource), workflowSourceOrigin.map(_.importPath), None, importResolvers)
+    lazy val parserCacheInputs =
+      ParserCacheInputs(Option(workflowSource), workflowSourceOrigin.map(_.importPath), None, importResolvers)
 
     for {
       _ <- enabledCheck
@@ -87,13 +112,16 @@ class WdlDraft3LanguageFactory(override val config: Config) extends LanguageFact
     } yield womBundle
   }
 
-  override def createExecutable(womBundle: WomBundle, inputsJson: WorkflowJson, ioFunctions: IoFunctionSet): Checked[ValidatedWomNamespace] = {
+  override def createExecutable(womBundle: WomBundle,
+                                inputsJson: WorkflowJson,
+                                ioFunctions: IoFunctionSet
+  ): Checked[ValidatedWomNamespace] =
     for {
       _ <- enabledCheck
       executable <- womBundle.toWomExecutable(Option(inputsJson), ioFunctions, strictValidation)
       validated <- LanguageFactoryUtil.validateWomNamespace(executable, ioFunctions)
     } yield validated
-  }
 
-  override def looksParsable(content: String): Boolean = LanguageFactoryUtil.simpleLooksParseable(List("version 1.0"), List("#"))(content)
+  override def looksParsable(content: String): Boolean =
+    LanguageFactoryUtil.simpleLooksParseable(List("version 1.0"), List("#"))(content)
 }
diff --git a/languageFactories/wdl-draft3/src/test/scala/languages/wdl/draft3/WdlDraft3CachingSpec.scala b/languageFactories/wdl-draft3/src/test/scala/languages/wdl/draft3/WdlDraft3CachingSpec.scala
index bca467e89c6..9ed41458025 100644
--- a/languageFactories/wdl-draft3/src/test/scala/languages/wdl/draft3/WdlDraft3CachingSpec.scala
+++ b/languageFactories/wdl-draft3/src/test/scala/languages/wdl/draft3/WdlDraft3CachingSpec.scala
@@ -14,7 +14,6 @@ import wom.core.{WorkflowOptionsJson, WorkflowSource}
 import wom.executable.WomBundle
 import wom.expression.NoIoFunctionSet
 
-
 class WdlDraft3CachingSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   val languageConfig = ConfigFactory.parseString(
@@ -29,11 +28,8 @@ class WdlDraft3CachingSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
       |  }
       |}
       |""".stripMargin
-
   )
 
-
-
   it should "only evaluate files once" in {
     val invalidWorkflowSource =
       """
@@ -124,9 +120,21 @@ object WdlDraft3CachingSpec {
 
     var evaluationCount = 0
 
-    override protected def makeWomBundle(workflowSource: WorkflowSource, workflowSourceOrigin: Option[ResolvedImportRecord], workflowOptionsJson: WorkflowOptionsJson, importResolvers: List[ImportResolver.ImportResolver], languageFactories: List[LanguageFactory], convertNestedScatterToSubworkflow: Boolean): ErrorOr[WomBundle] = {
+    override protected def makeWomBundle(workflowSource: WorkflowSource,
+                                         workflowSourceOrigin: Option[ResolvedImportRecord],
+                                         workflowOptionsJson: WorkflowOptionsJson,
+                                         importResolvers: List[ImportResolver.ImportResolver],
+                                         languageFactories: List[LanguageFactory],
+                                         convertNestedScatterToSubworkflow: Boolean
+    ): ErrorOr[WomBundle] = {
       evaluationCount = evaluationCount + 1
-      super.makeWomBundle(workflowSource, workflowSourceOrigin, workflowOptionsJson, importResolvers, languageFactories, convertNestedScatterToSubworkflow)
+      super.makeWomBundle(workflowSource,
+                          workflowSourceOrigin,
+                          workflowOptionsJson,
+                          importResolvers,
+                          languageFactories,
+                          convertNestedScatterToSubworkflow
+      )
     }
 
   }
diff --git a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
index 3fa11515118..9590b9f405f 100644
--- a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
+++ b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClient.scala
@@ -57,19 +57,19 @@ class DrsHubClientImpl[F[_]: Concurrent](client: Client[F], baseUrl: Uri) extend
     "localizationPath",
     "bondProvider"
   )(ResourceMetadata.apply)
-  implicit val resourceMetadataRequestEncoder: Encoder[ResourceMetadataRequest] = Encoder.forProduct2("url", "fields")(x =>
-    (x.url, x.fields)
-  )
-  implicit val resourceMetadataRequestEntityEncoder: EntityEncoder[F, ResourceMetadataRequest] = circeEntityEncoder[F, ResourceMetadataRequest]
+  implicit val resourceMetadataRequestEncoder: Encoder[ResourceMetadataRequest] =
+    Encoder.forProduct2("url", "fields")(x => (x.url, x.fields))
+  implicit val resourceMetadataRequestEntityEncoder: EntityEncoder[F, ResourceMetadataRequest] =
+    circeEntityEncoder[F, ResourceMetadataRequest]
   override def fetchSystemStatus(): F[Boolean] = {
     val request = Request[F](uri = baseUrl / "status").withHeaders(
       org.http4s.headers.Accept(MediaType.application.json)
     )
     client.run(request).use { resp =>
       resp.status match {
-        case Status.Ok                  => true.pure[F]
+        case Status.Ok => true.pure[F]
         case Status.InternalServerError => false.pure[F]
-        case _                          => UnknownError.raiseError
+        case _ => UnknownError.raiseError
       }
     }
   }
@@ -77,17 +77,17 @@ class DrsHubClientImpl[F[_]: Concurrent](client: Client[F], baseUrl: Uri) extend
   override def resolveDrsObject(drsPath: String, fields: List[String]): F[ResourceMetadata] = {
     val body = ResourceMetadataRequest(url = drsPath, fields = fields)
     val entityBody: EntityBody[F] = EntityEncoder[F, ResourceMetadataRequest].toEntity(body).body
-    val request = Request[F](uri = baseUrl / "api" / apiVersion / "drs" / "resolve", method=Method.POST, body=entityBody).withHeaders(
-      org.http4s.headers.`Content-Type`(MediaType.application.json)
-    )
+    val request =
+      Request[F](uri = baseUrl / "api" / apiVersion / "drs" / "resolve", method = Method.POST, body = entityBody)
+        .withHeaders(
+          org.http4s.headers.`Content-Type`(MediaType.application.json)
+        )
     client.run(request).use { resp =>
       resp.status match {
-        case Status.Ok                  => resp.as[ResourceMetadata]
-        case _                          => UnknownError.raiseError
+        case Status.Ok => resp.as[ResourceMetadata]
+        case _ => UnknownError.raiseError
       }
     }
   }
 
 }
-
-
diff --git a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
index ceeefc7479f..2a63324247a 100644
--- a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
+++ b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
@@ -14,7 +14,7 @@ object PactHelper {
                        status: Int,
                        responseHeaders: Seq[(String, String)],
                        body: DslPart
-                      ): PactDslResponse =
+  ): PactDslResponse =
     builder
       .`given`(state)
       .uponReceiving(uponReceiving)
@@ -33,8 +33,8 @@ object PactHelper {
                        path: String,
                        requestHeaders: Seq[(String, String)],
                        status: Int,
-                       responseHeaders: Seq[(String, String)],
-                      ): PactDslResponse =
+                       responseHeaders: Seq[(String, String)]
+  ): PactDslResponse =
     builder
       .`given`(state)
       .uponReceiving(uponReceiving)
@@ -52,7 +52,7 @@ object PactHelper {
                        path: String,
                        requestHeaders: Seq[(String, String)],
                        status: Int
-                      ): PactDslResponse =
+  ): PactDslResponse =
     builder
       .`given`(state)
       .uponReceiving(uponReceiving)
@@ -68,7 +68,7 @@ object PactHelper {
                        path: String,
                        requestHeaders: Seq[(String, String)],
                        status: Int
-                      ): PactDslResponse =
+  ): PactDslResponse =
     builder
       .uponReceiving(uponReceiving)
       .method(method)
@@ -86,7 +86,7 @@ object PactHelper {
                        status: Int,
                        responseHeaders: Seq[(String, String)],
                        body: DslPart
-                      ): PactDslResponse =
+  ): PactDslResponse =
     builder
       .`given`(state)
       .uponReceiving(uponReceiving)
@@ -109,7 +109,7 @@ object PactHelper {
                        status: Int,
                        responseHeaders: Seq[(String, String)],
                        responsBody: DslPart
-                      ): PactDslResponse =
+  ): PactDslResponse =
     builder
       .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
       .uponReceiving(uponReceiving)
@@ -132,7 +132,7 @@ object PactHelper {
                        status: Int,
                        responseHeaders: Seq[(String, String)],
                        body: DslPart
-                      ): PactDslResponse =
+  ): PactDslResponse =
     builder
       .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
       .uponReceiving(uponReceiving)
@@ -154,7 +154,7 @@ object PactHelper {
                           status: Int,
                           responseHeaders: Seq[(String, String)],
                           body: A
-                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
+  )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
     builder
       .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
       .uponReceiving(uponReceiving)
@@ -174,7 +174,7 @@ object PactHelper {
                           requestHeaders: Seq[(String, String)],
                           requestBody: A,
                           status: Int
-                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
+  )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
     builder
       .`given`(state)
       .uponReceiving(uponReceiving)
@@ -194,7 +194,7 @@ object PactHelper {
                           requestHeaders: Seq[(String, String)],
                           requestBody: A,
                           status: Int
-                         )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
+  )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
     builder
       .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
       .uponReceiving(uponReceiving)
diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
index f023257fef9..0e003b5d3fe 100644
--- a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
+++ b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/BlobFileSystemContractSpec.scala
@@ -13,6 +13,7 @@ class BlobFileSystemContractSpec extends AnyFlatSpec with Matchers with RequestR
 
   val resourceId = "";
   val workspaceId = "";
+
   /**
    * we can define the folder that the pact contracts get written to upon completion of this test suite.
    */
@@ -27,24 +28,27 @@ class BlobFileSystemContractSpec extends AnyFlatSpec with Matchers with RequestR
    * scala tests on build and if the tests pass when run a pact file will be generated locally
    */
   override def pact: RequestResponsePact = ConsumerPactBuilder
-      .consumer("cromwell-blob-filesystem-consumer")
-      .hasPactWith("wsm-provider")
-      .`given`(
-        "resource exists",
-        Map("id" -> resourceId.asJson, "value" -> 123.asJson) // we can use parameters to specify details about the provider state
-      )
-      .`given`(
-        "workspace exists",
-        Map("id" -> workspaceId, "value" -> 123) // we can use parameters to specify details about the provider state
-      )
-      .uponReceiving("Request to fetch SAS Token")
-      .method("POST")
-      .path(s"/api/workspaces/v1/${workspaceId}/resources/controlled/azure/storageContainer/${resourceId}/getSasToken")
-      .headers("Authorization" -> "sampleToken")
-      .willRespondWith()
-      .status(200)
-      .body(
-        Json.obj("id" -> "".asJson, "value" -> 123.asJson)
-      ).toPact()
+    .consumer("cromwell-blob-filesystem-consumer")
+    .hasPactWith("wsm-provider")
+    .`given`(
+      "resource exists",
+      Map("id" -> resourceId.asJson,
+          "value" -> 123.asJson
+      ) // we can use parameters to specify details about the provider state
+    )
+    .`given`(
+      "workspace exists",
+      Map("id" -> workspaceId, "value" -> 123) // we can use parameters to specify details about the provider state
+    )
+    .uponReceiving("Request to fetch SAS Token")
+    .method("POST")
+    .path(s"/api/workspaces/v1/${workspaceId}/resources/controlled/azure/storageContainer/${resourceId}/getSasToken")
+    .headers("Authorization" -> "sampleToken")
+    .willRespondWith()
+    .status(200)
+    .body(
+      Json.obj("id" -> "".asJson, "value" -> 123.asJson)
+    )
+    .toPact()
 
 }
diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
index a4ebe56d76a..ead29c29d4f 100644
--- a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
+++ b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
@@ -28,19 +28,19 @@ class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePac
     )
 
   private val requestFields = List(
-      "bucket",
-      "accessUrl",
-      "googleServiceAccount",
-      "fileName",
-      "hashes",
-      "localizationPath",
-      "bondProvider",
-      "name",
-      "size",
-      "timeCreated",
-      "timeUpdated",
-      "gsUri",
-      "contentType",
+    "bucket",
+    "accessUrl",
+    "googleServiceAccount",
+    "fileName",
+    "hashes",
+    "localizationPath",
+    "bondProvider",
+    "name",
+    "size",
+    "timeCreated",
+    "timeUpdated",
+    "gsUri",
+    "contentType"
   )
 
   val filesize = 123L
@@ -51,7 +51,6 @@ class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePac
   val fileHash = "a2317edbd2eb6cf6b0ee49cb81e3a556"
   val accessUrl = f"gs://${bucket}/${filename}"
 
-
   val drsResourceResponsePlaceholder: ResourceMetadata = ResourceMetadata(
     "application/octet-stream",
     filesize,
@@ -70,27 +69,33 @@ class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePac
 
   val resourceMetadataResponseDsl: DslPart = newJsonBody { o =>
     o.stringType("contentType", "application/octet-stream")
-      o.numberType("size", filesize)
-      o.stringType("timeCreated", timeCreated)
-      o.stringType("timeUpdated", timeCreated)
-      o.nullValue("gsUri")
-      o.nullValue("googleServiceAccount")
-      o.nullValue("fileName")
-      o.`object`("accessUrl" , { a =>
-        a.stringType("url", accessUrl)
-          a.`array`("headers", { h =>
-            h.stringType("Header")
-            h.stringType("Example")
-            ()
-          })
-        ()
-      })
-      o.`object`("hashes", { o =>
-        o.stringType("md5", fileHash)
-        ()
-      })
-      o.nullValue("localizationPath")
-      o.stringType("bondProvider", bondProvider)
+    o.numberType("size", filesize)
+    o.stringType("timeCreated", timeCreated)
+    o.stringType("timeUpdated", timeCreated)
+    o.nullValue("gsUri")
+    o.nullValue("googleServiceAccount")
+    o.nullValue("fileName")
+    o.`object`("accessUrl",
+               { a =>
+                 a.stringType("url", accessUrl)
+                 a.`array`("headers",
+                           { h =>
+                             h.stringType("Header")
+                             h.stringType("Example")
+                             ()
+                           }
+                 )
+                 ()
+               }
+    )
+    o.`object`("hashes",
+               { o =>
+                 o.stringType("md5", fileHash)
+                 ()
+               }
+    )
+    o.nullValue("localizationPath")
+    o.stringType("bondProvider", bondProvider)
     ()
   }.build
 
@@ -98,10 +103,12 @@ class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePac
 
   val resourceRequestDsl = newJsonBody { o =>
     o.stringType("url", f"drs://test.theanvil.io/${fileId}")
-    o.array("fields", { a =>
-      requestFields.map(a.stringType)
-      ()
-    })
+    o.array("fields",
+            { a =>
+              requestFields.map(a.stringType)
+              ()
+            }
+    )
     ()
   }.build
 
@@ -147,9 +154,8 @@ class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePac
 
   override val pact: RequestResponsePact = pactDslResponse.toPact
 
-  val client: Client[IO] = {
+  val client: Client[IO] =
     BlazeClientBuilder[IO](ExecutionContext.global).resource.allocated.unsafeRunSync()._1
-  }
 
   /*
   we should use these tests to ensure that our client class correctly handles responses from the provider - i.e. decoding, error mapping, validation
diff --git a/perf/src/main/scala/cromwell/perf/Call.scala b/perf/src/main/scala/cromwell/perf/Call.scala
index 3849cb4093d..b8e91589126 100644
--- a/perf/src/main/scala/cromwell/perf/Call.scala
+++ b/perf/src/main/scala/cromwell/perf/Call.scala
@@ -6,21 +6,21 @@ import io.circe.JsonObject
 
 case class CallCaching(hit: Option[Boolean],
                        result: Option[String],
-                       hitFailures: Option[Seq[Map[String, Seq[JsonObject]]]])
-
-
-case class ExecutionEvents(startTime: OffsetDateTime,
-                           description: String,
-                           endTime: OffsetDateTime)
+                       hitFailures: Option[Seq[Map[String, Seq[JsonObject]]]]
+)
 
+case class ExecutionEvents(startTime: OffsetDateTime, description: String, endTime: OffsetDateTime)
 
 case class Call(shardIndex: Int,
                 start: OffsetDateTime,
                 end: OffsetDateTime,
                 callCaching: Option[CallCaching],
-                executionEvents: Seq[ExecutionEvents]) {
-  val callCachingEventStates = List("CheckingCallCache", "FetchingCachedOutputsFromDatabase", "BackendIsCopyingCachedOutputs")
-  val jobPreparationEventStates = List("Pending", "RequestingExecutionToken", "WaitingForValueStore", "PreparingJob", "CheckingJobStore")
+                executionEvents: Seq[ExecutionEvents]
+) {
+  val callCachingEventStates =
+    List("CheckingCallCache", "FetchingCachedOutputsFromDatabase", "BackendIsCopyingCachedOutputs")
+  val jobPreparationEventStates =
+    List("Pending", "RequestingExecutionToken", "WaitingForValueStore", "PreparingJob", "CheckingJobStore")
   val cacheCopyingEventStates = List("FetchingCachedOutputsFromDatabase", "BackendIsCopyingCachedOutputs")
 
   /**
@@ -40,23 +40,24 @@ case class Call(shardIndex: Int,
     */
   val timeInCheckingCallCacheState: Duration = {
     val eventsRelatedToCC = executionEvents.collect {
-      case event if event.description.equalsIgnoreCase("CheckingCallCache") => Duration.between(event.startTime, event.endTime)
+      case event if event.description.equalsIgnoreCase("CheckingCallCache") =>
+        Duration.between(event.startTime, event.endTime)
     }
 
-    if(eventsRelatedToCC.nonEmpty) eventsRelatedToCC.reduce(_ plus _) else Duration.ZERO
+    if (eventsRelatedToCC.nonEmpty) eventsRelatedToCC.reduce(_ plus _) else Duration.ZERO
   }
 
   /**
     * @return Time (in Duration) job spent in Call Caching states
     */
   val timeInCallCachingState: Duration = {
-    val eventsRelatedToCC = executionEvents.filter(event => callCachingEventStates.exists(state => state.equalsIgnoreCase(event.description)))
+    val eventsRelatedToCC =
+      executionEvents.filter(event => callCachingEventStates.exists(state => state.equalsIgnoreCase(event.description)))
 
     if (eventsRelatedToCC.nonEmpty) {
       val eventsSortedByStartTime = eventsRelatedToCC.sortBy(_.startTime)
       Duration.between(eventsSortedByStartTime.head.startTime, eventsSortedByStartTime.last.endTime)
-    }
-    else Duration.ZERO
+    } else Duration.ZERO
   }
 
   /**
@@ -65,10 +66,12 @@ case class Call(shardIndex: Int,
     */
   val timeInJobPreparation: Duration = {
     val durationOfEventsInPreparationState = executionEvents.collect {
-      case event if jobPreparationEventStates.exists(_.equalsIgnoreCase(event.description)) => Duration.between(event.startTime, event.endTime)
+      case event if jobPreparationEventStates.exists(_.equalsIgnoreCase(event.description)) =>
+        Duration.between(event.startTime, event.endTime)
     }
 
-    if(durationOfEventsInPreparationState.nonEmpty) durationOfEventsInPreparationState.reduce(_ plus _) else Duration.ZERO
+    if (durationOfEventsInPreparationState.nonEmpty) durationOfEventsInPreparationState.reduce(_ plus _)
+    else Duration.ZERO
   }
 
   /**
@@ -77,9 +80,11 @@ case class Call(shardIndex: Int,
     */
   val timeForFetchingAndCopyingCacheHit: Duration = {
     val durationOfEventsInCacheCopyingState = executionEvents.collect {
-      case event if cacheCopyingEventStates.exists(_.equalsIgnoreCase(event.description)) => Duration.between(event.startTime, event.endTime)
+      case event if cacheCopyingEventStates.exists(_.equalsIgnoreCase(event.description)) =>
+        Duration.between(event.startTime, event.endTime)
     }
 
-    if(durationOfEventsInCacheCopyingState.nonEmpty) durationOfEventsInCacheCopyingState.reduce(_ plus _) else Duration.ZERO
+    if (durationOfEventsInCacheCopyingState.nonEmpty) durationOfEventsInCacheCopyingState.reduce(_ plus _)
+    else Duration.ZERO
   }
 }
diff --git a/perf/src/main/scala/cromwell/perf/CompareMetadata.scala b/perf/src/main/scala/cromwell/perf/CompareMetadata.scala
index 600bd38aba0..64e49d93807 100644
--- a/perf/src/main/scala/cromwell/perf/CompareMetadata.scala
+++ b/perf/src/main/scala/cromwell/perf/CompareMetadata.scala
@@ -15,7 +15,7 @@ import io.circe._
 import io.circe.generic.semiauto._
 import io.circe.parser._
 
-object CompareMetadata extends App with StrictLogging{
+object CompareMetadata extends App with StrictLogging {
   private val REGRESSION_CONST = 1.1
 
   // If removed, IntelliJ (Oct '18) thinks the import isn't used.
@@ -33,7 +33,6 @@ object CompareMetadata extends App with StrictLogging{
     decode[Metadata](metadataFileContent)
   }
 
-
   def parseMetadataFromGcsFile(gcsUrl: String, pathToServiceAccount: String): Either[Error, Metadata] = {
     val gcsUrlArray = gcsUrl.replace("gs://", "").split("/", 2)
     val Array(gcsBucket, fileToBeLocalized) = gcsUrlArray
@@ -46,13 +45,10 @@ object CompareMetadata extends App with StrictLogging{
     decode[Metadata](metadataFileContent)
   }
 
-
-  def parseMetadata(inputFile: String, pathToServiceAccount: String): Either[Error, Metadata] = {
+  def parseMetadata(inputFile: String, pathToServiceAccount: String): Either[Error, Metadata] =
     if (inputFile.startsWith("gs://"))
       parseMetadataFromGcsFile(inputFile, pathToServiceAccount)
     else parseMetadataFromLocalFile(inputFile)
-  }
-
 
   def displayComputedMetrics(metadata: Metadata, displayMsg: String): Unit = {
     logger.info(displayMsg)
@@ -64,59 +60,65 @@ object CompareMetadata extends App with StrictLogging{
     logger.info(s"Avg time job spent in Call Caching state: ${metadata.avgTimeInCallCachingState}")
     logger.info(s"Avg time job spent in just CheckingCallCache state: ${metadata.avgTimeInCheckingCallCacheState}")
     logger.info(s"Avg time job spent in Job Preparation state: ${metadata.avgTimeInJobPreparation}")
-    logger.info(s"Avg time job spent in fetching and copying cache hit(s) state: ${metadata.avgTimeForFetchingAndCopyingCacheHit}")
+    logger.info(
+      s"Avg time job spent in fetching and copying cache hit(s) state: ${metadata.avgTimeForFetchingAndCopyingCacheHit}"
+    )
   }
 
-
   /***
     * Compares the metrics in Metadata which have type 'Duration' (mostly the ones related to time metrics)
     */
-  def compareDurationMetrics(metadataOld: Metadata, metadataNew: Metadata, metricFunc: Metadata => Duration, metricName: String): ErrorOr[String] = {
-    if(metricFunc(metadataNew).toMillis > REGRESSION_CONST * metricFunc(metadataOld).toMillis){
+  def compareDurationMetrics(metadataOld: Metadata,
+                             metadataNew: Metadata,
+                             metricFunc: Metadata => Duration,
+                             metricName: String
+  ): ErrorOr[String] =
+    if (metricFunc(metadataNew).toMillis > REGRESSION_CONST * metricFunc(metadataOld).toMillis) {
       (s"$metricName of new metadata is greater than 10% of old metadata. " +
         s"New metric value: ${metricFunc(metadataNew)}. " +
         s"Old metric value: ${metricFunc(metadataOld)}.").invalidNel[String]
-    }
-    else s"$metricName hasn't regressed yet".valid
-  }
-
+    } else s"$metricName hasn't regressed yet".valid
 
   /***
     * Compares the metrics in Metadata which have type 'Int' (mostly the ones related to size metrics)
     */
-  def compareIntMetrics(metadataOld: Metadata, metadataNew: Metadata, metricFunc: Metadata => Int, metricName: String): ErrorOr[String] = {
-    if(metricFunc(metadataNew) > REGRESSION_CONST * metricFunc(metadataOld)){
+  def compareIntMetrics(metadataOld: Metadata,
+                        metadataNew: Metadata,
+                        metricFunc: Metadata => Int,
+                        metricName: String
+  ): ErrorOr[String] =
+    if (metricFunc(metadataNew) > REGRESSION_CONST * metricFunc(metadataOld)) {
       (s"$metricName of new metadata is greater than 10% of old metadata. " +
         s"New metric value: ${metricFunc(metadataNew)}. " +
         s"Old metric value: ${metricFunc(metadataOld)}.").invalidNel[String]
-    }
-    else s"$metricName hasn't regressed yet".valid
-  }
-
+    } else s"$metricName hasn't regressed yet".valid
 
   def compareMetadataMetrics(metadataOld: Metadata, metadataNew: Metadata): ErrorOr[List[String]] = {
-    val durationFuncList: List[(Metadata => Duration, String)] = List((_.workflowStartedAfter, "workflowStartedAfter"),
+    val durationFuncList: List[(Metadata => Duration, String)] = List(
+      (_.workflowStartedAfter, "workflowStartedAfter"),
       (_.workflowRunningTime, "workflowRunningTime"),
       (_.avgTimeInCallCachingState, "avgTimeInCallCachingState"),
       (_.avgTimeInCheckingCallCacheState, "avgTimeInCheckingCallCacheState"),
       (_.avgTimeInJobPreparation, "avgTimeInJobPreparation"),
-      (_.avgTimeForFetchingAndCopyingCacheHit, "avgTimeForFetchingAndCopyingCacheHit"))
+      (_.avgTimeForFetchingAndCopyingCacheHit, "avgTimeForFetchingAndCopyingCacheHit")
+    )
 
-    val intFuncList:  List[(Metadata => Int, String)] = List((_.totalJobsPerRootWf, "totalJobsPerRootWf"), (_.avgCacheRetries, "avgCacheRetries"))
+    val intFuncList: List[(Metadata => Int, String)] =
+      List((_.totalJobsPerRootWf, "totalJobsPerRootWf"), (_.avgCacheRetries, "avgCacheRetries"))
 
     val durationMetricsComp = durationFuncList.map(x => compareDurationMetrics(metadataOld, metadataNew, x._1, x._2))
     val intMetricsComp = intFuncList.map(x => compareIntMetrics(metadataOld, metadataNew, x._1, x._2))
     (durationMetricsComp ::: intMetricsComp).sequence[ErrorOr, String]
   }
 
-
   def printParseErrorToConsoleAndExit(metadataFile: String, error: Error, systemExit: Boolean): Unit = {
     logger.error(s"Something went wrong while parsing $metadataFile. Error: ${error.getLocalizedMessage}")
     if (systemExit) System.exit(1)
   }
 
-
-  def generateAndCompareMetrics(metadataOldEither: Either[Error, Metadata], metadataNewEither: Either[Error, Metadata]): Unit = {
+  def generateAndCompareMetrics(metadataOldEither: Either[Error, Metadata],
+                                metadataNewEither: Either[Error, Metadata]
+  ): Unit =
     (metadataOldEither, metadataNewEither) match {
       case (Right(metadataOld), Right(metadataNew)) =>
         val metadataOldMsg = s"Metrics for metadata generated from ${args(0)}"
@@ -136,16 +138,13 @@ object CompareMetadata extends App with StrictLogging{
         printParseErrorToConsoleAndExit(args(0), e1, systemExit = false)
         printParseErrorToConsoleAndExit(args(1), e2, systemExit = true)
     }
-  }
-
 
   args.length match {
     case 2 =>
       if (args(0).startsWith("gs://") || args(1).startsWith("gs://")) {
         logger.error("Path to service account is needed to download GCS file. Please pass it as 3rd argument.")
         System.exit(1)
-      }
-      else generateAndCompareMetrics(parseMetadataFromLocalFile(args(0)), parseMetadataFromLocalFile(args(1)))
+      } else generateAndCompareMetrics(parseMetadataFromLocalFile(args(0)), parseMetadataFromLocalFile(args(1)))
     case 3 => generateAndCompareMetrics(parseMetadata(args(0), args(2)), parseMetadata(args(1), args(2)))
     case _ =>
       logger.error("Please pass in 2 file paths!")
diff --git a/perf/src/main/scala/cromwell/perf/Metadata.scala b/perf/src/main/scala/cromwell/perf/Metadata.scala
index 190063e48b3..b61e88c795a 100644
--- a/perf/src/main/scala/cromwell/perf/Metadata.scala
+++ b/perf/src/main/scala/cromwell/perf/Metadata.scala
@@ -8,18 +8,18 @@ case class Metadata(id: String,
                     start: OffsetDateTime,
                     end: OffsetDateTime,
                     status: String,
-                    calls: Option[Map[String, Seq[Call]]]) {
+                    calls: Option[Map[String, Seq[Call]]]
+) {
 
   private def addInt(x: Int, y: Int): Int = x + y
 
   private def addDuration(x: Duration, y: Duration): Duration = x.plus(y)
 
-  private def sumElementsInOptionSeq[A](listOption: Option[Iterable[A]], op: (A, A) => A, default: A): A = {
+  private def sumElementsInOptionSeq[A](listOption: Option[Iterable[A]], op: (A, A) => A, default: A): A =
     listOption match {
-      case Some(list) => list.reduce[A]((a, b) => op(a,b))
+      case Some(list) => list.reduce[A]((a, b) => op(a, b))
       case None => default
     }
-  }
 
   /**
     * @return Time between the submission and start of workflow
@@ -28,47 +28,47 @@ case class Metadata(id: String,
 
   val workflowRunningTime: Duration = Duration.between(start, end)
 
-  val totalJobsPerRootWf: Int = sumElementsInOptionSeq(calls.map(taskMap => taskMap.map(callsPerTask => callsPerTask._2.size)), addInt, 0)
+  val totalJobsPerRootWf: Int =
+    sumElementsInOptionSeq(calls.map(taskMap => taskMap.map(callsPerTask => callsPerTask._2.size)), addInt, 0)
 
-  val avgCacheRetries: Int = {
+  val avgCacheRetries: Int =
     if (totalJobsPerRootWf > 0) {
-      val cacheRetriesList = calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.cacheCopyRetries)))
+      val cacheRetriesList =
+        calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.cacheCopyRetries)))
       sumElementsInOptionSeq(cacheRetriesList, addInt, 0) / totalJobsPerRootWf
-    }
-    else 0
-  }
+    } else 0
 
-  val avgTimeInCallCachingState: Duration = {
+  val avgTimeInCallCachingState: Duration =
     if (totalJobsPerRootWf > 0) {
-      val timeInCallCachingStateList = calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeInCallCachingState)))
-      sumElementsInOptionSeq(timeInCallCachingStateList, addDuration, Duration.ZERO).dividedBy(totalJobsPerRootWf.toLong)
-    }
-    else Duration.ZERO
-  }
+      val timeInCallCachingStateList =
+        calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeInCallCachingState)))
+      sumElementsInOptionSeq(timeInCallCachingStateList, addDuration, Duration.ZERO).dividedBy(
+        totalJobsPerRootWf.toLong
+      )
+    } else Duration.ZERO
 
-  val avgTimeInCheckingCallCacheState: Duration = {
+  val avgTimeInCheckingCallCacheState: Duration =
     if (totalJobsPerRootWf > 0) {
-      val timeInCheckingCallCacheStateList = calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeInCheckingCallCacheState)))
-      sumElementsInOptionSeq(timeInCheckingCallCacheStateList, addDuration, Duration.ZERO).dividedBy(totalJobsPerRootWf.toLong)
-    }
-    else Duration.ZERO
-  }
+      val timeInCheckingCallCacheStateList = calls.map(taskMap =>
+        taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeInCheckingCallCacheState))
+      )
+      sumElementsInOptionSeq(timeInCheckingCallCacheStateList, addDuration, Duration.ZERO).dividedBy(
+        totalJobsPerRootWf.toLong
+      )
+    } else Duration.ZERO
 
-  val avgTimeInJobPreparation: Duration = {
+  val avgTimeInJobPreparation: Duration =
     if (totalJobsPerRootWf > 0) {
-      val timeInJobPreparationList = calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeInJobPreparation)))
+      val timeInJobPreparationList =
+        calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeInJobPreparation)))
       sumElementsInOptionSeq(timeInJobPreparationList, addDuration, Duration.ZERO).dividedBy(totalJobsPerRootWf.toLong)
-    }
-    else Duration.ZERO
-  }
+    } else Duration.ZERO
 
-  val avgTimeForFetchingAndCopyingCacheHit: Duration = {
+  val avgTimeForFetchingAndCopyingCacheHit: Duration =
     if (totalJobsPerRootWf > 0) {
-      val timeInCopyingList = calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeForFetchingAndCopyingCacheHit)))
+      val timeInCopyingList = calls.map(taskMap =>
+        taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeForFetchingAndCopyingCacheHit))
+      )
       sumElementsInOptionSeq(timeInCopyingList, addDuration, Duration.ZERO).dividedBy(totalJobsPerRootWf.toLong)
-    }
-    else Duration.ZERO
-  }
+    } else Duration.ZERO
 }
-
-
diff --git a/project/ContinuousIntegration.scala b/project/ContinuousIntegration.scala
index e2b61994c22..d5dd3262f87 100644
--- a/project/ContinuousIntegration.scala
+++ b/project/ContinuousIntegration.scala
@@ -30,13 +30,20 @@ object ContinuousIntegration {
         "docker",
         "run",
         "--rm",
-        "-v", s"${vaultToken.value}:/root/.vault-token",
-        "-v", s"${srcCiResources.value}:${srcCiResources.value}",
-        "-v", s"${targetCiResources.value}:${targetCiResources.value}",
-        "-e", "ENVIRONMENT=not_used",
-        "-e", s"INPUT_PATH=${srcCiResources.value}",
-        "-e", s"OUT_PATH=${targetCiResources.value}",
-        "broadinstitute/dsde-toolbox:dev", "render-templates.sh"
+        "-v",
+        s"${vaultToken.value}:/root/.vault-token",
+        "-v",
+        s"${srcCiResources.value}:${srcCiResources.value}",
+        "-v",
+        s"${targetCiResources.value}:${targetCiResources.value}",
+        "-e",
+        "ENVIRONMENT=not_used",
+        "-e",
+        s"INPUT_PATH=${srcCiResources.value}",
+        "-e",
+        s"OUT_PATH=${targetCiResources.value}",
+        "broadinstitute/dsde-toolbox:dev",
+        "render-templates.sh"
       )
       val result = cmd ! log
       if (result != 0) {
@@ -45,7 +52,7 @@ object ContinuousIntegration {
             "https://hub.docker.com/r/broadinstitute/dsde-toolbox/"
         )
       }
-    },
+    }
   )
 
   def aggregateSettings(rootProject: Project): Seq[Setting[_]] = List(
@@ -54,7 +61,7 @@ object ContinuousIntegration {
       streams.value.log // make sure logger is loaded
       validateAggregatedProjects(rootProject, state.value)
       (Compile / compile).value
-    },
+    }
   )
 
   private val copyCiResources: TaskKey[Unit] = taskKey[Unit](s"Copy CI resources.")
@@ -74,9 +81,9 @@ object ContinuousIntegration {
     */
   private def getBuildSbtNames(rootProject: Project, state: State): Set[String] = {
     val extracted = Project.extract(state)
-    extracted.structure.units.flatMap({
-      case (_, loadedBuildUnit) => loadedBuildUnit.defined.keys
-    }).toSet - rootProject.id
+    extracted.structure.units.flatMap { case (_, loadedBuildUnit) =>
+      loadedBuildUnit.defined.keys
+    }.toSet - rootProject.id
   }
 
   /**
@@ -85,8 +92,8 @@ object ContinuousIntegration {
   private def validateAggregatedProjects(rootProject: Project, state: State): Unit = {
     // Get the list of projects explicitly aggregated
     val projectReferences: Seq[ProjectReference] = rootProject.aggregate
-    val localProjectReferences = projectReferences collect {
-      case localProject: LocalProject => localProject
+    val localProjectReferences = projectReferences collect { case localProject: LocalProject =>
+      localProject
     }
     val aggregatedNames = localProjectReferences.map(_.project).toSet
 
@@ -98,7 +105,7 @@ object ContinuousIntegration {
 
     val falseNames = unaggregatedProjects.filterKeys(aggregatedNames.contains)
     if (falseNames.nonEmpty) {
-      val reasons = falseNames.map({case (name, reason) => s"  ${name}: ${reason}"}).mkString("\n")
+      val reasons = falseNames.map { case (name, reason) => s"  ${name}: ${reason}" }.mkString("\n")
       sys.error(s"There are projects aggregated in build.sbt that shouldn't be:\n$reasons")
     }
   }
diff --git a/project/GenerateRestApiDocs.scala b/project/GenerateRestApiDocs.scala
index 9173a25c3c5..3e0297a09f5 100644
--- a/project/GenerateRestApiDocs.scala
+++ b/project/GenerateRestApiDocs.scala
@@ -65,7 +65,7 @@ object GenerateRestApiDocs {
     * @param content The original contents of the RESTAPI.md.
     * @return The contents with updated paths.
     */
-  private def replacePaths(content: String): String = {
+  private def replacePaths(content: String): String =
     content match {
       case PathsRegex(start, paths, end) =>
         val replacedPaths = paths.linesWithSeparators map {
@@ -73,12 +73,13 @@ object GenerateRestApiDocs {
           case other => other
         }
         replacedPaths.mkString(start, "", end)
-      case _ => throw new IllegalArgumentException(
-        "Content did not match expected regex. " +
-          "Did the swagger2markdown format change significantly? " +
-          "If so, a new regex may be required.")
+      case _ =>
+        throw new IllegalArgumentException(
+          "Content did not match expected regex. " +
+            "Did the swagger2markdown format change significantly? " +
+            "If so, a new regex may be required."
+        )
     }
-  }
 
   /**
     * Replaces generic strings in the generated RESTAPI.md.
@@ -86,9 +87,8 @@ object GenerateRestApiDocs {
     * @param content The contents of the RESTAPI.md.
     * @return The contents with generic replacements.
     */
-  private def replaceGenerics(content: String): String = {
+  private def replaceGenerics(content: String): String =
     GenericReplacements.foldRight(content)(replaceGeneric)
-  }
 
   /**
     * Replaces a single generic string in the generated RESTAPI.md.
@@ -118,12 +118,11 @@ object GenerateRestApiDocs {
     try {
       currentThread.setContextClassLoader(classUtilsClassLoader)
       block
-    } finally {
+    } finally
       currentThread.setContextClassLoader(originalThreadClassLoader)
-    }
   }
 
-  private def getModifiedMarkdown: String = {
+  private def getModifiedMarkdown: String =
     withPatchedClassLoader {
       val config = new Swagger2MarkupConfigBuilder()
         .withMarkupLanguage(MarkupLanguage.MARKDOWN)
@@ -135,7 +134,6 @@ object GenerateRestApiDocs {
       val contents = converter.toString
       replaceGenerics(replacePaths(contents))
     }
-  }
 
   /**
     * Generates the markdown from the swagger YAML, with some Cromwell customizations.
@@ -164,6 +162,6 @@ object GenerateRestApiDocs {
   // Returns a settings including the `generateRestApiDocs` task.
   val generateRestApiDocsSettings: Seq[Setting[_]] = List(
     generateRestApiDocs := writeModifiedMarkdown(),
-    checkRestApiDocs := checkModifiedMarkdown(streams.value.log),
+    checkRestApiDocs := checkModifiedMarkdown(streams.value.log)
   )
 }
diff --git a/project/Merging.scala b/project/Merging.scala
index 91b135e59eb..4ed133b82ac 100644
--- a/project/Merging.scala
+++ b/project/Merging.scala
@@ -4,23 +4,30 @@ import sbtassembly.{MergeStrategy, PathList}
 
 object Merging {
   val customMergeStrategy: Def.Initialize[String => MergeStrategy] = Def.setting {
-    case PathList(ps@_*) if Set("project.properties", "execution.interceptors").contains(ps.last) =>
+    case PathList(ps @ _*) if Set("project.properties", "execution.interceptors").contains(ps.last) =>
       // Merge/Filter files from AWS/Google jars that otherwise collide at merge time.
       MergeStrategy.filterDistinctLines
-    case PathList(ps@_*) if ps.last == "logback.xml" =>
+    case PathList(ps @ _*) if ps.last == "logback.xml" =>
       MergeStrategy.first
     // Merge mozilla/public-suffix-list.txt if duplicated
-    case PathList(ps@_*) if ps.last == "public-suffix-list.txt" =>
+    case PathList(ps @ _*) if ps.last == "public-suffix-list.txt" =>
       MergeStrategy.last
     // Merge kotlin modules if duplicated
-    case PathList(ps@_*) if ps.last == "kotlin-stdlib-common.kotlin_module" =>
+    case PathList(ps @ _*) if ps.last == "kotlin-stdlib-common.kotlin_module" =>
       MergeStrategy.last
-    case PathList(ps@_*) if ps.last == "kotlin-stdlib.kotlin_module" =>
+    case PathList(ps @ _*) if ps.last == "kotlin-stdlib.kotlin_module" =>
       MergeStrategy.last
     // AWS SDK v2 configuration files - can be discarded
-    case PathList(ps@_*) if Set("codegen.config" , "service-2.json" , "waiters-2.json" , "customization.config" , "examples-1.json" , "paginators-1.json").contains(ps.last) =>
+    case PathList(ps @ _*)
+        if Set("codegen.config",
+               "service-2.json",
+               "waiters-2.json",
+               "customization.config",
+               "examples-1.json",
+               "paginators-1.json"
+        ).contains(ps.last) =>
       MergeStrategy.discard
-    case x@PathList("META-INF", path@_*) =>
+    case x @ PathList("META-INF", path @ _*) =>
       path map {
         _.toLowerCase
       } match {
@@ -51,7 +58,7 @@ object Merging {
           val oldStrategy = (assembly / assemblyMergeStrategy).value
           oldStrategy(x)
       }
-    case x@PathList("OSGI-INF", path@_*) =>
+    case x @ PathList("OSGI-INF", path @ _*) =>
       path map {
         _.toLowerCase
       } match {
@@ -61,10 +68,11 @@ object Merging {
           val oldStrategy = (assembly / assemblyMergeStrategy).value
           oldStrategy(x)
       }
-    case "asm-license.txt" | "module-info.class" | "overview.html" | "cobertura.properties" | "grammar.hgr" | "CHANGELOG.txt" =>
+    case "asm-license.txt" | "module-info.class" | "overview.html" | "cobertura.properties" | "grammar.hgr" |
+        "CHANGELOG.txt" =>
       MergeStrategy.discard
     // inspired by https://github.com/ergoplatform/explorer-backend/blob/7364ecfdeabeb691f0f25525e577d6c48240c672/build.sbt#L14-L15
-    case other if other.contains("scala/annotation/nowarn.class")  => MergeStrategy.discard
+    case other if other.contains("scala/annotation/nowarn.class") => MergeStrategy.discard
     case other if other.contains("scala/annotation/nowarn$.class") => MergeStrategy.discard
     case PathList("mime.types") =>
       MergeStrategy.last
diff --git a/project/Publishing.scala b/project/Publishing.scala
index 1d4143fc13e..0af27e77147 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -34,7 +34,7 @@ object Publishing {
     `CROMWELL_SBT_DOCKER_TAGS=dev,develop sbt 'show docker::imageNames'` returns:
       ArrayBuffer(broadinstitute/womtool:dev, broadinstitute/womtool:develop)
       ArrayBuffer(broadinstitute/cromwell:dev, broadinstitute/cromwell:develop)
-    */
+     */
     dockerTags := {
       val versionsCsv = if (Version.isSnapshot) {
         // Tag looks like `85-443a6fc-SNAP`
@@ -113,19 +113,19 @@ object Publishing {
     docker / buildOptions := BuildOptions(
       cache = false,
       removeIntermediateContainers = BuildOptions.Remove.Always
-    ),
+    )
   )
 
-  def dockerPushSettings(pushEnabled: Boolean): Seq[Setting[_]] = {
+  def dockerPushSettings(pushEnabled: Boolean): Seq[Setting[_]] =
     if (pushEnabled) {
       List(
         dockerPushCheck := {
           val projectName = name.value
           val repositoryName = s"broadinstitute/$projectName"
           val repositoryUrl = s"https://registry.hub.docker.com/v2/repositories/$repositoryName/"
-          try {
+          try
             url(repositoryUrl).cat.lineStream
-          } catch {
+          catch {
             case exception: Exception =>
               throw new IllegalStateException(
                 s"""|Verify that public repository https://hub.docker.com/r/$repositoryName exists.
@@ -144,7 +144,6 @@ object Publishing {
         }
       )
     }
-  }
 
   private val broadArtifactoryResolver: Resolver =
     "Broad Artifactory" at
@@ -170,12 +169,11 @@ object Publishing {
   private val artifactoryCredentialsFile =
     file("target/ci/resources/artifactory_credentials.properties").getAbsoluteFile
 
-  private val artifactoryCredentials: Seq[Credentials] = {
+  private val artifactoryCredentials: Seq[Credentials] =
     if (artifactoryCredentialsFile.exists)
       List(Credentials(artifactoryCredentialsFile))
     else
       Nil
-  }
 
   // BT-250 Check if publishing will fail due to already published artifacts
   val checkAlreadyPublished = taskKey[Boolean]("Verifies if publishing has already occurred")
@@ -183,7 +181,8 @@ object Publishing {
 
   private case class CromwellMDArtifactType(artifactType: String,
                                             artifactExtension: String,
-                                            classifierOption: Option[String])
+                                            classifierOption: Option[String]
+  )
 
   /**
     * The types of MDArtifacts published by this sbt build.
@@ -201,18 +200,18 @@ object Publishing {
   /**
     * Retrieve the IBiblioResolver from sbt's Ivy setup.
     */
-  private def getIBiblioResolver(ivy: Ivy): IBiblioResolver = {
+  private def getIBiblioResolver(ivy: Ivy): IBiblioResolver =
     ivy.getSettings.getResolver(broadArtifactoryResolver.name) match {
       case iBiblioResolver: IBiblioResolver => iBiblioResolver
       case other => sys.error(s"Expected an IBiblioResolver, got $other")
     }
-  }
 
   /**
     * Maps an sbt artifact to the Apache Ivy artifact type.
     */
-  private def makeMDArtifact(moduleDescriptor: DefaultModuleDescriptor)
-                            (cromwellMDArtifactType: CromwellMDArtifactType): MDArtifact = {
+  private def makeMDArtifact(moduleDescriptor: DefaultModuleDescriptor)(
+    cromwellMDArtifactType: CromwellMDArtifactType
+  ): MDArtifact =
     new MDArtifact(
       moduleDescriptor,
       moduleDescriptor.getModuleRevisionId.getName,
@@ -221,7 +220,6 @@ object Publishing {
       null,
       cromwellMDArtifactType.classifierOption.map("classifier" -> _).toMap.asJava
     )
-  }
 
   /**
     * Returns true and prints out an error if an artifact already exists.
@@ -243,20 +241,19 @@ object Publishing {
       val module = ivyModule.value
       val log = streams.value.log
 
-      module.withModule(log) {
-        case (ivy, moduleDescriptor, _) =>
-          val resolver = getIBiblioResolver(ivy)
-          cromwellMDArtifactTypes
-            .map(makeMDArtifact(moduleDescriptor))
-            .map(existsMDArtifact(resolver, log))
-            .exists(identity)
+      module.withModule(log) { case (ivy, moduleDescriptor, _) =>
+        val resolver = getIBiblioResolver(ivy)
+        cromwellMDArtifactTypes
+          .map(makeMDArtifact(moduleDescriptor))
+          .map(existsMDArtifact(resolver, log))
+          .exists(identity)
       }
     },
     errorIfAlreadyPublished := {
       if (checkAlreadyPublished.value) {
         sys.error(
           s"Some ${version.value} artifacts were already published and will need to be manually deleted. " +
-          "See the errors above for the list of published artifacts."
+            "See the errors above for the list of published artifacts."
         )
       }
     }
diff --git a/project/Testing.scala b/project/Testing.scala
index 54ddc458353..6997e31960c 100644
--- a/project/Testing.scala
+++ b/project/Testing.scala
@@ -62,7 +62,7 @@ object Testing {
       spanScaleFactor,
       "-W",
       "300",
-      "300",
+      "300"
     )
 
   /** Run minnie-kenny only once per sbt invocation. */
@@ -71,7 +71,7 @@ object Testing {
     private var resultOption: Option[Int] = None
 
     /** Run using the logger, throwing an exception only on the first failure. */
-    def runOnce(log: Logger, args: Seq[String]): Unit = {
+    def runOnce(log: Logger, args: Seq[String]): Unit =
       mutex synchronized {
         if (resultOption.isEmpty) {
           log.debug(s"Running minnie-kenny.sh${args.mkString(" ", " ", "")}")
@@ -83,7 +83,6 @@ object Testing {
             sys.error("Running minnie-kenny.sh failed. Please double check for errors above.")
         }
       }
-    }
   }
 
   // Only run one minnie-kenny.sh at a time!
@@ -116,24 +115,24 @@ object Testing {
     Test / test := {
       minnieKenny.toTask("").value
       (Test / test).value
-    },
+    }
   )
 
   private val integrationTestSettings = List(
     libraryDependencies ++= testDependencies.map(_ % IntegrationTest)
   ) ++ itSettings
 
-  def addTestSettings(project: Project) = {
+  def addTestSettings(project: Project) =
     project
       .settings(testSettings)
-      .configs(AllTests).settings(inConfig(AllTests)(Defaults.testTasks): _*)
-      .configs(CromwellBenchmarkTest).settings(inConfig(CromwellBenchmarkTest)(Defaults.testTasks): _*)
-  }
+      .configs(AllTests)
+      .settings(inConfig(AllTests)(Defaults.testTasks): _*)
+      .configs(CromwellBenchmarkTest)
+      .settings(inConfig(CromwellBenchmarkTest)(Defaults.testTasks): _*)
 
-  def addIntegrationTestSettings(project: Project) = {
+  def addIntegrationTestSettings(project: Project) =
     project
       .settings(integrationTestSettings)
       .configs(IntegrationTest)
-  }
 
 }
diff --git a/project/Version.scala b/project/Version.scala
index 4de639d9d41..e530e54e62e 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -33,10 +33,10 @@ object Version {
       ThisBuild / git.versionProperty := "project.version",
       ThisBuild / git.baseVersion := cromwellVersion,
       ThisBuild / version :=
-        makeVersion(
-          versionProperty = git.versionProperty.value,
-          baseVersion = git.baseVersion.?.value,
-          headCommit = git.gitHeadCommit.value),
+        makeVersion(versionProperty = git.versionProperty.value,
+                    baseVersion = git.baseVersion.?.value,
+                    headCommit = git.gitHeadCommit.value
+        ),
       ThisBuild / shellPrompt := { state => "%s| %s> ".format(GitCommand.prompt.apply(state), cromwellVersion) }
     )
 
@@ -74,9 +74,7 @@ object Version {
     List(file)
   }
 
-  private def makeVersion(versionProperty: String,
-                          baseVersion: Option[String],
-                          headCommit: Option[String]): String = {
+  private def makeVersion(versionProperty: String, baseVersion: Option[String], headCommit: Option[String]): String = {
     // The version string passed in via command line settings, if desired.
     def overrideVersion = Option(sys.props(versionProperty))
 
@@ -88,7 +86,7 @@ object Version {
     // Version string fallback.
     val unknownVersion = basePrefix + "unknown"
 
-    //Now we fall through the potential version numbers...
+    // Now we fall through the potential version numbers...
     val version = overrideVersion orElse commitVersion getOrElse unknownVersion
 
     // For now, obfuscate SNAPSHOTs from sbt's developers: https://github.com/sbt/sbt/issues/2687#issuecomment-236586241
diff --git a/server/src/main/scala/cromwell/CommandLineArguments.scala b/server/src/main/scala/cromwell/CommandLineArguments.scala
index 986a33a4dc2..7cebb1b01ba 100644
--- a/server/src/main/scala/cromwell/CommandLineArguments.scala
+++ b/server/src/main/scala/cromwell/CommandLineArguments.scala
@@ -25,7 +25,8 @@ object CommandLineArguments {
                              worflowInputs: String,
                              workflowOptions: WorkflowOptions,
                              workflowLabels: String,
-                             dependencies: Option[File])
+                             dependencies: Option[File]
+  )
 
   case class WorkflowSourceOrUrl(source: Option[String], url: Option[String])
 }
@@ -41,52 +42,52 @@ case class CommandLineArguments(command: Option[Command] = None,
                                 imports: Option[Path] = None,
                                 metadataOutput: Option[Path] = None,
                                 host: URL = CommandLineArguments.DefaultCromwellHost
-                               ) {
+) {
   def validateSubmission(logger: Logger): ErrorOr[ValidSubmission] = {
 
-    def getWorkflowSourceFromPath(workflowPath: Path): ErrorOr[WorkflowSourceOrUrl] = {
+    def getWorkflowSourceFromPath(workflowPath: Path): ErrorOr[WorkflowSourceOrUrl] =
       WorkflowSourceOrUrl(None, Option(workflowPath.pathAsString)).validNel
-    }
 
     val workflowSourceAndUrl: ErrorOr[WorkflowSourceOrUrl] = DefaultPathBuilder.build(workflowSource.get) match {
-      case Success(workflowPath) => {
+      case Success(workflowPath) =>
         if (!workflowPath.exists) s"Workflow source path does not exist: $workflowPath".invalidNel
-        else if(!workflowPath.isReadable) s"Workflow source path is not readable: $workflowPath".invalidNel
+        else if (!workflowPath.isReadable) s"Workflow source path is not readable: $workflowPath".invalidNel
         else getWorkflowSourceFromPath(workflowPath)
-      }
       case Failure(e: InvalidPathException) => s"Invalid file path. Error: ${e.getMessage}".invalidNel
-      case Failure(_) => PartialWorkflowSources.validateWorkflowUrl(workflowSource.get).map(validUrl => WorkflowSourceOrUrl(None, Option(validUrl)))
+      case Failure(_) =>
+        PartialWorkflowSources
+          .validateWorkflowUrl(workflowSource.get)
+          .map(validUrl => WorkflowSourceOrUrl(None, Option(validUrl)))
     }
 
     val inputsJson: ErrorOr[String] = readOptionContent("Workflow inputs", workflowInputs)
 
     import common.validation.ErrorOr.ShortCircuitingFlatMap
-    val optionsJson = readOptionContent("Workflow options", workflowOptions).flatMap { WorkflowOptions.fromJsonString(_).toErrorOr }
+    val optionsJson = readOptionContent("Workflow options", workflowOptions).flatMap {
+      WorkflowOptions.fromJsonString(_).toErrorOr
+    }
 
     val labelsJson = readOptionContent("Workflow labels", workflowLabels)
 
     val workflowImports: Option[File] = imports.map(p => File(p.pathAsString))
 
-    (workflowSourceAndUrl, inputsJson, optionsJson, labelsJson) mapN {
-      case (srcOrUrl, i, o, l) =>
-        ValidSubmission(srcOrUrl.source, srcOrUrl.url, workflowRoot, i, o, l, workflowImports)
+    (workflowSourceAndUrl, inputsJson, optionsJson, labelsJson) mapN { case (srcOrUrl, i, o, l) =>
+      ValidSubmission(srcOrUrl.source, srcOrUrl.url, workflowRoot, i, o, l, workflowImports)
     }
   }
 
   /** Read the path to a string. */
-  private def readContent(inputDescription: String, path: Path): ErrorOr[String] = {
+  private def readContent(inputDescription: String, path: Path): ErrorOr[String] =
     if (!path.exists) {
       s"$inputDescription does not exist: $path".invalidNel
     } else if (!path.isReadable) {
       s"$inputDescription is not readable: $path".invalidNel
     } else path.contentAsString.validNel
-  }
 
   /** Read the path to a string, unless the path is None, in which case returns "{}". */
-  private def readOptionContent(inputDescription: String, pathOption: Option[Path]): ErrorOr[String] = {
+  private def readOptionContent(inputDescription: String, pathOption: Option[Path]): ErrorOr[String] =
     pathOption match {
       case Some(path) => readContent(inputDescription, path)
       case None => "{}".validNel
     }
-  }
 }
diff --git a/server/src/main/scala/cromwell/CommandLineParser.scala b/server/src/main/scala/cromwell/CommandLineParser.scala
index e8b30d5e008..60127905f6f 100644
--- a/server/src/main/scala/cromwell/CommandLineParser.scala
+++ b/server/src/main/scala/cromwell/CommandLineParser.scala
@@ -33,33 +33,29 @@ object CommandLineParser {
 //                           An optional JSON file path to output metadata.
 //  -h, --host               Cromwell server URL
 class CommandLineParser extends scopt.OptionParser[CommandLineArguments]("java -jar /path/to/cromwell.jar") {
-  
+
   private def commonSubmissionArguments = List(
-    arg[String]("workflow-source").text("Workflow source file or workflow url.").required().
-      action((s, c) =>
-        c.copy(workflowSource = Option(s))),
-    opt[String]("workflow-root").text("Workflow root.").
-      action((s, c) =>
-        c.copy(workflowRoot = Option(s))),
-    opt[String]('i', "inputs").text("Workflow inputs file.").
-      action((s, c) =>
-        c.copy(workflowInputs = Option(DefaultPathBuilder.get(s)))),
-    opt[String]('o', "options").text("Workflow options file.").
-      action((s, c) =>
-        c.copy(workflowOptions = Option(DefaultPathBuilder.get(s)))),
-    opt[String]('t', "type").text("Workflow type.").
-      action((s, c) =>
-        c.copy(workflowType = Option(s))),
-    opt[String]('v', "type-version").text("Workflow type version.").
-      action((s, c) =>
-        c.copy(workflowTypeVersion = Option(s))),
-    opt[String]('l', "labels").text("Workflow labels file.").
-      action((s, c) =>
-        c.copy(workflowLabels = Option(DefaultPathBuilder.get(s)))),
-    opt[String]('p', "imports").text(
-      "A zip file to search for workflow imports.").
-      action((s, c) =>
-        c.copy(imports = Option(DefaultPathBuilder.get(s))))
+    arg[String]("workflow-source")
+      .text("Workflow source file or workflow url.")
+      .required()
+      .action((s, c) => c.copy(workflowSource = Option(s))),
+    opt[String]("workflow-root").text("Workflow root.").action((s, c) => c.copy(workflowRoot = Option(s))),
+    opt[String]('i', "inputs")
+      .text("Workflow inputs file.")
+      .action((s, c) => c.copy(workflowInputs = Option(DefaultPathBuilder.get(s)))),
+    opt[String]('o', "options")
+      .text("Workflow options file.")
+      .action((s, c) => c.copy(workflowOptions = Option(DefaultPathBuilder.get(s)))),
+    opt[String]('t', "type").text("Workflow type.").action((s, c) => c.copy(workflowType = Option(s))),
+    opt[String]('v', "type-version")
+      .text("Workflow type version.")
+      .action((s, c) => c.copy(workflowTypeVersion = Option(s))),
+    opt[String]('l', "labels")
+      .text("Workflow labels file.")
+      .action((s, c) => c.copy(workflowLabels = Option(DefaultPathBuilder.get(s)))),
+    opt[String]('p', "imports")
+      .text("A zip file to search for workflow imports.")
+      .action((s, c) => c.copy(imports = Option(DefaultPathBuilder.get(s))))
   )
 
   head("cromwell", cromwellVersion)
@@ -68,29 +64,29 @@ class CommandLineParser extends scopt.OptionParser[CommandLineArguments]("java -
 
   version("version")
 
-  cmd("server").action((_, c) => c.copy(command = Option(Server))).text(
-    "Starts a web server on port 8000.  See the web server documentation for more details about the API endpoints.")
+  cmd("server")
+    .action((_, c) => c.copy(command = Option(Server)))
+    .text(
+      "Starts a web server on port 8000.  See the web server documentation for more details about the API endpoints."
+    )
 
-  cmd("run").
-    action((_, c) => c.copy(command = Option(Run))).
-    text("Run the workflow and print out the outputs in JSON format.").
-    children(
+  cmd("run")
+    .action((_, c) => c.copy(command = Option(Run)))
+    .text("Run the workflow and print out the outputs in JSON format.")
+    .children(
       commonSubmissionArguments ++ List(
-        opt[String]('m', "metadata-output").text(
-          "An optional JSON file path to output metadata.").
-          action((s, c) =>
-            c.copy(metadataOutput = Option(DefaultPathBuilder.get(s))))
+        opt[String]('m', "metadata-output")
+          .text("An optional JSON file path to output metadata.")
+          .action((s, c) => c.copy(metadataOutput = Option(DefaultPathBuilder.get(s))))
       ): _*
     )
 
   cmd("submit")
-    .action((_, c) => c.copy(command = Option(Submit))).
-    text("Submit the workflow to a Cromwell server.").
-    children(
+    .action((_, c) => c.copy(command = Option(Submit)))
+    .text("Submit the workflow to a Cromwell server.")
+    .children(
       commonSubmissionArguments ++ List(
-        opt[String]('h', "host").text("Cromwell server URL.").
-          action((h, c) =>
-            c.copy(host = new URL(h)))
+        opt[String]('h', "host").text("Cromwell server URL.").action((h, c) => c.copy(host = new URL(h)))
       ): _*
     )
 }
diff --git a/server/src/main/scala/cromwell/CromwellApp.scala b/server/src/main/scala/cromwell/CromwellApp.scala
index 9c814c4aeb9..6b843069493 100644
--- a/server/src/main/scala/cromwell/CromwellApp.scala
+++ b/server/src/main/scala/cromwell/CromwellApp.scala
@@ -6,17 +6,16 @@ object CromwellApp extends App {
   case object Run extends Command
   case object Server extends Command
   case object Submit extends Command
-  
+
   def buildParser(): scopt.OptionParser[CommandLineArguments] = new CommandLineParser()
 
-  def runCromwell(args: CommandLineArguments): Unit = {
+  def runCromwell(args: CommandLineArguments): Unit =
     args.command match {
       case Some(Run) => CromwellEntryPoint.runSingle(args)
       case Some(Server) => CromwellEntryPoint.runServer()
       case Some(Submit) => CromwellEntryPoint.submitToServer(args)
       case None => showUsageAndExitWithError()
     }
-  }
 
   val parser = buildParser()
 
diff --git a/server/src/main/scala/cromwell/CromwellEntryPoint.scala b/server/src/main/scala/cromwell/CromwellEntryPoint.scala
index d712ea71b28..cd3c3dd0458 100644
--- a/server/src/main/scala/cromwell/CromwellEntryPoint.scala
+++ b/server/src/main/scala/cromwell/CromwellEntryPoint.scala
@@ -18,7 +18,11 @@ import cromwell.api.CromwellClient
 import cromwell.api.model.{Label, LabelsJsonFormatter, WorkflowSingleSubmission}
 import cromwell.core.logging.JavaLoggingBridge
 import cromwell.core.path.{DefaultPathBuilder, Path}
-import cromwell.core.{WorkflowSourceFilesCollection, WorkflowSourceFilesWithDependenciesZip, WorkflowSourceFilesWithoutImports}
+import cromwell.core.{
+  WorkflowSourceFilesCollection,
+  WorkflowSourceFilesWithDependenciesZip,
+  WorkflowSourceFilesWithoutImports
+}
 import cromwell.engine.workflow.SingleWorkflowRunnerActor
 import cromwell.engine.workflow.SingleWorkflowRunnerActor.RunWorkflow
 import cromwell.server.{CromwellServer, CromwellShutdown, CromwellSystem}
@@ -78,7 +82,9 @@ object CromwellEntryPoint extends GracefulStopSupport {
     val runner = cromwellSystem.actorSystem.actorOf(runnerProps, "SingleWorkflowRunnerActor")
 
     import cromwell.util.PromiseActor.EnhancedActorRef
-    waitAndExit(() => runner.askNoTimeout(RunWorkflow), () => CromwellShutdown.instance(cromwellSystem.actorSystem).run(JvmExitReason))
+    waitAndExit(() => runner.askNoTimeout(RunWorkflow),
+                () => CromwellShutdown.instance(cromwellSystem.actorSystem).run(JvmExitReason)
+    )
   }
 
   def submitToServer(args: CommandLineArguments): Unit = {
@@ -123,11 +129,10 @@ object CromwellEntryPoint extends GracefulStopSupport {
       new CromwellSystem {
         override lazy val config: Config = CromwellEntryPoint.config
       }
-    } recoverWith {
-      case t: Throwable =>
-        Log.error(s"Failed to instantiate Cromwell System. Shutting down Cromwell.", t)
-        System.exit(1)
-        Failure(t)
+    } recoverWith { case t: Throwable =>
+      Log.error(s"Failed to instantiate Cromwell System. Shutting down Cromwell.", t)
+      System.exit(1)
+      Failure(t)
     } get
   }
 
@@ -184,11 +189,12 @@ object CromwellEntryPoint extends GracefulStopSupport {
     val futureResult = operation()
     Await.ready(futureResult, Duration.Inf)
 
-    try {
+    try
       Await.ready(shutdown(), 30.seconds)
-    } catch {
+    catch {
       case _: TimeoutException => Console.err.println("Timed out trying to shutdown actor system")
-      case other: Exception => Console.err.println(s"Unexpected error trying to shutdown actor system: ${other.getMessage}")
+      case other: Exception =>
+        Console.err.println(s"Unexpected error trying to shutdown actor system: ${other.getMessage}")
     }
 
     val returnCode = futureResult.value.get match {
@@ -201,34 +207,33 @@ object CromwellEntryPoint extends GracefulStopSupport {
     sys.exit(returnCode)
   }
 
-  private def waitAndExit(runner: CromwellSystem => Future[Any], workflowManagerSystem: CromwellSystem): Unit = {
+  private def waitAndExit(runner: CromwellSystem => Future[Any], workflowManagerSystem: CromwellSystem): Unit =
     waitAndExit(() => runner(workflowManagerSystem), () => workflowManagerSystem.shutdownActorSystem())
-  }
 
   def validateSubmitArguments(args: CommandLineArguments): WorkflowSingleSubmission = {
     import LabelsJsonFormatter._
     import spray.json._
 
-    val validation = args.validateSubmission(EntryPointLogger) map {
-      case ValidSubmission(s, u, r, i, o, l, z) =>
-        val finalWorkflowSourceAndUrl: WorkflowSourceOrUrl =
-          (s, u) match {
-            case (None, Some(url)) if !url.startsWith("http") => //case where url is a WDL/CWL file
-              WorkflowSourceOrUrl(Option(DefaultPathBuilder.get(url).contentAsString), None)
-            case _ =>
-              WorkflowSourceOrUrl(s, u)
-          }
-
-        WorkflowSingleSubmission(
-          workflowSource = finalWorkflowSourceAndUrl.source,
-          workflowUrl = finalWorkflowSourceAndUrl.url,
-          workflowRoot = r,
-          workflowType = args.workflowType,
-          workflowTypeVersion = args.workflowTypeVersion,
-          inputsJson = Option(i),
-          options = Option(o.asPrettyJson),
-          labels = Option(l.parseJson.convertTo[List[Label]]),
-          zippedImports = z)
+    val validation = args.validateSubmission(EntryPointLogger) map { case ValidSubmission(s, u, r, i, o, l, z) =>
+      val finalWorkflowSourceAndUrl: WorkflowSourceOrUrl =
+        (s, u) match {
+          case (None, Some(url)) if !url.startsWith("http") => // case where url is a WDL/CWL file
+            WorkflowSourceOrUrl(Option(DefaultPathBuilder.get(url).contentAsString), None)
+          case _ =>
+            WorkflowSourceOrUrl(s, u)
+        }
+
+      WorkflowSingleSubmission(
+        workflowSource = finalWorkflowSourceAndUrl.source,
+        workflowUrl = finalWorkflowSourceAndUrl.url,
+        workflowRoot = r,
+        workflowType = args.workflowType,
+        workflowTypeVersion = args.workflowTypeVersion,
+        inputsJson = Option(i),
+        options = Option(o.asPrettyJson),
+        labels = Option(l.parseJson.convertTo[List[Label]]),
+        zippedImports = z
+      )
     }
 
     validOrFailSubmission(validation)
@@ -236,37 +241,40 @@ object CromwellEntryPoint extends GracefulStopSupport {
 
   def validateRunArguments(args: CommandLineArguments): WorkflowSourceFilesCollection = {
 
-    val sourceFileCollection = (args.validateSubmission(EntryPointLogger), writeableMetadataPath(args.metadataOutput)) mapN {
-      case (ValidSubmission(s, u, r, i, o, l, Some(z)), _) =>
-        //noinspection RedundantDefaultArgument
-        WorkflowSourceFilesWithDependenciesZip.apply(
-          workflowSource = s,
-          workflowUrl = u,
-          workflowRoot = r,
-          workflowType = args.workflowType,
-          workflowTypeVersion = args.workflowTypeVersion,
-          inputsJson = i,
-          workflowOptions = o,
-          labelsJson = l,
-          importsZip = z.loadBytes,
-          warnings = Vector.empty,
-          workflowOnHold = false,
-          requestedWorkflowId = None)
-      case (ValidSubmission(s, u, r, i, o, l, None), _) =>
-        //noinspection RedundantDefaultArgument
-        WorkflowSourceFilesWithoutImports.apply(
-          workflowSource = s,
-          workflowUrl = u,
-          workflowRoot = r,
-          workflowType = args.workflowType,
-          workflowTypeVersion = args.workflowTypeVersion,
-          inputsJson = i,
-          workflowOptions = o,
-          labelsJson = l,
-          warnings = Vector.empty,
-          workflowOnHold = false,
-          requestedWorkflowId = None)
-    }
+    val sourceFileCollection =
+      (args.validateSubmission(EntryPointLogger), writeableMetadataPath(args.metadataOutput)) mapN {
+        case (ValidSubmission(s, u, r, i, o, l, Some(z)), _) =>
+          // noinspection RedundantDefaultArgument
+          WorkflowSourceFilesWithDependenciesZip.apply(
+            workflowSource = s,
+            workflowUrl = u,
+            workflowRoot = r,
+            workflowType = args.workflowType,
+            workflowTypeVersion = args.workflowTypeVersion,
+            inputsJson = i,
+            workflowOptions = o,
+            labelsJson = l,
+            importsZip = z.loadBytes,
+            warnings = Vector.empty,
+            workflowOnHold = false,
+            requestedWorkflowId = None
+          )
+        case (ValidSubmission(s, u, r, i, o, l, None), _) =>
+          // noinspection RedundantDefaultArgument
+          WorkflowSourceFilesWithoutImports.apply(
+            workflowSource = s,
+            workflowUrl = u,
+            workflowRoot = r,
+            workflowType = args.workflowType,
+            workflowTypeVersion = args.workflowTypeVersion,
+            inputsJson = i,
+            workflowOptions = o,
+            labelsJson = l,
+            warnings = Vector.empty,
+            workflowOnHold = false,
+            requestedWorkflowId = None
+          )
+      }
 
     val sourceFiles = for {
       sources <- sourceFileCollection
@@ -276,19 +284,19 @@ object CromwellEntryPoint extends GracefulStopSupport {
     validOrFailSubmission(sourceFiles)
   }
 
-  def validOrFailSubmission[A](validation: ErrorOr[A]): A = {
-    validation.valueOr(errors => throw new RuntimeException with MessageAggregation {
-      override def exceptionContext: String = "ERROR: Unable to submit workflow to Cromwell:"
-      override def errorMessages: Iterable[String] = errors.toList
-    })
-  }
+  def validOrFailSubmission[A](validation: ErrorOr[A]): A =
+    validation.valueOr(errors =>
+      throw new RuntimeException with MessageAggregation {
+        override def exceptionContext: String = "ERROR: Unable to submit workflow to Cromwell:"
+        override def errorMessages: Iterable[String] = errors.toList
+      }
+    )
 
-  private def writeableMetadataPath(path: Option[Path]): ErrorOr[Unit] = {
+  private def writeableMetadataPath(path: Option[Path]): ErrorOr[Unit] =
     path match {
       case Some(p) if !metadataPathIsWriteable(p) => s"Unable to write to metadata directory: $p".invalidNel
       case _ => ().validNel
     }
-  }
 
   private def metadataPathIsWriteable(metadataPath: Path): Boolean =
     Try(metadataPath.createIfNotExists(createParents = true).append("")).isSuccess
diff --git a/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala b/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
index 41b1edccb36..00ff1f7cdc4 100644
--- a/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
+++ b/server/src/test/scala/cromwell/CromwellCommandLineSpec.scala
@@ -51,12 +51,14 @@ class CromwellCommandLineSpec extends AnyFlatSpec with CromwellTimeoutSpec with
 
   it should "run single when supplying wdl and inputs" in {
     val threeStep = WdlAndInputs(ThreeStep)
-    val optionsLast = parser.parse(Array("run", threeStep.wdl, "--inputs", threeStep.inputs), CommandLineArguments()).get
+    val optionsLast =
+      parser.parse(Array("run", threeStep.wdl, "--inputs", threeStep.inputs), CommandLineArguments()).get
     optionsLast.command shouldBe Some(Run)
     optionsLast.workflowSource.get shouldBe threeStep.wdl
     optionsLast.workflowInputs.get.pathAsString shouldBe threeStep.inputs
 
-    val optionsFirst = parser.parse(Array("run", "--inputs", threeStep.inputs, threeStep.wdl), CommandLineArguments()).get
+    val optionsFirst =
+      parser.parse(Array("run", "--inputs", threeStep.inputs, threeStep.wdl), CommandLineArguments()).get
     optionsFirst.command shouldBe Some(Run)
     optionsFirst.workflowSource.get shouldBe threeStep.wdl
     optionsFirst.workflowInputs.get.pathAsString shouldBe threeStep.inputs
@@ -96,13 +98,21 @@ class CromwellCommandLineSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   }
 
   it should "run single when supplying wdl and inputs and options" in {
-    val optionsLast = parser.parse(Array("run", "3step.wdl", "--inputs", "3step.inputs", "--options", "3step.options"), CommandLineArguments()).get
+    val optionsLast = parser
+      .parse(Array("run", "3step.wdl", "--inputs", "3step.inputs", "--options", "3step.options"),
+             CommandLineArguments()
+      )
+      .get
     optionsLast.command shouldBe Some(Run)
     optionsLast.workflowSource.get shouldBe "3step.wdl"
     optionsLast.workflowInputs.get.pathAsString shouldBe "3step.inputs"
     optionsLast.workflowOptions.get.pathAsString shouldBe "3step.options"
 
-    val optionsFirst = parser.parse(Array("run", "--inputs", "3step.inputs", "--options", "3step.options", "3step.wdl"), CommandLineArguments()).get
+    val optionsFirst = parser
+      .parse(Array("run", "--inputs", "3step.inputs", "--options", "3step.options", "3step.wdl"),
+             CommandLineArguments()
+      )
+      .get
     optionsFirst.command shouldBe Some(Run)
     optionsFirst.workflowSource.get shouldBe "3step.wdl"
     optionsFirst.workflowInputs.get.pathAsString shouldBe "3step.inputs"
@@ -118,16 +128,29 @@ class CromwellCommandLineSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   }
 
   it should "fail if workflow url length is more than 2000 characters" in {
-    val veryLongUrl = "https://this_url_has_more_than_2000_characters/why_would_someone_have_such_long_urls_one_would_ask/beats_me/now_starts_lorem_ipsum/At_vero_eos_et_accusamus_et_iusto_odio_dignissimos_ducimus_qui_blanditiis_praesentium_voluptatum_deleniti_atque_corrupti_quos_dolores_et_quas_molestias_excepturi_sint_occaecati_cupiditate_non_provident,_similique_sunt_in_culpa_qui_officia_deserunt_mollitia_animi,_id_est_laborum_et_dolorum_fuga._Et_harum_quidem_rerum_facilis_est_et_expedita_distinctio._Nam_libero_tempore,_cum_soluta_nobis_est_eligendi_optio_cumque_nihil_impedit_quo_minus_id_quod_maxime_placeat_facere_possimus,_omnis_voluptas_assumenda_est,_omnis_dolor_repellendus._Temporibus_autem_quibusdam_et_aut_officiis_debitis_aut_rerum_necessitatibus_saepe_eveniet_ut_et_voluptates_repudiandae_sint_et_molestiae_non_recusandae._Itaque_earum_rerum_hic_tenetur_a_sapiente_delectus,_ut_aut_reiciendis_voluptatibus_maiores_alias_consequatur_aut_perferendis_doloribus_asperiores_repellat/Sed_ut_perspiciatis_unde_omnis_iste_natus_error_sit_voluptatem_accusantium_doloremque_laudantium,_totam_rem_aperiam,_eaque_ipsa_quae_ab_illo_inventore_veritatis_et_quasi_architecto_beatae_vitae_dicta_sunt_explicabo._Nemo_enim_ipsam_voluptatem_quia_voluptas_sit_aspernatur_aut_odit_aut_fugit,_sed_quia_consequuntur_magni_dolores_eos_qui_ratione_voluptatem_sequi_nesciunt._Neque_porro_quisquam_est,_qui_dolorem_ipsum_quia_dolor_sit_amet,_consectetur,_adipisci_velit,_sed_quia_non_numquam_eius_modi_tempora_incidunt_ut_labore_et_dolore_magnam_aliquam_quaerat_voluptatem._Ut_enim_ad_minima_veniam,_quis_nostrum_exercitationem_ullam_corporis_suscipit_laboriosam,_nisi_ut_aliquid_ex_ea_commodi_consequatur?_Quis_autem_vel_eum_iure_reprehenderit_qui_in_ea_voluptate_velit_esse_quam_nihil_molestiae_consequatur,_vel_illum_qui_dolorem_eum_fugiat_quo_voluptas_nulla_pariatur?/Lorem_ipsum_dolor_sit_amet,_consectetur_adipiscing_elit,_sed_do_eiusmod_tempor_incididunt_ut_labore_et_dolore_magna_aliqua._Ut_enim_ad_minim_veniam,_quis_nostrud_exercitation_ullamco_laboris_nisi_ut_aliquip_ex_ea_commodo_consequat._Duis_aute_irure_dolor_in_reprehenderit_in_voluptate_velit_esse_cillum_dolore_eu_fugiat_nulla_pariatur._Excepteur_sint_occaecat_cupidatat_non_proident,_sunt_in_culpa_qui_officia_deserunt_mollit_anim_id_est_laborum/hello.wdl/hello.wdl"
+    val veryLongUrl =
+      "https://this_url_has_more_than_2000_characters/why_would_someone_have_such_long_urls_one_would_ask/beats_me/now_starts_lorem_ipsum/At_vero_eos_et_accusamus_et_iusto_odio_dignissimos_ducimus_qui_blanditiis_praesentium_voluptatum_deleniti_atque_corrupti_quos_dolores_et_quas_molestias_excepturi_sint_occaecati_cupiditate_non_provident,_similique_sunt_in_culpa_qui_officia_deserunt_mollitia_animi,_id_est_laborum_et_dolorum_fuga._Et_harum_quidem_rerum_facilis_est_et_expedita_distinctio._Nam_libero_tempore,_cum_soluta_nobis_est_eligendi_optio_cumque_nihil_impedit_quo_minus_id_quod_maxime_placeat_facere_possimus,_omnis_voluptas_assumenda_est,_omnis_dolor_repellendus._Temporibus_autem_quibusdam_et_aut_officiis_debitis_aut_rerum_necessitatibus_saepe_eveniet_ut_et_voluptates_repudiandae_sint_et_molestiae_non_recusandae._Itaque_earum_rerum_hic_tenetur_a_sapiente_delectus,_ut_aut_reiciendis_voluptatibus_maiores_alias_consequatur_aut_perferendis_doloribus_asperiores_repellat/Sed_ut_perspiciatis_unde_omnis_iste_natus_error_sit_voluptatem_accusantium_doloremque_laudantium,_totam_rem_aperiam,_eaque_ipsa_quae_ab_illo_inventore_veritatis_et_quasi_architecto_beatae_vitae_dicta_sunt_explicabo._Nemo_enim_ipsam_voluptatem_quia_voluptas_sit_aspernatur_aut_odit_aut_fugit,_sed_quia_consequuntur_magni_dolores_eos_qui_ratione_voluptatem_sequi_nesciunt._Neque_porro_quisquam_est,_qui_dolorem_ipsum_quia_dolor_sit_amet,_consectetur,_adipisci_velit,_sed_quia_non_numquam_eius_modi_tempora_incidunt_ut_labore_et_dolore_magnam_aliquam_quaerat_voluptatem._Ut_enim_ad_minima_veniam,_quis_nostrum_exercitationem_ullam_corporis_suscipit_laboriosam,_nisi_ut_aliquid_ex_ea_commodi_consequatur?_Quis_autem_vel_eum_iure_reprehenderit_qui_in_ea_voluptate_velit_esse_quam_nihil_molestiae_consequatur,_vel_illum_qui_dolorem_eum_fugiat_quo_voluptas_nulla_pariatur?/Lorem_ipsum_dolor_sit_amet,_consectetur_adipiscing_elit,_sed_do_eiusmod_tempor_incididunt_ut_labore_et_dolore_magna_aliqua._Ut_enim_ad_minim_veniam,_quis_nostrud_exercitation_ullamco_laboris_nisi_ut_aliquip_ex_ea_commodo_consequat._Duis_aute_irure_dolor_in_reprehenderit_in_voluptate_velit_esse_cillum_dolore_eu_fugiat_nulla_pariatur._Excepteur_sint_occaecat_cupidatat_non_proident,_sunt_in_culpa_qui_officia_deserunt_mollit_anim_id_est_laborum/hello.wdl/hello.wdl"
     val command = parser.parse(Array("run", veryLongUrl), CommandLineArguments()).get
     val validation = Try(CromwellEntryPoint.validateRunArguments(command))
 
     validation.isFailure shouldBe true
-    validation.failed.get.getMessage should include("Invalid workflow url: url has length 2305, longer than the maximum allowed 2000 characters")
+    validation.failed.get.getMessage should include(
+      "Invalid workflow url: url has length 2305, longer than the maximum allowed 2000 characters"
+    )
   }
 
   it should "fail if input files do not exist" in {
-    val parsedArgs = parser.parse(Array("run", "xyzshouldnotexist.wdl", "--inputs", "xyzshouldnotexist.inputs", "--options", "xyzshouldnotexist.options"), CommandLineArguments()).get
+    val parsedArgs = parser
+      .parse(Array("run",
+                   "xyzshouldnotexist.wdl",
+                   "--inputs",
+                   "xyzshouldnotexist.inputs",
+                   "--options",
+                   "xyzshouldnotexist.options"
+             ),
+             CommandLineArguments()
+      )
+      .get
     val validation = Try(CromwellEntryPoint.validateRunArguments(parsedArgs))
 
     validation.isFailure shouldBe true
@@ -147,7 +170,11 @@ class CromwellCommandLineSpec extends AnyFlatSpec with CromwellTimeoutSpec with
 
   it should "fail if metadata output path is not writeable" in {
     val threeStep = WdlAndInputs(ThreeStep)
-    val parsedArgs = parser.parse(Array("run", threeStep.wdl, "--inputs", threeStep.inputs, "--metadata-output", threeStep.metadata), CommandLineArguments()).get
+    val parsedArgs = parser
+      .parse(Array("run", threeStep.wdl, "--inputs", threeStep.inputs, "--metadata-output", threeStep.metadata),
+             CommandLineArguments()
+      )
+      .get
     threeStep.metadataFile write "foo"
     threeStep.metadataFile setPermissions Set.empty
     val ccl = Try(CromwellEntryPoint.validateRunArguments(parsedArgs))
@@ -166,7 +193,8 @@ class CromwellCommandLineSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     val zippedDir = wdlDir.zip()
     val zippedPath = zippedDir.pathAsString
 
-    val parsedArgs = parser.parse(Array("run", filePassing.pathAsString, "--imports", zippedPath), CommandLineArguments()).get
+    val parsedArgs =
+      parser.parse(Array("run", filePassing.pathAsString, "--imports", zippedPath), CommandLineArguments()).get
     val ccl = Try(CromwellEntryPoint.validateRunArguments(parsedArgs))
     ccl.isFailure shouldBe false
 
diff --git a/server/src/test/scala/cromwell/CromwellTestKitSpec.scala b/server/src/test/scala/cromwell/CromwellTestKitSpec.scala
index 319b417e861..09688408552 100644
--- a/server/src/test/scala/cromwell/CromwellTestKitSpec.scala
+++ b/server/src/test/scala/cromwell/CromwellTestKitSpec.scala
@@ -9,21 +9,29 @@ import cromwell.CromwellTestKitSpec._
 import cromwell.core._
 import cromwell.core.path.BetterFileMethods.Cmds
 import cromwell.core.path.DefaultPathBuilder
-import cromwell.docker.DockerInfoActor.{DockerInfoSuccessResponse, DockerInformation}
+import cromwell.docker.DockerInfoActor.{DockerInformation, DockerInfoSuccessResponse}
 import cromwell.docker.{DockerHashResult, DockerInfoRequest}
 import cromwell.engine.MockCromwellTerminator
 import cromwell.engine.backend.{BackendConfiguration, CromwellBackends}
 import cromwell.engine.workflow.WorkflowManagerActor.RetrieveNewWorkflows
-import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadActor.{CacheLookupNoHit, CacheLookupRequest}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadActor.{
+  CacheLookupNoHit,
+  CacheLookupRequest
+}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheWriteActor.SaveCallCacheHashes
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheWriteSuccess
 import cromwell.engine.workflow.workflowstore.WorkflowStoreSubmitActor.WorkflowSubmittedToStore
 import cromwell.engine.workflow.workflowstore.{InMemorySubWorkflowStore, InMemoryWorkflowStore, WorkflowStoreActor}
-import cromwell.jobstore.JobStoreActor.{JobStoreWriteSuccess, JobStoreWriterCommand}
+import cromwell.jobstore.JobStoreActor.{JobStoreWriterCommand, JobStoreWriteSuccess}
 import cromwell.languages.config.{CromwellLanguages, LanguageConfiguration}
 import cromwell.server.{CromwellRootActor, CromwellSystem}
 import cromwell.services.metadata.MetadataService._
-import cromwell.services.{FailedMetadataJsonResponse, MetadataJsonResponse, ServiceRegistryActor, SuccessfulMetadataJsonResponse}
+import cromwell.services.{
+  FailedMetadataJsonResponse,
+  MetadataJsonResponse,
+  ServiceRegistryActor,
+  SuccessfulMetadataJsonResponse
+}
 import cromwell.subworkflowstore.EmptySubWorkflowStoreActor
 import cromwell.util.SampleWdl
 import org.scalactic.Equality
@@ -43,7 +51,8 @@ import scala.concurrent.duration._
 import scala.concurrent.{Await, ExecutionContext, Future}
 import scala.util.matching.Regex
 
-case class OutputNotFoundException(outputFqn: String, actualOutputs: String) extends RuntimeException(s"Expected output $outputFqn was not found in: '$actualOutputs'")
+case class OutputNotFoundException(outputFqn: String, actualOutputs: String)
+    extends RuntimeException(s"Expected output $outputFqn was not found in: '$actualOutputs'")
 case class LogNotFoundException(log: String) extends RuntimeException(s"Expected log $log was not found")
 
 object CromwellTestKitSpec {
@@ -108,33 +117,32 @@ object CromwellTestKitSpec {
   class TestWorkflowManagerSystem(testActorSystem: ActorSystem, override val config: Config) extends CromwellSystem {
     override protected def systemName: String = testActorSystem.name
     override protected def newActorSystem(): ActorSystem = testActorSystem
+
     /**
       * Do NOT shut down the test actor system inside the normal flow.
       * The actor system will be externally shutdown outside the block.
       */
     // -Ywarn-value-discard
-    override def shutdownActorSystem(): Future[Terminated] = { Future.successful(null) }
+    override def shutdownActorSystem(): Future[Terminated] = Future.successful(null)
   }
 
   /**
    * Wait for exactly one occurrence of the specified info pattern in the specified block.  The block is in its own
    * parameter list for usage syntax reasons.
    */
-  def waitForInfo[T](pattern: String, occurrences: Int = 1)(block: => T)(implicit system: ActorSystem): T = {
+  def waitForInfo[T](pattern: String, occurrences: Int = 1)(block: => T)(implicit system: ActorSystem): T =
     EventFilter.info(pattern = pattern, occurrences = occurrences).intercept {
       block
     }
-  }
 
   /**
    * Wait for occurrence(s) of the specified warning pattern in the specified block.  The block is in its own parameter
    * list for usage syntax reasons.
    */
-  def waitForWarning[T](pattern: String, occurrences: Int = 1)(block: => T)(implicit system: ActorSystem): T = {
+  def waitForWarning[T](pattern: String, occurrences: Int = 1)(block: => T)(implicit system: ActorSystem): T =
     EventFilter.warning(pattern = pattern, occurrences = occurrences).intercept {
       block
     }
-  }
 
   /**
    * Akka TestKit appears to be unable to match errors generated by `log.error(Throwable, String)` with the normal
@@ -144,40 +152,40 @@ object CromwellTestKitSpec {
    */
   def waitForErrorWithException[T](pattern: String,
                                    throwableClass: Class[_ <: Throwable] = classOf[Throwable],
-                                   occurrences: Int = 1)
-                                  (block: => T)
-                                  (implicit system: ActorSystem): T = {
+                                   occurrences: Int = 1
+  )(block: => T)(implicit system: ActorSystem): T = {
     val regex = Right[String, Regex](pattern.r)
     ErrorFilter(throwableClass, source = None, message = regex, complete = false)(occurrences = occurrences).intercept {
       block
     }
   }
 
-
   /**
     * Special case for validating outputs. Used when the test wants to check that an output exists, but doesn't care what
     * the actual value was.
     */
-  lazy val AnyValueIsFine: WomValue = WomString("Today you are you! That is truer than true! There is no one alive who is you-er than you!")
+  lazy val AnyValueIsFine: WomValue = WomString(
+    "Today you are you! That is truer than true! There is no one alive who is you-er than you!"
+  )
 
-  def replaceVariables(womValue: WomValue, workflowId: WorkflowId): WomValue = {
+  def replaceVariables(womValue: WomValue, workflowId: WorkflowId): WomValue =
     womValue match {
       case WomString(value) => WomString(replaceVariables(value, workflowId))
       case _ => womValue
     }
-  }
 
   def replaceVariables(value: String, workflowId: WorkflowId): String = {
     val variables = Map("PWD" -> Cmds.pwd.toString, "UUID" -> workflowId.toString)
-    variables.foldLeft(value) {
-      case (result, (variableName, variableValue)) => result.replace(s"<<$variableName>>", s"$variableValue")
+    variables.foldLeft(value) { case (result, (variableName, variableValue)) =>
+      result.replace(s"<<$variableName>>", s"$variableValue")
     }
   }
 
   lazy val DefaultConfig: Config = ConfigFactory.load
 
   lazy val NooPServiceActorConfig: Config = DefaultConfig.withValue(
-    "services.LoadController.class", ConfigValueFactory.fromAnyRef("cromwell.services.NooPServiceActor")
+    "services.LoadController.class",
+    ConfigValueFactory.fromAnyRef("cromwell.services.NooPServiceActor")
   )
 
   lazy val JesBackendConfig: Config = ConfigFactory.parseString(
@@ -215,7 +223,8 @@ object CromwellTestKitSpec {
       |    }
       |  }
       |}
-    """.stripMargin)
+    """.stripMargin
+  )
 
   /**
     * It turns out that tests using the metadata refresh actor running in parallel don't work so well if there are more
@@ -229,19 +238,23 @@ object CromwellTestKitSpec {
     */
   private val ServiceRegistryActorSystem = akka.actor.ActorSystem("cromwell-service-registry-system")
 
-  val ServiceRegistryActorInstance: ActorRef = {
-    ServiceRegistryActorSystem.actorOf(ServiceRegistryActor.props(CromwellTestKitSpec.DefaultConfig), "ServiceRegistryActor")
-  }
+  val ServiceRegistryActorInstance: ActorRef =
+    ServiceRegistryActorSystem.actorOf(ServiceRegistryActor.props(CromwellTestKitSpec.DefaultConfig),
+                                       "ServiceRegistryActor"
+    )
 
   class TestCromwellRootActor(config: Config)(implicit materializer: ActorMaterializer)
-    extends CromwellRootActor(MockCromwellTerminator, false, false, serverMode = true, config = config) {
+      extends CromwellRootActor(MockCromwellTerminator, false, false, serverMode = true, config = config) {
 
     override lazy val serviceRegistryActor: ActorRef = ServiceRegistryActorInstance
     override lazy val workflowStore = new InMemoryWorkflowStore
     override lazy val subWorkflowStore = new InMemorySubWorkflowStore(workflowStore)
     def submitWorkflow(sources: WorkflowSourceFilesCollection): WorkflowId = {
       val submitMessage = WorkflowStoreActor.SubmitWorkflow(sources)
-      val result = Await.result(workflowStoreActor.ask(submitMessage)(TimeoutDuration), Duration.Inf).asInstanceOf[WorkflowSubmittedToStore].workflowId
+      val result = Await
+        .result(workflowStoreActor.ask(submitMessage)(TimeoutDuration), Duration.Inf)
+        .asInstanceOf[WorkflowSubmittedToStore]
+        .workflowId
       workflowManagerActor ! RetrieveNewWorkflows
       result
     }
@@ -249,8 +262,14 @@ object CromwellTestKitSpec {
 }
 
 abstract class CromwellTestKitWordSpec extends CromwellTestKitSpec with AnyWordSpecLike
-abstract class CromwellTestKitSpec extends TestKitSuite
-  with DefaultTimeout with ImplicitSender with Matchers with ScalaFutures with Eventually with OneInstancePerTest {
+abstract class CromwellTestKitSpec
+    extends TestKitSuite
+    with DefaultTimeout
+    with ImplicitSender
+    with Matchers
+    with ScalaFutures
+    with Eventually
+    with OneInstancePerTest {
 
   override protected lazy val actorSystemConfig: Config = ConfigFactory.parseString(CromwellTestKitSpec.ConfigText)
 
@@ -273,7 +292,7 @@ abstract class CromwellTestKitSpec extends TestKitSuite
   lazy val dummyServiceRegistryActor: ActorRef = system.actorOf(Props.empty, "dummyServiceRegistryActor")
   lazy val dummyLogCopyRouter: ActorRef = system.actorOf(Props.empty, "dummyLogCopyRouter")
 
-  //noinspection ConvertExpressionToSAM
+  // noinspection ConvertExpressionToSAM
   // Allow to use shouldEqual between 2 WdlTypes while acknowledging for edge cases
   implicit val wdlTypeSoftEquality: Equality[WomType] = new Equality[WomType] {
     @tailrec
@@ -301,10 +320,10 @@ abstract class CromwellTestKitSpec extends TestKitSuite
         case (_: WomString, expectedFile: WomFile) => fileEquality(a.valueString, expectedFile.valueString)
         case (array: WomArray, expectedArray: WomArray) =>
           (array.value.length == expectedArray.value.length) &&
-            array.value.zip(expectedArray.value).map(Function.tupled(areEqual)).forall(identity)
+          array.value.zip(expectedArray.value).map(Function.tupled(areEqual)).forall(identity)
         case (map: WomMap, expectedMap: WomMap) =>
-          val mapped = map.value.map {
-            case (k, v) => expectedMap.value.contains(k) && areEqual(v, expectedMap.value(k))
+          val mapped = map.value.map { case (k, v) =>
+            expectedMap.value.contains(k) && areEqual(v, expectedMap.value(k))
           }
 
           (map.value.size == expectedMap.value.size) && mapped.forall(identity)
@@ -315,9 +334,8 @@ abstract class CromwellTestKitSpec extends TestKitSuite
     }
   }
 
-  protected def buildCromwellRootActor(config: Config, actorName: String): TestActorRef[TestCromwellRootActor] = {
+  protected def buildCromwellRootActor(config: Config, actorName: String): TestActorRef[TestCromwellRootActor] =
     TestActorRef(new TestCromwellRootActor(config), actorName)
-  }
 
   def runWdl(sampleWdl: SampleWdl,
              runtime: String = "",
@@ -326,8 +344,8 @@ abstract class CromwellTestKitSpec extends TestKitSuite
              terminalState: WorkflowState = WorkflowSucceeded,
              config: Config = NooPServiceActorConfig,
              patienceConfig: PatienceConfig = defaultPatience,
-             testActorName: String,
-            )(implicit ec: ExecutionContext): Map[FullyQualifiedName, WomValue] = {
+             testActorName: String
+  )(implicit ec: ExecutionContext): Map[FullyQualifiedName, WomValue] = {
 
     val rootActor = buildCromwellRootActor(config, testActorName)
     val sources = sampleWdl.asWorkflowSources(
@@ -338,7 +356,11 @@ abstract class CromwellTestKitSpec extends TestKitSuite
       labels = customLabels
     )
     val workflowId = rootActor.underlyingActor.submitWorkflow(sources)
-    eventually { verifyWorkflowComplete(rootActor.underlyingActor.serviceRegistryActor, workflowId) } (config = patienceConfig, pos = implicitly[org.scalactic.source.Position], retrying = implicitly[Retrying[Unit]])
+    eventually(verifyWorkflowComplete(rootActor.underlyingActor.serviceRegistryActor, workflowId))(
+      config = patienceConfig,
+      pos = implicitly[org.scalactic.source.Position],
+      retrying = implicitly[Retrying[Unit]]
+    )
     verifyWorkflowState(rootActor.underlyingActor.serviceRegistryActor, workflowId, terminalState)
 
     val outcome = getWorkflowOutputsFromMetadata(workflowId, rootActor.underlyingActor.serviceRegistryActor)
@@ -354,14 +376,17 @@ abstract class CromwellTestKitSpec extends TestKitSuite
                              allowOtherOutputs: Boolean = true,
                              config: Config = NooPServiceActorConfig,
                              patienceConfig: PatienceConfig = defaultPatience,
-                             testActorName: String,
-                            )
-                            (implicit ec: ExecutionContext): WorkflowId = {
+                             testActorName: String
+  )(implicit ec: ExecutionContext): WorkflowId = {
     val rootActor = buildCromwellRootActor(config, testActorName)
     val sources = sampleWdl.asWorkflowSources(runtime, workflowOptions)
 
     val workflowId = rootActor.underlyingActor.submitWorkflow(sources)
-    eventually { verifyWorkflowComplete(rootActor.underlyingActor.serviceRegistryActor, workflowId) } (config = patienceConfig, pos = implicitly[org.scalactic.source.Position], retrying = implicitly[Retrying[Unit]])
+    eventually(verifyWorkflowComplete(rootActor.underlyingActor.serviceRegistryActor, workflowId))(
+      config = patienceConfig,
+      pos = implicitly[org.scalactic.source.Position],
+      retrying = implicitly[Retrying[Unit]]
+    )
     verifyWorkflowState(rootActor.underlyingActor.serviceRegistryActor, workflowId, WorkflowSucceeded)
 
     val outputs = getWorkflowOutputsFromMetadata(workflowId, rootActor.underlyingActor.serviceRegistryActor)
@@ -374,7 +399,10 @@ abstract class CromwellTestKitSpec extends TestKitSuite
     }
     if (!allowOtherOutputs) {
       outputs foreach { case (actualFqn, actualValue) =>
-        val expectedValue = expectedOutputs.getOrElse(actualFqn, throw new RuntimeException(s"Actual output $actualFqn was not wanted in '$expectedOutputNames'"))
+        val expectedValue = expectedOutputs.getOrElse(
+          actualFqn,
+          throw new RuntimeException(s"Actual output $actualFqn was not wanted in '$expectedOutputNames'")
+        )
         if (expectedValue != AnyValueIsFine) actualValue shouldEqual expectedValue
       }
     }
@@ -383,9 +411,12 @@ abstract class CromwellTestKitSpec extends TestKitSuite
     workflowId
   }
 
-  private def getWorkflowState(workflowId: WorkflowId, serviceRegistryActor: ActorRef)(implicit ec: ExecutionContext): WorkflowState = {
+  private def getWorkflowState(workflowId: WorkflowId, serviceRegistryActor: ActorRef)(implicit
+    ec: ExecutionContext
+  ): WorkflowState = {
     val statusResponse = serviceRegistryActor.ask(GetStatus(workflowId))(TimeoutDuration).collect {
-      case SuccessfulMetadataJsonResponse(_, jsObject) => WorkflowState.withName(jsObject.fields("status").asInstanceOf[JsString].value)
+      case SuccessfulMetadataJsonResponse(_, jsObject) =>
+        WorkflowState.withName(jsObject.fields("status").asInstanceOf[JsString].value)
       case f => throw new RuntimeException(s"Unexpected status response for $workflowId: $f")
     }
     Await.result(statusResponse, TimeoutDuration)
@@ -394,20 +425,29 @@ abstract class CromwellTestKitSpec extends TestKitSuite
   /**
     * Verifies that a workflow is complete
     */
-  protected def verifyWorkflowComplete(serviceRegistryActor: ActorRef, workflowId: WorkflowId)(implicit ec: ExecutionContext): Unit = {
-    List(WorkflowSucceeded, WorkflowFailed, WorkflowAborted) should contain(getWorkflowState(workflowId, serviceRegistryActor))
+  protected def verifyWorkflowComplete(serviceRegistryActor: ActorRef, workflowId: WorkflowId)(implicit
+    ec: ExecutionContext
+  ): Unit = {
+    List(WorkflowSucceeded, WorkflowFailed, WorkflowAborted) should contain(
+      getWorkflowState(workflowId, serviceRegistryActor)
+    )
     ()
   }
 
   /**
     * Verifies that a state is correct.
     */
-  protected def verifyWorkflowState(serviceRegistryActor: ActorRef, workflowId: WorkflowId, expectedState: WorkflowState)(implicit ec: ExecutionContext): Unit = {
-    getWorkflowState(workflowId, serviceRegistryActor) should equal (expectedState)
+  protected def verifyWorkflowState(serviceRegistryActor: ActorRef,
+                                    workflowId: WorkflowId,
+                                    expectedState: WorkflowState
+  )(implicit ec: ExecutionContext): Unit = {
+    getWorkflowState(workflowId, serviceRegistryActor) should equal(expectedState)
     ()
   }
 
-  private def getWorkflowOutputsFromMetadata(id: WorkflowId, serviceRegistryActor: ActorRef): Map[FullyQualifiedName, WomValue] = {
+  private def getWorkflowOutputsFromMetadata(id: WorkflowId,
+                                             serviceRegistryActor: ActorRef
+  ): Map[FullyQualifiedName, WomValue] = {
 
     val response = serviceRegistryActor.ask(WorkflowOutputs(id)).mapTo[MetadataJsonResponse] collect {
       case SuccessfulMetadataJsonResponse(_, r) => r
@@ -416,12 +456,12 @@ abstract class CromwellTestKitSpec extends TestKitSuite
     val jsObject = Await.result(response, TimeoutDuration)
 
     jsObject.getFields(WorkflowMetadataKeys.Outputs).toList match {
-      case head::_ => head.asInstanceOf[JsObject].fields.map( x => (x._1, jsValueToWdlValue(x._2)))
+      case head :: _ => head.asInstanceOf[JsObject].fields.map(x => (x._1, jsValueToWdlValue(x._2)))
       case _ => Map.empty
     }
   }
 
-  private def jsValueToWdlValue(jsValue: JsValue): WomValue = {
+  private def jsValueToWdlValue(jsValue: JsValue): WomValue =
     jsValue match {
       case str: JsString => WomString(str.value)
       case JsNumber(number) if number.scale == 0 => WomInteger(number.intValue)
@@ -433,17 +473,18 @@ abstract class CromwellTestKitSpec extends TestKitSuite
         else WomArray(WomArrayType(valuesArray.head.womType), valuesArray)
       case map: JsObject =>
         // TODO: currently assuming all keys are String. But that's not WDL-complete...
-        val valuesMap: Map[WomValue, WomValue] = map.fields.map { case (fieldName, fieldValue) => (WomString(fieldName), jsValueToWdlValue(fieldValue)) }
+        val valuesMap: Map[WomValue, WomValue] = map.fields.map { case (fieldName, fieldValue) =>
+          (WomString(fieldName), jsValueToWdlValue(fieldValue))
+        }
         if (valuesMap.isEmpty) WomMap(WomMapType(WomStringType, WomStringType), Map.empty)
         else WomMap(WomMapType(WomStringType, valuesMap.head._2.womType), valuesMap)
       case oh => throw new RuntimeException(s"Programmer Error! Unexpected case match: $oh")
     }
-  }
 }
 
 class AlwaysHappyJobStoreActor extends Actor {
-  override def receive: Receive = {
-    case x: JobStoreWriterCommand => sender() ! JobStoreWriteSuccess(x)
+  override def receive: Receive = { case x: JobStoreWriterCommand =>
+    sender() ! JobStoreWriteSuccess(x)
   }
 }
 
@@ -456,14 +497,14 @@ object AlwaysHappyJobStoreActor {
 }
 
 class EmptyCallCacheReadActor extends Actor {
-  override def receive: Receive = {
-    case _: CacheLookupRequest => sender() ! CacheLookupNoHit
+  override def receive: Receive = { case _: CacheLookupRequest =>
+    sender() ! CacheLookupNoHit
   }
 }
 
 class EmptyCallCacheWriteActor extends Actor {
-  override def receive: Receive = {
-    case SaveCallCacheHashes => sender() ! CallCacheWriteSuccess
+  override def receive: Receive = { case SaveCallCacheHashes =>
+    sender() ! CallCacheWriteSuccess
   }
 }
 
@@ -476,8 +517,8 @@ object EmptyCallCacheWriteActor {
 }
 
 class EmptyDockerHashActor extends Actor {
-  override def receive: Receive = {
-    case request: DockerInfoRequest => sender() ! DockerInfoSuccessResponse(DockerInformation(DockerHashResult("alg", "hash"), None), request)
+  override def receive: Receive = { case request: DockerInfoRequest =>
+    sender() ! DockerInfoSuccessResponse(DockerInformation(DockerHashResult("alg", "hash"), None), request)
   }
 }
 
diff --git a/server/src/test/scala/cromwell/DeclarationWorkflowSpec.scala b/server/src/test/scala/cromwell/DeclarationWorkflowSpec.scala
index a2b8a4c8a8a..00b06994bcd 100644
--- a/server/src/test/scala/cromwell/DeclarationWorkflowSpec.scala
+++ b/server/src/test/scala/cromwell/DeclarationWorkflowSpec.scala
@@ -21,7 +21,11 @@ class DeclarationWorkflowSpec extends Matchers with AnyWordSpecLike {
       /*
        * WARNING: be aware that `workflow.inputs` is used by projects external to Cromwell (eg FC's input enumerator).
        */
-      val actualInputs = WdlNamespaceWithWorkflow.load(SampleWdl.DeclarationsWorkflow.workflowSource(), Seq.empty[Draft2ImportResolver]).get.workflow.inputs
+      val actualInputs = WdlNamespaceWithWorkflow
+        .load(SampleWdl.DeclarationsWorkflow.workflowSource(), Seq.empty[Draft2ImportResolver])
+        .get
+        .workflow
+        .inputs
 
       actualInputs foreach {
         case (inputName: FullyQualifiedName, actualRequiredInputDefinition: RequiredInputDefinition) =>
@@ -34,10 +38,13 @@ class DeclarationWorkflowSpec extends Matchers with AnyWordSpecLike {
           inputName should be("two_step.cat.flags2")
           inputDefinition.womType should be(WomOptionalType(WomStringType))
         case (inputName: FullyQualifiedName, inputDefinition: OverridableInputDefinitionWithDefault) =>
-          inputDefinition.localName.value should be ("two_step.static_string")
+          inputDefinition.localName.value should be("two_step.static_string")
           inputName should be("two_step.static_string")
           inputDefinition.womType should be(WomStringType)
-        case other => throw new RuntimeException(s"Programmer Error! Draft 2 isn't set up to produce or handle ${other.getClass.getSimpleName}")
+        case other =>
+          throw new RuntimeException(
+            s"Programmer Error! Draft 2 isn't set up to produce or handle ${other.getClass.getSimpleName}"
+          )
       }
     }
   }
diff --git a/server/src/test/scala/cromwell/FilePassingWorkflowSpec.scala b/server/src/test/scala/cromwell/FilePassingWorkflowSpec.scala
index 6a29981a44d..2690671e98d 100644
--- a/server/src/test/scala/cromwell/FilePassingWorkflowSpec.scala
+++ b/server/src/test/scala/cromwell/FilePassingWorkflowSpec.scala
@@ -21,7 +21,7 @@ class FilePassingWorkflowSpec extends CromwellTestKitWordSpec {
           "file_passing.b.contents" -> WomString("foo bar baz")
         ),
         patienceConfig = PatienceConfig(2.minutes.dilated),
-        testActorName = "TestCromwellRootActor-files",
+        testActorName = "TestCromwellRootActor-files"
       )
     }
   }
diff --git a/server/src/test/scala/cromwell/MultipleFilesWithSameNameWorkflowSpec.scala b/server/src/test/scala/cromwell/MultipleFilesWithSameNameWorkflowSpec.scala
index 0e64170f02d..63f184b4eea 100644
--- a/server/src/test/scala/cromwell/MultipleFilesWithSameNameWorkflowSpec.scala
+++ b/server/src/test/scala/cromwell/MultipleFilesWithSameNameWorkflowSpec.scala
@@ -12,7 +12,7 @@ class MultipleFilesWithSameNameWorkflowSpec extends CromwellTestKitWordSpec {
           "two.x.out" -> WomString("first file.txt"),
           "two.y.out" -> WomString("second file.txt")
         ),
-        testActorName = "TestCromwellRootActor-clobber",
+        testActorName = "TestCromwellRootActor-clobber"
       )
     }
   }
diff --git a/server/src/test/scala/cromwell/OptionalParamWorkflowSpec.scala b/server/src/test/scala/cromwell/OptionalParamWorkflowSpec.scala
index 7bee2c4cf7f..9c6081dae6e 100644
--- a/server/src/test/scala/cromwell/OptionalParamWorkflowSpec.scala
+++ b/server/src/test/scala/cromwell/OptionalParamWorkflowSpec.scala
@@ -11,17 +11,17 @@ class OptionalParamWorkflowSpec extends Matchers with AnyWordSpecLike {
   "A workflow with an optional parameter that has a prefix inside the tag" should {
     "not include that prefix if no value is specified" in {
       val wf = s"""
-         |task find {
-         |  String? pattern
-         |  File root
-         |  command {
-         |    find $${root} $${"-name " + pattern}
-         |  }
-         |}
-         |
-         |workflow wf {
-         |  call find
-         |}
+                  |task find {
+                  |  String? pattern
+                  |  File root
+                  |  command {
+                  |    find $${root} $${"-name " + pattern}
+                  |  }
+                  |}
+                  |
+                  |workflow wf {
+                  |  call find
+                  |}
        """.stripMargin
       val ns = WdlNamespace.loadUsingSource(wf, None, None).get
       val findTask = ns.findTask("find") getOrElse {
@@ -34,10 +34,16 @@ class OptionalParamWorkflowSpec extends Matchers with AnyWordSpecLike {
       )
       instantiateWithoutValue.toTry.get.head.commandString shouldEqual "find src"
 
-      val instantiateWithValue = findTask.instantiateCommand(findTask.inputsFromMap(Map(
-        "find.root" -> WomSingleFile("src"),
-        "find.pattern" -> WomString("*.java")
-      )), NoFunctions).getOrElse {fail("Expected instantiation to work")}
+      val instantiateWithValue = findTask
+        .instantiateCommand(findTask.inputsFromMap(
+                              Map(
+                                "find.root" -> WomSingleFile("src"),
+                                "find.pattern" -> WomString("*.java")
+                              )
+                            ),
+                            NoFunctions
+        )
+        .getOrElse(fail("Expected instantiation to work"))
       instantiateWithValue.head.commandString shouldEqual "find src -name *.java"
     }
   }
diff --git a/server/src/test/scala/cromwell/ReferenceConfSpec.scala b/server/src/test/scala/cromwell/ReferenceConfSpec.scala
index 993ba4da0e6..69e3349e4c7 100644
--- a/server/src/test/scala/cromwell/ReferenceConfSpec.scala
+++ b/server/src/test/scala/cromwell/ReferenceConfSpec.scala
@@ -40,12 +40,11 @@ class ReferenceConfSpec extends Suite with AnyFlatSpecLike with Matchers {
 
         val overlappingKeys = fileKeys.intersect(nonFileKeys).toSeq.sorted
         if (overlappingKeys.nonEmpty) {
-          fail(
-            s"""|Key(s) overlapping
-                |=> ${overlappingKeys.mkString("=> ")}
-                |between $fileUrl
-                |    and $nonFileUrl
-                |""".stripMargin)
+          fail(s"""|Key(s) overlapping
+                   |=> ${overlappingKeys.mkString("=> ")}
+                   |between $fileUrl
+                   |    and $nonFileUrl
+                   |""".stripMargin)
         }
       }
     }
diff --git a/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala b/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
index b3f4df64d07..4e67ac984a1 100644
--- a/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
+++ b/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
@@ -1,4 +1,3 @@
-
 package cromwell
 
 import java.time.OffsetDateTime
@@ -27,11 +26,11 @@ import scala.concurrent.{Await, Promise}
 
 object SimpleWorkflowActorSpec {
 
-  case class TestableWorkflowActorAndMetadataPromise
-  (
+  case class TestableWorkflowActorAndMetadataPromise(
     workflowActor: TestFSMRef[WorkflowActorState, WorkflowActorData, WorkflowActor],
     supervisor: TestProbe,
-    promise: Promise[Unit])
+    promise: Promise[Unit]
+  )
 }
 
 class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfter {
@@ -40,7 +39,8 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
   private def buildWorkflowActor(sampleWdl: SampleWdl,
                                  rawInputsOverride: String,
                                  workflowId: WorkflowId,
-                                 matchers: Matcher*): TestableWorkflowActorAndMetadataPromise = {
+                                 matchers: Matcher*
+  ): TestableWorkflowActorAndMetadataPromise = {
     val workflowSources = WorkflowSourceFilesWithoutImports(
       workflowSource = Option(sampleWdl.workflowSource()),
       workflowUrl = None,
@@ -55,34 +55,44 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
     )
 
     val promise = Promise[Unit]()
-    val watchActor = system.actorOf(MetadataWatchActor.props(promise, matchers: _*), s"service-registry-$workflowId-${UUID.randomUUID()}")
+    val watchActor = system.actorOf(MetadataWatchActor.props(promise, matchers: _*),
+                                    s"service-registry-$workflowId-${UUID.randomUUID()}"
+    )
     val supervisor = TestProbe()
     val config = ConfigFactory.load()
     val workflowToStart = WorkflowToStart(workflowId, OffsetDateTime.now(), workflowSources, Submitted, HogGroup("foo"))
-    val callCachingEnabled =false
-    val invalidateBadCacheResults =false
+    val callCachingEnabled = false
+    val invalidateBadCacheResults = false
     val workflowActor = TestFSMRef(
-      factory = new WorkflowActor(workflowToStart, config,
+      factory = new WorkflowActor(
+        workflowToStart,
+        config,
         ioActor = system.actorOf(SimpleIoActor.props),
         callCachingEnabled = callCachingEnabled,
         invalidateBadCacheResults = invalidateBadCacheResults,
         serviceRegistryActor = watchActor,
-        workflowLogCopyRouter = system.actorOf(Props.empty, s"workflow-copy-log-router-$workflowId-${UUID.randomUUID()}"),
+        workflowLogCopyRouter =
+          system.actorOf(Props.empty, s"workflow-copy-log-router-$workflowId-${UUID.randomUUID()}"),
         workflowCallbackActor = None,
         jobStoreActor = system.actorOf(AlwaysHappyJobStoreActor.props),
         subWorkflowStoreActor = system.actorOf(AlwaysHappySubWorkflowStoreActor.props),
         callCacheReadActor = system.actorOf(EmptyCallCacheReadActor.props),
         callCacheWriteActor = system.actorOf(EmptyCallCacheWriteActor.props),
         dockerHashActor = system.actorOf(EmptyDockerHashActor.props),
-        jobRestartCheckTokenDispenserActor = system.actorOf(JobTokenDispenserActor.props(serviceRegistry, Rate(100, 1.second), None, "execution", "Running")),
-        jobExecutionTokenDispenserActor = system.actorOf(JobTokenDispenserActor.props(serviceRegistry, Rate(100, 1.second), None, "execution", "Running")),
+        jobRestartCheckTokenDispenserActor = system.actorOf(
+          JobTokenDispenserActor.props(serviceRegistry, Rate(100, 1.second), None, "execution", "Running")
+        ),
+        jobExecutionTokenDispenserActor = system.actorOf(
+          JobTokenDispenserActor.props(serviceRegistry, Rate(100, 1.second), None, "execution", "Running")
+        ),
         backendSingletonCollection = BackendSingletonCollection(Map("Local" -> None)),
         serverMode = true,
         workflowStoreActor = system.actorOf(Props.empty),
         workflowHeartbeatConfig = WorkflowHeartbeatConfig(config),
         totalJobsByRootWf = new AtomicInteger(),
         fileHashCacheActorProps = None,
-        blacklistCache = None),
+        blacklistCache = None
+      ),
       supervisor = supervisor.ref,
       name = s"workflow-actor-$workflowId"
     )
@@ -96,16 +106,19 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
     workflowId = WorkflowId.randomId()
   }
 
-  def workflowManagerActorAwaitsSingleWorkCompleteMessage(workflowManagerActor: TestProbe, finalState: WorkflowState): Unit = {
-    workflowManagerActor.expectMsgPF(TestExecutionTimeout) {
-      case WorkflowActorWorkComplete(_, _, finalState) => finalState should be(finalState)
+  def workflowManagerActorAwaitsSingleWorkCompleteMessage(workflowManagerActor: TestProbe,
+                                                          finalState: WorkflowState
+  ): Unit = {
+    workflowManagerActor.expectMsgPF(TestExecutionTimeout) { case WorkflowActorWorkComplete(_, _, finalState) =>
+      finalState should be(finalState)
     }
     workflowManagerActor.expectNoMessage(AwaitAlmostNothing)
   }
 
   "A WorkflowActor" should {
     "start, run, succeed and die" in {
-      val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, _) = buildWorkflowActor(SampleWdl.HelloWorld, SampleWdl.HelloWorld.workflowJson, workflowId)
+      val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, _) =
+        buildWorkflowActor(SampleWdl.HelloWorld, SampleWdl.HelloWorld.workflowJson, workflowId)
       val probe = TestProbe()
       probe watch workflowActor
       startingCallsFilter("wf_hello.hello") {
@@ -120,7 +133,8 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
     "fail to construct with missing inputs" in {
       val expectedError = "Required workflow input 'wf_hello.hello.addressee' not specified"
       val failureMatcher = FailureMatcher(expectedError)
-      val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) = buildWorkflowActor(SampleWdl.HelloWorld, "{}", workflowId, failureMatcher)
+      val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) =
+        buildWorkflowActor(SampleWdl.HelloWorld, "{}", workflowId, failureMatcher)
       val probe = TestProbe()
       probe watch workflowActor
       workflowActor ! StartWorkflowCommand
@@ -140,18 +154,20 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
       // TODO WOM: restore offending offensive input name
       val expectedError = "No coercion defined from '3' of type 'spray.json.JsNumber' to 'String'."
       val failureMatcher = FailureMatcher(expectedError)
-      val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) = buildWorkflowActor(SampleWdl.HelloWorld, s""" { "$Addressee" : 3} """,
-        workflowId, failureMatcher)
+      val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) =
+        buildWorkflowActor(SampleWdl.HelloWorld, s""" { "$Addressee" : 3} """, workflowId, failureMatcher)
 
       val probe = TestProbe()
       probe watch workflowActor
       workflowActor ! StartWorkflowCommand
-      try {
+      try
         Await.result(promise.future, TestExecutionTimeout)
-      } catch {
+      catch {
         case _: Throwable =>
           val info = failureMatcher.nearMissInformation
-          fail(s"We didn't see the expected error message $expectedError within $TestExecutionTimeout. ${info.mkString(", ")}")
+          fail(
+            s"We didn't see the expected error message $expectedError within $TestExecutionTimeout. ${info.mkString(", ")}"
+          )
       }
       probe.expectTerminated(workflowActor, AwaitAlmostNothing)
       supervisor.expectMsgPF(AwaitAlmostNothing, "parent should get a failed response") {
@@ -165,9 +181,11 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
     }
 
     "fail when a call fails" in {
-      val expectedError = "Job wf_goodbye.goodbye:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
+      val expectedError =
+        "Job wf_goodbye.goodbye:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
       val failureMatcher = FailureMatcher(expectedError)
-      val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) = buildWorkflowActor(SampleWdl.GoodbyeWorld, SampleWdl.GoodbyeWorld.workflowJson, workflowId, failureMatcher)
+      val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) =
+        buildWorkflowActor(SampleWdl.GoodbyeWorld, SampleWdl.GoodbyeWorld.workflowJson, workflowId, failureMatcher)
       val probe = TestProbe()
       probe watch workflowActor
       startingCallsFilter("wf_goodbye.goodbye") {
@@ -188,18 +206,24 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
     "gracefully handle malformed WDL" in {
       val expectedError = "No input bfile found evaluating inputs for expression bfile"
       val failureMatcher = FailureMatcher(expectedError)
-      val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) = buildWorkflowActor(SampleWdl.CoercionNotDefined, SampleWdl.CoercionNotDefined.workflowJson, workflowId, failureMatcher)
+      val TestableWorkflowActorAndMetadataPromise(workflowActor, supervisor, promise) =
+        buildWorkflowActor(SampleWdl.CoercionNotDefined,
+                           SampleWdl.CoercionNotDefined.workflowJson,
+                           workflowId,
+                           failureMatcher
+        )
       val probe = TestProbe()
       probe watch workflowActor
       workflowActor ! StartWorkflowCommand
-      try {
+      try
         Await.result(promise.future, TestExecutionTimeout)
-      } catch {
+      catch {
         case _: Throwable =>
           val info = failureMatcher.nearMissInformation
           val errorString =
             if (info.nonEmpty) "We had a near miss: " + info.mkString(", ")
-            else s"The expected key was never seen. We saw: [\n  ${failureMatcher.fullEventList.map(e => s"${e.key} -> ${e.value}").mkString("\n  ")}\n]."
+            else
+              s"The expected key was never seen. We saw: [\n  ${failureMatcher.fullEventList.map(e => s"${e.key} -> ${e.value}").mkString("\n  ")}\n]."
           fail(s"We didn't see the expected error message '$expectedError' within $TestExecutionTimeout. $errorString}")
       }
       probe.expectTerminated(workflowActor, AwaitAlmostNothing)
@@ -223,4 +247,3 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
     }
   }
 }
-
diff --git a/server/src/test/scala/cromwell/WorkflowFailSlowSpec.scala b/server/src/test/scala/cromwell/WorkflowFailSlowSpec.scala
index 165a6bcea20..8b173b28979 100644
--- a/server/src/test/scala/cromwell/WorkflowFailSlowSpec.scala
+++ b/server/src/test/scala/cromwell/WorkflowFailSlowSpec.scala
@@ -3,7 +3,6 @@ package cromwell
 import cromwell.core.WorkflowFailed
 import cromwell.util.SampleWdl
 
-
 // TODO: These tests are (and were) somewhat unsatisfactory. They'd be much better if we use TestFSMRefs and TestProbes to simulate job completions against the WorkflowActor and make sure it only completes the workflow at the appropriate time.
 class WorkflowFailSlowSpec extends CromwellTestKitWordSpec {
   val FailFastOptions: String =
@@ -19,7 +18,7 @@ class WorkflowFailSlowSpec extends CromwellTestKitWordSpec {
         sampleWdl = SampleWdl.WorkflowFailSlow,
         workflowOptions = FailFastOptions,
         terminalState = WorkflowFailed,
-        testActorName = "TestCromwellRootActor-not-complete",
+        testActorName = "TestCromwellRootActor-not-complete"
       )
       outputs.size should be(0)
     }
@@ -30,7 +29,7 @@ class WorkflowFailSlowSpec extends CromwellTestKitWordSpec {
       val outputs = runWdl(
         sampleWdl = SampleWdl.WorkflowFailSlow,
         terminalState = WorkflowFailed,
-        testActorName = "TestCromwellRootActor-workflowFailureMode",
+        testActorName = "TestCromwellRootActor-workflowFailureMode"
       )
       outputs.size should be(0)
     }
diff --git a/server/src/test/scala/cromwell/WorkflowOutputsSpec.scala b/server/src/test/scala/cromwell/WorkflowOutputsSpec.scala
index f20b4d29c6c..2c164b51d51 100644
--- a/server/src/test/scala/cromwell/WorkflowOutputsSpec.scala
+++ b/server/src/test/scala/cromwell/WorkflowOutputsSpec.scala
@@ -14,7 +14,7 @@ class WorkflowOutputsSpec extends CromwellTestKitWordSpec {
           "three_step.wc.count" -> AnyValueIsFine
         ),
         allowOtherOutputs = false,
-        testActorName = "TestCromwellRootActor-use-all",
+        testActorName = "TestCromwellRootActor-use-all"
       )
     }
 
@@ -26,7 +26,7 @@ class WorkflowOutputsSpec extends CromwellTestKitWordSpec {
           "three_step.wc.count" -> AnyValueIsFine
         ),
         allowOtherOutputs = false,
-        testActorName = "TestCromwellRootActor-output",
+        testActorName = "TestCromwellRootActor-output"
       )
     }
 
@@ -38,7 +38,7 @@ class WorkflowOutputsSpec extends CromwellTestKitWordSpec {
           "scatter0.inside_scatter.out" -> AnyValueIsFine
         ),
         allowOtherOutputs = false,
-        testActorName = "TestCromwellRootActor-shards",
+        testActorName = "TestCromwellRootActor-shards"
       )
     }
 
@@ -49,7 +49,7 @@ class WorkflowOutputsSpec extends CromwellTestKitWordSpec {
           "scatter0.inside_scatter.out" -> AnyValueIsFine
         ),
         allowOtherOutputs = false,
-        testActorName = "TestCromwellRootActor-wildcards",
+        testActorName = "TestCromwellRootActor-wildcards"
       )
     }
   }
diff --git a/server/src/test/scala/cromwell/engine/WorkflowManagerActorSpec.scala b/server/src/test/scala/cromwell/engine/WorkflowManagerActorSpec.scala
index c1bcaf083b4..07645654b63 100644
--- a/server/src/test/scala/cromwell/engine/WorkflowManagerActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/WorkflowManagerActorSpec.scala
@@ -1,4 +1,3 @@
-
 package cromwell.engine
 
 import akka.actor.ActorSystem
@@ -14,7 +13,7 @@ import scala.concurrent.duration._
 import scala.language.postfixOps
 
 class WorkflowManagerActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorBuilderForSpecs {
-  override implicit val actorSystem: ActorSystem = system
+  implicit override val actorSystem: ActorSystem = system
 
   "A WorkflowManagerActor" should {
 
@@ -80,18 +79,21 @@ class WorkflowManagerActorSpec extends CromwellTestKitWordSpec with WorkflowDesc
           )
       }
 
-      val config = CromwellTestKitSpec.NooPServiceActorConfig.
-        withValue("system.max-concurrent-workflows", ConfigValueFactory.fromAnyRef(2)).
-        withValue("system.new-workflow-poll-rate", ConfigValueFactory.fromAnyRef(1))
+      val config = CromwellTestKitSpec.NooPServiceActorConfig
+        .withValue("system.max-concurrent-workflows", ConfigValueFactory.fromAnyRef(2))
+        .withValue("system.new-workflow-poll-rate", ConfigValueFactory.fromAnyRef(1))
 
       val rootActor = buildCromwellRootActor(config = config, actorName = "TestCromwellRootActor-pickup")
       val serviceRegistryActor = rootActor.underlyingActor.serviceRegistryActor
 
       val firstSources = SubWorkflows(naptime = 60 seconds).asWorkflowSources()
 
-      def waitForState(workflowId: WorkflowId, state: WorkflowState): Unit = {
-        eventually { verifyWorkflowState(serviceRegistryActor, workflowId, state) } (config = defaultPatience, pos = implicitly[org.scalactic.source.Position], retrying = implicitly[Retrying[Unit]])
-      }
+      def waitForState(workflowId: WorkflowId, state: WorkflowState): Unit =
+        eventually(verifyWorkflowState(serviceRegistryActor, workflowId, state))(
+          config = defaultPatience,
+          pos = implicitly[org.scalactic.source.Position],
+          retrying = implicitly[Retrying[Unit]]
+        )
 
       val firstWorkflowId = rootActor.underlyingActor.submitWorkflow(firstSources)
       waitForState(firstWorkflowId, WorkflowRunning)
diff --git a/server/src/test/scala/cromwell/engine/WorkflowStoreActorSpec.scala b/server/src/test/scala/cromwell/engine/WorkflowStoreActorSpec.scala
index d0f39fe8889..e9d5e6f1041 100644
--- a/server/src/test/scala/cromwell/engine/WorkflowStoreActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/WorkflowStoreActorSpec.scala
@@ -7,14 +7,22 @@ import akka.testkit._
 import cats.data.{NonEmptyList, NonEmptyVector}
 import common.assertion.CromwellTimeoutSpec
 import cromwell.core._
-import cromwell.core.abort.{AbortResponse, WorkflowAbortFailureResponse, WorkflowAbortRequestedResponse, WorkflowAbortedResponse}
+import cromwell.core.abort.{
+  AbortResponse,
+  WorkflowAbortedResponse,
+  WorkflowAbortFailureResponse,
+  WorkflowAbortRequestedResponse
+}
 import cromwell.engine.workflow.{CoordinatedWorkflowStoreActorBuilder, SqlWorkflowStoreBuilder}
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowNotFoundException
 import cromwell.engine.workflow.workflowstore.SqlWorkflowStore.WorkflowStoreState
 import cromwell.engine.workflow.workflowstore.WorkflowStoreActor._
 import cromwell.engine.workflow.workflowstore.WorkflowStoreCoordinatedAccessActor.WriteHeartbeats
 import cromwell.engine.workflow.workflowstore.WorkflowStoreEngineActor.{NewWorkflowsToStart, NoNewWorkflowsToStart}
-import cromwell.engine.workflow.workflowstore.WorkflowStoreSubmitActor.{WorkflowSubmittedToStore, WorkflowsBatchSubmittedToStore}
+import cromwell.engine.workflow.workflowstore.WorkflowStoreSubmitActor.{
+  WorkflowsBatchSubmittedToStore,
+  WorkflowSubmittedToStore
+}
 import cromwell.engine.workflow.workflowstore._
 import cromwell.services.metadata.MetadataQuery
 import cromwell.services.metadata.MetadataService.{GetMetadataAction, MetadataLookupResponse}
@@ -31,8 +39,14 @@ import scala.concurrent.Await
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-class WorkflowStoreActorSpec extends CromwellTestKitWordSpec with CoordinatedWorkflowStoreActorBuilder
-  with SqlWorkflowStoreBuilder with Matchers with BeforeAndAfter with Eventually with CromwellTimeoutSpec {
+class WorkflowStoreActorSpec
+    extends CromwellTestKitWordSpec
+    with CoordinatedWorkflowStoreActorBuilder
+    with SqlWorkflowStoreBuilder
+    with Matchers
+    with BeforeAndAfter
+    with Eventually
+    with CromwellTimeoutSpec {
   private val helloWorldSourceFiles = HelloWorld.asWorkflowSources().asInstanceOf[WorkflowSourceFilesWithoutImports]
   private val helloWorldSourceFilesOnHold = HelloWorld.asWorkflowSources(workflowOnHold = true)
   private val helloCwlWorldSourceFiles =
@@ -46,8 +60,7 @@ class WorkflowStoreActorSpec extends CromwellTestKitWordSpec with CoordinatedWor
       val (list, distinct) = knownDistinct
       if (!distinct) {
         (list :+ next, false)
-      }
-      else {
+      } else {
         (list :+ next, !list.map(_.id).contains(next.id))
       }
     }
@@ -89,8 +102,8 @@ class WorkflowStoreActorSpec extends CromwellTestKitWordSpec with CoordinatedWor
         "WorkflowStoreActor-CheckOnHold"
       )
       storeActor ! SubmitWorkflow(helloWorldSourceFilesOnHold)
-      expectMsgPF(10 seconds) {
-        case submit: WorkflowSubmittedToStore => submit.state shouldBe WorkflowOnHold
+      expectMsgPF(10 seconds) { case submit: WorkflowSubmittedToStore =>
+        submit.state shouldBe WorkflowOnHold
       }
     }
 
@@ -107,9 +120,11 @@ class WorkflowStoreActorSpec extends CromwellTestKitWordSpec with CoordinatedWor
         ),
         "WorkflowStoreActor-ReturnIdsForBatch"
       )
-      storeActor ! BatchSubmitWorkflows(NonEmptyList.of(helloWorldSourceFiles, helloWorldSourceFiles, helloWorldSourceFiles))
-      expectMsgPF(10 seconds) {
-        case WorkflowsBatchSubmittedToStore(ids, WorkflowSubmitted) => ids.toList.size shouldBe 3
+      storeActor ! BatchSubmitWorkflows(
+        NonEmptyList.of(helloWorldSourceFiles, helloWorldSourceFiles, helloWorldSourceFiles)
+      )
+      expectMsgPF(10 seconds) { case WorkflowsBatchSubmittedToStore(ids, WorkflowSubmitted) =>
+        ids.toList.size shouldBe 3
       }
     }
 
@@ -126,46 +141,42 @@ class WorkflowStoreActorSpec extends CromwellTestKitWordSpec with CoordinatedWor
         ),
         "WorkflowStoreActor-FetchExactlyN"
       )
-      storeActor ! BatchSubmitWorkflows(NonEmptyList.of(helloWorldSourceFiles, helloWorldSourceFiles, helloCwlWorldSourceFiles))
+      storeActor ! BatchSubmitWorkflows(
+        NonEmptyList.of(helloWorldSourceFiles, helloWorldSourceFiles, helloCwlWorldSourceFiles)
+      )
       val insertedIds = expectMsgType[WorkflowsBatchSubmittedToStore](10 seconds).workflowIds.toList
 
       storeActor ! FetchRunnableWorkflows(2, Set.empty)
-      expectMsgPF(10 seconds) {
-        case NewWorkflowsToStart(workflowNel) =>
-          workflowNel.toList.size shouldBe 2
-          checkDistinctIds(workflowNel.toList) shouldBe true
-          workflowNel map {
-            case WorkflowToStart(id, _, sources, state, _) =>
-              insertedIds.contains(id) shouldBe true
-              sources shouldBe helloWorldSourceFiles
-              state shouldBe Submitted
-          }
+      expectMsgPF(10 seconds) { case NewWorkflowsToStart(workflowNel) =>
+        workflowNel.toList.size shouldBe 2
+        checkDistinctIds(workflowNel.toList) shouldBe true
+        workflowNel map { case WorkflowToStart(id, _, sources, state, _) =>
+          insertedIds.contains(id) shouldBe true
+          sources shouldBe helloWorldSourceFiles
+          state shouldBe Submitted
+        }
       }
 
       storeActor ! FetchRunnableWorkflows(1, Set.empty)
-      expectMsgPF(10 seconds) {
-        case NewWorkflowsToStart(workflowNel) =>
-          workflowNel.toList.size shouldBe 1
-          checkDistinctIds(workflowNel.toList) shouldBe true
-          workflowNel map {
-            case WorkflowToStart(id, _, sources, state, _) =>
-              insertedIds.contains(id) shouldBe true
-              sources shouldBe helloCwlWorldSourceFiles
-              state shouldBe Submitted
-          }
+      expectMsgPF(10 seconds) { case NewWorkflowsToStart(workflowNel) =>
+        workflowNel.toList.size shouldBe 1
+        checkDistinctIds(workflowNel.toList) shouldBe true
+        workflowNel map { case WorkflowToStart(id, _, sources, state, _) =>
+          insertedIds.contains(id) shouldBe true
+          sources shouldBe helloCwlWorldSourceFiles
+          state shouldBe Submitted
+        }
       }
     }
 
     "fetch encrypted and cleared workflow options" in {
       EncryptionSpec.assumeAes256Cbc()
 
-      val optionedSourceFiles = HelloWorld.asWorkflowSources(workflowOptions =
-        s"""|{
-            |  "key": "value",
-            |  "refresh_token": "it's a secret"
-            |}
-            |""".stripMargin)
-
+      val optionedSourceFiles = HelloWorld.asWorkflowSources(workflowOptions = s"""|{
+                                                                                   |  "key": "value",
+                                                                                   |  "refresh_token": "it's a secret"
+                                                                                   |}
+                                                                                   |""".stripMargin)
 
       val store = new InMemoryWorkflowStore
       val storeActor = system.actorOf(
@@ -183,36 +194,35 @@ class WorkflowStoreActorSpec extends CromwellTestKitWordSpec with CoordinatedWor
       val insertedIds = expectMsgType[WorkflowsBatchSubmittedToStore](10 seconds).workflowIds.toList
 
       storeActor ! FetchRunnableWorkflows(1, Set.empty)
-      expectMsgPF(10 seconds) {
-        case NewWorkflowsToStart(workflowNel) =>
-          workflowNel.toList.size should be(1)
-          checkDistinctIds(workflowNel.toList) should be(true)
-          workflowNel.toList.foreach {
-            case WorkflowToStart(id, _, sources, state, _) =>
-              insertedIds.contains(id) should be(true)
-              sources.workflowSource should be(optionedSourceFiles.workflowSource)
-              sources.inputsJson should be(optionedSourceFiles.inputsJson)
-              state should be(Submitted)
-
-              import spray.json._
-
-              // We need to wait for workflow metadata to be flushed before we can successfully query for it
-              eventually(timeout(15.seconds.dilated), interval(500.millis.dilated)) {
-                val actorNameUniquificationString = UUID.randomUUID().toString.take(7)
-                val readMetadataActor = system.actorOf(
-                  ReadDatabaseMetadataWorkerActor.props(metadataReadTimeout = 30 seconds, metadataReadRowNumberSafetyThreshold = 20000),
-                  s"ReadMetadataActor-FetchEncryptedOptions-$actorNameUniquificationString"
-                )
-
-                readMetadataActor ! GetMetadataAction(MetadataQuery.forWorkflow(id))
-                expectMsgPF(10 seconds) {
-                  case MetadataLookupResponse(_, eventList) =>
-                    val optionsEvent = eventList.find(_.key.key == "submittedFiles:options").get
-                    val clearedJsObject = optionsEvent.value.get.value.parseJson.asJsObject
-                    clearedJsObject.fields("key") should be(JsString("value"))
-                }
-              }
+      expectMsgPF(10 seconds) { case NewWorkflowsToStart(workflowNel) =>
+        workflowNel.toList.size should be(1)
+        checkDistinctIds(workflowNel.toList) should be(true)
+        workflowNel.toList.foreach { case WorkflowToStart(id, _, sources, state, _) =>
+          insertedIds.contains(id) should be(true)
+          sources.workflowSource should be(optionedSourceFiles.workflowSource)
+          sources.inputsJson should be(optionedSourceFiles.inputsJson)
+          state should be(Submitted)
+
+          import spray.json._
+
+          // We need to wait for workflow metadata to be flushed before we can successfully query for it
+          eventually(timeout(15.seconds.dilated), interval(500.millis.dilated)) {
+            val actorNameUniquificationString = UUID.randomUUID().toString.take(7)
+            val readMetadataActor = system.actorOf(
+              ReadDatabaseMetadataWorkerActor.props(metadataReadTimeout = 30 seconds,
+                                                    metadataReadRowNumberSafetyThreshold = 20000
+              ),
+              s"ReadMetadataActor-FetchEncryptedOptions-$actorNameUniquificationString"
+            )
+
+            readMetadataActor ! GetMetadataAction(MetadataQuery.forWorkflow(id))
+            expectMsgPF(10 seconds) { case MetadataLookupResponse(_, eventList) =>
+              val optionsEvent = eventList.find(_.key.key == "submittedFiles:options").get
+              val clearedJsObject = optionsEvent.value.get.value.parseJson.asJsObject
+              clearedJsObject.fields("key") should be(JsString("value"))
+            }
           }
+        }
       }
     }
 
@@ -229,20 +239,20 @@ class WorkflowStoreActorSpec extends CromwellTestKitWordSpec with CoordinatedWor
         ),
         "WorkflowStoreActor-ReturnOnlyRemaining"
       )
-      storeActor ! BatchSubmitWorkflows(NonEmptyList.of(helloWorldSourceFiles, helloWorldSourceFiles, helloWorldSourceFiles))
+      storeActor ! BatchSubmitWorkflows(
+        NonEmptyList.of(helloWorldSourceFiles, helloWorldSourceFiles, helloWorldSourceFiles)
+      )
       val insertedIds = expectMsgType[WorkflowsBatchSubmittedToStore](10 seconds).workflowIds.toList
 
       storeActor ! FetchRunnableWorkflows(100, Set.empty)
-      expectMsgPF(10 seconds) {
-        case NewWorkflowsToStart(workflowNel) =>
-          workflowNel.toList.size shouldBe 3
-          checkDistinctIds(workflowNel.toList) shouldBe true
-          workflowNel map {
-            case WorkflowToStart(id, _, sources, state, _) =>
-              insertedIds.contains(id) shouldBe true
-              sources shouldBe helloWorldSourceFiles
-              state shouldBe Submitted
-          }
+      expectMsgPF(10 seconds) { case NewWorkflowsToStart(workflowNel) =>
+        workflowNel.toList.size shouldBe 3
+        checkDistinctIds(workflowNel.toList) shouldBe true
+        workflowNel map { case WorkflowToStart(id, _, sources, state, _) =>
+          insertedIds.contains(id) shouldBe true
+          sources shouldBe helloWorldSourceFiles
+          state shouldBe Submitted
+        }
       }
     }
 
@@ -426,7 +436,8 @@ class WorkflowStoreActorSpec extends CromwellTestKitWordSpec with CoordinatedWor
       abortResponse.asInstanceOf[WorkflowAbortFailureResponse].workflowId should be(notFoundWorkflowId)
       abortResponse.asInstanceOf[WorkflowAbortFailureResponse].failure should be(a[WorkflowNotFoundException])
       abortResponse.asInstanceOf[WorkflowAbortFailureResponse].failure.getMessage should be(
-        s"Couldn't abort 7ff8dff3-bc80-4500-af3b-57dbe7a6ecbb because no workflow with that ID is in progress")
+        s"Couldn't abort 7ff8dff3-bc80-4500-af3b-57dbe7a6ecbb because no workflow with that ID is in progress"
+      )
     }
 
   }
diff --git a/server/src/test/scala/cromwell/engine/workflow/CoordinatedWorkflowStoreActorBuilder.scala b/server/src/test/scala/cromwell/engine/workflow/CoordinatedWorkflowStoreActorBuilder.scala
index 33703ef0ea8..7bce743a166 100644
--- a/server/src/test/scala/cromwell/engine/workflow/CoordinatedWorkflowStoreActorBuilder.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/CoordinatedWorkflowStoreActorBuilder.scala
@@ -1,7 +1,11 @@
 package cromwell.engine.workflow
 
 import akka.testkit.TestKitBase
-import cromwell.engine.workflow.workflowstore.{CoordinatedWorkflowStoreAccess, WorkflowStore, WorkflowStoreCoordinatedAccessActor}
+import cromwell.engine.workflow.workflowstore.{
+  CoordinatedWorkflowStoreAccess,
+  WorkflowStore,
+  WorkflowStoreCoordinatedAccessActor
+}
 
 trait CoordinatedWorkflowStoreActorBuilder { testKit: TestKitBase =>
   def access(coordinatedAccessActorName: String)(store: WorkflowStore): CoordinatedWorkflowStoreAccess = {
diff --git a/server/src/test/scala/cromwell/engine/workflow/SqlWorkflowStoreBuilder.scala b/server/src/test/scala/cromwell/engine/workflow/SqlWorkflowStoreBuilder.scala
index 0b772789da7..59bdae414cc 100644
--- a/server/src/test/scala/cromwell/engine/workflow/SqlWorkflowStoreBuilder.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/SqlWorkflowStoreBuilder.scala
@@ -16,10 +16,11 @@ trait SqlWorkflowStoreBuilder {
 
   def runWithDatabase[T](databaseConfig: Config)(block: SqlWorkflowStore => T): T = {
     val database = new EngineSlickDatabase(databaseConfig).initialized(EngineServicesStore.EngineLiquibaseSettings)
-    val metadataDatabase = new MetadataSlickDatabase(databaseConfig).initialized(MetadataServicesStore.MetadataLiquibaseSettings)
-    try {
+    val metadataDatabase =
+      new MetadataSlickDatabase(databaseConfig).initialized(MetadataServicesStore.MetadataLiquibaseSettings)
+    try
       block(SqlWorkflowStore(database, metadataDatabase))
-    } finally {
+    finally {
       Try(database.close())
       ()
     }
diff --git a/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala b/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
index 6f7c57ae985..9d7eb2ad59b 100644
--- a/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/WorkflowActorSpec.scala
@@ -14,10 +14,24 @@ import cromwell.engine.backend.BackendSingletonCollection
 import cromwell.engine.workflow.WorkflowActor._
 import cromwell.engine.workflow.WorkflowManagerActor.WorkflowActorWorkComplete
 import cromwell.engine.workflow.lifecycle.EngineLifecycleActorAbortCommand
-import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{ExecuteWorkflowCommand, WorkflowExecutionAbortedResponse, WorkflowExecutionFailedResponse, WorkflowExecutionSucceededResponse}
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{
+  ExecuteWorkflowCommand,
+  WorkflowExecutionAbortedResponse,
+  WorkflowExecutionFailedResponse,
+  WorkflowExecutionSucceededResponse
+}
 import cromwell.engine.workflow.lifecycle.finalization.{CopyWorkflowLogsActor, WorkflowCallbackActor}
-import cromwell.engine.workflow.lifecycle.finalization.WorkflowFinalizationActor.{StartFinalizationCommand, WorkflowFinalizationFailedResponse, WorkflowFinalizationSucceededResponse}
-import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{StartInitializationCommand, WorkflowInitializationAbortedResponse, WorkflowInitializationFailedResponse, WorkflowInitializationSucceededResponse}
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowFinalizationActor.{
+  StartFinalizationCommand,
+  WorkflowFinalizationFailedResponse,
+  WorkflowFinalizationSucceededResponse
+}
+import cromwell.engine.workflow.lifecycle.initialization.WorkflowInitializationActor.{
+  StartInitializationCommand,
+  WorkflowInitializationAbortedResponse,
+  WorkflowInitializationFailedResponse,
+  WorkflowInitializationSucceededResponse
+}
 import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.MaterializeWorkflowDescriptorFailureResponse
 import cromwell.engine.workflow.workflowstore.{StartableState, Submitted, WorkflowHeartbeatConfig, WorkflowToStart}
 import cromwell.engine.{EngineFilesystems, EngineWorkflowDescriptor}
@@ -31,13 +45,18 @@ import wom.values.WomString
 import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future}
 
-class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorBuilderForSpecs with BeforeAndAfter with Eventually with StrictLogging {
+class WorkflowActorSpec
+    extends CromwellTestKitWordSpec
+    with WorkflowDescriptorBuilderForSpecs
+    with BeforeAndAfter
+    with Eventually
+    with StrictLogging {
 
   override protected lazy val actorSystemConfig: Config =
     ConfigFactory.parseString("""akka.loggers = ["akka.testkit.TestEventListener"]""")
   // https://doc.akka.io/docs/akka/current/testing.html#expecting-log-messages
 
-  override implicit lazy val actorSystem: ActorSystem = system
+  implicit override lazy val actorSystem: ActorSystem = system
 
   val mockServiceRegistryActor: TestActorRef[Actor] =
     TestActorRef(
@@ -48,7 +67,7 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
           case _ => // No action
         }
       },
-      "mockServiceRegistryActor",
+      "mockServiceRegistryActor"
     )
 
   val mockDir: Path = DefaultPathBuilder.get("/where/to/copy/wf/logs")
@@ -57,7 +76,8 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 
   var currentWorkflowId: WorkflowId = _
   val currentLifecycleActor: TestProbe = TestProbe("currentLifecycleActor")
-  val workflowSources: WorkflowSourceFilesCollection = ThreeStep.asWorkflowSources(workflowOptions = mockWorkflowOptions)
+  val workflowSources: WorkflowSourceFilesCollection =
+    ThreeStep.asWorkflowSources(workflowOptions = mockWorkflowOptions)
   lazy val descriptor: EngineWorkflowDescriptor =
     createMaterializedEngineWorkflowDescriptor(WorkflowId.randomId(), workflowSources = workflowSources)
   val supervisorProbe: TestProbe = TestProbe("supervisorProbe")
@@ -76,8 +96,8 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
     currentWorkflowId = WorkflowId.randomId()
     copyWorkflowLogsProbe = TestProbe(s"copyWorkflowLogsProbe-$currentWorkflowId")
     // Clear the supervisor probe of anything remaining from previous runs:
-    supervisorProbe.receiveWhile(max = 1.second, idle = 1.second) {
-      case _ => println("Ignoring excess message to WMA: ")
+    supervisorProbe.receiveWhile(max = 1.second, idle = 1.second) { case _ =>
+      println("Ignoring excess message to WMA: ")
     }
   }
 
@@ -87,7 +107,8 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
                                   extraPathBuilderFactory: Option[PathBuilderFactory] = None,
                                   workflowCallbackActor: Option[ActorRef] = None,
                                   initializationMaxRetries: Int = 3,
-                                  initializationInterval: FiniteDuration = 10.millis) = {
+                                  initializationInterval: FiniteDuration = 10.millis
+  ) = {
     val actor = TestFSMRef(
       factory = new WorkflowActorWithTestAddons(
         finalizationProbe = finalizationProbe,
@@ -119,10 +140,17 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
         workflowExecutionActorProbe = executionProbe
       ),
       supervisor = supervisorProbe.ref,
-      name = s"workflowActor-$currentWorkflowId",
+      name = s"workflowActor-$currentWorkflowId"
+    )
+    actor.setState(
+      stateName = state,
+      stateData = WorkflowActorData(Option(currentLifecycleActor.ref),
+                                    Option(descriptor),
+                                    AllBackendInitializationData.empty,
+                                    StateCheckpoint(InitializingWorkflowState),
+                                    Submitted
+      )
     )
-    actor.setState(stateName = state, stateData = WorkflowActorData(Option(currentLifecycleActor.ref), Option(descriptor),
-      AllBackendInitializationData.empty, StateCheckpoint(InitializingWorkflowState), Submitted))
     actor
   }
 
@@ -152,7 +180,9 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       finalizationProbe.expectMsg(StartFinalizationCommand)
       actor.stateName should be(FinalizingWorkflowState)
       actor ! WorkflowFinalizationSucceededResponse
-      supervisorProbe.expectMsgPF(TimeoutDuration) { case x: WorkflowFailedResponse => x.workflowId should be(currentWorkflowId) }
+      supervisorProbe.expectMsgPF(TimeoutDuration) { case x: WorkflowFailedResponse =>
+        x.workflowId should be(currentWorkflowId)
+      }
       workflowManagerActorExpectsSingleWorkCompleteNotification(WorkflowFailed)
       deathwatch.expectTerminated(actor)
     }
@@ -179,9 +209,9 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       val actor = createWorkflowActor(InitializingWorkflowState)
       deathwatch watch actor
       actor ! AbortWorkflowCommand
-      eventually { actor.stateName should be(WorkflowAbortingState) }
-      currentLifecycleActor.expectMsgPF(TimeoutDuration) {
-        case EngineLifecycleActorAbortCommand => actor ! WorkflowInitializationAbortedResponse
+      eventually(actor.stateName should be(WorkflowAbortingState))
+      currentLifecycleActor.expectMsgPF(TimeoutDuration) { case EngineLifecycleActorAbortCommand =>
+        actor ! WorkflowInitializationAbortedResponse
       }
       finalizationProbe.expectMsg(StartFinalizationCommand)
       actor.stateName should be(FinalizingWorkflowState)
@@ -201,11 +231,11 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       initializationProbe.expectMsg(StartInitializationCommand)
 
       actor ! AbortWorkflowCommand
-      eventually { actor.stateName should be(WorkflowAbortingState) }
+      eventually(actor.stateName should be(WorkflowAbortingState))
       // Because we failed a few times, the actor test's initial "currentLifecycleActor will have been replaced by this
       // new initializationProbe:
-      initializationProbe.expectMsgPF(TimeoutDuration) {
-        case EngineLifecycleActorAbortCommand => actor ! WorkflowInitializationAbortedResponse
+      initializationProbe.expectMsgPF(TimeoutDuration) { case EngineLifecycleActorAbortCommand =>
+        actor ! WorkflowInitializationAbortedResponse
       }
 
       finalizationProbe.expectMsg(StartFinalizationCommand)
@@ -222,12 +252,12 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 
       // Set the stage with a few unfortunate retries:
       actor ! WorkflowInitializationFailedResponse(Seq(new Exception("Initialization Failed (1)")))
-      eventually { actor.stateData.currentLifecycleStateActor should be(None) }
+      eventually(actor.stateData.currentLifecycleStateActor should be(None))
 
       actor ! AbortWorkflowCommand
       // Because there are no active lifecycle actors, this actor should jump to Finalizing without
       // needing any further input:
-      eventually { actor.stateName should be(FinalizingWorkflowState) }
+      eventually(actor.stateName should be(FinalizingWorkflowState))
 
       // Expect the mailboxes for the initialization actor to be empty (and check "currentLifecycleActor" for good measure)
       currentLifecycleActor.expectNoMessage(10.millis)
@@ -247,7 +277,9 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       finalizationProbe.expectMsg(StartFinalizationCommand)
       actor.stateName should be(FinalizingWorkflowState)
       actor ! WorkflowFinalizationSucceededResponse
-      supervisorProbe.expectMsgPF(TimeoutDuration) { case x: WorkflowFailedResponse => x.workflowId should be(currentWorkflowId) }
+      supervisorProbe.expectMsgPF(TimeoutDuration) { case x: WorkflowFailedResponse =>
+        x.workflowId should be(currentWorkflowId)
+      }
       workflowManagerActorExpectsSingleWorkCompleteNotification(WorkflowFailed)
       deathwatch.expectTerminated(actor)
     }
@@ -256,10 +288,9 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       val actor = createWorkflowActor(ExecutingWorkflowState)
       deathwatch watch actor
       actor ! AbortWorkflowCommand
-      eventually { actor.stateName should be(WorkflowAbortingState) }
-      currentLifecycleActor.expectMsgPF(CromwellTestKitSpec.TimeoutDuration) {
-        case EngineLifecycleActorAbortCommand =>
-          actor ! WorkflowExecutionAbortedResponse(Map.empty)
+      eventually(actor.stateName should be(WorkflowAbortingState))
+      currentLifecycleActor.expectMsgPF(CromwellTestKitSpec.TimeoutDuration) { case EngineLifecycleActorAbortCommand =>
+        actor ! WorkflowExecutionAbortedResponse(Map.empty)
       }
       finalizationProbe.expectMsg(StartFinalizationCommand)
       actor.stateName should be(FinalizingWorkflowState)
@@ -300,7 +331,9 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
       deathwatch watch actor
 
       copyWorkflowLogsProbe.expectNoMessage(AwaitAlmostNothing)
-      actor ! MaterializeWorkflowDescriptorFailureResponse(new Exception("Intentionally failing workflow materialization to test log copying"))
+      actor ! MaterializeWorkflowDescriptorFailureResponse(
+        new Exception("Intentionally failing workflow materialization to test log copying")
+      )
       copyWorkflowLogsProbe.expectMsg(CopyWorkflowLogsActor.Copy(currentWorkflowId, mockDir))
       supervisorProbe.expectMsgPF(TimeoutDuration) { case _: WorkflowFailedResponse => /* success! */ }
       workflowManagerActorExpectsSingleWorkCompleteNotification(WorkflowFailed)
@@ -313,10 +346,9 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 
       workflowActor.children.head ! Kill
 
-      eventually { workflowActor.stateName should be(WorkflowAbortingState) }
-      currentLifecycleActor.expectMsgPF(TimeoutDuration) {
-        case EngineLifecycleActorAbortCommand =>
-          workflowActor ! WorkflowExecutionAbortedResponse(Map.empty)
+      eventually(workflowActor.stateName should be(WorkflowAbortingState))
+      currentLifecycleActor.expectMsgPF(TimeoutDuration) { case EngineLifecycleActorAbortCommand =>
+        workflowActor ! WorkflowExecutionAbortedResponse(Map.empty)
       }
       finalizationProbe.expectMsg(StartFinalizationCommand)
       workflowActor.stateName should be(FinalizingWorkflowState)
@@ -327,22 +359,31 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
     }
 
     "log an error when a path builder factory initialization fails" in {
-      EventFilter.error(start = "Failed to copy workflow log", pattern = ".*Failing as requested.*", occurrences = 1).intercept {
-        val _ = createWorkflowActor(WorkflowSucceededState, Option(new FailingPathBuilderFactory()))
-      }
+      EventFilter
+        .error(start = "Failed to copy workflow log", pattern = ".*Failing as requested.*", occurrences = 1)
+        .intercept {
+          val _ = createWorkflowActor(WorkflowSucceededState, Option(new FailingPathBuilderFactory()))
+        }
     }
 
     "log an error when a path builder factory initialization throws" in {
-      EventFilter.error(start = "Failed to copy workflow log", pattern = ".*Throwing as requested.*", occurrences = 1).intercept {
-        val _ = createWorkflowActor(WorkflowSucceededState, Option(new ThrowingPathBuilderFactory()))
-      }
+      EventFilter
+        .error(start = "Failed to copy workflow log", pattern = ".*Throwing as requested.*", occurrences = 1)
+        .intercept {
+          val _ = createWorkflowActor(WorkflowSucceededState, Option(new ThrowingPathBuilderFactory()))
+        }
     }
 
     "send a workflow callback message" in {
       val actor = createWorkflowActor(ExecutingWorkflowState, workflowCallbackActor = Option(workflowCallbackProbe.ref))
       deathwatch watch actor
       val mockOutputs = WomMocks.mockOutputExpectations(Map("foo" -> WomString("bar")))
-      val msg = WorkflowCallbackActor.PerformCallbackCommand(currentWorkflowId, Some(mockUri), WorkflowSucceeded, mockOutputs, List.empty)
+      val msg = WorkflowCallbackActor.PerformCallbackCommand(currentWorkflowId,
+                                                             Some(mockUri),
+                                                             WorkflowSucceeded,
+                                                             mockOutputs,
+                                                             List.empty
+      )
 
       workflowCallbackProbe.expectNoMessage(AwaitAlmostNothing)
       actor ! WorkflowExecutionSucceededResponse(Map.empty, Set(currentWorkflowId), mockOutputs, Set.empty)
@@ -352,10 +393,16 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
     }
 
     "send a workflow callback message for a failing workflow" in {
-      val actor = createWorkflowActor(FinalizingWorkflowState, workflowCallbackActor = Option(workflowCallbackProbe.ref))
+      val actor =
+        createWorkflowActor(FinalizingWorkflowState, workflowCallbackActor = Option(workflowCallbackProbe.ref))
       deathwatch watch actor
       val errorText = "oh nooo :("
-      val msg = WorkflowCallbackActor.PerformCallbackCommand(currentWorkflowId, Some(mockUri), WorkflowFailed, CallOutputs.empty, List(errorText))
+      val msg = WorkflowCallbackActor.PerformCallbackCommand(currentWorkflowId,
+                                                             Some(mockUri),
+                                                             WorkflowFailed,
+                                                             CallOutputs.empty,
+                                                             List(errorText)
+      )
 
       workflowCallbackProbe.expectNoMessage(AwaitAlmostNothing)
       actor ! WorkflowFinalizationFailedResponse(Seq(new RuntimeException(errorText)))
@@ -366,15 +413,17 @@ class WorkflowActorSpec extends CromwellTestKitWordSpec with WorkflowDescriptorB
 }
 
 class FailingPathBuilderFactory() extends PathBuilderFactory {
-  override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] = {
+  override def withOptions(
+    options: WorkflowOptions
+  )(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] =
     Future(throw new Exception("Failing as requested"))
-  }
 }
 
 class ThrowingPathBuilderFactory() extends PathBuilderFactory {
-  override def withOptions(options: WorkflowOptions)(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] = {
+  override def withOptions(
+    options: WorkflowOptions
+  )(implicit as: ActorSystem, ec: ExecutionContext): Future[PathBuilder] =
     throw new Exception("Throwing as requested")
-  }
 }
 
 class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
@@ -402,36 +451,42 @@ class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
                                   initializationMaxRetries: Int,
                                   initializationInterval: FiniteDuration,
                                   workflowInitializationActorProbe: TestProbe,
-                                  workflowExecutionActorProbe: TestProbe) extends WorkflowActor(
-  workflowToStart = WorkflowToStart(id = workflowId,
-    submissionTime = OffsetDateTime.now,
-    state = startState,
-    sources = workflowSources,
-    hogGroup = HogGroup("foo")),
-  conf = conf,
-  callCachingEnabled = callCachingEnabled,
-  invalidateBadCacheResults = invalidateBadCacheResults,
-  ioActor = ioActor,
-  serviceRegistryActor = serviceRegistryActor,
-  workflowLogCopyRouter = workflowLogCopyRouter,
-  workflowCallbackActor,
-  jobStoreActor = jobStoreActor,
-  subWorkflowStoreActor = subWorkflowStoreActor,
-  callCacheReadActor = callCacheReadActor,
-  callCacheWriteActor = callCacheWriteActor,
-  dockerHashActor = dockerHashActor,
-  jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
-  jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
-  backendSingletonCollection = BackendSingletonCollection(Map.empty),
-  workflowStoreActor = workflowStoreActor,
-  serverMode = true,
-  workflowHeartbeatConfig = workflowHeartbeatConfig,
-  totalJobsByRootWf = totalJobsByRootWf,
-  fileHashCacheActorProps = None,
-  blacklistCache = None) {
-
-  override def createInitializationActor(workflowDescriptor: EngineWorkflowDescriptor, name: String): ActorRef = workflowInitializationActorProbe.ref
-  override def createWorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor, data: WorkflowActorData): ActorRef = workflowExecutionActorProbe.ref
+                                  workflowExecutionActorProbe: TestProbe
+) extends WorkflowActor(
+      workflowToStart = WorkflowToStart(id = workflowId,
+                                        submissionTime = OffsetDateTime.now,
+                                        state = startState,
+                                        sources = workflowSources,
+                                        hogGroup = HogGroup("foo")
+      ),
+      conf = conf,
+      callCachingEnabled = callCachingEnabled,
+      invalidateBadCacheResults = invalidateBadCacheResults,
+      ioActor = ioActor,
+      serviceRegistryActor = serviceRegistryActor,
+      workflowLogCopyRouter = workflowLogCopyRouter,
+      workflowCallbackActor,
+      jobStoreActor = jobStoreActor,
+      subWorkflowStoreActor = subWorkflowStoreActor,
+      callCacheReadActor = callCacheReadActor,
+      callCacheWriteActor = callCacheWriteActor,
+      dockerHashActor = dockerHashActor,
+      jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
+      jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
+      backendSingletonCollection = BackendSingletonCollection(Map.empty),
+      workflowStoreActor = workflowStoreActor,
+      serverMode = true,
+      workflowHeartbeatConfig = workflowHeartbeatConfig,
+      totalJobsByRootWf = totalJobsByRootWf,
+      fileHashCacheActorProps = None,
+      blacklistCache = None
+    ) {
+
+  override def createInitializationActor(workflowDescriptor: EngineWorkflowDescriptor, name: String): ActorRef =
+    workflowInitializationActorProbe.ref
+  override def createWorkflowExecutionActor(workflowDescriptor: EngineWorkflowDescriptor,
+                                            data: WorkflowActorData
+  ): ActorRef = workflowExecutionActorProbe.ref
 
   override val initializationRetryInterval: FiniteDuration = initializationInterval
   override val maxInitializationAttempts: Int = initializationMaxRetries
@@ -443,6 +498,6 @@ class WorkflowActorWithTestAddons(val finalizationProbe: TestProbe,
 
   override def makeFinalizationActor(workflowDescriptor: EngineWorkflowDescriptor,
                                      jobExecutionMap: JobExecutionMap,
-                                     workflowOutputs: CallOutputs,
-                                    ): ActorRef = finalizationProbe.ref
+                                     workflowOutputs: CallOutputs
+  ): ActorRef = finalizationProbe.ref
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/WorkflowDescriptorBuilderForSpecs.scala b/server/src/test/scala/cromwell/engine/workflow/WorkflowDescriptorBuilderForSpecs.scala
index ccec86872c8..86f7d1b0b48 100644
--- a/server/src/test/scala/cromwell/engine/workflow/WorkflowDescriptorBuilderForSpecs.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/WorkflowDescriptorBuilderForSpecs.scala
@@ -6,7 +6,12 @@ import cromwell.CromwellTestKitSpec
 import cromwell.core.{HogGroup, SimpleIoActor, WorkflowId, WorkflowSourceFilesCollection}
 import cromwell.engine.EngineWorkflowDescriptor
 import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor
-import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.{MaterializeWorkflowDescriptorCommand, MaterializeWorkflowDescriptorFailureResponse, MaterializeWorkflowDescriptorSuccessResponse, WorkflowDescriptorMaterializationResult}
+import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.{
+  MaterializeWorkflowDescriptorCommand,
+  MaterializeWorkflowDescriptorFailureResponse,
+  MaterializeWorkflowDescriptorSuccessResponse,
+  WorkflowDescriptorMaterializationResult
+}
 
 import scala.concurrent.Await
 
@@ -16,32 +21,40 @@ trait WorkflowDescriptorBuilderForSpecs {
   implicit val actorSystem: ActorSystem
   lazy val ioActor = actorSystem.actorOf(SimpleIoActor.props)
 
-  def createMaterializedEngineWorkflowDescriptor(id: WorkflowId, workflowSources: WorkflowSourceFilesCollection): EngineWorkflowDescriptor = {
+  def createMaterializedEngineWorkflowDescriptor(id: WorkflowId,
+                                                 workflowSources: WorkflowSourceFilesCollection
+  ): EngineWorkflowDescriptor = {
     import akka.pattern.ask
     implicit val timeout = akka.util.Timeout(awaitTimeout)
     implicit val ec = actorSystem.dispatcher
     val callCachingEnabled = true
     val invalidateBadCacheResults = true
     val serviceRegistryIgnorer = actorSystem.actorOf(Props.empty)
-    val actor = actorSystem.actorOf(MaterializeWorkflowDescriptorActor.props(
-      serviceRegistryIgnorer,
-      id,
-      importLocalFilesystem = false,
-      ioActorProxy = ioActor,
-      hogGroup = HogGroup("testcase")), "MaterializeWorkflowDescriptorActor-" + id.id)
-    val workflowDescriptorFuture = actor.ask(
-      MaterializeWorkflowDescriptorCommand(
-        workflowSources,
-        ConfigFactory.load,
-        callCachingEnabled,
-        invalidateBadCacheResults)
-    ).mapTo[WorkflowDescriptorMaterializationResult]
-
-    Await.result(workflowDescriptorFuture map {
-      case MaterializeWorkflowDescriptorSuccessResponse(workflowDescriptor) => workflowDescriptor
-      case MaterializeWorkflowDescriptorFailureResponse(reason) => throw reason
-    }, awaitTimeout)
+    val actor = actorSystem.actorOf(
+      MaterializeWorkflowDescriptorActor.props(serviceRegistryIgnorer,
+                                               id,
+                                               importLocalFilesystem = false,
+                                               ioActorProxy = ioActor,
+                                               hogGroup = HogGroup("testcase")
+      ),
+      "MaterializeWorkflowDescriptorActor-" + id.id
+    )
+    val workflowDescriptorFuture = actor
+      .ask(
+        MaterializeWorkflowDescriptorCommand(workflowSources,
+                                             ConfigFactory.load,
+                                             callCachingEnabled,
+                                             invalidateBadCacheResults
+        )
+      )
+      .mapTo[WorkflowDescriptorMaterializationResult]
+
+    Await.result(
+      workflowDescriptorFuture map {
+        case MaterializeWorkflowDescriptorSuccessResponse(workflowDescriptor) => workflowDescriptor
+        case MaterializeWorkflowDescriptorFailureResponse(reason) => throw reason
+      },
+      awaitTimeout
+    )
   }
 }
-
-
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala
index fb44db3003c..216afa6ee4f 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala
@@ -9,7 +9,11 @@ import cromwell.core._
 import cromwell.core.labels.Labels
 import cromwell.engine.backend.{BackendConfigurationEntry, CromwellBackends}
 import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor
-import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.{MaterializeWorkflowDescriptorCommand, MaterializeWorkflowDescriptorFailureResponse, MaterializeWorkflowDescriptorSuccessResponse}
+import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.{
+  MaterializeWorkflowDescriptorCommand,
+  MaterializeWorkflowDescriptorFailureResponse,
+  MaterializeWorkflowDescriptorSuccessResponse
+}
 import cromwell.util.SampleWdl.HelloWorld
 import cromwell.{CromwellTestKitSpec, CromwellTestKitWordSpec}
 import org.scalatest.BeforeAndAfter
@@ -23,29 +27,34 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
 
   private val ioActor = system.actorOf(SimpleIoActor.props)
   private val workflowId = WorkflowId.randomId()
-  private val minimumConf = ConfigFactory.parseString(
-    """
-      |backend {
-      |  default = "Local"
-      |}
-      |""".stripMargin
-  ).withFallback(CromwellTestKitSpec.DefaultConfig)
-  private val differentDefaultBackendConf = ConfigFactory.parseString(
-    """
-      |backend {
-      |  default = "DefaultBackend"
-      |  // These providers are empty here because the MaterializeWorkflowDescriptorActor won't introspect them:
-      |  providers {
-      |    DefaultBackend {}
-      |    SpecifiedBackend {}
-      |  }
-      |}
-      |""".stripMargin
-  ).withFallback(CromwellTestKitSpec.DefaultConfig)
+  private val minimumConf = ConfigFactory
+    .parseString(
+      """
+        |backend {
+        |  default = "Local"
+        |}
+        |""".stripMargin
+    )
+    .withFallback(CromwellTestKitSpec.DefaultConfig)
+  private val differentDefaultBackendConf = ConfigFactory
+    .parseString(
+      """
+        |backend {
+        |  default = "DefaultBackend"
+        |  // These providers are empty here because the MaterializeWorkflowDescriptorActor won't introspect them:
+        |  providers {
+        |    DefaultBackend {}
+        |    SpecifiedBackend {}
+        |  }
+        |}
+        |""".stripMargin
+    )
+    .withFallback(CromwellTestKitSpec.DefaultConfig)
   val unstructuredFile = "fubar badness!"
   private val validOptions = WorkflowOptions.fromJsonString(""" { "write_to_cache": true } """).get
-  val validCustomLabelsFile="""{ "label1": "value1", "label2": "value2", "Label1": "valu£1" }"""
-  val badCustomLabelsFile="""{ "key with characters more than 255-at vero eos et accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpas": "value with characters more than 255-at vero eos et accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpa" }"""
+  val validCustomLabelsFile = """{ "label1": "value1", "label2": "value2", "Label1": "valu£1" }"""
+  val badCustomLabelsFile =
+    """{ "key with characters more than 255-at vero eos et accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpas": "value with characters more than 255-at vero eos et accusamus et iusto odio dignissimos ducimus qui blanditiis praesentium voluptatum deleniti atque corrupti quos dolores et quas molestias excepturi sint occaecati cupiditate non provident, similique sunt in culpa" }"""
 
   private val validInputsJson = HelloWorld.rawInputs.toJson.toString()
   private val workflowSourceNoDocker = HelloWorld.workflowSource(""" runtime { } """)
@@ -71,8 +80,7 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
   private val invalidMemoryRetryOptions5 =
     WorkflowOptions.fromJsonString(""" { "memory_retry_multiplier": true } """).get
 
-  before {
-  }
+  before {}
 
   after {
     system.stop(NoBehaviorActor)
@@ -83,7 +91,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
 
   "MaterializeWorkflowDescriptorActor" should {
     "accept valid WDL, inputs and options files" in {
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = Option(workflowSourceNoDocker),
         workflowUrl = None,
@@ -94,9 +109,13 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = validOptions,
         labelsJson = validCustomLabelsFile,
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                minimumConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
@@ -126,9 +145,18 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
     }
 
     "accept valid workflowUrl" in {
-      val workflowUrl = Option("https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl")
+      val workflowUrl = Option(
+        "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"
+      )
       val inputs = Map("my_workflow.i" -> 5)
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = None,
         workflowUrl = workflowUrl,
@@ -139,9 +167,13 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = WorkflowOptions.empty,
         labelsJson = "{}",
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                minimumConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
@@ -181,11 +213,20 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
       val placeholdingActorFactoryClass = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
       val fauxBackendEntries = List(
         BackendConfigurationEntry("SpecifiedBackend", placeholdingActorFactoryClass, ConfigFactory.parseString("")),
-        BackendConfigurationEntry("DefaultBackend", placeholdingActorFactoryClass, ConfigFactory.parseString("")))
+        BackendConfigurationEntry("DefaultBackend", placeholdingActorFactoryClass, ConfigFactory.parseString(""))
+      )
       val cromwellBackends = CromwellBackends(fauxBackendEntries)
 
       // Run the test:
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, cromwellBackends, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 cromwellBackends,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = Option(wdl),
         workflowUrl = None,
@@ -196,9 +237,13 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = WorkflowOptions.empty,
         labelsJson = validCustomLabelsFile,
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, differentDefaultBackendConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                differentDefaultBackendConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
@@ -210,7 +255,8 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
                 wfDesc.backendAssignments(call) shouldBe "DefaultBackend"
               case call => fail(s"Unexpected task: ${call.callable.name}")
             }
-          case MaterializeWorkflowDescriptorFailureResponse(reason) => fail(s"Materialization unexpectedly failed ($reason)")
+          case MaterializeWorkflowDescriptorFailureResponse(reason) =>
+            fail(s"Materialization unexpectedly failed ($reason)")
           case unknown =>
             fail(s"Unexpected materialization response: $unknown")
         }
@@ -231,7 +277,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
           |}
         """.stripMargin
 
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = Option(wdl),
         workflowUrl = None,
@@ -242,16 +295,25 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = WorkflowOptions.empty,
         labelsJson = "{}",
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, differentDefaultBackendConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                differentDefaultBackendConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
-            if (!reason.getMessage.contains("Backend for call foo.a ('NoSuchBackend') not registered in configuration file"))
+            if (
+              !reason.getMessage.contains(
+                "Backend for call foo.a ('NoSuchBackend') not registered in configuration file"
+              )
+            )
               fail(s"Unexpected failure message from MaterializeWorkflowDescriptorActor: ${reason.getMessage}")
-          case _: MaterializeWorkflowDescriptorSuccessResponse => fail("This materialization should not have succeeded!")
+          case _: MaterializeWorkflowDescriptorSuccessResponse =>
+            fail("This materialization should not have succeeded!")
           case unknown =>
             fail(s"Unexpected materialization response: $unknown")
         }
@@ -261,7 +323,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
     }
 
     "reject an invalid WDL source" in {
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = Option(unstructuredFile),
         workflowUrl = None,
@@ -272,15 +341,22 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = validOptions,
         labelsJson = validCustomLabelsFile,
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                minimumConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
-            reason.getMessage should startWith("Workflow input processing failed:\nERROR: Finished parsing without consuming all tokens.")
-          case _: MaterializeWorkflowDescriptorSuccessResponse => fail("This materialization should not have succeeded!")
+            reason.getMessage should startWith(
+              "Workflow input processing failed:\nERROR: Finished parsing without consuming all tokens."
+            )
+          case _: MaterializeWorkflowDescriptorSuccessResponse =>
+            fail("This materialization should not have succeeded!")
           case unknown =>
             fail(s"Unexpected materialization response: $unknown")
         }
@@ -292,7 +368,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
     "reject workflow with invalid URL" in {
       val workflowUrl = Option("https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow")
       val inputs = Map("my_workflow.i" -> 5)
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = None,
         workflowUrl = workflowUrl,
@@ -303,18 +386,23 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = WorkflowOptions.empty,
         labelsJson = "{}",
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                minimumConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
             reason.getMessage should startWith(
               """Workflow input processing failed:
-                |Failed to resolve 'https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Failed to download https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow (reason 1 of 1): 404: Not Found"""
-                .stripMargin)
-          case _: MaterializeWorkflowDescriptorSuccessResponse => fail("This materialization should not have succeeded!")
+                |Failed to resolve 'https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Failed to download https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow (reason 1 of 1): 404: Not Found""".stripMargin
+            )
+          case _: MaterializeWorkflowDescriptorSuccessResponse =>
+            fail("This materialization should not have succeeded!")
           case unknown =>
             fail(s"Unexpected materialization response: $unknown")
         }
@@ -330,7 +418,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
           |
           |# no workflow foo { ... } block!!
         """.stripMargin
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = Option(noWorkflowWdl),
         workflowUrl = None,
@@ -341,15 +436,22 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = validOptions,
         labelsJson = validCustomLabelsFile,
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                minimumConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
-            reason.getMessage should startWith("Workflow input processing failed:\nNamespace does not have a local workflow to run")
-          case _: MaterializeWorkflowDescriptorSuccessResponse => fail("This materialization should not have succeeded!")
+            reason.getMessage should startWith(
+              "Workflow input processing failed:\nNamespace does not have a local workflow to run"
+            )
+          case _: MaterializeWorkflowDescriptorSuccessResponse =>
+            fail("This materialization should not have succeeded!")
           case unknown =>
             fail(s"Unexpected materialization response: $unknown")
         }
@@ -359,7 +461,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
     }
 
     "reject an invalid workflow inputs file" in {
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = Option(workflowSourceNoDocker),
         workflowUrl = None,
@@ -370,15 +479,20 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = validOptions,
         labelsJson = validCustomLabelsFile,
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                minimumConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
             reason.getMessage should startWith("Workflow input processing failed:\n")
-          case _: MaterializeWorkflowDescriptorSuccessResponse => fail("This materialization should not have succeeded!")
+          case _: MaterializeWorkflowDescriptorSuccessResponse =>
+            fail("This materialization should not have succeeded!")
           case unknown =>
             fail(s"Unexpected materialization response: $unknown")
         }
@@ -388,7 +502,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
     }
 
     "reject requests if any required inputs are missing" in {
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val noInputsJson = "{}"
       val badOptionsSources = WorkflowSourceFilesWithoutImports(
         workflowSource = Option(workflowSourceNoDocker),
@@ -400,15 +521,22 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = validOptions,
         labelsJson = validCustomLabelsFile,
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(badOptionsSources, minimumConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(badOptionsSources,
+                                                                minimumConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
-            reason.getMessage should startWith("Workflow input processing failed:\nRequired workflow input 'wf_hello.hello.addressee' not specified")
-          case _: MaterializeWorkflowDescriptorSuccessResponse => fail("This materialization should not have succeeded!")
+            reason.getMessage should startWith(
+              "Workflow input processing failed:\nRequired workflow input 'wf_hello.hello.addressee' not specified"
+            )
+          case _: MaterializeWorkflowDescriptorSuccessResponse =>
+            fail("This materialization should not have succeeded!")
           case unknown =>
             fail(s"Unexpected materialization response: $unknown")
         }
@@ -426,7 +554,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
           |  call bar
           |}
         """.stripMargin
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = Option(wdl),
         workflowUrl = None,
@@ -437,15 +572,22 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = validOptions,
         labelsJson = validCustomLabelsFile,
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                minimumConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
-            reason.getMessage should startWith("Workflow input processing failed:\nERROR: Value 'j' is declared as a 'Int' but the expression evaluates to 'String'")
-          case _: MaterializeWorkflowDescriptorSuccessResponse => fail("This materialization should not have succeeded!")
+            reason.getMessage should startWith(
+              "Workflow input processing failed:\nERROR: Value 'j' is declared as a 'Int' but the expression evaluates to 'String'"
+            )
+          case _: MaterializeWorkflowDescriptorSuccessResponse =>
+            fail("This materialization should not have succeeded!")
           case unknown => fail(s"Unexpected materialization response: $unknown")
         }
       }
@@ -472,7 +614,14 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         "foo.bad_two" -> "\"gs://another/bad/gcs/path.txt",
         "foo.bad_three" -> ""
       ).toJson.toString
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = Option(wdl),
         workflowUrl = None,
@@ -483,18 +632,27 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = validOptions,
         labelsJson = validCustomLabelsFile,
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                minimumConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
             reason.getMessage should startWith("Workflow input processing failed:\n")
-            reason.getMessage should include("Invalid value for File input 'foo.bad_one': \"gs://this/is/a/bad/gcs/path.txt starts with a '\"'")
-            reason.getMessage should include("Invalid value for File input 'foo.bad_two': \"gs://another/bad/gcs/path.txt starts with a '\"'")
+            reason.getMessage should include(
+              "Invalid value for File input 'foo.bad_one': \"gs://this/is/a/bad/gcs/path.txt starts with a '\"'"
+            )
+            reason.getMessage should include(
+              "Invalid value for File input 'foo.bad_two': \"gs://another/bad/gcs/path.txt starts with a '\"'"
+            )
             reason.getMessage should include("Invalid value for File input 'foo.bad_three': empty value")
-          case _: MaterializeWorkflowDescriptorSuccessResponse => fail("This materialization should not have succeeded!")
+          case _: MaterializeWorkflowDescriptorSuccessResponse =>
+            fail("This materialization should not have succeeded!")
           case unknown => fail(s"Unexpected materialization response: $unknown")
         }
       }
@@ -514,23 +672,36 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
     "reject invalid memory_retry_multiplier" in {
       List(invalidMemoryRetryOptions1, invalidMemoryRetryOptions2, invalidMemoryRetryOptions3) map { options =>
         MaterializeWorkflowDescriptorActor.validateMemoryRetryMultiplier(options) match {
-          case Invalid(errorsList) => errorsList.head should be("Workflow option 'memory_retry_multiplier' is invalid. " +
-            "It should be in the range 1.0 ≤ n ≤ 99.0")
+          case Invalid(errorsList) =>
+            errorsList.head should be(
+              "Workflow option 'memory_retry_multiplier' is invalid. " +
+                "It should be in the range 1.0 ≤ n ≤ 99.0"
+            )
           case Valid(_) => fail(s"memory_retry_multiplier validation for $options succeeded but should have failed!")
         }
       }
 
       List(invalidMemoryRetryOptions4, invalidMemoryRetryOptions5) map { options =>
         MaterializeWorkflowDescriptorActor.validateMemoryRetryMultiplier(options) match {
-          case Invalid(errorsList) => errorsList.head should startWith(s"Workflow option 'memory_retry_multiplier' is invalid. " +
-            "It should be of type Double and in the range 1.0 ≤ n ≤ 99.0. Error: NumberFormatException:")
+          case Invalid(errorsList) =>
+            errorsList.head should startWith(
+              s"Workflow option 'memory_retry_multiplier' is invalid. " +
+                "It should be of type Double and in the range 1.0 ≤ n ≤ 99.0. Error: NumberFormatException:"
+            )
           case Valid(_) => fail(s"memory_retry_multiplier validation for $options succeeded but should have failed!")
         }
       }
     }
 
     "fail materialization if memory_retry_multiplier is invalid" in {
-      val materializeWfActor = system.actorOf(MaterializeWorkflowDescriptorActor.props(NoBehaviorActor, workflowId, importLocalFilesystem = false, ioActorProxy = ioActor, hogGroup = fooHogGroup))
+      val materializeWfActor = system.actorOf(
+        MaterializeWorkflowDescriptorActor.props(NoBehaviorActor,
+                                                 workflowId,
+                                                 importLocalFilesystem = false,
+                                                 ioActorProxy = ioActor,
+                                                 hogGroup = fooHogGroup
+        )
+      )
       val sources = WorkflowSourceFilesWithoutImports(
         workflowSource = Option(workflowSourceNoDocker),
         workflowUrl = None,
@@ -541,16 +712,23 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
         workflowOptions = invalidMemoryRetryOptions1,
         labelsJson = validCustomLabelsFile,
         warnings = Vector.empty,
-        requestedWorkflowId = None)
-      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources, minimumConf, callCachingEnabled,
-        invalidateBadCacheResults)
+        requestedWorkflowId = None
+      )
+      materializeWfActor ! MaterializeWorkflowDescriptorCommand(sources,
+                                                                minimumConf,
+                                                                callCachingEnabled,
+                                                                invalidateBadCacheResults
+      )
 
       within(Timeout) {
         expectMsgPF() {
           case MaterializeWorkflowDescriptorFailureResponse(reason) =>
             reason.getMessage should startWith("Workflow input processing failed:\n")
-            reason.getMessage should include("Workflow option 'memory_retry_multiplier' is invalid. It should be in the range 1.0 ≤ n ≤ 99.0")
-          case _: MaterializeWorkflowDescriptorSuccessResponse => fail("This materialization should not have succeeded!")
+            reason.getMessage should include(
+              "Workflow option 'memory_retry_multiplier' is invalid. It should be in the range 1.0 ≤ n ≤ 99.0"
+            )
+          case _: MaterializeWorkflowDescriptorSuccessResponse =>
+            fail("This materialization should not have succeeded!")
           case unknown => fail(s"Unexpected materialization response: $unknown")
         }
       }
@@ -559,4 +737,3 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
     }
   }
 }
-
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorSpec.scala
index 5edba1ff413..06ad805e6f6 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/WorkflowExecutionActorSpec.scala
@@ -10,7 +10,10 @@ import cromwell.backend.AllBackendInitializationData
 import cromwell.core.{SimpleIoActor, WorkflowId}
 import cromwell.engine.backend.{BackendConfigurationEntry, BackendSingletonCollection, CromwellBackends}
 import cromwell.engine.workflow.WorkflowDescriptorBuilderForSpecs
-import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{ExecuteWorkflowCommand, WorkflowExecutionFailedResponse}
+import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.{
+  ExecuteWorkflowCommand,
+  WorkflowExecutionFailedResponse
+}
 import cromwell.engine.workflow.tokens.DynamicRateLimiter.Rate
 import cromwell.engine.workflow.tokens.JobTokenDispenserActor
 import cromwell.engine.workflow.workflowstore.Submitted
@@ -24,14 +27,18 @@ import org.scalatest.matchers.should.Matchers
 import scala.concurrent.duration._
 import scala.concurrent.{Await, Promise}
 
-class WorkflowExecutionActorSpec extends CromwellTestKitSpec with AnyFlatSpecLike with Matchers with BeforeAndAfter with WorkflowDescriptorBuilderForSpecs {
+class WorkflowExecutionActorSpec
+    extends CromwellTestKitSpec
+    with AnyFlatSpecLike
+    with Matchers
+    with BeforeAndAfter
+    with WorkflowDescriptorBuilderForSpecs {
 
-  override implicit val actorSystem = system
+  implicit override val actorSystem = system
   implicit val DefaultDuration = 60.seconds.dilated
 
   def mockServiceRegistryActor = TestActorRef(new Actor {
-    override def receive = {
-      case _ => // No action
+    override def receive = { case _ => // No action
     }
   })
 
@@ -57,17 +64,33 @@ class WorkflowExecutionActorSpec extends CromwellTestKitSpec with AnyFlatSpecLik
     import MetadataWatchActor.metadataKeyAttemptChecker
     val metadataSuccessPromise = Promise[Unit]()
     val requiredMetadataMatchers: Seq[MetadataWatchActor.Matcher] = List(
-      MetadataWatchActor.JobKeyMetadataKeyAndValueContainStringMatcher(metadataKeyAttemptChecker(1), "executionStatus", "RetryableFailure"),
-      MetadataWatchActor.JobKeyMetadataKeyAndValueContainStringMatcher(metadataKeyAttemptChecker(2), "executionStatus", "RetryableFailure"),
-      MetadataWatchActor.JobKeyMetadataKeyAndValueContainStringMatcher(metadataKeyAttemptChecker(3), "executionStatus", "Failed")
+      MetadataWatchActor.JobKeyMetadataKeyAndValueContainStringMatcher(metadataKeyAttemptChecker(1),
+                                                                       "executionStatus",
+                                                                       "RetryableFailure"
+      ),
+      MetadataWatchActor.JobKeyMetadataKeyAndValueContainStringMatcher(metadataKeyAttemptChecker(2),
+                                                                       "executionStatus",
+                                                                       "RetryableFailure"
+      ),
+      MetadataWatchActor.JobKeyMetadataKeyAndValueContainStringMatcher(metadataKeyAttemptChecker(3),
+                                                                       "executionStatus",
+                                                                       "Failed"
+      )
+    )
+    val metadataWatcherActor =
+      TestActorRef[MetadataWatchActor](Props(MetadataWatchActor(metadataSuccessPromise, requiredMetadataMatchers: _*)))
+    val serviceRegistryActor = system.actorOf(
+      ServiceRegistryActor.props(ConfigFactory.load(),
+                                 overrides = Map(MetadataService.MetadataServiceName -> metadataWatcherActor.props)
+      )
     )
-    val metadataWatcherActor = TestActorRef[MetadataWatchActor](Props(MetadataWatchActor(metadataSuccessPromise, requiredMetadataMatchers: _*)))
-    val serviceRegistryActor = system.actorOf(ServiceRegistryActor.props(ConfigFactory.load(), overrides = Map(MetadataService.MetadataServiceName -> metadataWatcherActor.props)))
     val jobStoreActor = system.actorOf(AlwaysHappyJobStoreActor.props)
     val ioActor = system.actorOf(SimpleIoActor.props)
     val subWorkflowStoreActor = system.actorOf(AlwaysHappySubWorkflowStoreActor.props)
-    val jobRestartCheckTokenDispenserActor = system.actorOf(JobTokenDispenserActor.props(serviceRegistry, Rate(100, 1.second), None, "execution", "Running"))
-    val jobExecutionTokenDispenserActor = system.actorOf(JobTokenDispenserActor.props(serviceRegistry, Rate(100, 1.second), None, "execution", "Running"))
+    val jobRestartCheckTokenDispenserActor =
+      system.actorOf(JobTokenDispenserActor.props(serviceRegistry, Rate(100, 1.second), None, "execution", "Running"))
+    val jobExecutionTokenDispenserActor =
+      system.actorOf(JobTokenDispenserActor.props(serviceRegistry, Rate(100, 1.second), None, "execution", "Running"))
     val MockBackendConfigEntry = BackendConfigurationEntry(
       name = "Mock",
       lifecycleActorFactoryClass = "cromwell.engine.backend.mock.RetryableBackendLifecycleActorFactory",
@@ -76,18 +99,38 @@ class WorkflowExecutionActorSpec extends CromwellTestKitSpec with AnyFlatSpecLik
     CromwellBackends.initBackends(List(MockBackendConfigEntry))
 
     val workflowId = WorkflowId.randomId()
-    val engineWorkflowDescriptor = createMaterializedEngineWorkflowDescriptor(workflowId, SampleWdl.HelloWorld.asWorkflowSources(runtime = runtimeSection))
+    val engineWorkflowDescriptor =
+      createMaterializedEngineWorkflowDescriptor(workflowId,
+                                                 SampleWdl.HelloWorld.asWorkflowSources(runtime = runtimeSection)
+      )
     val callCacheReadActor = TestProbe()
     val callCacheWriteActor = TestProbe()
     val dockerHashActor = TestProbe()
 
     val weaSupervisor = TestProbe()
     val workflowExecutionActor = TestActorRef(
-      props = WorkflowExecutionActor.props(engineWorkflowDescriptor, ioActor, serviceRegistryActor, jobStoreActor, subWorkflowStoreActor,
-        callCacheReadActor.ref, callCacheWriteActor.ref, dockerHashActor.ref, jobRestartCheckTokenDispenserActor, jobExecutionTokenDispenserActor, MockBackendSingletonCollection,
-        AllBackendInitializationData.empty, startState = Submitted, rootConfig, new AtomicInteger(), fileHashCacheActor = None, blacklistCache = None),
+      props = WorkflowExecutionActor.props(
+        engineWorkflowDescriptor,
+        ioActor,
+        serviceRegistryActor,
+        jobStoreActor,
+        subWorkflowStoreActor,
+        callCacheReadActor.ref,
+        callCacheWriteActor.ref,
+        dockerHashActor.ref,
+        jobRestartCheckTokenDispenserActor,
+        jobExecutionTokenDispenserActor,
+        MockBackendSingletonCollection,
+        AllBackendInitializationData.empty,
+        startState = Submitted,
+        rootConfig,
+        new AtomicInteger(),
+        fileHashCacheActor = None,
+        blacklistCache = None
+      ),
       name = "WorkflowExecutionActor",
-      supervisor = weaSupervisor.ref)
+      supervisor = weaSupervisor.ref
+    )
 
     EventFilter.info(pattern = "Starting wf_hello.hello", occurrences = 3).intercept {
       workflowExecutionActor ! ExecuteWorkflowCommand
@@ -96,10 +139,12 @@ class WorkflowExecutionActorSpec extends CromwellTestKitSpec with AnyFlatSpecLik
     weaSupervisor.expectMsgClass(classOf[WorkflowExecutionFailedResponse])
 
     // Super-helpful debug in case the metadata watcher is still unhappy:
-    if(metadataWatcherActor.underlyingActor.unsatisfiedMatchers.nonEmpty) {
+    if (metadataWatcherActor.underlyingActor.unsatisfiedMatchers.nonEmpty) {
       requiredMetadataMatchers foreach { matcher =>
         matcher.nearMissInformation.foreach { info =>
-          System.out.println("A matcher had a near miss (it might still get a matching value later!): " + info.replace("\n", "..."))
+          System.out.println(
+            "A matcher had a near miss (it might still get a matching value later!): " + info.replace("\n", "...")
+          )
         }
       }
     }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaBackendIsCopyingCachedOutputsSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaBackendIsCopyingCachedOutputsSpec.scala
index 8171eefeb34..e05d5958c1a 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaBackendIsCopyingCachedOutputsSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaBackendIsCopyingCachedOutputsSpec.scala
@@ -4,7 +4,12 @@ import cats.data.NonEmptyList
 import cromwell.core.callcaching._
 import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor._
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadingJobActor.NextHit
-import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.{CacheHit, CallCacheHashes, EJHAResponse, HashError}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.{
+  CacheHit,
+  CallCacheHashes,
+  EJHAResponse,
+  HashError
+}
 import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec._
 import cromwell.engine.workflow.lifecycle.execution.ejea.HasJobSuccessResponse.SuccessfulCallCacheHashes
 import cromwell.services.CallCaching.CallCachingEntryId
@@ -15,9 +20,16 @@ import scala.concurrent.duration._
 import scala.util.control.NoStackTrace
 import scala.util.{Failure, Success, Try}
 
-class EjeaBackendIsCopyingCachedOutputsSpec extends EngineJobExecutionActorSpec with HasJobSuccessResponse with HasCopyFailureResponses with HasJobFailureResponses with CanExpectJobStoreWrites with CanExpectCacheWrites with CanExpectCacheInvalidation {
+class EjeaBackendIsCopyingCachedOutputsSpec
+    extends EngineJobExecutionActorSpec
+    with HasJobSuccessResponse
+    with HasCopyFailureResponses
+    with HasJobFailureResponses
+    with CanExpectJobStoreWrites
+    with CanExpectCacheWrites
+    with CanExpectCacheInvalidation {
 
-  override implicit val stateUnderTest = BackendIsCopyingCachedOutputs
+  implicit override val stateUnderTest = BackendIsCopyingCachedOutputs
 
   "An EJEA in BackendIsCopyingCachedOutputs state" should {
 
@@ -32,179 +44,231 @@ class EjeaBackendIsCopyingCachedOutputsSpec extends EngineJobExecutionActorSpec
                                                          initialHashData: Option[Try[CallCacheHashes]],
                                                          ejhaResponse: Option[EJHAResponse],
                                                          expectedFinalHashData: Option[Try[CallCacheHashes]],
-                                                         validForMode: CallCachingMode => Boolean) {
-      def hashingCompletedSuccessfully = ejhaResponse == hashResultsEjhaResponse || initialHashData == hashResultsDataValue
+                                                         validForMode: CallCachingMode => Boolean
+    ) {
+      def hashingCompletedSuccessfully =
+        ejhaResponse == hashResultsEjhaResponse || initialHashData == hashResultsDataValue
     }
 
     val initialHashDataAndEjhaResponseCombinations = List(
       // The mode will NEVER have "writeToCache" in these scenarios:
       InitialHashDataAndEjhaResponseCombination("no hashes (ever)", None, None, None, mode => !mode.writeToCache),
-      InitialHashDataAndEjhaResponseCombination("unsuccessful hashes in initial data", hashErrorDataValue, None, hashErrorDataValue, mode => !mode.writeToCache),
+      InitialHashDataAndEjhaResponseCombination("unsuccessful hashes in initial data",
+                                                hashErrorDataValue,
+                                                None,
+                                                hashErrorDataValue,
+                                                mode => !mode.writeToCache
+      ),
       // The mode will ALWAYS have "writeToCache" in these scenarios:
-      InitialHashDataAndEjhaResponseCombination("unsuccessful hashes from EJHA", None, hashErrorEjhaResponse, hashErrorDataValue, mode => mode.writeToCache),
-      InitialHashDataAndEjhaResponseCombination("successful hashes from EJHA", None, hashResultsEjhaResponse, hashResultsDataValue, mode => mode.writeToCache),
-      InitialHashDataAndEjhaResponseCombination("successful hashes in initial data", hashResultsDataValue, None, hashResultsDataValue, mode => mode.writeToCache)
+      InitialHashDataAndEjhaResponseCombination("unsuccessful hashes from EJHA",
+                                                None,
+                                                hashErrorEjhaResponse,
+                                                hashErrorDataValue,
+                                                mode => mode.writeToCache
+      ),
+      InitialHashDataAndEjhaResponseCombination("successful hashes from EJHA",
+                                                None,
+                                                hashResultsEjhaResponse,
+                                                hashResultsDataValue,
+                                                mode => mode.writeToCache
+      ),
+      InitialHashDataAndEjhaResponseCombination("successful hashes in initial data",
+                                                hashResultsDataValue,
+                                                None,
+                                                hashResultsDataValue,
+                                                mode => mode.writeToCache
+      )
     )
 
     CallCachingModes.filter(_.readFromCache) foreach { mode =>
-      initialHashDataAndEjhaResponseCombinations filter { _.validForMode(mode) } foreach { case combo @ InitialHashDataAndEjhaResponseCombination(hashComboName, initialHashData, ejhaResponse, finalHashData, _) =>
-
-        val cacheUpdateRequired = combo.hashingCompletedSuccessfully && mode.writeToCache
-        val nextStepName = if (cacheUpdateRequired) "Update call cache" else "Update job store"
-        s"$nextStepName when call caching is $mode, the EJEA has $hashComboName and then gets a success result" in {
-          ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, mode)
-          // Send the response from the EJHA (if there was one!):
-          ejhaResponse foreach { ejea ! _ }
-
-          // Nothing should happen here:
-          helper.jobStoreProbe.expectNoMessage(awaitAlmostNothing)
-
-          // Send the response from the copying actor
-          ejea ! successResponse
-
-          if (cacheUpdateRequired) {
-            expectCacheWrite(successResponse, finalHashData.get.get)
-          } else {
-            expectJobStoreWrite(SucceededResponseData(successResponse, finalHashData))
-          }
-          // A separate check of the final effective call caching mode:
-          if (ejhaResponse == hashErrorEjhaResponse || initialHashData == hashErrorDataValue) {
-            ejea.underlyingActor.checkEffectiveCallCachingMode should be(mode.withoutWrite)
-          } else {
-            ejea.underlyingActor.checkEffectiveCallCachingMode should be(mode)
-          }
-        }
-
-        s"$nextStepName when it gets a success result and it then gets $hashComboName, if call caching is $mode" in {
-          ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, mode)
-          // Send the response from the copying actor
-          ejea ! successResponse
+      initialHashDataAndEjhaResponseCombinations filter { _.validForMode(mode) } foreach {
+        case combo @ InitialHashDataAndEjhaResponseCombination(hashComboName,
+                                                               initialHashData,
+                                                               ejhaResponse,
+                                                               finalHashData,
+                                                               _
+            ) =>
+          val cacheUpdateRequired = combo.hashingCompletedSuccessfully && mode.writeToCache
+          val nextStepName = if (cacheUpdateRequired) "Update call cache" else "Update job store"
+          s"$nextStepName when call caching is $mode, the EJEA has $hashComboName and then gets a success result" in {
+            ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, mode)
+            // Send the response from the EJHA (if there was one!):
+            ejhaResponse foreach { ejea ! _ }
 
-          ejhaResponse foreach { resp =>
-            // Nothing should have happened yet:
+            // Nothing should happen here:
             helper.jobStoreProbe.expectNoMessage(awaitAlmostNothing)
 
-            // Ok, now send the response from the EJHA (if there was one!):
-            ejea ! resp
-          }
+            // Send the response from the copying actor
+            ejea ! successResponse
 
-          if (cacheUpdateRequired) {
-            expectCacheWrite(successResponse, finalHashData.get.get)
-          } else {
-            expectJobStoreWrite(SucceededResponseData(successResponse, finalHashData))
-          }
-          // A separate check of the final effective call caching mode:
-          if (ejhaResponse == hashErrorEjhaResponse || initialHashData == hashErrorDataValue) {
-            ejea.underlyingActor.checkEffectiveCallCachingMode should be(mode.withoutWrite)
-          } else {
-            ejea.underlyingActor.checkEffectiveCallCachingMode should be(mode)
+            if (cacheUpdateRequired) {
+              expectCacheWrite(successResponse, finalHashData.get.get)
+            } else {
+              expectJobStoreWrite(SucceededResponseData(successResponse, finalHashData))
+            }
+            // A separate check of the final effective call caching mode:
+            if (ejhaResponse == hashErrorEjhaResponse || initialHashData == hashErrorDataValue) {
+              ejea.underlyingActor.checkEffectiveCallCachingMode should be(mode.withoutWrite)
+            } else {
+              ejea.underlyingActor.checkEffectiveCallCachingMode should be(mode)
+            }
           }
-        }
-
-        if (mode.readFromCache) {
-          s"invalidate a call for caching if backend copying failed when it was going to receive $hashComboName, if call caching is $mode" in {
 
+          s"$nextStepName when it gets a success result and it then gets $hashComboName, if call caching is $mode" in {
             ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, mode)
-
-            ejea.stateData should be(ResponsePendingData(
-              helper.backendJobDescriptor,
-              helper.bjeaProps,
-              initialHashData,
-              Option(helper.ejhaProbe.ref),
-              cacheHit,
-              None,
-              cacheHitFailureCount = 0,
-              failedCopyAttempts = 0
-            ))
-
             // Send the response from the copying actor
-            ejea ! copyAttemptFailedResponse(cacheHitNumber)
+            ejea ! successResponse
 
-            expectInvalidateCallCacheActor(cacheId)
-            eventually {
-              ejea.stateName should be(InvalidatingCacheEntry)
-            }
-            ejea.stateData should be(ResponsePendingData(
-              helper.backendJobDescriptor,
-              helper.bjeaProps,
-              initialHashData,
-              Option(helper.ejhaProbe.ref),
-              cacheHit,
-              None,
-              cacheHitFailureCount = 1,
-              failedCopyAttempts = 1
-            ))
-          }
+            ejhaResponse foreach { resp =>
+              // Nothing should have happened yet:
+              helper.jobStoreProbe.expectNoMessage(awaitAlmostNothing)
 
-          s"not invalidate a call for caching if backend copying failed when invalidation is disabled, when it was going to receive $hashComboName, if call caching is $mode" in {
-            val invalidationDisabledOptions = CallCachingOptions(invalidateBadCacheResults = false, workflowOptionCallCachePrefixes = None)
-            val cacheInvalidationDisabledMode = mode match {
-              case CallCachingActivity(rw, _) => CallCachingActivity(rw, invalidationDisabledOptions)
-              case _ => fail(s"Mode $mode not appropriate for cache invalidation tests")
+              // Ok, now send the response from the EJHA (if there was one!):
+              ejea ! resp
             }
-            ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, cacheInvalidationDisabledMode)
-            // Send the response from the copying actor
-            ejea ! copyAttemptFailedResponse(cacheHitNumber)
-
-            helper.ejhaProbe.expectMsg(NextHit)
 
-            eventually {
-              ejea.stateName should be(CheckingCallCache)
+            if (cacheUpdateRequired) {
+              expectCacheWrite(successResponse, finalHashData.get.get)
+            } else {
+              expectJobStoreWrite(SucceededResponseData(successResponse, finalHashData))
+            }
+            // A separate check of the final effective call caching mode:
+            if (ejhaResponse == hashErrorEjhaResponse || initialHashData == hashErrorDataValue) {
+              ejea.underlyingActor.checkEffectiveCallCachingMode should be(mode.withoutWrite)
+            } else {
+              ejea.underlyingActor.checkEffectiveCallCachingMode should be(mode)
             }
-            // Make sure we didn't start invalidating anything:
-            helper.invalidateCacheActorCreations.hasExactlyOne should be(false)
-            ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, initialHashData, Option(helper.ejhaProbe.ref), cacheHit, cacheHitFailureCount = 1, failedCopyAttempts = 1))
           }
 
-          def checkInvalidateOnCopyFailure(expectMetric: Boolean) = {
-            val metricsExpectationString = (if (expectMetric) "and " else "but not ") + "generate a metric"
-            s"invalidate a call for caching $metricsExpectationString if backend copying failed (preserving any received hashes) when call caching is $mode, the EJEA has $hashComboName and then gets a success result" in {
+          if (mode.readFromCache) {
+            s"invalidate a call for caching if backend copying failed when it was going to receive $hashComboName, if call caching is $mode" in {
+
               ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, mode)
-              // Send the response from the EJHA (if there was one!):
-              ejhaResponse foreach {
-                ejea ! _
-              }
 
-              // Nothing should happen here:
-              helper.jobStoreProbe.expectNoMessage(awaitAlmostNothing)
+              ejea.stateData should be(
+                ResponsePendingData(
+                  helper.backendJobDescriptor,
+                  helper.bjeaProps,
+                  initialHashData,
+                  Option(helper.ejhaProbe.ref),
+                  cacheHit,
+                  None,
+                  cacheHitFailureCount = 0,
+                  failedCopyAttempts = 0
+                )
+              )
 
               // Send the response from the copying actor
-              val copyFailureMessage = if (expectMetric) cacheHitBlacklistedResponse(cacheHitNumber) else copyAttemptFailedResponse(cacheHitNumber)
-              ejea ! copyFailureMessage
+              ejea ! copyAttemptFailedResponse(cacheHitNumber)
 
               expectInvalidateCallCacheActor(cacheId)
               eventually {
                 ejea.stateName should be(InvalidatingCacheEntry)
               }
-              ejea.stateData should be(ResponsePendingData(
-                helper.backendJobDescriptor,
-                helper.bjeaProps,
-                finalHashData,
-                Option(helper.ejhaProbe.ref),
-                cacheHit,
-                None,
-                cacheHitFailureCount = 1,
-                failedCopyAttempts = if (expectMetric) 0 else 1
-                // In this context `expectMetric` means "was blacklisted".
-                // If the cache hit was blacklisted there should have been no additional copy attempt so no failed copy attempt.
-              ))
-
-              if (expectMetric) {
-                helper.serviceRegistryProbe.fishForSpecificMessage(2.seconds) {
-                  case InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(prefix, path))) =>
-                    prefix should be(List.empty[String])
-                    path should be(NonEmptyList.of(
-                      "job",
-                      "callcaching", "read", "error", "bucketblacklisted", helper.taskName, helper.backendWorkflowDescriptor.hogGroup.value
-                    ))
+              ejea.stateData should be(
+                ResponsePendingData(
+                  helper.backendJobDescriptor,
+                  helper.bjeaProps,
+                  initialHashData,
+                  Option(helper.ejhaProbe.ref),
+                  cacheHit,
+                  None,
+                  cacheHitFailureCount = 1,
+                  failedCopyAttempts = 1
+                )
+              )
+            }
+
+            s"not invalidate a call for caching if backend copying failed when invalidation is disabled, when it was going to receive $hashComboName, if call caching is $mode" in {
+              val invalidationDisabledOptions =
+                CallCachingOptions(invalidateBadCacheResults = false, workflowOptionCallCachePrefixes = None)
+              val cacheInvalidationDisabledMode = mode match {
+                case CallCachingActivity(rw, _) => CallCachingActivity(rw, invalidationDisabledOptions)
+                case _ => fail(s"Mode $mode not appropriate for cache invalidation tests")
+              }
+              ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, cacheInvalidationDisabledMode)
+              // Send the response from the copying actor
+              ejea ! copyAttemptFailedResponse(cacheHitNumber)
+
+              helper.ejhaProbe.expectMsg(NextHit)
+
+              eventually {
+                ejea.stateName should be(CheckingCallCache)
+              }
+              // Make sure we didn't start invalidating anything:
+              helper.invalidateCacheActorCreations.hasExactlyOne should be(false)
+              ejea.stateData should be(
+                ResponsePendingData(helper.backendJobDescriptor,
+                                    helper.bjeaProps,
+                                    initialHashData,
+                                    Option(helper.ejhaProbe.ref),
+                                    cacheHit,
+                                    cacheHitFailureCount = 1,
+                                    failedCopyAttempts = 1
+                )
+              )
+            }
+
+            def checkInvalidateOnCopyFailure(expectMetric: Boolean) = {
+              val metricsExpectationString = (if (expectMetric) "and " else "but not ") + "generate a metric"
+              s"invalidate a call for caching $metricsExpectationString if backend copying failed (preserving any received hashes) when call caching is $mode, the EJEA has $hashComboName and then gets a success result" in {
+                ejea = ejeaInBackendIsCopyingCachedOutputsState(initialHashData, mode)
+                // Send the response from the EJHA (if there was one!):
+                ejhaResponse foreach {
+                  ejea ! _
+                }
+
+                // Nothing should happen here:
+                helper.jobStoreProbe.expectNoMessage(awaitAlmostNothing)
+
+                // Send the response from the copying actor
+                val copyFailureMessage =
+                  if (expectMetric) cacheHitBlacklistedResponse(cacheHitNumber)
+                  else copyAttemptFailedResponse(cacheHitNumber)
+                ejea ! copyFailureMessage
+
+                expectInvalidateCallCacheActor(cacheId)
+                eventually {
+                  ejea.stateName should be(InvalidatingCacheEntry)
+                }
+                ejea.stateData should be(
+                  ResponsePendingData(
+                    helper.backendJobDescriptor,
+                    helper.bjeaProps,
+                    finalHashData,
+                    Option(helper.ejhaProbe.ref),
+                    cacheHit,
+                    None,
+                    cacheHitFailureCount = 1,
+                    failedCopyAttempts = if (expectMetric) 0 else 1
+                    // In this context `expectMetric` means "was blacklisted".
+                    // If the cache hit was blacklisted there should have been no additional copy attempt so no failed copy attempt.
+                  )
+                )
+
+                if (expectMetric) {
+                  helper.serviceRegistryProbe.fishForSpecificMessage(2.seconds) {
+                    case InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(prefix, path))) =>
+                      prefix should be(List.empty[String])
+                      path should be(
+                        NonEmptyList.of(
+                          "job",
+                          "callcaching",
+                          "read",
+                          "error",
+                          "bucketblacklisted",
+                          helper.taskName,
+                          helper.backendWorkflowDescriptor.hogGroup.value
+                        )
+                      )
+                  }
                 }
               }
             }
-          }
 
-          checkInvalidateOnCopyFailure(expectMetric = false)
-          checkInvalidateOnCopyFailure(expectMetric = true)
-        }
+            checkInvalidateOnCopyFailure(expectMetric = false)
+            checkInvalidateOnCopyFailure(expectMetric = true)
+          }
       }
     }
   }
@@ -212,10 +276,13 @@ class EjeaBackendIsCopyingCachedOutputsSpec extends EngineJobExecutionActorSpec
   private val cacheId: CallCachingEntryId = CallCachingEntryId(74)
   private val cacheHitNumber = 3
   private val cacheHit = Option(EJEACacheHit(CacheHit(cacheId), hitNumber = cacheHitNumber, details = None))
-  def standardResponsePendingData(hashes: Option[Try[CallCacheHashes]]) = ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, hashes, Option(helper.ejhaProbe.ref), cacheHit)
-  def ejeaInBackendIsCopyingCachedOutputsState(initialHashes: Option[Try[CallCacheHashes]], callCachingMode: CallCachingMode, restarting: Boolean = false) = {
+  def standardResponsePendingData(hashes: Option[Try[CallCacheHashes]]) =
+    ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, hashes, Option(helper.ejhaProbe.ref), cacheHit)
+  def ejeaInBackendIsCopyingCachedOutputsState(initialHashes: Option[Try[CallCacheHashes]],
+                                               callCachingMode: CallCachingMode,
+                                               restarting: Boolean = false
+  ) =
     helper
       .buildEJEA(restarting = restarting, callCachingMode = callCachingMode)
       .setStateInline(data = standardResponsePendingData(initialHashes))
-  }
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingCacheEntryExistenceSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingCacheEntryExistenceSpec.scala
index 922c3b0f90a..af208492ce1 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingCacheEntryExistenceSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingCacheEntryExistenceSpec.scala
@@ -13,20 +13,23 @@ import scala.util.control.NoStackTrace
 
 class EjeaCheckingCacheEntryExistenceSpec extends EngineJobExecutionActorSpec {
 
-  override implicit val stateUnderTest = CheckingJobStore
+  implicit override val stateUnderTest = CheckingJobStore
 
   "An EJEA in EjeaCheckingCacheEntryExistence state should" should {
     "re-use the results from the cache hit" in {
       createCheckingCacheEntryExistenceEjea()
 
-      ejea ! CallCachingJoin(CallCachingEntry(helper.workflowId.toString, helper.jobFqn, 0, None, None, allowResultReuse = true),
+      ejea ! CallCachingJoin(
+        CallCachingEntry(helper.workflowId.toString, helper.jobFqn, 0, None, None, allowResultReuse = true),
         List(CallCachingHashEntry("runtime attribute: docker", "HASHVALUE")),
         None,
         List.empty,
         List.empty
       )
-      helper.serviceRegistryProbe.expectMsgPF(awaitTimeout) {
-        case put: PutMetadataAction => put.events.find(_.key.key.endsWith("runtime attribute:docker"))flatMap(_.value.map(_.value)) shouldBe Option("HASHVALUE")
+      helper.serviceRegistryProbe.expectMsgPF(awaitTimeout) { case put: PutMetadataAction =>
+        put.events.find(_.key.key.endsWith("runtime attribute:docker")) flatMap (_.value.map(_.value)) shouldBe Option(
+          "HASHVALUE"
+        )
       }
       helper.jobStoreProbe.expectMsgClass(classOf[RegisterJobCompleted])
       ejea.stateName should be(UpdatingJobStore)
@@ -49,7 +52,6 @@ class EjeaCheckingCacheEntryExistenceSpec extends EngineJobExecutionActorSpec {
     }
   }
 
-  private def createCheckingCacheEntryExistenceEjea(): Unit = {
+  private def createCheckingCacheEntryExistenceEjea(): Unit =
     ejea = helper.buildEJEA().setStateInline(state = CheckingCacheEntryExistence, data = NoData)
-  }
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingCallCacheSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingCallCacheSpec.scala
index 6ba6141daeb..a915e62b388 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingCallCacheSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingCallCacheSpec.scala
@@ -1,7 +1,12 @@
 package cromwell.engine.workflow.lifecycle.execution.ejea
 
 import cromwell.core.callcaching.{CallCachingActivity, CallCachingOff, ReadCache}
-import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor.{CheckingCallCache, FetchingCachedOutputsFromDatabase, ResponsePendingData, RunningJob}
+import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor.{
+  CheckingCallCache,
+  FetchingCachedOutputsFromDatabase,
+  ResponsePendingData,
+  RunningJob
+}
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.{CacheHit, CacheMiss, HashError}
 import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec.EnhancedTestEJEA
 import cromwell.services.CallCaching.CallCachingEntryId
@@ -11,7 +16,7 @@ import scala.util.control.NoStackTrace
 
 class EjeaCheckingCallCacheSpec extends EngineJobExecutionActorSpec with Eventually with CanExpectFetchCachedResults {
 
-  override implicit val stateUnderTest = CheckingCallCache
+  implicit override val stateUnderTest = CheckingCallCache
 
   "An EJEA in CheckingCallCache mode" should {
     "Try to fetch the call cache outputs if it gets a CacheHit" in {
@@ -21,29 +26,32 @@ class EjeaCheckingCallCacheSpec extends EngineJobExecutionActorSpec with Eventua
       ejea.stateName should be(FetchingCachedOutputsFromDatabase)
     }
 
-    RestartOrExecuteCommandTuples foreach { case RestartOrExecuteCommandTuple(operationName, restarting, expectedMessage) =>
-      s"$operationName the job if it receives a cache miss and restarting is $restarting" in {
-        createCheckingCallCacheEjea(restarting)
-        ejea ! CacheMiss
-        helper.bjeaProbe.expectMsg(awaitTimeout, expectedMessage)
-        ejea.stateName should be(RunningJob)
-      }
-
-      s"Disabling call caching and $operationName the job if it receives a HashError and restarting is $restarting" in {
-        createCheckingCallCacheEjea(restarting)
-        ejea ! HashError(new Exception("Anticipated exception. Part of test-flow") with NoStackTrace)
-        eventually {
-          ejea.underlyingActor.checkEffectiveCallCachingMode should be(CallCachingOff)
+    RestartOrExecuteCommandTuples foreach {
+      case RestartOrExecuteCommandTuple(operationName, restarting, expectedMessage) =>
+        s"$operationName the job if it receives a cache miss and restarting is $restarting" in {
+          createCheckingCallCacheEjea(restarting)
+          ejea ! CacheMiss
+          helper.bjeaProbe.expectMsg(awaitTimeout, expectedMessage)
+          ejea.stateName should be(RunningJob)
+        }
+
+        s"Disabling call caching and $operationName the job if it receives a HashError and restarting is $restarting" in {
+          createCheckingCallCacheEjea(restarting)
+          ejea ! HashError(new Exception("Anticipated exception. Part of test-flow") with NoStackTrace)
+          eventually {
+            ejea.underlyingActor.checkEffectiveCallCachingMode should be(CallCachingOff)
+          }
+          helper.bjeaProbe.expectMsg(awaitTimeout, expectedMessage)
+          ejea.stateName should be(RunningJob)
         }
-        helper.bjeaProbe.expectMsg(awaitTimeout, expectedMessage)
-        ejea.stateName should be(RunningJob)
-      }
     }
   }
 
   private def createCheckingCallCacheEjea(restarting: Boolean = false): Unit = {
     ejea = helper.buildEJEA(restarting = restarting, callCachingMode = CallCachingActivity(ReadCache))
-    ejea.setStateInline(state = CheckingCallCache, data = ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None))
+    ejea.setStateInline(state = CheckingCallCache,
+                        data = ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None)
+    )
     ()
   }
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingJobStoreSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingJobStoreSpec.scala
index e1f1a244b38..a9d3fdd8727 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingJobStoreSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaCheckingJobStoreSpec.scala
@@ -1,16 +1,24 @@
 package cromwell.engine.workflow.lifecycle.execution.ejea
 
-import cromwell.backend.BackendJobExecutionActor.{JobFailedNonRetryableResponse, JobFailedRetryableResponse, JobSucceededResponse}
+import cromwell.backend.BackendJobExecutionActor.{
+  JobFailedNonRetryableResponse,
+  JobFailedRetryableResponse,
+  JobSucceededResponse
+}
 import cromwell.core.CallOutputs
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadActor.CallCacheEntryForCall
 import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec.EnhancedTestEJEA
-import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor.{CheckingCacheEntryExistence, CheckingJobStore, NoData}
+import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor.{
+  CheckingCacheEntryExistence,
+  CheckingJobStore,
+  NoData
+}
 import cromwell.jobstore.JobStoreActor.{JobComplete, JobNotComplete}
 import cromwell.jobstore.{JobResultFailure, JobResultSuccess}
 
 class EjeaCheckingJobStoreSpec extends EngineJobExecutionActorSpec {
 
-  override implicit val stateUnderTest = CheckingJobStore
+  implicit override val stateUnderTest = CheckingJobStore
 
   "An EJEA in CheckingJobStore state should" should {
     "send a Job SucceededResponse if the job is already complete and successful" in {
@@ -21,17 +29,15 @@ class EjeaCheckingJobStoreSpec extends EngineJobExecutionActorSpec {
 
       ejea ! JobComplete(JobResultSuccess(returnCode, jobOutputs))
 
-      helper.replyToProbe.expectMsgPF(awaitTimeout) {
-        case response: JobSucceededResponse =>
-          response.returnCode shouldBe returnCode
-          response.jobOutputs shouldBe jobOutputs
+      helper.replyToProbe.expectMsgPF(awaitTimeout) { case response: JobSucceededResponse =>
+        response.returnCode shouldBe returnCode
+        response.jobOutputs shouldBe jobOutputs
       }
 
       helper.deathwatch.expectTerminated(ejea)
     }
 
     List(("FailedNonRetryableResponse", false), ("FailedRetryableResponse", true)) foreach { case (name, retryable) =>
-
       s"send a $name if the job is already complete and failed" in {
         createCheckingJobStoreEjea()
         val returnCode: Option[Int] = Option(1)
@@ -59,12 +65,16 @@ class EjeaCheckingJobStoreSpec extends EngineJobExecutionActorSpec {
       ejea.setState(CheckingJobStore)
       ejea ! JobNotComplete
 
-      helper.callCacheReadActorProbe.expectMsg(awaitTimeout, "expecting CallCacheEntryForCall", CallCacheEntryForCall(helper.workflowId, helper.jobDescriptorKey))
+      helper.callCacheReadActorProbe.expectMsg(awaitTimeout,
+                                               "expecting CallCacheEntryForCall",
+                                               CallCacheEntryForCall(helper.workflowId, helper.jobDescriptorKey)
+      )
       ejea.stateName should be(CheckingCacheEntryExistence)
 
       ejea.stop()
     }
   }
 
-  private def createCheckingJobStoreEjea(): Unit = { ejea = helper.buildEJEA(restarting = true).setStateInline(state = CheckingJobStore, data = NoData) }
+  private def createCheckingJobStoreEjea(): Unit = ejea =
+    helper.buildEJEA(restarting = true).setStateInline(state = CheckingJobStore, data = NoData)
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaFetchingCachedOutputsFromDatabaseSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaFetchingCachedOutputsFromDatabaseSpec.scala
index fab5cfa0b65..bc3f56dfe66 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaFetchingCachedOutputsFromDatabaseSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaFetchingCachedOutputsFromDatabaseSpec.scala
@@ -6,7 +6,10 @@ import cromwell.core.callcaching.{CallCachingActivity, ReadAndWriteCache}
 import cromwell.core.simpleton.WomValueSimpleton
 import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor._
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.{CacheHit, HashError}
-import cromwell.engine.workflow.lifecycle.execution.callcaching.FetchCachedResultsActor.{CachedOutputLookupFailed, CachedOutputLookupSucceeded}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.FetchCachedResultsActor.{
+  CachedOutputLookupFailed,
+  CachedOutputLookupSucceeded
+}
 import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec._
 import cromwell.engine.workflow.lifecycle.execution.ejea.HasJobSuccessResponse.SuccessfulCallCacheHashes
 import wom.values.WomString
@@ -21,10 +24,10 @@ class EjeaFetchingCachedOutputsFromDatabaseSpec extends EngineJobExecutionActorS
 
   "An EJEA in FetchingCachedOutputsFromDatabase state" should {
 
-    val possibleEjhaResponses = List(
-      ("no hashes", None),
-      ("hash results", Some(SuccessfulCallCacheHashes)),
-      ("hash error", Some(HashError(new Exception("blah")))))
+    val possibleEjhaResponses = List(("no hashes", None),
+                                     ("hash results", Some(SuccessfulCallCacheHashes)),
+                                     ("hash error", Some(HashError(new Exception("blah"))))
+    )
 
     possibleEjhaResponses foreach { case (name, ejhaResponse) =>
       s"Correctly receive $name then begin the backend-specific output copying actor when it gets a result-fetch success" in {
@@ -35,12 +38,20 @@ class EjeaFetchingCachedOutputsFromDatabaseSpec extends EngineJobExecutionActorS
         }
 
         // Send the response from the "Fetch" actor
-        val cachedSimpletons = Seq(WomValueSimpleton("a", WomString("hullo")), WomValueSimpleton("b", WomString("cheerio")))
+        val cachedSimpletons =
+          Seq(WomValueSimpleton("a", WomString("hullo")), WomValueSimpleton("b", WomString("cheerio")))
         val detritusMap = Map("stdout" -> "//somePath")
         val cachedReturnCode = Some(17)
         val sourceCacheDetails = s"${WorkflowId.randomId()}:call-someTask:1"
-        ejea ! CachedOutputLookupSucceeded(cachedSimpletons, detritusMap, cachedReturnCode, callCachingEntryId, sourceCacheDetails)
-        helper.callCacheHitCopyingProbe.expectMsg(CopyOutputsCommand(cachedSimpletons, detritusMap, callCachingEntryId, cachedReturnCode))
+        ejea ! CachedOutputLookupSucceeded(cachedSimpletons,
+                                           detritusMap,
+                                           cachedReturnCode,
+                                           callCachingEntryId,
+                                           sourceCacheDetails
+        )
+        helper.callCacheHitCopyingProbe.expectMsg(
+          CopyOutputsCommand(cachedSimpletons, detritusMap, callCachingEntryId, cachedReturnCode)
+        )
 
         // Check we end up in the right state:
         ejea.stateName should be(BackendIsCopyingCachedOutputs)
@@ -60,40 +71,49 @@ class EjeaFetchingCachedOutputsFromDatabaseSpec extends EngineJobExecutionActorS
         ejea.stateData.asInstanceOf[ResponsePendingData] shouldEqualFieldwise expectedData
       }
 
-      RestartOrExecuteCommandTuples foreach { case RestartOrExecuteCommandTuple(operationName, restarting, expectedMessage) =>
-        // Send the response from the "Fetch" actor
-        val failureReason = new Exception("You can't handle the truth!")
-        val lookupFailedMsg = CachedOutputLookupFailed(CallCachingEntryId(90210), failureReason)
-
-        s"Correctly receive $name then $operationName the job when it gets a ${lookupFailedMsg.getClass.getSimpleName} result-fetch failure" in {
-          ejea = ejeaInFetchingCachedOutputsFromDatabaseState(restarting)
-          // Send the response from the EJHA (if there was one!):
-          ejhaResponse foreach {
-            ejea ! _
+      RestartOrExecuteCommandTuples foreach {
+        case RestartOrExecuteCommandTuple(operationName, restarting, expectedMessage) =>
+          // Send the response from the "Fetch" actor
+          val failureReason = new Exception("You can't handle the truth!")
+          val lookupFailedMsg = CachedOutputLookupFailed(CallCachingEntryId(90210), failureReason)
+
+          s"Correctly receive $name then $operationName the job when it gets a ${lookupFailedMsg.getClass.getSimpleName} result-fetch failure" in {
+            ejea = ejeaInFetchingCachedOutputsFromDatabaseState(restarting)
+            // Send the response from the EJHA (if there was one!):
+            ejhaResponse foreach {
+              ejea ! _
+            }
+
+            ejea ! lookupFailedMsg
+
+            helper.bjeaProbe.expectMsg(awaitTimeout, expectedMessage)
+
+            // Check we end up in the right state:
+            ejea.stateName should be(RunningJob)
+            // Check we end up with the right data:
+            val expectedData = initialData.copy(
+              hashes = ejhaResponse map {
+                case SuccessfulCallCacheHashes => Success(SuccessfulCallCacheHashes)
+                case HashError(t) => Failure(t)
+                case _ => fail(s"Bad test wiring. We didn't expect $ejhaResponse here")
+              },
+              backendJobActor = Option(helper.bjeaProbe.ref)
+            )
+            ejea.stateData should be(expectedData)
           }
-
-          ejea ! lookupFailedMsg
-
-          helper.bjeaProbe.expectMsg(awaitTimeout, expectedMessage)
-
-          // Check we end up in the right state:
-          ejea.stateName should be(RunningJob)
-          // Check we end up with the right data:
-          val expectedData = initialData.copy(
-            hashes = ejhaResponse map {
-              case SuccessfulCallCacheHashes => Success(SuccessfulCallCacheHashes)
-              case HashError(t) => Failure(t)
-              case _ => fail(s"Bad test wiring. We didn't expect $ejhaResponse here")
-            },
-            backendJobActor = Option(helper.bjeaProbe.ref)
-          )
-          ejea.stateData should be(expectedData)
-        }
       }
     }
   }
 
   val callCachingEntryId = CallCachingEntryId(75)
-  def initialData = ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None, None, Some(EJEACacheHit(CacheHit(callCachingEntryId), 2, None)), None)
-  def ejeaInFetchingCachedOutputsFromDatabaseState(restarting: Boolean = false) = helper.buildEJEA(restarting = restarting, callCachingMode = CallCachingActivity(ReadAndWriteCache)).setStateInline(data = initialData)
+  def initialData = ResponsePendingData(helper.backendJobDescriptor,
+                                        helper.bjeaProps,
+                                        None,
+                                        None,
+                                        Some(EJEACacheHit(CacheHit(callCachingEntryId), 2, None)),
+                                        None
+  )
+  def ejeaInFetchingCachedOutputsFromDatabaseState(restarting: Boolean = false) = helper
+    .buildEJEA(restarting = restarting, callCachingMode = CallCachingActivity(ReadAndWriteCache))
+    .setStateInline(data = initialData)
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaInvalidatingCacheEntrySpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaInvalidatingCacheEntrySpec.scala
index bc860b8a7cc..f52e74017b4 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaInvalidatingCacheEntrySpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaInvalidatingCacheEntrySpec.scala
@@ -4,13 +4,16 @@ import akka.actor.ActorRef
 import cromwell.core.callcaching.{CallCachingActivity, ReadCache}
 import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor._
 import cromwell.engine.workflow.lifecycle.execution.callcaching.CallCacheReadingJobActor.NextHit
-import cromwell.engine.workflow.lifecycle.execution.callcaching.{CallCacheInvalidatedFailure, CallCacheInvalidatedSuccess}
+import cromwell.engine.workflow.lifecycle.execution.callcaching.{
+  CallCacheInvalidatedFailure,
+  CallCacheInvalidatedSuccess
+}
 import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec._
 import cromwell.services.CallCaching.CallCachingEntryId
 
 class EjeaInvalidatingCacheEntrySpec extends EngineJobExecutionActorSpec {
 
-  override implicit val stateUnderTest = InvalidatingCacheEntry
+  implicit override val stateUnderTest = InvalidatingCacheEntry
 
   "An EJEA in InvalidatingCacheEntry state" should {
 
@@ -27,24 +30,38 @@ class EjeaInvalidatingCacheEntrySpec extends EngineJobExecutionActorSpec {
 
         helper.bjeaProbe.expectNoMessage(awaitAlmostNothing)
         helper.ejhaProbe.expectMsg(NextHit)
-        eventually { ejea.stateName should be(CheckingCallCache) }
-        ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None, Option(helper.ejhaProbe.ref), None))
+        eventually(ejea.stateName should be(CheckingCallCache))
+        ejea.stateData should be(
+          ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None, Option(helper.ejhaProbe.ref), None)
+        )
       }
 
-      RestartOrExecuteCommandTuples foreach { case RestartOrExecuteCommandTuple(operationName, restarting, expectedMessage) =>
-        s"$operationName a job if there is no ejha when invalidate response is $invalidateActorResponse" in {
-          ejea = ejeaInvalidatingCacheEntryState(None, restarting = restarting)
-          // Send the response from the invalidate actor
-          ejea ! invalidateActorResponse
+      RestartOrExecuteCommandTuples foreach {
+        case RestartOrExecuteCommandTuple(operationName, restarting, expectedMessage) =>
+          s"$operationName a job if there is no ejha when invalidate response is $invalidateActorResponse" in {
+            ejea = ejeaInvalidatingCacheEntryState(None, restarting = restarting)
+            // Send the response from the invalidate actor
+            ejea ! invalidateActorResponse
 
-          helper.bjeaProbe.expectMsg(awaitTimeout, expectedMessage)
-          eventually { ejea.stateName should be(RunningJob) }
-          ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None, None, None, Option(helper.bjeaProbe.ref)))
-        }
+            helper.bjeaProbe.expectMsg(awaitTimeout, expectedMessage)
+            eventually(ejea.stateName should be(RunningJob))
+            ejea.stateData should be(
+              ResponsePendingData(helper.backendJobDescriptor,
+                                  helper.bjeaProps,
+                                  None,
+                                  None,
+                                  None,
+                                  Option(helper.bjeaProbe.ref)
+              )
+            )
+          }
       }
     }
   }
 
-  def standardResponsePendingData(ejha: Option[ActorRef]) = ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None, ejha, None, None)
-  def ejeaInvalidatingCacheEntryState(ejha: Option[ActorRef], restarting: Boolean = false) = helper.buildEJEA(restarting = restarting, callCachingMode = CallCachingActivity(ReadCache)).setStateInline(state = InvalidatingCacheEntry, data = standardResponsePendingData(ejha))
+  def standardResponsePendingData(ejha: Option[ActorRef]) =
+    ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None, ejha, None, None)
+  def ejeaInvalidatingCacheEntryState(ejha: Option[ActorRef], restarting: Boolean = false) = helper
+    .buildEJEA(restarting = restarting, callCachingMode = CallCachingActivity(ReadCache))
+    .setStateInline(state = InvalidatingCacheEntry, data = standardResponsePendingData(ejha))
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaMultipleCallCacheCopyAttemptsSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaMultipleCallCacheCopyAttemptsSpec.scala
index cd13165370a..f19bd3b42e2 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaMultipleCallCacheCopyAttemptsSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaMultipleCallCacheCopyAttemptsSpec.scala
@@ -16,14 +16,14 @@ import EjeaMultipleCallCacheCopyAttemptsSpec.bt140Debug
 import akka.testkit.TestFSMRef
 
 class EjeaMultipleCallCacheCopyAttemptsSpec
-  extends EngineJobExecutionActorSpec
+    extends EngineJobExecutionActorSpec
     with HasJobSuccessResponse
     with HasCopyFailureResponses
     with HasJobFailureResponses
     with CanExpectJobStoreWrites
     with CanExpectFetchCachedResults {
 
-  override implicit val stateUnderTest: EngineJobExecutionActorState = BackendIsCopyingCachedOutputs
+  implicit override val stateUnderTest: EngineJobExecutionActorState = BackendIsCopyingCachedOutputs
   override val allowMultipleCacheCycles: Boolean = true
 
   "An EJEA attempting to call cache copy" should {
@@ -45,19 +45,29 @@ class EjeaMultipleCallCacheCopyAttemptsSpec
 
     def fetchCachedResultsActorSendsResultSetToEjeaAndEjeaReacts(copyAttemptNumber: Int) = {
       val callCachingEntryId = cacheEntryIdFromCopyAttempt(copyAttemptNumber)
-      val cachedSimpletons = Seq(WomValueSimpleton("a", WomString("hullo")), WomValueSimpleton("b", WomString("cheerio")))
+      val cachedSimpletons =
+        Seq(WomValueSimpleton("a", WomString("hullo")), WomValueSimpleton("b", WomString("cheerio")))
       val detritusMap = Map("stdout" -> "//somePath")
       val cachedReturnCode = Some(17)
       val sourceCacheDetails = s"${WorkflowId.randomId()}:call-someTask:1"
-      ejea ! CachedOutputLookupSucceeded(cachedSimpletons, detritusMap, cachedReturnCode, callCachingEntryId, sourceCacheDetails)
-      helper.callCacheHitCopyingProbe.expectMsg(CopyOutputsCommand(cachedSimpletons, detritusMap, callCachingEntryId, cachedReturnCode))
+      ejea ! CachedOutputLookupSucceeded(cachedSimpletons,
+                                         detritusMap,
+                                         cachedReturnCode,
+                                         callCachingEntryId,
+                                         sourceCacheDetails
+      )
+      helper.callCacheHitCopyingProbe.expectMsg(
+        CopyOutputsCommand(cachedSimpletons, detritusMap, callCachingEntryId, cachedReturnCode)
+      )
       eventually {
         ejea.stateName should be(BackendIsCopyingCachedOutputs)
       }
     }
 
     def copyAttemptFailsAndEjeaLooksForNextHit(becauseBlacklisted: Boolean, copyAttemptNumber: Int) = {
-      val response = if (becauseBlacklisted) cacheHitBlacklistedResponse(copyAttemptNumber) else copyAttemptFailedResponse(copyAttemptNumber)
+      val response =
+        if (becauseBlacklisted) cacheHitBlacklistedResponse(copyAttemptNumber)
+        else copyAttemptFailedResponse(copyAttemptNumber)
 
       ejea ! response
       helper.ejhaProbe.expectMsg(NextHit)
@@ -95,14 +105,15 @@ class EjeaMultipleCallCacheCopyAttemptsSpec
       // First: A long series of copy failure:
       bt140Debug("'keep waiting' running 'series of copy failures'")
       val initialCopyFailures = maxFailedCopyAttempts - 1
-      0.until(initialCopyFailures). foreach { currentCopyAttemptNumber =>
+      0.until(initialCopyFailures).foreach { currentCopyAttemptNumber =>
         ejhaSendsHitIdToEjeaAndEjeaReacts(currentCopyAttemptNumber)
         fetchCachedResultsActorSendsResultSetToEjeaAndEjeaReacts(currentCopyAttemptNumber)
         copyAttemptFailsAndEjeaLooksForNextHit(becauseBlacklisted = false, currentCopyAttemptNumber)
       }
 
       // Then: A success:
-      val currentCopyAttemptNumber = initialCopyFailures // because the initial 0.until(...) is non-inclusive of the argument
+      val currentCopyAttemptNumber =
+        initialCopyFailures // because the initial 0.until(...) is non-inclusive of the argument
       bt140Debug("'keep waiting' running 'ejhaSendsHitIdToEjeaAndEjeaReacts'")
       ejhaSendsHitIdToEjeaAndEjeaReacts(copyAttemptNumber = currentCopyAttemptNumber)
       bt140Debug("'keep waiting' running 'fetchCachedResultsActorSendsResultSetToEjeaAndEjeaReacts'")
@@ -120,7 +131,7 @@ class EjeaMultipleCallCacheCopyAttemptsSpec
       // First: A long series of copy failure:
       bt140Debug("'fail fast' running 'longer series of (genuine) copy failures'")
       val initialCopyFailures = maxFailedCopyAttempts - 1
-      0.until(initialCopyFailures). foreach { currentCopyAttemptNumber =>
+      0.until(initialCopyFailures).foreach { currentCopyAttemptNumber =>
         ejhaSendsHitIdToEjeaAndEjeaReacts(currentCopyAttemptNumber)
         fetchCachedResultsActorSendsResultSetToEjeaAndEjeaReacts(currentCopyAttemptNumber)
         copyAttemptFailsAndEjeaLooksForNextHit(becauseBlacklisted = false, currentCopyAttemptNumber)
@@ -128,7 +139,8 @@ class EjeaMultipleCallCacheCopyAttemptsSpec
 
       // Then: Another failure:
       bt140Debug("'fail fast' running 'ejhaSendsHitIdToEjeaAndEjeaReacts'")
-      val currentCopyAttemptNumber = initialCopyFailures // because the initial 0.until(...) is non-inclusive of the argument
+      val currentCopyAttemptNumber =
+        initialCopyFailures // because the initial 0.until(...) is non-inclusive of the argument
       ejhaSendsHitIdToEjeaAndEjeaReacts(copyAttemptNumber = currentCopyAttemptNumber)
       bt140Debug("'fail fast' running 'fetchCachedResultsActorSendsResultSetToEjeaAndEjeaReacts'")
       fetchCachedResultsActorSendsResultSetToEjeaAndEjeaReacts(currentCopyAttemptNumber)
@@ -145,7 +157,7 @@ class EjeaMultipleCallCacheCopyAttemptsSpec
       // First: A long series of (genuine) copy failures:
       bt140Debug("'disregard' running 'longer series of (genuine) copy failures'")
       val initialCopyFailures = maxFailedCopyAttempts - 1
-      0.until(initialCopyFailures). foreach { currentCopyAttemptNumber =>
+      0.until(initialCopyFailures).foreach { currentCopyAttemptNumber =>
         ejhaSendsHitIdToEjeaAndEjeaReacts(currentCopyAttemptNumber)
         fetchCachedResultsActorSendsResultSetToEjeaAndEjeaReacts(currentCopyAttemptNumber)
         copyAttemptFailsAndEjeaLooksForNextHit(becauseBlacklisted = false, currentCopyAttemptNumber)
@@ -154,7 +166,7 @@ class EjeaMultipleCallCacheCopyAttemptsSpec
       // Second: An even longer series of (blacklist) copy failures:
       bt140Debug("'disregard' running 'longer series of (exclude list) copy failures'")
       val blacklistCopyFailures = maxFailedCopyAttempts + 2
-      initialCopyFailures.until(initialCopyFailures + blacklistCopyFailures). foreach { currentCopyAttemptNumber =>
+      initialCopyFailures.until(initialCopyFailures + blacklistCopyFailures).foreach { currentCopyAttemptNumber =>
         ejhaSendsHitIdToEjeaAndEjeaReacts(currentCopyAttemptNumber)
         fetchCachedResultsActorSendsResultSetToEjeaAndEjeaReacts(currentCopyAttemptNumber)
         copyAttemptFailsAndEjeaLooksForNextHit(becauseBlacklisted = true, currentCopyAttemptNumber)
@@ -171,18 +183,21 @@ class EjeaMultipleCallCacheCopyAttemptsSpec
       bt140Debug("'disregard' done")
     }
 
-
   }
 
   def buildEjea(maxFailedCopyAttempts: Int): TestFSMRef[EngineJobExecutionActorState, EJEAData, MockEjea] = helper
     .buildEJEA(
       restarting = false,
       callCachingMode = CallCachingActivity(ReadCache, CallCachingOptions(invalidateBadCacheResults = false)),
-      callCachingMaxFailedCopyAttempts = maxFailedCopyAttempts)
-    .setStateInline(state = CheckingCallCache, data = ResponsePendingData(
-      jobDescriptor = helper.backendJobDescriptor,
-      bjeaProps = helper.bjeaProps,
-      ejha = Some(helper.ejhaProbe.ref)))
+      callCachingMaxFailedCopyAttempts = maxFailedCopyAttempts
+    )
+    .setStateInline(
+      state = CheckingCallCache,
+      data = ResponsePendingData(jobDescriptor = helper.backendJobDescriptor,
+                                 bjeaProps = helper.bjeaProps,
+                                 ejha = Some(helper.ejhaProbe.ref)
+      )
+    )
 
 }
 
@@ -194,7 +209,6 @@ object EjeaMultipleCallCacheCopyAttemptsSpec extends StrictLogging {
   at any point someone decides that this is not actually helping, feel free to delete all calls to this method and the
   debug method itself.
    */
-  private def bt140Debug(message: String): Unit = {
+  private def bt140Debug(message: String): Unit =
     logger.info("BT-140 debug: " + message)
-  }
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPendingSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPendingSpec.scala
index 3d9ccdea718..4bbea403bfb 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPendingSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPendingSpec.scala
@@ -9,7 +9,7 @@ import org.scalatest.concurrent.Eventually
 
 class EjeaPendingSpec extends EngineJobExecutionActorSpec with CanValidateJobStoreKey with Eventually {
 
-  override implicit val stateUnderTest: EngineJobExecutionActorState = Pending
+  implicit override val stateUnderTest: EngineJobExecutionActorState = Pending
 
   "An EJEA in the Pending state" should {
 
@@ -36,7 +36,8 @@ class EjeaPendingSpec extends EngineJobExecutionActorSpec with CanValidateJobSto
         if (restarting) {
           helper.jobRestartCheckTokenDispenserProbe.expectMsgClass(max = awaitTimeout, classOf[JobTokenRequest])
         } else {
-          val tokenRequest = helper.jobExecutionTokenDispenserProbe.expectMsgClass(max = awaitTimeout, classOf[JobTokenRequest])
+          val tokenRequest =
+            helper.jobExecutionTokenDispenserProbe.expectMsgClass(max = awaitTimeout, classOf[JobTokenRequest])
           // 1 is the default hog-factor value defined in reference.conf
           tokenRequest.jobTokenType.hogFactor should be(1)
         }
@@ -45,14 +46,20 @@ class EjeaPendingSpec extends EngineJobExecutionActorSpec with CanValidateJobSto
       s"should use hog-factor defined in backend configuration in token request (with restarting=$restarting)" in {
         val expectedHogFactorValue = 123
         val overriddenHogFactorAttributeString = s"hog-factor: $expectedHogFactorValue"
-        val backendWithOverriddenHogFactorConfigDescriptor = BackendConfigurationDescriptor(backendConfig = ConfigFactory.parseString(overriddenHogFactorAttributeString), globalConfig)
-        ejea = helper.buildEJEA(restarting = restarting, backendConfigurationDescriptor = backendWithOverriddenHogFactorConfigDescriptor)
+        val backendWithOverriddenHogFactorConfigDescriptor =
+          BackendConfigurationDescriptor(backendConfig = ConfigFactory.parseString(overriddenHogFactorAttributeString),
+                                         globalConfig
+          )
+        ejea = helper.buildEJEA(restarting = restarting,
+                                backendConfigurationDescriptor = backendWithOverriddenHogFactorConfigDescriptor
+        )
         ejea ! Execute
 
         if (restarting) {
           helper.jobRestartCheckTokenDispenserProbe.expectMsgClass(max = awaitTimeout, classOf[JobTokenRequest])
         } else {
-          val tokenRequest = helper.jobExecutionTokenDispenserProbe.expectMsgClass(max = awaitTimeout, classOf[JobTokenRequest])
+          val tokenRequest =
+            helper.jobExecutionTokenDispenserProbe.expectMsgClass(max = awaitTimeout, classOf[JobTokenRequest])
           tokenRequest.jobTokenType.hogFactor should be(expectedHogFactorValue)
         }
       }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPreparingJobSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPreparingJobSpec.scala
index edb50af67bc..8bae0b275fe 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPreparingJobSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaPreparingJobSpec.scala
@@ -5,12 +5,15 @@ import cromwell.backend.BackendJobExecutionActor.JobFailedNonRetryableResponse
 import cromwell.core.callcaching.{CallCachingMode, DockerWithHash}
 import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor._
 import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec._
-import cromwell.engine.workflow.lifecycle.execution.job.preparation.CallPreparation.{BackendJobPreparationSucceeded, CallPreparationFailed}
+import cromwell.engine.workflow.lifecycle.execution.job.preparation.CallPreparation.{
+  BackendJobPreparationSucceeded,
+  CallPreparationFailed
+}
 import org.scalatest.concurrent.Eventually
 
 class EjeaPreparingJobSpec extends EngineJobExecutionActorSpec with CanExpectHashingInitialization with Eventually {
 
-  override implicit val stateUnderTest = PreparingJob
+  implicit override val stateUnderTest = PreparingJob
 
   "An EJEA in PreparingJob state" should {
 
@@ -22,30 +25,47 @@ class EjeaPreparingJobSpec extends EngineJobExecutionActorSpec with CanExpectHas
           ejea ! jobPrepSuccessResponse(jobDescriptor)
           expectHashingActorInitialization(mode, jobDescriptor)
           ejea.stateName should be(CheckingCallCache)
-          ejea.stateData should be(ResponsePendingData(jobDescriptor, helper.bjeaProps, None, Option(helper.ejhaProbe.ref)))
+          ejea.stateData should be(
+            ResponsePendingData(jobDescriptor, helper.bjeaProps, None, Option(helper.ejhaProbe.ref))
+          )
         }
 
         s"Not check for a cache hit when job preparation succeeds and no docker hash is available ($mode)" in {
           ejea = ejeaInPreparingState(mode)
           ejea ! jobPrepSuccessResponse(helper.backendJobDescriptor)
           ejea.stateName should be(RunningJob)
-          ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None, backendJobActor = Option(helper.bjeaProbe.ref)))
+          ejea.stateData should be(
+            ResponsePendingData(helper.backendJobDescriptor,
+                                helper.bjeaProps,
+                                None,
+                                backendJobActor = Option(helper.bjeaProbe.ref)
+            )
+          )
         }
       } else {
-        RestartOrExecuteCommandTuples foreach { case RestartOrExecuteCommandTuple(operationName, restarting, expectedMessage) =>
-          s"Send BJEA '$operationName' when job preparation succeeds ($mode)" in {
-            ejea = ejeaInPreparingState(mode = mode, restarting = restarting)
-            ejea ! jobPrepSuccessResponse(helper.backendJobDescriptor)
-            helper.bjeaProbe.expectMsg(awaitTimeout, "job preparation", expectedMessage)
-            ejea.stateName should be(RunningJob)
-            ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None, backendJobActor = Option(helper.bjeaProbe.ref)))
-          }
+        RestartOrExecuteCommandTuples foreach {
+          case RestartOrExecuteCommandTuple(operationName, restarting, expectedMessage) =>
+            s"Send BJEA '$operationName' when job preparation succeeds ($mode)" in {
+              ejea = ejeaInPreparingState(mode = mode, restarting = restarting)
+              ejea ! jobPrepSuccessResponse(helper.backendJobDescriptor)
+              helper.bjeaProbe.expectMsg(awaitTimeout, "job preparation", expectedMessage)
+              ejea.stateName should be(RunningJob)
+              ejea.stateData should be(
+                ResponsePendingData(helper.backendJobDescriptor,
+                                    helper.bjeaProps,
+                                    None,
+                                    backendJobActor = Option(helper.bjeaProbe.ref)
+                )
+              )
+            }
         }
       }
 
       s"Not proceed if Job Preparation fails ($mode)" in {
-        val prepActorResponse = CallPreparationFailed(helper.jobDescriptorKey, new Exception("The goggles! They do nothing!"))
-        val prepFailedEjeaResponse = JobFailedNonRetryableResponse(helper.jobDescriptorKey, prepActorResponse.throwable, None)
+        val prepActorResponse =
+          CallPreparationFailed(helper.jobDescriptorKey, new Exception("The goggles! They do nothing!"))
+        val prepFailedEjeaResponse =
+          JobFailedNonRetryableResponse(helper.jobDescriptorKey, prepActorResponse.throwable, None)
         ejea = ejeaInPreparingState(mode)
         ejea ! prepActorResponse
         helper.replyToProbe.expectMsg(prepFailedEjeaResponse)
@@ -54,8 +74,11 @@ class EjeaPreparingJobSpec extends EngineJobExecutionActorSpec with CanExpectHas
     }
   }
 
-  def jobPrepSuccessResponse(jobDescriptor: BackendJobDescriptor) = BackendJobPreparationSucceeded(jobDescriptor, helper.bjeaProps)
+  def jobPrepSuccessResponse(jobDescriptor: BackendJobDescriptor) =
+    BackendJobPreparationSucceeded(jobDescriptor, helper.bjeaProps)
 
-  def ejeaInPreparingState(mode: CallCachingMode, restarting: Boolean = false) = helper.buildEJEA(restarting = restarting, callCachingMode = mode).setStateInline(state = PreparingJob, data = NoData)
+  def ejeaInPreparingState(mode: CallCachingMode, restarting: Boolean = false) = helper
+    .buildEJEA(restarting = restarting, callCachingMode = mode)
+    .setStateInline(state = PreparingJob, data = NoData)
 
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingExecutionTokenSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingExecutionTokenSpec.scala
index bc710d98b0f..66c6c0adf4c 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingExecutionTokenSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingExecutionTokenSpec.scala
@@ -8,7 +8,7 @@ import org.scalatest.concurrent.Eventually
 
 class EjeaRequestingExecutionTokenSpec extends EngineJobExecutionActorSpec with CanValidateJobStoreKey with Eventually {
 
-  override implicit val stateUnderTest: EngineJobExecutionActorState = RequestingExecutionToken
+  implicit override val stateUnderTest: EngineJobExecutionActorState = RequestingExecutionToken
 
   "An EJEA in the RequestingExecutionToken state" should {
 
@@ -27,8 +27,14 @@ class EjeaRequestingExecutionTokenSpec extends EngineJobExecutionActorSpec with
         ejea = helper.buildEJEA(restarting = false)
         ejea ! JobTokenDispensed
 
-        helper.replyToProbe.expectMsg(max = awaitTimeout, hint = "Awaiting JobStarting message", JobStarting(helper.jobDescriptorKey))
-        helper.replyToProbe.expectMsg(max = awaitTimeout, hint = "Awaiting RequestValueStore message", RequestValueStore)
+        helper.replyToProbe.expectMsg(max = awaitTimeout,
+                                      hint = "Awaiting JobStarting message",
+                                      JobStarting(helper.jobDescriptorKey)
+        )
+        helper.replyToProbe.expectMsg(max = awaitTimeout,
+                                      hint = "Awaiting RequestValueStore message",
+                                      RequestValueStore
+        )
         ejea.stateName should be(WaitingForValueStore)
       }
     }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingRestartCheckTokenSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingRestartCheckTokenSpec.scala
index 186b67aa1af..968378414da 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingRestartCheckTokenSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRequestingRestartCheckTokenSpec.scala
@@ -5,9 +5,12 @@ import cromwell.engine.workflow.tokens.JobTokenDispenserActor.JobTokenDispensed
 import cromwell.jobstore.JobStoreActor.QueryJobCompletion
 import org.scalatest.concurrent.Eventually
 
-class EjeaRequestingRestartCheckTokenSpec extends EngineJobExecutionActorSpec with CanValidateJobStoreKey with Eventually {
+class EjeaRequestingRestartCheckTokenSpec
+    extends EngineJobExecutionActorSpec
+    with CanValidateJobStoreKey
+    with Eventually {
 
-  override implicit val stateUnderTest: EngineJobExecutionActorState = RequestingRestartCheckToken
+  implicit override val stateUnderTest: EngineJobExecutionActorState = RequestingRestartCheckToken
 
   "An EJEA in the RequestingRestartTokenCheck state" should {
 
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRunningJobSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRunningJobSpec.scala
index 774c334d098..599d0fca6c6 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRunningJobSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaRunningJobSpec.scala
@@ -4,15 +4,27 @@ import cromwell.core.callcaching._
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.HashError
 import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec.EnhancedTestEJEA
 import cromwell.engine.workflow.lifecycle.execution.ejea.HasJobSuccessResponse.SuccessfulCallCacheHashes
-import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor.{FailedResponseData, ResponsePendingData, RunningJob, SucceededResponseData}
+import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor.{
+  FailedResponseData,
+  ResponsePendingData,
+  RunningJob,
+  SucceededResponseData
+}
 import org.scalatest.concurrent.Eventually
 
 import scala.util.control.NoStackTrace
 import scala.util.{Failure, Success}
 
-class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually with CanValidateJobStoreKey with CanExpectJobStoreWrites with CanExpectCacheWrites with HasJobSuccessResponse with HasJobFailureResponses {
+class EjeaRunningJobSpec
+    extends EngineJobExecutionActorSpec
+    with Eventually
+    with CanValidateJobStoreKey
+    with CanExpectJobStoreWrites
+    with CanExpectCacheWrites
+    with HasJobSuccessResponse
+    with HasJobFailureResponses {
 
-  override implicit val stateUnderTest = RunningJob
+  implicit override val stateUnderTest = RunningJob
 
   val hashError = HashError(new Exception("ARGH!!!") with NoStackTrace)
 
@@ -23,7 +35,6 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
 
   "A 'RunningJob' EJEA" should {
     CallCachingModes foreach { mode =>
-
       /* *************************** */
       /* JobAbortedResponse Handling */
       /* *************************** */
@@ -43,7 +54,7 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
       s"Handle receiving a JobAbortedResponse correctly in $mode mode with successful hashes" in {
         ejea = ejeaInRunningState(mode)
         ejea ! SuccessfulCallCacheHashes
-        eventually { ejea.stateData should be(initialData.copy(hashes = Some(Success(SuccessfulCallCacheHashes)))) }
+        eventually(ejea.stateData should be(initialData.copy(hashes = Some(Success(SuccessfulCallCacheHashes)))))
         ejea.stateName should be(RunningJob)
 
         ejea ! abortedResponse
@@ -59,7 +70,7 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
       s"Handle receiving a JobAbortedResponse correctly in $mode mode with failed hashes" in {
         ejea = ejeaInRunningState(mode)
         ejea ! hashError
-        eventually { ejea.stateData should be(initialData.copy(hashes = Some(Failure(hashError.reason)))) }
+        eventually(ejea.stateData should be(initialData.copy(hashes = Some(Failure(hashError.reason)))))
         ejea.stateName should be(RunningJob)
 
         ejea ! abortedResponse
@@ -85,7 +96,7 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
         s"Handle receiving SuccessResponse then CallCacheHashes correctly in $mode mode" in {
           ejea = ejeaInRunningState(mode)
           ejea ! successResponse
-          eventually { ejea.stateData should be(SucceededResponseData(successResponse, None)) }
+          eventually(ejea.stateData should be(SucceededResponseData(successResponse, None)))
           ejea.stateName should be(RunningJob)
           ejea ! SuccessfulCallCacheHashes
           expectCacheWrite(successResponse, SuccessfulCallCacheHashes)
@@ -94,7 +105,7 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
         s"Handle receiving CallCacheHashes then SuccessResponse correctly in $mode mode" in {
           ejea = ejeaInRunningState(mode)
           ejea ! SuccessfulCallCacheHashes
-          eventually { ejea.stateData should be(initialData.copy(hashes = Some(Success(SuccessfulCallCacheHashes)))) }
+          eventually(ejea.stateData should be(initialData.copy(hashes = Some(Success(SuccessfulCallCacheHashes)))))
           ejea.stateName should be(RunningJob)
           ejea ! successResponse
           expectCacheWrite(successResponse, SuccessfulCallCacheHashes)
@@ -103,7 +114,7 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
         s"Handle receiving SuccessResponse then HashError correctly in $mode mode" in {
           ejea = ejeaInRunningState(mode)
           ejea ! successResponse
-          eventually { ejea.stateData should be(SucceededResponseData(successResponse, None)) }
+          eventually(ejea.stateData should be(SucceededResponseData(successResponse, None)))
           ejea.stateName should be(RunningJob)
           ejea ! hashError
           expectJobStoreWrite(SucceededResponseData(successResponse, Some(Failure(hashError.reason))))
@@ -112,7 +123,11 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
         s"Handle receiving HashError then SuccessResponse correctly in $mode mode" in {
           ejea = ejeaInRunningState(mode)
           ejea ! hashError
-          eventually { ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, Some(Failure(hashError.reason)))) }
+          eventually {
+            ejea.stateData should be(
+              ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, Some(Failure(hashError.reason)))
+            )
+          }
           ejea.stateName should be(RunningJob)
           ejea ! successResponse
           expectJobStoreWrite(SucceededResponseData(successResponse, Some(Failure(hashError.reason))))
@@ -125,11 +140,13 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
             val failedResponse = responseMaker()
             ejea = ejeaInRunningState(mode)
             ejea ! failedResponse
-            eventually { ejea.stateData should be(FailedResponseData(failedResponse, None)) }
+            eventually(ejea.stateData should be(FailedResponseData(failedResponse, None)))
             ejea.stateName should be(RunningJob)
             ejea ! SuccessfulCallCacheHashes
             // Don't expect cache write here (the job failed !) but do expect job store write
-            expectJobStoreWriteFailed(FailedResponseData(failedResponse, Option(Success(SuccessfulCallCacheHashes))), retryable)
+            expectJobStoreWriteFailed(FailedResponseData(failedResponse, Option(Success(SuccessfulCallCacheHashes))),
+                                      retryable
+            )
             helper.callCacheWriteActorProbe.expectNoMessage(awaitAlmostNothing)
           }
 
@@ -138,10 +155,12 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
             ejea = ejeaInRunningState(mode)
             ejea.stateName should be(RunningJob)
             ejea ! SuccessfulCallCacheHashes
-            eventually { ejea.stateData should be(initialData.copy(hashes = Some(Success(SuccessfulCallCacheHashes)))) }
+            eventually(ejea.stateData should be(initialData.copy(hashes = Some(Success(SuccessfulCallCacheHashes)))))
             ejea ! failedResponse
             // Don't expect cache write here (the job failed !) but do expect job store write
-            expectJobStoreWriteFailed(FailedResponseData(failedResponse, Option(Success(SuccessfulCallCacheHashes))), retryable)
+            expectJobStoreWriteFailed(FailedResponseData(failedResponse, Option(Success(SuccessfulCallCacheHashes))),
+                                      retryable
+            )
             helper.callCacheWriteActorProbe.expectNoMessage(awaitAlmostNothing)
           }
 
@@ -149,7 +168,7 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
             val failedResponse = responseMaker()
             ejea = ejeaInRunningState(mode)
             ejea ! failedResponse
-            eventually { ejea.stateData should be(FailedResponseData(failedResponse, None)) }
+            eventually(ejea.stateData should be(FailedResponseData(failedResponse, None)))
             ejea.stateName should be(RunningJob)
             ejea ! hashError
             expectJobStoreWriteFailed(FailedResponseData(failedResponse, Some(Failure(hashError.reason))), retryable)
@@ -160,7 +179,11 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
             val failedResponse = responseMaker()
             ejea = ejeaInRunningState(mode)
             ejea ! hashError
-            eventually { ejea.stateData should be(ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, Some(Failure(hashError.reason)))) }
+            eventually {
+              ejea.stateData should be(
+                ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, Some(Failure(hashError.reason)))
+              )
+            }
             ejea.stateName should be(RunningJob)
             ejea ! failedResponse
             expectJobStoreWriteFailed(FailedResponseData(failedResponse, Some(Failure(hashError.reason))), retryable)
@@ -179,7 +202,7 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
         s"Handle receiving a SucceededResponse correctly in $mode mode with successful hashes" in {
           ejea = ejeaInRunningState(mode)
           ejea ! SuccessfulCallCacheHashes
-          eventually { ejea.stateData should be(initialData.copy(hashes = Some(Success(SuccessfulCallCacheHashes)))) }
+          eventually(ejea.stateData should be(initialData.copy(hashes = Some(Success(SuccessfulCallCacheHashes)))))
           ejea.stateName should be(RunningJob)
           ejea ! successResponse
           // Even if we received hashes, writeToCache is false so we go straight to job store and don't write them to the cache
@@ -190,7 +213,7 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
         s"Handle receiving a SucceededResponse correctly in $mode mode with failed hashes" in {
           ejea = ejeaInRunningState(mode)
           ejea ! hashError
-          eventually { ejea.stateData should be(initialData.copy(hashes = Some(Failure(hashError.reason)))) }
+          eventually(ejea.stateData should be(initialData.copy(hashes = Some(Failure(hashError.reason)))))
           ejea.stateName should be(RunningJob)
           ejea ! successResponse
           // Even if we received hashes, writeToCache is false so we go straight to job store and don't write them to the cache
@@ -212,10 +235,12 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
             val failedResponse = responseMaker()
             ejea = ejeaInRunningState(mode)
             ejea ! SuccessfulCallCacheHashes
-            eventually { ejea.stateData should be(initialData.copy(hashes = Some(Success(SuccessfulCallCacheHashes)))) }
+            eventually(ejea.stateData should be(initialData.copy(hashes = Some(Success(SuccessfulCallCacheHashes)))))
             ejea.stateName should be(RunningJob)
             ejea ! failedResponse
-            expectJobStoreWriteFailed(FailedResponseData(failedResponse, Some(Success(SuccessfulCallCacheHashes))), retryable)
+            expectJobStoreWriteFailed(FailedResponseData(failedResponse, Some(Success(SuccessfulCallCacheHashes))),
+                                      retryable
+            )
             helper.callCacheWriteActorProbe.expectNoMessage(awaitAlmostNothing)
           }
 
@@ -223,7 +248,7 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
             val failedResponse = responseMaker()
             ejea = ejeaInRunningState(mode)
             ejea ! hashError
-            eventually { ejea.stateData should be(initialData.copy(hashes = Some(Failure(hashError.reason)))) }
+            eventually(ejea.stateData should be(initialData.copy(hashes = Some(Failure(hashError.reason)))))
             ejea.stateName should be(RunningJob)
             ejea ! failedResponse
             expectJobStoreWriteFailed(FailedResponseData(failedResponse, Some(Failure(hashError.reason))), retryable)
@@ -235,5 +260,6 @@ class EjeaRunningJobSpec extends EngineJobExecutionActorSpec with Eventually wit
   }
 
   def initialData = ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, None)
-  def ejeaInRunningState(mode: CallCachingMode = CallCachingActivity(ReadAndWriteCache)) = helper.buildEJEA(callCachingMode = mode).setStateInline(state = RunningJob, data = initialData)
+  def ejeaInRunningState(mode: CallCachingMode = CallCachingActivity(ReadAndWriteCache)) =
+    helper.buildEJEA(callCachingMode = mode).setStateInline(state = RunningJob, data = initialData)
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingCallCacheSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingCallCacheSpec.scala
index c12b3ffceeb..d9a273c4cc0 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingCallCacheSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingCallCacheSpec.scala
@@ -8,9 +8,13 @@ import cromwell.engine.workflow.lifecycle.execution.ejea.HasJobSuccessResponse.S
 import scala.util.Success
 import scala.util.control.NoStackTrace
 
-class EjeaUpdatingCallCacheSpec extends EngineJobExecutionActorSpec with HasJobSuccessResponse with CanExpectJobStoreWrites with HasJobFailureResponses {
+class EjeaUpdatingCallCacheSpec
+    extends EngineJobExecutionActorSpec
+    with HasJobSuccessResponse
+    with CanExpectJobStoreWrites
+    with HasJobFailureResponses {
 
-  override implicit val stateUnderTest = UpdatingCallCache
+  implicit override val stateUnderTest = UpdatingCallCache
 
   "An EJEA in UpdatingCallCache state" should {
 
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingJobStoreSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingJobStoreSpec.scala
index 61cb2eb693e..cd585df22b8 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingJobStoreSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaUpdatingJobStoreSpec.scala
@@ -8,9 +8,12 @@ import cromwell.engine.workflow.lifecycle.execution.ejea.HasJobSuccessResponse.S
 
 import scala.util.Success
 
-class EjeaUpdatingJobStoreSpec extends EngineJobExecutionActorSpec with HasJobSuccessResponse with HasJobFailureResponses {
+class EjeaUpdatingJobStoreSpec
+    extends EngineJobExecutionActorSpec
+    with HasJobSuccessResponse
+    with HasJobFailureResponses {
 
-  override implicit val stateUnderTest = UpdatingJobStore
+  implicit override val stateUnderTest = UpdatingJobStore
 
   "An EJEA in UpdatingJobStoreSpec" should {
 
@@ -31,7 +34,9 @@ class EjeaUpdatingJobStoreSpec extends EngineJobExecutionActorSpec with HasJobSu
     s"Create a suitable failure if the JobStore write fails" in {
       val response = successResponse
       ejea = ejeaInUpdatingJobStoreState(response)
-      val exception = new Exception("I loved Ophelia: forty thousand brothers\\ Could not, with all their quantity of love,\\ Make up my sum. What wilt thou do for her?")
+      val exception = new Exception(
+        "I loved Ophelia: forty thousand brothers\\ Could not, with all their quantity of love,\\ Make up my sum. What wilt thou do for her?"
+      )
       ejea ! JobStoreWriteFailure(exception)
       helper.replyToProbe.expectMsgPF(awaitTimeout) {
         case JobFailedNonRetryableResponse(jobDescriptorKey, reason, None) =>
@@ -43,7 +48,8 @@ class EjeaUpdatingJobStoreSpec extends EngineJobExecutionActorSpec with HasJobSu
   }
 
   def ejeaInUpdatingJobStoreState(response: BackendJobExecutionResponse) = {
-    val pendingResponseData = ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, Some(Success(SuccessfulCallCacheHashes)))
+    val pendingResponseData =
+      ResponsePendingData(helper.backendJobDescriptor, helper.bjeaProps, Some(Success(SuccessfulCallCacheHashes)))
     val newData = response match {
       case success: JobSucceededResponse => pendingResponseData.withSuccessResponse(success)
       case failed: BackendJobFailedResponse => pendingResponseData.withFailedResponse(failed)
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaWaitingForValueStoreSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaWaitingForValueStoreSpec.scala
index 983f622a22e..304d94303f7 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaWaitingForValueStoreSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EjeaWaitingForValueStoreSpec.scala
@@ -7,17 +7,21 @@ import cromwell.engine.workflow.lifecycle.execution.stores.ValueStore
 
 class EjeaWaitingForValueStoreSpec extends EngineJobExecutionActorSpec {
 
-  override implicit val stateUnderTest = CheckingJobStore
+  implicit override val stateUnderTest = CheckingJobStore
 
   "An EJEA in EjeaWaitingForValueStore state should" should {
     "prepare the job when receiving the output store" in {
       createWaitingForValueStoreEjea()
       val valueStore = ValueStore.empty
       ejea ! valueStore
-      helper.jobPreparationProbe.expectMsg(awaitTimeout, "expecting CallPreparation Start", CallPreparation.Start(valueStore))
+      helper.jobPreparationProbe.expectMsg(awaitTimeout,
+                                           "expecting CallPreparation Start",
+                                           CallPreparation.Start(valueStore)
+      )
       ejea.stateName should be(PreparingJob)
     }
   }
 
-  private def createWaitingForValueStoreEjea(): Unit = { ejea = helper.buildEJEA(restarting = true).setStateInline(state = WaitingForValueStore, data = NoData) }
+  private def createWaitingForValueStoreEjea(): Unit = ejea =
+    helper.buildEJEA(restarting = true).setStateInline(state = WaitingForValueStore, data = NoData)
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpec.scala
index e1e613a6189..24a6be01ffc 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpec.scala
@@ -16,8 +16,11 @@ import org.scalatest.wordspec.AnyWordSpecLike
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-trait EngineJobExecutionActorSpec extends AbstractEngineJobExecutionActorSpec
-  with Matchers with BeforeAndAfterAll with BeforeAndAfter {
+trait EngineJobExecutionActorSpec
+    extends AbstractEngineJobExecutionActorSpec
+    with Matchers
+    with BeforeAndAfterAll
+    with BeforeAndAfter {
 
   // If we WANT something to happen, make sure it happens within this window:
   val awaitTimeout: FiniteDuration = 10 seconds
@@ -28,7 +31,8 @@ trait EngineJobExecutionActorSpec extends AbstractEngineJobExecutionActorSpec
 
   val allowMultipleCacheCycles = false
 
-  implicit override val patienceConfig: PatienceConfig = PatienceConfig(timeout = scaled(awaitTimeout), interval = scaled(awaitAlmostNothing))
+  implicit override val patienceConfig: PatienceConfig =
+    PatienceConfig(timeout = scaled(awaitTimeout), interval = scaled(awaitAlmostNothing))
 
   // The default values for these are "null". The helper is created in "before", the ejea is up to the test cases
   private[ejea] var helper: PerTestHelper = _
@@ -42,7 +46,8 @@ trait EngineJobExecutionActorSpec extends AbstractEngineJobExecutionActorSpec
     List(
       ("FetchCachedResultsActor", helper.fetchCachedResultsActorCreations),
       ("JobHashingActor", helper.jobHashingInitializations),
-      ("CallCacheInvalidateActor", helper.invalidateCacheActorCreations)) foreach {
+      ("CallCacheInvalidateActor", helper.invalidateCacheActorCreations)
+    ) foreach {
       case (name, GotTooMany(list)) if !allowMultipleCacheCycles => fail(s"Too many $name creations (${list.size})")
       case _ => // Fine.
     }
@@ -51,15 +56,23 @@ trait EngineJobExecutionActorSpec extends AbstractEngineJobExecutionActorSpec
   }
 
   // Some helper lists
-  val CallCachingModes = List(CallCachingOff, CallCachingActivity(ReadCache), CallCachingActivity(WriteCache), CallCachingActivity(ReadAndWriteCache))
-  case class RestartOrExecuteCommandTuple(operationName: String, restarting: Boolean, expectedMessageToBjea: BackendJobExecutionActorCommand)
+  val CallCachingModes = List(CallCachingOff,
+                              CallCachingActivity(ReadCache),
+                              CallCachingActivity(WriteCache),
+                              CallCachingActivity(ReadAndWriteCache)
+  )
+  case class RestartOrExecuteCommandTuple(operationName: String,
+                                          restarting: Boolean,
+                                          expectedMessageToBjea: BackendJobExecutionActorCommand
+  )
   val RestartOrExecuteCommandTuples = List(
     RestartOrExecuteCommandTuple("execute", restarting = false, BackendJobExecutionActor.ExecuteJobCommand),
-    RestartOrExecuteCommandTuple("restart", restarting = true, BackendJobExecutionActor.RecoverJobCommand))
+    RestartOrExecuteCommandTuple("restart", restarting = true, BackendJobExecutionActor.RecoverJobCommand)
+  )
 }
 
 object EngineJobExecutionActorSpec {
-  implicit class EnhancedTestEJEA[S,D,T <: Actor](me: TestFSMRef[S, D, T]) {
+  implicit class EnhancedTestEJEA[S, D, T <: Actor](me: TestFSMRef[S, D, T]) {
     // Like setState, but mirrors back the EJEA (for easier inlining)
     def setStateInline(state: S = me.stateName, data: D = me.stateData): TestFSMRef[S, D, T] = {
       me.setState(state, data)
@@ -127,8 +140,16 @@ object AbstractEngineJobExecutionActorSpec {
   private lazy val testConfig = ConfigFactory.parseString(ConfigText)
 }
 
-abstract class AbstractEngineJobExecutionActorSpec extends TestKitSuite
-  with DefaultTimeout with ImplicitSender with Matchers with ScalaFutures with Eventually with Suite
-  with OneInstancePerTest with BeforeAndAfterAll with AnyWordSpecLike {
+abstract class AbstractEngineJobExecutionActorSpec
+    extends TestKitSuite
+    with DefaultTimeout
+    with ImplicitSender
+    with Matchers
+    with ScalaFutures
+    with Eventually
+    with Suite
+    with OneInstancePerTest
+    with BeforeAndAfterAll
+    with AnyWordSpecLike {
   override protected lazy val actorSystemConfig: Config = AbstractEngineJobExecutionActorSpec.testConfig
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpecUtil.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpecUtil.scala
index bf4722c6370..d9917f37404 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpecUtil.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorSpecUtil.scala
@@ -1,11 +1,16 @@
 package cromwell.engine.workflow.lifecycle.execution.ejea
 
-import cromwell.backend.BackendCacheHitCopyingActor.{CopyingOutputsFailedResponse, CopyAttemptError, BlacklistSkip}
+import cromwell.backend.BackendCacheHitCopyingActor.{BlacklistSkip, CopyAttemptError, CopyingOutputsFailedResponse}
 import cromwell.backend.{BackendJobDescriptor, MetricableCacheCopyErrorCategory}
 import cromwell.backend.BackendJobExecutionActor._
 import cromwell.core.callcaching._
 import cromwell.engine.workflow.lifecycle.execution.callcaching.EngineJobHashingActor.{CallCacheHashes, FileHashes}
-import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor.{EJEAData, SucceededResponseData, UpdatingCallCache, UpdatingJobStore}
+import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor.{
+  EJEAData,
+  SucceededResponseData,
+  UpdatingCallCache,
+  UpdatingJobStore
+}
 import cromwell.jobstore.JobStoreActor.RegisterJobCompleted
 import cromwell.jobstore.{JobResultFailure, JobResultSuccess, JobStoreKey}
 import cromwell.services.CallCaching.CallCachingEntryId
@@ -27,13 +32,14 @@ private[ejea] trait CanValidateJobStoreKey { self: EngineJobExecutionActorSpec =
 
 private[ejea] trait CanExpectCacheWrites extends Eventually { self: EngineJobExecutionActorSpec =>
   def expectCacheWrite(expectedResponse: JobSucceededResponse, expectedCallCacheHashes: CallCacheHashes): Unit = {
-    eventually { ejea.stateName should be(UpdatingCallCache) }
+    eventually(ejea.stateName should be(UpdatingCallCache))
     ejea.stateData should be(SucceededResponseData(expectedResponse, Some(Success(expectedCallCacheHashes))))
     ()
   }
 }
 
-private[ejea] trait CanExpectJobStoreWrites extends CanValidateJobStoreKey { self: EngineJobExecutionActorSpec with HasJobSuccessResponse with HasJobFailureResponses =>
+private[ejea] trait CanExpectJobStoreWrites extends CanValidateJobStoreKey {
+  self: EngineJobExecutionActorSpec with HasJobSuccessResponse with HasJobFailureResponses =>
 
   def expectJobStoreWrite(expectedData: EJEAData): Unit = {
     helper.jobStoreProbe.expectMsgPF(max = awaitTimeout, hint = "Job Store Write") {
@@ -63,7 +69,7 @@ private[ejea] trait CanExpectJobStoreWrites extends CanValidateJobStoreKey { sel
 
 private[ejea] trait CanExpectHashingInitialization extends Eventually { self: EngineJobExecutionActorSpec =>
   def expectHashingActorInitialization(mode: CallCachingMode, jobDescriptor: BackendJobDescriptor): Unit = {
-    eventually { helper.jobHashingInitializations.hasExactlyOne should be(true) }
+    eventually(helper.jobHashingInitializations.hasExactlyOne should be(true))
     helper.jobHashingInitializations.checkIt { initialization =>
       initialization._1 should be(jobDescriptor)
       initialization._2 should be(mode)
@@ -86,7 +92,7 @@ private[ejea] trait CanExpectFetchCachedResults extends Eventually { self: Engin
 
 private[ejea] trait CanExpectCacheInvalidation extends Eventually { self: EngineJobExecutionActorSpec =>
   def expectInvalidateCallCacheActor(expectedCacheId: CallCachingEntryId): Unit = {
-    eventually { helper.invalidateCacheActorCreations.hasExactlyOne should be(true) }
+    eventually(helper.invalidateCacheActorCreations.hasExactlyOne should be(true))
     helper.invalidateCacheActorCreations.checkIt { cacheId =>
       cacheId shouldBe expectedCacheId
     }
@@ -96,16 +102,25 @@ private[ejea] trait CanExpectCacheInvalidation extends Eventually { self: Engine
 private[ejea] trait HasJobSuccessResponse { self: EngineJobExecutionActorSpec =>
   val successRc = Option(171)
   val successOutputs = WomMocks.mockOutputExpectations(Map("a" -> WomInteger(3), "b" -> WomString("bee")))
-  def successResponse = JobSucceededResponse(helper.jobDescriptorKey, successRc, successOutputs, None, Seq.empty, None, resultGenerationMode = RunOnBackend)
+  def successResponse = JobSucceededResponse(helper.jobDescriptorKey,
+                                             successRc,
+                                             successOutputs,
+                                             None,
+                                             Seq.empty,
+                                             None,
+                                             resultGenerationMode = RunOnBackend
+  )
 }
 private[ejea] object HasJobSuccessResponse {
   val SuccessfulCallCacheHashes = CallCacheHashes(
     Set(HashResult(HashKey("whatever you want"), HashValue("whatever you need"))),
     "initialHash",
-    Option(FileHashes(
-      Set(HashResult(HashKey("whatever file you want"), HashValue("whatever file you need"))),
-      "fileHash"
-    ))
+    Option(
+      FileHashes(
+        Set(HashResult(HashKey("whatever file you want"), HashValue("whatever file you need"))),
+        "fileHash"
+      )
+    )
   )
 }
 
@@ -123,6 +138,11 @@ private[ejea] trait HasCopyFailureResponses { self: EngineJobExecutionActorSpec
     new Exception("Deliberate failure for test case: failed to copy cache outputs!") with NoStackTrace
 
   // Need to delay making the response because job descriptors come from the per-test "helper", which is null outside tests!
-  def copyAttemptFailedResponse(attemptNumber: Int) = CopyingOutputsFailedResponse(helper.jobDescriptorKey, attemptNumber, CopyAttemptError(copyFailureReason))
-  def cacheHitBlacklistedResponse(attemptNumber: Int) = CopyingOutputsFailedResponse(helper.jobDescriptorKey, attemptNumber, BlacklistSkip(MetricableCacheCopyErrorCategory.BucketBlacklisted))
+  def copyAttemptFailedResponse(attemptNumber: Int) =
+    CopyingOutputsFailedResponse(helper.jobDescriptorKey, attemptNumber, CopyAttemptError(copyFailureReason))
+  def cacheHitBlacklistedResponse(attemptNumber: Int) = CopyingOutputsFailedResponse(
+    helper.jobDescriptorKey,
+    attemptNumber,
+    BlacklistSkip(MetricableCacheCopyErrorCategory.BucketBlacklisted)
+  )
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorTransitionsSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorTransitionsSpec.scala
index c4b532f9453..dad095c7002 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorTransitionsSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/EngineJobExecutionActorTransitionsSpec.scala
@@ -20,13 +20,13 @@ class EngineJobExecutionActorTransitionsSpec extends AnyFlatSpec with CromwellTi
 
     val cacheReadCycles = 5
 
-    val longCallCachingCycleStateSequence = List(
-      Pending,
-      RequestingExecutionToken,
-      CheckingJobStore,
-      CheckingCallCache,
-      FetchingCachedOutputsFromDatabase,
-      CheckingCacheEntryExistence) ++ callCachingStateCycle * cacheReadCycles ++ List(
+    val longCallCachingCycleStateSequence = List(Pending,
+                                                 RequestingExecutionToken,
+                                                 CheckingJobStore,
+                                                 CheckingCallCache,
+                                                 FetchingCachedOutputsFromDatabase,
+                                                 CheckingCacheEntryExistence
+    ) ++ callCachingStateCycle * cacheReadCycles ++ List(
       WaitingForValueStore,
       PreparingJob,
       RunningJob,
@@ -39,26 +39,28 @@ class EngineJobExecutionActorTransitionsSpec extends AnyFlatSpec with CromwellTi
     val transitionSequence = longCallCachingCycleStateSequence.sliding(2) map {
       case fromState :: toState :: _ => EngineJobExecutionActorState.transitionEventString(fromState, toState)
       case _ => fail("Programmer blunder. This test writer had one job to do...")
-    } collect {
-      case Some(stateName) => stateName
+    } collect { case Some(stateName) =>
+      stateName
     }
 
-    transitionSequence.toList should be(List(
-      // "Pending", <-- NB: There's no transition into "Pending" because that was the start state
-      "RequestingExecutionToken",
-      "CheckingJobStore",
-      "CallCacheReading",
-      "WaitingForValueStore",
-      "PreparingJob",
-      "RunningJob",
-      "UpdatingCallCache",
-      "UpdatingJobStore",
-    ))
+    transitionSequence.toList should be(
+      List(
+        // "Pending", <-- NB: There's no transition into "Pending" because that was the start state
+        "RequestingExecutionToken",
+        "CheckingJobStore",
+        "CallCacheReading",
+        "WaitingForValueStore",
+        "PreparingJob",
+        "RunningJob",
+        "UpdatingCallCache",
+        "UpdatingJobStore"
+      )
+    )
   }
 }
 
 object EngineJobExecutionActorTransitionsSpec {
   implicit class MultipliableList[A](val list: List[A]) extends AnyVal {
-    final def *(i: Int): List[A] = if (i == 0 ) List.empty else if (i == 1) list else list ++ (list * (i - 1))
+    final def *(i: Int): List[A] = if (i == 0) List.empty else if (i == 1) list else list ++ (list * (i - 1))
   }
 }
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/ExpectOne.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/ExpectOne.scala
index efc5f5966fd..ff142e48a59 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/ExpectOne.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/ExpectOne.scala
@@ -1,8 +1,12 @@
 package cromwell.engine.workflow.lifecycle.execution.ejea
 
-private[ejea] sealed trait ExpectOne[+A] {
-  def checkIt(block: A => Any): Unit = throw new IllegalStateException("This ExpectOne must have exactly one element for checkIt to work")
-  def checkLatest(block: A => Any): Unit = throw new IllegalStateException("This ExpectOne must have at least one element for checkLatest to work")
+sealed private[ejea] trait ExpectOne[+A] {
+  def checkIt(block: A => Any): Unit = throw new IllegalStateException(
+    "This ExpectOne must have exactly one element for checkIt to work"
+  )
+  def checkLatest(block: A => Any): Unit = throw new IllegalStateException(
+    "This ExpectOne must have at least one element for checkLatest to work"
+  )
   def hasAtLeastOne: Boolean
   def hasExactlyOne: Boolean
   def foundOne[B >: A](theFoundOne: B) = this match {
@@ -25,7 +29,7 @@ private[ejea] case class GotOne[+A](theOne: A) extends ExpectOne[A] {
 }
 
 private[ejea] case class GotTooMany[+A](theOnes: List[A]) extends ExpectOne[A] {
-  override def checkLatest(block: A => Any): Unit = { block(theOnes.last); ()  }
+  override def checkLatest(block: A => Any): Unit = { block(theOnes.last); () }
   override def hasAtLeastOne = true
   override def hasExactlyOne = false
-}
\ No newline at end of file
+}
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/PerTestHelper.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/PerTestHelper.scala
index e1176318fc6..e72c8a90a45 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/PerTestHelper.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/execution/ejea/PerTestHelper.scala
@@ -10,7 +10,12 @@ import cromwell.core.{CallOutputs, HogGroup, WorkflowId, WorkflowOptions}
 import cromwell.engine.EngineWorkflowDescriptor
 import cromwell.engine.workflow.lifecycle.execution.ejea.EngineJobExecutionActorSpec._
 import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor
-import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor.{CallCachingParameters, EJEAData, EngineJobExecutionActorState, ResponsePendingData}
+import cromwell.engine.workflow.lifecycle.execution.job.EngineJobExecutionActor.{
+  CallCachingParameters,
+  EJEAData,
+  EngineJobExecutionActorState,
+  ResponsePendingData
+}
 import cromwell.engine.workflow.mocks.{DeclarationMock, TaskMock, WdlWomExpressionMock}
 import cromwell.services.CallCaching.CallCachingEntryId
 import cromwell.util.AkkaTestUtil._
@@ -26,7 +31,9 @@ import scala.concurrent.duration.FiniteDuration
 import scala.util.{Success, Try}
 
 private[ejea] class PerTestHelper(implicit val system: ActorSystem)
-  extends TaskMock with WdlWomExpressionMock with DeclarationMock {
+    extends TaskMock
+    with WdlWomExpressionMock
+    with DeclarationMock {
 
   val workflowId: WorkflowId = WorkflowId.randomId()
   val workflowName = "wf"
@@ -35,22 +42,26 @@ private[ejea] class PerTestHelper(implicit val system: ActorSystem)
   val jobIndex: Option[Int] = Option(1)
   val jobAttempt = 1
 
-  val task: CallableTaskDefinition = WomMocks.mockTaskDefinition(taskName).copy(
-    inputs = List(OverridableInputDefinitionWithDefault("inInt", WomIntegerType, mockIntExpression(543))),
-    outputs = List(OutputDefinition("outString", WomStringType, mockStringExpression("hello")))
-  )
+  val task: CallableTaskDefinition = WomMocks
+    .mockTaskDefinition(taskName)
+    .copy(
+      inputs = List(OverridableInputDefinitionWithDefault("inInt", WomIntegerType, mockIntExpression(543))),
+      outputs = List(OutputDefinition("outString", WomStringType, mockStringExpression("hello")))
+    )
 
   val call: CommandCallNode = WomMocks.mockTaskCall(WomIdentifier(taskName, jobFqn), task)
   val jobDescriptorKey: BackendJobDescriptorKey = BackendJobDescriptorKey(call, jobIndex, jobAttempt)
 
   val backendWorkflowDescriptor: BackendWorkflowDescriptor = BackendWorkflowDescriptor(id = workflowId,
-    callable = null,
-    knownValues = null,
-    workflowOptions = WorkflowOptions.empty,
-    customLabels = null,
-    hogGroup = HogGroup("foo"),
-    List.empty,
-    None)
+                                                                                       callable = null,
+                                                                                       knownValues = null,
+                                                                                       workflowOptions =
+                                                                                         WorkflowOptions.empty,
+                                                                                       customLabels = null,
+                                                                                       hogGroup = HogGroup("foo"),
+                                                                                       List.empty,
+                                                                                       None
+  )
   val backendJobDescriptor: BackendJobDescriptor =
     BackendJobDescriptor(
       workflowDescriptor = backendWorkflowDescriptor,
@@ -59,7 +70,7 @@ private[ejea] class PerTestHelper(implicit val system: ActorSystem)
       evaluatedTaskInputs = Map.empty,
       maybeCallCachingEligible = FloatingDockerTagWithoutHash("ubuntu:latest"),
       dockerSize = None,
-      prefetchedKvStoreEntries = Map.empty,
+      prefetchedKvStoreEntries = Map.empty
     )
 
   var fetchCachedResultsActorCreations: ExpectOne[(CallCachingEntryId, Seq[OutputDefinition])] = NothingYet
@@ -83,55 +94,75 @@ private[ejea] class PerTestHelper(implicit val system: ActorSystem)
   val jobExecutionTokenDispenserProbe: TestProbe = TestProbe()
   val ejhaProbe: TestProbe = TestProbe()
 
-  def buildFactory(backendConfigurationDescriptor: BackendConfigurationDescriptor): BackendLifecycleActorFactory = new BackendLifecycleActorFactory {
+  def buildFactory(backendConfigurationDescriptor: BackendConfigurationDescriptor): BackendLifecycleActorFactory =
+    new BackendLifecycleActorFactory {
 
-    override val name = "PerTestHelper"
+      override val name = "PerTestHelper"
 
-    override val configurationDescriptor: BackendConfigurationDescriptor = backendConfigurationDescriptor
+      override val configurationDescriptor: BackendConfigurationDescriptor = backendConfigurationDescriptor
 
-    override def jobExecutionActorProps(jobDescriptor: BackendJobDescriptor,
-                                        initializationData: Option[BackendInitializationData],
-                                        serviceRegistryActor: ActorRef,
-                                        ioActor: ActorRef,
-                                        backendSingletonActor: Option[ActorRef]): Props = bjeaProps
+      override def jobExecutionActorProps(jobDescriptor: BackendJobDescriptor,
+                                          initializationData: Option[BackendInitializationData],
+                                          serviceRegistryActor: ActorRef,
+                                          ioActor: ActorRef,
+                                          backendSingletonActor: Option[ActorRef]
+      ): Props = bjeaProps
 
-    override def cacheHitCopyingActorProps: Option[(BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Int, Option[BlacklistCache]) => Props] = Option((_, _, _, _, _, _) => callCacheHitCopyingProbe.props)
+      override def cacheHitCopyingActorProps: Option[
+        (BackendJobDescriptor,
+         Option[BackendInitializationData],
+         ActorRef,
+         ActorRef,
+         Int,
+         Option[BlacklistCache]
+        ) => Props
+      ] = Option((_, _, _, _, _, _) => callCacheHitCopyingProbe.props)
 
-    override def expressionLanguageFunctions(workflowDescriptor: BackendWorkflowDescriptor,
-                                             jobKey: BackendJobDescriptorKey,
-                                             initializationData: Option[BackendInitializationData],
-                                             ioActorProxy: ActorRef,
-                                             ec: ExecutionContext): IoFunctionSet = {
-      NoIoFunctionSet
-    }
+      override def expressionLanguageFunctions(workflowDescriptor: BackendWorkflowDescriptor,
+                                               jobKey: BackendJobDescriptorKey,
+                                               initializationData: Option[BackendInitializationData],
+                                               ioActorProxy: ActorRef,
+                                               ec: ExecutionContext
+      ): IoFunctionSet =
+        NoIoFunctionSet
 
-    override def fileHashingActorProps:
-    Option[(BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Option[ActorRef]) => Props] = {
-      Option((_, _, _, _, _) => Props.empty)
-    }
+      override def fileHashingActorProps: Option[
+        (BackendJobDescriptor, Option[BackendInitializationData], ActorRef, ActorRef, Option[ActorRef]) => Props
+      ] =
+        Option((_, _, _, _, _) => Props.empty)
 
-    // These two factory methods should never be called from EJEA or any of its descendants:
-    override def workflowFinalizationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                                ioActor: ActorRef,
-                                                calls: Set[CommandCallNode],
-                                                jobExecutionMap: JobExecutionMap,
-                                                workflowOutputs: CallOutputs,
-                                                initializationData: Option[BackendInitializationData]): Option[Props] = throw new UnsupportedOperationException("Unexpected finalization actor creation!")
-    override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
+      // These two factory methods should never be called from EJEA or any of its descendants:
+      override def workflowFinalizationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
                                                   ioActor: ActorRef,
                                                   calls: Set[CommandCallNode],
-                                                  serviceRegistryActor: ActorRef,
-                                                  restarting: Boolean): Option[Props] = throw new UnsupportedOperationException("Unexpected finalization actor creation!")
-  }
+                                                  jobExecutionMap: JobExecutionMap,
+                                                  workflowOutputs: CallOutputs,
+                                                  initializationData: Option[BackendInitializationData]
+      ): Option[Props] = throw new UnsupportedOperationException("Unexpected finalization actor creation!")
+      override def workflowInitializationActorProps(workflowDescriptor: BackendWorkflowDescriptor,
+                                                    ioActor: ActorRef,
+                                                    calls: Set[CommandCallNode],
+                                                    serviceRegistryActor: ActorRef,
+                                                    restarting: Boolean
+      ): Option[Props] = throw new UnsupportedOperationException("Unexpected finalization actor creation!")
+    }
 
   def buildEJEA(restarting: Boolean = true,
                 callCachingMode: CallCachingMode = CallCachingOff,
                 callCachingMaxFailedCopyAttempts: Int = 1000000,
-                backendConfigurationDescriptor: BackendConfigurationDescriptor = TestConfig.emptyBackendConfigDescriptor)
-               (implicit startingState: EngineJobExecutionActorState): TestFSMRef[EngineJobExecutionActorState, EJEAData, MockEjea] = {
+                backendConfigurationDescriptor: BackendConfigurationDescriptor = TestConfig.emptyBackendConfigDescriptor
+  )(implicit
+    startingState: EngineJobExecutionActorState
+  ): TestFSMRef[EngineJobExecutionActorState, EJEAData, MockEjea] = {
 
     val factory: BackendLifecycleActorFactory = buildFactory(backendConfigurationDescriptor)
-    val descriptor = EngineWorkflowDescriptor(WomMocks.mockWorkflowDefinition(workflowName), backendWorkflowDescriptor, null, null, null, callCachingMode)
+    val descriptor = EngineWorkflowDescriptor(WomMocks.mockWorkflowDefinition(workflowName),
+                                              backendWorkflowDescriptor,
+                                              null,
+                                              null,
+                                              null,
+                                              callCachingMode
+    )
 
     val callCachingParameters = CallCachingParameters(
       mode = callCachingMode,
@@ -143,23 +174,30 @@ private[ejea] class PerTestHelper(implicit val system: ActorSystem)
       fileHashBatchSize = 100
     )
 
-    val myBrandNewEjea = new TestFSMRef[EngineJobExecutionActorState, EJEAData, MockEjea](system, Props(new MockEjea(
-      helper = this,
-      jobPreparationProbe = jobPreparationProbe,
-      replyTo = replyToProbe.ref,
-      jobDescriptorKey = jobDescriptorKey,
-      workflowDescriptor = descriptor,
-      factory = factory,
-      initializationData = None,
-      restarting = restarting,
-      serviceRegistryActor = serviceRegistryProbe.ref,
-      ioActor = ioActorProbe.ref,
-      jobStoreActor = jobStoreProbe.ref,
-      dockerHashActor = dockerHashActorProbe.ref,
-      jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserProbe.ref,
-      jobExecutionTokenDispenserActor = jobExecutionTokenDispenserProbe.ref,
-      callCachingParameters = callCachingParameters
-    )), parentProbe.ref, s"EngineJobExecutionActorSpec-$workflowId")
+    val myBrandNewEjea = new TestFSMRef[EngineJobExecutionActorState, EJEAData, MockEjea](
+      system,
+      Props(
+        new MockEjea(
+          helper = this,
+          jobPreparationProbe = jobPreparationProbe,
+          replyTo = replyToProbe.ref,
+          jobDescriptorKey = jobDescriptorKey,
+          workflowDescriptor = descriptor,
+          factory = factory,
+          initializationData = None,
+          restarting = restarting,
+          serviceRegistryActor = serviceRegistryProbe.ref,
+          ioActor = ioActorProbe.ref,
+          jobStoreActor = jobStoreProbe.ref,
+          dockerHashActor = dockerHashActorProbe.ref,
+          jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserProbe.ref,
+          jobExecutionTokenDispenserActor = jobExecutionTokenDispenserProbe.ref,
+          callCachingParameters = callCachingParameters
+        )
+      ),
+      parentProbe.ref,
+      s"EngineJobExecutionActorSpec-$workflowId"
+    )
 
     deathwatch watch myBrandNewEjea
     myBrandNewEjea.setStateInline(state = startingState)
@@ -180,38 +218,41 @@ private[ejea] class MockEjea(helper: PerTestHelper,
                              dockerHashActor: ActorRef,
                              jobRestartCheckTokenDispenserActor: ActorRef,
                              jobExecutionTokenDispenserActor: ActorRef,
-                             callCachingParameters: EngineJobExecutionActor.CallCachingParameters) extends EngineJobExecutionActor(
-  replyTo = replyTo,
-  jobDescriptorKey = jobDescriptorKey,
-  workflowDescriptor = workflowDescriptor,
-  backendLifecycleActorFactory = factory,
-  initializationData = initializationData,
-  restarting = restarting,
-  serviceRegistryActor = serviceRegistryActor,
-  ioActor = ioActor,
-  jobStoreActor = jobStoreActor,
-  workflowDockerLookupActor = dockerHashActor,
-  jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
-  jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
-  backendSingletonActor = None,
-  command = if (restarting) RecoverJobCommand else ExecuteJobCommand,
-  callCachingParameters = callCachingParameters) {
+                             callCachingParameters: EngineJobExecutionActor.CallCachingParameters
+) extends EngineJobExecutionActor(
+      replyTo = replyTo,
+      jobDescriptorKey = jobDescriptorKey,
+      workflowDescriptor = workflowDescriptor,
+      backendLifecycleActorFactory = factory,
+      initializationData = initializationData,
+      restarting = restarting,
+      serviceRegistryActor = serviceRegistryActor,
+      ioActor = ioActor,
+      jobStoreActor = jobStoreActor,
+      workflowDockerLookupActor = dockerHashActor,
+      jobRestartCheckTokenDispenserActor = jobRestartCheckTokenDispenserActor,
+      jobExecutionTokenDispenserActor = jobExecutionTokenDispenserActor,
+      backendSingletonActor = None,
+      command = if (restarting) RecoverJobCommand else ExecuteJobCommand,
+      callCachingParameters = callCachingParameters
+    ) {
 
   implicit val system: ActorSystem = context.system
-  override def makeFetchCachedResultsActor(cacheId: CallCachingEntryId): Unit = {
-    helper.fetchCachedResultsActorCreations =
-      helper.fetchCachedResultsActorCreations.foundOne((cacheId, null))
-  }
+  override def makeFetchCachedResultsActor(cacheId: CallCachingEntryId): Unit =
+    helper.fetchCachedResultsActorCreations = helper.fetchCachedResultsActorCreations.foundOne((cacheId, null))
   override def initializeJobHashing(jobDescriptor: BackendJobDescriptor,
                                     activity: CallCachingActivity,
-                                    callCachingEligible: CallCachingEligible): Try[ActorRef] = {
+                                    callCachingEligible: CallCachingEligible
+  ): Try[ActorRef] = {
     helper.jobHashingInitializations = helper.jobHashingInitializations.foundOne((jobDescriptor, activity))
     Success(helper.ejhaProbe.ref)
   }
   override def createBackendJobExecutionActor(data: ResponsePendingData): ActorRef = helper.bjeaProbe.ref
-  override def invalidateCacheHit(cacheId: CallCachingEntryId): Unit = { helper.invalidateCacheActorCreations = helper.invalidateCacheActorCreations.foundOne(cacheId) }
+  override def invalidateCacheHit(cacheId: CallCachingEntryId): Unit = helper.invalidateCacheActorCreations =
+    helper.invalidateCacheActorCreations.foundOne(cacheId)
   override def createJobPreparationActor(jobPrepProps: Props, name: String): ActorRef = jobPreparationProbe.ref
   override def onTimedTransition(from: EngineJobExecutionActorState,
                                  to: EngineJobExecutionActorState,
-                                 duration: FiniteDuration): Unit = {}
+                                 duration: FiniteDuration
+  ): Unit = {}
 }
diff --git a/server/src/test/scala/cromwell/jobstore/JobStoreServiceSpec.scala b/server/src/test/scala/cromwell/jobstore/JobStoreServiceSpec.scala
index e2734b68fef..b1133d80e1d 100644
--- a/server/src/test/scala/cromwell/jobstore/JobStoreServiceSpec.scala
+++ b/server/src/test/scala/cromwell/jobstore/JobStoreServiceSpec.scala
@@ -24,8 +24,12 @@ object JobStoreServiceSpec {
   private val EmptyExpression = PlaceholderWomExpression(Set.empty, WomStringType)
 }
 
-class JobStoreServiceSpec extends CromwellTestKitWordSpec with Matchers with CoordinatedWorkflowStoreActorBuilder
-  with SqlWorkflowStoreBuilder with CromwellTimeoutSpec {
+class JobStoreServiceSpec
+    extends CromwellTestKitWordSpec
+    with Matchers
+    with CoordinatedWorkflowStoreActorBuilder
+    with SqlWorkflowStoreBuilder
+    with CromwellTimeoutSpec {
 
   "JobStoreService" should {
     "register Job and Workflow completions and read back (query) the result" in {
@@ -33,18 +37,18 @@ class JobStoreServiceSpec extends CromwellTestKitWordSpec with Matchers with Coo
         lazy val jobStore: JobStore = new SqlJobStore(EngineServicesStore.engineDatabaseInterface)
         val jobStoreService =
           system.actorOf(
-            props =
-              JobStoreActor.props(
-                database = jobStore,
-                registryActor = dummyServiceRegistryActor,
-                workflowStoreAccess = access("coordinatedAccessActor-register")(workflowStore)
-              ),
-            name = "jobStoreService-register",
+            props = JobStoreActor.props(
+              database = jobStore,
+              registryActor = dummyServiceRegistryActor,
+              workflowStoreAccess = access("coordinatedAccessActor-register")(workflowStore)
+            ),
+            name = "jobStoreService-register"
           )
 
         val workflowId = WorkflowId.randomId()
-        val mockTask = WomMocks.mockTaskDefinition("bar")
-        .copy(outputs = List(OutputDefinition("baz", WomStringType, EmptyExpression)))
+        val mockTask = WomMocks
+          .mockTaskDefinition("bar")
+          .copy(outputs = List(OutputDefinition("baz", WomStringType, EmptyExpression)))
         val successCall = WomMocks.mockTaskCall(WomIdentifier("bar"), definition = mockTask)
 
         val successKey = BackendJobDescriptorKey(successCall, None, 1).toJobStoreKey(workflowId)
@@ -68,12 +72,16 @@ class JobStoreServiceSpec extends CromwellTestKitWordSpec with Matchers with Coo
         jobStoreService ! QueryJobCompletion(failureKey, mockTask.outputs map WomMocks.mockOutputPort)
         expectMsgType[JobNotComplete.type](MaxWait)
 
-        jobStoreService ! RegisterJobCompleted(failureKey, JobResultFailure(Option(11), new IllegalArgumentException("Insufficient funds"), retryable = false))
+        jobStoreService ! RegisterJobCompleted(failureKey,
+                                               JobResultFailure(Option(11),
+                                                                new IllegalArgumentException("Insufficient funds"),
+                                                                retryable = false
+                                               )
+        )
         expectMsgType[JobStoreWriteSuccess](MaxWait)
 
         jobStoreService ! QueryJobCompletion(failureKey, mockTask.outputs map WomMocks.mockOutputPort)
-        expectMsgPF(MaxWait) {
-          case JobComplete(JobResultFailure(Some(11), _, false)) =>
+        expectMsgPF(MaxWait) { case JobComplete(JobResultFailure(Some(11), _, false)) =>
         }
 
         jobStoreService ! RegisterWorkflowCompleted(workflowId)
diff --git a/server/src/test/scala/cromwell/jobstore/JobStoreWriterSpec.scala b/server/src/test/scala/cromwell/jobstore/JobStoreWriterSpec.scala
index f8ba551dab5..50ee1c4281b 100644
--- a/server/src/test/scala/cromwell/jobstore/JobStoreWriterSpec.scala
+++ b/server/src/test/scala/cromwell/jobstore/JobStoreWriterSpec.scala
@@ -8,7 +8,12 @@ import cromwell.core.actor.BatchActor.{BatchActorState, CommandAndReplyTo, Proce
 import cromwell.core.{CallOutputs, WorkflowId}
 import cromwell.engine.workflow.{CoordinatedWorkflowStoreActorBuilder, SqlWorkflowStoreBuilder}
 import cromwell.jobstore.JobStore.{JobCompletion, WorkflowCompletion}
-import cromwell.jobstore.JobStoreActor.{JobStoreWriteSuccess, JobStoreWriterCommand, RegisterJobCompleted, RegisterWorkflowCompleted}
+import cromwell.jobstore.JobStoreActor.{
+  JobStoreWriterCommand,
+  JobStoreWriteSuccess,
+  RegisterJobCompleted,
+  RegisterWorkflowCompleted
+}
 import org.scalatest.BeforeAndAfter
 import org.scalatest.matchers.should.Matchers
 import wom.graph.GraphNodePort.OutputPort
@@ -17,7 +22,13 @@ import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future, Promise}
 import scala.language.postfixOps
 
-class JobStoreWriterSpec extends CromwellTestKitWordSpec with SqlWorkflowStoreBuilder with CoordinatedWorkflowStoreActorBuilder with Matchers with BeforeAndAfter with CromwellTimeoutSpec {
+class JobStoreWriterSpec
+    extends CromwellTestKitWordSpec
+    with SqlWorkflowStoreBuilder
+    with CoordinatedWorkflowStoreActorBuilder
+    with Matchers
+    with BeforeAndAfter
+    with CromwellTimeoutSpec {
 
   var database: WriteCountingJobStore = _
   var workflowId: WorkflowId = _
@@ -29,9 +40,13 @@ class JobStoreWriterSpec extends CromwellTestKitWordSpec with SqlWorkflowStoreBu
     workflowId = WorkflowId.randomId()
   }
 
-  private def sendRegisterCompletion(jobStoreWriter: TestFSMRef[BatchActorState, WeightedQueue[CommandAndReplyTo[JobStoreWriterCommand], Int], JobStoreWriterActor])(attempt: Int): Unit = {
+  private def sendRegisterCompletion(
+    jobStoreWriter: TestFSMRef[BatchActorState,
+                               WeightedQueue[CommandAndReplyTo[JobStoreWriterCommand], Int],
+                               JobStoreWriterActor
+    ]
+  )(attempt: Int): Unit =
     jobStoreWriter ! RegisterJobCompleted(jobKey(attempt), successResult)
-  }
 
   private def jobKey(attempt: Int): JobStoreKey = JobStoreKey(workflowId, s"call.fqn", None, attempt)
 
@@ -43,7 +58,7 @@ class JobStoreWriterSpec extends CromwellTestKitWordSpec with SqlWorkflowStoreBu
     ()
   }
 
-  //noinspection SameParameterValue
+  // noinspection SameParameterValue
   private def assertDb(totalWritesCalled: Int, jobCompletionsRecorded: Int, workflowCompletionsRecorded: Int): Unit = {
     database.totalWritesCalled shouldBe totalWritesCalled
     database.jobCompletionsRecorded shouldBe jobCompletionsRecorded
@@ -51,7 +66,7 @@ class JobStoreWriterSpec extends CromwellTestKitWordSpec with SqlWorkflowStoreBu
     ()
   }
 
-  //noinspection SameParameterValue
+  // noinspection SameParameterValue
   private def assertReceived(expectedJobStoreWriteAcks: Int): Unit = {
     val received = receiveN(expectedJobStoreWriteAcks, 10 seconds)
     received foreach {
@@ -73,9 +88,9 @@ class JobStoreWriterSpec extends CromwellTestKitWordSpec with SqlWorkflowStoreBu
               flushRate = flushFrequency,
               serviceRegistryActor = TestProbe("serviceRegistryActor-collapse").ref,
               threshold = 1000,
-              workflowStoreAccess = access("coordinatedAccessActor-collapse")(workflowStore),
+              workflowStoreAccess = access("coordinatedAccessActor-collapse")(workflowStore)
             ),
-            name = "jobStoreWriter-collapse",
+            name = "jobStoreWriter-collapse"
           )
 
         // Send a job completion. The database will hang.
@@ -111,9 +126,9 @@ class JobStoreWriterSpec extends CromwellTestKitWordSpec with SqlWorkflowStoreBu
               flushRate = flushFrequency,
               serviceRegistryActor = TestProbe("serviceRegistryActor-skip").ref,
               threshold = 1000,
-              workflowStoreAccess = access("coordinatedAccessActor-skip")(workflowStore),
+              workflowStoreAccess = access("coordinatedAccessActor-skip")(workflowStore)
             ),
-            "jobStoreWriter-skip",
+            "jobStoreWriter-skip"
           )
 
         // Send a job completion. The database will hang.
@@ -143,7 +158,10 @@ class JobStoreWriterSpec extends CromwellTestKitWordSpec with SqlWorkflowStoreBu
   }
 }
 
-class WriteCountingJobStore(var totalWritesCalled: Int, var jobCompletionsRecorded: Int, var workflowCompletionsRecorded: Int) extends JobStore {
+class WriteCountingJobStore(var totalWritesCalled: Int,
+                            var jobCompletionsRecorded: Int,
+                            var workflowCompletionsRecorded: Int
+) extends JobStore {
 
   // A Promise so that the calling tests can hang the writer on the db write.  Once the promise is completed the writer is
   // released and all further messages will be written immediately.
@@ -154,8 +172,10 @@ class WriteCountingJobStore(var totalWritesCalled: Int, var jobCompletionsRecord
     ()
   }
 
-  override def writeToDatabase(workflowCompletions: Seq[WorkflowCompletion], jobCompletions: Seq[JobCompletion], batchSize: Int)
-                              (implicit ec: ExecutionContext): Future[Unit] = {
+  override def writeToDatabase(workflowCompletions: Seq[WorkflowCompletion],
+                               jobCompletions: Seq[JobCompletion],
+                               batchSize: Int
+  )(implicit ec: ExecutionContext): Future[Unit] = {
 
     totalWritesCalled += 1
     jobCompletionsRecorded += jobCompletions.size
@@ -163,7 +183,9 @@ class WriteCountingJobStore(var totalWritesCalled: Int, var jobCompletionsRecord
     writePromise.future
   }
 
-  override def readJobResult(jobStoreKey: JobStoreKey, taskOutputs: Seq[OutputPort])(implicit ec: ExecutionContext): Future[Option[JobResult]] = throw new UnsupportedOperationException()
+  override def readJobResult(jobStoreKey: JobStoreKey, taskOutputs: Seq[OutputPort])(implicit
+    ec: ExecutionContext
+  ): Future[Option[JobResult]] = throw new UnsupportedOperationException()
 }
 
 object WriteCountingJobStore {
diff --git a/server/src/test/scala/cromwell/subworkflowstore/SubWorkflowStoreSpec.scala b/server/src/test/scala/cromwell/subworkflowstore/SubWorkflowStoreSpec.scala
index c52f356c87c..0b8aca0e890 100644
--- a/server/src/test/scala/cromwell/subworkflowstore/SubWorkflowStoreSpec.scala
+++ b/server/src/test/scala/cromwell/subworkflowstore/SubWorkflowStoreSpec.scala
@@ -29,14 +29,18 @@ object SubWorkflowStoreSpec {
   val EmptyExpression = WdlExpression.fromString(""" "" """)
 }
 
-class SubWorkflowStoreSpec extends CromwellTestKitWordSpec with CoordinatedWorkflowStoreActorBuilder
-  with CromwellTimeoutSpec with Matchers {
+class SubWorkflowStoreSpec
+    extends CromwellTestKitWordSpec
+    with CoordinatedWorkflowStoreActorBuilder
+    with CromwellTimeoutSpec
+    with Matchers {
   "SubWorkflowStore" should {
     "work" in {
       lazy val subWorkflowStore = new SqlSubWorkflowStore(EngineServicesStore.engineDatabaseInterface)
       val subWorkflowStoreService = system.actorOf(SubWorkflowStoreActor.props(subWorkflowStore))
 
-      lazy val workflowStore = SqlWorkflowStore(EngineServicesStore.engineDatabaseInterface, MetadataServicesStore.metadataDatabaseInterface)
+      lazy val workflowStore =
+        SqlWorkflowStore(EngineServicesStore.engineDatabaseInterface, MetadataServicesStore.metadataDatabaseInterface)
       val workflowHeartbeatConfig = WorkflowHeartbeatConfig(CromwellTestKitSpec.DefaultConfig)
       val workflowStoreService = system.actorOf(
         WorkflowStoreActor.props(
@@ -64,17 +68,19 @@ class SubWorkflowStoreSpec extends CromwellTestKitWordSpec with CoordinatedWorkf
         override def tag: String = "foobar"
       }
 
-      workflowStoreService ! SubmitWorkflow(WorkflowSourceFilesWithoutImports(
-        workflowSource = Option(""),
-        workflowUrl = None,
-        workflowRoot = None,
-        workflowType = Option("WDL"),
-        workflowTypeVersion = None,
-        inputsJson = "{}",
-        workflowOptions = WorkflowOptions.empty,
-        labelsJson = "{}",
-        warnings = Vector.empty,
-        requestedWorkflowId = None)
+      workflowStoreService ! SubmitWorkflow(
+        WorkflowSourceFilesWithoutImports(
+          workflowSource = Option(""),
+          workflowUrl = None,
+          workflowRoot = None,
+          workflowType = Option("WDL"),
+          workflowTypeVersion = None,
+          inputsJson = "{}",
+          workflowOptions = WorkflowOptions.empty,
+          labelsJson = "{}",
+          warnings = Vector.empty,
+          requestedWorkflowId = None
+        )
       )
       val rootWorkflowId = expectMsgType[WorkflowSubmittedToStore](10 seconds).workflowId
 
@@ -95,7 +101,7 @@ class SubWorkflowStoreSpec extends CromwellTestKitWordSpec with CoordinatedWorkf
         callIndex = jobKey.index.fromIndex,
         callAttempt = jobKey.attempt,
         subWorkflowExecutionUuid = subWorkflowId.toString,
-        subWorkflowStoreEntryId = Option(0),
+        subWorkflowStoreEntryId = Option(0)
       )
       expectMsg[SubWorkflowFound](SubWorkflowFound(subWorkflowEntry))
 
@@ -112,7 +118,7 @@ class SubWorkflowStoreSpec extends CromwellTestKitWordSpec with CoordinatedWorkf
         callIndex = jobKey.index.fromIndex,
         callAttempt = jobKey.attempt,
         subWorkflowExecutionUuid = subSubWorkflowId.toString,
-        subWorkflowStoreEntryId = Option(1),
+        subWorkflowStoreEntryId = Option(1)
       )
       expectMsg[SubWorkflowFound](SubWorkflowFound(subSubWorkflowEntry))
 
diff --git a/services/src/main/scala/cromwell/services/EnhancedBatchActor.scala b/services/src/main/scala/cromwell/services/EnhancedBatchActor.scala
index 6e6815f3f82..771b4fc388d 100644
--- a/services/src/main/scala/cromwell/services/EnhancedBatchActor.scala
+++ b/services/src/main/scala/cromwell/services/EnhancedBatchActor.scala
@@ -10,7 +10,7 @@ import scala.concurrent.duration.FiniteDuration
   * A BatchActor with instrumentation and load control traits mixed in to remove some boilerplate
   */
 abstract class EnhancedBatchActor[C](flushRate: FiniteDuration, batchSize: Int)
-  extends BatchActor[C](flushRate, batchSize)
+    extends BatchActor[C](flushRate, batchSize)
     with InstrumentedBatchActor[C]
     with CromwellInstrumentationActor
     with LoadControlledBatchActor[C] {
diff --git a/services/src/main/scala/cromwell/services/EnhancedThrottlerActor.scala b/services/src/main/scala/cromwell/services/EnhancedThrottlerActor.scala
index f0d127c93bc..2ae7ac5bcfe 100644
--- a/services/src/main/scala/cromwell/services/EnhancedThrottlerActor.scala
+++ b/services/src/main/scala/cromwell/services/EnhancedThrottlerActor.scala
@@ -8,9 +8,9 @@ import cromwell.services.loadcontroller.LoadControlledBatchActor
   * A ThrottlerActor with instrumentation and load control traits mixed in to remove some boilerplate
   */
 abstract class EnhancedThrottlerActor[C]
-  extends ThrottlerActor[C]
-  with InstrumentedBatchActor[C] 
-  with CromwellInstrumentationActor
-  with LoadControlledBatchActor[C] {
+    extends ThrottlerActor[C]
+    with InstrumentedBatchActor[C]
+    with CromwellInstrumentationActor
+    with LoadControlledBatchActor[C] {
   protected def enhancedReceive: Receive = loadControlReceive.orElse(instrumentationReceive).orElse(super.receive)
 }
diff --git a/services/src/main/scala/cromwell/services/IoActorRequester.scala b/services/src/main/scala/cromwell/services/IoActorRequester.scala
index 42c9d8eefb6..456c3ec392a 100644
--- a/services/src/main/scala/cromwell/services/IoActorRequester.scala
+++ b/services/src/main/scala/cromwell/services/IoActorRequester.scala
@@ -34,9 +34,10 @@ trait IoActorRequester extends StrictLogging { this: Actor =>
         promise.complete(Success(actorRef))
       case Success(NoIoActorRefAvailable) =>
         logger.warn(s"No IoActorRef available for ${self.path} yet. Retrying in $backoffInterval.")
-        context.system.scheduler.scheduleOnce(backoffInterval) { requestIoActorInner(promise, backoffInterval) }
+        context.system.scheduler.scheduleOnce(backoffInterval)(requestIoActorInner(promise, backoffInterval))
       case Success(other) =>
-        val message = s"Programmer Error: Unexpected response to a RequestIoActor message in ${self.path}'s IoActorRequester: $other"
+        val message =
+          s"Programmer Error: Unexpected response to a RequestIoActor message in ${self.path}'s IoActorRequester: $other"
         logger.error(message)
         promise.failure(new Exception(message))
       case Failure(reason) =>
diff --git a/services/src/main/scala/cromwell/services/ServiceRegistryActor.scala b/services/src/main/scala/cromwell/services/ServiceRegistryActor.scala
index 2e43e651b2b..5cd6c84df7a 100644
--- a/services/src/main/scala/cromwell/services/ServiceRegistryActor.scala
+++ b/services/src/main/scala/cromwell/services/ServiceRegistryActor.scala
@@ -31,34 +31,47 @@ object ServiceRegistryActor {
   def props(config: Config) = Props(new ServiceRegistryActor(config)).withDispatcher(ServiceDispatcher)
 
   // To enable testing, this lets us override a config value with a Props of our choice:
-  def props(config: Config, overrides: Map[String, Props]) = {
+  def props(config: Config, overrides: Map[String, Props]) =
     Props(new ServiceRegistryActor(config) {
       override def serviceProps = super.serviceProps ++ overrides
     }).withDispatcher(ServiceDispatcher)
-  }
 
   def serviceNameToPropsMap(globalConfig: Config, registryActor: ActorRef): Map[String, Props] = {
-    val serviceNamesToConfigStanzas = globalConfig.getObject("services").entrySet.asScala.map(x => x.getKey -> x.getValue).toMap
+    val serviceNamesToConfigStanzas =
+      globalConfig.getObject("services").entrySet.asScala.map(x => x.getKey -> x.getValue).toMap
     serviceNamesToConfigStanzas map {
-      case (serviceName, config: ConfigObject) => serviceName -> serviceProps(serviceName, globalConfig, config.toConfig, registryActor)
+      case (serviceName, config: ConfigObject) =>
+        serviceName -> serviceProps(serviceName, globalConfig, config.toConfig, registryActor)
       case (serviceName, _) => throw new Exception(s"Invalid configuration for service $serviceName")
     }
   }
 
-  private def serviceProps(serviceName: String, globalConfig: Config, serviceStanza: Config, registryActor: ActorRef): Props = {
+  private def serviceProps(serviceName: String,
+                           globalConfig: Config,
+                           serviceStanza: Config,
+                           registryActor: ActorRef
+  ): Props = {
     val serviceConfigStanza = serviceStanza.as[Option[Config]]("config").getOrElse(ConfigFactory.parseString(""))
 
     val dispatcher = serviceStanza.as[Option[String]]("dispatcher").getOrElse(ServiceDispatcher)
-    val className = serviceStanza.as[Option[String]]("class").getOrElse(
-      throw new IllegalArgumentException(s"Invalid configuration for service $serviceName: missing 'class' definition")
-    )
-
-    try {
-      Props.create(Class.forName(className), serviceConfigStanza, globalConfig, registryActor).withDispatcher(dispatcher)
-    } catch {
-      case e: ClassNotFoundException => throw new RuntimeException(
-        s"Class $className for service $serviceName cannot be found in the class path.", e
+    val className = serviceStanza
+      .as[Option[String]]("class")
+      .getOrElse(
+        throw new IllegalArgumentException(
+          s"Invalid configuration for service $serviceName: missing 'class' definition"
+        )
       )
+
+    try
+      Props
+        .create(Class.forName(className), serviceConfigStanza, globalConfig, registryActor)
+        .withDispatcher(dispatcher)
+    catch {
+      case e: ClassNotFoundException =>
+        throw new RuntimeException(
+          s"Class $className for service $serviceName cannot be found in the class path.",
+          e
+        )
     }
   }
 }
@@ -71,8 +84,8 @@ class ServiceRegistryActor(globalConfig: Config) extends Actor with ActorLogging
   // When the IO actor starts up, it can register itself here for other service registry actors to make use of it
   var ioActor: Option[ActorRef] = None
 
-  val services: Map[String, ActorRef] = serviceProps map {
-    case (name, props) => name -> context.actorOf(props, name)
+  val services: Map[String, ActorRef] = serviceProps map { case (name, props) =>
+    name -> context.actorOf(props, name)
   }
 
   private def transform(message: Any, from: ActorRef): Any = message match {
@@ -87,18 +100,28 @@ class ServiceRegistryActor(globalConfig: Config) extends Actor with ActorLogging
           debugLogLoadMessages(msg, sender())
           ref.tell(transform(msg, sender()), sender())
         case None =>
-          log.error("Received ServiceRegistryMessage requesting service '{}' for which no service is configured.  Message: {}", msg.serviceName, msg)
+          log.error(
+            "Received ServiceRegistryMessage requesting service '{}' for which no service is configured.  Message: {}",
+            msg.serviceName,
+            msg
+          )
           sender() ! ServiceRegistryFailure(msg.serviceName)
       }
-    case meta: ServiceRegistryMetaRequest => meta match {
-      case RequestIoActorRef => ioActor match {
-        case Some(ref) => sender() ! IoActorRef(ref)
-        case None => sender() ! NoIoActorRefAvailable
+    case meta: ServiceRegistryMetaRequest =>
+      meta match {
+        case RequestIoActorRef =>
+          ioActor match {
+            case Some(ref) => sender() ! IoActorRef(ref)
+            case None => sender() ! NoIoActorRefAvailable
+          }
+        case IoActorRef(ref) =>
+          if (ioActor.isEmpty) { ioActor = Option(ref) }
+          else {
+            log.error(
+              s"Programmer Error: More than one IoActor is trying to register itself in the service registry ($ref will *NOT* replace the existing $ioActor)"
+            )
+          }
       }
-      case IoActorRef(ref) =>
-        if (ioActor.isEmpty) { ioActor = Option(ref) }
-        else { log.error(s"Programmer Error: More than one IoActor is trying to register itself in the service registry ($ref will *NOT* replace the existing $ioActor)") }
-    }
     case ShutdownCommand =>
       services.values.toList match {
         case Nil => context stop self
@@ -110,14 +133,13 @@ class ServiceRegistryActor(globalConfig: Config) extends Actor with ActorLogging
       sender() ! ServiceRegistryFailure("Message is not a ServiceRegistryMessage: " + fool)
   }
 
-  private def debugLogLoadMessages(msg: ServiceRegistryMessage, sender: ActorRef): Unit = {
+  private def debugLogLoadMessages(msg: ServiceRegistryMessage, sender: ActorRef): Unit =
     msg match {
       case msg: LoadMetric =>
         log.debug(s"Service Registry Actor receiving $msg message from $sender")
       case _ =>
         ()
     }
-  }
 
   /**
     * Set the supervision strategy such that any of the individual service actors fails to initialize that we'll pass
diff --git a/services/src/main/scala/cromwell/services/healthmonitor/ProtoHealthMonitorServiceActor.scala b/services/src/main/scala/cromwell/services/healthmonitor/ProtoHealthMonitorServiceActor.scala
index 4d4a12e77d0..39d020bb701 100644
--- a/services/src/main/scala/cromwell/services/healthmonitor/ProtoHealthMonitorServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/healthmonitor/ProtoHealthMonitorServiceActor.scala
@@ -34,11 +34,18 @@ trait ProtoHealthMonitorServiceActor extends Actor with LazyLogging with Timers
 
   implicit val ec: ExecutionContext = context.system.dispatcher
 
-  lazy val sweepInterval = serviceConfig.as[Option[FiniteDuration]]("services.HealthMonitor.check-refresh-time").getOrElse(DefaultSweepTime)
-  lazy val futureTimeout: FiniteDuration = serviceConfig.as[Option[FiniteDuration]]("services.HealthMonitor.check-timeout").getOrElse(DefaultFutureTimeout)
-  lazy val staleThreshold: FiniteDuration = serviceConfig.as[Option[FiniteDuration]]("services.HealthMonitor.status-ttl").getOrElse(DefaultStaleThreshold)
-  lazy val failureRetryCount: Int = serviceConfig.as[Option[Int]]("services.HealthMonitor.check-failure-retry-count").getOrElse(DefaultFailureRetryCount)
-  lazy val failureRetryInterval: FiniteDuration = serviceConfig.as[Option[FiniteDuration]]("services.HealthMonitor.check-failure-retry-interval").getOrElse(DefaultFailureRetryInterval)
+  lazy val sweepInterval =
+    serviceConfig.as[Option[FiniteDuration]]("services.HealthMonitor.check-refresh-time").getOrElse(DefaultSweepTime)
+  lazy val futureTimeout: FiniteDuration =
+    serviceConfig.as[Option[FiniteDuration]]("services.HealthMonitor.check-timeout").getOrElse(DefaultFutureTimeout)
+  lazy val staleThreshold: FiniteDuration =
+    serviceConfig.as[Option[FiniteDuration]]("services.HealthMonitor.status-ttl").getOrElse(DefaultStaleThreshold)
+  lazy val failureRetryCount: Int = serviceConfig
+    .as[Option[Int]]("services.HealthMonitor.check-failure-retry-count")
+    .getOrElse(DefaultFailureRetryCount)
+  lazy val failureRetryInterval: FiniteDuration = serviceConfig
+    .as[Option[FiniteDuration]]("services.HealthMonitor.check-failure-retry-interval")
+    .getOrElse(DefaultFailureRetryInterval)
 
   /**
     * Contains each subsystem status along with a timestamp of when the entry was made so we know when the status
@@ -49,24 +56,20 @@ trait ProtoHealthMonitorServiceActor extends Actor with LazyLogging with Timers
     subsystems.map((_, CachedSubsystemStatus(UnknownStatus, now))).toMap
   }
 
-  private[healthmonitor] def initialize(): Unit = {
+  private[healthmonitor] def initialize(): Unit =
     subsystems foreach { s =>
       logger.info(s"Availability of '${s.name}' will be monitored and reported via the '/engine/v1/status' API")
       self ! Check(s, failureRetryCount)
     }
-  }
 
-  private def check(subsystem: MonitoredSubsystem, after: FiniteDuration, withRetriesLeft: Int): Unit = {
+  private def check(subsystem: MonitoredSubsystem, after: FiniteDuration, withRetriesLeft: Int): Unit =
     timers.startSingleTimer(UUID.randomUUID(), Check(subsystem, withRetriesLeft), after)
-  }
 
-  private[healthmonitor] def scheduleFailedRetryCheck(subsystem: MonitoredSubsystem, retriesLeft: Int): Unit = {
+  private[healthmonitor] def scheduleFailedRetryCheck(subsystem: MonitoredSubsystem, retriesLeft: Int): Unit =
     check(subsystem, after = failureRetryInterval, withRetriesLeft = retriesLeft - 1)
-  }
 
-  private[healthmonitor] def scheduleSweepCheck(subsystem: MonitoredSubsystem): Unit = {
+  private[healthmonitor] def scheduleSweepCheck(subsystem: MonitoredSubsystem): Unit =
     check(subsystem, after = sweepInterval, withRetriesLeft = failureRetryCount)
-  }
 
   initialize()
 
@@ -138,15 +141,21 @@ object ProtoHealthMonitorServiceActor {
 
   final case class MonitoredSubsystem(name: String, check: () => Future[SubsystemStatus])
   final case class SubsystemStatus(ok: Boolean, messages: Option[List[String]])
-  final case class CachedSubsystemStatus(status: SubsystemStatus, created: Long) // created is time in millis when status was captured
+  final case class CachedSubsystemStatus(status: SubsystemStatus,
+                                         created: Long
+  ) // created is time in millis when status was captured
 
   sealed abstract class HealthMonitorServiceActorRequest
   case class Check(subsystem: MonitoredSubsystem, retriesLeft: Int) extends HealthMonitorServiceActorRequest
-  final case class Store(subsystem: MonitoredSubsystem, status: SubsystemStatus) extends HealthMonitorServiceActorRequest
-  case object GetCurrentStatus extends HealthMonitorServiceActorRequest with ServiceRegistryMessage { override val serviceName = "HealthMonitor" }
+  final case class Store(subsystem: MonitoredSubsystem, status: SubsystemStatus)
+      extends HealthMonitorServiceActorRequest
+  case object GetCurrentStatus extends HealthMonitorServiceActorRequest with ServiceRegistryMessage {
+    override val serviceName = "HealthMonitor"
+  }
 
   sealed abstract class HealthMonitorServiceActorResponse
-  final case class StatusCheckResponse(ok: Boolean, systems: Map[String, SubsystemStatus]) extends HealthMonitorServiceActorResponse
+  final case class StatusCheckResponse(ok: Boolean, systems: Map[String, SubsystemStatus])
+      extends HealthMonitorServiceActorResponse
 
   /**
     * Adds non-blocking timeout support to futures.
@@ -157,8 +166,10 @@ object ProtoHealthMonitorServiceActor {
     *   // returns in 5 seconds
     * }}}
     */
-  private implicit class FutureWithTimeout[A](f: Future[A]) {
-    def withTimeout(duration: FiniteDuration, errMsg: String, scheduler: Scheduler)(implicit ec: ExecutionContext): Future[A] =
+  implicit private class FutureWithTimeout[A](f: Future[A]) {
+    def withTimeout(duration: FiniteDuration, errMsg: String, scheduler: Scheduler)(implicit
+      ec: ExecutionContext
+    ): Future[A] =
       Future.firstCompletedOf(List(f, after(duration, scheduler)(Future.failed(new TimeoutException(errMsg)))))
   }
 }
diff --git a/services/src/main/scala/cromwell/services/healthmonitor/impl/HealthMonitorServiceActor.scala b/services/src/main/scala/cromwell/services/healthmonitor/impl/HealthMonitorServiceActor.scala
index 908f0706551..5c5e13b0615 100644
--- a/services/src/main/scala/cromwell/services/healthmonitor/impl/HealthMonitorServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/healthmonitor/impl/HealthMonitorServiceActor.scala
@@ -6,8 +6,8 @@ import cromwell.services.healthmonitor.ProtoHealthMonitorServiceActor
 import cromwell.services.healthmonitor.impl.workbench.WorkbenchHealthMonitorServiceActor
 
 final class HealthMonitorServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
-  extends WorkbenchHealthMonitorServiceActor(serviceConfig, globalConfig, serviceRegistryActor) {
-  override implicit val system = context.system
+    extends WorkbenchHealthMonitorServiceActor(serviceConfig, globalConfig, serviceRegistryActor) {
+  implicit override val system = context.system
 
   override lazy val subsystems: Set[ProtoHealthMonitorServiceActor.MonitoredSubsystem] = {
 
@@ -18,7 +18,7 @@ final class HealthMonitorServiceActor(serviceConfig: Config, globalConfig: Confi
     Set(
       dockerHubSubsystemOption,
       engineDatabaseSubsystemOption,
-      gcsSubsystemOption,
+      gcsSubsystemOption
     ).flatten ++ PapiSubsystems
   }
 }
diff --git a/services/src/main/scala/cromwell/services/healthmonitor/impl/common/DockerHubMonitor.scala b/services/src/main/scala/cromwell/services/healthmonitor/impl/common/DockerHubMonitor.scala
index e56fbb98bdf..9170b6edd3a 100644
--- a/services/src/main/scala/cromwell/services/healthmonitor/impl/common/DockerHubMonitor.scala
+++ b/services/src/main/scala/cromwell/services/healthmonitor/impl/common/DockerHubMonitor.scala
@@ -24,7 +24,8 @@ trait DockerHubMonitor {
   implicit val timeout = Timeout(5.seconds)
 
   lazy val dockerHubFlow = List(new DockerHubRegistry(DockerRegistryConfig.default))
-  lazy val dockerHashActor = system.actorOf(DockerInfoActor.props(dockerHubFlow, 500, 0.minutes, 0), "HealthMonitorDockerHashActor")
+  lazy val dockerHashActor =
+    system.actorOf(DockerInfoActor.props(dockerHubFlow, 500, 0.minutes, 0), "HealthMonitorDockerHashActor")
 
   lazy val DockerHub = MonitoredSubsystem("DockerHub", checkDockerhub _)
 
@@ -32,13 +33,15 @@ trait DockerHubMonitor {
     * Demonstrates connectivity to Docker Hub by periodically pulling the hash of an image. If the hash is not returned
     * we assume that there is no connection to Docker Hub.
     */
-  private def checkDockerhub(): Future[SubsystemStatus] = {
+  private def checkDockerhub(): Future[SubsystemStatus] =
     dockerHashActor.ask(UbuntuLatestHashRequest).mapTo[DockerInfoResponse] map {
       case _: DockerInfoSuccessResponse => OkStatus
       case f: DockerInfoFailedResponse => throw f.failure
-      case huh => throw new RuntimeException("Encountered unexpected error when trying to contact DockerHub: " + huh.getClass.getCanonicalName)
+      case huh =>
+        throw new RuntimeException(
+          "Encountered unexpected error when trying to contact DockerHub: " + huh.getClass.getCanonicalName
+        )
     }
-  }
 }
 
 object DockerHubMonitor {
diff --git a/services/src/main/scala/cromwell/services/healthmonitor/impl/common/EngineDatabaseMonitor.scala b/services/src/main/scala/cromwell/services/healthmonitor/impl/common/EngineDatabaseMonitor.scala
index be518bf001a..a7707bf86fd 100644
--- a/services/src/main/scala/cromwell/services/healthmonitor/impl/common/EngineDatabaseMonitor.scala
+++ b/services/src/main/scala/cromwell/services/healthmonitor/impl/common/EngineDatabaseMonitor.scala
@@ -1,7 +1,7 @@
 package cromwell.services.healthmonitor.impl.common
 
 import cromwell.services.EngineServicesStore
-import cromwell.services.healthmonitor.ProtoHealthMonitorServiceActor.{MonitoredSubsystem, SubsystemStatus, OkStatus}
+import cromwell.services.healthmonitor.ProtoHealthMonitorServiceActor.{MonitoredSubsystem, OkStatus, SubsystemStatus}
 import cats.syntax.functor._
 import cats.instances.future._
 import scala.concurrent.{ExecutionContext, Future}
@@ -19,7 +19,6 @@ trait EngineDatabaseMonitor {
   /**
     * Demonstrates connectivity to the engine database by periodically making a small query
     */
-  private def checkEngineDb(): Future[SubsystemStatus] = {
+  private def checkEngineDb(): Future[SubsystemStatus] =
     EngineServicesStore.engineDatabaseInterface.queryDockerHashStoreEntries("DOESNOTEXIST") as OkStatus
-  }
 }
diff --git a/services/src/main/scala/cromwell/services/healthmonitor/impl/workbench/WorkbenchHealthMonitorServiceActor.scala b/services/src/main/scala/cromwell/services/healthmonitor/impl/workbench/WorkbenchHealthMonitorServiceActor.scala
index 6bbef784dfa..43a5c597c8a 100644
--- a/services/src/main/scala/cromwell/services/healthmonitor/impl/workbench/WorkbenchHealthMonitorServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/healthmonitor/impl/workbench/WorkbenchHealthMonitorServiceActor.scala
@@ -31,17 +31,20 @@ import scala.concurrent.{ExecutionContext, Future}
   * as GCS and PAPI. This implementation makes some assumptions of Cromwell's configuration which will be true
   * in a Workbench scenario but YMMV otherwise. Caveat emptor and all of that fun stuff.
   */
-abstract class WorkbenchHealthMonitorServiceActor(val serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
-  extends ProtoHealthMonitorServiceActor
+abstract class WorkbenchHealthMonitorServiceActor(val serviceConfig: Config,
+                                                  globalConfig: Config,
+                                                  serviceRegistryActor: ActorRef
+) extends ProtoHealthMonitorServiceActor
     with DockerHubMonitor
     with EngineDatabaseMonitor {
-  override implicit val system = context.system
+  implicit override val system = context.system
 
-  private lazy val papiBackendConfigurations = serviceConfig.as[Set[String]]("check-papi-backends").map(WorkbenchHealthMonitorServiceActor.PapiConfiguration.fromBackendNameValue(_, serviceConfig, globalConfig))
+  private lazy val papiBackendConfigurations = serviceConfig
+    .as[Set[String]]("check-papi-backends")
+    .map(WorkbenchHealthMonitorServiceActor.PapiConfiguration.fromBackendNameValue(_, serviceConfig, globalConfig))
 
-  def papiMonitoredSubsystem(papiConfiguration: PapiConfiguration): MonitoredSubsystem = {
+  def papiMonitoredSubsystem(papiConfiguration: PapiConfiguration): MonitoredSubsystem =
     MonitoredSubsystem(papiConfiguration.backendName, () => checkPapi(papiConfiguration))
-  }
 
   protected lazy val Gcs = MonitoredSubsystem("GCS", () => checkGcs())
   protected lazy val PapiSubsystems = papiBackendConfigurations map papiMonitoredSubsystem
@@ -54,7 +57,8 @@ abstract class WorkbenchHealthMonitorServiceActor(val serviceConfig: Config, glo
   private def getGoogleAuthConfigurationOrFail(googleAuthName: String): GoogleAuthMode =
     googleConfig.auth(googleAuthName) match {
       case Valid(a) => a
-      case Invalid(e) => throw new IllegalArgumentException("Unable to configure WorkbenchHealthMonitor: " + e.toList.mkString(", "))
+      case Invalid(e) =>
+        throw new IllegalArgumentException("Unable to configure WorkbenchHealthMonitor: " + e.toList.mkString(", "))
     }
 
   /**
@@ -80,12 +84,19 @@ abstract class WorkbenchHealthMonitorServiceActor(val serviceConfig: Config, glo
     val check = for {
       credentials <- Future(googleAuth.credentials(List(CloudLifeSciencesScopes.CLOUD_PLATFORM)))
       actorFactoryName = papiProviderConfig.as[String]("actor-factory")
-      genomicsChecker = if (actorFactoryName.contains("v2beta")) {
-        val location = papiConfig.as[String]("genomics.location")
-        GenomicsCheckerV2Beta(googleConfig.applicationName, googleAuth, endpointUrl, location, credentials, papiProjectId)
-      } else {
-        GenomicsCheckerV2Alpha1(googleConfig.applicationName, googleAuth, endpointUrl, credentials, papiProjectId)
-      }
+      genomicsChecker =
+        if (actorFactoryName.contains("v2beta")) {
+          val location = papiConfig.as[String]("genomics.location")
+          GenomicsCheckerV2Beta(googleConfig.applicationName,
+                                googleAuth,
+                                endpointUrl,
+                                location,
+                                credentials,
+                                papiProjectId
+          )
+        } else {
+          GenomicsCheckerV2Alpha1(googleConfig.applicationName, googleAuth, endpointUrl, credentials, papiProjectId)
+        }
       checked <- genomicsChecker.check
     } yield checked
 
@@ -98,9 +109,8 @@ object WorkbenchHealthMonitorServiceActor {
     protected def httpInitializer(credentials: Credentials) = {
       val delegate = new HttpCredentialsAdapter(credentials)
       new HttpRequestInitializer() {
-        def initialize(httpRequest: HttpRequest) = {
+        def initialize(httpRequest: HttpRequest) =
           delegate.initialize(httpRequest)
-        }
       }
     }
 
@@ -112,34 +122,42 @@ object WorkbenchHealthMonitorServiceActor {
                                    endpointUrl: URL,
                                    location: String,
                                    credentials: Credentials,
-                                   papiProjectId: String)(implicit val ec: ExecutionContext) extends GenomicsChecker {
-    val lifeSciences = new CloudLifeSciences.Builder(
-      GoogleAuthMode.httpTransport,
-      GoogleAuthMode.jsonFactory,
-      httpInitializer(credentials))
+                                   papiProjectId: String
+  )(implicit val ec: ExecutionContext)
+      extends GenomicsChecker {
+    val lifeSciences = new CloudLifeSciences.Builder(GoogleAuthMode.httpTransport,
+                                                     GoogleAuthMode.jsonFactory,
+                                                     httpInitializer(credentials)
+    )
       .setApplicationName(applicationName)
       .setRootUrl(endpointUrl.toString)
       .build
 
     override def check = Future {
       // https://cloud.google.com/life-sciences/docs/reference/rest/v2beta/projects.locations.operations
-      lifeSciences.projects().locations().operations().list(s"projects/$papiProjectId/locations/$location").setPageSize(1).execute()
+      lifeSciences
+        .projects()
+        .locations()
+        .operations()
+        .list(s"projects/$papiProjectId/locations/$location")
+        .setPageSize(1)
+        .execute()
       ()
     }
   }
 
   case class GenomicsCheckerV2Alpha1(applicationName: String,
-                                   authMode: GoogleAuthMode,
-                                   endpointUrl: URL,
-                                   credentials: Credentials,
-                                   papiProjectId: String)(implicit val ec: ExecutionContext) extends GenomicsChecker {
-    val genomics = new Genomics.Builder(
-      GoogleAuthMode.httpTransport,
-      GoogleAuthMode.jsonFactory,
-      httpInitializer(credentials))
-      .setApplicationName(applicationName)
-      .setRootUrl(endpointUrl.toString)
-      .build
+                                     authMode: GoogleAuthMode,
+                                     endpointUrl: URL,
+                                     credentials: Credentials,
+                                     papiProjectId: String
+  )(implicit val ec: ExecutionContext)
+      extends GenomicsChecker {
+    val genomics =
+      new Genomics.Builder(GoogleAuthMode.httpTransport, GoogleAuthMode.jsonFactory, httpInitializer(credentials))
+        .setApplicationName(applicationName)
+        .setRootUrl(endpointUrl.toString)
+        .build
 
     override def check = Future {
       // https://cloud.google.com/genomics/reference/rest/#rest-resource-v2alpha1projectsoperations
@@ -153,15 +171,16 @@ object WorkbenchHealthMonitorServiceActor {
   object PapiConfiguration {
     def fromBackendNameKey(backendNameKey: String,
                            serviceConfig: Config,
-                           globalConfig: Config): Option[PapiConfiguration] = {
+                           globalConfig: Config
+    ): Option[PapiConfiguration] =
       serviceConfig.as[Option[String]](backendNameKey) map {
         fromBackendNameValue(_, serviceConfig, globalConfig)
       }
-    }
 
     def fromBackendNameValue(papiBackendName: String,
                              serviceConfig: Config,
-                             globalConfig: Config): PapiConfiguration = {
+                             globalConfig: Config
+    ): PapiConfiguration = {
       val papiProviderConfig: Config = globalConfig.as[Config](s"backend.providers.$papiBackendName")
       val papiConfig: Config = papiProviderConfig.as[Config]("config")
       PapiConfiguration(papiBackendName, papiConfig, papiProviderConfig)
diff --git a/services/src/main/scala/cromwell/services/instrumentation/AsynchronousThrottlingGaugeMetricActor.scala b/services/src/main/scala/cromwell/services/instrumentation/AsynchronousThrottlingGaugeMetricActor.scala
index a079e1e7fb0..cf8df945532 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/AsynchronousThrottlingGaugeMetricActor.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/AsynchronousThrottlingGaugeMetricActor.scala
@@ -9,8 +9,8 @@ import scala.concurrent.{ExecutionContext, Future}
 
 class AsynchronousThrottlingGaugeMetricActor(metricPath: NonEmptyList[String],
                                              instrumentationPrefix: Option[String],
-                                             override val serviceRegistryActor: ActorRef)
-  extends LoggingFSM[AsynchronousThrottlingGaugeMetricActorState, Unit]
+                                             override val serviceRegistryActor: ActorRef
+) extends LoggingFSM[AsynchronousThrottlingGaugeMetricActorState, Unit]
     with CromwellInstrumentation {
 
   implicit val ec = context.dispatcher
@@ -42,10 +42,11 @@ class AsynchronousThrottlingGaugeMetricActor(metricPath: NonEmptyList[String],
       goto(WaitingForMetricCalculationRequestOrMetricValue)
   }
 
-  whenUnhandled {
-    case Event(unexpected, _) =>
-      log.warning(s"Programmer error: this actor should not receive message $unexpected from ${sender().path} while in state $stateName")
-      stay()
+  whenUnhandled { case Event(unexpected, _) =>
+    log.warning(
+      s"Programmer error: this actor should not receive message $unexpected from ${sender().path} while in state $stateName"
+    )
+    stay()
   }
 
   private def sendGaugeAndStay(metricValue: Long): State = {
diff --git a/services/src/main/scala/cromwell/services/instrumentation/CromwellInstrumentation.scala b/services/src/main/scala/cromwell/services/instrumentation/CromwellInstrumentation.scala
index 1c0bf4fd57f..cd7adef9c41 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/CromwellInstrumentation.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/CromwellInstrumentation.scala
@@ -1,6 +1,6 @@
 package cromwell.services.instrumentation
 
-import java.time.{OffsetDateTime, Duration => JDuration}
+import java.time.{Duration => JDuration, OffsetDateTime}
 import java.util.concurrent.TimeUnit
 
 import akka.actor.{Actor, ActorRef, Timers}
@@ -16,7 +16,8 @@ import scala.language.implicitConversions
 
 object CromwellInstrumentation {
 
-  val InstrumentationRate = ConfigFactory.load()
+  val InstrumentationRate = ConfigFactory
+    .load()
     .getConfig("system")
     .as[Option[FiniteDuration]]("instrumentation-rate")
     .getOrElse(5.seconds)
@@ -30,9 +31,8 @@ object CromwellInstrumentation {
       .map(c => path.concatNel(NonEmptyList.of(c.toString)))
       .getOrElse(path)
 
-    def withThrowable(failure: Throwable, statusCodeExtractor: Throwable => Option[Int]) = {
+    def withThrowable(failure: Throwable, statusCodeExtractor: Throwable => Option[Int]) =
       path.withStatusCodeFailure(statusCodeExtractor(failure))
-    }
   }
 }
 
@@ -50,70 +50,64 @@ trait CromwellInstrumentation {
     * The cromwell bucket prefix is always prepended:
     * cromwell.[prefix].path
     */
-  final private def makeBucket(path: InstrumentationPath, prefix: Option[String]): CromwellBucket = {
+  final private def makeBucket(path: InstrumentationPath, prefix: Option[String]): CromwellBucket =
     CromwellBucket(prefix.toList, path)
-  }
 
   /**
     * Creates an increment message for the given bucket
     */
-  private final def countMessage(path: InstrumentationPath, count: Long, prefix: Option[String]): InstrumentationServiceMessage = {
+  final private def countMessage(path: InstrumentationPath,
+                                 count: Long,
+                                 prefix: Option[String]
+  ): InstrumentationServiceMessage =
     InstrumentationServiceMessage(CromwellCount(makeBucket(path, prefix), count))
-  }
 
   /**
     * Increment the counter for the given bucket
     */
-  protected final def count(path: InstrumentationPath, count: Long, prefix: Option[String] = None): Unit = {
+  final protected def count(path: InstrumentationPath, count: Long, prefix: Option[String] = None): Unit =
     serviceRegistryActor.tell(countMessage(path, count, prefix), instrumentationSender)
-  }
 
   /**
     * Creates an increment message for the given bucket
     */
-  private final def incrementMessage(path: InstrumentationPath, prefix: Option[String]): InstrumentationServiceMessage = {
+  final private def incrementMessage(path: InstrumentationPath, prefix: Option[String]): InstrumentationServiceMessage =
     InstrumentationServiceMessage(CromwellIncrement(makeBucket(path, prefix)))
-  }
 
   /**
     * Increment the counter for the given bucket
     */
-  protected final def increment(path: InstrumentationPath, prefix: Option[String] = None): Unit = {
+  final protected def increment(path: InstrumentationPath, prefix: Option[String] = None): Unit =
     serviceRegistryActor.tell(incrementMessage(path, prefix), instrumentationSender)
-  }
 
   /**
     * Creates a gauge message for the given bucket
     */
-  private final def gaugeMessage(path: InstrumentationPath, value: Long, prefix: Option[String]) = {
+  final private def gaugeMessage(path: InstrumentationPath, value: Long, prefix: Option[String]) =
     InstrumentationServiceMessage(CromwellGauge(makeBucket(path, prefix), value))
-  }
 
   /**
     * Set the bucket to the gauge value
     */
-  protected final def sendGauge(path: InstrumentationPath, value: Long, prefix: Option[String] = None): Unit = {
+  final protected def sendGauge(path: InstrumentationPath, value: Long, prefix: Option[String] = None): Unit =
     serviceRegistryActor.tell(gaugeMessage(path, value, prefix), instrumentationSender)
-  }
 
   /**
     * Creates a timing message for the given bucket and duration
     */
-  private final def timingMessage(path: InstrumentationPath, duration: FiniteDuration, prefix: Option[String]) = {
+  final private def timingMessage(path: InstrumentationPath, duration: FiniteDuration, prefix: Option[String]) =
     InstrumentationServiceMessage(CromwellTiming(makeBucket(path, prefix), duration))
-  }
 
   /**
     * Add a timing information for the given bucket
     */
-  protected final def sendTiming(path: InstrumentationPath, duration: FiniteDuration, prefix: Option[String] = None) = {
+  final protected def sendTiming(path: InstrumentationPath, duration: FiniteDuration, prefix: Option[String] = None) =
     serviceRegistryActor.tell(timingMessage(path, duration, prefix), instrumentationSender)
-  }
 
-  def calculateTimeDifference(startTime: OffsetDateTime, endTime: OffsetDateTime): FiniteDuration = {
+  def calculateTimeDifference(startTime: OffsetDateTime, endTime: OffsetDateTime): FiniteDuration =
     FiniteDuration(JDuration.between(startTime, endTime).toMillis, TimeUnit.MILLISECONDS)
-  }
-  def calculateTimeSince(startTime: OffsetDateTime): FiniteDuration = calculateTimeDifference(startTime, OffsetDateTime.now())
+  def calculateTimeSince(startTime: OffsetDateTime): FiniteDuration =
+    calculateTimeDifference(startTime, OffsetDateTime.now())
 }
 
 /**
@@ -123,9 +117,8 @@ trait CromwellInstrumentationScheduler { this: Actor with Timers =>
   private case object InstrumentationTimerKey
   private case object InstrumentationTimerAction extends ControlMessage
 
-  def startInstrumentationTimer() = {
+  def startInstrumentationTimer() =
     timers.startSingleTimer(InstrumentationTimerKey, InstrumentationTimerAction, InstrumentationRate)
-  }
 
   protected def instrumentationReceive(instrumentationAction: () => Unit): Receive = {
     case InstrumentationTimerAction =>
diff --git a/services/src/main/scala/cromwell/services/instrumentation/CromwellMetric.scala b/services/src/main/scala/cromwell/services/instrumentation/CromwellMetric.scala
index 21c9dba1cd8..dbdc4525feb 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/CromwellMetric.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/CromwellMetric.scala
@@ -25,12 +25,15 @@ sealed trait CromwellMetric
 
 object CromwellCount {
   def apply(bucket: CromwellBucket, value: Long): CromwellCount = new CromwellCount(bucket, value)
-  def unapply(count: CromwellCount): Option[(CromwellBucket, Long, Double)] = Option((count.bucket, count.value, count.sampling))
+  def unapply(count: CromwellCount): Option[(CromwellBucket, Long, Double)] = Option(
+    (count.bucket, count.value, count.sampling)
+  )
 }
+
 /**
   * Count occurrences of an event
   */
-class CromwellCount(val bucket: CromwellBucket, val value: Long, val sampling: Double = 1.0D) extends CromwellMetric {
+class CromwellCount(val bucket: CromwellBucket, val value: Long, val sampling: Double = 1.0d) extends CromwellMetric {
   override def toString: String = s"CromwellCount($bucket, $value, $sampling)"
 }
 
@@ -42,7 +45,7 @@ case class CromwellIncrement(override val bucket: CromwellBucket) extends Cromwe
 /**
   * Measures a time value
   */
-case class CromwellTiming(bucket: CromwellBucket, value: FiniteDuration, sampling: Double = 1.0D) extends CromwellMetric
+case class CromwellTiming(bucket: CromwellBucket, value: FiniteDuration, sampling: Double = 1.0d) extends CromwellMetric
 
 /**
   * Measures a gauge value
diff --git a/services/src/main/scala/cromwell/services/instrumentation/InstrumentedBatchActor.scala b/services/src/main/scala/cromwell/services/instrumentation/InstrumentedBatchActor.scala
index 46ec07b1b33..0e08371829d 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/InstrumentedBatchActor.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/InstrumentedBatchActor.scala
@@ -40,10 +40,9 @@ trait InstrumentedBatchActor[C] { this: BatchActor[C] with CromwellInstrumentati
     * Don't forget to chain this into your receive method to instrument the queue size:
     * override def receive = instrumentationReceive.orElse(super.receive)
     */
-  protected def instrumentationReceive: Receive = {
-    case QueueSizeTimerAction => 
-      sendGauge(queueSizePath, stateData.weight.toLong, instrumentationPrefix)
-      timers.startSingleTimer(QueueSizeTimerKey, QueueSizeTimerAction, CromwellInstrumentation.InstrumentationRate)
+  protected def instrumentationReceive: Receive = { case QueueSizeTimerAction =>
+    sendGauge(queueSizePath, stateData.weight.toLong, instrumentationPrefix)
+    timers.startSingleTimer(QueueSizeTimerKey, QueueSizeTimerAction, CromwellInstrumentation.InstrumentationRate)
   }
 
   /**
@@ -59,7 +58,10 @@ trait InstrumentedBatchActor[C] { this: BatchActor[C] with CromwellInstrumentati
     action onComplete {
       case Success(numProcessed) =>
         count(processedPath, numProcessed.toLong, instrumentationPrefix)
-        sendTiming(durationPath, (OffsetDateTime.now().toEpochSecond - startTime.toEpochSecond).seconds, instrumentationPrefix)
+        sendTiming(durationPath,
+                   (OffsetDateTime.now().toEpochSecond - startTime.toEpochSecond).seconds,
+                   instrumentationPrefix
+        )
       case Failure(_) => count(failurePath, 1L, instrumentationPrefix)
     }
     action
diff --git a/services/src/main/scala/cromwell/services/instrumentation/impl/noop/NoopInstrumentationServiceActor.scala b/services/src/main/scala/cromwell/services/instrumentation/impl/noop/NoopInstrumentationServiceActor.scala
index e7385ed7991..5c8eb8c744a 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/impl/noop/NoopInstrumentationServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/impl/noop/NoopInstrumentationServiceActor.scala
@@ -6,13 +6,16 @@ import cromwell.services.instrumentation.InstrumentationService.InstrumentationS
 import cromwell.util.GracefulShutdownHelper.ShutdownCommand
 
 object NoopInstrumentationServiceActor {
-  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) = Props(new NoopInstrumentationServiceActor(serviceConfig, globalConfig, serviceRegistryActor))
+  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) = Props(
+    new NoopInstrumentationServiceActor(serviceConfig, globalConfig, serviceRegistryActor)
+  )
 }
 
 /**
   * Actor that ignores every InstrumentationServiceMessage - This is the default implementation of this service
   */
-class NoopInstrumentationServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor {
+class NoopInstrumentationServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
+    extends Actor {
   override def receive = {
     case InstrumentationServiceMessage(_) => // Drop all messages
     case ShutdownCommand => context stop self
diff --git a/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala b/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
index 4df3f966db6..de991711689 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala
@@ -9,7 +9,10 @@ import com.typesafe.config.Config
 import com.typesafe.scalalogging.StrictLogging
 import cromwell.services.instrumentation.{CromwellBucket, CromwellGauge, CromwellIncrement}
 import cromwell.services.instrumentation.InstrumentationService.InstrumentationServiceMessage
-import cromwell.services.instrumentation.impl.selectivetsv.SelectiveTsvInstrumentationServiceActor.{SnapshotState, StateHistory}
+import cromwell.services.instrumentation.impl.selectivetsv.SelectiveTsvInstrumentationServiceActor.{
+  SnapshotState,
+  StateHistory
+}
 import cromwell.util.GracefulShutdownHelper.ShutdownCommand
 
 import scala.concurrent.duration._
@@ -24,12 +27,14 @@ import scala.concurrent.ExecutionContext
   *
   *  This is a test/demonstration version of the actor. I strongly discourage deploying with it in any production usage!
   */
-class SelectiveTsvInstrumentationServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
-  extends Actor
+class SelectiveTsvInstrumentationServiceActor(serviceConfig: Config,
+                                              globalConfig: Config,
+                                              serviceRegistryActor: ActorRef
+) extends Actor
     with StrictLogging {
 
   implicit val ec: ExecutionContext = context.dispatcher
-  context.system.scheduler.schedule(10.seconds, 1.seconds) { self ! SnapshotState }
+  context.system.scheduler.schedule(10.seconds, 1.seconds)(self ! SnapshotState)
 
   var stateHistory: StateHistory = StateHistory.empty
 
@@ -59,14 +64,15 @@ class SelectiveTsvInstrumentationServiceActor(serviceConfig: Config, globalConfi
     case ShutdownCommand => context stop self
   }
 
-  private def checkTsvPrintout(): Boolean = {
-    if (stateHistory.stateHistory.size >= 2 &&
+  private def checkTsvPrintout(): Boolean =
+    if (
+      stateHistory.stateHistory.size >= 2 &&
       stateHistory.stateHistory.last._2.get("jobs.ejea.executing").contains(0) &&
-      stateHistory.stateHistory.init.last._2.get("jobs.ejea.executing").exists(_ != 0)) {
+      stateHistory.stateHistory.init.last._2.get("jobs.ejea.executing").exists(_ != 0)
+    ) {
       outputCountHistory()
       true
     } else false
-  }
 
   private def outputCountHistory(): Unit = {
     import java.io.BufferedWriter
@@ -93,7 +99,11 @@ object SelectiveTsvInstrumentationServiceActor {
 
   case object SnapshotState
 
-  final case class StateHistory(fields: Vector[String], currentState: Map[String, Int], stateHistory: Vector[(Long, Map[String, Int])], firstEntryTimestampMillis: Option[Long]) {
+  final case class StateHistory(fields: Vector[String],
+                                currentState: Map[String, Int],
+                                stateHistory: Vector[(Long, Map[String, Int])],
+                                firstEntryTimestampMillis: Option[Long]
+  ) {
     def increment(field: String): StateHistory = {
       val newState = currentState + (field -> (currentState.getOrElse(field, 0) + 1))
       if (fields.contains(field)) {
@@ -107,13 +117,12 @@ object SelectiveTsvInstrumentationServiceActor {
         )
       }
     }
-    def decrement(field: String): StateHistory = {
+    def decrement(field: String): StateHistory =
       this.copy(
         currentState = currentState + (field -> (currentState(field) - 1))
       )
-    }
 
-    def set(field: String, value: Long): StateHistory = {
+    def set(field: String, value: Long): StateHistory =
       if (fields.contains(field)) {
         this.copy(
           currentState = currentState + (field -> value.intValue)
@@ -124,22 +133,23 @@ object SelectiveTsvInstrumentationServiceActor {
           currentState = currentState + (field -> value.intValue)
         )
       }
-    }
 
-    def snapshotState(): StateHistory = {
+    def snapshotState(): StateHistory =
       if (this == StateHistory.empty) this
       else {
-        val creationTimestampEpochMillis = firstEntryTimestampMillis.getOrElse(OffsetDateTime.now.toInstant.toEpochMilli)
+        val creationTimestampEpochMillis =
+          firstEntryTimestampMillis.getOrElse(OffsetDateTime.now.toInstant.toEpochMilli)
         this.copy(
-          stateHistory = stateHistory :+ ((OffsetDateTime.now.toInstant.toEpochMilli - creationTimestampEpochMillis) -> currentState),
+          stateHistory =
+            stateHistory :+ ((OffsetDateTime.now.toInstant.toEpochMilli - creationTimestampEpochMillis) -> currentState),
           firstEntryTimestampMillis = Option(creationTimestampEpochMillis)
         )
       }
-    }
 
     def stateHistoryTsv(): Vector[String] = {
 
-      val interestingFields = fields.filter(field => stateHistory.exists(history => history._2.get(field).exists(_ != 0)))
+      val interestingFields =
+        fields.filter(field => stateHistory.exists(history => history._2.get(field).exists(_ != 0)))
 
       val header = (List("timestamp") ++ interestingFields).mkString("\t")
       val rows = stateHistory.map { case (timestamp, fieldMap) =>
diff --git a/services/src/main/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverConfig.scala b/services/src/main/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverConfig.scala
index 06fe0442da4..7fd6e79a708 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverConfig.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverConfig.scala
@@ -18,50 +18,57 @@ case class StackdriverConfig(googleProject: String,
                              flushRate: FiniteDuration,
                              cromwellInstanceIdentifier: Option[String],
                              cromwellInstanceRole: Option[String],
-                             cromwellPerfTestCase: Option[String])
+                             cromwellPerfTestCase: Option[String]
+)
 
 object StackdriverConfig {
   val CromwellInstanceIdentifier = "cromwell-instance-identifier"
   val CromwellInstanceRole = "cromwell-instance-role"
   val CromwellPerfTest = "cromwell-perf-test-case"
 
-  private def validateFlushRate(rateFunc: => FiniteDuration): ErrorOr[FiniteDuration] = {
+  private def validateFlushRate(rateFunc: => FiniteDuration): ErrorOr[FiniteDuration] =
     validate[FiniteDuration](rateFunc) match {
-      case Valid(duration) => duration match {
-        case _ if duration < 1.minute => (s"`flush-rate` must be 1 minute or longer, specified rate is `$duration`. " +
-          s"Google's Stackdriver API needs each metric to be sent not more than once per minute.").invalidNel
-        case _ => duration.validNel
-      }
+      case Valid(duration) =>
+        duration match {
+          case _ if duration < 1.minute =>
+            (s"`flush-rate` must be 1 minute or longer, specified rate is `$duration`. " +
+              s"Google's Stackdriver API needs each metric to be sent not more than once per minute.").invalidNel
+          case _ => duration.validNel
+        }
       case Invalid(e) => e.invalid
     }
-  }
 
-
-  private def validateAuth(authSchemeFunc: => String, googleConfiguration: GoogleConfiguration): ErrorOr[GoogleAuthMode] = {
+  private def validateAuth(authSchemeFunc: => String,
+                           googleConfiguration: GoogleConfiguration
+  ): ErrorOr[GoogleAuthMode] =
     validate[String](authSchemeFunc) match {
-      case Valid(schemeString) => googleConfiguration.auth(schemeString) match {
-        case Valid(auth @ (_:ApplicationDefaultMode | _:ServiceAccountMode)) => auth.valid
-        case Valid(auth @ (_: MockAuthMode)) => auth.valid // Allow mocking for tests
-        case Valid(_) => s"`auth` scheme: $schemeString is not allowed for Stackdriver instrumentation. Only `application_default` and `service_account` modes are valid.".invalidNel
-        case Invalid(error) => s"`auth` scheme is invalid. Errors: $error".invalidNel
-      }
+      case Valid(schemeString) =>
+        googleConfiguration.auth(schemeString) match {
+          case Valid(auth @ (_: ApplicationDefaultMode | _: ServiceAccountMode)) => auth.valid
+          case Valid(auth @ (_: MockAuthMode)) => auth.valid // Allow mocking for tests
+          case Valid(_) =>
+            s"`auth` scheme: $schemeString is not allowed for Stackdriver instrumentation. Only `application_default` and `service_account` modes are valid.".invalidNel
+          case Invalid(error) => s"`auth` scheme is invalid. Errors: $error".invalidNel
+        }
       case Invalid(e) => e.invalid
     }
-  }
-
 
   def apply(serviceConfig: Config, globalConfig: Config): StackdriverConfig = {
     val googleConfiguration: GoogleConfiguration = GoogleConfiguration(globalConfig)
     val cromwellInstanceId: ErrorOr[Option[String]] = globalConfig.getAs[String]("system.cromwell_id").validNel
 
-    val googleProject: ErrorOr[String] = validate[String] { serviceConfig.as[String]("google-project") }
+    val googleProject: ErrorOr[String] = validate[String](serviceConfig.as[String]("google-project"))
     val authScheme: ErrorOr[GoogleAuthMode] = validateAuth(serviceConfig.as[String]("auth"), googleConfiguration)
     val flushRate: ErrorOr[FiniteDuration] = validateFlushRate(serviceConfig.as[FiniteDuration]("flush-rate"))
     val cromwellInstanceRole: ErrorOr[Option[String]] = serviceConfig.getAs[String](CromwellInstanceRole).validNel
     val cromwellPerfTestCase: ErrorOr[Option[String]] = serviceConfig.getAs[String](CromwellPerfTest).validNel
 
-    (googleProject, authScheme, flushRate, cromwellInstanceId, cromwellInstanceRole, cromwellPerfTestCase).mapN({ (p, a, f, i, r, t) =>
-      new StackdriverConfig(p, a, f, i, r, t)
-    }).valueOr(errors => throw AggregatedMessageException("Stackdriver instrumentation config is invalid. Error(s)", errors.toList))
+    (googleProject, authScheme, flushRate, cromwellInstanceId, cromwellInstanceRole, cromwellPerfTestCase)
+      .mapN { (p, a, f, i, r, t) =>
+        new StackdriverConfig(p, a, f, i, r, t)
+      }
+      .valueOr(errors =>
+        throw AggregatedMessageException("Stackdriver instrumentation config is invalid. Error(s)", errors.toList)
+      )
   }
 }
diff --git a/services/src/main/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverInstrumentationServiceActor.scala b/services/src/main/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverInstrumentationServiceActor.scala
index 02dce2b78ad..28048becea8 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverInstrumentationServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverInstrumentationServiceActor.scala
@@ -20,8 +20,11 @@ import scala.jdk.CollectionConverters._
 import scala.concurrent.duration._
 import scala.util.Try
 
-
-class StackdriverInstrumentationServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor with StrictLogging {
+class StackdriverInstrumentationServiceActor(serviceConfig: Config,
+                                             globalConfig: Config,
+                                             serviceRegistryActor: ActorRef
+) extends Actor
+    with StrictLogging {
   implicit lazy val executionContext = context.dispatcher
 
   val stackdriverConfig = StackdriverConfig(serviceConfig, globalConfig)
@@ -33,7 +36,8 @@ class StackdriverInstrumentationServiceActor(serviceConfig: Config, globalConfig
   var metricsMap = Map.empty[StackdriverMetric, Vector[Double]]
 
   // Instantiates a client
-  val metricServiceSettings = MetricServiceSettings.newBuilder.setCredentialsProvider(FixedCredentialsProvider.create(credentials)).build
+  val metricServiceSettings =
+    MetricServiceSettings.newBuilder.setCredentialsProvider(FixedCredentialsProvider.create(credentials)).build
   final val metricServiceClient = MetricServiceClient.create(metricServiceSettings)
 
   // Prepares the monitored resource descriptor
@@ -43,16 +47,16 @@ class StackdriverInstrumentationServiceActor(serviceConfig: Config, globalConfig
   // Give the actor time to warm up, then start sending the metrics to Stackdriver at an interval
   context.system.scheduler.schedule(InitialDelay, stackdriverConfig.flushRate, self, SendStackdriverMetricCommand)
 
-
   override def receive = {
     case SendStackdriverMetricCommand => sendMetricData()
-    case InstrumentationServiceMessage(cromwellMetric) => cromwellMetric match {
-      case CromwellTiming(bucket, value, _) => updateMetricMap(bucket, value.toMillis.toDouble, StackdriverGauge)
-      case CromwellGauge(bucket, value) => updateMetricMap(bucket, value.toDouble, StackdriverGauge)
-      case CromwellCount(bucket, value, _) => updateMetricMap(bucket, value.toDouble, StackdriverCumulative)
-      case CromwellIncrement(bucket) => updateMetricMap(bucket, metricValue = 1D, metricKind = StackdriverCumulative)
-      case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-    }
+    case InstrumentationServiceMessage(cromwellMetric) =>
+      cromwellMetric match {
+        case CromwellTiming(bucket, value, _) => updateMetricMap(bucket, value.toMillis.toDouble, StackdriverGauge)
+        case CromwellGauge(bucket, value) => updateMetricMap(bucket, value.toDouble, StackdriverGauge)
+        case CromwellCount(bucket, value, _) => updateMetricMap(bucket, value.toDouble, StackdriverCumulative)
+        case CromwellIncrement(bucket) => updateMetricMap(bucket, metricValue = 1d, metricKind = StackdriverCumulative)
+        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
+      }
     case ShutdownCommand =>
       // flush out metrics (if any) before shut down
       sendMetricData()
@@ -60,29 +64,24 @@ class StackdriverInstrumentationServiceActor(serviceConfig: Config, globalConfig
       context stop self
   }
 
-
   private def generateMetricLabels(): Map[String, String] = {
-    def labelFromConfig(op: StackdriverConfig => Option[String], key: String): Option[(String, String)] = {
+    def labelFromConfig(op: StackdriverConfig => Option[String], key: String): Option[(String, String)] =
       op(stackdriverConfig).map(v => (key.replace("-", "_"), v))
-    }
 
     labelFromConfig(_.cromwellInstanceIdentifier, CromwellInstanceIdentifier).toMap ++
       labelFromConfig(_.cromwellInstanceRole, CromwellInstanceRole) ++
       labelFromConfig(_.cromwellPerfTestCase, CromwellPerfTest)
   }
 
-
   private def updateMetricMap(bucket: CromwellBucket, metricValue: Double, metricKind: StackdriverMetricKind): Unit = {
     val metricObj = StackdriverMetric(bucket.toStackdriverString, metricKind)
 
     if (metricsMap.contains(metricObj)) {
       val valueVector: Vector[Double] = metricsMap(metricObj) :+ metricValue
       metricsMap += metricObj -> valueVector
-    }
-    else metricsMap += metricObj -> Vector(metricValue)
+    } else metricsMap += metricObj -> Vector(metricValue)
   }
 
-
   private def sendMetricData(): Unit = {
     metricsMap.foreach { case (key, value: Vector[Double]) =>
       val dataPointVectorSum = value.sum
@@ -91,29 +90,42 @@ class StackdriverInstrumentationServiceActor(serviceConfig: Config, globalConfig
         case StackdriverCumulative => dataPointVectorSum
       }
 
-      writeMetrics(key, dataPoint) recover {
-        case e => logger.error(s"Failed to send metrics to Stackdriver API for metric ${key.name} with value $dataPoint.", e)
+      writeMetrics(key, dataPoint) recover { case e =>
+        logger.error(s"Failed to send metrics to Stackdriver API for metric ${key.name} with value $dataPoint.", e)
       }
     }
 
     metricsMap = Map.empty[StackdriverMetric, Vector[Double]]
   }
 
-
   private def writeMetrics(metricObj: StackdriverMetric, value: Double): Try[Unit] = {
-    def timeInterval(metricKind: StackdriverMetricKind): TimeInterval = {
+    def timeInterval(metricKind: StackdriverMetricKind): TimeInterval =
       metricKind match {
-        case StackdriverGauge => TimeInterval.newBuilder.setEndTime(Timestamps.fromMillis(System.currentTimeMillis)).build
-        case StackdriverCumulative => TimeInterval.newBuilder.setStartTime(ActorCreationTime).setEndTime(Timestamps.fromMillis(System.currentTimeMillis)).build
+        case StackdriverGauge =>
+          TimeInterval.newBuilder.setEndTime(Timestamps.fromMillis(System.currentTimeMillis)).build
+        case StackdriverCumulative =>
+          TimeInterval.newBuilder
+            .setStartTime(ActorCreationTime)
+            .setEndTime(Timestamps.fromMillis(System.currentTimeMillis))
+            .build
       }
-    }
 
-    def createTimeSeries(metricKind: StackdriverMetricKind, metric: Metric, resource: MonitoredResource, dataPointList: util.List[Point]): TimeSeries = {
+    def createTimeSeries(metricKind: StackdriverMetricKind,
+                         metric: Metric,
+                         resource: MonitoredResource,
+                         dataPointList: util.List[Point]
+    ): TimeSeries =
       metricKind match {
-        case StackdriverGauge => TimeSeries.newBuilder.setMetric(metric).setResource(resource).addAllPoints(dataPointList).build
-        case StackdriverCumulative => TimeSeries.newBuilder.setMetric(metric).setResource(resource).setMetricKind(MetricDescriptor.MetricKind.CUMULATIVE).addAllPoints(dataPointList).build
+        case StackdriverGauge =>
+          TimeSeries.newBuilder.setMetric(metric).setResource(resource).addAllPoints(dataPointList).build
+        case StackdriverCumulative =>
+          TimeSeries.newBuilder
+            .setMetric(metric)
+            .setResource(resource)
+            .setMetricKind(MetricDescriptor.MetricKind.CUMULATIVE)
+            .addAllPoints(dataPointList)
+            .build
       }
-    }
 
     // Prepares an individual data point
     val interval = timeInterval(metricObj.kind)
@@ -122,26 +134,25 @@ class StackdriverInstrumentationServiceActor(serviceConfig: Config, globalConfig
     val dataPointList: List[Point] = List[Point](dataPoint)
 
     // Prepares the metric descriptor
-    val metric: Metric = Metric.newBuilder.setType(s"$CustomMetricDomain/${metricObj.name}").putAllLabels(metricLabelsMap.asJava).build
+    val metric: Metric =
+      Metric.newBuilder.setType(s"$CustomMetricDomain/${metricObj.name}").putAllLabels(metricLabelsMap.asJava).build
 
     // Prepares the time series request
     val timeSeries = createTimeSeries(metricObj.kind, metric, monitoredResource, dataPointList.asJava)
     val timeSeriesList = List[TimeSeries](timeSeries)
 
-    val timeSeriesRequest = CreateTimeSeriesRequest.newBuilder.setName(projectName.toString).addAllTimeSeries(timeSeriesList.asJava).build
+    val timeSeriesRequest =
+      CreateTimeSeriesRequest.newBuilder.setName(projectName.toString).addAllTimeSeries(timeSeriesList.asJava).build
 
     // Writes time series data
     Try(sendTimeSeriesToStackdriver(timeSeriesRequest))
   }
 
-
   // This single line of code is a separate function to help with StackdriverInstrumentationActor tests
-  def sendTimeSeriesToStackdriver(timeSeriesRequest: CreateTimeSeriesRequest): Unit = {
+  def sendTimeSeriesToStackdriver(timeSeriesRequest: CreateTimeSeriesRequest): Unit =
     metricServiceClient.createTimeSeries(timeSeriesRequest)
-  }
 }
 
-
 object StackdriverInstrumentationServiceActor {
   val CromwellMetricPrefix = List("cromwell")
 
@@ -160,24 +171,24 @@ object StackdriverInstrumentationServiceActor {
 
   val InitialDelay = 1.minute
 
-  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) = Props(new StackdriverInstrumentationServiceActor(serviceConfig, globalConfig, serviceRegistryActor))
+  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) = Props(
+    new StackdriverInstrumentationServiceActor(serviceConfig, globalConfig, serviceRegistryActor)
+  )
 
   implicit class CromwellBucketEnhanced(val cromwellBucket: CromwellBucket) extends AnyVal {
+
     /**
       * Transforms a CromwellBucket to a Stackdriver path
       */
     def toStackdriverString = (CromwellMetricPrefix ++ cromwellBucket.prefix ++
-        cromwellBucket.path.toList).mkString("/").replaceAll(" ", "_").replaceAll("\\[|\\]", "")
+      cromwellBucket.path.toList).mkString("/").replaceAll(" ", "_").replaceAll("\\[|\\]", "")
   }
 }
 
-
 sealed trait StackdriverMetricKind
 object StackdriverGauge extends StackdriverMetricKind
 object StackdriverCumulative extends StackdriverMetricKind
 
-
 case class StackdriverMetric(name: String, kind: StackdriverMetricKind)
 
-
 object SendStackdriverMetricCommand
diff --git a/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/CromwellStatsD.scala b/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/CromwellStatsD.scala
index c9450c4efcd..2a7b559387e 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/CromwellStatsD.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/CromwellStatsD.scala
@@ -12,10 +12,9 @@ object CromwellStatsD {
   */
 case class CromwellStatsD(hostname: String, port: Int) extends StatsD(hostname, port) {
   val MetricSuffixesToFilter = Set("max", "min", "p50", "p75", "p98", "p99", "p999", "mean_rate", "m5_rate", "m15_rate")
-  
-  override def send(name: String, value: String): Unit = {
+
+  override def send(name: String, value: String): Unit =
     if (MetricSuffixesToFilter.exists(suffix => name.endsWith(suffix)))
       CromwellStatsD.logger.debug(s"Filtering metric with name [$name] and value [$value]")
     else super.send(name, value)
-  }
 }
diff --git a/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/StatsDConfig.scala b/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/StatsDConfig.scala
index d67eb348bdf..9dd063cf1cd 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/StatsDConfig.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/StatsDConfig.scala
@@ -15,16 +15,20 @@ case class StatsDConfig(hostname: String, port: Int, prefix: Option[String], flu
 object StatsDConfig {
   def apply(serviceConfig: Config): StatsDConfig = {
 
-    val hostname: ErrorOr[String] = validate[String] { serviceConfig.as[String]("hostname") }
-    val port: ErrorOr[Int] = validate[Int] { serviceConfig.as[Int]("port") }
-    val prefix: ErrorOr[Option[String]] = validate { serviceConfig.as[Option[String]]("prefix") }
-    val flushRate: ErrorOr[FiniteDuration] = validate[FiniteDuration] { serviceConfig.as[FiniteDuration]("flush-rate") }
+    val hostname: ErrorOr[String] = validate[String](serviceConfig.as[String]("hostname"))
+    val port: ErrorOr[Int] = validate[Int](serviceConfig.as[Int]("port"))
+    val prefix: ErrorOr[Option[String]] = validate(serviceConfig.as[Option[String]]("prefix"))
+    val flushRate: ErrorOr[FiniteDuration] = validate[FiniteDuration](serviceConfig.as[FiniteDuration]("flush-rate"))
 
-    (hostname, port, prefix, flushRate).mapN({ (h, p, n, f) => 
-      new StatsDConfig(h, p, n, f)
-    }).valueOr(errors => throw new IllegalArgumentException with MessageAggregation {
-      override val exceptionContext = "StatsD config is invalid"
-      override val errorMessages = errors.toList
-    })
+    (hostname, port, prefix, flushRate)
+      .mapN { (h, p, n, f) =>
+        new StatsDConfig(h, p, n, f)
+      }
+      .valueOr(errors =>
+        throw new IllegalArgumentException with MessageAggregation {
+          override val exceptionContext = "StatsD config is invalid"
+          override val errorMessages = errors.toList
+        }
+      )
   }
 }
diff --git a/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActor.scala b/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActor.scala
index a90c7f66a8c..06accb59cf4 100644
--- a/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActor.scala
@@ -22,6 +22,7 @@ object StatsDInstrumentationServiceActor {
     Props(new StatsDInstrumentationServiceActor(serviceConfig, globalConfig, serviceRegistryActor))
 
   implicit class CromwellBucketEnhanced(val cromwellBucket: CromwellBucket) extends AnyVal {
+
     /**
       * Transforms a CromwellBucket to a StatsD path, optionally inserting a value between prefix and path
       */
@@ -45,7 +46,9 @@ object StatsDInstrumentationServiceActor {
   * If performance or statistics accuracy becomes a problem one might implement a more efficient solution
   * by making use of downsampling and / or multi metrics packets: https://github.com/etsy/statsd/blob/master/docs/metric_types.md
   */
-class StatsDInstrumentationServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor with DefaultInstrumented {
+class StatsDInstrumentationServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
+    extends Actor
+    with DefaultInstrumented {
   val statsDConfig: StatsDConfig = StatsDConfig(serviceConfig)
   val cromwellInstanceIdOption: Option[String] = globalConfig.getAs[String]("system.cromwell_id")
 
@@ -63,13 +66,14 @@ class StatsDInstrumentationServiceActor(serviceConfig: Config, globalConfig: Con
     .start(statsDConfig.flushRate.toMillis, TimeUnit.MILLISECONDS)
 
   override def receive: Receive = {
-    case InstrumentationServiceMessage(cromwellMetric) => cromwellMetric match {
-      case CromwellIncrement(bucket) => increment(bucket)
-      case CromwellCount(bucket, value, _) => updateCounter(bucket, value)
-      case CromwellGauge(bucket, value) => updateGauge(bucket, value)
-      case CromwellTiming(bucket, value, _) => updateTiming(bucket, value)
-      case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
-    }
+    case InstrumentationServiceMessage(cromwellMetric) =>
+      cromwellMetric match {
+        case CromwellIncrement(bucket) => increment(bucket)
+        case CromwellCount(bucket, value, _) => updateCounter(bucket, value)
+        case CromwellGauge(bucket, value) => updateGauge(bucket, value)
+        case CromwellTiming(bucket, value, _) => updateTiming(bucket, value)
+        case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
+      }
     case ShutdownCommand => context stop self
   }
 
@@ -105,7 +109,7 @@ class StatsDInstrumentationServiceActor(serviceConfig: Config, globalConfig: Con
     val newGauge = !gaugeFunctions.containsKey(bucket)
     gaugeFunctions.put(bucket, value)
     if (newGauge) {
-      metrics.gauge(bucket.toStatsDString()){ gaugeFunctions.get(bucket) }
+      metrics.gauge(bucket.toStatsDString())(gaugeFunctions.get(bucket))
     }
     ()
   }
@@ -113,7 +117,6 @@ class StatsDInstrumentationServiceActor(serviceConfig: Config, globalConfig: Con
   /**
     * Adds a new timing value for this bucket
     */
-  private def updateTiming(bucket: CromwellBucket, value: FiniteDuration): Unit = {
+  private def updateTiming(bucket: CromwellBucket, value: FiniteDuration): Unit =
     metrics.timer(bucket.toStatsDString()).update(value)
-  }
 }
diff --git a/services/src/main/scala/cromwell/services/keyvalue/KeyValueReadActor.scala b/services/src/main/scala/cromwell/services/keyvalue/KeyValueReadActor.scala
index 7f166f02ffe..3a03906ac6f 100644
--- a/services/src/main/scala/cromwell/services/keyvalue/KeyValueReadActor.scala
+++ b/services/src/main/scala/cromwell/services/keyvalue/KeyValueReadActor.scala
@@ -11,9 +11,9 @@ import scala.concurrent.Future
 import scala.util.{Failure, Success}
 
 abstract class KeyValueReadActor(override val threshold: Int, override val serviceRegistryActor: ActorRef)
-  extends EnhancedThrottlerActor[CommandAndReplyTo[KvGet]] {
+    extends EnhancedThrottlerActor[CommandAndReplyTo[KvGet]] {
   override def receive = enhancedReceive.orElse(super.receive)
-  
+
   override def processHead(head: CommandAndReplyTo[KvGet]) = instrumentedProcess {
     val processed = processGet(head.command)
     processed onComplete {
@@ -24,12 +24,13 @@ abstract class KeyValueReadActor(override val threshold: Int, override val servi
     // In this case it's 1 because we processed 1 KvGet
     processed.map(_ => 1)
   }
-  
+
   def processGet(get: KvGet): Future[KvResponse]
 
-  override protected lazy val instrumentationPath = KeyValueServiceActor.InstrumentationPath.concatNel(NonEmptyList.one("read"))
+  override protected lazy val instrumentationPath =
+    KeyValueServiceActor.InstrumentationPath.concatNel(NonEmptyList.one("read"))
   override protected lazy val instrumentationPrefix = InstrumentationPrefixes.ServicesPrefix
-  override def commandToData(snd: ActorRef) = {
-    case get: KvGet => CommandAndReplyTo(get, snd)
+  override def commandToData(snd: ActorRef) = { case get: KvGet =>
+    CommandAndReplyTo(get, snd)
   }
 }
diff --git a/services/src/main/scala/cromwell/services/keyvalue/KeyValueServiceActor.scala b/services/src/main/scala/cromwell/services/keyvalue/KeyValueServiceActor.scala
index 96d7071e4f7..575209ffcee 100644
--- a/services/src/main/scala/cromwell/services/keyvalue/KeyValueServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/keyvalue/KeyValueServiceActor.scala
@@ -48,10 +48,10 @@ trait KeyValueServiceActor extends Actor with GracefulShutdownHelper with ActorL
     case _: ActorInitializationException => Escalate
     case t => super.supervisorStrategy.decider.applyOrElse(t, (_: Any) => Escalate)
   }
-  
+
   private val kvReadActor = context.actorOf(kvReadActorProps, "KvReadActor")
   private val kvWriteActor = context.actorOf(kvWriteActorProps, "KvWriteActor")
-  
+
   override def receive = {
     case get: KvGet => kvReadActor forward get
     case put: KvPut => kvWriteActor forward put
diff --git a/services/src/main/scala/cromwell/services/keyvalue/KeyValueWriteActor.scala b/services/src/main/scala/cromwell/services/keyvalue/KeyValueWriteActor.scala
index 372f7fea271..799ccf7d9a0 100644
--- a/services/src/main/scala/cromwell/services/keyvalue/KeyValueWriteActor.scala
+++ b/services/src/main/scala/cromwell/services/keyvalue/KeyValueWriteActor.scala
@@ -11,19 +11,22 @@ import scala.concurrent.Future
 import scala.concurrent.duration.FiniteDuration
 import scala.util.{Failure, Success}
 
-abstract class KeyValueWriteActor(override val serviceRegistryActor: ActorRef, flushRate: FiniteDuration, batchSize: Int)
-  extends EnhancedBatchActor[CommandAndReplyTo[KvPut]](flushRate, batchSize) {
+abstract class KeyValueWriteActor(override val serviceRegistryActor: ActorRef,
+                                  flushRate: FiniteDuration,
+                                  batchSize: Int
+) extends EnhancedBatchActor[CommandAndReplyTo[KvPut]](flushRate, batchSize) {
 
-  
   override protected def process(data: NonEmptyVector[CommandAndReplyTo[KvPut]]) = instrumentedProcess {
     val processed = processPut(data.map(_.command).toVector)
     processed onComplete {
-      case Success(_) => data.toVector.foreach({
-        case CommandAndReplyTo(command, replyTo) => replyTo ! KvPutSuccess(command)
-      })
-      case Failure(f) => data.toVector.foreach({
-        case CommandAndReplyTo(command, replyTo) => replyTo ! KvFailure(command, f)
-      })
+      case Success(_) =>
+        data.toVector.foreach { case CommandAndReplyTo(command, replyTo) =>
+          replyTo ! KvPutSuccess(command)
+        }
+      case Failure(f) =>
+        data.toVector.foreach { case CommandAndReplyTo(command, replyTo) =>
+          replyTo ! KvFailure(command, f)
+        }
     }
     // This method should return how many "operations" have been performed to enable instrumentation of throughput
     // Here we've processed all the KvPuts in "data"
@@ -31,13 +34,14 @@ abstract class KeyValueWriteActor(override val serviceRegistryActor: ActorRef, f
   }
 
   def processPut(put: Vector[KvPut]): Future[Unit]
-  
+
   // EnhancedBatchActor overrides
   override def receive = enhancedReceive.orElse(super.receive)
   override protected def weightFunction(command: CommandAndReplyTo[KvPut]) = 1
-  override protected def instrumentationPath = KeyValueServiceActor.InstrumentationPath.concatNel(NonEmptyList.one("write"))
+  override protected def instrumentationPath =
+    KeyValueServiceActor.InstrumentationPath.concatNel(NonEmptyList.one("write"))
   override protected def instrumentationPrefix = InstrumentationPrefixes.ServicesPrefix
-  override def commandToData(snd: ActorRef) = {
-    case put: KvPut => CommandAndReplyTo(put, snd)
+  override def commandToData(snd: ActorRef) = { case put: KvPut =>
+    CommandAndReplyTo(put, snd)
   }
 }
diff --git a/services/src/main/scala/cromwell/services/keyvalue/KvClient.scala b/services/src/main/scala/cromwell/services/keyvalue/KvClient.scala
index c8ddbcb880f..ed130b35773 100644
--- a/services/src/main/scala/cromwell/services/keyvalue/KvClient.scala
+++ b/services/src/main/scala/cromwell/services/keyvalue/KvClient.scala
@@ -10,18 +10,18 @@ trait KvClient { this: Actor with ActorLogging =>
   def serviceRegistryActor: ActorRef
   private[keyvalue] var currentKvClientRequests: Map[ScopedKey, Promise[KvResponse]] = Map.empty
 
-  final def makeKvRequest(actions: Seq[KvAction])(implicit ec: ExecutionContext): Future[Seq[KvResponse]] = {
+  final def makeKvRequest(actions: Seq[KvAction])(implicit ec: ExecutionContext): Future[Seq[KvResponse]] =
     if (actions.exists(action => currentKvClientRequests.contains(action.key))) {
-      val msg = "Programmer Error! KvClient does not support multiple KvActions active for the same ScopedKey concurrently. Mi Scusi!"
+      val msg =
+        "Programmer Error! KvClient does not support multiple KvActions active for the same ScopedKey concurrently. Mi Scusi!"
       log.error(msg)
       Future.failed(new RuntimeException(msg))
     } else {
       createResponseSet(actions)
     }
-  }
 
-  final def kvClientReceive: Actor.Receive = {
-    case response: KvResponse => fulfillOrLog(response)
+  final def kvClientReceive: Actor.Receive = { case response: KvResponse =>
+    fulfillOrLog(response)
   }
 
   private def createResponseSet(newActions: Seq[KvAction])(implicit ec: ExecutionContext) = {
@@ -35,7 +35,10 @@ trait KvClient { this: Actor with ActorLogging =>
     case Some(fulfilledPromise) =>
       fulfilledPromise.success(response)
       currentKvClientRequests -= response.key
-    case None => log.error(s"Programmer Error: Got a KV response for a request that was never sent: $response. Did you use the KV store without KvClient? Current key set: ${currentKvClientRequests.keys.mkString("")}")
+    case None =>
+      log.error(
+        s"Programmer Error: Got a KV response for a request that was never sent: $response. Did you use the KV store without KvClient? Current key set: ${currentKvClientRequests.keys
+            .mkString("")}"
+      )
   }
 }
-
diff --git a/services/src/main/scala/cromwell/services/keyvalue/impl/BackendKeyValueDatabaseAccess.scala b/services/src/main/scala/cromwell/services/keyvalue/impl/BackendKeyValueDatabaseAccess.scala
index 47fcbbb3a03..0bcf1c70fe4 100644
--- a/services/src/main/scala/cromwell/services/keyvalue/impl/BackendKeyValueDatabaseAccess.scala
+++ b/services/src/main/scala/cromwell/services/keyvalue/impl/BackendKeyValueDatabaseAccess.scala
@@ -17,27 +17,43 @@ object BackendKeyValueDatabaseAccess {
 
 trait BackendKeyValueDatabaseAccess {
 
-  def getBackendValueByKey(workflowId: WorkflowId, jobKey: KvJobKey, key: String)
-                           (implicit ec: ExecutionContext): Future[Option[String]] = {
-    EngineServicesStore.engineDatabaseInterface.queryStoreValue(
-      workflowId.toString, jobKey.callFqn, jobKey.callIndex.fromIndex, jobKey.callAttempt, key)
-  }
+  def getBackendValueByKey(workflowId: WorkflowId, jobKey: KvJobKey, key: String)(implicit
+    ec: ExecutionContext
+  ): Future[Option[String]] =
+    EngineServicesStore.engineDatabaseInterface.queryStoreValue(workflowId.toString,
+                                                                jobKey.callFqn,
+                                                                jobKey.callIndex.fromIndex,
+                                                                jobKey.callAttempt,
+                                                                key
+    )
 
   def updateBackendKeyValuePair(workflowId: WorkflowId,
                                 jobKey: KvJobKey,
                                 backendStoreKey: String,
-                                backendStoreValue: String)(implicit ec: ExecutionContext, actorSystem: ActorSystem): Future[Unit] = {
-    val jobKeyValueEntry = JobKeyValueEntry(workflowId.toString, jobKey.callFqn, jobKey.callIndex.fromIndex,
-      jobKey.callAttempt, backendStoreKey, backendStoreValue)
+                                backendStoreValue: String
+  )(implicit ec: ExecutionContext, actorSystem: ActorSystem): Future[Unit] = {
+    val jobKeyValueEntry = JobKeyValueEntry(workflowId.toString,
+                                            jobKey.callFqn,
+                                            jobKey.callIndex.fromIndex,
+                                            jobKey.callAttempt,
+                                            backendStoreKey,
+                                            backendStoreValue
+    )
     withRetry(() => EngineServicesStore.engineDatabaseInterface.addJobKeyValueEntry(jobKeyValueEntry))
   }
 
-  def updateBackendKeyValuePairs(pairs: Iterable[BackendKeyValuePair])(implicit ec: ExecutionContext, actorSystem: ActorSystem): Future[Unit] = {
-    val entries = pairs.map({
-      case (workflowId, jobKey, backendStoreKey, backendStoreValue) =>
-        JobKeyValueEntry(workflowId.toString, jobKey.callFqn, jobKey.callIndex.fromIndex,
-          jobKey.callAttempt, backendStoreKey, backendStoreValue)
-    })
+  def updateBackendKeyValuePairs(
+    pairs: Iterable[BackendKeyValuePair]
+  )(implicit ec: ExecutionContext, actorSystem: ActorSystem): Future[Unit] = {
+    val entries = pairs.map { case (workflowId, jobKey, backendStoreKey, backendStoreValue) =>
+      JobKeyValueEntry(workflowId.toString,
+                       jobKey.callFqn,
+                       jobKey.callIndex.fromIndex,
+                       jobKey.callAttempt,
+                       backendStoreKey,
+                       backendStoreValue
+      )
+    }
     withRetry(() => EngineServicesStore.engineDatabaseInterface.addJobKeyValueEntries(entries))
   }
 }
diff --git a/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueReadActor.scala b/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueReadActor.scala
index 21bc2fa41c5..751d5a82293 100644
--- a/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueReadActor.scala
+++ b/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueReadActor.scala
@@ -5,13 +5,13 @@ import cromwell.services.keyvalue.KeyValueServiceActor.{KvKeyLookupFailed, KvPai
 import cromwell.services.keyvalue.{KeyValueReadActor, KeyValueServiceActor}
 
 object SqlKeyValueReadActor {
-  def props(threshold: Int, serviceRegistryActor: ActorRef) = {
+  def props(threshold: Int, serviceRegistryActor: ActorRef) =
     Props(new SqlKeyValueReadActor(threshold, serviceRegistryActor))
-  }
 }
 
 class SqlKeyValueReadActor(threshold: Int, serviceRegistryActor: ActorRef)
-  extends KeyValueReadActor(threshold, serviceRegistryActor) with BackendKeyValueDatabaseAccess {
+    extends KeyValueReadActor(threshold, serviceRegistryActor)
+    with BackendKeyValueDatabaseAccess {
   override def processGet(get: KeyValueServiceActor.KvGet) = {
     val backendValue = getBackendValueByKey(
       get.key.workflowId,
diff --git a/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueServiceActor.scala b/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueServiceActor.scala
index 43edc284f42..b8311113a72 100644
--- a/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueServiceActor.scala
@@ -9,28 +9,27 @@ import net.ceedubs.ficus.Ficus._
 
 import scala.concurrent.duration._
 object SqlKeyValueServiceActor {
-  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) = Props(SqlKeyValueServiceActor(serviceConfig, globalConfig, serviceRegistryActor)).withDispatcher(ServiceDispatcher)
+  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) =
+    Props(SqlKeyValueServiceActor(serviceConfig, globalConfig, serviceRegistryActor)).withDispatcher(ServiceDispatcher)
 }
 
 final case class SqlKeyValueServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
-  extends KeyValueServiceActor {
+    extends KeyValueServiceActor {
 
   private lazy val dbFlushRate = serviceConfig.as[Option[FiniteDuration]]("db-flush-rate").getOrElse(5.seconds)
   private lazy val dbBatchSize = serviceConfig.as[Option[Int]]("db-batch-size").getOrElse(200)
 
-  override protected def kvReadActorProps = {
+  override protected def kvReadActorProps =
     SqlKeyValueReadActor.props(
       LoadConfig.KeyValueReadThreshold,
       serviceRegistryActor
     )
-  }
 
-  override protected def kvWriteActorProps = {
+  override protected def kvWriteActorProps =
     SqlKeyValueWriteActor.props(
       LoadConfig.KeyValueWriteThreshold,
       serviceRegistryActor,
       dbFlushRate,
       dbBatchSize
     )
-  }
 }
diff --git a/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueWriteActor.scala b/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueWriteActor.scala
index 0d25af74ff5..ebe6dc30a56 100644
--- a/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueWriteActor.scala
+++ b/services/src/main/scala/cromwell/services/keyvalue/impl/SqlKeyValueWriteActor.scala
@@ -6,22 +6,22 @@ import cromwell.services.keyvalue.{KeyValueServiceActor, KeyValueWriteActor}
 import scala.concurrent.duration.FiniteDuration
 
 object SqlKeyValueWriteActor {
-  def props(threshold: Int, serviceRegistryActor: ActorRef, flushRate: FiniteDuration, batchSize: Int) = {
+  def props(threshold: Int, serviceRegistryActor: ActorRef, flushRate: FiniteDuration, batchSize: Int) =
     Props(new SqlKeyValueWriteActor(threshold, serviceRegistryActor, flushRate, batchSize))
-  }
 }
 
-class SqlKeyValueWriteActor(override val threshold: Int, serviceRegistryActor: ActorRef, flushRate: FiniteDuration, batchSize: Int)
-  extends KeyValueWriteActor(serviceRegistryActor, flushRate, batchSize) with BackendKeyValueDatabaseAccess {
-  private implicit val system = context.system
+class SqlKeyValueWriteActor(override val threshold: Int,
+                            serviceRegistryActor: ActorRef,
+                            flushRate: FiniteDuration,
+                            batchSize: Int
+) extends KeyValueWriteActor(serviceRegistryActor, flushRate, batchSize)
+    with BackendKeyValueDatabaseAccess {
+  implicit private val system = context.system
 
   override def processPut(puts: Vector[KeyValueServiceActor.KvPut]) = {
-    val pairs = puts.map({put =>
-      (put.pair.key.workflowId,
-        put.pair.key.jobKey,
-        put.pair.key.key,
-        put.pair.value)
-    })
+    val pairs = puts.map { put =>
+      (put.pair.key.workflowId, put.pair.key.jobKey, put.pair.key.key, put.pair.value)
+    }
     updateBackendKeyValuePairs(pairs)
   }
 }
diff --git a/services/src/main/scala/cromwell/services/loadcontroller/LoadControlledBatchActor.scala b/services/src/main/scala/cromwell/services/loadcontroller/LoadControlledBatchActor.scala
index bb25febf5c0..30fc5935090 100644
--- a/services/src/main/scala/cromwell/services/loadcontroller/LoadControlledBatchActor.scala
+++ b/services/src/main/scala/cromwell/services/loadcontroller/LoadControlledBatchActor.scala
@@ -18,9 +18,13 @@ object LoadControlledBatchActor {
 trait LoadControlledBatchActor[C] { this: BatchActor[C] =>
   def threshold: Int
   def serviceRegistryActor: ActorRef
-  private val path = if (routed) NonEmptyList.of(context.parent.path.name, self.path.name) else NonEmptyList.one(self.path.name)
+  private val path =
+    if (routed) NonEmptyList.of(context.parent.path.name, self.path.name) else NonEmptyList.one(self.path.name)
 
-  timers.startSingleTimer(LoadControlledBatchActorTimerKey, LoadControlledBatchActorTimerAction, LoadConfig.MonitoringFrequency)
+  timers.startSingleTimer(LoadControlledBatchActorTimerKey,
+                          LoadControlledBatchActorTimerAction,
+                          LoadConfig.MonitoringFrequency
+  )
 
   private def weightToLoad(weight: Int) = if (weight > threshold) HighLoad else NormalLoad
 
@@ -28,9 +32,11 @@ trait LoadControlledBatchActor[C] { this: BatchActor[C] =>
     * Don't forget to chain this into your receive method to monitor the queue size:
     * override def receive = loadControlReceive.orElse(super.receive)
     */
-  protected def loadControlReceive: Receive = {
-    case LoadControlledBatchActorTimerAction => 
-      serviceRegistryActor ! LoadMetric(path, weightToLoad(stateData.weight))
-      timers.startSingleTimer(LoadControlledBatchActorTimerKey, LoadControlledBatchActorTimerAction, LoadConfig.MonitoringFrequency)
+  protected def loadControlReceive: Receive = { case LoadControlledBatchActorTimerAction =>
+    serviceRegistryActor ! LoadMetric(path, weightToLoad(stateData.weight))
+    timers.startSingleTimer(LoadControlledBatchActorTimerKey,
+                            LoadControlledBatchActorTimerAction,
+                            LoadConfig.MonitoringFrequency
+    )
   }
 }
diff --git a/services/src/main/scala/cromwell/services/loadcontroller/impl/LoadControllerServiceActor.scala b/services/src/main/scala/cromwell/services/loadcontroller/impl/LoadControllerServiceActor.scala
index 8dba38e7e99..8c4c878c4d2 100644
--- a/services/src/main/scala/cromwell/services/loadcontroller/impl/LoadControllerServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/loadcontroller/impl/LoadControllerServiceActor.scala
@@ -28,21 +28,27 @@ object LoadControllerServiceActor {
 class LoadControllerServiceActor(serviceConfig: Config,
                                  globalConfig: Config,
                                  override val serviceRegistryActor: ActorRef
-                                ) extends Actor
-  with ActorLogging with Listeners with Timers with CromwellInstrumentation {
+) extends Actor
+    with ActorLogging
+    with Listeners
+    with Timers
+    with CromwellInstrumentation {
   private val controlFrequency = serviceConfig
     .as[Option[Duration]]("control-frequency")
     .getOrElse(5.seconds)
 
-  private [impl] var loadLevel: LoadLevel = NormalLoad
-  private [impl] var monitoredActors: Set[ActorRef] = Set.empty
-  private [impl] var loadMetrics: Map[ActorAndMetric, LoadLevel] = Map.empty
+  private[impl] var loadLevel: LoadLevel = NormalLoad
+  private[impl] var monitoredActors: Set[ActorRef] = Set.empty
+  private[impl] var loadMetrics: Map[ActorAndMetric, LoadLevel] = Map.empty
 
   override def receive = listenerManagement.orElse(controlReceive)
 
   override def preStart() = {
     if (controlFrequency.isFinite)
-      timers.startPeriodicTimer(LoadControlTimerKey, LoadControlTimerAction, controlFrequency.asInstanceOf[FiniteDuration])
+      timers.startPeriodicTimer(LoadControlTimerKey,
+                                LoadControlTimerAction,
+                                controlFrequency.asInstanceOf[FiniteDuration]
+      )
     else
       log.info("Load control disabled")
     super.preStart()
@@ -74,7 +80,8 @@ class LoadControllerServiceActor(serviceConfig: Config,
     val backToNormal = loadLevel != NormalLoad && newLoadLevel == NormalLoad
     // If there's something to say, let it out !
     if (escalates || backToNormal) {
-      if (newLoadLevel == HighLoad) log.info(s"The following components have reported being overloaded: $highLoadMetricsForLogging")
+      if (newLoadLevel == HighLoad)
+        log.info(s"The following components have reported being overloaded: $highLoadMetricsForLogging")
       gossip(newLoadLevel)
     }
     loadLevel = newLoadLevel
@@ -83,14 +90,16 @@ class LoadControllerServiceActor(serviceConfig: Config,
 
   private def handleTerminated(terminee: ActorRef) = {
     monitoredActors = monitoredActors - terminee
-    loadMetrics = loadMetrics.view.filterKeys({
-      case ActorAndMetric(actor, _) => actor != terminee
-    }).toMap
+    loadMetrics = loadMetrics.view.filterKeys { case ActorAndMetric(actor, _) =>
+      actor != terminee
+    }.toMap
   }
 
-  private def highLoadMetricsForLogging = {
-    loadMetrics.collect({
-      case (ActorAndMetric(_, metricPath), HighLoad) => metricPath.head
-    }).toSet.mkString(", ")
-  }
+  private def highLoadMetricsForLogging =
+    loadMetrics
+      .collect { case (ActorAndMetric(_, metricPath), HighLoad) =>
+        metricPath.head
+      }
+      .toSet
+      .mkString(", ")
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/MetadataArchiveStatus.scala b/services/src/main/scala/cromwell/services/metadata/MetadataArchiveStatus.scala
index 0f32733f666..6c3e978d746 100644
--- a/services/src/main/scala/cromwell/services/metadata/MetadataArchiveStatus.scala
+++ b/services/src/main/scala/cromwell/services/metadata/MetadataArchiveStatus.scala
@@ -30,13 +30,15 @@ object MetadataArchiveStatus {
     case Some(other) => withName(other)
   }
 
-  def withName(str: String): ErrorOr[MetadataArchiveStatus] = MetadataArchiveStatusValues.find(_.toString.equalsIgnoreCase(str)) match {
-    case Some(value) => value.validNel
-    case None => s"No such MetadataArchiveStatus: $str".invalidNel
-  }
+  def withName(str: String): ErrorOr[MetadataArchiveStatus] =
+    MetadataArchiveStatusValues.find(_.toString.equalsIgnoreCase(str)) match {
+      case Some(value) => value.validNel
+      case None => s"No such MetadataArchiveStatus: $str".invalidNel
+    }
 
   case object Unarchived extends MetadataArchiveStatus
   case object Archived extends MetadataArchiveStatus
-  case object ArchivedAndDeleted extends MetadataArchiveStatus // this means that original data is deleted from METADATA_ENTRY table
+  case object ArchivedAndDeleted
+      extends MetadataArchiveStatus // this means that original data is deleted from METADATA_ENTRY table
   case object ArchiveFailed extends MetadataArchiveStatus
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/MetadataJsonSupport.scala b/services/src/main/scala/cromwell/services/metadata/MetadataJsonSupport.scala
index 42930f463d5..efc36c01d28 100644
--- a/services/src/main/scala/cromwell/services/metadata/MetadataJsonSupport.scala
+++ b/services/src/main/scala/cromwell/services/metadata/MetadataJsonSupport.scala
@@ -9,17 +9,23 @@ import common.util.TimeUtil._
 object MetadataJsonSupport extends DefaultJsonProtocol {
   implicit object WorkflowIdJsonFormatter extends RootJsonFormat[WorkflowId] {
     def write(id: WorkflowId) = JsString(id.id.toString)
-    def read(value: JsValue) = throw new UnsupportedOperationException("Reading WorkflowId from JSON is currently unsupported")
+    def read(value: JsValue) = throw new UnsupportedOperationException(
+      "Reading WorkflowId from JSON is currently unsupported"
+    )
   }
 
   implicit object MetadataTypeFormatter extends RootJsonFormat[MetadataType] {
     def write(t: MetadataType) = JsString(t.typeName)
-    def read(value: JsValue) = throw new UnsupportedOperationException("Reading MetadataType from JSON is currently unsupported")
+    def read(value: JsValue) = throw new UnsupportedOperationException(
+      "Reading MetadataType from JSON is currently unsupported"
+    )
   }
 
   implicit object OffsetDateTimeFormatter extends RootJsonFormat[OffsetDateTime] {
     def write(offsetDateTime: OffsetDateTime) = new JsString(offsetDateTime.toUtcMilliString)
-    def read(value: JsValue) = throw new UnsupportedOperationException("Reading OffsetDateTime from JSON is currently unsupported")
+    def read(value: JsValue) = throw new UnsupportedOperationException(
+      "Reading OffsetDateTime from JSON is currently unsupported"
+    )
   }
 
   implicit val MetadataValueFormat = jsonFormat2(MetadataValue.apply)
diff --git a/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala b/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala
index 1b38bd2f479..c88a142605b 100644
--- a/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala
+++ b/services/src/main/scala/cromwell/services/metadata/MetadataQuery.scala
@@ -17,9 +17,8 @@ object MetadataKey {
 
   val KeySeparator = ':'
 
-  def apply(workflowId: WorkflowId, jobKey: Option[MetadataJobKey], keys: String*): MetadataKey = {
-    new MetadataKey(workflowId, jobKey, compositeKey(keys:_*))
-  }
+  def apply(workflowId: WorkflowId, jobKey: Option[MetadataJobKey], keys: String*): MetadataKey =
+    new MetadataKey(workflowId, jobKey, compositeKey(keys: _*))
 
   def compositeKey(keys: String*): String = keys.toList.mkString(KeySeparator.toString)
 }
@@ -27,18 +26,18 @@ object MetadataKey {
 object MetadataEvent {
   def apply(key: MetadataKey, value: MetadataValue) = new MetadataEvent(key, Option(value), OffsetDateTime.now)
 
-  def apply(key: MetadataKey, optionalValue: Option[MetadataValue]) = new MetadataEvent(key, optionalValue, OffsetDateTime.now)
+  def apply(key: MetadataKey, optionalValue: Option[MetadataValue]) =
+    new MetadataEvent(key, optionalValue, OffsetDateTime.now)
 
   def empty(key: MetadataKey) = new MetadataEvent(key, None, OffsetDateTime.now)
 
-  def labelsToMetadataEvents(labels: Labels, workflowId: WorkflowId): Iterable[MetadataEvent] = {
+  def labelsToMetadataEvents(labels: Labels, workflowId: WorkflowId): Iterable[MetadataEvent] =
     labels.value map { label =>
       MetadataEvent(
         MetadataKey(workflowId, None, s"${WorkflowMetadataKeys.Labels}:${label.key}"),
         MetadataValue(label.value)
       )
     }
-  }
 }
 
 sealed trait MetadataType { def typeName: String }
@@ -47,13 +46,13 @@ case object MetadataInt extends MetadataType { override val typeName = "int" }
 case object MetadataNumber extends MetadataType { override val typeName = "number" }
 case object MetadataBoolean extends MetadataType { override val typeName = "boolean" }
 /* TODO Might be better to have MetadataNull be a value instead of a type ?
-  * We'd need to reorganize MetadataValue, maybe like spray does and have explicit case classes types
-  * instead of one generic MetadataValue(value, type)
-*/
+ * We'd need to reorganize MetadataValue, maybe like spray does and have explicit case classes types
+ * instead of one generic MetadataValue(value, type)
+ */
 case object MetadataNull extends MetadataType { override val typeName = "null" }
 
 object MetadataValue {
-  def apply(value: Any): MetadataValue = {
+  def apply(value: Any): MetadataValue =
     Option(value).getOrElse("") match {
       case WomInteger(i) => new MetadataValue(i.toString, MetadataInt)
       case WomFloat(f) => new MetadataValue(f.toString, MetadataNumber)
@@ -63,12 +62,12 @@ object MetadataValue {
       case WomOptionalValue(_, None) => new MetadataValue("", MetadataNull)
       case value: WomValue => new MetadataValue(value.valueString, MetadataString)
       case _: Int | Long | _: java.lang.Long | _: java.lang.Integer => new MetadataValue(value.toString, MetadataInt)
-      case _: Double | Float | _: java.lang.Double | _: java.lang.Float => new MetadataValue(value.toString, MetadataNumber)
+      case _: Double | Float | _: java.lang.Double | _: java.lang.Float =>
+        new MetadataValue(value.toString, MetadataNumber)
       case _: Boolean | _: java.lang.Boolean => new MetadataValue(value.toString, MetadataBoolean)
       case offsetDateTime: OffsetDateTime => new MetadataValue(offsetDateTime.toUtcMilliString, MetadataString)
       case other => new MetadataValue(other.toString, MetadataString)
     }
-  }
 }
 
 object MetadataType {
@@ -93,7 +92,8 @@ final case class MetadataEvent(key: MetadataKey, value: Option[MetadataValue], o
 final case class MetadataQueryJobKey(callFqn: String, index: Option[Int], attempt: Option[Int])
 
 object MetadataQueryJobKey {
-  def forMetadataJobKey(jobKey: MetadataJobKey) = MetadataQueryJobKey(jobKey.callFqn, jobKey.index, Option(jobKey.attempt))
+  def forMetadataJobKey(jobKey: MetadataJobKey) =
+    MetadataQueryJobKey(jobKey.callFqn, jobKey.index, Option(jobKey.attempt))
 }
 
 case class MetadataQuery(workflowId: WorkflowId,
@@ -101,16 +101,28 @@ case class MetadataQuery(workflowId: WorkflowId,
                          key: Option[String],
                          includeKeysOption: Option[NonEmptyList[String]],
                          excludeKeysOption: Option[NonEmptyList[String]],
-                         expandSubWorkflows: Boolean)
+                         expandSubWorkflows: Boolean
+)
 
 object MetadataQuery {
-  def forWorkflow(workflowId: WorkflowId) = MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
-
-  def forJob(workflowId: WorkflowId, jobKey: MetadataJobKey): MetadataQuery = {
-    MetadataQuery(workflowId, Option(MetadataQueryJobKey.forMetadataJobKey(jobKey)), None, None, None, expandSubWorkflows = false)
-  }
-
-  def forKey(key: MetadataKey): MetadataQuery = {
-    MetadataQuery(key.workflowId, key.jobKey map MetadataQueryJobKey.forMetadataJobKey, Option(key.key), None, None, expandSubWorkflows = false)
-  }
+  def forWorkflow(workflowId: WorkflowId) =
+    MetadataQuery(workflowId, None, None, None, None, expandSubWorkflows = false)
+
+  def forJob(workflowId: WorkflowId, jobKey: MetadataJobKey): MetadataQuery =
+    MetadataQuery(workflowId,
+                  Option(MetadataQueryJobKey.forMetadataJobKey(jobKey)),
+                  None,
+                  None,
+                  None,
+                  expandSubWorkflows = false
+    )
+
+  def forKey(key: MetadataKey): MetadataQuery =
+    MetadataQuery(key.workflowId,
+                  key.jobKey map MetadataQueryJobKey.forMetadataJobKey,
+                  Option(key.key),
+                  None,
+                  None,
+                  expandSubWorkflows = false
+    )
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/MetadataService.scala b/services/src/main/scala/cromwell/services/metadata/MetadataService.scala
index dd45cf5535d..57557a842b1 100644
--- a/services/src/main/scala/cromwell/services/metadata/MetadataService.scala
+++ b/services/src/main/scala/cromwell/services/metadata/MetadataService.scala
@@ -27,13 +27,15 @@ object MetadataService {
                                        labels: Option[Map[String, String]],
                                        parentWorkflowId: Option[String],
                                        rootWorkflowId: Option[String],
-                                       metadataArchiveStatus: MetadataArchiveStatus)
+                                       metadataArchiveStatus: MetadataArchiveStatus
+  )
 
   final case class WorkflowQueryResponse(results: Seq[WorkflowQueryResult], totalResultsCount: Int)
 
   final case class QueryMetadata(page: Option[Int], pageSize: Option[Int], totalRecords: Option[Int])
 
   trait MetadataServiceMessage
+
   /**
     * Command Actions
     */
@@ -66,8 +68,13 @@ object MetadataService {
         serviceRegistryActor ! PutMetadataAction(events)
       }
 
-      def putMetadataWithRawKey(workflowId: WorkflowId, jobKey: Option[(FullyQualifiedName, Option[Int], Int)], keyValue: Map[String, Any]) = {
-        val metadataJobKey = jobKey map { case (fullyQualifiedName, index, attempt) => MetadataJobKey(fullyQualifiedName, index, attempt) }
+      def putMetadataWithRawKey(workflowId: WorkflowId,
+                                jobKey: Option[(FullyQualifiedName, Option[Int], Int)],
+                                keyValue: Map[String, Any]
+      ) = {
+        val metadataJobKey = jobKey map { case (fullyQualifiedName, index, attempt) =>
+          MetadataJobKey(fullyQualifiedName, index, attempt)
+        }
 
         val events = keyValue map { case (key, value) =>
           val metadataKey = MetadataKey(workflowId, metadataJobKey, key)
@@ -85,8 +92,12 @@ object MetadataService {
   }
 
   val MaximumMetadataActionAttempts = 10
-  final case class PutMetadataAction(events: Iterable[MetadataEvent], maxAttempts: Int = MaximumMetadataActionAttempts) extends MetadataWriteAction
-  final case class PutMetadataActionAndRespond(events: Iterable[MetadataEvent], replyTo: ActorRef, maxAttempts: Int = MaximumMetadataActionAttempts) extends MetadataWriteAction
+  final case class PutMetadataAction(events: Iterable[MetadataEvent], maxAttempts: Int = MaximumMetadataActionAttempts)
+      extends MetadataWriteAction
+  final case class PutMetadataActionAndRespond(events: Iterable[MetadataEvent],
+                                               replyTo: ActorRef,
+                                               maxAttempts: Int = MaximumMetadataActionAttempts
+  ) extends MetadataWriteAction
 
   final case object ListenToMetadataWriteActor extends MetadataServiceAction with ListenToMessage
 
@@ -95,14 +106,13 @@ object MetadataService {
     def apply(workflowId: WorkflowId,
               includeKeysOption: Option[NonEmptyList[String]],
               excludeKeysOption: Option[NonEmptyList[String]],
-              expandSubWorkflows: Boolean): BuildWorkflowMetadataJsonAction = {
+              expandSubWorkflows: Boolean
+    ): BuildWorkflowMetadataJsonAction =
       GetMetadataAction(MetadataQuery(workflowId, None, None, includeKeysOption, excludeKeysOption, expandSubWorkflows))
-    }
   }
 
-  final case class GetMetadataAction(key: MetadataQuery,
-                                     checkTotalMetadataRowNumberBeforeQuerying: Boolean = true)
-    extends BuildWorkflowMetadataJsonWithOverridableSourceAction {
+  final case class GetMetadataAction(key: MetadataQuery, checkTotalMetadataRowNumberBeforeQuerying: Boolean = true)
+      extends BuildWorkflowMetadataJsonWithOverridableSourceAction {
 
     override def workflowId: WorkflowId = key.workflowId
   }
@@ -112,7 +122,8 @@ object MetadataService {
   final case class GetStatus(workflowId: WorkflowId) extends BuildWorkflowMetadataJsonAction
   final case class GetLabels(workflowId: WorkflowId) extends BuildWorkflowMetadataJsonAction
   final case class GetRootAndSubworkflowLabels(workflowId: WorkflowId) extends BuildWorkflowMetadataJsonAction
-  final case class QueryForWorkflowsMatchingParameters(parameters: Seq[(String, String)]) extends BuildMetadataJsonAction
+  final case class QueryForWorkflowsMatchingParameters(parameters: Seq[(String, String)])
+      extends BuildMetadataJsonAction
   final case class WorkflowOutputs(workflowId: WorkflowId) extends BuildWorkflowMetadataJsonWithOverridableSourceAction
   final case class GetLogs(workflowId: WorkflowId) extends BuildWorkflowMetadataJsonWithOverridableSourceAction
   case object RefreshSummary extends MetadataServiceAction
@@ -137,24 +148,33 @@ object MetadataService {
     def reason: Throwable
   }
 
-  final case class MetadataLookupStreamSuccess(id: WorkflowId, result: DatabasePublisher[MetadataEntry]) extends MetadataServiceResponse
+  final case class MetadataLookupStreamSuccess(id: WorkflowId, result: DatabasePublisher[MetadataEntry])
+      extends MetadataServiceResponse
   final case class MetadataLookupStreamFailed(id: WorkflowId, reason: Throwable) extends MetadataServiceResponse
-  final case class MetadataLookupFailedTooLargeResponse(query: MetadataQuery, metadataSizeRows: Int) extends MetadataServiceResponse
+  final case class MetadataLookupFailedTooLargeResponse(query: MetadataQuery, metadataSizeRows: Int)
+      extends MetadataServiceResponse
   final case class MetadataLookupFailedTimeoutResponse(query: MetadataQuery) extends MetadataServiceResponse
   final case class FetchFailedTasksTimeoutResponse(workflowId: WorkflowId) extends MetadataServiceResponse
-  final case class MetadataLookupResponse(query: MetadataQuery, eventList: Seq[MetadataEvent]) extends MetadataServiceResponse
+  final case class MetadataLookupResponse(query: MetadataQuery, eventList: Seq[MetadataEvent])
+      extends MetadataServiceResponse
   final case class FetchFailedJobsMetadataLookupResponse(events: Seq[MetadataEvent]) extends MetadataServiceResponse
-  final case class FetchFailedJobsMetadataLookupFailed(workflowId: WorkflowId, reason: Throwable) extends MetadataServiceFailure
-  final case class MetadataServiceKeyLookupFailed(query: MetadataQuery, reason: Throwable) extends MetadataServiceFailure
+  final case class FetchFailedJobsMetadataLookupFailed(workflowId: WorkflowId, reason: Throwable)
+      extends MetadataServiceFailure
+  final case class MetadataServiceKeyLookupFailed(query: MetadataQuery, reason: Throwable)
+      extends MetadataServiceFailure
 
   final case class StatusLookupResponse(workflowId: WorkflowId, status: WorkflowState) extends MetadataServiceResponse
   final case class StatusLookupFailed(workflowId: WorkflowId, reason: Throwable) extends MetadataServiceFailure
 
-  final case class LabelLookupResponse(workflowId: WorkflowId, labels: Map[String, String]) extends MetadataServiceResponse
+  final case class LabelLookupResponse(workflowId: WorkflowId, labels: Map[String, String])
+      extends MetadataServiceResponse
   final case class LabelLookupFailed(workflowId: WorkflowId, reason: Throwable) extends MetadataServiceFailure
 
-  final case class RootAndSubworkflowLabelsLookupResponse(rootWorkflowId: WorkflowId, labels: Map[WorkflowId, Map[String, String]]) extends MetadataServiceResponse
-  final case class RootAndSubworkflowLabelsLookupFailed(rootWorkflowId: WorkflowId, reason: Throwable) extends MetadataServiceFailure
+  final case class RootAndSubworkflowLabelsLookupResponse(rootWorkflowId: WorkflowId,
+                                                          labels: Map[WorkflowId, Map[String, String]]
+  ) extends MetadataServiceResponse
+  final case class RootAndSubworkflowLabelsLookupFailed(rootWorkflowId: WorkflowId, reason: Throwable)
+      extends MetadataServiceFailure
 
   final case class WorkflowOutputsResponse(id: WorkflowId, outputs: Seq[MetadataEvent]) extends MetadataServiceResponse
   final case class WorkflowOutputsFailure(id: WorkflowId, reason: Throwable) extends MetadataServiceFailure
@@ -163,7 +183,8 @@ object MetadataService {
   final case class LogsFailure(id: WorkflowId, reason: Throwable) extends MetadataServiceFailure
 
   final case class MetadataWriteSuccess(events: Iterable[MetadataEvent]) extends MetadataServiceResponse
-  final case class MetadataWriteFailure(reason: Throwable, events: Iterable[MetadataEvent]) extends MetadataServiceFailure
+  final case class MetadataWriteFailure(reason: Throwable, events: Iterable[MetadataEvent])
+      extends MetadataServiceFailure
 
   sealed abstract class WorkflowValidationResponse extends MetadataServiceResponse
   case object RecognizedWorkflowId extends WorkflowValidationResponse
@@ -171,26 +192,32 @@ object MetadataService {
   final case class FailedToCheckWorkflowId(cause: Throwable) extends WorkflowValidationResponse
 
   sealed abstract class FetchWorkflowArchiveStatusAndEndTimeResponse extends MetadataServiceResponse
-  final case class WorkflowMetadataArchivedStatusAndEndTime(archiveStatus: MetadataArchiveStatus, endTime: Option[OffsetDateTime]) extends FetchWorkflowArchiveStatusAndEndTimeResponse
-  final case class FailedToGetArchiveStatusAndEndTime(reason: Throwable) extends FetchWorkflowArchiveStatusAndEndTimeResponse
+  final case class WorkflowMetadataArchivedStatusAndEndTime(archiveStatus: MetadataArchiveStatus,
+                                                            endTime: Option[OffsetDateTime]
+  ) extends FetchWorkflowArchiveStatusAndEndTimeResponse
+  final case class FailedToGetArchiveStatusAndEndTime(reason: Throwable)
+      extends FetchWorkflowArchiveStatusAndEndTimeResponse
 
   sealed abstract class MetadataQueryResponse extends MetadataServiceResponse
-  final case class WorkflowQuerySuccess(response: WorkflowQueryResponse, meta: Option[QueryMetadata]) extends MetadataQueryResponse
+  final case class WorkflowQuerySuccess(response: WorkflowQueryResponse, meta: Option[QueryMetadata])
+      extends MetadataQueryResponse
   final case class WorkflowQueryFailure(reason: Throwable) extends MetadataQueryResponse
 
-  private implicit class EnhancedWomTraversable(val womValues: Iterable[WomValue]) extends AnyVal {
+  implicit private class EnhancedWomTraversable(val womValues: Iterable[WomValue]) extends AnyVal {
     def toEvents(metadataKey: MetadataKey): List[MetadataEvent] = if (womValues.isEmpty) {
       List(MetadataEvent.empty(metadataKey.copy(key = s"${metadataKey.key}[]")))
     } else {
-      womValues.toList
-        .zipWithIndex
-        .flatMap { case (value, index) => womValueToMetadataEvents(metadataKey.copy(key = s"${metadataKey.key}[$index]"), value) }
+      womValues.toList.zipWithIndex
+        .flatMap { case (value, index) =>
+          womValueToMetadataEvents(metadataKey.copy(key = s"${metadataKey.key}[$index]"), value)
+        }
     }
   }
 
   private def toPrimitiveEvent(metadataKey: MetadataKey, valueName: String)(value: Option[Any]) = value match {
     case Some(v) => MetadataEvent(metadataKey.copy(key = s"${metadataKey.key}:$valueName"), MetadataValue(v))
-    case None => MetadataEvent(metadataKey.copy(key = s"${metadataKey.key}:$valueName"), MetadataValue("", MetadataNull))
+    case None =>
+      MetadataEvent(metadataKey.copy(key = s"${metadataKey.key}:$valueName"), MetadataValue("", MetadataNull))
   }
 
   def womValueToMetadataEvents(metadataKey: MetadataKey, womValue: WomValue): Iterable[MetadataEvent] = womValue match {
@@ -199,13 +226,17 @@ object MetadataService {
       if (valueMap.isEmpty) {
         List(MetadataEvent.empty(metadataKey))
       } else {
-        valueMap.toList flatMap { case (key, value) => womValueToMetadataEvents(metadataKey.copy(key = metadataKey.key + s":${key.valueString}"), value) }
+        valueMap.toList flatMap { case (key, value) =>
+          womValueToMetadataEvents(metadataKey.copy(key = metadataKey.key + s":${key.valueString}"), value)
+        }
       }
     case objectLike: WomObjectLike =>
       if (objectLike.values.isEmpty) {
         List(MetadataEvent.empty(metadataKey))
       } else {
-        objectLike.values.toList flatMap { case (key, value) => womValueToMetadataEvents(metadataKey.copy(key = metadataKey.key + s":$key"), value) }
+        objectLike.values.toList flatMap { case (key, value) =>
+          womValueToMetadataEvents(metadataKey.copy(key = metadataKey.key + s":$key"), value)
+        }
       }
     case WomOptionalValue(_, Some(value)) =>
       womValueToMetadataEvents(metadataKey, value)
@@ -214,7 +245,8 @@ object MetadataService {
         womValueToMetadataEvents(metadataKey.copy(key = metadataKey.key + ":right"), right)
     case populated: WomMaybePopulatedFile =>
       import mouse.all._
-      val secondaryFiles = populated.secondaryFiles.toEvents(metadataKey.copy(key = s"${metadataKey.key}:secondaryFiles"))
+      val secondaryFiles =
+        populated.secondaryFiles.toEvents(metadataKey.copy(key = s"${metadataKey.key}:secondaryFiles"))
 
       List(
         MetadataEvent(metadataKey.copy(key = s"${metadataKey.key}:class"), MetadataValue("File")),
@@ -226,7 +258,8 @@ object MetadataService {
       ) ++ secondaryFiles
     case listedDirectory: WomMaybeListedDirectory =>
       import mouse.all._
-      val listing = listedDirectory.listingOption.toList.flatten.toEvents(metadataKey.copy(key = s"${metadataKey.key}:listing"))
+      val listing =
+        listedDirectory.listingOption.toList.flatten.toEvents(metadataKey.copy(key = s"${metadataKey.key}:listing"))
       List(
         MetadataEvent(metadataKey.copy(key = s"${metadataKey.key}:class"), MetadataValue("Directory")),
         listedDirectory.valueOption |> toPrimitiveEvent(metadataKey, "location")
@@ -235,13 +268,22 @@ object MetadataService {
       List(MetadataEvent(metadataKey, MetadataValue(value)))
   }
 
-  def throwableToMetadataEvents(metadataKey: MetadataKey, t: Throwable, failureIndex: Int = Random.nextInt(Int.MaxValue)): List[MetadataEvent] = {
-    val emptyCauseList = List(MetadataEvent.empty(metadataKey.copy(key = metadataKey.key + s"[$failureIndex]:causedBy[]")))
+  def throwableToMetadataEvents(metadataKey: MetadataKey,
+                                t: Throwable,
+                                failureIndex: Int = Random.nextInt(Int.MaxValue)
+  ): List[MetadataEvent] = {
+    val emptyCauseList = List(
+      MetadataEvent.empty(metadataKey.copy(key = metadataKey.key + s"[$failureIndex]:causedBy[]"))
+    )
     val metadataKeyAndFailureIndex = s"${metadataKey.key}[$failureIndex]"
 
     t match {
       case aggregation: ThrowableAggregation =>
-        val message = List(MetadataEvent(metadataKey.copy(key = s"$metadataKeyAndFailureIndex:message"), MetadataValue(aggregation.exceptionContext)))
+        val message = List(
+          MetadataEvent(metadataKey.copy(key = s"$metadataKeyAndFailureIndex:message"),
+                        MetadataValue(aggregation.exceptionContext)
+          )
+        )
         val indexedCauses = aggregation.throwables.toList.zipWithIndex
         val indexedCauseEvents = if (indexedCauses.nonEmpty) {
           indexedCauses flatMap { case (cause, index) =>
@@ -253,7 +295,11 @@ object MetadataService {
         }
         message ++ indexedCauseEvents
       case aggregation: MessageAggregation =>
-        val message = List(MetadataEvent(metadataKey.copy(key = s"$metadataKeyAndFailureIndex:message"), MetadataValue(aggregation.exceptionContext)))
+        val message = List(
+          MetadataEvent(metadataKey.copy(key = s"$metadataKeyAndFailureIndex:message"),
+                        MetadataValue(aggregation.exceptionContext)
+          )
+        )
         val indexedCauses = aggregation.errorMessages.toList.zipWithIndex
         val indexedCauseEvents = if (indexedCauses.nonEmpty) {
           indexedCauses flatMap { case (cause, index) =>
@@ -267,11 +313,14 @@ object MetadataService {
         message ++ indexedCauseEvents
 
       case _ =>
-        val message = List(MetadataEvent(metadataKey.copy(key = s"$metadataKeyAndFailureIndex:message"), MetadataValue(t.getMessage)))
+        val message = List(
+          MetadataEvent(metadataKey.copy(key = s"$metadataKeyAndFailureIndex:message"), MetadataValue(t.getMessage))
+        )
         val causeKey = metadataKey.copy(key = s"$metadataKeyAndFailureIndex:causedBy")
-        val cause = Option(t.getCause) map { cause => throwableToMetadataEvents(causeKey, cause, 0) } getOrElse emptyCauseList
+        val cause = Option(t.getCause) map { cause =>
+          throwableToMetadataEvents(causeKey, cause, 0)
+        } getOrElse emptyCauseList
         message ++ cause
     }
   }
 }
-
diff --git a/services/src/main/scala/cromwell/services/metadata/WorkflowQueryKey.scala b/services/src/main/scala/cromwell/services/metadata/WorkflowQueryKey.scala
index 726361f2cfc..ce6444128fc 100644
--- a/services/src/main/scala/cromwell/services/metadata/WorkflowQueryKey.scala
+++ b/services/src/main/scala/cromwell/services/metadata/WorkflowQueryKey.scala
@@ -65,7 +65,7 @@ object WorkflowQueryKey {
 
     override def validate(grouped: Map[String, Seq[(String, String)]]): ErrorOr[List[String]] = {
       val values = valuesFromMap(grouped).toList
-      val nels:List[data.ValidatedNel[String,String]] = values map {
+      val nels: List[data.ValidatedNel[String, String]] = values map {
         case Patterns.WorkflowName(n) => n.validNel[String]
         case v => v.invalidNel[String]
       }
@@ -77,18 +77,16 @@ object WorkflowQueryKey {
     override def validate(grouped: Map[String, Seq[(String, String)]]): ErrorOr[List[Label]] = {
       val values = valuesFromMap(grouped).toList
 
-      def validateLabelRegex(labelKeyValue: String): ErrorOr[Label] = {
+      def validateLabelRegex(labelKeyValue: String): ErrorOr[Label] =
         labelKeyValue.split("\\:", 2) match {
           case Array(k, v) => Label.validateLabel(k, v)
           case _ => labelKeyValue.invalidNel
         }
-      }
       val nels: List[ErrorOr[Label]] = values map validateLabelRegex
       sequenceListOfValidatedNels("Label values do not match allowed pattern label-key:label-value", nels)
     }
   }
 
-
   case object LabelAndKeyValue extends LabelLikeKeyValue {
     override val name = "Label"
   }
@@ -111,7 +109,8 @@ object WorkflowQueryKey {
     override def validate(grouped: Map[String, Seq[(String, String)]]): ErrorOr[List[String]] = {
       val values = valuesFromMap(grouped).toList
       val nels = values map { v =>
-        if (Try(WorkflowId.fromString(v.toLowerCase.capitalize)).isSuccess) v.validNel[String] else s"invalid Id value: '$v'".invalidNel[String]
+        if (Try(WorkflowId.fromString(v.toLowerCase.capitalize)).isSuccess) v.validNel[String]
+        else s"invalid Id value: '$v'".invalidNel[String]
       }
       sequenceListOfValidatedNels("Id values do match allowed workflow id pattern", nels)
     }
@@ -150,11 +149,11 @@ object WorkflowQueryKey {
       /*
         The inclusion of `WorkflowMetadataKeys.ParentWorkflowId` is for backwards compatibility. As of #4381
         parentWorkflowId is always included, but we did not want to break old automated queries
-        */
+       */
       val allowedValues = Seq(WorkflowMetadataKeys.Labels, WorkflowMetadataKeys.ParentWorkflowId)
-      val nels: List[ErrorOr[String]] = values map { v => {
+      val nels: List[ErrorOr[String]] = values map { v =>
         allowedValues.contains(v).fold(v.validNel[String], v.invalidNel[String])
-      }}
+      }
       sequenceListOfValidatedNels(s"Keys should be from $allowedValues. Unrecognized values", nels)
     }
   }
@@ -177,13 +176,12 @@ object WorkflowQueryKey {
 sealed trait WorkflowQueryKey[T] {
   def validate(grouped: Map[String, Seq[(String, String)]]): ErrorOr[T]
   def name: String
-  def valuesFromMap(grouped: Map[String, Seq[(String, String)]]): Seq[String] = {
+  def valuesFromMap(grouped: Map[String, Seq[(String, String)]]): Seq[String] =
     grouped.getOrElse(name, Seq.empty) map { _._2 }
-  }
 }
 
 sealed trait DateTimeWorkflowQueryKey extends WorkflowQueryKey[Option[OffsetDateTime]] {
-  override def validate(grouped: Map[String, Seq[(String, String)]]): ErrorOr[Option[OffsetDateTime]] = {
+  override def validate(grouped: Map[String, Seq[(String, String)]]): ErrorOr[Option[OffsetDateTime]] =
     valuesFromMap(grouped).toList match {
       case vs if vs.lengthCompare(1) > 0 =>
         s"Found ${vs.size} values for key '$name' but at most one is allowed.".invalidNel[Option[OffsetDateTime]]
@@ -195,11 +193,11 @@ sealed trait DateTimeWorkflowQueryKey extends WorkflowQueryKey[Option[OffsetDate
         }
       case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
     }
-  }
   def displayName: String
 }
 
 sealed trait SeqWorkflowQueryKey[A] extends WorkflowQueryKey[Seq[A]] {
+
   /** `sequence` the `List[ErrorOr[A]]` to a single `ErrorOr[List[A]]` */
   protected def sequenceListOfValidatedNels(prefix: String, errorOrList: List[ErrorOr[A]]): ErrorOr[List[A]] = {
     val errorOr = errorOrList.sequence[ErrorOr, A]
@@ -210,38 +208,36 @@ sealed trait SeqWorkflowQueryKey[A] extends WorkflowQueryKey[Seq[A]] {
 }
 
 sealed trait IntWorkflowQueryKey extends WorkflowQueryKey[Option[Int]] {
-  override def validate(grouped: Map[String, Seq[(String, String)]]): ErrorOr[Option[Int]] = {
+  override def validate(grouped: Map[String, Seq[(String, String)]]): ErrorOr[Option[Int]] =
     valuesFromMap(grouped).toList match {
       case vs if vs.lengthCompare(1) > 0 =>
         s"Found ${vs.size} values for key '$name' but at most one is allowed.".invalidNel[Option[Int]]
       case Nil => None.validNel
       case v :: Nil =>
         Try(v.toInt) match {
-          case Success(intVal) => if (intVal > 0) Option(intVal).validNel else s"Integer value not greater than 0".invalidNel[Option[Int]]
+          case Success(intVal) =>
+            if (intVal > 0) Option(intVal).validNel else s"Integer value not greater than 0".invalidNel[Option[Int]]
           case _ => s"Value given for $displayName does not parse as a integer: $v".invalidNel[Option[Int]]
         }
       case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
     }
-  }
   def displayName: String
 }
 
 sealed trait BooleanWorkflowQueryKey extends WorkflowQueryKey[Boolean] {
-  override def validate(grouped: Map[String, Seq[(String, String)]]): ErrorOr[Boolean] = {
+  override def validate(grouped: Map[String, Seq[(String, String)]]): ErrorOr[Boolean] =
     valuesFromMap(grouped).toList match {
-      case vs if vs.lengthCompare(1) > 0 => s"Found ${vs.size} values for key '$name' but at most one is allowed.".invalidNel[Boolean]
+      case vs if vs.lengthCompare(1) > 0 =>
+        s"Found ${vs.size} values for key '$name' but at most one is allowed.".invalidNel[Boolean]
       case Nil => defaultBooleanValue.validNel
-      case v :: Nil => {
+      case v :: Nil =>
         Try(v.toBoolean) match {
           case Success(bool) => bool.validNel
           case _ => s"Value given for $displayName does not parse as a boolean: $v".invalidNel[Boolean]
         }
-      }
       case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
     }
-  }
-   def displayName: String
+  def displayName: String
 
   def defaultBooleanValue: Boolean
 }
-
diff --git a/services/src/main/scala/cromwell/services/metadata/WorkflowQueryParameters.scala b/services/src/main/scala/cromwell/services/metadata/WorkflowQueryParameters.scala
index 55ebe102211..020bdfea5d9 100644
--- a/services/src/main/scala/cromwell/services/metadata/WorkflowQueryParameters.scala
+++ b/services/src/main/scala/cromwell/services/metadata/WorkflowQueryParameters.scala
@@ -11,26 +11,31 @@ import cromwell.core.labels.Label
 import cromwell.services.metadata.WorkflowQueryKey._
 import common.validation.ErrorOr._
 
-case class WorkflowQueryParameters private(statuses: Set[String],
-                                           names: Set[String],
-                                           ids: Set[WorkflowId],
-                                           labelsAnd: Set[Label],
-                                           labelsOr: Set[Label],
-                                           excludeLabelsAnd: Set[Label],
-                                           excludeLabelsOr: Set[Label],
-                                           submissionTime: Option[OffsetDateTime],
-                                           startDate: Option[OffsetDateTime],
-                                           endDate: Option[OffsetDateTime],
-                                           metadataArchiveStatus: Set[MetadataArchiveStatus],
-                                           page: Option[Int],
-                                           pageSize: Option[Int],
-                                           additionalQueryResultFields: Set[String],
-                                           includeSubworkflows: Boolean,
-                                           newestFirst: Boolean)
+case class WorkflowQueryParameters private (statuses: Set[String],
+                                            names: Set[String],
+                                            ids: Set[WorkflowId],
+                                            labelsAnd: Set[Label],
+                                            labelsOr: Set[Label],
+                                            excludeLabelsAnd: Set[Label],
+                                            excludeLabelsOr: Set[Label],
+                                            submissionTime: Option[OffsetDateTime],
+                                            startDate: Option[OffsetDateTime],
+                                            endDate: Option[OffsetDateTime],
+                                            metadataArchiveStatus: Set[MetadataArchiveStatus],
+                                            page: Option[Int],
+                                            pageSize: Option[Int],
+                                            additionalQueryResultFields: Set[String],
+                                            includeSubworkflows: Boolean,
+                                            newestFirst: Boolean
+)
 
 object WorkflowQueryParameters {
 
-  private def validateDate1BeforeDate2(date1: Option[OffsetDateTime], date2: Option[OffsetDateTime], date1Type: String, date2Type: String): ErrorOr[Unit] = {
+  private def validateDate1BeforeDate2(date1: Option[OffsetDateTime],
+                                       date2: Option[OffsetDateTime],
+                                       date1Type: String,
+                                       date2Type: String
+  ): ErrorOr[Unit] = {
     // Invert the notion of success/failure here to only "successfully" generate an error message if
     // both date1 and date2 dates have been specified and date1 is after date2.
     val date1AfterDate2Error = for {
@@ -62,7 +67,7 @@ object WorkflowQueryParameters {
    * Run the validation logic over the specified raw parameters, creating a `WorkflowQueryParameters` if all
    * validation succeeds, otherwise accumulate all validation messages within the `ValidationNel`.
    */
-  private [metadata] def runValidation(rawParameters: Seq[(String, String)]): ErrorOr[WorkflowQueryParameters] = {
+  private[metadata] def runValidation(rawParameters: Seq[(String, String)]): ErrorOr[WorkflowQueryParameters] = {
 
     val onlyRecognizedKeysValidation = validateOnlyRecognizedKeys(rawParameters)
 
@@ -74,16 +79,23 @@ object WorkflowQueryParameters {
     val submissionTimeValidation = SubmissionTime.validate(valuesByCanonicalCapitalization)
     val statusesValidation: ErrorOr[Set[String]] = Status.validate(valuesByCanonicalCapitalization).map(_.toSet)
     val namesValidation: ErrorOr[Set[String]] = Name.validate(valuesByCanonicalCapitalization).map(_.toSet)
-    val workflowIdsValidation: ErrorOr[Set[WorkflowId]] = WorkflowQueryKey.Id.validate(valuesByCanonicalCapitalization).map(ids => (ids map WorkflowId.fromString).toSet)
-    val labelsAndValidation: ErrorOr[Set[Label]] = WorkflowQueryKey.LabelAndKeyValue.validate(valuesByCanonicalCapitalization).map(_.toSet)
-    val labelsOrValidation: ErrorOr[Set[Label]] = WorkflowQueryKey.LabelOrKeyValue.validate(valuesByCanonicalCapitalization).map(_.toSet)
-    val excludeLabelsAndValidation: ErrorOr[Set[Label]] = WorkflowQueryKey.ExcludeLabelAndKeyValue.validate(valuesByCanonicalCapitalization).map(_.toSet)
-    val excludeLabelsOrValidation: ErrorOr[Set[Label]] = WorkflowQueryKey.ExcludeLabelOrKeyValue.validate(valuesByCanonicalCapitalization).map(_.toSet)
+    val workflowIdsValidation: ErrorOr[Set[WorkflowId]] =
+      WorkflowQueryKey.Id.validate(valuesByCanonicalCapitalization).map(ids => (ids map WorkflowId.fromString).toSet)
+    val labelsAndValidation: ErrorOr[Set[Label]] =
+      WorkflowQueryKey.LabelAndKeyValue.validate(valuesByCanonicalCapitalization).map(_.toSet)
+    val labelsOrValidation: ErrorOr[Set[Label]] =
+      WorkflowQueryKey.LabelOrKeyValue.validate(valuesByCanonicalCapitalization).map(_.toSet)
+    val excludeLabelsAndValidation: ErrorOr[Set[Label]] =
+      WorkflowQueryKey.ExcludeLabelAndKeyValue.validate(valuesByCanonicalCapitalization).map(_.toSet)
+    val excludeLabelsOrValidation: ErrorOr[Set[Label]] =
+      WorkflowQueryKey.ExcludeLabelOrKeyValue.validate(valuesByCanonicalCapitalization).map(_.toSet)
     val pageValidation = Page.validate(valuesByCanonicalCapitalization)
     val pageSizeValidation = PageSize.validate(valuesByCanonicalCapitalization)
-    val additionalQueryResultFieldsValidation: ErrorOr[Set[String]] = AdditionalQueryResultFields.validate(valuesByCanonicalCapitalization).map(_.toSet)
+    val additionalQueryResultFieldsValidation: ErrorOr[Set[String]] =
+      AdditionalQueryResultFields.validate(valuesByCanonicalCapitalization).map(_.toSet)
     val includeSubworkflowsValidation = IncludeSubworkflows.validate(valuesByCanonicalCapitalization)
-    val metadataArchiveStatusValidation: ErrorOr[Set[MetadataArchiveStatus]] = WorkflowQueryKey.MetadataArchiveStatus.validate(valuesByCanonicalCapitalization).map(_.toSet)
+    val metadataArchiveStatusValidation: ErrorOr[Set[MetadataArchiveStatus]] =
+      WorkflowQueryKey.MetadataArchiveStatus.validate(valuesByCanonicalCapitalization).map(_.toSet)
     val newestFirstValidation = NewestFirst.validate(valuesByCanonicalCapitalization)
 
     // Only validate start before end if both of the individual date parsing validations have already succeeded.
@@ -99,26 +111,45 @@ object WorkflowQueryParameters {
     }
 
     (onlyRecognizedKeysValidation,
-      startBeforeEndValidation,
-      submissionBeforeStartValidation,
-      statusesValidation,
-      namesValidation,
-      workflowIdsValidation,
-      labelsAndValidation,
-      labelsOrValidation,
-      excludeLabelsAndValidation,
-      excludeLabelsOrValidation,
-      submissionTimeValidation,
-      startDateValidation,
-      endDateValidation,
-      pageValidation,
-      pageSizeValidation,
-      additionalQueryResultFieldsValidation,
-      includeSubworkflowsValidation,
-      metadataArchiveStatusValidation,
-      newestFirstValidation
+     startBeforeEndValidation,
+     submissionBeforeStartValidation,
+     statusesValidation,
+     namesValidation,
+     workflowIdsValidation,
+     labelsAndValidation,
+     labelsOrValidation,
+     excludeLabelsAndValidation,
+     excludeLabelsOrValidation,
+     submissionTimeValidation,
+     startDateValidation,
+     endDateValidation,
+     pageValidation,
+     pageSizeValidation,
+     additionalQueryResultFieldsValidation,
+     includeSubworkflowsValidation,
+     metadataArchiveStatusValidation,
+     newestFirstValidation
     ) mapN {
-      (_, _, _, statuses, names, ids, labelsAnd, labelsOr, excludeLabelsAnd, excludeLabelsOr, submissionTime, startDate, endDate, page, pageSize, additionalQueryResultFields, includeSubworkflows, metadataArchiveStatus, newestFirst) =>
+      (_,
+       _,
+       _,
+       statuses,
+       names,
+       ids,
+       labelsAnd,
+       labelsOr,
+       excludeLabelsAnd,
+       excludeLabelsOr,
+       submissionTime,
+       startDate,
+       endDate,
+       page,
+       pageSize,
+       additionalQueryResultFields,
+       includeSubworkflows,
+       metadataArchiveStatus,
+       newestFirst
+      ) =>
         WorkflowQueryParameters(
           statuses,
           names,
@@ -140,10 +171,9 @@ object WorkflowQueryParameters {
     }
   }
 
-  def apply(rawParameters: Seq[(String, String)]): WorkflowQueryParameters = {
+  def apply(rawParameters: Seq[(String, String)]): WorkflowQueryParameters =
     runValidation(rawParameters) match {
       case Valid(queryParameters) => queryParameters
       case Invalid(x) => throw new IllegalArgumentException(x.toList.mkString("\n"))
     }
-  }
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala b/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala
index 0069ffe8821..13bb31463da 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/MetadataDatabaseAccess.scala
@@ -28,7 +28,8 @@ object MetadataDatabaseAccess {
 
   private lazy val WorkflowMetadataSummarySemigroup = new Semigroup[WorkflowMetadataSummaryEntry] {
     override def combine(summary1: WorkflowMetadataSummaryEntry,
-                         summary2: WorkflowMetadataSummaryEntry): WorkflowMetadataSummaryEntry = {
+                         summary2: WorkflowMetadataSummaryEntry
+    ): WorkflowMetadataSummaryEntry = {
       // Resolve the status if both `this` and `that` have defined statuses.  This will evaluate to `None`
       // if one or both of the statuses is not defined.
       val resolvedStatus = for {
@@ -45,7 +46,7 @@ object MetadataDatabaseAccess {
         submissionTimestamp = summary1.submissionTimestamp orElse summary2.submissionTimestamp,
         parentWorkflowExecutionUuid = summary1.parentWorkflowExecutionUuid orElse summary2.parentWorkflowExecutionUuid,
         rootWorkflowExecutionUuid = summary1.rootWorkflowExecutionUuid orElse summary2.rootWorkflowExecutionUuid,
-        metadataArchiveStatus = summary1.metadataArchiveStatus,
+        metadataArchiveStatus = summary1.metadataArchiveStatus
       )
     }
   }
@@ -75,17 +76,20 @@ object MetadataDatabaseAccess {
   }
 
   private def buildUpdatedSummary(existingSummary: Option[WorkflowMetadataSummaryEntry],
-                                  metadataForUuid: Seq[MetadataEntry]): WorkflowMetadataSummaryEntry = {
+                                  metadataForUuid: Seq[MetadataEntry]
+  ): WorkflowMetadataSummaryEntry = {
     implicit val wmss = WorkflowMetadataSummarySemigroup
 
     val base = existingSummary.getOrElse(baseSummary(metadataForUuid.head.workflowExecutionUuid))
-    metadataForUuid.foldLeft(base) {
-      case (metadataSummary, metadatum) => metadataSummary |+| metadatum.toSummary
+    metadataForUuid.foldLeft(base) { case (metadataSummary, metadatum) =>
+      metadataSummary |+| metadatum.toSummary
     }
   }
 
   final case class SummaryResult(rowsProcessedIncreasing: Long, rowsProcessedDecreasing: Long, decreasingGap: Long)
-  final case class WorkflowArchiveStatusAndEndTimestamp(archiveStatus: Option[String], endTimestamp: Option[OffsetDateTime])
+  final case class WorkflowArchiveStatusAndEndTimestamp(archiveStatus: Option[String],
+                                                        endTimestamp: Option[OffsetDateTime]
+  )
 }
 
 trait MetadataDatabaseAccess {
@@ -99,8 +103,15 @@ trait MetadataDatabaseAccess {
       val value = metadataEvent.value map { _.value }
       val valueType = metadataEvent.value map { _.valueType.typeName }
       val jobKey = key.jobKey map { jk => (jk.callFqn, jk.index, jk.attempt) }
-      MetadataEntry(workflowUuid, jobKey.map(_._1), jobKey.flatMap(_._2), jobKey.map(_._3),
-        key.key, value.toClobOption, valueType, timestamp)
+      MetadataEntry(workflowUuid,
+                    jobKey.map(_._1),
+                    jobKey.flatMap(_._2),
+                    jobKey.map(_._3),
+                    key.key,
+                    value.toClobOption,
+                    valueType,
+                    timestamp
+      )
     }
     metadataDatabaseInterface.addMetadataEntries(
       metadataEntries = metadata,
@@ -111,10 +122,11 @@ trait MetadataDatabaseAccess {
       submissionMetadataKey = WorkflowMetadataKeys.SubmissionTime,
       parentWorkflowIdKey = WorkflowMetadataKeys.ParentWorkflowId,
       rootWorkflowIdKey = WorkflowMetadataKeys.RootWorkflowId,
-      labelMetadataKey = WorkflowMetadataKeys.Labels)
+      labelMetadataKey = WorkflowMetadataKeys.Labels
+    )
   }
 
-  def metadataToMetadataEvents(workflowId: WorkflowId)(metadata: Seq[MetadataEntry]): Seq[MetadataEvent] = {
+  def metadataToMetadataEvents(workflowId: WorkflowId)(metadata: Seq[MetadataEntry]): Seq[MetadataEvent] =
     metadata map { m =>
       // If callFullyQualifiedName is non-null then attempt will also be non-null and there is a MetadataJobKey.
       val metadataJobKey: Option[MetadataJobKey] = for {
@@ -123,17 +135,16 @@ trait MetadataDatabaseAccess {
       } yield MetadataJobKey(callFqn, m.jobIndex, attempt)
 
       val key = MetadataKey(workflowId, metadataJobKey, m.metadataKey)
-      val value = m.metadataValueType.map(mType =>
-        MetadataValue(m.metadataValue.toRawString, MetadataType.fromString(mType))
-      )
+      val value =
+        m.metadataValueType.map(mType => MetadataValue(m.metadataValue.toRawString, MetadataType.fromString(mType)))
 
       MetadataEvent(key, value, m.metadataTimestamp.toSystemOffsetDateTime)
     }
-  }
 
   def getMetadataReadRowCount(query: MetadataQuery, timeout: Duration)(implicit ec: ExecutionContext): Future[Int] = {
 
-    def listKeyRequirements(keyRequirementsInput: Option[NonEmptyList[String]]): List[String] = keyRequirementsInput.map(_.toList).toList.flatten.map(_ + "%")
+    def listKeyRequirements(keyRequirementsInput: Option[NonEmptyList[String]]): List[String] =
+      keyRequirementsInput.map(_.toList).toList.flatten.map(_ + "%")
 
     val uuid = query.workflowId.id.toString
 
@@ -143,27 +154,60 @@ trait MetadataDatabaseAccess {
       case q @ MetadataQuery(_, None, Some(key), None, None, _) =>
         metadataDatabaseInterface.countMetadataEntries(uuid, key, q.expandSubWorkflows, timeout)
       case q @ MetadataQuery(_, Some(jobKey), None, None, None, _) =>
-        metadataDatabaseInterface.countMetadataEntries(uuid, jobKey.callFqn, jobKey.index, jobKey.attempt, q.expandSubWorkflows, timeout)
+        metadataDatabaseInterface.countMetadataEntries(uuid,
+                                                       jobKey.callFqn,
+                                                       jobKey.index,
+                                                       jobKey.attempt,
+                                                       q.expandSubWorkflows,
+                                                       timeout
+        )
       case q @ MetadataQuery(_, Some(jobKey), Some(key), None, None, _) =>
-        metadataDatabaseInterface.countMetadataEntries(uuid, key, jobKey.callFqn, jobKey.index, jobKey.attempt, q.expandSubWorkflows, timeout)
+        metadataDatabaseInterface.countMetadataEntries(uuid,
+                                                       key,
+                                                       jobKey.callFqn,
+                                                       jobKey.index,
+                                                       jobKey.attempt,
+                                                       q.expandSubWorkflows,
+                                                       timeout
+        )
       case q @ MetadataQuery(_, None, None, includeKeys, excludeKeys, _) =>
         val excludeKeyRequirements = listKeyRequirements(excludeKeys)
         val queryType = if (excludeKeyRequirements.contains("calls%")) WorkflowQuery else CallOrWorkflowQuery
 
-        metadataDatabaseInterface.countMetadataEntryWithKeyConstraints(uuid, listKeyRequirements(includeKeys), excludeKeyRequirements, queryType, q.expandSubWorkflows, timeout)
-      case q @ MetadataQuery(_, Some(MetadataQueryJobKey(callFqn, index, attempt)), None, includeKeys, excludeKeys, _) =>
-        metadataDatabaseInterface.countMetadataEntryWithKeyConstraints(uuid, listKeyRequirements(includeKeys), listKeyRequirements(excludeKeys), CallQuery(callFqn, index, attempt), q.expandSubWorkflows, timeout)
+        metadataDatabaseInterface.countMetadataEntryWithKeyConstraints(uuid,
+                                                                       listKeyRequirements(includeKeys),
+                                                                       excludeKeyRequirements,
+                                                                       queryType,
+                                                                       q.expandSubWorkflows,
+                                                                       timeout
+        )
+      case q @ MetadataQuery(_,
+                             Some(MetadataQueryJobKey(callFqn, index, attempt)),
+                             None,
+                             includeKeys,
+                             excludeKeys,
+                             _
+          ) =>
+        metadataDatabaseInterface.countMetadataEntryWithKeyConstraints(uuid,
+                                                                       listKeyRequirements(includeKeys),
+                                                                       listKeyRequirements(excludeKeys),
+                                                                       CallQuery(callFqn, index, attempt),
+                                                                       q.expandSubWorkflows,
+                                                                       timeout
+        )
       case _ => Future.failed(new IllegalArgumentException(s"Invalid MetadataQuery: $query"))
     }
   }
 
-  def metadataEventsStream(workflowId: WorkflowId): Try[DatabasePublisher[MetadataEntry]] = {
+  def metadataEventsStream(workflowId: WorkflowId): Try[DatabasePublisher[MetadataEntry]] =
     Try(metadataDatabaseInterface.streamMetadataEntries(workflowId.id.toString))
-  }
 
-  def queryMetadataEvents(query: MetadataQuery, timeout: Duration)(implicit ec: ExecutionContext): Future[Seq[MetadataEvent]] = {
+  def queryMetadataEvents(query: MetadataQuery, timeout: Duration)(implicit
+    ec: ExecutionContext
+  ): Future[Seq[MetadataEvent]] = {
 
-    def listKeyRequirements(keyRequirementsInput: Option[NonEmptyList[String]]): List[String] = keyRequirementsInput.map(_.toList).toList.flatten.map(_ + "%")
+    def listKeyRequirements(keyRequirementsInput: Option[NonEmptyList[String]]): List[String] =
+      keyRequirementsInput.map(_.toList).toList.flatten.map(_ + "%")
 
     val uuid = query.workflowId.id.toString
 
@@ -180,79 +224,97 @@ trait MetadataDatabaseAccess {
         val excludeKeyRequirements = listKeyRequirements(excludeKeys)
         val queryType = if (excludeKeyRequirements.contains("calls%")) WorkflowQuery else CallOrWorkflowQuery
 
-        metadataDatabaseInterface.queryMetadataEntryWithKeyConstraints(uuid, listKeyRequirements(includeKeys), excludeKeyRequirements, queryType, timeout)
+        metadataDatabaseInterface.queryMetadataEntryWithKeyConstraints(uuid,
+                                                                       listKeyRequirements(includeKeys),
+                                                                       excludeKeyRequirements,
+                                                                       queryType,
+                                                                       timeout
+        )
       case MetadataQuery(_, Some(MetadataQueryJobKey(callFqn, index, attempt)), None, includeKeys, excludeKeys, _) =>
-        metadataDatabaseInterface.queryMetadataEntryWithKeyConstraints(uuid, listKeyRequirements(includeKeys), listKeyRequirements(excludeKeys), CallQuery(callFqn, index, attempt), timeout)
+        metadataDatabaseInterface.queryMetadataEntryWithKeyConstraints(uuid,
+                                                                       listKeyRequirements(includeKeys),
+                                                                       listKeyRequirements(excludeKeys),
+                                                                       CallQuery(callFqn, index, attempt),
+                                                                       timeout
+        )
       case _ => Future.failed(new IllegalArgumentException(s"Invalid MetadataQuery: $query"))
     }
 
     futureMetadata map metadataToMetadataEvents(query.workflowId)
   }
 
-  def queryWorkflowOutputs(id: WorkflowId,
-                           timeout: Duration)
-                          (implicit ec: ExecutionContext): Future[Seq[MetadataEvent]] = {
+  def queryWorkflowOutputs(id: WorkflowId, timeout: Duration)(implicit
+    ec: ExecutionContext
+  ): Future[Seq[MetadataEvent]] = {
     val uuid = id.id.toString
-    metadataDatabaseInterface.queryMetadataEntryWithKeyConstraints(
-      uuid, List(s"${WorkflowMetadataKeys.Outputs}:%"), List.empty, WorkflowQuery, timeout).
-      map(metadataToMetadataEvents(id))
+    metadataDatabaseInterface
+      .queryMetadataEntryWithKeyConstraints(uuid,
+                                            List(s"${WorkflowMetadataKeys.Outputs}:%"),
+                                            List.empty,
+                                            WorkflowQuery,
+                                            timeout
+      )
+      .map(metadataToMetadataEvents(id))
   }
 
-  def queryLogs(id: WorkflowId,
-                timeout: Duration)
-               (implicit ec: ExecutionContext): Future[Seq[MetadataEvent]] = {
+  def queryLogs(id: WorkflowId, timeout: Duration)(implicit ec: ExecutionContext): Future[Seq[MetadataEvent]] = {
     import cromwell.services.metadata.CallMetadataKeys._
 
     val keys = List(Stdout, Stderr, BackendLogsPrefix + ":%")
-    metadataDatabaseInterface.queryMetadataEntryWithKeyConstraints(id.id.toString, keys, List.empty, CallOrWorkflowQuery, timeout) map
+    metadataDatabaseInterface.queryMetadataEntryWithKeyConstraints(id.id.toString,
+                                                                   keys,
+                                                                   List.empty,
+                                                                   CallOrWorkflowQuery,
+                                                                   timeout
+    ) map
       metadataToMetadataEvents(id)
   }
 
-  def refreshWorkflowMetadataSummaries(limit: Int)(implicit ec: ExecutionContext): Future[SummaryResult] = {
+  def refreshWorkflowMetadataSummaries(limit: Int)(implicit ec: ExecutionContext): Future[SummaryResult] =
     for {
       increasingProcessed <- metadataDatabaseInterface.summarizeIncreasing(
         labelMetadataKey = WorkflowMetadataKeys.Labels,
         limit = limit,
-        buildUpdatedSummary = MetadataDatabaseAccess.buildUpdatedSummary)
+        buildUpdatedSummary = MetadataDatabaseAccess.buildUpdatedSummary
+      )
       (decreasingProcessed, decreasingGap) <- metadataDatabaseInterface.summarizeDecreasing(
         summaryNameDecreasing = WorkflowMetadataKeys.SummaryNameDecreasing,
         summaryNameIncreasing = WorkflowMetadataKeys.SummaryNameIncreasing,
         labelMetadataKey = WorkflowMetadataKeys.Labels,
         limit = limit,
-        buildUpdatedSummary = MetadataDatabaseAccess.buildUpdatedSummary)
+        buildUpdatedSummary = MetadataDatabaseAccess.buildUpdatedSummary
+      )
     } yield SummaryResult(increasingProcessed, decreasingProcessed, decreasingGap)
-  }
 
   def updateMetadataArchiveStatus(workflowId: WorkflowId, newStatus: MetadataArchiveStatus): Future[Int] = {
     val databaseStatusValue = MetadataArchiveStatus.toDatabaseValue(newStatus)
     metadataDatabaseInterface.updateMetadataArchiveStatus(workflowId.toString, databaseStatusValue)
   }
 
-  def getWorkflowStatus(id: WorkflowId)
-                       (implicit ec: ExecutionContext): Future[Option[WorkflowState]] = {
+  def getWorkflowStatus(id: WorkflowId)(implicit ec: ExecutionContext): Future[Option[WorkflowState]] =
     metadataDatabaseInterface.getWorkflowStatus(id.toString) map { _ map WorkflowState.withName }
-  }
 
-  def getWorkflowLabels(id: WorkflowId)(implicit ec: ExecutionContext): Future[Map[String, String]] = {
+  def getWorkflowLabels(id: WorkflowId)(implicit ec: ExecutionContext): Future[Map[String, String]] =
     metadataDatabaseInterface.getWorkflowLabels(id.toString)
-  }
 
-  def getRootAndSubworkflowLabels(rootWorkflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Map[WorkflowId, Map[String, String]]] = {
+  def getRootAndSubworkflowLabels(
+    rootWorkflowId: WorkflowId
+  )(implicit ec: ExecutionContext): Future[Map[WorkflowId, Map[String, String]]] =
     metadataDatabaseInterface.getRootAndSubworkflowLabels(rootWorkflowId.toString) map {
       _ map { case (id, labelsForId) => WorkflowId.fromString(id) -> labelsForId }
     }
-  }
 
-  def workflowWithIdExistsInMetadata(possibleWorkflowId: String)(implicit ec: ExecutionContext): Future[Boolean] = {
+  def workflowWithIdExistsInMetadata(possibleWorkflowId: String)(implicit ec: ExecutionContext): Future[Boolean] =
     metadataDatabaseInterface.metadataEntryExists(possibleWorkflowId)
-  }
 
-  def workflowWithIdExistsInMetadataSummaries(possibleWorkflowId: String)(implicit ec: ExecutionContext): Future[Boolean] = {
+  def workflowWithIdExistsInMetadataSummaries(possibleWorkflowId: String)(implicit
+    ec: ExecutionContext
+  ): Future[Boolean] =
     metadataDatabaseInterface.metadataSummaryEntryExists(possibleWorkflowId)
-  }
 
-  def queryWorkflowSummaries(queryParameters: WorkflowQueryParameters)
-                            (implicit ec: ExecutionContext): Future[(WorkflowQueryResponse, Option[QueryMetadata])] = {
+  def queryWorkflowSummaries(
+    queryParameters: WorkflowQueryParameters
+  )(implicit ec: ExecutionContext): Future[(WorkflowQueryResponse, Option[QueryMetadata])] = {
 
     val labelsAndToQuery = queryParameters.labelsAnd.map(label => (label.key, label.value))
     val labelsOrToQuery = queryParameters.labelsOr.map(label => (label.key, label.value))
@@ -295,24 +357,27 @@ trait MetadataDatabaseAccess {
       queryParameters.includeSubworkflows
     )
 
-    def queryMetadata(count: Int): Option[QueryMetadata] = {
+    def queryMetadata(count: Int): Option[QueryMetadata] =
       (queryParameters.page, queryParameters.pageSize) match {
         case (None, None) => None
         case (Some(_), None) => None // Page without pagesize returns everything
         case (None, Some(_)) => Option(QueryMetadata(Option(1), queryParameters.pageSize, Option(count)))
         case _ => Option(QueryMetadata(queryParameters.page, queryParameters.pageSize, Option(count)))
       }
-    }
 
-    def summariesToQueryResults(workflows: Iterable[WorkflowMetadataSummaryEntry]): Future[List[MetadataService.WorkflowQueryResult]] = {
+    def summariesToQueryResults(
+      workflows: Iterable[WorkflowMetadataSummaryEntry]
+    ): Future[List[MetadataService.WorkflowQueryResult]] =
       workflows.toList.traverse(summaryToQueryResult)
-    }
 
     def summaryToQueryResult(workflow: WorkflowMetadataSummaryEntry): Future[MetadataService.WorkflowQueryResult] = {
 
       val workflowLabels: Future[Map[String, String]] =
-        queryParameters.additionalQueryResultFields.contains(WorkflowMetadataKeys.Labels).fold(
-          metadataDatabaseInterface.getWorkflowLabels(workflow.workflowExecutionUuid), Future.successful(Map.empty))
+        queryParameters.additionalQueryResultFields
+          .contains(WorkflowMetadataKeys.Labels)
+          .fold(metadataDatabaseInterface.getWorkflowLabels(workflow.workflowExecutionUuid),
+                Future.successful(Map.empty)
+          )
 
       val archiveStatus = MetadataArchiveStatus.fromDatabaseValue(workflow.metadataArchiveStatus)
 
@@ -320,17 +385,17 @@ trait MetadataDatabaseAccess {
         labels <- workflowLabels
         archived <- Future.fromTry(archiveStatus.toTry)
       } yield MetadataService.WorkflowQueryResult(
-          id = workflow.workflowExecutionUuid,
-          name = workflow.workflowName,
-          status = workflow.workflowStatus,
-          submission = workflow.submissionTimestamp map {_.toSystemOffsetDateTime},
-          start = workflow.startTimestamp map { _.toSystemOffsetDateTime },
-          end = workflow.endTimestamp map { _.toSystemOffsetDateTime },
-          labels = labels.nonEmpty.option(labels),
-          parentWorkflowId = workflow.parentWorkflowExecutionUuid,
-          rootWorkflowId = workflow.rootWorkflowExecutionUuid,
-          metadataArchiveStatus = archived
-        )
+        id = workflow.workflowExecutionUuid,
+        name = workflow.workflowName,
+        status = workflow.workflowStatus,
+        submission = workflow.submissionTimestamp map { _.toSystemOffsetDateTime },
+        start = workflow.startTimestamp map { _.toSystemOffsetDateTime },
+        end = workflow.endTimestamp map { _.toSystemOffsetDateTime },
+        labels = labels.nonEmpty.option(labels),
+        parentWorkflowId = workflow.parentWorkflowExecutionUuid,
+        rootWorkflowId = workflow.rootWorkflowExecutionUuid,
+        metadataArchiveStatus = archived
+      )
     }
 
     for {
@@ -340,49 +405,87 @@ trait MetadataDatabaseAccess {
     } yield (WorkflowQueryResponse(queryResults, count), queryMetadata(count))
   }
 
-  def deleteAllMetadataEntriesForWorkflowAndUpdateArchiveStatus(workflowId: WorkflowId, newArchiveStatus: Option[String])(implicit ec: ExecutionContext): Future[Int] = {
+  def deleteAllMetadataEntriesForWorkflowAndUpdateArchiveStatus(workflowId: WorkflowId,
+                                                                newArchiveStatus: Option[String]
+  )(implicit ec: ExecutionContext): Future[Int] = {
     import cromwell.core.WorkflowState
 
     (metadataDatabaseInterface.getWorkflowStatus(workflowId.toString)) flatMap {
       case None =>
-        Future.failed(new Exception(s"""Metadata deletion precondition failed: workflow ID "$workflowId" did not have a status in the summary table"""))
+        Future.failed(
+          new Exception(
+            s"""Metadata deletion precondition failed: workflow ID "$workflowId" did not have a status in the summary table"""
+          )
+        )
       case Some(status) =>
         if (WorkflowState.withName(status).isTerminal)
-          metadataDatabaseInterface.deleteAllMetadataForWorkflowAndUpdateArchiveStatus(workflowId.toString, newArchiveStatus)
+          metadataDatabaseInterface.deleteAllMetadataForWorkflowAndUpdateArchiveStatus(workflowId.toString,
+                                                                                       newArchiveStatus
+          )
         else
-          Future.failed(new Exception(s"""Metadata deletion precondition failed: workflow ID "$workflowId" was in non-terminal status "$status""""))
+          Future.failed(
+            new Exception(
+              s"""Metadata deletion precondition failed: workflow ID "$workflowId" was in non-terminal status "$status""""
+            )
+          )
 
     }
   }
 
-  def getRootWorkflowId(workflowId: String)(implicit ec: ExecutionContext): Future[Option[String]] = metadataDatabaseInterface.getRootWorkflowId(workflowId)
-
-  def queryWorkflowIdsByArchiveStatusAndOlderThanTimestamp(archiveStatus: Option[String], thresholdTimestamp: OffsetDateTime, batchSize: Long)(implicit ec: ExecutionContext): Future[Seq[String]] =
-    metadataDatabaseInterface.queryWorkflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp(archiveStatus, thresholdTimestamp.toSystemTimestamp, batchSize)
+  def getRootWorkflowId(workflowId: String)(implicit ec: ExecutionContext): Future[Option[String]] =
+    metadataDatabaseInterface.getRootWorkflowId(workflowId)
+
+  def queryWorkflowIdsByArchiveStatusAndOlderThanTimestamp(archiveStatus: Option[String],
+                                                           thresholdTimestamp: OffsetDateTime,
+                                                           batchSize: Long
+  )(implicit ec: ExecutionContext): Future[Seq[String]] =
+    metadataDatabaseInterface.queryWorkflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp(
+      archiveStatus,
+      thresholdTimestamp.toSystemTimestamp,
+      batchSize
+    )
 
   def getSummaryQueueSize()(implicit ec: ExecutionContext): Future[Int] =
     metadataDatabaseInterface.getSummaryQueueSize()
 
-  def getMetadataArchiveStatusAndEndTime(id: WorkflowId)(implicit ec: ExecutionContext): Future[WorkflowArchiveStatusAndEndTimestamp] = {
+  def getMetadataArchiveStatusAndEndTime(
+    id: WorkflowId
+  )(implicit ec: ExecutionContext): Future[WorkflowArchiveStatusAndEndTimestamp] =
     metadataDatabaseInterface.getMetadataArchiveStatusAndEndTime(id.toString).map {
-      case (statusOption, timestampOption) => WorkflowArchiveStatusAndEndTimestamp(statusOption, timestampOption.map(_.toSystemOffsetDateTime))
+      case (statusOption, timestampOption) =>
+        WorkflowArchiveStatusAndEndTimestamp(statusOption, timestampOption.map(_.toSystemOffsetDateTime))
     }
-  }
 
   def queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String],
                                                                    workflowEndTimestampThreshold: OffsetDateTime,
-                                                                   batchSize: Long)(implicit ec: ExecutionContext): Future[Seq[WorkflowMetadataSummaryEntry]] =
-    metadataDatabaseInterface.queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses, workflowEndTimestampThreshold.toSystemTimestamp, batchSize)
+                                                                   batchSize: Long
+  )(implicit ec: ExecutionContext): Future[Seq[WorkflowMetadataSummaryEntry]] =
+    metadataDatabaseInterface.queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(
+      workflowStatuses,
+      workflowEndTimestampThreshold.toSystemTimestamp,
+      batchSize
+    )
 
   def countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String],
-                                                                       workflowEndTimestampThreshold: OffsetDateTime)(implicit ec: ExecutionContext): Future[Int] =
-    metadataDatabaseInterface.countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses, workflowEndTimestampThreshold.toSystemTimestamp)
+                                                                       workflowEndTimestampThreshold: OffsetDateTime
+  )(implicit ec: ExecutionContext): Future[Int] =
+    metadataDatabaseInterface.countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(
+      workflowStatuses,
+      workflowEndTimestampThreshold.toSystemTimestamp
+    )
 
-  def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold: OffsetDateTime)(implicit ec: ExecutionContext): Future[Int] =
-    metadataDatabaseInterface.countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold.toSystemTimestamp)
+  def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(
+    workflowEndTimestampThreshold: OffsetDateTime
+  )(implicit ec: ExecutionContext): Future[Int] =
+    metadataDatabaseInterface.countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(
+      workflowEndTimestampThreshold.toSystemTimestamp
+    )
 
-  def getMetadataTableSizeInformation()(implicit ec: ExecutionContext): Future[Option[InformationSchemaEntry]] = metadataDatabaseInterface.getMetadataTableSizeInformation()
+  def getMetadataTableSizeInformation()(implicit ec: ExecutionContext): Future[Option[InformationSchemaEntry]] =
+    metadataDatabaseInterface.getMetadataTableSizeInformation()
 
-  def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: WorkflowId)(implicit ec: ExecutionContext): Future[Vector[MetadataEntry]] =
+  def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: WorkflowId)(implicit
+    ec: ExecutionContext
+  ): Future[Vector[MetadataEntry]] =
     metadataDatabaseInterface.getFailedJobsMetadataWithWorkflowId(rootWorkflowId.toString)
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala
index d320adb42ae..5b45d7bb1e0 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala
@@ -1,7 +1,16 @@
 package cromwell.services.metadata.impl
 
 import akka.actor.SupervisorStrategy.{Decider, Directive, Escalate, Resume}
-import akka.actor.{Actor, ActorContext, ActorInitializationException, ActorLogging, ActorRef, Cancellable, OneForOneStrategy, Props}
+import akka.actor.{
+  Actor,
+  ActorContext,
+  ActorInitializationException,
+  ActorLogging,
+  ActorRef,
+  Cancellable,
+  OneForOneStrategy,
+  Props
+}
 import akka.routing.Listen
 import cats.data.NonEmptyList
 import com.typesafe.config.Config
@@ -15,7 +24,11 @@ import cromwell.services.metadata.MetadataArchiveStatus
 import cromwell.services.metadata.MetadataService._
 import cromwell.services.metadata.impl.MetadataDatabaseAccess.WorkflowArchiveStatusAndEndTimestamp
 import cromwell.services.metadata.impl.MetadataStatisticsRecorder.MetadataStatisticsRecorderSettings
-import cromwell.services.metadata.impl.MetadataSummaryRefreshActor.{MetadataSummaryFailure, MetadataSummarySuccess, SummarizeMetadata}
+import cromwell.services.metadata.impl.MetadataSummaryRefreshActor.{
+  MetadataSummaryFailure,
+  MetadataSummarySuccess,
+  SummarizeMetadata
+}
 import cromwell.services.metadata.impl.archiver.{ArchiveMetadataConfig, ArchiveMetadataSchedulerActor}
 import cromwell.services.metadata.impl.builder.MetadataBuilderActor
 import cromwell.services.metadata.impl.deleter.{DeleteMetadataActor, DeleteMetadataConfig}
@@ -30,11 +43,12 @@ import scala.util.{Failure, Success}
 object MetadataServiceActor {
   val MetadataInstrumentationPrefix = NonEmptyList.of("metadata")
 
-  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) = Props(MetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor)).withDispatcher(ServiceDispatcher)
+  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) =
+    Props(MetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor)).withDispatcher(ServiceDispatcher)
 }
 
 case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
-  extends Actor
+    extends Actor
     with ActorLogging
     with MetadataDatabaseAccess
     with MetadataServicesStore
@@ -49,7 +63,10 @@ case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, ser
   override val supervisorStrategy = new OneForOneStrategy()(decider) {
     override def logFailure(context: ActorContext, child: ActorRef, cause: Throwable, decision: Directive) = {
       val childName = if (child == readActor) "Read" else "Write"
-      log.error(cause, s"The $childName Metadata Actor died unexpectedly, metadata events might have been lost. Restarting it...")
+      log.error(
+        cause,
+        s"The $childName Metadata Actor died unexpectedly, metadata events might have been lost. Restarting it..."
+      )
     }
   }
 
@@ -65,12 +82,14 @@ case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, ser
   private val metadataReadRowNumberSafetyThreshold: Int =
     serviceConfig.getOrElse[Int]("metadata-read-row-number-safety-threshold", 1000000)
 
-  private val metadataTableMetricsInterval: Option[FiniteDuration] = serviceConfig.getAs[FiniteDuration]("metadata-table-metrics-interval")
+  private val metadataTableMetricsInterval: Option[FiniteDuration] =
+    serviceConfig.getAs[FiniteDuration]("metadata-table-metrics-interval")
 
-  private val metadataTableMetricsPath: NonEmptyList[String] = MetadataServiceActor.MetadataInstrumentationPrefix :+ "table"
+  private val metadataTableMetricsPath: NonEmptyList[String] =
+    MetadataServiceActor.MetadataInstrumentationPrefix :+ "table"
   private val dataFreeMetricsPath: NonEmptyList[String] = metadataTableMetricsPath :+ "data_free"
   private val dataLengthMetricsPath: NonEmptyList[String] = metadataTableMetricsPath :+ "data_length"
-  private val indexLengthMetricsPath:  NonEmptyList[String] = metadataTableMetricsPath :+ "index_length"
+  private val indexLengthMetricsPath: NonEmptyList[String] = metadataTableMetricsPath :+ "index_length"
 
   def readMetadataWorkerActorProps(): Props =
     ReadDatabaseMetadataWorkerActor
@@ -81,15 +100,28 @@ case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, ser
     .props(readMetadataWorkerActorProps, metadataReadRowNumberSafetyThreshold)
     .withDispatcher(ServiceDispatcher)
 
-  val readActor = context.actorOf(ReadMetadataRegulatorActor.props(metadataBuilderActorProps, readMetadataWorkerActorProps), "ClassicMSA-ReadMetadataRegulatorActor")
+  val readActor = context.actorOf(
+    ReadMetadataRegulatorActor.props(metadataBuilderActorProps, readMetadataWorkerActorProps),
+    "ClassicMSA-ReadMetadataRegulatorActor"
+  )
 
   val dbFlushRate = serviceConfig.getOrElse("db-flush-rate", 5.seconds)
   val dbBatchSize = serviceConfig.getOrElse("db-batch-size", 200)
-  val metadataWriteStatisticsConfig = MetadataStatisticsRecorderSettings(serviceConfig.as[Option[Config]]("metadata-write-statistics"))
-  val writeActor = context.actorOf(WriteMetadataActor.props(dbBatchSize, dbFlushRate, serviceRegistryActor, LoadConfig.MetadataWriteThreshold, metadataWriteStatisticsConfig), "WriteMetadataActor")
+  val metadataWriteStatisticsConfig = MetadataStatisticsRecorderSettings(
+    serviceConfig.as[Option[Config]]("metadata-write-statistics")
+  )
+  val writeActor = context.actorOf(
+    WriteMetadataActor.props(dbBatchSize,
+                             dbFlushRate,
+                             serviceRegistryActor,
+                             LoadConfig.MetadataWriteThreshold,
+                             metadataWriteStatisticsConfig
+    ),
+    "WriteMetadataActor"
+  )
 
   implicit val ec = context.dispatcher
-  //noinspection ActorMutableStateInspection
+  // noinspection ActorMutableStateInspection
   private var summaryRefreshCancellable: Option[Cancellable] = None
 
   private val summaryActor: Option[ActorRef] = buildSummaryActor
@@ -101,13 +133,15 @@ case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, ser
   private val deleteMetadataActor: Option[ActorRef] = buildDeleteMetadataActor
 
   // if `metadata-table-size-metrics-interval` is specified, schedule sending size metrics at that interval
-  metadataTableMetricsInterval.map(context.system.scheduler.schedule(1.minute, _, self, SendMetadataTableSizeMetrics)(context.dispatcher, self))
+  metadataTableMetricsInterval.map(
+    context.system.scheduler.schedule(1.minute, _, self, SendMetadataTableSizeMetrics)(context.dispatcher, self)
+  )
 
-  private def scheduleSummary(): Unit = {
+  private def scheduleSummary(): Unit =
     metadataSummaryRefreshInterval foreach { interval =>
-      summaryRefreshCancellable = Option(context.system.scheduler.scheduleOnce(interval, self, RefreshSummary)(context.dispatcher, self))
+      summaryRefreshCancellable =
+        Option(context.system.scheduler.scheduleOnce(interval, self, RefreshSummary)(context.dispatcher, self))
     }
-  }
 
   override def postStop(): Unit = {
     summaryRefreshCancellable foreach { _.cancel() }
@@ -115,8 +149,8 @@ case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, ser
   }
 
   private def buildSummaryActor: Option[ActorRef] = {
-    val actor = metadataSummaryRefreshInterval map {
-      _ => context.actorOf(MetadataSummaryRefreshActor.props(serviceRegistryActor), "metadata-summary-actor")
+    val actor = metadataSummaryRefreshInterval map { _ =>
+      context.actorOf(MetadataSummaryRefreshActor.props(serviceRegistryActor), "metadata-summary-actor")
     }
     val message = metadataSummaryRefreshInterval match {
       case Some(interval) => s"Metadata summary refreshing every $interval."
@@ -126,60 +160,75 @@ case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, ser
     actor
   }
 
-  private def buildArchiveMetadataActor: Option[ActorRef] = {
+  private def buildArchiveMetadataActor: Option[ActorRef] =
     if (serviceConfig.hasPath("archive-metadata")) {
       log.info("Building metadata archiver from config")
       ArchiveMetadataConfig.parseConfig(serviceConfig.getConfig("archive-metadata"))(context.system) match {
-        case Right(config) => Option(context.actorOf(ArchiveMetadataSchedulerActor.props(config, serviceRegistryActor), "archive-metadata-scheduler"))
-        case Left(errorList) => throw AggregatedMessageException("Failed to parse the archive-metadata config", errorList.toList)
+        case Right(config) =>
+          Option(
+            context.actorOf(ArchiveMetadataSchedulerActor.props(config, serviceRegistryActor),
+                            "archive-metadata-scheduler"
+            )
+          )
+        case Left(errorList) =>
+          throw AggregatedMessageException("Failed to parse the archive-metadata config", errorList.toList)
       }
     } else {
       log.info("No metadata archiver defined in config")
       None
     }
-  }
 
-  private def buildDeleteMetadataActor: Option[ActorRef] = {
+  private def buildDeleteMetadataActor: Option[ActorRef] =
     if (serviceConfig.hasPath("delete-metadata")) {
       log.info("Building metadata deleter from config")
       DeleteMetadataConfig.parseConfig(serviceConfig.getConfig("delete-metadata")) match {
-        case Right(config) => Option(context.actorOf(DeleteMetadataActor.props(config, serviceRegistryActor), "delete-metadata-actor"))
-        case Left(errorList) => throw AggregatedMessageException("Failed to parse the archive-metadata config", errorList.toList)
+        case Right(config) =>
+          Option(context.actorOf(DeleteMetadataActor.props(config, serviceRegistryActor), "delete-metadata-actor"))
+        case Left(errorList) =>
+          throw AggregatedMessageException("Failed to parse the archive-metadata config", errorList.toList)
       }
     } else {
       log.info("No metadata deleter defined in config")
       None
     }
-  }
 
-  private def validateWorkflowIdInMetadata(possibleWorkflowId: WorkflowId, sender: ActorRef): Unit = {
+  private def validateWorkflowIdInMetadata(possibleWorkflowId: WorkflowId, sender: ActorRef): Unit =
     workflowWithIdExistsInMetadata(possibleWorkflowId.toString) onComplete {
       case Success(true) => sender ! RecognizedWorkflowId
       case Success(false) => sender ! UnrecognizedWorkflowId
-      case Failure(e) => sender ! FailedToCheckWorkflowId(new RuntimeException(s"Failed lookup attempt for workflow ID $possibleWorkflowId", e))
+      case Failure(e) =>
+        sender ! FailedToCheckWorkflowId(
+          new RuntimeException(s"Failed lookup attempt for workflow ID $possibleWorkflowId", e)
+        )
     }
-  }
 
-  private def validateWorkflowIdInMetadataSummaries(possibleWorkflowId: WorkflowId, sender: ActorRef): Unit = {
+  private def validateWorkflowIdInMetadataSummaries(possibleWorkflowId: WorkflowId, sender: ActorRef): Unit =
     workflowWithIdExistsInMetadataSummaries(possibleWorkflowId.toString) onComplete {
       case Success(true) => sender ! RecognizedWorkflowId
       case Success(false) => sender ! UnrecognizedWorkflowId
-      case Failure(e) => sender ! FailedToCheckWorkflowId(new RuntimeException(s"Failed lookup attempt for workflow ID $possibleWorkflowId", e))
+      case Failure(e) =>
+        sender ! FailedToCheckWorkflowId(
+          new RuntimeException(s"Failed lookup attempt for workflow ID $possibleWorkflowId", e)
+        )
     }
-  }
 
-  private def fetchWorkflowMetadataArchiveStatusAndEndTime(workflowId: WorkflowId, sender: ActorRef): Unit = {
+  private def fetchWorkflowMetadataArchiveStatusAndEndTime(workflowId: WorkflowId, sender: ActorRef): Unit =
     getMetadataArchiveStatusAndEndTime(workflowId) onComplete {
       case Success(WorkflowArchiveStatusAndEndTimestamp(status, endTime)) =>
         MetadataArchiveStatus.fromDatabaseValue(status).toTry match {
           case Success(archiveStatus) => sender ! WorkflowMetadataArchivedStatusAndEndTime(archiveStatus, endTime)
-          case Failure(e) => sender ! FailedToGetArchiveStatusAndEndTime(new RuntimeException(s"Failed to get metadata archive status for workflow ID $workflowId", e))
+          case Failure(e) =>
+            sender ! FailedToGetArchiveStatusAndEndTime(
+              new RuntimeException(s"Failed to get metadata archive status for workflow ID $workflowId", e)
+            )
         }
-      case Failure(e) => sender ! FailedToGetArchiveStatusAndEndTime(new RuntimeException(s"Failed to get metadata archive status for workflow ID $workflowId", e))
+      case Failure(e) =>
+        sender ! FailedToGetArchiveStatusAndEndTime(
+          new RuntimeException(s"Failed to get metadata archive status for workflow ID $workflowId", e)
+        )
     }
-  }
 
-  private def sendMetadataTableSizeMetrics(): Unit = {
+  private def sendMetadataTableSizeMetrics(): Unit =
     getMetadataTableSizeInformation() onComplete {
       case Success(v) =>
         v foreach { d =>
@@ -187,9 +236,9 @@ case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, ser
           sendGauge(indexLengthMetricsPath, d.indexLength)
           sendGauge(dataFreeMetricsPath, d.dataFree)
         }
-      case Failure(e) => log.error(e, s"Error fetching metadata table size metrics. Will try again in $metadataTableMetricsInterval...")
+      case Failure(e) =>
+        log.error(e, s"Error fetching metadata table size metrics. Will try again in $metadataTableMetricsInterval...")
     }
-  }
 
   def summarizerReceive: Receive = {
     case RefreshSummary => summaryActor foreach { _ ! SummarizeMetadata(metadataSummaryRefreshLimit, sender()) }
@@ -200,15 +249,18 @@ case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, ser
   }
 
   def receive = summarizerReceive orElse {
-    case ShutdownCommand => waitForActorsAndShutdown(NonEmptyList.of(writeActor) ++ archiveMetadataActor.toList ++ deleteMetadataActor.toList)
+    case ShutdownCommand =>
+      waitForActorsAndShutdown(NonEmptyList.of(writeActor) ++ archiveMetadataActor.toList ++ deleteMetadataActor.toList)
     case SendMetadataTableSizeMetrics => sendMetadataTableSizeMetrics()
     case action: PutMetadataAction => writeActor forward action
     case action: PutMetadataActionAndRespond => writeActor forward action
     // Assume that listen messages are directed to the write metadata actor
     case listen: Listen => writeActor forward listen
     case v: ValidateWorkflowIdInMetadata => validateWorkflowIdInMetadata(v.possibleWorkflowId, sender())
-    case v: ValidateWorkflowIdInMetadataSummaries => validateWorkflowIdInMetadataSummaries(v.possibleWorkflowId, sender())
-    case g: FetchWorkflowMetadataArchiveStatusAndEndTime => fetchWorkflowMetadataArchiveStatusAndEndTime(g.workflowId, sender())
+    case v: ValidateWorkflowIdInMetadataSummaries =>
+      validateWorkflowIdInMetadataSummaries(v.possibleWorkflowId, sender())
+    case g: FetchWorkflowMetadataArchiveStatusAndEndTime =>
+      fetchWorkflowMetadataArchiveStatusAndEndTime(g.workflowId, sender())
     case action: BuildMetadataJsonAction => readActor forward action
     case streamAction: GetMetadataStreamAction => readActor forward streamAction
   }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/MetadataStatisticsRecorder.scala b/services/src/main/scala/cromwell/services/metadata/impl/MetadataStatisticsRecorder.scala
index 5e9316ac89f..b3b802adfc7 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/MetadataStatisticsRecorder.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/MetadataStatisticsRecorder.scala
@@ -16,35 +16,42 @@ import scala.util.Try
 
 object MetadataStatisticsRecorder {
   final case class HeavyMetadataAlert(workflowId: WorkflowId, count: Long)
-  final case class WorkflowMetadataWriteStatistics(workflowId: WorkflowId, totalWrites: Long, lastLogged: Long, knownParent: Option[WorkflowId])
+  final case class WorkflowMetadataWriteStatistics(workflowId: WorkflowId,
+                                                   totalWrites: Long,
+                                                   lastLogged: Long,
+                                                   knownParent: Option[WorkflowId]
+  )
 
   sealed trait MetadataStatisticsRecorderSettings
   case object MetadataStatisticsDisabled extends MetadataStatisticsRecorderSettings
 
   final case class MetadataStatisticsEnabled(workflowCacheSize: Long,
-                                                      metadataAlertInterval: Long,
-                                                      bundleSubworkflowsIntoParents: Boolean) extends MetadataStatisticsRecorderSettings
-
-  def apply(statisticsRecorderSettings: MetadataStatisticsRecorderSettings): MetadataStatisticsRecorder = statisticsRecorderSettings match {
-    case MetadataStatisticsEnabled(cacheSize, interval, subworkflowBundling) => new ActiveMetadataStatisticsRecorder(cacheSize, interval, subworkflowBundling)
-    case MetadataStatisticsDisabled => new NoopMetadataStatisticsRecorder()
-  }
-
+                                             metadataAlertInterval: Long,
+                                             bundleSubworkflowsIntoParents: Boolean
+  ) extends MetadataStatisticsRecorderSettings
+
+  def apply(statisticsRecorderSettings: MetadataStatisticsRecorderSettings): MetadataStatisticsRecorder =
+    statisticsRecorderSettings match {
+      case MetadataStatisticsEnabled(cacheSize, interval, subworkflowBundling) =>
+        new ActiveMetadataStatisticsRecorder(cacheSize, interval, subworkflowBundling)
+      case MetadataStatisticsDisabled => new NoopMetadataStatisticsRecorder()
+    }
 
   object MetadataStatisticsRecorderSettings {
     val defaultCacheSize = 20000L
     val defaultAlertInterval = 100000L
     val defaultSubworkflowBundling = true
 
-    def apply(configSection: Option[Config]): MetadataStatisticsRecorderSettings = (configSection flatMap { conf: Config =>
-      if (conf.as[Option[Boolean]]("enabled").forall(identity)) {
-        val cacheSize: Long = conf.getOrElse("cache-size", defaultCacheSize)
-        val metadataAlertInterval: Long = conf.getOrElse("metadata-row-alert-interval", defaultAlertInterval)
-        val subworkflowBundling: Boolean = conf.getOrElse("sub-workflow-bundling", defaultSubworkflowBundling)
-        Option(MetadataStatisticsEnabled(cacheSize, metadataAlertInterval, subworkflowBundling))
-      } else None
+    def apply(configSection: Option[Config]): MetadataStatisticsRecorderSettings =
+      (configSection flatMap { conf: Config =>
+        if (conf.as[Option[Boolean]]("enabled").forall(identity)) {
+          val cacheSize: Long = conf.getOrElse("cache-size", defaultCacheSize)
+          val metadataAlertInterval: Long = conf.getOrElse("metadata-row-alert-interval", defaultAlertInterval)
+          val subworkflowBundling: Boolean = conf.getOrElse("sub-workflow-bundling", defaultSubworkflowBundling)
+          Option(MetadataStatisticsEnabled(cacheSize, metadataAlertInterval, subworkflowBundling))
+        } else None
 
-    }).getOrElse(MetadataStatisticsDisabled)
+      }).getOrElse(MetadataStatisticsDisabled)
   }
 }
 
@@ -57,49 +64,58 @@ final class NoopMetadataStatisticsRecorder extends MetadataStatisticsRecorder {
 }
 
 final class ActiveMetadataStatisticsRecorder(workflowCacheSize: Long = 100000L, // 100,000
-                                       metadataAlertInterval: Long = 100000L, // 100,000
-                                       bundleSubworkflowsIntoParents: Boolean = false
-                                      ) extends MetadataStatisticsRecorder {
+                                             metadataAlertInterval: Long = 100000L, // 100,000
+                                             bundleSubworkflowsIntoParents: Boolean = false
+) extends MetadataStatisticsRecorder {
 
   // Statistics for each workflow
-  private val metadataWriteStatisticsCache = CacheBuilder.newBuilder()
+  private val metadataWriteStatisticsCache = CacheBuilder
+    .newBuilder()
     .expireAfterAccess(JDuration.ofSeconds(4.hours.toSeconds))
     .maximumSize(workflowCacheSize)
     .build[WorkflowId, WorkflowMetadataWriteStatistics]()
 
-  def writeStatisticsLoader(workflowId: WorkflowId): Callable[WorkflowMetadataWriteStatistics] = () => WorkflowMetadataWriteStatistics(workflowId, 0L, 0L, None)
+  def writeStatisticsLoader(workflowId: WorkflowId): Callable[WorkflowMetadataWriteStatistics] = () =>
+    WorkflowMetadataWriteStatistics(workflowId, 0L, 0L, None)
 
-  def processEventsAndGenerateAlerts(putEvents: Iterable[MetadataEvent]): Vector[HeavyMetadataAlert] = {
-    putEvents.groupBy(_.key.workflowId).toVector.flatMap { case (id, list) => processEventsForWorkflow(id, list)}
-  }
+  def processEventsAndGenerateAlerts(putEvents: Iterable[MetadataEvent]): Vector[HeavyMetadataAlert] =
+    putEvents.groupBy(_.key.workflowId).toVector.flatMap { case (id, list) => processEventsForWorkflow(id, list) }
 
-  private def processEventsForWorkflow(workflowId: WorkflowId, events: Iterable[MetadataEvent]): Vector[HeavyMetadataAlert] = {
+  private def processEventsForWorkflow(workflowId: WorkflowId,
+                                       events: Iterable[MetadataEvent]
+  ): Vector[HeavyMetadataAlert] = {
     val workflowWriteStats = metadataWriteStatisticsCache.get(workflowId, writeStatisticsLoader(workflowId))
 
     // Find a new parent record if one exists and update the statistics to record it:
-    val parentallyUpdatedStatistics = {
+    val parentallyUpdatedStatistics =
       if (!bundleSubworkflowsIntoParents) workflowWriteStats
       else if (workflowWriteStats.knownParent.isDefined) workflowWriteStats
       else {
         val newParentId = events.collectFirst {
-          case MetadataEvent(MetadataKey(_, None, "parentWorkflowId"), Some(MetadataValue(value, MetadataString)), _) => Try(WorkflowId(UUID.fromString(value))).toOption
+          case MetadataEvent(MetadataKey(_, None, "parentWorkflowId"), Some(MetadataValue(value, MetadataString)), _) =>
+            Try(WorkflowId(UUID.fromString(value))).toOption
         }.flatten
         workflowWriteStats.copy(knownParent = newParentId)
       }
-    }
 
     updateStatisticsCacheAndGenerateAlerts(parentallyUpdatedStatistics, events.size.longValue)
   }
 
-  private def updateStatisticsCacheAndGenerateAlerts(workflowWriteStats: WorkflowMetadataWriteStatistics, count: Long): Vector[HeavyMetadataAlert] = {
+  private def updateStatisticsCacheAndGenerateAlerts(workflowWriteStats: WorkflowMetadataWriteStatistics,
+                                                     count: Long
+  ): Vector[HeavyMetadataAlert] = {
     val writesForWorkflow = workflowWriteStats.totalWrites + count
 
     val myAlerts = if (writesForWorkflow >= workflowWriteStats.lastLogged + metadataAlertInterval) {
-      metadataWriteStatisticsCache.put(workflowWriteStats.workflowId, workflowWriteStats.copy(totalWrites = writesForWorkflow, lastLogged = writesForWorkflow))
+      metadataWriteStatisticsCache.put(
+        workflowWriteStats.workflowId,
+        workflowWriteStats.copy(totalWrites = writesForWorkflow, lastLogged = writesForWorkflow)
+      )
       Vector(HeavyMetadataAlert(workflowWriteStats.workflowId, writesForWorkflow))
-    }
-    else {
-      metadataWriteStatisticsCache.put(workflowWriteStats.workflowId, workflowWriteStats.copy(totalWrites = writesForWorkflow))
+    } else {
+      metadataWriteStatisticsCache.put(workflowWriteStats.workflowId,
+                                       workflowWriteStats.copy(totalWrites = writesForWorkflow)
+      )
       Vector.empty
     }
 
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/MetadataSummaryRefreshActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/MetadataSummaryRefreshActor.scala
index 5a80b08e4cc..64fa240388d 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/MetadataSummaryRefreshActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/MetadataSummaryRefreshActor.scala
@@ -1,6 +1,5 @@
 package cromwell.services.metadata.impl
 
-
 import akka.actor.{ActorRef, LoggingFSM, Props}
 import cats.data.NonEmptyList
 import cromwell.core.Dispatcher.ServiceDispatcher
@@ -25,7 +24,8 @@ object MetadataSummaryRefreshActor {
   case object MetadataSummarySuccess extends MetadataSummaryActorMessage
   final case class MetadataSummaryFailure(t: Throwable) extends MetadataSummaryActorMessage
 
-  def props(serviceRegistryActor: ActorRef) = Props(new MetadataSummaryRefreshActor(serviceRegistryActor)).withDispatcher(ServiceDispatcher)
+  def props(serviceRegistryActor: ActorRef) =
+    Props(new MetadataSummaryRefreshActor(serviceRegistryActor)).withDispatcher(ServiceDispatcher)
 
   sealed trait SummaryRefreshState
   case object WaitingForRequest extends SummaryRefreshState
@@ -36,16 +36,17 @@ object MetadataSummaryRefreshActor {
 }
 
 class MetadataSummaryRefreshActor(override val serviceRegistryActor: ActorRef)
-  extends LoggingFSM[SummaryRefreshState, SummaryRefreshData.type]
+    extends LoggingFSM[SummaryRefreshState, SummaryRefreshData.type]
     with MetadataDatabaseAccess
     with MetadataServicesStore
     with CromwellInstrumentation {
 
   implicit val ec = context.dispatcher
 
-  private val summaryMetricsGapsPath: NonEmptyList[String] = MetadataServiceActor.MetadataInstrumentationPrefix :+ "summarizer" :+ "gap"
-  private val summaryMetricsProcessedPath: NonEmptyList[String] = MetadataServiceActor.MetadataInstrumentationPrefix :+ "summarizer" :+ "processed"
-
+  private val summaryMetricsGapsPath: NonEmptyList[String] =
+    MetadataServiceActor.MetadataInstrumentationPrefix :+ "summarizer" :+ "gap"
+  private val summaryMetricsProcessedPath: NonEmptyList[String] =
+    MetadataServiceActor.MetadataInstrumentationPrefix :+ "summarizer" :+ "processed"
 
   val increasingGapPath = summaryMetricsGapsPath :+ "increasing"
   val decreasingGapPath = summaryMetricsGapsPath :+ "decreasing"
@@ -56,38 +57,37 @@ class MetadataSummaryRefreshActor(override val serviceRegistryActor: ActorRef)
   private val instrumentationPrefix: Option[String] = InstrumentationPrefixes.ServicesPrefix
 
   private val summarizerQueueIncreasingGapMetricActor =
-    context.actorOf(AsynchronousThrottlingGaugeMetricActor.props(increasingGapPath, instrumentationPrefix, serviceRegistryActor))
+    context.actorOf(
+      AsynchronousThrottlingGaugeMetricActor.props(increasingGapPath, instrumentationPrefix, serviceRegistryActor)
+    )
 
   startWith(WaitingForRequest, SummaryRefreshData)
 
-  when (WaitingForRequest) {
-    case Event(SummarizeMetadata(limit, respondTo), _) =>
-      refreshWorkflowMetadataSummaries(limit) onComplete {
-        case Success(summaryResult) =>
-          summarizerQueueIncreasingGapMetricActor ! CalculateMetricValue { ec => getSummaryQueueSize()(ec) }
-          sendGauge(decreasingGapPath, summaryResult.decreasingGap, instrumentationPrefix)
-
-          count(increasingProcessedPath, summaryResult.rowsProcessedIncreasing, instrumentationPrefix)
-          count(decreasingProcessedPath, summaryResult.rowsProcessedDecreasing, instrumentationPrefix)
-
-          respondTo ! MetadataSummarySuccess
-          self ! MetadataSummaryComplete
-        case Failure(t) =>
-          log.error(t, "Failed to summarize metadata")
-          respondTo ! MetadataSummaryFailure(t)
-          self ! MetadataSummaryComplete
-      }
-      goto(SummarizingMetadata)
+  when(WaitingForRequest) { case Event(SummarizeMetadata(limit, respondTo), _) =>
+    refreshWorkflowMetadataSummaries(limit) onComplete {
+      case Success(summaryResult) =>
+        summarizerQueueIncreasingGapMetricActor ! CalculateMetricValue(ec => getSummaryQueueSize()(ec))
+        sendGauge(decreasingGapPath, summaryResult.decreasingGap, instrumentationPrefix)
+
+        count(increasingProcessedPath, summaryResult.rowsProcessedIncreasing, instrumentationPrefix)
+        count(decreasingProcessedPath, summaryResult.rowsProcessedDecreasing, instrumentationPrefix)
+
+        respondTo ! MetadataSummarySuccess
+        self ! MetadataSummaryComplete
+      case Failure(t) =>
+        log.error(t, "Failed to summarize metadata")
+        respondTo ! MetadataSummaryFailure(t)
+        self ! MetadataSummaryComplete
+    }
+    goto(SummarizingMetadata)
   }
 
-  when (SummarizingMetadata) {
-    case Event(MetadataSummaryComplete, _) =>
-      goto(WaitingForRequest) using SummaryRefreshData
+  when(SummarizingMetadata) { case Event(MetadataSummaryComplete, _) =>
+    goto(WaitingForRequest) using SummaryRefreshData
   }
 
-  whenUnhandled {
-    case Event(wut, _) =>
-      log.warning("Unrecognized or unexpected message while in state '{}': {}", stateName, wut)
-      stay()
+  whenUnhandled { case Event(wut, _) =>
+    log.warning("Unrecognized or unexpected message while in state '{}': {}", stateName, wut)
+    stay()
   }
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/ReadDatabaseMetadataWorkerActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/ReadDatabaseMetadataWorkerActor.scala
index 165c1bc2f14..25240577e37 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/ReadDatabaseMetadataWorkerActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/ReadDatabaseMetadataWorkerActor.scala
@@ -14,11 +14,12 @@ import scala.util.Try
 
 object ReadDatabaseMetadataWorkerActor {
   def props(metadataReadTimeout: Duration, metadataReadRowNumberSafetyThreshold: Int) =
-    Props(new ReadDatabaseMetadataWorkerActor(metadataReadTimeout, metadataReadRowNumberSafetyThreshold)).withDispatcher(ServiceDispatcher)
+    Props(new ReadDatabaseMetadataWorkerActor(metadataReadTimeout, metadataReadRowNumberSafetyThreshold))
+      .withDispatcher(ServiceDispatcher)
 }
 
 class ReadDatabaseMetadataWorkerActor(metadataReadTimeout: Duration, metadataReadRowNumberSafetyThreshold: Int)
-  extends Actor
+    extends Actor
     with ActorLogging
     with MetadataDatabaseAccess
     with MetadataServicesStore {
@@ -26,34 +27,41 @@ class ReadDatabaseMetadataWorkerActor(metadataReadTimeout: Duration, metadataRea
   implicit val ec = context.dispatcher
 
   def receive = {
-    case FetchFailedJobsMetadataWithWorkflowId(w: WorkflowId) => {
+    case FetchFailedJobsMetadataWithWorkflowId(w: WorkflowId) =>
       evaluateRespondAndStop(sender(), getFailedJobs(w))
-    }
     case GetMetadataAction(query: MetadataQuery, checkTotalMetadataRowNumberBeforeQuerying: Boolean) =>
       evaluateRespondAndStop(sender(), getMetadata(query, checkTotalMetadataRowNumberBeforeQuerying))
     case GetMetadataStreamAction(workflowId) =>
       evaluateRespondAndStop(sender(), Future.fromTry(getMetadataStream(workflowId)))
     case GetStatus(workflowId) => evaluateRespondAndStop(sender(), getStatus(workflowId))
     case GetLabels(workflowId) => evaluateRespondAndStop(sender(), queryLabelsAndRespond(workflowId))
-    case GetRootAndSubworkflowLabels(rootWorkflowId: WorkflowId) => evaluateRespondAndStop(sender(), queryRootAndSubworkflowLabelsAndRespond(rootWorkflowId))
+    case GetRootAndSubworkflowLabels(rootWorkflowId: WorkflowId) =>
+      evaluateRespondAndStop(sender(), queryRootAndSubworkflowLabelsAndRespond(rootWorkflowId))
     case GetLogs(workflowId) => evaluateRespondAndStop(sender(), queryLogsAndRespond(workflowId))
-    case QueryForWorkflowsMatchingParameters(parameters) => evaluateRespondAndStop(sender(), queryWorkflowsAndRespond(parameters))
+    case QueryForWorkflowsMatchingParameters(parameters) =>
+      evaluateRespondAndStop(sender(), queryWorkflowsAndRespond(parameters))
     case WorkflowOutputs(id) => evaluateRespondAndStop(sender(), queryWorkflowOutputsAndRespond(id))
-    case unexpected => log.warning(s"Programmer Error! Unexpected message received by ${getClass.getSimpleName}: $unexpected")
+    case unexpected =>
+      log.warning(s"Programmer Error! Unexpected message received by ${getClass.getSimpleName}: $unexpected")
   }
 
   private def evaluateRespondAndStop(sndr: ActorRef, f: Future[Any]) = {
     f map { result =>
       sndr ! result
-    } andThen {
-      case _ => self ! PoisonPill
-    } recover {
-      case t => log.error(t, s"Programmer Error! Unexpected error fall-through to 'evaluateRespondAndStop in ${getClass.getSimpleName}'")
+    } andThen { case _ =>
+      self ! PoisonPill
+    } recover { case t =>
+      log.error(
+        t,
+        s"Programmer Error! Unexpected error fall-through to 'evaluateRespondAndStop in ${getClass.getSimpleName}'"
+      )
     }
     ()
   }
 
-  private def getMetadata(query: MetadataQuery, checkResultSizeBeforeQuerying: Boolean): Future[MetadataServiceResponse] = {
+  private def getMetadata(query: MetadataQuery,
+                          checkResultSizeBeforeQuerying: Boolean
+  ): Future[MetadataServiceResponse] =
     if (checkResultSizeBeforeQuerying) {
       getMetadataReadRowCount(query, metadataReadTimeout) flatMap { count =>
         if (count > metadataReadRowNumberSafetyThreshold) {
@@ -68,94 +76,84 @@ class ReadDatabaseMetadataWorkerActor(metadataReadTimeout: Duration, metadataRea
     } else {
       queryMetadata(query)
     }
-  }
 
-  private def getMetadataStream(workflowId: WorkflowId): Try[MetadataServiceResponse] = {
-    metadataEventsStream(workflowId) map {
-      s => MetadataLookupStreamSuccess(workflowId, s)
-    } recover {
-      case t => MetadataLookupStreamFailed(workflowId, t)
+  private def getMetadataStream(workflowId: WorkflowId): Try[MetadataServiceResponse] =
+    metadataEventsStream(workflowId) map { s =>
+      MetadataLookupStreamSuccess(workflowId, s)
+    } recover { case t =>
+      MetadataLookupStreamFailed(workflowId, t)
     }
-  }
 
   private def queryMetadata(query: MetadataQuery): Future[MetadataServiceResponse] =
-    queryMetadataEvents(query, metadataReadTimeout) map {
-      m => MetadataLookupResponse(query, m)
+    queryMetadataEvents(query, metadataReadTimeout) map { m =>
+      MetadataLookupResponse(query, m)
     } recover {
       case _: SQLTimeoutException => MetadataLookupFailedTimeoutResponse(query)
       case t => MetadataServiceKeyLookupFailed(query, t)
     }
 
   private def getFailedJobs(workflowId: WorkflowId): Future[MetadataServiceResponse] = {
-   val futureEvents: Future[Seq[MetadataEvent]] = getFailedJobsMetadataWithWorkflowId(workflowId) map metadataToMetadataEvents(workflowId)
-    futureEvents map {
-      m => FetchFailedJobsMetadataLookupResponse(m)
+    val futureEvents: Future[Seq[MetadataEvent]] =
+      getFailedJobsMetadataWithWorkflowId(workflowId) map metadataToMetadataEvents(workflowId)
+    futureEvents map { m =>
+      FetchFailedJobsMetadataLookupResponse(m)
     } recover {
       case _: SQLTimeoutException => FetchFailedTasksTimeoutResponse(workflowId)
       case t => FetchFailedJobsMetadataLookupFailed(workflowId, t)
     }
   }
 
-  private def getStatus(id: WorkflowId): Future[MetadataServiceResponse] = {
-
+  private def getStatus(id: WorkflowId): Future[MetadataServiceResponse] =
     getWorkflowStatus(id) map {
       case Some(s) => StatusLookupResponse(id, s)
       // There's a workflow existence check at the API layer.  If the request has made it this far in the system
       // then the workflow exists but it must not have generated a status yet.
       case None => StatusLookupResponse(id, WorkflowSubmitted)
-    } recover {
-      case t => StatusLookupFailed(id, t)
+    } recover { case t =>
+      StatusLookupFailed(id, t)
     }
-  }
 
-  private def queryLabelsAndRespond(id: WorkflowId): Future[MetadataServiceResponse] = {
-
-    getWorkflowLabels(id) map {
-      ls => LabelLookupResponse(id, ls)
-    } recover {
-      case t => LabelLookupFailed(id, t)
+  private def queryLabelsAndRespond(id: WorkflowId): Future[MetadataServiceResponse] =
+    getWorkflowLabels(id) map { ls =>
+      LabelLookupResponse(id, ls)
+    } recover { case t =>
+      LabelLookupFailed(id, t)
     }
-  }
-
-  private def queryRootAndSubworkflowLabelsAndRespond(rootWorkflowId: WorkflowId): Future[MetadataServiceResponse] = {
 
+  private def queryRootAndSubworkflowLabelsAndRespond(rootWorkflowId: WorkflowId): Future[MetadataServiceResponse] =
     getRootAndSubworkflowLabels(rootWorkflowId) map { labels =>
       RootAndSubworkflowLabelsLookupResponse(rootWorkflowId, labels)
-    } recover {
-      case t => RootAndSubworkflowLabelsLookupFailed(rootWorkflowId, t)
+    } recover { case t =>
+      RootAndSubworkflowLabelsLookupFailed(rootWorkflowId, t)
     }
-  }
 
   private def queryWorkflowsAndRespond(rawParameters: Seq[(String, String)]): Future[MetadataServiceResponse] = {
-    def queryWorkflows: Future[(WorkflowQueryResponse, Option[QueryMetadata])] = {
+    def queryWorkflows: Future[(WorkflowQueryResponse, Option[QueryMetadata])] =
       for {
-      // Future/Try to wrap the exception that might be thrown from WorkflowQueryParameters.apply.
+        // Future/Try to wrap the exception that might be thrown from WorkflowQueryParameters.apply.
         parameters <- Future.fromTry(Try(WorkflowQueryParameters(rawParameters)))
         response <- queryWorkflowSummaries(parameters)
       } yield response
-    }
 
-    queryWorkflows map {
-      case (response, metadata) => WorkflowQuerySuccess(response, metadata)
-    } recover {
-      case t => WorkflowQueryFailure(t)
+    queryWorkflows map { case (response, metadata) =>
+      WorkflowQuerySuccess(response, metadata)
+    } recover { case t =>
+      WorkflowQueryFailure(t)
     }
   }
 
-  private def queryWorkflowOutputsAndRespond(id: WorkflowId): Future[MetadataServiceResponse] = {
-    queryWorkflowOutputs(id, metadataReadTimeout) map {
-      o => WorkflowOutputsResponse(id, o)
-    } recover {
-      case t => WorkflowOutputsFailure(id, t)
+  private def queryWorkflowOutputsAndRespond(id: WorkflowId): Future[MetadataServiceResponse] =
+    queryWorkflowOutputs(id, metadataReadTimeout) map { o =>
+      WorkflowOutputsResponse(id, o)
+    } recover { case t =>
+      WorkflowOutputsFailure(id, t)
     }
-  }
 
-  private def queryLogsAndRespond(id: WorkflowId): Future[MetadataServiceResponse] = {
-    queryLogs(id, metadataReadTimeout) map {
-      s => LogsResponse(id, s)
-    } recover {
-      case t => LogsFailure(id, t)
+  private def queryLogsAndRespond(id: WorkflowId): Future[MetadataServiceResponse] =
+    queryLogs(id, metadataReadTimeout) map { s =>
+      LogsResponse(id, s)
+    } recover { case t =>
+      LogsFailure(id, t)
     }
-  }
 
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataRegulatorActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataRegulatorActor.scala
index 869ae79e10f..45ddb1bf272 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataRegulatorActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/ReadMetadataRegulatorActor.scala
@@ -5,13 +5,25 @@ import akka.actor.{Actor, ActorLogging, ActorRef, Props}
 import cromwell.core.Dispatcher.ApiDispatcher
 import cromwell.services.MetadataJsonResponse
 import cromwell.services.metadata.MetadataService
-import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, BuildWorkflowMetadataJsonAction, FetchFailedJobsMetadataWithWorkflowId, GetMetadataStreamAction, MetadataLookupStreamSuccess, MetadataQueryResponse, MetadataServiceAction, MetadataServiceResponse, RootAndSubworkflowLabelsLookupResponse}
+import cromwell.services.metadata.MetadataService.{
+  BuildMetadataJsonAction,
+  BuildWorkflowMetadataJsonAction,
+  FetchFailedJobsMetadataWithWorkflowId,
+  GetMetadataStreamAction,
+  MetadataLookupStreamSuccess,
+  MetadataQueryResponse,
+  MetadataServiceAction,
+  MetadataServiceResponse,
+  RootAndSubworkflowLabelsLookupResponse
+}
 import cromwell.services.metadata.impl.ReadMetadataRegulatorActor.PropsMaker
 import cromwell.services.metadata.impl.builder.MetadataBuilderActor
 
 import scala.collection.mutable
 
-class ReadMetadataRegulatorActor(metadataBuilderActorProps: PropsMaker, readMetadataWorkerProps: PropsMaker) extends Actor with ActorLogging {
+class ReadMetadataRegulatorActor(metadataBuilderActorProps: PropsMaker, readMetadataWorkerProps: PropsMaker)
+    extends Actor
+    with ActorLogging {
   // This actor tracks all requests coming in from the API service and spins up new builders as needed to service them.
   // If the processing of an identical request is already in flight the requester will be added to a set of requesters
   // to notify when the response from the first request becomes available.
@@ -31,7 +43,10 @@ class ReadMetadataRegulatorActor(metadataBuilderActorProps: PropsMaker, readMeta
           val currentRequesters = apiRequests.getOrElse(fetchFailedJobsMetadataAction, Set.empty)
           apiRequests.put(fetchFailedJobsMetadataAction, currentRequesters + sender())
           if (currentRequesters.isEmpty) {
-            val builderActor = context.actorOf(metadataBuilderActorProps().withDispatcher(ApiDispatcher), MetadataBuilderActor.uniqueActorName(fetchFailedJobsMetadataAction.workflowId.toString))
+            val builderActor = context.actorOf(
+              metadataBuilderActorProps().withDispatcher(ApiDispatcher),
+              MetadataBuilderActor.uniqueActorName(fetchFailedJobsMetadataAction.workflowId.toString)
+            )
             builderRequests.put(builderActor, fetchFailedJobsMetadataAction)
             builderActor ! fetchFailedJobsMetadataAction
           }
@@ -39,7 +54,10 @@ class ReadMetadataRegulatorActor(metadataBuilderActorProps: PropsMaker, readMeta
           val currentRequesters = apiRequests.getOrElse(singleWorkflowAction, Set.empty)
           apiRequests.put(singleWorkflowAction, currentRequesters + sender())
           if (currentRequesters.isEmpty) {
-            val builderActor = context.actorOf(metadataBuilderActorProps().withDispatcher(ApiDispatcher), MetadataBuilderActor.uniqueActorName(singleWorkflowAction.workflowId.toString))
+            val builderActor = context.actorOf(
+              metadataBuilderActorProps().withDispatcher(ApiDispatcher),
+              MetadataBuilderActor.uniqueActorName(singleWorkflowAction.workflowId.toString)
+            )
             builderRequests.put(builderActor, singleWorkflowAction)
             builderActor ! singleWorkflowAction
           }
@@ -47,7 +65,9 @@ class ReadMetadataRegulatorActor(metadataBuilderActorProps: PropsMaker, readMeta
           val currentRequesters = apiRequests.getOrElse(crossWorkflowAction, Set.empty)
           apiRequests.put(crossWorkflowAction, currentRequesters + sender())
           if (currentRequesters.isEmpty) {
-            val readMetadataActor = context.actorOf(readMetadataWorkerProps.apply().withDispatcher(ApiDispatcher), s"MetadataQueryWorker-${UUID.randomUUID()}")
+            val readMetadataActor = context.actorOf(readMetadataWorkerProps.apply().withDispatcher(ApiDispatcher),
+                                                    s"MetadataQueryWorker-${UUID.randomUUID()}"
+            )
             builderRequests.put(readMetadataActor, crossWorkflowAction)
             readMetadataActor ! crossWorkflowAction
           }
@@ -55,14 +75,17 @@ class ReadMetadataRegulatorActor(metadataBuilderActorProps: PropsMaker, readMeta
     case streamRequest: GetMetadataStreamAction =>
       val currentRequesters = apiRequests.getOrElse(streamRequest, Set.empty)
       apiRequests.put(streamRequest, currentRequesters + sender())
-      if(currentRequesters.isEmpty) {
-        val readMetadataActor = context.actorOf(readMetadataWorkerProps.apply().withDispatcher(ApiDispatcher), s"MetadataQueryWorker-${UUID.randomUUID()}")
+      if (currentRequesters.isEmpty) {
+        val readMetadataActor = context.actorOf(readMetadataWorkerProps.apply().withDispatcher(ApiDispatcher),
+                                                s"MetadataQueryWorker-${UUID.randomUUID()}"
+        )
         builderRequests.put(readMetadataActor, streamRequest)
         readMetadataActor ! streamRequest
       }
     case serviceResponse: MetadataServiceResponse =>
       serviceResponse match {
-        case response @ (_: MetadataJsonResponse | _: MetadataQueryResponse | _: RootAndSubworkflowLabelsLookupResponse | _: MetadataLookupStreamSuccess) =>
+        case response @ (_: MetadataJsonResponse | _: MetadataQueryResponse |
+            _: RootAndSubworkflowLabelsLookupResponse | _: MetadataLookupStreamSuccess) =>
           handleResponseFromMetadataWorker(response)
       }
     case other => log.error(s"Programmer Error: Unexpected message $other received from ${sender()}")
@@ -75,16 +98,20 @@ class ReadMetadataRegulatorActor(metadataBuilderActorProps: PropsMaker, readMeta
         apiRequests.get(action) match {
           case Some(requesters) =>
             apiRequests.remove(action)
-            requesters foreach { _ ! response}
+            requesters foreach { _ ! response }
           case None =>
             // unpossible: there had to have been a request that corresponded to this response
-            log.error(s"Programmer Error: MetadataBuilderRegulatorActor has no registered requesters found for action: $action")
+            log.error(
+              s"Programmer Error: MetadataBuilderRegulatorActor has no registered requesters found for action: $action"
+            )
         }
         builderRequests.remove(sndr)
         ()
       case None =>
         // unpossible: this actor should know about all the child MetadataBuilderActors it has begotten
-        log.error(s"Programmer Error: MetadataBuilderRegulatorActor received a metadata response from an unrecognized sender $sndr")
+        log.error(
+          s"Programmer Error: MetadataBuilderRegulatorActor received a metadata response from an unrecognized sender $sndr"
+        )
     }
   }
 }
@@ -92,7 +119,6 @@ class ReadMetadataRegulatorActor(metadataBuilderActorProps: PropsMaker, readMeta
 object ReadMetadataRegulatorActor {
   type PropsMaker = () => Props
 
-  def props(singleWorkflowMetadataBuilderProps: PropsMaker, summarySearcherProps: PropsMaker): Props = {
+  def props(singleWorkflowMetadataBuilderProps: PropsMaker, summarySearcherProps: PropsMaker): Props =
     Props(new ReadMetadataRegulatorActor(singleWorkflowMetadataBuilderProps, summarySearcherProps))
-  }
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/WriteMetadataActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/WriteMetadataActor.scala
index 46af4a28ee7..16bf344ac6f 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/WriteMetadataActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/WriteMetadataActor.scala
@@ -14,13 +14,12 @@ import cromwell.services.{EnhancedBatchActor, MetadataServicesStore}
 import scala.concurrent.duration._
 import scala.util.{Failure, Success}
 
-
 class WriteMetadataActor(override val batchSize: Int,
                          override val flushRate: FiniteDuration,
                          override val serviceRegistryActor: ActorRef,
                          override val threshold: Int,
-                         metadataStatisticsRecorderSettings: MetadataStatisticsRecorderSettings)
-  extends EnhancedBatchActor[MetadataWriteAction](flushRate, batchSize)
+                         metadataStatisticsRecorderSettings: MetadataStatisticsRecorderSettings
+) extends EnhancedBatchActor[MetadataWriteAction](flushRate, batchSize)
     with ActorLogging
     with MetadataDatabaseAccess
     with MetadataServicesStore {
@@ -30,22 +29,23 @@ class WriteMetadataActor(override val batchSize: Int,
   override def process(e: NonEmptyVector[MetadataWriteAction]) = instrumentedProcess {
     val empty = (Vector.empty[MetadataEvent], List.empty[(Iterable[MetadataEvent], ActorRef)])
 
-    val (putWithoutResponse, putWithResponse) = e.foldLeft(empty)({
+    val (putWithoutResponse, putWithResponse) = e.foldLeft(empty) {
       case ((putEvents, putAndRespondEvents), action: PutMetadataAction) =>
         (putEvents ++ action.events, putAndRespondEvents)
       case ((putEvents, putAndRespondEvents), action: PutMetadataActionAndRespond) =>
         (putEvents, putAndRespondEvents :+ (action.events -> action.replyTo))
-    })
+    }
     val allPutEvents: Iterable[MetadataEvent] = putWithoutResponse ++ putWithResponse.flatMap(_._1)
     val dbAction = addMetadataEvents(allPutEvents)
 
-    statsRecorder.processEventsAndGenerateAlerts(allPutEvents) foreach(a => log.warning(s"${a.workflowId} has logged a heavy amount of metadata (${a.count} rows)"))
+    statsRecorder.processEventsAndGenerateAlerts(allPutEvents) foreach (a =>
+      log.warning(s"${a.workflowId} has logged a heavy amount of metadata (${a.count} rows)")
+    )
 
     dbAction onComplete {
       case Success(_) =>
         putWithResponse foreach { case (ev, replyTo) => replyTo ! MetadataWriteSuccess(ev) }
       case Failure(cause) =>
-
         val (outOfTries, stillGood) = e.toVector.partition(_.maxAttempts <= 1)
 
         handleOutOfTries(outOfTries, cause)
@@ -61,8 +61,15 @@ class WriteMetadataActor(override val batchSize: Int,
   private def enumerateWorkflowWriteFailures(writeActions: Vector[MetadataWriteAction]): String =
     countActionsByWorkflow(writeActions).map { case (wfid, size) => s"$wfid: $size" }.mkString(", ")
 
-  private def handleOutOfTries(writeActions: Vector[MetadataWriteAction], reason: Throwable): Unit = if (writeActions.nonEmpty) {
-    log.error(reason, "Metadata event writes have failed irretrievably for the following workflows. They will be lost: " + enumerateWorkflowWriteFailures(writeActions))
+  private def handleOutOfTries(writeActions: Vector[MetadataWriteAction], reason: Throwable): Unit = if (
+    writeActions.nonEmpty
+  ) {
+    log.error(
+      reason,
+      "Metadata event writes have failed irretrievably for the following workflows. They will be lost: " + enumerateWorkflowWriteFailures(
+        writeActions
+      )
+    )
 
     writeActions foreach {
       case PutMetadataActionAndRespond(ev, replyTo, _) => replyTo ! MetadataWriteFailure(reason, ev)
@@ -71,7 +78,11 @@ class WriteMetadataActor(override val batchSize: Int,
   }
 
   private def handleEventsToReconsider(writeActions: Vector[MetadataWriteAction]): Unit = if (writeActions.nonEmpty) {
-    log.warning("Metadata event writes have failed for the following workflows. They will be retried: " + enumerateWorkflowWriteFailures(writeActions))
+    log.warning(
+      "Metadata event writes have failed for the following workflows. They will be retried: " + enumerateWorkflowWriteFailures(
+        writeActions
+      )
+    )
 
     writeActions foreach {
       case action: PutMetadataAction => self ! action.copy(maxAttempts = action.maxAttempts - 1)
@@ -84,8 +95,8 @@ class WriteMetadataActor(override val batchSize: Int,
   override protected def weightFunction(command: MetadataWriteAction) = command.size
   override protected def instrumentationPath = MetadataServiceActor.MetadataInstrumentationPrefix
   override protected def instrumentationPrefix = InstrumentationPrefixes.ServicesPrefix
-  def commandToData(snd: ActorRef): PartialFunction[Any, MetadataWriteAction] = {
-    case command: MetadataWriteAction => command
+  def commandToData(snd: ActorRef): PartialFunction[Any, MetadataWriteAction] = { case command: MetadataWriteAction =>
+    command
   }
 }
 
@@ -95,7 +106,8 @@ object WriteMetadataActor {
             flushRate: FiniteDuration,
             serviceRegistryActor: ActorRef,
             threshold: Int,
-            statisticsRecorderSettings: MetadataStatisticsRecorderSettings): Props =
+            statisticsRecorderSettings: MetadataStatisticsRecorderSettings
+  ): Props =
     Props(new WriteMetadataActor(dbBatchSize, flushRate, serviceRegistryActor, threshold, statisticsRecorderSettings))
       .withDispatcher(ServiceDispatcher)
       .withMailbox(PriorityMailbox)
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataConfig.scala b/services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataConfig.scala
index 25390d94c39..f719116e60e 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataConfig.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataConfig.scala
@@ -21,8 +21,8 @@ final case class ArchiveMetadataConfig(pathBuilders: PathBuilders,
                                        archiveDelay: FiniteDuration,
                                        instrumentationInterval: FiniteDuration,
                                        debugLogging: Boolean,
-                                       batchSize: Long) {
-}
+                                       batchSize: Long
+) {}
 
 object ArchiveMetadataConfig {
   def parseConfig(archiveMetadataConfig: Config)(implicit system: ActorSystem): Checked[ArchiveMetadataConfig] = {
@@ -33,16 +33,34 @@ object ArchiveMetadataConfig {
     val defaultBatchSize: Long = 1
 
     for {
-      _ <- Try(archiveMetadataConfig.getConfig("filesystems.gcs")).toCheckedWithContext("parse archiver 'filesystems.gcs' field from config")
+      _ <- Try(archiveMetadataConfig.getConfig("filesystems.gcs"))
+        .toCheckedWithContext("parse archiver 'filesystems.gcs' field from config")
       pathBuilderFactories <- CromwellFileSystems.instance.factoriesFromConfig(archiveMetadataConfig)
-      pathBuilders <- Try(Await.result(PathBuilderFactory.instantiatePathBuilders(pathBuilderFactories.values.toList, WorkflowOptions.empty), 60.seconds))
+      pathBuilders <- Try(
+        Await.result(
+          PathBuilderFactory.instantiatePathBuilders(pathBuilderFactories.values.toList, WorkflowOptions.empty),
+          60.seconds
+        )
+      )
         .toCheckedWithContext("construct archiver path builders from factories")
-      bucket <- Try(archiveMetadataConfig.getString("bucket")).toCheckedWithContext("parse Carboniter 'bucket' field from config")
-      backoffInterval <- Try(archiveMetadataConfig.getOrElse[FiniteDuration]("backoff-interval", defaultMaxInterval)).toChecked
+      bucket <- Try(archiveMetadataConfig.getString("bucket"))
+        .toCheckedWithContext("parse Carboniter 'bucket' field from config")
+      backoffInterval <- Try(
+        archiveMetadataConfig.getOrElse[FiniteDuration]("backoff-interval", defaultMaxInterval)
+      ).toChecked
       archiveDelay <- Try(archiveMetadataConfig.getOrElse("archive-delay", defaultArchiveDelay)).toChecked
-      instrumentationInterval <- Try(archiveMetadataConfig.getOrElse("instrumentation-interval", defaultInstrumentationInterval)).toChecked
+      instrumentationInterval <- Try(
+        archiveMetadataConfig.getOrElse("instrumentation-interval", defaultInstrumentationInterval)
+      ).toChecked
       debugLogging <- Try(archiveMetadataConfig.getOrElse("debug-logging", defaultDebugLogging)).toChecked
       batchSize <- Try(archiveMetadataConfig.getOrElse("batch-size", defaultBatchSize)).toChecked
-    } yield ArchiveMetadataConfig(pathBuilders, bucket, backoffInterval, archiveDelay, instrumentationInterval, debugLogging, batchSize)
+    } yield ArchiveMetadataConfig(pathBuilders,
+                                  bucket,
+                                  backoffInterval,
+                                  archiveDelay,
+                                  instrumentationInterval,
+                                  debugLogging,
+                                  batchSize
+    )
   }
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataSchedulerActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataSchedulerActor.scala
index 1f5ac1f4460..1908a46438c 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataSchedulerActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/archiver/ArchiveMetadataSchedulerActor.scala
@@ -21,7 +21,11 @@ import cromwell.database.sql.SqlConverters.{ClobOptionToRawString, TimestampToSy
 import cromwell.database.sql.tables.{MetadataEntry, WorkflowMetadataSummaryEntry}
 import cromwell.services.instrumentation.CromwellInstrumentation
 import cromwell.services.metadata.MetadataArchiveStatus.Archived
-import cromwell.services.metadata.MetadataService.{GetMetadataStreamAction, MetadataLookupStreamFailed, MetadataLookupStreamSuccess}
+import cromwell.services.metadata.MetadataService.{
+  GetMetadataStreamAction,
+  MetadataLookupStreamFailed,
+  MetadataLookupStreamSuccess
+}
 import cromwell.services.metadata.impl.archiver.ArchiveMetadataSchedulerActor._
 import cromwell.services.metadata.impl.{MetadataDatabaseAccess, MetadataServiceActor}
 import cromwell.services.{IoActorRequester, MetadataServicesStore}
@@ -35,10 +39,9 @@ import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success, Try}
 
-
 class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig,
-                                    override val serviceRegistryActor: ActorRef)
-  extends Actor
+                                    override val serviceRegistryActor: ActorRef
+) extends Actor
     with ActorLogging
     with GracefulShutdownHelper
     with MetadataDatabaseAccess
@@ -48,25 +51,31 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
 
   implicit val ec: ExecutionContext = context.dispatcher
   implicit val askTimeout: Timeout = new Timeout(60.seconds)
-  lazy val futureAsyncIo: Future[AsyncIo] = requestIoActor() map { ioActor => {
+  lazy val futureAsyncIo: Future[AsyncIo] = requestIoActor() map { ioActor =>
     log.info(s"IoActor reference received by ${self.path.name}")
     new AsyncIo(ioActor, DefaultIoCommandBuilder)
-  } }
+  }
 
-  private val archiverMetricsBasePath: NonEmptyList[String] = MetadataServiceActor.MetadataInstrumentationPrefix :+ "archiver"
+  private val archiverMetricsBasePath: NonEmptyList[String] =
+    MetadataServiceActor.MetadataInstrumentationPrefix :+ "archiver"
   private val rowsProcessedMetricPath: NonEmptyList[String] = archiverMetricsBasePath :+ "rows_processed"
   private val rowsPerWorkflowMetricPath: NonEmptyList[String] = archiverMetricsBasePath :+ "rows_per_workflow"
   private val bytesProcessedMetricPath: NonEmptyList[String] = archiverMetricsBasePath :+ "bytes_processed"
   private val bytesPerWorkflowMetricPath: NonEmptyList[String] = archiverMetricsBasePath :+ "bytes_per_workflow"
-  private val workflowsProcessedSuccessMetricPath: NonEmptyList[String] = archiverMetricsBasePath :+ "workflows_processed" :+ "success"
-  private val workflowsProcessedFailureMetricPath: NonEmptyList[String] = archiverMetricsBasePath :+ "workflows_processed" :+ "failure"
-  private val timeBehindExpectedDelayMetricPath: NonEmptyList[String] = archiverMetricsBasePath :+ "time_behind_expected_delay"
-  private val workflowArchiveTotalTimeMetricPath: NonEmptyList[String] = archiverMetricsBasePath :+ "workflow_archive_total_time"
+  private val workflowsProcessedSuccessMetricPath: NonEmptyList[String] =
+    archiverMetricsBasePath :+ "workflows_processed" :+ "success"
+  private val workflowsProcessedFailureMetricPath: NonEmptyList[String] =
+    archiverMetricsBasePath :+ "workflows_processed" :+ "failure"
+  private val timeBehindExpectedDelayMetricPath: NonEmptyList[String] =
+    archiverMetricsBasePath :+ "time_behind_expected_delay"
+  private val workflowArchiveTotalTimeMetricPath: NonEmptyList[String] =
+    archiverMetricsBasePath :+ "workflow_archive_total_time"
   private val workflowsToArchiveMetricPath: NonEmptyList[String] = archiverMetricsBasePath :+ "workflows_to_archive"
   private val archiverTimingMetricsBasePath: NonEmptyList[String] = archiverMetricsBasePath :+ "timings"
   private val archiverStreamTimingMetricsBasePath: NonEmptyList[String] = archiverTimingMetricsBasePath :+ "streaming"
 
-  private val TerminalWorkflowStatuses: List[String] = List(WorkflowSucceeded, WorkflowAborted, WorkflowFailed).map(_.toString)
+  private val TerminalWorkflowStatuses: List[String] =
+    List(WorkflowSucceeded, WorkflowAborted, WorkflowFailed).map(_.toString)
 
   // kick off archiving immediately
   self ! ArchiveNextWorkflowMessage
@@ -80,7 +89,7 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
 
       // These handlers send metrics for most paths even when they're not incremented, so that the metrics
       // paths are actively receiving data points throughout:
-      archiveNextWorkflows.onComplete({
+      archiveNextWorkflows.onComplete {
         case Success(cnt) =>
           count(workflowsProcessedSuccessMetricPath, cnt, ServicesPrefix)
           count(workflowsProcessedFailureMetricPath, 0L, ServicesPrefix)
@@ -92,7 +101,10 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
             count(rowsProcessedMetricPath, 0L, ServicesPrefix)
             sendGauge(workflowsToArchiveMetricPath, 0L, ServicesPrefix)
             sendTiming(workflowArchiveTotalTimeMetricPath, calculateTimeSince(startTime), ServicesPrefix)
-            if (archiveMetadataConfig.debugLogging) log.info(s"No complete workflows which finished over ${archiveMetadataConfig.archiveDelay} ago remain to be archived. Scheduling next poll in ${archiveMetadataConfig.backoffInterval}.")
+            if (archiveMetadataConfig.debugLogging)
+              log.info(
+                s"No complete workflows which finished over ${archiveMetadataConfig.archiveDelay} ago remain to be archived. Scheduling next poll in ${archiveMetadataConfig.backoffInterval}."
+              )
             scheduleNextWorkflowToArchive()
           }
         case Failure(error) =>
@@ -102,9 +114,12 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
           sendTiming(workflowArchiveTotalTimeMetricPath, calculateTimeSince(startTime), ServicesPrefix)
           log.error(error, s"Error while archiving, will retry.")
           scheduleNextWorkflowToArchive()
-      })
-    case ShutdownCommand => context.stop(self)  // TODO: cancel any streaming that might be happening?
-    case other => log.info(s"Programmer Error! The ArchiveMetadataSchedulerActor received unexpected message! (${sender()} sent ${other.toPrettyElidedString(1000)}})")
+      }
+    case ShutdownCommand => context.stop(self) // TODO: cancel any streaming that might be happening?
+    case other =>
+      log.info(
+        s"Programmer Error! The ArchiveMetadataSchedulerActor received unexpected message! (${sender()} sent ${other.toPrettyElidedString(1000)}})"
+      )
   }
 
   def workflowsLeftToArchiveMetric(): Unit = {
@@ -112,17 +127,24 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
     countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(
       TerminalWorkflowStatuses,
       currentTimestampMinusDelay
-    ).onComplete({
+    ).onComplete {
       case Success(workflowsToArchive) =>
         sendGauge(workflowsToArchiveMetricPath, workflowsToArchive.longValue(), ServicesPrefix)
         // schedule next workflows left to archive query after interval
-        context.system.scheduler.scheduleOnce(archiveMetadataConfig.instrumentationInterval)(workflowsLeftToArchiveMetric())
+        context.system.scheduler.scheduleOnce(archiveMetadataConfig.instrumentationInterval)(
+          workflowsLeftToArchiveMetric()
+        )
       case Failure(exception) =>
-        log.error(exception, s"Something went wrong while fetching number of workflows left to archive. " +
-          s"Scheduling next poll in ${archiveMetadataConfig.instrumentationInterval}.")
+        log.error(
+          exception,
+          s"Something went wrong while fetching number of workflows left to archive. " +
+            s"Scheduling next poll in ${archiveMetadataConfig.instrumentationInterval}."
+        )
         // schedule next workflows left to archive query after interval
-        context.system.scheduler.scheduleOnce(archiveMetadataConfig.instrumentationInterval)(workflowsLeftToArchiveMetric())
-    })
+        context.system.scheduler.scheduleOnce(archiveMetadataConfig.instrumentationInterval)(
+          workflowsLeftToArchiveMetric()
+        )
+    }
   }
 
   def archiveNextWorkflows: Future[Long] = {
@@ -131,14 +153,21 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
     for {
       workflowSummaryEntries <- lookupNextWorkflowsToArchive(archiveMetadataConfig.batchSize)
       batchLookupEndTime = OffsetDateTime.now()
-      _ = sendTiming(archiverTimingMetricsBasePath :+ "lookup_next_workflows", calculateTimeDifference(batchLookupStartTime, batchLookupEndTime), ServicesPrefix)
-      _ = if (archiveMetadataConfig.debugLogging) log.info(s"About to archive batch of ${workflowSummaryEntries.size} workflows.")
+      _ = sendTiming(archiverTimingMetricsBasePath :+ "lookup_next_workflows",
+                     calculateTimeDifference(batchLookupStartTime, batchLookupEndTime),
+                     ServicesPrefix
+      )
+      _ = if (archiveMetadataConfig.debugLogging)
+        log.info(s"About to archive batch of ${workflowSummaryEntries.size} workflows.")
       result <- archiveSummaryEntries(workflowSummaryEntries)
-      _ = sendTiming(archiverTimingMetricsBasePath :+ "batch_lookup_and_archive_time", calculateTimeDifference(batchLookupStartTime, OffsetDateTime.now()), ServicesPrefix)
+      _ = sendTiming(archiverTimingMetricsBasePath :+ "batch_lookup_and_archive_time",
+                     calculateTimeDifference(batchLookupStartTime, OffsetDateTime.now()),
+                     ServicesPrefix
+      )
     } yield result
   }
 
-  private def archiveSummaryEntries(entries: Seq[WorkflowMetadataSummaryEntry]): Future[Long] = {
+  private def archiveSummaryEntries(entries: Seq[WorkflowMetadataSummaryEntry]): Future[Long] =
     if (entries.isEmpty) {
       sendGauge(timeBehindExpectedDelayMetricPath, 0L, ServicesPrefix)
       Future.successful(0L)
@@ -148,11 +177,16 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
 
       result.map(_.sum)
     }
-  }
 
   private def archiveSummaryEntry(entry: WorkflowMetadataSummaryEntry): Future[Long] = {
     entry.endTimestamp.foreach { workflowEndTime =>
-      sendGauge(timeBehindExpectedDelayMetricPath, calculateTimeSince(workflowEndTime.toSystemOffsetDateTime).toMillis - archiveMetadataConfig.archiveDelay.toMillis, ServicesPrefix)
+      sendGauge(
+        timeBehindExpectedDelayMetricPath,
+        calculateTimeSince(
+          workflowEndTime.toSystemOffsetDateTime
+        ).toMillis - archiveMetadataConfig.archiveDelay.toMillis,
+        ServicesPrefix
+      )
     }
 
     val archiveStartTime = OffsetDateTime.now()
@@ -163,14 +197,26 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
       dbStream <- fetchStreamFromDatabase(WorkflowId(UUID.fromString(workflowId)))
       _ = log.info(s"Archiving metadata for $workflowId to ${path.pathAsString}")
       readyToStreamTime = OffsetDateTime.now()
-      _ = sendTiming(archiverTimingMetricsBasePath :+ "prepare_to_stream", calculateTimeDifference(archiveStartTime, readyToStreamTime), ServicesPrefix)
+      _ = sendTiming(archiverTimingMetricsBasePath :+ "prepare_to_stream",
+                     calculateTimeDifference(archiveStartTime, readyToStreamTime),
+                     ServicesPrefix
+      )
       _ <- streamMetadataToGcs(path, dbStream)
       streamCompleteTime = OffsetDateTime.now()
-      _ = sendTiming(archiverTimingMetricsBasePath :+ "stream_to_gcs", calculateTimeDifference(readyToStreamTime, streamCompleteTime), ServicesPrefix)
+      _ = sendTiming(archiverTimingMetricsBasePath :+ "stream_to_gcs",
+                     calculateTimeDifference(readyToStreamTime, streamCompleteTime),
+                     ServicesPrefix
+      )
       _ <- updateMetadataArchiveStatus(WorkflowId(UUID.fromString(workflowId)), Archived)
       statusUpdatedTime = OffsetDateTime.now()
-      _ = sendTiming(archiverTimingMetricsBasePath :+ "archive_status_update", calculateTimeDifference(streamCompleteTime, statusUpdatedTime), ServicesPrefix)
-      _ = sendTiming(workflowArchiveTotalTimeMetricPath, calculateTimeDifference(archiveStartTime, statusUpdatedTime), ServicesPrefix)
+      _ = sendTiming(archiverTimingMetricsBasePath :+ "archive_status_update",
+                     calculateTimeDifference(streamCompleteTime, statusUpdatedTime),
+                     ServicesPrefix
+      )
+      _ = sendTiming(workflowArchiveTotalTimeMetricPath,
+                     calculateTimeDifference(archiveStartTime, statusUpdatedTime),
+                     ServicesPrefix
+      )
       _ = log.info(s"Archiving succeeded for $workflowId")
     } yield 1L
   }
@@ -184,14 +230,14 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
     )
   }
 
-  private def getGcsPathForMetadata(summaryEntry: WorkflowMetadataSummaryEntry): Try[Path] =  {
+  private def getGcsPathForMetadata(summaryEntry: WorkflowMetadataSummaryEntry): Try[Path] = {
     /*
       Note: The naming convention for archived workflows is:
         - if a workflow has no root workflow, its archived metadata is put in GCS at <workflow_id>/<workflow_id>.csv
         - if a workflow is a subworkflow, its archived metadata is put in GCS under it's root workflow's directory i.e.
           <root_workflow_id>/<subworkflow_id>.csv
       Changing this convention would break the expectations of where to find the archived metadata files.
-   */
+     */
     val bucket = archiveMetadataConfig.bucket
     val workflowId = summaryEntry.workflowExecutionUuid
     val rootWorkflowId = summaryEntry.rootWorkflowExecutionUuid.getOrElse(workflowId)
@@ -200,39 +246,53 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
     }
   }
 
-  def fetchStreamFromDatabase(workflowId: WorkflowId): Future[DatabasePublisher[MetadataEntry]] = {
+  def fetchStreamFromDatabase(workflowId: WorkflowId): Future[DatabasePublisher[MetadataEntry]] =
     (serviceRegistryActor ? GetMetadataStreamAction(workflowId)) flatMap {
       case MetadataLookupStreamSuccess(_, responseStream) => Future.successful(responseStream)
-      case MetadataLookupStreamFailed(_, reason) => Future.failed(new Exception(s"Failed to get metadata stream", reason))
+      case MetadataLookupStreamFailed(_, reason) =>
+        Future.failed(new Exception(s"Failed to get metadata stream", reason))
       case other => Future.failed(new Exception(s"Failed to get metadata stream: ${other.toPrettyElidedString(1000)}"))
     }
-  }
 
   def streamMetadataToGcs(path: Path, stream: DatabasePublisher[MetadataEntry]): Future[Unit] = {
     val streamStartTime = OffsetDateTime.now()
 
-    val rowsCounter = new CounterAndProgressiveLogger( logFunction = (newRows, totalRows) => {
-      if (archiveMetadataConfig.debugLogging) logger.info(s"Uploaded $newRows new rows to ${path.pathAsString}. Total uploaded is now ${totalRows}") else ()
-      count(rowsProcessedMetricPath, newRows, ServicesPrefix)
-    }, 100000)
+    val rowsCounter = new CounterAndProgressiveLogger(
+      logFunction = (newRows, totalRows) => {
+        if (archiveMetadataConfig.debugLogging)
+          logger.info(s"Uploaded $newRows new rows to ${path.pathAsString}. Total uploaded is now ${totalRows}")
+        else ()
+        count(rowsProcessedMetricPath, newRows, ServicesPrefix)
+      },
+      100000
+    )
 
     for {
       asyncIo <- futureAsyncIo
       gotAsyncIoTime = OffsetDateTime.now()
-      _ = sendTiming(archiverStreamTimingMetricsBasePath :+ "get_async_io", calculateTimeDifference(streamStartTime, gotAsyncIoTime), ServicesPrefix)
+      _ = sendTiming(archiverStreamTimingMetricsBasePath :+ "get_async_io",
+                     calculateTimeDifference(streamStartTime, gotAsyncIoTime),
+                     ServicesPrefix
+      )
       gcsStream = Files.newOutputStream(path.nioPath, StandardOpenOption.CREATE)
       gcsStreamCreatedTime = OffsetDateTime.now()
-      _ = sendTiming(archiverStreamTimingMetricsBasePath :+ "create_gcs_stream", calculateTimeDifference(gotAsyncIoTime, gcsStreamCreatedTime), ServicesPrefix)
+      _ = sendTiming(archiverStreamTimingMetricsBasePath :+ "create_gcs_stream",
+                     calculateTimeDifference(gotAsyncIoTime, gcsStreamCreatedTime),
+                     ServicesPrefix
+      )
       crc32cStream = new Crc32cStream()
       teeStream = new TeeingOutputStream(gcsStream, crc32cStream, new ByteCountingOutputStream())
       csvPrinter =
         new CSVPrinter(
           new OutputStreamWriter(teeStream),
-          CSVFormat.DEFAULT.builder().setHeader(CsvFileHeaders : _*).build(),
+          CSVFormat.DEFAULT.builder().setHeader(CsvFileHeaders: _*).build()
         )
       csvPrinterCreatedTime = OffsetDateTime.now()
-      _ = sendTiming(archiverStreamTimingMetricsBasePath :+ "create_csv_printer", calculateTimeDifference(gcsStreamCreatedTime, csvPrinterCreatedTime), ServicesPrefix)
-      _ <- stream.foreach(me => {
+      _ = sendTiming(archiverStreamTimingMetricsBasePath :+ "create_csv_printer",
+                     calculateTimeDifference(gcsStreamCreatedTime, csvPrinterCreatedTime),
+                     ServicesPrefix
+      )
+      _ <- stream.foreach { me =>
         csvPrinter.printRecord(
           me.metadataEntryId.map(_.toString).getOrElse(""),
           me.workflowExecutionUuid,
@@ -245,17 +305,30 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
           me.metadataValueType.getOrElse("")
         )
         rowsCounter.increment()
-      })
+      }
       _ = rowsCounter.manualLog()
       _ = sendGauge(rowsPerWorkflowMetricPath, rowsCounter.getTotalCount, ServicesPrefix)
       _ = csvPrinter.close()
       streamingCompleteTime = OffsetDateTime.now()
-      _ = sendTiming(archiverStreamTimingMetricsBasePath :+ "stream_data_to_gcs", calculateTimeDifference(csvPrinterCreatedTime, streamingCompleteTime), ServicesPrefix)
+      _ = sendTiming(archiverStreamTimingMetricsBasePath :+ "stream_data_to_gcs",
+                     calculateTimeDifference(csvPrinterCreatedTime, streamingCompleteTime),
+                     ServicesPrefix
+      )
       expectedChecksum = crc32cStream.checksumString
       uploadedChecksum <- asyncIo.hashAsync(path)
       checksumValidatedTime = OffsetDateTime.now()
-      _ = sendTiming(archiverStreamTimingMetricsBasePath :+ "checksum_validation", calculateTimeDifference(streamingCompleteTime, checksumValidatedTime), ServicesPrefix)
-      _ <- if (uploadedChecksum == expectedChecksum) Future.successful(()) else Future.failed(new Exception(s"Uploaded checksum '$uploadedChecksum' did not match local calculation ('$expectedChecksum')"))
+      _ = sendTiming(archiverStreamTimingMetricsBasePath :+ "checksum_validation",
+                     calculateTimeDifference(streamingCompleteTime, checksumValidatedTime),
+                     ServicesPrefix
+      )
+      _ <-
+        if (uploadedChecksum == expectedChecksum) Future.successful(())
+        else
+          Future.failed(
+            new Exception(
+              s"Uploaded checksum '$uploadedChecksum' did not match local calculation ('$expectedChecksum')"
+            )
+          )
     } yield ()
   }
 
@@ -265,10 +338,15 @@ class ArchiveMetadataSchedulerActor(archiveMetadataConfig: ArchiveMetadataConfig
   }
 
   final class ByteCountingOutputStream() extends OutputStream {
-    val byteCounter = new CounterAndProgressiveLogger( logFunction = (newBytes, totalBytes) => {
-      if (archiveMetadataConfig.debugLogging) logger.info(s"Uploaded $newBytes new bytes. Total uploaded is now $totalBytes") else ()
-      count(bytesProcessedMetricPath, newBytes, ServicesPrefix)
-    }, 100000)
+    val byteCounter = new CounterAndProgressiveLogger(
+      logFunction = (newBytes, totalBytes) => {
+        if (archiveMetadataConfig.debugLogging)
+          logger.info(s"Uploaded $newBytes new bytes. Total uploaded is now $totalBytes")
+        else ()
+        count(bytesProcessedMetricPath, newBytes, ServicesPrefix)
+      },
+      100000
+    )
 
     override def write(b: Int): Unit = byteCounter.increment()
     override def close(): Unit = {
@@ -298,9 +376,9 @@ object ArchiveMetadataSchedulerActor {
     Props(new ArchiveMetadataSchedulerActor(archiveMetadataConfig, serviceRegistryActor))
 
   final class TeeingOutputStream(streams: OutputStream*) extends OutputStream {
-    override def write(b: Int): Unit = { streams.foreach(_.write(b)) }
-    override def close(): Unit = { streams.foreach(_.close())}
-    override def flush(): Unit = { streams.foreach(_.flush())}
+    override def write(b: Int): Unit = streams.foreach(_.write(b))
+    override def close(): Unit = streams.foreach(_.close())
+    override def flush(): Unit = streams.foreach(_.flush())
   }
 
   final class Crc32cStream() extends OutputStream {
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala
index 05e494680a3..1f48bc8d12c 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataBuilderActor.scala
@@ -18,7 +18,6 @@ import spray.json._
 
 import scala.language.postfixOps
 
-
 object MetadataBuilderActor {
   sealed trait MetadataBuilderActorState
   case object Idle extends MetadataBuilderActorState
@@ -28,24 +27,26 @@ object MetadataBuilderActor {
   sealed trait MetadataBuilderActorData
 
   case object IdleData extends MetadataBuilderActorData
-  final case class HasWorkData(target: ActorRef,
-                               originalRequest: BuildMetadataJsonAction) extends MetadataBuilderActorData
+  final case class HasWorkData(target: ActorRef, originalRequest: BuildMetadataJsonAction)
+      extends MetadataBuilderActorData
   final case class HasReceivedEventsData(target: ActorRef,
                                          originalRequest: BuildMetadataJsonAction,
                                          originalQuery: MetadataQuery,
                                          originalEvents: Seq[MetadataEvent],
                                          subWorkflowsMetadata: Map[String, JsValue],
-                                         waitFor: Int) extends MetadataBuilderActorData {
-    def withSubWorkflow(id: String, metadata: JsValue) = {
+                                         waitFor: Int
+  ) extends MetadataBuilderActorData {
+    def withSubWorkflow(id: String, metadata: JsValue) =
       this.copy(subWorkflowsMetadata = subWorkflowsMetadata + ((id, metadata)))
-    }
 
     def isComplete = subWorkflowsMetadata.size == waitFor
   }
 
-  def props(readMetadataWorkerMaker: () => Props, metadataReadRowNumberSafetyThreshold: Int, isForSubworkflows: Boolean = false) = {
+  def props(readMetadataWorkerMaker: () => Props,
+            metadataReadRowNumberSafetyThreshold: Int,
+            isForSubworkflows: Boolean = false
+  ) =
     Props(new MetadataBuilderActor(readMetadataWorkerMaker, metadataReadRowNumberSafetyThreshold, isForSubworkflows))
-  }
 
   val log = LoggerFactory.getLogger("MetadataBuilder")
 
@@ -62,18 +63,27 @@ object MetadataBuilderActor {
     */
   private case class MetadataForIndex(index: Int, metadata: List[JsObject])
 
-  private def eventsToAttemptMetadata(subWorkflowMetadata: Map[String, JsValue])(attempt: Int, events: Seq[MetadataEvent]) = {
-    val withAttemptField = JsObject(MetadataComponent(events, subWorkflowMetadata).toJson.asJsObject.fields + (AttemptKey -> JsNumber(attempt)))
+  private def eventsToAttemptMetadata(
+    subWorkflowMetadata: Map[String, JsValue]
+  )(attempt: Int, events: Seq[MetadataEvent]) = {
+    val withAttemptField = JsObject(
+      MetadataComponent(events, subWorkflowMetadata).toJson.asJsObject.fields + (AttemptKey -> JsNumber(attempt))
+    )
     MetadataForAttempt(attempt, withAttemptField)
   }
 
   private def attemptMetadataToIndexMetadata(index: ExecutionIndex, attemptMetadata: Iterable[MetadataForAttempt]) = {
     def addIndexProperty(value: JsObject) = JsObject(value.fields + (ShardKey -> JsNumber(index.getOrElse(-1))))
-    val metadata = attemptMetadata.toList.sortBy(_.attempt) map { mdForAttempt => addIndexProperty(mdForAttempt.metadata) }
+    val metadata = attemptMetadata.toList.sortBy(_.attempt) map { mdForAttempt =>
+      addIndexProperty(mdForAttempt.metadata)
+    }
     MetadataForIndex(index.getOrElse(-1), metadata)
   }
 
-  private def buildMetadataJson(events: Seq[MetadataEvent], includeCallsIfEmpty: Boolean, expandedValues: Map[String, JsValue]): JsObject = {
+  private def buildMetadataJson(events: Seq[MetadataEvent],
+                                includeCallsIfEmpty: Boolean,
+                                expandedValues: Map[String, JsValue]
+  ): JsObject = {
     // Partition events into workflow level and call level events
     val (workflowLevel, callLevel) = events partition { _.key.jobKey.isEmpty }
     val workflowLevelJson = MetadataComponent(workflowLevel, Map.empty).toJson.asJsObject
@@ -112,12 +122,16 @@ object MetadataBuilderActor {
      *    ...
      * )
      */
-    val callsGroupedByFQNAndIndexAndAttempt = callsGroupedByFQNAndIndex safeMapValues { _ safeMapValues { _ groupBy { _.key.jobKey.get.attempt } } }
+    val callsGroupedByFQNAndIndexAndAttempt = callsGroupedByFQNAndIndex safeMapValues {
+      _ safeMapValues { _ groupBy { _.key.jobKey.get.attempt } }
+    }
 
     val eventsToAttemptFunction = Function.tupled(eventsToAttemptMetadata(expandedValues) _)
     val attemptToIndexFunction = (attemptMetadataToIndexMetadata _).tupled
 
-    val callsMap = callsGroupedByFQNAndIndexAndAttempt safeMapValues { _ safeMapValues { _ map eventsToAttemptFunction } map attemptToIndexFunction } safeMapValues { md =>
+    val callsMap = callsGroupedByFQNAndIndexAndAttempt safeMapValues {
+      _ safeMapValues { _ map eventsToAttemptFunction } map attemptToIndexFunction
+    } safeMapValues { md =>
       JsArray(md.toVector.sortBy(_.index) flatMap { _.metadata })
     }
 
@@ -126,24 +140,31 @@ object MetadataBuilderActor {
     JsObject(workflowLevelJson.fields ++ callData)
   }
 
-  private def parseWorkflowEvents(includeCallsIfEmpty: Boolean, expandedValues: Map[String, JsValue])(events: Seq[MetadataEvent]): JsObject = {
+  private def parseWorkflowEvents(includeCallsIfEmpty: Boolean, expandedValues: Map[String, JsValue])(
+    events: Seq[MetadataEvent]
+  ): JsObject =
     buildMetadataJson(events, includeCallsIfEmpty, expandedValues)
-  }
 
   /**
     * Parse a Seq of MetadataEvent into a full Json metadata response.
     */
-  private def parse(events: Seq[MetadataEvent], expandedValues: Map[String, JsValue]): JsObject = {
-    JsObject(events.groupBy(_.key.workflowId.toString) safeMapValues parseWorkflowEvents(includeCallsIfEmpty = true, expandedValues))
-  }
+  private def parse(events: Seq[MetadataEvent], expandedValues: Map[String, JsValue]): JsObject =
+    JsObject(
+      events.groupBy(_.key.workflowId.toString) safeMapValues parseWorkflowEvents(includeCallsIfEmpty = true,
+                                                                                  expandedValues
+      )
+    )
 
   val actorIdIterator = new AtomicLong(0)
 
-  def uniqueActorName(workflowId: String): String = s"${getClass.getSimpleName}.${actorIdIterator.getAndIncrement()}-for-$workflowId"
+  def uniqueActorName(workflowId: String): String =
+    s"${getClass.getSimpleName}.${actorIdIterator.getAndIncrement()}-for-$workflowId"
 
   case class JobKeyAndGrouping(jobKey: MetadataJobKey, grouping: String)
 
-  def makeSyntheticGroupedExecutionEvents(jobKeyAndGrouping: JobKeyAndGrouping, events: List[MetadataEvent]): List[MetadataEvent] = {
+  def makeSyntheticGroupedExecutionEvents(jobKeyAndGrouping: JobKeyAndGrouping,
+                                          events: List[MetadataEvent]
+  ): List[MetadataEvent] = {
     // The input list of `events` might be incoherent since some events that were logically generated may not (yet) have been
     // recorded in the database. This code is written defensively to check for a start date in the event list. If there isn't one,
     // just return the original list of events because we can't sanely construct a synthetic event.
@@ -152,8 +173,12 @@ object MetadataBuilderActor {
     if (startTimeEvents.isEmpty) {
       events
     } else {
-      val oldestStartTimeKey = startTimeEvents.minBy(_.value collect { case MetadataValue(s, _) => OffsetDateTime.parse(s).toEpochSecond } get)
-      val newestStartTimeKey = startTimeEvents.maxBy(_.value collect { case MetadataValue(s, _) => OffsetDateTime.parse(s).toEpochSecond } get)
+      val oldestStartTimeKey = startTimeEvents.minBy(_.value collect { case MetadataValue(s, _) =>
+        OffsetDateTime.parse(s).toEpochSecond
+      } get)
+      val newestStartTimeKey = startTimeEvents.maxBy(_.value collect { case MetadataValue(s, _) =>
+        OffsetDateTime.parse(s).toEpochSecond
+      } get)
       // Search for an end date event corresponding to the newest start date event. Use the same prefix as on the
       // newestStartDateEvent to search for it.
       val executionEventPrefix = newestStartTimeKey.key.key.takeWhile(_ != ':')
@@ -167,7 +192,9 @@ object MetadataBuilderActor {
       // generated from these events uses a consistent subscript.
       List(
         oldestStartTimeKey.copy(key = syntheticStartTimeKey),
-        oldestStartTimeKey.copy(key = syntheticDescriptionKey, value = Option(MetadataValue(jobKeyAndGrouping.grouping, MetadataString)))
+        oldestStartTimeKey.copy(key = syntheticDescriptionKey,
+                                value = Option(MetadataValue(jobKeyAndGrouping.grouping, MetadataString))
+        )
       ) ++ endTimeEvent.toList
     }
   }
@@ -181,54 +208,69 @@ object MetadataBuilderActor {
     val executionEventKeyPatternRe = "[^]]+".r
     // Group execution events by their execution event keys.
     // The `get` inside the `groupBy` is safe because there must be a closing brace on the opening brace.
-    val executionEventsByKeys = executionEvents groupBy { e => (e.key.key.substring("executionEvents[".length) |> executionEventKeyPatternRe.findFirstIn).get }
+    val executionEventsByKeys = executionEvents groupBy { e =>
+      (e.key.key.substring("executionEvents[".length) |> executionEventKeyPatternRe.findFirstIn).get
+    }
     // "grouped" and "ungrouped" refer to the ":grouping" attribute that may be present in execution event metadata.
-    val (groupedExecutionEvents, ungroupedExecutionEvents) = executionEventsByKeys partition { case (k, es) => es.exists(_.key.key == s"executionEvents[$k]:grouping") }
+    val (groupedExecutionEvents, ungroupedExecutionEvents) = executionEventsByKeys partition { case (k, es) =>
+      es.exists(_.key.key == s"executionEvents[$k]:grouping")
+    }
 
     // (jobKey + grouping) => eeKey => executionEvents
     val groupedExecutionEventsByGrouping = groupedExecutionEvents groupBy {
       // The `get` on the `jobKey` is safe because execution events are all job-based. The outer `get` is safe because we already verified
       // the presence of this "grouping" attribute in this data set above.
-      case (k, es) => es.collectFirst { case e if e.key.key == s"executionEvents[$k]:grouping" => JobKeyAndGrouping(e.key.jobKey.get, e.value.get.value) } get } map {
-        case (jkg, m) => jkg -> m.values.toList.flatten }
+      case (k, es) =>
+        es.collectFirst {
+          case e if e.key.key == s"executionEvents[$k]:grouping" =>
+            JobKeyAndGrouping(e.key.jobKey.get, e.value.get.value)
+        } get
+    } map { case (jkg, m) =>
+      jkg -> m.values.toList.flatten
+    }
 
     // Tuplize the grouping function so it can operate on the List elements directly.
     val tupledGrouper = (makeSyntheticGroupedExecutionEvents _).tupled
     nonExecutionEvents ++ ungroupedExecutionEvents.values.toList.flatten ++ (groupedExecutionEventsByGrouping.toList flatMap tupledGrouper)
   }
 
-
-
-  def processMetadataEvents(query: MetadataQuery, eventsList: Seq[MetadataEvent], expandedValues: Map[String, JsValue]): JsObject = {
+  def processMetadataEvents(query: MetadataQuery,
+                            eventsList: Seq[MetadataEvent],
+                            expandedValues: Map[String, JsValue]
+  ): JsObject =
     // Should we send back some message ? Or even fail the request instead ?
     if (eventsList.isEmpty) JsObject(Map.empty[String, JsValue])
     else {
       query match {
-        case mq: MetadataQuery => workflowMetadataResponse(mq.workflowId, eventsList, includeCallsIfEmpty = true, expandedValues)
+        case mq: MetadataQuery =>
+          workflowMetadataResponse(mq.workflowId, eventsList, includeCallsIfEmpty = true, expandedValues)
         case _ => MetadataBuilderActor.parse(eventsList, expandedValues)
       }
     }
-  }
 
-  def processStatusResponse(workflowId: WorkflowId, status: WorkflowState): JsObject = {
-    JsObject(Map(
-      WorkflowMetadataKeys.Status -> JsString(status.toString),
-      WorkflowMetadataKeys.Id -> JsString(workflowId.toString)
-    ))
-  }
+  def processStatusResponse(workflowId: WorkflowId, status: WorkflowState): JsObject =
+    JsObject(
+      Map(
+        WorkflowMetadataKeys.Status -> JsString(status.toString),
+        WorkflowMetadataKeys.Id -> JsString(workflowId.toString)
+      )
+    )
 
   def processLabelsResponse(workflowId: WorkflowId, labels: Map[String, String]): JsObject = {
     val jsLabels = labels map { case (k, v) => k -> JsString(v) }
-    JsObject(Map(
-      WorkflowMetadataKeys.Id -> JsString(workflowId.toString),
-      WorkflowMetadataKeys.Labels -> JsObject(jsLabels)
-    ))
+    JsObject(
+      Map(
+        WorkflowMetadataKeys.Id -> JsString(workflowId.toString),
+        WorkflowMetadataKeys.Labels -> JsObject(jsLabels)
+      )
+    )
   }
 
   def processOutputsResponse(id: WorkflowId, events: Seq[MetadataEvent]): JsObject = {
     // Add in an empty output event if there aren't already any output events.
     val hasOutputs = events exists { _.key.key.startsWith(WorkflowMetadataKeys.Outputs + ":") }
-    val updatedEvents = if (hasOutputs) events else MetadataEvent.empty(MetadataKey(id, None, WorkflowMetadataKeys.Outputs)) +: events
+    val updatedEvents =
+      if (hasOutputs) events else MetadataEvent.empty(MetadataKey(id, None, WorkflowMetadataKeys.Outputs)) +: events
 
     workflowMetadataResponse(id, updatedEvents, includeCallsIfEmpty = false, Map.empty)
   }
@@ -236,26 +278,31 @@ object MetadataBuilderActor {
   def workflowMetadataResponse(workflowId: WorkflowId,
                                eventsList: Seq[MetadataEvent],
                                includeCallsIfEmpty: Boolean,
-                               expandedValues: Map[String, JsValue]): JsObject = {
-    JsObject(MetadataBuilderActor.parseWorkflowEvents(includeCallsIfEmpty, expandedValues)(eventsList).fields + ("id" -> JsString(workflowId.toString)))
-  }
+                               expandedValues: Map[String, JsValue]
+  ): JsObject =
+    JsObject(
+      MetadataBuilderActor
+        .parseWorkflowEvents(includeCallsIfEmpty, expandedValues)(eventsList)
+        .fields + ("id" -> JsString(workflowId.toString))
+    )
 }
 
-class MetadataBuilderActor(readMetadataWorkerMaker: () => Props, metadataReadRowNumberSafetyThreshold: Int, isForSubworkflows: Boolean)
-  extends LoggingFSM[MetadataBuilderActorState, MetadataBuilderActorData] with DefaultJsonProtocol {
+class MetadataBuilderActor(readMetadataWorkerMaker: () => Props,
+                           metadataReadRowNumberSafetyThreshold: Int,
+                           isForSubworkflows: Boolean
+) extends LoggingFSM[MetadataBuilderActorState, MetadataBuilderActorData]
+    with DefaultJsonProtocol {
 
   import MetadataBuilderActor._
 
   startWith(Idle, IdleData)
   val tag = self.path.name
 
-  when(Idle) {
-    case Event(action: BuildMetadataJsonAction, IdleData) =>
+  when(Idle) { case Event(action: BuildMetadataJsonAction, IdleData) =>
+    val readActor = context.actorOf(readMetadataWorkerMaker.apply())
 
-      val readActor = context.actorOf(readMetadataWorkerMaker.apply())
-
-      readActor ! action
-      goto(WaitingForMetadataService) using HasWorkData(sender(), action)
+    readActor ! action
+    goto(WaitingForMetadataService) using HasWorkData(sender(), action)
   }
 
   private def allDone() = {
@@ -274,14 +321,20 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props, metadataReadRow
       target ! SuccessfulMetadataJsonResponse(originalRequest, processOutputsResponse(id, events))
       allDone()
     case Event(LogsResponse(w, l), HasWorkData(target, originalRequest)) =>
-      target ! SuccessfulMetadataJsonResponse(originalRequest, workflowMetadataResponse(w, l, includeCallsIfEmpty = false, Map.empty))
+      target ! SuccessfulMetadataJsonResponse(originalRequest,
+                                              workflowMetadataResponse(w, l, includeCallsIfEmpty = false, Map.empty)
+      )
       allDone()
     case Event(MetadataLookupResponse(query, metadata), HasWorkData(target, originalRequest)) =>
       processMetadataResponse(query, metadata, target, originalRequest)
     case Event(FetchFailedJobsMetadataLookupResponse(metadata), HasWorkData(target, originalRequest)) =>
       processFailedJobsMetadataResponse(metadata, target, originalRequest)
     case Event(MetadataLookupFailedTooLargeResponse(query, metadataSizeRows), HasWorkData(target, originalRequest)) =>
-      val metadataTooLargeNumberOfRowsException = new MetadataTooLargeNumberOfRowsException(query.workflowId, metadataSizeRows, metadataReadRowNumberSafetyThreshold)
+      val metadataTooLargeNumberOfRowsException =
+        new MetadataTooLargeNumberOfRowsException(query.workflowId,
+                                                  metadataSizeRows,
+                                                  metadataReadRowNumberSafetyThreshold
+        )
       target ! FailedMetadataJsonResponse(originalRequest, metadataTooLargeNumberOfRowsException)
       allDone()
     case Event(MetadataLookupFailedTimeoutResponse(query), HasWorkData(target, originalRequest)) =>
@@ -322,26 +375,34 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props, metadataReadRow
       stay()
   }
 
-  def processSubWorkflowMetadata(metadataResponse: MetadataJsonResponse, data: HasReceivedEventsData) = {
+  def processSubWorkflowMetadata(metadataResponse: MetadataJsonResponse, data: HasReceivedEventsData) =
     metadataResponse match {
       case SuccessfulMetadataJsonResponse(GetMetadataAction(queryKey, _), js) =>
         val subId: WorkflowId = queryKey.workflowId
         val newData = data.withSubWorkflow(subId.toString, js)
 
         if (newData.isComplete) {
-          buildAndStop(data.originalQuery, data.originalEvents, newData.subWorkflowsMetadata, data.target, data.originalRequest)
+          buildAndStop(data.originalQuery,
+                       data.originalEvents,
+                       newData.subWorkflowsMetadata,
+                       data.target,
+                       data.originalRequest
+          )
         } else {
           stay() using newData
         }
       case FailedMetadataJsonResponse(originalRequest, e) =>
-        failAndDie(new RuntimeException(s"Failed to retrieve metadata for a sub workflow ($originalRequest)", e), data.target, data.originalRequest)
+        failAndDie(new RuntimeException(s"Failed to retrieve metadata for a sub workflow ($originalRequest)", e),
+                   data.target,
+                   data.originalRequest
+        )
 
       case other =>
-        val message = s"Programmer Error: MetadataBuilderActor expected subworkflow metadata response type but got ${other.getClass.getSimpleName}"
+        val message =
+          s"Programmer Error: MetadataBuilderActor expected subworkflow metadata response type but got ${other.getClass.getSimpleName}"
         log.error(message)
         failAndDie(new Exception(message), data.target, data.originalRequest)
     }
-  }
 
   def failAndDie(reason: Throwable, target: ActorRef, originalRequest: BuildMetadataJsonAction) = {
     target ! FailedMetadataJsonResponse(originalRequest, reason)
@@ -349,36 +410,63 @@ class MetadataBuilderActor(readMetadataWorkerMaker: () => Props, metadataReadRow
     stay()
   }
 
-  def buildAndStop(query: MetadataQuery, eventsList: Seq[MetadataEvent], expandedValues: Map[String, JsValue], target: ActorRef, originalRequest: BuildMetadataJsonAction) = {
+  def buildAndStop(query: MetadataQuery,
+                   eventsList: Seq[MetadataEvent],
+                   expandedValues: Map[String, JsValue],
+                   target: ActorRef,
+                   originalRequest: BuildMetadataJsonAction
+  ) = {
     val groupedEvents = groupEvents(eventsList)
     val res = processMetadataEvents(query, groupedEvents, expandedValues).fields
     target ! SuccessfulMetadataJsonResponse(originalRequest, JsObject(res))
     allDone()
   }
 
-  def processMetadataResponse(query: MetadataQuery, eventsList: Seq[MetadataEvent], target: ActorRef, originalRequest: BuildMetadataJsonAction) = {
+  def processMetadataResponse(query: MetadataQuery,
+                              eventsList: Seq[MetadataEvent],
+                              target: ActorRef,
+                              originalRequest: BuildMetadataJsonAction
+  ) =
     if (query.expandSubWorkflows) {
       // Scan events for sub workflow ids
-      val subWorkflowIds = eventsList.collect({
-        case MetadataEvent(key, value, _) if key.key.endsWith(CallMetadataKeys.SubWorkflowId) => value map { _.value }
-      }).flatten.distinct
+      val subWorkflowIds = eventsList
+        .collect {
+          case MetadataEvent(key, value, _) if key.key.endsWith(CallMetadataKeys.SubWorkflowId) => value map { _.value }
+        }
+        .flatten
+        .distinct
 
       // If none is found just proceed to build metadata
       if (subWorkflowIds.isEmpty) buildAndStop(query, eventsList, Map.empty, target, originalRequest)
       else {
         // Otherwise spin up a metadata builder actor for each sub workflow
         subWorkflowIds foreach { subId =>
-          val subMetadataBuilder = context.actorOf(MetadataBuilderActor.props(readMetadataWorkerMaker, metadataReadRowNumberSafetyThreshold, isForSubworkflows = true), uniqueActorName(subId))
-          subMetadataBuilder ! GetMetadataAction(query.copy(workflowId = WorkflowId.fromString(subId)), checkTotalMetadataRowNumberBeforeQuerying = false)
+          val subMetadataBuilder = context.actorOf(MetadataBuilderActor.props(readMetadataWorkerMaker,
+                                                                              metadataReadRowNumberSafetyThreshold,
+                                                                              isForSubworkflows = true
+                                                   ),
+                                                   uniqueActorName(subId)
+          )
+          subMetadataBuilder ! GetMetadataAction(query.copy(workflowId = WorkflowId.fromString(subId)),
+                                                 checkTotalMetadataRowNumberBeforeQuerying = false
+          )
         }
-        goto(WaitingForSubWorkflows) using HasReceivedEventsData(target, originalRequest, query, eventsList, Map.empty, subWorkflowIds.size)
+        goto(WaitingForSubWorkflows) using HasReceivedEventsData(target,
+                                                                 originalRequest,
+                                                                 query,
+                                                                 eventsList,
+                                                                 Map.empty,
+                                                                 subWorkflowIds.size
+        )
       }
     } else {
       buildAndStop(query, eventsList, Map.empty, target, originalRequest)
     }
-  }
 
-  def processFailedJobsMetadataResponse(eventsList: Seq[MetadataEvent], target: ActorRef, originalRequest: BuildMetadataJsonAction) = {
+  def processFailedJobsMetadataResponse(eventsList: Seq[MetadataEvent],
+                                        target: ActorRef,
+                                        originalRequest: BuildMetadataJsonAction
+  ) = {
     val groupedEvents = groupEvents(eventsList)
     val res = MetadataBuilderActor.parse(groupedEvents, Map.empty)
     target ! SuccessfulMetadataJsonResponse(originalRequest, res)
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataComponent.scala b/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataComponent.scala
index 428feafe1a1..756744806b2 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataComponent.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/builder/MetadataComponent.scala
@@ -18,7 +18,7 @@ object MetadataComponent {
     private lazy val stringKeyMapSg = implicitly[Semigroup[Map[String, MetadataComponent]]]
     private lazy val intKeyMapSg = implicitly[Semigroup[Map[Int, MetadataComponent]]]
 
-    def combine(f1: MetadataComponent, f2: MetadataComponent): MetadataComponent = {
+    def combine(f1: MetadataComponent, f2: MetadataComponent): MetadataComponent =
       (f1, f2) match {
         case (MetadataObject(v1), MetadataObject(v2)) => MetadataObject(stringKeyMapSg.combine(v1, v2))
         case (MetadataList(v1), MetadataList(v2)) => MetadataList(intKeyMapSg.combine(v1, v2))
@@ -27,15 +27,17 @@ object MetadataComponent {
         // Otherwise assume it's ordered by default and take the new one
         case (_, o2) => o2
       }
-    }
 
     override def empty: MetadataComponent = MetadataObject.empty
   }
 
   val metadataPrimitiveJsonWriter: JsonWriter[MetadataPrimitive] = JsonWriter.func2Writer[MetadataPrimitive] {
-    case MetadataPrimitive(MetadataValue(value, MetadataInt), _) => Try(value.toInt) map JsNumber.apply getOrElse JsString(value)
-    case MetadataPrimitive(MetadataValue(value, MetadataNumber), _) => Try(value.toDouble) map JsNumber.apply getOrElse JsString(value)
-    case MetadataPrimitive(MetadataValue(value, MetadataBoolean), _) => Try(value.toBoolean) map JsBoolean.apply getOrElse JsString(value)
+    case MetadataPrimitive(MetadataValue(value, MetadataInt), _) =>
+      Try(value.toInt) map JsNumber.apply getOrElse JsString(value)
+    case MetadataPrimitive(MetadataValue(value, MetadataNumber), _) =>
+      Try(value.toDouble) map JsNumber.apply getOrElse JsString(value)
+    case MetadataPrimitive(MetadataValue(value, MetadataBoolean), _) =>
+      Try(value.toBoolean) map JsBoolean.apply getOrElse JsString(value)
     case MetadataPrimitive(MetadataValue(value, MetadataString), _) => JsString(value)
     case MetadataPrimitive(MetadataValue(_, MetadataNull), _) => JsNull
   }
@@ -58,7 +60,7 @@ object MetadataComponent {
   val KeySplitter = s"(?<!\\\\)$KeySeparator"
   private val bracketMatcher = """\[(\d*)\]""".r
 
-  private def parseKeyChunk(chunk: String, innerValue: MetadataComponent): MetadataComponent = {
+  private def parseKeyChunk(chunk: String, innerValue: MetadataComponent): MetadataComponent =
     chunk.indexOf('[') match {
       // If there's no bracket, it's an object. e.g.: "calls"
       case -1 => MetadataObject(Map(chunk -> innerValue))
@@ -77,7 +79,7 @@ object MetadataComponent {
         } yield asInt
         // Fold into a MetadataList: MetadataList(0 -> MetadataList(1 -> innerValue))
         val init = if (innerValue == MetadataEmptyComponent) {
-        // Empty value means empty list
+          // Empty value means empty list
           listIndices.toList.init.foldRight(MetadataList.empty)((index, acc) => MetadataList(TreeMap(index -> acc)))
         } else {
           listIndices.toList.foldRight(innerValue)((index, acc) => MetadataList(TreeMap(index -> acc)))
@@ -86,27 +88,29 @@ object MetadataComponent {
 
         MetadataObject(Map(objectName -> metadataList))
     }
-  }
 
   private def customOrdering(event: MetadataEvent): Option[Ordering[MetadataPrimitive]] = event match {
-    case MetadataEvent(MetadataKey(_, Some(_), key), _, _)
-      if key == CallMetadataKeys.ExecutionStatus => Option(MetadataPrimitive.ExecutionStatusOrdering)
-    case MetadataEvent(MetadataKey(_, _, key), _, _)
-      if key == CallMetadataKeys.Start || key == CallMetadataKeys.End => Option(MetadataPrimitive.TimestampOrdering)
-    case MetadataEvent(MetadataKey(_, None, key), _, _)
-      if key == WorkflowMetadataKeys.Status => Option(MetadataPrimitive.WorkflowStateOrdering)
+    case MetadataEvent(MetadataKey(_, Some(_), key), _, _) if key == CallMetadataKeys.ExecutionStatus =>
+      Option(MetadataPrimitive.ExecutionStatusOrdering)
+    case MetadataEvent(MetadataKey(_, _, key), _, _) if key == CallMetadataKeys.Start || key == CallMetadataKeys.End =>
+      Option(MetadataPrimitive.TimestampOrdering)
+    case MetadataEvent(MetadataKey(_, None, key), _, _) if key == WorkflowMetadataKeys.Status =>
+      Option(MetadataPrimitive.WorkflowStateOrdering)
     case _ => None
   }
 
   private def toMetadataComponent(subWorkflowMetadata: Map[String, JsValue])(event: MetadataEvent) = {
-    lazy val primitive = event.value map { MetadataPrimitive(_, customOrdering(event)) } getOrElse MetadataEmptyComponent
+    lazy val primitive = event.value map {
+      MetadataPrimitive(_, customOrdering(event))
+    } getOrElse MetadataEmptyComponent
     lazy val originalKeyAndPrimitive = (event.key.key, primitive)
 
     val keyAndPrimitive: (String, MetadataComponent) = if (event.key.key.endsWith(CallMetadataKeys.SubWorkflowId)) {
       (for {
         metadataValue <- event.value
         subWorkflowMetadata <- subWorkflowMetadata.get(metadataValue.value)
-        keyWithSubWorkflowMetadata = event.key.key.replace(CallMetadataKeys.SubWorkflowId, CallMetadataKeys.SubWorkflowMetadata)
+        keyWithSubWorkflowMetadata = event.key.key
+          .replace(CallMetadataKeys.SubWorkflowId, CallMetadataKeys.SubWorkflowMetadata)
         subWorkflowComponent = MetadataJsonComponent(subWorkflowMetadata)
       } yield (keyWithSubWorkflowMetadata, subWorkflowComponent)) getOrElse originalKeyAndPrimitive
     } else originalKeyAndPrimitive
@@ -115,15 +119,13 @@ object MetadataComponent {
   }
 
   /** Sort events by timestamp, transform them into MetadataComponent, and merge them together. */
-  def apply(events: Seq[MetadataEvent], subWorkflowMetadata: Map[String, JsValue] = Map.empty): MetadataComponent = {
+  def apply(events: Seq[MetadataEvent], subWorkflowMetadata: Map[String, JsValue] = Map.empty): MetadataComponent =
     // The `List` has a `Foldable` instance defined in scope, and because the `List`'s elements have a `Monoid` instance
     // defined in scope, `combineAll` can derive a sane `TimestampedJsValue` value even if the `List` of events is empty.
     events.toList map toMetadataComponent(subWorkflowMetadata) combineAll
-  }
 
-  def fromMetadataKeyAndPrimitive(metadataKey: String, innerComponent: MetadataComponent) = {
+  def fromMetadataKeyAndPrimitive(metadataKey: String, innerComponent: MetadataComponent) =
     metadataKey.split(KeySplitter).map(_.unescapeMeta).foldRight(innerComponent)(parseKeyChunk)
-  }
 }
 
 sealed trait MetadataComponent
@@ -133,9 +135,8 @@ case object MetadataNullComponent extends MetadataComponent
 // Metadata Object
 object MetadataObject {
   def empty = new MetadataObject(Map.empty)
-  def apply(kvPair: (String, MetadataComponent)*) = {
+  def apply(kvPair: (String, MetadataComponent)*) =
     new MetadataObject(kvPair.toMap)
-  }
 }
 
 case class MetadataObject(v: Map[String, MetadataComponent]) extends MetadataComponent
@@ -143,7 +144,9 @@ case class MetadataObject(v: Map[String, MetadataComponent]) extends MetadataCom
 // Metadata List
 object MetadataList {
   def empty = new MetadataList(Map.empty)
-  def apply(components: List[MetadataComponent]) = new MetadataList(components.zipWithIndex.map({case (c, i) => i -> c}).toMap)
+  def apply(components: List[MetadataComponent]) = new MetadataList(components.zipWithIndex.map { case (c, i) =>
+    i -> c
+  }.toMap)
 }
 case class MetadataList(v: Map[Int, MetadataComponent]) extends MetadataComponent
 
@@ -161,7 +164,8 @@ object MetadataPrimitive {
     Instant.parse(primitive.v.value)
   }.reverse
 }
-case class MetadataPrimitive(v: MetadataValue, customOrdering: Option[Ordering[MetadataPrimitive]] = None) extends MetadataComponent
+case class MetadataPrimitive(v: MetadataValue, customOrdering: Option[Ordering[MetadataPrimitive]] = None)
+    extends MetadataComponent
 
 // Metadata Component that owns an already computed JsValue
 case class MetadataJsonComponent(jsValue: JsValue) extends MetadataComponent
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/deleter/DeleteMetadataActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/deleter/DeleteMetadataActor.scala
index 92b1fff49ee..f1afcbde19f 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/deleter/DeleteMetadataActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/deleter/DeleteMetadataActor.scala
@@ -1,6 +1,6 @@
 package cromwell.services.metadata.impl.deleter
 
-import java.time.{OffsetDateTime, Duration => JDuration}
+import java.time.{Duration => JDuration, OffsetDateTime}
 import java.util.concurrent.TimeUnit
 
 import akka.actor.{Actor, ActorLogging, ActorRef, Props}
@@ -21,22 +21,25 @@ import scala.concurrent.duration._
 import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success}
 
-class DeleteMetadataActor(deleteMetadataConfig: DeleteMetadataConfig,
-                          override val serviceRegistryActor: ActorRef)
-  extends Actor
-  with ActorLogging
-  with MetadataDatabaseAccess
-  with MetadataServicesStore
-  with CromwellInstrumentation {
+class DeleteMetadataActor(deleteMetadataConfig: DeleteMetadataConfig, override val serviceRegistryActor: ActorRef)
+    extends Actor
+    with ActorLogging
+    with MetadataDatabaseAccess
+    with MetadataServicesStore
+    with CromwellInstrumentation {
 
   implicit val ec: ExecutionContext = context.dispatcher
   implicit val askTimeout: Timeout = new Timeout(60.seconds)
 
-  private val deleterMetricsBasePath: NonEmptyList[String] = MetadataServiceActor.MetadataInstrumentationPrefix :+ "deleter"
+  private val deleterMetricsBasePath: NonEmptyList[String] =
+    MetadataServiceActor.MetadataInstrumentationPrefix :+ "deleter"
   private val rowsDeletedMetricPath: NonEmptyList[String] = deleterMetricsBasePath :+ "rows_deleted"
-  private val workflowsDeletedSuccessMetricPath: NonEmptyList[String] = deleterMetricsBasePath :+ "workflows_deleted" :+ "success"
-  private val workflowsDeletedFailureMetricPath: NonEmptyList[String] = deleterMetricsBasePath :+ "workflows_deleted" :+ "failure"
-  private val workflowDeleteTotalTimeMetricPath: NonEmptyList[String] = deleterMetricsBasePath :+ "workflow_delete_total_time"
+  private val workflowsDeletedSuccessMetricPath: NonEmptyList[String] =
+    deleterMetricsBasePath :+ "workflows_deleted" :+ "success"
+  private val workflowsDeletedFailureMetricPath: NonEmptyList[String] =
+    deleterMetricsBasePath :+ "workflows_deleted" :+ "failure"
+  private val workflowDeleteTotalTimeMetricPath: NonEmptyList[String] =
+    deleterMetricsBasePath :+ "workflow_delete_total_time"
   private val workflowsToDeleteMetricPath: NonEmptyList[String] = deleterMetricsBasePath :+ "workflows_to_delete"
 
   // Send an initial delete message to get things started:
@@ -46,15 +49,14 @@ class DeleteMetadataActor(deleteMetadataConfig: DeleteMetadataConfig,
   context.system.scheduler.scheduleOnce(deleteMetadataConfig.instrumentationInterval)(workflowsLeftToDeleteMetric())
 
   override def receive: Receive = {
-    case DeleteNextWorkflowMessage => {
+    case DeleteNextWorkflowMessage =>
       val startTime = OffsetDateTime.now()
-      def calculateTimeSinceStart() = {
+      def calculateTimeSinceStart() =
         FiniteDuration(JDuration.between(startTime, OffsetDateTime.now()).toMillis, TimeUnit.MILLISECONDS)
-      }
 
       // These handlers send metrics for most paths even when they're not incremented, so that the metrics
       // paths are actively receiving data points throughout:
-      deleteNextWorkflow().onComplete({
+      deleteNextWorkflow().onComplete {
         case Success(true) =>
           increment(workflowsDeletedSuccessMetricPath, ServicesPrefix)
           count(workflowsDeletedFailureMetricPath, 0L, ServicesPrefix)
@@ -67,7 +69,10 @@ class DeleteMetadataActor(deleteMetadataConfig: DeleteMetadataConfig,
           sendGauge(workflowsToDeleteMetricPath, 0L, ServicesPrefix)
           sendTiming(workflowDeleteTotalTimeMetricPath, calculateTimeSinceStart(), ServicesPrefix)
           scheduleNextDeleteAttemptAfterInterval()
-          if (deleteMetadataConfig.debugLogging) log.info(s"No archived workflows which finished over ${deleteMetadataConfig.delayAfterWorkflowCompletion} ago remain to be deleted. Scheduling next poll in ${deleteMetadataConfig.backoffInterval}.")
+          if (deleteMetadataConfig.debugLogging)
+            log.info(
+              s"No archived workflows which finished over ${deleteMetadataConfig.delayAfterWorkflowCompletion} ago remain to be deleted. Scheduling next poll in ${deleteMetadataConfig.backoffInterval}."
+            )
         case Failure(error) =>
           count(rowsDeletedMetricPath, 0L, ServicesPrefix)
           count(workflowsDeletedSuccessMetricPath, 0L, ServicesPrefix)
@@ -75,26 +80,36 @@ class DeleteMetadataActor(deleteMetadataConfig: DeleteMetadataConfig,
           sendTiming(workflowDeleteTotalTimeMetricPath, calculateTimeSinceStart(), ServicesPrefix)
           log.error(error, s"Error while deleting, will wait ${deleteMetadataConfig.backoffInterval} then try again.")
           scheduleNextDeleteAttemptAfterInterval()
-      })
+      }
 
-    }
-    case ShutdownCommand => context.stop(self)  // TODO: cancel any deletion action that might be happening?
-    case other => log.info(s"Programmer Error! The DeleteMetadataSchedulerActor received unexpected message! (${sender()} sent ${other.toPrettyElidedString(1000)}})")
+    case ShutdownCommand => context.stop(self) // TODO: cancel any deletion action that might be happening?
+    case other =>
+      log.info(
+        s"Programmer Error! The DeleteMetadataSchedulerActor received unexpected message! (${sender()} sent ${other.toPrettyElidedString(1000)}})"
+      )
   }
 
   def workflowsLeftToDeleteMetric(): Unit = {
-    val currentTimestampMinusDelay = OffsetDateTime.now().minusSeconds(deleteMetadataConfig.delayAfterWorkflowCompletion.toSeconds)
-    countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(currentTimestampMinusDelay).onComplete({
+    val currentTimestampMinusDelay =
+      OffsetDateTime.now().minusSeconds(deleteMetadataConfig.delayAfterWorkflowCompletion.toSeconds)
+    countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(currentTimestampMinusDelay).onComplete {
       case Success(workflowsToDelete) =>
         sendGauge(workflowsToDeleteMetricPath, workflowsToDelete.longValue(), ServicesPrefix)
         // schedule next workflows left to delete query after interval
-        context.system.scheduler.scheduleOnce(deleteMetadataConfig.instrumentationInterval)(workflowsLeftToDeleteMetric())
+        context.system.scheduler.scheduleOnce(deleteMetadataConfig.instrumentationInterval)(
+          workflowsLeftToDeleteMetric()
+        )
       case Failure(exception) =>
-        log.error(exception, s"Something went wrong while fetching number of workflows left to delete. " +
-          s"Scheduling next poll in ${deleteMetadataConfig.instrumentationInterval}.")
+        log.error(
+          exception,
+          s"Something went wrong while fetching number of workflows left to delete. " +
+            s"Scheduling next poll in ${deleteMetadataConfig.instrumentationInterval}."
+        )
         // schedule next workflows left to delete query after interval
-        context.system.scheduler.scheduleOnce(deleteMetadataConfig.instrumentationInterval)(workflowsLeftToDeleteMetric())
-    })
+        context.system.scheduler.scheduleOnce(deleteMetadataConfig.instrumentationInterval)(
+          workflowsLeftToDeleteMetric()
+        )
+    }
   }
 
   def deleteNextWorkflow(): Future[Boolean] = for {
@@ -103,7 +118,10 @@ class DeleteMetadataActor(deleteMetadataConfig: DeleteMetadataConfig,
       case Some(id) =>
         log.info(s"Workflow $id identified for metadata deletion")
         for {
-          rowsDeleted <- deleteAllMetadataEntriesForWorkflowAndUpdateArchiveStatus(id, MetadataArchiveStatus.toDatabaseValue(ArchivedAndDeleted))
+          rowsDeleted <- deleteAllMetadataEntriesForWorkflowAndUpdateArchiveStatus(
+            id,
+            MetadataArchiveStatus.toDatabaseValue(ArchivedAndDeleted)
+          )
           _ = count(rowsDeletedMetricPath, rowsDeleted.longValue(), ServicesPrefix)
           _ = log.info(s"Deleted $rowsDeleted metadata rows for $id")
         } yield true
@@ -112,7 +130,8 @@ class DeleteMetadataActor(deleteMetadataConfig: DeleteMetadataConfig,
   } yield result
 
   def lookupNextWorkflowToDelete(): Future[Option[WorkflowId]] = {
-    val currentTimestampMinusDelay = OffsetDateTime.now().minusSeconds(deleteMetadataConfig.delayAfterWorkflowCompletion.toSeconds)
+    val currentTimestampMinusDelay =
+      OffsetDateTime.now().minusSeconds(deleteMetadataConfig.delayAfterWorkflowCompletion.toSeconds)
     queryWorkflowIdsByArchiveStatusAndOlderThanTimestamp(
       MetadataArchiveStatus.toDatabaseValue(Archived),
       currentTimestampMinusDelay,
@@ -130,5 +149,7 @@ class DeleteMetadataActor(deleteMetadataConfig: DeleteMetadataConfig,
 object DeleteMetadataActor {
   case object DeleteNextWorkflowMessage
 
-  def props(config: DeleteMetadataConfig, serviceRegistryActor: ActorRef): Props = Props(new DeleteMetadataActor(config, serviceRegistryActor))
+  def props(config: DeleteMetadataConfig, serviceRegistryActor: ActorRef): Props = Props(
+    new DeleteMetadataActor(config, serviceRegistryActor)
+  )
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/deleter/DeleteMetadataConfig.scala b/services/src/main/scala/cromwell/services/metadata/impl/deleter/DeleteMetadataConfig.scala
index 0be2f77655a..6fa278eba0d 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/deleter/DeleteMetadataConfig.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/deleter/DeleteMetadataConfig.scala
@@ -12,7 +12,8 @@ import scala.util.Try
 final case class DeleteMetadataConfig(backoffInterval: FiniteDuration,
                                       delayAfterWorkflowCompletion: FiniteDuration,
                                       instrumentationInterval: FiniteDuration,
-                                      debugLogging: Boolean)
+                                      debugLogging: Boolean
+)
 
 object DeleteMetadataConfig {
 
@@ -21,11 +22,14 @@ object DeleteMetadataConfig {
     val defaultInstrumentationInterval = 1 minute
     val defaultDebugLogging = true
 
-
     for {
-      backoffInterval <- Try(deleteMetadataConfig.getOrElse[FiniteDuration]("backoff-interval", defaultBackoffInterval)).toChecked
+      backoffInterval <- Try(
+        deleteMetadataConfig.getOrElse[FiniteDuration]("backoff-interval", defaultBackoffInterval)
+      ).toChecked
       delayAfterWorkflowCompletion <- Try(deleteMetadataConfig.as[FiniteDuration]("deletion-delay")).toChecked
-      instrumentationInterval <- Try(deleteMetadataConfig.getOrElse("instrumentation-interval", defaultInstrumentationInterval)).toChecked
+      instrumentationInterval <- Try(
+        deleteMetadataConfig.getOrElse("instrumentation-interval", defaultInstrumentationInterval)
+      ).toChecked
       debugLogging <- Try(deleteMetadataConfig.getOrElse("debug-logging", defaultDebugLogging)).toChecked
     } yield DeleteMetadataConfig(backoffInterval, delayAfterWorkflowCompletion, instrumentationInterval, debugLogging)
   }
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/hybridpubsub/HybridPubSubMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/hybridpubsub/HybridPubSubMetadataServiceActor.scala
index 20e62067cf8..89e5697cd60 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/hybridpubsub/HybridPubSubMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/hybridpubsub/HybridPubSubMetadataServiceActor.scala
@@ -6,7 +6,6 @@ import cromwell.services.metadata.MetadataService.{PutMetadataAction, PutMetadat
 import cromwell.services.metadata.impl.MetadataServiceActor
 import cromwell.services.metadata.impl.pubsub.PubSubMetadataServiceActor
 
-
 /**
   * A metadata service implementation which will function as a standard metadata service but also push all metadata
   * events to google pubsub.
@@ -19,9 +18,13 @@ import cromwell.services.metadata.impl.pubsub.PubSubMetadataServiceActor
   * It is expected that the user will supply any desired config fields for both MetadataServiceActor and
   * PubSubMetadataServiceActor as the serviceConfig block will be passed along to both of them.
   */
-class HybridPubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor with ActorLogging {
-  val standardMetadataActor: ActorRef = context.actorOf(MetadataServiceActor.props(serviceConfig, globalConfig, serviceRegistryActor))
-  val pubSubMetadataActor: ActorRef = context.actorOf(PubSubMetadataServiceActor.props(serviceConfig, globalConfig, serviceRegistryActor))
+class HybridPubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
+    extends Actor
+    with ActorLogging {
+  val standardMetadataActor: ActorRef =
+    context.actorOf(MetadataServiceActor.props(serviceConfig, globalConfig, serviceRegistryActor))
+  val pubSubMetadataActor: ActorRef =
+    context.actorOf(PubSubMetadataServiceActor.props(serviceConfig, globalConfig, serviceRegistryActor))
 
   override def receive = {
     case action: PutMetadataAction =>
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/pubsub/PubSubMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/pubsub/PubSubMetadataServiceActor.scala
index f139be5c27a..85fa1847301 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/pubsub/PubSubMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/pubsub/PubSubMetadataServiceActor.scala
@@ -11,7 +11,12 @@ import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.cloudsupport.gcp.auth.ServiceAccountMode
 import cromwell.cloudsupport.gcp.auth.ServiceAccountMode.JsonFileFormat
 import cromwell.core.Dispatcher._
-import cromwell.services.metadata.MetadataService.{MetadataWriteFailure, MetadataWriteSuccess, PutMetadataAction, PutMetadataActionAndRespond}
+import cromwell.services.metadata.MetadataService.{
+  MetadataWriteFailure,
+  MetadataWriteSuccess,
+  PutMetadataAction,
+  PutMetadataActionAndRespond
+}
 import cromwell.services.metadata._
 import net.ceedubs.ficus.Ficus._
 import org.broadinstitute.dsde.workbench.google.{GoogleCredentialModes, GooglePubSubDAO, HttpGooglePubSubDAO}
@@ -40,7 +45,9 @@ import scala.util.{Failure, Success}
   *  - Revisit the Alpakka connector instead of the workbench-lib version. There was a bug they fixed but hadn't released
   *     it yet. Also I'm pretty sure that same bug was repeated in a few other places.
   */
-class PubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor with ActorLogging {
+class PubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
+    extends Actor
+    with ActorLogging {
   implicit val ec = context.dispatcher
 
   // The auth *must* be a service account auth but it might not be named service-account.
@@ -74,14 +81,21 @@ class PubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, se
     // This class requires a service account auth due to the library used
     val googleAuth = googleConfig.auth(googleAuthName) match {
       case Valid(a: ServiceAccountMode) => a
-      case Valid(doh) => throw new IllegalArgumentException(s"Unable to configure PubSubMetadataServiceActor: ${doh.name} was not a service account auth")
-      case Invalid(e) => throw new IllegalArgumentException("Unable to configure PubSubMetadataServiceActor: " + e.toList.mkString(", "))
+      case Valid(doh) =>
+        throw new IllegalArgumentException(
+          s"Unable to configure PubSubMetadataServiceActor: ${doh.name} was not a service account auth"
+        )
+      case Invalid(e) =>
+        throw new IllegalArgumentException("Unable to configure PubSubMetadataServiceActor: " + e.toList.mkString(", "))
     }
     val jsonAuth = googleAuth.fileFormat match {
       case j: JsonFileFormat =>
         val jsonString = new String(Files.readAllBytes(Paths.get(j.file)))
         GoogleCredentialModes.Json(jsonString)
-      case _ => throw new IllegalArgumentException("Unable to configure PubSubMetadataServiceActor: the service account must supply a JSON file")
+      case _ =>
+        throw new IllegalArgumentException(
+          "Unable to configure PubSubMetadataServiceActor: the service account must supply a JSON file"
+        )
     }
 
     // The metric name is pretty useless. It's an artifact of the workbench libraries which we're not using
@@ -103,7 +117,7 @@ class PubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, se
     * return type of HttpGooglePubSubDAO.createSubscription and only caring about the success of the Future. It is not
     * considered an error if the subscription already exists (in fact, this is a likely circumstance).
     */
-  private def createSubscription(): Future[Unit] = {
+  private def createSubscription(): Future[Unit] =
     pubSubSubscriptionName match {
       case Some(name) =>
         log.info("Creating subscription " + name)
@@ -112,7 +126,6 @@ class PubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, se
         log.info("Not creating a subscription")
         Future.successful(())
     }
-  }
 
   private def publishMessages(events: Iterable[MetadataEvent]): Future[Unit] = {
     import PubSubMetadataServiceActor.EnhancedMetadataEvents
@@ -124,9 +137,9 @@ class PubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, se
 }
 
 object PubSubMetadataServiceActor {
-  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) = {
-    Props(new PubSubMetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor)).withDispatcher(ServiceDispatcher)
-  }
+  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) =
+    Props(new PubSubMetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor))
+      .withDispatcher(ServiceDispatcher)
 
   implicit class EnhancedMetadataEvents(val e: Iterable[MetadataEvent]) extends AnyVal {
     import MetadataJsonSupport._
@@ -134,4 +147,3 @@ object PubSubMetadataServiceActor {
     def toJson: Seq[String] = e.map(_.toJson.toString()).toSeq
   }
 }
-
diff --git a/services/src/main/scala/cromwell/services/metadata/metadata.scala b/services/src/main/scala/cromwell/services/metadata/metadata.scala
index 9e621cfad07..6860bb7c69b 100644
--- a/services/src/main/scala/cromwell/services/metadata/metadata.scala
+++ b/services/src/main/scala/cromwell/services/metadata/metadata.scala
@@ -35,5 +35,5 @@ object Patterns {
         \.                               #   Literal dot.
         (\d+)                            #   Captured shard digits.
       )?                                 # End outer optional noncapturing group for shard.
-                               """.trim.r                         // The trim is necessary as (?x) must be at the beginning of the regex.
+                               """.trim.r // The trim is necessary as (?x) must be at the beginning of the regex.
 }
diff --git a/services/src/main/scala/cromwell/services/metadata/package.scala b/services/src/main/scala/cromwell/services/metadata/package.scala
index 6ccbbcefa7f..279a82e858d 100644
--- a/services/src/main/scala/cromwell/services/metadata/package.scala
+++ b/services/src/main/scala/cromwell/services/metadata/package.scala
@@ -11,17 +11,19 @@ package object metadata {
 }
 
 sealed trait MetadataJsonResponse extends MetadataServiceResponse { def originalRequest: BuildMetadataJsonAction }
-final case class SuccessfulMetadataJsonResponse(originalRequest: BuildMetadataJsonAction, responseJson: JsObject) extends MetadataJsonResponse
-final case class FailedMetadataJsonResponse(originalRequest: BuildMetadataJsonAction, reason: Throwable) extends MetadataJsonResponse
+final case class SuccessfulMetadataJsonResponse(originalRequest: BuildMetadataJsonAction, responseJson: JsObject)
+    extends MetadataJsonResponse
+final case class FailedMetadataJsonResponse(originalRequest: BuildMetadataJsonAction, reason: Throwable)
+    extends MetadataJsonResponse
 
 class MetadataTooLargeException(message: String) extends RuntimeException(message) with NoStackTrace
 
 final class MetadataTooLargeNumberOfRowsException(workflowId: WorkflowId, metadataSizeRows: Int, metadataLimitRows: Int)
-  extends MetadataTooLargeException(
-    s"Metadata for workflow $workflowId exists in database but cannot be served because row count of $metadataSizeRows exceeds configured limit of $metadataLimitRows."
-  )
+    extends MetadataTooLargeException(
+      s"Metadata for workflow $workflowId exists in database but cannot be served because row count of $metadataSizeRows exceeds configured limit of $metadataLimitRows."
+    )
 
 final class MetadataTooLargeTimeoutException(workflowId: WorkflowId)
-  extends MetadataTooLargeException(
-    s"Metadata for workflow $workflowId exists in database but retrieval timed out, possibly due to large row count."
-  )
+    extends MetadataTooLargeException(
+      s"Metadata for workflow $workflowId exists in database but retrieval timed out, possibly due to large row count."
+    )
diff --git a/services/src/main/scala/cromwell/services/womtool/Describer.scala b/services/src/main/scala/cromwell/services/womtool/Describer.scala
index fa0a2331c62..7b8116001da 100644
--- a/services/src/main/scala/cromwell/services/womtool/Describer.scala
+++ b/services/src/main/scala/cromwell/services/womtool/Describer.scala
@@ -46,7 +46,8 @@ object Describer {
   private def describeWorkflowInner(factory: LanguageFactory,
                                     workflowSource: WorkflowSource,
                                     importResolvers: List[ImportResolver.ImportResolver],
-                                    workflowSourceFilesCollection: WorkflowSourceFilesCollection): WorkflowDescription = {
+                                    workflowSourceFilesCollection: WorkflowSourceFilesCollection
+  ): WorkflowDescription = {
 
     val submittedDescriptorType = Map(
       "descriptorType" -> factory.languageName,
@@ -56,7 +57,12 @@ object Describer {
     // Mirror of the inputs/no inputs fork in womtool.validate.Validate
     if (workflowSourceFilesCollection.inputsJson.isEmpty) {
       // No inputs: just load up the WomBundle
-      factory.getWomBundle(workflowSource, workflowSourceOrigin = None, workflowOptionsJson = "{}", importResolvers, List(factory)) match {
+      factory.getWomBundle(workflowSource,
+                           workflowSourceOrigin = None,
+                           workflowOptionsJson = "{}",
+                           importResolvers,
+                           List(factory)
+      ) match {
         case Right(bundle: WomBundle) =>
           WorkflowDescription.fromBundle(bundle, submittedDescriptorType, List.empty)
         case Left(workflowErrors) =>
@@ -64,7 +70,12 @@ object Describer {
       }
     } else {
       // Inputs: load up the WomBundle and then try creating an executable with WomBundle + inputs
-      factory.getWomBundle(workflowSource, workflowSourceOrigin = None, workflowOptionsJson = "{}", importResolvers, List(factory)) match {
+      factory.getWomBundle(workflowSource,
+                           workflowSourceOrigin = None,
+                           workflowOptionsJson = "{}",
+                           importResolvers,
+                           List(factory)
+      ) match {
         case Right(bundle) =>
           factory.createExecutable(bundle, workflowSourceFilesCollection.inputsJson, NoIoFunctionSet) match {
             // Throw away the executable, all we care about is whether it created successfully (i.e. the inputs are valid)
diff --git a/services/src/main/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActor.scala b/services/src/main/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActor.scala
index 35a950a6343..ac1c748281d 100644
--- a/services/src/main/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActor.scala
+++ b/services/src/main/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActor.scala
@@ -11,13 +11,14 @@ import cromwell.util.GracefulShutdownHelper.ShutdownCommand
 
 import scala.concurrent.{ExecutionContext, Future}
 
-class WomtoolServiceInCromwellActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor with LazyLogging {
+class WomtoolServiceInCromwellActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
+    extends Actor
+    with LazyLogging {
 
   implicit val ec: ExecutionContext = context.dispatcher
 
   override def receive: Receive = {
     case DescribeRequest(filesCollection) =>
-
       // We are consciously wrapping a Future around the Await.result way down in the HTTP import resolver until we can update the whole call hierarchy to async
       // https://doc.akka.io/docs/akka/2.5.16/actors.html?language=scala#ask-send-and-receive-future
       Future {
@@ -33,5 +34,6 @@ class WomtoolServiceInCromwellActor(serviceConfig: Config, globalConfig: Config,
 
 object WomtoolServiceInCromwellActor {
   def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) =
-    Props(new WomtoolServiceInCromwellActor(serviceConfig, globalConfig, serviceRegistryActor)).withDispatcher(ServiceDispatcher)
+    Props(new WomtoolServiceInCromwellActor(serviceConfig, globalConfig, serviceRegistryActor))
+      .withDispatcher(ServiceDispatcher)
 }
diff --git a/services/src/main/scala/cromwell/services/womtool/models/InputDescription.scala b/services/src/main/scala/cromwell/services/womtool/models/InputDescription.scala
index cb01ab5c920..142bda234a3 100644
--- a/services/src/main/scala/cromwell/services/womtool/models/InputDescription.scala
+++ b/services/src/main/scala/cromwell/services/womtool/models/InputDescription.scala
@@ -6,5 +6,10 @@ import io.circe.generic.JsonCodec
 import wom.expression.WomExpression
 import wom.types.WomType
 
-@JsonCodec(encodeOnly=true)
-case class InputDescription(name: String, valueType: WomType, typeDisplayName: String, optional: Boolean, default: Option[WomExpression])
+@JsonCodec(encodeOnly = true)
+case class InputDescription(name: String,
+                            valueType: WomType,
+                            typeDisplayName: String,
+                            optional: Boolean,
+                            default: Option[WomExpression]
+)
diff --git a/services/src/main/scala/cromwell/services/womtool/models/MetaValueElementJsonSupport.scala b/services/src/main/scala/cromwell/services/womtool/models/MetaValueElementJsonSupport.scala
index 0855c9e131c..d29edc6b6b7 100644
--- a/services/src/main/scala/cromwell/services/womtool/models/MetaValueElementJsonSupport.scala
+++ b/services/src/main/scala/cromwell/services/womtool/models/MetaValueElementJsonSupport.scala
@@ -9,7 +9,7 @@ object MetaValueElementJsonSupport {
 
   // We only implement the encoder, because currently, the decoder is not required.
   implicit val metaValueElementEncoder: Encoder[MetaValueElement] = new Encoder[MetaValueElement] {
-    final def apply(a : MetaValueElement) : Json = {
+    final def apply(a: MetaValueElement): Json =
       a match {
         case MetaValueElementNull =>
           Json.Null
@@ -30,10 +30,9 @@ object MetaValueElementJsonSupport {
           Json.fromValues(vec.map(apply))
 
         case MetaValueElementObject(m) =>
-          Json.fromFields(m.map{ case (key, value) =>
-                            key -> apply(value)
-                          })
+          Json.fromFields(m.map { case (key, value) =>
+            key -> apply(value)
+          })
       }
-    }
   }
 }
diff --git a/services/src/main/scala/cromwell/services/womtool/models/OutputDescription.scala b/services/src/main/scala/cromwell/services/womtool/models/OutputDescription.scala
index 255efee4df8..fcf520c5a6d 100644
--- a/services/src/main/scala/cromwell/services/womtool/models/OutputDescription.scala
+++ b/services/src/main/scala/cromwell/services/womtool/models/OutputDescription.scala
@@ -4,5 +4,5 @@ import cromwell.services.womtool.models.WomTypeJsonSupport.womTypeEncoder // Int
 import io.circe.generic.JsonCodec
 import wom.types.WomType
 
-@JsonCodec(encodeOnly=true)
+@JsonCodec(encodeOnly = true)
 case class OutputDescription(name: String, valueType: WomType, typeDisplayName: String)
diff --git a/services/src/main/scala/cromwell/services/womtool/models/WomTypeJsonSupport.scala b/services/src/main/scala/cromwell/services/womtool/models/WomTypeJsonSupport.scala
index 2bf4211a3b9..b8816383188 100644
--- a/services/src/main/scala/cromwell/services/womtool/models/WomTypeJsonSupport.scala
+++ b/services/src/main/scala/cromwell/services/womtool/models/WomTypeJsonSupport.scala
@@ -8,26 +8,26 @@ object WomTypeJsonSupport {
   // We use `wom.types.WomType.callCachingName` instead of `wom.types.WomType.displayName` here because
   // the type hierarchy is designed for machine readability and should similarly be stable.
   implicit val womTypeEncoder: Encoder[WomType] = new Encoder[WomType] {
-    final def apply(a: WomType): Json = {
+    final def apply(a: WomType): Json =
       a match {
         case a: WomMapType =>
           Json.obj(
             ("typeName", Json.fromString("Map")),
             ("mapType",
-              Json.obj(
-                ("keyType", womTypeEncoder.apply(a.keyType)),
-                ("valueType", womTypeEncoder.apply(a.valueType))
-              )
+             Json.obj(
+               ("keyType", womTypeEncoder.apply(a.keyType)),
+               ("valueType", womTypeEncoder.apply(a.valueType))
+             )
             )
           )
         case a: WomPairType =>
           Json.obj(
             ("typeName", Json.fromString("Pair")),
             ("pairType",
-              Json.obj(
-                ("leftType", womTypeEncoder.apply(a.leftType)),
-                ("rightType", womTypeEncoder.apply(a.rightType))
-              )
+             Json.obj(
+               ("leftType", womTypeEncoder.apply(a.leftType)),
+               ("rightType", womTypeEncoder.apply(a.rightType))
+             )
             )
           )
         case a: WomArrayType =>
@@ -39,14 +39,16 @@ object WomTypeJsonSupport {
         case a: WomCompositeType =>
           Json.obj(
             ("typeName", Json.fromString("Object")),
-            ("objectFieldTypes", Json.fromValues(
-              a.typeMap map { entry =>
-                Json.obj(
-                  ("fieldName", Json.fromString(entry._1)),
-                  ("fieldType", womTypeEncoder.apply(entry._2))
-                )
-              }
-            ))
+            ("objectFieldTypes",
+             Json.fromValues(
+               a.typeMap map { entry =>
+                 Json.obj(
+                   ("fieldName", Json.fromString(entry._1)),
+                   ("fieldType", womTypeEncoder.apply(entry._2))
+                 )
+               }
+             )
+            )
           )
         case a: WomOptionalType =>
           Json.obj(
@@ -58,7 +60,6 @@ object WomTypeJsonSupport {
             ("typeName", Json.fromString(a.stableName))
           )
       }
-    }
   }
 
 }
diff --git a/services/src/main/scala/cromwell/services/womtool/models/WorkflowDescription.scala b/services/src/main/scala/cromwell/services/womtool/models/WorkflowDescription.scala
index bea99387388..44e19dd758b 100644
--- a/services/src/main/scala/cromwell/services/womtool/models/WorkflowDescription.scala
+++ b/services/src/main/scala/cromwell/services/womtool/models/WorkflowDescription.scala
@@ -9,31 +9,34 @@ import wom.executable.WomBundle
 
 import MetaValueElementJsonSupport._
 
-case class WorkflowDescription( valid: Boolean,
-                                errors: List[String],
-                                validWorkflow: Boolean,
-                                name: String,
-                                inputs: List[InputDescription],
-                                outputs: List[OutputDescription],
-                                images: List[String],
-                                submittedDescriptorType: Map[String, String],
-                                importedDescriptorTypes: List[Map[String, String]],
-                                meta: Map[String, MetaValueElement],
-                                parameterMeta: Map[String, MetaValueElement],
-                                isRunnableWorkflow: Boolean)
+case class WorkflowDescription(valid: Boolean,
+                               errors: List[String],
+                               validWorkflow: Boolean,
+                               name: String,
+                               inputs: List[InputDescription],
+                               outputs: List[OutputDescription],
+                               images: List[String],
+                               submittedDescriptorType: Map[String, String],
+                               importedDescriptorTypes: List[Map[String, String]],
+                               meta: Map[String, MetaValueElement],
+                               parameterMeta: Map[String, MetaValueElement],
+                               isRunnableWorkflow: Boolean
+)
 
 case object WorkflowDescription {
 
-  def withErrors(errors: List[String], submittedDescriptorType: Map[String, String]): WorkflowDescription = {
+  def withErrors(errors: List[String], submittedDescriptorType: Map[String, String]): WorkflowDescription =
     WorkflowDescription(
       valid = false,
       errors = errors,
       validWorkflow = false,
       submittedDescriptorType = submittedDescriptorType
     )
-  }
 
-  def fromBundle(bundle: WomBundle, submittedDescriptorType: Map[String, String], inputErrors: List[String] = List.empty): WorkflowDescription = {
+  def fromBundle(bundle: WomBundle,
+                 submittedDescriptorType: Map[String, String],
+                 inputErrors: List[String] = List.empty
+  ): WorkflowDescription = {
 
     val images: List[String] = bundle.allCallables.values.toList flatMap { callable: Callable =>
       callable match {
@@ -51,31 +54,72 @@ case object WorkflowDescription {
 
       // There is a primary callable in the form of a workflow
       case (_, Some(primaryCallable: WorkflowDefinition)) =>
-        fromBundleInner(inputErrors, primaryCallable.name, submittedDescriptorType, primaryCallable.inputs, primaryCallable.outputs, primaryCallable.meta, primaryCallable.parameterMeta, images, isRunnableWorkflow = true)
+        fromBundleInner(
+          inputErrors,
+          primaryCallable.name,
+          submittedDescriptorType,
+          primaryCallable.inputs,
+          primaryCallable.outputs,
+          primaryCallable.meta,
+          primaryCallable.parameterMeta,
+          images,
+          isRunnableWorkflow = true
+        )
 
       // There is a primary callable in the form of a task
       case (_, Some(primaryCallable: CallableTaskDefinition)) =>
-        fromBundleInner(inputErrors, primaryCallable.name, submittedDescriptorType, primaryCallable.inputs, primaryCallable.outputs, primaryCallable.meta, primaryCallable.parameterMeta, images, isRunnableWorkflow = false)
+        fromBundleInner(
+          inputErrors,
+          primaryCallable.name,
+          submittedDescriptorType,
+          primaryCallable.inputs,
+          primaryCallable.outputs,
+          primaryCallable.meta,
+          primaryCallable.parameterMeta,
+          images,
+          isRunnableWorkflow = false
+        )
 
       // WDL draft-2: a solo task is not primary, but we should still use its name and IO
       case ((soloNonPrimaryTask: CallableTaskDefinition) :: Nil, None) =>
-        fromBundleInner(inputErrors, soloNonPrimaryTask.name, submittedDescriptorType, soloNonPrimaryTask.inputs, soloNonPrimaryTask.outputs, soloNonPrimaryTask.meta, soloNonPrimaryTask.parameterMeta, images, isRunnableWorkflow = false)
+        fromBundleInner(
+          inputErrors,
+          soloNonPrimaryTask.name,
+          submittedDescriptorType,
+          soloNonPrimaryTask.inputs,
+          soloNonPrimaryTask.outputs,
+          soloNonPrimaryTask.meta,
+          soloNonPrimaryTask.parameterMeta,
+          images,
+          isRunnableWorkflow = false
+        )
 
       // Multiple tasks
       case _ =>
-        fromBundleInner(inputErrors, "", submittedDescriptorType, List.empty, List.empty, Map.empty, Map.empty, images, isRunnableWorkflow = false)
+        fromBundleInner(inputErrors,
+                        "",
+                        submittedDescriptorType,
+                        List.empty,
+                        List.empty,
+                        Map.empty,
+                        Map.empty,
+                        images,
+                        isRunnableWorkflow = false
+        )
     }
   }
 
   private def fromBundleInner(
-                               inputErrors: List[String],
-                               name: String, submittedDescriptorType: Map[String, String],
-                               inputs: List[InputDefinition], outputs: List[OutputDefinition],
-                               meta: Map[String, MetaValueElement],
-                               parameterMeta: Map[String, MetaValueElement],
-                               images: List[String],
-                               isRunnableWorkflow: Boolean
-                             ): WorkflowDescription = {
+    inputErrors: List[String],
+    name: String,
+    submittedDescriptorType: Map[String, String],
+    inputs: List[InputDefinition],
+    outputs: List[OutputDefinition],
+    meta: Map[String, MetaValueElement],
+    parameterMeta: Map[String, MetaValueElement],
+    images: List[String],
+    isRunnableWorkflow: Boolean
+  ): WorkflowDescription = {
     val inputDescriptions = inputs.sortBy(_.name) map { input: InputDefinition =>
       input match {
         case i: InputDefinitionWithDefault =>
@@ -133,21 +177,30 @@ case object WorkflowDescription {
             importedDescriptorTypes: List[Map[String, String]] = List.empty,
             meta: Map[String, MetaValueElement] = Map.empty,
             parameterMeta: Map[String, MetaValueElement] = Map.empty,
-            isRunnableWorkflow: Boolean = false): WorkflowDescription = {
-    new WorkflowDescription(valid, errors, validWorkflow, name, inputs, outputs, images, submittedDescriptorType, importedDescriptorTypes, meta, parameterMeta, isRunnableWorkflow)
-  }
+            isRunnableWorkflow: Boolean = false
+  ): WorkflowDescription =
+    new WorkflowDescription(valid,
+                            errors,
+                            validWorkflow,
+                            name,
+                            inputs,
+                            outputs,
+                            images,
+                            submittedDescriptorType,
+                            importedDescriptorTypes,
+                            meta,
+                            parameterMeta,
+                            isRunnableWorkflow
+    )
 
   implicit val workflowDescriptionEncoder: Encoder[WorkflowDescription] = deriveEncoder[WorkflowDescription]
 
   // We need this decoder to exist for `responseAs[WorkflowDescription]` to work in `cromwell.webservice.routes.WomtoolRouteSupportSpec`
   // That test only inspects some fields in the JSON, so this works adequately for now.
-  implicit val workflowDescriptionDecoder: Decoder[WorkflowDescription] = (c: HCursor) => {
+  implicit val workflowDescriptionDecoder: Decoder[WorkflowDescription] = (c: HCursor) =>
     for {
       valid <- c.downField("valid").as[Boolean]
       errors <- c.downField("errors").as[List[String]]
       validWorkflow <- c.downField("validWorkflow").as[Boolean]
-    } yield {
-      WorkflowDescription(valid = valid, errors = errors, validWorkflow = validWorkflow)
-    }
-  }
+    } yield WorkflowDescription(valid = valid, errors = errors, validWorkflow = validWorkflow)
 }
diff --git a/services/src/test/scala/cromwell/services/IoActorRequesterSpec.scala b/services/src/test/scala/cromwell/services/IoActorRequesterSpec.scala
index d76e38c1fa0..93211d44666 100644
--- a/services/src/test/scala/cromwell/services/IoActorRequesterSpec.scala
+++ b/services/src/test/scala/cromwell/services/IoActorRequesterSpec.scala
@@ -21,7 +21,9 @@ class IoActorRequesterSpec extends TestKitSuite with ImplicitSender with AnyFlat
   it should "Allow actors to request and receive a reference to the IO Actor" in {
     val serviceRegistry = TestProbe()
     val ioActor = TestProbe()
-    val requester = TestActorRef[SimpleIoActorRequester](simpleIoActorRequesterProps(serviceRegistry.ref), "simple-io-requester-request-receive")
+    val requester = TestActorRef[SimpleIoActorRequester](simpleIoActorRequesterProps(serviceRegistry.ref),
+                                                         "simple-io-requester-request-receive"
+    )
 
     serviceRegistry.expectMsg(RequestIoActorRef)
     serviceRegistry.lastSender ! IoActorRef(ioActor.ref)
@@ -36,7 +38,9 @@ class IoActorRequesterSpec extends TestKitSuite with ImplicitSender with AnyFlat
   it should "keep asking if the IoActor is not available immediately" in {
     val serviceRegistry = TestProbe()
     val ioActor = TestProbe()
-    val requester = TestActorRef[SimpleIoActorRequester](simpleIoActorRequesterProps(serviceRegistry.ref), "simple-io-requester-not-ready-resilience")
+    val requester = TestActorRef[SimpleIoActorRequester](simpleIoActorRequesterProps(serviceRegistry.ref),
+                                                         "simple-io-requester-not-ready-resilience"
+    )
 
     10.times {
       serviceRegistry.expectMsg(RequestIoActorRef)
@@ -55,14 +59,17 @@ class IoActorRequesterSpec extends TestKitSuite with ImplicitSender with AnyFlat
 
   it should "fail if the IoActorRequest receives an unexpected response" in {
     val serviceRegistry = TestProbe()
-    val requester = TestActorRef[SimpleIoActorRequester](simpleIoActorRequesterProps(serviceRegistry.ref), "simple-io-requester-not-ready-resilience")
+    val requester = TestActorRef[SimpleIoActorRequester](simpleIoActorRequesterProps(serviceRegistry.ref),
+                                                         "simple-io-requester-not-ready-resilience"
+    )
 
     serviceRegistry.expectMsg(RequestIoActorRef)
     serviceRegistry.lastSender ! "!!!Bad Response!!!"
 
     eventually {
       requester.underlyingActor.ioActor.value match {
-        case Some(Failure(exception)) => exception.getMessage should startWith("Programmer Error: Unexpected response to a RequestIoActor message")
+        case Some(Failure(exception)) =>
+          exception.getMessage should startWith("Programmer Error: Unexpected response to a RequestIoActor message")
         case Some(Success(other)) => fail(s"Expected the IoActor ref to be empty, but got: $other")
         case None => fail("No IoActor received")
       }
@@ -77,10 +84,12 @@ object IoActorRequesterSpec {
 
     val ioActor: Future[ActorRef] = requestIoActor(backoffInterval = 10.millis)
 
-    override def receive: Receive = {
-      case other => throw new RuntimeException(s"Didn't expect a message but got: $other")
+    override def receive: Receive = { case other =>
+      throw new RuntimeException(s"Didn't expect a message but got: $other")
     }
   }
 
-  def simpleIoActorRequesterProps(serviceRegistryActor: ActorRef): Props = Props(new SimpleIoActorRequester(serviceRegistryActor))
+  def simpleIoActorRequesterProps(serviceRegistryActor: ActorRef): Props = Props(
+    new SimpleIoActorRequester(serviceRegistryActor)
+  )
 }
diff --git a/services/src/test/scala/cromwell/services/NooPServiceActor.scala b/services/src/test/scala/cromwell/services/NooPServiceActor.scala
index 649ea0a3ebe..dedfeeead73 100644
--- a/services/src/test/scala/cromwell/services/NooPServiceActor.scala
+++ b/services/src/test/scala/cromwell/services/NooPServiceActor.scala
@@ -5,7 +5,7 @@ import com.typesafe.config.Config
 import cromwell.util.GracefulShutdownHelper.ShutdownCommand
 
 class NooPServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef) extends Actor {
-  override def receive = {
-    case ShutdownCommand => context stop self
+  override def receive = { case ShutdownCommand =>
+    context stop self
   }
 }
diff --git a/services/src/test/scala/cromwell/services/ServiceRegistryActorSpec.scala b/services/src/test/scala/cromwell/services/ServiceRegistryActorSpec.scala
index ce639f89387..05d86ee680c 100644
--- a/services/src/test/scala/cromwell/services/ServiceRegistryActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/ServiceRegistryActorSpec.scala
@@ -1,6 +1,5 @@
 package cromwell.services
 
-
 import java.util.UUID
 
 import akka.actor.SupervisorStrategy.Stop
@@ -19,7 +18,6 @@ import org.scalatest.matchers.should.Matchers
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-
 abstract class EmptyActor extends Actor {
   override def receive: Receive = Actor.emptyBehavior
 }
@@ -67,8 +65,10 @@ object ServiceRegistryActorSpec {
          | $ServiceNameKey {
          |   class = "$ServiceClassKey"
          | }
-      """.stripMargin.replace(ServiceNameKey, serviceClass.serviceName)
-        .stripMargin.replace(ServiceClassKey, serviceClass.getCanonicalName)
+      """.stripMargin
+        .replace(ServiceNameKey, serviceClass.serviceName)
+        .stripMargin
+        .replace(ServiceClassKey, serviceClass.getCanonicalName)
   }
 
   val AwaitTimeout: FiniteDuration = 5 seconds
@@ -97,18 +97,17 @@ class ServiceRegistryActorSpec extends TestKitSuite with AnyFlatSpecLike with Ma
     system.actorOf(
       props = Props(new EmptyActor {
         context.actorOf(ServiceRegistryActor.props(config), s"ServiceRegistryActor-$uuid")
-        override val supervisorStrategy: SupervisorStrategy = OneForOneStrategy() {
-          case f => parentProbe.ref ! f; Stop
+        override val supervisorStrategy: SupervisorStrategy = OneForOneStrategy() { case f =>
+          parentProbe.ref ! f; Stop
         }
       }),
-      name = s"childActor-$uuid",
+      name = s"childActor-$uuid"
     )
     parentProbe
   }
 
-  private def buildServiceRegistry(config: Config): ActorRef = {
+  private def buildServiceRegistry(config: Config): ActorRef =
     system.actorOf(ServiceRegistryActor.props(config), s"ServiceRegistryActor-${UUID.randomUUID()}")
-  }
 
   behavior of "ServiceRegistryActorSpec"
 
@@ -121,10 +120,9 @@ class ServiceRegistryActorSpec extends TestKitSuite with AnyFlatSpecLike with Ma
     val configString = buildConfig(classOf[FooServiceActor])
     val missingServices = configString.replace("  services ", "  shmervices")
     val probe = buildProbeForInitializationException(ConfigFactory.parseString(missingServices))
-    probe.expectMsgPF(AwaitTimeout) {
-      case e: ActorInitializationException =>
-        e.getCause shouldBe a [ConfigException.Missing]
-        e.getCause.getMessage shouldBe "String: 1: No configuration setting found for key 'services'"
+    probe.expectMsgPF(AwaitTimeout) { case e: ActorInitializationException =>
+      e.getCause shouldBe a[ConfigException.Missing]
+      e.getCause.getMessage shouldBe "String: 1: No configuration setting found for key 'services'"
     }
   }
 
@@ -132,24 +130,24 @@ class ServiceRegistryActorSpec extends TestKitSuite with AnyFlatSpecLike with Ma
     val configString = buildConfig(classOf[FooServiceActor])
     val missingService = configString.replace("FooServiceActor", "FooWhoServiceActor")
     val probe = buildProbeForInitializationException(ConfigFactory.parseString(missingService))
-    probe.expectMsgPF(AwaitTimeout) {
-      case e: ActorInitializationException =>
-        // The class not found exception is wrapped in a Runtime Exception giving the name of the faulty service
-        val cause = e.getCause
-        cause shouldBe a [RuntimeException] 
-        val classNotFound = cause.getCause
-        classNotFound shouldBe a [ClassNotFoundException]
-        classNotFound.getMessage shouldBe "cromwell.services.FooWhoServiceActor"
+    probe.expectMsgPF(AwaitTimeout) { case e: ActorInitializationException =>
+      // The class not found exception is wrapped in a Runtime Exception giving the name of the faulty service
+      val cause = e.getCause
+      cause shouldBe a[RuntimeException]
+      val classNotFound = cause.getCause
+      classNotFound shouldBe a[ClassNotFoundException]
+      classNotFound.getMessage shouldBe "cromwell.services.FooWhoServiceActor"
     }
   }
 
   it should "die during construction if a service class lacks a proper constructor" in {
     val configString = buildConfig(classOf[NoAppropriateConstructorServiceActor])
     val probe = buildProbeForInitializationException(ConfigFactory.parseString(configString))
-    probe.expectMsgPF(AwaitTimeout) {
-      case e: ActorInitializationException =>
-        e.getCause shouldBe an [IllegalArgumentException]
-        e.getCause.getMessage should include("no matching constructor found on class cromwell.services.NoAppropriateConstructorServiceActor")
+    probe.expectMsgPF(AwaitTimeout) { case e: ActorInitializationException =>
+      e.getCause shouldBe an[IllegalArgumentException]
+      e.getCause.getMessage should include(
+        "no matching constructor found on class cromwell.services.NoAppropriateConstructorServiceActor"
+      )
     }
   }
 
@@ -157,10 +155,9 @@ class ServiceRegistryActorSpec extends TestKitSuite with AnyFlatSpecLike with Ma
     val configString = buildConfig(classOf[FooServiceActor])
     val missingService = configString.replace("class = \"cromwell.services.FooServiceActor\"", "")
     val probe = buildProbeForInitializationException(ConfigFactory.parseString(missingService))
-    probe.expectMsgPF(AwaitTimeout) {
-      case e: ActorInitializationException =>
-        e.getCause shouldBe an [IllegalArgumentException]
-        e.getCause.getMessage shouldBe "Invalid configuration for service Foo: missing 'class' definition"
+    probe.expectMsgPF(AwaitTimeout) { case e: ActorInitializationException =>
+      e.getCause shouldBe an[IllegalArgumentException]
+      e.getCause.getMessage shouldBe "Invalid configuration for service Foo: missing 'class' definition"
     }
   }
 
@@ -171,9 +168,8 @@ class ServiceRegistryActorSpec extends TestKitSuite with AnyFlatSpecLike with Ma
 
     service.tell("This is a String, not an appropriate ServiceRegistryActor message", probe.ref)
 
-    probe.expectMsgPF(AwaitTimeout) {
-      case e: ServiceRegistryFailure =>
-        e.serviceName should include("Message is not a ServiceRegistryMessage:")
+    probe.expectMsgPF(AwaitTimeout) { case e: ServiceRegistryFailure =>
+      e.serviceName should include("Message is not a ServiceRegistryMessage:")
     }
   }
 
@@ -185,9 +181,8 @@ class ServiceRegistryActorSpec extends TestKitSuite with AnyFlatSpecLike with Ma
 
     service.tell(ArbitraryBarMessage, probe.ref)
 
-    probe.expectMsgPF(AwaitTimeout) {
-      case e: ServiceRegistryFailure =>
-        e.serviceName shouldBe "Bar"
+    probe.expectMsgPF(AwaitTimeout) { case e: ServiceRegistryFailure =>
+      e.serviceName shouldBe "Bar"
     }
   }
 
@@ -204,7 +199,7 @@ class ServiceRegistryActorSpec extends TestKitSuite with AnyFlatSpecLike with Ma
       case x => fail("unexpected message: " + x)
     }
   }
-  
+
   it should "unpack ListenTo messages" in {
     val snd = TestProbe("snd").ref
     val configString = buildConfig(classOf[BarServiceActor])
diff --git a/services/src/test/scala/cromwell/services/ServicesSpec.scala b/services/src/test/scala/cromwell/services/ServicesSpec.scala
index 364d2e26bf6..ef7423ab34d 100644
--- a/services/src/test/scala/cromwell/services/ServicesSpec.scala
+++ b/services/src/test/scala/cromwell/services/ServicesSpec.scala
@@ -70,8 +70,7 @@ object ServicesSpec {
   val config: Config = ConfigFactory.parseString(ServicesSpec.configString)
 }
 
-abstract class ServicesSpec extends TestKitSuite
-  with Matchers with AnyWordSpecLike with ScalaFutures {
+abstract class ServicesSpec extends TestKitSuite with Matchers with AnyWordSpecLike with ScalaFutures {
 
   override protected lazy val actorSystemConfig: Config = ServicesSpec.config
   implicit val timeout: Timeout = Timeout(60.seconds.dilated)
diff --git a/services/src/test/scala/cromwell/services/database/ConnectionMetadata.scala b/services/src/test/scala/cromwell/services/database/ConnectionMetadata.scala
index 0ba8478ad4a..5f788ba2f9b 100644
--- a/services/src/test/scala/cromwell/services/database/ConnectionMetadata.scala
+++ b/services/src/test/scala/cromwell/services/database/ConnectionMetadata.scala
@@ -3,8 +3,7 @@ package cromwell.services.database
 /**
   * Metadata from the JDBC connection and driver.
   */
-case class ConnectionMetadata
-(
+case class ConnectionMetadata(
   databaseProductName: String,
   databaseProductVersion: String,
   databaseMajorVersion: Int,
@@ -14,5 +13,5 @@ case class ConnectionMetadata
   driverMajorVersion: Int,
   driverMinorVersion: Int,
   jdbcMajorVersion: Int,
-  jdbcMinorVersion: Int,
+  jdbcMinorVersion: Int
 )
diff --git a/services/src/test/scala/cromwell/services/database/CromwellDatabaseType.scala b/services/src/test/scala/cromwell/services/database/CromwellDatabaseType.scala
index 8a8ede69e19..97d1851c79a 100644
--- a/services/src/test/scala/cromwell/services/database/CromwellDatabaseType.scala
+++ b/services/src/test/scala/cromwell/services/database/CromwellDatabaseType.scala
@@ -20,7 +20,7 @@ sealed trait CromwellDatabaseType[T <: SlickDatabase] {
 object CromwellDatabaseType {
   val All: Seq[CromwellDatabaseType[_ <: SlickDatabase]] = List(
     EngineDatabaseType,
-    MetadataDatabaseType,
+    MetadataDatabaseType
   )
 }
 
@@ -28,16 +28,14 @@ object EngineDatabaseType extends CromwellDatabaseType[EngineSlickDatabase] {
   override val name: String = "Engine"
   override val liquibaseSettings: LiquibaseSettings = EngineServicesStore.EngineLiquibaseSettings
 
-  override def newDatabase(config: Config): EngineSlickDatabase with TestSlickDatabase = {
+  override def newDatabase(config: Config): EngineSlickDatabase with TestSlickDatabase =
     new EngineSlickDatabase(config) with TestSlickDatabase
-  }
 }
 
 object MetadataDatabaseType extends CromwellDatabaseType[MetadataSlickDatabase] {
   override val name: String = "Metadata"
   override val liquibaseSettings: LiquibaseSettings = MetadataServicesStore.MetadataLiquibaseSettings
 
-  override def newDatabase(config: Config): MetadataSlickDatabase with TestSlickDatabase = {
+  override def newDatabase(config: Config): MetadataSlickDatabase with TestSlickDatabase =
     new MetadataSlickDatabase(config) with TestSlickDatabase
-  }
 }
diff --git a/services/src/test/scala/cromwell/services/database/DatabaseSystem.scala b/services/src/test/scala/cromwell/services/database/DatabaseSystem.scala
index 8add5869502..490c7823c20 100644
--- a/services/src/test/scala/cromwell/services/database/DatabaseSystem.scala
+++ b/services/src/test/scala/cromwell/services/database/DatabaseSystem.scala
@@ -19,7 +19,7 @@ object DatabaseSystem {
     MysqlEarliestDatabaseSystem,
     MysqlLatestDatabaseSystem,
     PostgresqlEarliestDatabaseSystem,
-    PostgresqlLatestDatabaseSystem,
+    PostgresqlLatestDatabaseSystem
   )
 }
 
diff --git a/services/src/test/scala/cromwell/services/database/DatabaseTestKit.scala b/services/src/test/scala/cromwell/services/database/DatabaseTestKit.scala
index 651248b70cd..5ca41bc15bc 100644
--- a/services/src/test/scala/cromwell/services/database/DatabaseTestKit.scala
+++ b/services/src/test/scala/cromwell/services/database/DatabaseTestKit.scala
@@ -33,15 +33,15 @@ object DatabaseTestKit extends StrictLogging {
     * @tparam A       The return type of the block.
     * @return The return value of the block.
     */
-  def withConnection[Profile <: JdbcProfile, A](profile: Profile, database: Profile#Backend#Database)
-                                               (block: Connection => A): A = {
+  def withConnection[Profile <: JdbcProfile, A](profile: Profile, database: Profile#Backend#Database)(
+    block: Connection => A
+  ): A =
     /*
      TODO: Should this withConnection() method have a (implicit?) timeout parameter, that it passes on to Await.result?
      If we run completely asynchronously, nest calls to withConnection, and then call flatMap, the outer connection may
      already be closed before an inner block finishes running.
      */
     Await.result(database.run(profile.api.SimpleDBIO(context => block(context.connection))), Duration.Inf)
-  }
 
   /**
     * Lends two connections to a block of code.
@@ -56,15 +56,16 @@ object DatabaseTestKit extends StrictLogging {
     * @tparam A        The return type of the block.
     * @return The return value of the block.
     */
-  def withConnections[Profile1 <: JdbcProfile, Profile2 <: JdbcProfile, A]
-  (profile1: Profile1, database1: Profile1#Backend#Database, profile2: Profile2, database2: Profile2#Backend#Database)
-  (block: (Connection, Connection) => A): A = {
+  def withConnections[Profile1 <: JdbcProfile, Profile2 <: JdbcProfile, A](profile1: Profile1,
+                                                                           database1: Profile1#Backend#Database,
+                                                                           profile2: Profile2,
+                                                                           database2: Profile2#Backend#Database
+  )(block: (Connection, Connection) => A): A =
     withConnection(profile1, database1) { connection1 =>
       withConnection(profile2, database2) { connection2 =>
         block(connection1, connection2)
       }
     }
-  }
 
   /**
     * Creates a new in memory HSQLDB that should be closed after use.
@@ -83,7 +84,8 @@ object DatabaseTestKit extends StrictLogging {
     * Opens an initialized database.
     */
   def initializedDatabaseFromConfig[A <: SlickDatabase](databaseType: CromwellDatabaseType[A],
-                                                        databaseConfig: Config): A with TestSlickDatabase = {
+                                                        databaseConfig: Config
+  ): A with TestSlickDatabase = {
     val database = databaseType.newDatabase(databaseConfig)
     database.initialized(databaseType.liquibaseSettings)
   }
@@ -92,21 +94,23 @@ object DatabaseTestKit extends StrictLogging {
     * Opens an initialized database.
     */
   def initializedDatabaseFromSystem[A <: SlickDatabase](databaseType: CromwellDatabaseType[A],
-                                                        databaseSystem: DatabaseSystem): A with TestSlickDatabase = {
+                                                        databaseSystem: DatabaseSystem
+  ): A with TestSlickDatabase =
     initializeDatabaseByContainerOptTypeAndSystem(None, databaseType, databaseSystem)
-  }
 
   /**
    * Opens a database connection without any liquibase being performed.
    */
-  def schemalessDatabaseFromContainerOptAndSystem(containerOpt: Option[Container], databaseSystem: DatabaseSystem): SchemalessSlickDatabase with TestSlickDatabase = {
+  def schemalessDatabaseFromContainerOptAndSystem(containerOpt: Option[Container],
+                                                  databaseSystem: DatabaseSystem
+  ): SchemalessSlickDatabase with TestSlickDatabase =
     containerOpt match {
       case None => new SchemalessSlickDatabase(getConfig(databaseSystem, dbContainerOpt = None)) with TestSlickDatabase
       case Some(cont) if cont.isInstanceOf[JdbcDatabaseContainer] =>
-        new SchemalessSlickDatabase(getConfig(databaseSystem, Option(cont.asInstanceOf[JdbcDatabaseContainer]))) with TestSlickDatabase
+        new SchemalessSlickDatabase(getConfig(databaseSystem, Option(cont.asInstanceOf[JdbcDatabaseContainer])))
+          with TestSlickDatabase
       case Some(_) => throw new RuntimeException("ERROR: container is not a JdbcDatabaseContainer.")
     }
-  }
 
   def getDatabaseTestContainer(databaseSystem: DatabaseSystem): Option[Container] = {
     val containerOption: Option[SingleContainer[_ <: JavaJdbcDatabaseContainer[_]]] = databaseSystem match {
@@ -114,24 +118,32 @@ object DatabaseTestKit extends StrictLogging {
       case networkDbSystem: NetworkDatabaseSystem =>
         networkDbSystem.platform match {
           case MariadbDatabasePlatform =>
-            Option(MariaDBContainer(
-              dockerImageName = DockerImageName.parse(s"mariadb:${networkDbSystem.dockerImageVersion}"),
-              dbName = "cromwell_test",
-              dbUsername = "cromwell",
-              dbPassword = "test"
-            ))
+            Option(
+              MariaDBContainer(
+                dockerImageName = DockerImageName.parse(s"mariadb:${networkDbSystem.dockerImageVersion}"),
+                dbName = "cromwell_test",
+                dbUsername = "cromwell",
+                dbPassword = "test"
+              )
+            )
           case MysqlDatabasePlatform =>
-            Option(MySQLContainer(
-              mysqlImageVersion = DockerImageName.parse(s"mysql:${networkDbSystem.dockerImageVersion}"),
-              databaseName = "cromwell_test",
-              username = "cromwell",
-              password = "test"))
+            Option(
+              MySQLContainer(
+                mysqlImageVersion = DockerImageName.parse(s"mysql:${networkDbSystem.dockerImageVersion}"),
+                databaseName = "cromwell_test",
+                username = "cromwell",
+                password = "test"
+              )
+            )
           case PostgresqlDatabasePlatform =>
-            Option(PostgreSQLContainer(
-              dockerImageNameOverride = DockerImageName.parse(s"postgres:${networkDbSystem.dockerImageVersion}"),
-              databaseName = "cromwell_test",
-              username = "cromwell",
-              password = "test"))
+            Option(
+              PostgreSQLContainer(
+                dockerImageNameOverride = DockerImageName.parse(s"postgres:${networkDbSystem.dockerImageVersion}"),
+                databaseName = "cromwell_test",
+                username = "cromwell",
+                password = "test"
+              )
+            )
           case _ => None
         }
     }
@@ -145,22 +157,28 @@ object DatabaseTestKit extends StrictLogging {
 
   def initializeDatabaseByContainerOptTypeAndSystem[A <: SlickDatabase](containerOpt: Option[Container],
                                                                         databaseType: CromwellDatabaseType[A],
-                                                                        databaseSystem: DatabaseSystem): A with TestSlickDatabase = {
+                                                                        databaseSystem: DatabaseSystem
+  ): A with TestSlickDatabase =
     containerOpt match {
       case None => initializedDatabaseFromConfig(databaseType, getConfig(databaseSystem, None))
       case Some(cont) if cont.isInstanceOf[JdbcDatabaseContainer] =>
-        initializedDatabaseFromConfig(databaseType, getConfig(databaseSystem, Option(cont.asInstanceOf[JdbcDatabaseContainer])))
+        initializedDatabaseFromConfig(databaseType,
+                                      getConfig(databaseSystem, Option(cont.asInstanceOf[JdbcDatabaseContainer]))
+        )
       case Some(_) => throw new RuntimeException("ERROR: container is not a JdbcDatabaseContainer.")
     }
-  }
 
-  def getConfig(databaseSystem: DatabaseSystem, dbContainerOpt: Option[JdbcDatabaseContainer] = None): Config = {
+  def getConfig(databaseSystem: DatabaseSystem, dbContainerOpt: Option[JdbcDatabaseContainer] = None): Config =
     dbContainerOpt match {
       case None if databaseSystem == HsqldbDatabaseSystem => hsqldbDatabaseConfig
-      case None => throw new RuntimeException("ERROR: dbContainer option must be passed into `getConfig` method for all databases except HSQLDB.")
+      case None =>
+        throw new RuntimeException(
+          "ERROR: dbContainer option must be passed into `getConfig` method for all databases except HSQLDB."
+        )
       case Some(dbContainer) =>
         val (slickProfile, jdbcDriver) = databaseSystem.platform match {
-          case HsqldbDatabasePlatform => throw new RuntimeException("ERROR: dbContainer option cannot be defined for HSQLDB database.")
+          case HsqldbDatabasePlatform =>
+            throw new RuntimeException("ERROR: dbContainer option cannot be defined for HSQLDB database.")
           case MariadbDatabasePlatform => ("slick.jdbc.MySQLProfile$", "org.mariadb.jdbc.Driver")
           case MysqlDatabasePlatform => ("slick.jdbc.MySQLProfile$", "com.mysql.cj.jdbc.Driver")
           case PostgresqlDatabasePlatform => ("slick.jdbc.PostgresProfile$", "org.postgresql.Driver")
@@ -177,7 +195,6 @@ object DatabaseTestKit extends StrictLogging {
               |""".stripMargin
         )
     }
-  }
 
   /**
     * Run liquibase on a open database.
@@ -193,68 +210,61 @@ object DatabaseTestKit extends StrictLogging {
   /**
     * Returns a Liquibase snapshot of an open Slick database.
     */
-  def liquibaseSnapshot(database: SlickDatabase): DatabaseSnapshot = {
+  def liquibaseSnapshot(database: SlickDatabase): DatabaseSnapshot =
     withConnection(database.dataAccess.driver, database.database)(LiquibaseUtils.getSnapshot)
-  }
 
   /**
     * Returns the database connection metadata for an open Slick database.
     */
-  def connectionMetadata(database: SlickDatabase): ConnectionMetadata = {
-    withConnection(database.dataAccess.driver, database.database) {
-      connection =>
-        val metadata = connection.getMetaData
-        ConnectionMetadata(
-          databaseProductName = metadata.getDatabaseProductName,
-          databaseProductVersion = metadata.getDatabaseProductVersion,
-          databaseMajorVersion = metadata.getDatabaseMajorVersion,
-          databaseMinorVersion = metadata.getDatabaseMinorVersion,
-          driverName = metadata.getDriverName,
-          driverVersion = metadata.getDriverVersion,
-          driverMajorVersion = metadata.getDriverMajorVersion,
-          driverMinorVersion = metadata.getDriverMinorVersion,
-          jdbcMajorVersion = metadata.getJDBCMajorVersion,
-          jdbcMinorVersion = metadata.getJDBCMinorVersion,
-        )
+  def connectionMetadata(database: SlickDatabase): ConnectionMetadata =
+    withConnection(database.dataAccess.driver, database.database) { connection =>
+      val metadata = connection.getMetaData
+      ConnectionMetadata(
+        databaseProductName = metadata.getDatabaseProductName,
+        databaseProductVersion = metadata.getDatabaseProductVersion,
+        databaseMajorVersion = metadata.getDatabaseMajorVersion,
+        databaseMinorVersion = metadata.getDatabaseMinorVersion,
+        driverName = metadata.getDriverName,
+        driverVersion = metadata.getDriverVersion,
+        driverMajorVersion = metadata.getDriverMajorVersion,
+        driverMinorVersion = metadata.getDriverMinorVersion,
+        jdbcMajorVersion = metadata.getJDBCMajorVersion,
+        jdbcMinorVersion = metadata.getJDBCMinorVersion
+      )
     }
-  }
 
   /**
     * Returns a Liquibase snapshot of an in memory HSQLDB.
     */
   def inMemorySnapshot[A <: SlickDatabase](databaseType: CromwellDatabaseType[A],
-                       schemaManager: SchemaManager): DatabaseSnapshot = {
+                                           schemaManager: SchemaManager
+  ): DatabaseSnapshot = {
     var snapshot: DatabaseSnapshot = null
     for {
       database <- inMemoryDatabase(databaseType, schemaManager).autoClosed
-    } {
-      snapshot = liquibaseSnapshot(database)
     }
+      snapshot = liquibaseSnapshot(database)
     snapshot
   }
 
   /**
     * Returns true if the primary key was auto generated by the database.
     */
-  def isGenerated(primaryKey: MPrimaryKey): Boolean = {
+  def isGenerated(primaryKey: MPrimaryKey): Boolean =
     isGenerated(primaryKey.pkName.get)
-  }
 
   /**
     * Returns true if the index was auto generated by the database.
     */
-  def isGenerated(index: MIndexInfo): Boolean = {
+  def isGenerated(index: MIndexInfo): Boolean =
     isGenerated(index.indexName.get)
-  }
 
   /**
     * Returns true if the index was auto generated by the database.
     */
-  def isGenerated(index: Index): Boolean = {
+  def isGenerated(index: Index): Boolean =
     isGenerated(index.getName)
-  }
 
-  private def isGenerated(name: String): Boolean = {
+  private def isGenerated(name: String): Boolean =
     name.startsWith("SYS_")
-  }
 }
diff --git a/services/src/test/scala/cromwell/services/database/HsqldbTransactionIsolationSpec.scala b/services/src/test/scala/cromwell/services/database/HsqldbTransactionIsolationSpec.scala
index affca45d5b4..1bd8b0312f3 100644
--- a/services/src/test/scala/cromwell/services/database/HsqldbTransactionIsolationSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/HsqldbTransactionIsolationSpec.scala
@@ -14,7 +14,12 @@ import org.scalatest.matchers.should.Matchers
   * http://www.hsqldb.org/doc/guide/sessions-chapt.html#snc_tx_mvcc
   * https://en.wikipedia.org/wiki/Multiversion_concurrency_control
   */
-class HsqldbTransactionIsolationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalaFutures with StringNormalizations {
+class HsqldbTransactionIsolationSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalaFutures
+    with StringNormalizations {
 
   CromwellDatabaseType.All foreach { databaseType =>
     behavior of s"HSQLDB transaction isolation for ${databaseType.name}"
@@ -24,7 +29,7 @@ class HsqldbTransactionIsolationSpec extends AnyFlatSpec with CromwellTimeoutSpe
         slickDatabase <- DatabaseTestKit.initializedDatabaseFromSystem(databaseType, HsqldbDatabaseSystem).autoClosed
       } {
         import slickDatabase.dataAccess.driver.api._
-        //noinspection SqlDialectInspection
+        // noinspection SqlDialectInspection
         val getHsqldbTx =
           sql"""SELECT PROPERTY_VALUE
                 FROM INFORMATION_SCHEMA.SYSTEM_PROPERTIES
@@ -32,7 +37,7 @@ class HsqldbTransactionIsolationSpec extends AnyFlatSpec with CromwellTimeoutSpe
              """.as[String].head
 
         val future = slickDatabase.database.run(getHsqldbTx)
-        (future.futureValue shouldEqual "mvcc") (after being lowerCased)
+        (future.futureValue shouldEqual "mvcc")(after being lowerCased)
       }
     }
   }
diff --git a/services/src/test/scala/cromwell/services/database/LiquibaseChangeSetSpec.scala b/services/src/test/scala/cromwell/services/database/LiquibaseChangeSetSpec.scala
index 3943fb65423..0db3e34bff9 100644
--- a/services/src/test/scala/cromwell/services/database/LiquibaseChangeSetSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/LiquibaseChangeSetSpec.scala
@@ -32,7 +32,7 @@ class LiquibaseChangeSetSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
         withClue("the dbms attribute must explicitly list supported databases:") {
           changeSet.getDbmsSet shouldNot be(null)
           changeSet.getDbmsSet shouldNot be(empty)
-          changeSet.getDbmsSet shouldNot contain atLeastOneOf("none", "all")
+          changeSet.getDbmsSet shouldNot contain atLeastOneOf ("none", "all")
         }
         changeSet.getDbmsSet.asScala foreach { dbms =>
           withClue("do not use dbms excludes:") {
@@ -44,7 +44,7 @@ class LiquibaseChangeSetSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
       if (dbmsSet.contains("postgresql")) {
         it should s"check object quoting in $description" in {
           withClue("""databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS" must be set for PostgreSQL:""") {
-            changeSet.getObjectQuotingStrategy should be (ObjectQuotingStrategy.QUOTE_ALL_OBJECTS)
+            changeSet.getObjectQuotingStrategy should be(ObjectQuotingStrategy.QUOTE_ALL_OBJECTS)
           }
         }
       }
diff --git a/services/src/test/scala/cromwell/services/database/LiquibaseComparisonSpec.scala b/services/src/test/scala/cromwell/services/database/LiquibaseComparisonSpec.scala
index 255237b396f..c0cbd5383a0 100644
--- a/services/src/test/scala/cromwell/services/database/LiquibaseComparisonSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/LiquibaseComparisonSpec.scala
@@ -31,7 +31,6 @@ class LiquibaseComparisonSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     PatienceConfig(timeout = scaled(5.seconds), interval = scaled(100.millis))
 
   CromwellDatabaseType.All foreach { databaseType =>
-
     lazy val expectedSnapshot = DatabaseTestKit.inMemorySnapshot(databaseType, SlickSchemaManager)
     lazy val expectedColumns = get[Column](expectedSnapshot).sorted
     lazy val expectedPrimaryKeys = get[PrimaryKey](expectedSnapshot).sorted
@@ -40,12 +39,12 @@ class LiquibaseComparisonSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     lazy val expectedIndexes = get[Index](expectedSnapshot) filterNot DatabaseTestKit.isGenerated
 
     DatabaseSystem.All foreach { databaseSystem =>
-
       behavior of s"Liquibase Comparison for ${databaseType.name} ${databaseSystem.name}"
 
       val containerOpt: Option[Container] = DatabaseTestKit.getDatabaseTestContainer(databaseSystem)
 
-      lazy val liquibasedDatabase = DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, databaseType, databaseSystem)
+      lazy val liquibasedDatabase =
+        DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, databaseType, databaseSystem)
 
       lazy val connectionMetadata = DatabaseTestKit.connectionMetadata(liquibasedDatabase)
 
@@ -59,7 +58,7 @@ class LiquibaseComparisonSpec extends AnyFlatSpec with CromwellTimeoutSpec with
       lazy val columnMapping = getColumnMapping(databaseSystem)
 
       it should "start container if required" taggedAs DbmsTest in {
-        containerOpt.foreach { _.start }
+        containerOpt.foreach(_.start)
       }
 
       expectedColumns foreach { expectedColumn =>
@@ -71,9 +70,11 @@ class LiquibaseComparisonSpec extends AnyFlatSpec with CromwellTimeoutSpec with
           }
           val actualColumn = actualColumnOption getOrElse fail(s"Did not find $description")
 
-          withClue(s"for type " +
-            s"${actualColumn.getType.getTypeName}(default = ${actualColumn.getDefaultValue}) vs. " +
-            s"${expectedColumn.getType.getTypeName}(default = ${expectedColumn.getDefaultValue}):") {
+          withClue(
+            s"for type " +
+              s"${actualColumn.getType.getTypeName}(default = ${actualColumn.getDefaultValue}) vs. " +
+              s"${expectedColumn.getType.getTypeName}(default = ${expectedColumn.getDefaultValue}):"
+          ) {
 
             val actualColumnType = ColumnType.from(actualColumn)
 
@@ -98,7 +99,7 @@ class LiquibaseComparisonSpec extends AnyFlatSpec with CromwellTimeoutSpec with
                   None,
                   Option(DefaultNullBoolean),
                   Option(DefaultNullString),
-                  Option(DefaultNullFunction),
+                  Option(DefaultNullFunction)
                 )
                 List(Option(actualColumn.getDefaultValue)) should contain atLeastOneElementOf expectedOptions
               } else {
@@ -129,7 +130,7 @@ class LiquibaseComparisonSpec extends AnyFlatSpec with CromwellTimeoutSpec with
             val expectedSequenceTypeOption = sequenceTypeValidationOption(
               expectedColumn,
               databaseSystem,
-              connectionMetadata,
+              connectionMetadata
             )
             expectedSequenceTypeOption foreach { expectedSequenceType =>
               val dbio = sequenceTypeDbio(expectedColumn, databaseSystem, liquibasedDatabase)
@@ -225,14 +226,14 @@ class LiquibaseComparisonSpec extends AnyFlatSpec with CromwellTimeoutSpec with
       }
 
       it should "stop container if required" taggedAs DbmsTest in {
-        containerOpt.foreach { _.stop() }
+        containerOpt.foreach(_.stop())
       }
     }
   }
 }
 
 object LiquibaseComparisonSpec {
-  private def get[T <: DatabaseObject : ClassTag : Ordering](databaseSnapshot: DatabaseSnapshot): Seq[T] = {
+  private def get[T <: DatabaseObject: ClassTag: Ordering](databaseSnapshot: DatabaseSnapshot): Seq[T] = {
     val databaseObjectClass = classTag[T].runtimeClass.asInstanceOf[Class[T]]
     databaseSnapshot.get(databaseObjectClass).asScala.toSeq
   }
@@ -241,49 +242,42 @@ object LiquibaseComparisonSpec {
   private val DefaultNullString = "NULL"
   private val DefaultNullFunction = new DatabaseFunction(DefaultNullString)
 
-  private def isSlickDefaultNull(column: Column): Boolean = {
+  private def isSlickDefaultNull(column: Column): Boolean =
     Option(column.getDefaultValue).isEmpty || column.getDefaultValue == DefaultNullFunction
-  }
 
   case class ColumnDescription(tableName: String, columnName: String)
 
   object ColumnDescription {
-    def from(column: Column): ColumnDescription = {
+    def from(column: Column): ColumnDescription =
       ColumnDescription(column.getRelation.getName, column.getName)
-    }
   }
 
-  case class ColumnType
-  (
+  case class ColumnType(
     typeName: String,
-    sizeOption: Option[Int] = None,
+    sizeOption: Option[Int] = None
   )
 
   object ColumnType {
-    def from(column: Column): ColumnType = {
+    def from(column: Column): ColumnType =
       ColumnType(
         column.getType.getTypeName.toUpperCase,
-        Option(column.getType.getColumnSize).map(_.toInt),
+        Option(column.getType.getColumnSize).map(_.toInt)
       )
-    }
   }
 
-  case class ColumnDefault
-  (
+  case class ColumnDefault(
     columnType: ColumnType,
-    defaultValue: AnyRef,
+    defaultValue: AnyRef
   )
 
   object ColumnDefault {
-    def from(column: Column): ColumnDefault = {
+    def from(column: Column): ColumnDefault =
       ColumnDefault(ColumnType.from(column), column.getDefaultValue)
-    }
   }
 
-  case class ColumnMapping
-  (
+  case class ColumnMapping(
     typeMapping: PartialFunction[ColumnType, ColumnType] = PartialFunction.empty,
-    defaultMapping: Map[ColumnDefault, AnyRef] = Map.empty,
+    defaultMapping: Map[ColumnDefault, AnyRef] = Map.empty
   )
 
   /** Generate the expected PostgreSQL sequence name for a column. */
@@ -294,7 +288,7 @@ object LiquibaseComparisonSpec {
     // Postgres cuts of the length of names around this length
     val Count = 30
 
-    def shorten(name: String, isColumn: Boolean): String = {
+    def shorten(name: String, isColumn: Boolean): String =
       pad {
         // NOTE: Table and column name truncation seems slightly different.
         // This logic was empirically derived. Feel free to modify/simplify!
@@ -306,7 +300,6 @@ object LiquibaseComparisonSpec {
           name.take(Count - 1)
         }
       }
-    }
 
     val tableName = shorten(column.getRelation.getName, isColumn = false)
     val columnName = shorten(column.getName, isColumn = true)
@@ -330,19 +323,19 @@ object LiquibaseComparisonSpec {
   // Note: BIT vs. TINYINT may be yet another tabs vs. spaces
   // https://stackoverflow.com/questions/11167793/boolean-or-tinyint-confusion/17298805
   private val MysqldbColumnMapping =
-  ColumnMapping(
-    typeMapping = Map(
-      HsqldbTypeBigInt -> ColumnType("BIGINT", Option(19)),
-      HsqldbTypeBlob -> ColumnType("LONGBLOB", Option(2147483647)),
-      HsqldbTypeBoolean -> ColumnType("TINYINT", Option(3)),
-      HsqldbTypeClob -> ColumnType("LONGTEXT", Option(2147483647)),
-      HsqldbTypeInteger -> ColumnType("INT", Option(10)),
-      HsqldbTypeTimestamp -> ColumnType("DATETIME"),
-    ),
-    defaultMapping = Map(
-      HsqldbDefaultBooleanTrue -> Int.box(1)
-    ),
-  )
+    ColumnMapping(
+      typeMapping = Map(
+        HsqldbTypeBigInt -> ColumnType("BIGINT", Option(19)),
+        HsqldbTypeBlob -> ColumnType("LONGBLOB", Option(2147483647)),
+        HsqldbTypeBoolean -> ColumnType("TINYINT", Option(3)),
+        HsqldbTypeClob -> ColumnType("LONGTEXT", Option(2147483647)),
+        HsqldbTypeInteger -> ColumnType("INT", Option(10)),
+        HsqldbTypeTimestamp -> ColumnType("DATETIME")
+      ),
+      defaultMapping = Map(
+        HsqldbDefaultBooleanTrue -> Int.box(1)
+      )
+    )
 
   // MariaDB should behave similar to MySQL except that only LOBs have sizes
   private val MariadbColumnMapping =
@@ -353,11 +346,11 @@ object LiquibaseComparisonSpec {
         HsqldbTypeBoolean -> ColumnType("TINYINT"),
         HsqldbTypeClob -> ColumnType("LONGTEXT", Option(2147483647)),
         HsqldbTypeInteger -> ColumnType("INT"),
-        HsqldbTypeTimestamp -> ColumnType("DATETIME"),
+        HsqldbTypeTimestamp -> ColumnType("DATETIME")
       ),
       defaultMapping = Map(
-        HsqldbDefaultBooleanTrue -> Int.box(1),
-      ),
+        HsqldbDefaultBooleanTrue -> Int.box(1)
+      )
     )
 
   private val PostgresqlColumnMapping =
@@ -367,21 +360,20 @@ object LiquibaseComparisonSpec {
         HsqldbTypeBlob -> ColumnType("OID", None),
         HsqldbTypeBoolean -> ColumnType("BOOL", None),
         HsqldbTypeClob -> ColumnType("TEXT", None),
-        HsqldbTypeInteger -> ColumnType("INT4", None),
-      ),
+        HsqldbTypeInteger -> ColumnType("INT4", None)
+      )
     )
 
   /**
     * Returns the column mapping for the DBMS.
     */
-  private def getColumnMapping(databaseSystem: DatabaseSystem): ColumnMapping = {
+  private def getColumnMapping(databaseSystem: DatabaseSystem): ColumnMapping =
     databaseSystem.platform match {
       case HsqldbDatabasePlatform => HsqldbColumnMapping
       case MariadbDatabasePlatform => MariadbColumnMapping
       case MysqlDatabasePlatform => MysqldbColumnMapping
       case PostgresqlDatabasePlatform => PostgresqlColumnMapping
     }
-  }
 
   /**
     * Returns the column type, possibly mapped via the ColumnMapping.
@@ -394,9 +386,8 @@ object LiquibaseComparisonSpec {
   /**
     * Returns the default for the column, either from ColumnMapping or the column itself.
     */
-  private def getColumnDefault(column: Column, columnMapping: ColumnMapping): AnyRef = {
+  private def getColumnDefault(column: Column, columnMapping: ColumnMapping): AnyRef =
     columnMapping.defaultMapping.getOrElse(ColumnDefault.from(column), column.getDefaultValue)
-  }
 
   /**
     * Return the default for the auto increment column.
@@ -404,8 +395,8 @@ object LiquibaseComparisonSpec {
   private def getAutoIncrementDefault(column: Column,
                                       columnMapping: ColumnMapping,
                                       databaseSystem: DatabaseSystem,
-                                      connectionMetadata: ConnectionMetadata,
-                                     ): ColumnDefault = {
+                                      connectionMetadata: ConnectionMetadata
+  ): ColumnDefault =
     databaseSystem.platform match {
       case PostgresqlDatabasePlatform if connectionMetadata.databaseMajorVersion <= 9 =>
         val columnType = column.getType.getTypeName match {
@@ -416,7 +407,6 @@ object LiquibaseComparisonSpec {
         ColumnDefault(columnType, columnDefault)
       case _ => ColumnDefault(getColumnType(column, columnMapping), column.getDefaultValue)
     }
-  }
 
   /**
     * Returns an optional extra check to ensure that datetimes can store microseconds.
@@ -436,23 +426,23 @@ object LiquibaseComparisonSpec {
     *
     * This check also has to be done here, as Liquibase does not return the precision for Mysql datetime fields.
     */
-  private def columnTypeValidationOption(column: Column, databaseSystem: DatabaseSystem): Option[String] = {
+  private def columnTypeValidationOption(column: Column, databaseSystem: DatabaseSystem): Option[String] =
     databaseSystem.platform match {
       case MysqlDatabasePlatform | MariadbDatabasePlatform if column.getType.getTypeName == "TIMESTAMP" =>
         Option("datetime(6)")
       case _ => None
     }
-  }
 
   private def columnTypeDbio(column: Column,
                              databaseSystem: DatabaseSystem,
-                             database: SlickDatabase): database.dataAccess.driver.api.DBIO[String] = {
+                             database: SlickDatabase
+  ): database.dataAccess.driver.api.DBIO[String] = {
     import database.dataAccess.driver.api._
     databaseSystem.platform match {
       case MysqlDatabasePlatform | MariadbDatabasePlatform if column.getType.getTypeName == "TIMESTAMP" =>
         val getType = GetResult(_.rs.getString("Type"))
 
-        //noinspection SqlDialectInspection
+        // noinspection SqlDialectInspection
         sql"""SHOW COLUMNS
               FROM #${column.getRelation.getName}
               WHERE FIELD = '#${column.getName}'
@@ -472,23 +462,23 @@ object LiquibaseComparisonSpec {
     */
   private def sequenceTypeValidationOption(column: Column,
                                            databaseSystem: DatabaseSystem,
-                                           connectionMetadata: ConnectionMetadata,
-                                          ): Option[String] = {
+                                           connectionMetadata: ConnectionMetadata
+  ): Option[String] =
     databaseSystem.platform match {
       case PostgresqlDatabasePlatform if column.isAutoIncrement && connectionMetadata.databaseMajorVersion <= 9 =>
         // "this is currently always bigint" --> https://www.postgresql.org/docs/9.6/infoschema-sequences.html
         Option("bigint")
       case _ => None
     }
-  }
 
   private def sequenceTypeDbio(column: Column,
                                databaseSystem: DatabaseSystem,
-                               database: SlickDatabase): database.dataAccess.driver.api.DBIO[String] = {
+                               database: SlickDatabase
+  ): database.dataAccess.driver.api.DBIO[String] = {
     import database.dataAccess.driver.api._
     databaseSystem.platform match {
       case PostgresqlDatabasePlatform if column.isAutoIncrement =>
-        //noinspection SqlDialectInspection
+        // noinspection SqlDialectInspection
         sql"""select data_type
               from INFORMATION_SCHEMA.sequences
               where sequence_name = '#${postgresqlSeqName(column)}'
@@ -498,11 +488,11 @@ object LiquibaseComparisonSpec {
   }
 
   private def unsupportedColumnTypeException(column: Column,
-                                             databaseSystem: DatabaseSystem): UnsupportedOperationException = {
+                                             databaseSystem: DatabaseSystem
+  ): UnsupportedOperationException =
     new UnsupportedOperationException(
       s"${databaseSystem.name} ${column.getRelation.getName}.${column.getName}: ${column.getType.getTypeName}"
     )
-  }
 
   /**
     * Returns columns that are nullable, but shouldn't be.
@@ -512,7 +502,8 @@ object LiquibaseComparisonSpec {
     * TODO: make a changelog to fix, and then remove list of mistakes.
     */
   private def getNullTodos(databaseSystem: DatabaseSystem,
-                           databaseType: CromwellDatabaseType[_ <: SlickDatabase]): Seq[ColumnDescription] = {
+                           databaseType: CromwellDatabaseType[_ <: SlickDatabase]
+  ): Seq[ColumnDescription] =
     (databaseSystem.platform, databaseType) match {
       case (MysqlDatabasePlatform, EngineDatabaseType) =>
         List(
@@ -538,16 +529,15 @@ object LiquibaseComparisonSpec {
           ColumnDescription("JOB_STORE_SIMPLETON_ENTRY", "JOB_STORE_ENTRY_ID"),
           ColumnDescription("WORKFLOW_STORE_ENTRY", "IMPORTS_ZIP"),
           ColumnDescription("WORKFLOW_STORE_ENTRY", "WORKFLOW_EXECUTION_UUID"),
-          ColumnDescription("WORKFLOW_STORE_ENTRY", "WORKFLOW_STATE"),
+          ColumnDescription("WORKFLOW_STORE_ENTRY", "WORKFLOW_STATE")
         )
       case (MysqlDatabasePlatform, MetadataDatabaseType) =>
         List(
           ColumnDescription("CUSTOM_LABEL_ENTRY", "CUSTOM_LABEL_KEY"),
           ColumnDescription("CUSTOM_LABEL_ENTRY", "CUSTOM_LABEL_VALUE"),
           ColumnDescription("SUMMARY_STATUS_ENTRY", "SUMMARY_NAME"),
-          ColumnDescription("SUMMARY_STATUS_ENTRY", "SUMMARY_POSITION"),
+          ColumnDescription("SUMMARY_STATUS_ENTRY", "SUMMARY_POSITION")
         )
       case _ => Nil
     }
-  }
 }
diff --git a/services/src/test/scala/cromwell/services/database/LiquibaseOrdering.scala b/services/src/test/scala/cromwell/services/database/LiquibaseOrdering.scala
index 43ca64ee796..26d3885e003 100644
--- a/services/src/test/scala/cromwell/services/database/LiquibaseOrdering.scala
+++ b/services/src/test/scala/cromwell/services/database/LiquibaseOrdering.scala
@@ -15,9 +15,8 @@ object LiquibaseOrdering {
 
   implicit val liquibaseOrderingForeignKey: Ordering[ForeignKey] = Ordering.by[ForeignKey, String](_.getName)
 
-  implicit val liquibaseOrderingUniqueConstraint: Ordering[UniqueConstraint] = {
+  implicit val liquibaseOrderingUniqueConstraint: Ordering[UniqueConstraint] =
     Ordering.by[UniqueConstraint, String](_.getName)
-  }
 
   implicit val liquibaseOrderingIndex: Ordering[Index] = Ordering.by[Index, String](_.getName)
 }
diff --git a/services/src/test/scala/cromwell/services/database/LobSpec.scala b/services/src/test/scala/cromwell/services/database/LobSpec.scala
index eee252d31eb..2d140d24c81 100644
--- a/services/src/test/scala/cromwell/services/database/LobSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/LobSpec.scala
@@ -24,15 +24,15 @@ class LobSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with Sc
     PatienceConfig(timeout = scaled(5.seconds), interval = scaled(100.millis))
 
   DatabaseSystem.All foreach { databaseSystem =>
-
     behavior of s"CLOBs and BLOBs on ${databaseSystem.name}"
 
     val containerOpt: Option[Container] = DatabaseTestKit.getDatabaseTestContainer(databaseSystem)
 
-    lazy val database = DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, EngineDatabaseType, databaseSystem)
+    lazy val database =
+      DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, EngineDatabaseType, databaseSystem)
 
     it should "start container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.start }
+      containerOpt.foreach(_.start)
     }
 
     it should "store empty blobs" taggedAs DbmsTest in {
@@ -58,7 +58,7 @@ class LobSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with Sc
         submissionTime = OffsetDateTime.now.toSystemTimestamp,
         importsZip = Option(emptyBlob),
         customLabels = clob,
-        hogGroup = None,
+        hogGroup = None
       )
 
       val workflowStoreEntries = Seq(workflowStoreEntry)
@@ -122,7 +122,7 @@ class LobSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with Sc
         submissionTime = OffsetDateTime.now.toSystemTimestamp,
         importsZip = Option(Array.empty[Byte]).toBlobOption,
         customLabels = clob,
-        hogGroup = Option("abc-1"),
+        hogGroup = Option("abc-1")
       )
 
       val noneWorkflowUuid = WorkflowId.randomId().toString
@@ -141,7 +141,7 @@ class LobSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with Sc
         submissionTime = OffsetDateTime.now.toSystemTimestamp,
         importsZip = None,
         customLabels = clob,
-        hogGroup = Option("abc-1"),
+        hogGroup = Option("abc-1")
       )
 
       val aByte = 'a'.toByte
@@ -161,7 +161,7 @@ class LobSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with Sc
         submissionTime = OffsetDateTime.now.toSystemTimestamp,
         importsZip = Option(Array(aByte)).toBlobOption,
         customLabels = clob,
-        hogGroup = Option("abc-1"),
+        hogGroup = Option("abc-1")
       )
 
       val workflowStoreEntries = Seq(emptyWorkflowStoreEntry, noneWorkflowStoreEntry, aByteWorkflowStoreEntry)
@@ -201,7 +201,7 @@ class LobSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with Sc
     }
 
     it should "stop container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.stop() }
+      containerOpt.foreach(_.stop())
     }
   }
 }
diff --git a/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala b/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala
index 33dd2a73b66..7a914ba4a1b 100644
--- a/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/MetadataSlickDatabaseSpec.scala
@@ -24,20 +24,20 @@ import scala.language.postfixOps
 class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalaFutures {
 
   DatabaseSystem.All foreach { databaseSystem =>
-
     implicit val ec: ExecutionContextExecutor = ExecutionContext.global
 
     behavior of s"MetadataSlickDatabase on ${databaseSystem.name}"
 
     val containerOpt: Option[Container] = DatabaseTestKit.getDatabaseTestContainer(databaseSystem)
 
-    lazy val database = DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, MetadataDatabaseType, databaseSystem)
+    lazy val database =
+      DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, MetadataDatabaseType, databaseSystem)
     import cromwell.database.migration.metadata.table.symbol.MetadataStatement.OffsetDateTimeToSystemTimestamp
     import database.dataAccess.driver.api._
     val now = OffsetDateTime.now().toSystemTimestamp
 
     it should "start container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.start }
+      containerOpt.foreach(_.start)
     }
 
     val rootCountableId = "root workflow id: countable stuff"
@@ -59,87 +59,494 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val stdErrValue = Option(new SerialClob("test value".toCharArray()))
 
     it should "set up the test data" taggedAs DbmsTest in {
-      database.runTestTransaction(
-        database.dataAccess.metadataEntries ++= Seq(
-          MetadataEntry("workflow id: 4 to delete, including 1 label", None, None, None, "someKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry("workflow id: 4 to delete, including 1 label", None, None, None, "someKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry("workflow id: 4 to delete, including 1 label", None, None, None, "someKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry("workflow id: 4 to delete, including 1 label", None, None, None, "labels:do delete me", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-
-          MetadataEntry("workflow id: I am a root workflow with a subworkflow", None, None, None, "labels:do delete me", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry("workflow id: I am a root workflow with a subworkflow", None, None, None, "please do delete me", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry("workflow id: I am the subworkflow", None, None, None, "labels:do delete me", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry("workflow id: I am the subworkflow", None, None, None, "please do delete me", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-
-          MetadataEntry("nested subworkflows: root", None, None, None, "please do delete me", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry("nested subworkflows: first nesting", None, None, None, "please do delete me", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry("nested subworkflows: second nesting", None, None, None, "please do delete me", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry("nested subworkflows: third nesting", None, None, None, "please do delete me", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-
-          // Workflow level
-          MetadataEntry(rootCountableId, None, None, None, "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(rootCountableId, None, None, None, "excludableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          // Call level
-          MetadataEntry(rootCountableId, Option("includableCall"), Option(0), Option(1), "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(rootCountableId, Option("includableCall"), Option(0), Option(1), "excludableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          //   Excludable call index
-          MetadataEntry(rootCountableId, Option("includableCall"), Option(1), Option(1), "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          //   Excludable call attempt
-          MetadataEntry(rootCountableId, Option("includableCall"), Option(0), Option(2), "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(rootCountableId, Option("excludableCall"), Option(0), Option(1), "whateverKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-
-          // Subworkflow level
-          MetadataEntry(subWorkflowCountableId, None, None, None, "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(subWorkflowCountableId, None, None, None, "excludableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          // Call level
-          MetadataEntry(subWorkflowCountableId, Option("includableCall"), Option(0), Option(1), "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(subWorkflowCountableId, Option("includableCall"), Option(0), Option(1), "excludableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          //   Excludable call index
-          MetadataEntry(subWorkflowCountableId, Option("includableCall"), Option(1), Option(1), "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          //   Excludable call attempt
-          MetadataEntry(subWorkflowCountableId, Option("includableCall"), Option(0), Option(2), "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(subWorkflowCountableId, Option("excludableCall"), Option(0), Option(1), "whateverKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-
-          // Subsubworkflow level
-          MetadataEntry(subSubWorkflowCountableId, None, None, None, "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(subSubWorkflowCountableId, None, None, None, "excludableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          // Call level
-          MetadataEntry(subSubWorkflowCountableId, Option("includableCall"), Option(0), Option(1), "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(subSubWorkflowCountableId, Option("includableCall"), Option(0), Option(1), "excludableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          //   Excludable call index
-          MetadataEntry(subSubWorkflowCountableId, Option("includableCall"), Option(1), Option(1), "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          //   Excludable call attempt
-          MetadataEntry(subSubWorkflowCountableId, Option("includableCall"), Option(0), Option(2), "includableKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(subSubWorkflowCountableId, Option("excludableCall"), Option(0), Option(1), "whateverKey", None, None, OffsetDateTime.now().toSystemTimestamp, None),
+      database
+        .runTestTransaction(
+          database.dataAccess.metadataEntries ++= Seq(
+            MetadataEntry("workflow id: 4 to delete, including 1 label",
+                          None,
+                          None,
+                          None,
+                          "someKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("workflow id: 4 to delete, including 1 label",
+                          None,
+                          None,
+                          None,
+                          "someKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("workflow id: 4 to delete, including 1 label",
+                          None,
+                          None,
+                          None,
+                          "someKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("workflow id: 4 to delete, including 1 label",
+                          None,
+                          None,
+                          None,
+                          "labels:do delete me",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("workflow id: I am a root workflow with a subworkflow",
+                          None,
+                          None,
+                          None,
+                          "labels:do delete me",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("workflow id: I am a root workflow with a subworkflow",
+                          None,
+                          None,
+                          None,
+                          "please do delete me",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("workflow id: I am the subworkflow",
+                          None,
+                          None,
+                          None,
+                          "labels:do delete me",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("workflow id: I am the subworkflow",
+                          None,
+                          None,
+                          None,
+                          "please do delete me",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("nested subworkflows: root",
+                          None,
+                          None,
+                          None,
+                          "please do delete me",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("nested subworkflows: first nesting",
+                          None,
+                          None,
+                          None,
+                          "please do delete me",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("nested subworkflows: second nesting",
+                          None,
+                          None,
+                          None,
+                          "please do delete me",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry("nested subworkflows: third nesting",
+                          None,
+                          None,
+                          None,
+                          "please do delete me",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+
+            // Workflow level
+            MetadataEntry(rootCountableId,
+                          None,
+                          None,
+                          None,
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry(rootCountableId,
+                          None,
+                          None,
+                          None,
+                          "excludableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            // Call level
+            MetadataEntry(rootCountableId,
+                          Option("includableCall"),
+                          Option(0),
+                          Option(1),
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry(rootCountableId,
+                          Option("includableCall"),
+                          Option(0),
+                          Option(1),
+                          "excludableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            //   Excludable call index
+            MetadataEntry(rootCountableId,
+                          Option("includableCall"),
+                          Option(1),
+                          Option(1),
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            //   Excludable call attempt
+            MetadataEntry(rootCountableId,
+                          Option("includableCall"),
+                          Option(0),
+                          Option(2),
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry(rootCountableId,
+                          Option("excludableCall"),
+                          Option(0),
+                          Option(1),
+                          "whateverKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+
+            // Subworkflow level
+            MetadataEntry(subWorkflowCountableId,
+                          None,
+                          None,
+                          None,
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry(subWorkflowCountableId,
+                          None,
+                          None,
+                          None,
+                          "excludableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            // Call level
+            MetadataEntry(subWorkflowCountableId,
+                          Option("includableCall"),
+                          Option(0),
+                          Option(1),
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry(subWorkflowCountableId,
+                          Option("includableCall"),
+                          Option(0),
+                          Option(1),
+                          "excludableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            //   Excludable call index
+            MetadataEntry(subWorkflowCountableId,
+                          Option("includableCall"),
+                          Option(1),
+                          Option(1),
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            //   Excludable call attempt
+            MetadataEntry(subWorkflowCountableId,
+                          Option("includableCall"),
+                          Option(0),
+                          Option(2),
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry(subWorkflowCountableId,
+                          Option("excludableCall"),
+                          Option(0),
+                          Option(1),
+                          "whateverKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+
+            // Subsubworkflow level
+            MetadataEntry(subSubWorkflowCountableId,
+                          None,
+                          None,
+                          None,
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry(subSubWorkflowCountableId,
+                          None,
+                          None,
+                          None,
+                          "excludableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            // Call level
+            MetadataEntry(subSubWorkflowCountableId,
+                          Option("includableCall"),
+                          Option(0),
+                          Option(1),
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry(subSubWorkflowCountableId,
+                          Option("includableCall"),
+                          Option(0),
+                          Option(1),
+                          "excludableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            //   Excludable call index
+            MetadataEntry(subSubWorkflowCountableId,
+                          Option("includableCall"),
+                          Option(1),
+                          Option(1),
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            //   Excludable call attempt
+            MetadataEntry(subSubWorkflowCountableId,
+                          Option("includableCall"),
+                          Option(0),
+                          Option(2),
+                          "includableKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            ),
+            MetadataEntry(subSubWorkflowCountableId,
+                          Option("excludableCall"),
+                          Option(0),
+                          Option(1),
+                          "whateverKey",
+                          None,
+                          None,
+                          OffsetDateTime.now().toSystemTimestamp,
+                          None
+            )
+          )
         )
-      ).futureValue(Timeout(10.seconds))
-
-      database.runTestTransaction(
-        database.dataAccess.workflowMetadataSummaryEntries ++= Seq(
-          WorkflowMetadataSummaryEntry("workflow id: 3 to delete, 1 label", Option("workflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), None, None, None, None),
-
-          WorkflowMetadataSummaryEntry("workflow id: I am a root workflow with a subworkflow", Option("workflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), None, None, None, None),
-          WorkflowMetadataSummaryEntry("workflow id: I am the subworkflow", Option("workflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), Option("workflow id: I am a root workflow with a subworkflow"), Option("workflow id: I am a root workflow with a subworkflow"), None, None),
-
-          WorkflowMetadataSummaryEntry("nested subworkflows: root", Option("workflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), None, None, None, None),
-          WorkflowMetadataSummaryEntry("nested subworkflows: first nesting", Option("workflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), Option("nested subworkflows: root"), Option("nested subworkflows: root"), None, None),
-          WorkflowMetadataSummaryEntry("nested subworkflows: second nesting", Option("workflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), Option("nested subworkflows: first nesting"), Option("nested subworkflows: root"), None, None),
-          WorkflowMetadataSummaryEntry("nested subworkflows: third nesting", Option("workflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), Option("nested subworkflows: second nesting"), Option("nested subworkflows: root"), None, None),
-
-          WorkflowMetadataSummaryEntry(rootCountableId, Option("workflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), None, None, None, None),
-          WorkflowMetadataSummaryEntry(subWorkflowCountableId, Option("subworkflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), Option(rootCountableId), Option(rootCountableId), None, None),
-          WorkflowMetadataSummaryEntry(subSubWorkflowCountableId, Option("subsubworkflow name"), Option("Succeeded"), Option(now), Option(now), Option(now), Option(subWorkflowCountableId), Option(rootCountableId), None, None),
+        .futureValue(Timeout(10.seconds))
+
+      database
+        .runTestTransaction(
+          database.dataAccess.workflowMetadataSummaryEntries ++= Seq(
+            WorkflowMetadataSummaryEntry("workflow id: 3 to delete, 1 label",
+                                         Option("workflow name"),
+                                         Option("Succeeded"),
+                                         Option(now),
+                                         Option(now),
+                                         Option(now),
+                                         None,
+                                         None,
+                                         None,
+                                         None
+            ),
+            WorkflowMetadataSummaryEntry(
+              "workflow id: I am a root workflow with a subworkflow",
+              Option("workflow name"),
+              Option("Succeeded"),
+              Option(now),
+              Option(now),
+              Option(now),
+              None,
+              None,
+              None,
+              None
+            ),
+            WorkflowMetadataSummaryEntry(
+              "workflow id: I am the subworkflow",
+              Option("workflow name"),
+              Option("Succeeded"),
+              Option(now),
+              Option(now),
+              Option(now),
+              Option("workflow id: I am a root workflow with a subworkflow"),
+              Option("workflow id: I am a root workflow with a subworkflow"),
+              None,
+              None
+            ),
+            WorkflowMetadataSummaryEntry("nested subworkflows: root",
+                                         Option("workflow name"),
+                                         Option("Succeeded"),
+                                         Option(now),
+                                         Option(now),
+                                         Option(now),
+                                         None,
+                                         None,
+                                         None,
+                                         None
+            ),
+            WorkflowMetadataSummaryEntry(
+              "nested subworkflows: first nesting",
+              Option("workflow name"),
+              Option("Succeeded"),
+              Option(now),
+              Option(now),
+              Option(now),
+              Option("nested subworkflows: root"),
+              Option("nested subworkflows: root"),
+              None,
+              None
+            ),
+            WorkflowMetadataSummaryEntry(
+              "nested subworkflows: second nesting",
+              Option("workflow name"),
+              Option("Succeeded"),
+              Option(now),
+              Option(now),
+              Option(now),
+              Option("nested subworkflows: first nesting"),
+              Option("nested subworkflows: root"),
+              None,
+              None
+            ),
+            WorkflowMetadataSummaryEntry(
+              "nested subworkflows: third nesting",
+              Option("workflow name"),
+              Option("Succeeded"),
+              Option(now),
+              Option(now),
+              Option(now),
+              Option("nested subworkflows: second nesting"),
+              Option("nested subworkflows: root"),
+              None,
+              None
+            ),
+            WorkflowMetadataSummaryEntry(rootCountableId,
+                                         Option("workflow name"),
+                                         Option("Succeeded"),
+                                         Option(now),
+                                         Option(now),
+                                         Option(now),
+                                         None,
+                                         None,
+                                         None,
+                                         None
+            ),
+            WorkflowMetadataSummaryEntry(
+              subWorkflowCountableId,
+              Option("subworkflow name"),
+              Option("Succeeded"),
+              Option(now),
+              Option(now),
+              Option(now),
+              Option(rootCountableId),
+              Option(rootCountableId),
+              None,
+              None
+            ),
+            WorkflowMetadataSummaryEntry(
+              subSubWorkflowCountableId,
+              Option("subsubworkflow name"),
+              Option("Succeeded"),
+              Option(now),
+              Option(now),
+              Option(now),
+              Option(subWorkflowCountableId),
+              Option(rootCountableId),
+              None,
+              None
+            )
+          )
         )
-      ).futureValue(Timeout(10.seconds))
+        .futureValue(Timeout(10.seconds))
     }
 
     it should "delete the right number of rows for a root workflow without subworkflows" taggedAs DbmsTest in {
-      val delete = database.deleteAllMetadataForWorkflowAndUpdateArchiveStatus("workflow id: 4 to delete, including 1 label", None)
+      val delete =
+        database.deleteAllMetadataForWorkflowAndUpdateArchiveStatus("workflow id: 4 to delete, including 1 label", None)
       delete.futureValue(Timeout(10.seconds)) should be(4)
     }
 
     it should "delete the right number of rows for a root workflow with subworkflows" taggedAs DbmsTest in {
-      val delete = database.deleteAllMetadataForWorkflowAndUpdateArchiveStatus("workflow id: I am a root workflow with a subworkflow", None)
+      val delete = database.deleteAllMetadataForWorkflowAndUpdateArchiveStatus(
+        "workflow id: I am a root workflow with a subworkflow",
+        None
+      )
       delete.futureValue(Timeout(10.seconds)) should be(2)
     }
 
@@ -153,23 +560,41 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
         val expansionFactor = if (expandSubWorkflows) 3 else 1;
         // Everything
         {
-          val count = database.countMetadataEntries(rootCountableId, expandSubWorkflows = expandSubWorkflows, 10 seconds)
+          val count =
+            database.countMetadataEntries(rootCountableId, expandSubWorkflows = expandSubWorkflows, 10 seconds)
           count.futureValue(Timeout(10.seconds)) should be(7 * expansionFactor)
         }
 
         // Only includable keys - this looks for workflow level data only
         {
-          val count = database.countMetadataEntries(rootCountableId, "includableKey", expandSubWorkflows = expandSubWorkflows, 10 seconds)
+          val count = database.countMetadataEntries(rootCountableId,
+                                                    "includableKey",
+                                                    expandSubWorkflows = expandSubWorkflows,
+                                                    10 seconds
+          )
           count.futureValue(Timeout(10.seconds)) should be(1 * expansionFactor)
         }
 
         {
-          val count = database.countMetadataEntries(rootCountableId, "includableCall", Option(0), Option(1), expandSubWorkflows = expandSubWorkflows, 10 seconds)
+          val count = database.countMetadataEntries(rootCountableId,
+                                                    "includableCall",
+                                                    Option(0),
+                                                    Option(1),
+                                                    expandSubWorkflows = expandSubWorkflows,
+                                                    10 seconds
+          )
           count.futureValue(Timeout(10 seconds)) should be(2 * expansionFactor)
         }
 
         {
-          val count = database.countMetadataEntries(rootCountableId, "includableKey", "includableCall", Option(0), Option(1), expandSubWorkflows = expandSubWorkflows, 10 seconds)
+          val count = database.countMetadataEntries(rootCountableId,
+                                                    "includableKey",
+                                                    "includableCall",
+                                                    Option(0),
+                                                    Option(1),
+                                                    expandSubWorkflows = expandSubWorkflows,
+                                                    10 seconds
+          )
           count.futureValue(Timeout(10 seconds)) should be(1 * expansionFactor)
         }
 
@@ -180,7 +605,8 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
             metadataKeysToFilterOut = List("excludable%"),
             CallQuery("includableCall", Option(0), Option(1)),
             expandSubWorkflows = expandSubWorkflows,
-            10 seconds)
+            10 seconds
+          )
           count.futureValue(Timeout(10 seconds)) should be(1 * expansionFactor)
         }
 
@@ -211,76 +637,465 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
 
     it should "fetch failed tasks from a failed workflow" taggedAs DbmsTest in {
-      database.runTestTransaction(
-        database.dataAccess.metadataEntries ++= Seq(
-          //Failed parent workflow calls (successful calls and older attempts and runs mixed in for negative checks)
-          MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(0), Option(0), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(0), Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(1), Option(0), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(1), Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedParentWorkflowId, Option("failedWorkflowCall"), Option(1), Option(1), "stderr", stdErrValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedParentWorkflowId, Option("successfulWorkflowCall"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedParentWorkflowId, Option("successfulSubWorkflowCall"), Option(0), Option(0), "subWorkflowId", Option(new SerialClob(failedChildWorkflowId.toCharArray)), Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-
-          //ignored failed workflow calls. These should not be fetched since it's not part of the target workflow tree
-          MetadataEntry(ignoredFailedParentWorkflowId, Option("failedWorkflowCall"), Option(0), Option(0), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(ignoredFailedChildWorkflowId, Option("failedSubWorkflowCall"), None, Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-
-          //child workflow calls (successful calls and previous failed attempts/shards are mixed in for negative checks)
-          //notFailedSubWorkflowCall should not be returned since it succeeded on the last attempt and has no scatters
-          MetadataEntry(failedChildWorkflowId, Option("notActuallyFailedSubWorkflowCall"), None, Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("notActuallyFailedSubWorkflowCall"), None, Option(2), "backendStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("notActuallyFailedSubWorkflowCall"), None, Option(2), "stderr", stdErrValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-
-          //Failed child workflow calls (successful calls and previous failed attempts/shards are mixed in for negative checks)
-          //failedSubWorkflowCall should be returned since it never succeeded
-          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall"), None, Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall"), None, Option(2), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall"), None, Option(2), "stderr", stdErrValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall2"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-
-          //Third set of child workflow calls, similar to above however this set consists of retries and scatters
-          //It's safe to assume that if one scatter fails then they all fail, so pull the last scatter on the last attempt
-          //failedSubWorkflowCall2 should return since the scatters failed on the last attempt
-          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(1), Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(2), Option(1), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(1), Option(2), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(2), Option(2), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("failedSubWorkflowCall2"), Option(2), Option(2), "stderr", stdErrValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall3"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-
-          //Fourth set of child workflow calls
-          //This set should not return anything since the scatters succeeded on the last attempt
-          MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(1), Option(1), "executionStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(2), Option(1), "backendStatus", failedStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(1), Option(2), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(2), Option(2), "backendStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("notActuallySubWorkflowCall2"), Option(2), Option(2), "stderr", stdErrValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(failedChildWorkflowId, Option("successfulSubWorkflowCall4"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-
-          //Successful parent workflow call (negative check)
-          MetadataEntry(successfulParentWorkflowId, Option("successfulWorkflowCall"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-
-          //Successful child workflow calls (negative check)
-          MetadataEntry(successfulChildWorkflowId, Option("successfulSubWorkflowCall"), Option(0), Option(0), "executionStatus", doneStatusMetadataValue, Option("String"), OffsetDateTime.now().toSystemTimestamp, None),
-          MetadataEntry(successfulChildWorkflowId, Option("successfulSubWorkflowCall"), Option(0), Option(0), "subWorkflowId", Option(new SerialClob(successfulParentWorkflowId.toCharArray)), Option("String"), OffsetDateTime.now().toSystemTimestamp, None)
+      database
+        .runTestTransaction(
+          database.dataAccess.metadataEntries ++= Seq(
+            // Failed parent workflow calls (successful calls and older attempts and runs mixed in for negative checks)
+            MetadataEntry(
+              failedParentWorkflowId,
+              Option("failedWorkflowCall"),
+              Option(0),
+              Option(0),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedParentWorkflowId,
+              Option("failedWorkflowCall"),
+              Option(0),
+              Option(1),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedParentWorkflowId,
+              Option("failedWorkflowCall"),
+              Option(1),
+              Option(0),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedParentWorkflowId,
+              Option("failedWorkflowCall"),
+              Option(1),
+              Option(1),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedParentWorkflowId,
+              Option("failedWorkflowCall"),
+              Option(1),
+              Option(1),
+              "stderr",
+              stdErrValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedParentWorkflowId,
+              Option("successfulWorkflowCall"),
+              Option(0),
+              Option(0),
+              "executionStatus",
+              doneStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedParentWorkflowId,
+              Option("successfulSubWorkflowCall"),
+              Option(0),
+              Option(0),
+              "subWorkflowId",
+              Option(new SerialClob(failedChildWorkflowId.toCharArray)),
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+
+            // ignored failed workflow calls. These should not be fetched since it's not part of the target workflow tree
+            MetadataEntry(
+              ignoredFailedParentWorkflowId,
+              Option("failedWorkflowCall"),
+              Option(0),
+              Option(0),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              ignoredFailedChildWorkflowId,
+              Option("failedSubWorkflowCall"),
+              None,
+              Option(1),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+
+            // child workflow calls (successful calls and previous failed attempts/shards are mixed in for negative checks)
+            // notFailedSubWorkflowCall should not be returned since it succeeded on the last attempt and has no scatters
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("notActuallyFailedSubWorkflowCall"),
+              None,
+              Option(1),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("notActuallyFailedSubWorkflowCall"),
+              None,
+              Option(2),
+              "backendStatus",
+              doneStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("notActuallyFailedSubWorkflowCall"),
+              None,
+              Option(2),
+              "stderr",
+              stdErrValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("successfulSubWorkflowCall"),
+              Option(0),
+              Option(0),
+              "executionStatus",
+              doneStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+
+            // Failed child workflow calls (successful calls and previous failed attempts/shards are mixed in for negative checks)
+            // failedSubWorkflowCall should be returned since it never succeeded
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("failedSubWorkflowCall"),
+              None,
+              Option(1),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("failedSubWorkflowCall"),
+              None,
+              Option(2),
+              "backendStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("failedSubWorkflowCall"),
+              None,
+              Option(2),
+              "stderr",
+              stdErrValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("successfulSubWorkflowCall2"),
+              Option(0),
+              Option(0),
+              "executionStatus",
+              doneStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+
+            // Third set of child workflow calls, similar to above however this set consists of retries and scatters
+            // It's safe to assume that if one scatter fails then they all fail, so pull the last scatter on the last attempt
+            // failedSubWorkflowCall2 should return since the scatters failed on the last attempt
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("failedSubWorkflowCall2"),
+              Option(1),
+              Option(1),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("failedSubWorkflowCall2"),
+              Option(2),
+              Option(1),
+              "backendStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("failedSubWorkflowCall2"),
+              Option(1),
+              Option(2),
+              "backendStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("failedSubWorkflowCall2"),
+              Option(2),
+              Option(2),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("failedSubWorkflowCall2"),
+              Option(2),
+              Option(2),
+              "stderr",
+              stdErrValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("successfulSubWorkflowCall3"),
+              Option(0),
+              Option(0),
+              "executionStatus",
+              doneStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+
+            // Fourth set of child workflow calls
+            // This set should not return anything since the scatters succeeded on the last attempt
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("notActuallySubWorkflowCall2"),
+              Option(1),
+              Option(1),
+              "executionStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("notActuallySubWorkflowCall2"),
+              Option(2),
+              Option(1),
+              "backendStatus",
+              failedStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("notActuallySubWorkflowCall2"),
+              Option(1),
+              Option(2),
+              "executionStatus",
+              doneStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("notActuallySubWorkflowCall2"),
+              Option(2),
+              Option(2),
+              "backendStatus",
+              doneStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("notActuallySubWorkflowCall2"),
+              Option(2),
+              Option(2),
+              "stderr",
+              stdErrValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              failedChildWorkflowId,
+              Option("successfulSubWorkflowCall4"),
+              Option(0),
+              Option(0),
+              "executionStatus",
+              doneStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+
+            // Successful parent workflow call (negative check)
+            MetadataEntry(
+              successfulParentWorkflowId,
+              Option("successfulWorkflowCall"),
+              Option(0),
+              Option(0),
+              "executionStatus",
+              doneStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+
+            // Successful child workflow calls (negative check)
+            MetadataEntry(
+              successfulChildWorkflowId,
+              Option("successfulSubWorkflowCall"),
+              Option(0),
+              Option(0),
+              "executionStatus",
+              doneStatusMetadataValue,
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            ),
+            MetadataEntry(
+              successfulChildWorkflowId,
+              Option("successfulSubWorkflowCall"),
+              Option(0),
+              Option(0),
+              "subWorkflowId",
+              Option(new SerialClob(successfulParentWorkflowId.toCharArray)),
+              Option("String"),
+              OffsetDateTime.now().toSystemTimestamp,
+              None
+            )
+          )
         )
-      ).futureValue(Timeout(10.seconds))
-
-      database.runTestTransaction(
-        database.dataAccess.workflowMetadataSummaryEntries ++= Seq(
-          //Failed WorkflowMetadataSummaryEntry setup
-          WorkflowMetadataSummaryEntry(failedParentWorkflowId, Option("failedParentWorkflow"), Option("Failed"), Option(now), Option(now), Option(now), None, None, None, None),
-          WorkflowMetadataSummaryEntry(failedChildWorkflowId, Option("failedChildWorkflow"), Option("Failed"), Option(now), Option(now), Option(now), Option(failedParentWorkflowId), Option(failedParentWorkflowId), None, None),
-          WorkflowMetadataSummaryEntry(successfulParentWorkflowId, Option("successfulParentWorkflow"), Option("Succeeded"), Option(now), Option(now), Option(now), None, None, None, None),
-          WorkflowMetadataSummaryEntry(successfulChildWorkflowId, Option("successfulChildWorkflow"), Option("Succeeded"), Option(now), Option(now), Option(now), Option(successfulParentWorkflowId), Option(successfulParentWorkflowId), None, None),
-          WorkflowMetadataSummaryEntry(ignoredFailedParentWorkflowId, Option("ignoredFailedParentWorkflow"), Option("Failed"), Option(now), Option(now), Option(now), Option(ignoredFailedParentWorkflowId), Option(ignoredFailedParentWorkflowId), None, None),
-          WorkflowMetadataSummaryEntry(ignoredFailedChildWorkflowId, Option("ignoredFailedChildWorkflow"), Option("Failed"), Option(now), Option(now), Option(now), Option(ignoredFailedChildWorkflowId), Option(ignoredFailedChildWorkflowId), None, None)
+        .futureValue(Timeout(10.seconds))
+
+      database
+        .runTestTransaction(
+          database.dataAccess.workflowMetadataSummaryEntries ++= Seq(
+            // Failed WorkflowMetadataSummaryEntry setup
+            WorkflowMetadataSummaryEntry(failedParentWorkflowId,
+                                         Option("failedParentWorkflow"),
+                                         Option("Failed"),
+                                         Option(now),
+                                         Option(now),
+                                         Option(now),
+                                         None,
+                                         None,
+                                         None,
+                                         None
+            ),
+            WorkflowMetadataSummaryEntry(
+              failedChildWorkflowId,
+              Option("failedChildWorkflow"),
+              Option("Failed"),
+              Option(now),
+              Option(now),
+              Option(now),
+              Option(failedParentWorkflowId),
+              Option(failedParentWorkflowId),
+              None,
+              None
+            ),
+            WorkflowMetadataSummaryEntry(successfulParentWorkflowId,
+                                         Option("successfulParentWorkflow"),
+                                         Option("Succeeded"),
+                                         Option(now),
+                                         Option(now),
+                                         Option(now),
+                                         None,
+                                         None,
+                                         None,
+                                         None
+            ),
+            WorkflowMetadataSummaryEntry(
+              successfulChildWorkflowId,
+              Option("successfulChildWorkflow"),
+              Option("Succeeded"),
+              Option(now),
+              Option(now),
+              Option(now),
+              Option(successfulParentWorkflowId),
+              Option(successfulParentWorkflowId),
+              None,
+              None
+            ),
+            WorkflowMetadataSummaryEntry(
+              ignoredFailedParentWorkflowId,
+              Option("ignoredFailedParentWorkflow"),
+              Option("Failed"),
+              Option(now),
+              Option(now),
+              Option(now),
+              Option(ignoredFailedParentWorkflowId),
+              Option(ignoredFailedParentWorkflowId),
+              None,
+              None
+            ),
+            WorkflowMetadataSummaryEntry(
+              ignoredFailedChildWorkflowId,
+              Option("ignoredFailedChildWorkflow"),
+              Option("Failed"),
+              Option(now),
+              Option(now),
+              Option(now),
+              Option(ignoredFailedChildWorkflowId),
+              Option(ignoredFailedChildWorkflowId),
+              None,
+              None
+            )
+          )
         )
-      ).futureValue(Timeout(10.seconds))
+        .futureValue(Timeout(10.seconds))
 
-      val futureEntries: Future[Seq[MetadataEntry]] = database.getFailedJobsMetadataWithWorkflowId(failedParentWorkflowId)
+      val futureEntries: Future[Seq[MetadataEntry]] =
+        database.getFailedJobsMetadataWithWorkflowId(failedParentWorkflowId)
       var entriesFound = false
 
       val recordCount = Map(
@@ -294,69 +1109,65 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
         )
       )
 
-      whenReady(futureEntries, timeout(scaled(5 seconds))) {
-        entries =>
-          entries.foreach(entry => {
-            entriesFound = true
-            val workflowId = entry.workflowExecutionUuid
-            recordCount.getOrElse(workflowId, None) should not be(None)
-            recordCount(workflowId)("actual") += 1
-            val metadataValueClob = entry.metadataValue.get
-            val metadataValueString = metadataValueClob.getSubString(1, metadataValueClob.length().toInt)
-
-            entry.metadataKey match {
-              case "stderr" => {
-                metadataValueString should be("test value")
-              }
-              case "backendStatus" => {
-                metadataValueString should be("Failed")
-              }
-              case "executionStatus" => {
-                metadataValueString should be("Failed")
-              }
-              case _ => fail(s"Unexpected key ${entry.metadataKey} was included in result set")
-            }
-
-            entry.metadataKey should not be("subWorkflowId")
-            entry.callFullyQualifiedName.getOrElse("") match {
-              case "failedWorkflowCall" => {
-                entry.jobIndex.get should be(1)
-                entry.jobAttempt.get should be(1)
-                val isValidKey = List("executionStatus", "stderr").contains(entry.metadataKey)
-                isValidKey should be(true)
-              }
-              case "failedSubWorkflowCall" => {
-                entry.jobIndex should be(None)
-                entry.jobAttempt.get should be(2)
-                val isValidKey = List("backendStatus", "stderr").contains(entry.metadataKey)
-                isValidKey should be(true)
-              }
-              case "failedSubWorkflowCall2" => {
-                entry.jobIndex.get should be(2)
-                entry.jobAttempt.get should be(2)
-                val isValidKey = List("executionStatus", "stderr").contains(entry.metadataKey)
-                isValidKey should be(true)
-              }
-              case _ => fail(s"Entry ${entry.callFullyQualifiedName.getOrElse("N/A")} | Index: ${entry.jobIndex.get} | Attempt: ${entry.jobAttempt.get} should not be in result set")
-            }
-          })
-          entriesFound should be(true)
-          recordCount.foreach(record => {
-            record._2("actual") should be(record._2("expected"))
-          })
+      whenReady(futureEntries, timeout(scaled(5 seconds))) { entries =>
+        entries.foreach { entry =>
+          entriesFound = true
+          val workflowId = entry.workflowExecutionUuid
+          recordCount.getOrElse(workflowId, None) should not be None
+          recordCount(workflowId)("actual") += 1
+          val metadataValueClob = entry.metadataValue.get
+          val metadataValueString = metadataValueClob.getSubString(1, metadataValueClob.length().toInt)
+
+          entry.metadataKey match {
+            case "stderr" =>
+              metadataValueString should be("test value")
+            case "backendStatus" =>
+              metadataValueString should be("Failed")
+            case "executionStatus" =>
+              metadataValueString should be("Failed")
+            case _ => fail(s"Unexpected key ${entry.metadataKey} was included in result set")
+          }
+
+          entry.metadataKey should not be "subWorkflowId"
+          entry.callFullyQualifiedName.getOrElse("") match {
+            case "failedWorkflowCall" =>
+              entry.jobIndex.get should be(1)
+              entry.jobAttempt.get should be(1)
+              val isValidKey = List("executionStatus", "stderr").contains(entry.metadataKey)
+              isValidKey should be(true)
+            case "failedSubWorkflowCall" =>
+              entry.jobIndex should be(None)
+              entry.jobAttempt.get should be(2)
+              val isValidKey = List("backendStatus", "stderr").contains(entry.metadataKey)
+              isValidKey should be(true)
+            case "failedSubWorkflowCall2" =>
+              entry.jobIndex.get should be(2)
+              entry.jobAttempt.get should be(2)
+              val isValidKey = List("executionStatus", "stderr").contains(entry.metadataKey)
+              isValidKey should be(true)
+            case _ =>
+              fail(
+                s"Entry ${entry.callFullyQualifiedName.getOrElse("N/A")} | Index: ${entry.jobIndex.get} | Attempt: ${entry.jobAttempt.get} should not be in result set"
+              )
+          }
+        }
+        entriesFound should be(true)
+        recordCount.foreach(record => record._2("actual") should be(record._2("expected")))
       }
     }
 
     it should "clean up & close the database" taggedAs DbmsTest in {
       // Not relevant in Travis where all state gets nuked but useful for testing locally
       database.runTestTransaction(database.dataAccess.metadataEntries.delete).futureValue(Timeout(10.seconds))
-      database.runTestTransaction(database.dataAccess.workflowMetadataSummaryEntries.delete).futureValue(Timeout(10.seconds))
+      database
+        .runTestTransaction(database.dataAccess.workflowMetadataSummaryEntries.delete)
+        .futureValue(Timeout(10.seconds))
 
       database.close()
     }
 
     it should "stop container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.stop() }
+      containerOpt.foreach(_.stop())
     }
 
   }
@@ -364,7 +1175,7 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
   behavior of "MetadataSlickDatabase"
   it should "partition metadata for summarization correctly" in {
 
-    def partition(metadata: Seq[MetadataEntry]): SummarizationPartitionedMetadata = {
+    def partition(metadata: Seq[MetadataEntry]): SummarizationPartitionedMetadata =
       MetadataSlickDatabase.partitionSummarizationMetadata(
         rawMetadataEntries = metadata,
         startMetadataKey = WorkflowMetadataKeys.StartTime,
@@ -374,8 +1185,8 @@ class MetadataSlickDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
         submissionMetadataKey = WorkflowMetadataKeys.SubmissionTime,
         parentWorkflowIdKey = WorkflowMetadataKeys.ParentWorkflowId,
         rootWorkflowIdKey = WorkflowMetadataKeys.RootWorkflowId,
-        labelMetadataKey = WorkflowMetadataKeys.Labels)
-    }
+        labelMetadataKey = WorkflowMetadataKeys.Labels
+      )
 
     {
       // Edge condition: empty input
diff --git a/services/src/test/scala/cromwell/services/database/QueryTimeoutSpec.scala b/services/src/test/scala/cromwell/services/database/QueryTimeoutSpec.scala
index ad3277f4ae0..6beb304380a 100644
--- a/services/src/test/scala/cromwell/services/database/QueryTimeoutSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/QueryTimeoutSpec.scala
@@ -22,32 +22,34 @@ import scala.util.matching.Regex
 class QueryTimeoutSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalaFutures {
 
   DatabaseSystem.All foreach { databaseSystem =>
-    testOption(databaseSystem) foreach {
-      case (sleepCommand, errorMessageGenerator) =>
-        behavior of s"Query timeouts on ${databaseSystem.name}"
+    testOption(databaseSystem) foreach { case (sleepCommand, errorMessageGenerator) =>
+      behavior of s"Query timeouts on ${databaseSystem.name}"
 
-        val containerOpt: Option[Container] = DatabaseTestKit.getDatabaseTestContainer(databaseSystem)
+      val containerOpt: Option[Container] = DatabaseTestKit.getDatabaseTestContainer(databaseSystem)
 
-        it should "start container if required" taggedAs DbmsTest in {
-          containerOpt.foreach { _.start }
-        }
+      it should "start container if required" taggedAs DbmsTest in {
+        containerOpt.foreach(_.start)
+      }
 
-        it should "fail with a timeout" taggedAs DbmsTest in {
-          checkDatabaseSystem(containerOpt, databaseSystem, sleepCommand, errorMessageGenerator)
-        }
+      it should "fail with a timeout" taggedAs DbmsTest in {
+        checkDatabaseSystem(containerOpt, databaseSystem, sleepCommand, errorMessageGenerator)
+      }
 
-        it should "stop container if required" taggedAs DbmsTest in {
-          containerOpt.foreach { _.stop() }
-        }
+      it should "stop container if required" taggedAs DbmsTest in {
+        containerOpt.foreach(_.stop())
+      }
     }
   }
 
   private def checkDatabaseSystem(containerOpt: Option[Container],
                                   databaseSystem: DatabaseSystem,
                                   sleepCommand: String,
-                                  errorMessageGenerator: ErrorMessageGenerator): Unit = {
+                                  errorMessageGenerator: ErrorMessageGenerator
+  ): Unit =
     for {
-      testDatabase <- DatabaseTestKit.schemalessDatabaseFromContainerOptAndSystem(containerOpt, databaseSystem).autoClosed
+      testDatabase <- DatabaseTestKit
+        .schemalessDatabaseFromContainerOptAndSystem(containerOpt, databaseSystem)
+        .autoClosed
     } {
       import testDatabase.dataAccess.driver.api._
 
@@ -55,7 +57,7 @@ class QueryTimeoutSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
 
       val errorMessage = errorMessageGenerator(metadataGenerator)
 
-      //noinspection SqlDialectInspection
+      // noinspection SqlDialectInspection
       val future = testDatabase.runTestTransaction(sql"""#$sleepCommand""".as[Int].headOption, timeout = 5.seconds)
       errorMessage match {
         case IntErrorMessage(result) => future.futureValue(Timeout(10.seconds)) should be(Option(result))
@@ -64,21 +66,21 @@ class QueryTimeoutSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
           future.failed.futureValue(Timeout(10.seconds)).getMessage should fullyMatch regex pattern
       }
     }
-  }
 
-  private def testOption(databaseSystem: DatabaseSystem): Option[(String, ErrorMessageGenerator)] = {
+  private def testOption(databaseSystem: DatabaseSystem): Option[(String, ErrorMessageGenerator)] =
     databaseSystem.platform match {
       case HsqldbDatabasePlatform =>
         // HSQL does not document a SLEEP() function, which is essential for this test
         // The functionality being tested is not relevant to an HSQL user, so the omission is probably acceptable
         None
       case MariadbDatabasePlatform =>
-        Option((
-          "select sleep(10);",
-          (metadataGenerator: MetadataGenerator) => {
-            val metadata = metadataGenerator()
-            (metadata.databaseMajorVersion, metadata.databaseMinorVersion) match {
-              /*
+        Option(
+          (
+            "select sleep(10);",
+            (metadataGenerator: MetadataGenerator) => {
+              val metadata = metadataGenerator()
+              (metadata.databaseMajorVersion, metadata.databaseMinorVersion) match {
+                /*
               The docs say "If SLEEP() is interrupted, it returns 1."
 
               - https://mariadb.com/kb/en/sleep/
@@ -101,27 +103,31 @@ class QueryTimeoutSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
 
               Either way, we just need to make sure the sleep was interrupted and don't care if it was via an exception
               or returning `1`.
-               */
-              case (major, minor) if (major >= 10 && minor >= 3) || major >= 11 =>
-                RegexErrorMessage(
+                 */
+                case (major, minor) if (major >= 10 && minor >= 3) || major >= 11 =>
+                  RegexErrorMessage(
                     """(\(conn=\d+\) )?Query execution was interrupted \(max_statement_time exceeded\)""".r
-                )
-              case _ => IntErrorMessage(1)
+                  )
+                case _ => IntErrorMessage(1)
+              }
             }
-          }
-        ))
+          )
+        )
       case MysqlDatabasePlatform =>
-        Option((
-          "select sleep(10);",
-          _ => StringErrorMessage("Statement cancelled due to timeout or client request"),
-        ))
+        Option(
+          (
+            "select sleep(10);",
+            _ => StringErrorMessage("Statement cancelled due to timeout or client request")
+          )
+        )
       case PostgresqlDatabasePlatform =>
-        Option((
-          "select pg_sleep(10);",
-          _ => StringErrorMessage("ERROR: canceling statement due to user request"),
-        ))
+        Option(
+          (
+            "select pg_sleep(10);",
+            _ => StringErrorMessage("ERROR: canceling statement due to user request")
+          )
+        )
     }
-  }
 }
 
 object QueryTimeoutSpec {
diff --git a/services/src/test/scala/cromwell/services/database/RootAndSubworkflowLabelsSpec.scala b/services/src/test/scala/cromwell/services/database/RootAndSubworkflowLabelsSpec.scala
index 88fceef7063..7f7b7b7f27f 100644
--- a/services/src/test/scala/cromwell/services/database/RootAndSubworkflowLabelsSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/RootAndSubworkflowLabelsSpec.scala
@@ -32,28 +32,33 @@ class RootAndSubworkflowLabelsSpec extends AnyFlatSpec with CromwellTimeoutSpec
     println(now)
 
     it should "start container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.start }
+      containerOpt.foreach(_.start)
     }
 
     it should "set up the test data" taggedAs DbmsTest in {
-      database.runTestTransaction(
-        {
-          val root = summary(name = "root")
-          val branch = summary(name = "branch", parent = Option("root"), root = Option("root"))
-          val leaf = summary(name = "leaf", parent = Option("branch"), root = Option("root"))
-          val random = summary(name = "random")
-          database.dataAccess.workflowMetadataSummaryEntries ++= Seq(root, branch, leaf, random)
-        } andThen {
-          val root = label("root")
-          // intentionally not labeling the branch as a negative test
-          val leaf = label("leaf")
-          val random = label("random")
-          database.dataAccess.customLabelEntries ++= Seq(root, /* branch, */ leaf, random)
-        }
-      ).futureValue(Timeout(10.seconds))
+      database
+        .runTestTransaction(
+          {
+            val root = summary(name = "root")
+            val branch = summary(name = "branch", parent = Option("root"), root = Option("root"))
+            val leaf = summary(name = "leaf", parent = Option("branch"), root = Option("root"))
+            val random = summary(name = "random")
+            database.dataAccess.workflowMetadataSummaryEntries ++= Seq(root, branch, leaf, random)
+          } andThen {
+            val root = label("root")
+            // intentionally not labeling the branch as a negative test
+            val leaf = label("leaf")
+            val random = label("random")
+            database.dataAccess.customLabelEntries ++= Seq(root, /* branch, */ leaf, random)
+          }
+        )
+        .futureValue(Timeout(10.seconds))
     }
 
-    def summary(name: String, parent: Option[String] = None, root: Option[String] = None): WorkflowMetadataSummaryEntry = {
+    def summary(name: String,
+                parent: Option[String] = None,
+                root: Option[String] = None
+    ): WorkflowMetadataSummaryEntry =
       WorkflowMetadataSummaryEntry(
         workflowExecutionUuid = name,
         workflowStatus = Option("Succeeded"),
@@ -65,22 +70,19 @@ class RootAndSubworkflowLabelsSpec extends AnyFlatSpec with CromwellTimeoutSpec
         rootWorkflowExecutionUuid = root,
         metadataArchiveStatus = None
       )
-    }
 
-    def label(uuid: String): CustomLabelEntry = {
+    def label(uuid: String): CustomLabelEntry =
       CustomLabelEntry(customLabelKey = "key", customLabelValue = uuid, workflowExecutionUuid = uuid)
-    }
 
     it should "query root and subworkflow labels correctly" taggedAs DbmsTest in {
-      database.getRootAndSubworkflowLabels("root").
-        futureValue(Timeout(10.seconds)) shouldBe Map(
+      database.getRootAndSubworkflowLabels("root").futureValue(Timeout(10.seconds)) shouldBe Map(
         "root" -> Map("key" -> "root"),
         "leaf" -> Map("key" -> "leaf")
       )
     }
 
     it should "stop container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.stop() }
+      containerOpt.foreach(_.stop())
     }
   }
 }
diff --git a/services/src/test/scala/cromwell/services/database/SchemaManager.scala b/services/src/test/scala/cromwell/services/database/SchemaManager.scala
index 02ba7297883..f6e3cff0d88 100644
--- a/services/src/test/scala/cromwell/services/database/SchemaManager.scala
+++ b/services/src/test/scala/cromwell/services/database/SchemaManager.scala
@@ -13,7 +13,7 @@ sealed trait SchemaManager {
 object SchemaManager {
   val All: Seq[SchemaManager] = List(
     LiquibaseSchemaManager,
-    SlickSchemaManager,
+    SlickSchemaManager
   )
 }
 
diff --git a/services/src/test/scala/cromwell/services/database/SchemaManagerSpec.scala b/services/src/test/scala/cromwell/services/database/SchemaManagerSpec.scala
index a22188b34b6..17dc425182c 100644
--- a/services/src/test/scala/cromwell/services/database/SchemaManagerSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/SchemaManagerSpec.scala
@@ -67,12 +67,13 @@ class SchemaManagerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
         for {
           actualDatabase <- inMemoryDatabase(databaseType, schemaManager).autoClosed
           expectedDatabase <- inMemoryDatabase(databaseType, otherSchemaManager).autoClosed
-        } {
+        }
           compare(
-            expectedDatabase.dataAccess.driver, expectedDatabase.database,
-            actualDatabase.dataAccess.driver, actualDatabase.database,
+            expectedDatabase.dataAccess.driver,
+            expectedDatabase.database,
+            actualDatabase.dataAccess.driver,
+            actualDatabase.database
           ) { diffResult =>
-
             import cromwell.database.migration.liquibase.DiffResultFilter._
 
             /*
@@ -80,9 +81,7 @@ class SchemaManagerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
             See notes at the bottom of changelog.xml
              */
             val diffFilters = StandardTypeFilters
-            val filteredDiffResult = diffResult
-              .filterChangeLogs
-              .filterLiquibaseObjects
+            val filteredDiffResult = diffResult.filterChangeLogs.filterLiquibaseObjects
               .filterChangedObjects(diffFilters)
 
             val totalChanged =
@@ -98,14 +97,16 @@ class SchemaManagerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
               diffToChangeLog.print(printStream)
               val changeSetsScoped = XML.loadString(outputStream.toString) \ "changeSet" \ "_"
               val changeSets = changeSetsScoped map stripNodeScope
-              fail(changeSets.mkString(
-                s"The following changes are in $schemaManager but not in $otherSchemaManager:\n  ",
-                "\n  ",
-                "\nEnsure that the columns/fields exist, with the same lengths in " +
-                  s"$schemaManager and $otherSchemaManager and synchronize the two."))
+              fail(
+                changeSets.mkString(
+                  s"The following changes are in $schemaManager but not in $otherSchemaManager:\n  ",
+                  "\n  ",
+                  "\nEnsure that the columns/fields exist, with the same lengths in " +
+                    s"$schemaManager and $otherSchemaManager and synchronize the two."
+                )
+              )
             }
           }
-        }
       }
 
       it should "match expected generated names" taggedAs DbmsTest in {
@@ -113,9 +114,8 @@ class SchemaManagerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
 
         for {
           slickDatabase <- inMemoryDatabase(databaseType, schemaManager).autoClosed
-        } {
-          schemaMetadata = getSchemaMetadata(slickDatabase)
         }
+          schemaMetadata = getSchemaMetadata(slickDatabase)
 
         var misnamed = Seq.empty[String]
 
@@ -184,7 +184,9 @@ class SchemaManagerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
           if (missing.nonEmpty) {
             failMessage += missing.mkString(
               s"Based on the schema in $schemaManager, please ensure that the following tables/columns exist:\n",
-              "\n", "\n")
+              "\n",
+              "\n"
+            )
           }
 
           fail(failMessage)
@@ -196,33 +198,29 @@ class SchemaManagerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
 
 object SchemaManagerSpec {
   // strip the namespace from elems and their children
-  private def stripNodeScope(node: Node): Node = {
+  private def stripNodeScope(node: Node): Node =
     node match {
       case elem: Elem => elem.copy(scope = TopScope, child = elem.child map stripNodeScope)
       case other => other
     }
-  }
 
-  private def compare[ReferenceProfile <: JdbcProfile, ComparisonProfile <: JdbcProfile, T]
-  (referenceProfile: ReferenceProfile,
-   referenceDatabase: ReferenceProfile#Backend#Database,
-   comparisonProfile: ComparisonProfile,
-   comparisonDatabase: ComparisonProfile#Backend#Database)(block: DiffResult => T): T = {
+  private def compare[ReferenceProfile <: JdbcProfile, ComparisonProfile <: JdbcProfile, T](
+    referenceProfile: ReferenceProfile,
+    referenceDatabase: ReferenceProfile#Backend#Database,
+    comparisonProfile: ComparisonProfile,
+    comparisonDatabase: ComparisonProfile#Backend#Database
+  )(block: DiffResult => T): T =
     DatabaseTestKit.withConnections(referenceProfile, referenceDatabase, comparisonProfile, comparisonDatabase) {
       LiquibaseUtils.compare(_, _)(block)
     }
-  }
-
 
   private val SnakeRegex = "_([a-z])".r
 
-  private def snakeToCamel(value: String): String = {
+  private def snakeToCamel(value: String): String =
     SnakeRegex.replaceAllIn(value.toLowerCase, _.group(1).toUpperCase)
-  }
 
-  private def snakeAbbreviate(value: String): String = {
+  private def snakeAbbreviate(value: String): String =
     SnakeRegex.findAllMatchIn("_" + value.toLowerCase).map(_.group(1)).mkString("").toUpperCase
-  }
 
   private def tableClassName(tableName: String) = s"cromwell.database.sql.tables.$tableName"
 
@@ -246,40 +244,42 @@ object SchemaManagerSpec {
 
   case class DatabaseItem(tableName: String, itemName: String)
 
-  case class SchemaMetadata(tableMetadata: Seq[MTable], columnMetadata: Seq[MColumn], indexMetadata: Seq[MIndexInfo],
-                            primaryKeyMetadata: Seq[MPrimaryKey], foreignKeyMetadata: Seq[MForeignKey]) {
-    lazy val tables: Seq[TableClass] = tableMetadata.map({ table =>
+  case class SchemaMetadata(tableMetadata: Seq[MTable],
+                            columnMetadata: Seq[MColumn],
+                            indexMetadata: Seq[MIndexInfo],
+                            primaryKeyMetadata: Seq[MPrimaryKey],
+                            foreignKeyMetadata: Seq[MForeignKey]
+  ) {
+    lazy val tables: Seq[TableClass] = tableMetadata.map { table =>
       val tableName = snakeToCamel(table.name.name).capitalize
       TableClass(tableName)
-    }).distinct
+    }.distinct
 
-    lazy val columns: Seq[DatabaseItem] = columnMetadata.map({ column =>
+    lazy val columns: Seq[DatabaseItem] = columnMetadata.map { column =>
       val tableName = snakeToCamel(column.table.name).capitalize
       val columnName = snakeToCamel(column.name)
       DatabaseItem(tableName, columnName)
-    }).distinct
+    }.distinct
 
-    lazy val indexes: Seq[DatabaseItem] = indexMetadata.map({ index =>
+    lazy val indexes: Seq[DatabaseItem] = indexMetadata.map { index =>
       val tableName = snakeToCamel(index.table.name).capitalize
       val indexName = snakeToCamel(getIndexName(index))
       DatabaseItem(tableName, indexName)
-    }).distinct
+    }.distinct
 
-    lazy val foreignKeys: Seq[DatabaseItem] = foreignKeyMetadata.map({ foreignKey =>
+    lazy val foreignKeys: Seq[DatabaseItem] = foreignKeyMetadata.map { foreignKey =>
       val tableName = snakeToCamel(foreignKey.fkTable.name).capitalize
       val indexName = snakeToCamel(foreignKey.fkName.get)
       DatabaseItem(tableName, indexName)
-    }).distinct
+    }.distinct
 
     lazy val slickItems: Seq[DatabaseItem] = columns ++ indexes ++ foreignKeys
 
-    def existsTableItem(tableItem: DatabaseItem): Boolean = {
+    def existsTableItem(tableItem: DatabaseItem): Boolean =
       tables.find(_.tableName == tableItem.tableName).exists(_.existsTableField(tableItem.itemName))
-    }
 
-    def existsSlickMapping(tableItem: DatabaseItem): Boolean = {
+    def existsSlickMapping(tableItem: DatabaseItem): Boolean =
       tables.find(_.tableName == tableItem.tableName).exists(_.existsSlickMapping(tableItem.itemName))
-    }
   }
 
 }
diff --git a/services/src/test/scala/cromwell/services/database/SlickDeadlocksSpec.scala b/services/src/test/scala/cromwell/services/database/SlickDeadlocksSpec.scala
index f0823be7337..f5e95cb4dd2 100644
--- a/services/src/test/scala/cromwell/services/database/SlickDeadlocksSpec.scala
+++ b/services/src/test/scala/cromwell/services/database/SlickDeadlocksSpec.scala
@@ -31,13 +31,13 @@ class SlickDeadlocksSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   it should "not happen" in {
     val logger = Logger(LoggerFactory.getLogger(getClass.getName))
     // Test based on https://github.com/kwark/slick-deadlock/blob/82525fc/src/main/scala/SlickDeadlock.scala
-    val databaseConfig = ConfigFactory.parseString(
-      s"""|db.url = "jdbc:hsqldb:mem:$${uniqueSchema};shutdown=false;hsqldb.tx=mvcc"
-          |db.driver = "org.hsqldb.jdbcDriver"
-          |db.connectionTimeout = 3000
-          |db.numThreads = 2
-          |profile = "slick.jdbc.HsqldbProfile$$"
-          |""".stripMargin)
+    val databaseConfig =
+      ConfigFactory.parseString(s"""|db.url = "jdbc:hsqldb:mem:$${uniqueSchema};shutdown=false;hsqldb.tx=mvcc"
+                                    |db.driver = "org.hsqldb.jdbcDriver"
+                                    |db.connectionTimeout = 3000
+                                    |db.numThreads = 2
+                                    |profile = "slick.jdbc.HsqldbProfile$$"
+                                    |""".stripMargin)
     logger.info("Initializing deadlock-test database")
     for {
       database <- DatabaseTestKit.initializedDatabaseFromConfig(EngineDatabaseType, databaseConfig).autoClosed
diff --git a/services/src/test/scala/cromwell/services/database/TestSlickDatabase.scala b/services/src/test/scala/cromwell/services/database/TestSlickDatabase.scala
index c88ad81df79..8e1157a7797 100644
--- a/services/src/test/scala/cromwell/services/database/TestSlickDatabase.scala
+++ b/services/src/test/scala/cromwell/services/database/TestSlickDatabase.scala
@@ -16,8 +16,7 @@ trait TestSlickDatabase {
 
   def runTestTransaction[R](action: DBIO[R],
                             isolationLevel: TransactionIsolation = TransactionIsolation.RepeatableRead,
-                            timeout: Duration = Duration.Inf,
-                           ): Future[R] = {
+                            timeout: Duration = Duration.Inf
+  ): Future[R] =
     slickDatabase.runTransaction(action, isolationLevel, timeout)
-  }
 }
diff --git a/services/src/test/scala/cromwell/services/healthmonitor/HealthMonitorServiceActorSpec.scala b/services/src/test/scala/cromwell/services/healthmonitor/HealthMonitorServiceActorSpec.scala
index f4e5ff344e6..81c783656fd 100644
--- a/services/src/test/scala/cromwell/services/healthmonitor/HealthMonitorServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/healthmonitor/HealthMonitorServiceActorSpec.scala
@@ -14,9 +14,15 @@ import org.scalatest.time.{Millis, Seconds, Span}
 
 import scala.concurrent.duration._
 
-class HealthMonitorServiceActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with Eventually with AskSupport {
+class HealthMonitorServiceActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with Eventually
+    with AskSupport {
 
-  override implicit def patienceConfig = PatienceConfig(timeout = scaled(Span(15, Seconds)), interval = Span(500, Millis))
+  implicit override def patienceConfig =
+    PatienceConfig(timeout = scaled(Span(15, Seconds)), interval = Span(500, Millis))
 
   behavior of "HealthMonitorServiceActor"
 
@@ -29,14 +35,20 @@ class HealthMonitorServiceActorSpec extends TestKitSuite with AnyFlatSpecLike wi
         |check-papi-backends: []
         |""".stripMargin
 
-
     val globalConfigString =
       s"""services.HealthMonitor.config: {
          |$serviceConfigString
          |}
          |""".stripMargin
 
-    val actor = system.actorOf(Props(new HealthMonitorServiceActor(ConfigFactory.parseString(serviceConfigString), ConfigFactory.parseString(globalConfigString), null)))
+    val actor = system.actorOf(
+      Props(
+        new HealthMonitorServiceActor(ConfigFactory.parseString(serviceConfigString),
+                                      ConfigFactory.parseString(globalConfigString),
+                                      null
+        )
+      )
+    )
 
     val testProbe = TestProbe()
 
diff --git a/services/src/test/scala/cromwell/services/healthmonitor/ProtoHealthMonitorServiceActorSpec.scala b/services/src/test/scala/cromwell/services/healthmonitor/ProtoHealthMonitorServiceActorSpec.scala
index 1a9ce43bd31..12243a47ceb 100644
--- a/services/src/test/scala/cromwell/services/healthmonitor/ProtoHealthMonitorServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/healthmonitor/ProtoHealthMonitorServiceActorSpec.scala
@@ -20,14 +20,17 @@ import scala.language.postfixOps
 
 class ProtoHealthMonitorServiceActorSpec extends TestKitSuite with AnyFlatSpecLike with Eventually {
   implicit val timeout = Timeout(scaled(5.seconds))
-  final implicit val blockingEc: ExecutionContextExecutor = ExecutionContext.fromExecutor(
+  implicit final val blockingEc: ExecutionContextExecutor = ExecutionContext.fromExecutor(
     Executors.newCachedThreadPool()
   )
 
   override val patienceConfig = PatienceConfig(timeout = scaled(20 seconds), interval = scaled(1 second))
   implicit val patience = patienceConfig
 
-  private def eventualStatus(actorRef: ActorRef, ok: Boolean, systems: (MonitoredSubsystem, SubsystemStatus)*): Assertion = {
+  private def eventualStatus(actorRef: ActorRef,
+                             ok: Boolean,
+                             systems: (MonitoredSubsystem, SubsystemStatus)*
+  ): Assertion = {
     case class NameAndStatus(name: String, status: SubsystemStatus)
 
     eventually {
@@ -35,7 +38,7 @@ class ProtoHealthMonitorServiceActorSpec extends TestKitSuite with AnyFlatSpecLi
       assert(resp.ok == ok)
 
       val actual = resp.systems.toList.map(NameAndStatus.tupled).sortBy(_.name)
-      val expected = systems.map { case (m, s) => m.name -> s } map { NameAndStatus.tupled } sortBy(_.name)
+      val expected = systems.map { case (m, s) => m.name -> s } map NameAndStatus.tupled sortBy (_.name)
       assert(actual.length == expected.length)
 
       actual.zip(expected) map { case (a, e) =>
@@ -46,7 +49,10 @@ class ProtoHealthMonitorServiceActorSpec extends TestKitSuite with AnyFlatSpecLi
           am <- a.status.messages.toList.flatten.headOption
           em <- e.status.messages.toList.flatten.headOption
         } yield am.startsWith(em)
-        assert(isEmpty || actualPrefixedByExpected.contains(true), s"Instead, a.status.messages = ${a.status.messages.toList.flatten} and e.status.messages = ${e.status.messages.toList.flatten}")
+        assert(
+          isEmpty || actualPrefixedByExpected.contains(true),
+          s"Instead, a.status.messages = ${a.status.messages.toList.flatten} and e.status.messages = ${e.status.messages.toList.flatten}"
+        )
       } head
     }
   }
@@ -106,7 +112,7 @@ class ProtoHealthMonitorServiceActorSpec extends TestKitSuite with AnyFlatSpecLi
 
   it should "handle timed out futures" in {
     var first = true
-    def timeOutCheck(): Future[SubsystemStatus] = {
+    def timeOutCheck(): Future[SubsystemStatus] =
       if (first) {
         first = false
         Future.successful(OkStatus)
@@ -116,7 +122,6 @@ class ProtoHealthMonitorServiceActorSpec extends TestKitSuite with AnyFlatSpecLi
           OkStatus
         }
       }
-    }
 
     val timeoutSubsystem = MonitoredSubsystem("Timeout", () => timeOutCheck())
 
@@ -174,8 +179,8 @@ class ProtoHealthMonitorServiceActorSpec extends TestKitSuite with AnyFlatSpecLi
     val statusStoreMessages: List[Option[String]] = statusStores.map(_.messages.flatMap(_.headOption))
 
     val expectedMessagePrefixes = List(None, Option("womp womp"), Option("Timed out"))
-    statusStoreMessages.zip(expectedMessagePrefixes) foreach {
-      case (a, e) => assert(a.isEmpty && e.isEmpty || a.exists(_.startsWith(e.get)))
+    statusStoreMessages.zip(expectedMessagePrefixes) foreach { case (a, e) =>
+      assert(a.isEmpty && e.isEmpty || a.exists(_.startsWith(e.get)))
     }
   }
 }
@@ -189,16 +194,16 @@ object ProtoHealthMonitorServiceActorSpec {
   val TimedOutStatus = SubsystemStatus(ok = false, Option(List("Timed out")))
 
   abstract class TestHealthMonitorActor(override val serviceConfig: Config = ConfigFactory.empty())
-    extends ProtoHealthMonitorServiceActor with ScaledTimeSpans {
+      extends ProtoHealthMonitorServiceActor
+      with ScaledTimeSpans {
     override lazy val staleThreshold = scaled(3.seconds)
     override lazy val failureRetryInterval = scaled(100.milliseconds)
     override lazy val sweepInterval = scaled(200.milliseconds)
     override lazy val futureTimeout = scaled(1.second)
   }
 
-  private def mockCheckSuccess(): Future[SubsystemStatus] = {
+  private def mockCheckSuccess(): Future[SubsystemStatus] =
     Future.successful(OkStatus)
-  }
 
   private def mockCheckFailure(): Future[SubsystemStatus] = {
     // Pay no mind, just needed to make sure the checks for both subsystems in the "binning" test get to run.
diff --git a/services/src/test/scala/cromwell/services/instrumentation/AsynchronousThrottlingGaugeMetricActorSpec.scala b/services/src/test/scala/cromwell/services/instrumentation/AsynchronousThrottlingGaugeMetricActorSpec.scala
index 8b7c6979e8c..002e7f1296d 100644
--- a/services/src/test/scala/cromwell/services/instrumentation/AsynchronousThrottlingGaugeMetricActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/instrumentation/AsynchronousThrottlingGaugeMetricActorSpec.scala
@@ -4,7 +4,12 @@ import akka.testkit.{ImplicitSender, TestFSMRef, TestProbe}
 import cats.data.NonEmptyList
 import cromwell.core.TestKitSuite
 import cromwell.core.instrumentation.InstrumentationPrefixes
-import cromwell.services.instrumentation.AsynchronousThrottlingGaugeMetricActor.{CalculateMetricValue, MetricCalculationInProgress, MetricValue, WaitingForMetricCalculationRequestOrMetricValue}
+import cromwell.services.instrumentation.AsynchronousThrottlingGaugeMetricActor.{
+  CalculateMetricValue,
+  MetricCalculationInProgress,
+  MetricValue,
+  WaitingForMetricCalculationRequestOrMetricValue
+}
 import cromwell.services.instrumentation.InstrumentationService.InstrumentationServiceMessage
 import org.scalatest.concurrent.Eventually
 import org.scalatest.flatspec.AnyFlatSpecLike
@@ -14,7 +19,12 @@ import scala.concurrent.Promise
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-class AsynchronousThrottlingGaugeMetricActorSpec extends TestKitSuite with AnyFlatSpecLike with ImplicitSender with Matchers with Eventually {
+class AsynchronousThrottlingGaugeMetricActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with ImplicitSender
+    with Matchers
+    with Eventually {
 
   private val defaultTimeout = 5 seconds
 
@@ -23,7 +33,10 @@ class AsynchronousThrottlingGaugeMetricActorSpec extends TestKitSuite with AnyFl
     val serviceRegistryProbe = TestProbe()
     val calculatedValPromise = Promise[Int]()
     val metricActor = TestFSMRef {
-      new AsynchronousThrottlingGaugeMetricActor(NonEmptyList.of("metric"), InstrumentationPrefixes.ServicesPrefix, serviceRegistryProbe.ref)
+      new AsynchronousThrottlingGaugeMetricActor(NonEmptyList.of("metric"),
+                                                 InstrumentationPrefixes.ServicesPrefix,
+                                                 serviceRegistryProbe.ref
+      )
     }
     metricActor ! CalculateMetricValue(_ => calculatedValPromise.future)
     eventually {
@@ -33,7 +46,7 @@ class AsynchronousThrottlingGaugeMetricActorSpec extends TestKitSuite with AnyFl
     eventually {
       metricActor.stateName shouldBe WaitingForMetricCalculationRequestOrMetricValue
     }
-    serviceRegistryProbe.expectMsgPF(defaultTimeout){
+    serviceRegistryProbe.expectMsgPF(defaultTimeout) {
       case InstrumentationServiceMessage(CromwellGauge(_, actualValue)) =>
         actualValue shouldBe calculatedVal
     }
@@ -42,7 +55,10 @@ class AsynchronousThrottlingGaugeMetricActorSpec extends TestKitSuite with AnyFl
   it should "return into WaitingForMetricCalculationRequestOrMetricValue state if metric calculation resulted in error" in {
     val dbFailurePromise = Promise[Int]()
     val metricActor = TestFSMRef {
-      new AsynchronousThrottlingGaugeMetricActor(NonEmptyList.of("metric"), InstrumentationPrefixes.ServicesPrefix, TestProbe().ref)
+      new AsynchronousThrottlingGaugeMetricActor(NonEmptyList.of("metric"),
+                                                 InstrumentationPrefixes.ServicesPrefix,
+                                                 TestProbe().ref
+      )
     }
     metricActor ! CalculateMetricValue(_ => dbFailurePromise.future)
     eventually {
@@ -58,10 +74,13 @@ class AsynchronousThrottlingGaugeMetricActorSpec extends TestKitSuite with AnyFl
     val calculatedVal = -1L
     val serviceRegistryProbe = TestProbe()
     val metricActor = TestFSMRef {
-      new AsynchronousThrottlingGaugeMetricActor(NonEmptyList.of("metric"), InstrumentationPrefixes.ServicesPrefix, serviceRegistryProbe.ref)
+      new AsynchronousThrottlingGaugeMetricActor(NonEmptyList.of("metric"),
+                                                 InstrumentationPrefixes.ServicesPrefix,
+                                                 serviceRegistryProbe.ref
+      )
     }
     metricActor ! MetricValue(calculatedVal)
-    serviceRegistryProbe.expectMsgPF(defaultTimeout){
+    serviceRegistryProbe.expectMsgPF(defaultTimeout) {
       case InstrumentationServiceMessage(CromwellGauge(_, actualValue)) =>
         actualValue shouldBe calculatedVal
     }
@@ -73,7 +92,10 @@ class AsynchronousThrottlingGaugeMetricActorSpec extends TestKitSuite with AnyFl
     val serviceRegistryProbe = TestProbe()
     val calculatedValPromise = Promise[Int]()
     val metricActor = TestFSMRef {
-      new AsynchronousThrottlingGaugeMetricActor(NonEmptyList.of("metric"), InstrumentationPrefixes.ServicesPrefix, serviceRegistryProbe.ref)
+      new AsynchronousThrottlingGaugeMetricActor(NonEmptyList.of("metric"),
+                                                 InstrumentationPrefixes.ServicesPrefix,
+                                                 serviceRegistryProbe.ref
+      )
     }
     metricActor ! CalculateMetricValue(_ => calculatedValPromise.future)
     eventually {
@@ -82,7 +104,7 @@ class AsynchronousThrottlingGaugeMetricActorSpec extends TestKitSuite with AnyFl
 
     // interrupted by precalculated MetricValue
     metricActor ! MetricValue(precalculatedVal)
-    serviceRegistryProbe.expectMsgPF(defaultTimeout){
+    serviceRegistryProbe.expectMsgPF(defaultTimeout) {
       case InstrumentationServiceMessage(CromwellGauge(_, actualValue)) =>
         actualValue shouldBe precalculatedVal
     }
@@ -93,7 +115,7 @@ class AsynchronousThrottlingGaugeMetricActorSpec extends TestKitSuite with AnyFl
     eventually {
       metricActor.stateName shouldBe WaitingForMetricCalculationRequestOrMetricValue
     }
-    serviceRegistryProbe.expectMsgPF(defaultTimeout){
+    serviceRegistryProbe.expectMsgPF(defaultTimeout) {
       case InstrumentationServiceMessage(CromwellGauge(_, actualValue)) =>
         actualValue shouldBe calculatedVal
     }
@@ -102,7 +124,10 @@ class AsynchronousThrottlingGaugeMetricActorSpec extends TestKitSuite with AnyFl
   it should "successfully complete ongoing metric value calculation and ignore another calculation requests while in MetricCalculationInProgress state" in {
     val serviceRegistryProbe = TestProbe()
     val metricActor = TestFSMRef {
-      new AsynchronousThrottlingGaugeMetricActor(NonEmptyList.of("metric"), InstrumentationPrefixes.ServicesPrefix, serviceRegistryProbe.ref)
+      new AsynchronousThrottlingGaugeMetricActor(NonEmptyList.of("metric"),
+                                                 InstrumentationPrefixes.ServicesPrefix,
+                                                 serviceRegistryProbe.ref
+      )
     }
 
     val calculatedVal = -1
@@ -124,7 +149,7 @@ class AsynchronousThrottlingGaugeMetricActorSpec extends TestKitSuite with AnyFl
     eventually {
       metricActor.stateName shouldBe WaitingForMetricCalculationRequestOrMetricValue
     }
-    serviceRegistryProbe.expectMsgPF(defaultTimeout){
+    serviceRegistryProbe.expectMsgPF(defaultTimeout) {
       case InstrumentationServiceMessage(CromwellGauge(_, actualValue)) =>
         // should be calculatedVal, not calculatedValInterruptor
         actualValue shouldBe calculatedVal
diff --git a/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverConfigSpec.scala b/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverConfigSpec.scala
index 3ba42161222..8b64a8b4b0e 100644
--- a/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverConfigSpec.scala
+++ b/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverConfigSpec.scala
@@ -46,7 +46,6 @@ class StackdriverConfigSpec extends TestKitSuite with AnyFlatSpecLike with Befor
     stackdriverConfig.cromwellPerfTestCase shouldBe Option("perf-test-1")
   }
 
-
   it should "correctly parse config with optional values" in {
     val config = ConfigFactory.parseString(
       """
@@ -66,7 +65,6 @@ class StackdriverConfigSpec extends TestKitSuite with AnyFlatSpecLike with Befor
     stackdriverConfig.cromwellPerfTestCase shouldBe None
   }
 
-
   it should "correctly add cromwell instance identifier to config" in {
     val globalConfig = ConfigFactory.parseString(
       s"""
@@ -102,7 +100,6 @@ class StackdriverConfigSpec extends TestKitSuite with AnyFlatSpecLike with Befor
     stackdriverConfig.cromwellPerfTestCase shouldBe None
   }
 
-
   it should "throw error for invalid auth" in {
     val config = ConfigFactory.parseString(
       """
@@ -118,7 +115,6 @@ class StackdriverConfigSpec extends TestKitSuite with AnyFlatSpecLike with Befor
                                     |`auth` scheme is invalid. Errors: NonEmptyList(`google` configuration stanza does not contain an auth named 'my-auth'.  Known auth names: application-default)""".stripMargin
   }
 
-
   it should "throw error for invalid flush rate" in {
     val config = ConfigFactory.parseString(
       """
diff --git a/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverInstrumentationServiceActorSpec.scala b/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverInstrumentationServiceActorSpec.scala
index d97f63ab48d..5059dc7eb78 100644
--- a/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverInstrumentationServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/StackdriverInstrumentationServiceActorSpec.scala
@@ -12,7 +12,11 @@ import org.scalatest.matchers.should.Matchers
 
 import scala.concurrent.duration._
 
-class StackdriverInstrumentationServiceActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with Eventually {
+class StackdriverInstrumentationServiceActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with Eventually {
   behavior of "StackdriverInstrumentationServiceActor"
 
   private val MaxWaitTime = 2.minutes
@@ -39,7 +43,6 @@ class StackdriverInstrumentationServiceActorSpec extends TestKitSuite with AnyFl
   private val testGaugeBucket =
     CromwellBucket(List("test_prefix"), NonEmptyList.of("test", "gauge", "metric", "bucket"))
 
-
   it should "correctly receive the metrics with resource labels" in {
     val stackdriverConfig = ConfigFactory.parseString(
       """
@@ -64,22 +67,28 @@ class StackdriverInstrumentationServiceActorSpec extends TestKitSuite with AnyFl
     val expectedGaugeMetrics = ("custom.googleapis.com/cromwell/test_prefix/test/gauge/metric/bucket", 40.0)
     val expectedTimingMetrics = ("custom.googleapis.com/cromwell/test_prefix/test/metric/bucket/timing", 7500.0)
 
-    val stackdriverActor = TestActorRef(new TestStackdriverInstrumentationServiceActor(stackdriverConfig, globalConfig, registryProbe))
+    val stackdriverActor =
+      TestActorRef(new TestStackdriverInstrumentationServiceActor(stackdriverConfig, globalConfig, registryProbe))
 
     rawMetricList foreach (metric => stackdriverActor ! InstrumentationServiceMessage(metric))
 
     eventually {
       stackdriverActor.underlyingActor.metricsReceived should have length 3
 
-      stackdriverActor.underlyingActor.metricsReceived.map(m => (m.metricPath, m.metricValue)) should contain (expectedCumulativeMetrics)
-      stackdriverActor.underlyingActor.metricsReceived.map(m => (m.metricPath, m.metricValue)) should contain (expectedGaugeMetrics)
-      stackdriverActor.underlyingActor.metricsReceived.map(m => (m.metricPath, m.metricValue)) should contain (expectedTimingMetrics)
-
-      stackdriverActor.underlyingActor.metricsReceived.map(_.resourceLabels) should contain (resourceLabels)
+      stackdriverActor.underlyingActor.metricsReceived.map(m => (m.metricPath, m.metricValue)) should contain(
+        expectedCumulativeMetrics
+      )
+      stackdriverActor.underlyingActor.metricsReceived.map(m => (m.metricPath, m.metricValue)) should contain(
+        expectedGaugeMetrics
+      )
+      stackdriverActor.underlyingActor.metricsReceived.map(m => (m.metricPath, m.metricValue)) should contain(
+        expectedTimingMetrics
+      )
+
+      stackdriverActor.underlyingActor.metricsReceived.map(_.resourceLabels) should contain(resourceLabels)
     }
   }
 
-
   it should "correctly receive metrics with metric labels" in {
     val stackdriverConfig = ConfigFactory.parseString(
       """
@@ -99,15 +108,18 @@ class StackdriverInstrumentationServiceActorSpec extends TestKitSuite with AnyFl
     val expectedCumulativeMetrics = ("custom.googleapis.com/cromwell/test_prefix/test/metric/bucket", 50.0)
     val metricLabels = Map("cromwell_instance_role" -> "backend", "cromwell_perf_test_case" -> "perf-test-1")
 
-    val stackdriverActor = TestActorRef(new TestStackdriverInstrumentationServiceActor(stackdriverConfig, globalConfig, registryProbe))
+    val stackdriverActor =
+      TestActorRef(new TestStackdriverInstrumentationServiceActor(stackdriverConfig, globalConfig, registryProbe))
 
     rawMetricList foreach (metric => stackdriverActor ! InstrumentationServiceMessage(metric))
 
     eventually {
       stackdriverActor.underlyingActor.metricsReceived should have length 1
-      stackdriverActor.underlyingActor.metricsReceived.map(m => (m.metricPath, m.metricValue)) should contain (expectedCumulativeMetrics)
-      stackdriverActor.underlyingActor.metricsReceived.map(_.resourceLabels) should contain (resourceLabels)
-      stackdriverActor.underlyingActor.metricsReceived.map(_.metricLabels) should contain (metricLabels)
+      stackdriverActor.underlyingActor.metricsReceived.map(m => (m.metricPath, m.metricValue)) should contain(
+        expectedCumulativeMetrics
+      )
+      stackdriverActor.underlyingActor.metricsReceived.map(_.resourceLabels) should contain(resourceLabels)
+      stackdriverActor.underlyingActor.metricsReceived.map(_.metricLabels) should contain(metricLabels)
     }
   }
 }
diff --git a/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/TestStackdriverInstrumentationServiceActor.scala b/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/TestStackdriverInstrumentationServiceActor.scala
index e1b708b6a72..d186864969d 100644
--- a/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/TestStackdriverInstrumentationServiceActor.scala
+++ b/services/src/test/scala/cromwell/services/instrumentation/impl/stackdriver/TestStackdriverInstrumentationServiceActor.scala
@@ -5,8 +5,10 @@ import com.google.monitoring.v3.CreateTimeSeriesRequest
 import com.typesafe.config.Config
 import scala.jdk.CollectionConverters._
 
-class TestStackdriverInstrumentationServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
-  extends StackdriverInstrumentationServiceActor(serviceConfig, globalConfig, serviceRegistryActor) {
+class TestStackdriverInstrumentationServiceActor(serviceConfig: Config,
+                                                 globalConfig: Config,
+                                                 serviceRegistryActor: ActorRef
+) extends StackdriverInstrumentationServiceActor(serviceConfig, globalConfig, serviceRegistryActor) {
 
   var metricsReceived = List[TimeSeriesRequest]()
 
@@ -15,14 +17,15 @@ class TestStackdriverInstrumentationServiceActor(serviceConfig: Config, globalCo
     val metric = timeSeries.getMetric
 
     metricsReceived = metricsReceived :+ TimeSeriesRequest(metric.getType,
-      timeSeries.getPoints(0).getValue.getDoubleValue,
-      timeSeries.getResource.getLabelsMap.asScala.toMap,
-      metric.getLabelsMap.asScala.toMap)
+                                                           timeSeries.getPoints(0).getValue.getDoubleValue,
+                                                           timeSeries.getResource.getLabelsMap.asScala.toMap,
+                                                           metric.getLabelsMap.asScala.toMap
+    )
   }
 }
 
-
 case class TimeSeriesRequest(metricPath: String,
                              metricValue: Double,
                              resourceLabels: Map[String, String],
-                             metricLabels: Map[String, String])
+                             metricLabels: Map[String, String]
+)
diff --git a/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDConfigSpec.scala b/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDConfigSpec.scala
index b109b785c42..b22ce0b2ef1 100644
--- a/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDConfigSpec.scala
+++ b/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDConfigSpec.scala
@@ -9,7 +9,7 @@ import scala.concurrent.duration._
 
 class StatsDConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "StatsDConfig"
-  
+
   it should "parse correct service configuration" in {
     val config = ConfigFactory.parseString(
       """
diff --git a/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActorBenchmarkSpec.scala b/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActorBenchmarkSpec.scala
index 82b3183faef..1275a64e231 100644
--- a/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActorBenchmarkSpec.scala
+++ b/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActorBenchmarkSpec.scala
@@ -15,7 +15,12 @@ import org.scalatest.matchers.should.Matchers
 import scala.jdk.CollectionConverters._
 import scala.concurrent.duration._
 
-class StatsDInstrumentationServiceActorBenchmarkSpec extends TestKitSuite with AnyFlatSpecLike with BeforeAndAfterAll with Matchers with Eventually {
+class StatsDInstrumentationServiceActorBenchmarkSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with BeforeAndAfterAll
+    with Matchers
+    with Eventually {
   behavior of "StatsDInstrumentationServiceActor"
 
   val config = ConfigFactory.parseString(
@@ -28,18 +33,20 @@ class StatsDInstrumentationServiceActorBenchmarkSpec extends TestKitSuite with A
   )
 
   val registryProbe = TestProbe().ref
-  override implicit val patienceConfig: PatienceConfig = PatienceConfig(scaled(3.seconds))
+  implicit override val patienceConfig: PatienceConfig = PatienceConfig(scaled(3.seconds))
   val testBucket = CromwellBucket(List("test_prefix"), NonEmptyList.of("test", "metric", "benchmark", "bucket"))
 
-
   it should "have good throughput for gauges" in {
-    val instrumentationActor = TestActorRef(new StatsDInstrumentationServiceActor(config, ConfigFactory.load(), registryProbe))
+    val instrumentationActor =
+      TestActorRef(new StatsDInstrumentationServiceActor(config, ConfigFactory.load(), registryProbe))
     val gaugeName = instrumentationActor.underlyingActor.metricBaseName.append(testBucket.toStatsDString()).name
-    LazyList.range(0, 1 * 1000 * 1000, 1).foreach({ i =>
+    LazyList.range(0, 1 * 1000 * 1000, 1).foreach { i =>
       instrumentationActor ! InstrumentationServiceMessage(CromwellGauge(testBucket, i.toLong))
-    })
+    }
     eventually {
-      instrumentationActor.underlyingActor.metricRegistry.getGauges.asScala.get(gaugeName).map(_.getValue) shouldBe Some(999999)
+      instrumentationActor.underlyingActor.metricRegistry.getGauges.asScala
+        .get(gaugeName)
+        .map(_.getValue) shouldBe Some(999999)
     }
   }
 }
diff --git a/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActorSpec.scala b/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActorSpec.scala
index ed913606191..93237709c2a 100644
--- a/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/instrumentation/impl/statsd/StatsDInstrumentationServiceActorSpec.scala
@@ -16,7 +16,11 @@ import org.scalatest.matchers.should.Matchers
 
 import scala.concurrent.duration._
 
-class StatsDInstrumentationServiceActorSpec extends TestKitSuite with AnyFlatSpecLike with BeforeAndAfterAll with Matchers {
+class StatsDInstrumentationServiceActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with BeforeAndAfterAll
+    with Matchers {
   behavior of "StatsDInstrumentationServiceActor"
 
   val config = ConfigFactory.parseString(
@@ -35,12 +39,13 @@ class StatsDInstrumentationServiceActorSpec extends TestKitSuite with AnyFlatSpe
   val patience = 1.second
   val testBucket = CromwellBucket(List("test_prefix"), NonEmptyList.of("test", "metric", "bucket"))
   val testGaugeBucket = CromwellBucket(List("test_prefix"), NonEmptyList.of("test", "gauge", "metric", "bucket"))
-  
+
   var udpListenerActor: ActorRef = _
-  
+
   override def beforeAll(): Unit = {
     // Start an actor listening to the UDP port and forwarding messages to the udpProbe
-    udpListenerActor = system.actorOf(Props(new UDPListenerActor(new InetSocketAddress("localhost", 8125), udpProbe.ref)))
+    udpListenerActor =
+      system.actorOf(Props(new UDPListenerActor(new InetSocketAddress("localhost", 8125), udpProbe.ref)))
     // Give a sec to the actor to open an UDP socket
     Thread.sleep(1.second.toMillis)
     super.beforeAll()
@@ -56,45 +61,63 @@ class StatsDInstrumentationServiceActorSpec extends TestKitSuite with AnyFlatSpe
                            metric: CromwellMetric,
                            expectedExactPackets: Set[String],
                            expectedFuzzyPackets: Set[String] = Set.empty,
-                           prependCromwellInstancePrefix: Boolean = false)
-  
+                           prependCromwellInstancePrefix: Boolean = false
+  )
+
   // Note: The current StatsD implementation sends everything as StatsD gauges so we expect all packets to be "...|g"
   List(
-    StatsDTestBit("increment counters", CromwellIncrement(testBucket),
+    StatsDTestBit(
+      "increment counters",
+      CromwellIncrement(testBucket),
       Set("prefix_value.cromwell.test_prefix.test.metric.bucket.samples:1|g"),
       Set("prefix_value.cromwell.test_prefix.test.metric.bucket.m1_rate")
     ),
-    StatsDTestBit("add count", CromwellCount(testBucket, 80),
+    StatsDTestBit(
+      "add count",
+      CromwellCount(testBucket, 80),
       Set("prefix_value.cromwell.test_prefix.test.metric.bucket.samples:81|g"),
       Set("prefix_value.cromwell.test_prefix.test.metric.bucket.m1_rate")
     ),
-    StatsDTestBit("set gauges", CromwellGauge(testGaugeBucket, 89),
-      Set("prefix_value.cromwell.test_prefix.test.gauge.metric.bucket:89|g")
+    StatsDTestBit("set gauges",
+                  CromwellGauge(testGaugeBucket, 89),
+                  Set("prefix_value.cromwell.test_prefix.test.gauge.metric.bucket:89|g")
     ),
-    StatsDTestBit("set timings", CromwellTiming(testBucket.expand("timing"), 5.seconds),
-      Set("prefix_value.cromwell.test_prefix.test.metric.bucket.timing.stddev:0.00|g",
+    StatsDTestBit(
+      "set timings",
+      CromwellTiming(testBucket.expand("timing"), 5.seconds),
+      Set(
+        "prefix_value.cromwell.test_prefix.test.metric.bucket.timing.stddev:0.00|g",
         "prefix_value.cromwell.test_prefix.test.metric.bucket.timing.samples:1|g",
         "prefix_value.cromwell.test_prefix.test.metric.bucket.timing.p95:5000.00|g",
         "prefix_value.cromwell.test_prefix.test.metric.bucket.timing.mean:5000.00|g"
       ),
       Set("prefix_value.cromwell.test_prefix.test.metric.bucket.timing.m1_rate")
     ),
-    StatsDTestBit("increment counters with cromwell id prefix", CromwellIncrement(testBucket),
+    StatsDTestBit(
+      "increment counters with cromwell id prefix",
+      CromwellIncrement(testBucket),
       Set("prefix_value.cromwell.cromwell-101.test_prefix.test.metric.bucket.samples:1|g"),
       Set("prefix_value.cromwell.cromwell-101.test_prefix.test.metric.bucket.m1_rate"),
       prependCromwellInstancePrefix = true
     ),
-    StatsDTestBit("add count with cromwell id prefix", CromwellCount(testBucket, 80),
+    StatsDTestBit(
+      "add count with cromwell id prefix",
+      CromwellCount(testBucket, 80),
       Set("prefix_value.cromwell.cromwell-101.test_prefix.test.metric.bucket.samples:81|g"),
       Set("prefix_value.cromwell.cromwell-101.test_prefix.test.metric.bucket.m1_rate"),
       prependCromwellInstancePrefix = true
     ),
-    StatsDTestBit("set gauges with cromwell id prefix", CromwellGauge(testGaugeBucket, 89),
+    StatsDTestBit(
+      "set gauges with cromwell id prefix",
+      CromwellGauge(testGaugeBucket, 89),
       Set("prefix_value.cromwell.cromwell-101.test_prefix.test.gauge.metric.bucket:89|g"),
       prependCromwellInstancePrefix = true
     ),
-    StatsDTestBit("set timings with cromwell id prefix", CromwellTiming(testBucket.expand("timing"), 5.seconds),
-      Set("prefix_value.cromwell.cromwell-101.test_prefix.test.metric.bucket.timing.stddev:0.00|g",
+    StatsDTestBit(
+      "set timings with cromwell id prefix",
+      CromwellTiming(testBucket.expand("timing"), 5.seconds),
+      Set(
+        "prefix_value.cromwell.cromwell-101.test_prefix.test.metric.bucket.timing.stddev:0.00|g",
         "prefix_value.cromwell.cromwell-101.test_prefix.test.metric.bucket.timing.samples:1|g",
         "prefix_value.cromwell.cromwell-101.test_prefix.test.metric.bucket.timing.p95:5000.00|g",
         "prefix_value.cromwell.cromwell-101.test_prefix.test.metric.bucket.timing.mean:5000.00|g"
@@ -103,38 +126,49 @@ class StatsDInstrumentationServiceActorSpec extends TestKitSuite with AnyFlatSpe
       prependCromwellInstancePrefix = true
     )
   ) foreach {
-    case StatsDTestBit(description, metric, expectedExactPackets, expectedFuzzyPackets, prependCromwellInstancePrefix) =>
+    case StatsDTestBit(description,
+                       metric,
+                       expectedExactPackets,
+                       expectedFuzzyPackets,
+                       prependCromwellInstancePrefix
+        ) =>
       it should description in {
 
         val globalConfig = if (prependCromwellInstancePrefix) cromwellInstanceConfig else ConfigFactory.empty()
 
-        val instrumentationActor = TestActorRef(new StatsDInstrumentationServiceActor(config, globalConfig, registryProbe))
+        val instrumentationActor =
+          TestActorRef(new StatsDInstrumentationServiceActor(config, globalConfig, registryProbe))
         instrumentationActor ! InstrumentationServiceMessage(metric)
-        val received = udpProbe.receiveWhile(patience) {
-          case Udp.Received(data, _) => data.utf8String
+        val received = udpProbe.receiveWhile(patience) { case Udp.Received(data, _) =>
+          data.utf8String
         }
 
-        expectedExactPackets foreach { packet => if (!received.contains(packet)) {
-          val prefix = packet.split(":").head
-          received.find(_.startsWith(prefix)) match {
-            case Some(sharedPrefix) => fail(s"Missing packet: $packet, but found: $sharedPrefix. Should this be a fuzzy packet?")
-            case None => fail(s"Missing packet: $packet, and no packets received with prefix $prefix")
+        expectedExactPackets foreach { packet =>
+          if (!received.contains(packet)) {
+            val prefix = packet.split(":").head
+            received.find(_.startsWith(prefix)) match {
+              case Some(sharedPrefix) =>
+                fail(s"Missing packet: $packet, but found: $sharedPrefix. Should this be a fuzzy packet?")
+              case None => fail(s"Missing packet: $packet, and no packets received with prefix $prefix")
+            }
           }
-        }}
-        expectedFuzzyPackets foreach { packet => if (!received.exists(_.contains(packet))) fail(s"Missing fuzzy packet: $packet") }
+        }
+        expectedFuzzyPackets foreach { packet =>
+          if (!received.exists(_.contains(packet))) fail(s"Missing fuzzy packet: $packet")
+        }
       }
   }
-  
+
   private class UDPListenerActor(remote: InetSocketAddress, sendTo: ActorRef) extends Actor with ActorLogging {
-    implicit val system =  context.system
+    implicit val system = context.system
     IO(Udp) ! Udp.Bind(sendTo, remote)
 
-    def receive = {
-      case Udp.Bound(_) => context.become(ready(sender()))
+    def receive = { case Udp.Bound(_) =>
+      context.become(ready(sender()))
     }
 
     def ready(socket: ActorRef): Receive = {
-      case Udp.Unbind  => socket ! Udp.Unbind
+      case Udp.Unbind => socket ! Udp.Unbind
       case Udp.Unbound => context.stop(self)
       case other => log.error(s"received unexpected message: $other")
     }
diff --git a/services/src/test/scala/cromwell/services/keyvalue/InMemoryKvServiceActor.scala b/services/src/test/scala/cromwell/services/keyvalue/InMemoryKvServiceActor.scala
index c4f0c6177c0..b57ef9a931b 100644
--- a/services/src/test/scala/cromwell/services/keyvalue/InMemoryKvServiceActor.scala
+++ b/services/src/test/scala/cromwell/services/keyvalue/InMemoryKvServiceActor.scala
@@ -30,10 +30,9 @@ final class InMemoryKvServiceActor extends KeyValueServiceActor {
 
   override protected def kvWriteActorProps = Props.empty
 
-  private def respond(replyTo: ActorRef, action: KvAction, response: Future[KvResponse]): Unit = {
+  private def respond(replyTo: ActorRef, action: KvAction, response: Future[KvResponse]): Unit =
     response.onComplete {
       case Success(x) => replyTo ! x
       case Failure(ex) => replyTo ! KvFailure(action, ex)
     }
-  }
 }
diff --git a/services/src/test/scala/cromwell/services/keyvalue/KvClientSpec.scala b/services/src/test/scala/cromwell/services/keyvalue/KvClientSpec.scala
index f8af9a21132..00d8dd02079 100644
--- a/services/src/test/scala/cromwell/services/keyvalue/KvClientSpec.scala
+++ b/services/src/test/scala/cromwell/services/keyvalue/KvClientSpec.scala
@@ -58,5 +58,3 @@ class KvClientSpec extends TestKitSuite with AnyFlatSpecLike with Matchers {
 class KvTestClientActor(val serviceRegistryActor: ActorRef) extends Actor with ActorLogging with KvClient {
   override def receive: Receive = kvClientReceive orElse Actor.ignoringBehavior
 }
-
-
diff --git a/services/src/test/scala/cromwell/services/keyvalue/impl/KeyValueDatabaseSpec.scala b/services/src/test/scala/cromwell/services/keyvalue/impl/KeyValueDatabaseSpec.scala
index e673b6f012f..4485f23f347 100644
--- a/services/src/test/scala/cromwell/services/keyvalue/impl/KeyValueDatabaseSpec.scala
+++ b/services/src/test/scala/cromwell/services/keyvalue/impl/KeyValueDatabaseSpec.scala
@@ -18,7 +18,12 @@ import org.scalatest.time.{Millis, Seconds, Span}
 
 import scala.concurrent.{ExecutionContext, Future}
 
-class KeyValueDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalaFutures with RecoverMethods {
+class KeyValueDatabaseSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalaFutures
+    with RecoverMethods {
 
   implicit val ec: ExecutionContext = ExecutionContext.global
   implicit val defaultPatience: PatienceConfig = PatienceConfig(scaled(Span(5, Seconds)), scaled(Span(100, Millis)))
@@ -28,7 +33,8 @@ class KeyValueDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
 
     val containerOpt: Option[Container] = DatabaseTestKit.getDatabaseTestContainer(databaseSystem)
 
-    lazy val dataAccess = DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, EngineDatabaseType, databaseSystem)
+    lazy val dataAccess =
+      DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, EngineDatabaseType, databaseSystem)
 
     val workflowId = WorkflowId.randomId().toString
     val callFqn = "AwesomeWorkflow.GoodJob"
@@ -70,7 +76,7 @@ class KeyValueDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     )
 
     it should "start database container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.start }
+      containerOpt.foreach(_.start)
     }
 
     it should "upsert and retrieve kv pairs correctly" taggedAs DbmsTest in {
@@ -116,13 +122,13 @@ class KeyValueDatabaseSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     }
 
     it should "stop container" taggedAs DbmsTest in {
-      containerOpt.foreach { _.stop() }
+      containerOpt.foreach(_.stop())
     }
   }
 }
 
 object KeyValueDatabaseSpec {
-  private def getFailureRegex(databaseSystem: DatabaseSystem): String = {
+  private def getFailureRegex(databaseSystem: DatabaseSystem): String =
     databaseSystem.platform match {
       case HsqldbDatabasePlatform =>
         """integrity constraint violation: NOT NULL check constraint; """ +
@@ -133,14 +139,12 @@ object KeyValueDatabaseSpec {
         """ERROR: null value in column "STORE_VALUE" """ +
           """(of relation "JOB_KEY_VALUE_ENTRY" )?violates not-null constraint"""
     }
-  }
 
-  private def getFailureClass(databaseSystem: DatabaseSystem): Class[_ <: Exception] = {
+  private def getFailureClass(databaseSystem: DatabaseSystem): Class[_ <: Exception] =
     databaseSystem.platform match {
       case HsqldbDatabasePlatform => classOf[SQLIntegrityConstraintViolationException]
       case MariadbDatabasePlatform => classOf[BatchUpdateException]
       case MysqlDatabasePlatform => classOf[BatchUpdateException]
       case PostgresqlDatabasePlatform => classOf[PSQLException]
     }
-  }
 }
diff --git a/services/src/test/scala/cromwell/services/keyvalue/impl/KeyValueServiceActorSpec.scala b/services/src/test/scala/cromwell/services/keyvalue/impl/KeyValueServiceActorSpec.scala
index 1faee0ac315..781c163164b 100644
--- a/services/src/test/scala/cromwell/services/keyvalue/impl/KeyValueServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/keyvalue/impl/KeyValueServiceActorSpec.scala
@@ -16,13 +16,13 @@ class KeyValueServiceActorSpec extends ServicesSpec with Eventually {
 
   val cromwellConfig: Config = ConfigFactory.parseString(
     s"""services: {
-        |  KeyValue: {
-        |    class: "cromwell.services.keyvalue.KeyValueServiceActor"
-        |    config {
-        |      option1: "value1"
-        |    }
-        |  }
-        |}
+       |  KeyValue: {
+       |    class: "cromwell.services.keyvalue.KeyValueServiceActor"
+       |    config {
+       |      option1: "value1"
+       |    }
+       |  }
+       |}
      """.stripMargin
   )
 
@@ -30,7 +30,7 @@ class KeyValueServiceActorSpec extends ServicesSpec with Eventually {
   val sqlKvServiceActor: ActorRef =
     system.actorOf(
       props = SqlKeyValueServiceActor.props(emptyConfig, emptyConfig, TestProbe("serviceRegistryActor").ref),
-      name = "sqlKvServiceActor",
+      name = "sqlKvServiceActor"
     )
   val wfID: WorkflowId = WorkflowId.randomId()
 
@@ -53,23 +53,23 @@ class KeyValueServiceActorSpec extends ServicesSpec with Eventually {
     "insert a key/value" in {
       val kvPut1 = KvPut(KvPair(ScopedKey(wfID, jobKey1, "k1"), "v1"))
 
-          (for {
-            putResult <- (sqlKvServiceActor ? kvPut1).mapTo[KvResponse]
-            _ = putResult shouldEqual KvPutSuccess(kvPut1)
-            putResult <- (sqlKvServiceActor ? KvPut(kvPair2)).mapTo[KvResponse]
-            _ = putResult shouldEqual KvPutSuccess(KvPut(kvPair2))
-            putResult <- (sqlKvServiceActor ? KvPut(kvPair3)).mapTo[KvResponse]
-            _ = putResult shouldEqual KvPutSuccess(KvPut(kvPair3))
-          } yield ()).futureValue
+      (for {
+        putResult <- (sqlKvServiceActor ? kvPut1).mapTo[KvResponse]
+        _ = putResult shouldEqual KvPutSuccess(kvPut1)
+        putResult <- (sqlKvServiceActor ? KvPut(kvPair2)).mapTo[KvResponse]
+        _ = putResult shouldEqual KvPutSuccess(KvPut(kvPair2))
+        putResult <- (sqlKvServiceActor ? KvPut(kvPair3)).mapTo[KvResponse]
+        _ = putResult shouldEqual KvPutSuccess(KvPut(kvPair3))
+      } yield ()).futureValue
     }
 
     "return error if key doesn't exist" in {
       val scopedKeyNeverPut = ScopedKey(wfID, jobKey2, "k2")
 
-          (for {
-            getResult <- (sqlKvServiceActor ? KvGet(scopedKeyNeverPut)).mapTo[KvResponse]
-            _ = getResult shouldEqual KvKeyLookupFailed(KvGet(scopedKeyNeverPut))
-          } yield ()).futureValue
+      (for {
+        getResult <- (sqlKvServiceActor ? KvGet(scopedKeyNeverPut)).mapTo[KvResponse]
+        _ = getResult shouldEqual KvKeyLookupFailed(KvGet(scopedKeyNeverPut))
+      } yield ()).futureValue
     }
 
     "be able to overwrite values" in {
diff --git a/services/src/test/scala/cromwell/services/loadcontroller/impl/LoadControllerServiceActorSpec.scala b/services/src/test/scala/cromwell/services/loadcontroller/impl/LoadControllerServiceActorSpec.scala
index 531f7106460..e5d6f9d9bfc 100644
--- a/services/src/test/scala/cromwell/services/loadcontroller/impl/LoadControllerServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/loadcontroller/impl/LoadControllerServiceActorSpec.scala
@@ -19,9 +19,14 @@ object LoadControllerServiceActorSpec {
   val Config = ConfigFactory.parseString("control-frequency = 1 second")
 }
 
-class LoadControllerServiceActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with Eventually with ImplicitSender {
+class LoadControllerServiceActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with Eventually
+    with ImplicitSender {
   behavior of "LoadControllerServiceActor"
-  override implicit val patienceConfig: PatienceConfig = PatienceConfig(scaled(2.seconds))
+  implicit override val patienceConfig: PatienceConfig = PatienceConfig(scaled(2.seconds))
 
   it should "record metrics" in {
     val loadActor = TestActorRef(new LoadControllerServiceActor(Config, Config, TestProbe().ref))
diff --git a/services/src/test/scala/cromwell/services/metadata/MetadataQuerySpec.scala b/services/src/test/scala/cromwell/services/metadata/MetadataQuerySpec.scala
index 5a908aaf092..83737c37d11 100644
--- a/services/src/test/scala/cromwell/services/metadata/MetadataQuerySpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/MetadataQuerySpec.scala
@@ -4,13 +4,22 @@ import akka.actor.{Actor, ActorRef, Props}
 import akka.testkit.TestProbe
 import com.typesafe.config.{Config, ConfigFactory}
 import cromwell.core.TestKitSuite
-import cromwell.services.metadata.MetadataQuerySpec.{CannedResponseReadMetadataWorker, MetadataServiceActor_CustomizeRead}
-import cromwell.services.metadata.MetadataService.{BuildMetadataJsonAction, MetadataServiceResponse, QueryForWorkflowsMatchingParameters, WorkflowQueryResponse, WorkflowQuerySuccess}
+import cromwell.services.metadata.MetadataQuerySpec.{
+  CannedResponseReadMetadataWorker,
+  MetadataServiceActor_CustomizeRead
+}
+import cromwell.services.metadata.MetadataService.{
+  BuildMetadataJsonAction,
+  MetadataServiceResponse,
+  QueryForWorkflowsMatchingParameters,
+  WorkflowQueryResponse,
+  WorkflowQuerySuccess
+}
 import cromwell.services.metadata.impl.{MetadataServiceActor, MetadataServiceActorSpec}
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 
-class MetadataQuerySpec extends TestKitSuite with AnyFlatSpecLike with Matchers  {
+class MetadataQuerySpec extends TestKitSuite with AnyFlatSpecLike with Matchers {
 
   it should "correctly forward requests to read workers and responses back to requesters" in {
 
@@ -26,7 +35,9 @@ class MetadataQuerySpec extends TestKitSuite with AnyFlatSpecLike with Matchers
     val requester = TestProbe("MetadataServiceClientProbe")
     def readWorkerProps() = Props(new CannedResponseReadMetadataWorker(Map(request -> response)))
     val serviceRegistry = TestProbe("ServiceRegistryProbe")
-    val metadataService = system.actorOf(MetadataServiceActor_CustomizeRead.props(readWorkerProps, serviceRegistry), "MetadataServiceUnderTest")
+    val metadataService = system.actorOf(MetadataServiceActor_CustomizeRead.props(readWorkerProps, serviceRegistry),
+                                         "MetadataServiceUnderTest"
+    )
 
     requester.send(metadataService, request)
     requester.expectMsg(response)
@@ -35,12 +46,17 @@ class MetadataQuerySpec extends TestKitSuite with AnyFlatSpecLike with Matchers
 
 }
 
-
 object MetadataQuerySpec {
-  final class MetadataServiceActor_CustomizeRead(config: Config, serviceRegistryActor: ActorRef, readWorkerMaker: () => Props)
-    extends MetadataServiceActor(MetadataServiceActorSpec.globalConfigToMetadataServiceConfig(config), config, serviceRegistryActor) {
-
-    override def readMetadataWorkerActorProps(): Props = readWorkerMaker.apply().withDispatcher(cromwell.core.Dispatcher.ServiceDispatcher)
+  final class MetadataServiceActor_CustomizeRead(config: Config,
+                                                 serviceRegistryActor: ActorRef,
+                                                 readWorkerMaker: () => Props
+  ) extends MetadataServiceActor(MetadataServiceActorSpec.globalConfigToMetadataServiceConfig(config),
+                                 config,
+                                 serviceRegistryActor
+      ) {
+
+    override def readMetadataWorkerActorProps(): Props =
+      readWorkerMaker.apply().withDispatcher(cromwell.core.Dispatcher.ServiceDispatcher)
   }
 
   object MetadataServiceActor_CustomizeRead {
@@ -50,10 +66,10 @@ object MetadataQuerySpec {
       Props(new MetadataServiceActor_CustomizeRead(config, serviceRegistryProbe.ref, readActorProps))
   }
 
-
-  final class CannedResponseReadMetadataWorker(cannedResponses: Map[BuildMetadataJsonAction, MetadataServiceResponse]) extends Actor {
-    override def receive: Receive = {
-      case msg: BuildMetadataJsonAction => sender() ! cannedResponses.getOrElse(msg, throw new Exception(s"Unexpected inbound message: $msg"))
+  final class CannedResponseReadMetadataWorker(cannedResponses: Map[BuildMetadataJsonAction, MetadataServiceResponse])
+      extends Actor {
+    override def receive: Receive = { case msg: BuildMetadataJsonAction =>
+      sender() ! cannedResponses.getOrElse(msg, throw new Exception(s"Unexpected inbound message: $msg"))
     }
   }
 }
diff --git a/services/src/test/scala/cromwell/services/metadata/MetadataServiceSpec.scala b/services/src/test/scala/cromwell/services/metadata/MetadataServiceSpec.scala
index da4587c55f3..d3d596e45ce 100644
--- a/services/src/test/scala/cromwell/services/metadata/MetadataServiceSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/MetadataServiceSpec.scala
@@ -32,12 +32,16 @@ class MetadataServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     val womArray = WomArray(WomArrayType(WomStringType), Seq(WomString("Hello"), WomString("world!")))
     val emptyWomArray = WomArray(WomArrayType(WomStringType), Seq.empty)
 
-    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"), womArray).toList should contain theSameElementsInOrderAs List(
+    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"),
+                             womArray
+    ).toList should contain theSameElementsInOrderAs List(
       MetadataEvent(MetadataKey(workflowId, None, "root[0]"), MetadataValue("Hello")),
       MetadataEvent(MetadataKey(workflowId, None, "root[1]"), MetadataValue("world!"))
     )
 
-    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"), emptyWomArray).toList should contain theSameElementsAs List(
+    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"),
+                             emptyWomArray
+    ).toList should contain theSameElementsAs List(
       MetadataEvent.empty(MetadataKey(workflowId, None, "root[]"))
     )
   }
@@ -45,18 +49,24 @@ class MetadataServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   it should "convert a WomMap to MetadataEvents" in {
     import MetadataService._
     val workflowId = WorkflowId.randomId()
-    val womMap = WomMap(WomMapType(WomStringType, WomStringType), Map(
-      WomString("Hello") -> WomString("world!"),
-      WomString("Goodbye") -> WomString("world!")
-    ))
+    val womMap = WomMap(WomMapType(WomStringType, WomStringType),
+                        Map(
+                          WomString("Hello") -> WomString("world!"),
+                          WomString("Goodbye") -> WomString("world!")
+                        )
+    )
     val emptyWomMap = WomMap(WomMapType(WomStringType, WomStringType), Map.empty)
 
-    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"), womMap).toList should contain theSameElementsInOrderAs List(
+    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"),
+                             womMap
+    ).toList should contain theSameElementsInOrderAs List(
       MetadataEvent(MetadataKey(workflowId, None, "root:Hello"), MetadataValue("world!")),
       MetadataEvent(MetadataKey(workflowId, None, "root:Goodbye"), MetadataValue("world!"))
     )
 
-    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"), emptyWomMap).toList should contain theSameElementsAs List(
+    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"),
+                             emptyWomMap
+    ).toList should contain theSameElementsAs List(
       MetadataEvent.empty(MetadataKey(workflowId, None, "root"))
     )
   }
@@ -82,7 +92,9 @@ class MetadataServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
       )
     )
 
-    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"), womMaybePopulatedFileOuter).toList should contain theSameElementsInOrderAs List(
+    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"),
+                             womMaybePopulatedFileOuter
+    ).toList should contain theSameElementsInOrderAs List(
       MetadataEvent(MetadataKey(workflowId, None, "root:class"), MetadataValue("File")),
       MetadataEvent(MetadataKey(workflowId, None, "root:location"), MetadataValue("fileValue")),
       MetadataEvent(MetadataKey(workflowId, None, "root:checksum"), MetadataValue("checksum")),
@@ -119,7 +131,9 @@ class MetadataServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
       )
     )
 
-    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"), womMaybeListedDirectoryOuter).toList should contain theSameElementsInOrderAs List(
+    womValueToMetadataEvents(MetadataKey(workflowId, None, "root"),
+                             womMaybeListedDirectoryOuter
+    ).toList should contain theSameElementsInOrderAs List(
       MetadataEvent(MetadataKey(workflowId, None, "root:class"), MetadataValue("Directory")),
       MetadataEvent(MetadataKey(workflowId, None, "root:location"), MetadataValue("directoryValue")),
       MetadataEvent(MetadataKey(workflowId, None, "root:listing[0]:class"), MetadataValue("Directory")),
@@ -137,12 +151,14 @@ class MetadataServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
       ("womValue", "metadataValue"),
       (WomString("hi"), MetadataValue("hi", MetadataString)),
       (WomInteger(1), MetadataValue("1", MetadataInt)),
-      (WomFloat(1F), MetadataValue("1.0", MetadataNumber)),
+      (WomFloat(1f), MetadataValue("1.0", MetadataNumber)),
       (WomBoolean(true), MetadataValue("true", MetadataBoolean))
     )
 
     forAll(values) { (womValue, metadataValue) =>
-      womValueToMetadataEvents(MetadataKey(workflowId, None, "root"), womValue).toList should contain theSameElementsAs List(
+      womValueToMetadataEvents(MetadataKey(workflowId, None, "root"),
+                               womValue
+      ).toList should contain theSameElementsAs List(
         metadata.MetadataEvent(MetadataKey(workflowId, None, "root"), metadataValue)
       )
     }
@@ -192,7 +208,8 @@ class MetadataServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
 
     val (outerPrefix, outerCausedBys, outerFailureId) = validateExceptionMessage(events.head, workflowId, tMsg)
     val (cause1Prefix, cause1CausedBys, cause1FailureId) = validateExceptionMessage(events(1), workflowId, causeMsg)
-    val (cause2Prefix, cause2CausedBys, cause2FailureId) = validateExceptionMessage(events(2), workflowId, innerCauseMsg)
+    val (cause2Prefix, cause2CausedBys, cause2FailureId) =
+      validateExceptionMessage(events(2), workflowId, innerCauseMsg)
     events(3).key.key should be(s"$cause2Prefix[$cause2FailureId]$cause2CausedBys:causedBy[]")
 
     outerPrefix should be(pathToFailures)
@@ -236,7 +253,8 @@ class MetadataServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     runtimeCausedBys should be("")
 
     // Aggregate exception:
-    val (aggregatePrefix, aggregateCausedBys, aggregateFailureId) = validateExceptionMessage(events(1), workflowId, causeContext)
+    val (aggregatePrefix, aggregateCausedBys, aggregateFailureId) =
+      validateExceptionMessage(events(1), workflowId, causeContext)
     aggregatePrefix should be(pathToFailures)
     aggregateCausedBys should be(":causedBy[0]")
     aggregateFailureId should be(runtimeFailureId)
@@ -250,7 +268,8 @@ class MetadataServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
 
     // cause2, caused by innerCause caused by []
     val (cause2Prefix, cause2CausedBys, cause2FailureId) = validateExceptionMessage(events(4), workflowId, cause2Msg)
-    val (innerCausePrefix, innerCauseCausedBys, innerCauseFailureIds) = validateExceptionMessage(events(5), workflowId, innerCauseMsg)
+    val (innerCausePrefix, innerCauseCausedBys, innerCauseFailureIds) =
+      validateExceptionMessage(events(5), workflowId, innerCauseMsg)
     cause2Prefix should be(pathToFailures)
     cause2CausedBys should be(":causedBy[0]:causedBy[1]")
     cause2FailureId should be(runtimeFailureId)
@@ -277,6 +296,9 @@ class MetadataServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
         case failureMessageRegex(prefix, failureIndex, causedBys) => (prefix, causedBys, failureIndex)
         case _ => fail("Unexpected failure key format: " + k.key)
       }
-    case _ => fail("throwableToMetadataEvents generated a metadata event without a metadata value! Bad throwableToMetadataEvents! Very bad!")
+    case _ =>
+      fail(
+        "throwableToMetadataEvents generated a metadata event without a metadata value! Bad throwableToMetadataEvents! Very bad!"
+      )
   }
 }
diff --git a/services/src/test/scala/cromwell/services/metadata/MetadataStatisticsRecorderSpec.scala b/services/src/test/scala/cromwell/services/metadata/MetadataStatisticsRecorderSpec.scala
index 2096e3f9553..d10d8146250 100644
--- a/services/src/test/scala/cromwell/services/metadata/MetadataStatisticsRecorderSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/MetadataStatisticsRecorderSpec.scala
@@ -16,10 +16,18 @@ class MetadataStatisticsRecorderSpec extends AnyFlatSpec with Matchers {
 
   behavior of "MetadataStatisticsRecorder"
 
-  def uninterestingWriteEvent(workflowId: WorkflowId)(): MetadataEvent = MetadataEvent(MetadataKey(workflowId, None, "foo"), MetadataValue(WomInteger(1)))
-  def parentNotificationEvent(rootWorkflowId: WorkflowId, parentWorkflowId: WorkflowId, subWorkflowId: WorkflowId): Vector[MetadataEvent] = Vector(
-    MetadataEvent(MetadataKey(subWorkflowId, None, "rootWorkflowId"), MetadataValue(WomString(rootWorkflowId.toString))),
-    MetadataEvent(MetadataKey(subWorkflowId, None, "parentWorkflowId"), MetadataValue(WomString(parentWorkflowId.toString)))
+  def uninterestingWriteEvent(workflowId: WorkflowId)(): MetadataEvent =
+    MetadataEvent(MetadataKey(workflowId, None, "foo"), MetadataValue(WomInteger(1)))
+  def parentNotificationEvent(rootWorkflowId: WorkflowId,
+                              parentWorkflowId: WorkflowId,
+                              subWorkflowId: WorkflowId
+  ): Vector[MetadataEvent] = Vector(
+    MetadataEvent(MetadataKey(subWorkflowId, None, "rootWorkflowId"),
+                  MetadataValue(WomString(rootWorkflowId.toString))
+    ),
+    MetadataEvent(MetadataKey(subWorkflowId, None, "parentWorkflowId"),
+                  MetadataValue(WomString(parentWorkflowId.toString))
+    )
   )
 
   it should "count rows for one workflow and create alerts every interval" in {
@@ -28,7 +36,9 @@ class MetadataStatisticsRecorderSpec extends AnyFlatSpec with Matchers {
 
     (1 to 10) foreach { i =>
       recorder.processEventsAndGenerateAlerts(9 of uninterestingWriteEvent(workflowId)) should be(Vector.empty)
-      recorder.processEventsAndGenerateAlerts(1 of uninterestingWriteEvent(workflowId)) should be(Vector(HeavyMetadataAlert(workflowId, 10L * i)))
+      recorder.processEventsAndGenerateAlerts(1 of uninterestingWriteEvent(workflowId)) should be(
+        Vector(HeavyMetadataAlert(workflowId, 10L * i))
+      )
       ()
     }
   }
@@ -42,7 +52,9 @@ class MetadataStatisticsRecorderSpec extends AnyFlatSpec with Matchers {
       val bigMetadataDump = Math.abs(Random.nextInt(101)) + 10
       val expectedCountAfterProcessing = runningCounter + bigMetadataDump
 
-      recorder.processEventsAndGenerateAlerts(bigMetadataDump of uninterestingWriteEvent(workflowId)) should be(Vector(HeavyMetadataAlert(workflowId, expectedCountAfterProcessing)))
+      recorder.processEventsAndGenerateAlerts(bigMetadataDump of uninterestingWriteEvent(workflowId)) should be(
+        Vector(HeavyMetadataAlert(workflowId, expectedCountAfterProcessing))
+      )
       runningCounter = expectedCountAfterProcessing
       ()
     }
@@ -60,11 +72,13 @@ class MetadataStatisticsRecorderSpec extends AnyFlatSpec with Matchers {
         (7 of uninterestingWriteEvent(workflowId3))
     ) should be(Vector.empty)
 
-    recorder.processEventsAndGenerateAlerts(
-      (3 of uninterestingWriteEvent(workflowId1)) ++
-        (5 of uninterestingWriteEvent(workflowId2)) ++
-        (7 of uninterestingWriteEvent(workflowId3))
-    ).toSet should be(Set(HeavyMetadataAlert(workflowId2, 10), HeavyMetadataAlert(workflowId3, 14)))
+    recorder
+      .processEventsAndGenerateAlerts(
+        (3 of uninterestingWriteEvent(workflowId1)) ++
+          (5 of uninterestingWriteEvent(workflowId2)) ++
+          (7 of uninterestingWriteEvent(workflowId3))
+      )
+      .toSet should be(Set(HeavyMetadataAlert(workflowId2, 10), HeavyMetadataAlert(workflowId3, 14)))
 
     recorder.processEventsAndGenerateAlerts(
       (3 of uninterestingWriteEvent(workflowId1)) ++
@@ -72,11 +86,15 @@ class MetadataStatisticsRecorderSpec extends AnyFlatSpec with Matchers {
         (7 of uninterestingWriteEvent(workflowId3))
     ) should be(Vector.empty)
 
-    recorder.processEventsAndGenerateAlerts(
-      (3 of uninterestingWriteEvent(workflowId1)) ++
-        (5 of uninterestingWriteEvent(workflowId2)) ++
-        (7 of uninterestingWriteEvent(workflowId3))
-    ).toSet should be(Set(HeavyMetadataAlert(workflowId1, 12), HeavyMetadataAlert(workflowId2, 20), HeavyMetadataAlert(workflowId3, 28)))
+    recorder
+      .processEventsAndGenerateAlerts(
+        (3 of uninterestingWriteEvent(workflowId1)) ++
+          (5 of uninterestingWriteEvent(workflowId2)) ++
+          (7 of uninterestingWriteEvent(workflowId3))
+      )
+      .toSet should be(
+      Set(HeavyMetadataAlert(workflowId1, 12), HeavyMetadataAlert(workflowId2, 20), HeavyMetadataAlert(workflowId3, 28))
+    )
   }
 
   it should "be able to accumulate counts from subworkflows" in {
@@ -89,41 +107,55 @@ class MetadataStatisticsRecorderSpec extends AnyFlatSpec with Matchers {
 
     // Recording SW1 parentage adds 2 events against subWorkflowId1 (and thus rootWorkflowId)
     withClue(recorder.statusString()) {
-      recorder.processEventsAndGenerateAlerts(parentNotificationEvent(rootWorkflowId, rootWorkflowId, subWorkflow1Id)) should be(Vector.empty)
+      recorder.processEventsAndGenerateAlerts(
+        parentNotificationEvent(rootWorkflowId, rootWorkflowId, subWorkflow1Id)
+      ) should be(Vector.empty)
     }
 
     // Recording SW2 parentage adds 2 events against subWorkflowId2 (and thus subWorkflow1Id and thus rootWorkflowId)
     withClue(recorder.statusString()) {
-      recorder.processEventsAndGenerateAlerts(parentNotificationEvent(rootWorkflowId, subWorkflow1Id, subWorkflow2Id)) should be(Vector.empty)
+      recorder.processEventsAndGenerateAlerts(
+        parentNotificationEvent(rootWorkflowId, subWorkflow1Id, subWorkflow2Id)
+      ) should be(Vector.empty)
     }
 
     // To get started, add 7 events to the root subworkflow:
     withClue(recorder.statusString()) {
-      recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(rootWorkflowId)) should be(Vector(HeavyMetadataAlert(rootWorkflowId, 11)))
+      recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(rootWorkflowId)) should be(
+        Vector(HeavyMetadataAlert(rootWorkflowId, 11))
+      )
     }
 
     // Current standing: root: 11, sub1: 4, sub2: 2
 
     withClue(recorder.statusString()) {
-      recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow1Id)) should be(Vector(HeavyMetadataAlert(subWorkflow1Id, 11)))
+      recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow1Id)) should be(
+        Vector(HeavyMetadataAlert(subWorkflow1Id, 11))
+      )
     }
 
     // Current standing: root: 18, sub1: 11, sub2: 2
 
     withClue(recorder.statusString()) {
-      recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow2Id)) should be(Vector(HeavyMetadataAlert(rootWorkflowId, 25)))
+      recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow2Id)) should be(
+        Vector(HeavyMetadataAlert(rootWorkflowId, 25))
+      )
     }
 
     // Current standing: root: 25, sub1: 18, sub2: 9
 
     withClue(recorder.statusString()) {
-      recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow1Id)) should be(Vector(HeavyMetadataAlert(subWorkflow1Id, 25)))
+      recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow1Id)) should be(
+        Vector(HeavyMetadataAlert(subWorkflow1Id, 25))
+      )
     }
 
     // Current standing: root: 32, sub1: 25, sub2: 9
 
     withClue(recorder.statusString()) {
-      recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow2Id)).toSet should be(Set(HeavyMetadataAlert(rootWorkflowId, 39), HeavyMetadataAlert(subWorkflow2Id, 16)))
+      recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow2Id)).toSet should be(
+        Set(HeavyMetadataAlert(rootWorkflowId, 39), HeavyMetadataAlert(subWorkflow2Id, 16))
+      )
     }
 
     // Current standing: root: 39, sub1: 32, sub2: 16
@@ -135,8 +167,12 @@ class MetadataStatisticsRecorderSpec extends AnyFlatSpec with Matchers {
     val subWorkflow1Id = WorkflowId(UUID.randomUUID())
     val subWorkflow2Id = WorkflowId(UUID.randomUUID())
 
-    recorder.processEventsAndGenerateAlerts(parentNotificationEvent(rootWorkflowId, rootWorkflowId, subWorkflow1Id)) should be(Vector.empty)
-    recorder.processEventsAndGenerateAlerts(parentNotificationEvent(rootWorkflowId, subWorkflow1Id, subWorkflow2Id)) should be(Vector.empty)
+    recorder.processEventsAndGenerateAlerts(
+      parentNotificationEvent(rootWorkflowId, rootWorkflowId, subWorkflow1Id)
+    ) should be(Vector.empty)
+    recorder.processEventsAndGenerateAlerts(
+      parentNotificationEvent(rootWorkflowId, subWorkflow1Id, subWorkflow2Id)
+    ) should be(Vector.empty)
 
     // If we were accumulating these would alert, but we see nothing if not accumulating:
     recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow1Id)) should be(Vector.empty)
@@ -144,7 +180,11 @@ class MetadataStatisticsRecorderSpec extends AnyFlatSpec with Matchers {
 
     // When we trip the limits, we should only see alerts for individual workflows.
     // Note: it's 16 not 14 because of the two parent notification entries above
-    recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow1Id)) should be(Vector(HeavyMetadataAlert(subWorkflow1Id, 16)))
-    recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow2Id)) should be(Vector(HeavyMetadataAlert(subWorkflow2Id, 16)))
+    recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow1Id)) should be(
+      Vector(HeavyMetadataAlert(subWorkflow1Id, 16))
+    )
+    recorder.processEventsAndGenerateAlerts(7 of uninterestingWriteEvent(subWorkflow2Id)) should be(
+      Vector(HeavyMetadataAlert(subWorkflow2Id, 16))
+    )
   }
 }
diff --git a/services/src/test/scala/cromwell/services/metadata/QueryForWorkflowsMatchingParametersSpec.scala b/services/src/test/scala/cromwell/services/metadata/QueryForWorkflowsMatchingParametersSpec.scala
index 344b01ef410..fff625d2500 100644
--- a/services/src/test/scala/cromwell/services/metadata/QueryForWorkflowsMatchingParametersSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/QueryForWorkflowsMatchingParametersSpec.scala
@@ -25,10 +25,10 @@ class QueryForWorkflowsMatchingParametersSpec extends AnyWordSpec with CromwellT
           r.endDate should be(Symbol("empty"))
           r.names should be(Symbol("empty"))
           r.statuses should be(Symbol("empty"))
-          r.labelsAnd should be (Symbol("empty"))
-          r.labelsOr should be (Symbol("empty"))
-          r.excludeLabelsAnd should be (Symbol("empty"))
-          r.excludeLabelsOr should be (Symbol("empty"))
+          r.labelsAnd should be(Symbol("empty"))
+          r.labelsOr should be(Symbol("empty"))
+          r.excludeLabelsAnd should be(Symbol("empty"))
+          r.excludeLabelsOr should be(Symbol("empty"))
           r.submissionTime should be(Symbol("empty"))
         case Invalid(fs) =>
           throw new RuntimeException(fs.toList.mkString(", "))
@@ -200,7 +200,7 @@ class QueryForWorkflowsMatchingParametersSpec extends AnyWordSpec with CromwellT
       )
       val result = WorkflowQueryParameters.runValidation(rawParameters)
       result match {
-        case Valid(_) => //good
+        case Valid(_) => // good
         case Invalid(fs) =>
           fs.toList should have size 1
       }
@@ -230,7 +230,7 @@ class QueryForWorkflowsMatchingParametersSpec extends AnyWordSpec with CromwellT
       )
       val result = WorkflowQueryParameters.runValidation(rawParameters)
       result match {
-        case Valid(_) => //good
+        case Valid(_) => // good
         case Invalid(fs) =>
           fs.toList should have size 1
       }
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
index 2a812419775..c97969abf02 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala
@@ -38,8 +38,13 @@ object MetadataDatabaseAccessSpec {
   val Subworkflow2Name = "test_subworkflow_2"
 }
 
-class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with ScalaFutures
-  with BeforeAndAfterAll with Eventually {
+class MetadataDatabaseAccessSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with ScalaFutures
+    with BeforeAndAfterAll
+    with Eventually {
   import MetadataDatabaseAccessSpec._
 
   implicit val ec: ExecutionContext = ExecutionContext.global
@@ -53,9 +58,11 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
 
     lazy val dataAccess: MetadataDatabaseAccess with MetadataServicesStore =
       new MetadataDatabaseAccess with MetadataServicesStore {
-        override val metadataDatabaseInterface: MetadataSlickDatabase = {
-          DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, MetadataDatabaseType, databaseSystem)
-        }
+        override val metadataDatabaseInterface: MetadataSlickDatabase =
+          DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt,
+                                                                        MetadataDatabaseType,
+                                                                        databaseSystem
+          )
       }
 
     def publishMetadataEvents(baseKey: MetadataKey, keyValues: Array[(String, String)]): Future[Unit] = {
@@ -65,9 +72,13 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       dataAccess.addMetadataEvents(events)
     }
 
-    def baseWorkflowMetadata(name: String, labels: Set[Label] = Set.empty, workflowId: WorkflowId = WorkflowId.randomId()): Future[WorkflowId] = {
+    def baseWorkflowMetadata(name: String,
+                             labels: Set[Label] = Set.empty,
+                             workflowId: WorkflowId = WorkflowId.randomId()
+    ): Future[WorkflowId] = {
       val defaultLabels = Set(Label("cromwell-workflow-name", name))
-      val labelMetadata = (labels ++ defaultLabels).map(label => (s"${WorkflowMetadataKeys.Labels}:${label.key}", label.value)).toArray
+      val labelMetadata =
+        (labels ++ defaultLabels).map(label => (s"${WorkflowMetadataKeys.Labels}:${label.key}", label.value)).toArray
 
       val workflowKey = MetadataKey(workflowId, jobKey = None, key = null)
       def keyAndValue(name: String) = Array(
@@ -80,14 +91,17 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       publishMetadataEvents(workflowKey, keyAndValue(name)).map(_ => workflowId)
     }
 
-    def subworkflowMetadata(parentWorkflowId: WorkflowId, subworkflowName: String, workflowId: WorkflowId = WorkflowId.randomId()): Future[WorkflowId] = {
+    def subworkflowMetadata(parentWorkflowId: WorkflowId,
+                            subworkflowName: String,
+                            workflowId: WorkflowId = WorkflowId.randomId()
+    ): Future[WorkflowId] = {
       val workflowKey = MetadataKey(workflowId, jobKey = None, key = null)
       val metadataKeys = Array(
         (WorkflowMetadataKeys.Status, WorkflowRunning.toString),
         (WorkflowMetadataKeys.Name, subworkflowName),
         (WorkflowMetadataKeys.StartTime, OffsetDateTime.now.toUtcMilliString),
         (WorkflowMetadataKeys.ParentWorkflowId, parentWorkflowId.toString),
-        (WorkflowMetadataKeys.RootWorkflowId, parentWorkflowId.toString),
+        (WorkflowMetadataKeys.RootWorkflowId, parentWorkflowId.toString)
       )
 
       publishMetadataEvents(workflowKey, metadataKeys).map(_ => workflowId)
@@ -98,13 +112,14 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       val keyAndValue = Array(
         (WorkflowMetadataKeys.Status, WorkflowRunning.toString),
         (WorkflowMetadataKeys.Status, WorkflowSucceeded.toString),
-        (WorkflowMetadataKeys.EndTime, OffsetDateTime.now.toUtcMilliString))
+        (WorkflowMetadataKeys.EndTime, OffsetDateTime.now.toUtcMilliString)
+      )
 
       publishMetadataEvents(workflowKey, keyAndValue).map(_ => id)
     }
 
     it should "start container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.start }
+      containerOpt.foreach(_.start)
     }
 
     it should "properly get next workflow to archive and number of workflows left to archive" taggedAs DbmsTest in {
@@ -125,14 +140,21 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
 
       // both workflows should be available for archiving
       eventually(Timeout(2.minutes)) {
-        val workflowsLeftToArchiveFuture = dataAccess.countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(terminalWorkflowStatuses, OffsetDateTime.now().minusSeconds(10))
+        val workflowsLeftToArchiveFuture = dataAccess.countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(
+          terminalWorkflowStatuses,
+          OffsetDateTime.now().minusSeconds(10)
+        )
         val workflowsLeftToArchiveResponse = Await.result(workflowsLeftToArchiveFuture, defaultTimeout)
         workflowsLeftToArchiveResponse shouldBe 2
       }
 
       // check that the first workflow should be the one to be archived first
       val workflowToArchiveResponse1 = eventually(Timeout(2.minutes)) {
-        val workflowToArchiveFuture = dataAccess.queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(terminalWorkflowStatuses, OffsetDateTime.now().minusSeconds(10), 1)
+        val workflowToArchiveFuture =
+          dataAccess.queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(terminalWorkflowStatuses,
+                                                                                  OffsetDateTime.now().minusSeconds(10),
+                                                                                  1
+          )
         val workflowToArchiveResponse = Await.result(workflowToArchiveFuture, defaultTimeout)
         workflowToArchiveResponse should not be empty
         workflowToArchiveResponse
@@ -142,19 +164,27 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       workflowToArchiveResponse1.head.workflowExecutionUuid shouldBe workflowId1.toString
 
       // assume first workflow has been archived
-      val updateMetadataArchiveStatusFuture = dataAccess.updateMetadataArchiveStatus(workflowId1, MetadataArchiveStatus.Archived)
+      val updateMetadataArchiveStatusFuture =
+        dataAccess.updateMetadataArchiveStatus(workflowId1, MetadataArchiveStatus.Archived)
       Await.result(updateMetadataArchiveStatusFuture, defaultTimeout)
 
       // only 1 workflow should be left for archiving
       eventually(Timeout(2.minutes)) {
-        val workflowsLeftToArchiveFuture = dataAccess.countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(terminalWorkflowStatuses, OffsetDateTime.now().minusSeconds(10))
+        val workflowsLeftToArchiveFuture = dataAccess.countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(
+          terminalWorkflowStatuses,
+          OffsetDateTime.now().minusSeconds(10)
+        )
         val workflowsLeftToArchiveResponse = Await.result(workflowsLeftToArchiveFuture, defaultTimeout)
         workflowsLeftToArchiveResponse shouldBe 1
       }
 
       // check that the second workflow should be the one to be archived next
       val workflowToArchiveResponse2 = eventually(Timeout(2.minutes)) {
-        val workflowToArchiveFuture = dataAccess.queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(terminalWorkflowStatuses, OffsetDateTime.now().minusSeconds(10), 1)
+        val workflowToArchiveFuture =
+          dataAccess.queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(terminalWorkflowStatuses,
+                                                                                  OffsetDateTime.now().minusSeconds(10),
+                                                                                  1
+          )
         val workflowToArchiveResponse = Await.result(workflowToArchiveFuture, defaultTimeout)
         workflowToArchiveResponse should not be empty
         workflowToArchiveResponse
@@ -167,23 +197,23 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     it should "return pagination metadata only when page and pagesize query params are specified" taggedAs DbmsTest in {
       (for {
         _ <- baseWorkflowMetadata(Workflow1Name)
-        //get metadata when page and pagesize are specified
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.Page.name -> "1", WorkflowQueryKey.PageSize.name -> "50"))) map { case (_, meta) =>
+        // get metadata when page and pagesize are specified
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(Seq(WorkflowQueryKey.Page.name -> "1", WorkflowQueryKey.PageSize.name -> "50"))
+        ) map { case (_, meta) =>
           meta match {
             case Some(_) =>
             case None => fail("Should have metadata when page and pagesize are specified.")
           }
         }
-        //don't get metadata when page and pagesize are not specified
-        _ <- dataAccess.queryWorkflowSummaries(
-          WorkflowQueryParameters(Seq())) map { case (_, meta) =>
+        // don't get metadata when page and pagesize are not specified
+        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq())) map { case (_, meta) =>
           meta match {
             case Some(_) => fail("Should not have metadata when page and pagesize are not specified")
             case None =>
           }
         }
-      } yield()).futureValue
+      } yield ()).futureValue
     }
 
     it should "sort metadata events by timestamp from older to newer" taggedAs DbmsTest in {
@@ -194,9 +224,14 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         val yesterday = now.minusDays(1)
         val tomorrow = now.plusDays(1)
 
-        val yesterdayEvent = MetadataEvent(workflowKey.copy(key = WorkflowMetadataKeys.WorkflowRoot), Option(MetadataValue("A")), yesterday)
-        val nowEvent = MetadataEvent(workflowKey.copy(key = WorkflowMetadataKeys.WorkflowRoot), Option(MetadataValue("B")), now)
-        val tomorrowEvent = MetadataEvent(workflowKey.copy(key = WorkflowMetadataKeys.WorkflowRoot), Option(MetadataValue("C")), tomorrow)
+        val yesterdayEvent = MetadataEvent(workflowKey.copy(key = WorkflowMetadataKeys.WorkflowRoot),
+                                           Option(MetadataValue("A")),
+                                           yesterday
+        )
+        val nowEvent =
+          MetadataEvent(workflowKey.copy(key = WorkflowMetadataKeys.WorkflowRoot), Option(MetadataValue("B")), now)
+        val tomorrowEvent =
+          MetadataEvent(workflowKey.copy(key = WorkflowMetadataKeys.WorkflowRoot), Option(MetadataValue("C")), tomorrow)
 
         val events = Vector(tomorrowEvent, yesterdayEvent, nowEvent)
 
@@ -208,19 +243,26 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       (for {
         workflow1Id <- baseWorkflowMetadata(Workflow1Name)
         expected <- unorderedEvents(workflow1Id)
-        response <- dataAccess.queryMetadataEvents(MetadataQuery(workflow1Id, None, Option(WorkflowMetadataKeys.WorkflowRoot), None, None, expandSubWorkflows = false), 5.seconds)
+        response <- dataAccess.queryMetadataEvents(MetadataQuery(workflow1Id,
+                                                                 None,
+                                                                 Option(WorkflowMetadataKeys.WorkflowRoot),
+                                                                 None,
+                                                                 None,
+                                                                 expandSubWorkflows = false
+                                                   ),
+                                                   5.seconds
+        )
         _ = response shouldBe expected
-      } yield()).futureValue
+      } yield ()).futureValue
     }
 
-    def assertRowsProcessedAndSummarizationComplete(summaryResult: SummaryResult) = {
+    def assertRowsProcessedAndSummarizationComplete(summaryResult: SummaryResult) =
       withClue(s"asserting correctness of $summaryResult") {
         summaryResult.rowsProcessedIncreasing should be > 0L
         summaryResult.rowsProcessedDecreasing should be(0L)
 
         summaryResult.decreasingGap should be(0L)
       }
-    }
 
     it should "create and query a workflow" taggedAs DbmsTest in {
 
@@ -242,14 +284,14 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
 
         // Query with no filters
         (workflowQueryResult, workflowQueryResult2) <-
-        dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq.empty)) map { case (response, _) =>
-          val result = response.results find { r => r.name.contains(Workflow1Name) && r.end.isDefined } getOrElse
-            fail(s"$Workflow1Name with an end not found in ${response.results}")
-          val result2 = response.results find {
-            _.name.contains(Workflow2Name)
-          } getOrElse fail(s"$Workflow2Name not found in ${response.results}")
-          (result, result2)
-        }
+          dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq.empty)) map { case (response, _) =>
+            val result = response.results find { r => r.name.contains(Workflow1Name) && r.end.isDefined } getOrElse
+              fail(s"$Workflow1Name with an end not found in ${response.results}")
+            val result2 = response.results find {
+              _.name.contains(Workflow2Name)
+            } getOrElse fail(s"$Workflow2Name not found in ${response.results}")
+            (result, result2)
+          }
         // Filter by name
         _ <- dataAccess.queryWorkflowSummaries(
           WorkflowQueryParameters(Seq(WorkflowQueryKey.Name.name -> Workflow1Name))
@@ -257,95 +299,133 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
           val resultsByName = response.results groupBy {
             _.name
           }
-          withClue("Filter by name") { resultsByName.keys.toSet.flatten should equal(Set(Workflow1Name)) }
+          withClue("Filter by name")(resultsByName.keys.toSet.flatten should equal(Set(Workflow1Name)))
         }
         // Filter by multiple names
         _ <- dataAccess.queryWorkflowSummaries(
-          WorkflowQueryParameters(Seq(
-            WorkflowQueryKey.Name.name -> Workflow1Name, WorkflowQueryKey.Name.name -> Workflow2Name))
+          WorkflowQueryParameters(
+            Seq(WorkflowQueryKey.Name.name -> Workflow1Name, WorkflowQueryKey.Name.name -> Workflow2Name)
+          )
         ) map { case (response, _) =>
           val resultsByName = response.results groupBy {
             _.name
           }
-          withClue("Filter by multiple names") { resultsByName.keys.toSet.flatten should equal(Set(Workflow1Name, Workflow2Name)) }
+          withClue("Filter by multiple names") {
+            resultsByName.keys.toSet.flatten should equal(Set(Workflow1Name, Workflow2Name))
+          }
         }
         // Filter by workflow id
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          Seq(WorkflowQueryKey.Id.name -> workflow1Id.toString))) map { case (response, _) =>
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(Seq(WorkflowQueryKey.Id.name -> workflow1Id.toString))
+        ) map { case (response, _) =>
           val resultsById = response.results groupBy {
             _.name
           }
-          withClue("Filter by workflow ID") { resultsById.keys.toSet.flatten should equal(Set(Workflow1Name)) }
+          withClue("Filter by workflow ID")(resultsById.keys.toSet.flatten should equal(Set(Workflow1Name)))
         }
         // Filter by multiple workflow ids
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          Seq(workflow1Id, workflow2Id).map(id => WorkflowQueryKey.Id.name -> id.toString))) map { case (response, _) =>
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(Seq(workflow1Id, workflow2Id).map(id => WorkflowQueryKey.Id.name -> id.toString))
+        ) map { case (response, _) =>
           val resultsById = response.results groupBy {
             _.name
           }
-          withClue("Filter by multiple workflow IDs") { resultsById.keys.toSet.flatten should equal(Set(Workflow1Name, Workflow2Name)) }
+          withClue("Filter by multiple workflow IDs") {
+            resultsById.keys.toSet.flatten should equal(Set(Workflow1Name, Workflow2Name))
+          }
         }
         // Filter by workflow id within random Ids
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          (randomIds :+ workflow1Id.toString).map(id => WorkflowQueryKey.Id.name -> id))) map { case (response, _) =>
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters((randomIds :+ workflow1Id.toString).map(id => WorkflowQueryKey.Id.name -> id))
+        ) map { case (response, _) =>
           val resultsById = response.results groupBy {
             _.name
           }
-          withClue("Filter by workflow ID within random IDs") { resultsById.keys.toSet.flatten should equal(Set(Workflow1Name)) }
+          withClue("Filter by workflow ID within random IDs") {
+            resultsById.keys.toSet.flatten should equal(Set(Workflow1Name))
+          }
         }
         // Filter by status
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.Status.name -> "Submitted"))) map { case (response, _) =>
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(Seq(WorkflowQueryKey.Status.name -> "Submitted"))
+        ) map { case (response, _) =>
           val resultsByStatus = response.results groupBy (_.status)
-          withClue("Filter by status") { resultsByStatus.keys.toSet.flatten should equal(Set("Submitted")) }
+          withClue("Filter by status")(resultsByStatus.keys.toSet.flatten should equal(Set("Submitted")))
         }
         // Filter by multiple statuses
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.Status.name -> "Submitted",
-          WorkflowQueryKey.Status.name -> "Succeeded"))) map { case (response, _) =>
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(WorkflowQueryKey.Status.name -> "Submitted", WorkflowQueryKey.Status.name -> "Succeeded")
+          )
+        ) map { case (response, _) =>
           val resultsByStatus = response.results groupBy (_.status)
-          withClue("Filter by multiple statuses") { resultsByStatus.keys.toSet.flatten should equal(Set("Submitted", "Succeeded")) }
+          withClue("Filter by multiple statuses") {
+            resultsByStatus.keys.toSet.flatten should equal(Set("Submitted", "Succeeded"))
+          }
         }
         // Filter by label using AND
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.LabelAndKeyValue.name -> s"${testLabel2.key}:${testLabel2.value}"))) map { case (response, _) =>
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(WorkflowQueryKey.LabelAndKeyValue.name -> s"${testLabel2.key}:${testLabel2.value}")
+          )
+        ) map { case (response, _) =>
           val resultByName = response.results groupBy (_.name)
-          withClue("Filter by label using AND") { resultByName.keys.toSet.flatten should equal(Set(Workflow1Name, Workflow2Name)) }
+          withClue("Filter by label using AND") {
+            resultByName.keys.toSet.flatten should equal(Set(Workflow1Name, Workflow2Name))
+          }
         }
         // Filter by multiple labels using AND
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          Seq(testLabel2, testLabel3)
-            .map(label => WorkflowQueryKey.LabelAndKeyValue.name -> s"${label.key}:${label.value}"))
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(testLabel2, testLabel3)
+              .map(label => WorkflowQueryKey.LabelAndKeyValue.name -> s"${label.key}:${label.value}")
+          )
         ) map { case (response, _) =>
           val resultByName = response.results groupBy (_.name)
-          withClue("Filter by multiple labels using AND") { resultByName.keys.toSet.flatten should equal(Set(Workflow2Name)) }
+          withClue("Filter by multiple labels using AND") {
+            resultByName.keys.toSet.flatten should equal(Set(Workflow2Name))
+          }
         }
         // Filter by label using OR
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.LabelOrKeyValue.name -> s"${testLabel2.key}:${testLabel2.value}"))) map { case (response, _) =>
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(WorkflowQueryKey.LabelOrKeyValue.name -> s"${testLabel2.key}:${testLabel2.value}")
+          )
+        ) map { case (response, _) =>
           val resultByName = response.results groupBy (_.name)
-          withClue("Filter by label using OR") { resultByName.keys.toSet.flatten should equal(Set(Workflow1Name, Workflow2Name)) }
+          withClue("Filter by label using OR") {
+            resultByName.keys.toSet.flatten should equal(Set(Workflow1Name, Workflow2Name))
+          }
         }
         // Filter by multiple labels using OR
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          Seq(testLabel2, testLabel3)
-            .map(label => WorkflowQueryKey.LabelOrKeyValue.name -> s"${label.key}:${label.value}"))
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(testLabel2, testLabel3)
+              .map(label => WorkflowQueryKey.LabelOrKeyValue.name -> s"${label.key}:${label.value}")
+          )
         ) map { case (response, _) =>
           val resultByName = response.results groupBy (_.name)
-          withClue("Filter by multiple label using OR") { resultByName.keys.toSet.flatten should equal(Set(Workflow1Name, Workflow2Name)) }
+          withClue("Filter by multiple label using OR") {
+            resultByName.keys.toSet.flatten should equal(Set(Workflow1Name, Workflow2Name))
+          }
         }
         // Filter by exclude label using AND
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.ExcludeLabelAndKeyValue.name -> s"${testLabel2.key}:${testLabel2.value}"))) map { case (response, _) =>
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(WorkflowQueryKey.ExcludeLabelAndKeyValue.name -> s"${testLabel2.key}:${testLabel2.value}")
+          )
+        ) map { case (response, _) =>
           val resultByName = response.results groupBy (_.name)
           withClue("Filter by exclude label using AND") {
             resultByName.keys.toSet.flatten should contain(Workflow1Name)
           }
         }
         // Filter by multiple exclude labels using AND
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          Seq(testLabel2, testLabel3)
-            .map(label => WorkflowQueryKey.ExcludeLabelAndKeyValue.name -> s"${label.key}:${label.value}"))
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(testLabel2, testLabel3)
+              .map(label => WorkflowQueryKey.ExcludeLabelAndKeyValue.name -> s"${label.key}:${label.value}")
+          )
         ) map { case (response, _) =>
           val resultByName = response.results groupBy (_.name)
           val ids = response.results.map(_.id)
@@ -356,17 +436,22 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
           }
         }
         // Filter by exclude label using OR
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.ExcludeLabelOrKeyValue.name -> s"${testLabel2.key}:${testLabel2.value}"))) map { case (response, _) =>
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(WorkflowQueryKey.ExcludeLabelOrKeyValue.name -> s"${testLabel2.key}:${testLabel2.value}")
+          )
+        ) map { case (response, _) =>
           val resultByName = response.results groupBy (_.name)
           withClue("Filter to exclude label using OR") {
             resultByName.keys.toSet.flatten should contain(Workflow1Name)
           }
         }
         // Filter by multiple exclude labels using OR
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          Seq(testLabel2, testLabel3)
-            .map(label => WorkflowQueryKey.ExcludeLabelOrKeyValue.name -> s"${label.key}:${label.value}"))
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(testLabel2, testLabel3)
+              .map(label => WorkflowQueryKey.ExcludeLabelOrKeyValue.name -> s"${label.key}:${label.value}")
+          )
         ) map { case (response, _) =>
           // NOTE: On persistent databases other workflows will be returned. Just verify that our two workflows are not.
           val ids = response.results.map(_.id)
@@ -376,49 +461,56 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
           }
         }
         // Filter by start date
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.StartDate.name -> workflowQueryResult2.start.get.toUtcMilliString))) map {
-          case (response, _) =>
-            response.results partition {
-              r => r.start.isDefined && r.start.get.compareTo(workflowQueryResult.start.get) >= 0
-            } match {
-              case (y, n) if y.nonEmpty && n.isEmpty => // good
-              case (y, n) => fail(s"Found ${y.size} later workflows and ${n.size} earlier")
-            }
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(WorkflowQueryKey.StartDate.name -> workflowQueryResult2.start.get.toUtcMilliString)
+          )
+        ) map { case (response, _) =>
+          response.results partition { r =>
+            r.start.isDefined && r.start.get.compareTo(workflowQueryResult.start.get) >= 0
+          } match {
+            case (y, n) if y.nonEmpty && n.isEmpty => // good
+            case (y, n) => fail(s"Found ${y.size} later workflows and ${n.size} earlier")
+          }
         }
         // Filter by end date
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.EndDate.name -> workflowQueryResult.end.get.toUtcMilliString))) map {
-          case (response, _) =>
-            response.results partition {
-              r => r.end.isDefined && r.end.get.compareTo(workflowQueryResult.end.get) <= 0
-            } match {
-              case (y, n) if y.nonEmpty && n.isEmpty => // good
-              case (y, n) => fail(s"Found ${y.size} earlier workflows and ${n.size} later")
-            }
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(Seq(WorkflowQueryKey.EndDate.name -> workflowQueryResult.end.get.toUtcMilliString))
+        ) map { case (response, _) =>
+          response.results partition { r =>
+            r.end.isDefined && r.end.get.compareTo(workflowQueryResult.end.get) <= 0
+          } match {
+            case (y, n) if y.nonEmpty && n.isEmpty => // good
+            case (y, n) => fail(s"Found ${y.size} earlier workflows and ${n.size} later")
+          }
         }
         // Filter by submission time
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.SubmissionTime.name -> workflowQueryResult2.submission.get.toUtcMilliString))) map {
-          case (response, _) =>
-            response.results partition { r =>
-              r.submission.isDefined && r.submission.get.compareTo(workflowQueryResult2.submission.get) <= 0
-            } match {
-              case (y, n) if y.nonEmpty && n.isEmpty => // good
-              case (y, n) =>
-                fail(s"Found ${y.size} earlier workflows and ${n.size} later while filtering by submission timestamp")
-            }
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(WorkflowQueryKey.SubmissionTime.name -> workflowQueryResult2.submission.get.toUtcMilliString)
+          )
+        ) map { case (response, _) =>
+          response.results partition { r =>
+            r.submission.isDefined && r.submission.get.compareTo(workflowQueryResult2.submission.get) <= 0
+          } match {
+            case (y, n) if y.nonEmpty && n.isEmpty => // good
+            case (y, n) =>
+              fail(s"Found ${y.size} earlier workflows and ${n.size} later while filtering by submission timestamp")
+          }
         }
         // Check for labels in query response
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.AdditionalQueryResultFields.name -> "labels"))) map {
-          case (response, _) =>
-            response.results filter {
-              workflowQueryResult => List(workflow1Id.toString, workflow1Id.toString).contains(workflowQueryResult.id)
-            } partition { r => r.labels.isDefined } match {
-              case (y, n) if y.nonEmpty && n.isEmpty => //good
-              case (y, n) => fail(s"Something went horribly wrong since labels were populated for ${y.size} and were missing for ${n.size} workflow(s)!")
-            }
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(Seq(WorkflowQueryKey.AdditionalQueryResultFields.name -> "labels"))
+        ) map { case (response, _) =>
+          response.results filter { workflowQueryResult =>
+            List(workflow1Id.toString, workflow1Id.toString).contains(workflowQueryResult.id)
+          } partition { r => r.labels.isDefined } match {
+            case (y, n) if y.nonEmpty && n.isEmpty => // good
+            case (y, n) =>
+              fail(
+                s"Something went horribly wrong since labels were populated for ${y.size} and were missing for ${n.size} workflow(s)!"
+              )
+          }
         }
       } yield ()).futureValue(Timeout(scaled(Span(30, Seconds))), Interval(scaled(Span(500, Millis))))
     }
@@ -430,18 +522,28 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         _ <- baseWorkflowMetadata(uniqueWorkflow3Name)
         // refresh the metadata
         _ <- dataAccess.refreshWorkflowMetadataSummaries(1000) map assertRowsProcessedAndSummarizationComplete
-        //get totalResultsCount when page and pagesize are specified
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          // name being added to the query parameters so as to exclude workflows being populated by the other tests in this spec
-          WorkflowQueryKey.Name.name -> uniqueWorkflow3Name,
-          WorkflowQueryKey.Page.name -> "1", WorkflowQueryKey.PageSize.name -> "1"))) map { case (resp, _) =>
+        // get totalResultsCount when page and pagesize are specified
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(
+              // name being added to the query parameters so as to exclude workflows being populated by the other tests in this spec
+              WorkflowQueryKey.Name.name -> uniqueWorkflow3Name,
+              WorkflowQueryKey.Page.name -> "1",
+              WorkflowQueryKey.PageSize.name -> "1"
+            )
+          )
+        ) map { case (resp, _) =>
           resp.totalResultsCount match {
             case 2 =>
-            case 1 => fail("totalResultsCount is suspiciously equal to the pageSize and not the expected total results count. Please fix!")
-            case other => fail(s"totalResultsCount is expected to be 2 but is actually $other. Something has gone horribly wrong!")
+            case 1 =>
+              fail(
+                "totalResultsCount is suspiciously equal to the pageSize and not the expected total results count. Please fix!"
+              )
+            case other =>
+              fail(s"totalResultsCount is expected to be 2 but is actually $other. Something has gone horribly wrong!")
           }
         }
-      } yield()).futureValue
+      } yield ()).futureValue
     }
 
     it should "revert to an prior label value" taggedAs DbmsTest in {
@@ -488,10 +590,14 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         // refresh metadata
         _ <- dataAccess.refreshWorkflowMetadataSummaries(1000)
         // include subworkflows
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(WorkflowQueryKey.IncludeSubworkflows.name -> true.toString))) map { case (resp, _) =>
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(Seq(WorkflowQueryKey.IncludeSubworkflows.name -> true.toString))
+        ) map { case (resp, _) =>
           val resultByName = resp.results groupBy (_.name)
           withClue("include subworkflows:") {
-            List(ParentWorkflowName, SubworkflowName, ParentWorkflow2Name, Subworkflow2Name).foreach { n => resultByName.keys.toSet.flatten should contain(n) }
+            List(ParentWorkflowName, SubworkflowName, ParentWorkflow2Name, Subworkflow2Name).foreach { n =>
+              resultByName.keys.toSet.flatten should contain(n)
+            }
           }
         }
         // exclude subworkflows - make sure we get 2 results in the right order:
@@ -521,22 +627,29 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
           case (resp, _) =>
             val resultByName = resp.results groupBy (_.name)
             // This time we can do a strict equality check rather than 'contains', because we know these two should be the most recent (non-sub-) workflows:
-            withClue("exclude subworkflows and assert page size:") { resultByName.keys.flatten should be(Set(ParentWorkflowName, ParentWorkflow2Name)) }
+            withClue("exclude subworkflows and assert page size:") {
+              resultByName.keys.flatten should be(Set(ParentWorkflowName, ParentWorkflow2Name))
+            }
         }
 
-
         // check for parentWorkflow1 in query response
-        _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(
-          WorkflowQueryKey.AdditionalQueryResultFields.name -> "parentWorkflowId",
-          WorkflowQueryKey.Name.name -> SubworkflowName))) map {
-          case (response, _) =>
-            response.results partition { r => r.parentWorkflowId.isDefined} match {
-              case (y, n) if y.nonEmpty && n.isEmpty => //good
-              case (y, n) => fail(s"parentWorkflow1 should be populated for a subworkflow. It was populated correctly for ${y.size} " +
-                s"and was missing in ${n.size} subworkflow(s). Something went horribly wrong!")
-            }
+        _ <- dataAccess.queryWorkflowSummaries(
+          WorkflowQueryParameters(
+            Seq(WorkflowQueryKey.AdditionalQueryResultFields.name -> "parentWorkflowId",
+                WorkflowQueryKey.Name.name -> SubworkflowName
+            )
+          )
+        ) map { case (response, _) =>
+          response.results partition { r => r.parentWorkflowId.isDefined } match {
+            case (y, n) if y.nonEmpty && n.isEmpty => // good
+            case (y, n) =>
+              fail(
+                s"parentWorkflow1 should be populated for a subworkflow. It was populated correctly for ${y.size} " +
+                  s"and was missing in ${n.size} subworkflow(s). Something went horribly wrong!"
+              )
+          }
         }
-      } yield()).futureValue
+      } yield ()).futureValue
     }
 
     it should "properly query metadata summaries based on archived status and timestamp and update archive status after metadata deletion" taggedAs DbmsTest in {
@@ -550,25 +663,37 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       val refreshSummariesFuture = dataAccess.refreshWorkflowMetadataSummaries(1000)
       Await.result(refreshSummariesFuture, defaultTimeout)
 
-      val updateMetadataArchiveStatusFuture = dataAccess.updateMetadataArchiveStatus(workflowId1, MetadataArchiveStatus.Archived)
+      val updateMetadataArchiveStatusFuture =
+        dataAccess.updateMetadataArchiveStatus(workflowId1, MetadataArchiveStatus.Archived)
       Await.result(updateMetadataArchiveStatusFuture, defaultTimeout)
 
-      val responseEmptyFuture = dataAccess.queryWorkflowIdsByArchiveStatusAndOlderThanTimestamp(Option("Archived"), OffsetDateTime.now().minusMinutes(1), 200)
+      val responseEmptyFuture =
+        dataAccess.queryWorkflowIdsByArchiveStatusAndOlderThanTimestamp(Option("Archived"),
+                                                                        OffsetDateTime.now().minusMinutes(1),
+                                                                        200
+        )
       val responseEmpty = Await.result(responseEmptyFuture, defaultTimeout)
       responseEmpty shouldBe empty
 
       eventually(Timeout(2.minutes)) {
-        val responseNonEmptyFuture = dataAccess.queryWorkflowIdsByArchiveStatusAndOlderThanTimestamp (Option ("Archived"), OffsetDateTime.now().minusMinutes(1), 200)
+        val responseNonEmptyFuture =
+          dataAccess.queryWorkflowIdsByArchiveStatusAndOlderThanTimestamp(Option("Archived"),
+                                                                          OffsetDateTime.now().minusMinutes(1),
+                                                                          200
+          )
         val responseNonEmpty = Await.result(responseNonEmptyFuture, 10.seconds)
         responseNonEmpty should not be empty
         responseNonEmpty should contain allElementsOf Seq(workflowId1.toString)
         responseNonEmpty should contain noElementsOf Seq(workflowId2.toString)
       }
 
-      val deleteMetadataFuture = dataAccess.deleteAllMetadataEntriesForWorkflowAndUpdateArchiveStatus(workflowId1, Option("ArchivedAndDeleted"))
+      val deleteMetadataFuture =
+        dataAccess.deleteAllMetadataEntriesForWorkflowAndUpdateArchiveStatus(workflowId1, Option("ArchivedAndDeleted"))
       Await.result(deleteMetadataFuture, defaultTimeout)
 
-      val summaryResponseFuture = dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(Seq(WorkflowQueryKey.Id.name -> workflowId1.toString)))
+      val summaryResponseFuture = dataAccess.queryWorkflowSummaries(
+        WorkflowQueryParameters(Seq(WorkflowQueryKey.Id.name -> workflowId1.toString))
+      )
       val summaryResponse = Await.result(summaryResponseFuture, defaultTimeout)
       summaryResponse._1.results should not be empty
       summaryResponse._1.results.head.metadataArchiveStatus.toString shouldBe "ArchivedAndDeleted"
@@ -576,21 +701,30 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
 
     it should "error when deleting metadata for a root workflow that does not exist" taggedAs DbmsTest in {
       dataAccess
-        .deleteAllMetadataEntriesForWorkflowAndUpdateArchiveStatus(WorkflowId.fromString("00000000-0000-0000-0000-000000000000"), None)
-        .failed.futureValue(Timeout(10.seconds))
-        .getMessage should be("""Metadata deletion precondition failed: workflow ID "00000000-0000-0000-0000-000000000000" did not have a status in the summary table""")
+        .deleteAllMetadataEntriesForWorkflowAndUpdateArchiveStatus(
+          WorkflowId.fromString("00000000-0000-0000-0000-000000000000"),
+          None
+        )
+        .failed
+        .futureValue(Timeout(10.seconds))
+        .getMessage should be(
+        """Metadata deletion precondition failed: workflow ID "00000000-0000-0000-0000-000000000000" did not have a status in the summary table"""
+      )
     }
 
     it should "refuse to delete a non-terminal workflow" taggedAs DbmsTest in {
       val test = for {
-        rootWorkflowId <- baseWorkflowMetadata("root workflow name", workflowId = WorkflowId.fromString("33333333-3333-3333-3333-333333333333"))
+        rootWorkflowId <- baseWorkflowMetadata("root workflow name",
+                                               workflowId =
+                                                 WorkflowId.fromString("33333333-3333-3333-3333-333333333333")
+        )
         _ <- dataAccess.refreshWorkflowMetadataSummaries(1000)
         _ <- dataAccess.deleteAllMetadataEntriesForWorkflowAndUpdateArchiveStatus(rootWorkflowId, None)
       } yield ()
 
-      test
-        .failed.futureValue(Timeout(10.seconds))
-        .getMessage should be(s"""Metadata deletion precondition failed: workflow ID "33333333-3333-3333-3333-333333333333" was in non-terminal status "Submitted"""")
+      test.failed.futureValue(Timeout(10.seconds)).getMessage should be(
+        s"""Metadata deletion precondition failed: workflow ID "33333333-3333-3333-3333-333333333333" was in non-terminal status "Submitted""""
+      )
     }
 
     it should "close the database" taggedAs DbmsTest in {
@@ -598,7 +732,7 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     }
 
     it should "stop container if required" taggedAs DbmsTest in {
-      containerOpt.foreach { _.stop() }
+      containerOpt.foreach(_.stop())
     }
   }
 }
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/MetadataServiceActorSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/MetadataServiceActorSpec.scala
index 22ff8c78d5e..f738e56d395 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/MetadataServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/MetadataServiceActorSpec.scala
@@ -26,20 +26,19 @@ class MetadataServiceActorSpec extends ServicesSpec {
   val config: Config = ConfigFactory.parseString(Config)
   lazy val actor: ActorRef =
     system.actorOf(
-      props =
-        MetadataServiceActor.props(
-          serviceConfig = globalConfigToMetadataServiceConfig(config),
-          globalConfig = config,
-          serviceRegistryActor = TestProbe("serviceRegistryActor").ref,
-        ),
-      name = "MetadataServiceActor-for-MetadataServiceActorSpec",
+      props = MetadataServiceActor.props(
+        serviceConfig = globalConfigToMetadataServiceConfig(config),
+        globalConfig = config,
+        serviceRegistryActor = TestProbe("serviceRegistryActor").ref
+      ),
+      name = "MetadataServiceActor-for-MetadataServiceActorSpec"
     )
 
   val workflowId: WorkflowId = WorkflowId.randomId()
 
-    /*
+  /*
     Simple store / retrieve
-     */
+   */
 
   val key1: MetadataKey = MetadataKey(workflowId, None, "key1")
   val key2: MetadataKey = MetadataKey(workflowId, None, "key2")
@@ -71,50 +70,64 @@ class MetadataServiceActorSpec extends ServicesSpec {
   val query4: MetadataQuery = MetadataQuery.forWorkflow(workflowId)
   val query5: MetadataQuery = MetadataQuery.forJob(workflowId, supJob)
 
-  val testCases: List[(String, MetadataQuery, String)] = List[(String, MetadataQuery, String)] (
-    ("query1", query1, s"""{
-                          |  "key1": "value2",
-                          |  "calls": {},
-                          |  "id": "$workflowId"
-                          |}""".stripMargin),
-    ("query2", query2, s"""{
-                          |  "key2": "value1",
-                          |  "calls": {},
-                          |  "id": "$workflowId"
-                          |}""".stripMargin),
-    ("query3", query3, s"""{
-                          |  "calls": {
-                          |    "sup.sup": [{
-                          |      "dog": {},
-                          |      "attempt": 1,
-                          |      "shardIndex": -1
-                          |    }]
-                          |  },
-                          |  "id": "$workflowId"
-                          |}""".stripMargin),
-    ("query4", query4, s"""{
-                          |  "key1": "value2",
-                          |  "key2": "value1",
-                          |  "calls": {
-                          |    "sup.sup": [{
-                          |      "dog": {},
-                          |      "attempt": 1,
-                          |      "shardIndex": -1
-                          |    }]
-                          |  },
-                          |  "id": "$workflowId"
-                          |}""".stripMargin),
-    ("query5", query5, s"""{
-                          |  "calls": {
-                          |    "sup.sup": [{
-                          |      "dog": {},
-                          |      "attempt": 1,
-                          |      "shardIndex": -1
-                          |    }]
-                          |  },
-                          |  "id": "$workflowId"
-                          |}""".stripMargin),
-
+  val testCases: List[(String, MetadataQuery, String)] = List[(String, MetadataQuery, String)](
+    ("query1",
+     query1,
+     s"""{
+        |  "key1": "value2",
+        |  "calls": {},
+        |  "id": "$workflowId"
+        |}""".stripMargin
+    ),
+    ("query2",
+     query2,
+     s"""{
+        |  "key2": "value1",
+        |  "calls": {},
+        |  "id": "$workflowId"
+        |}""".stripMargin
+    ),
+    ("query3",
+     query3,
+     s"""{
+        |  "calls": {
+        |    "sup.sup": [{
+        |      "dog": {},
+        |      "attempt": 1,
+        |      "shardIndex": -1
+        |    }]
+        |  },
+        |  "id": "$workflowId"
+        |}""".stripMargin
+    ),
+    ("query4",
+     query4,
+     s"""{
+        |  "key1": "value2",
+        |  "key2": "value1",
+        |  "calls": {
+        |    "sup.sup": [{
+        |      "dog": {},
+        |      "attempt": 1,
+        |      "shardIndex": -1
+        |    }]
+        |  },
+        |  "id": "$workflowId"
+        |}""".stripMargin
+    ),
+    ("query5",
+     query5,
+     s"""{
+        |  "calls": {
+        |    "sup.sup": [{
+        |      "dog": {},
+        |      "attempt": 1,
+        |      "shardIndex": -1
+        |    }]
+        |  },
+        |  "id": "$workflowId"
+        |}""".stripMargin
+    )
   )
 
   actorName should {
@@ -126,10 +139,10 @@ class MetadataServiceActorSpec extends ServicesSpec {
     }
 
     testCases foreach { case (name, query, expectation) =>
-
       s"perform $name correctly" in {
         eventually(Timeout(10.seconds), Interval(2.seconds)) {
-          val response = Await.result((actor ? GetMetadataAction(query)).mapTo[SuccessfulMetadataJsonResponse], 1.seconds)
+          val response =
+            Await.result((actor ? GetMetadataAction(query)).mapTo[SuccessfulMetadataJsonResponse], 1.seconds)
 
           response.responseJson shouldBe expectation.parseJson
         }
@@ -138,19 +151,26 @@ class MetadataServiceActorSpec extends ServicesSpec {
 
     "be able to query by Unarchived metadataArchiveStatus" in {
 
-      val summarizableStatusUpdate = PutMetadataAction(MetadataEvent(
-        MetadataKey(workflowId, None, WorkflowMetadataKeys.Status),
-        Option(MetadataValue("Running")),
-        moment.plusSeconds(1)
-      ))
+      val summarizableStatusUpdate = PutMetadataAction(
+        MetadataEvent(
+          MetadataKey(workflowId, None, WorkflowMetadataKeys.Status),
+          Option(MetadataValue("Running")),
+          moment.plusSeconds(1)
+        )
+      )
       actor ! summarizableStatusUpdate
 
       eventually(Timeout(10.seconds), Interval(2.seconds)) {
-        val queryEverythingResponse = Await.result((actor ? QueryForWorkflowsMatchingParameters(List.empty)).mapTo[WorkflowQuerySuccess], 1.seconds)
+        val queryEverythingResponse =
+          Await.result((actor ? QueryForWorkflowsMatchingParameters(List.empty)).mapTo[WorkflowQuerySuccess], 1.seconds)
         queryEverythingResponse.response.results.length should be(1)
         println(queryEverythingResponse)
 
-        val response1 = Await.result((actor ? QueryForWorkflowsMatchingParameters(List(("metadataArchiveStatus", "Unarchived")))).mapTo[WorkflowQuerySuccess], 1.seconds)
+        val response1 =
+          Await.result((actor ? QueryForWorkflowsMatchingParameters(List(("metadataArchiveStatus", "Unarchived"))))
+                         .mapTo[WorkflowQuerySuccess],
+                       1.seconds
+          )
         // We submitted one workflow, so we should should see one value here:
         response1.response.results.length should be(1)
       }
@@ -158,21 +178,35 @@ class MetadataServiceActorSpec extends ServicesSpec {
 
     "be able to query by Archived metadataArchiveStatus" in {
 
-      val response2 = Await.result((actor ? QueryForWorkflowsMatchingParameters(List(("metadataArchiveStatus", "Archived")))).mapTo[WorkflowQuerySuccess], 1.seconds)
+      val response2 =
+        Await.result((actor ? QueryForWorkflowsMatchingParameters(List(("metadataArchiveStatus", "Archived"))))
+                       .mapTo[WorkflowQuerySuccess],
+                     1.seconds
+        )
       // That workflow hasn't been marked as archived so this result set is empty:
       response2.response.results.length should be(0)
     }
 
     "be able to query by ArchiveFailed metadataArchiveStatus" in {
-      val response3 = Await.result((actor ? QueryForWorkflowsMatchingParameters(List(("metadataArchiveStatus", "ArchiveFailed")))).mapTo[WorkflowQuerySuccess], 1.seconds)
+      val response3 =
+        Await.result((actor ? QueryForWorkflowsMatchingParameters(List(("metadataArchiveStatus", "ArchiveFailed"))))
+                       .mapTo[WorkflowQuerySuccess],
+                     1.seconds
+        )
       // That workflow hasn't been marked as archived so this result set is empty:
       response3.response.results.length should be(0)
     }
 
     "not be able to query by an invalid metadataArchiveStatus" in {
-      val response4 = Await.result((actor ? QueryForWorkflowsMatchingParameters(List(("metadataArchiveStatus", "!!OOPS!!")))).mapTo[WorkflowQueryFailure], 1.seconds)
+      val response4 =
+        Await.result((actor ? QueryForWorkflowsMatchingParameters(List(("metadataArchiveStatus", "!!OOPS!!"))))
+                       .mapTo[WorkflowQueryFailure],
+                     1.seconds
+        )
       // That workflow hasn't been marked as archived so this result set is empty:
-      response4.reason.getMessage should be("Unrecognized 'metadata archive status' value(s): No such MetadataArchiveStatus: !!OOPS!!")
+      response4.reason.getMessage should be(
+        "Unrecognized 'metadata archive status' value(s): No such MetadataArchiveStatus: !!OOPS!!"
+      )
     }
   }
 }
@@ -184,12 +218,15 @@ object MetadataServiceActorSpec {
       |services.MetadataService.config.db-flush-rate = 100 millis
     """.stripMargin
 
-  val ConfigWithoutSummarizer: String = Config + """
-      |services.MetadataService.config.metadata-summary-refresh-interval = "Inf"
+  val ConfigWithoutSummarizer: String =
+    Config + """
+               |services.MetadataService.config.metadata-summary-refresh-interval = "Inf"
     """.stripMargin
 
   // Use this to convert the above "global" configs into metadata service specific "service config"s:
-  def globalConfigToMetadataServiceConfig(config: Config): Config = if (config.hasPath("services.MetadataService.config")) {
+  def globalConfigToMetadataServiceConfig(config: Config): Config = if (
+    config.hasPath("services.MetadataService.config")
+  ) {
     config.getConfig("services.MetadataService.config")
   } else {
     ConfigFactory.empty()
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorBenchmark.scala b/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorBenchmark.scala
index 96418047723..1a4783dee87 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorBenchmark.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorBenchmark.scala
@@ -16,16 +16,15 @@ import org.scalatest.matchers.should.Matchers
 import scala.concurrent.duration._
 
 class WriteMetadataActorBenchmark extends TestKitSuite with AnyFlatSpecLike with Eventually with Matchers {
-  override implicit val patienceConfig = PatienceConfig(scaled(30.seconds), 1.second)
+  implicit override val patienceConfig = PatienceConfig(scaled(30.seconds), 1.second)
 
   behavior of "WriteMetadataActor"
 
   val workflowId = WorkflowId.randomId()
   val registry = TestProbe().ref
 
-  def makeEvent = {
+  def makeEvent =
     MetadataEvent(MetadataKey(workflowId, None, "metadata_key"), MetadataValue("My Value"))
-  }
 
   def time[T](description: String)(thunk: => T): T = {
     val t1 = System.currentTimeMillis
@@ -38,16 +37,18 @@ class WriteMetadataActorBenchmark extends TestKitSuite with AnyFlatSpecLike with
   private val databaseSystem = MysqlEarliestDatabaseSystem
   private val containerOpt: Option[Container] = DatabaseTestKit.getDatabaseTestContainer(databaseSystem)
 
-  private lazy val dataAccess = DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, MetadataDatabaseType, databaseSystem)
+  private lazy val dataAccess =
+    DatabaseTestKit.initializeDatabaseByContainerOptTypeAndSystem(containerOpt, MetadataDatabaseType, databaseSystem)
 
   it should "start container if required" taggedAs IntegrationTest in {
-    containerOpt.foreach { _.start }
+    containerOpt.foreach(_.start)
   }
 
   it should "provide good throughput" taggedAs IntegrationTest in {
-    val writeActor = TestFSMRef(new WriteMetadataActor(1000, 5.seconds, registry, Int.MaxValue, MetadataStatisticsDisabled) {
-      override val metadataDatabaseInterface: MetadataSlickDatabase = dataAccess
-    })
+    val writeActor =
+      TestFSMRef(new WriteMetadataActor(1000, 5.seconds, registry, Int.MaxValue, MetadataStatisticsDisabled) {
+        override val metadataDatabaseInterface: MetadataSlickDatabase = dataAccess
+      })
 
     time("metadata write") {
       (0 to 1 * 1000 * 1000)
@@ -67,6 +68,6 @@ class WriteMetadataActorBenchmark extends TestKitSuite with AnyFlatSpecLike with
   }
 
   it should "stop container if required" taggedAs IntegrationTest in {
-    containerOpt.foreach { _.stop() }
+    containerOpt.foreach(_.stop())
   }
 }
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala
index 6ed7fa6c402..9b9e4f75ccd 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala
@@ -10,7 +10,13 @@ import cromwell.core.{TestKitSuite, WorkflowId}
 import cromwell.database.sql.joins.MetadataJobQueryValue
 import cromwell.database.sql.tables.{InformationSchemaEntry, MetadataEntry, WorkflowMetadataSummaryEntry}
 import cromwell.database.sql.{MetadataSqlDatabase, SqlDatabase}
-import cromwell.services.metadata.MetadataService.{MetadataWriteAction, MetadataWriteFailure, MetadataWriteSuccess, PutMetadataAction, PutMetadataActionAndRespond}
+import cromwell.services.metadata.MetadataService.{
+  MetadataWriteAction,
+  MetadataWriteFailure,
+  MetadataWriteSuccess,
+  PutMetadataAction,
+  PutMetadataActionAndRespond
+}
 import cromwell.services.metadata.impl.MetadataStatisticsRecorder.MetadataStatisticsDisabled
 import cromwell.services.metadata.impl.WriteMetadataActorSpec.BatchSizeCountingWriteMetadataActor
 import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
@@ -36,17 +42,22 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
       override val metadataDatabaseInterface = mockDatabaseInterface(0)
     })
 
-    def metadataEvent(index: Int) = PutMetadataAction(MetadataEvent(MetadataKey(WorkflowId.randomId(), None, s"metadata_key_$index"), MetadataValue(s"hello_$index")))
+    def metadataEvent(index: Int) = PutMetadataAction(
+      MetadataEvent(MetadataKey(WorkflowId.randomId(), None, s"metadata_key_$index"), MetadataValue(s"hello_$index"))
+    )
 
-    val probes = (0 until 27).map({ _ =>
-      val probe = TestProbe()
-      probe
-    }).zipWithIndex.map {
-      case (probe, index) => probe -> metadataEvent(index)
-    }
+    val probes = (0 until 27)
+      .map { _ =>
+        val probe = TestProbe()
+        probe
+      }
+      .zipWithIndex
+      .map { case (probe, index) =>
+        probe -> metadataEvent(index)
+      }
 
-    probes foreach {
-      case (probe, msg) => probe.send(writeActor, msg)
+    probes foreach { case (probe, msg) =>
+      probe.send(writeActor, msg)
     }
 
     eventually {
@@ -64,24 +75,34 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
         override val metadataDatabaseInterface = mockDatabaseInterface(failureRate)
       })
 
-      def metadataEvent(index: Int, probe: ActorRef) = PutMetadataActionAndRespond(List(MetadataEvent(MetadataKey(WorkflowId.randomId(), None, s"metadata_key_$index"), MetadataValue(s"hello_$index"))), probe)
-
-      val probes = (0 until 43).map({ _ =>
-        val probe = TestProbe()
-        probe
-      }).zipWithIndex.map {
-        case (probe, index) => probe -> metadataEvent(index, probe.ref)
-      }
-
-      probes foreach {
-        case (probe, msg) => probe.send(writeActor, msg)
+      def metadataEvent(index: Int, probe: ActorRef) =
+        PutMetadataActionAndRespond(List(
+                                      MetadataEvent(MetadataKey(WorkflowId.randomId(), None, s"metadata_key_$index"),
+                                                    MetadataValue(s"hello_$index")
+                                      )
+                                    ),
+                                    probe
+        )
+
+      val probes = (0 until 43)
+        .map { _ =>
+          val probe = TestProbe()
+          probe
+        }
+        .zipWithIndex
+        .map { case (probe, index) =>
+          probe -> metadataEvent(index, probe.ref)
+        }
+
+      probes foreach { case (probe, msg) =>
+        probe.send(writeActor, msg)
       }
 
-      probes.foreach {
-        case (probe, msg) => probe.expectMsg(MetadataWriteSuccess(msg.events))
+      probes.foreach { case (probe, msg) =>
+        probe.expectMsg(MetadataWriteSuccess(msg.events))
       }
       eventually {
-        writeActor.underlyingActor.failureCount should be (5 * failureRate)
+        writeActor.underlyingActor.failureCount should be(5 * failureRate)
       }
 
       writeActor.stop()
@@ -94,24 +115,32 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
       override val metadataDatabaseInterface = mockDatabaseInterface(100)
     })
 
-    def metadataEvent(index: Int, probe: ActorRef) = PutMetadataActionAndRespond(List(MetadataEvent(MetadataKey(WorkflowId.randomId(), None, s"metadata_key_$index"), MetadataValue(s"hello_$index"))), probe)
-
-    val probes = (0 until 43).map({ _ =>
-      val probe = TestProbe()
+    def metadataEvent(index: Int, probe: ActorRef) = PutMetadataActionAndRespond(
+      List(
+        MetadataEvent(MetadataKey(WorkflowId.randomId(), None, s"metadata_key_$index"), MetadataValue(s"hello_$index"))
+      ),
       probe
-    }).zipWithIndex.map {
-      case (probe, index) => probe -> metadataEvent(index, probe.ref)
-    }
+    )
+
+    val probes = (0 until 43)
+      .map { _ =>
+        val probe = TestProbe()
+        probe
+      }
+      .zipWithIndex
+      .map { case (probe, index) =>
+        probe -> metadataEvent(index, probe.ref)
+      }
 
-    probes foreach {
-      case (probe, msg) => probe.send(writeActor, msg)
+    probes foreach { case (probe, msg) =>
+      probe.send(writeActor, msg)
     }
 
-    probes.foreach {
-      case (probe, msg) => probe.expectMsg(MetadataWriteFailure(WriteMetadataActorSpec.IntermittentException, msg.events))
+    probes.foreach { case (probe, msg) =>
+      probe.expectMsg(MetadataWriteFailure(WriteMetadataActorSpec.IntermittentException, msg.events))
     }
     eventually {
-      writeActor.underlyingActor.failureCount should be (5 * 10)
+      writeActor.underlyingActor.failureCount should be(5 * 10)
     }
 
     writeActor.stop()
@@ -127,8 +156,7 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
 
     override def connectionDescription: String = "Mock Database"
 
-    override def existsMetadataEntries()(
-      implicit ec: ExecutionContext): Nothing = notImplemented()
+    override def existsMetadataEntries()(implicit ec: ExecutionContext): Nothing = notImplemented()
 
     var requestsSinceLastSuccess = 0
     // Return successful
@@ -140,8 +168,8 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
                                     submissionMetadataKey: String,
                                     parentWorkflowIdKey: String,
                                     rootWorkflowIdKey: String,
-                                    labelMetadataKey: String)
-                                   (implicit ec: ExecutionContext): Future[Unit] = {
+                                    labelMetadataKey: String
+    )(implicit ec: ExecutionContext): Future[Unit] =
       if (requestsSinceLastSuccess == failuresBetweenEachSuccess) {
         requestsSinceLastSuccess = 0
         Future.successful(())
@@ -149,50 +177,50 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
         requestsSinceLastSuccess += 1
         Future.failed(WriteMetadataActorSpec.IntermittentException)
       }
-    }
 
-    override def metadataEntryExists(workflowExecutionUuid: String)
-                                    (implicit ec: ExecutionContext): Nothing = notImplemented()
+    override def metadataEntryExists(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Nothing =
+      notImplemented()
 
-    override def metadataSummaryEntryExists(workflowExecutionUuid: String)
-                                           (implicit ec: ExecutionContext): Nothing = notImplemented()
+    override def metadataSummaryEntryExists(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Nothing =
+      notImplemented()
 
-    override def queryMetadataEntries(workflowExecutionUuid: String,
-                                      timeout: Duration)
-                                     (implicit ec: ExecutionContext): Nothing = notImplemented()
+    override def queryMetadataEntries(workflowExecutionUuid: String, timeout: Duration)(implicit
+      ec: ExecutionContext
+    ): Nothing = notImplemented()
 
     override def streamMetadataEntries(workflowExecutionUuid: String): Nothing = notImplemented()
 
-    override def queryMetadataEntries(workflowExecutionUuid: String,
-                                      metadataKey: String,
-                                      timeout: Duration)(implicit ec: ExecutionContext): Nothing = notImplemented()
+    override def queryMetadataEntries(workflowExecutionUuid: String, metadataKey: String, timeout: Duration)(implicit
+      ec: ExecutionContext
+    ): Nothing = notImplemented()
 
     override def queryMetadataEntries(workflowExecutionUuid: String,
                                       callFullyQualifiedName: String,
                                       jobIndex: Option[Int],
                                       jobAttempt: Option[Int],
-                                      timeout: Duration)(implicit ec: ExecutionContext): Nothing = notImplemented()
+                                      timeout: Duration
+    )(implicit ec: ExecutionContext): Nothing = notImplemented()
 
     override def queryMetadataEntries(workflowUuid: String,
                                       metadataKey: String,
                                       callFullyQualifiedName: String,
                                       jobIndex: Option[Int],
                                       jobAttempt: Option[Int],
-                                      timeout: Duration)(implicit ec: ExecutionContext): Nothing = notImplemented()
+                                      timeout: Duration
+    )(implicit ec: ExecutionContext): Nothing = notImplemented()
 
     override def queryMetadataEntryWithKeyConstraints(workflowExecutionUuid: String,
-                                             metadataKeysToFilterFor: List[String],
-                                             metadataKeysToFilterAgainst: List[String],
-                                             metadataJobQueryValue: MetadataJobQueryValue,
-                                             timeout: Duration)
-                                            (implicit ec: ExecutionContext): Nothing = notImplemented()
-
-    override def summarizeIncreasing(labelMetadataKey: String,
-                                     limit: Int,
-                                     buildUpdatedSummary:
-                                     (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry])
-                                       => WorkflowMetadataSummaryEntry)
-                                    (implicit ec: ExecutionContext): Nothing = notImplemented()
+                                                      metadataKeysToFilterFor: List[String],
+                                                      metadataKeysToFilterAgainst: List[String],
+                                                      metadataJobQueryValue: MetadataJobQueryValue,
+                                                      timeout: Duration
+    )(implicit ec: ExecutionContext): Nothing = notImplemented()
+
+    override def summarizeIncreasing(
+      labelMetadataKey: String,
+      limit: Int,
+      buildUpdatedSummary: (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry]) => WorkflowMetadataSummaryEntry
+    )(implicit ec: ExecutionContext): Nothing = notImplemented()
 
     /**
       * Retrieves a window of summarizable metadata satisfying the specified criteria.
@@ -200,23 +228,23 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
       * @param buildUpdatedSummary Takes in the optional existing summary and the metadata, returns the new summary.
       * @return A `Future` with the maximum metadataEntryId summarized by the invocation of this method.
       */
-    override def summarizeDecreasing(summaryNameDecreasing: String,
-                                     summaryNameIncreasing: String,
-                                     labelMetadataKey: String,
-                                     limit: Int,
-                                     buildUpdatedSummary:
-                                     (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry])
-                                       => WorkflowMetadataSummaryEntry)
-                                    (implicit ec: ExecutionContext): Nothing = notImplemented()
-
-    override def getWorkflowStatus(workflowExecutionUuid: String)
-                                  (implicit ec: ExecutionContext): Nothing = notImplemented()
+    override def summarizeDecreasing(
+      summaryNameDecreasing: String,
+      summaryNameIncreasing: String,
+      labelMetadataKey: String,
+      limit: Int,
+      buildUpdatedSummary: (Option[WorkflowMetadataSummaryEntry], Seq[MetadataEntry]) => WorkflowMetadataSummaryEntry
+    )(implicit ec: ExecutionContext): Nothing = notImplemented()
+
+    override def getWorkflowStatus(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Nothing =
+      notImplemented()
 
-    override def getWorkflowLabels(workflowExecutionUuid: String)
-                                  (implicit ec: ExecutionContext): Nothing = notImplemented()
+    override def getWorkflowLabels(workflowExecutionUuid: String)(implicit ec: ExecutionContext): Nothing =
+      notImplemented()
 
-    override def getRootAndSubworkflowLabels(rootWorkflowExecutionUuid: String)
-                                  (implicit ec: ExecutionContext): Nothing = notImplemented()
+    override def getRootAndSubworkflowLabels(rootWorkflowExecutionUuid: String)(implicit
+      ec: ExecutionContext
+    ): Nothing = notImplemented()
 
     override def queryWorkflowSummaries(parentWorkflowIdMetadataKey: String,
                                         workflowStatuses: Set[String],
@@ -233,10 +261,9 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
                                         includeSubworkflows: Boolean,
                                         page: Option[Int],
                                         pageSize: Option[Int],
-                                        newestFirst: Boolean)
-                                       (implicit ec: ExecutionContext): Nothing = {
+                                        newestFirst: Boolean
+    )(implicit ec: ExecutionContext): Nothing =
       notImplemented()
-    }
 
     override def countWorkflowSummaries(parentWorkflowIdMetadataKey: String,
                                         workflowStatuses: Set[String],
@@ -250,66 +277,101 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
                                         startTimestampOption: Option[Timestamp],
                                         endTimestampOption: Option[Timestamp],
                                         metadataArchiveStatus: Set[Option[String]],
-                                        includeSubworkflows: Boolean)
-                                       (implicit ec: ExecutionContext): Nothing = {
+                                        includeSubworkflows: Boolean
+    )(implicit ec: ExecutionContext): Nothing =
       notImplemented()
-    }
 
-    override def updateMetadataArchiveStatus(workflowExecutionUuid: String, newArchiveStatus: Option[String]): Future[Int] = notImplemented()
+    override def updateMetadataArchiveStatus(workflowExecutionUuid: String,
+                                             newArchiveStatus: Option[String]
+    ): Future[Int] = notImplemented()
 
-    override def withConnection[A](block: Connection => A): Nothing = {
+    override def withConnection[A](block: Connection => A): Nothing =
       notImplemented()
-    }
 
     override def close(): Nothing = notImplemented()
 
-    override def deleteAllMetadataForWorkflowAndUpdateArchiveStatus(workflowId: String, newArchiveStatus: Option[String])(implicit ec: ExecutionContext): Future[Int] = {
+    override def deleteAllMetadataForWorkflowAndUpdateArchiveStatus(workflowId: String,
+                                                                    newArchiveStatus: Option[String]
+    )(implicit ec: ExecutionContext): Future[Int] =
       notImplemented()
-    }
 
-    override def getRootWorkflowId(workflowId: String)(implicit ec: ExecutionContext): Future[Option[String]] = {
+    override def getRootWorkflowId(workflowId: String)(implicit ec: ExecutionContext): Future[Option[String]] =
       notImplemented()
-    }
 
-    override def queryWorkflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp(archiveStatus: Option[String], thresholdTimestamp: Timestamp, batchSize: Long)(implicit ec: ExecutionContext): Future[Seq[String]] = {
+    override def queryWorkflowIdsByArchiveStatusAndEndedOnOrBeforeThresholdTimestamp(archiveStatus: Option[String],
+                                                                                     thresholdTimestamp: Timestamp,
+                                                                                     batchSize: Long
+    )(implicit ec: ExecutionContext): Future[Seq[String]] =
       notImplemented()
-    }
 
-    override def getSummaryQueueSize()(implicit ec: ExecutionContext): Future[Int] = {
+    override def getSummaryQueueSize()(implicit ec: ExecutionContext): Future[Int] =
       notImplemented()
-    }
 
-    override def countMetadataEntries(workflowExecutionUuid: String, expandSubWorkflows: Boolean, timeout: Duration)(implicit ec: ExecutionContext): Future[Int] = {
+    override def countMetadataEntries(workflowExecutionUuid: String, expandSubWorkflows: Boolean, timeout: Duration)(
+      implicit ec: ExecutionContext
+    ): Future[Int] =
       notImplemented()
-    }
 
-    override def countMetadataEntries(workflowExecutionUuid: String, metadataKey: String, expandSubWorkflows: Boolean, timeout: Duration)(implicit ec: ExecutionContext): Future[Int] = {
+    override def countMetadataEntries(workflowExecutionUuid: String,
+                                      metadataKey: String,
+                                      expandSubWorkflows: Boolean,
+                                      timeout: Duration
+    )(implicit ec: ExecutionContext): Future[Int] =
       notImplemented()
-    }
 
-    override def countMetadataEntries(workflowExecutionUuid: String, callFullyQualifiedName: String, jobIndex: Option[Int], jobAttempt: Option[Int], expandSubWorkflows: Boolean, timeout: Duration)(implicit ec: ExecutionContext): Future[Int] = {
+    override def countMetadataEntries(workflowExecutionUuid: String,
+                                      callFullyQualifiedName: String,
+                                      jobIndex: Option[Int],
+                                      jobAttempt: Option[Int],
+                                      expandSubWorkflows: Boolean,
+                                      timeout: Duration
+    )(implicit ec: ExecutionContext): Future[Int] =
       notImplemented()
-    }
 
-    override def countMetadataEntries(workflowUuid: String, metadataKey: String, callFullyQualifiedName: String, jobIndex: Option[Int], jobAttempt: Option[Int], expandSubWorkflows: Boolean, timeout: Duration)(implicit ec: ExecutionContext): Future[Int] = {
+    override def countMetadataEntries(workflowUuid: String,
+                                      metadataKey: String,
+                                      callFullyQualifiedName: String,
+                                      jobIndex: Option[Int],
+                                      jobAttempt: Option[Int],
+                                      expandSubWorkflows: Boolean,
+                                      timeout: Duration
+    )(implicit ec: ExecutionContext): Future[Int] =
       notImplemented()
-    }
 
-    override def countMetadataEntryWithKeyConstraints(workflowExecutionUuid: String, metadataKeysToFilterFor: List[String], metadataKeysToFilterAgainst: List[String], metadataJobQueryValue: MetadataJobQueryValue, expandSubWorkflows: Boolean, timeout: Duration)(implicit ec: ExecutionContext): Future[Int] = {
+    override def countMetadataEntryWithKeyConstraints(workflowExecutionUuid: String,
+                                                      metadataKeysToFilterFor: List[String],
+                                                      metadataKeysToFilterAgainst: List[String],
+                                                      metadataJobQueryValue: MetadataJobQueryValue,
+                                                      expandSubWorkflows: Boolean,
+                                                      timeout: Duration
+    )(implicit ec: ExecutionContext): Future[Int] =
       notImplemented()
-    }
 
-    override def getMetadataArchiveStatusAndEndTime(workflowId: String)(implicit ec: ExecutionContext):  Future[(Option[String], Option[Timestamp])] = notImplemented()
+    override def getMetadataArchiveStatusAndEndTime(workflowId: String)(implicit
+      ec: ExecutionContext
+    ): Future[(Option[String], Option[Timestamp])] = notImplemented()
 
-    override def queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String], workflowEndTimestampThreshold: Timestamp, batchSize: Long)(implicit ec: ExecutionContext): Future[Seq[WorkflowMetadataSummaryEntry]] = notImplemented()
+    override def queryWorkflowsToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String],
+                                                                              workflowEndTimestampThreshold: Timestamp,
+                                                                              batchSize: Long
+    )(implicit ec: ExecutionContext): Future[Seq[WorkflowMetadataSummaryEntry]] = notImplemented()
 
-    override def countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(workflowStatuses: List[String], workflowEndTimestampThreshold: Timestamp)(implicit ec: ExecutionContext): Future[Int] = notImplemented()
+    override def countWorkflowsLeftToArchiveThatEndedOnOrBeforeThresholdTimestamp(
+      workflowStatuses: List[String],
+      workflowEndTimestampThreshold: Timestamp
+    )(implicit ec: ExecutionContext): Future[Int] = notImplemented()
 
-    override def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(workflowEndTimestampThreshold: Timestamp)(implicit ec: ExecutionContext): Future[Int] = notImplemented()
+    override def countWorkflowsLeftToDeleteThatEndedOnOrBeforeThresholdTimestamp(
+      workflowEndTimestampThreshold: Timestamp
+    )(implicit ec: ExecutionContext): Future[Int] = notImplemented()
 
-    override def getMetadataTableSizeInformation()(implicit ec: ExecutionContext): Future[Option[InformationSchemaEntry]] = notImplemented()
+    override def getMetadataTableSizeInformation()(implicit
+      ec: ExecutionContext
+    ): Future[Option[InformationSchemaEntry]] = notImplemented()
 
-    override def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: String)(implicit ec: ExecutionContext): Future[Vector[MetadataEntry]] = notImplemented()
+    override def getFailedJobsMetadataWithWorkflowId(rootWorkflowId: String)(implicit
+      ec: ExecutionContext
+    ): Future[Vector[MetadataEntry]] = notImplemented()
   }
 }
 
@@ -320,7 +382,8 @@ object WriteMetadataActorSpec {
   class BatchSizeCountingWriteMetadataActor(override val batchSize: Int,
                                             override val flushRate: FiniteDuration,
                                             override val serviceRegistryActor: ActorRef,
-                                            override val threshold: Int) extends WriteMetadataActor(batchSize, flushRate, serviceRegistryActor, threshold, MetadataStatisticsDisabled) {
+                                            override val threshold: Int
+  ) extends WriteMetadataActor(batchSize, flushRate, serviceRegistryActor, threshold, MetadataStatisticsDisabled) {
 
     var batchSizes: Vector[Int] = Vector.empty
     var failureCount: Int = 0
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/pubsub/PubSubMetadataServiceActorSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/pubsub/PubSubMetadataServiceActorSpec.scala
index 3caee16eb11..8b4219e1d5e 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/pubsub/PubSubMetadataServiceActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/pubsub/PubSubMetadataServiceActorSpec.scala
@@ -8,7 +8,12 @@ import com.google.api.services.pubsub.model.Topic
 import com.typesafe.config.{Config, ConfigFactory}
 import cromwell.core.WorkflowId
 import cromwell.services.ServicesSpec
-import cromwell.services.metadata.MetadataService.{MetadataWriteFailure, MetadataWriteSuccess, PutMetadataAction, PutMetadataActionAndRespond}
+import cromwell.services.metadata.MetadataService.{
+  MetadataWriteFailure,
+  MetadataWriteSuccess,
+  PutMetadataAction,
+  PutMetadataActionAndRespond
+}
 import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
 import org.broadinstitute.dsde.workbench.google.GooglePubSubDAO
 import org.broadinstitute.dsde.workbench.google.GooglePubSubDAO.PubSubMessage
@@ -177,29 +182,36 @@ class PubSubMetadataServiceActorSpec extends ServicesSpec {
 }
 
 object PubSubMetadataServiceActorSpec {
+
   /** A variant of PubSubMetadataServiceActor with a GooglePubSubDAO which will always return success */
-  class SuccessfulMockPubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
-    extends PubSubMetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor) {
+  class SuccessfulMockPubSubMetadataServiceActor(serviceConfig: Config,
+                                                 globalConfig: Config,
+                                                 serviceRegistryActor: ActorRef
+  ) extends PubSubMetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor) {
 
     override def createPubSubConnection(): GooglePubSubDAO = new SuccessfulMockGooglePubSubDao
   }
 
   /** A variant of PubSubMetadataServiceActor with a GooglePubSubDAO which will always return failure */
-  class FailingToCreateTopicMockPubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
-    extends PubSubMetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor) {
+  class FailingToCreateTopicMockPubSubMetadataServiceActor(serviceConfig: Config,
+                                                           globalConfig: Config,
+                                                           serviceRegistryActor: ActorRef
+  ) extends PubSubMetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor) {
 
     override def createPubSubConnection(): GooglePubSubDAO = new FailingToCreateTopicMockGooglePubSubDao
   }
 
   /** A variant of PubSubMetadataServiceActor which will fail on message publication */
-  class FailToPublishMockPubSubMetadataServiceActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
-    extends PubSubMetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor) {
+  class FailToPublishMockPubSubMetadataServiceActor(serviceConfig: Config,
+                                                    globalConfig: Config,
+                                                    serviceRegistryActor: ActorRef
+  ) extends PubSubMetadataServiceActor(serviceConfig, globalConfig, serviceRegistryActor) {
 
     override def createPubSubConnection(): GooglePubSubDAO = new FailToPublishMockGooglePubSubDao
   }
 
   trait MockGooglePubSubDao extends GooglePubSubDAO {
-    override implicit val executionContext: ExecutionContext = ExecutionContext.global
+    implicit override val executionContext: ExecutionContext = ExecutionContext.global
 
     override def createTopic(topicName: String): Future[Boolean]
     override def createSubscription(topicName: String, subscriptionName: String): Future[Boolean]
@@ -207,26 +219,36 @@ object PubSubMetadataServiceActorSpec {
 
     // The following aren't used so leaving them empty
     override def deleteTopic(topicName: String): Future[Boolean] = throw new UnsupportedOperationException
-    override def getTopic(topicName: String)(implicit executionContext: ExecutionContext): Future[Option[Topic]] = throw new UnsupportedOperationException
+    override def getTopic(topicName: String)(implicit executionContext: ExecutionContext): Future[Option[Topic]] =
+      throw new UnsupportedOperationException
     override def deleteSubscription(subscriptionName: String): Future[Boolean] = throw new UnsupportedOperationException
-    override def acknowledgeMessages(subscriptionName: String, messages: scala.collection.Seq[PubSubMessage]): Future[Unit] = throw new UnsupportedOperationException
-    override def acknowledgeMessagesById(subscriptionName: String, ackIds: scala.collection.Seq[String]): Future[Unit] = throw new UnsupportedOperationException
-    override def pullMessages(subscriptionName: String, maxMessages: Int): Future[scala.collection.Seq[PubSubMessage]] = throw new UnsupportedOperationException
-    override def setTopicIamPermissions(topicName: String, permissions: Map[WorkbenchEmail, String]): Future[Unit] = throw new UnsupportedOperationException
+    override def acknowledgeMessages(subscriptionName: String,
+                                     messages: scala.collection.Seq[PubSubMessage]
+    ): Future[Unit] = throw new UnsupportedOperationException
+    override def acknowledgeMessagesById(subscriptionName: String, ackIds: scala.collection.Seq[String]): Future[Unit] =
+      throw new UnsupportedOperationException
+    override def pullMessages(subscriptionName: String, maxMessages: Int): Future[scala.collection.Seq[PubSubMessage]] =
+      throw new UnsupportedOperationException
+    override def setTopicIamPermissions(topicName: String, permissions: Map[WorkbenchEmail, String]): Future[Unit] =
+      throw new UnsupportedOperationException
   }
 
   class SuccessfulMockGooglePubSubDao extends MockGooglePubSubDao {
     override def createTopic(topicName: String): Future[Boolean] = Future.successful(true)
-    override def createSubscription(topicName: String, subscriptionName: String): Future[Boolean] = Future.successful(true)
-    override def publishMessages(topicName: String, messages: scala.collection.Seq[String]): Future[Unit] = Future.successful(())
+    override def createSubscription(topicName: String, subscriptionName: String): Future[Boolean] =
+      Future.successful(true)
+    override def publishMessages(topicName: String, messages: scala.collection.Seq[String]): Future[Unit] =
+      Future.successful(())
   }
 
   class FailingToCreateTopicMockGooglePubSubDao extends SuccessfulMockGooglePubSubDao {
-    override def createTopic(topicName: String): Future[Boolean] = Future.failed(new RuntimeException("Unable to create topic"))
+    override def createTopic(topicName: String): Future[Boolean] =
+      Future.failed(new RuntimeException("Unable to create topic"))
   }
 
   class FailToPublishMockGooglePubSubDao extends SuccessfulMockGooglePubSubDao {
-    override def publishMessages(topicName: String, messages: scala.collection.Seq[String]): Future[Unit] = Future.failed(new RuntimeException("sorry charlie"))
+    override def publishMessages(topicName: String, messages: scala.collection.Seq[String]): Future[Unit] =
+      Future.failed(new RuntimeException("sorry charlie"))
   }
 
   // This doesn't include a project so should be a failure
diff --git a/services/src/test/scala/cromwell/services/womtool/DescriberSpec.scala b/services/src/test/scala/cromwell/services/womtool/DescriberSpec.scala
index 95a0f64fd96..47fba0684fc 100644
--- a/services/src/test/scala/cromwell/services/womtool/DescriberSpec.scala
+++ b/services/src/test/scala/cromwell/services/womtool/DescriberSpec.scala
@@ -79,8 +79,10 @@ class DescriberSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
 object DescriberSpec {
   sealed trait DescriberSpecTestCase { def expectedDescription: String }
-  final case class FileAndDescription(file: String, override val expectedDescription: String) extends DescriberSpecTestCase
-  final case class UrlAndDescription(url: String, override val expectedDescription: String) extends DescriberSpecTestCase
+  final case class FileAndDescription(file: String, override val expectedDescription: String)
+      extends DescriberSpecTestCase
+  final case class UrlAndDescription(url: String, override val expectedDescription: String)
+      extends DescriberSpecTestCase
 
   def interpretTestCase(caseDirectory: Path): DescriberSpecTestCase = {
     val description = caseDirectory.resolve("description.json").contentAsString
diff --git a/services/src/test/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActorSpec.scala b/services/src/test/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActorSpec.scala
index a37f4021650..08b9955dcc1 100644
--- a/services/src/test/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActorSpec.scala
@@ -19,13 +19,17 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
 
   val womtoolActor: ActorRef =
     system.actorOf(
-      props = WomtoolServiceInCromwellActor.props(ConfigFactory.empty(), ConfigFactory.empty(), TestProbe("serviceRegistryActor").ref),
-      name = "womtoolActor",
+      props = WomtoolServiceInCromwellActor.props(ConfigFactory.empty(),
+                                                  ConfigFactory.empty(),
+                                                  TestProbe("serviceRegistryActor").ref
+      ),
+      name = "womtoolActor"
     )
   CromwellLanguages.initLanguages(LanguageConfiguration.AllLanguageEntries)
 
   object TestData {
-    val workflowUrlValid = "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"
+    val workflowUrlValid =
+      "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/womtool/src/test/resources/validate/wdl_draft3/valid/callable_imports/my_workflow.wdl"
     val workflowUrlNotFound = "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow"
     val workflowUrlBadHost = "https://zardoz.zardoz"
     val workflowUrlNotAUrl = "Zardoz"
@@ -167,33 +171,40 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
 
       val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlValid), inputsJson = TestData.bogusInputs)
 
-      check(DescribeRequest(wsfc), DescribeSuccess(
-        description = WorkflowDescription(
-          valid = false,
-          errors = List("Required workflow input 'wf_hello.hello.addressee' not specified"),
-          validWorkflow = true,
-          name = "wf_hello",
-          inputs = List(InputDescription("hello.addressee", WomStringType, "String", optional = false, None)),
-          submittedDescriptorType = Map("descriptorType" -> "WDL", "descriptorTypeVersion" -> "1.0"),
-          isRunnableWorkflow = true,
+      check(
+        DescribeRequest(wsfc),
+        DescribeSuccess(
+          description = WorkflowDescription(
+            valid = false,
+            errors = List("Required workflow input 'wf_hello.hello.addressee' not specified"),
+            validWorkflow = true,
+            name = "wf_hello",
+            inputs = List(InputDescription("hello.addressee", WomStringType, "String", optional = false, None)),
+            submittedDescriptorType = Map("descriptorType" -> "WDL", "descriptorTypeVersion" -> "1.0"),
+            isRunnableWorkflow = true
+          )
         )
-      ))
+      )
     }
 
     "return valid = false, validWorkflow = true for a valid inputs-requiring workflow with an empty inputs JSON" in {
 
       val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlValid), inputsJson = TestData.emptyInputs)
 
-      check(DescribeRequest(wsfc), DescribeSuccess(
-        description = WorkflowDescription(
-          valid = false,
-          errors = List("Required workflow input 'wf_hello.hello.addressee' not specified"),
-          validWorkflow = true,
-          name = "wf_hello",
-          inputs = List(InputDescription("hello.addressee", WomStringType, "String", optional = false, None)),
-          submittedDescriptorType = Map("descriptorType" -> "WDL", "descriptorTypeVersion" -> "1.0"),
-          isRunnableWorkflow = true),
-      ))
+      check(
+        DescribeRequest(wsfc),
+        DescribeSuccess(
+          description = WorkflowDescription(
+            valid = false,
+            errors = List("Required workflow input 'wf_hello.hello.addressee' not specified"),
+            validWorkflow = true,
+            name = "wf_hello",
+            inputs = List(InputDescription("hello.addressee", WomStringType, "String", optional = false, None)),
+            submittedDescriptorType = Map("descriptorType" -> "WDL", "descriptorTypeVersion" -> "1.0"),
+            isRunnableWorkflow = true
+          )
+        )
+      )
     }
 
     "return valid for a valid no-inputs workflow with empty inputs" in {
@@ -228,14 +239,27 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
 
       val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlValidNoInputs), inputsJson = TestData.bogusInputs)
 
-      check(DescribeRequest(wsfc), DescribeSuccess(
-        description = WorkflowDescription(valid = false, errors = List("WARNING: Unexpected input provided: foo.bar (expected inputs: [])"), validWorkflow = true, name = "wf_hello", inputs = List.empty, submittedDescriptorType = Map("descriptorType" -> "WDL", "descriptorTypeVersion" -> "1.0"), isRunnableWorkflow = true)))
+      check(
+        DescribeRequest(wsfc),
+        DescribeSuccess(
+          description = WorkflowDescription(
+            valid = false,
+            errors = List("WARNING: Unexpected input provided: foo.bar (expected inputs: [])"),
+            validWorkflow = true,
+            name = "wf_hello",
+            inputs = List.empty,
+            submittedDescriptorType = Map("descriptorType" -> "WDL", "descriptorTypeVersion" -> "1.0"),
+            isRunnableWorkflow = true
+          )
+        )
+      )
     }
 
     // In draft-2 we allow extraneous inputs for legacy reasons - e.g. users put comments in them
     "return valid for a valid no-inputs draft-2 workflow with extraneous inputs" in {
 
-      val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlValidDraft2NoInputs), inputsJson = TestData.bogusInputs)
+      val wsfc =
+        wsfcConjurer(workflowSource = Option(TestData.wdlValidDraft2NoInputs), inputsJson = TestData.bogusInputs)
 
       check(
         DescribeRequest(wsfc),
@@ -298,7 +322,8 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
 
     "return an error when both workflow URL and workflow source specified" in {
 
-      val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlInvalid), workflowUrl = Option(TestData.workflowUrlValid))
+      val wsfc =
+        wsfcConjurer(workflowSource = Option(TestData.wdlInvalid), workflowUrl = Option(TestData.workflowUrlValid))
 
       check(DescribeRequest(wsfc), DescribeFailure("Both workflow source and url can't be supplied"))
     }
@@ -307,9 +332,12 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
 
       val wsfc = wsfcConjurer(workflowUrl = Option(TestData.workflowUrlNotFound))
 
-      check(DescribeRequest(wsfc),
+      check(
+        DescribeRequest(wsfc),
         DescribeFailure(
-          "Failed to resolve 'https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Failed to download https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow (reason 1 of 1): 404: Not Found"))
+          "Failed to resolve 'https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Failed to download https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow (reason 1 of 1): 404: Not Found"
+        )
+      )
     }
 
     "return an error when the workflow URL's host can't be resolved" in {
@@ -320,9 +348,17 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       (for {
         result <- (womtoolActor ? DescribeRequest(wsfc)).mapTo[DescribeResult]
         _ = result should (
-          be(DescribeFailure("Failed to resolve 'https://zardoz.zardoz' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Failed to download https://zardoz.zardoz (reason 1 of 1): HTTP resolver with headers had an unexpected error (zardoz.zardoz: Name or service not known)"))
-          or
-          be(DescribeFailure("Failed to resolve 'https://zardoz.zardoz' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Failed to download https://zardoz.zardoz (reason 1 of 1): HTTP resolver with headers had an unexpected error (zardoz.zardoz: nodename nor servname provided, or not known)"))
+          be(
+            DescribeFailure(
+              "Failed to resolve 'https://zardoz.zardoz' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Failed to download https://zardoz.zardoz (reason 1 of 1): HTTP resolver with headers had an unexpected error (zardoz.zardoz: Name or service not known)"
+            )
+          )
+            or
+              be(
+                DescribeFailure(
+                  "Failed to resolve 'https://zardoz.zardoz' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Failed to download https://zardoz.zardoz (reason 1 of 1): HTTP resolver with headers had an unexpected error (zardoz.zardoz: nodename nor servname provided, or not known)"
+                )
+              )
         )
       } yield ()).futureValue
     }
@@ -332,7 +368,12 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc = wsfcConjurer(workflowUrl = Option(TestData.workflowUrlNotAUrl))
 
       // The HTTP resolver has figured out that you have not given it a URL and assumes it's a relative path
-      check(DescribeRequest(wsfc), DescribeFailure("Failed to resolve 'Zardoz' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path"))
+      check(
+        DescribeRequest(wsfc),
+        DescribeFailure(
+          "Failed to resolve 'Zardoz' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path"
+        )
+      )
     }
 
   }
@@ -346,7 +387,8 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
                            workflowUrl: Option[WorkflowUrl] = None,
                            workflowType: Option[WorkflowType] = None,
                            workflowTypeVersion: Option[WorkflowTypeVersion] = None,
-                           inputsJson: WorkflowJson = ""): WorkflowSourceFilesCollection = {
+                           inputsJson: WorkflowJson = ""
+  ): WorkflowSourceFilesCollection =
     WorkflowSourceFilesCollection(
       workflowSource = workflowSource,
       workflowUrl = workflowUrl,
@@ -361,6 +403,5 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       warnings = Seq.empty,
       requestedWorkflowId = None
     )
-  }
 
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index fed3b2c09e0..bbd552b4325 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -81,21 +81,27 @@ object AwsBatchAsyncBackendJobExecutionActor {
 }
 
 class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
-  extends BackendJobLifecycleActor with StandardAsyncExecutionActor with AwsBatchJobCachingActorHelper
-    with KvClient with AskSupport {
+    extends BackendJobLifecycleActor
+    with StandardAsyncExecutionActor
+    with AwsBatchJobCachingActorHelper
+    with KvClient
+    with AskSupport {
 
   /**
     * The builder for `IoCommands` to the storage system used by jobs executed by this backend
     */
-  override lazy val ioCommandBuilder: IoCommandBuilder = configuration.fileSystem match  {
+  override lazy val ioCommandBuilder: IoCommandBuilder = configuration.fileSystem match {
     case AWSBatchStorageSystems.s3 => S3BatchCommandBuilder
-    case _ =>  DefaultIoCommandBuilder
+    case _ => DefaultIoCommandBuilder
   }
 
   // the cromwell backend Actor
   val backendSingletonActor: ActorRef =
     standardParams.backendSingletonActorOption.getOrElse(
-      throw new RuntimeException(s"AWS Backend actor cannot exist without its backend singleton (of type ${AwsBatchSingletonActor.getClass.getSimpleName})"))
+      throw new RuntimeException(
+        s"AWS Backend actor cannot exist without its backend singleton (of type ${AwsBatchSingletonActor.getClass.getSimpleName})"
+      )
+    )
 
   import AwsBatchAsyncBackendJobExecutionActor._
 
@@ -115,11 +121,12 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
   override lazy val pollBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(1.second, 5.minutes, 1.1)
 
-  override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(
-    initialInterval = 3 seconds, maxInterval = 20 seconds, multiplier = 1.1)
+  override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff =
+    SimpleExponentialBackoff(initialInterval = 3 seconds, maxInterval = 20 seconds, multiplier = 1.1)
 
-  //the name (String) of the docker image that will be used to contain this job
-  private lazy val jobDockerImage = jobDescriptor.maybeCallCachingEligible.dockerHash.getOrElse(runtimeAttributes.dockerImage)
+  // the name (String) of the docker image that will be used to contain this job
+  private lazy val jobDockerImage =
+    jobDescriptor.maybeCallCachingEligible.dockerHash.getOrElse(runtimeAttributes.dockerImage)
 
   override lazy val dockerImageUsed: Option[String] = Option(jobDockerImage)
 
@@ -128,7 +135,6 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         |$jobShell ${jobPaths.script.pathWithoutScheme}
         |""".stripMargin
 
-
   /* Batch job object (see AwsBatchJob). This has the configuration necessary
    * to perform all operations with the AWS Batch infrastructure. This is
    * where the real work happens
@@ -163,23 +169,26 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
    */
 
   lazy val cmdScript = configuration.fileSystem match {
-     case AWSBatchStorageSystems.s3 => commandScriptContents.toEither.toOption.get
-     case _ => execScript
+    case AWSBatchStorageSystems.s3 => commandScriptContents.toEither.toOption.get
+    case _ => execScript
   }
 
-  lazy val batchJob: AwsBatchJob = {
+  lazy val batchJob: AwsBatchJob =
     AwsBatchJob(
       jobDescriptor,
       runtimeAttributes,
       instantiatedCommand.commandString,
       cmdScript,
-      rcPath.toString, executionStdout, executionStderr,
+      rcPath.toString,
+      executionStdout,
+      executionStderr,
       generateAwsBatchInputs(jobDescriptor),
       generateAwsBatchOutputs(jobDescriptor),
-      jobPaths, Seq.empty[AwsBatchParameter],
+      jobPaths,
+      Seq.empty[AwsBatchParameter],
       configuration.awsConfig.region,
-      Option(configuration.awsAuth))
-  }
+      Option(configuration.awsAuth)
+    )
   /* Tries to abort the job in flight
    *
    * @param job A StandardAsyncJob object (has jobId value) to cancel
@@ -188,7 +197,9 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
    */
   override def tryAbort(job: StandardAsyncJob): Unit = {
     batchJob.abort(job.jobId) // job.JobId should be the AWS Batch Job Id based on analysis of other backends
-    Log.info(s"Attempted CancelJob operation in AWS Batch for Job ID ${job.jobId}. There were no errors during the operation")
+    Log.info(
+      s"Attempted CancelJob operation in AWS Batch for Job ID ${job.jobId}. There were no errors during the operation"
+    )
     Log.info(s"We have normality. Anything you still can't cope with is therefore your own problem")
     Log.info(s"https://www.youtube.com/watch?v=YCRxnjE7JVs")
     ()
@@ -200,14 +211,19 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     * Takes two arrays of remote and local WOM File paths and generates the necessary AwsBatchInputs.
     */
   private def inputsFromWomFiles(namePrefix: String,
-                                    remotePathArray: Seq[WomFile],
-                                    localPathArray: Seq[WomFile],
-                                    jobDescriptor: BackendJobDescriptor): Iterable[AwsBatchInput] = {
-    (remotePathArray zip localPathArray zipWithIndex) flatMap {
-      case ((remotePath, localPath), index) =>
-        Seq(AwsBatchFileInput(s"$namePrefix-$index", remotePath.valueString, DefaultPathBuilder.get(localPath.valueString), workingDisk))
+                                 remotePathArray: Seq[WomFile],
+                                 localPathArray: Seq[WomFile],
+                                 jobDescriptor: BackendJobDescriptor
+  ): Iterable[AwsBatchInput] =
+    (remotePathArray zip localPathArray zipWithIndex) flatMap { case ((remotePath, localPath), index) =>
+      Seq(
+        AwsBatchFileInput(s"$namePrefix-$index",
+                          remotePath.valueString,
+                          DefaultPathBuilder.get(localPath.valueString),
+                          workingDisk
+        )
+      )
     }
-  }
 
   /**
     * Turns WomFiles into relative paths.  These paths are relative to the working disk.
@@ -215,18 +231,17 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     * relativeLocalizationPath("foo/bar.txt") -> "foo/bar.txt"
     * relativeLocalizationPath("s3://some/bucket/foo.txt") -> "some/bucket/foo.txt"
     */
-  override protected def relativeLocalizationPath(file: WomFile): WomFile = {
+  override protected def relativeLocalizationPath(file: WomFile): WomFile =
     file.mapFile(value =>
       getPath(value) match {
         case Success(path) =>
-          configuration.fileSystem match  {
+          configuration.fileSystem match {
             case AWSBatchStorageSystems.s3 => path.pathWithoutScheme
-            case _ =>  path.toString
+            case _ => path.toString
           }
         case _ => value
       }
     )
-  }
 
   /**
     * Generate a set of inputs based on a job description
@@ -236,28 +251,28 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   private[aws] def generateAwsBatchInputs(jobDescriptor: BackendJobDescriptor): Set[AwsBatchInput] = {
     val writeFunctionFiles = instantiatedCommand.createdFiles map { f => f.file.value.md5SumShort -> List(f) } toMap
 
-    val writeFunctionInputs = writeFunctionFiles flatMap {
-      case (name, files) => inputsFromWomFiles(name, files.map(_.file), files.map(localizationPath), jobDescriptor)
+    val writeFunctionInputs = writeFunctionFiles flatMap { case (name, files) =>
+      inputsFromWomFiles(name, files.map(_.file), files.map(localizationPath), jobDescriptor)
     }
 
     // Collect all WomFiles from inputs to the call.
     val callInputFiles: Map[FullyQualifiedName, Seq[WomFile]] = jobDescriptor.fullyQualifiedInputs safeMapValues {
       womFile =>
-        val arrays: Seq[WomArray] = womFile collectAsSeq {
-          case womFile: WomFile =>
-            val files: List[WomSingleFile] = DirectoryFunctions
-              .listWomSingleFiles(womFile, callPaths.workflowPaths)
-              .toTry(s"Error getting single files for $womFile").get
-            WomArray(WomArrayType(WomSingleFileType), files)
+        val arrays: Seq[WomArray] = womFile collectAsSeq { case womFile: WomFile =>
+          val files: List[WomSingleFile] = DirectoryFunctions
+            .listWomSingleFiles(womFile, callPaths.workflowPaths)
+            .toTry(s"Error getting single files for $womFile")
+            .get
+          WomArray(WomArrayType(WomSingleFileType), files)
         }
 
-        arrays.flatMap(_.value).collect {
-          case womFile: WomFile => womFile
+        arrays.flatMap(_.value).collect { case womFile: WomFile =>
+          womFile
         }
     }
 
-    val callInputInputs = callInputFiles flatMap {
-      case (name, files) => inputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor)
+    val callInputInputs = callInputFiles flatMap { case (name, files) =>
+      inputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor)
     }
 
     val scriptInput: AwsBatchInput = AwsBatchFileInput(
@@ -278,12 +293,11 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     */
   private def relativePathAndVolume(path: String, disks: Seq[AwsBatchVolume]): (Path, AwsBatchVolume) = {
 
-    def getAbsolutePath(path: Path) = {
+    def getAbsolutePath(path: Path) =
       configuration.fileSystem match {
         case AWSBatchStorageSystems.s3 => AwsBatchWorkingDisk.MountPoint.resolve(path)
         case _ => DefaultPathBuilder.get(configuration.root).resolve(path)
       }
-  }
     val absolutePath = DefaultPathBuilder.get(path) match {
       case p if !p.isAbsolute => getAbsolutePath(p)
       case p => p
@@ -292,7 +306,9 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     disks.find(d => absolutePath.startsWith(d.mountPoint)) match {
       case Some(disk) => (disk.mountPoint.relativize(absolutePath), disk)
       case None =>
-        throw new Exception(s"Absolute path $path doesn't appear to be under any mount points: ${disks.map(_.toString).mkString(", ")}")
+        throw new Exception(
+          s"Absolute path $path doesn't appear to be under any mount points: ${disks.map(_.toString).mkString(", ")}"
+        )
     }
   }
 
@@ -301,18 +317,18 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     * @param referenceName the name to make safe
     * @return the name or the MD5sum of that name if the name is >= 128 characters
     */
-  private def makeSafeAwsBatchReferenceName(referenceName: String) = {
+  private def makeSafeAwsBatchReferenceName(referenceName: String) =
     if (referenceName.length <= 127) referenceName else referenceName.md5Sum
-  }
 
   private[aws] def generateAwsBatchOutputs(jobDescriptor: BackendJobDescriptor): Set[AwsBatchFileOutput] = {
     import cats.syntax.validated._
-    def evaluateFiles(output: OutputDefinition): List[WomFile] = {
+    def evaluateFiles(output: OutputDefinition): List[WomFile] =
       Try(
-        output.expression.evaluateFiles(jobDescriptor.localInputs, NoIoFunctionSet, output.womType).map(_.toList map { _.file })
+        output.expression
+          .evaluateFiles(jobDescriptor.localInputs, NoIoFunctionSet, output.womType)
+          .map(_.toList map { _.file })
       ).getOrElse(List.empty[WomFile].validNel)
-       .getOrElse(List.empty)
-    }
+        .getOrElse(List.empty)
 
     val womFileOutputs = jobDescriptor.taskCall.callable.outputs.flatMap(evaluateFiles) map relativeLocalizationPath
 
@@ -324,7 +340,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       }
     }
 
-    val additionalGlobOutput = jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateAwsBatchGlobFileOutputs).toSet
+    val additionalGlobOutput =
+      jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateAwsBatchGlobFileOutputs).toSet
 
     outputs.toSet ++ additionalGlobOutput
   }
@@ -360,11 +377,12 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   // used by generateAwsBatchOutputs, could potentially move this def within that function
   private def generateAwsBatchSingleFileOutputs(womFile: WomSingleFile): List[AwsBatchFileOutput] = {
     val destination = configuration.fileSystem match {
-      case  AWSBatchStorageSystems.s3 =>  callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
-      case _ => DefaultPathBuilder.get(womFile.valueString) match {
-        case p if !p.isAbsolute =>  callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
-        case p => p.pathAsString
-      }
+      case AWSBatchStorageSystems.s3 => callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
+      case _ =>
+        DefaultPathBuilder.get(womFile.valueString) match {
+          case p if !p.isAbsolute => callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
+          case p => p.pathAsString
+        }
 
     }
     val (relpath, disk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
@@ -385,64 +403,79 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     // We need both the glob directory and the glob list:
     List(
       // The glob directory:
-      AwsBatchFileOutput(makeSafeAwsBatchReferenceName(globDirectory), globDirectoryDestinationPath, DefaultPathBuilder.get(globDirectory + "*"), globDirectoryDisk),
+      AwsBatchFileOutput(makeSafeAwsBatchReferenceName(globDirectory),
+                         globDirectoryDestinationPath,
+                         DefaultPathBuilder.get(globDirectory + "*"),
+                         globDirectoryDisk
+      ),
       // The glob list file:
-      AwsBatchFileOutput(makeSafeAwsBatchReferenceName(globListFile), globListFileDestinationPath, DefaultPathBuilder.get(globListFile), globDirectoryDisk)
+      AwsBatchFileOutput(makeSafeAwsBatchReferenceName(globListFile),
+                         globListFileDestinationPath,
+                         DefaultPathBuilder.get(globListFile),
+                         globDirectoryDisk
+      )
     )
   }
 
-  override lazy val commandDirectory: Path = configuration.fileSystem match  {
+  override lazy val commandDirectory: Path = configuration.fileSystem match {
     case AWSBatchStorageSystems.s3 => AwsBatchWorkingDisk.MountPoint
-    case _ =>  jobPaths.callExecutionRoot
+    case _ => jobPaths.callExecutionRoot
   }
 
   override def globParentDirectory(womGlobFile: WomGlobFile): Path =
     configuration.fileSystem match {
-      case  AWSBatchStorageSystems.s3 =>
+      case AWSBatchStorageSystems.s3 =>
         val (_, disk) = relativePathAndVolume(womGlobFile.value, runtimeAttributes.disks)
         disk.mountPoint
       case _ => commandDirectory
     }
 
-  override def isTerminal(runStatus: RunStatus): Boolean = {
+  override def isTerminal(runStatus: RunStatus): Boolean =
     runStatus match {
       case _: TerminalRunStatus => true
       case _ => false
     }
-  }
 
   /**
     * Asynchronously upload the command script to the script path
     * @return a `Future` for the asynch operation
     */
-  def uploadScriptFile(): Future[Unit] = {
+  def uploadScriptFile(): Future[Unit] =
     commandScriptContents.fold(
       errors => Future.failed(new RuntimeException(errors.toList.mkString(", "))),
       asyncIo.writeAsync(jobPaths.script, _, Seq.empty)
     )
-  }
 
   // Primary entry point for cromwell to actually run something
-  override def executeAsync(): Future[ExecutionHandle] = {
-
+  override def executeAsync(): Future[ExecutionHandle] =
     for {
-      //upload the command script
+      // upload the command script
       _ <- uploadScriptFile()
       completionPromise = Promise[SubmitJobResponse]()
-      //send a message to the Actor requesting a job submission
+      // send a message to the Actor requesting a job submission
       _ = backendSingletonActor ! SubmitAwsJobRequest(batchJob, attributes, completionPromise)
-      //the future response of the submit job request
+      // the future response of the submit job request
       submitJobResponse <- completionPromise.future
-      //send a notify of status method to the Actor
-      _ = backendSingletonActor ! NotifyOfStatus(runtimeAttributes.queueArn, submitJobResponse.jobId, Option(Initializing))
-    } yield PendingExecutionHandle(jobDescriptor, StandardAsyncJob(submitJobResponse.jobId), Option(batchJob), previousState = None)
-  }
-
+      // send a notify of status method to the Actor
+      _ = backendSingletonActor ! NotifyOfStatus(runtimeAttributes.queueArn,
+                                                 submitJobResponse.jobId,
+                                                 Option(Initializing)
+      )
+    } yield PendingExecutionHandle(jobDescriptor,
+                                   StandardAsyncJob(submitJobResponse.jobId),
+                                   Option(batchJob),
+                                   previousState = None
+    )
 
-  override def recoverAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] =  reconnectAsync(jobId)
+  override def recoverAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] = reconnectAsync(jobId)
 
   override def reconnectAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] = {
-    val handle = PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState](jobDescriptor, jobId, Option(batchJob), previousState = None)
+    val handle = PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState](jobDescriptor,
+                                                                                                       jobId,
+                                                                                                       Option(batchJob),
+                                                                                                       previousState =
+                                                                                                         None
+    )
     Future.successful(handle)
   }
 
@@ -475,7 +508,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         jobLogger.info("Having to fall back to AWS query for status")
         Future.fromTry(job.status(jobId))
       case other =>
-        val message = s"Programmer Error (please report this): Received an unexpected message from the OccasionalPollingActor: $other"
+        val message =
+          s"Programmer Error (please report this): Received an unexpected message from the OccasionalPollingActor: $other"
         jobLogger.error(message)
         Future.failed(new Exception(message) with NoStackTrace)
     }
@@ -492,69 +526,66 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     case _ => super.isFatal(throwable)
   }
 
-  override lazy val startMetadataKeyValues: Map[String, Any] = super[AwsBatchJobCachingActorHelper].startMetadataKeyValues
+  override lazy val startMetadataKeyValues: Map[String, Any] =
+    super[AwsBatchJobCachingActorHelper].startMetadataKeyValues
 
-  //opportunity to send custom metadata when the run is in a terminal state, currently we don't
-  override def getTerminalMetadata(runStatus: RunStatus): Map[String, Any] = {
+  // opportunity to send custom metadata when the run is in a terminal state, currently we don't
+  override def getTerminalMetadata(runStatus: RunStatus): Map[String, Any] =
     runStatus match {
       case _: TerminalRunStatus => Map()
       case unknown => throw new RuntimeException(s"Attempt to get terminal metadata from non terminal status: $unknown")
     }
-  }
   def hostAbsoluteFilePath(jobPaths: JobPaths, pathString: String): Path = {
 
-    val pathBuilders:List[PathBuilder]  = List(DefaultPathBuilder)
+    val pathBuilders: List[PathBuilder] = List(DefaultPathBuilder)
     val path = PathFactory.buildPath(pathString, pathBuilders)
     if (!path.isAbsolute)
       jobPaths.callExecutionRoot.resolve(path).toAbsolutePath
-    else if(jobPaths.isInExecution(path.pathAsString))
+    else if (jobPaths.isInExecution(path.pathAsString))
       jobPaths.hostPathFromContainerPath(path.pathAsString)
     else
       jobPaths.hostPathFromContainerInputs(path.pathAsString)
   }
 
   override def mapOutputWomFile(womFile: WomFile): WomFile = {
-    val wfile  =  configuration.fileSystem match {
-      case  AWSBatchStorageSystems.s3 =>
+    val wfile = configuration.fileSystem match {
+      case AWSBatchStorageSystems.s3 =>
         womFile
       case _ =>
         val hostPath = hostAbsoluteFilePath(jobPaths, womFile.valueString)
-        if (!hostPath.exists) throw new FileNotFoundException(s"Could not process output, file not found: ${hostPath.pathAsString}")
+        if (!hostPath.exists)
+          throw new FileNotFoundException(s"Could not process output, file not found: ${hostPath.pathAsString}")
         womFile mapFile { _ => hostPath.pathAsString }
     }
     womFileToPath(generateAwsBatchOutputs(jobDescriptor))(wfile)
   }
 
-  private[aws] def womFileToPath(outputs: Set[AwsBatchFileOutput])(womFile: WomFile): WomFile = {
+  private[aws] def womFileToPath(outputs: Set[AwsBatchFileOutput])(womFile: WomFile): WomFile =
     womFile mapFile { path =>
       outputs collectFirst {
         case output if output.name == makeSafeAwsBatchReferenceName(path) => output.s3key
       } getOrElse path
     }
-  }
 
-  override def getTerminalEvents(runStatus: RunStatus): Seq[ExecutionEvent] = {
+  override def getTerminalEvents(runStatus: RunStatus): Seq[ExecutionEvent] =
     runStatus match {
       case successStatus: RunStatus.Succeeded => successStatus.eventList
       case unknown =>
         throw new RuntimeException(s"handleExecutionSuccess not called with RunStatus.Success. Instead got $unknown")
     }
-  }
 
-  override def retryEvaluateOutputs(exception: Exception): Boolean = {
+  override def retryEvaluateOutputs(exception: Exception): Boolean =
     exception match {
       case aggregated: CromwellAggregatedException =>
         aggregated.throwables.collectFirst { case s: SocketTimeoutException => s }.isDefined
       case _ => false
     }
-  }
 
-  override def mapCommandLineWomFile(womFile: WomFile): WomFile = {
+  override def mapCommandLineWomFile(womFile: WomFile): WomFile =
     womFile.mapFile(value =>
       getPath(value) match {
         case Success(path: S3Path) => workingDisk.mountPoint.resolve(path.pathWithoutScheme).pathAsString
         case _ => value
       }
     )
-  }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index e0dd8951550..3b05654d879 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -39,7 +39,11 @@ import common.exception.MessageAggregation
 import common.validation.ErrorOr._
 import common.validation.Validation._
 import cromwell.backend.CommonBackendConfigurationAttributes
-import cromwell.backend.impl.aws.callcaching.{AwsBatchCacheHitDuplicationStrategy, CopyCachedOutputs, UseOriginalCachedOutputs}
+import cromwell.backend.impl.aws.callcaching.{
+  AwsBatchCacheHitDuplicationStrategy,
+  CopyCachedOutputs,
+  UseOriginalCachedOutputs
+}
 import cromwell.cloudsupport.aws.AwsConfiguration
 import cromwell.cloudsupport.aws.auth.AwsAuthMode
 import eu.timepit.refined._
@@ -57,7 +61,8 @@ case class AwsBatchAttributes(fileSystem: String,
                               executionBucket: String,
                               duplicationStrategy: AwsBatchCacheHitDuplicationStrategy,
                               submitAttempts: Int Refined Positive,
-                              createDefinitionAttempts: Int Refined Positive)
+                              createDefinitionAttempts: Int Refined Positive
+)
 
 object AwsBatchAttributes {
   lazy val Logger = LoggerFactory.getLogger(this.getClass)
@@ -77,49 +82,54 @@ object AwsBatchAttributes {
 
   private val context = "AwsBatch"
 
-  implicit val urlReader: ValueReader[URL] = StringReader.stringValueReader.map { URI.create(_).toURL }
+  implicit val urlReader: ValueReader[URL] = StringReader.stringValueReader.map(URI.create(_).toURL)
 
   def fromConfigs(awsConfig: AwsConfiguration, backendConfig: Config): AwsBatchAttributes = {
-    val configKeys = backendConfig.entrySet().asScala.toSet map { entry: java.util.Map.Entry[String, ConfigValue] => entry.getKey }
+    val configKeys = backendConfig.entrySet().asScala.toSet map { entry: java.util.Map.Entry[String, ConfigValue] =>
+      entry.getKey
+    }
     warnNotRecognized(configKeys, availableConfigKeys, context, Logger)
 
     def warnDeprecated(keys: Set[String], deprecated: Map[String, String], context: String, logger: Logger) = {
       val deprecatedKeys = keys.intersect(deprecated.keySet)
-      deprecatedKeys foreach { key => logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}") }
+      deprecatedKeys foreach { key =>
+        logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}")
+      }
     }
 
     warnDeprecated(configKeys, deprecatedAwsBatchKeys, context, Logger)
 
-    val executionBucket: ErrorOr[String] = validate { backendConfig.as[String]("root") }
+    val executionBucket: ErrorOr[String] = validate(backendConfig.as[String]("root"))
 
-    val fileSysStr:ErrorOr[String] =  validate {backendConfig.hasPath("filesystems.s3") match {
-      case true => "s3"
-      case false => "local"
-    }}
+    val fileSysStr: ErrorOr[String] = validate {
+      backendConfig.hasPath("filesystems.s3") match {
+        case true => "s3"
+        case false => "local"
+      }
+    }
 
     val fileSysPath = backendConfig.hasPath("filesystems.s3") match {
       case true => "filesystems.s3"
       case false => "filesystems.local"
     }
-    val filesystemAuthMode: ErrorOr[AwsAuthMode] = {
+    val filesystemAuthMode: ErrorOr[AwsAuthMode] =
       (for {
         authName <- validate {
           backendConfig.as[String](s"${fileSysPath}.auth")
         }.toEither
         validAuth <- awsConfig.auth(authName).toEither
       } yield validAuth).toValidated
-    }
-
 
     val duplicationStrategy: ErrorOr[AwsBatchCacheHitDuplicationStrategy] =
       validate {
-        backendConfig.
-          as[Option[String]](s"${fileSysPath}.caching.duplication-strategy").
-          getOrElse("copy") match {
-            case "copy" => CopyCachedOutputs
-            case "reference" => UseOriginalCachedOutputs
-            case other => throw new IllegalArgumentException(s"Unrecognized caching duplication strategy: $other. Supported strategies are copy and reference. See reference.conf for more details.")
-          }
+        backendConfig.as[Option[String]](s"${fileSysPath}.caching.duplication-strategy").getOrElse("copy") match {
+          case "copy" => CopyCachedOutputs
+          case "reference" => UseOriginalCachedOutputs
+          case other =>
+            throw new IllegalArgumentException(
+              s"Unrecognized caching duplication strategy: $other. Supported strategies are copy and reference. See reference.conf for more details."
+            )
+        }
       }
 
     (
@@ -144,8 +154,6 @@ object AwsBatchAttributes {
       override def read(config: Config, path: String): ErrorOr[Refined[Int, Positive]] = {
         val int = config.getInt(path)
         refineV[Positive](int).toValidatedNel
+      }
     }
-  }
 }
-
-
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala
index edfbd560362..ae34cd958f8 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendInitializationData.scala
@@ -34,20 +34,23 @@ package cromwell.backend.impl.aws
 import cromwell.backend.standard.{StandardInitializationData, StandardValidatedRuntimeAttributesBuilder}
 import software.amazon.awssdk.auth.credentials.AwsCredentialsProvider
 
-case class AwsBatchBackendInitializationData
-(
+case class AwsBatchBackendInitializationData(
   override val workflowPaths: AwsBatchWorkflowPaths,
   override val runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder,
   configuration: AwsBatchConfiguration,
-  provider: AwsCredentialsProvider,
+  provider: AwsCredentialsProvider
   // TODO: We'll need something specific for batch probably, but I need to
   //       understand more about the genomics node first
-  //genomics: Genomics
-) extends StandardInitializationData(workflowPaths, runtimeAttributesBuilder, AwsBatchBackendInitializationDataUtility.getExpressionFunctionsClass(configuration.fileSystem))
+  // genomics: Genomics
+) extends StandardInitializationData(
+      workflowPaths,
+      runtimeAttributesBuilder,
+      AwsBatchBackendInitializationDataUtility.getExpressionFunctionsClass(configuration.fileSystem)
+    )
 
-object  AwsBatchBackendInitializationDataUtility {
-   def getExpressionFunctionsClass(fs: String) = fs match {
-      case AWSBatchStorageSystems.s3 => classOf[AwsBatchExpressionFunctions]
-      case _ => classOf[AwsBatchExpressionFunctionsForFS]
-   }
+object AwsBatchBackendInitializationDataUtility {
+  def getExpressionFunctionsClass(fs: String) = fs match {
+    case AWSBatchStorageSystems.s3 => classOf[AwsBatchExpressionFunctions]
+    case _ => classOf[AwsBatchExpressionFunctionsForFS]
+  }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
index c0ae9210852..498bee626b1 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
@@ -32,8 +32,20 @@
 package cromwell.backend.impl.aws
 
 import akka.actor.{ActorRef, Props}
-import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor, JobExecutionMap}
-import cromwell.backend.standard.{StandardAsyncExecutionActor, StandardFinalizationActor, StandardFinalizationActorParams, StandardInitializationActor, StandardInitializationActorParams, StandardLifecycleActorFactory}
+import cromwell.backend.{
+  BackendConfigurationDescriptor,
+  BackendInitializationData,
+  BackendWorkflowDescriptor,
+  JobExecutionMap
+}
+import cromwell.backend.standard.{
+  StandardAsyncExecutionActor,
+  StandardFinalizationActor,
+  StandardFinalizationActorParams,
+  StandardInitializationActor,
+  StandardInitializationActorParams,
+  StandardLifecycleActorFactory
+}
 import cromwell.core.CallOutputs
 import wom.graph.CommandCallNode
 
@@ -43,41 +55,38 @@ import wom.graph.CommandCallNode
   * @param name Factory name
   * @param configurationDescriptor configuration descriptor for the backend
   */
-case class AwsBatchBackendLifecycleActorFactory(
-  name: String,
-  configurationDescriptor: BackendConfigurationDescriptor)
+case class AwsBatchBackendLifecycleActorFactory(name: String, configurationDescriptor: BackendConfigurationDescriptor)
     extends StandardLifecycleActorFactory {
 
-  override lazy val initializationActorClass: Class[_ <: StandardInitializationActor]
-    = classOf[AwsBatchInitializationActor]
+  override lazy val initializationActorClass: Class[_ <: StandardInitializationActor] =
+    classOf[AwsBatchInitializationActor]
 
-  override lazy val asyncExecutionActorClass: Class[_ <: StandardAsyncExecutionActor]
-    = classOf[AwsBatchAsyncBackendJobExecutionActor]
+  override lazy val asyncExecutionActorClass: Class[_ <: StandardAsyncExecutionActor] =
+    classOf[AwsBatchAsyncBackendJobExecutionActor]
 
-  override lazy val finalizationActorClassOption: Option[Class[_ <: StandardFinalizationActor]]
-    = Option(classOf[AwsBatchFinalizationActor])
+  override lazy val finalizationActorClassOption: Option[Class[_ <: StandardFinalizationActor]] = Option(
+    classOf[AwsBatchFinalizationActor]
+  )
 
-  override lazy val jobIdKey: String
-    = AwsBatchAsyncBackendJobExecutionActor.AwsBatchOperationIdKey
+  override lazy val jobIdKey: String = AwsBatchAsyncBackendJobExecutionActor.AwsBatchOperationIdKey
 
   val configuration = new AwsBatchConfiguration(configurationDescriptor)
 
-  override def workflowInitializationActorParams(
-                                                  workflowDescriptor: BackendWorkflowDescriptor,
-                                                  ioActor: ActorRef,
-                                                  calls: Set[CommandCallNode],
-                                                  serviceRegistryActor: ActorRef,
-                                                  restart: Boolean): StandardInitializationActorParams = {
+  override def workflowInitializationActorParams(workflowDescriptor: BackendWorkflowDescriptor,
+                                                 ioActor: ActorRef,
+                                                 calls: Set[CommandCallNode],
+                                                 serviceRegistryActor: ActorRef,
+                                                 restart: Boolean
+  ): StandardInitializationActorParams =
     AwsBatchInitializationActorParams(workflowDescriptor, ioActor, calls, configuration, serviceRegistryActor, restart)
-  }
 
-  override def workflowFinalizationActorParams(
-                                                workflowDescriptor: BackendWorkflowDescriptor,
-                                                ioActor: ActorRef,
-                                                calls: Set[CommandCallNode],
-                                                jobExecutionMap: JobExecutionMap,
-                                                workflowOutputs: CallOutputs,
-                                                initializationDataOption: Option[BackendInitializationData]): StandardFinalizationActorParams = {
+  override def workflowFinalizationActorParams(workflowDescriptor: BackendWorkflowDescriptor,
+                                               ioActor: ActorRef,
+                                               calls: Set[CommandCallNode],
+                                               jobExecutionMap: JobExecutionMap,
+                                               workflowOutputs: CallOutputs,
+                                               initializationDataOption: Option[BackendInitializationData]
+  ): StandardFinalizationActorParams =
     // The `AwsBatchInitializationActor` will only return a non-`Empty`
     // `AwsBatchBackendInitializationData` from a successful `beforeAll`
     // invocation.  HOWEVER, the finalization actor is created regardless
@@ -86,10 +95,15 @@ case class AwsBatchBackendLifecycleActorFactory(
     // `AwsBatchBackendInitializationData` option, and there is no `.get`
     // on the initialization data as there is with the execution or cache
     // hit copying actor methods.
-    AwsBatchFinalizationActorParams(workflowDescriptor, ioActor, calls, configuration, jobExecutionMap, workflowOutputs, initializationDataOption)
-  }
+    AwsBatchFinalizationActorParams(workflowDescriptor,
+                                    ioActor,
+                                    calls,
+                                    configuration,
+                                    jobExecutionMap,
+                                    workflowOutputs,
+                                    initializationDataOption
+    )
 
-  override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] = {
+  override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] =
     Option(AwsBatchSingletonActor.props(configuration.awsConfig.region, Option(configuration.awsAuth)))
-  }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
index 2bc76d4bb0b..a5ef13cdf23 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
@@ -33,7 +33,7 @@ package cromwell.backend.impl.aws
 
 import cromwell.filesystems.s3.S3PathBuilderFactory
 import cromwell.backend.BackendConfigurationDescriptor
-import cromwell.core.{BackendDockerConfiguration}
+import cromwell.core.BackendDockerConfiguration
 import cromwell.core.path.PathBuilderFactory
 import cromwell.cloudsupport.aws.AwsConfiguration
 
@@ -48,20 +48,19 @@ class AwsBatchConfiguration(val configurationDescriptor: BackendConfigurationDes
   val dockerCredentials = BackendDockerConfiguration.build(configurationDescriptor.backendConfig).dockerCredentials
   val fileSystem =
     configurationDescriptor.backendConfig.hasPath("filesystems.s3") match {
-      case true =>  "s3"
+      case true => "s3"
       case false => "local"
-  }
+    }
   val pathBuilderFactory = configurationDescriptor.backendConfig.hasPath("filesystems.s3") match {
     case true => S3PathBuilderFactory(configurationDescriptor.globalConfig, configurationDescriptor.backendConfig)
     case false =>
-    PathBuilderFactory
+      PathBuilderFactory
   }
 }
 
 object AWSBatchStorageSystems {
-  val s3:String = "s3"
-  val efs:String = "efs"
-  val ebs:String = "ebs"
-  val local:String = "local"
+  val s3: String = "s3"
+  val efs: String = "efs"
+  val ebs: String = "ebs"
+  val local: String = "local"
 }
-
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala
index b75d4d6b00f..5cf2ef424bd 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchExpressionFunctions.scala
@@ -39,24 +39,22 @@ import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
 import cromwell.core.path.{DefaultPath, Path}
 
 class AwsBatchExpressionFunctions(standardParams: StandardExpressionFunctionsParams)
-  extends StandardExpressionFunctions(standardParams) {
+    extends StandardExpressionFunctions(standardParams) {
   override lazy val ioCommandBuilder: IoCommandBuilder = S3BatchCommandBuilder
 
-  override def preMapping(str: String) = {
+  override def preMapping(str: String) =
     S3PathBuilder.validatePath(str) match {
       case _: ValidFullS3Path => str
       case PossiblyValidRelativeS3Path => callContext.root.resolve(str.stripPrefix("/")).pathAsString
       case invalid: InvalidS3Path => throw new IllegalArgumentException(invalid.errorMessage)
     }
-  }
 }
 
 class AwsBatchExpressionFunctionsForFS(standardParams: StandardExpressionFunctionsParams)
-  extends StandardExpressionFunctions(standardParams) {
-  override def postMapping(path: Path) = {
+    extends StandardExpressionFunctions(standardParams) {
+  override def postMapping(path: Path) =
     path match {
       case _: DefaultPath if !path.isAbsolute => callContext.root.resolve(path)
       case _ => path
     }
-  }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchFinalizationActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchFinalizationActor.scala
index 6fdccf995eb..ba09f871abd 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchFinalizationActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchFinalizationActor.scala
@@ -40,8 +40,7 @@ import cromwell.core.io.DefaultIoCommandBuilder
 import wom.graph.CommandCallNode
 import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
 
-case class AwsBatchFinalizationActorParams
-(
+case class AwsBatchFinalizationActorParams(
   workflowDescriptor: BackendWorkflowDescriptor,
   ioActor: ActorRef,
   calls: Set[CommandCallNode],
@@ -54,13 +53,14 @@ case class AwsBatchFinalizationActorParams
 }
 
 class AwsBatchFinalizationActor(val params: AwsBatchFinalizationActorParams)
-  extends StandardFinalizationActor(params) with AsyncIoActorClient {
+    extends StandardFinalizationActor(params)
+    with AsyncIoActorClient {
 
   lazy val configuration: AwsBatchConfiguration = params.configuration
 
-  override lazy val ioCommandBuilder =  configuration.fileSystem match {
-    case  AWSBatchStorageSystems.s3 =>  S3BatchCommandBuilder
-    case _ =>   DefaultIoCommandBuilder
+  override lazy val ioCommandBuilder = configuration.fileSystem match {
+    case AWSBatchStorageSystems.s3 => S3BatchCommandBuilder
+    case _ => DefaultIoCommandBuilder
   }
 
   override def ioActor: ActorRef = params.ioActor
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
index fe3668f9b00..aadf35bff14 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchInitializationActor.scala
@@ -36,8 +36,12 @@ import java.io.IOException
 import akka.actor.ActorRef
 import software.amazon.awssdk.auth.credentials.AwsCredentialsProvider
 import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
-import cromwell.backend.standard.{StandardInitializationActor, StandardInitializationActorParams, StandardValidatedRuntimeAttributesBuilder}
-import cromwell.backend.{BackendConfigurationDescriptor, BackendWorkflowDescriptor, BackendInitializationData}
+import cromwell.backend.standard.{
+  StandardInitializationActor,
+  StandardInitializationActorParams,
+  StandardValidatedRuntimeAttributesBuilder
+}
+import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor}
 import cromwell.core.io.DefaultIoCommandBuilder
 import cromwell.core.io.AsyncIoActorClient
 import cromwell.core.path.Path
@@ -45,8 +49,7 @@ import wom.graph.CommandCallNode
 
 import scala.concurrent.Future
 
-case class AwsBatchInitializationActorParams
-(
+case class AwsBatchInitializationActorParams(
   workflowDescriptor: BackendWorkflowDescriptor,
   ioActor: ActorRef,
   calls: Set[CommandCallNode],
@@ -58,34 +61,36 @@ case class AwsBatchInitializationActorParams
 }
 
 object AwsBatchInitializationActor {
-  private case class AuthFileAlreadyExistsException(path: Path) extends IOException(s"Failed to upload authentication file at $path:" +
-    s" there was already a file at the same location and this workflow was not being restarted.")
+  private case class AuthFileAlreadyExistsException(path: Path)
+      extends IOException(
+        s"Failed to upload authentication file at $path:" +
+          s" there was already a file at the same location and this workflow was not being restarted."
+      )
 }
 
 class AwsBatchInitializationActor(params: AwsBatchInitializationActorParams)
-  extends StandardInitializationActor(params) with AsyncIoActorClient {
+    extends StandardInitializationActor(params)
+    with AsyncIoActorClient {
 
   override lazy val ioActor = params.ioActor
   private val configuration = params.configuration
-  override implicit val system = context.system
+  implicit override val system = context.system
 
-  override def beforeAll(): Future[Option[BackendInitializationData]] = {
+  override def beforeAll(): Future[Option[BackendInitializationData]] =
     configuration.fileSystem match {
-      case AWSBatchStorageSystems.s3  => super.beforeAll()
-      case _ => {
+      case AWSBatchStorageSystems.s3 => super.beforeAll()
+      case _ =>
         initializationData map { data =>
           publishWorkflowRoot(data.workflowPaths.workflowRoot.pathAsString)
           Option(data)
         }
-      }
     }
-  }
 
   override lazy val runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder =
     AwsBatchRuntimeAttributes.runtimeAttributesBuilder(configuration)
 
   private lazy val provider: Future[AwsCredentialsProvider] =
-    Future { configuration.awsAuth.provider() }
+    Future(configuration.awsAuth.provider())
 
   override lazy val workflowPaths: Future[AwsBatchWorkflowPaths] = for {
     prov <- provider
@@ -96,14 +101,14 @@ class AwsBatchInitializationActor(params: AwsBatchInitializationActorParams)
     prov <- provider
   } yield AwsBatchBackendInitializationData(workflowPaths, runtimeAttributesBuilder, configuration, prov)
 
-  override lazy val ioCommandBuilder =  {
+  override lazy val ioCommandBuilder = {
     val conf = Option(configuration) match {
       case Some(cf) => cf
-      case None =>  new  AwsBatchConfiguration(params.configurationDescriptor)
+      case None => new AwsBatchConfiguration(params.configurationDescriptor)
     }
     conf.fileSystem match {
-      case  AWSBatchStorageSystems.s3 =>  S3BatchCommandBuilder
-      case _ =>   DefaultIoCommandBuilder
+      case AWSBatchStorageSystems.s3 => S3BatchCommandBuilder
+      case _ => DefaultIoCommandBuilder
     }
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index de4617ad786..3e2ba2d482b 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -50,7 +50,12 @@ import software.amazon.awssdk.services.batch.model._
 import software.amazon.awssdk.services.cloudwatchlogs.CloudWatchLogsClient
 import software.amazon.awssdk.services.cloudwatchlogs.model.{GetLogEventsRequest, OutputLogEvent}
 import software.amazon.awssdk.services.s3.S3Client
-import software.amazon.awssdk.services.s3.model.{GetObjectRequest, HeadObjectRequest, NoSuchKeyException, PutObjectRequest}
+import software.amazon.awssdk.services.s3.model.{
+  GetObjectRequest,
+  HeadObjectRequest,
+  NoSuchKeyException,
+  PutObjectRequest
+}
 import wdl4s.parser.MemoryUnit
 
 import scala.jdk.CollectionConverters._
@@ -67,20 +72,21 @@ import scala.util.{Random, Try}
   *  @param commandLine command line to be passed to the job
   *  @param commandScript the `commandLine` with additional commands to setup the context and localize/ de-localize files
   */
-final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
-                             runtimeAttributes: AwsBatchRuntimeAttributes, // config or WDL/CWL
-                             commandLine: String, // WDL/CWL
-                             commandScript: String, // WDL/CWL
-                             dockerRc: String, // Calculated from StandardAsyncExecutionActor
-                             dockerStdout: String, // Calculated from StandardAsyncExecutionActor
-                             dockerStderr: String, // Calculated from StandardAsyncExecutionActor
-                             inputs: Set[AwsBatchInput],
-                             outputs: Set[AwsBatchFileOutput],
-                             jobPaths: JobPaths, // Based on config, calculated in Job Paths, key to all things outside container
-                             parameters: Seq[AwsBatchParameter],
-                             configRegion: Option[Region],
-                             optAwsAuthMode: Option[AwsAuthMode] = None
-                            ) {
+final case class AwsBatchJob(
+  jobDescriptor: BackendJobDescriptor, // WDL/CWL
+  runtimeAttributes: AwsBatchRuntimeAttributes, // config or WDL/CWL
+  commandLine: String, // WDL/CWL
+  commandScript: String, // WDL/CWL
+  dockerRc: String, // Calculated from StandardAsyncExecutionActor
+  dockerStdout: String, // Calculated from StandardAsyncExecutionActor
+  dockerStderr: String, // Calculated from StandardAsyncExecutionActor
+  inputs: Set[AwsBatchInput],
+  outputs: Set[AwsBatchFileOutput],
+  jobPaths: JobPaths, // Based on config, calculated in Job Paths, key to all things outside container
+  parameters: Seq[AwsBatchParameter],
+  configRegion: Option[Region],
+  optAwsAuthMode: Option[AwsAuthMode] = None
+) {
 
   // values for container environment
   val AWS_MAX_ATTEMPTS: String = "AWS_MAX_ATTEMPTS"
@@ -90,7 +96,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
 
   val Log: Logger = LoggerFactory.getLogger(AwsBatchJob.getClass)
 
-  //this will be the "folder" that scripts will live in (underneath the script bucket)
+  // this will be the "folder" that scripts will live in (underneath the script bucket)
   val scriptKeyPrefix = "scripts/"
 
   // TODO: Auth, endpoint
@@ -115,38 +121,40 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     * 3. at the end of the script sync all content with the s3 bucket
     */
   lazy val reconfiguredScript: String = {
-    //this is the location of the aws cli mounted into the container by the ec2 launch template
+    // this is the location of the aws cli mounted into the container by the ec2 launch template
     val s3Cmd = "/usr/local/aws-cli/v2/current/bin/aws s3"
-    //internal to the container, therefore not mounted
+    // internal to the container, therefore not mounted
     val workDir = "/tmp/scratch"
-    //working in a mount will cause collisions in long running workers
+    // working in a mount will cause collisions in long running workers
     val replaced = commandScript.replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
-    val insertionPoint = replaced.indexOf("\n", replaced.indexOf("#!")) +1 //just after the new line after the shebang!
+    val insertionPoint =
+      replaced.indexOf("\n", replaced.indexOf("#!")) + 1 // just after the new line after the shebang!
 
     /* generate a series of s3 copy statements to copy any s3 files into the container. We randomize the order
        so that large scatters don't all attempt to copy the same thing at the same time. */
-    val inputCopyCommand = Random.shuffle(inputs.map {
-      case input: AwsBatchFileInput if input.s3key.startsWith("s3://") && input.s3key.endsWith(".tmp") =>
-        //we are localizing a tmp file which may contain workdirectory paths that need to be reconfigured
-        s"""
-           |$s3Cmd cp --no-progress ${input.s3key} $workDir/${input.local}
-           |sed -i 's#${AwsBatchWorkingDisk.MountPoint.pathAsString}#$workDir#g' $workDir/${input.local}
-           |""".stripMargin
-
-
-      case input: AwsBatchFileInput if input.s3key.startsWith("s3://") =>
-        s"$s3Cmd cp --no-progress ${input.s3key} ${input.mount.mountPoint.pathAsString}/${input.local}"
-          .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
-
-      case input: AwsBatchFileInput =>
-        //here we don't need a copy command but the centaurTests expect us to verify the existence of the file
-        val filePath = s"${input.mount.mountPoint.pathAsString}/${input.local.pathAsString}"
-          .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
-
-        s"test -e $filePath || echo 'input file: $filePath does not exist' && exit 1"
-
-      case _ => ""
-    }.toList).mkString("\n")
+    val inputCopyCommand = Random
+      .shuffle(inputs.map {
+        case input: AwsBatchFileInput if input.s3key.startsWith("s3://") && input.s3key.endsWith(".tmp") =>
+          // we are localizing a tmp file which may contain workdirectory paths that need to be reconfigured
+          s"""
+             |$s3Cmd cp --no-progress ${input.s3key} $workDir/${input.local}
+             |sed -i 's#${AwsBatchWorkingDisk.MountPoint.pathAsString}#$workDir#g' $workDir/${input.local}
+             |""".stripMargin
+
+        case input: AwsBatchFileInput if input.s3key.startsWith("s3://") =>
+          s"$s3Cmd cp --no-progress ${input.s3key} ${input.mount.mountPoint.pathAsString}/${input.local}"
+            .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
+
+        case input: AwsBatchFileInput =>
+          // here we don't need a copy command but the centaurTests expect us to verify the existence of the file
+          val filePath = s"${input.mount.mountPoint.pathAsString}/${input.local.pathAsString}"
+            .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
+
+          s"test -e $filePath || echo 'input file: $filePath does not exist' && exit 1"
+
+        case _ => ""
+      }.toList)
+      .mkString("\n")
 
     // this goes at the start of the script after the #!
     val preamble =
@@ -166,42 +174,45 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     val stdOut = dockerStdout.replace("/cromwell_root", workDir)
     val stdErr = dockerStderr.replace("/cromwell_root", workDir)
 
-    //generate a series of s3 commands to delocalize artifacts from the container to storage at the end of the task
-    val outputCopyCommand = outputs.map {
-      case output: AwsBatchFileOutput if output.local.pathAsString.contains("*") => "" //filter out globs
-      case output: AwsBatchFileOutput if output.name.endsWith(".list") && output.name.contains("glob-") =>
-
-        val s3GlobOutDirectory = output.s3key.replace(".list", "")
-        val globDirectory = output.name.replace(".list", "")
-        /*
-         * Need to process this list and de-localize each file if the list file actually exists
-         * if it doesn't exist then 'touch' it so that it can be copied otherwise later steps will get upset
-         * about the missing file
-         */
-        s"""
-           |touch ${output.name}
-           |$s3Cmd cp --no-progress ${output.name} ${output.s3key}
-           |if [ -e $globDirectory ]; then $s3Cmd cp --no-progress $globDirectory $s3GlobOutDirectory --recursive --exclude "cromwell_glob_control_file"; fi
-           |""".stripMargin
-
-      case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
-        //output is on working disk mount
-        s"""
-           |$s3Cmd cp --no-progress $workDir/${output.local.pathAsString} ${output.s3key}
-           |""".stripMargin
-      case output: AwsBatchFileOutput =>
-        //output on a different mount
-        s"$s3Cmd cp --no-progress ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
-      case _ => ""
-    }.mkString("\n") + "\n" +
+    // generate a series of s3 commands to delocalize artifacts from the container to storage at the end of the task
+    val outputCopyCommand = outputs
+      .map {
+        case output: AwsBatchFileOutput if output.local.pathAsString.contains("*") => "" // filter out globs
+        case output: AwsBatchFileOutput if output.name.endsWith(".list") && output.name.contains("glob-") =>
+          val s3GlobOutDirectory = output.s3key.replace(".list", "")
+          val globDirectory = output.name.replace(".list", "")
+          /*
+           * Need to process this list and de-localize each file if the list file actually exists
+           * if it doesn't exist then 'touch' it so that it can be copied otherwise later steps will get upset
+           * about the missing file
+           */
+          s"""
+             |touch ${output.name}
+             |$s3Cmd cp --no-progress ${output.name} ${output.s3key}
+             |if [ -e $globDirectory ]; then $s3Cmd cp --no-progress $globDirectory $s3GlobOutDirectory --recursive --exclude "cromwell_glob_control_file"; fi
+             |""".stripMargin
+
+        case output: AwsBatchFileOutput
+            if output.s3key.startsWith(
+              "s3://"
+            ) && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
+          // output is on working disk mount
+          s"""
+             |$s3Cmd cp --no-progress $workDir/${output.local.pathAsString} ${output.s3key}
+             |""".stripMargin
+        case output: AwsBatchFileOutput =>
+          // output on a different mount
+          s"$s3Cmd cp --no-progress ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
+        case _ => ""
+      }
+      .mkString("\n") + "\n" +
       s"""
          |if [ -f $workDir/${jobPaths.returnCodeFilename} ]; then $s3Cmd cp --no-progress $workDir/${jobPaths.returnCodeFilename} ${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename} ; fi\n
          |if [ -f $stdErr ]; then $s3Cmd cp --no-progress $stdErr ${jobPaths.standardPaths.error.pathAsString}; fi
          |if [ -f $stdOut ]; then $s3Cmd cp --no-progress $stdOut ${jobPaths.standardPaths.output.pathAsString}; fi
          |""".stripMargin
 
-
-    //insert the preamble at the insertion point and the postscript copy command at the end
+    // insert the preamble at the insertion point and the postscript copy command at the end
     replaced.patch(insertionPoint, preamble, 0) +
       s"""
          |{
@@ -212,87 +223,106 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |}
          |""".stripMargin
   }
-  private def batch_file_s3_url(scriptBucketName: String, scriptKeyPrefix: String, scriptKey: String): String  = runtimeAttributes.fileSystem match {
-       case AWSBatchStorageSystems.s3  => s"s3://${runtimeAttributes.scriptS3BucketName}/$scriptKeyPrefix$scriptKey"
-       case _ => ""
-  }
+  private def batch_file_s3_url(scriptBucketName: String, scriptKeyPrefix: String, scriptKey: String): String =
+    runtimeAttributes.fileSystem match {
+      case AWSBatchStorageSystems.s3 => s"s3://${runtimeAttributes.scriptS3BucketName}/$scriptKeyPrefix$scriptKey"
+      case _ => ""
+    }
 
-  private def generateEnvironmentKVPairs(scriptBucketName: String, scriptKeyPrefix: String, scriptKey: String): List[KeyValuePair] = {
-    List(buildKVPair(AWS_MAX_ATTEMPTS, AWS_MAX_ATTEMPTS_DEFAULT_VALUE),
+  private def generateEnvironmentKVPairs(scriptBucketName: String,
+                                         scriptKeyPrefix: String,
+                                         scriptKey: String
+  ): List[KeyValuePair] =
+    List(
+      buildKVPair(AWS_MAX_ATTEMPTS, AWS_MAX_ATTEMPTS_DEFAULT_VALUE),
       buildKVPair(AWS_RETRY_MODE, AWS_RETRY_MODE_DEFAULT_VALUE),
       buildKVPair("BATCH_FILE_TYPE", "script"),
-      buildKVPair("BATCH_FILE_S3_URL",batch_file_s3_url(scriptBucketName,scriptKeyPrefix,scriptKey)))
-  }
+      buildKVPair("BATCH_FILE_S3_URL", batch_file_s3_url(scriptBucketName, scriptKeyPrefix, scriptKey))
+    )
 
-  def submitJob[F[_]]()( implicit timer: Timer[F], async: Async[F]): Aws[F, SubmitJobResponse] = {
+  def submitJob[F[_]]()(implicit timer: Timer[F], async: Async[F]): Aws[F, SubmitJobResponse] = {
 
-    val taskId = jobDescriptor.key.call.fullyQualifiedName + "-" + jobDescriptor.key.index + "-" + jobDescriptor.key.attempt
+    val taskId =
+      jobDescriptor.key.call.fullyQualifiedName + "-" + jobDescriptor.key.index + "-" + jobDescriptor.key.attempt
 
-    //find or create the script in s3 to execute for s3 fileSystem
-    val scriptKey =  runtimeAttributes.fileSystem match {
-       case AWSBatchStorageSystems.s3  =>  findOrCreateS3Script(reconfiguredScript, runtimeAttributes.scriptS3BucketName)
-       case _ => ""
+    // find or create the script in s3 to execute for s3 fileSystem
+    val scriptKey = runtimeAttributes.fileSystem match {
+      case AWSBatchStorageSystems.s3 => findOrCreateS3Script(reconfiguredScript, runtimeAttributes.scriptS3BucketName)
+      case _ => ""
     }
 
-    if(runtimeAttributes.fileSystem == AWSBatchStorageSystems.s3) {
-       val regex = "s3://([^/]*)/(.*)".r
-       val regex(bucketName, key) = jobPaths.callExecutionRoot.toString
-       writeReconfiguredScriptForAudit(reconfiguredScript, bucketName, key+"/reconfigured-script.sh")
+    if (runtimeAttributes.fileSystem == AWSBatchStorageSystems.s3) {
+      val regex = "s3://([^/]*)/(.*)".r
+      val regex(bucketName, key) = jobPaths.callExecutionRoot.toString
+      writeReconfiguredScriptForAudit(reconfiguredScript, bucketName, key + "/reconfigured-script.sh")
     }
 
-
     val batch_script = runtimeAttributes.fileSystem match {
-       case AWSBatchStorageSystems.s3  => s"s3://${runtimeAttributes.scriptS3BucketName}/$scriptKeyPrefix$scriptKey"
-       case _  => commandScript
+      case AWSBatchStorageSystems.s3 => s"s3://${runtimeAttributes.scriptS3BucketName}/$scriptKeyPrefix$scriptKey"
+      case _ => commandScript
     }
 
-    //calls the client to submit the job
+    // calls the client to submit the job
     def callClient(definitionArn: String, awsBatchAttributes: AwsBatchAttributes): Aws[F, SubmitJobResponse] = {
 
       Log.info(s"Submitting taskId: $taskId, job definition : $definitionArn, script: $batch_script")
 
       val submit: F[SubmitJobResponse] =
-        async.delay(batchClient.submitJob(
-          SubmitJobRequest.builder()
-            .jobName(sanitize(jobDescriptor.taskCall.fullyQualifiedName))
-            .parameters(parameters.collect({ case i: AwsBatchInput => i.toStringString }).toMap.asJava)
-
-            //provide job environment variables, vcpu and memory
-            .containerOverrides(
-              ContainerOverrides.builder
-                .environment(
-
-                  generateEnvironmentKVPairs(runtimeAttributes.scriptS3BucketName, scriptKeyPrefix, scriptKey): _*
-                )
-                .resourceRequirements(
-                  ResourceRequirement.builder()
-                    .`type`(ResourceType.VCPU)
-                    .value(runtimeAttributes.cpu.value.toString)
-                    .build(),
-                  ResourceRequirement.builder()
-                    .`type`(ResourceType.MEMORY)
-                    .value(runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString)
-                    .build(),
-                )
-                .build()
-            )
-            .jobQueue(runtimeAttributes.queueArn)
-            .jobDefinition(definitionArn)
-            .build
-        ))
+        async.delay(
+          batchClient.submitJob(
+            SubmitJobRequest
+              .builder()
+              .jobName(sanitize(jobDescriptor.taskCall.fullyQualifiedName))
+              .parameters(parameters.collect { case i: AwsBatchInput => i.toStringString }.toMap.asJava)
+
+              // provide job environment variables, vcpu and memory
+              .containerOverrides(
+                ContainerOverrides.builder
+                  .environment(
+                    generateEnvironmentKVPairs(runtimeAttributes.scriptS3BucketName, scriptKeyPrefix, scriptKey): _*
+                  )
+                  .resourceRequirements(
+                    ResourceRequirement
+                      .builder()
+                      .`type`(ResourceType.VCPU)
+                      .value(runtimeAttributes.cpu.value.toString)
+                      .build(),
+                    ResourceRequirement
+                      .builder()
+                      .`type`(ResourceType.MEMORY)
+                      .value(runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString)
+                      .build()
+                  )
+                  .build()
+              )
+              .jobQueue(runtimeAttributes.queueArn)
+              .jobDefinition(definitionArn)
+              .build
+          )
+        )
 
       ReaderT.liftF(
-        Stream.retry(submit, 0.millis, duration => duration.plus(duration), awsBatchAttributes.submitAttempts.value, {
-          // RegisterJobDefinition is eventually consistent, so it may not be there
-          case e: ClientException => e.statusCode() == 404
-          case _ => false
-        }).compile.last.map(_.get)) //if successful there is guaranteed to be a value emitted, hence we can .get this option
+        Stream
+          .retry(
+            submit,
+            0.millis,
+            duration => duration.plus(duration),
+            awsBatchAttributes.submitAttempts.value,
+            {
+              // RegisterJobDefinition is eventually consistent, so it may not be there
+              case e: ClientException => e.statusCode() == 404
+              case _ => false
+            }
+          )
+          .compile
+          .last
+          .map(_.get)
+      ) // if successful there is guaranteed to be a value emitted, hence we can .get this option
     }
 
     (findOrCreateDefinition[F]() product Kleisli.ask[F, AwsBatchAttributes]).flatMap((callClient _).tupled)
   }
 
-
   /**
     * Performs an md5 digest the script, checks in s3 bucket for that script, if it's not already there then persists it.
     *
@@ -300,31 +330,38 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     * @param scriptS3BucketName the bucket that stores the scripts
     * @return the name of the script that was found or created
     */
-  private def findOrCreateS3Script(commandLine :String, scriptS3BucketName: String) :String = {
+  private def findOrCreateS3Script(commandLine: String, scriptS3BucketName: String): String = {
 
     val bucketName = scriptS3BucketName
 
-    val key = MessageDigest.getInstance("MD5")
+    val key = MessageDigest
+      .getInstance("MD5")
       .digest(commandLine.getBytes())
       .foldLeft("")(_ + "%02x".format(_))
 
     Log.debug(s"s3 object name for script is calculated to be s3://$bucketName/$scriptKeyPrefix$key")
 
-    try { //try and get the object
+    try { // try and get the object
 
-      s3Client.getObject( GetObjectRequest.builder().bucket(bucketName).key( scriptKeyPrefix + key).build )
-      s3Client.headObject(HeadObjectRequest.builder()
-        .bucket(bucketName)
-        .key( scriptKeyPrefix + key )
-        .build
-      ).eTag().equals(key)
+      s3Client.getObject(GetObjectRequest.builder().bucket(bucketName).key(scriptKeyPrefix + key).build)
+      s3Client
+        .headObject(
+          HeadObjectRequest
+            .builder()
+            .bucket(bucketName)
+            .key(scriptKeyPrefix + key)
+            .build
+        )
+        .eTag()
+        .equals(key)
 
       // if there's no exception then the script already exists
       Log.debug(s"""Found script $bucketName/$scriptKeyPrefix$key""")
     } catch {
-      case _: NoSuchKeyException =>  //this happens if there is no object with that key in the bucket
-        val putRequest = PutObjectRequest.builder()
-          .bucket(bucketName) //remove the "s3://" prefix
+      case _: NoSuchKeyException => // this happens if there is no object with that key in the bucket
+        val putRequest = PutObjectRequest
+          .builder()
+          .bucket(bucketName) // remove the "s3://" prefix
           .key(scriptKeyPrefix + key)
           .build
 
@@ -335,7 +372,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     key
   }
 
-  private def writeReconfiguredScriptForAudit( reconfiguredScript: String, bucketName: String, key: String) = {
+  private def writeReconfiguredScriptForAudit(reconfiguredScript: String, bucketName: String, key: String) = {
     val putObjectRequest = PutObjectRequest.builder().bucket(bucketName).key(key).build()
     s3Client.putObject(putObjectRequest, RequestBody.fromString(reconfiguredScript))
   }
@@ -345,95 +382,100 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     * @return Arn for newly created job definition
     *
     */
-  private def findOrCreateDefinition[F[_]]()
-                                          (implicit async: Async[F], timer: Timer[F]): Aws[F, String] = ReaderT { awsBatchAttributes =>
-
-    // this is a call back that is executed below by the async.recoverWithRetry(retry)
-    val submit = async.delay({
-
-      val commandStr = awsBatchAttributes.fileSystem match {
-        case AWSBatchStorageSystems.s3 => reconfiguredScript
-        case _ => commandScript
-      }
-      val jobDefinitionContext = AwsBatchJobDefinitionContext(
-        runtimeAttributes = runtimeAttributes,
-        commandText = commandStr,
-        dockerRcPath = dockerRc,
-        dockerStdoutPath = dockerStdout,
-        dockerStderrPath = dockerStderr,
-        jobDescriptor = jobDescriptor,
-        jobPaths = jobPaths,
-        inputs = inputs,
-        outputs = outputs)
-
-      val jobDefinitionBuilder = StandardAwsBatchJobDefinitionBuilder
-      val jobDefinition = jobDefinitionBuilder.build(jobDefinitionContext)
-
-
-      //check if there is already a suitable definition based on the calculated job definition name
-      val jobDefinitionName = jobDefinition.name
-
-      Log.debug(s"Checking for existence of job definition called: $jobDefinitionName")
-
-      val describeJobDefinitionRequest = DescribeJobDefinitionsRequest.builder()
-        .jobDefinitionName( jobDefinitionName )
-        .status("ACTIVE")
-        .build()
-
-      val describeJobDefinitionResponse = batchClient.describeJobDefinitions(describeJobDefinitionRequest)
-
-      if ( !describeJobDefinitionResponse.jobDefinitions.isEmpty ) {
-        //sort the definitions so that the latest revision is at the head
-        val definitions = describeJobDefinitionResponse.jobDefinitions().asScala.toList.sortWith(_.revision > _.revision)
-
-        //return the arn of the job
-        definitions.head.jobDefinitionArn()
-      } else {
-        Log.debug(s"No job definition found. Creating job definition: $jobDefinitionName")
-
-        // See:
-        //
-        // http://aws-java-sdk-javadoc.s3-website-us-west-2.amazonaws.com/latest/software/amazon/awssdk/services/batch/model/RegisterJobDefinitionRequest.Builder.html
-        val definitionRequest = RegisterJobDefinitionRequest.builder
-          .containerProperties(jobDefinition.containerProperties)
+  private def findOrCreateDefinition[F[_]]()(implicit async: Async[F], timer: Timer[F]): Aws[F, String] = ReaderT {
+    awsBatchAttributes =>
+      // this is a call back that is executed below by the async.recoverWithRetry(retry)
+      val submit = async.delay {
+
+        val commandStr = awsBatchAttributes.fileSystem match {
+          case AWSBatchStorageSystems.s3 => reconfiguredScript
+          case _ => commandScript
+        }
+        val jobDefinitionContext = AwsBatchJobDefinitionContext(
+          runtimeAttributes = runtimeAttributes,
+          commandText = commandStr,
+          dockerRcPath = dockerRc,
+          dockerStdoutPath = dockerStdout,
+          dockerStderrPath = dockerStderr,
+          jobDescriptor = jobDescriptor,
+          jobPaths = jobPaths,
+          inputs = inputs,
+          outputs = outputs
+        )
+
+        val jobDefinitionBuilder = StandardAwsBatchJobDefinitionBuilder
+        val jobDefinition = jobDefinitionBuilder.build(jobDefinitionContext)
+
+        // check if there is already a suitable definition based on the calculated job definition name
+        val jobDefinitionName = jobDefinition.name
+
+        Log.debug(s"Checking for existence of job definition called: $jobDefinitionName")
+
+        val describeJobDefinitionRequest = DescribeJobDefinitionsRequest
+          .builder()
           .jobDefinitionName(jobDefinitionName)
-          // See https://stackoverflow.com/questions/24349517/scala-method-named-type
-          .`type`(JobDefinitionType.CONTAINER)
-          .build
+          .status("ACTIVE")
+          .build()
+
+        val describeJobDefinitionResponse = batchClient.describeJobDefinitions(describeJobDefinitionRequest)
+
+        if (!describeJobDefinitionResponse.jobDefinitions.isEmpty) {
+          // sort the definitions so that the latest revision is at the head
+          val definitions =
+            describeJobDefinitionResponse.jobDefinitions().asScala.toList.sortWith(_.revision > _.revision)
+
+          // return the arn of the job
+          definitions.head.jobDefinitionArn()
+        } else {
+          Log.debug(s"No job definition found. Creating job definition: $jobDefinitionName")
+
+          // See:
+          //
+          // http://aws-java-sdk-javadoc.s3-website-us-west-2.amazonaws.com/latest/software/amazon/awssdk/services/batch/model/RegisterJobDefinitionRequest.Builder.html
+          val definitionRequest = RegisterJobDefinitionRequest.builder
+            .containerProperties(jobDefinition.containerProperties)
+            .jobDefinitionName(jobDefinitionName)
+            // See https://stackoverflow.com/questions/24349517/scala-method-named-type
+            .`type`(JobDefinitionType.CONTAINER)
+            .build
 
-        Log.debug(s"Submitting definition request: $definitionRequest")
+          Log.debug(s"Submitting definition request: $definitionRequest")
 
-        val response: RegisterJobDefinitionResponse = batchClient.registerJobDefinition(definitionRequest)
-        Log.info(s"Definition created: $response")
-        response.jobDefinitionArn()
+          val response: RegisterJobDefinitionResponse = batchClient.registerJobDefinition(definitionRequest)
+          Log.info(s"Definition created: $response")
+          response.jobDefinitionArn()
+        }
       }
-    })
-
-
-    // a function to retry submissions, returns a higher kind parameterized on a String (where the String is an arn)
-    val retry: F[String] = Stream.retry(
-      fo = submit, //the value to attempt to get
-      delay = 0.millis, //how long to wait
-      nextDelay = _ * 2, //how long to back off after a failure
-      maxAttempts = awsBatchAttributes.createDefinitionAttempts.value, //how many times to try
-      retriable = { //a function to say if we should retry or not
-        // RegisterJobDefinition throws 404s every once in a while
-        case e: ClientException => e.statusCode() == 404 || e.statusCode() == 409
-        // a 409 means an eventual consistency collision has happened, most likely during a scatter.
-        // Just wait and retry as job definition names are canonical and if another thread succeeds in making one then
-        // that will be used and if there really isn't one, then the definition will be created.
-        case _ => false  //don't retry other cases
-      }
-    ).compile.last.map(_.get)
 
-    // attempt to register the job definition
-    async.recoverWith(submit){
-      case e: ClientException if e.statusCode == 404 ||
-        e.statusCode == 409 || e.statusCode == 429  => retry  //probably worth trying again
-    }
+      // a function to retry submissions, returns a higher kind parameterized on a String (where the String is an arn)
+      val retry: F[String] = Stream
+        .retry(
+          fo = submit, // the value to attempt to get
+          delay = 0.millis, // how long to wait
+          nextDelay = _ * 2, // how long to back off after a failure
+          maxAttempts = awsBatchAttributes.createDefinitionAttempts.value, // how many times to try
+          retriable = { // a function to say if we should retry or not
+            // RegisterJobDefinition throws 404s every once in a while
+            case e: ClientException => e.statusCode() == 404 || e.statusCode() == 409
+            // a 409 means an eventual consistency collision has happened, most likely during a scatter.
+            // Just wait and retry as job definition names are canonical and if another thread succeeds in making one then
+            // that will be used and if there really isn't one, then the definition will be created.
+            case _ => false // don't retry other cases
+          }
+        )
+        .compile
+        .last
+        .map(_.get)
+
+      // attempt to register the job definition
+      async.recoverWith(submit) {
+        case e: ClientException
+            if e.statusCode == 404 ||
+              e.statusCode == 409 || e.statusCode == 429 =>
+          retry // probably worth trying again
+      }
   }
 
-
   /** Gets the status of a job by its Id, converted to a RunStatus
     *
     *  @param jobId Job ID as defined in AWS Batch
@@ -446,54 +488,62 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
   } yield runStatus
 
   def detail(jobId: String): JobDetail = {
-    //TODO: This client call should be wrapped in a cats Effect
+    // TODO: This client call should be wrapped in a cats Effect
     val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(jobId).build)
 
-    val jobDetail = describeJobsResponse.jobs.asScala.headOption.
-      getOrElse(throw new RuntimeException(s"Expected a job Detail to be present from this request: $describeJobsResponse and this response: $describeJobsResponse "))
+    val jobDetail = describeJobsResponse.jobs.asScala.headOption.getOrElse(
+      throw new RuntimeException(
+        s"Expected a job Detail to be present from this request: $describeJobsResponse and this response: $describeJobsResponse "
+      )
+    )
 
     jobDetail
   }
 
-  def rc(detail: JobDetail): Integer = {
+  def rc(detail: JobDetail): Integer =
     detail.container.exitCode
-  }
 
   def output(detail: JobDetail): String = {
-    val events: Seq[OutputLogEvent] = cloudWatchLogsClient.getLogEvents(GetLogEventsRequest.builder
-      // http://aws-java-sdk-javadoc.s3-website-us-west-2.amazonaws.com/latest/software/amazon/awssdk/services/batch/model/ContainerDetail.html#logStreamName--
-      .logGroupName("/aws/batch/job")
-      .logStreamName(detail.container.logStreamName)
-      .startFromHead(true)
-      .build).events.asScala.toList
-    val eventMessages = for ( event <- events ) yield event.message
+    val events: Seq[OutputLogEvent] = cloudWatchLogsClient
+      .getLogEvents(
+        GetLogEventsRequest.builder
+          // http://aws-java-sdk-javadoc.s3-website-us-west-2.amazonaws.com/latest/software/amazon/awssdk/services/batch/model/ContainerDetail.html#logStreamName--
+          .logGroupName("/aws/batch/job")
+          .logStreamName(detail.container.logStreamName)
+          .startFromHead(true)
+          .build
+      )
+      .events
+      .asScala
+      .toList
+    val eventMessages = for (event <- events) yield event.message
     eventMessages mkString "\n"
   }
 
-  def abort(jobId: String): TerminateJobResponse = {
+  def abort(jobId: String): TerminateJobResponse =
     /*
      * Using Terminate here because it will work on jobs at any stage of their lifecycle whereas cancel will only work
      * on jobs that are not yet at the STARTING or RUNNING phase
      */
     batchClient.terminateJob(TerminateJobRequest.builder.jobId(jobId).reason("cromwell abort called").build())
-  }
 
   /**
     * Generate a `String` describing the instance. Mainly for debugging
     * @return a description of the instance
     */
-  override def toString: String = {
+  override def toString: String =
     new ToStringBuilder(this, ToStringStyle.JSON_STYLE)
       .append("jobDescriptor", jobDescriptor)
       .append("runtimeAttributes", runtimeAttributes)
       .append("commandLine", commandLine)
       .append("commandScript", commandScript)
-      .append("dockerRc", dockerRc).append("dockerStderr", dockerStderr).append("dockerStdout", dockerStdout)
+      .append("dockerRc", dockerRc)
+      .append("dockerStderr", dockerStderr)
+      .append("dockerStdout", dockerStdout)
       .append("inputs", inputs)
       .append("outputs", outputs)
       .append("jobPaths", jobPaths)
       .append("configRegion", configRegion)
       .append("awsAuthMode", optAwsAuthMode)
       .build
-  }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
index 903f88a1cc4..c1d99620ac7 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobCachingActorHelper.scala
@@ -44,22 +44,25 @@ import cromwell.core.path.Path
 trait AwsBatchJobCachingActorHelper extends StandardCachingActorHelper {
   this: Actor with JobLogging =>
 
-  lazy val initializationData: AwsBatchBackendInitializationData = {
+  lazy val initializationData: AwsBatchBackendInitializationData =
     backendInitializationDataAs[AwsBatchBackendInitializationData]
-  }
 
   lazy val configuration: AwsBatchConfiguration = initializationData.configuration
 
   // TODO: Determine if call paths are relevant
   lazy val callPaths: AwsBatchJobPaths = jobPaths.asInstanceOf[AwsBatchJobPaths]
 
-  lazy val runtimeAttributes: AwsBatchRuntimeAttributes = AwsBatchRuntimeAttributes(validatedRuntimeAttributes, configuration.runtimeConfig, configuration.fileSystem)
-
-  lazy val workingDisk: AwsBatchVolume = runtimeAttributes.disks.find(x => configuration.fileSystem match {
-    case AWSBatchStorageSystems.s3 => x.name == AwsBatchWorkingDisk.Name
-    case _ =>  configuration.root.startsWith(x.mountPoint.pathAsString)
-  }).get
+  lazy val runtimeAttributes: AwsBatchRuntimeAttributes =
+    AwsBatchRuntimeAttributes(validatedRuntimeAttributes, configuration.runtimeConfig, configuration.fileSystem)
 
+  lazy val workingDisk: AwsBatchVolume = runtimeAttributes.disks
+    .find(x =>
+      configuration.fileSystem match {
+        case AWSBatchStorageSystems.s3 => x.name == AwsBatchWorkingDisk.Name
+        case _ => configuration.root.startsWith(x.mountPoint.pathAsString)
+      }
+    )
+    .get
 
   lazy val callRootPath: Path = callPaths.callExecutionRoot
   lazy val returnCodeFilename: String = callPaths.returnCodeFilename
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index 549d3c65185..1dab976fb70 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -34,7 +34,15 @@ package cromwell.backend.impl.aws
 import scala.collection.mutable.ListBuffer
 import cromwell.backend.BackendJobDescriptor
 import cromwell.backend.io.JobPaths
-import software.amazon.awssdk.services.batch.model.{ContainerProperties, Host, KeyValuePair, MountPoint, ResourceRequirement, ResourceType, Volume}
+import software.amazon.awssdk.services.batch.model.{
+  ContainerProperties,
+  Host,
+  KeyValuePair,
+  MountPoint,
+  ResourceRequirement,
+  ResourceType,
+  Volume
+}
 import cromwell.backend.impl.aws.io.AwsBatchVolume
 
 import scala.jdk.CollectionConverters._
@@ -43,7 +51,6 @@ import org.apache.commons.lang3.builder.{ToStringBuilder, ToStringStyle}
 import org.slf4j.{Logger, LoggerFactory}
 import wdl4s.parser.MemoryUnit
 
-
 /**
   * Responsible for the creation of the job definition.
   *
@@ -62,18 +69,16 @@ sealed trait AwsBatchJobDefinition {
   def containerProperties: ContainerProperties
   def name: String
 
-  override def toString: String = {
+  override def toString: String =
     new ToStringBuilder(this, ToStringStyle.JSON_STYLE)
       .append("name", name)
       .append("containerProperties", containerProperties)
       .build
-  }
 }
 
 trait AwsBatchJobDefinitionBuilder {
   val Log: Logger = LoggerFactory.getLogger(StandardAwsBatchJobDefinitionBuilder.getClass)
 
-
   /** Gets a builder, seeded with appropriate portions of the container properties
    *
    *  @param dockerImage docker image with which to run
@@ -83,71 +88,77 @@ trait AwsBatchJobDefinitionBuilder {
   def builder(dockerImage: String): ContainerProperties.Builder =
     ContainerProperties.builder().image(dockerImage)
 
-
   def buildResources(builder: ContainerProperties.Builder,
-                     context: AwsBatchJobDefinitionContext): (ContainerProperties.Builder, String) = {
+                     context: AwsBatchJobDefinitionContext
+  ): (ContainerProperties.Builder, String) = {
     // The initial buffer should only contain one item - the hostpath of the
     // local disk mount point, which will be needed by the docker container
     // that copies data around
 
     val environment = List.empty[KeyValuePair]
 
-
-    def buildVolumes(disks: Seq[AwsBatchVolume]): List[Volume] = {
-
-      //all the configured disks plus the fetch and run volume and the aws-cli volume
+    def buildVolumes(disks: Seq[AwsBatchVolume]): List[Volume] =
+      // all the configured disks plus the fetch and run volume and the aws-cli volume
       disks.map(d => d.toVolume()).toList ++ List(
-        Volume.builder()
-        .name("fetchAndRunScript")
-        .host(Host.builder().sourcePath("/usr/local/bin/fetch_and_run.sh").build())
-        .build(),
-        //the aws-cli location on the EC2
-        Volume.builder()
+        Volume
+          .builder()
+          .name("fetchAndRunScript")
+          .host(Host.builder().sourcePath("/usr/local/bin/fetch_and_run.sh").build())
+          .build(),
+        // the aws-cli location on the EC2
+        Volume
+          .builder()
           .name("awsCliHome")
           .host(Host.builder().sourcePath("/usr/local/aws-cli").build())
           .build()
       )
-    }
-
-    def buildMountPoints(disks: Seq[AwsBatchVolume]): List[MountPoint] = {
 
-      //all the configured disks plus the fetch and run mount point and the AWS cli mount point
+    def buildMountPoints(disks: Seq[AwsBatchVolume]): List[MountPoint] =
+      // all the configured disks plus the fetch and run mount point and the AWS cli mount point
       disks.map(_.toMountPoint).toList ++ List(
-        MountPoint.builder()
+        MountPoint
+          .builder()
           .readOnly(true)
           .sourceVolume("fetchAndRunScript")
           .containerPath("/var/scratch/fetch_and_run.sh")
           .build(),
-
-        MountPoint.builder()
+        MountPoint
+          .builder()
           .readOnly(true)
           .sourceVolume("awsCliHome")
-          //where the aws-cli will be on the container
+          // where the aws-cli will be on the container
           .containerPath("/usr/local/aws-cli")
           .build()
       )
-    }
 
-    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair]): String = {
-      val str = s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}"
+    def buildName(imageName: String,
+                  packedCommand: String,
+                  volumes: List[Volume],
+                  mountPoints: List[MountPoint],
+                  env: Seq[KeyValuePair]
+    ): String = {
+      val str = s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints
+          .map(_.toString)
+          .mkString(",")}:${env.map(_.toString).mkString(",")}"
 
-      val sha1 = MessageDigest.getInstance("SHA-1")
-            .digest( str.getBytes("UTF-8") )
-            .map("%02x".format(_)).mkString
+      val sha1 = MessageDigest
+        .getInstance("SHA-1")
+        .digest(str.getBytes("UTF-8"))
+        .map("%02x".format(_))
+        .mkString
 
-      val prefix = s"cromwell_$imageName".slice(0,88) // will be joined to a 40 character SHA1 for total length of 128
+      val prefix = s"cromwell_$imageName".slice(0, 88) // will be joined to a 40 character SHA1 for total length of 128
 
       sanitize(prefix + sha1)
     }
 
-
     val cmdName = context.runtimeAttributes.fileSystem match {
-       case AWSBatchStorageSystems.s3 => "/var/scratch/fetch_and_run.sh"
-       case _ =>  context.commandText
+      case AWSBatchStorageSystems.s3 => "/var/scratch/fetch_and_run.sh"
+      case _ => context.commandText
     }
     val packedCommand = packCommand("/bin/bash", "-c", cmdName)
-    val volumes =  buildVolumes( context.runtimeAttributes.disks )
-    val mountPoints = buildMountPoints( context.runtimeAttributes.disks)
+    val volumes = buildVolumes(context.runtimeAttributes.disks)
+    val mountPoints = buildMountPoints(context.runtimeAttributes.disks)
     val jobDefinitionName = buildName(
       context.runtimeAttributes.dockerImage,
       packedCommand.mkString(","),
@@ -158,21 +169,23 @@ trait AwsBatchJobDefinitionBuilder {
 
     (builder
        .command(packedCommand.asJava)
-      .resourceRequirements(
-        ResourceRequirement.builder()
-          .`type`(ResourceType.MEMORY)
-          .value(context.runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString)
-          .build(),
-        ResourceRequirement.builder()
-          .`type`(ResourceType.VCPU)
-          .value(context.runtimeAttributes.cpu.value.toString)
-          .build(),
-      )
-        .volumes( volumes.asJava)
-        .mountPoints( mountPoints.asJava)
-        .environment(environment.asJava),
-
-      jobDefinitionName)
+       .resourceRequirements(
+         ResourceRequirement
+           .builder()
+           .`type`(ResourceType.MEMORY)
+           .value(context.runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString)
+           .build(),
+         ResourceRequirement
+           .builder()
+           .`type`(ResourceType.VCPU)
+           .value(context.runtimeAttributes.cpu.value.toString)
+           .build()
+       )
+       .volumes(volumes.asJava)
+       .mountPoints(mountPoints.asJava)
+       .environment(environment.asJava),
+     jobDefinitionName
+    )
   }
 
   private def packCommand(shell: String, options: String, mainCommand: String): Seq[String] = {
@@ -180,10 +193,9 @@ trait AwsBatchJobDefinitionBuilder {
     val lim = 1024
     val packedCommand = mainCommand.length() match {
       case len if len <= lim => mainCommand
-      case len if len > lim => {
+      case len if len > lim =>
         rc += "gzipdata" // This is hard coded in our agent and must be the first item
         gzip(mainCommand)
-      }
     }
     rc += shell
     rc += options
@@ -196,7 +208,7 @@ trait AwsBatchJobDefinitionBuilder {
 
 object StandardAwsBatchJobDefinitionBuilder extends AwsBatchJobDefinitionBuilder {
   def build(context: AwsBatchJobDefinitionContext): AwsBatchJobDefinition = {
-    //instantiate a builder with the name of the docker image
+    // instantiate a builder with the name of the docker image
     val builderInst = builder(context.runtimeAttributes.dockerImage)
     val (b, name) = buildResources(builderInst, context)
 
@@ -204,32 +216,32 @@ object StandardAwsBatchJobDefinitionBuilder extends AwsBatchJobDefinitionBuilder
   }
 }
 
-case class StandardAwsBatchJobDefinitionBuilder private(containerProperties: ContainerProperties, name: String) extends AwsBatchJobDefinition
+case class StandardAwsBatchJobDefinitionBuilder private (containerProperties: ContainerProperties, name: String)
+    extends AwsBatchJobDefinition
 
 object AwsBatchJobDefinitionContext
 
-case class AwsBatchJobDefinitionContext(
-            runtimeAttributes: AwsBatchRuntimeAttributes,
-            commandText: String,
-            dockerRcPath: String,
-            dockerStdoutPath: String,
-            dockerStderrPath: String,
-            jobDescriptor: BackendJobDescriptor,
-            jobPaths: JobPaths,
-            inputs: Set[AwsBatchInput],
-            outputs: Set[AwsBatchFileOutput]){
-
-  override def toString: String = {
+case class AwsBatchJobDefinitionContext(runtimeAttributes: AwsBatchRuntimeAttributes,
+                                        commandText: String,
+                                        dockerRcPath: String,
+                                        dockerStdoutPath: String,
+                                        dockerStderrPath: String,
+                                        jobDescriptor: BackendJobDescriptor,
+                                        jobPaths: JobPaths,
+                                        inputs: Set[AwsBatchInput],
+                                        outputs: Set[AwsBatchFileOutput]
+) {
+
+  override def toString: String =
     new ToStringBuilder(this, ToStringStyle.JSON_STYLE)
       .append("runtimeAttributes", runtimeAttributes)
       .append("commandText", commandText)
       .append("dockerRcPath", dockerRcPath)
-      .append("dockerStderrPath",dockerStderrPath)
+      .append("dockerStderrPath", dockerStderrPath)
       .append("dockerStdoutPath", dockerStdoutPath)
       .append("jobDescriptor", jobDescriptor)
       .append("jobPaths", jobPaths)
       .append("inputs", inputs)
       .append("outputs", outputs)
       .build
-  }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala
index e8d93570dbc..5725bea6001 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobPaths.scala
@@ -45,7 +45,10 @@ object AwsBatchJobPaths {
  * @param workflowPaths the paths for the job
  * @param jobKey the job
  */
-final case class AwsBatchJobPaths(override val workflowPaths: AwsBatchWorkflowPaths, jobKey: BackendJobDescriptorKey, override val isCallCacheCopyAttempt: Boolean = false) extends JobPaths {
+final case class AwsBatchJobPaths(override val workflowPaths: AwsBatchWorkflowPaths,
+                                  jobKey: BackendJobDescriptorKey,
+                                  override val isCallCacheCopyAttempt: Boolean = false
+) extends JobPaths {
 
   def logBasename = {
     val index = jobKey.index.map(s => s"-$s").getOrElse("")
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchMetadataKeys.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchMetadataKeys.scala
index 1a884fd886b..cf7ec9bea94 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchMetadataKeys.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchMetadataKeys.scala
@@ -31,7 +31,6 @@
 
 package cromwell.backend.impl.aws
 
-
 object AwsBatchMetadataKeys {
   val ExecutionBucket = "batch:executionBucket"
   // TODO: This will be needed later
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchParameters.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchParameters.scala
index ff9a75156f7..61a61e60a5f 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchParameters.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchParameters.scala
@@ -42,12 +42,13 @@ import software.amazon.awssdk.services.batch.model.KeyValuePair
 sealed trait AwsBatchParameter {
   def name: String
   def toKeyValuePair: KeyValuePair
-  def toStringString: (String,String)
+  def toStringString: (String, String)
 }
 
 sealed trait AwsBatchInput extends AwsBatchParameter
 
-final case class AwsBatchFileInput(name: String, s3key: String, local: Path, mount: AwsBatchVolume) extends AwsBatchInput {
+final case class AwsBatchFileInput(name: String, s3key: String, local: Path, mount: AwsBatchVolume)
+    extends AwsBatchInput {
   def toKeyValuePair = KeyValuePair.builder.name(name).value(s3key).build
   def toStringString = (name, s3key)
   def containerPath: Path = mount.mountPoint.resolve(local)
@@ -58,7 +59,8 @@ final case class AwsBatchLiteralInput(name: String, value: String) extends AwsBa
   def toStringString = (name, value)
 }
 
-final case class AwsBatchFileOutput(name: String, s3key: String, local: Path, mount: AwsBatchVolume) extends AwsBatchParameter {
+final case class AwsBatchFileOutput(name: String, s3key: String, local: Path, mount: AwsBatchVolume)
+    extends AwsBatchParameter {
   def toKeyValuePair = KeyValuePair.builder.name(name).value(s3key).build
   def toStringString = (name, s3key)
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index ca0eeb9b10c..87f04cc44dc 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -71,7 +71,8 @@ case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      continueOnReturnCode: ContinueOnReturnCode,
                                      noAddress: Boolean,
                                      scriptS3BucketName: String,
-                                     fileSystem:String= "s3")
+                                     fileSystem: String = "s3"
+)
 
 object AwsBatchRuntimeAttributes {
 
@@ -92,96 +93,125 @@ object AwsBatchRuntimeAttributes {
 
   private val MemoryDefaultValue = "2 GB"
 
-  private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] = CpuValidation.instance
-    .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
+  private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] =
+    CpuValidation.instance
+      .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
-  private def cpuMinValidation(runtimeConfig: Option[Config]):RuntimeAttributesValidation[Int Refined Positive] = CpuValidation.instanceMin
-    .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
+  private def cpuMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] =
+    CpuValidation.instanceMin
+      .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
   private def failOnStderrValidation(runtimeConfig: Option[Config]) = FailOnStderrValidation.default(runtimeConfig)
 
-  private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) = ContinueOnReturnCodeValidation.default(runtimeConfig)
+  private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) =
+    ContinueOnReturnCodeValidation.default(runtimeConfig)
 
-  private def disksValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Seq[AwsBatchVolume]] = DisksValidation
-    .withDefault(DisksValidation.configDefaultWomValue(runtimeConfig) getOrElse DisksDefaultValue)
+  private def disksValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Seq[AwsBatchVolume]] =
+    DisksValidation
+      .withDefault(DisksValidation.configDefaultWomValue(runtimeConfig) getOrElse DisksDefaultValue)
 
-  private def zonesValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[String]] = ZonesValidation
-    .withDefault(ZonesValidation.configDefaultWomValue(runtimeConfig) getOrElse ZonesDefaultValue)
+  private def zonesValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[String]] =
+    ZonesValidation
+      .withDefault(ZonesValidation.configDefaultWomValue(runtimeConfig) getOrElse ZonesDefaultValue)
 
-  private def memoryValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] = {
+  private def memoryValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] =
     MemoryValidation.withDefaultMemory(
       RuntimeAttributesKeys.MemoryKey,
-      MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, runtimeConfig) getOrElse MemoryDefaultValue)
-  }
+      MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, runtimeConfig) getOrElse MemoryDefaultValue
+    )
 
-  private def memoryMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] = {
-    MemoryValidation.withDefaultMemory(
-      RuntimeAttributesKeys.MemoryMinKey,
-      MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMinKey, runtimeConfig) getOrElse MemoryDefaultValue)
-  }
+  private def memoryMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] =
+    MemoryValidation.withDefaultMemory(RuntimeAttributesKeys.MemoryMinKey,
+                                       MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMinKey,
+                                                                            runtimeConfig
+                                       ) getOrElse MemoryDefaultValue
+    )
 
-  private def noAddressValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = noAddressValidationInstance
-    .withDefault(noAddressValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue)
+  private def noAddressValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] =
+    noAddressValidationInstance
+      .withDefault(noAddressValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue)
 
-  private def scriptS3BucketNameValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[String] = {
-    ScriptS3BucketNameValidation(scriptS3BucketKey).withDefault(ScriptS3BucketNameValidation(scriptS3BucketKey)
-      .configDefaultWomValue(runtimeConfig).getOrElse( throw new RuntimeException( "scriptBucketName is required" )))
-  }
+  private def scriptS3BucketNameValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[String] =
+    ScriptS3BucketNameValidation(scriptS3BucketKey).withDefault(
+      ScriptS3BucketNameValidation(scriptS3BucketKey)
+        .configDefaultWomValue(runtimeConfig)
+        .getOrElse(throw new RuntimeException("scriptBucketName is required"))
+    )
 
   private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
 
   private def queueArnValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[String] =
-    QueueArnValidation.withDefault(QueueArnValidation.configDefaultWomValue(runtimeConfig) getOrElse
-      (throw new RuntimeException("queueArn is required")))
+    QueueArnValidation.withDefault(
+      QueueArnValidation.configDefaultWomValue(runtimeConfig) getOrElse
+        (throw new RuntimeException("queueArn is required"))
+    )
 
   def runtimeAttributesBuilder(configuration: AwsBatchConfiguration): StandardValidatedRuntimeAttributesBuilder = {
     val runtimeConfig = configuration.runtimeConfig
-    def validationsS3backend = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
-                        cpuValidation(runtimeConfig),
-                        cpuMinValidation(runtimeConfig),
-                        disksValidation(runtimeConfig),
-                        zonesValidation(runtimeConfig),
-                        memoryValidation(runtimeConfig),
-                        memoryMinValidation(runtimeConfig),
-                        noAddressValidation(runtimeConfig),
-                        dockerValidation,
-                        queueArnValidation(runtimeConfig),
-                        scriptS3BucketNameValidation(runtimeConfig)
-                      )
-   def validationsLocalBackend  = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
-      cpuValidation(runtimeConfig),
-      cpuMinValidation(runtimeConfig),
-      disksValidation(runtimeConfig),
-      zonesValidation(runtimeConfig),
-      memoryValidation(runtimeConfig),
-      memoryMinValidation(runtimeConfig),
-      noAddressValidation(runtimeConfig),
-      dockerValidation,
-      queueArnValidation(runtimeConfig)
-    )
-
-    configuration.fileSystem match  {
-       case AWSBatchStorageSystems.s3 =>  validationsS3backend
-
-       case _ => validationsLocalBackend
+    def validationsS3backend = StandardValidatedRuntimeAttributesBuilder
+      .default(runtimeConfig)
+      .withValidation(
+        cpuValidation(runtimeConfig),
+        cpuMinValidation(runtimeConfig),
+        disksValidation(runtimeConfig),
+        zonesValidation(runtimeConfig),
+        memoryValidation(runtimeConfig),
+        memoryMinValidation(runtimeConfig),
+        noAddressValidation(runtimeConfig),
+        dockerValidation,
+        queueArnValidation(runtimeConfig),
+        scriptS3BucketNameValidation(runtimeConfig)
+      )
+    def validationsLocalBackend = StandardValidatedRuntimeAttributesBuilder
+      .default(runtimeConfig)
+      .withValidation(
+        cpuValidation(runtimeConfig),
+        cpuMinValidation(runtimeConfig),
+        disksValidation(runtimeConfig),
+        zonesValidation(runtimeConfig),
+        memoryValidation(runtimeConfig),
+        memoryMinValidation(runtimeConfig),
+        noAddressValidation(runtimeConfig),
+        dockerValidation,
+        queueArnValidation(runtimeConfig)
+      )
+
+    configuration.fileSystem match {
+      case AWSBatchStorageSystems.s3 => validationsS3backend
+
+      case _ => validationsLocalBackend
     }
   }
 
-  def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes, runtimeAttrsConfig: Option[Config], fileSystem:String): AwsBatchRuntimeAttributes = {
-    val cpu: Int Refined Positive = RuntimeAttributesValidation.extract(cpuValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+  def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes,
+            runtimeAttrsConfig: Option[Config],
+            fileSystem: String
+  ): AwsBatchRuntimeAttributes = {
+    val cpu: Int Refined Positive =
+      RuntimeAttributesValidation.extract(cpuValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val zones: Vector[String] = RuntimeAttributesValidation.extract(ZonesValidation, validatedRuntimeAttributes)
-    val memory: MemorySize = RuntimeAttributesValidation.extract(memoryValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val disks: Seq[AwsBatchVolume] = RuntimeAttributesValidation.extract(disksValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val memory: MemorySize =
+      RuntimeAttributesValidation.extract(memoryValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val disks: Seq[AwsBatchVolume] =
+      RuntimeAttributesValidation.extract(disksValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val docker: String = RuntimeAttributesValidation.extract(dockerValidation, validatedRuntimeAttributes)
-    val queueArn: String = RuntimeAttributesValidation.extract(queueArnValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val failOnStderr: Boolean = RuntimeAttributesValidation.extract(failOnStderrValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val continueOnReturnCode: ContinueOnReturnCode = RuntimeAttributesValidation.extract(continueOnReturnCodeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val noAddress: Boolean = RuntimeAttributesValidation.extract(noAddressValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val scriptS3BucketName = fileSystem match  {
-       case AWSBatchStorageSystems.s3 => RuntimeAttributesValidation.extract(scriptS3BucketNameValidation(runtimeAttrsConfig) , validatedRuntimeAttributes)
-       case _ => ""
-     }
-
+    val queueArn: String =
+      RuntimeAttributesValidation.extract(queueArnValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val failOnStderr: Boolean =
+      RuntimeAttributesValidation.extract(failOnStderrValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val continueOnReturnCode: ContinueOnReturnCode = RuntimeAttributesValidation.extract(
+      continueOnReturnCodeValidation(runtimeAttrsConfig),
+      validatedRuntimeAttributes
+    )
+    val noAddress: Boolean =
+      RuntimeAttributesValidation.extract(noAddressValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val scriptS3BucketName = fileSystem match {
+      case AWSBatchStorageSystems.s3 =>
+        RuntimeAttributesValidation.extract(scriptS3BucketNameValidation(runtimeAttrsConfig),
+                                            validatedRuntimeAttributes
+        )
+      case _ => ""
+    }
 
     new AwsBatchRuntimeAttributes(
       cpu,
@@ -203,23 +233,21 @@ object ScriptS3BucketNameValidation {
   def apply(key: String): ScriptS3BucketNameValidation = new ScriptS3BucketNameValidation(key)
 }
 
-class ScriptS3BucketNameValidation( key: String ) extends StringRuntimeAttributesValidation(key) {
+class ScriptS3BucketNameValidation(key: String) extends StringRuntimeAttributesValidation(key) {
 
-  //a reasonable but not perfect regex for a bucket. see https://stackoverflow.com/a/50484916/3573553
-  protected val s3BucketNameRegex: Regex = "(?=^.{3,63}$)(?!^(\\d+\\.)+\\d+$)(^(([a-z0-9]|[a-z0-9][a-z0-9\\-]*[a-z0-9])\\.)*([a-z0-9]|[a-z0-9][a-z0-9\\-]*[a-z0-9])$)"
-    .r
+  // a reasonable but not perfect regex for a bucket. see https://stackoverflow.com/a/50484916/3573553
+  protected val s3BucketNameRegex: Regex =
+    "(?=^.{3,63}$)(?!^(\\d+\\.)+\\d+$)(^(([a-z0-9]|[a-z0-9][a-z0-9\\-]*[a-z0-9])\\.)*([a-z0-9]|[a-z0-9][a-z0-9\\-]*[a-z0-9])$)".r
 
-
-  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = {
-    case WomString(s) => validateBucketName(s)
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = { case WomString(s) =>
+    validateBucketName(s)
   }
 
-  private def validateBucketName(possibleBucketName: String): ErrorOr[String] = {
+  private def validateBucketName(possibleBucketName: String): ErrorOr[String] =
     possibleBucketName match {
-      case s3BucketNameRegex(_@_*) => possibleBucketName.validNel
+      case s3BucketNameRegex(_ @_*) => possibleBucketName.validNel
       case _ => "The Script Bucket name has an invalid s3 bucket format".invalidNel
     }
-  }
 }
 
 object QueueArnValidation extends ArnValidation(AwsBatchRuntimeAttributes.QueueArnKey) {
@@ -227,7 +255,7 @@ object QueueArnValidation extends ArnValidation(AwsBatchRuntimeAttributes.QueueA
   // https://docs.aws.amazon.com/en_us/general/latest/gr/aws-arns-and-namespaces.html#arn-syntax-batch
   // arn:aws:batch:region:account-id:job-queue/queue-name
   override protected val arnRegex: Regex =
-  s"""
+    s"""
       (?x)                            # Turn on comments and whitespace insensitivity
       (arn)                           # Every AWS ARN starts with "arn"
       :
@@ -259,22 +287,21 @@ object ArnValidation {
 }
 
 class ArnValidation(override val key: String) extends StringRuntimeAttributesValidation(key) {
-  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = {
-    case WomString(s) => validateArn(s)
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = { case WomString(s) =>
+    validateArn(s)
   }
 
-  private def validateArn(possibleArn: String): ErrorOr[String] = {
+  private def validateArn(possibleArn: String): ErrorOr[String] =
     possibleArn match {
-      case arnRegex(_@_*) => possibleArn.validNel
+      case arnRegex(_ @_*) => possibleArn.validNel
       case _ => "ARN has invalid format".invalidNel
     }
-  }
 
   // Possible ARN formats can be found here
   // https://docs.aws.amazon.com/en_us/general/latest/gr/aws-arns-and-namespaces.html
   // This is quite vague regex, but it allows to support a lot of ARN formats
   protected val arnRegex: Regex =
-  s"""
+    s"""
       (?x)                            # Turn on comments and whitespace insensitivity
       (arn)                           # Every ARN starts with "arn"
       :
@@ -347,27 +374,25 @@ object DisksValidation extends RuntimeAttributesValidation[Seq[AwsBatchVolume]]
     defaulted
   }
 
-  private def validateLocalDisk(disk: String): ErrorOr[AwsBatchVolume] = {
+  private def validateLocalDisk(disk: String): ErrorOr[AwsBatchVolume] =
     AwsBatchVolume.parse(disk) match {
       case scala.util.Success(attachedDisk) => attachedDisk.validNel
       case scala.util.Failure(ex) => ex.getMessage.invalidNel
     }
-  }
 
   private def sequenceNels(nels: Seq[ErrorOr[AwsBatchVolume]]): ErrorOr[Seq[AwsBatchVolume]] = {
     val emptyDiskNel: ErrorOr[Vector[AwsBatchVolume]] = Vector.empty[AwsBatchVolume].validNel
-    val disksNel: ErrorOr[Vector[AwsBatchVolume]] = nels.foldLeft(emptyDiskNel) {
-      (acc, v) => (acc, v) mapN { (a, v) => a :+ v }
+    val disksNel: ErrorOr[Vector[AwsBatchVolume]] = nels.foldLeft(emptyDiskNel) { (acc, v) =>
+      (acc, v) mapN { (a, v) => a :+ v }
     }
     disksNel
   }
 
-  private def addDefault(disksNel: ErrorOr[Seq[AwsBatchVolume]]): ErrorOr[Seq[AwsBatchVolume]] = {
+  private def addDefault(disksNel: ErrorOr[Seq[AwsBatchVolume]]): ErrorOr[Seq[AwsBatchVolume]] =
     disksNel map {
       case disks if disks.exists(_.name == AwsBatchWorkingDisk.Name) || disks.exists(_.fsType == "efs") => disks
       case disks => disks :+ AwsBatchWorkingDisk.Default
     }
-  }
 
   override protected def missingValueMessage: String =
     s"Expecting $key runtime attribute to be a comma separated String or Array[String]"
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchSingletonActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchSingletonActor.scala
index ed32d0bd3d8..185a8fcac90 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchSingletonActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchSingletonActor.scala
@@ -7,9 +7,17 @@ import cromwell.cloudsupport.aws.auth.AwsAuthMode
 import cromwell.core.Mailbox
 import software.amazon.awssdk.regions.Region
 
-class AwsBatchSingletonActor(configRegion: Option[Region], optAwsAuthMode: Option[AwsAuthMode] = None) extends Actor with ActorLogging {
-  val awsOccasionalStatusPoller: ActorRef = context.actorOf(OccasionalStatusPollingActor.props(configRegion, optAwsAuthMode).withMailbox(Mailbox.PriorityMailbox), "OccasionalStatusPollingActor")
-  val awsIntervalLimitedSubmitActor: ActorRef = context.actorOf(IntervalLimitedAwsJobSubmitActor.props(configRegion).withMailbox(Mailbox.PriorityMailbox), "IntervalLimitedAWSSubmitActor")
+class AwsBatchSingletonActor(configRegion: Option[Region], optAwsAuthMode: Option[AwsAuthMode] = None)
+    extends Actor
+    with ActorLogging {
+  val awsOccasionalStatusPoller: ActorRef = context.actorOf(
+    OccasionalStatusPollingActor.props(configRegion, optAwsAuthMode).withMailbox(Mailbox.PriorityMailbox),
+    "OccasionalStatusPollingActor"
+  )
+  val awsIntervalLimitedSubmitActor: ActorRef = context.actorOf(
+    IntervalLimitedAwsJobSubmitActor.props(configRegion).withMailbox(Mailbox.PriorityMailbox),
+    "IntervalLimitedAWSSubmitActor"
+  )
 
   override def receive = {
 
@@ -23,5 +31,7 @@ class AwsBatchSingletonActor(configRegion: Option[Region], optAwsAuthMode: Optio
 }
 
 object AwsBatchSingletonActor {
-  def props(configRegion: Option[Region], optAwsAuthMode: Option[AwsAuthMode] = None) = Props(new AwsBatchSingletonActor(configRegion, optAwsAuthMode))
+  def props(configRegion: Option[Region], optAwsAuthMode: Option[AwsAuthMode] = None) = Props(
+    new AwsBatchSingletonActor(configRegion, optAwsAuthMode)
+  )
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala
index 45d3eafe75d..1212aa24100 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPaths.scala
@@ -53,25 +53,28 @@ object AwsBatchWorkflowPaths {
  */
 case class AwsBatchWorkflowPaths(workflowDescriptor: BackendWorkflowDescriptor,
                                  provider: AwsCredentialsProvider,
-                                 configuration: AwsBatchConfiguration)(implicit actorSystem: ActorSystem) extends WorkflowPaths {
+                                 configuration: AwsBatchConfiguration
+)(implicit actorSystem: ActorSystem)
+    extends WorkflowPaths {
 
-  override lazy val executionRootString: String =  configuration.fileSystem match {
-    case AWSBatchStorageSystems.s3  => workflowDescriptor.workflowOptions.getOrElse(AwsBatchWorkflowPaths.RootOptionKey, configuration.root)
+  override lazy val executionRootString: String = configuration.fileSystem match {
+    case AWSBatchStorageSystems.s3 =>
+      workflowDescriptor.workflowOptions.getOrElse(AwsBatchWorkflowPaths.RootOptionKey, configuration.root)
     case _ => configuration.root
   }
   private val workflowOptions: WorkflowOptions = workflowDescriptor.workflowOptions
 
-  override def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): AwsBatchJobPaths = {
+  override def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): AwsBatchJobPaths =
     new AwsBatchJobPaths(workflowPaths.asInstanceOf[AwsBatchWorkflowPaths], jobKey)
-  }
 
-  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths = this.copy(workflowDescriptor = workflowDescriptor)
+  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths =
+    this.copy(workflowDescriptor = workflowDescriptor)
 
   override def config: Config = configuration.configurationDescriptor.backendConfig
-  override def pathBuilders: List[PathBuilder] = {
+  override def pathBuilders: List[PathBuilder] =
     if (configuration.fileSystem == "s3") {
       List(configuration.pathBuilderFactory.asInstanceOf[S3PathBuilderFactory].fromProvider(workflowOptions, provider))
     } else {
-      WorkflowPaths.DefaultPathBuilders}
-  }
+      WorkflowPaths.DefaultPathBuilders
+    }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/IntervalLimitedAwsJobSubmitActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/IntervalLimitedAwsJobSubmitActor.scala
index f16aa95eb12..3c4cbfe6457 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/IntervalLimitedAwsJobSubmitActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/IntervalLimitedAwsJobSubmitActor.scala
@@ -20,7 +20,8 @@ import scala.util.{Failure, Success}
 class IntervalLimitedAwsJobSubmitActor(configRegion: Option[Region]) extends Actor with ActorLogging {
 
   implicit val ec: ExecutionContext = context.dispatcher
-  implicit val timer: Timer[IO] = cats.effect.IO.timer(ExecutionContext.fromExecutor(Executors.newSingleThreadScheduledExecutor))
+  implicit val timer: Timer[IO] =
+    cats.effect.IO.timer(ExecutionContext.fromExecutor(Executors.newSingleThreadScheduledExecutor))
 
   val WorkInterval = 100.millis
 
@@ -33,30 +34,30 @@ class IntervalLimitedAwsJobSubmitActor(configRegion: Option[Region]) extends Act
   // Maps job ID to status
   private var workQueue: Vector[SubmitAwsJobRequest] = Vector.empty
 
-
   override def receive = {
     case sfm: SubmitAwsJobRequest =>
       workQueue :+= sfm
 
-    case CheckForWork => workQueue.headOption match {
-      case Some(SubmitAwsJobRequest(batchJob, attributes, completionPromise)) =>
-        batchJob.submitJob[IO]().run(attributes).unsafeToFuture() onComplete {
-          case Success(value) =>
-            completionPromise.success(value)
-            scheduleWorkCheck(WorkInterval)
-          case Failure(error) =>
-            completionPromise.failure(error)
-            log.error(error, s"Submission of new AWS job failed")
-            scheduleWorkCheck(WorkInterval)
-        }
-        workQueue = workQueue.tail
-      case None =>
-        scheduleWorkCheck(WorkInterval)
-    }
+    case CheckForWork =>
+      workQueue.headOption match {
+        case Some(SubmitAwsJobRequest(batchJob, attributes, completionPromise)) =>
+          batchJob.submitJob[IO]().run(attributes).unsafeToFuture() onComplete {
+            case Success(value) =>
+              completionPromise.success(value)
+              scheduleWorkCheck(WorkInterval)
+            case Failure(error) =>
+              completionPromise.failure(error)
+              log.error(error, s"Submission of new AWS job failed")
+              scheduleWorkCheck(WorkInterval)
+          }
+          workQueue = workQueue.tail
+        case None =>
+          scheduleWorkCheck(WorkInterval)
+      }
   }
 
   def scheduleWorkCheck(in: FiniteDuration): Unit = {
-    context.system.scheduler.scheduleOnce(in) { self ! CheckForWork }
+    context.system.scheduler.scheduleOnce(in)(self ! CheckForWork)
     ()
   }
 
@@ -67,7 +68,10 @@ object IntervalLimitedAwsJobSubmitActor {
 
   sealed trait IntervalLimitedAwsJobSubmitActorMessage
   case object CheckForWork
-  final case class SubmitAwsJobRequest(job: AwsBatchJob, attributes: AwsBatchAttributes, completionPromise: Promise[SubmitJobResponse]) extends IntervalLimitedAwsJobSubmitActorMessage
+  final case class SubmitAwsJobRequest(job: AwsBatchJob,
+                                       attributes: AwsBatchAttributes,
+                                       completionPromise: Promise[SubmitJobResponse]
+  ) extends IntervalLimitedAwsJobSubmitActorMessage
 
   def props(configRegion: Option[Region]) = Props(new IntervalLimitedAwsJobSubmitActor(configRegion))
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/OccasionalStatusPollingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/OccasionalStatusPollingActor.scala
index 152130745f5..dda0e614ef4 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/OccasionalStatusPollingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/OccasionalStatusPollingActor.scala
@@ -26,7 +26,9 @@ import scala.util.{Failure, Success, Try}
   *   - The 'queuesToMonitor' get added to but never cleared out (so on a multi-tenant system, will grow indefinitely)
   *   - We don't track completed jobs - so when a job completes the caller will get a None, and have to fall back to an AWS query anyway.
   */
-class OccasionalStatusPollingActor(configRegion: Option[Region], optAwsAuthMode: Option[AwsAuthMode] = None) extends Actor with ActorLogging {
+class OccasionalStatusPollingActor(configRegion: Option[Region], optAwsAuthMode: Option[AwsAuthMode] = None)
+    extends Actor
+    with ActorLogging {
 
   implicit val ec: ExecutionContext = context.dispatcher
 
@@ -61,7 +63,10 @@ class OccasionalStatusPollingActor(configRegion: Option[Region], optAwsAuthMode:
       statuses += jobId -> status
       queuesToMonitor += queueArn // Set addition so expectation is a no-op almost every time
     case NotifyOfStatus(_, jobId, None) =>
-      log.error("Programmer Error: OccasionalStatusPollerActor was given an empty status update for {}. It was probably intended to be filled.", jobId)
+      log.error(
+        "Programmer Error: OccasionalStatusPollerActor was given an empty status update for {}. It was probably intended to be filled.",
+        jobId
+      )
   }
 
   private def updateStatuses() = {
@@ -69,14 +74,18 @@ class OccasionalStatusPollingActor(configRegion: Option[Region], optAwsAuthMode:
     final case class PageAccumulation(nextPageToken: String, currentList: Vector[String])
 
     @tailrec
-    def findJobsInStatus(awsStatusName: String, queueName: String, pageAccumulation: Option[PageAccumulation]): Vector[String] = {
+    def findJobsInStatus(awsStatusName: String,
+                         queueName: String,
+                         pageAccumulation: Option[PageAccumulation]
+    ): Vector[String] = {
 
-      val requestBuilder = ListJobsRequest.builder()
+      val requestBuilder = ListJobsRequest
+        .builder()
         .jobStatus(awsStatusName)
         .jobQueue(queueName)
-          .maxResults(100)
+        .maxResults(100)
 
-      pageAccumulation.foreach { pa => requestBuilder.nextToken(pa.nextPageToken) }
+      pageAccumulation.foreach(pa => requestBuilder.nextToken(pa.nextPageToken))
 
       val request = requestBuilder.build()
 
@@ -103,19 +112,18 @@ class OccasionalStatusPollingActor(configRegion: Option[Region], optAwsAuthMode:
         // Remove the old values and add the new values
 
         statuses = statuses.filterNot(_._2 == mapToRunStatus) ++ jobIdsInStatus.map(_ -> mapToRunStatus)
-      } recover {
-        case e =>
-          log.error(e, s"Failure fetching statuses for AWS jobs in $mapToRunStatus. No updates will occur.")
+      } recover { case e =>
+        log.error(e, s"Failure fetching statuses for AWS jobs in $mapToRunStatus. No updates will occur.")
       }
       ()
     }
 
-      updateForStatusNames(List("SUBMITTED", "PENDING", "RUNNABLE"), Initializing)
-      updateForStatusNames(List("STARTING", "RUNNING"), Running)
+    updateForStatusNames(List("SUBMITTED", "PENDING", "RUNNABLE"), Initializing)
+    updateForStatusNames(List("STARTING", "RUNNING"), Running)
   }
 
   def scheduleStatusUpdate(in: FiniteDuration): Unit = {
-    context.system.scheduler.scheduleOnce(in) { self ! UpdateStatuses }
+    context.system.scheduler.scheduleOnce(in)(self ! UpdateStatuses)
     ()
   }
 
@@ -129,8 +137,11 @@ object OccasionalStatusPollingActor {
   case object UpdateStatuses extends OccasionalStatusPollingActorMessage
   case class StatusUpdates(newState: Map[String, RunStatus]) extends OccasionalStatusPollingActorMessage
 
-  final case class NotifyOfStatus(queueArn: String, jobId: String, runStatus: Option[RunStatus]) extends OccasionalStatusPollingActorMessage
+  final case class NotifyOfStatus(queueArn: String, jobId: String, runStatus: Option[RunStatus])
+      extends OccasionalStatusPollingActorMessage
   final case class WhatsMyStatus(queueArn: String, jobId: String) extends OccasionalStatusPollingActorMessage
 
-  def props(configRegion: Option[Region], optAwsAuthMode: Option[AwsAuthMode] = None) = Props(new OccasionalStatusPollingActor(configRegion, optAwsAuthMode))
+  def props(configRegion: Option[Region], optAwsAuthMode: Option[AwsAuthMode] = None) = Props(
+    new OccasionalStatusPollingActor(configRegion, optAwsAuthMode)
+  )
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/RunStatus.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/RunStatus.scala
index f3218c9ca47..bdf34d38063 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/RunStatus.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/RunStatus.scala
@@ -50,8 +50,11 @@ sealed trait RunStatus {
 }
 
 object RunStatus {
-  def fromJobStatus(status: JobStatus, jobId: String, errorMessage: Option[String] = None,
-                    eventList: Seq[ExecutionEvent] = Seq.empty): Try[RunStatus] = {
+  def fromJobStatus(status: JobStatus,
+                    jobId: String,
+                    errorMessage: Option[String] = None,
+                    eventList: Seq[ExecutionEvent] = Seq.empty
+  ): Try[RunStatus] =
     status match {
       case JobStatus.FAILED => Success(Failed(jobId, errorMessage, eventList))
       case JobStatus.PENDING => Success(Initializing)
@@ -63,7 +66,6 @@ object RunStatus {
       // JobStatus.UNKNOWN_TO_SDK_VERSION
       case _ => Failure(new RuntimeException(s"job {$jobId} has an unknown status {$status}"))
     }
-  }
 
   case object Initializing extends RunStatus
   case object Running extends RunStatus
@@ -82,33 +84,30 @@ object RunStatus {
   }
 
   object UnsuccessfulRunStatus {
-    def apply(jobId: String, status: String, errorMessage: Option[String], eventList: Seq[ExecutionEvent]): UnsuccessfulRunStatus = {
+    def apply(jobId: String,
+              status: String,
+              errorMessage: Option[String],
+              eventList: Seq[ExecutionEvent]
+    ): UnsuccessfulRunStatus =
       if (status == "Stopped") { // TODO: Verify this
         Stopped(jobId, errorMessage, eventList)
       } else {
         Failed(jobId, errorMessage, eventList)
       }
-    }
   }
 
-  final case class Stopped(jobId: String,
-                          errorMessage: Option[String],
-                          eventList: Seq[ExecutionEvent],
-                          ) extends UnsuccessfulRunStatus {
+  final case class Stopped(jobId: String, errorMessage: Option[String], eventList: Seq[ExecutionEvent])
+      extends UnsuccessfulRunStatus {
     override def toString = "Stopped"
   }
 
-  final case class Failed(jobId: String,
-                          errorMessage: Option[String],
-                          eventList: Seq[ExecutionEvent],
-                          ) extends UnsuccessfulRunStatus {
+  final case class Failed(jobId: String, errorMessage: Option[String], eventList: Seq[ExecutionEvent])
+      extends UnsuccessfulRunStatus {
     override def toString = "Failed"
   }
 
-  final case class Cancelled(jobId: String,
-                          errorMessage: Option[String],
-                          eventList: Seq[ExecutionEvent],
-                          ) extends UnsuccessfulRunStatus {
+  final case class Cancelled(jobId: String, errorMessage: Option[String], eventList: Seq[ExecutionEvent])
+      extends UnsuccessfulRunStatus {
     override def toString = "Cancelled"
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
index 86bfd46e754..568f4d5a0a3 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
@@ -33,7 +33,7 @@ package cromwell.backend.impl.aws.callcaching
 import com.google.cloud.storage.contrib.nio.CloudStorageOptions
 import common.util.TryUtil
 import cromwell.backend.BackendInitializationData
-import cromwell.backend.impl.aws.{AWSBatchStorageSystems, AwsBatchBackendInitializationData}
+import cromwell.backend.impl.aws.{AwsBatchBackendInitializationData, AWSBatchStorageSystems}
 import cromwell.backend.io.JobPaths
 import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardCacheHitCopyingActorParams}
 import cromwell.core.CallOutputs
@@ -46,20 +46,22 @@ import wom.values.WomFile
 import scala.language.postfixOps
 import scala.util.Try
 
-class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams) extends StandardCacheHitCopyingActor(standardParams) {
+class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams)
+    extends StandardCacheHitCopyingActor(standardParams) {
   private val batchAttributes = BackendInitializationData
     .as[AwsBatchBackendInitializationData](standardParams.backendInitializationDataOption)
-    .configuration.batchAttributes
+    .configuration
+    .batchAttributes
 
   override protected val commandBuilder: IoCommandBuilder = batchAttributes.fileSystem match {
-    case AWSBatchStorageSystems.s3  => S3BatchCommandBuilder
-    case  _ => DefaultIoCommandBuilder
+    case AWSBatchStorageSystems.s3 => S3BatchCommandBuilder
+    case _ => DefaultIoCommandBuilder
   }
   private val cachingStrategy = batchAttributes.duplicationStrategy
 
   override def processSimpletons(womValueSimpletons: Seq[WomValueSimpleton],
-                                 sourceCallRootPath: Path,
-                                ): Try[(CallOutputs, Set[IoCommand[_]])] = {
+                                 sourceCallRootPath: Path
+  ): Try[(CallOutputs, Set[IoCommand[_]])] =
     (batchAttributes.fileSystem, cachingStrategy) match {
       case (AWSBatchStorageSystems.s3, UseOriginalCachedOutputs) =>
         val touchCommands: Seq[Try[IoTouchCommand]] = womValueSimpletons collect {
@@ -72,10 +74,10 @@ class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyin
         }
       case (_, _) => super.processSimpletons(womValueSimpletons, sourceCallRootPath)
     }
-  }
 
-  override def processDetritus(sourceJobDetritusFiles: Map[String, String]
-                              ): Try[(Map[String, Path], Set[IoCommand[_]])] =
+  override def processDetritus(
+    sourceJobDetritusFiles: Map[String, String]
+  ): Try[(Map[String, Path], Set[IoCommand[_]])] =
     (batchAttributes.fileSystem, cachingStrategy) match {
       case (AWSBatchStorageSystems.s3, UseOriginalCachedOutputs) =>
         // apply getPath on each detritus string file
@@ -92,33 +94,40 @@ class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyin
           }
         }
       case (_, _) => super.processDetritus(sourceJobDetritusFiles)
-   }
+    }
 
   override protected def additionalIoCommands(sourceCallRootPath: Path,
                                               originalSimpletons: Seq[WomValueSimpleton],
                                               newOutputs: CallOutputs,
-                                              originalDetritus:  Map[String, String],
-                                              newDetritus: Map[String, Path]): Try[List[Set[IoCommand[_]]]] = Try {
-    (batchAttributes.fileSystem, cachingStrategy)  match {
+                                              originalDetritus: Map[String, String],
+                                              newDetritus: Map[String, Path]
+  ): Try[List[Set[IoCommand[_]]]] = Try {
+    (batchAttributes.fileSystem, cachingStrategy) match {
       case (AWSBatchStorageSystems.s3, UseOriginalCachedOutputs) =>
-            val content =
-              s"""
-                 |This directory does not contain any output files because this job matched an identical job that was previously run, thus it was a cache-hit.
-                 |Cromwell is configured to not copy outputs during call caching. To change this, edit the filesystems.aws.caching.duplication-strategy field in your backend configuration.
-                 |The original outputs can be found at this location: ${sourceCallRootPath.pathAsString}
+        val content =
+          s"""
+             |This directory does not contain any output files because this job matched an identical job that was previously run, thus it was a cache-hit.
+             |Cromwell is configured to not copy outputs during call caching. To change this, edit the filesystems.aws.caching.duplication-strategy field in your backend configuration.
+             |The original outputs can be found at this location: ${sourceCallRootPath.pathAsString}
       """.stripMargin
 
         // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
-        List(Set(
-          S3BatchCommandBuilder.writeCommand(
-            path = jobPaths.forCallCacheCopyAttempts.callExecutionRoot / "call_caching_placeholder.txt",
-            content = content,
-            options = Seq(CloudStorageOptions.withMimeType("text/plain")),
-          ).get
-        ))
-       case (AWSBatchStorageSystems.s3, CopyCachedOutputs) => List.empty
-       case (_, _) =>
-         super.additionalIoCommands(sourceCallRootPath,originalSimpletons, newOutputs, originalDetritus,newDetritus).get
+        List(
+          Set(
+            S3BatchCommandBuilder
+              .writeCommand(
+                path = jobPaths.forCallCacheCopyAttempts.callExecutionRoot / "call_caching_placeholder.txt",
+                content = content,
+                options = Seq(CloudStorageOptions.withMimeType("text/plain"))
+              )
+              .get
+          )
+        )
+      case (AWSBatchStorageSystems.s3, CopyCachedOutputs) => List.empty
+      case (_, _) =>
+        super
+          .additionalIoCommands(sourceCallRootPath, originalSimpletons, newOutputs, originalDetritus, newDetritus)
+          .get
     }
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
index f731fb1b44a..0a3e781bdb3 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
@@ -37,11 +37,15 @@ import cromwell.backend.impl.aws.AwsBatchBackendInitializationData
 import cromwell.backend.impl.aws.AWSBatchStorageSystems
 import cromwell.core.io.DefaultIoCommandBuilder
 
-class AwsBatchBackendFileHashingActor(standardParams: StandardFileHashingActorParams) extends StandardFileHashingActor(standardParams) {
+class AwsBatchBackendFileHashingActor(standardParams: StandardFileHashingActorParams)
+    extends StandardFileHashingActor(standardParams) {
 
-  override val ioCommandBuilder = BackendInitializationData.as[AwsBatchBackendInitializationData](standardParams.backendInitializationDataOption)
-    .configuration.batchAttributes.fileSystem match {
-       case AWSBatchStorageSystems.s3  => S3BatchCommandBuilder
-       case _ =>  DefaultIoCommandBuilder
+  override val ioCommandBuilder = BackendInitializationData
+    .as[AwsBatchBackendInitializationData](standardParams.backendInitializationDataOption)
+    .configuration
+    .batchAttributes
+    .fileSystem match {
+    case AWSBatchStorageSystems.s3 => S3BatchCommandBuilder
+    case _ => DefaultIoCommandBuilder
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchCacheHitDuplicationStrategy.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchCacheHitDuplicationStrategy.scala
index 24b92d5b62f..9efec4b9330 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchCacheHitDuplicationStrategy.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchCacheHitDuplicationStrategy.scala
@@ -33,4 +33,4 @@ package cromwell.backend.impl.aws.callcaching
 sealed trait AwsBatchCacheHitDuplicationStrategy
 
 case object CopyCachedOutputs extends AwsBatchCacheHitDuplicationStrategy
-case object UseOriginalCachedOutputs extends AwsBatchCacheHitDuplicationStrategy
\ No newline at end of file
+case object UseOriginalCachedOutputs extends AwsBatchCacheHitDuplicationStrategy
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/errors/AwsBatchKnownJobFailure.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/errors/AwsBatchKnownJobFailure.scala
index 654fc81be49..0ea8c7a7fd6 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/errors/AwsBatchKnownJobFailure.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/errors/AwsBatchKnownJobFailure.scala
@@ -6,11 +6,11 @@ import cromwell.core.path.Path
 sealed trait AwsBatchKnownJobFailure extends KnownJobFailureException
 
 case class FailedToDelocalizeFailure(message: String, jobTag: String, stderrPath: Option[Path])
-  extends AwsBatchKnownJobFailure {
+    extends AwsBatchKnownJobFailure {
   lazy val stderrMessage = stderrPath map { p =>
     s"3) Look into the stderr (${p.pathAsString}) file for evidence that some of the output files the command is expected to create were not created."
   } getOrElse ""
-  
+
   lazy val missingFilesMessage = if (message.contains("No URLs matched")) {
     s"""It appears that some of the expected output files for task $jobTag did not exist when the command exited.
        |A few things to try
@@ -19,6 +19,6 @@ case class FailedToDelocalizeFailure(message: String, jobTag: String, stderrPath
        |$stderrMessage
      """.stripMargin
   } else ""
-  
+
   override def getMessage = missingFilesMessage + message
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala
index 769c2c2f5d8..9f9003e2dcd 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchVolume.scala
@@ -42,7 +42,6 @@ import wom.values._
 import scala.util.Try
 import scala.util.matching.Regex
 
-
 /*
  * This will handle volumes that are defined in the configuration. It will
  * *not* attach new block storage, as that is handled a priori as part of the
@@ -66,7 +65,7 @@ object AwsBatchVolume {
       case DiskPatterns.WorkingDiskPattern(_, _) =>
         Valid(AwsBatchWorkingDisk())
       case DiskPatterns.MountedDiskPattern(mountPoint, _, fsType) =>
-        Valid(AwsBatchEmptyMountedDisk(DefaultPathBuilder.get(mountPoint),fsType))
+        Valid(AwsBatchEmptyMountedDisk(DefaultPathBuilder.get(mountPoint), fsType))
       case _ =>
         s"Disk strings should be of the format 'local-disk' or '/mount/point' but got: '$s'".invalidNel
     }
@@ -86,29 +85,24 @@ trait AwsBatchVolume {
   def name: String
   def mountPoint: Path
   def fsType: String
-  def getHostPath(id: Option[String]) : String =  {
+  def getHostPath(id: Option[String]): String =
     id match {
       case Some(id) => mountPoint.toAbsolutePath.pathAsString + "/" + id
-      case None   =>   mountPoint.toAbsolutePath.pathAsString
+      case None => mountPoint.toAbsolutePath.pathAsString
     }
-  }
-  def toVolume(id: Option[String]=None): Volume = {
-    Volume
-      .builder
+  def toVolume(id: Option[String] = None): Volume =
+    Volume.builder
       .name(name)
       .host(Host.builder.sourcePath(getHostPath(id)).build)
       .build
-  }
-  def toMountPoint: MountPoint = {
-    MountPoint
-      .builder
+  def toMountPoint: MountPoint =
+    MountPoint.builder
       .containerPath(mountPoint.toAbsolutePath.pathAsString)
       .sourceVolume(name)
       .build
-  }
 }
 
-case class AwsBatchEmptyMountedDisk(mountPoint: Path, ftype:String="ebs") extends AwsBatchVolume {
+case class AwsBatchEmptyMountedDisk(mountPoint: Path, ftype: String = "ebs") extends AwsBatchVolume {
   val name = s"d-${mountPoint.pathAsString.md5Sum}"
   val fsType = ftype.toLowerCase
   override def toString: String = s"$name $mountPoint"
@@ -117,7 +111,7 @@ case class AwsBatchEmptyMountedDisk(mountPoint: Path, ftype:String="ebs") extend
 object AwsBatchWorkingDisk {
   val MountPoint: Path = DefaultPathBuilder.get("/cromwell_root")
   val Name = "local-disk"
-  val fsType=  "ebs"
+  val fsType = "ebs"
   val Default = AwsBatchWorkingDisk()
 }
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/package.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/package.scala
index 9b171741471..18dbb9d17b3 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/package.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/package.scala
@@ -14,11 +14,10 @@ package object aws {
 
   type Aws[F[_], A] = ReaderT[F, AwsBatchAttributes, A]
 
-  def sanitize(name: String): String ={
+  def sanitize(name: String): String =
     // Up to 128 letters (uppercase and lowercase), numbers, hyphens, and underscores are allowed.
     // We'll replace all invalid characters with an underscore
     name.replaceAll("[^A-Za-z0-9_\\-]", "_").slice(0, 128)
-  }
 
   def buildKVPair(key: String, value: String): KeyValuePair =
     KeyValuePair.builder.name(key).value(value).build
@@ -67,9 +66,11 @@ package object aws {
     * @tparam ClientT the type of the client that you will get back
     * @return a configured client for the AWS service
     */
-  def configureClient[BuilderT <: AwsClientBuilder[BuilderT, ClientT], ClientT](builder: AwsClientBuilder[BuilderT, ClientT],
-                                                                                 awsAuthMode: Option[AwsAuthMode],
-                                                                                 configRegion: Option[Region]): ClientT = {
+  def configureClient[BuilderT <: AwsClientBuilder[BuilderT, ClientT], ClientT](
+    builder: AwsClientBuilder[BuilderT, ClientT],
+    awsAuthMode: Option[AwsAuthMode],
+    configRegion: Option[Region]
+  ): ClientT = {
     awsAuthMode.foreach { awsAuthMode =>
       builder.credentialsProvider(awsAuthMode.provider())
     }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
index ba2e5580b3f..089ac4257cf 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
@@ -43,7 +43,13 @@ import cromwell.backend.impl.aws.AwsBatchAsyncBackendJobExecutionActor.AwsBatchP
 import cromwell.backend.impl.aws.RunStatus.UnsuccessfulRunStatus
 import cromwell.backend.impl.aws.io.AwsBatchWorkingDisk
 import cromwell.backend.io.JobPathsSpecHelper._
-import cromwell.backend.standard.{DefaultStandardAsyncExecutionActorParams, StandardAsyncExecutionActorParams, StandardAsyncJob, StandardExpressionFunctions, StandardExpressionFunctionsParams}
+import cromwell.backend.standard.{
+  DefaultStandardAsyncExecutionActorParams,
+  StandardAsyncExecutionActorParams,
+  StandardAsyncJob,
+  StandardExpressionFunctions,
+  StandardExpressionFunctionsParams
+}
 import cromwell.cloudsupport.aws.s3.S3Storage
 import cromwell.core.Tags.AwsTest
 import cromwell.core._
@@ -80,8 +86,14 @@ import scala.concurrent.{Await, ExecutionContext, Future, Promise}
 import scala.language.postfixOps
 import scala.util.Success
 
-class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
-  with AnyFlatSpecLike with Matchers with ImplicitSender with BackendSpec with BeforeAndAfter with DefaultJsonProtocol {
+class AwsBatchAsyncBackendJobExecutionActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with ImplicitSender
+    with BackendSpec
+    with BeforeAndAfter
+    with DefaultJsonProtocol {
   lazy val mockPathBuilderS3: S3PathBuilder = S3PathBuilder.fromProvider(
     AnonymousCredentialsProvider.create,
     S3Storage.DefaultConfiguration,
@@ -98,23 +110,23 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
   val YoSup: String =
     s"""
-      |task sup {
-      |  String addressee
-      |  command {
-      |    echo "yo sup $${addressee}!"
-      |  }
-      |  output {
-      |    String salutation = read_string(stdout())
-      |  }
-      |  runtime {
-      |    docker: "alpine:latest"
-      |    queueArn: "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue"
-      |  }
-      |}
-      |
-      |workflow wf_sup {
-      |  call sup
-      |}
+       |task sup {
+       |  String addressee
+       |  command {
+       |    echo "yo sup $${addressee}!"
+       |  }
+       |  output {
+       |    String salutation = read_string(stdout())
+       |  }
+       |  runtime {
+       |    docker: "alpine:latest"
+       |    queueArn: "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue"
+       |  }
+       |}
+       |
+       |workflow wf_sup {
+       |  call sup
+       |}
     """.stripMargin
 
   private val Inputs: Map[FullyQualifiedName, WomValue] = Map("wf_sup.sup.addressee" -> WomString("dog"))
@@ -128,11 +140,11 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
   lazy val TestableStandardExpressionFunctionsParamsS3: StandardExpressionFunctionsParams =
     new StandardExpressionFunctionsParams {
-    override lazy val pathBuilders: List[PathBuilder] = List(mockPathBuilderS3)
-    override lazy val callContext: CallContext = TestableCallContextS3
-    override val ioActorProxy: ActorRef = simpleIoActor
-    override val executionContext: ExecutionContext = system.dispatcher
-  }
+      override lazy val pathBuilders: List[PathBuilder] = List(mockPathBuilderS3)
+      override lazy val callContext: CallContext = TestableCallContextS3
+      override val ioActorProxy: ActorRef = simpleIoActor
+      override val executionContext: ExecutionContext = system.dispatcher
+    }
   lazy val TestableStandardExpressionFunctionsParamsLocal: StandardExpressionFunctionsParams =
     new StandardExpressionFunctionsParams {
       override lazy val pathBuilders: List[PathBuilder] = List(mockPathBuilderLocal)
@@ -140,12 +152,10 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
       override val ioActorProxy: ActorRef = simpleIoActor
       override val executionContext: ExecutionContext = system.dispatcher
     }
-  lazy val TestableAwsBatchExpressionFunctions: AwsBatchExpressionFunctions = {
+  lazy val TestableAwsBatchExpressionFunctions: AwsBatchExpressionFunctions =
     new AwsBatchExpressionFunctions(TestableStandardExpressionFunctionsParamsS3)
-  }
-  lazy val TestableAwsBatchExpressionFunctionsLocal: AwsBatchExpressionFunctions = {
+  lazy val TestableAwsBatchExpressionFunctionsLocal: AwsBatchExpressionFunctions =
     new AwsBatchExpressionFunctions(TestableStandardExpressionFunctionsParamsLocal)
-  }
   private def buildInitializationData(jobDescriptor: BackendJobDescriptor, configuration: AwsBatchConfiguration) = {
     val workflowPaths = AwsBatchWorkflowPaths(
       jobDescriptor.workflowDescriptor,
@@ -156,17 +166,18 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     AwsBatchBackendInitializationData(workflowPaths, runtimeAttributesBuilder, configuration, null)
   }
 
-  class TestableAwsBatchJobExecutionActor(params: StandardAsyncExecutionActorParams, functions: StandardExpressionFunctions)
-    extends AwsBatchAsyncBackendJobExecutionActor(params) {
+  class TestableAwsBatchJobExecutionActor(params: StandardAsyncExecutionActorParams,
+                                          functions: StandardExpressionFunctions
+  ) extends AwsBatchAsyncBackendJobExecutionActor(params) {
 
     def this(jobDescriptor: BackendJobDescriptor,
              promise: Promise[BackendJobExecutionResponse],
              configuration: AwsBatchConfiguration,
-             //functions: AwsBatchExpressionFunctions = TestableAwsBatchExpressionFunctions,
+             // functions: AwsBatchExpressionFunctions = TestableAwsBatchExpressionFunctions,
              functions: StandardExpressionFunctions = TestableAwsBatchExpressionFunctions,
              singletonActor: ActorRef = emptyActor,
-             ioActor: ActorRef = mockIoActor) = {
-
+             ioActor: ActorRef = mockIoActor
+    ) =
       this(
         DefaultStandardAsyncExecutionActorParams(
           jobIdKey = AwsBatchAsyncBackendJobExecutionActor.AwsBatchOperationIdKey,
@@ -181,7 +192,6 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
         ),
         functions
       )
-    }
 
     override lazy val jobLogger: JobLogger = new JobLogger(
       "TestLogger",
@@ -213,7 +223,9 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
   private def buildJobDescriptor(): BackendJobDescriptor = {
     val attempt = 1
     val wdlNamespace = WdlNamespaceWithWorkflow.load(YoSup, Seq.empty[Draft2ImportResolver]).get
-    val womDefinition = wdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    val womDefinition = wdlNamespace.workflow
+      .toWomWorkflowDefinition(isASubworkflow = false)
+      .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
 
     wdlNamespace.toWomExecutable(Option(Inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
       case Right(womExecutable) =>
@@ -238,7 +250,14 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
         val key = BackendJobDescriptorKey(job, None, attempt)
         val runtimeAttributes = makeRuntimeAttributes(job)
         val prefetchedKvEntries = Map[String, KvResponse]()
-        BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(Inputs), NoDocker, None, prefetchedKvEntries)
+        BackendJobDescriptor(workflowDescriptor,
+                             key,
+                             runtimeAttributes,
+                             fqnWdlMapToDeclarationMap(Inputs),
+                             NoDocker,
+                             None,
+                             prefetchedKvEntries
+        )
       case Left(badtimes) => fail(badtimes.toList.mkString(", "))
     }
   }
@@ -282,15 +301,19 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
   //   Await.result(promise.future, Timeout)
   // }
 
-  def buildTestActorRef(functions:StandardExpressionFunctions): TestActorRef[TestableAwsBatchJobExecutionActor] = {
+  def buildTestActorRef(functions: StandardExpressionFunctions): TestActorRef[TestableAwsBatchJobExecutionActor] = {
     // For this test we say that all previous attempts were preempted:
     val jobDescriptor = buildJobDescriptor()
-    val props = Props(new TestableAwsBatchJobExecutionActor(jobDescriptor, Promise(),
-      configuration,
-      //TestableAwsBatchExpressionFunctions,
-      functions,
-      emptyActor,
-      failIoActor))
+    val props = Props(
+      new TestableAwsBatchJobExecutionActor(jobDescriptor,
+                                            Promise(),
+                                            configuration,
+                                            // TestableAwsBatchExpressionFunctions,
+                                            functions,
+                                            emptyActor,
+                                            failIoActor
+      )
+    )
     TestActorRef(props, s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
   }
 
@@ -427,7 +450,7 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     checkFailedResult(None).isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
     // TODO: Determine the actual error message that comes back and special-case it in handlExecutionFailure
     //       in AwsBatchBackendJobExecutionActor
-    //checkFailedResult(Option("Operation canceled at")) shouldBe AbortedExecutionHandle
+    // checkFailedResult(Option("Operation canceled at")) shouldBe AbortedExecutionHandle
 
     actorRef.stop()
   }
@@ -446,12 +469,15 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
       fileKey -> fileVal
     )
 
-    val wdlNamespace = WdlNamespaceWithWorkflow.load(YoSup,
-      Seq.empty[Draft2ImportResolver]).get
-    val womWorkflow = wdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    val wdlNamespace = WdlNamespaceWithWorkflow.load(YoSup, Seq.empty[Draft2ImportResolver]).get
+    val womWorkflow = wdlNamespace.workflow
+      .toWomWorkflowDefinition(isASubworkflow = false)
+      .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
     wdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
 
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
@@ -464,19 +490,34 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
           None
         )
 
-        val call: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst({ case t: CommandCallNode => t }).get
+        val call: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst { case t: CommandCallNode =>
+          t
+        }.get
         val key = BackendJobDescriptorKey(call, None, 1)
         val runtimeAttributes = makeRuntimeAttributes(call)
-        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
 
-        val props = Props(new TestableAwsBatchJobExecutionActor(jobDescriptor, Promise(), configuration, TestableAwsBatchExpressionFunctions))
+        val props = Props(
+          new TestableAwsBatchJobExecutionActor(jobDescriptor,
+                                                Promise(),
+                                                configuration,
+                                                TestableAwsBatchExpressionFunctions
+          )
+        )
         val testActorRef = TestActorRef[TestableAwsBatchJobExecutionActor](
-          props, s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
-
+          props,
+          s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
 
-        def pathToLocal(womValue: WomValue): WomValue = {
+        def pathToLocal(womValue: WomValue): WomValue =
           WomFileMapper.mapWomFiles(testActorRef.underlyingActor.mapCommandLineWomFile)(womValue).get
-        }
 
         val mappedInputs = jobDescriptor.localInputs safeMapValues pathToLocal
 
@@ -498,37 +539,59 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     }
   }
 
-  private val dockerAndDiskWdlNamespace = WdlNamespaceWithWorkflow.load(SampleWdl.CurrentDirectory.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-    Seq.empty[Draft2ImportResolver]).get
+  private val dockerAndDiskWdlNamespace = WdlNamespaceWithWorkflow
+    .load(SampleWdl.CurrentDirectory.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+          Seq.empty[Draft2ImportResolver]
+    )
+    .get
 
   it should "generate correct AwsBatchFileInputs from a WdlMap" taggedAs AwsTest ignore {
     val inputs: Map[String, WomValue] = Map(
-      "stringToFileMap" -> WomMap(WomMapType(WomStringType, WomSingleFileType), Map(
-        WomString("stringTofile1") -> WomSingleFile("s3://path/to/stringTofile1"),
-        WomString("stringTofile2") -> WomSingleFile("s3://path/to/stringTofile2")
-      )),
-      "fileToStringMap" -> WomMap(WomMapType(WomSingleFileType, WomStringType), Map(
-        WomSingleFile("s3://path/to/fileToString1") -> WomString("fileToString1"),
-        WomSingleFile("s3://path/to/fileToString2") -> WomString("fileToString2")
-      )),
-      "fileToFileMap" -> WomMap(WomMapType(WomSingleFileType, WomSingleFileType), Map(
-        WomSingleFile("s3://path/to/fileToFile1Key") -> WomSingleFile("s3://path/to/fileToFile1Value"),
-        WomSingleFile("s3://path/to/fileToFile2Key") -> WomSingleFile("s3://path/to/fileToFile2Value")
-      )),
-      "stringToString" -> WomMap(WomMapType(WomStringType, WomStringType), Map(
-        WomString("stringToString1") -> WomString("path/to/stringToString1"),
-        WomString("stringToString2") -> WomString("path/to/stringToString2")
-      ))
+      "stringToFileMap" -> WomMap(
+        WomMapType(WomStringType, WomSingleFileType),
+        Map(
+          WomString("stringTofile1") -> WomSingleFile("s3://path/to/stringTofile1"),
+          WomString("stringTofile2") -> WomSingleFile("s3://path/to/stringTofile2")
+        )
+      ),
+      "fileToStringMap" -> WomMap(
+        WomMapType(WomSingleFileType, WomStringType),
+        Map(
+          WomSingleFile("s3://path/to/fileToString1") -> WomString("fileToString1"),
+          WomSingleFile("s3://path/to/fileToString2") -> WomString("fileToString2")
+        )
+      ),
+      "fileToFileMap" -> WomMap(
+        WomMapType(WomSingleFileType, WomSingleFileType),
+        Map(
+          WomSingleFile("s3://path/to/fileToFile1Key") -> WomSingleFile("s3://path/to/fileToFile1Value"),
+          WomSingleFile("s3://path/to/fileToFile2Key") -> WomSingleFile("s3://path/to/fileToFile2Value")
+        )
+      ),
+      "stringToString" -> WomMap(
+        WomMapType(WomStringType, WomStringType),
+        Map(
+          WomString("stringToString1") -> WomString("path/to/stringToString1"),
+          WomString("stringToString2") -> WomString("path/to/stringToString2")
+        )
+      )
     )
 
-    val workflowInputs = inputs map {
-      case (k, v) => s"wf_whereami.whereami$k" -> v
+    val workflowInputs = inputs map { case (k, v) =>
+      s"wf_whereami.whereami$k" -> v
     }
 
-    val womWorkflow = dockerAndDiskWdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
-    dockerAndDiskWdlNamespace.toWomExecutable(Option(workflowInputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
+    val womWorkflow = dockerAndDiskWdlNamespace.workflow
+      .toWomWorkflowDefinition(isASubworkflow = false)
+      .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    dockerAndDiskWdlNamespace.toWomExecutable(Option(workflowInputs.toJson.compactPrint),
+                                              NoIoFunctionSet,
+                                              strictValidation = true
+    ) match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
           womWorkflow,
@@ -543,43 +606,103 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
         val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
         val runtimeAttributes = makeRuntimeAttributes(job)
         val key = BackendJobDescriptorKey(job, None, 1)
-        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
 
         val props = Props(new TestableAwsBatchJobExecutionActor(jobDescriptor, Promise(), configuration))
         val testActorRef = TestActorRef[TestableAwsBatchJobExecutionActor](
-          props, s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+          props,
+          s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
 
         val batchInputs = testActorRef.underlyingActor.generateAwsBatchInputs(jobDescriptor)
         batchInputs should have size 8
-        batchInputs should contain(AwsBatchFileInput(
-          "stringToFileMap-0", "s3://path/to/stringTofile1", DefaultPathBuilder.get("path/to/stringTofile1"), workingDisk))
-        batchInputs should contain(AwsBatchFileInput(
-          "stringToFileMap-1", "s3://path/to/stringTofile2", DefaultPathBuilder.get("path/to/stringTofile2"), workingDisk))
-        batchInputs should contain(AwsBatchFileInput(
-          "fileToStringMap-0", "s3://path/to/fileToString1", DefaultPathBuilder.get("path/to/fileToString1"), workingDisk))
-        batchInputs should contain(AwsBatchFileInput(
-          "fileToStringMap-1", "s3://path/to/fileToString2", DefaultPathBuilder.get("path/to/fileToString2"), workingDisk))
-        batchInputs should contain(AwsBatchFileInput(
-          "fileToFileMap-0", "s3://path/to/fileToFile1Key", DefaultPathBuilder.get("path/to/fileToFile1Key"), workingDisk))
-        batchInputs should contain(AwsBatchFileInput(
-          "fileToFileMap-1", "s3://path/to/fileToFile1Value", DefaultPathBuilder.get("path/to/fileToFile1Value"), workingDisk))
-        batchInputs should contain(AwsBatchFileInput(
-          "fileToFileMap-2", "s3://path/to/fileToFile2Key", DefaultPathBuilder.get("path/to/fileToFile2Key"), workingDisk))
-        batchInputs should contain(AwsBatchFileInput(
-          "fileToFileMap-3", "s3://path/to/fileToFile2Value", DefaultPathBuilder.get("path/to/fileToFile2Value"), workingDisk))
+        batchInputs should contain(
+          AwsBatchFileInput("stringToFileMap-0",
+                            "s3://path/to/stringTofile1",
+                            DefaultPathBuilder.get("path/to/stringTofile1"),
+                            workingDisk
+          )
+        )
+        batchInputs should contain(
+          AwsBatchFileInput("stringToFileMap-1",
+                            "s3://path/to/stringTofile2",
+                            DefaultPathBuilder.get("path/to/stringTofile2"),
+                            workingDisk
+          )
+        )
+        batchInputs should contain(
+          AwsBatchFileInput("fileToStringMap-0",
+                            "s3://path/to/fileToString1",
+                            DefaultPathBuilder.get("path/to/fileToString1"),
+                            workingDisk
+          )
+        )
+        batchInputs should contain(
+          AwsBatchFileInput("fileToStringMap-1",
+                            "s3://path/to/fileToString2",
+                            DefaultPathBuilder.get("path/to/fileToString2"),
+                            workingDisk
+          )
+        )
+        batchInputs should contain(
+          AwsBatchFileInput("fileToFileMap-0",
+                            "s3://path/to/fileToFile1Key",
+                            DefaultPathBuilder.get("path/to/fileToFile1Key"),
+                            workingDisk
+          )
+        )
+        batchInputs should contain(
+          AwsBatchFileInput("fileToFileMap-1",
+                            "s3://path/to/fileToFile1Value",
+                            DefaultPathBuilder.get("path/to/fileToFile1Value"),
+                            workingDisk
+          )
+        )
+        batchInputs should contain(
+          AwsBatchFileInput("fileToFileMap-2",
+                            "s3://path/to/fileToFile2Key",
+                            DefaultPathBuilder.get("path/to/fileToFile2Key"),
+                            workingDisk
+          )
+        )
+        batchInputs should contain(
+          AwsBatchFileInput("fileToFileMap-3",
+                            "s3://path/to/fileToFile2Value",
+                            DefaultPathBuilder.get("path/to/fileToFile2Value"),
+                            workingDisk
+          )
+        )
 
       case Left(badness) => fail(badness.toList.mkString(", "))
     }
   }
 
-  def makeAwsBatchActorRef(sampleWdl: SampleWdl, callName: LocallyQualifiedName, inputs: Map[FullyQualifiedName, WomValue],
-                      functions: StandardExpressionFunctions = TestableAwsBatchExpressionFunctions):
-  TestActorRef[TestableAwsBatchJobExecutionActor] = {
-    val womWorkflow = WdlNamespaceWithWorkflow.load(sampleWdl.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-      Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
-    dockerAndDiskWdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
+  def makeAwsBatchActorRef(sampleWdl: SampleWdl,
+                           callName: LocallyQualifiedName,
+                           inputs: Map[FullyQualifiedName, WomValue],
+                           functions: StandardExpressionFunctions = TestableAwsBatchExpressionFunctions
+  ): TestActorRef[TestableAwsBatchJobExecutionActor] = {
+    val womWorkflow = WdlNamespaceWithWorkflow
+      .load(sampleWdl.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get, Seq.empty[Draft2ImportResolver])
+      .get
+      .workflow
+      .toWomWorkflowDefinition(isASubworkflow = false)
+      .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    dockerAndDiskWdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint),
+                                              NoIoFunctionSet,
+                                              strictValidation = true
+    ) match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
           womWorkflow,
@@ -594,10 +717,20 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
         val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == callName).get
         val key = BackendJobDescriptorKey(call, None, 1)
         val runtimeAttributes = makeRuntimeAttributes(call)
-        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
 
         val props = Props(new TestableAwsBatchJobExecutionActor(jobDescriptor, Promise(), configuration, functions))
-        TestActorRef[TestableAwsBatchJobExecutionActor](props, s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+        TestActorRef[TestableAwsBatchJobExecutionActor](
+          props,
+          s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
       case Left(badness) => fail(badness.toList.mkString(", "))
     }
   }
@@ -611,11 +744,18 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val workflowId = backend.workflowDescriptor.id
     val batchInputs = backend.generateAwsBatchInputs(jobDescriptor)
     batchInputs should have size 1
-    batchInputs should contain(AwsBatchFileInput("in-0", "s3://blah/b/c.txt", DefaultPathBuilder.get("blah/b/c.txt"), workingDisk))
+    batchInputs should contain(
+      AwsBatchFileInput("in-0", "s3://blah/b/c.txt", DefaultPathBuilder.get("blah/b/c.txt"), workingDisk)
+    )
     val outputs = backend.generateAwsBatchOutputs(jobDescriptor)
     outputs should have size 1
-    outputs should contain(AwsBatchFileOutput("out",
-      s"s3://my-cromwell-workflows-bucket/file_passing/$workflowId/call-a/out", DefaultPathBuilder.get("out"), workingDisk))
+    outputs should contain(
+      AwsBatchFileOutput("out",
+                         s"s3://my-cromwell-workflows-bucket/file_passing/$workflowId/call-a/out",
+                         DefaultPathBuilder.get("out"),
+                         workingDisk
+      )
+    )
   }
 
   it should "generate correct AwsBatchInputs when a command line contains a write_lines call in it" taggedAs AwsTest ignore {
@@ -623,23 +763,28 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
       "strs" -> WomArray(WomArrayType(WomStringType), Seq("A", "B", "C").map(WomString))
     )
 
-    class TestAwsBatchExpressionFunctions extends AwsBatchExpressionFunctions(TestableStandardExpressionFunctionsParamsS3) {
-      override def writeFile(path: String, content: String): Future[WomSingleFile] = {
+    class TestAwsBatchExpressionFunctions
+        extends AwsBatchExpressionFunctions(TestableStandardExpressionFunctionsParamsS3) {
+      override def writeFile(path: String, content: String): Future[WomSingleFile] =
         Future.fromTry(Success(WomSingleFile(s"s3://some/path/file.txt")))
-      }
     }
-    class TestAwsBatchExpressionFunctionsLocal extends AwsBatchExpressionFunctionsForFS(TestableStandardExpressionFunctionsParamsLocal) {
-      override def writeFile(path: String, content: String): Future[WomSingleFile] = {
+    class TestAwsBatchExpressionFunctionsLocal
+        extends AwsBatchExpressionFunctionsForFS(TestableStandardExpressionFunctionsParamsLocal) {
+      override def writeFile(path: String, content: String): Future[WomSingleFile] =
         Future.fromTry(Success(WomSingleFile(s"/some/path/file.txt")))
-      }
     }
     val functions = new TestAwsBatchExpressionFunctions
     val backend = makeAwsBatchActorRef(SampleWdl.ArrayIO, "serialize", inputs, functions).underlyingActor
     val jobDescriptor = backend.jobDescriptor
     val batchInputs = backend.generateAwsBatchInputs(jobDescriptor)
     batchInputs should have size 1
-    batchInputs should contain(AwsBatchFileInput(
-      "c6fd5c91-0", "s3://some/path/file.txt", DefaultPathBuilder.get("some/path/file.txt"), workingDisk))
+    batchInputs should contain(
+      AwsBatchFileInput("c6fd5c91-0",
+                        "s3://some/path/file.txt",
+                        DefaultPathBuilder.get("some/path/file.txt"),
+                        workingDisk
+      )
+    )
     val outputs = backend.generateAwsBatchOutputs(jobDescriptor)
     outputs should have size 0
 
@@ -648,8 +793,9 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val jobDescriptorLocal = backendLocal.jobDescriptor
     val batchInputsLocal = backend.generateAwsBatchInputs(jobDescriptorLocal)
     batchInputsLocal should have size 1
-    batchInputsLocal should contain(AwsBatchFileInput(
-      "c6fd5c91-0", "/some/path/file.txt", DefaultPathBuilder.get("some/path/file.txt"), workingDisk))
+    batchInputsLocal should contain(
+      AwsBatchFileInput("c6fd5c91-0", "/some/path/file.txt", DefaultPathBuilder.get("some/path/file.txt"), workingDisk)
+    )
     val outputsLocal = backendLocal.generateAwsBatchOutputs(jobDescriptorLocal)
     outputsLocal should have size 0
   }
@@ -657,13 +803,22 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
   it should "generate correct AwsBatchFileInputs from a WdlArray" taggedAs AwsTest ignore {
     val inputs: Map[String, WomValue] = Map(
       "fileArray" ->
-        WomArray(WomArrayType(WomSingleFileType), Seq(WomSingleFile("s3://path/to/file1"), WomSingleFile("s3://path/to/file2")))
+        WomArray(WomArrayType(WomSingleFileType),
+                 Seq(WomSingleFile("s3://path/to/file1"), WomSingleFile("s3://path/to/file2"))
+        )
     )
 
-    val womWorkflow = dockerAndDiskWdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
-    dockerAndDiskWdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
+    val womWorkflow = dockerAndDiskWdlNamespace.workflow
+      .toWomWorkflowDefinition(isASubworkflow = false)
+      .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    dockerAndDiskWdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint),
+                                              NoIoFunctionSet,
+                                              strictValidation = true
+    ) match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
           womWorkflow,
@@ -678,16 +833,29 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
         val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
         val runtimeAttributes = makeRuntimeAttributes(job)
         val key = BackendJobDescriptorKey(job, None, 1)
-        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
 
         val props = Props(new TestableAwsBatchJobExecutionActor(jobDescriptor, Promise(), configuration))
         val testActorRef = TestActorRef[TestableAwsBatchJobExecutionActor](
-          props, s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+          props,
+          s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
 
         val batchInputs = testActorRef.underlyingActor.generateAwsBatchInputs(jobDescriptor)
         batchInputs should have size 2
-        batchInputs should contain(AwsBatchFileInput("fileArray-0", "s3://path/to/file1", DefaultPathBuilder.get("path/to/file1"), workingDisk))
-        batchInputs should contain(AwsBatchFileInput("fileArray-1", "s3://path/to/file2", DefaultPathBuilder.get("path/to/file2"), workingDisk))
+        batchInputs should contain(
+          AwsBatchFileInput("fileArray-0", "s3://path/to/file1", DefaultPathBuilder.get("path/to/file1"), workingDisk)
+        )
+        batchInputs should contain(
+          AwsBatchFileInput("fileArray-1", "s3://path/to/file2", DefaultPathBuilder.get("path/to/file2"), workingDisk)
+        )
       case Left(badness) => fail(badness.toList.mkString(", "))
     }
   }
@@ -698,10 +866,17 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
       "file2" -> WomSingleFile("s3://path/to/file2")
     )
 
-    val womWorkflow = dockerAndDiskWdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
-    dockerAndDiskWdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
+    val womWorkflow = dockerAndDiskWdlNamespace.workflow
+      .toWomWorkflowDefinition(isASubworkflow = false)
+      .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    dockerAndDiskWdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint),
+                                              NoIoFunctionSet,
+                                              strictValidation = true
+    ) match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
           womWorkflow,
@@ -716,16 +891,29 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
         val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
         val runtimeAttributes = makeRuntimeAttributes(job)
         val key = BackendJobDescriptorKey(job, None, 1)
-        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
 
         val props = Props(new TestableAwsBatchJobExecutionActor(jobDescriptor, Promise(), configuration))
         val testActorRef = TestActorRef[TestableAwsBatchJobExecutionActor](
-          props, s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+          props,
+          s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
 
         val batchInputs = testActorRef.underlyingActor.generateAwsBatchInputs(jobDescriptor)
         batchInputs should have size 2
-        batchInputs should contain(AwsBatchFileInput("file1-0", "s3://path/to/file1", DefaultPathBuilder.get("path/to/file1"), workingDisk))
-        batchInputs should contain(AwsBatchFileInput("file2-0", "s3://path/to/file2", DefaultPathBuilder.get("path/to/file2"), workingDisk))
+        batchInputs should contain(
+          AwsBatchFileInput("file1-0", "s3://path/to/file1", DefaultPathBuilder.get("path/to/file1"), workingDisk)
+        )
+        batchInputs should contain(
+          AwsBatchFileInput("file2-0", "s3://path/to/file2", DefaultPathBuilder.get("path/to/file2"), workingDisk)
+        )
 
       case Left(badness) => fail(badness.toList.mkString(", "))
     }
@@ -733,30 +921,54 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
   it should "convert local Paths back to corresponding foreign paths in AwsBatchOutputs" taggedAs AwsTest in {
     val outputs = Set(
-      AwsBatchFileOutput("/cromwell_root/path/to/file1", "s3://path/to/file1",
-        DefaultPathBuilder.get("/cromwell_root/path/to/file1"), workingDisk),
-      AwsBatchFileOutput("/cromwell_root/path/to/file2", "s3://path/to/file2",
-        DefaultPathBuilder.get("/cromwell_root/path/to/file2"), workingDisk),
-      AwsBatchFileOutput("/cromwell_root/path/to/file3", "s3://path/to/file3",
-        DefaultPathBuilder.get("/cromwell_root/path/to/file3"), workingDisk),
-      AwsBatchFileOutput("/cromwell_root/path/to/file4", "s3://path/to/file4",
-        DefaultPathBuilder.get("/cromwell_root/path/to/file4"), workingDisk),
-      AwsBatchFileOutput("/cromwell_root/path/to/file5", "s3://path/to/file5",
-        DefaultPathBuilder.get("/cromwell_root/path/to/file5"), workingDisk)
+      AwsBatchFileOutput("/cromwell_root/path/to/file1",
+                         "s3://path/to/file1",
+                         DefaultPathBuilder.get("/cromwell_root/path/to/file1"),
+                         workingDisk
+      ),
+      AwsBatchFileOutput("/cromwell_root/path/to/file2",
+                         "s3://path/to/file2",
+                         DefaultPathBuilder.get("/cromwell_root/path/to/file2"),
+                         workingDisk
+      ),
+      AwsBatchFileOutput("/cromwell_root/path/to/file3",
+                         "s3://path/to/file3",
+                         DefaultPathBuilder.get("/cromwell_root/path/to/file3"),
+                         workingDisk
+      ),
+      AwsBatchFileOutput("/cromwell_root/path/to/file4",
+                         "s3://path/to/file4",
+                         DefaultPathBuilder.get("/cromwell_root/path/to/file4"),
+                         workingDisk
+      ),
+      AwsBatchFileOutput("/cromwell_root/path/to/file5",
+                         "s3://path/to/file5",
+                         DefaultPathBuilder.get("/cromwell_root/path/to/file5"),
+                         workingDisk
+      )
     )
     val outputValues = Seq(
       WomSingleFile("/cromwell_root/path/to/file1"),
-      WomArray(WomArrayType(WomSingleFileType), Seq(
-        WomSingleFile("/cromwell_root/path/to/file2"), WomSingleFile("/cromwell_root/path/to/file3"))),
-      WomMap(WomMapType(WomSingleFileType, WomSingleFileType), Map(
-        WomSingleFile("/cromwell_root/path/to/file4") -> WomSingleFile("/cromwell_root/path/to/file5")
-      ))
+      WomArray(WomArrayType(WomSingleFileType),
+               Seq(WomSingleFile("/cromwell_root/path/to/file2"), WomSingleFile("/cromwell_root/path/to/file3"))
+      ),
+      WomMap(WomMapType(WomSingleFileType, WomSingleFileType),
+             Map(
+               WomSingleFile("/cromwell_root/path/to/file4") -> WomSingleFile("/cromwell_root/path/to/file5")
+             )
+      )
     )
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+              Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
       NoOptions,
       Labels.empty,
@@ -768,33 +980,44 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestableAwsBatchJobExecutionActor(jobDescriptor, Promise(), configuration))
     val testActorRef = TestActorRef[TestableAwsBatchJobExecutionActor](
-      props, s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
-    def wdlValueToS3Path(outputs: Set[AwsBatchFileOutput])(womValue: WomValue): WomValue = {
+    def wdlValueToS3Path(outputs: Set[AwsBatchFileOutput])(womValue: WomValue): WomValue =
       WomFileMapper.mapWomFiles(testActorRef.underlyingActor.womFileToPath(outputs))(womValue).get
-    }
 
     val result = outputValues map wdlValueToS3Path(outputs)
     result should have size 3
     result should contain(WomSingleFile("s3://path/to/file1"))
-    result should contain(WomArray(WomArrayType(WomSingleFileType),
-      Seq(WomSingleFile("s3://path/to/file2"), WomSingleFile("s3://path/to/file3")))
+    result should contain(
+      WomArray(WomArrayType(WomSingleFileType),
+               Seq(WomSingleFile("s3://path/to/file2"), WomSingleFile("s3://path/to/file3"))
+      )
     )
-    result should contain(WomMap(WomMapType(WomSingleFileType, WomSingleFileType),
-      Map(WomSingleFile("s3://path/to/file4") -> WomSingleFile("s3://path/to/file5")))
+    result should contain(
+      WomMap(WomMapType(WomSingleFileType, WomSingleFileType),
+             Map(WomSingleFile("s3://path/to/file4") -> WomSingleFile("s3://path/to/file5"))
+      )
     )
   }
 
   it should "return log paths for non-scattered call" taggedAs AwsTest in {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId(UUID.fromString("e6236763-c518-41d0-9688-432549a8bf7c")),
-      WdlNamespaceWithWorkflow.load(
-        SampleWdl.HelloWorld.asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(SampleWdl.HelloWorld.asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
+              Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
       WorkflowOptions.fromJsonString(""" {"aws_s3_root": "s3://path/to/root"} """).get,
       Labels.empty,
@@ -806,11 +1029,14 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "hello").get
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestableAwsBatchJobExecutionActor(jobDescriptor, Promise(), configuration))
     val testActorRef = TestActorRef[TestableAwsBatchJobExecutionActor](
-      props, s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     val backend = testActorRef.underlyingActor
 
@@ -825,9 +1051,15 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
   it should "return log paths for scattered call" taggedAs AwsTest ignore {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId(UUID.fromString("e6236763-c518-41d0-9688-432549a8bf7d")),
-      WdlNamespaceWithWorkflow.load(
-        new SampleWdl.ScatterWdl().asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(
+          new SampleWdl.ScatterWdl().asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
+          Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
       WorkflowOptions.fromJsonString(""" {"root": "s3://path/to/root"} """).get,
       Labels.empty,
@@ -839,11 +1071,14 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "B").get
     val key = BackendJobDescriptorKey(call, Option(2), 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestableAwsBatchJobExecutionActor(jobDescriptor, Promise(), configuration))
     val testActorRef = TestActorRef[TestableAwsBatchJobExecutionActor](
-      props, s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableAwsBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     val backend = testActorRef.underlyingActor
 
@@ -862,11 +1097,12 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
     val jobId = "the-job-id"
 
-    def execute:Future[ExecutionHandle] ={ backend.recoverAsync(StandardAsyncJob(jobId)) }
+    def execute: Future[ExecutionHandle] = backend.recoverAsync(StandardAsyncJob(jobId))
 
     whenReady(execute, PatienceConfiguration.Timeout(10.seconds.dilated)) { executionResponse =>
-      executionResponse should be(a[PendingExecutionHandle[_,_,_]])
-      val pendingExecutionResponse = executionResponse.asInstanceOf[PendingExecutionHandle[StandardAsyncJob, AwsBatchJob, RunStatus]]
+      executionResponse should be(a[PendingExecutionHandle[_, _, _]])
+      val pendingExecutionResponse =
+        executionResponse.asInstanceOf[PendingExecutionHandle[StandardAsyncJob, AwsBatchJob, RunStatus]]
       pendingExecutionResponse.isDone should be(false)
       pendingExecutionResponse.jobDescriptor should be(jobDescriptor)
       pendingExecutionResponse.pendingJob should be(StandardAsyncJob(jobId))
@@ -876,8 +1112,10 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
   }
 
   private def makeRuntimeAttributes(job: CommandCallNode) = {
-    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(job.callable.runtimeAttributes, null, Map.empty)
-    RuntimeAttributeDefinition.addDefaultsToAttributes(
-      runtimeAttributesBuilder.definitions.toSet, NoOptions)(evaluatedAttributes.getOrElse(fail("Failed to evaluate runtime attributes")))
+    val evaluatedAttributes =
+      RuntimeAttributeDefinition.evaluateRuntimeAttributes(job.callable.runtimeAttributes, null, Map.empty)
+    RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributesBuilder.definitions.toSet, NoOptions)(
+      evaluatedAttributes.getOrElse(fail("Failed to evaluate runtime attributes"))
+    )
   }
 }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAttachedDiskSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAttachedDiskSpec.scala
index f2022fe3456..d76a745c4bc 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAttachedDiskSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAttachedDiskSpec.scala
@@ -40,15 +40,16 @@ import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks._
 import org.scalatest.prop.Tables.Table
 
-
 class AwsBatchAttachedDiskSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TryValues {
   val validTable = Table(
     ("unparsed", "parsed"),
     // AwsBatchEmptyMountedDisk has a toString override that uses the MD5sum of
     // the mount path in the return value, so these values are deterministic
     ("d-39de0dbcfb68c8735bd088c62fa061a4 /mnt", AwsBatchEmptyMountedDisk(DefaultPathBuilder.get("/mnt"))),
-    ("d-753b3ff55ce6e29b10951ad6190f7c84 /mnt/my_path", AwsBatchEmptyMountedDisk(DefaultPathBuilder.get("/mnt/my_path"))),
-    ("local-disk /cromwell_root", AwsBatchWorkingDisk()),
+    ("d-753b3ff55ce6e29b10951ad6190f7c84 /mnt/my_path",
+     AwsBatchEmptyMountedDisk(DefaultPathBuilder.get("/mnt/my_path"))
+    ),
+    ("local-disk /cromwell_root", AwsBatchWorkingDisk())
   )
 
   // TODO: Work through this syntax
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAttributesSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAttributesSpec.scala
index e3a6d099e66..aeb9d825f83 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAttributesSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAttributesSpec.scala
@@ -58,10 +58,9 @@ class AwsBatchAttributesSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
   it should "not parse invalid config" taggedAs IntegrationTest in {
     val nakedConfig =
-      ConfigFactory.parseString(
-        """
-          |{
-          |}
+      ConfigFactory.parseString("""
+                                  |{
+                                  |}
         """.stripMargin)
 
     val exception = intercept[IllegalArgumentException with MessageAggregation] {
@@ -76,21 +75,21 @@ class AwsBatchAttributesSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
   def configString(): String =
     s"""
-      |{
-      |   root = "s3://myBucket"
-      |   maximum-polling-interval = 600
-      |   numSubmitAttempts = 6
-      |   numCreateDefinitionAttempts = 6
-      |
-      |
-      |   filesystems = {
-      |     local {
-      |       // A reference to a potentially different auth for manipulating files via engine functions.
-      |       auth = "default"
-      |     }
-      |   }
-      |}
-      | """.stripMargin
+       |{
+       |   root = "s3://myBucket"
+       |   maximum-polling-interval = 600
+       |   numSubmitAttempts = 6
+       |   numCreateDefinitionAttempts = 6
+       |
+       |
+       |   filesystems = {
+       |     local {
+       |       // A reference to a potentially different auth for manipulating files via engine functions.
+       |       auth = "default"
+       |     }
+       |   }
+       |}
+       | """.stripMargin
   def configStringS3(): String =
     s"""
        |{
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchConfigurationSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchConfigurationSpec.scala
index 829c0b0514f..0e7ff6c8a56 100755
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchConfigurationSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchConfigurationSpec.scala
@@ -40,7 +40,12 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks
 
-class AwsBatchConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks with BeforeAndAfterAll {
+class AwsBatchConfigurationSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks
+    with BeforeAndAfterAll {
 
   behavior of "AwsBatchConfigurationSpec"
 
@@ -51,32 +56,31 @@ class AwsBatchConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     ()
   }
 
-  val globalConfig = ConfigFactory.parseString(
-    s"""
-      |aws {
-      |
-      |  application-name = "cromwell"
-      |   numSubmitAttempts = 6
-      |   numCreateDefinitionAttempts = 6
-      |
-      |  auths = [
-      |    {
-      |      name = "application-default"
-      |      scheme = "default"
-      |    },
-      |    {
-      |      name = "user-via-refresh"
-      |      scheme = "custom_keys"
-      |      access-key = "secret_key"
-      |      secret-key = "${mockFile.pathAsString}"
-      |    },
-      |    {
-      |      name = "service-account"
-      |      scheme = "default"
-      |    }
-      |  ]
-      |}
-      |
+  val globalConfig = ConfigFactory.parseString(s"""
+                                                  |aws {
+                                                  |
+                                                  |  application-name = "cromwell"
+                                                  |   numSubmitAttempts = 6
+                                                  |   numCreateDefinitionAttempts = 6
+                                                  |
+                                                  |  auths = [
+                                                  |    {
+                                                  |      name = "application-default"
+                                                  |      scheme = "default"
+                                                  |    },
+                                                  |    {
+                                                  |      name = "user-via-refresh"
+                                                  |      scheme = "custom_keys"
+                                                  |      access-key = "secret_key"
+                                                  |      secret-key = "${mockFile.pathAsString}"
+                                                  |    },
+                                                  |    {
+                                                  |      name = "service-account"
+                                                  |      scheme = "default"
+                                                  |    }
+                                                  |  ]
+                                                  |}
+                                                  |
     """.stripMargin)
 
   val backendConfig = ConfigFactory.parseString(
@@ -110,7 +114,8 @@ class AwsBatchConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       |    }
       |  }
       |
-    """.stripMargin)
+    """.stripMargin
+  )
 
   it should "fail to instantiate if any required configuration is missing" in {
 
@@ -131,11 +136,14 @@ class AwsBatchConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
   }
 
   it should "have correct root" in {
-    new AwsBatchConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig)).root shouldBe "s3://my-cromwell-workflows-bucket"
+    new AwsBatchConfiguration(
+      BackendConfigurationDescriptor(backendConfig, globalConfig)
+    ).root shouldBe "s3://my-cromwell-workflows-bucket"
   }
 
   it should "have correct docker" in {
-    val dockerConf = new AwsBatchConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig)).dockerCredentials
+    val dockerConf =
+      new AwsBatchConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig)).dockerCredentials
     dockerConf shouldBe defined
     dockerConf.get.token shouldBe "dockerToken"
   }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchInitializationActorSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchInitializationActorSpec.scala
index f1e2eb40bf9..762830d78dc 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchInitializationActorSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchInitializationActorSpec.scala
@@ -50,45 +50,43 @@ import wom.graph.CommandCallNode
 
 import scala.concurrent.duration._
 
-class AwsBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
-  with ImplicitSender {
+class AwsBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with ImplicitSender {
   val Timeout: FiniteDuration = 30.second.dilated
 
   import BackendSpec._
 
   val HelloWorld: String =
     s"""
-      |task hello {
-      |  String addressee = "you"
-      |  command {
-      |    echo "Hello $${addressee}!"
-      |  }
-      |  output {
-      |    String salutation = read_string(stdout())
-      |  }
-      |
-      |  RUNTIME
-      |}
-      |
-      |workflow wf_hello {
-      |  call hello
-      |}
+       |task hello {
+       |  String addressee = "you"
+       |  command {
+       |    echo "Hello $${addressee}!"
+       |  }
+       |  output {
+       |    String salutation = read_string(stdout())
+       |  }
+       |
+       |  RUNTIME
+       |}
+       |
+       |workflow wf_hello {
+       |  call hello
+       |}
     """.stripMargin
 
-  val globalConfig: Config = ConfigFactory.parseString(
-    """
-      |aws {
-      |
-      |  application-name = "cromwell"
-      |
-      |  auths = [
-      |    {
-      |      name = "default"
-      |      scheme = "default"
-      |    }
-      |  ]
-      |}
-      |""".stripMargin)
+  val globalConfig: Config = ConfigFactory.parseString("""
+                                                         |aws {
+                                                         |
+                                                         |  application-name = "cromwell"
+                                                         |
+                                                         |  auths = [
+                                                         |    {
+                                                         |      name = "default"
+                                                         |      scheme = "default"
+                                                         |    }
+                                                         |  ]
+                                                         |}
+                                                         |""".stripMargin)
 
   val backendConfigTemplate: String =
     """
@@ -157,28 +155,42 @@ class AwsBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike
 
   val backendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[DOCKERHUBCONFIG]", ""))
 
-  val dockerBackendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[DOCKERHUBCONFIG]",
-    """
-      |dockerhub {
-      |  account = "my@docker.account"
-      |  # no secrets here guys this is just `echo -n username:password | base64`
-      |  token = "dXNlcm5hbWU6cGFzc3dvcmQ="
-      |}
-      | """.stripMargin))
+  val dockerBackendConfig: Config = ConfigFactory.parseString(
+    backendConfigTemplate.replace(
+      "[DOCKERHUBCONFIG]",
+      """
+        |dockerhub {
+        |  account = "my@docker.account"
+        |  # no secrets here guys this is just `echo -n username:password | base64`
+        |  token = "dXNlcm5hbWU6cGFzc3dvcmQ="
+        |}
+        | """.stripMargin
+    )
+  )
 
   val defaultBackendConfig: BackendConfigurationDescriptor = BackendConfigurationDescriptor(backendConfig, globalConfig)
 
   val refreshTokenConfig: Config = ConfigFactory.parseString(refreshTokenConfigTemplate)
 
   private def getAwsBatchBackendProps(workflowDescriptor: BackendWorkflowDescriptor,
-                                 calls: Set[CommandCallNode],
-                                 configuration: AwsBatchConfiguration): Props = {
+                                      calls: Set[CommandCallNode],
+                                      configuration: AwsBatchConfiguration
+  ): Props = {
     val ioActor = mockIoActor
-    val params = AwsBatchInitializationActorParams(workflowDescriptor, ioActor, calls, configuration, emptyActor, restarting = false)
+    val params = AwsBatchInitializationActorParams(workflowDescriptor,
+                                                   ioActor,
+                                                   calls,
+                                                   configuration,
+                                                   emptyActor,
+                                                   restarting = false
+    )
     Props(new AwsBatchInitializationActor(params)).withDispatcher(BackendDispatcher)
   }
 
-  private def getAwsBatchBackend(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[CommandCallNode], conf: BackendConfigurationDescriptor) = {
+  private def getAwsBatchBackend(workflowDescriptor: BackendWorkflowDescriptor,
+                                 calls: Set[CommandCallNode],
+                                 conf: BackendConfigurationDescriptor
+  ) = {
     val props = getAwsBatchBackendProps(workflowDescriptor, calls, new AwsBatchConfiguration(conf))
     system.actorOf(props, "TestableAwsBatchInitializationActor-" + UUID.randomUUID)
   }
@@ -188,17 +200,17 @@ class AwsBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike
   it should "log a warning message when there are unsupported runtime attributes" taggedAs IntegrationTest in {
 
     within(Timeout) {
-      val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld,
-        runtime = """runtime { docker: "ubuntu/latest" test: true }""")
-      val backend = getAwsBatchBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes,
-        defaultBackendConfig)
+      val workflowDescriptor =
+        buildWdlWorkflowDescriptor(HelloWorld, runtime = """runtime { docker: "ubuntu/latest" test: true }""")
+      val backend =
+        getAwsBatchBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes, defaultBackendConfig)
       val eventPattern =
         "Key/s [test] is/are not supported by backend. Unsupported attributes will not be part of job executions."
       EventFilter.warning(pattern = escapePattern(eventPattern), occurrences = 1) intercept {
         backend ! Initialize
       }
       expectMsgPF() {
-        case InitializationSuccess(_) => //Docker entry is present.
+        case InitializationSuccess(_) => // Docker entry is present.
         case InitializationFailed(failure) => fail(s"InitializationSuccess was expected but got $failure")
       }
     }
@@ -207,26 +219,32 @@ class AwsBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike
   it should "return InitializationFailed when docker runtime attribute key is not present" taggedAs IntegrationTest in {
     within(Timeout) {
       val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld, runtime = """runtime { }""")
-      val backend = getAwsBatchBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes,
-        defaultBackendConfig)
+      val backend =
+        getAwsBatchBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes, defaultBackendConfig)
       backend ! Initialize
-      expectMsgPF() {
-        case InitializationFailed(failure) =>
-          failure match {
-            case exception: RuntimeAttributeValidationFailures =>
-              if (!exception.getMessage.equals("Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!"))
-                fail("Exception message is not equal to 'Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!'.")
-          }
+      expectMsgPF() { case InitializationFailed(failure) =>
+        failure match {
+          case exception: RuntimeAttributeValidationFailures =>
+            if (
+              !exception.getMessage.equals(
+                "Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!"
+              )
+            )
+              fail(
+                "Exception message is not equal to 'Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!'."
+              )
+        }
       }
     }
   }
 
-  private case class TestingBits(actorRef: TestActorRef[AwsBatchInitializationActor], configuration: AwsBatchConfiguration)
+  private case class TestingBits(actorRef: TestActorRef[AwsBatchInitializationActor],
+                                 configuration: AwsBatchConfiguration
+  )
 
 }
 
 object AwsBatchInitializationActorSpec {
-  def normalize(str: String): String = {
+  def normalize(str: String): String =
     str.parseJson.prettyPrint
-  }
 }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobExecutionActorSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobExecutionActorSpec.scala
index be384d2af77..37b9ebaef99 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobExecutionActorSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobExecutionActorSpec.scala
@@ -35,7 +35,11 @@ import akka.actor.{Actor, ActorRef, Props}
 import akka.testkit._
 import cromwell.backend.BackendJobExecutionActor.{ExecuteJobCommand, JobFailedNonRetryableResponse}
 import cromwell.backend.impl.aws.ControllableFailingJabjea.JabjeaExplode
-import cromwell.backend.standard.{DefaultStandardSyncExecutionActorParams, StandardSyncExecutionActor, StandardSyncExecutionActorParams}
+import cromwell.backend.standard.{
+  DefaultStandardSyncExecutionActorParams,
+  StandardSyncExecutionActor,
+  StandardSyncExecutionActorParams
+}
 import cromwell.backend.{BackendJobDescriptor, MinimumRuntimeSettings}
 import cromwell.core.TestKitSuite
 import org.scalatest.flatspec.AnyFlatSpecLike
@@ -67,12 +71,21 @@ class AwsBatchJobExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
 
     val parent = TestProbe("parent")
     val deathwatch = TestProbe("deathwatch")
-    val params = DefaultStandardSyncExecutionActorParams(AwsBatchAsyncBackendJobExecutionActor.AwsBatchOperationIdKey, serviceRegistryActor, ioActor,
-      jobDescriptor, null, Option(initializationData), backendSingletonActor,
-      classOf[AwsBatchAsyncBackendJobExecutionActor], MinimumRuntimeSettings())
+    val params = DefaultStandardSyncExecutionActorParams(
+      AwsBatchAsyncBackendJobExecutionActor.AwsBatchOperationIdKey,
+      serviceRegistryActor,
+      ioActor,
+      jobDescriptor,
+      null,
+      Option(initializationData),
+      backendSingletonActor,
+      classOf[AwsBatchAsyncBackendJobExecutionActor],
+      MinimumRuntimeSettings()
+    )
     val testJJEA = TestActorRef[TestAwsBatchJobExecutionActor](
       props = Props(new TestAwsBatchJobExecutionActor(params, Props(new ConstructorFailingJABJEA))),
-      supervisor = parent.ref)
+      supervisor = parent.ref
+    )
     deathwatch watch testJJEA
 
     // Nothing happens:
@@ -81,9 +94,10 @@ class AwsBatchJobExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
 
     testJJEA.tell(msg = ExecuteJobCommand, sender = parent.ref)
 
-    parent.expectMsgPF(max = TimeoutDuration) {
-      case JobFailedNonRetryableResponse(_, throwable, _) =>
-        throwable.getMessage should be("AwsBatchAsyncBackendJobExecutionActor failed and didn't catch its exception. This condition has been handled and the job will be marked as failed.")
+    parent.expectMsgPF(max = TimeoutDuration) { case JobFailedNonRetryableResponse(_, throwable, _) =>
+      throwable.getMessage should be(
+        "AwsBatchAsyncBackendJobExecutionActor failed and didn't catch its exception. This condition has been handled and the job will be marked as failed."
+      )
     }
   }
 
@@ -100,13 +114,22 @@ class AwsBatchJobExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
     val parent = TestProbe("parent")
     val deathwatch = TestProbe("deathwatch")
     val constructionPromise = Promise[ActorRef]()
-    val params = DefaultStandardSyncExecutionActorParams(AwsBatchAsyncBackendJobExecutionActor.AwsBatchOperationIdKey, serviceRegistryActor, ioActor,
-      jobDescriptor, null, Option(initializationData), backendSingletonActor,
+    val params = DefaultStandardSyncExecutionActorParams(
+      AwsBatchAsyncBackendJobExecutionActor.AwsBatchOperationIdKey,
+      serviceRegistryActor,
+      ioActor,
+      jobDescriptor,
+      null,
+      Option(initializationData),
+      backendSingletonActor,
       classOf[AwsBatchAsyncBackendJobExecutionActor],
-      MinimumRuntimeSettings())
+      MinimumRuntimeSettings()
+    )
     val testJJEA = TestActorRef[TestAwsBatchJobExecutionActor](
-      props = Props(new TestAwsBatchJobExecutionActor(params, Props(new ControllableFailingJabjea(constructionPromise)))),
-      supervisor = parent.ref)
+      props =
+        Props(new TestAwsBatchJobExecutionActor(params, Props(new ControllableFailingJabjea(constructionPromise)))),
+      supervisor = parent.ref
+    )
     deathwatch watch testJJEA
 
     // Nothing happens:
@@ -127,15 +150,16 @@ class AwsBatchJobExecutionActorSpec extends TestKitSuite with AnyFlatSpecLike wi
         throw exception
     }
 
-    parent.expectMsgPF(max = TimeoutDuration) {
-      case JobFailedNonRetryableResponse(_, throwable, _) =>
-        throwable.getMessage should be("AwsBatchAsyncBackendJobExecutionActor failed and didn't catch its exception. This condition has been handled and the job will be marked as failed.")
+    parent.expectMsgPF(max = TimeoutDuration) { case JobFailedNonRetryableResponse(_, throwable, _) =>
+      throwable.getMessage should be(
+        "AwsBatchAsyncBackendJobExecutionActor failed and didn't catch its exception. This condition has been handled and the job will be marked as failed."
+      )
     }
   }
 }
 
-class TestAwsBatchJobExecutionActor(params: StandardSyncExecutionActorParams,
-                               fakeJabjeaProps: Props) extends StandardSyncExecutionActor(params) {
+class TestAwsBatchJobExecutionActor(params: StandardSyncExecutionActorParams, fakeJabjeaProps: Props)
+    extends StandardSyncExecutionActor(params) {
   override def createAsyncProps(): Props = fakeJabjeaProps
 }
 
@@ -147,12 +171,12 @@ class ConstructorFailingJABJEA extends ControllableFailingJabjea(Promise[ActorRe
 class ControllableFailingJabjea(constructionPromise: Promise[ActorRef]) extends Actor {
   def explode(): Unit = {
     val boom = 1 == 1
-    if (boom) throw new RuntimeException("Test Exception! Don't panic if this appears during a test run!")
-      with NoStackTrace
+    if (boom)
+      throw new RuntimeException("Test Exception! Don't panic if this appears during a test run!") with NoStackTrace
   }
   constructionPromise.trySuccess(self)
-  override def receive: Receive = {
-    case JabjeaExplode => explode()
+  override def receive: Receive = { case JabjeaExplode =>
+    explode()
   }
 }
 
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index e9a5f1f86d9..32d0cfab6bb 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -102,30 +102,51 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
 
   val cpu: Int Refined Positive = 2
   val runtimeAttributes: AwsBatchRuntimeAttributes = new AwsBatchRuntimeAttributes(
-      cpu = cpu,
-      zones = Vector("us-east-1"),
-      memory = MemorySize(2.0, MemoryUnit.GB),
-      disks = Seq.empty,
-      dockerImage = "ubuntu:latest",
-      queueArn = "arn:aws:batch:us-east-1:123456789:job-queue/default-gwf-core",
-      failOnStderr = true,
-      continueOnReturnCode = ContinueOnReturnCodeFlag(false),
-      noAddress = false,
-      scriptS3BucketName = "script-bucket",
-      fileSystem = "s3")
+    cpu = cpu,
+    zones = Vector("us-east-1"),
+    memory = MemorySize(2.0, MemoryUnit.GB),
+    disks = Seq.empty,
+    dockerImage = "ubuntu:latest",
+    queueArn = "arn:aws:batch:us-east-1:123456789:job-queue/default-gwf-core",
+    failOnStderr = true,
+    continueOnReturnCode = ContinueOnReturnCodeFlag(false),
+    noAddress = false,
+    scriptS3BucketName = "script-bucket",
+    fileSystem = "s3"
+  )
 
   private def generateBasicJob: AwsBatchJob = {
-    val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
-      "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
-      Seq.empty[AwsBatchInput].toSet, Seq.empty[AwsBatchFileOutput].toSet,
-      jobPaths, Seq.empty[AwsBatchParameter], None)
+    val job = AwsBatchJob(
+      null,
+      runtimeAttributes,
+      "commandLine",
+      script,
+      "/cromwell_root/hello-rc.txt",
+      "/cromwell_root/hello-stdout.log",
+      "/cromwell_root/hello-stderr.log",
+      Seq.empty[AwsBatchInput].toSet,
+      Seq.empty[AwsBatchFileOutput].toSet,
+      jobPaths,
+      Seq.empty[AwsBatchParameter],
+      None
+    )
     job
   }
   private def generateBasicJobForLocalFS: AwsBatchJob = {
-    val job = AwsBatchJob(null, runtimeAttributes.copy(fileSystem="local"), "commandLine", script,
-      "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
-      Seq.empty[AwsBatchInput].toSet, Seq.empty[AwsBatchFileOutput].toSet,
-      jobPaths, Seq.empty[AwsBatchParameter], None)
+    val job = AwsBatchJob(
+      null,
+      runtimeAttributes.copy(fileSystem = "local"),
+      "commandLine",
+      script,
+      "/cromwell_root/hello-rc.txt",
+      "/cromwell_root/hello-stdout.log",
+      "/cromwell_root/hello-stderr.log",
+      Seq.empty[AwsBatchInput].toSet,
+      Seq.empty[AwsBatchFileOutput].toSet,
+      jobPaths,
+      Seq.empty[AwsBatchParameter],
+      None
+    )
     job
   }
 
@@ -136,10 +157,10 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
 
     val job: AwsBatchJob = generateBasicJob
 
-    job.AWS_RETRY_MODE should be ("AWS_RETRY_MODE")
-    job.AWS_RETRY_MODE_DEFAULT_VALUE should be ("adaptive")
-    job.AWS_MAX_ATTEMPTS should be ("AWS_MAX_ATTEMPTS")
-    job.AWS_MAX_ATTEMPTS_DEFAULT_VALUE should be ("14")
+    job.AWS_RETRY_MODE should be("AWS_RETRY_MODE")
+    job.AWS_RETRY_MODE_DEFAULT_VALUE should be("adaptive")
+    job.AWS_MAX_ATTEMPTS should be("AWS_MAX_ATTEMPTS")
+    job.AWS_MAX_ATTEMPTS_DEFAULT_VALUE should be("14")
   }
 
   it should "generate appropriate KV pairs for the container environment for S3" in {
@@ -149,10 +170,10 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     // testing a private method see https://www.scalatest.org/user_guide/using_PrivateMethodTester
     val kvPairs = job invokePrivate generateEnvironmentKVPairs("script-bucket", "prefix-", "key")
 
-    kvPairs should contain (buildKVPair(job.AWS_MAX_ATTEMPTS, job.AWS_MAX_ATTEMPTS_DEFAULT_VALUE))
-    kvPairs should contain (buildKVPair(job.AWS_RETRY_MODE, "adaptive"))
-    kvPairs should contain (buildKVPair("BATCH_FILE_TYPE", "script"))
-    kvPairs should contain (buildKVPair("BATCH_FILE_S3_URL", "s3://script-bucket/prefix-key"))
+    kvPairs should contain(buildKVPair(job.AWS_MAX_ATTEMPTS, job.AWS_MAX_ATTEMPTS_DEFAULT_VALUE))
+    kvPairs should contain(buildKVPair(job.AWS_RETRY_MODE, "adaptive"))
+    kvPairs should contain(buildKVPair("BATCH_FILE_TYPE", "script"))
+    kvPairs should contain(buildKVPair("BATCH_FILE_S3_URL", "s3://script-bucket/prefix-key"))
   }
 
   it should "generate appropriate KV pairs for the container environment for Local FS" in {
@@ -162,9 +183,9 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     // testing a private method see https://www.scalatest.org/user_guide/using_PrivateMethodTester
     val kvPairs = job invokePrivate generateEnvironmentKVPairs("script-bucket", "prefix-", "key")
 
-    kvPairs should contain (buildKVPair(job.AWS_MAX_ATTEMPTS, job.AWS_MAX_ATTEMPTS_DEFAULT_VALUE))
-    kvPairs should contain (buildKVPair(job.AWS_RETRY_MODE, "adaptive"))
-    kvPairs should contain (buildKVPair("BATCH_FILE_TYPE", "script"))
-    kvPairs should contain (buildKVPair("BATCH_FILE_S3_URL", ""))
+    kvPairs should contain(buildKVPair(job.AWS_MAX_ATTEMPTS, job.AWS_MAX_ATTEMPTS_DEFAULT_VALUE))
+    kvPairs should contain(buildKVPair(job.AWS_RETRY_MODE, "adaptive"))
+    kvPairs should contain(buildKVPair("BATCH_FILE_TYPE", "script"))
+    kvPairs should contain(buildKVPair("BATCH_FILE_S3_URL", ""))
   }
 }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
index fbab5a81a23..957126da9ad 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
@@ -50,32 +50,41 @@ import wom.values._
 
 class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec with Matchers {
 
-  def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]): WorkflowOptions = {
-    WorkflowOptions(JsObject(Map(
-      "default_runtime_attributes" -> JsObject(defaults)
-    )))
-  }
-
-  val expectedDefaults = new AwsBatchRuntimeAttributes(refineMV[Positive](1), Vector("us-east-1a", "us-east-1b"),
+  def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]): WorkflowOptions =
+    WorkflowOptions(
+      JsObject(
+        Map(
+          "default_runtime_attributes" -> JsObject(defaults)
+        )
+      )
+    )
 
-    MemorySize(2, MemoryUnit.GB), Vector(AwsBatchWorkingDisk()),
+  val expectedDefaults = new AwsBatchRuntimeAttributes(
+    refineMV[Positive](1),
+    Vector("us-east-1a", "us-east-1b"),
+    MemorySize(2, MemoryUnit.GB),
+    Vector(AwsBatchWorkingDisk()),
     "ubuntu:latest",
     "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue",
     false,
     ContinueOnReturnCodeSet(Set(0)),
     false,
-    "my-stuff")
-
-  val expectedDefaultsLocalFS = new AwsBatchRuntimeAttributes(refineMV[Positive](1), Vector("us-east-1a", "us-east-1b"),
-
-    MemorySize(2, MemoryUnit.GB), Vector(AwsBatchWorkingDisk()),
+    "my-stuff"
+  )
+
+  val expectedDefaultsLocalFS = new AwsBatchRuntimeAttributes(
+    refineMV[Positive](1),
+    Vector("us-east-1a", "us-east-1b"),
+    MemorySize(2, MemoryUnit.GB),
+    Vector(AwsBatchWorkingDisk()),
     "ubuntu:latest",
     "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue",
     false,
     ContinueOnReturnCodeSet(Set(0)),
     false,
     "",
-    "local")
+    "local"
+  )
 
   "AwsBatchRuntimeAttributes" should {
 
@@ -106,12 +115,16 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
 
     "fail to validate a scriptBucketName with trailing slash entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff/"))
-      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "The Script Bucket name has an invalid s3 bucket format")
+      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+                                                    "The Script Bucket name has an invalid s3 bucket format"
+      )
     }
 
     "fail to validate an invalid scriptBucketName entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my**Bucket"))
-      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "The Script Bucket name has an invalid s3 bucket format")
+      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+                                                    "The Script Bucket name has an invalid s3 bucket format"
+      )
     }
 
     "validate a valid Docker entry" in {
@@ -122,113 +135,196 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
 
     "fail to validate an invalid Docker entry" in {
       val runtimeAttributes = Map("docker" -> WomInteger(1))
-      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting docker runtime attribute to be a String")
+      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+                                                    "Expecting docker runtime attribute to be a String"
+      )
     }
 
     "validate a valid failOnStderr entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "failOnStderr" -> WomBoolean(true))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "failOnStderr" -> WomBoolean(true)
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(failOnStderr = true)
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid failOnStderr entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "failOnStderr" -> WomString("yes"))
-      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'")
+      assertAwsBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'"
+      )
     }
 
     "validate a valid continueOnReturnCode integer entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "continueOnReturnCode" -> WomInteger(1))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "continueOnReturnCode" -> WomInteger(1)
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1)))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "validate a valid continueOnReturnCode boolean entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "continueOnReturnCode" -> WomBoolean(false))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "continueOnReturnCode" -> WomBoolean(false)
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(continueOnReturnCode = ContinueOnReturnCodeFlag(false))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "validate a valid continueOnReturnCode array entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "continueOnReturnCode" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2))))
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "scriptBucketName" -> WomString("my-stuff"),
+        "continueOnReturnCode" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2)))
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1, 2)))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "coerce then validate a valid continueOnReturnCode array entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "continueOnReturnCode" -> WomArray(WomArrayType(WomStringType), List(WomString("1"), WomString("2"))))
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "scriptBucketName" -> WomString("my-stuff"),
+        "continueOnReturnCode" -> WomArray(WomArrayType(WomStringType), List(WomString("1"), WomString("2")))
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1, 2)))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid continueOnReturnCode entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "continueOnReturnCode" -> WomString("value"))
-      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]")
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "continueOnReturnCode" -> WomString("value")
+      )
+      assertAwsBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+      )
     }
 
     "validate a valid cpu entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "cpu" -> WomInteger(2))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "cpu" -> WomInteger(2))
       val expectedRuntimeAttributes = expectedDefaults.copy(cpu = refineMV[Positive](2))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "validate a valid cpu string entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "cpu" -> WomString("2"))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "cpu" -> WomString("2")
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(cpu = refineMV[Positive](2))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
     "validate a valid Filesystem string entry S3" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "filesystem" -> WomString("s3"))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "filesystem" -> WomString("s3")
+      )
       val expectedRuntimeAttributes = expectedDefaults
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
     "validate a valid Filesystem string entry local Filesystem" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),"scriptBucketName" -> WomString(""), "filesystem" -> WomString("local"))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString(""),
+                                  "filesystem" -> WomString("local")
+      )
       val expectedRuntimeAttributes = expectedDefaultsLocalFS
-      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes,WorkflowOptions.fromMap(Map.empty).get,
-        NonEmptyList.of("us-east-1a", "us-east-1b"), new AwsBatchConfiguration(AwsBatchTestConfigForLocalFS.AwsBatchBackendConfigurationDescriptor))
+      assertAwsBatchRuntimeAttributesSuccessfulCreation(
+        runtimeAttributes,
+        expectedRuntimeAttributes,
+        WorkflowOptions.fromMap(Map.empty).get,
+        NonEmptyList.of("us-east-1a", "us-east-1b"),
+        new AwsBatchConfiguration(AwsBatchTestConfigForLocalFS.AwsBatchBackendConfigurationDescriptor)
+      )
     }
 
     "fail to validate an invalid cpu entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "cpu" -> WomString("value"))
-      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting cpu runtime attribute to be an Integer")
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "cpu" -> WomString("value")
+      )
+      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+                                                    "Expecting cpu runtime attribute to be an Integer"
+      )
     }
 
     "validate a valid zones entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "zones" -> WomString("us-east-1a"))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "zones" -> WomString("us-east-1a")
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(zones = Vector("us-east-1a"))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid zones entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "zones" -> WomInteger(1))
-      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]")
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "zones" -> WomInteger(1)
+      )
+      assertAwsBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]"
+      )
     }
 
     "validate a valid array zones entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "zones" -> WomArray(WomArrayType(WomStringType), List(WomString("us-east-1a"), WomString("us-east-1b"))))
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "scriptBucketName" -> WomString("my-stuff"),
+        "zones" -> WomArray(WomArrayType(WomStringType), List(WomString("us-east-1a"), WomString("us-east-1b")))
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(zones = Vector("us-east-1a", "us-east-1b"))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid array zones entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "zones" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2))))
-      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]")
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "scriptBucketName" -> WomString("my-stuff"),
+        "zones" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2)))
+      )
+      assertAwsBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]"
+      )
     }
 
     "validate a valid disks entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "disks" -> WomString("local-disk"))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "disks" -> WomString("local-disk")
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(disks = Seq(AwsBatchVolume.parse("local-disk").get))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid disks entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "disks" -> WomInteger(10))
-      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting disks runtime attribute to be a comma separated String or Array[String]")
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "disks" -> WomInteger(10)
+      )
+      assertAwsBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting disks runtime attribute to be a comma separated String or Array[String]"
+      )
     }
 
     "validate a valid disks array entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "disks" -> WomArray(WomArrayType(WomStringType), List(WomString("local-disk"), WomString("local-disk"))))
-      val expectedRuntimeAttributes = expectedDefaults.copy(disks = Seq(AwsBatchVolume.parse("local-disk").get, AwsBatchVolume.parse("local-disk").get))
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "scriptBucketName" -> WomString("my-stuff"),
+        "disks" -> WomArray(WomArrayType(WomStringType), List(WomString("local-disk"), WomString("local-disk")))
+      )
+      val expectedRuntimeAttributes = expectedDefaults.copy(disks =
+        Seq(AwsBatchVolume.parse("local-disk").get, AwsBatchVolume.parse("local-disk").get)
+      )
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
@@ -239,26 +335,42 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     // }
 
     "validate a valid memory entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "memory" -> WomString("1 GB"))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "memory" -> WomString("1 GB")
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(memory = MemorySize(1, MemoryUnit.GB))
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid memory entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "memory" -> WomString("blah"))
-      assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting memory runtime attribute to be an Integer or String with format '8 GB'")
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "memory" -> WomString("blah")
+      )
+      assertAwsBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting memory runtime attribute to be an Integer or String with format '8 GB'"
+      )
     }
 
     "validate a valid noAddress entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "noAddress" -> WomBoolean(true))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "noAddress" -> WomBoolean(true)
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(noAddress = true)
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid noAddress entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "noAddress" -> WomInteger(1))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "scriptBucketName" -> WomString("my-stuff"),
+                                  "noAddress" -> WomInteger(1)
+      )
       assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes,
-        "Expecting noAddress runtime attribute to be a Boolean")
+                                                    "Expecting noAddress runtime attribute to be a Boolean"
+      )
     }
 
     "validate a valid queueArn entry" in {
@@ -269,10 +381,13 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
         "arn:aws-cn:batch:us-west-2:123456789012:job-queue/default-a4e50e00-b850-11e9",
         "arn:aws-cn:batch:us-gov-west-1:123456789012:job-queue/default-a4e50e00-b850-11e9",
         "arn:aws-us-gov:batch:us-west-2:123456789012:job-queue/default-a4e50e00-b850-11e9",
-        "arn:aws:batch:us-east-1:123456789012:job-queue/my_queue",
+        "arn:aws:batch:us-east-1:123456789012:job-queue/my_queue"
       )
       validArnsAsStrings foreach { validArn =>
-        val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "queueArn" -> WomString(validArn))
+        val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                    "scriptBucketName" -> WomString("my-stuff"),
+                                    "queueArn" -> WomString(validArn)
+        )
         val expectedRuntimeAttributes = expectedDefaults.copy(queueArn = validArn)
         assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
       }
@@ -292,13 +407,12 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
       )
       invalidArnsAsStrings foreach { invalidArn =>
         val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "queueArn" -> WomString(invalidArn))
-        assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes,
-          "ARN has invalid format")
+        assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes, "ARN has invalid format")
       }
     }
 
     "override config default attributes with default attributes declared in workflow options" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff") )
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"))
 
       val workflowOptionsJson =
         """{
@@ -312,7 +426,8 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     }
 
     "override config default runtime attributes with task runtime attributes" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"),  "cpu" -> WomInteger(4))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "cpu" -> WomInteger(4))
 
       val workflowOptionsJson =
         """{
@@ -326,7 +441,8 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     }
 
     "override invalid config default attributes with task runtime attributes" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),"scriptBucketName" -> WomString("my-stuff"),  "cpu" -> WomInteger(4))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "cpu" -> WomInteger(4))
 
       val workflowOptionsJson =
         """{
@@ -341,10 +457,11 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
   }
 
   private def assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes: Map[String, WomValue],
-                                                           expectedRuntimeAttributes: AwsBatchRuntimeAttributes,
-                                                           workflowOptions: WorkflowOptions = emptyWorkflowOptions,
-                                                           defaultZones: NonEmptyList[String] = defaultZones,
-                                                           configuration: AwsBatchConfiguration = configuration): Unit = {
+                                                                expectedRuntimeAttributes: AwsBatchRuntimeAttributes,
+                                                                workflowOptions: WorkflowOptions = emptyWorkflowOptions,
+                                                                defaultZones: NonEmptyList[String] = defaultZones,
+                                                                configuration: AwsBatchConfiguration = configuration
+  ): Unit = {
     try {
       val actualRuntimeAttributes = toAwsBatchRuntimeAttributes(runtimeAttributes, workflowOptions, configuration)
       assert(actualRuntimeAttributes == expectedRuntimeAttributes)
@@ -355,8 +472,9 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
   }
 
   private def assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue],
-                                                       exMsg: String,
-                                                       workflowOptions: WorkflowOptions = emptyWorkflowOptions): Unit = {
+                                                            exMsg: String,
+                                                            workflowOptions: WorkflowOptions = emptyWorkflowOptions
+  ): Unit = {
     try {
       toAwsBatchRuntimeAttributes(runtimeAttributes, workflowOptions, configuration)
       fail(s"A RuntimeException was expected with message: $exMsg")
@@ -367,11 +485,14 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
   }
 
   private def toAwsBatchRuntimeAttributes(runtimeAttributes: Map[String, WomValue],
-                                     workflowOptions: WorkflowOptions,
-                                     configuration: AwsBatchConfiguration): AwsBatchRuntimeAttributes = {
+                                          workflowOptions: WorkflowOptions,
+                                          configuration: AwsBatchConfiguration
+  ): AwsBatchRuntimeAttributes = {
     val runtimeAttributesBuilder = AwsBatchRuntimeAttributes.runtimeAttributesBuilder(configuration)
-    val defaultedAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(
-      staticRuntimeAttributeDefinitions, workflowOptions)(runtimeAttributes)
+    val defaultedAttributes =
+      RuntimeAttributeDefinition.addDefaultsToAttributes(staticRuntimeAttributeDefinitions, workflowOptions)(
+        runtimeAttributes
+      )
     val validatedRuntimeAttributes = runtimeAttributesBuilder.build(defaultedAttributes, NOPLogger.NOP_LOGGER)
     AwsBatchRuntimeAttributes(validatedRuntimeAttributes, configuration.runtimeConfig, configuration.fileSystem)
   }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
index 38545c7e472..d5095989c2c 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
@@ -109,8 +109,10 @@ object AwsBatchTestConfig {
   val AwsBatchBackendConfig = ConfigFactory.parseString(AwsBatchBackendConfigString)
   val AwsBatchGlobalConfig = ConfigFactory.parseString(AwsBatchGlobalConfigString)
   val AwsBatchBackendNoDefaultConfig = ConfigFactory.parseString(NoDefaultsConfigString)
-  val AwsBatchBackendConfigurationDescriptor = BackendConfigurationDescriptor(AwsBatchBackendConfig, AwsBatchGlobalConfig)
-  val NoDefaultsConfigurationDescriptor = BackendConfigurationDescriptor(AwsBatchBackendNoDefaultConfig, AwsBatchGlobalConfig)
+  val AwsBatchBackendConfigurationDescriptor =
+    BackendConfigurationDescriptor(AwsBatchBackendConfig, AwsBatchGlobalConfig)
+  val NoDefaultsConfigurationDescriptor =
+    BackendConfigurationDescriptor(AwsBatchBackendNoDefaultConfig, AwsBatchGlobalConfig)
 }
 
 object AwsBatchTestConfigForLocalFS {
@@ -188,6 +190,8 @@ object AwsBatchTestConfigForLocalFS {
   val AwsBatchBackendConfig = ConfigFactory.parseString(AwsBatchBackendConfigString)
   val AwsBatchGlobalConfig = ConfigFactory.parseString(AwsBatchGlobalConfigString)
   val AwsBatchBackendNoDefaultConfig = ConfigFactory.parseString(NoDefaultsConfigString)
-  val AwsBatchBackendConfigurationDescriptor = BackendConfigurationDescriptor(AwsBatchBackendConfig, AwsBatchGlobalConfig)
-  val NoDefaultsConfigurationDescriptor = BackendConfigurationDescriptor(AwsBatchBackendNoDefaultConfig, AwsBatchGlobalConfig)
-}
\ No newline at end of file
+  val AwsBatchBackendConfigurationDescriptor =
+    BackendConfigurationDescriptor(AwsBatchBackendConfig, AwsBatchGlobalConfig)
+  val NoDefaultsConfigurationDescriptor =
+    BackendConfigurationDescriptor(AwsBatchBackendNoDefaultConfig, AwsBatchGlobalConfig)
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala
index 1bf708e8f8c..456fd822e7b 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala
@@ -3,29 +3,40 @@ package cromwell.backend.google.batch
 import akka.actor.{ActorRef, Props}
 import com.google.api.client.util.ExponentialBackOff
 import com.typesafe.scalalogging.StrictLogging
-import cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory.{preemptionCountKey, robustBuildAttributes, unexpectedRetryCountKey}
+import cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory.{
+  preemptionCountKey,
+  robustBuildAttributes,
+  unexpectedRetryCountKey
+}
 import cromwell.backend.google.batch.actors._
 import cromwell.backend.google.batch.api.{GcpBatchApiRequestHandler, GcpBatchRequestFactoryImpl}
 import cromwell.backend.google.batch.models.{GcpBatchConfiguration, GcpBatchConfigurationAttributes}
 import cromwell.backend.google.batch.callcaching.{BatchBackendCacheHitCopyingActor, BatchBackendFileHashingActor}
 import cromwell.backend.standard._
 import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardFileHashingActor}
-import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor, JobExecutionMap}
+import cromwell.backend.{
+  BackendConfigurationDescriptor,
+  BackendInitializationData,
+  BackendWorkflowDescriptor,
+  JobExecutionMap
+}
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.core.CallOutputs
 import wom.graph.CommandCallNode
 
 import scala.util.{Failure, Try}
 
-class GcpBatchBackendLifecycleActorFactory(override val name: String, override val configurationDescriptor: BackendConfigurationDescriptor)
-  extends StandardLifecycleActorFactory {
+class GcpBatchBackendLifecycleActorFactory(override val name: String,
+                                           override val configurationDescriptor: BackendConfigurationDescriptor
+) extends StandardLifecycleActorFactory {
 
   override val requestedKeyValueStoreKeys: Seq[String] = Seq(preemptionCountKey, unexpectedRetryCountKey)
 
   override def jobIdKey: String = "__gcp_batch"
   protected val googleConfig: GoogleConfiguration = GoogleConfiguration(configurationDescriptor.globalConfig)
 
-  override lazy val initializationActorClass: Class[_ <: StandardInitializationActor] = classOf[GcpBatchInitializationActor]
+  override lazy val initializationActorClass: Class[_ <: StandardInitializationActor] =
+    classOf[GcpBatchInitializationActor]
 
   override def asyncExecutionActorClass: Class[_ <: StandardAsyncExecutionActor] =
     classOf[GcpBatchAsyncBackendJobExecutionActor]
@@ -33,47 +44,58 @@ class GcpBatchBackendLifecycleActorFactory(override val name: String, override v
   override lazy val finalizationActorClassOption: Option[Class[_ <: StandardFinalizationActor]] =
     Option(classOf[GcpBatchFinalizationActor])
 
-
-
   protected val batchAttributes: GcpBatchConfigurationAttributes = {
-    def defaultBuildAttributes()=
+    def defaultBuildAttributes() =
       GcpBatchConfigurationAttributes(googleConfig, configurationDescriptor.backendConfig, "batchConfig")
     robustBuildAttributes(defaultBuildAttributes)
   }
 
   val batchConfiguration = new GcpBatchConfiguration(configurationDescriptor, googleConfig, batchAttributes)
 
-  override def workflowInitializationActorParams(
-
-                                                  workflowDescriptor: BackendWorkflowDescriptor,
-                                                  ioActor: ActorRef,
-                                                  calls: Set[CommandCallNode],
-                                                  serviceRegistryActor: ActorRef,
-                                                  restart: Boolean): StandardInitializationActorParams = {
-    GcpBatchInitializationActorParams(workflowDescriptor, ioActor , calls, batchConfiguration, serviceRegistryActor, restart)
-  }
-
-  override def workflowFinalizationActorParams(
-                                           workflowDescriptor: BackendWorkflowDescriptor,
-                                           ioActor: ActorRef,
-                                           //batchConfiguration: GcpBatchConfiguration,
-                                           calls: Set[CommandCallNode],
-                                           jobExecutionMap: JobExecutionMap,
-                                           workflowOutputs: CallOutputs,
-                                           initializationDataOption: Option[BackendInitializationData]): StandardFinalizationActorParams = {
-    GcpBatchFinalizationActorParams(workflowDescriptor, ioActor, batchConfiguration, calls, jobExecutionMap, workflowOutputs, initializationDataOption)
-  }
-
-  override lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] = {
+  override def workflowInitializationActorParams(workflowDescriptor: BackendWorkflowDescriptor,
+                                                 ioActor: ActorRef,
+                                                 calls: Set[CommandCallNode],
+                                                 serviceRegistryActor: ActorRef,
+                                                 restart: Boolean
+  ): StandardInitializationActorParams =
+    GcpBatchInitializationActorParams(workflowDescriptor,
+                                      ioActor,
+                                      calls,
+                                      batchConfiguration,
+                                      serviceRegistryActor,
+                                      restart
+    )
+
+  override def workflowFinalizationActorParams(workflowDescriptor: BackendWorkflowDescriptor,
+                                               ioActor: ActorRef,
+                                               // batchConfiguration: GcpBatchConfiguration,
+                                               calls: Set[CommandCallNode],
+                                               jobExecutionMap: JobExecutionMap,
+                                               workflowOutputs: CallOutputs,
+                                               initializationDataOption: Option[BackendInitializationData]
+  ): StandardFinalizationActorParams =
+    GcpBatchFinalizationActorParams(workflowDescriptor,
+                                    ioActor,
+                                    batchConfiguration,
+                                    calls,
+                                    jobExecutionMap,
+                                    workflowOutputs,
+                                    initializationDataOption
+    )
+
+  override lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] =
     Option(classOf[BatchBackendCacheHitCopyingActor])
-  }
 
-  override lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(classOf[BatchBackendFileHashingActor])
+  override lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(
+    classOf[BatchBackendFileHashingActor]
+  )
 
   override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] = {
     val requestHandler = new GcpBatchApiRequestHandler
     val requestFactory = new GcpBatchRequestFactoryImpl()(batchConfiguration.batchAttributes.gcsTransferConfiguration)
-    Option(GcpBatchBackendSingletonActor.props(requestFactory, serviceRegistryActor = serviceRegistryActor)(requestHandler))
+    Option(
+      GcpBatchBackendSingletonActor.props(requestFactory, serviceRegistryActor = serviceRegistryActor)(requestHandler)
+    )
   }
 }
 
@@ -81,13 +103,13 @@ object GcpBatchBackendLifecycleActorFactory extends StrictLogging {
   val preemptionCountKey = "PreemptionCount"
   val unexpectedRetryCountKey = "UnexpectedRetryCount"
 
-
-  private [batch] def robustBuildAttributes(buildAttributes: () => GcpBatchConfigurationAttributes,
-                                            maxAttempts: Int = 3,
-                                            initialIntervalMillis: Int = 5000,
-                                            maxIntervalMillis: Int = 10000,
-                                            multiplier: Double = 1.5,
-                                            randomizationFactor: Double = 0.5): GcpBatchConfigurationAttributes = {
+  private[batch] def robustBuildAttributes(buildAttributes: () => GcpBatchConfigurationAttributes,
+                                           maxAttempts: Int = 3,
+                                           initialIntervalMillis: Int = 5000,
+                                           maxIntervalMillis: Int = 10000,
+                                           multiplier: Double = 1.5,
+                                           randomizationFactor: Double = 0.5
+  ): GcpBatchConfigurationAttributes = {
     val backoff = new ExponentialBackOff.Builder()
       .setInitialIntervalMillis(initialIntervalMillis)
       .setMaxIntervalMillis(maxIntervalMillis)
@@ -96,7 +118,7 @@ object GcpBatchBackendLifecycleActorFactory extends StrictLogging {
       .build()
 
     // `attempt` is 1-based
-    def build(attempt: Int): Try[GcpBatchConfigurationAttributes] = {
+    def build(attempt: Int): Try[GcpBatchConfigurationAttributes] =
       Try {
         buildAttributes()
       } recoverWith {
@@ -106,9 +128,13 @@ object GcpBatchBackendLifecycleActorFactory extends StrictLogging {
             .warn(s"Failed to build GcpBatchConfigurationAttributes on attempt $attempt of $maxAttempts, retrying.", ex)
           Thread.sleep(backoff.nextBackOffMillis())
           build(attempt + 1)
-        case e => Failure(new RuntimeException(s"Failed to build GcpBatchConfigurationAttributes on attempt $attempt of $maxAttempts", e))
+        case e =>
+          Failure(
+            new RuntimeException(s"Failed to build GcpBatchConfigurationAttributes on attempt $attempt of $maxAttempts",
+                                 e
+            )
+          )
       }
-    }
     // This intentionally throws if the final result of `build` is a `Failure`.
     build(attempt = 1).get
   }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiAbortClient.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiAbortClient.scala
index f025ae05282..892980441bf 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiAbortClient.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiAbortClient.scala
@@ -6,9 +6,8 @@ import cromwell.backend.google.batch.monitoring.BatchInstrumentation
 
 trait BatchApiAbortClient { this: Actor with ActorLogging with BatchInstrumentation =>
 
-  def abortJob(jobName: JobName, backendSingletonActor: ActorRef): Unit = {
+  def abortJob(jobName: JobName, backendSingletonActor: ActorRef): Unit =
     backendSingletonActor ! GcpBatchBackendSingletonActor.Action.AbortJob(jobName)
-  }
 
   def abortActorClientReceive: Actor.Receive = {
     case GcpBatchBackendSingletonActor.Event.JobAbortRequestSent(job) =>
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiFetchJobClient.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiFetchJobClient.scala
index e502bb18c2e..b18bdc23f4e 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiFetchJobClient.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiFetchJobClient.scala
@@ -33,7 +33,7 @@ trait BatchApiFetchJobClient { this: Actor with ActorLogging with BatchInstrumen
     pollingActorClientPromise = None
   }
 
-  def fetchJob(jobName: JobName, backendSingletonActor: ActorRef): Future[Job] = {
+  def fetchJob(jobName: JobName, backendSingletonActor: ActorRef): Future[Job] =
     pollingActorClientPromise match {
       case Some(p) => p.future
       case None =>
@@ -43,5 +43,4 @@ trait BatchApiFetchJobClient { this: Actor with ActorLogging with BatchInstrumen
         pollingActorClientPromise = Option(newPromise)
         newPromise.future
     }
-  }
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiRunCreationClient.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiRunCreationClient.scala
index 0763369dc50..0825f865f77 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiRunCreationClient.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/BatchApiRunCreationClient.scala
@@ -35,7 +35,7 @@ trait BatchApiRunCreationClient { this: Actor with ActorLogging with BatchInstru
     runCreationClientPromise = None
   }
 
-  def runBatchJob(request: GcpBatchRequest, backendSingletonActor: ActorRef): Future[StandardAsyncJob] = {
+  def runBatchJob(request: GcpBatchRequest, backendSingletonActor: ActorRef): Future[StandardAsyncJob] =
     runCreationClientPromise match {
       case Some(p) =>
         p.future
@@ -46,5 +46,4 @@ trait BatchApiRunCreationClient { this: Actor with ActorLogging with BatchInstru
         runCreationClientPromise = Option(newPromise)
         newPromise.future
     }
-  }
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
index b3f9d47d316..eba54bdc4c3 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
@@ -25,7 +25,13 @@ import cromwell.filesystems.gcs.GcsPathBuilder
 import cromwell.filesystems.gcs.GcsPathBuilder.ValidFullGcsPath
 
 import java.io.FileNotFoundException
-import cromwell.backend.standard.{ScriptPreambleData, StandardAdHocValue, StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
+import cromwell.backend.standard.{
+  ScriptPreambleData,
+  StandardAdHocValue,
+  StandardAsyncExecutionActor,
+  StandardAsyncExecutionActorParams,
+  StandardAsyncJob
+}
 import cromwell.core._
 import cromwell.core.io.IoCommandBuilder
 import cromwell.core.path.{DefaultPathBuilder, Path}
@@ -84,7 +90,9 @@ object GcpBatchAsyncBackendJobExecutionActor {
 
   val plainTextContentType: Option[ContentType.WithCharset] = Option(ContentTypes.`text/plain(UTF-8)`)
 
-  private[batch] def groupParametersByGcsBucket[T <: BatchParameter](parameters: List[T]): Map[String, NonEmptyList[T]] = {
+  private[batch] def groupParametersByGcsBucket[T <: BatchParameter](
+    parameters: List[T]
+  ): Map[String, NonEmptyList[T]] =
     parameters.map { param =>
       def pathTypeString = if (param.isFileParameter) "File" else "Directory"
       val regexToUse = if (param.isFileParameter) gcsFilePathMatcher else gcsDirectoryPathMatcher
@@ -93,16 +101,17 @@ object GcpBatchAsyncBackendJobExecutionActor {
         case regexToUse(bucket) => Map(bucket -> NonEmptyList.of(param))
         case regexToUse(bucket, _) => Map(bucket -> NonEmptyList.of(param))
         case other =>
-          throw new Exception(s"$pathTypeString path '$other' did not match the expected regex: ${regexToUse.pattern.toString}")  with NoStackTrace
+          throw new Exception(
+            s"$pathTypeString path '$other' did not match the expected regex: ${regexToUse.pattern.toString}"
+          ) with NoStackTrace
       }
     } combineAll
-  }
 
   private[batch] def generateDrsLocalizerManifest(inputs: List[GcpBatchInput]): String = {
     val outputStream = new ByteArrayOutputStream()
     val csvPrinter = new CSVPrinter(new OutputStreamWriter(outputStream), CSVFormat.DEFAULT)
-    val drsFileInputs = inputs collect {
-      case drsInput@GcpBatchFileInput(_, drsPath: DrsPath, _, _) => (drsInput, drsPath)
+    val drsFileInputs = inputs collect { case drsInput @ GcpBatchFileInput(_, drsPath: DrsPath, _, _) =>
+      (drsInput, drsPath)
     }
     drsFileInputs foreach { case (drsInput, drsPath) =>
       csvPrinter.printRecord(drsPath.pathAsString, drsInput.containerPath.pathAsString)
@@ -114,7 +123,7 @@ object GcpBatchAsyncBackendJobExecutionActor {
 }
 
 class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
-  extends BackendJobLifecycleActor
+    extends BackendJobLifecycleActor
     with StandardAsyncExecutionActor
     with BatchApiRunCreationClient
     with BatchApiFetchJobClient
@@ -137,7 +146,8 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   /** The type of the run status returned during each poll. */
   override type StandardAsyncRunState = RunStatus
 
-  override def receive: Receive = runCreationClientReceive orElse pollingActorClientReceive orElse abortActorClientReceive orElse kvClientReceive orElse super.receive
+  override def receive: Receive =
+    runCreationClientReceive orElse pollingActorClientReceive orElse abortActorClientReceive orElse kvClientReceive orElse super.receive
 
   /** Should return true if the status contained in `thiz` is equivalent to `that`, delta any other data that might be carried around
    * in the state type.
@@ -145,17 +155,22 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   def statusEquivalentTo(thiz: StandardAsyncRunState)(that: StandardAsyncRunState): Boolean = thiz == that
 
   protected lazy val cmdInput: GcpBatchFileInput =
-    GcpBatchFileInput(GcpBatchJobPaths.BatchExecParamName, gcpBatchCallPaths.script, DefaultPathBuilder.get(gcpBatchCallPaths.scriptFilename), workingDisk)
+    GcpBatchFileInput(GcpBatchJobPaths.BatchExecParamName,
+                      gcpBatchCallPaths.script,
+                      DefaultPathBuilder.get(gcpBatchCallPaths.scriptFilename),
+                      workingDisk
+    )
 
   private lazy val jobDockerImage = jobDescriptor.maybeCallCachingEligible.dockerHash
     .getOrElse(runtimeAttributes.dockerImage)
 
   override def dockerImageUsed: Option[String] = Option(jobDockerImage)
 
-  //noinspection ActorMutableStateInspection
+  // noinspection ActorMutableStateInspection
 
   // Need to add previousRetryReasons and preemptible in order to get preemptible to work in the tests
-  protected val previousRetryReasons: ErrorOr[PreviousRetryReasons] = PreviousRetryReasons.tryApply(jobDescriptor.prefetchedKvStoreEntries, jobDescriptor.key.attempt)
+  protected val previousRetryReasons: ErrorOr[PreviousRetryReasons] =
+    PreviousRetryReasons.tryApply(jobDescriptor.prefetchedKvStoreEntries, jobDescriptor.key.attempt)
 
   lazy val preemptible: Boolean = previousRetryReasons match {
     case Valid(PreviousRetryReasons(p, _)) => p < maxPreemption
@@ -167,32 +182,56 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   val backendSingletonActor: ActorRef = standardParams.backendSingletonActorOption
     .getOrElse(throw new RuntimeException("GCP Batch actor cannot exist without its backend singleton 2"))
 
-
   /**
    * Takes two arrays of remote and local WOM File paths and generates the necessary `GcpBatchInput`s.
    */
   protected def gcpBatchInputsFromWomFiles(inputName: String,
                                            remotePathArray: Seq[WomFile],
                                            localPathArray: Seq[WomFile],
-                                           jobDescriptor: BackendJobDescriptor): Iterable[GcpBatchInput] = {
-        (remotePathArray zip localPathArray) flatMap {
-          case (remotePath: WomMaybeListedDirectory, localPath) =>
-            maybeListedDirectoryToBatchParameters(inputName, remotePath, localPath.valueString)
-          case (remotePath: WomUnlistedDirectory, localPath) =>
-            Seq(GcpBatchDirectoryInput(inputName, getPath(remotePath.valueString).get, DefaultPathBuilder.get(localPath.valueString), workingDisk))
-          case (remotePath: WomMaybePopulatedFile, localPath) =>
-            maybePopulatedFileToBatchParameters(inputName, remotePath, localPath.valueString)
-          case (remotePath, localPath) =>
-            Seq(GcpBatchFileInput(inputName, getPath(remotePath.valueString).get, DefaultPathBuilder.get(localPath.valueString), workingDisk))
-        }
-  }
+                                           jobDescriptor: BackendJobDescriptor
+  ): Iterable[GcpBatchInput] =
+    (remotePathArray zip localPathArray) flatMap {
+      case (remotePath: WomMaybeListedDirectory, localPath) =>
+        maybeListedDirectoryToBatchParameters(inputName, remotePath, localPath.valueString)
+      case (remotePath: WomUnlistedDirectory, localPath) =>
+        Seq(
+          GcpBatchDirectoryInput(inputName,
+                                 getPath(remotePath.valueString).get,
+                                 DefaultPathBuilder.get(localPath.valueString),
+                                 workingDisk
+          )
+        )
+      case (remotePath: WomMaybePopulatedFile, localPath) =>
+        maybePopulatedFileToBatchParameters(inputName, remotePath, localPath.valueString)
+      case (remotePath, localPath) =>
+        Seq(
+          GcpBatchFileInput(inputName,
+                            getPath(remotePath.valueString).get,
+                            DefaultPathBuilder.get(localPath.valueString),
+                            workingDisk
+          )
+        )
+    }
 
-  private def maybePopulatedFileToBatchParameters(inputName: String, maybePopulatedFile: WomMaybePopulatedFile, localPath: String) = {
-    val secondaryFiles = maybePopulatedFile.secondaryFiles.flatMap({ secondaryFile =>
-      gcpBatchInputsFromWomFiles(secondaryFile.valueString, List(secondaryFile), List(relativeLocalizationPath(secondaryFile)), jobDescriptor)
-    })
+  private def maybePopulatedFileToBatchParameters(inputName: String,
+                                                  maybePopulatedFile: WomMaybePopulatedFile,
+                                                  localPath: String
+  ) = {
+    val secondaryFiles = maybePopulatedFile.secondaryFiles.flatMap { secondaryFile =>
+      gcpBatchInputsFromWomFiles(secondaryFile.valueString,
+                                 List(secondaryFile),
+                                 List(relativeLocalizationPath(secondaryFile)),
+                                 jobDescriptor
+      )
+    }
 
-    Seq(GcpBatchFileInput(inputName, getPath(maybePopulatedFile.valueString).get, DefaultPathBuilder.get(localPath), workingDisk)) ++ secondaryFiles
+    Seq(
+      GcpBatchFileInput(inputName,
+                        getPath(maybePopulatedFile.valueString).get,
+                        DefaultPathBuilder.get(localPath),
+                        workingDisk
+      )
+    ) ++ secondaryFiles
   }
 
   /**
@@ -201,7 +240,7 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
    * relativeLocalizationPath("foo/bar.txt") -> "foo/bar.txt"
    * relativeLocalizationPath("gs://some/bucket/foo.txt") -> "some/bucket/foo.txt"
    */
-  override protected def relativeLocalizationPath(file: WomFile): WomFile = {
+  override protected def relativeLocalizationPath(file: WomFile): WomFile =
     file.mapFile(value =>
       getPath(value) match {
         case Success(drsPath: DrsPath) => DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
@@ -209,21 +248,21 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         case _ => value
       }
     )
-  }
 
   lazy val localMonitoringImageScriptPath: Path =
     DefaultPathBuilder.get(gcpBatchCallPaths.batchMonitoringImageScriptFilename)
 
-  override protected def fileName(file: WomFile): WomFile = {
+  override protected def fileName(file: WomFile): WomFile =
     file.mapFile(value =>
       getPath(value) match {
-        case Success(drsPath: DrsPath) => DefaultPathBuilder
-          .get(DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()).name
+        case Success(drsPath: DrsPath) =>
+          DefaultPathBuilder
+            .get(DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync())
+            .name
         case Success(path) => path.name
         case _ => value
       }
     )
-  }
 
   override lazy val inputsToNotLocalize: Set[WomFile] = {
     val localizeOptional = jobDescriptor.findInputFilesByParameterMeta {
@@ -252,21 +291,20 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   }
 
   // The original implementation recursively finds all non directory files, in V2 we can keep directory as is
-  protected lazy val callInputFiles: Map[FullyQualifiedName, Seq[WomFile]] = {
-
+  protected lazy val callInputFiles: Map[FullyQualifiedName, Seq[WomFile]] =
     // NOTE: This causes the tests to fail
-      jobDescriptor.localInputs map {
-        case (key, womFile) =>
-          key -> womFile.collectAsSeq({
-            case womFile: WomFile if !inputsToNotLocalize.contains(womFile) => womFile
-          })
+    jobDescriptor.localInputs map { case (key, womFile) =>
+      key -> womFile.collectAsSeq {
+        case womFile: WomFile if !inputsToNotLocalize.contains(womFile) => womFile
       }
-  }
+    }
 
   private lazy val gcsTransferLibrary =
     Source.fromInputStream(Thread.currentThread.getContextClassLoader.getResourceAsStream("gcs_transfer.sh")).mkString
 
-  private def gcsLocalizationTransferBundle[T <: GcpBatchInput](gcsTransferConfiguration: GcsTransferConfiguration)(bucket: String, inputs: NonEmptyList[T]): String = {
+  private def gcsLocalizationTransferBundle[T <: GcpBatchInput](
+    gcsTransferConfiguration: GcsTransferConfiguration
+  )(bucket: String, inputs: NonEmptyList[T]): String = {
     val project = inputs.head.cloudPath.asInstanceOf[GcsPath].projectId
     val maxAttempts = gcsTransferConfiguration.transferAttempts
 
@@ -285,25 +323,27 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     // Deduplicate any inputs since parallel localization can't deal with this.
     val uniqueFilesByContainerParentDirectory = filesByContainerParentDirectory map { case (p, fs) => p -> fs.toSet }
 
-    val filesWithSameNamesTransferBundles: List[String] = uniqueFilesByContainerParentDirectory.toList map { case (containerParent, filesWithSameParent) =>
-      val arrayIdentifier = s"files_to_localize_" + DigestUtils.md5Hex(bucket + containerParent)
-      val entries = filesWithSameParent.map(_.cloudPath) mkString("\"", "\"\n|  \"", "\"")
+    val filesWithSameNamesTransferBundles: List[String] = uniqueFilesByContainerParentDirectory.toList map {
+      case (containerParent, filesWithSameParent) =>
+        val arrayIdentifier = s"files_to_localize_" + DigestUtils.md5Hex(bucket + containerParent)
+        val entries = filesWithSameParent.map(_.cloudPath) mkString ("\"", "\"\n|  \"", "\"")
 
-      s"""
-         |# Localize files from source bucket '$bucket' to container parent directory '$containerParent'.
-         |$arrayIdentifier=(
-         |  "$project"   # project to use if requester pays
-         |  "$maxAttempts" # max transfer attempts
-         |  "${containerParent.ensureSlashed}" # container parent directory
-         |  $entries
-         |)
-         |
-         |localize_files "$${$arrayIdentifier[@]}"
+        s"""
+           |# Localize files from source bucket '$bucket' to container parent directory '$containerParent'.
+           |$arrayIdentifier=(
+           |  "$project"   # project to use if requester pays
+           |  "$maxAttempts" # max transfer attempts
+           |  "${containerParent.ensureSlashed}" # container parent directory
+           |  $entries
+           |)
+           |
+           |localize_files "$${$arrayIdentifier[@]}"
        """.stripMargin
     }
 
     val filesWithDifferentNamesTransferBundles = filesWithDifferentNames map { f =>
-      val arrayIdentifier = s"singleton_file_to_localize_" + DigestUtils.md5Hex(f.cloudPath.pathAsString + f.containerPath.pathAsString)
+      val arrayIdentifier =
+        s"singleton_file_to_localize_" + DigestUtils.md5Hex(f.cloudPath.pathAsString + f.containerPath.pathAsString)
       s"""
          |# Localize singleton file '${f.cloudPath.pathAsString}' to '${f.containerPath.pathAsString}'.
          |$arrayIdentifier=(
@@ -319,27 +359,31 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
     // Only write a transfer bundle for directories if there are directories to be localized. Emptiness isn't a concern
     // for files since there is always at least the command script to be localized.
-    val directoryTransferBundle = if (directories.isEmpty) "" else {
-      val entries = directories flatMap { i => List(i.cloudPath, i.containerPath) } mkString("\"", "\"\n|  \"", "\"")
+    val directoryTransferBundle =
+      if (directories.isEmpty) ""
+      else {
+        val entries = directories flatMap { i => List(i.cloudPath, i.containerPath) } mkString ("\"", "\"\n|  \"", "\"")
 
-      val arrayIdentifier = s"directories_to_localize_" + DigestUtils.md5Hex(bucket)
+        val arrayIdentifier = s"directories_to_localize_" + DigestUtils.md5Hex(bucket)
 
-      s"""
-         |# Directories from source bucket '$bucket'.
-         |$arrayIdentifier=(
-         |  "$project"    # project to use if requester pays
-         |  "$maxAttempts" # max transfer attempts
-         |  $entries
-         |)
-         |
-         |localize_directories "$${$arrayIdentifier[@]}"
+        s"""
+           |# Directories from source bucket '$bucket'.
+           |$arrayIdentifier=(
+           |  "$project"    # project to use if requester pays
+           |  "$maxAttempts" # max transfer attempts
+           |  $entries
+           |)
+           |
+           |localize_directories "$${$arrayIdentifier[@]}"
        """.stripMargin
-    }
+      }
 
     (directoryTransferBundle :: (filesWithSameNamesTransferBundles ++ filesWithDifferentNamesTransferBundles)) mkString "\n\n"
   }
 
-  private def gcsDelocalizationTransferBundle[T <: GcpBatchOutput](transferConfiguration: GcsTransferConfiguration)(bucket: String, outputs: NonEmptyList[T]): String = {
+  private def gcsDelocalizationTransferBundle[T <: GcpBatchOutput](
+    transferConfiguration: GcsTransferConfiguration
+  )(bucket: String, outputs: NonEmptyList[T]): String = {
     val project = outputs.head.cloudPath.asInstanceOf[GcsPath].projectId
     val maxAttempts = transferConfiguration.transferAttempts
 
@@ -350,14 +394,16 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         case _: GcpBatchDirectoryOutput => "directory" // a primary directory
       }
 
-      val optional = Option(output) collectFirst { case o: GcpBatchFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
+      val optional = Option(output) collectFirst {
+        case o: GcpBatchFileOutput if o.secondary || o.optional => "optional"
+      } getOrElse "required"
       val contentType = output.contentType.map(_.toString).getOrElse("")
 
       List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
-    } mkString("\"", "\"\n|  \"", "\"")
+    } mkString ("\"", "\"\n|  \"", "\"")
 
-    val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(
-      "parallel_composite_upload_threshold", transferConfiguration.parallelCompositeUploadThreshold)
+    val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions
+      .getOrElse("parallel_composite_upload_threshold", transferConfiguration.parallelCompositeUploadThreshold)
 
     // Use a digest as bucket names can contain characters that are not legal in bash identifiers.
     val arrayIdentifier = s"delocalize_" + DigestUtils.md5Hex(bucket)
@@ -374,13 +420,12 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       """.stripMargin
   }
 
-  private def bracketTransfersWithMessages(activity: String)(transferBody: String): String = {
+  private def bracketTransfersWithMessages(activity: String)(transferBody: String): String =
     List(
       s"timestamped_message '$activity script execution started...'",
       transferBody,
       s"timestamped_message '$activity script execution complete.'"
     ) mkString "\n"
-  }
 
   def uploadDrsLocalizationManifest(createParameters: CreateBatchJobParameters, cloudPath: Path): Future[Unit] = {
     val content = generateDrsLocalizerManifest(createParameters.inputOutputParameters.fileInputParameters)
@@ -390,21 +435,24 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       Future.unit
   }
 
-  def uploadScriptFile(): Future[Unit] = {
+  def uploadScriptFile(): Future[Unit] =
     commandScriptContents
       .fold(
-        errors => Future
-          .failed(new RuntimeException(errors
-            .toList
-            .mkString(", "))),
+        errors =>
+          Future
+            .failed(
+              new RuntimeException(
+                errors.toList
+                  .mkString(", ")
+              )
+            ),
         asyncIo
-          .writeAsync(jobPaths
-            .script, _, Seq(CloudStorageOptions.withMimeType("text/plain")))
+          .writeAsync(jobPaths.script, _, Seq(CloudStorageOptions.withMimeType("text/plain")))
       )
-  }
 
   def sendGoogleLabelsToMetadata(customLabels: Seq[GcpLabel]): Unit = {
-    lazy val backendLabelEvents: Map[String, String] = ((backendLabels ++ customLabels) map { l => s"${CallMetadataKeys.BackendLabels}:${l.key}" -> l.value }).toMap
+    lazy val backendLabelEvents: Map[String, String] =
+      ((backendLabels ++ customLabels) map { l => s"${CallMetadataKeys.BackendLabels}:${l.key}" -> l.value }).toMap
     tellMetadata(backendLabelEvents)
   }
 
@@ -415,34 +463,37 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       case Failure(OptionNotFoundException(_)) => false
       case Failure(f) =>
         // Should not happen, this case should have been screened for and fast-failed during workflow materialization.
-        log.error(f, s"Programmer error: unexpected failure attempting to read value for workflow option '$optionName' as a Boolean")
+        log.error(
+          f,
+          s"Programmer error: unexpected failure attempting to read value for workflow option '$optionName' as a Boolean"
+        )
         false
     }
   }
 
-
-  def getReferenceInputsToMountedPathsOpt(createParameters: CreateBatchJobParameters): Option[Map[GcpBatchInput, String]] = {
+  def getReferenceInputsToMountedPathsOpt(
+    createParameters: CreateBatchJobParameters
+  ): Option[Map[GcpBatchInput, String]] =
     if (useReferenceDisks) {
-      batchAttributes
-        .referenceFileToDiskImageMappingOpt
+      batchAttributes.referenceFileToDiskImageMappingOpt
         .map(getReferenceInputsToMountedPathMappings(_, createParameters.inputOutputParameters.fileInputParameters))
     } else {
       None
     }
-  }
 
   private def generateGcsLocalizationScript(inputs: List[GcpBatchInput],
-                                            referenceInputsToMountedPathsOpt: Option[Map[GcpBatchInput, String]])
-                                           (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+                                            referenceInputsToMountedPathsOpt: Option[Map[GcpBatchInput, String]]
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
     import cromwell.backend.google.batch.runnable.RunnableUtils.shellEscaped
 
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
-        referenceInputsToMountedPaths map {
-          case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
+        referenceInputsToMountedPaths map { case (input, absolutePathOnRefDisk) =>
+          s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(
+              absolutePathOnRefDisk
+            )} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }
 
@@ -464,9 +515,9 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       }
 
     val regularFilesLocalizationScript = {
-      val regularFiles = referenceInputsToMountedPathsOpt.map(maybeReferenceInputsToMountedPaths =>
-        inputs diff maybeReferenceInputsToMountedPaths.keySet.toList
-      ).getOrElse(inputs)
+      val regularFiles = referenceInputsToMountedPathsOpt
+        .map(maybeReferenceInputsToMountedPaths => inputs diff maybeReferenceInputsToMountedPaths.keySet.toList)
+        .getOrElse(inputs)
       if (regularFiles.nonEmpty) {
         val bundleFunction = (gcsLocalizationTransferBundle(gcsTransferConfiguration) _).tupled
         generateGcsTransferScript(regularFiles, bundleFunction)
@@ -485,12 +536,16 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     combinedLocalizationScript |> bracketTransfersWithMessages("Localization")
   }
 
-  private def generateGcsDelocalizationScript(outputs: List[GcpBatchOutput])(implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  private def generateGcsDelocalizationScript(
+    outputs: List[GcpBatchOutput]
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     val bundleFunction = (gcsDelocalizationTransferBundle(gcsTransferConfiguration) _).tupled
     generateGcsTransferScript(outputs, bundleFunction) |> bracketTransfersWithMessages("Delocalization")
   }
 
-  private def generateGcsTransferScript[T <: BatchParameter](items: List[T], bundleFunction: ((String, NonEmptyList[T])) => String): String = {
+  private def generateGcsTransferScript[T <: BatchParameter](items: List[T],
+                                                             bundleFunction: ((String, NonEmptyList[T])) => String
+  ): String = {
     val gcsItems = items collect { case i if i.cloudPath.isInstanceOf[GcsPath] => i }
     groupParametersByGcsBucket(gcsItems) map bundleFunction mkString "\n"
   }
@@ -499,24 +554,35 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
                                   cloudPath: Path,
                                   transferLibraryContainerPath: Path,
                                   gcsTransferConfiguration: GcsTransferConfiguration,
-                                  referenceInputsToMountedPathsOpt: Option[Map[GcpBatchInput, String]]): Future[Unit] = {
-    val content = generateGcsLocalizationScript(createParameters.inputOutputParameters.fileInputParameters, referenceInputsToMountedPathsOpt)(gcsTransferConfiguration)
-    asyncIo.writeAsync(cloudPath, s"source '$transferLibraryContainerPath'\n\n" + content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+                                  referenceInputsToMountedPathsOpt: Option[Map[GcpBatchInput, String]]
+  ): Future[Unit] = {
+    val content = generateGcsLocalizationScript(createParameters.inputOutputParameters.fileInputParameters,
+                                                referenceInputsToMountedPathsOpt
+    )(gcsTransferConfiguration)
+    asyncIo.writeAsync(cloudPath,
+                       s"source '$transferLibraryContainerPath'\n\n" + content,
+                       Seq(CloudStorageOptions.withMimeType("text/plain"))
+    )
   }
 
   def uploadGcsDelocalizationScript(createParameters: CreateBatchJobParameters,
                                     cloudPath: Path,
                                     transferLibraryContainerPath: Path,
-                                    gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = {
-    val content = generateGcsDelocalizationScript(createParameters.inputOutputParameters.fileOutputParameters)(gcsTransferConfiguration)
-    asyncIo.writeAsync(cloudPath, s"source '$transferLibraryContainerPath'\n\n" + content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+                                    gcsTransferConfiguration: GcsTransferConfiguration
+  ): Future[Unit] = {
+    val content = generateGcsDelocalizationScript(createParameters.inputOutputParameters.fileOutputParameters)(
+      gcsTransferConfiguration
+    )
+    asyncIo.writeAsync(cloudPath,
+                       s"source '$transferLibraryContainerPath'\n\n" + content,
+                       Seq(CloudStorageOptions.withMimeType("text/plain"))
+    )
   }
 
-
   // TAG DISK
   private def createBatchParameters(inputOutputParameters: InputOutputParameters,
-                                       customLabels: Seq[GcpLabel],
-                                      ): CreateBatchJobParameters = {
+                                    customLabels: Seq[GcpLabel]
+  ): CreateBatchJobParameters =
     standardParams.backendInitializationDataOption match {
       case Some(data: GcpBackendInitializationData) =>
         val dockerKeyAndToken: Option[CreateBatchDockerKeyAndToken] = for {
@@ -525,36 +591,39 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         } yield CreateBatchDockerKeyAndToken(key, token)
 
         /*
-           * Right now this doesn't cost anything, because sizeOption returns the size if it was previously already fetched
-           * for some reason (expression evaluation for instance), but otherwise does not retrieve it and returns None.
-           * In CWL-land we tend to be aggressive in pre-fetching the size in order to be able to evaluate JS expressions,
-           * but less in WDL as we can get it last minute and on demand because size is a WDL function, whereas in CWL
-           * we don't inspect the JS to know if size is called and therefore always pre-fetch it.
-           *
-           * We could decide to call withSize before in which case we would retrieve the size for all files and have
-           * a guaranteed more accurate total size, but there might be performance impacts ?
-           */
+         * Right now this doesn't cost anything, because sizeOption returns the size if it was previously already fetched
+         * for some reason (expression evaluation for instance), but otherwise does not retrieve it and returns None.
+         * In CWL-land we tend to be aggressive in pre-fetching the size in order to be able to evaluate JS expressions,
+         * but less in WDL as we can get it last minute and on demand because size is a WDL function, whereas in CWL
+         * we don't inspect the JS to know if size is called and therefore always pre-fetch it.
+         *
+         * We could decide to call withSize before in which case we would retrieve the size for all files and have
+         * a guaranteed more accurate total size, but there might be performance impacts ?
+         */
         val inputFileSize = Option(callInputFiles.values.flatMap(_.flatMap(_.sizeOption)).sum)
 
         // Attempt to adjust the disk size by taking into account the size of input files
-        val adjustedSizeDisks = inputFileSize.map(size => MemorySize.apply(size.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB)) map { inputFileSizeInformation =>
-          runtimeAttributes.disks.adjustWorkingDiskWithNewMin(
-            inputFileSizeInformation,
-            jobLogger.info(s"Adjusted working disk size to ${inputFileSizeInformation.amount} GB to account for input files")
-          )
-        } getOrElse runtimeAttributes.disks
+        val adjustedSizeDisks =
+          inputFileSize.map(size => MemorySize.apply(size.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB)) map {
+            inputFileSizeInformation =>
+              runtimeAttributes.disks.adjustWorkingDiskWithNewMin(
+                inputFileSizeInformation,
+                jobLogger.info(
+                  s"Adjusted working disk size to ${inputFileSizeInformation.amount} GB to account for input files"
+                )
+              )
+          } getOrElse runtimeAttributes.disks
 
         val inputFilePaths = inputOutputParameters.jobInputParameters.map(_.cloudPath.pathAsString).toSet
 
         val referenceDisksToMount =
           batchAttributes.referenceFileToDiskImageMappingOpt.map(getReferenceDisksToMount(_, inputFilePaths))
 
-        val dockerhubCredentials: (String, String) = {
+        val dockerhubCredentials: (String, String) =
           new String(Base64.getDecoder.decode(batchAttributes.dockerhubToken), "UTF-8").split(":", 2) match {
             case Array(username, password) => (username, password)
             case _ => ("", "")
           }
-        }
 
         val workflowOptions = workflowDescriptor.workflowOptions
 
@@ -564,7 +633,7 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
           workflowPaths = workflowPaths,
           commandDirectory = commandDirectory,
           workingDisk = workingDisk,
-          localMonitoringImageScriptPath = localMonitoringImageScriptPath,
+          localMonitoringImageScriptPath = localMonitoringImageScriptPath
         )
 
         val checkpointingConfiguration =
@@ -614,9 +683,10 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       case None =>
         throw new RuntimeException("No batch backend initialization data found?")
     }
-  }
 
-  protected def relativePathAndAttachedDisk(path: String, disks: Seq[GcpBatchAttachedDisk]): (Path, GcpBatchAttachedDisk) = {
+  protected def relativePathAndAttachedDisk(path: String,
+                                            disks: Seq[GcpBatchAttachedDisk]
+  ): (Path, GcpBatchAttachedDisk) = {
     val absolutePath = DefaultPathBuilder.get(path) match {
       case p if !p.isAbsolute => GcpBatchWorkingDisk.MountPoint.resolve(p)
       case p => p
@@ -625,13 +695,14 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     disks.find(d => absolutePath.startsWith(d.mountPoint)) match {
       case Some(disk) => (disk.mountPoint.relativize(absolutePath), disk)
       case None =>
-        throw new Exception(s"Absolute path $path doesn't appear to be under any mount points: ${disks.map(_.toString).mkString(", ")}")
+        throw new Exception(
+          s"Absolute path $path doesn't appear to be under any mount points: ${disks.map(_.toString).mkString(", ")}"
+        )
     }
   }
 
-  protected def makeSafeReferenceName(referenceName: String): String = {
+  protected def makeSafeReferenceName(referenceName: String): String =
     if (referenceName.length <= 127) referenceName else referenceName.md5Sum
-  }
 
   // De-localize the glob directory as a GcpBatchDirectoryOutput instead of using * pattern match
   protected def generateGlobFileOutputs(womFile: WomGlobFile): List[GcpBatchOutput] = {
@@ -646,9 +717,23 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     // We need both the glob directory and the glob list:
     List(
       // The glob directory:
-      GcpBatchDirectoryOutput(makeSafeReferenceName(globDirectory), gcsGlobDirectoryDestinationPath, DefaultPathBuilder.get(globDirectory), globDirectoryDisk, optional = false, secondary = false),
+      GcpBatchDirectoryOutput(
+        makeSafeReferenceName(globDirectory),
+        gcsGlobDirectoryDestinationPath,
+        DefaultPathBuilder.get(globDirectory),
+        globDirectoryDisk,
+        optional = false,
+        secondary = false
+      ),
       // The glob list file:
-      GcpBatchFileOutput(makeSafeReferenceName(globListFile), gcsGlobListFileDestinationPath, DefaultPathBuilder.get(globListFile), globDirectoryDisk, optional = false, secondary = false)
+      GcpBatchFileOutput(
+        makeSafeReferenceName(globListFile),
+        gcsGlobListFileDestinationPath,
+        DefaultPathBuilder.get(globListFile),
+        globDirectoryDisk,
+        optional = false,
+        secondary = false
+      )
     )
   }
 
@@ -656,23 +741,22 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   lazy val localMonitoringLogPath: Path = DefaultPathBuilder.get(gcpBatchCallPaths.batchMonitoringLogFilename)
   lazy val localMonitoringScriptPath: Path = DefaultPathBuilder.get(gcpBatchCallPaths.batchMonitoringScriptFilename)
 
-  lazy val monitoringScript: Option[GcpBatchFileInput] = {
+  lazy val monitoringScript: Option[GcpBatchFileInput] =
     gcpBatchCallPaths.workflowPaths.monitoringScriptPath map { path =>
       GcpBatchFileInput(s"$batchMonitoringParamName-in", path, localMonitoringScriptPath, workingDisk)
     }
-  }
 
-  private val DockerMonitoringLogPath: Path = GcpBatchWorkingDisk.MountPoint.resolve(gcpBatchCallPaths.batchMonitoringLogFilename)
-  private val DockerMonitoringScriptPath: Path = GcpBatchWorkingDisk.MountPoint.resolve(gcpBatchCallPaths.batchMonitoringScriptFilename)
+  private val DockerMonitoringLogPath: Path =
+    GcpBatchWorkingDisk.MountPoint.resolve(gcpBatchCallPaths.batchMonitoringLogFilename)
+  private val DockerMonitoringScriptPath: Path =
+    GcpBatchWorkingDisk.MountPoint.resolve(gcpBatchCallPaths.batchMonitoringScriptFilename)
 
-  override def scriptPreamble: ErrorOr[ScriptPreambleData] = {
+  override def scriptPreamble: ErrorOr[ScriptPreambleData] =
     if (monitoringOutput.isDefined)
-      ScriptPreambleData(
-      s"""|touch $DockerMonitoringLogPath
-          |chmod u+x $DockerMonitoringScriptPath
-          |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin).valid
+      ScriptPreambleData(s"""|touch $DockerMonitoringLogPath
+                             |chmod u+x $DockerMonitoringScriptPath
+                             |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin).valid
     else ScriptPreambleData("").valid
-  }
 
   private[actors] def generateInputs(jobDescriptor: BackendJobDescriptor): Set[GcpBatchInput] = {
     // We need to tell PAPI about files that were created as part of command instantiation (these need to be defined
@@ -680,38 +764,57 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     // md5's of their paths.
     val writeFunctionFiles = instantiatedCommand.createdFiles map { f => f.file.value.md5SumShort -> List(f) } toMap
 
-    val writeFunctionInputs = writeFunctionFiles flatMap {
-      case (name, files) => gcpBatchInputsFromWomFiles(name, files.map(_.file), files.map(localizationPath), jobDescriptor)
+    val writeFunctionInputs = writeFunctionFiles flatMap { case (name, files) =>
+      gcpBatchInputsFromWomFiles(name, files.map(_.file), files.map(localizationPath), jobDescriptor)
     }
 
-    val callInputInputs = callInputFiles flatMap {
-      case (name, files) => gcpBatchInputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor)
+    val callInputInputs = callInputFiles flatMap { case (name, files) =>
+      gcpBatchInputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor)
     }
 
     (writeFunctionInputs ++ callInputInputs).toSet
   }
 
   // Simply create a GcpBatchDirectoryOutput instead of globbing
-  protected def generateUnlistedDirectoryOutputs(unlistedDirectory: WomUnlistedDirectory, fileEvaluation: FileEvaluation): List[GcpBatchOutput] = {
+  protected def generateUnlistedDirectoryOutputs(unlistedDirectory: WomUnlistedDirectory,
+                                                 fileEvaluation: FileEvaluation
+  ): List[GcpBatchOutput] = {
     val destination = callRootPath.resolve(unlistedDirectory.value.stripPrefix("/"))
     val (relpath, disk) = relativePathAndAttachedDisk(unlistedDirectory.value, runtimeAttributes.disks)
-    val directoryOutput = GcpBatchDirectoryOutput(makeSafeReferenceName(unlistedDirectory.value), destination, relpath, disk, fileEvaluation.optional, fileEvaluation.secondary)
+    val directoryOutput = GcpBatchDirectoryOutput(makeSafeReferenceName(unlistedDirectory.value),
+                                                  destination,
+                                                  relpath,
+                                                  disk,
+                                                  fileEvaluation.optional,
+                                                  fileEvaluation.secondary
+    )
     List(directoryOutput)
   }
 
-  private def maybeListedDirectoryToBatchParameters(inputName: String, womMaybeListedDirectory: WomMaybeListedDirectory, localPath: String) = womMaybeListedDirectory match {
+  private def maybeListedDirectoryToBatchParameters(inputName: String,
+                                                    womMaybeListedDirectory: WomMaybeListedDirectory,
+                                                    localPath: String
+  ) = womMaybeListedDirectory match {
     // If there is a path, simply localize as a directory
     case WomMaybeListedDirectory(Some(path), _, _, _) =>
       List(GcpBatchDirectoryInput(inputName, getPath(path).get, DefaultPathBuilder.get(localPath), workingDisk))
 
     // If there is a listing, recurse and call gcpBatchInputsFromWomFiles on all the listed files
     case WomMaybeListedDirectory(_, Some(listing), _, _) if listing.nonEmpty =>
-      listing.flatMap({
+      listing.flatMap {
         case womFile: WomFile if isAdHocFile(womFile) =>
-          gcpBatchInputsFromWomFiles(makeSafeReferenceName(womFile.valueString), List(womFile), List(fileName(womFile)), jobDescriptor)
+          gcpBatchInputsFromWomFiles(makeSafeReferenceName(womFile.valueString),
+                                     List(womFile),
+                                     List(fileName(womFile)),
+                                     jobDescriptor
+          )
         case womFile: WomFile =>
-          gcpBatchInputsFromWomFiles(makeSafeReferenceName(womFile.valueString), List(womFile), List(relativeLocalizationPath(womFile)), jobDescriptor)
-      })
+          gcpBatchInputsFromWomFiles(makeSafeReferenceName(womFile.valueString),
+                                     List(womFile),
+                                     List(relativeLocalizationPath(womFile)),
+                                     jobDescriptor
+          )
+      }
     case _ => List.empty
   }
 
@@ -719,58 +822,69 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     val (relpath, disk) = relativePathAndAttachedDisk(womFile.value, runtimeAttributes.disks)
     // If the file is on a custom mount point, resolve it so that the full mount path will show up in the cloud path
     // For the default one (cromwell_root), the expectation is that it does not appear
-    val mountedPath = if (!disk.mountPoint.isSamePathAs(GcpBatchWorkingDisk.Default.mountPoint)) disk.mountPoint.resolve(relpath) else relpath
+    val mountedPath =
+      if (!disk.mountPoint.isSamePathAs(GcpBatchWorkingDisk.Default.mountPoint)) disk.mountPoint.resolve(relpath)
+      else relpath
     // Normalize the local path (to get rid of ".." and "."). Also strip any potential leading / so that it gets appended to the call root
     val normalizedPath = mountedPath.normalize().pathAsString.stripPrefix("/")
     val destination = callRootPath.resolve(normalizedPath)
-    val batchFileOutput = GcpBatchFileOutput(makeSafeReferenceName(womFile.value), destination, relpath, disk, fileEvaluation.optional, fileEvaluation.secondary)
+    val batchFileOutput = GcpBatchFileOutput(makeSafeReferenceName(womFile.value),
+                                             destination,
+                                             relpath,
+                                             disk,
+                                             fileEvaluation.optional,
+                                             fileEvaluation.secondary
+    )
     List(batchFileOutput)
   }
 
   private[actors] def generateOutputs(jobDescriptor: BackendJobDescriptor): Set[GcpBatchOutput] = {
-    def evaluateFiles(output: OutputDefinition): List[FileEvaluation] = {
+    def evaluateFiles(output: OutputDefinition): List[FileEvaluation] =
       Try(
         output.expression.evaluateFiles(jobDescriptor.localInputs, NoIoFunctionSet, output.womType).map(_.toList)
       ).getOrElse(List.empty[FileEvaluation].validNel)
         .getOrElse(List.empty)
-    }
 
-    def relativeFileEvaluation(evaluation: FileEvaluation): FileEvaluation = {
+    def relativeFileEvaluation(evaluation: FileEvaluation): FileEvaluation =
       evaluation.copy(file = relativeLocalizationPath(evaluation.file))
-    }
 
     val womFileOutputs = jobDescriptor.taskCall.callable.outputs.flatMap(evaluateFiles) map relativeFileEvaluation
 
     val outputs: Seq[GcpBatchOutput] = womFileOutputs.distinct flatMap { fileEvaluation =>
       fileEvaluation.file.flattenFiles flatMap {
-        case unlistedDirectory: WomUnlistedDirectory => generateUnlistedDirectoryOutputs(unlistedDirectory, fileEvaluation)
+        case unlistedDirectory: WomUnlistedDirectory =>
+          generateUnlistedDirectoryOutputs(unlistedDirectory, fileEvaluation)
         case singleFile: WomSingleFile => generateSingleFileOutputs(singleFile, fileEvaluation)
         case globFile: WomGlobFile => generateGlobFileOutputs(globFile) // Assumes optional = false for globs.
       }
     }
 
-    val additionalGlobOutput = jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateGlobFileOutputs).toSet
+    val additionalGlobOutput =
+      jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateGlobFileOutputs).toSet
 
     outputs.toSet ++ additionalGlobOutput
   }
 
   protected def uploadGcsTransferLibrary(createBatchParameters: CreateBatchJobParameters,
                                          cloudPath: Path,
-                                         gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = {
-
+                                         gcsTransferConfiguration: GcsTransferConfiguration
+  ): Future[Unit] =
     asyncIo.writeAsync(cloudPath, gcsTransferLibrary, Seq(CloudStorageOptions.withMimeType("text/plain")))
-  }
-
 
   lazy val monitoringOutput: Option[GcpBatchFileOutput] = monitoringScript map { _ =>
-    GcpBatchFileOutput(s"$batchMonitoringParamName-out",
-      gcpBatchCallPaths.batchMonitoringLogPath, localMonitoringLogPath, workingDisk, optional = false, secondary = false,
-      contentType = plainTextContentType)
+    GcpBatchFileOutput(
+      s"$batchMonitoringParamName-out",
+      gcpBatchCallPaths.batchMonitoringLogPath,
+      localMonitoringLogPath,
+      workingDisk,
+      optional = false,
+      secondary = false,
+      contentType = plainTextContentType
+    )
   }
 
   override lazy val commandDirectory: Path = GcpBatchWorkingDisk.MountPoint
 
-
   // Primary entry point for cromwell to run GCP Batch job
   override def executeAsync(): Future[ExecutionHandle] = {
 
@@ -778,8 +892,15 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     def evaluateRuntimeAttributes = Future.fromTry(Try(runtimeAttributes))
 
     def generateInputOutputParameters: Future[InputOutputParameters] = Future.fromTry(Try {
-      val rcFileOutput = GcpBatchFileOutput(returnCodeFilename, returnCodeGcsPath, DefaultPathBuilder.get(returnCodeFilename), workingDisk, optional = false, secondary = false,
-        contentType = plainTextContentType)
+      val rcFileOutput = GcpBatchFileOutput(
+        returnCodeFilename,
+        returnCodeGcsPath,
+        DefaultPathBuilder.get(returnCodeFilename),
+        workingDisk,
+        optional = false,
+        secondary = false,
+        contentType = plainTextContentType
+      )
 
       val memoryRetryRCFileOutput = GcpBatchFileOutput(
         memoryRetryRCFilename,
@@ -799,8 +920,16 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         StandardStream("stdout", _.output),
         StandardStream("stderr", _.error)
       ) map { s =>
-        GcpBatchFileOutput(s.name, returnCodeGcsPath.sibling(s.filename), DefaultPathBuilder.get(s.filename),
-          workingDisk, optional = false, secondary = false, uploadPeriod = batchAttributes.logFlushPeriod, contentType = plainTextContentType)
+        GcpBatchFileOutput(
+          s.name,
+          returnCodeGcsPath.sibling(s.filename),
+          DefaultPathBuilder.get(s.filename),
+          workingDisk,
+          optional = false,
+          secondary = false,
+          uploadPeriod = batchAttributes.logFlushPeriod,
+          contentType = plainTextContentType
+        )
       }
 
       InputOutputParameters(
@@ -820,13 +949,13 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
     })
 
-
     val gcpBatchParameters = CreateGcpBatchParameters(
       jobDescriptor = jobDescriptor,
       runtimeAttributes = runtimeAttributes,
       batchAttributes = batchAttributes,
       projectId = batchAttributes.project,
-      region = batchAttributes.location)
+      region = batchAttributes.location
+    )
 
     val runBatchResponse = for {
       _ <- evaluateRuntimeAttributes
@@ -842,9 +971,18 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       _ <- uploadGcsTransferLibrary(createParameters, gcsTransferLibraryCloudPath, gcsTransferConfiguration)
       gcsLocalizationScriptCloudPath = jobPaths.callExecutionRoot / GcpBatchJobPaths.GcsLocalizationScriptName
       referenceInputsToMountedPathsOpt = getReferenceInputsToMountedPathsOpt(createParameters)
-      _ <- uploadGcsLocalizationScript(createParameters, gcsLocalizationScriptCloudPath, transferLibraryContainerPath, gcsTransferConfiguration, referenceInputsToMountedPathsOpt)
+      _ <- uploadGcsLocalizationScript(createParameters,
+                                       gcsLocalizationScriptCloudPath,
+                                       transferLibraryContainerPath,
+                                       gcsTransferConfiguration,
+                                       referenceInputsToMountedPathsOpt
+      )
       gcsDelocalizationScriptCloudPath = jobPaths.callExecutionRoot / GcpBatchJobPaths.GcsDelocalizationScriptName
-      _ <- uploadGcsDelocalizationScript(createParameters, gcsDelocalizationScriptCloudPath, transferLibraryContainerPath, gcsTransferConfiguration)
+      _ <- uploadGcsDelocalizationScript(createParameters,
+                                         gcsDelocalizationScriptCloudPath,
+                                         transferLibraryContainerPath,
+                                         gcsTransferConfiguration
+      )
       _ = createParameters.privateDockerKeyAndEncryptedToken.isDefined
       jobName = "job-" + java.util.UUID.randomUUID.toString
       request = GcpBatchRequest(workflowId, createParameters, jobName = jobName, gcpBatchParameters)
@@ -856,34 +994,37 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
     // TODO: Handle when the job gets aborted before it starts being processed
     runBatchResponse.map { runId =>
-      PendingExecutionHandle(
-        jobDescriptor = jobDescriptor,
-        pendingJob = runId,
-        runInfo = Option(Run(runId)),
-        previousState = None)
+      PendingExecutionHandle(jobDescriptor = jobDescriptor,
+                             pendingJob = runId,
+                             runInfo = Option(Run(runId)),
+                             previousState = None
+      )
     }
   }
 
   override def reconnectAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] = {
     log.info("reconnect async runs") // in for debugging remove later
-    val handle = PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState](jobDescriptor, jobId, Option(Run(jobId)), previousState = None)
+    val handle = PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState](
+      jobDescriptor,
+      jobId,
+      Option(Run(jobId)),
+      previousState = None
+    )
     Future.successful(handle)
   }
 
-  override lazy val pollBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(5
-    .second, 5
-    .minutes, 1.1)
+  override lazy val pollBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(5.second, 5.minutes, 1.1)
 
-  override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(
-    initialInterval = 5
-      .seconds, maxInterval = 20
-      .seconds, multiplier = 1.1)
+  override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff =
+    SimpleExponentialBackoff(initialInterval = 5.seconds, maxInterval = 20.seconds, multiplier = 1.1)
 
-  override lazy val runtimeEnvironment: RuntimeEnvironment = {
-    RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes, GcpBatchWorkingDisk.MountPoint, GcpBatchWorkingDisk.MountPoint)(standardParams.minimumRuntimeSettings)
-  }
+  override lazy val runtimeEnvironment: RuntimeEnvironment =
+    RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes,
+                              GcpBatchWorkingDisk.MountPoint,
+                              GcpBatchWorkingDisk.MountPoint
+    )(standardParams.minimumRuntimeSettings)
 
-  protected def sendIncrementMetricsForReferenceFiles(referenceInputFilesOpt: Option[Set[GcpBatchInput]]): Unit = {
+  protected def sendIncrementMetricsForReferenceFiles(referenceInputFilesOpt: Option[Set[GcpBatchInput]]): Unit =
     referenceInputFilesOpt match {
       case Some(referenceInputFiles) =>
         referenceInputFiles.foreach { referenceInputFile =>
@@ -892,18 +1033,20 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       case _ =>
       // do nothing - reference disks feature is either not configured in Cromwell or disabled in workflow options
     }
-  }
 
   protected def sendIncrementMetricsForDockerImageCache(dockerImageCacheDiskOpt: Option[String],
                                                         dockerImageAsSpecifiedByUser: String,
-                                                        isDockerImageCacheUsageRequested: Boolean): Unit = {
+                                                        isDockerImageCacheUsageRequested: Boolean
+  ): Unit =
     (isDockerImageCacheUsageRequested, dockerImageCacheDiskOpt) match {
-      case (true, None) => increment(NonEmptyList("docker", List("image", "cache", "image_not_in_cache", dockerImageAsSpecifiedByUser)))
-      case (true, Some(_)) => increment(NonEmptyList("docker", List("image", "cache", "used_image_from_cache", dockerImageAsSpecifiedByUser)))
-      case (false, Some(_)) => increment(NonEmptyList("docker", List("image", "cache", "cached_image_not_used", dockerImageAsSpecifiedByUser)))
+      case (true, None) =>
+        increment(NonEmptyList("docker", List("image", "cache", "image_not_in_cache", dockerImageAsSpecifiedByUser)))
+      case (true, Some(_)) =>
+        increment(NonEmptyList("docker", List("image", "cache", "used_image_from_cache", dockerImageAsSpecifiedByUser)))
+      case (false, Some(_)) =>
+        increment(NonEmptyList("docker", List("image", "cache", "cached_image_not_used", dockerImageAsSpecifiedByUser)))
       case _ => // docker image cache not requested and image is not in cache anyway - do nothing
     }
-  }
 
   override def pollStatusAsync(handle: GcpBatchPendingExecutionHandle): Future[RunStatus] = {
     // yes, we use the whole jobName as the id
@@ -917,7 +1060,7 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     } yield RunStatus.fromJobStatus(job.getStatus.getState)
   }
 
-  override def isTerminal(runStatus: RunStatus): Boolean = {
+  override def isTerminal(runStatus: RunStatus): Boolean =
     runStatus match {
       case _: RunStatus.TerminalRunStatus =>
         log.info(s"isTerminal match terminal run status with $runStatus")
@@ -926,9 +1069,8 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         log.info(f"isTerminal match _ running with status $other")
         false
     }
-  }
 
-  override def isDone(runStatus: RunStatus): Boolean = {
+  override def isDone(runStatus: RunStatus): Boolean =
     runStatus match {
       case _: RunStatus.Succeeded =>
         log.info("GCP batch job succeeded matched isDone")
@@ -938,11 +1080,12 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         false
       case _ =>
         log.info(s"did not match isDone: $runStatus")
-        throw new RuntimeException(s"Cromwell programmer blunder: isDone was called on an incomplete RunStatus ($runStatus).")
+        throw new RuntimeException(
+          s"Cromwell programmer blunder: isDone was called on an incomplete RunStatus ($runStatus)."
+        )
     }
-  }
 
-  override def getTerminalEvents(runStatus: RunStatus): Seq[ExecutionEvent] = {
+  override def getTerminalEvents(runStatus: RunStatus): Seq[ExecutionEvent] =
     runStatus match {
       case t: RunStatus.TerminalRunStatus =>
         log.warning(s"Tried to get terminal events on a terminal status without events: $runStatus")
@@ -951,46 +1094,40 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       case unknown =>
         throw new RuntimeException(s"handleExecutionSuccess not called with RunStatus.Success. Instead got $unknown")
     }
-  }
 
-  override lazy val startMetadataKeyValues: Map[String, Any] = super[GcpBatchJobCachingActorHelper].startMetadataKeyValues
+  override lazy val startMetadataKeyValues: Map[String, Any] =
+    super[GcpBatchJobCachingActorHelper].startMetadataKeyValues
 
   // TODO: review sending machine and Instance type
-  override def getTerminalMetadata(runStatus: RunStatus): Map[String, Any] = {
+  override def getTerminalMetadata(runStatus: RunStatus): Map[String, Any] =
     runStatus match {
       case _: TerminalRunStatus => Map()
       case unknown => throw new RuntimeException(s"Attempt to get terminal metadata from non terminal status: $unknown")
     }
-  }
 
-  override def mapOutputWomFile(womFile: WomFile): WomFile = {
+  override def mapOutputWomFile(womFile: WomFile): WomFile =
     womFileToGcsPath(generateOutputs(jobDescriptor))(womFile)
-  }
-
 
   override def globParentDirectory(womGlobFile: WomGlobFile): Path = {
     val (_, disk) = relativePathAndAttachedDisk(womGlobFile.value, runtimeAttributes.disks)
     disk.mountPoint
   }
 
-
-  protected def googleProject(descriptor: BackendWorkflowDescriptor): String = {
+  protected def googleProject(descriptor: BackendWorkflowDescriptor): String =
     descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleProject, batchAttributes.project)
-  }
 
-  protected def computeServiceAccount(descriptor: BackendWorkflowDescriptor): String = {
-    descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleComputeServiceAccount, batchAttributes.computeServiceAccount)
-  }
+  protected def computeServiceAccount(descriptor: BackendWorkflowDescriptor): String =
+    descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleComputeServiceAccount,
+                                         batchAttributes.computeServiceAccount
+    )
 
-  protected def fuseEnabled(descriptor: BackendWorkflowDescriptor): Boolean = {
+  protected def fuseEnabled(descriptor: BackendWorkflowDescriptor): Boolean =
     descriptor.workflowOptions.getBoolean(WorkflowOptionKeys.EnableFuse).toOption.getOrElse(batchAttributes.enableFuse)
-  }
 
-  protected def useDockerImageCache(descriptor: BackendWorkflowDescriptor): Boolean = {
+  protected def useDockerImageCache(descriptor: BackendWorkflowDescriptor): Boolean =
     descriptor.workflowOptions.getBoolean(WorkflowOptionKeys.UseDockerImageCache).getOrElse(false)
-  }
 
-  override def cloudResolveWomFile(womFile: WomFile): WomFile = {
+  override def cloudResolveWomFile(womFile: WomFile): WomFile =
     womFile.mapFile { value =>
       getPath(value) match {
         case Success(drsPath: DrsPath) => DrsResolver.getSimpleGsUri(drsPath).unsafeRunSync().getOrElse(value)
@@ -998,16 +1135,15 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         case _ => value
       }
     }
-  }
 
-  override def mapCommandLineWomFile(womFile: WomFile): WomFile = {
+  override def mapCommandLineWomFile(womFile: WomFile): WomFile =
     womFile.mapFile { value =>
       (getPath(value), asAdHocFile(womFile)) match {
         case (Success(gcsPath: GcsPath), Some(adHocFile)) =>
           // Ad hoc files will be placed directly at the root ("/cromwell_root/ad_hoc_file.txt") unlike other input files
           // for which the full path is being propagated ("/cromwell_root/path/to/input_file.txt")
           workingDisk.mountPoint.resolve(adHocFile.alternativeName.getOrElse(gcsPath.name)).pathAsString
-        case (Success(path@(_: GcsPath | _: HttpPath)), _) =>
+        case (Success(path @ (_: GcsPath | _: HttpPath)), _) =>
           workingDisk.mountPoint.resolve(path.pathWithoutScheme).pathAsString
         case (Success(drsPath: DrsPath), _) =>
           val filePath = DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
@@ -1017,9 +1153,8 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         case _ => value
       }
     }
-  }
 
-  override def mapCommandLineJobInputWomFile(womFile: WomFile): WomFile = {
+  override def mapCommandLineJobInputWomFile(womFile: WomFile): WomFile =
     womFile.mapFile(value =>
       getPath(value) match {
         case Success(gcsPath: GcsPath) => workingDisk.mountPoint.resolve(gcsPath.pathWithoutScheme).pathAsString
@@ -1029,9 +1164,8 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         case _ => value
       }
     )
-  }
 
-  def womFileToGcsPath(batchOutputs: Set[GcpBatchOutput])(womFile: WomFile): WomFile = {
+  def womFileToGcsPath(batchOutputs: Set[GcpBatchOutput])(womFile: WomFile): WomFile =
     womFile mapFile { path =>
       batchOutputs collectFirst {
         case batchOutput if batchOutput.name == makeSafeReferenceName(path) =>
@@ -1048,37 +1182,32 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
           case _: ValidFullGcsPath => path
 
           /*
-            * Strip the prefixes in RuntimeOutputMapping.prefixFilters from the path, one at a time.
-            * For instance
-            * file:///cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt will progressively become
-            *
-            * /cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
-            * bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
-            * call-A/file.txt
-            *
-            * This code is called as part of a path mapper that will be applied to the WOMified cwl.output.json.
-            * The cwl.output.json when it's being read by Cromwell from the bucket still contains local paths
-            * (as they were created by the cwl tool).
-            * In order to keep things working we need to map those local paths to where they were actually delocalized,
-            * which is determined in cromwell.backend.google.pipelines.v2beta.api.Delocalization.
-            */
-          case _ => (callRootPath /
-            RuntimeOutputMapping
-              .prefixFilters(workflowPaths.workflowRoot)
-              .foldLeft(path)({
-                case (newPath, prefix) => newPath.stripPrefix(prefix)
-              })
-            ).pathAsString
+           * Strip the prefixes in RuntimeOutputMapping.prefixFilters from the path, one at a time.
+           * For instance
+           * file:///cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt will progressively become
+           *
+           * /cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
+           * bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
+           * call-A/file.txt
+           *
+           * This code is called as part of a path mapper that will be applied to the WOMified cwl.output.json.
+           * The cwl.output.json when it's being read by Cromwell from the bucket still contains local paths
+           * (as they were created by the cwl tool).
+           * In order to keep things working we need to map those local paths to where they were actually delocalized,
+           * which is determined in cromwell.backend.google.pipelines.v2beta.api.Delocalization.
+           */
+          case _ =>
+            (callRootPath /
+              RuntimeOutputMapping
+                .prefixFilters(workflowPaths.workflowRoot)
+                .foldLeft(path) { case (newPath, prefix) =>
+                  newPath.stripPrefix(prefix)
+                }).pathAsString
         }
       }
     }
-  }
 
   // No need for Cromwell-performed localization in the PAPI backend, ad hoc values are localized directly from GCS to the VM by PAPI.
-  override lazy val localizeAdHocValues: List[AdHocValue] => ErrorOr[List[StandardAdHocValue]] = _.map(Coproduct[StandardAdHocValue](_)).validNel
+  override lazy val localizeAdHocValues: List[AdHocValue] => ErrorOr[List[StandardAdHocValue]] =
+    _.map(Coproduct[StandardAdHocValue](_)).validNel
 }
-
-
-
-
-
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchBackendSingletonActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchBackendSingletonActor.scala
index 66e74b3f2c8..1e17767f029 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchBackendSingletonActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchBackendSingletonActor.scala
@@ -14,10 +14,11 @@ import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success}
 
 object GcpBatchBackendSingletonActor {
-  def props(requestFactory: GcpBatchRequestFactory, serviceRegistryActor: ActorRef)(implicit requestHandler: GcpBatchApiRequestHandler): Props = {
+  def props(requestFactory: GcpBatchRequestFactory, serviceRegistryActor: ActorRef)(implicit
+    requestHandler: GcpBatchApiRequestHandler
+  ): Props =
     Props(new GcpBatchBackendSingletonActor(requestFactory, serviceRegistryActor = serviceRegistryActor))
       .withDispatcher(BackendDispatcher)
-  }
 
   // This is the only type of messages that can be processed by this actor from this actor
   sealed trait Action extends Product with Serializable
@@ -38,8 +39,10 @@ object GcpBatchBackendSingletonActor {
 
 }
 
-final class GcpBatchBackendSingletonActor(requestFactory: GcpBatchRequestFactory, override val serviceRegistryActor: ActorRef)(implicit requestHandler: GcpBatchApiRequestHandler)
-  extends Actor
+final class GcpBatchBackendSingletonActor(requestFactory: GcpBatchRequestFactory,
+                                          override val serviceRegistryActor: ActorRef
+)(implicit requestHandler: GcpBatchApiRequestHandler)
+    extends Actor
     with ActorLogging
     with BatchInstrumentation
     with CromwellInstrumentationScheduler
@@ -47,7 +50,7 @@ final class GcpBatchBackendSingletonActor(requestFactory: GcpBatchRequestFactory
 
   import GcpBatchBackendSingletonActor._
 
-  private implicit val ec: ExecutionContext = context.dispatcher
+  implicit private val ec: ExecutionContext = context.dispatcher
 
   override def preStart() = {
     startInstrumentationTimer()
@@ -81,8 +84,8 @@ final class GcpBatchBackendSingletonActor(requestFactory: GcpBatchRequestFactory
           replyTo ! Event.JobStatusRetrieved(job)
 
         case Failure(exception) =>
-          log.error(exception,  s"Failed to query job status ($jobName) from GCP")
-          replyTo ! Event.ActionFailed(jobName.toString ,exception)
+          log.error(exception, s"Failed to query job status ($jobName) from GCP")
+          replyTo ! Event.ActionFailed(jobName.toString, exception)
       }
 
     case Action.AbortJob(jobName) =>
@@ -108,7 +111,8 @@ final class GcpBatchBackendSingletonActor(requestFactory: GcpBatchRequestFactory
       // that are on a final state.
       log.info(s"Cromwell requested to abort workflow $workflowId")
 
-    case other => log.error(s"Unexpected message from {} to ${this.getClass.getSimpleName}: {}", sender().path.name, other)
+    case other =>
+      log.error(s"Unexpected message from {} to ${this.getClass.getSimpleName}: {}", sender().path.name, other)
   }
 
   override def receive = instrumentationReceive(loadMetricHandler _).orElse(normalReceive)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchFinalizationActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchFinalizationActor.scala
index dd57edc8b4e..1749a229621 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchFinalizationActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchFinalizationActor.scala
@@ -9,8 +9,7 @@ import cromwell.core.io.AsyncIoActorClient
 import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
 import wom.graph.CommandCallNode
 
-case class GcpBatchFinalizationActorParams
-(
+case class GcpBatchFinalizationActorParams(
   workflowDescriptor: BackendWorkflowDescriptor,
   ioActor: ActorRef,
   batchConfiguration: GcpBatchConfiguration,
@@ -22,7 +21,9 @@ case class GcpBatchFinalizationActorParams
   override def configurationDescriptor: BackendConfigurationDescriptor = batchConfiguration.configurationDescriptor
 }
 
-class GcpBatchFinalizationActor(val batchParams: GcpBatchFinalizationActorParams) extends StandardFinalizationActor(batchParams) with AsyncIoActorClient {
+class GcpBatchFinalizationActor(val batchParams: GcpBatchFinalizationActorParams)
+    extends StandardFinalizationActor(batchParams)
+    with AsyncIoActorClient {
 
   lazy val batchConfiguration: GcpBatchConfiguration = batchParams.batchConfiguration
 
@@ -30,6 +31,4 @@ class GcpBatchFinalizationActor(val batchParams: GcpBatchFinalizationActorParams
   override def ioActor: ActorRef = batchParams.ioActor
 }
 
-object GcpBatchFinalizationActor {
-
-}
\ No newline at end of file
+object GcpBatchFinalizationActor {}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActor.scala
index 466a4f20d7e..5456c28ccbe 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActor.scala
@@ -16,10 +16,18 @@ import com.google.auth.http.HttpCredentialsAdapter
 import com.google.auth.oauth2.OAuth2Credentials
 import cromwell.backend.google.batch._
 import cromwell.backend.google.batch.actors.GcpBatchInitializationActor._
-import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.{VirtualPrivateCloudConfiguration, VirtualPrivateCloudLabels, VirtualPrivateCloudLiterals}
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.{
+  VirtualPrivateCloudConfiguration,
+  VirtualPrivateCloudLabels,
+  VirtualPrivateCloudLiterals
+}
 import cromwell.backend.google.batch.models._
 import cromwell.backend.google.batch.runnable.WorkflowOptionKeys
-import cromwell.backend.standard.{StandardInitializationActor, StandardInitializationActorParams, StandardValidatedRuntimeAttributesBuilder}
+import cromwell.backend.standard.{
+  StandardInitializationActor,
+  StandardInitializationActorParams,
+  StandardValidatedRuntimeAttributesBuilder
+}
 import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor}
 import cromwell.cloudsupport.gcp.auth.GoogleAuthMode.{httpTransport, jsonFactory}
 import cromwell.cloudsupport.gcp.auth.{GoogleAuthMode, UserServiceAccountMode}
@@ -36,8 +44,7 @@ import scala.concurrent.Future
 import scala.util.Try
 import scala.util.control.NonFatal
 
-case class GcpBatchInitializationActorParams
-(
+case class GcpBatchInitializationActorParams(
   workflowDescriptor: BackendWorkflowDescriptor,
   ioActor: ActorRef,
   calls: Set[CommandCallNode],
@@ -48,7 +55,9 @@ case class GcpBatchInitializationActorParams
   override val configurationDescriptor: BackendConfigurationDescriptor = batchConfiguration.configurationDescriptor
 
 }
-class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams) extends StandardInitializationActor(batchParams) with AsyncIoActorClient {
+class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams)
+    extends StandardInitializationActor(batchParams)
+    with AsyncIoActorClient {
 
   override lazy val ioActor: ActorRef = batchParams.ioActor
   protected val gcpBatchConfiguration: GcpBatchConfiguration = batchParams.batchConfiguration
@@ -65,11 +74,12 @@ class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams
 
   // Credentials object for the Genomics API
   private lazy val genomicsCredentials: Future[Credentials] = gcpBatchConfiguration.batchAttributes.auths.genomics
-                                                                                    .retryCredentials(workflowOptions, List(
-                                                                                      CloudLifeSciencesScopes
-                                                                                        .CLOUD_PLATFORM,
-                                                                                      GenomicsScopes.GENOMICS
-                                                                                    ))
+    .retryCredentials(workflowOptions,
+                      List(
+                        CloudLifeSciencesScopes.CLOUD_PLATFORM,
+                        GenomicsScopes.GENOMICS
+                      )
+    )
 
   val privateDockerEncryptionKeyName: Option[String] = {
     val optionsEncryptionKey = workflowOptions.get(GoogleAuthMode.DockerCredentialsEncryptionKeyNameKey).toOption
@@ -89,11 +99,14 @@ class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams
       // That doesn't seem great but it's effectively what the existing code around user service accounts appears to be doing.
       val userServiceAccountAuth: Option[GoogleAuthMode] = for {
         _ <- workflowOptions.get(GoogleAuthMode.UserServiceAccountKey).toOption
-        usaAuth <- gcpBatchConfiguration.googleConfig.authsByName.values collectFirst { case u: UserServiceAccountMode => u }
+        usaAuth <- gcpBatchConfiguration.googleConfig.authsByName.values collectFirst {
+          case u: UserServiceAccountMode => u
+        }
       } yield usaAuth
 
-      def encryptionAuthFromConfig: Option[GoogleAuthMode] = gcpBatchConfiguration.dockerEncryptionAuthName.flatMap { name =>
-        gcpBatchConfiguration.googleConfig.auth(name).toOption
+      def encryptionAuthFromConfig: Option[GoogleAuthMode] = gcpBatchConfiguration.dockerEncryptionAuthName.flatMap {
+        name =>
+          gcpBatchConfiguration.googleConfig.auth(name).toOption
       }
       // If there's no user service account auth in the workflow options fall back to an auth specified in config.
       userServiceAccountAuth orElse encryptionAuthFromConfig
@@ -103,12 +116,18 @@ class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams
       new String(Base64.decodeBase64(dockerToken)).split(':') match {
         case Array(username, password) =>
           // unencrypted tokens are base64-encoded username:password
-          Option(JsObject(
-            Map(
-              "username" -> JsString(username),
-              "password" -> JsString(password)
-            )).compactPrint)
-        case _ => throw new RuntimeException(s"provided dockerhub token '$dockerToken' is not a base64-encoded username:password")
+          Option(
+            JsObject(
+              Map(
+                "username" -> JsString(username),
+                "password" -> JsString(password)
+              )
+            ).compactPrint
+          )
+        case _ =>
+          throw new RuntimeException(
+            s"provided dockerhub token '$dockerToken' is not a base64-encoded username:password"
+          )
       }
     }
 
@@ -122,17 +141,25 @@ class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams
   }
 
   private def vpcNetworkAndSubnetworkProjectLabelsFuture(): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
-    def googleProject(descriptor: BackendWorkflowDescriptor): String = {
-      descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleProject, batchParams.batchConfiguration.batchAttributes.project)
-    }
+    def googleProject(descriptor: BackendWorkflowDescriptor): String =
+      descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleProject,
+                                           batchParams.batchConfiguration.batchAttributes.project
+      )
 
-    def projectMetadataRequest(vpcConfig: VirtualPrivateCloudLabels): Future[HttpRequest] = {
+    def projectMetadataRequest(vpcConfig: VirtualPrivateCloudLabels): Future[HttpRequest] =
       Future {
-        val credentials = vpcConfig.auth.credentials(workflowOptions.get(_).getOrElse(throw new RuntimeException("Unable to find the necessary workflow option for auth credentials")), List(CloudResourceManagerScopes.CLOUD_PLATFORM))
+        val credentials = vpcConfig.auth.credentials(
+          workflowOptions
+            .get(_)
+            .getOrElse(throw new RuntimeException("Unable to find the necessary workflow option for auth credentials")),
+          List(CloudResourceManagerScopes.CLOUD_PLATFORM)
+        )
 
         val httpCredentialsAdapter = new HttpCredentialsAdapter(credentials)
-        val cloudResourceManagerBuilder = new CloudResourceManager
-        .Builder(GoogleAuthMode.httpTransport, GoogleAuthMode.jsonFactory, httpCredentialsAdapter)
+        val cloudResourceManagerBuilder = new CloudResourceManager.Builder(GoogleAuthMode.httpTransport,
+                                                                           GoogleAuthMode.jsonFactory,
+                                                                           httpCredentialsAdapter
+        )
           .setApplicationName(gcpBatchConfiguration.googleConfig.applicationName)
           .build()
 
@@ -140,19 +167,23 @@ class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams
 
         project.buildHttpRequest()
       }
-    }
 
     def projectMetadataResponseToLabels(httpResponse: HttpResponse): Future[ProjectLabels] = {
       implicit val googleProjectMetadataLabelDecoder: Decoder[ProjectLabels] = deriveDecoder
-      Future.fromTry(decode[ProjectLabels](httpResponse.parseAsString()).toTry).recoverWith {
-        case NonFatal(e) => Future.failed(new RuntimeException(s"Failed to parse labels from project metadata response from Google Cloud Resource Manager API. " +
-          s"${ExceptionUtils.getMessage(e)}", e))
+      Future.fromTry(decode[ProjectLabels](httpResponse.parseAsString()).toTry).recoverWith { case NonFatal(e) =>
+        Future.failed(
+          new RuntimeException(
+            s"Failed to parse labels from project metadata response from Google Cloud Resource Manager API. " +
+              s"${ExceptionUtils.getMessage(e)}",
+            e
+          )
+        )
       }
     }
 
     def networkLabelsFromProjectLabels(vpcConfig: VirtualPrivateCloudLabels,
-                                       projectLabels: ProjectLabels,
-                                      ): Option[VpcAndSubnetworkProjectLabelValues] = {
+                                       projectLabels: ProjectLabels
+    ): Option[VpcAndSubnetworkProjectLabelValues] =
       projectLabels.labels.get(vpcConfig.network) map { vpcNetworkLabelValue =>
         val subnetworkLabelOption = vpcConfig.subnetwork.flatMap { s =>
           projectLabels.labels.collectFirst {
@@ -162,22 +193,22 @@ class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams
 
         VpcAndSubnetworkProjectLabelValues(vpcNetworkLabelValue, subnetworkLabelOption)
       }
-    }
 
-    def fetchVpcLabelsFromProjectMetadata(vpcConfig: VirtualPrivateCloudLabels
-                                         ): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
+    def fetchVpcLabelsFromProjectMetadata(
+      vpcConfig: VirtualPrivateCloudLabels
+    ): Future[Option[VpcAndSubnetworkProjectLabelValues]] =
       for {
         projectMetadataResponse <- projectMetadataRequest(vpcConfig).map(_.executeAsync().get())
         projectLabels <- projectMetadataResponseToLabels(projectMetadataResponse)
       } yield networkLabelsFromProjectLabels(vpcConfig, projectLabels)
-    }
 
     /*
     First, try to fetch the network information from labels, where that fetch may still return None.
     Then, if we did not discover a network via labels for whatever reason try to look for literal values.
      */
-    def fetchVpcLabels(vpcConfig: VirtualPrivateCloudConfiguration
-                      ): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
+    def fetchVpcLabels(
+      vpcConfig: VirtualPrivateCloudConfiguration
+    ): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
       // Added explicit types to hopefully help future devs who stumble across this two-step code
       val fetchedFromLabels: Future[Option[VpcAndSubnetworkProjectLabelValues]] = vpcConfig.labelsOption match {
         case Some(labels: VirtualPrivateCloudLabels) => fetchVpcLabelsFromProjectMetadata(labels)
@@ -201,9 +232,13 @@ class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams
     gcsCred <- gcsCredentials
     genomicsCred <- genomicsCredentials
     validatedPathBuilders <- pathBuilders
-  } yield new GcpBatchWorkflowPaths(
-      workflowDescriptor, gcsCred, genomicsCred, gcpBatchConfiguration, validatedPathBuilders, standardStreamNameToFileNameMetadataMapper)(ioEc)
-
+  } yield new GcpBatchWorkflowPaths(workflowDescriptor,
+                                    gcsCred,
+                                    genomicsCred,
+                                    gcpBatchConfiguration,
+                                    validatedPathBuilders,
+                                    standardStreamNameToFileNameMetadataMapper
+  )(ioEc)
 
   override lazy val initializationData: Future[GcpBackendInitializationData] = for {
     batchWorkflowPaths <- workflowPaths
@@ -221,13 +256,12 @@ class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams
 
   override def validateWorkflowOptions(): Try[Unit] = GcpLabel.fromWorkflowOptions(workflowOptions).map(_ => ())
 
-  override def beforeAll(): Future[Option[BackendInitializationData]] = {
+  override def beforeAll(): Future[Option[BackendInitializationData]] =
     for {
       paths <- workflowPaths
       _ = publishWorkflowRoot(paths.workflowRoot.pathAsString)
       data <- initializationData
     } yield Option(data)
-  }
 
   def standardStreamNameToFileNameMetadataMapper(gcpBatchJobPaths: GcpBatchJobPaths, streamName: String): String =
     GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper(gcpBatchJobPaths, streamName)
@@ -238,7 +272,9 @@ class GcpBatchInitializationActor(batchParams: GcpBatchInitializationActorParams
 
 object GcpBatchInitializationActor {
   // For metadata publishing purposes default to using the name of a standard stream as the stream's filename.
-  def defaultStandardStreamNameToFileNameMetadataMapper(gcpBatchJobPaths: GcpBatchJobPaths, streamName: String): String = streamName
+  def defaultStandardStreamNameToFileNameMetadataMapper(gcpBatchJobPaths: GcpBatchJobPaths,
+                                                        streamName: String
+  ): String = streamName
 
   def encryptKms(keyName: String, credentials: OAuth2Credentials, plainText: String): String = {
     val httpCredentialsAdapter = new HttpCredentialsAdapter(credentials)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchJobCachingActorHelper.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchJobCachingActorHelper.scala
index e86404bef1e..8f305778f29 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchJobCachingActorHelper.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchJobCachingActorHelper.scala
@@ -14,22 +14,19 @@ import scala.language.postfixOps
 trait GcpBatchJobCachingActorHelper extends StandardCachingActorHelper {
   this: GcpBatchAsyncBackendJobExecutionActor with JobLogging =>
 
-  lazy val initializationData: GcpBackendInitializationData = {
+  lazy val initializationData: GcpBackendInitializationData =
     backendInitializationDataAs[GcpBackendInitializationData]
-  }
   lazy val batchConfiguration: GcpBatchConfiguration = initializationData.gcpBatchConfiguration
 
   lazy val gcpBatchCallPaths: GcpBatchJobPaths = jobPaths.asInstanceOf[GcpBatchJobPaths]
 
   lazy val runtimeAttributes = GcpBatchRuntimeAttributes(
     validatedRuntimeAttributes,
-    batchConfiguration
-      .runtimeConfig
+    batchConfiguration.runtimeConfig
   )
 
   lazy val maxPreemption: Int = runtimeAttributes.preemptible
 
-
   lazy val workingDisk: GcpBatchAttachedDisk = runtimeAttributes.disks.find(_.name == GcpBatchWorkingDisk.Name).get
 
   lazy val callRootPath: Path = gcpBatchCallPaths.callExecutionRoot
@@ -45,16 +42,18 @@ trait GcpBatchJobCachingActorHelper extends StandardCachingActorHelper {
     val workflow = jobDescriptor.workflowDescriptor
     val call = jobDescriptor.taskCall
     val subWorkflow = workflow.callable
-    val subWorkflowLabels = if (!subWorkflow.equals(workflow.rootWorkflow))
-      Labels("cromwell-sub-workflow-name" -> subWorkflow.name)
-    else
-      Labels.empty
+    val subWorkflowLabels =
+      if (!subWorkflow.equals(workflow.rootWorkflow))
+        Labels("cromwell-sub-workflow-name" -> subWorkflow.name)
+      else
+        Labels.empty
 
     val alias = call.localName
-    val aliasLabels = if (!alias.equals(call.callable.name))
-      Labels("wdl-call-alias" -> alias)
-    else
-      Labels.empty
+    val aliasLabels =
+      if (!alias.equals(call.callable.name))
+        Labels("wdl-call-alias" -> alias)
+      else
+        Labels.empty
 
     Labels(
       "cromwell-workflow-id" -> s"cromwell-${workflow.rootWorkflowId}",
@@ -62,18 +61,16 @@ trait GcpBatchJobCachingActorHelper extends StandardCachingActorHelper {
     ) ++ subWorkflowLabels ++ aliasLabels
   }
 
-
   lazy val originalLabels: Labels = defaultLabels
 
   lazy val backendLabels: Seq[GcpLabel] = GcpLabel.safeLabels(originalLabels.asTuple: _*)
 
-  lazy val originalLabelEvents: Map[String, String] = originalLabels.value map { l => s"${CallMetadataKeys.Labels}:${l.key}" -> l.value } toMap
+  lazy val originalLabelEvents: Map[String, String] = originalLabels.value map { l =>
+    s"${CallMetadataKeys.Labels}:${l.key}" -> l.value
+  } toMap
 
   override protected def nonStandardMetadata: Map[String, Any] = {
-    val googleProject = initializationData
-      .workflowPaths
-      .workflowDescriptor
-      .workflowOptions
+    val googleProject = initializationData.workflowPaths.workflowDescriptor.workflowOptions
       .get(WorkflowOptionKeys.GoogleProject)
       .getOrElse(batchAttributes.project)
 
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchApiRequestHandler.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchApiRequestHandler.scala
index 1a877558942..b10b8361130 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchApiRequestHandler.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchApiRequestHandler.scala
@@ -25,10 +25,9 @@ class GcpBatchApiRequestHandler {
     val headerProvider = FixedHeaderProvider.create(headers)
     val batchSettings = BatchServiceSettings.newBuilder.setHeaderProvider(headerProvider).build
     val client = BatchServiceClient.create(batchSettings)
-    try {
+    try
       f(client)
-    } finally {
+    finally
       client.close()
-    }
   }
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala
index 6976bd09867..3c69c3c8fb4 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala
@@ -28,9 +28,9 @@ object GcpBatchRequestFactory {
     * Input parameters that are not strictly needed by the user's command but are Cromwell byproducts.
     */
   case class DetritusInputParameters(
-                                      executionScriptInputParameter: GcpBatchFileInput,
-                                      monitoringScriptInputParameter: Option[GcpBatchFileInput]
-                                    ) {
+    executionScriptInputParameter: GcpBatchFileInput,
+    monitoringScriptInputParameter: Option[GcpBatchFileInput]
+  ) {
     def all: List[GcpBatchFileInput] = List(executionScriptInputParameter) ++ monitoringScriptInputParameter
   }
 
@@ -38,11 +38,12 @@ object GcpBatchRequestFactory {
     * Output parameters that are not produced by the user's command but are Cromwell byproducts.
     */
   case class DetritusOutputParameters(
-                                       monitoringScriptOutputParameter: Option[GcpBatchFileOutput],
-                                       rcFileOutputParameter: GcpBatchFileOutput,
-                                       memoryRetryRCFileOutputParameter: GcpBatchFileOutput
-                                     ) {
-    def all: List[GcpBatchFileOutput] = memoryRetryRCFileOutputParameter :: List(rcFileOutputParameter) ++ monitoringScriptOutputParameter
+    monitoringScriptOutputParameter: Option[GcpBatchFileOutput],
+    rcFileOutputParameter: GcpBatchFileOutput,
+    memoryRetryRCFileOutputParameter: GcpBatchFileOutput
+  ) {
+    def all: List[GcpBatchFileOutput] =
+      memoryRetryRCFileOutputParameter :: List(rcFileOutputParameter) ++ monitoringScriptOutputParameter
   }
 
   /**
@@ -51,12 +52,12 @@ object GcpBatchRequestFactory {
     * to treat them differently.
     */
   case class InputOutputParameters(
-                                    detritusInputParameters: DetritusInputParameters,
-                                    jobInputParameters: List[GcpBatchInput],
-                                    jobOutputParameters: List[GcpBatchOutput],
-                                    detritusOutputParameters: DetritusOutputParameters,
-                                    literalInputParameters: List[GcpBatchLiteralInput]
-                                  ) {
+    detritusInputParameters: DetritusInputParameters,
+    jobInputParameters: List[GcpBatchInput],
+    jobOutputParameters: List[GcpBatchOutput],
+    detritusOutputParameters: DetritusOutputParameters,
+    literalInputParameters: List[GcpBatchLiteralInput]
+  ) {
     lazy val fileInputParameters: List[GcpBatchInput] = jobInputParameters ++ detritusInputParameters.all
     lazy val fileOutputParameters: List[GcpBatchOutput] = detritusOutputParameters.all ++ jobOutputParameters
   }
@@ -89,7 +90,7 @@ object GcpBatchRequestFactory {
                                       enableSshAccess: Boolean,
                                       vpcNetworkAndSubnetworkProjectLabels: Option[VpcAndSubnetworkProjectLabelValues],
                                       dockerhubCredentials: (String, String)
-                                     ) {
+  ) {
     def literalInputs = inputOutputParameters.literalInputParameters
 
     def inputParameters = inputOutputParameters.fileInputParameters
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
index 9c482d852d1..a8f6519b7a5 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
@@ -2,7 +2,21 @@ package cromwell.backend.google.batch.api
 
 import com.google.cloud.batch.v1.AllocationPolicy._
 import com.google.cloud.batch.v1.LogsPolicy.Destination
-import com.google.cloud.batch.v1.{AllocationPolicy, ComputeResource, CreateJobRequest, DeleteJobRequest, GetJobRequest, Job, JobName, LogsPolicy, Runnable, ServiceAccount, TaskGroup, TaskSpec, Volume}
+import com.google.cloud.batch.v1.{
+  AllocationPolicy,
+  ComputeResource,
+  CreateJobRequest,
+  DeleteJobRequest,
+  GetJobRequest,
+  Job,
+  JobName,
+  LogsPolicy,
+  Runnable,
+  ServiceAccount,
+  TaskGroup,
+  TaskSpec,
+  Volume
+}
 import com.google.protobuf.Duration
 import cromwell.backend.google.batch.io.GcpBatchAttachedDisk
 import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
@@ -12,25 +26,27 @@ import cromwell.backend.google.batch.util.BatchUtilityConversions
 
 import scala.jdk.CollectionConverters._
 
-class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransferConfiguration) extends GcpBatchRequestFactory
-  with BatchUtilityConversions
-  with UserRunnable
-  with ContainerSetup
-  with Localization
-  with Delocalization
-  with MemoryRetryCheckRunnable
-  with MonitoringRunnable
-  with CheckpointingRunnable {
+class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransferConfiguration)
+    extends GcpBatchRequestFactory
+    with BatchUtilityConversions
+    with UserRunnable
+    with ContainerSetup
+    with Localization
+    with Delocalization
+    with MemoryRetryCheckRunnable
+    with MonitoringRunnable
+    with CheckpointingRunnable {
 
   override def queryRequest(jobName: JobName): GetJobRequest = GetJobRequest.newBuilder.setName(jobName.toString).build
 
-  override def abortRequest(jobName: JobName): DeleteJobRequest = DeleteJobRequest.newBuilder.setName(jobName.toString).build()
-
+  override def abortRequest(jobName: JobName): DeleteJobRequest =
+    DeleteJobRequest.newBuilder.setName(jobName.toString).build()
 
-  def createNetworkWithVPC(vpcAndSubnetworkProjectLabelValues: VpcAndSubnetworkProjectLabelValues, data: GcpBatchRequest): NetworkInterface.Builder = {
+  def createNetworkWithVPC(vpcAndSubnetworkProjectLabelValues: VpcAndSubnetworkProjectLabelValues,
+                           data: GcpBatchRequest
+  ): NetworkInterface.Builder = {
 
-    val network = NetworkInterface
-      .newBuilder
+    val network = NetworkInterface.newBuilder
       .setNoExternalIpAddress(data.gcpBatchParameters.runtimeAttributes.noAddress)
       .setNetwork(vpcAndSubnetworkProjectLabelValues.networkName(data.gcpBatchParameters.projectId))
 
@@ -42,35 +58,35 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
 
   }
 
-  def createNetwork(data: GcpBatchRequest): NetworkInterface.Builder = {
+  def createNetwork(data: GcpBatchRequest): NetworkInterface.Builder =
     data.createParameters.vpcNetworkAndSubnetworkProjectLabels match {
       case Some(vpcAndSubnetworkProjectLabelValues) => createNetworkWithVPC(vpcAndSubnetworkProjectLabelValues, data)
       case _ => NetworkInterface.newBuilder().setNoExternalIpAddress(data.createParameters.runtimeAttributes.noAddress)
     }
-  }
 
-  private def createComputeResource(cpu: Long, memory: Long, bootDiskSizeMb: Long) = {
-    ComputeResource
-      .newBuilder
+  private def createComputeResource(cpu: Long, memory: Long, bootDiskSizeMb: Long) =
+    ComputeResource.newBuilder
       .setCpuMilli(cpu)
       .setMemoryMib(memory)
       .setBootDiskMib(bootDiskSizeMb)
       .build
-  }
 
-  private def createInstancePolicy(cpuPlatform: String, spotModel: ProvisioningModel, accelerators: Option[Accelerator.Builder], attachedDisks: List[AttachedDisk]): InstancePolicy.Builder = {
+  private def createInstancePolicy(cpuPlatform: String,
+                                   spotModel: ProvisioningModel,
+                                   accelerators: Option[Accelerator.Builder],
+                                   attachedDisks: List[AttachedDisk]
+  ): InstancePolicy.Builder = {
 
-    //set GPU count to 0 if not included in workflow
+    // set GPU count to 0 if not included in workflow
     val gpuAccelerators = accelerators.getOrElse(Accelerator.newBuilder.setCount(0).setType("")) // TODO: Driver version
 
-    val instancePolicy = InstancePolicy
-      .newBuilder
+    val instancePolicy = InstancePolicy.newBuilder
       .setProvisioningModel(spotModel)
       .addAllDisks(attachedDisks.asJava)
       .setMinCpuPlatform(cpuPlatform)
       .buildPartial()
 
-    //add GPUs if GPU count is greater than 1
+    // add GPUs if GPU count is greater than 1
     if (gpuAccelerators.getCount >= 1) {
       val instancePolicyGpu = instancePolicy.toBuilder
       instancePolicyGpu.addAccelerators(gpuAccelerators).build
@@ -81,65 +97,71 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
 
   }
 
-  private def createNetworkPolicy(networkInterface: NetworkInterface): NetworkPolicy = {
-    NetworkPolicy
-      .newBuilder
+  private def createNetworkPolicy(networkInterface: NetworkInterface): NetworkPolicy =
+    NetworkPolicy.newBuilder
       .addNetworkInterfaces(0, networkInterface)
       .build
-  }
 
-  private def createTaskSpec(runnables: List[Runnable], computeResource: ComputeResource, retryCount: Int, durationInSeconds: Long, volumes: List[Volume]) = {
-    TaskSpec
-      .newBuilder
+  private def createTaskSpec(runnables: List[Runnable],
+                             computeResource: ComputeResource,
+                             retryCount: Int,
+                             durationInSeconds: Long,
+                             volumes: List[Volume]
+  ) =
+    TaskSpec.newBuilder
       .addAllRunnables(runnables.asJava)
       .setComputeResource(computeResource)
       .addAllVolumes(volumes.asJava)
       .setMaxRetryCount(retryCount)
-      .setMaxRunDuration(Duration
-        .newBuilder
-        .setSeconds(durationInSeconds)
-        .build)
-  }
+      .setMaxRunDuration(
+        Duration.newBuilder
+          .setSeconds(durationInSeconds)
+          .build
+      )
 
-  private def createTaskGroup(taskCount: Long, task: TaskSpec.Builder): TaskGroup = {
-    TaskGroup
-      .newBuilder
+  private def createTaskGroup(taskCount: Long, task: TaskSpec.Builder): TaskGroup =
+    TaskGroup.newBuilder
       .setTaskCount(taskCount)
       .setTaskSpec(task)
       .build
 
-  }
-
-  private def createAllocationPolicy(data: GcpBatchRequest, locationPolicy: LocationPolicy, instancePolicy: InstancePolicy, networkPolicy: NetworkPolicy, serviceAccount: ServiceAccount, accelerators: Option[Accelerator.Builder]) = {
+  private def createAllocationPolicy(data: GcpBatchRequest,
+                                     locationPolicy: LocationPolicy,
+                                     instancePolicy: InstancePolicy,
+                                     networkPolicy: NetworkPolicy,
+                                     serviceAccount: ServiceAccount,
+                                     accelerators: Option[Accelerator.Builder]
+  ) = {
 
-    val allocationPolicy = AllocationPolicy
-      .newBuilder
+    val allocationPolicy = AllocationPolicy.newBuilder
       .setLocation(locationPolicy)
       .setNetwork(networkPolicy)
-      .putLabels("cromwell-workflow-id", toLabel(data.workflowId.toString)) //label for workflow from WDL
+      .putLabels("cromwell-workflow-id", toLabel(data.workflowId.toString)) // label for workflow from WDL
       .putLabels("goog-batch-worker", "true")
-      .putAllLabels((data.createParameters.googleLabels.map(label => label.key -> label.value).toMap.asJava))
+      .putAllLabels(data.createParameters.googleLabels.map(label => label.key -> label.value).toMap.asJava)
       .setServiceAccount(serviceAccount)
       .buildPartial()
 
     val gpuAccelerators = accelerators.getOrElse(Accelerator.newBuilder.setCount(0).setType(""))
 
-    //add GPUs if GPU count is greater than or equal to 1
+    // add GPUs if GPU count is greater than or equal to 1
     if (gpuAccelerators.getCount >= 1) {
-      allocationPolicy.toBuilder.addInstances(InstancePolicyOrTemplate.newBuilder.setPolicy(instancePolicy).setInstallGpuDrivers(true).build)
+      allocationPolicy.toBuilder.addInstances(
+        InstancePolicyOrTemplate.newBuilder.setPolicy(instancePolicy).setInstallGpuDrivers(true).build
+      )
     } else {
       allocationPolicy.toBuilder.addInstances(InstancePolicyOrTemplate.newBuilder.setPolicy(instancePolicy).build)
     }
   }
 
-
   override def submitRequest(data: GcpBatchRequest): CreateJobRequest = {
 
     val batchAttributes = data.gcpBatchParameters.batchAttributes
     val runtimeAttributes = data.gcpBatchParameters.runtimeAttributes
     val createParameters = data.createParameters
     val retryCount = data.gcpBatchParameters.runtimeAttributes.preemptible
-    val allDisksToBeMounted: Seq[GcpBatchAttachedDisk] = createParameters.adjustedSizeDisks ++ createParameters.referenceDisksForLocalizationOpt.getOrElse(List.empty)
+    val allDisksToBeMounted: Seq[GcpBatchAttachedDisk] =
+      createParameters.adjustedSizeDisks ++ createParameters.referenceDisksForLocalizationOpt.getOrElse(List.empty)
     val gcpBootDiskSizeMb = convertGbToMib(runtimeAttributes)
 
     // set parent for metadata storage of job information
@@ -184,43 +206,44 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
     val monitoringShutdown: List[Runnable] = monitoringShutdownRunnables(createParameters)
     val checkpointingStart: List[Runnable] = checkpointingSetupRunnables(createParameters, allVolumes)
     val checkpointingShutdown: List[Runnable] = checkpointingShutdownRunnables(createParameters, allVolumes)
-    val sshAccess: List[Runnable] = List.empty //sshAccessActions(createPipelineParameters, mounts)
+    val sshAccess: List[Runnable] = List.empty // sshAccessActions(createPipelineParameters, mounts)
 
     val sortedRunnables: List[Runnable] = RunnableUtils.sortRunnables(
       containerSetup = containerSetup,
-        localization = localization,
-        userRunnable = userRunnable,
-        memoryRetryRunnable = memoryRetryRunnable,
-        deLocalization = deLocalization,
-        monitoringSetup = monitoringSetup,
-        monitoringShutdown = monitoringShutdown,
-        checkpointingStart = checkpointingStart,
-        checkpointingShutdown = checkpointingShutdown,
-        sshAccess = sshAccess,
-        isBackground = _.getBackground,
-      )
+      localization = localization,
+      userRunnable = userRunnable,
+      memoryRetryRunnable = memoryRetryRunnable,
+      deLocalization = deLocalization,
+      monitoringSetup = monitoringSetup,
+      monitoringShutdown = monitoringShutdown,
+      checkpointingStart = checkpointingStart,
+      checkpointingShutdown = checkpointingShutdown,
+      sshAccess = sshAccess,
+      isBackground = _.getBackground
+    )
 
     val computeResource = createComputeResource(cpuCores, memory, gcpBootDiskSizeMb)
     val taskSpec = createTaskSpec(sortedRunnables, computeResource, retryCount, durationInSeconds, allVolumes)
     val taskGroup: TaskGroup = createTaskGroup(taskCount, taskSpec)
     val instancePolicy = createInstancePolicy(cpuPlatform, spotModel, accelerators, allDisks)
     val locationPolicy = LocationPolicy.newBuilder.addAllowedLocations(zones).build
-    val allocationPolicy = createAllocationPolicy(data, locationPolicy, instancePolicy.build, networkPolicy, gcpSa, accelerators)
-    val job = Job
-      .newBuilder
+    val allocationPolicy =
+      createAllocationPolicy(data, locationPolicy, instancePolicy.build, networkPolicy, gcpSa, accelerators)
+    val job = Job.newBuilder
       .addTaskGroups(taskGroup)
       .setAllocationPolicy(allocationPolicy.build())
-      .putLabels("submitter", "cromwell") // label to signify job submitted by cromwell for larger tracking purposes within GCP batch
+      .putLabels("submitter",
+                 "cromwell"
+      ) // label to signify job submitted by cromwell for larger tracking purposes within GCP batch
       .putLabels("goog-batch-worker", "true")
-      .putAllLabels((data.createParameters.googleLabels.map(label => label.key -> label.value).toMap.asJava))
-      .setLogsPolicy(LogsPolicy
-        .newBuilder
-        .setDestination(Destination.CLOUD_LOGGING)
-        .build)
-
+      .putAllLabels(data.createParameters.googleLabels.map(label => label.key -> label.value).toMap.asJava)
+      .setLogsPolicy(
+        LogsPolicy.newBuilder
+          .setDestination(Destination.CLOUD_LOGGING)
+          .build
+      )
 
-    CreateJobRequest
-      .newBuilder
+    CreateJobRequest.newBuilder
       .setParent(parent)
       .setJob(job)
       .setJobId(data.jobName)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchVMAuthentication.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchVMAuthentication.scala
index 4f14d1b92b1..7858429ebd4 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchVMAuthentication.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/authentication/GcpBatchVMAuthentication.scala
@@ -28,7 +28,9 @@ object GcpBatchDockerCredentials {
       case None => ().validNel // fine
       case _ =>
         for {
-          authName <- dockerCredentials.authName.toErrorOr("KMS Encryption key defined for private Docker but no auth specified")
+          authName <- dockerCredentials.authName.toErrorOr(
+            "KMS Encryption key defined for private Docker but no auth specified"
+          )
           _ <- googleConfig.auth(authName)
         } yield ()
     }
@@ -37,10 +39,10 @@ object GcpBatchDockerCredentials {
       case Invalid(errors) =>
         throw new RuntimeException(errors.toList.mkString(", "))
       case Valid(_) =>
-        new GcpBatchDockerCredentials(
-          token = dockerCredentials.token,
-          keyName = dockerCredentials.keyName,
-          authName = dockerCredentials.authName)
+        new GcpBatchDockerCredentials(token = dockerCredentials.token,
+                                      keyName = dockerCredentials.keyName,
+                                      authName = dockerCredentials.authName
+        )
     }
   }
 }
@@ -50,11 +52,12 @@ object GcpBatchDockerCredentials {
   */
 case class GcpBatchDockerCredentials(override val token: String,
                                      override val keyName: Option[String],
-                                     override val authName: Option[String])
-  extends DockerCredentials(token = token, keyName = keyName, authName = authName) with GcpBatchAuthObject {
+                                     override val authName: Option[String]
+) extends DockerCredentials(token = token, keyName = keyName, authName = authName)
+    with GcpBatchAuthObject {
 
   override val context = "docker"
   override val map = Map(
     "token" -> JsString(token)
   )
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendCacheHitCopyingActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendCacheHitCopyingActor.scala
index a0fc2e96317..82fd47735f7 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendCacheHitCopyingActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendCacheHitCopyingActor.scala
@@ -16,20 +16,24 @@ import wom.values.WomFile
 import scala.language.postfixOps
 import scala.util.Try
 
-class BatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams) extends StandardCacheHitCopyingActor(standardParams){
+class BatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams)
+    extends StandardCacheHitCopyingActor(standardParams) {
   override protected val commandBuilder: GcsBatchCommandBuilder.type = GcsBatchCommandBuilder
   private val cachingStrategy: BatchCacheHitDuplicationStrategy = BackendInitializationData
     .as[GcpBackendInitializationData](standardParams.backendInitializationDataOption)
-    .gcpBatchConfiguration.batchAttributes.cacheHitDuplicationStrategy
+    .gcpBatchConfiguration
+    .batchAttributes
+    .cacheHitDuplicationStrategy
 
   override def processSimpletons(womValueSimpletons: Seq[WomValueSimpleton],
-                                 sourceCallRootPath: Path,
-                                ): Try[(CallOutputs, Set[IoCommand[_]])] =
+                                 sourceCallRootPath: Path
+  ): Try[(CallOutputs, Set[IoCommand[_]])] =
     cachingStrategy match {
       case CopyCachedOutputs => super.processSimpletons(womValueSimpletons, sourceCallRootPath)
       case UseOriginalCachedOutputs =>
         val touchCommands: Seq[Try[IoTouchCommand]] = womValueSimpletons collect {
-          case WomValueSimpleton(_, wdlFile: WomFile) => getPath(wdlFile.value) flatMap GcsBatchCommandBuilder.touchCommand
+          case WomValueSimpleton(_, wdlFile: WomFile) =>
+            getPath(wdlFile.value) flatMap GcsBatchCommandBuilder.touchCommand
         }
 
         TryUtil.sequence(touchCommands) map {
@@ -37,10 +41,13 @@ class BatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingAc
         }
     }
 
-  override def extractBlacklistPrefix(path: String): Option[String] = Option(path.stripPrefix("gs://").takeWhile(_ != '/'))
+  override def extractBlacklistPrefix(path: String): Option[String] = Option(
+    path.stripPrefix("gs://").takeWhile(_ != '/')
+  )
 
-  override def processDetritus(sourceJobDetritusFiles: Map[String, String]
-                              ): Try[(Map[String, Path], Set[IoCommand[_]])] =
+  override def processDetritus(
+    sourceJobDetritusFiles: Map[String, String]
+  ): Try[(Map[String, Path], Set[IoCommand[_]])] =
     cachingStrategy match {
       case CopyCachedOutputs => super.processDetritus(sourceJobDetritusFiles)
       case UseOriginalCachedOutputs =>
@@ -63,7 +70,8 @@ class BatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingAc
                                               originalSimpletons: Seq[WomValueSimpleton],
                                               newOutputs: CallOutputs,
                                               originalDetritus: Map[String, String],
-                                              newDetritus: Map[String, Path]): Try[List[Set[IoCommand[_]]]] = Try {
+                                              newDetritus: Map[String, Path]
+  ): Try[List[Set[IoCommand[_]]]] = Try {
     cachingStrategy match {
       case UseOriginalCachedOutputs =>
         val content =
@@ -74,13 +82,17 @@ class BatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingAc
     """.stripMargin
 
         // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
-        List(Set(
-          GcsBatchCommandBuilder.writeCommand(
-            path = jobPaths.forCallCacheCopyAttempts.callExecutionRoot / "call_caching_placeholder.txt",
-            content = content,
-            options = Seq(CloudStorageOptions.withMimeType("text/plain")),
-          ).get
-        ))
+        List(
+          Set(
+            GcsBatchCommandBuilder
+              .writeCommand(
+                path = jobPaths.forCallCacheCopyAttempts.callExecutionRoot / "call_caching_placeholder.txt",
+                content = content,
+                options = Seq(CloudStorageOptions.withMimeType("text/plain"))
+              )
+              .get
+          )
+        )
       case CopyCachedOutputs => List.empty
     }
   }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendFileHashingActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendFileHashingActor.scala
index a3f000e7085..20f34876403 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendFileHashingActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchBackendFileHashingActor.scala
@@ -3,6 +3,7 @@ package cromwell.backend.google.batch.callcaching
 import cromwell.backend.standard.callcaching.{StandardFileHashingActor, StandardFileHashingActorParams}
 import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
 
-class BatchBackendFileHashingActor(standardParams: StandardFileHashingActorParams) extends StandardFileHashingActor(standardParams) {
+class BatchBackendFileHashingActor(standardParams: StandardFileHashingActorParams)
+    extends StandardFileHashingActor(standardParams) {
   override val ioCommandBuilder = GcsBatchCommandBuilder
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchCacheHitDuplicationStrategy.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchCacheHitDuplicationStrategy.scala
index 778a0c2fefe..37467fc5e32 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchCacheHitDuplicationStrategy.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/callcaching/BatchCacheHitDuplicationStrategy.scala
@@ -4,4 +4,3 @@ sealed trait BatchCacheHitDuplicationStrategy
 
 case object CopyCachedOutputs extends BatchCacheHitDuplicationStrategy
 case object UseOriginalCachedOutputs extends BatchCacheHitDuplicationStrategy
-
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/errors/InvalidGcsPathsInManifestFileException.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/errors/InvalidGcsPathsInManifestFileException.scala
index 708906e8f17..abd0b447d25 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/errors/InvalidGcsPathsInManifestFileException.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/errors/InvalidGcsPathsInManifestFileException.scala
@@ -3,5 +3,6 @@ package cromwell.backend.google.batch.errors
 import scala.util.control.NoStackTrace
 
 class InvalidGcsPathsInManifestFileException(paths: List[String]) extends Exception with NoStackTrace {
-  override def getMessage: String = s"Some of the paths in manifest file are not valid GCS paths: \n${paths.mkString("\n")}"
-}
\ No newline at end of file
+  override def getMessage: String =
+    s"Some of the paths in manifest file are not valid GCS paths: \n${paths.mkString("\n")}"
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala
index 0e49985e24f..50a0704dd4e 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala
@@ -21,11 +21,16 @@ object GcpBatchAttachedDisk {
     def diskTypeValidation(diskTypeString: String): ErrorOr[DiskType] = validateDiskType(diskTypeString)
 
     val validation: ErrorOr[GcpBatchAttachedDisk] = s match {
-      case WorkingDiskPattern(sizeGb, diskType) => (validateDiskType(diskType), sizeGbValidation(sizeGb)) mapN {
-        GcpBatchWorkingDisk.apply
-      }
-      case MountedDiskPattern(mountPoint, sizeGb, diskType) => (sizeGbValidation(sizeGb), diskTypeValidation(diskType)) mapN { (s, dt) => PipelinesApiEmptyMountedDisk(dt, s, DefaultPathBuilder.get(mountPoint)) }
-      case _ => s"Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: '$s'".invalidNel
+      case WorkingDiskPattern(sizeGb, diskType) =>
+        (validateDiskType(diskType), sizeGbValidation(sizeGb)) mapN {
+          GcpBatchWorkingDisk.apply
+        }
+      case MountedDiskPattern(mountPoint, sizeGb, diskType) =>
+        (sizeGbValidation(sizeGb), diskTypeValidation(diskType)) mapN { (s, dt) =>
+          PipelinesApiEmptyMountedDisk(dt, s, DefaultPathBuilder.get(mountPoint))
+        }
+      case _ =>
+        s"Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: '$s'".invalidNel
     }
 
     Try(validation match {
@@ -38,26 +43,25 @@ object GcpBatchAttachedDisk {
     })
   }
 
-  private def validateDiskType(diskTypeName: String): ErrorOr[DiskType] = {
+  private def validateDiskType(diskTypeName: String): ErrorOr[DiskType] =
     DiskType.values().find(_.diskTypeName == diskTypeName) match {
       case Some(diskType) => diskType.validNel
       case None =>
         val diskTypeNames = DiskType.values.map(_.diskTypeName).mkString(", ")
         s"Disk TYPE $diskTypeName should be one of $diskTypeNames".invalidNel
     }
-  }
 
-  private def validateLong(value: String): ErrorOr[Long] = {
-    try {
+  private def validateLong(value: String): ErrorOr[Long] =
+    try
       value.toLong.validNel
-    } catch {
+    catch {
       case _: IllegalArgumentException => s"$value not convertible to a Long".invalidNel
     }
-  }
 
   implicit class EnhancedDisks(val disks: Seq[GcpBatchAttachedDisk]) extends AnyVal {
     def adjustWorkingDiskWithNewMin(minimum: MemorySize, onAdjustment: => Unit): Seq[GcpBatchAttachedDisk] = disks map {
-      case disk: GcpBatchWorkingDisk if disk == GcpBatchWorkingDisk.Default && disk.sizeGb < minimum.to(MemoryUnit.GB).amount.toInt =>
+      case disk: GcpBatchWorkingDisk
+          if disk == GcpBatchWorkingDisk.Default && disk.sizeGb < minimum.to(MemoryUnit.GB).amount.toInt =>
         onAdjustment
         disk.copy(sizeGb = minimum.to(MemoryUnit.GB).amount.toInt)
       case other => other
@@ -72,7 +76,8 @@ trait GcpBatchAttachedDisk {
   def mountPoint: Path
 }
 
-case class PipelinesApiEmptyMountedDisk(diskType: DiskType, sizeGb: Int, mountPoint: Path) extends GcpBatchAttachedDisk {
+case class PipelinesApiEmptyMountedDisk(diskType: DiskType, sizeGb: Int, mountPoint: Path)
+    extends GcpBatchAttachedDisk {
   val name = s"d-${mountPoint.pathAsString.md5Sum}"
 
   override def toString: String = s"$mountPoint $sizeGb ${diskType.diskTypeName}"
@@ -95,4 +100,4 @@ case class GcpBatchReferenceFilesDisk(image: String, sizeGb: Int) extends GcpBat
   val mountPoint: Path = DefaultPathBuilder.get(s"/mnt/${image.md5Sum}")
   val name: String = s"d-${mountPoint.pathAsString.md5Sum}"
   val diskType: DiskType = DiskType.HDD
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/package.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/package.scala
index 25489ff6869..50a2fbdcb31 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/package.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/package.scala
@@ -1,4 +1,3 @@
-
 package cromwell.backend.google.batch
 
 import com.google.api.client.http.HttpResponseException
@@ -8,24 +7,22 @@ import cromwell.core.path.Path
 package object io {
   implicit class PathEnhanced(val path: Path) extends AnyVal {
 
-    def writeAsJson(content: String): Path = {
+    def writeAsJson(content: String): Path =
       path.writeBytes(content.getBytes.iterator)(Seq(CloudStorageOptions.withMimeType("application/json")))
-    }
 
-    def writeAsText(content: String): Path = {
+    def writeAsText(content: String): Path =
       path.writeBytes(content.getBytes.iterator)(Seq(CloudStorageOptions.withMimeType("text/plain")))
-    }
   }
 
-  private [batch] def isFatalJesException(t: Throwable): Boolean = t match {
+  private[batch] def isFatalJesException(t: Throwable): Boolean = t match {
     case e: HttpResponseException if e.getStatusCode == 403 => true
     case e: HttpResponseException if e.getStatusCode == 400 && e.getContent.contains("INVALID_ARGUMENT") => true
     case _ => false
   }
 
-  private [batch] def isTransientJesException(t: Throwable): Boolean = t match {
+  private[batch] def isTransientJesException(t: Throwable): Boolean = t match {
     // Quota exceeded
     case e: HttpResponseException if e.getStatusCode == 429 => true
     case _ => false
   }
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/CreateGcpBatchParameters.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/CreateGcpBatchParameters.scala
index d6258169fa8..456f7115ae8 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/CreateGcpBatchParameters.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/CreateGcpBatchParameters.scala
@@ -7,4 +7,4 @@ case class CreateGcpBatchParameters(jobDescriptor: BackendJobDescriptor,
                                     batchAttributes: GcpBatchConfigurationAttributes,
                                     projectId: String,
                                     region: String
-                                   )
+)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBackendInitializationData.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBackendInitializationData.scala
index 47169b30f0a..a64b78fb7d2 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBackendInitializationData.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBackendInitializationData.scala
@@ -5,12 +5,11 @@ import cromwell.backend.google.batch.util.BatchExpressionFunctions
 import cromwell.backend.standard.{StandardInitializationData, StandardValidatedRuntimeAttributesBuilder}
 
 case class GcpBackendInitializationData(
-                                         override val workflowPaths: GcpBatchWorkflowPaths,
-                                         override val runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder,
-                                         gcpBatchConfiguration: GcpBatchConfiguration,
-                                         gcsCredentials: Credentials,
-                                         privateDockerEncryptionKeyName: Option[String],
-                                         privateDockerEncryptedToken: Option[String],
-                                         vpcNetworkAndSubnetworkProjectLabels: Option[VpcAndSubnetworkProjectLabelValues]
-
-                                       ) extends StandardInitializationData(workflowPaths, runtimeAttributesBuilder, classOf[BatchExpressionFunctions] )
+  override val workflowPaths: GcpBatchWorkflowPaths,
+  override val runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder,
+  gcpBatchConfiguration: GcpBatchConfiguration,
+  gcsCredentials: Credentials,
+  privateDockerEncryptionKeyName: Option[String],
+  privateDockerEncryptedToken: Option[String],
+  vpcNetworkAndSubnetworkProjectLabels: Option[VpcAndSubnetworkProjectLabelValues]
+) extends StandardInitializationData(workflowPaths, runtimeAttributesBuilder, classOf[BatchExpressionFunctions])
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfiguration.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfiguration.scala
index dc397c5755e..7e7db17ddf5 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfiguration.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfiguration.scala
@@ -10,29 +10,27 @@ import spray.json._
 
 import scala.concurrent.duration.FiniteDuration
 
-
 class GcpBatchConfiguration(val configurationDescriptor: BackendConfigurationDescriptor,
                             val googleConfig: GoogleConfiguration,
                             val batchAttributes: GcpBatchConfigurationAttributes
-                           ) extends DefaultJsonProtocol {
+) extends DefaultJsonProtocol {
 
   val batchAuths: GcpBatchAuths = batchAttributes.auths
   val root: String = configurationDescriptor.backendConfig.getString("root")
   val batchTimeout: FiniteDuration = batchAttributes.batchTimeout
   val runtimeConfig: Option[Config] = configurationDescriptor.backendRuntimeAttributesConfig
 
-
-  val dockerCredentials: Option[GcpBatchDockerCredentials] = {
+  val dockerCredentials: Option[GcpBatchDockerCredentials] =
     BackendDockerConfiguration.build(configurationDescriptor.backendConfig).dockerCredentials map { creds =>
       GcpBatchDockerCredentials.apply(creds, googleConfig)
-   }
-  }
+    }
 
   val dockerEncryptionKeyName: Option[String] = dockerCredentials flatMap { _.keyName }
   val dockerEncryptionAuthName: Option[String] = dockerCredentials flatMap { _.authName }
   val dockerToken: Option[String] = dockerCredentials map { _.token }
 
-  val jobShell: String = configurationDescriptor.backendConfig.as[Option[String]]("job-shell").getOrElse(
-    configurationDescriptor.globalConfig.getOrElse("system.job-shell", "/bin/bash"))
+  val jobShell: String = configurationDescriptor.backendConfig
+    .as[Option[String]]("job-shell")
+    .getOrElse(configurationDescriptor.globalConfig.getOrElse("system.job-shell", "/bin/bash"))
 
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributes.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributes.scala
index 0a57b0a2a5e..a212ad35f2b 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributes.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributes.scala
@@ -11,10 +11,22 @@ import common.validation.Validation._
 import cromwell.backend.CommonBackendConfigurationAttributes
 import cromwell.backend.google.batch._
 import cromwell.backend.google.batch.authentication.GcpBatchAuths
-import cromwell.backend.google.batch.callcaching.{BatchCacheHitDuplicationStrategy, CopyCachedOutputs, UseOriginalCachedOutputs}
+import cromwell.backend.google.batch.callcaching.{
+  BatchCacheHitDuplicationStrategy,
+  CopyCachedOutputs,
+  UseOriginalCachedOutputs
+}
 import cromwell.backend.google.batch.io.GcpBatchReferenceFilesDisk
-import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.{BatchRequestTimeoutConfiguration, GcsTransferConfiguration, VirtualPrivateCloudConfiguration}
-import cromwell.backend.google.batch.util.{DockerImageCacheEntry, GcpBatchDockerCacheMappingOperations, GcpBatchReferenceFilesMappingOperations}
+import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.{
+  BatchRequestTimeoutConfiguration,
+  GcsTransferConfiguration,
+  VirtualPrivateCloudConfiguration
+}
+import cromwell.backend.google.batch.util.{
+  DockerImageCacheEntry,
+  GcpBatchDockerCacheMappingOperations,
+  GcpBatchReferenceFilesMappingOperations
+}
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
 import cromwell.filesystems.gcs.GcsPathBuilder
@@ -30,29 +42,33 @@ import scala.jdk.CollectionConverters._
 import scala.util.matching.Regex
 import scala.util.{Failure, Success, Try}
 
-case class GcpBatchConfigurationAttributes(project: String,
-                                           computeServiceAccount: String,
-                                           auths: GcpBatchAuths,
-                                           restrictMetadataAccess: Boolean,
-                                           dockerhubToken: String,
-                                           enableFuse: Boolean,
-                                           executionBucket: String,
-                                           location: String,
-                                           maxPollingInterval: Int,
-                                           qps: Int Refined Positive,
-                                           cacheHitDuplicationStrategy: BatchCacheHitDuplicationStrategy,
-                                           requestWorkers: Int Refined Positive,
-                                           batchTimeout: FiniteDuration,
-                                           logFlushPeriod: Option[FiniteDuration],
-                                           gcsTransferConfiguration: GcsTransferConfiguration,
-                                           virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
-                                           batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration,
-                                           referenceFileToDiskImageMappingOpt: Option[Map[String, GcpBatchReferenceFilesDisk]],
-                                           dockerImageToCacheDiskImageMappingOpt: Option[Map[String, DockerImageCacheEntry]],
-                                           checkpointingInterval: FiniteDuration
-                                          )
-
-object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperations with GcpBatchReferenceFilesMappingOperations with StrictLogging {
+case class GcpBatchConfigurationAttributes(
+  project: String,
+  computeServiceAccount: String,
+  auths: GcpBatchAuths,
+  restrictMetadataAccess: Boolean,
+  dockerhubToken: String,
+  enableFuse: Boolean,
+  executionBucket: String,
+  location: String,
+  maxPollingInterval: Int,
+  qps: Int Refined Positive,
+  cacheHitDuplicationStrategy: BatchCacheHitDuplicationStrategy,
+  requestWorkers: Int Refined Positive,
+  batchTimeout: FiniteDuration,
+  logFlushPeriod: Option[FiniteDuration],
+  gcsTransferConfiguration: GcsTransferConfiguration,
+  virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
+  batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration,
+  referenceFileToDiskImageMappingOpt: Option[Map[String, GcpBatchReferenceFilesDisk]],
+  dockerImageToCacheDiskImageMappingOpt: Option[Map[String, DockerImageCacheEntry]],
+  checkpointingInterval: FiniteDuration
+)
+
+object GcpBatchConfigurationAttributes
+    extends GcpBatchDockerCacheMappingOperations
+    with GcpBatchReferenceFilesMappingOperations
+    with StrictLogging {
 
   /**
     * param transferAttempts This is the number of attempts, not retries, hence it is positive.
@@ -64,11 +80,12 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
   final case class VirtualPrivateCloudLiterals(network: String, subnetwork: Option[String])
 
   final case class VirtualPrivateCloudConfiguration(labelsOption: Option[VirtualPrivateCloudLabels],
-                                                    literalsOption: Option[VirtualPrivateCloudLiterals],
-                                                   )
-
-  final case class BatchRequestTimeoutConfiguration(readTimeoutMillis: Option[Int Refined Positive], connectTimeoutMillis: Option[Int Refined Positive])
+                                                    literalsOption: Option[VirtualPrivateCloudLiterals]
+  )
 
+  final case class BatchRequestTimeoutConfiguration(readTimeoutMillis: Option[Int Refined Positive],
+                                                    connectTimeoutMillis: Option[Int Refined Positive]
+  )
 
   lazy val Logger: Logger = LoggerFactory.getLogger("BatchConfiguration")
 
@@ -119,45 +136,47 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
     "genomics.default-zones" -> "default-runtime-attributes.zones"
   )
 
-  def apply(googleConfig: GoogleConfiguration, backendConfig: Config, backendName: String): GcpBatchConfigurationAttributes = {
-
+  def apply(googleConfig: GoogleConfiguration,
+            backendConfig: Config,
+            backendName: String
+  ): GcpBatchConfigurationAttributes = {
 
-    def vpcErrorMessage(missingKeys: List[String]) = s"Virtual Private Cloud configuration is invalid. Missing keys: `${missingKeys.mkString(",")}`.".invalidNel
+    def vpcErrorMessage(missingKeys: List[String]) =
+      s"Virtual Private Cloud configuration is invalid. Missing keys: `${missingKeys.mkString(",")}`.".invalidNel
 
     def validateVPCLabelsConfig(networkOption: Option[String],
                                 subnetworkOption: Option[String],
-                                authOption: Option[String],
-                               ): ErrorOr[Option[VirtualPrivateCloudLabels]] = {
+                                authOption: Option[String]
+    ): ErrorOr[Option[VirtualPrivateCloudLabels]] =
       (networkOption, subnetworkOption, authOption) match {
-        case (Some(network), _, Some(auth)) => googleConfig.auth(auth) match {
-          case Valid(validAuth) =>
-            Option(VirtualPrivateCloudLabels(network, subnetworkOption, validAuth)).validNel
-          case Invalid(error) => s"Auth $auth is not valid for Virtual Private Cloud configuration. Reason: $error".invalidNel
-        }
+        case (Some(network), _, Some(auth)) =>
+          googleConfig.auth(auth) match {
+            case Valid(validAuth) =>
+              Option(VirtualPrivateCloudLabels(network, subnetworkOption, validAuth)).validNel
+            case Invalid(error) =>
+              s"Auth $auth is not valid for Virtual Private Cloud configuration. Reason: $error".invalidNel
+          }
         case (Some(_), _, None) => vpcErrorMessage(List("auth"))
         case (None, _, Some(_)) => vpcErrorMessage(List("network-label-key"))
         case (None, Some(_), None) => vpcErrorMessage(List("network-label-key", "auth"))
         case (None, None, None) => None.validNel
       }
-    }
-
 
     def validateVPCLiteralsConfig(networkNameOption: Option[String],
-                                  subnetworkNameOption: Option[String],
-                                 ): ErrorOr[Option[VirtualPrivateCloudLiterals]] = {
+                                  subnetworkNameOption: Option[String]
+    ): ErrorOr[Option[VirtualPrivateCloudLiterals]] =
       (networkNameOption, subnetworkNameOption) match {
         case (None, Some(_)) => vpcErrorMessage(List("network-name"))
         case (Some(networkName), _) => Option(VirtualPrivateCloudLiterals(networkName, subnetworkNameOption)).valid
         case (None, None) => None.valid
       }
-    }
 
     def validateVPCConfig(networkNameOption: Option[String],
                           subnetworkNameOption: Option[String],
                           networkLabelOption: Option[String],
                           subnetworkLabelOption: Option[String],
-                          authOption: Option[String],
-                         ): ErrorOr[VirtualPrivateCloudConfiguration] = {
+                          authOption: Option[String]
+    ): ErrorOr[VirtualPrivateCloudConfiguration] = {
       val vpcLabelsValidation =
         validateVPCLabelsConfig(networkLabelOption, subnetworkLabelOption, authOption)
       val vpcLiteralsValidation =
@@ -165,18 +184,20 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
       (vpcLabelsValidation, vpcLiteralsValidation) mapN VirtualPrivateCloudConfiguration
     }
 
-    val configKeys = backendConfig.entrySet().asScala.toSet map { entry: java.util.Map.Entry[String, ConfigValue] => entry.getKey }
+    val configKeys = backendConfig.entrySet().asScala.toSet map { entry: java.util.Map.Entry[String, ConfigValue] =>
+      entry.getKey
+    }
     warnNotRecognized(configKeys, batchKeys, backendName, Logger)
 
-
     def warnDeprecated(keys: Set[String], deprecated: Map[String, String], logger: Logger): Unit = {
       val deprecatedKeys = keys.intersect(deprecated.keySet)
-      deprecatedKeys foreach { key => logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}") }
+      deprecatedKeys foreach { key =>
+        logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}")
+      }
     }
 
     warnDeprecated(configKeys, deprecatedJesKeys, Logger)
 
-
     val project: ErrorOr[String] = validate {
       backendConfig.as[String]("project")
     }
@@ -187,7 +208,8 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
       backendConfig.as[String]("genomics.location")
     }
     val maxPollingInterval: Int = backendConfig.as[Option[Int]]("maximum-polling-interval").getOrElse(600)
-    val computeServiceAccount: String = backendConfig.as[Option[String]]("genomics.compute-service-account").getOrElse("default")
+    val computeServiceAccount: String =
+      backendConfig.as[Option[String]]("genomics.compute-service-account").getOrElse("default")
     val genomicsAuthName: ErrorOr[String] = validate {
       backendConfig.as[String]("genomics.auth")
     }
@@ -210,10 +232,14 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
       backendConfig.as[Option[String]]("filesystems.gcs.caching.duplication-strategy").getOrElse("copy") match {
         case "copy" => CopyCachedOutputs
         case "reference" => UseOriginalCachedOutputs
-        case other => throw new IllegalArgumentException(s"Unrecognized caching duplication strategy: $other. Supported strategies are copy and reference. See reference.conf for more details.")
+        case other =>
+          throw new IllegalArgumentException(
+            s"Unrecognized caching duplication strategy: $other. Supported strategies are copy and reference. See reference.conf for more details."
+          )
       }
     }
-    val requestWorkers: ErrorOr[Int Refined Positive] = validatePositiveInt(backendConfig.as[Option[Int]]("request-workers").getOrElse(3), "request-workers")
+    val requestWorkers: ErrorOr[Int Refined Positive] =
+      validatePositiveInt(backendConfig.as[Option[Int]]("request-workers").getOrElse(3), "request-workers")
 
     val batchTimeout: FiniteDuration = backendConfig.getOrElse("batch-timeout", 7.days)
 
@@ -225,9 +251,11 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
       case None => Option(1.minute)
     }
 
-    val parallelCompositeUploadThreshold = validateGsutilMemorySpecification(backendConfig, "genomics.parallel-composite-upload-threshold")
+    val parallelCompositeUploadThreshold =
+      validateGsutilMemorySpecification(backendConfig, "genomics.parallel-composite-upload-threshold")
 
-    val localizationAttempts: ErrorOr[Int Refined Positive] = backendConfig.as[Option[Int]]("genomics.localization-attempts")
+    val localizationAttempts: ErrorOr[Int Refined Positive] = backendConfig
+      .as[Option[Int]]("genomics.localization-attempts")
       .map(attempts => validatePositiveInt(attempts, "genomics.localization-attempts"))
       .getOrElse(DefaultGcsTransferAttempts.validNel)
 
@@ -250,88 +278,93 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
       backendConfig.getAs[String]("virtual-private-cloud.auth")
     }
 
-    val virtualPrivateCloudConfiguration: ErrorOr[VirtualPrivateCloudConfiguration] = {
+    val virtualPrivateCloudConfiguration: ErrorOr[VirtualPrivateCloudConfiguration] =
       (vpcNetworkName, vpcSubnetworkName, vpcNetworkLabel, vpcSubnetworkLabel, vpcAuth) flatMapN validateVPCConfig
-    }
 
-    val batchRequestsReadTimeout = readOptionalPositiveMillisecondsIntFromDuration(backendConfig, "batch-requests.timeouts.read")
-    val batchRequestsConnectTimeout = readOptionalPositiveMillisecondsIntFromDuration(backendConfig, "batch-requests.timeouts.connect")
+    val batchRequestsReadTimeout =
+      readOptionalPositiveMillisecondsIntFromDuration(backendConfig, "batch-requests.timeouts.read")
+    val batchRequestsConnectTimeout =
+      readOptionalPositiveMillisecondsIntFromDuration(backendConfig, "batch-requests.timeouts.connect")
 
-    val batchRequestTimeoutConfigurationValidation = (batchRequestsReadTimeout, batchRequestsConnectTimeout) mapN { (read, connect) =>
-      BatchRequestTimeoutConfiguration(readTimeoutMillis = read, connectTimeoutMillis = connect)
+    val batchRequestTimeoutConfigurationValidation = (batchRequestsReadTimeout, batchRequestsConnectTimeout) mapN {
+      (read, connect) =>
+        BatchRequestTimeoutConfiguration(readTimeoutMillis = read, connectTimeoutMillis = connect)
     }
 
-    val referenceDiskLocalizationManifestFiles: ErrorOr[Option[List[ManifestFile]]] = validateReferenceDiskManifestConfigs(backendConfig, backendName)
+    val referenceDiskLocalizationManifestFiles: ErrorOr[Option[List[ManifestFile]]] =
+      validateReferenceDiskManifestConfigs(backendConfig, backendName)
 
-    val dockerImageCacheManifestFile: ErrorOr[Option[ValidFullGcsPath]] = validateGcsPathToDockerImageCacheManifestFile(backendConfig)
+    val dockerImageCacheManifestFile: ErrorOr[Option[ValidFullGcsPath]] = validateGcsPathToDockerImageCacheManifestFile(
+      backendConfig
+    )
 
     val checkpointingInterval: FiniteDuration = backendConfig.getOrElse(checkpointingIntervalKey, 10.minutes)
 
-    def authGoogleConfigForBatchConfigurationAttributes(project: String,
-                                                        bucket: String,
-                                                        genomicsName: String,
-                                                        location: String,
-                                                        restrictMetadata: Boolean,
-                                                        dockerhubToken: String,
-                                                        enableFuse: Boolean,
-                                                        gcsName: String,
-                                                        qps: Int Refined Positive,
-                                                        cacheHitDuplicationStrategy: BatchCacheHitDuplicationStrategy,
-                                                        requestWorkers: Int Refined Positive,
-                                                        gcsTransferConfiguration: GcsTransferConfiguration,
-                                                        virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
-                                                        batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration,
-                                                        referenceDiskLocalizationManifestFilesOpt: Option[List[ManifestFile]],
-                                                        dockerImageCacheManifestFileOpt: Option[ValidFullGcsPath]): ErrorOr[GcpBatchConfigurationAttributes] =
-      (googleConfig.auth(genomicsName), googleConfig.auth(gcsName)) mapN {
-        (genomicsAuth, gcsAuth) =>
-          val generatedReferenceFilesMappingOpt = referenceDiskLocalizationManifestFilesOpt map {
-            generateReferenceFilesMapping(genomicsAuth, _)
-          }
-          val dockerImageToCacheDiskImageMappingOpt = dockerImageCacheManifestFileOpt map {
-            generateDockerImageToDiskImageMapping(genomicsAuth, _)
-          }
-          models.GcpBatchConfigurationAttributes(
-            project = project,
-            computeServiceAccount = computeServiceAccount,
-            auths = GcpBatchAuths(genomicsAuth, gcsAuth),
-            restrictMetadataAccess = restrictMetadata,
-            dockerhubToken = dockerhubToken,
-            enableFuse = enableFuse,
-            executionBucket = bucket,
-            location = location,
-            maxPollingInterval = maxPollingInterval,
-            qps = qps,
-            cacheHitDuplicationStrategy = cacheHitDuplicationStrategy,
-            requestWorkers = requestWorkers,
-            batchTimeout = batchTimeout,
-            logFlushPeriod = logFlushPeriod,
-            gcsTransferConfiguration = gcsTransferConfiguration,
-            virtualPrivateCloudConfiguration = virtualPrivateCloudConfiguration,
-            batchRequestTimeoutConfiguration = batchRequestTimeoutConfiguration,
-            referenceFileToDiskImageMappingOpt = generatedReferenceFilesMappingOpt,
-            dockerImageToCacheDiskImageMappingOpt = dockerImageToCacheDiskImageMappingOpt,
-            checkpointingInterval = checkpointingInterval
-          )
+    def authGoogleConfigForBatchConfigurationAttributes(
+      project: String,
+      bucket: String,
+      genomicsName: String,
+      location: String,
+      restrictMetadata: Boolean,
+      dockerhubToken: String,
+      enableFuse: Boolean,
+      gcsName: String,
+      qps: Int Refined Positive,
+      cacheHitDuplicationStrategy: BatchCacheHitDuplicationStrategy,
+      requestWorkers: Int Refined Positive,
+      gcsTransferConfiguration: GcsTransferConfiguration,
+      virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
+      batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration,
+      referenceDiskLocalizationManifestFilesOpt: Option[List[ManifestFile]],
+      dockerImageCacheManifestFileOpt: Option[ValidFullGcsPath]
+    ): ErrorOr[GcpBatchConfigurationAttributes] =
+      (googleConfig.auth(genomicsName), googleConfig.auth(gcsName)) mapN { (genomicsAuth, gcsAuth) =>
+        val generatedReferenceFilesMappingOpt = referenceDiskLocalizationManifestFilesOpt map {
+          generateReferenceFilesMapping(genomicsAuth, _)
+        }
+        val dockerImageToCacheDiskImageMappingOpt = dockerImageCacheManifestFileOpt map {
+          generateDockerImageToDiskImageMapping(genomicsAuth, _)
+        }
+        models.GcpBatchConfigurationAttributes(
+          project = project,
+          computeServiceAccount = computeServiceAccount,
+          auths = GcpBatchAuths(genomicsAuth, gcsAuth),
+          restrictMetadataAccess = restrictMetadata,
+          dockerhubToken = dockerhubToken,
+          enableFuse = enableFuse,
+          executionBucket = bucket,
+          location = location,
+          maxPollingInterval = maxPollingInterval,
+          qps = qps,
+          cacheHitDuplicationStrategy = cacheHitDuplicationStrategy,
+          requestWorkers = requestWorkers,
+          batchTimeout = batchTimeout,
+          logFlushPeriod = logFlushPeriod,
+          gcsTransferConfiguration = gcsTransferConfiguration,
+          virtualPrivateCloudConfiguration = virtualPrivateCloudConfiguration,
+          batchRequestTimeoutConfiguration = batchRequestTimeoutConfiguration,
+          referenceFileToDiskImageMappingOpt = generatedReferenceFilesMappingOpt,
+          dockerImageToCacheDiskImageMappingOpt = dockerImageToCacheDiskImageMappingOpt,
+          checkpointingInterval = checkpointingInterval
+        )
       }
 
-
     (project,
-      executionBucket,
-      genomicsAuthName,
-      location,
-      genomicsRestrictMetadataAccess,
-      dockerhubToken,
-      genomicsEnableFuse,
-      gcsFilesystemAuthName,
-      qpsValidation,
-      duplicationStrategy,
-      requestWorkers,
-      gcsTransferConfiguration,
-      virtualPrivateCloudConfiguration,
-      batchRequestTimeoutConfigurationValidation,
-      referenceDiskLocalizationManifestFiles,
-      dockerImageCacheManifestFile
+     executionBucket,
+     genomicsAuthName,
+     location,
+     genomicsRestrictMetadataAccess,
+     dockerhubToken,
+     genomicsEnableFuse,
+     gcsFilesystemAuthName,
+     qpsValidation,
+     duplicationStrategy,
+     requestWorkers,
+     gcsTransferConfiguration,
+     virtualPrivateCloudConfiguration,
+     batchRequestTimeoutConfigurationValidation,
+     referenceDiskLocalizationManifestFiles,
+     dockerImageCacheManifestFile
     ) flatMapN authGoogleConfigForBatchConfigurationAttributes match {
       case Valid(r) => r
       case Invalid(f) =>
@@ -342,25 +375,27 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
     }
   }
 
-  private def validateSingleGcsPath(gcsPath: String): ErrorOr[ValidFullGcsPath] = {
+  private def validateSingleGcsPath(gcsPath: String): ErrorOr[ValidFullGcsPath] =
     GcsPathBuilder.validateGcsPath(gcsPath) match {
       case validPath: ValidFullGcsPath => validPath.validNel
       case invalidPath => s"Invalid GCS path: $invalidPath".invalidNel
     }
-  }
 
-  private[batch] def validateGcsPathToDockerImageCacheManifestFile(backendConfig: Config): ErrorOr[Option[ValidFullGcsPath]] = {
+  private[batch] def validateGcsPathToDockerImageCacheManifestFile(
+    backendConfig: Config
+  ): ErrorOr[Option[ValidFullGcsPath]] =
     backendConfig.getAs[String]("docker-image-cache-manifest-file") match {
       case Some(gcsPath) => validateSingleGcsPath(gcsPath).map(Option.apply)
       case None => None.validNel
     }
-  }
 
   /**
     * Validate that the entries corresponding to "reference-disk-localization-manifests" in the specified
     * backend are parseable as `ManifestFile`s.
     */
-  private[batch] def validateReferenceDiskManifestConfigs(backendConfig: Config, backendName: String): ErrorOr[Option[List[ManifestFile]]] = {
+  private[batch] def validateReferenceDiskManifestConfigs(backendConfig: Config,
+                                                          backendName: String
+  ): ErrorOr[Option[List[ManifestFile]]] =
     Try(backendConfig.getAs[List[Config]]("reference-disk-localization-manifests")) match {
       case Failure(e) =>
         ("Error attempting to parse value for 'reference-disk-localization-manifests' as List[Config]: " +
@@ -375,10 +410,13 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
             // equivalent using clunkier syntax:
             configs traverse parser.decode[ManifestFile] match {
               case Right(manifests) =>
-                logger.info(s"Reference disks feature for $backendName backend is configured with the following reference images: ${manifests.map(_.imageIdentifier).mkString(", ")}.")
+                logger.info(
+                  s"Reference disks feature for $backendName backend is configured with the following reference images: ${manifests.map(_.imageIdentifier).mkString(", ")}."
+                )
                 Option(manifests).validNel
               case Left(err) =>
-                val message = s"Reference disks misconfigured for backend $backendName, could not parse as List[ManifestFile]"
+                val message =
+                  s"Reference disks misconfigured for backend $backendName, could not parse as List[ManifestFile]"
                 logger.error(message, err.getCause)
                 s"$message: ${err.getMessage}".invalidNel
             }
@@ -387,7 +425,6 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
             None.validNel
         }
     }
-  }
 
   def validateQps(config: Config): ErrorOr[Int Refined Positive] = {
     import eu.timepit.refined._
@@ -396,7 +433,8 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
     val qpsCandidate = qp100s / 100
 
     refineV[Positive](qpsCandidate) match {
-      case Left(_) => s"Calculated QPS for Google Genomics API ($qpsCandidate/s) was not a positive integer (supplied value was $qp100s per 100s)".invalidNel
+      case Left(_) =>
+        s"Calculated QPS for Google Genomics API ($qpsCandidate/s) was not a positive integer (supplied value was $qp100s per 100s)".invalidNel
       case Right(refined) => refined.validNel
     }
   }
@@ -405,19 +443,21 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
     val entry = config.as[Option[String]](configPath)
     entry match {
       case None => "0".validNel
-      case Some(v@GsutilHumanBytes(_, _)) => v.validNel
-      case Some(bad) => s"Invalid gsutil memory specification in Cromwell configuration at path '$configPath': '$bad'".invalidNel
+      case Some(v @ GsutilHumanBytes(_, _)) => v.validNel
+      case Some(bad) =>
+        s"Invalid gsutil memory specification in Cromwell configuration at path '$configPath': '$bad'".invalidNel
     }
   }
 
-  def validatePositiveInt(n: Int, configPath: String): Validated[NonEmptyList[String], Refined[Int, Positive]] = {
+  def validatePositiveInt(n: Int, configPath: String): Validated[NonEmptyList[String], Refined[Int, Positive]] =
     refineV[Positive](n) match {
       case Left(_) => s"Value $n for $configPath is not strictly positive".invalidNel
       case Right(refined) => refined.validNel
     }
-  }
 
-  def readOptionalPositiveMillisecondsIntFromDuration(backendConfig: Config, configPath: String): ErrorOr[Option[Int Refined Positive]] = {
+  def readOptionalPositiveMillisecondsIntFromDuration(backendConfig: Config,
+                                                      configPath: String
+  ): ErrorOr[Option[Int Refined Positive]] = {
 
     def validate(n: FiniteDuration) = {
       val result: ErrorOr[Int Refined Positive] = Try(n.toMillis.toInt).toErrorOr flatMap { millisInt =>
@@ -445,7 +485,7 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
       List("GiB", "Gibit", "G"),
       List("TiB", "Tibit", "T"),
       List("PiB", "Pibit", "P"),
-      List("EiB", "Eibit", "E"),
+      List("EiB", "Eibit", "E")
     )
 
     val suffixes = for {
@@ -454,7 +494,7 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
     } yield name
 
     // Differs from the Python original in a couple of ways:
-    //* The Python original uses named groups which are not supported in Scala regexes.
+    // * The Python original uses named groups which are not supported in Scala regexes.
     //   (?P<num>\d*\.\d+|\d+)\s*(?P<suffix>%s)?
     //
     // * The Python original lowercases both the units and the human string before running the matcher.
@@ -462,4 +502,4 @@ object GcpBatchConfigurationAttributes extends GcpBatchDockerCacheMappingOperati
     val orSuffixes = suffixes.mkString("|")
     "(?i)(\\d*\\.\\d+|\\d+)\\s*(%s)?".format(orSuffixes).r
   }
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchCustomMachineType.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchCustomMachineType.scala
index 84366f4e969..cf5db4df9e9 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchCustomMachineType.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchCustomMachineType.scala
@@ -21,6 +21,7 @@ import scala.math.{log, pow}
   * - https://cloud.google.com/sdk/gcloud/reference/compute/instances/create#--custom-vm-type
   */
 trait CustomMachineType {
+
   /**
     * The vm prefix to create this custom machine type.
     */
@@ -54,10 +55,7 @@ trait CustomMachineType {
   /**
     * Generates a custom machine type based on the requested memory and cpu
     */
-  def machineType(requestedMemory: MemorySize,
-                  requestedCpu: Int Refined Positive,
-                  jobLogger: Logger,
-                 ): String = {
+  def machineType(requestedMemory: MemorySize, requestedCpu: Int Refined Positive, jobLogger: Logger): String = {
     val memory = requestedMemory |> validateMemory
     val cpu = requestedCpu |> validateCpu
 
@@ -92,8 +90,8 @@ trait CustomMachineType {
                             adjustedCpu: Int,
                             originalMemory: MemorySize,
                             adjustedMemory: MemorySize,
-                            logger: Logger,
-                           ): Unit = {
+                            logger: Logger
+  ): Unit = {
     def memoryAdjustmentLog = s"memory was adjusted from ${originalMemory.toMBString} to ${adjustedMemory.toMBString}"
 
     def cpuAdjustmentLog = s"cpu was adjusted from $originalCpu to $adjustedCpu"
@@ -101,7 +99,7 @@ trait CustomMachineType {
     val messageOption =
       (
         originalCpu == adjustedCpu,
-        originalMemory.to(MemoryUnit.MB).amount == adjustedMemory.to(MemoryUnit.MB).amount,
+        originalMemory.to(MemoryUnit.MB).amount == adjustedMemory.to(MemoryUnit.MB).amount
       ) match {
         case (true, false) => Option(memoryAdjustmentLog)
         case (false, true) => Option(cpuAdjustmentLog)
@@ -129,17 +127,15 @@ case object N1CustomMachineType extends CustomMachineType {
   override val maxMemoryPerCpu: MemorySize = MemorySize(6.5, MemoryUnit.GB)
   override val memoryFactor: MemorySize = MemorySize(256, MemoryUnit.MB)
 
-  override def validateCpu(cpu: Refined[Int, Positive]): Int = {
+  override def validateCpu(cpu: Refined[Int, Positive]): Int =
     // Either one cpu, or an even number of cpus
     cpu.value match {
       case 1 => 1
       case cpu => cpu + (cpu % 2)
     }
-  }
 
-  override def validateMemory(memory: MemorySize): MemorySize = {
+  override def validateMemory(memory: MemorySize): MemorySize =
     memory.asMultipleOf(memoryFactor)
-  }
 }
 
 case object N2CustomMachineType extends CustomMachineType {
@@ -148,18 +144,16 @@ case object N2CustomMachineType extends CustomMachineType {
   override val maxMemoryPerCpu: MemorySize = MemorySize(8.0, MemoryUnit.GB)
   override val memoryFactor: MemorySize = MemorySize(256, MemoryUnit.MB)
 
-  override def validateCpu(cpu: Refined[Int, Positive]): Int = {
+  override def validateCpu(cpu: Refined[Int, Positive]): Int =
     // cpus must be divisible by 2 up to 32, and higher numbers must be divisible by 4
     cpu.value match {
       case cpu if cpu <= 32 => cpu + (cpu % 2)
       case cpu if cpu % 4 == 0 => cpu
       case cpu => cpu + (4 - (cpu % 4))
     }
-  }
 
-  override def validateMemory(memory: MemorySize): MemorySize = {
+  override def validateMemory(memory: MemorySize): MemorySize =
     memory.asMultipleOf(memoryFactor)
-  }
 }
 
 case object N2DCustomMachineType extends CustomMachineType {
@@ -167,18 +161,15 @@ case object N2DCustomMachineType extends CustomMachineType {
   override val minMemoryPerCpu: MemorySize = MemorySize(0.5, MemoryUnit.GB)
   override val maxMemoryPerCpu: MemorySize = MemorySize(8.0, MemoryUnit.GB)
   override val memoryFactor: MemorySize = MemorySize(256, MemoryUnit.MB)
-  
-  override def validateCpu(cpu: Refined[Int, Positive]): Int = {
+
+  override def validateCpu(cpu: Refined[Int, Positive]): Int =
     cpu.value match {
-      case cpu if cpu <= 16 => 2 max pow(2, (log(cpu.toDouble)/log(2)).ceil).toInt
+      case cpu if cpu <= 16 => 2 max pow(2, (log(cpu.toDouble) / log(2)).ceil).toInt
       case cpu if cpu > 16 && cpu <= 96 && cpu % 16 == 0 => cpu
       case cpu if cpu > 16 && cpu <= 96 => cpu + 16 - (cpu % 16)
       case cpu if cpu > 96 => 96
     }
-  }
 
-  override def validateMemory(memory: MemorySize): MemorySize = {
+  override def validateMemory(memory: MemorySize): MemorySize =
     memory.asMultipleOf(memoryFactor)
-  }
 }
-
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchJobPaths.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchJobPaths.scala
index 923e5dc16f5..494eb6b0faa 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchJobPaths.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchJobPaths.scala
@@ -16,18 +16,16 @@ object GcpBatchJobPaths {
   val DrsLocalizationManifestName = "drs_manifest"
 
 }
-case class GcpBatchJobPaths(override val workflowPaths: GcpBatchWorkflowPaths, jobKey: BackendJobDescriptorKey, override val isCallCacheCopyAttempt: Boolean = false) extends JobPaths {
+case class GcpBatchJobPaths(override val workflowPaths: GcpBatchWorkflowPaths,
+                            jobKey: BackendJobDescriptorKey,
+                            override val isCallCacheCopyAttempt: Boolean = false
+) extends JobPaths {
 
   def batchLogBasename = {
-    val index = jobKey
-      .index
+    val index = jobKey.index
       .map(s => s"-$s")
       .getOrElse("")
-    s"${
-      jobKey
-        .node
-        .localName
-    }$index"
+    s"${jobKey.node.localName}$index"
   }
 
   val batchLogFilename: String = s"$batchLogBasename.log"
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchParameters.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchParameters.scala
index c2c75ce5667..010ee9d2fdb 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchParameters.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchParameters.scala
@@ -52,32 +52,33 @@ sealed trait GcpBatchOutput extends BatchParameter {
   def contentType: Option[ContentType] = None
 }
 
-final case class GcpBatchFileInput(name: String,
-                                       cloudPath: Path,
-                                       relativeHostPath: Path,
-                                       mount: GcpBatchAttachedDisk) extends GcpBatchInput
+final case class GcpBatchFileInput(name: String, cloudPath: Path, relativeHostPath: Path, mount: GcpBatchAttachedDisk)
+    extends GcpBatchInput
 
 final case class GcpBatchDirectoryInput(name: String,
-                                            cloudPath: Path,
-                                            relativeHostPath: Path,
-                                            mount: GcpBatchAttachedDisk) extends GcpBatchInput
-
-final case class GcpBatchFileOutput(name: String,
                                         cloudPath: Path,
                                         relativeHostPath: Path,
-                                        mount: GcpBatchAttachedDisk,
-                                        optional: Boolean,
-                                        secondary: Boolean,
-                                        uploadPeriod: Option[FiniteDuration] = None,
-                                        override val contentType: Option[ContentType] = None) extends GcpBatchOutput
+                                        mount: GcpBatchAttachedDisk
+) extends GcpBatchInput
+
+final case class GcpBatchFileOutput(name: String,
+                                    cloudPath: Path,
+                                    relativeHostPath: Path,
+                                    mount: GcpBatchAttachedDisk,
+                                    optional: Boolean,
+                                    secondary: Boolean,
+                                    uploadPeriod: Option[FiniteDuration] = None,
+                                    override val contentType: Option[ContentType] = None
+) extends GcpBatchOutput
 
 final case class GcpBatchDirectoryOutput(name: String,
-                                             cloudPath: Path,
-                                             relativeHostPath: Path,
-                                             mount: GcpBatchAttachedDisk,
-                                             optional: Boolean,
-                                             secondary: Boolean,
-                                             override val contentType: Option[ContentType] = None) extends GcpBatchOutput
+                                         cloudPath: Path,
+                                         relativeHostPath: Path,
+                                         mount: GcpBatchAttachedDisk,
+                                         optional: Boolean,
+                                         secondary: Boolean,
+                                         override val contentType: Option[ContentType] = None
+) extends GcpBatchOutput
 
 // TODO: Remove when support for V1 is stopped, this is only used to pass the extra_param auth file
-final case class GcpBatchLiteralInput(name: String, value: String)
\ No newline at end of file
+final case class GcpBatchLiteralInput(name: String, value: String)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRequest.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRequest.scala
index 3c616c0ba4e..df0e8a9cede 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRequest.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRequest.scala
@@ -6,4 +6,5 @@ import cromwell.core.WorkflowId
 case class GcpBatchRequest(workflowId: WorkflowId,
                            createParameters: CreateBatchJobParameters,
                            jobName: String,
-                           gcpBatchParameters: CreateGcpBatchParameters)
+                           gcpBatchParameters: CreateGcpBatchParameters
+)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
index c9dc62b0cc7..cdf3826f7af 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
@@ -37,21 +37,21 @@ object GpuResource {
 
 final case class GpuResource(gpuType: GpuType, gpuCount: Int Refined Positive)
 
-final case class GcpBatchRuntimeAttributes(
-                                      cpu: Int Refined Positive,
-                                      cpuPlatform: Option[String],
-                                      gpuResource: Option[GpuResource],
-                                      zones: Vector[String],
-                                      preemptible: Int,
-                                      bootDiskSize: Int,
-                                      memory: MemorySize,
-                                      disks: Seq[GcpBatchAttachedDisk],
-                                      dockerImage: String,
-                                      failOnStderr: Boolean,
-                                      continueOnReturnCode: ContinueOnReturnCode,
-                                      noAddress: Boolean,
-                                      useDockerImageCache: Option[Boolean],
-                                      checkpointFilename: Option[String])
+final case class GcpBatchRuntimeAttributes(cpu: Int Refined Positive,
+                                           cpuPlatform: Option[String],
+                                           gpuResource: Option[GpuResource],
+                                           zones: Vector[String],
+                                           preemptible: Int,
+                                           bootDiskSize: Int,
+                                           memory: MemorySize,
+                                           disks: Seq[GcpBatchAttachedDisk],
+                                           dockerImage: String,
+                                           failOnStderr: Boolean,
+                                           continueOnReturnCode: ContinueOnReturnCode,
+                                           noAddress: Boolean,
+                                           useDockerImageCache: Option[Boolean],
+                                           checkpointFilename: Option[String]
+)
 
 object GcpBatchRuntimeAttributes {
 
@@ -74,147 +74,188 @@ object GcpBatchRuntimeAttributes {
   private val DisksDefaultValue = WomString(s"${GcpBatchWorkingDisk.Name} 10 SSD")
 
   val CpuPlatformKey = "cpuPlatform"
-  private val cpuPlatformValidationInstance = new StringRuntimeAttributesValidation(CpuPlatformKey)
-    .optional
+  private val cpuPlatformValidationInstance = new StringRuntimeAttributesValidation(CpuPlatformKey).optional
   // via `gcloud compute zones describe us-central1-a`
   val CpuPlatformIntelCascadeLakeValue = "Intel Cascade Lake"
   val CpuPlatformAMDRomeValue = "AMD Rome"
 
-  private def cpuMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] = CpuValidation
-    .instanceMin
-    .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
+  private def cpuMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] =
+    CpuValidation.instanceMin
+      .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
   val UseDockerImageCacheKey = "useDockerImageCache"
-  private val useDockerImageCacheValidationInstance = new BooleanRuntimeAttributesValidation(UseDockerImageCacheKey)
-    .optional
+  private val useDockerImageCacheValidationInstance = new BooleanRuntimeAttributesValidation(
+    UseDockerImageCacheKey
+  ).optional
 
   val CheckpointFileKey = "checkpointFile"
   private val checkpointFileValidationInstance = new StringRuntimeAttributesValidation(CheckpointFileKey).optional
 
   private val MemoryDefaultValue = "2048 MB"
 
-  private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] = CpuValidation
-    .instance
-    .withDefault(CpuValidation
-      .configDefaultWomValue(runtimeConfig) getOrElse CpuValidation
-      .defaultMin)
-  private def cpuPlatformValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] = cpuPlatformValidationInstance
-  private def gpuTypeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[GpuType] = GpuTypeValidation.optional
+  private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] =
+    CpuValidation.instance
+      .withDefault(
+        CpuValidation
+          .configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin
+      )
+  private def cpuPlatformValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] =
+    cpuPlatformValidationInstance
+  private def gpuTypeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[GpuType] =
+    GpuTypeValidation.optional
 
   val GpuDriverVersionKey = "nvidiaDriverVersion"
-  private def gpuDriverValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] = new StringRuntimeAttributesValidation(GpuDriverVersionKey).optional
+  private def gpuDriverValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] =
+    new StringRuntimeAttributesValidation(GpuDriverVersionKey).optional
 
-  private def gpuCountValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optional
-  private def gpuMinValidation(runtimeConfig: Option[Config]):OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optionalMin
+  private def gpuCountValidation(
+    runtimeConfig: Option[Config]
+  ): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optional
+  private def gpuMinValidation(
+    runtimeConfig: Option[Config]
+  ): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optionalMin
 
   private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
 
   private def failOnStderrValidation(runtimeConfig: Option[Config]) = FailOnStderrValidation.default(runtimeConfig)
 
-  private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) = ContinueOnReturnCodeValidation.default(runtimeConfig)
+  private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) =
+    ContinueOnReturnCodeValidation.default(runtimeConfig)
 
-  private def disksValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Seq[GcpBatchAttachedDisk]] = DisksValidation
-    .withDefault(DisksValidation.configDefaultWomValue(runtimeConfig) getOrElse DisksDefaultValue)
+  private def disksValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Seq[GcpBatchAttachedDisk]] =
+    DisksValidation
+      .withDefault(DisksValidation.configDefaultWomValue(runtimeConfig) getOrElse DisksDefaultValue)
 
-  private def zonesValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[String]] = ZonesValidation
-    .withDefault(ZonesValidation
-      .configDefaultWomValue(runtimeConfig) getOrElse ZonesDefaultValue)
+  private def zonesValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[String]] =
+    ZonesValidation
+      .withDefault(
+        ZonesValidation
+          .configDefaultWomValue(runtimeConfig) getOrElse ZonesDefaultValue
+      )
 
-  private def preemptibleValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = preemptibleValidationInstance
-    .withDefault(preemptibleValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse PreemptibleDefaultValue)
+  private def preemptibleValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] =
+    preemptibleValidationInstance
+      .withDefault(preemptibleValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse PreemptibleDefaultValue)
 
-  private def memoryValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] = {
+  private def memoryValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] =
     MemoryValidation.withDefaultMemory(
       RuntimeAttributesKeys.MemoryKey,
-      MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, runtimeConfig) getOrElse MemoryDefaultValue)
-  }
+      MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, runtimeConfig) getOrElse MemoryDefaultValue
+    )
 
-  private def memoryMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] = {
+  private def memoryMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] =
     MemoryValidation.withDefaultMemory(
       RuntimeAttributesKeys.MemoryMinKey,
       MemoryValidation
-        .configDefaultString(RuntimeAttributesKeys.MemoryMinKey, runtimeConfig) getOrElse MemoryDefaultValue)
-  }
-
+        .configDefaultString(RuntimeAttributesKeys.MemoryMinKey, runtimeConfig) getOrElse MemoryDefaultValue
+    )
 
-  private def bootDiskSizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = bootDiskValidationInstance
-    .withDefault(bootDiskValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse BootDiskDefaultValue)
+  private def bootDiskSizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] =
+    bootDiskValidationInstance
+      .withDefault(bootDiskValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse BootDiskDefaultValue)
 
-  private def noAddressValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = noAddressValidationInstance
-    .withDefault(noAddressValidationInstance
-      .configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue)
+  private def noAddressValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] =
+    noAddressValidationInstance
+      .withDefault(
+        noAddressValidationInstance
+          .configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue
+      )
 
-  private def useDockerImageCacheValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Boolean] =
+  private def useDockerImageCacheValidation(
+    runtimeConfig: Option[Config]
+  ): OptionalRuntimeAttributesValidation[Boolean] =
     useDockerImageCacheValidationInstance
 
-  private val outDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] = {
+  private val outDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
     InformationValidation.optional(RuntimeAttributesKeys.OutDirMinKey, MemoryUnit.MB, allowZero = true)
-  }
 
-  private val tmpDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] = {
+  private val tmpDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
     InformationValidation.optional(RuntimeAttributesKeys.TmpDirMinKey, MemoryUnit.MB, allowZero = true)
-  }
 
-  private val inputDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] = {
+  private val inputDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
     InformationValidation.optional(RuntimeAttributesKeys.DnaNexusInputDirMinKey, MemoryUnit.MB, allowZero = true)
-  }
 
   def runtimeAttributesBuilder(batchConfiguration: GcpBatchConfiguration): StandardValidatedRuntimeAttributesBuilder = {
     val runtimeConfig = batchConfiguration.runtimeConfig
-    StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
-      gpuCountValidation(runtimeConfig),
-      gpuTypeValidation(runtimeConfig),
-      gpuDriverValidation(runtimeConfig),
-      cpuValidation(runtimeConfig),
-      cpuPlatformValidation(runtimeConfig),
-      cpuMinValidation(runtimeConfig),
-      gpuMinValidation(runtimeConfig),
-      disksValidation(runtimeConfig),
-      noAddressValidation(runtimeConfig),
-      zonesValidation(runtimeConfig),
-      preemptibleValidation(runtimeConfig),
-      memoryValidation(runtimeConfig),
-      memoryMinValidation(runtimeConfig),
-      bootDiskSizeValidation(runtimeConfig),
-      useDockerImageCacheValidation(runtimeConfig),
-      checkpointFileValidationInstance,
-      dockerValidation,
-      outDirMinValidation,
-      tmpDirMinValidation,
-      inputDirMinValidation
-    )
+    StandardValidatedRuntimeAttributesBuilder
+      .default(runtimeConfig)
+      .withValidation(
+        gpuCountValidation(runtimeConfig),
+        gpuTypeValidation(runtimeConfig),
+        gpuDriverValidation(runtimeConfig),
+        cpuValidation(runtimeConfig),
+        cpuPlatformValidation(runtimeConfig),
+        cpuMinValidation(runtimeConfig),
+        gpuMinValidation(runtimeConfig),
+        disksValidation(runtimeConfig),
+        noAddressValidation(runtimeConfig),
+        zonesValidation(runtimeConfig),
+        preemptibleValidation(runtimeConfig),
+        memoryValidation(runtimeConfig),
+        memoryMinValidation(runtimeConfig),
+        bootDiskSizeValidation(runtimeConfig),
+        useDockerImageCacheValidation(runtimeConfig),
+        checkpointFileValidationInstance,
+        dockerValidation,
+        outDirMinValidation,
+        tmpDirMinValidation,
+        inputDirMinValidation
+      )
   }
 
-  def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes, runtimeAttrsConfig: Option[Config]): GcpBatchRuntimeAttributes = {
-    val cpu: Int Refined Positive = RuntimeAttributesValidation.extract(cpuValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val cpuPlatform: Option[String] = RuntimeAttributesValidation.extractOption(cpuPlatformValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
-    val checkpointFileName: Option[String] = RuntimeAttributesValidation.extractOption(checkpointFileValidationInstance.key, validatedRuntimeAttributes)
+  def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes,
+            runtimeAttrsConfig: Option[Config]
+  ): GcpBatchRuntimeAttributes = {
+    val cpu: Int Refined Positive =
+      RuntimeAttributesValidation.extract(cpuValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val cpuPlatform: Option[String] = RuntimeAttributesValidation.extractOption(
+      cpuPlatformValidation(runtimeAttrsConfig).key,
+      validatedRuntimeAttributes
+    )
+    val checkpointFileName: Option[String] =
+      RuntimeAttributesValidation.extractOption(checkpointFileValidationInstance.key, validatedRuntimeAttributes)
 
-    //GPU
+    // GPU
     lazy val gpuType: Option[GpuType] = RuntimeAttributesValidation
       .extractOption(gpuTypeValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
     lazy val gpuCount: Option[Int Refined Positive] = RuntimeAttributesValidation
       .extractOption(gpuCountValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
-    lazy val gpuDriver: Option[String] = RuntimeAttributesValidation.extractOption(gpuDriverValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+    lazy val gpuDriver: Option[String] =
+      RuntimeAttributesValidation.extractOption(gpuDriverValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
 
     val gpuResource: Option[GpuResource] = if (gpuType.isDefined || gpuCount.isDefined || gpuDriver.isDefined) {
-      Option(GpuResource(gpuType.getOrElse(GpuType.DefaultGpuType), gpuCount
-        .getOrElse(GpuType.DefaultGpuCount)))
+      Option(
+        GpuResource(gpuType.getOrElse(GpuType.DefaultGpuType),
+                    gpuCount
+                      .getOrElse(GpuType.DefaultGpuCount)
+        )
+      )
     } else {
       None
     }
 
-
     val docker: String = RuntimeAttributesValidation.extract(dockerValidation, validatedRuntimeAttributes)
-    val failOnStderr: Boolean = RuntimeAttributesValidation.extract(failOnStderrValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val continueOnReturnCode: ContinueOnReturnCode = RuntimeAttributesValidation.extract(continueOnReturnCodeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val noAddress: Boolean = RuntimeAttributesValidation.extract(noAddressValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val failOnStderr: Boolean =
+      RuntimeAttributesValidation.extract(failOnStderrValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val continueOnReturnCode: ContinueOnReturnCode = RuntimeAttributesValidation.extract(
+      continueOnReturnCodeValidation(runtimeAttrsConfig),
+      validatedRuntimeAttributes
+    )
+    val noAddress: Boolean =
+      RuntimeAttributesValidation.extract(noAddressValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val zones: Vector[String] = RuntimeAttributesValidation.extract(ZonesValidation, validatedRuntimeAttributes)
-    val preemptible: Int = RuntimeAttributesValidation.extract(preemptibleValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val bootDiskSize: Int = RuntimeAttributesValidation.extract(bootDiskSizeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val memory: MemorySize = RuntimeAttributesValidation.extract(memoryValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val disks: Seq[GcpBatchAttachedDisk] = RuntimeAttributesValidation.extract(disksValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val useDockerImageCache: Option[Boolean] = RuntimeAttributesValidation.extractOption(useDockerImageCacheValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+    val preemptible: Int =
+      RuntimeAttributesValidation.extract(preemptibleValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val bootDiskSize: Int =
+      RuntimeAttributesValidation.extract(bootDiskSizeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val memory: MemorySize =
+      RuntimeAttributesValidation.extract(memoryValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val disks: Seq[GcpBatchAttachedDisk] =
+      RuntimeAttributesValidation.extract(disksValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val useDockerImageCache: Option[Boolean] = RuntimeAttributesValidation.extractOption(
+      useDockerImageCacheValidation(runtimeAttrsConfig).key,
+      validatedRuntimeAttributes
+    )
 
     val outDirMin: Option[MemorySize] = RuntimeAttributesValidation
       .extractOption(outDirMinValidation.key, validatedRuntimeAttributes)
@@ -223,9 +264,10 @@ object GcpBatchRuntimeAttributes {
     val inputDirMin: Option[MemorySize] = RuntimeAttributesValidation
       .extractOption(inputDirMinValidation.key, validatedRuntimeAttributes)
 
-
-    val totalExecutionDiskSizeBytes = List(inputDirMin.map(_.bytes), outDirMin.map(_.bytes), tmpDirMin.map(_.bytes))
-      .flatten.fold(MemorySize(0, MemoryUnit.Bytes).bytes)(_ + _)
+    val totalExecutionDiskSizeBytes = List(inputDirMin.map(_.bytes),
+                                           outDirMin.map(_.bytes),
+                                           tmpDirMin.map(_.bytes)
+    ).flatten.fold(MemorySize(0, MemoryUnit.Bytes).bytes)(_ + _)
     val totalExecutionDiskSize = MemorySize(totalExecutionDiskSizeBytes, MemoryUnit.Bytes)
 
     val adjustedDisks = disks.adjustWorkingDiskWithNewMin(totalExecutionDiskSize, ())
@@ -244,10 +286,10 @@ object GcpBatchRuntimeAttributes {
       continueOnReturnCode,
       noAddress,
       useDockerImageCache,
-      checkpointFileName)
+      checkpointFileName
+    )
   }
 
-
 }
 
 object ZonesValidation extends RuntimeAttributesValidation[Vector[String]] {
@@ -277,24 +319,23 @@ object DisksValidation extends RuntimeAttributesValidation[Seq[GcpBatchAttachedD
   }
 
   private def validateLocalDisks(disks: Seq[String]): ErrorOr[Seq[GcpBatchAttachedDisk]] = {
-    val diskNels: ErrorOr[Seq[GcpBatchAttachedDisk]] = disks.toList.traverse[ErrorOr, GcpBatchAttachedDisk](validateLocalDisk)
+    val diskNels: ErrorOr[Seq[GcpBatchAttachedDisk]] =
+      disks.toList.traverse[ErrorOr, GcpBatchAttachedDisk](validateLocalDisk)
     val defaulted: ErrorOr[Seq[GcpBatchAttachedDisk]] = addDefault(diskNels)
     defaulted
   }
 
-  private def validateLocalDisk(disk: String): ErrorOr[GcpBatchAttachedDisk] = {
+  private def validateLocalDisk(disk: String): ErrorOr[GcpBatchAttachedDisk] =
     GcpBatchAttachedDisk.parse(disk) match {
       case scala.util.Success(attachedDisk) => attachedDisk.validNel
       case scala.util.Failure(ex) => ex.getMessage.invalidNel
     }
-  }
 
-  private def addDefault(disksNel: ErrorOr[Seq[GcpBatchAttachedDisk]]): ErrorOr[Seq[GcpBatchAttachedDisk]] = {
+  private def addDefault(disksNel: ErrorOr[Seq[GcpBatchAttachedDisk]]): ErrorOr[Seq[GcpBatchAttachedDisk]] =
     disksNel map {
       case disks if disks.exists(_.name == GcpBatchWorkingDisk.Name) => disks
       case disks => disks :+ GcpBatchWorkingDisk.Default
     }
-  }
 
   override protected def missingValueMessage: String =
     s"Expecting $key runtime attribute to be a comma separated String or Array[String]"
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchWorkflowPaths.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchWorkflowPaths.scala
index fcb80241b21..5fdadce45d0 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchWorkflowPaths.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchWorkflowPaths.scala
@@ -21,10 +21,9 @@ object GcpBatchWorkflowPaths {
   private val AuthFilePathOptionKey = "auth_bucket"
   private val GcsPrefix = "gs://"
 
-  private def callCachePathPrefixFromExecutionRoot(executionRoot: String): String = {
+  private def callCachePathPrefixFromExecutionRoot(executionRoot: String): String =
     // If the root looks like gs://bucket/stuff-under-bucket this should return gs://bucket
     GcsPrefix + executionRoot.substring(GcsPrefix.length).takeWhile(_ != '/')
-  }
 }
 case class GcpBatchWorkflowPaths(workflowDescriptor: BackendWorkflowDescriptor,
                                  gcsCredentials: Credentials,
@@ -35,20 +34,25 @@ case class GcpBatchWorkflowPaths(workflowDescriptor: BackendWorkflowDescriptor,
                                  // combined controller + job standard output and error files. PAPI v1 controls the periodic
                                  // delocalization of these files so the metadata Cromwell publishes for these files needs
                                  // to match the PAPI v1 names.
-                                 standardStreamNameToFileNameMetadataMapper: (GcpBatchJobPaths, String) => String)(implicit ec: ExecutionContext) extends WorkflowPaths {
+                                 standardStreamNameToFileNameMetadataMapper: (GcpBatchJobPaths, String) => String
+)(implicit ec: ExecutionContext)
+    extends WorkflowPaths {
 
-  override lazy val executionRootString: String = workflowDescriptor.workflowOptions.getOrElse(GcpBatchWorkflowPaths.GcsRootOptionKey, gcpBatchConfiguration.root)
-  override lazy val callCacheRootPrefix: Option[String] = Option(callCachePathPrefixFromExecutionRoot(executionRootString))
+  override lazy val executionRootString: String =
+    workflowDescriptor.workflowOptions.getOrElse(GcpBatchWorkflowPaths.GcsRootOptionKey, gcpBatchConfiguration.root)
+  override lazy val callCacheRootPrefix: Option[String] = Option(
+    callCachePathPrefixFromExecutionRoot(executionRootString)
+  )
 
   private val workflowOptions: WorkflowOptions = workflowDescriptor.workflowOptions
 
   val gcsAuthFilePath: Path = {
     // The default auth file bucket is always at the root of the root workflow
-    val defaultBucket = executionRoot.resolve(workflowDescriptor.rootWorkflow.name)
-                                     .resolve(workflowDescriptor.rootWorkflowId.toString)
+    val defaultBucket = executionRoot
+      .resolve(workflowDescriptor.rootWorkflow.name)
+      .resolve(workflowDescriptor.rootWorkflowId.toString)
     val bucket = workflowDescriptor.workflowOptions
-                                   .get(GcpBatchWorkflowPaths.AuthFilePathOptionKey) getOrElse defaultBucket
-      .pathAsString
+      .get(GcpBatchWorkflowPaths.AuthFilePathOptionKey) getOrElse defaultBucket.pathAsString
 
     /*
      * This is an "exception". The filesystem used here is built from genomicsAuth
@@ -63,24 +67,21 @@ case class GcpBatchWorkflowPaths(workflowDescriptor: BackendWorkflowDescriptor,
       Option(gcpBatchConfiguration.batchAttributes.project)
     )
 
-    val authBucket = pathBuilderWithGenomicsAuth.build(bucket) recover {
-      case ex => throw new Exception(s"Invalid gcs auth_bucket path $bucket", ex)
+    val authBucket = pathBuilderWithGenomicsAuth.build(bucket) recover { case ex =>
+      throw new Exception(s"Invalid gcs auth_bucket path $bucket", ex)
     } get
 
     authBucket.resolve(s"${workflowDescriptor.rootWorkflowId}_auth.json")
   }
 
-  val monitoringScriptPath: Option[Path] = workflowOptions.get(WorkflowOptionKeys.MonitoringScript)
-                                                          .toOption map { path =>
-    // Fail here if the path exists but can't be built
-    getPath(path).get
+  val monitoringScriptPath: Option[Path] = workflowOptions.get(WorkflowOptionKeys.MonitoringScript).toOption map {
+    path =>
+      // Fail here if the path exists but can't be built
+      getPath(path).get
   }
-  override def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): GcpBatchJobPaths = {
+  override def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): GcpBatchJobPaths =
     new GcpBatchJobPaths(workflowPaths.asInstanceOf[GcpBatchWorkflowPaths], jobKey)
-  }
-  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths = this.copy(workflowDescriptor = workflowDescriptor)
+  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths =
+    this.copy(workflowDescriptor = workflowDescriptor)
   override def config: Config = gcpBatchConfiguration.configurationDescriptor.backendConfig
 }
-
-
-
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala
index 49e2941bf59..303b2ec85f2 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala
@@ -23,18 +23,16 @@ object GcpLabel {
 
   // This function is used to coerce a string into one that meets the requirements for a label submission to Google Pipelines API.
   // See 'labels' in https://cloud.google.com/genomics/reference/rpc/google.genomics.v1alpha2#google.genomics.v1alpha2.RunPipelineArgs
-  def safeGoogleName(mainText: String, emptyAllowed: Boolean = false): String = {
-
+  def safeGoogleName(mainText: String, emptyAllowed: Boolean = false): String =
     validateLabelRegex(mainText) match {
       case Valid(labelText) => labelText
       case invalid @ _ if mainText.equals("") && emptyAllowed => mainText
       case invalid @ _ =>
-        def appendSafe(current: String, nextChar: Char): String = {
+        def appendSafe(current: String, nextChar: Char): String =
           nextChar match {
             case c if c.isLetterOrDigit || c == '-' => current + c.toLower
             case _ => current + '-'
           }
-        }
 
         val foldResult = mainText.toCharArray.foldLeft("")(appendSafe)
 
@@ -50,51 +48,64 @@ object GcpLabel {
         if (tooLong) {
           val middleSeparator = "---"
           val subSectionLength = (MaxLabelLength - middleSeparator.length) / 2
-          validStartAndEnd.substring(0, subSectionLength) + middleSeparator + validStartAndEnd.substring(length - subSectionLength, length)
+          validStartAndEnd.substring(0, subSectionLength) + middleSeparator + validStartAndEnd.substring(
+            length - subSectionLength,
+            length
+          )
         } else {
           validStartAndEnd
         }
     }
-  }
 
-  def validateLabelRegex(s: String): ErrorOr[String] = {
+  def validateLabelRegex(s: String): ErrorOr[String] =
     (GoogleLabelRegex.pattern.matcher(s).matches, s.length <= MaxLabelLength) match {
       case (true, true) => s.validNel
-      case (false, false) => s"Invalid label field: `$s` did not match regex '$GoogleLabelRegexPattern' and it is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
+      case (false, false) =>
+        s"Invalid label field: `$s` did not match regex '$GoogleLabelRegexPattern' and it is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
       case (false, _) => s"Invalid label field: `$s` did not match the regex '$GoogleLabelRegexPattern'".invalidNel
-      case (_, false) => s"Invalid label field: `$s` is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
+      case (_, false) =>
+        s"Invalid label field: `$s` is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
     }
-  }
-
 
   def safeLabels(values: (String, String)*): Seq[GcpLabel] = {
-    def safeGoogleLabel(kvp: (String, String)): GcpLabel = {
+    def safeGoogleLabel(kvp: (String, String)): GcpLabel =
       GcpLabel(safeGoogleName(kvp._1), safeGoogleName(kvp._2, emptyAllowed = true))
-    }
     values.map(safeGoogleLabel)
   }
 
-  def validateLabel(key: String, value: String): ErrorOr[GcpLabel] = {
-    (validateLabelRegex(key), validateLabelRegex(value)).mapN { (validKey, validValue) => GcpLabel(validKey, validValue)  }
-  }
+  def validateLabel(key: String, value: String): ErrorOr[GcpLabel] =
+    (validateLabelRegex(key), validateLabelRegex(value)).mapN { (validKey, validValue) =>
+      GcpLabel(validKey, validValue)
+    }
 
   def fromWorkflowOptions(workflowOptions: WorkflowOptions): Try[Seq[GcpLabel]] = {
 
     def extractGoogleLabelsFromJsObject(jsObject: JsObject): Try[Seq[GcpLabel]] = {
       val asErrorOr = jsObject.fields.toList.traverse {
         case (key: String, value: JsString) => GcpLabel.validateLabel(key, value.value)
-        case (key, other) => s"Bad label value type for '$key'. Expected simple string but got $other".invalidNel : ErrorOr[GcpLabel]
+        case (key, other) =>
+          s"Bad label value type for '$key'. Expected simple string but got $other".invalidNel: ErrorOr[GcpLabel]
       }
 
       asErrorOr match {
         case Valid(value) => Success(value)
-        case Invalid(errors) => Failure(new AggregatedMessageException("Invalid 'google_labels' in workflow options", errors.toList) with CromwellFatalExceptionMarker with NoStackTrace)
+        case Invalid(errors) =>
+          Failure(
+            new AggregatedMessageException("Invalid 'google_labels' in workflow options", errors.toList)
+              with CromwellFatalExceptionMarker
+              with NoStackTrace
+          )
       }
     }
 
     workflowOptions.toMap.get("google_labels") match {
       case Some(obj: JsObject) => extractGoogleLabelsFromJsObject(obj)
-      case Some(other) => Failure(new Exception(s"Invalid 'google_labels' in workflow options. Must be a simple JSON object mapping string keys to string values. Got $other") with NoStackTrace with CromwellFatalExceptionMarker)
+      case Some(other) =>
+        Failure(
+          new Exception(
+            s"Invalid 'google_labels' in workflow options. Must be a simple JSON object mapping string keys to string values. Got $other"
+          ) with NoStackTrace with CromwellFatalExceptionMarker
+        )
       case None => Success(Seq.empty)
     }
   }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/PreviousRetryReasons.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/PreviousRetryReasons.scala
index 521dec4ee57..0bd3c1e1535 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/PreviousRetryReasons.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/PreviousRetryReasons.scala
@@ -14,9 +14,10 @@ object PreviousRetryReasons {
 
   def tryApply(prefetchedKvEntries: Map[String, KvResponse], attemptNumber: Int): ErrorOr[PreviousRetryReasons] = {
     val validatedPreemptionCount = validatedKvResponse(prefetchedKvEntries.get(preemptionCountKey), preemptionCountKey)
-    val validatedUnexpectedRetryCount = validatedKvResponse(prefetchedKvEntries.get(unexpectedRetryCountKey), unexpectedRetryCountKey)
+    val validatedUnexpectedRetryCount =
+      validatedKvResponse(prefetchedKvEntries.get(unexpectedRetryCountKey), unexpectedRetryCountKey)
 
-    (validatedPreemptionCount, validatedUnexpectedRetryCount) mapN { PreviousRetryReasons.apply }
+    (validatedPreemptionCount, validatedUnexpectedRetryCount) mapN PreviousRetryReasons.apply
   }
 
   def apply(knownPreemptedCount: Int, knownUnexpectedRetryCount: Int, attempt: Int): PreviousRetryReasons = {
@@ -35,10 +36,9 @@ object PreviousRetryReasons {
     case None => s"Programmer Error: Engine made no effort to prefetch $fromKey".invalidNel
   }
 
-  private def validatedInt(s: String, fromKey: String): ErrorOr[Int] = {
+  private def validatedInt(s: String, fromKey: String): ErrorOr[Int] =
     Try(s.toInt) match {
       case Success(i) => i.validNel
       case Failure(_) => s"Unexpected value found in the KV store: $fromKey='$s'".invalidNel
     }
-  }
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/Run.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/Run.scala
index 418d8ee2a35..5b475196906 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/Run.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/Run.scala
@@ -2,4 +2,4 @@ package cromwell.backend.google.batch.models
 
 import cromwell.backend.standard.StandardAsyncJob
 
-case class Run(job: StandardAsyncJob)
\ No newline at end of file
+case class Run(job: StandardAsyncJob)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/RunStatus.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/RunStatus.scala
index f5631ef6afa..334dca4b0f2 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/RunStatus.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/RunStatus.scala
@@ -8,55 +8,54 @@ sealed trait RunStatus
 
 object RunStatus {
 
-    private val log: Logger = LoggerFactory.getLogger(RunStatus.toString)
-
-    def fromJobStatus(status: JobStatus.State): RunStatus = status match {
-        case JobStatus.State.QUEUED =>
-            log.info("job queued")
-            Running
-        case JobStatus.State.SCHEDULED =>
-            log.info("job scheduled")
-            Running
-        case JobStatus.State.RUNNING =>
-            log.info("job running")
-            Running
-        case JobStatus.State.SUCCEEDED =>
-            log.info("job scheduled")
-            Succeeded(List(ExecutionEvent("complete in GCP Batch"))) //update to more specific
-        case JobStatus.State.FAILED =>
-            log.info("job failed")
-            Failed(List.empty)
-        case JobStatus.State.DELETION_IN_PROGRESS =>
-            log.info("deletion in progress")
-            DeletionInProgress
-        case JobStatus.State.STATE_UNSPECIFIED =>
-            log.info("state unspecified")
-            StateUnspecified
-        case JobStatus.State.UNRECOGNIZED =>
-            log.info("state unrecognized")
-            Unrecognized
-        case _ =>
-            log.info(s"job status not matched: $status")
-            Running
-    }
-
-
-    sealed trait TerminalRunStatus extends RunStatus {
-        def eventList: Seq[ExecutionEvent]
-    }
-
-    sealed trait UnsuccessfulRunStatus extends TerminalRunStatus
-
-    case object Running extends RunStatus
-    case object DeletionInProgress extends RunStatus
-    case object StateUnspecified extends RunStatus
-    case object Unrecognized extends RunStatus
-
-    case class Succeeded(override val eventList: Seq[ExecutionEvent]) extends TerminalRunStatus {
-        override def toString = "Succeeded"
-    }
-
-    final case class Failed(override val eventList: Seq[ExecutionEvent]) extends UnsuccessfulRunStatus {
-        override def toString = "Failed"
-    }
+  private val log: Logger = LoggerFactory.getLogger(RunStatus.toString)
+
+  def fromJobStatus(status: JobStatus.State): RunStatus = status match {
+    case JobStatus.State.QUEUED =>
+      log.info("job queued")
+      Running
+    case JobStatus.State.SCHEDULED =>
+      log.info("job scheduled")
+      Running
+    case JobStatus.State.RUNNING =>
+      log.info("job running")
+      Running
+    case JobStatus.State.SUCCEEDED =>
+      log.info("job scheduled")
+      Succeeded(List(ExecutionEvent("complete in GCP Batch"))) // update to more specific
+    case JobStatus.State.FAILED =>
+      log.info("job failed")
+      Failed(List.empty)
+    case JobStatus.State.DELETION_IN_PROGRESS =>
+      log.info("deletion in progress")
+      DeletionInProgress
+    case JobStatus.State.STATE_UNSPECIFIED =>
+      log.info("state unspecified")
+      StateUnspecified
+    case JobStatus.State.UNRECOGNIZED =>
+      log.info("state unrecognized")
+      Unrecognized
+    case _ =>
+      log.info(s"job status not matched: $status")
+      Running
+  }
+
+  sealed trait TerminalRunStatus extends RunStatus {
+    def eventList: Seq[ExecutionEvent]
+  }
+
+  sealed trait UnsuccessfulRunStatus extends TerminalRunStatus
+
+  case object Running extends RunStatus
+  case object DeletionInProgress extends RunStatus
+  case object StateUnspecified extends RunStatus
+  case object Unrecognized extends RunStatus
+
+  case class Succeeded(override val eventList: Seq[ExecutionEvent]) extends TerminalRunStatus {
+    override def toString = "Succeeded"
+  }
+
+  final case class Failed(override val eventList: Seq[ExecutionEvent]) extends UnsuccessfulRunStatus {
+    override def toString = "Failed"
+  }
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/VpcAndSubnetworkProjectLabelValues.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/VpcAndSubnetworkProjectLabelValues.scala
index a77bcd96d87..1dd4ce4bda7 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/VpcAndSubnetworkProjectLabelValues.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/VpcAndSubnetworkProjectLabelValues.scala
@@ -3,6 +3,7 @@ package cromwell.backend.google.batch.models
 import cromwell.backend.google.batch.models.VpcAndSubnetworkProjectLabelValues._
 
 final case class VpcAndSubnetworkProjectLabelValues(vpcName: String, subnetNameOpt: Option[String]) {
+
   /**
    * Returns a qualified network name replacing the string `\${projectId}` in the network name if found.
    */
@@ -20,9 +21,8 @@ final case class VpcAndSubnetworkProjectLabelValues(vpcName: String, subnetNameO
   /**
    * Replaces the string `\${projectId}` in the subnet name if found.
    */
-  def subnetNameOption(projectId: String): Option[String] = {
+  def subnetNameOption(projectId: String): Option[String] =
     subnetNameOpt map { _.replace(ProjectIdToken, projectId) }
-  }
 }
 
 object VpcAndSubnetworkProjectLabelValues {
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/CheckpointingConfiguration.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/CheckpointingConfiguration.scala
index ab04a4a71a9..d706168d96e 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/CheckpointingConfiguration.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/CheckpointingConfiguration.scala
@@ -10,18 +10,21 @@ final class CheckpointingConfiguration(jobDescriptor: BackendJobDescriptor,
                                        workflowPaths: WorkflowPaths,
                                        commandDirectory: Path,
                                        checkpointInterval: FiniteDuration
-                                      ) {
-  def checkpointFileCloud(checkpointFileName: String): String = {
+) {
+  def checkpointFileCloud(checkpointFileName: String): String =
     // The checkpoint file for ANY attempt always goes in the "attempt 1" directory. That way we guarantee that
     // every attempt is able to recover from the single source of checkpointing truth.
-    workflowPaths.toJobPaths(jobDescriptor.key.copy(attempt = 1), jobDescriptor.workflowDescriptor)
-      .callExecutionRoot.resolve("__checkpointing").resolve(checkpointFileName).toAbsolutePath.pathAsString
-  }
+    workflowPaths
+      .toJobPaths(jobDescriptor.key.copy(attempt = 1), jobDescriptor.workflowDescriptor)
+      .callExecutionRoot
+      .resolve("__checkpointing")
+      .resolve(checkpointFileName)
+      .toAbsolutePath
+      .pathAsString
   def tmpCheckpointFileCloud(checkpointFileName: String): String = checkpointFileCloud(checkpointFileName) + "-tmp"
 
-  def checkpointFileLocal(checkpointFileName: String): String = {
+  def checkpointFileLocal(checkpointFileName: String): String =
     commandDirectory.resolve(checkpointFileName).toAbsolutePath.pathAsString
-  }
   def tmpCheckpointFileLocal(checkpointFileName: String): String = checkpointFileLocal(checkpointFileName) + "-tmp"
 
   def localizePreviousCheckpointCommand(checkpointFileName: String): String = {
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/Env.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/Env.scala
index df0cb3b070c..396334d7de0 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/Env.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/Env.scala
@@ -3,6 +3,7 @@ package cromwell.backend.google.batch.monitoring
 import cromwell.backend.BackendJobDescriptor
 
 object Env {
+
   /**
    * Name of an environmental variable
    */
@@ -12,13 +13,12 @@ object Env {
   val TaskCallAttempt = "TASK_CALL_ATTEMPT"
   val DiskMounts = "DISK_MOUNTS"
 
-  def monitoringImageEnvironment(jobDescriptor: BackendJobDescriptor)
-                                (mountPaths: List[String]): Map[String, String] =
+  def monitoringImageEnvironment(jobDescriptor: BackendJobDescriptor)(mountPaths: List[String]): Map[String, String] =
     Map(
       Env.WorkflowId -> jobDescriptor.workflowDescriptor.id.toString,
       Env.TaskCallName -> jobDescriptor.taskCall.localName,
       Env.TaskCallIndex -> jobDescriptor.key.index.map(_.toString).getOrElse("NA"),
       Env.TaskCallAttempt -> jobDescriptor.key.attempt.toString,
-      Env.DiskMounts -> mountPaths.mkString(" "),
+      Env.DiskMounts -> mountPaths.mkString(" ")
     )
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/MonitoringImage.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/MonitoringImage.scala
index 578081dc46f..81e17d4d135 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/MonitoringImage.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/monitoring/MonitoringImage.scala
@@ -13,8 +13,8 @@ final class MonitoringImage(jobDescriptor: BackendJobDescriptor,
                             workflowPaths: WorkflowPaths,
                             commandDirectory: Path,
                             workingDisk: GcpBatchAttachedDisk,
-                            localMonitoringImageScriptPath: Path,
-                           ) {
+                            localMonitoringImageScriptPath: Path
+) {
 
   val monitoringImageOption: Option[String] = workflowOptions.get(WorkflowOptionKeys.MonitoringImage).toOption
 
@@ -24,22 +24,21 @@ final class MonitoringImage(jobDescriptor: BackendJobDescriptor,
     for {
       _ <- monitoringImageOption // Only use the monitoring_image_script when monitoring_image provided
       monitoringImageScript <- workflowOptions.get(WorkflowOptionKeys.MonitoringImageScript).toOption
-    } yield {
-      PathFactory.buildPath(
-        monitoringImageScript,
-        workflowPaths.pathBuilders,
-      )
-    }
+    } yield PathFactory.buildPath(
+      monitoringImageScript,
+      workflowPaths.pathBuilders
+    )
 
   val monitoringImageCommand: List[String] =
     monitoringImageScriptOption match {
-      case Some(_) => List(
-        "/bin/sh",
-        "-c",
-        s"cd '${commandDirectory.pathAsString}' && " +
-          s"chmod +x '${monitoringImageScriptContainerPath.pathAsString}' && " +
-          s"'${monitoringImageScriptContainerPath.pathAsString}'"
-      )
+      case Some(_) =>
+        List(
+          "/bin/sh",
+          "-c",
+          s"cd '${commandDirectory.pathAsString}' && " +
+            s"chmod +x '${monitoringImageScriptContainerPath.pathAsString}' && " +
+            s"'${monitoringImageScriptContainerPath.pathAsString}'"
+        )
       case None => Nil
     }
 
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/CheckpointingRunnable.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/CheckpointingRunnable.scala
index 5ad8d2b21f9..081cbc1ee52 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/CheckpointingRunnable.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/CheckpointingRunnable.scala
@@ -4,45 +4,65 @@ import com.google.cloud.batch.v1.{Runnable, Volume}
 import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobParameters
 
 trait CheckpointingRunnable {
-  def checkpointingSetupRunnables(createParameters: CreateBatchJobParameters,
-                                  volumes: List[Volume]
-                               ): List[Runnable] = {
-    val result = createParameters.runtimeAttributes.checkpointFilename.map { checkpointFilename =>
-      val checkpointingImage = RunnableUtils.CloudSdkImage
-      val checkpointingCommand = createParameters.checkpointingConfiguration.checkpointingCommand(checkpointFilename, RunnableCommands.multiLineBinBashCommand)
-      val checkpointingEnvironment = Map.empty[String, String]
-
-      // Initial sync from cloud:
-      val initialCheckpointSyncRunnable = RunnableBuilder.cloudSdkShellRunnable(
-        createParameters.checkpointingConfiguration.localizePreviousCheckpointCommand(checkpointFilename)
-      )(volumes = volumes, flags = List.empty, labels = Map.empty)
-      val describeInitialCheckpointingSyncRunnable = RunnableBuilder.describeDocker("initial checkpointing sync", initialCheckpointSyncRunnable)
-
-      // Background upload runnable:
-      val backgroundCheckpointingRunnable = RunnableBuilder.backgroundRunnable(
-        image = checkpointingImage,
-        command = checkpointingCommand,
-        environment = checkpointingEnvironment,
-        volumes = volumes
-      )
-      val describeBackgroundCheckpointingRunnable = RunnableBuilder.describeDocker("begin checkpointing background runnable", backgroundCheckpointingRunnable)
-
-      List(describeInitialCheckpointingSyncRunnable, initialCheckpointSyncRunnable, describeBackgroundCheckpointingRunnable, backgroundCheckpointingRunnable)
-    }.getOrElse(Nil)
+  def checkpointingSetupRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume]): List[Runnable] = {
+    val result = createParameters.runtimeAttributes.checkpointFilename
+      .map { checkpointFilename =>
+        val checkpointingImage = RunnableUtils.CloudSdkImage
+        val checkpointingCommand =
+          createParameters.checkpointingConfiguration.checkpointingCommand(checkpointFilename,
+                                                                           RunnableCommands.multiLineBinBashCommand
+          )
+        val checkpointingEnvironment = Map.empty[String, String]
+
+        // Initial sync from cloud:
+        val initialCheckpointSyncRunnable = RunnableBuilder.cloudSdkShellRunnable(
+          createParameters.checkpointingConfiguration.localizePreviousCheckpointCommand(checkpointFilename)
+        )(volumes = volumes, flags = List.empty, labels = Map.empty)
+        val describeInitialCheckpointingSyncRunnable =
+          RunnableBuilder.describeDocker("initial checkpointing sync", initialCheckpointSyncRunnable)
+
+        // Background upload runnable:
+        val backgroundCheckpointingRunnable = RunnableBuilder.backgroundRunnable(
+          image = checkpointingImage,
+          command = checkpointingCommand,
+          environment = checkpointingEnvironment,
+          volumes = volumes
+        )
+        val describeBackgroundCheckpointingRunnable =
+          RunnableBuilder.describeDocker("begin checkpointing background runnable", backgroundCheckpointingRunnable)
+
+        List(describeInitialCheckpointingSyncRunnable,
+             initialCheckpointSyncRunnable,
+             describeBackgroundCheckpointingRunnable,
+             backgroundCheckpointingRunnable
+        )
+      }
+      .getOrElse(Nil)
 
     result.map(_.build)
   }
 
-  def checkpointingShutdownRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume]): List[Runnable] = {
-    val result = createParameters.runtimeAttributes.checkpointFilename.map { checkpointFilename =>
-      val terminationRunnable = RunnableBuilder.terminateBackgroundRunnablesRunnable()
-      val describeTerminationRunnable = RunnableBuilder.describeDocker("terminate checkpointing runnable", terminationRunnable)
+  def checkpointingShutdownRunnables(createParameters: CreateBatchJobParameters,
+                                     volumes: List[Volume]
+  ): List[Runnable] = {
+    val result = createParameters.runtimeAttributes.checkpointFilename
+      .map { checkpointFilename =>
+        val terminationRunnable = RunnableBuilder.terminateBackgroundRunnablesRunnable()
+        val describeTerminationRunnable =
+          RunnableBuilder.describeDocker("terminate checkpointing runnable", terminationRunnable)
 
-      val deleteCheckpointRunnable = RunnableBuilder.gcsFileDeletionRunnable(createParameters.checkpointingConfiguration.checkpointFileCloud(checkpointFilename), volumes)
-      val deleteTmpCheckpointRunnable = RunnableBuilder.gcsFileDeletionRunnable(createParameters.checkpointingConfiguration.tmpCheckpointFileCloud(checkpointFilename), volumes)
+        val deleteCheckpointRunnable = RunnableBuilder.gcsFileDeletionRunnable(
+          createParameters.checkpointingConfiguration.checkpointFileCloud(checkpointFilename),
+          volumes
+        )
+        val deleteTmpCheckpointRunnable = RunnableBuilder.gcsFileDeletionRunnable(
+          createParameters.checkpointingConfiguration.tmpCheckpointFileCloud(checkpointFilename),
+          volumes
+        )
 
-      List(describeTerminationRunnable, terminationRunnable, deleteCheckpointRunnable, deleteTmpCheckpointRunnable)
-    }.getOrElse(Nil)
+        List(describeTerminationRunnable, terminationRunnable, deleteCheckpointRunnable, deleteTmpCheckpointRunnable)
+      }
+      .getOrElse(Nil)
 
     result.map(_.build)
   }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Delocalization.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Delocalization.scala
index f1b28598a28..4e1ab74104b 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Delocalization.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Delocalization.scala
@@ -21,8 +21,9 @@ trait Delocalization {
   import RunnableUtils._
 
   private def runtimeOutputExtractorRunnable(containerCallRoot: String,
-                                           outputFile: String,
-                                           womOutputRuntimeExtractor: WomOutputRuntimeExtractor): Runnable.Builder = {
+                                             outputFile: String,
+                                             womOutputRuntimeExtractor: WomOutputRuntimeExtractor
+  ): Runnable.Builder = {
     val commands = List(
       "-c",
       // Create the directory where the fofn will be written
@@ -39,7 +40,9 @@ trait Delocalization {
       .withLabels(Map(Key.Tag -> Value.Delocalization))
   }
 
-  private def delocalizeRuntimeOutputsScript(fofnPath: String, workflowRoot: Path, cloudCallRoot: Path)(implicit gcsTransferConfiguration: GcsTransferConfiguration) = {
+  private def delocalizeRuntimeOutputsScript(fofnPath: String, workflowRoot: Path, cloudCallRoot: Path)(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ) = {
     val gsutilCommand: String => String = { flag =>
       s"""rm -f $$HOME/.config/gcloud/gce && gsutil -m $flag cp -r $$line "${cloudCallRoot.pathAsString.ensureSlashed}$$gcs_path""""
     }
@@ -70,13 +73,21 @@ trait Delocalization {
         |fi""".stripMargin
   }
 
-  private def delocalizeRuntimeOutputsRunnable(cloudCallRoot: Path, inputFile: String, workflowRoot: Path, volumes: List[Volume])(implicit gcsTransferConfiguration: GcsTransferConfiguration): Runnable.Builder = {
+  private def delocalizeRuntimeOutputsRunnable(cloudCallRoot: Path,
+                                               inputFile: String,
+                                               workflowRoot: Path,
+                                               volumes: List[Volume]
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): Runnable.Builder = {
     val command = multiLineCommand(delocalizeRuntimeOutputsScript(inputFile, workflowRoot, cloudCallRoot))
-    RunnableBuilder.cloudSdkShellRunnable(command)(volumes = volumes, labels = Map(Key.Tag -> Value.Delocalization), flags = List.empty)
+    RunnableBuilder.cloudSdkShellRunnable(command)(volumes = volumes,
+                                                   labels = Map(Key.Tag -> Value.Delocalization),
+                                                   flags = List.empty
+    )
   }
 
-  def deLocalizeRunnables(createParameters: CreateBatchJobParameters,
-                          volumes: List[Volume])(implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable] = {
+  def deLocalizeRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): List[Runnable] = {
     val cloudCallRoot = createParameters.cloudCallRoot
     val callExecutionContainerRoot = createParameters.commandScriptContainerPath.parent
 
@@ -84,25 +95,37 @@ trait Delocalization {
      * Ideally temporaryFofnForRuntimeOutputFiles should be somewhere else than the execution directory (we could mount anther directory)
      * However because it runs after everything else there's no risk of polluting the task's results and the random ID ensures we don't override anything
      */
-    val temporaryFofnDirectoryForRuntimeOutputFiles = callExecutionContainerRoot.pathAsString.ensureSlashed + UUID.randomUUID().toString.split("-")(0)
+    val temporaryFofnDirectoryForRuntimeOutputFiles =
+      callExecutionContainerRoot.pathAsString.ensureSlashed + UUID.randomUUID().toString.split("-")(0)
     val temporaryFofnForRuntimeOutputFiles = temporaryFofnDirectoryForRuntimeOutputFiles + "/runtime_output_files.txt"
 
     val runtimeExtractionRunnables = createParameters.womOutputRuntimeExtractor.toList flatMap { extractor =>
-      List (
-        runtimeOutputExtractorRunnable(callExecutionContainerRoot.pathAsString, temporaryFofnForRuntimeOutputFiles, extractor),
-        delocalizeRuntimeOutputsRunnable(cloudCallRoot, temporaryFofnForRuntimeOutputFiles, createParameters.cloudWorkflowRoot, volumes)
+      List(
+        runtimeOutputExtractorRunnable(callExecutionContainerRoot.pathAsString,
+                                       temporaryFofnForRuntimeOutputFiles,
+                                       extractor
+        ),
+        delocalizeRuntimeOutputsRunnable(cloudCallRoot,
+                                         temporaryFofnForRuntimeOutputFiles,
+                                         createParameters.cloudWorkflowRoot,
+                                         volumes
+        )
       )
     }
 
-    val gcsDelocalizationContainerPath = createParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
+    val gcsDelocalizationContainerPath =
+      createParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
 
     val delocalizationLabel = Map(Key.Tag -> Value.Delocalization)
-    val runGcsDelocalizationScript = cloudSdkShellRunnable(
-      s"/bin/bash $gcsDelocalizationContainerPath")(volumes = volumes, labels = delocalizationLabel, flags = List.empty)
+    val runGcsDelocalizationScript = cloudSdkShellRunnable(s"/bin/bash $gcsDelocalizationContainerPath")(
+      volumes = volumes,
+      labels = delocalizationLabel,
+      flags = List.empty
+    )
 
     val annotatedRunnables: List[Runnable.Builder] = runGcsDelocalizationScript ::
       createParameters.outputParameters.flatMap(_.toRunnables(volumes)) ++
-        runtimeExtractionRunnables
+      runtimeExtractionRunnables
 
     // NOTE: papiv2 delocalizes logs from /google but such logs are not available on batch
     // See: https://cloud.google.com/life-sciences/docs/reference/rpc/google.cloud.lifesciences.v2beta
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Localization.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Localization.scala
index 07fe3e848c4..04ff33c16e8 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Localization.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/Localization.scala
@@ -17,47 +17,63 @@ trait Localization {
   import RunnableCommands._
   import RunnableLabels._
 
-  def localizeRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume])
-                       (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable] = {
+  def localizeRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): List[Runnable] = {
     val localizationLabel = Map(Key.Tag -> Value.Localization)
 
     val gcsTransferLibraryContainerPath = createParameters.commandScriptContainerPath.sibling(GcsTransferLibraryName)
-    val localizeGcsTransferLibrary = cloudSdkShellRunnable(localizeFile(
-      cloudPath = createParameters.cloudCallRoot / GcsTransferLibraryName,
-      containerPath = gcsTransferLibraryContainerPath))(volumes = volumes, labels = localizationLabel, flags = List.empty)
+    val localizeGcsTransferLibrary = cloudSdkShellRunnable(
+      localizeFile(cloudPath = createParameters.cloudCallRoot / GcsTransferLibraryName,
+                   containerPath = gcsTransferLibraryContainerPath
+      )
+    )(volumes = volumes, labels = localizationLabel, flags = List.empty)
 
     val gcsLocalizationContainerPath = createParameters.commandScriptContainerPath.sibling(GcsLocalizationScriptName)
-    val localizeGcsLocalizationScript = cloudSdkShellRunnable(localizeFile(
-      cloudPath = createParameters.cloudCallRoot / GcsLocalizationScriptName,
-      containerPath = gcsLocalizationContainerPath))(volumes = volumes, labels = localizationLabel, flags = List.empty)
-
-    val gcsDelocalizationContainerPath = createParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
-    val localizeGcsDelocalizationScript = cloudSdkShellRunnable(localizeFile(
-      cloudPath = createParameters.cloudCallRoot / GcsDelocalizationScriptName,
-      containerPath = gcsDelocalizationContainerPath))(volumes = volumes, labels = localizationLabel, flags = List.empty)
-
-    val runGcsLocalizationScript = cloudSdkShellRunnable(
-      s"/bin/bash $gcsLocalizationContainerPath")(volumes = volumes, labels = localizationLabel, flags = List.empty)
+    val localizeGcsLocalizationScript = cloudSdkShellRunnable(
+      localizeFile(cloudPath = createParameters.cloudCallRoot / GcsLocalizationScriptName,
+                   containerPath = gcsLocalizationContainerPath
+      )
+    )(volumes = volumes, labels = localizationLabel, flags = List.empty)
+
+    val gcsDelocalizationContainerPath =
+      createParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
+    val localizeGcsDelocalizationScript = cloudSdkShellRunnable(
+      localizeFile(cloudPath = createParameters.cloudCallRoot / GcsDelocalizationScriptName,
+                   containerPath = gcsDelocalizationContainerPath
+      )
+    )(volumes = volumes, labels = localizationLabel, flags = List.empty)
+
+    val runGcsLocalizationScript = cloudSdkShellRunnable(s"/bin/bash $gcsLocalizationContainerPath")(
+      volumes = volumes,
+      labels = localizationLabel,
+      flags = List.empty
+    )
 
     val drsInputs: List[DrsPath] = createParameters.inputOutputParameters.fileInputParameters.collect {
       case GcpBatchFileInput(_, drsPath: DrsPath, _, _) => drsPath
     }
 
     val drsLocalizationRunnable = if (drsInputs.nonEmpty) {
-      val drsLocalizationManifestContainerPath = createParameters.commandScriptContainerPath.sibling(DrsLocalizationManifestName)
-      val localizeDrsLocalizationManifest = cloudSdkShellRunnable(localizeFile(
-        cloudPath = createParameters.cloudCallRoot / DrsLocalizationManifestName,
-        containerPath = drsLocalizationManifestContainerPath))(volumes = volumes, labels = localizationLabel, flags = List.empty)
+      val drsLocalizationManifestContainerPath =
+        createParameters.commandScriptContainerPath.sibling(DrsLocalizationManifestName)
+      val localizeDrsLocalizationManifest = cloudSdkShellRunnable(
+        localizeFile(cloudPath = createParameters.cloudCallRoot / DrsLocalizationManifestName,
+                     containerPath = drsLocalizationManifestContainerPath
+        )
+      )(volumes = volumes, labels = localizationLabel, flags = List.empty)
 
       // Requester pays project id is stored on each DrsPath, but will be the same for all DRS inputs to a
       // particular workflow because it's determined by the Google project set in workflow options.
       val requesterPaysProjectId: Option[String] = drsInputs.flatMap(_.requesterPaysProjectIdOption).headOption
-      val runDrsLocalization = Localization.drsRunnable(drsLocalizationManifestContainerPath, localizationLabel, requesterPaysProjectId)
+      val runDrsLocalization =
+        Localization.drsRunnable(drsLocalizationManifestContainerPath, localizationLabel, requesterPaysProjectId)
       List(localizeDrsLocalizationManifest, runDrsLocalization)
     } else List[Runnable.Builder]()
 
     // Any "classic" PAPI v2 one-at-a-time localizations for non-GCS inputs.
-    val singletonLocalizations = createParameters.inputOutputParameters.fileInputParameters.flatMap(_.toRunnables(volumes))
+    val singletonLocalizations =
+      createParameters.inputOutputParameters.fileInputParameters.flatMap(_.toRunnables(volumes))
 
     val localizations =
       localizeGcsTransferLibrary ::
@@ -79,7 +95,7 @@ object Localization {
   def drsRunnable(manifestPath: Path,
                   labels: Map[String, String],
                   requesterPaysProjectId: Option[String]
-                 ): Runnable.Builder = {
+  ): Runnable.Builder = {
     import RunnableBuilder.EnhancedRunnableBuilder
 
     val drsResolverConfig = config.getConfig("filesystems.drs.global.config.resolver")
@@ -98,4 +114,4 @@ object Localization {
       .withEnvironment(drsResolverEnv)
       .withLabels(labels)
   }
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MemoryRetryCheckRunnable.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MemoryRetryCheckRunnable.scala
index 3c728b21775..3ab2a64fddc 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MemoryRetryCheckRunnable.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MemoryRetryCheckRunnable.scala
@@ -5,10 +5,9 @@ import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobPa
 
 trait MemoryRetryCheckRunnable {
 
-  def checkForMemoryRetryRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume]): List[Runnable] = {
+  def checkForMemoryRetryRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume]): List[Runnable] =
     createParameters.retryWithMoreMemoryKeys match {
       case Some(keys) => List(RunnableBuilder.checkForMemoryRetryRunnable(keys, volumes)).map(_.build)
       case None => List.empty[Runnable]
     }
-  }
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MonitoringRunnable.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MonitoringRunnable.scala
index b48918610b2..d1fc27b4c89 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MonitoringRunnable.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/MonitoringRunnable.scala
@@ -5,9 +5,9 @@ import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobPa
 import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
 
 trait MonitoringRunnable {
-  def monitoringSetupRunnables(createParameters: CreateBatchJobParameters,
-                               volumes: List[Volume]
-                            )(implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable] = {
+  def monitoringSetupRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): List[Runnable] = {
 
     val monitoringImageScriptRunnables =
       createParameters.monitoringImage.monitoringImageScriptOption match {
@@ -21,7 +21,7 @@ trait MonitoringRunnable {
           val describeLocalizeScriptRunnable =
             RunnableBuilder.describeDocker(
               "localizing monitoring image script runnable",
-              localizeScriptRunnable,
+              localizeScriptRunnable
             )
           List(describeLocalizeScriptRunnable, localizeScriptRunnable)
         case None => Nil
@@ -30,7 +30,6 @@ trait MonitoringRunnable {
     val monitoringImageRunnables =
       createParameters.monitoringImage.monitoringImageOption match {
         case Some(image) =>
-
           val monitoringImage = image
           val monitoringImageCommand = createParameters.monitoringImage.monitoringImageCommand
           val monitoringImageEnvironment = createParameters.monitoringImage.monitoringImageEnvironment
@@ -52,15 +51,15 @@ trait MonitoringRunnable {
     (monitoringImageScriptRunnables ++ monitoringImageRunnables).map(_.build)
   }
 
-  def monitoringShutdownRunnables(createParameters: CreateBatchJobParameters): List[Runnable] = {
+  def monitoringShutdownRunnables(createParameters: CreateBatchJobParameters): List[Runnable] =
     createParameters.monitoringImage.monitoringImageOption match {
       case Some(_) =>
         val terminationRunnable = RunnableBuilder.terminateBackgroundRunnablesRunnable()
 
-        val describeTerminationRunnable = RunnableBuilder.describeDocker("terminate monitoring runnable", terminationRunnable)
+        val describeTerminationRunnable =
+          RunnableBuilder.describeDocker("terminate monitoring runnable", terminationRunnable)
 
         List(describeTerminationRunnable, terminationRunnable).map(_.build)
       case None => Nil
     }
-  }
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala
index 7f35528fad3..d69502295cd 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableBuilder.scala
@@ -1,7 +1,7 @@
 package cromwell.backend.google.batch.runnable
 
 import com.google.cloud.batch.v1.Runnable.Container
-import com.google.cloud.batch.v1.{Environment,Runnable, Volume}
+import com.google.cloud.batch.v1.{Environment, Runnable, Volume}
 import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
 import cromwell.backend.google.batch.models.{BatchParameter, GcpBatchInput, GcpBatchOutput}
 import cromwell.core.path.Path
@@ -19,6 +19,7 @@ object RunnableBuilder {
   import RunnableUtils._
 
   implicit class EnhancedRunnableBuilder(val builder: Runnable.Builder) extends AnyVal {
+
     /**
       * Only for use with docker images KNOWN to not have entrypoints already set,
       * or used with accompanying call to setEntrypoint("non-empty-string").
@@ -31,31 +32,30 @@ object RunnableBuilder {
       builder.setContainer(container)
     }
 
-    def withEntrypointCommand(command: String*): Runnable.Builder = {
+    def withEntrypointCommand(command: String*): Runnable.Builder =
       builder
         .setContainer(
           builder.getContainerBuilder
-            .setEntrypoint(command.headOption.getOrElse(""))  //set to blank string instead of null because batch does not support null
+            .setEntrypoint(
+              command.headOption.getOrElse("")
+            ) // set to blank string instead of null because batch does not support null
             .addAllCommands(
               command.drop(1).asJava
             )
         )
-    }
 
-    def withFlags(flags: List[RunnableFlag]): Runnable.Builder = {
+    def withFlags(flags: List[RunnableFlag]): Runnable.Builder =
       flags.foldLeft(builder) {
         case (acc, RunnableFlag.IgnoreExitStatus) => acc.setIgnoreExitStatus(true)
         case (acc, RunnableFlag.RunInBackground) => acc.setBackground(true)
         case (acc, RunnableFlag.AlwaysRun) => acc.setAlwaysRun(true)
       }
-    }
 
     def withEnvironment(environment: Map[String, String]): Runnable.Builder = {
       val env = Environment.newBuilder.putAllVariables(environment.asJava)
       builder.setEnvironment(env)
     }
 
-
     def withVolumes(volumes: List[Volume]): Runnable.Builder = {
       val formattedVolumes = volumes.map { volume =>
         val mountPath = volume.getMountPath
@@ -98,17 +98,17 @@ object RunnableBuilder {
     }
   }
 
-  def withImage(image: String): Runnable.Builder = {
-    Runnable.newBuilder()
+  def withImage(image: String): Runnable.Builder =
+    Runnable
+      .newBuilder()
       .setContainer(Container.newBuilder.setImageUri(image))
-  }
 
-  private def cloudSdkContainerBuilder: Container.Builder = {
+  private def cloudSdkContainerBuilder: Container.Builder =
     Container.newBuilder.setImageUri(CloudSdkImage)
-  }
 
-  def monitoringImageScriptRunnable(cloudPath: Path, containerPath: Path, volumes: List[Volume])
-                                 (implicit gcsTransferConfiguration: GcsTransferConfiguration): Runnable.Builder = {
+  def monitoringImageScriptRunnable(cloudPath: Path, containerPath: Path, volumes: List[Volume])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): Runnable.Builder = {
     val command = RunnableCommands.localizeFile(cloudPath, containerPath)
     val labels = Map(Key.Tag -> Value.Localization)
     cloudSdkShellRunnable(command)(volumes = volumes, flags = List.empty, labels = labels)
@@ -118,7 +118,7 @@ object RunnableBuilder {
                          command: List[String],
                          environment: Map[String, String],
                          volumes: List[Volume]
-                      ): Runnable.Builder = {
+  ): Runnable.Builder =
     withImage(image)
       .withEntrypointCommand(command: _*)
       .withRunInBackground(true)
@@ -126,18 +126,15 @@ object RunnableBuilder {
       .withEnvironment(environment)
       .withFlags(List(RunnableFlag.RunInBackground, RunnableFlag.IgnoreExitStatus))
       .withLabels(Map(Key.Tag -> Value.Monitoring))
-  }
-
 
-  def terminateBackgroundRunnablesRunnable(): Runnable.Builder = {
+  def terminateBackgroundRunnablesRunnable(): Runnable.Builder =
     cloudSdkShellRunnable(terminateAllBackgroundRunnablesCommand)(
       volumes = List.empty,
       flags = List(RunnableFlag.AlwaysRun),
       labels = Map(Key.Tag -> Value.Monitoring)
     )
-  }
 
-  def gcsFileDeletionRunnable(cloudPath: String, volumes: List[Volume]): Runnable.Builder = {
+  def gcsFileDeletionRunnable(cloudPath: String, volumes: List[Volume]): Runnable.Builder =
     cloudSdkShellRunnable(
       s"""gsutil rm '$cloudPath'"""
     )(
@@ -145,13 +142,13 @@ object RunnableBuilder {
       flags = List(RunnableFlag.IgnoreExitStatus),
       labels = Map(Key.Tag -> Value.Monitoring)
     )
-  }
 
   def userRunnable(docker: String,
                    scriptContainerPath: String,
                    jobShell: String,
                    volumes: List[Volume],
-                   dockerhubCredentials: (String, String)): Runnable.Builder = {
+                   dockerhubCredentials: (String, String)
+  ): Runnable.Builder = {
 
     val container = (dockerhubCredentials._1, dockerhubCredentials._2) match {
       case (username, password) if username.nonEmpty && password.nonEmpty =>
@@ -167,52 +164,57 @@ object RunnableBuilder {
           .setEntrypoint(jobShell)
           .addCommands(scriptContainerPath)
     }
-    Runnable.newBuilder()
+    Runnable
+      .newBuilder()
       .setContainer(container)
       .withVolumes(volumes)
       .putLabels(Key.Tag, Value.UserRunnable)
   }
 
-  def checkForMemoryRetryRunnable(retryLookupKeys: List[String], volumes: List[Volume]): Runnable.Builder = {
+  def checkForMemoryRetryRunnable(retryLookupKeys: List[String], volumes: List[Volume]): Runnable.Builder =
     cloudSdkShellRunnable(RunnableCommands.checkIfStderrContainsRetryKeys(retryLookupKeys))(
       volumes = volumes,
       flags = List(RunnableFlag.AlwaysRun),
       labels = Map(Key.Tag -> Value.RetryWithMoreMemory)
     ).withAlwaysRun(true)
-  }
 
   // Creates a Runnable that logs the docker command for the passed in runnable.
-  def describeDocker(description: String, runnable: Runnable.Builder): Runnable.Builder = {
+  def describeDocker(description: String, runnable: Runnable.Builder): Runnable.Builder =
     logTimestampedRunnable(
       s"Running $description: ${toDockerRun(runnable)}",
       List.empty,
       List.empty,
       runnable.scalaLabels
     )
-  }
 
   private def timestampedMessage(message: String): String =
     s"""printf '%s %s\\n' "$$(date -u '+%Y/%m/%d %H:%M:%S')" ${shellEscaped(message)}"""
 
-  private def logTimestampedRunnable(message: String, volumes: List[Volume], flags: List[RunnableFlag], runnableLabels: Map[String, String]): Runnable.Builder = {
+  private def logTimestampedRunnable(message: String,
+                                     volumes: List[Volume],
+                                     flags: List[RunnableFlag],
+                                     runnableLabels: Map[String, String]
+  ): Runnable.Builder =
     // Uses the cloudSdk image as that image will be used for other operations as well.
     cloudSdkShellRunnable(
       timestampedMessage(message)
-    )(volumes, flags, labels = runnableLabels collect {
-      case (key, value) if key == Key.Tag => Key.Logging -> value
-      case (key, value) => key -> value
-    }).withTimeout(timeout = 300.seconds)
-  }
+    )(volumes,
+      flags,
+      labels = runnableLabels collect {
+        case (key, value) if key == Key.Tag => Key.Logging -> value
+        case (key, value) => key -> value
+      }
+    ).withTimeout(timeout = 300.seconds)
 
   def cloudSdkRunnable: Runnable.Builder = Runnable.newBuilder.setContainer(cloudSdkContainerBuilder)
 
-  def cloudSdkShellRunnable(shellCommand: String)(
-    volumes: List[Volume],
-    flags: List[RunnableFlag],
-    labels: Map[String, String],
-    timeout: Duration = Duration.Inf): Runnable.Builder = {
-
-    Runnable.newBuilder.setContainer(cloudSdkContainerBuilder)
+  def cloudSdkShellRunnable(shellCommand: String)(volumes: List[Volume],
+                                                  flags: List[RunnableFlag],
+                                                  labels: Map[String, String],
+                                                  timeout: Duration = Duration.Inf
+  ): Runnable.Builder =
+    Runnable.newBuilder
+      .setContainer(cloudSdkContainerBuilder)
       .withVolumes(volumes)
       .withLabels(labels)
       .withEntrypointCommand(
@@ -222,19 +224,17 @@ object RunnableBuilder {
       )
       .withFlags(flags)
       .withTimeout(timeout)
-  }
 
-    def annotateTimestampedRunnable(description: String,
-                                    loggingLabelValue: String,
-                                    isAlwaysRun: Boolean = false)(
-                                    volumes: List[Volume],
-                                    runnables: List[Runnable.Builder]): List[Runnable.Builder] = {
-
-      val flags = if (isAlwaysRun) List(RunnableFlag.AlwaysRun) else List()
-      val labels = Map(Key.Logging -> loggingLabelValue)
-      val starting = logTimestampedRunnable(s"Starting $description.", volumes, flags, labels)
-      val done = logTimestampedRunnable(s"Done $description.", volumes, flags, labels)
-      List(starting) ++ runnables ++ List(done)
+  def annotateTimestampedRunnable(description: String,
+                                  loggingLabelValue: String,
+                                  isAlwaysRun: Boolean = false
+  )(volumes: List[Volume], runnables: List[Runnable.Builder]): List[Runnable.Builder] = {
+
+    val flags = if (isAlwaysRun) List(RunnableFlag.AlwaysRun) else List()
+    val labels = Map(Key.Logging -> loggingLabelValue)
+    val starting = logTimestampedRunnable(s"Starting $description.", volumes, flags, labels)
+    val done = logTimestampedRunnable(s"Done $description.", volumes, flags, labels)
+    List(starting) ++ runnables ++ List(done)
   }
 
   /**
@@ -243,7 +243,7 @@ object RunnableBuilder {
     * @param parameter Input or output parameter to label.
     * @return The labels.
     */
-  def parameterLabels(parameter: BatchParameter): Map[String, String] = {
+  def parameterLabels(parameter: BatchParameter): Map[String, String] =
     parameter match {
       case _: GcpBatchInput =>
         Map(
@@ -256,33 +256,31 @@ object RunnableBuilder {
           Key.OutputName -> parameter.name
         )
     }
-  }
 
   /** Creates a Runnable that describes the parameter localization or delocalization. */
-  def describeParameter(parameter: BatchParameter, volumes: List[Volume], labels: Map[String, String]): Runnable.Builder = {
+  def describeParameter(parameter: BatchParameter,
+                        volumes: List[Volume],
+                        labels: Map[String, String]
+  ): Runnable.Builder =
     parameter match {
       case _: GcpBatchInput =>
         val message = "Localizing input %s -> %s".format(
           shellEscaped(parameter.cloudPath),
-          shellEscaped(parameter.containerPath),
+          shellEscaped(parameter.containerPath)
         )
         logTimestampedRunnable(message, volumes, List.empty, labels)
       case _: GcpBatchOutput =>
         val message = "Delocalizing output %s -> %s".format(
           shellEscaped(parameter.containerPath),
-          shellEscaped(parameter.cloudPath),
+          shellEscaped(parameter.cloudPath)
         )
         logTimestampedRunnable(message, volumes, List(RunnableFlag.AlwaysRun), labels)
     }
-  }
 
   // Converts an Runnable to a `docker run ...` command runnable in the shell.
   private[runnable] def toDockerRun(runnable: Runnable.Builder): String = {
-    runnable.getContainer
-      .getCommandsList
-      .asScala
-      .toList
-      .map { cmd => shellEscaped(cmd) }
+    runnable.getContainer.getCommandsList.asScala.toList
+      .map(cmd => shellEscaped(cmd))
       .mkString(" ")
 
     val commandArgs: String = Option(runnable.getContainerBuilder.getCommandsList) match {
@@ -313,11 +311,6 @@ object RunnableBuilder {
         } mkString ""
     }
 
-    List("docker run",
-      mountArgs,
-      entrypointArg,
-      imageArg,
-      commandArgs,
-    ).mkString
+    List("docker run", mountArgs, entrypointArg, imageArg, commandArgs).mkString
   }
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableCommands.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableCommands.scala
index 0bbd1c50d53..8c7c024691e 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableCommands.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableCommands.scala
@@ -32,19 +32,20 @@ object RunnableCommands {
     def escape: String = StringEscapeUtils.escapeXSI(path.pathAsString)
   }
 
-  private def makeContentTypeFlag(contentType: Option[ContentType]) = contentType.map(ct => s"""-h "Content-Type: $ct"""").getOrElse("")
+  private def makeContentTypeFlag(contentType: Option[ContentType]) =
+    contentType.map(ct => s"""-h "Content-Type: $ct"""").getOrElse("")
 
   def makeContainerDirectory(containerPath: Path) = s"mkdir -p ${containerPath.escape}"
 
-  def delocalizeDirectory(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
-                         (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def delocalizeDirectory(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     retry {
       recoverRequesterPaysError(cloudPath) { flag =>
         s"rm -f $$HOME/.config/gcloud/gce && " +
           s"gsutil $flag ${contentType |> makeContentTypeFlag} -m rsync -r ${containerPath.escape} ${cloudPath.escape}"
       }
     }
-  }
 
   /**
     * As per https://cloud.google.com/storage/docs/gsutil/addlhelp/HowSubdirectoriesWork, rule #2
@@ -58,29 +59,29 @@ object RunnableCommands {
     * By instead using the parent directory (and ensuring it ends with a slash), gsutil will treat that as a directory and put the file under it.
     * So the final gsutil command will look something like gsutil cp /local/file.txt gs://bucket/subdir/
     */
-  def delocalizeFile(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
-                    (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def delocalizeFile(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     retry {
       recoverRequesterPaysError(cloudPath) { flag =>
         s"rm -f $$HOME/.config/gcloud/gce && " +
           s"gsutil $flag ${contentType |> makeContentTypeFlag} cp ${containerPath.escape} ${cloudPath.parent.escape.ensureSlashed}"
       }
     }
-  }
 
   /**
     * delocalizeFile necessarily copies the file to the same name. Use this if you want to to specify a name different from the original
     * Make sure that there's no object named "yourfinalname_something" (see above) in the same cloud directory.
     */
-  def delocalizeFileTo(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
-                      (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def delocalizeFileTo(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     retry {
       recoverRequesterPaysError(cloudPath) { flag =>
         s"rm -f $$HOME/.config/gcloud/gce && " +
           s"gsutil $flag ${contentType |> makeContentTypeFlag} cp ${containerPath.escape} ${cloudPath.escape}"
       }
     }
-  }
 
   def ifExist(containerPath: Path)(f: => String) = s"if [ -e ${containerPath.escape} ]; then $f; fi"
 
@@ -92,7 +93,7 @@ object RunnableCommands {
        |  sleep ${duration.toSeconds}
        |done""".stripMargin
 
-  def retry(f: => String)(implicit gcsTransferConfiguration: GcsTransferConfiguration, wait: FiniteDuration): String = {
+  def retry(f: => String)(implicit gcsTransferConfiguration: GcsTransferConfiguration, wait: FiniteDuration): String =
     s"""for i in $$(seq ${gcsTransferConfiguration.transferAttempts}); do
        |  (
        |    $f
@@ -107,35 +108,34 @@ object RunnableCommands {
        |  fi
        |done
        |exit "$$RC"""".stripMargin
-  }
 
-  def delocalizeFileOrDirectory(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
-                               (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def delocalizeFileOrDirectory(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     s"""if [ -d ${containerPath.escape} ]; then
        |  ${delocalizeDirectory(containerPath, cloudPath, contentType)}
        |else
        |  ${delocalizeFile(containerPath, cloudPath, contentType)}
        |fi""".stripMargin
-  }
 
-  def localizeDirectory(cloudPath: Path, containerPath: Path)
-                       (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def localizeDirectory(cloudPath: Path, containerPath: Path)(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     retry {
       recoverRequesterPaysError(cloudPath) { flag =>
         s"${containerPath |> makeContainerDirectory} && " +
           s"rm -f $$HOME/.config/gcloud/gce && gsutil $flag -m rsync -r ${cloudPath.escape} ${containerPath.escape}"
       }
     }
-  }
 
-  def localizeFile(cloudPath: Path, containerPath: Path)
-                  (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def localizeFile(cloudPath: Path, containerPath: Path)(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     retry {
       recoverRequesterPaysError(cloudPath) { flag =>
         s"rm -f $$HOME/.config/gcloud/gce && gsutil $flag cp ${cloudPath.escape} ${containerPath.escape}"
       }
     }
-  }
 
   def recoverRequesterPaysError(path: Path)(f: String => String): String = {
     val commandWithoutProject = f("")
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableLabels.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableLabels.scala
index 7d9978c42c1..35624215443 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableLabels.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableLabels.scala
@@ -2,6 +2,7 @@ package cromwell.backend.google.batch.runnable
 
 object RunnableLabels {
   object Key {
+
     /**
       * Very short description of the runnable
       */
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala
index 7df2a4bff79..f60baed0608 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala
@@ -6,6 +6,7 @@ import net.ceedubs.ficus.Ficus._
 import org.apache.commons.text.StringEscapeUtils
 
 object RunnableUtils {
+
   /** Image to use for ssh access. */
   val sshImage = "gcr.io/cloud-genomics-pipelines/tools"
 
@@ -32,7 +33,7 @@ object RunnableUtils {
     * When updating this value, also consider updating the CromwellImagesSizeRoundedUpInGB below.
     */
   val CloudSdkImage: String =
-    //config.getOrElse("cloud-sdk-image-url", "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine")
+    // config.getOrElse("cloud-sdk-image-url", "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine")
     config.getOrElse("cloud-sdk-image-url", "gcr.io/google.com/cloudsdktool/cloud-sdk:434.0.0-alpine")
   /*
    * At the moment, cloud-sdk (584MB for 354.0.0-alpine) and stedolan/jq (182MB) decompressed ~= 0.8 GB
@@ -55,27 +56,28 @@ object RunnableUtils {
 
   private val backgroundRunnableTerminationGraceTime = 10
 
-  val terminateAllBackgroundRunnablesCommand: String = s"kill -TERM -1 && sleep $backgroundRunnableTerminationGraceTime || true"
+  val terminateAllBackgroundRunnablesCommand: String =
+    s"kill -TERM -1 && sleep $backgroundRunnableTerminationGraceTime || true"
 
   def timestampedMessage(message: String): String =
     s"""printf '%s %s\\n' "$$(date -u '+%Y/%m/%d %H:%M:%S')" ${shellEscaped(message)}"""
 
   /** Start background runnables first, leave the rest as is */
   def sortRunnables(containerSetup: List[Runnable],
-                            localization: List[Runnable],
-                            userRunnable: List[Runnable],
-                            memoryRetryRunnable: List[Runnable],
-                            deLocalization: List[Runnable],
-                            monitoringSetup: List[Runnable],
-                            monitoringShutdown: List[Runnable],
-                            checkpointingStart: List[Runnable],
-                            checkpointingShutdown: List[Runnable],
-                            sshAccess: List[Runnable],
-                            isBackground: Runnable => Boolean,
-                         ): List[Runnable] = {
+                    localization: List[Runnable],
+                    userRunnable: List[Runnable],
+                    memoryRetryRunnable: List[Runnable],
+                    deLocalization: List[Runnable],
+                    monitoringSetup: List[Runnable],
+                    monitoringShutdown: List[Runnable],
+                    checkpointingStart: List[Runnable],
+                    checkpointingShutdown: List[Runnable],
+                    sshAccess: List[Runnable],
+                    isBackground: Runnable => Boolean
+  ): List[Runnable] = {
     val toBeSortedRunnables = localization ++ userRunnable ++ memoryRetryRunnable ++ deLocalization
-    val sortedRunnables = toBeSortedRunnables.sortWith {
-      case (runnable, _) => isBackground(runnable)
+    val sortedRunnables = toBeSortedRunnables.sortWith { case (runnable, _) =>
+      isBackground(runnable)
     }
 
     sshAccess ++ containerSetup ++ monitoringSetup ++ checkpointingStart ++ sortedRunnables ++ checkpointingShutdown ++ monitoringShutdown
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala
index d2d499b3127..cba665dbf9e 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/UserRunnable.scala
@@ -3,7 +3,6 @@ package cromwell.backend.google.batch.runnable
 import com.google.cloud.batch.v1.{Runnable, Volume}
 import cromwell.backend.google.batch.api.GcpBatchRequestFactory.CreateBatchJobParameters
 
-
 trait UserRunnable {
 
   def userRunnables(createParameters: CreateBatchJobParameters, volumes: List[Volume]): List[Runnable] = {
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchExpressionFunctions.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchExpressionFunctions.scala
index 4ad6cc45b61..dcec7ec3799 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchExpressionFunctions.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchExpressionFunctions.scala
@@ -10,26 +10,25 @@ import cromwell.filesystems.gcs.GcsPathBuilder
 import cromwell.filesystems.gcs.GcsPathBuilder.{InvalidGcsPath, PossiblyValidRelativeGcsPath, ValidFullGcsPath}
 import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
 
-class BatchPathFunctions(pathBuilders: PathBuilders, callContext: CallContext) extends CallCorePathFunctionSet(pathBuilders, callContext) {
-  override def relativeToHostCallRoot(path: String) = {
+class BatchPathFunctions(pathBuilders: PathBuilders, callContext: CallContext)
+    extends CallCorePathFunctionSet(pathBuilders, callContext) {
+  override def relativeToHostCallRoot(path: String) =
     GcsPathBuilder.validateGcsPath(path) match {
       case _: ValidFullGcsPath => path
       case _ => callContext.root.resolve(path.stripPrefix("file://").stripPrefix("/")).pathAsString
     }
-  }
 }
 
 class BatchExpressionFunctions(standardParams: StandardExpressionFunctionsParams)
-  extends StandardExpressionFunctions(standardParams) {
+    extends StandardExpressionFunctions(standardParams) {
   override lazy val ioCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder
 
-  override def preMapping(str: String) = {
+  override def preMapping(str: String) =
     GcsPathBuilder.validateGcsPath(str) match {
       case _: ValidFullGcsPath => str
       case PossiblyValidRelativeGcsPath => callContext.root.resolve(str.stripPrefix("/")).pathAsString
       case _: InvalidGcsPath => str
     }
-  }
 
   override lazy val pathFunctions = new BatchPathFunctions(pathBuilders, callContext)
 
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchParameterConversions.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchParameterConversions.scala
index ad7c942b4f9..2a230e58d6b 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchParameterConversions.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchParameterConversions.scala
@@ -12,7 +12,9 @@ import cromwell.filesystems.http.HttpPath
 import simulacrum.typeclass
 
 @typeclass trait ToParameter[A <: BatchParameter] {
-  def toRunnables(p: A, volumes: List[Volume])(implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable.Builder]
+  def toRunnables(p: A, volumes: List[Volume])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): List[Runnable.Builder]
 }
 
 trait GcpBatchParameterConversions {
@@ -20,16 +22,17 @@ trait GcpBatchParameterConversions {
   import RunnableCommands._
   import RunnableLabels._
 
-
   implicit val fileInputToParameter: ToParameter[GcpBatchFileInput] = new ToParameter[GcpBatchFileInput] {
-    override def toRunnables(fileInput: GcpBatchFileInput, volumes: List[Volume])
-                          (implicit retryPolicy: GcsTransferConfiguration): List[Runnable.Builder] = {
+    override def toRunnables(fileInput: GcpBatchFileInput, volumes: List[Volume])(implicit
+      retryPolicy: GcsTransferConfiguration
+    ): List[Runnable.Builder] = {
 
       val labels = RunnableBuilder.parameterLabels(fileInput)
       fileInput.cloudPath match {
         case _: HttpPath =>
           val command = s"curl --silent --create-dirs --output ${fileInput.containerPath} ${fileInput.cloudPath}"
-          val localizationRunnables = RunnableBuilder.cloudSdkShellRunnable(command)(volumes = volumes, labels = labels, flags = List.empty)
+          val localizationRunnables =
+            RunnableBuilder.cloudSdkShellRunnable(command)(volumes = volumes, labels = labels, flags = List.empty)
           List(RunnableBuilder.describeParameter(fileInput, volumes, labels), localizationRunnables)
 
         case _: GcsPath =>
@@ -44,8 +47,9 @@ trait GcpBatchParameterConversions {
 
   implicit val directoryInputToParameter: ToParameter[GcpBatchDirectoryInput] =
     new ToParameter[GcpBatchDirectoryInput] {
-      override def toRunnables(directoryInput: GcpBatchDirectoryInput, volumes: List[Volume])
-                            (implicit retryPolicy: GcsTransferConfiguration): List[Runnable.Builder] = {
+      override def toRunnables(directoryInput: GcpBatchDirectoryInput, volumes: List[Volume])(implicit
+        retryPolicy: GcsTransferConfiguration
+      ): List[Runnable.Builder] =
         directoryInput.cloudPath match {
           case _: GcsPath => Nil // GCS paths will be localized with a separate localization script.
           case _ =>
@@ -56,19 +60,23 @@ trait GcpBatchParameterConversions {
             )(volumes = volumes, labels = labels, flags = List.empty)
             List(describeRunnables, localizationRunnables)
         }
-      }
     }
 
   implicit val fileOutputToParameter: ToParameter[GcpBatchFileOutput] = new ToParameter[GcpBatchFileOutput] {
-    override def toRunnables(fileOutput: GcpBatchFileOutput, volumes: List[Volume])
-                          (implicit retryPolicy: GcsTransferConfiguration): List[Runnable.Builder] = {
+    override def toRunnables(fileOutput: GcpBatchFileOutput, volumes: List[Volume])(implicit
+      retryPolicy: GcsTransferConfiguration
+    ): List[Runnable.Builder] = {
 
       // If the output is a "secondary file", it actually could be a directory but we won't know before runtime.
       // The fileOrDirectory method will generate a command that can cover both cases
-      lazy val copy = if (fileOutput.secondary)
-        RunnableCommands.delocalizeFileOrDirectory(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
-      else
-        RunnableCommands.delocalizeFile(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
+      lazy val copy =
+        if (fileOutput.secondary)
+          RunnableCommands.delocalizeFileOrDirectory(fileOutput.containerPath,
+                                                     fileOutput.cloudPath,
+                                                     fileOutput.contentType
+          )
+        else
+          RunnableCommands.delocalizeFile(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
 
       lazy val copyOnlyIfExists = RunnableCommands.ifExist(fileOutput.containerPath) {
         copy
@@ -97,11 +105,13 @@ trait GcpBatchParameterConversions {
             case (key, _) if key == Key.Tag => key -> Value.Background
             case (key, value) => key -> value
           }
-          val periodic = RunnableBuilder.cloudSdkShellRunnable(
-            every(period) {
-              copyCommand
-            }
-          )(volumes = volumes, labels = periodicLabels, flags = List.empty).withRunInBackground(true)
+          val periodic = RunnableBuilder
+            .cloudSdkShellRunnable(
+              every(period) {
+                copyCommand
+              }
+            )(volumes = volumes, labels = periodicLabels, flags = List.empty)
+            .withRunInBackground(true)
 
           finalDelocalizationRunnables :+ periodic
 
@@ -112,34 +122,37 @@ trait GcpBatchParameterConversions {
 
   implicit val directoryOutputToParameter: ToParameter[GcpBatchDirectoryOutput] =
     new ToParameter[GcpBatchDirectoryOutput] {
-      override def toRunnables(directoryOutput: GcpBatchDirectoryOutput, volumes: List[Volume])
-                            (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable.Builder] = {
+      override def toRunnables(directoryOutput: GcpBatchDirectoryOutput, volumes: List[Volume])(implicit
+        gcsTransferConfiguration: GcsTransferConfiguration
+      ): List[Runnable.Builder] =
         directoryOutput.cloudPath match {
           case _: GcsPath => Nil // GCS paths will be delocalized with a separate delocalization script.
           case _ =>
             val labels = RunnableBuilder.parameterLabels(directoryOutput)
             val describeRunnable = RunnableBuilder.describeParameter(directoryOutput, volumes, labels)
-            val delocalizationRunnable = RunnableBuilder.cloudSdkShellRunnable(
-              delocalizeDirectory(directoryOutput.containerPath, directoryOutput.cloudPath, None)
-            )(volumes = volumes, labels = labels, flags = List.empty)
+            val delocalizationRunnable = RunnableBuilder
+              .cloudSdkShellRunnable(
+                delocalizeDirectory(directoryOutput.containerPath, directoryOutput.cloudPath, None)
+              )(volumes = volumes, labels = labels, flags = List.empty)
               .withAlwaysRun(true)
 
             List(describeRunnable, delocalizationRunnable)
         }
-      }
     }
 
   implicit val inputToParameter: ToParameter[GcpBatchInput] = new ToParameter[GcpBatchInput] {
-    override def toRunnables(p: GcpBatchInput, volumes: List[Volume])
-                          (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable.Builder] = p match {
+    override def toRunnables(p: GcpBatchInput, volumes: List[Volume])(implicit
+      gcsTransferConfiguration: GcsTransferConfiguration
+    ): List[Runnable.Builder] = p match {
       case fileInput: GcpBatchFileInput => fileInputToParameter.toRunnables(fileInput, volumes)
       case directoryInput: GcpBatchDirectoryInput => directoryInputToParameter.toRunnables(directoryInput, volumes)
     }
   }
 
   implicit val outputToParameter: ToParameter[GcpBatchOutput] = new ToParameter[GcpBatchOutput] {
-    override def toRunnables(p: GcpBatchOutput, volumes: List[Volume])
-                          (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Runnable.Builder] = p match {
+    override def toRunnables(p: GcpBatchOutput, volumes: List[Volume])(implicit
+      gcsTransferConfiguration: GcsTransferConfiguration
+    ): List[Runnable.Builder] = p match {
       case fileOutput: GcpBatchFileOutput => fileOutputToParameter.toRunnables(fileOutput, volumes)
       case directoryOutput: GcpBatchDirectoryOutput => directoryOutputToParameter.toRunnables(directoryOutput, volumes)
     }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala
index 612c95651e9..d27344c42b9 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/BatchUtilityConversions.scala
@@ -9,14 +9,12 @@ import wom.format.MemorySize
 trait BatchUtilityConversions {
 
   // construct zones string
-  def toZonesPath(zones: Vector[String]): String = {
+  def toZonesPath(zones: Vector[String]): String =
     zones.map(zone => "zones/" + zone).mkString(" ")
-  }
 
   // lowercase text to match gcp label requirements
-  def toLabel(text: String): String = {
+  def toLabel(text: String): String =
     text.toLowerCase
-  }
 
   // creates batch run time location from zones entered in runtime.  This is needed if network not defined by user to place on right network.
   def toBatchRunLocation(zones: Vector[String]): String = {
@@ -25,14 +23,12 @@ trait BatchUtilityConversions {
   }
 
   // convert cpu cores to millicores that Batch expects
-  def toCpuCores(cpu: Long): Long = {
+  def toCpuCores(cpu: Long): Long =
     cpu * 1000
-  }
 
   // convert memory to MiB that Batch expects
-  def toMemMib(memory: MemorySize): Long = {
+  def toMemMib(memory: MemorySize): Long =
     (memory.amount * 1024).toLong
-  }
 
   // set Standard or Spot instances
   def toProvisioningModel(preemption: Int): ProvisioningModel = preemption compare 0 match {
@@ -45,39 +41,33 @@ trait BatchUtilityConversions {
   def toVolumes(disks: Seq[GcpBatchAttachedDisk]): List[Volume] = disks.map(toVolume).toList
 
   def toVolume(disk: GcpBatchAttachedDisk): Volume = {
-    val volume = Volume
-      .newBuilder
+    val volume = Volume.newBuilder
       .setDeviceName(disk.name)
       .setMountPath(disk.mountPoint.pathAsString)
 
-
     disk match {
       case _: GcpBatchReferenceFilesDisk =>
         volume
           .addMountOptions("async, rw")
           .build
       case _ =>
-        volume
-          .build
+        volume.build
     }
   }
 
   private def toDisk(disk: GcpBatchAttachedDisk): AttachedDisk = {
-    val googleDisk = Disk
-      .newBuilder
+    val googleDisk = Disk.newBuilder
       .setSizeGb(disk.sizeGb.toLong)
       .setType(toBatchDiskType(disk.diskType))
 
     disk match {
       case refDisk: GcpBatchReferenceFilesDisk =>
-        googleDisk.setImage(refDisk.image)
-          .build
+        googleDisk.setImage(refDisk.image).build
       case _ =>
         googleDisk.build
     }
 
-    val googleAttachedDisk = AttachedDisk
-      .newBuilder
+    val googleAttachedDisk = AttachedDisk.newBuilder
       .setDeviceName(disk.name)
       .setNewDisk(googleDisk)
       .build
@@ -91,11 +81,11 @@ trait BatchUtilityConversions {
     case DiskType.LOCAL => "local-ssd"
   }
 
-  def convertGbToMib(runtimeAttributes: GcpBatchRuntimeAttributes): Long = {
+  def convertGbToMib(runtimeAttributes: GcpBatchRuntimeAttributes): Long =
     (runtimeAttributes.bootDiskSize * 953.7).toLong
-  }
 
   // Create accelerators for GPUs
-  def toAccelerator(gpuResource: GpuResource): Accelerator.Builder = Accelerator.newBuilder.setCount(gpuResource.gpuCount.value.toLong).setType(gpuResource.gpuType.toString)
+  def toAccelerator(gpuResource: GpuResource): Accelerator.Builder =
+    Accelerator.newBuilder.setCount(gpuResource.gpuCount.value.toLong).setType(gpuResource.gpuType.toString)
 
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchDockerCacheMappingOperations.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchDockerCacheMappingOperations.scala
index e7ca7a0e6a8..233413b6d4b 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchDockerCacheMappingOperations.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchDockerCacheMappingOperations.scala
@@ -20,7 +20,8 @@ trait GcpBatchDockerCacheMappingOperations {
   private class DockerImageManifestVersionError(message: String) extends RuntimeException(message) with NoStackTrace
 
   def generateDockerImageToDiskImageMapping(auth: GoogleAuthMode,
-                                            dockerImageCacheManifestFile: ValidFullGcsPath): Map[String, DockerImageCacheEntry] = {
+                                            dockerImageCacheManifestFile: ValidFullGcsPath
+  ): Map[String, DockerImageCacheEntry] = {
 
     val gcsClient = StorageOptions
       .newBuilder()
@@ -34,35 +35,42 @@ trait GcpBatchDockerCacheMappingOperations {
   def getDockerCacheDiskImageForAJob(dockerImageToCacheDiskImageMappingOpt: Option[Map[String, DockerImageCacheEntry]],
                                      dockerImageAsSpecifiedByUser: String,
                                      dockerImageWithDigest: String,
-                                     jobLogger: JobLogger): Option[String] = {
+                                     jobLogger: JobLogger
+  ): Option[String] =
     dockerImageToCacheDiskImageMappingOpt
       .flatMap(_.get(dockerImageAsSpecifiedByUser))
       .filter { cachedDockerImageDigestAndDiskName =>
         val hashStartingPositionInActualDockerImage = dockerImageWithDigest.indexOf('@')
         if (hashStartingPositionInActualDockerImage != -1) {
-          val actualDigestOfDesiredDockerImage = dockerImageWithDigest.substring(hashStartingPositionInActualDockerImage + 1)
+          val actualDigestOfDesiredDockerImage =
+            dockerImageWithDigest.substring(hashStartingPositionInActualDockerImage + 1)
           if (cachedDockerImageDigestAndDiskName.dockerImageDigest == actualDigestOfDesiredDockerImage) {
             true
           } else {
-            jobLogger.info(s"Cached Docker image digest mismatch. Requested docker image $dockerImageAsSpecifiedByUser has different digest than " +
-              s"corresponding cached image located at the ${cachedDockerImageDigestAndDiskName.diskImageName} disk image. " +
-              s"Digest of requested image is $actualDigestOfDesiredDockerImage, but digest of cached image is ${cachedDockerImageDigestAndDiskName.dockerImageDigest}. " +
-              s"Docker image cache feature will not be used for this task.")
+            jobLogger.info(
+              s"Cached Docker image digest mismatch. Requested docker image $dockerImageAsSpecifiedByUser has different digest than " +
+                s"corresponding cached image located at the ${cachedDockerImageDigestAndDiskName.diskImageName} disk image. " +
+                s"Digest of requested image is $actualDigestOfDesiredDockerImage, but digest of cached image is ${cachedDockerImageDigestAndDiskName.dockerImageDigest}. " +
+                s"Docker image cache feature will not be used for this task."
+            )
 
             false
           }
         } else {
-          jobLogger.error(s"Programmer error ! Odd docker image name where supposed to be name with digest: $dockerImageWithDigest")
+          jobLogger.error(
+            s"Programmer error ! Odd docker image name where supposed to be name with digest: $dockerImageWithDigest"
+          )
           false
         }
       }
       .map(_.diskImageName)
-  }
 
-  private[batch] def readDockerImageCacheManifestFileFromGCS(gcsClient: Storage, gcsPath: ValidFullGcsPath): IO[DockerImageCacheManifest] = {
-    val manifestFileBlobIo = IO { gcsClient.get(BlobId.of(gcsPath.bucket, gcsPath.path.substring(1))) }
+  private[batch] def readDockerImageCacheManifestFileFromGCS(gcsClient: Storage,
+                                                             gcsPath: ValidFullGcsPath
+  ): IO[DockerImageCacheManifest] = {
+    val manifestFileBlobIo = IO(gcsClient.get(BlobId.of(gcsPath.bucket, gcsPath.path.substring(1))))
     manifestFileBlobIo flatMap { manifestFileBlob =>
-      val jsonStringIo = IO { manifestFileBlob.getContent().map(_.toChar).mkString }
+      val jsonStringIo = IO(manifestFileBlob.getContent().map(_.toChar).mkString)
       jsonStringIo.flatMap { jsonStr =>
         decode[DockerImageCacheManifest](jsonStr) match {
           case Left(error) => IO.raiseError(error)
@@ -70,12 +78,16 @@ trait GcpBatchDockerCacheMappingOperations {
             if (parsedManifest.manifestFormatVersion == CURRENT_SUPPORTED_MANIFEST_FORMAT_VERSION) {
               IO.pure(parsedManifest)
             } else {
-              IO.raiseError(new DockerImageManifestVersionError(s"Current supported docker image cache manifest format version " +
-                s"is $CURRENT_SUPPORTED_MANIFEST_FORMAT_VERSION, but got ${parsedManifest.manifestFormatVersion}"))
+              IO.raiseError(
+                new DockerImageManifestVersionError(
+                  s"Current supported docker image cache manifest format version " +
+                    s"is $CURRENT_SUPPORTED_MANIFEST_FORMAT_VERSION, but got ${parsedManifest.manifestFormatVersion}"
+                )
+              )
             }
         }
       }
     }
   }
 
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchExpressionFunctions.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchExpressionFunctions.scala
index 2cb2b86b34c..bdf358f1914 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchExpressionFunctions.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchExpressionFunctions.scala
@@ -10,26 +10,25 @@ import cromwell.filesystems.gcs.GcsPathBuilder
 import cromwell.filesystems.gcs.GcsPathBuilder.{InvalidGcsPath, PossiblyValidRelativeGcsPath, ValidFullGcsPath}
 import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
 
-class GcpBatchPathFunctions(pathBuilders: PathBuilders, callContext: CallContext) extends CallCorePathFunctionSet(pathBuilders, callContext) {
-  override def relativeToHostCallRoot(path: String) = {
+class GcpBatchPathFunctions(pathBuilders: PathBuilders, callContext: CallContext)
+    extends CallCorePathFunctionSet(pathBuilders, callContext) {
+  override def relativeToHostCallRoot(path: String) =
     GcsPathBuilder.validateGcsPath(path) match {
       case _: ValidFullGcsPath => path
       case _ => callContext.root.resolve(path.stripPrefix("file://").stripPrefix("/")).pathAsString
     }
-  }
 }
 
 class GcpBatchExpressionFunctions(standardParams: StandardExpressionFunctionsParams)
-  extends StandardExpressionFunctions(standardParams) {
+    extends StandardExpressionFunctions(standardParams) {
   override lazy val ioCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder
 
-  override def preMapping(str: String) = {
+  override def preMapping(str: String) =
     GcsPathBuilder.validateGcsPath(str) match {
       case _: ValidFullGcsPath => str
       case PossiblyValidRelativeGcsPath => callContext.root.resolve(str.stripPrefix("/")).pathAsString
       case _: InvalidGcsPath => str
     }
-  }
 
   override lazy val pathFunctions = new GcpBatchPathFunctions(pathBuilders, callContext)
 
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraints.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraints.scala
index 83b4796e039..2bbf835eeef 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraints.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraints.scala
@@ -1,6 +1,11 @@
 package cromwell.backend.google.batch.util
 
-import cromwell.backend.google.batch.models.{GcpBatchRuntimeAttributes, N1CustomMachineType, N2CustomMachineType, N2DCustomMachineType}
+import cromwell.backend.google.batch.models.{
+  GcpBatchRuntimeAttributes,
+  N1CustomMachineType,
+  N2CustomMachineType,
+  N2DCustomMachineType
+}
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
 import org.slf4j.Logger
@@ -12,20 +17,19 @@ object GcpBatchMachineConstraints {
                   cpu: Int Refined Positive,
                   cpuPlatformOption: Option[String],
                   googleLegacyMachineSelection: Boolean,
-                  jobLogger: Logger,
-                 ): String = {
+                  jobLogger: Logger
+  ): String =
     if (googleLegacyMachineSelection) {
       s"predefined-$cpu-${memory.to(MemoryUnit.MB).amount.intValue()}"
     } else {
       // If someone requests Intel Cascade Lake as their CPU platform then switch the machine type to n2.
-      // Similarly, CPU platform of AMD Rome corresponds to the machine type n2d.  
+      // Similarly, CPU platform of AMD Rome corresponds to the machine type n2d.
       val customMachineType =
         cpuPlatformOption match {
           case Some(GcpBatchRuntimeAttributes.CpuPlatformIntelCascadeLakeValue) => N2CustomMachineType
-          case Some(GcpBatchRuntimeAttributes.CpuPlatformAMDRomeValue)          => N2DCustomMachineType
+          case Some(GcpBatchRuntimeAttributes.CpuPlatformAMDRomeValue) => N2DCustomMachineType
           case _ => N1CustomMachineType
         }
       customMachineType.machineType(memory, cpu, jobLogger)
     }
-  }
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchReferenceFilesMappingOperations.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchReferenceFilesMappingOperations.scala
index f472263f51c..b03347b2e5b 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchReferenceFilesMappingOperations.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GcpBatchReferenceFilesMappingOperations.scala
@@ -25,7 +25,8 @@ trait GcpBatchReferenceFilesMappingOperations {
     * may take a significant amount of time.
     */
   def generateReferenceFilesMapping(auth: GoogleAuthMode,
-                                    referenceDiskLocalizationManifests: List[ManifestFile]): Map[String, GcpBatchReferenceFilesDisk] = {
+                                    referenceDiskLocalizationManifests: List[ManifestFile]
+  ): Map[String, GcpBatchReferenceFilesDisk] = {
     val gcsClient = StorageOptions
       .newBuilder()
       .setCredentials(auth.credentials(Set(StorageScopes.DEVSTORAGE_READ_ONLY)))
@@ -40,26 +41,31 @@ trait GcpBatchReferenceFilesMappingOperations {
   }
 
   def getReferenceInputsToMountedPathMappings(referenceFileToDiskImageMapping: Map[String, GcpBatchReferenceFilesDisk],
-                                              inputFiles: List[GcpBatchInput]): Map[GcpBatchInput, String] = {
-    val gcsPathsToInputs = inputFiles.collect { case i if i.cloudPath.isInstanceOf[GcsPath] => (i.cloudPath.asInstanceOf[GcsPath].pathAsString, i) }.toMap
+                                              inputFiles: List[GcpBatchInput]
+  ): Map[GcpBatchInput, String] = {
+    val gcsPathsToInputs = inputFiles.collect {
+      case i if i.cloudPath.isInstanceOf[GcsPath] => (i.cloudPath.asInstanceOf[GcsPath].pathAsString, i)
+    }.toMap
     referenceFileToDiskImageMapping.collect {
-      case (path, disk) if gcsPathsToInputs.keySet.contains(s"gs://$path")  =>
+      case (path, disk) if gcsPathsToInputs.keySet.contains(s"gs://$path") =>
         (gcsPathsToInputs(s"gs://$path"), s"${disk.mountPoint.pathAsString}/$path")
     }
   }
 
   def getReferenceDisksToMount(referenceFileToDiskImageMapping: Map[String, GcpBatchReferenceFilesDisk],
-                               inputFilePaths: Set[String]): List[GcpBatchReferenceFilesDisk] = {
+                               inputFilePaths: Set[String]
+  ): List[GcpBatchReferenceFilesDisk] =
     referenceFileToDiskImageMapping.view.filterKeys(key => inputFilePaths.contains(s"gs://$key")).values.toList.distinct
-  }
 
-  private def getReferenceFileToValidatedGcsPathMap(referenceFiles: Set[ReferenceFile]): IO[Map[ReferenceFile, ValidFullGcsPath]] = {
-    val filesAndValidatedPaths = referenceFiles.map {
-      referenceFile => (referenceFile, GcsPathBuilder.validateGcsPath(s"gs://${referenceFile.path}"))
+  private def getReferenceFileToValidatedGcsPathMap(
+    referenceFiles: Set[ReferenceFile]
+  ): IO[Map[ReferenceFile, ValidFullGcsPath]] = {
+    val filesAndValidatedPaths = referenceFiles.map { referenceFile =>
+      (referenceFile, GcsPathBuilder.validateGcsPath(s"gs://${referenceFile.path}"))
     }.toMap
 
-    val filesWithValidPaths = filesAndValidatedPaths.collect {
-      case (referenceFile, validPath: ValidFullGcsPath) => (referenceFile, validPath)
+    val filesWithValidPaths = filesAndValidatedPaths.collect { case (referenceFile, validPath: ValidFullGcsPath) =>
+      (referenceFile, validPath)
     }
     val filesWithInvalidPaths = filesAndValidatedPaths.collect {
       case (referenceFile, invalidPath: InvalidFullGcsPath) => (referenceFile, invalidPath)
@@ -73,30 +79,30 @@ trait GcpBatchReferenceFilesMappingOperations {
   }
 
   protected def bulkValidateCrc32cs(gcsClient: Storage,
-                                    filesWithValidPaths: Map[ReferenceFile, ValidFullGcsPath]): IO[Map[ReferenceFile, Boolean]] = {
+                                    filesWithValidPaths: Map[ReferenceFile, ValidFullGcsPath]
+  ): IO[Map[ReferenceFile, Boolean]] =
     IO {
       val gcsBatch = gcsClient.batch()
-      val filesAndBlobResults = filesWithValidPaths map {
-        case (referenceFile, ValidFullGcsPath(bucket, path)) =>
-          val blobGetResult = gcsBatch.get(BlobId.of(bucket, path.substring(1)), BlobGetOption.fields(BlobField.CRC32C))
-          (referenceFile, blobGetResult)
+      val filesAndBlobResults = filesWithValidPaths map { case (referenceFile, ValidFullGcsPath(bucket, path)) =>
+        val blobGetResult = gcsBatch.get(BlobId.of(bucket, path.substring(1)), BlobGetOption.fields(BlobField.CRC32C))
+        (referenceFile, blobGetResult)
       }
       gcsBatch.submit()
 
-      filesAndBlobResults map {
-        case (referenceFile, blobGetResult) =>
-          val crc32cFromManifest = BaseEncoding.base64.encode(
-            // drop 4 leading bytes from Long crc32c value
-            // https://stackoverflow.com/a/25111119/1794750
-            util.Arrays.copyOfRange(Longs.toByteArray(referenceFile.crc32c), 4, 8)
-          )
+      filesAndBlobResults map { case (referenceFile, blobGetResult) =>
+        val crc32cFromManifest = BaseEncoding.base64.encode(
+          // drop 4 leading bytes from Long crc32c value
+          // https://stackoverflow.com/a/25111119/1794750
+          util.Arrays.copyOfRange(Longs.toByteArray(referenceFile.crc32c), 4, 8)
+        )
 
-          (referenceFile, crc32cFromManifest === blobGetResult.get().getCrc32c)
+        (referenceFile, crc32cFromManifest === blobGetResult.get().getCrc32c)
       }
     }
-  }
 
-  private def getMapOfValidReferenceFilePathsToDisks(gcsClient: Storage, manifestFile: ManifestFile): IO[Map[String, GcpBatchReferenceFilesDisk]] = {
+  private def getMapOfValidReferenceFilePathsToDisks(gcsClient: Storage,
+                                                     manifestFile: ManifestFile
+  ): IO[Map[String, GcpBatchReferenceFilesDisk]] = {
     val refDisk = GcpBatchReferenceFilesDisk(manifestFile.imageIdentifier, manifestFile.diskSizeGb)
     val allReferenceFilesFromManifestMap = manifestFile.files.map(refFile => (refFile, refDisk)).toMap
 
@@ -109,10 +115,13 @@ trait GcpBatchReferenceFilesMappingOperations {
     validReferenceFilesFromManifestMapIo map { validReferenceFilesFromManifestMap =>
       val invalidReferenceFiles = allReferenceFilesFromManifestMap.keySet -- validReferenceFilesFromManifestMap.keySet
       if (invalidReferenceFiles.nonEmpty) {
-        logger.warn(s"The following files listed in references manifest have checksum mismatch with actual files in GCS: ${invalidReferenceFiles.mkString(",")}")
+        logger.warn(
+          s"The following files listed in references manifest have checksum mismatch with actual files in GCS: ${invalidReferenceFiles
+              .mkString(",")}"
+        )
       }
-      validReferenceFilesFromManifestMap.map {
-        case (refFile, disk) => (refFile.path, disk)
+      validReferenceFilesFromManifestMap.map { case (refFile, disk) =>
+        (refFile.path, disk)
       }.toMap
     }
   }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuTypeValidation.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuTypeValidation.scala
index e7ade1bc46a..de53b2a0206 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuTypeValidation.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuTypeValidation.scala
@@ -8,7 +8,6 @@ import wom.RuntimeAttributesKeys
 import wom.types.{WomStringType, WomType}
 import wom.values.{WomString, WomValue}
 
-
 object GpuTypeValidation {
   lazy val instance: RuntimeAttributesValidation[GpuType] = new GpuTypeValidation
   lazy val optional: OptionalRuntimeAttributesValidation[GpuType] = instance.optional
@@ -20,6 +19,7 @@ class GpuTypeValidation extends RuntimeAttributesValidation[GpuType] {
   override def coercion: Iterable[WomType] = Set(WomStringType)
   override def validateValue: PartialFunction[WomValue, ErrorOr[GpuType]] = {
     case WomString(s) => GpuType(s).validNel
-    case other => s"Invalid '$key': String value required but got ${other.womType.friendlyName}. See ${GpuType.MoreDetailsURL} for a list of options".invalidNel
+    case other =>
+      s"Invalid '$key': String value required but got ${other.womType.friendlyName}. See ${GpuType.MoreDetailsURL} for a list of options".invalidNel
   }
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala
index 4b24c9aeacf..51c19813229 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala
@@ -5,7 +5,11 @@ import cats.syntax.either._
 import cats.syntax.validated._
 import com.typesafe.config.Config
 import common.validation.ErrorOr.ErrorOr
-import cromwell.backend.validation.{OptionalRuntimeAttributesValidation, PositiveIntRuntimeAttributesValidation, RuntimeAttributesValidation}
+import cromwell.backend.validation.{
+  OptionalRuntimeAttributesValidation,
+  PositiveIntRuntimeAttributesValidation,
+  RuntimeAttributesValidation
+}
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
 import eu.timepit.refined.refineV
@@ -37,4 +41,4 @@ class GpuValidation(attributeName: String) extends PositiveIntRuntimeAttributesV
     case other =>
       s"Invalid gpu count. Expected positive Int but got ${other.womType.friendlyName} ${other.toWomString}".invalidNel
   }
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/GcpBatchIoSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/GcpBatchIoSpec.scala
index 186152c0768..9a42728510d 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/GcpBatchIoSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/GcpBatchIoSpec.scala
@@ -1,7 +1,12 @@
 package cromwell.backend.google.batch
 
 import com.google.api.client.http.HttpResponseException
-import com.google.api.client.testing.http.{HttpTesting, MockHttpTransport, MockLowLevelHttpRequest, MockLowLevelHttpResponse}
+import com.google.api.client.testing.http.{
+  HttpTesting,
+  MockHttpTransport,
+  MockLowLevelHttpRequest,
+  MockLowLevelHttpResponse
+}
 import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
@@ -25,10 +30,9 @@ class GcpBatchIoSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   }
 
   private def mockTransport(statusCode: Int) = new MockHttpTransport() {
-    override def buildRequest(method: String, url: String) = {
+    override def buildRequest(method: String, url: String) =
       new MockLowLevelHttpRequest() {
         override def execute() = new MockLowLevelHttpResponse().setStatusCode(statusCode)
       }
-    }
   }
 }
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
index 711f59d6845..4253b1877be 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
@@ -18,7 +18,12 @@ import cromwell.backend.google.batch.io.{DiskType, GcpBatchWorkingDisk}
 import cromwell.backend.google.batch.models._
 import cromwell.backend.google.batch.util.BatchExpressionFunctions
 import cromwell.backend.io.JobPathsSpecHelper._
-import cromwell.backend.standard.{DefaultStandardAsyncExecutionActorParams, StandardAsyncExecutionActorParams, StandardAsyncJob, StandardExpressionFunctionsParams}
+import cromwell.backend.standard.{
+  DefaultStandardAsyncExecutionActorParams,
+  StandardAsyncExecutionActorParams,
+  StandardAsyncJob,
+  StandardExpressionFunctionsParams
+}
 import cromwell.core._
 import cromwell.core.callcaching.NoDocker
 import cromwell.core.labels.Labels
@@ -53,14 +58,15 @@ import scala.language.postfixOps
 import common.mock.MockSugar
 import org.mockito.Mockito._
 
-class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
-  with AnyFlatSpecLike
-  with Matchers
-  with ImplicitSender
-  with BackendSpec
-  with BeforeAndAfter
-  with MockSugar
-  with DefaultJsonProtocol {
+class GcpBatchAsyncBackendJobExecutionActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with ImplicitSender
+    with BackendSpec
+    with BeforeAndAfter
+    with MockSugar
+    with DefaultJsonProtocol {
 
   val mockPathBuilder: GcsPathBuilder = MockGcsPathBuilder.instance
   import MockGcsPathBuilder._
@@ -68,7 +74,7 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
   private def gcsPath(str: String) = mockPathBuilder.build(str).getOrElse(fail(s"Invalid gcs path: $str"))
 
-  //import GcpBatchTestConfig._
+  // import GcpBatchTestConfig._
   import cromwell.backend.google.batch.models.GcpBatchTestConfig._
 
   implicit val Timeout: FiniteDuration = 25.seconds.dilated
@@ -98,31 +104,39 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
   private val NoOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))
 
-  private lazy val TestableCallContext = CallContext(mockPathBuilder.build("gs://root").get, DummyStandardPaths, isDocker = false)
+  private lazy val TestableCallContext =
+    CallContext(mockPathBuilder.build("gs://root").get, DummyStandardPaths, isDocker = false)
 
-  private lazy val TestableStandardExpressionFunctionsParams: StandardExpressionFunctionsParams
-  = new StandardExpressionFunctionsParams {
-    override lazy val pathBuilders: List[PathBuilder] = List(mockPathBuilder)
-    override lazy val callContext: CallContext = TestableCallContext
-    override val ioActorProxy: ActorRef = simpleIoActor
-    override val executionContext: ExecutionContext = system.dispatcher
-  }
+  private lazy val TestableStandardExpressionFunctionsParams: StandardExpressionFunctionsParams =
+    new StandardExpressionFunctionsParams {
+      override lazy val pathBuilders: List[PathBuilder] = List(mockPathBuilder)
+      override lazy val callContext: CallContext = TestableCallContext
+      override val ioActorProxy: ActorRef = simpleIoActor
+      override val executionContext: ExecutionContext = system.dispatcher
+    }
 
-  lazy val TestableGcpBatchExpressionFunctions: BatchExpressionFunctions = {
+  lazy val TestableGcpBatchExpressionFunctions: BatchExpressionFunctions =
     new BatchExpressionFunctions(TestableStandardExpressionFunctionsParams)
-  }
 
   private def buildInitializationData(jobDescriptor: BackendJobDescriptor, configuration: GcpBatchConfiguration) = {
-    val pathBuilders = Await.result(configuration.configurationDescriptor.pathBuilders(WorkflowOptions.empty), 5.seconds)
+    val pathBuilders =
+      Await.result(configuration.configurationDescriptor.pathBuilders(WorkflowOptions.empty), 5.seconds)
     val workflowPaths = GcpBatchWorkflowPaths(
-      jobDescriptor.workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), configuration, pathBuilders, GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+      jobDescriptor.workflowDescriptor,
+      NoCredentials.getInstance(),
+      NoCredentials.getInstance(),
+      configuration,
+      pathBuilders,
+      GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper
+    )
     val runtimeAttributesBuilder = GcpBatchRuntimeAttributes.runtimeAttributesBuilder(configuration)
 
     GcpBackendInitializationData(workflowPaths, runtimeAttributesBuilder, configuration, null, None, None, None)
   }
 
-  class TestableGcpBatchJobExecutionActor(params: StandardAsyncExecutionActorParams, functions: BatchExpressionFunctions)
-    extends GcpBatchAsyncBackendJobExecutionActor(params) {
+  class TestableGcpBatchJobExecutionActor(params: StandardAsyncExecutionActorParams,
+                                          functions: BatchExpressionFunctions
+  ) extends GcpBatchAsyncBackendJobExecutionActor(params) {
 
     def this(jobDescriptor: BackendJobDescriptor,
              promise: Promise[BackendJobExecutionResponse],
@@ -130,8 +144,8 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
              functions: BatchExpressionFunctions = TestableGcpBatchExpressionFunctions,
              batchSingletonActor: ActorRef = emptyActor,
              ioActor: ActorRef = mockIoActor,
-             serviceRegistryActor: ActorRef = kvService) = {
-
+             serviceRegistryActor: ActorRef = kvService
+    ) =
       this(
         DefaultStandardAsyncExecutionActorParams(
           jobIdKey = GcpBatchAsyncBackendJobExecutionActor.GcpBatchOperationIdKey,
@@ -146,7 +160,6 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
         ),
         functions
       )
-    }
 
     override lazy val jobLogger: JobLogger = new JobLogger(
       loggerName = "TestLogger",
@@ -162,7 +175,6 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     override lazy val backendEngineFunctions: BatchExpressionFunctions = functions
   }
 
-
   private val runtimeAttributesBuilder = GcpBatchRuntimeAttributes.runtimeAttributesBuilder(gcpBatchConfiguration)
   private val workingDisk = GcpBatchWorkingDisk(DiskType.SSD, 200)
 
@@ -174,11 +186,18 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
       |}
     """.stripMargin
 
-  private def buildPreemptibleJobDescriptor(preemptible: Int, previousPreemptions: Int, previousUnexpectedRetries: Int, failedRetriesCountOpt: Option[Int] = None): BackendJobDescriptor = {
+  private def buildPreemptibleJobDescriptor(preemptible: Int,
+                                            previousPreemptions: Int,
+                                            previousUnexpectedRetries: Int,
+                                            failedRetriesCountOpt: Option[Int] = None
+  ): BackendJobDescriptor = {
     val attempt = previousPreemptions + previousUnexpectedRetries + 1
-    val wdlNamespace = WdlNamespaceWithWorkflow.load(YoSup.replace("[PREEMPTIBLE]", s"preemptible: $preemptible"),
-      Seq.empty[Draft2ImportResolver]).get
-    val womDefinition = wdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    val wdlNamespace = WdlNamespaceWithWorkflow
+      .load(YoSup.replace("[PREEMPTIBLE]", s"preemptible: $preemptible"), Seq.empty[Draft2ImportResolver])
+      .get
+    val womDefinition = wdlNamespace.workflow
+      .toWomWorkflowDefinition(isASubworkflow = false)
+      .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
 
     wdlNamespace.toWomExecutable(Option(Inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
       case Right(womExecutable) =>
@@ -203,21 +222,42 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
         val key = BackendJobDescriptorKey(job, None, attempt)
         val runtimeAttributes = makeRuntimeAttributes(job)
         val prefetchedKvEntries = Map(
-          GcpBatchBackendLifecycleActorFactory.preemptionCountKey -> KvPair(ScopedKey(workflowDescriptor.id, KvJobKey(key), GcpBatchBackendLifecycleActorFactory.preemptionCountKey), previousPreemptions.toString),
-          GcpBatchBackendLifecycleActorFactory.unexpectedRetryCountKey -> KvPair(ScopedKey(workflowDescriptor.id, KvJobKey(key), GcpBatchBackendLifecycleActorFactory.unexpectedRetryCountKey), previousUnexpectedRetries.toString))
-        val prefetchedKvEntriesUpd = if(failedRetriesCountOpt.isEmpty) {
+          GcpBatchBackendLifecycleActorFactory.preemptionCountKey -> KvPair(
+            ScopedKey(workflowDescriptor.id, KvJobKey(key), GcpBatchBackendLifecycleActorFactory.preemptionCountKey),
+            previousPreemptions.toString
+          ),
+          GcpBatchBackendLifecycleActorFactory.unexpectedRetryCountKey -> KvPair(
+            ScopedKey(workflowDescriptor.id,
+                      KvJobKey(key),
+                      GcpBatchBackendLifecycleActorFactory.unexpectedRetryCountKey
+            ),
+            previousUnexpectedRetries.toString
+          )
+        )
+        val prefetchedKvEntriesUpd = if (failedRetriesCountOpt.isEmpty) {
           prefetchedKvEntries
         } else {
-          prefetchedKvEntries + (BackendLifecycleActorFactory.FailedRetryCountKey -> KvPair(ScopedKey(workflowDescriptor.id, KvJobKey(key), BackendLifecycleActorFactory.FailedRetryCountKey), failedRetriesCountOpt.get.toString ))
+          prefetchedKvEntries + (BackendLifecycleActorFactory.FailedRetryCountKey -> KvPair(
+            ScopedKey(workflowDescriptor.id, KvJobKey(key), BackendLifecycleActorFactory.FailedRetryCountKey),
+            failedRetriesCountOpt.get.toString
+          ))
         }
-        BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(Inputs), NoDocker, None, prefetchedKvEntriesUpd)
+        BackendJobDescriptor(workflowDescriptor,
+                             key,
+                             runtimeAttributes,
+                             fqnWdlMapToDeclarationMap(Inputs),
+                             NoDocker,
+                             None,
+                             prefetchedKvEntriesUpd
+        )
       case Left(badtimes) => fail(badtimes.toList.mkString(", "))
     }
   }
 
   private case class DockerImageCacheTestingParameters(dockerImageCacheDiskOpt: Option[String],
                                                        dockerImageAsSpecifiedByUser: String,
-                                                       isDockerImageCacheUsageRequested: Boolean)
+                                                       isDockerImageCacheUsageRequested: Boolean
+  )
 
   private def executionActor(jobDescriptor: BackendJobDescriptor,
                              promise: Promise[BackendJobExecutionResponse],
@@ -226,13 +266,19 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
                              serviceRegistryActor: ActorRef = kvService,
                              referenceInputFilesOpt: Option[Set[GcpBatchInput]] = None,
                              dockerImageCacheTestingParamsOpt: Option[DockerImageCacheTestingParameters] = None
-                            ): ActorRef = {
+  ): ActorRef = {
 
     val job = generateStandardAsyncJob
     val run = Run(job)
     val handle = new GcpBatchPendingExecutionHandle(jobDescriptor, run.job, Option(run), None)
 
-    class ExecuteOrRecoverActor extends TestableGcpBatchJobExecutionActor(jobDescriptor, promise, gcpBatchConfiguration, batchSingletonActor = batchSingletonActor, serviceRegistryActor = serviceRegistryActor) {
+    class ExecuteOrRecoverActor
+        extends TestableGcpBatchJobExecutionActor(jobDescriptor,
+                                                  promise,
+                                                  gcpBatchConfiguration,
+                                                  batchSingletonActor = batchSingletonActor,
+                                                  serviceRegistryActor = serviceRegistryActor
+        ) {
       override def executeOrRecover(mode: ExecutionMode)(implicit ec: ExecutionContext): Future[ExecutionHandle] = {
         sendIncrementMetricsForReferenceFiles(referenceInputFilesOpt)
         dockerImageCacheTestingParamsOpt.foreach { dockerImageCacheTestingParams =>
@@ -251,17 +297,23 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     system.actorOf(Props(new ExecuteOrRecoverActor), "ExecuteOrRecoverActor-" + UUID.randomUUID)
   }
 
-  def runAndFail(previousPreemptions: Int, previousUnexpectedRetries: Int, preemptible: Int, errorCode: Status, innerErrorMessage: String, expectPreemptible: Boolean): BackendJobExecutionResponse = {
+  def runAndFail(previousPreemptions: Int,
+                 previousUnexpectedRetries: Int,
+                 preemptible: Int,
+                 errorCode: Status,
+                 innerErrorMessage: String,
+                 expectPreemptible: Boolean
+  ): BackendJobExecutionResponse = {
 
     val runStatus: RunStatus = RunStatus.Failed(List.empty)
     //    val runStatus = UnsuccessfulRunStatus(errorCode, Option(innerErrorMessage), Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), expectPreemptible)
     val statusPoller = TestProbe("statusPoller")
 
     val promise = Promise[BackendJobExecutionResponse]()
-    val jobDescriptor =  buildPreemptibleJobDescriptor(preemptible, previousPreemptions, previousUnexpectedRetries)
+    val jobDescriptor = buildPreemptibleJobDescriptor(preemptible, previousPreemptions, previousUnexpectedRetries)
 
     // TODO: Use this to check the new KV entries are there!  From PAPI
-    //val kvProbe = TestProbe("kvProbe")
+    // val kvProbe = TestProbe("kvProbe")
 
     val backend = executionActor(jobDescriptor, promise, statusPoller.ref, expectPreemptible)
     backend ! Execute
@@ -277,20 +329,35 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
           case RunStatus.Unrecognized => com.google.cloud.batch.v1.JobStatus.State.UNRECOGNIZED
         }
 
-        backend ! GcpBatchBackendSingletonActor.Event.JobStatusRetrieved(Job.newBuilder.setStatus(com.google.cloud.batch.v1.JobStatus.newBuilder.setState(internalStatus).build()).build())
+        backend ! GcpBatchBackendSingletonActor.Event.JobStatusRetrieved(
+          Job.newBuilder
+            .setStatus(com.google.cloud.batch.v1.JobStatus.newBuilder.setState(internalStatus).build())
+            .build()
+        )
     }
 
     Await.result(promise.future, Timeout)
   }
 
-  def buildPreemptibleTestActorRef(attempt: Int, preemptible: Int, failedRetriesCountOpt: Option[Int] = None): TestActorRef[TestableGcpBatchJobExecutionActor] = {
+  def buildPreemptibleTestActorRef(attempt: Int,
+                                   preemptible: Int,
+                                   failedRetriesCountOpt: Option[Int] = None
+  ): TestActorRef[TestableGcpBatchJobExecutionActor] = {
     // For this test we say that all previous attempts were preempted:
-    val jobDescriptor = buildPreemptibleJobDescriptor(preemptible, attempt - 1, previousUnexpectedRetries = 0, failedRetriesCountOpt = failedRetriesCountOpt)
-    val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(),
-      gcpBatchConfiguration,
-      TestableGcpBatchExpressionFunctions,
-      emptyActor,
-      failIoActor))
+    val jobDescriptor = buildPreemptibleJobDescriptor(preemptible,
+                                                      attempt - 1,
+                                                      previousUnexpectedRetries = 0,
+                                                      failedRetriesCountOpt = failedRetriesCountOpt
+    )
+    val props = Props(
+      new TestableGcpBatchJobExecutionActor(jobDescriptor,
+                                            Promise(),
+                                            gcpBatchConfiguration,
+                                            TestableGcpBatchExpressionFunctions,
+                                            emptyActor,
+                                            failIoActor
+      )
+    )
     TestActorRef(props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
   }
 
@@ -331,12 +398,30 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
   it should "send proper value for \"number of reference files used gauge\" metric, or don't send anything if reference disks feature is disabled" in {
 
-    val expectedInput1 = GcpBatchFileInput(name = "testfile1", relativeHostPath = DefaultPathBuilder.build(Paths.get(s"test/reference/path/file1")), mount = null, cloudPath = null)
-    val expectedInput2 = GcpBatchFileInput(name = "testfile2", relativeHostPath = DefaultPathBuilder.build(Paths.get(s"test/reference/path/file2")), mount = null, cloudPath = null)
+    val expectedInput1 = GcpBatchFileInput(name = "testfile1",
+                                           relativeHostPath =
+                                             DefaultPathBuilder.build(Paths.get(s"test/reference/path/file1")),
+                                           mount = null,
+                                           cloudPath = null
+    )
+    val expectedInput2 = GcpBatchFileInput(name = "testfile2",
+                                           relativeHostPath =
+                                             DefaultPathBuilder.build(Paths.get(s"test/reference/path/file2")),
+                                           mount = null,
+                                           cloudPath = null
+    )
     val expectedReferenceInputFiles = Set[GcpBatchInput](expectedInput1, expectedInput2)
 
-    val expectedMsg1 = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList.of("referencefiles", expectedInput1.relativeHostPath.pathAsString))))
-    val expectedMsg2 = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList.of("referencefiles", expectedInput2.relativeHostPath.pathAsString))))
+    val expectedMsg1 = InstrumentationServiceMessage(
+      CromwellIncrement(
+        CromwellBucket(List.empty, NonEmptyList.of("referencefiles", expectedInput1.relativeHostPath.pathAsString))
+      )
+    )
+    val expectedMsg2 = InstrumentationServiceMessage(
+      CromwellIncrement(
+        CromwellBucket(List.empty, NonEmptyList.of("referencefiles", expectedInput2.relativeHostPath.pathAsString))
+      )
+    )
 
     val jobDescriptor = buildPreemptibleJobDescriptor(0, 0, 0)
     val serviceRegistryProbe = TestProbe()
@@ -370,59 +455,74 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val serviceRegistryProbe = TestProbe()
     val madeUpDockerImageName = "test_madeup_docker_image_name"
 
-    val expectedMessageWhenRequestedNotFound = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList("docker", List("image", "cache", "image_not_in_cache", madeUpDockerImageName)))))
+    val expectedMessageWhenRequestedNotFound = InstrumentationServiceMessage(
+      CromwellIncrement(
+        CromwellBucket(List.empty,
+                       NonEmptyList("docker", List("image", "cache", "image_not_in_cache", madeUpDockerImageName))
+        )
+      )
+    )
     val backendDockerCacheRequestedButNotFound = executionActor(
       jobDescriptor,
       Promise[BackendJobExecutionResponse](),
       TestProbe().ref,
       shouldBePreemptible = false,
       serviceRegistryActor = serviceRegistryProbe.ref,
-      dockerImageCacheTestingParamsOpt =
-        Option(
-          DockerImageCacheTestingParameters(
-            None,
-            "test_madeup_docker_image_name",
-            isDockerImageCacheUsageRequested = true
-          )
+      dockerImageCacheTestingParamsOpt = Option(
+        DockerImageCacheTestingParameters(
+          None,
+          "test_madeup_docker_image_name",
+          isDockerImageCacheUsageRequested = true
         )
+      )
     )
     backendDockerCacheRequestedButNotFound ! Execute
     serviceRegistryProbe.expectMsg(expectedMessageWhenRequestedNotFound)
 
-    val expectedMessageWhenRequestedAndFound = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList("docker", List("image", "cache", "used_image_from_cache", madeUpDockerImageName)))))
+    val expectedMessageWhenRequestedAndFound = InstrumentationServiceMessage(
+      CromwellIncrement(
+        CromwellBucket(List.empty,
+                       NonEmptyList("docker", List("image", "cache", "used_image_from_cache", madeUpDockerImageName))
+        )
+      )
+    )
     val backendDockerCacheRequestedAndFound = executionActor(
       jobDescriptor,
       Promise[BackendJobExecutionResponse](),
       TestProbe().ref,
       shouldBePreemptible = false,
       serviceRegistryActor = serviceRegistryProbe.ref,
-      dockerImageCacheTestingParamsOpt =
-        Option(
-          DockerImageCacheTestingParameters(
-            Option("test_madeup_disk_image_name"),
-            "test_madeup_docker_image_name",
-            isDockerImageCacheUsageRequested = true
-          )
+      dockerImageCacheTestingParamsOpt = Option(
+        DockerImageCacheTestingParameters(
+          Option("test_madeup_disk_image_name"),
+          "test_madeup_docker_image_name",
+          isDockerImageCacheUsageRequested = true
         )
+      )
     )
     backendDockerCacheRequestedAndFound ! Execute
     serviceRegistryProbe.expectMsg(expectedMessageWhenRequestedAndFound)
 
-    val expectedMessageWhenNotRequestedButFound = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList("docker", List("image", "cache", "cached_image_not_used", madeUpDockerImageName)))))
+    val expectedMessageWhenNotRequestedButFound = InstrumentationServiceMessage(
+      CromwellIncrement(
+        CromwellBucket(List.empty,
+                       NonEmptyList("docker", List("image", "cache", "cached_image_not_used", madeUpDockerImageName))
+        )
+      )
+    )
     val backendDockerCacheNotRequestedButFound = executionActor(
       jobDescriptor,
       Promise[BackendJobExecutionResponse](),
       TestProbe().ref,
       shouldBePreemptible = false,
       serviceRegistryActor = serviceRegistryProbe.ref,
-      dockerImageCacheTestingParamsOpt =
-        Option(
-          DockerImageCacheTestingParameters(
-            Option("test_madeup_disk_image_name"),
-            "test_madeup_docker_image_name",
-            isDockerImageCacheUsageRequested = false
-          )
+      dockerImageCacheTestingParamsOpt = Option(
+        DockerImageCacheTestingParameters(
+          Option("test_madeup_disk_image_name"),
+          "test_madeup_docker_image_name",
+          isDockerImageCacheUsageRequested = false
         )
+      )
     )
     backendDockerCacheNotRequestedButFound ! Execute
     serviceRegistryProbe.expectMsg(expectedMessageWhenNotRequestedButFound)
@@ -433,14 +533,13 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
       TestProbe().ref,
       shouldBePreemptible = false,
       serviceRegistryActor = serviceRegistryProbe.ref,
-      dockerImageCacheTestingParamsOpt =
-        Option(
-          DockerImageCacheTestingParameters(
-            None,
-            "test_madeup_docker_image_name",
-            isDockerImageCacheUsageRequested = false
-          )
+      dockerImageCacheTestingParamsOpt = Option(
+        DockerImageCacheTestingParameters(
+          None,
+          "test_madeup_docker_image_name",
+          isDockerImageCacheUsageRequested = false
         )
+      )
     )
     backendDockerCacheNotRequestedNotFound ! Execute
     serviceRegistryProbe.expectNoMessage(timeout)
@@ -475,8 +574,10 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
     checkFailedResult(Status.ABORTED, Option("15: Other type of error."))
       .isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
-    checkFailedResult(Status.OUT_OF_RANGE, Option("14: Wrong errorCode.")).isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
-    checkFailedResult(Status.ABORTED, Option("Weird error message.")).isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
+    checkFailedResult(Status.OUT_OF_RANGE, Option("14: Wrong errorCode."))
+      .isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
+    checkFailedResult(Status.ABORTED, Option("Weird error message."))
+      .isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
     checkFailedResult(Status.ABORTED, Option("UnparsableInt: Even weirder error message."))
       .isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
     checkFailedResult(Status.ABORTED, None).isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
@@ -511,14 +612,20 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
       gcsFileKey -> gcsFileVal
     )
 
-    val wdlNamespace = WdlNamespaceWithWorkflow.load(
-      wdlString,
-      Seq.empty[Draft2ImportResolver],
-    ).get
-    val womWorkflow = wdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    val wdlNamespace = WdlNamespaceWithWorkflow
+      .load(
+        wdlString,
+        Seq.empty[Draft2ImportResolver]
+      )
+      .get
+    val womWorkflow = wdlNamespace.workflow
+      .toWomWorkflowDefinition(isASubworkflow = false)
+      .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
     wdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
 
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
@@ -531,19 +638,28 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
           None
         )
 
-        val call: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst({ case t: CommandCallNode => t }).get
+        val call: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst { case t: CommandCallNode =>
+          t
+        }.get
         val key = BackendJobDescriptorKey(call, None, 1)
         val runtimeAttributes = makeRuntimeAttributes(call)
-        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
 
         val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
         val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
-          props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
-
+          props,
+          s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
 
-        def gcsPathToLocal(womValue: WomValue): WomValue = {
+        def gcsPathToLocal(womValue: WomValue): WomValue =
           WomFileMapper.mapWomFiles(testActorRef.underlyingActor.mapCommandLineWomFile)(womValue).get
-        }
 
         val mappedInputs = jobDescriptor.localInputs safeMapValues gcsPathToLocal
 
@@ -569,8 +685,14 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+              Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
       WorkflowOptions.fromJsonString("""{"monitoring_script": "gs://path/to/script"}""").get,
       Labels.empty,
@@ -582,22 +704,37 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
     val runtimeAttributes = makeRuntimeAttributes(job)
     val key = BackendJobDescriptorKey(job, None, 1)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
     val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
-      props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     testActorRef.underlyingActor.monitoringScript shouldBe
-      Option(GcpBatchFileInput("monitoring-in", gcsPath("gs://path/to/script"), DefaultPathBuilder.get("monitoring.sh"), workingDisk))
+      Option(
+        GcpBatchFileInput("monitoring-in",
+                          gcsPath("gs://path/to/script"),
+                          DefaultPathBuilder.get("monitoring.sh"),
+                          workingDisk
+        )
+      )
   }
 
   it should "not create a GcpBatchFileInput for the monitoring script, when not specified" in {
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+              Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
       NoOptions,
       Labels.empty,
@@ -606,14 +743,17 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
       None
     )
 
-    val job: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst({case t: CommandCallNode => t}).get
+    val job: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst { case t: CommandCallNode => t }.get
     val key = BackendJobDescriptorKey(job, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(job)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
     val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
-      props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     testActorRef.underlyingActor.monitoringScript shouldBe None
   }
@@ -622,11 +762,18 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId(UUID.fromString("e6236763-c518-41d0-9688-432549a8bf7c")),
-      WdlNamespaceWithWorkflow.load(
-        SampleWdl.HelloWorld.asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(SampleWdl.HelloWorld.asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
+              Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
-      WorkflowOptions.fromJsonString(s""" {"${GcpBatchWorkflowPaths.GcsRootOptionKey}": "gs://path/to/gcs_root"} """).get,
+      WorkflowOptions
+        .fromJsonString(s""" {"${GcpBatchWorkflowPaths.GcsRootOptionKey}": "gs://path/to/gcs_root"} """)
+        .get,
       Labels.empty,
       HogGroup("foo"),
       List.empty,
@@ -636,11 +783,14 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "hello").get
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
     val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
-      props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     val batchBackend = testActorRef.underlyingActor
 
@@ -659,11 +809,19 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId(UUID.fromString("e6236763-c518-41d0-9688-432549a8bf7d")),
-      WdlNamespaceWithWorkflow.load(
-        new SampleWdl.ScatterWdl().asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(
+          new SampleWdl.ScatterWdl().asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
+          Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
-      WorkflowOptions.fromJsonString(s""" {"${GcpBatchWorkflowPaths.GcsRootOptionKey}": "gs://path/to/gcs_root"} """).get,
+      WorkflowOptions
+        .fromJsonString(s""" {"${GcpBatchWorkflowPaths.GcsRootOptionKey}": "gs://path/to/gcs_root"} """)
+        .get,
       Labels.empty,
       HogGroup("foo"),
       List.empty,
@@ -673,11 +831,14 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "B").get
     val key = BackendJobDescriptorKey(call, Option(2), 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
     val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
-      props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     val batchBackend = testActorRef.underlyingActor
 
@@ -694,9 +855,8 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
   it should "return preemptible = true only in the correct cases" in {
 
-    def attempt(max: Int, attempt: Int): GcpBatchAsyncBackendJobExecutionActor = {
+    def attempt(max: Int, attempt: Int): GcpBatchAsyncBackendJobExecutionActor =
       buildPreemptibleTestActorRef(attempt, max).underlyingActor
-    }
     def attempt1(max: Int) = attempt(max, 1)
     def attempt2(max: Int) = attempt(max, 2)
 
@@ -733,13 +893,15 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
         .toWomWorkflowDefinition(isASubworkflow = false)
         .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
-      WorkflowOptions.fromJsonString(
-        s"""|{
-            |  "google_project": "$googleProject",
-            |  "${GcpBatchWorkflowPaths.GcsRootOptionKey}": "$batchGcsRoot"
-            |}
-            |""".stripMargin
-      ).get,
+      WorkflowOptions
+        .fromJsonString(
+          s"""|{
+              |  "google_project": "$googleProject",
+              |  "${GcpBatchWorkflowPaths.GcsRootOptionKey}": "$batchGcsRoot"
+              |}
+              |""".stripMargin
+        )
+        .get,
       Labels.empty,
       HogGroup("foo"),
       List.empty,
@@ -749,11 +911,14 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "goodbye").get
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
     val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
-      props, s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableGcpBatchJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     val batchBackend = testActorRef.underlyingActor
 
@@ -789,12 +954,15 @@ class GcpBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
   }
 
   private def makeRuntimeAttributes(job: CommandCallNode) = {
-    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(job.callable.runtimeAttributes, null, Map.empty)
-    RuntimeAttributeDefinition.addDefaultsToAttributes(
-      runtimeAttributesBuilder.definitions.toSet, NoOptions)(evaluatedAttributes.getOrElse(fail("Failed to evaluate runtime attributes")))
+    val evaluatedAttributes =
+      RuntimeAttributeDefinition.evaluateRuntimeAttributes(job.callable.runtimeAttributes, null, Map.empty)
+    RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributesBuilder.definitions.toSet, NoOptions)(
+      evaluatedAttributes.getOrElse(fail("Failed to evaluate runtime attributes"))
+    )
   }
 
-  private def generateStandardAsyncJob = {
-    StandardAsyncJob(JobName.newBuilder().setJob(UUID.randomUUID().toString).setProject("test").setLocation("local").build().toString)
-  }
-}
\ No newline at end of file
+  private def generateStandardAsyncJob =
+    StandardAsyncJob(
+      JobName.newBuilder().setJob(UUID.randomUUID().toString).setProject("test").setLocation("local").build().toString
+    )
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchBackendLifecycleActorFactorySpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchBackendLifecycleActorFactorySpec.scala
index d3bf3a7a3d1..a872ae7090a 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchBackendLifecycleActorFactorySpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchBackendLifecycleActorFactorySpec.scala
@@ -11,7 +11,6 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-
 class GcpBatchBackendLifecycleActorFactorySpec extends AnyFlatSpecLike with Matchers with TableDrivenPropertyChecks {
 
   "GcpBatchBackendLifecycleActorFactory" should "robustly build configuration attributes" in {
@@ -36,7 +35,8 @@ class GcpBatchBackendLifecycleActorFactorySpec extends AnyFlatSpecLike with Matc
       batchRequestTimeoutConfiguration = null,
       referenceFileToDiskImageMappingOpt = None,
       dockerImageToCacheDiskImageMappingOpt = None,
-      checkpointingInterval = 1 second)
+      checkpointingInterval = 1 second
+    )
 
     GcpBatchBackendLifecycleActorFactory.robustBuildAttributes(() => attributes) shouldBe attributes
   }
@@ -54,7 +54,10 @@ class GcpBatchBackendLifecycleActorFactorySpec extends AnyFlatSpecLike with Matc
     forAll(fails) { (attempts, description, function) =>
       it should s"$description: make $attempts attribute creation attempts before giving up" in {
         val e = the[RuntimeException] thrownBy {
-          GcpBatchBackendLifecycleActorFactory.robustBuildAttributes(function, initialIntervalMillis = 1, maxIntervalMillis = 5)
+          GcpBatchBackendLifecycleActorFactory.robustBuildAttributes(function,
+                                                                     initialIntervalMillis = 1,
+                                                                     maxIntervalMillis = 5
+          )
         }
         e.getMessage should startWith(s"Failed to build GcpBatchConfigurationAttributes on attempt $attempts of 3")
       }
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActorSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActorSpec.scala
index c57902531c8..cdfaa931755 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActorSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchInitializationActorSpec.scala
@@ -8,7 +8,7 @@ import cromwell.backend.BackendWorkflowInitializationActor.{InitializationFailed
 import cromwell.backend.async.RuntimeAttributeValidationFailures
 import cromwell.backend.google.batch.models.GcpBatchConfiguration
 import cromwell.backend.google.batch.actors.GcpBatchInitializationActorSpec._
-import cromwell.backend.google.batch.models.GcpBatchTestConfig.{BatchGlobalConfig, googleConfiguration, batchAttributes}
+import cromwell.backend.google.batch.models.GcpBatchTestConfig.{batchAttributes, googleConfiguration, BatchGlobalConfig}
 import cromwell.backend.{BackendConfigurationDescriptor, BackendSpec, BackendWorkflowDescriptor}
 import cromwell.core.Dispatcher.BackendDispatcher
 import cromwell.core.TestKitSuite
@@ -20,8 +20,7 @@ import wom.graph.CommandCallNode
 
 import scala.concurrent.duration._
 
-class GcpBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
-  with ImplicitSender {
+class GcpBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with ImplicitSender {
   val Timeout: FiniteDuration = 30.second.dilated
 
   import BackendSpec._
@@ -47,14 +46,27 @@ class GcpBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike
 
   private def getJesBackendProps(workflowDescriptor: BackendWorkflowDescriptor,
                                  calls: Set[CommandCallNode],
-                                 jesConfiguration: GcpBatchConfiguration): Props = {
+                                 jesConfiguration: GcpBatchConfiguration
+  ): Props = {
     val ioActor = mockIoActor
-    val params = GcpBatchInitializationActorParams(workflowDescriptor, ioActor, calls, jesConfiguration, emptyActor, restarting = false)
+    val params = GcpBatchInitializationActorParams(workflowDescriptor,
+                                                   ioActor,
+                                                   calls,
+                                                   jesConfiguration,
+                                                   emptyActor,
+                                                   restarting = false
+    )
     Props(new GcpBatchInitializationActor(params)).withDispatcher(BackendDispatcher)
   }
 
-  private def getJesBackend(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[CommandCallNode], conf: BackendConfigurationDescriptor) = {
-    val props = getJesBackendProps(workflowDescriptor, calls, new GcpBatchConfiguration(conf, googleConfiguration, batchAttributes))
+  private def getJesBackend(workflowDescriptor: BackendWorkflowDescriptor,
+                            calls: Set[CommandCallNode],
+                            conf: BackendConfigurationDescriptor
+  ) = {
+    val props = getJesBackendProps(workflowDescriptor,
+                                   calls,
+                                   new GcpBatchConfiguration(conf, googleConfiguration, batchAttributes)
+    )
     system.actorOf(props, "TestableJesInitializationActor-" + UUID.randomUUID)
   }
 
@@ -63,17 +75,16 @@ class GcpBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike
   it should "log a warning message when there are unsupported runtime attributes" in {
 
     within(Timeout) {
-      val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld,
-        runtime = """runtime { docker: "ubuntu/latest" test: true }""")
-      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes,
-        defaultBackendConfig)
+      val workflowDescriptor =
+        buildWdlWorkflowDescriptor(HelloWorld, runtime = """runtime { docker: "ubuntu/latest" test: true }""")
+      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes, defaultBackendConfig)
       val eventPattern =
         "Key/s [test] is/are not supported by backend. Unsupported attributes will not be part of job executions."
       EventFilter.warning(pattern = escapePattern(eventPattern), occurrences = 1) intercept {
         backend ! Initialize
       }
       expectMsgPF() {
-        case InitializationSuccess(_) => //Docker entry is present.
+        case InitializationSuccess(_) => // Docker entry is present.
         case InitializationFailed(failure) => fail(s"InitializationSuccess was expected but got $failure")
       }
     }
@@ -82,36 +93,39 @@ class GcpBatchInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike
   it should "return InitializationFailed when docker runtime attribute key is not present" in {
     within(Timeout) {
       val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld, runtime = """runtime { }""")
-      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes,
-        defaultBackendConfig)
+      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes, defaultBackendConfig)
       backend ! Initialize
-      expectMsgPF() {
-        case InitializationFailed(failure) =>
-          failure match {
-            case exception: RuntimeAttributeValidationFailures =>
-              if (!exception.getMessage.equals("Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!"))
-                fail("Exception message is not equal to 'Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!'.")
-          }
+      expectMsgPF() { case InitializationFailed(failure) =>
+        failure match {
+          case exception: RuntimeAttributeValidationFailures =>
+            if (
+              !exception.getMessage.equals(
+                "Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!"
+              )
+            )
+              fail(
+                "Exception message is not equal to 'Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!'."
+              )
+        }
       }
     }
   }
 }
 
 object GcpBatchInitializationActorSpec {
-  val globalConfig: Config = ConfigFactory.parseString(
-    """
-      |google {
-      |
-      |  application-name = "cromwell"
-      |
-      |  auths = [
-      |    {
-      |      name = "application-default"
-      |      scheme = "mock"
-      |    }
-      |  ]
-      |}
-      |""".stripMargin)
+  val globalConfig: Config = ConfigFactory.parseString("""
+                                                         |google {
+                                                         |
+                                                         |  application-name = "cromwell"
+                                                         |
+                                                         |  auths = [
+                                                         |    {
+                                                         |      name = "application-default"
+                                                         |      scheme = "mock"
+                                                         |    }
+                                                         |  ]
+                                                         |}
+                                                         |""".stripMargin)
 
   val backendConfigTemplate: String =
     """
@@ -158,28 +172,40 @@ object GcpBatchInitializationActorSpec {
       |[DOCKERHUBCONFIG]
       |""".stripMargin
 
-  val backendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[VPCCONFIG]", "").replace("[DOCKERHUBCONFIG]", ""))
-
-  val dockerBackendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[VPCCONFIG]", "").replace("[DOCKERHUBCONFIG]",
-    """
-      |dockerhub {
-      |  account = "my@docker.account"
-      |  # no secrets here guys this is just `echo -n username:password | base64`
-      |  token = "dXNlcm5hbWU6cGFzc3dvcmQ="
-      |}
-      | """.stripMargin))
-
-  val vpcBackendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[DOCKERHUBCONFIG]", "").replace("[VPCCONFIG]",
-    """
-      |virtual-private-cloud {
-      |  network-label-key = "cromwell-ci-network"
-      |  subnetwork-label-key = "cromwell-ci-subnetwork"
-      |  auth = "service_account"
-      |}
-      | """.stripMargin))
+  val backendConfig: Config =
+    ConfigFactory.parseString(backendConfigTemplate.replace("[VPCCONFIG]", "").replace("[DOCKERHUBCONFIG]", ""))
+
+  val dockerBackendConfig: Config = ConfigFactory.parseString(
+    backendConfigTemplate
+      .replace("[VPCCONFIG]", "")
+      .replace(
+        "[DOCKERHUBCONFIG]",
+        """
+          |dockerhub {
+          |  account = "my@docker.account"
+          |  # no secrets here guys this is just `echo -n username:password | base64`
+          |  token = "dXNlcm5hbWU6cGFzc3dvcmQ="
+          |}
+          | """.stripMargin
+      )
+  )
+
+  val vpcBackendConfig: Config = ConfigFactory.parseString(
+    backendConfigTemplate
+      .replace("[DOCKERHUBCONFIG]", "")
+      .replace(
+        "[VPCCONFIG]",
+        """
+          |virtual-private-cloud {
+          |  network-label-key = "cromwell-ci-network"
+          |  subnetwork-label-key = "cromwell-ci-subnetwork"
+          |  auth = "service_account"
+          |}
+          | """.stripMargin
+      )
+  )
 
   private val defaultBackendConfig = new BackendConfigurationDescriptor(backendConfig, globalConfig) {
     override private[backend] lazy val cromwellFileSystems = new CromwellFileSystems(BatchGlobalConfig)
   }
 }
-
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDiskSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDiskSpec.scala
index a168743db8f..7e0f03cc422 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDiskSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDiskSpec.scala
@@ -40,7 +40,7 @@ class GcpBatchAttachedDiskSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   )
 
   it should "reject malformed disk mounts" in {
-    forAll(invalidTable) { (unparsed) =>
+    forAll(invalidTable) { unparsed =>
       GcpBatchAttachedDisk.parse(unparsed) should be(a[Failure[_]])
     }
   }
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchAttributeSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchAttributeSpec.scala
index 6743962a4e0..fc012ec5ff8 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchAttributeSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchAttributeSpec.scala
@@ -6,28 +6,22 @@ import org.scalatest.matchers.should.Matchers
 import org.scalatest.wordspec.AnyWordSpecLike
 import wom.values.{WomFloat, WomInteger, WomSingleFile, WomString, WomValue}
 
-class GcpBatchGpuAttributesSpec
-  extends AnyWordSpecLike
-    with Matchers
-    with GcpBatchRuntimeAttributesSpecsMixin {
+class GcpBatchGpuAttributesSpec extends AnyWordSpecLike with Matchers with GcpBatchRuntimeAttributesSpecsMixin {
 
   val validGpuTypes = List(
     (Option(WomString("nvidia-tesla-k80")), Option(GpuType.NVIDIATeslaK80)),
-    (Option(WomString("nvidia-tesla-p100")), Option( GpuType.NVIDIATeslaP100)),
-    (Option(WomString("custom-gpu-24601")), Option( GpuType("custom-gpu-24601"))),
-    (None, None))
-  val invalidGpuTypes = List(
-    WomSingleFile("nvidia-tesla-k80"),
-    WomInteger(100))
+    (Option(WomString("nvidia-tesla-p100")), Option(GpuType.NVIDIATeslaP100)),
+    (Option(WomString("custom-gpu-24601")), Option(GpuType("custom-gpu-24601"))),
+    (None, None)
+  )
+  val invalidGpuTypes = List(WomSingleFile("nvidia-tesla-k80"), WomInteger(100))
 
   val validGpuCounts = List(
     (Option(WomInteger(1)), Option(1)),
     (Option(WomInteger(100)), Option(100)),
     (None, None)
   )
-  val invalidGpuCounts = List(
-    WomString("ten"),
-    WomFloat(1.0))
+  val invalidGpuCounts = List(WomString("ten"), WomFloat(1.0))
 
   validGpuTypes foreach { case (validGpuType, expectedGpuTypeValue) =>
     validGpuCounts foreach { case (validGpuCount, expectedGpuCountValue) =>
@@ -36,7 +30,8 @@ class GcpBatchGpuAttributesSpec
           "docker" -> WomString("ubuntu:latest")
         ) ++ validGpuType.map(t => "gpuType" -> t) ++ validGpuCount.map(c => "gpuCount" -> c)
 
-        val actualRuntimeAttributes = toBatchRuntimeAttributes(runtimeAttributes, emptyWorkflowOptions, gcpBatchConfiguration)
+        val actualRuntimeAttributes =
+          toBatchRuntimeAttributes(runtimeAttributes, emptyWorkflowOptions, gcpBatchConfiguration)
 
         expectedGpuTypeValue match {
           case Some(v) => actualRuntimeAttributes.gpuResource.exists(_.gpuType == v)
@@ -57,9 +52,9 @@ class GcpBatchGpuAttributesSpec
           "docker" -> WomString("ubuntu:latest")
         ) ++ validGpuType.map(t => "gpuType" -> t) + ("gpuCount" -> invalidGpuCount)
 
-        assertBatchRuntimeAttributesFailedCreation(
-          runtimeAttributes,
-          s"Invalid gpu count. Expected positive Int but got")
+        assertBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+                                                   s"Invalid gpu count. Expected positive Int but got"
+        )
       }
     }
   }
@@ -71,10 +66,10 @@ class GcpBatchGpuAttributesSpec
           "docker" -> WomString("ubuntu:latest")
         ) + ("gpuType" -> invalidGpuType) + ("gpuCount" -> invalidGpuCount)
 
-        assertBatchRuntimeAttributesFailedCreation(
-          runtimeAttributes,
-          s"Invalid gpu count. Expected positive Int but got")
+        assertBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+                                                   s"Invalid gpu count. Expected positive Int but got"
+        )
       }
     }
   }
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributesSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributesSpec.scala
index d914e9f2978..47044de002d 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributesSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationAttributesSpec.scala
@@ -17,8 +17,11 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 //import java.net.URL
 import scala.concurrent.duration._
 
-class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
-  with TableDrivenPropertyChecks {
+class GcpBatchConfigurationAttributesSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks {
 
   behavior of "GcpBatchAttributes"
 
@@ -50,7 +53,7 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
     gcpBatchAttributes.maxPollingInterval should be(600)
   }
 
-  it should "parse batch-requests.timeouts values correctly" in  {
+  it should "parse batch-requests.timeouts values correctly" in {
 
     val customContent =
       """
@@ -66,7 +69,9 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
     val gcpBatchAttributes = GcpBatchConfigurationAttributes(googleConfig, backendConfig, "batch")
 
     gcpBatchAttributes.batchRequestTimeoutConfiguration.readTimeoutMillis.get.value should be(100.hours.toMillis.toInt)
-    gcpBatchAttributes.batchRequestTimeoutConfiguration.connectTimeoutMillis.get.value should be(10.seconds.toMillis.toInt)
+    gcpBatchAttributes.batchRequestTimeoutConfiguration.connectTimeoutMillis.get.value should be(
+      10.seconds.toMillis.toInt
+    )
   }
 
   it should "parse an empty batch-requests.timeouts section correctly" in {
@@ -143,8 +148,8 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
         |""".stripMargin,
       VirtualPrivateCloudConfiguration(
         Option(VirtualPrivateCloudLabels("my-network", Option("my-subnetwork"), mockAuth)),
-        None,
-      ),
+        None
+      )
     ),
     (
       "labels config without subnetwork key",
@@ -155,8 +160,8 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
         |""".stripMargin,
       VirtualPrivateCloudConfiguration(
         Option(VirtualPrivateCloudLabels("my-network", None, mockAuth)),
-        None,
-      ),
+        None
+      )
     ),
     (
       "literal config",
@@ -167,8 +172,8 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
         |""".stripMargin,
       VirtualPrivateCloudConfiguration(
         None,
-        Option(VirtualPrivateCloudLiterals("my-network", Option("my-subnetwork"))),
-      ),
+        Option(VirtualPrivateCloudLiterals("my-network", Option("my-subnetwork")))
+      )
     ),
     (
       "literal config without subnetwork name",
@@ -178,9 +183,9 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
         |""".stripMargin,
       VirtualPrivateCloudConfiguration(
         None,
-        Option(VirtualPrivateCloudLiterals("my-network", None)),
-      ),
-    ),
+        Option(VirtualPrivateCloudLiterals("my-network", None))
+      )
+    )
   )
 
   private val invalidVPCConfigTests = Table(
@@ -191,7 +196,7 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
         |  network-label-key = my-network
         |}
         |""".stripMargin,
-      List("Virtual Private Cloud configuration is invalid. Missing keys: `auth`."),
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `auth`.")
     ),
     (
       "without network label-key",
@@ -199,7 +204,7 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
         |  auth = mock
         |}
         |""".stripMargin,
-      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key`."),
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key`.")
     ),
     (
       "with just a subnetwork label key",
@@ -207,7 +212,7 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
         |  subnetwork-label-key = my-subnetwork
         |}
         |""".stripMargin,
-      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key,auth`."),
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key,auth`.")
     ),
     (
       "with subnetwork label network key and auth",
@@ -216,8 +221,8 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
         |   auth = mock
         | }
         |""".stripMargin,
-      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key`."),
-    ),
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key`.")
+    )
   )
 
   forAll(validVpcConfigTests) { (description, customConfig, vpcConfig) =>
@@ -243,13 +248,12 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
   it should "not parse invalid config" in {
 
     val nakedConfig =
-      ConfigFactory.parseString(
-        """
-          |{
-          |   genomics {
-          |
-          |   }
-          |}
+      ConfigFactory.parseString("""
+                                  |{
+                                  |   genomics {
+                                  |
+                                  |   }
+                                  |}
         """.stripMargin)
 
     val exception = intercept[IllegalArgumentException with MessageAggregation] {
@@ -302,7 +306,8 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
     val invalids = List("-1", "150MB", "14PB")
 
     invalids foreach {
-      case invalid@GcpBatchConfigurationAttributes.GsutilHumanBytes(_, _) => fail(s"Memory specification $invalid not expected to be accepted")
+      case invalid @ GcpBatchConfigurationAttributes.GsutilHumanBytes(_, _) =>
+        fail(s"Memory specification $invalid not expected to be accepted")
       case _ =>
     }
   }
@@ -332,32 +337,32 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
     // Highly abridged versions of hg19 and hg38 manifests just to test for correctness
     // of parsing.
     val manifestConfig =
-    """
-      |reference-disk-localization-manifests = [
-      |{
-      |  "imageIdentifier" : "hg19-public-2020-10-26",
-      |  "diskSizeGb" : 10,
-      |  "files" : [ {
-      |    "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
-      |    "crc32c" : 159565724
-      |  }, {
-      |    "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
-      |    "crc32c" : 1679459712
-      |  }]
-      |},
-      |{
-      |  "imageIdentifier" : "hg38-public-2020-10-26",
-      |  "diskSizeGb" : 20,
-      |  "files" : [ {
-      |    "path" : "gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
-      |    "crc32c" : 930173616
-      |  }, {
-      |    "path" : "gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
-      |    "crc32c" : 289077232
-      |  }]
-      |}
-      |]
-      |""".stripMargin
+      """
+        |reference-disk-localization-manifests = [
+        |{
+        |  "imageIdentifier" : "hg19-public-2020-10-26",
+        |  "diskSizeGb" : 10,
+        |  "files" : [ {
+        |    "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
+        |    "crc32c" : 159565724
+        |  }, {
+        |    "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
+        |    "crc32c" : 1679459712
+        |  }]
+        |},
+        |{
+        |  "imageIdentifier" : "hg38-public-2020-10-26",
+        |  "diskSizeGb" : 20,
+        |  "files" : [ {
+        |    "path" : "gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
+        |    "crc32c" : 930173616
+        |  }, {
+        |    "path" : "gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
+        |    "crc32c" : 289077232
+        |  }]
+        |}
+        |]
+        |""".stripMargin
     val backendConfig = ConfigFactory.parseString(configString(manifestConfig))
     val validation = GcpBatchConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "batch")
     val manifests: List[ManifestFile] = validation.toEither.toOption.get.get
@@ -422,7 +427,7 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
          |   "imageIdentifier" : "hg19-public-2020-10-26",
          |   "diskSizeGb" : 10,
          |   # missing files
-         |}]""",
+         |}]"""
     )
 
     badValues foreach { badValue =>
@@ -433,19 +438,21 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
     }
   }
 
-
   it should "parse correct existing docker-image-cache-manifest-file config" in {
 
     val dockerImageCacheManifest1Path = "gs://bucket/manifest1.json"
     val dockerImageCacheManifestConfigStr = s"""docker-image-cache-manifest-file = "$dockerImageCacheManifest1Path""""
     val backendConfig = ConfigFactory.parseString(configString(dockerImageCacheManifestConfigStr))
 
-    val validatedGcsPathToDockerImageCacheManifestFileErrorOr = GcpBatchConfigurationAttributes.validateGcsPathToDockerImageCacheManifestFile(backendConfig)
+    val validatedGcsPathToDockerImageCacheManifestFileErrorOr =
+      GcpBatchConfigurationAttributes.validateGcsPathToDockerImageCacheManifestFile(backendConfig)
     validatedGcsPathToDockerImageCacheManifestFileErrorOr match {
       case Valid(validatedGcsPathToDockerImageCacheManifestFileOpt) =>
         validatedGcsPathToDockerImageCacheManifestFileOpt match {
           case Some(validatedGcsPathToDockerCacheManifestFile) =>
-            validatedGcsPathToDockerCacheManifestFile shouldBe GcsPathBuilder.validateGcsPath(dockerImageCacheManifest1Path)
+            validatedGcsPathToDockerCacheManifestFile shouldBe GcsPathBuilder.validateGcsPath(
+              dockerImageCacheManifest1Path
+            )
           case None =>
             fail("GCS paths to docker image cache manifest files, parsed from config, should not be empty")
         }
@@ -458,7 +465,8 @@ class GcpBatchConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeo
 
     val backendConfig = ConfigFactory.parseString(configString())
 
-    val validatedGcsPathsToDockerImageCacheManifestFilesErrorOr = GcpBatchConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "unit-test-backend")
+    val validatedGcsPathsToDockerImageCacheManifestFilesErrorOr =
+      GcpBatchConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "unit-test-backend")
     validatedGcsPathsToDockerImageCacheManifestFilesErrorOr match {
       case Valid(validatedGcsPathsToDockerImageCacheManifestFilesOpt) =>
         validatedGcsPathsToDockerImageCacheManifestFilesOpt shouldBe None
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala
index 46b7c147b34..42ae487b5fb 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala
@@ -11,7 +11,12 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks
 
-class GcpBatchConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks with BeforeAndAfterAll {
+class GcpBatchConfigurationSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks
+    with BeforeAndAfterAll {
 
   behavior of "GcpBatchConfigurationSpec"
 
@@ -22,26 +27,25 @@ class GcpBatchConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     ()
   }
 
-  val globalConfig = ConfigFactory.parseString(
-    s"""
-       |google {
-       |
-       |  application-name = "cromwell"
-       |
-       |  auths = [
-       |    {
-       |      name = "application-default"
-       |      scheme = "application_default"
-       |    },
-       |    {
-       |      name = "service-account"
-       |      scheme = "service_account"
-       |      service-account-id = "my-service-account"
-       |      pem-file = "${mockFile.pathAsString}"
-       |    }
-       |  ]
-       |}
-       |
+  val globalConfig = ConfigFactory.parseString(s"""
+                                                  |google {
+                                                  |
+                                                  |  application-name = "cromwell"
+                                                  |
+                                                  |  auths = [
+                                                  |    {
+                                                  |      name = "application-default"
+                                                  |      scheme = "application_default"
+                                                  |    },
+                                                  |    {
+                                                  |      name = "service-account"
+                                                  |      scheme = "service_account"
+                                                  |      service-account-id = "my-service-account"
+                                                  |      pem-file = "${mockFile.pathAsString}"
+                                                  |    }
+                                                  |  ]
+                                                  |}
+                                                  |
     """.stripMargin)
 
   val backendConfig = ConfigFactory.parseString(
@@ -87,7 +91,8 @@ class GcpBatchConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       |    }
       |  }
       |
-    """.stripMargin)
+    """.stripMargin
+  )
 
   it should "fail to instantiate if any required configuration is missing" in {
 
@@ -113,12 +118,15 @@ class GcpBatchConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
   }
 
   it should "have correct root" in {
-    new GcpBatchConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig), googleConfiguration, batchAttributes).root shouldBe "gs://my-cromwell-workflows-bucket"
+    new GcpBatchConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig),
+                              googleConfiguration,
+                              batchAttributes
+    ).root shouldBe "gs://my-cromwell-workflows-bucket"
   }
 
-  //it should "have correct docker" in {
+  // it should "have correct docker" in {
   //  val dockerConf = new GcpBatchConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig), googleConfiguration, batchAttributes).dockerCredentials
   //  dockerConf shouldBe defined
   //  dockerConf.get.token shouldBe "dockerToken"
-  //}
+  // }
 }
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchJobPathsSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchJobPathsSpec.scala
index ed2baf4fd06..933d2958689 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchJobPathsSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchJobPathsSpec.scala
@@ -27,7 +27,14 @@ class GcpBatchJobPathsSpec extends TestKitSuite with AnyFlatSpecLike with Matche
     )
     val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
 
-    val workflowPaths = GcpBatchWorkflowPaths(workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), gcpBatchConfiguration, pathBuilders(), GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+    val workflowPaths = GcpBatchWorkflowPaths(
+      workflowDescriptor,
+      NoCredentials.getInstance(),
+      NoCredentials.getInstance(),
+      gcpBatchConfiguration,
+      pathBuilders(),
+      GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper
+    )
 
     val callPaths = GcpBatchJobPaths(workflowPaths, jobDescriptorKey)
 
@@ -44,7 +51,14 @@ class GcpBatchJobPathsSpec extends TestKitSuite with AnyFlatSpecLike with Matche
     )
     val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
 
-    val workflowPaths = GcpBatchWorkflowPaths(workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), gcpBatchConfiguration, pathBuilders(), GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+    val workflowPaths = GcpBatchWorkflowPaths(
+      workflowDescriptor,
+      NoCredentials.getInstance(),
+      NoCredentials.getInstance(),
+      gcpBatchConfiguration,
+      pathBuilders(),
+      GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper
+    )
 
     val callPaths = GcpBatchJobPaths(workflowPaths, jobDescriptorKey)
 
@@ -66,7 +80,14 @@ class GcpBatchJobPathsSpec extends TestKitSuite with AnyFlatSpecLike with Matche
     )
     val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
 
-    val workflowPaths = GcpBatchWorkflowPaths(workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), gcpBatchConfiguration, pathBuilders(), GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+    val workflowPaths = GcpBatchWorkflowPaths(
+      workflowDescriptor,
+      NoCredentials.getInstance(),
+      NoCredentials.getInstance(),
+      gcpBatchConfiguration,
+      pathBuilders(),
+      GcpBatchInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper
+    )
 
     val callPaths = GcpBatchJobPaths(workflowPaths, jobDescriptorKey)
 
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
index 569a2af58eb..beb9b865c1b 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
@@ -21,7 +21,7 @@ import wom.values._
 import scala.util.{Failure, Success, Try}
 
 final class GcpBatchRuntimeAttributesSpec
-  extends AnyWordSpecLike
+    extends AnyWordSpecLike
     with Matchers
     with GcpBatchRuntimeAttributesSpecsMixin {
 
@@ -35,7 +35,10 @@ final class GcpBatchRuntimeAttributesSpec
     "use hardcoded defaults if not declared in task, workflow options, or config (except for docker)" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"))
       val expectedRuntimeAttributes = expectedDefaults
-      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes, batchConfiguration = noDefaultsBatchConfiguration)
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes,
+                                                     expectedRuntimeAttributes,
+                                                     batchConfiguration = noDefaultsBatchConfiguration
+      )
     }
 
     "validate a valid Docker entry" in {
@@ -58,12 +61,18 @@ final class GcpBatchRuntimeAttributesSpec
 
     "fail to validate an invalid failOnStderr entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "failOnStderr" -> WomString("yes"))
-      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'")
+      assertBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'"
+      )
     }
 
     "fail to validate an invalid continueOnReturnCode entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomString("value"))
-      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]")
+      assertBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+      )
     }
 
     "validate a valid cpu entry" in {
@@ -91,18 +100,30 @@ final class GcpBatchRuntimeAttributesSpec
 
     "fail to validate an invalid zones entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "zones" -> WomInteger(1))
-      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]")
+      assertBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]"
+      )
     }
 
     "validate a valid array zones entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "zones" -> WomArray(WomArrayType(WomStringType), List(WomString("us-central1-y"), WomString("us-central1-z"))))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "zones" -> WomArray(WomArrayType(WomStringType),
+                                                      List(WomString("us-central1-y"), WomString("us-central1-z"))
+                                  )
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(zones = Vector("us-central1-y", "us-central1-z"))
       assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid array zones entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "zones" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2))))
-      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]")
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "zones" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2)))
+      )
+      assertBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]"
+      )
     }
 
     "validate a valid preemptible entry" in {
@@ -114,7 +135,8 @@ final class GcpBatchRuntimeAttributesSpec
     "fail to validate an invalid preemptible entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "preemptible" -> WomString("value"))
       assertBatchRuntimeAttributesFailedCreation(runtimeAttributes,
-        "Expecting preemptible runtime attribute to be an Integer")
+                                                 "Expecting preemptible runtime attribute to be an Integer"
+      )
     }
 
     "validate a valid bootDiskSizeGb entry" in {
@@ -125,7 +147,9 @@ final class GcpBatchRuntimeAttributesSpec
 
     "fail to validate an invalid bootDiskSizeGb entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "bootDiskSizeGb" -> WomString("4GB"))
-      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting bootDiskSizeGb runtime attribute to be an Integer")
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+                                                 "Expecting bootDiskSizeGb runtime attribute to be an Integer"
+      )
     }
 
     //    "validate a valid disks entry" in {
@@ -134,15 +158,15 @@ final class GcpBatchRuntimeAttributesSpec
     //      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     //    }
 
-    //"fail to validate an invalid disks entry" in {
+    // "fail to validate an invalid disks entry" in {
     //  val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomInteger(10))
     //  assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting disks runtime attribute to be a comma separated String or Array[String]")
-    //}
+    // }
 
-    //"fail to validate a valid disks array entry" in {
+    // "fail to validate a valid disks array entry" in {
     //  val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomArray(WomArrayType(WomStringType), List(WomString("blah"), WomString("blah blah"))))
     //  assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE'")
-    //}
+    // }
 
     "validate a valid memory entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "memory" -> WomString("1 GB"))
@@ -152,7 +176,10 @@ final class GcpBatchRuntimeAttributesSpec
 
     "fail to validate an invalid memory entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "memory" -> WomString("blah"))
-      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting memory runtime attribute to be an Integer or String with format '8 GB'")
+      assertBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting memory runtime attribute to be an Integer or String with format '8 GB'"
+      )
     }
 
     "validate a valid noAddress entry" in {
@@ -164,7 +191,8 @@ final class GcpBatchRuntimeAttributesSpec
     "fail to validate an invalid noAddress entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "noAddress" -> WomInteger(1))
       assertBatchRuntimeAttributesFailedCreation(runtimeAttributes,
-        "Expecting noAddress runtime attribute to be a Boolean")
+                                                 "Expecting noAddress runtime attribute to be a Boolean"
+      )
     }
 
     "override config default attributes with default attributes declared in workflow options" in {
@@ -226,11 +254,14 @@ final class GcpBatchRuntimeAttributesSpec
 trait GcpBatchRuntimeAttributesSpecsMixin {
   this: TestSuite =>
 
-  def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]): WorkflowOptions = {
-    WorkflowOptions(JsObject(Map(
-      "default_runtime_attributes" -> JsObject(defaults)
-    )))
-  }
+  def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]): WorkflowOptions =
+    WorkflowOptions(
+      JsObject(
+        Map(
+          "default_runtime_attributes" -> JsObject(defaults)
+        )
+      )
+    )
 
   val expectedDefaults = new GcpBatchRuntimeAttributes(
     cpu = refineMV(1),
@@ -253,7 +284,8 @@ trait GcpBatchRuntimeAttributesSpecsMixin {
                                                      expectedRuntimeAttributes: GcpBatchRuntimeAttributes,
                                                      workflowOptions: WorkflowOptions = emptyWorkflowOptions,
                                                      defaultZones: NonEmptyList[String] = defaultZones,
-                                                     batchConfiguration: GcpBatchConfiguration = gcpBatchConfiguration): Unit = {
+                                                     batchConfiguration: GcpBatchConfiguration = gcpBatchConfiguration
+  ): Unit = {
     try {
       val actualRuntimeAttributes = toBatchRuntimeAttributes(runtimeAttributes, workflowOptions, batchConfiguration)
       assert(actualRuntimeAttributes == expectedRuntimeAttributes)
@@ -265,10 +297,13 @@ trait GcpBatchRuntimeAttributesSpecsMixin {
 
   def assertBatchRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue],
                                                  exMsgs: List[String],
-                                                 workflowOptions: WorkflowOptions): Unit = {
+                                                 workflowOptions: WorkflowOptions
+  ): Unit = {
     Try(toBatchRuntimeAttributes(runtimeAttributes, workflowOptions, gcpBatchConfiguration)) match {
       case Success(oops) =>
-        fail(s"Expected error containing strings: ${exMsgs.map(s => s"'$s'").mkString(", ")} but instead got Success($oops)")
+        fail(
+          s"Expected error containing strings: ${exMsgs.map(s => s"'$s'").mkString(", ")} but instead got Success($oops)"
+        )
       case Failure(ex) => exMsgs foreach { exMsg => assert(ex.getMessage.contains(exMsg)) }
     }
     ()
@@ -276,23 +311,29 @@ trait GcpBatchRuntimeAttributesSpecsMixin {
 
   def assertBatchRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue],
                                                  exMsg: String,
-                                                 workflowOptions: WorkflowOptions = emptyWorkflowOptions): Unit = {
+                                                 workflowOptions: WorkflowOptions = emptyWorkflowOptions
+  ): Unit =
     assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, List(exMsg), workflowOptions)
-  }
 
   def toBatchRuntimeAttributes(runtimeAttributes: Map[String, WomValue],
                                workflowOptions: WorkflowOptions,
-                               batchConfiguration: GcpBatchConfiguration): GcpBatchRuntimeAttributes = {
+                               batchConfiguration: GcpBatchConfiguration
+  ): GcpBatchRuntimeAttributes = {
     val runtimeAttributesBuilder = GcpBatchRuntimeAttributes.runtimeAttributesBuilder(batchConfiguration)
-    val defaultedAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(
-      staticRuntimeAttributeDefinitions, workflowOptions)(runtimeAttributes)
+    val defaultedAttributes =
+      RuntimeAttributeDefinition.addDefaultsToAttributes(staticRuntimeAttributeDefinitions, workflowOptions)(
+        runtimeAttributes
+      )
     val validatedRuntimeAttributes = runtimeAttributesBuilder.build(defaultedAttributes, NOPLogger.NOP_LOGGER)
     GcpBatchRuntimeAttributes(validatedRuntimeAttributes, batchConfiguration.runtimeConfig)
   }
 
   val emptyWorkflowOptions: WorkflowOptions = WorkflowOptions.fromMap(Map.empty).get
   val defaultZones: NonEmptyList[String] = NonEmptyList.of("us-central1-b", "us-central1-a")
-  val noDefaultsBatchConfiguration = new GcpBatchConfiguration(GcpBatchTestConfig.NoDefaultsConfigurationDescriptor, googleConfiguration, batchAttributes)
+  val noDefaultsBatchConfiguration = new GcpBatchConfiguration(GcpBatchTestConfig.NoDefaultsConfigurationDescriptor,
+                                                               googleConfiguration,
+                                                               batchAttributes
+  )
   val staticRuntimeAttributeDefinitions: Set[RuntimeAttributeDefinition] =
     GcpBatchRuntimeAttributes.runtimeAttributesBuilder(GcpBatchTestConfig.gcpBatchConfiguration).definitions.toSet
 }
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchTestConfig.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchTestConfig.scala
index fc8b1333170..4d41f5436ea 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchTestConfig.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchTestConfig.scala
@@ -98,11 +98,10 @@ object GcpBatchTestConfig {
   val BatchBackendConfig: Config = ConfigFactory.parseString(BatchBackendConfigString)
   val BatchGlobalConfig: Config = ConfigFactory.parseString(BatchGlobalConfigString)
   val BatchBackendNoDefaultConfig: Config = ConfigFactory.parseString(NoDefaultsConfigString)
-  val BatchBackendConfigurationDescriptor: BackendConfigurationDescriptor = {
+  val BatchBackendConfigurationDescriptor: BackendConfigurationDescriptor =
     new BackendConfigurationDescriptor(BatchBackendConfig, BatchGlobalConfig) {
       override private[backend] lazy val cromwellFileSystems = new CromwellFileSystems(BatchGlobalConfig)
     }
-  }
   val NoDefaultsConfigurationDescriptor: BackendConfigurationDescriptor =
     BackendConfigurationDescriptor(BatchBackendNoDefaultConfig, BatchGlobalConfig)
   def pathBuilders()(implicit as: ActorSystem): List[PathBuilder] =
@@ -110,5 +109,6 @@ object GcpBatchTestConfig {
   val googleConfiguration: GoogleConfiguration = GoogleConfiguration(BatchGlobalConfig)
   val batchAttributes: GcpBatchConfigurationAttributes =
     GcpBatchConfigurationAttributes(googleConfiguration, BatchBackendConfig, "batch")
-  val gcpBatchConfiguration = new GcpBatchConfiguration(BatchBackendConfigurationDescriptor, googleConfiguration,batchAttributes)
-}
\ No newline at end of file
+  val gcpBatchConfiguration =
+    new GcpBatchConfiguration(BatchBackendConfigurationDescriptor, googleConfiguration, batchAttributes)
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchVpcAndSubnetworkProjectLabelValuesSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchVpcAndSubnetworkProjectLabelValuesSpec.scala
index e24b3fc809e..e28b912a1fb 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchVpcAndSubnetworkProjectLabelValuesSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchVpcAndSubnetworkProjectLabelValuesSpec.scala
@@ -21,15 +21,15 @@ class GcpBatchVpcAndSubnetworkProjectLabelValuesSpec extends AnyFlatSpec with Ma
       s"slashed/$${projectId}/net",
       None,
       "slashed/my-project/net",
-      None,
+      None
     ),
     (
       "a subnet with a project token",
       "slashed/net",
       Option(s"slashed/$${projectId}/sub"),
       "slashed/net",
-      Option("slashed/my-project/sub"),
-    ),
+      Option("slashed/my-project/sub")
+    )
   )
 
   forAll(labelsTests) { (description, network, subnetOption, networkName, subnetNameOption) =>
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/LocalizationSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/LocalizationSpec.scala
index 12be65744e0..3e7beb90d0a 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/LocalizationSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/LocalizationSpec.scala
@@ -24,14 +24,21 @@ class LocalizationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     fields.keySet.map(_.getName) should contain theSameElementsAs Set("commands", "image_uri")
     //      Set("commands", "environment", "imageUri", "labels", "mounts")
 
-    fields.find(_._1.getName == "commands").value.asInstanceOf[(_, java.util.List[_])]._2 should contain theSameElementsAs List(
-      "-m", manifestPathString
+    fields
+      .find(_._1.getName == "commands")
+      .value
+      .asInstanceOf[(_, java.util.List[_])]
+      ._2 should contain theSameElementsAs List(
+      "-m",
+      manifestPathString
     )
 
     //    runnable.get("mounts") should be(a[java.util.List[_]])
     //    runnable.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
     //
-    fields.find(_._1.getName == "image_uri").value.asInstanceOf[(_, String)]._2 should be("somerepo/drs-downloader:tagged")
+    fields.find(_._1.getName == "image_uri").value.asInstanceOf[(_, String)]._2 should be(
+      "somerepo/drs-downloader:tagged"
+    )
     //
     //    val actionLabels = runnable.get("labels").asInstanceOf[java.util.Map[_, _]]
     //    actionLabels.keySet.asScala should contain theSameElementsAs List("tag")
@@ -46,19 +53,29 @@ class LocalizationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     val tagLabel = "myLabel"
     val requesterPaysProjectId = "123"
 
-    val container = Localization.drsRunnable(manifestPath, Map(tagKey -> tagLabel), Option(requesterPaysProjectId)).getContainer
+    val container =
+      Localization.drsRunnable(manifestPath, Map(tagKey -> tagLabel), Option(requesterPaysProjectId)).getContainer
     val fields = container.getAllFields.asScala
     fields.keySet.map(_.getName) should contain theSameElementsAs Set("commands", "image_uri")
     //      Set("commands", "environment", "imageUri", "labels", "mounts")
 
-    fields.find(_._1.getName == "commands").value.asInstanceOf[(_, java.util.List[_])]._2 should contain theSameElementsAs List(
-      "-m", manifestPathString, "-r", requesterPaysProjectId
+    fields
+      .find(_._1.getName == "commands")
+      .value
+      .asInstanceOf[(_, java.util.List[_])]
+      ._2 should contain theSameElementsAs List(
+      "-m",
+      manifestPathString,
+      "-r",
+      requesterPaysProjectId
     )
 
     //    runnable.get("mounts") should be(a[java.util.List[_]])
     //    runnable.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
 
-    fields.find(_._1.getName == "image_uri").value.asInstanceOf[(_, String)]._2 should be("somerepo/drs-downloader:tagged")
+    fields.find(_._1.getName == "image_uri").value.asInstanceOf[(_, String)]._2 should be(
+      "somerepo/drs-downloader:tagged"
+    )
 
     //    val actionLabels = runnable.get("labels").asInstanceOf[java.util.Map[_, _]]
     //    actionLabels.keySet.asScala should contain theSameElementsAs List("tag")
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala
index 04d2c7d43f5..ef657ad11ca 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableBuilderSpec.scala
@@ -18,31 +18,42 @@ class RunnableBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     ("description", "runnable", "command"),
     ("a cloud sdk runnable", RunnableBuilder.cloudSdkRunnable, s"docker run ${RunnableUtils.CloudSdkImage}"),
     ("a cloud sdk runnable with args",
-      RunnableBuilder.cloudSdkRunnable.withCommand("bash", "-c", "echo hello"),
-      s"docker run ${RunnableUtils.CloudSdkImage} bash -c echo\\ hello"
+     RunnableBuilder.cloudSdkRunnable.withCommand("bash", "-c", "echo hello"),
+     s"docker run ${RunnableUtils.CloudSdkImage} bash -c echo\\ hello"
     ),
     ("a cloud sdk runnable with quotes in the args",
-      RunnableBuilder.cloudSdkRunnable.withCommand("bash", "-c", "echo hello m'lord"),
-      s"docker run ${RunnableUtils.CloudSdkImage} bash -c echo\\ hello\\ m\\'lord"
+     RunnableBuilder.cloudSdkRunnable.withCommand("bash", "-c", "echo hello m'lord"),
+     s"docker run ${RunnableUtils.CloudSdkImage} bash -c echo\\ hello\\ m\\'lord"
     ),
     ("a cloud sdk runnable with a newline in the args",
-      RunnableBuilder.cloudSdkRunnable.withCommand("bash", "-c", "echo hello\\\nworld"),
-      s"docker run ${RunnableUtils.CloudSdkImage} bash -c echo\\ hello\\\\world"
+     RunnableBuilder.cloudSdkRunnable.withCommand("bash", "-c", "echo hello\\\nworld"),
+     s"docker run ${RunnableUtils.CloudSdkImage} bash -c echo\\ hello\\\\world"
     ),
     ("an runnable with multiple args",
-      Runnable.newBuilder()
-        .setContainer(Runnable.Container.newBuilder.setImageUri("ubuntu"))
-        .withEntrypointCommand("")
-        .withCommand("bash", "-c", "echo hello")
-        .withAlwaysRun(true)
-        .withVolumes(List(
-          Volume.newBuilder().setDeviceName("read-only-disk").setMountPath("/mnt/read/only/container").addMountOptions("ro"),
-          Volume.newBuilder().setDeviceName("read-write-disk").setMountPath("/mnt/read/write/container").addMountOptions("rw"),
-        ).map(_.build())),
-      "docker run" +
-        " -v /mnt/read/only/container:/mnt/read/only/container -v /mnt/read/write/container:/mnt/read/write/container" +
-        " ubuntu bash -c echo\\ hello"
-    ),
+     Runnable
+       .newBuilder()
+       .setContainer(Runnable.Container.newBuilder.setImageUri("ubuntu"))
+       .withEntrypointCommand("")
+       .withCommand("bash", "-c", "echo hello")
+       .withAlwaysRun(true)
+       .withVolumes(
+         List(
+           Volume
+             .newBuilder()
+             .setDeviceName("read-only-disk")
+             .setMountPath("/mnt/read/only/container")
+             .addMountOptions("ro"),
+           Volume
+             .newBuilder()
+             .setDeviceName("read-write-disk")
+             .setMountPath("/mnt/read/write/container")
+             .addMountOptions("rw")
+         ).map(_.build())
+       ),
+     "docker run" +
+       " -v /mnt/read/only/container:/mnt/read/only/container -v /mnt/read/write/container:/mnt/read/write/container" +
+       " ubuntu bash -c echo\\ hello"
+    )
   )
 
   forAll(dockerRunRunnables) { (description, runnable, command) =>
@@ -53,15 +64,17 @@ class RunnableBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
 
   private val memoryRetryExpectedEntrypoint = "/bin/sh"
 
-  def memoryRetryExpectedCommand(lookupString: String): List[String] = {
+  def memoryRetryExpectedCommand(lookupString: String): List[String] =
     List(
       "-c",
       s"grep -E -q '$lookupString' /cromwell_root/stderr ; echo $$? > /cromwell_root/memory_retry_rc"
     )
-  }
 
   val volumes = List(
-    Volume.newBuilder().setDeviceName("read-only-disk").setMountPath("/mnt/read/only/container")/*.addMountOptions("ro")*/
+    Volume
+      .newBuilder()
+      .setDeviceName("read-only-disk")
+      .setMountPath("/mnt/read/only/container") /*.addMountOptions("ro")*/
   ).map(_.build())
 
   private val memoryRetryRunnableExpectedLabels = Map(Key.Tag -> Value.RetryWithMoreMemory).asJava
@@ -76,7 +89,9 @@ class RunnableBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     runnable.getContainer.getCommandsList.asScala shouldBe expectedCommand
     runnable.getAlwaysRun shouldBe true
     runnable.getLabelsMap shouldBe memoryRetryRunnableExpectedLabels
-    runnable.getContainer.getVolumesList.asScala.toList shouldBe volumes.map(v => s"${v.getMountPath}:${v.getMountPath}")
+    runnable.getContainer.getVolumesList.asScala.toList shouldBe volumes.map(v =>
+      s"${v.getMountPath}:${v.getMountPath}"
+    )
   }
 
   it should "return cloud sdk runnable for multiple keys in retry-with-double-memory" in {
@@ -89,6 +104,8 @@ class RunnableBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     runnable.getContainer.getCommandsList.asScala shouldBe expectedCommand
     runnable.getAlwaysRun shouldBe true
     runnable.getLabelsMap shouldBe memoryRetryRunnableExpectedLabels
-    runnable.getContainer.getVolumesList.asScala.toList shouldBe volumes.map(v => s"${v.getMountPath}:${v.getMountPath}")
+    runnable.getContainer.getVolumesList.asScala.toList shouldBe volumes.map(v =>
+      s"${v.getMountPath}:${v.getMountPath}"
+    )
   }
-}
\ No newline at end of file
+}
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableCommandSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableCommandSpec.scala
index 6e6c9f2d0af..546f8c9997e 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableCommandSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/runnable/RunnableCommandSpec.scala
@@ -1,6 +1,5 @@
 package cromwell.backend.google.batch.runnable
 
-
 import java.nio.file.Path
 import common.assertion.CromwellTimeoutSpec
 import cromwell.backend.google.batch.models.GcpBatchConfigurationAttributes.GcsTransferConfiguration
@@ -19,7 +18,7 @@ class RunnableCommandsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
       mock[Path],
       mock[com.google.api.services.storage.Storage],
       mock[com.google.cloud.storage.Storage],
-      "my-project",
+      "my-project"
     )
     val recovered = recoverRequesterPaysError(path) { flag =>
       s"flag is $flag"
@@ -46,22 +45,23 @@ class RunnableCommandsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
   }
 
   it should "use GcsTransferConfiguration to set the number of localization retries" in {
-    implicit val gcsTransferConfiguration: GcsTransferConfiguration = GcsTransferConfiguration(
-      transferAttempts = refineMV(31380), parallelCompositeUploadThreshold = "0")
-    retry("I'm very flaky") shouldBe """for i in $(seq 31380); do
-                                       |  (
-                                       |    I'm very flaky
-                                       |  )
-                                       |  RC=$?
-                                       |  if [ "$RC" = "0" ]; then
-                                       |    break
-                                       |  fi
-                                       |  if [ $i -lt 31380 ]; then
-                                       |    printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" Waiting\ 5\ seconds\ and\ retrying
-                                       |    sleep 5
-                                       |  fi
-                                       |done
-                                       |exit "$RC"""".stripMargin
+    implicit val gcsTransferConfiguration: GcsTransferConfiguration =
+      GcsTransferConfiguration(transferAttempts = refineMV(31380), parallelCompositeUploadThreshold = "0")
+    retry(
+      "I'm very flaky"
+    ) shouldBe """for i in $(seq 31380); do
+                 |  (
+                 |    I'm very flaky
+                 |  )
+                 |  RC=$?
+                 |  if [ "$RC" = "0" ]; then
+                 |    break
+                 |  fi
+                 |  if [ $i -lt 31380 ]; then
+                 |    printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" Waiting\ 5\ seconds\ and\ retrying
+                 |    sleep 5
+                 |  fi
+                 |done
+                 |exit "$RC"""".stripMargin
   }
 }
-
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraintsSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraintsSpec.scala
index 968ab545cbf..417b1e829d1 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraintsSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/util/GcpBatchMachineConstraintsSpec.scala
@@ -65,9 +65,9 @@ class GcpBatchMachineConstraintsSpec extends AnyFlatSpec with CromwellTimeoutSpe
 
       // Same tests but with AMD Rome (n2d) #cpu > 16 are in increments of 16
       (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1024"),
-      (MemorySize(4,  MemoryUnit.GB), refineMV[Positive](3), n2dOption, false, "n2d-custom-4-4096"),
+      (MemorySize(4, MemoryUnit.GB), refineMV[Positive](3), n2dOption, false, "n2d-custom-4-4096"),
       (MemorySize(1, MemoryUnit.GB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1024"),
-      (MemorySize(1 , MemoryUnit.GB), refineMV[Positive](4), n2dOption, false, "n2d-custom-4-2048"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](4), n2dOption, false, "n2d-custom-4-2048"),
       (MemorySize(14, MemoryUnit.GB), refineMV[Positive](16), n2dOption, false, "n2d-custom-16-14336"),
       (MemorySize(13.65, MemoryUnit.GB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-14080"),
       (MemorySize(1520.96, MemoryUnit.MB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1536"),
@@ -83,7 +83,7 @@ class GcpBatchMachineConstraintsSpec extends AnyFlatSpec with CromwellTimeoutSpe
         cpu = cpu,
         cpuPlatformOption = cpuPlatformOption,
         googleLegacyMachineSelection = googleLegacyMachineSelection,
-        jobLogger = NOPLogger.NOP_LOGGER,
+        jobLogger = NOPLogger.NOP_LOGGER
       ) shouldBe expected
     }
   }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/CustomMachineType.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/CustomMachineType.scala
index 33cbd346abf..d7855890641 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/CustomMachineType.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/CustomMachineType.scala
@@ -20,6 +20,7 @@ import math.{log, pow}
   * - https://cloud.google.com/sdk/gcloud/reference/compute/instances/create#--custom-vm-type
   */
 trait CustomMachineType {
+
   /**
     * The vm prefix to create this custom machine type.
     */
@@ -53,10 +54,7 @@ trait CustomMachineType {
   /**
     * Generates a custom machine type based on the requested memory and cpu
     */
-  def machineType(requestedMemory: MemorySize,
-                  requestedCpu: Int Refined Positive,
-                  jobLogger: Logger,
-                 ): String = {
+  def machineType(requestedMemory: MemorySize, requestedCpu: Int Refined Positive, jobLogger: Logger): String = {
     val memory = requestedMemory |> validateMemory
     val cpu = requestedCpu |> validateCpu
 
@@ -91,8 +89,8 @@ trait CustomMachineType {
                             adjustedCpu: Int,
                             originalMemory: MemorySize,
                             adjustedMemory: MemorySize,
-                            logger: Logger,
-                           ): Unit = {
+                            logger: Logger
+  ): Unit = {
     def memoryAdjustmentLog = s"memory was adjusted from ${originalMemory.toMBString} to ${adjustedMemory.toMBString}"
 
     def cpuAdjustmentLog = s"cpu was adjusted from $originalCpu to $adjustedCpu"
@@ -100,7 +98,7 @@ trait CustomMachineType {
     val messageOption =
       (
         originalCpu == adjustedCpu,
-        originalMemory.to(MemoryUnit.MB).amount == adjustedMemory.to(MemoryUnit.MB).amount,
+        originalMemory.to(MemoryUnit.MB).amount == adjustedMemory.to(MemoryUnit.MB).amount
       ) match {
         case (true, false) => Option(memoryAdjustmentLog)
         case (false, true) => Option(cpuAdjustmentLog)
@@ -128,17 +126,15 @@ case object N1CustomMachineType extends CustomMachineType {
   override val maxMemoryPerCpu: MemorySize = MemorySize(6.5, MemoryUnit.GB)
   override val memoryFactor: MemorySize = MemorySize(256, MemoryUnit.MB)
 
-  override def validateCpu(cpu: Refined[Int, Positive]): Int = {
+  override def validateCpu(cpu: Refined[Int, Positive]): Int =
     // Either one cpu, or an even number of cpus
     cpu.value match {
       case 1 => 1
       case cpu => cpu + (cpu % 2)
     }
-  }
 
-  override def validateMemory(memory: MemorySize): MemorySize = {
+  override def validateMemory(memory: MemorySize): MemorySize =
     memory.asMultipleOf(memoryFactor)
-  }
 }
 
 case object N2CustomMachineType extends CustomMachineType {
@@ -147,18 +143,16 @@ case object N2CustomMachineType extends CustomMachineType {
   override val maxMemoryPerCpu: MemorySize = MemorySize(8.0, MemoryUnit.GB)
   override val memoryFactor: MemorySize = MemorySize(256, MemoryUnit.MB)
 
-  override def validateCpu(cpu: Refined[Int, Positive]): Int = {
+  override def validateCpu(cpu: Refined[Int, Positive]): Int =
     // cpus must be divisible by 2 up to 32, and higher numbers must be divisible by 4
     cpu.value match {
       case cpu if cpu <= 32 => cpu + (cpu % 2)
       case cpu if cpu % 4 == 0 => cpu
       case cpu => cpu + (4 - (cpu % 4))
     }
-  }
 
-  override def validateMemory(memory: MemorySize): MemorySize = {
+  override def validateMemory(memory: MemorySize): MemorySize =
     memory.asMultipleOf(memoryFactor)
-  }
 }
 
 case object N2DCustomMachineType extends CustomMachineType {
@@ -166,18 +160,15 @@ case object N2DCustomMachineType extends CustomMachineType {
   override val minMemoryPerCpu: MemorySize = MemorySize(0.5, MemoryUnit.GB)
   override val maxMemoryPerCpu: MemorySize = MemorySize(8.0, MemoryUnit.GB)
   override val memoryFactor: MemorySize = MemorySize(256, MemoryUnit.MB)
-  
-  override def validateCpu(cpu: Refined[Int, Positive]): Int = {
+
+  override def validateCpu(cpu: Refined[Int, Positive]): Int =
     cpu.value match {
-      case cpu if cpu <= 16 => 2 max pow(2, (log(cpu.toDouble)/log(2)).ceil).toInt
+      case cpu if cpu <= 16 => 2 max pow(2, (log(cpu.toDouble) / log(2)).ceil).toInt
       case cpu if cpu > 16 && cpu <= 96 && cpu % 16 == 0 => cpu
       case cpu if cpu > 16 && cpu <= 96 => cpu + 16 - (cpu % 16)
       case cpu if cpu > 96 => 96
     }
-  }
 
-  override def validateMemory(memory: MemorySize): MemorySize = {
+  override def validateMemory(memory: MemorySize): MemorySize =
     memory.asMultipleOf(memoryFactor)
-  }
 }
-
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GoogleCloudScopes.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GoogleCloudScopes.scala
index 5adc03ba1a8..02c40b6f11a 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GoogleCloudScopes.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GoogleCloudScopes.scala
@@ -4,6 +4,7 @@ package cromwell.backend.google.pipelines.common
   * Google cloud scopes that don't have constants defined elsewhere in Google Cloud Java API.
   */
 object GoogleCloudScopes {
+
   /**
     * More restricted version of com.google.api.services.cloudkms.v1.CloudKMSScopes.CLOUD_PLATFORM
     * Could use that scope to keep things simple, but docs say to use a more restricted scope:
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GoogleLabels.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GoogleLabels.scala
index 3eacb82393b..0599594fdf8 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GoogleLabels.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GoogleLabels.scala
@@ -23,18 +23,16 @@ object GoogleLabels {
 
   // This function is used to coerce a string into one that meets the requirements for a label submission to Google Pipelines API.
   // See 'labels' in https://cloud.google.com/genomics/reference/rpc/google.genomics.v1alpha2#google.genomics.v1alpha2.RunPipelineArgs
-  def safeGoogleName(mainText: String, emptyAllowed: Boolean = false): String = {
-
+  def safeGoogleName(mainText: String, emptyAllowed: Boolean = false): String =
     validateLabelRegex(mainText) match {
       case Valid(labelText) => labelText
       case invalid @ _ if mainText.equals("") && emptyAllowed => mainText
       case invalid @ _ =>
-        def appendSafe(current: String, nextChar: Char): String = {
+        def appendSafe(current: String, nextChar: Char): String =
           nextChar match {
             case c if c.isLetterOrDigit || c == '-' => current + c.toLower
             case _ => current + '-'
           }
-        }
 
         val foldResult = mainText.toCharArray.foldLeft("")(appendSafe)
 
@@ -50,51 +48,64 @@ object GoogleLabels {
         if (tooLong) {
           val middleSeparator = "---"
           val subSectionLength = (MaxLabelLength - middleSeparator.length) / 2
-          validStartAndEnd.substring(0, subSectionLength) + middleSeparator + validStartAndEnd.substring(length - subSectionLength, length)
+          validStartAndEnd.substring(0, subSectionLength) + middleSeparator + validStartAndEnd.substring(
+            length - subSectionLength,
+            length
+          )
         } else {
           validStartAndEnd
         }
     }
-  }
 
-  def validateLabelRegex(s: String): ErrorOr[String] = {
+  def validateLabelRegex(s: String): ErrorOr[String] =
     (GoogleLabelRegex.pattern.matcher(s).matches, s.length <= MaxLabelLength) match {
       case (true, true) => s.validNel
-      case (false, false) => s"Invalid label field: `$s` did not match regex '$GoogleLabelRegexPattern' and it is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
+      case (false, false) =>
+        s"Invalid label field: `$s` did not match regex '$GoogleLabelRegexPattern' and it is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
       case (false, _) => s"Invalid label field: `$s` did not match the regex '$GoogleLabelRegexPattern'".invalidNel
-      case (_, false) => s"Invalid label field: `$s` is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
+      case (_, false) =>
+        s"Invalid label field: `$s` is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
     }
-  }
-
 
   def safeLabels(values: (String, String)*): Seq[GoogleLabel] = {
-    def safeGoogleLabel(kvp: (String, String)): GoogleLabel = {
+    def safeGoogleLabel(kvp: (String, String)): GoogleLabel =
       GoogleLabel(safeGoogleName(kvp._1), safeGoogleName(kvp._2, emptyAllowed = true))
-    }
     values.map(safeGoogleLabel)
   }
 
-  def validateLabel(key: String, value: String): ErrorOr[GoogleLabel] = {
-    (validateLabelRegex(key), validateLabelRegex(value)).mapN { (validKey, validValue) => GoogleLabel(validKey, validValue)  }
-  }
+  def validateLabel(key: String, value: String): ErrorOr[GoogleLabel] =
+    (validateLabelRegex(key), validateLabelRegex(value)).mapN { (validKey, validValue) =>
+      GoogleLabel(validKey, validValue)
+    }
 
   def fromWorkflowOptions(workflowOptions: WorkflowOptions): Try[Seq[GoogleLabel]] = {
 
     def extractGoogleLabelsFromJsObject(jsObject: JsObject): Try[Seq[GoogleLabel]] = {
       val asErrorOr = jsObject.fields.toList.traverse {
         case (key: String, value: JsString) => GoogleLabels.validateLabel(key, value.value)
-        case (key, other) => s"Bad label value type for '$key'. Expected simple string but got $other".invalidNel : ErrorOr[GoogleLabel]
+        case (key, other) =>
+          s"Bad label value type for '$key'. Expected simple string but got $other".invalidNel: ErrorOr[GoogleLabel]
       }
 
       asErrorOr match {
         case Valid(value) => Success(value)
-        case Invalid(errors) => Failure(new AggregatedMessageException("Invalid 'google_labels' in workflow options", errors.toList) with CromwellFatalExceptionMarker with NoStackTrace)
+        case Invalid(errors) =>
+          Failure(
+            new AggregatedMessageException("Invalid 'google_labels' in workflow options", errors.toList)
+              with CromwellFatalExceptionMarker
+              with NoStackTrace
+          )
       }
     }
 
     workflowOptions.toMap.get("google_labels") match {
       case Some(obj: JsObject) => extractGoogleLabelsFromJsObject(obj)
-      case Some(other) => Failure(new Exception(s"Invalid 'google_labels' in workflow options. Must be a simple JSON object mapping string keys to string values. Got $other") with NoStackTrace with CromwellFatalExceptionMarker)
+      case Some(other) =>
+        Failure(
+          new Exception(
+            s"Invalid 'google_labels' in workflow options. Must be a simple JSON object mapping string keys to string values. Got $other"
+          ) with NoStackTrace with CromwellFatalExceptionMarker
+        )
       case None => Success(Seq.empty)
     }
   }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuTypeValidation.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuTypeValidation.scala
index 540888f9180..7ef5dfb0232 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuTypeValidation.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuTypeValidation.scala
@@ -19,6 +19,7 @@ class GpuTypeValidation extends RuntimeAttributesValidation[GpuType] {
   override def coercion: Iterable[WomType] = Set(WomStringType)
   override def validateValue: PartialFunction[WomValue, ErrorOr[GpuType]] = {
     case WomString(s) => GpuType(s).validNel
-    case other => s"Invalid '$key': String value required but got ${other.womType.friendlyName}. See ${GpuType.MoreDetailsURL} for a list of options".invalidNel
+    case other =>
+      s"Invalid '$key': String value required but got ${other.womType.friendlyName}. See ${GpuType.MoreDetailsURL} for a list of options".invalidNel
   }
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuValidation.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuValidation.scala
index adbb44565a9..916410df293 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuValidation.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuValidation.scala
@@ -5,7 +5,11 @@ import cats.syntax.either._
 import cats.syntax.validated._
 import com.typesafe.config.Config
 import common.validation.ErrorOr.ErrorOr
-import cromwell.backend.validation.{OptionalRuntimeAttributesValidation, PositiveIntRuntimeAttributesValidation, RuntimeAttributesValidation}
+import cromwell.backend.validation.{
+  OptionalRuntimeAttributesValidation,
+  PositiveIntRuntimeAttributesValidation,
+  RuntimeAttributesValidation
+}
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
 import eu.timepit.refined.refineV
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/MachineConstraints.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/MachineConstraints.scala
index 7e707f959e1..b92e9ceeeb7 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/MachineConstraints.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/MachineConstraints.scala
@@ -11,8 +11,8 @@ object MachineConstraints {
                   cpu: Int Refined Positive,
                   cpuPlatformOption: Option[String],
                   googleLegacyMachineSelection: Boolean,
-                  jobLogger: Logger,
-                 ): String = {
+                  jobLogger: Logger
+  ): String =
     if (googleLegacyMachineSelection) {
       s"predefined-$cpu-${memory.to(MemoryUnit.MB).amount.intValue()}"
     } else {
@@ -26,10 +26,9 @@ object MachineConstraints {
         cpuPlatformOption match {
           case Some(PipelinesApiRuntimeAttributes.CpuPlatformIntelIceLakeValue) => N2CustomMachineType
           case Some(PipelinesApiRuntimeAttributes.CpuPlatformIntelCascadeLakeValue) => N2CustomMachineType
-          case Some(PipelinesApiRuntimeAttributes.CpuPlatformAMDRomeValue)          => N2DCustomMachineType 
+          case Some(PipelinesApiRuntimeAttributes.CpuPlatformAMDRomeValue) => N2DCustomMachineType
           case _ => N1CustomMachineType
         }
       customMachineType.machineType(memory, cpu, jobLogger)
     }
-  }
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PapiInstrumentation.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PapiInstrumentation.scala
index 656597cf29f..e0f40fe2670 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PapiInstrumentation.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PapiInstrumentation.scala
@@ -23,9 +23,8 @@ object PapiInstrumentation {
   private val PapiAbortRetriedKey = PapiAbortKey.concatNel(RetryKey)
 
   implicit class StatsDPathGoogleEnhanced(val statsDPath: InstrumentationPath) extends AnyVal {
-    def withGoogleThrowable(failure: Throwable) = {
+    def withGoogleThrowable(failure: Throwable) =
       statsDPath.withThrowable(failure, GoogleUtil.extractStatusCode)
-    }
   }
 }
 
@@ -35,15 +34,21 @@ trait PapiInstrumentation extends CromwellInstrumentation {
   def abortSuccess() = increment(PapiAbortKey.concatNel(SuccessKey), BackendPrefix)
 
   def failedQuery(failedQuery: PAPIApiRequestFailed) = failedQuery.query match {
-    case _: PAPIStatusPollRequest => increment(PapiPollFailedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
-    case _: PAPIRunCreationRequest => increment(PapiRunFailedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
-    case _: PAPIAbortRequest => increment(PapiAbortFailedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
+    case _: PAPIStatusPollRequest =>
+      increment(PapiPollFailedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
+    case _: PAPIRunCreationRequest =>
+      increment(PapiRunFailedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
+    case _: PAPIAbortRequest =>
+      increment(PapiAbortFailedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
   }
 
   def retriedQuery(failedQuery: PAPIApiRequestFailed) = failedQuery.query match {
-    case _: PAPIStatusPollRequest => increment(PapiPollRetriedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
-    case _: PAPIRunCreationRequest => increment(PapiRunRetriedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
-    case _: PAPIAbortRequest => increment(PapiAbortRetriedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
+    case _: PAPIStatusPollRequest =>
+      increment(PapiPollRetriedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
+    case _: PAPIRunCreationRequest =>
+      increment(PapiRunRetriedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
+    case _: PAPIAbortRequest =>
+      increment(PapiAbortRetriedKey.withGoogleThrowable(failedQuery.cause.cause), BackendPrefix)
   }
 
   def updateQueueSize(size: Int) = sendGauge(PapiKey.concatNel("queue_size"), size.toLong, BackendPrefix)
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
index fee63573ff1..fa079ea86b2 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -13,20 +13,36 @@ import common.util.StringUtil._
 import common.validation.ErrorOr._
 import common.validation.Validation._
 import cromwell.backend._
-import cromwell.backend.async.{AbortedExecutionHandle, ExecutionHandle, FailedNonRetryableExecutionHandle, FailedRetryableExecutionHandle, PendingExecutionHandle}
+import cromwell.backend.async.{
+  AbortedExecutionHandle,
+  ExecutionHandle,
+  FailedNonRetryableExecutionHandle,
+  FailedRetryableExecutionHandle,
+  PendingExecutionHandle
+}
 import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.GcsTransferConfiguration
 import cromwell.backend.google.pipelines.common.PipelinesApiJobPaths.GcsTransferLibraryName
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory._
 import cromwell.backend.google.pipelines.common.api.RunStatus.TerminalRunStatus
 import cromwell.backend.google.pipelines.common.api._
 import cromwell.backend.google.pipelines.common.api.clients.PipelinesApiRunCreationClient.JobAbortedException
-import cromwell.backend.google.pipelines.common.api.clients.{PipelinesApiAbortClient, PipelinesApiRunCreationClient, PipelinesApiStatusRequestClient}
+import cromwell.backend.google.pipelines.common.api.clients.{
+  PipelinesApiAbortClient,
+  PipelinesApiRunCreationClient,
+  PipelinesApiStatusRequestClient
+}
 import cromwell.backend.google.pipelines.common.authentication.PipelinesApiDockerCredentials
 import cromwell.backend.google.pipelines.common.errors.FailedToDelocalizeFailure
 import cromwell.backend.google.pipelines.common.io._
 import cromwell.backend.google.pipelines.common.monitoring.{CheckpointingConfiguration, MonitoringImage}
 import cromwell.backend.io.DirectoryFunctions
-import cromwell.backend.standard.{ScriptPreambleData, StandardAdHocValue, StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
+import cromwell.backend.standard.{
+  ScriptPreambleData,
+  StandardAdHocValue,
+  StandardAsyncExecutionActor,
+  StandardAsyncExecutionActorParams,
+  StandardAsyncJob
+}
 import cromwell.core._
 import cromwell.core.io.IoCommandBuilder
 import cromwell.core.path.{DefaultPathBuilder, Path}
@@ -80,7 +96,8 @@ object PipelinesApiAsyncBackendJobExecutionActor {
                         message: String,
                         jobTag: String,
                         returnCodeOption: Option[Int],
-                        stderrPath: Path): Exception = {
+                        stderrPath: Path
+  ): Exception = {
     val returnCodeMessage = returnCodeOption match {
       case Some(returnCode) if returnCode == 0 => "Job exited without an error, exit code 0."
       case Some(returnCode) => s"Job exit code $returnCode. Check $stderrPath for more information."
@@ -92,7 +109,7 @@ object PipelinesApiAsyncBackendJobExecutionActor {
 }
 
 class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
-  extends BackendJobLifecycleActor
+    extends BackendJobLifecycleActor
     with StandardAsyncExecutionActor
     with PipelinesApiJobCachingActorHelper
     with PipelinesApiStatusRequestClient
@@ -111,7 +128,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
 
   val jesBackendSingletonActor: ActorRef =
     standardParams.backendSingletonActorOption.getOrElse(
-      throw new RuntimeException("JES Backend actor cannot exist without the JES backend singleton actor"))
+      throw new RuntimeException("JES Backend actor cannot exist without the JES backend singleton actor")
+    )
 
   override type StandardAsyncRunInfo = Run
 
@@ -122,23 +140,35 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
   override val papiApiActor: ActorRef = jesBackendSingletonActor
 
   override lazy val pollBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(
-    initialInterval = 30 seconds, maxInterval = jesAttributes.maxPollingInterval seconds, multiplier = 1.1)
+    initialInterval = 30 seconds,
+    maxInterval = jesAttributes.maxPollingInterval seconds,
+    multiplier = 1.1
+  )
 
-  override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff = SimpleExponentialBackoff(
-    initialInterval = 3 seconds, maxInterval = 20 seconds, multiplier = 1.1)
+  override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff =
+    SimpleExponentialBackoff(initialInterval = 3 seconds, maxInterval = 20 seconds, multiplier = 1.1)
 
-  override lazy val runtimeEnvironment: RuntimeEnvironment = {
-    RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes, PipelinesApiWorkingDisk.MountPoint, PipelinesApiWorkingDisk.MountPoint)(standardParams.minimumRuntimeSettings)
-  }
+  override lazy val runtimeEnvironment: RuntimeEnvironment =
+    RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes,
+                              PipelinesApiWorkingDisk.MountPoint,
+                              PipelinesApiWorkingDisk.MountPoint
+    )(standardParams.minimumRuntimeSettings)
 
   protected lazy val cmdInput: PipelinesApiFileInput =
-    PipelinesApiFileInput(PipelinesApiJobPaths.JesExecParamName, pipelinesApiCallPaths.script, DefaultPathBuilder.get(pipelinesApiCallPaths.scriptFilename), workingDisk)
+    PipelinesApiFileInput(PipelinesApiJobPaths.JesExecParamName,
+                          pipelinesApiCallPaths.script,
+                          DefaultPathBuilder.get(pipelinesApiCallPaths.scriptFilename),
+                          workingDisk
+    )
 
-  protected lazy val dockerConfiguration: Option[PipelinesApiDockerCredentials] = pipelinesConfiguration.dockerCredentials
+  protected lazy val dockerConfiguration: Option[PipelinesApiDockerCredentials] =
+    pipelinesConfiguration.dockerCredentials
 
-  protected val previousRetryReasons: ErrorOr[PreviousRetryReasons] = PreviousRetryReasons.tryApply(jobDescriptor.prefetchedKvStoreEntries, jobDescriptor.key.attempt)
+  protected val previousRetryReasons: ErrorOr[PreviousRetryReasons] =
+    PreviousRetryReasons.tryApply(jobDescriptor.prefetchedKvStoreEntries, jobDescriptor.key.attempt)
 
-  protected lazy val jobDockerImage: String = jobDescriptor.maybeCallCachingEligible.dockerHash.getOrElse(runtimeAttributes.dockerImage)
+  protected lazy val jobDockerImage: String =
+    jobDescriptor.maybeCallCachingEligible.dockerHash.getOrElse(runtimeAttributes.dockerImage)
 
   override lazy val dockerImageUsed: Option[String] = Option(jobDockerImage)
 
@@ -152,7 +182,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
   override def requestsAbortAndDiesImmediately: Boolean = false
 
   /*_*/ // Silence an errant IntelliJ warning
-  override def receive: Receive = pollingActorClientReceive orElse runCreationClientReceive orElse abortActorClientReceive orElse kvClientReceive orElse super.receive
+  override def receive: Receive =
+    pollingActorClientReceive orElse runCreationClientReceive orElse abortActorClientReceive orElse kvClientReceive orElse super.receive
   /*_*/ // https://stackoverflow.com/questions/36679973/controlling-false-intellij-code-editor-error-in-scala-plugin
 
   /**
@@ -161,12 +192,17 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
   protected def pipelinesApiInputsFromWomFiles(jesNamePrefix: String,
                                                remotePathArray: Seq[WomFile],
                                                localPathArray: Seq[WomFile],
-                                               jobDescriptor: BackendJobDescriptor): Iterable[PipelinesApiInput] = {
-    (remotePathArray zip localPathArray zipWithIndex) flatMap {
-      case ((remotePath, localPath), index) =>
-        Seq(PipelinesApiFileInput(s"$jesNamePrefix-$index", getPath(remotePath.valueString).get, DefaultPathBuilder.get(localPath.valueString), workingDisk))
+                                               jobDescriptor: BackendJobDescriptor
+  ): Iterable[PipelinesApiInput] =
+    (remotePathArray zip localPathArray zipWithIndex) flatMap { case ((remotePath, localPath), index) =>
+      Seq(
+        PipelinesApiFileInput(s"$jesNamePrefix-$index",
+                              getPath(remotePath.valueString).get,
+                              DefaultPathBuilder.get(localPath.valueString),
+                              workingDisk
+        )
+      )
     }
-  }
 
   /**
     * Turns WomFiles into relative paths.  These paths are relative to the working disk.
@@ -174,7 +210,7 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     * relativeLocalizationPath("foo/bar.txt") -> "foo/bar.txt"
     * relativeLocalizationPath("gs://some/bucket/foo.txt") -> "some/bucket/foo.txt"
     */
-  override protected def relativeLocalizationPath(file: WomFile): WomFile = {
+  override protected def relativeLocalizationPath(file: WomFile): WomFile =
     file.mapFile(value =>
       getPath(value) match {
         case Success(drsPath: DrsPath) => DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
@@ -182,17 +218,16 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
         case _ => value
       }
     )
-  }
 
-  override protected def fileName(file: WomFile): WomFile = {
+  override protected def fileName(file: WomFile): WomFile =
     file.mapFile(value =>
       getPath(value) match {
-        case Success(drsPath: DrsPath) => DefaultPathBuilder.get(DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()).name
+        case Success(drsPath: DrsPath) =>
+          DefaultPathBuilder.get(DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()).name
         case Success(path) => path.name
         case _ => value
       }
     )
-  }
 
   override lazy val inputsToNotLocalize: Set[WomFile] = {
     val localizeOptional = jobDescriptor.findInputFilesByParameterMeta {
@@ -204,23 +239,21 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     localizeSkipped ++ localizeMapped
   }
 
-  protected def callInputFiles: Map[FullyQualifiedName, Seq[WomFile]] = {
-
-    jobDescriptor.fullyQualifiedInputs map {
-      case (key, womFile) =>
-        val arrays: Seq[WomArray] = womFile collectAsSeq {
-          case womFile: WomFile if !inputsToNotLocalize.contains(womFile) =>
-            val files: List[WomSingleFile] = DirectoryFunctions
-              .listWomSingleFiles(womFile, pipelinesApiCallPaths.workflowPaths)
-              .toTry(s"Error getting single files for $womFile").get
-            WomArray(WomArrayType(WomSingleFileType), files)
-        }
+  protected def callInputFiles: Map[FullyQualifiedName, Seq[WomFile]] =
+    jobDescriptor.fullyQualifiedInputs map { case (key, womFile) =>
+      val arrays: Seq[WomArray] = womFile collectAsSeq {
+        case womFile: WomFile if !inputsToNotLocalize.contains(womFile) =>
+          val files: List[WomSingleFile] = DirectoryFunctions
+            .listWomSingleFiles(womFile, pipelinesApiCallPaths.workflowPaths)
+            .toTry(s"Error getting single files for $womFile")
+            .get
+          WomArray(WomArrayType(WomSingleFileType), files)
+      }
 
-        key -> arrays.flatMap(_.value).collect {
-          case womFile: WomFile => womFile
-        }
+      key -> arrays.flatMap(_.value).collect { case womFile: WomFile =>
+        womFile
+      }
     }
-  }
 
   private[pipelines] def generateInputs(jobDescriptor: BackendJobDescriptor): Set[PipelinesApiInput] = {
     // We need to tell PAPI about files that were created as part of command instantiation (these need to be defined
@@ -228,12 +261,12 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     // md5's of their paths.
     val writeFunctionFiles = instantiatedCommand.createdFiles map { f => f.file.value.md5SumShort -> List(f) } toMap
 
-    val writeFunctionInputs = writeFunctionFiles flatMap {
-      case (name, files) => pipelinesApiInputsFromWomFiles(name, files.map(_.file), files.map(localizationPath), jobDescriptor)
+    val writeFunctionInputs = writeFunctionFiles flatMap { case (name, files) =>
+      pipelinesApiInputsFromWomFiles(name, files.map(_.file), files.map(localizationPath), jobDescriptor)
     }
 
-    val callInputInputs = callInputFiles flatMap {
-      case (name, files) => pipelinesApiInputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor)
+    val callInputInputs = callInputFiles flatMap { case (name, files) =>
+      pipelinesApiInputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor)
     }
 
     (writeFunctionInputs ++ callInputInputs).toSet
@@ -245,7 +278,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     *
     * @throws Exception if the `path` does not live in one of the supplied `disks`
     */
-  protected def relativePathAndAttachedDisk(path: String, disks: Seq[PipelinesApiAttachedDisk]): (Path, PipelinesApiAttachedDisk) = {
+  protected def relativePathAndAttachedDisk(path: String,
+                                            disks: Seq[PipelinesApiAttachedDisk]
+  ): (Path, PipelinesApiAttachedDisk) = {
     val absolutePath = DefaultPathBuilder.get(path) match {
       case p if !p.isAbsolute => PipelinesApiWorkingDisk.MountPoint.resolve(p)
       case p => p
@@ -254,7 +289,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     disks.find(d => absolutePath.startsWith(d.mountPoint)) match {
       case Some(disk) => (disk.mountPoint.relativize(absolutePath), disk)
       case None =>
-        throw new Exception(s"Absolute path $path doesn't appear to be under any mount points: ${disks.map(_.toString).mkString(", ")}")
+        throw new Exception(
+          s"Absolute path $path doesn't appear to be under any mount points: ${disks.map(_.toString).mkString(", ")}"
+        )
     }
   }
 
@@ -262,39 +299,40 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     * If the desired reference name is too long, we don't want to break JES or risk collisions by arbitrary truncation. So,
     * just use a hash. We only do this when needed to give better traceability in the normal case.
     */
-  protected def makeSafeReferenceName(referenceName: String): String = {
+  protected def makeSafeReferenceName(referenceName: String): String =
     if (referenceName.length <= 127) referenceName else referenceName.md5Sum
-  }
 
-  protected [pipelines] def generateOutputs(jobDescriptor: BackendJobDescriptor): Set[PipelinesApiOutput] = {
+  protected[pipelines] def generateOutputs(jobDescriptor: BackendJobDescriptor): Set[PipelinesApiOutput] = {
     import cats.syntax.validated._
-    def evaluateFiles(output: OutputDefinition): List[FileEvaluation] = {
+    def evaluateFiles(output: OutputDefinition): List[FileEvaluation] =
       Try(
         output.expression.evaluateFiles(jobDescriptor.localInputs, NoIoFunctionSet, output.womType).map(_.toList)
       ).getOrElse(List.empty[FileEvaluation].validNel)
         .getOrElse(List.empty)
-    }
 
-    def relativeFileEvaluation(evaluation: FileEvaluation): FileEvaluation = {
+    def relativeFileEvaluation(evaluation: FileEvaluation): FileEvaluation =
       evaluation.copy(file = relativeLocalizationPath(evaluation.file))
-    }
 
     val womFileOutputs = jobDescriptor.taskCall.callable.outputs.flatMap(evaluateFiles) map relativeFileEvaluation
 
     val outputs: Seq[PipelinesApiOutput] = womFileOutputs.distinct flatMap { fileEvaluation =>
       fileEvaluation.file.flattenFiles flatMap {
-        case unlistedDirectory: WomUnlistedDirectory => generateUnlistedDirectoryOutputs(unlistedDirectory, fileEvaluation)
+        case unlistedDirectory: WomUnlistedDirectory =>
+          generateUnlistedDirectoryOutputs(unlistedDirectory, fileEvaluation)
         case singleFile: WomSingleFile => generateSingleFileOutputs(singleFile, fileEvaluation)
         case globFile: WomGlobFile => generateGlobFileOutputs(globFile) // Assumes optional = false for globs.
       }
     }
 
-    val additionalGlobOutput = jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateGlobFileOutputs).toSet
+    val additionalGlobOutput =
+      jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateGlobFileOutputs).toSet
 
     outputs.toSet ++ additionalGlobOutput
   }
 
-  protected def generateUnlistedDirectoryOutputs(womFile: WomUnlistedDirectory, fileEvaluation: FileEvaluation): List[PipelinesApiOutput] = {
+  protected def generateUnlistedDirectoryOutputs(womFile: WomUnlistedDirectory,
+                                                 fileEvaluation: FileEvaluation
+  ): List[PipelinesApiOutput] = {
     val directoryPath = womFile.value.ensureSlashed
     val directoryListFile = womFile.value.ensureUnslashed + ".list"
     val gcsDirDestinationPath = callRootPath.resolve(directoryPath)
@@ -325,10 +363,18 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     )
   }
 
-  protected def generateSingleFileOutputs(womFile: WomSingleFile, fileEvaluation: FileEvaluation): List[PipelinesApiFileOutput] = {
+  protected def generateSingleFileOutputs(womFile: WomSingleFile,
+                                          fileEvaluation: FileEvaluation
+  ): List[PipelinesApiFileOutput] = {
     val destination = callRootPath.resolve(womFile.value.stripPrefix("/"))
     val (relpath, disk) = relativePathAndAttachedDisk(womFile.value, runtimeAttributes.disks)
-    val jesFileOutput = PipelinesApiFileOutput(makeSafeReferenceName(womFile.value), destination, relpath, disk, fileEvaluation.optional, fileEvaluation.secondary)
+    val jesFileOutput = PipelinesApiFileOutput(makeSafeReferenceName(womFile.value),
+                                               destination,
+                                               relpath,
+                                               disk,
+                                               fileEvaluation.optional,
+                                               fileEvaluation.secondary
+    )
     List(jesFileOutput)
   }
 
@@ -344,11 +390,23 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     // We need both the glob directory and the glob list:
     List(
       // The glob directory:
-      PipelinesApiFileOutput(makeSafeReferenceName(globDirectory), gcsGlobDirectoryDestinationPath, DefaultPathBuilder.get(globDirectory + "*"), globDirectoryDisk,
-        optional = false, secondary = false),
+      PipelinesApiFileOutput(
+        makeSafeReferenceName(globDirectory),
+        gcsGlobDirectoryDestinationPath,
+        DefaultPathBuilder.get(globDirectory + "*"),
+        globDirectoryDisk,
+        optional = false,
+        secondary = false
+      ),
       // The glob list file:
-      PipelinesApiFileOutput(makeSafeReferenceName(globListFile), gcsGlobListFileDestinationPath, DefaultPathBuilder.get(globListFile), globDirectoryDisk,
-        optional = false, secondary = false)
+      PipelinesApiFileOutput(
+        makeSafeReferenceName(globListFile),
+        gcsGlobListFileDestinationPath,
+        DefaultPathBuilder.get(globListFile),
+        globDirectoryDisk,
+        optional = false,
+        secondary = false
+      )
     )
   }
 
@@ -358,71 +416,73 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
   lazy val localMonitoringImageScriptPath: Path =
     DefaultPathBuilder.get(pipelinesApiCallPaths.jesMonitoringImageScriptFilename)
 
-  lazy val monitoringScript: Option[PipelinesApiFileInput] = {
+  lazy val monitoringScript: Option[PipelinesApiFileInput] =
     pipelinesApiCallPaths.workflowPaths.monitoringScriptPath map { path =>
       PipelinesApiFileInput(s"$jesMonitoringParamName-in", path, localMonitoringScriptPath, workingDisk)
     }
-  }
 
   lazy val monitoringOutput: Option[PipelinesApiFileOutput] = monitoringScript map { _ =>
-    PipelinesApiFileOutput(s"$jesMonitoringParamName-out",
-      pipelinesApiCallPaths.jesMonitoringLogPath, localMonitoringLogPath, workingDisk, optional = false, secondary = false,
-      contentType = plainTextContentType)
+    PipelinesApiFileOutput(
+      s"$jesMonitoringParamName-out",
+      pipelinesApiCallPaths.jesMonitoringLogPath,
+      localMonitoringLogPath,
+      workingDisk,
+      optional = false,
+      secondary = false,
+      contentType = plainTextContentType
+    )
   }
 
   override lazy val commandDirectory: Path = PipelinesApiWorkingDisk.MountPoint
 
-  private val DockerMonitoringLogPath: Path = PipelinesApiWorkingDisk.MountPoint.resolve(pipelinesApiCallPaths.jesMonitoringLogFilename)
-  private val DockerMonitoringScriptPath: Path = PipelinesApiWorkingDisk.MountPoint.resolve(pipelinesApiCallPaths.jesMonitoringScriptFilename)
-  //noinspection ActorMutableStateInspection
+  private val DockerMonitoringLogPath: Path =
+    PipelinesApiWorkingDisk.MountPoint.resolve(pipelinesApiCallPaths.jesMonitoringLogFilename)
+  private val DockerMonitoringScriptPath: Path =
+    PipelinesApiWorkingDisk.MountPoint.resolve(pipelinesApiCallPaths.jesMonitoringScriptFilename)
+  // noinspection ActorMutableStateInspection
   private var hasDockerCredentials: Boolean = false
 
-  private lazy val isDockerImageCacheUsageRequested = runtimeAttributes.useDockerImageCache.getOrElse(useDockerImageCache(jobDescriptor.workflowDescriptor))
+  private lazy val isDockerImageCacheUsageRequested =
+    runtimeAttributes.useDockerImageCache.getOrElse(useDockerImageCache(jobDescriptor.workflowDescriptor))
 
-  override def scriptPreamble: ErrorOr[ScriptPreambleData] = {
+  override def scriptPreamble: ErrorOr[ScriptPreambleData] =
     if (monitoringOutput.isDefined)
-      ScriptPreambleData(
-      s"""|touch $DockerMonitoringLogPath
-          |chmod u+x $DockerMonitoringScriptPath
-          |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin).valid
-     else ScriptPreambleData("").valid
-  }
+      ScriptPreambleData(s"""|touch $DockerMonitoringLogPath
+                             |chmod u+x $DockerMonitoringScriptPath
+                             |$DockerMonitoringScriptPath > $DockerMonitoringLogPath &""".stripMargin).valid
+    else ScriptPreambleData("").valid
 
   override def globParentDirectory(womGlobFile: WomGlobFile): Path = {
     val (_, disk) = relativePathAndAttachedDisk(womGlobFile.value, runtimeAttributes.disks)
     disk.mountPoint
   }
 
-  protected def googleProject(descriptor: BackendWorkflowDescriptor): String = {
+  protected def googleProject(descriptor: BackendWorkflowDescriptor): String =
     descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleProject, jesAttributes.project)
-  }
 
-  protected def computeServiceAccount(descriptor: BackendWorkflowDescriptor): String = {
-    descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleComputeServiceAccount, jesAttributes.computeServiceAccount)
-  }
+  protected def computeServiceAccount(descriptor: BackendWorkflowDescriptor): String =
+    descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleComputeServiceAccount,
+                                         jesAttributes.computeServiceAccount
+    )
 
-  protected def fuseEnabled(descriptor: BackendWorkflowDescriptor): Boolean = {
+  protected def fuseEnabled(descriptor: BackendWorkflowDescriptor): Boolean =
     descriptor.workflowOptions.getBoolean(WorkflowOptionKeys.EnableFuse).toOption.getOrElse(jesAttributes.enableFuse)
-  }
 
-  protected def googleLegacyMachineSelection(descriptor: BackendWorkflowDescriptor): Boolean = {
+  protected def googleLegacyMachineSelection(descriptor: BackendWorkflowDescriptor): Boolean =
     descriptor.workflowOptions.getBoolean(WorkflowOptionKeys.GoogleLegacyMachineSelection).getOrElse(false)
-  }
 
-  protected def useDockerImageCache(descriptor: BackendWorkflowDescriptor): Boolean = {
+  protected def useDockerImageCache(descriptor: BackendWorkflowDescriptor): Boolean =
     descriptor.workflowOptions.getBoolean(WorkflowOptionKeys.UseDockerImageCache).getOrElse(false)
-  }
 
-  override def isTerminal(runStatus: RunStatus): Boolean = {
+  override def isTerminal(runStatus: RunStatus): Boolean =
     runStatus match {
       case _: TerminalRunStatus => true
       case _ => false
     }
-  }
 
   private def createPipelineParameters(inputOutputParameters: InputOutputParameters,
-                                       customLabels: Seq[GoogleLabel],
-                                       ): CreatePipelineParameters = {
+                                       customLabels: Seq[GoogleLabel]
+  ): CreatePipelineParameters =
     standardParams.backendInitializationDataOption match {
       case Some(data: PipelinesApiBackendInitializationData) =>
         val dockerKeyAndToken: Option[CreatePipelineDockerKeyAndToken] = for {
@@ -431,24 +491,28 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
         } yield CreatePipelineDockerKeyAndToken(key, token)
 
         /*
-           * Right now this doesn't cost anything, because sizeOption returns the size if it was previously already fetched
-           * for some reason (expression evaluation for instance), but otherwise does not retrieve it and returns None.
-           * In CWL-land we tend to be aggressive in pre-fetching the size in order to be able to evaluate JS expressions,
-           * but less in WDL as we can get it last minute and on demand because size is a WDL function, whereas in CWL
-           * we don't inspect the JS to know if size is called and therefore always pre-fetch it.
-           *
-           * We could decide to call withSize before in which case we would retrieve the size for all files and have
-           * a guaranteed more accurate total size, but there might be performance impacts ?
-           */
+         * Right now this doesn't cost anything, because sizeOption returns the size if it was previously already fetched
+         * for some reason (expression evaluation for instance), but otherwise does not retrieve it and returns None.
+         * In CWL-land we tend to be aggressive in pre-fetching the size in order to be able to evaluate JS expressions,
+         * but less in WDL as we can get it last minute and on demand because size is a WDL function, whereas in CWL
+         * we don't inspect the JS to know if size is called and therefore always pre-fetch it.
+         *
+         * We could decide to call withSize before in which case we would retrieve the size for all files and have
+         * a guaranteed more accurate total size, but there might be performance impacts ?
+         */
         val inputFileSize = Option(callInputFiles.values.flatMap(_.flatMap(_.sizeOption)).sum)
 
         // Attempt to adjust the disk size by taking into account the size of input files
-        val adjustedSizeDisks = inputFileSize.map(size => MemorySize.apply(size.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB)) map { inputFileSizeInformation =>
-          runtimeAttributes.disks.adjustWorkingDiskWithNewMin(
-            inputFileSizeInformation,
-            jobLogger.info(s"Adjusted working disk size to ${inputFileSizeInformation.amount} GB to account for input files")
-          )
-        } getOrElse runtimeAttributes.disks
+        val adjustedSizeDisks =
+          inputFileSize.map(size => MemorySize.apply(size.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB)) map {
+            inputFileSizeInformation =>
+              runtimeAttributes.disks.adjustWorkingDiskWithNewMin(
+                inputFileSizeInformation,
+                jobLogger.info(
+                  s"Adjusted working disk size to ${inputFileSizeInformation.amount} GB to account for input files"
+                )
+              )
+          } getOrElse runtimeAttributes.disks
 
         val inputFilePaths = inputOutputParameters.jobInputParameters.map(_.cloudPath.pathAsString).toSet
         val referenceDisksToMount =
@@ -465,7 +529,7 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
             workflowPaths = workflowPaths,
             commandDirectory = commandDirectory,
             workingDisk = workingDisk,
-            localMonitoringImageScriptPath = localMonitoringImageScriptPath,
+            localMonitoringImageScriptPath = localMonitoringImageScriptPath
           )
 
         val checkpointingConfiguration =
@@ -523,7 +587,6 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
       case None =>
         throw new RuntimeException("No pipelines API backend initialization data found?")
     }
-  }
 
   override def isFatal(throwable: Throwable): Boolean = super.isFatal(throwable) || isFatalJesException(throwable)
 
@@ -531,33 +594,44 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
 
   override def executeAsync(): Future[ExecutionHandle] = createNewJob()
 
-  val futureKvJobKey: KvJobKey = KvJobKey(jobDescriptor.key.call.fullyQualifiedName, jobDescriptor.key.index, jobDescriptor.key.attempt + 1)
+  val futureKvJobKey: KvJobKey =
+    KvJobKey(jobDescriptor.key.call.fullyQualifiedName, jobDescriptor.key.index, jobDescriptor.key.attempt + 1)
 
   override def recoverAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] = reconnectToExistingJob(jobId)
 
   override def reconnectAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] = reconnectToExistingJob(jobId)
 
-  override def reconnectToAbortAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] = reconnectToExistingJob(jobId, forceAbort = true)
+  override def reconnectToAbortAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] =
+    reconnectToExistingJob(jobId, forceAbort = true)
 
   private def reconnectToExistingJob(jobForResumption: StandardAsyncJob, forceAbort: Boolean = false) = {
     if (forceAbort) tryAbort(jobForResumption)
-    Future.successful(PendingExecutionHandle(jobDescriptor, jobForResumption, Option(Run(jobForResumption)), previousState = None))
+    Future.successful(
+      PendingExecutionHandle(jobDescriptor, jobForResumption, Option(Run(jobForResumption)), previousState = None)
+    )
   }
 
-  protected def uploadDrsLocalizationManifest(createPipelineParameters: CreatePipelineParameters, cloudPath: Path): Future[Unit] = Future.successful(())
+  protected def uploadDrsLocalizationManifest(createPipelineParameters: CreatePipelineParameters,
+                                              cloudPath: Path
+  ): Future[Unit] = Future.successful(())
 
-  protected def uploadGcsTransferLibrary(createPipelineParameters: CreatePipelineParameters, cloudPath: Path, gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = Future.successful(())
+  protected def uploadGcsTransferLibrary(createPipelineParameters: CreatePipelineParameters,
+                                         cloudPath: Path,
+                                         gcsTransferConfiguration: GcsTransferConfiguration
+  ): Future[Unit] = Future.successful(())
 
   protected def uploadGcsLocalizationScript(createPipelineParameters: CreatePipelineParameters,
                                             cloudPath: Path,
                                             transferLibraryContainerPath: Path,
                                             gcsTransferConfiguration: GcsTransferConfiguration,
-                                            referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]]): Future[Unit] = Future.successful(())
+                                            referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]]
+  ): Future[Unit] = Future.successful(())
 
   protected def uploadGcsDelocalizationScript(createPipelineParameters: CreatePipelineParameters,
                                               cloudPath: Path,
                                               transferLibraryContainerPath: Path,
-                                              gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = Future.successful(())
+                                              gcsTransferConfiguration: GcsTransferConfiguration
+  ): Future[Unit] = Future.successful(())
 
   protected val useReferenceDisks: Boolean = {
     val optionName = WorkflowOptions.UseReferenceDisks.name
@@ -566,7 +640,10 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
       case Failure(OptionNotFoundException(_)) => false
       case Failure(f) =>
         // Should not happen, this case should have been screened for and fast-failed during workflow materialization.
-        log.error(f, s"Programmer error: unexpected failure attempting to read value for workflow option '$optionName' as a Boolean")
+        log.error(
+          f,
+          s"Programmer error: unexpected failure attempting to read value for workflow option '$optionName' as a Boolean"
+        )
         false
     }
   }
@@ -576,8 +653,15 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     def evaluateRuntimeAttributes = Future.fromTry(Try(runtimeAttributes))
 
     def generateInputOutputParameters: Future[InputOutputParameters] = Future.fromTry(Try {
-      val rcFileOutput = PipelinesApiFileOutput(returnCodeFilename, returnCodeGcsPath, DefaultPathBuilder.get(returnCodeFilename), workingDisk, optional = false, secondary = false,
-        contentType = plainTextContentType)
+      val rcFileOutput = PipelinesApiFileOutput(
+        returnCodeFilename,
+        returnCodeGcsPath,
+        DefaultPathBuilder.get(returnCodeFilename),
+        workingDisk,
+        optional = false,
+        secondary = false,
+        contentType = plainTextContentType
+      )
 
       val memoryRetryRCFileOutput = PipelinesApiFileOutput(
         memoryRetryRCFilename,
@@ -597,8 +681,16 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
         StandardStream("stdout", _.output),
         StandardStream("stderr", _.error)
       ) map { s =>
-        PipelinesApiFileOutput(s.name, returnCodeGcsPath.sibling(s.filename), DefaultPathBuilder.get(s.filename),
-          workingDisk, optional = false, secondary = false, uploadPeriod = jesAttributes.logFlushPeriod, contentType = plainTextContentType)
+        PipelinesApiFileOutput(
+          s.name,
+          returnCodeGcsPath.sibling(s.filename),
+          DefaultPathBuilder.get(s.filename),
+          workingDisk,
+          optional = false,
+          secondary = false,
+          uploadPeriod = jesAttributes.logFlushPeriod,
+          contentType = plainTextContentType
+        )
       }
 
       InputOutputParameters(
@@ -623,19 +715,24 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     )
 
     def sendGoogleLabelsToMetadata(customLabels: Seq[GoogleLabel]): Unit = {
-      lazy val backendLabelEvents: Map[String, String] = ((backendLabels ++ customLabels) map { l => s"${CallMetadataKeys.BackendLabels}:${l.key}" -> l.value }).toMap
+      lazy val backendLabelEvents: Map[String, String] =
+        ((backendLabels ++ customLabels) map { l => s"${CallMetadataKeys.BackendLabels}:${l.key}" -> l.value }).toMap
       tellMetadata(backendLabelEvents)
     }
 
-    def getReferenceInputsToMountedPathsOpt(createPipelinesParameters: CreatePipelineParameters): Option[Map[PipelinesApiInput, String]] = {
+    def getReferenceInputsToMountedPathsOpt(
+      createPipelinesParameters: CreatePipelineParameters
+    ): Option[Map[PipelinesApiInput, String]] =
       if (useReferenceDisks) {
-        jesAttributes
-          .referenceFileToDiskImageMappingOpt
-          .map(getReferenceInputsToMountedPathMappings(_, createPipelinesParameters.inputOutputParameters.fileInputParameters))
+        jesAttributes.referenceFileToDiskImageMappingOpt
+          .map(
+            getReferenceInputsToMountedPathMappings(_,
+                                                    createPipelinesParameters.inputOutputParameters.fileInputParameters
+            )
+          )
       } else {
         None
       }
-    }
 
     val runPipelineResponse = for {
       _ <- evaluateRuntimeAttributes
@@ -651,9 +748,18 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
       _ <- uploadGcsTransferLibrary(createParameters, gcsTransferLibraryCloudPath, gcsTransferConfiguration)
       gcsLocalizationScriptCloudPath = jobPaths.callExecutionRoot / PipelinesApiJobPaths.GcsLocalizationScriptName
       referenceInputsToMountedPathsOpt = getReferenceInputsToMountedPathsOpt(createParameters)
-      _ <- uploadGcsLocalizationScript(createParameters, gcsLocalizationScriptCloudPath, transferLibraryContainerPath, gcsTransferConfiguration, referenceInputsToMountedPathsOpt)
+      _ <- uploadGcsLocalizationScript(createParameters,
+                                       gcsLocalizationScriptCloudPath,
+                                       transferLibraryContainerPath,
+                                       gcsTransferConfiguration,
+                                       referenceInputsToMountedPathsOpt
+      )
       gcsDelocalizationScriptCloudPath = jobPaths.callExecutionRoot / PipelinesApiJobPaths.GcsDelocalizationScriptName
-      _ <- uploadGcsDelocalizationScript(createParameters, gcsDelocalizationScriptCloudPath, transferLibraryContainerPath, gcsTransferConfiguration)
+      _ <- uploadGcsDelocalizationScript(createParameters,
+                                         gcsDelocalizationScriptCloudPath,
+                                         transferLibraryContainerPath,
+                                         gcsTransferConfiguration
+      )
       _ = this.hasDockerCredentials = createParameters.privateDockerKeyAndEncryptedToken.isDefined
       runId <- runPipeline(workflowId, createParameters, jobLogger)
       _ = sendGoogleLabelsToMetadata(customLabels)
@@ -667,48 +773,50 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
 
     runPipelineResponse map { runId =>
       PendingExecutionHandle(jobDescriptor, runId, Option(Run(runId)), previousState = None)
-    } recover {
-      case JobAbortedException => AbortedExecutionHandle
+    } recover { case JobAbortedException =>
+      AbortedExecutionHandle
     }
   }
 
-  protected def sendIncrementMetricsForReferenceFiles(referenceInputFilesOpt: Option[Set[PipelinesApiInput]]): Unit = {
+  protected def sendIncrementMetricsForReferenceFiles(referenceInputFilesOpt: Option[Set[PipelinesApiInput]]): Unit =
     referenceInputFilesOpt match {
       case Some(referenceInputFiles) =>
         referenceInputFiles.foreach { referenceInputFile =>
           increment(NonEmptyList.of("referencefiles", referenceInputFile.relativeHostPath.pathAsString))
         }
       case _ =>
-        // do nothing - reference disks feature is either not configured in Cromwell or disabled in workflow options
+      // do nothing - reference disks feature is either not configured in Cromwell or disabled in workflow options
     }
-  }
 
   protected def sendIncrementMetricsForDockerImageCache(dockerImageCacheDiskOpt: Option[String],
                                                         dockerImageAsSpecifiedByUser: String,
-                                                        isDockerImageCacheUsageRequested: Boolean): Unit = {
+                                                        isDockerImageCacheUsageRequested: Boolean
+  ): Unit =
     (isDockerImageCacheUsageRequested, dockerImageCacheDiskOpt) match {
-      case (true, None) => increment(NonEmptyList("docker", List("image", "cache", "image_not_in_cache", dockerImageAsSpecifiedByUser)))
-      case (true, Some(_)) => increment(NonEmptyList("docker", List("image", "cache", "used_image_from_cache", dockerImageAsSpecifiedByUser)))
-      case (false, Some(_)) => increment(NonEmptyList("docker", List("image", "cache", "cached_image_not_used", dockerImageAsSpecifiedByUser)))
+      case (true, None) =>
+        increment(NonEmptyList("docker", List("image", "cache", "image_not_in_cache", dockerImageAsSpecifiedByUser)))
+      case (true, Some(_)) =>
+        increment(NonEmptyList("docker", List("image", "cache", "used_image_from_cache", dockerImageAsSpecifiedByUser)))
+      case (false, Some(_)) =>
+        increment(NonEmptyList("docker", List("image", "cache", "cached_image_not_used", dockerImageAsSpecifiedByUser)))
       case _ => // docker image cache not requested and image is not in cache anyway - do nothing
     }
-  }
 
-  override def pollStatusAsync(handle: JesPendingExecutionHandle): Future[RunStatus] = {
+  override def pollStatusAsync(handle: JesPendingExecutionHandle): Future[RunStatus] =
     super[PipelinesApiStatusRequestClient].pollStatus(workflowId, handle.pendingJob)
-  }
 
   override def customPollStatusFailure: PartialFunction[(ExecutionHandle, Exception), ExecutionHandle] = {
-    case (_: JesPendingExecutionHandle@unchecked, JobAbortedException) =>
+    case (_: JesPendingExecutionHandle @unchecked, JobAbortedException) =>
       AbortedExecutionHandle
-    case (oldHandle: JesPendingExecutionHandle@unchecked, e: GoogleJsonResponseException) if e.getStatusCode == 404 =>
+    case (oldHandle: JesPendingExecutionHandle @unchecked, e: GoogleJsonResponseException) if e.getStatusCode == 404 =>
       jobLogger.error(s"JES Job ID ${oldHandle.runInfo.get.job} has not been found, failing call")
       FailedNonRetryableExecutionHandle(e, kvPairsToSave = None)
   }
 
-  override lazy val startMetadataKeyValues: Map[String, Any] = super[PipelinesApiJobCachingActorHelper].startMetadataKeyValues
+  override lazy val startMetadataKeyValues: Map[String, Any] =
+    super[PipelinesApiJobCachingActorHelper].startMetadataKeyValues
 
-  override def getTerminalMetadata(runStatus: RunStatus): Map[String, Any] = {
+  override def getTerminalMetadata(runStatus: RunStatus): Map[String, Any] =
     runStatus match {
       case terminalRunStatus: TerminalRunStatus =>
         Map(
@@ -718,66 +826,61 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
         )
       case unknown => throw new RuntimeException(s"Attempt to get terminal metadata from non terminal status: $unknown")
     }
-  }
 
-  override def mapOutputWomFile(womFile: WomFile): WomFile = {
+  override def mapOutputWomFile(womFile: WomFile): WomFile =
     womFileToGcsPath(generateOutputs(jobDescriptor))(womFile)
-  }
 
-  protected [pipelines] def womFileToGcsPath(jesOutputs: Set[PipelinesApiOutput])(womFile: WomFile): WomFile = {
+  protected[pipelines] def womFileToGcsPath(jesOutputs: Set[PipelinesApiOutput])(womFile: WomFile): WomFile =
     womFile mapFile { path =>
       jesOutputs collectFirst {
         case jesOutput if jesOutput.name == makeSafeReferenceName(path) => jesOutput.cloudPath.pathAsString
       } getOrElse path
     }
-  }
 
-  override def isDone(runStatus: RunStatus): Boolean = {
+  override def isDone(runStatus: RunStatus): Boolean =
     runStatus match {
       case _: RunStatus.Success => true
       case _: RunStatus.UnsuccessfulRunStatus => false
-      case _ => throw new RuntimeException(s"Cromwell programmer blunder: isSuccess was called on an incomplete RunStatus ($runStatus).")
+      case _ =>
+        throw new RuntimeException(
+          s"Cromwell programmer blunder: isSuccess was called on an incomplete RunStatus ($runStatus)."
+        )
     }
-  }
 
-  override def getTerminalEvents(runStatus: RunStatus): Seq[ExecutionEvent] = {
+  override def getTerminalEvents(runStatus: RunStatus): Seq[ExecutionEvent] =
     runStatus match {
       case successStatus: RunStatus.Success => successStatus.eventList
       case unknown =>
         throw new RuntimeException(s"handleExecutionSuccess not called with RunStatus.Success. Instead got $unknown")
     }
-  }
 
-  override def retryEvaluateOutputs(exception: Exception): Boolean = {
+  override def retryEvaluateOutputs(exception: Exception): Boolean =
     exception match {
       case aggregated: CromwellAggregatedException =>
         aggregated.throwables.collectFirst { case s: SocketTimeoutException => s }.isDefined
       case _ => false
     }
-  }
 
   private lazy val standardPaths = jobPaths.standardPaths
 
-  override def handleExecutionFailure(runStatus: RunStatus,
-                                      returnCode: Option[Int]): Future[ExecutionHandle] = {
+  override def handleExecutionFailure(runStatus: RunStatus, returnCode: Option[Int]): Future[ExecutionHandle] = {
 
-    def generateBetterErrorMsg(runStatus: RunStatus.UnsuccessfulRunStatus, errorMsg: String): String = {
-      if (runStatus.errorCode.getCode.value == PapiFailedPreConditionErrorCode
-          && errorMsg.contains("Execution failed")
-          && (errorMsg.contains("Localization") || errorMsg.contains("Delocalization"))) {
+    def generateBetterErrorMsg(runStatus: RunStatus.UnsuccessfulRunStatus, errorMsg: String): String =
+      if (
+        runStatus.errorCode.getCode.value == PapiFailedPreConditionErrorCode
+        && errorMsg.contains("Execution failed")
+        && (errorMsg.contains("Localization") || errorMsg.contains("Delocalization"))
+      ) {
         s"Please check the log file for more details: $jesLogPath."
       }
-      //If error code 10, add some extra messaging to the server logging
+      // If error code 10, add some extra messaging to the server logging
       else if (runStatus.errorCode.getCode.value == PapiMysteriouslyCrashedErrorCode) {
         jobLogger.info(s"Job Failed with Error Code 10 for a machine where Preemptible is set to $preemptible")
         errorMsg
-      }
-      else errorMsg
-    }
+      } else errorMsg
 
     // Inner function: Handles a 'Failed' runStatus (or Preempted if preemptible was false)
-    def handleFailedRunStatus(runStatus: RunStatus.UnsuccessfulRunStatus,
-                              returnCode: Option[Int]): ExecutionHandle = {
+    def handleFailedRunStatus(runStatus: RunStatus.UnsuccessfulRunStatus, returnCode: Option[Int]): ExecutionHandle = {
 
       lazy val prettyError = runStatus.prettyPrintedError
 
@@ -793,10 +896,12 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
           handleUnexpectedTermination(runStatus.errorCode, prettyError, returnCode)
         case _ if isDockerPullFailure =>
           val unable = s"Unable to pull Docker image '$jobDockerImage' "
-          val details = if (hasDockerCredentials)
-            "but Docker credentials are present; is this Docker account authorized to pull the image? " else
-            "and there are effectively no Docker credentials present (one or more of token, authorization, or Google KMS key may be missing). " +
-            "Please check your private Docker configuration and/or the pull access for this image. "
+          val details =
+            if (hasDockerCredentials)
+              "but Docker credentials are present; is this Docker account authorized to pull the image? "
+            else
+              "and there are effectively no Docker credentials present (one or more of token, authorization, or Google KMS key may be missing). " +
+                "Please check your private Docker configuration and/or the pull access for this image. "
           val message = unable + details + prettyError
           FailedNonRetryableExecutionHandle(
             StandardException(runStatus.errorCode, message, jobTag, returnCode, standardPaths.error),
@@ -819,34 +924,43 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
           case preemptedStatus: RunStatus.Preempted if preemptible => handlePreemption(preemptedStatus, returnCode)
           case _: RunStatus.Cancelled => AbortedExecutionHandle
           case failedStatus: RunStatus.UnsuccessfulRunStatus => handleFailedRunStatus(failedStatus, returnCode)
-          case unknown => throw new RuntimeException(s"handleExecutionFailure not called with RunStatus.Failed or RunStatus.Preempted. Instead got $unknown")
+          case unknown =>
+            throw new RuntimeException(
+              s"handleExecutionFailure not called with RunStatus.Failed or RunStatus.Preempted. Instead got $unknown"
+            )
         }
       }
     }
   }
 
-  private def nextAttemptPreemptedAndUnexpectedRetryCountsToKvPairs(p: Int, ur: Int): Seq[KvPair] = {
+  private def nextAttemptPreemptedAndUnexpectedRetryCountsToKvPairs(p: Int, ur: Int): Seq[KvPair] =
     Seq(
-      KvPair(ScopedKey(workflowId, futureKvJobKey, PipelinesApiBackendLifecycleActorFactory.unexpectedRetryCountKey), ur.toString),
-      KvPair(ScopedKey(workflowId, futureKvJobKey, PipelinesApiBackendLifecycleActorFactory.preemptionCountKey), p.toString)
+      KvPair(ScopedKey(workflowId, futureKvJobKey, PipelinesApiBackendLifecycleActorFactory.unexpectedRetryCountKey),
+             ur.toString
+      ),
+      KvPair(ScopedKey(workflowId, futureKvJobKey, PipelinesApiBackendLifecycleActorFactory.preemptionCountKey),
+             p.toString
+      )
     )
-  }
 
-  private def handleUnexpectedTermination(errorCode: Status, errorMessage: String, jobReturnCode: Option[Int]): ExecutionHandle = {
+  private def handleUnexpectedTermination(errorCode: Status,
+                                          errorMessage: String,
+                                          jobReturnCode: Option[Int]
+  ): ExecutionHandle = {
     val msg = s"Retrying. $errorMessage"
     previousRetryReasons match {
       case Valid(PreviousRetryReasons(p, ur)) =>
         val thisUnexpectedRetry = ur + 1
         if (thisUnexpectedRetry <= maxUnexpectedRetries) {
-          val preemptionAndUnexpectedRetryCountsKvPairs = nextAttemptPreemptedAndUnexpectedRetryCountsToKvPairs(p, thisUnexpectedRetry)
+          val preemptionAndUnexpectedRetryCountsKvPairs =
+            nextAttemptPreemptedAndUnexpectedRetryCountsToKvPairs(p, thisUnexpectedRetry)
           // Increment unexpected retry count and preemption count stays the same
           FailedRetryableExecutionHandle(
             StandardException(errorCode, msg, jobTag, jobReturnCode, standardPaths.error),
             jobReturnCode,
             kvPairsToSave = Option(preemptionAndUnexpectedRetryCountsKvPairs)
           )
-        }
-        else {
+        } else {
           FailedNonRetryableExecutionHandle(
             StandardException(errorCode, errorMessage, jobTag, jobReturnCode, standardPaths.error),
             jobReturnCode,
@@ -873,7 +987,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
         val taskName = s"${workflowDescriptor.id}:${call.localName}"
         val baseMsg = s"Task $taskName was preempted for the ${thisPreemption.toOrdinal} time."
 
-        val preemptionAndUnexpectedRetryCountsKvPairs = nextAttemptPreemptedAndUnexpectedRetryCountsToKvPairs(thisPreemption, ur)
+        val preemptionAndUnexpectedRetryCountsKvPairs =
+          nextAttemptPreemptedAndUnexpectedRetryCountsToKvPairs(thisPreemption, ur)
         if (thisPreemption < maxPreemption) {
           // Increment preemption count and unexpectedRetryCount stays the same
           val msg =
@@ -884,12 +999,14 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
             jobReturnCode,
             kvPairsToSave = Option(preemptionAndUnexpectedRetryCountsKvPairs)
           )
-        }
-        else {
+        } else {
           val msg = s"$baseMsg The maximum number of preemptible attempts ($maxPreemption) has been reached. The " +
             s"call will be restarted with a non-preemptible VM. Error code $errorCode.$prettyPrintedError)"
-          FailedRetryableExecutionHandle(StandardException(
-            errorCode, msg, jobTag, jobReturnCode, standardPaths.error), jobReturnCode, kvPairsToSave = Option(preemptionAndUnexpectedRetryCountsKvPairs))
+          FailedRetryableExecutionHandle(
+            StandardException(errorCode, msg, jobTag, jobReturnCode, standardPaths.error),
+            jobReturnCode,
+            kvPairsToSave = Option(preemptionAndUnexpectedRetryCountsKvPairs)
+          )
         }
       case Invalid(_) =>
         FailedNonRetryableExecutionHandle(
@@ -916,7 +1033,7 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
     canSkipLocalize
   }
 
-  override def cloudResolveWomFile(womFile: WomFile): WomFile = {
+  override def cloudResolveWomFile(womFile: WomFile): WomFile =
     womFile.mapFile { value =>
       getPath(value) match {
         case Success(drsPath: DrsPath) => DrsResolver.getSimpleGsUri(drsPath).unsafeRunSync().getOrElse(value)
@@ -924,16 +1041,15 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
         case _ => value
       }
     }
-  }
 
-  override def mapCommandLineWomFile(womFile: WomFile): WomFile = {
+  override def mapCommandLineWomFile(womFile: WomFile): WomFile =
     womFile.mapFile { value =>
       (getPath(value), asAdHocFile(womFile)) match {
         case (Success(gcsPath: GcsPath), Some(adHocFile)) =>
           // Ad hoc files will be placed directly at the root ("/cromwell_root/ad_hoc_file.txt") unlike other input files
           // for which the full path is being propagated ("/cromwell_root/path/to/input_file.txt")
           workingDisk.mountPoint.resolve(adHocFile.alternativeName.getOrElse(gcsPath.name)).pathAsString
-        case (Success(path @ ( _: GcsPath | _: HttpPath)), _) =>
+        case (Success(path @ (_: GcsPath | _: HttpPath)), _) =>
           workingDisk.mountPoint.resolve(path.pathWithoutScheme).pathAsString
         case (Success(drsPath: DrsPath), _) =>
           val filePath = DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
@@ -943,9 +1059,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
         case _ => value
       }
     }
-  }
 
-  override def mapCommandLineJobInputWomFile(womFile: WomFile): WomFile = {
+  override def mapCommandLineJobInputWomFile(womFile: WomFile): WomFile =
     womFile.mapFile(value =>
       getPath(value) match {
         case Success(gcsPath: GcsPath) => workingDisk.mountPoint.resolve(gcsPath.pathWithoutScheme).pathAsString
@@ -955,8 +1070,8 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
         case _ => value
       }
     )
-  }
 
   // No need for Cromwell-performed localization in the PAPI backend, ad hoc values are localized directly from GCS to the VM by PAPI.
-  override lazy val localizeAdHocValues: List[AdHocValue] => ErrorOr[List[StandardAdHocValue]] = _.map(Coproduct[StandardAdHocValue](_)).validNel
+  override lazy val localizeAdHocValues: List[AdHocValue] => ErrorOr[List[StandardAdHocValue]] =
+    _.map(Coproduct[StandardAdHocValue](_)).validNel
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendInitializationData.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendInitializationData.scala
index d8634fcf016..22a298a9738 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendInitializationData.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendInitializationData.scala
@@ -4,8 +4,7 @@ import com.google.auth.Credentials
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory
 import cromwell.backend.standard.{StandardInitializationData, StandardValidatedRuntimeAttributesBuilder}
 
-case class PipelinesApiBackendInitializationData
-(
+case class PipelinesApiBackendInitializationData(
   override val workflowPaths: PipelinesApiWorkflowPaths,
   override val runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder,
   papiConfiguration: PipelinesApiConfiguration,
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactory.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactory.scala
index 91061161ac9..e993985f985 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactory.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactory.scala
@@ -4,9 +4,16 @@ import akka.actor.{ActorRef, Props}
 import com.google.api.client.util.ExponentialBackOff
 import com.typesafe.scalalogging.StrictLogging
 import cromwell.backend._
-import cromwell.backend.google.pipelines.common.PipelinesApiBackendLifecycleActorFactory.{preemptionCountKey, robustBuildAttributes, unexpectedRetryCountKey}
+import cromwell.backend.google.pipelines.common.PipelinesApiBackendLifecycleActorFactory.{
+  preemptionCountKey,
+  robustBuildAttributes,
+  unexpectedRetryCountKey
+}
 import cromwell.backend.google.pipelines.common.authentication.PipelinesApiDockerCredentials
-import cromwell.backend.google.pipelines.common.callcaching.{PipelinesApiBackendCacheHitCopyingActor, PipelinesApiBackendFileHashingActor}
+import cromwell.backend.google.pipelines.common.callcaching.{
+  PipelinesApiBackendCacheHitCopyingActor,
+  PipelinesApiBackendFileHashingActor
+}
 import cromwell.backend.standard._
 import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardFileHashingActor}
 import cromwell.cloudsupport.gcp.GoogleConfiguration
@@ -16,8 +23,10 @@ import wom.graph.CommandCallNode
 
 import scala.util.{Failure, Success, Try}
 
-abstract class PipelinesApiBackendLifecycleActorFactory(override val name: String, override val configurationDescriptor: BackendConfigurationDescriptor)
-  extends StandardLifecycleActorFactory {
+abstract class PipelinesApiBackendLifecycleActorFactory(
+  override val name: String,
+  override val configurationDescriptor: BackendConfigurationDescriptor
+) extends StandardLifecycleActorFactory {
 
   // Abstract members
   protected def requiredBackendSingletonActor(serviceRegistryActor: ActorRef): Props
@@ -34,7 +43,8 @@ abstract class PipelinesApiBackendLifecycleActorFactory(override val name: Strin
     robustBuildAttributes(defaultBuildAttributes)
   }
 
-  override lazy val initializationActorClass: Class[_ <: StandardInitializationActor] = classOf[PipelinesApiInitializationActor]
+  override lazy val initializationActorClass: Class[_ <: StandardInitializationActor] =
+    classOf[PipelinesApiInitializationActor]
 
   override lazy val asyncExecutionActorClass: Class[_ <: StandardAsyncExecutionActor] =
     classOf[PipelinesApiAsyncBackendJobExecutionActor]
@@ -42,36 +52,61 @@ abstract class PipelinesApiBackendLifecycleActorFactory(override val name: Strin
     Option(classOf[PipelinesApiFinalizationActor])
   override lazy val jobIdKey: String = PipelinesApiAsyncBackendJobExecutionActor.JesOperationIdKey
 
-  override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] = Option(requiredBackendSingletonActor(serviceRegistryActor))
-
-  override def workflowInitializationActorParams(workflowDescriptor: BackendWorkflowDescriptor, ioActor: ActorRef, calls: Set[CommandCallNode],
-                                                 serviceRegistryActor: ActorRef, restart: Boolean): StandardInitializationActorParams = {
-    PipelinesApiInitializationActorParams(workflowDescriptor, ioActor, calls, jesConfiguration, serviceRegistryActor, restart)
-  }
-
-  override def workflowFinalizationActorParams(workflowDescriptor: BackendWorkflowDescriptor, ioActor: ActorRef, calls: Set[CommandCallNode],
-                                               jobExecutionMap: JobExecutionMap, workflowOutputs: CallOutputs,
-                                               initializationDataOption: Option[BackendInitializationData]):
-  StandardFinalizationActorParams = {
+  override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] = Option(
+    requiredBackendSingletonActor(serviceRegistryActor)
+  )
+
+  override def workflowInitializationActorParams(workflowDescriptor: BackendWorkflowDescriptor,
+                                                 ioActor: ActorRef,
+                                                 calls: Set[CommandCallNode],
+                                                 serviceRegistryActor: ActorRef,
+                                                 restart: Boolean
+  ): StandardInitializationActorParams =
+    PipelinesApiInitializationActorParams(workflowDescriptor,
+                                          ioActor,
+                                          calls,
+                                          jesConfiguration,
+                                          serviceRegistryActor,
+                                          restart
+    )
+
+  override def workflowFinalizationActorParams(workflowDescriptor: BackendWorkflowDescriptor,
+                                               ioActor: ActorRef,
+                                               calls: Set[CommandCallNode],
+                                               jobExecutionMap: JobExecutionMap,
+                                               workflowOutputs: CallOutputs,
+                                               initializationDataOption: Option[BackendInitializationData]
+  ): StandardFinalizationActorParams =
     // The `PipelinesApiInitializationActor` will only return a non-`Empty` `PipelinesApiBackendInitializationData` from a successful `beforeAll`
     // invocation.  HOWEVER, the finalization actor is created regardless of whether workflow initialization was successful
     // or not.  So the finalization actor must be able to handle an empty `PipelinesApiBackendInitializationData` option, and there is no
     // `.get` on the initialization data as there is with the execution or cache hit copying actor methods.
-    PipelinesApiFinalizationActorParams(workflowDescriptor, ioActor, calls, jesConfiguration, jobExecutionMap, workflowOutputs,
-      initializationDataOption)
-  }
-
-  override lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] = {
+    PipelinesApiFinalizationActorParams(workflowDescriptor,
+                                        ioActor,
+                                        calls,
+                                        jesConfiguration,
+                                        jobExecutionMap,
+                                        workflowOutputs,
+                                        initializationDataOption
+    )
+
+  override lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] =
     Option(classOf[PipelinesApiBackendCacheHitCopyingActor])
-  }
 
-  override lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(classOf[PipelinesApiBackendFileHashingActor])
+  override lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(
+    classOf[PipelinesApiBackendFileHashingActor]
+  )
 
-  override def dockerHashCredentials(workflowDescriptor: BackendWorkflowDescriptor, initializationData: Option[BackendInitializationData]): List[Any] = {
+  override def dockerHashCredentials(workflowDescriptor: BackendWorkflowDescriptor,
+                                     initializationData: Option[BackendInitializationData]
+  ): List[Any] =
     Try(BackendInitializationData.as[PipelinesApiBackendInitializationData](initializationData)) match {
       case Success(papiData) =>
-        val tokenFromWorkflowOptions = workflowDescriptor.workflowOptions.get(GoogleAuthMode.DockerCredentialsTokenKey).toOption
-        val effectiveToken = tokenFromWorkflowOptions.orElse(papiData.papiConfiguration.dockerCredentials map { _.token })
+        val tokenFromWorkflowOptions =
+          workflowDescriptor.workflowOptions.get(GoogleAuthMode.DockerCredentialsTokenKey).toOption
+        val effectiveToken = tokenFromWorkflowOptions.orElse(papiData.papiConfiguration.dockerCredentials map {
+          _.token
+        })
 
         val dockerCredentials: Option[PipelinesApiDockerCredentials] = effectiveToken map { token =>
           // These credentials are being returned for hashing and all that matters in this context is the token
@@ -83,19 +118,19 @@ abstract class PipelinesApiBackendLifecycleActorFactory(override val name: Strin
         List(dockerCredentials, googleCredentials).flatten
       case _ => List.empty[Any]
     }
-  }
 }
 
 object PipelinesApiBackendLifecycleActorFactory extends StrictLogging {
   val preemptionCountKey = "PreemptionCount"
   val unexpectedRetryCountKey = "UnexpectedRetryCount"
 
-  private [common] def robustBuildAttributes(buildAttributes: () => PipelinesApiConfigurationAttributes,
-                                             maxAttempts: Int = 3,
-                                             initialIntervalMillis: Int = 5000,
-                                             maxIntervalMillis: Int = 10000,
-                                             multiplier: Double = 1.5,
-                                             randomizationFactor: Double = 0.5): PipelinesApiConfigurationAttributes = {
+  private[common] def robustBuildAttributes(buildAttributes: () => PipelinesApiConfigurationAttributes,
+                                            maxAttempts: Int = 3,
+                                            initialIntervalMillis: Int = 5000,
+                                            maxIntervalMillis: Int = 10000,
+                                            multiplier: Double = 1.5,
+                                            randomizationFactor: Double = 0.5
+  ): PipelinesApiConfigurationAttributes = {
     val backoff = new ExponentialBackOff.Builder()
       .setInitialIntervalMillis(initialIntervalMillis)
       .setMaxIntervalMillis(maxIntervalMillis)
@@ -104,18 +139,26 @@ object PipelinesApiBackendLifecycleActorFactory extends StrictLogging {
       .build()
 
     // `attempt` is 1-based
-    def build(attempt: Int): Try[PipelinesApiConfigurationAttributes] = {
+    def build(attempt: Int): Try[PipelinesApiConfigurationAttributes] =
       Try {
         buildAttributes()
       } recoverWith {
         // Try again if this was an Exception (as opposed to an Error) and we have not hit maxAttempts
         case ex: Exception if attempt < maxAttempts =>
-          logger.warn(s"Failed to build PipelinesApiConfigurationAttributes on attempt $attempt of $maxAttempts, retrying.", ex)
+          logger.warn(
+            s"Failed to build PipelinesApiConfigurationAttributes on attempt $attempt of $maxAttempts, retrying.",
+            ex
+          )
           Thread.sleep(backoff.nextBackOffMillis())
           build(attempt + 1)
-        case e => Failure(new RuntimeException(s"Failed to build PipelinesApiConfigurationAttributes on attempt $attempt of $maxAttempts", e))
+        case e =>
+          Failure(
+            new RuntimeException(
+              s"Failed to build PipelinesApiConfigurationAttributes on attempt $attempt of $maxAttempts",
+              e
+            )
+          )
       }
-    }
     // This intentionally throws if the final result of `build` is a `Failure`.
     build(attempt = 1).get
   }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendSingletonActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendSingletonActor.scala
index 468e5006cf7..2e5bcccb0a8 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendSingletonActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendSingletonActor.scala
@@ -9,10 +9,17 @@ import cromwell.core.Mailbox
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
 
-final class PipelinesApiBackendSingletonActor(qps: Int Refined Positive, requestWorkers: Int Refined Positive, serviceRegistryActor: ActorRef)
-                                                  (implicit batchHandler: PipelinesApiRequestHandler) extends Actor with ActorLogging {
+final class PipelinesApiBackendSingletonActor(qps: Int Refined Positive,
+                                              requestWorkers: Int Refined Positive,
+                                              serviceRegistryActor: ActorRef
+)(implicit batchHandler: PipelinesApiRequestHandler)
+    extends Actor
+    with ActorLogging {
 
-  val jesApiQueryManager = context.actorOf(PipelinesApiRequestManager.props(qps, requestWorkers, serviceRegistryActor).withMailbox(Mailbox.PriorityMailbox), "PAPIQueryManager")
+  val jesApiQueryManager = context.actorOf(
+    PipelinesApiRequestManager.props(qps, requestWorkers, serviceRegistryActor).withMailbox(Mailbox.PriorityMailbox),
+    "PAPIQueryManager"
+  )
 
   override def receive = {
     case abort: BackendSingletonActorAbortWorkflow => jesApiQueryManager.forward(abort)
@@ -23,6 +30,8 @@ final class PipelinesApiBackendSingletonActor(qps: Int Refined Positive, request
 }
 
 object PipelinesApiBackendSingletonActor {
-  def props[O](qps: Int Refined Positive, requestWorkers: Int Refined Positive, serviceRegistryActor: ActorRef)
-              (implicit batchHandler: PipelinesApiRequestHandler): Props = Props(new PipelinesApiBackendSingletonActor(qps, requestWorkers, serviceRegistryActor)).withDispatcher(BackendDispatcher)
+  def props[O](qps: Int Refined Positive, requestWorkers: Int Refined Positive, serviceRegistryActor: ActorRef)(implicit
+    batchHandler: PipelinesApiRequestHandler
+  ): Props = Props(new PipelinesApiBackendSingletonActor(qps, requestWorkers, serviceRegistryActor))
+    .withDispatcher(BackendDispatcher)
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfiguration.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfiguration.scala
index 2b380143441..f279728d102 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfiguration.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfiguration.scala
@@ -14,23 +14,24 @@ import scala.concurrent.duration.FiniteDuration
 class PipelinesApiConfiguration(val configurationDescriptor: BackendConfigurationDescriptor,
                                 val genomicsFactory: PipelinesApiFactoryInterface,
                                 val googleConfig: GoogleConfiguration,
-                                val papiAttributes: PipelinesApiConfigurationAttributes) extends DefaultJsonProtocol {
+                                val papiAttributes: PipelinesApiConfigurationAttributes
+) extends DefaultJsonProtocol {
 
   val jesAuths: PipelinesApiAuths = papiAttributes.auths
   val root: String = configurationDescriptor.backendConfig.getString("root")
   val pipelineTimeout: FiniteDuration = papiAttributes.pipelineTimeout
   val runtimeConfig: Option[Config] = configurationDescriptor.backendRuntimeAttributesConfig
 
-  val dockerCredentials: Option[PipelinesApiDockerCredentials] = {
+  val dockerCredentials: Option[PipelinesApiDockerCredentials] =
     BackendDockerConfiguration.build(configurationDescriptor.backendConfig).dockerCredentials map { creds =>
       PipelinesApiDockerCredentials.apply(creds, googleConfig)
     }
-  }
 
   val dockerEncryptionKeyName: Option[String] = dockerCredentials flatMap { _.keyName }
   val dockerEncryptionAuthName: Option[String] = dockerCredentials flatMap { _.authName }
   val dockerToken: Option[String] = dockerCredentials map { _.token }
 
-  val jobShell: String = configurationDescriptor.backendConfig.as[Option[String]]("job-shell").getOrElse(
-    configurationDescriptor.globalConfig.getOrElse("system.job-shell", "/bin/bash"))
+  val jobShell: String = configurationDescriptor.backendConfig
+    .as[Option[String]]("job-shell")
+    .getOrElse(configurationDescriptor.globalConfig.getOrElse("system.job-shell", "/bin/bash"))
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationAttributes.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationAttributes.scala
index adfaa54c1d5..9f279c4350c 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationAttributes.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationAttributes.scala
@@ -9,9 +9,17 @@ import common.exception.MessageAggregation
 import common.validation.ErrorOr._
 import common.validation.Validation._
 import cromwell.backend.CommonBackendConfigurationAttributes
-import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.{BatchRequestTimeoutConfiguration, GcsTransferConfiguration, VirtualPrivateCloudConfiguration}
+import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.{
+  BatchRequestTimeoutConfiguration,
+  GcsTransferConfiguration,
+  VirtualPrivateCloudConfiguration
+}
 import cromwell.backend.google.pipelines.common.authentication.PipelinesApiAuths
-import cromwell.backend.google.pipelines.common.callcaching.{CopyCachedOutputs, PipelinesCacheHitDuplicationStrategy, UseOriginalCachedOutputs}
+import cromwell.backend.google.pipelines.common.callcaching.{
+  CopyCachedOutputs,
+  PipelinesCacheHitDuplicationStrategy,
+  UseOriginalCachedOutputs
+}
 import cromwell.backend.google.pipelines.common.io.PipelinesApiReferenceFilesDisk
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
@@ -29,30 +37,31 @@ import scala.concurrent.duration._
 import scala.util.matching.Regex
 import scala.util.{Failure, Success, Try}
 
-case class PipelinesApiConfigurationAttributes(project: String,
-                                               computeServiceAccount: String,
-                                               auths: PipelinesApiAuths,
-                                               restrictMetadataAccess: Boolean,
-                                               enableFuse: Boolean,
-                                               executionBucket: String,
-                                               endpointUrl: URL,
-                                               location: String,
-                                               maxPollingInterval: Int,
-                                               qps: Int Refined Positive,
-                                               cacheHitDuplicationStrategy: PipelinesCacheHitDuplicationStrategy,
-                                               requestWorkers: Int Refined Positive,
-                                               pipelineTimeout: FiniteDuration,
-                                               logFlushPeriod: Option[FiniteDuration],
-                                               gcsTransferConfiguration: GcsTransferConfiguration,
-                                               virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
-                                               batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration,
-                                               referenceFileToDiskImageMappingOpt: Option[Map[String, PipelinesApiReferenceFilesDisk]],
-                                               dockerImageToCacheDiskImageMappingOpt: Option[Map[String, DockerImageCacheEntry]],
-                                               checkpointingInterval: FiniteDuration
-                                              )
+case class PipelinesApiConfigurationAttributes(
+  project: String,
+  computeServiceAccount: String,
+  auths: PipelinesApiAuths,
+  restrictMetadataAccess: Boolean,
+  enableFuse: Boolean,
+  executionBucket: String,
+  endpointUrl: URL,
+  location: String,
+  maxPollingInterval: Int,
+  qps: Int Refined Positive,
+  cacheHitDuplicationStrategy: PipelinesCacheHitDuplicationStrategy,
+  requestWorkers: Int Refined Positive,
+  pipelineTimeout: FiniteDuration,
+  logFlushPeriod: Option[FiniteDuration],
+  gcsTransferConfiguration: GcsTransferConfiguration,
+  virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
+  batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration,
+  referenceFileToDiskImageMappingOpt: Option[Map[String, PipelinesApiReferenceFilesDisk]],
+  dockerImageToCacheDiskImageMappingOpt: Option[Map[String, DockerImageCacheEntry]],
+  checkpointingInterval: FiniteDuration
+)
 
 object PipelinesApiConfigurationAttributes
-  extends PipelinesApiDockerCacheMappingOperations
+    extends PipelinesApiDockerCacheMappingOperations
     with PipelinesApiReferenceFilesMappingOperations
     with StrictLogging {
 
@@ -64,10 +73,11 @@ object PipelinesApiConfigurationAttributes
   final case class VirtualPrivateCloudLabels(network: String, subnetwork: Option[String], auth: GoogleAuthMode)
   final case class VirtualPrivateCloudLiterals(network: String, subnetwork: Option[String])
   final case class VirtualPrivateCloudConfiguration(labelsOption: Option[VirtualPrivateCloudLabels],
-                                                    literalsOption: Option[VirtualPrivateCloudLiterals],
-                                                   )
-  final case class BatchRequestTimeoutConfiguration(readTimeoutMillis: Option[Int Refined Positive], connectTimeoutMillis: Option[Int Refined Positive])
-
+                                                    literalsOption: Option[VirtualPrivateCloudLiterals]
+  )
+  final case class BatchRequestTimeoutConfiguration(readTimeoutMillis: Option[Int Refined Positive],
+                                                    connectTimeoutMillis: Option[Int Refined Positive]
+  )
 
   lazy val Logger: Logger = LoggerFactory.getLogger("PipelinesApiConfiguration")
 
@@ -119,43 +129,47 @@ object PipelinesApiConfigurationAttributes
     "genomics.default-zones" -> "default-runtime-attributes.zones"
   )
 
-  def apply(googleConfig: GoogleConfiguration, backendConfig: Config, backendName: String): PipelinesApiConfigurationAttributes = {
+  def apply(googleConfig: GoogleConfiguration,
+            backendConfig: Config,
+            backendName: String
+  ): PipelinesApiConfigurationAttributes = {
 
-    def vpcErrorMessage(missingKeys: List[String]) = s"Virtual Private Cloud configuration is invalid. Missing keys: `${missingKeys.mkString(",")}`.".invalidNel
+    def vpcErrorMessage(missingKeys: List[String]) =
+      s"Virtual Private Cloud configuration is invalid. Missing keys: `${missingKeys.mkString(",")}`.".invalidNel
 
     def validateVPCLabelsConfig(networkOption: Option[String],
                                 subnetworkOption: Option[String],
-                                authOption: Option[String],
-                               ): ErrorOr[Option[VirtualPrivateCloudLabels]] = {
+                                authOption: Option[String]
+    ): ErrorOr[Option[VirtualPrivateCloudLabels]] =
       (networkOption, subnetworkOption, authOption) match {
-        case (Some(network), _, Some(auth)) => googleConfig.auth(auth) match {
-          case Valid(validAuth) =>
-            Option(VirtualPrivateCloudLabels(network, subnetworkOption, validAuth)).validNel
-          case Invalid(error) => s"Auth $auth is not valid for Virtual Private Cloud configuration. Reason: $error" .invalidNel
-        }
+        case (Some(network), _, Some(auth)) =>
+          googleConfig.auth(auth) match {
+            case Valid(validAuth) =>
+              Option(VirtualPrivateCloudLabels(network, subnetworkOption, validAuth)).validNel
+            case Invalid(error) =>
+              s"Auth $auth is not valid for Virtual Private Cloud configuration. Reason: $error".invalidNel
+          }
         case (Some(_), _, None) => vpcErrorMessage(List("auth"))
         case (None, _, Some(_)) => vpcErrorMessage(List("network-label-key"))
         case (None, Some(_), None) => vpcErrorMessage(List("network-label-key", "auth"))
         case (None, None, None) => None.validNel
       }
-    }
 
     def validateVPCLiteralsConfig(networkNameOption: Option[String],
-                                  subnetworkNameOption: Option[String],
-                                 ): ErrorOr[Option[VirtualPrivateCloudLiterals]] = {
+                                  subnetworkNameOption: Option[String]
+    ): ErrorOr[Option[VirtualPrivateCloudLiterals]] =
       (networkNameOption, subnetworkNameOption) match {
         case (None, Some(_)) => vpcErrorMessage(List("network-name"))
         case (Some(networkName), _) => Option(VirtualPrivateCloudLiterals(networkName, subnetworkNameOption)).valid
         case (None, None) => None.valid
       }
-    }
 
     def validateVPCConfig(networkNameOption: Option[String],
                           subnetworkNameOption: Option[String],
                           networkLabelOption: Option[String],
                           subnetworkLabelOption: Option[String],
-                          authOption: Option[String],
-                         ): ErrorOr[VirtualPrivateCloudConfiguration] = {
+                          authOption: Option[String]
+    ): ErrorOr[VirtualPrivateCloudConfiguration] = {
       val vpcLabelsValidation =
         validateVPCLabelsConfig(networkLabelOption, subnetworkLabelOption, authOption)
       val vpcLiteralsValidation =
@@ -163,33 +177,49 @@ object PipelinesApiConfigurationAttributes
       (vpcLabelsValidation, vpcLiteralsValidation) mapN VirtualPrivateCloudConfiguration
     }
 
-    val configKeys = backendConfig.entrySet().asScala.toSet map { entry: java.util.Map.Entry[String, ConfigValue] => entry.getKey }
+    val configKeys = backendConfig.entrySet().asScala.toSet map { entry: java.util.Map.Entry[String, ConfigValue] =>
+      entry.getKey
+    }
     warnNotRecognized(configKeys, papiKeys, backendName, Logger)
 
     def warnDeprecated(keys: Set[String], deprecated: Map[String, String], context: String, logger: Logger): Unit = {
       val deprecatedKeys = keys.intersect(deprecated.keySet)
-      deprecatedKeys foreach { key => logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}") }
+      deprecatedKeys foreach { key =>
+        logger.warn(s"Found deprecated configuration key $key, replaced with ${deprecated.get(key)}")
+      }
     }
 
     warnDeprecated(configKeys, deprecatedJesKeys, backendName, Logger)
 
-    val project: ErrorOr[String] = validate { backendConfig.as[String]("project") }
-    val executionBucket: ErrorOr[String] = validate { backendConfig.as[String]("root") }
-    val endpointUrl: ErrorOr[URL] = validate { backendConfig.as[URL]("genomics.endpoint-url") }
-    val location: ErrorOr[String] = validateGenomicsLocation(endpointUrl, backendConfig.as[Option[String]]("genomics.location"))
+    val project: ErrorOr[String] = validate(backendConfig.as[String]("project"))
+    val executionBucket: ErrorOr[String] = validate(backendConfig.as[String]("root"))
+    val endpointUrl: ErrorOr[URL] = validate(backendConfig.as[URL]("genomics.endpoint-url"))
+    val location: ErrorOr[String] =
+      validateGenomicsLocation(endpointUrl, backendConfig.as[Option[String]]("genomics.location"))
     val maxPollingInterval: Int = backendConfig.as[Option[Int]]("maximum-polling-interval").getOrElse(600)
-    val computeServiceAccount: String = backendConfig.as[Option[String]]("genomics.compute-service-account").getOrElse("default")
-    val genomicsAuthName: ErrorOr[String] = validate { backendConfig.as[String]("genomics.auth") }
-    val genomicsRestrictMetadataAccess: ErrorOr[Boolean] = validate { backendConfig.as[Option[Boolean]]("genomics.restrict-metadata-access").getOrElse(false) }
-    val genomicsEnableFuse: ErrorOr[Boolean] = validate { backendConfig.as[Option[Boolean]]("genomics.enable-fuse").getOrElse(false) }
-    val gcsFilesystemAuthName: ErrorOr[String] = validate { backendConfig.as[String]("filesystems.gcs.auth") }
+    val computeServiceAccount: String =
+      backendConfig.as[Option[String]]("genomics.compute-service-account").getOrElse("default")
+    val genomicsAuthName: ErrorOr[String] = validate(backendConfig.as[String]("genomics.auth"))
+    val genomicsRestrictMetadataAccess: ErrorOr[Boolean] = validate {
+      backendConfig.as[Option[Boolean]]("genomics.restrict-metadata-access").getOrElse(false)
+    }
+    val genomicsEnableFuse: ErrorOr[Boolean] = validate {
+      backendConfig.as[Option[Boolean]]("genomics.enable-fuse").getOrElse(false)
+    }
+    val gcsFilesystemAuthName: ErrorOr[String] = validate(backendConfig.as[String]("filesystems.gcs.auth"))
     val qpsValidation = validateQps(backendConfig)
-    val duplicationStrategy = validate { backendConfig.as[Option[String]]("filesystems.gcs.caching.duplication-strategy").getOrElse("copy") match {
-      case "copy" => CopyCachedOutputs
-      case "reference" => UseOriginalCachedOutputs
-      case other => throw new IllegalArgumentException(s"Unrecognized caching duplication strategy: $other. Supported strategies are copy and reference. See reference.conf for more details.")
-    } }
-    val requestWorkers: ErrorOr[Int Refined Positive] = validatePositiveInt(backendConfig.as[Option[Int]]("request-workers").getOrElse(3), "request-workers")
+    val duplicationStrategy = validate {
+      backendConfig.as[Option[String]]("filesystems.gcs.caching.duplication-strategy").getOrElse("copy") match {
+        case "copy" => CopyCachedOutputs
+        case "reference" => UseOriginalCachedOutputs
+        case other =>
+          throw new IllegalArgumentException(
+            s"Unrecognized caching duplication strategy: $other. Supported strategies are copy and reference. See reference.conf for more details."
+          )
+      }
+    }
+    val requestWorkers: ErrorOr[Int Refined Positive] =
+      validatePositiveInt(backendConfig.as[Option[Int]]("request-workers").getOrElse(3), "request-workers")
 
     val pipelineTimeout: FiniteDuration = backendConfig.getOrElse("pipeline-timeout", 7.days)
 
@@ -201,9 +231,11 @@ object PipelinesApiConfigurationAttributes
       case None => Option(1.minute)
     }
 
-    val parallelCompositeUploadThreshold = validateGsutilMemorySpecification(backendConfig, "genomics.parallel-composite-upload-threshold")
+    val parallelCompositeUploadThreshold =
+      validateGsutilMemorySpecification(backendConfig, "genomics.parallel-composite-upload-threshold")
 
-    val localizationAttempts: ErrorOr[Int Refined Positive] = backendConfig.as[Option[Int]]("genomics.localization-attempts")
+    val localizationAttempts: ErrorOr[Int Refined Positive] = backendConfig
+      .as[Option[Int]]("genomics.localization-attempts")
       .map(attempts => validatePositiveInt(attempts, "genomics.localization-attempts"))
       .getOrElse(DefaultGcsTransferAttempts.validNel)
 
@@ -216,91 +248,101 @@ object PipelinesApiConfigurationAttributes
     val vpcSubnetworkName: ErrorOr[Option[String]] = validate {
       backendConfig.getAs[String]("virtual-private-cloud.subnetwork-name")
     }
-    val vpcNetworkLabel: ErrorOr[Option[String]] = validate { backendConfig.getAs[String]("virtual-private-cloud.network-label-key") }
-    val vpcSubnetworkLabel: ErrorOr[Option[String]] = validate { backendConfig.getAs[String]("virtual-private-cloud.subnetwork-label-key") }
-    val vpcAuth: ErrorOr[Option[String]] = validate { backendConfig.getAs[String]("virtual-private-cloud.auth")}
+    val vpcNetworkLabel: ErrorOr[Option[String]] = validate {
+      backendConfig.getAs[String]("virtual-private-cloud.network-label-key")
+    }
+    val vpcSubnetworkLabel: ErrorOr[Option[String]] = validate {
+      backendConfig.getAs[String]("virtual-private-cloud.subnetwork-label-key")
+    }
+    val vpcAuth: ErrorOr[Option[String]] = validate(backendConfig.getAs[String]("virtual-private-cloud.auth"))
 
-    val virtualPrivateCloudConfiguration: ErrorOr[VirtualPrivateCloudConfiguration] = {
+    val virtualPrivateCloudConfiguration: ErrorOr[VirtualPrivateCloudConfiguration] =
       (vpcNetworkName, vpcSubnetworkName, vpcNetworkLabel, vpcSubnetworkLabel, vpcAuth) flatMapN validateVPCConfig
-    }
 
-    val batchRequestsReadTimeout = readOptionalPositiveMillisecondsIntFromDuration(backendConfig, "batch-requests.timeouts.read")
-    val batchRequestsConnectTimeout = readOptionalPositiveMillisecondsIntFromDuration(backendConfig, "batch-requests.timeouts.connect")
+    val batchRequestsReadTimeout =
+      readOptionalPositiveMillisecondsIntFromDuration(backendConfig, "batch-requests.timeouts.read")
+    val batchRequestsConnectTimeout =
+      readOptionalPositiveMillisecondsIntFromDuration(backendConfig, "batch-requests.timeouts.connect")
 
-    val batchRequestTimeoutConfigurationValidation = (batchRequestsReadTimeout, batchRequestsConnectTimeout) mapN { (read, connect) =>
-      BatchRequestTimeoutConfiguration(readTimeoutMillis = read, connectTimeoutMillis = connect)
+    val batchRequestTimeoutConfigurationValidation = (batchRequestsReadTimeout, batchRequestsConnectTimeout) mapN {
+      (read, connect) =>
+        BatchRequestTimeoutConfiguration(readTimeoutMillis = read, connectTimeoutMillis = connect)
     }
 
-    val referenceDiskLocalizationManifestFiles: ErrorOr[Option[List[ManifestFile]]] = validateReferenceDiskManifestConfigs(backendConfig, backendName)
+    val referenceDiskLocalizationManifestFiles: ErrorOr[Option[List[ManifestFile]]] =
+      validateReferenceDiskManifestConfigs(backendConfig, backendName)
 
-    val dockerImageCacheManifestFile: ErrorOr[Option[ValidFullGcsPath]] = validateGcsPathToDockerImageCacheManifestFile(backendConfig)
+    val dockerImageCacheManifestFile: ErrorOr[Option[ValidFullGcsPath]] = validateGcsPathToDockerImageCacheManifestFile(
+      backendConfig
+    )
 
     val checkpointingInterval: FiniteDuration = backendConfig.getOrElse(checkpointingIntervalKey, 10.minutes)
 
-    def authGoogleConfigForPapiConfigurationAttributes(project: String,
-                                                       bucket: String,
-                                                       endpointUrl: URL,
-                                                       genomicsName: String,
-                                                       location: String,
-                                                       restrictMetadata: Boolean,
-                                                       enableFuse: Boolean,
-                                                       gcsName: String,
-                                                       qps: Int Refined Positive,
-                                                       cacheHitDuplicationStrategy: PipelinesCacheHitDuplicationStrategy,
-                                                       requestWorkers: Int Refined Positive,
-                                                       gcsTransferConfiguration: GcsTransferConfiguration,
-                                                       virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
-                                                       batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration,
-                                                       referenceDiskLocalizationManifestFilesOpt: Option[List[ManifestFile]],
-                                                       dockerImageCacheManifestFileOpt: Option[ValidFullGcsPath]): ErrorOr[PipelinesApiConfigurationAttributes] =
-      (googleConfig.auth(genomicsName), googleConfig.auth(gcsName)) mapN {
-        (genomicsAuth, gcsAuth) =>
-          val generatedReferenceFilesMappingOpt = referenceDiskLocalizationManifestFilesOpt map {
-            generateReferenceFilesMapping(genomicsAuth, _)
-          }
-          val dockerImageToCacheDiskImageMappingOpt = dockerImageCacheManifestFileOpt map {
-            generateDockerImageToDiskImageMapping(genomicsAuth, _)
-          }
-          PipelinesApiConfigurationAttributes(
-            project = project,
-            computeServiceAccount = computeServiceAccount,
-            auths = PipelinesApiAuths(genomicsAuth, gcsAuth),
-            restrictMetadataAccess = restrictMetadata,
-            enableFuse = enableFuse,
-            executionBucket = bucket,
-            endpointUrl = endpointUrl,
-            location = location,
-            maxPollingInterval = maxPollingInterval,
-            qps = qps,
-            cacheHitDuplicationStrategy = cacheHitDuplicationStrategy,
-            requestWorkers = requestWorkers,
-            pipelineTimeout = pipelineTimeout,
-            logFlushPeriod = logFlushPeriod,
-            gcsTransferConfiguration = gcsTransferConfiguration,
-            virtualPrivateCloudConfiguration = virtualPrivateCloudConfiguration,
-            batchRequestTimeoutConfiguration = batchRequestTimeoutConfiguration,
-            referenceFileToDiskImageMappingOpt = generatedReferenceFilesMappingOpt,
-            dockerImageToCacheDiskImageMappingOpt = dockerImageToCacheDiskImageMappingOpt,
-            checkpointingInterval = checkpointingInterval
-          )
-    }
+    def authGoogleConfigForPapiConfigurationAttributes(
+      project: String,
+      bucket: String,
+      endpointUrl: URL,
+      genomicsName: String,
+      location: String,
+      restrictMetadata: Boolean,
+      enableFuse: Boolean,
+      gcsName: String,
+      qps: Int Refined Positive,
+      cacheHitDuplicationStrategy: PipelinesCacheHitDuplicationStrategy,
+      requestWorkers: Int Refined Positive,
+      gcsTransferConfiguration: GcsTransferConfiguration,
+      virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
+      batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration,
+      referenceDiskLocalizationManifestFilesOpt: Option[List[ManifestFile]],
+      dockerImageCacheManifestFileOpt: Option[ValidFullGcsPath]
+    ): ErrorOr[PipelinesApiConfigurationAttributes] =
+      (googleConfig.auth(genomicsName), googleConfig.auth(gcsName)) mapN { (genomicsAuth, gcsAuth) =>
+        val generatedReferenceFilesMappingOpt = referenceDiskLocalizationManifestFilesOpt map {
+          generateReferenceFilesMapping(genomicsAuth, _)
+        }
+        val dockerImageToCacheDiskImageMappingOpt = dockerImageCacheManifestFileOpt map {
+          generateDockerImageToDiskImageMapping(genomicsAuth, _)
+        }
+        PipelinesApiConfigurationAttributes(
+          project = project,
+          computeServiceAccount = computeServiceAccount,
+          auths = PipelinesApiAuths(genomicsAuth, gcsAuth),
+          restrictMetadataAccess = restrictMetadata,
+          enableFuse = enableFuse,
+          executionBucket = bucket,
+          endpointUrl = endpointUrl,
+          location = location,
+          maxPollingInterval = maxPollingInterval,
+          qps = qps,
+          cacheHitDuplicationStrategy = cacheHitDuplicationStrategy,
+          requestWorkers = requestWorkers,
+          pipelineTimeout = pipelineTimeout,
+          logFlushPeriod = logFlushPeriod,
+          gcsTransferConfiguration = gcsTransferConfiguration,
+          virtualPrivateCloudConfiguration = virtualPrivateCloudConfiguration,
+          batchRequestTimeoutConfiguration = batchRequestTimeoutConfiguration,
+          referenceFileToDiskImageMappingOpt = generatedReferenceFilesMappingOpt,
+          dockerImageToCacheDiskImageMappingOpt = dockerImageToCacheDiskImageMappingOpt,
+          checkpointingInterval = checkpointingInterval
+        )
+      }
 
     (project,
-      executionBucket,
-      endpointUrl,
-      genomicsAuthName,
-      location,
-      genomicsRestrictMetadataAccess,
-      genomicsEnableFuse,
-      gcsFilesystemAuthName,
-      qpsValidation,
-      duplicationStrategy,
-      requestWorkers,
-      gcsTransferConfiguration,
-      virtualPrivateCloudConfiguration,
-      batchRequestTimeoutConfigurationValidation,
-      referenceDiskLocalizationManifestFiles,
-      dockerImageCacheManifestFile
+     executionBucket,
+     endpointUrl,
+     genomicsAuthName,
+     location,
+     genomicsRestrictMetadataAccess,
+     genomicsEnableFuse,
+     gcsFilesystemAuthName,
+     qpsValidation,
+     duplicationStrategy,
+     requestWorkers,
+     gcsTransferConfiguration,
+     virtualPrivateCloudConfiguration,
+     batchRequestTimeoutConfigurationValidation,
+     referenceDiskLocalizationManifestFiles,
+     dockerImageCacheManifestFile
     ) flatMapN authGoogleConfigForPapiConfigurationAttributes match {
       case Valid(r) => r
       case Invalid(f) =>
@@ -311,25 +353,27 @@ object PipelinesApiConfigurationAttributes
     }
   }
 
-  private def validateSingleGcsPath(gcsPath: String): ErrorOr[ValidFullGcsPath] = {
+  private def validateSingleGcsPath(gcsPath: String): ErrorOr[ValidFullGcsPath] =
     GcsPathBuilder.validateGcsPath(gcsPath) match {
       case validPath: ValidFullGcsPath => validPath.validNel
       case invalidPath => s"Invalid GCS path: $invalidPath".invalidNel
     }
-  }
 
-  private [common] def validateGcsPathToDockerImageCacheManifestFile(backendConfig: Config): ErrorOr[Option[ValidFullGcsPath]] = {
+  private[common] def validateGcsPathToDockerImageCacheManifestFile(
+    backendConfig: Config
+  ): ErrorOr[Option[ValidFullGcsPath]] =
     backendConfig.getAs[String]("docker-image-cache-manifest-file") match {
       case Some(gcsPath) => validateSingleGcsPath(gcsPath).map(Option.apply)
       case None => None.validNel
     }
-  }
 
   /**
     * Validate that the entries corresponding to "reference-disk-localization-manifests" in the specified
     * backend are parseable as `ManifestFile`s.
     */
-  private [common] def validateReferenceDiskManifestConfigs(backendConfig: Config, backendName: String): ErrorOr[Option[List[ManifestFile]]] = {
+  private[common] def validateReferenceDiskManifestConfigs(backendConfig: Config,
+                                                           backendName: String
+  ): ErrorOr[Option[List[ManifestFile]]] =
     Try(backendConfig.getAs[List[Config]]("reference-disk-localization-manifests")) match {
       case Failure(e) =>
         ("Error attempting to parse value for 'reference-disk-localization-manifests' as List[Config]: " +
@@ -344,10 +388,13 @@ object PipelinesApiConfigurationAttributes
             // equivalent using clunkier syntax:
             configs traverse parser.decode[ManifestFile] match {
               case Right(manifests) =>
-                logger.info(s"Reference disks feature for $backendName backend is configured with the following reference images: ${manifests.map(_.imageIdentifier).mkString(", ")}.")
+                logger.info(
+                  s"Reference disks feature for $backendName backend is configured with the following reference images: ${manifests.map(_.imageIdentifier).mkString(", ")}."
+                )
                 Option(manifests).validNel
               case Left(err) =>
-                val message = s"Reference disks misconfigured for backend $backendName, could not parse as List[ManifestFile]"
+                val message =
+                  s"Reference disks misconfigured for backend $backendName, could not parse as List[ManifestFile]"
                 logger.error(message, err.getCause)
                 s"$message: ${err.getMessage}".invalidNel
             }
@@ -356,7 +403,6 @@ object PipelinesApiConfigurationAttributes
             None.validNel
         }
     }
-  }
 
   def validateQps(config: Config): ErrorOr[Int Refined Positive] = {
     import eu.timepit.refined._
@@ -365,12 +411,13 @@ object PipelinesApiConfigurationAttributes
     val qpsCandidate = qp100s / 100
 
     refineV[Positive](qpsCandidate) match {
-      case Left(_) => s"Calculated QPS for Google Genomics API ($qpsCandidate/s) was not a positive integer (supplied value was $qp100s per 100s)".invalidNel
+      case Left(_) =>
+        s"Calculated QPS for Google Genomics API ($qpsCandidate/s) was not a positive integer (supplied value was $qp100s per 100s)".invalidNel
       case Right(refined) => refined.validNel
     }
   }
 
-  def validateGenomicsLocation(genomicsUrl: ErrorOr[URL], location: Option[String]): ErrorOr[String] = {
+  def validateGenomicsLocation(genomicsUrl: ErrorOr[URL], location: Option[String]): ErrorOr[String] =
     genomicsUrl match {
       case Valid(url) if url.toString.contains("lifesciences") =>
         location match {
@@ -379,25 +426,26 @@ object PipelinesApiConfigurationAttributes
         }
       case _ => location.getOrElse("").validNel
     }
-  }
 
   def validateGsutilMemorySpecification(config: Config, configPath: String): ErrorOr[String] = {
     val entry = config.as[Option[String]](configPath)
     entry match {
       case None => "0".validNel
       case Some(v @ GsutilHumanBytes(_, _)) => v.validNel
-      case Some(bad) => s"Invalid gsutil memory specification in Cromwell configuration at path '$configPath': '$bad'".invalidNel
+      case Some(bad) =>
+        s"Invalid gsutil memory specification in Cromwell configuration at path '$configPath': '$bad'".invalidNel
     }
   }
 
-  def validatePositiveInt(n: Int, configPath: String): Validated[NonEmptyList[String], Refined[Int, Positive]] = {
+  def validatePositiveInt(n: Int, configPath: String): Validated[NonEmptyList[String], Refined[Int, Positive]] =
     refineV[Positive](n) match {
       case Left(_) => s"Value $n for $configPath is not strictly positive".invalidNel
       case Right(refined) => refined.validNel
     }
-  }
 
-  def readOptionalPositiveMillisecondsIntFromDuration(backendConfig: Config, configPath: String): ErrorOr[Option[Int Refined Positive]] = {
+  def readOptionalPositiveMillisecondsIntFromDuration(backendConfig: Config,
+                                                      configPath: String
+  ): ErrorOr[Option[Int Refined Positive]] = {
 
     def validate(n: FiniteDuration) = {
       val result: ErrorOr[Int Refined Positive] = Try(n.toMillis.toInt).toErrorOr flatMap { millisInt =>
@@ -417,7 +465,7 @@ object PipelinesApiConfigurationAttributes
   }
 
   // Copy/port of gsutil's "_GenerateSuffixRegex"
-  private [common] lazy val GsutilHumanBytes: Regex = {
+  private[common] lazy val GsutilHumanBytes: Regex = {
     val _EXP_STRINGS = List(
       List("B", "bit"),
       List("KiB", "Kibit", "K"),
@@ -425,7 +473,7 @@ object PipelinesApiConfigurationAttributes
       List("GiB", "Gibit", "G"),
       List("TiB", "Tibit", "T"),
       List("PiB", "Pibit", "P"),
-      List("EiB", "Eibit", "E"),
+      List("EiB", "Eibit", "E")
     )
 
     val suffixes = for {
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiDockerCacheMappingOperations.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiDockerCacheMappingOperations.scala
index 97a0b1a1da5..b9728272153 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiDockerCacheMappingOperations.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiDockerCacheMappingOperations.scala
@@ -20,7 +20,8 @@ trait PipelinesApiDockerCacheMappingOperations {
   private class DockerImageManifestVersionError(message: String) extends RuntimeException(message) with NoStackTrace
 
   def generateDockerImageToDiskImageMapping(auth: GoogleAuthMode,
-                                            dockerImageCacheManifestFile: ValidFullGcsPath): Map[String, DockerImageCacheEntry] = {
+                                            dockerImageCacheManifestFile: ValidFullGcsPath
+  ): Map[String, DockerImageCacheEntry] = {
 
     val gcsClient = StorageOptions
       .newBuilder()
@@ -34,35 +35,42 @@ trait PipelinesApiDockerCacheMappingOperations {
   def getDockerCacheDiskImageForAJob(dockerImageToCacheDiskImageMappingOpt: Option[Map[String, DockerImageCacheEntry]],
                                      dockerImageAsSpecifiedByUser: String,
                                      dockerImageWithDigest: String,
-                                     jobLogger: JobLogger): Option[String] = {
+                                     jobLogger: JobLogger
+  ): Option[String] =
     dockerImageToCacheDiskImageMappingOpt
       .flatMap(_.get(dockerImageAsSpecifiedByUser))
       .filter { cachedDockerImageDigestAndDiskName =>
         val hashStartingPositionInActualDockerImage = dockerImageWithDigest.indexOf('@')
         if (hashStartingPositionInActualDockerImage != -1) {
-          val actualDigestOfDesiredDockerImage = dockerImageWithDigest.substring(hashStartingPositionInActualDockerImage + 1)
+          val actualDigestOfDesiredDockerImage =
+            dockerImageWithDigest.substring(hashStartingPositionInActualDockerImage + 1)
           if (cachedDockerImageDigestAndDiskName.dockerImageDigest == actualDigestOfDesiredDockerImage) {
             true
           } else {
-            jobLogger.info(s"Cached Docker image digest mismatch. Requested docker image $dockerImageAsSpecifiedByUser has different digest than " +
-              s"corresponding cached image located at the ${cachedDockerImageDigestAndDiskName.diskImageName} disk image. " +
-              s"Digest of requested image is $actualDigestOfDesiredDockerImage, but digest of cached image is ${cachedDockerImageDigestAndDiskName.dockerImageDigest}. " +
-              s"Docker image cache feature will not be used for this task.")
+            jobLogger.info(
+              s"Cached Docker image digest mismatch. Requested docker image $dockerImageAsSpecifiedByUser has different digest than " +
+                s"corresponding cached image located at the ${cachedDockerImageDigestAndDiskName.diskImageName} disk image. " +
+                s"Digest of requested image is $actualDigestOfDesiredDockerImage, but digest of cached image is ${cachedDockerImageDigestAndDiskName.dockerImageDigest}. " +
+                s"Docker image cache feature will not be used for this task."
+            )
 
             false
           }
         } else {
-          jobLogger.error(s"Programmer error ! Odd docker image name where supposed to be name with digest: $dockerImageWithDigest")
+          jobLogger.error(
+            s"Programmer error ! Odd docker image name where supposed to be name with digest: $dockerImageWithDigest"
+          )
           false
         }
       }
       .map(_.diskImageName)
-  }
 
-  private[common] def readDockerImageCacheManifestFileFromGCS(gcsClient: Storage, gcsPath: ValidFullGcsPath): IO[DockerImageCacheManifest] = {
-    val manifestFileBlobIo = IO { gcsClient.get(BlobId.of(gcsPath.bucket, gcsPath.path.substring(1))) }
+  private[common] def readDockerImageCacheManifestFileFromGCS(gcsClient: Storage,
+                                                              gcsPath: ValidFullGcsPath
+  ): IO[DockerImageCacheManifest] = {
+    val manifestFileBlobIo = IO(gcsClient.get(BlobId.of(gcsPath.bucket, gcsPath.path.substring(1))))
     manifestFileBlobIo flatMap { manifestFileBlob =>
-      val jsonStringIo = IO { manifestFileBlob.getContent().map(_.toChar).mkString }
+      val jsonStringIo = IO(manifestFileBlob.getContent().map(_.toChar).mkString)
       jsonStringIo.flatMap { jsonStr =>
         decode[DockerImageCacheManifest](jsonStr) match {
           case Left(error) => IO.raiseError(error)
@@ -70,8 +78,12 @@ trait PipelinesApiDockerCacheMappingOperations {
             if (parsedManifest.manifestFormatVersion == CURRENT_SUPPORTED_MANIFEST_FORMAT_VERSION) {
               IO.pure(parsedManifest)
             } else {
-              IO.raiseError(new DockerImageManifestVersionError(s"Current supported docker image cache manifest format version " +
-                s"is $CURRENT_SUPPORTED_MANIFEST_FORMAT_VERSION, but got ${parsedManifest.manifestFormatVersion}"))
+              IO.raiseError(
+                new DockerImageManifestVersionError(
+                  s"Current supported docker image cache manifest format version " +
+                    s"is $CURRENT_SUPPORTED_MANIFEST_FORMAT_VERSION, but got ${parsedManifest.manifestFormatVersion}"
+                )
+              )
             }
         }
       }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiExpressionFunctions.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiExpressionFunctions.scala
index bbd1aed9ecc..e90042bad2c 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiExpressionFunctions.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiExpressionFunctions.scala
@@ -10,26 +10,25 @@ import cromwell.filesystems.gcs.GcsPathBuilder
 import cromwell.filesystems.gcs.GcsPathBuilder.{InvalidGcsPath, PossiblyValidRelativeGcsPath, ValidFullGcsPath}
 import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
 
-class PipelinesApiPathFunctions(pathBuilders: PathBuilders, callContext: CallContext) extends CallCorePathFunctionSet(pathBuilders, callContext) {
-  override def relativeToHostCallRoot(path: String) = {
+class PipelinesApiPathFunctions(pathBuilders: PathBuilders, callContext: CallContext)
+    extends CallCorePathFunctionSet(pathBuilders, callContext) {
+  override def relativeToHostCallRoot(path: String) =
     GcsPathBuilder.validateGcsPath(path) match {
       case _: ValidFullGcsPath => path
       case _ => callContext.root.resolve(path.stripPrefix("file://").stripPrefix("/")).pathAsString
     }
-  }
 }
 
 class PipelinesApiExpressionFunctions(standardParams: StandardExpressionFunctionsParams)
-  extends StandardExpressionFunctions(standardParams) {
+    extends StandardExpressionFunctions(standardParams) {
   override lazy val ioCommandBuilder: IoCommandBuilder = GcsBatchCommandBuilder
 
-  override def preMapping(str: String) = {
+  override def preMapping(str: String) =
     GcsPathBuilder.validateGcsPath(str) match {
       case _: ValidFullGcsPath => str
       case PossiblyValidRelativeGcsPath => callContext.root.resolve(str.stripPrefix("/")).pathAsString
       case _: InvalidGcsPath => str
     }
-  }
 
   override lazy val pathFunctions = new PipelinesApiPathFunctions(pathBuilders, callContext)
 
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiFinalizationActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiFinalizationActor.scala
index 9be35d11bd9..08d91b414dd 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiFinalizationActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiFinalizationActor.scala
@@ -8,8 +8,7 @@ import cromwell.core.io.AsyncIoActorClient
 import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
 import wom.graph.CommandCallNode
 
-case class PipelinesApiFinalizationActorParams
-(
+case class PipelinesApiFinalizationActorParams(
   workflowDescriptor: BackendWorkflowDescriptor,
   ioActor: ActorRef,
   calls: Set[CommandCallNode],
@@ -22,7 +21,8 @@ case class PipelinesApiFinalizationActorParams
 }
 
 class PipelinesApiFinalizationActor(val pipelinesParams: PipelinesApiFinalizationActorParams)
-  extends StandardFinalizationActor(pipelinesParams) with AsyncIoActorClient {
+    extends StandardFinalizationActor(pipelinesParams)
+    with AsyncIoActorClient {
 
   lazy val jesConfiguration: PipelinesApiConfiguration = pipelinesParams.jesConfiguration
 
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiInitializationActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiInitializationActor.scala
index a97b8f7f9df..b3533c05b97 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiInitializationActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiInitializationActor.scala
@@ -14,7 +14,11 @@ import com.google.auth.oauth2.OAuth2Credentials
 import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes._
 import cromwell.backend.google.pipelines.common.PipelinesApiInitializationActor._
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory
-import cromwell.backend.standard.{StandardInitializationActor, StandardInitializationActorParams, StandardValidatedRuntimeAttributesBuilder}
+import cromwell.backend.standard.{
+  StandardInitializationActor,
+  StandardInitializationActorParams,
+  StandardValidatedRuntimeAttributesBuilder
+}
 import cromwell.backend.{BackendConfigurationDescriptor, BackendInitializationData, BackendWorkflowDescriptor}
 import cromwell.cloudsupport.gcp.auth.GoogleAuthMode.{httpTransport, jsonFactory}
 import cromwell.cloudsupport.gcp.auth.{GoogleAuthMode, UserServiceAccountMode}
@@ -33,8 +37,7 @@ import wom.graph.CommandCallNode
 import scala.concurrent.Future
 import scala.util.Try
 
-case class PipelinesApiInitializationActorParams
-(
+case class PipelinesApiInitializationActorParams(
   workflowDescriptor: BackendWorkflowDescriptor,
   ioActor: ActorRef,
   calls: Set[CommandCallNode],
@@ -46,7 +49,8 @@ case class PipelinesApiInitializationActorParams
 }
 
 class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializationActorParams)
-  extends StandardInitializationActor(pipelinesParams) with AsyncIoActorClient {
+    extends StandardInitializationActor(pipelinesParams)
+    with AsyncIoActorClient {
 
   override lazy val ioActor: ActorRef = pipelinesParams.ioActor
   protected val pipelinesConfiguration: PipelinesApiConfiguration = pipelinesParams.jesConfiguration
@@ -58,19 +62,20 @@ class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializatio
 
   // Credentials object for the GCS API
   private lazy val gcsCredentials: Future[Credentials] = pipelinesConfiguration.papiAttributes.auths.gcs
-      .retryCredentials(workflowOptions, List(StorageScopes.DEVSTORAGE_FULL_CONTROL))
+    .retryCredentials(workflowOptions, List(StorageScopes.DEVSTORAGE_FULL_CONTROL))
 
   // Credentials object for the Genomics API
   private lazy val genomicsCredentials: Future[Credentials] = pipelinesConfiguration.papiAttributes.auths.genomics
-    .retryCredentials(workflowOptions, List(
-      CloudLifeSciencesScopes.CLOUD_PLATFORM,
-      GenomicsScopes.GENOMICS
-    ))
+    .retryCredentials(workflowOptions,
+                      List(
+                        CloudLifeSciencesScopes.CLOUD_PLATFORM,
+                        GenomicsScopes.GENOMICS
+                      )
+    )
 
   // Genomics object to access the Genomics API
-  private lazy val genomics: Future[PipelinesApiRequestFactory] = {
+  private lazy val genomics: Future[PipelinesApiRequestFactory] =
     genomicsCredentials map pipelinesConfiguration.genomicsFactory.fromCredentials
-  }
 
   val privateDockerEncryptionKeyName: Option[String] = {
     val optionsEncryptionKey = workflowOptions.get(GoogleAuthMode.DockerCredentialsEncryptionKeyNameKey).toOption
@@ -90,11 +95,14 @@ class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializatio
       // That doesn't seem great but it's effectively what the existing code around user service accounts appears to be doing.
       val userServiceAccountAuth: Option[GoogleAuthMode] = for {
         _ <- workflowOptions.get(GoogleAuthMode.UserServiceAccountKey).toOption
-        usaAuth <- pipelinesConfiguration.googleConfig.authsByName.values collectFirst { case u: UserServiceAccountMode => u }
+        usaAuth <- pipelinesConfiguration.googleConfig.authsByName.values collectFirst {
+          case u: UserServiceAccountMode => u
+        }
       } yield usaAuth
 
-      def encryptionAuthFromConfig: Option[GoogleAuthMode] = pipelinesConfiguration.dockerEncryptionAuthName.flatMap { name =>
-        pipelinesConfiguration.googleConfig.auth(name).toOption
+      def encryptionAuthFromConfig: Option[GoogleAuthMode] = pipelinesConfiguration.dockerEncryptionAuthName.flatMap {
+        name =>
+          pipelinesConfiguration.googleConfig.auth(name).toOption
       }
       // If there's no user service account auth in the workflow options fall back to an auth specified in config.
       userServiceAccountAuth orElse encryptionAuthFromConfig
@@ -104,12 +112,18 @@ class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializatio
       new String(Base64.decodeBase64(dockerToken)).split(':') match {
         case Array(username, password) =>
           // unencrypted tokens are base64-encoded username:password
-          Option(JsObject(
-            Map(
-              "username" -> JsString(username),
-              "password" -> JsString(password)
-            )).compactPrint)
-        case _ => throw new RuntimeException(s"provided dockerhub token '$dockerToken' is not a base64-encoded username:password")
+          Option(
+            JsObject(
+              Map(
+                "username" -> JsString(username),
+                "password" -> JsString(password)
+              )
+            ).compactPrint
+          )
+        case _ =>
+          throw new RuntimeException(
+            s"provided dockerhub token '$dockerToken' is not a base64-encoded username:password"
+          )
       }
     }
 
@@ -123,17 +137,21 @@ class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializatio
   }
 
   private def vpcNetworkAndSubnetworkProjectLabelsFuture(): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
-    def googleProject(descriptor: BackendWorkflowDescriptor): String = {
-      descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleProject, pipelinesParams.jesConfiguration.papiAttributes.project)
-    }
+    def googleProject(descriptor: BackendWorkflowDescriptor): String =
+      descriptor.workflowOptions.getOrElse(WorkflowOptionKeys.GoogleProject,
+                                           pipelinesParams.jesConfiguration.papiAttributes.project
+      )
 
-    def projectMetadataRequest(vpcConfig: VirtualPrivateCloudLabels): Future[HttpRequest] = {
+    def projectMetadataRequest(vpcConfig: VirtualPrivateCloudLabels): Future[HttpRequest] =
       Future {
-        val credentials = vpcConfig.auth.credentials(workflowOptions.get(_).get, List(CloudLifeSciencesScopes.CLOUD_PLATFORM))
+        val credentials =
+          vpcConfig.auth.credentials(workflowOptions.get(_).get, List(CloudLifeSciencesScopes.CLOUD_PLATFORM))
 
         val httpCredentialsAdapter = new HttpCredentialsAdapter(credentials)
-        val cloudResourceManagerBuilder = new CloudResourceManager
-        .Builder(GoogleAuthMode.httpTransport, GoogleAuthMode.jsonFactory, httpCredentialsAdapter)
+        val cloudResourceManagerBuilder = new CloudResourceManager.Builder(GoogleAuthMode.httpTransport,
+                                                                           GoogleAuthMode.jsonFactory,
+                                                                           httpCredentialsAdapter
+        )
           .setApplicationName(pipelinesConfiguration.googleConfig.applicationName)
           .build()
 
@@ -141,19 +159,23 @@ class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializatio
 
         project.buildHttpRequest()
       }
-    }
 
     def projectMetadataResponseToLabels(httpResponse: HttpResponse): Future[ProjectLabels] = {
       implicit val googleProjectMetadataLabelDecoder: Decoder[ProjectLabels] = deriveDecoder
-      Future.fromTry(decode[ProjectLabels](httpResponse.parseAsString()).toTry).recoverWith {
-        case e: Throwable => Future.failed(new RuntimeException(s"Failed to parse labels from project metadata response from Google Cloud Resource Manager API. " +
-          s"${ExceptionUtils.getMessage(e)}", e))
+      Future.fromTry(decode[ProjectLabels](httpResponse.parseAsString()).toTry).recoverWith { case e: Throwable =>
+        Future.failed(
+          new RuntimeException(
+            s"Failed to parse labels from project metadata response from Google Cloud Resource Manager API. " +
+              s"${ExceptionUtils.getMessage(e)}",
+            e
+          )
+        )
       }
     }
 
     def networkLabelsFromProjectLabels(vpcConfig: VirtualPrivateCloudLabels,
-                                       projectLabels: ProjectLabels,
-                                      ): Option[VpcAndSubnetworkProjectLabelValues] = {
+                                       projectLabels: ProjectLabels
+    ): Option[VpcAndSubnetworkProjectLabelValues] =
       projectLabels.labels.get(vpcConfig.network) map { vpcNetworkLabelValue =>
         val subnetworkLabelOption = vpcConfig.subnetwork.flatMap { s =>
           projectLabels.labels.collectFirst {
@@ -163,22 +185,22 @@ class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializatio
 
         VpcAndSubnetworkProjectLabelValues(vpcNetworkLabelValue, subnetworkLabelOption)
       }
-    }
 
-    def fetchVpcLabelsFromProjectMetadata(vpcConfig: VirtualPrivateCloudLabels
-                                         ): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
+    def fetchVpcLabelsFromProjectMetadata(
+      vpcConfig: VirtualPrivateCloudLabels
+    ): Future[Option[VpcAndSubnetworkProjectLabelValues]] =
       for {
         projectMetadataResponse <- projectMetadataRequest(vpcConfig).map(_.executeAsync().get())
         projectLabels <- projectMetadataResponseToLabels(projectMetadataResponse)
       } yield networkLabelsFromProjectLabels(vpcConfig, projectLabels)
-    }
 
     /*
     First, try to fetch the network information from labels, where that fetch may still return None.
     Then, if we did not discover a network via labels for whatever reason try to look for literal values.
      */
-    def fetchVpcLabels(vpcConfig: VirtualPrivateCloudConfiguration
-                      ): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
+    def fetchVpcLabels(
+      vpcConfig: VirtualPrivateCloudConfiguration
+    ): Future[Option[VpcAndSubnetworkProjectLabelValues]] = {
       // Added explicit types to hopefully help future devs who stumble across this two-step code
       val fetchedFromLabels: Future[Option[VpcAndSubnetworkProjectLabelValues]] = vpcConfig.labelsOption match {
         case Some(labels: VirtualPrivateCloudLabels) => fetchVpcLabelsFromProjectMetadata(labels)
@@ -202,8 +224,13 @@ class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializatio
     gcsCred <- gcsCredentials
     genomicsCred <- genomicsCredentials
     validatedPathBuilders <- pathBuilders
-  } yield new PipelinesApiWorkflowPaths(
-    workflowDescriptor, gcsCred, genomicsCred, pipelinesConfiguration, validatedPathBuilders, standardStreamNameToFileNameMetadataMapper)(ioEc)
+  } yield new PipelinesApiWorkflowPaths(workflowDescriptor,
+                                        gcsCred,
+                                        genomicsCred,
+                                        pipelinesConfiguration,
+                                        validatedPathBuilders,
+                                        standardStreamNameToFileNameMetadataMapper
+  )(ioEc)
 
   override lazy val initializationData: Future[PipelinesApiBackendInitializationData] = for {
     jesWorkflowPaths <- workflowPaths
@@ -218,19 +245,21 @@ class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializatio
     genomicsRequestFactory = genomicsFactory,
     privateDockerEncryptionKeyName = privateDockerEncryptionKeyName,
     privateDockerEncryptedToken = privateDockerEncryptedToken,
-    vpcNetworkAndSubnetworkProjectLabels = vpcNetworkAndSubnetworkProjectLabels)
+    vpcNetworkAndSubnetworkProjectLabels = vpcNetworkAndSubnetworkProjectLabels
+  )
 
   override def validateWorkflowOptions(): Try[Unit] = GoogleLabels.fromWorkflowOptions(workflowOptions).map(_ => ())
 
-  override def beforeAll(): Future[Option[BackendInitializationData]] = {
+  override def beforeAll(): Future[Option[BackendInitializationData]] =
     for {
       paths <- workflowPaths
       _ = publishWorkflowRoot(paths.workflowRoot.pathAsString)
       data <- initializationData
     } yield Option(data)
-  }
 
-  def standardStreamNameToFileNameMetadataMapper(pipelinesApiJobPaths: PipelinesApiJobPaths, streamName: String): String =
+  def standardStreamNameToFileNameMetadataMapper(pipelinesApiJobPaths: PipelinesApiJobPaths,
+                                                 streamName: String
+  ): String =
     PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper(pipelinesApiJobPaths, streamName)
 
   override lazy val ioCommandBuilder: GcsBatchCommandBuilder.type = GcsBatchCommandBuilder
@@ -238,7 +267,9 @@ class PipelinesApiInitializationActor(pipelinesParams: PipelinesApiInitializatio
 
 object PipelinesApiInitializationActor {
   // For metadata publishing purposes default to using the name of a standard stream as the stream's filename.
-  def defaultStandardStreamNameToFileNameMetadataMapper(pipelinesApiJobPaths: PipelinesApiJobPaths, streamName: String): String = streamName
+  def defaultStandardStreamNameToFileNameMetadataMapper(pipelinesApiJobPaths: PipelinesApiJobPaths,
+                                                        streamName: String
+  ): String = streamName
 
   def encryptKms(keyName: String, credentials: OAuth2Credentials, plainText: String): String = {
     val httpCredentialsAdapter = new HttpCredentialsAdapter(credentials)
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
index 353e33a5019..74fb944fe51 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala
@@ -12,9 +12,8 @@ import scala.language.postfixOps
 trait PipelinesApiJobCachingActorHelper extends StandardCachingActorHelper {
   this: PipelinesApiAsyncBackendJobExecutionActor with JobLogging =>
 
-  lazy val initializationData: PipelinesApiBackendInitializationData = {
+  lazy val initializationData: PipelinesApiBackendInitializationData =
     backendInitializationDataAs[PipelinesApiBackendInitializationData]
-  }
 
   lazy val pipelinesConfiguration: PipelinesApiConfiguration = initializationData.papiConfiguration
 
@@ -26,7 +25,8 @@ trait PipelinesApiJobCachingActorHelper extends StandardCachingActorHelper {
     googleLegacyMachineSelection(jobDescriptor.workflowDescriptor)
   )
 
-  lazy val workingDisk: PipelinesApiAttachedDisk = runtimeAttributes.disks.find(_.name == PipelinesApiWorkingDisk.Name).get
+  lazy val workingDisk: PipelinesApiAttachedDisk =
+    runtimeAttributes.disks.find(_.name == PipelinesApiWorkingDisk.Name).get
 
   lazy val callRootPath: Path = pipelinesApiCallPaths.callExecutionRoot
   lazy val returnCodeFilename: String = pipelinesApiCallPaths.returnCodeFilename
@@ -44,16 +44,18 @@ trait PipelinesApiJobCachingActorHelper extends StandardCachingActorHelper {
     val workflow = jobDescriptor.workflowDescriptor
     val call = jobDescriptor.taskCall
     val subWorkflow = workflow.callable
-    val subWorkflowLabels = if (!subWorkflow.equals(workflow.rootWorkflow))
-      Labels("cromwell-sub-workflow-name" -> subWorkflow.name)
-    else
-      Labels.empty
+    val subWorkflowLabels =
+      if (!subWorkflow.equals(workflow.rootWorkflow))
+        Labels("cromwell-sub-workflow-name" -> subWorkflow.name)
+      else
+        Labels.empty
 
     val alias = call.localName
-    val aliasLabels = if (!alias.equals(call.callable.name))
-      Labels("wdl-call-alias" -> alias)
-    else
-      Labels.empty
+    val aliasLabels =
+      if (!alias.equals(call.callable.name))
+        Labels("wdl-call-alias" -> alias)
+      else
+        Labels.empty
 
     Labels(
       "cromwell-workflow-id" -> s"cromwell-${workflow.rootWorkflowId}",
@@ -63,15 +65,14 @@ trait PipelinesApiJobCachingActorHelper extends StandardCachingActorHelper {
 
   lazy val originalLabels: Labels = defaultLabels
 
-  lazy val backendLabels: Seq[GoogleLabel] = GoogleLabels.safeLabels(originalLabels.asTuple :_*)
+  lazy val backendLabels: Seq[GoogleLabel] = GoogleLabels.safeLabels(originalLabels.asTuple: _*)
 
-  lazy val originalLabelEvents: Map[String, String] = originalLabels.value map { l => s"${CallMetadataKeys.Labels}:${l.key}" -> l.value } toMap
+  lazy val originalLabelEvents: Map[String, String] = originalLabels.value map { l =>
+    s"${CallMetadataKeys.Labels}:${l.key}" -> l.value
+  } toMap
 
   override protected def nonStandardMetadata: Map[String, Any] = {
-    val googleProject = initializationData
-      .workflowPaths
-      .workflowDescriptor
-      .workflowOptions
+    val googleProject = initializationData.workflowPaths.workflowDescriptor.workflowOptions
       .get(WorkflowOptionKeys.GoogleProject)
       .getOrElse(jesAttributes.project)
 
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
index ae047187825..ec4af5344cf 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobPaths.scala
@@ -19,7 +19,10 @@ object PipelinesApiJobPaths {
 // Non-`final` as this is mocked for testing since using a real instance proved too difficult.
 // Do not subclass this or other case classes in production code, at least without understanding the pitfalls:
 // https://nrinaudo.github.io/scala-best-practices/tricky_behaviours/final_case_classes.html
-case class PipelinesApiJobPaths(override val workflowPaths: PipelinesApiWorkflowPaths, jobKey: BackendJobDescriptorKey, override val isCallCacheCopyAttempt: Boolean = false) extends JobPaths {
+case class PipelinesApiJobPaths(override val workflowPaths: PipelinesApiWorkflowPaths,
+                                jobKey: BackendJobDescriptorKey,
+                                override val isCallCacheCopyAttempt: Boolean = false
+) extends JobPaths {
 
   // `jesLogBasename` is a `def` rather than a `val` because it is referenced polymorphically from
   // the initialization code of the extended `JobPaths` trait, but this class will not have initialized its `val`s
@@ -41,8 +44,11 @@ case class PipelinesApiJobPaths(override val workflowPaths: PipelinesApiWorkflow
   override lazy val customMetadataPaths = Map(
     CallMetadataKeys.BackendLogsPrefix + ":log" -> jesLogPath
   ) ++ (
-    workflowPaths.monitoringScriptPath map { p => Map(PipelinesApiMetadataKeys.MonitoringScript -> p,
-                                                      PipelinesApiMetadataKeys.MonitoringLog -> jesMonitoringLogPath) } getOrElse Map.empty
+    workflowPaths.monitoringScriptPath map { p =>
+      Map(PipelinesApiMetadataKeys.MonitoringScript -> p,
+          PipelinesApiMetadataKeys.MonitoringLog -> jesMonitoringLogPath
+      )
+    } getOrElse Map.empty
   )
 
   override lazy val customDetritusPaths: Map[String, Path] = Map(
@@ -53,12 +59,11 @@ case class PipelinesApiJobPaths(override val workflowPaths: PipelinesApiWorkflow
     PipelinesApiJobPaths.JesLogPathKey -> jesLogPath
   )
 
-  override def standardOutputAndErrorPaths: Map[String, Path] = {
+  override def standardOutputAndErrorPaths: Map[String, Path] =
     super.standardOutputAndErrorPaths map { case (k, v) =>
       val updated = workflowPaths.standardStreamNameToFileNameMetadataMapper(this, k)
       k -> v.parent.resolve(updated)
     }
-  }
 
   override def forCallCacheCopyAttempts: JobPaths = this.copy(isCallCacheCopyAttempt = true)
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiParameters.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiParameters.scala
index 88fb0cdaafc..9076e08e0d0 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiParameters.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiParameters.scala
@@ -55,12 +55,14 @@ sealed trait PipelinesApiOutput extends PipelinesParameter {
 final case class PipelinesApiFileInput(name: String,
                                        cloudPath: Path,
                                        relativeHostPath: Path,
-                                       mount: PipelinesApiAttachedDisk) extends PipelinesApiInput
+                                       mount: PipelinesApiAttachedDisk
+) extends PipelinesApiInput
 
 final case class PipelinesApiDirectoryInput(name: String,
                                             cloudPath: Path,
                                             relativeHostPath: Path,
-                                            mount: PipelinesApiAttachedDisk) extends PipelinesApiInput
+                                            mount: PipelinesApiAttachedDisk
+) extends PipelinesApiInput
 
 final case class PipelinesApiFileOutput(name: String,
                                         cloudPath: Path,
@@ -69,7 +71,8 @@ final case class PipelinesApiFileOutput(name: String,
                                         optional: Boolean,
                                         secondary: Boolean,
                                         uploadPeriod: Option[FiniteDuration] = None,
-                                        override val contentType: Option[ContentType] = None) extends PipelinesApiOutput
+                                        override val contentType: Option[ContentType] = None
+) extends PipelinesApiOutput
 
 final case class PipelinesApiDirectoryOutput(name: String,
                                              cloudPath: Path,
@@ -77,7 +80,8 @@ final case class PipelinesApiDirectoryOutput(name: String,
                                              mount: PipelinesApiAttachedDisk,
                                              optional: Boolean,
                                              secondary: Boolean,
-                                             override val contentType: Option[ContentType] = None) extends PipelinesApiOutput
+                                             override val contentType: Option[ContentType] = None
+) extends PipelinesApiOutput
 
 // TODO: Remove when support for V1 is stopped, this is only used to pass the extra_param auth file
 final case class PipelinesApiLiteralInput(name: String, value: String)
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiReferenceFilesMappingOperations.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiReferenceFilesMappingOperations.scala
index d190325f0cd..e4a6d6e2d0d 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiReferenceFilesMappingOperations.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiReferenceFilesMappingOperations.scala
@@ -27,7 +27,8 @@ trait PipelinesApiReferenceFilesMappingOperations {
     * may take a significant amount of time.
    */
   def generateReferenceFilesMapping(auth: GoogleAuthMode,
-                                    referenceDiskLocalizationManifests: List[ManifestFile]): Map[String, PipelinesApiReferenceFilesDisk] = {
+                                    referenceDiskLocalizationManifests: List[ManifestFile]
+  ): Map[String, PipelinesApiReferenceFilesDisk] = {
     val gcsClient = StorageOptions
       .newBuilder()
       .setCredentials(auth.credentials(Set(StorageScopes.DEVSTORAGE_READ_ONLY)))
@@ -35,33 +36,39 @@ trait PipelinesApiReferenceFilesMappingOperations {
       .getService
 
     val validReferenceFilesMapIO = referenceDiskLocalizationManifests
-        .traverse(manifestFile => getMapOfValidReferenceFilePathsToDisks(gcsClient, manifestFile))
-        .map(_.flatten.toMap)
+      .traverse(manifestFile => getMapOfValidReferenceFilePathsToDisks(gcsClient, manifestFile))
+      .map(_.flatten.toMap)
 
     validReferenceFilesMapIO.unsafeRunSync()
   }
 
-  def getReferenceInputsToMountedPathMappings(referenceFileToDiskImageMapping: Map[String, PipelinesApiReferenceFilesDisk],
-                                              inputFiles: List[PipelinesApiInput]): Map[PipelinesApiInput, String] = {
-    val gcsPathsToInputs = inputFiles.collect { case i if i.cloudPath.isInstanceOf[GcsPath] => (i.cloudPath.asInstanceOf[GcsPath].pathAsString, i) }.toMap
+  def getReferenceInputsToMountedPathMappings(
+    referenceFileToDiskImageMapping: Map[String, PipelinesApiReferenceFilesDisk],
+    inputFiles: List[PipelinesApiInput]
+  ): Map[PipelinesApiInput, String] = {
+    val gcsPathsToInputs = inputFiles.collect {
+      case i if i.cloudPath.isInstanceOf[GcsPath] => (i.cloudPath.asInstanceOf[GcsPath].pathAsString, i)
+    }.toMap
     referenceFileToDiskImageMapping.collect {
-      case (path, disk) if gcsPathsToInputs.keySet.contains(s"gs://$path")  =>
+      case (path, disk) if gcsPathsToInputs.keySet.contains(s"gs://$path") =>
         (gcsPathsToInputs(s"gs://$path"), s"${disk.mountPoint.pathAsString}/$path")
     }
   }
 
   def getReferenceDisksToMount(referenceFileToDiskImageMapping: Map[String, PipelinesApiReferenceFilesDisk],
-                               inputFilePaths: Set[String]): List[PipelinesApiReferenceFilesDisk] = {
+                               inputFilePaths: Set[String]
+  ): List[PipelinesApiReferenceFilesDisk] =
     referenceFileToDiskImageMapping.view.filterKeys(key => inputFilePaths.contains(s"gs://$key")).values.toList.distinct
-  }
 
-  private def getReferenceFileToValidatedGcsPathMap(referenceFiles: Set[ReferenceFile]): IO[Map[ReferenceFile, ValidFullGcsPath]] = {
-    val filesAndValidatedPaths = referenceFiles.map {
-      referenceFile => (referenceFile, GcsPathBuilder.validateGcsPath(s"gs://${referenceFile.path}"))
+  private def getReferenceFileToValidatedGcsPathMap(
+    referenceFiles: Set[ReferenceFile]
+  ): IO[Map[ReferenceFile, ValidFullGcsPath]] = {
+    val filesAndValidatedPaths = referenceFiles.map { referenceFile =>
+      (referenceFile, GcsPathBuilder.validateGcsPath(s"gs://${referenceFile.path}"))
     }.toMap
 
-    val filesWithValidPaths = filesAndValidatedPaths.collect {
-      case (referenceFile, validPath: ValidFullGcsPath) => (referenceFile, validPath)
+    val filesWithValidPaths = filesAndValidatedPaths.collect { case (referenceFile, validPath: ValidFullGcsPath) =>
+      (referenceFile, validPath)
     }
     val filesWithInvalidPaths = filesAndValidatedPaths.collect {
       case (referenceFile, invalidPath: InvalidFullGcsPath) => (referenceFile, invalidPath)
@@ -75,30 +82,30 @@ trait PipelinesApiReferenceFilesMappingOperations {
   }
 
   protected def bulkValidateCrc32cs(gcsClient: Storage,
-                                    filesWithValidPaths: Map[ReferenceFile, ValidFullGcsPath]): IO[Map[ReferenceFile, Boolean]] = {
+                                    filesWithValidPaths: Map[ReferenceFile, ValidFullGcsPath]
+  ): IO[Map[ReferenceFile, Boolean]] =
     IO {
       val gcsBatch = gcsClient.batch()
-      val filesAndBlobResults = filesWithValidPaths map {
-        case (referenceFile, ValidFullGcsPath(bucket, path)) =>
-          val blobGetResult = gcsBatch.get(BlobId.of(bucket, path.substring(1)), BlobGetOption.fields(BlobField.CRC32C))
-          (referenceFile, blobGetResult)
+      val filesAndBlobResults = filesWithValidPaths map { case (referenceFile, ValidFullGcsPath(bucket, path)) =>
+        val blobGetResult = gcsBatch.get(BlobId.of(bucket, path.substring(1)), BlobGetOption.fields(BlobField.CRC32C))
+        (referenceFile, blobGetResult)
       }
       gcsBatch.submit()
 
-      filesAndBlobResults map {
-        case (referenceFile, blobGetResult) =>
-          val crc32cFromManifest = BaseEncoding.base64.encode(
-            // drop 4 leading bytes from Long crc32c value
-            // https://stackoverflow.com/a/25111119/1794750
-            util.Arrays.copyOfRange(Longs.toByteArray(referenceFile.crc32c), 4, 8)
-          )
+      filesAndBlobResults map { case (referenceFile, blobGetResult) =>
+        val crc32cFromManifest = BaseEncoding.base64.encode(
+          // drop 4 leading bytes from Long crc32c value
+          // https://stackoverflow.com/a/25111119/1794750
+          util.Arrays.copyOfRange(Longs.toByteArray(referenceFile.crc32c), 4, 8)
+        )
 
-          (referenceFile, crc32cFromManifest === blobGetResult.get().getCrc32c)
+        (referenceFile, crc32cFromManifest === blobGetResult.get().getCrc32c)
       }
     }
-  }
 
-  private def getMapOfValidReferenceFilePathsToDisks(gcsClient: Storage, manifestFile: ManifestFile): IO[Map[String, PipelinesApiReferenceFilesDisk]] = {
+  private def getMapOfValidReferenceFilePathsToDisks(gcsClient: Storage,
+                                                     manifestFile: ManifestFile
+  ): IO[Map[String, PipelinesApiReferenceFilesDisk]] = {
     val refDisk = PipelinesApiReferenceFilesDisk(manifestFile.imageIdentifier, manifestFile.diskSizeGb)
     val allReferenceFilesFromManifestMap = manifestFile.files.map(refFile => (refFile, refDisk)).toMap
 
@@ -111,10 +118,13 @@ trait PipelinesApiReferenceFilesMappingOperations {
     validReferenceFilesFromManifestMapIo map { validReferenceFilesFromManifestMap =>
       val invalidReferenceFiles = allReferenceFilesFromManifestMap.keySet -- validReferenceFilesFromManifestMap.keySet
       if (invalidReferenceFiles.nonEmpty) {
-        logger.warn(s"The following files listed in references manifest have checksum mismatch with actual files in GCS: ${invalidReferenceFiles.mkString(",")}")
+        logger.warn(
+          s"The following files listed in references manifest have checksum mismatch with actual files in GCS: ${invalidReferenceFiles
+              .mkString(",")}"
+        )
       }
-      validReferenceFilesFromManifestMap.map {
-        case (refFile, disk) => (refFile.path, disk)
+      validReferenceFilesFromManifestMap.map { case (refFile, disk) =>
+        (refFile.path, disk)
       }.toMap
     }
   }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala
index db87797de37..3e2ee2446e0 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala
@@ -35,7 +35,10 @@ object GpuResource {
   }
 }
 
-final case class GpuResource(gpuType: GpuType, gpuCount: Int Refined Positive, nvidiaDriverVersion: String = GpuResource.DefaultNvidiaDriverVersion)
+final case class GpuResource(gpuType: GpuType,
+                             gpuCount: Int Refined Positive,
+                             nvidiaDriverVersion: String = GpuResource.DefaultNvidiaDriverVersion
+)
 
 final case class PipelinesApiRuntimeAttributes(cpu: Int Refined Positive,
                                                cpuPlatform: Option[String],
@@ -51,7 +54,8 @@ final case class PipelinesApiRuntimeAttributes(cpu: Int Refined Positive,
                                                noAddress: Boolean,
                                                googleLegacyMachineSelection: Boolean,
                                                useDockerImageCache: Option[Boolean],
-                                               checkpointFilename: Option[String])
+                                               checkpointFilename: Option[String]
+)
 
 object PipelinesApiRuntimeAttributes {
 
@@ -81,138 +85,193 @@ object PipelinesApiRuntimeAttributes {
   val CpuPlatformIntelIceLakeValue = "Intel Ice Lake"
 
   val UseDockerImageCacheKey = "useDockerImageCache"
-  private val useDockerImageCacheValidationInstance = new BooleanRuntimeAttributesValidation(UseDockerImageCacheKey).optional
+  private val useDockerImageCacheValidationInstance = new BooleanRuntimeAttributesValidation(
+    UseDockerImageCacheKey
+  ).optional
 
   val CheckpointFileKey = "checkpointFile"
   private val checkpointFileValidationInstance = new StringRuntimeAttributesValidation(CheckpointFileKey).optional
 
   private val MemoryDefaultValue = "2048 MB"
 
-  private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] = CpuValidation.instance
-    .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
+  private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] =
+    CpuValidation.instance
+      .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
-  private def cpuPlatformValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] = cpuPlatformValidationInstance
+  private def cpuPlatformValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] =
+    cpuPlatformValidationInstance
 
-  private def cpuMinValidation(runtimeConfig: Option[Config]):RuntimeAttributesValidation[Int Refined Positive] = CpuValidation.instanceMin
-    .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
+  private def cpuMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] =
+    CpuValidation.instanceMin
+      .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
-  private def gpuTypeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[GpuType] = GpuTypeValidation.optional
+  private def gpuTypeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[GpuType] =
+    GpuTypeValidation.optional
 
   val GpuDriverVersionKey = "nvidiaDriverVersion"
-  private def gpuDriverValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] = new StringRuntimeAttributesValidation(GpuDriverVersionKey).optional
+  private def gpuDriverValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] =
+    new StringRuntimeAttributesValidation(GpuDriverVersionKey).optional
 
-  private def gpuCountValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optional
+  private def gpuCountValidation(
+    runtimeConfig: Option[Config]
+  ): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optional
 
-  private def gpuMinValidation(runtimeConfig: Option[Config]):OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optionalMin
+  private def gpuMinValidation(
+    runtimeConfig: Option[Config]
+  ): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optionalMin
 
   private def failOnStderrValidation(runtimeConfig: Option[Config]) = FailOnStderrValidation.default(runtimeConfig)
 
-  private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) = ContinueOnReturnCodeValidation.default(runtimeConfig)
+  private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) =
+    ContinueOnReturnCodeValidation.default(runtimeConfig)
 
-  private def disksValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Seq[PipelinesApiAttachedDisk]] = DisksValidation
+  private def disksValidation(
+    runtimeConfig: Option[Config]
+  ): RuntimeAttributesValidation[Seq[PipelinesApiAttachedDisk]] = DisksValidation
     .withDefault(DisksValidation.configDefaultWomValue(runtimeConfig) getOrElse DisksDefaultValue)
 
-  private def zonesValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[String]] = ZonesValidation
-    .withDefault(ZonesValidation.configDefaultWomValue(runtimeConfig) getOrElse ZonesDefaultValue)
+  private def zonesValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[String]] =
+    ZonesValidation
+      .withDefault(ZonesValidation.configDefaultWomValue(runtimeConfig) getOrElse ZonesDefaultValue)
 
-  private def preemptibleValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = preemptibleValidationInstance
-    .withDefault(preemptibleValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse PreemptibleDefaultValue)
+  private def preemptibleValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] =
+    preemptibleValidationInstance
+      .withDefault(preemptibleValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse PreemptibleDefaultValue)
 
-  private def memoryValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] = {
+  private def memoryValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] =
     MemoryValidation.withDefaultMemory(
       RuntimeAttributesKeys.MemoryKey,
-      MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, runtimeConfig) getOrElse MemoryDefaultValue)
-  }
+      MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, runtimeConfig) getOrElse MemoryDefaultValue
+    )
 
-  private def memoryMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] = {
-    MemoryValidation.withDefaultMemory(
-      RuntimeAttributesKeys.MemoryMinKey,
-      MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMinKey, runtimeConfig) getOrElse MemoryDefaultValue)
-  }
+  private def memoryMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] =
+    MemoryValidation.withDefaultMemory(RuntimeAttributesKeys.MemoryMinKey,
+                                       MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMinKey,
+                                                                            runtimeConfig
+                                       ) getOrElse MemoryDefaultValue
+    )
 
-  private def bootDiskSizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = bootDiskValidationInstance
-    .withDefault(bootDiskValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse BootDiskDefaultValue)
+  private def bootDiskSizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] =
+    bootDiskValidationInstance
+      .withDefault(bootDiskValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse BootDiskDefaultValue)
 
-  private def noAddressValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = noAddressValidationInstance
-    .withDefault(noAddressValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue)
+  private def noAddressValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] =
+    noAddressValidationInstance
+      .withDefault(noAddressValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue)
 
-  private def useDockerImageCacheValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Boolean] =
+  private def useDockerImageCacheValidation(
+    runtimeConfig: Option[Config]
+  ): OptionalRuntimeAttributesValidation[Boolean] =
     useDockerImageCacheValidationInstance
 
-
   private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
 
-  private val outDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] = {
+  private val outDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
     InformationValidation.optional(RuntimeAttributesKeys.OutDirMinKey, MemoryUnit.MB, allowZero = true)
-  }
 
-  private val tmpDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] = {
+  private val tmpDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
     InformationValidation.optional(RuntimeAttributesKeys.TmpDirMinKey, MemoryUnit.MB, allowZero = true)
-  }
 
-  private val inputDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] = {
+  private val inputDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
     InformationValidation.optional(RuntimeAttributesKeys.DnaNexusInputDirMinKey, MemoryUnit.MB, allowZero = true)
-  }
 
-  def runtimeAttributesBuilder(jesConfiguration: PipelinesApiConfiguration): StandardValidatedRuntimeAttributesBuilder = {
+  def runtimeAttributesBuilder(
+    jesConfiguration: PipelinesApiConfiguration
+  ): StandardValidatedRuntimeAttributesBuilder = {
     val runtimeConfig = jesConfiguration.runtimeConfig
-    StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
-      gpuCountValidation(runtimeConfig),
-      gpuTypeValidation(runtimeConfig),
-      gpuDriverValidation(runtimeConfig),
-      cpuValidation(runtimeConfig),
-      cpuMinValidation(runtimeConfig),
-      gpuMinValidation(runtimeConfig),
-      disksValidation(runtimeConfig),
-      zonesValidation(runtimeConfig),
-      preemptibleValidation(runtimeConfig),
-      memoryValidation(runtimeConfig),
-      memoryMinValidation(runtimeConfig),
-      bootDiskSizeValidation(runtimeConfig),
-      noAddressValidation(runtimeConfig),
-      cpuPlatformValidation(runtimeConfig),
-      useDockerImageCacheValidation(runtimeConfig),
-      checkpointFileValidationInstance,
-      dockerValidation,
-      outDirMinValidation,
-      tmpDirMinValidation,
-      inputDirMinValidation
-    )
+    StandardValidatedRuntimeAttributesBuilder
+      .default(runtimeConfig)
+      .withValidation(
+        gpuCountValidation(runtimeConfig),
+        gpuTypeValidation(runtimeConfig),
+        gpuDriverValidation(runtimeConfig),
+        cpuValidation(runtimeConfig),
+        cpuMinValidation(runtimeConfig),
+        gpuMinValidation(runtimeConfig),
+        disksValidation(runtimeConfig),
+        zonesValidation(runtimeConfig),
+        preemptibleValidation(runtimeConfig),
+        memoryValidation(runtimeConfig),
+        memoryMinValidation(runtimeConfig),
+        bootDiskSizeValidation(runtimeConfig),
+        noAddressValidation(runtimeConfig),
+        cpuPlatformValidation(runtimeConfig),
+        useDockerImageCacheValidation(runtimeConfig),
+        checkpointFileValidationInstance,
+        dockerValidation,
+        outDirMinValidation,
+        tmpDirMinValidation,
+        inputDirMinValidation
+      )
   }
 
-  def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes, runtimeAttrsConfig: Option[Config], googleLegacyMachineSelection: Boolean = false): PipelinesApiRuntimeAttributes = {
-    val cpu: Int Refined Positive = RuntimeAttributesValidation.extract(cpuValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val cpuPlatform: Option[String] = RuntimeAttributesValidation.extractOption(cpuPlatformValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+  def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes,
+            runtimeAttrsConfig: Option[Config],
+            googleLegacyMachineSelection: Boolean = false
+  ): PipelinesApiRuntimeAttributes = {
+    val cpu: Int Refined Positive =
+      RuntimeAttributesValidation.extract(cpuValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val cpuPlatform: Option[String] = RuntimeAttributesValidation.extractOption(
+      cpuPlatformValidation(runtimeAttrsConfig).key,
+      validatedRuntimeAttributes
+    )
 
-    val checkpointFileName: Option[String] = RuntimeAttributesValidation.extractOption(checkpointFileValidationInstance.key, validatedRuntimeAttributes)
+    val checkpointFileName: Option[String] =
+      RuntimeAttributesValidation.extractOption(checkpointFileValidationInstance.key, validatedRuntimeAttributes)
 
     // GPU
-    lazy val gpuType: Option[GpuType] = RuntimeAttributesValidation.extractOption(gpuTypeValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
-    lazy val gpuCount: Option[Int Refined Positive] = RuntimeAttributesValidation.extractOption(gpuCountValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
-    lazy val gpuDriver: Option[String] = RuntimeAttributesValidation.extractOption(gpuDriverValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+    lazy val gpuType: Option[GpuType] =
+      RuntimeAttributesValidation.extractOption(gpuTypeValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+    lazy val gpuCount: Option[Int Refined Positive] =
+      RuntimeAttributesValidation.extractOption(gpuCountValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
+    lazy val gpuDriver: Option[String] =
+      RuntimeAttributesValidation.extractOption(gpuDriverValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
 
     val gpuResource: Option[GpuResource] = if (gpuType.isDefined || gpuCount.isDefined || gpuDriver.isDefined) {
-      Option(GpuResource(gpuType.getOrElse(GpuType.DefaultGpuType), gpuCount.getOrElse(GpuType.DefaultGpuCount), gpuDriver.getOrElse(GpuResource.DefaultNvidiaDriverVersion)))
+      Option(
+        GpuResource(gpuType.getOrElse(GpuType.DefaultGpuType),
+                    gpuCount.getOrElse(GpuType.DefaultGpuCount),
+                    gpuDriver.getOrElse(GpuResource.DefaultNvidiaDriverVersion)
+        )
+      )
     } else {
       None
     }
 
     val zones: Vector[String] = RuntimeAttributesValidation.extract(ZonesValidation, validatedRuntimeAttributes)
-    val preemptible: Int = RuntimeAttributesValidation.extract(preemptibleValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val bootDiskSize: Int = RuntimeAttributesValidation.extract(bootDiskSizeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val memory: MemorySize = RuntimeAttributesValidation.extract(memoryValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val disks: Seq[PipelinesApiAttachedDisk] = RuntimeAttributesValidation.extract(disksValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val preemptible: Int =
+      RuntimeAttributesValidation.extract(preemptibleValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val bootDiskSize: Int =
+      RuntimeAttributesValidation.extract(bootDiskSizeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val memory: MemorySize =
+      RuntimeAttributesValidation.extract(memoryValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val disks: Seq[PipelinesApiAttachedDisk] =
+      RuntimeAttributesValidation.extract(disksValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val docker: String = RuntimeAttributesValidation.extract(dockerValidation, validatedRuntimeAttributes)
-    val failOnStderr: Boolean = RuntimeAttributesValidation.extract(failOnStderrValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val continueOnReturnCode: ContinueOnReturnCode = RuntimeAttributesValidation.extract(continueOnReturnCodeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val noAddress: Boolean = RuntimeAttributesValidation.extract(noAddressValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
-    val useDockerImageCache: Option[Boolean] = RuntimeAttributesValidation.extractOption(useDockerImageCacheValidation(runtimeAttrsConfig).key, validatedRuntimeAttributes)
-
-    val outDirMin: Option[MemorySize] = RuntimeAttributesValidation.extractOption(outDirMinValidation.key, validatedRuntimeAttributes)
-    val tmpDirMin: Option[MemorySize] = RuntimeAttributesValidation.extractOption(tmpDirMinValidation.key, validatedRuntimeAttributes)
-    val inputDirMin: Option[MemorySize] = RuntimeAttributesValidation.extractOption(inputDirMinValidation.key, validatedRuntimeAttributes)
+    val failOnStderr: Boolean =
+      RuntimeAttributesValidation.extract(failOnStderrValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val continueOnReturnCode: ContinueOnReturnCode = RuntimeAttributesValidation.extract(
+      continueOnReturnCodeValidation(runtimeAttrsConfig),
+      validatedRuntimeAttributes
+    )
+    val noAddress: Boolean =
+      RuntimeAttributesValidation.extract(noAddressValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val useDockerImageCache: Option[Boolean] = RuntimeAttributesValidation.extractOption(
+      useDockerImageCacheValidation(runtimeAttrsConfig).key,
+      validatedRuntimeAttributes
+    )
 
-    val totalExecutionDiskSizeBytes = List(inputDirMin.map(_.bytes), outDirMin.map(_.bytes), tmpDirMin.map(_.bytes)).flatten.fold(MemorySize(0, MemoryUnit.Bytes).bytes)(_ + _)
+    val outDirMin: Option[MemorySize] =
+      RuntimeAttributesValidation.extractOption(outDirMinValidation.key, validatedRuntimeAttributes)
+    val tmpDirMin: Option[MemorySize] =
+      RuntimeAttributesValidation.extractOption(tmpDirMinValidation.key, validatedRuntimeAttributes)
+    val inputDirMin: Option[MemorySize] =
+      RuntimeAttributesValidation.extractOption(inputDirMinValidation.key, validatedRuntimeAttributes)
+
+    val totalExecutionDiskSizeBytes = List(inputDirMin.map(_.bytes),
+                                           outDirMin.map(_.bytes),
+                                           tmpDirMin.map(_.bytes)
+    ).flatten.fold(MemorySize(0, MemoryUnit.Bytes).bytes)(_ + _)
     val totalExecutionDiskSize = MemorySize(totalExecutionDiskSizeBytes, MemoryUnit.Bytes)
 
     val adjustedDisks = disks.adjustWorkingDiskWithNewMin(totalExecutionDiskSize, ())
@@ -264,24 +323,23 @@ object DisksValidation extends RuntimeAttributesValidation[Seq[PipelinesApiAttac
   }
 
   private def validateLocalDisks(disks: Seq[String]): ErrorOr[Seq[PipelinesApiAttachedDisk]] = {
-    val diskNels: ErrorOr[Seq[PipelinesApiAttachedDisk]] = disks.toList.traverse[ErrorOr, PipelinesApiAttachedDisk](validateLocalDisk)
+    val diskNels: ErrorOr[Seq[PipelinesApiAttachedDisk]] =
+      disks.toList.traverse[ErrorOr, PipelinesApiAttachedDisk](validateLocalDisk)
     val defaulted: ErrorOr[Seq[PipelinesApiAttachedDisk]] = addDefault(diskNels)
     defaulted
   }
 
-  private def validateLocalDisk(disk: String): ErrorOr[PipelinesApiAttachedDisk] = {
+  private def validateLocalDisk(disk: String): ErrorOr[PipelinesApiAttachedDisk] =
     PipelinesApiAttachedDisk.parse(disk) match {
       case scala.util.Success(attachedDisk) => attachedDisk.validNel
       case scala.util.Failure(ex) => ex.getMessage.invalidNel
     }
-  }
 
-  private def addDefault(disksNel: ErrorOr[Seq[PipelinesApiAttachedDisk]]): ErrorOr[Seq[PipelinesApiAttachedDisk]] = {
+  private def addDefault(disksNel: ErrorOr[Seq[PipelinesApiAttachedDisk]]): ErrorOr[Seq[PipelinesApiAttachedDisk]] =
     disksNel map {
       case disks if disks.exists(_.name == PipelinesApiWorkingDisk.Name) => disks
       case disks => disks :+ PipelinesApiWorkingDisk.Default
     }
-  }
 
   override protected def missingValueMessage: String =
     s"Expecting $key runtime attribute to be a comma separated String or Array[String]"
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiWorkflowPaths.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiWorkflowPaths.scala
index 959112587ab..aad39a6f565 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiWorkflowPaths.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiWorkflowPaths.scala
@@ -20,34 +20,41 @@ object PipelinesApiWorkflowPaths {
   private val AuthFilePathOptionKey = "auth_bucket"
   private val GcsPrefix = "gs://"
 
-  private[common] def callCachePathPrefixFromExecutionRoot(executionRoot: String): String = {
+  private[common] def callCachePathPrefixFromExecutionRoot(executionRoot: String): String =
     // If the root looks like gs://bucket/stuff-under-bucket this should return gs://bucket
     GcsPrefix + executionRoot.substring(GcsPrefix.length).takeWhile(_ != '/')
-  }
 }
 
-case class PipelinesApiWorkflowPaths(workflowDescriptor: BackendWorkflowDescriptor,
-                                     gcsCredentials: Credentials,
-                                     genomicsCredentials: Credentials,
-                                     papiConfiguration: PipelinesApiConfiguration,
-                                     override val pathBuilders: PathBuilders,
-                                     // This allows for the adjustment of the standard stream file names in PAPI v1 to match the
-                                     // combined controller + job standard output and error files. PAPI v1 controls the periodic
-                                     // delocalization of these files so the metadata Cromwell publishes for these files needs
-                                     // to match the PAPI v1 names.
-                                     standardStreamNameToFileNameMetadataMapper: (PipelinesApiJobPaths, String) => String)(implicit ec: ExecutionContext) extends WorkflowPaths {
+case class PipelinesApiWorkflowPaths(
+  workflowDescriptor: BackendWorkflowDescriptor,
+  gcsCredentials: Credentials,
+  genomicsCredentials: Credentials,
+  papiConfiguration: PipelinesApiConfiguration,
+  override val pathBuilders: PathBuilders,
+  // This allows for the adjustment of the standard stream file names in PAPI v1 to match the
+  // combined controller + job standard output and error files. PAPI v1 controls the periodic
+  // delocalization of these files so the metadata Cromwell publishes for these files needs
+  // to match the PAPI v1 names.
+  standardStreamNameToFileNameMetadataMapper: (PipelinesApiJobPaths, String) => String
+)(implicit ec: ExecutionContext)
+    extends WorkflowPaths {
 
   override lazy val executionRootString: String =
     workflowDescriptor.workflowOptions.getOrElse(PipelinesApiWorkflowPaths.GcsRootOptionKey, papiConfiguration.root)
 
-  override lazy val callCacheRootPrefix: Option[String] = Option(callCachePathPrefixFromExecutionRoot(executionRootString))
+  override lazy val callCacheRootPrefix: Option[String] = Option(
+    callCachePathPrefixFromExecutionRoot(executionRootString)
+  )
 
   private val workflowOptions: WorkflowOptions = workflowDescriptor.workflowOptions
 
   val gcsAuthFilePath: Path = {
     // The default auth file bucket is always at the root of the root workflow
-    val defaultBucket = executionRoot.resolve(workflowDescriptor.rootWorkflow.name).resolve(workflowDescriptor.rootWorkflowId.toString)
-    val bucket = workflowDescriptor.workflowOptions.get(PipelinesApiWorkflowPaths.AuthFilePathOptionKey) getOrElse defaultBucket.pathAsString
+    val defaultBucket =
+      executionRoot.resolve(workflowDescriptor.rootWorkflow.name).resolve(workflowDescriptor.rootWorkflowId.toString)
+    val bucket = workflowDescriptor.workflowOptions.get(
+      PipelinesApiWorkflowPaths.AuthFilePathOptionKey
+    ) getOrElse defaultBucket.pathAsString
 
     /*
      * This is an "exception". The filesystem used here is built from genomicsAuth
@@ -62,23 +69,24 @@ case class PipelinesApiWorkflowPaths(workflowDescriptor: BackendWorkflowDescript
       Option(papiConfiguration.papiAttributes.project)
     )
 
-    val authBucket = pathBuilderWithGenomicsAuth.build(bucket) recover {
-      case ex => throw new Exception(s"Invalid gcs auth_bucket path $bucket", ex)
+    val authBucket = pathBuilderWithGenomicsAuth.build(bucket) recover { case ex =>
+      throw new Exception(s"Invalid gcs auth_bucket path $bucket", ex)
     } get
 
     authBucket.resolve(s"${workflowDescriptor.rootWorkflowId}_auth.json")
   }
 
-  val monitoringScriptPath: Option[Path] = workflowOptions.get(WorkflowOptionKeys.MonitoringScript).toOption map { path =>
-    // Fail here if the path exists but can't be built
-    getPath(path).get
+  val monitoringScriptPath: Option[Path] = workflowOptions.get(WorkflowOptionKeys.MonitoringScript).toOption map {
+    path =>
+      // Fail here if the path exists but can't be built
+      getPath(path).get
   }
 
-  override def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): PipelinesApiJobPaths = {
+  override def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): PipelinesApiJobPaths =
     new PipelinesApiJobPaths(workflowPaths.asInstanceOf[PipelinesApiWorkflowPaths], jobKey)
-  }
 
-  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths = this.copy(workflowDescriptor = workflowDescriptor)
+  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths =
+    this.copy(workflowDescriptor = workflowDescriptor)
 
   override def config: Config = papiConfiguration.configurationDescriptor.backendConfig
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PreviousRetryReasons.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PreviousRetryReasons.scala
index 01819ce0082..50a372bc027 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PreviousRetryReasons.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PreviousRetryReasons.scala
@@ -3,7 +3,10 @@ package cromwell.google.pipelines.common
 import cats.syntax.apply._
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
-import cromwell.backend.google.pipelines.common.PipelinesApiBackendLifecycleActorFactory.{preemptionCountKey, unexpectedRetryCountKey}
+import cromwell.backend.google.pipelines.common.PipelinesApiBackendLifecycleActorFactory.{
+  preemptionCountKey,
+  unexpectedRetryCountKey
+}
 import cromwell.services.keyvalue.KeyValueServiceActor._
 
 import scala.util.{Failure, Success, Try}
@@ -14,9 +17,10 @@ object PreviousRetryReasons {
 
   def tryApply(prefetchedKvEntries: Map[String, KvResponse], attemptNumber: Int): ErrorOr[PreviousRetryReasons] = {
     val validatedPreemptionCount = validatedKvResponse(prefetchedKvEntries.get(preemptionCountKey), preemptionCountKey)
-    val validatedUnexpectedRetryCount = validatedKvResponse(prefetchedKvEntries.get(unexpectedRetryCountKey), unexpectedRetryCountKey)
+    val validatedUnexpectedRetryCount =
+      validatedKvResponse(prefetchedKvEntries.get(unexpectedRetryCountKey), unexpectedRetryCountKey)
 
-    (validatedPreemptionCount, validatedUnexpectedRetryCount) mapN { PreviousRetryReasons.apply }
+    (validatedPreemptionCount, validatedUnexpectedRetryCount) mapN PreviousRetryReasons.apply
   }
 
   def apply(knownPreemptedCount: Int, knownUnexpectedRetryCount: Int, attempt: Int): PreviousRetryReasons = {
@@ -35,10 +39,9 @@ object PreviousRetryReasons {
     case None => s"Programmer Error: Engine made no effort to prefetch $fromKey".invalidNel
   }
 
-  private def validatedInt(s: String, fromKey: String): ErrorOr[Int] = {
+  private def validatedInt(s: String, fromKey: String): ErrorOr[Int] =
     Try(s.toInt) match {
       case Success(i) => i.validNel
       case Failure(_) => s"Unexpected value found in the KV store: $fromKey='$s'".invalidNel
     }
-  }
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/VpcAndSubnetworkProjectLabelValues.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/VpcAndSubnetworkProjectLabelValues.scala
index 53e4203c6a9..267d360376a 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/VpcAndSubnetworkProjectLabelValues.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/VpcAndSubnetworkProjectLabelValues.scala
@@ -3,6 +3,7 @@ package cromwell.backend.google.pipelines.common
 import cromwell.backend.google.pipelines.common.VpcAndSubnetworkProjectLabelValues._
 
 final case class VpcAndSubnetworkProjectLabelValues(vpcName: String, subnetNameOpt: Option[String]) {
+
   /**
     * Returns a qualified network name replacing the string `\${projectId}` in the network name if found.
     */
@@ -20,9 +21,8 @@ final case class VpcAndSubnetworkProjectLabelValues(vpcName: String, subnetNameO
   /**
     * Replaces the string `\${projectId}` in the subnet name if found.
     */
-  def subnetNameOption(projectId: String): Option[String] = {
+  def subnetNameOption(projectId: String): Option[String] =
     subnetNameOpt map { _.replace(ProjectIdToken, projectId) }
-  }
 }
 
 object VpcAndSubnetworkProjectLabelValues {
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionCommands.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionCommands.scala
index 2357db6cf25..54af3200acb 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionCommands.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionCommands.scala
@@ -33,19 +33,20 @@ object ActionCommands {
     def escape: String = StringEscapeUtils.escapeXSI(path.pathAsString)
   }
 
-  private def makeContentTypeFlag(contentType: Option[ContentType]) = contentType.map(ct => s"""-h "Content-Type: $ct"""").getOrElse("")
+  private def makeContentTypeFlag(contentType: Option[ContentType]) =
+    contentType.map(ct => s"""-h "Content-Type: $ct"""").getOrElse("")
 
   def makeContainerDirectory(containerPath: Path) = s"mkdir -p ${containerPath.escape}"
 
-  def delocalizeDirectory(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
-                         (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def delocalizeDirectory(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     retry {
       recoverRequesterPaysError(cloudPath) { flag =>
         s"rm -f $$HOME/.config/gcloud/gce && " +
           s"gsutil $flag ${contentType |> makeContentTypeFlag} -m rsync -r ${containerPath.escape} ${cloudPath.escape}"
       }
     }
-  }
 
   /**
     * As per https://cloud.google.com/storage/docs/gsutil/addlhelp/HowSubdirectoriesWork, rule #2
@@ -59,29 +60,29 @@ object ActionCommands {
     * By instead using the parent directory (and ensuring it ends with a slash), gsutil will treat that as a directory and put the file under it.
     * So the final gsutil command will look something like gsutil cp /local/file.txt gs://bucket/subdir/
     */
-  def delocalizeFile(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
-                    (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def delocalizeFile(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     retry {
       recoverRequesterPaysError(cloudPath) { flag =>
         s"rm -f $$HOME/.config/gcloud/gce && " +
           s"gsutil $flag ${contentType |> makeContentTypeFlag} cp ${containerPath.escape} ${cloudPath.parent.escape.ensureSlashed}"
       }
     }
-  }
 
   /**
     * delocalizeFile necessarily copies the file to the same name. Use this if you want to to specify a name different from the original
     * Make sure that there's no object named "yourfinalname_something" (see above) in the same cloud directory.
     */
-  def delocalizeFileTo(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
-                      (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def delocalizeFileTo(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     retry {
       recoverRequesterPaysError(cloudPath) { flag =>
         s"rm -f $$HOME/.config/gcloud/gce && " +
           s"gsutil $flag ${contentType |> makeContentTypeFlag} cp ${containerPath.escape} ${cloudPath.escape}"
       }
     }
-  }
 
   def ifExist(containerPath: Path)(f: => String) = s"if [ -e ${containerPath.escape} ]; then $f; fi"
 
@@ -93,7 +94,7 @@ object ActionCommands {
        |  sleep ${duration.toSeconds}
        |done""".stripMargin
 
-  def retry(f: => String)(implicit gcsTransferConfiguration: GcsTransferConfiguration, wait: FiniteDuration): String = {
+  def retry(f: => String)(implicit gcsTransferConfiguration: GcsTransferConfiguration, wait: FiniteDuration): String =
     s"""for i in $$(seq ${gcsTransferConfiguration.transferAttempts}); do
        |  (
        |    $f
@@ -108,35 +109,34 @@ object ActionCommands {
        |  fi
        |done
        |exit "$$RC"""".stripMargin
-  }
 
-  def delocalizeFileOrDirectory(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])
-                               (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def delocalizeFileOrDirectory(containerPath: Path, cloudPath: Path, contentType: Option[ContentType])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     s"""if [ -d ${containerPath.escape} ]; then
        |  ${delocalizeDirectory(containerPath, cloudPath, contentType)}
        |else
        |  ${delocalizeFile(containerPath, cloudPath, contentType)}
        |fi""".stripMargin
-  }
 
-  def localizeDirectory(cloudPath: Path, containerPath: Path)
-                       (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def localizeDirectory(cloudPath: Path, containerPath: Path)(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     retry {
       recoverRequesterPaysError(cloudPath) { flag =>
         s"${containerPath |> makeContainerDirectory} && " +
           s"rm -f $$HOME/.config/gcloud/gce && gsutil $flag -m rsync -r ${cloudPath.escape} ${containerPath.escape}"
       }
     }
-  }
 
-  def localizeFile(cloudPath: Path, containerPath: Path)
-                  (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  def localizeFile(cloudPath: Path, containerPath: Path)(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): String =
     retry {
       recoverRequesterPaysError(cloudPath) { flag =>
         s"rm -f $$HOME/.config/gcloud/gce && gsutil $flag cp ${cloudPath.escape} ${containerPath.escape}"
       }
     }
-  }
 
   def recoverRequesterPaysError(path: Path)(f: String => String): String = {
     val commandWithoutProject = f("")
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionLabels.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionLabels.scala
index 09941f5b6ba..6e136215398 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionLabels.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionLabels.scala
@@ -2,6 +2,7 @@ package cromwell.backend.google.pipelines.common.action
 
 object ActionLabels {
   object Key {
+
     /**
       * Very short description of the action
       */
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionUtils.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionUtils.scala
index a30e27f48ca..b05971a13ad 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionUtils.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionUtils.scala
@@ -5,6 +5,7 @@ import org.apache.commons.text.StringEscapeUtils
 import net.ceedubs.ficus.Ficus._
 
 object ActionUtils {
+
   /** Image to use for ssh access. */
   val sshImage = "gcr.io/cloud-genomics-pipelines/tools"
 
@@ -72,7 +73,8 @@ object ActionUtils {
     */
   private val backgroundActionTerminationGraceTime = 10
 
-  val terminateAllBackgroundActionsCommand: String = s"kill -TERM -1 && sleep $backgroundActionTerminationGraceTime || true"
+  val terminateAllBackgroundActionsCommand: String =
+    s"kill -TERM -1 && sleep $backgroundActionTerminationGraceTime || true"
 
   def timestampedMessage(message: String): String =
     s"""printf '%s %s\\n' "$$(date -u '+%Y/%m/%d %H:%M:%S')" ${shellEscaped(message)}"""
@@ -88,12 +90,12 @@ object ActionUtils {
                           checkpointingStart: List[Action],
                           checkpointingShutdown: List[Action],
                           sshAccess: List[Action],
-                          isBackground: Action => Boolean,
-                         ): List[Action] = {
+                          isBackground: Action => Boolean
+  ): List[Action] = {
     val toBeSortedActions = localization ++ userAction ++ memoryRetryAction ++ deLocalization
-    val sortedActions = toBeSortedActions.sortWith({
-      case (action, _) => isBackground(action)
-    })
+    val sortedActions = toBeSortedActions.sortWith { case (action, _) =>
+      isBackground(action)
+    }
 
     sshAccess ++ containerSetup ++ monitoringSetup ++ checkpointingStart ++ sortedActions ++ checkpointingShutdown ++ monitoringShutdown
   }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiBatchHandler.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiBatchHandler.scala
index c88d52e33c6..0dbb4e50466 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiBatchHandler.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiBatchHandler.scala
@@ -9,5 +9,8 @@ import scala.util.Try
 
 trait PipelinesApiBatchHandler {
   def makeBatchRequest: BatchRequest
-  def enqueue[T <: PAPIApiRequest](papiApiRequest: T, batchRequest: BatchRequest, pollingManager: ActorRef): Future[Try[Unit]]
+  def enqueue[T <: PAPIApiRequest](papiApiRequest: T,
+                                   batchRequest: BatchRequest,
+                                   pollingManager: ActorRef
+  ): Future[Try[Unit]]
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiFactoryInterface.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiFactoryInterface.scala
index fe5908fae9b..4e0ec2cba5b 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiFactoryInterface.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiFactoryInterface.scala
@@ -16,7 +16,7 @@ abstract class PipelinesApiFactoryInterface {
     val httpCredentialsAdapter = new HttpCredentialsAdapter(credentials)
     build(httpCredentialsAdapter)
   }
-  
+
   protected def build(httpRequestInitializer: HttpRequestInitializer): PipelinesApiRequestFactory
 
   def usesEncryptedDocker: Boolean
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestFactory.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestFactory.scala
index 2ed2e50c6cf..71bc4203b62 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestFactory.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestFactory.scala
@@ -31,9 +31,9 @@ object PipelinesApiRequestFactory {
     * Input parameters that are not strictly needed by the user's command but are Cromwell byproducts.
     */
   case class DetritusInputParameters(
-                                      executionScriptInputParameter: PipelinesApiFileInput,
-                                      monitoringScriptInputParameter: Option[PipelinesApiFileInput]
-                                    ) {
+    executionScriptInputParameter: PipelinesApiFileInput,
+    monitoringScriptInputParameter: Option[PipelinesApiFileInput]
+  ) {
     def all: List[PipelinesApiFileInput] = List(executionScriptInputParameter) ++ monitoringScriptInputParameter
   }
 
@@ -41,11 +41,12 @@ object PipelinesApiRequestFactory {
     * Output parameters that are not produced by the user's command but are Cromwell byproducts.
     */
   case class DetritusOutputParameters(
-                                       monitoringScriptOutputParameter: Option[PipelinesApiFileOutput],
-                                       rcFileOutputParameter: PipelinesApiFileOutput,
-                                       memoryRetryRCFileOutputParameter: PipelinesApiFileOutput
-                                    ) {
-    def all: List[PipelinesApiFileOutput] = memoryRetryRCFileOutputParameter :: List(rcFileOutputParameter) ++ monitoringScriptOutputParameter
+    monitoringScriptOutputParameter: Option[PipelinesApiFileOutput],
+    rcFileOutputParameter: PipelinesApiFileOutput,
+    memoryRetryRCFileOutputParameter: PipelinesApiFileOutput
+  ) {
+    def all: List[PipelinesApiFileOutput] =
+      memoryRetryRCFileOutputParameter :: List(rcFileOutputParameter) ++ monitoringScriptOutputParameter
   }
 
   /**
@@ -54,12 +55,12 @@ object PipelinesApiRequestFactory {
     * to treat them differently.
     */
   case class InputOutputParameters(
-                                    detritusInputParameters: DetritusInputParameters,
-                                    jobInputParameters: List[PipelinesApiInput],
-                                    jobOutputParameters: List[PipelinesApiOutput],
-                                    detritusOutputParameters: DetritusOutputParameters,
-                                    literalInputParameters: List[PipelinesApiLiteralInput]
-                                  ) {
+    detritusInputParameters: DetritusInputParameters,
+    jobInputParameters: List[PipelinesApiInput],
+    jobOutputParameters: List[PipelinesApiOutput],
+    detritusOutputParameters: DetritusOutputParameters,
+    literalInputParameters: List[PipelinesApiLiteralInput]
+  ) {
     lazy val fileInputParameters: List[PipelinesApiInput] = jobInputParameters ++ detritusInputParameters.all
     lazy val fileOutputParameters: List[PipelinesApiOutput] = detritusOutputParameters.all ++ jobOutputParameters
   }
@@ -92,7 +93,7 @@ object PipelinesApiRequestFactory {
                                       enableSshAccess: Boolean,
                                       vpcNetworkAndSubnetworkProjectLabels: Option[VpcAndSubnetworkProjectLabelValues],
                                       dockerImageCacheDiskOpt: Option[String]
-                                     ) {
+  ) {
     def literalInputs = inputOutputParameters.literalInputParameters
     def inputParameters = inputOutputParameters.fileInputParameters
     def outputParameters = inputOutputParameters.fileOutputParameters
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestHandler.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestHandler.scala
index efae1a922bb..e5426b1c339 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestHandler.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestHandler.scala
@@ -10,16 +10,19 @@ import scala.concurrent.{ExecutionContext, Future}
 import scala.util.Try
 
 trait PipelinesApiRequestHandler {
-  def initializeHttpRequest(batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration)
-                           (httpRequest: HttpRequest): Unit = {
-    batchRequestTimeoutConfiguration.readTimeoutMillis foreach {
-      timeout => httpRequest.setReadTimeout(timeout.value)
+  def initializeHttpRequest(
+    batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration
+  )(httpRequest: HttpRequest): Unit = {
+    batchRequestTimeoutConfiguration.readTimeoutMillis foreach { timeout =>
+      httpRequest.setReadTimeout(timeout.value)
     }
-    batchRequestTimeoutConfiguration.connectTimeoutMillis foreach {
-      timeout => httpRequest.setConnectTimeout(timeout.value)
+    batchRequestTimeoutConfiguration.connectTimeoutMillis foreach { timeout =>
+      httpRequest.setConnectTimeout(timeout.value)
     }
   }
 
   def makeBatchRequest: BatchRequest
-  def enqueue[T <: PAPIApiRequest](papiApiRequest: T, batchRequest: BatchRequest, pollingManager: ActorRef)(implicit ec: ExecutionContext): Future[Try[Unit]]
+  def enqueue[T <: PAPIApiRequest](papiApiRequest: T, batchRequest: BatchRequest, pollingManager: ActorRef)(implicit
+    ec: ExecutionContext
+  ): Future[Try[Unit]]
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManager.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManager.scala
index 81e3c2d9fda..f67b027f0c4 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManager.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManager.scala
@@ -28,53 +28,62 @@ import scala.util.control.NoStackTrace
 /**
   * Holds a set of PAPI request until a PipelinesApiRequestActor pulls the work.
   */
-class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers: Int Refined Positive, override val serviceRegistryActor: ActorRef)
-                                   (implicit batchHandler: PipelinesApiRequestHandler) extends Actor
-  with ActorLogging with PapiInstrumentation with CromwellInstrumentationScheduler with Timers {
+class PipelinesApiRequestManager(val qps: Int Refined Positive,
+                                 requestWorkers: Int Refined Positive,
+                                 override val serviceRegistryActor: ActorRef
+)(implicit batchHandler: PipelinesApiRequestHandler)
+    extends Actor
+    with ActorLogging
+    with PapiInstrumentation
+    with CromwellInstrumentationScheduler
+    with Timers {
 
   override val supervisorStrategy = SupervisorStrategy.stoppingStrategy
 
   private val maxRetries = 10
   /*
-    * Context: the batch.execute() method throws an IOException("insufficient data written") in certain conditions.
-    * Here is what we know about it and how this attempts to address the issue.
-    *
-    * It was determined empirically that errors start to be thrown when the batch request approaches 15MB.
-    * Looking more closely at timing it appears that the exception takes almost exactly 60 seconds to be thrown
-    * from the batch.execute method, which suggests that this might be time related rather than byte size related and that
-    * the 15MB limit is just an artifact of how much data can be sent / received in 60 seconds by the client / server.
-    *
-    * In an attempt to provide a fix for this issue, the total size of the batch size is limited to 14MB, which is a rather
-    * arbitrary value only supported by local testing.
-    *
-    * Result of further investigation on the cause:
-    * IOException("insufficient data written") is being thrown because the http request attempts to close() its output stream.
-    * The close() method throws the "insufficient data written" exception because it still had data to send.
-    * The close() method was called as part of a finally, because an exception was thrown earlier when attempting to write to the
-    * stream. This exception is however swallowed by the one thrown in the close().
-    * This commit https://github.com/google/google-http-java-client/pull/333 fixes the swallowing issue so the original
-    * exception is thrown instead: IOException(“Error writing request body to server”).
-    * Tracing back why this exception is being thrown, it appears that at some point the socket gets closed externally
-    * (maybe the google server closes it ?)
-    * which results in a SocketException("broken pipe") being thrown and eventually bubbles up to the IOExceptions above.
-    *
-    * see sun.net.www.protocol.http.HttpURLConnection
-    * and com.google.api.client.http.javanet.NetHttpRequest
-    *
-  */
+   * Context: the batch.execute() method throws an IOException("insufficient data written") in certain conditions.
+   * Here is what we know about it and how this attempts to address the issue.
+   *
+   * It was determined empirically that errors start to be thrown when the batch request approaches 15MB.
+   * Looking more closely at timing it appears that the exception takes almost exactly 60 seconds to be thrown
+   * from the batch.execute method, which suggests that this might be time related rather than byte size related and that
+   * the 15MB limit is just an artifact of how much data can be sent / received in 60 seconds by the client / server.
+   *
+   * In an attempt to provide a fix for this issue, the total size of the batch size is limited to 14MB, which is a rather
+   * arbitrary value only supported by local testing.
+   *
+   * Result of further investigation on the cause:
+   * IOException("insufficient data written") is being thrown because the http request attempts to close() its output stream.
+   * The close() method throws the "insufficient data written" exception because it still had data to send.
+   * The close() method was called as part of a finally, because an exception was thrown earlier when attempting to write to the
+   * stream. This exception is however swallowed by the one thrown in the close().
+   * This commit https://github.com/google/google-http-java-client/pull/333 fixes the swallowing issue so the original
+   * exception is thrown instead: IOException(“Error writing request body to server”).
+   * Tracing back why this exception is being thrown, it appears that at some point the socket gets closed externally
+   * (maybe the google server closes it ?)
+   * which results in a SocketException("broken pipe") being thrown and eventually bubbles up to the IOExceptions above.
+   *
+   * see sun.net.www.protocol.http.HttpURLConnection
+   * and com.google.api.client.http.javanet.NetHttpRequest
+   *
+   */
   private val maxBatchRequestSize: Long = 14L * 1024L * 1024L
   private val requestTooLargeException = new UserPAPIApiException(
-    cause = new IllegalArgumentException(s"The task run request has exceeded the maximum PAPI request size ($maxBatchRequestSize bytes)."),
-    helpfulHint = Option("If you have a task with a very large number of inputs and / or outputs in your workflow you should try to reduce it. " +
-      "Depending on your case you could: 1) Zip your input files together and unzip them in the command. 2) Use a file of file names " +
-      "and localize the files yourself.")
+    cause = new IllegalArgumentException(
+      s"The task run request has exceeded the maximum PAPI request size ($maxBatchRequestSize bytes)."
+    ),
+    helpfulHint = Option(
+      "If you have a task with a very large number of inputs and / or outputs in your workflow you should try to reduce it. " +
+        "Depending on your case you could: 1) Zip your input files together and unzip them in the command. 2) Use a file of file names " +
+        "and localize the files yourself."
+    )
   )
 
   private[api] lazy val nbWorkers = requestWorkers.value
 
   private lazy val workerBatchInterval = determineBatchInterval(qps) * nbWorkers.toLong
 
-
   // workQueue is protected for the unit tests, not intended to be generally overridden
   protected[api] var workQueue: Queue[PAPIApiRequest] = Queue.empty
   private var workInProgress: Map[ActorRef, PipelinesApiWorkBatch] = Map.empty
@@ -82,7 +91,9 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
   // the scheduled delay, unless the workflow is aborted in the meantime in which case they will be cancelled.
   private var queriesWaitingForRetry: Set[PAPIApiRequest] = Set.empty[PAPIApiRequest]
 
-  private def papiRequestWorkerProps = PipelinesApiRequestWorker.props(self, workerBatchInterval, serviceRegistryActor).withMailbox(Mailbox.PriorityMailbox)
+  private def papiRequestWorkerProps = PipelinesApiRequestWorker
+    .props(self, workerBatchInterval, serviceRegistryActor)
+    .withMailbox(Mailbox.PriorityMailbox)
 
   // statusPollers is protected for the unit tests, not intended to be generally overridden
   protected[api] var statusPollers: Vector[ActorRef] = Vector.empty
@@ -100,7 +111,9 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
     val newLoad = if (workQueue.size > LoadConfig.PAPIThreshold) HighLoad else NormalLoad
 
     if (previousLoad == NormalLoad && newLoad == HighLoad)
-      log.warning(s"PAPI Request Manager transitioned to HighLoad with queue size ${workQueue.size} exceeding limit of ${LoadConfig.PAPIThreshold}")
+      log.warning(
+        s"PAPI Request Manager transitioned to HighLoad with queue size ${workQueue.size} exceeding limit of ${LoadConfig.PAPIThreshold}"
+      )
     else if (previousLoad == HighLoad && newLoad == NormalLoad)
       log.info("PAPI Request Manager transitioned back to NormaLoad")
 
@@ -122,30 +135,35 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
     case PipelinesWorkerRequestWork(maxBatchSize) => handleWorkerAskingForWork(sender(), maxBatchSize)
     case failure: PAPIApiRequestFailed =>
       handleQueryFailure(failure)
-    case Terminated(actorRef) => onFailure(actorRef, new RuntimeException("PipelinesApiRequestHandler actor termination caught by manager") with NoStackTrace)
-    case other => log.error(s"Unexpected message from {} to ${this.getClass.getSimpleName}: {}", sender().path.name, other)
+    case Terminated(actorRef) =>
+      onFailure(actorRef,
+                new RuntimeException("PipelinesApiRequestHandler actor termination caught by manager") with NoStackTrace
+      )
+    case other =>
+      log.error(s"Unexpected message from {} to ${this.getClass.getSimpleName}: {}", sender().path.name, other)
   }
 
   override def receive = instrumentationReceive(monitorQueueSize _).orElse(requestManagerReceive)
 
   private def abort(workflowId: WorkflowId) = {
-    def aborted(query: PAPIRunCreationRequest) = query.requester ! PipelinesApiRunCreationQueryFailed(query, JobAbortedException)
+    def aborted(query: PAPIRunCreationRequest) =
+      query.requester ! PipelinesApiRunCreationQueryFailed(query, JobAbortedException)
 
-    workQueue = workQueue.filterNot({
+    workQueue = workQueue.filterNot {
       case query: PAPIRunCreationRequest if query.workflowId == workflowId =>
         aborted(query)
         true
       case _ => false
-    })
+    }
 
-    queriesWaitingForRetry = queriesWaitingForRetry.filterNot({
+    queriesWaitingForRetry = queriesWaitingForRetry.filterNot {
       case query: PAPIRunCreationRequest if query.workflowId == workflowId =>
         timers.cancel(query)
         queriesWaitingForRetry = queriesWaitingForRetry - query
         aborted(query)
         true
       case _ => false
-    })
+    }
   }
 
   private def handleQueryFailure(failure: PAPIApiRequestFailed) = {
@@ -155,7 +173,9 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
       // NB: we don't count user errors towards the PAPI failed queries count in our metrics:
       if (!userError) {
         failedQuery(failure)
-        log.warning(s"PAPI request workers tried and failed ${failure.query.failedAttempts} times to make ${failure.query.getClass.getSimpleName} request to PAPI")
+        log.warning(
+          s"PAPI request workers tried and failed ${failure.query.failedAttempts} times to make ${failure.query.getClass.getSimpleName} request to PAPI"
+        )
       }
 
       failure.query.requester ! failure
@@ -169,7 +189,7 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
       timers.startSingleTimer(nextRequest, nextRequest, delay)
     }
 
-    if (userError || failure.query.failedAttempts >= maxRetries ) {
+    if (userError || failure.query.failedAttempts >= maxRetries) {
       failQuery()
     } else {
       retryQuery()
@@ -177,7 +197,12 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
   }
 
   private def handleWorkerAskingForWork(papiRequestWorkerActor: ActorRef, maxBatchSize: Int) = {
-    log.debug("Request for PAPI requests received from {} (max batch size is {}, current queue size is {})", papiRequestWorkerActor.path.name, maxBatchSize, workQueue.size)
+    log.debug(
+      "Request for PAPI requests received from {} (max batch size is {}, current queue size is {})",
+      papiRequestWorkerActor.path.name,
+      maxBatchSize,
+      workQueue.size
+    )
 
     workInProgress -= papiRequestWorkerActor
     val beheaded = beheadWorkQueue(maxBatchSize)
@@ -196,10 +221,13 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
   }
 
   // Intentionally not final, this runs afoul of SI-4440 (I believe)
-  private case class BeheadedWorkQueue(workToDo: Option[NonEmptyList[PAPIApiRequest]], newWorkQueue: Queue[PAPIApiRequest])
+  private case class BeheadedWorkQueue(workToDo: Option[NonEmptyList[PAPIApiRequest]],
+                                       newWorkQueue: Queue[PAPIApiRequest]
+  )
   private def beheadWorkQueue(maxBatchSize: Int): BeheadedWorkQueue = {
     import common.collections.EnhancedCollections._
-    val DeQueued(head, tail) = workQueue.takeWhileWeighted(maxBatchRequestSize, _.contentLength, Option(maxBatchSize), strict = true)
+    val DeQueued(head, tail) =
+      workQueue.takeWhileWeighted(maxBatchRequestSize, _.contentLength, Option(maxBatchSize), strict = true)
 
     head.toList match {
       case h :: t => BeheadedWorkQueue(Option(NonEmptyList(h, t)), tail)
@@ -240,7 +268,12 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
             s"Exception details: $throwable"
         )
       case None =>
-        log.error(throwable, "The PAPI request worker '{}' terminated ({}). The request manager did not know what work the actor was doing so cannot resubmit any requests or inform any requesters of failures. This should never happen - please report this as a programmer error.", terminee.path.name, throwable.getMessage)
+        log.error(
+          throwable,
+          "The PAPI request worker '{}' terminated ({}). The request manager did not know what work the actor was doing so cannot resubmit any requests or inform any requesters of failures. This should never happen - please report this as a programmer error.",
+          terminee.path.name,
+          throwable.getMessage
+        )
     }
 
     resetWorker(terminee)
@@ -249,7 +282,10 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
   private def resetWorker(worker: ActorRef): Unit = {
 
     if (!statusPollers.contains(worker)) {
-      log.warning("PAPI request worker {} is being reset but was never registered in the pool of workers. This should never happen - please report this as a programmer error.", worker.path.name)
+      log.warning(
+        "PAPI request worker {} is being reset but was never registered in the pool of workers. This should never happen - please report this as a programmer error.",
+        worker.path.name
+      )
     }
 
     val stillGoodWorkers = statusPollers.filterNot(_ == worker)
@@ -257,12 +293,16 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
 
     statusPollers = stillGoodWorkers :+ newWorker
 
-    log.info("PAPI request worker {} has been removed and replaced by {} in the pool of {} workers", worker.path.name, newWorker.path.name, statusPollers.size)
+    log.info("PAPI request worker {} has been removed and replaced by {} in the pool of {} workers",
+             worker.path.name,
+             newWorker.path.name,
+             statusPollers.size
+    )
   }
 
   private[api] def resetAllWorkers() = {
     log.info("'resetAllWorkers()' called to fill vector with {} new workers", nbWorkers)
-    val result = Vector.fill(nbWorkers) { makeAndWatchWorkerActor() }
+    val result = Vector.fill(nbWorkers)(makeAndWatchWorkerActor())
     statusPollers = result
   }
 
@@ -275,7 +315,9 @@ class PipelinesApiRequestManager(val qps: Int Refined Positive, requestWorkers:
   // Separate method to allow overriding in tests:
   private[api] def makeWorkerActor(): ActorRef = {
     val result = context.actorOf(papiRequestWorkerProps, s"PAPIQueryWorker-${UUID.randomUUID()}")
-    log.info(s"Request manager ${self.path.name} created new PAPI request worker ${result.path.name} with batch interval of ${workerBatchInterval}")
+    log.info(
+      s"Request manager ${self.path.name} created new PAPI request worker ${result.path.name} with batch interval of ${workerBatchInterval}"
+    )
     result
   }
 }
@@ -284,8 +326,10 @@ object PipelinesApiRequestManager {
   case object ResetAllRequestWorkers
   case object QueueMonitoringTimerKey
   case object QueueMonitoringTimerAction extends ControlMessage
-  def props(qps: Int Refined Positive, requestWorkers: Int Refined Positive, serviceRegistryActor: ActorRef)
-              (implicit batchHandler: PipelinesApiRequestHandler): Props = Props(new PipelinesApiRequestManager(qps, requestWorkers, serviceRegistryActor)).withDispatcher(BackendDispatcher)
+  def props(qps: Int Refined Positive, requestWorkers: Int Refined Positive, serviceRegistryActor: ActorRef)(implicit
+    batchHandler: PipelinesApiRequestHandler
+  ): Props =
+    Props(new PipelinesApiRequestManager(qps, requestWorkers, serviceRegistryActor)).withDispatcher(BackendDispatcher)
 
   /**
     * Given the Genomics API queries per 100 seconds and given MaxBatchSize will determine a batch interval which
@@ -320,7 +364,8 @@ object PipelinesApiRequestManager {
                                    httpRequest: HttpRequest,
                                    jobId: StandardAsyncJob,
                                    failedAttempts: Int = 0,
-                                   backoff: Backoff = PAPIApiRequest.backoff) extends PAPIApiRequest {
+                                   backoff: Backoff = PAPIApiRequest.backoff
+  ) extends PAPIApiRequest {
     override def withFailedAttempt = this.copy(failedAttempts = failedAttempts + 1, backoff = backoff.next)
   }
 
@@ -328,7 +373,8 @@ object PipelinesApiRequestManager {
                                     requester: ActorRef,
                                     httpRequest: HttpRequest,
                                     failedAttempts: Int = 0,
-                                    backoff: Backoff = PAPIApiRequest.backoff) extends PAPIApiRequest {
+                                    backoff: Backoff = PAPIApiRequest.backoff
+  ) extends PAPIApiRequest {
     override def withFailedAttempt = this.copy(failedAttempts = failedAttempts + 1, backoff = backoff.next)
   }
 
@@ -337,7 +383,8 @@ object PipelinesApiRequestManager {
                               httpRequest: HttpRequest,
                               jobId: StandardAsyncJob,
                               failedAttempts: Int = 0,
-                              backoff: Backoff = PAPIApiRequest.backoff) extends PAPIApiRequest {
+                              backoff: Backoff = PAPIApiRequest.backoff
+  ) extends PAPIApiRequest {
     override def withFailedAttempt = this.copy(failedAttempts = failedAttempts + 1, backoff = backoff.next)
   }
 
@@ -346,16 +393,21 @@ object PipelinesApiRequestManager {
     val cause: PAPIApiException
   }
 
-  final case class PipelinesApiStatusQueryFailed(query: PAPIApiRequest, cause: PAPIApiException) extends PAPIApiRequestFailed
-  final case class PipelinesApiRunCreationQueryFailed(query: PAPIApiRequest, cause: PAPIApiException) extends PAPIApiRequestFailed
-  final case class PipelinesApiAbortQueryFailed(query: PAPIApiRequest, cause: PAPIApiException) extends PAPIApiRequestFailed
+  final case class PipelinesApiStatusQueryFailed(query: PAPIApiRequest, cause: PAPIApiException)
+      extends PAPIApiRequestFailed
+  final case class PipelinesApiRunCreationQueryFailed(query: PAPIApiRequest, cause: PAPIApiException)
+      extends PAPIApiRequestFailed
+  final case class PipelinesApiAbortQueryFailed(query: PAPIApiRequest, cause: PAPIApiException)
+      extends PAPIApiRequestFailed
 
-  private[api] final case class PipelinesApiWorkBatch(workBatch: NonEmptyList[PAPIApiRequest])
+  final private[api] case class PipelinesApiWorkBatch(workBatch: NonEmptyList[PAPIApiRequest])
   private[api] case object NoWorkToDo
 
-  private[api] final case class PipelinesWorkerRequestWork(maxBatchSize: Int) extends ControlMessage
+  final private[api] case class PipelinesWorkerRequestWork(maxBatchSize: Int) extends ControlMessage
 
-  final case class GoogleJsonException(e: GoogleJsonError, responseHeaders: HttpHeaders) extends IOException with CromwellFatalExceptionMarker {
+  final case class GoogleJsonException(e: GoogleJsonError, responseHeaders: HttpHeaders)
+      extends IOException
+      with CromwellFatalExceptionMarker {
     override def getMessage: String = e.getMessage
   }
 
@@ -365,10 +417,12 @@ object PipelinesApiRequestManager {
   }
 
   class SystemPAPIApiException(val cause: Throwable) extends PAPIApiException {
-    override def getMessage: String = s"Unable to complete PAPI request due to system or connection error (${cause.getMessage})"
+    override def getMessage: String =
+      s"Unable to complete PAPI request due to system or connection error (${cause.getMessage})"
   }
 
   final class UserPAPIApiException(val cause: Throwable, helpfulHint: Option[String]) extends PAPIApiException {
-    override def getMessage: String = s"Unable to complete PAPI request due to a problem with the request (${cause.getMessage}). ${helpfulHint.getOrElse("")}"
+    override def getMessage: String =
+      s"Unable to complete PAPI request due to a problem with the request (${cause.getMessage}). ${helpfulHint.getOrElse("")}"
   }
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestWorker.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestWorker.scala
index 2ccadf54ed5..694dc68390e 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestWorker.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestWorker.scala
@@ -17,9 +17,13 @@ import scala.util.{Failure, Success, Try}
 /**
   * Sends batched requests to JES as a worker to the JesApiQueryManager
   */
-class PipelinesApiRequestWorker(val pollingManager: ActorRef, val batchInterval: FiniteDuration, override val serviceRegistryActor: ActorRef)
-                               (implicit val batchHandler: PipelinesApiRequestHandler)
-  extends Actor with ActorLogging with CromwellInstrumentationActor {
+class PipelinesApiRequestWorker(val pollingManager: ActorRef,
+                                val batchInterval: FiniteDuration,
+                                override val serviceRegistryActor: ActorRef
+)(implicit val batchHandler: PipelinesApiRequestHandler)
+    extends Actor
+    with ActorLogging
+    with CromwellInstrumentationActor {
 
   self ! NoWorkToDo // Starts the check-for-work cycle when the actor is fully initialized.
 
@@ -51,18 +55,18 @@ class PipelinesApiRequestWorker(val pollingManager: ActorRef, val batchInterval:
     runBatch(batch)
     Future.sequence(batchFutures.toList)
   }
-  
+
   // These are separate functions so that the tests can hook in and replace the JES-side stuff
   private[api] def createBatch(): BatchRequest = batch
-  private[api] def runBatch(batch: BatchRequest): Unit = {
-    try {
+  private[api] def runBatch(batch: BatchRequest): Unit =
+    try
       if (batch.size() > 0) batch.execute()
-    } catch {
+    catch {
       case e: java.io.IOException =>
-        val msg = s"A batch of PAPI status requests failed. The request manager will retry automatically up to 10 times. The error was: ${e.getMessage}"
+        val msg =
+          s"A batch of PAPI status requests failed. The request manager will retry automatically up to 10 times. The error was: ${e.getMessage}"
         throw new Exception(msg, e.getCause) with NoStackTrace
     }
-  }
 
   // TODO: FSMify this actor?
   private def interstitialRecombobulation: PartialFunction[Try[List[Try[Unit]]], Unit] = {
@@ -71,11 +75,17 @@ class PipelinesApiRequestWorker(val pollingManager: ActorRef, val batchInterval:
       scheduleCheckForWork()
     case Success(someFailures) =>
       val errors = someFailures collect { case Failure(t) => t.getMessage }
-      log.warning("PAPI request worker had {} failures making {} requests: {}", errors.size, someFailures.size, errors.mkString(System.lineSeparator, "," + System.lineSeparator, ""))
+      log.warning(
+        "PAPI request worker had {} failures making {} requests: {}",
+        errors.size,
+        someFailures.size,
+        errors.mkString(System.lineSeparator, "," + System.lineSeparator, "")
+      )
       scheduleCheckForWork()
     case Failure(t) =>
       // NB: Should be impossible since we only ever do completionPromise.trySuccess()
-      val msg = "Programmer Error: Completion promise unexpectedly set to Failure: {}. Don't do this, otherwise the Future.sequence is short-circuited on the first failure"
+      val msg =
+        "Programmer Error: Completion promise unexpectedly set to Failure: {}. Don't do this, otherwise the Future.sequence is short-circuited on the first failure"
       log.error(msg, t.getMessage)
       scheduleCheckForWork()
   }
@@ -85,16 +95,19 @@ class PipelinesApiRequestWorker(val pollingManager: ActorRef, val batchInterval:
     * Warning: Only use this from inside a receive method.
     */
   private def scheduleCheckForWork(): Unit = {
-    context.system.scheduler.scheduleOnce(batchInterval) { pollingManager ! PipelinesApiRequestManager.PipelinesWorkerRequestWork(MaxBatchSize) }
+    context.system.scheduler.scheduleOnce(batchInterval) {
+      pollingManager ! PipelinesApiRequestManager.PipelinesWorkerRequestWork(MaxBatchSize)
+    }
     ()
   }
 }
 
 object PipelinesApiRequestWorker {
-  def props(pollingManager: ActorRef, batchInterval: FiniteDuration, serviceRegistryActor: ActorRef)
-              (implicit batchHandler: PipelinesApiRequestHandler) = {
-    Props(new PipelinesApiRequestWorker(pollingManager, batchInterval, serviceRegistryActor)).withDispatcher(BackendDispatcher)
-  }
+  def props(pollingManager: ActorRef, batchInterval: FiniteDuration, serviceRegistryActor: ActorRef)(implicit
+    batchHandler: PipelinesApiRequestHandler
+  ) =
+    Props(new PipelinesApiRequestWorker(pollingManager, batchInterval, serviceRegistryActor))
+      .withDispatcher(BackendDispatcher)
 
   // The Batch API limits us to 100 at a time
   val MaxBatchSize = 100
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/RunStatus.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/RunStatus.scala
index 51064deff21..933a6139344 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/RunStatus.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/RunStatus.scala
@@ -34,7 +34,8 @@ object RunStatus {
   case class Success(eventList: Seq[ExecutionEvent],
                      machineType: Option[String],
                      zone: Option[String],
-                     instanceName: Option[String]) extends TerminalRunStatus {
+                     instanceName: Option[String]
+  ) extends TerminalRunStatus {
     override def toString = "Success"
   }
 
@@ -45,19 +46,36 @@ object RunStatus {
               machineType: Option[String],
               zone: Option[String],
               instanceName: Option[String],
-              wasPreemptible: Boolean): UnsuccessfulRunStatus = {
+              wasPreemptible: Boolean
+    ): UnsuccessfulRunStatus = {
       val jesCode: Option[Int] = errorMessage flatMap { em => Try(em.substring(0, em.indexOf(':')).toInt).toOption }
 
       // Because of Reasons, sometimes errors which aren't indicative of preemptions are treated as preemptions.
       val unsuccessfulStatusBuilder = errorCode match {
-        case Status.ABORTED if jesCode.contains(PipelinesApiAsyncBackendJobExecutionActor.JesPreemption) => Preempted.apply _
-        case Status.ABORTED if jesCode.contains(PipelinesApiAsyncBackendJobExecutionActor.JesUnexpectedTermination) && wasPreemptible => Preempted.apply _
-        case Status.ABORTED if errorMessage.exists(_.contains(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style)) => Preempted.apply _
-        case Status.UNKNOWN if errorMessage.exists(_.contains(PipelinesApiAsyncBackendJobExecutionActor.FailedToStartDueToPreemptionSubstring)) => Preempted.apply _
+        case Status.ABORTED if jesCode.contains(PipelinesApiAsyncBackendJobExecutionActor.JesPreemption) =>
+          Preempted.apply _
+        case Status.ABORTED
+            if jesCode.contains(PipelinesApiAsyncBackendJobExecutionActor.JesUnexpectedTermination) && wasPreemptible =>
+          Preempted.apply _
+        case Status.ABORTED
+            if errorMessage.exists(_.contains(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style)) =>
+          Preempted.apply _
+        case Status.UNKNOWN
+            if errorMessage.exists(
+              _.contains(PipelinesApiAsyncBackendJobExecutionActor.FailedToStartDueToPreemptionSubstring)
+            ) =>
+          Preempted.apply _
         case Status.CANCELLED => Cancelled.apply _
         case _ => Failed.apply _
       }
-      unsuccessfulStatusBuilder.apply(errorCode, jesCode, errorMessage.toList, eventList, machineType, zone, instanceName)
+      unsuccessfulStatusBuilder.apply(errorCode,
+                                      jesCode,
+                                      errorMessage.toList,
+                                      eventList,
+                                      machineType,
+                                      zone,
+                                      instanceName
+      )
     }
   }
 
@@ -67,7 +85,8 @@ object RunStatus {
                           eventList: Seq[ExecutionEvent],
                           machineType: Option[String],
                           zone: Option[String],
-                          instanceName: Option[String]) extends UnsuccessfulRunStatus {
+                          instanceName: Option[String]
+  ) extends UnsuccessfulRunStatus {
     override def toString = "Failed"
   }
 
@@ -75,12 +94,13 @@ object RunStatus {
     * What Cromwell calls Aborted, PAPI calls Cancelled. This means the job was "cancelled" by the user
     */
   final case class Cancelled(errorCode: Status,
-                          jesCode: Option[Int],
-                          errorMessages: List[String],
-                          eventList: Seq[ExecutionEvent],
-                          machineType: Option[String],
-                          zone: Option[String],
-                          instanceName: Option[String]) extends UnsuccessfulRunStatus {
+                             jesCode: Option[Int],
+                             errorMessages: List[String],
+                             eventList: Seq[ExecutionEvent],
+                             machineType: Option[String],
+                             zone: Option[String],
+                             instanceName: Option[String]
+  ) extends UnsuccessfulRunStatus {
     override def toString = "Cancelled"
   }
 
@@ -90,7 +110,8 @@ object RunStatus {
                              eventList: Seq[ExecutionEvent],
                              machineType: Option[String],
                              zone: Option[String],
-                             instanceName: Option[String]) extends UnsuccessfulRunStatus {
+                             instanceName: Option[String]
+  ) extends UnsuccessfulRunStatus {
     override def toString = "Preempted"
   }
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiAbortClient.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiAbortClient.scala
index 0654f2699c5..90fcd293f07 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiAbortClient.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiAbortClient.scala
@@ -3,8 +3,14 @@ package cromwell.backend.google.pipelines.common.api.clients
 import akka.actor.{Actor, ActorLogging, ActorRef}
 import cromwell.backend.google.pipelines.common.PapiInstrumentation
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory
-import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.{PAPIAbortRequest, PipelinesApiAbortQueryFailed}
-import cromwell.backend.google.pipelines.common.api.clients.PipelinesApiAbortClient.{PAPIAbortRequestSuccessful, PAPIOperationIsAlreadyTerminal}
+import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.{
+  PAPIAbortRequest,
+  PipelinesApiAbortQueryFailed
+}
+import cromwell.backend.google.pipelines.common.api.clients.PipelinesApiAbortClient.{
+  PAPIAbortRequestSuccessful,
+  PAPIOperationIsAlreadyTerminal
+}
 import cromwell.backend.standard.StandardAsyncJob
 import cromwell.core.WorkflowId
 import cromwell.core.logging.JobLogging
@@ -23,9 +29,8 @@ trait PipelinesApiAbortClient { this: Actor with ActorLogging with JobLogging wi
   val papiApiActor: ActorRef
   val requestFactory: PipelinesApiRequestFactory
 
-  def abortJob(jobId: StandardAsyncJob) = {
+  def abortJob(jobId: StandardAsyncJob) =
     papiApiActor ! PAPIAbortRequest(workflowId, self, requestFactory.cancelRequest(jobId), jobId)
-  }
 
   def abortActorClientReceive: Actor.Receive = {
     case PAPIAbortRequestSuccessful(jobId) =>
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiRunCreationClient.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiRunCreationClient.scala
index 0ff1920b732..ef585129f3b 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiRunCreationClient.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiRunCreationClient.scala
@@ -3,7 +3,10 @@ package cromwell.backend.google.pipelines.common.api.clients
 import akka.actor.{Actor, ActorLogging, ActorRef}
 import cromwell.backend.google.pipelines.common.PapiInstrumentation
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.CreatePipelineParameters
-import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.{PipelinesApiRunCreationQueryFailed, SystemPAPIApiException}
+import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.{
+  PipelinesApiRunCreationQueryFailed,
+  SystemPAPIApiException
+}
 import cromwell.backend.google.pipelines.common.api.{PipelinesApiRequestFactory, PipelinesApiRequestManager}
 import cromwell.backend.standard.StandardAsyncJob
 import cromwell.core.WorkflowId
@@ -18,7 +21,10 @@ object PipelinesApiRunCreationClient {
     * Exception used to represent the fact that a job was aborted before a creation attempt was made.
     * Meaning it was in the queue when the abort request was made, so it was just removed from the queue.
     */
-  case object JobAbortedException extends SystemPAPIApiException(new Exception("The job was removed from the queue before a PAPI creation request was made"))
+  case object JobAbortedException
+      extends SystemPAPIApiException(
+        new Exception("The job was removed from the queue before a PAPI creation request was made")
+      )
 }
 
 /**
@@ -45,15 +51,21 @@ trait PipelinesApiRunCreationClient { this: Actor with ActorLogging with PapiIns
     runCreationClientPromise = None
   }
 
-  def runPipeline(workflowId: WorkflowId, createPipelineParameters: CreatePipelineParameters, jobLogger: JobLogger): Future[StandardAsyncJob] = {
+  def runPipeline(workflowId: WorkflowId,
+                  createPipelineParameters: CreatePipelineParameters,
+                  jobLogger: JobLogger
+  ): Future[StandardAsyncJob] =
     runCreationClientPromise match {
       case Some(p) =>
         p.future
       case None =>
-        papiApiActor ! PipelinesApiRequestManager.PAPIRunCreationRequest(workflowId, self, requestFactory.runRequest(createPipelineParameters, jobLogger))
+        papiApiActor ! PipelinesApiRequestManager.PAPIRunCreationRequest(
+          workflowId,
+          self,
+          requestFactory.runRequest(createPipelineParameters, jobLogger)
+        )
         val newPromise = Promise[StandardAsyncJob]()
         runCreationClientPromise = Option(newPromise)
         newPromise.future
     }
-  }
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiStatusRequestClient.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiStatusRequestClient.scala
index cb6cf2f9940..1f266484489 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiStatusRequestClient.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/clients/PipelinesApiStatusRequestClient.scala
@@ -38,14 +38,17 @@ trait PipelinesApiStatusRequestClient { this: Actor with ActorLogging with PapiI
     pollingActorClientPromise = None
   }
 
-  def pollStatus(workflowId: WorkflowId, jobId: StandardAsyncJob): Future[RunStatus] = {
+  def pollStatus(workflowId: WorkflowId, jobId: StandardAsyncJob): Future[RunStatus] =
     pollingActorClientPromise match {
       case Some(p) => p.future
       case None =>
-        papiApiActor ! PipelinesApiRequestManager.PAPIStatusPollRequest(workflowId, self, requestFactory.getRequest(jobId), jobId)
+        papiApiActor ! PipelinesApiRequestManager.PAPIStatusPollRequest(workflowId,
+                                                                        self,
+                                                                        requestFactory.getRequest(jobId),
+                                                                        jobId
+        )
         val newPromise = Promise[RunStatus]()
         pollingActorClientPromise = Option(newPromise)
         newPromise.future
     }
-  }
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/authentication/PipelinesApiVMAuthentication.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/authentication/PipelinesApiVMAuthentication.scala
index 583ac380851..c00e2a6c16a 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/authentication/PipelinesApiVMAuthentication.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/authentication/PipelinesApiVMAuthentication.scala
@@ -7,6 +7,7 @@ import common.validation.Validation._
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.core.DockerCredentials
 import spray.json.{JsString, JsValue}
+
 /**
  * Interface for Authentication information that can be included as a json object in the file uploaded to GCS
  * upon workflow creation and used in the VM.
@@ -15,7 +16,7 @@ sealed trait PipelinesApiAuthObject {
   def context: String
   def map: Map[String, JsValue]
 
-  def toMap: Map[String, Map[String, JsValue]] =  Map(context -> map)
+  def toMap: Map[String, Map[String, JsValue]] = Map(context -> map)
 }
 
 object PipelinesApiDockerCredentials {
@@ -26,7 +27,9 @@ object PipelinesApiDockerCredentials {
       case None => ().validNel // fine
       case _ =>
         for {
-          authName <- dockerCredentials.authName.toErrorOr("KMS Encryption key defined for private Docker but no auth specified")
+          authName <- dockerCredentials.authName.toErrorOr(
+            "KMS Encryption key defined for private Docker but no auth specified"
+          )
           _ <- googleConfig.auth(authName)
         } yield ()
     }
@@ -35,10 +38,10 @@ object PipelinesApiDockerCredentials {
       case Invalid(errors) =>
         throw new RuntimeException(errors.toList.mkString(", "))
       case Valid(_) =>
-        new PipelinesApiDockerCredentials(
-          token = dockerCredentials.token,
-          keyName = dockerCredentials.keyName,
-          authName = dockerCredentials.authName)
+        new PipelinesApiDockerCredentials(token = dockerCredentials.token,
+                                          keyName = dockerCredentials.keyName,
+                                          authName = dockerCredentials.authName
+        )
     }
   }
 }
@@ -48,8 +51,9 @@ object PipelinesApiDockerCredentials {
  */
 case class PipelinesApiDockerCredentials(override val token: String,
                                          override val keyName: Option[String],
-                                         override val authName: Option[String])
-  extends DockerCredentials(token = token, keyName = keyName, authName = authName) with PipelinesApiAuthObject {
+                                         override val authName: Option[String]
+) extends DockerCredentials(token = token, keyName = keyName, authName = authName)
+    with PipelinesApiAuthObject {
 
   override val context = "docker"
   override val map = Map(
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendCacheHitCopyingActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendCacheHitCopyingActor.scala
index 90d9fd88d2d..55f2ab0a278 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendCacheHitCopyingActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendCacheHitCopyingActor.scala
@@ -16,54 +16,62 @@ import wom.values.WomFile
 import scala.language.postfixOps
 import scala.util.Try
 
-class PipelinesApiBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams) extends StandardCacheHitCopyingActor(standardParams) {
+class PipelinesApiBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams)
+    extends StandardCacheHitCopyingActor(standardParams) {
   override protected val commandBuilder: GcsBatchCommandBuilder.type = GcsBatchCommandBuilder
   private val cachingStrategy = BackendInitializationData
     .as[PipelinesApiBackendInitializationData](standardParams.backendInitializationDataOption)
-    .papiConfiguration.papiAttributes.cacheHitDuplicationStrategy
-  
+    .papiConfiguration
+    .papiAttributes
+    .cacheHitDuplicationStrategy
+
   override def processSimpletons(womValueSimpletons: Seq[WomValueSimpleton],
-                                 sourceCallRootPath: Path,
-                                ): Try[(CallOutputs, Set[IoCommand[_]])] =
+                                 sourceCallRootPath: Path
+  ): Try[(CallOutputs, Set[IoCommand[_]])] =
     cachingStrategy match {
-    case CopyCachedOutputs => super.processSimpletons(womValueSimpletons, sourceCallRootPath)
-    case UseOriginalCachedOutputs =>
-      val touchCommands: Seq[Try[IoTouchCommand]] = womValueSimpletons collect {
-        case WomValueSimpleton(_, wdlFile: WomFile) => getPath(wdlFile.value) flatMap GcsBatchCommandBuilder.touchCommand
-      }
-      
-      TryUtil.sequence(touchCommands) map {
-        WomValueBuilder.toJobOutputs(jobDescriptor.taskCall.outputPorts, womValueSimpletons) -> _.toSet
-      }
-  }
+      case CopyCachedOutputs => super.processSimpletons(womValueSimpletons, sourceCallRootPath)
+      case UseOriginalCachedOutputs =>
+        val touchCommands: Seq[Try[IoTouchCommand]] = womValueSimpletons collect {
+          case WomValueSimpleton(_, wdlFile: WomFile) =>
+            getPath(wdlFile.value) flatMap GcsBatchCommandBuilder.touchCommand
+        }
+
+        TryUtil.sequence(touchCommands) map {
+          WomValueBuilder.toJobOutputs(jobDescriptor.taskCall.outputPorts, womValueSimpletons) -> _.toSet
+        }
+    }
 
-  override def extractBlacklistPrefix(path: String): Option[String] = Option(path.stripPrefix("gs://").takeWhile(_ != '/'))
+  override def extractBlacklistPrefix(path: String): Option[String] = Option(
+    path.stripPrefix("gs://").takeWhile(_ != '/')
+  )
 
-  override def processDetritus(sourceJobDetritusFiles: Map[String, String]
-                              ): Try[(Map[String, Path], Set[IoCommand[_]])] = 
+  override def processDetritus(
+    sourceJobDetritusFiles: Map[String, String]
+  ): Try[(Map[String, Path], Set[IoCommand[_]])] =
     cachingStrategy match {
-    case CopyCachedOutputs => super.processDetritus(sourceJobDetritusFiles)
-    case UseOriginalCachedOutputs =>
-      // apply getPath on each detritus string file
-      val detritusAsPaths = detritusFileKeys(sourceJobDetritusFiles).toSeq map { key =>
-        key -> getPath(sourceJobDetritusFiles(key))
-      } toMap
+      case CopyCachedOutputs => super.processDetritus(sourceJobDetritusFiles)
+      case UseOriginalCachedOutputs =>
+        // apply getPath on each detritus string file
+        val detritusAsPaths = detritusFileKeys(sourceJobDetritusFiles).toSeq map { key =>
+          key -> getPath(sourceJobDetritusFiles(key))
+        } toMap
 
-      // Don't forget to re-add the CallRootPathKey that has been filtered out by detritusFileKeys
-      TryUtil.sequenceMap(detritusAsPaths, "Failed to make paths out of job detritus") flatMap { newDetritus =>
-        Try {
-          // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
-          (newDetritus + (JobPaths.CallRootPathKey -> destinationCallRootPath)) ->
-            newDetritus.values.map(GcsBatchCommandBuilder.touchCommand(_).get).toSet
+        // Don't forget to re-add the CallRootPathKey that has been filtered out by detritusFileKeys
+        TryUtil.sequenceMap(detritusAsPaths, "Failed to make paths out of job detritus") flatMap { newDetritus =>
+          Try {
+            // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
+            (newDetritus + (JobPaths.CallRootPathKey -> destinationCallRootPath)) ->
+              newDetritus.values.map(GcsBatchCommandBuilder.touchCommand(_).get).toSet
+          }
         }
-      }
-  }
+    }
 
   override protected def additionalIoCommands(sourceCallRootPath: Path,
                                               originalSimpletons: Seq[WomValueSimpleton],
                                               newOutputs: CallOutputs,
-                                              originalDetritus:  Map[String, String],
-                                              newDetritus: Map[String, Path]): Try[List[Set[IoCommand[_]]]] = Try {
+                                              originalDetritus: Map[String, String],
+                                              newDetritus: Map[String, Path]
+  ): Try[List[Set[IoCommand[_]]]] = Try {
     cachingStrategy match {
       case UseOriginalCachedOutputs =>
         val content =
@@ -74,13 +82,17 @@ class PipelinesApiBackendCacheHitCopyingActor(standardParams: StandardCacheHitCo
       """.stripMargin
 
         // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
-        List(Set(
-          GcsBatchCommandBuilder.writeCommand(
-            path = jobPaths.forCallCacheCopyAttempts.callExecutionRoot / "call_caching_placeholder.txt",
-            content = content,
-            options = Seq(CloudStorageOptions.withMimeType("text/plain")),
-          ).get
-        ))
+        List(
+          Set(
+            GcsBatchCommandBuilder
+              .writeCommand(
+                path = jobPaths.forCallCacheCopyAttempts.callExecutionRoot / "call_caching_placeholder.txt",
+                content = content,
+                options = Seq(CloudStorageOptions.withMimeType("text/plain"))
+              )
+              .get
+          )
+        )
       case CopyCachedOutputs => List.empty
     }
   }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendFileHashingActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendFileHashingActor.scala
index 030b8cf8a70..e275a322ea4 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendFileHashingActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendFileHashingActor.scala
@@ -3,6 +3,7 @@ package cromwell.backend.google.pipelines.common.callcaching
 import cromwell.backend.standard.callcaching.{StandardFileHashingActor, StandardFileHashingActorParams}
 import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
 
-class PipelinesApiBackendFileHashingActor(standardParams: StandardFileHashingActorParams) extends StandardFileHashingActor(standardParams) {
+class PipelinesApiBackendFileHashingActor(standardParams: StandardFileHashingActorParams)
+    extends StandardFileHashingActor(standardParams) {
   override val ioCommandBuilder = GcsBatchCommandBuilder
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/errors/InvalidGcsPathsInManifestFileException.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/errors/InvalidGcsPathsInManifestFileException.scala
index 982caa9f80a..14344a2a45a 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/errors/InvalidGcsPathsInManifestFileException.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/errors/InvalidGcsPathsInManifestFileException.scala
@@ -3,5 +3,6 @@ package cromwell.backend.google.pipelines.common.errors
 import scala.util.control.NoStackTrace
 
 class InvalidGcsPathsInManifestFileException(paths: List[String]) extends Exception with NoStackTrace {
-  override def getMessage: String = s"Some of the paths in manifest file are not valid GCS paths: \n${paths.mkString("\n")}"
+  override def getMessage: String =
+    s"Some of the paths in manifest file are not valid GCS paths: \n${paths.mkString("\n")}"
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/errors/PipelinesApiKnownJobFailure.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/errors/PipelinesApiKnownJobFailure.scala
index 7c232c04700..e2842a78e95 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/errors/PipelinesApiKnownJobFailure.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/errors/PipelinesApiKnownJobFailure.scala
@@ -10,7 +10,7 @@ case class FailToLocalizeFailure(messages: List[String]) extends PipelinesApiKno
 }
 
 case class FailedToDelocalizeFailure(message: String, jobTag: String, stderrPath: Option[Path])
-  extends PipelinesApiKnownJobFailure {
+    extends PipelinesApiKnownJobFailure {
   lazy val stderrMessage = stderrPath map { p =>
     s"3) Look into the stderr (${p.pathAsString}) file for evidence that some of the output files the command is expected to create were not created."
   } getOrElse ""
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/PipelinesApiAttachedDisk.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/PipelinesApiAttachedDisk.scala
index fb686ec4371..fec1ad22c52 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/PipelinesApiAttachedDisk.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/PipelinesApiAttachedDisk.scala
@@ -20,9 +20,14 @@ object PipelinesApiAttachedDisk {
     def diskTypeValidation(diskTypeString: String): ErrorOr[DiskType] = validateDiskType(diskTypeString)
 
     val validation: ErrorOr[PipelinesApiAttachedDisk] = s match {
-      case WorkingDiskPattern(sizeGb, diskType) => (validateDiskType(diskType), sizeGbValidation(sizeGb)) mapN { PipelinesApiWorkingDisk.apply }
-      case MountedDiskPattern(mountPoint, sizeGb, diskType) => (sizeGbValidation(sizeGb), diskTypeValidation(diskType)) mapN { (s, dt) => PipelinesApiEmptyMountedDisk(dt, s, DefaultPathBuilder.get(mountPoint)) }
-      case _ => s"Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: '$s'".invalidNel
+      case WorkingDiskPattern(sizeGb, diskType) =>
+        (validateDiskType(diskType), sizeGbValidation(sizeGb)) mapN PipelinesApiWorkingDisk.apply
+      case MountedDiskPattern(mountPoint, sizeGb, diskType) =>
+        (sizeGbValidation(sizeGb), diskTypeValidation(diskType)) mapN { (s, dt) =>
+          PipelinesApiEmptyMountedDisk(dt, s, DefaultPathBuilder.get(mountPoint))
+        }
+      case _ =>
+        s"Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: '$s'".invalidNel
     }
 
     Try(validation match {
@@ -35,30 +40,30 @@ object PipelinesApiAttachedDisk {
     })
   }
 
-  private def validateDiskType(diskTypeName: String): ErrorOr[DiskType] = {
+  private def validateDiskType(diskTypeName: String): ErrorOr[DiskType] =
     DiskType.values().find(_.diskTypeName == diskTypeName) match {
       case Some(diskType) => diskType.validNel
       case None =>
         val diskTypeNames = DiskType.values.map(_.diskTypeName).mkString(", ")
         s"Disk TYPE $diskTypeName should be one of $diskTypeNames".invalidNel
     }
-  }
 
-  private def validateLong(value: String): ErrorOr[Long] = {
-    try {
+  private def validateLong(value: String): ErrorOr[Long] =
+    try
       value.toLong.validNel
-    } catch {
+    catch {
       case _: IllegalArgumentException => s"$value not convertible to a Long".invalidNel
     }
-  }
-  
+
   implicit class EnhancedDisks(val disks: Seq[PipelinesApiAttachedDisk]) extends AnyVal {
-    def adjustWorkingDiskWithNewMin(minimum: MemorySize, onAdjustment: => Unit): Seq[PipelinesApiAttachedDisk] = disks map {
-      case disk: PipelinesApiWorkingDisk if disk == PipelinesApiWorkingDisk.Default && disk.sizeGb < minimum.to(MemoryUnit.GB).amount.toInt =>
-        onAdjustment
-        disk.copy(sizeGb = minimum.to(MemoryUnit.GB).amount.toInt)
-      case other => other
-    }
+    def adjustWorkingDiskWithNewMin(minimum: MemorySize, onAdjustment: => Unit): Seq[PipelinesApiAttachedDisk] =
+      disks map {
+        case disk: PipelinesApiWorkingDisk
+            if disk == PipelinesApiWorkingDisk.Default && disk.sizeGb < minimum.to(MemoryUnit.GB).amount.toInt =>
+          onAdjustment
+          disk.copy(sizeGb = minimum.to(MemoryUnit.GB).amount.toInt)
+        case other => other
+      }
   }
 }
 
@@ -69,7 +74,8 @@ trait PipelinesApiAttachedDisk {
   def mountPoint: Path
 }
 
-case class PipelinesApiEmptyMountedDisk(diskType: DiskType, sizeGb: Int, mountPoint: Path) extends PipelinesApiAttachedDisk {
+case class PipelinesApiEmptyMountedDisk(diskType: DiskType, sizeGb: Int, mountPoint: Path)
+    extends PipelinesApiAttachedDisk {
   val name = s"d-${mountPoint.pathAsString.md5Sum}"
   override def toString: String = s"$mountPoint $sizeGb ${diskType.diskTypeName}"
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/package.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/package.scala
index 01bbc913e87..56b70e049fd 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/package.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/package.scala
@@ -7,22 +7,20 @@ import cromwell.core.path.Path
 package object io {
   implicit class PathEnhanced(val path: Path) extends AnyVal {
 
-    def writeAsJson(content: String): Path = {
+    def writeAsJson(content: String): Path =
       path.writeBytes(content.getBytes.iterator)(Seq(CloudStorageOptions.withMimeType("application/json")))
-    }
 
-    def writeAsText(content: String): Path = {
+    def writeAsText(content: String): Path =
       path.writeBytes(content.getBytes.iterator)(Seq(CloudStorageOptions.withMimeType("text/plain")))
-    }
   }
 
-  private [pipelines] def isFatalJesException(t: Throwable): Boolean = t match {
+  private[pipelines] def isFatalJesException(t: Throwable): Boolean = t match {
     case e: HttpResponseException if e.getStatusCode == 403 => true
     case e: HttpResponseException if e.getStatusCode == 400 && e.getContent.contains("INVALID_ARGUMENT") => true
     case _ => false
   }
 
-  private [pipelines] def isTransientJesException(t: Throwable): Boolean = t match {
+  private[pipelines] def isTransientJesException(t: Throwable): Boolean = t match {
     // Quota exceeded
     case e: HttpResponseException if e.getStatusCode == 429 => true
     case _ => false
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/CheckpointingConfiguration.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/CheckpointingConfiguration.scala
index c55ccdcda0a..95351449060 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/CheckpointingConfiguration.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/CheckpointingConfiguration.scala
@@ -10,18 +10,21 @@ final class CheckpointingConfiguration(jobDescriptor: BackendJobDescriptor,
                                        workflowPaths: WorkflowPaths,
                                        commandDirectory: Path,
                                        checkpointInterval: FiniteDuration
-                                      ) {
-  def checkpointFileCloud(checkpointFileName: String): String = {
+) {
+  def checkpointFileCloud(checkpointFileName: String): String =
     // The checkpoint file for ANY attempt always goes in the "attempt 1" directory. That way we guarantee that
     // every attempt is able to recover from the single source of checkpointing truth.
-    workflowPaths.toJobPaths(jobDescriptor.key.copy(attempt = 1), jobDescriptor.workflowDescriptor)
-      .callExecutionRoot.resolve("__checkpointing").resolve(checkpointFileName).toAbsolutePath.pathAsString
-  }
+    workflowPaths
+      .toJobPaths(jobDescriptor.key.copy(attempt = 1), jobDescriptor.workflowDescriptor)
+      .callExecutionRoot
+      .resolve("__checkpointing")
+      .resolve(checkpointFileName)
+      .toAbsolutePath
+      .pathAsString
   def tmpCheckpointFileCloud(checkpointFileName: String): String = checkpointFileCloud(checkpointFileName) + "-tmp"
 
-  def checkpointFileLocal(checkpointFileName: String): String = {
+  def checkpointFileLocal(checkpointFileName: String): String =
     commandDirectory.resolve(checkpointFileName).toAbsolutePath.pathAsString
-  }
   def tmpCheckpointFileLocal(checkpointFileName: String): String = checkpointFileLocal(checkpointFileName) + "-tmp"
 
   def localizePreviousCheckpointCommand(checkpointFileName: String): String = {
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/Env.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/Env.scala
index 62bb2c2d12a..a886cc7a819 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/Env.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/Env.scala
@@ -3,6 +3,7 @@ package cromwell.backend.google.pipelines.common.monitoring
 import cromwell.backend.BackendJobDescriptor
 
 object Env {
+
   /**
     * Name of an environmental variable
     */
@@ -12,13 +13,12 @@ object Env {
   val TaskCallAttempt = "TASK_CALL_ATTEMPT"
   val DiskMounts = "DISK_MOUNTS"
 
-  def monitoringImageEnvironment(jobDescriptor: BackendJobDescriptor)
-                                (mountPaths: List[String]): Map[String, String] =
+  def monitoringImageEnvironment(jobDescriptor: BackendJobDescriptor)(mountPaths: List[String]): Map[String, String] =
     Map(
       Env.WorkflowId -> jobDescriptor.workflowDescriptor.id.toString,
       Env.TaskCallName -> jobDescriptor.taskCall.localName,
       Env.TaskCallIndex -> jobDescriptor.key.index.map(_.toString).getOrElse("NA"),
       Env.TaskCallAttempt -> jobDescriptor.key.attempt.toString,
-      Env.DiskMounts -> mountPaths.mkString(" "),
+      Env.DiskMounts -> mountPaths.mkString(" ")
     )
 }
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/MonitoringImage.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/MonitoringImage.scala
index 24e7e424e80..d953b1a2168 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/MonitoringImage.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/monitoring/MonitoringImage.scala
@@ -13,8 +13,8 @@ final class MonitoringImage(jobDescriptor: BackendJobDescriptor,
                             workflowPaths: WorkflowPaths,
                             commandDirectory: Path,
                             workingDisk: PipelinesApiAttachedDisk,
-                            localMonitoringImageScriptPath: Path,
-                           ) {
+                            localMonitoringImageScriptPath: Path
+) {
 
   val monitoringImageOption: Option[String] = workflowOptions.get(WorkflowOptionKeys.MonitoringImage).toOption
 
@@ -24,22 +24,21 @@ final class MonitoringImage(jobDescriptor: BackendJobDescriptor,
     for {
       _ <- monitoringImageOption // Only use the monitoring_image_script when monitoring_image provided
       monitoringImageScript <- workflowOptions.get(WorkflowOptionKeys.MonitoringImageScript).toOption
-    } yield {
-      PathFactory.buildPath(
-        monitoringImageScript,
-        workflowPaths.pathBuilders,
-      )
-    }
+    } yield PathFactory.buildPath(
+      monitoringImageScript,
+      workflowPaths.pathBuilders
+    )
 
   val monitoringImageCommand: List[String] =
     monitoringImageScriptOption match {
-      case Some(_) => List(
-        "/bin/sh",
-        "-c",
-        s"cd '${commandDirectory.pathAsString}' && " +
-          s"chmod +x '${monitoringImageScriptContainerPath.pathAsString}' && " +
-          s"'${monitoringImageScriptContainerPath.pathAsString}'"
-      )
+      case Some(_) =>
+        List(
+          "/bin/sh",
+          "-c",
+          s"cd '${commandDirectory.pathAsString}' && " +
+            s"chmod +x '${monitoringImageScriptContainerPath.pathAsString}' && " +
+            s"'${monitoringImageScriptContainerPath.pathAsString}'"
+        )
       case None => Nil
     }
 
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/IoSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/IoSpec.scala
index 80cfc3543b9..de2434ca90b 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/IoSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/IoSpec.scala
@@ -1,7 +1,12 @@
 package cromwell.backend.google.pipelines.common
 
 import com.google.api.client.http.HttpResponseException
-import com.google.api.client.testing.http.{HttpTesting, MockHttpTransport, MockLowLevelHttpRequest, MockLowLevelHttpResponse}
+import com.google.api.client.testing.http.{
+  HttpTesting,
+  MockHttpTransport,
+  MockLowLevelHttpRequest,
+  MockLowLevelHttpResponse
+}
 import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
@@ -25,10 +30,9 @@ class IoSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   private def mockTransport(statusCode: Int) = new MockHttpTransport() {
-    override def buildRequest(method: String, url: String) = {
+    override def buildRequest(method: String, url: String) =
       new MockLowLevelHttpRequest() {
         override def execute() = new MockLowLevelHttpResponse().setStatusCode(statusCode)
       }
-    }
   }
 }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/MachineConstraintsSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/MachineConstraintsSpec.scala
index 48ace9666e0..919ee49a255 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/MachineConstraintsSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/MachineConstraintsSpec.scala
@@ -74,16 +74,16 @@ class MachineConstraintsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
       (MemorySize(1024.0, MemoryUnit.MB), refineMV[Positive](1), n2OptionIceLake, false, "n2-custom-2-2048"),
       (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), n2OptionIceLake, false, "n2-custom-36-36864"),
 
-      // Same tests but with AMD Rome (n2d) #cpu > 16 are in increments of 16  
+      // Same tests but with AMD Rome (n2d) #cpu > 16 are in increments of 16
       (MemorySize(1024, MemoryUnit.MB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1024"),
-      (MemorySize(4,  MemoryUnit.GB), refineMV[Positive](3), n2dOption, false, "n2d-custom-4-4096"),
+      (MemorySize(4, MemoryUnit.GB), refineMV[Positive](3), n2dOption, false, "n2d-custom-4-4096"),
       (MemorySize(1, MemoryUnit.GB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1024"),
-      (MemorySize(1 , MemoryUnit.GB), refineMV[Positive](4), n2dOption, false, "n2d-custom-4-2048"),
+      (MemorySize(1, MemoryUnit.GB), refineMV[Positive](4), n2dOption, false, "n2d-custom-4-2048"),
       (MemorySize(14, MemoryUnit.GB), refineMV[Positive](16), n2dOption, false, "n2d-custom-16-14336"),
       (MemorySize(13.65, MemoryUnit.GB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-14080"),
       (MemorySize(1520.96, MemoryUnit.MB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1536"),
       (MemorySize(1024.0, MemoryUnit.MB), refineMV[Positive](1), n2dOption, false, "n2d-custom-2-1024"),
-      (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), n2dOption, false, "n2d-custom-48-24576"), 
+      (MemorySize(2, MemoryUnit.GB), refineMV[Positive](33), n2dOption, false, "n2d-custom-48-24576"),
       (MemorySize(2, MemoryUnit.GB), refineMV[Positive](81), n2dOption, false, "n2d-custom-96-49152"),
       (MemorySize(256, MemoryUnit.GB), refineMV[Positive](128), n2dOption, false, "n2d-custom-96-262144")
     )
@@ -94,7 +94,7 @@ class MachineConstraintsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
         cpu = cpu,
         cpuPlatformOption = cpuPlatformOption,
         googleLegacyMachineSelection = googleLegacyMachineSelection,
-        jobLogger = NOPLogger.NOP_LOGGER,
+        jobLogger = NOPLogger.NOP_LOGGER
       ) shouldBe expected
     }
   }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
index 828112b557d..37221ff8534 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
@@ -11,17 +11,31 @@ import cats.data.NonEmptyList
 import com.google.api.client.http.HttpRequest
 import com.google.cloud.NoCredentials
 import common.collections.EnhancedCollections._
-import cromwell.backend.BackendJobExecutionActor.{BackendJobExecutionResponse, JobFailedNonRetryableResponse, JobFailedRetryableResponse}
+import cromwell.backend.BackendJobExecutionActor.{
+  BackendJobExecutionResponse,
+  JobFailedNonRetryableResponse,
+  JobFailedRetryableResponse
+}
 import cromwell.backend._
 import cromwell.backend.async.AsyncBackendJobExecutionActor.{Execute, ExecutionMode}
-import cromwell.backend.async.{AbortedExecutionHandle, ExecutionHandle, FailedNonRetryableExecutionHandle, FailedRetryableExecutionHandle}
+import cromwell.backend.async.{
+  AbortedExecutionHandle,
+  ExecutionHandle,
+  FailedNonRetryableExecutionHandle,
+  FailedRetryableExecutionHandle
+}
 import cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.JesPendingExecutionHandle
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.PAPIStatusPollRequest
 import cromwell.backend.google.pipelines.common.api.RunStatus.UnsuccessfulRunStatus
 import cromwell.backend.google.pipelines.common.io.{DiskType, PipelinesApiWorkingDisk}
 import cromwell.backend.io.JobPathsSpecHelper._
-import cromwell.backend.standard.{DefaultStandardAsyncExecutionActorParams, StandardAsyncExecutionActorParams, StandardAsyncJob, StandardExpressionFunctionsParams}
+import cromwell.backend.standard.{
+  DefaultStandardAsyncExecutionActorParams,
+  StandardAsyncExecutionActorParams,
+  StandardAsyncJob,
+  StandardExpressionFunctionsParams
+}
 import cromwell.core._
 import cromwell.core.callcaching.NoDocker
 import cromwell.core.labels.Labels
@@ -55,13 +69,14 @@ import scala.concurrent.{Await, ExecutionContext, Future, Promise}
 import scala.language.postfixOps
 import scala.util.Success
 
-class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
-  with AnyFlatSpecLike
-  with Matchers
-  with ImplicitSender
-  with BackendSpec
-  with BeforeAndAfter
-  with DefaultJsonProtocol {
+class PipelinesApiAsyncBackendJobExecutionActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with ImplicitSender
+    with BackendSpec
+    with BeforeAndAfter
+    with DefaultJsonProtocol {
 
   val mockPathBuilder: GcsPathBuilder = MockGcsPathBuilder.instance
   import MockGcsPathBuilder._
@@ -75,60 +90,76 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
   val YoSup: String =
     s"""
-      |task sup {
-      |  String addressee
-      |  command {
-      |    echo "yo sup $${addressee}!"
-      |  }
-      |  output {
-      |    String salutation = read_string(stdout())
-      |  }
-      |  runtime {
-      |    docker: "ubuntu:latest"
-      |    [PREEMPTIBLE]
-      |  }
-      |}
-      |
-      |workflow wf_sup {
-      |  call sup
-      |}
+       |task sup {
+       |  String addressee
+       |  command {
+       |    echo "yo sup $${addressee}!"
+       |  }
+       |  output {
+       |    String salutation = read_string(stdout())
+       |  }
+       |  runtime {
+       |    docker: "ubuntu:latest"
+       |    [PREEMPTIBLE]
+       |  }
+       |}
+       |
+       |workflow wf_sup {
+       |  call sup
+       |}
     """.stripMargin
 
   val Inputs: Map[FullyQualifiedName, WomValue] = Map("wf_sup.sup.addressee" -> WomString("dog"))
 
   private val NoOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))
 
-  private lazy val TestableCallContext = CallContext(mockPathBuilder.build("gs://root").get, DummyStandardPaths, isDocker = false)
+  private lazy val TestableCallContext =
+    CallContext(mockPathBuilder.build("gs://root").get, DummyStandardPaths, isDocker = false)
 
-  private lazy val TestableStandardExpressionFunctionsParams: StandardExpressionFunctionsParams
-  = new StandardExpressionFunctionsParams {
-    override lazy val pathBuilders: List[PathBuilder] = List(mockPathBuilder)
-    override lazy val callContext: CallContext = TestableCallContext
-    override val ioActorProxy: ActorRef = simpleIoActor
-    override val executionContext: ExecutionContext = system.dispatcher
-  }
+  private lazy val TestableStandardExpressionFunctionsParams: StandardExpressionFunctionsParams =
+    new StandardExpressionFunctionsParams {
+      override lazy val pathBuilders: List[PathBuilder] = List(mockPathBuilder)
+      override lazy val callContext: CallContext = TestableCallContext
+      override val ioActorProxy: ActorRef = simpleIoActor
+      override val executionContext: ExecutionContext = system.dispatcher
+    }
 
-  lazy val TestableJesExpressionFunctions: PipelinesApiExpressionFunctions = {
+  lazy val TestableJesExpressionFunctions: PipelinesApiExpressionFunctions =
     new PipelinesApiExpressionFunctions(TestableStandardExpressionFunctionsParams)
-  }
 
   private def buildInitializationData(jobDescriptor: BackendJobDescriptor, configuration: PipelinesApiConfiguration) = {
-    val pathBuilders = Await.result(configuration.configurationDescriptor.pathBuilders(WorkflowOptions.empty), 5.seconds)
+    val pathBuilders =
+      Await.result(configuration.configurationDescriptor.pathBuilders(WorkflowOptions.empty), 5.seconds)
     val workflowPaths = PipelinesApiWorkflowPaths(
-      jobDescriptor.workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), configuration, pathBuilders, PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+      jobDescriptor.workflowDescriptor,
+      NoCredentials.getInstance(),
+      NoCredentials.getInstance(),
+      configuration,
+      pathBuilders,
+      PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper
+    )
     val runtimeAttributesBuilder = PipelinesApiRuntimeAttributes.runtimeAttributesBuilder(configuration)
     val requestFactory: PipelinesApiRequestFactory = new PipelinesApiRequestFactory {
       override def cancelRequest(job: StandardAsyncJob): HttpRequest = null
       override def getRequest(job: StandardAsyncJob): HttpRequest = null
       override def runRequest(createPipelineParameters: PipelinesApiRequestFactory.CreatePipelineParameters,
-                              jobLogger: JobLogger,
-                             ): HttpRequest = null
+                              jobLogger: JobLogger
+      ): HttpRequest = null
     }
-    PipelinesApiBackendInitializationData(workflowPaths, runtimeAttributesBuilder, configuration, null, requestFactory, None, None, None)
+    PipelinesApiBackendInitializationData(workflowPaths,
+                                          runtimeAttributesBuilder,
+                                          configuration,
+                                          null,
+                                          requestFactory,
+                                          None,
+                                          None,
+                                          None
+    )
   }
 
-  class TestablePipelinesApiJobExecutionActor(params: StandardAsyncExecutionActorParams, functions: PipelinesApiExpressionFunctions)
-    extends PipelinesApiAsyncBackendJobExecutionActor(params) {
+  class TestablePipelinesApiJobExecutionActor(params: StandardAsyncExecutionActorParams,
+                                              functions: PipelinesApiExpressionFunctions
+  ) extends PipelinesApiAsyncBackendJobExecutionActor(params) {
 
     def this(jobDescriptor: BackendJobDescriptor,
              promise: Promise[BackendJobExecutionResponse],
@@ -136,8 +167,8 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
              functions: PipelinesApiExpressionFunctions = TestableJesExpressionFunctions,
              jesSingletonActor: ActorRef = emptyActor,
              ioActor: ActorRef = mockIoActor,
-             serviceRegistryActor: ActorRef = kvService) = {
-
+             serviceRegistryActor: ActorRef = kvService
+    ) =
       this(
         DefaultStandardAsyncExecutionActorParams(
           jobIdKey = PipelinesApiAsyncBackendJobExecutionActor.JesOperationIdKey,
@@ -152,7 +183,6 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
         ),
         functions
       )
-    }
 
     override lazy val jobLogger: JobLogger = new JobLogger(
       loggerName = "TestLogger",
@@ -168,7 +198,6 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     override lazy val backendEngineFunctions: PipelinesApiExpressionFunctions = functions
   }
 
-
   private val runtimeAttributesBuilder = PipelinesApiRuntimeAttributes.runtimeAttributesBuilder(papiConfiguration)
   private val workingDisk = PipelinesApiWorkingDisk(DiskType.SSD, 200)
 
@@ -180,11 +209,18 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
       |}
     """.stripMargin
 
-  private def buildPreemptibleJobDescriptor(preemptible: Int, previousPreemptions: Int, previousUnexpectedRetries: Int, failedRetriesCountOpt: Option[Int] = None): BackendJobDescriptor = {
+  private def buildPreemptibleJobDescriptor(preemptible: Int,
+                                            previousPreemptions: Int,
+                                            previousUnexpectedRetries: Int,
+                                            failedRetriesCountOpt: Option[Int] = None
+  ): BackendJobDescriptor = {
     val attempt = previousPreemptions + previousUnexpectedRetries + 1
-    val wdlNamespace = WdlNamespaceWithWorkflow.load(YoSup.replace("[PREEMPTIBLE]", s"preemptible: $preemptible"),
-      Seq.empty[Draft2ImportResolver]).get
-    val womDefinition = wdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    val wdlNamespace = WdlNamespaceWithWorkflow
+      .load(YoSup.replace("[PREEMPTIBLE]", s"preemptible: $preemptible"), Seq.empty[Draft2ImportResolver])
+      .get
+    val womDefinition = wdlNamespace.workflow
+      .toWomWorkflowDefinition(isASubworkflow = false)
+      .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
 
     wdlNamespace.toWomExecutable(Option(Inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
       case Right(womExecutable) =>
@@ -209,21 +245,45 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
         val key = BackendJobDescriptorKey(job, None, attempt)
         val runtimeAttributes = makeRuntimeAttributes(job)
         val prefetchedKvEntries = Map(
-          PipelinesApiBackendLifecycleActorFactory.preemptionCountKey -> KvPair(ScopedKey(workflowDescriptor.id, KvJobKey(key), PipelinesApiBackendLifecycleActorFactory.preemptionCountKey), previousPreemptions.toString),
-          PipelinesApiBackendLifecycleActorFactory.unexpectedRetryCountKey -> KvPair(ScopedKey(workflowDescriptor.id, KvJobKey(key), PipelinesApiBackendLifecycleActorFactory.unexpectedRetryCountKey), previousUnexpectedRetries.toString))
-        val prefetchedKvEntriesUpd = if(failedRetriesCountOpt.isEmpty) {
+          PipelinesApiBackendLifecycleActorFactory.preemptionCountKey -> KvPair(
+            ScopedKey(workflowDescriptor.id,
+                      KvJobKey(key),
+                      PipelinesApiBackendLifecycleActorFactory.preemptionCountKey
+            ),
+            previousPreemptions.toString
+          ),
+          PipelinesApiBackendLifecycleActorFactory.unexpectedRetryCountKey -> KvPair(
+            ScopedKey(workflowDescriptor.id,
+                      KvJobKey(key),
+                      PipelinesApiBackendLifecycleActorFactory.unexpectedRetryCountKey
+            ),
+            previousUnexpectedRetries.toString
+          )
+        )
+        val prefetchedKvEntriesUpd = if (failedRetriesCountOpt.isEmpty) {
           prefetchedKvEntries
         } else {
-          prefetchedKvEntries + (BackendLifecycleActorFactory.FailedRetryCountKey -> KvPair(ScopedKey(workflowDescriptor.id, KvJobKey(key), BackendLifecycleActorFactory.FailedRetryCountKey), failedRetriesCountOpt.get.toString ))
+          prefetchedKvEntries + (BackendLifecycleActorFactory.FailedRetryCountKey -> KvPair(
+            ScopedKey(workflowDescriptor.id, KvJobKey(key), BackendLifecycleActorFactory.FailedRetryCountKey),
+            failedRetriesCountOpt.get.toString
+          ))
         }
-        BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(Inputs), NoDocker, None, prefetchedKvEntriesUpd)
+        BackendJobDescriptor(workflowDescriptor,
+                             key,
+                             runtimeAttributes,
+                             fqnWdlMapToDeclarationMap(Inputs),
+                             NoDocker,
+                             None,
+                             prefetchedKvEntriesUpd
+        )
       case Left(badtimes) => fail(badtimes.toList.mkString(", "))
     }
   }
 
   private case class DockerImageCacheTestingParameters(dockerImageCacheDiskOpt: Option[String],
                                                        dockerImageAsSpecifiedByUser: String,
-                                                       isDockerImageCacheUsageRequested: Boolean)
+                                                       isDockerImageCacheUsageRequested: Boolean
+  )
 
   private def executionActor(jobDescriptor: BackendJobDescriptor,
                              promise: Promise[BackendJobExecutionResponse],
@@ -232,13 +292,19 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
                              serviceRegistryActor: ActorRef = kvService,
                              referenceInputFilesOpt: Option[Set[PipelinesApiInput]] = None,
                              dockerImageCacheTestingParamsOpt: Option[DockerImageCacheTestingParameters] = None
-                            ): ActorRef = {
+  ): ActorRef = {
 
     val job = StandardAsyncJob(UUID.randomUUID().toString)
     val run = Run(job)
     val handle = new JesPendingExecutionHandle(jobDescriptor, run.job, Option(run), None)
 
-    class ExecuteOrRecoverActor extends TestablePipelinesApiJobExecutionActor(jobDescriptor, promise, papiConfiguration, jesSingletonActor = jesSingletonActor, serviceRegistryActor = serviceRegistryActor) {
+    class ExecuteOrRecoverActor
+        extends TestablePipelinesApiJobExecutionActor(jobDescriptor,
+                                                      promise,
+                                                      papiConfiguration,
+                                                      jesSingletonActor = jesSingletonActor,
+                                                      serviceRegistryActor = serviceRegistryActor
+        ) {
       override def executeOrRecover(mode: ExecutionMode)(implicit ec: ExecutionContext): Future[ExecutionHandle] = {
         sendIncrementMetricsForReferenceFiles(referenceInputFilesOpt)
         dockerImageCacheTestingParamsOpt.foreach { dockerImageCacheTestingParams =>
@@ -257,34 +323,58 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     system.actorOf(Props(new ExecuteOrRecoverActor), "ExecuteOrRecoverActor-" + UUID.randomUUID)
   }
 
-  private def runAndFail(previousPreemptions: Int, previousUnexpectedRetries: Int, preemptible: Int, errorCode: Status, innerErrorMessage: String, expectPreemptible: Boolean): BackendJobExecutionResponse = {
-
-    val runStatus = UnsuccessfulRunStatus(errorCode, Option(innerErrorMessage), Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), expectPreemptible)
+  private def runAndFail(previousPreemptions: Int,
+                         previousUnexpectedRetries: Int,
+                         preemptible: Int,
+                         errorCode: Status,
+                         innerErrorMessage: String,
+                         expectPreemptible: Boolean
+  ): BackendJobExecutionResponse = {
+
+    val runStatus = UnsuccessfulRunStatus(errorCode,
+                                          Option(innerErrorMessage),
+                                          Seq.empty,
+                                          Option("fakeMachine"),
+                                          Option("fakeZone"),
+                                          Option("fakeInstance"),
+                                          expectPreemptible
+    )
     val statusPoller = TestProbe("statusPoller")
 
     val promise = Promise[BackendJobExecutionResponse]()
-    val jobDescriptor =  buildPreemptibleJobDescriptor(preemptible, previousPreemptions, previousUnexpectedRetries)
+    val jobDescriptor = buildPreemptibleJobDescriptor(preemptible, previousPreemptions, previousUnexpectedRetries)
 
     // TODO: Use this to check the new KV entries are there!
-    //val kvProbe = TestProbe("kvProbe")
+    // val kvProbe = TestProbe("kvProbe")
 
     val backend = executionActor(jobDescriptor, promise, statusPoller.ref, expectPreemptible)
     backend ! Execute
-    statusPoller.expectMsgPF(max = Timeout, hint = "awaiting status poll") {
-      case _: PAPIStatusPollRequest => backend ! runStatus
+    statusPoller.expectMsgPF(max = Timeout, hint = "awaiting status poll") { case _: PAPIStatusPollRequest =>
+      backend ! runStatus
     }
 
     Await.result(promise.future, Timeout)
   }
 
-  def buildPreemptibleTestActorRef(attempt: Int, preemptible: Int, failedRetriesCountOpt: Option[Int] = None): TestActorRef[TestablePipelinesApiJobExecutionActor] = {
+  def buildPreemptibleTestActorRef(attempt: Int,
+                                   preemptible: Int,
+                                   failedRetriesCountOpt: Option[Int] = None
+  ): TestActorRef[TestablePipelinesApiJobExecutionActor] = {
     // For this test we say that all previous attempts were preempted:
-    val jobDescriptor = buildPreemptibleJobDescriptor(preemptible, attempt - 1, previousUnexpectedRetries = 0, failedRetriesCountOpt = failedRetriesCountOpt)
-    val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(),
-      papiConfiguration,
-      TestableJesExpressionFunctions,
-      emptyActor,
-      failIoActor))
+    val jobDescriptor = buildPreemptibleJobDescriptor(preemptible,
+                                                      attempt - 1,
+                                                      previousUnexpectedRetries = 0,
+                                                      failedRetriesCountOpt = failedRetriesCountOpt
+    )
+    val props = Props(
+      new TestablePipelinesApiJobExecutionActor(jobDescriptor,
+                                                Promise(),
+                                                papiConfiguration,
+                                                TestableJesExpressionFunctions,
+                                                emptyActor,
+                                                failIoActor
+      )
+    )
     TestActorRef(props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
   }
 
@@ -294,12 +384,33 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
   { // Set of "handle call failures appropriately with respect to preemption and failure" tests
     val expectations = Table(
-      ("previous_preemptions", "previous_unexpectedRetries", "preemptible", "errorCode", "message", "shouldRunAsPreemptible", "shouldRetry"),
+      ("previous_preemptions",
+       "previous_unexpectedRetries",
+       "preemptible",
+       "errorCode",
+       "message",
+       "shouldRunAsPreemptible",
+       "shouldRetry"
+      ),
       // No preemptible attempts allowed, but standard failures should be retried.
-      (0, 0, 0, Status.ABORTED, "13: retryable error", false, true), // This is the new "unexpected failure" mode, which is now retried
+      (0,
+       0,
+       0,
+       Status.ABORTED,
+       "13: retryable error",
+       false,
+       true
+      ), // This is the new "unexpected failure" mode, which is now retried
       (0, 1, 0, Status.ABORTED, "13: retryable error", false, true),
       (0, 2, 0, Status.ABORTED, "13: retryable error", false, false), // The third unexpected failure is a real failure.
-      (0, 0, 0, Status.ABORTED, "14: usually means preempted...?", false, false), // Usually means "preempted', but this wasn't a preemptible VM, so this should just be a failure.
+      (0,
+       0,
+       0,
+       Status.ABORTED,
+       "14: usually means preempted...?",
+       false,
+       false
+      ), // Usually means "preempted', but this wasn't a preemptible VM, so this should just be a failure.
       (0, 0, 0, Status.ABORTED, "15: other error", false, false),
       (0, 0, 0, Status.OUT_OF_RANGE, "13: unexpected error", false, false),
       (0, 0, 0, Status.OUT_OF_RANGE, "14: test error msg", false, false),
@@ -328,27 +439,62 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
       (1, 0, 1, Status.OUT_OF_RANGE, "Instance failed to start due to preemption.", false, false)
     )
 
-    expectations foreach { case (previousPreemptions, previousUnexpectedRetries, preemptible, errorCode, innerErrorMessage, shouldBePreemptible, shouldRetry) =>
-      val descriptor = s"previousPreemptions=$previousPreemptions, previousUnexpectedRetries=$previousUnexpectedRetries preemptible=$preemptible, errorCode=$errorCode, innerErrorMessage=$innerErrorMessage"
-      it should s"handle call failures appropriately with respect to preemption and failure ($descriptor)" in {
-        runAndFail(previousPreemptions, previousUnexpectedRetries, preemptible, errorCode, innerErrorMessage, shouldBePreemptible) match {
-          case response: JobFailedNonRetryableResponse =>
-            if(shouldRetry) fail(s"A should-be-retried job ($descriptor) was sent back to the engine with: $response")
-          case response: JobFailedRetryableResponse =>
-            if(!shouldRetry) fail(s"A shouldn't-be-retried job ($descriptor) was sent back to the engine with $response")
-          case huh => fail(s"Unexpected response: $huh")
+    expectations foreach {
+      case (previousPreemptions,
+            previousUnexpectedRetries,
+            preemptible,
+            errorCode,
+            innerErrorMessage,
+            shouldBePreemptible,
+            shouldRetry
+          ) =>
+        val descriptor =
+          s"previousPreemptions=$previousPreemptions, previousUnexpectedRetries=$previousUnexpectedRetries preemptible=$preemptible, errorCode=$errorCode, innerErrorMessage=$innerErrorMessage"
+        it should s"handle call failures appropriately with respect to preemption and failure ($descriptor)" in {
+          runAndFail(previousPreemptions,
+                     previousUnexpectedRetries,
+                     preemptible,
+                     errorCode,
+                     innerErrorMessage,
+                     shouldBePreemptible
+          ) match {
+            case response: JobFailedNonRetryableResponse =>
+              if (shouldRetry)
+                fail(s"A should-be-retried job ($descriptor) was sent back to the engine with: $response")
+            case response: JobFailedRetryableResponse =>
+              if (!shouldRetry)
+                fail(s"A shouldn't-be-retried job ($descriptor) was sent back to the engine with $response")
+            case huh => fail(s"Unexpected response: $huh")
+          }
         }
-      }
     }
   }
 
   it should "send proper value for \"number of reference files used gauge\" metric, or don't send anything if reference disks feature is disabled" in {
-    val expectedInput1 = PipelinesApiFileInput(name = "testfile1", relativeHostPath = DefaultPathBuilder.build(Paths.get(s"test/reference/path/file1")), mount = null, cloudPath = null)
-    val expectedInput2 = PipelinesApiFileInput(name = "testfile2", relativeHostPath = DefaultPathBuilder.build(Paths.get(s"test/reference/path/file2")), mount = null, cloudPath = null)
+    val expectedInput1 = PipelinesApiFileInput(name = "testfile1",
+                                               relativeHostPath =
+                                                 DefaultPathBuilder.build(Paths.get(s"test/reference/path/file1")),
+                                               mount = null,
+                                               cloudPath = null
+    )
+    val expectedInput2 = PipelinesApiFileInput(name = "testfile2",
+                                               relativeHostPath =
+                                                 DefaultPathBuilder.build(Paths.get(s"test/reference/path/file2")),
+                                               mount = null,
+                                               cloudPath = null
+    )
     val expectedReferenceInputFiles = Set[PipelinesApiInput](expectedInput1, expectedInput2)
 
-    val expectedMsg1 = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList.of("referencefiles", expectedInput1.relativeHostPath.pathAsString))))
-    val expectedMsg2 = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList.of("referencefiles", expectedInput2.relativeHostPath.pathAsString))))
+    val expectedMsg1 = InstrumentationServiceMessage(
+      CromwellIncrement(
+        CromwellBucket(List.empty, NonEmptyList.of("referencefiles", expectedInput1.relativeHostPath.pathAsString))
+      )
+    )
+    val expectedMsg2 = InstrumentationServiceMessage(
+      CromwellIncrement(
+        CromwellBucket(List.empty, NonEmptyList.of("referencefiles", expectedInput2.relativeHostPath.pathAsString))
+      )
+    )
 
     val jobDescriptor = buildPreemptibleJobDescriptor(0, 0, 0)
     val serviceRegistryProbe = TestProbe()
@@ -381,59 +527,74 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val serviceRegistryProbe = TestProbe()
     val madeUpDockerImageName = "test_madeup_docker_image_name"
 
-    val expectedMessageWhenRequestedNotFound = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList("docker", List("image", "cache", "image_not_in_cache", madeUpDockerImageName)))))
+    val expectedMessageWhenRequestedNotFound = InstrumentationServiceMessage(
+      CromwellIncrement(
+        CromwellBucket(List.empty,
+                       NonEmptyList("docker", List("image", "cache", "image_not_in_cache", madeUpDockerImageName))
+        )
+      )
+    )
     val backendDockerCacheRequestedButNotFound = executionActor(
       jobDescriptor,
       Promise[BackendJobExecutionResponse](),
       TestProbe().ref,
       shouldBePreemptible = false,
       serviceRegistryActor = serviceRegistryProbe.ref,
-      dockerImageCacheTestingParamsOpt =
-        Option(
-          DockerImageCacheTestingParameters(
-            None,
-            "test_madeup_docker_image_name",
-            isDockerImageCacheUsageRequested = true
-          )
+      dockerImageCacheTestingParamsOpt = Option(
+        DockerImageCacheTestingParameters(
+          None,
+          "test_madeup_docker_image_name",
+          isDockerImageCacheUsageRequested = true
         )
+      )
     )
     backendDockerCacheRequestedButNotFound ! Execute
     serviceRegistryProbe.expectMsg(expectedMessageWhenRequestedNotFound)
 
-    val expectedMessageWhenRequestedAndFound = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList("docker", List("image", "cache", "used_image_from_cache", madeUpDockerImageName)))))
+    val expectedMessageWhenRequestedAndFound = InstrumentationServiceMessage(
+      CromwellIncrement(
+        CromwellBucket(List.empty,
+                       NonEmptyList("docker", List("image", "cache", "used_image_from_cache", madeUpDockerImageName))
+        )
+      )
+    )
     val backendDockerCacheRequestedAndFound = executionActor(
       jobDescriptor,
       Promise[BackendJobExecutionResponse](),
       TestProbe().ref,
       shouldBePreemptible = false,
       serviceRegistryActor = serviceRegistryProbe.ref,
-      dockerImageCacheTestingParamsOpt =
-        Option(
-          DockerImageCacheTestingParameters(
-            Option("test_madeup_disk_image_name"),
-            "test_madeup_docker_image_name",
-            isDockerImageCacheUsageRequested = true
-          )
+      dockerImageCacheTestingParamsOpt = Option(
+        DockerImageCacheTestingParameters(
+          Option("test_madeup_disk_image_name"),
+          "test_madeup_docker_image_name",
+          isDockerImageCacheUsageRequested = true
         )
+      )
     )
     backendDockerCacheRequestedAndFound ! Execute
     serviceRegistryProbe.expectMsg(expectedMessageWhenRequestedAndFound)
 
-    val expectedMessageWhenNotRequestedButFound = InstrumentationServiceMessage(CromwellIncrement(CromwellBucket(List.empty, NonEmptyList("docker", List("image", "cache", "cached_image_not_used", madeUpDockerImageName)))))
+    val expectedMessageWhenNotRequestedButFound = InstrumentationServiceMessage(
+      CromwellIncrement(
+        CromwellBucket(List.empty,
+                       NonEmptyList("docker", List("image", "cache", "cached_image_not_used", madeUpDockerImageName))
+        )
+      )
+    )
     val backendDockerCacheNotRequestedButFound = executionActor(
       jobDescriptor,
       Promise[BackendJobExecutionResponse](),
       TestProbe().ref,
       shouldBePreemptible = false,
       serviceRegistryActor = serviceRegistryProbe.ref,
-      dockerImageCacheTestingParamsOpt =
-        Option(
-          DockerImageCacheTestingParameters(
-            Option("test_madeup_disk_image_name"),
-            "test_madeup_docker_image_name",
-            isDockerImageCacheUsageRequested = false
-          )
+      dockerImageCacheTestingParamsOpt = Option(
+        DockerImageCacheTestingParameters(
+          Option("test_madeup_disk_image_name"),
+          "test_madeup_docker_image_name",
+          isDockerImageCacheUsageRequested = false
         )
+      )
     )
     backendDockerCacheNotRequestedButFound ! Execute
     serviceRegistryProbe.expectMsg(expectedMessageWhenNotRequestedButFound)
@@ -444,14 +605,13 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
       TestProbe().ref,
       shouldBePreemptible = false,
       serviceRegistryActor = serviceRegistryProbe.ref,
-      dockerImageCacheTestingParamsOpt =
-        Option(
-          DockerImageCacheTestingParameters(
-            None,
-            "test_madeup_docker_image_name",
-            isDockerImageCacheUsageRequested = false
-          )
+      dockerImageCacheTestingParamsOpt = Option(
+        DockerImageCacheTestingParameters(
+          None,
+          "test_madeup_docker_image_name",
+          isDockerImageCacheUsageRequested = false
         )
+      )
     )
     backendDockerCacheNotRequestedNotFound ! Execute
     serviceRegistryProbe.expectNoMessage(timeout)
@@ -463,7 +623,15 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val runId = StandardAsyncJob(UUID.randomUUID().toString)
     val handle = new JesPendingExecutionHandle(null, runId, None, None)
 
-    val failedStatus = UnsuccessfulRunStatus(Status.ABORTED, Option("14: VM XXX shut down unexpectedly."), Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), wasPreemptible = true)
+    val failedStatus = UnsuccessfulRunStatus(
+      Status.ABORTED,
+      Option("14: VM XXX shut down unexpectedly."),
+      Seq.empty,
+      Option("fakeMachine"),
+      Option("fakeZone"),
+      Option("fakeInstance"),
+      wasPreemptible = true
+    )
     val executionResult = jesBackend.handleExecutionResult(failedStatus, handle)
     val result = Await.result(executionResult, timeout)
     result.isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
@@ -477,7 +645,15 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val runId = StandardAsyncJob(UUID.randomUUID().toString)
     val handle = new JesPendingExecutionHandle(null, runId, None, None)
 
-    val failedStatus = UnsuccessfulRunStatus(Status.ABORTED, Option("14: VM XXX shut down unexpectedly."), Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), wasPreemptible = true)
+    val failedStatus = UnsuccessfulRunStatus(
+      Status.ABORTED,
+      Option("14: VM XXX shut down unexpectedly."),
+      Seq.empty,
+      Option("fakeMachine"),
+      Option("fakeZone"),
+      Option("fakeInstance"),
+      wasPreemptible = true
+    )
     val executionResult = jesBackend.handleExecutionResult(failedStatus, handle)
     val result = Await.result(executionResult, timeout)
     result.isInstanceOf[FailedRetryableExecutionHandle] shouldBe true
@@ -492,7 +668,15 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val runId = StandardAsyncJob(UUID.randomUUID().toString)
     val handle = new JesPendingExecutionHandle(null, runId, None, None)
 
-    val failedStatus = UnsuccessfulRunStatus(Status.ABORTED, Option("14: VM XXX shut down unexpectedly."), Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), wasPreemptible = true)
+    val failedStatus = UnsuccessfulRunStatus(
+      Status.ABORTED,
+      Option("14: VM XXX shut down unexpectedly."),
+      Seq.empty,
+      Option("fakeMachine"),
+      Option("fakeZone"),
+      Option("fakeInstance"),
+      wasPreemptible = true
+    )
     val executionResult = jesBackend.handleExecutionResult(failedStatus, handle)
     val result = Await.result(executionResult, timeout)
     result.isInstanceOf[FailedRetryableExecutionHandle] shouldBe true
@@ -507,7 +691,14 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val runId = StandardAsyncJob(UUID.randomUUID().toString)
     val handle = new JesPendingExecutionHandle(null, runId, None, None)
 
-    val failedStatus = UnsuccessfulRunStatus(Status.ABORTED, Option("13: Retryable Error."), Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), wasPreemptible = true)
+    val failedStatus = UnsuccessfulRunStatus(Status.ABORTED,
+                                             Option("13: Retryable Error."),
+                                             Seq.empty,
+                                             Option("fakeMachine"),
+                                             Option("fakeZone"),
+                                             Option("fakeInstance"),
+                                             wasPreemptible = true
+    )
     val executionResult = jesBackend.handleExecutionResult(failedStatus, handle)
     val result = Await.result(executionResult, timeout)
     result.isInstanceOf[FailedRetryableExecutionHandle] shouldBe true
@@ -522,7 +713,15 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val runId = StandardAsyncJob(UUID.randomUUID().toString)
     val handle = new JesPendingExecutionHandle(null, runId, None, None)
 
-    val failedStatus = UnsuccessfulRunStatus(Status.ABORTED, Option(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style), Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), wasPreemptible = true)
+    val failedStatus = UnsuccessfulRunStatus(
+      Status.ABORTED,
+      Option(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style),
+      Seq.empty,
+      Option("fakeMachine"),
+      Option("fakeZone"),
+      Option("fakeInstance"),
+      wasPreemptible = true
+    )
     val executionResult = jesBackend.handleExecutionResult(failedStatus, handle)
     val result = Await.result(executionResult, timeout)
     result.isInstanceOf[FailedRetryableExecutionHandle] shouldBe true
@@ -537,7 +736,15 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val runId = StandardAsyncJob(UUID.randomUUID().toString)
     val handle = new JesPendingExecutionHandle(null, runId, None, None)
 
-    val failedStatus = UnsuccessfulRunStatus(Status.ABORTED, Option(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style), Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), wasPreemptible = true)
+    val failedStatus = UnsuccessfulRunStatus(
+      Status.ABORTED,
+      Option(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style),
+      Seq.empty,
+      Option("fakeMachine"),
+      Option("fakeZone"),
+      Option("fakeInstance"),
+      wasPreemptible = true
+    )
     val executionResult = jesBackend.handleExecutionResult(failedStatus, handle)
     val result = Await.result(executionResult, timeout)
     result.isInstanceOf[FailedRetryableExecutionHandle] shouldBe true
@@ -552,32 +759,42 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val runId = StandardAsyncJob(UUID.randomUUID().toString)
     val handle = new JesPendingExecutionHandle(null, runId, None, None)
 
-    val failedStatus = UnsuccessfulRunStatus(Status.ABORTED, Option(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style), Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), wasPreemptible = true)
+    val failedStatus = UnsuccessfulRunStatus(
+      Status.ABORTED,
+      Option(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style),
+      Seq.empty,
+      Option("fakeMachine"),
+      Option("fakeZone"),
+      Option("fakeInstance"),
+      wasPreemptible = true
+    )
     val executionResult = jesBackend.handleExecutionResult(failedStatus, handle)
     val result = Await.result(executionResult, timeout)
     result.isInstanceOf[FailedRetryableExecutionHandle] shouldBe true
 
-
     val probe = TestProbe("probe")
     val job = jesBackend.workflowDescriptor.callable.taskCallNodes.head
     val key = BackendJobDescriptorKey(job, None, attempt = 2)
 
-    val scopedKeyPreempt = ScopedKey(jesBackend.workflowId, KvJobKey(key), PipelinesApiBackendLifecycleActorFactory.preemptionCountKey)
+    val scopedKeyPreempt =
+      ScopedKey(jesBackend.workflowId, KvJobKey(key), PipelinesApiBackendLifecycleActorFactory.preemptionCountKey)
     probe.send(kvService, KvGet(scopedKeyPreempt))
-    probe.expectMsgPF(5.seconds) {
-      case kvPreempt: KvPair => kvPreempt.value shouldBe 1.toString
+    probe.expectMsgPF(5.seconds) { case kvPreempt: KvPair =>
+      kvPreempt.value shouldBe 1.toString
     }
 
-    val scopedKeyUnexpected = ScopedKey(jesBackend.workflowId, KvJobKey(key), PipelinesApiBackendLifecycleActorFactory.unexpectedRetryCountKey)
+    val scopedKeyUnexpected =
+      ScopedKey(jesBackend.workflowId, KvJobKey(key), PipelinesApiBackendLifecycleActorFactory.unexpectedRetryCountKey)
     probe.send(kvService, KvGet(scopedKeyUnexpected))
-    probe.expectMsgPF(5.seconds) {
-      case kvUnexpected: KvPair => kvUnexpected.value shouldBe 0.toString
+    probe.expectMsgPF(5.seconds) { case kvUnexpected: KvPair =>
+      kvUnexpected.value shouldBe 0.toString
     }
 
-    val scopedKeyFailedAttempts = ScopedKey(jesBackend.workflowId, KvJobKey(key), BackendLifecycleActorFactory.FailedRetryCountKey)
+    val scopedKeyFailedAttempts =
+      ScopedKey(jesBackend.workflowId, KvJobKey(key), BackendLifecycleActorFactory.FailedRetryCountKey)
     probe.send(kvService, KvGet(scopedKeyFailedAttempts))
-    probe.expectMsgPF(5.seconds) {
-      case kvFailedRetry: KvPair => kvFailedRetry.value shouldBe 1.toString
+    probe.expectMsgPF(5.seconds) { case kvFailedRetry: KvPair =>
+      kvFailedRetry.value shouldBe 1.toString
     }
   }
 
@@ -588,14 +805,23 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val handle = new JesPendingExecutionHandle(null, runId, None, None)
 
     def checkFailedResult(errorCode: Status, errorMessage: Option[String]): ExecutionHandle = {
-      val failed = UnsuccessfulRunStatus(errorCode, errorMessage, Seq.empty, Option("fakeMachine"), Option("fakeZone"), Option("fakeInstance"), wasPreemptible = true)
+      val failed = UnsuccessfulRunStatus(errorCode,
+                                         errorMessage,
+                                         Seq.empty,
+                                         Option("fakeMachine"),
+                                         Option("fakeZone"),
+                                         Option("fakeInstance"),
+                                         wasPreemptible = true
+      )
       Await.result(jesBackend.handleExecutionResult(failed, handle), timeout)
     }
 
     checkFailedResult(Status.ABORTED, Option("15: Other type of error."))
       .isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
-    checkFailedResult(Status.OUT_OF_RANGE, Option("14: Wrong errorCode.")).isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
-    checkFailedResult(Status.ABORTED, Option("Weird error message.")).isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
+    checkFailedResult(Status.OUT_OF_RANGE, Option("14: Wrong errorCode."))
+      .isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
+    checkFailedResult(Status.ABORTED, Option("Weird error message."))
+      .isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
     checkFailedResult(Status.ABORTED, Option("UnparsableInt: Even weirder error message."))
       .isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
     checkFailedResult(Status.ABORTED, None).isInstanceOf[FailedNonRetryableExecutionHandle] shouldBe true
@@ -632,14 +858,20 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
       gcsFileKey -> gcsFileVal
     )
 
-    val wdlNamespace = WdlNamespaceWithWorkflow.load(
-      wdlString,
-      Seq.empty[Draft2ImportResolver],
-    ).get
-    val womWorkflow = wdlNamespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    val wdlNamespace = WdlNamespaceWithWorkflow
+      .load(
+        wdlString,
+        Seq.empty[Draft2ImportResolver]
+      )
+      .get
+    val womWorkflow = wdlNamespace.workflow
+      .toWomWorkflowDefinition(isASubworkflow = false)
+      .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
     wdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
 
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
@@ -652,19 +884,28 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
           None
         )
 
-        val call: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst({ case t: CommandCallNode => t }).get
+        val call: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst { case t: CommandCallNode =>
+          t
+        }.get
         val key = BackendJobDescriptorKey(call, None, 1)
         val runtimeAttributes = makeRuntimeAttributes(call)
-        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
 
         val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration))
         val testActorRef = TestActorRef[TestablePipelinesApiJobExecutionActor](
-          props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
-
+          props,
+          s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
 
-        def gcsPathToLocal(womValue: WomValue): WomValue = {
+        def gcsPathToLocal(womValue: WomValue): WomValue =
           WomFileMapper.mapWomFiles(testActorRef.underlyingActor.mapCommandLineWomFile)(womValue).get
-        }
 
         val mappedInputs = jobDescriptor.localInputs safeMapValues gcsPathToLocal
 
@@ -687,50 +928,67 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
   }
 
   private val dockerAndDiskMapsWdlNamespace =
-    WdlNamespaceWithWorkflow.load(
-      SampleWdl.CurrentDirectoryMaps.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-      Seq.empty[Draft2ImportResolver],
-    ).get
+    WdlNamespaceWithWorkflow
+      .load(
+        SampleWdl.CurrentDirectoryMaps.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+        Seq.empty[Draft2ImportResolver]
+      )
+      .get
 
   private val dockerAndDiskArrayWdlNamespace =
-    WdlNamespaceWithWorkflow.load(
-      SampleWdl.CurrentDirectoryArray.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-      Seq.empty[Draft2ImportResolver],
-    ).get
+    WdlNamespaceWithWorkflow
+      .load(
+        SampleWdl.CurrentDirectoryArray.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+        Seq.empty[Draft2ImportResolver]
+      )
+      .get
 
   private val dockerAndDiskFilesWdlNamespace =
-    WdlNamespaceWithWorkflow.load(
-      SampleWdl.CurrentDirectoryFiles.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-      Seq.empty[Draft2ImportResolver],
-    ).get
+    WdlNamespaceWithWorkflow
+      .load(
+        SampleWdl.CurrentDirectoryFiles.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+        Seq.empty[Draft2ImportResolver]
+      )
+      .get
 
   it should "generate correct JesFileInputs from a WdlMap" in {
     val inputs: Map[String, WomValue] = Map(
-      "stringToFileMap" -> WomMap(WomMapType(WomStringType, WomSingleFileType), Map(
-        WomString("stringTofile1") -> WomSingleFile("gs://path/to/stringTofile1"),
-        WomString("stringTofile2") -> WomSingleFile("gs://path/to/stringTofile2")
-      )),
-      "fileToStringMap" -> WomMap(WomMapType(WomSingleFileType, WomStringType), Map(
-        WomSingleFile("gs://path/to/fileToString1") -> WomString("fileToString1"),
-        WomSingleFile("gs://path/to/fileToString2") -> WomString("fileToString2")
-      )),
-      "fileToFileMap" -> WomMap(WomMapType(WomSingleFileType, WomSingleFileType), Map(
-        WomSingleFile("gs://path/to/fileToFile1Key") -> WomSingleFile("gs://path/to/fileToFile1Value"),
-        WomSingleFile("gs://path/to/fileToFile2Key") -> WomSingleFile("gs://path/to/fileToFile2Value")
-      )),
-      "stringToString" -> WomMap(WomMapType(WomStringType, WomStringType), Map(
-        WomString("stringToString1") -> WomString("path/to/stringToString1"),
-        WomString("stringToString2") -> WomString("path/to/stringToString2")
-      ))
+      "stringToFileMap" -> WomMap(
+        WomMapType(WomStringType, WomSingleFileType),
+        Map(
+          WomString("stringTofile1") -> WomSingleFile("gs://path/to/stringTofile1"),
+          WomString("stringTofile2") -> WomSingleFile("gs://path/to/stringTofile2")
+        )
+      ),
+      "fileToStringMap" -> WomMap(
+        WomMapType(WomSingleFileType, WomStringType),
+        Map(
+          WomSingleFile("gs://path/to/fileToString1") -> WomString("fileToString1"),
+          WomSingleFile("gs://path/to/fileToString2") -> WomString("fileToString2")
+        )
+      ),
+      "fileToFileMap" -> WomMap(
+        WomMapType(WomSingleFileType, WomSingleFileType),
+        Map(
+          WomSingleFile("gs://path/to/fileToFile1Key") -> WomSingleFile("gs://path/to/fileToFile1Value"),
+          WomSingleFile("gs://path/to/fileToFile2Key") -> WomSingleFile("gs://path/to/fileToFile2Value")
+        )
+      ),
+      "stringToString" -> WomMap(
+        WomMapType(WomStringType, WomStringType),
+        Map(
+          WomString("stringToString1") -> WomString("path/to/stringToString1"),
+          WomString("stringToString2") -> WomString("path/to/stringToString2")
+        )
+      )
     )
 
-    val workflowInputs = inputs map {
-      case (key, value) => (s"wf_whereami.whereami.$key", value)
+    val workflowInputs = inputs map { case (key, value) =>
+      (s"wf_whereami.whereami.$key", value)
     }
 
     val womWorkflow =
-      dockerAndDiskMapsWdlNamespace
-        .workflow
+      dockerAndDiskMapsWdlNamespace.workflow
         .toWomWorkflowDefinition(isASubworkflow = false)
         .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
     val womExecutableChecked =
@@ -738,7 +996,9 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
         .toWomExecutable(Option(workflowInputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true)
     womExecutableChecked match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
           womWorkflow,
@@ -753,62 +1013,87 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
         val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
         val runtimeAttributes = makeRuntimeAttributes(job)
         val key = BackendJobDescriptorKey(job, None, 1)
-        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
 
         val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration))
         val testActorRef = TestActorRef[TestablePipelinesApiJobExecutionActor](
-          props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+          props,
+          s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
 
         val jesInputs = testActorRef.underlyingActor.generateInputs(jobDescriptor)
         jesInputs should have size 8
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.stringToFileMap-0",
-          cloudPath = gcsPath("gs://path/to/stringTofile1"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/stringTofile1"),
-          mount = workingDisk,
-        ))
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.stringToFileMap-1",
-          cloudPath = gcsPath("gs://path/to/stringTofile2"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/stringTofile2"),
-          mount = workingDisk,
-        ))
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.fileToStringMap-0",
-          cloudPath = gcsPath("gs://path/to/fileToString1"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/fileToString1"),
-          mount = workingDisk,
-        ))
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.fileToStringMap-1",
-          cloudPath = gcsPath("gs://path/to/fileToString2"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/fileToString2"),
-          mount = workingDisk,
-        ))
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.fileToFileMap-0",
-          cloudPath = gcsPath("gs://path/to/fileToFile1Key"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile1Key"),
-          mount = workingDisk,
-        ))
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.fileToFileMap-1",
-          cloudPath = gcsPath("gs://path/to/fileToFile1Value"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile1Value"),
-          mount = workingDisk,
-        ))
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.fileToFileMap-2",
-          cloudPath = gcsPath("gs://path/to/fileToFile2Key"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile2Key"),
-          mount = workingDisk,
-        ))
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.fileToFileMap-3",
-          cloudPath = gcsPath("gs://path/to/fileToFile2Value"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile2Value"),
-          mount = workingDisk,
-        ))
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.stringToFileMap-0",
+            cloudPath = gcsPath("gs://path/to/stringTofile1"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/stringTofile1"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.stringToFileMap-1",
+            cloudPath = gcsPath("gs://path/to/stringTofile2"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/stringTofile2"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.fileToStringMap-0",
+            cloudPath = gcsPath("gs://path/to/fileToString1"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToString1"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.fileToStringMap-1",
+            cloudPath = gcsPath("gs://path/to/fileToString2"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToString2"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.fileToFileMap-0",
+            cloudPath = gcsPath("gs://path/to/fileToFile1Key"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile1Key"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.fileToFileMap-1",
+            cloudPath = gcsPath("gs://path/to/fileToFile1Value"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile1Value"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.fileToFileMap-2",
+            cloudPath = gcsPath("gs://path/to/fileToFile2Key"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile2Key"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.fileToFileMap-3",
+            cloudPath = gcsPath("gs://path/to/fileToFile2Value"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile2Value"),
+            mount = workingDisk
+          )
+        )
 
       case Left(badness) => fail(badness.toList.mkString(", "))
     }
@@ -818,17 +1103,17 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
                               workflowInputs: Map[FullyQualifiedName, WomValue],
                               callName: LocallyQualifiedName,
                               callInputs: Map[LocallyQualifiedName, WomValue],
-                              functions: PipelinesApiExpressionFunctions = TestableJesExpressionFunctions,
-                             ):
-  TestActorRef[TestablePipelinesApiJobExecutionActor] = {
+                              functions: PipelinesApiExpressionFunctions = TestableJesExpressionFunctions
+  ): TestActorRef[TestablePipelinesApiJobExecutionActor] = {
     val wdlNamespaceWithWorkflow =
-      WdlNamespaceWithWorkflow.load(
-        sampleWdl.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-        Seq.empty[Draft2ImportResolver],
-      ).get
+      WdlNamespaceWithWorkflow
+        .load(
+          sampleWdl.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+          Seq.empty[Draft2ImportResolver]
+        )
+        .get
     val womWorkflow =
-      wdlNamespaceWithWorkflow
-        .workflow
+      wdlNamespaceWithWorkflow.workflow
         .toWomWorkflowDefinition(isASubworkflow = false)
         .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
     val womExecutableChecked =
@@ -836,11 +1121,13 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
         .toWomExecutable(
           Option(workflowInputs.toJson.compactPrint),
           NoIoFunctionSet,
-          strictValidation = true,
+          strictValidation = true
         )
     womExecutableChecked match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
           womWorkflow,
@@ -863,11 +1150,16 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
             evaluatedTaskInputs = fqnWdlMapToDeclarationMap(callInputs),
             maybeCallCachingEligible = NoDocker,
             dockerSize = None,
-            prefetchedKvStoreEntries = Map.empty,
+            prefetchedKvStoreEntries = Map.empty
           )
 
-        val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration, functions))
-        TestActorRef[TestablePipelinesApiJobExecutionActor](props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+        val props = Props(
+          new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration, functions)
+        )
+        TestActorRef[TestablePipelinesApiJobExecutionActor](
+          props,
+          s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
       case Left(badness) => fail(badness.toList.mkString(", "))
     }
   }
@@ -877,23 +1169,33 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val workflowInputs = Map("file_passing.f" -> womFile)
     val callInputs = Map(
       "in" -> womFile, // how does one programmatically map the wf inputs to the call inputs?
-      "out_name" -> WomString("out"), // is it expected that this isn't using the default?
+      "out_name" -> WomString("out") // is it expected that this isn't using the default?
     )
     val jesBackend = makeJesActorRef(SampleWdl.FilePassingWorkflow, workflowInputs, "a", callInputs).underlyingActor
     val jobDescriptor = jesBackend.jobDescriptor
     val workflowId = jesBackend.workflowId
     val jesInputs = jesBackend.generateInputs(jobDescriptor)
     jesInputs should have size 1
-    jesInputs should contain(PipelinesApiFileInput(
-      name = "file_passing.a.in-0",
-      cloudPath = gcsPath("gs://blah/b/c.txt"),
-      relativeHostPath = DefaultPathBuilder.get("blah/b/c.txt"),
-      mount = workingDisk,
-    ))
+    jesInputs should contain(
+      PipelinesApiFileInput(
+        name = "file_passing.a.in-0",
+        cloudPath = gcsPath("gs://blah/b/c.txt"),
+        relativeHostPath = DefaultPathBuilder.get("blah/b/c.txt"),
+        mount = workingDisk
+      )
+    )
     val jesOutputs = jesBackend.generateOutputs(jobDescriptor)
     jesOutputs should have size 1
-    jesOutputs should contain(PipelinesApiFileOutput("out",
-      gcsPath(s"gs://my-cromwell-workflows-bucket/file_passing/$workflowId/call-a/out"), DefaultPathBuilder.get("out"), workingDisk, optional = false, secondary = false))
+    jesOutputs should contain(
+      PipelinesApiFileOutput(
+        "out",
+        gcsPath(s"gs://my-cromwell-workflows-bucket/file_passing/$workflowId/call-a/out"),
+        DefaultPathBuilder.get("out"),
+        workingDisk,
+        optional = false,
+        secondary = false
+      )
+    )
   }
 
   it should "generate correct JesInputs when a command line contains a write_lines call in it" in {
@@ -901,10 +1203,10 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
       "strs" -> WomArray(WomArrayType(WomStringType), Seq("A", "B", "C").map(WomString))
     )
 
-    class TestPipelinesApiExpressionFunctions extends PipelinesApiExpressionFunctions(TestableStandardExpressionFunctionsParams) {
-      override def writeFile(path: String, content: String): Future[WomSingleFile] = {
+    class TestPipelinesApiExpressionFunctions
+        extends PipelinesApiExpressionFunctions(TestableStandardExpressionFunctionsParams) {
+      override def writeFile(path: String, content: String): Future[WomSingleFile] =
         Future.fromTry(Success(WomSingleFile(s"gs://some/path/file.txt")))
-      }
     }
 
     val functions = new TestPipelinesApiExpressionFunctions
@@ -912,12 +1214,14 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val jobDescriptor = jesBackend.jobDescriptor
     val jesInputs = jesBackend.generateInputs(jobDescriptor)
     jesInputs should have size 1
-    jesInputs should contain(PipelinesApiFileInput(
-      name = "c35ad8d3-0",
-      cloudPath = gcsPath("gs://some/path/file.txt"),
-      relativeHostPath = DefaultPathBuilder.get("some/path/file.txt"),
-      mount = workingDisk,
-    ))
+    jesInputs should contain(
+      PipelinesApiFileInput(
+        name = "c35ad8d3-0",
+        cloudPath = gcsPath("gs://some/path/file.txt"),
+        relativeHostPath = DefaultPathBuilder.get("some/path/file.txt"),
+        mount = workingDisk
+      )
+    )
     val jesOutputs = jesBackend.generateOutputs(jobDescriptor)
     jesOutputs should have size 0
   }
@@ -925,16 +1229,17 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
   it should "generate correct JesFileInputs from a WdlArray" in {
     val inputs: Map[String, WomValue] = Map(
       "fileArray" ->
-        WomArray(WomArrayType(WomSingleFileType), Seq(WomSingleFile("gs://path/to/file1"), WomSingleFile("gs://path/to/file2")))
+        WomArray(WomArrayType(WomSingleFileType),
+                 Seq(WomSingleFile("gs://path/to/file1"), WomSingleFile("gs://path/to/file2"))
+        )
     )
 
-    val workflowInputs = inputs map {
-      case (key, value) => (s"wf_whereami.whereami.$key", value)
+    val workflowInputs = inputs map { case (key, value) =>
+      (s"wf_whereami.whereami.$key", value)
     }
 
     val womWorkflow =
-      dockerAndDiskArrayWdlNamespace
-        .workflow
+      dockerAndDiskArrayWdlNamespace.workflow
         .toWomWorkflowDefinition(isASubworkflow = false)
         .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
     val womExecutableChecked =
@@ -942,7 +1247,9 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
         .toWomExecutable(Option(workflowInputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true)
     womExecutableChecked match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
           womWorkflow,
@@ -957,26 +1264,39 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
         val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
         val runtimeAttributes = makeRuntimeAttributes(job)
         val key = BackendJobDescriptorKey(job, None, 1)
-        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
 
         val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration))
         val testActorRef = TestActorRef[TestablePipelinesApiJobExecutionActor](
-          props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+          props,
+          s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
 
         val jesInputs = testActorRef.underlyingActor.generateInputs(jobDescriptor)
         jesInputs should have size 2
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.fileArray-0",
-          cloudPath = gcsPath("gs://path/to/file1"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/file1"),
-          mount = workingDisk,
-        ))
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.fileArray-1",
-          cloudPath = gcsPath("gs://path/to/file2"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/file2"),
-          mount = workingDisk,
-        ))
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.fileArray-0",
+            cloudPath = gcsPath("gs://path/to/file1"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/file1"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.fileArray-1",
+            cloudPath = gcsPath("gs://path/to/file2"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/file2"),
+            mount = workingDisk
+          )
+        )
       case Left(badness) => fail(badness.toList.mkString(", "))
     }
   }
@@ -987,13 +1307,12 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
       "file2" -> WomSingleFile("gs://path/to/file2")
     )
 
-    val workflowInputs = inputs map {
-      case (key, value) => (s"wf_whereami.whereami.$key", value)
+    val workflowInputs = inputs map { case (key, value) =>
+      (s"wf_whereami.whereami.$key", value)
     }
 
     val womWorkflow =
-      dockerAndDiskFilesWdlNamespace
-        .workflow
+      dockerAndDiskFilesWdlNamespace.workflow
         .toWomWorkflowDefinition(isASubworkflow = false)
         .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
     val womExecutableChecked =
@@ -1001,7 +1320,9 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
         .toWomExecutable(Option(workflowInputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true)
     womExecutableChecked match {
       case Right(womExecutable) =>
-        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap({case (port, v) => v.select[WomValue] map { port -> _ }})
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map { port -> _ }
+        }
         val workflowDescriptor = BackendWorkflowDescriptor(
           WorkflowId.randomId(),
           womWorkflow,
@@ -1016,26 +1337,39 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
         val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
         val runtimeAttributes = makeRuntimeAttributes(job)
         val key = BackendJobDescriptorKey(job, None, 1)
-        val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, fqnWdlMapToDeclarationMap(inputs), NoDocker, None, Map.empty)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
 
         val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration))
         val testActorRef = TestActorRef[TestablePipelinesApiJobExecutionActor](
-          props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+          props,
+          s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
 
         val jesInputs = testActorRef.underlyingActor.generateInputs(jobDescriptor)
         jesInputs should have size 2
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.file1-0",
-          cloudPath = gcsPath("gs://path/to/file1"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/file1"),
-          mount = workingDisk,
-        ))
-        jesInputs should contain(PipelinesApiFileInput(
-          name = "wf_whereami.whereami.file2-0",
-          cloudPath = gcsPath("gs://path/to/file2"),
-          relativeHostPath = DefaultPathBuilder.get("path/to/file2"),
-          mount = workingDisk,
-        ))
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.file1-0",
+            cloudPath = gcsPath("gs://path/to/file1"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/file1"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          PipelinesApiFileInput(
+            name = "wf_whereami.whereami.file2-0",
+            cloudPath = gcsPath("gs://path/to/file2"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/file2"),
+            mount = workingDisk
+          )
+        )
 
       case Left(badness) => fail(badness.toList.mkString(", "))
     }
@@ -1043,30 +1377,69 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
 
   it should "convert local Paths back to corresponding GCS paths in JesOutputs" in {
     val jesOutputs = Set(
-      PipelinesApiFileOutput("/cromwell_root/path/to/file1", gcsPath("gs://path/to/file1"),
-        DefaultPathBuilder.get("/cromwell_root/path/to/file1"), workingDisk, optional = false, secondary = false),
-      PipelinesApiFileOutput("/cromwell_root/path/to/file2", gcsPath("gs://path/to/file2"),
-        DefaultPathBuilder.get("/cromwell_root/path/to/file2"), workingDisk, optional = false, secondary = false),
-      PipelinesApiFileOutput("/cromwell_root/path/to/file3", gcsPath("gs://path/to/file3"),
-        DefaultPathBuilder.get("/cromwell_root/path/to/file3"), workingDisk, optional = false, secondary = false),
-      PipelinesApiFileOutput("/cromwell_root/path/to/file4", gcsPath("gs://path/to/file4"),
-        DefaultPathBuilder.get("/cromwell_root/path/to/file4"), workingDisk, optional = false, secondary = false),
-      PipelinesApiFileOutput("/cromwell_root/path/to/file5", gcsPath("gs://path/to/file5"),
-        DefaultPathBuilder.get("/cromwell_root/path/to/file5"), workingDisk, optional = false, secondary = false)
+      PipelinesApiFileOutput(
+        "/cromwell_root/path/to/file1",
+        gcsPath("gs://path/to/file1"),
+        DefaultPathBuilder.get("/cromwell_root/path/to/file1"),
+        workingDisk,
+        optional = false,
+        secondary = false
+      ),
+      PipelinesApiFileOutput(
+        "/cromwell_root/path/to/file2",
+        gcsPath("gs://path/to/file2"),
+        DefaultPathBuilder.get("/cromwell_root/path/to/file2"),
+        workingDisk,
+        optional = false,
+        secondary = false
+      ),
+      PipelinesApiFileOutput(
+        "/cromwell_root/path/to/file3",
+        gcsPath("gs://path/to/file3"),
+        DefaultPathBuilder.get("/cromwell_root/path/to/file3"),
+        workingDisk,
+        optional = false,
+        secondary = false
+      ),
+      PipelinesApiFileOutput(
+        "/cromwell_root/path/to/file4",
+        gcsPath("gs://path/to/file4"),
+        DefaultPathBuilder.get("/cromwell_root/path/to/file4"),
+        workingDisk,
+        optional = false,
+        secondary = false
+      ),
+      PipelinesApiFileOutput(
+        "/cromwell_root/path/to/file5",
+        gcsPath("gs://path/to/file5"),
+        DefaultPathBuilder.get("/cromwell_root/path/to/file5"),
+        workingDisk,
+        optional = false,
+        secondary = false
+      )
     )
     val outputValues = Seq(
       WomSingleFile("/cromwell_root/path/to/file1"),
-      WomArray(WomArrayType(WomSingleFileType), Seq(
-        WomSingleFile("/cromwell_root/path/to/file2"), WomSingleFile("/cromwell_root/path/to/file3"))),
-      WomMap(WomMapType(WomSingleFileType, WomSingleFileType), Map(
-        WomSingleFile("/cromwell_root/path/to/file4") -> WomSingleFile("/cromwell_root/path/to/file5")
-      ))
+      WomArray(WomArrayType(WomSingleFileType),
+               Seq(WomSingleFile("/cromwell_root/path/to/file2"), WomSingleFile("/cromwell_root/path/to/file3"))
+      ),
+      WomMap(WomMapType(WomSingleFileType, WomSingleFileType),
+             Map(
+               WomSingleFile("/cromwell_root/path/to/file4") -> WomSingleFile("/cromwell_root/path/to/file5")
+             )
+      )
     )
 
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+              Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
       NoOptions,
       Labels.empty,
@@ -1078,32 +1451,44 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration))
     val testActorRef = TestActorRef[TestablePipelinesApiJobExecutionActor](
-      props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
-    def wdlValueToGcsPath(jesOutputs: Set[PipelinesApiFileOutput])(womValue: WomValue): WomValue = {
+    def wdlValueToGcsPath(jesOutputs: Set[PipelinesApiFileOutput])(womValue: WomValue): WomValue =
       WomFileMapper.mapWomFiles(testActorRef.underlyingActor.womFileToGcsPath(jesOutputs.toSet))(womValue).get
-    }
 
     val result = outputValues map wdlValueToGcsPath(jesOutputs)
     result should have size 3
     result should contain(WomSingleFile("gs://path/to/file1"))
-    result should contain(WomArray(WomArrayType(WomSingleFileType),
-      Seq(WomSingleFile("gs://path/to/file2"), WomSingleFile("gs://path/to/file3")))
+    result should contain(
+      WomArray(WomArrayType(WomSingleFileType),
+               Seq(WomSingleFile("gs://path/to/file2"), WomSingleFile("gs://path/to/file3"))
+      )
     )
-    result should contain(WomMap(WomMapType(WomSingleFileType, WomSingleFileType),
-      Map(WomSingleFile("gs://path/to/file4") -> WomSingleFile("gs://path/to/file5")))
+    result should contain(
+      WomMap(WomMapType(WomSingleFileType, WomSingleFileType),
+             Map(WomSingleFile("gs://path/to/file4") -> WomSingleFile("gs://path/to/file5"))
+      )
     )
   }
 
   it should "create a JesFileInput for the monitoring script, when specified" in {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+              Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
       WorkflowOptions.fromJsonString("""{"monitoring_script": "gs://path/to/script"}""").get,
       Labels.empty,
@@ -1115,21 +1500,36 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
     val runtimeAttributes = makeRuntimeAttributes(job)
     val key = BackendJobDescriptorKey(job, None, 1)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration))
     val testActorRef = TestActorRef[TestablePipelinesApiJobExecutionActor](
-      props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     testActorRef.underlyingActor.monitoringScript shouldBe
-      Option(PipelinesApiFileInput("monitoring-in", gcsPath("gs://path/to/script"), DefaultPathBuilder.get("monitoring.sh"), workingDisk))
+      Option(
+        PipelinesApiFileInput("monitoring-in",
+                              gcsPath("gs://path/to/script"),
+                              DefaultPathBuilder.get("monitoring.sh"),
+                              workingDisk
+        )
+      )
   }
 
   it should "not create a JesFileInput for the monitoring script, when not specified" in {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId.randomId(),
-      WdlNamespaceWithWorkflow.load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(SampleWdl.EmptyString.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+              Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
       NoOptions,
       Labels.empty,
@@ -1138,14 +1538,17 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
       None
     )
 
-    val job: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst({case t: CommandCallNode => t}).get
+    val job: CommandCallNode = workflowDescriptor.callable.graph.nodes.collectFirst { case t: CommandCallNode => t }.get
     val key = BackendJobDescriptorKey(job, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(job)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration))
     val testActorRef = TestActorRef[TestablePipelinesApiJobExecutionActor](
-      props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     testActorRef.underlyingActor.monitoringScript shouldBe None
   }
@@ -1153,9 +1556,14 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
   it should "return JES log paths for non-scattered call" in {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId(UUID.fromString("e6236763-c518-41d0-9688-432549a8bf7c")),
-      WdlNamespaceWithWorkflow.load(
-        SampleWdl.HelloWorld.asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(SampleWdl.HelloWorld.asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
+              Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
       WorkflowOptions.fromJsonString(""" {"jes_gcs_root": "gs://path/to/gcs_root"} """).get,
       Labels.empty,
@@ -1167,11 +1575,14 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "hello").get
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration))
     val testActorRef = TestActorRef[TestablePipelinesApiJobExecutionActor](
-      props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     val jesBackend = testActorRef.underlyingActor
 
@@ -1189,9 +1600,15 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
   it should "return JES log paths for scattered call" in {
     val workflowDescriptor = BackendWorkflowDescriptor(
       WorkflowId(UUID.fromString("e6236763-c518-41d0-9688-432549a8bf7d")),
-      WdlNamespaceWithWorkflow.load(
-        new SampleWdl.ScatterWdl().asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
-        Seq.empty[Draft2ImportResolver]).get.workflow.toWomWorkflowDefinition(isASubworkflow = false).getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
+      WdlNamespaceWithWorkflow
+        .load(
+          new SampleWdl.ScatterWdl().asWorkflowSources(""" runtime {docker: "ubuntu:latest"} """).workflowSource.get,
+          Seq.empty[Draft2ImportResolver]
+        )
+        .get
+        .workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
       WorkflowOptions.fromJsonString(""" {"jes_gcs_root": "gs://path/to/gcs_root"} """).get,
       Labels.empty,
@@ -1203,11 +1620,14 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "B").get
     val key = BackendJobDescriptorKey(call, Option(2), 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration))
     val testActorRef = TestActorRef[TestablePipelinesApiJobExecutionActor](
-      props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     val jesBackend = testActorRef.underlyingActor
 
@@ -1223,9 +1643,8 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
   }
 
   it should "return preemptible = true only in the correct cases" in {
-    def attempt(max: Int, attempt: Int): PipelinesApiAsyncBackendJobExecutionActor = {
+    def attempt(max: Int, attempt: Int): PipelinesApiAsyncBackendJobExecutionActor =
       buildPreemptibleTestActorRef(attempt, max).underlyingActor
-    }
     def attempt1(max: Int) = attempt(max, 1)
     def attempt2(max: Int) = attempt(max, 2)
 
@@ -1261,13 +1680,15 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
         .toWomWorkflowDefinition(isASubworkflow = false)
         .getOrElse(fail("failed to get WomDefinition from WdlWorkflow")),
       Map.empty,
-      WorkflowOptions.fromJsonString(
-        s"""|{
-            |  "google_project": "$googleProject",
-            |  "jes_gcs_root": "$jesGcsRoot"
-            |}
-            |""".stripMargin
-      ).get,
+      WorkflowOptions
+        .fromJsonString(
+          s"""|{
+              |  "google_project": "$googleProject",
+              |  "jes_gcs_root": "$jesGcsRoot"
+              |}
+              |""".stripMargin
+        )
+        .get,
       Labels.empty,
       HogGroup("foo"),
       List.empty,
@@ -1277,11 +1698,14 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
     val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == "goodbye").get
     val key = BackendJobDescriptorKey(call, None, 1)
     val runtimeAttributes = makeRuntimeAttributes(call)
-    val jobDescriptor = BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
+    val jobDescriptor =
+      BackendJobDescriptor(workflowDescriptor, key, runtimeAttributes, Map.empty, NoDocker, None, Map.empty)
 
     val props = Props(new TestablePipelinesApiJobExecutionActor(jobDescriptor, Promise(), papiConfiguration))
     val testActorRef = TestActorRef[TestablePipelinesApiJobExecutionActor](
-      props, s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}")
+      props,
+      s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+    )
 
     val jesBackend = testActorRef.underlyingActor
 
@@ -1317,8 +1741,10 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends TestKitSuite
   }
 
   private def makeRuntimeAttributes(job: CommandCallNode) = {
-    val evaluatedAttributes = RuntimeAttributeDefinition.evaluateRuntimeAttributes(job.callable.runtimeAttributes, null, Map.empty)
-    RuntimeAttributeDefinition.addDefaultsToAttributes(
-      runtimeAttributesBuilder.definitions.toSet, NoOptions)(evaluatedAttributes.getOrElse(fail("Failed to evaluate runtime attributes")))
+    val evaluatedAttributes =
+      RuntimeAttributeDefinition.evaluateRuntimeAttributes(job.callable.runtimeAttributes, null, Map.empty)
+    RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributesBuilder.definitions.toSet, NoOptions)(
+      evaluatedAttributes.getOrElse(fail("Failed to evaluate runtime attributes"))
+    )
   }
 }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAttachedDiskSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAttachedDiskSpec.scala
index 0d15ed46574..5b19bfe48f1 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAttachedDiskSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAttachedDiskSpec.scala
@@ -1,7 +1,12 @@
 package cromwell.backend.google.pipelines.common
 
 import common.assertion.CromwellTimeoutSpec
-import cromwell.backend.google.pipelines.common.io.{DiskType, PipelinesApiAttachedDisk, PipelinesApiEmptyMountedDisk, PipelinesApiWorkingDisk}
+import cromwell.backend.google.pipelines.common.io.{
+  DiskType,
+  PipelinesApiAttachedDisk,
+  PipelinesApiEmptyMountedDisk,
+  PipelinesApiWorkingDisk
+}
 import cromwell.core.path.DefaultPathBuilder
 import org.scalatest.TryValues
 import org.scalatest.flatspec.AnyFlatSpec
@@ -41,7 +46,7 @@ class PipelinesApiAttachedDiskSpec extends AnyFlatSpec with CromwellTimeoutSpec
   )
 
   it should "reject malformed disk mounts" in {
-    forAll(invalidTable) { (unparsed) =>
+    forAll(invalidTable) { unparsed =>
       PipelinesApiAttachedDisk.parse(unparsed) should be(a[Failure[_]])
     }
   }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactorySpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactorySpec.scala
index d997bedbd1c..f2ba65c65db 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactorySpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactorySpec.scala
@@ -9,7 +9,10 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 import scala.concurrent.duration._
 import scala.language.postfixOps
 
-class PipelinesApiBackendLifecycleActorFactorySpec extends AnyFlatSpecLike with Matchers with TableDrivenPropertyChecks {
+class PipelinesApiBackendLifecycleActorFactorySpec
+    extends AnyFlatSpecLike
+    with Matchers
+    with TableDrivenPropertyChecks {
 
   "PipelinesApiBackendLifecycleActorFactory" should "robustly build configuration attributes" in {
 
@@ -33,7 +36,8 @@ class PipelinesApiBackendLifecycleActorFactorySpec extends AnyFlatSpecLike with
       batchRequestTimeoutConfiguration = null,
       referenceFileToDiskImageMappingOpt = None,
       dockerImageToCacheDiskImageMappingOpt = None,
-      checkpointingInterval = 1 second)
+      checkpointingInterval = 1 second
+    )
 
     PipelinesApiBackendLifecycleActorFactory.robustBuildAttributes(() => attributes) shouldBe attributes
   }
@@ -50,8 +54,11 @@ class PipelinesApiBackendLifecycleActorFactorySpec extends AnyFlatSpecLike with
     )
     forAll(fails) { (attempts, description, function) =>
       it should s"$description: make $attempts attribute creation attempts before giving up" in {
-        val e = the [RuntimeException] thrownBy {
-          PipelinesApiBackendLifecycleActorFactory.robustBuildAttributes(function, initialIntervalMillis = 1, maxIntervalMillis = 5)
+        val e = the[RuntimeException] thrownBy {
+          PipelinesApiBackendLifecycleActorFactory.robustBuildAttributes(function,
+                                                                         initialIntervalMillis = 1,
+                                                                         maxIntervalMillis = 5
+          )
         }
         e.getMessage should startWith(s"Failed to build PipelinesApiConfigurationAttributes on attempt $attempts of 3")
       }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiCallPathsSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiCallPathsSpec.scala
index 64971449373..80bc309bf35 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiCallPathsSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiCallPathsSpec.scala
@@ -24,7 +24,14 @@ class PipelinesApiCallPathsSpec extends TestKitSuite with AnyFlatSpecLike with M
       inputFileAsJson = Option(JsObject(SampleWdl.HelloWorld.rawInputs.safeMapValues(JsString.apply)).compactPrint)
     )
     val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
-    val workflowPaths = PipelinesApiWorkflowPaths(workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), papiConfiguration, pathBuilders(), PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+    val workflowPaths = PipelinesApiWorkflowPaths(
+      workflowDescriptor,
+      NoCredentials.getInstance(),
+      NoCredentials.getInstance(),
+      papiConfiguration,
+      pathBuilders(),
+      PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper
+    )
 
     val callPaths = PipelinesApiJobPaths(workflowPaths, jobDescriptorKey)
 
@@ -40,7 +47,14 @@ class PipelinesApiCallPathsSpec extends TestKitSuite with AnyFlatSpecLike with M
       inputFileAsJson = Option(JsObject(SampleWdl.HelloWorld.rawInputs.safeMapValues(JsString.apply)).compactPrint)
     )
     val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
-    val workflowPaths = PipelinesApiWorkflowPaths(workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), papiConfiguration, pathBuilders(), PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+    val workflowPaths = PipelinesApiWorkflowPaths(
+      workflowDescriptor,
+      NoCredentials.getInstance(),
+      NoCredentials.getInstance(),
+      papiConfiguration,
+      pathBuilders(),
+      PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper
+    )
 
     val callPaths = PipelinesApiJobPaths(workflowPaths, jobDescriptorKey)
 
@@ -60,7 +74,14 @@ class PipelinesApiCallPathsSpec extends TestKitSuite with AnyFlatSpecLike with M
       inputFileAsJson = Option(JsObject(SampleWdl.HelloWorld.rawInputs.safeMapValues(JsString.apply)).compactPrint)
     )
     val jobDescriptorKey = firstJobDescriptorKey(workflowDescriptor)
-    val workflowPaths = PipelinesApiWorkflowPaths(workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), papiConfiguration, pathBuilders(), PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+    val workflowPaths = PipelinesApiWorkflowPaths(
+      workflowDescriptor,
+      NoCredentials.getInstance(),
+      NoCredentials.getInstance(),
+      papiConfiguration,
+      pathBuilders(),
+      PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper
+    )
 
     val callPaths = PipelinesApiJobPaths(workflowPaths, jobDescriptorKey)
 
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationAttributesSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationAttributesSpec.scala
index 59625afa4a0..c1c25199e4e 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationAttributesSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationAttributesSpec.scala
@@ -16,8 +16,11 @@ import org.scalatest.prop.TableDrivenPropertyChecks
 import java.net.URL
 import scala.concurrent.duration._
 
-class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
-  with TableDrivenPropertyChecks {
+class PipelinesApiConfigurationAttributesSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks {
 
   import PipelinesApiTestConfig._
 
@@ -64,8 +67,12 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
     val backendConfig = ConfigFactory.parseString(configString(customContent = customContent))
     val pipelinesApiAttributes = PipelinesApiConfigurationAttributes(googleConfig, backendConfig, "papi")
 
-    pipelinesApiAttributes.batchRequestTimeoutConfiguration.readTimeoutMillis.get.value should be(100.hours.toMillis.toInt)
-    pipelinesApiAttributes.batchRequestTimeoutConfiguration.connectTimeoutMillis.get.value should be(10.seconds.toMillis.toInt)
+    pipelinesApiAttributes.batchRequestTimeoutConfiguration.readTimeoutMillis.get.value should be(
+      100.hours.toMillis.toInt
+    )
+    pipelinesApiAttributes.batchRequestTimeoutConfiguration.connectTimeoutMillis.get.value should be(
+      10.seconds.toMillis.toInt
+    )
   }
 
   it should "parse an empty batch-requests.timeouts section correctly" in {
@@ -136,8 +143,8 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
         |""".stripMargin,
       VirtualPrivateCloudConfiguration(
         Option(VirtualPrivateCloudLabels("my-network", Option("my-subnetwork"), mockAuth)),
-        None,
-      ),
+        None
+      )
     ),
     (
       "labels config without subnetwork key",
@@ -148,8 +155,8 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
         |""".stripMargin,
       VirtualPrivateCloudConfiguration(
         Option(VirtualPrivateCloudLabels("my-network", None, mockAuth)),
-        None,
-      ),
+        None
+      )
     ),
     (
       "literal config",
@@ -160,8 +167,8 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
         |""".stripMargin,
       VirtualPrivateCloudConfiguration(
         None,
-        Option(VirtualPrivateCloudLiterals("my-network", Option("my-subnetwork"))),
-      ),
+        Option(VirtualPrivateCloudLiterals("my-network", Option("my-subnetwork")))
+      )
     ),
     (
       "literal config without subnetwork name",
@@ -171,9 +178,9 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
         |""".stripMargin,
       VirtualPrivateCloudConfiguration(
         None,
-        Option(VirtualPrivateCloudLiterals("my-network", None)),
-      ),
-    ),
+        Option(VirtualPrivateCloudLiterals("my-network", None))
+      )
+    )
   )
 
   private val invalidVPCConfigTests = Table(
@@ -184,7 +191,7 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
         |  network-label-key = my-network
         |}
         |""".stripMargin,
-      List("Virtual Private Cloud configuration is invalid. Missing keys: `auth`."),
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `auth`.")
     ),
     (
       "without network label-key",
@@ -192,7 +199,7 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
         |  auth = mock
         |}
         |""".stripMargin,
-      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key`."),
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key`.")
     ),
     (
       "with just a subnetwork label key",
@@ -200,7 +207,7 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
         |  subnetwork-label-key = my-subnetwork
         |}
         |""".stripMargin,
-      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key,auth`."),
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key,auth`.")
     ),
     (
       "with subnetwork label network key and auth",
@@ -209,8 +216,8 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
         |   auth = mock
         | }
         |""".stripMargin,
-      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key`."),
-    ),
+      List("Virtual Private Cloud configuration is invalid. Missing keys: `network-label-key`.")
+    )
   )
 
   forAll(validVpcConfigTests) { (description, customConfig, vpcConfig) =>
@@ -233,13 +240,12 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
 
   it should "not parse invalid config" in {
     val nakedConfig =
-      ConfigFactory.parseString(
-        """
-          |{
-          |   genomics {
-          |     endpoint-url = "myEndpoint"
-          |   }
-          |}
+      ConfigFactory.parseString("""
+                                  |{
+                                  |   genomics {
+                                  |     endpoint-url = "myEndpoint"
+                                  |   }
+                                  |}
         """.stripMargin)
 
     val exception = intercept[IllegalArgumentException with MessageAggregation] {
@@ -255,27 +261,27 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
 
   def configString(customContent: String = "", genomics: String = ""): String =
     s"""
-      |{
-      |   project = "myProject"
-      |   root = "gs://myBucket"
-      |   maximum-polling-interval = 600
-      |   $customContent
-      |   genomics {
-      |     // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
-      |     // Pipelines and manipulate auth JSONs.
-      |     auth = "mock"
-      |    $genomics
-      |     endpoint-url = "http://myEndpoint"
-      |   }
-      |
-      |   filesystems = {
-      |     gcs {
-      |       // A reference to a potentially different auth for manipulating files via engine functions.
-      |       auth = "mock"
-      |     }
-      |   }
-      |}
-      | """.stripMargin
+       |{
+       |   project = "myProject"
+       |   root = "gs://myBucket"
+       |   maximum-polling-interval = 600
+       |   $customContent
+       |   genomics {
+       |     // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
+       |     // Pipelines and manipulate auth JSONs.
+       |     auth = "mock"
+       |    $genomics
+       |     endpoint-url = "http://myEndpoint"
+       |   }
+       |
+       |   filesystems = {
+       |     gcs {
+       |       // A reference to a potentially different auth for manipulating files via engine functions.
+       |       auth = "mock"
+       |     }
+       |   }
+       |}
+       | """.stripMargin
 
   it should "parse gsutil memory specifications" in {
     val valids = List("0", "150M", "14   PIBIT", "6kib")
@@ -290,7 +296,8 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
     val invalids = List("-1", "150MB", "14PB")
 
     invalids foreach {
-      case invalid@PipelinesApiConfigurationAttributes.GsutilHumanBytes(_, _) => fail(s"Memory specification $invalid not expected to be accepted")
+      case invalid @ PipelinesApiConfigurationAttributes.GsutilHumanBytes(_, _) =>
+        fail(s"Memory specification $invalid not expected to be accepted")
       case _ =>
     }
   }
@@ -317,32 +324,32 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
     // Highly abridged versions of hg19 and hg38 manifests just to test for correctness
     // of parsing.
     val manifestConfig =
-    """
-      |reference-disk-localization-manifests = [
-      |{
-      |  "imageIdentifier" : "hg19-public-2020-10-26",
-      |  "diskSizeGb" : 10,
-      |  "files" : [ {
-      |    "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
-      |    "crc32c" : 159565724
-      |  }, {
-      |    "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
-      |    "crc32c" : 1679459712
-      |  }]
-      |},
-      |{
-      |  "imageIdentifier" : "hg38-public-2020-10-26",
-      |  "diskSizeGb" : 20,
-      |  "files" : [ {
-      |    "path" : "gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
-      |    "crc32c" : 930173616
-      |  }, {
-      |    "path" : "gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
-      |    "crc32c" : 289077232
-      |  }]
-      |}
-      |]
-      |""".stripMargin
+      """
+        |reference-disk-localization-manifests = [
+        |{
+        |  "imageIdentifier" : "hg19-public-2020-10-26",
+        |  "diskSizeGb" : 10,
+        |  "files" : [ {
+        |    "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
+        |    "crc32c" : 159565724
+        |  }, {
+        |    "path" : "gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
+        |    "crc32c" : 1679459712
+        |  }]
+        |},
+        |{
+        |  "imageIdentifier" : "hg38-public-2020-10-26",
+        |  "diskSizeGb" : 20,
+        |  "files" : [ {
+        |    "path" : "gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
+        |    "crc32c" : 930173616
+        |  }, {
+        |    "path" : "gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
+        |    "crc32c" : 289077232
+        |  }]
+        |}
+        |]
+        |""".stripMargin
     val backendConfig = ConfigFactory.parseString(configString(manifestConfig))
     val validation = PipelinesApiConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "papi")
     val manifests: List[ManifestFile] = validation.toEither.toOption.get.get
@@ -406,7 +413,7 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
          |   "imageIdentifier" : "hg19-public-2020-10-26",
          |   "diskSizeGb" : 10,
          |   # missing files
-         |}]""",
+         |}]"""
     )
 
     badValues foreach { badValue =>
@@ -417,18 +424,20 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
     }
   }
 
-
   it should "parse correct existing docker-image-cache-manifest-file config" in {
     val dockerImageCacheManifest1Path = "gs://bucket/manifest1.json"
     val dockerImageCacheManifestConfigStr = s"""docker-image-cache-manifest-file = "$dockerImageCacheManifest1Path""""
     val backendConfig = ConfigFactory.parseString(configString(dockerImageCacheManifestConfigStr))
 
-    val validatedGcsPathToDockerImageCacheManifestFileErrorOr = PipelinesApiConfigurationAttributes.validateGcsPathToDockerImageCacheManifestFile(backendConfig)
+    val validatedGcsPathToDockerImageCacheManifestFileErrorOr =
+      PipelinesApiConfigurationAttributes.validateGcsPathToDockerImageCacheManifestFile(backendConfig)
     validatedGcsPathToDockerImageCacheManifestFileErrorOr match {
       case Valid(validatedGcsPathToDockerImageCacheManifestFileOpt) =>
         validatedGcsPathToDockerImageCacheManifestFileOpt match {
           case Some(validatedGcsPathToDockerCacheManifestFile) =>
-            validatedGcsPathToDockerCacheManifestFile shouldBe GcsPathBuilder.validateGcsPath(dockerImageCacheManifest1Path)
+            validatedGcsPathToDockerCacheManifestFile shouldBe GcsPathBuilder.validateGcsPath(
+              dockerImageCacheManifest1Path
+            )
           case None =>
             fail("GCS paths to docker image cache manifest files, parsed from config, should not be empty")
         }
@@ -440,7 +449,8 @@ class PipelinesApiConfigurationAttributesSpec extends AnyFlatSpec with CromwellT
   it should "parse correct missing docker-image-cache-manifest-file config" in {
     val backendConfig = ConfigFactory.parseString(configString())
 
-    val validatedGcsPathsToDockerImageCacheManifestFilesErrorOr = PipelinesApiConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "unit-test-backend")
+    val validatedGcsPathsToDockerImageCacheManifestFilesErrorOr =
+      PipelinesApiConfigurationAttributes.validateReferenceDiskManifestConfigs(backendConfig, "unit-test-backend")
     validatedGcsPathsToDockerImageCacheManifestFilesErrorOr match {
       case Valid(validatedGcsPathsToDockerImageCacheManifestFilesOpt) =>
         validatedGcsPathsToDockerImageCacheManifestFilesOpt shouldBe None
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationSpec.scala
index 04dfdf72740..ee592d3ce1c 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiConfigurationSpec.scala
@@ -11,7 +11,12 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks
 
-class PipelinesApiConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks with BeforeAndAfterAll {
+class PipelinesApiConfigurationSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks
+    with BeforeAndAfterAll {
 
   behavior of "PipelinesApiConfigurationSpec"
 
@@ -22,26 +27,25 @@ class PipelinesApiConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec
     ()
   }
 
-  val globalConfig = ConfigFactory.parseString(
-    s"""
-      |google {
-      |
-      |  application-name = "cromwell"
-      |
-      |  auths = [
-      |    {
-      |      name = "application-default"
-      |      scheme = "application_default"
-      |    },
-      |    {
-      |      name = "service-account"
-      |      scheme = "service_account"
-      |      service-account-id = "my-service-account"
-      |      pem-file = "${mockFile.pathAsString}"
-      |    }
-      |  ]
-      |}
-      |
+  val globalConfig = ConfigFactory.parseString(s"""
+                                                  |google {
+                                                  |
+                                                  |  application-name = "cromwell"
+                                                  |
+                                                  |  auths = [
+                                                  |    {
+                                                  |      name = "application-default"
+                                                  |      scheme = "application_default"
+                                                  |    },
+                                                  |    {
+                                                  |      name = "service-account"
+                                                  |      scheme = "service_account"
+                                                  |      service-account-id = "my-service-account"
+                                                  |      pem-file = "${mockFile.pathAsString}"
+                                                  |    }
+                                                  |  ]
+                                                  |}
+                                                  |
     """.stripMargin)
 
   val backendConfig = ConfigFactory.parseString(
@@ -88,7 +92,8 @@ class PipelinesApiConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec
       |    }
       |  }
       |
-    """.stripMargin)
+    """.stripMargin
+  )
 
   it should "fail to instantiate if any required configuration is missing" in {
 
@@ -108,17 +113,29 @@ class PipelinesApiConfigurationSpec extends AnyFlatSpec with CromwellTimeoutSpec
       an[Exception] shouldBe thrownBy {
         val failingGoogleConf = GoogleConfiguration(global)
         val failingAttributes = PipelinesApiConfigurationAttributes(failingGoogleConf, backend, "papi")
-        new PipelinesApiConfiguration(BackendConfigurationDescriptor(backend, global), genomicsFactory, failingGoogleConf, failingAttributes)
+        new PipelinesApiConfiguration(BackendConfigurationDescriptor(backend, global),
+                                      genomicsFactory,
+                                      failingGoogleConf,
+                                      failingAttributes
+        )
       }
     }
   }
 
   it should "have correct root" in {
-    new PipelinesApiConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig), genomicsFactory, googleConfiguration, papiAttributes).root shouldBe "gs://my-cromwell-workflows-bucket"
+    new PipelinesApiConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig),
+                                  genomicsFactory,
+                                  googleConfiguration,
+                                  papiAttributes
+    ).root shouldBe "gs://my-cromwell-workflows-bucket"
   }
 
   it should "have correct docker" in {
-    val dockerConf = new PipelinesApiConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig), genomicsFactory, googleConfiguration, papiAttributes).dockerCredentials
+    val dockerConf = new PipelinesApiConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig),
+                                                   genomicsFactory,
+                                                   googleConfiguration,
+                                                   papiAttributes
+    ).dockerCredentials
     dockerConf shouldBe defined
     dockerConf.get.token shouldBe "dockerToken"
   }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiDockerCacheMappingOperationsSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiDockerCacheMappingOperationsSpec.scala
index 8fd8d7dd581..dbd1d747390 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiDockerCacheMappingOperationsSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiDockerCacheMappingOperationsSpec.scala
@@ -14,7 +14,7 @@ import common.mock.MockSugar
 import scala.io.Source
 
 class PipelinesApiDockerCacheMappingOperationsSpec
-  extends AnyFlatSpecLike
+    extends AnyFlatSpecLike
     with CromwellTimeoutSpec
     with Matchers
     with MockSugar
@@ -25,19 +25,18 @@ class PipelinesApiDockerCacheMappingOperationsSpec
   it should "successfully parse docker image cache manifest JSON file as instance of Map[String, String]" in {
     val expectedManifest = DockerImageCacheManifest(
       manifestFormatVersion = 2,
-      dockerImageCacheMap =
-        Map(
-          "project1/dockerImage1" ->
-            DockerImageCacheEntry(
-              "sha256:c73e11b1a7854f31ff12c607738bef7b0560a880dc9d0445dde084acc0e9da09",
-              "projects/some-google-project/global/images/dockerCacheDiskForDockerImage1"
-            ),
-          "project2/dockerImage2" ->
-            DockerImageCacheEntry(
-              "sha256:7eb386481d87e41ebddceb948f25379bb339784df5247a3dfbdea2ac101b10c0",
-              "projects/another-google-project/global/images/dockerCacheDiskForDockerImage2"
-            )
-        )
+      dockerImageCacheMap = Map(
+        "project1/dockerImage1" ->
+          DockerImageCacheEntry(
+            "sha256:c73e11b1a7854f31ff12c607738bef7b0560a880dc9d0445dde084acc0e9da09",
+            "projects/some-google-project/global/images/dockerCacheDiskForDockerImage1"
+          ),
+        "project2/dockerImage2" ->
+          DockerImageCacheEntry(
+            "sha256:7eb386481d87e41ebddceb948f25379bb339784df5247a3dfbdea2ac101b10c0",
+            "projects/another-google-project/global/images/dockerCacheDiskForDockerImage2"
+          )
+      )
     )
 
     val testJsonFileName = "docker-image-cache-manifest.json"
@@ -46,9 +45,12 @@ class PipelinesApiDockerCacheMappingOperationsSpec
 
     val mockJsonBlob = {
       val mockBlob = mock[Blob]
-      val testJsonAsByteArray = Source.fromInputStream(
-        Thread.currentThread.getContextClassLoader.getResourceAsStream(testJsonFileName)
-      ).mkString.getBytes
+      val testJsonAsByteArray = Source
+        .fromInputStream(
+          Thread.currentThread.getContextClassLoader.getResourceAsStream(testJsonFileName)
+        )
+        .mkString
+        .getBytes
 
       when(mockBlob.getContent()).thenReturn(testJsonAsByteArray)
       mockBlob
@@ -60,8 +62,12 @@ class PipelinesApiDockerCacheMappingOperationsSpec
       mockClient
     }
 
-    val readFileFromGcsPrivateMethod = PrivateMethod[IO[DockerImageCacheManifest]](Symbol("readDockerImageCacheManifestFileFromGCS"))
-    val parsedJsonAsManifestIO = pipelinesApiDockerCacheMappingOperationsMock invokePrivate readFileFromGcsPrivateMethod(mockGcsClient, testJsonGcsPath)
+    val readFileFromGcsPrivateMethod =
+      PrivateMethod[IO[DockerImageCacheManifest]](Symbol("readDockerImageCacheManifestFileFromGCS"))
+    val parsedJsonAsManifestIO =
+      pipelinesApiDockerCacheMappingOperationsMock invokePrivate readFileFromGcsPrivateMethod(mockGcsClient,
+                                                                                              testJsonGcsPath
+      )
     val parsedJsonAsManifest = parsedJsonAsManifestIO.unsafeRunSync()
 
     parsedJsonAsManifest.equals(expectedManifest) shouldBe true
@@ -72,7 +78,8 @@ class PipelinesApiDockerCacheMappingOperationsSpec
     val testDockerImageName = "test_madeup_docker_image"
     val testDockerImageDigest = "fake_docker_image_digest"
     val testDiskImageName = "fake_disk_image_name"
-    val dockerImageToCacheDiskImageMapping = Map(testDockerImageName -> DockerImageCacheEntry(testDockerImageDigest, testDiskImageName))
+    val dockerImageToCacheDiskImageMapping =
+      Map(testDockerImageName -> DockerImageCacheEntry(testDockerImageDigest, testDiskImageName))
     val dockerImageCacheDiskOpt =
       pipelinesApiDockerCacheMappingOperationsMock.getDockerCacheDiskImageForAJob(
         dockerImageToCacheDiskImageMappingOpt = Option(dockerImageToCacheDiskImageMapping),
@@ -89,7 +96,8 @@ class PipelinesApiDockerCacheMappingOperationsSpec
     val testDockerImageName = "test_madeup_docker_image"
     val testDockerImageDigest = "fake_docker_image_digest"
     val expectedDiskImageName = "fake_disk_image_name"
-    val dockerImageToCacheDiskImageMapping = Map(testDockerImageName -> DockerImageCacheEntry(testDockerImageDigest, expectedDiskImageName))
+    val dockerImageToCacheDiskImageMapping =
+      Map(testDockerImageName -> DockerImageCacheEntry(testDockerImageDigest, expectedDiskImageName))
     val dockerImageCacheDiskOpt =
       pipelinesApiDockerCacheMappingOperationsMock.getDockerCacheDiskImageForAJob(
         dockerImageToCacheDiskImageMappingOpt = Option(dockerImageToCacheDiskImageMapping),
@@ -107,7 +115,8 @@ class PipelinesApiDockerCacheMappingOperationsSpec
     val testDockerImageNameSpecifiedByUser = "test_non_cached_docker_image"
     val testDockerImageDigest = "fake_docker_image_digest"
     val testDiskImageName = "fake_disk_image_name"
-    val dockerImageToCacheDiskImageMapping = Map(testCachedDockerImageName -> DockerImageCacheEntry(testDockerImageDigest, testDiskImageName))
+    val dockerImageToCacheDiskImageMapping =
+      Map(testCachedDockerImageName -> DockerImageCacheEntry(testDockerImageDigest, testDiskImageName))
     val dockerImageCacheDiskOpt =
       pipelinesApiDockerCacheMappingOperationsMock.getDockerCacheDiskImageForAJob(
         dockerImageToCacheDiskImageMappingOpt = Option(dockerImageToCacheDiskImageMapping),
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiGpuAttributesSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiGpuAttributesSpec.scala
index 23f4659b49c..52507e3d256 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiGpuAttributesSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiGpuAttributesSpec.scala
@@ -6,28 +6,22 @@ import org.scalatest.matchers.should.Matchers
 import org.scalatest.wordspec.AnyWordSpecLike
 import wom.values.{WomFloat, WomInteger, WomSingleFile, WomString, WomValue}
 
-class PipelinesApiGpuAttributesSpec
-  extends AnyWordSpecLike
-    with Matchers
-    with PipelinesApiRuntimeAttributesSpecsMixin {
+class PipelinesApiGpuAttributesSpec extends AnyWordSpecLike with Matchers with PipelinesApiRuntimeAttributesSpecsMixin {
 
   val validGpuTypes = List(
     (Option(WomString("nvidia-tesla-k80")), Option(GpuType.NVIDIATeslaK80)),
-    (Option(WomString("nvidia-tesla-p100")), Option( GpuType.NVIDIATeslaP100)),
-    (Option(WomString("custom-gpu-24601")), Option( GpuType("custom-gpu-24601"))),
-    (None, None))
-  val invalidGpuTypes = List(
-    WomSingleFile("nvidia-tesla-k80"),
-    WomInteger(100))
+    (Option(WomString("nvidia-tesla-p100")), Option(GpuType.NVIDIATeslaP100)),
+    (Option(WomString("custom-gpu-24601")), Option(GpuType("custom-gpu-24601"))),
+    (None, None)
+  )
+  val invalidGpuTypes = List(WomSingleFile("nvidia-tesla-k80"), WomInteger(100))
 
   val validGpuCounts = List(
     (Option(WomInteger(1)), Option(1)),
     (Option(WomInteger(100)), Option(100)),
     (None, None)
   )
-  val invalidGpuCounts = List(
-    WomString("ten"),
-    WomFloat(1.0))
+  val invalidGpuCounts = List(WomString("ten"), WomFloat(1.0))
 
   validGpuTypes foreach { case (validGpuType, expectedGpuTypeValue) =>
     validGpuCounts foreach { case (validGpuCount, expectedGpuCountValue) =>
@@ -36,7 +30,8 @@ class PipelinesApiGpuAttributesSpec
           "docker" -> WomString("ubuntu:latest")
         ) ++ validGpuType.map(t => "gpuType" -> t) ++ validGpuCount.map(c => "gpuCount" -> c)
 
-        val actualRuntimeAttributes = toPapiRuntimeAttributes(runtimeAttributes, emptyWorkflowOptions, papiConfiguration)
+        val actualRuntimeAttributes =
+          toPapiRuntimeAttributes(runtimeAttributes, emptyWorkflowOptions, papiConfiguration)
 
         expectedGpuTypeValue match {
           case Some(v) => actualRuntimeAttributes.gpuResource.exists(_.gpuType == v)
@@ -57,9 +52,9 @@ class PipelinesApiGpuAttributesSpec
           "docker" -> WomString("ubuntu:latest")
         ) ++ validGpuType.map(t => "gpuType" -> t) + ("gpuCount" -> invalidGpuCount)
 
-        assertPapiRuntimeAttributesFailedCreation(
-          runtimeAttributes,
-          s"Invalid gpu count. Expected positive Int but got")
+        assertPapiRuntimeAttributesFailedCreation(runtimeAttributes,
+                                                  s"Invalid gpu count. Expected positive Int but got"
+        )
       }
     }
   }
@@ -71,9 +66,9 @@ class PipelinesApiGpuAttributesSpec
           "docker" -> WomString("ubuntu:latest")
         ) + ("gpuType" -> invalidGpuType) + ("gpuCount" -> invalidGpuCount)
 
-        assertPapiRuntimeAttributesFailedCreation(
-          runtimeAttributes,
-          s"Invalid gpu count. Expected positive Int but got")
+        assertPapiRuntimeAttributesFailedCreation(runtimeAttributes,
+                                                  s"Invalid gpu count. Expected positive Int but got"
+        )
       }
     }
   }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiInitializationActorSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiInitializationActorSpec.scala
index 918a8a436ef..c51ab46e9f4 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiInitializationActorSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiInitializationActorSpec.scala
@@ -8,7 +8,12 @@ import com.typesafe.config.{Config, ConfigFactory}
 import cromwell.backend.BackendWorkflowInitializationActor.{InitializationFailed, InitializationSuccess, Initialize}
 import cromwell.backend.async.RuntimeAttributeValidationFailures
 import cromwell.backend.google.pipelines.common.PipelinesApiInitializationActorSpec._
-import cromwell.backend.google.pipelines.common.PipelinesApiTestConfig.{PapiGlobalConfig, genomicsFactory, googleConfiguration, papiAttributes}
+import cromwell.backend.google.pipelines.common.PipelinesApiTestConfig.{
+  genomicsFactory,
+  googleConfiguration,
+  papiAttributes,
+  PapiGlobalConfig
+}
 import cromwell.backend.{BackendConfigurationDescriptor, BackendSpec, BackendWorkflowDescriptor}
 import cromwell.core.Dispatcher.BackendDispatcher
 import cromwell.core.TestKitSuite
@@ -20,41 +25,54 @@ import wom.graph.CommandCallNode
 
 import scala.concurrent.duration._
 
-class PipelinesApiInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
-  with ImplicitSender {
+class PipelinesApiInitializationActorSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with ImplicitSender {
   val Timeout: FiniteDuration = 30.second.dilated
 
   import BackendSpec._
 
   val HelloWorld: String =
     s"""
-      |task hello {
-      |  String addressee = "you"
-      |  command {
-      |    echo "Hello $${addressee}!"
-      |  }
-      |  output {
-      |    String salutation = read_string(stdout())
-      |  }
-      |
-      |  RUNTIME
-      |}
-      |
-      |workflow wf_hello {
-      |  call hello
-      |}
+       |task hello {
+       |  String addressee = "you"
+       |  command {
+       |    echo "Hello $${addressee}!"
+       |  }
+       |  output {
+       |    String salutation = read_string(stdout())
+       |  }
+       |
+       |  RUNTIME
+       |}
+       |
+       |workflow wf_hello {
+       |  call hello
+       |}
     """.stripMargin
 
   private def getJesBackendProps(workflowDescriptor: BackendWorkflowDescriptor,
                                  calls: Set[CommandCallNode],
-                                 jesConfiguration: PipelinesApiConfiguration): Props = {
+                                 jesConfiguration: PipelinesApiConfiguration
+  ): Props = {
     val ioActor = mockIoActor
-    val params = PipelinesApiInitializationActorParams(workflowDescriptor, ioActor, calls, jesConfiguration, emptyActor, restarting = false)
+    val params = PipelinesApiInitializationActorParams(workflowDescriptor,
+                                                       ioActor,
+                                                       calls,
+                                                       jesConfiguration,
+                                                       emptyActor,
+                                                       restarting = false
+    )
     Props(new PipelinesApiInitializationActor(params)).withDispatcher(BackendDispatcher)
   }
 
-  private def getJesBackend(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[CommandCallNode], conf: BackendConfigurationDescriptor) = {
-    val props = getJesBackendProps(workflowDescriptor, calls, new PipelinesApiConfiguration(conf, genomicsFactory, googleConfiguration, papiAttributes))
+  private def getJesBackend(workflowDescriptor: BackendWorkflowDescriptor,
+                            calls: Set[CommandCallNode],
+                            conf: BackendConfigurationDescriptor
+  ) = {
+    val props = getJesBackendProps(
+      workflowDescriptor,
+      calls,
+      new PipelinesApiConfiguration(conf, genomicsFactory, googleConfiguration, papiAttributes)
+    )
     system.actorOf(props, "TestableJesInitializationActor-" + UUID.randomUUID)
   }
 
@@ -63,17 +81,16 @@ class PipelinesApiInitializationActorSpec extends TestKitSuite with AnyFlatSpecL
   it should "log a warning message when there are unsupported runtime attributes" in {
 
     within(Timeout) {
-      val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld,
-        runtime = """runtime { docker: "ubuntu/latest" test: true }""")
-      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes,
-        defaultBackendConfig)
+      val workflowDescriptor =
+        buildWdlWorkflowDescriptor(HelloWorld, runtime = """runtime { docker: "ubuntu/latest" test: true }""")
+      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes, defaultBackendConfig)
       val eventPattern =
         "Key/s [test] is/are not supported by backend. Unsupported attributes will not be part of job executions."
       EventFilter.warning(pattern = escapePattern(eventPattern), occurrences = 1) intercept {
         backend ! Initialize
       }
       expectMsgPF() {
-        case InitializationSuccess(_) => //Docker entry is present.
+        case InitializationSuccess(_) => // Docker entry is present.
         case InitializationFailed(failure) => fail(s"InitializationSuccess was expected but got $failure")
       }
     }
@@ -82,36 +99,39 @@ class PipelinesApiInitializationActorSpec extends TestKitSuite with AnyFlatSpecL
   it should "return InitializationFailed when docker runtime attribute key is not present" in {
     within(Timeout) {
       val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld, runtime = """runtime { }""")
-      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes,
-        defaultBackendConfig)
+      val backend = getJesBackend(workflowDescriptor, workflowDescriptor.callable.taskCallNodes, defaultBackendConfig)
       backend ! Initialize
-      expectMsgPF() {
-        case InitializationFailed(failure) =>
-          failure match {
-            case exception: RuntimeAttributeValidationFailures =>
-              if (!exception.getMessage.equals("Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!"))
-                fail("Exception message is not equal to 'Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!'.")
-          }
+      expectMsgPF() { case InitializationFailed(failure) =>
+        failure match {
+          case exception: RuntimeAttributeValidationFailures =>
+            if (
+              !exception.getMessage.equals(
+                "Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!"
+              )
+            )
+              fail(
+                "Exception message is not equal to 'Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!'."
+              )
+        }
       }
     }
   }
 }
 
 object PipelinesApiInitializationActorSpec {
-  val globalConfig: Config = ConfigFactory.parseString(
-    """
-      |google {
-      |
-      |  application-name = "cromwell"
-      |
-      |  auths = [
-      |    {
-      |      name = "application-default"
-      |      scheme = "mock"
-      |    }
-      |  ]
-      |}
-      |""".stripMargin)
+  val globalConfig: Config = ConfigFactory.parseString("""
+                                                         |google {
+                                                         |
+                                                         |  application-name = "cromwell"
+                                                         |
+                                                         |  auths = [
+                                                         |    {
+                                                         |      name = "application-default"
+                                                         |      scheme = "mock"
+                                                         |    }
+                                                         |  ]
+                                                         |}
+                                                         |""".stripMargin)
 
   val backendConfigTemplate: String =
     """
@@ -158,25 +178,38 @@ object PipelinesApiInitializationActorSpec {
       |[DOCKERHUBCONFIG]
       |""".stripMargin
 
-  val backendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[VPCCONFIG]", "").replace("[DOCKERHUBCONFIG]", ""))
-
-  val dockerBackendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[VPCCONFIG]", "").replace("[DOCKERHUBCONFIG]",
-    """
-      |dockerhub {
-      |  account = "my@docker.account"
-      |  # no secrets here guys this is just `echo -n username:password | base64`
-      |  token = "dXNlcm5hbWU6cGFzc3dvcmQ="
-      |}
-      | """.stripMargin))
-
-  val vpcBackendConfig: Config = ConfigFactory.parseString(backendConfigTemplate.replace("[DOCKERHUBCONFIG]", "").replace("[VPCCONFIG]",
-    """
-      |virtual-private-cloud {
-      |  network-label-key = "cromwell-ci-network"
-      |  subnetwork-label-key = "cromwell-ci-subnetwork"
-      |  auth = "service_account"
-      |}
-      | """.stripMargin))
+  val backendConfig: Config =
+    ConfigFactory.parseString(backendConfigTemplate.replace("[VPCCONFIG]", "").replace("[DOCKERHUBCONFIG]", ""))
+
+  val dockerBackendConfig: Config = ConfigFactory.parseString(
+    backendConfigTemplate
+      .replace("[VPCCONFIG]", "")
+      .replace(
+        "[DOCKERHUBCONFIG]",
+        """
+          |dockerhub {
+          |  account = "my@docker.account"
+          |  # no secrets here guys this is just `echo -n username:password | base64`
+          |  token = "dXNlcm5hbWU6cGFzc3dvcmQ="
+          |}
+          | """.stripMargin
+      )
+  )
+
+  val vpcBackendConfig: Config = ConfigFactory.parseString(
+    backendConfigTemplate
+      .replace("[DOCKERHUBCONFIG]", "")
+      .replace(
+        "[VPCCONFIG]",
+        """
+          |virtual-private-cloud {
+          |  network-label-key = "cromwell-ci-network"
+          |  subnetwork-label-key = "cromwell-ci-subnetwork"
+          |  auth = "service_account"
+          |}
+          | """.stripMargin
+      )
+  )
 
   private val defaultBackendConfig = new BackendConfigurationDescriptor(backendConfig, globalConfig) {
     override private[backend] lazy val cromwellFileSystems = new CromwellFileSystems(PapiGlobalConfig)
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobExecutionActorSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobExecutionActorSpec.scala
index 37b2ba6f02c..50b9a4d0862 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobExecutionActorSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobExecutionActorSpec.scala
@@ -4,7 +4,11 @@ import akka.actor.{Actor, ActorRef, Props}
 import akka.testkit._
 import cromwell.backend.BackendJobExecutionActor.{ExecuteJobCommand, JobFailedNonRetryableResponse}
 import cromwell.backend.google.pipelines.common.ControllableFailingPabjea.JabjeaExplode
-import cromwell.backend.standard.{DefaultStandardSyncExecutionActorParams, StandardSyncExecutionActor, StandardSyncExecutionActorParams}
+import cromwell.backend.standard.{
+  DefaultStandardSyncExecutionActorParams,
+  StandardSyncExecutionActor,
+  StandardSyncExecutionActorParams
+}
 import cromwell.backend.{BackendJobDescriptor, MinimumRuntimeSettings}
 import cromwell.core.TestKitSuite
 import org.scalatest.flatspec.AnyFlatSpecLike
@@ -36,12 +40,21 @@ class PipelinesApiJobExecutionActorSpec extends TestKitSuite with AnyFlatSpecLik
 
     val parent = TestProbe("parent")
     val deathwatch = TestProbe("deathwatch")
-    val params = DefaultStandardSyncExecutionActorParams(PipelinesApiAsyncBackendJobExecutionActor.JesOperationIdKey, serviceRegistryActor, ioActor,
-      jobDescriptor, null, Option(initializationData), jesBackendSingletonActor,
-      classOf[PipelinesApiAsyncBackendJobExecutionActor], MinimumRuntimeSettings())
+    val params = DefaultStandardSyncExecutionActorParams(
+      PipelinesApiAsyncBackendJobExecutionActor.JesOperationIdKey,
+      serviceRegistryActor,
+      ioActor,
+      jobDescriptor,
+      null,
+      Option(initializationData),
+      jesBackendSingletonActor,
+      classOf[PipelinesApiAsyncBackendJobExecutionActor],
+      MinimumRuntimeSettings()
+    )
     val testJJEA = TestActorRef[TestPipelinesApiJobExecutionActor](
       props = Props(new TestPipelinesApiJobExecutionActor(params, Props(new ConstructorFailingJABJEA))),
-      supervisor = parent.ref)
+      supervisor = parent.ref
+    )
     deathwatch watch testJJEA
 
     // Nothing happens:
@@ -50,9 +63,10 @@ class PipelinesApiJobExecutionActorSpec extends TestKitSuite with AnyFlatSpecLik
 
     testJJEA.tell(msg = ExecuteJobCommand, sender = parent.ref)
 
-    parent.expectMsgPF(max = TimeoutDuration) {
-      case JobFailedNonRetryableResponse(_, throwable, _) =>
-        throwable.getMessage should be("PipelinesApiAsyncBackendJobExecutionActor failed and didn't catch its exception. This condition has been handled and the job will be marked as failed.")
+    parent.expectMsgPF(max = TimeoutDuration) { case JobFailedNonRetryableResponse(_, throwable, _) =>
+      throwable.getMessage should be(
+        "PipelinesApiAsyncBackendJobExecutionActor failed and didn't catch its exception. This condition has been handled and the job will be marked as failed."
+      )
     }
   }
 
@@ -69,13 +83,23 @@ class PipelinesApiJobExecutionActorSpec extends TestKitSuite with AnyFlatSpecLik
     val parent = TestProbe("parent")
     val deathwatch = TestProbe("deathwatch")
     val jabjeaConstructionPromise = Promise[ActorRef]()
-    val params = DefaultStandardSyncExecutionActorParams(PipelinesApiAsyncBackendJobExecutionActor.JesOperationIdKey, serviceRegistryActor, ioActor,
-      jobDescriptor, null, Option(initializationData), jesBackendSingletonActor,
+    val params = DefaultStandardSyncExecutionActorParams(
+      PipelinesApiAsyncBackendJobExecutionActor.JesOperationIdKey,
+      serviceRegistryActor,
+      ioActor,
+      jobDescriptor,
+      null,
+      Option(initializationData),
+      jesBackendSingletonActor,
       classOf[PipelinesApiAsyncBackendJobExecutionActor],
-      MinimumRuntimeSettings())
+      MinimumRuntimeSettings()
+    )
     val testJJEA = TestActorRef[TestPipelinesApiJobExecutionActor](
-      props = Props(new TestPipelinesApiJobExecutionActor(params, Props(new ControllableFailingPabjea(jabjeaConstructionPromise)))),
-      supervisor = parent.ref)
+      props = Props(
+        new TestPipelinesApiJobExecutionActor(params, Props(new ControllableFailingPabjea(jabjeaConstructionPromise)))
+      ),
+      supervisor = parent.ref
+    )
     deathwatch watch testJJEA
 
     // Nothing happens:
@@ -96,15 +120,16 @@ class PipelinesApiJobExecutionActorSpec extends TestKitSuite with AnyFlatSpecLik
         throw exception
     }
 
-    parent.expectMsgPF(max = TimeoutDuration) {
-      case JobFailedNonRetryableResponse(_, throwable, _) =>
-        throwable.getMessage should be("PipelinesApiAsyncBackendJobExecutionActor failed and didn't catch its exception. This condition has been handled and the job will be marked as failed.")
+    parent.expectMsgPF(max = TimeoutDuration) { case JobFailedNonRetryableResponse(_, throwable, _) =>
+      throwable.getMessage should be(
+        "PipelinesApiAsyncBackendJobExecutionActor failed and didn't catch its exception. This condition has been handled and the job will be marked as failed."
+      )
     }
   }
 }
 
-class TestPipelinesApiJobExecutionActor(params: StandardSyncExecutionActorParams,
-                                        fakeJabjeaProps: Props) extends StandardSyncExecutionActor(params) {
+class TestPipelinesApiJobExecutionActor(params: StandardSyncExecutionActorParams, fakeJabjeaProps: Props)
+    extends StandardSyncExecutionActor(params) {
   override def createAsyncProps(): Props = fakeJabjeaProps
 }
 
@@ -116,12 +141,12 @@ class ConstructorFailingJABJEA extends ControllableFailingPabjea(Promise[ActorRe
 class ControllableFailingPabjea(constructionPromise: Promise[ActorRef]) extends Actor {
   def explode(): Unit = {
     val boom = 1 == 1
-    if (boom) throw new RuntimeException("Test Exception! Don't panic if this appears during a test run!")
-      with NoStackTrace
+    if (boom)
+      throw new RuntimeException("Test Exception! Don't panic if this appears during a test run!") with NoStackTrace
   }
   constructionPromise.trySuccess(self)
-  override def receive: Receive = {
-    case JabjeaExplode => explode()
+  override def receive: Receive = { case JabjeaExplode =>
+    explode()
   }
 }
 
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiReferenceFilesMappingOperationsSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiReferenceFilesMappingOperationsSpec.scala
index e9ce34f964a..7ae6944ed2f 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiReferenceFilesMappingOperationsSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiReferenceFilesMappingOperationsSpec.scala
@@ -22,41 +22,61 @@ class PipelinesApiReferenceFilesMappingOperationsSpec extends AnyFlatSpecLike wi
   private val papiReferenceFilesMappingOperationsMockObject: PipelinesApiReferenceFilesMappingOperations =
     new PipelinesApiReferenceFilesMappingOperations {
 
-      override def bulkValidateCrc32cs(gcsClient: Storage, filesWithValidPaths: Map[ReferenceFile, ValidFullGcsPath]): IO[Map[ReferenceFile, Boolean]] =
+      override def bulkValidateCrc32cs(gcsClient: Storage,
+                                       filesWithValidPaths: Map[ReferenceFile, ValidFullGcsPath]
+      ): IO[Map[ReferenceFile, Boolean]] =
         IO.pure(filesWithValidPaths.keySet.map(file => (file, file.path != refFile4Disk2MismatchingChecksum)).toMap)
     }
 
   private val refFileMappingsMock = papiReferenceFilesMappingOperationsMockObject.generateReferenceFilesMapping(
     MockAuthMode("default"),
     List(
-      ManifestFile(imageIdentifier = disk1.image, diskSizeGb = disk1.sizeGb, files = List(
-        ReferenceFile(path = refFile1Disk1, crc32c = 5),
-        ReferenceFile(path = refFile2Disk1, crc32c = 6)
-      )),
-      ManifestFile(imageIdentifier = disk2.image, diskSizeGb = disk2.sizeGb, files = List(
-        ReferenceFile(path = refFile3Disk2, crc32c = 7)
-      ))
+      ManifestFile(imageIdentifier = disk1.image,
+                   diskSizeGb = disk1.sizeGb,
+                   files = List(
+                     ReferenceFile(path = refFile1Disk1, crc32c = 5),
+                     ReferenceFile(path = refFile2Disk1, crc32c = 6)
+                   )
+      ),
+      ManifestFile(imageIdentifier = disk2.image,
+                   diskSizeGb = disk2.sizeGb,
+                   files = List(
+                     ReferenceFile(path = refFile3Disk2, crc32c = 7)
+                   )
+      )
     )
   )
 
   it should "correctly figure out which disks have to be mounted based on provided input file paths" in {
     val nonReferenceInputFilePaths = Set("gs://not/a/reference/file")
-    val forNonReferenceFile = papiReferenceFilesMappingOperationsMockObject.getReferenceDisksToMount(refFileMappingsMock, nonReferenceInputFilePaths)
+    val forNonReferenceFile =
+      papiReferenceFilesMappingOperationsMockObject.getReferenceDisksToMount(refFileMappingsMock,
+                                                                             nonReferenceInputFilePaths
+      )
     forNonReferenceFile.isEmpty shouldBe true
 
     val referenceInputFilePathsFrom2Disks = Set(s"gs://$refFile1Disk1", s"gs://$refFile3Disk2")
-    val forReferencesFrom2Disks = papiReferenceFilesMappingOperationsMockObject.getReferenceDisksToMount(refFileMappingsMock, referenceInputFilePathsFrom2Disks)
+    val forReferencesFrom2Disks =
+      papiReferenceFilesMappingOperationsMockObject.getReferenceDisksToMount(refFileMappingsMock,
+                                                                             referenceInputFilePathsFrom2Disks
+      )
     forReferencesFrom2Disks should contain theSameElementsAs List(disk1, disk2)
 
     val referenceInputFilePathsFromSingleDisk = Set(s"gs://$refFile1Disk1", s"gs://$refFile2Disk1")
-    val forReferencesFromSingleDisk = papiReferenceFilesMappingOperationsMockObject.getReferenceDisksToMount(refFileMappingsMock, referenceInputFilePathsFromSingleDisk)
+    val forReferencesFromSingleDisk =
+      papiReferenceFilesMappingOperationsMockObject.getReferenceDisksToMount(refFileMappingsMock,
+                                                                             referenceInputFilePathsFromSingleDisk
+      )
     forReferencesFromSingleDisk.size shouldBe 1
     forReferencesFromSingleDisk.head shouldBe disk1
   }
 
   it should "not consider valid a reference file with mismatching checksum" in {
     val mismatchingChecksumReferenceFile = Set(refFile4Disk2MismatchingChecksum)
-    val forMismatchingChecksumReferenceFile = papiReferenceFilesMappingOperationsMockObject.getReferenceDisksToMount(refFileMappingsMock, mismatchingChecksumReferenceFile)
+    val forMismatchingChecksumReferenceFile =
+      papiReferenceFilesMappingOperationsMockObject.getReferenceDisksToMount(refFileMappingsMock,
+                                                                             mismatchingChecksumReferenceFile
+      )
     forMismatchingChecksumReferenceFile.isEmpty shouldBe true
   }
 }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributesSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributesSpec.scala
index aa9812e4b3c..a7a880cb28c 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributesSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributesSpec.scala
@@ -20,7 +20,7 @@ import wom.values._
 import scala.util.{Failure, Success, Try}
 
 final class PipelinesApiRuntimeAttributesSpec
-  extends AnyWordSpecLike
+    extends AnyWordSpecLike
     with Matchers
     with PipelinesApiRuntimeAttributesSpecsMixin {
 
@@ -34,7 +34,10 @@ final class PipelinesApiRuntimeAttributesSpec
     "use hardcoded defaults if not declared in task, workflow options, or config (except for docker)" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"))
       val expectedRuntimeAttributes = expectedDefaults
-      assertPapiRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes, papiConfiguration = noDefaultsPapiConfiguration)
+      assertPapiRuntimeAttributesSuccessfulCreation(runtimeAttributes,
+                                                    expectedRuntimeAttributes,
+                                                    papiConfiguration = noDefaultsPapiConfiguration
+      )
     }
 
     "validate a valid Docker entry" in {
@@ -56,7 +59,10 @@ final class PipelinesApiRuntimeAttributesSpec
 
     "fail to validate an invalid failOnStderr entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "failOnStderr" -> WomString("yes"))
-      assertPapiRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'")
+      assertPapiRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'"
+      )
     }
 
     "validate a valid continueOnReturnCode integer entry" in {
@@ -72,20 +78,29 @@ final class PipelinesApiRuntimeAttributesSpec
     }
 
     "validate a valid continueOnReturnCode array entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2))))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"),
+            "continueOnReturnCode" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2)))
+        )
       val expectedRuntimeAttributes = expectedDefaults.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1, 2)))
       assertPapiRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "coerce then validate a valid continueOnReturnCode array entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomArray(WomArrayType(WomStringType), List(WomString("1"), WomString("2"))))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"),
+            "continueOnReturnCode" -> WomArray(WomArrayType(WomStringType), List(WomString("1"), WomString("2")))
+        )
       val expectedRuntimeAttributes = expectedDefaults.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1, 2)))
       assertPapiRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid continueOnReturnCode entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomString("value"))
-      assertPapiRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]")
+      assertPapiRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+      )
     }
 
     "validate a valid cpu entry" in {
@@ -113,18 +128,30 @@ final class PipelinesApiRuntimeAttributesSpec
 
     "fail to validate an invalid zones entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "zones" -> WomInteger(1))
-      assertPapiRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]")
+      assertPapiRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]"
+      )
     }
 
     "validate a valid array zones entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "zones" -> WomArray(WomArrayType(WomStringType), List(WomString("us-central1-y"), WomString("us-central1-z"))))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "zones" -> WomArray(WomArrayType(WomStringType),
+                                                      List(WomString("us-central1-y"), WomString("us-central1-z"))
+                                  )
+      )
       val expectedRuntimeAttributes = expectedDefaults.copy(zones = Vector("us-central1-y", "us-central1-z"))
       assertPapiRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid array zones entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "zones" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2))))
-      assertPapiRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]")
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  "zones" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2)))
+      )
+      assertPapiRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting zones runtime attribute to be either a whitespace separated String or an Array[String]"
+      )
     }
 
     "validate a valid preemptible entry" in {
@@ -136,7 +163,8 @@ final class PipelinesApiRuntimeAttributesSpec
     "fail to validate an invalid preemptible entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "preemptible" -> WomString("value"))
       assertPapiRuntimeAttributesFailedCreation(runtimeAttributes,
-        "Expecting preemptible runtime attribute to be an Integer")
+                                                "Expecting preemptible runtime attribute to be an Integer"
+      )
     }
 
     "validate a valid bootDiskSizeGb entry" in {
@@ -147,29 +175,50 @@ final class PipelinesApiRuntimeAttributesSpec
 
     "fail to validate an invalid bootDiskSizeGb entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "bootDiskSizeGb" -> WomString("4GB"))
-      assertPapiRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting bootDiskSizeGb runtime attribute to be an Integer")
+      assertPapiRuntimeAttributesFailedCreation(runtimeAttributes,
+                                                "Expecting bootDiskSizeGb runtime attribute to be an Integer"
+      )
     }
 
     "validate a valid disks entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 20 SSD"))
-      val expectedRuntimeAttributes = expectedDefaults.copy(disks = Seq(PipelinesApiAttachedDisk.parse("local-disk 20 SSD").get))
+      val expectedRuntimeAttributes =
+        expectedDefaults.copy(disks = Seq(PipelinesApiAttachedDisk.parse("local-disk 20 SSD").get))
       assertPapiRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid disks entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomInteger(10))
-      assertPapiRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting disks runtime attribute to be a comma separated String or Array[String]")
+      assertPapiRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting disks runtime attribute to be a comma separated String or Array[String]"
+      )
     }
 
     "validate a valid disks array entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomArray(WomArrayType(WomStringType), List(WomString("local-disk 20 SSD"), WomString("local-disk 30 SSD"))))
-      val expectedRuntimeAttributes = expectedDefaults.copy(disks = Seq(PipelinesApiAttachedDisk.parse("local-disk 20 SSD").get, PipelinesApiAttachedDisk.parse("local-disk 30 SSD").get))
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "disks" -> WomArray(WomArrayType(WomStringType),
+                            List(WomString("local-disk 20 SSD"), WomString("local-disk 30 SSD"))
+        )
+      )
+      val expectedRuntimeAttributes = expectedDefaults.copy(disks =
+        Seq(PipelinesApiAttachedDisk.parse("local-disk 20 SSD").get,
+            PipelinesApiAttachedDisk.parse("local-disk 30 SSD").get
+        )
+      )
       assertPapiRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate a valid disks array entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomArray(WomArrayType(WomStringType), List(WomString("blah"), WomString("blah blah"))))
-      assertPapiRuntimeAttributesFailedCreation(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE'")
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"),
+            "disks" -> WomArray(WomArrayType(WomStringType), List(WomString("blah"), WomString("blah blah")))
+        )
+      assertPapiRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE'"
+      )
     }
 
     "validate a valid memory entry" in {
@@ -180,7 +229,10 @@ final class PipelinesApiRuntimeAttributesSpec
 
     "fail to validate an invalid memory entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "memory" -> WomString("blah"))
-      assertPapiRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting memory runtime attribute to be an Integer or String with format '8 GB'")
+      assertPapiRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting memory runtime attribute to be an Integer or String with format '8 GB'"
+      )
     }
 
     "validate a valid noAddress entry" in {
@@ -192,7 +244,8 @@ final class PipelinesApiRuntimeAttributesSpec
     "fail to validate an invalid noAddress entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "noAddress" -> WomInteger(1))
       assertPapiRuntimeAttributesFailedCreation(runtimeAttributes,
-        "Expecting noAddress runtime attribute to be a Boolean")
+                                                "Expecting noAddress runtime attribute to be a Boolean"
+      )
     }
 
     "override config default attributes with default attributes declared in workflow options" in {
@@ -253,21 +306,39 @@ final class PipelinesApiRuntimeAttributesSpec
 
 trait PipelinesApiRuntimeAttributesSpecsMixin { this: TestSuite =>
 
-  def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]): WorkflowOptions = {
-    WorkflowOptions(JsObject(Map(
-      "default_runtime_attributes" -> JsObject(defaults)
-    )))
-  }
-
-  val expectedDefaults = new PipelinesApiRuntimeAttributes(refineMV(1), None, None, Vector("us-central1-b", "us-central1-a"), 0, 10,
-    MemorySize(2, MemoryUnit.GB), Vector(PipelinesApiWorkingDisk(DiskType.SSD, 10)), "ubuntu:latest", false,
-    ContinueOnReturnCodeSet(Set(0)), false, false, None, None)
+  def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]): WorkflowOptions =
+    WorkflowOptions(
+      JsObject(
+        Map(
+          "default_runtime_attributes" -> JsObject(defaults)
+        )
+      )
+    )
+
+  val expectedDefaults = new PipelinesApiRuntimeAttributes(
+    refineMV(1),
+    None,
+    None,
+    Vector("us-central1-b", "us-central1-a"),
+    0,
+    10,
+    MemorySize(2, MemoryUnit.GB),
+    Vector(PipelinesApiWorkingDisk(DiskType.SSD, 10)),
+    "ubuntu:latest",
+    false,
+    ContinueOnReturnCodeSet(Set(0)),
+    false,
+    false,
+    None,
+    None
+  )
 
   def assertPapiRuntimeAttributesSuccessfulCreation(runtimeAttributes: Map[String, WomValue],
                                                     expectedRuntimeAttributes: PipelinesApiRuntimeAttributes,
                                                     workflowOptions: WorkflowOptions = emptyWorkflowOptions,
                                                     defaultZones: NonEmptyList[String] = defaultZones,
-                                                    papiConfiguration: PipelinesApiConfiguration = papiConfiguration): Unit = {
+                                                    papiConfiguration: PipelinesApiConfiguration = papiConfiguration
+  ): Unit = {
     try {
       val actualRuntimeAttributes = toPapiRuntimeAttributes(runtimeAttributes, workflowOptions, papiConfiguration)
       assert(actualRuntimeAttributes == expectedRuntimeAttributes)
@@ -279,34 +350,45 @@ trait PipelinesApiRuntimeAttributesSpecsMixin { this: TestSuite =>
 
   def assertPapiRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue],
                                                 exMsgs: List[String],
-                                                workflowOptions: WorkflowOptions): Unit = {
+                                                workflowOptions: WorkflowOptions
+  ): Unit = {
     Try(toPapiRuntimeAttributes(runtimeAttributes, workflowOptions, papiConfiguration)) match {
       case Success(oops) =>
-        fail(s"Expected error containing strings: ${exMsgs.map(s => s"'$s'").mkString(", ")} but instead got Success($oops)")
-      case Failure(ex) => exMsgs foreach { exMsg =>  assert(ex.getMessage.contains(exMsg)) }
+        fail(
+          s"Expected error containing strings: ${exMsgs.map(s => s"'$s'").mkString(", ")} but instead got Success($oops)"
+        )
+      case Failure(ex) => exMsgs foreach { exMsg => assert(ex.getMessage.contains(exMsg)) }
     }
     ()
   }
 
   def assertPapiRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue],
                                                 exMsg: String,
-                                                workflowOptions: WorkflowOptions = emptyWorkflowOptions): Unit = {
+                                                workflowOptions: WorkflowOptions = emptyWorkflowOptions
+  ): Unit =
     assertPapiRuntimeAttributesFailedCreation(runtimeAttributes, List(exMsg), workflowOptions)
-  }
 
   def toPapiRuntimeAttributes(runtimeAttributes: Map[String, WomValue],
                               workflowOptions: WorkflowOptions,
-                              papiConfiguration: PipelinesApiConfiguration): PipelinesApiRuntimeAttributes = {
+                              papiConfiguration: PipelinesApiConfiguration
+  ): PipelinesApiRuntimeAttributes = {
     val runtimeAttributesBuilder = PipelinesApiRuntimeAttributes.runtimeAttributesBuilder(papiConfiguration)
-    val defaultedAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(
-      staticRuntimeAttributeDefinitions, workflowOptions)(runtimeAttributes)
+    val defaultedAttributes =
+      RuntimeAttributeDefinition.addDefaultsToAttributes(staticRuntimeAttributeDefinitions, workflowOptions)(
+        runtimeAttributes
+      )
     val validatedRuntimeAttributes = runtimeAttributesBuilder.build(defaultedAttributes, NOPLogger.NOP_LOGGER)
     PipelinesApiRuntimeAttributes(validatedRuntimeAttributes, papiConfiguration.runtimeConfig)
   }
 
   val emptyWorkflowOptions: WorkflowOptions = WorkflowOptions.fromMap(Map.empty).get
   val defaultZones: NonEmptyList[String] = NonEmptyList.of("us-central1-b", "us-central1-a")
-  val noDefaultsPapiConfiguration = new PipelinesApiConfiguration(PipelinesApiTestConfig.NoDefaultsConfigurationDescriptor, genomicsFactory, googleConfiguration, papiAttributes)
+  val noDefaultsPapiConfiguration = new PipelinesApiConfiguration(
+    PipelinesApiTestConfig.NoDefaultsConfigurationDescriptor,
+    genomicsFactory,
+    googleConfiguration,
+    papiAttributes
+  )
   val staticRuntimeAttributeDefinitions: Set[RuntimeAttributeDefinition] =
     PipelinesApiRuntimeAttributes.runtimeAttributesBuilder(PipelinesApiTestConfig.papiConfiguration).definitions.toSet
 }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiTestConfig.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiTestConfig.scala
index 2df2de9467d..8de64e27ff9 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiTestConfig.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiTestConfig.scala
@@ -104,24 +104,21 @@ object PipelinesApiTestConfig {
   val PapiBackendConfig: Config = ConfigFactory.parseString(PapiBackendConfigString)
   val PapiGlobalConfig: Config = ConfigFactory.parseString(PapiGlobalConfigString)
   val PapiBackendNoDefaultConfig: Config = ConfigFactory.parseString(NoDefaultsConfigString)
-  val PapiBackendConfigurationDescriptor: BackendConfigurationDescriptor = {
+  val PapiBackendConfigurationDescriptor: BackendConfigurationDescriptor =
     new BackendConfigurationDescriptor(PapiBackendConfig, PapiGlobalConfig) {
       override private[backend] lazy val cromwellFileSystems = new CromwellFileSystems(PapiGlobalConfig)
     }
-  }
   val NoDefaultsConfigurationDescriptor: BackendConfigurationDescriptor =
     BackendConfigurationDescriptor(PapiBackendNoDefaultConfig, PapiGlobalConfig)
   val genomicsFactory: PipelinesApiFactoryInterface = new PipelinesApiFactoryInterface {
-    override def build(httpRequestInitializer: HttpRequestInitializer): PipelinesApiRequestFactory = {
+    override def build(httpRequestInitializer: HttpRequestInitializer): PipelinesApiRequestFactory =
       new PipelinesApiRequestFactory {
         override def cancelRequest(job: StandardAsyncJob) = throw new UnsupportedOperationException
         override def getRequest(job: StandardAsyncJob) = throw new UnsupportedOperationException
-        override def runRequest(createPipelineParameters:
-                                PipelinesApiRequestFactory.CreatePipelineParameters,
-                                jobLogger: JobLogger,
-                               ) = throw new UnsupportedOperationException
+        override def runRequest(createPipelineParameters: PipelinesApiRequestFactory.CreatePipelineParameters,
+                                jobLogger: JobLogger
+        ) = throw new UnsupportedOperationException
       }
-    }
     override def usesEncryptedDocker: Boolean = false
   }
   def pathBuilders()(implicit as: ActorSystem): List[PathBuilder] =
@@ -129,5 +126,9 @@ object PipelinesApiTestConfig {
   val googleConfiguration: GoogleConfiguration = GoogleConfiguration(PapiGlobalConfig)
   val papiAttributes: PipelinesApiConfigurationAttributes =
     PipelinesApiConfigurationAttributes(googleConfiguration, PapiBackendConfig, "papi")
-  val papiConfiguration = new PipelinesApiConfiguration(PapiBackendConfigurationDescriptor, genomicsFactory, googleConfiguration, papiAttributes)
+  val papiConfiguration = new PipelinesApiConfiguration(PapiBackendConfigurationDescriptor,
+                                                        genomicsFactory,
+                                                        googleConfiguration,
+                                                        papiAttributes
+  )
 }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiWorkflowPathsSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiWorkflowPathsSpec.scala
index db7b189e79e..5c68eedeb82 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiWorkflowPathsSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiWorkflowPathsSpec.scala
@@ -24,7 +24,14 @@ class PipelinesApiWorkflowPathsSpec extends TestKitSuite with AnyFlatSpecLike wi
       SampleWdl.HelloWorld.workflowSource(),
       inputFileAsJson = Option(JsObject(SampleWdl.HelloWorld.rawInputs.safeMapValues(JsString.apply)).compactPrint)
     )
-    workflowPaths = PipelinesApiWorkflowPaths(workflowDescriptor, NoCredentials.getInstance(), NoCredentials.getInstance(), papiConfiguration, pathBuilders(), PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper)
+    workflowPaths = PipelinesApiWorkflowPaths(
+      workflowDescriptor,
+      NoCredentials.getInstance(),
+      NoCredentials.getInstance(),
+      papiConfiguration,
+      pathBuilders(),
+      PipelinesApiInitializationActor.defaultStandardStreamNameToFileNameMetadataMapper
+    )
   }
 
   it should "map the correct paths" in {
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/VpcAndSubnetworkProjectLabelValuesSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/VpcAndSubnetworkProjectLabelValuesSpec.scala
index 4b4f2fe35a7..2c8572cf146 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/VpcAndSubnetworkProjectLabelValuesSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/VpcAndSubnetworkProjectLabelValuesSpec.scala
@@ -21,15 +21,15 @@ class VpcAndSubnetworkProjectLabelValuesSpec extends AnyFlatSpec with Matchers w
       s"slashed/$${projectId}/net",
       None,
       "slashed/my-project/net",
-      None,
+      None
     ),
     (
       "a subnet with a project token",
       "slashed/net",
       Option(s"slashed/$${projectId}/sub"),
       "slashed/net",
-      Option("slashed/my-project/sub"),
-    ),
+      Option("slashed/my-project/sub")
+    )
   )
 
   forAll(labelsTests) { (description, network, subnetOption, networkName, subnetNameOption) =>
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManagerSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManagerSpec.scala
index 7da9484167a..3b7ccd59038 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManagerSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestManagerSpec.scala
@@ -33,20 +33,22 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
   val registryProbe: ActorRef = TestProbe("registryProbe").ref
   val workflowId: WorkflowId = WorkflowId.randomId()
 
-  private def makePollRequest(snd: ActorRef, jobId: StandardAsyncJob) = new PAPIStatusPollRequest(workflowId, snd, null, jobId) {
-    override def contentLength = 0
-  }
+  private def makePollRequest(snd: ActorRef, jobId: StandardAsyncJob) =
+    new PAPIStatusPollRequest(workflowId, snd, null, jobId) {
+      override def contentLength = 0
+    }
 
-  private def makeCreateRequest(contentSize: Long, snd: ActorRef, workflowId: WorkflowId = workflowId) = new PAPIRunCreationRequest(workflowId, snd, null) {
-    override def contentLength: Long = contentSize
-  }
+  private def makeCreateRequest(contentSize: Long, snd: ActorRef, workflowId: WorkflowId = workflowId) =
+    new PAPIRunCreationRequest(workflowId, snd, null) {
+      override def contentLength: Long = contentSize
+    }
 
   it should "queue up and dispense status poll requests, in order" in {
     val statusPoller = TestProbe(name = "StatusPoller")
     val jaqmActor: TestActorRef[TestPipelinesApiRequestManager] =
       TestActorRef(
         props = TestPipelinesApiRequestManager.props(registryProbe, statusPoller.ref),
-        name = "jaqmActor-queue",
+        name = "jaqmActor-queue"
       )
 
     var statusRequesters = ((0 until BatchSize * 2) map { i => i -> TestProbe(name = s"StatusRequester_$i") }).toMap
@@ -92,7 +94,7 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
     val jaqmActor: TestActorRef[TestPipelinesApiRequestManager] =
       TestActorRef(
         props = TestPipelinesApiRequestManager.props(registryProbe, statusPoller.ref),
-        name = "jaqmActor-reject-create",
+        name = "jaqmActor-reject-create"
       )
 
     val statusRequester = TestProbe("statusRequester")
@@ -111,7 +113,7 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
     // maxBatchSize is 14MB, which mean we can take 2 queries of 5MB but not 3
     val jaqmActor: TestActorRef[TestPipelinesApiRequestManager] = TestActorRef(
       props = TestPipelinesApiRequestManager.props(registryProbe, statusPoller.ref),
-      name = "jaqmActor-maxBatchSize",
+      name = "jaqmActor-maxBatchSize"
     )
 
     val statusRequester = TestProbe("statusRequester")
@@ -149,22 +151,22 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
       val statusPoller1 = TestActorRef[TestPapiWorkerActor](
         props = Props(new TestPapiWorkerActor()),
         supervisor = TestActorRef(new AkkaTestUtil.StoppingSupervisor()),
-        name = s"statusPoller1-$name",
+        name = s"statusPoller1-$name"
       )
       val statusPoller2 = TestActorRef[TestPapiWorkerActor](
         props = Props(new TestPapiWorkerActor()),
         supervisor = TestActorRef(new AkkaTestUtil.StoppingSupervisor()),
-        name = s"statusPoller2-$name",
+        name = s"statusPoller2-$name"
       )
       val statusPoller3 = TestActorRef[TestPapiWorkerActor](
         props = Props(new TestPapiWorkerActor()),
         supervisor = TestActorRef(new AkkaTestUtil.StoppingSupervisor()),
-        name = s"statusPoller3-$name",
+        name = s"statusPoller3-$name"
       )
       val jaqmActor: TestActorRef[TestPipelinesApiRequestManager] =
         TestActorRef(
           props = TestPipelinesApiRequestManager.props(registryProbe, statusPoller1, statusPoller2, statusPoller3),
-          name = s"TestJesApiQueryManage-$name",
+          name = s"TestJesApiQueryManage-$name"
         )
 
       val emptyActor = system.actorOf(Props.empty, s"emptyActor-$name")
@@ -177,8 +179,8 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
 
       // The work queue should be filled and the manager should have one poller active:
       eventually {
-        jaqmActor.underlyingActor.queueSize should be (BatchSize)
-        jaqmActor.underlyingActor.testPollerCreations should be (1)
+        jaqmActor.underlyingActor.queueSize should be(BatchSize)
+        jaqmActor.underlyingActor.testPollerCreations should be(1)
         jaqmActor.underlyingActor.statusPollers.size should be(1)
         jaqmActor.underlyingActor.statusPollers.head should be(statusPoller1)
       }
@@ -188,7 +190,7 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
 
       // Therefore, there's no work left in the work queue because it's all been given to the worker:
       eventually {
-        jaqmActor.underlyingActor.queueSize should be (0)
+        jaqmActor.underlyingActor.queueSize should be(0)
         statusPoller1.underlyingActor.workToDo.map(_.size) should be(Some(BatchSize))
       }
 
@@ -197,8 +199,8 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
 
       // The work queue receives all the work that couldn't be completed, and a new poller is created:
       eventually {
-        jaqmActor.underlyingActor.queueSize should be (BatchSize)
-        jaqmActor.underlyingActor.testPollerCreations should be (2)
+        jaqmActor.underlyingActor.queueSize should be(BatchSize)
+        jaqmActor.underlyingActor.testPollerCreations should be(2)
         jaqmActor.underlyingActor.statusPollers.size should be(1)
         jaqmActor.underlyingActor.statusPollers.head should be(statusPoller2)
       }
@@ -208,7 +210,7 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
 
       // The queue is emptied again and this time statusPoller2 has it:
       eventually {
-        jaqmActor.underlyingActor.queueSize should be (0)
+        jaqmActor.underlyingActor.queueSize should be(0)
         statusPoller2.underlyingActor.workToDo.map(_.size) should be(Some(BatchSize))
       }
 
@@ -217,8 +219,8 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
 
       // The work queue receives all the work that couldn't be completed *again*, and a new poller is created *again*:
       eventually {
-        jaqmActor.underlyingActor.queueSize should be (BatchSize)
-        jaqmActor.underlyingActor.testPollerCreations should be (3)
+        jaqmActor.underlyingActor.queueSize should be(BatchSize)
+        jaqmActor.underlyingActor.testPollerCreations should be(3)
         jaqmActor.underlyingActor.statusPollers.size should be(1)
         jaqmActor.underlyingActor.statusPollers.head should be(statusPoller3)
       }
@@ -231,7 +233,7 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
     val jaqmActor: TestActorRef[TestPipelinesApiRequestManager] =
       TestActorRef(
         props = TestPipelinesApiRequestManager.props(registryProbe, statusPoller.ref),
-        name = "jaqmActor-run",
+        name = "jaqmActor-run"
       )
 
     // Enqueue 3 create requests
@@ -247,7 +249,9 @@ class PipelinesApiRequestManagerSpec extends TestKitSuite with AnyFlatSpecLike w
     // It should remove all and only run requests for workflow A
     eventually {
       jaqmActor.underlyingActor.queueSize shouldBe 1
-      jaqmActor.underlyingActor.workQueue.head.asInstanceOf[PipelinesApiRequestManager.PAPIRunCreationRequest].workflowId shouldBe workflowIdB
+      jaqmActor.underlyingActor.workQueue.head
+        .asInstanceOf[PipelinesApiRequestManager.PAPIRunCreationRequest]
+        .workflowId shouldBe workflowIdB
     }
   }
 }
@@ -265,14 +269,14 @@ object TestPipelinesApiRequestManagerSpec {
 class TestPipelinesApiRequestManager(qps: Int Refined Positive,
                                      requestWorkers: Int Refined Positive,
                                      registry: ActorRef,
-                                     availableRequestWorkers: ActorRef*)
-  extends PipelinesApiRequestManager(qps, requestWorkers, registry)(new MockPipelinesRequestHandler) {
+                                     availableRequestWorkers: ActorRef*
+) extends PipelinesApiRequestManager(qps, requestWorkers, registry)(new MockPipelinesRequestHandler) {
 
   var testProbeQueue: Queue[ActorRef] = _
   var testPollerCreations: Int = _
 
-  private def askForWorkReceive: PartialFunction[Any, Unit] = {
-    case afw: SpecOnly_TriggerRequestForWork => statusPollers.head ! afw
+  private def askForWorkReceive: PartialFunction[Any, Unit] = { case afw: SpecOnly_TriggerRequestForWork =>
+    statusPollers.head ! afw
   }
 
   override def receive: PartialFunction[Any, Unit] = askForWorkReceive orElse super.receive
@@ -284,7 +288,7 @@ class TestPipelinesApiRequestManager(qps: Int Refined Positive,
 
   override private[api] lazy val nbWorkers = 1
   override private[api] def resetAllWorkers(): Unit = {
-    val pollers = Vector.fill(1) { makeAndWatchWorkerActor() }
+    val pollers = Vector.fill(1)(makeAndWatchWorkerActor())
     statusPollers = pollers
   }
 
@@ -325,28 +329,29 @@ class TestPapiWorkerActor() extends DeathTestActor with ActorLogging {
     case SpecOnly_TriggerRequestForWork(manager, batchSize) => requestWork(manager, batchSize)
   }
 
-  def requestWork(papiRequestManager: ActorRef, batchSize: Int): Unit = {
+  def requestWork(papiRequestManager: ActorRef, batchSize: Int): Unit =
     papiRequestManager ! PipelinesWorkerRequestWork(batchSize)
-  }
 }
 
 case class SpecOnly_TriggerRequestForWork(papiRequestManager: ActorRef, batchSize: Int)
 
 class MockPipelinesRequestHandler extends PipelinesApiRequestHandler {
   override def makeBatchRequest = throw new UnsupportedOperationException
-  override def enqueue[T <: PipelinesApiRequestManager.PAPIApiRequest](papiApiRequest: T, batchRequest: BatchRequest, pollingManager: ActorRef)
-                                                                      (implicit ec: ExecutionContext)= throw new UnsupportedOperationException
+  override def enqueue[T <: PipelinesApiRequestManager.PAPIApiRequest](papiApiRequest: T,
+                                                                       batchRequest: BatchRequest,
+                                                                       pollingManager: ActorRef
+  )(implicit ec: ExecutionContext) = throw new UnsupportedOperationException
 }
 
 object TestPipelinesApiRequestManager {
   import PipelinesApiTestConfig._
 
-  def props(registryProbe: ActorRef, statusPollers: ActorRef*): Props = {
-    Props(new TestPipelinesApiRequestManager(
-      papiConfiguration.papiAttributes.qps,
-      papiConfiguration.papiAttributes.requestWorkers,
-      registryProbe,
-      statusPollers: _*)
+  def props(registryProbe: ActorRef, statusPollers: ActorRef*): Props =
+    Props(
+      new TestPipelinesApiRequestManager(papiConfiguration.papiAttributes.qps,
+                                         papiConfiguration.papiAttributes.requestWorkers,
+                                         registryProbe,
+                                         statusPollers: _*
+      )
     )
-  }
 }
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestWorkerSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestWorkerSpec.scala
index d189735eab0..0736b5c051c 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestWorkerSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestWorkerSpec.scala
@@ -8,8 +8,17 @@ import com.google.api.client.googleapis.batch.json.JsonBatchCallback
 import com.google.api.client.googleapis.json.GoogleJsonError
 import com.google.api.client.http.HttpRequest
 import cromwell.backend.google.pipelines.common.PipelinesApiConfiguration
-import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.{PAPIApiException, PAPIApiRequestFailed, PAPIStatusPollRequest, PipelinesWorkerRequestWork}
-import cromwell.backend.google.pipelines.common.api.TestPipelinesApiRequestWorker.{CallbackFailure, CallbackSuccess, PipelinesApiBatchCallbackResponse}
+import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.{
+  PAPIApiException,
+  PAPIApiRequestFailed,
+  PAPIStatusPollRequest,
+  PipelinesWorkerRequestWork
+}
+import cromwell.backend.google.pipelines.common.api.TestPipelinesApiRequestWorker.{
+  CallbackFailure,
+  CallbackSuccess,
+  PipelinesApiBatchCallbackResponse
+}
 import cromwell.core.{ExecutionEvent, TestKitSuite}
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
@@ -25,7 +34,11 @@ import scala.concurrent.{Future, Promise}
 import scala.util.Try
 
 abstract class PipelinesApiRequestWorkerSpec[O >: Null]
-  extends TestKitSuite with AnyFlatSpecLike with Matchers with Eventually with BeforeAndAfter {
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with Eventually
+    with BeforeAndAfter {
 
   implicit var batchHandler: TestPipelinesApiBatchHandler[O]
 
@@ -45,12 +58,16 @@ abstract class PipelinesApiRequestWorkerSpec[O >: Null]
   }
 
   it should "query for work and wait for a reply" in {
-    managerProbe.expectMsgClass(max = TestExecutionTimeout, c = classOf[PipelinesApiRequestManager.PipelinesWorkerRequestWork])
+    managerProbe.expectMsgClass(max = TestExecutionTimeout,
+                                c = classOf[PipelinesApiRequestManager.PipelinesWorkerRequestWork]
+    )
     managerProbe.expectNoMessage(max = AwaitAlmostNothing)
   }
 
   it should "respond correctly with various run statuses" in {
-    managerProbe.expectMsgClass(max = TestExecutionTimeout, c = classOf[PipelinesApiRequestManager.PipelinesWorkerRequestWork])
+    managerProbe.expectMsgClass(max = TestExecutionTimeout,
+                                c = classOf[PipelinesApiRequestManager.PipelinesWorkerRequestWork]
+    )
 
     val requester1 = TestProbe("requester1")
     val query1 = PAPIStatusPollRequest(null, requester1.ref, null, null)
@@ -72,13 +89,15 @@ abstract class PipelinesApiRequestWorkerSpec[O >: Null]
       machineType = None,
       zone = None,
       instanceName = None,
-      wasPreemptible = false,
+      wasPreemptible = false
     )
     batchHandler.operationStatusResponses :+= successStatus
     batchHandler.operationStatusResponses :+= failureStatus
 
-    workerActor.tell(msg = PipelinesApiRequestManager.PipelinesApiWorkBatch(NonEmptyList(query1, List(query2, query3))), sender = managerProbe.ref)
-    eventually { batchHandler.runBatchRequested should be(true) }
+    workerActor.tell(msg = PipelinesApiRequestManager.PipelinesApiWorkBatch(NonEmptyList(query1, List(query2, query3))),
+                     sender = managerProbe.ref
+    )
+    eventually(batchHandler.runBatchRequested should be(true))
 
     // The manager shouldn't have been asked for more work yet:
     managerProbe.expectNoMessage(max = AwaitAlmostNothing)
@@ -91,10 +110,10 @@ abstract class PipelinesApiRequestWorkerSpec[O >: Null]
     requester3.expectNoMessage(max = AwaitAlmostNothing)
 
     // Requester3 expected nothing... Instead, the manager expects an API failure notification and then a request for more work:
-    managerProbe.expectMsgPF(TestExecutionTimeout) {
-      case failure: PAPIApiRequestFailed =>
-        if (!failure.cause.isInstanceOf[PAPIApiException]) fail("Unexpected failure cause class: " + failure.cause.getClass.getSimpleName)
-        if (failure.query != query2 && failure.query != query3) fail("Unexpected query caused failure: " + failure.query)
+    managerProbe.expectMsgPF(TestExecutionTimeout) { case failure: PAPIApiRequestFailed =>
+      if (!failure.cause.isInstanceOf[PAPIApiException])
+        fail("Unexpected failure cause class: " + failure.cause.getClass.getSimpleName)
+      if (failure.query != query2 && failure.query != query3) fail("Unexpected query caused failure: " + failure.query)
     }
     managerProbe.expectMsg(PipelinesWorkerRequestWork(PipelinesApiRequestWorker.MaxBatchSize))
     managerProbe.expectNoMessage(max = AwaitAlmostNothing)
@@ -102,8 +121,9 @@ abstract class PipelinesApiRequestWorkerSpec[O >: Null]
 }
 
 //noinspection ScalaUnusedSymbol
-class TestPipelinesApiRequestWorker(manager: ActorRef, qps: Int Refined Positive, registryProbe: ActorRef)(implicit batchHandler: TestPipelinesApiBatchHandler[_])
-  extends PipelinesApiRequestWorker(manager, 10.milliseconds, registryProbe) {
+class TestPipelinesApiRequestWorker(manager: ActorRef, qps: Int Refined Positive, registryProbe: ActorRef)(implicit
+  batchHandler: TestPipelinesApiBatchHandler[_]
+) extends PipelinesApiRequestWorker(manager, 10.milliseconds, registryProbe) {
   override def createBatch(): BatchRequest = null
   override def runBatch(batch: BatchRequest): Unit = batchHandler.runBatch()
 }
@@ -118,14 +138,15 @@ abstract class TestPipelinesApiBatchHandler[O >: Null] extends PipelinesApiReque
   def createBatch(genomicsInterface: O): BatchRequest = null
   def runBatch(): Unit = runBatchRequested = true
 
-  def executeBatch(): Unit = {
-    resultHandlers.zip(callbackResponses) foreach { case (handler, response) => response match {
-      case CallbackSuccess => handler.onSuccess(null, null)
-      case CallbackFailure =>
-        val error: GoogleJsonError = new GoogleJsonError()
-        handler.onFailure(error, null)
-    }}
-  }
+  def executeBatch(): Unit =
+    resultHandlers.zip(callbackResponses) foreach { case (handler, response) =>
+      response match {
+        case CallbackSuccess => handler.onSuccess(null, null)
+        case CallbackFailure =>
+          val error: GoogleJsonError = new GoogleJsonError()
+          handler.onFailure(error, null)
+      }
+    }
 
   def enqueueStatusPollInBatch(pollingRequest: PAPIStatusPollRequest, batch: BatchRequest): Future[Try[Unit]] = {
     val completionPromise = Promise[Try[Unit]]()
@@ -134,9 +155,12 @@ abstract class TestPipelinesApiBatchHandler[O >: Null] extends PipelinesApiReque
     completionPromise.future
   }
 
-  def statusPollResultHandler(pollRequest: PAPIStatusPollRequest, completionPromise: Promise[Try[Unit]]): JsonBatchCallback[O]
+  def statusPollResultHandler(pollRequest: PAPIStatusPollRequest,
+                              completionPromise: Promise[Try[Unit]]
+  ): JsonBatchCallback[O]
 
-  def addStatusPollToBatch(httpRequest: HttpRequest, batch: BatchRequest, resultHandler: JsonBatchCallback[O]): Unit = resultHandlers :+= resultHandler
+  def addStatusPollToBatch(httpRequest: HttpRequest, batch: BatchRequest, resultHandler: JsonBatchCallback[O]): Unit =
+    resultHandlers :+= resultHandler
 
   def mockStatusInterpreter(operation: O): RunStatus = {
     val (status, newQueue) = operationStatusResponses.dequeue
@@ -146,14 +170,16 @@ abstract class TestPipelinesApiBatchHandler[O >: Null] extends PipelinesApiReque
 }
 
 object TestPipelinesApiRequestWorker {
-  def props(manager: ActorRef, jesConfiguration: PipelinesApiConfiguration, registryProbe: ActorRef)
-           (implicit batchHandler: TestPipelinesApiBatchHandler[_]): Props = {
-    Props(new TestPipelinesApiRequestWorker(
-      manager,
-      jesConfiguration.papiAttributes.qps,
-      registryProbe
-    ))
-  }
+  def props(manager: ActorRef, jesConfiguration: PipelinesApiConfiguration, registryProbe: ActorRef)(implicit
+    batchHandler: TestPipelinesApiBatchHandler[_]
+  ): Props =
+    Props(
+      new TestPipelinesApiRequestWorker(
+        manager,
+        jesConfiguration.papiAttributes.qps,
+        registryProbe
+      )
+    )
 
   sealed trait PipelinesApiBatchCallbackResponse
   case object CallbackSuccess extends PipelinesApiBatchCallbackResponse
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendCacheHitCopyingActorSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendCacheHitCopyingActorSpec.scala
index 1c40fa38590..368b631c6ce 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendCacheHitCopyingActorSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/callcaching/PipelinesApiBackendCacheHitCopyingActorSpec.scala
@@ -3,7 +3,7 @@ package cromwell.backend.google.pipelines.common.callcaching
 import akka.event.NoLogging
 import akka.testkit.{ImplicitSender, TestFSMRef, TestProbe}
 import com.typesafe.config.ConfigFactory
-import cromwell.backend.BackendCacheHitCopyingActor.{CopyOutputsCommand, CopyingOutputsFailedResponse}
+import cromwell.backend.BackendCacheHitCopyingActor.{CopyingOutputsFailedResponse, CopyOutputsCommand}
 import cromwell.backend.BackendJobExecutionActor.JobSucceededResponse
 import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes._
 import cromwell.backend.google.pipelines.common._
@@ -38,9 +38,13 @@ import scala.concurrent.duration._
 import scala.language.postfixOps
 import scala.util.{Success, Try}
 
-
-class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
-  with AnyFlatSpecLike with Matchers with ImplicitSender with MockSugar with Eventually {
+class PipelinesApiBackendCacheHitCopyingActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with ImplicitSender
+    with MockSugar
+    with Eventually {
 
   behavior of "PipelinesApiBackendCacheHitCopyingActor"
 
@@ -72,7 +76,8 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
     // Make sure we got the expected type of cache
     blacklistCache match {
       case _: GroupingBlacklistCache =>
-      case bad => fail(s"Unexpected blacklist cache type, expected GroupingBlacklistCache: ${bad.getClass.getSimpleName}")
+      case bad =>
+        fail(s"Unexpected blacklist cache type, expected GroupingBlacklistCache: ${bad.getClass.getSimpleName}")
     }
 
     {
@@ -86,7 +91,8 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
         fakeIoActor = ioActor,
         fakeServiceRegistryActor = serviceRegistryActor,
         supervisor = supervisor,
-        grouping = grouping)
+        grouping = grouping
+      )
 
       val copyCommand = buildCopyCommand(hitId = 0, bucket = WideOpenBucket)
       supervisor watch copyActor
@@ -97,9 +103,8 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
         copyActor.underlyingActor.stateName shouldBe WaitingForIoResponses
       }
 
-      ioActor.expectMsgPF(5 seconds) {
-        case ioCommand: DefaultIoCopyCommand =>
-          ioActor.reply(IoSuccess(ioCommand, ()))
+      ioActor.expectMsgPF(5 seconds) { case ioCommand: DefaultIoCopyCommand =>
+        ioActor.reply(IoSuccess(ioCommand, ()))
       }
 
       supervisor.expectMsgPF(5 seconds) { case _: JobSucceededResponse => }
@@ -135,7 +140,8 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
         fakeIoActor = ioActor,
         fakeServiceRegistryActor = serviceRegistryActor,
         supervisor = supervisor,
-        grouping = grouping)
+        grouping = grouping
+      )
 
       val command = buildCopyCommand(hitId = 1, bucket = LockedDownBucket)
       supervisor watch copyActor
@@ -146,10 +152,9 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
         copyActor.underlyingActor.stateName shouldBe WaitingForIoResponses
       }
 
-      ioActor.expectMsgPF(5 seconds) {
-        case ioCommand: DefaultIoCopyCommand =>
-          val failedPath = command.jobDetritusFiles(JobPaths.ReturnCodePathKey)
-          ioActor.reply(IoReadForbiddenFailure(ioCommand, new RuntimeException(), failedPath))
+      ioActor.expectMsgPF(5 seconds) { case ioCommand: DefaultIoCopyCommand =>
+        val failedPath = command.jobDetritusFiles(JobPaths.ReturnCodePathKey)
+        ioActor.reply(IoReadForbiddenFailure(ioCommand, new RuntimeException(), failedPath))
       }
 
       supervisor.expectMsgPF(5 seconds) { case _: CopyingOutputsFailedResponse => }
@@ -193,7 +198,8 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
         fakeIoActor = ioActor,
         fakeServiceRegistryActor = serviceRegistryActor,
         supervisor = supervisor,
-        grouping = grouping)
+        grouping = grouping
+      )
 
       supervisor watch copyActor
 
@@ -234,7 +240,8 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
         fakeIoActor = ioActor,
         fakeServiceRegistryActor = serviceRegistryActor,
         supervisor = supervisor,
-        grouping = grouping)
+        grouping = grouping
+      )
 
       supervisor watch copyActor
 
@@ -245,12 +252,12 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
         copyActor.underlyingActor.stateName shouldBe WaitingForIoResponses
       }
 
-      ioActor.expectMsgPF(5 seconds) {
-        case ioCommand: DefaultIoCopyCommand =>
-          ioActor.reply(IoFailure(ioCommand, new RuntimeException()))
+      ioActor.expectMsgPF(5 seconds) { case ioCommand: DefaultIoCopyCommand =>
+        ioActor.reply(IoFailure(ioCommand, new RuntimeException()))
       }
 
-      val List(readHit, readBucket, writeHit) = instrumentationCounts(n = 3, serviceRegistryActor = serviceRegistryActor)
+      val List(readHit, readBucket, writeHit) =
+        instrumentationCounts(n = 3, serviceRegistryActor = serviceRegistryActor)
 
       readHit.bucket.path.toList shouldBe expectedMetric(Hit, Read, UntestedCacheResult)
       readBucket.bucket.path.toList shouldBe expectedMetric(Bucket, Read, GoodCacheResult)
@@ -286,15 +293,15 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
         fakeIoActor = ioActor,
         fakeServiceRegistryActor = serviceRegistryActor,
         supervisor = supervisor,
-        grouping = grouping)
+        grouping = grouping
+      )
 
       supervisor watch copyActor
 
       val command = buildCopyCommand(hitId = 3, bucket = WideOpenBucket)
       copyActor ! command
 
-      supervisor.expectMsgPF(5 seconds) {
-        case _: CopyingOutputsFailedResponse =>
+      supervisor.expectMsgPF(5 seconds) { case _: CopyingOutputsFailedResponse =>
       }
       // The IoActor should not be consulted and the copying actor should simply stop itself without transitioning.
       supervisor.expectTerminated(copyActor)
@@ -328,15 +335,15 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
         fakeIoActor = ioActor,
         fakeServiceRegistryActor = serviceRegistryActor,
         supervisor = supervisor,
-        grouping = grouping)
+        grouping = grouping
+      )
 
       supervisor watch copyActor
 
       val command = buildCopyCommand(hitId = 4, bucket = LockedDownBucket)
       copyActor ! command
 
-      supervisor.expectMsgPF(5 seconds) {
-        case _: CopyingOutputsFailedResponse =>
+      supervisor.expectMsgPF(5 seconds) { case _: CopyingOutputsFailedResponse =>
       }
       // The IoActor should not be consulted and the copying actor should simply stop itself without transitioning.
       supervisor.expectTerminated(copyActor)
@@ -364,7 +371,9 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
 
   private def instrumentationCounts(n: Int, serviceRegistryActor: TestProbe): List[CromwellCount] = {
     val received = serviceRegistryActor.receiveN(n = n, max = 5 seconds).toList
-    val instrumentationCounts = received collect { case InstrumentationServiceMessage(c) => c } collect { case c: CromwellCount => c }
+    val instrumentationCounts = received collect { case InstrumentationServiceMessage(c) => c } collect {
+      case c: CromwellCount => c
+    }
     instrumentationCounts foreach { c => c.value shouldBe 1; c.sampling shouldBe 1.0 }
 
     instrumentationCounts
@@ -399,7 +408,8 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
                              fakeIoActor: TestProbe,
                              fakeServiceRegistryActor: TestProbe,
                              supervisor: TestProbe,
-                             grouping: Option[String]): TestFSMRefPipelinesApiBackendCacheHitCopyingActor = {
+                             grouping: Option[String]
+  ): TestFSMRefPipelinesApiBackendCacheHitCopyingActor = {
     // Couldn't mock this, possibly due to the use of `Refined` in two parameters:
     //
     // Underlying exception : java.lang.IllegalArgumentException: Cannot cast to primitive type: int
@@ -449,7 +459,7 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
       attempt = 1
     )
 
-    //noinspection ScalaUnusedSymbol
+    // noinspection ScalaUnusedSymbol
     def mapper(jobPaths: PipelinesApiJobPaths, originalPath: String): String = originalPath
 
     val workflowDescriptor = mock[BackendWorkflowDescriptor]
@@ -524,9 +534,7 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
 
     CopyOutputsCommand(
       womValueSimpletons = List.empty,
-      jobDetritusFiles = Map(
-        JobPaths.CallRootPathKey -> callRoot,
-        JobPaths.ReturnCodePathKey -> rcFile),
+      jobDetritusFiles = Map(JobPaths.CallRootPathKey -> callRoot, JobPaths.ReturnCodePathKey -> rcFile),
       returnCode = Option(0),
       cacheHit = CallCachingEntryId(hitId)
     )
@@ -540,10 +548,15 @@ class PipelinesApiBackendCacheHitCopyingActorSpec extends TestKitSuite
   case object Read extends CacheAccessType
   case object Write extends CacheAccessType
 
-  private def expectedMetric(hitOrBucket: BlacklistingType, accessType: CacheAccessType, status: BlacklistStatus): List[String] = {
-    List("job", "callcaching", "blacklist",
-      accessType.metricFormat,
-      hitOrBucket.metricFormat,
-      status.getClass.getSimpleName.dropRight(1))
-  }
+  private def expectedMetric(hitOrBucket: BlacklistingType,
+                             accessType: CacheAccessType,
+                             status: BlacklistStatus
+  ): List[String] =
+    List("job",
+         "callcaching",
+         "blacklist",
+         accessType.metricFormat,
+         hitOrBucket.metricFormat,
+         status.getClass.getSimpleName.dropRight(1)
+    )
 }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
index 7710f3de98e..3b38f578d6a 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
@@ -26,32 +26,29 @@ import wom.format.MemorySize
 
 import scala.jdk.CollectionConverters._
 
-case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, endpointUrl: URL)(implicit gcsTransferConfiguration: GcsTransferConfiguration) extends PipelinesApiFactoryInterface
-  with ContainerSetup
-  with MonitoringAction
-  with CheckpointingAction
-  with Localization
-  with UserAction
-  with Delocalization
-  with MemoryRetryCheckAction
-  with SSHAccessAction {
+case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, endpointUrl: URL)(implicit
+  gcsTransferConfiguration: GcsTransferConfiguration
+) extends PipelinesApiFactoryInterface
+    with ContainerSetup
+    with MonitoringAction
+    with CheckpointingAction
+    with Localization
+    with UserAction
+    with Delocalization
+    with MemoryRetryCheckAction
+    with SSHAccessAction {
 
   override def build(initializer: HttpRequestInitializer): PipelinesApiRequestFactory = new PipelinesApiRequestFactory {
-    val genomics: Genomics = new Genomics.Builder(
-      GoogleAuthMode.httpTransport,
-      GoogleAuthMode.jsonFactory,
-      initializer)
+    val genomics: Genomics = new Genomics.Builder(GoogleAuthMode.httpTransport, GoogleAuthMode.jsonFactory, initializer)
       .setApplicationName(applicationName)
       .setRootUrl(endpointUrl.toString)
       .build
 
-    override def cancelRequest(job: StandardAsyncJob): HttpRequest = {
+    override def cancelRequest(job: StandardAsyncJob): HttpRequest =
       genomics.projects().operations().cancel(job.jobId, new CancelOperationRequest()).buildHttpRequest()
-    }
 
-    override def getRequest(job: StandardAsyncJob): HttpRequest = {
+    override def getRequest(job: StandardAsyncJob): HttpRequest =
       genomics.projects().operations().get(job.jobId).buildHttpRequest()
-    }
 
     override def runRequest(createPipelineParameters: CreatePipelineParameters, jobLogger: JobLogger): HttpRequest = {
       def createNetworkWithVPC(vpcAndSubnetworkProjectLabelValues: VpcAndSubnetworkProjectLabelValues): Network = {
@@ -66,12 +63,11 @@ case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, en
         network
       }
 
-      def createNetwork(): Network = {
+      def createNetwork(): Network =
         createPipelineParameters.vpcNetworkAndSubnetworkProjectLabels match {
           case Some(vpcAndSubnetworkProjectLabelValues) => createNetworkWithVPC(vpcAndSubnetworkProjectLabelValues)
           case _ => new Network().setUsePrivateAddress(createPipelineParameters.runtimeAttributes.noAddress)
         }
-      }
 
       val allDisksToBeMounted = createPipelineParameters.adjustedSizeDisks ++
         createPipelineParameters.referenceDisksForLocalizationOpt.getOrElse(List.empty)
@@ -95,7 +91,8 @@ case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, en
       // adding memory as environment variables makes it easy for a user to retrieve the new value of memory
       // on the machine to utilize in their command blocks if needed
       val runtimeMemory = createPipelineParameters.runtimeAttributes.memory
-      val environment = Map("MEM_UNIT" -> runtimeMemory.unit.toString, "MEM_SIZE" -> runtimeMemory.amount.toString).asJava
+      val environment =
+        Map("MEM_UNIT" -> runtimeMemory.unit.toString, "MEM_SIZE" -> runtimeMemory.amount.toString).asJava
 
       val sortedActions =
         ActionUtils.sortActions[Action](
@@ -109,13 +106,12 @@ case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, en
           checkpointingStart = checkpointingStart,
           checkpointingShutdown = checkpointingShutdown,
           sshAccess = sshAccess,
-          isBackground =
-            action =>
-              Option(action.getFlags)
-                .map(_.asScala)
-                .toList
-                .flatten
-                .contains(ActionFlag.RunInBackground.toString),
+          isBackground = action =>
+            Option(action.getFlags)
+              .map(_.asScala)
+              .toList
+              .flatten
+              .contains(ActionFlag.RunInBackground.toString)
         )
 
       val serviceAccount = new ServiceAccount()
@@ -138,8 +134,7 @@ case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, en
 
       val network: Network = createNetwork()
 
-      val accelerators = createPipelineParameters.runtimeAttributes
-        .gpuResource.map(toAccelerator).toList.asJava
+      val accelerators = createPipelineParameters.runtimeAttributes.gpuResource.map(toAccelerator).toList.asJava
 
       /*
        * Adjust using docker images used by Cromwell as well as the tool's docker image size if available
@@ -147,12 +142,18 @@ case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, en
       val adjustedBootDiskSize = {
         val fromRuntimeAttributes = createPipelineParameters.runtimeAttributes.bootDiskSize
         // Compute the decompressed size based on the information available
-        val userCommandImageSizeInBytes = createPipelineParameters.jobDescriptor.dockerSize.map(_.toFullSize(DockerConfiguration.instance.sizeCompressionFactor)).getOrElse(0L)
-        val userCommandImageSizeInGB = MemorySize(userCommandImageSizeInBytes.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB).amount
+        val userCommandImageSizeInBytes = createPipelineParameters.jobDescriptor.dockerSize
+          .map(_.toFullSize(DockerConfiguration.instance.sizeCompressionFactor))
+          .getOrElse(0L)
+        val userCommandImageSizeInGB =
+          MemorySize(userCommandImageSizeInBytes.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB).amount
         val userCommandImageSizeRoundedUpInGB = userCommandImageSizeInGB.ceil.toInt
 
-        val totalSize = fromRuntimeAttributes + userCommandImageSizeRoundedUpInGB + ActionUtils.cromwellImagesSizeRoundedUpInGB
-        jobLogger.info(s"Adjusting boot disk size to $totalSize GB: $fromRuntimeAttributes GB (runtime attributes) + $userCommandImageSizeRoundedUpInGB GB (user command image) + ${ActionUtils.cromwellImagesSizeRoundedUpInGB} GB (Cromwell support images)")
+        val totalSize =
+          fromRuntimeAttributes + userCommandImageSizeRoundedUpInGB + ActionUtils.cromwellImagesSizeRoundedUpInGB
+        jobLogger.info(
+          s"Adjusting boot disk size to $totalSize GB: $fromRuntimeAttributes GB (runtime attributes) + $userCommandImageSizeRoundedUpInGB GB (user command image) + ${ActionUtils.cromwellImagesSizeRoundedUpInGB} GB (Cromwell support images)"
+        )
         totalSize
       }
 
@@ -166,10 +167,12 @@ case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, en
         .setNetwork(network)
         .setAccelerators(accelerators)
 
-      if(createPipelineParameters.dockerImageCacheDiskOpt.isDefined) {
-        jobLogger.info("Docker image cache requested for the job, but the job is being executed by Google " +
-          "Genomics API v2alpha1, while the feature is only supported by from Google Life Scielnces API starting from" +
-          "the version v2beta")
+      if (createPipelineParameters.dockerImageCacheDiskOpt.isDefined) {
+        jobLogger.info(
+          "Docker image cache requested for the job, but the job is being executed by Google " +
+            "Genomics API v2alpha1, while the feature is only supported by from Google Life Scielnces API starting from" +
+            "the version v2beta"
+        )
       }
 
       createPipelineParameters.runtimeAttributes.gpuResource foreach { resource =>
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
index 481f7d6c5a8..d31d311fc28 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -17,7 +17,15 @@ import cromwell.filesystems.gcs.{GcsPath, GcsPathBuilder}
 import org.apache.commons.codec.digest.DigestUtils
 import wom.core.FullyQualifiedName
 import wom.expression.FileEvaluation
-import wom.values.{GlobFunctions, WomFile, WomGlobFile, WomMaybeListedDirectory, WomMaybePopulatedFile, WomSingleFile, WomUnlistedDirectory}
+import wom.values.{
+  GlobFunctions,
+  WomFile,
+  WomGlobFile,
+  WomMaybeListedDirectory,
+  WomMaybePopulatedFile,
+  WomSingleFile,
+  WomUnlistedDirectory
+}
 
 import java.io.FileNotFoundException
 import scala.concurrent.Future
@@ -26,7 +34,7 @@ import scala.language.postfixOps
 import scala.util.control.NoStackTrace
 
 class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExecutionActorParams)
-  extends cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor(standardParams)
+    extends cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor(standardParams)
     with PipelinesApiReferenceFilesMappingOperations {
 
   // The original implementation assumes the WomFiles are all WomMaybePopulatedFiles and wraps everything in a PipelinesApiFileInput
@@ -34,31 +42,45 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
   override protected def pipelinesApiInputsFromWomFiles(inputName: String,
                                                         remotePathArray: Seq[WomFile],
                                                         localPathArray: Seq[WomFile],
-                                                        jobDescriptor: BackendJobDescriptor): Iterable[PipelinesApiInput] = {
+                                                        jobDescriptor: BackendJobDescriptor
+  ): Iterable[PipelinesApiInput] =
     (remotePathArray zip localPathArray) flatMap {
       case (remotePath: WomMaybeListedDirectory, localPath) =>
         maybeListedDirectoryToPipelinesParameters(inputName, remotePath, localPath.valueString)
       case (remotePath: WomUnlistedDirectory, localPath) =>
-        Seq(PipelinesApiDirectoryInput(inputName, getPath(remotePath.valueString).get, DefaultPathBuilder.get(localPath.valueString), workingDisk))
+        Seq(
+          PipelinesApiDirectoryInput(inputName,
+                                     getPath(remotePath.valueString).get,
+                                     DefaultPathBuilder.get(localPath.valueString),
+                                     workingDisk
+          )
+        )
       case (remotePath: WomMaybePopulatedFile, localPath) =>
         maybePopulatedFileToPipelinesParameters(inputName, remotePath, localPath.valueString)
       case (remotePath, localPath) =>
-        Seq(PipelinesApiFileInput(inputName, getPath(remotePath.valueString).get, DefaultPathBuilder.get(localPath.valueString), workingDisk))
+        Seq(
+          PipelinesApiFileInput(inputName,
+                                getPath(remotePath.valueString).get,
+                                DefaultPathBuilder.get(localPath.valueString),
+                                workingDisk
+          )
+        )
     }
-  }
 
   // The original implementation recursively finds all non directory files, in V2 we can keep directory as is
   override protected lazy val callInputFiles: Map[FullyQualifiedName, Seq[WomFile]] = jobDescriptor.localInputs map {
     case (key, womFile) =>
-      key -> womFile.collectAsSeq({
+      key -> womFile.collectAsSeq {
         case womFile: WomFile if !inputsToNotLocalize.contains(womFile) => womFile
-      })
+      }
   }
 
   private lazy val gcsTransferLibrary =
     Source.fromInputStream(Thread.currentThread.getContextClassLoader.getResourceAsStream("gcs_transfer.sh")).mkString
 
-  private def gcsLocalizationTransferBundle[T <: PipelinesApiInput](gcsTransferConfiguration: GcsTransferConfiguration)(bucket: String, inputs: NonEmptyList[T]): String = {
+  private def gcsLocalizationTransferBundle[T <: PipelinesApiInput](
+    gcsTransferConfiguration: GcsTransferConfiguration
+  )(bucket: String, inputs: NonEmptyList[T]): String = {
     val project = inputs.head.cloudPath.asInstanceOf[GcsPath].projectId
     val maxAttempts = gcsTransferConfiguration.transferAttempts
 
@@ -73,27 +95,29 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
 
     val filesByContainerParentDirectory = filesWithSameNames.groupBy(_.containerPath.parent.toString)
     // Deduplicate any inputs since parallel localization can't deal with this.
-    val uniqueFilesByContainerParentDirectory = filesByContainerParentDirectory map { case (p, fs) => p -> fs.toSet  }
+    val uniqueFilesByContainerParentDirectory = filesByContainerParentDirectory map { case (p, fs) => p -> fs.toSet }
 
-    val filesWithSameNamesTransferBundles: List[String] = uniqueFilesByContainerParentDirectory.toList map { case (containerParent, filesWithSameParent) =>
-      val arrayIdentifier = s"files_to_localize_" + DigestUtils.md5Hex(bucket + containerParent)
-      val entries = filesWithSameParent.map(_.cloudPath) mkString("\"", "\"\n|  \"", "\"")
+    val filesWithSameNamesTransferBundles: List[String] = uniqueFilesByContainerParentDirectory.toList map {
+      case (containerParent, filesWithSameParent) =>
+        val arrayIdentifier = s"files_to_localize_" + DigestUtils.md5Hex(bucket + containerParent)
+        val entries = filesWithSameParent.map(_.cloudPath) mkString ("\"", "\"\n|  \"", "\"")
 
-      s"""
-         |# Localize files from source bucket '$bucket' to container parent directory '$containerParent'.
-         |$arrayIdentifier=(
-         |  "$project"   # project to use if requester pays
-         |  "$maxAttempts" # max transfer attempts
-         |  "${containerParent.ensureSlashed}" # container parent directory
-         |  $entries
-         |)
-         |
-         |localize_files "$${$arrayIdentifier[@]}"
+        s"""
+           |# Localize files from source bucket '$bucket' to container parent directory '$containerParent'.
+           |$arrayIdentifier=(
+           |  "$project"   # project to use if requester pays
+           |  "$maxAttempts" # max transfer attempts
+           |  "${containerParent.ensureSlashed}" # container parent directory
+           |  $entries
+           |)
+           |
+           |localize_files "$${$arrayIdentifier[@]}"
        """.stripMargin
     }
 
     val filesWithDifferentNamesTransferBundles = filesWithDifferentNames map { f =>
-      val arrayIdentifier = s"singleton_file_to_localize_" + DigestUtils.md5Hex(f.cloudPath.pathAsString + f.containerPath.pathAsString)
+      val arrayIdentifier =
+        s"singleton_file_to_localize_" + DigestUtils.md5Hex(f.cloudPath.pathAsString + f.containerPath.pathAsString)
       s"""
          |# Localize singleton file '${f.cloudPath.pathAsString}' to '${f.containerPath.pathAsString}'.
          |$arrayIdentifier=(
@@ -109,27 +133,31 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
 
     // Only write a transfer bundle for directories if there are directories to be localized. Emptiness isn't a concern
     // for files since there is always at least the command script to be localized.
-    val directoryTransferBundle = if (directories.isEmpty) "" else {
-      val entries = directories flatMap { i => List(i.cloudPath, i.containerPath) } mkString("\"", "\"\n|  \"", "\"")
+    val directoryTransferBundle =
+      if (directories.isEmpty) ""
+      else {
+        val entries = directories flatMap { i => List(i.cloudPath, i.containerPath) } mkString ("\"", "\"\n|  \"", "\"")
 
-      val arrayIdentifier = s"directories_to_localize_" + DigestUtils.md5Hex(bucket)
+        val arrayIdentifier = s"directories_to_localize_" + DigestUtils.md5Hex(bucket)
 
-      s"""
-         |# Directories from source bucket '$bucket'.
-         |$arrayIdentifier=(
-         |  "$project"    # project to use if requester pays
-         |  "$maxAttempts" # max transfer attempts
-         |  $entries
-         |)
-         |
-         |localize_directories "$${$arrayIdentifier[@]}"
+        s"""
+           |# Directories from source bucket '$bucket'.
+           |$arrayIdentifier=(
+           |  "$project"    # project to use if requester pays
+           |  "$maxAttempts" # max transfer attempts
+           |  $entries
+           |)
+           |
+           |localize_directories "$${$arrayIdentifier[@]}"
        """.stripMargin
-    }
+      }
 
     (directoryTransferBundle :: (filesWithSameNamesTransferBundles ++ filesWithDifferentNamesTransferBundles)) mkString "\n\n"
   }
 
-  private def gcsDelocalizationTransferBundle[T <: PipelinesApiOutput](transferConfiguration: GcsTransferConfiguration)(bucket: String, outputs: NonEmptyList[T]): String = {
+  private def gcsDelocalizationTransferBundle[T <: PipelinesApiOutput](
+    transferConfiguration: GcsTransferConfiguration
+  )(bucket: String, outputs: NonEmptyList[T]): String = {
     val project = outputs.head.cloudPath.asInstanceOf[GcsPath].projectId
     val maxAttempts = transferConfiguration.transferAttempts
 
@@ -140,14 +168,16 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
         case _: PipelinesApiDirectoryOutput => "directory" // a primary directory
       }
 
-      val optional = Option(output) collectFirst { case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
+      val optional = Option(output) collectFirst {
+        case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional"
+      } getOrElse "required"
       val contentType = output.contentType.map(_.toString).getOrElse("")
 
       List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
-    } mkString("\"", "\"\n|  \"", "\"")
+    } mkString ("\"", "\"\n|  \"", "\"")
 
-    val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(
-      "parallel_composite_upload_threshold", transferConfiguration.parallelCompositeUploadThreshold)
+    val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions
+      .getOrElse("parallel_composite_upload_threshold", transferConfiguration.parallelCompositeUploadThreshold)
 
     // Use a digest as bucket names can contain characters that are not legal in bash identifiers.
     val arrayIdentifier = s"delocalize_" + DigestUtils.md5Hex(bucket)
@@ -164,27 +194,27 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       """.stripMargin
   }
 
-  private def bracketTransfersWithMessages(activity: String)(transferBody: String): String = {
+  private def bracketTransfersWithMessages(activity: String)(transferBody: String): String =
     List(
       s"timestamped_message '$activity script execution started...'",
       transferBody,
       s"timestamped_message '$activity script execution complete.'"
     ) mkString "\n"
-  }
 
   import mouse.all._
 
   private def generateGcsLocalizationScript(inputs: List[PipelinesApiInput],
-                                            referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]])
-                                           (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+                                            referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]]
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
     import cromwell.backend.google.pipelines.common.action.ActionUtils.shellEscaped
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
-        referenceInputsToMountedPaths map {
-          case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
+        referenceInputsToMountedPaths map { case (input, absolutePathOnRefDisk) =>
+          s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(
+              absolutePathOnRefDisk
+            )} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }
 
@@ -206,9 +236,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       }
 
     val regularFilesLocalizationScript = {
-      val regularFiles = referenceInputsToMountedPathsOpt.map(maybeReferenceInputsToMountedPaths =>
-        inputs diff maybeReferenceInputsToMountedPaths.keySet.toList
-      ).getOrElse(inputs)
+      val regularFiles = referenceInputsToMountedPathsOpt
+        .map(maybeReferenceInputsToMountedPaths => inputs diff maybeReferenceInputsToMountedPaths.keySet.toList)
+        .getOrElse(inputs)
       if (regularFiles.nonEmpty) {
         val bundleFunction = (gcsLocalizationTransferBundle(gcsTransferConfiguration) _).tupled
         generateGcsTransferScript(regularFiles, bundleFunction)
@@ -227,45 +257,68 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
     combinedLocalizationScript |> bracketTransfersWithMessages("Localization")
   }
 
-  private def generateGcsDelocalizationScript(outputs: List[PipelinesApiOutput])(implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  private def generateGcsDelocalizationScript(
+    outputs: List[PipelinesApiOutput]
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     val bundleFunction = (gcsDelocalizationTransferBundle(gcsTransferConfiguration) _).tupled
     generateGcsTransferScript(outputs, bundleFunction) |> bracketTransfersWithMessages("Delocalization")
   }
 
-  private def generateGcsTransferScript[T <: PipelinesParameter](items: List[T], bundleFunction: ((String, NonEmptyList[T])) => String): String = {
+  private def generateGcsTransferScript[T <: PipelinesParameter](items: List[T],
+                                                                 bundleFunction: ((String, NonEmptyList[T])) => String
+  ): String = {
     val gcsItems = items collect { case i if i.cloudPath.isInstanceOf[GcsPath] => i }
     groupParametersByGcsBucket(gcsItems) map bundleFunction mkString "\n"
   }
 
   override protected def uploadGcsTransferLibrary(createPipelineParameters: CreatePipelineParameters,
                                                   cloudPath: Path,
-                                                  gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = {
-
+                                                  gcsTransferConfiguration: GcsTransferConfiguration
+  ): Future[Unit] =
     asyncIo.writeAsync(cloudPath, gcsTransferLibrary, Seq(CloudStorageOptions.withMimeType("text/plain")))
-  }
 
   override def uploadGcsLocalizationScript(createPipelineParameters: CreatePipelineParameters,
                                            cloudPath: Path,
                                            transferLibraryContainerPath: Path,
                                            gcsTransferConfiguration: GcsTransferConfiguration,
-                                           referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]]): Future[Unit] = {
-    val content = generateGcsLocalizationScript(createPipelineParameters.inputOutputParameters.fileInputParameters, referenceInputsToMountedPathsOpt)(gcsTransferConfiguration)
-    asyncIo.writeAsync(cloudPath, s"source '$transferLibraryContainerPath'\n\n" + content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+                                           referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]]
+  ): Future[Unit] = {
+    val content = generateGcsLocalizationScript(createPipelineParameters.inputOutputParameters.fileInputParameters,
+                                                referenceInputsToMountedPathsOpt
+    )(gcsTransferConfiguration)
+    asyncIo.writeAsync(cloudPath,
+                       s"source '$transferLibraryContainerPath'\n\n" + content,
+                       Seq(CloudStorageOptions.withMimeType("text/plain"))
+    )
   }
 
   override def uploadGcsDelocalizationScript(createPipelineParameters: CreatePipelineParameters,
                                              cloudPath: Path,
                                              transferLibraryContainerPath: Path,
-                                             gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = {
-    val content = generateGcsDelocalizationScript(createPipelineParameters.inputOutputParameters.fileOutputParameters)(gcsTransferConfiguration)
-    asyncIo.writeAsync(cloudPath, s"source '$transferLibraryContainerPath'\n\n" + content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+                                             gcsTransferConfiguration: GcsTransferConfiguration
+  ): Future[Unit] = {
+    val content = generateGcsDelocalizationScript(createPipelineParameters.inputOutputParameters.fileOutputParameters)(
+      gcsTransferConfiguration
+    )
+    asyncIo.writeAsync(cloudPath,
+                       s"source '$transferLibraryContainerPath'\n\n" + content,
+                       Seq(CloudStorageOptions.withMimeType("text/plain"))
+    )
   }
 
   // Simply create a PipelinesApiDirectoryOutput in v2 instead of globbing
-  override protected def generateUnlistedDirectoryOutputs(unlistedDirectory: WomUnlistedDirectory, fileEvaluation: FileEvaluation): List[PipelinesApiOutput] = {
+  override protected def generateUnlistedDirectoryOutputs(unlistedDirectory: WomUnlistedDirectory,
+                                                          fileEvaluation: FileEvaluation
+  ): List[PipelinesApiOutput] = {
     val destination = callRootPath.resolve(unlistedDirectory.value.stripPrefix("/"))
     val (relpath, disk) = relativePathAndAttachedDisk(unlistedDirectory.value, runtimeAttributes.disks)
-    val directoryOutput = PipelinesApiDirectoryOutput(makeSafeReferenceName(unlistedDirectory.value), destination, relpath, disk, fileEvaluation.optional, fileEvaluation.secondary)
+    val directoryOutput = PipelinesApiDirectoryOutput(makeSafeReferenceName(unlistedDirectory.value),
+                                                      destination,
+                                                      relpath,
+                                                      disk,
+                                                      fileEvaluation.optional,
+                                                      fileEvaluation.secondary
+    )
     List(directoryOutput)
   }
 
@@ -282,13 +335,27 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
     // We need both the glob directory and the glob list:
     List(
       // The glob directory:
-      PipelinesApiDirectoryOutput(makeSafeReferenceName(globDirectory), gcsGlobDirectoryDestinationPath, DefaultPathBuilder.get(globDirectory), globDirectoryDisk, optional = false, secondary = false),
+      PipelinesApiDirectoryOutput(
+        makeSafeReferenceName(globDirectory),
+        gcsGlobDirectoryDestinationPath,
+        DefaultPathBuilder.get(globDirectory),
+        globDirectoryDisk,
+        optional = false,
+        secondary = false
+      ),
       // The glob list file:
-      PipelinesApiFileOutput(makeSafeReferenceName(globListFile), gcsGlobListFileDestinationPath, DefaultPathBuilder.get(globListFile), globDirectoryDisk, optional = false, secondary = false)
+      PipelinesApiFileOutput(
+        makeSafeReferenceName(globListFile),
+        gcsGlobListFileDestinationPath,
+        DefaultPathBuilder.get(globListFile),
+        globDirectoryDisk,
+        optional = false,
+        secondary = false
+      )
     )
   }
 
-  override def womFileToGcsPath(jesOutputs: Set[PipelinesApiOutput])(womFile: WomFile): WomFile = {
+  override def womFileToGcsPath(jesOutputs: Set[PipelinesApiOutput])(womFile: WomFile): WomFile =
     womFile mapFile { path =>
       jesOutputs collectFirst {
         case jesOutput if jesOutput.name == makeSafeReferenceName(path) =>
@@ -305,65 +372,98 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
           case _: ValidFullGcsPath => path
 
           /*
-            * Strip the prefixes in RuntimeOutputMapping.prefixFilters from the path, one at a time.
-            * For instance
-            * file:///cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt will progressively become
-            *
-            * /cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
-            * bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
-            * call-A/file.txt
-            *
-            * This code is called as part of a path mapper that will be applied to the WOMified cwl.output.json.
-            * The cwl.output.json when it's being read by Cromwell from the bucket still contains local paths
-            * (as they were created by the cwl tool).
-            * In order to keep things working we need to map those local paths to where they were actually delocalized,
-            * which is determined in cromwell.backend.google.pipelines.v2alpha1.api.Delocalization.
-            */
-          case _ => (callRootPath /
-            RuntimeOutputMapping
+           * Strip the prefixes in RuntimeOutputMapping.prefixFilters from the path, one at a time.
+           * For instance
+           * file:///cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt will progressively become
+           *
+           * /cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
+           * bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
+           * call-A/file.txt
+           *
+           * This code is called as part of a path mapper that will be applied to the WOMified cwl.output.json.
+           * The cwl.output.json when it's being read by Cromwell from the bucket still contains local paths
+           * (as they were created by the cwl tool).
+           * In order to keep things working we need to map those local paths to where they were actually delocalized,
+           * which is determined in cromwell.backend.google.pipelines.v2alpha1.api.Delocalization.
+           */
+          case _ =>
+            (callRootPath /
+              RuntimeOutputMapping
                 .prefixFilters(workflowPaths.workflowRoot)
-                .foldLeft(path)({
-                  case (newPath, prefix) => newPath.stripPrefix(prefix)
-                })
-            ).pathAsString
+                .foldLeft(path) { case (newPath, prefix) =>
+                  newPath.stripPrefix(prefix)
+                }).pathAsString
         }
       }
     }
-  }
 
-  private def maybePopulatedFileToPipelinesParameters(inputName: String, maybePopulatedFile: WomMaybePopulatedFile, localPath: String) = {
-    val secondaryFiles = maybePopulatedFile.secondaryFiles.flatMap({ secondaryFile =>
-      pipelinesApiInputsFromWomFiles(secondaryFile.valueString, List(secondaryFile), List(relativeLocalizationPath(secondaryFile)), jobDescriptor)
-    })
+  private def maybePopulatedFileToPipelinesParameters(inputName: String,
+                                                      maybePopulatedFile: WomMaybePopulatedFile,
+                                                      localPath: String
+  ) = {
+    val secondaryFiles = maybePopulatedFile.secondaryFiles.flatMap { secondaryFile =>
+      pipelinesApiInputsFromWomFiles(secondaryFile.valueString,
+                                     List(secondaryFile),
+                                     List(relativeLocalizationPath(secondaryFile)),
+                                     jobDescriptor
+      )
+    }
 
-    Seq(PipelinesApiFileInput(inputName, getPath(maybePopulatedFile.valueString).get, DefaultPathBuilder.get(localPath), workingDisk)) ++ secondaryFiles
+    Seq(
+      PipelinesApiFileInput(inputName,
+                            getPath(maybePopulatedFile.valueString).get,
+                            DefaultPathBuilder.get(localPath),
+                            workingDisk
+      )
+    ) ++ secondaryFiles
   }
 
-  private def maybeListedDirectoryToPipelinesParameters(inputName: String, womMaybeListedDirectory: WomMaybeListedDirectory, localPath: String) = womMaybeListedDirectory match {
+  private def maybeListedDirectoryToPipelinesParameters(inputName: String,
+                                                        womMaybeListedDirectory: WomMaybeListedDirectory,
+                                                        localPath: String
+  ) = womMaybeListedDirectory match {
     // If there is a path, simply localize as a directory
     case WomMaybeListedDirectory(Some(path), _, _, _) =>
       List(PipelinesApiDirectoryInput(inputName, getPath(path).get, DefaultPathBuilder.get(localPath), workingDisk))
 
     // If there is a listing, recurse and call pipelinesApiInputsFromWomFiles on all the listed files
     case WomMaybeListedDirectory(_, Some(listing), _, _) if listing.nonEmpty =>
-      listing.flatMap({
+      listing.flatMap {
         case womFile: WomFile if isAdHocFile(womFile) =>
-          pipelinesApiInputsFromWomFiles(makeSafeReferenceName(womFile.valueString), List(womFile), List(fileName(womFile)), jobDescriptor)
+          pipelinesApiInputsFromWomFiles(makeSafeReferenceName(womFile.valueString),
+                                         List(womFile),
+                                         List(fileName(womFile)),
+                                         jobDescriptor
+          )
         case womFile: WomFile =>
-          pipelinesApiInputsFromWomFiles(makeSafeReferenceName(womFile.valueString), List(womFile), List(relativeLocalizationPath(womFile)), jobDescriptor)
-      })
+          pipelinesApiInputsFromWomFiles(makeSafeReferenceName(womFile.valueString),
+                                         List(womFile),
+                                         List(relativeLocalizationPath(womFile)),
+                                         jobDescriptor
+          )
+      }
     case _ => List.empty
   }
 
-  override def generateSingleFileOutputs(womFile: WomSingleFile, fileEvaluation: FileEvaluation): List[PipelinesApiFileOutput] = {
+  override def generateSingleFileOutputs(womFile: WomSingleFile,
+                                         fileEvaluation: FileEvaluation
+  ): List[PipelinesApiFileOutput] = {
     val (relpath, disk) = relativePathAndAttachedDisk(womFile.value, runtimeAttributes.disks)
     // If the file is on a custom mount point, resolve it so that the full mount path will show up in the cloud path
     // For the default one (cromwell_root), the expectation is that it does not appear
-    val mountedPath = if (!disk.mountPoint.isSamePathAs(PipelinesApiWorkingDisk.Default.mountPoint)) disk.mountPoint.resolve(relpath) else relpath
+    val mountedPath =
+      if (!disk.mountPoint.isSamePathAs(PipelinesApiWorkingDisk.Default.mountPoint)) disk.mountPoint.resolve(relpath)
+      else relpath
     // Normalize the local path (to get rid of ".." and "."). Also strip any potential leading / so that it gets appended to the call root
     val normalizedPath = mountedPath.normalize().pathAsString.stripPrefix("/")
     val destination = callRootPath.resolve(normalizedPath)
-    val jesFileOutput = PipelinesApiFileOutput(makeSafeReferenceName(womFile.value), destination, relpath, disk, fileEvaluation.optional, fileEvaluation.secondary)
+    val jesFileOutput = PipelinesApiFileOutput(makeSafeReferenceName(womFile.value),
+                                               destination,
+                                               relpath,
+                                               disk,
+                                               fileEvaluation.optional,
+                                               fileEvaluation.secondary
+    )
     List(jesFileOutput)
   }
 }
@@ -381,10 +481,12 @@ object PipelinesApiAsyncBackendJobExecutionActor {
   //  - There must be at least one '/', followed by some content in the file name.
   // - Or, then, for directories:
   //  - If we got this far, we already have a valid directory path. Allow it to optionally end with a `/` character.
-  private val gcsFilePathMatcher =      "(?s)^gs://([a-zA-Z0-9][^/]+)(/[^/]+)*/[^/]+$".r
+  private val gcsFilePathMatcher = "(?s)^gs://([a-zA-Z0-9][^/]+)(/[^/]+)*/[^/]+$".r
   private val gcsDirectoryPathMatcher = "(?s)^gs://([a-zA-Z0-9][^/]+)(/[^/]+)*/?$".r
 
-  private [v2alpha1] def groupParametersByGcsBucket[T <: PipelinesParameter](parameters: List[T]): Map[String, NonEmptyList[T]] = {
+  private[v2alpha1] def groupParametersByGcsBucket[T <: PipelinesParameter](
+    parameters: List[T]
+  ): Map[String, NonEmptyList[T]] =
     parameters.map { param =>
       def pathTypeString = if (param.isFileParameter) "File" else "Directory"
       val regexToUse = if (param.isFileParameter) gcsFilePathMatcher else gcsDirectoryPathMatcher
@@ -393,8 +495,9 @@ object PipelinesApiAsyncBackendJobExecutionActor {
         case regexToUse(bucket) => Map(bucket -> NonEmptyList.of(param))
         case regexToUse(bucket, _) => Map(bucket -> NonEmptyList.of(param))
         case other =>
-          throw new Exception(s"$pathTypeString path '$other' did not match the expected regex: ${regexToUse.pattern.toString}") with NoStackTrace
+          throw new Exception(
+            s"$pathTypeString path '$other' did not match the expected regex: ${regexToUse.pattern.toString}"
+          ) with NoStackTrace
       }
     } combineAll
-  }
 }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiLifecycleActorFactory.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiLifecycleActorFactory.scala
index aad8c49eec8..95d4965d6f6 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiLifecycleActorFactory.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiLifecycleActorFactory.scala
@@ -2,17 +2,21 @@ package cromwell.backend.google.pipelines.v2alpha1
 
 import akka.actor.{ActorRef, Props}
 import cromwell.backend.BackendConfigurationDescriptor
-import cromwell.backend.google.pipelines.common.{PipelinesApiBackendLifecycleActorFactory, PipelinesApiBackendSingletonActor, PipelinesApiConfiguration}
+import cromwell.backend.google.pipelines.common.{
+  PipelinesApiBackendLifecycleActorFactory,
+  PipelinesApiBackendSingletonActor,
+  PipelinesApiConfiguration
+}
 import cromwell.backend.google.pipelines.v2alpha1.api.request.RequestHandler
 import cromwell.backend.standard.StandardAsyncExecutionActor
 
 class PipelinesApiLifecycleActorFactory(name: String, configurationDescriptor: BackendConfigurationDescriptor)
-  extends PipelinesApiBackendLifecycleActorFactory(name, configurationDescriptor) {
+    extends PipelinesApiBackendLifecycleActorFactory(name, configurationDescriptor) {
   private val genomicsFactory =
     GenomicsFactory(
       googleConfig.applicationName,
       papiAttributes.auths.genomics,
-      papiAttributes.endpointUrl,
+      papiAttributes.endpointUrl
     )(papiAttributes.gcsTransferConfiguration)
   override protected val jesConfiguration =
     new PipelinesApiConfiguration(configurationDescriptor, genomicsFactory, googleConfig, papiAttributes)
@@ -21,7 +25,7 @@ class PipelinesApiLifecycleActorFactory(name: String, configurationDescriptor: B
       new RequestHandler(
         googleConfig.applicationName,
         papiAttributes.endpointUrl,
-        papiAttributes.batchRequestTimeoutConfiguration,
+        papiAttributes.batchRequestTimeoutConfiguration
       )
     PipelinesApiBackendSingletonActor.props(
       jesConfiguration.papiAttributes.qps,
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
index 19774a4cc41..dc21f3ea11c 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesParameterConversions.scala
@@ -21,14 +21,14 @@ import simulacrum.typeclass
 
 trait PipelinesParameterConversions {
   implicit val fileInputToParameter: ToParameter[PipelinesApiFileInput] = new ToParameter[PipelinesApiFileInput] {
-    override def toActions(fileInput: PipelinesApiFileInput, mounts: List[Mount])
-                          (implicit retryPolicy: GcsTransferConfiguration): List[Action] = {
+    override def toActions(fileInput: PipelinesApiFileInput, mounts: List[Mount])(implicit
+      retryPolicy: GcsTransferConfiguration
+    ): List[Action] = {
       lazy val config = ConfigFactory.load
 
       val labels = ActionBuilder.parameterLabels(fileInput)
       fileInput.cloudPath match {
         case drsPath: DrsPath =>
-
           import scala.jdk.CollectionConverters._
 
           val drsFileSystemProvider = drsPath.drsPath.getFileSystem.provider.asInstanceOf[DrsCloudNioFileSystemProvider]
@@ -49,13 +49,12 @@ trait PipelinesParameterConversions {
         case sraPath: SraPath =>
           val sraConfig = config.getConfig("filesystems.sra")
 
-          def getString(key: String): Option[String] = {
+          def getString(key: String): Option[String] =
             if (sraConfig.hasPath(key)) {
               Some(sraConfig.getString(key))
             } else {
               None
             }
-          }
 
           val image = getString("docker-image") getOrElse "fusera/fusera:alpine"
           val (createNgc, ngcArgs) = getString("ngc") match {
@@ -83,31 +82,33 @@ trait PipelinesParameterConversions {
 
   implicit val directoryInputToParameter: ToParameter[PipelinesApiDirectoryInput] =
     new ToParameter[PipelinesApiDirectoryInput] {
-    override def toActions(directoryInput: PipelinesApiDirectoryInput, mounts: List[Mount])
-                          (implicit retryPolicy: GcsTransferConfiguration): List[Action] = {
-      directoryInput.cloudPath match {
-        case _: GcsPath => Nil // GCS paths will be localized with a separate localization script.
-        case _ =>
-          val labels = ActionBuilder.parameterLabels(directoryInput)
-          val describeAction = ActionBuilder.describeParameter(directoryInput, labels)
-          val localizationAction = cloudSdkShellAction(
-            localizeDirectory(directoryInput.cloudPath, directoryInput.containerPath)
-          )(mounts = mounts, labels = labels)
-          List(describeAction, localizationAction)
-      }
+      override def toActions(directoryInput: PipelinesApiDirectoryInput, mounts: List[Mount])(implicit
+        retryPolicy: GcsTransferConfiguration
+      ): List[Action] =
+        directoryInput.cloudPath match {
+          case _: GcsPath => Nil // GCS paths will be localized with a separate localization script.
+          case _ =>
+            val labels = ActionBuilder.parameterLabels(directoryInput)
+            val describeAction = ActionBuilder.describeParameter(directoryInput, labels)
+            val localizationAction = cloudSdkShellAction(
+              localizeDirectory(directoryInput.cloudPath, directoryInput.containerPath)
+            )(mounts = mounts, labels = labels)
+            List(describeAction, localizationAction)
+        }
     }
-  }
 
   implicit val fileOutputToParameter: ToParameter[PipelinesApiFileOutput] = new ToParameter[PipelinesApiFileOutput] {
-    override def toActions(fileOutput: PipelinesApiFileOutput, mounts: List[Mount])
-                          (implicit retryPolicy: GcsTransferConfiguration): List[Action] = {
+    override def toActions(fileOutput: PipelinesApiFileOutput, mounts: List[Mount])(implicit
+      retryPolicy: GcsTransferConfiguration
+    ): List[Action] = {
 
       // If the output is a "secondary file", it actually could be a directory but we won't know before runtime.
       // The fileOrDirectory method will generate a command that can cover both cases
-      lazy val copy = if (fileOutput.secondary)
-        delocalizeFileOrDirectory(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
-      else
-        delocalizeFile(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
+      lazy val copy =
+        if (fileOutput.secondary)
+          delocalizeFileOrDirectory(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
+        else
+          delocalizeFile(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
 
       lazy val copyOnlyIfExists = ifExist(fileOutput.containerPath) {
         copy
@@ -150,32 +151,34 @@ trait PipelinesParameterConversions {
 
   implicit val directoryOutputToParameter: ToParameter[PipelinesApiDirectoryOutput] =
     new ToParameter[PipelinesApiDirectoryOutput] {
-    override def toActions(directoryOutput: PipelinesApiDirectoryOutput, mounts: List[Mount])
-                          (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = {
-      directoryOutput.cloudPath match {
-        case _: GcsPath => Nil // GCS paths will be delocalized with a separate delocalization script.
-        case _ =>
-          val labels = ActionBuilder.parameterLabels(directoryOutput)
-          val describeAction = ActionBuilder.describeParameter(directoryOutput, labels)
-          val delocalizationAction = cloudSdkShellAction(
-            delocalizeDirectory(directoryOutput.containerPath, directoryOutput.cloudPath, None)
-          )(mounts = mounts, flags = List(ActionFlag.AlwaysRun), labels = labels)
-          List(describeAction, delocalizationAction)
-      }
+      override def toActions(directoryOutput: PipelinesApiDirectoryOutput, mounts: List[Mount])(implicit
+        gcsTransferConfiguration: GcsTransferConfiguration
+      ): List[Action] =
+        directoryOutput.cloudPath match {
+          case _: GcsPath => Nil // GCS paths will be delocalized with a separate delocalization script.
+          case _ =>
+            val labels = ActionBuilder.parameterLabels(directoryOutput)
+            val describeAction = ActionBuilder.describeParameter(directoryOutput, labels)
+            val delocalizationAction = cloudSdkShellAction(
+              delocalizeDirectory(directoryOutput.containerPath, directoryOutput.cloudPath, None)
+            )(mounts = mounts, flags = List(ActionFlag.AlwaysRun), labels = labels)
+            List(describeAction, delocalizationAction)
+        }
     }
-  }
 
   implicit val inputToParameter: ToParameter[PipelinesApiInput] = new ToParameter[PipelinesApiInput] {
-    override def toActions(p: PipelinesApiInput, mounts: List[Mount])
-                          (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = p match {
+    override def toActions(p: PipelinesApiInput, mounts: List[Mount])(implicit
+      gcsTransferConfiguration: GcsTransferConfiguration
+    ): List[Action] = p match {
       case fileInput: PipelinesApiFileInput => fileInputToParameter.toActions(fileInput, mounts)
       case directoryInput: PipelinesApiDirectoryInput => directoryInputToParameter.toActions(directoryInput, mounts)
     }
   }
 
   implicit val outputToParameter: ToParameter[PipelinesApiOutput] = new ToParameter[PipelinesApiOutput] {
-    override def toActions(p: PipelinesApiOutput, mounts: List[Mount])
-                          (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = p match {
+    override def toActions(p: PipelinesApiOutput, mounts: List[Mount])(implicit
+      gcsTransferConfiguration: GcsTransferConfiguration
+    ): List[Action] = p match {
       case fileOutput: PipelinesApiFileOutput => fileOutputToParameter.toActions(fileOutput, mounts)
       case directoryOutput: PipelinesApiDirectoryOutput => directoryOutputToParameter.toActions(directoryOutput, mounts)
     }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesUtilityConversions.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesUtilityConversions.scala
index 41ed815eb73..be672df5df2 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesUtilityConversions.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesUtilityConversions.scala
@@ -12,14 +12,15 @@ import scala.language.postfixOps
 import scala.util.Try
 
 trait PipelinesUtilityConversions {
-  def toAccelerator(gpuResource: GpuResource): Accelerator = new Accelerator().setCount(gpuResource.gpuCount.value.toLong).setType(gpuResource.gpuType.toString)
+  def toAccelerator(gpuResource: GpuResource): Accelerator =
+    new Accelerator().setCount(gpuResource.gpuCount.value.toLong).setType(gpuResource.gpuType.toString)
   def toMachineType(jobLogger: JobLogger)(attributes: PipelinesApiRuntimeAttributes): String =
     MachineConstraints.machineType(
       memory = attributes.memory,
       cpu = attributes.cpu,
       cpuPlatformOption = attributes.cpuPlatform,
       googleLegacyMachineSelection = attributes.googleLegacyMachineSelection,
-      jobLogger = jobLogger,
+      jobLogger = jobLogger
     )
   def toMounts(disks: Seq[PipelinesApiAttachedDisk]): List[Mount] = disks.map(toMount).toList
   def toDisks(disks: Seq[PipelinesApiAttachedDisk]): List[Disk] = disks.map(toDisk).toList
@@ -58,7 +59,9 @@ trait PipelinesUtilityConversions {
     // There are both "Started pulling" and "Stopped pulling" events but these are confusing for metadata, especially on the
     // timing diagram. Create a single "Pulling <docker image>" grouping to absorb these events.
     def groupingFromPull: Option[String] = List("Started", "Stopped") flatMap { k =>
-      Option(event.getDescription) collect { case d if d.startsWith(s"$k pulling") => "Pulling" + d.substring(s"$k pulling".length)}
+      Option(event.getDescription) collect {
+        case d if d.startsWith(s"$k pulling") => "Pulling" + d.substring(s"$k pulling".length)
+      }
     } headOption
 
     ExecutionEvent(
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionBuilder.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionBuilder.scala
index 0d38d9f2398..82787262cf5 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionBuilder.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionBuilder.scala
@@ -36,7 +36,7 @@ object ActionBuilder {
       * Useful for any externally provided images that _might_ have entrypoints already set. This is a workaround for
       * the issue detailed in BA-6406. See underlying google issue in that ticket for more info.
       */
-    def withEntrypointCommand(command: String*): Action = {
+    def withEntrypointCommand(command: String*): Action =
       action
         .setEntrypoint(command.headOption.orNull)
         .setCommands(
@@ -45,7 +45,6 @@ object ActionBuilder {
             .map(_.asJava)
             .orNull
         )
-    }
 
     def withFlags(flags: List[ActionFlag]): Action = action.setFlags(flags |> javaFlags)
     def withMounts(mounts: List[Mount]): Action = action.setMounts(mounts.asJava)
@@ -55,7 +54,6 @@ object ActionBuilder {
       case _ => action
     }
 
-
     def scalaLabels: Map[String, String] = {
       val list = for {
         keyValueList <- Option(action.getLabels).toList
@@ -70,8 +68,9 @@ object ActionBuilder {
   def withImage(image: String): Action = new Action()
     .setImageUri(image)
 
-  def monitoringImageScriptAction(cloudPath: Path, containerPath: Path, mounts: List[Mount])
-                                 (implicit gcsTransferConfiguration: GcsTransferConfiguration): Action = {
+  def monitoringImageScriptAction(cloudPath: Path, containerPath: Path, mounts: List[Mount])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): Action = {
     val command = ActionCommands.localizeFile(cloudPath, containerPath)
     val labels = Map(Key.Tag -> Value.Localization)
     ActionBuilder.cloudSdkShellAction(command)(mounts = mounts, labels = labels)
@@ -80,8 +79,8 @@ object ActionBuilder {
   def backgroundAction(image: String,
                        command: List[String],
                        environment: Map[String, String],
-                       mounts: List[Mount],
-                      ): Action = {
+                       mounts: List[Mount]
+  ): Action =
     new Action()
       .setImageUri(image)
       .withEntrypointCommand(command: _*)
@@ -90,7 +89,6 @@ object ActionBuilder {
       .setEnvironment(environment.asJava)
       .withLabels(Map(Key.Tag -> Value.Monitoring))
       .setPidNamespace(backgroundActionPidNamespace)
-  }
 
   def terminateBackgroundActionsAction(): Action =
     cloudSdkShellAction(terminateAllBackgroundActionsCommand)(
@@ -109,13 +107,16 @@ object ActionBuilder {
                  mounts: List[Mount],
                  jobShell: String,
                  privateDockerKeyAndToken: Option[CreatePipelineDockerKeyAndToken],
-                 fuseEnabled: Boolean): Action = {
+                 fuseEnabled: Boolean
+  ): Action = {
 
     val dockerImageIdentifier = DockerImageIdentifier.fromString(docker)
 
     val secret = for {
       imageId <- dockerImageIdentifier.toOption
-      if DockerHub.isValidDockerHubHost(imageId.host) // This token only works for Docker Hub and not other repositories.
+      if DockerHub.isValidDockerHubHost(
+        imageId.host
+      ) // This token only works for Docker Hub and not other repositories.
       keyAndToken <- privateDockerKeyAndToken
       s = new Secret().setKeyName(keyAndToken.key).setCipherText(keyAndToken.encryptedToken)
     } yield s
@@ -130,22 +131,22 @@ object ActionBuilder {
       .setFlags((if (fuseEnabled) List(ActionFlag.EnableFuse.toString) else List.empty).asJava)
   }
 
-  def checkForMemoryRetryAction(retryLookupKeys: List[String], mounts: List[Mount]): Action = {
+  def checkForMemoryRetryAction(retryLookupKeys: List[String], mounts: List[Mount]): Action =
     cloudSdkShellAction(ActionCommands.checkIfStderrContainsRetryKeys(retryLookupKeys))(
       mounts = mounts,
-      labels = Map(Key.Tag -> Value.RetryWithMoreMemory),
+      labels = Map(Key.Tag -> Value.RetryWithMoreMemory)
     ).withFlags(List(ActionFlag.AlwaysRun))
-  }
 
   def cloudSdkShellAction(shellCommand: String)(mounts: List[Mount] = List.empty,
                                                 flags: List[ActionFlag] = List.empty,
                                                 labels: Map[String, String] = Map.empty,
-                                                timeout: Duration = Duration.Inf): Action =
+                                                timeout: Duration = Duration.Inf
+  ): Action =
     cloudSdkAction
       .withEntrypointCommand(
         "/bin/sh",
         "-c",
-        if (shellCommand.contains("\n")) shellCommand |> ActionCommands.multiLineCommand else shellCommand,
+        if (shellCommand.contains("\n")) shellCommand |> ActionCommands.multiLineCommand else shellCommand
       )
       .withFlags(flags)
       .withMounts(mounts)
@@ -158,7 +159,7 @@ object ActionBuilder {
     * @param pipelinesParameter Input or output parameter to label.
     * @return The labels.
     */
-  def parameterLabels(pipelinesParameter: PipelinesParameter): Map[String, String] = {
+  def parameterLabels(pipelinesParameter: PipelinesParameter): Map[String, String] =
     pipelinesParameter match {
       case _: PipelinesApiInput =>
         Map(
@@ -171,7 +172,6 @@ object ActionBuilder {
           Key.OutputName -> pipelinesParameter.name
         )
     }
-  }
 
   /**
     * Surrounds the list of Actions with a pair of starting and done Actions.
@@ -182,8 +182,9 @@ object ActionBuilder {
     * @param actions           The list of Actions to surround.
     * @return The starting Action, the passed in list, and then a done Action.
     */
-  def annotateTimestampedActions(description: String, loggingLabelValue: String, isAlwaysRun: Boolean = false)
-                                (actions: List[Action]): List[Action] = {
+  def annotateTimestampedActions(description: String, loggingLabelValue: String, isAlwaysRun: Boolean = false)(
+    actions: List[Action]
+  ): List[Action] = {
     val flags = if (isAlwaysRun) List(ActionFlag.AlwaysRun) else List()
     val labels = Map(Key.Logging -> loggingLabelValue)
     val starting = List(logTimestampedAction(s"Starting $description.", flags, labels))
@@ -192,32 +193,29 @@ object ActionBuilder {
   }
 
   /** Creates an Action that describes the parameter localization or delocalization. */
-  def describeParameter(pipelinesParameter: PipelinesParameter,
-                        actionLabels: Map[String, String]): Action = {
+  def describeParameter(pipelinesParameter: PipelinesParameter, actionLabels: Map[String, String]): Action =
     pipelinesParameter match {
       case _: PipelinesApiInput =>
         val message = "Localizing input %s -> %s".format(
           shellEscaped(pipelinesParameter.cloudPath),
-          shellEscaped(pipelinesParameter.containerPath),
+          shellEscaped(pipelinesParameter.containerPath)
         )
         ActionBuilder.logTimestampedAction(message, List(), actionLabels)
       case _: PipelinesApiOutput =>
         val message = "Delocalizing output %s -> %s".format(
           shellEscaped(pipelinesParameter.containerPath),
-          shellEscaped(pipelinesParameter.cloudPath),
+          shellEscaped(pipelinesParameter.cloudPath)
         )
         ActionBuilder.logTimestampedAction(message, List(ActionFlag.AlwaysRun), actionLabels)
     }
-  }
 
   /** Creates an Action that logs the docker command for the passed in action. */
-  def describeDocker(description: String, action: Action): Action = {
+  def describeDocker(description: String, action: Action): Action =
     ActionBuilder.logTimestampedAction(
       s"Running $description: ${ActionBuilder.toDockerRun(action)}",
       Nil,
       action.scalaLabels
     )
-  }
 
   /**
     * Creates an Action that logs the time as UTC plus prints the message. The original actionLabels will also be
@@ -233,7 +231,8 @@ object ActionBuilder {
     */
   private def logTimestampedAction(message: String,
                                    actionFlags: List[ActionFlag],
-                                   actionLabels: Map[String, String]): Action = {
+                                   actionLabels: Map[String, String]
+  ): Action =
     // Uses the cloudSdk image as that image will be used for other operations as well.
     cloudSdkShellAction(
       timestampedMessage(message)
@@ -245,7 +244,6 @@ object ActionBuilder {
       },
       timeout = 300.seconds
     )
-  }
 
   /** Converts an Action to a `docker run ...` command runnable in the shell. */
   private[api] def toDockerRun(action: Action): String = {
@@ -266,7 +264,8 @@ object ActionBuilder {
     val environmentArgs: String = Option(action.getEnvironment) match {
       case Some(environment) =>
         environment.asScala map {
-          case (key, value) if Option(key).isDefined && Option(value).isDefined => s" -e ${shellEscaped(s"$key:$value")}"
+          case (key, value) if Option(key).isDefined && Option(value).isDefined =>
+            s" -e ${shellEscaped(s"$key:$value")}"
           case (key, _) if Option(key).isDefined => s" -e ${shellEscaped(key)}"
           case _ => ""
         } mkString ""
@@ -319,15 +318,15 @@ object ActionBuilder {
     }
 
     Array("docker run",
-      nameArg,
-      mountArgs,
-      environmentArgs,
-      pidNamespaceArg,
-      flagsArgs,
-      portMappingArgs,
-      entrypointArg,
-      imageArg,
-      commandArgs,
+          nameArg,
+          mountArgs,
+          environmentArgs,
+          pidNamespaceArg,
+          flagsArgs,
+          portMappingArgs,
+          entrypointArg,
+          imageArg,
+          commandArgs
     ).mkString
   }
 }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/CheckpointingAction.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/CheckpointingAction.scala
index c723fca7800..1688863dc48 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/CheckpointingAction.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/CheckpointingAction.scala
@@ -6,19 +6,21 @@ import cromwell.backend.google.pipelines.common.action.ActionUtils
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.CreatePipelineParameters
 
 trait CheckpointingAction {
-  def checkpointingSetupActions(createPipelineParameters: CreatePipelineParameters,
-                                mounts: List[Mount]
-                            ): List[Action] =
+  def checkpointingSetupActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount]): List[Action] =
     createPipelineParameters.runtimeAttributes.checkpointFilename map { checkpointFilename =>
       val checkpointingImage = ActionUtils.CloudSdkImage
-      val checkpointingCommand = createPipelineParameters.checkpointingConfiguration.checkpointingCommand(checkpointFilename, ActionCommands.multiLineBinBashCommand)
+      val checkpointingCommand =
+        createPipelineParameters.checkpointingConfiguration.checkpointingCommand(checkpointFilename,
+                                                                                 ActionCommands.multiLineBinBashCommand
+        )
       val checkpointingEnvironment = Map.empty[String, String]
 
       // Initial sync from cloud:
       val initialCheckpointSyncAction = ActionBuilder.cloudSdkShellAction(
         createPipelineParameters.checkpointingConfiguration.localizePreviousCheckpointCommand(checkpointFilename)
       )(mounts = mounts)
-      val describeInitialCheckpointingSyncAction = ActionBuilder.describeDocker("initial checkpointing sync", initialCheckpointSyncAction)
+      val describeInitialCheckpointingSyncAction =
+        ActionBuilder.describeDocker("initial checkpointing sync", initialCheckpointSyncAction)
 
       // Background upload action:
       val backgroundCheckpointingAction = ActionBuilder.backgroundAction(
@@ -27,19 +29,28 @@ trait CheckpointingAction {
         environment = checkpointingEnvironment,
         mounts = mounts
       )
-      val describeBackgroundCheckpointingAction = ActionBuilder.describeDocker("begin checkpointing background action", backgroundCheckpointingAction)
+      val describeBackgroundCheckpointingAction =
+        ActionBuilder.describeDocker("begin checkpointing background action", backgroundCheckpointingAction)
 
-      List(describeInitialCheckpointingSyncAction, initialCheckpointSyncAction, describeBackgroundCheckpointingAction, backgroundCheckpointingAction)
-    } getOrElse(Nil)
+      List(describeInitialCheckpointingSyncAction,
+           initialCheckpointSyncAction,
+           describeBackgroundCheckpointingAction,
+           backgroundCheckpointingAction
+      )
+    } getOrElse Nil
 
   def checkpointingShutdownActions(createPipelineParameters: CreatePipelineParameters): List[Action] =
     createPipelineParameters.runtimeAttributes.checkpointFilename map { checkpointFilename =>
       val terminationAction = ActionBuilder.terminateBackgroundActionsAction()
       val describeTerminationAction = ActionBuilder.describeDocker("terminate checkpointing action", terminationAction)
 
-      val deleteCheckpointAction = ActionBuilder.gcsFileDeletionAction(createPipelineParameters.checkpointingConfiguration.checkpointFileCloud(checkpointFilename))
-      val deleteTmpCheckpointAction = ActionBuilder.gcsFileDeletionAction(createPipelineParameters.checkpointingConfiguration.tmpCheckpointFileCloud(checkpointFilename))
+      val deleteCheckpointAction = ActionBuilder.gcsFileDeletionAction(
+        createPipelineParameters.checkpointingConfiguration.checkpointFileCloud(checkpointFilename)
+      )
+      val deleteTmpCheckpointAction = ActionBuilder.gcsFileDeletionAction(
+        createPipelineParameters.checkpointingConfiguration.tmpCheckpointFileCloud(checkpointFilename)
+      )
 
       List(describeTerminationAction, terminationAction, deleteCheckpointAction, deleteTmpCheckpointAction)
-    } getOrElse(Nil)
+    } getOrElse Nil
 }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Delocalization.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Delocalization.scala
index efb3b017f89..41a5dbbc81c 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Delocalization.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Delocalization.scala
@@ -21,42 +21,54 @@ import wom.runtime.WomOutputRuntimeExtractor
 import scala.jdk.CollectionConverters._
 import scala.concurrent.duration._
 
-object Delocalization {
-}
+object Delocalization {}
 
 trait Delocalization {
 
-  private def delocalizeLogsAction(gcsLogPath: Path)(implicit gcsTransferConfiguration: GcsTransferConfiguration) = {
+  private def delocalizeLogsAction(gcsLogPath: Path)(implicit gcsTransferConfiguration: GcsTransferConfiguration) =
     cloudSdkShellAction(
-    delocalizeDirectory(DefaultPathBuilder.build(logsRoot).get, gcsLogPath, PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType)
+      delocalizeDirectory(DefaultPathBuilder.build(logsRoot).get,
+                          gcsLogPath,
+                          PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType
+      )
     )(flags = List(ActionFlag.AlwaysRun), labels = Map(Key.Tag -> Value.Delocalization))
-  }
 
   // Used for the final copy of the logs to make sure we have the most up to date version before terminating the job
-  private def copyAggregatedLogToLegacyPath(gcsLegacyLogPath: Path)(implicit gcsTransferConfiguration: GcsTransferConfiguration): Action = {
+  private def copyAggregatedLogToLegacyPath(
+    gcsLegacyLogPath: Path
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): Action =
     cloudSdkShellAction(
-      delocalizeFileTo(DefaultPathBuilder.build(aggregatedLog).get, gcsLegacyLogPath, PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType)
+      delocalizeFileTo(DefaultPathBuilder.build(aggregatedLog).get,
+                       gcsLegacyLogPath,
+                       PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType
+      )
     )(flags = List(ActionFlag.AlwaysRun), labels = Map(Key.Tag -> Value.Delocalization))
-  }
 
   // Periodically copies the logs out to GCS
-  private def copyAggregatedLogToLegacyPathPeriodic(gcsLegacyLogPath: Path)(implicit gcsTransferConfiguration: GcsTransferConfiguration): Action = {
+  private def copyAggregatedLogToLegacyPathPeriodic(
+    gcsLegacyLogPath: Path
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): Action =
     cloudSdkShellAction(
-      every(30.seconds) { delocalizeFileTo(DefaultPathBuilder.build(aggregatedLog).get, gcsLegacyLogPath, PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType) }
+      every(30.seconds) {
+        delocalizeFileTo(DefaultPathBuilder.build(aggregatedLog).get,
+                         gcsLegacyLogPath,
+                         PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType
+        )
+      }
     )(flags = List(ActionFlag.RunInBackground), labels = Map(Key.Tag -> Value.Background))
-  }
 
   private def runtimeOutputExtractorAction(containerCallRoot: String,
-                                    outputFile: String,
-                                    mounts: List[Mount],
-                                    womOutputRuntimeExtractor: WomOutputRuntimeExtractor): Action = {
+                                           outputFile: String,
+                                           mounts: List[Mount],
+                                           womOutputRuntimeExtractor: WomOutputRuntimeExtractor
+  ): Action = {
     val commands = List(
       "-c",
       // Create the directory where the fofn will be written
       s"mkdir -p $$(dirname $outputFile) && " +
-      s"cd $containerCallRoot && " +
-      """echo "Runtime output files to be delocalized:" && """ +
-      s"${womOutputRuntimeExtractor.command} | tee $outputFile"
+        s"cd $containerCallRoot && " +
+        """echo "Runtime output files to be delocalized:" && """ +
+        s"${womOutputRuntimeExtractor.command} | tee $outputFile"
     )
 
     ActionBuilder
@@ -69,7 +81,9 @@ trait Delocalization {
       .withLabels(Map(Key.Tag -> Value.Delocalization))
   }
 
-  private def delocalizeRuntimeOutputsScript(fofnPath: String, workflowRoot: Path, cloudCallRoot: Path)(implicit gcsTransferConfiguration: GcsTransferConfiguration) = {
+  private def delocalizeRuntimeOutputsScript(fofnPath: String, workflowRoot: Path, cloudCallRoot: Path)(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ) = {
     val gsutilCommand: String => String = { flag =>
       s"""rm -f $$HOME/.config/gcloud/gce && gsutil -m $flag cp -r $$line "${cloudCallRoot.pathAsString.ensureSlashed}$$gcs_path""""
     }
@@ -100,13 +114,21 @@ trait Delocalization {
         |fi""".stripMargin
   }
 
-  private def delocalizeRuntimeOutputsAction(cloudCallRoot: Path, inputFile: String, workflowRoot: Path, mounts: List[Mount])(implicit gcsTransferConfiguration: GcsTransferConfiguration): Action = {
+  private def delocalizeRuntimeOutputsAction(cloudCallRoot: Path,
+                                             inputFile: String,
+                                             workflowRoot: Path,
+                                             mounts: List[Mount]
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): Action = {
     val command = multiLineCommand(delocalizeRuntimeOutputsScript(inputFile, workflowRoot, cloudCallRoot))
-    ActionBuilder.cloudSdkShellAction(command)(mounts, flags = List(ActionFlag.DisableImagePrefetch), labels = Map(Key.Tag -> Value.Delocalization))
+    ActionBuilder.cloudSdkShellAction(command)(mounts,
+                                               flags = List(ActionFlag.DisableImagePrefetch),
+                                               labels = Map(Key.Tag -> Value.Delocalization)
+    )
   }
 
-  def deLocalizeActions(createPipelineParameters: CreatePipelineParameters,
-                        mounts: List[Mount])(implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = {
+  def deLocalizeActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): List[Action] = {
     val cloudCallRoot = createPipelineParameters.cloudCallRoot
     val callExecutionContainerRoot = createPipelineParameters.commandScriptContainerPath.parent
 
@@ -117,21 +139,31 @@ trait Delocalization {
      * Ideally temporaryFofnForRuntimeOutputFiles should be somewhere else than the execution directory (we could mount anther directory)
      * However because it runs after everything else there's no risk of polluting the task's results and the random ID ensures we don't override anything
      */
-    val temporaryFofnDirectoryForRuntimeOutputFiles = callExecutionContainerRoot.pathAsString.ensureSlashed + UUID.randomUUID().toString.split("-")(0)
+    val temporaryFofnDirectoryForRuntimeOutputFiles =
+      callExecutionContainerRoot.pathAsString.ensureSlashed + UUID.randomUUID().toString.split("-")(0)
     val temporaryFofnForRuntimeOutputFiles = temporaryFofnDirectoryForRuntimeOutputFiles + "/runtime_output_files.txt"
 
     val runtimeExtractionActions = createPipelineParameters.womOutputRuntimeExtractor.toList flatMap { extractor =>
-      List (
-        runtimeOutputExtractorAction(callExecutionContainerRoot.pathAsString, temporaryFofnForRuntimeOutputFiles, mounts, extractor),
-        delocalizeRuntimeOutputsAction(cloudCallRoot, temporaryFofnForRuntimeOutputFiles, createPipelineParameters.cloudWorkflowRoot, mounts)
+      List(
+        runtimeOutputExtractorAction(callExecutionContainerRoot.pathAsString,
+                                     temporaryFofnForRuntimeOutputFiles,
+                                     mounts,
+                                     extractor
+        ),
+        delocalizeRuntimeOutputsAction(cloudCallRoot,
+                                       temporaryFofnForRuntimeOutputFiles,
+                                       createPipelineParameters.cloudWorkflowRoot,
+                                       mounts
+        )
       )
     }
 
-    val gcsDelocalizationContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
+    val gcsDelocalizationContainerPath =
+      createPipelineParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
 
     val delocalizationLabel = Map(Key.Tag -> Value.Delocalization)
-    val runGcsDelocalizationScript: Action = cloudSdkShellAction(
-      s"/bin/bash $gcsDelocalizationContainerPath")(mounts = mounts, labels = delocalizationLabel)
+    val runGcsDelocalizationScript: Action =
+      cloudSdkShellAction(s"/bin/bash $gcsDelocalizationContainerPath")(mounts = mounts, labels = delocalizationLabel)
 
     ActionBuilder.annotateTimestampedActions("delocalization", Value.Delocalization)(
       runGcsDelocalizationScript ::
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Deserialization.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Deserialization.scala
index f2883b6b285..57d9f7b60ce 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Deserialization.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Deserialization.scala
@@ -25,17 +25,19 @@ import scala.util.{Failure, Success, Try}
   * This uses reflection and is therefore not great performance-wise.
   * However it is only used once, when the job completes, which should limit the performance hit.
   */
-private [api] object Deserialization {
-  def findEvent[T <: GenericJson](events: List[Event],
-                                  filter: T => Boolean = Function.const(true)(_: T))
-                                 (implicit tag: ClassTag[T]): Option[RequestContextReader[Option[T]]] =
-    events.to(LazyList)
+private[api] object Deserialization {
+  def findEvent[T <: GenericJson](events: List[Event], filter: T => Boolean = Function.const(true)(_: T))(implicit
+    tag: ClassTag[T]
+  ): Option[RequestContextReader[Option[T]]] =
+    events
+      .to(LazyList)
       .map(_.details(tag))
-      .collectFirst({
+      .collectFirst {
         case Some(event) if event.map(filter).getOrElse(false) => event.toErrorOr.fallBack
-      })
+      }
 
   implicit class EventDeserialization(val event: Event) extends AnyVal {
+
     /**
       * Attempts to deserialize the details map to T
       * Returns None if the details are not of type T
@@ -62,17 +64,19 @@ private [api] object Deserialization {
   }
 
   implicit class OperationDeserialization(val operation: Operation) extends AnyVal {
+
     /**
       * Deserializes the events to com.google.api.services.genomics.v2alpha1.model.Event
       */
     def events: ErrorOr[List[Event]] = {
       val eventsErrorOrOption = for {
         eventsMap <- metadata.get("events")
-        eventsErrorOr <- Option(eventsMap
-          .asInstanceOf[JArrayList[JMap[String, Object]]]
-          .asScala
-          .toList
-          .traverse[ErrorOr, Event](deserializeTo[Event](_).toErrorOr)
+        eventsErrorOr <- Option(
+          eventsMap
+            .asInstanceOf[JArrayList[JMap[String, Object]]]
+            .asScala
+            .toList
+            .traverse[ErrorOr, Event](deserializeTo[Event](_).toErrorOr)
         )
       } yield eventsErrorOr
       eventsErrorOrOption.getOrElse(Nil.validNel)
@@ -81,11 +85,10 @@ private [api] object Deserialization {
     /**
       * Deserializes the pipeline to com.google.api.services.genomics.v2alpha1.model.Pipeline
       */
-    def pipeline: Option[Try[Pipeline]] = {
+    def pipeline: Option[Try[Pipeline]] =
       metadata
         .get("pipeline")
         .map(_.asInstanceOf[JMap[String, Object]] |> deserializeTo[Pipeline])
-    }
 
     // If there's a WorkerAssignedEvent it means a VM was created - which we consider as the job started
     // Note that the VM might still be booting
@@ -103,19 +106,23 @@ private [api] object Deserialization {
   /**
     * Deserializes a java.util.Map[String, Object] to an instance of T
     */
-  private [api] def deserializeTo[T <: GenericJson](attributes: JMap[String, Object])(implicit tag: ClassTag[T]): Try[T] = Try {
+  private[api] def deserializeTo[T <: GenericJson](
+    attributes: JMap[String, Object]
+  )(implicit tag: ClassTag[T]): Try[T] = Try {
     // Create a new instance, because it's a GenericJson there's always a 0-arg constructor
     val newT = tag.runtimeClass.asInstanceOf[Class[T]].getConstructor().newInstance()
 
     // Optionally returns the field with the given name
     def field(name: String) = Option(newT.getClassInfo.getField(name))
 
-    def handleMap(key: String, value: Object) = {
+    def handleMap(key: String, value: Object) =
       (field(key), value) match {
         // If the serialized value is a list, we need to check if its elements need to be deserialized
         case (Some(f), list: java.util.List[java.util.Map[String, Object]] @unchecked) =>
           // Try to get the generic type of the declared field (the field should have a list type since the value is a list)
-          Try(f.getGenericType.asInstanceOf[ParameterizedType].getActualTypeArguments.toList.head.asInstanceOf[Class[_]]) match {
+          Try(
+            f.getGenericType.asInstanceOf[ParameterizedType].getActualTypeArguments.toList.head.asInstanceOf[Class[_]]
+          ) match {
             // If we can get it and its a GenericJson, it means we need to deserialize the elements to their proper type
             case Success(genericListType) if classOf[GenericJson].isAssignableFrom(genericListType) =>
               // The get throws at the first error and hence doesn't aggregate the errors but it seems
@@ -134,7 +141,8 @@ private [api] object Deserialization {
         // If it can't be assigned and the value is a map, it is very likely that the field "key" of T is of some type U
         // but has been deserialized to a Map[String, Object]. In this case we retrieve the type U from the field and recurse
         // to deserialize properly
-        case (Some(f), map: java.util.Map[String, Object] @unchecked) if classOf[GenericJson].isAssignableFrom(f.getType) =>
+        case (Some(f), map: java.util.Map[String, Object] @unchecked)
+            if classOf[GenericJson].isAssignableFrom(f.getType) =>
           // This whole function is wrapped in a try so just .get to throw
           val deserializedInnerAttribute = deserializeTo(map)(ClassTag[GenericJson](f.getType)).get
           newT.set(key, deserializedInnerAttribute)
@@ -151,7 +159,6 @@ private [api] object Deserialization {
         // and losing properly deserialized attributes
         case _ =>
       }
-    }
 
     // Go over the map entries and use the "set" method of GenericJson to set the attributes.
     Option(attributes).map(_.asScala).getOrElse(Map.empty).foreach((handleMap _).tupled)
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Localization.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Localization.scala
index 1d4666a4cf8..23bb29224b6 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Localization.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/Localization.scala
@@ -10,32 +10,42 @@ import cromwell.backend.google.pipelines.v2alpha1.PipelinesConversions._
 import cromwell.backend.google.pipelines.v2alpha1.ToParameter.ops._
 import cromwell.backend.google.pipelines.v2alpha1.api.ActionBuilder.cloudSdkShellAction
 
-
 trait Localization {
-  def localizeActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount])
-                     (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = {
+  def localizeActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): List[Action] = {
     val localizationLabel = Map(Key.Tag -> Value.Localization)
 
-    val gcsTransferLibraryContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(GcsTransferLibraryName)
-    val localizeGcsTransferLibrary = cloudSdkShellAction(localizeFile(
-      cloudPath = createPipelineParameters.cloudCallRoot / GcsTransferLibraryName,
-      containerPath = gcsTransferLibraryContainerPath))(mounts = mounts, labels = localizationLabel)
-
-    val gcsLocalizationContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(GcsLocalizationScriptName)
-    val localizeGcsLocalizationScript = cloudSdkShellAction(localizeFile(
-      cloudPath = createPipelineParameters.cloudCallRoot / GcsLocalizationScriptName,
-      containerPath = gcsLocalizationContainerPath))(mounts = mounts, labels = localizationLabel)
-
-    val gcsDelocalizationContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
-    val localizeGcsDelocalizationScript = cloudSdkShellAction(localizeFile(
-      cloudPath = createPipelineParameters.cloudCallRoot / GcsDelocalizationScriptName,
-      containerPath = gcsDelocalizationContainerPath))(mounts = mounts, labels = localizationLabel)
-
-    val runGcsLocalizationScript = cloudSdkShellAction(
-      s"/bin/bash $gcsLocalizationContainerPath")(mounts = mounts, labels = localizationLabel)
+    val gcsTransferLibraryContainerPath =
+      createPipelineParameters.commandScriptContainerPath.sibling(GcsTransferLibraryName)
+    val localizeGcsTransferLibrary = cloudSdkShellAction(
+      localizeFile(cloudPath = createPipelineParameters.cloudCallRoot / GcsTransferLibraryName,
+                   containerPath = gcsTransferLibraryContainerPath
+      )
+    )(mounts = mounts, labels = localizationLabel)
+
+    val gcsLocalizationContainerPath =
+      createPipelineParameters.commandScriptContainerPath.sibling(GcsLocalizationScriptName)
+    val localizeGcsLocalizationScript = cloudSdkShellAction(
+      localizeFile(cloudPath = createPipelineParameters.cloudCallRoot / GcsLocalizationScriptName,
+                   containerPath = gcsLocalizationContainerPath
+      )
+    )(mounts = mounts, labels = localizationLabel)
+
+    val gcsDelocalizationContainerPath =
+      createPipelineParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
+    val localizeGcsDelocalizationScript = cloudSdkShellAction(
+      localizeFile(cloudPath = createPipelineParameters.cloudCallRoot / GcsDelocalizationScriptName,
+                   containerPath = gcsDelocalizationContainerPath
+      )
+    )(mounts = mounts, labels = localizationLabel)
+
+    val runGcsLocalizationScript =
+      cloudSdkShellAction(s"/bin/bash $gcsLocalizationContainerPath")(mounts = mounts, labels = localizationLabel)
 
     // Any "classic" PAPI v2 one-at-a-time localizations for non-GCS inputs.
-    val singletonLocalizations = createPipelineParameters.inputOutputParameters.fileInputParameters.flatMap(_.toActions(mounts).toList)
+    val singletonLocalizations =
+      createPipelineParameters.inputOutputParameters.fileInputParameters.flatMap(_.toActions(mounts).toList)
 
     val localizations =
       localizeGcsTransferLibrary ::
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/MemoryRetryCheckAction.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/MemoryRetryCheckAction.scala
index 46e3fc9dbb9..099ba635c8c 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/MemoryRetryCheckAction.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/MemoryRetryCheckAction.scala
@@ -5,10 +5,11 @@ import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.C
 
 trait MemoryRetryCheckAction {
 
-  def checkForMemoryRetryActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount]): List[Action] = {
+  def checkForMemoryRetryActions(createPipelineParameters: CreatePipelineParameters,
+                                 mounts: List[Mount]
+  ): List[Action] =
     createPipelineParameters.retryWithMoreMemoryKeys match {
       case Some(keys) => List(ActionBuilder.checkForMemoryRetryAction(keys, mounts))
       case None => List.empty[Action]
     }
-  }
 }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/MonitoringAction.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/MonitoringAction.scala
index b65177480a8..d0edefbb24a 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/MonitoringAction.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/MonitoringAction.scala
@@ -5,9 +5,9 @@ import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttribu
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.CreatePipelineParameters
 
 trait MonitoringAction {
-  def monitoringSetupActions(createPipelineParameters: CreatePipelineParameters,
-                             mounts: List[Mount]
-                            )(implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = {
+  def monitoringSetupActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): List[Action] = {
 
     val monitoringImageScriptActions =
       createPipelineParameters.monitoringImage.monitoringImageScriptOption match {
@@ -16,12 +16,12 @@ trait MonitoringAction {
             ActionBuilder.monitoringImageScriptAction(
               script,
               createPipelineParameters.monitoringImage.monitoringImageScriptContainerPath,
-              mounts,
+              mounts
             )
           val describeLocalizeScriptAction =
             ActionBuilder.describeDocker(
               "localizing monitoring image script action",
-              localizeScriptAction,
+              localizeScriptAction
             )
           List(describeLocalizeScriptAction, localizeScriptAction)
         case None => Nil
@@ -30,7 +30,6 @@ trait MonitoringAction {
     val monitoringImageActions =
       createPipelineParameters.monitoringImage.monitoringImageOption match {
         case Some(image) =>
-
           val monitoringImage = image
           val monitoringImageCommand = createPipelineParameters.monitoringImage.monitoringImageCommand
           val monitoringImageEnvironment = createPipelineParameters.monitoringImage.monitoringImageEnvironment
@@ -39,7 +38,7 @@ trait MonitoringAction {
             monitoringImage,
             monitoringImageCommand,
             monitoringImageEnvironment(mounts.map(_.getPath)),
-            mounts,
+            mounts
           )
 
           val describeMonitoringAction = ActionBuilder.describeDocker("monitoring action", monitoringAction)
@@ -52,7 +51,7 @@ trait MonitoringAction {
     monitoringImageScriptActions ++ monitoringImageActions
   }
 
-  def monitoringShutdownActions(createPipelineParameters: CreatePipelineParameters): List[Action] = {
+  def monitoringShutdownActions(createPipelineParameters: CreatePipelineParameters): List[Action] =
     createPipelineParameters.monitoringImage.monitoringImageOption match {
       case Some(_) =>
         val terminationAction = ActionBuilder.terminateBackgroundActionsAction()
@@ -62,5 +61,4 @@ trait MonitoringAction {
         List(describeTerminationAction, terminationAction)
       case None => Nil
     }
-  }
 }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/SSHAccessAction.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/SSHAccessAction.scala
index a1fd56bf1d1..feab74eb2a3 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/SSHAccessAction.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/SSHAccessAction.scala
@@ -8,16 +8,16 @@ import scala.jdk.CollectionConverters._
 
 trait SSHAccessAction {
 
-  def sshAccessActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount]) : List[Action] = {
+  def sshAccessActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount]): List[Action] =
     if (createPipelineParameters.enableSshAccess) {
       sshAccessAction(mounts)
     } else {
       Nil
     }
-  }
 
   private def sshAccessAction(mounts: List[Mount]): List[Action] = {
-    val sshAction = ActionBuilder.withImage(ActionUtils.sshImage)
+    val sshAction = ActionBuilder
+      .withImage(ActionUtils.sshImage)
       .setEntrypoint(ActionUtils.sshEntryPoint)
       .setPortMappings(ActionUtils.sshPortMappings.asJava)
       .setFlags(List(ActionFlag.RunInBackground.toString).asJava)
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/AbortRequestHandler.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/AbortRequestHandler.scala
index 8806e88cd94..fce24460ee7 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/AbortRequestHandler.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/AbortRequestHandler.scala
@@ -6,7 +6,10 @@ import com.google.api.client.googleapis.json.GoogleJsonError
 import com.google.api.client.http.HttpHeaders
 import com.typesafe.scalalogging.LazyLogging
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager._
-import cromwell.backend.google.pipelines.common.api.clients.PipelinesApiAbortClient.{PAPIAbortRequestSuccessful, PAPIOperationIsAlreadyTerminal}
+import cromwell.backend.google.pipelines.common.api.clients.PipelinesApiAbortClient.{
+  PAPIAbortRequestSuccessful,
+  PAPIOperationIsAlreadyTerminal
+}
 import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
 import org.apache.commons.lang3.StringUtils
 
@@ -14,7 +17,11 @@ import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success, Try}
 
 trait AbortRequestHandler extends LazyLogging { this: RequestHandler =>
-  protected def handleGoogleError(abortQuery: PAPIAbortRequest, pollingManager: ActorRef, e: GoogleJsonError, responseHeaders: HttpHeaders): Try[Unit] = {
+  protected def handleGoogleError(abortQuery: PAPIAbortRequest,
+                                  pollingManager: ActorRef,
+                                  e: GoogleJsonError,
+                                  responseHeaders: HttpHeaders
+  ): Try[Unit] =
     // This condition is telling us that the job we tried to cancel is already in a terminal state. Technically PAPI
     // was not able to cancel the job because the job could not be transitioned from 'Running' to 'Cancelled'. But from
     // Cromwell's perspective a job cancellation is really just a request for the job to be in a terminal state, so
@@ -23,30 +30,34 @@ trait AbortRequestHandler extends LazyLogging { this: RequestHandler =>
     // If/when Google implements https://partnerissuetracker.corp.google.com/issues/171993833 we could break these cases
     // out and make our logging more specific if we wanted to.
     if (Option(e.getCode).contains(400) || StringUtils.contains(e.getMessage, "Precondition check failed")) {
-      logger.info(s"PAPI declined to abort job ${abortQuery.jobId.jobId} in workflow ${abortQuery.workflowId}, most likely because it is no longer running. Marking as finished. Message: ${e.getMessage}")
+      logger.info(
+        s"PAPI declined to abort job ${abortQuery.jobId.jobId} in workflow ${abortQuery.workflowId}, most likely because it is no longer running. Marking as finished. Message: ${e.getMessage}"
+      )
       abortQuery.requester ! PAPIOperationIsAlreadyTerminal(abortQuery.jobId.jobId)
       Success(())
     } else {
-      pollingManager ! PipelinesApiAbortQueryFailed(abortQuery, new SystemPAPIApiException(GoogleJsonException(e, responseHeaders)))
+      pollingManager ! PipelinesApiAbortQueryFailed(abortQuery,
+                                                    new SystemPAPIApiException(GoogleJsonException(e, responseHeaders))
+      )
       Failure(new Exception(mkErrorString(e)))
     }
-  }
 
   // The Genomics batch endpoint doesn't seem to be able to handle abort requests on V2 operations at the moment
   // For now, don't batch the request and execute it on its own
-  def handleRequest(abortQuery: PAPIAbortRequest, batch: BatchRequest, pollingManager: ActorRef)(implicit ec: ExecutionContext): Future[Try[Unit]] = {
+  def handleRequest(abortQuery: PAPIAbortRequest, batch: BatchRequest, pollingManager: ActorRef)(implicit
+    ec: ExecutionContext
+  ): Future[Try[Unit]] =
     Future(abortQuery.httpRequest.execute()) map {
       case response if response.isSuccessStatusCode =>
         abortQuery.requester ! PAPIAbortRequestSuccessful(abortQuery.jobId.jobId)
         Success(())
-      case response => for {
-        asGoogleError <- Try(GoogleJsonError.parse(GoogleAuthMode.jsonFactory, response))
-        handled <- handleGoogleError(abortQuery, pollingManager, asGoogleError, response.getHeaders)
-      } yield handled
-    } recover {
-      case e =>
-        pollingManager ! PipelinesApiAbortQueryFailed(abortQuery, new SystemPAPIApiException(e))
-        Failure(e)
+      case response =>
+        for {
+          asGoogleError <- Try(GoogleJsonError.parse(GoogleAuthMode.jsonFactory, response))
+          handled <- handleGoogleError(abortQuery, pollingManager, asGoogleError, response.getHeaders)
+        } yield handled
+    } recover { case e =>
+      pollingManager ! PipelinesApiAbortQueryFailed(abortQuery, new SystemPAPIApiException(e))
+      Failure(e)
     }
-  }
 }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/ErrorReporter.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/ErrorReporter.scala
index 9b88a2f54bd..70cadeb229f 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/ErrorReporter.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/ErrorReporter.scala
@@ -22,28 +22,27 @@ object ErrorReporter {
 
   // This can be used to log non-critical deserialization failures and not fail the task
   implicit class ErrorOrLogger[A](val t: ErrorOr[A]) extends AnyVal {
-    private def logErrors(errors: NonEmptyList[String], workflowId: WorkflowId, operation: Operation): Unit = {
-      logger.error(s"[$workflowId] Failed to parse PAPI response. Operation Id: ${operation.getName}" + s"${errors.toList.mkString(", ")}")
+    private def logErrors(errors: NonEmptyList[String], workflowId: WorkflowId, operation: Operation): Unit =
+      logger.error(
+        s"[$workflowId] Failed to parse PAPI response. Operation Id: ${operation.getName}" + s"${errors.toList.mkString(", ")}"
+      )
+
+    def fallBack: RequestContextReader[Option[A]] = Reader { case (workflowId, operation) =>
+      t match {
+        case Valid(s) => Option(s)
+        case Invalid(f) =>
+          logErrors(f, workflowId, operation)
+          None
+      }
     }
 
-    def fallBack: RequestContextReader[Option[A]] = Reader {
-      case (workflowId, operation) =>
-        t match {
-          case Valid(s) => Option(s)
-          case Invalid(f) =>
-            logErrors(f, workflowId, operation)
-            None
-        }
-    }
-
-    def fallBackTo(to: A): RequestContextReader[A] = Reader {
-      case (workflowId, operation) =>
-        t match {
-          case Valid(s) => s
-          case Invalid(f) =>
-            logErrors(f, workflowId, operation)
-            to
-        }
+    def fallBackTo(to: A): RequestContextReader[A] = Reader { case (workflowId, operation) =>
+      t match {
+        case Valid(s) => s
+        case Invalid(f) =>
+          logErrors(f, workflowId, operation)
+          to
+      }
     }
   }
 }
@@ -55,7 +54,8 @@ class ErrorReporter(machineType: Option[String],
                     instanceName: Option[String],
                     actions: List[Action],
                     operation: Operation,
-                    workflowId: WorkflowId) {
+                    workflowId: WorkflowId
+) {
   import ErrorReporter._
 
   def toUnsuccessfulRunStatus(error: Status, events: List[Event]): UnsuccessfulRunStatus = {
@@ -67,7 +67,11 @@ class ErrorReporter(machineType: Option[String],
     val status = statusOption.getOrElse(GStatus.UNAVAILABLE)
     val builder = status match {
       case GStatus.UNAVAILABLE if wasPreemptible => Preempted.apply _
-      case GStatus.ABORTED if wasPreemptible && Option(error.getMessage).exists(_.contains(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style)) => Preempted.apply _
+      case GStatus.ABORTED
+          if wasPreemptible && Option(error.getMessage).exists(
+            _.contains(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style)
+          ) =>
+        Preempted.apply _
       case GStatus.CANCELLED => Cancelled.apply _
       case _ => Failed.apply _
     }
@@ -80,7 +84,7 @@ class ErrorReporter(machineType: Option[String],
   }
 
   // There's maybe one FailedEvent per operation with a summary error message
-  private def unexpectedExitStatusErrorStrings(events: List[Event], actions: List[Action]): List[String] = {
+  private def unexpectedExitStatusErrorStrings(events: List[Event], actions: List[Action]): List[String] =
     for {
       event <- events
       detail <- event.details[UnexpectedExitStatusEvent].flatMap(_.toErrorOr.fallBack(workflowId -> operation))
@@ -90,33 +94,32 @@ class ErrorReporter(machineType: Option[String],
       labelTag = action.flatMap(actionLabelTag)
       inputNameTag = action.flatMap(actionLabelInputName)
     } yield unexpectedStatusErrorString(event, stderr, labelTag, inputNameTag)
-  }
 
   // It would probably be good to define a richer error structure than String, but right now that's what the backend interface expects
-  private def unexpectedStatusErrorString(event: Event, stderr: Option[String], labelTag: Option[String], inputNameTag: Option[String]) = {
+  private def unexpectedStatusErrorString(event: Event,
+                                          stderr: Option[String],
+                                          labelTag: Option[String],
+                                          inputNameTag: Option[String]
+  ) =
     labelTag.map("[" + _ + "] ").getOrElse("") +
-      inputNameTag.map("Input name: " +  _ + " - ").getOrElse("") +
+      inputNameTag.map("Input name: " + _ + " - ").getOrElse("") +
       Option(event).flatMap(eventValue => Option(eventValue.getDescription)).getOrElse("") +
       stderr.map(": " + _).getOrElse("")
-  }
 
   // There may be one FailedEvent per operation with a summary error message
-  private def summaryFailure(events: List[Event]): Option[String] = {
+  private def summaryFailure(events: List[Event]): Option[String] =
     findEvent[FailedEvent](events)
       .flatMap(_(workflowId -> operation))
       .map(_.getCause)
-  }
 
   // Try to find the stderr for the given action ID
-  private def stderrForAction(events: List[Event])(actionId: Integer) = {
+  private def stderrForAction(events: List[Event])(actionId: Integer) =
     findEvent[ContainerStoppedEvent](events, _.getActionId == actionId)
       .flatMap(_(workflowId -> operation))
       .map(_.getStderr)
-  }
 
-  private def actionLabelValue(action: Action, k: String): Option[String] = {
+  private def actionLabelValue(action: Action, k: String): Option[String] =
     Option(action).flatMap(actionValue => Option(actionValue.getLabels)).map(_.asScala).flatMap(_.get(k))
-  }
 
   private def actionLabelTag(action: Action) = actionLabelValue(action, Key.Tag)
   private def actionLabelInputName(action: Action) = actionLabelValue(action, Key.InputName)
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/GetRequestHandler.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/GetRequestHandler.scala
index 9a1c239fbbe..15fefc02910 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/GetRequestHandler.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/GetRequestHandler.scala
@@ -22,37 +22,46 @@ import org.apache.commons.lang3.exception.ExceptionUtils
 import scala.jdk.CollectionConverters._
 import scala.concurrent.{ExecutionContext, Future}
 import scala.language.postfixOps
-import scala.util.{Failure, Try, Success => TrySuccess}
+import scala.util.{Failure, Success => TrySuccess, Try}
 
 trait GetRequestHandler { this: RequestHandler =>
   // the Genomics batch endpoint doesn't seem to be able to handle get requests on V2 operations at the moment
   // For now, don't batch the request and execute it on its own
-  def handleRequest(pollingRequest: PAPIStatusPollRequest, batch: BatchRequest, pollingManager: ActorRef)(implicit ec: ExecutionContext): Future[Try[Unit]] = Future(pollingRequest.httpRequest.execute()) map {
+  def handleRequest(pollingRequest: PAPIStatusPollRequest, batch: BatchRequest, pollingManager: ActorRef)(implicit
+    ec: ExecutionContext
+  ): Future[Try[Unit]] = Future(pollingRequest.httpRequest.execute()) map {
     case response if response.isSuccessStatusCode =>
       val operation = response.parseAs(classOf[Operation])
       pollingRequest.requester ! interpretOperationStatus(operation, pollingRequest)
       TrySuccess(())
     case response =>
       val failure = Try(GoogleJsonError.parse(GoogleAuthMode.jsonFactory, response)) match {
-        case TrySuccess(googleError) => new SystemPAPIApiException(GoogleJsonException(googleError, response.getHeaders))
-        case Failure(_) => new SystemPAPIApiException(new RuntimeException(s"Failed to get status for operation ${pollingRequest.jobId.jobId}: HTTP Status Code: ${response.getStatusCode}"))
+        case TrySuccess(googleError) =>
+          new SystemPAPIApiException(GoogleJsonException(googleError, response.getHeaders))
+        case Failure(_) =>
+          new SystemPAPIApiException(
+            new RuntimeException(
+              s"Failed to get status for operation ${pollingRequest.jobId.jobId}: HTTP Status Code: ${response.getStatusCode}"
+            )
+          )
       }
       pollingManager ! PipelinesApiStatusQueryFailed(pollingRequest, failure)
       Failure(failure)
-  } recover {
-    case e =>
-      pollingManager ! PipelinesApiStatusQueryFailed(pollingRequest, new SystemPAPIApiException(e))
-      Failure(e)
+  } recover { case e =>
+    pollingManager ! PipelinesApiStatusQueryFailed(pollingRequest, new SystemPAPIApiException(e))
+    Failure(e)
   }
 
-  private [request] def interpretOperationStatus(operation: Operation, pollingRequest: PAPIStatusPollRequest): RunStatus = {
+  private[request] def interpretOperationStatus(operation: Operation,
+                                                pollingRequest: PAPIStatusPollRequest
+  ): RunStatus =
     if (Option(operation).isEmpty) {
       // It is possible to receive a null via an HTTP 200 with no response. If that happens, handle it and don't crash.
       // https://github.com/googleapis/google-http-java-client/blob/v1.28.0/google-http-client/src/main/java/com/google/api/client/http/HttpResponse.java#L456-L458
       val errorMessage = "Operation returned as empty"
       UnsuccessfulRunStatus(Status.UNKNOWN, Option(errorMessage), Nil, None, None, None, wasPreemptible = false)
     } else {
-      try {
+      try
         if (operation.getDone) {
           val metadata = operation.metadata
           // Deserialize the response
@@ -66,7 +75,7 @@ trait GetRequestHandler { this: RequestHandler =>
             .toList
             .flatten
           val workerEvent: Option[WorkerAssignedEvent] =
-            findEvent[WorkerAssignedEvent](events).flatMap(_ (pollingRequest.workflowId -> operation))
+            findEvent[WorkerAssignedEvent](events).flatMap(_(pollingRequest.workflowId -> operation))
           val executionEvents = getEventList(metadata, events, actions)
           val virtualMachineOption = for {
             pipelineValue <- pipeline
@@ -111,7 +120,7 @@ trait GetRequestHandler { this: RequestHandler =>
         } else {
           Initializing
         }
-      } catch {
+      catch {
         case nullPointerException: NullPointerException =>
           throw new RuntimeException(
             s"Caught NPE while interpreting operation ${operation.getName}: " +
@@ -121,20 +130,25 @@ trait GetRequestHandler { this: RequestHandler =>
           )
       }
     }
-  }
 
-  private def getEventList(metadata: Map[String, AnyRef], events: List[Event], actions: List[Action]): List[ExecutionEvent] = {
-    val starterEvent: Option[ExecutionEvent] = {
-      metadata.get("createTime") map { time => ExecutionEvent("waiting for quota", OffsetDateTime.parse(time.toString)) }
-    }
+  private def getEventList(metadata: Map[String, AnyRef],
+                           events: List[Event],
+                           actions: List[Action]
+  ): List[ExecutionEvent] = {
+    val starterEvent: Option[ExecutionEvent] =
+      metadata.get("createTime") map { time =>
+        ExecutionEvent("waiting for quota", OffsetDateTime.parse(time.toString))
+      }
 
-    val completionEvent: Option[ExecutionEvent] = {
-      metadata.get("endTime") map { time => ExecutionEvent("Complete in GCE / Cromwell Poll Interval", OffsetDateTime.parse(time.toString)) }
-    }
+    val completionEvent: Option[ExecutionEvent] =
+      metadata.get("endTime") map { time =>
+        ExecutionEvent("Complete in GCE / Cromwell Poll Interval", OffsetDateTime.parse(time.toString))
+      }
 
     // Map action indexes to event types. Action indexes are 1-based for some reason.
     val actionIndexToEventType: Map[Int, String] = List(Key.Logging, Key.Tag).flatMap { k =>
-      actions.zipWithIndex collect { case (a, i) if a.getLabels.containsKey(k) => (i + 1) -> a.getLabels.get(k) } } toMap
+      actions.zipWithIndex collect { case (a, i) if a.getLabels.containsKey(k) => (i + 1) -> a.getLabels.get(k) }
+    } toMap
 
     val executionEvents = events.map(toExecutionEvent(actionIndexToEventType))
     // The Docker image used for CWL output parsing causes some complications for the timing diagram. Docker image
@@ -152,7 +166,10 @@ trait GetRequestHandler { this: RequestHandler =>
     val filteredExecutionEvents = startDelocalization match {
       case None => executionEvents // Can't do filtering without a start time for Delocalization.
       case Some(start) =>
-        executionEvents filterNot { e => (e.name.startsWith("Started pulling ") || e.name.startsWith("Stopped pulling ")) && e.offsetDateTime.compareTo(start.offsetDateTime) > 0 }
+        executionEvents filterNot { e =>
+          (e.name.startsWith("Started pulling ") || e.name.startsWith("Stopped pulling ")) && e.offsetDateTime
+            .compareTo(start.offsetDateTime) > 0
+        }
     }
 
     starterEvent.toList ++ filteredExecutionEvents ++ completionEvent
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/RequestHandler.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/RequestHandler.scala
index 6cb2b148a58..50ec0fd239e 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/RequestHandler.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/RequestHandler.scala
@@ -5,7 +5,11 @@ import com.google.api.client.googleapis.batch.BatchRequest
 import com.google.api.client.googleapis.json.GoogleJsonError
 import com.google.api.services.genomics.v2alpha1.Genomics
 import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.BatchRequestTimeoutConfiguration
-import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.{PAPIAbortRequest, PAPIRunCreationRequest, PAPIStatusPollRequest}
+import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.{
+  PAPIAbortRequest,
+  PAPIRunCreationRequest,
+  PAPIStatusPollRequest
+}
 import cromwell.backend.google.pipelines.common.api.{PipelinesApiRequestHandler, PipelinesApiRequestManager}
 import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
 import org.slf4j.{Logger, LoggerFactory}
@@ -21,18 +25,18 @@ object RequestHandler {
 
 class RequestHandler(applicationName: String,
                      endpointUrl: URL,
-                     batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration)
-  extends PipelinesApiRequestHandler
-  with RunRequestHandler
-  with GetRequestHandler
-  with AbortRequestHandler {
+                     batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration
+) extends PipelinesApiRequestHandler
+    with RunRequestHandler
+    with GetRequestHandler
+    with AbortRequestHandler {
 
   override def makeBatchRequest: BatchRequest = {
     val builder =
       new Genomics.Builder(
         GoogleAuthMode.httpTransport,
         GoogleAuthMode.jsonFactory,
-        initializeHttpRequest(batchRequestTimeoutConfiguration) _,
+        initializeHttpRequest(batchRequestTimeoutConfiguration) _
       )
         .setApplicationName(applicationName)
         .setRootUrl(endpointUrl.toString)
@@ -42,9 +46,8 @@ class RequestHandler(applicationName: String,
 
   override def enqueue[T <: PipelinesApiRequestManager.PAPIApiRequest](papiApiRequest: T,
                                                                        batchRequest: BatchRequest,
-                                                                       pollingManager: ActorRef)
-                                                                      (implicit ec: ExecutionContext)
-  : Future[Try[Unit]] = papiApiRequest match {
+                                                                       pollingManager: ActorRef
+  )(implicit ec: ExecutionContext): Future[Try[Unit]] = papiApiRequest match {
     case create: PAPIRunCreationRequest => handleRequest(create, batchRequest, pollingManager)
     case status: PAPIStatusPollRequest => handleRequest(status, batchRequest, pollingManager)
     case abort: PAPIAbortRequest => handleRequest(abort, batchRequest, pollingManager)
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/RunRequestHandler.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/RunRequestHandler.scala
index 1b655b41edb..8b791125335 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/RunRequestHandler.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/RunRequestHandler.scala
@@ -14,7 +14,10 @@ import scala.concurrent.{Future, Promise}
 import scala.util.{Failure, Success, Try}
 
 trait RunRequestHandler { this: RequestHandler =>
-  private def runCreationResultHandler(originalRequest: PAPIApiRequest, completionPromise: Promise[Try[Unit]], pollingManager: ActorRef) = new JsonBatchCallback[Operation] {
+  private def runCreationResultHandler(originalRequest: PAPIApiRequest,
+                                       completionPromise: Promise[Try[Unit]],
+                                       pollingManager: ActorRef
+  ) = new JsonBatchCallback[Operation] {
     override def onSuccess(operation: Operation, responseHeaders: HttpHeaders): Unit = {
       originalRequest.requester ! getJob(operation)
       completionPromise.trySuccess(Success(()))
@@ -41,17 +44,23 @@ trait RunRequestHandler { this: RequestHandler =>
     }
   }
 
-  def handleRequest(runCreationQuery: PAPIRunCreationRequest, batch: BatchRequest, pollingManager: ActorRef): Future[Try[Unit]] = {
+  def handleRequest(runCreationQuery: PAPIRunCreationRequest,
+                    batch: BatchRequest,
+                    pollingManager: ActorRef
+  ): Future[Try[Unit]] = {
     val completionPromise = Promise[Try[Unit]]()
     val resultHandler = runCreationResultHandler(runCreationQuery, completionPromise, pollingManager)
     addRunCreationToBatch(runCreationQuery.httpRequest, batch, resultHandler)
     completionPromise.future
   }
 
-  private def addRunCreationToBatch(request: HttpRequest, batch: BatchRequest, resultHandler: JsonBatchCallback[Operation]): Unit = {
+  private def addRunCreationToBatch(request: HttpRequest,
+                                    batch: BatchRequest,
+                                    resultHandler: JsonBatchCallback[Operation]
+  ): Unit = {
     /*
-      * Manually enqueue the request instead of doing it through the RunPipelineRequest
-      * as it would unnecessarily rebuild the request (which we already have)
+     * Manually enqueue the request instead of doing it through the RunPipelineRequest
+     * as it would unnecessarily rebuild the request (which we already have)
      */
     batch.queue(request, classOf[Operation], classOf[GoogleJsonErrorContainer], resultHandler)
     ()
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
index 510f4a80742..3a119c1cf77 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
@@ -10,8 +10,11 @@ import org.mockito.Mockito._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
-  with MockSugar {
+class PipelinesApiAsyncBackendJobExecutionActorSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with MockSugar {
   behavior of "PipelinesParameterConversions"
 
   it should "group files by bucket" in {
@@ -39,8 +42,8 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Cro
 
     val expected =
       Map("foo" -> (NonEmptyList.of(0, 1) map inputs.apply)) ++
-      Map("bar" -> (NonEmptyList.of(2, 3, 4) map inputs.apply)) ++
-      Map("baz" -> NonEmptyList.of(inputs(5)))
+        Map("bar" -> (NonEmptyList.of(2, 3, 4) map inputs.apply)) ++
+        Map("baz" -> NonEmptyList.of(inputs(5)))
 
     PipelinesApiAsyncBackendJobExecutionActor.groupParametersByGcsBucket(inputs) shouldEqual expected
   }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
index 18c84ee66eb..a325c8c0a01 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesConversionsSpec.scala
@@ -34,13 +34,18 @@ class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
   private lazy val fakeCredentials = NoCredentials.getInstance
 
   private val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
-    throw new UnsupportedOperationException("Currently PipelinesConversionsSpec doesn't need to use drs read interpreter.")
+    throw new UnsupportedOperationException(
+      "Currently PipelinesConversionsSpec doesn't need to use drs read interpreter."
+    )
 
   it should "create a DRS input parameter" in {
 
     val drsPathBuilder = DrsPathBuilder(
-      new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
-      None,
+      new DrsCloudNioFileSystemProvider(drsResolverConfig,
+                                        GoogleOauthDrsCredentials(fakeCredentials, 1.minutes),
+                                        drsReadInterpreter
+      ),
+      None
     )
     val drsPath = drsPathBuilder.build("drs://drs.example.org/aaaabbbb-cccc-dddd-eeee-abcd0000dcba").get
     val containerRelativePath = DefaultPathBuilder.get("path/to/file.bai")
@@ -62,10 +67,10 @@ class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     )
 
     logging.get("flags") should be(a[java.util.List[_]])
-    logging.get("flags").asInstanceOf[java.util.List[_]] should be (empty)
+    logging.get("flags").asInstanceOf[java.util.List[_]] should be(empty)
 
     logging.get("mounts") should be(a[java.util.List[_]])
-    logging.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+    logging.get("mounts").asInstanceOf[java.util.List[_]] should be(empty)
 
     logging.get("imageUri") should be(ActionUtils.CloudSdkImage)
 
@@ -86,7 +91,7 @@ class PipelinesConversionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
     )
 
     action.get("mounts") should be(a[java.util.List[_]])
-    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+    action.get("mounts").asInstanceOf[java.util.List[_]] should be(empty)
 
     action.get("imageUri") should be("somerepo/drs-downloader:tagged")
 
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionBuilderSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionBuilderSpec.scala
index 83d1be04e74..4cd37c0cc60 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionBuilderSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionBuilderSpec.scala
@@ -19,35 +19,37 @@ class ActionBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     ("description", "action", "command"),
     ("a cloud sdk action", ActionBuilder.cloudSdkAction, s"docker run ${ActionUtils.CloudSdkImage}"),
     ("a cloud sdk action with args",
-      ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello").asJava),
-      s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello"
+     ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello").asJava),
+     s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello"
     ),
     ("a cloud sdk action with quotes in the args",
-      ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello m'lord").asJava),
-      s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello\\ m\\'lord"
+     ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello m'lord").asJava),
+     s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello\\ m\\'lord"
     ),
     ("a cloud sdk action with a newline in the args",
-      ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello\\\nworld").asJava),
-      s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello\\\\world"
+     ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello\\\nworld").asJava),
+     s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello\\\\world"
     ),
     ("an action with multiple args",
-      new Action()
-        .setImageUri("ubuntu")
-        .setEnvironment(Map("ENV" -> "dev").asJava)
-        .setEntrypoint("")
-        .setCommands(List("bash", "-c", "echo hello").asJava)
-        .setFlags(List(ActionFlag.PublishExposedPorts, ActionFlag.AlwaysRun).map(_.toString).asJava)
-        .setMounts(List(
-          new Mount().setDisk("read-only-disk").setPath("/read/only/container").setReadOnly(true),
-          new Mount().setDisk("read-write-disk").setPath("/read/write/container"),
-        ).asJava)
-        .setName("my_container_name")
-        .setPidNamespace("host")
-        .setPortMappings(Map("8008" -> Int.box(8000)).asJava),
-      "docker run --name my_container_name" +
-        " -v /mnt/read-only-disk:/read/only/container:ro -v /mnt/read-write-disk:/read/write/container" +
-        " -e ENV:dev --pid=host -P -p 8008:8000 --entrypoint= ubuntu bash -c echo\\ hello"
-    ),
+     new Action()
+       .setImageUri("ubuntu")
+       .setEnvironment(Map("ENV" -> "dev").asJava)
+       .setEntrypoint("")
+       .setCommands(List("bash", "-c", "echo hello").asJava)
+       .setFlags(List(ActionFlag.PublishExposedPorts, ActionFlag.AlwaysRun).map(_.toString).asJava)
+       .setMounts(
+         List(
+           new Mount().setDisk("read-only-disk").setPath("/read/only/container").setReadOnly(true),
+           new Mount().setDisk("read-write-disk").setPath("/read/write/container")
+         ).asJava
+       )
+       .setName("my_container_name")
+       .setPidNamespace("host")
+       .setPortMappings(Map("8008" -> Int.box(8000)).asJava),
+     "docker run --name my_container_name" +
+       " -v /mnt/read-only-disk:/read/only/container:ro -v /mnt/read-write-disk:/read/write/container" +
+       " -e ENV:dev --pid=host -P -p 8008:8000 --entrypoint= ubuntu bash -c echo\\ hello"
+    )
   )
 
   forAll(dockerRunActions) { (description, action, command) =>
@@ -56,15 +58,13 @@ class ActionBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     }
   }
 
-
   private val memoryRetryExpectedEntrypoint = "/bin/sh"
 
-  def memoryRetryExpectedCommand(lookupString: String): util.List[String] = {
+  def memoryRetryExpectedCommand(lookupString: String): util.List[String] =
     List(
       "-c",
       s"grep -E -q '$lookupString' /cromwell_root/stderr ; echo $$? > /cromwell_root/memory_retry_rc"
     ).asJava
-  }
 
   val mounts = List(new Mount().setDisk("read-only-disk").setPath("/read/only/container"))
   private val memoryRetryActionExpectedFlags = List(ActionFlag.AlwaysRun.toString).asJava
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionCommandsSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionCommandsSpec.scala
index 31d1300d4db..20c9e1fe6e3 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionCommandsSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/ActionCommandsSpec.scala
@@ -19,7 +19,7 @@ class ActionCommandsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
       mock[Path],
       mock[com.google.api.services.storage.Storage],
       mock[com.google.cloud.storage.Storage],
-      "my-project",
+      "my-project"
     )
     val recovered = recoverRequesterPaysError(path) { flag =>
       s"flag is $flag"
@@ -46,21 +46,23 @@ class ActionCommandsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   it should "use GcsTransferConfiguration to set the number of localization retries" in {
-    implicit val gcsTransferConfiguration: GcsTransferConfiguration = GcsTransferConfiguration(
-      transferAttempts = refineMV(31380), parallelCompositeUploadThreshold = "0")
-    retry("I'm very flaky") shouldBe """for i in $(seq 31380); do
-                                       |  (
-                                       |    I'm very flaky
-                                       |  )
-                                       |  RC=$?
-                                       |  if [ "$RC" = "0" ]; then
-                                       |    break
-                                       |  fi
-                                       |  if [ $i -lt 31380 ]; then
-                                       |    printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" Waiting\ 5\ seconds\ and\ retrying
-                                       |    sleep 5
-                                       |  fi
-                                       |done
-                                       |exit "$RC"""".stripMargin
+    implicit val gcsTransferConfiguration: GcsTransferConfiguration =
+      GcsTransferConfiguration(transferAttempts = refineMV(31380), parallelCompositeUploadThreshold = "0")
+    retry(
+      "I'm very flaky"
+    ) shouldBe """for i in $(seq 31380); do
+                 |  (
+                 |    I'm very flaky
+                 |  )
+                 |  RC=$?
+                 |  if [ "$RC" = "0" ]; then
+                 |    break
+                 |  fi
+                 |  if [ $i -lt 31380 ]; then
+                 |    printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" Waiting\ 5\ seconds\ and\ retrying
+                 |    sleep 5
+                 |  fi
+                 |done
+                 |exit "$RC"""".stripMargin
   }
 }
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
index 7f10580b700..f78f2dce9f4 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala
@@ -120,7 +120,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
         "resources" -> Map[String, Object](
           "projectId" -> "project",
           "virtualMachine" -> Map(
-            "machineType" -> "custom-1-1024",
+            "machineType" -> "custom-1-1024"
           ).asJava
         ).asJava
       ).asJava
@@ -153,15 +153,19 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
       )
     ).asJava
 
-    val metadataMapStarted = makeMetadata(Map[String, Object](
-      "@type" -> "WorkerAssignedEvent",
-      "zone" -> "event 1 Zone",
-      "instance" -> "event 1 Instance"
-    ))
+    val metadataMapStarted = makeMetadata(
+      Map[String, Object](
+        "@type" -> "WorkerAssignedEvent",
+        "zone" -> "event 1 Zone",
+        "instance" -> "event 1 Instance"
+      )
+    )
     val metadataMapNotStarted = makeMetadata(Map.empty)
-    val metadataMapNotStarted2 = makeMetadata(Map[String, Object](
-      "@type" -> "ContainerStartedEvent"
-    ))
+    val metadataMapNotStarted2 = makeMetadata(
+      Map[String, Object](
+        "@type" -> "ContainerStartedEvent"
+      )
+    )
 
     operation.setMetadata(metadataMapStarted)
     operation.hasStarted shouldBe true
@@ -174,8 +178,8 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   it should "deserialize big decimals correctly" in {
     val valueMap = Map[String, Object](
       "integerValue" -> BigDecimal(5),
-      "doubleValue" -> BigDecimal.decimal(6D),
-      "floatValue" -> BigDecimal.decimal(7F),
+      "doubleValue" -> BigDecimal.decimal(6d),
+      "floatValue" -> BigDecimal.decimal(7f),
       "longValue" -> BigDecimal.decimal(8L)
     ).asJava
 
@@ -183,8 +187,8 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     deserialized.isSuccess shouldBe true
     val deserializedSuccess = deserialized.get
     deserializedSuccess.integerValue shouldBe 5
-    deserializedSuccess.doubleValue shouldBe 6D
-    deserializedSuccess.floatValue shouldBe 7F
+    deserializedSuccess.doubleValue shouldBe 6d
+    deserializedSuccess.floatValue shouldBe 7f
     deserializedSuccess.longValue shouldBe 8L
   }
 
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/GetRequestHandlerSpec.scala b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/GetRequestHandlerSpec.scala
index 6efca44f5a5..5bc340f22ed 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/GetRequestHandlerSpec.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/request/GetRequestHandlerSpec.scala
@@ -25,7 +25,7 @@ class GetRequestHandlerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   private val requestHandler: GetRequestHandler = new RequestHandler(
     "GetRequestHandlerSpec",
     new URL("file:///getrequesthandlerspec"),
-    BatchRequestTimeoutConfiguration(None, None),
+    BatchRequestTimeoutConfiguration(None, None)
   )
 
   private val workflowId = WorkflowId.randomId()
@@ -37,260 +37,270 @@ class GetRequestHandlerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
 
   private val interpretedStatus = Table(
     ("description", "json", "status"),
-    ("parse null operation json", null, UnsuccessfulRunStatus(
-      Status.UNKNOWN,
-      Option("Operation returned as empty"),
-      Nil,
-      None,
-      None,
-      None,
-      wasPreemptible = false
-    )),
+    ("parse null operation json",
+     null,
+     UnsuccessfulRunStatus(
+       Status.UNKNOWN,
+       Option("Operation returned as empty"),
+       Nil,
+       None,
+       None,
+       None,
+       wasPreemptible = false
+     )
+    ),
     ("parse empty operation json", "{}", Initializing),
     ("parse error operation json without resources",
-      """|{
-         |  "done": true,
-         |  "error": {}
-         |}
-         |""".stripMargin,
-      Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
+     """|{
+        |  "done": true,
+        |  "error": {}
+        |}
+        |""".stripMargin,
+     Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
     ),
     ("parse error operation json without virtualMachine",
-      """|{
-         |  "done": true,
-         |  "resources": {
-         |  },
-         |  "error": {}
-         |}
-         |""".stripMargin,
-      Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
+     """|{
+        |  "done": true,
+        |  "resources": {
+        |  },
+        |  "error": {}
+        |}
+        |""".stripMargin,
+     Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
     ),
     ("parse error operation json without preemptible",
-      """|{
-         |  "done": true,
-         |  "resources": {
-         |    "virtualMachine": {
-         |    }
-         |  },
-         |  "error": {}
-         |}
-         |""".stripMargin,
-      Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
+     """|{
+        |  "done": true,
+        |  "resources": {
+        |    "virtualMachine": {
+        |    }
+        |  },
+        |  "error": {}
+        |}
+        |""".stripMargin,
+     Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
     ),
     ("parse error operation json with preemptible true",
-      """|{
-         |  "done": true,
-         |  "resources": {
-         |    "virtualMachine": {
-         |      "preemptible": true
-         |    }
-         |  },
-         |  "error": {}
-         |}
-         |""".stripMargin,
-      Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
+     """|{
+        |  "done": true,
+        |  "resources": {
+        |    "virtualMachine": {
+        |      "preemptible": true
+        |    }
+        |  },
+        |  "error": {}
+        |}
+        |""".stripMargin,
+     Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
     ),
     ("parse error operation json with preemptible false",
-      """|{
-         |  "done": true,
-         |  "resources": {
-         |    "virtualMachine": {
-         |      "preemptible": false
-         |    }
-         |  },
-         |  "error": {}
-         |}
-         |""".stripMargin,
-      Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
-    ),
-    ("check that we classify error code 10 as a preemption on a preemptible VM",
-      """{
+     """|{
         |  "done": true,
-        |  "error": {
-        |    "code": 10,
-        |    "message": "The assigned worker has failed to complete the operation"
+        |  "resources": {
+        |    "virtualMachine": {
+        |      "preemptible": false
+        |    }
         |  },
-        |  "metadata": {
-        |    "@type": "type.googleapis.com/google.genomics.v2alpha1.Metadata",
-        |    "createTime": "2019-08-18T12:04:38.082650Z",
-        |    "endTime": "2019-08-18T15:58:26.659602622Z",
-        |    "events": [],
-        |    "labels": {
-        |      "cromwell-sub-workflow-name": "bamtocram",
-        |      "cromwell-workflow-id": "asdfasdf",
-        |      "wdl-call-alias": "validatecram",
-        |      "wdl-task-name": "validatesamfile"
-        |    },
-        |    "pipeline": {
-        |      "actions": [],
-        |      "environment": {},
-        |      "resources": {
-        |        "projectId": "",
-        |        "regions": [],
-        |        "virtualMachine": {
-        |          "accelerators": [],
-        |          "bootDiskSizeGb": 11,
-        |          "bootImage": "asdfasdf",
-        |          "cpuPlatform": "",
-        |          "disks": [
-        |            {
-        |              "name": "local-disk",
-        |              "sizeGb": 41,
-        |              "sourceImage": "",
-        |              "type": "pd-standard"
-        |            }
-        |          ],
-        |          "enableStackdriverMonitoring": false,
-        |          "labels": {
-        |            "cromwell-sub-workflow-name": "bamtocram",
-        |            "cromwell-workflow-id": "asdfasdf",
-        |            "goog-pipelines-worker": "true",
-        |            "wdl-call-alias": "validatecram",
-        |            "wdl-task-name": "validatesamfile"
-        |          },
-        |          "machineType": "custom-2-7168",
-        |          "network": {
-        |            "name": "",
-        |            "subnetwork": "",
-        |            "usePrivateAddress": false
-        |          },
-        |          "nvidiaDriverVersion": "",
-        |          "preemptible": true,
-        |          "serviceAccount": {
-        |            "email": "default",
-        |            "scopes": [
-        |              "https://www.googleapis.com/auth/genomics",
-        |              "https://www.googleapis.com/auth/compute",
-        |              "https://www.googleapis.com/auth/devstorage.full_control",
-        |              "https://www.googleapis.com/auth/cloudkms",
-        |              "https://www.googleapis.com/auth/userinfo.email",
-        |              "https://www.googleapis.com/auth/userinfo.profile",
-        |              "https://www.googleapis.com/auth/monitoring.write",
-        |              "https://www.googleapis.com/auth/cloud-platform"
-        |            ]
-        |          }
-        |        },
-        |        "zones": [
-        |          "us-central1-a",
-        |          "us-central1-b",
-        |          "us-east1-d",
-        |          "us-central1-c",
-        |          "us-central1-f",
-        |          "us-east1-c"
-        |        ]
-        |      },
-        |      "timeout": "604800s"
-        |    },
-        |    "startTime": "2019-08-18T12:04:39.192909594Z"
-        |  },
-        |  "name": "asdfasdf"
-        |}""".stripMargin,
-      Preempted(
-        Status.ABORTED,
-        None,
-        Nil,
-        List(
-          ExecutionEvent("waiting for quota", OffsetDateTime.parse("2019-08-18T12:04:38.082650Z"),None),
-          ExecutionEvent("Complete in GCE / Cromwell Poll Interval", OffsetDateTime.parse("2019-08-18T15:58:26.659602622Z"),None),
-        ),
-        Some("custom-2-7168"),
-        None,
-        None)
+        |  "error": {}
+        |}
+        |""".stripMargin,
+     Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
+    ),
+    ("check that we classify error code 10 as a preemption on a preemptible VM",
+     """{
+       |  "done": true,
+       |  "error": {
+       |    "code": 10,
+       |    "message": "The assigned worker has failed to complete the operation"
+       |  },
+       |  "metadata": {
+       |    "@type": "type.googleapis.com/google.genomics.v2alpha1.Metadata",
+       |    "createTime": "2019-08-18T12:04:38.082650Z",
+       |    "endTime": "2019-08-18T15:58:26.659602622Z",
+       |    "events": [],
+       |    "labels": {
+       |      "cromwell-sub-workflow-name": "bamtocram",
+       |      "cromwell-workflow-id": "asdfasdf",
+       |      "wdl-call-alias": "validatecram",
+       |      "wdl-task-name": "validatesamfile"
+       |    },
+       |    "pipeline": {
+       |      "actions": [],
+       |      "environment": {},
+       |      "resources": {
+       |        "projectId": "",
+       |        "regions": [],
+       |        "virtualMachine": {
+       |          "accelerators": [],
+       |          "bootDiskSizeGb": 11,
+       |          "bootImage": "asdfasdf",
+       |          "cpuPlatform": "",
+       |          "disks": [
+       |            {
+       |              "name": "local-disk",
+       |              "sizeGb": 41,
+       |              "sourceImage": "",
+       |              "type": "pd-standard"
+       |            }
+       |          ],
+       |          "enableStackdriverMonitoring": false,
+       |          "labels": {
+       |            "cromwell-sub-workflow-name": "bamtocram",
+       |            "cromwell-workflow-id": "asdfasdf",
+       |            "goog-pipelines-worker": "true",
+       |            "wdl-call-alias": "validatecram",
+       |            "wdl-task-name": "validatesamfile"
+       |          },
+       |          "machineType": "custom-2-7168",
+       |          "network": {
+       |            "name": "",
+       |            "subnetwork": "",
+       |            "usePrivateAddress": false
+       |          },
+       |          "nvidiaDriverVersion": "",
+       |          "preemptible": true,
+       |          "serviceAccount": {
+       |            "email": "default",
+       |            "scopes": [
+       |              "https://www.googleapis.com/auth/genomics",
+       |              "https://www.googleapis.com/auth/compute",
+       |              "https://www.googleapis.com/auth/devstorage.full_control",
+       |              "https://www.googleapis.com/auth/cloudkms",
+       |              "https://www.googleapis.com/auth/userinfo.email",
+       |              "https://www.googleapis.com/auth/userinfo.profile",
+       |              "https://www.googleapis.com/auth/monitoring.write",
+       |              "https://www.googleapis.com/auth/cloud-platform"
+       |            ]
+       |          }
+       |        },
+       |        "zones": [
+       |          "us-central1-a",
+       |          "us-central1-b",
+       |          "us-east1-d",
+       |          "us-central1-c",
+       |          "us-central1-f",
+       |          "us-east1-c"
+       |        ]
+       |      },
+       |      "timeout": "604800s"
+       |    },
+       |    "startTime": "2019-08-18T12:04:39.192909594Z"
+       |  },
+       |  "name": "asdfasdf"
+       |}""".stripMargin,
+     Preempted(
+       Status.ABORTED,
+       None,
+       Nil,
+       List(
+         ExecutionEvent("waiting for quota", OffsetDateTime.parse("2019-08-18T12:04:38.082650Z"), None),
+         ExecutionEvent("Complete in GCE / Cromwell Poll Interval",
+                        OffsetDateTime.parse("2019-08-18T15:58:26.659602622Z"),
+                        None
+         )
+       ),
+       Some("custom-2-7168"),
+       None,
+       None
+     )
     ),
     ("check that we classify error code 10 as a failure on a non-preemptible VM",
-      """{
-        |  "done": true,
-        |  "error": {
-        |    "code": 10,
-        |    "message": "The assigned worker has failed to complete the operation"
-        |  },
-        |  "metadata": {
-        |    "@type": "type.googleapis.com/google.genomics.v2alpha1.Metadata",
-        |    "createTime": "2019-08-18T12:04:38.082650Z",
-        |    "endTime": "2019-08-18T15:58:26.659602622Z",
-        |    "events": [],
-        |    "labels": {
-        |      "cromwell-sub-workflow-name": "bamtocram",
-        |      "cromwell-workflow-id": "asdfasdf",
-        |      "wdl-call-alias": "validatecram",
-        |      "wdl-task-name": "validatesamfile"
-        |    },
-        |    "pipeline": {
-        |      "actions": [],
-        |      "environment": {},
-        |      "resources": {
-        |        "projectId": "",
-        |        "regions": [],
-        |        "virtualMachine": {
-        |          "accelerators": [],
-        |          "bootDiskSizeGb": 11,
-        |          "bootImage": "asdfasdf",
-        |          "cpuPlatform": "",
-        |          "disks": [
-        |            {
-        |              "name": "local-disk",
-        |              "sizeGb": 41,
-        |              "sourceImage": "",
-        |              "type": "pd-standard"
-        |            }
-        |          ],
-        |          "enableStackdriverMonitoring": false,
-        |          "labels": {
-        |            "cromwell-sub-workflow-name": "bamtocram",
-        |            "cromwell-workflow-id": "asdfasdf",
-        |            "goog-pipelines-worker": "true",
-        |            "wdl-call-alias": "validatecram",
-        |            "wdl-task-name": "validatesamfile"
-        |          },
-        |          "machineType": "custom-2-7168",
-        |          "network": {
-        |            "name": "",
-        |            "subnetwork": "",
-        |            "usePrivateAddress": false
-        |          },
-        |          "nvidiaDriverVersion": "",
-        |          "preemptible": false,
-        |          "serviceAccount": {
-        |            "email": "default",
-        |            "scopes": [
-        |              "https://www.googleapis.com/auth/genomics",
-        |              "https://www.googleapis.com/auth/compute",
-        |              "https://www.googleapis.com/auth/devstorage.full_control",
-        |              "https://www.googleapis.com/auth/cloudkms",
-        |              "https://www.googleapis.com/auth/userinfo.email",
-        |              "https://www.googleapis.com/auth/userinfo.profile",
-        |              "https://www.googleapis.com/auth/monitoring.write",
-        |              "https://www.googleapis.com/auth/cloud-platform"
-        |            ]
-        |          }
-        |        },
-        |        "zones": [
-        |          "us-central1-a",
-        |          "us-central1-b",
-        |          "us-east1-d",
-        |          "us-central1-c",
-        |          "us-central1-f",
-        |          "us-east1-c"
-        |        ]
-        |      },
-        |      "timeout": "604800s"
-        |    },
-        |    "startTime": "2019-08-18T12:04:39.192909594Z"
-        |  },
-        |  "name": "asdfasdf"
-        |}""".stripMargin,
-      Failed(
-        Status.ABORTED,
-        None,
-        Nil,
-        List(
-          ExecutionEvent("waiting for quota", OffsetDateTime.parse("2019-08-18T12:04:38.082650Z"),None),
-          ExecutionEvent("Complete in GCE / Cromwell Poll Interval", OffsetDateTime.parse("2019-08-18T15:58:26.659602622Z"),None),
-        ),
-        Some("custom-2-7168"),
-        None,
-        None
-      )
+     """{
+       |  "done": true,
+       |  "error": {
+       |    "code": 10,
+       |    "message": "The assigned worker has failed to complete the operation"
+       |  },
+       |  "metadata": {
+       |    "@type": "type.googleapis.com/google.genomics.v2alpha1.Metadata",
+       |    "createTime": "2019-08-18T12:04:38.082650Z",
+       |    "endTime": "2019-08-18T15:58:26.659602622Z",
+       |    "events": [],
+       |    "labels": {
+       |      "cromwell-sub-workflow-name": "bamtocram",
+       |      "cromwell-workflow-id": "asdfasdf",
+       |      "wdl-call-alias": "validatecram",
+       |      "wdl-task-name": "validatesamfile"
+       |    },
+       |    "pipeline": {
+       |      "actions": [],
+       |      "environment": {},
+       |      "resources": {
+       |        "projectId": "",
+       |        "regions": [],
+       |        "virtualMachine": {
+       |          "accelerators": [],
+       |          "bootDiskSizeGb": 11,
+       |          "bootImage": "asdfasdf",
+       |          "cpuPlatform": "",
+       |          "disks": [
+       |            {
+       |              "name": "local-disk",
+       |              "sizeGb": 41,
+       |              "sourceImage": "",
+       |              "type": "pd-standard"
+       |            }
+       |          ],
+       |          "enableStackdriverMonitoring": false,
+       |          "labels": {
+       |            "cromwell-sub-workflow-name": "bamtocram",
+       |            "cromwell-workflow-id": "asdfasdf",
+       |            "goog-pipelines-worker": "true",
+       |            "wdl-call-alias": "validatecram",
+       |            "wdl-task-name": "validatesamfile"
+       |          },
+       |          "machineType": "custom-2-7168",
+       |          "network": {
+       |            "name": "",
+       |            "subnetwork": "",
+       |            "usePrivateAddress": false
+       |          },
+       |          "nvidiaDriverVersion": "",
+       |          "preemptible": false,
+       |          "serviceAccount": {
+       |            "email": "default",
+       |            "scopes": [
+       |              "https://www.googleapis.com/auth/genomics",
+       |              "https://www.googleapis.com/auth/compute",
+       |              "https://www.googleapis.com/auth/devstorage.full_control",
+       |              "https://www.googleapis.com/auth/cloudkms",
+       |              "https://www.googleapis.com/auth/userinfo.email",
+       |              "https://www.googleapis.com/auth/userinfo.profile",
+       |              "https://www.googleapis.com/auth/monitoring.write",
+       |              "https://www.googleapis.com/auth/cloud-platform"
+       |            ]
+       |          }
+       |        },
+       |        "zones": [
+       |          "us-central1-a",
+       |          "us-central1-b",
+       |          "us-east1-d",
+       |          "us-central1-c",
+       |          "us-central1-f",
+       |          "us-east1-c"
+       |        ]
+       |      },
+       |      "timeout": "604800s"
+       |    },
+       |    "startTime": "2019-08-18T12:04:39.192909594Z"
+       |  },
+       |  "name": "asdfasdf"
+       |}""".stripMargin,
+     Failed(
+       Status.ABORTED,
+       None,
+       Nil,
+       List(
+         ExecutionEvent("waiting for quota", OffsetDateTime.parse("2019-08-18T12:04:38.082650Z"), None),
+         ExecutionEvent("Complete in GCE / Cromwell Poll Interval",
+                        OffsetDateTime.parse("2019-08-18T15:58:26.659602622Z"),
+                        None
+         )
+       ),
+       Some("custom-2-7168"),
+       None,
+       None
+     )
     )
   )
 
@@ -299,7 +309,7 @@ class GetRequestHandlerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
       // Operation responses could come back as null. Handle it and don't crash.
       // https://github.com/googleapis/google-http-java-client/blob/v1.28.0/google-http-client/src/main/java/com/google/api/client/http/HttpResponse.java#L456-L458
       val operation =
-      Option(json).map(GoogleAuthMode.jsonFactory.createJsonParser).map(_.parse(classOf[Operation])).orNull
+        Option(json).map(GoogleAuthMode.jsonFactory.createJsonParser).map(_.parse(classOf[Operation])).orNull
       val runStatus = requestHandler.interpretOperationStatus(operation, pollingRequest)
 
       runStatus should be(expectedStatus)
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
index 8d8f52d3773..2c601007e2e 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
@@ -26,32 +26,35 @@ import wom.format.MemorySize
 
 import scala.jdk.CollectionConverters._
 
-case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode, endpointUrl: URL, location: String)(implicit gcsTransferConfiguration: GcsTransferConfiguration) extends PipelinesApiFactoryInterface
-  with ContainerSetup
-  with MonitoringAction
-  with CheckpointingAction
-  with Localization
-  with UserAction
-  with Delocalization
-  with MemoryRetryCheckAction
-  with SSHAccessAction {
+case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode, endpointUrl: URL, location: String)(
+  implicit gcsTransferConfiguration: GcsTransferConfiguration
+) extends PipelinesApiFactoryInterface
+    with ContainerSetup
+    with MonitoringAction
+    with CheckpointingAction
+    with Localization
+    with UserAction
+    with Delocalization
+    with MemoryRetryCheckAction
+    with SSHAccessAction {
 
   override def build(initializer: HttpRequestInitializer): PipelinesApiRequestFactory = new PipelinesApiRequestFactory {
-    val lifeSciences: CloudLifeSciences = new CloudLifeSciences.Builder(
-      GoogleAuthMode.httpTransport,
-      GoogleAuthMode.jsonFactory,
-      initializer)
-      .setApplicationName(applicationName)
-      .setRootUrl(endpointUrl.toString)
-      .build
-
-    override def cancelRequest(job: StandardAsyncJob): HttpRequest = {
-      lifeSciences.projects().locations().operations().cancel(job.jobId, new CancelOperationRequest()).buildHttpRequest()
-    }
-
-    override def getRequest(job: StandardAsyncJob): HttpRequest = {
+    val lifeSciences: CloudLifeSciences =
+      new CloudLifeSciences.Builder(GoogleAuthMode.httpTransport, GoogleAuthMode.jsonFactory, initializer)
+        .setApplicationName(applicationName)
+        .setRootUrl(endpointUrl.toString)
+        .build
+
+    override def cancelRequest(job: StandardAsyncJob): HttpRequest =
+      lifeSciences
+        .projects()
+        .locations()
+        .operations()
+        .cancel(job.jobId, new CancelOperationRequest())
+        .buildHttpRequest()
+
+    override def getRequest(job: StandardAsyncJob): HttpRequest =
       lifeSciences.projects().locations().operations().get(job.jobId).buildHttpRequest()
-    }
 
     override def runRequest(createPipelineParameters: CreatePipelineParameters, jobLogger: JobLogger): HttpRequest = {
       def createNetworkWithVPC(vpcAndSubnetworkProjectLabelValues: VpcAndSubnetworkProjectLabelValues): Network = {
@@ -66,12 +69,11 @@ case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode
         network
       }
 
-      def createNetwork(): Network = {
+      def createNetwork(): Network =
         createPipelineParameters.vpcNetworkAndSubnetworkProjectLabels match {
           case Some(vpcAndSubnetworkProjectLabelValues) => createNetworkWithVPC(vpcAndSubnetworkProjectLabelValues)
           case _ => new Network().setUsePrivateAddress(createPipelineParameters.runtimeAttributes.noAddress)
         }
-      }
 
       val allDisksToBeMounted = createPipelineParameters.adjustedSizeDisks ++
         createPipelineParameters.referenceDisksForLocalizationOpt.getOrElse(List.empty)
@@ -95,7 +97,8 @@ case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode
       // adding memory as environment variables makes it easy for a user to retrieve the new value of memory
       // on the machine to utilize in their command blocks if needed
       val runtimeMemory = createPipelineParameters.runtimeAttributes.memory
-      val environment = Map("MEM_UNIT" -> runtimeMemory.unit.toString, "MEM_SIZE" -> runtimeMemory.amount.toString).asJava
+      val environment =
+        Map("MEM_UNIT" -> runtimeMemory.unit.toString, "MEM_SIZE" -> runtimeMemory.amount.toString).asJava
 
       val sortedActions: List[Action] =
         ActionUtils.sortActions[Action](
@@ -109,7 +112,7 @@ case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode
           checkpointingStart = checkpointingStart,
           checkpointingShutdown = checkpointingShutdown,
           sshAccess = sshAccess,
-          isBackground = _.getRunInBackground,
+          isBackground = _.getRunInBackground
         )
 
       val serviceAccount = new ServiceAccount()
@@ -131,8 +134,7 @@ case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode
 
       val network: Network = createNetwork()
 
-      val accelerators = createPipelineParameters.runtimeAttributes
-        .gpuResource.map(toAccelerator).toList.asJava
+      val accelerators = createPipelineParameters.runtimeAttributes.gpuResource.map(toAccelerator).toList.asJava
 
       val virtualMachine = new VirtualMachine()
         .setDisks(disks.asJava)
@@ -153,18 +155,24 @@ case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode
       val adjustedBootDiskSize = {
         val fromRuntimeAttributes = createPipelineParameters.runtimeAttributes.bootDiskSize
         // Compute the decompressed size based on the information available
-        val userCommandImageSizeInBytes = createPipelineParameters.jobDescriptor.dockerSize.map(_.toFullSize(DockerConfiguration.instance.sizeCompressionFactor)).getOrElse(0L)
-        val userCommandImageSizeInGB = MemorySize(userCommandImageSizeInBytes.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB).amount
+        val userCommandImageSizeInBytes = createPipelineParameters.jobDescriptor.dockerSize
+          .map(_.toFullSize(DockerConfiguration.instance.sizeCompressionFactor))
+          .getOrElse(0L)
+        val userCommandImageSizeInGB =
+          MemorySize(userCommandImageSizeInBytes.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB).amount
         val userCommandImageSizeRoundedUpInGB = userCommandImageSizeInGB.ceil.toInt
 
         val totalSize = fromRuntimeAttributes +
-          createPipelineParameters
-            .dockerImageCacheDiskOpt
-            .map(_ => 0) // if we are using docker image cache then we don't need this additional volume for the boot disk
+          createPipelineParameters.dockerImageCacheDiskOpt
+            .map(_ =>
+              0
+            ) // if we are using docker image cache then we don't need this additional volume for the boot disk
             .getOrElse(userCommandImageSizeRoundedUpInGB + ActionUtils.cromwellImagesSizeRoundedUpInGB)
 
         if (totalSize != fromRuntimeAttributes) {
-          jobLogger.info(s"Adjusting boot disk size to $totalSize GB: $fromRuntimeAttributes GB (runtime attributes) + $userCommandImageSizeRoundedUpInGB GB (user command image) + ${ActionUtils.cromwellImagesSizeRoundedUpInGB} GB (Cromwell support images)")
+          jobLogger.info(
+            s"Adjusting boot disk size to $totalSize GB: $fromRuntimeAttributes GB (runtime attributes) + $userCommandImageSizeRoundedUpInGB GB (user command image) + ${ActionUtils.cromwellImagesSizeRoundedUpInGB} GB (Cromwell support images)"
+          )
         }
 
         totalSize
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
index 3c0f5ca63f9..c664aadf066 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -20,7 +20,15 @@ import org.apache.commons.csv.{CSVFormat, CSVPrinter}
 import org.apache.commons.io.output.ByteArrayOutputStream
 import wom.core.FullyQualifiedName
 import wom.expression.FileEvaluation
-import wom.values.{GlobFunctions, WomFile, WomGlobFile, WomMaybeListedDirectory, WomMaybePopulatedFile, WomSingleFile, WomUnlistedDirectory}
+import wom.values.{
+  GlobFunctions,
+  WomFile,
+  WomGlobFile,
+  WomMaybeListedDirectory,
+  WomMaybePopulatedFile,
+  WomSingleFile,
+  WomUnlistedDirectory
+}
 
 import java.nio.charset.Charset
 
@@ -31,7 +39,7 @@ import scala.language.postfixOps
 import scala.util.control.NoStackTrace
 
 class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExecutionActorParams)
-  extends cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor(standardParams)
+    extends cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor(standardParams)
     with PipelinesApiReferenceFilesMappingOperations {
 
   // The original implementation assumes the WomFiles are all WomMaybePopulatedFiles and wraps everything in a PipelinesApiFileInput
@@ -39,31 +47,45 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
   override protected def pipelinesApiInputsFromWomFiles(inputName: String,
                                                         remotePathArray: Seq[WomFile],
                                                         localPathArray: Seq[WomFile],
-                                                        jobDescriptor: BackendJobDescriptor): Iterable[PipelinesApiInput] = {
+                                                        jobDescriptor: BackendJobDescriptor
+  ): Iterable[PipelinesApiInput] =
     (remotePathArray zip localPathArray) flatMap {
       case (remotePath: WomMaybeListedDirectory, localPath) =>
         maybeListedDirectoryToPipelinesParameters(inputName, remotePath, localPath.valueString)
       case (remotePath: WomUnlistedDirectory, localPath) =>
-        Seq(PipelinesApiDirectoryInput(inputName, getPath(remotePath.valueString).get, DefaultPathBuilder.get(localPath.valueString), workingDisk))
+        Seq(
+          PipelinesApiDirectoryInput(inputName,
+                                     getPath(remotePath.valueString).get,
+                                     DefaultPathBuilder.get(localPath.valueString),
+                                     workingDisk
+          )
+        )
       case (remotePath: WomMaybePopulatedFile, localPath) =>
         maybePopulatedFileToPipelinesParameters(inputName, remotePath, localPath.valueString)
       case (remotePath, localPath) =>
-        Seq(PipelinesApiFileInput(inputName, getPath(remotePath.valueString).get, DefaultPathBuilder.get(localPath.valueString), workingDisk))
+        Seq(
+          PipelinesApiFileInput(inputName,
+                                getPath(remotePath.valueString).get,
+                                DefaultPathBuilder.get(localPath.valueString),
+                                workingDisk
+          )
+        )
     }
-  }
 
   // The original implementation recursively finds all non directory files, in V2 we can keep directory as is
   override protected lazy val callInputFiles: Map[FullyQualifiedName, Seq[WomFile]] = jobDescriptor.localInputs map {
     case (key, womFile) =>
-      key -> womFile.collectAsSeq({
+      key -> womFile.collectAsSeq {
         case womFile: WomFile if !inputsToNotLocalize.contains(womFile) => womFile
-      })
+      }
   }
 
   private lazy val gcsTransferLibrary =
     Source.fromInputStream(Thread.currentThread.getContextClassLoader.getResourceAsStream("gcs_transfer.sh")).mkString
 
-  private def gcsLocalizationTransferBundle[T <: PipelinesApiInput](gcsTransferConfiguration: GcsTransferConfiguration)(bucket: String, inputs: NonEmptyList[T]): String = {
+  private def gcsLocalizationTransferBundle[T <: PipelinesApiInput](
+    gcsTransferConfiguration: GcsTransferConfiguration
+  )(bucket: String, inputs: NonEmptyList[T]): String = {
     val project = inputs.head.cloudPath.asInstanceOf[GcsPath].projectId
     val maxAttempts = gcsTransferConfiguration.transferAttempts
 
@@ -78,27 +100,29 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
 
     val filesByContainerParentDirectory = filesWithSameNames.groupBy(_.containerPath.parent.toString)
     // Deduplicate any inputs since parallel localization can't deal with this.
-    val uniqueFilesByContainerParentDirectory = filesByContainerParentDirectory map { case (p, fs) => p -> fs.toSet  }
+    val uniqueFilesByContainerParentDirectory = filesByContainerParentDirectory map { case (p, fs) => p -> fs.toSet }
 
-    val filesWithSameNamesTransferBundles: List[String] = uniqueFilesByContainerParentDirectory.toList map { case (containerParent, filesWithSameParent) =>
-      val arrayIdentifier = s"files_to_localize_" + DigestUtils.md5Hex(bucket + containerParent)
-      val entries = filesWithSameParent.map(_.cloudPath) mkString("\"", "\"\n|  \"", "\"")
+    val filesWithSameNamesTransferBundles: List[String] = uniqueFilesByContainerParentDirectory.toList map {
+      case (containerParent, filesWithSameParent) =>
+        val arrayIdentifier = s"files_to_localize_" + DigestUtils.md5Hex(bucket + containerParent)
+        val entries = filesWithSameParent.map(_.cloudPath) mkString ("\"", "\"\n|  \"", "\"")
 
-      s"""
-         |# Localize files from source bucket '$bucket' to container parent directory '$containerParent'.
-         |$arrayIdentifier=(
-         |  "$project"   # project to use if requester pays
-         |  "$maxAttempts" # max transfer attempts
-         |  "${containerParent.ensureSlashed}" # container parent directory
-         |  $entries
-         |)
-         |
-         |localize_files "$${$arrayIdentifier[@]}"
+        s"""
+           |# Localize files from source bucket '$bucket' to container parent directory '$containerParent'.
+           |$arrayIdentifier=(
+           |  "$project"   # project to use if requester pays
+           |  "$maxAttempts" # max transfer attempts
+           |  "${containerParent.ensureSlashed}" # container parent directory
+           |  $entries
+           |)
+           |
+           |localize_files "$${$arrayIdentifier[@]}"
        """.stripMargin
     }
 
     val filesWithDifferentNamesTransferBundles = filesWithDifferentNames map { f =>
-      val arrayIdentifier = s"singleton_file_to_localize_" + DigestUtils.md5Hex(f.cloudPath.pathAsString + f.containerPath.pathAsString)
+      val arrayIdentifier =
+        s"singleton_file_to_localize_" + DigestUtils.md5Hex(f.cloudPath.pathAsString + f.containerPath.pathAsString)
       s"""
          |# Localize singleton file '${f.cloudPath.pathAsString}' to '${f.containerPath.pathAsString}'.
          |$arrayIdentifier=(
@@ -114,27 +138,31 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
 
     // Only write a transfer bundle for directories if there are directories to be localized. Emptiness isn't a concern
     // for files since there is always at least the command script to be localized.
-    val directoryTransferBundle = if (directories.isEmpty) "" else {
-      val entries = directories flatMap { i => List(i.cloudPath, i.containerPath) } mkString("\"", "\"\n|  \"", "\"")
+    val directoryTransferBundle =
+      if (directories.isEmpty) ""
+      else {
+        val entries = directories flatMap { i => List(i.cloudPath, i.containerPath) } mkString ("\"", "\"\n|  \"", "\"")
 
-      val arrayIdentifier = s"directories_to_localize_" + DigestUtils.md5Hex(bucket)
+        val arrayIdentifier = s"directories_to_localize_" + DigestUtils.md5Hex(bucket)
 
-      s"""
-         |# Directories from source bucket '$bucket'.
-         |$arrayIdentifier=(
-         |  "$project"    # project to use if requester pays
-         |  "$maxAttempts" # max transfer attempts
-         |  $entries
-         |)
-         |
-         |localize_directories "$${$arrayIdentifier[@]}"
+        s"""
+           |# Directories from source bucket '$bucket'.
+           |$arrayIdentifier=(
+           |  "$project"    # project to use if requester pays
+           |  "$maxAttempts" # max transfer attempts
+           |  $entries
+           |)
+           |
+           |localize_directories "$${$arrayIdentifier[@]}"
        """.stripMargin
-    }
+      }
 
     (directoryTransferBundle :: (filesWithSameNamesTransferBundles ++ filesWithDifferentNamesTransferBundles)) mkString "\n\n"
   }
 
-  private def gcsDelocalizationTransferBundle[T <: PipelinesApiOutput](transferConfiguration: GcsTransferConfiguration)(bucket: String, outputs: NonEmptyList[T]): String = {
+  private def gcsDelocalizationTransferBundle[T <: PipelinesApiOutput](
+    transferConfiguration: GcsTransferConfiguration
+  )(bucket: String, outputs: NonEmptyList[T]): String = {
     val project = outputs.head.cloudPath.asInstanceOf[GcsPath].projectId
     val maxAttempts = transferConfiguration.transferAttempts
 
@@ -145,14 +173,16 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
         case _: PipelinesApiDirectoryOutput => "directory" // a primary directory
       }
 
-      val optional = Option(output) collectFirst { case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
+      val optional = Option(output) collectFirst {
+        case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional"
+      } getOrElse "required"
       val contentType = output.contentType.map(_.toString).getOrElse("")
 
       List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
-    } mkString("\"", "\"\n|  \"", "\"")
+    } mkString ("\"", "\"\n|  \"", "\"")
 
-    val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(
-      "parallel_composite_upload_threshold", transferConfiguration.parallelCompositeUploadThreshold)
+    val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions
+      .getOrElse("parallel_composite_upload_threshold", transferConfiguration.parallelCompositeUploadThreshold)
 
     // Use a digest as bucket names can contain characters that are not legal in bash identifiers.
     val arrayIdentifier = s"delocalize_" + DigestUtils.md5Hex(bucket)
@@ -169,17 +199,18 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       """.stripMargin
   }
 
-  private def bracketTransfersWithMessages(activity: String)(transferBody: String): String = {
+  private def bracketTransfersWithMessages(activity: String)(transferBody: String): String =
     List(
       s"timestamped_message '$activity script execution started...'",
       transferBody,
       s"timestamped_message '$activity script execution complete.'"
     ) mkString "\n"
-  }
 
   import mouse.all._
 
-  override def uploadDrsLocalizationManifest(createPipelineParameters: CreatePipelineParameters, cloudPath: Path): Future[Unit] = {
+  override def uploadDrsLocalizationManifest(createPipelineParameters: CreatePipelineParameters,
+                                             cloudPath: Path
+  ): Future[Unit] = {
     val content = generateDrsLocalizerManifest(createPipelineParameters.inputOutputParameters.fileInputParameters)
     if (content.nonEmpty)
       asyncIo.writeAsync(cloudPath, content, Seq(CloudStorageOptions.withMimeType("text/plain")))
@@ -188,16 +219,17 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
   }
 
   private def generateGcsLocalizationScript(inputs: List[PipelinesApiInput],
-                                            referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]])
-                                           (implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+                                            referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]]
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     // Generate a mapping of reference inputs to their mounted paths and a section of the localization script to
     // "faux localize" these reference inputs with symlinks to their locations on mounted reference disks.
     import cromwell.backend.google.pipelines.common.action.ActionUtils.shellEscaped
     val referenceFilesLocalizationScript = {
       val symlinkCreationCommandsOpt = referenceInputsToMountedPathsOpt map { referenceInputsToMountedPaths =>
-        referenceInputsToMountedPaths map {
-          case (input, absolutePathOnRefDisk) =>
-            s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(absolutePathOnRefDisk)} ${shellEscaped(input.containerPath.pathAsString)}"
+        referenceInputsToMountedPaths map { case (input, absolutePathOnRefDisk) =>
+          s"mkdir -p ${shellEscaped(input.containerPath.parent.pathAsString)} && ln -s ${shellEscaped(
+              absolutePathOnRefDisk
+            )} ${shellEscaped(input.containerPath.pathAsString)}"
         }
       }
 
@@ -219,9 +251,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       }
 
     val regularFilesLocalizationScript = {
-      val regularFiles = referenceInputsToMountedPathsOpt.map(maybeReferenceInputsToMountedPaths =>
-        inputs diff maybeReferenceInputsToMountedPaths.keySet.toList
-      ).getOrElse(inputs)
+      val regularFiles = referenceInputsToMountedPathsOpt
+        .map(maybeReferenceInputsToMountedPaths => inputs diff maybeReferenceInputsToMountedPaths.keySet.toList)
+        .getOrElse(inputs)
       if (regularFiles.nonEmpty) {
         val bundleFunction = (gcsLocalizationTransferBundle(gcsTransferConfiguration) _).tupled
         generateGcsTransferScript(regularFiles, bundleFunction)
@@ -240,45 +272,68 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
     combinedLocalizationScript |> bracketTransfersWithMessages("Localization")
   }
 
-  private def generateGcsDelocalizationScript(outputs: List[PipelinesApiOutput])(implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
+  private def generateGcsDelocalizationScript(
+    outputs: List[PipelinesApiOutput]
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): String = {
     val bundleFunction = (gcsDelocalizationTransferBundle(gcsTransferConfiguration) _).tupled
     generateGcsTransferScript(outputs, bundleFunction) |> bracketTransfersWithMessages("Delocalization")
   }
 
-  private def generateGcsTransferScript[T <: PipelinesParameter](items: List[T], bundleFunction: ((String, NonEmptyList[T])) => String): String = {
+  private def generateGcsTransferScript[T <: PipelinesParameter](items: List[T],
+                                                                 bundleFunction: ((String, NonEmptyList[T])) => String
+  ): String = {
     val gcsItems = items collect { case i if i.cloudPath.isInstanceOf[GcsPath] => i }
     groupParametersByGcsBucket(gcsItems) map bundleFunction mkString "\n"
   }
 
   override protected def uploadGcsTransferLibrary(createPipelineParameters: CreatePipelineParameters,
                                                   cloudPath: Path,
-                                                  gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = {
-
+                                                  gcsTransferConfiguration: GcsTransferConfiguration
+  ): Future[Unit] =
     asyncIo.writeAsync(cloudPath, gcsTransferLibrary, Seq(CloudStorageOptions.withMimeType("text/plain")))
-  }
 
   override def uploadGcsLocalizationScript(createPipelineParameters: CreatePipelineParameters,
                                            cloudPath: Path,
                                            transferLibraryContainerPath: Path,
                                            gcsTransferConfiguration: GcsTransferConfiguration,
-                                           referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]]): Future[Unit] = {
-    val content = generateGcsLocalizationScript(createPipelineParameters.inputOutputParameters.fileInputParameters, referenceInputsToMountedPathsOpt)(gcsTransferConfiguration)
-    asyncIo.writeAsync(cloudPath, s"source '$transferLibraryContainerPath'\n\n" + content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+                                           referenceInputsToMountedPathsOpt: Option[Map[PipelinesApiInput, String]]
+  ): Future[Unit] = {
+    val content = generateGcsLocalizationScript(createPipelineParameters.inputOutputParameters.fileInputParameters,
+                                                referenceInputsToMountedPathsOpt
+    )(gcsTransferConfiguration)
+    asyncIo.writeAsync(cloudPath,
+                       s"source '$transferLibraryContainerPath'\n\n" + content,
+                       Seq(CloudStorageOptions.withMimeType("text/plain"))
+    )
   }
 
   override def uploadGcsDelocalizationScript(createPipelineParameters: CreatePipelineParameters,
                                              cloudPath: Path,
                                              transferLibraryContainerPath: Path,
-                                             gcsTransferConfiguration: GcsTransferConfiguration): Future[Unit] = {
-    val content = generateGcsDelocalizationScript(createPipelineParameters.inputOutputParameters.fileOutputParameters)(gcsTransferConfiguration)
-    asyncIo.writeAsync(cloudPath, s"source '$transferLibraryContainerPath'\n\n" + content, Seq(CloudStorageOptions.withMimeType("text/plain")))
+                                             gcsTransferConfiguration: GcsTransferConfiguration
+  ): Future[Unit] = {
+    val content = generateGcsDelocalizationScript(createPipelineParameters.inputOutputParameters.fileOutputParameters)(
+      gcsTransferConfiguration
+    )
+    asyncIo.writeAsync(cloudPath,
+                       s"source '$transferLibraryContainerPath'\n\n" + content,
+                       Seq(CloudStorageOptions.withMimeType("text/plain"))
+    )
   }
 
   // Simply create a PipelinesApiDirectoryOutput in v2 instead of globbing
-  override protected def generateUnlistedDirectoryOutputs(unlistedDirectory: WomUnlistedDirectory, fileEvaluation: FileEvaluation): List[PipelinesApiOutput] = {
+  override protected def generateUnlistedDirectoryOutputs(unlistedDirectory: WomUnlistedDirectory,
+                                                          fileEvaluation: FileEvaluation
+  ): List[PipelinesApiOutput] = {
     val destination = callRootPath.resolve(unlistedDirectory.value.stripPrefix("/"))
     val (relpath, disk) = relativePathAndAttachedDisk(unlistedDirectory.value, runtimeAttributes.disks)
-    val directoryOutput = PipelinesApiDirectoryOutput(makeSafeReferenceName(unlistedDirectory.value), destination, relpath, disk, fileEvaluation.optional, fileEvaluation.secondary)
+    val directoryOutput = PipelinesApiDirectoryOutput(makeSafeReferenceName(unlistedDirectory.value),
+                                                      destination,
+                                                      relpath,
+                                                      disk,
+                                                      fileEvaluation.optional,
+                                                      fileEvaluation.secondary
+    )
     List(directoryOutput)
   }
 
@@ -295,13 +350,27 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
     // We need both the glob directory and the glob list:
     List(
       // The glob directory:
-      PipelinesApiDirectoryOutput(makeSafeReferenceName(globDirectory), gcsGlobDirectoryDestinationPath, DefaultPathBuilder.get(globDirectory), globDirectoryDisk, optional = false, secondary = false),
+      PipelinesApiDirectoryOutput(
+        makeSafeReferenceName(globDirectory),
+        gcsGlobDirectoryDestinationPath,
+        DefaultPathBuilder.get(globDirectory),
+        globDirectoryDisk,
+        optional = false,
+        secondary = false
+      ),
       // The glob list file:
-      PipelinesApiFileOutput(makeSafeReferenceName(globListFile), gcsGlobListFileDestinationPath, DefaultPathBuilder.get(globListFile), globDirectoryDisk, optional = false, secondary = false)
+      PipelinesApiFileOutput(
+        makeSafeReferenceName(globListFile),
+        gcsGlobListFileDestinationPath,
+        DefaultPathBuilder.get(globListFile),
+        globDirectoryDisk,
+        optional = false,
+        secondary = false
+      )
     )
   }
 
-  override def womFileToGcsPath(jesOutputs: Set[PipelinesApiOutput])(womFile: WomFile): WomFile = {
+  override def womFileToGcsPath(jesOutputs: Set[PipelinesApiOutput])(womFile: WomFile): WomFile =
     womFile mapFile { path =>
       jesOutputs collectFirst {
         case jesOutput if jesOutput.name == makeSafeReferenceName(path) =>
@@ -318,65 +387,98 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
           case _: ValidFullGcsPath => path
 
           /*
-            * Strip the prefixes in RuntimeOutputMapping.prefixFilters from the path, one at a time.
-            * For instance
-            * file:///cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt will progressively become
-            *
-            * /cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
-            * bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
-            * call-A/file.txt
-            *
-            * This code is called as part of a path mapper that will be applied to the WOMified cwl.output.json.
-            * The cwl.output.json when it's being read by Cromwell from the bucket still contains local paths
-            * (as they were created by the cwl tool).
-            * In order to keep things working we need to map those local paths to where they were actually delocalized,
-            * which is determined in cromwell.backend.google.pipelines.v2beta.api.Delocalization.
-            */
-          case _ => (callRootPath /
-            RuntimeOutputMapping
+           * Strip the prefixes in RuntimeOutputMapping.prefixFilters from the path, one at a time.
+           * For instance
+           * file:///cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt will progressively become
+           *
+           * /cromwell_root/bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
+           * bucket/workflow_name/6d777414-5ee7-4c60-8b9e-a02ec44c398e/call-A/file.txt
+           * call-A/file.txt
+           *
+           * This code is called as part of a path mapper that will be applied to the WOMified cwl.output.json.
+           * The cwl.output.json when it's being read by Cromwell from the bucket still contains local paths
+           * (as they were created by the cwl tool).
+           * In order to keep things working we need to map those local paths to where they were actually delocalized,
+           * which is determined in cromwell.backend.google.pipelines.v2beta.api.Delocalization.
+           */
+          case _ =>
+            (callRootPath /
+              RuntimeOutputMapping
                 .prefixFilters(workflowPaths.workflowRoot)
-                .foldLeft(path)({
-                  case (newPath, prefix) => newPath.stripPrefix(prefix)
-                })
-            ).pathAsString
+                .foldLeft(path) { case (newPath, prefix) =>
+                  newPath.stripPrefix(prefix)
+                }).pathAsString
         }
       }
     }
-  }
 
-  private def maybePopulatedFileToPipelinesParameters(inputName: String, maybePopulatedFile: WomMaybePopulatedFile, localPath: String) = {
-    val secondaryFiles = maybePopulatedFile.secondaryFiles.flatMap({ secondaryFile =>
-      pipelinesApiInputsFromWomFiles(secondaryFile.valueString, List(secondaryFile), List(relativeLocalizationPath(secondaryFile)), jobDescriptor)
-    })
+  private def maybePopulatedFileToPipelinesParameters(inputName: String,
+                                                      maybePopulatedFile: WomMaybePopulatedFile,
+                                                      localPath: String
+  ) = {
+    val secondaryFiles = maybePopulatedFile.secondaryFiles.flatMap { secondaryFile =>
+      pipelinesApiInputsFromWomFiles(secondaryFile.valueString,
+                                     List(secondaryFile),
+                                     List(relativeLocalizationPath(secondaryFile)),
+                                     jobDescriptor
+      )
+    }
 
-    Seq(PipelinesApiFileInput(inputName, getPath(maybePopulatedFile.valueString).get, DefaultPathBuilder.get(localPath), workingDisk)) ++ secondaryFiles
+    Seq(
+      PipelinesApiFileInput(inputName,
+                            getPath(maybePopulatedFile.valueString).get,
+                            DefaultPathBuilder.get(localPath),
+                            workingDisk
+      )
+    ) ++ secondaryFiles
   }
 
-  private def maybeListedDirectoryToPipelinesParameters(inputName: String, womMaybeListedDirectory: WomMaybeListedDirectory, localPath: String) = womMaybeListedDirectory match {
+  private def maybeListedDirectoryToPipelinesParameters(inputName: String,
+                                                        womMaybeListedDirectory: WomMaybeListedDirectory,
+                                                        localPath: String
+  ) = womMaybeListedDirectory match {
     // If there is a path, simply localize as a directory
     case WomMaybeListedDirectory(Some(path), _, _, _) =>
       List(PipelinesApiDirectoryInput(inputName, getPath(path).get, DefaultPathBuilder.get(localPath), workingDisk))
 
     // If there is a listing, recurse and call pipelinesApiInputsFromWomFiles on all the listed files
     case WomMaybeListedDirectory(_, Some(listing), _, _) if listing.nonEmpty =>
-      listing.flatMap({
+      listing.flatMap {
         case womFile: WomFile if isAdHocFile(womFile) =>
-          pipelinesApiInputsFromWomFiles(makeSafeReferenceName(womFile.valueString), List(womFile), List(fileName(womFile)), jobDescriptor)
+          pipelinesApiInputsFromWomFiles(makeSafeReferenceName(womFile.valueString),
+                                         List(womFile),
+                                         List(fileName(womFile)),
+                                         jobDescriptor
+          )
         case womFile: WomFile =>
-          pipelinesApiInputsFromWomFiles(makeSafeReferenceName(womFile.valueString), List(womFile), List(relativeLocalizationPath(womFile)), jobDescriptor)
-      })
+          pipelinesApiInputsFromWomFiles(makeSafeReferenceName(womFile.valueString),
+                                         List(womFile),
+                                         List(relativeLocalizationPath(womFile)),
+                                         jobDescriptor
+          )
+      }
     case _ => List.empty
   }
 
-  override def generateSingleFileOutputs(womFile: WomSingleFile, fileEvaluation: FileEvaluation): List[PipelinesApiFileOutput] = {
+  override def generateSingleFileOutputs(womFile: WomSingleFile,
+                                         fileEvaluation: FileEvaluation
+  ): List[PipelinesApiFileOutput] = {
     val (relpath, disk) = relativePathAndAttachedDisk(womFile.value, runtimeAttributes.disks)
     // If the file is on a custom mount point, resolve it so that the full mount path will show up in the cloud path
     // For the default one (cromwell_root), the expectation is that it does not appear
-    val mountedPath = if (!disk.mountPoint.isSamePathAs(PipelinesApiWorkingDisk.Default.mountPoint)) disk.mountPoint.resolve(relpath) else relpath
+    val mountedPath =
+      if (!disk.mountPoint.isSamePathAs(PipelinesApiWorkingDisk.Default.mountPoint)) disk.mountPoint.resolve(relpath)
+      else relpath
     // Normalize the local path (to get rid of ".." and "."). Also strip any potential leading / so that it gets appended to the call root
     val normalizedPath = mountedPath.normalize().pathAsString.stripPrefix("/")
     val destination = callRootPath.resolve(normalizedPath)
-    val jesFileOutput = PipelinesApiFileOutput(makeSafeReferenceName(womFile.value), destination, relpath, disk, fileEvaluation.optional, fileEvaluation.secondary)
+    val jesFileOutput = PipelinesApiFileOutput(makeSafeReferenceName(womFile.value),
+                                               destination,
+                                               relpath,
+                                               disk,
+                                               fileEvaluation.optional,
+                                               fileEvaluation.secondary
+    )
     List(jesFileOutput)
   }
 }
@@ -394,10 +496,12 @@ object PipelinesApiAsyncBackendJobExecutionActor {
   //  - There must be at least one '/', followed by some content in the file name.
   // - Or, then, for directories:
   //  - If we got this far, we already have a valid directory path. Allow it to optionally end with a `/` character.
-  private val gcsFilePathMatcher =      "(?s)^gs://([a-zA-Z0-9][^/]+)(/[^/]+)*/[^/]+$".r
+  private val gcsFilePathMatcher = "(?s)^gs://([a-zA-Z0-9][^/]+)(/[^/]+)*/[^/]+$".r
   private val gcsDirectoryPathMatcher = "(?s)^gs://([a-zA-Z0-9][^/]+)(/[^/]+)*/?$".r
 
-  private [v2beta] def groupParametersByGcsBucket[T <: PipelinesParameter](parameters: List[T]): Map[String, NonEmptyList[T]] = {
+  private[v2beta] def groupParametersByGcsBucket[T <: PipelinesParameter](
+    parameters: List[T]
+  ): Map[String, NonEmptyList[T]] =
     parameters.map { param =>
       def pathTypeString = if (param.isFileParameter) "File" else "Directory"
       val regexToUse = if (param.isFileParameter) gcsFilePathMatcher else gcsDirectoryPathMatcher
@@ -406,16 +510,17 @@ object PipelinesApiAsyncBackendJobExecutionActor {
         case regexToUse(bucket) => Map(bucket -> NonEmptyList.of(param))
         case regexToUse(bucket, _) => Map(bucket -> NonEmptyList.of(param))
         case other =>
-          throw new Exception(s"$pathTypeString path '$other' did not match the expected regex: ${regexToUse.pattern.toString}") with NoStackTrace
+          throw new Exception(
+            s"$pathTypeString path '$other' did not match the expected regex: ${regexToUse.pattern.toString}"
+          ) with NoStackTrace
       }
     } combineAll
-  }
 
-  private [v2beta] def generateDrsLocalizerManifest(inputs: List[PipelinesApiInput]): String = {
+  private[v2beta] def generateDrsLocalizerManifest(inputs: List[PipelinesApiInput]): String = {
     val outputStream = new ByteArrayOutputStream()
     val csvPrinter = new CSVPrinter(new OutputStreamWriter(outputStream), CSVFormat.DEFAULT)
-    val drsFileInputs = inputs collect {
-      case drsInput@PipelinesApiFileInput(_, drsPath: DrsPath, _, _) => (drsInput, drsPath)
+    val drsFileInputs = inputs collect { case drsInput @ PipelinesApiFileInput(_, drsPath: DrsPath, _, _) =>
+      (drsInput, drsPath)
     }
     drsFileInputs foreach { case (drsInput, drsPath) =>
       csvPrinter.printRecord(drsPath.pathAsString, drsInput.containerPath.pathAsString)
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiLifecycleActorFactory.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiLifecycleActorFactory.scala
index 9a0f3b7334e..ff43845ccd1 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiLifecycleActorFactory.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiLifecycleActorFactory.scala
@@ -2,18 +2,22 @@ package cromwell.backend.google.pipelines.v2beta
 
 import akka.actor.{ActorRef, Props}
 import cromwell.backend.BackendConfigurationDescriptor
-import cromwell.backend.google.pipelines.common.{PipelinesApiBackendLifecycleActorFactory, PipelinesApiBackendSingletonActor, PipelinesApiConfiguration}
+import cromwell.backend.google.pipelines.common.{
+  PipelinesApiBackendLifecycleActorFactory,
+  PipelinesApiBackendSingletonActor,
+  PipelinesApiConfiguration
+}
 import cromwell.backend.google.pipelines.v2beta.api.request.RequestHandler
 import cromwell.backend.standard.StandardAsyncExecutionActor
 
 class PipelinesApiLifecycleActorFactory(name: String, configurationDescriptor: BackendConfigurationDescriptor)
-  extends PipelinesApiBackendLifecycleActorFactory(name, configurationDescriptor) {
+    extends PipelinesApiBackendLifecycleActorFactory(name, configurationDescriptor) {
   private val genomicsFactory =
     LifeSciencesFactory(
       googleConfig.applicationName,
       papiAttributes.auths.genomics,
       papiAttributes.endpointUrl,
-      papiAttributes.location,
+      papiAttributes.location
     )(papiAttributes.gcsTransferConfiguration)
   override protected val jesConfiguration =
     new PipelinesApiConfiguration(configurationDescriptor, genomicsFactory, googleConfig, papiAttributes)
@@ -22,7 +26,7 @@ class PipelinesApiLifecycleActorFactory(name: String, configurationDescriptor: B
       new RequestHandler(
         googleConfig.applicationName,
         papiAttributes.endpointUrl,
-        papiAttributes.batchRequestTimeoutConfiguration,
+        papiAttributes.batchRequestTimeoutConfiguration
       )
     PipelinesApiBackendSingletonActor.props(
       jesConfiguration.papiAttributes.qps,
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
index 64365fe404f..0ce16f1e4a8 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesParameterConversions.scala
@@ -20,8 +20,9 @@ import simulacrum.typeclass
 
 trait PipelinesParameterConversions {
   implicit val fileInputToParameter: ToParameter[PipelinesApiFileInput] = new ToParameter[PipelinesApiFileInput] {
-    override def toActions(fileInput: PipelinesApiFileInput, mounts: List[Mount])
-                          (implicit retryPolicy: GcsTransferConfiguration): List[Action] = {
+    override def toActions(fileInput: PipelinesApiFileInput, mounts: List[Mount])(implicit
+      retryPolicy: GcsTransferConfiguration
+    ): List[Action] = {
       lazy val config = ConfigFactory.load
 
       val labels = ActionBuilder.parameterLabels(fileInput)
@@ -29,13 +30,12 @@ trait PipelinesParameterConversions {
         case sraPath: SraPath =>
           val sraConfig = config.getConfig("filesystems.sra")
 
-          def getString(key: String): Option[String] = {
+          def getString(key: String): Option[String] =
             if (sraConfig.hasPath(key)) {
               Some(sraConfig.getString(key))
             } else {
               None
             }
-          }
 
           val image = getString("docker-image") getOrElse "fusera/fusera:alpine"
           val (createNgc, ngcArgs) = getString("ngc") match {
@@ -67,31 +67,33 @@ trait PipelinesParameterConversions {
 
   implicit val directoryInputToParameter: ToParameter[PipelinesApiDirectoryInput] =
     new ToParameter[PipelinesApiDirectoryInput] {
-    override def toActions(directoryInput: PipelinesApiDirectoryInput, mounts: List[Mount])
-                          (implicit retryPolicy: GcsTransferConfiguration): List[Action] = {
-      directoryInput.cloudPath match {
-        case _: GcsPath => Nil // GCS paths will be localized with a separate localization script.
-        case _ =>
-          val labels = ActionBuilder.parameterLabels(directoryInput)
-          val describeAction = ActionBuilder.describeParameter(directoryInput, labels)
-          val localizationAction = cloudSdkShellAction(
-            localizeDirectory(directoryInput.cloudPath, directoryInput.containerPath)
-          )(mounts = mounts, labels = labels)
-          List(describeAction, localizationAction)
-      }
+      override def toActions(directoryInput: PipelinesApiDirectoryInput, mounts: List[Mount])(implicit
+        retryPolicy: GcsTransferConfiguration
+      ): List[Action] =
+        directoryInput.cloudPath match {
+          case _: GcsPath => Nil // GCS paths will be localized with a separate localization script.
+          case _ =>
+            val labels = ActionBuilder.parameterLabels(directoryInput)
+            val describeAction = ActionBuilder.describeParameter(directoryInput, labels)
+            val localizationAction = cloudSdkShellAction(
+              localizeDirectory(directoryInput.cloudPath, directoryInput.containerPath)
+            )(mounts = mounts, labels = labels)
+            List(describeAction, localizationAction)
+        }
     }
-  }
 
   implicit val fileOutputToParameter: ToParameter[PipelinesApiFileOutput] = new ToParameter[PipelinesApiFileOutput] {
-    override def toActions(fileOutput: PipelinesApiFileOutput, mounts: List[Mount])
-                          (implicit retryPolicy: GcsTransferConfiguration): List[Action] = {
+    override def toActions(fileOutput: PipelinesApiFileOutput, mounts: List[Mount])(implicit
+      retryPolicy: GcsTransferConfiguration
+    ): List[Action] = {
 
       // If the output is a "secondary file", it actually could be a directory but we won't know before runtime.
       // The fileOrDirectory method will generate a command that can cover both cases
-      lazy val copy = if (fileOutput.secondary)
-        delocalizeFileOrDirectory(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
-      else
-        delocalizeFile(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
+      lazy val copy =
+        if (fileOutput.secondary)
+          delocalizeFileOrDirectory(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
+        else
+          delocalizeFile(fileOutput.containerPath, fileOutput.cloudPath, fileOutput.contentType)
 
       lazy val copyOnlyIfExists = ifExist(fileOutput.containerPath) {
         copy
@@ -106,7 +108,8 @@ trait PipelinesParameterConversions {
         case _ =>
           val describeAction = ActionBuilder.describeParameter(fileOutput, labels)
 
-          val delocalizationAction = cloudSdkShellAction(copyCommand)(mounts = mounts, labels = labels).withAlwaysRun(true)
+          val delocalizationAction =
+            cloudSdkShellAction(copyCommand)(mounts = mounts, labels = labels).withAlwaysRun(true)
           List(describeAction, delocalizationAction)
       }
 
@@ -132,32 +135,34 @@ trait PipelinesParameterConversions {
 
   implicit val directoryOutputToParameter: ToParameter[PipelinesApiDirectoryOutput] =
     new ToParameter[PipelinesApiDirectoryOutput] {
-    override def toActions(directoryOutput: PipelinesApiDirectoryOutput, mounts: List[Mount])
-                          (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = {
-      directoryOutput.cloudPath match {
-        case _: GcsPath => Nil // GCS paths will be delocalized with a separate delocalization script.
-        case _ =>
-          val labels = ActionBuilder.parameterLabels(directoryOutput)
-          val describeAction = ActionBuilder.describeParameter(directoryOutput, labels)
-          val delocalizationAction = cloudSdkShellAction(
-            delocalizeDirectory(directoryOutput.containerPath, directoryOutput.cloudPath, None)
-          )(mounts = mounts, labels = labels).withAlwaysRun(true)
-          List(describeAction, delocalizationAction)
-      }
+      override def toActions(directoryOutput: PipelinesApiDirectoryOutput, mounts: List[Mount])(implicit
+        gcsTransferConfiguration: GcsTransferConfiguration
+      ): List[Action] =
+        directoryOutput.cloudPath match {
+          case _: GcsPath => Nil // GCS paths will be delocalized with a separate delocalization script.
+          case _ =>
+            val labels = ActionBuilder.parameterLabels(directoryOutput)
+            val describeAction = ActionBuilder.describeParameter(directoryOutput, labels)
+            val delocalizationAction = cloudSdkShellAction(
+              delocalizeDirectory(directoryOutput.containerPath, directoryOutput.cloudPath, None)
+            )(mounts = mounts, labels = labels).withAlwaysRun(true)
+            List(describeAction, delocalizationAction)
+        }
     }
-  }
 
   implicit val inputToParameter: ToParameter[PipelinesApiInput] = new ToParameter[PipelinesApiInput] {
-    override def toActions(p: PipelinesApiInput, mounts: List[Mount])
-                          (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = p match {
+    override def toActions(p: PipelinesApiInput, mounts: List[Mount])(implicit
+      gcsTransferConfiguration: GcsTransferConfiguration
+    ): List[Action] = p match {
       case fileInput: PipelinesApiFileInput => fileInputToParameter.toActions(fileInput, mounts)
       case directoryInput: PipelinesApiDirectoryInput => directoryInputToParameter.toActions(directoryInput, mounts)
     }
   }
 
   implicit val outputToParameter: ToParameter[PipelinesApiOutput] = new ToParameter[PipelinesApiOutput] {
-    override def toActions(p: PipelinesApiOutput, mounts: List[Mount])
-                          (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = p match {
+    override def toActions(p: PipelinesApiOutput, mounts: List[Mount])(implicit
+      gcsTransferConfiguration: GcsTransferConfiguration
+    ): List[Action] = p match {
       case fileOutput: PipelinesApiFileOutput => fileOutputToParameter.toActions(fileOutput, mounts)
       case directoryOutput: PipelinesApiDirectoryOutput => directoryOutputToParameter.toActions(directoryOutput, mounts)
     }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala
index 09359428d01..a1e08007b05 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala
@@ -12,14 +12,15 @@ import PipelinesUtilityConversions._
 import scala.language.postfixOps
 
 trait PipelinesUtilityConversions {
-  def toAccelerator(gpuResource: GpuResource): Accelerator = new Accelerator().setCount(gpuResource.gpuCount.value.toLong).setType(gpuResource.gpuType.toString)
+  def toAccelerator(gpuResource: GpuResource): Accelerator =
+    new Accelerator().setCount(gpuResource.gpuCount.value.toLong).setType(gpuResource.gpuType.toString)
   def toMachineType(jobLogger: JobLogger)(attributes: PipelinesApiRuntimeAttributes): String =
     MachineConstraints.machineType(
       memory = attributes.memory,
       cpu = attributes.cpu,
       cpuPlatformOption = attributes.cpuPlatform,
       googleLegacyMachineSelection = attributes.googleLegacyMachineSelection,
-      jobLogger = jobLogger,
+      jobLogger = jobLogger
     )
   def toMounts(disks: Seq[PipelinesApiAttachedDisk]): List[Mount] = disks.map(toMount).toList
   def toDisks(disks: Seq[PipelinesApiAttachedDisk]): List[Disk] = disks.map(toDisk).toList
@@ -57,7 +58,9 @@ trait PipelinesUtilityConversions {
     // There are both "Started pulling" and "Stopped pulling" events but these are confusing for metadata, especially on the
     // timing diagram. Create a single "Pulling <docker image>" grouping to absorb these events.
     def groupingFromPull: Option[String] = List("Started", "Stopped") flatMap { k =>
-      Option(event.getDescription) collect { case d if d.startsWith(s"$k pulling") => "Pulling" + d.substring(s"$k pulling".length)}
+      Option(event.getDescription) collect {
+        case d if d.startsWith(s"$k pulling") => "Pulling" + d.substring(s"$k pulling".length)
+      }
     } headOption
 
     // See WX-1137. ContainerStoppedEvent descriptions contain the stderr, which may include 4-byte unicode
@@ -85,7 +88,7 @@ trait PipelinesUtilityConversions {
 object PipelinesUtilityConversions {
 
   implicit class EnhancedEvent(val event: Event) extends AnyVal {
-    def getActionId: Option[Integer] = {
+    def getActionId: Option[Integer] =
       if (event.getContainerKilled != null) {
         Option(event.getContainerKilled.getActionId)
       } else if (event.getContainerStarted != null) {
@@ -97,12 +100,10 @@ object PipelinesUtilityConversions {
       } else {
         None
       }
-    }
   }
 
   lazy val utf8mb4Regex = "[\\x{10000}-\\x{FFFFF}]"
-  lazy val utf8mb3Replacement = "\uFFFD"  // This is the standard char for replacing invalid/unknown unicode chars
-  def cleanUtf8mb4(in: String): String = {
+  lazy val utf8mb3Replacement = "\uFFFD" // This is the standard char for replacing invalid/unknown unicode chars
+  def cleanUtf8mb4(in: String): String =
     in.replaceAll(utf8mb4Regex, utf8mb3Replacement)
-  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/ActionBuilder.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/ActionBuilder.scala
index 8a1a3bfc97e..a2cbb69980f 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/ActionBuilder.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/ActionBuilder.scala
@@ -20,6 +20,7 @@ import scala.concurrent.duration._
   */
 object ActionBuilder {
   implicit class EnhancedAction(val action: Action) extends AnyVal {
+
     /**
       * Only for use with docker images KNOWN to not have entrypoints already set,
       * or used with accompanying call to setEntrypoint("non-empty-string").
@@ -33,7 +34,7 @@ object ActionBuilder {
       * Useful for any externally provided images that _might_ have entrypoints already set. This is a workaround for
       * the issue detailed in BA-6406. See underlying google issue in that ticket for more info.
       */
-    def withEntrypointCommand(command: String*): Action = {
+    def withEntrypointCommand(command: String*): Action =
       action
         .setEntrypoint(command.headOption.orNull)
         .setCommands(
@@ -42,7 +43,6 @@ object ActionBuilder {
             .map(_.asJava)
             .orNull
         )
-    }
 
     def withMounts(mounts: List[Mount]): Action = action.setMounts(mounts.asJava)
     def withLabels(labels: Map[String, String]): Action = action.setLabels(labels.asJava)
@@ -54,8 +54,10 @@ object ActionBuilder {
     def withRunInBackground(runInBackground: Boolean): Action = action.setRunInBackground(runInBackground)
     def withAlwaysRun(alwaysRun: Boolean): Action = action.setAlwaysRun(alwaysRun)
     def withEnableFuse(enableFuse: Boolean): Action = action.setEnableFuse(enableFuse)
-    def withPublishExposedPorts(publishExposedPorts: Boolean): Action = action.setPublishExposedPorts(publishExposedPorts)
-    def withDisableImagePrefetch(disableImagePrefetch: Boolean): Action = action.setDisableImagePrefetch(disableImagePrefetch)
+    def withPublishExposedPorts(publishExposedPorts: Boolean): Action =
+      action.setPublishExposedPorts(publishExposedPorts)
+    def withDisableImagePrefetch(disableImagePrefetch: Boolean): Action =
+      action.setDisableImagePrefetch(disableImagePrefetch)
 
     def scalaLabels: Map[String, String] = {
       val list = for {
@@ -71,8 +73,9 @@ object ActionBuilder {
   def withImage(image: String): Action = new Action()
     .setImageUri(image)
 
-  def monitoringImageScriptAction(cloudPath: Path, containerPath: Path, mounts: List[Mount])
-                                 (implicit gcsTransferConfiguration: GcsTransferConfiguration): Action = {
+  def monitoringImageScriptAction(cloudPath: Path, containerPath: Path, mounts: List[Mount])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): Action = {
     val command = ActionCommands.localizeFile(cloudPath, containerPath)
     val labels = Map(Key.Tag -> Value.Localization)
     ActionBuilder.cloudSdkShellAction(command)(mounts = mounts, labels = labels)
@@ -81,8 +84,8 @@ object ActionBuilder {
   def backgroundAction(image: String,
                        command: List[String],
                        environment: Map[String, String],
-                       mounts: List[Mount],
-                      ): Action = {
+                       mounts: List[Mount]
+  ): Action =
     new Action()
       .setImageUri(image)
       .withEntrypointCommand(command: _*)
@@ -92,7 +95,6 @@ object ActionBuilder {
       .setEnvironment(environment.asJava)
       .withLabels(Map(Key.Tag -> Value.Monitoring))
       .setPidNamespace(backgroundActionPidNamespace)
-  }
 
   def terminateBackgroundActionsAction(): Action =
     cloudSdkShellAction(terminateAllBackgroundActionsCommand)(labels = Map(Key.Tag -> Value.Monitoring))
@@ -110,13 +112,16 @@ object ActionBuilder {
                  mounts: List[Mount],
                  jobShell: String,
                  privateDockerKeyAndToken: Option[CreatePipelineDockerKeyAndToken],
-                 fuseEnabled: Boolean): Action = {
+                 fuseEnabled: Boolean
+  ): Action = {
 
     val dockerImageIdentifier = DockerImageIdentifier.fromString(docker)
 
     val secret = for {
       imageId <- dockerImageIdentifier.toOption
-      if DockerHub.isValidDockerHubHost(imageId.host) // This token only works for Docker Hub and not other repositories.
+      if DockerHub.isValidDockerHubHost(
+        imageId.host
+      ) // This token only works for Docker Hub and not other repositories.
       keyAndToken <- privateDockerKeyAndToken
       s = new Secret().setKeyName(keyAndToken.key).setCipherText(keyAndToken.encryptedToken)
     } yield s
@@ -131,16 +136,16 @@ object ActionBuilder {
       .setEnableFuse(fuseEnabled)
   }
 
-  def checkForMemoryRetryAction(retryLookupKeys: List[String], mounts: List[Mount]): Action = {
+  def checkForMemoryRetryAction(retryLookupKeys: List[String], mounts: List[Mount]): Action =
     cloudSdkShellAction(ActionCommands.checkIfStderrContainsRetryKeys(retryLookupKeys))(
       mounts = mounts,
       labels = Map(Key.Tag -> Value.RetryWithMoreMemory)
     ).withAlwaysRun(true)
-  }
 
   def cloudSdkShellAction(shellCommand: String)(mounts: List[Mount] = List.empty,
                                                 labels: Map[String, String] = Map.empty,
-                                                timeout: Duration = Duration.Inf): Action =
+                                                timeout: Duration = Duration.Inf
+  ): Action =
     cloudSdkAction
       .withEntrypointCommand(
         "/bin/sh",
@@ -157,7 +162,7 @@ object ActionBuilder {
     * @param pipelinesParameter Input or output parameter to label.
     * @return The labels.
     */
-  def parameterLabels(pipelinesParameter: PipelinesParameter): Map[String, String] = {
+  def parameterLabels(pipelinesParameter: PipelinesParameter): Map[String, String] =
     pipelinesParameter match {
       case _: PipelinesApiInput =>
         Map(
@@ -170,7 +175,6 @@ object ActionBuilder {
           Key.OutputName -> pipelinesParameter.name
         )
     }
-  }
 
   /**
     * Surrounds the list of Actions with a pair of starting and done Actions.
@@ -181,8 +185,9 @@ object ActionBuilder {
     * @param actions           The list of Actions to surround.
     * @return The starting Action, the passed in list, and then a done Action.
     */
-  def annotateTimestampedActions(description: String, loggingLabelValue: String, isAlwaysRun: Boolean = false)
-                                (actions: List[Action]): List[Action] = {
+  def annotateTimestampedActions(description: String, loggingLabelValue: String, isAlwaysRun: Boolean = false)(
+    actions: List[Action]
+  ): List[Action] = {
     val labels = Map(Key.Logging -> loggingLabelValue)
     val starting = List(logTimestampedAction(s"Starting $description.", labels).withAlwaysRun(isAlwaysRun))
     val done = List(logTimestampedAction(s"Done $description.", labels).withAlwaysRun(isAlwaysRun))
@@ -190,31 +195,28 @@ object ActionBuilder {
   }
 
   /** Creates an Action that describes the parameter localization or delocalization. */
-  def describeParameter(pipelinesParameter: PipelinesParameter,
-                        actionLabels: Map[String, String]): Action = {
+  def describeParameter(pipelinesParameter: PipelinesParameter, actionLabels: Map[String, String]): Action =
     pipelinesParameter match {
       case _: PipelinesApiInput =>
         val message = "Localizing input %s -> %s".format(
           shellEscaped(pipelinesParameter.cloudPath),
-          shellEscaped(pipelinesParameter.containerPath),
+          shellEscaped(pipelinesParameter.containerPath)
         )
         ActionBuilder.logTimestampedAction(message, actionLabels)
       case _: PipelinesApiOutput =>
         val message = "Delocalizing output %s -> %s".format(
           shellEscaped(pipelinesParameter.containerPath),
-          shellEscaped(pipelinesParameter.cloudPath),
+          shellEscaped(pipelinesParameter.cloudPath)
         )
         ActionBuilder.logTimestampedAction(message, actionLabels).withAlwaysRun(true)
     }
-  }
 
   /** Creates an Action that logs the docker command for the passed in action. */
-  def describeDocker(description: String, action: Action): Action = {
+  def describeDocker(description: String, action: Action): Action =
     ActionBuilder.logTimestampedAction(
       s"Running $description: ${ActionBuilder.toDockerRun(action)}",
       action.scalaLabels
     )
-  }
 
   def timestampedMessage(message: String): String =
     s"""printf '%s %s\\n' "$$(date -u '+%Y/%m/%d %H:%M:%S')" ${shellEscaped(message)}"""
@@ -230,8 +232,7 @@ object ActionBuilder {
     * @param actionLabels Labels from the original Action to modify and apply to the logging Action.
     * @return A new Action that will log the time and print the message.
     */
-  private def logTimestampedAction(message: String,
-                                   actionLabels: Map[String, String]): Action = {
+  private def logTimestampedAction(message: String, actionLabels: Map[String, String]): Action =
     // Uses the cloudSdk image as that image will be used for other operations as well.
     cloudSdkShellAction(
       timestampedMessage(message)
@@ -242,7 +243,6 @@ object ActionBuilder {
       },
       timeout = 300.seconds
     )
-  }
 
   /** Converts an Action to a `docker run ...` command runnable in the shell. */
   private[api] def toDockerRun(action: Action): String = {
@@ -263,7 +263,8 @@ object ActionBuilder {
     val environmentArgs: String = Option(action.getEnvironment) match {
       case Some(environment) =>
         environment.asScala map {
-          case (key, value) if Option(key).isDefined && Option(value).isDefined => s" -e ${shellEscaped(s"$key:$value")}"
+          case (key, value) if Option(key).isDefined && Option(value).isDefined =>
+            s" -e ${shellEscaped(s"$key:$value")}"
           case (key, _) if Option(key).isDefined => s" -e ${shellEscaped(key)}"
           case _ => ""
         } mkString ""
@@ -307,15 +308,15 @@ object ActionBuilder {
     val publishExposedPortsFlag: String = if (action.getPublishExposedPorts) " -P" else ""
 
     Array("docker run",
-      nameArg,
-      mountArgs,
-      environmentArgs,
-      pidNamespaceArg,
-      publishExposedPortsFlag,
-      portMappingArgs,
-      entrypointArg,
-      imageArg,
-      commandArgs,
+          nameArg,
+          mountArgs,
+          environmentArgs,
+          pidNamespaceArg,
+          publishExposedPortsFlag,
+          portMappingArgs,
+          entrypointArg,
+          imageArg,
+          commandArgs
     ).mkString
   }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/CheckpointingAction.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/CheckpointingAction.scala
index 658ea88ffff..fca9b0c6f9b 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/CheckpointingAction.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/CheckpointingAction.scala
@@ -6,19 +6,21 @@ import cromwell.backend.google.pipelines.common.action.ActionUtils
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.CreatePipelineParameters
 
 trait CheckpointingAction {
-  def checkpointingSetupActions(createPipelineParameters: CreatePipelineParameters,
-                                mounts: List[Mount]
-                            ): List[Action] =
+  def checkpointingSetupActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount]): List[Action] =
     createPipelineParameters.runtimeAttributes.checkpointFilename map { checkpointFilename =>
       val checkpointingImage = ActionUtils.CloudSdkImage
-      val checkpointingCommand = createPipelineParameters.checkpointingConfiguration.checkpointingCommand(checkpointFilename, ActionCommands.multiLineBinBashCommand)
+      val checkpointingCommand =
+        createPipelineParameters.checkpointingConfiguration.checkpointingCommand(checkpointFilename,
+                                                                                 ActionCommands.multiLineBinBashCommand
+        )
       val checkpointingEnvironment = Map.empty[String, String]
 
       // Initial sync from cloud:
       val initialCheckpointSyncAction = ActionBuilder.cloudSdkShellAction(
         createPipelineParameters.checkpointingConfiguration.localizePreviousCheckpointCommand(checkpointFilename)
       )(mounts = mounts)
-      val describeInitialCheckpointingSyncAction = ActionBuilder.describeDocker("initial checkpointing sync", initialCheckpointSyncAction)
+      val describeInitialCheckpointingSyncAction =
+        ActionBuilder.describeDocker("initial checkpointing sync", initialCheckpointSyncAction)
 
       // Background upload action:
       val backgroundCheckpointingAction = ActionBuilder.backgroundAction(
@@ -27,20 +29,28 @@ trait CheckpointingAction {
         environment = checkpointingEnvironment,
         mounts = mounts
       )
-      val describeBackgroundCheckpointingAction = ActionBuilder.describeDocker("begin checkpointing background action", backgroundCheckpointingAction)
+      val describeBackgroundCheckpointingAction =
+        ActionBuilder.describeDocker("begin checkpointing background action", backgroundCheckpointingAction)
 
-      List(describeInitialCheckpointingSyncAction, initialCheckpointSyncAction, describeBackgroundCheckpointingAction, backgroundCheckpointingAction)
-    } getOrElse(Nil)
+      List(describeInitialCheckpointingSyncAction,
+           initialCheckpointSyncAction,
+           describeBackgroundCheckpointingAction,
+           backgroundCheckpointingAction
+      )
+    } getOrElse Nil
 
-  def checkpointingShutdownActions(createPipelineParameters: CreatePipelineParameters): List[Action] = {
+  def checkpointingShutdownActions(createPipelineParameters: CreatePipelineParameters): List[Action] =
     createPipelineParameters.runtimeAttributes.checkpointFilename map { checkpointFilename =>
       val terminationAction = ActionBuilder.terminateBackgroundActionsAction()
       val describeTerminationAction = ActionBuilder.describeDocker("terminate checkpointing action", terminationAction)
 
-      val deleteCheckpointAction = ActionBuilder.gcsFileDeletionAction(createPipelineParameters.checkpointingConfiguration.checkpointFileCloud(checkpointFilename))
-      val deleteTmpCheckpointAction = ActionBuilder.gcsFileDeletionAction(createPipelineParameters.checkpointingConfiguration.tmpCheckpointFileCloud(checkpointFilename))
+      val deleteCheckpointAction = ActionBuilder.gcsFileDeletionAction(
+        createPipelineParameters.checkpointingConfiguration.checkpointFileCloud(checkpointFilename)
+      )
+      val deleteTmpCheckpointAction = ActionBuilder.gcsFileDeletionAction(
+        createPipelineParameters.checkpointingConfiguration.tmpCheckpointFileCloud(checkpointFilename)
+      )
 
       List(describeTerminationAction, terminationAction, deleteCheckpointAction, deleteTmpCheckpointAction)
-    } getOrElse(Nil)
-  }
+    } getOrElse Nil
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Delocalization.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Delocalization.scala
index 8fc0d81cff1..4d8416c46af 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Delocalization.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Delocalization.scala
@@ -23,39 +23,50 @@ import scala.concurrent.duration._
 
 trait Delocalization {
 
-  private def delocalizeLogsAction(gcsLogPath: Path)(implicit gcsTransferConfiguration: GcsTransferConfiguration) = {
+  private def delocalizeLogsAction(gcsLogPath: Path)(implicit gcsTransferConfiguration: GcsTransferConfiguration) =
     cloudSdkShellAction(
-    delocalizeDirectory(DefaultPathBuilder.build(logsRoot).get, gcsLogPath, PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType)
+      delocalizeDirectory(DefaultPathBuilder.build(logsRoot).get,
+                          gcsLogPath,
+                          PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType
+      )
     )(labels = Map(Key.Tag -> Value.Delocalization)).withAlwaysRun(true)
-  }
 
   // Used for the final copy of the logs to make sure we have the most up to date version before terminating the job
-  private def copyAggregatedLogToLegacyPath(gcsLegacyLogPath: Path)
-                                           (implicit gcsTransferConfiguration: GcsTransferConfiguration): Action = {
+  private def copyAggregatedLogToLegacyPath(
+    gcsLegacyLogPath: Path
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): Action =
     cloudSdkShellAction(
-      delocalizeFileTo(DefaultPathBuilder.build(aggregatedLog).get, gcsLegacyLogPath, PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType)
+      delocalizeFileTo(DefaultPathBuilder.build(aggregatedLog).get,
+                       gcsLegacyLogPath,
+                       PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType
+      )
     )(labels = Map(Key.Tag -> Value.Delocalization)).withAlwaysRun(true)
-  }
 
   // Periodically copies the logs out to GCS
-  private def copyAggregatedLogToLegacyPathPeriodic(gcsLegacyLogPath: Path)
-                                                   (implicit gcsTransferConfiguration: GcsTransferConfiguration): Action = {
+  private def copyAggregatedLogToLegacyPathPeriodic(
+    gcsLegacyLogPath: Path
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): Action =
     cloudSdkShellAction(
-      every(30.seconds) { delocalizeFileTo(DefaultPathBuilder.build(aggregatedLog).get, gcsLegacyLogPath, PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType) }
+      every(30.seconds) {
+        delocalizeFileTo(DefaultPathBuilder.build(aggregatedLog).get,
+                         gcsLegacyLogPath,
+                         PipelinesApiAsyncBackendJobExecutionActor.plainTextContentType
+        )
+      }
     )(labels = Map(Key.Tag -> Value.Background)).withRunInBackground(true)
-  }
 
   private def runtimeOutputExtractorAction(containerCallRoot: String,
-                                    outputFile: String,
-                                    mounts: List[Mount],
-                                    womOutputRuntimeExtractor: WomOutputRuntimeExtractor): Action = {
+                                           outputFile: String,
+                                           mounts: List[Mount],
+                                           womOutputRuntimeExtractor: WomOutputRuntimeExtractor
+  ): Action = {
     val commands = List(
       "-c",
       // Create the directory where the fofn will be written
       s"mkdir -p $$(dirname $outputFile) && " +
-      s"cd $containerCallRoot && " +
-      """echo "Runtime output files to be delocalized:" && """ +
-      s"${womOutputRuntimeExtractor.command} | tee $outputFile"
+        s"cd $containerCallRoot && " +
+        """echo "Runtime output files to be delocalized:" && """ +
+        s"${womOutputRuntimeExtractor.command} | tee $outputFile"
     )
 
     ActionBuilder
@@ -68,7 +79,9 @@ trait Delocalization {
       .withLabels(Map(Key.Tag -> Value.Delocalization))
   }
 
-  private def delocalizeRuntimeOutputsScript(fofnPath: String, workflowRoot: Path, cloudCallRoot: Path)(implicit gcsTransferConfiguration: GcsTransferConfiguration) = {
+  private def delocalizeRuntimeOutputsScript(fofnPath: String, workflowRoot: Path, cloudCallRoot: Path)(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ) = {
     val gsutilCommand: String => String = { flag =>
       s"""rm -f $$HOME/.config/gcloud/gce && gsutil -m $flag cp -r $$line "${cloudCallRoot.pathAsString.ensureSlashed}$$gcs_path""""
     }
@@ -99,13 +112,20 @@ trait Delocalization {
         |fi""".stripMargin
   }
 
-  private def delocalizeRuntimeOutputsAction(cloudCallRoot: Path, inputFile: String, workflowRoot: Path, mounts: List[Mount])(implicit gcsTransferConfiguration: GcsTransferConfiguration): Action = {
+  private def delocalizeRuntimeOutputsAction(cloudCallRoot: Path,
+                                             inputFile: String,
+                                             workflowRoot: Path,
+                                             mounts: List[Mount]
+  )(implicit gcsTransferConfiguration: GcsTransferConfiguration): Action = {
     val command = multiLineCommand(delocalizeRuntimeOutputsScript(inputFile, workflowRoot, cloudCallRoot))
-    ActionBuilder.cloudSdkShellAction(command)(mounts, labels = Map(Key.Tag -> Value.Delocalization)).withDisableImagePrefetch(true)
+    ActionBuilder
+      .cloudSdkShellAction(command)(mounts, labels = Map(Key.Tag -> Value.Delocalization))
+      .withDisableImagePrefetch(true)
   }
 
-  def deLocalizeActions(createPipelineParameters: CreatePipelineParameters,
-                        mounts: List[Mount])(implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = {
+  def deLocalizeActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): List[Action] = {
     val cloudCallRoot = createPipelineParameters.cloudCallRoot
     val callExecutionContainerRoot = createPipelineParameters.commandScriptContainerPath.parent
 
@@ -116,21 +136,31 @@ trait Delocalization {
      * Ideally temporaryFofnForRuntimeOutputFiles should be somewhere else than the execution directory (we could mount anther directory)
      * However because it runs after everything else there's no risk of polluting the task's results and the random ID ensures we don't override anything
      */
-    val temporaryFofnDirectoryForRuntimeOutputFiles = callExecutionContainerRoot.pathAsString.ensureSlashed + UUID.randomUUID().toString.split("-")(0)
+    val temporaryFofnDirectoryForRuntimeOutputFiles =
+      callExecutionContainerRoot.pathAsString.ensureSlashed + UUID.randomUUID().toString.split("-")(0)
     val temporaryFofnForRuntimeOutputFiles = temporaryFofnDirectoryForRuntimeOutputFiles + "/runtime_output_files.txt"
 
     val runtimeExtractionActions = createPipelineParameters.womOutputRuntimeExtractor.toList flatMap { extractor =>
-      List (
-        runtimeOutputExtractorAction(callExecutionContainerRoot.pathAsString, temporaryFofnForRuntimeOutputFiles, mounts, extractor),
-        delocalizeRuntimeOutputsAction(cloudCallRoot, temporaryFofnForRuntimeOutputFiles, createPipelineParameters.cloudWorkflowRoot, mounts)
+      List(
+        runtimeOutputExtractorAction(callExecutionContainerRoot.pathAsString,
+                                     temporaryFofnForRuntimeOutputFiles,
+                                     mounts,
+                                     extractor
+        ),
+        delocalizeRuntimeOutputsAction(cloudCallRoot,
+                                       temporaryFofnForRuntimeOutputFiles,
+                                       createPipelineParameters.cloudWorkflowRoot,
+                                       mounts
+        )
       )
     }
 
-    val gcsDelocalizationContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
+    val gcsDelocalizationContainerPath =
+      createPipelineParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
 
     val delocalizationLabel = Map(Key.Tag -> Value.Delocalization)
-    val runGcsDelocalizationScript: Action = cloudSdkShellAction(
-      s"/bin/bash $gcsDelocalizationContainerPath")(mounts = mounts, labels = delocalizationLabel)
+    val runGcsDelocalizationScript: Action =
+      cloudSdkShellAction(s"/bin/bash $gcsDelocalizationContainerPath")(mounts = mounts, labels = delocalizationLabel)
 
     ActionBuilder.annotateTimestampedActions("delocalization", Value.Delocalization)(
       runGcsDelocalizationScript ::
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Deserialization.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Deserialization.scala
index 54de52e74be..8699983ca63 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Deserialization.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Deserialization.scala
@@ -23,9 +23,10 @@ import scala.util.{Failure, Success, Try}
   * for which there's an existing class.
   * This class provides implicit functions to deserialize those map to their proper type.
   */
-private [api] object Deserialization {
+private[api] object Deserialization {
 
   implicit class OperationDeserialization(val operation: Operation) extends AnyVal {
+
     /**
       * Deserializes the events to com.google.api.services.genomics.v2beta.model.Event
       *
@@ -35,11 +36,12 @@ private [api] object Deserialization {
     def events: ErrorOr[List[Event]] = {
       val eventsErrorOrOption = for {
         eventsMap <- metadata.get("events")
-        eventsErrorOr <- Option(eventsMap
-          .asInstanceOf[JArrayList[JMap[String, Object]]]
-          .asScala
-          .toList
-          .traverse[ErrorOr, Event](deserializeTo[Event](_).toErrorOr)
+        eventsErrorOr <- Option(
+          eventsMap
+            .asInstanceOf[JArrayList[JMap[String, Object]]]
+            .asScala
+            .toList
+            .traverse[ErrorOr, Event](deserializeTo[Event](_).toErrorOr)
         )
       } yield eventsErrorOr
       eventsErrorOrOption.getOrElse(Nil.validNel)
@@ -48,11 +50,10 @@ private [api] object Deserialization {
     /**
       * Deserializes the pipeline to com.google.api.services.genomics.v2beta.model.Pipeline
       */
-    def pipeline: Option[Try[Pipeline]] = {
+    def pipeline: Option[Try[Pipeline]] =
       metadata
         .get("pipeline")
         .map(_.asInstanceOf[JMap[String, Object]] |> deserializeTo[Pipeline])
-    }
 
     // If there's a WorkerAssignedEvent it means a VM was created - which we consider as the job started
     // Note that the VM might still be booting
@@ -70,19 +71,23 @@ private [api] object Deserialization {
   /**
     * Deserializes a java.util.Map[String, Object] to an instance of T
     */
-  private [api] def deserializeTo[T <: GenericJson](attributes: JMap[String, Object])(implicit tag: ClassTag[T]): Try[T] = Try {
+  private[api] def deserializeTo[T <: GenericJson](
+    attributes: JMap[String, Object]
+  )(implicit tag: ClassTag[T]): Try[T] = Try {
     // Create a new instance, because it's a GenericJson there's always a 0-arg constructor
     val newT = tag.runtimeClass.asInstanceOf[Class[T]].getConstructor().newInstance()
 
     // Optionally returns the field with the given name
     def field(name: String) = Option(newT.getClassInfo.getField(name))
 
-    def handleMap(key: String, value: Object) = {
+    def handleMap(key: String, value: Object) =
       (field(key), value) match {
         // If the serialized value is a list, we need to check if its elements need to be deserialized
         case (Some(f), list: java.util.List[java.util.Map[String, Object]] @unchecked) =>
           // Try to get the generic type of the declared field (the field should have a list type since the value is a list)
-          Try(f.getGenericType.asInstanceOf[ParameterizedType].getActualTypeArguments.toList.head.asInstanceOf[Class[_]]) match {
+          Try(
+            f.getGenericType.asInstanceOf[ParameterizedType].getActualTypeArguments.toList.head.asInstanceOf[Class[_]]
+          ) match {
             // If we can get it and its a GenericJson, it means we need to deserialize the elements to their proper type
             case Success(genericListType) if classOf[GenericJson].isAssignableFrom(genericListType) =>
               // The get throws at the first error and hence doesn't aggregate the errors but it seems
@@ -101,7 +106,8 @@ private [api] object Deserialization {
         // If it can't be assigned and the value is a map, it is very likely that the field "key" of T is of some type U
         // but has been deserialized to a Map[String, Object]. In this case we retrieve the type U from the field and recurse
         // to deserialize properly
-        case (Some(f), map: java.util.Map[String, Object] @unchecked) if classOf[GenericJson].isAssignableFrom(f.getType) =>
+        case (Some(f), map: java.util.Map[String, Object] @unchecked)
+            if classOf[GenericJson].isAssignableFrom(f.getType) =>
           // This whole function is wrapped in a try so just .get to throw
           val deserializedInnerAttribute = deserializeTo(map)(ClassTag[GenericJson](f.getType)).get
           newT.set(key, deserializedInnerAttribute)
@@ -118,7 +124,6 @@ private [api] object Deserialization {
         // and losing properly deserialized attributes
         case _ =>
       }
-    }
 
     // Go over the map entries and use the "set" method of GenericJson to set the attributes.
     Option(attributes).map(_.asScala).getOrElse(Map.empty).foreach((handleMap _).tupled)
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
index 3b470b9096b..5779c42cbeb 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/Localization.scala
@@ -11,55 +11,69 @@ import cromwell.backend.google.pipelines.common.PipelinesApiJobPaths._
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.CreatePipelineParameters
 import cromwell.backend.google.pipelines.v2beta.PipelinesConversions._
 import cromwell.backend.google.pipelines.v2beta.ToParameter.ops._
-import cromwell.backend.google.pipelines.v2beta.api.ActionBuilder.{EnhancedAction, cloudSdkShellAction}
+import cromwell.backend.google.pipelines.v2beta.api.ActionBuilder.{cloudSdkShellAction, EnhancedAction}
 import cromwell.core.path.Path
 import cromwell.filesystems.drs.DrsPath
 
 import scala.jdk.CollectionConverters._
 
-
 trait Localization {
-  def localizeActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount])
-                     (implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = {
+  def localizeActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): List[Action] = {
     val localizationLabel = Map(Key.Tag -> Value.Localization)
 
-    val gcsTransferLibraryContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(GcsTransferLibraryName)
-    val localizeGcsTransferLibrary = cloudSdkShellAction(localizeFile(
-      cloudPath = createPipelineParameters.cloudCallRoot / GcsTransferLibraryName,
-      containerPath = gcsTransferLibraryContainerPath))(mounts = mounts, labels = localizationLabel)
-
-    val gcsLocalizationContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(GcsLocalizationScriptName)
-    val localizeGcsLocalizationScript = cloudSdkShellAction(localizeFile(
-      cloudPath = createPipelineParameters.cloudCallRoot / GcsLocalizationScriptName,
-      containerPath = gcsLocalizationContainerPath))(mounts = mounts, labels = localizationLabel)
-
-    val gcsDelocalizationContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
-    val localizeGcsDelocalizationScript = cloudSdkShellAction(localizeFile(
-      cloudPath = createPipelineParameters.cloudCallRoot / GcsDelocalizationScriptName,
-      containerPath = gcsDelocalizationContainerPath))(mounts = mounts, labels = localizationLabel)
-
-    val runGcsLocalizationScript = cloudSdkShellAction(
-      s"/bin/bash $gcsLocalizationContainerPath")(mounts = mounts, labels = localizationLabel)
+    val gcsTransferLibraryContainerPath =
+      createPipelineParameters.commandScriptContainerPath.sibling(GcsTransferLibraryName)
+    val localizeGcsTransferLibrary = cloudSdkShellAction(
+      localizeFile(cloudPath = createPipelineParameters.cloudCallRoot / GcsTransferLibraryName,
+                   containerPath = gcsTransferLibraryContainerPath
+      )
+    )(mounts = mounts, labels = localizationLabel)
+
+    val gcsLocalizationContainerPath =
+      createPipelineParameters.commandScriptContainerPath.sibling(GcsLocalizationScriptName)
+    val localizeGcsLocalizationScript = cloudSdkShellAction(
+      localizeFile(cloudPath = createPipelineParameters.cloudCallRoot / GcsLocalizationScriptName,
+                   containerPath = gcsLocalizationContainerPath
+      )
+    )(mounts = mounts, labels = localizationLabel)
+
+    val gcsDelocalizationContainerPath =
+      createPipelineParameters.commandScriptContainerPath.sibling(GcsDelocalizationScriptName)
+    val localizeGcsDelocalizationScript = cloudSdkShellAction(
+      localizeFile(cloudPath = createPipelineParameters.cloudCallRoot / GcsDelocalizationScriptName,
+                   containerPath = gcsDelocalizationContainerPath
+      )
+    )(mounts = mounts, labels = localizationLabel)
+
+    val runGcsLocalizationScript =
+      cloudSdkShellAction(s"/bin/bash $gcsLocalizationContainerPath")(mounts = mounts, labels = localizationLabel)
 
     val drsInputs: List[DrsPath] = createPipelineParameters.inputOutputParameters.fileInputParameters.collect {
       case PipelinesApiFileInput(_, drsPath: DrsPath, _, _) => drsPath
     }
 
     val drsLocalizationActions = if (drsInputs.nonEmpty) {
-      val drsLocalizationManifestContainerPath = createPipelineParameters.commandScriptContainerPath.sibling(DrsLocalizationManifestName)
-      val localizeDrsLocalizationManifest = cloudSdkShellAction(localizeFile(
-        cloudPath = createPipelineParameters.cloudCallRoot / DrsLocalizationManifestName,
-        containerPath = drsLocalizationManifestContainerPath))(mounts = mounts, labels = localizationLabel)
+      val drsLocalizationManifestContainerPath =
+        createPipelineParameters.commandScriptContainerPath.sibling(DrsLocalizationManifestName)
+      val localizeDrsLocalizationManifest = cloudSdkShellAction(
+        localizeFile(cloudPath = createPipelineParameters.cloudCallRoot / DrsLocalizationManifestName,
+                     containerPath = drsLocalizationManifestContainerPath
+        )
+      )(mounts = mounts, labels = localizationLabel)
 
       // Requester pays project id is stored on each DrsPath, but will be the same for all DRS inputs to a
       // particular workflow because it's determined by the Google project set in workflow options.
       val requesterPaysProjectId: Option[String] = drsInputs.flatMap(_.requesterPaysProjectIdOption).headOption
-      val runDrsLocalization = Localization.drsAction(drsLocalizationManifestContainerPath, mounts, localizationLabel, requesterPaysProjectId)
+      val runDrsLocalization =
+        Localization.drsAction(drsLocalizationManifestContainerPath, mounts, localizationLabel, requesterPaysProjectId)
       List(localizeDrsLocalizationManifest, runDrsLocalization)
     } else List[Action]()
 
     // Any "classic" PAPI v2 one-at-a-time localizations for non-GCS inputs.
-    val singletonLocalizations = createPipelineParameters.inputOutputParameters.fileInputParameters.flatMap(_.toActions(mounts).toList)
+    val singletonLocalizations =
+      createPipelineParameters.inputOutputParameters.fileInputParameters.flatMap(_.toActions(mounts).toList)
 
     val localizations =
       localizeGcsTransferLibrary ::
@@ -78,7 +92,7 @@ object Localization {
                 mounts: List[Mount],
                 labels: Map[String, String],
                 requesterPaysProjectId: Option[String]
-               ): Action = {
+  ): Action = {
     val config = ConfigFactory.load
     val drsResolverConfig = config.getConfig("filesystems.drs.global.config.resolver")
     val drsConfig = DrsConfig.fromConfig(drsResolverConfig)
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/MemoryRetryCheckAction.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/MemoryRetryCheckAction.scala
index 07bc213d1bd..ed223394376 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/MemoryRetryCheckAction.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/MemoryRetryCheckAction.scala
@@ -5,10 +5,11 @@ import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.C
 
 trait MemoryRetryCheckAction {
 
-  def checkForMemoryRetryActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount]): List[Action] = {
+  def checkForMemoryRetryActions(createPipelineParameters: CreatePipelineParameters,
+                                 mounts: List[Mount]
+  ): List[Action] =
     createPipelineParameters.retryWithMoreMemoryKeys match {
       case Some(keys) => List(ActionBuilder.checkForMemoryRetryAction(keys, mounts))
       case None => List.empty[Action]
     }
-  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/MonitoringAction.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/MonitoringAction.scala
index 5b86d75cbcf..b51b6577de3 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/MonitoringAction.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/MonitoringAction.scala
@@ -5,9 +5,9 @@ import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttribu
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestFactory.CreatePipelineParameters
 
 trait MonitoringAction {
-  def monitoringSetupActions(createPipelineParameters: CreatePipelineParameters,
-                             mounts: List[Mount]
-                            )(implicit gcsTransferConfiguration: GcsTransferConfiguration): List[Action] = {
+  def monitoringSetupActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount])(implicit
+    gcsTransferConfiguration: GcsTransferConfiguration
+  ): List[Action] = {
 
     val monitoringImageScriptActions =
       createPipelineParameters.monitoringImage.monitoringImageScriptOption match {
@@ -16,12 +16,12 @@ trait MonitoringAction {
             ActionBuilder.monitoringImageScriptAction(
               script,
               createPipelineParameters.monitoringImage.monitoringImageScriptContainerPath,
-              mounts,
+              mounts
             )
           val describeLocalizeScriptAction =
             ActionBuilder.describeDocker(
               "localizing monitoring image script action",
-              localizeScriptAction,
+              localizeScriptAction
             )
           List(describeLocalizeScriptAction, localizeScriptAction)
         case None => Nil
@@ -30,7 +30,6 @@ trait MonitoringAction {
     val monitoringImageActions =
       createPipelineParameters.monitoringImage.monitoringImageOption match {
         case Some(image) =>
-
           val monitoringImage = image
           val monitoringImageCommand = createPipelineParameters.monitoringImage.monitoringImageCommand
           val monitoringImageEnvironment = createPipelineParameters.monitoringImage.monitoringImageEnvironment
@@ -39,7 +38,7 @@ trait MonitoringAction {
             monitoringImage,
             monitoringImageCommand,
             monitoringImageEnvironment(mounts.map(_.getPath)),
-            mounts,
+            mounts
           )
 
           val describeMonitoringAction = ActionBuilder.describeDocker("monitoring action", monitoringAction)
@@ -52,7 +51,7 @@ trait MonitoringAction {
     monitoringImageScriptActions ++ monitoringImageActions
   }
 
-  def monitoringShutdownActions(createPipelineParameters: CreatePipelineParameters): List[Action] = {
+  def monitoringShutdownActions(createPipelineParameters: CreatePipelineParameters): List[Action] =
     createPipelineParameters.monitoringImage.monitoringImageOption match {
       case Some(_) =>
         val terminationAction = ActionBuilder.terminateBackgroundActionsAction()
@@ -62,5 +61,4 @@ trait MonitoringAction {
         List(describeTerminationAction, terminationAction)
       case None => Nil
     }
-  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/SSHAccessAction.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/SSHAccessAction.scala
index 342b5701847..a2b91178c1b 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/SSHAccessAction.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/SSHAccessAction.scala
@@ -9,16 +9,16 @@ import scala.jdk.CollectionConverters._
 
 trait SSHAccessAction {
 
-  def sshAccessActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount]) : List[Action] = {
+  def sshAccessActions(createPipelineParameters: CreatePipelineParameters, mounts: List[Mount]): List[Action] =
     if (createPipelineParameters.enableSshAccess) {
       sshAccessAction(mounts)
     } else {
       Nil
     }
-  }
 
   private def sshAccessAction(mounts: List[Mount]): List[Action] = {
-    val sshAction = ActionBuilder.withImage(ActionUtils.sshImage)
+    val sshAction = ActionBuilder
+      .withImage(ActionUtils.sshImage)
       .withEntrypointCommand(ActionUtils.sshEntryPoint)
       .setPortMappings(ActionUtils.sshPortMappings.asJava)
       .setRunInBackground(true)
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/AbortRequestHandler.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/AbortRequestHandler.scala
index b4d9421b451..26905f51d2f 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/AbortRequestHandler.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/AbortRequestHandler.scala
@@ -6,7 +6,10 @@ import com.google.api.client.googleapis.json.GoogleJsonError
 import com.google.api.client.http.HttpHeaders
 import com.typesafe.scalalogging.LazyLogging
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager._
-import cromwell.backend.google.pipelines.common.api.clients.PipelinesApiAbortClient.{PAPIAbortRequestSuccessful, PAPIOperationIsAlreadyTerminal}
+import cromwell.backend.google.pipelines.common.api.clients.PipelinesApiAbortClient.{
+  PAPIAbortRequestSuccessful,
+  PAPIOperationIsAlreadyTerminal
+}
 import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
 import org.apache.commons.lang3.StringUtils
 
@@ -14,7 +17,11 @@ import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success, Try}
 
 trait AbortRequestHandler extends LazyLogging { this: RequestHandler =>
-  protected def handleGoogleError(abortQuery: PAPIAbortRequest, pollingManager: ActorRef, e: GoogleJsonError, responseHeaders: HttpHeaders): Try[Unit] = {
+  protected def handleGoogleError(abortQuery: PAPIAbortRequest,
+                                  pollingManager: ActorRef,
+                                  e: GoogleJsonError,
+                                  responseHeaders: HttpHeaders
+  ): Try[Unit] =
     // This condition is telling us that the job we tried to cancel is already in a terminal state. Technically PAPI
     // was not able to cancel the job because the job could not be transitioned from 'Running' to 'Cancelled'. But from
     // Cromwell's perspective a job cancellation is really just a request for the job to be in a terminal state, so
@@ -23,30 +30,34 @@ trait AbortRequestHandler extends LazyLogging { this: RequestHandler =>
     // If/when Google implements https://partnerissuetracker.corp.google.com/issues/171993833 we could break these cases
     // out and make our logging more specific if we wanted to.
     if (Option(e.getCode).contains(400) || StringUtils.contains(e.getMessage, "Precondition check failed")) {
-      logger.info(s"PAPI declined to abort job ${abortQuery.jobId.jobId} in workflow ${abortQuery.workflowId}, most likely because it is no longer running. Marking as finished. Message: ${e.getMessage}")
+      logger.info(
+        s"PAPI declined to abort job ${abortQuery.jobId.jobId} in workflow ${abortQuery.workflowId}, most likely because it is no longer running. Marking as finished. Message: ${e.getMessage}"
+      )
       abortQuery.requester ! PAPIOperationIsAlreadyTerminal(abortQuery.jobId.jobId)
       Success(())
     } else {
-      pollingManager ! PipelinesApiAbortQueryFailed(abortQuery, new SystemPAPIApiException(GoogleJsonException(e, responseHeaders)))
+      pollingManager ! PipelinesApiAbortQueryFailed(abortQuery,
+                                                    new SystemPAPIApiException(GoogleJsonException(e, responseHeaders))
+      )
       Failure(new Exception(mkErrorString(e)))
     }
-  }
 
   // The Genomics batch endpoint doesn't seem to be able to handle abort requests on V2 operations at the moment
   // For now, don't batch the request and execute it on its own
-  def handleRequest(abortQuery: PAPIAbortRequest, batch: BatchRequest, pollingManager: ActorRef)(implicit ec: ExecutionContext): Future[Try[Unit]] = {
+  def handleRequest(abortQuery: PAPIAbortRequest, batch: BatchRequest, pollingManager: ActorRef)(implicit
+    ec: ExecutionContext
+  ): Future[Try[Unit]] =
     Future(abortQuery.httpRequest.setThrowExceptionOnExecuteError(false).execute()) map {
       case response if response.isSuccessStatusCode =>
         abortQuery.requester ! PAPIAbortRequestSuccessful(abortQuery.jobId.jobId)
         Success(())
-      case response => for {
-        asGoogleError <- Try(GoogleJsonError.parse(GoogleAuthMode.jsonFactory, response))
-        handled <- handleGoogleError(abortQuery, pollingManager, asGoogleError, response.getHeaders)
-      } yield handled
-    } recover {
-      case e =>
-        pollingManager ! PipelinesApiAbortQueryFailed(abortQuery, new SystemPAPIApiException(e))
-        Failure(e)
+      case response =>
+        for {
+          asGoogleError <- Try(GoogleJsonError.parse(GoogleAuthMode.jsonFactory, response))
+          handled <- handleGoogleError(abortQuery, pollingManager, asGoogleError, response.getHeaders)
+        } yield handled
+    } recover { case e =>
+      pollingManager ! PipelinesApiAbortQueryFailed(abortQuery, new SystemPAPIApiException(e))
+      Failure(e)
     }
-  }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/ErrorReporter.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/ErrorReporter.scala
index 1c57c3ba2ce..2329af494c0 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/ErrorReporter.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/ErrorReporter.scala
@@ -20,28 +20,27 @@ object ErrorReporter {
 
   // This can be used to log non-critical deserialization failures and not fail the task
   implicit class ErrorOrLogger[A](val t: ErrorOr[A]) extends AnyVal {
-    private def logErrors(errors: NonEmptyList[String], workflowId: WorkflowId, operation: Operation): Unit = {
-      logger.error(s"[$workflowId] Failed to parse PAPI response. Operation Id: ${operation.getName}" + s"${errors.toList.mkString(", ")}")
+    private def logErrors(errors: NonEmptyList[String], workflowId: WorkflowId, operation: Operation): Unit =
+      logger.error(
+        s"[$workflowId] Failed to parse PAPI response. Operation Id: ${operation.getName}" + s"${errors.toList.mkString(", ")}"
+      )
+
+    def fallBack: RequestContextReader[Option[A]] = Reader { case (workflowId, operation) =>
+      t match {
+        case Valid(s) => Option(s)
+        case Invalid(f) =>
+          logErrors(f, workflowId, operation)
+          None
+      }
     }
 
-    def fallBack: RequestContextReader[Option[A]] = Reader {
-      case (workflowId, operation) =>
-        t match {
-          case Valid(s) => Option(s)
-          case Invalid(f) =>
-            logErrors(f, workflowId, operation)
-            None
-        }
-    }
-
-    def fallBackTo(to: A): RequestContextReader[A] = Reader {
-      case (workflowId, operation) =>
-        t match {
-          case Valid(s) => s
-          case Invalid(f) =>
-            logErrors(f, workflowId, operation)
-            to
-        }
+    def fallBackTo(to: A): RequestContextReader[A] = Reader { case (workflowId, operation) =>
+      t match {
+        case Valid(s) => s
+        case Invalid(f) =>
+          logErrors(f, workflowId, operation)
+          to
+      }
     }
   }
 }
@@ -53,7 +52,8 @@ class ErrorReporter(machineType: Option[String],
                     instanceName: Option[String],
                     actions: List[Action],
                     operation: Operation,
-                    workflowId: WorkflowId) {
+                    workflowId: WorkflowId
+) {
 
   def toUnsuccessfulRunStatus(error: Status, events: List[Event]): UnsuccessfulRunStatus = {
     // If for some reason the status is null, set it as UNAVAILABLE
@@ -64,7 +64,11 @@ class ErrorReporter(machineType: Option[String],
     val status = statusOption.getOrElse(GStatus.UNAVAILABLE)
     val builder = status match {
       case GStatus.UNAVAILABLE if wasPreemptible => Preempted.apply _
-      case GStatus.ABORTED if wasPreemptible && Option(error.getMessage).exists(_.contains(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style)) => Preempted.apply _
+      case GStatus.ABORTED
+          if wasPreemptible && Option(error.getMessage).exists(
+            _.contains(PipelinesApiAsyncBackendJobExecutionActor.FailedV2Style)
+          ) =>
+        Preempted.apply _
       case GStatus.CANCELLED => Cancelled.apply _
       case _ => Failed.apply _
     }
@@ -77,7 +81,7 @@ class ErrorReporter(machineType: Option[String],
   }
 
   // There's maybe one FailedEvent per operation with a summary error message
-  private def unexpectedExitStatusErrorStrings(events: List[Event], actions: List[Action]): List[String] = {
+  private def unexpectedExitStatusErrorStrings(events: List[Event], actions: List[Action]): List[String] =
     for {
       event <- events
       unexpectedStatusEvent <- Option(event.getUnexpectedExitStatus)
@@ -87,33 +91,33 @@ class ErrorReporter(machineType: Option[String],
       labelTag = action.flatMap(actionLabelTag)
       inputNameTag = action.flatMap(actionLabelInputName)
     } yield unexpectedStatusErrorString(event, stderr, labelTag, inputNameTag)
-  }
 
   // It would probably be good to define a richer error structure than String, but right now that's what the backend interface expects
-  private def unexpectedStatusErrorString(event: Event, stderr: Option[String], labelTag: Option[String], inputNameTag: Option[String]) = {
+  private def unexpectedStatusErrorString(event: Event,
+                                          stderr: Option[String],
+                                          labelTag: Option[String],
+                                          inputNameTag: Option[String]
+  ) =
     labelTag.map("[" + _ + "] ").getOrElse("") +
-      inputNameTag.map("Input name: " +  _ + " - ").getOrElse("") +
+      inputNameTag.map("Input name: " + _ + " - ").getOrElse("") +
       Option(event).flatMap(eventValue => Option(eventValue.getDescription)).getOrElse("") +
       stderr.map(": " + _).getOrElse("")
-  }
 
   // There may be one FailedEvent per operation with a summary error message
-  private def summaryFailure(events: List[Event]): Option[String] = {
+  private def summaryFailure(events: List[Event]): Option[String] =
     events.collectFirst {
       case event if event.getFailed != null => event.getFailed.getCause
     }
-  }
 
   // Try to find the stderr for the given action ID
-  private def stderrForAction(events: List[Event])(actionId: Integer) = {
+  private def stderrForAction(events: List[Event])(actionId: Integer) =
     events.collectFirst {
-      case event if event.getContainerStopped != null && event.getContainerStopped.getActionId == actionId  => event.getContainerStopped.getStderr
+      case event if event.getContainerStopped != null && event.getContainerStopped.getActionId == actionId =>
+        event.getContainerStopped.getStderr
     }
-  }
 
-  private def actionLabelValue(action: Action, k: String): Option[String] = {
+  private def actionLabelValue(action: Action, k: String): Option[String] =
     Option(action).flatMap(actionValue => Option(actionValue.getLabels)).map(_.asScala).flatMap(_.get(k))
-  }
 
   private def actionLabelTag(action: Action) = actionLabelValue(action, Key.Tag)
   private def actionLabelInputName(action: Action) = actionLabelValue(action, Key.InputName)
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/GetRequestHandler.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/GetRequestHandler.scala
index 5bcb9c812f4..0473aecaa36 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/GetRequestHandler.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/GetRequestHandler.scala
@@ -10,7 +10,13 @@ import common.validation.Validation._
 import cromwell.backend.google.pipelines.common.action.ActionLabels._
 import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager._
 import cromwell.backend.google.pipelines.common.api.RunStatus
-import cromwell.backend.google.pipelines.common.api.RunStatus.{AwaitingCloudQuota, Initializing, Running, Success, UnsuccessfulRunStatus}
+import cromwell.backend.google.pipelines.common.api.RunStatus.{
+  AwaitingCloudQuota,
+  Initializing,
+  Running,
+  Success,
+  UnsuccessfulRunStatus
+}
 import cromwell.backend.google.pipelines.v2beta.PipelinesConversions._
 import cromwell.backend.google.pipelines.v2beta.api.Deserialization._
 import cromwell.backend.google.pipelines.v2beta.api.request.ErrorReporter._
@@ -22,30 +28,39 @@ import org.apache.commons.lang3.exception.ExceptionUtils
 import scala.jdk.CollectionConverters._
 import scala.concurrent.{ExecutionContext, Future}
 import scala.language.postfixOps
-import scala.util.{Failure, Try, Success => TrySuccess}
+import scala.util.{Failure, Success => TrySuccess, Try}
 
 trait GetRequestHandler { this: RequestHandler =>
   // the Genomics batch endpoint doesn't seem to be able to handle get requests on V2 operations at the moment
   // For now, don't batch the request and execute it on its own
-  def handleRequest(pollingRequest: PAPIStatusPollRequest, batch: BatchRequest, pollingManager: ActorRef)(implicit ec: ExecutionContext): Future[Try[Unit]] = Future(pollingRequest.httpRequest.execute()) map {
+  def handleRequest(pollingRequest: PAPIStatusPollRequest, batch: BatchRequest, pollingManager: ActorRef)(implicit
+    ec: ExecutionContext
+  ): Future[Try[Unit]] = Future(pollingRequest.httpRequest.execute()) map {
     case response if response.isSuccessStatusCode =>
       val operation = response.parseAs(classOf[Operation])
       pollingRequest.requester ! interpretOperationStatus(operation, pollingRequest)
       TrySuccess(())
     case response =>
       val failure = Try(GoogleJsonError.parse(GoogleAuthMode.jsonFactory, response)) match {
-        case TrySuccess(googleError) => new SystemPAPIApiException(GoogleJsonException(googleError, response.getHeaders))
-        case Failure(_) => new SystemPAPIApiException(new RuntimeException(s"Failed to get status for operation ${pollingRequest.jobId.jobId}: HTTP Status Code: ${response.getStatusCode}"))
+        case TrySuccess(googleError) =>
+          new SystemPAPIApiException(GoogleJsonException(googleError, response.getHeaders))
+        case Failure(_) =>
+          new SystemPAPIApiException(
+            new RuntimeException(
+              s"Failed to get status for operation ${pollingRequest.jobId.jobId}: HTTP Status Code: ${response.getStatusCode}"
+            )
+          )
       }
       pollingManager ! PipelinesApiStatusQueryFailed(pollingRequest, failure)
       Failure(failure)
-  } recover {
-    case e =>
-      pollingManager ! PipelinesApiStatusQueryFailed(pollingRequest, new SystemPAPIApiException(e))
-      Failure(e)
+  } recover { case e =>
+    pollingManager ! PipelinesApiStatusQueryFailed(pollingRequest, new SystemPAPIApiException(e))
+    Failure(e)
   }
 
-  private [request] def interpretOperationStatus(operation: Operation, pollingRequest: PAPIStatusPollRequest): RunStatus = {
+  private[request] def interpretOperationStatus(operation: Operation,
+                                                pollingRequest: PAPIStatusPollRequest
+  ): RunStatus =
     if (Option(operation).isEmpty) {
       // It is possible to receive a null via an HTTP 200 with no response. If that happens, handle it and don't crash.
       // https://github.com/googleapis/google-http-java-client/blob/v1.28.0/google-http-client/src/main/java/com/google/api/client/http/HttpResponse.java#L456-L458
@@ -125,16 +140,20 @@ trait GetRequestHandler { this: RequestHandler =>
           )
       }
     }
-  }
 
-  private def getEventList(metadata: Map[String, AnyRef], events: List[Event], actions: List[Action]): List[ExecutionEvent] = {
-    val starterEvent: Option[ExecutionEvent] = {
-      metadata.get("createTime") map { time => ExecutionEvent("waiting for quota", OffsetDateTime.parse(time.toString)) }
-    }
+  private def getEventList(metadata: Map[String, AnyRef],
+                           events: List[Event],
+                           actions: List[Action]
+  ): List[ExecutionEvent] = {
+    val starterEvent: Option[ExecutionEvent] =
+      metadata.get("createTime") map { time =>
+        ExecutionEvent("waiting for quota", OffsetDateTime.parse(time.toString))
+      }
 
-    val completionEvent: Option[ExecutionEvent] = {
-      metadata.get("endTime") map { time => ExecutionEvent("Complete in GCE / Cromwell Poll Interval", OffsetDateTime.parse(time.toString)) }
-    }
+    val completionEvent: Option[ExecutionEvent] =
+      metadata.get("endTime") map { time =>
+        ExecutionEvent("Complete in GCE / Cromwell Poll Interval", OffsetDateTime.parse(time.toString))
+      }
 
     // Map action indexes to event types. Action indexes are 1-based for some reason.
     // BA-6455: since v2beta version of Life Sciences API, `a.getLabels` would return `null` for empty labels, unlike
@@ -161,7 +180,10 @@ trait GetRequestHandler { this: RequestHandler =>
     val filteredExecutionEvents = startDelocalization match {
       case None => executionEvents // Can't do filtering without a start time for Delocalization.
       case Some(start) =>
-        executionEvents filterNot { e => (e.name.startsWith("Started pulling ") || e.name.startsWith("Stopped pulling ")) && e.offsetDateTime.compareTo(start.offsetDateTime) > 0 }
+        executionEvents filterNot { e =>
+          (e.name.startsWith("Started pulling ") || e.name.startsWith("Stopped pulling ")) && e.offsetDateTime
+            .compareTo(start.offsetDateTime) > 0
+        }
     }
 
     starterEvent.toList ++ filteredExecutionEvents ++ completionEvent
@@ -172,7 +194,7 @@ trait GetRequestHandler { this: RequestHandler =>
   //   "metrics": [
   //     "CPUS"
   //   ]
-  private def isQuotaDelayed(events: List[Event]): Boolean = {
+  private def isQuotaDelayed(events: List[Event]): Boolean =
     events.sortBy(_.getTimestamp).reverse.headOption match {
       case Some(event) =>
         quotaMessages.exists(event.getDescription.contains)
@@ -180,7 +202,6 @@ trait GetRequestHandler { this: RequestHandler =>
         // If the events list is empty, we're not waiting for quota yet
         false
     }
-  }
 
   private val quotaMessages = List(
     "A resource limit has delayed the operation",
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/RequestHandler.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/RequestHandler.scala
index 523556e378d..a8eccb027f7 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/RequestHandler.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/RequestHandler.scala
@@ -5,7 +5,11 @@ import com.google.api.client.googleapis.batch.BatchRequest
 import com.google.api.client.googleapis.json.GoogleJsonError
 import com.google.api.services.lifesciences.v2beta.CloudLifeSciences
 import cromwell.backend.google.pipelines.common.PipelinesApiConfigurationAttributes.BatchRequestTimeoutConfiguration
-import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.{PAPIAbortRequest, PAPIRunCreationRequest, PAPIStatusPollRequest}
+import cromwell.backend.google.pipelines.common.api.PipelinesApiRequestManager.{
+  PAPIAbortRequest,
+  PAPIRunCreationRequest,
+  PAPIStatusPollRequest
+}
 import cromwell.backend.google.pipelines.common.api.{PipelinesApiRequestHandler, PipelinesApiRequestManager}
 import cromwell.cloudsupport.gcp.auth.GoogleAuthMode
 import org.slf4j.{Logger, LoggerFactory}
@@ -21,18 +25,18 @@ object RequestHandler {
 
 class RequestHandler(applicationName: String,
                      endpointUrl: URL,
-                     batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration)
-  extends PipelinesApiRequestHandler
-  with RunRequestHandler
-  with GetRequestHandler
-  with AbortRequestHandler {
+                     batchRequestTimeoutConfiguration: BatchRequestTimeoutConfiguration
+) extends PipelinesApiRequestHandler
+    with RunRequestHandler
+    with GetRequestHandler
+    with AbortRequestHandler {
 
   override def makeBatchRequest: BatchRequest = {
     val builder =
       new CloudLifeSciences.Builder(
         GoogleAuthMode.httpTransport,
         GoogleAuthMode.jsonFactory,
-        initializeHttpRequest(batchRequestTimeoutConfiguration) _,
+        initializeHttpRequest(batchRequestTimeoutConfiguration) _
       )
         .setApplicationName(applicationName)
         .setRootUrl(endpointUrl.toString)
@@ -42,9 +46,8 @@ class RequestHandler(applicationName: String,
 
   override def enqueue[T <: PipelinesApiRequestManager.PAPIApiRequest](papiApiRequest: T,
                                                                        batchRequest: BatchRequest,
-                                                                       pollingManager: ActorRef)
-                                                                      (implicit ec: ExecutionContext)
-  : Future[Try[Unit]] = papiApiRequest match {
+                                                                       pollingManager: ActorRef
+  )(implicit ec: ExecutionContext): Future[Try[Unit]] = papiApiRequest match {
     case create: PAPIRunCreationRequest => handleRequest(create, batchRequest, pollingManager)
     case status: PAPIStatusPollRequest => handleRequest(status, batchRequest, pollingManager)
     case abort: PAPIAbortRequest => handleRequest(abort, batchRequest, pollingManager)
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/RunRequestHandler.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/RunRequestHandler.scala
index ca815944d77..9de5a91d85c 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/RunRequestHandler.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/api/request/RunRequestHandler.scala
@@ -14,7 +14,10 @@ import scala.concurrent.{Future, Promise}
 import scala.util.{Failure, Success, Try}
 
 trait RunRequestHandler { this: RequestHandler =>
-  private def runCreationResultHandler(originalRequest: PAPIApiRequest, completionPromise: Promise[Try[Unit]], pollingManager: ActorRef) = new JsonBatchCallback[Operation] {
+  private def runCreationResultHandler(originalRequest: PAPIApiRequest,
+                                       completionPromise: Promise[Try[Unit]],
+                                       pollingManager: ActorRef
+  ) = new JsonBatchCallback[Operation] {
     override def onSuccess(operation: Operation, responseHeaders: HttpHeaders): Unit = {
       originalRequest.requester ! getJob(operation)
       completionPromise.trySuccess(Success(()))
@@ -41,17 +44,23 @@ trait RunRequestHandler { this: RequestHandler =>
     }
   }
 
-  def handleRequest(runCreationQuery: PAPIRunCreationRequest, batch: BatchRequest, pollingManager: ActorRef): Future[Try[Unit]] = {
+  def handleRequest(runCreationQuery: PAPIRunCreationRequest,
+                    batch: BatchRequest,
+                    pollingManager: ActorRef
+  ): Future[Try[Unit]] = {
     val completionPromise = Promise[Try[Unit]]()
     val resultHandler = runCreationResultHandler(runCreationQuery, completionPromise, pollingManager)
     addRunCreationToBatch(runCreationQuery.httpRequest, batch, resultHandler)
     completionPromise.future
   }
 
-  private def addRunCreationToBatch(request: HttpRequest, batch: BatchRequest, resultHandler: JsonBatchCallback[Operation]): Unit = {
+  private def addRunCreationToBatch(request: HttpRequest,
+                                    batch: BatchRequest,
+                                    resultHandler: JsonBatchCallback[Operation]
+  ): Unit = {
     /*
-      * Manually enqueue the request instead of doing it through the RunPipelineRequest
-      * as it would unnecessarily rebuild the request (which we already have)
+     * Manually enqueue the request instead of doing it through the RunPipelineRequest
+     * as it would unnecessarily rebuild the request (which we already have)
      */
     batch.queue(request, classOf[Operation], classOf[GoogleJsonErrorContainer], resultHandler)
     ()
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
index e7189d453ad..97a06617721 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
@@ -18,8 +18,11 @@ import org.scalatest.matchers.should.Matchers
 
 import scala.concurrent.duration.DurationInt
 
-class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
-  with MockSugar {
+class PipelinesApiAsyncBackendJobExecutionActorSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with MockSugar {
   behavior of "PipelinesParameterConversions"
 
   it should "group files by bucket" in {
@@ -47,8 +50,8 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Cro
 
     val expected =
       Map("foo" -> (NonEmptyList.of(0, 1) map inputs.apply)) ++
-      Map("bar" -> (NonEmptyList.of(2, 3, 4) map inputs.apply)) ++
-      Map("baz" -> NonEmptyList.of(inputs(5)))
+        Map("bar" -> (NonEmptyList.of(2, 3, 4) map inputs.apply)) ++
+        Map("baz" -> NonEmptyList.of(inputs(5)))
 
     PipelinesApiAsyncBackendJobExecutionActor.groupParametersByGcsBucket(inputs) shouldEqual expected
   }
@@ -65,11 +68,16 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Cro
       val fakeCredentials = NoCredentials.getInstance
 
       val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
-        throw new UnsupportedOperationException("PipelinesApiAsyncBackendJobExecutionActorSpec doesn't need to use drs read interpreter.")
+        throw new UnsupportedOperationException(
+          "PipelinesApiAsyncBackendJobExecutionActorSpec doesn't need to use drs read interpreter."
+        )
 
       DrsPathBuilder(
-        new DrsCloudNioFileSystemProvider(drsResolverConfig, GoogleOauthDrsCredentials(fakeCredentials, 1.minutes), drsReadInterpreter),
-        None,
+        new DrsCloudNioFileSystemProvider(drsResolverConfig,
+                                          GoogleOauthDrsCredentials(fakeCredentials, 1.minutes),
+                                          drsReadInterpreter
+        ),
+        None
       )
     }
 
@@ -82,7 +90,10 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Cro
     }
 
     val nonDrsInput: PipelinesApiFileInput = PipelinesApiFileInput("nnn",
-      DefaultPathBuilder.get("/local/nnn.bai"), DefaultPathBuilder.get("/path/to/nnn.bai"), mount)
+                                                                   DefaultPathBuilder.get("/local/nnn.bai"),
+                                                                   DefaultPathBuilder.get("/path/to/nnn.bai"),
+                                                                   mount
+    )
 
     val inputs = List(
       makeDrsInput("aaa", "drs://drs.example.org/aaa", "path/to/aaa.bai"),
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/ActionBuilderSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/ActionBuilderSpec.scala
index 44abde7862c..233f168a257 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/ActionBuilderSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/ActionBuilderSpec.scala
@@ -19,36 +19,38 @@ class ActionBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     ("description", "action", "command"),
     ("a cloud sdk action", ActionBuilder.cloudSdkAction, s"docker run ${ActionUtils.CloudSdkImage}"),
     ("a cloud sdk action with args",
-      ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello").asJava),
-      s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello"
+     ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello").asJava),
+     s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello"
     ),
     ("a cloud sdk action with quotes in the args",
-      ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello m'lord").asJava),
-      s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello\\ m\\'lord"
+     ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello m'lord").asJava),
+     s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello\\ m\\'lord"
     ),
     ("a cloud sdk action with a newline in the args",
-      ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello\\\nworld").asJava),
-      s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello\\\\world"
+     ActionBuilder.cloudSdkAction.setCommands(List("bash", "-c", "echo hello\\\nworld").asJava),
+     s"docker run ${ActionUtils.CloudSdkImage} bash -c echo\\ hello\\\\world"
     ),
     ("an action with multiple args",
-      new Action()
-        .setImageUri("ubuntu")
-        .setEnvironment(Map("ENV" -> "dev").asJava)
-        .setEntrypoint("")
-        .setCommands(List("bash", "-c", "echo hello").asJava)
-        .setPublishExposedPorts(true)
-        .setAlwaysRun(true)
-        .setMounts(List(
-          new Mount().setDisk("read-only-disk").setPath("/read/only/container").setReadOnly(true),
-          new Mount().setDisk("read-write-disk").setPath("/read/write/container"),
-        ).asJava)
-        .setContainerName("my_container_name")
-        .setPidNamespace("host")
-        .setPortMappings(Map("8008" -> Int.box(8000)).asJava),
-      "docker run --name my_container_name" +
-        " -v /mnt/read-only-disk:/read/only/container:ro -v /mnt/read-write-disk:/read/write/container" +
-        " -e ENV:dev --pid=host -P -p 8008:8000 --entrypoint= ubuntu bash -c echo\\ hello"
-    ),
+     new Action()
+       .setImageUri("ubuntu")
+       .setEnvironment(Map("ENV" -> "dev").asJava)
+       .setEntrypoint("")
+       .setCommands(List("bash", "-c", "echo hello").asJava)
+       .setPublishExposedPorts(true)
+       .setAlwaysRun(true)
+       .setMounts(
+         List(
+           new Mount().setDisk("read-only-disk").setPath("/read/only/container").setReadOnly(true),
+           new Mount().setDisk("read-write-disk").setPath("/read/write/container")
+         ).asJava
+       )
+       .setContainerName("my_container_name")
+       .setPidNamespace("host")
+       .setPortMappings(Map("8008" -> Int.box(8000)).asJava),
+     "docker run --name my_container_name" +
+       " -v /mnt/read-only-disk:/read/only/container:ro -v /mnt/read-write-disk:/read/write/container" +
+       " -e ENV:dev --pid=host -P -p 8008:8000 --entrypoint= ubuntu bash -c echo\\ hello"
+    )
   )
 
   forAll(dockerRunActions) { (description, action, command) =>
@@ -59,12 +61,11 @@ class ActionBuilderSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
 
   private val memoryRetryExpectedEntrypoint = "/bin/sh"
 
-  def memoryRetryExpectedCommand(lookupString: String): util.List[String] = {
+  def memoryRetryExpectedCommand(lookupString: String): util.List[String] =
     List(
       "-c",
       s"grep -E -q '$lookupString' /cromwell_root/stderr ; echo $$? > /cromwell_root/memory_retry_rc"
     ).asJava
-  }
 
   val mounts = List(new Mount().setDisk("read-only-disk").setPath("/read/only/container"))
   private val memoryRetryActionExpectedLabels = Map(Key.Tag -> Value.RetryWithMoreMemory).asJava
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/ActionCommandsSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/ActionCommandsSpec.scala
index 257fb094b0d..4356c5f0418 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/ActionCommandsSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/ActionCommandsSpec.scala
@@ -19,7 +19,7 @@ class ActionCommandsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
       mock[Path],
       mock[com.google.api.services.storage.Storage],
       mock[com.google.cloud.storage.Storage],
-      "my-project",
+      "my-project"
     )
     val recovered = recoverRequesterPaysError(path) { flag =>
       s"flag is $flag"
@@ -46,21 +46,23 @@ class ActionCommandsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   it should "use GcsTransferConfiguration to set the number of localization retries" in {
-    implicit val gcsTransferConfiguration: GcsTransferConfiguration = GcsTransferConfiguration(
-      transferAttempts = refineMV(31380), parallelCompositeUploadThreshold = "0")
-    retry("I'm very flaky") shouldBe """for i in $(seq 31380); do
-                                       |  (
-                                       |    I'm very flaky
-                                       |  )
-                                       |  RC=$?
-                                       |  if [ "$RC" = "0" ]; then
-                                       |    break
-                                       |  fi
-                                       |  if [ $i -lt 31380 ]; then
-                                       |    printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" Waiting\ 5\ seconds\ and\ retrying
-                                       |    sleep 5
-                                       |  fi
-                                       |done
-                                       |exit "$RC"""".stripMargin
+    implicit val gcsTransferConfiguration: GcsTransferConfiguration =
+      GcsTransferConfiguration(transferAttempts = refineMV(31380), parallelCompositeUploadThreshold = "0")
+    retry(
+      "I'm very flaky"
+    ) shouldBe """for i in $(seq 31380); do
+                 |  (
+                 |    I'm very flaky
+                 |  )
+                 |  RC=$?
+                 |  if [ "$RC" = "0" ]; then
+                 |    break
+                 |  fi
+                 |  if [ $i -lt 31380 ]; then
+                 |    printf '%s %s\n' "$(date -u '+%Y/%m/%d %H:%M:%S')" Waiting\ 5\ seconds\ and\ retrying
+                 |    sleep 5
+                 |  fi
+                 |done
+                 |exit "$RC"""".stripMargin
   }
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
index 6afd75adbd6..c2e8920301b 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala
@@ -37,7 +37,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
               "portMappings" -> Map(
                 "8000" -> Integer.valueOf(8008)
               ).asJava
-            ).asJava,
+            ).asJava
           ).asJava
         ).asJava
       )
@@ -118,7 +118,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
         "resources" -> Map[String, Object](
           "projectId" -> "project",
           "virtualMachine" -> Map(
-            "machineType" -> "custom-1-1024",
+            "machineType" -> "custom-1-1024"
           ).asJava
         ).asJava
       ).asJava
@@ -149,15 +149,20 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
       )
     ).asJava
 
-    val metadataMapStarted = makeMetadata(Map[String, Object](
-      "workerAssigned" -> Map(
-        "zone" -> "event 1 Zone",
-        "instance" -> "event 1 Instance"
-      ).asJava))
+    val metadataMapStarted = makeMetadata(
+      Map[String, Object](
+        "workerAssigned" -> Map(
+          "zone" -> "event 1 Zone",
+          "instance" -> "event 1 Instance"
+        ).asJava
+      )
+    )
     val metadataMapNotStarted = makeMetadata(Map.empty)
-    val metadataMapNotStarted2 = makeMetadata(Map[String, Object](
-      "containerStarted" -> Map().asJava
-    ))
+    val metadataMapNotStarted2 = makeMetadata(
+      Map[String, Object](
+        "containerStarted" -> Map().asJava
+      )
+    )
 
     operation.setMetadata(metadataMapStarted)
     operation.hasStarted shouldBe true
@@ -170,8 +175,8 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
   it should "deserialize big decimals correctly" in {
     val valueMap = Map[String, Object](
       "integerValue" -> BigDecimal(5),
-      "doubleValue" -> BigDecimal.decimal(6D),
-      "floatValue" -> BigDecimal.decimal(7F),
+      "doubleValue" -> BigDecimal.decimal(6d),
+      "floatValue" -> BigDecimal.decimal(7f),
       "longValue" -> BigDecimal.decimal(8L)
     ).asJava
 
@@ -179,8 +184,8 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     deserialized match {
       case Success(deserializedSuccess) =>
         deserializedSuccess.integerValue shouldBe 5
-        deserializedSuccess.doubleValue shouldBe 6D
-        deserializedSuccess.floatValue shouldBe 7F
+        deserializedSuccess.doubleValue shouldBe 6d
+        deserializedSuccess.floatValue shouldBe 7f
         deserializedSuccess.longValue shouldBe 8L
       case Failure(f) =>
         fail("Bad deserialization", f)
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala
index f815ceebd14..2ddf991d0f7 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/LocalizationSpec.scala
@@ -25,11 +25,12 @@ class LocalizationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
 
     action.get("commands") should be(a[java.util.List[_]])
     action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
-      "-m", manifestPathString
+      "-m",
+      manifestPathString
     )
 
     action.get("mounts") should be(a[java.util.List[_]])
-    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+    action.get("mounts").asInstanceOf[java.util.List[_]] should be(empty)
 
     action.get("imageUri") should be("somerepo/drs-downloader:tagged")
 
@@ -52,11 +53,14 @@ class LocalizationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
 
     action.get("commands") should be(a[java.util.List[_]])
     action.get("commands").asInstanceOf[java.util.List[_]] should contain theSameElementsAs List(
-      "-m", manifestPathString, "-r", requesterPaysProjectId
+      "-m",
+      manifestPathString,
+      "-r",
+      requesterPaysProjectId
     )
 
     action.get("mounts") should be(a[java.util.List[_]])
-    action.get("mounts").asInstanceOf[java.util.List[_]] should be (empty)
+    action.get("mounts").asInstanceOf[java.util.List[_]] should be(empty)
 
     action.get("imageUri") should be("somerepo/drs-downloader:tagged")
 
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/request/GetRequestHandlerSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/request/GetRequestHandlerSpec.scala
index 802a7b68106..7f0ae47135f 100644
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/request/GetRequestHandlerSpec.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/request/GetRequestHandlerSpec.scala
@@ -25,7 +25,7 @@ class GetRequestHandlerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
   private val requestHandler: GetRequestHandler = new RequestHandler(
     "GetRequestHandlerSpec",
     new URL("file:///getrequesthandlerspec"),
-    BatchRequestTimeoutConfiguration(None, None),
+    BatchRequestTimeoutConfiguration(None, None)
   )
 
   private val workflowId = WorkflowId.randomId()
@@ -37,623 +37,656 @@ class GetRequestHandlerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
 
   private val interpretedStatus = Table(
     ("description", "json", "status"),
-    ("parse null operation json", null, UnsuccessfulRunStatus(
-      Status.UNKNOWN,
-      Option("Operation returned as empty"),
-      Nil,
-      None,
-      None,
-      None,
-      wasPreemptible = false
-    )),
+    ("parse null operation json",
+     null,
+     UnsuccessfulRunStatus(
+       Status.UNKNOWN,
+       Option("Operation returned as empty"),
+       Nil,
+       None,
+       None,
+       None,
+       wasPreemptible = false
+     )
+    ),
     ("parse empty operation json", "{}", Initializing),
     ("parse error operation json without resources",
-      """|{
-         |  "done": true,
-         |  "error": {}
-         |}
-         |""".stripMargin,
-      Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
+     """|{
+        |  "done": true,
+        |  "error": {}
+        |}
+        |""".stripMargin,
+     Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
     ),
     ("parse error operation json without virtualMachine",
-      """|{
-         |  "done": true,
-         |  "resources": {
-         |  },
-         |  "error": {}
-         |}
-         |""".stripMargin,
-      Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
+     """|{
+        |  "done": true,
+        |  "resources": {
+        |  },
+        |  "error": {}
+        |}
+        |""".stripMargin,
+     Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
     ),
     ("parse error operation json without preemptible",
-      """|{
-         |  "done": true,
-         |  "resources": {
-         |    "virtualMachine": {
-         |    }
-         |  },
-         |  "error": {}
-         |}
-         |""".stripMargin,
-      Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
+     """|{
+        |  "done": true,
+        |  "resources": {
+        |    "virtualMachine": {
+        |    }
+        |  },
+        |  "error": {}
+        |}
+        |""".stripMargin,
+     Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
     ),
     ("parse error operation json with preemptible true",
-      """|{
-         |  "done": true,
-         |  "resources": {
-         |    "virtualMachine": {
-         |      "preemptible": true
-         |    }
-         |  },
-         |  "error": {}
-         |}
-         |""".stripMargin,
-      Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
+     """|{
+        |  "done": true,
+        |  "resources": {
+        |    "virtualMachine": {
+        |      "preemptible": true
+        |    }
+        |  },
+        |  "error": {}
+        |}
+        |""".stripMargin,
+     Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
     ),
     ("parse error operation json with preemptible false",
-      """|{
-         |  "done": true,
-         |  "resources": {
-         |    "virtualMachine": {
-         |      "preemptible": false
-         |    }
-         |  },
-         |  "error": {}
-         |}
-         |""".stripMargin,
-      Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
-    ),
-    ("check that we classify error code 10 as a preemption on a preemptible VM",
-      """{
+     """|{
         |  "done": true,
-        |  "error": {
-        |    "code": 10,
-        |    "message": "The assigned worker has failed to complete the operation"
-        |  },
-        |  "metadata": {
-        |    "@type": "type.googleapis.com/google.genomics.v2alpha1.Metadata",
-        |    "createTime": "2019-08-18T12:04:38.082650Z",
-        |    "endTime": "2019-08-18T15:58:26.659602622Z",
-        |    "events": [],
-        |    "labels": {
-        |      "cromwell-sub-workflow-name": "bamtocram",
-        |      "cromwell-workflow-id": "asdfasdf",
-        |      "wdl-call-alias": "validatecram",
-        |      "wdl-task-name": "validatesamfile"
-        |    },
-        |    "pipeline": {
-        |      "actions": [],
-        |      "environment": {},
-        |      "resources": {
-        |        "projectId": "",
-        |        "regions": [],
-        |        "virtualMachine": {
-        |          "accelerators": [],
-        |          "bootDiskSizeGb": 11,
-        |          "bootImage": "asdfasdf",
-        |          "cpuPlatform": "",
-        |          "disks": [
-        |            {
-        |              "name": "local-disk",
-        |              "sizeGb": 41,
-        |              "sourceImage": "",
-        |              "type": "pd-standard"
-        |            }
-        |          ],
-        |          "enableStackdriverMonitoring": false,
-        |          "labels": {
-        |            "cromwell-sub-workflow-name": "bamtocram",
-        |            "cromwell-workflow-id": "asdfasdf",
-        |            "goog-pipelines-worker": "true",
-        |            "wdl-call-alias": "validatecram",
-        |            "wdl-task-name": "validatesamfile"
-        |          },
-        |          "machineType": "custom-2-7168",
-        |          "network": {
-        |            "name": "",
-        |            "subnetwork": "",
-        |            "usePrivateAddress": false
-        |          },
-        |          "nvidiaDriverVersion": "",
-        |          "preemptible": true,
-        |          "serviceAccount": {
-        |            "email": "default",
-        |            "scopes": [
-        |              "https://www.googleapis.com/auth/genomics",
-        |              "https://www.googleapis.com/auth/compute",
-        |              "https://www.googleapis.com/auth/devstorage.full_control",
-        |              "https://www.googleapis.com/auth/cloudkms",
-        |              "https://www.googleapis.com/auth/userinfo.email",
-        |              "https://www.googleapis.com/auth/userinfo.profile",
-        |              "https://www.googleapis.com/auth/monitoring.write",
-        |              "https://www.googleapis.com/auth/cloud-platform"
-        |            ]
-        |          }
-        |        },
-        |        "zones": [
-        |          "us-central1-a",
-        |          "us-central1-b",
-        |          "us-east1-d",
-        |          "us-central1-c",
-        |          "us-central1-f",
-        |          "us-east1-c"
-        |        ]
-        |      },
-        |      "timeout": "604800s"
-        |    },
-        |    "startTime": "2019-08-18T12:04:39.192909594Z"
+        |  "resources": {
+        |    "virtualMachine": {
+        |      "preemptible": false
+        |    }
         |  },
-        |  "name": "asdfasdf"
-        |}""".stripMargin,
-      Preempted(
-        Status.ABORTED,
-        None,
-        Nil,
-        List(
-          ExecutionEvent("waiting for quota", OffsetDateTime.parse("2019-08-18T12:04:38.082650Z"),None),
-          ExecutionEvent("Complete in GCE / Cromwell Poll Interval", OffsetDateTime.parse("2019-08-18T15:58:26.659602622Z"),None),
-        ),
-        Some("custom-2-7168"),
-        None,
-        None)
+        |  "error": {}
+        |}
+        |""".stripMargin,
+     Failed(Status.UNAVAILABLE, None, Nil, Nil, None, None, None)
+    ),
+    ("check that we classify error code 10 as a preemption on a preemptible VM",
+     """{
+       |  "done": true,
+       |  "error": {
+       |    "code": 10,
+       |    "message": "The assigned worker has failed to complete the operation"
+       |  },
+       |  "metadata": {
+       |    "@type": "type.googleapis.com/google.genomics.v2alpha1.Metadata",
+       |    "createTime": "2019-08-18T12:04:38.082650Z",
+       |    "endTime": "2019-08-18T15:58:26.659602622Z",
+       |    "events": [],
+       |    "labels": {
+       |      "cromwell-sub-workflow-name": "bamtocram",
+       |      "cromwell-workflow-id": "asdfasdf",
+       |      "wdl-call-alias": "validatecram",
+       |      "wdl-task-name": "validatesamfile"
+       |    },
+       |    "pipeline": {
+       |      "actions": [],
+       |      "environment": {},
+       |      "resources": {
+       |        "projectId": "",
+       |        "regions": [],
+       |        "virtualMachine": {
+       |          "accelerators": [],
+       |          "bootDiskSizeGb": 11,
+       |          "bootImage": "asdfasdf",
+       |          "cpuPlatform": "",
+       |          "disks": [
+       |            {
+       |              "name": "local-disk",
+       |              "sizeGb": 41,
+       |              "sourceImage": "",
+       |              "type": "pd-standard"
+       |            }
+       |          ],
+       |          "enableStackdriverMonitoring": false,
+       |          "labels": {
+       |            "cromwell-sub-workflow-name": "bamtocram",
+       |            "cromwell-workflow-id": "asdfasdf",
+       |            "goog-pipelines-worker": "true",
+       |            "wdl-call-alias": "validatecram",
+       |            "wdl-task-name": "validatesamfile"
+       |          },
+       |          "machineType": "custom-2-7168",
+       |          "network": {
+       |            "name": "",
+       |            "subnetwork": "",
+       |            "usePrivateAddress": false
+       |          },
+       |          "nvidiaDriverVersion": "",
+       |          "preemptible": true,
+       |          "serviceAccount": {
+       |            "email": "default",
+       |            "scopes": [
+       |              "https://www.googleapis.com/auth/genomics",
+       |              "https://www.googleapis.com/auth/compute",
+       |              "https://www.googleapis.com/auth/devstorage.full_control",
+       |              "https://www.googleapis.com/auth/cloudkms",
+       |              "https://www.googleapis.com/auth/userinfo.email",
+       |              "https://www.googleapis.com/auth/userinfo.profile",
+       |              "https://www.googleapis.com/auth/monitoring.write",
+       |              "https://www.googleapis.com/auth/cloud-platform"
+       |            ]
+       |          }
+       |        },
+       |        "zones": [
+       |          "us-central1-a",
+       |          "us-central1-b",
+       |          "us-east1-d",
+       |          "us-central1-c",
+       |          "us-central1-f",
+       |          "us-east1-c"
+       |        ]
+       |      },
+       |      "timeout": "604800s"
+       |    },
+       |    "startTime": "2019-08-18T12:04:39.192909594Z"
+       |  },
+       |  "name": "asdfasdf"
+       |}""".stripMargin,
+     Preempted(
+       Status.ABORTED,
+       None,
+       Nil,
+       List(
+         ExecutionEvent("waiting for quota", OffsetDateTime.parse("2019-08-18T12:04:38.082650Z"), None),
+         ExecutionEvent("Complete in GCE / Cromwell Poll Interval",
+                        OffsetDateTime.parse("2019-08-18T15:58:26.659602622Z"),
+                        None
+         )
+       ),
+       Some("custom-2-7168"),
+       None,
+       None
+     )
     ),
     ("check that we classify error code 10 as a failure on a non-preemptible VM",
-      """{
-        |  "done": true,
-        |  "error": {
-        |    "code": 10,
-        |    "message": "The assigned worker has failed to complete the operation"
-        |  },
-        |  "metadata": {
-        |    "@type": "type.googleapis.com/google.genomics.v2alpha1.Metadata",
-        |    "createTime": "2019-08-18T12:04:38.082650Z",
-        |    "endTime": "2019-08-18T15:58:26.659602622Z",
-        |    "events": [],
-        |    "labels": {
-        |      "cromwell-sub-workflow-name": "bamtocram",
-        |      "cromwell-workflow-id": "asdfasdf",
-        |      "wdl-call-alias": "validatecram",
-        |      "wdl-task-name": "validatesamfile"
-        |    },
-        |    "pipeline": {
-        |      "actions": [],
-        |      "environment": {},
-        |      "resources": {
-        |        "projectId": "",
-        |        "regions": [],
-        |        "virtualMachine": {
-        |          "accelerators": [],
-        |          "bootDiskSizeGb": 11,
-        |          "bootImage": "asdfasdf",
-        |          "cpuPlatform": "",
-        |          "disks": [
-        |            {
-        |              "name": "local-disk",
-        |              "sizeGb": 41,
-        |              "sourceImage": "",
-        |              "type": "pd-standard"
-        |            }
-        |          ],
-        |          "enableStackdriverMonitoring": false,
-        |          "labels": {
-        |            "cromwell-sub-workflow-name": "bamtocram",
-        |            "cromwell-workflow-id": "asdfasdf",
-        |            "goog-pipelines-worker": "true",
-        |            "wdl-call-alias": "validatecram",
-        |            "wdl-task-name": "validatesamfile"
-        |          },
-        |          "machineType": "custom-2-7168",
-        |          "network": {
-        |            "name": "",
-        |            "subnetwork": "",
-        |            "usePrivateAddress": false
-        |          },
-        |          "nvidiaDriverVersion": "",
-        |          "preemptible": false,
-        |          "serviceAccount": {
-        |            "email": "default",
-        |            "scopes": [
-        |              "https://www.googleapis.com/auth/genomics",
-        |              "https://www.googleapis.com/auth/compute",
-        |              "https://www.googleapis.com/auth/devstorage.full_control",
-        |              "https://www.googleapis.com/auth/cloudkms",
-        |              "https://www.googleapis.com/auth/userinfo.email",
-        |              "https://www.googleapis.com/auth/userinfo.profile",
-        |              "https://www.googleapis.com/auth/monitoring.write",
-        |              "https://www.googleapis.com/auth/cloud-platform"
-        |            ]
-        |          }
-        |        },
-        |        "zones": [
-        |          "us-central1-a",
-        |          "us-central1-b",
-        |          "us-east1-d",
-        |          "us-central1-c",
-        |          "us-central1-f",
-        |          "us-east1-c"
-        |        ]
-        |      },
-        |      "timeout": "604800s"
-        |    },
-        |    "startTime": "2019-08-18T12:04:39.192909594Z"
-        |  },
-        |  "name": "asdfasdf"
-        |}""".stripMargin,
-      Failed(
-        Status.ABORTED,
-        None,
-        Nil,
-        List(
-          ExecutionEvent("waiting for quota", OffsetDateTime.parse("2019-08-18T12:04:38.082650Z"),None),
-          ExecutionEvent("Complete in GCE / Cromwell Poll Interval", OffsetDateTime.parse("2019-08-18T15:58:26.659602622Z"),None),
-        ),
-        Some("custom-2-7168"),
-        None,
-        None
-      )
+     """{
+       |  "done": true,
+       |  "error": {
+       |    "code": 10,
+       |    "message": "The assigned worker has failed to complete the operation"
+       |  },
+       |  "metadata": {
+       |    "@type": "type.googleapis.com/google.genomics.v2alpha1.Metadata",
+       |    "createTime": "2019-08-18T12:04:38.082650Z",
+       |    "endTime": "2019-08-18T15:58:26.659602622Z",
+       |    "events": [],
+       |    "labels": {
+       |      "cromwell-sub-workflow-name": "bamtocram",
+       |      "cromwell-workflow-id": "asdfasdf",
+       |      "wdl-call-alias": "validatecram",
+       |      "wdl-task-name": "validatesamfile"
+       |    },
+       |    "pipeline": {
+       |      "actions": [],
+       |      "environment": {},
+       |      "resources": {
+       |        "projectId": "",
+       |        "regions": [],
+       |        "virtualMachine": {
+       |          "accelerators": [],
+       |          "bootDiskSizeGb": 11,
+       |          "bootImage": "asdfasdf",
+       |          "cpuPlatform": "",
+       |          "disks": [
+       |            {
+       |              "name": "local-disk",
+       |              "sizeGb": 41,
+       |              "sourceImage": "",
+       |              "type": "pd-standard"
+       |            }
+       |          ],
+       |          "enableStackdriverMonitoring": false,
+       |          "labels": {
+       |            "cromwell-sub-workflow-name": "bamtocram",
+       |            "cromwell-workflow-id": "asdfasdf",
+       |            "goog-pipelines-worker": "true",
+       |            "wdl-call-alias": "validatecram",
+       |            "wdl-task-name": "validatesamfile"
+       |          },
+       |          "machineType": "custom-2-7168",
+       |          "network": {
+       |            "name": "",
+       |            "subnetwork": "",
+       |            "usePrivateAddress": false
+       |          },
+       |          "nvidiaDriverVersion": "",
+       |          "preemptible": false,
+       |          "serviceAccount": {
+       |            "email": "default",
+       |            "scopes": [
+       |              "https://www.googleapis.com/auth/genomics",
+       |              "https://www.googleapis.com/auth/compute",
+       |              "https://www.googleapis.com/auth/devstorage.full_control",
+       |              "https://www.googleapis.com/auth/cloudkms",
+       |              "https://www.googleapis.com/auth/userinfo.email",
+       |              "https://www.googleapis.com/auth/userinfo.profile",
+       |              "https://www.googleapis.com/auth/monitoring.write",
+       |              "https://www.googleapis.com/auth/cloud-platform"
+       |            ]
+       |          }
+       |        },
+       |        "zones": [
+       |          "us-central1-a",
+       |          "us-central1-b",
+       |          "us-east1-d",
+       |          "us-central1-c",
+       |          "us-central1-f",
+       |          "us-east1-c"
+       |        ]
+       |      },
+       |      "timeout": "604800s"
+       |    },
+       |    "startTime": "2019-08-18T12:04:39.192909594Z"
+       |  },
+       |  "name": "asdfasdf"
+       |}""".stripMargin,
+     Failed(
+       Status.ABORTED,
+       None,
+       Nil,
+       List(
+         ExecutionEvent("waiting for quota", OffsetDateTime.parse("2019-08-18T12:04:38.082650Z"), None),
+         ExecutionEvent("Complete in GCE / Cromwell Poll Interval",
+                        OffsetDateTime.parse("2019-08-18T15:58:26.659602622Z"),
+                        None
+         )
+       ),
+       Some("custom-2-7168"),
+       None,
+       None
+     )
     ),
     // As of 2022-01 the zone `us-west3` in `broad-dsde-cromwell-dev` has its CPU quota purposely de-rated to 1 for testing
     ("check that a job is AwaitingCloudQuota if its most recent event is quota exhaustion",
-      """{
-        |  "metadata": {
-        |    "@type": "type.googleapis.com/google.cloud.lifesciences.v2beta.Metadata",
-        |    "createTime": "2022-01-19T21:53:55.138960Z",
-        |    "events": [
-        |      {
-        |        "delayed": {
-        |          "cause": "generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
-        |          "metrics": [
-        |            "CPUS"
-        |          ]
-        |        },
-        |        "description": "A resource limit has delayed the operation: generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
-        |        "timestamp": "2022-01-19T21:54:07.717679160Z"
-        |      }
-        |    ],
-        |    "labels": {
-        |      "cromwell-workflow-id": "cromwell-ac888b4e-2e6b-4dcc-a537-3c6db7764037",
-        |      "wdl-task-name": "sleep"
-        |    },
-        |    "pipeline": {
-        |      "actions": [
-        |        {
-        |          "commands": [
-        |            "-c",
-        |            "printf '%s %s\\n' \"$(date -u '+%Y/%m/%d %H:%M:%S')\" Starting\\ container\\ setup."
-        |          ],
-        |          "entrypoint": "/bin/sh",
-        |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine",
-        |          "labels": {
-        |            "logging": "ContainerSetup"
-        |          },
-        |          "timeout": "300s"
-        |        }
-        |      ],
-        |      "environment": {
-        |        "MEM_SIZE": "2.0",
-        |        "MEM_UNIT": "GB"
-        |      },
-        |      "resources": {
-        |        "virtualMachine": {
-        |          "bootDiskSizeGb": 12,
-        |          "bootImage": "projects/cos-cloud/global/images/family/cos-stable",
-        |          "disks": [
-        |            {
-        |              "name": "local-disk",
-        |              "sizeGb": 10,
-        |              "type": "pd-ssd"
-        |            }
-        |          ],
-        |          "labels": {
-        |            "cromwell-workflow-id": "cromwell-ac888b4e-2e6b-4dcc-a537-3c6db7764037",
-        |            "goog-pipelines-worker": "true",
-        |            "wdl-task-name": "sleep"
-        |          },
-        |          "machineType": "custom-1-2048",
-        |          "network": {},
-        |          "nvidiaDriverVersion": "450.51.06",
-        |          "serviceAccount": {
-        |            "email": "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com",
-        |            "scopes": [
-        |              "https://www.googleapis.com/auth/compute",
-        |              "https://www.googleapis.com/auth/devstorage.full_control",
-        |              "https://www.googleapis.com/auth/cloudkms",
-        |              "https://www.googleapis.com/auth/userinfo.email",
-        |              "https://www.googleapis.com/auth/userinfo.profile",
-        |              "https://www.googleapis.com/auth/monitoring.write",
-        |              "https://www.googleapis.com/auth/bigquery",
-        |              "https://www.googleapis.com/auth/cloud-platform"
-        |            ]
-        |          },
-        |          "volumes": [
-        |            {
-        |              "persistentDisk": {
-        |                "sizeGb": 10,
-        |                "type": "pd-ssd"
-        |              },
-        |              "volume": "local-disk"
-        |            }
-        |          ]
-        |        },
-        |        "zones": [
-        |          "us-west3-a",
-        |          "us-west3-b",
-        |          "us-west3-c"
-        |        ]
-        |      },
-        |      "timeout": "604800s"
-        |    }
-        |  },
-        |  "name": "projects/1005074806481/locations/us-central1/operations/3874882033889365536"
-        |}""".stripMargin,
-      AwaitingCloudQuota
+     """{
+       |  "metadata": {
+       |    "@type": "type.googleapis.com/google.cloud.lifesciences.v2beta.Metadata",
+       |    "createTime": "2022-01-19T21:53:55.138960Z",
+       |    "events": [
+       |      {
+       |        "delayed": {
+       |          "cause": "generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
+       |          "metrics": [
+       |            "CPUS"
+       |          ]
+       |        },
+       |        "description": "A resource limit has delayed the operation: generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
+       |        "timestamp": "2022-01-19T21:54:07.717679160Z"
+       |      }
+       |    ],
+       |    "labels": {
+       |      "cromwell-workflow-id": "cromwell-ac888b4e-2e6b-4dcc-a537-3c6db7764037",
+       |      "wdl-task-name": "sleep"
+       |    },
+       |    "pipeline": {
+       |      "actions": [
+       |        {
+       |          "commands": [
+       |            "-c",
+       |            "printf '%s %s\\n' \"$(date -u '+%Y/%m/%d %H:%M:%S')\" Starting\\ container\\ setup."
+       |          ],
+       |          "entrypoint": "/bin/sh",
+       |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine",
+       |          "labels": {
+       |            "logging": "ContainerSetup"
+       |          },
+       |          "timeout": "300s"
+       |        }
+       |      ],
+       |      "environment": {
+       |        "MEM_SIZE": "2.0",
+       |        "MEM_UNIT": "GB"
+       |      },
+       |      "resources": {
+       |        "virtualMachine": {
+       |          "bootDiskSizeGb": 12,
+       |          "bootImage": "projects/cos-cloud/global/images/family/cos-stable",
+       |          "disks": [
+       |            {
+       |              "name": "local-disk",
+       |              "sizeGb": 10,
+       |              "type": "pd-ssd"
+       |            }
+       |          ],
+       |          "labels": {
+       |            "cromwell-workflow-id": "cromwell-ac888b4e-2e6b-4dcc-a537-3c6db7764037",
+       |            "goog-pipelines-worker": "true",
+       |            "wdl-task-name": "sleep"
+       |          },
+       |          "machineType": "custom-1-2048",
+       |          "network": {},
+       |          "nvidiaDriverVersion": "450.51.06",
+       |          "serviceAccount": {
+       |            "email": "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com",
+       |            "scopes": [
+       |              "https://www.googleapis.com/auth/compute",
+       |              "https://www.googleapis.com/auth/devstorage.full_control",
+       |              "https://www.googleapis.com/auth/cloudkms",
+       |              "https://www.googleapis.com/auth/userinfo.email",
+       |              "https://www.googleapis.com/auth/userinfo.profile",
+       |              "https://www.googleapis.com/auth/monitoring.write",
+       |              "https://www.googleapis.com/auth/bigquery",
+       |              "https://www.googleapis.com/auth/cloud-platform"
+       |            ]
+       |          },
+       |          "volumes": [
+       |            {
+       |              "persistentDisk": {
+       |                "sizeGb": 10,
+       |                "type": "pd-ssd"
+       |              },
+       |              "volume": "local-disk"
+       |            }
+       |          ]
+       |        },
+       |        "zones": [
+       |          "us-west3-a",
+       |          "us-west3-b",
+       |          "us-west3-c"
+       |        ]
+       |      },
+       |      "timeout": "604800s"
+       |    }
+       |  },
+       |  "name": "projects/1005074806481/locations/us-central1/operations/3874882033889365536"
+       |}""".stripMargin,
+     AwaitingCloudQuota
     ),
     ("check that a job is Running and no longer AwaitingCloudQuota once a worker assigns",
-      """{
-        |  "metadata": {
-        |    "@type": "type.googleapis.com/google.cloud.lifesciences.v2beta.Metadata",
-        |    "createTime": "2022-01-19T21:53:55.138960Z",
-        |    "events": [
-        |      {
-        |        "description": "Started pulling \"gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine\"",
-        |        "pullStarted": {
-        |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine"
-        |        },
-        |        "timestamp": "2022-01-19T22:09:55.410251187Z"
-        |      },
-        |      {
-        |        "description": "Worker \"google-pipelines-worker-e6c8bf8035860b2cd69488497bd602d8\" assigned in \"us-west3-c\" on a \"custom-1-2048\" machine",
-        |        "timestamp": "2022-01-19T22:09:20.363771714Z",
-        |        "workerAssigned": {
-        |          "instance": "google-pipelines-worker-e6c8bf8035860b2cd69488497bd602d8",
-        |          "machineType": "custom-1-2048",
-        |          "zone": "us-west3-c"
-        |        }
-        |      },
-        |      {
-        |        "delayed": {
-        |          "cause": "generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
-        |          "metrics": [
-        |            "CPUS"
-        |          ]
-        |        },
-        |        "description": "A resource limit has delayed the operation: generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
-        |        "timestamp": "2022-01-19T21:54:07.717679160Z"
-        |      }
-        |    ],
-        |    "labels": {
-        |      "cromwell-workflow-id": "cromwell-ac888b4e-2e6b-4dcc-a537-3c6db7764037",
-        |      "wdl-task-name": "sleep"
-        |    },
-        |    "pipeline": {
-        |      "actions": [
-        |        {
-        |          "commands": [
-        |            "-c",
-        |            "printf '%s %s\\n' \"$(date -u '+%Y/%m/%d %H:%M:%S')\" Starting\\ container\\ setup."
-        |          ],
-        |          "entrypoint": "/bin/sh",
-        |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine",
-        |          "labels": {
-        |            "logging": "ContainerSetup"
-        |          },
-        |          "timeout": "300s"
-        |        }
-        |      ],
-        |      "environment": {
-        |        "MEM_SIZE": "2.0",
-        |        "MEM_UNIT": "GB"
-        |      },
-        |      "resources": {
-        |        "virtualMachine": {
-        |          "bootDiskSizeGb": 12,
-        |          "bootImage": "projects/cos-cloud/global/images/family/cos-stable",
-        |          "disks": [
-        |            {
-        |              "name": "local-disk",
-        |              "sizeGb": 10,
-        |              "type": "pd-ssd"
-        |            }
-        |          ],
-        |          "labels": {
-        |            "cromwell-workflow-id": "cromwell-ac888b4e-2e6b-4dcc-a537-3c6db7764037",
-        |            "goog-pipelines-worker": "true",
-        |            "wdl-task-name": "sleep"
-        |          },
-        |          "machineType": "custom-1-2048",
-        |          "network": {},
-        |          "nvidiaDriverVersion": "450.51.06",
-        |          "serviceAccount": {
-        |            "email": "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com",
-        |            "scopes": [
-        |              "https://www.googleapis.com/auth/compute",
-        |              "https://www.googleapis.com/auth/devstorage.full_control",
-        |              "https://www.googleapis.com/auth/cloudkms",
-        |              "https://www.googleapis.com/auth/userinfo.email",
-        |              "https://www.googleapis.com/auth/userinfo.profile",
-        |              "https://www.googleapis.com/auth/monitoring.write",
-        |              "https://www.googleapis.com/auth/bigquery",
-        |              "https://www.googleapis.com/auth/cloud-platform"
-        |            ]
-        |          },
-        |          "volumes": [
-        |            {
-        |              "persistentDisk": {
-        |                "sizeGb": 10,
-        |                "type": "pd-ssd"
-        |              },
-        |              "volume": "local-disk"
-        |            }
-        |          ]
-        |        },
-        |        "zones": [
-        |          "us-west3-a",
-        |          "us-west3-b",
-        |          "us-west3-c"
-        |        ]
-        |      },
-        |      "timeout": "604800s"
-        |    },
-        |    "startTime": "2022-01-19T22:09:20.363771714Z"
-        |  },
-        |  "name": "projects/1005074806481/locations/us-central1/operations/3874882033889365536"
-        |}
-        |
-        |
-        |""".stripMargin,
-      Running
+     """{
+       |  "metadata": {
+       |    "@type": "type.googleapis.com/google.cloud.lifesciences.v2beta.Metadata",
+       |    "createTime": "2022-01-19T21:53:55.138960Z",
+       |    "events": [
+       |      {
+       |        "description": "Started pulling \"gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine\"",
+       |        "pullStarted": {
+       |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine"
+       |        },
+       |        "timestamp": "2022-01-19T22:09:55.410251187Z"
+       |      },
+       |      {
+       |        "description": "Worker \"google-pipelines-worker-e6c8bf8035860b2cd69488497bd602d8\" assigned in \"us-west3-c\" on a \"custom-1-2048\" machine",
+       |        "timestamp": "2022-01-19T22:09:20.363771714Z",
+       |        "workerAssigned": {
+       |          "instance": "google-pipelines-worker-e6c8bf8035860b2cd69488497bd602d8",
+       |          "machineType": "custom-1-2048",
+       |          "zone": "us-west3-c"
+       |        }
+       |      },
+       |      {
+       |        "delayed": {
+       |          "cause": "generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
+       |          "metrics": [
+       |            "CPUS"
+       |          ]
+       |        },
+       |        "description": "A resource limit has delayed the operation: generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
+       |        "timestamp": "2022-01-19T21:54:07.717679160Z"
+       |      }
+       |    ],
+       |    "labels": {
+       |      "cromwell-workflow-id": "cromwell-ac888b4e-2e6b-4dcc-a537-3c6db7764037",
+       |      "wdl-task-name": "sleep"
+       |    },
+       |    "pipeline": {
+       |      "actions": [
+       |        {
+       |          "commands": [
+       |            "-c",
+       |            "printf '%s %s\\n' \"$(date -u '+%Y/%m/%d %H:%M:%S')\" Starting\\ container\\ setup."
+       |          ],
+       |          "entrypoint": "/bin/sh",
+       |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine",
+       |          "labels": {
+       |            "logging": "ContainerSetup"
+       |          },
+       |          "timeout": "300s"
+       |        }
+       |      ],
+       |      "environment": {
+       |        "MEM_SIZE": "2.0",
+       |        "MEM_UNIT": "GB"
+       |      },
+       |      "resources": {
+       |        "virtualMachine": {
+       |          "bootDiskSizeGb": 12,
+       |          "bootImage": "projects/cos-cloud/global/images/family/cos-stable",
+       |          "disks": [
+       |            {
+       |              "name": "local-disk",
+       |              "sizeGb": 10,
+       |              "type": "pd-ssd"
+       |            }
+       |          ],
+       |          "labels": {
+       |            "cromwell-workflow-id": "cromwell-ac888b4e-2e6b-4dcc-a537-3c6db7764037",
+       |            "goog-pipelines-worker": "true",
+       |            "wdl-task-name": "sleep"
+       |          },
+       |          "machineType": "custom-1-2048",
+       |          "network": {},
+       |          "nvidiaDriverVersion": "450.51.06",
+       |          "serviceAccount": {
+       |            "email": "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com",
+       |            "scopes": [
+       |              "https://www.googleapis.com/auth/compute",
+       |              "https://www.googleapis.com/auth/devstorage.full_control",
+       |              "https://www.googleapis.com/auth/cloudkms",
+       |              "https://www.googleapis.com/auth/userinfo.email",
+       |              "https://www.googleapis.com/auth/userinfo.profile",
+       |              "https://www.googleapis.com/auth/monitoring.write",
+       |              "https://www.googleapis.com/auth/bigquery",
+       |              "https://www.googleapis.com/auth/cloud-platform"
+       |            ]
+       |          },
+       |          "volumes": [
+       |            {
+       |              "persistentDisk": {
+       |                "sizeGb": 10,
+       |                "type": "pd-ssd"
+       |              },
+       |              "volume": "local-disk"
+       |            }
+       |          ]
+       |        },
+       |        "zones": [
+       |          "us-west3-a",
+       |          "us-west3-b",
+       |          "us-west3-c"
+       |        ]
+       |      },
+       |      "timeout": "604800s"
+       |    },
+       |    "startTime": "2022-01-19T22:09:20.363771714Z"
+       |  },
+       |  "name": "projects/1005074806481/locations/us-central1/operations/3874882033889365536"
+       |}
+       |
+       |
+       |""".stripMargin,
+     Running
     ),
     ("check that a job is no longer AwaitingCloudQuota once it finishes",
-      """{
-        |  "done": true,
-        |  "metadata": {
-        |    "@type": "type.googleapis.com/google.cloud.lifesciences.v2beta.Metadata",
-        |    "createTime": "2022-01-19T19:17:13.175579Z",
-        |    "endTime": "2022-01-19T19:37:22.764120036Z",
-        |    "events": [
-        |      {
-        |        "description": "Worker released",
-        |        "timestamp": "2022-01-19T19:37:22.764120036Z",
-        |        "workerReleased": {
-        |          "instance": "google-pipelines-worker-8eff543e6858c204c8f67520aee75432",
-        |          "zone": "us-west3-c"
-        |        }
-        |      },
-        |      {
-        |        "containerStopped": {
-        |          "actionId": 19
-        |        },
-        |        "description": "Stopped running shortened for test",
-        |        "timestamp": "2022-01-19T19:37:19.822873814Z"
-        |      },
-        |      {
-        |        "description": "Started pulling \"gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine\"",
-        |        "pullStarted": {
-        |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine"
-        |        },
-        |        "timestamp": "2022-01-19T19:32:55.709674372Z"
-        |      },
-        |      {
-        |        "description": "Worker \"google-pipelines-worker-8eff543e6858c204c8f67520aee75432\" assigned in \"us-west3-c\" on a \"custom-1-2048\" machine",
-        |        "timestamp": "2022-01-19T19:32:19.204055448Z",
-        |        "workerAssigned": {
-        |          "instance": "google-pipelines-worker-8eff543e6858c204c8f67520aee75432",
-        |          "machineType": "custom-1-2048",
-        |          "zone": "us-west3-c"
-        |        }
-        |      },
-        |      {
-        |        "delayed": {
-        |          "cause": "generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
-        |          "metrics": [
-        |            "CPUS"
-        |          ]
-        |        },
-        |        "description": "A resource limit has delayed the operation: generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
-        |        "timestamp": "2022-01-19T19:17:14.948193837Z"
-        |      }
-        |    ],
-        |    "labels": {
-        |      "cromwell-workflow-id": "cromwell-058bff35-4a55-4c0f-9113-0885f4119cd9",
-        |      "wdl-task-name": "sleep"
-        |    },
-        |    "pipeline": {
-        |      "actions": [
-        |        {
-        |          "commands": [
-        |            "-c",
-        |            "printf '%s %s\\n' \"$(date -u '+%Y/%m/%d %H:%M:%S')\" Starting\\ container\\ setup."
-        |          ],
-        |          "entrypoint": "/bin/sh",
-        |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine",
-        |          "labels": {
-        |            "logging": "ContainerSetup"
-        |          },
-        |          "timeout": "300s"
-        |        },
-        |        {
-        |          "alwaysRun": true,
-        |          "commands": [
-        |            "-c",
-        |            "python3 -c 'import base64; shortened for test"
-        |          ],
-        |          "entrypoint": "/bin/sh",
-        |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine",
-        |          "labels": {
-        |            "tag": "Delocalization"
-        |          }
-        |        }
-        |      ],
-        |      "environment": {
-        |        "MEM_SIZE": "2.0",
-        |        "MEM_UNIT": "GB"
-        |      },
-        |      "resources": {
-        |        "virtualMachine": {
-        |          "bootDiskSizeGb": 12,
-        |          "bootImage": "projects/cos-cloud/global/images/family/cos-stable",
-        |          "disks": [
-        |            {
-        |              "name": "local-disk",
-        |              "sizeGb": 10,
-        |              "type": "pd-ssd"
-        |            }
-        |          ],
-        |          "labels": {
-        |            "cromwell-workflow-id": "cromwell-058bff35-4a55-4c0f-9113-0885f4119cd9",
-        |            "goog-pipelines-worker": "true",
-        |            "wdl-task-name": "sleep"
-        |          },
-        |          "machineType": "custom-1-2048",
-        |          "network": {},
-        |          "nvidiaDriverVersion": "450.51.06",
-        |          "serviceAccount": {
-        |            "email": "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com",
-        |            "scopes": [
-        |              "https://www.googleapis.com/auth/compute",
-        |              "https://www.googleapis.com/auth/devstorage.full_control",
-        |              "https://www.googleapis.com/auth/cloudkms",
-        |              "https://www.googleapis.com/auth/userinfo.email",
-        |              "https://www.googleapis.com/auth/userinfo.profile",
-        |              "https://www.googleapis.com/auth/monitoring.write",
-        |              "https://www.googleapis.com/auth/bigquery",
-        |              "https://www.googleapis.com/auth/cloud-platform"
-        |            ]
-        |          },
-        |          "volumes": [
-        |            {
-        |              "persistentDisk": {
-        |                "sizeGb": 10,
-        |                "type": "pd-ssd"
-        |              },
-        |              "volume": "local-disk"
-        |            }
-        |          ]
-        |        },
-        |        "zones": [
-        |          "us-west3-a",
-        |          "us-west3-b",
-        |          "us-west3-c"
-        |        ]
-        |      },
-        |      "timeout": "604800s"
-        |    },
-        |    "startTime": "2022-01-19T19:32:19.204055448Z"
-        |  },
-        |  "name": "projects/1005074806481/locations/us-central1/operations/5001350794958839237",
-        |  "response": {
-        |    "@type": "type.googleapis.com/cloud.lifesciences.pipelines.RunPipelineResponse"
-        |  }
-        |}""".stripMargin,
-      Success(List(
-        new ExecutionEvent("waiting for quota", OffsetDateTime.parse("2022-01-19T19:17:13.175579Z"), None),
-        new ExecutionEvent("Worker released", OffsetDateTime.parse("2022-01-19T19:37:22.764120036Z"), None),
-        new ExecutionEvent("Stopped running shortened for test", OffsetDateTime.parse("2022-01-19T19:37:19.822873814Z"), None),
-        new ExecutionEvent("Started pulling \"gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine\"", OffsetDateTime.parse("2022-01-19T19:32:55.709674372Z"), Option("Pulling \"gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine\"")),
-        new ExecutionEvent("Worker \"google-pipelines-worker-8eff543e6858c204c8f67520aee75432\" assigned in \"us-west3-c\" on a \"custom-1-2048\" machine", OffsetDateTime.parse("2022-01-19T19:32:19.204055448Z"), None),
-        new ExecutionEvent("A resource limit has delayed the operation: generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high", OffsetDateTime.parse("2022-01-19T19:17:14.948193837Z"), None),
-        new ExecutionEvent("Complete in GCE / Cromwell Poll Interval", OffsetDateTime.parse("2022-01-19T19:37:22.764120036Z"), None)
-      ), Option("custom-1-2048"), Option("us-west3-c"), Option("google-pipelines-worker-8eff543e6858c204c8f67520aee75432"))
+     """{
+       |  "done": true,
+       |  "metadata": {
+       |    "@type": "type.googleapis.com/google.cloud.lifesciences.v2beta.Metadata",
+       |    "createTime": "2022-01-19T19:17:13.175579Z",
+       |    "endTime": "2022-01-19T19:37:22.764120036Z",
+       |    "events": [
+       |      {
+       |        "description": "Worker released",
+       |        "timestamp": "2022-01-19T19:37:22.764120036Z",
+       |        "workerReleased": {
+       |          "instance": "google-pipelines-worker-8eff543e6858c204c8f67520aee75432",
+       |          "zone": "us-west3-c"
+       |        }
+       |      },
+       |      {
+       |        "containerStopped": {
+       |          "actionId": 19
+       |        },
+       |        "description": "Stopped running shortened for test",
+       |        "timestamp": "2022-01-19T19:37:19.822873814Z"
+       |      },
+       |      {
+       |        "description": "Started pulling \"gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine\"",
+       |        "pullStarted": {
+       |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine"
+       |        },
+       |        "timestamp": "2022-01-19T19:32:55.709674372Z"
+       |      },
+       |      {
+       |        "description": "Worker \"google-pipelines-worker-8eff543e6858c204c8f67520aee75432\" assigned in \"us-west3-c\" on a \"custom-1-2048\" machine",
+       |        "timestamp": "2022-01-19T19:32:19.204055448Z",
+       |        "workerAssigned": {
+       |          "instance": "google-pipelines-worker-8eff543e6858c204c8f67520aee75432",
+       |          "machineType": "custom-1-2048",
+       |          "zone": "us-west3-c"
+       |        }
+       |      },
+       |      {
+       |        "delayed": {
+       |          "cause": "generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
+       |          "metrics": [
+       |            "CPUS"
+       |          ]
+       |        },
+       |        "description": "A resource limit has delayed the operation: generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
+       |        "timestamp": "2022-01-19T19:17:14.948193837Z"
+       |      }
+       |    ],
+       |    "labels": {
+       |      "cromwell-workflow-id": "cromwell-058bff35-4a55-4c0f-9113-0885f4119cd9",
+       |      "wdl-task-name": "sleep"
+       |    },
+       |    "pipeline": {
+       |      "actions": [
+       |        {
+       |          "commands": [
+       |            "-c",
+       |            "printf '%s %s\\n' \"$(date -u '+%Y/%m/%d %H:%M:%S')\" Starting\\ container\\ setup."
+       |          ],
+       |          "entrypoint": "/bin/sh",
+       |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine",
+       |          "labels": {
+       |            "logging": "ContainerSetup"
+       |          },
+       |          "timeout": "300s"
+       |        },
+       |        {
+       |          "alwaysRun": true,
+       |          "commands": [
+       |            "-c",
+       |            "python3 -c 'import base64; shortened for test"
+       |          ],
+       |          "entrypoint": "/bin/sh",
+       |          "imageUri": "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine",
+       |          "labels": {
+       |            "tag": "Delocalization"
+       |          }
+       |        }
+       |      ],
+       |      "environment": {
+       |        "MEM_SIZE": "2.0",
+       |        "MEM_UNIT": "GB"
+       |      },
+       |      "resources": {
+       |        "virtualMachine": {
+       |          "bootDiskSizeGb": 12,
+       |          "bootImage": "projects/cos-cloud/global/images/family/cos-stable",
+       |          "disks": [
+       |            {
+       |              "name": "local-disk",
+       |              "sizeGb": 10,
+       |              "type": "pd-ssd"
+       |            }
+       |          ],
+       |          "labels": {
+       |            "cromwell-workflow-id": "cromwell-058bff35-4a55-4c0f-9113-0885f4119cd9",
+       |            "goog-pipelines-worker": "true",
+       |            "wdl-task-name": "sleep"
+       |          },
+       |          "machineType": "custom-1-2048",
+       |          "network": {},
+       |          "nvidiaDriverVersion": "450.51.06",
+       |          "serviceAccount": {
+       |            "email": "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com",
+       |            "scopes": [
+       |              "https://www.googleapis.com/auth/compute",
+       |              "https://www.googleapis.com/auth/devstorage.full_control",
+       |              "https://www.googleapis.com/auth/cloudkms",
+       |              "https://www.googleapis.com/auth/userinfo.email",
+       |              "https://www.googleapis.com/auth/userinfo.profile",
+       |              "https://www.googleapis.com/auth/monitoring.write",
+       |              "https://www.googleapis.com/auth/bigquery",
+       |              "https://www.googleapis.com/auth/cloud-platform"
+       |            ]
+       |          },
+       |          "volumes": [
+       |            {
+       |              "persistentDisk": {
+       |                "sizeGb": 10,
+       |                "type": "pd-ssd"
+       |              },
+       |              "volume": "local-disk"
+       |            }
+       |          ]
+       |        },
+       |        "zones": [
+       |          "us-west3-a",
+       |          "us-west3-b",
+       |          "us-west3-c"
+       |        ]
+       |      },
+       |      "timeout": "604800s"
+       |    },
+       |    "startTime": "2022-01-19T19:32:19.204055448Z"
+       |  },
+       |  "name": "projects/1005074806481/locations/us-central1/operations/5001350794958839237",
+       |  "response": {
+       |    "@type": "type.googleapis.com/cloud.lifesciences.pipelines.RunPipelineResponse"
+       |  }
+       |}""".stripMargin,
+     Success(
+       List(
+         new ExecutionEvent("waiting for quota", OffsetDateTime.parse("2022-01-19T19:17:13.175579Z"), None),
+         new ExecutionEvent("Worker released", OffsetDateTime.parse("2022-01-19T19:37:22.764120036Z"), None),
+         new ExecutionEvent("Stopped running shortened for test",
+                            OffsetDateTime.parse("2022-01-19T19:37:19.822873814Z"),
+                            None
+         ),
+         new ExecutionEvent(
+           "Started pulling \"gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine\"",
+           OffsetDateTime.parse("2022-01-19T19:32:55.709674372Z"),
+           Option("Pulling \"gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine\"")
+         ),
+         new ExecutionEvent(
+           "Worker \"google-pipelines-worker-8eff543e6858c204c8f67520aee75432\" assigned in \"us-west3-c\" on a \"custom-1-2048\" machine",
+           OffsetDateTime.parse("2022-01-19T19:32:19.204055448Z"),
+           None
+         ),
+         new ExecutionEvent(
+           "A resource limit has delayed the operation: generic::resource_exhausted: allocating: selecting resources: selecting region and zone: no available zones: us-west3: 1 CPUS (0/1 available) usage too high",
+           OffsetDateTime.parse("2022-01-19T19:17:14.948193837Z"),
+           None
+         ),
+         new ExecutionEvent("Complete in GCE / Cromwell Poll Interval",
+                            OffsetDateTime.parse("2022-01-19T19:37:22.764120036Z"),
+                            None
+         )
+       ),
+       Option("custom-1-2048"),
+       Option("us-west3-c"),
+       Option("google-pipelines-worker-8eff543e6858c204c8f67520aee75432")
+     )
     )
   )
 
@@ -662,7 +695,7 @@ class GetRequestHandlerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
       // Operation responses could come back as null. Handle it and don't crash.
       // https://github.com/googleapis/google-http-java-client/blob/v1.28.0/google-http-client/src/main/java/com/google/api/client/http/HttpResponse.java#L456-L458
       val operation =
-      Option(json).map(GoogleAuthMode.jsonFactory.createJsonParser).map(_.parse(classOf[Operation])).orNull
+        Option(json).map(GoogleAuthMode.jsonFactory.createJsonParser).map(_.parse(classOf[Operation])).orNull
       val runStatus = requestHandler.interpretOperationStatus(operation, pollingRequest)
 
       runStatus should be(expectedStatus)
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala
index 0cf90bf9f1d..6e8bfba564e 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala
@@ -57,8 +57,9 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
     * @param inputs   The customized inputs to this task.
     */
   def writeTaskScript(script: Path, taskName: String, inputs: WorkflowCoercedInputs): Unit = {
-    val task = configInitializationData.wdlNamespace.findTask(taskName).
-      getOrElse(throw new RuntimeException(s"Unable to find task $taskName"))
+    val task = configInitializationData.wdlNamespace
+      .findTask(taskName)
+      .getOrElse(throw new RuntimeException(s"Unable to find task $taskName"))
 
     val taskDefinition = task.toWomTaskDefinition.toTry.get
 
@@ -103,8 +104,8 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
       if !inputs.contains(optional.localName.value)
     } yield optional -> WomOptionalValue.none(optional.womType.memberType)
 
-
-    val runtimeEnvironment = RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes, jobPaths)(standardParams.minimumRuntimeSettings)
+    val runtimeEnvironment =
+      RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes, jobPaths)(standardParams.minimumRuntimeSettings)
     val allInputs = providedWomInputs ++ optionalsForciblyInitializedToNone
     val womInstantiation = taskDefinition.instantiateCommand(allInputs, NoIoFunctionSet, identity, runtimeEnvironment)
 
@@ -122,14 +123,15 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
     * The inputs that are not specified by the config, that will be passed into a command for both submit and
     * submit-docker.
     */
-  private lazy val standardInputs: WorkflowCoercedInputs = {
+  private lazy val standardInputs: WorkflowCoercedInputs =
     Map(
       JobNameInput -> WomString(jobName),
       CwdInput -> WomString(jobPaths.callRoot.pathAsString)
     )
-  }
 
-  private [config] def dockerCidInputValue: WomString = WomString(jobPaths.callExecutionRoot.resolve(jobPaths.dockerCid).pathAsString)
+  private[config] def dockerCidInputValue: WomString = WomString(
+    jobPaths.callExecutionRoot.resolve(jobPaths.dockerCid).pathAsString
+  )
 
   /**
     * The inputs that are not specified by the config, that will be passed into a command for either submit or
@@ -142,7 +144,7 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
         DockerStdoutInput -> WomString(jobPathsWithDocker.toDockerPath(standardPaths.output).pathAsString),
         DockerStderrInput -> WomString(jobPathsWithDocker.toDockerPath(standardPaths.error).pathAsString),
         DockerScriptInput -> WomString(jobPathsWithDocker.toDockerPath(jobPaths.script).pathAsString),
-        DockerCidInput -> dockerCidInputValue,
+        DockerCidInput -> dockerCidInputValue
       ),
       Map.empty
     )
@@ -151,7 +153,7 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
       StdoutInput -> WomString(standardPaths.output.pathAsString),
       StderrInput -> WomString(standardPaths.error.pathAsString),
       ScriptInput -> WomString(jobPaths.script.pathAsString),
-      JobShellInput -> WomString(jobShell),
+      JobShellInput -> WomString(jobShell)
     )).toMap
   }
 
@@ -163,7 +165,8 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
     val declarationValidations = configInitializationData.declarationValidations
     val inputOptions = declarationValidations map {
       // Is it always the right thing to pass the Docker hash to a config backend?  What if it can't use hashes?
-      case declarationValidation if declarationValidation.key == DockerValidation.instance.key && jobDescriptor.maybeCallCachingEligible.dockerHash.isDefined =>
+      case declarationValidation
+          if declarationValidation.key == DockerValidation.instance.key && jobDescriptor.maybeCallCachingEligible.dockerHash.isDefined =>
         val dockerHash = jobDescriptor.maybeCallCachingEligible.dockerHash.get
         Option(declarationValidation.key -> WomString(dockerHash))
       case declarationValidation =>
@@ -175,7 +178,8 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
   }
 
   // `runtimeAttributeInputs` has already adjusted for the case of a `JobDescriptor` with `DockerWithHash`.
-  override lazy val dockerImageUsed: Option[String] = runtimeAttributeInputs.get(DockerValidation.instance.key).map(_.valueString)
+  override lazy val dockerImageUsed: Option[String] =
+    runtimeAttributeInputs.get(DockerValidation.instance.key).map(_.valueString)
 
   /**
     * Generates a command for a job id, using a config task.
@@ -185,7 +189,11 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
     * @param task   The config task that defines the command.
     * @return A runnable command.
     */
-  protected def jobScriptArgs(job: StandardAsyncJob, suffix: String, task: String, extraInputs: Map[String, WomValue] = Map.empty): SharedFileSystemCommand = {
+  protected def jobScriptArgs(job: StandardAsyncJob,
+                              suffix: String,
+                              task: String,
+                              extraInputs: Map[String, WomValue] = Map.empty
+  ): SharedFileSystemCommand = {
     val script = jobPaths.script.plusExt(suffix)
     writeTaskScript(script, task, Map(JobIdInput -> WomString(job.jobId)) ++ extraInputs)
     SharedFileSystemCommand("/bin/bash", script)
@@ -198,12 +206,12 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
   * @param standardParams Params for running a shared file system job.
   */
 class BackgroundConfigAsyncJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
-  extends ConfigAsyncJobExecutionActor with BackgroundAsyncJobExecutionActor {
+    extends ConfigAsyncJobExecutionActor
+    with BackgroundAsyncJobExecutionActor {
 
-  override def killArgs(job: StandardAsyncJob): SharedFileSystemCommand = {
+  override def killArgs(job: StandardAsyncJob): SharedFileSystemCommand =
     if (isDockerRun) jobScriptArgs(job, "kill", KillDockerTask, Map(DockerCidInput -> dockerCidInputValue))
     else super[BackgroundAsyncJobExecutionActor].killArgs(job)
-  }
 }
 
 /**
@@ -213,7 +221,7 @@ class BackgroundConfigAsyncJobExecutionActor(override val standardParams: Standa
   * @param standardParams Params for running a shared file system job.
   */
 class DispatchedConfigAsyncJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
-  extends ConfigAsyncJobExecutionActor {
+    extends ConfigAsyncJobExecutionActor {
 
   lazy val jobIdRegexString = configurationDescriptor.backendConfig.getString(JobIdRegexConfig)
 
@@ -234,9 +242,8 @@ class DispatchedConfigAsyncJobExecutionActor(override val standardParams: Standa
     * @param job The job to check.
     * @return A command that checks if the job is alive.
     */
-  override def checkAliveArgs(job: StandardAsyncJob): SharedFileSystemCommand = {
+  override def checkAliveArgs(job: StandardAsyncJob): SharedFileSystemCommand =
     jobScriptArgs(job, "check", CheckAliveTask)
-  }
 
   /**
     * Kills the job using the kill command from the config.
@@ -244,19 +251,23 @@ class DispatchedConfigAsyncJobExecutionActor(override val standardParams: Standa
     * @param job The job id to kill.
     * @return A command that may be used to kill the job.
     */
-  override def killArgs(job: StandardAsyncJob): SharedFileSystemCommand = {
+  override def killArgs(job: StandardAsyncJob): SharedFileSystemCommand =
     if (isDockerRun) jobScriptArgs(job, "kill", KillDockerTask, Map(DockerCidInput -> dockerCidInputValue))
     else jobScriptArgs(job, "kill", KillTask)
-  }
 
   protected lazy val exitCodeTimeout: Option[Long] = {
     val timeout = configurationDescriptor.backendConfig.as[Option[Long]](ExitCodeTimeoutConfig)
     timeout match {
       case Some(x) =>
-        jobLogger.info("Cromwell will watch for an rc file *and* double-check every {} seconds to make sure this job is still alive", x)
+        jobLogger.info(
+          "Cromwell will watch for an rc file *and* double-check every {} seconds to make sure this job is still alive",
+          x
+        )
         if (x < 0) throw new IllegalArgumentException(s"config value '$ExitCodeTimeoutConfig' must be 0 or higher")
       case None =>
-        jobLogger.info("Cromwell will watch for an rc file but will *not* double-check whether this job is actually alive (unless Cromwell restarts)")
+        jobLogger.info(
+          "Cromwell will watch for an rc file but will *not* double-check whether this job is actually alive (unless Cromwell restarts)"
+        )
     }
     timeout
   }
@@ -286,7 +297,10 @@ class DispatchedConfigAsyncJobExecutionActor(override val standardParams: Standa
               // The job has stopped but we don't have an RC yet. We'll wait one more 'timeout' for the RC to arrive:
               SharedFileSystemJobWaitingForReturnCode(nextTimeout)
             case Failure(e) =>
-              log.error(e, s"Failed to check status for ${handle.jobDescriptor.key.tag} using command: ${checkAliveArgs(handle.pendingJob)}")
+              log.error(
+                e,
+                s"Failed to check status for ${handle.jobDescriptor.key.tag} using command: ${checkAliveArgs(handle.pendingJob)}"
+              )
               SharedFileSystemJobRunning(nextTimeout)
           }
         } else {
@@ -300,8 +314,11 @@ class DispatchedConfigAsyncJobExecutionActor(override val standardParams: Standa
           // `isAlive` is not called anymore from this point
 
           // If exit-code-timeout is set in the config cromwell will create a fake exitcode file
-          val backupError = "??? (!! Programmer Error: It should be impossible to give up on 'waiting' without having set a maximum wait timeout. Please report this as a bug in the Cromwell Github repository !!)"
-          jobLogger.error(s"Return file not found after ${exitCodeTimeout.getOrElse(backupError)} seconds, assuming external kill")
+          val backupError =
+            "??? (!! Programmer Error: It should be impossible to give up on 'waiting' without having set a maximum wait timeout. Please report this as a bug in the Cromwell Github repository !!)"
+          jobLogger.error(
+            s"Return file not found after ${exitCodeTimeout.getOrElse(backupError)} seconds, assuming external kill"
+          )
 
           val returnCodeTemp = jobPaths.returnCode.plusExt("kill")
 
@@ -323,7 +340,9 @@ class DispatchedConfigAsyncJobExecutionActor(override val standardParams: Standa
               // Essentially, this covers the rare race condition whereby the task completes between starting to write the
               // fake RC, and trying to copy it:
 
-              log.error(s"An RC file appeared at ${jobPaths.returnCode} whilst trying to copy a fake exitcode file from ${returnCodeTemp}. Not to worry: the real file should now be picked up on the next poll.")
+              log.error(
+                s"An RC file appeared at ${jobPaths.returnCode} whilst trying to copy a fake exitcode file from ${returnCodeTemp}. Not to worry: the real file should now be picked up on the next poll."
+              )
 
               // Delete the fake file since it's not needed:
               returnCodeTemp.delete(true)
@@ -347,7 +366,6 @@ class DispatchedConfigAsyncJobExecutionActor(override val standardParams: Standa
   override def isTerminal(runStatus: SharedFileSystemRunState): Boolean = runStatus.terminal
 }
 
-
 object DispatchedConfigAsyncJobExecutionActor {
   def getJob(stdoutContent: String, stderr: Path, jobIdRegexString: String): StandardAsyncJob = {
     val jobIdRegex = jobIdRegexString.r
@@ -355,9 +373,10 @@ object DispatchedConfigAsyncJobExecutionActor {
     jobIdRegex findFirstIn output match {
       case Some(jobIdRegex(jobId)) => StandardAsyncJob(jobId)
       case _ =>
-        throw new RuntimeException("Could not find job ID from stdout file." +
-          s"Check the stderr file for possible errors: $stderr")
+        throw new RuntimeException(
+          "Could not find job ID from stdout file." +
+            s"Check the stderr file for possible errors: $stderr"
+        )
     }
   }
 }
-
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashing.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashing.scala
index 8676479883a..e3a62b549c6 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashing.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashing.scala
@@ -9,9 +9,9 @@ import scala.language.postfixOps
 import scala.util.Try
 
 private[config] object ConfigBackendFileHashing {
-  def getMd5Result(request: SingleFileHashRequest, log: LoggingAdapter): Try[String] ={
-    val path = DefaultPathBuilder.build(request.file.valueString) recover {
-      case failure => throw new RuntimeException("Failed to construct path to hash", failure)
+  def getMd5Result(request: SingleFileHashRequest, log: LoggingAdapter): Try[String] = {
+    val path = DefaultPathBuilder.build(request.file.valueString) recover { case failure =>
+      throw new RuntimeException("Failed to construct path to hash", failure)
     } get
 
     tryWithResource(() => path.newInputStream) { inputStream =>
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashingActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashingActor.scala
index a406730afa6..d18d828eed8 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashingActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendFileHashingActor.scala
@@ -13,14 +13,16 @@ object ConfigBackendFileHashingActor {
   def props(standardParams: StandardFileHashingActorParams) = Props(new ConfigBackendFileHashingActor(standardParams))
 }
 
-class ConfigBackendFileHashingActor(standardParams: StandardFileHashingActorParams) extends StandardFileHashingActor(standardParams) {
+class ConfigBackendFileHashingActor(standardParams: StandardFileHashingActorParams)
+    extends StandardFileHashingActor(standardParams) {
 
   override val ioCommandBuilder = GcsBatchCommandBuilder
-  
-  lazy val hashingStrategy: ConfigHashingStrategy = {
-    configurationDescriptor.backendConfig.as[Option[Config]]("filesystems.local.caching") map ConfigHashingStrategy.apply getOrElse ConfigHashingStrategy.defaultStrategy
-  }
-  
+
+  lazy val hashingStrategy: ConfigHashingStrategy =
+    configurationDescriptor.backendConfig.as[Option[Config]](
+      "filesystems.local.caching"
+    ) map ConfigHashingStrategy.apply getOrElse ConfigHashingStrategy.defaultStrategy
+
   override def customHashStrategy(fileRequest: SingleFileHashRequest): Option[Try[String]] = {
     log.debug(hashingStrategy.toString)
     Option(hashingStrategy.getHash(fileRequest, log))
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendLifecycleActorFactory.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendLifecycleActorFactory.scala
index 9ce1538cb00..1211e39fc80 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendLifecycleActorFactory.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigBackendLifecycleActorFactory.scala
@@ -14,22 +14,26 @@ import org.slf4j.{Logger, LoggerFactory}
   * @param configurationDescriptor The config information.
   */
 class ConfigBackendLifecycleActorFactory(val name: String, val configurationDescriptor: BackendConfigurationDescriptor)
-  extends SharedFileSystemBackendLifecycleActorFactory {
+    extends SharedFileSystemBackendLifecycleActorFactory {
 
   lazy val logger: Logger = LoggerFactory.getLogger(getClass)
-  lazy val hashingStrategy: ConfigHashingStrategy = {
-    configurationDescriptor.backendConfig.as[Option[Config]]("filesystems.local.caching") map ConfigHashingStrategy.apply getOrElse ConfigHashingStrategy.defaultStrategy
-  }
+  lazy val hashingStrategy: ConfigHashingStrategy =
+    configurationDescriptor.backendConfig.as[Option[Config]](
+      "filesystems.local.caching"
+    ) map ConfigHashingStrategy.apply getOrElse ConfigHashingStrategy.defaultStrategy
 
   override lazy val initializationActorClass: Class[ConfigInitializationActor] = classOf[ConfigInitializationActor]
 
   override lazy val asyncExecutionActorClass: Class[_ <: ConfigAsyncJobExecutionActor] = {
-    val runInBackground = configurationDescriptor.backendConfig.as[Option[Boolean]](RunInBackgroundConfig).getOrElse(false)
+    val runInBackground =
+      configurationDescriptor.backendConfig.as[Option[Boolean]](RunInBackgroundConfig).getOrElse(false)
     if (runInBackground)
       classOf[BackgroundConfigAsyncJobExecutionActor]
     else
       classOf[DispatchedConfigAsyncJobExecutionActor]
   }
 
-  override lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(classOf[ConfigBackendFileHashingActor])
+  override lazy val fileHashingActorClassOption: Option[Class[_ <: StandardFileHashingActor]] = Option(
+    classOf[ConfigBackendFileHashingActor]
+  )
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategy.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategy.scala
index 1478819f72a..2c70739af57 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategy.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategy.scala
@@ -20,24 +20,24 @@ object ConfigHashingStrategy {
   val defaultStrategy = HashFileMd5Strategy(checkSiblingMd5 = false)
 
   def apply(hashingConfig: Config): ConfigHashingStrategy = {
-      val checkSiblingMd5 = hashingConfig.as[Option[Boolean]]("check-sibling-md5").getOrElse(false)
-
-      // Fingerprint strategy by default checks the first 10 MiB (10485760 bytes) for performance reasons.
-      // 100 MB will take to much time on network file systems. 1 MB might not be unique enough.
-      // The value is user configurable.
-      lazy val fingerprintSize = hashingConfig.as[Option[Long]]("fingerprint-size").getOrElse(10L * 1024 * 1024)
-
-      hashingConfig.as[Option[String]]("hashing-strategy").getOrElse("file") match {
-        case "path" => HashPathStrategy(checkSiblingMd5)
-        case "file" => HashFileMd5Strategy(checkSiblingMd5)
-        case "md5" => HashFileMd5Strategy(checkSiblingMd5)
-        case "path+modtime" => HashPathModTimeStrategy(checkSiblingMd5)
-        case "xxh64" => HashFileXxH64Strategy(checkSiblingMd5)
-        case "fingerprint" => FingerprintStrategy(checkSiblingMd5, fingerprintSize)
-        case what =>
-          logger.warn(s"Unrecognized hashing strategy $what.")
-          HashPathStrategy(checkSiblingMd5)
-      }
+    val checkSiblingMd5 = hashingConfig.as[Option[Boolean]]("check-sibling-md5").getOrElse(false)
+
+    // Fingerprint strategy by default checks the first 10 MiB (10485760 bytes) for performance reasons.
+    // 100 MB will take to much time on network file systems. 1 MB might not be unique enough.
+    // The value is user configurable.
+    lazy val fingerprintSize = hashingConfig.as[Option[Long]]("fingerprint-size").getOrElse(10L * 1024 * 1024)
+
+    hashingConfig.as[Option[String]]("hashing-strategy").getOrElse("file") match {
+      case "path" => HashPathStrategy(checkSiblingMd5)
+      case "file" => HashFileMd5Strategy(checkSiblingMd5)
+      case "md5" => HashFileMd5Strategy(checkSiblingMd5)
+      case "path+modtime" => HashPathModTimeStrategy(checkSiblingMd5)
+      case "xxh64" => HashFileXxH64Strategy(checkSiblingMd5)
+      case "fingerprint" => FingerprintStrategy(checkSiblingMd5, fingerprintSize)
+      case what =>
+        logger.warn(s"Unrecognized hashing strategy $what.")
+        HashPathStrategy(checkSiblingMd5)
+    }
   }
 }
 
@@ -53,7 +53,8 @@ abstract class ConfigHashingStrategy {
     def usingStandardInitData(initData: StandardInitializationData) = {
       val pathBuilders = initData.workflowPaths.pathBuilders
       val file = PathFactory.buildPath(request.file.valueString, pathBuilders).followSymbolicLinks
-      if (!file.exists) Failure(new FileNotFoundException(s"Cannot hash file $file because it can't be found")) else {
+      if (!file.exists) Failure(new FileNotFoundException(s"Cannot hash file $file because it can't be found"))
+      else {
         if (checkSiblingMd5) {
           precomputedMd5(file) match {
             case Some(md5) => Try(md5.contentAsString.trim)
@@ -65,7 +66,8 @@ abstract class ConfigHashingStrategy {
 
     request.initializationData match {
       case Some(initData: StandardInitializationData) => usingStandardInitData(initData)
-      case _ => Failure(new IllegalArgumentException("Need SharedFileSystemBackendInitializationData to calculate hash."))
+      case _ =>
+        Failure(new IllegalArgumentException("Need SharedFileSystemBackendInitializationData to calculate hash."))
     }
   }
 
@@ -74,54 +76,51 @@ abstract class ConfigHashingStrategy {
     if (md5.exists) Option(md5) else None
   }
 
-  override def toString: String = {
+  override def toString: String =
     s"Call caching hashing strategy: $checkSiblingMessage$description."
-  }
 }
 
 final case class HashPathStrategy(checkSiblingMd5: Boolean) extends ConfigHashingStrategy {
-  override def hash(file: Path): Try[String] = {
+  override def hash(file: Path): Try[String] =
     Try(DigestUtils.md5Hex(file.toAbsolutePath.pathAsString))
-  }
 
   override val description = "hash file path"
 }
 
 final case class HashPathModTimeStrategy(checkSiblingMd5: Boolean) extends ConfigHashingStrategy {
-  override def hash(file: Path): Try[String] = {
+  override def hash(file: Path): Try[String] =
     // Add the last modified date here to make sure these are the files we are looking for.
     Try(DigestUtils.md5Hex(file.toAbsolutePath.pathAsString + file.lastModifiedTime.toString))
-  }
 
   override val description = "hash file path and last modified time"
 }
 
 final case class HashFileMd5Strategy(checkSiblingMd5: Boolean) extends ConfigHashingStrategy {
-  override protected def hash(file: Path): Try[String] = {
-    tryWithResource(() => file.newInputStream) { DigestUtils.md5Hex }
-  }
+  override protected def hash(file: Path): Try[String] =
+    tryWithResource(() => file.newInputStream)(DigestUtils.md5Hex)
 
   override val description = "hash file content with md5"
 }
 
 final case class HashFileXxH64Strategy(checkSiblingMd5: Boolean) extends ConfigHashingStrategy {
-  override protected def hash(file: Path): Try[String] = {
-    tryWithResource(() => file.newInputStream) {HashFileXxH64StrategyMethods.xxh64sum(_)}
-  }
+  override protected def hash(file: Path): Try[String] =
+    tryWithResource(() => file.newInputStream)(HashFileXxH64StrategyMethods.xxh64sum(_))
   override val description = "hash file content with xxh64"
 }
 
 final case class FingerprintStrategy(checkSiblingMd5: Boolean, fingerprintSize: Long) extends ConfigHashingStrategy {
-  override protected def hash(file: Path): Try[String] = {
+  override protected def hash(file: Path): Try[String] =
     Try {
       // Calculate the xxh64 hash of last modified time and filesize. These are NOT added, as it will lead to loss of
       // information. Instead their hexstrings are concatenated and then hashed.
-      HashFileXxH64StrategyMethods.xxh64sumString(file.lastModifiedTime.toEpochMilli.toHexString +
-      file.size.toHexString) +
-      HashFileXxH64StrategyMethods.xxh64sum(file.newInputStream, maxSize = fingerprintSize)
-      }
+      HashFileXxH64StrategyMethods.xxh64sumString(
+        file.lastModifiedTime.toEpochMilli.toHexString +
+          file.size.toHexString
+      ) +
+        HashFileXxH64StrategyMethods.xxh64sum(file.newInputStream, maxSize = fingerprintSize)
     }
-  override val description = "fingerprint the file with last modified time, size and a xxh64 hash of the first part of the file"
+  override val description =
+    "fingerprint the file with last modified time, size and a xxh64 hash of the first part of the file"
 }
 
 object HashFileXxH64StrategyMethods {
@@ -139,17 +138,17 @@ object HashFileXxH64StrategyMethods {
   def xxh64sum(inputStream: InputStream,
                bufferSize: Int = defaultBufferSize,
                maxSize: Long = Long.MaxValue,
-               seed: Long = 0L): String = {
+               seed: Long = 0L
+  ): String = {
     val hasher = xxhashFactory.newStreamingHash64(seed)
     val buffer: Array[Byte] = new Array[Byte](bufferSize)
     var byteCounter: Long = 0
-    try {
+    try
       while (inputStream.available() > 0 && byteCounter < maxSize) {
         val length: Int = inputStream.read(buffer)
         hasher.update(buffer, 0, length)
         byteCounter += length
       }
-    }
     finally inputStream.close()
     // Long.toHexString does not add leading zero's
     f"%%16s".format(hasher.getValue.toHexString).replace(" ", "0")
@@ -165,4 +164,3 @@ object HashFileXxH64StrategyMethods {
     f"%%16s".format(hash.toHexString).replace(" ", "0")
   }
 }
-
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigInitializationActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigInitializationActor.scala
index ea34521c8a8..b1e30ab7506 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigInitializationActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigInitializationActor.scala
@@ -2,7 +2,11 @@ package cromwell.backend.impl.sfs.config
 
 import cromwell.backend.io.WorkflowPaths
 import cromwell.backend.sfs._
-import cromwell.backend.standard.{StandardInitializationActorParams, StandardInitializationData, StandardValidatedRuntimeAttributesBuilder}
+import cromwell.backend.standard.{
+  StandardInitializationActorParams,
+  StandardInitializationData,
+  StandardValidatedRuntimeAttributesBuilder
+}
 import wdl.draft2.model.WdlNamespace
 
 import scala.concurrent.Future
@@ -17,14 +21,14 @@ import scala.concurrent.Future
   * @param declarationValidations   A collection of validations for each declaration.
   * @param wdlNamespace             A collection of WDL tasks for submitting, killing, etc.
   */
-class ConfigInitializationData
-(
-  workflowPaths: WorkflowPaths,
-  runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder,
-  val declarationValidations: Seq[DeclarationValidation],
-  val wdlNamespace: WdlNamespace)
-  extends StandardInitializationData(workflowPaths, runtimeAttributesBuilder,
-    classOf[SharedFileSystemExpressionFunctions])
+class ConfigInitializationData(workflowPaths: WorkflowPaths,
+                               runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder,
+                               val declarationValidations: Seq[DeclarationValidation],
+                               val wdlNamespace: WdlNamespace
+) extends StandardInitializationData(workflowPaths,
+                                     runtimeAttributesBuilder,
+                                     classOf[SharedFileSystemExpressionFunctions]
+    )
 
 /**
   * Extends the SharedFileSystemInitializationActor to create an instance of the ConfigInitializationData.
@@ -34,13 +38,14 @@ class ConfigInitializationData
   * @param params Parameters to create an initialization actor.
   */
 class ConfigInitializationActor(params: StandardInitializationActorParams)
-  extends SharedFileSystemInitializationActor(params) {
+    extends SharedFileSystemInitializationActor(params) {
 
   private lazy val configWdlNamespace = new ConfigWdlNamespace(params.configurationDescriptor.backendConfig)
 
-  lazy val declarationValidations: Seq[DeclarationValidation] = {
-    DeclarationValidation.fromDeclarations(configWdlNamespace.runtimeDeclarations, configWdlNamespace.callCachedRuntimeAttributes)
-  }
+  lazy val declarationValidations: Seq[DeclarationValidation] =
+    DeclarationValidation.fromDeclarations(configWdlNamespace.runtimeDeclarations,
+                                           configWdlNamespace.callCachedRuntimeAttributes
+    )
 
   override lazy val initializationData: Future[ConfigInitializationData] = {
     val wdlNamespace = configWdlNamespace.wdlNamespace
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigWdlNamespace.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigWdlNamespace.scala
index e5d84f38331..e06ebf66e84 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigWdlNamespace.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigWdlNamespace.scala
@@ -20,22 +20,27 @@ class ConfigWdlNamespace(backendConfig: Config) {
   private val configRuntimeAttributes = backendConfig.as[Option[String]](RuntimeAttributesConfig).getOrElse("")
 
   private val submitCommandOption = backendConfig.as[Option[String]](SubmitConfig)
-  private val submitSourceOption = submitCommandOption.map(makeWdlSource(
-    SubmitTask, _, submitRuntimeAttributes + configRuntimeAttributes))
+  private val submitSourceOption =
+    submitCommandOption.map(makeWdlSource(SubmitTask, _, submitRuntimeAttributes + configRuntimeAttributes))
 
   private val submitDockerCommandOption = backendConfig.as[Option[String]](SubmitDockerConfig)
-  private val submitDockerSourceOption = submitDockerCommandOption.map(makeWdlSource(
-    SubmitDockerTask, _, submitRuntimeAttributes + submitDockerRuntimeAttributes + configRuntimeAttributes))
+  private val submitDockerSourceOption = submitDockerCommandOption.map(
+    makeWdlSource(SubmitDockerTask,
+                  _,
+                  submitRuntimeAttributes + submitDockerRuntimeAttributes + configRuntimeAttributes
+    )
+  )
 
   private val killCommandOption = backendConfig.as[Option[String]](KillConfig)
   private val killSourceOption = killCommandOption.map(makeWdlSource(KillTask, _, jobIdRuntimeAttributes))
 
   private val killDockerCommandOption = backendConfig.as[Option[String]](KillDockerConfig)
-  private val killDockerSourceOption = killDockerCommandOption.map(makeWdlSource(KillDockerTask, _, jobIdRuntimeAttributes))
+  private val killDockerSourceOption =
+    killDockerCommandOption.map(makeWdlSource(KillDockerTask, _, jobIdRuntimeAttributes))
 
   private val checkAliveCommandOption = backendConfig.as[Option[String]](CheckAliveConfig)
-  private val checkAliveSourceOption = checkAliveCommandOption.map(makeWdlSource(
-    CheckAliveTask, _, jobIdRuntimeAttributes))
+  private val checkAliveSourceOption =
+    checkAliveCommandOption.map(makeWdlSource(CheckAliveTask, _, jobIdRuntimeAttributes))
 
   private val workflowSource =
     s"""
@@ -49,12 +54,11 @@ class ConfigWdlNamespace(backendConfig: Config) {
   /**
     * The wdl namespace containing the submit, kill, and check alive tasks.
     */
-  val wdlNamespace = {
+  val wdlNamespace =
     WdlNamespace.loadUsingSource(workflowSource, None, None) match {
       case Success(ns) => ns
       case Failure(f) => throw new RuntimeException(s"Error parsing generated wdl:\n$workflowSource".stripMargin, f)
     }
-  }
 
   private val runtimeAttributesTask = makeTask(RuntimeAttributesTask, "", configRuntimeAttributes)
 
@@ -62,12 +66,13 @@ class ConfigWdlNamespace(backendConfig: Config) {
     * The declarations of runtime attributes.
     */
   val runtimeDeclarations = runtimeAttributesTask.declarations
-  val callCachedRuntimeAttributes = backendConfig.as[Option[Map[String, Boolean]]](RuntimeAttributesCachingConfig).getOrElse(Map.empty)
+  val callCachedRuntimeAttributes =
+    backendConfig.as[Option[Map[String, Boolean]]](RuntimeAttributesCachingConfig).getOrElse(Map.empty)
 
 }
 
 object ConfigWdlNamespace {
-  private def makeWdlSource(taskName: String, command: String, declarations: String): WorkflowSource = {
+  private def makeWdlSource(taskName: String, command: String, declarations: String): WorkflowSource =
     s"""
        |task $taskName {
        |$declarations
@@ -76,7 +81,6 @@ object ConfigWdlNamespace {
        |}
        |}
        |""".stripMargin
-  }
 
   private def makeTask(taskName: String, command: String, declarations: String): WdlTask = {
     val workflowSource = makeWdlSource(taskName, command, declarations)
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/CpuDeclarationValidation.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/CpuDeclarationValidation.scala
index 455cf2bec81..19721aeef7c 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/CpuDeclarationValidation.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/CpuDeclarationValidation.scala
@@ -6,12 +6,12 @@ import eu.timepit.refined.numeric.Positive
 import wdl.draft2.model.Declaration
 import wom.values.WomValue
 
-class CpuDeclarationValidation(declaration: Declaration, instanceValidation: RuntimeAttributesValidation[Int Refined Positive])
-  extends DeclarationValidation(declaration, instanceValidation, usedInCallCachingOverride = Option(false)) {
+class CpuDeclarationValidation(declaration: Declaration,
+                               instanceValidation: RuntimeAttributesValidation[Int Refined Positive]
+) extends DeclarationValidation(declaration, instanceValidation, usedInCallCachingOverride = Option(false)) {
 
-  override def extractWdlValueOption(validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[WomValue] = {
+  override def extractWdlValueOption(validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[WomValue] =
     RuntimeAttributesValidation.extractOption(instanceValidation, validatedRuntimeAttributes) map { refined =>
       declaration.womType.coerceRawValue(refined.value).get
     }
-  }
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala
index 221f4d16fb7..7b5bcd4e7fc 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala
@@ -14,9 +14,10 @@ import scala.annotation.tailrec
   * Creates instances of runtime attribute validations from WDL declarations.
   */
 object DeclarationValidation {
-  def fromDeclarations(declarations: Seq[Declaration], callCachedRuntimeAttributes: Map[String, Boolean]): Seq[DeclarationValidation] = {
+  def fromDeclarations(declarations: Seq[Declaration],
+                       callCachedRuntimeAttributes: Map[String, Boolean]
+  ): Seq[DeclarationValidation] =
     declarations map fromDeclaration(callCachedRuntimeAttributesMap = callCachedRuntimeAttributes) _
-  }
 
   /**
     * Create a runtime attribute validation from a WDL declaration.
@@ -24,7 +25,9 @@ object DeclarationValidation {
     * @param declaration The declaration.
     * @return The DeclarationValidation object for the declaration.
     */
-  def fromDeclaration(callCachedRuntimeAttributesMap: Map[String, Boolean])(declaration: Declaration): DeclarationValidation = {
+  def fromDeclaration(
+    callCachedRuntimeAttributesMap: Map[String, Boolean]
+  )(declaration: Declaration): DeclarationValidation =
     declaration.unqualifiedName match {
       // Docker and CPU are special keys understood by cromwell.
       case name if name == DockerValidation.instance.key =>
@@ -33,13 +36,26 @@ object DeclarationValidation {
       case RuntimeAttributesKeys.CpuMinKey => new CpuDeclarationValidation(declaration, CpuValidation.instanceMin)
       case RuntimeAttributesKeys.CpuMaxKey => new CpuDeclarationValidation(declaration, CpuValidation.instanceMax)
       // See MemoryDeclarationValidation for more info
-      case name if MemoryDeclarationValidation.isMemoryDeclaration(name, MemoryRuntimeAttribute, MemoryRuntimeAttributePrefix) =>
+      case name
+          if MemoryDeclarationValidation.isMemoryDeclaration(name,
+                                                             MemoryRuntimeAttribute,
+                                                             MemoryRuntimeAttributePrefix
+          ) =>
         new MemoryDeclarationValidation(declaration, MemoryRuntimeAttribute, MemoryRuntimeAttributePrefix)
-      case name if MemoryDeclarationValidation.isMemoryDeclaration(name, MemoryMinRuntimeAttribute, MemoryRuntimeAttributePrefix) =>
+      case name
+          if MemoryDeclarationValidation.isMemoryDeclaration(name,
+                                                             MemoryMinRuntimeAttribute,
+                                                             MemoryRuntimeAttributePrefix
+          ) =>
         new MemoryDeclarationValidation(declaration, MemoryMinRuntimeAttribute, MemoryMinRuntimeAttributePrefix)
-      case name if MemoryDeclarationValidation.isMemoryDeclaration(name, MemoryMaxRuntimeAttribute, MemoryRuntimeAttributePrefix) =>
+      case name
+          if MemoryDeclarationValidation.isMemoryDeclaration(name,
+                                                             MemoryMaxRuntimeAttribute,
+                                                             MemoryRuntimeAttributePrefix
+          ) =>
         new MemoryDeclarationValidation(declaration, MemoryMaxRuntimeAttribute, MemoryMaxRuntimeAttributePrefix)
-      case name if MemoryDeclarationValidation.isMemoryDeclaration(name, DiskRuntimeAttribute, DiskRuntimeAttributePrefix) =>
+      case name
+          if MemoryDeclarationValidation.isMemoryDeclaration(name, DiskRuntimeAttribute, DiskRuntimeAttributePrefix) =>
         new MemoryDeclarationValidation(declaration, DiskRuntimeAttribute, DiskRuntimeAttributePrefix)
       // All other declarations must be a Boolean, Float, Integer, or String.
       case _ =>
@@ -50,10 +66,9 @@ object DeclarationValidation {
           usedInCallCachingOverride = callCachedRuntimeAttributesMap.get(declaration.unqualifiedName)
         )
     }
-  }
 
   @tailrec
-  private def validator(womType: WomType, unqualifiedName: String): PrimitiveRuntimeAttributesValidation[_, _] = {
+  private def validator(womType: WomType, unqualifiedName: String): PrimitiveRuntimeAttributesValidation[_, _] =
     womType match {
       case WomBooleanType => new BooleanRuntimeAttributesValidation(unqualifiedName)
       case WomFloatType => new FloatRuntimeAttributesValidation(unqualifiedName)
@@ -62,7 +77,6 @@ object DeclarationValidation {
       case WomOptionalType(x) => validator(x, unqualifiedName)
       case other => throw new RuntimeException(s"Unsupported config runtime attribute $other $unqualifiedName")
     }
-  }
 }
 
 /**
@@ -71,7 +85,10 @@ object DeclarationValidation {
   * @param declaration        The declaration from the config "runtime-attributes".
   * @param instanceValidation A basic instance validation for the declaration.
   */
-class DeclarationValidation(declaration: Declaration, instanceValidation: RuntimeAttributesValidation[_], usedInCallCachingOverride: Option[Boolean]) {
+class DeclarationValidation(declaration: Declaration,
+                            instanceValidation: RuntimeAttributesValidation[_],
+                            usedInCallCachingOverride: Option[Boolean]
+) {
   val key: String = declaration.unqualifiedName
 
   /**
@@ -97,12 +114,16 @@ class DeclarationValidation(declaration: Declaration, instanceValidation: Runtim
     // As a first approximation, think "caseClass.copy, but for validation functions"
     // In this case, we might (or might not) want to make our validations:
     // 1. have defaults:
-    val validationWithDefault = if (declaration.expression.isDefined) default(instanceValidation, declaration.expression.get) else instanceValidation
+    val validationWithDefault =
+      if (declaration.expression.isDefined) default(instanceValidation, declaration.expression.get)
+      else instanceValidation
     // 2. be optional:
-    val validationWithDefaultAndOptionality = if (declaration.womType.isInstanceOf[WomOptionalType]) validationWithDefault.optional else validationWithDefault
+    val validationWithDefaultAndOptionality =
+      if (declaration.womType.isInstanceOf[WomOptionalType]) validationWithDefault.optional else validationWithDefault
     // Or 3. have customized call caching properties:
     val validationWithDefaultAndOptionalityAndCallCaching = usedInCallCachingOverride match {
-      case Some(usedInCallCachingValue) => RuntimeAttributesValidation.withUsedInCallCaching(validationWithDefaultAndOptionality, usedInCallCachingValue)
+      case Some(usedInCallCachingValue) =>
+        RuntimeAttributesValidation.withUsedInCallCaching(validationWithDefaultAndOptionality, usedInCallCachingValue)
       case None => validationWithDefaultAndOptionality
     }
 
@@ -117,9 +138,9 @@ class DeclarationValidation(declaration: Declaration, instanceValidation: Runtim
     * @return A new copy of the validation with the default value.
     */
   protected def default(validation: RuntimeAttributesValidation[_],
-                        wdlExpression: WdlExpression): RuntimeAttributesValidation[_] = {
+                        wdlExpression: WdlExpression
+  ): RuntimeAttributesValidation[_] =
     validation.withDefault(wdlExpression.evaluate(NoLookup, NoFunctions).get)
-  }
 
   /**
     * Utility to get the value of this declaration from a collection of validated runtime attributes.
@@ -127,9 +148,8 @@ class DeclarationValidation(declaration: Declaration, instanceValidation: Runtim
     * @param validatedRuntimeAttributes The validated attributes.
     * @return The value from the collection wrapped in `Some`, or `None` if the value wasn't found.
     */
-  def extractWdlValueOption(validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[WomValue] = {
+  def extractWdlValueOption(validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[WomValue] =
     RuntimeAttributesValidation.extractOption(instanceValidation, validatedRuntimeAttributes) map {
       declaration.womType.coerceRawValue(_).get
     }
-  }
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidation.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidation.scala
index 7eab2f58b78..df712cd0fd6 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidation.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidation.scala
@@ -31,7 +31,10 @@ import wom.values._
   * @param declaration The declaration used to create this memory validation.
   */
 class MemoryDeclarationValidation(declaration: Declaration, attributeName: String, attributeNamePrefix: String)
-  extends DeclarationValidation(declaration, MemoryValidation.instance(attributeName), usedInCallCachingOverride = Option(false)) {
+    extends DeclarationValidation(declaration,
+                                  MemoryValidation.instance(attributeName),
+                                  usedInCallCachingOverride = Option(false)
+    ) {
 
   import MemoryDeclarationValidation._
 
@@ -46,14 +49,15 @@ class MemoryDeclarationValidation(declaration: Declaration, attributeName: Strin
     * @return The new validation.
     */
   override protected def default(validation: RuntimeAttributesValidation[_],
-                                 wdlExpression: WdlExpression): RuntimeAttributesValidation[_] = {
+                                 wdlExpression: WdlExpression
+  ): RuntimeAttributesValidation[_] = {
     val womValue = declaration.expression.get.evaluate(NoLookup, NoFunctions).get
     val amount: Double = defaultAmount(womValue)
     val memorySize = MemorySize(amount, declarationMemoryUnit)
     validation.withDefault(WomLong(memorySize.bytes.toLong))
   }
 
-  private def defaultAmount(womValue: WomValue): Double = {
+  private def defaultAmount(womValue: WomValue): Double =
     womValue match {
       case WomInteger(value) => value.toDouble
       case WomLong(value) => value.toDouble
@@ -61,7 +65,6 @@ class MemoryDeclarationValidation(declaration: Declaration, attributeName: Strin
       case WomOptionalValue(_, Some(optionalWdlValue)) => defaultAmount(optionalWdlValue)
       case other => throw new RuntimeException(s"Unsupported memory default: $other")
     }
-  }
 
   private lazy val declarationMemoryUnit: MemoryUnit = {
     val suffix = memoryUnitSuffix(declaration.unqualifiedName, attributeName, attributeNamePrefix)
@@ -78,10 +81,9 @@ class MemoryDeclarationValidation(declaration: Declaration, attributeName: Strin
     * @param validatedRuntimeAttributes The validated attributes.
     * @return The value from the collection wrapped in `Some`, or `None` if the value wasn't found.
     */
-  override def extractWdlValueOption(validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[WomValue] = {
+  override def extractWdlValueOption(validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[WomValue] =
     RuntimeAttributesValidation.extractOption(MemoryValidation.instance(attributeName), validatedRuntimeAttributes) map
       coerceMemorySize(declaration.womType)
-  }
 
   private def coerceMemorySize(womType: WomType)(value: MemorySize): WomValue = {
     val amount = value.to(declarationMemoryUnit).amount
@@ -95,7 +97,7 @@ class MemoryDeclarationValidation(declaration: Declaration, attributeName: Strin
 }
 
 object MemoryDeclarationValidation {
-  def isMemoryDeclaration(name: String, attributeName: String, attributeNamePrefix: String): Boolean = {
+  def isMemoryDeclaration(name: String, attributeName: String, attributeNamePrefix: String): Boolean =
     name match {
       case `attributeName` => true
       case prefixed if prefixed.startsWith(attributeNamePrefix) =>
@@ -105,12 +107,10 @@ object MemoryDeclarationValidation {
         }
       case _ => false
     }
-  }
 
-  private def memoryUnitSuffix(name: String, attributeName: String, attributeNamePrefix: String) = {
+  private def memoryUnitSuffix(name: String, attributeName: String, attributeNamePrefix: String) =
     if (name == attributeName)
       MemoryUnit.Bytes.suffixes.head
     else
       name.substring(attributeNamePrefix.length)
-  }
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/BackgroundAsyncJobExecutionActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/BackgroundAsyncJobExecutionActor.scala
index 199c08787a0..9648d7ea411 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/BackgroundAsyncJobExecutionActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/BackgroundAsyncJobExecutionActor.scala
@@ -8,9 +8,8 @@ trait BackgroundAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecution
 
   lazy val backgroundScript = jobPaths.script.plusExt("background")
 
-  override def writeScriptContents(): Either[ExecutionHandle, Unit] = {
+  override def writeScriptContents(): Either[ExecutionHandle, Unit] =
     super.writeScriptContents().flatMap(_ => writeBackgroundScriptContents())
-  }
 
   /**
     * Run the command via bash in the background, and echo the PID.
@@ -18,11 +17,10 @@ trait BackgroundAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecution
   private def writeBackgroundScriptContents(): Either[ExecutionHandle, Unit] = {
     val backgroundCommand = redirectOutputs(processArgs.argv.mkString("'", "' '", "'"))
     // $! contains the previous background command's process id (PID)
-    backgroundScript.write(
-      s"""|#!/bin/bash
-          |BACKGROUND_COMMAND &
-          |echo $$!
-          |""".stripMargin.replace("BACKGROUND_COMMAND", backgroundCommand))
+    backgroundScript.write(s"""|#!/bin/bash
+                               |BACKGROUND_COMMAND &
+                               |echo $$!
+                               |""".stripMargin.replace("BACKGROUND_COMMAND", backgroundCommand))
     Right(())
   }
 
@@ -38,9 +36,8 @@ trait BackgroundAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecution
     StandardAsyncJob(pid)
   }
 
-  override def checkAliveArgs(job: StandardAsyncJob): SharedFileSystemCommand = {
+  override def checkAliveArgs(job: StandardAsyncJob): SharedFileSystemCommand =
     SharedFileSystemCommand("ps", job.jobId)
-  }
 
   override def killArgs(job: StandardAsyncJob): SharedFileSystemCommand = {
     val killScript = jobPaths.script.plusExt("kill")
@@ -52,21 +49,20 @@ trait BackgroundAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecution
     /*
     Use pgrep to find the children of a process, and recursively kill the children before killing the parent.
      */
-    killScript.write(
-      s"""|#!/bin/bash
-          |kill_tree() {
-          |  local pid
-          |  local cpid
-          |  pid=$$1
-          |  for cpid in $$(pgrep -P "$$pid"); do
-          |    kill_tree "$$cpid"
-          |  done
-          |  echo killing "$$pid"
-          |  kill "$$pid"
-          |}
-          |
-          |kill_tree "${job.jobId}"
-          |""".stripMargin)
+    killScript.write(s"""|#!/bin/bash
+                         |kill_tree() {
+                         |  local pid
+                         |  local cpid
+                         |  pid=$$1
+                         |  for cpid in $$(pgrep -P "$$pid"); do
+                         |    kill_tree "$$cpid"
+                         |  done
+                         |  echo killing "$$pid"
+                         |  kill "$$pid"
+                         |}
+                         |
+                         |kill_tree "${job.jobId}"
+                         |""".stripMargin)
     ()
   }
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystem.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystem.scala
index eaf087f50c7..f1ab13d9234 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystem.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystem.scala
@@ -33,8 +33,8 @@ object SharedFileSystem extends StrictLogging {
 
   object AttemptedLookupResult {
     implicit class AugmentedAttemptedLookupSequence(s: Seq[AttemptedLookupResult]) {
-      def toLookupMap: Map[String, WomValue] = s collect {
-        case AttemptedLookupResult(name, Success(value)) => (name, value)
+      def toLookupMap: Map[String, WomValue] = s collect { case AttemptedLookupResult(name, Success(value)) =>
+        (name, value)
       } toMap
     }
   }
@@ -42,10 +42,9 @@ object SharedFileSystem extends StrictLogging {
   case class PairOfFiles(src: Path, dst: Path)
   type DuplicationStrategy = (Path, Path, Boolean) => Try[Unit]
 
-  private def createParentDirectory(executionPath: Path, docker: Boolean) = {
+  private def createParentDirectory(executionPath: Path, docker: Boolean) =
     if (docker) executionPath.parent.createPermissionedDirectories()
     else executionPath.parent.createDirectories()
-  }
 
   /**
     * Return a `Success` result if the file has already been localized, otherwise `Failure`.
@@ -71,24 +70,29 @@ object SharedFileSystem extends StrictLogging {
     logOnFailure(action, "hard link")
   }
 
-  private def localizePathViaSymbolicLink(originalPath: Path, executionPath: Path, docker: Boolean): Try[Unit] = {
-      if (originalPath.isDirectory) Failure(new UnsupportedOperationException("Cannot localize directory with symbolic links"))
-      else if (!originalPath.exists) Failure(new FileNotFoundException(originalPath.pathAsString))
-      else {
-        val action = Try {
-          createParentDirectory(executionPath, docker)
-          executionPath.linkTo(originalPath, symbolic = true)
-        }.void
-        logOnFailure(action, "symbolic link")
-      }
-  }
+  private def localizePathViaSymbolicLink(originalPath: Path, executionPath: Path, docker: Boolean): Try[Unit] =
+    if (originalPath.isDirectory)
+      Failure(new UnsupportedOperationException("Cannot localize directory with symbolic links"))
+    else if (!originalPath.exists) Failure(new FileNotFoundException(originalPath.pathAsString))
+    else {
+      val action = Try {
+        createParentDirectory(executionPath, docker)
+        executionPath.linkTo(originalPath, symbolic = true)
+      }.void
+      logOnFailure(action, "symbolic link")
+    }
 
   private def logOnFailure(action: Try[Unit], actionLabel: String): Try[Unit] = {
     if (action.isFailure) logger.warn(s"Localization via $actionLabel has failed: ${action.failed.get.getMessage}")
     action
   }
 
-  private def duplicate(description: String, source: Path, dest: Path, strategies: LazyList[DuplicationStrategy], docker: Boolean): Try[Unit] = {
+  private def duplicate(description: String,
+                        source: Path,
+                        dest: Path,
+                        strategies: LazyList[DuplicationStrategy],
+                        docker: Boolean
+  ): Try[Unit] = {
     val attempts: LazyList[Try[Unit]] = strategies.map(_.apply(source.followSymbolicLinks, dest, docker))
     attempts.find(_.isSuccess) getOrElse {
       TryUtil.sequence(attempts, s"Could not $description $source -> $dest").void
@@ -97,22 +101,20 @@ object SharedFileSystem extends StrictLogging {
 
   private lazy val beingCopied: mutable.Map[Path, Boolean] = mutable.Map[Path, Boolean]()
 
-  private def waitOnCopy(path: Path, lockFile: Path): Unit = {
-    while (beingCopied.getOrElse(path, false) || lockFile.exists)  {
+  private def waitOnCopy(path: Path, lockFile: Path): Unit =
+    while (beingCopied.getOrElse(path, false) || lockFile.exists)
       Thread.sleep(1)
-    }
-  }
 
-  private def countLinks(path: Path): Int = {
+  private def countLinks(path: Path): Int =
     path.getAttribute("unix:nlink").asInstanceOf[Int]
-  }
 }
 
 trait SharedFileSystem extends PathFactory {
   import SharedFileSystem._
 
   def sharedFileSystemConfig: Config
-  lazy val maxHardLinks: Int = sharedFileSystemConfig.getOrElse[Int]("max-hardlinks",950)  // Windows limit 1024. Keep a safe margin.
+  lazy val maxHardLinks: Int =
+    sharedFileSystemConfig.getOrElse[Int]("max-hardlinks", 950) // Windows limit 1024. Keep a safe margin.
   lazy val cachedCopyDir: Option[Path] = None
 
   private def localizePathViaCachedCopy(originalPath: Path, executionPath: Path, docker: Boolean): Try[Unit] = {
@@ -121,7 +123,8 @@ trait SharedFileSystem extends PathFactory {
       // Hash the parent. This will make sure bamfiles and their indexes stay in the same dir. This is not ideal. But should work.
       // There should be no file collisions because two files with the same name cannot exist in the same parent dir.
       // use .get . This strategy should not be used when there is no cachedCopyDir
-      val cachedCopySubDir: Path = cachedCopyDir.get.createChild(originalPath.toAbsolutePath.parent.hashCode.toString, asDirectory = true)
+      val cachedCopySubDir: Path =
+        cachedCopyDir.get.createChild(originalPath.toAbsolutePath.parent.hashCode.toString, asDirectory = true)
 
       // By prepending the modtime we prevent collisions in the cache from files that have changed in between.
       // Md5 is safer but much much slower and way too CPU intensive for big files.
@@ -142,9 +145,11 @@ trait SharedFileSystem extends PathFactory {
           // The copying may have been started while waiting on the lock.
           // If it is not there or the maxHardLinks are exceeded, is it already being copied by another thread?
           // if not copied by another thread, is it copied by another cromwell process? (Lock file present)
-          if ((!cachedCopyPath.exists || countLinks(cachedCopyPath) >= maxHardLinks) &&
+          if (
+            (!cachedCopyPath.exists || countLinks(cachedCopyPath) >= maxHardLinks) &&
             !SharedFileSystem.beingCopied.getOrElse(cachedCopyPath, false) &&
-            !cachedCopyPathLockFile.exists) {
+            !cachedCopyPathLockFile.exists
+          ) {
             // Create a lock file so other cromwell processes know copying has started
             try {
               cachedCopyPathLockFile.touch()
@@ -174,8 +179,7 @@ trait SharedFileSystem extends PathFactory {
             originalPath.copyTo(cachedCopyTmpPath, overwrite = true).moveTo(cachedCopyPath, overwrite = true)
           } catch {
             case e: Exception => throw e
-          }
-          finally {
+          } finally {
             // Always remove the locks after copying. Even if there is an exception.
             // We remove the key! Not set it to false. We don't want this map being flooded with
             // keys if the cromwell process is active for months in server mode. (Memory leak!)
@@ -197,19 +201,20 @@ trait SharedFileSystem extends PathFactory {
   lazy val DefaultStrategies = Seq("hard-link", "soft-link", "copy")
 
   lazy val LocalizationStrategyNames: Seq[String] = getConfigStrategies("localization")
-  lazy val LocalizationStrategies: Seq[DuplicationStrategy] = createStrategies(LocalizationStrategyNames, docker = false)
-  lazy val DockerLocalizationStrategies: Seq[DuplicationStrategy] = createStrategies(LocalizationStrategyNames, docker = true)
+  lazy val LocalizationStrategies: Seq[DuplicationStrategy] =
+    createStrategies(LocalizationStrategyNames, docker = false)
+  lazy val DockerLocalizationStrategies: Seq[DuplicationStrategy] =
+    createStrategies(LocalizationStrategyNames, docker = true)
 
   lazy val CachingStrategies: Seq[String] = getConfigStrategies("caching.duplication-strategy")
   lazy val Cachers: Seq[DuplicationStrategy] = createStrategies(CachingStrategies, docker = false)
 
-  private def getConfigStrategies(configPath: String): Seq[String] = {
+  private def getConfigStrategies(configPath: String): Seq[String] =
     if (sharedFileSystemConfig.hasPath(configPath)) {
       sharedFileSystemConfig.getStringList(configPath).asScala.toList
     } else {
       DefaultStrategies
     }
-  }
 
   private def createStrategies(configStrategies: Seq[String], docker: Boolean): Seq[DuplicationStrategy] = {
     // If localizing for a docker job, remove soft-link as an option
@@ -238,42 +243,41 @@ trait SharedFileSystem extends PathFactory {
     val path = PathFactory.buildPath(pathString, pathBuilders)
     path match {
       case _: DefaultPath if !path.isAbsolute => jobPaths.callExecutionRoot.resolve(path).toAbsolutePath
-      case _: DefaultPath if jobPaths.isInExecution(path.pathAsString) => jobPaths.hostPathFromContainerPath(path.pathAsString)
+      case _: DefaultPath if jobPaths.isInExecution(path.pathAsString) =>
+        jobPaths.hostPathFromContainerPath(path.pathAsString)
       case _: DefaultPath => jobPaths.hostPathFromContainerInputs(path.pathAsString)
     }
   }
 
-  def outputMapper(job: JobPaths)(womValue: WomValue): Try[WomValue] = {
+  def outputMapper(job: JobPaths)(womValue: WomValue): Try[WomValue] =
     WomFileMapper.mapWomFiles(mapJobWomFile(job))(womValue)
-  }
 
   def mapJobWomFile(jobPaths: JobPaths)(womFile: WomFile): WomFile = {
     val hostPath = hostAbsoluteFilePath(jobPaths, womFile.valueString)
     def hostAbsolute(pathString: String): String = hostAbsoluteFilePath(jobPaths, pathString).pathAsString
 
-    if (!hostPath.exists) throw new FileNotFoundException(s"Could not process output, file not found: ${hostAbsolute(womFile.valueString)}")
+    if (!hostPath.exists)
+      throw new FileNotFoundException(s"Could not process output, file not found: ${hostAbsolute(womFile.valueString)}")
 
     // There are composite WomFile types like WomMaybeListedDirectoryType that need to make the paths of contained
     // WomFiles host absolute, so don't just pass in a `const` of the function call result above.
     womFile mapFile hostAbsolute
   }
 
-  def cacheCopy(sourceFilePath: Path, destinationFilePath: Path): Try[Unit] = {
+  def cacheCopy(sourceFilePath: Path, destinationFilePath: Path): Try[Unit] =
     duplicate("cache", sourceFilePath, destinationFilePath, Cachers.to(LazyList), docker = false)
-  }
 
   /**
    * Return a possibly altered copy of inputs reflecting any localization of input file paths that might have
    * been performed for this `Backend` implementation.
    */
-  def localizeInputs(inputsRoot: Path, docker: Boolean)(inputs: WomEvaluatedCallInputs): Try[WomEvaluatedCallInputs] = {
+  def localizeInputs(inputsRoot: Path, docker: Boolean)(inputs: WomEvaluatedCallInputs): Try[WomEvaluatedCallInputs] =
     TryUtil.sequenceMap(
       inputs safeMapValues WomFileMapper.mapWomFiles(localizeWomFile(inputsRoot, docker)),
       "Failures during localization"
-    ) recoverWith {
-      case e => Failure(new IOException(e.getMessage) with CromwellFatalExceptionMarker)
+    ) recoverWith { case e =>
+      Failure(new IOException(e.getMessage) with CromwellFatalExceptionMarker)
     }
-  }
 
   def localizeWomFile(inputsRoot: Path, docker: Boolean)(value: WomFile): WomFile = {
     val strategies = if (docker) DockerLocalizationStrategies else LocalizationStrategies
@@ -282,23 +286,27 @@ trait SharedFileSystem extends PathFactory {
     def stripProtocolScheme(path: Path): Path = DefaultPathBuilder.get(path.pathWithoutScheme)
 
     /*
-      * Transform an original input path to a path in the call directory.
-      * The new path matches the original path, it only "moves" the root to be the call directory.
-      */
+     * Transform an original input path to a path in the call directory.
+     * The new path matches the original path, it only "moves" the root to be the call directory.
+     */
 
     def toCallPath(womFile: WomFile)(path: String): Try[PairOfFiles] = Try {
       val src = buildPath(path)
       // Strip out potential prefix protocol
       val localInputPath = stripProtocolScheme(src)
-      val dest = if (inputsRoot.isParentOf(localInputPath)) localInputPath
-      else {
-        val nameOverride = womFile match {
-          case directory: WomMaybeListedDirectory => directory.basename
-          case _ => None
+      val dest =
+        if (inputsRoot.isParentOf(localInputPath)) localInputPath
+        else {
+          val nameOverride = womFile match {
+            case directory: WomMaybeListedDirectory => directory.basename
+            case _ => None
+          }
+          // Concatenate call directory with absolute input path
+          DefaultPathBuilder.get(inputsRoot.pathAsString,
+                                 localInputPath.parent.pathAsString.hashCode.toString,
+                                 nameOverride.getOrElse(localInputPath.name)
+          )
         }
-        // Concatenate call directory with absolute input path
-        DefaultPathBuilder.get(inputsRoot.pathAsString, localInputPath.parent.pathAsString.hashCode.toString, nameOverride.getOrElse(localInputPath.name))
-      }
 
       PairOfFiles(src, dest)
     }
@@ -306,12 +314,12 @@ trait SharedFileSystem extends PathFactory {
     // A possibly staged version of the input file suitable for downstream processing, or just the original input
     // file if no staging was required.
     val staged: WomFile = value.mapFile { input =>
-      pathBuilders.collectFirst({ case h: HttpPathBuilder if HttpPathBuilder.accepts(input) => h }) match {
+      pathBuilders.collectFirst { case h: HttpPathBuilder if HttpPathBuilder.accepts(input) => h } match {
         case Some(httpPathBuilder) =>
           implicit val materializer = ActorMaterializer()
           implicit val ec: ExecutionContext = actorContext.dispatcher
 
-          Await.result(httpPathBuilder.content(input).map { _.toString }, Duration.Inf)
+          Await.result(httpPathBuilder.content(input).map(_.toString), Duration.Inf)
         case _ => input
       }
     }
@@ -328,16 +336,18 @@ trait SharedFileSystem extends PathFactory {
     * @param womFile WomFile to localize
     * @return localized WomFile
     */
-  private def localizeWomFile(toDestPath: WomFile => String => Try[PairOfFiles], strategies: LazyList[DuplicationStrategy], docker: Boolean)
-                             (womFile: WomFile): WomFile = {
+  private def localizeWomFile(toDestPath: WomFile => String => Try[PairOfFiles],
+                              strategies: LazyList[DuplicationStrategy],
+                              docker: Boolean
+  )(womFile: WomFile): WomFile = {
     val localized = womFile mapWomFile { file =>
-      val result = toDestPath(file)(file.value) flatMap {
-        case PairOfFiles(src, dst) => duplicate("localize", src, dst, strategies, docker).map(_ => dst.pathAsString)
+      val result = toDestPath(file)(file.value) flatMap { case PairOfFiles(src, dst) =>
+        duplicate("localize", src, dst, strategies, docker).map(_ => dst.pathAsString)
       }
       result.get
     }
     val sized = localized collect {
-      case womMaybePopulatedFile@WomMaybePopulatedFile(Some(path), _, None, _, _, _, _) =>
+      case womMaybePopulatedFile @ WomMaybePopulatedFile(Some(path), _, None, _, _, _, _) =>
         val pair = toDestPath(womMaybePopulatedFile)(path).get
         val srcSize = pair.src.size
         womMaybePopulatedFile.copy(sizeOption = Option(srcSize))
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemAsyncJobExecutionActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemAsyncJobExecutionActor.scala
index 1d55ead7860..24eb4d97a70 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemAsyncJobExecutionActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemAsyncJobExecutionActor.scala
@@ -76,7 +76,9 @@ object SharedFileSystemAsyncJobExecutionActor {
   * messages.
   */
 trait SharedFileSystemAsyncJobExecutionActor
-  extends BackendJobLifecycleActor with StandardAsyncExecutionActor with SharedFileSystemJobCachingActorHelper {
+    extends BackendJobLifecycleActor
+    with StandardAsyncExecutionActor
+    with SharedFileSystemJobCachingActorHelper {
 
   override type StandardAsyncRunInfo = Any
 
@@ -85,7 +87,8 @@ trait SharedFileSystemAsyncJobExecutionActor
   /** True if the status contained in `thiz` is equivalent to `that`, delta any other data that might be carried around
     * in the state type.
     */
-  override def statusEquivalentTo(thiz: StandardAsyncRunState)(that: StandardAsyncRunState): Boolean = thiz.status == that.status
+  override def statusEquivalentTo(thiz: StandardAsyncRunState)(that: StandardAsyncRunState): Boolean =
+    thiz.status == that.status
 
   override lazy val pollBackOff = SimpleExponentialBackoff(1.second, 5.minutes, 1.1)
 
@@ -129,28 +132,26 @@ trait SharedFileSystemAsyncJobExecutionActor
 
   lazy val jobPathsWithDocker: JobPathsWithDocker = jobPaths.asInstanceOf[JobPathsWithDocker]
 
-  def jobName: String = s"cromwell_${jobDescriptor.workflowDescriptor.id.shortString}_${jobDescriptor.taskCall.localName}"
+  def jobName: String =
+    s"cromwell_${jobDescriptor.workflowDescriptor.id.shortString}_${jobDescriptor.taskCall.localName}"
 
   /**
     * Localizes the file, run outside of docker.
     */
-  override def preProcessWomFile(womFile: WomFile): WomFile = {
+  override def preProcessWomFile(womFile: WomFile): WomFile =
     sharedFileSystem.localizeWomFile(jobPathsWithDocker.callInputsRoot, isDockerRun)(womFile)
-  }
 
   /**
     * Returns the paths to the file, inside of docker.
     */
-  override def mapCommandLineWomFile(womFile: WomFile): WomFile = {
+  override def mapCommandLineWomFile(womFile: WomFile): WomFile =
     womFile mapFile { path =>
       val cleanPath = DefaultPathBuilder.build(path).get
       if (isDockerRun) jobPathsWithDocker.toDockerPath(cleanPath).pathAsString else cleanPath.pathAsString
     }
-  }
 
-  override lazy val commandDirectory: Path = {
+  override lazy val commandDirectory: Path =
     if (isDockerRun) jobPathsWithDocker.callExecutionDockerRoot else jobPaths.callExecutionRoot
-  }
 
   override def execute(): ExecutionHandle = {
     if (isDockerRun) jobPaths.callExecutionRoot.createPermissionedDirectories()
@@ -161,22 +162,34 @@ trait SharedFileSystemAsyncJobExecutionActor
         val runner = makeProcessRunner()
         val exitValue = runner.run()
         if (exitValue != 0) {
-          FailedNonRetryableExecutionHandle(new RuntimeException("Unable to start job. " +
-            s"Check the stderr file for possible errors: ${runner.stderrPath}"), kvPairsToSave = None)
+          FailedNonRetryableExecutionHandle(new RuntimeException(
+                                              "Unable to start job. " +
+                                                s"Check the stderr file for possible errors: ${runner.stderrPath}"
+                                            ),
+                                            kvPairsToSave = None
+          )
         } else {
           val runningJob = getJob(exitValue, runner.stdoutPath, runner.stderrPath)
           PendingExecutionHandle(jobDescriptor, runningJob, None, None)
         }
-    }
+      }
     )
   }
 
   def writeScriptContents(): Either[ExecutionHandle, Unit] =
     commandScriptContents.fold(
-      errors => Left(FailedNonRetryableExecutionHandle(new RuntimeException("Unable to start job due to: " + errors.toList.mkString(", ")), kvPairsToSave = None)),
-      {script => jobPaths.script.write(script); Right(())} )
+      errors =>
+        Left(
+          FailedNonRetryableExecutionHandle(
+            new RuntimeException("Unable to start job due to: " + errors.toList.mkString(", ")),
+            kvPairsToSave = None
+          )
+        ),
+      { script => jobPaths.script.write(script); Right(()) }
+    )
 
   lazy val standardPaths = jobPaths.standardPaths
+
   /**
     * Creates a script to submit the script for asynchronous processing. The default implementation assumes the
     * processArgs already runs the script asynchronously. If not, mix in the `BackgroundAsyncJobExecutionActor` that
@@ -192,15 +205,13 @@ trait SharedFileSystemAsyncJobExecutionActor
 
   override def recover(job: StandardAsyncJob): ExecutionHandle = reconnectToExistingJob(job)
 
-  override def reconnectAsync(job: StandardAsyncJob): Future[ExecutionHandle] = {
+  override def reconnectAsync(job: StandardAsyncJob): Future[ExecutionHandle] =
     Future.successful(reconnectToExistingJob(job))
-  }
 
-  override def reconnectToAbortAsync(job: StandardAsyncJob): Future[ExecutionHandle] = {
+  override def reconnectToAbortAsync(job: StandardAsyncJob): Future[ExecutionHandle] =
     Future.successful(reconnectToExistingJob(job, forceAbort = true))
-  }
 
-  private def reconnectToExistingJob(job: StandardAsyncJob, forceAbort: Boolean = false): ExecutionHandle = {
+  private def reconnectToExistingJob(job: StandardAsyncJob, forceAbort: Boolean = false): ExecutionHandle =
     // To avoid race conditions, check for the rc file after checking if the job is alive.
     isAlive(job) match {
       case Success(true) =>
@@ -215,12 +226,16 @@ trait SharedFileSystemAsyncJobExecutionActor
           PendingExecutionHandle(jobDescriptor, job, None, None)
         } else {
           // Could start executeScript(), but for now fail because we shouldn't be in this state.
-          FailedNonRetryableExecutionHandle(new RuntimeException(
-            s"Unable to determine that ${job.jobId} is alive, and ${jobPaths.returnCode} does not exist."), None, kvPairsToSave = None)
+          FailedNonRetryableExecutionHandle(
+            new RuntimeException(
+              s"Unable to determine that ${job.jobId} is alive, and ${jobPaths.returnCode} does not exist."
+            ),
+            None,
+            kvPairsToSave = None
+          )
         }
       case Failure(f) => FailedNonRetryableExecutionHandle(f, None, kvPairsToSave = None)
     }
-  }
 
   def isAlive(job: StandardAsyncJob): Try[Boolean] = Try {
     val argv = checkAliveArgs(job).argv
@@ -235,18 +250,18 @@ trait SharedFileSystemAsyncJobExecutionActor
   override def tryAbort(job: StandardAsyncJob): Unit = {
     val returnCodeTmp = jobPaths.returnCode.plusExt("kill")
     returnCodeTmp.write(s"$SIGTERM\n")
-    try {
+    try
       returnCodeTmp.moveTo(jobPaths.returnCode)
-    } catch {
+    catch {
       case _: FileAlreadyExistsException =>
         // If the process has already completed, there will be an existing rc file.
         returnCodeTmp.delete(true)
     }
     val stderrTmp = standardPaths.error.plusExt("kill")
     stderrTmp.touch()
-    try {
+    try
       stderrTmp.moveTo(standardPaths.error)
-    } catch {
+    catch {
       case _: FileAlreadyExistsException =>
         // If the process has already started, there will be an existing stderr file.
         stderrTmp.delete(true)
@@ -259,16 +274,13 @@ trait SharedFileSystemAsyncJobExecutionActor
     ()
   }
 
-  override def pollStatus(handle: StandardAsyncPendingExecutionHandle): SharedFileSystemRunState = {
+  override def pollStatus(handle: StandardAsyncPendingExecutionHandle): SharedFileSystemRunState =
     if (jobPaths.returnCode.exists) SharedFileSystemJobDone
     else SharedFileSystemJobWaitingForReturnCode(waitUntil = None)
-  }
 
-  override def isTerminal(runStatus: StandardAsyncRunState): Boolean = {
+  override def isTerminal(runStatus: StandardAsyncRunState): Boolean =
     runStatus.terminal
-  }
 
-  override def mapOutputWomFile(womFile: WomFile): WomFile = {
+  override def mapOutputWomFile(womFile: WomFile): WomFile =
     sharedFileSystem.mapJobWomFile(jobPaths)(womFile)
-  }
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemBackendLifecycleActorFactory.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemBackendLifecycleActorFactory.scala
index 7e991a6ec5f..bf9f10a4da6 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemBackendLifecycleActorFactory.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemBackendLifecycleActorFactory.scala
@@ -12,7 +12,6 @@ trait SharedFileSystemBackendLifecycleActorFactory extends StandardLifecycleActo
 
   override def jobIdKey: String = SharedFileSystemAsyncJobExecutionActor.JobIdKey
 
-  override lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] = {
+  override lazy val cacheHitCopyingActorClassOption: Option[Class[_ <: StandardCacheHitCopyingActor]] =
     Option(classOf[SharedFileSystemCacheHitCopyingActor])
-  }
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemCacheHitCopyingActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemCacheHitCopyingActor.scala
index 042cc8759cd..2ad334002f3 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemCacheHitCopyingActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemCacheHitCopyingActor.scala
@@ -9,24 +9,23 @@ import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, Stan
 import scala.util.{Failure, Try}
 
 class SharedFileSystemCacheHitCopyingActor(standardParams: StandardCacheHitCopyingActorParams)
-  extends StandardCacheHitCopyingActor(standardParams) with SharedFileSystemJobCachingActorHelper {
+    extends StandardCacheHitCopyingActor(standardParams)
+    with SharedFileSystemJobCachingActorHelper {
 
   override protected def duplicate(copyPairs: Set[PathPair]): Option[Try[Unit]] = Option {
-    val copies = copyPairs map {
-      case (source, destination) => 
-        sharedFileSystem.cacheCopy(source, destination)
+    val copies = copyPairs map { case (source, destination) =>
+      sharedFileSystem.cacheCopy(source, destination)
     }
 
-    TryUtil.sequence(copies.toList).void recoverWith {
-      case failure =>
-        // If one or more of the copies failed, we want to delete all the files that were successfully copied
-        // before that. Especially if they've been symlinked, leaving them could lead to rewriting the original
-        // files when the job gets re-run
-        // TODO: this could be done more generally in the StandardCacheHitCopyingActor
-        copyPairs foreach {
-          case (_, dst) => dst.delete(swallowIOExceptions = true)
-        }
-        Failure(failure)
+    TryUtil.sequence(copies.toList).void recoverWith { case failure =>
+      // If one or more of the copies failed, we want to delete all the files that were successfully copied
+      // before that. Especially if they've been symlinked, leaving them could lead to rewriting the original
+      // files when the job gets re-run
+      // TODO: this could be done more generally in the StandardCacheHitCopyingActor
+      copyPairs foreach { case (_, dst) =>
+        dst.delete(swallowIOExceptions = true)
+      }
+      Failure(failure)
     }
   }
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemExpressionFunctions.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemExpressionFunctions.scala
index 303e8d621e0..3b3bc978878 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemExpressionFunctions.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemExpressionFunctions.scala
@@ -2,7 +2,11 @@ package cromwell.backend.sfs
 
 import akka.actor.ActorRef
 import cromwell.backend.io._
-import cromwell.backend.standard.{DefaultStandardExpressionFunctionsParams, StandardExpressionFunctions, StandardExpressionFunctionsParams}
+import cromwell.backend.standard.{
+  DefaultStandardExpressionFunctionsParams,
+  StandardExpressionFunctions,
+  StandardExpressionFunctionsParams
+}
 import cromwell.core.CallContext
 import cromwell.core.path.{DefaultPath, DefaultPathBuilder, Path, PathBuilder}
 import wom.expression.IoFunctionSet
@@ -13,43 +17,39 @@ object SharedFileSystemExpressionFunctions {
   def apply(jobPaths: JobPaths,
             pathBuilders: List[PathBuilder],
             ioActorProxy: ActorRef,
-            ec: ExecutionContext): SharedFileSystemExpressionFunctions = {
+            ec: ExecutionContext
+  ): SharedFileSystemExpressionFunctions =
     new SharedFileSystemExpressionFunctions(pathBuilders, jobPaths.callContext, ioActorProxy, ec)
-  }
 }
 
 class SharedFileSystemExpressionFunctions(standardParams: StandardExpressionFunctionsParams)
-  extends StandardExpressionFunctions(standardParams) {
+    extends StandardExpressionFunctions(standardParams) {
 
-  def this(pathBuilders: List[PathBuilder],
-           callContext: CallContext,
-           ioActorProxy: ActorRef,
-           ec: ExecutionContext) = {
+  def this(pathBuilders: List[PathBuilder], callContext: CallContext, ioActorProxy: ActorRef, ec: ExecutionContext) =
     this(DefaultStandardExpressionFunctionsParams(pathBuilders, callContext, ioActorProxy, ec))
-  }
 
-  override def makeInputSpecificFunctions(): IoFunctionSet = new SharedFileSystemExpressionFunctionsForInput(standardParams)
+  override def makeInputSpecificFunctions(): IoFunctionSet = new SharedFileSystemExpressionFunctionsForInput(
+    standardParams
+  )
 
-  override def postMapping(path: Path) = {
+  override def postMapping(path: Path) =
     path match {
       case _: DefaultPath if !path.isAbsolute => callContext.root.resolve(path)
       case _ => path
     }
-  }
 }
 
 class SharedFileSystemExpressionFunctionsForInput(standardParams: StandardExpressionFunctionsParams)
-  extends SharedFileSystemExpressionFunctions(standardParams) {
+    extends SharedFileSystemExpressionFunctions(standardParams) {
 
   // override needed to prevent class self-reference
   override def makeInputSpecificFunctions(): IoFunctionSet = this
 
   lazy val cromwellCwd: Path = DefaultPathBuilder.build(sys.props("user.dir")).get
 
-  override def postMapping(path: Path) = {
+  override def postMapping(path: Path) =
     path match {
       case _: DefaultPath if !path.isAbsolute => cromwellCwd.resolve(path)
       case _ => path
     }
-  }
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemInitializationActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemInitializationActor.scala
index 74392610465..75b5a09a8a3 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemInitializationActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemInitializationActor.scala
@@ -2,17 +2,20 @@ package cromwell.backend.sfs
 
 import cromwell.backend.BackendInitializationData
 import cromwell.backend.io.WorkflowPaths
-import cromwell.backend.standard.{StandardExpressionFunctions, StandardInitializationActor, StandardInitializationActorParams}
+import cromwell.backend.standard.{
+  StandardExpressionFunctions,
+  StandardInitializationActor,
+  StandardInitializationActorParams
+}
 import cromwell.backend.wfs.WorkflowPathBuilder
 
 import scala.concurrent.Future
 
 class SharedFileSystemInitializationActor(standardParams: StandardInitializationActorParams)
-  extends StandardInitializationActor(standardParams) {
+    extends StandardInitializationActor(standardParams) {
 
-  override lazy val pathBuilders = {
+  override lazy val pathBuilders =
     standardParams.configurationDescriptor.pathBuildersWithDefault(workflowDescriptor.workflowOptions)
-  }
 
   override lazy val workflowPaths: Future[WorkflowPaths] = pathBuilders map {
     WorkflowPathBuilder.workflowPaths(configurationDescriptor, workflowDescriptor, _)
@@ -21,11 +24,10 @@ class SharedFileSystemInitializationActor(standardParams: StandardInitialization
   override lazy val expressionFunctions: Class[_ <: StandardExpressionFunctions] =
     classOf[SharedFileSystemExpressionFunctions]
 
-  override def beforeAll(): Future[Option[BackendInitializationData]] = {
+  override def beforeAll(): Future[Option[BackendInitializationData]] =
     initializationData map { data =>
       publishWorkflowRoot(data.workflowPaths.workflowRoot.pathAsString)
       data.workflowPaths.workflowRoot.createDirectories()
       Option(data)
     }
-  }
 }
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemJobCachingActorHelper.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemJobCachingActorHelper.scala
index 2897d8a1ac1..699c9ab534d 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemJobCachingActorHelper.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/sfs/SharedFileSystemJobCachingActorHelper.scala
@@ -12,18 +12,18 @@ trait SharedFileSystemJobCachingActorHelper extends StandardCachingActorHelper {
 
   lazy val sharedFileSystem = new SharedFileSystem {
 
-    override implicit def actorContext: ActorContext = context
+    implicit override def actorContext: ActorContext = context
 
     override lazy val pathBuilders: List[PathBuilder] = standardInitializationData.workflowPaths.pathBuilders
 
-    override lazy val sharedFileSystemConfig: Config = {
+    override lazy val sharedFileSystemConfig: Config =
       configurationDescriptor.backendConfig.as[Option[Config]]("filesystems.local").getOrElse(ConfigFactory.empty())
-    }
 
     // cachedCopyDir should be on the same physical filesystem as the execution root.
     // WDL workflow names may not contain '-' so using 'cached-inputs' will certainly
     // not collide with any workflows in the root directory.
     override lazy val cachedCopyDir: Option[Path] = Option(
-      workflowPaths.executionRoot.createChild("cached-inputs", asDirectory = true))
+      workflowPaths.executionRoot.createChild("cached-inputs", asDirectory = true)
+    )
   }
 }
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActorSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActorSpec.scala
index f20267053e9..fce1e05a60b 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActorSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActorSpec.scala
@@ -4,18 +4,18 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class ConfigAsyncJobExecutionActorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "getJobRegex"
 
   val successfulTestCases = Map(
     ("Job <03957>... blah blah blah", "Job <(\\d+)>.*") -> "03957",
-
     ("""mxq_group_id=...
-      |mxq_group_name=...
-      |mxq_job_id=16988030
-      |""".stripMargin, "mxq_job_id=(\\d+)") -> "16988030"
+       |mxq_group_name=...
+       |mxq_job_id=16988030
+       |""".stripMargin,
+     "mxq_job_id=(\\d+)"
+    ) -> "16988030"
   )
 
   successfulTestCases foreach { case ((fileContent, jobIdRegex), expectedJobId) =>
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategySpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategySpec.scala
index 0cc6267374e..2814eb821a1 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategySpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigHashingStrategySpec.scala
@@ -19,8 +19,13 @@ import wom.values.WomSingleFile
 
 import scala.util.Success
 
-class ConfigHashingStrategySpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
-  with TableDrivenPropertyChecks with MockSugar with BeforeAndAfterAll {
+class ConfigHashingStrategySpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks
+    with MockSugar
+    with BeforeAndAfterAll {
 
   behavior of "ConfigHashingStrategy"
 
@@ -60,7 +65,9 @@ class ConfigHashingStrategySpec extends AnyFlatSpec with CromwellTimeoutSpec wit
   private def makeStrategy(strategy: String, checkSibling: Option[Boolean] = None) = {
     val conf = ConfigFactory.parseString(s"""hashing-strategy: "$strategy"""")
     ConfigHashingStrategy(
-      checkSibling map { check => conf.withValue("check-sibling-md5", ConfigValueFactory.fromAnyRef(check)) } getOrElse conf
+      checkSibling map { check =>
+        conf.withValue("check-sibling-md5", ConfigValueFactory.fromAnyRef(check))
+      } getOrElse conf
     )
   }
 
@@ -233,15 +240,14 @@ class ConfigHashingStrategySpec extends AnyFlatSpec with CromwellTimeoutSpec wit
   }
 
   it should "create a fingerprint strategy from config" in {
-    val defaultFingerprint:  FingerprintStrategy = makeStrategy("fingerprint").asInstanceOf[FingerprintStrategy]
+    val defaultFingerprint: FingerprintStrategy = makeStrategy("fingerprint").asInstanceOf[FingerprintStrategy]
     defaultFingerprint.isInstanceOf[FingerprintStrategy] shouldBe true
     defaultFingerprint.checkSiblingMd5 shouldBe false
     defaultFingerprint.fingerprintSize shouldBe 10 * 1024 * 1024
 
-    val config = ConfigFactory.parseString(
-      """|hashing-strategy: "fingerprint"
-         |fingerprint-size: 123456789
-         |""".stripMargin)
+    val config = ConfigFactory.parseString("""|hashing-strategy: "fingerprint"
+                                              |fingerprint-size: 123456789
+                                              |""".stripMargin)
     val otherFingerprint: FingerprintStrategy = ConfigHashingStrategy.apply(config).asInstanceOf[FingerprintStrategy]
     otherFingerprint.fingerprintSize shouldBe 123456789
     otherFingerprint.isInstanceOf[FingerprintStrategy] shouldBe true
@@ -261,8 +267,10 @@ class ConfigHashingStrategySpec extends AnyFlatSpec with CromwellTimeoutSpec wit
   }
 
   it should "have a fingerprint strategy and use md5 sibling file when appropriate" in {
-    val fingerPrintHash = HashFileXxH64StrategyMethods.xxh64sumString(file.lastModifiedTime.toEpochMilli.toHexString +
-                                                              file.size.toHexString) + steakXxh64
+    val fingerPrintHash = HashFileXxH64StrategyMethods.xxh64sumString(
+      file.lastModifiedTime.toEpochMilli.toHexString +
+        file.size.toHexString
+    ) + steakXxh64
     val table = Table(
       ("check", "withMd5", "expected"),
       (true, true, md5FileHash),
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigInitializationActorSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigInitializationActorSpec.scala
index fe2f320c562..085ac5cd974 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigInitializationActorSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/ConfigInitializationActorSpec.scala
@@ -11,34 +11,38 @@ class ConfigInitializationActorSpec extends AnyFlatSpec with CromwellTimeoutSpec
     val tripleQuote = "\"\"\""
     val singularityBackendConfigString =
       s"""run-in-background = true
-        | runtime-attributes = ${tripleQuote}
-        |       String singularity
-        |       Int uncacheworthy1
-        |       Int uncacheworthy2
-        |     ${tripleQuote}
-        | runtime-attributes-for-caching = {
-        |   "singularity": true
-        |   "uncacheworthy1": false
-        |   # NB: no specific entry for uncacheworthy2 - the default should already be 'false'.
-        | }
-        | submit-docker = ${tripleQuote}
-        |       singularity exec --bind $${cwd}:$${docker_cwd} docker://$${singularity} $${job_shell} $${script}
-        |     ${tripleQuote}
-        |""".stripMargin
+         | runtime-attributes = ${tripleQuote}
+         |       String singularity
+         |       Int uncacheworthy1
+         |       Int uncacheworthy2
+         |     ${tripleQuote}
+         | runtime-attributes-for-caching = {
+         |   "singularity": true
+         |   "uncacheworthy1": false
+         |   # NB: no specific entry for uncacheworthy2 - the default should already be 'false'.
+         | }
+         | submit-docker = ${tripleQuote}
+         |       singularity exec --bind $${cwd}:$${docker_cwd} docker://$${singularity} $${job_shell} $${script}
+         |     ${tripleQuote}
+         |""".stripMargin
 
     val singularityBackendConfig = ConfigFactory.parseString(singularityBackendConfigString)
 
     // Mirroring how the declarations are made in ConfigInitializationActor:
     lazy val configWdlNamespace = new ConfigWdlNamespace(singularityBackendConfig)
-    lazy val declarationValidations: Seq[DeclarationValidation] = {
-      DeclarationValidation.fromDeclarations(configWdlNamespace.runtimeDeclarations, configWdlNamespace.callCachedRuntimeAttributes)
-    }
+    lazy val declarationValidations: Seq[DeclarationValidation] =
+      DeclarationValidation.fromDeclarations(configWdlNamespace.runtimeDeclarations,
+                                             configWdlNamespace.callCachedRuntimeAttributes
+      )
 
     declarationValidations.exists(p => p.key == "singularity" && p.makeValidation().usedInCallCaching) should be(true)
-    declarationValidations.exists(p => p.key == "uncacheworthy1" && p.makeValidation().usedInCallCaching) should be(false)
-    declarationValidations.exists(p => p.key == "uncacheworthy2" && p.makeValidation().usedInCallCaching) should be(false)
+    declarationValidations.exists(p => p.key == "uncacheworthy1" && p.makeValidation().usedInCallCaching) should be(
+      false
+    )
+    declarationValidations.exists(p => p.key == "uncacheworthy2" && p.makeValidation().usedInCallCaching) should be(
+      false
+    )
 
   }
 
 }
-
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidationSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidationSpec.scala
index bd00982a49a..48722a0dc66 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidationSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidationSpec.scala
@@ -11,7 +11,11 @@ import wdl4s.parser.MemoryUnit
 import wom.format.MemorySize
 import wom.values.{WomFloat, WomLong}
 
-class MemoryDeclarationValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
+class MemoryDeclarationValidationSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks {
   behavior of "MemoryDeclarationValidation"
 
   val validDeclaredAmounts = Table(
@@ -24,7 +28,7 @@ class MemoryDeclarationValidationSpec extends AnyFlatSpec with CromwellTimeoutSp
     ("Int? memory_gb", Option(2), None, Option(WomLong(2))),
     ("Int? memory_gb = 3", None, Option(3), None),
     ("Int? memory_gb = 3", Option(2), Option(3), Option(WomLong(2))),
-    ("Float memory", Option(2), None, Option(WomFloat(2F * 1024F * 1024F * 1024F))),
+    ("Float memory", Option(2), None, Option(WomFloat(2f * 1024f * 1024f * 1024f))),
     ("Float memory_gb", Option(2), None, Option(WomFloat(2))),
     ("Float memory_gb = 3.0", None, Option(3), None),
     ("Float memory_gb = 3.0", Option(2), Option(3), Option(WomFloat(2))),
@@ -44,7 +48,7 @@ class MemoryDeclarationValidationSpec extends AnyFlatSpec with CromwellTimeoutSp
     ("Int? memoryMin_gb", Option(2), None, Option(WomLong(2))),
     ("Int? memoryMin_gb = 3", None, Option(3), None),
     ("Int? memoryMin_gb = 3", Option(2), Option(3), Option(WomLong(2))),
-    ("Float memoryMin", Option(2), None, Option(WomFloat(2F * 1024F * 1024F * 1024F))),
+    ("Float memoryMin", Option(2), None, Option(WomFloat(2f * 1024f * 1024f * 1024f))),
     ("Float memoryMin_gb", Option(2), None, Option(WomFloat(2))),
     ("Float memoryMin_gb = 3.0", None, Option(3), None),
     ("Float memoryMin_gb = 3.0", Option(2), Option(3), Option(WomFloat(2))),
@@ -60,7 +64,7 @@ class MemoryDeclarationValidationSpec extends AnyFlatSpec with CromwellTimeoutSp
     ("Int? memoryMax_gb", Option(2), None, Option(WomLong(2))),
     ("Int? memoryMax_gb = 3", None, Option(3), None),
     ("Int? memoryMax_gb = 3", Option(2), Option(3), Option(WomLong(2))),
-    ("Float memoryMax", Option(2), None, Option(WomFloat(2F * 1024F * 1024F * 1024F))),
+    ("Float memoryMax", Option(2), None, Option(WomFloat(2f * 1024f * 1024f * 1024f))),
     ("Float memoryMax_gb", Option(2), None, Option(WomFloat(2))),
     ("Float memoryMax_gb = 3.0", None, Option(3), None),
     ("Float memoryMax_gb = 3.0", Option(2), Option(3), Option(WomFloat(2))),
@@ -72,23 +76,23 @@ class MemoryDeclarationValidationSpec extends AnyFlatSpec with CromwellTimeoutSp
 
   forAll(validDeclaredAmounts) { (declaration, runtimeAmount, expectedDefaultAmount, expectedExtracted) =>
     it should s"extract memory from declared $declaration with memory set to ${runtimeAmount.getOrElse("none")}" in {
-      val memoryKey = if (declaration.contains("Min")) MemoryMinRuntimeAttribute
-      else if (declaration.contains("Max")) MemoryMaxRuntimeAttribute
-      else MemoryRuntimeAttribute
-
-      val memoryPrefix = if (declaration.contains("Min")) MemoryMinRuntimeAttributePrefix
-      else if (declaration.contains("Max")) MemoryMaxRuntimeAttributePrefix
-      else MemoryRuntimeAttributePrefix
-      
-      val config = ConfigFactory.parseString(
-        s"""|submit = "anything"
-            |${ConfigConstants.RuntimeAttributesConfig} = "$declaration"
-            |""".stripMargin)
+      val memoryKey =
+        if (declaration.contains("Min")) MemoryMinRuntimeAttribute
+        else if (declaration.contains("Max")) MemoryMaxRuntimeAttribute
+        else MemoryRuntimeAttribute
+
+      val memoryPrefix =
+        if (declaration.contains("Min")) MemoryMinRuntimeAttributePrefix
+        else if (declaration.contains("Max")) MemoryMaxRuntimeAttributePrefix
+        else MemoryRuntimeAttributePrefix
+
+      val config = ConfigFactory.parseString(s"""|submit = "anything"
+                                                 |${ConfigConstants.RuntimeAttributesConfig} = "$declaration"
+                                                 |""".stripMargin)
 
       val configWdlNamespace = new ConfigWdlNamespace(config)
       val runtimeDeclaration = configWdlNamespace.runtimeDeclarations.head
-      val memoryDeclarationValidation = new MemoryDeclarationValidation(runtimeDeclaration,
-        memoryKey, memoryPrefix)
+      val memoryDeclarationValidation = new MemoryDeclarationValidation(runtimeDeclaration, memoryKey, memoryPrefix)
       val attributes = runtimeAmount
         .map(amount => memoryKey -> MemorySize(amount.toDouble, MemoryUnit.GB))
         .toMap
@@ -101,7 +105,9 @@ class MemoryDeclarationValidationSpec extends AnyFlatSpec with CromwellTimeoutSp
         .map(amount => WomLong(MemorySize(amount.toDouble, MemoryUnit.GB).bytes.toLong))
 
       MemoryDeclarationValidation.isMemoryDeclaration(runtimeDeclaration.unqualifiedName,
-        memoryKey, memoryPrefix) should be(true)
+                                                      memoryKey,
+                                                      memoryPrefix
+      ) should be(true)
       default should be(expectedDefault)
       extracted should be(expectedExtracted)
     }
@@ -114,10 +120,9 @@ class MemoryDeclarationValidationSpec extends AnyFlatSpec with CromwellTimeoutSp
 
   forAll(badSyntaxDeclarations) { declaration =>
     it should s"throw a syntax error for memory declaration $declaration" in {
-      val config = ConfigFactory.parseString(
-        s"""|submit = "anything"
-            |${ConfigConstants.RuntimeAttributesConfig} = "$declaration"
-            |""".stripMargin)
+      val config = ConfigFactory.parseString(s"""|submit = "anything"
+                                                 |${ConfigConstants.RuntimeAttributesConfig} = "$declaration"
+                                                 |""".stripMargin)
 
       val expectedException = intercept[RuntimeException](new ConfigWdlNamespace(config))
       expectedException.getMessage should startWith("Error parsing generated wdl:\n")
@@ -133,15 +138,16 @@ class MemoryDeclarationValidationSpec extends AnyFlatSpec with CromwellTimeoutSp
 
   forAll(invalidDeclarations) { declaration =>
     it should s"not identify $declaration as a memory declaration" in {
-      val config = ConfigFactory.parseString(
-        s"""|submit = "anything"
-            |${ConfigConstants.RuntimeAttributesConfig} = "$declaration"
-            |""".stripMargin)
+      val config = ConfigFactory.parseString(s"""|submit = "anything"
+                                                 |${ConfigConstants.RuntimeAttributesConfig} = "$declaration"
+                                                 |""".stripMargin)
 
       val configWdlNamespace = new ConfigWdlNamespace(config)
       val runtimeDeclaration = configWdlNamespace.runtimeDeclarations.head
       MemoryDeclarationValidation.isMemoryDeclaration(runtimeDeclaration.unqualifiedName,
-        MemoryRuntimeAttribute, MemoryRuntimeAttributePrefix) should be(false)
+                                                      MemoryRuntimeAttribute,
+                                                      MemoryRuntimeAttributePrefix
+      ) should be(false)
     }
   }
 }
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemInitializationActorSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemInitializationActorSpec.scala
index cd74a247b8c..ee10f41ba48 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemInitializationActorSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemInitializationActorSpec.scala
@@ -18,32 +18,38 @@ import wom.graph.CommandCallNode
 
 import scala.concurrent.duration._
 
-class SharedFileSystemInitializationActorSpec extends TestKitSuite
-  with AnyWordSpecLike with Matchers with ImplicitSender {
+class SharedFileSystemInitializationActorSpec
+    extends TestKitSuite
+    with AnyWordSpecLike
+    with Matchers
+    with ImplicitSender {
   val Timeout: FiniteDuration = 10.second.dilated
 
   val HelloWorld: String =
     s"""
-      |task hello {
-      |  String addressee = "you"
-      |  command {
-      |    echo "Hello $${addressee}!"
-      |  }
-      |  output {
-      |    String salutation = read_string(stdout())
-      |  }
-      |
-      |  RUNTIME
-      |}
-      |
-      |workflow wf_hello {
-      |  call hello
-      |}
+       |task hello {
+       |  String addressee = "you"
+       |  command {
+       |    echo "Hello $${addressee}!"
+       |  }
+       |  output {
+       |    String salutation = read_string(stdout())
+       |  }
+       |
+       |  RUNTIME
+       |}
+       |
+       |workflow wf_hello {
+       |  call hello
+       |}
     """.stripMargin
 
-  private def getActorRef(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[CommandCallNode],
-                          conf: BackendConfigurationDescriptor) = {
-    val params = DefaultInitializationActorParams(workflowDescriptor, emptyActor, calls, emptyActor, conf, restarting = false)
+  private def getActorRef(workflowDescriptor: BackendWorkflowDescriptor,
+                          calls: Set[CommandCallNode],
+                          conf: BackendConfigurationDescriptor
+  ) = {
+    val params =
+      DefaultInitializationActorParams(workflowDescriptor, emptyActor, calls, emptyActor, conf, restarting = false)
     val props = Props(new SharedFileSystemInitializationActor(params))
     system.actorOf(props, "SharedFileSystemInitializationActor")
   }
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
index 848b5e56c6b..5d1b1e02c12 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
@@ -4,7 +4,12 @@ import _root_.wdl.draft2.model.LocallyQualifiedName
 import akka.testkit.{TestDuration, TestProbe}
 import com.typesafe.config.ConfigFactory
 import common.collections.EnhancedCollections._
-import cromwell.backend.BackendJobExecutionActor.{JobAbortedResponse, JobFailedNonRetryableResponse, JobSucceededResponse, RunOnBackend}
+import cromwell.backend.BackendJobExecutionActor.{
+  JobAbortedResponse,
+  JobFailedNonRetryableResponse,
+  JobSucceededResponse,
+  RunOnBackend
+}
 import cromwell.backend.BackendLifecycleActor.AbortJobCommand
 import cromwell.backend._
 import cromwell.backend.async.WrongReturnCode
@@ -33,8 +38,12 @@ import java.io.FileNotFoundException
 import scala.concurrent.duration._
 import scala.sys.process._
 
-class SharedFileSystemJobExecutionActorSpec extends TestKitSuite
-  with AnyFlatSpecLike with BackendSpec with TableDrivenPropertyChecks with OptionValues {
+class SharedFileSystemJobExecutionActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with BackendSpec
+    with TableDrivenPropertyChecks
+    with OptionValues {
 
   behavior of "SharedFileSystemJobExecutionActor"
 
@@ -45,13 +54,27 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite
   private val mockBackendJobDescriptorKey = BackendJobDescriptorKey(call, None, 1)
 
   def executeSpec(docker: Boolean): Any = {
-    val expectedOutputs: CallOutputs = WomMocks.mockOutputExpectations(Map("hello.salutation" -> WomString("Hello you !")))
-
-    val expectedResponse = JobSucceededResponse(mockBackendJobDescriptorKey, Some(0), expectedOutputs, None, Seq.empty, None, resultGenerationMode = RunOnBackend)
+    val expectedOutputs: CallOutputs =
+      WomMocks.mockOutputExpectations(Map("hello.salutation" -> WomString("Hello you !")))
+
+    val expectedResponse = JobSucceededResponse(mockBackendJobDescriptorKey,
+                                                Some(0),
+                                                expectedOutputs,
+                                                None,
+                                                Seq.empty,
+                                                None,
+                                                resultGenerationMode = RunOnBackend
+    )
     val runtime = if (docker) s"""runtime { docker: "$dockerImageUbuntu" }""" else ""
     val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld, runtime = runtime)
     val workflow = TestWorkflow(workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor, expectedResponse)
-    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor, Map.empty, WorkflowOptions.empty, runtimeAttributeDefinitions), workflow.config)
+    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
+                                                                    Map.empty,
+                                                                    WorkflowOptions.empty,
+                                                                    runtimeAttributeDefinitions
+                                ),
+                                workflow.config
+    )
     testWorkflow(workflow, backend)
   }
 
@@ -76,37 +99,53 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite
 
   it should "send back an execution failure if the task fails" in {
     val expectedResponse =
-      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey, WrongReturnCode("wf_goodbye.goodbye:NA:1", 1, None), Option(1))
-    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(GoodbyeWorld), TestConfig.backendRuntimeConfigDescriptor, expectedResponse)
-    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor, Map.empty, WorkflowOptions.empty, runtimeAttributeDefinitions), workflow.config)
+      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
+                                    WrongReturnCode("wf_goodbye.goodbye:NA:1", 1, None),
+                                    Option(1)
+      )
+    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(GoodbyeWorld),
+                                TestConfig.backendRuntimeConfigDescriptor,
+                                expectedResponse
+    )
+    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
+                                                                    Map.empty,
+                                                                    WorkflowOptions.empty,
+                                                                    runtimeAttributeDefinitions
+                                ),
+                                workflow.config
+    )
     testWorkflow(workflow, backend)
   }
 
   def localizationSpec(docker: Boolean): Assertion = {
-    def templateConf(localizers: String) = BackendConfigurationDescriptor(ConfigFactory.parseString(
-                s"""|{
-                    |  root = "local-cromwell-executions"
-                    |  filesystems {
-                    |    local {
-                    |      localization = [
-                    |        $localizers
-                    |      ]
-                    |    }
-                    |  }
-                    |  default-runtime-attributes {
-                    |  cpu: 1
-                    |  failOnStderr: false
-                    |  continueOnReturnCode: 0
-                    |  }
-                    |}
-                    |""".stripMargin), ConfigFactory.parseString("{}"))
+    def templateConf(localizers: String) = BackendConfigurationDescriptor(
+      ConfigFactory.parseString(s"""|{
+                                    |  root = "local-cromwell-executions"
+                                    |  filesystems {
+                                    |    local {
+                                    |      localization = [
+                                    |        $localizers
+                                    |      ]
+                                    |    }
+                                    |  }
+                                    |  default-runtime-attributes {
+                                    |  cpu: 1
+                                    |  failOnStderr: false
+                                    |  continueOnReturnCode: 0
+                                    |  }
+                                    |}
+                                    |""".stripMargin),
+      ConfigFactory.parseString("{}")
+    )
 
     val hardConf = templateConf("hard-link")
     val symConf = templateConf("soft-link")
     val copyConf = templateConf("copy")
 
-    val jsonInputFile = createCannedFile("localize", "content from json inputs", Option(DefaultPathBuilder.build(".").get))
-    val callInputFile = createCannedFile("localize", "content from call inputs", Option(DefaultPathBuilder.build(".").get))
+    val jsonInputFile =
+      createCannedFile("localize", "content from json inputs", Option(DefaultPathBuilder.build(".").get))
+    val callInputFile =
+      createCannedFile("localize", "content from call inputs", Option(DefaultPathBuilder.build(".").get))
     val inputs = Option(s"""{
       "wf_localize.workflowFile": "${callInputFile.pathAsString}",
       "wf_localize.localize.inputFileFromJson": "${jsonInputFile.pathAsString}"
@@ -115,9 +154,8 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite
     val expectedOutputs: CallOutputs = WomMocks.mockOutputExpectations(
       Map(
         "localize.out" -> WomArray(WomArrayType(WomStringType),
-          List(
-            WomString("content from json inputs"),
-            WomString("content from call inputs")))
+                                   List(WomString("content from json inputs"), WomString("content from call inputs"))
+        )
       )
     )
 
@@ -135,24 +173,50 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite
       val runtime = if (docker) s"""runtime { docker: "$dockerImageUbuntu" } """ else ""
       val workflowDescriptor = buildWdlWorkflowDescriptor(InputFiles, inputs, runtime = runtime)
       val callInputs = Map(
-        "inputFileFromCallInputs" -> workflowDescriptor.knownValues.collectFirst({
-          case (outputPort, resolvedValue) if outputPort.fullyQualifiedName == "wf_localize.workflowFile" => resolvedValue
-        }).get,
-        "inputFileFromJson" -> workflowDescriptor.knownValues.collectFirst({
-          case (outputPort, resolvedValue) if outputPort.fullyQualifiedName == "wf_localize.localize.inputFileFromJson" => resolvedValue
-        }).get
+        "inputFileFromCallInputs" -> workflowDescriptor.knownValues.collectFirst {
+          case (outputPort, resolvedValue) if outputPort.fullyQualifiedName == "wf_localize.workflowFile" =>
+            resolvedValue
+        }.get,
+        "inputFileFromJson" -> workflowDescriptor.knownValues.collectFirst {
+          case (outputPort, resolvedValue)
+              if outputPort.fullyQualifiedName == "wf_localize.localize.inputFileFromJson" =>
+            resolvedValue
+        }.get
       )
 
-      val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflowDescriptor, callInputs, WorkflowOptions.empty, runtimeAttributeDefinitions), conf)
-      val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor, callInputs, WorkflowOptions.empty, runtimeAttributeDefinitions)
-      val expectedResponse = JobSucceededResponse(jobDescriptor.key, Some(0), expectedOutputs, None, Seq.empty, None, resultGenerationMode = RunOnBackend)
+      val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                      callInputs,
+                                                                      WorkflowOptions.empty,
+                                                                      runtimeAttributeDefinitions
+                                  ),
+                                  conf
+      )
+      val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                    callInputs,
+                                                                                    WorkflowOptions.empty,
+                                                                                    runtimeAttributeDefinitions
+      )
+      val expectedResponse = JobSucceededResponse(jobDescriptor.key,
+                                                  Some(0),
+                                                  expectedOutputs,
+                                                  None,
+                                                  Seq.empty,
+                                                  None,
+                                                  resultGenerationMode = RunOnBackend
+      )
 
       val jobPaths = JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, conf.backendConfig)
 
       whenReady(backend.execute) { executionResponse =>
         assertResponse(executionResponse, expectedResponse)
-        val localizedJsonInputFile = DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString, jsonInputFile.parent.pathAsString.hashCode.toString + "/" + jsonInputFile.name)
-        val localizedCallInputFile = DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString, callInputFile.parent.pathAsString.hashCode.toString + "/" + callInputFile.name)
+        val localizedJsonInputFile =
+          DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString,
+                                 jsonInputFile.parent.pathAsString.hashCode.toString + "/" + jsonInputFile.name
+          )
+        val localizedCallInputFile =
+          DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString,
+                                 callInputFile.parent.pathAsString.hashCode.toString + "/" + callInputFile.name
+          )
 
         localizedJsonInputFile.isSymbolicLink shouldBe isSymlink
         val realJsonInputFile =
@@ -177,7 +241,11 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite
 
   it should "abort a job and kill a process" in {
     val workflowDescriptor = buildWdlWorkflowDescriptor(Sleep20)
-    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor, Map.empty, WorkflowOptions.empty, runtimeAttributeDefinitions)
+    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                  Map.empty,
+                                                                                  WorkflowOptions.empty,
+                                                                                  runtimeAttributeDefinitions
+    )
     val backendRef = createBackendRef(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
     val backend = backendRef.underlyingActor
 
@@ -191,7 +259,11 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite
 
   def recoverSpec(completed: Boolean, writeReturnCode: Boolean = true): Assertion = {
     val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld)
-    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor, Map.empty, WorkflowOptions.empty, runtimeAttributeDefinitions)
+    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                  Map.empty,
+                                                                                  WorkflowOptions.empty,
+                                                                                  runtimeAttributeDefinitions
+    )
     val backendRef = createBackendRef(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
     val backend = backendRef.underlyingActor
 
@@ -267,14 +339,33 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite
       // If this is not the case, more context/logic will need to be moved to the backend so it can figure it out by itself
       val symbolMaps: Map[LocallyQualifiedName, WomInteger] = Map("intNumber" -> WomInteger(shard))
 
-      val evaluatedAttributes = call.callable.runtimeAttributes.attributes.safeMapValues(_.evaluateValue(Map.empty, NoIoFunctionSet).getOrElse(fail("Can't evaluate runtime attribute")))
-      val runtimeAttributes: Map[LocallyQualifiedName, WomValue] = RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, WorkflowOptions.empty)(evaluatedAttributes)
+      val evaluatedAttributes = call.callable.runtimeAttributes.attributes
+        .safeMapValues(_.evaluateValue(Map.empty, NoIoFunctionSet).getOrElse(fail("Can't evaluate runtime attribute")))
+      val runtimeAttributes: Map[LocallyQualifiedName, WomValue] =
+        RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, WorkflowOptions.empty)(
+          evaluatedAttributes
+        )
 
       val jobDescriptor: BackendJobDescriptor =
-        BackendJobDescriptor(workflowDescriptor, BackendJobDescriptorKey(call, Option(shard), 1), runtimeAttributes, fqnWdlMapToDeclarationMap(symbolMaps), NoDocker, None, Map.empty)
+        BackendJobDescriptor(workflowDescriptor,
+                             BackendJobDescriptorKey(call, Option(shard), 1),
+                             runtimeAttributes,
+                             fqnWdlMapToDeclarationMap(symbolMaps),
+                             NoDocker,
+                             None,
+                             Map.empty
+        )
       val backend = createBackend(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
       val response =
-        JobSucceededResponse(mockBackendJobDescriptorKey, Some(0), WomMocks.mockOutputExpectations(Map("scattering.out" -> WomInteger(shard))), None, Seq.empty, None, resultGenerationMode = RunOnBackend)
+        JobSucceededResponse(
+          mockBackendJobDescriptorKey,
+          Some(0),
+          WomMocks.mockOutputExpectations(Map("scattering.out" -> WomInteger(shard))),
+          None,
+          Seq.empty,
+          None,
+          resultGenerationMode = RunOnBackend
+        )
       executeJobAndAssertOutputs(backend, response)
     }
   }
@@ -285,30 +376,55 @@ class SharedFileSystemJobExecutionActorSpec extends TestKitSuite
       "wf_localize.localize.inputFile": "$inputFile"
     }""")
     val workflowDescriptor = buildWdlWorkflowDescriptor(OutputProcess, inputs)
-    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor, Map.empty, WorkflowOptions.empty, runtimeAttributeDefinitions)
+    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                  Map.empty,
+                                                                                  WorkflowOptions.empty,
+                                                                                  runtimeAttributeDefinitions
+    )
     val backend = createBackend(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
-    val jobPaths = JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor.backendConfig)
+    val jobPaths =
+      JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor.backendConfig)
     val expectedA = WomSingleFile(jobPaths.callExecutionRoot.resolve("a").toAbsolutePath.pathAsString)
     val expectedB = WomSingleFile(jobPaths.callExecutionRoot.resolve("dir").toAbsolutePath.resolve("b").pathAsString)
-    val expectedOutputs = WomMocks.mockOutputExpectations(Map(
-      "localize.o1" -> expectedA,
-      "localize.o2" -> WomArray(WomArrayType(WomSingleFileType), Seq(expectedA, expectedB)),
-      "localize.o3" -> WomSingleFile(inputFile)
-    ))
-    val expectedResponse = JobSucceededResponse(jobDescriptor.key, Some(0), expectedOutputs, None, Seq.empty, None, resultGenerationMode = RunOnBackend)
+    val expectedOutputs = WomMocks.mockOutputExpectations(
+      Map(
+        "localize.o1" -> expectedA,
+        "localize.o2" -> WomArray(WomArrayType(WomSingleFileType), Seq(expectedA, expectedB)),
+        "localize.o3" -> WomSingleFile(inputFile)
+      )
+    )
+    val expectedResponse = JobSucceededResponse(jobDescriptor.key,
+                                                Some(0),
+                                                expectedOutputs,
+                                                None,
+                                                Seq.empty,
+                                                None,
+                                                resultGenerationMode = RunOnBackend
+    )
 
     executeJobAndAssertOutputs(backend, expectedResponse)
   }
 
   it should "fail post processing if an output file is not found" in {
-    val expectedResponse = JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
-      new FileNotFoundException("Could not process output, file not found:"), Option(0))
-    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(MissingOutputProcess), TestConfig.backendRuntimeConfigDescriptor, expectedResponse)
-    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor, Map.empty, WorkflowOptions.empty, runtimeAttributeDefinitions), workflow.config)
+    val expectedResponse =
+      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
+                                    new FileNotFoundException("Could not process output, file not found:"),
+                                    Option(0)
+      )
+    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(MissingOutputProcess),
+                                TestConfig.backendRuntimeConfigDescriptor,
+                                expectedResponse
+    )
+    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
+                                                                    Map.empty,
+                                                                    WorkflowOptions.empty,
+                                                                    runtimeAttributeDefinitions
+                                ),
+                                workflow.config
+    )
     testWorkflow(workflow, backend)
   }
 
-  def createCannedFile(prefix: String, contents: String, parent: Option[Path] = None): Path = {
+  def createCannedFile(prefix: String, contents: String, parent: Option[Path] = None): Path =
     DefaultPathBuilder.createTempFile(prefix, ".out", parent).write(contents)
-  }
 }
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemSpec.scala
index 34d5ca3cc73..409ef3c281f 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemSpec.scala
@@ -14,8 +14,12 @@ import wom.values.WomSingleFile
 
 import scala.io.Source
 
-class SharedFileSystemSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
-  with TableDrivenPropertyChecks with BackendSpec {
+class SharedFileSystemSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks
+    with BackendSpec {
 
   behavior of "SharedFileSystem"
 
@@ -27,14 +31,14 @@ class SharedFileSystemSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     ConfigFactory.parseString("""{localization: [cached-copy], max-hardlinks: 3 }""")
   private val localPathBuilder = List(DefaultPathBuilder)
 
-
   def localizationTest(config: Config,
                        docker: Boolean,
                        fileInCallDir: Boolean = false,
                        fileAlreadyExists: Boolean = false,
                        symlink: Boolean = false,
                        cachedCopy: Boolean = false,
-                       linkNb: Int = 1): Path = {
+                       linkNb: Int = 1
+  ): Path = {
     val callDir = DefaultPathBuilder.createTempDirectory("SharedFileSystem")
     val orig = if (fileInCallDir) callDir.createChild("inputFile") else DefaultPathBuilder.createTempFile("inputFile")
     val dest = if (fileInCallDir) orig else callDir./(orig.parent.pathAsString.hashCode.toString)./(orig.name)
@@ -54,11 +58,12 @@ class SharedFileSystemSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     val sharedFS: SharedFileSystem = new SharedFileSystem {
       override val pathBuilders: PathBuilders = localPathBuilder
       override val sharedFileSystemConfig: Config = config
-      override implicit def actorContext: ActorContext = null
+      implicit override def actorContext: ActorContext = null
       override lazy val cachedCopyDir: Option[Path] = Option(DefaultPathBuilder.createTempDirectory("cached-copy"))
     }
     val cachedFile: Option[Path] = sharedFS.cachedCopyDir.map(
-      _./(orig.parent.pathAsString.hashCode.toString)./(orig.lastModifiedTime.toEpochMilli.toString + orig.name))
+      _./(orig.parent.pathAsString.hashCode.toString)./(orig.lastModifiedTime.toEpochMilli.toString + orig.name)
+    )
     val localizedinputs = Map(inputs.head._1 -> WomSingleFile(dest.pathAsString))
     val result = sharedFS.localizeInputs(callDir, docker = docker)(inputs)
 
@@ -114,7 +119,7 @@ class SharedFileSystemSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     val sharedFS: SharedFileSystem = new SharedFileSystem {
       override val pathBuilders: PathBuilders = localPathBuilder
       override val sharedFileSystemConfig: Config = defaultLocalization
-      override implicit def actorContext: ActorContext = null
+      implicit override def actorContext: ActorContext = null
     }
     val result = sharedFS.localizeInputs(callDir, docker = false)(inputs)
     result.isFailure shouldBe true
@@ -130,11 +135,12 @@ class SharedFileSystemSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     val sharedFS: SharedFileSystem = new SharedFileSystem {
       override val pathBuilders: PathBuilders = localPathBuilder
       override val sharedFileSystemConfig: Config = cachedCopyLocalization
-      override implicit def actorContext: ActorContext = null
+      implicit override def actorContext: ActorContext = null
       override lazy val cachedCopyDir: Option[Path] = Option(DefaultPathBuilder.createTempDirectory("cached-copy"))
     }
     val cachedFile: Option[Path] = sharedFS.cachedCopyDir.map(
-      _./(orig.parent.pathAsString.hashCode.toString)./(orig.lastModifiedTime.toEpochMilli.toString + orig.name))
+      _./(orig.parent.pathAsString.hashCode.toString)./(orig.lastModifiedTime.toEpochMilli.toString + orig.name)
+    )
 
     val results = callDirs.map(sharedFS.localizeInputs(_, docker = true)(inputs))
 
@@ -148,7 +154,7 @@ class SharedFileSystemSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     dests.foreach(_.delete(swallowIOExceptions = true))
   }
 
-it should "copy the file again when the copy-cached file has exceeded the maximum number of hardlinks" in {
+  it should "copy the file again when the copy-cached file has exceeded the maximum number of hardlinks" in {
     val callDirs: IndexedSeq[Path] = 1 to 3 map { _ => DefaultPathBuilder.createTempDirectory("SharedFileSystem") }
     val orig = DefaultPathBuilder.createTempFile("inputFile")
     val dests = callDirs.map(_./(orig.parent.pathAsString.hashCode.toString)./(orig.name))
@@ -157,11 +163,12 @@ it should "copy the file again when the copy-cached file has exceeded the maximu
     val sharedFS: SharedFileSystem = new SharedFileSystem {
       override val pathBuilders: PathBuilders = localPathBuilder
       override val sharedFileSystemConfig: Config = cachedCopyLocalizationMaxHardlinks
-      override implicit def actorContext: ActorContext = null
+      implicit override def actorContext: ActorContext = null
       override lazy val cachedCopyDir: Option[Path] = Option(DefaultPathBuilder.createTempDirectory("cached-copy"))
     }
     val cachedFile: Option[Path] = sharedFS.cachedCopyDir.map(
-      _./(orig.parent.pathAsString.hashCode.toString)./(orig.lastModifiedTime.toEpochMilli.toString + orig.name))
+      _./(orig.parent.pathAsString.hashCode.toString)./(orig.lastModifiedTime.toEpochMilli.toString + orig.name)
+    )
 
     val results = callDirs.map(sharedFS.localizeInputs(_, docker = true)(inputs))
 
@@ -175,7 +182,6 @@ it should "copy the file again when the copy-cached file has exceeded the maximu
     dests.foreach(_.delete(swallowIOExceptions = true))
   }
 
-
   private[this] def countLinks(file: Path): Int = file.getAttribute("unix:nlink").asInstanceOf[Int]
 
   private[this] def isSymLink(file: Path): Boolean = file.isSymbolicLink
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/TestLocalAsyncJobExecutionActor.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/TestLocalAsyncJobExecutionActor.scala
index 58fec3dd74f..f9881908894 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/TestLocalAsyncJobExecutionActor.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/TestLocalAsyncJobExecutionActor.scala
@@ -10,15 +10,14 @@ import cromwell.core.SimpleIoActor
 import cromwell.services.keyvalue.InMemoryKvServiceActor
 
 class TestLocalAsyncJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
-  extends BackgroundAsyncJobExecutionActor {
+    extends BackgroundAsyncJobExecutionActor {
   override lazy val processArgs: SharedFileSystemCommand = {
     val script = jobPaths.script.pathAsString
     if (isDockerRun) {
       val docker = RuntimeAttributesValidation.extract(DockerValidation.instance, validatedRuntimeAttributes)
       val cwd = jobPaths.callRoot.pathAsString
       val dockerCwd = jobPathsWithDocker.callDockerRoot.pathAsString
-      SharedFileSystemCommand("/bin/bash", "-c",
-        s"docker run --rm -v $cwd:$dockerCwd -i $docker /bin/bash < $script")
+      SharedFileSystemCommand("/bin/bash", "-c", s"docker run --rm -v $cwd:$dockerCwd -i $docker /bin/bash < $script")
     } else {
       SharedFileSystemCommand("/bin/bash", script)
     }
@@ -28,19 +27,26 @@ class TestLocalAsyncJobExecutionActor(override val standardParams: StandardAsync
 }
 
 object TestLocalAsyncJobExecutionActor {
-  def createBackend(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor)
-                   (implicit system: ActorSystem): StandardSyncExecutionActor = {
+  def createBackend(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor)(
+    implicit system: ActorSystem
+  ): StandardSyncExecutionActor =
     createBackendRef(jobDescriptor, configurationDescriptor).underlyingActor
-  }
 
-  def createBackendRef(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor)
-                      (implicit system: ActorSystem): TestActorRef[StandardSyncExecutionActor] = {
-    val serviceRegistryActor = system.actorOf(Props(new InMemoryKvServiceActor)) // We only really need the KV store for now
+  def createBackendRef(jobDescriptor: BackendJobDescriptor, configurationDescriptor: BackendConfigurationDescriptor)(
+    implicit system: ActorSystem
+  ): TestActorRef[StandardSyncExecutionActor] = {
+    val serviceRegistryActor =
+      system.actorOf(Props(new InMemoryKvServiceActor)) // We only really need the KV store for now
     val ioActor = system.actorOf(SimpleIoActor.props)
-    val workflowPaths = new WorkflowPathsWithDocker(jobDescriptor.workflowDescriptor, configurationDescriptor.backendConfig)
-    val initializationData = new StandardInitializationData(workflowPaths,
-      StandardValidatedRuntimeAttributesBuilder.default(configurationDescriptor.backendRuntimeAttributesConfig).withValidation(DockerValidation.optional),
-      classOf[SharedFileSystemExpressionFunctions])
+    val workflowPaths =
+      new WorkflowPathsWithDocker(jobDescriptor.workflowDescriptor, configurationDescriptor.backendConfig)
+    val initializationData = new StandardInitializationData(
+      workflowPaths,
+      StandardValidatedRuntimeAttributesBuilder
+        .default(configurationDescriptor.backendRuntimeAttributesConfig)
+        .withValidation(DockerValidation.optional),
+      classOf[SharedFileSystemExpressionFunctions]
+    )
     val asyncClass = classOf[TestLocalAsyncJobExecutionActor]
 
     val params = DefaultStandardSyncExecutionActorParams(
@@ -52,7 +58,8 @@ object TestLocalAsyncJobExecutionActor {
       backendInitializationDataOption = Option(initializationData),
       backendSingletonActorOption = None,
       asyncJobExecutionActorClass = asyncClass,
-      MinimumRuntimeSettings())
+      MinimumRuntimeSettings()
+    )
 
     TestActorRef(new StandardSyncExecutionActor(params))
   }
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/DeclarationValidationSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/DeclarationValidationSpec.scala
index 4a6a28a47ba..681e4a91baa 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/DeclarationValidationSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/DeclarationValidationSpec.scala
@@ -12,16 +12,23 @@ import wdl.draft2.model._
 import wom.types.WomIntegerType
 import wom.values.WomInteger
 
-class DeclarationValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
+class DeclarationValidationSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks {
   behavior of "DeclarationValidation"
-  
+
   def validateCpu(key: String) = {
     val expression = WdlExpression.fromString("5")
     val declarationValidation = DeclarationValidation.fromDeclaration(callCachedRuntimeAttributesMap = Map.empty)(
-      Declaration(WomIntegerType, key, Option(expression), None, null))
-    declarationValidation.extractWdlValueOption(ValidatedRuntimeAttributes(Map(key -> refineMV[Positive](5)))) shouldBe Some(WomInteger(5))
+      Declaration(WomIntegerType, key, Option(expression), None, null)
+    )
+    declarationValidation.extractWdlValueOption(
+      ValidatedRuntimeAttributes(Map(key -> refineMV[Positive](5)))
+    ) shouldBe Some(WomInteger(5))
   }
-  
+
   it should "validate cpu attributes" in {
     val keys = Table(
       "key",
@@ -29,7 +36,7 @@ class DeclarationValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       "cpuMin",
       "cpuMax"
     )
-    
-    forAll(keys) { validateCpu }
+
+    forAll(keys)(validateCpu)
   }
 }
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/HttpFilesystemEnablementSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/HttpFilesystemEnablementSpec.scala
index 0c63b2b8db8..bb96ce4b1ee 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/HttpFilesystemEnablementSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/HttpFilesystemEnablementSpec.scala
@@ -10,7 +10,11 @@ import org.scalatest.BeforeAndAfterAll
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.wordspec.AnyWordSpecLike
 
-class HttpFilesystemEnablementSpec extends AnyWordSpecLike with CromwellTimeoutSpec with Matchers with BeforeAndAfterAll {
+class HttpFilesystemEnablementSpec
+    extends AnyWordSpecLike
+    with CromwellTimeoutSpec
+    with Matchers
+    with BeforeAndAfterAll {
   "The http filesystem on the default Local backend" should {
     "be enabled unless explicitly disabled" in {
       configuredFilesystems(LocalConfig) shouldEqual Set("http")
@@ -20,7 +24,6 @@ class HttpFilesystemEnablementSpec extends AnyWordSpecLike with CromwellTimeoutS
   }
 }
 
-
 object HttpFilesystemEnablementSpec {
   def configuredFilesystems(configs: Configurations): Set[String] = {
     val descriptor = new BackendConfigurationDescriptor(configs.local, configs.global) {
@@ -34,10 +37,10 @@ object HttpFilesystemEnablementSpec {
     // This is only checking the http filesystem, no need to load all those other filesystems with their
     // filesystem classes that live in other subprojects.
     val globalFilesystemsConfig =
-    """
-      |http {
-      |  class = "cromwell.filesystems.http.HttpPathBuilderFactory"
-      |}
+      """
+        |http {
+        |  class = "cromwell.filesystems.http.HttpPathBuilderFactory"
+        |}
     """.stripMargin
 
     val globalFilesystems = ConfigFactory.parseString(globalFilesystemsConfig)
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index bd171d757b4..d7a19685cd8 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -14,10 +14,23 @@ import common.exception.AggregatedMessageException
 import common.validation.ErrorOr.ErrorOr
 import common.validation.Validation._
 import cromwell.backend.BackendJobLifecycleActor
-import cromwell.backend.async.{AbortedExecutionHandle, ExecutionHandle, FailedNonRetryableExecutionHandle, PendingExecutionHandle}
-import cromwell.backend.impl.tes.TesAsyncBackendJobExecutionActor.{determineWSMSasEndpointFromInputs, generateLocalizedSasScriptPreamble}
+import cromwell.backend.async.{
+  AbortedExecutionHandle,
+  ExecutionHandle,
+  FailedNonRetryableExecutionHandle,
+  PendingExecutionHandle
+}
+import cromwell.backend.impl.tes.TesAsyncBackendJobExecutionActor.{
+  determineWSMSasEndpointFromInputs,
+  generateLocalizedSasScriptPreamble
+}
 import cromwell.backend.impl.tes.TesResponseJsonFormatter._
-import cromwell.backend.standard.{ScriptPreambleData, StandardAsyncExecutionActor, StandardAsyncExecutionActorParams, StandardAsyncJob}
+import cromwell.backend.standard.{
+  ScriptPreambleData,
+  StandardAsyncExecutionActor,
+  StandardAsyncExecutionActorParams,
+  StandardAsyncJob
+}
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.{DefaultPathBuilder, Path}
 import cromwell.core.retry.Retry._
@@ -63,7 +76,7 @@ case object Cancelled extends TesRunStatus {
 object TesAsyncBackendJobExecutionActor {
   val JobIdKey = "tes_job_id"
 
-  def generateLocalizedSasScriptPreamble(environmentVariableName: String, getSasWsmEndpoint: String) : String = {
+  def generateLocalizedSasScriptPreamble(environmentVariableName: String, getSasWsmEndpoint: String): String =
     // BEARER_TOKEN: https://learn.microsoft.com/en-us/azure/active-directory/managed-identities-azure-resources/how-to-use-vm-token#get-a-token-using-http
     // NB: Scala string interpolation and bash variable substitution use similar syntax. $$ is an escaped $, much like \\ is an escaped \.
     s"""
@@ -128,11 +141,9 @@ object TesAsyncBackendJobExecutionActor {
        |echo "Saving sas token: $${$environmentVariableName:0:4}**** to environment variable $environmentVariableName..."
        |### END ACQUIRE LOCAL SAS TOKEN ###
        |""".stripMargin
-  }
 
-  private def maybeConvertToBlob(pathToTest: Try[Path]): Try[BlobPath] = {
+  private def maybeConvertToBlob(pathToTest: Try[Path]): Try[BlobPath] =
     pathToTest.collect { case blob: BlobPath => blob }
-  }
 
   /**
    * Computes an endpoint that can be used to retrieve a sas token for a particular blob storage container.
@@ -149,29 +160,44 @@ object TesAsyncBackendJobExecutionActor {
   def determineWSMSasEndpointFromInputs(taskInputs: List[Input],
                                         pathGetter: String => Try[Path],
                                         logger: JobLogger,
-                                        blobConverter: Try[Path] => Try[BlobPath] = maybeConvertToBlob): Try[String] = {
+                                        blobConverter: Try[Path] => Try[BlobPath] = maybeConvertToBlob
+  ): Try[String] = {
     // Collect all of the inputs that are valid blob paths
     val blobFiles = taskInputs
-      .collect{ case Input(_, _, Some(url), _, _, _) => blobConverter(pathGetter(url)) }
-      .collect{ case Success(blob) => blob }
+      .collect { case Input(_, _, Some(url), _, _, _) => blobConverter(pathGetter(url)) }
+      .collect { case Success(blob) => blob }
 
     // Log if not all input files live in the same container.
     if (blobFiles.map(_.container).distinct.size > 1) {
-      logger.info(s"While parsing blob inputs, found more than one container. Generating SAS token based on first file in the list.")
+      logger.info(
+        s"While parsing blob inputs, found more than one container. Generating SAS token based on first file in the list."
+      )
     }
 
     // We use the first blob file in the list to determine the correct blob container.
-    blobFiles.headOption.map{blobPath =>
-      blobPath.getFilesystemManager.blobTokenGenerator match {
-        case wsmGenerator: WSMBlobSasTokenGenerator => wsmGenerator.getWSMSasFetchEndpoint(blobPath, Some(Duration.of(24, ChronoUnit.HOURS)))
-        case _ => Failure(new UnsupportedOperationException("Blob file does not have an associated WSMBlobSasTokenGenerator"))
+    blobFiles.headOption
+      .map { blobPath =>
+        blobPath.getFilesystemManager.blobTokenGenerator match {
+          case wsmGenerator: WSMBlobSasTokenGenerator =>
+            wsmGenerator.getWSMSasFetchEndpoint(blobPath, Some(Duration.of(24, ChronoUnit.HOURS)))
+          case _ =>
+            Failure(new UnsupportedOperationException("Blob file does not have an associated WSMBlobSasTokenGenerator"))
+        }
       }
-    }.getOrElse(Failure(new NoSuchElementException("Could not infer blob storage container from task inputs: No valid blob files provided.")))
+      .getOrElse(
+        Failure(
+          new NoSuchElementException(
+            "Could not infer blob storage container from task inputs: No valid blob files provided."
+          )
+        )
+      )
   }
 }
 
 class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
-  extends BackendJobLifecycleActor with StandardAsyncExecutionActor with TesJobCachingActorHelper {
+    extends BackendJobLifecycleActor
+    with StandardAsyncExecutionActor
+    with TesJobCachingActorHelper {
   implicit val actorSystem = context.system
   implicit val materializer = ActorMaterializer()
 
@@ -183,7 +209,8 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
   override lazy val pollBackOff: SimpleExponentialBackoff = tesConfiguration.pollBackoff
   override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff = tesConfiguration.executeOrRecoverBackoff
 
-  private lazy val realDockerImageUsed: String = jobDescriptor.maybeCallCachingEligible.dockerHash.getOrElse(runtimeAttributes.dockerImage)
+  private lazy val realDockerImageUsed: String =
+    jobDescriptor.maybeCallCachingEligible.dockerHash.getOrElse(runtimeAttributes.dockerImage)
   override lazy val dockerImageUsed: Option[String] = Option(realDockerImageUsed)
 
   private val tesEndpoint = workflowDescriptor.workflowOptions.getOrElse("endpoint", tesConfiguration.endpointURL)
@@ -194,7 +221,8 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
     OutputMode.withName(
       configurationDescriptor.backendConfig
         .getAs[String]("output-mode")
-        .getOrElse("granular").toUpperCase
+        .getOrElse("granular")
+        .toUpperCase
     )
   }
 
@@ -215,22 +243,28 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
    *
    * @return Bash code to run at the start of a task.
    */
-  override def scriptPreamble: ErrorOr[ScriptPreambleData] = {
+  override def scriptPreamble: ErrorOr[ScriptPreambleData] =
     runtimeAttributes.localizedSasEnvVar match {
-      case Some(environmentVariableName) => { // Case: user wants a sas token. Return the computed preamble or die trying.
-        val workflowName = workflowDescriptor.callable.name
-        val callInputFiles = jobDescriptor.fullyQualifiedInputs.safeMapValues {
-          _.collectAsSeq { case w: WomFile => w }
-        }
-        val taskInputs: List[Input] = TesTask.buildTaskInputs(callInputFiles, workflowName, mapCommandLineWomFile)
-        val computedEndpoint = determineWSMSasEndpointFromInputs(taskInputs, getPath, jobLogger)
-        computedEndpoint.map(endpoint => ScriptPreambleData(generateLocalizedSasScriptPreamble(environmentVariableName, endpoint), executeInSubshell =  false))
-      }.toErrorOr
-      case _ => ScriptPreambleData("", executeInSubshell = false).valid // Case: user doesn't want a sas token. Empty preamble is the correct preamble.
+      case Some(environmentVariableName) =>
+        { // Case: user wants a sas token. Return the computed preamble or die trying.
+          val workflowName = workflowDescriptor.callable.name
+          val callInputFiles = jobDescriptor.fullyQualifiedInputs.safeMapValues {
+            _.collectAsSeq { case w: WomFile => w }
+          }
+          val taskInputs: List[Input] = TesTask.buildTaskInputs(callInputFiles, workflowName, mapCommandLineWomFile)
+          val computedEndpoint = determineWSMSasEndpointFromInputs(taskInputs, getPath, jobLogger)
+          computedEndpoint.map(endpoint =>
+            ScriptPreambleData(generateLocalizedSasScriptPreamble(environmentVariableName, endpoint),
+                               executeInSubshell = false
+            )
+          )
+        }.toErrorOr
+      case _ =>
+        ScriptPreambleData("",
+                           executeInSubshell = false
+        ).valid // Case: user doesn't want a sas token. Empty preamble is the correct preamble.
     }
-  }
-
-  override def mapCommandLineWomFile(womFile: WomFile): WomFile = {
+  override def mapCommandLineWomFile(womFile: WomFile): WomFile =
     womFile.mapFile(value =>
       (getPath(value), asAdHocFile(womFile)) match {
         case (Success(path: Path), Some(adHocFile)) =>
@@ -240,9 +274,8 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
         case _ => mapCommandLineJobInputWomFile(womFile).value
       }
     )
-  }
 
-  override def mapCommandLineJobInputWomFile(womFile: WomFile): WomFile = {
+  override def mapCommandLineJobInputWomFile(womFile: WomFile): WomFile =
     womFile.mapFile(value =>
       getPath(value) match {
         case Success(drsPath: DrsPath) =>
@@ -261,33 +294,35 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
           // lives in the workflow execution directory, strip off that prefix from the path we're
           // generating inside `inputs/` to keep the total path length under control.
           // In Terra on Azure, this saves us 200+ characters.
-          tesJobPaths.callInputsDockerRoot.resolve(
-            path.pathStringWithoutPrefix(tesJobPaths.workflowPaths.workflowRoot)
-          ).pathAsString
+          tesJobPaths.callInputsDockerRoot
+            .resolve(
+              path.pathStringWithoutPrefix(tesJobPaths.workflowPaths.workflowRoot)
+            )
+            .pathAsString
         case Success(path: BlobPath) if path.startsWith(tesJobPaths.workflowPaths.executionRoot) =>
           // See comment above... if this file is in the execution root, strip that off.
           // In Terra on Azure, this saves us 160+ characters.
-          tesJobPaths.callInputsDockerRoot.resolve(
-            path.pathStringWithoutPrefix(tesJobPaths.workflowPaths.executionRoot)
-          ).pathAsString
+          tesJobPaths.callInputsDockerRoot
+            .resolve(
+              path.pathStringWithoutPrefix(tesJobPaths.workflowPaths.executionRoot)
+            )
+            .pathAsString
         case Success(path: Path) =>
           tesJobPaths.callInputsDockerRoot.resolve(path.pathWithoutScheme.stripPrefix("/")).pathAsString
         case _ =>
           value
       }
     )
-  }
 
-  override lazy val commandDirectory: Path = {
+  override lazy val commandDirectory: Path =
     runtimeAttributes.dockerWorkingDir match {
       case Some(path) => DefaultPathBuilder.get(path)
       case None => tesJobPaths.callExecutionDockerRoot
     }
-  }
 
   def createTaskMessage(): ErrorOr[Task] = {
-    val tesTask = (commandScriptContents, outputMode).mapN({
-      case (contents, mode) => TesTask(
+    val tesTask = (commandScriptContents, outputMode).mapN { case (contents, mode) =>
+      TesTask(
         jobDescriptor,
         configurationDescriptor,
         jobLogger,
@@ -299,25 +334,26 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
         realDockerImageUsed,
         mapCommandLineWomFile,
         jobShell,
-        mode)
-    })
+        mode
+      )
+    }
 
     tesTask.map(TesTask.makeTask)
   }
 
-  def writeScriptFile(): Future[Unit] = {
+  def writeScriptFile(): Future[Unit] =
     commandScriptContents.fold(
       errors => Future.failed(new RuntimeException(errors.toList.mkString(", "))),
       asyncIo.writeAsync(jobPaths.script, _, Seq.empty)
     )
-  }
 
   override def executeAsync(): Future[ExecutionHandle] = {
     // create call exec dir
     tesJobPaths.callExecutionRoot.createPermissionedDirectories()
     val taskMessageFuture = createTaskMessage().fold(
       errors => Future.failed(new RuntimeException(errors.toList.mkString(", "))),
-      Future.successful)
+      Future.successful
+    )
 
     for {
       _ <- writeScriptFile()
@@ -328,7 +364,12 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
   }
 
   override def reconnectAsync(jobId: StandardAsyncJob) = {
-    val handle = PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState](jobDescriptor, jobId, None, previousState = None)
+    val handle = PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState](jobDescriptor,
+                                                                                                       jobId,
+                                                                                                       None,
+                                                                                                       previousState =
+                                                                                                         None
+    )
     Future.successful(handle)
   }
 
@@ -343,15 +384,17 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
 
     val returnCodeTmp = jobPaths.returnCode.plusExt("kill")
     returnCodeTmp.write(s"$SIGTERM\n")
-    try {
+    try
       returnCodeTmp.moveTo(jobPaths.returnCode)
-    } catch {
+    catch {
       case _: FileAlreadyExistsException =>
         // If the process has already completed, there will be an existing rc file.
         returnCodeTmp.delete(true)
     }
 
-    makeRequest[CancelTaskResponse](HttpRequest(method = HttpMethods.POST, uri = s"$tesEndpoint/${job.jobId}:cancel")) onComplete {
+    makeRequest[CancelTaskResponse](
+      HttpRequest(method = HttpMethods.POST, uri = s"$tesEndpoint/${job.jobId}:cancel")
+    ) onComplete {
       case Success(_) => jobLogger.info("{} Aborted {}", tag: Any, job.jobId)
       case Failure(ex) => jobLogger.warn("{} Failed to abort {}: {}", tag, job.jobId, ex.getMessage)
     }
@@ -361,12 +404,12 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
 
   override def requestsAbortAndDiesImmediately: Boolean = false
 
-  override def pollStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[TesRunStatus] = {
+  override def pollStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[TesRunStatus] =
     for {
       status <- queryStatusAsync(handle)
       errorLog <- status match {
-          case Error(_) | Failed(_) => getErrorLogs(handle)
-          case _ => Future.successful(Seq.empty[String])
+        case Error(_) | Failed(_) => getErrorLogs(handle)
+        case _ => Future.successful(Seq.empty[String])
       }
       statusWithLog = status match {
         case Error(_) => Error(errorLog)
@@ -374,9 +417,8 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
         case _ => status
       }
     } yield statusWithLog
-  }
 
-  private def queryStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[TesRunStatus] = {
+  private def queryStatusAsync(handle: StandardAsyncPendingExecutionHandle): Future[TesRunStatus] =
     makeRequest[MinimalTaskView](HttpRequest(uri = s"$tesEndpoint/${handle.pendingJob.jobId}?view=MINIMAL")) map {
       response =>
         val state = response.state
@@ -400,16 +442,14 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
           case _ => Running
         }
     }
-  }
 
-  private def getErrorLogs(handle: StandardAsyncPendingExecutionHandle): Future[Seq[String]] = {
+  private def getErrorLogs(handle: StandardAsyncPendingExecutionHandle): Future[Seq[String]] =
     makeRequest[Task](HttpRequest(uri = s"$tesEndpoint/${handle.pendingJob.jobId}?view=FULL")) map { response =>
       response.logs.flatMap(_.lastOption).flatMap(_.system_logs).getOrElse(Seq.empty[String])
     }
-  }
 
   override def customPollStatusFailure: PartialFunction[(ExecutionHandle, Exception), ExecutionHandle] = {
-    case (oldHandle: StandardAsyncPendingExecutionHandle@unchecked, e: Exception) =>
+    case (oldHandle: StandardAsyncPendingExecutionHandle @unchecked, e: Exception) =>
       jobLogger.error(s"$tag TES Job ${oldHandle.pendingJob.jobId} has not been found, failing call")
       FailedNonRetryableExecutionHandle(e, kvPairsToSave = None)
   }
@@ -421,26 +461,23 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
     Future.successful(FailedNonRetryableExecutionHandle(exception, returnCode, None))
   }
 
-  override def handleExecutionFailure(status: StandardAsyncRunState, returnCode: Option[Int]) = {
+  override def handleExecutionFailure(status: StandardAsyncRunState, returnCode: Option[Int]) =
     status match {
       case Cancelled => Future.successful(AbortedExecutionHandle)
       case Error(_) | Failed(_) => handleExecutionError(status, returnCode)
       case _ => super.handleExecutionFailure(status, returnCode)
     }
-  }
 
-  override def isTerminal(runStatus: TesRunStatus): Boolean = {
+  override def isTerminal(runStatus: TesRunStatus): Boolean =
     runStatus.isTerminal
-  }
 
-  override def isDone(runStatus: TesRunStatus): Boolean = {
+  override def isDone(runStatus: TesRunStatus): Boolean =
     runStatus match {
       case Complete => true
       case _ => false
     }
-  }
 
-  override def mapOutputWomFile(womFile: WomFile): WomFile = {
+  override def mapOutputWomFile(womFile: WomFile): WomFile =
     womFile mapFile { path =>
       val absPath = getPath(path) match {
         case Success(absoluteOutputPath) if absoluteOutputPath.isAbsolute => absoluteOutputPath
@@ -451,7 +488,6 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
         throw new FileNotFoundException(s"Could not process output, file not found: ${absPath.pathAsString}")
       } else absPath.pathAsString
     }
-  }
 
   // Headers that should be included with all requests to the TES server
   private def requestHeaders: List[HttpHeader] =
@@ -462,16 +498,18 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
       }
     }.toList
 
-  private def makeRequest[A](request: HttpRequest)(implicit um: Unmarshaller[ResponseEntity, A]): Future[A] = {
+  private def makeRequest[A](request: HttpRequest)(implicit um: Unmarshaller[ResponseEntity, A]): Future[A] =
     for {
       response <- withRetry(() => Http().singleRequest(request.withHeaders(requestHeaders)))
-      data <- if (response.status.isFailure()) {
-        response.entity.dataBytes.runFold(ByteString(""))(_ ++ _).map(_.utf8String) flatMap { errorBody =>
-          Future.failed(new RuntimeException(s"Failed TES request: Code ${response.status.intValue()}, Body = $errorBody"))
+      data <-
+        if (response.status.isFailure()) {
+          response.entity.dataBytes.runFold(ByteString(""))(_ ++ _).map(_.utf8String) flatMap { errorBody =>
+            Future.failed(
+              new RuntimeException(s"Failed TES request: Code ${response.status.intValue()}, Body = $errorBody")
+            )
+          }
+        } else {
+          Unmarshal(response.entity).to[A]
         }
-      } else {
-        Unmarshal(response.entity).to[A]
-      }
     } yield data
-  }
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendInitializationData.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendInitializationData.scala
index 48f55e2f30b..53385ebb284 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendInitializationData.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendInitializationData.scala
@@ -2,8 +2,7 @@ package cromwell.backend.impl.tes
 
 import cromwell.backend.standard.{StandardInitializationData, StandardValidatedRuntimeAttributesBuilder}
 
-case class TesBackendInitializationData
-(
+case class TesBackendInitializationData(
   override val workflowPaths: TesWorkflowPaths,
   override val runtimeAttributesBuilder: StandardValidatedRuntimeAttributesBuilder,
   tesConfiguration: TesConfiguration
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendLifecycleActorFactory.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendLifecycleActorFactory.scala
index 46770e40032..9cb502ef952 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendLifecycleActorFactory.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendLifecycleActorFactory.scala
@@ -6,7 +6,7 @@ import cromwell.backend.standard._
 import wom.graph.CommandCallNode
 
 case class TesBackendLifecycleActorFactory(name: String, configurationDescriptor: BackendConfigurationDescriptor)
-  extends StandardLifecycleActorFactory {
+    extends StandardLifecycleActorFactory {
 
   override lazy val initializationActorClass: Class[_ <: StandardInitializationActor] = classOf[TesInitializationActor]
 
@@ -17,8 +17,11 @@ case class TesBackendLifecycleActorFactory(name: String, configurationDescriptor
 
   val tesConfiguration = new TesConfiguration(configurationDescriptor)
 
-  override def workflowInitializationActorParams(workflowDescriptor: BackendWorkflowDescriptor, ioActor: ActorRef, calls: Set[CommandCallNode],
-                                                 serviceRegistryActor: ActorRef, restarting: Boolean): StandardInitializationActorParams = {
+  override def workflowInitializationActorParams(workflowDescriptor: BackendWorkflowDescriptor,
+                                                 ioActor: ActorRef,
+                                                 calls: Set[CommandCallNode],
+                                                 serviceRegistryActor: ActorRef,
+                                                 restarting: Boolean
+  ): StandardInitializationActorParams =
     TesInitializationActorParams(workflowDescriptor, calls, tesConfiguration, serviceRegistryActor)
-  }
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
index 253f60114be..b90b406569a 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
@@ -13,34 +13,30 @@ class TesConfiguration(val configurationDescriptor: BackendConfigurationDescript
   val endpointURL = configurationDescriptor.backendConfig.getString("endpoint")
   val runtimeConfig = configurationDescriptor.backendRuntimeAttributesConfig
   val useBackendParameters =
-    configurationDescriptor
-      .backendConfig
+    configurationDescriptor.backendConfig
       .as[Option[Boolean]](TesConfiguration.useBackendParametersKey)
       .getOrElse(false)
 
   val pollBackoff =
-    configurationDescriptor
-      .backendConfig
+    configurationDescriptor.backendConfig
       .as[Option[Config]]("poll-backoff")
       .map(SimpleExponentialBackoff(_))
       .getOrElse(TesConfiguration.defaultPollBackoff)
 
   val executeOrRecoverBackoff =
-    configurationDescriptor
-      .backendConfig
+    configurationDescriptor.backendConfig
       .as[Option[Config]]("execute-or-recover-backoff")
       .map(SimpleExponentialBackoff(_))
       .getOrElse(TesConfiguration.defaultExecOrRecoverBackoff)
 
   // Used for testing only. Include a bearer token for authenticating with the TES server
   final val bearerPrefix: String = "Bearer "
-  val token: Option[String] = {
+  val token: Option[String] =
     configurationDescriptor.backendConfig.as[Option[String]]("bearer-token").map { t =>
       if (!t.startsWith(bearerPrefix))
         s"${bearerPrefix}${t}"
       else t
     }
-  }
 }
 
 object TesConfiguration {
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesExpressionFunctions.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesExpressionFunctions.scala
index 11b3b2bfb1b..19fe187c0f7 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesExpressionFunctions.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesExpressionFunctions.scala
@@ -3,10 +3,10 @@ package cromwell.backend.impl.tes
 import cromwell.backend.sfs.SharedFileSystemExpressionFunctions
 import cromwell.backend.standard.StandardExpressionFunctionsParams
 
-class TesExpressionFunctions(standardParams: StandardExpressionFunctionsParams) extends SharedFileSystemExpressionFunctions(standardParams) {
+class TesExpressionFunctions(standardParams: StandardExpressionFunctionsParams)
+    extends SharedFileSystemExpressionFunctions(standardParams) {
 
-  override def preMapping(str: String) = {
+  override def preMapping(str: String) =
     if (str.startsWith("/") || str.startsWith("ftp://")) str
     else standardParams.callContext.root.resolve(str).toString
-  }
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesInitializationActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesInitializationActor.scala
index 101187e2364..9d4d1b4be53 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesInitializationActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesInitializationActor.scala
@@ -12,8 +12,7 @@ import wom.graph.CommandCallNode
 import scala.concurrent.Future
 import scala.util.Try
 
-case class TesInitializationActorParams
-(
+case class TesInitializationActorParams(
   workflowDescriptor: BackendWorkflowDescriptor,
   calls: Set[CommandCallNode],
   tesConfiguration: TesConfiguration,
@@ -22,14 +21,12 @@ case class TesInitializationActorParams
   override val configurationDescriptor: BackendConfigurationDescriptor = tesConfiguration.configurationDescriptor
 }
 
-class TesInitializationActor(params: TesInitializationActorParams)
-  extends StandardInitializationActor(params) {
+class TesInitializationActor(params: TesInitializationActorParams) extends StandardInitializationActor(params) {
 
   private val tesConfiguration = params.tesConfiguration
 
-  override lazy val pathBuilders: Future[List[PathBuilder]] = {
+  override lazy val pathBuilders: Future[List[PathBuilder]] =
     standardParams.configurationDescriptor.pathBuildersWithDefault(workflowDescriptor.workflowOptions)
-  }
 
   override lazy val workflowPaths: Future[TesWorkflowPaths] = pathBuilders map {
     new TesWorkflowPaths(workflowDescriptor, tesConfiguration.configurationDescriptor.backendConfig, _)
@@ -41,10 +38,13 @@ class TesInitializationActor(params: TesInitializationActorParams)
   override def validateWorkflowOptions(): Try[Unit] = {
     def validateIdentities() = {
       val optionsMap = workflowDescriptor.workflowOptions.toMap
-      (optionsMap.get(TesWorkflowOptionKeys.WorkflowExecutionIdentity), optionsMap.get(TesWorkflowOptionKeys.DataAccessIdentity)) match {
+      (optionsMap.get(TesWorkflowOptionKeys.WorkflowExecutionIdentity),
+       optionsMap.get(TesWorkflowOptionKeys.DataAccessIdentity)
+      ) match {
         case (None, None) => ().validNel
         case (Some(_), Some(_)) => ().validNel
-        case _ => s"Workflow options ${TesWorkflowOptionKeys.WorkflowExecutionIdentity} and ${TesWorkflowOptionKeys.DataAccessIdentity} are both required if one is provided.".invalidNel
+        case _ =>
+          s"Workflow options ${TesWorkflowOptionKeys.WorkflowExecutionIdentity} and ${TesWorkflowOptionKeys.DataAccessIdentity} are both required if one is provided.".invalidNel
       }
     }
 
@@ -76,8 +76,7 @@ class TesInitializationActor(params: TesInitializationActorParams)
           // This is difficult because we're dealing with WomExpression rather than WomValue.
           s"Key/s [$notSupportedAttrString] is/are not explicitly supported by backend. Those with string values will " +
             "be passed to TES server in backend_parameters map, other attributes will not be part of job executions."
-        }
-        else {
+        } else {
           s"Key/s [$notSupportedAttrString] is/are not supported by backend. " +
             s"Unsupported attributes will not be part of job executions."
         }
@@ -86,11 +85,10 @@ class TesInitializationActor(params: TesInitializationActorParams)
     }
   }
 
-  override def beforeAll(): Future[Option[BackendInitializationData]] = {
+  override def beforeAll(): Future[Option[BackendInitializationData]] =
     workflowPaths map { paths =>
       publishWorkflowRoot(paths.workflowRoot.toString)
       paths.workflowRoot.createPermissionedDirectories()
       Option(TesBackendInitializationData(paths, runtimeAttributesBuilder, tesConfiguration))
     }
-  }
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobCachingActorHelper.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobCachingActorHelper.scala
index 6c4b495d362..0f132e55cc6 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobCachingActorHelper.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobCachingActorHelper.scala
@@ -1,6 +1,5 @@
 package cromwell.backend.impl.tes
 
-
 import akka.actor.Actor
 import cromwell.backend.standard.StandardCachingActorHelper
 import cromwell.core.logging.JobLogging
@@ -8,9 +7,8 @@ import cromwell.core.logging.JobLogging
 trait TesJobCachingActorHelper extends StandardCachingActorHelper {
   this: Actor with JobLogging =>
 
-  lazy val initializationData: TesBackendInitializationData = {
+  lazy val initializationData: TesBackendInitializationData =
     backendInitializationDataAs[TesBackendInitializationData]
-  }
 
   lazy val tesWorkflowPaths: TesWorkflowPaths = workflowPaths.asInstanceOf[TesWorkflowPaths]
 
@@ -18,7 +16,9 @@ trait TesJobCachingActorHelper extends StandardCachingActorHelper {
 
   lazy val tesConfiguration: TesConfiguration = initializationData.tesConfiguration
 
-  lazy val runtimeAttributes = TesRuntimeAttributes(validatedRuntimeAttributes, jobDescriptor.runtimeAttributes, tesConfiguration)
-  override protected def nonStandardMetadata: Map[String, Any] = super.nonStandardMetadata ++ tesJobPaths.azureLogPathsForMetadata
+  lazy val runtimeAttributes =
+    TesRuntimeAttributes(validatedRuntimeAttributes, jobDescriptor.runtimeAttributes, tesConfiguration)
+  override protected def nonStandardMetadata: Map[String, Any] =
+    super.nonStandardMetadata ++ tesJobPaths.azureLogPathsForMetadata
 
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
index ab7b2b27916..05887fc3fa5 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesJobPaths.scala
@@ -7,9 +7,7 @@ import cromwell.core.path._
 import cromwell.filesystems.blob.BlobPath
 
 object TesJobPaths {
-  def apply(jobKey: BackendJobDescriptorKey,
-  workflowDescriptor: BackendWorkflowDescriptor,
-  config: Config) = {
+  def apply(jobKey: BackendJobDescriptorKey, workflowDescriptor: BackendWorkflowDescriptor, config: Config) = {
     val workflowPaths = TesWorkflowPaths(workflowDescriptor, config, WorkflowPaths.DefaultPathBuilders)
     new TesJobPaths(workflowPaths, jobKey)
   }
@@ -17,13 +15,13 @@ object TesJobPaths {
 
 case class TesJobPaths private[tes] (override val workflowPaths: TesWorkflowPaths,
                                      jobKey: BackendJobDescriptorKey,
-                                     override val isCallCacheCopyAttempt: Boolean = false) extends JobPaths {
+                                     override val isCallCacheCopyAttempt: Boolean = false
+) extends JobPaths {
 
   import JobPaths._
 
-  override lazy val callExecutionRoot = {
+  override lazy val callExecutionRoot =
     callRoot.resolve("execution")
-  }
   val callDockerRoot = callPathBuilder(workflowPaths.dockerWorkflowRoot, jobKey, isCallCacheCopyAttempt)
   val callExecutionDockerRoot = callDockerRoot.resolve("execution")
   val callInputsDockerRoot = callDockerRoot.resolve("inputs")
@@ -38,22 +36,21 @@ case class TesJobPaths private[tes] (override val workflowPaths: TesWorkflowPath
    * While passing it outside of terra won't do any harm, we could consider making this optional and/or configurable.
    */
   private val taskFullPath = callRoot./("tes_task")
-  val tesTaskRoot : String = taskFullPath match {
+  val tesTaskRoot: String = taskFullPath match {
     case blob: BlobPath => blob.pathWithoutContainer
     case anyOtherPath: Path => anyOtherPath.pathAsString
   }
 
   // Like above: Nothing should rely on these files existing, since only the Azure TES implementation will actually create them.
   // Used to send the Azure TES log paths to the frontend.
-  val azureLogPathsForMetadata : Map[String, Any] = Map(
+  val azureLogPathsForMetadata: Map[String, Any] = Map(
     "tes_stdout" -> taskFullPath./("stdout.txt").pathAsString,
     "tes_stderr" -> taskFullPath./("stderr.txt").pathAsString
   )
 
   // Given an output path, return a path localized to the storage file system
-  def storageOutput(path: String): String = {
+  def storageOutput(path: String): String =
     callExecutionRoot.resolve(path).toString
-  }
 
   // Given an output path, return a path localized to the container file system
   def containerOutput(cwd: Path, path: String): String = containerExec(cwd, path)
@@ -62,9 +59,8 @@ case class TesJobPaths private[tes] (override val workflowPaths: TesWorkflowPath
   // callDockerRoot.resolve("outputs").resolve(name).toString
 
   // Given an file name, return a path localized to the container's execution directory
-  def containerExec(cwd: Path, path: String): String = {
+  def containerExec(cwd: Path, path: String): String =
     cwd.resolve(path).toString
-  }
 
   override def forCallCacheCopyAttempts: JobPaths = this.copy(isCallCacheCopyAttempt = true)
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
index 48ade7b234a..117e0ee79a7 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesRuntimeAttributes.scala
@@ -5,7 +5,11 @@ import cats.syntax.validated._
 import com.typesafe.config.Config
 import common.validation.ErrorOr.ErrorOr
 import cromwell.backend.google.pipelines.common.DisksValidation
-import cromwell.backend.google.pipelines.common.io.{PipelinesApiAttachedDisk, PipelinesApiEmptyMountedDisk, PipelinesApiWorkingDisk}
+import cromwell.backend.google.pipelines.common.io.{
+  PipelinesApiAttachedDisk,
+  PipelinesApiEmptyMountedDisk,
+  PipelinesApiWorkingDisk
+}
 import cromwell.backend.standard.StandardValidatedRuntimeAttributesBuilder
 import cromwell.backend.validation._
 import eu.timepit.refined.api.Refined
@@ -27,7 +31,8 @@ case class TesRuntimeAttributes(continueOnReturnCode: ContinueOnReturnCode,
                                 disk: Option[MemorySize],
                                 preemptible: Boolean,
                                 localizedSasEnvVar: Option[String],
-                                backendParameters: Map[String, Option[String]])
+                                backendParameters: Map[String, Option[String]]
+)
 
 object TesRuntimeAttributes {
   val DockerWorkingDirKey = "dockerWorkingDir"
@@ -35,22 +40,29 @@ object TesRuntimeAttributes {
   val PreemptibleKey = "preemptible"
   val LocalizedSasKey = "azureSasEnvironmentVariable"
 
-  private def cpuValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Int Refined Positive] = CpuValidation.optional
+  private def cpuValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Int Refined Positive] =
+    CpuValidation.optional
 
   private def failOnStderrValidation(runtimeConfig: Option[Config]) = FailOnStderrValidation.default(runtimeConfig)
 
-  private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) = ContinueOnReturnCodeValidation.default(runtimeConfig)
+  private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) =
+    ContinueOnReturnCodeValidation.default(runtimeConfig)
 
-  private def diskSizeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[MemorySize] = MemoryValidation.optional(DiskSizeKey)
+  private def diskSizeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[MemorySize] =
+    MemoryValidation.optional(DiskSizeKey)
 
-  private def diskSizeCompatValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[Seq[PipelinesApiAttachedDisk]] =
+  private def diskSizeCompatValidation(
+    runtimeConfig: Option[Config]
+  ): OptionalRuntimeAttributesValidation[Seq[PipelinesApiAttachedDisk]] =
     DisksValidation.optional
 
-  private def memoryValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[MemorySize] = MemoryValidation.optional(RuntimeAttributesKeys.MemoryKey)
+  private def memoryValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[MemorySize] =
+    MemoryValidation.optional(RuntimeAttributesKeys.MemoryKey)
 
   private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
 
-  private val dockerWorkingDirValidation: OptionalRuntimeAttributesValidation[String] = DockerWorkingDirValidation.optional
+  private val dockerWorkingDirValidation: OptionalRuntimeAttributesValidation[String] =
+    DockerWorkingDirValidation.optional
   private def preemptibleValidation(runtimeConfig: Option[Config]) = PreemptibleValidation.default(runtimeConfig)
   private def localizedSasValidation: OptionalRuntimeAttributesValidation[String] = LocalizedSasValidation.optional
 
@@ -58,40 +70,44 @@ object TesRuntimeAttributes {
     // !! NOTE !! If new validated attributes are added to TesRuntimeAttributes, be sure to include
     // their validations here so that they will be handled correctly with backendParameters.
     // Location 2 of 2
-    StandardValidatedRuntimeAttributesBuilder.default(backendRuntimeConfig).withValidation(
-      cpuValidation(backendRuntimeConfig),
-      memoryValidation(backendRuntimeConfig),
-      diskSizeValidation(backendRuntimeConfig),
-      diskSizeCompatValidation(backendRuntimeConfig),
-      dockerValidation,
-      dockerWorkingDirValidation,
-      preemptibleValidation(backendRuntimeConfig),
-      localizedSasValidation
-    )
+    StandardValidatedRuntimeAttributesBuilder
+      .default(backendRuntimeConfig)
+      .withValidation(
+        cpuValidation(backendRuntimeConfig),
+        memoryValidation(backendRuntimeConfig),
+        diskSizeValidation(backendRuntimeConfig),
+        diskSizeCompatValidation(backendRuntimeConfig),
+        dockerValidation,
+        dockerWorkingDirValidation,
+        preemptibleValidation(backendRuntimeConfig),
+        localizedSasValidation
+      )
 
   def makeBackendParameters(runtimeAttributes: Map[String, WomValue],
                             keysToExclude: Set[String],
-                            config: TesConfiguration): Map[String, Option[String]] = {
-
+                            config: TesConfiguration
+  ): Map[String, Option[String]] =
     if (config.useBackendParameters)
-      runtimeAttributes
-        .view.filterKeys(k => !keysToExclude.contains(k))
-        .flatMap( _ match {
+      runtimeAttributes.view
+        .filterKeys(k => !keysToExclude.contains(k))
+        .flatMap(_ match {
           case (key, WomString(s)) => Option((key, Option(s)))
           case (key, WomOptionalValue(WomStringType, Some(WomString(optS)))) => Option((key, Option(optS)))
           case (key, WomOptionalValue(WomStringType, None)) => Option((key, None))
           case _ => None
-        }).toMap
+        })
+        .toMap
     else
       Map.empty
-  }
 
-  private def detectDiskFormat(backendRuntimeConfig: Option[Config], validatedRuntimeAttributes: ValidatedRuntimeAttributes): Option[MemorySize] = {
+  private def detectDiskFormat(backendRuntimeConfig: Option[Config],
+                               validatedRuntimeAttributes: ValidatedRuntimeAttributes
+  ): Option[MemorySize] = {
 
-    def adaptPapiDisks(disks: Seq[PipelinesApiAttachedDisk]): MemorySize = {
+    def adaptPapiDisks(disks: Seq[PipelinesApiAttachedDisk]): MemorySize =
       disks match {
         case disk :: Nil if disk.isInstanceOf[PipelinesApiWorkingDisk] =>
-            MemorySize(disk.sizeGb.toDouble, MemoryUnit.GB)
+          MemorySize(disk.sizeGb.toDouble, MemoryUnit.GB)
         case _ :: _ =>
           // When a user specifies only a custom disk, we add the default disk in the background, so we technically have multiple disks.
           // But we don't want to confuse the user with `multiple disks` message when they only put one.
@@ -101,16 +117,21 @@ object TesRuntimeAttributes {
             // Multiple `local-disk` is not legal, but possible and should be detected
             throw new IllegalArgumentException("Expecting exactly one disk definition on this backend, found multiple")
       }
-    }
 
     val maybeTesDisk: Option[MemorySize] =
-      RuntimeAttributesValidation.extractOption(diskSizeValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+      RuntimeAttributesValidation.extractOption(diskSizeValidation(backendRuntimeConfig).key,
+                                                validatedRuntimeAttributes
+      )
     val maybePapiDisk: Option[Seq[PipelinesApiAttachedDisk]] =
-      RuntimeAttributesValidation.extractOption(diskSizeCompatValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+      RuntimeAttributesValidation.extractOption(diskSizeCompatValidation(backendRuntimeConfig).key,
+                                                validatedRuntimeAttributes
+      )
 
     (maybeTesDisk, maybePapiDisk) match {
       case (Some(tesDisk: MemorySize), _) =>
-        Option(tesDisk) // If WDLs are in circulation with both `disk` and `disks`, pick the one intended for this backend
+        Option(
+          tesDisk
+        ) // If WDLs are in circulation with both `disk` and `disks`, pick the one intended for this backend
       case (None, Some(papiDisks: Seq[PipelinesApiAttachedDisk])) =>
         Option(adaptPapiDisks(papiDisks))
       case _ =>
@@ -118,21 +139,29 @@ object TesRuntimeAttributes {
     }
   }
 
-  def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes, rawRuntimeAttributes: Map[String, WomValue], config: TesConfiguration): TesRuntimeAttributes = {
+  def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes,
+            rawRuntimeAttributes: Map[String, WomValue],
+            config: TesConfiguration
+  ): TesRuntimeAttributes = {
     val backendRuntimeConfig = config.runtimeConfig
     val docker: String = RuntimeAttributesValidation.extract(dockerValidation, validatedRuntimeAttributes)
-    val dockerWorkingDir: Option[String] = RuntimeAttributesValidation.extractOption(dockerWorkingDirValidation.key, validatedRuntimeAttributes)
-    val cpu: Option[Int Refined Positive] = RuntimeAttributesValidation.extractOption(cpuValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
-    val memory: Option[MemorySize] = RuntimeAttributesValidation.extractOption(memoryValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+    val dockerWorkingDir: Option[String] =
+      RuntimeAttributesValidation.extractOption(dockerWorkingDirValidation.key, validatedRuntimeAttributes)
+    val cpu: Option[Int Refined Positive] =
+      RuntimeAttributesValidation.extractOption(cpuValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
+    val memory: Option[MemorySize] =
+      RuntimeAttributesValidation.extractOption(memoryValidation(backendRuntimeConfig).key, validatedRuntimeAttributes)
     val disk: Option[MemorySize] = detectDiskFormat(backendRuntimeConfig, validatedRuntimeAttributes)
     val failOnStderr: Boolean =
       RuntimeAttributesValidation.extract(failOnStderrValidation(backendRuntimeConfig), validatedRuntimeAttributes)
     val continueOnReturnCode: ContinueOnReturnCode =
-      RuntimeAttributesValidation.extract(continueOnReturnCodeValidation(backendRuntimeConfig), validatedRuntimeAttributes)
-    val preemptible: Boolean = {
+      RuntimeAttributesValidation.extract(continueOnReturnCodeValidation(backendRuntimeConfig),
+                                          validatedRuntimeAttributes
+      )
+    val preemptible: Boolean =
       RuntimeAttributesValidation.extract(preemptibleValidation(backendRuntimeConfig), validatedRuntimeAttributes)
-    }
-    val localizedSas: Option[String] = RuntimeAttributesValidation.extractOption(localizedSasValidation.key, validatedRuntimeAttributes)
+    val localizedSas: Option[String] =
+      RuntimeAttributesValidation.extractOption(localizedSasValidation.key, validatedRuntimeAttributes)
 
     // !! NOTE !! If new validated attributes are added to TesRuntimeAttributes, be sure to include
     // their validations here so that they will be handled correctly with backendParameters.
@@ -177,8 +206,8 @@ object DockerWorkingDirValidation {
 
 class DockerWorkingDirValidation extends StringRuntimeAttributesValidation(TesRuntimeAttributes.DockerWorkingDirKey) {
   // NOTE: Docker's current test specs don't like WdlInteger, etc. auto converted to WdlString.
-  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = {
-    case WomString(value) => value.validNel
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = { case WomString(value) =>
+    value.validNel
   }
 }
 
@@ -196,9 +225,10 @@ class DockerWorkingDirValidation extends StringRuntimeAttributesValidation(TesRu
 
 object PreemptibleValidation {
   lazy val instance: RuntimeAttributesValidation[Boolean] = new PreemptibleValidation
-  def default(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = instance.withDefault(
-    configDefaultWdlValue(runtimeConfig) getOrElse WomBoolean(false))
-  def configDefaultWdlValue(runtimeConfig: Option[Config]): Option[WomValue] = instance.configDefaultWomValue(runtimeConfig)
+  def default(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] =
+    instance.withDefault(configDefaultWdlValue(runtimeConfig) getOrElse WomBoolean(false))
+  def configDefaultWdlValue(runtimeConfig: Option[Config]): Option[WomValue] =
+    instance.configDefaultWomValue(runtimeConfig)
 }
 
 class PreemptibleValidation extends BooleanRuntimeAttributesValidation(TesRuntimeAttributes.PreemptibleKey) {
@@ -241,11 +271,10 @@ class LocalizedSasValidation extends StringRuntimeAttributesValidation(TesRuntim
     matcher.find
   }
 
-  override protected def invalidValueMessage(value: WomValue): String = {
+  override protected def invalidValueMessage(value: WomValue): String =
     s"Invalid Runtime Attribute value for ${TesRuntimeAttributes.LocalizedSasKey}. Value must be a string containing only letters, numbers, and underscores."
-  }
 
-  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = {
-    case WomString(value) => if(isValidBashVariableName(value)) value.validNel else Validated.invalidNel(invalidValueMessage(WomString(value)))
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = { case WomString(value) =>
+    if (isValidBashVariableName(value)) value.validNel else Validated.invalidNel(invalidValueMessage(WomString(value)))
   }
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index d775367ac74..54df895d617 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -18,8 +18,8 @@ import wom.values._
 
 import scala.collection.immutable.Map
 
-final case class WorkflowExecutionIdentityConfig(value: String) {override def toString: String = value.toString}
-final case class WorkflowExecutionIdentityOption(value: String) {override def toString: String = value}
+final case class WorkflowExecutionIdentityConfig(value: String) { override def toString: String = value.toString }
+final case class WorkflowExecutionIdentityOption(value: String) { override def toString: String = value }
 final case class TesTask(jobDescriptor: BackendJobDescriptor,
                          configurationDescriptor: BackendConfigurationDescriptor,
                          jobLogger: JobLogger,
@@ -31,7 +31,8 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
                          dockerImageUsed: String,
                          mapCommandLineWomFile: WomFile => WomFile,
                          jobShell: String,
-                         outputMode: OutputMode) {
+                         outputMode: OutputMode
+) {
 
   private val workflowDescriptor = jobDescriptor.workflowDescriptor
   private val workflowName = workflowDescriptor.callable.name
@@ -41,8 +42,7 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
       .getAs[String]("workflow-execution-identity")
       .map(WorkflowExecutionIdentityConfig)
   private val workflowExecutionIdentityOption: Option[WorkflowExecutionIdentityOption] =
-    workflowDescriptor
-      .workflowOptions
+    workflowDescriptor.workflowOptions
       .get(TesWorkflowOptionKeys.WorkflowExecutionIdentity)
       .toOption
       .map(WorkflowExecutionIdentityOption)
@@ -50,9 +50,8 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
   val description: String = jobDescriptor.toString
 
   // TODO validate "project" field of workflowOptions
-  val project = {
+  val project =
     workflowDescriptor.workflowOptions.getOrElse("project", "")
-  }
 
   // contains the script to be executed
   private val commandScript = Input(
@@ -74,28 +73,34 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
   private def writeFunctionFiles: Map[FullyQualifiedName, Seq[WomFile]] =
     instantiatedCommand.createdFiles map { f => f.file.value.md5SumShort -> List(f.file) } toMap
 
-  private val callInputFiles: Map[FullyQualifiedName, Seq[WomFile]] = jobDescriptor
-    .fullyQualifiedInputs
+  private val callInputFiles: Map[FullyQualifiedName, Seq[WomFile]] = jobDescriptor.fullyQualifiedInputs
     .safeMapValues {
       _.collectAsSeq { case w: WomFile => w }
     }
 
   lazy val inputs: Seq[Input] = {
-    val result = TesTask.buildTaskInputs(callInputFiles ++ writeFunctionFiles, workflowName, mapCommandLineWomFile) ++ Seq(commandScript)
-    jobLogger.info(s"Calculated TES inputs (found ${result.size}): " + result.mkString(System.lineSeparator(),System.lineSeparator(),System.lineSeparator()))
+    val result =
+      TesTask.buildTaskInputs(callInputFiles ++ writeFunctionFiles, workflowName, mapCommandLineWomFile) ++ Seq(
+        commandScript
+      )
+    jobLogger.info(
+      s"Calculated TES inputs (found ${result.size}): " + result.mkString(System.lineSeparator(),
+                                                                          System.lineSeparator(),
+                                                                          System.lineSeparator()
+      )
+    )
     result
   }
 
   // TODO add TES logs to standard outputs
-  private lazy val standardOutputs = Seq("rc", "stdout", "stderr").map {
-    f =>
-      Output(
-        name = Option(f),
-        description = Option(fullyQualifiedTaskName + "." + f),
-        url = Option(tesPaths.storageOutput(f)),
-        path = tesPaths.containerOutput(containerWorkDir, f),
-        `type` = Option("FILE")
-      )
+  private lazy val standardOutputs = Seq("rc", "stdout", "stderr").map { f =>
+    Output(
+      name = Option(f),
+      description = Option(fullyQualifiedTaskName + "." + f),
+      url = Option(tesPaths.storageOutput(f)),
+      path = tesPaths.containerOutput(containerWorkDir, f),
+      `type` = Option("FILE")
+    )
   }
 
   // TODO extract output file variable names and match with Files below
@@ -113,12 +118,13 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
     // TODO WOM: this should be pushed back into WOM.
     // It's also a mess, evaluateFiles returns an ErrorOr but can still throw. We might want to use an EitherT, although
     // if it fails we just want to fallback to an empty list anyway...
-    def evaluateFiles(output: OutputDefinition): List[WomFile] = {
-      Try (
-        output.expression.evaluateFiles(jobDescriptor.localInputs, NoIoFunctionSet, output.womType).map(_.toList map { _.file })
+    def evaluateFiles(output: OutputDefinition): List[WomFile] =
+      Try(
+        output.expression
+          .evaluateFiles(jobDescriptor.localInputs, NoIoFunctionSet, output.womType)
+          .map(_.toList map { _.file })
       ).getOrElse(List.empty[WomFile].validNel)
-       .getOrElse(List.empty)
-    }
+        .getOrElse(List.empty)
 
     jobDescriptor.taskCall.callable.outputs
       .flatMap(evaluateFiles)
@@ -129,7 +135,7 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
     val globName = GlobFunctions.globName(g.value)
     val globDirName = "globDir." + index
     val globDirectory = globName + "/"
-    val globListName =  "globList." + index
+    val globListName = "globList." + index
     val globListFile = globName + ".list"
     Seq(
       Output(
@@ -140,7 +146,7 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
         `type` = Option("DIRECTORY")
       ),
       Output(
-        name  = Option(globListName),
+        name = Option(globListName),
         description = Option(fullyQualifiedTaskName + "." + globListName),
         url = Option(tesPaths.storageOutput(globListFile)),
         path = tesPaths.containerOutput(containerWorkDir, globListFile),
@@ -149,7 +155,8 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
     )
   }
 
-  private val womOutputs = outputWomFiles.flatMap(_.flattenFiles)
+  private val womOutputs = outputWomFiles
+    .flatMap(_.flattenFiles)
     .zipWithIndex
     .flatMap {
       case (f: WomSingleFile, index) =>
@@ -167,7 +174,7 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
       case (d: WomUnlistedDirectory, index) =>
         val directoryPathName = "dirPath." + index
         val directoryPath = d.value.ensureSlashed
-        val directoryListName =  "dirList." + index
+        val directoryListName = "dirList." + index
         val directoryList = d.value.ensureUnslashed + ".list"
         Seq(
           Output(
@@ -178,7 +185,7 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
             `type` = Option("DIRECTORY")
           ),
           Output(
-            name  = Option(directoryListName),
+            name = Option(directoryListName),
             description = Option(fullyQualifiedTaskName + "." + directoryListName),
             url = Option(tesPaths.storageOutput(directoryList)),
             path = tesPaths.containerOutput(containerWorkDir, directoryList),
@@ -187,7 +194,8 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
         )
     }
 
-  private val additionalGlobOutput = jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(handleGlobFile(_, womOutputs.size))
+  private val additionalGlobOutput =
+    jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(handleGlobFile(_, womOutputs.size))
 
   private lazy val cwdOutput = Output(
     name = Option("execution.dir.output"),
@@ -198,30 +206,37 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
   )
 
   val outputs: Seq[Output] = {
-    val result =  outputMode match {
+    val result = outputMode match {
       case OutputMode.GRANULAR => standardOutputs ++ Seq(commandScriptOut) ++ womOutputs ++ additionalGlobOutput
       case OutputMode.ROOT => List(cwdOutput) ++ additionalGlobOutput
     }
 
-    jobLogger.info(s"Calculated TES outputs (found ${result.size}): " + result.mkString(System.lineSeparator(),System.lineSeparator(),System.lineSeparator()))
+    jobLogger.info(
+      s"Calculated TES outputs (found ${result.size}): " + result.mkString(System.lineSeparator(),
+                                                                           System.lineSeparator(),
+                                                                           System.lineSeparator()
+      )
+    )
 
     result
   }
 
   val preferedWorkflowExecutionIdentity = TesTask.getPreferredWorkflowExecutionIdentity(
-      workflowExecutionIdentityConfig,
-      workflowExecutionIdentityOption
+    workflowExecutionIdentityConfig,
+    workflowExecutionIdentityOption
   )
 
-  val executors = Seq(Executor(
-    image = dockerImageUsed,
-    command = Seq(jobShell, commandScript.path),
-    workdir = runtimeAttributes.dockerWorkingDir,
-    stdout = Option(tesPaths.containerOutput(containerWorkDir, "stdout")),
-    stderr = Option(tesPaths.containerOutput(containerWorkDir, "stderr")),
-    stdin = None,
-    env = None
-  ))
+  val executors = Seq(
+    Executor(
+      image = dockerImageUsed,
+      command = Seq(jobShell, commandScript.path),
+      workdir = runtimeAttributes.dockerWorkingDir,
+      stdout = Option(tesPaths.containerOutput(containerWorkDir, "stdout")),
+      stderr = Option(tesPaths.containerOutput(containerWorkDir, "stderr")),
+      stdin = None,
+      env = None
+    )
+  )
 
   val resources: Resources = TesTask.makeResources(
     runtimeAttributes,
@@ -235,11 +250,13 @@ final case class TesTask(jobDescriptor: BackendJobDescriptor,
 object TesTask {
   // Helper to determine which source to use for a workflowExecutionIdentity
   def getPreferredWorkflowExecutionIdentity(configIdentity: Option[WorkflowExecutionIdentityConfig],
-                                           workflowOptionsIdentity: Option[WorkflowExecutionIdentityOption]): Option[String] = {
+                                            workflowOptionsIdentity: Option[WorkflowExecutionIdentityOption]
+  ): Option[String] =
     configIdentity.map(_.value).orElse(workflowOptionsIdentity.map(_.value))
-  }
   def makeResources(runtimeAttributes: TesRuntimeAttributes,
-                    workflowExecutionId: Option[String], internalPathPrefix: Option[String]): Resources = {
+                    workflowExecutionId: Option[String],
+                    internalPathPrefix: Option[String]
+  ): Resources = {
     /*
      * workflowExecutionId: This was added in BT-409 to let us pass information to an Azure
      * TES server about which user identity to run tasks as.
@@ -249,7 +266,7 @@ object TesTask {
      * a working directory that the TES task can use.
      */
     val internalPathPrefixKey = "internal_path_prefix"
-    val backendParameters : Map[String, Option[String]] = runtimeAttributes.backendParameters ++
+    val backendParameters: Map[String, Option[String]] = runtimeAttributes.backendParameters ++
       workflowExecutionId
         .map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option(_))
         .toMap ++
@@ -273,26 +290,27 @@ object TesTask {
     )
   }
 
-  def buildTaskInputs(taskFiles: Map[FullyQualifiedName, Seq[WomFile]], workflowName: String, womMapFn: WomFile => WomFile): List[Input] = {
-    taskFiles.flatMap {
-      case (fullyQualifiedName, files) => files.flatMap(_.flattenFiles).zipWithIndex.map {
-        case (f, index) =>
-          val inputType = f match {
-            case _: WomUnlistedDirectory => "DIRECTORY"
-            case _: WomSingleFile => "FILE"
-            case _: WomGlobFile => "FILE"
-          }
-          Input(
-            name = Option(fullyQualifiedName + "." + index),
-            description = Option(workflowName + "." + fullyQualifiedName + "." + index),
-            url = Option(f.value),
-            path = womMapFn(f).value,
-            `type` = Option(inputType),
-            content = None
-          )
+  def buildTaskInputs(taskFiles: Map[FullyQualifiedName, Seq[WomFile]],
+                      workflowName: String,
+                      womMapFn: WomFile => WomFile
+  ): List[Input] =
+    taskFiles.flatMap { case (fullyQualifiedName, files) =>
+      files.flatMap(_.flattenFiles).zipWithIndex.map { case (f, index) =>
+        val inputType = f match {
+          case _: WomUnlistedDirectory => "DIRECTORY"
+          case _: WomSingleFile => "FILE"
+          case _: WomGlobFile => "FILE"
+        }
+        Input(
+          name = Option(fullyQualifiedName + "." + index),
+          description = Option(workflowName + "." + fullyQualifiedName + "." + index),
+          url = Option(f.value),
+          path = womMapFn(f).value,
+          `type` = Option(inputType),
+          content = None
+        )
       }
     }.toList
-  }
 
   def makeTags(workflowDescriptor: BackendWorkflowDescriptor): Map[String, Option[String]] = {
     // In addition to passing through any workflow labels, include relevant workflow ids as tags.
@@ -304,7 +322,7 @@ object TesTask {
     )
   }
 
-  def makeTask(tesTask: TesTask): Task = {
+  def makeTask(tesTask: TesTask): Task =
     Task(
       id = None,
       state = None,
@@ -318,7 +336,6 @@ object TesTask {
       tags = Option(tesTask.tags),
       logs = None
     )
-  }
 }
 
 // Field requirements in classes below based off GA4GH schema
@@ -332,7 +349,8 @@ final case class Task(id: Option[String],
                       executors: Seq[Executor],
                       volumes: Option[Seq[String]],
                       tags: Option[Map[String, Option[String]]],
-                      logs: Option[Seq[TaskLog]])
+                      logs: Option[Seq[TaskLog]]
+)
 
 final case class Executor(image: String,
                           command: Seq[String],
@@ -340,42 +358,45 @@ final case class Executor(image: String,
                           stdout: Option[String],
                           stderr: Option[String],
                           stdin: Option[String],
-                          env: Option[Map[String, String]])
+                          env: Option[Map[String, String]]
+)
 
 final case class Input(name: Option[String],
                        description: Option[String],
                        url: Option[String],
                        path: String,
                        `type`: Option[String],
-                       content: Option[String])
+                       content: Option[String]
+)
 
 final case class Output(name: Option[String],
                         description: Option[String],
                         url: Option[String],
                         path: String,
-                        `type`: Option[String])
+                        `type`: Option[String]
+)
 
 final case class Resources(cpu_cores: Option[Int],
                            ram_gb: Option[Double],
                            disk_gb: Option[Double],
                            preemptible: Option[Boolean],
                            zones: Option[Seq[String]],
-                           backend_parameters: Option[Map[String, Option[String]]])
+                           backend_parameters: Option[Map[String, Option[String]]]
+)
 
-final case class OutputFileLog(url: String,
-                               path: String,
-                               size_bytes: Int)
+final case class OutputFileLog(url: String, path: String, size_bytes: Int)
 
 final case class TaskLog(start_time: Option[String],
                          end_time: Option[String],
                          metadata: Option[Map[String, String]],
                          logs: Option[Seq[ExecutorLog]],
                          outputs: Option[Seq[OutputFileLog]],
-                         system_logs: Option[Seq[String]])
+                         system_logs: Option[Seq[String]]
+)
 
 final case class ExecutorLog(start_time: Option[String],
                              end_time: Option[String],
                              stdout: Option[String],
                              stderr: Option[String],
-                             exit_code: Option[Int])
-
+                             exit_code: Option[Int]
+)
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesWorkflowPaths.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesWorkflowPaths.scala
index c85cee1a0c7..0b6db1fa9a4 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesWorkflowPaths.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesWorkflowPaths.scala
@@ -7,8 +7,9 @@ import cromwell.core.path.{PathBuilder, PathFactory}
 import net.ceedubs.ficus.Ficus._
 
 case class TesWorkflowPaths(override val workflowDescriptor: BackendWorkflowDescriptor,
-                       override val config: Config,
-                       override val pathBuilders: List[PathBuilder] = WorkflowPaths.DefaultPathBuilders) extends WorkflowPaths {
+                            override val config: Config,
+                            override val pathBuilders: List[PathBuilder] = WorkflowPaths.DefaultPathBuilders
+) extends WorkflowPaths {
 
   val DockerRootString = config.as[Option[String]]("dockerRoot").getOrElse("/cromwell-executions")
   var DockerRoot = PathFactory.buildPath(DockerRootString, pathBuilders)
@@ -17,10 +18,9 @@ case class TesWorkflowPaths(override val workflowDescriptor: BackendWorkflowDesc
   }
   val dockerWorkflowRoot = workflowPathBuilder(DockerRoot)
 
-  override def toJobPaths(workflowPaths: WorkflowPaths,
-                          jobKey: BackendJobDescriptorKey): TesJobPaths = {
+  override def toJobPaths(workflowPaths: WorkflowPaths, jobKey: BackendJobDescriptorKey): TesJobPaths =
     new TesJobPaths(workflowPaths.asInstanceOf[TesWorkflowPaths], jobKey)
-  }
 
-  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths = this.copy(workflowDescriptor = workflowDescriptor)
+  override protected def withDescriptor(workflowDescriptor: BackendWorkflowDescriptor): WorkflowPaths =
+    this.copy(workflowDescriptor = workflowDescriptor)
 }
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
index 11267d238cf..53ba95606d0 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
@@ -17,7 +17,8 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
 
   val fullyQualifiedName = "this.name.is.more.than.qualified"
   val workflowName = "mockWorkflow"
-  val someBlobUrl = "https://lz813a3d637adefec2c6e88f.blob.core.windows.net/sc-d8143fd8-aa07-446d-9ba0-af72203f1794/nyxp6c/tes-internal/configuration/supported-vm-sizes"
+  val someBlobUrl =
+    "https://lz813a3d637adefec2c6e88f.blob.core.windows.net/sc-d8143fd8-aa07-446d-9ba0-af72203f1794/nyxp6c/tes-internal/configuration/supported-vm-sizes"
   val someNotBlobUrl = "https://www.google.com/path/to/exile"
   var index = 0
 
@@ -29,7 +30,7 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
     `type` = Option("FILE"),
     content = None
   )
-  index = index+1
+  index = index + 1
 
   val blobInput_1 = Input(
     name = Option(fullyQualifiedName + "." + index),
@@ -39,7 +40,7 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
     `type` = Option("FILE"),
     content = None
   )
-  index = index+1
+  index = index + 1
 
   val notBlobInput_1 = Input(
     name = Option(fullyQualifiedName + "." + index),
@@ -49,7 +50,7 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
     `type` = Option("FILE"),
     content = None
   )
-  index = index+1
+  index = index + 1
 
   val notBlobInput_2 = Input(
     name = Option(fullyQualifiedName + "." + index),
@@ -68,7 +69,9 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
   def generateMockWsmTokenGenerator: WSMBlobSasTokenGenerator = {
     val mockTokenGenerator = mock[WSMBlobSasTokenGenerator]
     val expectedTokenDuration: Duration = Duration.of(24, ChronoUnit.HOURS)
-    mockTokenGenerator.getWSMSasFetchEndpoint(any[BlobPath], any[Option[Duration]]) returns Try(s"$testWsmEndpoint/api/workspaces/v1/$testWorkspaceId/resources/controlled/azure/storageContainer/$testContainerResourceId/getSasToken?sasExpirationDuration=${expectedTokenDuration.getSeconds.toInt}")
+    mockTokenGenerator.getWSMSasFetchEndpoint(any[BlobPath], any[Option[Duration]]) returns Try(
+      s"$testWsmEndpoint/api/workspaces/v1/$testWorkspaceId/resources/controlled/azure/storageContainer/$testContainerResourceId/getSasToken?sasExpirationDuration=${expectedTokenDuration.getSeconds.toInt}"
+    )
     mockTokenGenerator
   }
   def generateMockFsm: BlobFileSystemManager = {
@@ -77,7 +80,7 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
     mockFsm.blobTokenGenerator returns mockGenerator
     mockFsm
   }
-  //path to a blob file
+  // path to a blob file
   def generateMockBlobPath: BlobPath = {
     val mockBlobPath = mock[BlobPath]
     mockBlobPath.pathAsString returns someBlobUrl
@@ -90,7 +93,7 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
     mockBlobPath
   }
 
-  //Path to a file that isn't a blob file
+  // Path to a file that isn't a blob file
   def generateMockDefaultPath: cromwell.core.path.Path = {
     val mockDefaultPath: cromwell.core.path.Path = mock[cromwell.core.path.Path]
     mockDefaultPath.pathAsString returns someNotBlobUrl
@@ -99,60 +102,77 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
   def pathGetter(pathString: String): Try[cromwell.core.path.Path] = {
     val mockBlob: BlobPath = generateMockBlobPath
     val mockDefault: cromwell.core.path.Path = generateMockDefaultPath
-    if(pathString.contains(someBlobUrl)) Try(mockBlob) else Try(mockDefault)
+    if (pathString.contains(someBlobUrl)) Try(mockBlob) else Try(mockDefault)
   }
 
   def blobConverter(pathToConvert: Try[cromwell.core.path.Path]): Try[BlobPath] = {
     val mockBlob: BlobPath = generateMockBlobPath
-    if(pathToConvert.get.pathAsString.contains(someBlobUrl)) Try(mockBlob) else Failure(new Exception("failed"))
+    if (pathToConvert.get.pathAsString.contains(someBlobUrl)) Try(mockBlob) else Failure(new Exception("failed"))
   }
 
   it should "not return sas endpoint when no blob paths are provided" in {
     val mockLogger: JobLogger = mock[JobLogger]
     val emptyInputs: List[Input] = List()
     val bloblessInputs: List[Input] = List(notBlobInput_1, notBlobInput_2)
-    TesAsyncBackendJobExecutionActor.determineWSMSasEndpointFromInputs(emptyInputs, pathGetter, mockLogger, blobConverter).isFailure shouldBe true
-    TesAsyncBackendJobExecutionActor.determineWSMSasEndpointFromInputs(bloblessInputs, pathGetter, mockLogger, blobConverter).isFailure shouldBe true
+    TesAsyncBackendJobExecutionActor
+      .determineWSMSasEndpointFromInputs(emptyInputs, pathGetter, mockLogger, blobConverter)
+      .isFailure shouldBe true
+    TesAsyncBackendJobExecutionActor
+      .determineWSMSasEndpointFromInputs(bloblessInputs, pathGetter, mockLogger, blobConverter)
+      .isFailure shouldBe true
   }
 
   it should "return a sas endpoint based on inputs when blob paths are provided" in {
     val mockLogger: JobLogger = mock[JobLogger]
-    val expectedTokenLifetimeSeconds = 24 * 60 * 60 //assert that cromwell asks for 24h token duration.
-    val expected = s"$testWsmEndpoint/api/workspaces/v1/$testWorkspaceId/resources/controlled/azure/storageContainer/$testContainerResourceId/getSasToken?sasExpirationDuration=${expectedTokenLifetimeSeconds}"
+    val expectedTokenLifetimeSeconds = 24 * 60 * 60 // assert that cromwell asks for 24h token duration.
+    val expected =
+      s"$testWsmEndpoint/api/workspaces/v1/$testWorkspaceId/resources/controlled/azure/storageContainer/$testContainerResourceId/getSasToken?sasExpirationDuration=${expectedTokenLifetimeSeconds}"
     val blobInput: List[Input] = List(blobInput_0)
     val blobInputs: List[Input] = List(blobInput_0, blobInput_1)
     val mixedInputs: List[Input] = List(notBlobInput_1, blobInput_0, blobInput_1)
-    TesAsyncBackendJobExecutionActor.determineWSMSasEndpointFromInputs(blobInput, pathGetter, mockLogger, blobConverter).get shouldEqual expected
-    TesAsyncBackendJobExecutionActor.determineWSMSasEndpointFromInputs(blobInputs, pathGetter, mockLogger, blobConverter).get shouldEqual expected
-    TesAsyncBackendJobExecutionActor.determineWSMSasEndpointFromInputs(mixedInputs, pathGetter, mockLogger,  blobConverter).get shouldEqual expected
+    TesAsyncBackendJobExecutionActor
+      .determineWSMSasEndpointFromInputs(blobInput, pathGetter, mockLogger, blobConverter)
+      .get shouldEqual expected
+    TesAsyncBackendJobExecutionActor
+      .determineWSMSasEndpointFromInputs(blobInputs, pathGetter, mockLogger, blobConverter)
+      .get shouldEqual expected
+    TesAsyncBackendJobExecutionActor
+      .determineWSMSasEndpointFromInputs(mixedInputs, pathGetter, mockLogger, blobConverter)
+      .get shouldEqual expected
   }
 
   it should "contain expected strings in the bash script" in {
     val mockEnvironmentVariableNameFromWom = "mock_env_var_for_storing_sas_token"
-    val expectedEndpoint = s"$testWsmEndpoint/api/workspaces/v1/$testWorkspaceId/resources/controlled/azure/storageContainer/$testContainerResourceId/getSasToken"
+    val expectedEndpoint =
+      s"$testWsmEndpoint/api/workspaces/v1/$testWorkspaceId/resources/controlled/azure/storageContainer/$testContainerResourceId/getSasToken"
 
     val beginSubstring = "### BEGIN ACQUIRE LOCAL SAS TOKEN ###"
     val endSubstring = "### END ACQUIRE LOCAL SAS TOKEN ###"
     val curlCommandSubstring =
       s"""
-        |sas_response_json=$$(curl -s \\
-        |                    --retry 3 \\
-        |                    --retry-delay 2 \\
-        |                    -X POST "$expectedEndpoint" \\
-        |                    -H "Content-Type: application/json" \\
-        |                    -H "accept: */*" \\
-        |                    -H "Authorization: Bearer $${BEARER_TOKEN}" \\
-        |                    -H "Content-Length: 0" \\
-        |                    -d "")
-        |""".stripMargin
-    val exportCommandSubstring = s"""export $mockEnvironmentVariableNameFromWom=$$(echo "$${sas_response_json}" | jq -r '.token')"""
-    val echoCommandSubstring = s"""echo "Saving sas token: $${$mockEnvironmentVariableNameFromWom:0:4}**** to environment variable $mockEnvironmentVariableNameFromWom...""""
-    val generatedBashScript = TesAsyncBackendJobExecutionActor.generateLocalizedSasScriptPreamble(mockEnvironmentVariableNameFromWom, expectedEndpoint)
-
-    generatedBashScript should include (beginSubstring)
-    generatedBashScript should include (endSubstring)
-    generatedBashScript should include (curlCommandSubstring)
-    generatedBashScript should include (echoCommandSubstring)
-    generatedBashScript should include (exportCommandSubstring)
+         |sas_response_json=$$(curl -s \\
+         |                    --retry 3 \\
+         |                    --retry-delay 2 \\
+         |                    -X POST "$expectedEndpoint" \\
+         |                    -H "Content-Type: application/json" \\
+         |                    -H "accept: */*" \\
+         |                    -H "Authorization: Bearer $${BEARER_TOKEN}" \\
+         |                    -H "Content-Length: 0" \\
+         |                    -d "")
+         |""".stripMargin
+    val exportCommandSubstring =
+      s"""export $mockEnvironmentVariableNameFromWom=$$(echo "$${sas_response_json}" | jq -r '.token')"""
+    val echoCommandSubstring =
+      s"""echo "Saving sas token: $${$mockEnvironmentVariableNameFromWom:0:4}**** to environment variable $mockEnvironmentVariableNameFromWom...""""
+    val generatedBashScript =
+      TesAsyncBackendJobExecutionActor.generateLocalizedSasScriptPreamble(mockEnvironmentVariableNameFromWom,
+                                                                          expectedEndpoint
+      )
+
+    generatedBashScript should include(beginSubstring)
+    generatedBashScript should include(endSubstring)
+    generatedBashScript should include(curlCommandSubstring)
+    generatedBashScript should include(echoCommandSubstring)
+    generatedBashScript should include(exportCommandSubstring)
   }
 }
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesConfigurationSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesConfigurationSpec.scala
index a695e5d6e33..144941859c3 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesConfigurationSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesConfigurationSpec.scala
@@ -20,13 +20,15 @@ class TesConfigurationSpec extends AnyFlatSpec with Matchers {
     )
   )
 
-  def backoffsAreEquivalent(expectedBackoff: SimpleExponentialBackoff, actualBackoff: SimpleExponentialBackoff): Boolean = {
+  def backoffsAreEquivalent(expectedBackoff: SimpleExponentialBackoff,
+                            actualBackoff: SimpleExponentialBackoff
+  ): Boolean = {
     val b1 = expectedBackoff.googleBackoff
     val b2 = actualBackoff.googleBackoff
     b1.getInitialIntervalMillis == b2.getInitialIntervalMillis &&
-      b1.getMaxIntervalMillis == b2.getMaxIntervalMillis &&
-      b1.getMultiplier == b2.getMultiplier &&
-      b1.getRandomizationFactor == b2.getRandomizationFactor
+    b1.getMaxIntervalMillis == b2.getMaxIntervalMillis &&
+    b1.getMultiplier == b2.getMultiplier &&
+    b1.getRandomizationFactor == b2.getRandomizationFactor
   }
 
   it should "use default backoffs when no custom config provided" in {
@@ -38,7 +40,9 @@ class TesConfigurationSpec extends AnyFlatSpec with Matchers {
   it should "use configured backoffs if they exist" in {
     val tesConfig = makeTesConfig(TesTestConfig.backendConfigWithBackoffs)
     backoffsAreEquivalent(SimpleExponentialBackoff(5 seconds, 1 minute, 2.5, .7), tesConfig.pollBackoff) shouldBe true
-    backoffsAreEquivalent(SimpleExponentialBackoff(3 minutes, 1 hours, 5, .1), tesConfig.executeOrRecoverBackoff) shouldBe true
+    backoffsAreEquivalent(SimpleExponentialBackoff(3 minutes, 1 hours, 5, .1),
+                          tesConfig.executeOrRecoverBackoff
+    ) shouldBe true
   }
 
   it should "fail if user defines an invalid backoff" in {
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesInitializationActorSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesInitializationActorSpec.scala
index a081f26c910..a34062b3e88 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesInitializationActorSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesInitializationActorSpec.scala
@@ -18,8 +18,7 @@ import wom.graph.CommandCallNode
 
 import scala.concurrent.duration._
 
-class TesInitializationActorSpec extends TestKitSuite
-  with AnyWordSpecLike with Matchers with ImplicitSender {
+class TesInitializationActorSpec extends TestKitSuite with AnyWordSpecLike with Matchers with ImplicitSender {
   val Timeout: FiniteDuration = 10.second.dilated
 
   val HelloWorld: String =
@@ -67,9 +66,10 @@ class TesInitializationActorSpec extends TestKitSuite
       |}
       |""".stripMargin
 
-
-  private def getActorRef(workflowDescriptor: BackendWorkflowDescriptor, calls: Set[CommandCallNode],
-                          conf: BackendConfigurationDescriptor) = {
+  private def getActorRef(workflowDescriptor: BackendWorkflowDescriptor,
+                          calls: Set[CommandCallNode],
+                          conf: BackendConfigurationDescriptor
+  ) = {
     val params = TesInitializationActorParams(workflowDescriptor, calls, new TesConfiguration(conf), emptyActor)
     val props = Props(new TesInitializationActor(params))
     system.actorOf(props, "TesInitializationActor" + UUID.randomUUID)
@@ -84,8 +84,8 @@ class TesInitializationActorSpec extends TestKitSuite
   "TesInitializationActor" should {
     "log a warning message when there are unsupported runtime attributes" in {
       within(Timeout) {
-        val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld,
-          runtime = """runtime { docker: "ubuntu/latest" test: true }""")
+        val workflowDescriptor =
+          buildWdlWorkflowDescriptor(HelloWorld, runtime = """runtime { docker: "ubuntu/latest" test: true }""")
         val backend = getActorRef(workflowDescriptor, workflowDescriptor.callable.taskCallNodes, conf)
         val eventPattern =
           "Key/s [test] is/are not supported by backend. Unsupported attributes will not be part of job executions."
@@ -101,15 +101,17 @@ class TesInitializationActorSpec extends TestKitSuite
 
     def initializeActor(workflowOptions: WorkflowOptions): Unit = {
       val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld,
-        runtime = """runtime { docker: "ubuntu/latest" }""",
-        options = workflowOptions)
+                                                          runtime = """runtime { docker: "ubuntu/latest" }""",
+                                                          options = workflowOptions
+      )
       val backend = getActorRef(workflowDescriptor, workflowDescriptor.callable.taskCallNodes, conf)
       backend ! Initialize
     }
 
     def nonStringErrorMessage(key: String) = s"Workflow option $key must be a string"
 
-    val bothRequiredErrorMessage = s"Workflow options ${TesWorkflowOptionKeys.WorkflowExecutionIdentity} and ${TesWorkflowOptionKeys.DataAccessIdentity} are both required if one is provided"
+    val bothRequiredErrorMessage =
+      s"Workflow options ${TesWorkflowOptionKeys.WorkflowExecutionIdentity} and ${TesWorkflowOptionKeys.DataAccessIdentity} are both required if one is provided"
 
     "fail when WorkflowExecutionIdentity is not a string and DataAccessIdentity is missing" in {
       within(Timeout) {
@@ -121,9 +123,13 @@ class TesInitializationActorSpec extends TestKitSuite
           case InitializationSuccess(s) => fail(s"InitializationFailed was expected but got $s")
           case InitializationFailed(failure) =>
             val expectedMsg = nonStringErrorMessage(TesWorkflowOptionKeys.WorkflowExecutionIdentity)
-            if (!(failure.getMessage.contains(expectedMsg) &&
-              failure.getMessage.contains(bothRequiredErrorMessage))) {
-              fail(s"Exception message did not contain both '$expectedMsg' and '$bothRequiredErrorMessage'. Was '$failure'")
+            if (
+              !(failure.getMessage.contains(expectedMsg) &&
+                failure.getMessage.contains(bothRequiredErrorMessage))
+            ) {
+              fail(
+                s"Exception message did not contain both '$expectedMsg' and '$bothRequiredErrorMessage'. Was '$failure'"
+              )
             }
         }
       }
@@ -131,10 +137,14 @@ class TesInitializationActorSpec extends TestKitSuite
 
     "fail when WorkflowExecutionIdentity is a string but DataAccessIdentity is not a string" in {
       within(Timeout) {
-        val workflowOptions = WorkflowOptions(JsObject(Map(
-          TesWorkflowOptionKeys.WorkflowExecutionIdentity -> JsString("5"),
-          TesWorkflowOptionKeys.DataAccessIdentity -> JsNumber(6)
-        )))
+        val workflowOptions = WorkflowOptions(
+          JsObject(
+            Map(
+              TesWorkflowOptionKeys.WorkflowExecutionIdentity -> JsString("5"),
+              TesWorkflowOptionKeys.DataAccessIdentity -> JsNumber(6)
+            )
+          )
+        )
         initializeActor(workflowOptions)
         expectMsgPF() {
           case InitializationSuccess(s) => fail(s"InitializationFailed was expected but got $s")
@@ -147,10 +157,14 @@ class TesInitializationActorSpec extends TestKitSuite
 
     "successfully start when both WorkflowExecutionIdentity and DataAccessIdentity are strings" in {
       within(Timeout) {
-        val workflowOptions = WorkflowOptions(JsObject(Map(
-          TesWorkflowOptionKeys.WorkflowExecutionIdentity -> JsString("5"),
-          TesWorkflowOptionKeys.DataAccessIdentity -> JsString("6")
-        )))
+        val workflowOptions = WorkflowOptions(
+          JsObject(
+            Map(
+              TesWorkflowOptionKeys.WorkflowExecutionIdentity -> JsString("5"),
+              TesWorkflowOptionKeys.DataAccessIdentity -> JsString("6")
+            )
+          )
+        )
         initializeActor(workflowOptions)
         expectMsgPF() {
           case InitializationSuccess(_) =>
@@ -164,13 +178,18 @@ class TesInitializationActorSpec extends TestKitSuite
         val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld, runtime = """runtime { }""")
         val backend = getActorRef(workflowDescriptor, workflowDescriptor.callable.taskCallNodes, conf)
         backend ! Initialize
-        expectMsgPF() {
-          case InitializationFailed(failure) =>
-            failure match {
-              case exception: RuntimeAttributeValidationFailures =>
-                if (!exception.getMessage.equals("Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!"))
-                  fail("Exception message is not equal to 'Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!'.")
-            }
+        expectMsgPF() { case InitializationFailed(failure) =>
+          failure match {
+            case exception: RuntimeAttributeValidationFailures =>
+              if (
+                !exception.getMessage.equals(
+                  "Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!"
+                )
+              )
+                fail(
+                  "Exception message is not equal to 'Runtime validation failed:\nTask hello has an invalid runtime attribute docker = !! NOT FOUND !!'."
+                )
+          }
         }
       }
     }
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
index 830e0cbe70c..1fb43503fb6 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
@@ -31,11 +31,14 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
 
   val expectedDefaultsPlusUbuntuDocker = expectedDefaults.copy(dockerImage = "ubuntu:latest")
 
-  def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]) = {
-    WorkflowOptions(JsObject(Map(
-      "default_runtime_attributes" -> JsObject(defaults)
-    )))
-  }
+  def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]) =
+    WorkflowOptions(
+      JsObject(
+        Map(
+          "default_runtime_attributes" -> JsObject(defaults)
+        )
+      )
+    )
 
   "TesRuntimeAttributes" should {
 
@@ -63,7 +66,10 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
 
     "fail to validate an invalid failOnStderr entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "failOnStderr" -> WomString("yes"))
-      assertFailure(runtimeAttributes, "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'")
+      assertFailure(
+        runtimeAttributes,
+        "Expecting failOnStderr runtime attribute to be a Boolean or a String with values of 'true' or 'false'"
+      )
     }
 
     "validate a valid preemptible entry" in {
@@ -73,13 +79,16 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
     }
 
     "validate a valid azureSasEnvironmentVariable entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), TesRuntimeAttributes.LocalizedSasKey -> WomString("THIS_IS_VALID"))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"), TesRuntimeAttributes.LocalizedSasKey -> WomString("THIS_IS_VALID"))
       val expectedRuntimeAttributes = expectedDefaultsPlusUbuntuDocker.copy(localizedSasEnvVar = Some("THIS_IS_VALID"))
       assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid azureSasEnvironmentVariable entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), TesRuntimeAttributes.LocalizedSasKey -> WomString("THIS IS INVALID"))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),
+                                  TesRuntimeAttributes.LocalizedSasKey -> WomString("THIS IS INVALID")
+      )
       assertFailure(runtimeAttributes, "Value must be a string containing only letters, numbers, and underscores.")
     }
 
@@ -103,35 +112,53 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
 
     "fail to validate an invalid string preemptible entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "preemptible" -> WomString("yes"))
-      assertFailure(runtimeAttributes, "Expecting preemptible runtime attribute to be an Integer, Boolean, or a String with values of 'true' or 'false'")
+      assertFailure(
+        runtimeAttributes,
+        "Expecting preemptible runtime attribute to be an Integer, Boolean, or a String with values of 'true' or 'false'"
+      )
     }
 
     "fail to validate an invalid type preemptible entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "preemptible" -> WomFloat(3.14))
-      assertFailure(runtimeAttributes, "Expecting preemptible runtime attribute to be an Integer, Boolean, or a String with values of 'true' or 'false'")
+      assertFailure(
+        runtimeAttributes,
+        "Expecting preemptible runtime attribute to be an Integer, Boolean, or a String with values of 'true' or 'false'"
+      )
     }
 
     "validate a valid continueOnReturnCode entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomInteger(1))
-      val expectedRuntimeAttributes = expectedDefaultsPlusUbuntuDocker.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1)))
+      val expectedRuntimeAttributes =
+        expectedDefaultsPlusUbuntuDocker.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1)))
       assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "validate a valid continueOnReturnCode array entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2))))
-      val expectedRuntimeAttributes = expectedDefaultsPlusUbuntuDocker.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1, 2)))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"),
+            "continueOnReturnCode" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2)))
+        )
+      val expectedRuntimeAttributes =
+        expectedDefaultsPlusUbuntuDocker.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1, 2)))
       assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "coerce then validate a valid continueOnReturnCode array entry" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomArray(WomArrayType(WomStringType), List(WomString("1"), WomString("2"))))
-      val expectedRuntimeAttributes = expectedDefaultsPlusUbuntuDocker.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1, 2)))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"),
+            "continueOnReturnCode" -> WomArray(WomArrayType(WomStringType), List(WomString("1"), WomString("2")))
+        )
+      val expectedRuntimeAttributes =
+        expectedDefaultsPlusUbuntuDocker.copy(continueOnReturnCode = ContinueOnReturnCodeSet(Set(1, 2)))
       assertSuccess(runtimeAttributes, expectedRuntimeAttributes)
     }
 
     "fail to validate an invalid continueOnReturnCode entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomString("value"))
-      assertFailure(runtimeAttributes, "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]")
+      assertFailure(
+        runtimeAttributes,
+        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+      )
     }
 
     "validate a valid cpu entry" in assertSuccess(
@@ -158,7 +185,9 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
 
     "fail to validate an invalid memory entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "memory" -> WomString("blah"))
-      assertFailure(runtimeAttributes, "Expecting memory runtime attribute to be an Integer or String with format '8 GB'")
+      assertFailure(runtimeAttributes,
+                    "Expecting memory runtime attribute to be an Integer or String with format '8 GB'"
+      )
     }
 
     "validate a valid disk entry" in {
@@ -185,7 +214,8 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
     }
 
     "refuse multiple `local-disk` instances" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 SSD, local-disk 20 SSD"))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 10 SSD, local-disk 20 SSD"))
       assertFailure(runtimeAttributes, "Expecting exactly one disk definition on this backend, found multiple")
     }
 
@@ -195,29 +225,41 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
     }
 
     "refuse custom AND multiple mount points" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("/mnt/tmp 10 LOCAL, local-disk 20 HDD"))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("/mnt/tmp 10 LOCAL, local-disk 20 HDD"))
       assertFailure(runtimeAttributes, "Disks with custom mount points are not supported by this backend")
     }
 
     "not accept a single comma" ignore {
       // Surprisingly, the PAPI code we call under the covers validates `,` and give the user a default disk.
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString(","))
-      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: ','")
+      assertFailure(
+        runtimeAttributes,
+        "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: ','"
+      )
     }
 
     "not accept empty string" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString(""))
-      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: ''")
+      assertFailure(
+        runtimeAttributes,
+        "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: ''"
+      )
     }
 
     "not accept `banana`" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("banana"))
-      assertFailure(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: 'banana'")
+      assertFailure(
+        runtimeAttributes,
+        "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' but got: 'banana'"
+      )
     }
 
     "not accept a random number (chosen by fair dice roll)" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomInteger(4))
-      assertFailure(runtimeAttributes, "Expecting disks runtime attribute to be a comma separated String or Array[String]")
+      assertFailure(runtimeAttributes,
+                    "Expecting disks runtime attribute to be a comma separated String or Array[String]"
+      )
     }
 
     "validate a valid dockerWorkingDir entry" in {
@@ -248,12 +290,12 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
     }
 
     "exclude unknown non-string attributes from backend parameters" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "foo" -> WomInteger(5), "bar" -> WomString("baz"))
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"), "foo" -> WomInteger(5), "bar" -> WomString("baz"))
       val expectedRuntimeAttributes = expectedDefaults.copy(backendParameters = Map("bar" -> Option("baz")))
       assertSuccess(runtimeAttributes, expectedRuntimeAttributes, tesConfig = mockTesConfigWithBackendParams)
     }
 
-
     "turn populated optional unknown string attributes into backend parameters" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "foo" -> WomOptionalValue(WomString("bar")))
       val expectedRuntimeAttributes = expectedDefaults.copy(backendParameters = Map("foo" -> Option("bar")))
@@ -267,7 +309,8 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
     }
   }
 
-  private val mockConfigurationDescriptor = BackendConfigurationDescriptor(TesTestConfig.backendConfig, TestConfig.globalConfig)
+  private val mockConfigurationDescriptor =
+    BackendConfigurationDescriptor(TesTestConfig.backendConfig, TestConfig.globalConfig)
   private val mockTesConfiguration = new TesConfiguration(mockConfigurationDescriptor)
   private val mockTesConfigWithBackendParams = new TesConfiguration(
     mockConfigurationDescriptor.copy(backendConfig = TesTestConfig.backendConfigWithBackendParams)
@@ -276,7 +319,8 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
   private def assertSuccess(runtimeAttributes: Map[String, WomValue],
                             expectedRuntimeAttributes: TesRuntimeAttributes,
                             workflowOptions: WorkflowOptions = emptyWorkflowOptions,
-                            tesConfig: TesConfiguration = mockTesConfiguration): Unit = {
+                            tesConfig: TesConfiguration = mockTesConfiguration
+  ): Unit = {
 
     try {
       val actualRuntimeAttributes = toTesRuntimeAttributes(runtimeAttributes, workflowOptions, tesConfig)
@@ -290,7 +334,8 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
   private def assertFailure(runtimeAttributes: Map[String, WomValue],
                             exMsg: String,
                             workflowOptions: WorkflowOptions = emptyWorkflowOptions,
-                            tesConfig: TesConfiguration = mockTesConfiguration): Unit = {
+                            tesConfig: TesConfiguration = mockTesConfiguration
+  ): Unit = {
     try {
       toTesRuntimeAttributes(runtimeAttributes, workflowOptions, tesConfig)
       fail("A RuntimeException was expected.")
@@ -304,13 +349,15 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
   private val staticRuntimeAttributeDefinitions: Set[RuntimeAttributeDefinition] =
     TesRuntimeAttributes.runtimeAttributesBuilder(mockTesConfiguration.runtimeConfig).definitions.toSet
 
-
   private def toTesRuntimeAttributes(runtimeAttributes: Map[String, WomValue],
                                      workflowOptions: WorkflowOptions,
-                                     tesConfiguration: TesConfiguration): TesRuntimeAttributes = {
+                                     tesConfiguration: TesConfiguration
+  ): TesRuntimeAttributes = {
     val runtimeAttributesBuilder = TesRuntimeAttributes.runtimeAttributesBuilder(tesConfiguration.runtimeConfig)
-    val defaultedAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(
-      staticRuntimeAttributeDefinitions, workflowOptions)(runtimeAttributes)
+    val defaultedAttributes =
+      RuntimeAttributeDefinition.addDefaultsToAttributes(staticRuntimeAttributeDefinitions, workflowOptions)(
+        runtimeAttributes
+      )
     val validatedRuntimeAttributes = runtimeAttributesBuilder.build(defaultedAttributes, NOPLogger.NOP_LOGGER)
     TesRuntimeAttributes(validatedRuntimeAttributes, runtimeAttributes, tesConfiguration)
   }
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index a5fd3a3a7e2..21e818bbc5a 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -15,12 +15,7 @@ import wom.InstantiatedCommand
 
 import java.util.UUID
 
-class TesTaskSpec
-  extends AnyFlatSpec
-    with CromwellTimeoutSpec
-    with Matchers
-    with BackendSpec
-    with MockSugar {
+class TesTaskSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with BackendSpec with MockSugar {
 
   val runtimeAttributes = new TesRuntimeAttributes(
     ContinueOnReturnCodeSet(Set(0)),
@@ -40,19 +35,25 @@ class TesTaskSpec
   it should "create the correct resources when an identity is passed in WorkflowOptions" in {
     val wei = Option("abc123")
     TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
-        Resources(None, None, None, Option(false), None,
-          Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"),
-            expectedTuple))
-    )
+      Resources(None,
+                None,
+                None,
+                Option(false),
+                None,
+                Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"), expectedTuple))
+      )
   }
 
   it should "create the correct resources when an empty identity is passed in WorkflowOptions" in {
     val wei = Option("")
     TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
-      Resources(None, None, None, Option(false), None,
-        Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option(""),
-          expectedTuple))
-    )
+      Resources(None,
+                None,
+                None,
+                Option(false),
+                None,
+                Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option(""), expectedTuple))
+      )
   }
 
   it should "create the correct resources when no identity is passed in WorkflowOptions" in {
@@ -66,9 +67,13 @@ class TesTaskSpec
     val weio = Option(WorkflowExecutionIdentityOption("def456"))
     val wei = TesTask.getPreferredWorkflowExecutionIdentity(weic, weio)
     TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
-        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"),
-          expectedTuple))
-    )
+      Resources(None,
+                None,
+                None,
+                Option(false),
+                None,
+                Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"), expectedTuple))
+      )
   }
 
   it should "create the correct resources when no identity is passed in via backend config" in {
@@ -76,58 +81,65 @@ class TesTaskSpec
     val weio = Option(WorkflowExecutionIdentityOption("def456"))
     val wei = TesTask.getPreferredWorkflowExecutionIdentity(weic, weio)
     TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
-        Resources(None, None, None, Option(false), None, Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("def456"),
-          expectedTuple))
-    )
+      Resources(None,
+                None,
+                None,
+                Option(false),
+                None,
+                Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("def456"), expectedTuple))
+      )
   }
 
   it should "correctly set the internal path prefix when provided as a backend parameter" in {
     val wei = Option("abc123")
     val internalPathPrefix = Option("mock/path/to/tes/task")
     TesTask.makeResources(runtimeAttributes, wei, internalPathPrefix) shouldEqual
-      Resources(None, None, None, Option(false), None,
-        Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"),
-          "internal_path_prefix" -> internalPathPrefix)
-      ))
+      Resources(
+        None,
+        None,
+        None,
+        Option(false),
+        None,
+        Option(
+          Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"),
+              "internal_path_prefix" -> internalPathPrefix
+          )
+        )
+      )
   }
 
   it should "correctly resolve the path to .../tes_task and add the k/v pair to backend parameters" in {
     val emptyWorkflowOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))
-    val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld,
-      labels = Labels("foo" -> "bar"))
-    val jobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-      Map.empty,
-      emptyWorkflowOptions,
-      Set.empty)
-    val tesPaths = TesJobPaths(jobDescriptor.key,
-      jobDescriptor.workflowDescriptor,
-      TestConfig.emptyConfig)
+    val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld, labels = Labels("foo" -> "bar"))
+    val jobDescriptor =
+      jobDescriptorFromSingleCallWorkflow(workflowDescriptor, Map.empty, emptyWorkflowOptions, Set.empty)
+    val tesPaths = TesJobPaths(jobDescriptor.key, jobDescriptor.workflowDescriptor, TestConfig.emptyConfig)
 
     val expectedKey = "internal_path_prefix"
     val expectedValue = Option(tesPaths.tesTaskRoot)
 
-    //Assert path correctly ends up in the resources
+    // Assert path correctly ends up in the resources
     val wei = Option("abc123")
     TesTask.makeResources(runtimeAttributes, wei, expectedValue) shouldEqual
-      Resources(None, None, None, Option(false), None,
-        Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"),
-          expectedKey -> expectedValue))
+      Resources(
+        None,
+        None,
+        None,
+        Option(false),
+        None,
+        Option(Map(TesWorkflowOptionKeys.WorkflowExecutionIdentity -> Option("abc123"), expectedKey -> expectedValue))
       )
   }
 
   it should "copy labels to tags" in {
     val jobLogger = mock[JobLogger]
     val emptyWorkflowOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))
-    val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld,
-                                                        labels = Labels("foo" -> "bar"))
-    val jobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-      Map.empty,
-      emptyWorkflowOptions,
-      Set.empty)
-    val tesPaths = TesJobPaths(jobDescriptor.key,
-      jobDescriptor.workflowDescriptor,
-      TestConfig.emptyConfig)
-    val tesTask = TesTask(jobDescriptor,
+    val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld, labels = Labels("foo" -> "bar"))
+    val jobDescriptor =
+      jobDescriptorFromSingleCallWorkflow(workflowDescriptor, Map.empty, emptyWorkflowOptions, Set.empty)
+    val tesPaths = TesJobPaths(jobDescriptor.key, jobDescriptor.workflowDescriptor, TestConfig.emptyConfig)
+    val tesTask = TesTask(
+      jobDescriptor,
       TestConfig.emptyBackendConfigDescriptor,
       jobLogger,
       tesPaths,
@@ -138,7 +150,8 @@ class TesTaskSpec
       "",
       Map.empty,
       "",
-      OutputMode.ROOT)
+      OutputMode.ROOT
+    )
 
     val task = TesTask.makeTask(tesTask)
 
@@ -156,25 +169,23 @@ class TesTaskSpec
     val jobLogger = mock[JobLogger]
     val emptyWorkflowOptions = WorkflowOptions(JsObject(Map.empty[String, JsValue]))
     val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld)
-    val jobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                            Map.empty,
-                                                            emptyWorkflowOptions,
-                                                            Set.empty)
-    val tesPaths = TesJobPaths(jobDescriptor.key,
-                               jobDescriptor.workflowDescriptor,
-                               TestConfig.emptyConfig)
-    val tesTask = TesTask(jobDescriptor,
-                          TestConfig.emptyBackendConfigDescriptor,
-                          jobLogger,
-                          tesPaths,
-                          runtimeAttributes,
-                          DefaultPathBuilder.build("").get,
-                          "",
-                          InstantiatedCommand("command"),
-                          "",
-                          Map.empty,
-                          "",
-                          OutputMode.ROOT)
+    val jobDescriptor =
+      jobDescriptorFromSingleCallWorkflow(workflowDescriptor, Map.empty, emptyWorkflowOptions, Set.empty)
+    val tesPaths = TesJobPaths(jobDescriptor.key, jobDescriptor.workflowDescriptor, TestConfig.emptyConfig)
+    val tesTask = TesTask(
+      jobDescriptor,
+      TestConfig.emptyBackendConfigDescriptor,
+      jobLogger,
+      tesPaths,
+      runtimeAttributes,
+      DefaultPathBuilder.build("").get,
+      "",
+      InstantiatedCommand("command"),
+      "",
+      Map.empty,
+      "",
+      OutputMode.ROOT
+    )
 
     val task = TesTask.makeTask(tesTask)
 
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTestConfig.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTestConfig.scala
index 7cbfd7e5348..7bb14c02a61 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTestConfig.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTestConfig.scala
@@ -112,4 +112,3 @@ object TesTestConfig {
 
   val backendConfigWithInvalidBackoffs = ConfigFactory.parseString(backendConfigStringWithInvalidBackoffs)
 }
-
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesWorkflowPathsSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesWorkflowPathsSpec.scala
index 8d06277dbb5..e9d913eef0f 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesWorkflowPathsSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesWorkflowPathsSpec.scala
@@ -48,7 +48,9 @@ class TesWorkflowPathsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Mat
     subWd.id returns subWorkflowId
 
     val workflowPaths = TesWorkflowPaths(subWd, TesTestConfig.backendConfig)
-    workflowPaths.workflowRoot.toString shouldBe File(s"local-cromwell-executions/rootWorkflow/$rootWorkflowId/call-call1/shard-1/attempt-2/subWorkflow/$subWorkflowId").pathAsString
+    workflowPaths.workflowRoot.toString shouldBe File(
+      s"local-cromwell-executions/rootWorkflow/$rootWorkflowId/call-call1/shard-1/attempt-2/subWorkflow/$subWorkflowId"
+    ).pathAsString
     workflowPaths.dockerWorkflowRoot.toString shouldBe s"/cromwell-executions/rootWorkflow/$rootWorkflowId/call-call1/shard-1/attempt-2/subWorkflow/$subWorkflowId"
   }
 }
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TestWorkflows.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TestWorkflows.scala
index e98ca521075..8c73d36d49a 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TestWorkflows.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TestWorkflows.scala
@@ -7,26 +7,27 @@ object TestWorkflows {
 
   case class TestWorkflow(workflowDescriptor: BackendWorkflowDescriptor,
                           config: BackendConfigurationDescriptor,
-                          expectedResponse: BackendJobExecutionResponse)
+                          expectedResponse: BackendJobExecutionResponse
+  )
 
   val HelloWorld =
     s"""
-      |task hello {
-      |  String addressee = "you "
-      |  command {
-      |    echo "Hello $${addressee}!"
-      |  }
-      |  output {
-      |    String salutation = read_string(stdout())
-      |  }
-      |
-      |  RUNTIME
-      |}
-      |
-      |workflow wf_hello {
-      |  call hello
-      |}
-      |""".stripMargin
+       |task hello {
+       |  String addressee = "you "
+       |  command {
+       |    echo "Hello $${addressee}!"
+       |  }
+       |  output {
+       |    String salutation = read_string(stdout())
+       |  }
+       |
+       |  RUNTIME
+       |}
+       |
+       |workflow wf_hello {
+       |  call hello
+       |}
+       |""".stripMargin
 
   val GoodbyeWorld =
     """
@@ -46,26 +47,26 @@ object TestWorkflows {
 
   val InputFiles =
     s"""
-      |task localize {
-      |  File inputFileFromJson
-      |  File inputFileFromCallInputs
-      |  command {
-      |    cat $${inputFileFromJson}
-      |    echo ""
-      |    cat $${inputFileFromCallInputs}
-      |  }
-      |  output {
-      |    Array[String] out = read_lines(stdout())
-      |  }
-      |
-      |  RUNTIME
-      |}
-      |
-      |workflow wf_localize {
-      |  File workflowFile
-      |  call localize { input: inputFileFromCallInputs = workflowFile }
-      |}
-      |""".stripMargin
+       |task localize {
+       |  File inputFileFromJson
+       |  File inputFileFromCallInputs
+       |  command {
+       |    cat $${inputFileFromJson}
+       |    echo ""
+       |    cat $${inputFileFromCallInputs}
+       |  }
+       |  output {
+       |    Array[String] out = read_lines(stdout())
+       |  }
+       |
+       |  RUNTIME
+       |}
+       |
+       |workflow wf_localize {
+       |  File workflowFile
+       |  call localize { input: inputFileFromCallInputs = workflowFile }
+       |}
+       |""".stripMargin
 
   val Sleep10 =
     """
@@ -83,25 +84,25 @@ object TestWorkflows {
 
   val Scatter =
     s"""
-      |task scattering {
-      |  Int intNumber
-      |  command {
-      |    echo $${intNumber}
-      |  }
-      |  output {
-      |    Int out = read_string(stdout())
-      |  }
-      |}
-      |
-      |workflow wf_scattering {
-      |  Array[Int] numbers = [1, 2, 3]
-      |  scatter (i in numbers) {
-      |     call scattering { input: intNumber = i }
-      |  }
-      |}
-      |""".stripMargin
+       |task scattering {
+       |  Int intNumber
+       |  command {
+       |    echo $${intNumber}
+       |  }
+       |  output {
+       |    Int out = read_string(stdout())
+       |  }
+       |}
+       |
+       |workflow wf_scattering {
+       |  Array[Int] numbers = [1, 2, 3]
+       |  scatter (i in numbers) {
+       |     call scattering { input: intNumber = i }
+       |  }
+       |}
+       |""".stripMargin
 
-  val OutputProcess = {
+  val OutputProcess =
     """
       |task localize {
       |  File inputFile
@@ -121,9 +122,8 @@ object TestWorkflows {
       |  call localize
       |}
       |""".stripMargin
-  }
 
-  val MissingOutputProcess = {
+  val MissingOutputProcess =
     """
       |task localize {
       |  command {
@@ -137,5 +137,4 @@ object TestWorkflows {
       |  call localize
       |}
       |""".stripMargin
-  }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
index 24194807f17..f681b45ad62 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala
@@ -16,102 +16,113 @@ import scala.language.postfixOps
 
 object AstTools {
 
-  class InterpolatedTerminal(val rootTerminal: Terminal, innerTerminal: Terminal, columnOffset: Int) extends Terminal(
-    innerTerminal.getId,
-    innerTerminal.getTerminalStr,
-    innerTerminal.getSourceString,
-    innerTerminal.getResource,
-    // We want the line of the rootTerminal because innerTerminal is created purely from the expression string
-    // So its first line will be line 0, which is very unlikely to be line 0 in the WDL file
-    rootTerminal.getLine,
-    // Column offset tells us the position of innerTerminal in the rootTerminal string
-    // Therefore rootTerminal.getColumn + columnOffset gives us the column position for innerTerminal in the file (+1 to be on the $)
-    rootTerminal.getColumn + columnOffset + 1
-  )
+  class InterpolatedTerminal(val rootTerminal: Terminal, innerTerminal: Terminal, columnOffset: Int)
+      extends Terminal(
+        innerTerminal.getId,
+        innerTerminal.getTerminalStr,
+        innerTerminal.getSourceString,
+        innerTerminal.getResource,
+        // We want the line of the rootTerminal because innerTerminal is created purely from the expression string
+        // So its first line will be line 0, which is very unlikely to be line 0 in the WDL file
+        rootTerminal.getLine,
+        // Column offset tells us the position of innerTerminal in the rootTerminal string
+        // Therefore rootTerminal.getColumn + columnOffset gives us the column position for innerTerminal in the file (+1 to be on the $)
+        rootTerminal.getColumn + columnOffset + 1
+      )
 
   implicit class EnhancedAstNode(val astNode: AstNode) extends AnyVal {
     def findAsts(name: String): Seq[Ast] = AstTools.findAsts(astNode, name)
-    def findAstsWithTrail(name: String, trail: Seq[AstNode] = Seq.empty): Map[Ast, Seq[AstNode]] = {
+    def findAstsWithTrail(name: String, trail: Seq[AstNode] = Seq.empty): Map[Ast, Seq[AstNode]] =
       astNode match {
         case x: Ast =>
           val thisAst = if (x.getName.equals(name)) Map(x -> trail) else Map.empty[Ast, Seq[AstNode]]
-          combine(x.getAttributes.values.asScala.flatMap{_.findAstsWithTrail(name, trail :+ x)}.toMap, thisAst)
-        case x: AstList => x.asScala.toVector.flatMap{_.findAstsWithTrail(name, trail :+ x)}.toMap
+          combine(x.getAttributes.values.asScala.flatMap(_.findAstsWithTrail(name, trail :+ x)).toMap, thisAst)
+        case x: AstList => x.asScala.toVector.flatMap(_.findAstsWithTrail(name, trail :+ x)).toMap
         case _: Terminal => Map.empty[Ast, Seq[AstNode]]
         case _ => Map.empty[Ast, Seq[AstNode]]
       }
-    }
 
     private def findTerminalsInInterpolatedString(t: Terminal,
                                                   terminalType: String,
                                                   trail: Seq[AstNode],
                                                   parentTerminal: Option[Terminal],
-                                                  columnOffset: Int) = {
+                                                  columnOffset: Int
+    ) = {
       /*
-        * Find all interpolations in the string terminal.
-        * e.g: String a = "hello ${you}"
-        * We'll create an expression from "you" and remember the position in the string
-        * "hello ${you}" at which we found "${you}".
+       * Find all interpolations in the string terminal.
+       * e.g: String a = "hello ${you}"
+       * We'll create an expression from "you" and remember the position in the string
+       * "hello ${you}" at which we found "${you}".
        */
       val interpolatedExpressionAstNodesAndTheirMatchPosition = InterpolationTagPattern
         .findAllMatchIn(t.getSourceString)
-        .foldLeft(List.empty[(AstNode, Int)])((nodes, exprValue) => {
+        .foldLeft(List.empty[(AstNode, Int)]) { (nodes, exprValue) =>
           // This is the interpolated expression e.g ${my_var}
           val v = exprValue.group(0)
           // Create an expression from the content and remember the position of the match in the overall terminal string
           // so we can point to it in the error message if needed
           (WdlExpression.fromString(v.substring(2, v.length - 1)).ast, exprValue.start) +: nodes
-        })
+        }
 
       interpolatedExpressionAstNodesAndTheirMatchPosition match {
         // If there's no interpolated expression and the parent terminal is of the right type,
         // create an interpolated terminal and we're done
         case Nil if t.getTerminalStr == terminalType =>
-          val finalTerminal = parentTerminal map { parent => new InterpolatedTerminal(parent, t, columnOffset) } getOrElse t
+          val finalTerminal = parentTerminal map { parent =>
+            new InterpolatedTerminal(parent, t, columnOffset)
+          } getOrElse t
           Map(finalTerminal -> trail)
         // No interpolated terminal and the parent terminal is not of the right type, we're done
         case Nil => Map.empty[Terminal, Seq[AstNode]]
         // We found some interpolated terminals, recursively find their inner terminals and propagate the root terminal.
         // Also propagate the accumulated columnOffset. The regex index match will start
         // over at 0 in the next round of matching so we need to keep track of the offset as we recurse
-        case expressions => expressions.flatMap({
-          case (innerNode, offset) => innerNode.findTerminalsWithTrail(terminalType, trail :+ t, Option(parentTerminal.getOrElse(t)), columnOffset + offset)
-        }).toMap
+        case expressions =>
+          expressions.flatMap { case (innerNode, offset) =>
+            innerNode.findTerminalsWithTrail(terminalType,
+                                             trail :+ t,
+                                             Option(parentTerminal.getOrElse(t)),
+                                             columnOffset + offset
+            )
+          }.toMap
       }
     }
 
     def findTerminalsWithTrail(terminalType: String,
                                trail: Seq[AstNode] = Seq.empty,
                                parentTerminal: Option[Terminal] = None,
-                               columnOffset: Int = 0): Map[Terminal, Seq[AstNode]] = {
+                               columnOffset: Int = 0
+    ): Map[Terminal, Seq[AstNode]] =
       astNode match {
-        case o: Ast if o.isObjectLiteral => o.getAttribute("map").astListAsVector flatMap {
-          case a: Ast => a.getAttribute("value").findTerminalsWithTrail(terminalType, trail :+ o, parentTerminal)
-          case _: AstNode => Seq.empty
-        } toMap
-        case a: Ast => a.getAttributes.values.asScala flatMap { _.findTerminalsWithTrail(terminalType, trail :+ a) } toMap
+        case o: Ast if o.isObjectLiteral =>
+          o.getAttribute("map").astListAsVector flatMap {
+            case a: Ast => a.getAttribute("value").findTerminalsWithTrail(terminalType, trail :+ o, parentTerminal)
+            case _: AstNode => Seq.empty
+          } toMap
+        case a: Ast =>
+          a.getAttributes.values.asScala flatMap { _.findTerminalsWithTrail(terminalType, trail :+ a) } toMap
         case a: AstList => a.asScala.toVector flatMap { _.findTerminalsWithTrail(terminalType, trail :+ a) } toMap
         case t: Terminal if t.getTerminalStr == terminalType =>
-          val finalTerminal = parentTerminal map { parent => new InterpolatedTerminal(parent, t, columnOffset) } getOrElse t
+          val finalTerminal = parentTerminal map { parent =>
+            new InterpolatedTerminal(parent, t, columnOffset)
+          } getOrElse t
           Map(finalTerminal -> trail)
         case t: Terminal => findTerminalsInInterpolatedString(t, terminalType, trail, parentTerminal, columnOffset)
         case _ => Map.empty[Terminal, Seq[AstNode]]
       }
-    }
-    def findFirstTerminal: Option[Terminal] = {
+    def findFirstTerminal: Option[Terminal] =
       Option(astNode) flatMap {
         case l: AstList => l.astListAsVector.flatMap(_.findFirstTerminal).headOption
-        case a: Ast => a.getAttributes.asScala.toMap.flatMap({ case (_, v) => v.findFirstTerminal }).headOption
+        case a: Ast => a.getAttributes.asScala.toMap.flatMap { case (_, v) => v.findFirstTerminal }.headOption
         case t: Terminal => Option(t)
       }
-    }
     def findTopLevelMemberAccesses(): Iterable[Ast] = AstTools.findTopLevelMemberAccesses(astNode)
     def sourceString: String = astNode match {
       case t: Terminal => t.getSourceString
       case a: Ast => a.toPrettyString
     }
     def astListAsVector: Seq[AstNode] = astNode.asInstanceOf[AstList].asScala.toVector
-    def womType(wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter): WomType = {
+    def womType(wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter): WomType =
       astNode match {
         case t: Terminal =>
           t.getSourceString match {
@@ -150,10 +161,11 @@ object AstTools {
           }
         case _ => throw new UnsupportedOperationException(s"Unexpected WDL type AST: ${astNode.sourceString}")
       }
-    }
 
     def isOptionalType(a: Ast) = a.getName.equals("OptionalType")
-    def optionalType(a: Ast, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter) = WomOptionalType(a.getAttribute("innerType").womType(wdlSyntaxErrorFormatter))
+    def optionalType(a: Ast, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter) = WomOptionalType(
+      a.getAttribute("innerType").womType(wdlSyntaxErrorFormatter)
+    )
 
     def isNonEmptyType(a: Ast) = a.getName.equals("NonEmptyType")
     def nonEmptyType(a: Ast, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter) = {
@@ -168,21 +180,33 @@ object AstTools {
 
       def astToMap(ast: Ast) = {
         val mapType = womType.asInstanceOf[WomMapType]
-        val elements = ast.getAttribute("map").asInstanceOf[AstList].asScala.toVector.map({ kvnode =>
-          val k = kvnode.asInstanceOf[Ast].getAttribute("key").womValue(mapType.keyType, wdlSyntaxErrorFormatter)
-          val v = kvnode.asInstanceOf[Ast].getAttribute("value").womValue(mapType.valueType, wdlSyntaxErrorFormatter)
-          k -> v
-        }).toMap
+        val elements = ast
+          .getAttribute("map")
+          .asInstanceOf[AstList]
+          .asScala
+          .toVector
+          .map { kvnode =>
+            val k = kvnode.asInstanceOf[Ast].getAttribute("key").womValue(mapType.keyType, wdlSyntaxErrorFormatter)
+            val v = kvnode.asInstanceOf[Ast].getAttribute("value").womValue(mapType.valueType, wdlSyntaxErrorFormatter)
+            k -> v
+          }
+          .toMap
 
         WomMap(mapType, elements)
       }
 
       def astToObject(ast: Ast) = {
-        val elements = ast.getAttribute("map").asInstanceOf[AstList].asScala.toVector.map({ kvnode =>
-          val k = kvnode.asInstanceOf[Ast].getAttribute("key").sourceString
-          val v = kvnode.asInstanceOf[Ast].getAttribute("value").womValue(WomStringType, wdlSyntaxErrorFormatter)
-          k -> v
-        }).toMap
+        val elements = ast
+          .getAttribute("map")
+          .asInstanceOf[AstList]
+          .asScala
+          .toVector
+          .map { kvnode =>
+            val k = kvnode.asInstanceOf[Ast].getAttribute("key").sourceString
+            val v = kvnode.asInstanceOf[Ast].getAttribute("value").womValue(WomStringType, wdlSyntaxErrorFormatter)
+            k -> v
+          }
+          .toMap
 
         WomObject(elements)
       }
@@ -194,9 +218,13 @@ object AstTools {
           a.womValue(womType, wdlSyntaxErrorFormatter)
         } else if (subElements.lengthCompare(2) == 0 && womType.isInstanceOf[WomPairType]) {
           val pairType = womType.asInstanceOf[WomPairType]
-          WomPair(subElements.head.womValue(pairType.leftType, wdlSyntaxErrorFormatter), subElements(1).womValue(pairType.rightType, wdlSyntaxErrorFormatter))
+          WomPair(subElements.head.womValue(pairType.leftType, wdlSyntaxErrorFormatter),
+                  subElements(1).womValue(pairType.rightType, wdlSyntaxErrorFormatter)
+          )
         } else {
-          throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})")
+          throw new SyntaxError(
+            s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})"
+          )
         }
       }
 
@@ -208,31 +236,41 @@ object AstTools {
           WomSingleFile(t.getSourceString)
         case t: Terminal if t.getTerminalStr == "string" && womType == WomGlobFileType =>
           WomGlobFile(t.getSourceString)
-        case t: Terminal if t.getTerminalStr == "integer" && womType == WomIntegerType => WomInteger(t.getSourceString.toInt)
-        case t: Terminal if t.getTerminalStr == "float" && womType == WomFloatType => WomFloat(t.getSourceString.toDouble)
-        case t: Terminal if t.getTerminalStr == "boolean" && womType == WomBooleanType => t.getSourceString.toLowerCase match {
-          case "true" => WomBoolean.True
-          case "false" => WomBoolean.False
-        }
+        case t: Terminal if t.getTerminalStr == "integer" && womType == WomIntegerType =>
+          WomInteger(t.getSourceString.toInt)
+        case t: Terminal if t.getTerminalStr == "float" && womType == WomFloatType =>
+          WomFloat(t.getSourceString.toDouble)
+        case t: Terminal if t.getTerminalStr == "boolean" && womType == WomBooleanType =>
+          t.getSourceString.toLowerCase match {
+            case "true" => WomBoolean.True
+            case "false" => WomBoolean.False
+          }
         // TODO: The below cases, ArrayLiteral and MapLiteral, ObjectLiteral are brittle. They recursively call this womValue().
         // However, those recursive calls might contain full-on expressions instead of just other literals.  This
         // whole thing ought to be part of the regular expression evaluator, though I imagine that's non-trivial.
         case a: Ast if a.getName == "ArrayLiteral" && womType.isInstanceOf[WomArrayType] =>
           val arrType = womType.asInstanceOf[WomArrayType]
-          val elements = a.getAttribute("values").astListAsVector map {node => node.womValue(arrType.memberType, wdlSyntaxErrorFormatter)}
+          val elements = a.getAttribute("values").astListAsVector map { node =>
+            node.womValue(arrType.memberType, wdlSyntaxErrorFormatter)
+          }
           WomArray(arrType, elements)
         case a: Ast if a.getName == "TupleLiteral" => astTupleToValue(a)
         case a: Ast if a.getName == "MapLiteral" && womType.isInstanceOf[WomMapType] => astToMap(a)
         case a: Ast if a.getName == "ObjectLiteral" && womType == WomObjectType => astToObject(a)
-        case _ => throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})")
+        case _ =>
+          throw new SyntaxError(
+            s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})"
+          )
       }
     }
   }
 
   implicit class EnhancedAstSeq(val astSeq: Seq[Ast]) extends AnyVal {
-    def duplicatesByName: Seq[Ast] = {
-      astSeq.groupBy(_.getAttribute("name").sourceString).collect({case (_ ,v) if v.lengthCompare(1) > 0 => v.head}).toVector
-    }
+    def duplicatesByName: Seq[Ast] =
+      astSeq
+        .groupBy(_.getAttribute("name").sourceString)
+        .collect { case (_, v) if v.lengthCompare(1) > 0 => v.head }
+        .toVector
   }
 
   object AstNodeName {
@@ -261,7 +299,7 @@ object AstTools {
   def getAst(workflowSource: WorkflowSource, resource: String): Ast = {
     val parser = new WdlParser()
     val tokens = parser.lex(workflowSource, resource)
-    val terminalMap = (tokens.asScala.toVector map {(_, workflowSource)}).toMap
+    val terminalMap = (tokens.asScala.toVector map { (_, workflowSource) }).toMap
     val syntaxErrorFormatter = WdlSyntaxErrorFormatter(terminalMap)
     parser.parse(tokens, syntaxErrorFormatter).toAst.asInstanceOf[Ast]
   }
@@ -275,7 +313,7 @@ object AstTools {
     */
   def getAst(wdlFile: Path): Ast = getAst(File(wdlFile).contentAsString, File(wdlFile).name)
 
-  def findAsts(ast: AstNode, name: String): Seq[Ast] = {
+  def findAsts(ast: AstNode, name: String): Seq[Ast] =
     ast match {
       case x: Ast =>
         val thisAst = if (x.getName.equals(name)) Seq(x) else Seq.empty[Ast]
@@ -284,16 +322,14 @@ object AstTools {
       case _: Terminal => Seq.empty[Ast]
       case _ => Seq.empty[Ast]
     }
-  }
 
-  def findTerminals(ast: AstNode): Seq[Terminal] = {
+  def findTerminals(ast: AstNode): Seq[Terminal] =
     ast match {
       case x: Ast => x.getAttributes.values.asScala.flatMap(findTerminals).toSeq
       case x: AstList => x.asScala.toVector.flatMap(findTerminals)
       case x: Terminal => Seq(x)
       case _ => Seq.empty[Terminal]
     }
-  }
 
   /**
     * All MemberAccess ASTs that are not contained in other MemberAccess ASTs
@@ -301,14 +337,18 @@ object AstTools {
     * The reason this returns a collection would be expressions such as "a.b.c + a.b.d", each one of those
     * would have its own MemberAccess - "a.b.c" and "a.b.d"
     */
-  def findTopLevelMemberAccesses(expr: AstNode): Iterable[Ast] = expr.findAstsWithTrail("MemberAccess").filterNot {
-    case (_, v) => v exists {
-      case a: Ast => a.getName == "MemberAccess"
-      case _ => false
+  def findTopLevelMemberAccesses(expr: AstNode): Iterable[Ast] = expr
+    .findAstsWithTrail("MemberAccess")
+    .filterNot { case (_, v) =>
+      v exists {
+        case a: Ast => a.getName == "MemberAccess"
+        case _ => false
+      }
     }
-  }.keys
+    .keys
+
+  final case class VariableReference private[wdl] (terminal: Terminal, trail: Iterable[AstNode], from: Scope) {
 
-  final case class VariableReference private[wdl](terminal: Terminal, trail: Iterable[AstNode], from: Scope) {
     /**
       * If this is a simple MemberAccess (both sides are terminals),
       * find the rhs corresponding to "terminal" in the trail.
@@ -318,31 +358,34 @@ object AstTools {
       * this will return Some(Terminal("b"))
       */
     private lazy val terminalSubIdentifier: Option[Terminal] = trail.collectFirst {
-      case a: Ast if a.isMemberAccess
-        && a.getAttribute("lhs") == terminal
-        && a.getAttribute("rhs").isTerminal => a.getAttribute("rhs").asInstanceOf[Terminal]
+      case a: Ast
+          if a.isMemberAccess
+            && a.getAttribute("lhs") == terminal
+            && a.getAttribute("rhs").isTerminal =>
+        a.getAttribute("rhs").asInstanceOf[Terminal]
     }
 
-    private lazy val fullVariableReferenceString: String = terminal.getSourceString + (terminalSubIdentifier map { "." + _.getSourceString } getOrElse "")
+    private lazy val fullVariableReferenceString: String =
+      terminal.getSourceString + (terminalSubIdentifier map { "." + _.getSourceString } getOrElse "")
 
     private def findResolvableSubstring(name: String, previous: String): Option[String] = {
-      lazy val popLastNamePiece: Option[String] = {
+      lazy val popLastNamePiece: Option[String] =
         name.lastIndexOf(".") match {
           case -1 => None
           case i => Option(name.substring(0, i))
         }
-      }
 
       from.resolveVariable(name) match {
-        case Some(_: WdlTaskCall | _ : WdlWorkflowCall) => Option(previous)
+        case Some(_: WdlTaskCall | _: WdlWorkflowCall) => Option(previous)
         case Some(_) => Option(name)
         case None => popLastNamePiece.flatMap(findResolvableSubstring(_, name))
       }
     }
 
-    lazy val referencedVariableName: String = {
-      findResolvableSubstring(fullVariableReferenceString, fullVariableReferenceString).getOrElse(fullVariableReferenceString)
-    }
+    lazy val referencedVariableName: String =
+      findResolvableSubstring(fullVariableReferenceString, fullVariableReferenceString).getOrElse(
+        fullVariableReferenceString
+      )
   }
 
   /**
@@ -351,16 +394,14 @@ object AstTools {
     * These represent anything that would need to be have scope resolution done on it to determine the value
     */
   def findVariableReferences(expr: AstNode, from: Scope): Iterable[VariableReference] = {
-    def isMemberAccessRhs(identifier: Terminal, trail: Seq[AstNode]): Boolean = {
+    def isMemberAccessRhs(identifier: Terminal, trail: Seq[AstNode]): Boolean =
       // e.g. for MemberAccess ast representing source code A.B.C, this would return true for only B,C and not A
-      trail.collect({ case a: Ast if a.isMemberAccess && a.getAttribute("rhs") == identifier => a }).nonEmpty
-    }
-    def isFunctionName(identifier: Terminal, trail: Seq[AstNode]): Boolean = {
+      trail.collect { case a: Ast if a.isMemberAccess && a.getAttribute("rhs") == identifier => a }.nonEmpty
+    def isFunctionName(identifier: Terminal, trail: Seq[AstNode]): Boolean =
       trail.lastOption match {
         case Some(last: Ast) if last.isFunctionCall && last.getAttribute("name") == identifier => true
         case _ => false
       }
-    }
 
     /* terminal is the "lefter" lhs
      * trail is how we arrived to identifier from the original ast
@@ -391,9 +432,10 @@ object AstTools {
      *
      * There also might be other types of nodes in trail than MemberAccess depending the expression.
      */
-    expr.findTerminalsWithTrail("identifier").collect({
-      case (terminal, trail) if !isMemberAccessRhs(terminal, trail) && !isFunctionName(terminal, trail) => VariableReference(terminal, trail, from)
-    })
+    expr.findTerminalsWithTrail("identifier").collect {
+      case (terminal, trail) if !isMemberAccessRhs(terminal, trail) && !isFunctionName(terminal, trail) =>
+        VariableReference(terminal, trail, from)
+    }
 
   }
 
@@ -410,9 +452,10 @@ object AstTools {
     val callTaskName = ast.getAttribute("task").asInstanceOf[Terminal]
 
     /* Filter out all empty 'input' sections first */
-    val callInputSections = ast.findAsts(AstNodeName.Inputs).map {inputSectionAst =>
+    val callInputSections = ast.findAsts(AstNodeName.Inputs).map { inputSectionAst =>
       inputSectionAst.getAttribute("map").findAsts(AstNodeName.IOMapping) match {
-        case kvPairs: Seq[Ast] if kvPairs.isEmpty => throw new SyntaxError(wdlSyntaxErrorFormatter.emptyInputSection(callTaskName))
+        case kvPairs: Seq[Ast] if kvPairs.isEmpty =>
+          throw new SyntaxError(wdlSyntaxErrorFormatter.emptyInputSection(callTaskName))
         case _ => inputSectionAst
       }
     }
@@ -424,34 +467,42 @@ object AstTools {
       case asts: Seq[Ast] =>
         /* Uses of .head here are assumed by the above code that ensures that there are no empty maps */
         val secondInputSectionIOMappings = asts(1).getAttribute("map").astListAsVector
-        val firstKeyTerminal = secondInputSectionIOMappings.head.asInstanceOf[Ast].getAttribute("key").asInstanceOf[Terminal]
+        val firstKeyTerminal =
+          secondInputSectionIOMappings.head.asInstanceOf[Ast].getAttribute("key").asInstanceOf[Terminal]
         throw new SyntaxError(wdlSyntaxErrorFormatter.multipleInputStatementsOnCall(firstKeyTerminal))
     }
   }
 
-  def terminalMap(ast: Ast, source: WorkflowSource) = (findTerminals(ast) map {(_, source)}).toMap
+  def terminalMap(ast: Ast, source: WorkflowSource) = (findTerminals(ast) map { (_, source) }).toMap
 
-  def wdlSectionToStringMap(ast: Ast, node: String, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter): Map[String, String] = {
+  def wdlSectionToStringMap(ast: Ast,
+                            node: String,
+                            wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter
+  ): Map[String, String] =
     ast.findAsts(node) match {
       case a if a.isEmpty => Map.empty[String, String]
       case a if a.lengthCompare(1) == 0 =>
         // Yes, even 'meta {}' and 'parameter_meta {}' sections have RuntimeAttribute ASTs.
         // In hindsight, this was a poor name for the AST.
-        a.head.findAsts(AstNodeName.RuntimeAttribute).map({ ast =>
-          val key = ast.getAttribute("key").asInstanceOf[Terminal]
-          val value = ast.getAttribute("value")
-          if (!value.isInstanceOf[Terminal] || value.asInstanceOf[Terminal].getTerminalStr != "string") {
-            // Keys are parsed as identifiers, but values are parsed as expressions.
-            // For now, only accept expressions that are strings
-            throw new SyntaxError(wdlSyntaxErrorFormatter.expressionExpectedToBeString(key))
+        a.head
+          .findAsts(AstNodeName.RuntimeAttribute)
+          .map { ast =>
+            val key = ast.getAttribute("key").asInstanceOf[Terminal]
+            val value = ast.getAttribute("value")
+            if (!value.isInstanceOf[Terminal] || value.asInstanceOf[Terminal].getTerminalStr != "string") {
+              // Keys are parsed as identifiers, but values are parsed as expressions.
+              // For now, only accept expressions that are strings
+              throw new SyntaxError(wdlSyntaxErrorFormatter.expressionExpectedToBeString(key))
+            }
+            key.sourceString -> value.sourceString
           }
-          key.sourceString -> value.sourceString
-        }).toMap
-      case _ => throw new SyntaxError(wdlSyntaxErrorFormatter.expectedAtMostOneSectionPerTask(node, ast.getAttribute("name").asInstanceOf[Terminal]))
+          .toMap
+      case _ =>
+        throw new SyntaxError(
+          wdlSyntaxErrorFormatter.expectedAtMostOneSectionPerTask(node, ast.getAttribute("name").asInstanceOf[Terminal])
+        )
     }
-  }
 
-  private def combine[T, U](map1: Map[T, Seq[U]], map2: Map[T, Seq[U]]): Map[T, Seq[U]] = {
-    map1 ++ map2.map{ case (k,v) => k -> (v ++ map1.getOrElse(k, Seq.empty)) }
-  }
+  private def combine[T, U](map1: Map[T, Seq[U]], map2: Map[T, Seq[U]]): Map[T, Seq[U]] =
+    map1 ++ map2.map { case (k, v) => k -> (v ++ map1.getOrElse(k, Seq.empty)) }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/Declaration.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/Declaration.scala
index 0d6d5ed49e0..9956562a753 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/Declaration.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/Declaration.scala
@@ -6,12 +6,18 @@ import common.validation.ErrorOr.{ErrorOr, ShortCircuitingFlatMap}
 import wdl.draft2.model
 import wdl.draft2.model.AstTools.EnhancedAstNode
 import wdl.draft2.parser.WdlParser.{Ast, AstNode}
-import wom.callable.Callable.{InputDefinition, OverridableInputDefinitionWithDefault, OptionalInputDefinition, RequiredInputDefinition}
+import wom.callable.Callable.{
+  InputDefinition,
+  OptionalInputDefinition,
+  OverridableInputDefinitionWithDefault,
+  RequiredInputDefinition
+}
 import wom.graph._
 import wom.graph.expression.{ExposedExpressionNode, ExpressionNode}
 import wom.types.{WomArrayType, WomOptionalType, WomType}
 
 object DeclarationInterface {
+
   /**
     * Depending on who is asking, the type of a declaration can vary.
     * e.g
@@ -30,15 +36,14 @@ object DeclarationInterface {
     *   Array[String] s2 = a.o # Outside the scatter it's an Array[String]
     * }
     */
-  def relativeWdlType(from: Scope, target: DeclarationInterface, womType: WomType): WomType = {
+  def relativeWdlType(from: Scope, target: DeclarationInterface, womType: WomType): WomType =
     target.closestCommonAncestor(from) map { ancestor =>
-      target.ancestrySafe.takeWhile(_ != ancestor).foldLeft(womType){
+      target.ancestrySafe.takeWhile(_ != ancestor).foldLeft(womType) {
         case (acc, _: Scatter) => WomArrayType(acc)
         case (acc, _: If) => WomOptionalType(acc).flatOptionalType
         case (acc, _) => acc
       }
     } getOrElse womType
-  }
 }
 
 /**
@@ -90,9 +95,8 @@ trait DeclarationInterface extends WdlGraphNodeWithUpstreamReferences {
 
   final lazy val upstreamReferences = expression.toSeq.flatMap(_.variableReferences(this))
 
-  override def toString: String = {
+  override def toString: String =
     s"[Declaration type=${womType.stableName} name=$unqualifiedName expr=${expression.map(_.toWomString)}]"
-  }
 }
 
 object Declaration {
@@ -114,7 +118,7 @@ object Declaration {
   final case class IntermediateValueDeclarationNode(expressionNode: ExpressionNode) extends WdlDeclarationNode
   final case class GraphOutputDeclarationNode(graphOutputNode: GraphOutputNode) extends WdlDeclarationNode
 
-  def apply(ast: Ast, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter, parent: Option[Scope]): Declaration = {
+  def apply(ast: Ast, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter, parent: Option[Scope]): Declaration =
     Declaration(
       ast.getAttribute("type").womType(wdlSyntaxErrorFormatter),
       ast.getAttribute("name").sourceString,
@@ -125,31 +129,62 @@ object Declaration {
       parent,
       ast
     )
-  }
 
-  def buildWdlDeclarationNode(decl: DeclarationInterface, localLookup: Map[String, GraphNodePort.OutputPort], outerLookup: Map[String, GraphNodePort.OutputPort], preserveIndexForOuterLookups: Boolean): ErrorOr[WdlDeclarationNode] = {
+  def buildWdlDeclarationNode(decl: DeclarationInterface,
+                              localLookup: Map[String, GraphNodePort.OutputPort],
+                              outerLookup: Map[String, GraphNodePort.OutputPort],
+                              preserveIndexForOuterLookups: Boolean
+  ): ErrorOr[WdlDeclarationNode] = {
 
     def declarationAsExpressionNode(wdlExpression: WdlExpression) = {
       val womExpression = WdlWomExpression(wdlExpression, decl)
       for {
-        inputMapping <- WdlWomExpression.findInputsforExpression(womExpression, localLookup, outerLookup, preserveIndexForOuterLookups, decl)
-        expressionNode <- ExposedExpressionNode.fromInputMapping(decl.womIdentifier, womExpression, decl.womType, inputMapping)
+        inputMapping <- WdlWomExpression.findInputsforExpression(womExpression,
+                                                                 localLookup,
+                                                                 outerLookup,
+                                                                 preserveIndexForOuterLookups,
+                                                                 decl
+        )
+        expressionNode <- ExposedExpressionNode.fromInputMapping(decl.womIdentifier,
+                                                                 womExpression,
+                                                                 decl.womType,
+                                                                 inputMapping
+        )
       } yield IntermediateValueDeclarationNode(expressionNode)
     }
 
     def workflowOutputAsGraphOutputNode(wdlExpression: WdlExpression) = {
       val womExpression = WdlWomExpression(wdlExpression, decl)
       for {
-        inputMapping <- WdlWomExpression.findInputsforExpression(womExpression, localLookup, outerLookup, preserveIndexForOuterLookups, decl)
-        graphOutputNode <- ExpressionBasedGraphOutputNode.fromInputMapping(decl.womIdentifier, womExpression, decl.womType, inputMapping)
+        inputMapping <- WdlWomExpression.findInputsforExpression(womExpression,
+                                                                 localLookup,
+                                                                 outerLookup,
+                                                                 preserveIndexForOuterLookups,
+                                                                 decl
+        )
+        graphOutputNode <- ExpressionBasedGraphOutputNode.fromInputMapping(decl.womIdentifier,
+                                                                           womExpression,
+                                                                           decl.womType,
+                                                                           inputMapping
+        )
       } yield GraphOutputDeclarationNode(graphOutputNode)
     }
 
     def asWorkflowInput(inputDefinition: InputDefinition): GraphInputNode = inputDefinition match {
-      case RequiredInputDefinition(_, womType, _, _) => RequiredGraphInputNode(decl.womIdentifier, womType, decl.womIdentifier.fullyQualifiedName.value)
-      case OptionalInputDefinition(_, optionalType, _, _) => OptionalGraphInputNode(decl.womIdentifier, optionalType, decl.womIdentifier.fullyQualifiedName.value)
-      case OverridableInputDefinitionWithDefault(_, womType, default, _, _) => OptionalGraphInputNodeWithDefault(decl.womIdentifier, womType, default, decl.womIdentifier.fullyQualifiedName.value)
-      case other => throw new RuntimeException(s"Programmer Error! If you got here you probably changed draft 2 to try to do some draft 3 like things, but this draft 2 function isn't set up to produce or handle ${other.getClass.getSimpleName} yet!")
+      case RequiredInputDefinition(_, womType, _, _) =>
+        RequiredGraphInputNode(decl.womIdentifier, womType, decl.womIdentifier.fullyQualifiedName.value)
+      case OptionalInputDefinition(_, optionalType, _, _) =>
+        OptionalGraphInputNode(decl.womIdentifier, optionalType, decl.womIdentifier.fullyQualifiedName.value)
+      case OverridableInputDefinitionWithDefault(_, womType, default, _, _) =>
+        OptionalGraphInputNodeWithDefault(decl.womIdentifier,
+                                          womType,
+                                          default,
+                                          decl.womIdentifier.fullyQualifiedName.value
+        )
+      case other =>
+        throw new RuntimeException(
+          s"Programmer Error! If you got here you probably changed draft 2 to try to do some draft 3 like things, but this draft 2 function isn't set up to produce or handle ${other.getClass.getSimpleName} yet!"
+        )
     }
 
     (decl.asWorkflowInput, decl) match {
@@ -165,4 +200,5 @@ case class Declaration(womType: WomType,
                        unqualifiedName: String,
                        expression: Option[WdlExpression],
                        override val parent: Option[Scope],
-                       ast: Ast) extends DeclarationInterface
+                       ast: Ast
+) extends DeclarationInterface
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/If.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/If.scala
index 9bba2d1797d..e6bcdcce9b8 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/If.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/If.scala
@@ -8,7 +8,9 @@ import wdl.draft2.parser.WdlParser.Ast
   * @param index Index of the if block. The index is computed during tree generation to reflect WDL scope structure.
   * @param condition WDL Expression representing the condition in which to execute this If-block
   */
-case class If(index: Int, condition: WdlExpression, ast: Ast) extends WdlGraphNodeWithUpstreamReferences with WorkflowScoped {
+case class If(index: Int, condition: WdlExpression, ast: Ast)
+    extends WdlGraphNodeWithUpstreamReferences
+    with WorkflowScoped {
   val unqualifiedName = s"${If.FQNIdentifier}_$index"
   override def appearsInFqn = false
 
@@ -23,7 +25,6 @@ object If {
   /**
     * @param index Index of the if block. The index is computed during tree generation to reflect WDL scope structure.
     */
-  def apply(ast: Ast, index: Int): If = {
+  def apply(ast: Ast, index: Int): If =
     new If(index, WdlExpression(ast.getAttribute("expression")), ast)
-  }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/Scatter.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/Scatter.scala
index 9613b27bafb..aac86ce859c 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/Scatter.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/Scatter.scala
@@ -8,7 +8,9 @@ import wdl.draft2.parser.WdlParser.{Ast, Terminal}
   * @param item Item which this block is scattering over
   * @param collection Wdl Expression corresponding to the collection this scatter is looping through
   */
-case class Scatter(index: Int, item: String, collection: WdlExpression, ast: Ast) extends WdlGraphNodeWithUpstreamReferences with WorkflowScoped {
+case class Scatter(index: Int, item: String, collection: WdlExpression, ast: Ast)
+    extends WdlGraphNodeWithUpstreamReferences
+    with WorkflowScoped {
   val unqualifiedName = s"${Scatter.FQNIdentifier}_$index"
   override def appearsInFqn = false
 
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/Scope.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/Scope.scala
index caeec3ef3a8..243a1235b20 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/Scope.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/Scope.scala
@@ -26,21 +26,19 @@ trait Scope {
     */
   def parent: Option[Scope] = _parent
   private var _parent: Option[Scope] = None
-  def parent_=[Child <: Scope](scope: Scope): Unit = {
+  def parent_=[Child <: Scope](scope: Scope): Unit =
     if (this._parent.isEmpty) this._parent = Option(scope)
     else throw new UnsupportedOperationException("parent is write-once")
-  }
 
   /**
     * Child scopes, in the order that they appear in the source code
     */
   def children: Seq[Scope] = _children
   private var _children: Seq[Scope] = Seq.empty
-  def children_=[Child <: Scope](children: Seq[Child]): Unit = {
+  def children_=[Child <: Scope](children: Seq[Child]): Unit =
     if (this._children.isEmpty) {
       this._children = children
     } else throw new UnsupportedOperationException("children is write-once")
-  }
 
   lazy val childGraphNodes: Set[WdlGraphNode] = children.toSet.filterByType[WdlGraphNode]
   lazy val childGraphNodesSorted: Checked[List[WdlGraphNode]] = {
@@ -56,7 +54,8 @@ trait Scope {
       case Left(_) =>
         val cycleNodes = childGraphNodes.filter(cgn => cgn.upstreamAncestry.contains(cgn)).map(_.toString).toList.sorted
         s"This workflow contains cyclic dependencies containing these edges: ${cycleNodes.mkString(", ")}".invalidNelCheck
-      case Right(topologicalOrder) => topologicalOrder.toList.map(_.value).filter(childGraphNodes.contains).validNelCheck
+      case Right(topologicalOrder) =>
+        topologicalOrder.toList.map(_.value).filter(childGraphNodes.contains).validNelCheck
     }
   }
 
@@ -65,11 +64,10 @@ trait Scope {
     */
   def namespace: WdlNamespace = _namespace
   private var _namespace: WdlNamespace = _
-  def namespace_=[Child <: WdlNamespace](ns: WdlNamespace): Unit = {
+  def namespace_=[Child <: WdlNamespace](ns: WdlNamespace): Unit =
     if (Option(this._namespace).isEmpty) {
       this._namespace = ns
     } else throw new UnsupportedOperationException("namespace is write-once")
-  }
 
   /**
     * Seq(parent, grandparent, great grandparent, ..., WdlNamespace)
@@ -82,7 +80,7 @@ trait Scope {
   // This is needed in one specific case during WdlNamespace validation
   // where we need to compute the ancestries at a point where the full
   // parent branch has not been set yet.
-  private [wdl] def ancestrySafe: Seq[Scope] = parent match {
+  private[wdl] def ancestrySafe: Seq[Scope] = parent match {
     case Some(p) => Seq(p) ++ p.ancestrySafe
     case None => Seq.empty[Scope]
   }
@@ -95,7 +93,7 @@ trait Scope {
   /**
     * Descendants that are Calls
     */
-  lazy val calls: Set[WdlCall] = descendants.collect({ case c: WdlCall => c })
+  lazy val calls: Set[WdlCall] = descendants.collect { case c: WdlCall => c }
 
   lazy val taskCalls: Set[WdlTaskCall] = calls collect { case c: WdlTaskCall => c }
 
@@ -104,28 +102,27 @@ trait Scope {
   /**
     * Descendants that are Scatters
     */
-  lazy val scatters: Set[Scatter] = descendants.collect({ case s: Scatter => s })
+  lazy val scatters: Set[Scatter] = descendants.collect { case s: Scatter => s }
 
   /**
     * Declarations within this Scope, in the order that they appear in source code
     */
-  lazy val declarations: Seq[Declaration] = children.collect({ case d: Declaration => d})
+  lazy val declarations: Seq[Declaration] = children.collect { case d: Declaration => d }
 
   /**
     * String identifier for this scope.  this.namespace.resolve(this.fullyQualifiedName) == this
     */
-  lazy val fullyQualifiedName = {
+  lazy val fullyQualifiedName =
     (ancestry.filter(_.appearsInFqn).map(_.unqualifiedName).reverse :+ unqualifiedName).mkString(".")
-  }
-  
+
   lazy val womIdentifier = {
     /* Limit the fully qualified name to the parent workflow, if it exists.
      * The reason for this is if this scope comes from an imported namespace,
      * the name of the namespace will be part of the FQN. While useful to construct the hierarchy and dependencies,
      * this is not desirable when being used by underlying engines.
-    */
-    val womFullyQualifiedName = ancestry.collectFirst {
-      case workflow: WdlWorkflow => locallyQualifiedName(workflow)
+     */
+    val womFullyQualifiedName = ancestry.collectFirst { case workflow: WdlWorkflow =>
+      locallyQualifiedName(workflow)
     } getOrElse fullyQualifiedName
 
     WomIdentifier(unqualifiedName, womFullyQualifiedName)
@@ -141,31 +138,30 @@ trait Scope {
     * o.locallyQualified(a) = "a.o"
     * o.locallyQualified(w) = o.fullyQualifiedName = "w.a.o"
     */
-  def locallyQualifiedName(relativeTo: Scope): String = {
+  def locallyQualifiedName(relativeTo: Scope): String =
     // Take ancestries until we reach relativeTo
-    (ancestry.takeWhile(_ != relativeTo)
+    (ancestry
+      .takeWhile(_ != relativeTo)
       // we want relativeTo in the lqn but it's been rejected by takeWhile wo add it back
       .:+(relativeTo)
-      // Reverse because we start from the scope and climb up the ancestry tree but in the end we want a top-bottom lqn 
+      // Reverse because we start from the scope and climb up the ancestry tree but in the end we want a top-bottom lqn
       .reverse
       // Get rid of scatters, ifs... because we don't want them here
       .filter(_.appearsInFqn)
       // Take the unqualifiedName of each scope
       .map(_.unqualifiedName)
-      // Add the current scope
+    // Add the current scope
       :+ unqualifiedName)
       // Concatenate all of this
       .mkString(".")
-  }
 
   /**
     * String identifier for this scope, with hidden scope information.
     *
     * this.namespace.resolve(this.fullyQualifiedNameWithIndexScopes) == this
     */
-  def fullyQualifiedNameWithIndexScopes = {
+  def fullyQualifiedNameWithIndexScopes =
     (Seq(this) ++ ancestry).reverse.map(_.unqualifiedName).filter(_.nonEmpty).mkString(".")
-  }
 
   /**
     * Given another scope, returns the closest common ancestor between the two scopes,
@@ -180,7 +176,7 @@ trait Scope {
 
   def closestCommonScatter(other: Scope): Option[Scatter] = {
     val otherAncestry = other.ancestrySafe
-    ancestrySafe collectFirst  {
+    ancestrySafe collectFirst {
       case s: Scatter if otherAncestry.contains(s) => s
     }
   }
@@ -190,10 +186,11 @@ trait Scope {
     * until it finds a GraphNode with the `name` as its unqualifiedName
     */
   def resolveVariable(name: String, relativeTo: Scope = this, ignoreLocal: Boolean = false): Option[WdlGraphNode] = {
-    val siblingScopes = if (children.contains(relativeTo))
-    // For declarations, only resolve to declarations that are lexically before this declaration
-      children.dropRight(children.size - children.indexOf(relativeTo) )
-    else children
+    val siblingScopes =
+      if (children.contains(relativeTo))
+        // For declarations, only resolve to declarations that are lexically before this declaration
+        children.dropRight(children.size - children.indexOf(relativeTo))
+      else children
 
     val siblingCallOutputs = siblingScopes flatMap {
       case c: WdlTaskCall => c.outputs
@@ -203,12 +200,13 @@ trait Scope {
     val localLookup =
       if (ignoreLocal)
         Seq.empty
-      else (siblingScopes ++ siblingCallOutputs) collect {
-        case d: Declaration if d.unqualifiedName == name => d
-        case c: WdlTaskCall if c.unqualifiedName == name => c
-        case co: CallOutput if co.unqualifiedName == name => co
-        case o: TaskOutput if o.unqualifiedName == name => o
-      }
+      else
+        (siblingScopes ++ siblingCallOutputs) collect {
+          case d: Declaration if d.unqualifiedName == name => d
+          case c: WdlTaskCall if c.unqualifiedName == name => c
+          case co: CallOutput if co.unqualifiedName == name => co
+          case o: TaskOutput if o.unqualifiedName == name => o
+        }
 
     // If this is a scatter and the variable being resolved is the item
     val scatterLookup = Seq(this) collect {
@@ -237,39 +235,63 @@ trait Scope {
                      wdlFunctions: WdlFunctions[WomValue],
                      outputResolver: OutputResolver = NoOutputResolver,
                      shards: Map[Scatter, Int] = Map.empty[Scatter, Int],
-                     relativeTo: Scope = this): String => WomValue = {
+                     relativeTo: Scope = this
+  ): String => WomValue = {
 
     def handleScatterResolution(scatter: Scatter): Try[WomValue] = {
       // This case will happen if `name` references a Scatter.item (i.e. `x` in expression scatter(x in y) {...})
-      val evaluatedCollection = scatter.collection.evaluate(scatter.lookupFunction(knownInputs, wdlFunctions, outputResolver, shards), wdlFunctions)
+      val evaluatedCollection = scatter.collection.evaluate(
+        scatter.lookupFunction(knownInputs, wdlFunctions, outputResolver, shards),
+        wdlFunctions
+      )
       val scatterShard = shards.get(scatter)
 
       (evaluatedCollection, scatterShard) match {
         case (Success(WomArrayLike(array)), Some(shard)) if 0 <= shard && shard < array.value.size =>
           array.value.lift(shard) match {
             case Some(v) => Success(v)
-            case None => Failure(new VariableLookupException(s"Could not find value for shard index $shard in scatter collection $array"))
+            case None =>
+              Failure(
+                new VariableLookupException(s"Could not find value for shard index $shard in scatter collection $array")
+              )
           }
         case (Success(WomArrayLike(array)), Some(shard)) =>
-          Failure(new VariableLookupException(s"Scatter expression (${scatter.collection.toWomString}) evaluated to an array of ${array.value.size} elements, but element $shard was requested."))
+          Failure(
+            new VariableLookupException(
+              s"Scatter expression (${scatter.collection.toWomString}) evaluated to an array of ${array.value.size} elements, but element $shard was requested."
+            )
+          )
         case (Success(_: WomArrayLike), None) =>
-          Failure(ScatterIndexNotFound(s"Could not find the shard mapping to this scatter ${scatter.fullyQualifiedName}"))
+          Failure(
+            ScatterIndexNotFound(s"Could not find the shard mapping to this scatter ${scatter.fullyQualifiedName}")
+          )
         case (Success(value: WomValue), _) =>
-          Failure(new VariableLookupException(s"Expected scatter expression (${scatter.collection.toWomString}) to evaluate to an Array.  Instead, got a $value"))
+          Failure(
+            new VariableLookupException(
+              s"Expected scatter expression (${scatter.collection.toWomString}) to evaluate to an Array.  Instead, got a $value"
+            )
+          )
         case (failure @ Failure(_), _) => failure
         case (_, None) =>
-          Failure(new VariableLookupException(s"Could not find a shard for scatter block with expression (${scatter.collection.toWomString})"))
+          Failure(
+            new VariableLookupException(
+              s"Could not find a shard for scatter block with expression (${scatter.collection.toWomString})"
+            )
+          )
       }
     }
 
     def fromOutputs(node: WdlGraphNode) = {
-      def withShard(s: Scatter) = {
+      def withShard(s: Scatter) =
         shards.get(s) map { shard =>
           outputResolver(node, Option(shard))
         } getOrElse {
-          Failure(ScatterIndexNotFound(s"Could not find a shard for scatter block with expression (${s.collection.toWomString})"))
+          Failure(
+            ScatterIndexNotFound(
+              s"Could not find a shard for scatter block with expression (${s.collection.toWomString})"
+            )
+          )
         }
-      }
 
       this match {
         case s: Scatter if descendants.contains(node) => withShard(s)
@@ -282,18 +304,22 @@ trait Scope {
     }
 
     def handleDeclarationEvaluation(declaration: DeclarationInterface): Try[WomValue] = {
-      def declarationExcludingLookup(lookup: String => WomValue): String => WomValue = name => {
-        if (name.equals(declaration.unqualifiedName)) throw new IllegalArgumentException(s"Declaration for '$name' refers to its own value")
+      def declarationExcludingLookup(lookup: String => WomValue): String => WomValue = name =>
+        if (name.equals(declaration.unqualifiedName))
+          throw new IllegalArgumentException(s"Declaration for '$name' refers to its own value")
         else lookup(name)
-      }
 
       def evaluate =
         declaration.expression match {
           case Some(e) =>
-            val parentLookup = declaration.parent.map(_.lookupFunction(knownInputs, wdlFunctions, outputResolver, shards)).getOrElse(NoLookup)
+            val parentLookup = declaration.parent
+              .map(_.lookupFunction(knownInputs, wdlFunctions, outputResolver, shards))
+              .getOrElse(NoLookup)
             e.evaluate(declarationExcludingLookup(parentLookup), wdlFunctions)
           case None =>
-            Failure(new VariableLookupException(s"Declaration ${declaration.fullyQualifiedName} does not have an expression"))
+            Failure(
+              new VariableLookupException(s"Declaration ${declaration.fullyQualifiedName} does not have an expression")
+            )
         }
 
       fromOutputs(declaration) recoverWith { case _ => evaluate }
@@ -308,14 +334,32 @@ trait Scope {
           knownInputs.get(scope.fullyQualifiedName) map Success.apply getOrElse {
             Failure(new VariableLookupException(s"Could not find value in inputs map."))
           }
-        case callOutput: CallOutput => handleCallEvaluation(callOutput.call) flatMap {
-          case outputs: WdlCallOutputsObject => outputs.outputs.get(callOutput.unqualifiedName).map(Success(_)).getOrElse(Failure(new Exception(s"No output ${callOutput.unqualifiedName} found in ${callOutput.call.unqualifiedName}'s outputs")))
-          case other => Failure(new Exception(s"Call outputs unexpectedly evaluated to a ${other.womType.stableName}"))
-        }
+        case callOutput: CallOutput =>
+          handleCallEvaluation(callOutput.call) flatMap {
+            case outputs: WdlCallOutputsObject =>
+              outputs.outputs
+                .get(callOutput.unqualifiedName)
+                .map(Success(_))
+                .getOrElse(
+                  Failure(
+                    new Exception(
+                      s"No output ${callOutput.unqualifiedName} found in ${callOutput.call.unqualifiedName}'s outputs"
+                    )
+                  )
+                )
+            case other =>
+              Failure(new Exception(s"Call outputs unexpectedly evaluated to a ${other.womType.stableName}"))
+          }
         case call: WdlCall => handleCallEvaluation(call)
         case scatter: Scatter => handleScatterResolution(scatter)
-        case declaration: DeclarationInterface if declaration.expression.isDefined => handleDeclarationEvaluation(declaration)
-        case scope => Failure(new VariableLookupException(s"Variable $name resolved to scope ${scope.fullyQualifiedName} but cannot be evaluated."))
+        case declaration: DeclarationInterface if declaration.expression.isDefined =>
+          handleDeclarationEvaluation(declaration)
+        case scope =>
+          Failure(
+            new VariableLookupException(
+              s"Variable $name resolved to scope ${scope.fullyQualifiedName} but cannot be evaluated."
+            )
+          )
       } getOrElse {
         Failure(VariableNotFoundException(name))
       }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/TaskOutput.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/TaskOutput.scala
index 569ccc84cf1..34df17efad4 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/TaskOutput.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/TaskOutput.scala
@@ -14,11 +14,18 @@ object TaskOutput {
     TaskOutput(name, womType, expression, ast, parent)
   }
 
-  def buildWomOutputDefinition(taskOutput: TaskOutput) = {
-    OutputDefinition(LocalName(taskOutput.unqualifiedName), taskOutput.womType, WdlWomExpression(taskOutput.requiredExpression, from = taskOutput))
-  }
+  def buildWomOutputDefinition(taskOutput: TaskOutput) =
+    OutputDefinition(LocalName(taskOutput.unqualifiedName),
+                     taskOutput.womType,
+                     WdlWomExpression(taskOutput.requiredExpression, from = taskOutput)
+    )
 }
 
-final case class TaskOutput(unqualifiedName: String, womType: WomType, requiredExpression: WdlExpression, ast: Ast, override val parent: Option[Scope]) extends Output {
+final case class TaskOutput(unqualifiedName: String,
+                            womType: WomType,
+                            requiredExpression: WdlExpression,
+                            ast: Ast,
+                            override val parent: Option[Scope]
+) extends Output {
   lazy val womOutputDefinition: OutputDefinition = TaskOutput.buildWomOutputDefinition(this)
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlCall.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlCall.scala
index 8d1973bd109..42723ee9a97 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlCall.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlCall.scala
@@ -16,7 +16,8 @@ object WdlCall {
             namespaces: Seq[WdlNamespace],
             tasks: Seq[WdlTask],
             workflows: Seq[WdlWorkflow],
-            wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter): WdlCall = {
+            wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter
+  ): WdlCall = {
     val alias: Option[String] = ast.getAttribute("alias") match {
       case x: Terminal => Option(x.getSourceString)
       case _ => None
@@ -36,14 +37,12 @@ object WdlCall {
     }
   }
 
-  private def processCallInput(ast: Ast,
-                               wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter): Map[String, WdlExpression] = {
+  private def processCallInput(ast: Ast, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter): Map[String, WdlExpression] =
     AstTools.callInputSectionIOMappings(ast, wdlSyntaxErrorFormatter) map { a =>
       val key = a.getAttribute("key").sourceString
       val expression = new WdlExpression(a.getAttribute("value"))
       (key, expression)
     } toMap
-  }
 }
 
 /**
@@ -61,7 +60,9 @@ object WdlCall {
 sealed abstract class WdlCall(val alias: Option[String],
                               val callable: WdlCallable,
                               val inputMappings: Map[String, WdlExpression],
-                              val ast: Ast) extends WdlGraphNodeWithInputs with WorkflowScoped {
+                              val ast: Ast
+) extends WdlGraphNodeWithInputs
+    with WorkflowScoped {
   val unqualifiedName: String = alias getOrElse callable.unqualifiedName
 
   def callType: String
@@ -83,7 +84,8 @@ sealed abstract class WdlCall(val alias: Option[String],
     *
     * NB Only used in tests, womtool and some external tools (eg FC's workflow input enumerator)
     */
-  def workflowInputs: Seq[InputDefinition] = declarations.filterNot(i => inputMappings.contains(i.unqualifiedName)).flatMap(_.asWorkflowInput)
+  def workflowInputs: Seq[InputDefinition] =
+    declarations.filterNot(i => inputMappings.contains(i.unqualifiedName)).flatMap(_.asWorkflowInput)
 
   override def toString: String = s"[Call $fullyQualifiedName]"
 
@@ -98,12 +100,13 @@ sealed abstract class WdlCall(val alias: Option[String],
   def evaluateTaskInputs(inputs: WorkflowCoercedInputs,
                          wdlFunctions: WdlFunctions[WomValue],
                          outputResolver: OutputResolver = NoOutputResolver,
-                         shards: Map[Scatter, Int] = Map.empty[Scatter, Int]): Try[EvaluatedTaskInputs] = {
+                         shards: Map[Scatter, Int] = Map.empty[Scatter, Int]
+  ): Try[EvaluatedTaskInputs] = {
 
     type EvaluatedDeclarations = Map[Declaration, Try[WomValue]]
     def doDeclaration(currentInputs: EvaluatedDeclarations, declaration: Declaration): EvaluatedDeclarations = {
-      val newInputs = inputs ++ currentInputs.collect{
-        case (decl, Success(value)) => decl.fullyQualifiedName -> value
+      val newInputs = inputs ++ currentInputs.collect { case (decl, Success(value)) =>
+        decl.fullyQualifiedName -> value
       }
       val lookup = lookupFunction(newInputs, wdlFunctions, outputResolver, shards, relativeTo = declaration)
       val evaluatedDeclaration = Try(lookup(declaration.unqualifiedName))
@@ -141,21 +144,30 @@ sealed abstract class WdlCall(val alias: Option[String],
                               wdlFunctions: WdlFunctions[WomValue],
                               outputResolver: OutputResolver = NoOutputResolver,
                               shards: Map[Scatter, Int] = Map.empty[Scatter, Int],
-                              relativeTo: Scope = this): (String => WomValue) =
+                              relativeTo: Scope = this
+  ): (String => WomValue) =
     (name: String) => {
 
       val inputMappingsWithMatchingName = Try(
-        inputMappings.getOrElse(name, throw new Exception(s"Could not find $name in input section of call $fullyQualifiedName"))
+        inputMappings.getOrElse(
+          name,
+          throw new Exception(s"Could not find $name in input section of call $fullyQualifiedName")
+        )
       )
 
       val declarationsWithMatchingName = Try(
-        declarations.find(_.unqualifiedName == name).getOrElse(throw new Exception(s"No declaration named $name for call $fullyQualifiedName"))
+        declarations
+          .find(_.unqualifiedName == name)
+          .getOrElse(throw new Exception(s"No declaration named $name for call $fullyQualifiedName"))
       )
 
       val inputMappingsLookup = for {
         inputExpr <- inputMappingsWithMatchingName
         parent <- Try(parent.getOrElse(throw new Exception(s"Call $unqualifiedName has no parent")))
-        evaluatedExpr <- inputExpr.evaluate(parent.lookupFunction(inputs, wdlFunctions, outputResolver, shards, relativeTo), wdlFunctions)
+        evaluatedExpr <- inputExpr.evaluate(
+          parent.lookupFunction(inputs, wdlFunctions, outputResolver, shards, relativeTo),
+          wdlFunctions
+        )
         // Coerce the input into the declared type:
         declaration <- declarationsWithMatchingName
         coerced <- declaration.womType.coerceRawValue(evaluatedExpr)
@@ -174,7 +186,10 @@ sealed abstract class WdlCall(val alias: Option[String],
       val declarationExprLookup = for {
         declaration <- declarationsWithMatchingName
         declarationExpr <- Try(declaration.expression.getOrElse(throw VariableNotFoundException(declaration)))
-        evaluatedExpr <- declarationExpr.evaluate(lookupFunction(inputs, wdlFunctions, outputResolver, shards, relativeTo), wdlFunctions)
+        evaluatedExpr <- declarationExpr.evaluate(
+          lookupFunction(inputs, wdlFunctions, outputResolver, shards, relativeTo),
+          wdlFunctions
+        )
       } yield evaluatedExpr
 
       val taskParentResolution = for {
@@ -185,11 +200,11 @@ sealed abstract class WdlCall(val alias: Option[String],
       val resolutions = Seq(inputMappingsLookup, declarationExprLookup, declarationLookup, taskParentResolution)
 
       resolutions collectFirst { case Success(value) => value } getOrElse {
-        resolutions.toList.flatMap({
+        resolutions.toList.flatMap {
           case Failure(_: VariableNotFoundException) => None
           case Failure(ex) => Option(ex) // Only take failures that are not VariableNotFoundExceptions
           case _ => None
-        }) match {
+        } match {
           case Nil => throw VariableNotFoundException(name)
           case exs => throw new VariableLookupException(name, exs)
         }
@@ -197,9 +212,17 @@ sealed abstract class WdlCall(val alias: Option[String],
     }
 }
 
-case class WdlTaskCall(override val alias: Option[String], task: WdlTask, override val inputMappings: Map[String, WdlExpression], override val ast: Ast) extends WdlCall(alias, task, inputMappings, ast) {
+case class WdlTaskCall(override val alias: Option[String],
+                       task: WdlTask,
+                       override val inputMappings: Map[String, WdlExpression],
+                       override val ast: Ast
+) extends WdlCall(alias, task, inputMappings, ast) {
   override val callType = "call"
 }
-case class WdlWorkflowCall(override val alias: Option[String], calledWorkflow: WdlWorkflow, override val inputMappings: Map[String, WdlExpression], override val ast: Ast) extends WdlCall(alias, calledWorkflow, inputMappings, ast) {
+case class WdlWorkflowCall(override val alias: Option[String],
+                           calledWorkflow: WdlWorkflow,
+                           override val inputMappings: Map[String, WdlExpression],
+                           override val ast: Ast
+) extends WdlCall(alias, calledWorkflow, inputMappings, ast) {
   override val callType = "workflow"
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlExpression.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlExpression.scala
index 14e32d76ce0..0784371cdfe 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlExpression.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlExpression.scala
@@ -47,9 +47,11 @@ object WdlExpression {
     def isMapLiteral: Boolean = ast.getName == "MapLiteral"
     def isObjectLiteral: Boolean = ast.getName == "ObjectLiteral"
     def isArrayOrMapLookup: Boolean = ast.getName == "ArrayOrMapLookup"
-    def params: Vector[AstNode] = Option(ast.getAttribute("params")).map(_.asInstanceOf[AstList].asScala.toVector).getOrElse(Vector.empty)
+    def params: Vector[AstNode] =
+      Option(ast.getAttribute("params")).map(_.asInstanceOf[AstList].asScala.toVector).getOrElse(Vector.empty)
     def name = ast.getAttribute("name").asInstanceOf[Terminal].getSourceString
-    def isFunctionCallWithFirstParameterBeingFile = ast.isFunctionCall && ast.params.nonEmpty && WdlFunctionsWithFirstParameterBeingFile.contains(ast.functionName)
+    def isFunctionCallWithFirstParameterBeingFile =
+      ast.isFunctionCall && ast.params.nonEmpty && WdlFunctionsWithFirstParameterBeingFile.contains(ast.functionName)
     def isGlobFunctionCall = ast.isFunctionCall && ast.params.size == 1 && "glob".equals(ast.functionName)
   }
 
@@ -76,9 +78,19 @@ object WdlExpression {
   type ScopedLookupFunction = String => WomValue
 
   val BinaryOperators = Set(
-    "Add", "Subtract", "Multiply", "Divide", "Remainder",
-    "GreaterThan", "LessThan", "GreaterThanOrEqual", "LessThanOrEqual",
-    "Equals", "NotEquals", "LogicalAnd", "LogicalOr"
+    "Add",
+    "Subtract",
+    "Multiply",
+    "Divide",
+    "Remainder",
+    "GreaterThan",
+    "LessThan",
+    "GreaterThanOrEqual",
+    "LessThanOrEqual",
+    "Equals",
+    "NotEquals",
+    "LogicalAnd",
+    "LogicalOr"
   )
 
   val UnaryOperators = Set("LogicalNot", "UnaryPlus", "UnaryNegation")
@@ -100,24 +112,33 @@ object WdlExpression {
   def evaluate(ast: AstNode, lookup: ScopedLookupFunction, functions: WdlFunctions[WomValue]): Try[WomValue] =
     ValueEvaluator(lookup, functions).evaluate(ast)
 
-  def evaluateFiles(ast: AstNode, lookup: ScopedLookupFunction, functions: WdlFunctions[WomValue], coerceTo: WomType = WomAnyType) =
+  def evaluateFiles(ast: AstNode,
+                    lookup: ScopedLookupFunction,
+                    functions: WdlFunctions[WomValue],
+                    coerceTo: WomType = WomAnyType
+  ) =
     FileEvaluator(ValueEvaluator(lookup, functions), coerceTo).evaluate(ast)
 
-  def evaluateType(ast: AstNode, lookup: (String) => WomType, functions: WdlFunctions[WomType], from: Option[Scope] = None) =
+  def evaluateType(ast: AstNode,
+                   lookup: (String) => WomType,
+                   functions: WdlFunctions[WomType],
+                   from: Option[Scope] = None
+  ) =
     TypeEvaluator(lookup, functions, from).evaluate(ast)
 
   def fromString(expression: WorkflowSource): WdlExpression = {
     val tokens = parser.lex(expression, "string")
-    val terminalMap = (tokens.asScala.toVector map {(_, expression)}).toMap
+    val terminalMap = (tokens.asScala.toVector map { (_, expression) }).toMap
     val parseTree = parser.parse_e(tokens, WdlSyntaxErrorFormatter(terminalMap))
     new WdlExpression(parseTree.toAst)
   }
 
-  def toString(ast: AstNode, highlighter: SyntaxHighlighter = NullSyntaxHighlighter): String = {
+  def toString(ast: AstNode, highlighter: SyntaxHighlighter = NullSyntaxHighlighter): String =
     ast match {
-      case t: Terminal if Seq("identifier", "integer", "float", "boolean").contains(t.getTerminalStr) => t.getSourceString
+      case t: Terminal if Seq("identifier", "integer", "float", "boolean").contains(t.getTerminalStr) =>
+        t.getSourceString
       case t: Terminal if t.getTerminalStr == "string" => s""""${t.getSourceString.replaceAll("\"", "\\" + "\"")}""""
-      case a:Ast if a.isBinaryOperator =>
+      case a: Ast if a.isBinaryOperator =>
         val lhs = Option(a.getAttribute("lhs")).map(toString(_, highlighter)).getOrElse("")
         val rhs = Option(a.getAttribute("rhs")).map(toString(_, highlighter)).getOrElse("")
         a.getName match {
@@ -148,10 +169,10 @@ object WdlExpression {
         val f = toString(ifFalse, highlighter)
         s"if $c then $t else $f"
       case a: Ast if a.isArrayLiteral =>
-        val evaluatedElements = a.getAttribute("values").astListAsVector map {x => toString(x, highlighter)}
+        val evaluatedElements = a.getAttribute("values").astListAsVector map { x => toString(x, highlighter) }
         s"[${evaluatedElements.mkString(", ")}]"
       case a: Ast if a.isTupleLiteral =>
-        val evaluatedElements = a.getAttribute("values").astListAsVector map { x => toString(x, highlighter)}
+        val evaluatedElements = a.getAttribute("values").astListAsVector map { x => toString(x, highlighter) }
         s"(${evaluatedElements.mkString(", ")})"
       case a: Ast if a.isMapLiteral =>
         val evaluatedMap = a.getAttribute("map").astListAsVector map { kv =>
@@ -179,7 +200,6 @@ object WdlExpression {
         val params = a.params map { a => toString(a, highlighter) }
         s"${highlighter.function(a.name)}(${params.mkString(", ")})"
     }
-  }
 }
 
 case class WdlExpression(ast: AstNode) extends WomValue {
@@ -188,23 +208,27 @@ case class WdlExpression(ast: AstNode) extends WomValue {
   def evaluate(lookup: ScopedLookupFunction, functions: WdlFunctions[WomValue]): Try[WomValue] =
     WdlExpression.evaluate(ast, lookup, functions)
 
-  def evaluateFiles(lookup: ScopedLookupFunction, functions: WdlFunctions[WomValue], coerceTo: WomType): Try[Seq[WomFile]] =
+  def evaluateFiles(lookup: ScopedLookupFunction,
+                    functions: WdlFunctions[WomValue],
+                    coerceTo: WomType
+  ): Try[Seq[WomFile]] =
     WdlExpression.evaluateFiles(ast, lookup, functions, coerceTo)
 
-  def evaluateType(lookup: String => WomType, functions: WdlFunctions[WomType], from: Option[Scope] = None): Try[WomType] =
+  def evaluateType(lookup: String => WomType,
+                   functions: WdlFunctions[WomType],
+                   from: Option[Scope] = None
+  ): Try[WomType] =
     WdlExpression.evaluateType(ast, lookup, functions, from)
 
   def containsFunctionCall = ast.containsFunctionCalls
 
-  def toString(highlighter: SyntaxHighlighter): String = {
+  def toString(highlighter: SyntaxHighlighter): String =
     WdlExpression.toString(ast, highlighter)
-  }
 
   override def toWomString: String = toString(NullSyntaxHighlighter)
 
-  def prerequisiteCallNames: Set[String] = {
+  def prerequisiteCallNames: Set[String] =
     this.topLevelMemberAccesses map { _.lhsString }
-  }
   def topLevelMemberAccesses: Set[MemberAccess] = AstTools.findTopLevelMemberAccesses(ast) map { MemberAccess(_) } toSet
   def variableReferences(from: Scope): Iterable[VariableReference] = AstTools.findVariableReferences(ast, from)
 }
@@ -220,7 +244,8 @@ final case class WdlWomExpression(wdlExpression: WdlExpression, from: Scope) ext
   override def inputs: Set[String] = wdlExpression.variableReferences(from) map { _.referencedVariableName } toSet
 
   override def evaluateValue(variableValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = {
-    lazy val wdlFunctions = WdlStandardLibraryFunctions.fromIoFunctionSet(ioFunctionSet, FileSizeLimitationConfig.fileSizeLimitationConfig)
+    lazy val wdlFunctions =
+      WdlStandardLibraryFunctions.fromIoFunctionSet(ioFunctionSet, FileSizeLimitationConfig.fileSizeLimitationConfig)
     wdlExpression.evaluate(variableValues.apply, wdlFunctions).toErrorOr
   }
 
@@ -229,26 +254,42 @@ final case class WdlWomExpression(wdlExpression: WdlExpression, from: Scope) ext
     // case in the brave new WOM-world.
     wdlExpression.evaluateType(inputTypes.apply, new WdlStandardLibraryFunctionsType, Option(from)).toErrorOr
 
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
+  override def evaluateFiles(inputTypes: Map[String, WomValue],
+                             ioFunctionSet: IoFunctionSet,
+                             coerceTo: WomType
+  ): ErrorOr[Set[FileEvaluation]] = {
     lazy val wdlFunctions = new WdlStandardLibraryFunctions {
 
-      override def readFile(path: String, sizeLimit: Int): String = Await.result(ioFunctionSet.readFile(path, Option(sizeLimit), failOnOverflow = true), Duration.Inf)
+      override def readFile(path: String, sizeLimit: Int): String =
+        Await.result(ioFunctionSet.readFile(path, Option(sizeLimit), failOnOverflow = true), Duration.Inf)
 
-      override def writeFile(path: String, content: String): Try[WomFile] = Try(Await.result(ioFunctionSet.writeFile(path, content), Duration.Inf))
+      override def writeFile(path: String, content: String): Try[WomFile] = Try(
+        Await.result(ioFunctionSet.writeFile(path, content), Duration.Inf)
+      )
 
-      override def stdout(params: Seq[Try[WomValue]]): Try[WomFile] = Success(WomSingleFile(ioFunctionSet.pathFunctions.stdout))
+      override def stdout(params: Seq[Try[WomValue]]): Try[WomFile] = Success(
+        WomSingleFile(ioFunctionSet.pathFunctions.stdout)
+      )
 
-      override def stderr(params: Seq[Try[WomValue]]): Try[WomFile] = Success(WomSingleFile(ioFunctionSet.pathFunctions.stderr))
+      override def stderr(params: Seq[Try[WomValue]]): Try[WomFile] = Success(
+        WomSingleFile(ioFunctionSet.pathFunctions.stderr)
+      )
 
       override def globHelper(pattern: String): Seq[String] = Await.result(ioFunctionSet.glob(pattern), Duration.Inf)
 
-      override def size(params: Seq[Try[WomValue]]): Try[WomFloat] = Failure(new Exception("You shouldn't call 'size' from a FileEvaluator"))
+      override def size(params: Seq[Try[WomValue]]): Try[WomFloat] = Failure(
+        new Exception("You shouldn't call 'size' from a FileEvaluator")
+      )
 
-      override protected val fileSizeLimitationConfig: FileSizeLimitationConfig = FileSizeLimitationConfig.fileSizeLimitationConfig
+      override protected val fileSizeLimitationConfig: FileSizeLimitationConfig =
+        FileSizeLimitationConfig.fileSizeLimitationConfig
     }
-    wdlExpression.evaluateFiles(inputTypes.apply, wdlFunctions, coerceTo).toErrorOr.map(_.toSet[WomFile] map { file =>
-      FileEvaluation(file, optional = areAllFileTypesInWomTypeOptional(coerceTo), secondary = false)
-    })
+    wdlExpression
+      .evaluateFiles(inputTypes.apply, wdlFunctions, coerceTo)
+      .toErrorOr
+      .map(_.toSet[WomFile] map { file =>
+        FileEvaluation(file, optional = areAllFileTypesInWomTypeOptional(coerceTo), secondary = false)
+      })
   }
 }
 
@@ -263,7 +304,8 @@ object WdlWomExpression {
                               innerLookup: Map[String, GraphNodePort.OutputPort],
                               outerLookup: Map[String, GraphNodePort.OutputPort],
                               preserveIndexForOuterLookups: Boolean,
-                              owningScope: Scope): ErrorOr[Map[String, GraphNodePort.OutputPort]] = {
+                              owningScope: Scope
+  ): ErrorOr[Map[String, GraphNodePort.OutputPort]] = {
 
     def resolveVariable(v: AstTools.VariableReference): ErrorOr[(String, GraphNodePort.OutputPort)] = {
       val name = v.referencedVariableName
@@ -272,8 +314,11 @@ object WdlWomExpression {
           // If we can find the value locally, use it.
           // It might be a local value or it might be an OGIN already created by another Node for an outerLookup.
           Valid(name -> port)
-        case (None, Some(port)) => Valid(name -> OuterGraphInputNode(WomIdentifier(name), port, preserveIndexForOuterLookups).singleOutputPort)
-        case (None, None) => s"No input $name found evaluating inputs for expression ${expression.wdlExpression.toWomString} in (${(innerLookup.keys ++ outerLookup.keys).mkString(", ")})".invalidNel
+        case (None, Some(port)) =>
+          Valid(name -> OuterGraphInputNode(WomIdentifier(name), port, preserveIndexForOuterLookups).singleOutputPort)
+        case (None, None) =>
+          s"No input $name found evaluating inputs for expression ${expression.wdlExpression.toWomString} in (${(innerLookup.keys ++ outerLookup.keys)
+              .mkString(", ")})".invalidNel
       }
     }
 
@@ -288,21 +333,22 @@ object WdlWomExpression {
                                                               outerLookup: Map[String, GraphNodePort.OutputPort],
                                                               preserveIndexForOuterLookups: Boolean,
                                                               owningScope: Scope,
-                                                              constructor: AnonymousExpressionConstructor[T]): ErrorOr[T] = {
+                                                              constructor: AnonymousExpressionConstructor[T]
+  ): ErrorOr[T] = {
     import common.validation.ErrorOr.ShortCircuitingFlatMap
 
-    findInputsforExpression(expression, innerLookup, outerLookup, preserveIndexForOuterLookups, owningScope) flatMap { resolvedVariables =>
-      AnonymousExpressionNode.fromInputMapping(nodeIdentifier, expression, resolvedVariables, constructor)
+    findInputsforExpression(expression, innerLookup, outerLookup, preserveIndexForOuterLookups, owningScope) flatMap {
+      resolvedVariables =>
+        AnonymousExpressionNode.fromInputMapping(nodeIdentifier, expression, resolvedVariables, constructor)
     }
   }
 }
 
 object TernaryIf {
-  def unapply(arg: Ast): Option[(AstNode, AstNode, AstNode)] = {
+  def unapply(arg: Ast): Option[(AstNode, AstNode, AstNode)] =
     if (arg.getName.equals("TernaryIf")) {
       Option((arg.getAttribute("cond"), arg.getAttribute("iftrue"), arg.getAttribute("iffalse")))
     } else {
       None
     }
-  }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlGraphNode.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlGraphNode.scala
index a2c4eaaf9fa..b833dfeeca3 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlGraphNode.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlGraphNode.scala
@@ -3,7 +3,6 @@ package wdl.draft2.model
 import common.collections.EnhancedCollections._
 import wdl.draft2.model.AstTools.{EnhancedAstNode, VariableReference}
 
-
 sealed trait WdlGraphNode extends Scope {
 
   /**
@@ -19,9 +18,9 @@ sealed trait WdlGraphNode extends Scope {
   final lazy val upstream: Set[WdlGraphNode] = {
     // If we are inside the scope of another graph node (i.e. via document element ancestry), then
     // that is also upstream of us.
-    val closestScopedAncestor = ancestry.collectFirst({
-      case ancestor: WdlGraphNode => ancestor
-    })
+    val closestScopedAncestor = ancestry.collectFirst { case ancestor: WdlGraphNode =>
+      ancestor
+    }
 
     // We want:
     // - Nodes that this node references
@@ -30,21 +29,20 @@ sealed trait WdlGraphNode extends Scope {
     // But because our children's upstream might also include these (which we don't want), filter out:
     // - This
     // - Any other WdlGraphNode descendants of this
-    (referencedNodes ++ closestScopedAncestor.toSeq ++ childGraphNodes.flatMap(_.upstream)).toSet - this -- descendants.filterByType[WdlGraphNode]
+    (referencedNodes ++ closestScopedAncestor.toSeq ++ childGraphNodes.flatMap(_.upstream)).toSet - this -- descendants
+      .filterByType[WdlGraphNode]
   }
 
-  final lazy val downstream: Set[WdlGraphNode] = {
+  final lazy val downstream: Set[WdlGraphNode] =
     for {
-      node <- namespace.descendants.collect({
+      node <- namespace.descendants.collect {
         case n: WdlGraphNode if n.fullyQualifiedName != fullyQualifiedName => n
-      })
+      }
       if node.upstream.contains(this)
     } yield node
-  }
 
-  def isUpstreamFrom(other: WdlGraphNode): Boolean = {
+  def isUpstreamFrom(other: WdlGraphNode): Boolean =
     other.upstreamAncestry.contains(this) || (other.childGraphNodes exists isUpstreamFrom)
-  }
 }
 
 object WdlGraphNode {
@@ -59,17 +57,17 @@ trait WdlGraphNodeWithUpstreamReferences extends WdlGraphNode {
   def upstreamReferences: Iterable[VariableReference]
 
   // If we have variable reference to other graph nodes, then they are upstream from us.
-  override final def referencedNodes = for {
-      variable <- upstreamReferences
-      node <- resolveVariable(variable.terminal.sourceString)
-      if node.fullyQualifiedNameWithIndexScopes != fullyQualifiedNameWithIndexScopes
-    } yield node
+  final override def referencedNodes = for {
+    variable <- upstreamReferences
+    node <- resolveVariable(variable.terminal.sourceString)
+    if node.fullyQualifiedNameWithIndexScopes != fullyQualifiedNameWithIndexScopes
+  } yield node
 }
 
 trait WdlGraphNodeWithInputs extends WdlGraphNode {
   def inputMappings: Map[String, WdlExpression]
 
-  override final def referencedNodes = for {
+  final override def referencedNodes = for {
     expr <- inputMappings.values
     variable <- expr.variableReferences(this)
     scope <- parent
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlNamespace.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlNamespace.scala
index d1f75461a46..8691c55ab57 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlNamespace.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlNamespace.scala
@@ -23,7 +23,6 @@ import scala.jdk.CollectionConverters._
 import scala.collection.mutable
 import scala.util.{Failure, Success, Try}
 
-
 /**
   * Represents a parsed WDL file
   */
@@ -34,10 +33,10 @@ sealed trait WdlNamespace extends WomValue with Scope {
   def importedAs: Option[String] // Used when imported with `as`
   def imports: Seq[Import]
   def namespaces: Seq[WdlNamespace]
+
   /** Return this `WdlNamespace` and its child `WdlNamespace`s recursively. */
-  def allNamespacesRecursively: List[WdlNamespace] = {
+  def allNamespacesRecursively: List[WdlNamespace] =
     this +: (namespaces.toList flatMap { _.allNamespacesRecursively })
-  }
   def tasks: Seq[WdlTask]
   def workflows: Seq[WdlWorkflow]
   def terminalMap: Map[Terminal, WorkflowSource]
@@ -45,9 +44,8 @@ sealed trait WdlNamespace extends WomValue with Scope {
   override def unqualifiedName: LocallyQualifiedName = importedAs.getOrElse("")
   override def appearsInFqn: Boolean = importedAs.isDefined
   override def namespace: WdlNamespace = this
-  def resolve(fqn: FullyQualifiedName): Option[Scope] = {
+  def resolve(fqn: FullyQualifiedName): Option[Scope] =
     (descendants + this).find(d => d.fullyQualifiedName == fqn || d.fullyQualifiedNameWithIndexScopes == fqn)
-  }
   def resolveCallOrOutputOrDeclaration(fqn: FullyQualifiedName): Option[Scope] = {
     val callsAndOutputs = descendants collect {
       case c: WdlCall => c
@@ -73,7 +71,9 @@ case class WdlNamespaceWithoutWorkflow(importedAs: Option[String],
                                        ast: Ast,
                                        sourceString: String,
                                        importUri: Option[String] = None,
-                                       resolvedImportRecords: Set[ResolvedImportRecord] = Set.empty[ResolvedImportRecord]) extends WdlNamespace {
+                                       resolvedImportRecords: Set[ResolvedImportRecord] =
+                                         Set.empty[ResolvedImportRecord]
+) extends WdlNamespace {
   val workflows = Seq.empty[WdlWorkflow]
 
 }
@@ -91,7 +91,8 @@ case class WdlNamespaceWithWorkflow(importedAs: Option[String],
                                     ast: Ast,
                                     sourceString: String,
                                     importUri: Option[String] = None,
-                                    resolvedImportRecords: Set[ResolvedImportRecord] = Set.empty[ResolvedImportRecord]) extends WdlNamespace {
+                                    resolvedImportRecords: Set[ResolvedImportRecord] = Set.empty[ResolvedImportRecord]
+) extends WdlNamespace {
 
   override val workflows = Seq(workflow)
 
@@ -102,26 +103,36 @@ case class WdlNamespaceWithWorkflow(importedAs: Option[String],
     * For the declarations that have an expression attached to it already, evaluate the expression
     * and return the value. Only evaluates workflow level declarations. Other declarations will be evaluated at runtime.
     */
-  def staticDeclarationsRecursive(userInputs: WorkflowCoercedInputs, wdlFunctions: WdlStandardLibraryFunctions): Try[WorkflowCoercedInputs] = {
+  def staticDeclarationsRecursive(userInputs: WorkflowCoercedInputs,
+                                  wdlFunctions: WdlStandardLibraryFunctions
+  ): Try[WorkflowCoercedInputs] = {
     import common.exception.Aggregation._
 
-    def evalDeclaration(accumulated: Map[FullyQualifiedName, Try[WomValue]], current: Declaration): Map[FullyQualifiedName, Try[WomValue]] = {
+    def evalDeclaration(accumulated: Map[FullyQualifiedName, Try[WomValue]],
+                        current: Declaration
+    ): Map[FullyQualifiedName, Try[WomValue]] =
       current.expression match {
         case Some(expr) =>
-          val successfulAccumulated = accumulated.collect({ case (k, v) if v.isSuccess => k -> v.get })
-          val value = expr.evaluate(current.lookupFunction(successfulAccumulated ++ userInputs, wdlFunctions, NoOutputResolver, Map.empty[Scatter, Int]), wdlFunctions)
+          val successfulAccumulated = accumulated.collect { case (k, v) if v.isSuccess => k -> v.get }
+          val value = expr.evaluate(current.lookupFunction(successfulAccumulated ++ userInputs,
+                                                           wdlFunctions,
+                                                           NoOutputResolver,
+                                                           Map.empty[Scatter, Int]
+                                    ),
+                                    wdlFunctions
+          )
           val correctlyCoerced = value flatMap current.womType.coerceRawValue
           accumulated + (current.fullyQualifiedName -> correctlyCoerced)
         case None => accumulated
       }
-    }
 
     def evalScope: Map[FullyQualifiedName, Try[WomValue]] = {
-      val workflowDeclarations = children.collect({ case w: WdlWorkflow => w.declarations }).flatten
+      val workflowDeclarations = children.collect { case w: WdlWorkflow => w.declarations }.flatten
       (declarations ++ workflowDeclarations).foldLeft(Map.empty[FullyQualifiedName, Try[WomValue]])(evalDeclaration)
     }
 
-    val filteredExceptions: Set[Class[_ <: Throwable]] = Set(classOf[OutputVariableLookupException], classOf[ScatterIndexNotFound])
+    val filteredExceptions: Set[Class[_ <: Throwable]] =
+      Set(classOf[OutputVariableLookupException], classOf[ScatterIndexNotFound])
 
     // Filter out declarations for which evaluation failed because a call output variable could not be resolved, or a shard could not be found,
     // as this method is meant for pre-execution validation
@@ -153,27 +164,34 @@ object WdlNamespace {
 
   val WorkflowResourceString = "string"
 
-  def loadUsingPath(wdlFile: Path, resource: Option[String], importResolver: Option[Seq[Draft2ImportResolver]]): Try[WdlNamespace] = {
+  def loadUsingPath(wdlFile: Path,
+                    resource: Option[String],
+                    importResolver: Option[Seq[Draft2ImportResolver]]
+  ): Try[WdlNamespace] =
     load(readFile(wdlFile), resource.getOrElse(wdlFile.toString), importResolver.getOrElse(Seq(fileResolver)), None)
-  }
 
-  def loadUsingSource(workflowSource: WorkflowSource, resource: Option[String], importResolver: Option[Seq[Draft2ImportResolver]]): Try[WdlNamespace] = {
+  def loadUsingSource(workflowSource: WorkflowSource,
+                      resource: Option[String],
+                      importResolver: Option[Seq[Draft2ImportResolver]]
+  ): Try[WdlNamespace] =
     load(workflowSource, resource.getOrElse(WorkflowResourceString), importResolver.getOrElse(Seq(fileResolver)), None)
-  }
 
   private def load(workflowSource: WorkflowSource,
                    resource: String,
                    importResolver: Seq[Draft2ImportResolver],
                    importedAs: Option[String],
                    resolvedImportRecords: Set[ResolvedImportRecord] = Set.empty[ResolvedImportRecord],
-                   root: Boolean = true): Try[WdlNamespace] = Try {
+                   root: Boolean = true
+  ): Try[WdlNamespace] = Try {
     val maybeAst = Option(AstTools.getAst(workflowSource, resource))
 
     maybeAst match {
       case Some(ast) =>
         WdlNamespace(ast, resource, workflowSource, importResolver, importedAs, resolvedImportRecords, root = root)
       case None =>
-        throw new IllegalArgumentException("Could not build AST from workflow source. Source is empty or contains only comments and whitespace.")
+        throw new IllegalArgumentException(
+          "Could not build AST from workflow source. Source is empty or contains only comments and whitespace."
+        )
     }
   }
 
@@ -183,14 +201,18 @@ object WdlNamespace {
             importResolvers: Seq[Draft2ImportResolver],
             namespaceName: Option[String],
             resolvedImportRecords: Set[ResolvedImportRecord],
-            root: Boolean = false): WdlNamespace = {
+            root: Boolean = false
+  ): WdlNamespace = {
 
     val imports = for {
       importAst <- Option(ast).map(_.getAttribute("imports")).toSeq
       importStatement <- importAst.astListAsVector.map(Import(_))
     } yield importStatement
 
-    def tryResolve(str: String, remainingResolvers: Seq[Draft2ImportResolver], errors: List[Throwable]): Draft2ResolvedImportBundle = {
+    def tryResolve(str: String,
+                   remainingResolvers: Seq[Draft2ImportResolver],
+                   errors: List[Throwable]
+    ): Draft2ResolvedImportBundle =
       remainingResolvers match {
         case resolver :: tail =>
           Try(resolver(str)) match {
@@ -203,27 +225,28 @@ object WdlNamespace {
             case _ => throw ValidationException(s"Failed to import workflow $str.", errors)
           }
       }
-    }
 
     // Translates all import statements to sub-namespaces
     val namespaces: Seq[WdlNamespace] = for {
       imp <- imports
       draft2ResolvedImportBundle = tryResolve(imp.uri, importResolvers, List.empty)
-    } yield WdlNamespace.load(
-      draft2ResolvedImportBundle.source,
-      imp.uri,
-      importResolvers,
-      Option(imp.namespaceName),
-      resolvedImportRecords + draft2ResolvedImportBundle.resolvedImportRecord,
-      root = false
-    ).get
+    } yield WdlNamespace
+      .load(
+        draft2ResolvedImportBundle.source,
+        imp.uri,
+        importResolvers,
+        Option(imp.namespaceName),
+        resolvedImportRecords + draft2ResolvedImportBundle.resolvedImportRecord,
+        root = false
+      )
+      .get
 
     // Map of Terminal -> WDL Source Code so the syntax error formatter can show line numbers
     val terminalMap = AstTools.terminalMap(ast, source)
     val combinedTerminalMap = ((namespaces map { x => x.terminalMap }) ++ Seq(terminalMap)) reduce (_ ++ _)
     val wdlSyntaxErrorFormatter = WdlSyntaxErrorFormatter(combinedTerminalMap)
 
-    val topLevelAsts = ast.getAttribute("body").astListAsVector.collect({ case a: Ast => a })
+    val topLevelAsts = ast.getAttribute("body").astListAsVector.collect { case a: Ast => a }
 
     // All `task` definitions of primary workflow.
     val topLevelTasks: Seq[WdlTask] = for {
@@ -259,13 +282,18 @@ object WdlNamespace {
 
     def getChildren(scopeAst: Ast, scope: Option[Scope]): Seq[Scope] = {
       val ScopeAstNames = Seq(
-        AstNodeName.Call, AstNodeName.Workflow, AstNodeName.Namespace,
-        AstNodeName.Scatter, AstNodeName.If, AstNodeName.Declaration
+        AstNodeName.Call,
+        AstNodeName.Workflow,
+        AstNodeName.Namespace,
+        AstNodeName.Scatter,
+        AstNodeName.If,
+        AstNodeName.Declaration
       )
 
-      def getScopeAsts(root: Ast, astAttribute: String): Seq[Ast] = {
-        root.getAttribute(astAttribute).astListAsVector.collect({ case a: Ast if ScopeAstNames.contains(a.getName) => a })
-      }
+      def getScopeAsts(root: Ast, astAttribute: String): Seq[Ast] =
+        root.getAttribute(astAttribute).astListAsVector.collect {
+          case a: Ast if ScopeAstNames.contains(a.getName) => a
+        }
 
       def getTaskInputsOutputs(ast: Ast) = {
         val inputDeclarations = getScopeAsts(ast, "declarations").map(getScope(_, scope))
@@ -279,7 +307,8 @@ object WdlNamespace {
         case AstNodeName.Task => getTaskInputsOutputs(scopeAst)
         case AstNodeName.Declaration | AstNodeName.Output | AstNodeName.WorkflowOutputDeclaration => Seq.empty[Scope]
         case AstNodeName.Call =>
-          val referencedTask = findCallable(scopeAst.getAttribute("task").sourceString, namespaces, topLevelTasks ++ workflows)
+          val referencedTask =
+            findCallable(scopeAst.getAttribute("task").sourceString, namespaces, topLevelTasks ++ workflows)
           referencedTask match {
             case Some(task: WdlTask) =>
               getScopeAsts(task.ast, "declarations").map(d => getScope(d, scope))
@@ -301,45 +330,49 @@ object WdlNamespace {
       if ast.getName != AstNodeName.Task && ast.getName != AstNodeName.Workflow
     } yield ast
 
-    val children = topLevelTasks ++ namespaces ++ workflows ++ topLevelDeclarationScopes.map(ast => getScope(ast, parent = None))
+    val children =
+      topLevelTasks ++ namespaces ++ workflows ++ topLevelDeclarationScopes.map(ast => getScope(ast, parent = None))
 
     val newResolvedImportRecordsSet = resolvedImportRecords ++ namespaces.flatMap(_.resolvedImportRecords).toSet
 
     val namespace = workflows match {
-      case Nil => WdlNamespaceWithoutWorkflow(
-        importedAs = namespaceName,
-        imports = imports,
-        namespaces = namespaces,
-        tasks = topLevelTasks,
-        terminalMap = terminalMap,
-        ast = ast,
-        sourceString = source,
-        importUri = Option(uri),
-        resolvedImportRecords = newResolvedImportRecordsSet
-      )
-      case Seq(w) => WdlNamespaceWithWorkflow(
-        ast = ast,
-        workflow = w,
-        namespace = namespaceName,
-        imports = imports,
-        namespaces = namespaces,
-        tasks = topLevelTasks,
-        terminalMap = terminalMap,
-        wdlSyntaxErrorFormatter = wdlSyntaxErrorFormatter,
-        sourceString = source,
-        importUri = Option(uri),
-        resolvedImportRecords = newResolvedImportRecordsSet
-      )
-      case _ => throw new SyntaxError(wdlSyntaxErrorFormatter.tooManyWorkflows(ast.findAsts(AstNodeName.Workflow).asJava))
+      case Nil =>
+        WdlNamespaceWithoutWorkflow(
+          importedAs = namespaceName,
+          imports = imports,
+          namespaces = namespaces,
+          tasks = topLevelTasks,
+          terminalMap = terminalMap,
+          ast = ast,
+          sourceString = source,
+          importUri = Option(uri),
+          resolvedImportRecords = newResolvedImportRecordsSet
+        )
+      case Seq(w) =>
+        WdlNamespaceWithWorkflow(
+          ast = ast,
+          workflow = w,
+          namespace = namespaceName,
+          imports = imports,
+          namespaces = namespaces,
+          tasks = topLevelTasks,
+          terminalMap = terminalMap,
+          wdlSyntaxErrorFormatter = wdlSyntaxErrorFormatter,
+          sourceString = source,
+          importUri = Option(uri),
+          resolvedImportRecords = newResolvedImportRecordsSet
+        )
+      case _ =>
+        throw new SyntaxError(wdlSyntaxErrorFormatter.tooManyWorkflows(ast.findAsts(AstNodeName.Workflow).asJava))
     }
 
     // Write-once var setting for parent/child relationships
     def descendants(scope: Scope): Seq[Scope] = {
       val children = scope.children
-      val childDescendants = scope.children.flatMap({
+      val childDescendants = scope.children.flatMap {
         case _: WdlNamespace => Seq.empty
         case s => descendants(s)
-      })
+      }
       children ++ childDescendants
     }
 
@@ -359,9 +392,11 @@ object WdlNamespace {
     descendants(namespace).foreach(_.namespace = namespace)
 
     // SYNTAX CHECKS
-    val callInputSectionErrors = namespace.descendants.collect({ case c: WdlCall => c }).flatMap(
-      validateCallInputSection(_, wdlSyntaxErrorFormatter)
-    )
+    val callInputSectionErrors = namespace.descendants
+      .collect { case c: WdlCall => c }
+      .flatMap(
+        validateCallInputSection(_, wdlSyntaxErrorFormatter)
+      )
 
     val workflowOutputErrors = workflows flatMap { _.workflowCalls map { _.calledWorkflow } } collect {
       case calledWorkflow if calledWorkflow.workflowOutputWildcards.nonEmpty =>
@@ -400,37 +435,39 @@ object WdlNamespace {
       scatter <- namespace.descendants.collect { case sc: Scatter => sc }
       expression = scatter.collection
       badVariable <- referencesToAbsentValues(scatter, expression)
-    } yield new SyntaxError(wdlSyntaxErrorFormatter.scatterCollectionContainsInvalidVariableReference(scatter, badVariable))
+    } yield new SyntaxError(
+      wdlSyntaxErrorFormatter.scatterCollectionContainsInvalidVariableReference(scatter, badVariable)
+    )
 
-    def scopeNameAndTerminal(scope: Scope): (String, Terminal) = {
+    def scopeNameAndTerminal(scope: Scope): (String, Terminal) =
       scope match {
         case ns: WdlNamespace => ("Namespace", imports.find(_.uri == ns.resource).get.namespaceTerminal)
         case s: Scope => (s.getClass.getSimpleName, s.ast.findFirstTerminal.get)
       }
-    }
 
     case class ScopeAccumulator(accumulated: Seq[Scope] = Seq.empty, errors: Seq[String] = Seq.empty)
 
-    def lookForDuplicates(scopes: Iterable[Scope]) = {
+    def lookForDuplicates(scopes: Iterable[Scope]) =
       scopes.foldLeft(ScopeAccumulator()) { (acc, cur) =>
         val possibleError = acc.accumulated.find(_.unqualifiedName == cur.unqualifiedName) map { duplicate =>
           val (dupName, dupTerminal) = scopeNameAndTerminal(duplicate)
           val (curName, curTerminal) = scopeNameAndTerminal(cur)
           wdlSyntaxErrorFormatter.twoSiblingScopesHaveTheSameName(
-            dupName, dupTerminal, curName, curTerminal
+            dupName,
+            dupTerminal,
+            curName,
+            curTerminal
           )
         }
         ScopeAccumulator(acc.accumulated :+ cur, acc.errors ++ possibleError.toSeq)
       }
-    }
 
     val scopeDuplicationErrors = (namespace.descendants + namespace) collect {
       case scope if scope.namespace == namespace => lookForDuplicates(scope.children)
     }
 
-    val expandedWorkflowOutputsDuplicationErrors = {
+    val expandedWorkflowOutputsDuplicationErrors =
       (namespace.descendants + namespace) collect { case workflow: WdlWorkflow => lookForDuplicates(workflow.outputs) }
-    }
 
     val accumulatedErrors = expandedWorkflowOutputsDuplicationErrors ++ scopeDuplicationErrors
 
@@ -438,14 +475,20 @@ object WdlNamespace {
 
     val taskCommandReferenceErrors = for {
       task <- namespace.tasks
-      param <- task.commandTemplate.collect({ case p: ParameterCommandPart => p })
+      param <- task.commandTemplate.collect { case p: ParameterCommandPart => p }
       variable <- param.expression.variableReferences(task)
       if !task.declarations.map(_.unqualifiedName).contains(variable.terminal.getSourceString)
-    } yield new SyntaxError(wdlSyntaxErrorFormatter.commandExpressionContainsInvalidVariableReference(task.ast.getAttribute("name").asInstanceOf[Terminal], variable.terminal))
+    } yield new SyntaxError(
+      wdlSyntaxErrorFormatter.commandExpressionContainsInvalidVariableReference(
+        task.ast.getAttribute("name").asInstanceOf[Terminal],
+        variable.terminal
+      )
+    )
 
-    val all = workflowOutputErrors ++ declarationErrors ++ runtimeErrors ++ scatterErrors ++ callInputSectionErrors ++ taskCommandReferenceErrors ++ duplicateSiblingScopeNameErrors
+    val all =
+      workflowOutputErrors ++ declarationErrors ++ runtimeErrors ++ scatterErrors ++ callInputSectionErrors ++ taskCommandReferenceErrors ++ duplicateSiblingScopeNameErrors
 
-    all.sortWith({ case (l, r) => l.getMessage < r.getMessage }) match {
+    all.sortWith { case (l, r) => l.getMessage < r.getMessage } match {
       case s: Seq[SyntaxError] if s.nonEmpty => throw s.head
       case _ =>
     }
@@ -453,37 +496,46 @@ object WdlNamespace {
     namespace
   }
 
-  private def getDecls(scope: Scope): Seq[DeclarationInterface] = {
+  private def getDecls(scope: Scope): Seq[DeclarationInterface] =
     scope match {
       case t: WdlTask => t.declarations ++ t.outputs
       case w: WdlWorkflow => w.declarations ++ w.outputs
       case s => s.declarations
     }
-  }
 
-  private def declarationName(declarationAst: Ast): Terminal = declarationAst.getAttribute("name").asInstanceOf[Terminal]
+  private def declarationName(declarationAst: Ast): Terminal =
+    declarationAst.getAttribute("name").asInstanceOf[Terminal]
 
   /**
     * Determine the list of references in this expression to values which were never declared
     */
   private def referencesToAbsentValues(container: Scope, expression: WdlExpression): Iterable[Terminal] =
-    expression.variableReferences(container) collect { case variable if container.resolveVariable(variable.terminal.sourceString).isEmpty => variable.terminal }
+    expression.variableReferences(container) collect {
+      case variable if container.resolveVariable(variable.terminal.sourceString).isEmpty => variable.terminal
+    }
 
-  private def validateDeclaration(declaration: DeclarationInterface, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter): Seq[SyntaxError] = {
+  private def validateDeclaration(declaration: DeclarationInterface,
+                                  wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter
+  ): Seq[SyntaxError] = {
     val invalidVariableReferences = for {
       expr <- declaration.expression.toSeq
       variable <- referencesToAbsentValues(declaration, expr)
-    } yield new SyntaxError(wdlSyntaxErrorFormatter.declarationContainsReferenceToAbsentValue(
-      declaration.parent,
-      variable
-    ))
+    } yield new SyntaxError(
+      wdlSyntaxErrorFormatter.declarationContainsReferenceToAbsentValue(
+        declaration.parent,
+        variable
+      )
+    )
 
     val typeMismatches = typeCheckDeclaration(declaration, wdlSyntaxErrorFormatter).toSeq
 
     invalidVariableReferences ++ typeMismatches
   }
 
-  private def validateRuntime(attributeExpression: WdlExpression, task: WdlTask, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter): Seq[SyntaxError] = {
+  private def validateRuntime(attributeExpression: WdlExpression,
+                              task: WdlTask,
+                              wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter
+  ): Seq[SyntaxError] = {
     val invalidVariableReferences = for {
       variable <- referencesToAbsentValues(task, attributeExpression)
     } yield new SyntaxError(wdlSyntaxErrorFormatter.declarationContainsReferenceToAbsentValue(Option(task), variable))
@@ -491,50 +543,80 @@ object WdlNamespace {
     invalidVariableReferences.toSeq
   }
 
-  private [wdl] def lookupType(from: Scope)(n: String): WomType = {
+  private[wdl] def lookupType(from: Scope)(n: String): WomType = {
     val resolved = from.resolveVariable(n)
     resolved match {
       case Some(d: DeclarationInterface) => d.relativeWdlType(from)
       case Some(c: WdlCall) => WdlCallOutputsObjectType(c)
-      case Some(s: Scatter) => s.collection.evaluateType(lookupType(s), new WdlStandardLibraryFunctionsType, Option(from)) match {
-        case Success(WomArrayType(aType)) => aType
-        // We don't need to check for a WOM map type, because
-        // of the custom unapply in object WomArrayType
-        case _ => throw new VariableLookupException(s"Variable $n references a scatter block ${s.fullyQualifiedName}, but the collection does not evaluate to an array")
-      }
+      case Some(s: Scatter) =>
+        s.collection.evaluateType(lookupType(s), new WdlStandardLibraryFunctionsType, Option(from)) match {
+          case Success(WomArrayType(aType)) => aType
+          // We don't need to check for a WOM map type, because
+          // of the custom unapply in object WomArrayType
+          case _ =>
+            throw new VariableLookupException(
+              s"Variable $n references a scatter block ${s.fullyQualifiedName}, but the collection does not evaluate to an array"
+            )
+        }
       case Some(_: WdlNamespace) => WdlNamespaceType
       case _ => throw new VariableLookupException(s"Could not resolve $n from scope ${from.fullyQualifiedName}")
     }
   }
 
-  private def typeCheckDeclaration(decl: DeclarationInterface, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter): Option[SyntaxError] = {
+  private def typeCheckDeclaration(decl: DeclarationInterface,
+                                   wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter
+  ): Option[SyntaxError] =
     decl.expression flatMap { expr =>
       expr.evaluateType(lookupType(decl), new WdlStandardLibraryFunctionsType, Option(decl)) match {
         case Success(womType) =>
           if (!decl.womType.isCoerceableFrom(womType)) {
-            Option(new SyntaxError(wdlSyntaxErrorFormatter.taskOutputExpressionTypeDoesNotMatchDeclaredType(
-              declarationName(decl.ast), decl.womType, womType
-            )))
+            Option(
+              new SyntaxError(
+                wdlSyntaxErrorFormatter.taskOutputExpressionTypeDoesNotMatchDeclaredType(
+                  declarationName(decl.ast),
+                  decl.womType,
+                  womType
+                )
+              )
+            )
           } else {
             expr.evaluate(NoLookup, NoFunctions) match {
               case Success(value) if decl.womType.coerceRawValue(value).isFailure =>
-                Option(new SyntaxError(wdlSyntaxErrorFormatter.declarationExpressionNotCoerceableToTargetType(declarationName(decl.ast), decl.womType, value.womType)))
+                Option(
+                  new SyntaxError(
+                    wdlSyntaxErrorFormatter.declarationExpressionNotCoerceableToTargetType(declarationName(decl.ast),
+                                                                                           decl.womType,
+                                                                                           value.womType
+                    )
+                  )
+                )
               case _ => None
             }
           }
         case Failure(_) => None
       }
     }
-  }
 
-  private def validateCallInputSection(call: WdlCall, wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter): Seq[SyntaxError] = {
+  private def validateCallInputSection(call: WdlCall,
+                                       wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter
+  ): Seq[SyntaxError] = {
     val callInputSections = AstTools.callInputSectionIOMappings(call.ast, wdlSyntaxErrorFormatter)
 
     val invalidCallInputReferences = callInputSections flatMap { ast =>
       val lhs = ast.getAttribute("key").sourceString
       call.callable.inputNames.find(_ == lhs) match {
         case Some(_) => None
-        case None => Option(new SyntaxError(wdlSyntaxErrorFormatter.callReferencesAbsentTaskInput(ast, call.callable.ast, lhs, call.unqualifiedName, call.isInstanceOf[WdlWorkflowCall])))
+        case None =>
+          Option(
+            new SyntaxError(
+              wdlSyntaxErrorFormatter.callReferencesAbsentTaskInput(ast,
+                                                                    call.callable.ast,
+                                                                    lhs,
+                                                                    call.unqualifiedName,
+                                                                    call.isInstanceOf[WdlWorkflowCall]
+              )
+            )
+          )
       }
     }
 
@@ -552,24 +634,32 @@ object WdlNamespace {
         case Some(s: Scatter) =>
           s.collection.evaluateType(lookupType(s), new WdlStandardLibraryFunctionsType) map {
             case WomArrayType(WomObjectType) => None
-            case WomArrayType(_: WomPairType) if memberAccess.rhsString == "left" || memberAccess.rhsString == "right" => None
+            case WomArrayType(_: WomPairType)
+                if memberAccess.rhsString == "left" || memberAccess.rhsString == "right" =>
+              None
             // Maps get coerced into arrays of pairs, so this is also ok:
             case _: WomMapType if memberAccess.rhsString == "left" || memberAccess.rhsString == "right" => None
-            case other => Option(new SyntaxError(wdlSyntaxErrorFormatter.badTargetTypeForMemberAccess(memberAccess, other)))
+            case other =>
+              Option(new SyntaxError(wdlSyntaxErrorFormatter.badTargetTypeForMemberAccess(memberAccess, other)))
           } getOrElse None
-        case Some(d: DeclarationInterface) => d.womType match {
-          case _: WomPairType if memberAccess.rhsString == "left" || memberAccess.rhsString == "right" => None
-          case WomObjectType => None
-          case other => Option(new SyntaxError(wdlSyntaxErrorFormatter.badTargetTypeForMemberAccess(memberAccess, other)))
-        }
-        case Some(other) => Option(new SyntaxError(wdlSyntaxErrorFormatter.badTargetScopeForMemberAccess(memberAccess, other)))
-        case None => None
+        case Some(d: DeclarationInterface) =>
+          d.womType match {
+            case _: WomPairType if memberAccess.rhsString == "left" || memberAccess.rhsString == "right" => None
+            case WomObjectType => None
+            case other =>
+              Option(new SyntaxError(wdlSyntaxErrorFormatter.badTargetTypeForMemberAccess(memberAccess, other)))
+          }
+        case Some(other) =>
+          Option(new SyntaxError(wdlSyntaxErrorFormatter.badTargetScopeForMemberAccess(memberAccess, other)))
+        case None =>
+          None
           // In cases where there are many member accesses in the same Ast, it might be we can look up one layer but
           // not an inner layer.
           // It looks like we couldn't find this layer, so check whether there's an outer layer we can test access
           // for instead.
           memberAccess.lhsAst match {
-            case outerMemberAccessAst: Ast if outerMemberAccessAst.getName == "MemberAccess" => checkValidityOfMemberAccess(outerMemberAccessAst)
+            case outerMemberAccessAst: Ast if outerMemberAccessAst.getName == "MemberAccess" =>
+              checkValidityOfMemberAccess(outerMemberAccessAst)
             case _ => Option(new SyntaxError(wdlSyntaxErrorFormatter.noTargetForMemberAccess(memberAccess)))
           }
       }
@@ -594,18 +684,17 @@ object WdlNamespace {
     * Given a name, a collection of WdlNamespaces and a collection of Tasks, this method will attempt to find
     * a Task with that name within those collections.
     */
-  def findTask(name: String, namespaces: Seq[WdlNamespace], tasks: Seq[WdlTask]): Option[WdlTask] = {
+  def findTask(name: String, namespaces: Seq[WdlNamespace], tasks: Seq[WdlTask]): Option[WdlTask] =
     findCallable(name, namespaces, tasks) collect { case t: WdlTask => t }
-  }
 
-  def findCallable(name: String, namespaces: Seq[WdlNamespace], callables: Seq[WdlCallable]): Option[WdlCallable] = {
+  def findCallable(name: String, namespaces: Seq[WdlNamespace], callables: Seq[WdlCallable]): Option[WdlCallable] =
     if (name.contains(".")) {
       val parts = name.split("\\.", 2)
 
-      namespaces find (_.importedAs.contains(parts(0))) flatMap { x => findCallable(parts(1), x.namespaces, x.workflows ++ x.tasks) }
+      namespaces find (_.importedAs.contains(parts(0))) flatMap { x =>
+        findCallable(parts(1), x.namespaces, x.workflows ++ x.tasks)
+      }
     } else callables.find(_.unqualifiedName == name)
-  }
-
 
   private def readFile(wdlFile: Path): WorkflowSource = File(wdlFile).contentAsString
 
@@ -626,38 +715,52 @@ object WdlNamespace {
 }
 
 object WdlNamespaceWithWorkflow {
-  def load(workflowSource: WorkflowSource, importsResolvers: Seq[Draft2ImportResolver]): Try[WdlNamespaceWithWorkflow] = {
+  def load(workflowSource: WorkflowSource, importsResolvers: Seq[Draft2ImportResolver]): Try[WdlNamespaceWithWorkflow] =
     from(WdlNamespace.loadUsingSource(workflowSource, None, Option(importsResolvers)))
-  }
 
-  @deprecated("To avoid unexpected default resolutions, I recommend using the load(String, Seq[ImportResolver] method of loading.", "23")
-  def load(workflowSource: WorkflowSource): Try[WdlNamespaceWithWorkflow] = from(WdlNamespace.loadUsingSource(workflowSource, None, None))
-
-  @deprecated("To avoid unexpected default resolutions, I recommend using the load(String, Seq[ImportResolver] method of loading.", "23")
+  @deprecated(
+    "To avoid unexpected default resolutions, I recommend using the load(String, Seq[ImportResolver] method of loading.",
+    "23"
+  )
+  def load(workflowSource: WorkflowSource): Try[WdlNamespaceWithWorkflow] = from(
+    WdlNamespace.loadUsingSource(workflowSource, None, None)
+  )
+
+  @deprecated(
+    "To avoid unexpected default resolutions, I recommend using the load(String, Seq[ImportResolver] method of loading.",
+    "23"
+  )
   def load(workflowSource: WorkflowSource, importsDirectory: File): Try[WdlNamespaceWithWorkflow] = {
-    val resolvers: Seq[Draft2ImportResolver] = Seq(WdlNamespace.directoryResolver(importsDirectory), WdlNamespace.fileResolver)
+    val resolvers: Seq[Draft2ImportResolver] =
+      Seq(WdlNamespace.directoryResolver(importsDirectory), WdlNamespace.fileResolver)
     load(workflowSource, resolvers)
   }
 
-  @deprecated("To avoid unexpected default resolutions, I recommend using the load(String, Seq[ImportResolver] method of loading.", "23")
-  def load(wdlFile: Path, importResolver: Draft2ImportResolver): Try[WdlNamespaceWithWorkflow] = from(WdlNamespace.loadUsingPath(wdlFile, None, Option(Seq(importResolver))))
-
-  @deprecated("To avoid unexpected default resolutions, I recommend using the load(String, Seq[ImportResolver] method of loading.", "23")
-  def load(workflowSource: WorkflowSource, importResolver: Draft2ImportResolver): Try[WdlNamespaceWithWorkflow] = {
+  @deprecated(
+    "To avoid unexpected default resolutions, I recommend using the load(String, Seq[ImportResolver] method of loading.",
+    "23"
+  )
+  def load(wdlFile: Path, importResolver: Draft2ImportResolver): Try[WdlNamespaceWithWorkflow] = from(
+    WdlNamespace.loadUsingPath(wdlFile, None, Option(Seq(importResolver)))
+  )
+
+  @deprecated(
+    "To avoid unexpected default resolutions, I recommend using the load(String, Seq[ImportResolver] method of loading.",
+    "23"
+  )
+  def load(workflowSource: WorkflowSource, importResolver: Draft2ImportResolver): Try[WdlNamespaceWithWorkflow] =
     WdlNamespaceWithWorkflow.from(WdlNamespace.loadUsingSource(workflowSource, None, Option(Seq(importResolver))))
-  }
 
   /**
     * Used to safely cast a WdlNamespace to a NamespaceWithWorkflow. Throws an IllegalArgumentException if another
     * form of WdlNamespace is passed to it
     */
-  private def from(namespace: Try[WdlNamespace]): Try[WdlNamespaceWithWorkflow] = {
+  private def from(namespace: Try[WdlNamespace]): Try[WdlNamespaceWithWorkflow] =
     namespace match {
       case Success(n: WdlNamespaceWithWorkflow) => Success(n)
       case Success(_) => Failure(new IllegalArgumentException("Namespace does not have a local workflow to run"))
       case Failure(f) => Failure(f)
     }
-  }
 
   def apply(ast: Ast,
             workflow: WdlWorkflow,
@@ -669,7 +772,18 @@ object WdlNamespaceWithWorkflow {
             wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter,
             sourceString: String,
             importUri: Option[String],
-            resolvedImportRecords: Set[ResolvedImportRecord]): WdlNamespaceWithWorkflow = {
-    new WdlNamespaceWithWorkflow(namespace, workflow, imports, namespaces, tasks, terminalMap, wdlSyntaxErrorFormatter, ast, sourceString, importUri, resolvedImportRecords)
-  }
+            resolvedImportRecords: Set[ResolvedImportRecord]
+  ): WdlNamespaceWithWorkflow =
+    new WdlNamespaceWithWorkflow(namespace,
+                                 workflow,
+                                 imports,
+                                 namespaces,
+                                 tasks,
+                                 terminalMap,
+                                 wdlSyntaxErrorFormatter,
+                                 ast,
+                                 sourceString,
+                                 importUri,
+                                 resolvedImportRecords
+    )
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlRuntimeAttributes.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlRuntimeAttributes.scala
index 84508d001c6..3b30379f281 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlRuntimeAttributes.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlRuntimeAttributes.scala
@@ -15,7 +15,8 @@ object WdlRuntimeAttributes {
   def apply(ast: Ast): WdlRuntimeAttributes = {
     val asts = ast.findAsts(AstNodeName.Runtime)
     if (asts.size > 1) throw new UnsupportedOperationException("Only one runtime block may be defined per task")
-    val kvPairAsts = asts.headOption.map(_.getAttribute("map").asInstanceOf[AstList].asScala.toVector.map(_.asInstanceOf[Ast]))
+    val kvPairAsts =
+      asts.headOption.map(_.getAttribute("map").asInstanceOf[AstList].asScala.toVector.map(_.asInstanceOf[Ast]))
     val runtimeAttributeMap: Map[String, WdlExpression] = kvPairAsts match {
       case Some(vector) => vector.map(ast => processRuntimeAttribute(ast)).toMap
       case None => Map.empty[String, WdlExpression]
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlSyntaxErrorFormatter.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlSyntaxErrorFormatter.scala
index 158037a6105..bc1a7764efd 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlSyntaxErrorFormatter.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlSyntaxErrorFormatter.scala
@@ -21,94 +21,110 @@ case class WdlSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) e
     case classicTerminal => terminalMap.get(classicTerminal)
   }
 
-  private def line(t:Terminal): String = getTerminal(t).map(_.split("\n")(t.getLine - 1)).getOrElse(s"Cannot highlight line. It was probably in an imported file.")
+  private def line(t: Terminal): String = getTerminal(t)
+    .map(_.split("\n")(t.getLine - 1))
+    .getOrElse(s"Cannot highlight line. It was probably in an imported file.")
 
-  def unexpectedEof(method: String, expected: java.util.List[TerminalIdentifier], nt_rules: java.util.List[String]): String = "ERROR: Unexpected end of file"
+  def unexpectedEof(method: String,
+                    expected: java.util.List[TerminalIdentifier],
+                    nt_rules: java.util.List[String]
+  ): String = "ERROR: Unexpected end of file"
 
-  def excessTokens(method: String, terminal: Terminal): String = {
+  def excessTokens(method: String, terminal: Terminal): String =
     s"""ERROR: Finished parsing without consuming all tokens.
-        |
-        |${pointToSource(terminal)}
+       |
+       |${pointToSource(terminal)}
      """.stripMargin
-  }
 
-  def unexpectedSymbol(method: String, actual: Terminal, expected: java.util.List[TerminalIdentifier], rule: String): String = {
+  def unexpectedSymbol(method: String,
+                       actual: Terminal,
+                       expected: java.util.List[TerminalIdentifier],
+                       rule: String
+  ): String = {
     val expectedTokens = expected.asScala.map(_.string).mkString(", ")
     s"""ERROR: Unexpected symbol (line ${actual.getLine}, col ${actual.getColumn}) when parsing '$method'.
-        |
-        |Expected $expectedTokens, got ${actual.getSourceString}.
-        |
-        |${pointToSource(actual)}
-        |
-        |$rule
+       |
+       |Expected $expectedTokens, got ${actual.getSourceString}.
+       |
+       |${pointToSource(actual)}
+       |
+       |$rule
      """.stripMargin
   }
 
-  def noMoreTokens(method: String, expecting: TerminalIdentifier, last: Terminal): String = {
+  def noMoreTokens(method: String, expecting: TerminalIdentifier, last: Terminal): String =
     s"""ERROR: No more tokens.  Expecting ${expecting.string}
-        |
-        |${pointToSource(last)}
+       |
+       |${pointToSource(last)}
      """.stripMargin
-  }
 
-  def invalidTerminal(method: String, invalid: Terminal): String = {
+  def invalidTerminal(method: String, invalid: Terminal): String =
     s"""ERROR: Invalid symbol ID: ${invalid.getId} (${invalid.getTerminalStr})
-        |
-        |${pointToSource(invalid)}
+       |
+       |${pointToSource(invalid)}
      """.stripMargin
-  }
 
   // TODO: these next two methods won't be called by the parser because there are no lists in the WDL grammar that
   // cause these to be triggered.  Currently the parser is passing in 'null' for the value of 'last' and when that
   // changes, these errors can be made more helpful.
 
-  def missingListItems(method: String, required: Int, found: Int, last: Terminal): String = {
+  def missingListItems(method: String, required: Int, found: Int, last: Terminal): String =
     s"ERROR: $method requires $required items, but only found $found"
-  }
 
-  def missingTerminator(method: String, terminal: TerminalIdentifier, last: Terminal): String = {
+  def missingTerminator(method: String, terminal: TerminalIdentifier, last: Terminal): String =
     s"ERROR: $method requires a terminator after each element"
-  }
 
   def tooManyWorkflows(workflowAsts: java.util.List[Ast]): String = {
-    val otherWorkflows = workflowAsts.asScala.map({ ast =>
-      val name: Terminal = ast.getAttribute("name").asInstanceOf[Terminal]
-      s"""Prior workflow definition (line ${name.getLine} col ${name.getColumn}):
-          |
-          |${pointToSource(name)}
+    val otherWorkflows = workflowAsts.asScala
+      .map { ast =>
+        val name: Terminal = ast.getAttribute("name").asInstanceOf[Terminal]
+        s"""Prior workflow definition (line ${name.getLine} col ${name.getColumn}):
+           |
+           |${pointToSource(name)}
        """.stripMargin
-    }).mkString("\n")
+      }
+      .mkString("\n")
 
     s"""ERROR: Only one workflow definition allowed, found ${workflowAsts.size} workflows:
-        |
-        |$otherWorkflows
+       |
+       |$otherWorkflows
      """.stripMargin
   }
 
   def duplicateTask(taskAsts: Seq[Ast]): String = {
-    val otherTasks = taskAsts.map({ ast =>
-      val name: Terminal = ast.getAttribute("name").asInstanceOf[Terminal]
-      s"""Prior task definition (line ${name.getLine} col ${name.getColumn}):
-       |
-       |${pointToSource(name)}
+    val otherTasks = taskAsts
+      .map { ast =>
+        val name: Terminal = ast.getAttribute("name").asInstanceOf[Terminal]
+        s"""Prior task definition (line ${name.getLine} col ${name.getColumn}):
+           |
+           |${pointToSource(name)}
        """.stripMargin
-    }).mkString("\n")
+      }
+      .mkString("\n")
 
-    s"""ERROR: Two tasks defined with the name '${taskAsts.head.getAttribute("name").asInstanceOf[Terminal].getSourceString}':
-     |
-     |$otherTasks
+    s"""ERROR: Two tasks defined with the name '${taskAsts.head
+        .getAttribute("name")
+        .asInstanceOf[Terminal]
+        .getSourceString}':
+       |
+       |$otherTasks
      """.stripMargin
   }
 
   def callReferencesBadTaskName(callAst: Ast, taskName: String): String = {
     val callTask: Terminal = callAst.getAttribute("task").asInstanceOf[Terminal]
     s"""ERROR: Call references a task ($taskName) that doesn't exist (line ${callTask.getLine}, col ${callTask.getColumn})
-        |
-        |${pointToSource(callTask)}
+       |
+       |${pointToSource(callTask)}
      """.stripMargin
   }
 
-  def callReferencesAbsentTaskInput(callInputAst: Ast, taskAst: Ast, missingInput: String, callName: String, forSubworkflowCall: Boolean): String = {
+  def callReferencesAbsentTaskInput(callInputAst: Ast,
+                                    taskAst: Ast,
+                                    missingInput: String,
+                                    callName: String,
+                                    forSubworkflowCall: Boolean
+  ): String = {
     val callParameter: Terminal = callInputAst.getAttribute("key").asInstanceOf[Terminal]
     val taskName: Terminal = taskAst.getAttribute("name").asInstanceOf[Terminal]
     val taskNameString = taskName.getSourceString
@@ -129,44 +145,48 @@ case class WdlSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) e
     } else { "" }
 
     s"""ERROR: Call supplied an unexpected input: The '$taskNameString' task doesn't have an input called '$missingInput':
-        |
-        |${pointToSource(callParameter)}
-        |
-        |Options:
-        | - Add the input '$missingInput' to the '$taskNameString' task (defined on line ${taskName.getLine}).$subworkflowWarning
-        | - Remove '$missingInput = ...' from $callName's inputs (on line ${callParameter.getLine}).
+       |
+       |${pointToSource(callParameter)}
+       |
+       |Options:
+       | - Add the input '$missingInput' to the '$taskNameString' task (defined on line ${taskName.getLine}).$subworkflowWarning
+       | - Remove '$missingInput = ...' from $callName's inputs (on line ${callParameter.getLine}).
      """.stripMargin
   }
 
   def taskAndNamespaceHaveSameName(taskAst: Ast, namespace: Terminal): String = {
     val taskName = taskAst.getAttribute("name").asInstanceOf[Terminal]
     s"""ERROR: Task and namespace have the same name:
-     |
-     |Task defined here (line ${taskName.getLine}, col ${taskName.getColumn}):
-     |
-     |${pointToSource(taskName)}
-     |
-     |Import statement defined here (line ${namespace.getLine}, col ${namespace.getColumn}):
-     |
-     |${pointToSource(namespace)}
+       |
+       |Task defined here (line ${taskName.getLine}, col ${taskName.getColumn}):
+       |
+       |${pointToSource(taskName)}
+       |
+       |Import statement defined here (line ${namespace.getLine}, col ${namespace.getColumn}):
+       |
+       |${pointToSource(namespace)}
      """.stripMargin
   }
 
   def workflowAndNamespaceHaveSameName(workflowAst: Ast, namespace: Terminal): String = {
     val workflowName = workflowAst.getAttribute("name").asInstanceOf[Terminal]
     s"""ERROR: Workflow and namespace have the same name:
-     |
-     |Task defined here (line ${workflowName.getLine}, col ${workflowName.getColumn}):
-     |
-     |${pointToSource(workflowName)}
-     |
-     |Import statement defined here (line ${namespace.getLine}, col ${namespace.getColumn}):
-     |
-     |${pointToSource(namespace)}
+       |
+       |Task defined here (line ${workflowName.getLine}, col ${workflowName.getColumn}):
+       |
+       |${pointToSource(workflowName)}
+       |
+       |Import statement defined here (line ${namespace.getLine}, col ${namespace.getColumn}):
+       |
+       |${pointToSource(namespace)}
      """.stripMargin
   }
 
-  def twoSiblingScopesHaveTheSameName(firstScopeType: String, firstScopeName: Terminal, secondScopeType: String, secondScopeName: Terminal): String = {
+  def twoSiblingScopesHaveTheSameName(firstScopeType: String,
+                                      firstScopeName: Terminal,
+                                      secondScopeType: String,
+                                      secondScopeName: Terminal
+  ): String =
     s"""ERROR: Sibling nodes have conflicting names:
        |
        |$firstScopeType defined here (line ${firstScopeName.getLine}, col ${firstScopeName.getColumn}):
@@ -177,13 +197,12 @@ case class WdlSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) e
        |
        |${pointToSource(secondScopeName)}
      """.stripMargin
-  }
 
   def multipleCallsAndHaveSameName(names: Seq[(String, Terminal)]): String = {
     val duplicatedCallNames = names.map { case (astType, name) =>
       s"""$astType statement here (line ${name.getLine}, column ${name.getColumn}):
-        |
-        |${pointToSource(name)}
+         |
+         |${pointToSource(name)}
       """.stripMargin
     }
 
@@ -193,28 +212,26 @@ case class WdlSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) e
      """.stripMargin
   }
 
-  def multipleInputStatementsOnCall(secondInputStatement: Terminal): String = {
+  def multipleInputStatementsOnCall(secondInputStatement: Terminal): String =
     s"""ERROR: Call has multiple 'input' sections defined:
        |
        |${pointToSource(secondInputStatement)}
        |
        |Instead of multiple 'input' sections, use commas to separate the values.
      """.stripMargin
-  }
 
-  def emptyInputSection(callTaskName: Terminal) = {
+  def emptyInputSection(callTaskName: Terminal) =
     s"""ERROR: empty "input" section for call '${callTaskName.getSourceString}':
        |
        |${pointToSource(callTaskName)}
      """.stripMargin
-  }
 
   def noTargetForMemberAccess(memberAccess: MemberAccess): String = {
     val rhsAst = memberAccess.ast.getAttribute("rhs").asInstanceOf[Terminal]
 
     s"""ERROR: Cannot find reference to '${memberAccess.lhsString}' for member access '${memberAccess.memberAccessString}' (line ${rhsAst.getLine}, col ${rhsAst.getColumn}):
-     |
-     |${pointToSource(rhsAst)}
+       |
+       |${pointToSource(rhsAst)}
      """.stripMargin
   }
 
@@ -223,7 +240,7 @@ case class WdlSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) e
 
     s"""ERROR: Bad target for member access '${memberAccess.memberAccessString}': '${memberAccess.lhsString}' was a ${unexpectedType.stableName} (line ${rhsAst.getLine}, col ${rhsAst.getColumn}):
        |
-     |${pointToSource(rhsAst)}
+       |${pointToSource(rhsAst)}
      """.stripMargin
   }
 
@@ -232,7 +249,7 @@ case class WdlSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) e
 
     s"""ERROR: Bad target for member access '${memberAccess.memberAccessString}': '${memberAccess.lhsString}' was a ${unexpectedScope.getClass.getSimpleName} (line ${rhsAst.getLine}, col ${rhsAst.getColumn}):
        |
-     |${pointToSource(rhsAst)}
+       |${pointToSource(rhsAst)}
      """.stripMargin
   }
 
@@ -240,15 +257,16 @@ case class WdlSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) e
     val rhsAst = memberAccessAst.getAttribute("rhs").asInstanceOf[Terminal]
     val memberAccess = MemberAccess(memberAccessAst)
     val taskName = call.unqualifiedName
-    val goodOutputs = s" (current outputs of '$taskName': " + call.outputs.map("'" + _.unqualifiedName + "'").mkString(", ") + ")"
+    val goodOutputs =
+      s" (current outputs of '$taskName': " + call.outputs.map("'" + _.unqualifiedName + "'").mkString(", ") + ")"
 
     s"""ERROR: Call output not found: Call '${memberAccess.lhsString}' doesn't have an output '${memberAccess.rhsString}' (line ${rhsAst.getLine}, col ${rhsAst.getColumn}).
-     |
-     |${pointToSource(rhsAst)}
-     |
-     |Options:
-     | - Add the output '${memberAccess.rhsString}' to '$taskName'.
-     | - Modify the member access (on line ${rhsAst.getLine}) to use an existing output$goodOutputs.
+       |
+       |${pointToSource(rhsAst)}
+       |
+       |Options:
+       | - Add the output '${memberAccess.rhsString}' to '$taskName'.
+       | - Modify the member access (on line ${rhsAst.getLine}) to use an existing output$goodOutputs.
      """.stripMargin
   }
 
@@ -256,104 +274,95 @@ case class WdlSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) e
     val rhsAst = ast.getAttribute("fqn").asInstanceOf[Terminal]
 
     s"""ERROR: Old style workflow output references '${rhsAst.getSourceString}' which doesn't exist (line ${rhsAst.getLine}, col ${rhsAst.getColumn}):
-        |
-        |${pointToSource(rhsAst)}
-        |""".stripMargin
+       |
+       |${pointToSource(rhsAst)}
+       |""".stripMargin
   }
 
-  def pairMustHaveExactlyTwoTypeParameters(arrayDecl: Terminal): String = {
+  def pairMustHaveExactlyTwoTypeParameters(arrayDecl: Terminal): String =
     s"""ERROR: Pair type should have exactly two parameterized types (line ${arrayDecl.getLine}, col ${arrayDecl.getColumn}):
-        |
-     |${pointToSource(arrayDecl)}
+       |
+       |${pointToSource(arrayDecl)}
      """.stripMargin
-  }
 
-  def arrayMustHaveOnlyOneTypeParameter(arrayDecl: Terminal): String = {
+  def arrayMustHaveOnlyOneTypeParameter(arrayDecl: Terminal): String =
     s"""ERROR: Array type should only have one parameterized type (line ${arrayDecl.getLine}, col ${arrayDecl.getColumn}):
-     |
-     |${pointToSource(arrayDecl)}
+       |
+       |${pointToSource(arrayDecl)}
      """.stripMargin
-  }
 
-  def mapMustHaveExactlyTwoTypeParameters(mapDecl: Terminal): String = {
+  def mapMustHaveExactlyTwoTypeParameters(mapDecl: Terminal): String =
     s"""ERROR: Map type should have two parameterized types (line ${mapDecl.getLine}, col ${mapDecl.getColumn}):
-     |
-     |${pointToSource(mapDecl)}
+       |
+       |${pointToSource(mapDecl)}
      """.stripMargin
-  }
 
-  def arrayMustHaveATypeParameter(arrayDecl: Terminal): String = {
+  def arrayMustHaveATypeParameter(arrayDecl: Terminal): String =
     s"""ERROR: Array type should have exactly one parameterized type (line ${arrayDecl.getLine}, col ${arrayDecl.getColumn}):
-     |
-     |${pointToSource(arrayDecl)}
+       |
+       |${pointToSource(arrayDecl)}
      """.stripMargin
-  }
 
-  def taskOutputExpressionTypeDoesNotMatchDeclaredType(outputName: Terminal, outputType: WomType, expressionType: WomType) = {
+  def taskOutputExpressionTypeDoesNotMatchDeclaredType(outputName: Terminal,
+                                                       outputType: WomType,
+                                                       expressionType: WomType
+  ) =
     s"""ERROR: ${outputName.getSourceString} is declared as a ${outputType.stableName} but the expression evaluates to a ${expressionType.stableName}:
        |
        |${pointToSource(outputName)}
      """.stripMargin
-  }
 
-  def declarationExpressionNotCoerceableToTargetType(declName: Terminal, declType: WomType, evaluatedType: WomType) = {
+  def declarationExpressionNotCoerceableToTargetType(declName: Terminal, declType: WomType, evaluatedType: WomType) =
     s"""ERROR: Value '${declName.getSourceString}' is declared as a '${declType.stableName}' but the expression evaluates to '${evaluatedType.stableName}':
-        |
+       |
        |${pointToSource(declName)}
      """.stripMargin
-  }
 
-  def failedToDetermineTypeOfDeclaration(declName: Terminal) = {
+  def failedToDetermineTypeOfDeclaration(declName: Terminal) =
     s"""ERROR: Could not determine type of declaration ${declName.getSourceString}:
        |
        |${pointToSource(declName)}
      """.stripMargin
-  }
 
-  def trueAndFalseAttributesAreRequired(firstAttribute: Terminal) = {
+  def trueAndFalseAttributesAreRequired(firstAttribute: Terminal) =
     s"""ERROR: Both 'true' and 'false' attributes must be specified if either is specified:
        |
        |${pointToSource(firstAttribute)}
      """.stripMargin
-  }
 
-  def expressionExpectedToBeString(key: Terminal) = {
+  def expressionExpectedToBeString(key: Terminal) =
     s"""ERROR: Value for this attribute is expected to be a string:
        |
        |${pointToSource(key)}
      """.stripMargin
-  }
 
-  def expectedAtMostOneSectionPerTask(section: String, taskName: Terminal) = {
+  def expectedAtMostOneSectionPerTask(section: String, taskName: Terminal) =
     s"""ERROR: Expecting to find at most one '$section' section in the task:
        |
        |${pointToSource(taskName)}
      """.stripMargin
-  }
 
-  def expectedExactlyOneCommandSectionPerTask(taskName: Terminal) = {
+  def expectedExactlyOneCommandSectionPerTask(taskName: Terminal) =
     s"""ERROR: Expecting to find at most one 'command' section in the task:
        |
        |${pointToSource(taskName)}
      """.stripMargin
-  }
 
-  def commandExpressionContainsInvalidVariableReference(taskName: Terminal, variable: Terminal) = {
+  def commandExpressionContainsInvalidVariableReference(taskName: Terminal, variable: Terminal) =
     s"""ERROR: Variable ${variable.getSourceString} does not reference any declaration in the task (line ${variable.getLine}, col ${variable.getColumn}):
-        |
-        |${pointToSource(variable)}
-        |
-        |Task defined here (line ${taskName.getLine}, col ${taskName.getColumn}):
-        |
-        |${pointToSource(taskName)}
+       |
+       |${pointToSource(variable)}
+       |
+       |Task defined here (line ${taskName.getLine}, col ${taskName.getColumn}):
+       |
+       |${pointToSource(taskName)}
      """.stripMargin
-  }
 
   def declarationContainsReferenceToAbsentValue(parent: Option[Scope], variable: Terminal) = {
 
     val (parentName, missingType) = parent match {
-      case Some(t: WdlTask) => (s"task '${t.unqualifiedName}'" , "value")
-      case Some(t: WdlTaskCall) => (s"task '${t.task.unqualifiedName}'" , "value")
+      case Some(t: WdlTask) => (s"task '${t.unqualifiedName}'", "value")
+      case Some(t: WdlTaskCall) => (s"task '${t.task.unqualifiedName}'", "value")
       case Some(_) => ("workflow", "value or call")
       case None => ("", "")
     }
@@ -361,7 +370,8 @@ case class WdlSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) e
     invalidVariableReference(variable, missingType, parentName)
   }
 
-  def scatterCollectionContainsInvalidVariableReference(scatter: Scatter, variable: Terminal) = invalidVariableReference(variable, "value", "workflow")
+  def scatterCollectionContainsInvalidVariableReference(scatter: Scatter, variable: Terminal) =
+    invalidVariableReference(variable, "value", "workflow")
 
   private def invalidVariableReference(variable: Terminal, missingType: String, parentName: String) =
     s"""
@@ -370,12 +380,11 @@ case class WdlSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSource]) e
        |${pointToSource(variable)}
        |""".stripMargin
 
-  def memoryRuntimeAttributeInvalid(expressionStart: Terminal) = {
+  def memoryRuntimeAttributeInvalid(expressionStart: Terminal) =
     s"""ERROR: 'memory' runtime attribute should have the format "size unit" (e.g. "8 GB").
-        |
-        |Expression starts here (line ${expressionStart.getLine}, col ${expressionStart.getColumn}):
-        |
-        |${pointToSource(expressionStart)}
+       |
+       |Expression starts here (line ${expressionStart.getLine}, col ${expressionStart.getColumn}):
+       |
+       |${pointToSource(expressionStart)}
      """.stripMargin
-  }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlTask.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlTask.scala
index 130c4b0f706..89ea5d67aab 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlTask.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlTask.scala
@@ -19,7 +19,7 @@ import scala.language.postfixOps
 
 object WdlTask {
   val Ws = Pattern.compile("[\\ \\t]+")
-  private implicit val instantiatedCommandMonoid = cats.derived.MkMonoid[InstantiatedCommand]
+  implicit private val instantiatedCommandMonoid = cats.derived.MkMonoid[InstantiatedCommand]
 
   /** The function validateDeclaration() and the DeclarationAccumulator class are used
     * to accumulate errors and keep track of which Declarations/TaskOutputs have been examined.
@@ -38,7 +38,8 @@ object WdlTask {
     val meta = AstTools.wdlSectionToStringMap(ast, AstNodeName.Meta, wdlSyntaxErrorFormatter)
     val parameterMeta = AstTools.wdlSectionToStringMap(ast, AstNodeName.ParameterMeta, wdlSyntaxErrorFormatter)
 
-    if (commandAsts.size != 1) throw new SyntaxError(wdlSyntaxErrorFormatter.expectedExactlyOneCommandSectionPerTask(taskNameTerminal))
+    if (commandAsts.size != 1)
+      throw new SyntaxError(wdlSyntaxErrorFormatter.expectedExactlyOneCommandSectionPerTask(taskNameTerminal))
     val commandTemplate = commandAsts.head.getAttribute("parts").asInstanceOf[AstList].asScala.toVector map {
       case x: Terminal => StringCommandPart(x.getSourceString)
       case x: Ast => ParameterCommandPart(x, wdlSyntaxErrorFormatter)
@@ -47,7 +48,13 @@ object WdlTask {
     WdlTask(name, commandTemplate, runtimeAttributes, meta, parameterMeta, ast)
   }
 
-  def empty: WdlTask = new WdlTask("taskName", Seq.empty, WdlRuntimeAttributes(Map.empty[String, WdlExpression]), Map.empty, Map.empty, null)
+  def empty: WdlTask = new WdlTask("taskName",
+                                   Seq.empty,
+                                   WdlRuntimeAttributes(Map.empty[String, WdlExpression]),
+                                   Map.empty,
+                                   Map.empty,
+                                   null
+  )
 
 }
 
@@ -66,7 +73,8 @@ case class WdlTask(name: String,
                    runtimeAttributes: WdlRuntimeAttributes,
                    meta: Map[String, String],
                    parameterMeta: Map[String, String],
-                   ast: Ast) extends WdlCallable {
+                   ast: Ast
+) extends WdlCallable {
 
   override val unqualifiedName: LocallyQualifiedName = name
 
@@ -111,18 +119,20 @@ case class WdlTask(name: String,
     */
   def instantiateCommand(taskInputs: EvaluatedTaskInputs,
                          functions: WdlFunctions[WomValue],
-                         valueMapper: WomValue => WomValue = identity): ErrorOr[List[InstantiatedCommand]] = {
+                         valueMapper: WomValue => WomValue = identity
+  ): ErrorOr[List[InstantiatedCommand]] = {
 
-    val mappedInputs = taskInputs.map({case (k, v) => k.unqualifiedName -> v})
+    val mappedInputs = taskInputs.map { case (k, v) => k.unqualifiedName -> v }
     // `foldMap`: `map` over the elements of the `List[WdlCommandPart]`s, transforming each `WdlCommandPart` to an
     // `ErrorOr[InstantiatedCommand]`. Then fold the resulting `List[ErrorOr[InstantiatedCommand]]` into a single
     // `ErrorOr[InstantiatedCommand]`.
     import WdlTask.instantiatedCommandMonoid
     val fullInstantiatedCommand: ErrorOr[InstantiatedCommand] = commandTemplate.toList
-      .flatTraverse(_.instantiate(declarations, mappedInputs, functions, valueMapper)).map(_.combineAll)
+      .flatTraverse(_.instantiate(declarations, mappedInputs, functions, valueMapper))
+      .map(_.combineAll)
 
     // `normalize` the instantiation (i.e. don't break Python code indentation)
-    fullInstantiatedCommand map { c => List(c.copy(commandString = StringUtil.normalize(c.commandString)))}
+    fullInstantiatedCommand map { c => List(c.copy(commandString = StringUtil.normalize(c.commandString))) }
   }
 
   def commandTemplateString: String = StringUtil.normalize(commandTemplate.map(_.toString).mkString)
@@ -139,10 +149,10 @@ case class WdlTask(name: String,
     * inputMap = Map("t.s" -> WdlString("hello"))
     */
   // TODO WOM: Unused except in Specs
-  def inputsFromMap(inputs: Map[FullyQualifiedName, WomValue]): EvaluatedTaskInputs = {
+  def inputsFromMap(inputs: Map[FullyQualifiedName, WomValue]): EvaluatedTaskInputs =
     declarations flatMap { declaration =>
       inputs collectFirst {
-        case (fqn, value) if fqn == declaration.fullyQualifiedName => declaration -> value }
+        case (fqn, value) if fqn == declaration.fullyQualifiedName => declaration -> value
+      }
     } toMap
-  }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlWorkflow.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlWorkflow.scala
index 8f92f7db363..0eeef921775 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlWorkflow.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WdlWorkflow.scala
@@ -13,10 +13,10 @@ object WdlWorkflow {
       throw new UnsupportedOperationException(s"Expecting Workflow AST, got a ${ast.getName} AST")
     }
     val name = ast.getAttribute("name").asInstanceOf[Terminal].getSourceString
-    val callNames = ast.findAsts(AstNodeName.Call).map {call =>
+    val callNames = ast.findAsts(AstNodeName.Call).map { call =>
       ("Call", Option(call.getAttribute("alias")).getOrElse(call.getAttribute("task")))
     }
-    val declarationNames = ast.findAsts(AstNodeName.Declaration).map {decl =>
+    val declarationNames = ast.findAsts(AstNodeName.Declaration).map { decl =>
       ("Declaration", decl.getAttribute("name"))
     }
 
@@ -28,7 +28,8 @@ object WdlWorkflow {
 
     (callNames ++ declarationNames) groupBy { _._2.sourceString } foreach {
       case (_, terminals) if terminals.size > 1 =>
-        val castedToTerminal = terminals map { case (astType, terminalAst) => (astType, terminalAst.asInstanceOf[Terminal])
+        val castedToTerminal = terminals map { case (astType, terminalAst) =>
+          (astType, terminalAst.asInstanceOf[Terminal])
 
         }
 
@@ -48,7 +49,8 @@ case class WdlWorkflow(unqualifiedName: String,
                        wdlSyntaxErrorFormatter: WdlSyntaxErrorFormatter,
                        meta: Map[String, String],
                        parameterMeta: Map[String, String],
-                       ast: Ast) extends WdlCallable {
+                       ast: Ast
+) extends WdlCallable {
 
   /**
     * Also include workflow outputs which are not technically children but should be processed as such
@@ -79,9 +81,13 @@ case class WdlWorkflow(unqualifiedName: String,
   /** First tries to find any Call with name `name`.  If not found,
     * Fallback to looking at immediate children or delegating to parent node
     */
-  override def resolveVariable(name: String, relativeTo: Scope = this, ignoreLocal: Boolean = false): Option[WdlGraphNode] = {
-    findCallByName(name) orElse findDeclarationByName(name) orElse findWorkflowOutputByName(name, relativeTo) orElse super.resolveVariable(name, relativeTo)
-  }
+  override def resolveVariable(name: String,
+                               relativeTo: Scope = this,
+                               ignoreLocal: Boolean = false
+  ): Option[WdlGraphNode] =
+    findCallByName(name) orElse findDeclarationByName(name) orElse findWorkflowOutputByName(name,
+                                                                                            relativeTo
+    ) orElse super.resolveVariable(name, relativeTo)
 
   /**
     * Find a Call object by name.  For example,
@@ -104,28 +110,27 @@ case class WdlWorkflow(unqualifiedName: String,
     * Declarations within the workflow scope (including inside scatters and ifs)
     */
   lazy val transitiveDeclarations = {
-    def isValid(d: Declaration) = {
+    def isValid(d: Declaration) =
       d.parent match {
         case Some(w: WdlWorkflow) if w == this => true
         case Some(_: Scatter) => true
         case Some(_: If) => true
         case _ => false
       }
-    }
 
     descendants collect {
       case declaration: Declaration if isValid(declaration) => declaration
     }
   }
 
-  def findDeclarationByName(name: String): Option[Declaration] = {
+  def findDeclarationByName(name: String): Option[Declaration] =
     transitiveDeclarations.find(_.unqualifiedName == name)
-  }
 
   def findWorkflowOutputByName(name: String, relativeTo: Scope) = {
-    val leftOutputs = if (outputs.contains(relativeTo))
-      outputs.dropRight(outputs.size - outputs.indexOf(relativeTo))
-    else outputs
+    val leftOutputs =
+      if (outputs.contains(relativeTo))
+        outputs.dropRight(outputs.size - outputs.indexOf(relativeTo))
+      else outputs
     leftOutputs.find(_.unqualifiedName == name)
   }
 
@@ -142,7 +147,8 @@ case class WdlWorkflow(unqualifiedName: String,
    * @return a Map[FullyQualifiedName, WomType] representing the union
    *         of all outputs from all `call`s within this workflow
    */
-  lazy val expandedWildcardOutputs: Seq[WorkflowOutput] = if (isTopLevelWorkflow) calculateExpandedWildcardOutputs else Seq.empty
+  lazy val expandedWildcardOutputs: Seq[WorkflowOutput] =
+    if (isTopLevelWorkflow) calculateExpandedWildcardOutputs else Seq.empty
 
   private def calculateExpandedWildcardOutputs = {
 
@@ -151,7 +157,12 @@ case class WdlWorkflow(unqualifiedName: String,
         throw new RuntimeException(s"output ${output.fullyQualifiedName} has no parent Scope")
       }
 
-      new WorkflowOutput(locallyQualifiedName, womType, WdlExpression.fromString(locallyQualifiedName), output.ast, Option(this))
+      new WorkflowOutput(locallyQualifiedName,
+                         womType,
+                         WdlExpression.fromString(locallyQualifiedName),
+                         output.ast,
+                         Option(this)
+      )
     }
 
     def toWorkflowOutputs(scope: Scope): Seq[WorkflowOutput] = {
@@ -159,7 +170,7 @@ case class WdlWorkflow(unqualifiedName: String,
       val outputs = scope match {
         case call: WdlCall => call.outputs
         case outputDeclaration: Output => Seq(outputDeclaration)
-          // For non output declaration, don't return an array but return the raw value
+        // For non output declaration, don't return an array but return the raw value
         case otherDeclaration: DeclarationInterface => Seq(otherDeclaration)
         case _ => Seq.empty
       }
@@ -169,7 +180,9 @@ case class WdlWorkflow(unqualifiedName: String,
 
     // No outputs means all outputs
     val effectiveOutputWildcards = if (hasEmptyOutputSection) {
-      calls map { call => WorkflowOutputWildcard(unqualifiedName + "." + call.unqualifiedName, wildcard = true, call.ast) } toSeq
+      calls map { call =>
+        WorkflowOutputWildcard(unqualifiedName + "." + call.unqualifiedName, wildcard = true, call.ast)
+      } toSeq
     } else workflowOutputWildcards
 
     effectiveOutputWildcards flatMap { output =>
@@ -180,13 +193,16 @@ case class WdlWorkflow(unqualifiedName: String,
       }
       namespace.resolveCallOrOutputOrDeclaration(outputFqn) match {
         case Some(call: WdlCall) if output.wildcard && calls.contains(call) => toWorkflowOutputs(call)
-        case Some(declaration: DeclarationInterface) if descendants.contains(declaration) => toWorkflowOutputs(declaration)
+        case Some(declaration: DeclarationInterface) if descendants.contains(declaration) =>
+          toWorkflowOutputs(declaration)
         case _ => throw new SyntaxError(wdlSyntaxErrorFormatter.badOldStyleWorkflowOutput(output.ast))
       }
     }
   }
 
-  override lazy val outputs: Seq[WorkflowOutput] = expandedWildcardOutputs ++ children collect { case o: WorkflowOutput => o }
+  override lazy val outputs: Seq[WorkflowOutput] = expandedWildcardOutputs ++ children collect {
+    case o: WorkflowOutput => o
+  }
 
   override def toString = s"[Workflow $fullyQualifiedName]"
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowOutput.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowOutput.scala
index 0369618373e..878502a8adc 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowOutput.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowOutput.scala
@@ -13,4 +13,9 @@ object WorkflowOutput {
   }
 }
 
-case class WorkflowOutput(unqualifiedName: String, womType: WomType, requiredExpression: WdlExpression, ast: Ast, override val parent: Option[Scope]) extends Output
+case class WorkflowOutput(unqualifiedName: String,
+                          womType: WomType,
+                          requiredExpression: WdlExpression,
+                          ast: Ast,
+                          override val parent: Option[Scope]
+) extends Output
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowOutputWildcard.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowOutputWildcard.scala
index 556595592b8..78f5b1d7f38 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowOutputWildcard.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowOutputWildcard.scala
@@ -4,12 +4,11 @@ import wdl.draft2.parser.WdlParser.Ast
 
 case class WorkflowOutputWildcard(fqn: String, wildcard: Boolean, ast: Ast) {
 
-  def outputMatchesDeclaration(outputFqn: String, wildcardsAllowed: Boolean): Boolean = {
+  def outputMatchesDeclaration(outputFqn: String, wildcardsAllowed: Boolean): Boolean =
     if (wildcard) {
       val callFqn = outputFqn.substring(0, outputFqn.lastIndexOf('.'))
       wildcardsAllowed && callFqn.equals(fqn)
     } else {
       outputFqn.equals(fqn)
     }
-  }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowScoped.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowScoped.scala
index 0b64be6cf52..0ed48e61c0a 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowScoped.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/WorkflowScoped.scala
@@ -1,7 +1,11 @@
 package wdl.draft2.model
 
 trait WorkflowScoped extends Scope {
-  def parentWorkflow: WdlWorkflow = ancestry.collectFirst({ case w: WdlWorkflow => w }).getOrElse(
-    throw new IllegalStateException(s"Grammar constraint violation: $fullyQualifiedName should be contained in a workflow")
-  )
+  def parentWorkflow: WdlWorkflow = ancestry
+    .collectFirst { case w: WdlWorkflow => w }
+    .getOrElse(
+      throw new IllegalStateException(
+        s"Grammar constraint violation: $fullyQualifiedName should be contained in a workflow"
+      )
+    )
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/ParameterCommandPart.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/ParameterCommandPart.scala
index d1347a35a1e..aea8d35aefa 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/ParameterCommandPart.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/ParameterCommandPart.scala
@@ -21,9 +21,13 @@ object ParameterCommandPart {
       (ast.getAttribute("key").sourceString, ast.getAttribute("value").sourceString)
     } toMap
     val expression = WdlExpression(ast.getAttribute("expr"))
-    if ((attributes.contains("true") && !attributes.contains("false")) || (attributes.contains("false") && !attributes.contains("true"))) {
+    if (
+      (attributes.contains("true") && !attributes.contains("false")) || (attributes.contains("false") && !attributes
+        .contains("true"))
+    ) {
       // .head because we can't get here without there being at least one attribute
-      val firstAttr = ast.getAttribute("attributes").astListAsVector.head.asInstanceOf[Ast].getAttribute("key").asInstanceOf[Terminal]
+      val firstAttr =
+        ast.getAttribute("attributes").astListAsVector.head.asInstanceOf[Ast].getAttribute("key").asInstanceOf[Terminal]
       throw new SyntaxError(wdlSyntaxErrorFormatter.trueAndFalseAttributesAreRequired(firstAttr))
     }
     new ParameterCommandPart(attributes, expression)
@@ -31,11 +35,16 @@ object ParameterCommandPart {
 }
 
 case class ParameterCommandPart(attributes: Map[String, String], expression: WdlExpression) extends WdlCommandPart {
-  def attributesToString: String = if (attributes.nonEmpty) attributes.map({case (k,v) => s"$k=${WomString(v).toWomString}"}).mkString(" ") + " " else ""
+  def attributesToString: String = if (attributes.nonEmpty)
+    attributes.map { case (k, v) => s"$k=${WomString(v).toWomString}" }.mkString(" ") + " "
+  else ""
   override def toString: String = "${" + s"$attributesToString${expression.toWomString}" + "}"
 
-  override def instantiate(declarations: Seq[Declaration], inputs: Map[String, WomValue], functions: WdlFunctions[WomValue],
-                           valueMapper: (WomValue) => WomValue): ErrorOr[List[InstantiatedCommand]] = {
+  override def instantiate(declarations: Seq[Declaration],
+                           inputs: Map[String, WomValue],
+                           functions: WdlFunctions[WomValue],
+                           valueMapper: (WomValue) => WomValue
+  ): ErrorOr[List[InstantiatedCommand]] = {
     // This is a safety net.
     // In Cromwell's production code, optional declarations are always passed to instantiate, as WdlOptionalValue.none(type) if necessary.
     def lookupDeclaration(s: String) = declarations.collectFirst {
@@ -48,17 +57,17 @@ case class ParameterCommandPart(attributes: Map[String, String], expression: Wdl
     // Note that evaluating this expression may have the side effect of causing a file to be created if `writeFile`
     // is invoked. That file will be written to an "engine-relative" location which may be in cloud storage.
     val evaluatedCommandPartExpression: ErrorOr[WomValue] = expression.evaluate(lookup, functions) match {
-      case Success(v) => v match {
-        case WomOptionalValue(_, opt) => opt.getOrElse(defaultString).validNel
-        case _ => v.validNel
-      }
+      case Success(v) =>
+        v match {
+          case WomOptionalValue(_, opt) => opt.getOrElse(defaultString).validNel
+          case _ => v.validNel
+        }
       case Failure(OptionalNotSuppliedException(_)) => defaultString.validNel
       case Failure(e) => s"Could not evaluate expression: ${expression.toWomString}: ${e.getMessage}".invalidNel
     }
 
     // Create the stringified version of the command and record any file created in the process.
-    def instantiateCommand(value: WomValue): ErrorOr[InstantiatedCommand] = {
-
+    def instantiateCommand(value: WomValue): ErrorOr[InstantiatedCommand] =
       (valueMapper(value), value) match {
         case (b: WomBoolean, _) if attributes.contains("true") && attributes.contains("false") =>
           InstantiatedCommand(if (b.value) attributes.get("true").head else attributes.get("false").head).validNel
@@ -66,7 +75,9 @@ case class ParameterCommandPart(attributes: Map[String, String], expression: Wdl
           // Files generated by writeFiles have "engine-relative" paths which will be different from the container paths
           // calculated by `valueMapper`. "engine-relative" may mean either the non-Docker container path on the host
           // running Cromwell, or a cloud path. Capture these newly created files and their engine paths here.
-          InstantiatedCommand(commandString = f.valueString, createdFiles = List(CommandSetupSideEffectFile(unmappedFile))).validNel
+          InstantiatedCommand(commandString = f.valueString,
+                              createdFiles = List(CommandSetupSideEffectFile(unmappedFile))
+          ).validNel
         case (f: WomFile, _) =>
           InstantiatedCommand(f.valueString).validNel
         case (p: WomPrimitive, _) => InstantiatedCommand(p.valueString).validNel
@@ -77,7 +88,6 @@ case class ParameterCommandPart(attributes: Map[String, String], expression: Wdl
         case _ =>
           s"Could not string-ify value: $value".invalidNel
       }
-    }
 
     for {
       value <- evaluatedCommandPartExpression
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/StringCommandPart.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/StringCommandPart.scala
index ecb522eb02f..aa003949628 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/StringCommandPart.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/StringCommandPart.scala
@@ -10,6 +10,9 @@ import wom.values.WomValue
 case class StringCommandPart(literal: String) extends WdlCommandPart {
   override def toString: String = literal
 
-  override def instantiate(declarations: Seq[Declaration], inputsMap: Map[String, WomValue], functions: WdlFunctions[WomValue],
-                           valueMapper: (WomValue) => WomValue): ErrorOr[List[InstantiatedCommand]] = List(InstantiatedCommand(literal)).validNel
+  override def instantiate(declarations: Seq[Declaration],
+                           inputsMap: Map[String, WomValue],
+                           functions: WdlFunctions[WomValue],
+                           valueMapper: (WomValue) => WomValue
+  ): ErrorOr[List[InstantiatedCommand]] = List(InstantiatedCommand(literal)).validNel
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/WdlCommandPart.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/WdlCommandPart.scala
index 39aea939c39..c2657b2eaf0 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/WdlCommandPart.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/WdlCommandPart.scala
@@ -10,19 +10,25 @@ import wom.graph.LocalName
 import wom.values.WomValue
 import wom.{CommandPart, InstantiatedCommand}
 
-
 trait WdlCommandPart extends CommandPart {
 
   def instantiate(declarations: Seq[Declaration],
                   inputsMap: Map[String, WomValue],
                   functions: WdlFunctions[WomValue],
-                  valueMapper: WomValue => WomValue): ErrorOr[List[InstantiatedCommand]]
+                  valueMapper: WomValue => WomValue
+  ): ErrorOr[List[InstantiatedCommand]]
 
   override def instantiate(inputsMap: Map[LocalName, WomValue],
                            functions: IoFunctionSet,
                            valueMapper: WomValue => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] = {
-    val wdlFunctions = WdlStandardLibraryFunctions.fromIoFunctionSet(functions, FileSizeLimitationConfig.fileSizeLimitationConfig)
-    instantiate(Seq.empty, inputsMap.map({case (localName, value) => localName.value -> value}), wdlFunctions, valueMapper)
+                           runtimeEnvironment: RuntimeEnvironment
+  ): ErrorOr[List[InstantiatedCommand]] = {
+    val wdlFunctions =
+      WdlStandardLibraryFunctions.fromIoFunctionSet(functions, FileSizeLimitationConfig.fileSizeLimitationConfig)
+    instantiate(Seq.empty,
+                inputsMap.map { case (localName, value) => localName.value -> value },
+                wdlFunctions,
+                valueMapper
+    )
   }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex1.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex1.scala
index 6bf3c7e8316..906776c460b 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex1.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex1.scala
@@ -5,21 +5,21 @@ import wdl.draft2.model.WdlNamespaceWithWorkflow
 object ex1 {
   def main(args: Array[String]): Unit = {
     val wdl = """
-    |task a {
-    |  command { ps }
-    |}
-    |workflow wf {
-    | call a
-    |}""".stripMargin
+                |task a {
+                |  command { ps }
+                |}
+                |workflow wf {
+                | call a
+                |}""".stripMargin
 
     val ns = WdlNamespaceWithWorkflow.load(wdl, Seq.empty).get
 
     println(s"Workflow: ${ns.workflow.unqualifiedName}")
-    ns.workflow.calls foreach {call =>
+    ns.workflow.calls foreach { call =>
       println(s"Call: ${call.unqualifiedName}")
     }
 
-    ns.tasks foreach {task =>
+    ns.tasks foreach { task =>
       println(s"Task: ${task.name}")
       println(s"Command: ${task.commandTemplate}")
     }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex2.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex2.scala
index bfceb9754c2..f246712fa3c 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex2.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex2.scala
@@ -7,26 +7,26 @@ import wom.ResolvedImportRecord
 object ex2 {
   def main(args: Array[String]): Unit = {
     val wdl = """
-      |import "some_string"
-      |task a {
-      |  command { ps }
-      |}
-      |workflow wf {
-      | call a
-      |}""".stripMargin
+                |import "some_string"
+                |task a {
+                |  command { ps }
+                |}
+                |workflow wf {
+                | call a
+                |}""".stripMargin
 
-    def resolver(importString: String): Draft2ResolvedImportBundle = {
+    def resolver(importString: String): Draft2ResolvedImportBundle =
       importString match {
-        case "some_string" => Draft2ResolvedImportBundle("task imported { command {ps} }", ResolvedImportRecord("some_string"))
+        case "some_string" =>
+          Draft2ResolvedImportBundle("task imported { command {ps} }", ResolvedImportRecord("some_string"))
         case s if s.startsWith("http://") =>
           // issue HTTP request
           throw new UnsupportedOperationException("not implemented")
       }
-    }
 
     val ns = WdlNamespaceWithWorkflow.load(wdl, Seq(resolver _)).get
 
-    ns.tasks foreach {task =>
+    ns.tasks foreach { task =>
       println(s"Task: ${task.name}")
     }
   }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex3.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex3.scala
index f9f78754e49..98f80e0c90a 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex3.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex3.scala
@@ -7,24 +7,24 @@ import wom.ResolvedImportRecord
 object ex3 {
   def main(args: Array[String]): Unit = {
     val wdl = """
-      |import "some_string" as my_namespace
-      |task a {
-      |  command { ps }
-      |}
-      |workflow wf {
-      | call a
-      |}""".stripMargin
+                |import "some_string" as my_namespace
+                |task a {
+                |  command { ps }
+                |}
+                |workflow wf {
+                | call a
+                |}""".stripMargin
 
-    def resolver(importString: String): Draft2ResolvedImportBundle = {
+    def resolver(importString: String): Draft2ResolvedImportBundle =
       importString match {
-        case "some_string" => Draft2ResolvedImportBundle("task imported { command {ps} }", ResolvedImportRecord("some_string"))
+        case "some_string" =>
+          Draft2ResolvedImportBundle("task imported { command {ps} }", ResolvedImportRecord("some_string"))
         case _ => throw new UnsupportedOperationException()
       }
-    }
 
     val ns = WdlNamespaceWithWorkflow.load(wdl, Seq(resolver _)).get
 
-    ns.tasks foreach {task =>
+    ns.tasks foreach { task =>
       println(s"Task: ${task.name}")
     }
 
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex4.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex4.scala
index 7573f414ace..7f1b3b803b2 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex4.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex4.scala
@@ -5,13 +5,13 @@ import wdl.draft2.model.WdlNamespaceWithWorkflow
 object ex4 {
   def main(args: Array[String]): Unit = {
     val wdl = """
-      |task a {
-      |  command { ps }
-      |}
-      |workflow wf {
-      | call a
-      | call a as b
-      |}""".stripMargin
+                |task a {
+                |  command { ps }
+                |}
+                |workflow wf {
+                | call a
+                | call a as b
+                |}""".stripMargin
 
     val ns = WdlNamespaceWithWorkflow.load(wdl, Seq.empty).get
 
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex5.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex5.scala
index a796737f1fc..3c868058066 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex5.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex5.scala
@@ -5,20 +5,20 @@ import wdl.draft2.model.{WdlNamespaceWithWorkflow, WdlTaskCall}
 object ex5 {
   def main(args: Array[String]): Unit = {
     val wdl = """
-      |task a {
-      |  command { ps }
-      |  output { File procs = stdout() }
-      |}
-      |
-      |task b {
-      |  File s
-      |  command { wc -l ${s} }
-      |}
-      |
-      |workflow wf {
-      | call a
-      | call b {input: s=a.procs}
-      |}""".stripMargin
+                |task a {
+                |  command { ps }
+                |  output { File procs = stdout() }
+                |}
+                |
+                |task b {
+                |  File s
+                |  command { wc -l ${s} }
+                |}
+                |
+                |workflow wf {
+                | call a
+                | call b {input: s=a.procs}
+                |}""".stripMargin
 
     val ns = WdlNamespaceWithWorkflow.load(wdl, Seq.empty).get
 
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex6.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex6.scala
index 01fbd4735b8..13de4743697 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex6.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex6.scala
@@ -7,19 +7,18 @@ import wom.values.{WomString, WomValue}
 object ex6 {
   def main(args: Array[String]): Unit = {
     val wdl = """
-      |workflow wf {
-      |  String a = "foo" + "bar"
-      |  String b = "hello " + variable
-      |  String c = "hello " + other_variable
-      |}""".stripMargin
+                |workflow wf {
+                |  String a = "foo" + "bar"
+                |  String b = "hello " + variable
+                |  String c = "hello " + other_variable
+                |}""".stripMargin
 
     val ns = WdlNamespaceWithWorkflow.load(wdl, Seq.empty).get
-    def lookup(name: String): WomValue = {
+    def lookup(name: String): WomValue =
       name match {
         case "variable" => WomString("world")
         case _ => throw new NoSuchElementException
       }
-    }
     ns.workflow.declarations foreach { decl =>
       val value = decl.expression.get.evaluate(lookup, NoFunctions)
       println(s"Declaration '${decl.toWdlString}' evaluates to: $value")
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex7.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex7.scala
index 7bf0638cb58..6e347e16a43 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex7.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex7.scala
@@ -11,31 +11,30 @@ import scala.util.{Success, Try}
 object ex7 {
   def main(args: Array[String]): Unit = {
     val wdl = s"""
-      |task a {
-      |  String prefix
-      |  Array[Int] ints
-      |  command {
-      |    python script.py $${write_lines(ints)} > $${prefix + ".out"}
-      |  }
-      |}
-      |workflow wf {
-      |  call a
-      |}""".stripMargin
+                 |task a {
+                 |  String prefix
+                 |  Array[Int] ints
+                 |  command {
+                 |    python script.py $${write_lines(ints)} > $${prefix + ".out"}
+                 |  }
+                 |}
+                 |workflow wf {
+                 |  call a
+                 |}""".stripMargin
 
     val ns = WdlNamespaceWithWorkflow.load(wdl, Seq.empty).get
     val inputs = Map(
       "prefix" -> WomString("some_prefix"),
-      "ints" -> WomArray(WomArrayType(WomIntegerType), Seq(1,2,3,4,5).map(WomInteger.apply))
+      "ints" -> WomArray(WomArrayType(WomIntegerType), Seq(1, 2, 3, 4, 5).map(WomInteger.apply))
     )
 
     class CustomFunctions extends WdlFunctions[WomValue] {
-      def write_lines(params: Seq[Try[WomValue]]): Try[WomValue] = {
+      def write_lines(params: Seq[Try[WomValue]]): Try[WomValue] =
         // Validate `params`, write the result to a file, return file path
         Success(WomSingleFile("/tmp/array.txt"))
-      }
     }
 
-    ns.taskCalls.find( _.unqualifiedName == "a") foreach { call =>
+    ns.taskCalls.find(_.unqualifiedName == "a") foreach { call =>
       val wdlFunctions: CustomFunctions = new CustomFunctions
       val evaluatedInputs = call.evaluateTaskInputs(inputs, wdlFunctions).get
       println(call.task.instantiateCommand(evaluatedInputs, wdlFunctions).toTry.get)
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex8.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex8.scala
index 40fe900b670..12a69a10482 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex8.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/examples/ex8.scala
@@ -20,7 +20,7 @@ object ex8 {
     println(ast.toPrettyString)
 
     /* Traverse the tree to find all Task definitions */
-    AstTools.findAsts(ast, "Task") foreach {ast =>
+    AstTools.findAsts(ast, "Task") foreach { ast =>
       println(s"Task name: ${ast.getAttribute("name").sourceString}")
     }
   }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/LookupException.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/LookupException.scala
index 4222d289b86..2790746a0d2 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/LookupException.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/LookupException.scala
@@ -9,19 +9,28 @@ sealed trait LookupException { this: Exception => }
 /**
   * When a variable does not reference any known scope in the namespace.
   */
-sealed abstract case class VariableNotFoundException(variable: String, quoteName: Boolean = true) extends Exception(s"Variable $variable not found") with LookupException
+sealed abstract case class VariableNotFoundException(variable: String, quoteName: Boolean = true)
+    extends Exception(s"Variable $variable not found")
+    with LookupException
 
 object VariableNotFoundException {
   def apply(variable: String): VariableNotFoundException = new VariableNotFoundException(s"'$variable'") {}
-  def apply(variable: String, variableType: WomType): VariableNotFoundException= new VariableNotFoundException(s"'$variable': ${variableType.stableName}") {}
-  def apply(declaration: Declaration): VariableNotFoundException = VariableNotFoundException.apply(declaration.fullyQualifiedName, declaration.womType)
+  def apply(variable: String, variableType: WomType): VariableNotFoundException = new VariableNotFoundException(
+    s"'$variable': ${variableType.stableName}"
+  ) {}
+  def apply(declaration: Declaration): VariableNotFoundException =
+    VariableNotFoundException.apply(declaration.fullyQualifiedName, declaration.womType)
 }
 
 /**
   * When an unexpected exception occurred while attempting to resolve a variable.
   * Might act a single exception or aggregate multiple exceptions.
   */
-class VariableLookupException(override val exceptionContext: String, override val throwables: List[Throwable] = List.empty) extends RuntimeException with ThrowableAggregation with LookupException
+class VariableLookupException(override val exceptionContext: String,
+                              override val throwables: List[Throwable] = List.empty
+) extends RuntimeException
+    with ThrowableAggregation
+    with LookupException
 
 /**
   * Raised when attempting to resolve a variable in a scatter but the index could not be found.
@@ -31,4 +40,5 @@ final case class ScatterIndexNotFound(message: String) extends VariableLookupExc
 /**
   * Raised when attempting to resolve an output variable but the output resolver failed to return a value.
   */
-final case class OutputVariableLookupException(node: WdlGraphNode, index: Option[Int]) extends VariableLookupException(s"Could not find outputs for call ${node.fullyQualifiedName} at index $index")
+final case class OutputVariableLookupException(node: WdlGraphNode, index: Option[Int])
+    extends VariableLookupException(s"Could not find outputs for call ${node.fullyQualifiedName} at index $index")
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/UnsatisfiedInputException.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/UnsatisfiedInputException.scala
index c35906b8228..a4cc56bd30b 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/UnsatisfiedInputException.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/UnsatisfiedInputException.scala
@@ -1,3 +1,3 @@
 package wdl.draft2.model.exception
 
-class UnsatisfiedInputException(message: String) extends Exception(message)
\ No newline at end of file
+class UnsatisfiedInputException(message: String) extends Exception(message)
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/ValidationException.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/ValidationException.scala
index 1d1580519b6..d7933d4d089 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/ValidationException.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/exception/ValidationException.scala
@@ -2,4 +2,4 @@ package wdl.draft2.model.exception
 
 import common.exception.ThrowableAggregation
 
-case class ValidationException(exceptionContext: String, throwables: List[Throwable]) extends ThrowableAggregation
\ No newline at end of file
+case class ValidationException(exceptionContext: String, throwables: List[Throwable]) extends ThrowableAggregation
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/Evaluator.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/Evaluator.scala
index 221f899e0aa..4594f6200c1 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/Evaluator.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/Evaluator.scala
@@ -12,4 +12,3 @@ trait Evaluator {
   def functions: Functions
   def evaluate(ast: AstNode): Try[T]
 }
-
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala
index 224ced12d50..7b01cecfa17 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/FileEvaluator.scala
@@ -37,21 +37,20 @@ case class FileEvaluator(valueEvaluator: ValueEvaluator, coerceTo: WomType = Wom
 
   private def evalValue(ast: AstNode): Try[WomValue] = valueEvaluator.evaluate(ast)
 
-  private def evalValueToWdlFile(ast: AstNode): Try[WomFile] = {
+  private def evalValueToWdlFile(ast: AstNode): Try[WomFile] =
     evalValue(ast) match {
       case Success(p: WomPrimitive) => Success(WomSingleFile(p.valueString))
-      case Success(_) => Failure(new WomExpressionException(s"Expecting a primitive type from AST:\n${ast.toPrettyString}"))
+      case Success(_) =>
+        Failure(new WomExpressionException(s"Expecting a primitive type from AST:\n${ast.toPrettyString}"))
       case Failure(e) => Failure(e)
     }
-  }
 
-  def evaluate(ast: AstNode, anticipatedType: WomType = coerceTo): Try[Seq[WomFile]] = {
+  def evaluate(ast: AstNode, anticipatedType: WomType = coerceTo): Try[Seq[WomFile]] =
     valueEvaluator.evaluate(ast) match {
-        // If the ast can successfully be evaluated, then just find the WdlFiles that it contains
+      // If the ast can successfully be evaluated, then just find the WdlFiles that it contains
       case Success(v) => Success(FileEvaluatorUtil.findFilesToDelocalize(v, coerceTo))
       case Failure(_) => evaluateRecursive(ast, anticipatedType)
     }
-  }
 
   /**
     * Recursively traverse the ast and collect asts that evaluate successfully to a WdlFile
@@ -69,7 +68,7 @@ case class FileEvaluator(valueEvaluator: ValueEvaluator, coerceTo: WomType = Wom
     * Because we know that read_string takes a file parameter, WdlString("out") is transformed to a WdlFile (see evalValueToWdlFile)
     * We can now deduce that this task is expected to produce a WdlFile called "out"
     */
-  private def evaluateRecursive(ast: AstNode, anticipatedType: WomType): Try[Seq[WomFile]] = {
+  private def evaluateRecursive(ast: AstNode, anticipatedType: WomType): Try[Seq[WomFile]] =
     ast match {
       case a: Ast if a.isGlobFunctionCall =>
         evalValueToWdlFile(a.params.head) map { wdlFile => Seq(WomGlobFile(wdlFile.value)) }
@@ -83,17 +82,18 @@ case class FileEvaluator(valueEvaluator: ValueEvaluator, coerceTo: WomType = Wom
       case a: Ast if a.isBinaryOperator =>
         evalValueToWdlFile(a) match {
           case Success(f: WomFile) => Success(Seq(f))
-          case _ => for {
-            left <- evaluateRecursive(a.getAttribute("lhs"), anticipatedType)
-            right <- evaluateRecursive(a.getAttribute("rhs"), anticipatedType)
-          } yield left ++ right
+          case _ =>
+            for {
+              left <- evaluateRecursive(a.getAttribute("lhs"), anticipatedType)
+              right <- evaluateRecursive(a.getAttribute("rhs"), anticipatedType)
+            } yield left ++ right
         }
       case a: Ast if a.isUnaryOperator =>
         evalValueToWdlFile(a) match {
           case Success(f: WomFile) => Success(Seq(f))
           case _ =>
             evaluateRecursive(a.getAttribute("expression"), anticipatedType) match {
-              case Success(a:Seq[WomFile]) => Success(a)
+              case Success(a: Seq[WomFile]) => Success(a)
               case _ => Failure(new WomExpressionException(s"Could not evaluate:\n${a.toPrettyString}"))
             }
         }
@@ -106,10 +106,11 @@ case class FileEvaluator(valueEvaluator: ValueEvaluator, coerceTo: WomType = Wom
       case a: Ast if a.isArrayOrMapLookup =>
         evalValue(a) match {
           case Success(f: WomFile) => Success(Seq(f))
-          case _ => for {
-            left <- evaluateRecursive(a.getAttribute("lhs"), anticipatedType)
-            right <- evaluateRecursive(a.getAttribute("rhs"), anticipatedType)
-          } yield left ++ right
+          case _ =>
+            for {
+              left <- evaluateRecursive(a.getAttribute("lhs"), anticipatedType)
+              right <- evaluateRecursive(a.getAttribute("rhs"), anticipatedType)
+            } yield left ++ right
         }
       case a: Ast if a.isMemberAccess =>
         evalValue(a) match {
@@ -124,7 +125,12 @@ case class FileEvaluator(valueEvaluator: ValueEvaluator, coerceTo: WomType = Wom
               case Success(v) => Success(v.flatten)
               case f => f.map(_.flatten)
             }
-          case _ => Failure(new WomExpressionException(s"Failed to parse $a for files. Found an unexpected Array literal but anticipated a ${anticipatedType.stableName}"))
+          case _ =>
+            Failure(
+              new WomExpressionException(
+                s"Failed to parse $a for files. Found an unexpected Array literal but anticipated a ${anticipatedType.stableName}"
+              )
+            )
         }
       case a: Ast if a.isTupleLiteral =>
         val unevaluatedElements = a.getAttribute("values").astListAsVector
@@ -137,7 +143,12 @@ case class FileEvaluator(valueEvaluator: ValueEvaluator, coerceTo: WomType = Wom
                 left <- evaluate(unevaluatedElements.head, leftType)
                 right <- evaluate(unevaluatedElements(1), rightType)
               } yield left ++ right
-            case _ => Failure(new WomExpressionException(s"Failed to parse $a for files. Found an unexpected Pair literal but anticipated a ${anticipatedType.stableName}"))
+            case _ =>
+              Failure(
+                new WomExpressionException(
+                  s"Failed to parse $a for files. Found an unexpected Pair literal but anticipated a ${anticipatedType.stableName}"
+                )
+              )
           }
 
         } else {
@@ -152,20 +163,22 @@ case class FileEvaluator(valueEvaluator: ValueEvaluator, coerceTo: WomType = Wom
               key -> value
             }
 
-            val flattenedTries = evaluatedMap flatMap { case (k,v) => Seq(k,v) }
-            flattenedTries partition {_.isSuccess} match {
+            val flattenedTries = evaluatedMap flatMap { case (k, v) => Seq(k, v) }
+            flattenedTries partition { _.isSuccess } match {
               case (_, failures) if failures.nonEmpty =>
                 val message = failures.collect { case f: Failure[_] => f.exception.getMessage }.mkString("\n")
                 Failure(new WomExpressionException(s"Could not evaluate expression:\n$message"))
               case (successes, _) =>
                 Success(successes.flatMap(_.get))
             }
-          case _ => Failure(new WomExpressionException(s"Failed to parse $a for files. Found an unexpected Map literal but anticipated a ${anticipatedType.stableName}"))
+          case _ =>
+            Failure(
+              new WomExpressionException(
+                s"Failed to parse $a for files. Found an unexpected Map literal but anticipated a ${anticipatedType.stableName}"
+              )
+            )
         }
 
-
       case _ => Success(Seq.empty[WomFile])
     }
-  }
 }
-
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala
index be3fe3cb9a6..ac8fe551cc1 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/TypeEvaluator.scala
@@ -11,7 +11,10 @@ import wom.types._
 
 import scala.util.{Failure, Success, Try}
 
-case class TypeEvaluator(override val lookup: String => WomType, override val functions: WdlFunctions[WomType], from: Option[Scope] = None) extends Evaluator {
+case class TypeEvaluator(override val lookup: String => WomType,
+                         override val functions: WdlFunctions[WomType],
+                         from: Option[Scope] = None
+) extends Evaluator {
   override type T = WomType
 
   override def evaluate(ast: AstNode): Try[WomType] = ast match {
@@ -25,35 +28,36 @@ case class TypeEvaluator(override val lookup: String => WomType, override val fu
       val lhs = evaluate(a.getAttribute("lhs"))
       val rhs = evaluate(a.getAttribute("rhs"))
       a.getName match {
-        case "Add" => for(l <- lhs; r <- rhs) yield l.add(r).get
-        case "Subtract" => for(l <- lhs; r <- rhs) yield l.subtract(r).get
-        case "Multiply" => for(l <- lhs; r <- rhs) yield l.multiply(r).get
-        case "Divide" => for(l <- lhs; r <- rhs) yield l.divide(r).get
-        case "Remainder" => for(l <- lhs; r <- rhs) yield l.mod(r).get
-        case "Equals" => for(l <- lhs; r <- rhs) yield l.equalsType(r).get
-        case "NotEquals" => for(l <- lhs; r <- rhs) yield l.notEquals(r).get
-        case "LessThan" => for(l <- lhs; r <- rhs) yield l.lessThan(r).get
-        case "LessThanOrEqual" => for(l <- lhs; r <- rhs) yield l.lessThanOrEqual(r).get
-        case "GreaterThan" => for(l <- lhs; r <- rhs) yield l.greaterThan(r).get
-        case "GreaterThanOrEqual" => for(l <- lhs; r <- rhs) yield l.greaterThanOrEqual(r).get
-        case "LogicalOr" => for(l <- lhs; r <- rhs) yield l.or(r).get
-        case "LogicalAnd" => for(l <- lhs; r <- rhs) yield l.and(r).get
+        case "Add" => for (l <- lhs; r <- rhs) yield l.add(r).get
+        case "Subtract" => for (l <- lhs; r <- rhs) yield l.subtract(r).get
+        case "Multiply" => for (l <- lhs; r <- rhs) yield l.multiply(r).get
+        case "Divide" => for (l <- lhs; r <- rhs) yield l.divide(r).get
+        case "Remainder" => for (l <- lhs; r <- rhs) yield l.mod(r).get
+        case "Equals" => for (l <- lhs; r <- rhs) yield l.equalsType(r).get
+        case "NotEquals" => for (l <- lhs; r <- rhs) yield l.notEquals(r).get
+        case "LessThan" => for (l <- lhs; r <- rhs) yield l.lessThan(r).get
+        case "LessThanOrEqual" => for (l <- lhs; r <- rhs) yield l.lessThanOrEqual(r).get
+        case "GreaterThan" => for (l <- lhs; r <- rhs) yield l.greaterThan(r).get
+        case "GreaterThanOrEqual" => for (l <- lhs; r <- rhs) yield l.greaterThanOrEqual(r).get
+        case "LogicalOr" => for (l <- lhs; r <- rhs) yield l.or(r).get
+        case "LogicalAnd" => for (l <- lhs; r <- rhs) yield l.and(r).get
         case _ => Failure(new WomExpressionException(s"Invalid operator: ${a.getName}"))
       }
     case a: Ast if a.isUnaryOperator =>
       val expression = evaluate(a.getAttribute("expression"))
       a.getName match {
-        case "LogicalNot" => for(e <- expression) yield e.not.get
-        case "UnaryPlus" => for(e <- expression) yield e.unaryPlus.get
-        case "UnaryNegation" => for(e <- expression) yield e.unaryMinus.get
+        case "LogicalNot" => for (e <- expression) yield e.not.get
+        case "UnaryPlus" => for (e <- expression) yield e.unaryPlus.get
+        case "UnaryNegation" => for (e <- expression) yield e.unaryMinus.get
         case _ => Failure(new WomExpressionException(s"Invalid operator: ${a.getName}"))
       }
     case TernaryIf(condition, ifTrue, ifFalse) =>
       evaluate(condition) flatMap {
-        case WomBooleanType => for {
-          ifTrueType <- evaluate(ifTrue)
-          ifFalseType <- evaluate(ifFalse)
-        } yield WomType.lowestCommonSubtype(Seq(ifTrueType, ifFalseType))
+        case WomBooleanType =>
+          for {
+            ifTrueType <- evaluate(ifTrue)
+            ifFalseType <- evaluate(ifFalse)
+          } yield WomType.lowestCommonSubtype(Seq(ifTrueType, ifFalseType))
         case _ => Failure(new WomExpressionException("The condition of a ternary 'if' must be a Boolean."))
       }
     case a: Ast if a.isArrayLiteral =>
@@ -71,14 +75,14 @@ case class TypeEvaluator(override val lookup: String => WomType, override val fu
         key -> value
       }
 
-      val flattenedTries = evaluatedMap flatMap { case (k,v) => Seq(k,v) }
-      flattenedTries partition {_.isSuccess} match {
+      val flattenedTries = evaluatedMap flatMap { case (k, v) => Seq(k, v) }
+      flattenedTries partition { _.isSuccess } match {
         case (_, failures) if failures.nonEmpty =>
           val message = failures.collect { case f: Failure[_] => f.exception.getMessage }.mkString("\n")
           Failure(new WomExpressionException(s"Could not evaluate expression:\n$message"))
         case good @ _ =>
-          val keyType = WomType.homogeneousTypeFromTypes(evaluatedMap map { case (k, _) => k.get} )
-          val valueType = WomType.homogeneousTypeFromTypes(evaluatedMap map { case (_, v) => v.get} )
+          val keyType = WomType.homogeneousTypeFromTypes(evaluatedMap map { case (k, _) => k.get })
+          val valueType = WomType.homogeneousTypeFromTypes(evaluatedMap map { case (_, v) => v.get })
           Success(WomMapType(keyType, valueType))
       }
     case a: Ast if a.isMemberAccess =>
@@ -102,10 +106,12 @@ case class TypeEvaluator(override val lookup: String => WomType, override val fu
                 case "right" => Success(rightType)
               }
             case WomObjectType => Success(WomAnyType)
-            case ns: WdlNamespace => Success(lookup(ns.importedAs.map{ n => s"$n.${rhs.getSourceString}" }.getOrElse(rhs.getSourceString)))
-            case _ => Failure(new WomExpressionException("Left-hand side of expression must be a WdlObject or Namespace"))
-          } recoverWith {
-            case _ => Try(lookup(a.getAttribute("lhs").sourceString + "." + rhs.sourceString))
+            case ns: WdlNamespace =>
+              Success(lookup(ns.importedAs.map(n => s"$n.${rhs.getSourceString}").getOrElse(rhs.getSourceString)))
+            case _ =>
+              Failure(new WomExpressionException("Left-hand side of expression must be a WdlObject or Namespace"))
+          } recoverWith { case _ =>
+            Try(lookup(a.getAttribute("lhs").sourceString + "." + rhs.sourceString))
           }
         case _ => Failure(new WomExpressionException("Right-hand side of expression must be identifier"))
       }
@@ -113,7 +119,12 @@ case class TypeEvaluator(override val lookup: String => WomType, override val fu
       (evaluate(a.getAttribute("lhs")), evaluate(a.getAttribute("rhs"))) match {
         case (Success(a: WomArrayType), Success(WomIntegerType)) => Success(a.memberType)
         case (Success(m: WomMapType), Success(_: WomType)) => Success(m.valueType)
-        case (Success(otherLhs), Success(_)) => Failure(new WomExpressionException(s"Invalid indexing target. You cannot index a value of type '${otherLhs.stableName}'"))
+        case (Success(otherLhs), Success(_)) =>
+          Failure(
+            new WomExpressionException(
+              s"Invalid indexing target. You cannot index a value of type '${otherLhs.stableName}'"
+            )
+          )
         case (f: Failure[_], _) => f
         case (_, f: Failure[_]) => f
       }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala
index e57ead11abb..c60cb511b56 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/ValueEvaluator.scala
@@ -16,13 +16,15 @@ object ValueEvaluator {
   val InterpolationTagPattern = "\\$\\{\\s*([^\\}]*)\\s*\\}".r
 }
 
-case class ValueEvaluator(override val lookup: String => WomValue, override val functions: WdlFunctions[WomValue]) extends Evaluator {
+case class ValueEvaluator(override val lookup: String => WomValue, override val functions: WdlFunctions[WomValue])
+    extends Evaluator {
   override type T = WomValue
 
   private val InterpolationTagPattern = "\\$\\{\\s*([^\\}]*)\\s*\\}".r
 
-
-  private def interpolate(strToProcess: String, resultSoFar: Try[WomString] = Success(WomString(""))): Try[WomString] = {
+  private def interpolate(strToProcess: String,
+                          resultSoFar: Try[WomString] = Success(WomString(""))
+  ): Try[WomString] = {
 
     def evaluateTag(tag: String): Try[WomString] = {
       val expr = WdlExpression.fromString(tag.substring(2, tag.length - 1))
@@ -57,40 +59,47 @@ case class ValueEvaluator(override val lookup: String => WomValue, override val
         val lhs = evaluate(a.getAttribute("lhs"))
         val rhs = () => evaluate(a.getAttribute("rhs"))
         a.getName match {
-          case "Add" => for(l <- lhs; r <- rhs()) yield l.add(r).get
-          case "Subtract" => for(l <- lhs; r <- rhs()) yield l.subtract(r).get
-          case "Multiply" => for(l <- lhs; r <- rhs()) yield l.multiply(r).get
-          case "Divide" => for(l <- lhs; r <- rhs()) yield l.divide(r).get
-          case "Remainder" => for(l <- lhs; r <- rhs()) yield l.mod(r).get
-          case "Equals" => for(l <- lhs; r <- rhs()) yield l.equals(r).get
-          case "NotEquals" => for(l <- lhs; r <- rhs()) yield l.notEquals(r).get
-          case "LessThan" => for(l <- lhs; r <- rhs()) yield l.lessThan(r).get
-          case "LessThanOrEqual" => for(l <- lhs; r <- rhs()) yield l.lessThanOrEqual(r).get
-          case "GreaterThan" => for(l <- lhs; r <- rhs()) yield l.greaterThan(r).get
-          case "GreaterThanOrEqual" => for(l <- lhs; r <- rhs()) yield l.greaterThanOrEqual(r).get
-          case "LogicalOr" => lhs flatMap {
-            case WomBoolean(true) => Success(WomBoolean(true))
-            case b => rhs() flatMap b.or
-          }
-          case "LogicalAnd" => lhs flatMap {
-            case WomBoolean(false) => Success(WomBoolean(false))
-            case b => rhs() flatMap b.and
-          }
+          case "Add" => for (l <- lhs; r <- rhs()) yield l.add(r).get
+          case "Subtract" => for (l <- lhs; r <- rhs()) yield l.subtract(r).get
+          case "Multiply" => for (l <- lhs; r <- rhs()) yield l.multiply(r).get
+          case "Divide" => for (l <- lhs; r <- rhs()) yield l.divide(r).get
+          case "Remainder" => for (l <- lhs; r <- rhs()) yield l.mod(r).get
+          case "Equals" => for (l <- lhs; r <- rhs()) yield l.equals(r).get
+          case "NotEquals" => for (l <- lhs; r <- rhs()) yield l.notEquals(r).get
+          case "LessThan" => for (l <- lhs; r <- rhs()) yield l.lessThan(r).get
+          case "LessThanOrEqual" => for (l <- lhs; r <- rhs()) yield l.lessThanOrEqual(r).get
+          case "GreaterThan" => for (l <- lhs; r <- rhs()) yield l.greaterThan(r).get
+          case "GreaterThanOrEqual" => for (l <- lhs; r <- rhs()) yield l.greaterThanOrEqual(r).get
+          case "LogicalOr" =>
+            lhs flatMap {
+              case WomBoolean(true) => Success(WomBoolean(true))
+              case b => rhs() flatMap b.or
+            }
+          case "LogicalAnd" =>
+            lhs flatMap {
+              case WomBoolean(false) => Success(WomBoolean(false))
+              case b => rhs() flatMap b.and
+            }
           case _ => Failure(new WomExpressionException(s"Invalid operator: ${a.getName}"))
         }
       case a: Ast if a.isUnaryOperator =>
         val expression = evaluate(a.getAttribute("expression"))
         a.getName match {
-          case "LogicalNot" => for(e <- expression) yield e.not.get
-          case "UnaryPlus" => for(e <- expression) yield e.unaryPlus.get
-          case "UnaryNegation" => for(e <- expression) yield e.unaryMinus.get
+          case "LogicalNot" => for (e <- expression) yield e.not.get
+          case "UnaryPlus" => for (e <- expression) yield e.unaryPlus.get
+          case "UnaryNegation" => for (e <- expression) yield e.unaryMinus.get
           case _ => Failure(new WomExpressionException(s"Invalid operator: ${a.getName}"))
         }
       case TernaryIf(condition, ifTrue, ifFalse) =>
         evaluate(condition) flatMap {
           case WomBoolean(true) => evaluate(ifTrue)
           case WomBoolean(false) => evaluate(ifFalse)
-          case other => Failure(new WomExpressionException("'if' expression must be given a boolean argument but got: " + other.toWomString))
+          case other =>
+            Failure(
+              new WomExpressionException(
+                "'if' expression must be given a boolean argument but got: " + other.toWomString
+              )
+            )
         }
       case a: Ast if a.isArrayLiteral =>
         val evaluatedElements = a.getAttribute("values").astListAsVector map evaluate
@@ -134,56 +143,66 @@ case class ValueEvaluator(override val lookup: String => WomValue, override val
         }
       case a: Ast if a.isMemberAccess =>
         a.getAttribute("rhs") match {
-          case rhs:Terminal if rhs.getTerminalStr == "identifier" =>
+          case rhs: Terminal if rhs.getTerminalStr == "identifier" =>
             val memberAccessAsString = s"${a.getAttribute("lhs").sourceString}.${a.getAttribute("rhs").sourceString}"
-            Try(lookup(memberAccessAsString)).recoverWith {
-              case _ =>
-                evaluate(a.getAttribute("lhs")).flatMap {
-                  case o: WomObjectLike =>
-                    o.values.get(rhs.getSourceString) match {
-                      case Some(v:WomValue) => Success(v)
-                      case None =>
-                        o match {
-                          // o is a CallOutputsObject which means we failed to find an output value for rhs
-                          // Give a specific error message based on the type of Callable
-                          case callOutputObject: WdlCallOutputsObject =>
-                            callOutputObject.call match {
-                              case workflowCall: WdlWorkflowCall =>
-                                Failure(new WomExpressionException(
+            Try(lookup(memberAccessAsString)).recoverWith { case _ =>
+              evaluate(a.getAttribute("lhs")).flatMap {
+                case o: WomObjectLike =>
+                  o.values.get(rhs.getSourceString) match {
+                    case Some(v: WomValue) => Success(v)
+                    case None =>
+                      o match {
+                        // o is a CallOutputsObject which means we failed to find an output value for rhs
+                        // Give a specific error message based on the type of Callable
+                        case callOutputObject: WdlCallOutputsObject =>
+                          callOutputObject.call match {
+                            case workflowCall: WdlWorkflowCall =>
+                              Failure(
+                                new WomExpressionException(
                                   s"""${rhs.getSourceString} is not declared as an output of the sub workflow ${workflowCall.calledWorkflow.fullyQualifiedName}.
                                      |If you want to use workflow ${workflowCall.calledWorkflow.fullyQualifiedName} as a sub workflow, make sure that its output section is up to date with the latest syntax.
                                      |See the WDL specification for how to write outputs: https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#outputs""".stripMargin
-                                ))
-                              case taskCall: WdlTaskCall =>
-                                Failure(new WomExpressionException(
+                                )
+                              )
+                            case taskCall: WdlTaskCall =>
+                              Failure(
+                                new WomExpressionException(
                                   s"""${rhs.getSourceString} is not declared as an output of the task ${taskCall.task.fullyQualifiedName}.
                                      |Make sure to declare it as an output to be able to use it in the workflow.""".stripMargin
-                                ))
-                              case unknownCall =>
-                                Failure(new WomExpressionException(
+                                )
+                              )
+                            case unknownCall =>
+                              Failure(
+                                new WomExpressionException(
                                   s"Could not find key ${rhs.getSourceString} in Call ${unknownCall.fullyQualifiedName} of unknown type."
-                                ))
-                            }
-                          case _ => Failure(new WomExpressionException(s"Could not find key ${rhs.getSourceString} in WdlObject"))
-                        }
-                    }
-                  case array: WomArray if array.womType == WomArrayType(WomObjectType) =>
-                    /*
-                     * This case is for slicing an Array[Object], used mainly for scatter-gather.
-                     * For example, if 'call foo' was in a scatter block, foo's outputs (e.g. Int x)
-                     * would be an Array[Int].  If a downstream call has an input expression "foo.x",
-                     * then 'foo' would evaluate to an Array[Objects] and foo.x would result in an
-                     * Array[Int]
-                     */
-                    Success(array map {_.asInstanceOf[WomObject].values.get(rhs.sourceString).get})
-                  case p: WomPair =>
-                    val identifier = rhs.getSourceString
-                    if (identifier.equals("left")) Success(p.left)
-                    else if (identifier.equals("right")) Success(p.right)
-                    else Failure(new WomExpressionException("A pair only has the members: 'left' and 'right'"))
-                  case ns: WdlNamespace => Success(lookup(ns.importedAs.map{ n => s"$n.${rhs.getSourceString}" }.getOrElse(rhs.getSourceString)))
-                  case _ => Failure(new WomExpressionException("Left-hand side of expression must be a WdlObject or Namespace"))
-                }
+                                )
+                              )
+                          }
+                        case _ =>
+                          Failure(new WomExpressionException(s"Could not find key ${rhs.getSourceString} in WdlObject"))
+                      }
+                  }
+                case array: WomArray if array.womType == WomArrayType(WomObjectType) =>
+                  /*
+                   * This case is for slicing an Array[Object], used mainly for scatter-gather.
+                   * For example, if 'call foo' was in a scatter block, foo's outputs (e.g. Int x)
+                   * would be an Array[Int].  If a downstream call has an input expression "foo.x",
+                   * then 'foo' would evaluate to an Array[Objects] and foo.x would result in an
+                   * Array[Int]
+                   */
+                  Success(array map { _.asInstanceOf[WomObject].values.get(rhs.sourceString).get })
+                case p: WomPair =>
+                  val identifier = rhs.getSourceString
+                  if (identifier.equals("left")) Success(p.left)
+                  else if (identifier.equals("right")) Success(p.right)
+                  else Failure(new WomExpressionException("A pair only has the members: 'left' and 'right'"))
+                case ns: WdlNamespace =>
+                  Success(
+                    lookup(ns.importedAs.map(n => s"$n.${rhs.getSourceString}").getOrElse(rhs.getSourceString))
+                  )
+                case _ =>
+                  Failure(new WomExpressionException("Left-hand side of expression must be a WdlObject or Namespace"))
+              }
             }
           case _ => Failure(new WomExpressionException("Right-hand side of expression must be identifier"))
         }
@@ -193,8 +212,13 @@ case class ValueEvaluator(override val lookup: String => WomValue, override val
         (mapOrArray, index) match {
           case (Success(a: WomArray), Success(i: WomInteger)) =>
             Try(a.value(i.value)) match {
-              case s:Success[WomValue] => s
-              case Failure(ex) => Failure(new WomExpressionException(s"Failed to find index $index on array:\n\n$mapOrArray\n\n${ex.getMessage}"))
+              case s: Success[WomValue] => s
+              case Failure(ex) =>
+                Failure(
+                  new WomExpressionException(
+                    s"Failed to find index $index on array:\n\n$mapOrArray\n\n${ex.getMessage}"
+                  )
+                )
             }
           case (Success(m: WomMap), Success(v: WomValue)) =>
             m.value.get(v) match {
@@ -212,4 +236,3 @@ case class ValueEvaluator(override val lookup: String => WomValue, override val
     }
   }
 }
-
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlFunctions.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlFunctions.scala
index 087210de953..cd00d6fd754 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlFunctions.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlFunctions.scala
@@ -15,10 +15,10 @@ trait WdlFunctions[T] {
     * Extract a single `WomValue` from the specified `Seq`, returning `Failure` if the parameters
     * represent something other than a single `WomValue`.
     */
-  def extractSingleArgument(functionName: String, params: Seq[Try[T]]): Try[T] = {
-    if (params.length != 1) Failure(new UnsupportedOperationException(s"Expected one argument for $functionName, got ${params.length}"))
+  def extractSingleArgument(functionName: String, params: Seq[Try[T]]): Try[T] =
+    if (params.length != 1)
+      Failure(new UnsupportedOperationException(s"Expected one argument for $functionName, got ${params.length}"))
     else params.head
-  }
 
   /*
    * Below are methods that can be overridden, if necessary, by engine implementations of the standard library
@@ -27,5 +27,7 @@ trait WdlFunctions[T] {
   /**
     * Path where to write files created by standard functions (write_*).
    */
-  def tempFilePath: String = throw new UnsupportedOperationException("write_* functions are not supported by this implementation")
+  def tempFilePath: String = throw new UnsupportedOperationException(
+    "write_* functions are not supported by this implementation"
+  )
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlStandardLibraryFunctions.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlStandardLibraryFunctions.scala
index 5cd98ad7a61..0a9d6480174 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlStandardLibraryFunctions.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/expression/WdlStandardLibraryFunctions.scala
@@ -34,75 +34,97 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
 
   protected def fileSizeLimitationConfig: FileSizeLimitationConfig
 
-  private def writeContent(baseName: String, content: String): Try[WomFile] = writeFile(s"${baseName}_${content.md5Sum}.tmp", content)
+  private def writeContent(baseName: String, content: String): Try[WomFile] =
+    writeFile(s"${baseName}_${content.md5Sum}.tmp", content)
 
-  private def writeToTsv[A <: WomValue with TsvSerializable](functionName: String, params: Seq[Try[WomValue]], defaultIfOptionalEmpty: A): Try[WomFile] = {
+  private def writeToTsv[A <: WomValue with TsvSerializable](functionName: String,
+                                                             params: Seq[Try[WomValue]],
+                                                             defaultIfOptionalEmpty: A
+  ): Try[WomFile] =
     for {
       singleArgument <- extractSingleArgument(functionName, params)
       serialized <- ValueEvaluation.serializeWomValue(functionName, singleArgument, defaultIfOptionalEmpty)
       file <- writeContent(functionName, serialized)
     } yield file
-  }
 
-  def read_objects(params: Seq[Try[WomValue]]): Try[WomArray] = extractObjects("read_objects", params) map { a => WomArray(WomArrayType(WomObjectType), a.toIndexedSeq) }
-  def read_string(params: Seq[Try[WomValue]]): Try[WomString] = readContentsFromSingleFileParameter("read_string", params, fileSizeLimitationConfig.readStringLimit).map(s => WomString(s.trim))
-  def read_json(params: Seq[Try[WomValue]]): Try[WomValue] = readContentsFromSingleFileParameter("read_json", params, fileSizeLimitationConfig.readJsonLimit).map(_.parseJson).flatMap(WomObjectType.coerceRawValue)
-  def read_int(params: Seq[Try[WomValue]]): Try[WomInteger] = readContentsFromSingleFileParameter("read_int", params, fileSizeLimitationConfig.readIntLimit).map(s => WomString(s.trim)) map { s => WomInteger(s.value.trim.toInt) }
-  def read_float(params: Seq[Try[WomValue]]): Try[WomFloat] = readContentsFromSingleFileParameter("read_float", params, fileSizeLimitationConfig.readFloatLimit).map(s => WomString(s.trim)) map { s => WomFloat(s.value.trim.toDouble) }
-
-  def write_lines(params: Seq[Try[WomValue]]): Try[WomFile] = writeToTsv("write_lines", params, WomArray(WomArrayType(WomStringType), List.empty[WomValue]))
-  def write_map(params: Seq[Try[WomValue]]): Try[WomFile] = writeToTsv("write_map", params, WomMap(WomMapType(WomStringType, WomStringType), Map.empty[WomValue, WomValue]))
-  def write_object(params: Seq[Try[WomValue]]): Try[WomFile] = writeToTsv("write_object", params, WomObject(Map.empty[String, WomValue]))
-  def write_objects(params: Seq[Try[WomValue]]): Try[WomFile] = writeToTsv("write_objects", params, WomArray(WomArrayType(WomObjectType), List.empty[WomObject]))
-  def write_tsv(params: Seq[Try[WomValue]]): Try[WomFile] = writeToTsv("write_tsv", params, WomArray(WomArrayType(WomStringType), List.empty[WomValue]))
+  def read_objects(params: Seq[Try[WomValue]]): Try[WomArray] = extractObjects("read_objects", params) map { a =>
+    WomArray(WomArrayType(WomObjectType), a.toIndexedSeq)
+  }
+  def read_string(params: Seq[Try[WomValue]]): Try[WomString] =
+    readContentsFromSingleFileParameter("read_string", params, fileSizeLimitationConfig.readStringLimit).map(s =>
+      WomString(s.trim)
+    )
+  def read_json(params: Seq[Try[WomValue]]): Try[WomValue] = readContentsFromSingleFileParameter(
+    "read_json",
+    params,
+    fileSizeLimitationConfig.readJsonLimit
+  ).map(_.parseJson).flatMap(WomObjectType.coerceRawValue)
+  def read_int(params: Seq[Try[WomValue]]): Try[WomInteger] =
+    readContentsFromSingleFileParameter("read_int", params, fileSizeLimitationConfig.readIntLimit).map(s =>
+      WomString(s.trim)
+    ) map { s => WomInteger(s.value.trim.toInt) }
+  def read_float(params: Seq[Try[WomValue]]): Try[WomFloat] =
+    readContentsFromSingleFileParameter("read_float", params, fileSizeLimitationConfig.readFloatLimit).map(s =>
+      WomString(s.trim)
+    ) map { s => WomFloat(s.value.trim.toDouble) }
+
+  def write_lines(params: Seq[Try[WomValue]]): Try[WomFile] =
+    writeToTsv("write_lines", params, WomArray(WomArrayType(WomStringType), List.empty[WomValue]))
+  def write_map(params: Seq[Try[WomValue]]): Try[WomFile] =
+    writeToTsv("write_map", params, WomMap(WomMapType(WomStringType, WomStringType), Map.empty[WomValue, WomValue]))
+  def write_object(params: Seq[Try[WomValue]]): Try[WomFile] =
+    writeToTsv("write_object", params, WomObject(Map.empty[String, WomValue]))
+  def write_objects(params: Seq[Try[WomValue]]): Try[WomFile] =
+    writeToTsv("write_objects", params, WomArray(WomArrayType(WomObjectType), List.empty[WomObject]))
+  def write_tsv(params: Seq[Try[WomValue]]): Try[WomFile] =
+    writeToTsv("write_tsv", params, WomArray(WomArrayType(WomStringType), List.empty[WomValue]))
   def write_json(params: Seq[Try[WomValue]]): Try[WomFile] = for {
     value <- extractSingleArgument("write_json", params)
     jsonContent = ValueEvaluation.valueToJson(value)
     written <- writeContent("write_json", jsonContent.compactPrint)
   } yield written
 
-  def read_lines(params: Seq[Try[WomValue]]): Try[WomArray] = {
+  def read_lines(params: Seq[Try[WomValue]]): Try[WomArray] =
     for {
       contents <- readContentsFromSingleFileParameter("read_lines", params, fileSizeLimitationConfig.readLinesLimit)
       lines = contents.split("\n")
     } yield WomArray(WomArrayType(WomStringType), lines.toIndexedSeq map WomString)
-  }
 
-  def read_map(params: Seq[Try[WomValue]]): Try[WomMap] = {
+  def read_map(params: Seq[Try[WomValue]]): Try[WomMap] =
     for {
       contents <- readContentsFromSingleFileParameter("read_map", params, fileSizeLimitationConfig.readMapLimit)
       wdlMap <- WomMap.fromTsv(contents, WomMapType(WomAnyType, WomAnyType))
     } yield wdlMap
-  }
 
-  def read_object(params: Seq[Try[WomValue]]): Try[WomObject] = {
+  def read_object(params: Seq[Try[WomValue]]): Try[WomObject] =
     extractObjects("read_object", params) map {
       case array if array.length == 1 => array.head
-      case _ => throw new IllegalArgumentException("read_object yields an Object and thus can only read 2-rows TSV files. Try using read_objects instead.")
+      case _ =>
+        throw new IllegalArgumentException(
+          "read_object yields an Object and thus can only read 2-rows TSV files. Try using read_objects instead."
+        )
     }
-  }
 
-  def read_tsv(params: Seq[Try[WomValue]]): Try[WomArray] = {
+  def read_tsv(params: Seq[Try[WomValue]]): Try[WomArray] =
     for {
       contents <- readContentsFromSingleFileParameter("read_tsv", params, fileSizeLimitationConfig.readTsvLimit)
       wdlArray = WomArray.fromTsv(contents)
     } yield wdlArray
-  }
 
-  def read_boolean(params: Seq[Try[WomValue]]): Try[WomBoolean] = {
-    readContentsFromSingleFileParameter("read_boolean", params, fileSizeLimitationConfig.readBoolLimit).map(s => WomString(s.trim)) map { s => WomBoolean(java.lang.Boolean.parseBoolean(s.value.trim.toLowerCase)) }
-  }
+  def read_boolean(params: Seq[Try[WomValue]]): Try[WomBoolean] =
+    readContentsFromSingleFileParameter("read_boolean", params, fileSizeLimitationConfig.readBoolLimit).map(s =>
+      WomString(s.trim)
+    ) map { s => WomBoolean(java.lang.Boolean.parseBoolean(s.value.trim.toLowerCase)) }
 
   def globHelper(pattern: String): Seq[String]
 
-  final def glob(params: Seq[Try[WomValue]]): Try[WomArray] = {
+  final def glob(params: Seq[Try[WomValue]]): Try[WomArray] =
     for {
       pattern <- extractSingleArgument("glob", params)
       womString <- WomStringType.coerceRawValue(pattern)
       patternString = womString.valueString
       filePaths <- Try(globHelper(patternString))
     } yield WomArray(WomArrayType(WomSingleFileType), filePaths.map(WomSingleFile))
-  }
 
   def basename(params: Seq[Try[WomValue]]): Try[WomString] = {
 
@@ -113,8 +135,8 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
         val message = s"Bad number of arguments to basename(filename, suffixToStrip = ''): ${params.size}"
         Failure(new IllegalArgumentException(message))
       case _ =>
-        val failures = params collect {
-          case Failure(e) => e
+        val failures = params collect { case Failure(e) =>
+          e
         }
         Failure(AggregatedException("Failures evaluating basename parameters", failures))
     }
@@ -128,34 +150,51 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
     } yield WomString(suffixless)
   }
 
-  def floor(params: Seq[Try[WomValue]]): Try[WomInteger] = {
-    extractSingleArgument("floor", params) flatMap { f => WomFloatType.coerceRawValue(f) } map { f => WomInteger(Math.floor(f.asInstanceOf[WomFloat].value).toInt) }
-  }
+  def floor(params: Seq[Try[WomValue]]): Try[WomInteger] =
+    extractSingleArgument("floor", params) flatMap { f => WomFloatType.coerceRawValue(f) } map { f =>
+      WomInteger(Math.floor(f.asInstanceOf[WomFloat].value).toInt)
+    }
 
-  def round(params: Seq[Try[WomValue]]): Try[WomInteger] = {
-    extractSingleArgument("round", params) flatMap { f => WomFloatType.coerceRawValue(f) } map { f => WomInteger(Math.round(f.asInstanceOf[WomFloat].value).toInt) }
-  }
+  def round(params: Seq[Try[WomValue]]): Try[WomInteger] =
+    extractSingleArgument("round", params) flatMap { f => WomFloatType.coerceRawValue(f) } map { f =>
+      WomInteger(Math.round(f.asInstanceOf[WomFloat].value).toInt)
+    }
 
-  def ceil(params: Seq[Try[WomValue]]): Try[WomInteger] = {
-    extractSingleArgument("ceil", params) flatMap { f => WomFloatType.coerceRawValue(f) } map { f => WomInteger(Math.ceil(f.asInstanceOf[WomFloat].value).toInt) }
-  }
+  def ceil(params: Seq[Try[WomValue]]): Try[WomInteger] =
+    extractSingleArgument("ceil", params) flatMap { f => WomFloatType.coerceRawValue(f) } map { f =>
+      WomInteger(Math.ceil(f.asInstanceOf[WomFloat].value).toInt)
+    }
 
-  def transpose(params: Seq[Try[WomValue]]): Try[WomArray] = {
+  def transpose(params: Seq[Try[WomValue]]): Try[WomArray] =
     params.size match {
       case 1 => params.head flatMap EngineFunctions.transpose
-      case n => Failure(new IllegalArgumentException(s"Invalid number of parameters for engine function transpose: $n. Ensure transpose(x: Array[Array[X]]) takes exactly 1 parameters."))
+      case n =>
+        Failure(
+          new IllegalArgumentException(
+            s"Invalid number of parameters for engine function transpose: $n. Ensure transpose(x: Array[Array[X]]) takes exactly 1 parameters."
+          )
+        )
     }
-  }
 
   def length(params: Seq[Try[WomValue]]): Try[WomInteger] = {
     def extractArguments: Try[WomValue] = params.size match {
       case 1 => params.head
-      case n => Failure(new IllegalArgumentException(s"Invalid number of parameters for engine function length(): $n. length() takes exactly 1 parameter."))
+      case n =>
+        Failure(
+          new IllegalArgumentException(
+            s"Invalid number of parameters for engine function length(): $n. length() takes exactly 1 parameter."
+          )
+        )
     }
 
     def arrayLength(value: WomValue): Try[WomInteger] = value match {
       case WomArray(_, arrayValues) => Success(WomInteger(arrayValues.length))
-      case bad => Failure(new UnsupportedOperationException(s"length() expects one parameter of type Array but got one parameter of type ${bad.womType.stableName}"))
+      case bad =>
+        Failure(
+          new UnsupportedOperationException(
+            s"length() expects one parameter of type Array but got one parameter of type ${bad.womType.stableName}"
+          )
+        )
     }
 
     extractArguments flatMap arrayLength
@@ -164,7 +203,12 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
   def flatten(params: Seq[Try[WomValue]]): Try[WomValue] = {
     def getFlatValues(v: WomValue): Try[Seq[WomValue]] = v match {
       case WomArrayLike(WomArray(_, values)) => Success(values.toList)
-      case other => Failure(new IllegalArgumentException(s"Invalid argument to flatten: ${other.womType.stableName}, flatten requires an Array[Array[_]]"))
+      case other =>
+        Failure(
+          new IllegalArgumentException(
+            s"Invalid argument to flatten: ${other.womType.stableName}, flatten requires an Array[Array[_]]"
+          )
+        )
     }
 
     val arg: Try[WomValue] = extractSingleArgument("flatten", params)
@@ -173,7 +217,11 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
         val llt: Try[Seq[Seq[WomValue]]] = TryUtil.sequence(arrayValues.map(getFlatValues))
         llt.map(ll => WomArray(WomArrayType(elemType), ll.flatten))
       case bad =>
-        Failure(new UnsupportedOperationException(s"flatten() expects one parameter of type Array[Array[T]] but got one parameter of type ${bad.womType.stableName}"))
+        Failure(
+          new UnsupportedOperationException(
+            s"flatten() expects one parameter of type Array[Array[T]] but got one parameter of type ${bad.womType.stableName}"
+          )
+        )
     }
   }
 
@@ -183,13 +231,18 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
       case n => Failure(new UnsupportedOperationException(s"prefix() expects two parameters but got $n"))
     }
 
-    val makePrefixedString = (prefixString: WomValue, elements: WomValue) => (prefixString, elements) match {
-      case (WomString(p), WomArray(WomArrayType(etype), es)) if etype.isInstanceOf[WomPrimitiveType] =>
-        val result = es map { e => WomString(p + e.valueString) }
-        Success(WomArray(WomArrayType(WomStringType), result))
-      case (_, _) =>
-        Failure(new UnsupportedOperationException(s"The function prefix expect arguments (String, Array[X]) where X is a primitive type, but got (${prefixString.womType.stableName}, ${elements.womType.stableName})"))
-    }
+    val makePrefixedString = (prefixString: WomValue, elements: WomValue) =>
+      (prefixString, elements) match {
+        case (WomString(p), WomArray(WomArrayType(etype), es)) if etype.isInstanceOf[WomPrimitiveType] =>
+          val result = es map { e => WomString(p + e.valueString) }
+          Success(WomArray(WomArrayType(WomStringType), result))
+        case (_, _) =>
+          Failure(
+            new UnsupportedOperationException(
+              s"The function prefix expect arguments (String, Array[X]) where X is a primitive type, but got (${prefixString.womType.stableName}, ${elements.womType.stableName})"
+            )
+          )
+      }
 
     extractTwoArguments flatMap makePrefixedString.tupled
   }
@@ -197,31 +250,44 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
   def range(params: Seq[Try[WomValue]]): Try[WomArray] = {
     def extractAndValidateArguments = params.size match {
       case 1 => validateArguments(params.head)
-      case n => Failure(new IllegalArgumentException(s"Invalid number of parameters for engine function range: $n. Ensure range(x: WdlInteger) takes exactly 1 parameters."))
+      case n =>
+        Failure(
+          new IllegalArgumentException(
+            s"Invalid number of parameters for engine function range: $n. Ensure range(x: WdlInteger) takes exactly 1 parameters."
+          )
+        )
     }
 
     def validateArguments(value: Try[WomValue]) = value match {
       case Success(intValue: WomValue) if WomIntegerType.isCoerceableFrom(intValue.womType) =>
         Integer.valueOf(intValue.valueString) match {
           case i if i >= 0 => Success(i)
-          case n => Failure(new IllegalArgumentException(s"Parameter to seq must be greater than or equal to 0 (but got $n)"))
+          case n =>
+            Failure(new IllegalArgumentException(s"Parameter to seq must be greater than or equal to 0 (but got $n)"))
         }
       case _ => Failure(new IllegalArgumentException(s"Invalid parameter for engine function seq: $value."))
     }
 
-    extractAndValidateArguments map { intValue => WomArray(WomArrayType(WomIntegerType), (0 until intValue).map(WomInteger)) }
+    extractAndValidateArguments map { intValue =>
+      WomArray(WomArrayType(WomIntegerType), (0 until intValue).map(WomInteger))
+    }
   }
 
   def sub(params: Seq[Try[WomValue]]): Try[WomString] = {
     def extractArguments = params.size match {
       case 3 => Success((params.head, params(1), params(2)))
-      case n => Failure(new IllegalArgumentException(s"Invalid number of parameters for engine function sub: $n. sub takes exactly 3 parameters."))
+      case n =>
+        Failure(
+          new IllegalArgumentException(
+            s"Invalid number of parameters for engine function sub: $n. sub takes exactly 3 parameters."
+          )
+        )
     }
 
     def validateArguments(values: (Try[WomValue], Try[WomValue], Try[WomValue])) = values match {
       case (Success(strValue), Success(WomString(pattern)), Success(replaceValue))
-        if WomStringType.isCoerceableFrom(strValue.womType) &&
-          WomStringType.isCoerceableFrom(replaceValue.womType) =>
+          if WomStringType.isCoerceableFrom(strValue.womType) &&
+            WomStringType.isCoerceableFrom(replaceValue.womType) =>
         Success((strValue.valueString, pattern, replaceValue.valueString))
       case _ => Failure(new IllegalArgumentException(s"Invalid parameters for engine function sub: $values."))
     }
@@ -232,23 +298,40 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
     } yield WomString(pattern.r.replaceAllIn(str, replace))
   }
 
-  private val SelectFirstEmptyInput = Failure(new IllegalArgumentException("select_first failed. The input array was empty."))
+  private val SelectFirstEmptyInput = Failure(
+    new IllegalArgumentException("select_first failed. The input array was empty.")
+  )
   def select_first(params: Seq[Try[WomValue]]): Try[WomValue] = extractSingleArgument("select_first", params) flatMap {
     case WomArray(WomArrayType(WomOptionalType(memberType)), arrayValue) =>
-      if (arrayValue.isEmpty) SelectFirstEmptyInput else (arrayValue collectFirst {
-        case WomOptionalValue(_, Some(womValue)) => womValue
-        case womValue if memberType.isCoerceableFrom(womValue.womType) =>
-          memberType.coerceRawValue(womValue).get}).map(Success(_)).getOrElse(Failure(new IllegalArgumentException("select_first failed. All provided values were empty.")))
-    case WomArray(WomArrayType(_), arrayValue) => if (arrayValue.isEmpty) SelectFirstEmptyInput else Success(arrayValue.head)
-    case other => Failure(new IllegalArgumentException(s"select_first must take an array but got ${other.womType.stableName}: ${other.toWomString}"))
+      if (arrayValue.isEmpty) SelectFirstEmptyInput
+      else
+        (arrayValue collectFirst {
+          case WomOptionalValue(_, Some(womValue)) => womValue
+          case womValue if memberType.isCoerceableFrom(womValue.womType) =>
+            memberType.coerceRawValue(womValue).get
+        }).map(Success(_))
+          .getOrElse(Failure(new IllegalArgumentException("select_first failed. All provided values were empty.")))
+    case WomArray(WomArrayType(_), arrayValue) =>
+      if (arrayValue.isEmpty) SelectFirstEmptyInput else Success(arrayValue.head)
+    case other =>
+      Failure(
+        new IllegalArgumentException(
+          s"select_first must take an array but got ${other.womType.stableName}: ${other.toWomString}"
+        )
+      )
   }
 
   def select_all(params: Seq[Try[WomValue]]): Try[WomArray] = extractSingleArgument("select_all", params) flatMap {
     case WomArray(WomArrayType(WomOptionalType(memberType)), arrayValue) =>
-      Success(WomArray(WomArrayType(memberType), arrayValue collect {
-        case WomOptionalValue(_, Some(womValue)) => womValue
-        case womValue if memberType.isCoerceableFrom(womValue.womType) => memberType.coerceRawValue(womValue).get
-      }))
+      Success(
+        WomArray(
+          WomArrayType(memberType),
+          arrayValue collect {
+            case WomOptionalValue(_, Some(womValue)) => womValue
+            case womValue if memberType.isCoerceableFrom(womValue.womType) => memberType.coerceRawValue(womValue).get
+          }
+        )
+      )
     case allValid @ WomArray(WomArrayType(_), _) => Success(allValid)
     case other => Failure(new IllegalArgumentException("select_all must take an array but got: " + other.toWomString))
   }
@@ -259,26 +342,34 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
   }
 
   def zip(params: Seq[Try[WomValue]]): Try[WomArray] = {
-    val badArgsFailure = Failure(new IllegalArgumentException(s"Invalid parameters for engine function zip: $params. Requires exactly two evaluated array values of equal length."))
+    val badArgsFailure = Failure(
+      new IllegalArgumentException(
+        s"Invalid parameters for engine function zip: $params. Requires exactly two evaluated array values of equal length."
+      )
+    )
 
     for {
       values <- extractTwoParams(params, badArgsFailure)
       (left, right) <- assertEquallySizedArrays(values, badArgsFailure)
       leftType = left.womType.memberType
       rightType = right.womType.memberType
-      zipped = left.value.zip(right.value) map { case (l,r) => WomPair(l, r) }
+      zipped = left.value.zip(right.value) map { case (l, r) => WomPair(l, r) }
     } yield WomArray(WomArrayType(WomPairType(leftType, rightType)), zipped)
   }
 
   def cross(params: Seq[Try[WomValue]]): Try[WomArray] = {
-    val badArgsFailure = Failure(new IllegalArgumentException(s"Invalid parameters for engine function cross: $params. Requires exactly two evaluated array values of equal length."))
+    val badArgsFailure = Failure(
+      new IllegalArgumentException(
+        s"Invalid parameters for engine function cross: $params. Requires exactly two evaluated array values of equal length."
+      )
+    )
 
     for {
       values <- extractTwoParams(params, badArgsFailure)
       (left, right) <- assertArrays(values, badArgsFailure)
       leftType = left.womType.memberType
       rightType = right.womType.memberType
-      crossed = stdLibCrossProduct(left.value, right.value) map { case (l,r) => WomPair(l, r) }
+      crossed = stdLibCrossProduct(left.value, right.value) map { case (l, r) => WomPair(l, r) }
     } yield WomArray(WomArrayType(WomPairType(leftType, rightType)), crossed)
   }
 
@@ -287,12 +378,14 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
     * as a File and attempts to read the contents of that file and returns back the contents
     * as a String
     */
-  private def readContentsFromSingleFileParameter(functionName: String, params: Seq[Try[WomValue]], sizeLimit: Int): Try[String] = {
+  private def readContentsFromSingleFileParameter(functionName: String,
+                                                  params: Seq[Try[WomValue]],
+                                                  sizeLimit: Int
+  ): Try[String] =
     for {
       singleArgument <- extractSingleArgument(functionName, params)
       string = readFile(singleArgument.valueString, sizeLimit)
     } yield string
-  }
 
   private def extractObjects(functionName: String, params: Seq[Try[WomValue]]): Try[Array[WomObject]] = for {
     contents <- readContentsFromSingleFileParameter(functionName, params, fileSizeLimitationConfig.readObjectLimit)
@@ -301,18 +394,26 @@ trait WdlStandardLibraryFunctions extends WdlFunctions[WomValue] {
 }
 
 object WdlStandardLibraryFunctions {
-  def fromIoFunctionSet(ioFunctionSet: IoFunctionSet, _fileSizeLimitationConfig: FileSizeLimitationConfig) = new WdlStandardLibraryFunctions {
-    override def readFile(path: String, sizeLimit: Int): String = Await.result(ioFunctionSet.readFile(path, Option(sizeLimit), failOnOverflow = true), Duration.Inf)
+  def fromIoFunctionSet(ioFunctionSet: IoFunctionSet, _fileSizeLimitationConfig: FileSizeLimitationConfig) =
+    new WdlStandardLibraryFunctions {
+      override def readFile(path: String, sizeLimit: Int): String =
+        Await.result(ioFunctionSet.readFile(path, Option(sizeLimit), failOnOverflow = true), Duration.Inf)
 
-    override def writeFile(path: String, content: String): Try[WomFile] = Try(Await.result(ioFunctionSet.writeFile(path, content), Duration.Inf))
+      override def writeFile(path: String, content: String): Try[WomFile] = Try(
+        Await.result(ioFunctionSet.writeFile(path, content), Duration.Inf)
+      )
 
-    override def stdout(params: Seq[Try[WomValue]]): Try[WomFile] = Success(WomSingleFile(ioFunctionSet.pathFunctions.stdout))
+      override def stdout(params: Seq[Try[WomValue]]): Try[WomFile] = Success(
+        WomSingleFile(ioFunctionSet.pathFunctions.stdout)
+      )
 
-    override def stderr(params: Seq[Try[WomValue]]): Try[WomFile] = Success(WomSingleFile(ioFunctionSet.pathFunctions.stderr))
+      override def stderr(params: Seq[Try[WomValue]]): Try[WomFile] = Success(
+        WomSingleFile(ioFunctionSet.pathFunctions.stderr)
+      )
 
-    override def globHelper(pattern: String): Seq[String] = Await.result(ioFunctionSet.glob(pattern), Duration.Inf)
+      override def globHelper(pattern: String): Seq[String] = Await.result(ioFunctionSet.glob(pattern), Duration.Inf)
 
-    override def size(params: Seq[Try[WomValue]]): Try[WomFloat] = {
+      override def size(params: Seq[Try[WomValue]]): Try[WomFloat] = {
         // Inner function: get the memory unit from the second (optional) parameter
         def toUnit(womValue: Try[WomValue]) = womValue flatMap { unit => Try(MemoryUnit.fromSuffix(unit.valueString)) }
 
@@ -325,68 +426,98 @@ object WdlStandardLibraryFunctions {
 
         // Inner function: Get the file size, allowing for unpacking of optionals
         def optionalSafeFileSize(value: WomValue): Try[Long] = value match {
-          case f if f.isInstanceOf[WomSingleFile] || WomSingleFileType.isCoerceableFrom(f.womType) => Try(Await.result(ioFunctionSet.size(f.valueString), Duration.Inf))
+          case f if f.isInstanceOf[WomSingleFile] || WomSingleFileType.isCoerceableFrom(f.womType) =>
+            Try(Await.result(ioFunctionSet.size(f.valueString), Duration.Inf))
           case WomOptionalValue(_, Some(o)) => optionalSafeFileSize(o)
           case WomOptionalValue(f, None) if isOptionalOfFileType(f) => Success(0L)
-          case _ => Failure(new Exception(s"The 'size' method expects a 'File' or 'File?' argument but instead got ${value.womType.stableName}."))
+          case _ =>
+            Failure(
+              new Exception(
+                s"The 'size' method expects a 'File' or 'File?' argument but instead got ${value.womType.stableName}."
+              )
+            )
         }
 
         // Inner function: get the file size and convert into the requested memory unit
-        def fileSize(womValue: Try[WomValue], convertTo: Try[MemoryUnit] = Success(MemoryUnit.Bytes)): Try[Double] = {
+        def fileSize(womValue: Try[WomValue], convertTo: Try[MemoryUnit] = Success(MemoryUnit.Bytes)): Try[Double] =
           for {
             value <- womValue
             unit <- convertTo
             fileSize <- optionalSafeFileSize(value)
           } yield MemorySize(fileSize.toDouble, MemoryUnit.Bytes).to(unit).amount
-        }
 
         params match {
           case _ if params.length == 1 => fileSize(params.head) map WomFloat.apply
           case _ if params.length == 2 => fileSize(params.head, toUnit(params.tail.head)) map WomFloat.apply
-          case _ => Failure(new UnsupportedOperationException(s"Expected one or two parameters but got ${params.length} instead."))
+          case _ =>
+            Failure(
+              new UnsupportedOperationException(s"Expected one or two parameters but got ${params.length} instead.")
+            )
         }
-    }
+      }
 
-    override protected def fileSizeLimitationConfig: FileSizeLimitationConfig = _fileSizeLimitationConfig
-  }
+      override protected def fileSizeLimitationConfig: FileSizeLimitationConfig = _fileSizeLimitationConfig
+    }
 
   def crossProduct[A, B](as: Seq[A], bs: Seq[B]): Seq[(A, B)] = for {
     a <- as
     b <- bs
   } yield (a, b)
 
-  def extractTwoParams[A](params: Seq[Try[A]], badArgsFailure: Failure[Nothing]): Try[(A, A)] = {
+  def extractTwoParams[A](params: Seq[Try[A]], badArgsFailure: Failure[Nothing]): Try[(A, A)] =
     if (params.lengthCompare(2) != 0) { badArgsFailure }
-    else for {
-      left <- params.head
-      right <- params(1)
-    } yield (left, right)
-  }
-
-  def assertEquallySizedArrays[A](values: (WomValue, WomValue), badArgsFailure: Failure[Nothing] ): Try[(WomArray, WomArray)] = values match {
-    case (leftArray: WomArray, rightArray: WomArray) if leftArray.value.lengthCompare(rightArray.value.size) == 0 => Success((leftArray, rightArray))
+    else
+      for {
+        left <- params.head
+        right <- params(1)
+      } yield (left, right)
+
+  def assertEquallySizedArrays[A](values: (WomValue, WomValue),
+                                  badArgsFailure: Failure[Nothing]
+  ): Try[(WomArray, WomArray)] = values match {
+    case (leftArray: WomArray, rightArray: WomArray) if leftArray.value.lengthCompare(rightArray.value.size) == 0 =>
+      Success((leftArray, rightArray))
     case _ => badArgsFailure
   }
 
-  def assertArrays(values: (WomValue, WomValue), badArgsFailure: Failure[Nothing] ): Try[(WomArray, WomArray)] = values match {
-    case (leftArray: WomArray, rightArray: WomArray) => Success((leftArray, rightArray))
-    case _ => badArgsFailure
-  }
+  def assertArrays(values: (WomValue, WomValue), badArgsFailure: Failure[Nothing]): Try[(WomArray, WomArray)] =
+    values match {
+      case (leftArray: WomArray, rightArray: WomArray) => Success((leftArray, rightArray))
+      case _ => badArgsFailure
+    }
 }
 
 trait PureStandardLibraryFunctionsLike extends WdlStandardLibraryFunctions {
 
   def className = this.getClass.getCanonicalName
 
-  override def readFile(path: String, sizeLimit: Int): String = throw new UnsupportedOperationException(s"readFile not available in $className.")
-  override def writeFile(path: String, content: String): Try[WomFile] = throw new UnsupportedOperationException(s"writeFile not available in $className.")
-  override def read_json(params: Seq[Try[WomValue]]): Try[WomValue] = Failure(new UnsupportedOperationException(s"read_json not available in $className."))
-  override def write_json(params: Seq[Try[WomValue]]): Try[WomFile] = Failure(new UnsupportedOperationException(s"write_json not available in $className."))
-  override def size(params: Seq[Try[WomValue]]): Try[WomFloat] = Failure(new UnsupportedOperationException(s"size not available in $className."))
-  override def write_tsv(params: Seq[Try[WomValue]]): Try[WomFile] = Failure(new UnsupportedOperationException(s"write_tsv not available in $className."))
-  override def stdout(params: Seq[Try[WomValue]]): Try[WomFile] = Failure(new UnsupportedOperationException(s"stdout not available in $className."))
-  override def globHelper(pattern: String): Seq[String] = throw new UnsupportedOperationException(s"glob not available in $className.")
-  override def stderr(params: Seq[Try[WomValue]]): Try[WomFile] = Failure(new UnsupportedOperationException(s"stderr not available in $className."))
+  override def readFile(path: String, sizeLimit: Int): String = throw new UnsupportedOperationException(
+    s"readFile not available in $className."
+  )
+  override def writeFile(path: String, content: String): Try[WomFile] = throw new UnsupportedOperationException(
+    s"writeFile not available in $className."
+  )
+  override def read_json(params: Seq[Try[WomValue]]): Try[WomValue] = Failure(
+    new UnsupportedOperationException(s"read_json not available in $className.")
+  )
+  override def write_json(params: Seq[Try[WomValue]]): Try[WomFile] = Failure(
+    new UnsupportedOperationException(s"write_json not available in $className.")
+  )
+  override def size(params: Seq[Try[WomValue]]): Try[WomFloat] = Failure(
+    new UnsupportedOperationException(s"size not available in $className.")
+  )
+  override def write_tsv(params: Seq[Try[WomValue]]): Try[WomFile] = Failure(
+    new UnsupportedOperationException(s"write_tsv not available in $className.")
+  )
+  override def stdout(params: Seq[Try[WomValue]]): Try[WomFile] = Failure(
+    new UnsupportedOperationException(s"stdout not available in $className.")
+  )
+  override def globHelper(pattern: String): Seq[String] = throw new UnsupportedOperationException(
+    s"glob not available in $className."
+  )
+  override def stderr(params: Seq[Try[WomValue]]): Try[WomFile] = Failure(
+    new UnsupportedOperationException(s"stderr not available in $className.")
+  )
   override def fileSizeLimitationConfig: FileSizeLimitationConfig = FileSizeLimitationConfig.default
 }
 
@@ -422,20 +553,36 @@ class WdlStandardLibraryFunctionsType extends WdlFunctions[WomType] {
     params.toList match {
       case Success(f) :: Nil if isGoodFirstSizeParam(f) => Success(WomFloatType)
       case Success(f) :: Success(WomStringType) :: Nil if isGoodFirstSizeParam(f) => Success(WomFloatType)
-      case other => Failure(new Exception(s"Unexpected arguments to function `size`. Expected 'size(file: File [, unit: String])' but got 'size(${other.map(_.map(_.stableName)).mkString(", ")})'"))
+      case other =>
+        Failure(
+          new Exception(
+            s"Unexpected arguments to function `size`. Expected 'size(file: File [, unit: String])' but got 'size(${other
+                .map(_.map(_.stableName))
+                .mkString(", ")})'"
+          )
+        )
     }
   }
   def length(params: Seq[Try[WomType]]): Try[WomType] = params.toList match {
     case Success(WomArrayType(_)) :: Nil => Success(WomIntegerType)
     case _ =>
       val badArgs = params.mkString(", ")
-      Failure(new Exception(s"Unexpected arguments to function `length`. `length` takes a parameter of type Array but got: $badArgs"))
+      Failure(
+        new Exception(
+          s"Unexpected arguments to function `length`. `length` takes a parameter of type Array but got: $badArgs"
+        )
+      )
   }
   def prefix(params: Seq[Try[WomType]]): Try[WomType] = params.toList match {
-    case Success(WomStringType) :: Success(WomArrayType(_: WomPrimitiveType)) :: Nil => Success(WomArrayType(WomStringType))
+    case Success(WomStringType) :: Success(WomArrayType(_: WomPrimitiveType)) :: Nil =>
+      Success(WomArrayType(WomStringType))
     case _ =>
       val badArgs = params.mkString(", ")
-      Failure(new Exception(s"Unexpected arguments to function `prefix`.  `prefix` takes parameters of type String and Array[<primitive>] but got: $badArgs"))
+      Failure(
+        new Exception(
+          s"Unexpected arguments to function `prefix`.  `prefix` takes parameters of type String and Array[<primitive>] but got: $badArgs"
+        )
+      )
   }
   def sub(params: Seq[Try[WomType]]): Try[WomType] = Success(WomStringType)
   def range(params: Seq[Try[WomType]]): Try[WomType] = Success(WomArrayType(WomIntegerType))
@@ -453,7 +600,9 @@ class WdlStandardLibraryFunctionsType extends WdlFunctions[WomType] {
   }
   def basename(params: Seq[Try[WomType]]): Try[WomType] = params.toList match {
     case Success(fType) :: Nil if WomStringType.isCoerceableFrom(fType) => Success(WomStringType)
-    case Success(fType) :: Success(sType) :: Nil if WomStringType.isCoerceableFrom(fType) && WomStringType.isCoerceableFrom(sType) => Success(WomStringType)
+    case Success(fType) :: Success(sType) :: Nil
+        if WomStringType.isCoerceableFrom(fType) && WomStringType.isCoerceableFrom(sType) =>
+      Success(WomStringType)
     case _ => Failure(new Exception(s"Unexpected basename arguments: $params"))
   }
   def transpose(params: Seq[Try[WomType]]): Try[WomType] = params.toList match {
@@ -462,17 +611,29 @@ class WdlStandardLibraryFunctionsType extends WdlFunctions[WomType] {
   }
   def select_first(params: Seq[Try[WomType]]): Try[WomType] = extractSingleArgument("select_first", params) flatMap {
     case WomArrayType(WomOptionalType(innerType)) => Success(innerType)
-    case other => Failure(new IllegalArgumentException(s"select_first failed. It expects an array of optional values but got ${other.stableName}."))
+    case other =>
+      Failure(
+        new IllegalArgumentException(
+          s"select_first failed. It expects an array of optional values but got ${other.stableName}."
+        )
+      )
   }
   def select_all(params: Seq[Try[WomType]]): Try[WomType] = extractSingleArgument("select_all", params) flatMap {
     case WomArrayType(WomOptionalType(innerType)) => Success(WomArrayType(innerType))
-    case other => Failure(new IllegalArgumentException(s"select_all failed. It expects an array of optional values but got ${other.stableName}."))
-  }
-  def defined(params: Seq[Try[WomType]]): Try[WomType] = extractSingleArgument("defined", params).map(_ => WomBooleanType)
+    case other =>
+      Failure(
+        new IllegalArgumentException(
+          s"select_all failed. It expects an array of optional values but got ${other.stableName}."
+        )
+      )
+  }
+  def defined(params: Seq[Try[WomType]]): Try[WomType] =
+    extractSingleArgument("defined", params).map(_ => WomBooleanType)
   def zip(params: Seq[Try[WomType]]): Try[WomType] = {
     val badArgsFailure = Failure(new Exception(s"Unexpected zip parameters: $params"))
     WdlStandardLibraryFunctions.extractTwoParams(params, badArgsFailure) flatMap {
-      case (arrayType1: WomArrayType, arrayType2: WomArrayType) => Success(WomArrayType(WomPairType(arrayType1.memberType, arrayType2.memberType)))
+      case (arrayType1: WomArrayType, arrayType2: WomArrayType) =>
+        Success(WomArrayType(WomPairType(arrayType1.memberType, arrayType2.memberType)))
       case _ => badArgsFailure
     }
   }
@@ -480,7 +641,8 @@ class WdlStandardLibraryFunctionsType extends WdlFunctions[WomType] {
 
   def flatten(params: Seq[Try[WomType]]): Try[WomType] = extractSingleArgument("flatten", params) flatMap {
     case WomArrayType(inner @ WomArrayType(_)) => Success(inner)
-    case otherType => Failure(new Exception(s"flatten requires an Array[Array[_]] argument but instead got ${otherType.stableName}"))
+    case otherType =>
+      Failure(new Exception(s"flatten requires an Array[Array[_]] argument but instead got ${otherType.stableName}"))
   }
 }
 
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/formatter/SyntaxFormatter.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/formatter/SyntaxFormatter.scala
index d96b8fee102..4a1dbcfd651 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/formatter/SyntaxFormatter.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/formatter/SyntaxFormatter.scala
@@ -48,9 +48,8 @@ object HtmlSyntaxHighlighter extends SyntaxHighlighter {
 class SyntaxFormatter(highlighter: SyntaxHighlighter = NullSyntaxHighlighter) {
   val indentLevel = 2
 
-  private def indent(s: String, i: Int): String = {
-    s.split("\n").map {" " * (i * indentLevel) + _}.mkString("\n")
-  }
+  private def indent(s: String, i: Int): String =
+    s.split("\n").map(" " * (i * indentLevel) + _).mkString("\n")
 
   def format(namespace: WdlNamespace): String = {
     val imports = namespace.imports.map(formatImport) match {
@@ -61,16 +60,22 @@ class SyntaxFormatter(highlighter: SyntaxHighlighter = NullSyntaxHighlighter) {
     /*
      TODO/FIXME: If 'body' is really a function of `namespace` then `WdlNamespace` should have a func which
      does the first part, and `NamespaceWithWorkflow` override it, call super and then adds on the second part
-    */
+     */
 
     val namespaceDefinitions = namespace.ast.getAttribute("body").asInstanceOf[AstList].asScala.toVector
 
-    val taskDefinitions = namespaceDefinitions collect { case a: Ast if a.getName == "Task" =>
-      formatTask(namespace.findTask(a.getAttribute("name").sourceString).getOrElse(throw new UnsupportedOperationException("Shouldn't happen")))
+    val taskDefinitions = namespaceDefinitions collect {
+      case a: Ast if a.getName == "Task" =>
+        formatTask(
+          namespace
+            .findTask(a.getAttribute("name").sourceString)
+            .getOrElse(throw new UnsupportedOperationException("Shouldn't happen"))
+        )
     }
 
     val workflowDefinitions = namespace match {
-      case n: WdlNamespaceWithWorkflow => namespaceDefinitions collect {case a: Ast if a.getName == "Workflow" => formatWorkflow(n.workflow)}
+      case n: WdlNamespaceWithWorkflow =>
+        namespaceDefinitions collect { case a: Ast if a.getName == "Workflow" => formatWorkflow(n.workflow) }
       case _ => Vector.empty[AstNode]
     }
     val definitions = taskDefinitions ++ workflowDefinitions
@@ -96,39 +101,38 @@ class SyntaxFormatter(highlighter: SyntaxHighlighter = NullSyntaxHighlighter) {
     val parameterMeta = formatMetaSection("parameter_meta", task.parameterMeta, 1)
     val sections = List(declarations, command, outputs, runtime, meta, parameterMeta).filter(_.nonEmpty)
     val header = s"""${highlighter.keyword("task")} ${highlighter.name(task.name)} {
-       |${sections.mkString("\n")}
-       |}"""
-     .stripMargin
+                    |${sections.mkString("\n")}
+                    |}""".stripMargin
     header
   }
 
-  private def formatMetaSection(section: String, attrs: Map[String, String], level: Int): String = {
+  private def formatMetaSection(section: String, attrs: Map[String, String], level: Int): String =
     attrs match {
       case m: Map[String, String] if m.nonEmpty =>
         val wdlAttrs = m map { case (k, v) => indent(s"$k: " + "\"" + v + "\"", 1) }
-        indent(
-          s"""${highlighter.keyword(section)} {
-             |${wdlAttrs.mkString("\n")}
-             |}""".stripMargin, level)
+        indent(s"""${highlighter.keyword(section)} {
+                  |${wdlAttrs.mkString("\n")}
+                  |}""".stripMargin,
+               level
+        )
       case _ => ""
     }
-  }
 
-  private def formatRuntimeSection(runtimeAttributes: WdlRuntimeAttributes, level: Int): String = {
+  private def formatRuntimeSection(runtimeAttributes: WdlRuntimeAttributes, level: Int): String =
     runtimeAttributes.attrs match {
       case m if m.nonEmpty =>
         val attrs = m map { case (k, v) => indent(s"$k: ${v.toWomString}", level) }
-        indent(
-          s"""${highlighter.keyword("runtime")} {
-             |${attrs.mkString("\n")}
-             |}""".stripMargin, level)
+        indent(s"""${highlighter.keyword("runtime")} {
+                  |${attrs.mkString("\n")}
+                  |}""".stripMargin,
+               level
+        )
       case _ => ""
     }
-  }
 
-  private def formatCommandSection(task: WdlTask, level:Int): String = {
+  private def formatCommandSection(task: WdlTask, level: Int): String = {
     val (sdelim: String, edelim: String) =
-      if (task.commandTemplate.collect({case s:StringCommandPart => s.literal}).mkString.contains("}")) ("<<<", ">>>")
+      if (task.commandTemplate.collect { case s: StringCommandPart => s.literal }.mkString.contains("}")) ("<<<", ">>>")
       else ("{", "}")
 
     val section = s"""${highlighter.section("command")} $sdelim
@@ -137,46 +141,48 @@ class SyntaxFormatter(highlighter: SyntaxHighlighter = NullSyntaxHighlighter) {
     indent(section.stripMargin, level)
   }
 
-  private def formatOutputs(outputs: Seq[TaskOutput], level:Int): String = {
+  private def formatOutputs(outputs: Seq[TaskOutput], level: Int): String = {
     val section = s"""${highlighter.section("output")} {
         |${outputs.map(formatOutput(_, 1)).mkString("\n")}
         |}"""
     indent(section.stripMargin, level)
   }
 
-  private def formatOutput(output: TaskOutput, level:Int): String = {
-    indent(s"${highlighter.womType(output.womType)} ${highlighter.variable(output.unqualifiedName)} = ${output.requiredExpression.toString(highlighter)}", level)
-  }
+  private def formatOutput(output: TaskOutput, level: Int): String =
+    indent(s"${highlighter.womType(output.womType)} ${highlighter
+               .variable(output.unqualifiedName)} = ${output.requiredExpression.toString(highlighter)}",
+           level
+    )
 
   private def formatWorkflow(workflow: WdlWorkflow): String = {
     val declarations = workflow.declarations.map(formatDeclaration(_, 1))
-    val children = workflow.children.collect({case c if !workflow.declarations.contains(c) => formatScope(c, 1) })
+    val children = workflow.children.collect { case c if !workflow.declarations.contains(c) => formatScope(c, 1) }
     val outputs = formatWorkflowOutputs(workflow.workflowOutputWildcards, 1)
     val meta = formatMetaSection("meta", workflow.meta, 1)
     val parameterMeta = formatMetaSection("parameter_meta", workflow.parameterMeta, 1)
     val sections = (declarations ++ children ++ Seq(meta, parameterMeta, outputs)).filter(_.nonEmpty)
     s"""${highlighter.keyword("workflow")} ${highlighter.name(workflow.unqualifiedName)} {
-        |${sections.mkString("\n")}
-        |}""".stripMargin
+       |${sections.mkString("\n")}
+       |}""".stripMargin
   }
 
-  private def formatWorkflowOutputs(outputs: Seq[WorkflowOutputWildcard], level: Int): String = {
+  private def formatWorkflowOutputs(outputs: Seq[WorkflowOutputWildcard], level: Int): String =
     outputs match {
       case x: Seq[WorkflowOutputWildcard] if x.nonEmpty =>
         val outputStrings = outputs.map(formatWorkflowOutput(_, 1))
         indent(s"""${highlighter.keyword("output")} {
                   |${outputStrings.mkString("\n")}
-                  |}""".stripMargin, level)
+                  |}""".stripMargin,
+               level
+        )
       case _ => ""
     }
-  }
 
-  private def formatWorkflowOutput(output: WorkflowOutputWildcard, level: Int): String = {
+  private def formatWorkflowOutput(output: WorkflowOutputWildcard, level: Int): String =
     output.wildcard match {
       case true => indent(s"${formatWorkflowOutputFqn(output.fqn)}.*", level)
       case false => indent(formatWorkflowOutputFqn(output.fqn), level)
     }
-  }
 
   private def formatWorkflowOutputFqn(fqn: String) = fqn.replaceFirst("[a-zA-Z0-9]+\\.", "")
 
@@ -196,24 +202,29 @@ class SyntaxFormatter(highlighter: SyntaxHighlighter = NullSyntaxHighlighter) {
     if (call.inputMappings.isEmpty) {
       indent(header, level)
     } else {
-      val inputString = call.inputMappings.map {case (k, v) =>
-        s"$k=${v.toString(highlighter)}"
-      }.mkString(", ")
+      val inputString = call.inputMappings
+        .map { case (k, v) =>
+          s"$k=${v.toString(highlighter)}"
+        }
+        .mkString(", ")
       indent(s"""$header {
-         |  input: $inputString
-         |}""".stripMargin, level)
+                |  input: $inputString
+                |}""".stripMargin,
+             level
+      )
     }
   }
 
   private def formatScatter(scatter: Scatter, level: Int): String = {
-    val children = scatter.children.collect({case c if !c.isInstanceOf[Declaration] => formatScope(c, 1) })
+    val children = scatter.children.collect { case c if !c.isInstanceOf[Declaration] => formatScope(c, 1) }
     indent(
       s"""${highlighter.keyword("scatter")} (${scatter.item} in ${scatter.collection.toString(highlighter)}) {
-       |${children.mkString("\n")}
-       |}""".stripMargin, level)
+         |${children.mkString("\n")}
+         |}""".stripMargin,
+      level
+    )
   }
 
-  private def formatCallAlias(call: WdlTaskCall): String = {
-    call.alias.map {a => s" as ${highlighter.alias(a)}"}.getOrElse("")
-  }
+  private def formatCallAlias(call: WdlTaskCall): String =
+    call.alias.map(a => s" as ${highlighter.alias(a)}").getOrElse("")
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/package.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/package.scala
index c3326d26f36..4dd52a9eabf 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/package.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/package.scala
@@ -18,5 +18,6 @@ package object model {
   type Draft2ImportResolver = String => Draft2ResolvedImportBundle
   type OutputResolver = (WdlGraphNode, Option[Int]) => Try[WomValue]
 
-  val NoOutputResolver: OutputResolver = (node: WdlGraphNode, i: Option[Int]) => Failure(OutputVariableLookupException(node, i))
+  val NoOutputResolver: OutputResolver = (node: WdlGraphNode, i: Option[Int]) =>
+    Failure(OutputVariableLookupException(node, i))
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlCallOutputsObjectType.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlCallOutputsObjectType.scala
index 257eca6dd59..107a68410e5 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlCallOutputsObjectType.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlCallOutputsObjectType.scala
@@ -7,7 +7,7 @@ import wom.types.WomObjectTypeLike
 case class WdlCallOutputsObjectType(call: WdlCall) extends WomObjectTypeLike {
   val stableName: String = "Object"
 
-  override protected def coercion = {
-    case o: WdlCallOutputsObject => o
+  override protected def coercion = { case o: WdlCallOutputsObject =>
+    o
   }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlFlavoredWomType.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlFlavoredWomType.scala
index 4a74ef94842..fb38714109e 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlFlavoredWomType.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlFlavoredWomType.scala
@@ -13,23 +13,25 @@ object WdlFlavoredWomType {
   private val parser = new WdlParser()
 
   implicit class FromString(val womType: WomType) extends AnyVal {
+
     /**
       * Converts WDL source into a WomValue of this type, if possible.
       *
       * @param workflowSource source code representing the WomValue
       * @return The WomValue
       */
-    //TODO: return a Try ?
-    def fromWorkflowSource(workflowSource: WorkflowSource): WomValue = {
+    // TODO: return a Try ?
+    def fromWorkflowSource(workflowSource: WorkflowSource): WomValue =
       womType match {
         case WomFloatType => WomFloat(workflowSource.toDouble)
         case WomIntegerType => WomInteger(workflowSource.toInt)
         case WdlExpressionType => WdlExpression.fromString(workflowSource)
         case WomBooleanType => WomBoolean(workflowSource.toBoolean)
-        case WdlNamespaceType => throw new UnsupportedOperationException // This is what the original code was doing and clearly this is right.
+        case WdlNamespaceType =>
+          throw new UnsupportedOperationException // This is what the original code was doing and clearly this is right.
         case _ =>
           val tokens = parser.lex(workflowSource, "string")
-          val terminalMap = tokens.asScala.toVector.map {(_, workflowSource)}.toMap
+          val terminalMap = tokens.asScala.toVector.map((_, workflowSource)).toMap
           val wdlSyntaxErrorFormatter = WdlSyntaxErrorFormatter(terminalMap)
 
           /* Parsing as an expression is not sufficient... only a subset of these
@@ -40,15 +42,14 @@ object WdlFlavoredWomType {
 
           ast.womValue(womType, wdlSyntaxErrorFormatter)
       }
-    }
   }
 
-  def fromDisplayString(wdlString: String): WomType = {
+  def fromDisplayString(wdlString: String): WomType =
     wdlString match {
       case "Expression" => WdlExpressionType
       case _ =>
         val tokens = parser.lex(wdlString, "string")
-        val terminalMap = tokens.asScala.toVector.map {(_, wdlString)}.toMap
+        val terminalMap = tokens.asScala.toVector.map((_, wdlString)).toMap
         val wdlSyntaxErrorFormatter = WdlSyntaxErrorFormatter(terminalMap)
 
         /* parse_type_e() is the parse function for the $type_e nonterminal in grammar.hgr */
@@ -56,5 +57,4 @@ object WdlFlavoredWomType {
 
         ast.womType(wdlSyntaxErrorFormatter)
     }
-  }
 }
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlNamespaceType.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlNamespaceType.scala
index 41431bd6248..7e83ec259e0 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlNamespaceType.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/types/WdlNamespaceType.scala
@@ -6,7 +6,7 @@ import wom.types.WomType
 case object WdlNamespaceType extends WomType {
   override def stableName: String = "Namespace"
 
-  override protected def coercion = {
-    case n: WdlNamespace => n
+  override protected def coercion = { case n: WdlNamespace =>
+    n
   }
 }
diff --git a/wdl/model/draft2/src/test/scala/wdl/AstSpec.scala b/wdl/model/draft2/src/test/scala/wdl/AstSpec.scala
index 1800ef2669e..20ca07d83a7 100644
--- a/wdl/model/draft2/src/test/scala/wdl/AstSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/AstSpec.scala
@@ -17,9 +17,11 @@ class AstSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   }
 
   it should "produce AST with 3 Call nodes in the Workflow node" in {
-    AstTools.findAsts(
-      AstTools.findAsts(namespace.ast, "Workflow").head,
-      "Call"
-    ).size shouldEqual 3
+    AstTools
+      .findAsts(
+        AstTools.findAsts(namespace.ast, "Workflow").head,
+        "Call"
+      )
+      .size shouldEqual 3
   }
 }
diff --git a/wdl/model/draft2/src/test/scala/wdl/DeclarationSpec.scala b/wdl/model/draft2/src/test/scala/wdl/DeclarationSpec.scala
index 91303d3482c..9a66f5abc9e 100644
--- a/wdl/model/draft2/src/test/scala/wdl/DeclarationSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/DeclarationSpec.scala
@@ -10,7 +10,6 @@ import wom.values._
 
 import scala.util.{Failure, Success}
 
-
 class DeclarationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   lazy val wdlSource = (new SampleWdl.DeclarationsWdl).workflowSource()
   lazy val namespace = WdlNamespaceWithWorkflow.load(wdlSource, Seq.empty).get
@@ -148,44 +147,44 @@ class DeclarationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   }
 
   "A workflow" should "allow for JIT evaluation of declarations" in {
-    val wdl =  """task t {
-                 |    String i
-                 |    command {
-                 |        echo "${i}"
-                 |    }
-                 |    output {
-                 |        String o = read_string(stdout())
-                 |    }
-                 |}
-                 |
-                 |workflow declarations_as_nodes {
-                 |    call t as t1 { input: i = "hello" }
-                 |    
-                 |    String a = t1.o + " world"
-                 |    
-                 |    call t as t2 { input: i = a }
-                 |    
-                 |    Array[String] arr = [t1.o, t2.o]
-                 |    
-                 |    Map[String, String] map = { "key": t1.o }
-                 |    
-                 |    scatter(i in arr) {
-                 |        call t as t3 { input: i = i }
-                 |        String b = i + t3.o
-                 |        call t as t4 { input: i = b }
-                 |        String c = t3.o + " " + t4.o
-                 |    }
-                 |    
-                 |    Array[String] d = c
-                 |     
-                 |    output {
-                 |        String o1 = a
-                 |        Array[String] o2 = t4.o
-                 |        Array[String] o3 = d
-                 |        Array[String] o4 = b
-                 |        Array[String] o5 = c
-                 |    }
-                 |}
+    val wdl = """task t {
+                |    String i
+                |    command {
+                |        echo "${i}"
+                |    }
+                |    output {
+                |        String o = read_string(stdout())
+                |    }
+                |}
+                |
+                |workflow declarations_as_nodes {
+                |    call t as t1 { input: i = "hello" }
+                |    
+                |    String a = t1.o + " world"
+                |    
+                |    call t as t2 { input: i = a }
+                |    
+                |    Array[String] arr = [t1.o, t2.o]
+                |    
+                |    Map[String, String] map = { "key": t1.o }
+                |    
+                |    scatter(i in arr) {
+                |        call t as t3 { input: i = i }
+                |        String b = i + t3.o
+                |        call t as t4 { input: i = b }
+                |        String c = t3.o + " " + t4.o
+                |    }
+                |    
+                |    Array[String] d = c
+                |     
+                |    output {
+                |        String o1 = a
+                |        Array[String] o2 = t4.o
+                |        Array[String] o3 = d
+                |        Array[String] o4 = b
+                |        Array[String] o5 = c
+                |    }
+                |}
             """.stripMargin
     val ns = WdlNamespaceWithWorkflow.load(wdl, Seq.empty).get
     ns.staticDeclarationsRecursive(Map.empty[String, WomValue], NoFunctions) match {
@@ -195,4 +194,3 @@ class DeclarationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     }
   }
 }
-
diff --git a/wdl/model/draft2/src/test/scala/wdl/NamespaceSpec.scala b/wdl/model/draft2/src/test/scala/wdl/NamespaceSpec.scala
index 24e3a0b8916..0c65778b5eb 100644
--- a/wdl/model/draft2/src/test/scala/wdl/NamespaceSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/NamespaceSpec.scala
@@ -9,7 +9,10 @@ class NamespaceSpec extends WdlTest {
       val namespace = Try(loadWdl("type_checks.wdl"))
 
       namespace match {
-        case Failure(f) => f.getMessage should startWith("ERROR: oopsNotOptionalArray is declared as a Array[Int] but the expression evaluates to a Array[Int?]")
+        case Failure(f) =>
+          f.getMessage should startWith(
+            "ERROR: oopsNotOptionalArray is declared as a Array[Int] but the expression evaluates to a Array[Int?]"
+          )
         case Success(_) => fail("Should have failed to load namespace")
       }
     }
diff --git a/wdl/model/draft2/src/test/scala/wdl/ParameterWdlCommandPartSpec.scala b/wdl/model/draft2/src/test/scala/wdl/ParameterWdlCommandPartSpec.scala
index fe636fba4c9..997c1c3d595 100644
--- a/wdl/model/draft2/src/test/scala/wdl/ParameterWdlCommandPartSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/ParameterWdlCommandPartSpec.scala
@@ -18,7 +18,7 @@ class ParameterWdlCommandPartSpec extends WdlTest {
     val task = namespace.tasks.find(_.name == "param_test") getOrElse {
       fail("task 'param_test' not found")
     }
-    val paramsByName = task.commandTemplate.collect({ case p: ParameterCommandPart => p })
+    val paramsByName = task.commandTemplate.collect { case p: ParameterCommandPart => p }
 
     s"Stringify the $${...} tags correctly" in {
       paramsByName.size shouldEqual 6
@@ -33,15 +33,18 @@ class ParameterWdlCommandPartSpec extends WdlTest {
     "raise exception if 'true' attribute is specified but 'false' is not" in {
       WdlNamespace.loadUsingSource(
         s"""task param_test {
-            |  Boolean f
-            |
-            |  command <<<
-            |  ./binary $${true="--true" f}
-            |  >>>
-            |}
-            |
-            |workflow wf {call param_test}
-          """.stripMargin, None, None) match {
+           |  Boolean f
+           |
+           |  command <<<
+           |  ./binary $${true="--true" f}
+           |  >>>
+           |}
+           |
+           |workflow wf {call param_test}
+          """.stripMargin,
+        None,
+        None
+      ) match {
         case Failure(_: SyntaxError) => // expected
         case x => fail(s"Expecting a syntax error but got $x")
       }
@@ -60,24 +63,29 @@ class ParameterWdlCommandPartSpec extends WdlTest {
 
       val ns = WdlNamespace.loadUsingSource(wdl, None, None).get
       val task: WdlTask = ns.findTask("t").get
-      val command = task.instantiateCommand(Map(task.declarations.head -> WomString("world")), NoFunctions).toTry.get.head
+      val command =
+        task.instantiateCommand(Map(task.declarations.head -> WomString("world")), NoFunctions).toTry.get.head
       command.commandString shouldBe "echo hello world"
     }
-    
+
     "replace undefined values by their default value after evaluation" in {
       val wdl =
         s"""
-          |task t {
-          |  String? none
-          |  command {
-          |     echo $${"hello" + none}
-          |  }
-          |}
+           |task t {
+           |  String? none
+           |  command {
+           |     echo $${"hello" + none}
+           |  }
+           |}
         """.stripMargin
-      
+
       val ns = WdlNamespace.loadUsingSource(wdl, None, None).get
       val task = ns.findTask("t").get
-      val command = task.instantiateCommand(Map(task.declarations.head -> WomOptionalValue.none(WomStringType)), NoFunctions).toTry.get.head
+      val command = task
+        .instantiateCommand(Map(task.declarations.head -> WomOptionalValue.none(WomStringType)), NoFunctions)
+        .toTry
+        .get
+        .head
       command.commandString shouldBe "echo"
     }
   }
diff --git a/wdl/model/draft2/src/test/scala/wdl/RuntimeAttributeSpec.scala b/wdl/model/draft2/src/test/scala/wdl/RuntimeAttributeSpec.scala
index da6b6b6d96f..6ff8c27d0e9 100644
--- a/wdl/model/draft2/src/test/scala/wdl/RuntimeAttributeSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/RuntimeAttributeSpec.scala
@@ -79,15 +79,15 @@ object RuntimeAttributeSpec {
     """.stripMargin
 }
 
-  class RuntimeAttributeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with EitherValues {
-    val NamespaceWithRuntime = WdlNamespaceWithWorkflow.load(WorkflowWithRuntime, Seq.empty).get
-    val NamespaceWithoutRuntime = WdlNamespaceWithWorkflow.load(WorkflowWithoutRuntime, Seq.empty).get
+class RuntimeAttributeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with EitherValues {
+  val NamespaceWithRuntime = WdlNamespaceWithWorkflow.load(WorkflowWithRuntime, Seq.empty).get
+  val NamespaceWithoutRuntime = WdlNamespaceWithWorkflow.load(WorkflowWithoutRuntime, Seq.empty).get
 
-    "WDL file with runtime attributes" should "have attribute maps" in {
-      NamespaceWithRuntime.tasks.forall(_.runtimeAttributes.attrs.nonEmpty) should be(true)
-    }
+  "WDL file with runtime attributes" should "have attribute maps" in {
+    NamespaceWithRuntime.tasks.forall(_.runtimeAttributes.attrs.nonEmpty) should be(true)
+  }
 
-    "WDL file without runtime attributes" should "not have attribute maps" in {
-      NamespaceWithoutRuntime.tasks.forall(_.runtimeAttributes.attrs.isEmpty) should be(true)
-    }
+  "WDL file without runtime attributes" should "not have attribute maps" in {
+    NamespaceWithoutRuntime.tasks.forall(_.runtimeAttributes.attrs.isEmpty) should be(true)
   }
+}
diff --git a/wdl/model/draft2/src/test/scala/wdl/SameNameParametersSpec.scala b/wdl/model/draft2/src/test/scala/wdl/SameNameParametersSpec.scala
index c55583d38cc..79143389baa 100644
--- a/wdl/model/draft2/src/test/scala/wdl/SameNameParametersSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/SameNameParametersSpec.scala
@@ -9,15 +9,18 @@ import wdl.draft2.model.expression.NoFunctions
 import wom.values.WomString
 
 class SameNameParametersSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  val namespace1 = WdlNamespaceWithWorkflow.load(
-    """
-       |task test {
-       |  String x
-       |  command { ./script ${x} ${x} ${x} }
-       |}
-       |workflow wf { call test }
-     """.stripMargin, Seq.empty
-  ).get
+  val namespace1 = WdlNamespaceWithWorkflow
+    .load(
+      """
+        |task test {
+        |  String x
+        |  command { ./script ${x} ${x} ${x} }
+        |}
+        |workflow wf { call test }
+     """.stripMargin,
+      Seq.empty
+    )
+    .get
   val task = namespace1.findTask("test").get
 
   "A task with command that uses the same parameter more than once" should "only count it as one input" in {
diff --git a/wdl/model/draft2/src/test/scala/wdl/SampleWdl.scala b/wdl/model/draft2/src/test/scala/wdl/SampleWdl.scala
index c3b90302302..f756f81c700 100644
--- a/wdl/model/draft2/src/test/scala/wdl/SampleWdl.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/SampleWdl.scala
@@ -79,147 +79,145 @@ object SampleWdl {
       withPlaceholders.stripMargin.replace(outputSectionPlaceholder, outputsSection)
     }
 
-    val PatternKey ="three_step.cgrep.pattern"
+    val PatternKey = "three_step.cgrep.pattern"
   }
 
   object ThreeStep extends ThreeStepTemplate
 
-
   object NestedScatterWdl extends SampleWdl {
     override def workflowSource(runtime: String = "") =
       s"""
         task A {
-        |  command {
-        |    echo -n -e "jeff\nchris\nmiguel\nthibault\nkhalid\nscott"
-        |  }
-        |  output {
-        |    Array[String] A_out = read_lines(stdout())
-        |  }
-        |}
-        |
-        |task B {
-        |  String B_in
-        |  command {
-        |    python -c "print(len('$${B_in}'))"
-        |  }
-        |  output {
-        |    Int B_out = read_int(stdout())
-        |  }
-        |}
-        |
-        |task C {
-        |  Int C_in
-        |  command {
-        |    python -c "print($${C_in}*100)"
-        |  }
-        |  output {
-        |    Int C_out = read_int(stdout())
-        |  }
-        |}
-        |
-        |task D {
-        |  Array[Int] D_in
-        |  command {
-        |    python -c "print($${sep = '+' D_in})"
-        |  }
-        |  output {
-        |    Int D_out = read_int(stdout())
-        |  }
-        |}
-        |
-        |task E {
-        |  command {
-        |    python -c "import random; print(random.randint(1,100))"
-        |  }
-        |  output {
-        |    Int E_out = read_int(stdout())
-        |  }
-        |}
-        |
-        |workflow w {
-        |  call A
-        |  scatter (item in A.A_out) { # scatter 0
-        |    call B {input: B_in = item}
-        |    call C {input: C_in = B.B_out}
-        |    call E
-        |    scatter (itemB in B.B_out) { # scatter 1
-        |      call E as G
-        |    }
-        |    scatter (itemB in B.B_out) { # scatter 2
-        |      call E as H
-        |    }
-        |  }
-        |  scatter (item in A.A_out) { # scatter 3
-        |    call E as F
-        |  }
-        |  call D {input: D_in = B.B_out}
-        |}
+         |  command {
+         |    echo -n -e "jeff\nchris\nmiguel\nthibault\nkhalid\nscott"
+         |  }
+         |  output {
+         |    Array[String] A_out = read_lines(stdout())
+         |  }
+         |}
+         |
+         |task B {
+         |  String B_in
+         |  command {
+         |    python -c "print(len('$${B_in}'))"
+         |  }
+         |  output {
+         |    Int B_out = read_int(stdout())
+         |  }
+         |}
+         |
+         |task C {
+         |  Int C_in
+         |  command {
+         |    python -c "print($${C_in}*100)"
+         |  }
+         |  output {
+         |    Int C_out = read_int(stdout())
+         |  }
+         |}
+         |
+         |task D {
+         |  Array[Int] D_in
+         |  command {
+         |    python -c "print($${sep = '+' D_in})"
+         |  }
+         |  output {
+         |    Int D_out = read_int(stdout())
+         |  }
+         |}
+         |
+         |task E {
+         |  command {
+         |    python -c "import random; print(random.randint(1,100))"
+         |  }
+         |  output {
+         |    Int E_out = read_int(stdout())
+         |  }
+         |}
+         |
+         |workflow w {
+         |  call A
+         |  scatter (item in A.A_out) { # scatter 0
+         |    call B {input: B_in = item}
+         |    call C {input: C_in = B.B_out}
+         |    call E
+         |    scatter (itemB in B.B_out) { # scatter 1
+         |      call E as G
+         |    }
+         |    scatter (itemB in B.B_out) { # scatter 2
+         |      call E as H
+         |    }
+         |  }
+         |  scatter (item in A.A_out) { # scatter 3
+         |    call E as F
+         |  }
+         |  call D {input: D_in = B.B_out}
+         |}
       """.stripMargin
   }
 
-
   class ScatterWdl extends SampleWdl {
     val tasks = s"""task A {
-      |  command {
-      |    echo -n -e "jeff\nchris\nmiguel\nthibault\nkhalid\nscott"
-      |  }
-      |  output {
-      |    Array[String] A_out = read_lines(stdout())
-      |  }
-      |}
-      |
-      |task B {
-      |  String B_in
-      |  command {
-      |    python -c "print(len('$${B_in}'))"
-      |  }
-      |  output {
-      |    Int B_out = read_int(stdout())
-      |  }
-      |}
-      |
-      |task C {
-      |  Int C_in
-      |  command {
-      |    python -c "print($${C_in}*100)"
-      |  }
-      |  output {
-      |    Int C_out = read_int(stdout())
-      |  }
-      |}
-      |
-      |task D {
-      |  Array[Int] D_in
-      |  command {
-      |    python -c "print($${sep = '+' D_in})"
-      |  }
-      |  output {
-      |    Int D_out = read_int(stdout())
-      |  }
-      |}
-      |
-      |task E {
-      |  command {
-      |    python -c "print(9)"
-      |  }
-      |  output {
-      |    Int E_out = read_int(stdout())
-      |  }
-      |}
+                   |  command {
+                   |    echo -n -e "jeff\nchris\nmiguel\nthibault\nkhalid\nscott"
+                   |  }
+                   |  output {
+                   |    Array[String] A_out = read_lines(stdout())
+                   |  }
+                   |}
+                   |
+                   |task B {
+                   |  String B_in
+                   |  command {
+                   |    python -c "print(len('$${B_in}'))"
+                   |  }
+                   |  output {
+                   |    Int B_out = read_int(stdout())
+                   |  }
+                   |}
+                   |
+                   |task C {
+                   |  Int C_in
+                   |  command {
+                   |    python -c "print($${C_in}*100)"
+                   |  }
+                   |  output {
+                   |    Int C_out = read_int(stdout())
+                   |  }
+                   |}
+                   |
+                   |task D {
+                   |  Array[Int] D_in
+                   |  command {
+                   |    python -c "print($${sep = '+' D_in})"
+                   |  }
+                   |  output {
+                   |    Int D_out = read_int(stdout())
+                   |  }
+                   |}
+                   |
+                   |task E {
+                   |  command {
+                   |    python -c "print(9)"
+                   |  }
+                   |  output {
+                   |    Int E_out = read_int(stdout())
+                   |  }
+                   |}
     """.stripMargin
 
     override def workflowSource(runtime: String = "") =
       s"""$tasks
-        |
-        |workflow w {
-        |  call A
-        |  scatter (item in A.A_out) {
-        |    call B {input: B_in = item}
-        |    call C {input: C_in = B.B_out}
-        |    call E
-        |  }
-        |  call D {input: D_in = B.B_out}
-        |}
+         |
+         |workflow w {
+         |  call A
+         |  scatter (item in A.A_out) {
+         |    call B {input: B_in = item}
+         |    call C {input: C_in = B.B_out}
+         |    call E
+         |  }
+         |  call D {input: D_in = B.B_out}
+         |}
       """.stripMargin
   }
 
@@ -263,67 +261,66 @@ object SampleWdl {
   object TaskDeclarationsWdl extends SampleWdl {
     override def workflowSource(runtime: String = "") =
       """
-      |task t {
-      |   String s
-      |   command {
-      |     echo ${s}
-      |   }
-      |   output {
-      |     String o = s
-      |     Array[Int] outputArray = [0, 1, 2]
-      |   }
-      |}
-      |
-      |task u {
-      |   String a
-      |   String b
-      |   String c
-      |   Int d
-      |   String e = "e"
-      |   String f
-      |   String? g
-      |   String? h
-      |   String i
-      |   File j
-      |   Array[File] k
-      |   String? l
-      |
-      |   command {
-      |     echo ${a}
-      |     echo ${b}
-      |     echo ${c}
-      |     echo ${d}
-      |     echo ${e}
-      |     echo ${f}
-      |     echo ${g}
-      |     echo ${h}
-      |     echo ${i}
-      |   }
-      |}
-      |
-      |workflow wf {
-      | String workflowDeclarationFromInput
-      | String workflowDeclaration = "b"
-      | Array[File] files = ["a", "b", "c"]
-      |
-      | call t as t2 {input: s = "hey" }
-      |
-      | scatter (i in t2.outputArray) {
-      |   call t {input: s = "c"}
-      |   if (true) {
-      |     call t as t3 {input: s = "c"}
-      |   }
-      |   call u as v {input: a = workflowDeclarationFromInput,
-      |                       b = workflowDeclaration,
-      |                       c = t.o,
-      |                       d = i,
-      |                       i = "${workflowDeclaration}",
-      |                       k = files,
-      |                       l = t3.o }
-      | }
-      |}
-    """.
-        stripMargin
+        |task t {
+        |   String s
+        |   command {
+        |     echo ${s}
+        |   }
+        |   output {
+        |     String o = s
+        |     Array[Int] outputArray = [0, 1, 2]
+        |   }
+        |}
+        |
+        |task u {
+        |   String a
+        |   String b
+        |   String c
+        |   Int d
+        |   String e = "e"
+        |   String f
+        |   String? g
+        |   String? h
+        |   String i
+        |   File j
+        |   Array[File] k
+        |   String? l
+        |
+        |   command {
+        |     echo ${a}
+        |     echo ${b}
+        |     echo ${c}
+        |     echo ${d}
+        |     echo ${e}
+        |     echo ${f}
+        |     echo ${g}
+        |     echo ${h}
+        |     echo ${i}
+        |   }
+        |}
+        |
+        |workflow wf {
+        | String workflowDeclarationFromInput
+        | String workflowDeclaration = "b"
+        | Array[File] files = ["a", "b", "c"]
+        |
+        | call t as t2 {input: s = "hey" }
+        |
+        | scatter (i in t2.outputArray) {
+        |   call t {input: s = "c"}
+        |   if (true) {
+        |     call t as t3 {input: s = "c"}
+        |   }
+        |   call u as v {input: a = workflowDeclarationFromInput,
+        |                       b = workflowDeclaration,
+        |                       c = t.o,
+        |                       d = i,
+        |                       i = "${workflowDeclaration}",
+        |                       k = files,
+        |                       l = t3.o }
+        | }
+        |}
+    """.stripMargin
 
     val workflowInputs = Map(
       "wf.workflowDeclarationFromInput" -> WomString("a"),
diff --git a/wdl/model/draft2/src/test/scala/wdl/ScopeSpec.scala b/wdl/model/draft2/src/test/scala/wdl/ScopeSpec.scala
index e3003f5d0cf..317bc0d2777 100644
--- a/wdl/model/draft2/src/test/scala/wdl/ScopeSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/ScopeSpec.scala
@@ -11,12 +11,14 @@ class ScopeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   val namespace = WdlNamespaceWithWorkflow.load(SampleWdl.NestedScatterWdl.workflowSource(), Seq.empty).get
 
   it should "throw an exception if trying to re-assign children on a scope" in {
-    the [UnsupportedOperationException] thrownBy { namespace.workflow.children = Seq.empty } should have message "children is write-once"
+    the[UnsupportedOperationException] thrownBy {
+      namespace.workflow.children = Seq.empty
+    } should have message "children is write-once"
   }
 
   it should "throw an exception if trying to generate a workflow from a non-workflow ast" in {
     val callAst: Ast = AstTools.findAsts(namespace.ast, AstNodeName.Call).head
-    the [UnsupportedOperationException] thrownBy {
+    the[UnsupportedOperationException] thrownBy {
       WdlWorkflow(callAst, namespace.wdlSyntaxErrorFormatter)
     } should have message "Expecting Workflow AST, got a Call AST"
   }
diff --git a/wdl/model/draft2/src/test/scala/wdl/SyntaxErrorSpec.scala b/wdl/model/draft2/src/test/scala/wdl/SyntaxErrorSpec.scala
index 0ddad39acad..6cea8fec619 100644
--- a/wdl/model/draft2/src/test/scala/wdl/SyntaxErrorSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/SyntaxErrorSpec.scala
@@ -16,36 +16,36 @@ import scala.util.{Failure, Success}
 
 class SyntaxErrorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   private val psTaskWdl = """
-      |task ps {
-      |  command {
-      |    ps
-      |  }
-      |  output {
-      |    File procs = stdout()
-      |  }
-      |}""".stripMargin
+                            |task ps {
+                            |  command {
+                            |    ps
+                            |  }
+                            |  output {
+                            |    File procs = stdout()
+                            |  }
+                            |}""".stripMargin
 
   private val cgrepTaskWdl = s"""
-     |task cgrep {
-     |  String pattern
-     |  File in_file
-     |  command {
-     |    grep '$${pattern}' $${in_file} | wc -l
-     |  }
-     |  output {
-     |    Int count = read_int(stdout())
-     |  }
-     |}""".stripMargin
-
-  private def resolver(importUri: String): Draft2ResolvedImportBundle = {
+                                |task cgrep {
+                                |  String pattern
+                                |  File in_file
+                                |  command {
+                                |    grep '$${pattern}' $${in_file} | wc -l
+                                |  }
+                                |  output {
+                                |    Int count = read_int(stdout())
+                                |  }
+                                |}""".stripMargin
+
+  private def resolver(importUri: String): Draft2ResolvedImportBundle =
     importUri match {
       case "ps" => Draft2ResolvedImportBundle(psTaskWdl, ResolvedImportRecord("ps"))
       case "cgrep" => Draft2ResolvedImportBundle(cgrepTaskWdl, ResolvedImportRecord("cgrep"))
       case _ => throw new RuntimeException(s"Can't resolve $importUri")
     }
-  }
 
-  private def normalizeErrorMessage(msg: String) = StringUtil.stripAll(msg, " \t\n\r", " \t\n\r").replaceAll("[ \t]+\n", "\n")
+  private def normalizeErrorMessage(msg: String) =
+    StringUtil.stripAll(msg, " \t\n\r", " \t\n\r").replaceAll("[ \t]+\n", "\n")
 
   trait ErrorWdl {
     def testString: String
@@ -384,17 +384,17 @@ class SyntaxErrorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     val testString = "detect when a call has multiple input sections"
     val wdl =
       s"""task x {
-        |  String a
-        |  String b
-        |  command {  ./script $${a} $${b} }
-        |}
-        |
-        |workflow wf {
-        |  call x {
-        |    input: a = "a"
-        |    input: b = "b"
-        |  }
-        |}
+         |  String a
+         |  String b
+         |  command {  ./script $${a} $${b} }
+         |}
+         |
+         |workflow wf {
+         |  call x {
+         |    input: a = "a"
+         |    input: b = "b"
+         |  }
+         |}
       """.stripMargin
 
     val errors =
@@ -495,7 +495,7 @@ class SyntaxErrorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
         |    Boolean o = a.x
         |            ^""".stripMargin
   }
-  
+
   case object TypeMismatch4 extends ErrorWdl {
     val testString = "detect when a call output has a type mismatch (4)"
     val wdl =
@@ -573,25 +573,25 @@ class SyntaxErrorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     val testString = s"detect when expressions in command section reference missing task inputs"
     val wdl =
       s"""task a {
-        |  Int x
-        |  command { ./script $${x+y} }
-        |}
-        |
-        |workflow w {
-        |  call a
-        |}
+         |  Int x
+         |  command { ./script $${x+y} }
+         |}
+         |
+         |workflow w {
+         |  call a
+         |}
       """.stripMargin
 
     val errors =
       s"""ERROR: Variable y does not reference any declaration in the task (line 3, col 26):
-        |
-        |  command { ./script $${x+y} }
-        |                         ^
-        |
-        |Task defined here (line 1, col 6):
-        |
-        |task a {
-        |     ^
+         |
+         |  command { ./script $${x+y} }
+         |                         ^
+         |
+         |Task defined here (line 1, col 6):
+         |
+         |task a {
+         |     ^
       """.stripMargin
   }
 
@@ -673,11 +673,11 @@ class SyntaxErrorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     val testString = "detect when a variable is declared more than once (1)"
     val wdl =
       s"""task inputOops {
-        |  Int a = 5
-        |  Int a = 10
-        |  command { echo $${a} }
-        |}
-        |workflow a { call inputOops }
+         |  Int a = 5
+         |  Int a = 10
+         |  command { echo $${a} }
+         |}
+         |workflow a { call inputOops }
       """.stripMargin
 
     val errors =
@@ -799,16 +799,16 @@ class SyntaxErrorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
     val errors =
       """|ERROR: Sibling nodes have conflicting names:
-        |
-        |WorkflowOutput defined here (line 4, col 4):
-        |
-        |   String o = "output"
-        |   ^
-        |
-        |WorkflowOutput statement defined here (line 4, col 4):
-        |
-        |   String o = "output"
-        |   ^
+         |
+         |WorkflowOutput defined here (line 4, col 4):
+         |
+         |   String o = "output"
+         |   ^
+         |
+         |WorkflowOutput statement defined here (line 4, col 4):
+         |
+         |   String o = "output"
+         |   ^
       """.stripMargin
   }
 
@@ -1036,14 +1036,14 @@ class SyntaxErrorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     UnknownVariableInDeclaration
   )
 
-  forAll(syntaxErrorWdlTable) { (errorWdl) =>
+  forAll(syntaxErrorWdlTable) { errorWdl =>
     it should errorWdl.testString in {
-        WdlNamespace.loadUsingSource(errorWdl.wdl, None, Option(Seq(resolver))) match {
-          case Failure(e: SyntaxError) => normalizeErrorMessage(e.getMessage) shouldEqual normalizeErrorMessage(errorWdl.errors)
-          case Failure(x) => throw new Exception(s"Expecting a SyntaxError but got $x", x)
-          case Success(_) => fail("Bad WDL unexpectedly validated.")
+      WdlNamespace.loadUsingSource(errorWdl.wdl, None, Option(Seq(resolver))) match {
+        case Failure(e: SyntaxError) =>
+          normalizeErrorMessage(e.getMessage) shouldEqual normalizeErrorMessage(errorWdl.errors)
+        case Failure(x) => throw new Exception(s"Expecting a SyntaxError but got $x", x)
+        case Success(_) => fail("Bad WDL unexpectedly validated.")
       }
     }
   }
 }
-
diff --git a/wdl/model/draft2/src/test/scala/wdl/SyntaxHighlightSpec.scala b/wdl/model/draft2/src/test/scala/wdl/SyntaxHighlightSpec.scala
index 95cf4333c2a..697ed979b97 100644
--- a/wdl/model/draft2/src/test/scala/wdl/SyntaxHighlightSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/SyntaxHighlightSpec.scala
@@ -12,96 +12,101 @@ import scala.annotation.nowarn
 
 class SyntaxHighlightSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers {
   "SyntaxFormatter for typical workflow" should {
-    val namespace = WdlNamespace.loadUsingSource(
-      """
-        |task PairedFastQsToUnmappedBAM {
-        |  File fastq_1
-        |  File fastq_2
-        |  String readgroup_name
-        |  String sample_name
-        |  String library_name
-        |  String platform_unit
-        |  String run_date
-        |  String platform_name
-        |  String sequencing_center
-        |  Int disk_size
-        |  String mem_size
-        |
-        |  command {
-        |    java -Xmx3000m -jar /usr/gitc/picard.jar \
-        |      FastqToSam \
-        |      FASTQ=${fastq_1} \
-        |      FASTQ2=${fastq_2} \
-        |      OUTPUT=${readgroup_name}.bam \
-        |      READ_GROUP_NAME=${readgroup_name} \
-        |      SAMPLE_NAME=${sample_name} \
-        |      LIBRARY_NAME=${library_name} \
-        |      PLATFORM_UNIT=${platform_unit} \
-        |      RUN_DATE=${run_date} \
-        |      PLATFORM=${platform_name} \
-        |      SEQUENCING_CENTER=${sequencing_center}
-        |  }
-        |  runtime {
-        |    docker: "broadinstitute/genomes-in-the-cloud:2.2.4-1469632282"
-        |    memory: mem_size
-        |    cpu: "1"
-        |    disks: "local-disk " + disk_size + " HDD"
-        |  }
-        |  output {
-        |    File output_bam = "${readgroup_name}.bam"
-        |  }
-        |  	parameter_meta {
-        |    memory_mb: "Amount of memory to allocate to the JVM"
-        |    param: "Some arbitrary parameter"
-        |    sample_id: "The ID of the sample in format foo_bar_baz"
-        |  }
-        |  meta {
-        |    author: "Joe Somebody"
-        |    email: "joe@company.org"
-        |  }
-        |}
-        |
-        |# WORKFLOW DEFINITION
-        |workflow ConvertPairedFastQsToUnmappedBamWf {
-        |  Array[String] readgroup_list
-        |  Map[String, Array[File]] fastq_pairs
-        |  Map[String, Array[String]] metadata
-        |
-        |  # Convert multiple pairs of input fastqs in parallel
-        |  scatter (readgroup in readgroup_list) {
-        |
-        |    # Convert pair of FASTQs to uBAM
-        |    call PairedFastQsToUnmappedBAM {
-        |      input:
-        |        fastq_1 = fastq_pairs[readgroup][0],
-        |        fastq_2 = fastq_pairs[readgroup][1],
-        |        readgroup_name = readgroup,
-        |        sample_name = metadata[readgroup][0],
-        |        library_name = metadata[readgroup][1],
-        |        platform_unit = metadata[readgroup][2],
-        |        run_date = metadata[readgroup][3],
-        |        platform_name = metadata[readgroup][4],
-        |        sequencing_center = metadata[readgroup][5]
-        |    }
-        |  }
-        |
-        |  # Outputs that will be retained when execution is complete
-        |  output {
-        |    Array[File] output_bams = PairedFastQsToUnmappedBAM.output_bam
-        |  }
-        |
-        |  	parameter_meta {
-        |    memory_mb: "Amount of memory to allocate to the JVM"
-        |    param: "Some arbitrary parameter"
-        |    sample_id: "The ID of the sample in format foo_bar_baz"
-        |  }
-        |
-        |  meta {
-        |   author: "Joe Somebody"
-        |   email: "joe@company.org"
-        |  }
-        |}
-     """.stripMargin, None, None).get
+    val namespace = WdlNamespace
+      .loadUsingSource(
+        """
+          |task PairedFastQsToUnmappedBAM {
+          |  File fastq_1
+          |  File fastq_2
+          |  String readgroup_name
+          |  String sample_name
+          |  String library_name
+          |  String platform_unit
+          |  String run_date
+          |  String platform_name
+          |  String sequencing_center
+          |  Int disk_size
+          |  String mem_size
+          |
+          |  command {
+          |    java -Xmx3000m -jar /usr/gitc/picard.jar \
+          |      FastqToSam \
+          |      FASTQ=${fastq_1} \
+          |      FASTQ2=${fastq_2} \
+          |      OUTPUT=${readgroup_name}.bam \
+          |      READ_GROUP_NAME=${readgroup_name} \
+          |      SAMPLE_NAME=${sample_name} \
+          |      LIBRARY_NAME=${library_name} \
+          |      PLATFORM_UNIT=${platform_unit} \
+          |      RUN_DATE=${run_date} \
+          |      PLATFORM=${platform_name} \
+          |      SEQUENCING_CENTER=${sequencing_center}
+          |  }
+          |  runtime {
+          |    docker: "broadinstitute/genomes-in-the-cloud:2.2.4-1469632282"
+          |    memory: mem_size
+          |    cpu: "1"
+          |    disks: "local-disk " + disk_size + " HDD"
+          |  }
+          |  output {
+          |    File output_bam = "${readgroup_name}.bam"
+          |  }
+          |  	parameter_meta {
+          |    memory_mb: "Amount of memory to allocate to the JVM"
+          |    param: "Some arbitrary parameter"
+          |    sample_id: "The ID of the sample in format foo_bar_baz"
+          |  }
+          |  meta {
+          |    author: "Joe Somebody"
+          |    email: "joe@company.org"
+          |  }
+          |}
+          |
+          |# WORKFLOW DEFINITION
+          |workflow ConvertPairedFastQsToUnmappedBamWf {
+          |  Array[String] readgroup_list
+          |  Map[String, Array[File]] fastq_pairs
+          |  Map[String, Array[String]] metadata
+          |
+          |  # Convert multiple pairs of input fastqs in parallel
+          |  scatter (readgroup in readgroup_list) {
+          |
+          |    # Convert pair of FASTQs to uBAM
+          |    call PairedFastQsToUnmappedBAM {
+          |      input:
+          |        fastq_1 = fastq_pairs[readgroup][0],
+          |        fastq_2 = fastq_pairs[readgroup][1],
+          |        readgroup_name = readgroup,
+          |        sample_name = metadata[readgroup][0],
+          |        library_name = metadata[readgroup][1],
+          |        platform_unit = metadata[readgroup][2],
+          |        run_date = metadata[readgroup][3],
+          |        platform_name = metadata[readgroup][4],
+          |        sequencing_center = metadata[readgroup][5]
+          |    }
+          |  }
+          |
+          |  # Outputs that will be retained when execution is complete
+          |  output {
+          |    Array[File] output_bams = PairedFastQsToUnmappedBAM.output_bam
+          |  }
+          |
+          |  	parameter_meta {
+          |    memory_mb: "Amount of memory to allocate to the JVM"
+          |    param: "Some arbitrary parameter"
+          |    sample_id: "The ID of the sample in format foo_bar_baz"
+          |  }
+          |
+          |  meta {
+          |   author: "Joe Somebody"
+          |   email: "joe@company.org"
+          |  }
+          |}
+     """.stripMargin,
+        None,
+        None
+      )
+      .get
 
     @nowarn("msg=Unicode escapes in triple quoted strings are deprecated, use the literal character instead")
     val console =
@@ -264,117 +269,116 @@ class SyntaxHighlightSpec extends AnyWordSpec with CromwellTimeoutSpec with Matc
                        |}
                      """.stripMargin
 
-    def resolver(importUri: String): Draft2ResolvedImportBundle = {
+    def resolver(importUri: String): Draft2ResolvedImportBundle =
       importUri match {
         case "foo.wdl" => Draft2ResolvedImportBundle(fooTaskWdl, ResolvedImportRecord("foo.wdl"))
         case _ => throw new RuntimeException(s"Can't resolve $importUri")
       }
-    }
 
     val source = s"""
-        |import "foo.wdl" as foo_ns
-        |
-        |task t {
-        |  String f
-        |  Int p
-        |  command {
-        |    ./cmd $${f} $${p}
-        |  }
-        |}
-        |
-        |task s {
-        |  Array[File] input_file
-        |  command <<<
-        |    cat $${sep=' ' input_file} | awk '{s+=$$1} END {print s}'
-        |  >>>
-        |  output {
-        |    String s = read_string(stdout())
-        |  }
-        |}
-        |
-        |task r {
-        |  command { python -c "import random; print(random.randint(1,100))" }
-        |}
-        |
-        |workflow w {
-        |  Int p = 2+2
-        |  call t
-        |  call t as u {
-        |    input: f="abc", p=p
-        |  }
-        |}""".stripMargin
+                    |import "foo.wdl" as foo_ns
+                    |
+                    |task t {
+                    |  String f
+                    |  Int p
+                    |  command {
+                    |    ./cmd $${f} $${p}
+                    |  }
+                    |}
+                    |
+                    |task s {
+                    |  Array[File] input_file
+                    |  command <<<
+                    |    cat $${sep=' ' input_file} | awk '{s+=$$1} END {print s}'
+                    |  >>>
+                    |  output {
+                    |    String s = read_string(stdout())
+                    |  }
+                    |}
+                    |
+                    |task r {
+                    |  command { python -c "import random; print(random.randint(1,100))" }
+                    |}
+                    |
+                    |workflow w {
+                    |  Int p = 2+2
+                    |  call t
+                    |  call t as u {
+                    |    input: f="abc", p=p
+                    |  }
+                    |}""".stripMargin
 
     val namespace = WdlNamespace.loadUsingSource(source, None, Option(Seq(resolver))).get
 
     val console =
       s"""\u001b[38;5;214mimport\u001b[0m 'foo.wdl' as foo_ns
-        |
-        |\u001b[38;5;214mtask\u001b[0m \u001b[38;5;253mt\u001b[0m {
-        |  \u001b[38;5;33mString\u001b[0m \u001b[38;5;112mf\u001b[0m
-        |  \u001b[38;5;33mInt\u001b[0m \u001b[38;5;112mp\u001b[0m
-        |  \u001b[38;5;214mcommand\u001b[0m {
-        |    ./cmd $${f} $${p}
-        |  }
-        |}
-        |
-        |\u001b[38;5;214mtask\u001b[0m \u001b[38;5;253ms\u001b[0m {
-        |  \u001b[38;5;33mArray[File]\u001b[0m \u001b[38;5;112minput_file\u001b[0m
-        |  \u001b[38;5;214mcommand\u001b[0m <<<
-        |    cat $${sep=" " input_file} | awk '{s+=$$1} END {print s}'
-        |  >>>
-        |  \u001b[38;5;214moutput\u001b[0m {
-        |    \u001b[38;5;33mString\u001b[0m \u001b[38;5;112ms\u001b[0m = \u001b[38;5;13mread_string\u001b[0m(\u001b[38;5;13mstdout\u001b[0m())
-        |  }
-        |}
-        |
-        |\u001b[38;5;214mtask\u001b[0m \u001b[38;5;253mr\u001b[0m {
-        |  \u001b[38;5;214mcommand\u001b[0m {
-        |    python -c "import random; print(random.randint(1,100))"
-        |  }
-        |}
-        |
-        |\u001b[38;5;214mworkflow\u001b[0m \u001b[38;5;253mw\u001b[0m {
-        |  \u001b[38;5;33mInt\u001b[0m \u001b[38;5;112mp\u001b[0m = 2 + 2
-        |  \u001b[38;5;214mcall\u001b[0m \u001b[38;5;253mt\u001b[0m
-        |  \u001b[38;5;214mcall\u001b[0m \u001b[38;5;253mt\u001b[0m as u {
-        |    input: f="abc", p=p
-        |  }
-        |}""".stripMargin
+         |
+         |\u001b[38;5;214mtask\u001b[0m \u001b[38;5;253mt\u001b[0m {
+         |  \u001b[38;5;33mString\u001b[0m \u001b[38;5;112mf\u001b[0m
+         |  \u001b[38;5;33mInt\u001b[0m \u001b[38;5;112mp\u001b[0m
+         |  \u001b[38;5;214mcommand\u001b[0m {
+         |    ./cmd $${f} $${p}
+         |  }
+         |}
+         |
+         |\u001b[38;5;214mtask\u001b[0m \u001b[38;5;253ms\u001b[0m {
+         |  \u001b[38;5;33mArray[File]\u001b[0m \u001b[38;5;112minput_file\u001b[0m
+         |  \u001b[38;5;214mcommand\u001b[0m <<<
+         |    cat $${sep=" " input_file} | awk '{s+=$$1} END {print s}'
+         |  >>>
+         |  \u001b[38;5;214moutput\u001b[0m {
+         |    \u001b[38;5;33mString\u001b[0m \u001b[38;5;112ms\u001b[0m = \u001b[38;5;13mread_string\u001b[0m(\u001b[38;5;13mstdout\u001b[0m())
+         |  }
+         |}
+         |
+         |\u001b[38;5;214mtask\u001b[0m \u001b[38;5;253mr\u001b[0m {
+         |  \u001b[38;5;214mcommand\u001b[0m {
+         |    python -c "import random; print(random.randint(1,100))"
+         |  }
+         |}
+         |
+         |\u001b[38;5;214mworkflow\u001b[0m \u001b[38;5;253mw\u001b[0m {
+         |  \u001b[38;5;33mInt\u001b[0m \u001b[38;5;112mp\u001b[0m = 2 + 2
+         |  \u001b[38;5;214mcall\u001b[0m \u001b[38;5;253mt\u001b[0m
+         |  \u001b[38;5;214mcall\u001b[0m \u001b[38;5;253mt\u001b[0m as u {
+         |    input: f="abc", p=p
+         |  }
+         |}""".stripMargin
 
     val html =
       s"""<span class="keyword">import</span> 'foo.wdl' as foo_ns
-        |
-        |<span class="keyword">task</span> <span class="name">t</span> {
-        |  <span class="type">String</span> <span class="variable">f</span>
-        |  <span class="type">Int</span> <span class="variable">p</span>
-        |  <span class="section">command</span> {
-        |    <span class="command">./cmd $${f} $${p}</span>
-        |  }
-        |}
-        |
-        |<span class="keyword">task</span> <span class="name">s</span> {
-        |  <span class="type">Array[File]</span> <span class="variable">input_file</span>
-        |  <span class="section">command</span> <<<
-        |    <span class="command">cat $${sep=" " input_file} | awk '{s+=$$1} END {print s}'</span>
-        |  >>>
-        |  <span class="section">output</span> {
-        |    <span class="type">String</span> <span class="variable">s</span> = <span class="function">read_string</span>(<span class="function">stdout</span>())
-        |  }
-        |}
-        |
-        |<span class="keyword">task</span> <span class="name">r</span> {
-        |  <span class="section">command</span> {
-        |    <span class="command">python -c "import random; print(random.randint(1,100))"</span>
-        |  }
-        |}
-        |
-        |<span class="keyword">workflow</span> <span class="name">w</span> {
-        |  <span class="type">Int</span> <span class="variable">p</span> = 2 + 2
-        |  <span class="keyword">call</span> <span class="name">t</span>
-        |  <span class="keyword">call</span> <span class="name">t</span> as <span class="alias">u</span> {
-        |    input: f="abc", p=p
-        |  }
-        |}""".stripMargin
+         |
+         |<span class="keyword">task</span> <span class="name">t</span> {
+         |  <span class="type">String</span> <span class="variable">f</span>
+         |  <span class="type">Int</span> <span class="variable">p</span>
+         |  <span class="section">command</span> {
+         |    <span class="command">./cmd $${f} $${p}</span>
+         |  }
+         |}
+         |
+         |<span class="keyword">task</span> <span class="name">s</span> {
+         |  <span class="type">Array[File]</span> <span class="variable">input_file</span>
+         |  <span class="section">command</span> <<<
+         |    <span class="command">cat $${sep=" " input_file} | awk '{s+=$$1} END {print s}'</span>
+         |  >>>
+         |  <span class="section">output</span> {
+         |    <span class="type">String</span> <span class="variable">s</span> = <span class="function">read_string</span>(<span class="function">stdout</span>())
+         |  }
+         |}
+         |
+         |<span class="keyword">task</span> <span class="name">r</span> {
+         |  <span class="section">command</span> {
+         |    <span class="command">python -c "import random; print(random.randint(1,100))"</span>
+         |  }
+         |}
+         |
+         |<span class="keyword">workflow</span> <span class="name">w</span> {
+         |  <span class="type">Int</span> <span class="variable">p</span> = 2 + 2
+         |  <span class="keyword">call</span> <span class="name">t</span>
+         |  <span class="keyword">call</span> <span class="name">t</span> as <span class="alias">u</span> {
+         |    input: f="abc", p=p
+         |  }
+         |}""".stripMargin
 
     "format to console properly" in {
       val actual = new SyntaxFormatter(AnsiSyntaxHighlighter).format(namespace)
diff --git a/wdl/model/draft2/src/test/scala/wdl/TaskSpec.scala b/wdl/model/draft2/src/test/scala/wdl/TaskSpec.scala
index aee550334ee..45fab30c9a4 100644
--- a/wdl/model/draft2/src/test/scala/wdl/TaskSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/TaskSpec.scala
@@ -21,12 +21,17 @@ class TaskSpec extends WdlTest {
     s"have a task with name 'wc'" in {
       wcTask.name shouldEqual "wc"
       wcTask.declarations.map(_.toWdlString) shouldEqual Vector("File in_file")
-      wcTask.instantiateCommand(
-        wcTask.inputsFromMap(
-          Map("wc.in_file" -> WomSingleFile("/path/to/file"))
-        ),
-        NoFunctions
-      ).toTry.get.head.commandString shouldEqual "cat /path/to/file | wc -l"
+      wcTask
+        .instantiateCommand(
+          wcTask.inputsFromMap(
+            Map("wc.in_file" -> WomSingleFile("/path/to/file"))
+          ),
+          NoFunctions
+        )
+        .toTry
+        .get
+        .head
+        .commandString shouldEqual "cat /path/to/file | wc -l"
       wcTask.outputs.size shouldEqual 1
       wcTask.outputs.head.unqualifiedName shouldEqual "count"
       wcTask.outputs.head.womType shouldEqual WomIntegerType
@@ -38,12 +43,17 @@ class TaskSpec extends WdlTest {
         "String pattern",
         "File in_file"
       )
-      cgrepTask.instantiateCommand(
-        cgrepTask.inputsFromMap(
-          Map("cgrep.pattern" -> WomString("^...$"), "cgrep.in_file" -> WomSingleFile("/path/to/file"))
-        ),
-        NoFunctions
-      ).toTry.get.head.commandString shouldEqual "grep '^...$' /path/to/file | wc -l"
+      cgrepTask
+        .instantiateCommand(
+          cgrepTask.inputsFromMap(
+            Map("cgrep.pattern" -> WomString("^...$"), "cgrep.in_file" -> WomSingleFile("/path/to/file"))
+          ),
+          NoFunctions
+        )
+        .toTry
+        .get
+        .head
+        .commandString shouldEqual "grep '^...$' /path/to/file | wc -l"
       cgrepTask.outputs.size shouldEqual 1
       cgrepTask.outputs.head.unqualifiedName shouldEqual "count"
       cgrepTask.outputs.head.womType shouldEqual WomIntegerType
@@ -72,7 +82,12 @@ class TaskSpec extends WdlTest {
         "param_test.e" -> WomArray(WomArrayType(WomIntegerType), Seq(0, 1, 2) map WomInteger.apply),
         "param_test.f" -> WomBoolean.False
       )
-      paramTestTask.instantiateCommand(paramTestTask.inputsFromMap(inputs), NoFunctions).toTry.get.head.commandString shouldEqual "./binary a_val -p b_val c0,c1,c2 1 0\t1\t2 --false"
+      paramTestTask
+        .instantiateCommand(paramTestTask.inputsFromMap(inputs), NoFunctions)
+        .toTry
+        .get
+        .head
+        .commandString shouldEqual "./binary a_val -p b_val c0,c1,c2 1 0\t1\t2 --false"
     }
 
     s"instantiate command (1)" in {
@@ -83,7 +98,12 @@ class TaskSpec extends WdlTest {
         "param_test.e" -> WomArray(WomArrayType(WomIntegerType), Seq(0, 1, 2) map WomInteger.apply),
         "param_test.f" -> WomBoolean.True
       )
-      paramTestTask.instantiateCommand(paramTestTask.inputsFromMap(inputs), NoFunctions).toTry.get.head.commandString shouldEqual "./binary a_val -p b_val c0,c1,c2 9 0\t1\t2 --true"
+      paramTestTask
+        .instantiateCommand(paramTestTask.inputsFromMap(inputs), NoFunctions)
+        .toTry
+        .get
+        .head
+        .commandString shouldEqual "./binary a_val -p b_val c0,c1,c2 9 0\t1\t2 --true"
     }
 
     s"instantiate command (2)" in {
@@ -95,7 +115,12 @@ class TaskSpec extends WdlTest {
         "param_test.e" -> WomArray(WomArrayType(WomIntegerType), Seq()),
         "param_test.f" -> WomBoolean.True
       )
-      paramTestTask.instantiateCommand(paramTestTask.inputsFromMap(inputs), NoFunctions).toTry.get.head.commandString shouldEqual "./binary a_val -p b_val c0 1  --true"
+      paramTestTask
+        .instantiateCommand(paramTestTask.inputsFromMap(inputs), NoFunctions)
+        .toTry
+        .get
+        .head
+        .commandString shouldEqual "./binary a_val -p b_val c0 1  --true"
     }
 
     s"instantiate command (3)" in {
@@ -107,11 +132,18 @@ class TaskSpec extends WdlTest {
         "param_test.e" -> WomArray(WomArrayType(WomIntegerType), Seq()),
         "param_test.f" -> WomBoolean.True
       )
-      paramTestTask.instantiateCommand(paramTestTask.inputsFromMap(inputs), NoFunctions).toTry.get.head.commandString shouldEqual "./binary a_val -p b_val  1  --true"
+      paramTestTask
+        .instantiateCommand(paramTestTask.inputsFromMap(inputs), NoFunctions)
+        .toTry
+        .get
+        .head
+        .commandString shouldEqual "./binary a_val -p b_val  1  --true"
     }
 
     s"fail to instantiate command if missing a required input" in {
-      paramTestTask.instantiateCommand(paramTestTask.inputsFromMap(Map("param_test.a" -> WomString("a_val"))), NoFunctions).toTry match {
+      paramTestTask
+        .instantiateCommand(paramTestTask.inputsFromMap(Map("param_test.a" -> WomString("a_val"))), NoFunctions)
+        .toTry match {
         case Failure(_) => // expected
         case _ => fail("Expected an exception")
       }
diff --git a/wdl/model/draft2/src/test/scala/wdl/TestFileUtil.scala b/wdl/model/draft2/src/test/scala/wdl/TestFileUtil.scala
index 12f6850347b..bda7e929db2 100644
--- a/wdl/model/draft2/src/test/scala/wdl/TestFileUtil.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/TestFileUtil.scala
@@ -14,7 +14,6 @@ trait TestFileUtil {
     File(file).write(contents).path
   }
 
-  def createFile(name: String, dir: Path, contents: String) = {
+  def createFile(name: String, dir: Path, contents: String) =
     File(dir).createDirectories()./(name).write(contents).path
-  }
 }
diff --git a/wdl/model/draft2/src/test/scala/wdl/ThreeStepImportNamespaceSpec.scala b/wdl/model/draft2/src/test/scala/wdl/ThreeStepImportNamespaceSpec.scala
index 54e41467e1b..3b49adc5175 100644
--- a/wdl/model/draft2/src/test/scala/wdl/ThreeStepImportNamespaceSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/ThreeStepImportNamespaceSpec.scala
@@ -12,65 +12,63 @@ import scala.util.Failure
 
 class ThreeStepImportNamespaceSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   val psTaskWdl = """
-    |task ps {
-    |  command {
-    |    ps
-    |  }
-    |  output {
-    |    File procs = stdout()
-    |  }
-    |}""".stripMargin
+                    |task ps {
+                    |  command {
+                    |    ps
+                    |  }
+                    |  output {
+                    |    File procs = stdout()
+                    |  }
+                    |}""".stripMargin
 
   val cgrepTaskWdl = """
-    |task cgrep {
-    |  String pattern
-    |  String in_file
-    |  command {
-    |    grep '${pattern}' ${in_file} | wc -l
-    |  }
-    |  output {
-    |    Int count = read_int(stdout())
-    |  }
-    |}""".stripMargin
+                       |task cgrep {
+                       |  String pattern
+                       |  String in_file
+                       |  command {
+                       |    grep '${pattern}' ${in_file} | wc -l
+                       |  }
+                       |  output {
+                       |    Int count = read_int(stdout())
+                       |  }
+                       |}""".stripMargin
 
   val wcTaskWdl = """
-    |task wc {
-    |  File in_file
-    |  command {
-    |    cat ${in_file} | wc -l
-    |  }
-    |  output {
-    |    Int count = read_int(stdout())
-    |  }
-    |}""".stripMargin
+                    |task wc {
+                    |  File in_file
+                    |  command {
+                    |    cat ${in_file} | wc -l
+                    |  }
+                    |  output {
+                    |    Int count = read_int(stdout())
+                    |  }
+                    |}""".stripMargin
 
   val workflowWdl = """
-    |import "ps" as ns1
-    |import "cgrep" as ns2
-    |import "wc" as ns3
-    |
-    |workflow three_step {
-    |  call ns1.ps
-    |  call ns2.cgrep {
-    |    input: in_file=ps.procs
-    |  }
-    |  call ns3.wc {
-    |    input: in_file=ps.procs
-    |  }
-    |}""".stripMargin
+                      |import "ps" as ns1
+                      |import "cgrep" as ns2
+                      |import "wc" as ns3
+                      |
+                      |workflow three_step {
+                      |  call ns1.ps
+                      |  call ns2.cgrep {
+                      |    input: in_file=ps.procs
+                      |  }
+                      |  call ns3.wc {
+                      |    input: in_file=ps.procs
+                      |  }
+                      |}""".stripMargin
 
-  def resolver(importUri: String): Draft2ResolvedImportBundle = {
+  def resolver(importUri: String): Draft2ResolvedImportBundle =
     importUri match {
       case "ps" => Draft2ResolvedImportBundle(psTaskWdl, ResolvedImportRecord("ps"))
       case "cgrep" => Draft2ResolvedImportBundle(cgrepTaskWdl, ResolvedImportRecord("cgrep"))
       case "wc" => Draft2ResolvedImportBundle(wcTaskWdl, ResolvedImportRecord("wc"))
       case _ => throw new RuntimeException(s"Can't resolve $importUri")
     }
-  }
 
   val namespace = WdlNamespaceWithWorkflow.load(workflowWdl, Seq(resolver _)).get
 
-
   "WDL file with imports" should "Have 0 tasks (3 tasks are in separate namespace)" in {
     namespace.tasks.size shouldEqual 0
   }
@@ -78,16 +76,14 @@ class ThreeStepImportNamespaceSpec extends AnyFlatSpec with CromwellTimeoutSpec
     namespace.namespaces.size shouldEqual 3
   }
   it should "Have 3 imported WdlNamespaces with tasks 'ps', 'cgrep', and 'wc'" in {
-    namespace.namespaces flatMap {_.tasks} map {_.name} shouldEqual Seq("ps", "cgrep", "wc")
+    namespace.namespaces flatMap { _.tasks } map { _.name } shouldEqual Seq("ps", "cgrep", "wc")
   }
   it should "Throw an exception if the import resolver fails to resolve an import" in {
-    def badResolver(s: String): Draft2ResolvedImportBundle = {
+    def badResolver(s: String): Draft2ResolvedImportBundle =
       throw new RuntimeException(s"Can't Resolve")
-    }
     WdlNamespace.loadUsingSource(workflowWdl, None, Option(Seq(badResolver))) match {
       case Failure(_: ValidationException) =>
       case x => fail(s"Expecting ValidationException to be thrown when using badResolver but got $x")
     }
   }
 }
-
diff --git a/wdl/model/draft2/src/test/scala/wdl/ThreeStepImportSpec.scala b/wdl/model/draft2/src/test/scala/wdl/ThreeStepImportSpec.scala
index 61272990382..e2dd8cbf208 100644
--- a/wdl/model/draft2/src/test/scala/wdl/ThreeStepImportSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/ThreeStepImportSpec.scala
@@ -12,61 +12,60 @@ import scala.util.Failure
 
 class ThreeStepImportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   val psTaskWdl = """
-    |task ps {
-    |  command {
-    |    ps
-    |  }
-    |  output {
-    |    File procs = stdout()
-    |  }
-    |}""".stripMargin
+                    |task ps {
+                    |  command {
+                    |    ps
+                    |  }
+                    |  output {
+                    |    File procs = stdout()
+                    |  }
+                    |}""".stripMargin
 
   val cgrepTaskWdl = s"""
-    |task cgrep {
-    |  String pattern
-    |  File in_file
-    |  command {
-    |    grep '$${pattern}' $${in_file} | wc -l
-    |  }
-    |  output {
-    |    Int count = read_int(stdout())
-    |  }
-    |}""".stripMargin
+                        |task cgrep {
+                        |  String pattern
+                        |  File in_file
+                        |  command {
+                        |    grep '$${pattern}' $${in_file} | wc -l
+                        |  }
+                        |  output {
+                        |    Int count = read_int(stdout())
+                        |  }
+                        |}""".stripMargin
 
   val wcTaskWdl = s"""
-    |task wc {
-    |  File in_file
-    |  command {
-    |    cat $${in_file} | wc -l
-    |  }
-    |  output {
-    |    Int count = read_int(stdout())
-    |  }
-    |}""".stripMargin
+                     |task wc {
+                     |  File in_file
+                     |  command {
+                     |    cat $${in_file} | wc -l
+                     |  }
+                     |  output {
+                     |    Int count = read_int(stdout())
+                     |  }
+                     |}""".stripMargin
 
   val workflowWdl = """
-    |import "ps"
-    |import "cgrep"
-    |import "wc"
-    |
-    |workflow three_step {
-    |  call ps.ps
-    |  call cgrep.cgrep {
-    |    input: in_file=ps.procs
-    |  }
-    |  call wc.wc {
-    |    input: in_file=ps.procs
-    |  }
-    |}""".stripMargin
+                      |import "ps"
+                      |import "cgrep"
+                      |import "wc"
+                      |
+                      |workflow three_step {
+                      |  call ps.ps
+                      |  call cgrep.cgrep {
+                      |    input: in_file=ps.procs
+                      |  }
+                      |  call wc.wc {
+                      |    input: in_file=ps.procs
+                      |  }
+                      |}""".stripMargin
 
-  def resolver(importUri: String): Draft2ResolvedImportBundle = {
+  def resolver(importUri: String): Draft2ResolvedImportBundle =
     importUri match {
       case "ps" => Draft2ResolvedImportBundle(psTaskWdl, ResolvedImportRecord("ps"))
       case "cgrep" => Draft2ResolvedImportBundle(cgrepTaskWdl, ResolvedImportRecord("cgrep"))
       case "wc" => Draft2ResolvedImportBundle(wcTaskWdl, ResolvedImportRecord("wc"))
       case _ => throw new RuntimeException(s"Can't resolve $importUri")
     }
-  }
 
   val namespace = WdlNamespaceWithWorkflow.load(workflowWdl, Seq(resolver _)).get
 
@@ -78,12 +77,11 @@ class ThreeStepImportSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     namespace.namespaces.size shouldEqual 3
   }
   it should "Have imported namespaces with tasks named 'ps', 'cgrep' and 'wc'" in {
-    namespace.namespaces flatMap {_.tasks} map {_.name} shouldEqual Seq("ps", "cgrep", "wc")
+    namespace.namespaces flatMap { _.tasks } map { _.name } shouldEqual Seq("ps", "cgrep", "wc")
   }
   it should "Throw an exception if the import resolver fails to resolve an import" in {
-    def badResolver(s: String): Draft2ResolvedImportBundle = {
+    def badResolver(s: String): Draft2ResolvedImportBundle =
       throw new RuntimeException(s"Can't Resolve")
-    }
 
     WdlNamespace.loadUsingSource(workflowWdl, None, Option(Seq(badResolver))) match {
       case Failure(_: ValidationException) =>
diff --git a/wdl/model/draft2/src/test/scala/wdl/WdlCallSpec.scala b/wdl/model/draft2/src/test/scala/wdl/WdlCallSpec.scala
index 5b943bf13be..61459adb0d8 100644
--- a/wdl/model/draft2/src/test/scala/wdl/WdlCallSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/WdlCallSpec.scala
@@ -25,17 +25,25 @@ class WdlCallSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers {
 
     val inputs: WorkflowCoercedInputs = SampleWdl.TaskDeclarationsWdl.workflowInputs
 
-    def outputResolver(call: WdlGraphNode, index: Option[Int]): Try[WomValue] = {
+    def outputResolver(call: WdlGraphNode, index: Option[Int]): Try[WomValue] =
       (call, index) match {
-        case (`callT`, Some(2)) => Success(WdlCallOutputsObject(callT, Map("o" -> WomString(s"c ${index.getOrElse(-1)}"))))
-        case (`callT3`, Some(2)) => Success(WdlCallOutputsObject(callT, Map("o" -> WomString(s"c ${index.getOrElse(-1)}"))))
-        case (`callT2`, None) => Success(WdlCallOutputsObject(callT2, Map(
-          "outputArray" -> WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(0), WomInteger(1), WomInteger(2)))
-        )))
+        case (`callT`, Some(2)) =>
+          Success(WdlCallOutputsObject(callT, Map("o" -> WomString(s"c ${index.getOrElse(-1)}"))))
+        case (`callT3`, Some(2)) =>
+          Success(WdlCallOutputsObject(callT, Map("o" -> WomString(s"c ${index.getOrElse(-1)}"))))
+        case (`callT2`, None) =>
+          Success(
+            WdlCallOutputsObject(callT2,
+                                 Map(
+                                   "outputArray" -> WomArray(WomArrayType(WomIntegerType),
+                                                             Seq(WomInteger(0), WomInteger(1), WomInteger(2))
+                                   )
+                                 )
+            )
+          )
         case _ => Failure(new Exception(s"no output found for call ${call.fullyQualifiedName}"))
       }
-    }
-    
+
     val shardMap = Map(namespace.scatters.head -> 2)
 
     val declarations = callV.evaluateTaskInputs(inputs, NoFunctions, outputResolver, shardMap).get
@@ -56,7 +64,7 @@ class WdlCallSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers {
       WomArray(WomArrayType(WomSingleFileType), Seq(WomSingleFile("a"), WomSingleFile("b"), WomSingleFile("c")))
     declarations.find(_._1.unqualifiedName == "l").get._2 shouldBe WomOptionalValue(WomString("c 2"))
   }
-  
+
   "accumulate input evaluation errors and throw an exception" in {
     val wdl =
       """
@@ -70,7 +78,7 @@ class WdlCallSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers {
         | call t
         |}
       """.stripMargin
-    
+
     val namespace = WdlNamespace.loadUsingSource(wdl, None, None).get
     val callT = namespace.calls.find(_.unqualifiedName == "t").get
     val exception = the[ValidationException] thrownBy {
@@ -83,30 +91,30 @@ class WdlCallSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers {
 
     val wdl =
       s"""
-        |workflow x {
-        |  call cram
-        |  call y as shouldntBeProblematic {
-        |    input:
-        |      cram = cram.scram
-        |  }
-        |
-        |}
-        |
-        |task cram {
-        |  command {
-        |    echo "."
-        |  }
-        |  output {
-        |    String scram = "."
-        |  }
-        |}
-        |
-        |task y {
-        |  String cram
-        |  command {
-        |    echo "."
-        |  }
-        |}""".stripMargin
+         |workflow x {
+         |  call cram
+         |  call y as shouldntBeProblematic {
+         |    input:
+         |      cram = cram.scram
+         |  }
+         |
+         |}
+         |
+         |task cram {
+         |  command {
+         |    echo "."
+         |  }
+         |  output {
+         |    String scram = "."
+         |  }
+         |}
+         |
+         |task y {
+         |  String cram
+         |  command {
+         |    echo "."
+         |  }
+         |}""".stripMargin
 
     val namespace = WdlNamespace.loadUsingSource(wdl, None, None).get
     namespace.workflows.head.calls.exists(_.alias == Option("shouldntBeProblematic")) shouldBe true
@@ -116,115 +124,116 @@ class WdlCallSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers {
 
     val wdl =
       s"""
-        |workflow x {
-        |  call cram
-        |  call y as shouldntBeProblematic {
-        |    input:
-        |      cram = "asdf",
-        |      slam = cram.scram
-        |  }
-        |
-        |}
-        |
-        |task cram {
-        |  command {
-        |    echo "."
-        |  }
-        |  output {
-        |    String scram = "."
-        |  }
-        |}
-        |
-        |task y {
-        |  String cram
-        |  String slam
-        |  command {
-        |    echo "."
-        |  }
-        |}""".stripMargin
+         |workflow x {
+         |  call cram
+         |  call y as shouldntBeProblematic {
+         |    input:
+         |      cram = "asdf",
+         |      slam = cram.scram
+         |  }
+         |
+         |}
+         |
+         |task cram {
+         |  command {
+         |    echo "."
+         |  }
+         |  output {
+         |    String scram = "."
+         |  }
+         |}
+         |
+         |task y {
+         |  String cram
+         |  String slam
+         |  command {
+         |    echo "."
+         |  }
+         |}""".stripMargin
 
     val namespace = WdlNamespace.loadUsingSource(wdl, None, None).get
     namespace.workflows.head.calls.exists(_.alias == Option("shouldntBeProblematic")) shouldBe true
   }
-  
+
   "find workflows" in {
 
     val subWorkflow =
       s"""
-        |task hello2 {
-        |  String addressee = "hey"
-        |  command {
-        |    echo "Hello $${addressee}!"
-        |  }
-        |  output {
-        |    String salutation = read_string(stdout())
-        |  }
-        |}
-        |
-        |workflow sub_hello {
-        |  call hello2
-        |  output {
-        |    String result = hello2.salutation
-        |  }
-        |}
+         |task hello2 {
+         |  String addressee = "hey"
+         |  command {
+         |    echo "Hello $${addressee}!"
+         |  }
+         |  output {
+         |    String salutation = read_string(stdout())
+         |  }
+         |}
+         |
+         |workflow sub_hello {
+         |  call hello2
+         |  output {
+         |    String result = hello2.salutation
+         |  }
+         |}
       """.stripMargin
 
     val wdl =
       s"""
-        |import "placeholder" as sub
-        |
-        |task hello {
-        |  String addressee
-        |  command {
-        |    echo "Hello $${addressee}!"
-        |  }
-        |  output {
-        |    String salutation = read_string(stdout())
-        |  }
-        |}
-        |
-        |workflow wf_hello {
-        |  call sub.sub_hello
-        |  call hello {input: addressee = sub_hello.result }
-        |}
+         |import "placeholder" as sub
+         |
+         |task hello {
+         |  String addressee
+         |  command {
+         |    echo "Hello $${addressee}!"
+         |  }
+         |  output {
+         |    String salutation = read_string(stdout())
+         |  }
+         |}
+         |
+         |workflow wf_hello {
+         |  call sub.sub_hello
+         |  call hello {input: addressee = sub_hello.result }
+         |}
       """.stripMargin
 
-    val ns = WdlNamespaceWithWorkflow.load(wdl, Seq((uri: String) => Draft2ResolvedImportBundle(subWorkflow, ResolvedImportRecord(uri)))).get
+    val ns = WdlNamespaceWithWorkflow
+      .load(wdl, Seq((uri: String) => Draft2ResolvedImportBundle(subWorkflow, ResolvedImportRecord(uri))))
+      .get
     ns.workflow.workflowCalls.size shouldBe 1
     ns.workflow.taskCalls.size shouldBe 1
   }
-  
+
   "bubble up evaluation exception" in {
     val wdl =
       s"""
-        |task hello {
-        |  String addressee
-        |  command {
-        |    echo "Hello $${addressee}!"
-        |  }
-        |  runtime {
-        |      docker: "ubuntu:latest"
-        |    }
-        |  output {
-        |    String salutation = read_string(stdout())
-        |  }
-        |}
-        |
-        |workflow wf_hello {
-        |  File wf_hello_input
-        |  File wf_hello_input2
-        |  String read = read_string(wf_hello_input)
-        |  String read2 = read_string(wf_hello_input2)
-        |  
-        |  call hello {input: addressee = read_string(wf_hello_input) }
-        |  call hello as hello2 {input: addressee = read }
-        |  
-        |  output {
-        |    String salutation = hello.salutation
-        |  }
-        |}""".stripMargin
-    
-    
+         |task hello {
+         |  String addressee
+         |  command {
+         |    echo "Hello $${addressee}!"
+         |  }
+         |  runtime {
+         |      docker: "ubuntu:latest"
+         |    }
+         |  output {
+         |    String salutation = read_string(stdout())
+         |  }
+         |}
+         |
+         |workflow wf_hello {
+         |  File wf_hello_input
+         |  File wf_hello_input2
+         |  String read = read_string(wf_hello_input)
+         |  String read2 = read_string(wf_hello_input2)
+         |  
+         |  call hello {input: addressee = read_string(wf_hello_input) }
+         |  call hello as hello2 {input: addressee = read }
+         |  
+         |  output {
+         |    String salutation = hello.salutation
+         |  }
+         |}""".stripMargin
+
     val functionsWithRead = new PureStandardLibraryFunctionsLike {
       override def readFile(path: String, sizeLimit: Int): String = {
         import better.files._
@@ -234,18 +243,25 @@ class WdlCallSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers {
 
     val ns = WdlNamespaceWithWorkflow.load(wdl, Seq.empty).get
     val exception = intercept[ValidationException] {
-        ns.workflow.findCallByName("hello2").get.evaluateTaskInputs(
+      ns.workflow
+        .findCallByName("hello2")
+        .get
+        .evaluateTaskInputs(
           Map("wf_hello.wf_hello_input" -> WomSingleFile("/do/not/exist")),
           functionsWithRead
-        ).get
+        )
+        .get
     }
     exception.getMessage shouldBe "Input evaluation for Call wf_hello.hello2 failed.:\naddressee:\n\tFile not found /do/not/exist"
 
-    val staticEvaluation = ns.staticDeclarationsRecursive(Map(
-      "wf_hello.wf_hello_input" -> WomSingleFile("/do/not/exist"),
-      "wf_hello.wf_hello_input2" -> WomSingleFile("/do/not/exist2")
-    ), functionsWithRead)
-    
+    val staticEvaluation =
+      ns.staticDeclarationsRecursive(Map(
+                                       "wf_hello.wf_hello_input" -> WomSingleFile("/do/not/exist"),
+                                       "wf_hello.wf_hello_input2" -> WomSingleFile("/do/not/exist2")
+                                     ),
+                                     functionsWithRead
+      )
+
     staticEvaluation.isFailure shouldBe true
     val exception2 = staticEvaluation.failed.get
     exception2.getMessage shouldBe "Could not evaluate workflow declarations:\nwf_hello.read:\n\tFile not found /do/not/exist\nwf_hello.read2:\n\tFile not found /do/not/exist2"
diff --git a/wdl/model/draft2/src/test/scala/wdl/WdlTest.scala b/wdl/model/draft2/src/test/scala/wdl/WdlTest.scala
index 9bef617b390..11de27dcfcb 100644
--- a/wdl/model/draft2/src/test/scala/wdl/WdlTest.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/WdlTest.scala
@@ -11,23 +11,24 @@ import wom.ResolvedImportRecord
 trait WdlTest extends Matchers with AnyWordSpecLike {
   def resolver(root: File)(relPath: String): Draft2ResolvedImportBundle =
     Draft2ResolvedImportBundle((root / relPath).contentAsString, ResolvedImportRecord((root / relPath).pathAsString))
-  def loadWdl(path: String) = loadWdlFile(currentWorkingDirectory/"wom"/"src"/"test"/"resources"/path)
+  def loadWdl(path: String) = loadWdlFile(currentWorkingDirectory / "wom" / "src" / "test" / "resources" / path)
   def loadWdlFile(wdlFile: File) =
     WdlNamespaceWithWorkflow.load(wdlFile.contentAsString, Seq(resolver(wdlFile / "..") _)).get
   def getTask(ns: WdlNamespace, name: String): WdlTask = ns.tasks.find(_.unqualifiedName == name).get
-  def getCall(ns: WdlNamespaceWithWorkflow, name: String): WdlTaskCall = ns.workflow.taskCalls.find(_.unqualifiedName == name) getOrElse {
-    fail(s"Expecting call with name '$name'")
-  }
+  def getCall(ns: WdlNamespaceWithWorkflow, name: String): WdlTaskCall =
+    ns.workflow.taskCalls.find(_.unqualifiedName == name) getOrElse {
+      fail(s"Expecting call with name '$name'")
+    }
   def getScatter(ns: WdlNamespaceWithWorkflow, index: Int): Scatter = {
     val scatterFqn = ns.workflow.unqualifiedName + ".$scatter_" + index
-    val resolution = ns.resolve(scatterFqn).collect({ case s: Scatter => s})
+    val resolution = ns.resolve(scatterFqn).collect { case s: Scatter => s }
     resolution getOrElse {
       fail(s"Expecting a scatter block with FQN $scatterFqn")
     }
   }
   def getIf(ns: WdlNamespaceWithWorkflow, index: Int): If = {
     val ifFqn = ns.workflow.unqualifiedName + ".$if_" + index
-    val resolution = ns.resolve(ifFqn).collect({ case i: If => i })
+    val resolution = ns.resolve(ifFqn).collect { case i: If => i }
     resolution getOrElse {
       fail(s"Expecting a scatter block with FQN $ifFqn")
     }
diff --git a/wdl/model/draft2/src/test/scala/wdl/WdlWiringSpec.scala b/wdl/model/draft2/src/test/scala/wdl/WdlWiringSpec.scala
index 5ab30d7d57c..44181e6b2ab 100644
--- a/wdl/model/draft2/src/test/scala/wdl/WdlWiringSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/WdlWiringSpec.scala
@@ -19,7 +19,11 @@ class WdlWiringSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val wdlFile = testDir / "test.wdl"
     if (!wdlFile.exists) fail(s"Expecting a 'test.wdl' file in directory 'cases/${testDir.name}'")
     def resolvers: Seq[Draft2ImportResolver] =
-      Seq((relPath: String) => Draft2ResolvedImportBundle((testDir / relPath).contentAsString, ResolvedImportRecord((testDir / relPath).pathAsString)))
+      Seq((relPath: String) =>
+        Draft2ResolvedImportBundle((testDir / relPath).contentAsString,
+                                   ResolvedImportRecord((testDir / relPath).pathAsString)
+        )
+      )
     val namespace = WdlNamespaceWithWorkflow.load(File(wdlFile.path).contentAsString, resolvers).get
     val wdlFileRelPath = File(".").relativize(wdlFile)
 
@@ -98,12 +102,17 @@ class WdlWiringSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       expectedWorkflowInputsFile.write(jsObject.prettyPrint + "\n")
     }
 
-    expectedWorkflowInputsFile.contentAsString.parseJson.asInstanceOf[JsObject].fields.asInstanceOf[Map[String, JsString]] map {
-      case (k, v) => k -> v.value
+    expectedWorkflowInputsFile.contentAsString.parseJson
+      .asInstanceOf[JsObject]
+      .fields
+      .asInstanceOf[Map[String, JsString]] map { case (k, v) =>
+      k -> v.value
     }
   }
 
-  private def expectedParents(testDir: File, namespace: WdlNamespaceWithWorkflow): Map[FullyQualifiedName, Option[FullyQualifiedName]] = {
+  private def expectedParents(testDir: File,
+                              namespace: WdlNamespaceWithWorkflow
+  ): Map[FullyQualifiedName, Option[FullyQualifiedName]] = {
     val expectedParentsFile = testDir / "parents.expectations"
 
     if (!expectedParentsFile.exists) {
@@ -120,7 +129,9 @@ class WdlWiringSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     }
   }
 
-  private def expectedChildren(testDir: File, namespace: WdlNamespaceWithWorkflow): Map[FullyQualifiedName, Seq[Scope]] = {
+  private def expectedChildren(testDir: File,
+                               namespace: WdlNamespaceWithWorkflow
+  ): Map[FullyQualifiedName, Seq[Scope]] = {
     val expectedChildrenFile = testDir / "children.expectations"
 
     if (!expectedChildrenFile.exists) {
@@ -131,14 +142,18 @@ class WdlWiringSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       expectedChildrenFile.write(jsObject.prettyPrint + "\n")
     }
 
-    expectedChildrenFile.contentAsString.parseJson.asInstanceOf[JsObject].fields.asInstanceOf[Map[String, JsArray]] map {
-      case (k, v) =>
-        val children = v.elements.collect({ case s: JsString => s }).map(s => namespace.resolve(s.value).get)
-        k -> children
+    expectedChildrenFile.contentAsString.parseJson
+      .asInstanceOf[JsObject]
+      .fields
+      .asInstanceOf[Map[String, JsArray]] map { case (k, v) =>
+      val children = v.elements.collect { case s: JsString => s }.map(s => namespace.resolve(s.value).get)
+      k -> children
     }
   }
 
-  private def expectedFullyQualifiedNames(testDir: File, namespace: WdlNamespaceWithWorkflow): Map[FullyQualifiedName, String] = {
+  private def expectedFullyQualifiedNames(testDir: File,
+                                          namespace: WdlNamespaceWithWorkflow
+  ): Map[FullyQualifiedName, String] = {
     val expectedFqnsAndClassFile = testDir / "fqn.expectations"
 
     if (!expectedFqnsAndClassFile.exists) {
@@ -149,12 +164,17 @@ class WdlWiringSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       expectedFqnsAndClassFile.write(jsObject.prettyPrint + "\n")
     }
 
-    expectedFqnsAndClassFile.contentAsString.parseJson.asInstanceOf[JsObject].fields.asInstanceOf[Map[String, JsString]] map {
-      case (k, v) => k -> v.value
+    expectedFqnsAndClassFile.contentAsString.parseJson
+      .asInstanceOf[JsObject]
+      .fields
+      .asInstanceOf[Map[String, JsString]] map { case (k, v) =>
+      k -> v.value
     }
   }
 
-  private def expectedFullyQualifiedNamesWithIndexScopes(testDir: File, namespace: WdlNamespaceWithWorkflow): Map[FullyQualifiedName, String] = {
+  private def expectedFullyQualifiedNamesWithIndexScopes(testDir: File,
+                                                         namespace: WdlNamespaceWithWorkflow
+  ): Map[FullyQualifiedName, String] = {
     val expectedFqnsAndClassFile = testDir / "fqn_index_scopes.expectations"
 
     if (!expectedFqnsAndClassFile.exists) {
@@ -165,8 +185,11 @@ class WdlWiringSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       expectedFqnsAndClassFile.write(jsObject.prettyPrint + "\n")
     }
 
-    expectedFqnsAndClassFile.contentAsString.parseJson.asInstanceOf[JsObject].fields.asInstanceOf[Map[String, JsString]] map {
-      case (k, v) => k -> v.value
+    expectedFqnsAndClassFile.contentAsString.parseJson
+      .asInstanceOf[JsObject]
+      .fields
+      .asInstanceOf[Map[String, JsString]] map { case (k, v) =>
+      k -> v.value
     }
   }
 
@@ -181,30 +204,39 @@ class WdlWiringSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       expectedAncestryFile.write(jsObject.prettyPrint + "\n")
     }
 
-    expectedAncestryFile.contentAsString.parseJson.asInstanceOf[JsObject].fields.asInstanceOf[Map[String, JsArray]] map {
-      case (k, v) =>
-        val expectedAncestry = v.elements.asInstanceOf[Vector[JsString]].map(n => namespace.resolve(n.value).get)
-        val resolvedFqn = namespace.resolve(k).get
-        resolvedFqn -> expectedAncestry
+    expectedAncestryFile.contentAsString.parseJson
+      .asInstanceOf[JsObject]
+      .fields
+      .asInstanceOf[Map[String, JsArray]] map { case (k, v) =>
+      val expectedAncestry = v.elements.asInstanceOf[Vector[JsString]].map(n => namespace.resolve(n.value).get)
+      val resolvedFqn = namespace.resolve(k).get
+      resolvedFqn -> expectedAncestry
     }
   }
 
-  private def expectedUpstreamAncestry(testDir: File, namespace: WdlNamespaceWithWorkflow): Map[WdlGraphNode, Set[Scope]] = {
+  private def expectedUpstreamAncestry(testDir: File,
+                                       namespace: WdlNamespaceWithWorkflow
+  ): Map[WdlGraphNode, Set[Scope]] = {
     val expectedUpstreamFile = testDir / "upstreamAncestry.expectations"
 
     if (!expectedUpstreamFile.exists) {
-      val upstreamFqns = namespace.descendants.collect({ case n: WdlGraphNode => n }) map { node =>
-        node.fullyQualifiedName -> JsArray(node.upstreamAncestry.toVector.map(_.fullyQualifiedName).sorted.map(JsString(_)))
+      val upstreamFqns = namespace.descendants.collect { case n: WdlGraphNode => n } map { node =>
+        node.fullyQualifiedName -> JsArray(
+          node.upstreamAncestry.toVector.map(_.fullyQualifiedName).sorted.map(JsString(_))
+        )
       }
       val jsObject = JsObject(ListMap(upstreamFqns.toSeq.sortBy(_._1): _*))
       expectedUpstreamFile.write(jsObject.prettyPrint + "\n")
     }
 
-    expectedUpstreamFile.contentAsString.parseJson.asInstanceOf[JsObject].fields.asInstanceOf[Map[String, JsArray]] map {
-      case (k, v) =>
-        val expectedUpstreamAncestors = v.elements.asInstanceOf[Vector[JsString]].map(n => namespace.resolve(n.value).get).toSet
-        val resolvedFqn = namespace.resolve(k).get.asInstanceOf[WdlGraphNode]
-        resolvedFqn -> expectedUpstreamAncestors
+    expectedUpstreamFile.contentAsString.parseJson
+      .asInstanceOf[JsObject]
+      .fields
+      .asInstanceOf[Map[String, JsArray]] map { case (k, v) =>
+      val expectedUpstreamAncestors =
+        v.elements.asInstanceOf[Vector[JsString]].map(n => namespace.resolve(n.value).get).toSet
+      val resolvedFqn = namespace.resolve(k).get.asInstanceOf[WdlGraphNode]
+      resolvedFqn -> expectedUpstreamAncestors
     }
   }
 
@@ -212,18 +244,20 @@ class WdlWiringSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val expectedUpstreamFile = testDir / "upstream.expectations"
 
     if (!expectedUpstreamFile.exists) {
-      val upstreamFqns = namespace.descendants.collect({ case n: WdlGraphNode => n }) map { node =>
+      val upstreamFqns = namespace.descendants.collect { case n: WdlGraphNode => n } map { node =>
         node.fullyQualifiedName -> JsArray(node.upstream.toVector.map(_.fullyQualifiedName).sorted.map(JsString(_)))
       }
       val jsObject = JsObject(ListMap(upstreamFqns.toSeq.sortBy(_._1): _*))
       expectedUpstreamFile.write(jsObject.prettyPrint + "\n")
     }
 
-    expectedUpstreamFile.contentAsString.parseJson.asInstanceOf[JsObject].fields.asInstanceOf[Map[String, JsArray]] map {
-      case (k, v) =>
-        val expectedUpstream = v.elements.asInstanceOf[Vector[JsString]].map(n => namespace.resolve(n.value).get).toSet
-        val resolvedFqn = namespace.resolve(k).get.asInstanceOf[WdlGraphNode]
-        resolvedFqn -> expectedUpstream
+    expectedUpstreamFile.contentAsString.parseJson
+      .asInstanceOf[JsObject]
+      .fields
+      .asInstanceOf[Map[String, JsArray]] map { case (k, v) =>
+      val expectedUpstream = v.elements.asInstanceOf[Vector[JsString]].map(n => namespace.resolve(n.value).get).toSet
+      val resolvedFqn = namespace.resolve(k).get.asInstanceOf[WdlGraphNode]
+      resolvedFqn -> expectedUpstream
     }
   }
 
@@ -231,14 +265,17 @@ class WdlWiringSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val expectedDownstreamFile = testDir / "downstream.expectations"
 
     if (!expectedDownstreamFile.exists) {
-      val downstreamFqns = namespace.descendants.collect({ case n: WdlGraphNode => n }) map { node =>
+      val downstreamFqns = namespace.descendants.collect { case n: WdlGraphNode => n } map { node =>
         node.fullyQualifiedName -> JsArray(node.downstream.toVector.map(_.fullyQualifiedName).sorted.map(JsString(_)))
       }
       val jsObject = JsObject(ListMap(downstreamFqns.toSeq.sortBy(_._1): _*))
       expectedDownstreamFile.write(jsObject.prettyPrint + "\n")
     }
 
-    expectedDownstreamFile.contentAsString.parseJson.asInstanceOf[JsObject].fields.asInstanceOf[Map[String, JsArray]] map { case (k, v) =>
+    expectedDownstreamFile.contentAsString.parseJson
+      .asInstanceOf[JsObject]
+      .fields
+      .asInstanceOf[Map[String, JsArray]] map { case (k, v) =>
       val expectedDownstream = v.elements.asInstanceOf[Vector[JsString]].map(n => namespace.resolve(n.value).get).toSet
       val resolvedFqn = namespace.resolve(k).get.asInstanceOf[WdlGraphNode]
       resolvedFqn -> expectedDownstream
diff --git a/wdl/model/draft2/src/test/scala/wdl/WdlWorkflowImportsSpec.scala b/wdl/model/draft2/src/test/scala/wdl/WdlWorkflowImportsSpec.scala
index 38d84429af6..b6d7e5701b8 100644
--- a/wdl/model/draft2/src/test/scala/wdl/WdlWorkflowImportsSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/WdlWorkflowImportsSpec.scala
@@ -45,79 +45,79 @@ class WdlWorkflowImportsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
   val basicWdl =
     s"""
-      |import "$echoHelloWdlFile"
+       |import "$echoHelloWdlFile"
       """.stripMargin +
-    """
-      |
-      |task ls {
-      |  command {
-      |    ls -l
-      |  }
-      |  output {
-      |    String fileList = read_string(stdout())
-      |  }
-      |}
-      |
-      |task pwd {
-      |   command {
-      |     pwd
-      |   }
-      |   output {
-      |     String current = read_string(stdout())
-      |   }
-      |}
-      |
-      |workflow basic {
-      |  call ls
-      |  call pwd
-      |  output {
-      |       ls.fileList
-      |   }
-      |}
+      """
+        |
+        |task ls {
+        |  command {
+        |    ls -l
+        |  }
+        |  output {
+        |    String fileList = read_string(stdout())
+        |  }
+        |}
+        |
+        |task pwd {
+        |   command {
+        |     pwd
+        |   }
+        |   output {
+        |     String current = read_string(stdout())
+        |   }
+        |}
+        |
+        |workflow basic {
+        |  call ls
+        |  call pwd
+        |  output {
+        |       ls.fileList
+        |   }
+        |}
     """.stripMargin
 
   val printNumsWdl =
     s"""
-      |import "$echoHelloWdlFile" as multilingualEcho
-      |
+       |import "$echoHelloWdlFile" as multilingualEcho
+       |
       """.stripMargin +
-    """
-      |task ls {
-      |  command {
-      |    ls
-      |  }
-      |}
-      |
-      |
-      |task print1 {
-      |  Int x = 10
-      |  command {
-      |    for i in `seq 1 ${x}`
-      |      do
-      |        echo $i
-      |      done
-      |  }
-      |}
-      |
-      |task print2 {
-      |  Int x = 20
-      |  command {
-      |    for i in `seq 1 ${x}`
-      |      do
-      |        echo $i
-      |      done
-      |  }
-      |}
-      |
-      |task print3 {
-      |  Int x = 30
-      |  command {
-      |    for i in `seq 1 ${x}`
-      |      do
-      |        echo $i
-      |      done
-      |  }
-      |}
+      """
+        |task ls {
+        |  command {
+        |    ls
+        |  }
+        |}
+        |
+        |
+        |task print1 {
+        |  Int x = 10
+        |  command {
+        |    for i in `seq 1 ${x}`
+        |      do
+        |        echo $i
+        |      done
+        |  }
+        |}
+        |
+        |task print2 {
+        |  Int x = 20
+        |  command {
+        |    for i in `seq 1 ${x}`
+        |      do
+        |        echo $i
+        |      done
+        |  }
+        |}
+        |
+        |task print3 {
+        |  Int x = 30
+        |  command {
+        |    for i in `seq 1 ${x}`
+        |      do
+        |        echo $i
+        |      done
+        |  }
+        |}
     """.stripMargin
 
   val snoozeWdl =
@@ -176,11 +176,10 @@ class WdlWorkflowImportsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
       |}
     """.stripMargin
 
-
   val threeStepWdlWithImports =
     s"""
-      |import "$echoHelloWdlFile" as funEcho
-      |
+       |import "$echoHelloWdlFile" as funEcho
+       |
       """.stripMargin + threeStepWdl
 
   val basicWdlImportFile = addAndGetFile("basic", basicWdl)
@@ -188,8 +187,7 @@ class WdlWorkflowImportsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
   val snoozeWdlImportFile = addAndGetFile("snooze", snoozeWdl)
   val printNumsWdlImportFile = addAndGetFile("printNums", printNumsWdl)
 
-  def noExtension(fileName: String) = fileName.replace(".wdl","")
-
+  def noExtension(fileName: String) = fileName.replace(".wdl", "")
 
   val imports =
     s"""
@@ -202,41 +200,42 @@ class WdlWorkflowImportsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
   val primaryWorkflow =
     s"""
-    |
-    |task testCaseTask {
-    |  command {
-    |     echo "Ruchi's birthday: 01/19"
-    |  }
-    |}
-    |
-    |workflow testCases {
-    |  call ${noExtension(basicWdlImportFile)}.ls as ls1
-    |  call ${noExtension(printNumsWdlImportFile)}.ls as ls2
-    |
-    |  #call ${noExtension(basicWdlImportFile)}.pwd as soBasic
-    |
-    |  #call ${noExtension(printNumsWdlImportFile)}.print1
-    |  #call ${noExtension(printNumsWdlImportFile)}.print2 as printingFun
-    |
-    |
-    |  call classicThreeStep.ps
-    |  call classicThreeStep.ps as psAgain
-    |
-    |  call trySleep.sleep
-    |  call trySleep.sleep2 as sleepMore
-    |
-    |  call ${noExtension(basicWdlImportFile)}.${noExtension(echoHelloWdlFile)}.inFrench
-    |  call classicThreeStep.funEcho.inSpanish
-    |  call classicThreeStep.funEcho.inSpanish as inPortugese
-    |  call ${noExtension(printNumsWdlImportFile)}.multilingualEcho.inItalian
-    |
-    |}
-    |""".stripMargin
+       |
+       |task testCaseTask {
+       |  command {
+       |     echo "Ruchi's birthday: 01/19"
+       |  }
+       |}
+       |
+       |workflow testCases {
+       |  call ${noExtension(basicWdlImportFile)}.ls as ls1
+       |  call ${noExtension(printNumsWdlImportFile)}.ls as ls2
+       |
+       |  #call ${noExtension(basicWdlImportFile)}.pwd as soBasic
+       |
+       |  #call ${noExtension(printNumsWdlImportFile)}.print1
+       |  #call ${noExtension(printNumsWdlImportFile)}.print2 as printingFun
+       |
+       |
+       |  call classicThreeStep.ps
+       |  call classicThreeStep.ps as psAgain
+       |
+       |  call trySleep.sleep
+       |  call trySleep.sleep2 as sleepMore
+       |
+       |  call ${noExtension(basicWdlImportFile)}.${noExtension(echoHelloWdlFile)}.inFrench
+       |  call classicThreeStep.funEcho.inSpanish
+       |  call classicThreeStep.funEcho.inSpanish as inPortugese
+       |  call ${noExtension(printNumsWdlImportFile)}.multilingualEcho.inItalian
+       |
+       |}
+       |""".stripMargin
 
   val wdlWithImports = imports + primaryWorkflow
 
   val namespace = {
-    val resolvers: Seq[Draft2ImportResolver] = Seq(WdlNamespace.directoryResolver(wdlDirectory), WdlNamespace.fileResolver)
+    val resolvers: Seq[Draft2ImportResolver] =
+      Seq(WdlNamespace.directoryResolver(wdlDirectory), WdlNamespace.fileResolver)
     WdlNamespaceWithWorkflow.load(wdlWithImports, resolvers).get
   }
 
@@ -256,7 +255,8 @@ class WdlWorkflowImportsSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
   }
   it should "import two WDL file (with clashing task names) and be able to reference all tasks by FQN" in {
     val clashingTaskNames = Seq(namespace.resolve(s"${noExtension(basicWdlImportFile)}.ls"),
-                            namespace.resolve(s"${noExtension(printNumsWdlImportFile)}.ls"))
+                                namespace.resolve(s"${noExtension(printNumsWdlImportFile)}.ls")
+    )
 
     clashingTaskNames.size shouldEqual 2
   }
diff --git a/wdl/model/draft2/src/test/scala/wdl/WdlWorkflowSpec.scala b/wdl/model/draft2/src/test/scala/wdl/WdlWorkflowSpec.scala
index 4b5f2811760..96d31533fd3 100644
--- a/wdl/model/draft2/src/test/scala/wdl/WdlWorkflowSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/WdlWorkflowSpec.scala
@@ -77,82 +77,114 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
 
     val workflowInputs = Map("main_workflow.workflow_input" -> WomString("workflow_input"))
 
-    def outputResolverForWorkflow(workflow: WdlWorkflow)(call: WdlGraphNode, index: Option[Int])= {
+    def outputResolverForWorkflow(workflow: WdlWorkflow)(call: WdlGraphNode, index: Option[Int]) =
       call match {
         // Main Task
         case c: WdlCall if c == workflow.findCallByName("main_task").get =>
-          Success(WdlCallOutputsObject(c, Map(
-            "task_o1" -> WomString("MainTaskOutputString"),
-            "task_o2" -> WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(8)))
-          )))
+          Success(
+            WdlCallOutputsObject(c,
+                                 Map(
+                                   "task_o1" -> WomString("MainTaskOutputString"),
+                                   "task_o2" -> WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(8)))
+                                 )
+            )
+          )
         case c: WdlCall if c == workflow.findCallByName("main_task2").get =>
-          Success(WdlCallOutputsObject(c, Map(
-            "task_o1" -> WomString("MainTask2OutputString"),
-            "task_o2" -> WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(16)))
-          )))
+          Success(
+            WdlCallOutputsObject(c,
+                                 Map(
+                                   "task_o1" -> WomString("MainTask2OutputString"),
+                                   "task_o2" -> WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(16)))
+                                 )
+            )
+          )
         case c: WdlCall if c == workflow.findCallByName("main_task_in_scatter").get =>
-          Success(WdlCallOutputsObject(c, Map(
-            "task_o1" -> WomArray(WomArrayType(WomStringType), Seq(WomString("MainTaskOutputString")))
-          )))
+          Success(
+            WdlCallOutputsObject(c,
+                                 Map(
+                                   "task_o1" -> WomArray(WomArrayType(WomStringType),
+                                                         Seq(WomString("MainTaskOutputString"))
+                                   )
+                                 )
+            )
+          )
 
-        //Sub Task
+        // Sub Task
         case c: WdlCall if c == workflow.findCallByName("sub_task").get =>
-          Success(WdlCallOutputsObject(c, Map(
-            "sub_task_o1" -> WomString("SubTaskOutputString")
-          )))
+          Success(
+            WdlCallOutputsObject(c,
+                                 Map(
+                                   "sub_task_o1" -> WomString("SubTaskOutputString")
+                                 )
+            )
+          )
         case c: WdlCall if c == workflow.findCallByName("sub_task2").get =>
-          Success(WdlCallOutputsObject(c, Map(
-            "sub_task_o1" -> WomString("SubTask2OutputString")
-          )))
+          Success(
+            WdlCallOutputsObject(c,
+                                 Map(
+                                   "sub_task_o1" -> WomString("SubTask2OutputString")
+                                 )
+            )
+          )
 
         // Workflow Task
         case c: WdlCall if c == workflow.findCallByName("sub_workflow").get =>
-          Success(WdlCallOutputsObject(c, Map(
-            "sub_sub_workflow_sub_task_sub_task_o1" -> WomString("SubWorkflowSubTaskOutputString"),
-            "sub_o1" -> WomString("SubWorkflowOutputString")
-          )))
+          Success(
+            WdlCallOutputsObject(
+              c,
+              Map(
+                "sub_sub_workflow_sub_task_sub_task_o1" -> WomString("SubWorkflowSubTaskOutputString"),
+                "sub_o1" -> WomString("SubWorkflowOutputString")
+              )
+            )
+          )
         case c: WdlCall if c == workflow.findCallByName("sub_workflow2").get =>
-          Success(WdlCallOutputsObject(c, Map(
-            "sub_sub_workflow_sub_task_sub_task_o1" -> WomString("SubWorkflow2SubTaskOutputString"),
-            "sub_o1" -> WomString("SubWorkflow2OutputString")
-          )))
+          Success(
+            WdlCallOutputsObject(
+              c,
+              Map(
+                "sub_sub_workflow_sub_task_sub_task_o1" -> WomString("SubWorkflow2SubTaskOutputString"),
+                "sub_o1" -> WomString("SubWorkflow2OutputString")
+              )
+            )
+          )
         case c: WdlCall => fail(s"No output found for call ${c.unqualifiedName}")
         case _ => Failure(new Exception())
       }
-    }
 
     case class WorkflowOutputExpectation(unqualifiedName: FullyQualifiedName, womType: WomType, sourceString: String)
 
     implicit val workflowOutputEquality = new Equality[WorkflowOutput] {
-      override def areEqual(src: WorkflowOutput, expectation: Any): Boolean = {
+      override def areEqual(src: WorkflowOutput, expectation: Any): Boolean =
         expectation match {
           case output: WorkflowOutputExpectation =>
             output.unqualifiedName == src.unqualifiedName &&
             "main_workflow." + output.unqualifiedName == src.locallyQualifiedName(src.parent.get) &&
-              output.womType.stableName == src.womType.stableName &&
-              output.sourceString == src.requiredExpression.toWomString
+            output.womType.stableName == src.womType.stableName &&
+            output.sourceString == src.requiredExpression.toWomString
           case _ => false
         }
-      }
     }
 
     def evaluateOutputs(workflow: WdlWorkflow,
                         knownInputs: WorkflowCoercedInputs,
                         wdlFunctions: WdlFunctions[WomValue],
                         outputResolver: OutputResolver,
-                        shards: Map[Scatter, Int] = Map.empty[Scatter, Int]): Try[Map[WorkflowOutput, WomValue]] = {
+                        shards: Map[Scatter, Int] = Map.empty[Scatter, Int]
+    ): Try[Map[WorkflowOutput, WomValue]] = {
 
-      val evaluatedOutputs = workflow.outputs.foldLeft(Map.empty[WorkflowOutput, Try[WomValue]])((outputMap, output) => {
-        val currentOutputs = outputMap collect {
-          case (outputName, outputValue) if outputValue.isSuccess => outputName.fullyQualifiedName -> outputValue.get
-        }
-        def knownValues = currentOutputs ++ knownInputs
-        val lookup = workflow.lookupFunction(knownValues, wdlFunctions, outputResolver, shards, output)
-        val coerced = output.requiredExpression.evaluate(lookup, wdlFunctions) flatMap output.womType.coerceRawValue
-        val workflowOutput = output -> coerced
+      val evaluatedOutputs = workflow.outputs.foldLeft(Map.empty[WorkflowOutput, Try[WomValue]]) {
+        (outputMap, output) =>
+          val currentOutputs = outputMap collect {
+            case (outputName, outputValue) if outputValue.isSuccess => outputName.fullyQualifiedName -> outputValue.get
+          }
+          def knownValues = currentOutputs ++ knownInputs
+          val lookup = workflow.lookupFunction(knownValues, wdlFunctions, outputResolver, shards, output)
+          val coerced = output.requiredExpression.evaluate(lookup, wdlFunctions) flatMap output.womType.coerceRawValue
+          val workflowOutput = output -> coerced
 
-        outputMap + workflowOutput
-      })
+          outputMap + workflowOutput
+      }
 
       TryUtil.sequenceMap(evaluatedOutputs, "Failed to evaluate workflow outputs.\n")
     }
@@ -160,36 +192,52 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
     def verifyOutputsForNamespace(ns: WdlNamespaceWithWorkflow,
                                   declarationExpectations: Seq[WorkflowOutputExpectation],
                                   evaluationExpectations: Map[String, WomValue],
-                                  outputResolver: OutputResolver) = {
+                                  outputResolver: OutputResolver
+    ) = {
       val outputs = ns.workflow.outputs
       outputs should contain theSameElementsAs declarationExpectations
 
       val evaluatedOutputs = evaluateOutputs(ns.workflow, workflowInputs, NoFunctions, outputResolver)
       evaluatedOutputs match {
-        case Success(v) => v.map { case (output, outputValue) => output.unqualifiedName -> outputValue }.toList should contain theSameElementsAs evaluationExpectations
+        case Success(v) =>
+          v.map { case (output, outputValue) =>
+            output.unqualifiedName -> outputValue
+          }.toList should contain theSameElementsAs evaluationExpectations
         case Failure(e) => fail(e)
       }
     }
-    
-    def verifyOutputs(outputString: String, declarationExpectations: Seq[WorkflowOutputExpectation], evaluationExpectations: Map[String, WomValue]) = {
-      val ns = WdlNamespaceWithWorkflow.load(
-        wdl.replace("<<OUTPUTS>>", outputString), Seq((uri: String) => Draft2ResolvedImportBundle(subWorkflow, ResolvedImportRecord(uri)))).get
-      verifyOutputsForNamespace(ns, declarationExpectations, evaluationExpectations, outputResolverForWorkflow(ns.workflow))
+
+    def verifyOutputs(outputString: String,
+                      declarationExpectations: Seq[WorkflowOutputExpectation],
+                      evaluationExpectations: Map[String, WomValue]
+    ) = {
+      val ns = WdlNamespaceWithWorkflow
+        .load(wdl.replace("<<OUTPUTS>>", outputString),
+              Seq((uri: String) => Draft2ResolvedImportBundle(subWorkflow, ResolvedImportRecord(uri)))
+        )
+        .get
+      verifyOutputsForNamespace(ns,
+                                declarationExpectations,
+                                evaluationExpectations,
+                                outputResolverForWorkflow(ns.workflow)
+      )
     }
 
-    case class WorkflowOutputTestCase(description: String, output: String,
+    case class WorkflowOutputTestCase(description: String,
+                                      output: String,
                                       declarationExpectation: Seq[WorkflowOutputExpectation],
-                                      evaluatedOutputExpectation: Map[String, WomValue])
-    
+                                      evaluatedOutputExpectation: Map[String, WomValue]
+    )
+
     Seq(
       /*  WILDCARD OUTPUTS  */
       /*
         main_task.*                                # task wildcard
         main_task2.*                               # aliased task wildcard
-        
+
         sub_task.*                                 # sub task wildcard
         sub_task2.*                                # aliased sub task wildcard
-           
+
         sub_workflow.*                             # sub workflow wildcard
         sub_workflow2.*                            # aliased sub workflow wildcard
        */
@@ -229,16 +277,16 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
         Seq(WorkflowOutputExpectation("sub_task2.sub_task_o1", WomStringType, "sub_task2.sub_task_o1")),
         Map("sub_task2.sub_task_o1" -> WomString("SubTask2OutputString"))
       ),
-      
+
       /*  DIRECT OUTPUT REFERENCES  */
       /*
         main_task.task_o1                          # task output
         main_task2.task_o2                         # aliased task output
         main_task_in_scatter.task_o1               # task output in scatter
-        
+
         sub_task.sub_task_o1                       # sub task output
         sub_task2.sub_task_o1                      # aliased sub task output
-           
+
         sub_workflow.sub_o1                        # sub workflow output
         sub_workflow2.sub_o1                       # aliased sub workflow output
        */
@@ -257,15 +305,24 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
       WorkflowOutputTestCase(
         "task output in scatter",
         "main_task_in_scatter.task_o1",
-        Seq(WorkflowOutputExpectation("main_task_in_scatter.task_o1", WomArrayType(WomStringType), "main_task_in_scatter.task_o1")),
-        Map("main_task_in_scatter.task_o1" -> WomArray(WomArrayType(WomStringType), Seq(WomString("MainTaskOutputString"))))
+        Seq(
+          WorkflowOutputExpectation("main_task_in_scatter.task_o1",
+                                    WomArrayType(WomStringType),
+                                    "main_task_in_scatter.task_o1"
+          )
+        ),
+        Map(
+          "main_task_in_scatter.task_o1" -> WomArray(WomArrayType(WomStringType),
+                                                     Seq(WomString("MainTaskOutputString"))
+          )
+        )
       ),
       WorkflowOutputTestCase(
         "sub task output",
         "sub_task.sub_task_o1",
         Seq(WorkflowOutputExpectation("sub_task.sub_task_o1", WomStringType, "sub_task.sub_task_o1")),
         Map("sub_task.sub_task_o1" -> WomString("SubTaskOutputString"))
-        ),
+      ),
       WorkflowOutputTestCase(
         "aliased sub task output",
         "sub_task2.sub_task_o1",
@@ -289,21 +346,21 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
       /*
         String o1 = main_task.task_o1                       # task output
         Array[Int] o2 = main_task2.task_o2                  # aliased task output
-        
+
         String o3 = sub_task.sub_task_o1                    # sub task output
         String o4 = sub_task2.sub_task_o1                   # aliased sub task output
-        
+
         String o5 = sub_workflow.sub_o1                     # sub workflow output
         String o6 = sub_workflow2.sub_o1                    # aliased sub workflow output
-        
+
         String o7 = o1                                      # reference to output
-        String o8 = workflow_input                          # reference to empty input declaration 
+        String o8 = workflow_input                          # reference to empty input declaration
         String o9 = workflow_input2                         # reference to provided input declaration
         File o10 = workflow_input2                          # coercion 1
         Array[Int] o11 = main_task2.task_o2                 # complex type
         Map[Int, String] o12 = {1: "1"}                     # inline declaration with complex type
         String o13 = o1 + " " + o3                          # simple expression
-        
+
         Array[String] o14 = main_task_in_scatter.task_o1    # task in scatter
         String? o15 = optionalValue                         # optional value
        */
@@ -386,7 +443,7 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
         "inline declaration with complex type",
         "Map[Int, String] o12 = {1: \"1\"}",
         Seq(WorkflowOutputExpectation("o12", WomMapType(WomIntegerType, WomStringType), "{1: \"1\"}")),
-        Map("o12" -> WomMap(WomMapType(WomIntegerType,WomStringType), Map(WomInteger(1) -> WomString("1"))))
+        Map("o12" -> WomMap(WomMapType(WomIntegerType, WomStringType), Map(WomInteger(1) -> WomString("1"))))
       ),
       WorkflowOutputTestCase(
         "simple expression",
@@ -406,7 +463,7 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
         Seq(WorkflowOutputExpectation("o15", WomOptionalType(WomStringType), "optionalValue")),
         Map("o15" -> WomOptionalValue(WomString("optional")))
       ),
-      
+
       /* LEGACY SYNTAX FOLLOWED BY NEW SYNTAX */
       WorkflowOutputTestCase(
         "support legacy syntax followed by new syntax",
@@ -437,7 +494,11 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
         """.stripMargin
 
       a[SyntaxError] should be thrownBy {
-        WdlNamespaceWithWorkflow.load(wdl.replace("<<OUTPUTS>>", output), Seq((uri: String) => Draft2ResolvedImportBundle(subWorkflow, ResolvedImportRecord(uri)))).get
+        WdlNamespaceWithWorkflow
+          .load(wdl.replace("<<OUTPUTS>>", output),
+                Seq((uri: String) => Draft2ResolvedImportBundle(subWorkflow, ResolvedImportRecord(uri)))
+          )
+          .get
       }
     }
 
@@ -460,7 +521,7 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
         WorkflowOutputExpectation("t.o1", WomStringType, "t.o1"),
         WorkflowOutputExpectation("t.o2", WomStringType, "t.o2")
       )
-      
+
       val expectedEvaluatedOutputs = Map(
         "t.o1" -> WomString("o1"),
         "t.o2" -> WomString("o2")
@@ -468,21 +529,23 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
 
       val ns = WdlNamespaceWithWorkflow.load(wdl, Seq.empty).get
 
-      def outputResolver(call: WdlGraphNode, index: Option[Int])= {
+      def outputResolver(call: WdlGraphNode, index: Option[Int]) =
         call match {
           case c: WdlCall if c == ns.workflow.findCallByName("t").get =>
-            Success(WdlCallOutputsObject(c, Map(
-              "o1" -> WomString("o1"),
-              "o2" -> WomString("o2")
+            Success(
+              WdlCallOutputsObject(c,
+                                   Map(
+                                     "o1" -> WomString("o1"),
+                                     "o2" -> WomString("o2")
+                                   )
               )
-            ))
+            )
           case _ => Failure(new Exception())
         }
-      }
-      
+
       verifyOutputsForNamespace(ns, expectedDeclarations, expectedEvaluatedOutputs, outputResolver)
     }
-    
+
     "Throw a clear error when trying to use outputs declared with the old syntax in a parent workflow" in {
       val subWorkflow =
         """
@@ -511,12 +574,16 @@ class WdlWorkflowSpec extends AnyWordSpec with CromwellTimeoutSpec with Matchers
           |  call sub.sub_workflow
           |}
         """.stripMargin
-      
+
       val exception = the[SyntaxError] thrownBy
-        WdlNamespaceWithWorkflow.load(parentWorkflow, Seq((uri: String) => Draft2ResolvedImportBundle(subWorkflow, ResolvedImportRecord(uri)))).get
+        WdlNamespaceWithWorkflow
+          .load(parentWorkflow,
+                Seq((uri: String) => Draft2ResolvedImportBundle(subWorkflow, ResolvedImportRecord(uri)))
+          )
+          .get
       exception.getMessage shouldBe s"""Workflow sub_workflow is used as a sub workflow but has outputs declared with a deprecated syntax not compatible with sub workflows.
-                                        |To use this workflow as a sub workflow please update the workflow outputs section to the latest WDL specification.
-                                        |See https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#outputs""".stripMargin
+                                       |To use this workflow as a sub workflow please update the workflow outputs section to the latest WDL specification.
+                                       |See https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#outputs""".stripMargin
     }
   }
 }
diff --git a/wdl/model/draft2/src/test/scala/wdl/expression/DNAxTypeEvalTest.scala b/wdl/model/draft2/src/test/scala/wdl/expression/DNAxTypeEvalTest.scala
index 42e1740ed17..46f776e0e18 100644
--- a/wdl/model/draft2/src/test/scala/wdl/expression/DNAxTypeEvalTest.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/expression/DNAxTypeEvalTest.scala
@@ -43,31 +43,26 @@ class DNAxTypeEvalTest extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
        |}
        |""".stripMargin
 
-
   // Figure out the type of an expression
-  def evalType(expr: WdlExpression, parent: Scope) : Try[WomType] = {
-    expr.evaluateType(WdlNamespace.lookupType(parent),
-                      new WdlStandardLibraryFunctionsType,
-                      Some(parent))
-  }
+  def evalType(expr: WdlExpression, parent: Scope): Try[WomType] =
+    expr.evaluateType(WdlNamespace.lookupType(parent), new WdlStandardLibraryFunctionsType, Some(parent))
 
   it should "correctly evaluate expression types" in {
     val ns = WdlNamespaceWithWorkflow.load(wdlCode, Seq.empty).get
     val wf = ns.workflow
 
-    val call:WdlCall = wf.findCallByName("Add") match {
+    val call: WdlCall = wf.findCallByName("Add") match {
       case None => throw new Exception(s"Call Add not found in WDL file")
       case Some(call) => call
     }
-    val ssc:Scatter = wf.scatters.head
+    val ssc: Scatter = wf.scatters.head
 
     call.inputMappings.foreach { case (_, expr) =>
-      val t:Try[WomType] = evalType(expr, ssc)
+      val t: Try[WomType] = evalType(expr, ssc)
       t should equal(Success(WomIntegerType))
     }
   }
 
-
   val wdlCode2 =
     """|task Copy {
        |  File src
@@ -100,7 +95,7 @@ class DNAxTypeEvalTest extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     val ns = WdlNamespaceWithWorkflow.load(wdlCode2, Seq.empty).get
     val wf = ns.workflow
 
-    val copy2call:WdlCall = wf.findCallByName("Copy2") match {
+    val copy2call: WdlCall = wf.findCallByName("Copy2") match {
       case None => throw new Exception(s"Call Add not found in WDL file")
       case Some(call) => call
     }
@@ -114,7 +109,6 @@ class DNAxTypeEvalTest extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     t2 should equal(Success(WomStringType))
   }
 
-
   val wdlCode3 =
     """|
        |task Inc {
@@ -160,7 +154,7 @@ class DNAxTypeEvalTest extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     val ns = WdlNamespaceWithWorkflow.load(wdlCode3, Seq.empty).get
     val wf = ns.workflow
 
-    val incCall:WdlCall = wf.findCallByName("Inc") match {
+    val incCall: WdlCall = wf.findCallByName("Inc") match {
       case None => throw new Exception(s"Call Add not found in WDL file")
       case Some(call) => call
     }
diff --git a/wdl/model/draft2/src/test/scala/wdl/expression/Draft2SizeFunctionSpec.scala b/wdl/model/draft2/src/test/scala/wdl/expression/Draft2SizeFunctionSpec.scala
index 075d8910003..e6aac8c0f0d 100644
--- a/wdl/model/draft2/src/test/scala/wdl/expression/Draft2SizeFunctionSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/expression/Draft2SizeFunctionSpec.scala
@@ -20,74 +20,102 @@ class Draft2SizeFunctionSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
   it should "correctly report a 2048 byte file, in bytes by default" in {
     val readLike = testFunctions(Success(2048L))
-    validate(readLike.size(Seq(Success(WomSingleFile("blah"))))) { res => assert(res == WomFloat(2048d)) }
+    validate(readLike.size(Seq(Success(WomSingleFile("blah")))))(res => assert(res == WomFloat(2048d)))
   }
 
   it should "correctly report a 2048 byte file, in bytes" in {
     val readLike = testFunctions(Success(2048L))
-    validate(readLike.size(Seq(Success(WomSingleFile("blah")), Success(WomString("B"))))) { res => assert(res == WomFloat(2048d)) }
+    validate(readLike.size(Seq(Success(WomSingleFile("blah")), Success(WomString("B"))))) { res =>
+      assert(res == WomFloat(2048d))
+    }
   }
 
   it should "correctly report a 2048 byte file, in KB" in {
     val readLike = testFunctions(Success(2048L))
-    validate(readLike.size(Seq(Success(WomSingleFile("blah")), Success(WomString("KB"))))) { res => assert(res == WomFloat(2d)) }
+    validate(readLike.size(Seq(Success(WomSingleFile("blah")), Success(WomString("KB"))))) { res =>
+      assert(res == WomFloat(2d))
+    }
   }
 
   it should "correctly report a 2048 byte file, in KiB" in {
     val readLike = testFunctions(Success(2048L))
-    validate(readLike.size(Seq(Success(WomSingleFile("blah")), Success(WomString("Ki"))))) { res => assert(res == WomFloat(2d)) }
+    validate(readLike.size(Seq(Success(WomSingleFile("blah")), Success(WomString("Ki"))))) { res =>
+      assert(res == WomFloat(2d))
+    }
   }
 
   it should "correctly report the size of a supplied, optional, 2048 byte file" in {
     val readLike = testFunctions(Success(2048L))
-    validate(readLike.size(Seq(Success(WomOptionalValue(WomSingleFileType, Option(WomSingleFile("blah"))))))) { res => assert(res == WomFloat(2048d)) }
+    validate(readLike.size(Seq(Success(WomOptionalValue(WomSingleFileType, Option(WomSingleFile("blah"))))))) { res =>
+      assert(res == WomFloat(2048d))
+    }
   }
 
   it should "correctly report the size of a supplied, optional optional, 2048 byte file" in {
     val readLike = testFunctions(Success(2048L))
-    validate(readLike.size(Seq(Success(WomOptionalValue(
-      WomOptionalType(WomSingleFileType),
-      Option(WomOptionalValue(WomSingleFileType, Option(WomSingleFile("blah"))))
-    ))))) { res => assert(res == WomFloat(2048d)) }
+    validate(
+      readLike.size(
+        Seq(
+          Success(
+            WomOptionalValue(
+              WomOptionalType(WomSingleFileType),
+              Option(WomOptionalValue(WomSingleFileType, Option(WomSingleFile("blah"))))
+            )
+          )
+        )
+      )
+    )(res => assert(res == WomFloat(2048d)))
   }
 
   it should "correctly report the size of a supplied, optional, 2048 byte file, in MB" in {
     val readLike = testFunctions(Success(2048L))
-    validate(readLike.size(Seq(Success(WomOptionalValue(
-      WomSingleFileType, Option(WomSingleFile("blah")))), Success(WomString("MB")
-    )))) { res => assert(res == WomFloat(0.001953125d)) }
+    validate(
+      readLike.size(
+        Seq(Success(WomOptionalValue(WomSingleFileType, Option(WomSingleFile("blah")))), Success(WomString("MB")))
+      )
+    )(res => assert(res == WomFloat(0.001953125d)))
   }
 
   it should "correctly report that an unsupplied optional file is empty" in {
     val readLike = testFunctions(Success(2048L))
-    validate(readLike.size(Seq(Success(WomOptionalValue(WomSingleFileType, None))))) { res => assert(res == WomFloat(0d)) }
+    validate(readLike.size(Seq(Success(WomOptionalValue(WomSingleFileType, None))))) { res =>
+      assert(res == WomFloat(0d))
+    }
   }
 
   it should "correctly report that an unsupplied File?? is empty" in {
     val readLike = testFunctions(Success(2048L))
-    validate(readLike.size(Seq(Success(WomOptionalValue(WomOptionalType(WomSingleFileType), None))))) { res => assert(res == WomFloat(0d)) }
+    validate(readLike.size(Seq(Success(WomOptionalValue(WomOptionalType(WomSingleFileType), None))))) { res =>
+      assert(res == WomFloat(0d))
+    }
   }
 
   it should "correctly report that an unsupplied optional file is empty, even in MB" in {
     val readLike = testFunctions(Success(2048L))
-    validate(readLike.size(Seq(Success(WomOptionalValue(WomSingleFileType, None)), Success(WomString("MB")))))  { res => assert(res == WomFloat(0d)) }
+    validate(readLike.size(Seq(Success(WomOptionalValue(WomSingleFileType, None)), Success(WomString("MB"))))) { res =>
+      assert(res == WomFloat(0d))
+    }
   }
 
   it should "refuse to report file sizes for Ints" in {
-    val readLike = testFunctions(Failure(new Exception("Bad result: WdlIntegers shouldn't even be tried for getting file size")))
+    val readLike =
+      testFunctions(Failure(new Exception("Bad result: WdlIntegers shouldn't even be tried for getting file size")))
     val oops = readLike.size(Seq(Success(WomInteger(7))))
     oops match {
       case Success(x) => fail(s"Expected a string to not have a file length but instead got $x")
-      case Failure(e) => e.getMessage should be("The 'size' method expects a 'File' or 'File?' argument but instead got Int.")
+      case Failure(e) =>
+        e.getMessage should be("The 'size' method expects a 'File' or 'File?' argument but instead got Int.")
     }
   }
 
   it should "refuse to report file sizes for Int?s" in {
-    val readLike = testFunctions(Failure(new Exception("Bad result: WdlIntegers shouldn't even be tried for getting file size")))
+    val readLike =
+      testFunctions(Failure(new Exception("Bad result: WdlIntegers shouldn't even be tried for getting file size")))
     val oops = readLike.size(Seq(Success(WomOptionalValue(WomIntegerType, None))))
     oops match {
       case Success(x) => fail(s"Expected a string to not have a file length but instead got $x")
-      case Failure(e) => e.getMessage should be("The 'size' method expects a 'File' or 'File?' argument but instead got Int?.")
+      case Failure(e) =>
+        e.getMessage should be("The 'size' method expects a 'File' or 'File?' argument but instead got Int?.")
     }
   }
 
@@ -95,7 +123,8 @@ class Draft2SizeFunctionSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
     val readLike = testFunctions(Failure(new Exception("'size' inner exception, expect me to be passed on")))
     val oops = readLike.size(Seq(Success(WomSingleFile("blah"))))
     oops match {
-      case Success(_) => fail(s"The 'size' engine function didn't return the error generated in the inner 'size' method")
+      case Success(_) =>
+        fail(s"The 'size' engine function didn't return the error generated in the inner 'size' method")
       case Failure(e) => e.getMessage should be("'size' inner exception, expect me to be passed on")
     }
   }
@@ -107,7 +136,10 @@ class Draft2SizeFunctionSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 }
 
 object Draft2SizeFunctionSpec {
-  def testFunctions(sizeResult: Try[Long]): WdlStandardLibraryFunctions = WdlStandardLibraryFunctions.fromIoFunctionSet( new EmptyIoFunctionSet {
-    override def size(path: String): Future[Long] = Future.fromTry(sizeResult)
-  }, FileSizeLimitationConfig.default)
+  def testFunctions(sizeResult: Try[Long]): WdlStandardLibraryFunctions = WdlStandardLibraryFunctions.fromIoFunctionSet(
+    new EmptyIoFunctionSet {
+      override def size(path: String): Future[Long] = Future.fromTry(sizeResult)
+    },
+    FileSizeLimitationConfig.default
+  )
 }
diff --git a/wdl/model/draft2/src/test/scala/wdl/expression/FileEvaluatorSpec.scala b/wdl/model/draft2/src/test/scala/wdl/expression/FileEvaluatorSpec.scala
index a36d1112839..4614dfcad6a 100644
--- a/wdl/model/draft2/src/test/scala/wdl/expression/FileEvaluatorSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/expression/FileEvaluatorSpec.scala
@@ -20,39 +20,61 @@ class FileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     ("read_int(stdout() + 3)", Seq.empty[WomSingleFile], WomIntegerType),
     ("""read_int("/etc/" + read_int("somefile") + ".txt"))""", Seq(WomSingleFile("somefile")), WomIntegerType),
     ("""-read_int("/etc/file1")""", Seq(WomSingleFile("/etc/file1")), WomIntegerType),
-    ("""read_int("/etc/file1") + read_string("/bin/file2")""", Seq(WomSingleFile("/etc/file1"), WomSingleFile("/bin/file2")), WomStringType),
-    ("""read_int("/etc/file1") + read_string("/bin/file2") + read_string("/bin/file3") + read_string("/bin/file4") + read_string("/bin/file5")""", Seq(
-      WomSingleFile("/etc/file1"),
-      WomSingleFile("/bin/file2"),
-      WomSingleFile("/bin/file3"),
-      WomSingleFile("/bin/file4"),
-      WomSingleFile("/bin/file5")
-    ), WomStringType),
+    ("""read_int("/etc/file1") + read_string("/bin/file2")""",
+     Seq(WomSingleFile("/etc/file1"), WomSingleFile("/bin/file2")),
+     WomStringType
+    ),
+    ("""read_int("/etc/file1") + read_string("/bin/file2") + read_string("/bin/file3") + read_string("/bin/file4") + read_string("/bin/file5")""",
+     Seq(
+       WomSingleFile("/etc/file1"),
+       WomSingleFile("/bin/file2"),
+       WomSingleFile("/bin/file3"),
+       WomSingleFile("/bin/file4"),
+       WomSingleFile("/bin/file5")
+     ),
+     WomStringType
+    ),
     (""" "foo" + "bar" """, Seq(WomSingleFile("foobar")), WomSingleFileType),
     (""" "foo" + "bar" """, Seq.empty[WomSingleFile], WomStringType),
     (""" ["a", "b", "c"] """,
-      Seq(WomSingleFile("a"), WomSingleFile("b"), WomSingleFile("c")), WomArrayType(WomSingleFileType)),
+     Seq(WomSingleFile("a"), WomSingleFile("b"), WomSingleFile("c")),
+     WomArrayType(WomSingleFileType)
+    ),
     (""" ["a", "b", "c"] """, Seq.empty[WomSingleFile], WomArrayType(WomStringType)),
-    (""" {"a": "1", "b": "2", "c":"3"} """, Seq(
-      WomSingleFile("a"),
-      WomSingleFile("1"),
-      WomSingleFile("b"),
-      WomSingleFile("2"),
-      WomSingleFile("c"),
-      WomSingleFile("3")
-    ), WomMapType(WomSingleFileType, WomSingleFileType)),
-    (""" [read_string("x"), read_string("y")] """, Seq(WomSingleFile("x"), WomSingleFile("y")), WomArrayType(WomStringType)),
+    (""" {"a": "1", "b": "2", "c":"3"} """,
+     Seq(
+       WomSingleFile("a"),
+       WomSingleFile("1"),
+       WomSingleFile("b"),
+       WomSingleFile("2"),
+       WomSingleFile("c"),
+       WomSingleFile("3")
+     ),
+     WomMapType(WomSingleFileType, WomSingleFileType)
+    ),
+    (""" [read_string("x"), read_string("y")] """,
+     Seq(WomSingleFile("x"), WomSingleFile("y")),
+     WomArrayType(WomStringType)
+    ),
     (""" [fileNameAsStringInput, "${fileNameAsStringInput}.bai"] """,
-      Seq(WomSingleFile("sommat.bam"), WomSingleFile("sommat.bam.bai")), WomArrayType(WomSingleFileType)),
+     Seq(WomSingleFile("sommat.bam"), WomSingleFile("sommat.bam.bai")),
+     WomArrayType(WomSingleFileType)
+    ),
     (""" [ fileNameAsStringInput, mapToFileName["Chris"] ] """,
-      Seq(WomSingleFile("sommat.bam"), WomSingleFile("sommatStupid.bam")), WomArrayType(WomSingleFileType)),
+     Seq(WomSingleFile("sommat.bam"), WomSingleFile("sommatStupid.bam")),
+     WomArrayType(WomSingleFileType)
+    ),
     (""" {read_int("a"): read_string("x"), 4: read_string("y")} """,
-      Seq(WomSingleFile("a"), WomSingleFile("x"), WomSingleFile("y")), WomMapType(WomIntegerType, WomStringType)),
+     Seq(WomSingleFile("a"), WomSingleFile("x"), WomSingleFile("y")),
+     WomMapType(WomIntegerType, WomStringType)
+    ),
     (""" glob("out-*.txt") """, Seq(WomGlobFile("out-*.txt")), WomSingleFileType),
     (""" glob("out-*.txt")[0] """, Seq(WomGlobFile("out-*.txt")), WomSingleFileType),
     (""" read_tsv("my_file") """, Seq(WomSingleFile("my_file")), WomSingleFileType),
     (""" if read_int("i.txt") == 10 then "a.txt" else "b.txt" """,
-      Seq(WomSingleFile("a.txt"), WomSingleFile("b.txt"), WomSingleFile("i.txt")), WomSingleFileType),
+     Seq(WomSingleFile("a.txt"), WomSingleFile("b.txt"), WomSingleFile("i.txt")),
+     WomSingleFileType
+    ),
     (""" if "a" == "b" then "a.txt" else "b.txt" """, Seq(WomSingleFile("b.txt")), WomSingleFileType),
     (""" if b then read_string("t") else "nope" """, Seq(WomSingleFile("t")), WomStringType),
     (""" read_string(basename(fileInput, ".txt") + ".bam") """, Seq(WomSingleFile("input.bam")), WomStringType),
@@ -60,7 +82,6 @@ class FileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     (""" round(size("foo.txt")) """, Seq(WomSingleFile("foo.txt")), WomIntegerType),
     (""" size("foo.txt", "GB") """, Seq(WomSingleFile("foo.txt")), WomIntegerType),
     (""" round(size("foo.txt", "GB")) """, Seq(WomSingleFile("foo.txt")), WomIntegerType)
-
   )
 
   val lookupFunction = Map(
@@ -70,9 +91,13 @@ class FileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     "mapToFileName" -> WomMap(Map(WomString("Chris") -> WomString("sommatStupid.bam")))
   )
 
-  forAll (expressions) { (expression, files, anticipatedType) =>
+  forAll(expressions) { (expression, files, anticipatedType) =>
     it should s"evaluate $expression (coerced to: $anticipatedType) => $files" in {
-      WdlExpression.fromString(expression).evaluateFiles(lookupFunction, PureStandardLibraryFunctions, anticipatedType).get.toSet should be(files.toSet)
+      WdlExpression
+        .fromString(expression)
+        .evaluateFiles(lookupFunction, PureStandardLibraryFunctions, anticipatedType)
+        .get
+        .toSet should be(files.toSet)
     }
   }
 }
diff --git a/wdl/model/draft2/src/test/scala/wdl/expression/PureStandardLibraryFunctionsSpec.scala b/wdl/model/draft2/src/test/scala/wdl/expression/PureStandardLibraryFunctionsSpec.scala
index 8d0406aa203..a7208b80341 100644
--- a/wdl/model/draft2/src/test/scala/wdl/expression/PureStandardLibraryFunctionsSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/expression/PureStandardLibraryFunctionsSpec.scala
@@ -14,16 +14,22 @@ class PureStandardLibraryFunctionsSpec extends AnyFlatSpec with CromwellTimeoutS
   behavior of "transpose"
 
   it should "transpose a 2x3 into a 3x2" in {
-    val inArray = WomArray(WomArrayType(WomArrayType(WomIntegerType)), List(
-      WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2), WomInteger(3))),
-      WomArray(WomArrayType(WomIntegerType), List(WomInteger(4), WomInteger(5), WomInteger(6)))
-    ))
-
-    val expectedResult = WomArray(WomArrayType(WomArrayType(WomIntegerType)), List(
-      WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(4))),
-      WomArray(WomArrayType(WomIntegerType), List(WomInteger(2), WomInteger(5))),
-      WomArray(WomArrayType(WomIntegerType), List(WomInteger(3), WomInteger(6)))
-    ))
+    val inArray = WomArray(
+      WomArrayType(WomArrayType(WomIntegerType)),
+      List(
+        WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2), WomInteger(3))),
+        WomArray(WomArrayType(WomIntegerType), List(WomInteger(4), WomInteger(5), WomInteger(6)))
+      )
+    )
+
+    val expectedResult = WomArray(
+      WomArrayType(WomArrayType(WomIntegerType)),
+      List(
+        WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(4))),
+        WomArray(WomArrayType(WomIntegerType), List(WomInteger(2), WomInteger(5))),
+        WomArray(WomArrayType(WomIntegerType), List(WomInteger(3), WomInteger(6)))
+      )
+    )
 
     PureStandardLibraryFunctions.transpose(Seq(Success(inArray))) should be(Success(expectedResult))
   }
@@ -47,9 +53,10 @@ class PureStandardLibraryFunctionsSpec extends AnyFlatSpec with CromwellTimeoutS
     val ar3 = WomArray(WomArrayType(WomIntegerType), List.empty)
     val ar4 = WomArray(WomArrayType(WomIntegerType), List(WomInteger(6)))
     val aar = WomArray(WomArrayType(WomArrayType(WomIntegerType)), List(ar1, ar2, ar3, ar4))
-    val flat_ar = WomArray(WomArrayType(WomIntegerType), List(WomInteger(1), WomInteger(2),
-                                                              WomInteger(3), WomInteger(4),
-                                                              WomInteger(5), WomInteger(6)))
+    val flat_ar =
+      WomArray(WomArrayType(WomIntegerType),
+               List(WomInteger(1), WomInteger(2), WomInteger(3), WomInteger(4), WomInteger(5), WomInteger(6))
+      )
     PureStandardLibraryFunctions.flatten(Seq(Success(aar))) should be(Success(flat_ar))
   }
 
@@ -57,9 +64,10 @@ class PureStandardLibraryFunctionsSpec extends AnyFlatSpec with CromwellTimeoutS
     val sar1 = WomArray(WomArrayType(WomStringType), List(WomString("chatting"), WomString("is")))
     val sar2 = WomArray(WomArrayType(WomStringType), List(WomString("great"), WomString("for"), WomString("you")))
     val saar = WomArray(WomArrayType(WomArrayType(WomStringType)), List(sar1, sar2))
-    val flat_sar = WomArray(WomArrayType(WomStringType), List(WomString("chatting"), WomString("is"),
-                                                              WomString("great"), WomString("for"),
-                                                              WomString("you")))
+    val flat_sar =
+      WomArray(WomArrayType(WomStringType),
+               List(WomString("chatting"), WomString("is"), WomString("great"), WomString("for"), WomString("you"))
+      )
     PureStandardLibraryFunctions.flatten(Seq(Success(saar))) should be(Success(flat_sar))
   }
 
@@ -72,10 +80,8 @@ class PureStandardLibraryFunctionsSpec extends AnyFlatSpec with CromwellTimeoutS
   }
 
   it should "return errors for arguments which are not arrays" in {
-    val nonArrays: List[WomValue] = List(WomInteger(17),
-                                         WomString("banana"),
-                                         WomSingleFile("/tmp/bubbles"))
-    nonArrays.foreach{ elem =>
+    val nonArrays: List[WomValue] = List(WomInteger(17), WomString("banana"), WomSingleFile("/tmp/bubbles"))
+    nonArrays.foreach { elem =>
       PureStandardLibraryFunctions.flatten(Seq(Success(elem))) should be(a[Failure[_]])
     }
   }
@@ -86,16 +92,23 @@ class PureStandardLibraryFunctionsSpec extends AnyFlatSpec with CromwellTimeoutS
 
     val strings = List("foo", "bar", "baz")
     val stringWdlValues = WomArray(WomArrayType(WomStringType), strings map WomString.apply)
-    val stringsExpectation = WomArray(WomArrayType(WomStringType), strings map { f => WomString("-f " + f) } )
-    PureStandardLibraryFunctions.prefix(Seq(Success(WomString("-f ")), Success(stringWdlValues))) should be(Success(stringsExpectation))
+    val stringsExpectation = WomArray(WomArrayType(WomStringType), strings map { f => WomString("-f " + f) })
+    PureStandardLibraryFunctions.prefix(Seq(Success(WomString("-f ")), Success(stringWdlValues))) should be(
+      Success(stringsExpectation)
+    )
 
     val noStringWdlValues = WomArray(WomArrayType(WomStringType), List.empty)
-    PureStandardLibraryFunctions.prefix(Seq(Success(WomString("-f ")), Success(noStringWdlValues))) should be(Success(WomArray(WomArrayType(WomStringType), Seq.empty)))
+    PureStandardLibraryFunctions.prefix(Seq(Success(WomString("-f ")), Success(noStringWdlValues))) should be(
+      Success(WomArray(WomArrayType(WomStringType), Seq.empty))
+    )
 
     val integers = List(1, 2, 3)
-    val integerWdlValues = WomArray(WomArrayType(WomIntegerType), integers map { i => WomInteger.apply(Integer.valueOf(i)) })
-    val integersExpectation = WomArray(WomArrayType(WomStringType), integers map { i => WomString("-f " + i)})
-    PureStandardLibraryFunctions.prefix(Seq(Success(WomString("-f ")), Success(integerWdlValues))) should be(Success(integersExpectation))
+    val integerWdlValues =
+      WomArray(WomArrayType(WomIntegerType), integers map { i => WomInteger.apply(Integer.valueOf(i)) })
+    val integersExpectation = WomArray(WomArrayType(WomStringType), integers map { i => WomString("-f " + i) })
+    PureStandardLibraryFunctions.prefix(Seq(Success(WomString("-f ")), Success(integerWdlValues))) should be(
+      Success(integersExpectation)
+    )
   }
 
   behavior of "basename"
@@ -106,11 +119,15 @@ class PureStandardLibraryFunctionsSpec extends AnyFlatSpec with CromwellTimeoutS
     ("gs://bucket/charlie.bucket", "charlie.bucket", ".wonka", "charlie.bucket")
   ) foreach { case (full, baseWithExtension, suffixToStrip, suffixStripped) =>
     it should s"get the file name for $full" in {
-      PureStandardLibraryFunctions.basename(Seq(Success(WomString(full)))) should be(Success(WomString(baseWithExtension)))
+      PureStandardLibraryFunctions.basename(Seq(Success(WomString(full)))) should be(
+        Success(WomString(baseWithExtension))
+      )
     }
 
     it should s"get the file name for $full and strip the suffix '$suffixToStrip'" in {
-      PureStandardLibraryFunctions.basename(Seq(Success(WomString(full)), Success(WomString(suffixToStrip)))) should be(Success(WomString(suffixStripped)))
+      PureStandardLibraryFunctions.basename(Seq(Success(WomString(full)), Success(WomString(suffixToStrip)))) should be(
+        Success(WomString(suffixStripped))
+      )
     }
   }
 }
diff --git a/wdl/model/draft2/src/test/scala/wdl/expression/TypeEvaluatorSpec.scala b/wdl/model/draft2/src/test/scala/wdl/expression/TypeEvaluatorSpec.scala
index 97912908565..e5f22226fd0 100644
--- a/wdl/model/draft2/src/test/scala/wdl/expression/TypeEvaluatorSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/expression/TypeEvaluatorSpec.scala
@@ -19,20 +19,23 @@ class TypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
 
   def noLookup(String: String): WomType = fail("No identifiers should be looked up in this test")
 
-  def identifierLookup(String: String): WomType = {
+  def identifierLookup(String: String): WomType =
     String match {
       case "cgrep" => WdlCallOutputsObjectType(namespace.workflow.calls.find(_.unqualifiedName == "cgrep").get)
       case "ps" => WdlCallOutputsObjectType(namespace.workflow.calls.find(_.unqualifiedName == "ps").get)
     }
-  }
 
-  def identifierEval(exprStr: String): WomPrimitiveType = expr(exprStr).evaluateType(identifierLookup, new WdlStandardLibraryFunctionsType).asInstanceOf[Try[WomPrimitiveType]].get
-  def identifierEvalError(exprStr: String): Unit = {
-    expr(exprStr).evaluateType(identifierLookup, new WdlStandardLibraryFunctionsType).asInstanceOf[Try[WomPrimitive]] match {
+  def identifierEval(exprStr: String): WomPrimitiveType = expr(exprStr)
+    .evaluateType(identifierLookup, new WdlStandardLibraryFunctionsType)
+    .asInstanceOf[Try[WomPrimitiveType]]
+    .get
+  def identifierEvalError(exprStr: String): Unit =
+    expr(exprStr)
+      .evaluateType(identifierLookup, new WdlStandardLibraryFunctionsType)
+      .asInstanceOf[Try[WomPrimitive]] match {
       case Failure(_) => // Expected
       case Success(badValue) => fail(s"Operation was supposed to fail, instead I got value: $badValue")
     }
-  }
 
   private def operate(lhs: WomType, op: String, rhs: WomType): Try[WomType] = op match {
     case "+" => lhs.add(rhs)
@@ -384,13 +387,13 @@ class TypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     (WomBooleanType, "&&", WomSingleFileType)
   )
 
-  forAll (validOperations) { (lhs, op, rhs, expectedType) =>
+  forAll(validOperations) { (lhs, op, rhs, expectedType) =>
     it should s"validate the output type for the expression: $lhs $op $rhs = $expectedType" in {
       operate(lhs, op, rhs) shouldEqual Success(expectedType)
     }
   }
 
-  forAll (invalidOperations) { (lhs, op, rhs) =>
+  forAll(invalidOperations) { (lhs, op, rhs) =>
     it should s"not allow the expression: $lhs $op $rhs" in {
       operate(lhs, op, rhs) should be(a[Failure[_]])
     }
diff --git a/wdl/model/draft2/src/test/scala/wdl/expression/ValueEvaluatorSpec.scala b/wdl/model/draft2/src/test/scala/wdl/expression/ValueEvaluatorSpec.scala
index 42004e1e8a5..0c5a3c93227 100644
--- a/wdl/model/draft2/src/test/scala/wdl/expression/ValueEvaluatorSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/expression/ValueEvaluatorSpec.scala
@@ -26,11 +26,14 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     case "b" => WomInteger(2)
     case "s" => WomString("s")
     case "array_str" => WomArray(WomArrayType(WomStringType), Seq("foo", "bar", "baz").map(WomString))
-    case "map_str_int" => WomMap(WomMapType(WomStringType, WomIntegerType), Map(
-      WomString("a") -> WomInteger(0),
-      WomString("b") -> WomInteger(1),
-      WomString("c") -> WomInteger(2)
-    ))
+    case "map_str_int" =>
+      WomMap(WomMapType(WomStringType, WomIntegerType),
+             Map(
+               WomString("a") -> WomInteger(0),
+               WomString("b") -> WomInteger(1),
+               WomString("c") -> WomInteger(2)
+             )
+      )
     case "o" => WomObject(Map("key1" -> WomString("value1"), "key2" -> WomInteger(9)))
     case "myPair" => WomPair(WomInteger(3), WomString("hello"))
     case "etc_f" => WomSingleFile("/etc")
@@ -38,14 +41,14 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     case "etc_s" => WomString("/etc")
     case "sudoers_f" => WomSingleFile("/sudoers")
     case "sudoers_s" => WomString("/sudoers")
-    case "f" => WomFloat(0.5F)
+    case "f" => WomFloat(0.5f)
     case "t" => WomBoolean(true)
     case "someIntAsString" => WomOptionalValue(WomString("1"))
     case "someFloatAsString" => WomOptionalValue(WomString("0.5"))
     case "someStr" => WomOptionalValue(WomString("someStr"))
     case "someInt" => WomOptionalValue(WomInteger(1))
     case "someBoolean" => WomOptionalValue(WomBoolean(false))
-    case "someFloat" => WomOptionalValue(WomFloat(0.5F))
+    case "someFloat" => WomOptionalValue(WomFloat(0.5f))
     case "someFile" => WomOptionalValue(WomSingleFile("file"))
     case "noneStr" => WomOptionalValue.none(WomStringType)
     case "noneInt" => WomOptionalValue.none(WomIntegerType)
@@ -54,7 +57,6 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     case "noneFile" => WomOptionalValue.none(WomSingleFileType)
   }
 
-
   def identifierTypeLookup(name: String): WomType = identifierLookup(name).womType
 
   class TestValueFunctions extends WdlStandardLibraryFunctions {
@@ -62,7 +64,9 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
 
     override def readFile(path: String, sizeLimit: Int): String = throw new UnsupportedOperationException()
 
-    override def writeFile(path: String, content: String): Try[WomSingleFile] = Failure(new UnsupportedOperationException())
+    override def writeFile(path: String, content: String): Try[WomSingleFile] = Failure(
+      new UnsupportedOperationException()
+    )
 
     override def stdout(params: Seq[Try[WomValue]]): Try[WomSingleFile] = Failure(new UnsupportedOperationException())
 
@@ -70,9 +74,13 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
 
     override def read_json(params: Seq[Try[WomValue]]): Try[WomValue] = Failure(new UnsupportedOperationException())
 
-    override def write_tsv(params: Seq[Try[WomValue]]): Try[WomSingleFile] = Failure(new UnsupportedOperationException())
+    override def write_tsv(params: Seq[Try[WomValue]]): Try[WomSingleFile] = Failure(
+      new UnsupportedOperationException()
+    )
 
-    override def write_json(params: Seq[Try[WomValue]]): Try[WomSingleFile] = Failure(new UnsupportedOperationException())
+    override def write_json(params: Seq[Try[WomValue]]): Try[WomSingleFile] = Failure(
+      new UnsupportedOperationException()
+    )
 
     override def size(params: Seq[Try[WomValue]]): Try[WomFloat] = Failure(new UnsupportedOperationException())
 
@@ -101,23 +109,23 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
 
   def constEval(exprStr: String): WomValue = expr(exprStr).evaluate(noLookup, new TestValueFunctions()).get
 
-  def constEvalType(exprStr: String): WomType = expr(exprStr).evaluateType(identifierTypeLookup, new TestTypeFunctions).get
+  def constEvalType(exprStr: String): WomType =
+    expr(exprStr).evaluateType(identifierTypeLookup, new TestTypeFunctions).get
 
-  def constEvalError(exprStr: String): Throwable = {
+  def constEvalError(exprStr: String): Throwable =
     expr(exprStr).evaluate(noLookup, new TestValueFunctions()).asInstanceOf[Try[WomPrimitive]] match {
       case Failure(ex) => ex
       case Success(v) => fail(s"Operation was supposed to fail, instead I got value: $v")
     }
-  }
 
-  def identifierEval(exprStr: String): WomPrimitive = expr(exprStr).evaluate(identifierLookup, new TestValueFunctions()).asInstanceOf[Try[WomPrimitive]].get
+  def identifierEval(exprStr: String): WomPrimitive =
+    expr(exprStr).evaluate(identifierLookup, new TestValueFunctions()).asInstanceOf[Try[WomPrimitive]].get
 
-  def identifierEvalError(exprStr: String): Unit = {
+  def identifierEvalError(exprStr: String): Unit =
     expr(exprStr).evaluate(identifierLookup, new TestValueFunctions()).asInstanceOf[Try[WomPrimitive]] match {
       case Failure(_) => // Expected
       case Success(v) => fail(s"Operation was supposed to fail, instead I got value: $v")
     }
-  }
 
   val constantExpressions = Table(
     ("expression", "value"),
@@ -227,128 +235,137 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     ("(1)", WomInteger(1)),
 
     // Array in pair:
-    ("(\"hello\", [ 1, 2, 3 ])", WomPair(WomString("hello"), WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(1), WomInteger(2), WomInteger(3))))),
+    ("(\"hello\", [ 1, 2, 3 ])",
+     WomPair(WomString("hello"),
+             WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(1), WomInteger(2), WomInteger(3)))
+     )
+    ),
 
     // Map to pairs:
     ("""{
-    | 1: (1, 2),
-    | 2: (2, 3)
-    |}
-    """.stripMargin, WomMap(WomMapType(WomIntegerType, WomPairType(WomIntegerType, WomIntegerType)), Map(
-      WomInteger(1) -> WomPair(WomInteger(1), WomInteger(2)),
-      WomInteger(2) -> WomPair(WomInteger(2), WomInteger(3))
-    )))
+       | 1: (1, 2),
+       | 2: (2, 3)
+       |}
+    """.stripMargin,
+     WomMap(
+       WomMapType(WomIntegerType, WomPairType(WomIntegerType, WomIntegerType)),
+       Map(
+         WomInteger(1) -> WomPair(WomInteger(1), WomInteger(2)),
+         WomInteger(2) -> WomPair(WomInteger(2), WomInteger(3))
+       )
+     )
+    )
   )
 
   val badExpressions = Table(
-    ("expression"),
+    "expression",
 
     // Integers
-    ("1+true"),
-    ("1-true"),
-    (""" 1-"s"  """),
-    ("1*true"),
-    (""" 1*"s"  """),
-    ("1 / 0"),
-    ("1 / 0.0"),
-    ("25/0.0"),
-    ("1/true"),
-    (""" 1/"s"  """),
-    ("1%false"),
-    (""" 1%"s"  """),
-    ("1%0"),
-    (" 24 == false "),
-    (""" 1 == "s"  """),
-    (" 24 != false "),
-    (""" 1 != "s"  """),
-    (" 24 < false "),
-    (""" 1 < "s"  """),
-    (" 24 <= false "),
-    (""" 1 <= "s"  """),
-    ("4 > false"),
-    (""" 1 > "s"  """),
-    ("4 >= false"),
-    (""" 1 >= "s"  """),
+    "1+true",
+    "1-true",
+    """ 1-"s"  """,
+    "1*true",
+    """ 1*"s"  """,
+    "1 / 0",
+    "1 / 0.0",
+    "25/0.0",
+    "1/true",
+    """ 1/"s"  """,
+    "1%false",
+    """ 1%"s"  """,
+    "1%0",
+    " 24 == false ",
+    """ 1 == "s"  """,
+    " 24 != false ",
+    """ 1 != "s"  """,
+    " 24 < false ",
+    """ 1 < "s"  """,
+    " 24 <= false ",
+    """ 1 <= "s"  """,
+    "4 > false",
+    """ 1 > "s"  """,
+    "4 >= false",
+    """ 1 >= "s"  """,
 
     // Floats
-    ("1.0+true"),
-    ("1.0-true"),
-    (""" 1.0-"s"  """),
-    ("1.0*true"),
-    (""" 1.0*"s"  """),
-    ("1.0/true"),
-    ("1.0/0.0"),
-    ("1.0/0"),
-    (""" 1.0/"s"  """),
-    ("10.0 % 0"),
-    ("10.0 % 0.0"),
-    ("1.0%false"),
-    (""" 1.0%"s"  """),
-    ("24.0 == false "),
-    (""" 1.0 == "s"  """),
-    ("24.0 != false "),
-    (""" 1.0 != "s"  """),
-    ("24.0 < false "),
-    (""" 1.0 < "s"  """),
-    ("24.0 <= false "),
-    (""" 1.0 <= "s"  """),
-    ("4.0 > false"),
-    (""" 1.0 > "s"  """),
-    ("4.0 >= false"),
-    (""" 1.0 >= "s"  """),
+    "1.0+true",
+    "1.0-true",
+    """ 1.0-"s"  """,
+    "1.0*true",
+    """ 1.0*"s"  """,
+    "1.0/true",
+    "1.0/0.0",
+    "1.0/0",
+    """ 1.0/"s"  """,
+    "10.0 % 0",
+    "10.0 % 0.0",
+    "1.0%false",
+    """ 1.0%"s"  """,
+    "24.0 == false ",
+    """ 1.0 == "s"  """,
+    "24.0 != false ",
+    """ 1.0 != "s"  """,
+    "24.0 < false ",
+    """ 1.0 < "s"  """,
+    "24.0 <= false ",
+    """ 1.0 <= "s"  """,
+    "4.0 > false",
+    """ 1.0 > "s"  """,
+    "4.0 >= false",
+    """ 1.0 >= "s"  """,
 
     // Booleans
-    (""" true + "String" """),
-    ("true+2"),
-    ("true+2.3"),
-    ("false+true"),
-    ("false-5"),
-    ("false-6.6"),
-    ("true-true"),
-    (""" true-"s"  """),
-    ("false * 7"),
-    ("false * 7.2"),
-    ("false*true"),
-    (""" false*"s"  """),
-    ("false / 4"),
-    ("false/2.0"),
-    ("false/true"),
-    (""" true/"s"  """),
-    ("true % 3"),
-    ("true % 3.5"),
-    ("false%false"),
-    (""" true % "s"  """),
-    ("true == 24 "),
-    ("true == 24.0 "),
-    ("""true == "s"  """),
-    ("true != 0 "),
-    ("true != 0.0 "),
-    ("""true != "s"  """),
-    ("true < 3"),
-    ("true < 3.0"),
-    ("true < 5.0"),
-    ("""true < "s"  """),
-    ("true <= 4"),
-    ("true <= 3.0"),
-    ("""true <= "s"  """),
-    ("true > 3"),
-    ("true > 3.0"),
-    ("true >= 4"),
-    ("true >= 4.0"),
-    ("""true >= "s"  """),
-    ("false || 4"),
-    ("false || 4.0"),
-    ("""false || "s"  """),
-    ("true && 4"),
-    ("true && 4.0"),
-    ("""true && "s"  """),
+    """ true + "String" """,
+    "true+2",
+    "true+2.3",
+    "false+true",
+    "false-5",
+    "false-6.6",
+    "true-true",
+    """ true-"s"  """,
+    "false * 7",
+    "false * 7.2",
+    "false*true",
+    """ false*"s"  """,
+    "false / 4",
+    "false/2.0",
+    "false/true",
+    """ true/"s"  """,
+    "true % 3",
+    "true % 3.5",
+    "false%false",
+    """ true % "s"  """,
+    "true == 24 ",
+    "true == 24.0 ",
+    """true == "s"  """,
+    "true != 0 ",
+    "true != 0.0 ",
+    """true != "s"  """,
+    "true < 3",
+    "true < 3.0",
+    "true < 5.0",
+    """true < "s"  """,
+    "true <= 4",
+    "true <= 3.0",
+    """true <= "s"  """,
+    "true > 3",
+    "true > 3.0",
+    "true >= 4",
+    "true >= 4.0",
+    """true >= "s"  """,
+    "false || 4",
+    "false || 4.0",
+    """false || "s"  """,
+    "true && 4",
+    "true && 4.0",
+    """true && "s"  """,
 
     // Strings
-    (""" "hello" + true """),
-    (""" "hello" == true """),
-    (""" "hello" != true """),
-    (""" "hello" < true """),
-    (""" "hello" > true """)
+    """ "hello" + true """,
+    """ "hello" == true """,
+    """ "hello" != true """,
+    """ "hello" < true """,
+    """ "hello" > true """
   )
 
   val identifierLookupExpressions = Table(
@@ -413,7 +430,6 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     ("s == someStr", WomBoolean(false)),
     ("s < someStr", WomBoolean(true)),
     ("s > someStr", WomBoolean(false)),
-
     ("someStr + s", WomString("someStrs")),
     ("someInt + s", WomString("1s")),
     ("someFloat + s", WomString("0.5s")),
@@ -430,7 +446,6 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     ("a == someInt", WomBoolean(true)),
     ("a > someInt", WomBoolean(false)),
     ("a < someInt", WomBoolean(false)),
-
     ("someIntAsString + a", WomString("11")),
     ("someInt + a", WomInteger(2)),
     ("someInt * a", WomInteger(1)),
@@ -438,7 +453,6 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     ("someInt == a", WomBoolean(true)),
     ("someInt > a", WomBoolean(false)),
     ("someInt < a", WomBoolean(false)),
-
     ("-someInt", WomInteger(-1)),
     ("+someInt", WomInteger(1)),
 
@@ -450,7 +464,6 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     ("f == someFloat", WomBoolean(true)),
     ("f > someFloat", WomBoolean(false)),
     ("f < someFloat", WomBoolean(false)),
-
     ("someFloatAsString + f", WomString("0.50.5")),
     ("someFloat + f", WomFloat(1)),
     ("someFloat * f", WomFloat(0.25)),
@@ -458,7 +471,6 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     ("someFloat == f", WomBoolean(true)),
     ("someFloat > f", WomBoolean(false)),
     ("someFloat < f", WomBoolean(false)),
-
     ("-someFloat", WomFloat(-0.5)),
     ("+someFloat", WomFloat(0.5)),
 
@@ -468,64 +480,61 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     ("t < someBoolean", WomBoolean(false)),
     ("t && someBoolean", WomBoolean(false)),
     ("t || someBoolean", WomBoolean(true)),
-
     ("someBoolean == t", WomBoolean(false)),
     ("someBoolean > t", WomBoolean(false)),
     ("someBoolean < t", WomBoolean(true)),
     ("someBoolean && t", WomBoolean(false)),
     ("someBoolean || t", WomBoolean(true)),
-
     ("!someBoolean", WomBoolean(true)),
 
     // File
     ("etc_f + someStr", WomSingleFile("/etcsomeStr")),
     ("etc_f == someStr", WomBoolean(false)),
     ("etc_f == someFile", WomBoolean(false)),
-
     ("someFile == etc_f", WomBoolean(false))
   )
 
   val badIdentifierExpressions = Table(
-    ("expression"),
-    ("etc_f + 1"),
-    ("etc_f == 1"),
-    ("0.key3"),
-    ("array_str[3]"),
-    ("""map_str_int["d"]""")
+    "expression",
+    "etc_f + 1",
+    "etc_f == 1",
+    "0.key3",
+    "array_str[3]",
+    """map_str_int["d"]"""
   )
 
-  forAll (constantExpressions) { (expression, value) =>
+  forAll(constantExpressions) { (expression, value) =>
     it should s"evaluate $expression into ${value.valueString} (${value.womType.stableName})" in {
       constEval(expression) shouldEqual value
     }
   }
 
-  forAll (constantExpressions) { (expression, value) =>
+  forAll(constantExpressions) { (expression, value) =>
     it should s"evaluate $expression into type ${value.womType.stableName}" in {
       constEvalType(expression) shouldEqual value.womType
     }
   }
 
-  forAll (identifierLookupExpressions) { (expression, value) =>
+  forAll(identifierLookupExpressions) { (expression, value) =>
     it should s"evaluate $expression into ${value.valueString} (${value.womType.stableName})" in {
       identifierEval(expression) shouldEqual value
     }
   }
 
-  forAll (identifierLookupExpressions) { (expression, value) =>
+  forAll(identifierLookupExpressions) { (expression, value) =>
     it should s"evaluate $expression into type ${value.womType.stableName}" in {
       // need to skip the object expressions because we don't know the types of sub-objects
       if (!expression.startsWith("o.key")) constEvalType(expression) shouldEqual value.womType
     }
   }
 
-  forAll (badExpressions) { (expression) =>
+  forAll(badExpressions) { expression =>
     it should s"error when evaluating: $expression" in {
       constEvalError(expression)
     }
   }
 
-  forAll (badIdentifierExpressions) { (expression) =>
+  forAll(badIdentifierExpressions) { expression =>
     it should s"error when evaluating: $expression" in {
       identifierEvalError(expression)
     }
@@ -534,7 +543,9 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   "A string with special characters in it" should "convert to escape sequences when converted to WDL" in {
     WomString("a\nb").toWomString shouldEqual "\"a\\nb\""
     WomString("a\nb\t").toWomString shouldEqual "\"a\\nb\\t\""
-    WomString("be \u266f or be \u266e, just don't be \u266d").toWomString shouldEqual "\"be \\u266F or be \\u266E, just don't be \\u266D\""
+    WomString(
+      "be \u266f or be \u266e, just don't be \u266d"
+    ).toWomString shouldEqual "\"be \\u266F or be \\u266E, just don't be \\u266D\""
   }
 
   "Optional values" should "fail to perform addition with the + operator if the argument is None" in {
@@ -552,15 +563,21 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   "Ternary if blocks" should "fail to evaluate if the condition is not a boolean" in {
-    constEvalError(""" if 5 + 6 then 6 + 7 else 14 * 15 """).getMessage should be("'if' expression must be given a boolean argument but got: 11")
+    constEvalError(""" if 5 + 6 then 6 + 7 else 14 * 15 """).getMessage should be(
+      "'if' expression must be given a boolean argument but got: 11"
+    )
   }
 
   "Ternary if blocks" should "fail to evaluate if the chosen LHS expression fails to evaluate" in {
-    constEvalError(""" if (5 == 4 + 1) then fail() else 13 """).getClass.getSimpleName should be("NoSuchMethodException")
+    constEvalError(""" if (5 == 4 + 1) then fail() else 13 """).getClass.getSimpleName should be(
+      "NoSuchMethodException"
+    )
   }
 
   "Ternary if blocks" should "fail to evaluate if the chosen RHS expression fails to evaluate" in {
-    constEvalError(""" if (5 == 6 + 1) then 13 else fail() """).getClass.getSimpleName should be("NoSuchMethodException")
+    constEvalError(""" if (5 == 6 + 1) then 13 else fail() """).getClass.getSimpleName should be(
+      "NoSuchMethodException"
+    )
   }
 
   "WdlMaps" should "be coerced to their lowest common WomType" in {
@@ -583,10 +600,13 @@ class ValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     )
     val exp = model.WdlExpression.fromString(str)
 
-    val expectedMap: WomMap = WomMap(WomMapType(WomStringType, WomOptionalType(WomStringType)), Map (
-      WomString("i") -> WomOptionalValue(WomStringType, Some(WomString("1"))),
-      WomString("s") -> WomOptionalValue(WomStringType, Some(WomString("two")))
-    ))
+    val expectedMap: WomMap = WomMap(
+      WomMapType(WomStringType, WomOptionalType(WomStringType)),
+      Map(
+        WomString("i") -> WomOptionalValue(WomStringType, Some(WomString("1"))),
+        WomString("s") -> WomOptionalValue(WomStringType, Some(WomString("two")))
+      )
+    )
 
     val evaluated = exp.evaluate(lookup, NoFunctions)
 
diff --git a/wdl/model/draft2/src/test/scala/wdl/expression/WdlStandardLibraryFunctionsSpec.scala b/wdl/model/draft2/src/test/scala/wdl/expression/WdlStandardLibraryFunctionsSpec.scala
index c314a8ad80b..47d6cdfba5f 100644
--- a/wdl/model/draft2/src/test/scala/wdl/expression/WdlStandardLibraryFunctionsSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/expression/WdlStandardLibraryFunctionsSpec.scala
@@ -11,7 +11,6 @@ import wom.values._
 
 import scala.util.{Success, Try}
 
-
 class WdlStandardLibraryFunctionsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   import TableDrivenPropertyChecks._
@@ -26,7 +25,6 @@ class WdlStandardLibraryFunctionsSpec extends AnyFlatSpec with CromwellTimeoutSp
   )
 
   selectionTable foreach { case (input, select_first_ifAppropriate, select_all) =>
-
     val functionInput = Seq(Success(mkWdlArray(input)))
     if (select_first_ifAppropriate.isDefined) {
       val select_first = select_first_ifAppropriate.get
diff --git a/wdl/model/draft2/src/test/scala/wdl/types/WdlArrayTypeSpec.scala b/wdl/model/draft2/src/test/scala/wdl/types/WdlArrayTypeSpec.scala
index 4d3dd0469a4..0de95db815b 100644
--- a/wdl/model/draft2/src/test/scala/wdl/types/WdlArrayTypeSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/types/WdlArrayTypeSpec.scala
@@ -8,7 +8,7 @@ import wdl.draft2.parser.WdlParser.SyntaxError
 import wom.types.{WomArrayType, WomIntegerType}
 import wom.values.{WomArray, WomInteger}
 
-class WdlArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers  {
+class WdlArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   val intArray = WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(1), WomInteger(2), WomInteger(3)))
 
   it should "convert WDL source code to WdlArray" in {
diff --git a/wdl/model/draft2/src/test/scala/wdl/types/WdlMapTypeSpec.scala b/wdl/model/draft2/src/test/scala/wdl/types/WdlMapTypeSpec.scala
index 8af3f0409bd..a05facb6da6 100644
--- a/wdl/model/draft2/src/test/scala/wdl/types/WdlMapTypeSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/types/WdlMapTypeSpec.scala
@@ -1,6 +1,5 @@
 package wdl.types
 
-
 import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
@@ -9,15 +8,19 @@ import wdl.draft2.parser.WdlParser.SyntaxError
 import wom.types.{WomIntegerType, WomMapType, WomStringType}
 import wom.values.{WomInteger, WomMap, WomString}
 
-class WdlMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers  {
-  val stringIntMap = WomMap(WomMapType(WomStringType, WomIntegerType), Map(
-    WomString("a") -> WomInteger(1),
-    WomString("b") -> WomInteger(2),
-    WomString("c") -> WomInteger(3)
-  ))
-  
+class WdlMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+  val stringIntMap = WomMap(WomMapType(WomStringType, WomIntegerType),
+                            Map(
+                              WomString("a") -> WomInteger(1),
+                              WomString("b") -> WomInteger(2),
+                              WomString("c") -> WomInteger(3)
+                            )
+  )
+
   it should "convert WDL source code to WdlMap" in {
-    WomMapType(WomStringType, WomIntegerType).fromWorkflowSource("{\"a\": 1, \"b\": 2, \"c\": 3}") shouldEqual stringIntMap
+    WomMapType(WomStringType, WomIntegerType).fromWorkflowSource(
+      "{\"a\": 1, \"b\": 2, \"c\": 3}"
+    ) shouldEqual stringIntMap
   }
   it should "NOT successfully convert WDL source code to WdlMap if passed a bogus AST" in {
     try {
@@ -52,4 +55,3 @@ class WdlMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     }
   }
 }
-
diff --git a/wdl/model/draft2/src/test/scala/wdl/types/WdlObjectTypeSpec.scala b/wdl/model/draft2/src/test/scala/wdl/types/WdlObjectTypeSpec.scala
index 4b86b5b5f7c..1292d359223 100644
--- a/wdl/model/draft2/src/test/scala/wdl/types/WdlObjectTypeSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/types/WdlObjectTypeSpec.scala
@@ -9,22 +9,25 @@ import wom.types.{WomMapType, WomObjectType, WomStringType}
 import wom.values.{WomMap, WomObject, WomString}
 
 class WdlObjectTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  val abcObject = WomObject(Map(
-    "a" -> WomString("one"),
-    "b" -> WomString("two"),
-    "c" -> WomString("three")
-  ))
+  val abcObject = WomObject(
+    Map(
+      "a" -> WomString("one"),
+      "b" -> WomString("two"),
+      "c" -> WomString("three")
+    )
+  )
 
-  val coerceableMap = WomMap(WomMapType(WomStringType, WomStringType), Map(
-    WomString("a") -> WomString("one"),
-    WomString("b") -> WomString("two"),
-    WomString("c") -> WomString("three"))
+  val coerceableMap = WomMap(
+    WomMapType(WomStringType, WomStringType),
+    Map(WomString("a") -> WomString("one"), WomString("b") -> WomString("two"), WomString("c") -> WomString("three"))
   )
 
-  val nonCoerceableMap = WomMap(WomMapType(WomStringType, WomObjectType), Map(
-    WomString("a") -> WomObject(Map.empty),
-    WomString("b") -> WomObject(Map.empty),
-    WomString("c") -> WomObject(Map.empty))
+  val nonCoerceableMap = WomMap(
+    WomMapType(WomStringType, WomObjectType),
+    Map(WomString("a") -> WomObject(Map.empty),
+        WomString("b") -> WomObject(Map.empty),
+        WomString("c") -> WomObject(Map.empty)
+    )
   )
 
   it should "convert WDL source code to WdlMap" in {
diff --git a/wdl/model/draft2/src/test/scala/wdl/types/WdlPairTypeSpec.scala b/wdl/model/draft2/src/test/scala/wdl/types/WdlPairTypeSpec.scala
index 0ea14e14819..49e2208455d 100644
--- a/wdl/model/draft2/src/test/scala/wdl/types/WdlPairTypeSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/types/WdlPairTypeSpec.scala
@@ -17,26 +17,35 @@ class WdlPairTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
   val simplePair = WomPair(WomString("a"), WomInteger(1))
 
-  val stringIntMap = WomMap(WomMapType(WomStringType, WomIntegerType), Map(
-    WomString("a") -> WomInteger(1),
-    WomString("b") -> WomInteger(2),
-    WomString("c") -> WomInteger(3)
-  ))
-
-  val arrayOfPairs = WomArray(WomArrayType(WomPairType(WomStringType, WomIntegerType)), Seq(
-    WomPair(WomString("a"),WomInteger(1)),
-    WomPair(WomString("b"),WomInteger(2)),
-    WomPair(WomString("c"),WomInteger(3))
-  ))
-
-  val arrayOfPairsOfArrays = WomArray(WomArrayType(WomPairType(WomArrayType(WomStringType), WomArrayType(WomIntegerType))),
+  val stringIntMap = WomMap(WomMapType(WomStringType, WomIntegerType),
+                            Map(
+                              WomString("a") -> WomInteger(1),
+                              WomString("b") -> WomInteger(2),
+                              WomString("c") -> WomInteger(3)
+                            )
+  )
+
+  val arrayOfPairs = WomArray(
+    WomArrayType(WomPairType(WomStringType, WomIntegerType)),
+    Seq(
+      WomPair(WomString("a"), WomInteger(1)),
+      WomPair(WomString("b"), WomInteger(2)),
+      WomPair(WomString("c"), WomInteger(3))
+    )
+  )
+
+  val arrayOfPairsOfArrays = WomArray(
+    WomArrayType(WomPairType(WomArrayType(WomStringType), WomArrayType(WomIntegerType))),
     Seq(
-    WomPair(WomArray(WomArrayType(WomStringType), Seq(WomString("a"), WomString("b"))),
-      WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(1), WomInteger(11)))),
-    WomPair(WomArray(WomArrayType(WomStringType), Seq(WomString("c"), WomString("d"))),
-      WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(2), WomInteger(21)))),
-    WomPair(WomArray(WomArrayType(WomStringType), Seq(WomString("e"), WomString("f"))),
-      WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(3), WomInteger(31))))
+      WomPair(WomArray(WomArrayType(WomStringType), Seq(WomString("a"), WomString("b"))),
+              WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(1), WomInteger(11)))
+      ),
+      WomPair(WomArray(WomArrayType(WomStringType), Seq(WomString("c"), WomString("d"))),
+              WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(2), WomInteger(21)))
+      ),
+      WomPair(WomArray(WomArrayType(WomStringType), Seq(WomString("e"), WomString("f"))),
+              WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(3), WomInteger(31)))
+      )
     )
   )
 
@@ -47,31 +56,41 @@ class WdlPairTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
       WomPairType(WomStringType, WomStringType),
       Some(WomPair(WomString("1"), WomString("2")))
     ),
-
     (
-      WomPair(WomMap(WomMapType(WomIntegerType, WomStringType), Map(
-      WomInteger(1) -> WomString("100"),
-      WomInteger(2) -> WomString("200")
-      )), WomString("300")),
+      WomPair(WomMap(WomMapType(WomIntegerType, WomStringType),
+                     Map(
+                       WomInteger(1) -> WomString("100"),
+                       WomInteger(2) -> WomString("200")
+                     )
+              ),
+              WomString("300")
+      ),
       WomPairType(WomMapType(WomStringType, WomIntegerType), WomIntegerType),
-      Some(WomPair(WomMap(WomMapType(WomStringType, WomIntegerType), Map(
-        WomString("1") -> WomInteger(100),
-        WomString("2") -> WomInteger(200)
-      )), WomInteger(300)))
+      Some(
+        WomPair(WomMap(WomMapType(WomStringType, WomIntegerType),
+                       Map(
+                         WomString("1") -> WomInteger(100),
+                         WomString("2") -> WomInteger(200)
+                       )
+                ),
+                WomInteger(300)
+        )
+      )
     ),
-
-    (
-      WomPair(WomMap(WomMapType(WomIntegerType, WomStringType), Map(
-        WomInteger(1) -> WomString("100"),
-        WomInteger(2) -> WomString("200")
-      )), WomString("300")),
-      WomPairType(WomArrayType(WomStringType), WomStringType),
-      None)
-
+    (WomPair(WomMap(WomMapType(WomIntegerType, WomStringType),
+                    Map(
+                      WomInteger(1) -> WomString("100"),
+                      WomInteger(2) -> WomString("200")
+                    )
+             ),
+             WomString("300")
+     ),
+     WomPairType(WomArrayType(WomStringType), WomStringType),
+     None
+    )
   )
 
   coerceables foreach { case (fromValue, toType, coercedValue) =>
-
     val notString = coercedValue map { _ => "" } getOrElse "not "
     val coercionDefined = coercedValue.isDefined
 
@@ -85,7 +104,8 @@ class WdlPairTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
         case (Success(actualValue), Some(expectedValue)) => actualValue should be(expectedValue)
         case (Success(actualValue), None) => fail(s"Coercion should have failed but instead got $actualValue")
         case (Failure(_), None) => // Correctly failed to coerce
-        case (Failure(t), Some(expectedValue)) => fail(s"Expected coercion to produce $expectedValue but instead got exception $t")
+        case (Failure(t), Some(expectedValue)) =>
+          fail(s"Expected coercion to produce $expectedValue but instead got exception $t")
       }
     }
   }
@@ -153,7 +173,8 @@ class WdlPairTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
         |]
       """.stripMargin.parseJson
 
-    WomArrayType(WomPairType(WomArrayType(WomStringType), WomArrayType(WomIntegerType))).coerceRawValue(complexJsArray) match {
+    WomArrayType(WomPairType(WomArrayType(WomStringType), WomArrayType(WomIntegerType)))
+      .coerceRawValue(complexJsArray) match {
       case Success(array) => array shouldEqual arrayOfPairsOfArrays
       case Failure(f) => fail(s"exception while coercing JsObject to WdlPair: $f")
     }
@@ -196,7 +217,9 @@ class WdlPairTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     val results = WomPairType(WomStringType, WomIntegerType).coerceRawValue(invalidPair)
     results match {
       case Failure(ex) =>
-        ex.getMessage should (startWith("Failed to coerce") and endWith("requires for Right/Left value(s) to be defined.)"))
+        ex.getMessage should (startWith("Failed to coerce") and endWith(
+          "requires for Right/Left value(s) to be defined.)"
+        ))
       case Success(_) => fail("Unexpected successful coercion to WdlPair")
     }
   }
diff --git a/wdl/model/draft2/src/test/scala/wdl/types/WomArrayTypeSpec.scala b/wdl/model/draft2/src/test/scala/wdl/types/WomArrayTypeSpec.scala
index 41c54345b7f..69f58ef6407 100644
--- a/wdl/model/draft2/src/test/scala/wdl/types/WomArrayTypeSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/types/WomArrayTypeSpec.scala
@@ -10,22 +10,28 @@ import wom.values.{WomArray, WomValue}
 
 import scala.util.{Failure, Success}
 
-
-class WomArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers  {
+class WomArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "WomArrayType"
 
-  List(WomStringType, WomArrayType(WomIntegerType), WomPairType(WomIntegerType, WomPairType(WomIntegerType, WomIntegerType)), WomOptionalType(WomStringType)) foreach { desiredMemberType =>
+  List(WomStringType,
+       WomArrayType(WomIntegerType),
+       WomPairType(WomIntegerType, WomPairType(WomIntegerType, WomIntegerType)),
+       WomOptionalType(WomStringType)
+  ) foreach { desiredMemberType =>
     it should s"be able to construct an empty Array[${desiredMemberType.stableName}] value" in {
 
       val desiredArrayType = WomArrayType(desiredMemberType)
       WdlExpression.fromString("[]").evaluate(noLookup, NoFunctions) match {
-        case Success(emptyArray @ WomArray(actualArrayType @ WomMaybeEmptyArrayType(actualMemberType), actualArrayValue)) =>
+        case Success(
+              emptyArray @ WomArray(actualArrayType @ WomMaybeEmptyArrayType(actualMemberType), actualArrayValue)
+            ) =>
           actualMemberType should be(WomNothingType)
           actualArrayValue should be(Seq.empty)
           desiredArrayType.isCoerceableFrom(actualArrayType) should be(true)
           desiredArrayType.coerceRawValue(emptyArray) should be(Success(WomArray(desiredArrayType, Seq.empty)))
-        case Success(WomArray(WomNonEmptyArrayType(_), _)) => fail("Empty arrays should not be created with an Array[_]+ type")
+        case Success(WomArray(WomNonEmptyArrayType(_), _)) =>
+          fail("Empty arrays should not be created with an Array[_]+ type")
         case Success(other) => fail(s"Array literal somehow got evaluated as a ${other.womType} type?!?")
         case Failure(f) => fail("Unable to create an empty array.", f)
       }
@@ -44,16 +50,24 @@ class WomArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
 
   val nonEmptyLiteral = "[1, 2, 3]"
 
-  List(WomNonEmptyArrayType(WomIntegerType), WomOptionalType(WomNonEmptyArrayType(WomIntegerType))) foreach { targetType =>
-    it should s"be able to coerce an array literal into ${targetType.stableName}" in {
+  List(WomNonEmptyArrayType(WomIntegerType), WomOptionalType(WomNonEmptyArrayType(WomIntegerType))) foreach {
+    targetType =>
+      it should s"be able to coerce an array literal into ${targetType.stableName}" in {
 
-      val evaluatedLiteral: WomValue = WdlExpression.fromString(nonEmptyLiteral).evaluate(noLookup, NoFunctions).getOrElse(fail(s"Unable to evaluate non-empty literal $nonEmptyLiteral"))
+        val evaluatedLiteral: WomValue = WdlExpression
+          .fromString(nonEmptyLiteral)
+          .evaluate(noLookup, NoFunctions)
+          .getOrElse(fail(s"Unable to evaluate non-empty literal $nonEmptyLiteral"))
 
-      targetType.coerceRawValue(evaluatedLiteral) match {
-        case Success(womValue) => womValue.womType should be(targetType)
-        case Failure(e) => fail(s"Unable to coerce $evaluatedLiteral (${evaluatedLiteral.womType.stableName}) into ${targetType.stableName}", e)
+        targetType.coerceRawValue(evaluatedLiteral) match {
+          case Success(womValue) => womValue.womType should be(targetType)
+          case Failure(e) =>
+            fail(
+              s"Unable to coerce $evaluatedLiteral (${evaluatedLiteral.womType.stableName}) into ${targetType.stableName}",
+              e
+            )
+        }
       }
-    }
   }
 
   def noLookup(String: String): WomValue = fail("No identifiers should be looked up in this test")
diff --git a/wdl/model/draft2/src/test/scala/wdl/util/StringUtilSpec.scala b/wdl/model/draft2/src/test/scala/wdl/util/StringUtilSpec.scala
index 42af69a0405..7c466aca30e 100644
--- a/wdl/model/draft2/src/test/scala/wdl/util/StringUtilSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/util/StringUtilSpec.scala
@@ -5,7 +5,6 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks
 
-
 class StringUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
 
   behavior of "StringUtilSpec"
diff --git a/wdl/model/draft2/src/test/scala/wdl/values/WdlValueSpec.scala b/wdl/model/draft2/src/test/scala/wdl/values/WdlValueSpec.scala
index 225c7b6b98f..da7d53576a8 100644
--- a/wdl/model/draft2/src/test/scala/wdl/values/WdlValueSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/values/WdlValueSpec.scala
@@ -59,7 +59,8 @@ class WdlValueSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     (WdlExpression.fromString("a + b"), "a + b"),
     (WdlExpression.fromString("a(b, c)"), "a(b, c)"),
     (WdlExpression.fromString("\"a\" + \"b\""), "\"a\" + \"b\""),
-    (WdlExpression.fromString("a.b.c"), "a.b.c"))
+    (WdlExpression.fromString("a.b.c"), "a.b.c")
+  )
 
   forAll(wdlExpressionRawStrings) { (womValue, rawString) =>
     it should s"resemble a ${womValue.typeName} to/from raw string '$rawString'" in {
@@ -98,41 +99,64 @@ class WdlValueSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       WomObject(Map("0" -> WomString("zero")))
     ),
     (
-      WomObject(Map(
-        "0" -> WomString("zero"), "1" -> WomString("one"), "2" -> WomString("two"), "3" -> WomString("three")
-      )),
-      WomObject(Map(
-        "0" -> WomString("zero"), "1" -> WomString("one"), "2" -> WomString("two")
-      ))
+      WomObject(
+        Map(
+          "0" -> WomString("zero"),
+          "1" -> WomString("one"),
+          "2" -> WomString("two"),
+          "3" -> WomString("three")
+        )
+      ),
+      WomObject(
+        Map(
+          "0" -> WomString("zero"),
+          "1" -> WomString("one"),
+          "2" -> WomString("two")
+        )
+      )
     ),
     (
       WdlCallOutputsObject(testCall, Map("0" -> WomString("zero"))),
       WdlCallOutputsObject(testCall, Map("0" -> WomString("zero")))
     ),
     (
-      WdlCallOutputsObject(testCall, Map(
-        "0" -> WomString("zero"), "1" -> WomString("one"), "2" -> WomString("two"), "3" -> WomString("three")
-      )),
-      WdlCallOutputsObject(testCall, Map(
-        "0" -> WomString("zero"), "1" -> WomString("one"), "2" -> WomString("two")
-      ))
+      WdlCallOutputsObject(testCall,
+                           Map(
+                             "0" -> WomString("zero"),
+                             "1" -> WomString("one"),
+                             "2" -> WomString("two"),
+                             "3" -> WomString("three")
+                           )
+      ),
+      WdlCallOutputsObject(testCall,
+                           Map(
+                             "0" -> WomString("zero"),
+                             "1" -> WomString("one"),
+                             "2" -> WomString("two")
+                           )
+      )
     ),
     (
       WomMap(WomMapType(WomStringType, WomStringType), Map(WomString("0") -> WomString("zero"))),
       WomMap(WomMapType(WomStringType, WomStringType), Map(WomString("0") -> WomString("zero")))
     ),
     (
-      WomMap(WomMapType(WomStringType, WomStringType), Map(
-        WomString("0") -> WomString("zero"),
-        WomString("1") -> WomString("one"),
-        WomString("2") -> WomString("two"),
-        WomString("3") -> WomString("three")
-      )),
-      WomMap(WomMapType(WomStringType, WomStringType), Map(
-        WomString("0") -> WomString("zero"),
-        WomString("1") -> WomString("one"),
-        WomString("2") -> WomString("two")
-      ))
+      WomMap(
+        WomMapType(WomStringType, WomStringType),
+        Map(
+          WomString("0") -> WomString("zero"),
+          WomString("1") -> WomString("one"),
+          WomString("2") -> WomString("two"),
+          WomString("3") -> WomString("three")
+        )
+      ),
+      WomMap(WomMapType(WomStringType, WomStringType),
+             Map(
+               WomString("0") -> WomString("zero"),
+               WomString("1") -> WomString("one"),
+               WomString("2") -> WomString("two")
+             )
+      )
     ),
     (
       WomArray(WomArrayType(WomStringType), Seq(WomString("0"))),
@@ -146,18 +170,38 @@ class WdlValueSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       WomArray(
         WomArrayType(WomArrayType(WomStringType)),
         Seq(
-          WomArray(WomArrayType(WomStringType), Seq(
-            WomString("a0"), WomString("a1"), WomString("a2"), WomString("a3")
-          )),
-          WomArray(WomArrayType(WomStringType), Seq(
-            WomString("b0"), WomString("b1"), WomString("b2"), WomString("b3")
-          )),
-          WomArray(WomArrayType(WomStringType), Seq(
-            WomString("c0"), WomString("c1"), WomString("c2"), WomString("c3")
-          )),
-          WomArray(WomArrayType(WomStringType), Seq(
-            WomString("d0"), WomString("d1"), WomString("d2"), WomString("d3")
-          ))
+          WomArray(WomArrayType(WomStringType),
+                   Seq(
+                     WomString("a0"),
+                     WomString("a1"),
+                     WomString("a2"),
+                     WomString("a3")
+                   )
+          ),
+          WomArray(WomArrayType(WomStringType),
+                   Seq(
+                     WomString("b0"),
+                     WomString("b1"),
+                     WomString("b2"),
+                     WomString("b3")
+                   )
+          ),
+          WomArray(WomArrayType(WomStringType),
+                   Seq(
+                     WomString("c0"),
+                     WomString("c1"),
+                     WomString("c2"),
+                     WomString("c3")
+                   )
+          ),
+          WomArray(WomArrayType(WomStringType),
+                   Seq(
+                     WomString("d0"),
+                     WomString("d1"),
+                     WomString("d2"),
+                     WomString("d3")
+                   )
+          )
         )
       ),
       WomArray(
@@ -171,13 +215,12 @@ class WdlValueSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     )
   )
 
-  private def describe(womValue: WomValue): String = {
+  private def describe(womValue: WomValue): String =
     womValue match {
       case WdlCallOutputsObject(call, outputs) =>
         s"WdlCallOutputsObject(${call.unqualifiedName}, ${outputs.safeMapValues(_.toWomString)})"
       case _ => womValue.toWomString
     }
-  }
 
   forAll(wdlValueMaxedElements) { (womValue, expected) =>
     it should s"take max elements for ${describe(womValue)}" in {
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CallElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CallElement.scala
index 35b7f8be3cc..1d4a3e428ca 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CallElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CallElement.scala
@@ -5,5 +5,6 @@ final case class CallElement(callableReference: String,
                              alias: Option[String],
                              afters: Vector[String],
                              body: Option[CallBodyElement],
-                             override val sourceLocation : Option[SourceFileLocation])
-    extends LanguageElement with WorkflowGraphElement
+                             override val sourceLocation: Option[SourceFileLocation]
+) extends LanguageElement
+    with WorkflowGraphElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CommandPartElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CommandPartElement.scala
index cb8049fb4a8..2d89d6a20ed 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CommandPartElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CommandPartElement.scala
@@ -4,5 +4,7 @@ sealed trait CommandPartElement extends TaskSectionElement
 
 object CommandPartElement {
   final case class StringCommandPartElement(value: String) extends CommandPartElement
-  final case class PlaceholderCommandPartElement(expressionElement: ExpressionElement, attributes: PlaceholderAttributeSet) extends CommandPartElement
+  final case class PlaceholderCommandPartElement(expressionElement: ExpressionElement,
+                                                 attributes: PlaceholderAttributeSet
+  ) extends CommandPartElement
 }
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/DeclarationElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/DeclarationElement.scala
index 1a1bf71e8dd..ef85d3973bf 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/DeclarationElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/DeclarationElement.scala
@@ -8,25 +8,35 @@ final case class DeclarationContent(typeElement: TypeElement, name: String, expr
 /**
   * A Declaration outside of an input or output block
   */
-final case class IntermediateValueDeclarationElement(typeElement: TypeElement, name: String, expression: ExpressionElement) extends WorkflowGraphElement with TaskSectionElement
+final case class IntermediateValueDeclarationElement(typeElement: TypeElement,
+                                                     name: String,
+                                                     expression: ExpressionElement
+) extends WorkflowGraphElement
+    with TaskSectionElement
 
 object IntermediateValueDeclarationElement {
-  def fromContent(content: DeclarationContent): IntermediateValueDeclarationElement = IntermediateValueDeclarationElement(content.typeElement, content.name, content.expression)
+  def fromContent(content: DeclarationContent): IntermediateValueDeclarationElement =
+    IntermediateValueDeclarationElement(content.typeElement, content.name, content.expression)
 }
 
 /**
   * A declaration in an output block
   */
-final case class OutputDeclarationElement(typeElement: TypeElement, name: String, expression: ExpressionElement) extends LanguageElement with WorkflowGraphElement
+final case class OutputDeclarationElement(typeElement: TypeElement, name: String, expression: ExpressionElement)
+    extends LanguageElement
+    with WorkflowGraphElement
 
 object OutputDeclarationElement {
-  def fromContent(content: DeclarationContent): OutputDeclarationElement = OutputDeclarationElement(content.typeElement, content.name, content.expression)
+  def fromContent(content: DeclarationContent): OutputDeclarationElement =
+    OutputDeclarationElement(content.typeElement, content.name, content.expression)
 }
 
 /**
   * A declaration in an input block
   */
-final case class InputDeclarationElement(typeElement: TypeElement, name: String, expression: Option[ExpressionElement]) extends LanguageElement with WorkflowGraphElement
+final case class InputDeclarationElement(typeElement: TypeElement, name: String, expression: Option[ExpressionElement])
+    extends LanguageElement
+    with WorkflowGraphElement
 
 object DeclarationElement {
   /* Custom unapply so that elsewhere we can do things like this, and otherwise treat all declarations the same:
@@ -34,10 +44,11 @@ object DeclarationElement {
     case DeclarationElement(typeElement, name, Some(expr)) => ...
   }
    */
-  def unapply(languageElement: LanguageElement): Option[(TypeElement, String, Option[ExpressionElement])] = languageElement match {
-    case IntermediateValueDeclarationElement(typeElement, name, expr) => Option((typeElement, name, Option(expr)))
-    case OutputDeclarationElement(typeElement, name, expr) => Option((typeElement, name, Option(expr)))
-    case InputDeclarationElement(typeElement, name, expr) => Option((typeElement, name, expr))
-    case _ => None
-  }
+  def unapply(languageElement: LanguageElement): Option[(TypeElement, String, Option[ExpressionElement])] =
+    languageElement match {
+      case IntermediateValueDeclarationElement(typeElement, name, expr) => Option((typeElement, name, Option(expr)))
+      case OutputDeclarationElement(typeElement, name, expr) => Option((typeElement, name, Option(expr)))
+      case InputDeclarationElement(typeElement, name, expr) => Option((typeElement, name, expr))
+      case _ => None
+    }
 }
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
index ced84d77d75..a2fc6202193 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
@@ -31,7 +31,6 @@ object ExpressionElement {
     override val unescape: String = codePoint.toChar.toString
   }
 
-
   final case class KvPair(key: String, value: ExpressionElement)
   final case class ObjectLiteral(elements: Map[String, ExpressionElement]) extends ExpressionElement
   final case class ArrayLiteral(elements: Seq[ExpressionElement]) extends ExpressionElement
@@ -42,6 +41,7 @@ object ExpressionElement {
     * Represents a unary operation (i.e. a operator symbol followed by a single argument expression)
     */
   sealed trait UnaryOperation extends ExpressionElement {
+
     /**
       * The expression which follows the unary operator. The argument to the operation.
       */
@@ -56,6 +56,7 @@ object ExpressionElement {
     * A two-argument expression. Almost certainly comes from an infix operation in WDL (eg the '+' in  '7 + read_int(x)')
     */
   sealed trait BinaryOperation extends ExpressionElement {
+
     /**
       * The left-hand-side of the operation ('7' in the example above).
       */
@@ -67,21 +68,35 @@ object ExpressionElement {
     def right: ExpressionElement
   }
 
-  final case class LogicalOr(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class LogicalAnd(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class Equals(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class NotEquals(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class LessThan(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class LessThanOrEquals(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class GreaterThan(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class GreaterThanOrEquals(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class Add(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class Subtract(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class Multiply(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class Divide(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-  final case class Remainder(override val left: ExpressionElement, override val right: ExpressionElement) extends BinaryOperation
-
-  final case class TernaryIf(condition: ExpressionElement, ifTrue: ExpressionElement, ifFalse: ExpressionElement) extends ExpressionElement
+  final case class LogicalOr(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class LogicalAnd(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class Equals(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class NotEquals(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class LessThan(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class LessThanOrEquals(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class GreaterThan(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class GreaterThanOrEquals(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class Add(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class Subtract(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class Multiply(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class Divide(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+  final case class Remainder(override val left: ExpressionElement, override val right: ExpressionElement)
+      extends BinaryOperation
+
+  final case class TernaryIf(condition: ExpressionElement, ifTrue: ExpressionElement, ifFalse: ExpressionElement)
+      extends ExpressionElement
 
   sealed trait FunctionCallElement extends ExpressionElement
   // 0-param functions
@@ -127,11 +142,13 @@ object ExpressionElement {
     def firstParam: ExpressionElement
     def secondParam: Option[ExpressionElement]
   }
-  final case class Size(file: ExpressionElement, unit: Option[ExpressionElement]) extends OneOrTwoParamFunctionCallElement {
+  final case class Size(file: ExpressionElement, unit: Option[ExpressionElement])
+      extends OneOrTwoParamFunctionCallElement {
     override def firstParam: ExpressionElement = file
     override def secondParam: Option[ExpressionElement] = unit
   }
-  final case class Basename(param: ExpressionElement, suffixToRemove: Option[ExpressionElement]) extends OneOrTwoParamFunctionCallElement {
+  final case class Basename(param: ExpressionElement, suffixToRemove: Option[ExpressionElement])
+      extends OneOrTwoParamFunctionCallElement {
     override def firstParam: ExpressionElement = param
     override def secondParam: Option[ExpressionElement] = suffixToRemove
   }
@@ -157,7 +174,8 @@ object ExpressionElement {
     def arg2: ExpressionElement
     def arg3: ExpressionElement
   }
-  final case class Sub(input: ExpressionElement, pattern: ExpressionElement, replace: ExpressionElement) extends ThreeParamFunctionCallElement {
+  final case class Sub(input: ExpressionElement, pattern: ExpressionElement, replace: ExpressionElement)
+      extends ThreeParamFunctionCallElement {
     override def arg1: ExpressionElement = input
     override def arg2: ExpressionElement = pattern
     override def arg3: ExpressionElement = replace
@@ -203,7 +221,8 @@ object ExpressionElement {
     *  - But, the second element might be part of the identifier to look up (eg my_task.pair_of_pairs) OR it might
     *      be part of a member access chain (eg pair_of_pairs.left.right). We won't know until we do the linking.
     */
-  final case class IdentifierMemberAccess(first: String, second: String, memberAccessTail: Seq[String]) extends ExpressionElement
+  final case class IdentifierMemberAccess(first: String, second: String, memberAccessTail: Seq[String])
+      extends ExpressionElement
 
   /**
     * A member access which is based on an expression rather than an identifier.
@@ -211,7 +230,8 @@ object ExpressionElement {
     * eg:
     * (1, 2).left
     */
-  final case class ExpressionMemberAccess(expression: ExpressionElement, memberAccessTail: NonEmptyList[String]) extends ExpressionElement
+  final case class ExpressionMemberAccess(expression: ExpressionElement, memberAccessTail: NonEmptyList[String])
+      extends ExpressionElement
 
   /**
     *
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/FileElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/FileElement.scala
index 65f11aded9d..ecf45a1a193 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/FileElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/FileElement.scala
@@ -1,6 +1,7 @@
 package wdl.model.draft3.elements
 
 final case class FileElement(imports: Seq[ImportElement],
-                       structs: Seq[StructElement],
-                       workflows: Seq[WorkflowDefinitionElement],
-                       tasks: Seq[TaskDefinitionElement]) extends LanguageElement
+                             structs: Seq[StructElement],
+                             workflows: Seq[WorkflowDefinitionElement],
+                             tasks: Seq[TaskDefinitionElement]
+) extends LanguageElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/IfElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/IfElement.scala
index 36620018803..24d851abead 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/IfElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/IfElement.scala
@@ -1,4 +1,4 @@
 package wdl.model.draft3.elements
 
-final case class IfElement(conditionExpression: ExpressionElement,
-                           graphElements: Seq[WorkflowGraphElement]) extends WorkflowGraphElement
+final case class IfElement(conditionExpression: ExpressionElement, graphElements: Seq[WorkflowGraphElement])
+    extends WorkflowGraphElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ImportElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ImportElement.scala
index 835e81d6a92..92bf4a6289b 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ImportElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ImportElement.scala
@@ -1,5 +1,4 @@
 package wdl.model.draft3.elements
 
-final case class ImportElement(importUrl: String,
-                               namespace: Option[String],
-                               structRenames: Map[String, String]) extends LanguageElement
+final case class ImportElement(importUrl: String, namespace: Option[String], structRenames: Map[String, String])
+    extends LanguageElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/InputsSectionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/InputsSectionElement.scala
index 4b060b39b4d..58b537d8446 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/InputsSectionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/InputsSectionElement.scala
@@ -1,3 +1,5 @@
 package wdl.model.draft3.elements
 
-final case class InputsSectionElement(inputDeclarations: Seq[InputDeclarationElement]) extends WorkflowBodyElement with TaskSectionElement
+final case class InputsSectionElement(inputDeclarations: Seq[InputDeclarationElement])
+    extends WorkflowBodyElement
+    with TaskSectionElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/LanguageElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/LanguageElement.scala
index 8839cf8c2d3..ea29be54dcd 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/LanguageElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/LanguageElement.scala
@@ -2,5 +2,5 @@ package wdl.model.draft3.elements
 import wom.SourceFileLocation
 
 trait LanguageElement {
-    val sourceLocation : Option[SourceFileLocation] = None
+  val sourceLocation: Option[SourceFileLocation] = None
 }
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/MetaSectionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/MetaSectionElement.scala
index 0f318f10309..74020102db6 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/MetaSectionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/MetaSectionElement.scala
@@ -2,4 +2,6 @@ package wdl.model.draft3.elements
 
 import wom.callable.MetaValueElement
 
-final case class MetaSectionElement(meta: Map[String, MetaValueElement]) extends WorkflowBodyElement with TaskSectionElement
+final case class MetaSectionElement(meta: Map[String, MetaValueElement])
+    extends WorkflowBodyElement
+    with TaskSectionElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/OutputsSectionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/OutputsSectionElement.scala
index cea7438e1f5..96b88e94cb7 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/OutputsSectionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/OutputsSectionElement.scala
@@ -1,3 +1,5 @@
 package wdl.model.draft3.elements
 
-final case class OutputsSectionElement(outputs: Seq[OutputDeclarationElement]) extends WorkflowBodyElement with TaskSectionElement
+final case class OutputsSectionElement(outputs: Seq[OutputDeclarationElement])
+    extends WorkflowBodyElement
+    with TaskSectionElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ParameterMetaSectionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ParameterMetaSectionElement.scala
index f951103b5d6..8eb74929abc 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ParameterMetaSectionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ParameterMetaSectionElement.scala
@@ -2,4 +2,6 @@ package wdl.model.draft3.elements
 
 import wom.callable.MetaValueElement
 
-final case class ParameterMetaSectionElement(metaAttributes: Map[String, MetaValueElement]) extends WorkflowBodyElement with TaskSectionElement
+final case class ParameterMetaSectionElement(metaAttributes: Map[String, MetaValueElement])
+    extends WorkflowBodyElement
+    with TaskSectionElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/PlaceholderAttributeElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/PlaceholderAttributeElement.scala
index b21f2946078..9b955dcd158 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/PlaceholderAttributeElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/PlaceholderAttributeElement.scala
@@ -7,7 +7,11 @@ final case class TrueAttributeElement(value: String) extends PlaceholderAttribut
 final case class FalseAttributeElement(value: String) extends PlaceholderAttributeElement
 final case class SepAttributeElement(value: String) extends PlaceholderAttributeElement
 
-final case class PlaceholderAttributeSet(defaultAttribute: Option[String], trueAttribute: Option[String], falseAttribute: Option[String], sepAttribute: Option[String])
+final case class PlaceholderAttributeSet(defaultAttribute: Option[String],
+                                         trueAttribute: Option[String],
+                                         falseAttribute: Option[String],
+                                         sepAttribute: Option[String]
+)
 
 object PlaceholderAttributeSet {
   val empty = PlaceholderAttributeSet(None, None, None, None)
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ScatterElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ScatterElement.scala
index 59a242fb6d7..d9374e4aea9 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ScatterElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ScatterElement.scala
@@ -6,11 +6,12 @@ final case class ScatterElement(scatterName: String,
                                 scatterExpression: ExpressionElement,
                                 scatterVariableName: String,
                                 graphElements: Seq[WorkflowGraphElement],
-                                override val sourceLocation : Option[SourceFileLocation]) extends WorkflowGraphElement {
+                                override val sourceLocation: Option[SourceFileLocation]
+) extends WorkflowGraphElement {
 
   // Scatter names do not contain intrinsic information about the scatter; rather they are a sort
   // of hash based on the declarations's physical location in the source.
-  override def equals(other: scala.Any): Boolean = {
+  override def equals(other: scala.Any): Boolean =
     other match {
       case otherScatter: ScatterElement =>
         this.scatterExpression == otherScatter.scatterExpression &&
@@ -18,7 +19,6 @@ final case class ScatterElement(scatterName: String,
         this.graphElements == otherScatter.graphElements
       case _ => false
     }
-  }
 
   // Shorthand to only include certain members for hashing purposes
   // https://stackoverflow.com/a/31915429/818054
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/StringEscapeSequence.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/StringEscapeSequence.scala
index d2abab6ca58..b88453d1ede 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/StringEscapeSequence.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/StringEscapeSequence.scala
@@ -2,7 +2,15 @@ package wdl.model.draft3.elements
 
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
-import wdl.model.draft3.elements.ExpressionElement.{BackslashEscape, DoubleQuoteEscape, NewlineEscape, SingleQuoteEscape, StringEscapeSequence, TabEscape, UnicodeCharacterEscape}
+import wdl.model.draft3.elements.ExpressionElement.{
+  BackslashEscape,
+  DoubleQuoteEscape,
+  NewlineEscape,
+  SingleQuoteEscape,
+  StringEscapeSequence,
+  TabEscape,
+  UnicodeCharacterEscape
+}
 
 object StringEscapeSequence {
   val Octal = "\\\\([0-7]{3})".r
@@ -21,7 +29,6 @@ object StringEscapeSequence {
     case FourDigitUnicode(codePoint) => UnicodeCharacterEscape(BigInt(codePoint, 16).intValue).validNel
     case EightDigitUnicode(codePoint) => UnicodeCharacterEscape(BigInt(codePoint, 16).intValue).validNel
 
-
     case _ => s"Unrecognized escape sequence '$seq'".invalidNel
   }
 }
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/TaskDefinitionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/TaskDefinitionElement.scala
index 84a08b3715c..c952f69b468 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/TaskDefinitionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/TaskDefinitionElement.scala
@@ -9,4 +9,5 @@ final case class TaskDefinitionElement(name: String,
                                        runtimeSection: Option[RuntimeAttributesSectionElement],
                                        metaSection: Option[MetaSectionElement],
                                        parameterMetaSection: Option[ParameterMetaSectionElement],
-                                       override val sourceLocation : Option[SourceFileLocation]) extends FileBodyElement
+                                       override val sourceLocation: Option[SourceFileLocation]
+) extends FileBodyElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/TypeElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/TypeElement.scala
index 67e5598abb9..ed44c25f39d 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/TypeElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/TypeElement.scala
@@ -7,7 +7,7 @@ sealed trait TypeElement extends LanguageElement
 case class PrimitiveTypeElement(primitiveType: WomPrimitiveType) extends TypeElement
 
 case class ArrayTypeElement(inner: TypeElement) extends TypeElement
-case class MapTypeElement(keyType: TypeElement, valueType: TypeElement ) extends TypeElement
+case class MapTypeElement(keyType: TypeElement, valueType: TypeElement) extends TypeElement
 case class OptionalTypeElement(maybeType: TypeElement) extends TypeElement
 case class NonEmptyTypeElement(arrayType: TypeElement) extends TypeElement
 case class PairTypeElement(leftType: TypeElement, rightType: TypeElement) extends TypeElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/WorkflowDefinitionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/WorkflowDefinitionElement.scala
index d6aec431f88..de48042e9fb 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/WorkflowDefinitionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/WorkflowDefinitionElement.scala
@@ -7,4 +7,5 @@ final case class WorkflowDefinitionElement(name: String,
                                            outputsSection: Option[OutputsSectionElement],
                                            metaSection: Option[MetaSectionElement],
                                            parameterMetaSection: Option[ParameterMetaSectionElement],
-                                           override val sourceLocation : Option[SourceFileLocation]) extends FileBodyElement
+                                           override val sourceLocation: Option[SourceFileLocation]
+) extends FileBodyElement
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/GeneratedValueHandle.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/GeneratedValueHandle.scala
index 034854c56d6..e9e32149cfd 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/GeneratedValueHandle.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/GeneratedValueHandle.scala
@@ -8,7 +8,8 @@ sealed trait GeneratedValueHandle {
 }
 
 final case class GeneratedIdentifierValueHandle(linkableName: String, womType: WomType) extends GeneratedValueHandle
-final case class GeneratedCallOutputValueHandle(callName: String, outputName: String, womType: WomType) extends GeneratedValueHandle {
+final case class GeneratedCallOutputValueHandle(callName: String, outputName: String, womType: WomType)
+    extends GeneratedValueHandle {
   override def linkableName: String = s"$callName.$outputName"
 }
 
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/LinkedGraph.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/LinkedGraph.scala
index 26c0a84f693..2ca92b8bd34 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/LinkedGraph.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/LinkedGraph.scala
@@ -7,7 +7,7 @@ final case class LinkedGraph(elements: Set[WorkflowGraphElement],
                              edges: Set[LinkedGraphEdge],
                              generatedHandles: Set[GeneratedValueHandle],
                              consumedValueLookup: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
-                             typeAliases: Map[String, WomType]) {
-}
+                             typeAliases: Map[String, WomType]
+) {}
 
 final case class LinkedGraphEdge(upstream: WorkflowGraphElement, downstream: WorkflowGraphElement)
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedConsumedValueHook.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedConsumedValueHook.scala
index 0a2a3a2ed06..de43a0edc52 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedConsumedValueHook.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedConsumedValueHook.scala
@@ -14,7 +14,7 @@ final case class UnlinkedIdentifierHook(name: String) extends UnlinkedConsumedVa
   * Until we do the linking, we can't tell whether a consumed 'x.y' is a call output or a member access for 'y' on
   * a variable called 'x'.
   */
-final case class UnlinkedCallOutputOrIdentifierAndMemberAccessHook(name: String,
-                                                                   firstLookup: String) extends UnlinkedConsumedValueHook
+final case class UnlinkedCallOutputOrIdentifierAndMemberAccessHook(name: String, firstLookup: String)
+    extends UnlinkedConsumedValueHook
 
 final case class UnlinkedAfterCallHook(upstreamCallName: String) extends UnlinkedConsumedValueHook
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedValueConsumer.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedValueConsumer.scala
index 33104de1b3e..2fcaf0e4070 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedValueConsumer.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedValueConsumer.scala
@@ -8,14 +8,14 @@ import wom.types.WomType
 
 @typeclass
 trait GraphElementValueConsumer[A] {
-  def graphElementConsumedValueHooks(a: A,
-                                     typeAliases: Map[String, WomType],
-                                     callables: Map[String, Callable])
-                                    (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): ErrorOr[Set[UnlinkedConsumedValueHook]]
+  def graphElementConsumedValueHooks(a: A, typeAliases: Map[String, WomType], callables: Map[String, Callable])(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+  ): ErrorOr[Set[UnlinkedConsumedValueHook]]
 }
 
 @typeclass
 trait ExpressionValueConsumer[A] {
-  def expressionConsumedValueHooks(a: A)
-                                  (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook]
+  def expressionConsumedValueHooks(a: A)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+  ): Set[UnlinkedConsumedValueHook]
 }
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedValueGenerator.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedValueGenerator.scala
index e21e2cf2582..8e7af412f39 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedValueGenerator.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/UnlinkedValueGenerator.scala
@@ -7,5 +7,8 @@ import wom.types.WomType
 
 @typeclass
 trait UnlinkedValueGenerator[A] {
-  def generatedValueHandles(a: A, typeAliases: Map[String, WomType], callables: Map[String, Callable]): ErrorOr[Set[GeneratedValueHandle]]
+  def generatedValueHandles(a: A,
+                            typeAliases: Map[String, WomType],
+                            callables: Map[String, Callable]
+  ): ErrorOr[Set[GeneratedValueHandle]]
 }
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/FileEvaluator.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/FileEvaluator.scala
index 8c9c4b4578e..62b5e662860 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/FileEvaluator.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/FileEvaluator.scala
@@ -15,19 +15,22 @@ trait FileEvaluator[A <: ExpressionElement] {
   final def evaluateFilesNeededToEvaluate(a: A,
                                           inputs: Map[String, WomValue],
                                           ioFunctionSet: IoFunctionSet,
-                                          coerceTo: WomType)
-                                         (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                          valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+                                          coerceTo: WomType
+  )(implicit
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[Set[WomFile]] =
     valueEvaluator.evaluateValue(a, inputs, ioFunctionSet, None) match {
       case Valid(womValue) => FileEvaluatorUtil.findFilesToDelocalize(womValue.value, coerceTo).toSet.validNel
       case _ => predictFilesNeededToEvaluate(a, inputs, ioFunctionSet, coerceTo)
     }
-  }
 
   def predictFilesNeededToEvaluate(a: A,
                                    inputs: Map[String, WomValue],
                                    ioFunctionSet: IoFunctionSet,
-                                   coerceTo: WomType)
-                                  (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                   valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]]
+                                   coerceTo: WomType
+  )(implicit
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[Set[WomFile]]
 }
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/TypeEvaluator.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/TypeEvaluator.scala
index 068e99537c1..b7910478d83 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/TypeEvaluator.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/TypeEvaluator.scala
@@ -8,7 +8,7 @@ import wom.types.WomType
 
 @typeclass
 trait TypeEvaluator[A] {
-  def evaluateType(a: A,
-                   linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                  (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType]
+  def evaluateType(a: A, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+  ): ErrorOr[WomType]
 }
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/ValueEvaluator.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/ValueEvaluator.scala
index aba476675a8..4acb2612845 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/ValueEvaluator.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/ValueEvaluator.scala
@@ -9,6 +9,7 @@ import wom.values.WomValue
 
 @typeclass
 trait ValueEvaluator[A] {
+
   /**
     * Evaluate a value from an A
     * @param a The A to evaluate
@@ -20,8 +21,8 @@ trait ValueEvaluator[A] {
   def evaluateValue(a: A,
                     inputs: Map[String, WomValue],
                     ioFunctionSet: IoFunctionSet,
-                    forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                   (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]]
+                    forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+  )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]]
 }
 
 final case class ForCommandInstantiationOptions(valueMapper: WomValue => WomValue)
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/WomExpressionMaker.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/WomExpressionMaker.scala
index 02f5fdf8796..039b96ee768 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/WomExpressionMaker.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/WomExpressionMaker.scala
@@ -10,5 +10,6 @@ import wom.types.WomType
 trait WomExpressionMaker[A] {
   def makeWomExpression(a: A,
                         typeAliases: Map[String, WomType],
-                        consumedValueLookup: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]): ErrorOr[WomExpression]
+                        consumedValueLookup: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+  ): ErrorOr[WomExpression]
 }
diff --git a/wdl/model/shared/src/main/scala/wdl/shared/FileSizeLimitationConfig.scala b/wdl/model/shared/src/main/scala/wdl/shared/FileSizeLimitationConfig.scala
index 51af5d175da..205e149f7d4 100644
--- a/wdl/model/shared/src/main/scala/wdl/shared/FileSizeLimitationConfig.scala
+++ b/wdl/model/shared/src/main/scala/wdl/shared/FileSizeLimitationConfig.scala
@@ -42,19 +42,18 @@ object FileSizeLimitationConfig {
 
   lazy val fileSizeLimitationConfig: FileSizeLimitationConfig = config.as[FileSizeLimitationConfig]("input-read-limits")
 
-  implicit val configReader : ValueReader[FileSizeLimitationConfig] = ValueReader.relative{c =>
+  implicit val configReader: ValueReader[FileSizeLimitationConfig] = ValueReader.relative { c =>
     def f(s: String) = c.as[Int](s)
     new FileSizeLimitationConfig {
-      val readLinesLimit =  f("lines")
-      val readBoolLimit =   f("bool")
-      val readIntLimit =    f("int")
-      val readFloatLimit =  f("float")
+      val readLinesLimit = f("lines")
+      val readBoolLimit = f("bool")
+      val readIntLimit = f("int")
+      val readFloatLimit = f("float")
       val readStringLimit = f("string")
-      val readJsonLimit =   f("json")
-      val readTsvLimit =    f("tsv")
-      val readMapLimit =    f("map")
+      val readJsonLimit = f("json")
+      val readTsvLimit = f("tsv")
+      val readMapLimit = f("map")
       val readObjectLimit = f("object")
     }
   }
 }
-
diff --git a/wdl/model/shared/src/main/scala/wdl/shared/model/expression/FileEvaluatorUtil.scala b/wdl/model/shared/src/main/scala/wdl/shared/model/expression/FileEvaluatorUtil.scala
index cfadaed56f6..1fb4f0f12d3 100644
--- a/wdl/model/shared/src/main/scala/wdl/shared/model/expression/FileEvaluatorUtil.scala
+++ b/wdl/model/shared/src/main/scala/wdl/shared/model/expression/FileEvaluatorUtil.scala
@@ -11,12 +11,17 @@ object FileEvaluatorUtil {
     coercedValue match {
       case Success(f: WomFile) => Seq(f)
       case Success(a: WomArray) =>
-        a.value.flatMap(findFilesToDelocalize(_, coerceTo, coerce=false))
+        a.value.flatMap(findFilesToDelocalize(_, coerceTo, coerce = false))
       case Success(m: WomMap) =>
-        (m.value flatMap { case (k, v) => Seq(k, v) } flatMap(findFilesToDelocalize(_, coerceTo, coerce=false))).toSeq
-      case Success(WomOptionalValue(_, Some(v))) => findFilesToDelocalize(v, coerceTo, coerce=false)
-      case Success(WomPair(l, r)) => findFilesToDelocalize(l, coerceTo, coerce = false) ++ findFilesToDelocalize(r, coerceTo, coerce = false)
-      case Success(o: WomObject) => o.values.values.flatMap(inner => findFilesToDelocalize(inner, inner.womType, coerce = false)).toSeq
+        (m.value flatMap { case (k, v) => Seq(k, v) } flatMap (findFilesToDelocalize(_,
+                                                                                     coerceTo,
+                                                                                     coerce = false
+        ))).toSeq
+      case Success(WomOptionalValue(_, Some(v))) => findFilesToDelocalize(v, coerceTo, coerce = false)
+      case Success(WomPair(l, r)) =>
+        findFilesToDelocalize(l, coerceTo, coerce = false) ++ findFilesToDelocalize(r, coerceTo, coerce = false)
+      case Success(o: WomObject) =>
+        o.values.values.flatMap(inner => findFilesToDelocalize(inner, inner.womType, coerce = false)).toSeq
       case _ => Seq.empty[WomFile]
     }
   }
diff --git a/wdl/model/shared/src/main/scala/wdl/shared/model/expression/ValueEvaluation.scala b/wdl/model/shared/src/main/scala/wdl/shared/model/expression/ValueEvaluation.scala
index e8b4e72eccb..e15ac113e27 100644
--- a/wdl/model/shared/src/main/scala/wdl/shared/model/expression/ValueEvaluation.scala
+++ b/wdl/model/shared/src/main/scala/wdl/shared/model/expression/ValueEvaluation.scala
@@ -2,12 +2,27 @@ package wdl.shared.model.expression
 
 import spray.json.{JsArray, JsBoolean, JsNull, JsNumber, JsObject, JsString, JsValue}
 import wom.TsvSerializable
-import wom.values.{WomArray, WomBoolean, WomFile, WomFloat, WomInteger, WomMap, WomObjectLike, WomOptionalValue, WomPair, WomString, WomValue}
+import wom.values.{
+  WomArray,
+  WomBoolean,
+  WomFile,
+  WomFloat,
+  WomInteger,
+  WomMap,
+  WomObjectLike,
+  WomOptionalValue,
+  WomPair,
+  WomString,
+  WomValue
+}
 
 import scala.util.Try
 
 object ValueEvaluation {
-  def serializeWomValue[A <: WomValue with TsvSerializable](functionName: String, womValue: WomValue, defaultIfOptionalEmpty: A): Try[String] = {
+  def serializeWomValue[A <: WomValue with TsvSerializable](functionName: String,
+                                                            womValue: WomValue,
+                                                            defaultIfOptionalEmpty: A
+  ): Try[String] = {
     val wdlClass = defaultIfOptionalEmpty.getClass
     def castOrDefault(womValue: WomValue): A = womValue match {
       case WomOptionalValue(_, None) => defaultIfOptionalEmpty
@@ -31,9 +46,10 @@ object ValueEvaluation {
     case WomArray(_, values) => JsArray(values.map(valueToJson).toVector)
     case WomMap(_, value) => JsObject(value map { case (k, v) => k.valueString -> valueToJson(v) })
     case o: WomObjectLike => JsObject(o.values map { case (k, v) => k -> valueToJson(v) })
-    case opt: WomOptionalValue => opt.value match {
-      case Some(inner) => valueToJson(inner)
-      case None => JsNull
-    }
+    case opt: WomOptionalValue =>
+      opt.value match {
+        case Some(inner) => valueToJson(inner)
+        case None => JsNull
+      }
   }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
index b0c77565a77..52ac86b10a6 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
@@ -3,7 +3,7 @@ package wdl.transforms.biscayne.ast2wdlom
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
 import wdl.model.draft3.elements.ExpressionElement
-import wdl.model.draft3.elements.ExpressionElement.{Keys, AsMap, AsPairs, CollectByKey, Min, Max, Sep}
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep}
 import wdl.transforms.base.ast2wdlom.AstNodeToExpressionElement
 
 object AstToNewExpressionElements {
@@ -12,15 +12,20 @@ object AstToNewExpressionElements {
     "as_map" -> AstNodeToExpressionElement.validateOneParamEngineFunction(AsMap, "as_map"),
     "as_pairs" -> AstNodeToExpressionElement.validateOneParamEngineFunction(AsPairs, "as_pairs"),
     "collect_by_key" -> AstNodeToExpressionElement.validateOneParamEngineFunction(CollectByKey, "collect_by_key"),
-
     "min" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Min, "min"),
     "max" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Max, "max"),
-
     "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
-
-    "read_object" -> (_ => "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel),
-    "read_objects" -> (_ => "read_objects is no longer available in this WDL version. Consider using read_json instead".invalidNel),
-    "write_object" -> (_ => "write_object is no longer available in this WDL version. Consider using write_json instead".invalidNel),
-    "write_objects" -> (_ => "write_objects is no longer available in this WDL version. Consider using write_json instead".invalidNel),
+    "read_object" -> (_ =>
+      "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel
+    ),
+    "read_objects" -> (_ =>
+      "read_objects is no longer available in this WDL version. Consider using read_json instead".invalidNel
+    ),
+    "write_object" -> (_ =>
+      "write_object is no longer available in this WDL version. Consider using write_json instead".invalidNel
+    ),
+    "write_objects" -> (_ =>
+      "write_objects is no longer available in this WDL version. Consider using write_json instead".invalidNel
+    )
   )
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/BiscayneGenericAstNode.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/BiscayneGenericAstNode.scala
index cdfbc8569b3..bf063b4ea70 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/BiscayneGenericAstNode.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/BiscayneGenericAstNode.scala
@@ -5,7 +5,8 @@ import wdl.transforms.base.ast2wdlom.{GenericAst, GenericAstList, GenericAstNode
 import scala.jdk.CollectionConverters._
 
 case class BiscayneGenericAst(ast: Ast) extends GenericAst {
-  override def getAttribute(attr: String): GenericAstNode = Option(ast.getAttribute(attr)).map(BiscayneGenericAstNode.apply).orNull
+  override def getAttribute(attr: String): GenericAstNode =
+    Option(ast.getAttribute(attr)).map(BiscayneGenericAstNode.apply).orNull
   override def getAttributes: Map[String, GenericAstNode] = ast.getAttributes.asScala.toMap collect {
     case (key, value) if value != null => key -> BiscayneGenericAstNode(value)
   }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/ast2wdlom.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/ast2wdlom.scala
index 6bc3bcd94bc..1f84e5c142c 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/ast2wdlom.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/ast2wdlom.scala
@@ -13,50 +13,81 @@ import wom.callable.MetaKvPair
 
 package object ast2wdlom {
 
-  val wrapAst: CheckedAtoB[Ast, GenericAst] = CheckedAtoB.fromCheck { a => BiscayneGenericAst(a).validNelCheck }
-  val wrapAstNode: CheckedAtoB[AstNode, GenericAstNode] = CheckedAtoB.fromCheck { a => BiscayneGenericAstNode(a).validNelCheck }
+  val wrapAst: CheckedAtoB[Ast, GenericAst] = CheckedAtoB.fromCheck(a => BiscayneGenericAst(a).validNelCheck)
+  val wrapAstNode: CheckedAtoB[AstNode, GenericAstNode] = CheckedAtoB.fromCheck { a =>
+    BiscayneGenericAstNode(a).validNelCheck
+  }
 
-  implicit val astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString] = AstNodeToStaticString.astNodeToStaticStringElement()
+  implicit val astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString] =
+    AstNodeToStaticString.astNodeToStaticStringElement()
 
   // meta sections
   implicit val astNodeToMetaKvPair: CheckedAtoB[GenericAstNode, MetaKvPair] = AstNodeToMetaKvPair.astNodeToMetaKvPair
-  implicit val astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement] = astNodeToAst andThen AstToMetaSectionElement.astToMetaSectionElement
-  implicit val astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement] = astNodeToAst andThen AstToParameterMetaSectionElement.astToParameterMetaSectionElement
+  implicit val astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement] =
+    astNodeToAst andThen AstToMetaSectionElement.astToMetaSectionElement
+  implicit val astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement] =
+    astNodeToAst andThen AstToParameterMetaSectionElement.astToParameterMetaSectionElement
 
-  implicit val astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement] = AstNodeToExpressionElement.astNodeToExpressionElement(customEngineFunctionMakers = AstToNewExpressionElements.newBiscayneEngineFunctionMakers)
-  implicit val astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair] = AstNodeToKvPair.astNodeToKvPair(astNodeToExpressionElement)
+  implicit val astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement] =
+    AstNodeToExpressionElement.astNodeToExpressionElement(customEngineFunctionMakers =
+      AstToNewExpressionElements.newBiscayneEngineFunctionMakers
+    )
+  implicit val astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair] =
+    AstNodeToKvPair.astNodeToKvPair(astNodeToExpressionElement)
 
-  implicit val astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement] = AstNodeToTypeElement.astNodeToTypeElement(Map.empty)
+  implicit val astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement] =
+    AstNodeToTypeElement.astNodeToTypeElement(Map.empty)
   implicit val astToStructElement: CheckedAtoB[GenericAst, StructElement] = AstToStructElement.astToStructElement
-  implicit val astNodeToImportElement: CheckedAtoB[GenericAstNode, ImportElement] = astNodeToAst andThen AstToImportElement.astToImportElement
+  implicit val astNodeToImportElement: CheckedAtoB[GenericAstNode, ImportElement] =
+    astNodeToAst andThen AstToImportElement.astToImportElement
 
-  implicit val astNodeToInputDeclarationElement: CheckedAtoB[GenericAstNode, InputDeclarationElement] = astNodeToAst andThen AstToInputDeclarationElement.astToInputDeclarationElement
-  implicit val astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement] = astNodeToAst andThen AstToInputsSectionElement.astToInputsSectionElement
+  implicit val astNodeToInputDeclarationElement: CheckedAtoB[GenericAstNode, InputDeclarationElement] =
+    astNodeToAst andThen AstToInputDeclarationElement.astToInputDeclarationElement
+  implicit val astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement] =
+    astNodeToAst andThen AstToInputsSectionElement.astToInputsSectionElement
 
-  implicit val astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent] = astNodeToAst andThen AstToDeclarationContent.astToDeclarationContent
-  implicit val astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement] = astNodeToAst andThen AstToOutputsSectionElement.astToOutputSectionElement
+  implicit val astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent] =
+    astNodeToAst andThen AstToDeclarationContent.astToDeclarationContent
+  implicit val astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement] =
+    astNodeToAst andThen AstToOutputsSectionElement.astToOutputSectionElement
 
   val astToWorkflowGraphNodeElementConverterMaker = new AstToWorkflowGraphNodeElementConverterMaker()
-  implicit val astNodeToGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement] = astNodeToAst andThen astToWorkflowGraphNodeElementConverterMaker.converter
-  implicit val astNodeToCallElement: CheckedAtoB[GenericAstNode, CallElement] = astNodeToAst andThen AstToCallElement.astToCallElement
-  implicit val astNodeToScatterElement: CheckedAtoB[GenericAstNode, ScatterElement] = astNodeToAst andThen AstToScatterElement.astToScatterElement
-  implicit val astNodeToIfElement: CheckedAtoB[GenericAstNode, IfElement] = astNodeToAst andThen AstToIfElement.astToIfElement
+  implicit val astNodeToGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement] =
+    astNodeToAst andThen astToWorkflowGraphNodeElementConverterMaker.converter
+  implicit val astNodeToCallElement: CheckedAtoB[GenericAstNode, CallElement] =
+    astNodeToAst andThen AstToCallElement.astToCallElement
+  implicit val astNodeToScatterElement: CheckedAtoB[GenericAstNode, ScatterElement] =
+    astNodeToAst andThen AstToScatterElement.astToScatterElement
+  implicit val astNodeToIfElement: CheckedAtoB[GenericAstNode, IfElement] =
+    astNodeToAst andThen AstToIfElement.astToIfElement
   astToWorkflowGraphNodeElementConverterMaker.astNodeToScatterElement = Some(astNodeToScatterElement)
   astToWorkflowGraphNodeElementConverterMaker.astNodeToIfElement = Some(astNodeToIfElement)
   astToWorkflowGraphNodeElementConverterMaker.astNodeToCallElement = Some(astNodeToCallElement)
   astToWorkflowGraphNodeElementConverterMaker.astNodeToDeclarationContent = Some(astNodeToDeclarationContent)
 
-  implicit val astNodeToWorkflowBodyElement: CheckedAtoB[GenericAstNode, WorkflowBodyElement] = astNodeToAst andThen AstToWorkflowBodyElement.astToWorkflowBodyElement
-  implicit val astToWorkflowDefinitionElement: CheckedAtoB[GenericAst, WorkflowDefinitionElement] = AstToWorkflowDefinitionElement.astToWorkflowDefinitionElement
+  implicit val astNodeToWorkflowBodyElement: CheckedAtoB[GenericAstNode, WorkflowBodyElement] =
+    astNodeToAst andThen AstToWorkflowBodyElement.astToWorkflowBodyElement
+  implicit val astToWorkflowDefinitionElement: CheckedAtoB[GenericAst, WorkflowDefinitionElement] =
+    AstToWorkflowDefinitionElement.astToWorkflowDefinitionElement
 
-  implicit val astNodeToPlaceholderAttributeSet: CheckedAtoB[GenericAstNode, PlaceholderAttributeSet] = astNodeToAstList andThen AstNodeToPlaceholderAttributeSet.attributeKvpConverter
-  implicit val astNodeToCommandPartElement: CheckedAtoB[GenericAstNode, CommandPartElement] = AstNodeToCommandPartElement.astNodeToCommandPartElement
-  implicit val astNodeToCommandSectionElement: CheckedAtoB[GenericAstNode, CommandSectionElement] = astNodeToAst andThen AstToCommandSectionElement.astToCommandSectionElement
-  implicit val astNodeToRuntimeAttributesSectionElement: CheckedAtoB[GenericAstNode, RuntimeAttributesSectionElement] = astNodeToAst andThen AstToRuntimeAttributesSectionElement.astToRuntimeSectionElement
-  implicit val astNodeToTaskSectionElement: CheckedAtoB[GenericAstNode, TaskSectionElement] = astNodeToAst andThen AstToTaskSectionElement.astToTaskSectionElement
-  implicit val astToTaskDefinitionElement: CheckedAtoB[GenericAst, TaskDefinitionElement] = AstToTaskDefinitionElement.astToTaskDefinitionElement
+  implicit val astNodeToPlaceholderAttributeSet: CheckedAtoB[GenericAstNode, PlaceholderAttributeSet] =
+    astNodeToAstList andThen AstNodeToPlaceholderAttributeSet.attributeKvpConverter
+  implicit val astNodeToCommandPartElement: CheckedAtoB[GenericAstNode, CommandPartElement] =
+    AstNodeToCommandPartElement.astNodeToCommandPartElement
+  implicit val astNodeToCommandSectionElement: CheckedAtoB[GenericAstNode, CommandSectionElement] =
+    astNodeToAst andThen AstToCommandSectionElement.astToCommandSectionElement
+  implicit val astNodeToRuntimeAttributesSectionElement: CheckedAtoB[GenericAstNode, RuntimeAttributesSectionElement] =
+    astNodeToAst andThen AstToRuntimeAttributesSectionElement.astToRuntimeSectionElement
+  implicit val astNodeToTaskSectionElement: CheckedAtoB[GenericAstNode, TaskSectionElement] =
+    astNodeToAst andThen AstToTaskSectionElement.astToTaskSectionElement
+  implicit val astToTaskDefinitionElement: CheckedAtoB[GenericAst, TaskDefinitionElement] =
+    AstToTaskDefinitionElement.astToTaskDefinitionElement
 
-  implicit val astToFileBodyElement: CheckedAtoB[GenericAstNode, FileBodyElement] = astNodeToAst andThen AstToFileBodyElement.astToFileBodyElement(astToWorkflowDefinitionElement, astToTaskDefinitionElement, astToStructElement)
+  implicit val astToFileBodyElement: CheckedAtoB[GenericAstNode, FileBodyElement] =
+    astNodeToAst andThen AstToFileBodyElement.astToFileBodyElement(astToWorkflowDefinitionElement,
+                                                                   astToTaskDefinitionElement,
+                                                                   astToStructElement
+    )
 
   implicit val astToFileElement: CheckedAtoB[GenericAst, FileElement] = AstToFileElement.astToFileElement
   implicit val fileToFileElement: CheckedAtoB[File, FileElement] = fileToAst andThen wrapAst andThen astToFileElement
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
index 99c929f9c4a..ad168067177 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
@@ -6,52 +6,64 @@ import wdl.model.draft3.graph.{ExpressionValueConsumer, UnlinkedConsumedValueHoo
 
 object BiscayneExpressionValueConsumers {
   implicit val keysExpressionValueConsumer: ExpressionValueConsumer[Keys] = new ExpressionValueConsumer[Keys] {
-    override def expressionConsumedValueHooks(a: Keys)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: Keys)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
-    }
   }
 
   implicit val asMapExpressionValueConsumer: ExpressionValueConsumer[AsMap] = new ExpressionValueConsumer[AsMap] {
-    override def expressionConsumedValueHooks(a: AsMap)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: AsMap)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
-    }
   }
 
   implicit val asPairsExpressionValueConsumer: ExpressionValueConsumer[AsPairs] = new ExpressionValueConsumer[AsPairs] {
-    override def expressionConsumedValueHooks(a: AsPairs)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: AsPairs)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
-    }
   }
 
-  implicit val collectByKeyExpressionValueConsumer: ExpressionValueConsumer[CollectByKey] = new ExpressionValueConsumer[CollectByKey] {
-    override def expressionConsumedValueHooks(a: CollectByKey)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
-      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+  implicit val collectByKeyExpressionValueConsumer: ExpressionValueConsumer[CollectByKey] =
+    new ExpressionValueConsumer[CollectByKey] {
+      override def expressionConsumedValueHooks(a: CollectByKey)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
     }
-  }
 
   implicit val minExpressionValueConsumer: ExpressionValueConsumer[Min] = new ExpressionValueConsumer[Min] {
-    override def expressionConsumedValueHooks(a: Min)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
-      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++ expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
-    }
+    override def expressionConsumedValueHooks(
+      a: Min
+    )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++ expressionValueConsumer
+        .expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
   implicit val maxExpressionValueConsumer: ExpressionValueConsumer[Max] = new ExpressionValueConsumer[Max] {
-    override def expressionConsumedValueHooks(a: Max)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
-      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++ expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
-    }
+    override def expressionConsumedValueHooks(
+      a: Max
+    )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++ expressionValueConsumer
+        .expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
   implicit val sepExpressionValueConsumer: ExpressionValueConsumer[Sep] = new ExpressionValueConsumer[Sep] {
-    override def expressionConsumedValueHooks(a: Sep)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: Sep)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++
         expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
-    }
   }
 
-  implicit val noneLiteralExpressionValueConsumer: ExpressionValueConsumer[NoneLiteralElement.type] = new ExpressionValueConsumer[NoneLiteralElement.type] {
-    override def expressionConsumedValueHooks(a: NoneLiteralElement.type)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
-      // None literals consume no values:
-      Set.empty[UnlinkedConsumedValueHook]
+  implicit val noneLiteralExpressionValueConsumer: ExpressionValueConsumer[NoneLiteralElement.type] =
+    new ExpressionValueConsumer[NoneLiteralElement.type] {
+      override def expressionConsumedValueHooks(a: NoneLiteralElement.type)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        // None literals consume no values:
+        Set.empty[UnlinkedConsumedValueHook]
     }
-  }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
index a370f42ca29..f70c3603b4a 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
@@ -14,97 +14,101 @@ import wdl.transforms.biscayne.linking.expression.consumed.BiscayneExpressionVal
 
 package object consumed {
 
-  implicit val expressionElementUnlinkedValueConsumer: ExpressionValueConsumer[ExpressionElement] = new ExpressionValueConsumer[ExpressionElement] {
-    override def expressionConsumedValueHooks(a: ExpressionElement)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = a match {
-      case _: PrimitiveLiteralExpressionElement | _: StringLiteral => Set.empty[UnlinkedConsumedValueHook]
-      case a: NoneLiteralElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: StringExpression => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ObjectLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: PairLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ArrayLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: MapLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      // Member access:
-      case a: IdentifierLookup => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: IdentifierMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ExpressionMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: IndexAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      // Unary operators:
-      case a: UnaryNegation => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: UnaryPlus => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LogicalNot => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      // Binary operators:
-      case a: LogicalOr => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LogicalAnd => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Equals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: NotEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LessThan => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LessThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: GreaterThan => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: GreaterThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Add => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Subtract => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Multiply => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Divide => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Remainder => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: TernaryIf => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      // Engine functions:
-      case a: StdoutElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: StderrElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: ReadLines => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadMap => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadObject => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadJson => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadInt => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadString => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadFloat => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadBoolean => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteLines => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteMap => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteObject => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteJson => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Range => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Transpose => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Length => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Flatten => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Prefix => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: SelectFirst => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: SelectAll => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Defined => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Floor => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Ceil => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Round => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Glob => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: Size => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Basename => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: Zip => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Cross => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: Sub => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      // New WDL biscayne expressions:
-      case a: Keys => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: AsMap => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: AsPairs => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: CollectByKey => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Sep => sepExpressionValueConsumer.expressionConsumedValueHooks(a)(expressionValueConsumer)
-
-      case a: Min => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Max => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case other => throw new Exception(s"Cannot generate consumed values for ExpressionElement ${other.getClass.getSimpleName}")
+  implicit val expressionElementUnlinkedValueConsumer: ExpressionValueConsumer[ExpressionElement] =
+    new ExpressionValueConsumer[ExpressionElement] {
+      override def expressionConsumedValueHooks(a: ExpressionElement)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] = a match {
+        case _: PrimitiveLiteralExpressionElement | _: StringLiteral => Set.empty[UnlinkedConsumedValueHook]
+        case a: NoneLiteralElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: StringExpression => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ObjectLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: PairLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ArrayLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: MapLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        // Member access:
+        case a: IdentifierLookup => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: IdentifierMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ExpressionMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: IndexAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        // Unary operators:
+        case a: UnaryNegation => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: UnaryPlus => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LogicalNot => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        // Binary operators:
+        case a: LogicalOr => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LogicalAnd => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Equals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: NotEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LessThan => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LessThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: GreaterThan => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: GreaterThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Add => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Subtract => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Multiply => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Divide => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Remainder => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: TernaryIf => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        // Engine functions:
+        case a: StdoutElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: StderrElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: ReadLines => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadObject => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadJson => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadInt => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadString => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadFloat => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadBoolean => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteLines => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteObject => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteJson => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Range => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Transpose => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Length => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Flatten => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Prefix => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: SelectFirst => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: SelectAll => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Defined => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Floor => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Ceil => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Round => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Glob => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: Size => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Basename => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: Zip => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Cross => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: Sub => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        // New WDL biscayne expressions:
+        case a: Keys => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: AsMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: AsPairs => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: CollectByKey => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Sep => sepExpressionValueConsumer.expressionConsumedValueHooks(a)(expressionValueConsumer)
+
+        case a: Min => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Max => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case other =>
+          throw new Exception(s"Cannot generate consumed values for ExpressionElement ${other.getClass.getSimpleName}")
+      }
     }
-  }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
index 2e8fec5e815..fa968525bbc 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
@@ -8,9 +8,12 @@ import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.two
 object BiscayneFileEvaluators {
 
   implicit val keysFileEvaluator: FileEvaluator[Keys] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
-  implicit val asMapFileEvaluator: FileEvaluator[AsMap] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
-  implicit val asPairsFileEvaluator: FileEvaluator[AsPairs] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
-  implicit val collectByKeyFileEvaluator: FileEvaluator[CollectByKey] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val asMapFileEvaluator: FileEvaluator[AsMap] =
+    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val asPairsFileEvaluator: FileEvaluator[AsPairs] =
+    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val collectByKeyFileEvaluator: FileEvaluator[CollectByKey] =
+    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
 
   implicit val sepFunctionEvaluator: FileEvaluator[Sep] = twoParameterFunctionPassthroughFileEvaluator[Sep]
 
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
index 00a9a89ccd6..d143e948272 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
@@ -21,82 +21,134 @@ package object files {
 
   implicit val expressionFileEvaluator: FileEvaluator[ExpressionElement] = new FileEvaluator[ExpressionElement] {
 
-    override def predictFilesNeededToEvaluate(a: ExpressionElement, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
-
+    override def predictFilesNeededToEvaluate(a: ExpressionElement,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       a match {
         // Literals:
-        case a: PrimitiveLiteralExpressionElement => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: StringLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ObjectLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: MapLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ArrayLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: PairLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: PrimitiveLiteralExpressionElement =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: StringLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ObjectLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: MapLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ArrayLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: PairLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Lookups and member accesses:
-        case a: IdentifierLookup => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ExpressionMemberAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: IdentifierMemberAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: IndexAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IdentifierLookup =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ExpressionMemberAccess =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IdentifierMemberAccess =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IndexAccess =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Unary operators:
-        case a: UnaryNegation => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: UnaryPlus => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LogicalNot => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: UnaryNegation =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: UnaryPlus =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalNot =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Binary operators (at some point we might want to split these into separate cases):
-        case a: LogicalOr => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LogicalAnd => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalOr =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalAnd =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Equals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: NotEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LessThan => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LessThanOrEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: GreaterThan => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: GreaterThanOrEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: NotEquals =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LessThan =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LessThanOrEquals =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: GreaterThan =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: GreaterThanOrEquals =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Add => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Subtract => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Multiply => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Subtract =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Multiply =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Divide => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Remainder => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Remainder =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
-        case a: TernaryIf => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: TernaryIf =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Engine functions:
-        case StdoutElement => StdoutElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case StderrElement => StderrElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-
-        case a: ReadLines => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadTsv => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadObject => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadObjects => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadJson => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadInt => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadString => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadFloat => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadBoolean => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteLines => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteTsv => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteObject => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteObjects => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteJson => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case StdoutElement =>
+          StdoutElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case StderrElement =>
+          StderrElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        case a: ReadLines =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadTsv =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadMap =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadObject =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadObjects =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadJson =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadInt =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadString =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadFloat =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadBoolean =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteLines =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteTsv =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteMap =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteObject =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteObjects =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteJson =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Range => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Transpose => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Transpose =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Length => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Flatten => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Flatten =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Prefix => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: SelectFirst => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: SelectAll => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Defined => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SelectFirst =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SelectAll =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Defined =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Floor => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Ceil => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Round => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Glob => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: Size => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Basename => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Basename =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: Zip => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Cross => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
@@ -105,8 +157,10 @@ package object files {
 
         case a: Keys => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: AsMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: AsPairs => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: CollectByKey => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: AsPairs =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: CollectByKey =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Sep => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: Min => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
@@ -114,6 +168,5 @@ package object files {
 
         case other => s"No implementation of FileEvaluator[${other.getClass.getSimpleName}]".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
index 173dac60f14..9a993f6b5b8 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
@@ -11,59 +11,64 @@ import wom.types._
 
 object BiscayneTypeEvaluators {
   implicit val keysFunctionEvaluator: TypeEvaluator[Keys] = new TypeEvaluator[Keys] {
-    override def evaluateType(a: Keys, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Keys, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)) flatMap {
         case WomMapType(keyType, _) => WomArrayType(keyType).validNel
         case other => s"Cannot invoke 'keys' on type '${other.stableName}'. Expected a map".invalidNel
       }
-    }
   }
 
   implicit val asMapFunctionEvaluator: TypeEvaluator[AsMap] = new TypeEvaluator[AsMap] {
-    override def evaluateType(a: AsMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: AsMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
         case WomArrayType(WomPairType(x: WomPrimitiveType, y)) => WomMapType(x, y).validNel
-        case other @ WomArrayType(WomPairType(x, _)) => s"Cannot invoke 'as_map' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
+        case other @ WomArrayType(WomPairType(x, _)) =>
+          s"Cannot invoke 'as_map' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
         case other => s"Cannot invoke 'as_map' on type '${other.stableName}'. Expected an array of pairs".invalidNel
       }
-    }
   }
 
   implicit val asPairsFunctionEvaluator: TypeEvaluator[AsPairs] = new TypeEvaluator[AsPairs] {
-    override def evaluateType(a: AsPairs, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: AsPairs, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)) flatMap {
         case WomMapType(x, y) => WomArrayType(WomPairType(x, y)).validNel
         case other => s"Cannot invoke 'as_pairs' on type '${other.stableName}'. Expected a map".invalidNel
       }
-    }
   }
 
   implicit val collectByKeyFunctionEvaluator: TypeEvaluator[CollectByKey] = new TypeEvaluator[CollectByKey] {
-    override def evaluateType(a: CollectByKey, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: CollectByKey, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
         case WomArrayType(WomPairType(x: WomPrimitiveType, y)) => WomMapType(x, WomArrayType(y)).validNel
-        case other @ WomArrayType(WomPairType(x, _)) => s"Cannot invoke 'collect_by_key' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
-        case other => s"Cannot invoke 'collect_by_key' on type '${other.stableName}'. Expected an array of pairs".invalidNel
+        case other @ WomArrayType(WomPairType(x, _)) =>
+          s"Cannot invoke 'collect_by_key' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
+        case other =>
+          s"Cannot invoke 'collect_by_key' on type '${other.stableName}'. Expected an array of pairs".invalidNel
       }
-    }
   }
 
-  private def resultTypeOfIntVsFloat(functionName: String)(type1: WomType, type2: WomType): ErrorOr[WomType] = (type1, type2) match {
-    case (WomIntegerType, WomIntegerType) => WomIntegerType.validNel
-    case (WomIntegerType, WomFloatType) => WomFloatType.validNel
-    case (WomFloatType, WomIntegerType) => WomFloatType.validNel
-    case (WomFloatType, WomFloatType) => WomFloatType.validNel
-    case (other1, other2) => s"Cannot call '$functionName' with arguments (${other1.friendlyName}, ${other2.friendlyName}). Must be Int or Long.".invalidNel
-  }
+  private def resultTypeOfIntVsFloat(functionName: String)(type1: WomType, type2: WomType): ErrorOr[WomType] =
+    (type1, type2) match {
+      case (WomIntegerType, WomIntegerType) => WomIntegerType.validNel
+      case (WomIntegerType, WomFloatType) => WomFloatType.validNel
+      case (WomFloatType, WomIntegerType) => WomFloatType.validNel
+      case (WomFloatType, WomFloatType) => WomFloatType.validNel
+      case (other1, other2) =>
+        s"Cannot call '$functionName' with arguments (${other1.friendlyName}, ${other2.friendlyName}). Must be Int or Long.".invalidNel
+    }
 
   implicit val minFunctionEvaluator: TypeEvaluator[Min] = new TypeEvaluator[Min] {
-    override def evaluateType(a: Min,
-                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Min, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = {
       val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
       val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
 
@@ -72,9 +77,9 @@ object BiscayneTypeEvaluators {
   }
 
   implicit val maxFunctionEvaluator: TypeEvaluator[Max] = new TypeEvaluator[Max] {
-    override def evaluateType(a: Max,
-                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Max, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = {
       val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
       val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
 
@@ -83,15 +88,16 @@ object BiscayneTypeEvaluators {
   }
 
   implicit val sepFunctionEvaluator: TypeEvaluator[Sep] = new TypeEvaluator[Sep] {
-    override def evaluateType(a: Sep, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Sep, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.arg2, linkedValues, WomArrayType(WomAnyType)) flatMap {
-        case WomArrayType(WomArrayType(_)) => s"Cannot invoke 'sep' on type 'Array[Array[_]]'. Expected an Array[String].".invalidNel
+        case WomArrayType(WomArrayType(_)) =>
+          s"Cannot invoke 'sep' on type 'Array[Array[_]]'. Expected an Array[String].".invalidNel
         case WomArrayType(_) => WomStringType.validNel
 
         case other => s"Cannot invoke 'sep' on type '${other.stableName}'. Expected an Array[String].".invalidNel
 
       }
-    }
   }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
index 904baf2f076..0b61f7fd71c 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
@@ -18,9 +18,9 @@ import wdl.transforms.biscayne.linking.expression.types.BiscayneTypeEvaluators._
 
 package object types {
   implicit val expressionTypeEvaluator: TypeEvaluator[ExpressionElement] = new TypeEvaluator[ExpressionElement] {
-    override def evaluateType(a: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit typeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
-
+    override def evaluateType(a: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit typeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       a match {
         // Literals:
         case a: PrimitiveLiteralExpressionElement => a.evaluateType(linkedValues)(typeEvaluator)
@@ -111,8 +111,8 @@ package object types {
         case a: Min => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Max => a.evaluateType(linkedValues)(typeEvaluator)
 
-        case other => s"Unable to process ${other.getClass.getSimpleName}: No evaluateType exists for that type.".invalidNel
+        case other =>
+          s"Unable to process ${other.getClass.getSimpleName}: No evaluateType exists for that type.".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
index b55afa916c2..bdb3516f787 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
@@ -9,40 +9,54 @@ import common.collections.EnhancedCollections._
 import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement._
 import wdl.model.draft3.graph.expression.{EvaluatedValue, ForCommandInstantiationOptions, ValueEvaluator}
-import wdl.transforms.base.linking.expression.values.EngineFunctionEvaluators.{processValidatedSingleValue, processTwoValidatedValues}
+import wdl.transforms.base.linking.expression.values.EngineFunctionEvaluators.{
+  processTwoValidatedValues,
+  processValidatedSingleValue
+}
 import wom.expression.IoFunctionSet
 import wom.types._
-import wom.values.{WomArray, WomInteger, WomFloat, WomMap, WomOptionalValue, WomPair, WomValue, WomString}
+import wom.values.{WomArray, WomFloat, WomInteger, WomMap, WomOptionalValue, WomPair, WomString, WomValue}
 import wom.types.coercion.defaults._
 
 object BiscayneValueEvaluators {
 
-  implicit val noneLiteralEvaluator: ValueEvaluator[NoneLiteralElement.type] = new ValueEvaluator[ExpressionElement.NoneLiteralElement.type] {
-    override def evaluateValue(a: ExpressionElement.NoneLiteralElement.type, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      EvaluatedValue(
-        value = WomOptionalValue(WomNothingType, None),
-        sideEffectFiles = Seq.empty).validNel
+  implicit val noneLiteralEvaluator: ValueEvaluator[NoneLiteralElement.type] =
+    new ValueEvaluator[ExpressionElement.NoneLiteralElement.type] {
+      override def evaluateValue(a: ExpressionElement.NoneLiteralElement.type,
+                                 inputs: Map[String, WomValue],
+                                 ioFunctionSet: IoFunctionSet,
+                                 forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+      )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+        EvaluatedValue(value = WomOptionalValue(WomNothingType, None), sideEffectFiles = Seq.empty).validNel
     }
-  }
 
   implicit val asMapFunctionEvaluator: ValueEvaluator[AsMap] = new ValueEvaluator[AsMap] {
-    override def evaluateValue(a: AsMap, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      processValidatedSingleValue[WomArray, WomMap](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
+    override def evaluateValue(a: AsMap,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+      processValidatedSingleValue[WomArray, WomMap](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) {
         case WomArray(WomArrayType(WomPairType(_: WomPrimitiveType, _)), values) =>
           val validPairs: ErrorOr[List[(WomValue, WomValue)]] = values.toList traverse {
             case WomPair(l, r) => (l, r).validNel
-            case other => s"Unexpected array element. Expected a Pair[X, Y] but array contained ${other.toWomString}]".invalidNel
-          } leftMap {
-            errors => NonEmptyList.fromListUnsafe(errors.toList.distinct)
+            case other =>
+              s"Unexpected array element. Expected a Pair[X, Y] but array contained ${other.toWomString}]".invalidNel
+          } leftMap { errors =>
+            NonEmptyList.fromListUnsafe(errors.toList.distinct)
           }
           validPairs flatMap { pairs =>
             val grouped = pairs.groupBy(_._1)
             val tooManyKeyErrors = grouped collect {
-              case (name, list) if list.length != 1 => s"keys can only appear once but ${name.toWomString} appeared ${list.size} times."
+              case (name, list) if list.length != 1 =>
+                s"keys can only appear once but ${name.toWomString} appeared ${list.size} times."
             }
             if (tooManyKeyErrors.isEmpty) {
-              val pairs = grouped map { case (key, value) => (key -> value.head._2) }
+              val pairs = grouped map { case (key, value) => key -> value.head._2 }
 
               EvaluatedValue(WomMap(pairs), Seq.empty).validNel
             } else {
@@ -50,49 +64,69 @@ object BiscayneValueEvaluators {
             }
           }
 
-        case WomArray(womType@WomArrayType(WomPairType(x, _)), _) => s"Cannot evaluate 'as_map' on type ${womType.stableName}. Keys must be primitive but got ${x.stableName}.".invalidNel
-        case other => s"Invalid call of 'as_map' on parameter of type '${other.womType.stableName}' (expected Array[Pair[X, Y]])".invalidNel
-      } (coercer = WomArrayType(WomPairType(WomAnyType, WomAnyType)))
-    }
+        case WomArray(womType @ WomArrayType(WomPairType(x, _)), _) =>
+          s"Cannot evaluate 'as_map' on type ${womType.stableName}. Keys must be primitive but got ${x.stableName}.".invalidNel
+        case other =>
+          s"Invalid call of 'as_map' on parameter of type '${other.womType.stableName}' (expected Array[Pair[X, Y]])".invalidNel
+      }(coercer = WomArrayType(WomPairType(WomAnyType, WomAnyType)))
   }
 
   implicit val keysFunctionEvaluator: ValueEvaluator[Keys] = new ValueEvaluator[Keys] {
     override def evaluateValue(a: Keys,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-
-      processValidatedSingleValue[WomMap, WomArray](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
-        case WomMap(WomMapType(keyType, _), values) => EvaluatedValue(WomArray(WomArrayType(keyType), values.keys.toList), Seq.empty).validNel
-        case other => s"Invalid call of 'keys' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomMap, WomArray](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) {
+        case WomMap(WomMapType(keyType, _), values) =>
+          EvaluatedValue(WomArray(WomArrayType(keyType), values.keys.toList), Seq.empty).validNel
+        case other =>
+          s"Invalid call of 'keys' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
       }
-    }
   }
 
   implicit val asPairsFunctionEvaluator: ValueEvaluator[AsPairs] = new ValueEvaluator[AsPairs] {
-    override def evaluateValue(a: AsPairs, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      processValidatedSingleValue[WomMap, WomArray](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
+    override def evaluateValue(a: AsPairs,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+      processValidatedSingleValue[WomMap, WomArray](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) {
         case WomMap(WomMapType(keyType, valueType), values) =>
-          val validPairs: List[WomPair] = values.toList map {
-            case (l, r) => WomPair(l, r)
+          val validPairs: List[WomPair] = values.toList map { case (l, r) =>
+            WomPair(l, r)
           }
           EvaluatedValue(WomArray(WomArrayType(WomPairType(keyType, valueType)), validPairs), Seq.empty).validNel
 
-        case other => s"Invalid call of 'as_pairs' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
+        case other =>
+          s"Invalid call of 'as_pairs' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
       }
-    }
   }
 
   implicit val collectByKeyFunctionEvaluator: ValueEvaluator[CollectByKey] = new ValueEvaluator[CollectByKey] {
-    override def evaluateValue(a: CollectByKey, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      processValidatedSingleValue[WomArray, WomMap](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
+    override def evaluateValue(a: CollectByKey,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+      processValidatedSingleValue[WomArray, WomMap](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) {
         case WomArray(WomArrayType(WomPairType(_: WomPrimitiveType, _)), values) =>
           val validPairs: ErrorOr[List[(WomValue, WomValue)]] = values.toList traverse {
             case WomPair(l, r) => (l, r).validNel
-            case other => s"Unexpected array element. Expected a Pair[X, Y] but array contained ${other.toWomString}]".invalidNel
+            case other =>
+              s"Unexpected array element. Expected a Pair[X, Y] but array contained ${other.toWomString}]".invalidNel
           }
           validPairs flatMap { kvpairs =>
             val grouped: Map[WomValue, WomArray] = kvpairs.groupBy(_._1).safeMapValues(v => WomArray(v.map(_._2)))
@@ -100,22 +134,24 @@ object BiscayneValueEvaluators {
 
           }
 
-        case WomArray(womType@WomArrayType(WomPairType(x, _)), _) => s"Cannot evaluate 'collect_by_key' on type ${womType.stableName}. Keys must be primitive but got ${x.stableName}.".invalidNel
-        case other => s"Invalid call of 'collect_by_key' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
-      } (coercer = WomArrayType(WomPairType(WomAnyType, WomAnyType)))
-    }
+        case WomArray(womType @ WomArrayType(WomPairType(x, _)), _) =>
+          s"Cannot evaluate 'collect_by_key' on type ${womType.stableName}. Keys must be primitive but got ${x.stableName}.".invalidNel
+        case other =>
+          s"Invalid call of 'collect_by_key' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
+      }(coercer = WomArrayType(WomPairType(WomAnyType, WomAnyType)))
   }
 
   private def resultOfIntVsFloat(functionName: String,
                                  intFunc: (Int, Int) => Int,
-                                 doubleFunc: (Double, Double) => Double)
-                                (value1: EvaluatedValue[_], value2: EvaluatedValue[_]): ErrorOr[EvaluatedValue[WomValue]] = {
+                                 doubleFunc: (Double, Double) => Double
+  )(value1: EvaluatedValue[_], value2: EvaluatedValue[_]): ErrorOr[EvaluatedValue[WomValue]] = {
     val newValue = (value1.value, value2.value) match {
       case (WomInteger(i1), WomInteger(i2)) => WomInteger(intFunc(i1, i2)).validNel
       case (WomInteger(i1), WomFloat(l2)) => WomFloat(doubleFunc(i1.doubleValue, l2)).validNel
       case (WomFloat(l1), WomInteger(i2)) => WomFloat(doubleFunc(l1, i2.doubleValue)).validNel
       case (WomFloat(l1), WomFloat(l2)) => WomFloat(doubleFunc(l1, l2)).validNel
-      case (other1, other2) => s"Invalid arguments to '$functionName':(${other1.typeName}, ${other2.typeName})".invalidNel
+      case (other1, other2) =>
+        s"Invalid arguments to '$functionName':(${other1.typeName}, ${other2.typeName})".invalidNel
     }
     newValue map { v => EvaluatedValue(v, value1.sideEffectFiles ++ value2.sideEffectFiles) }
   }
@@ -124,10 +160,16 @@ object BiscayneValueEvaluators {
     override def evaluateValue(a: Min,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
-      val value1 = expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-      val value2 = expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
+      val value1 =
+        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      val value2 =
+        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
 
       val intFunc = (i1: Int, i2: Int) => Math.min(i1, i2)
       val doubleFunc = (l1: Double, l2: Double) => Math.min(l1, l2)
@@ -140,9 +182,16 @@ object BiscayneValueEvaluators {
     override def evaluateValue(a: Max,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
-      val value1 = expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-      val value2 = expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
+      val value1 =
+        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      val value2 =
+        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
 
       val intFunc = (i1: Int, i2: Int) => Math.max(i1, i2)
       val doubleFunc = (l1: Double, l2: Double) => Math.max(l1, l2)
@@ -155,15 +204,17 @@ object BiscayneValueEvaluators {
     override def evaluateValue(a: Sep,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] = {
-
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] =
       processTwoValidatedValues[WomString, WomArray, WomString](
-        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator),
-        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        ),
+        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
       ) { (sepvalue, arr) =>
         EvaluatedValue(WomString(arr.value.map(v => v.valueString).mkString(sepvalue.value)), Seq.empty).validNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
index 49590a31ba6..338c8676906 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
@@ -24,94 +24,154 @@ package object values {
     override def evaluateValue(a: ExpressionElement,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
       a match {
         // Literals:
-        case a: PrimitiveLiteralExpressionElement => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: NoneLiteralElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-
-        case a: StringLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: StringExpression => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ObjectLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: MapLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ArrayLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: PairLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: PrimitiveLiteralExpressionElement =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: NoneLiteralElement.type =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: StringLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: StringExpression =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ObjectLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: MapLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ArrayLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: PairLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         // Lookups and member accesses:
-        case a: IdentifierLookup => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ExpressionMemberAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: IdentifierMemberAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: IndexAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: IdentifierLookup =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ExpressionMemberAccess =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: IdentifierMemberAccess =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: IndexAccess =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         // Unary operators:
-        case a: UnaryNegation => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: UnaryPlus => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: LogicalNot => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: UnaryNegation =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: UnaryPlus =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LogicalNot =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         // Binary operators (at some point we might want to split these into separate cases):
-        case a: LogicalOr => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: LogicalAnd => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Equals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: NotEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: LessThan => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: LessThanOrEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: GreaterThan => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: GreaterThanOrEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LogicalOr =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LogicalAnd =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Equals =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: NotEquals =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LessThan =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LessThanOrEquals =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: GreaterThan =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: GreaterThanOrEquals =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Add => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Subtract => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Multiply => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Divide => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Remainder => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-
-        case a: TernaryIf => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Subtract =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Multiply =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Divide =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Remainder =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: TernaryIf =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         // Engine functions:
-        case a: StdoutElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: StderrElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-
-        case a: ReadLines => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadTsv => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadMap => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadObject => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadObjects => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadJson => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadInt => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadString => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadFloat => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadBoolean => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteLines => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteTsv => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteMap => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteObject => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteObjects => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteJson => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Range => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Transpose => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Length => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Flatten => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Prefix => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: SelectFirst => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: SelectAll => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Defined => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Floor => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: StdoutElement.type =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: StderrElement.type =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: ReadLines =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadTsv =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadMap =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadObject =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadObjects =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadJson =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadInt =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadString =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadFloat =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadBoolean =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteLines =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteTsv =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteMap =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteObject =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteObjects =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteJson =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Range =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Transpose =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Length =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Flatten =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Prefix =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: SelectFirst =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: SelectAll =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Defined =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Floor =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Ceil => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Round => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Round =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Glob => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Size => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Basename => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Basename =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Zip => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Cross => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Cross =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Sub => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Keys => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: AsMap => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: AsPairs => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: CollectByKey => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: AsMap =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: AsPairs =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: CollectByKey =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Sep => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Min => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
@@ -119,6 +179,5 @@ package object values {
 
         case other => s"Unable to process ${other.toWdlV1}: No evaluateValue exists for that type in WDL 1.1".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/BiscayneParser.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/BiscayneParser.scala
index d0d7ad82f89..5e989e7d235 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/BiscayneParser.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/BiscayneParser.scala
@@ -15,7 +15,7 @@ object StringParser {
   def convert(a: FileStringParserInput): Checked[Ast] = Try {
     val parser = new WdlParser()
     val tokens = parser.lex(a.workflowSource, a.resource)
-    val terminalMap = (tokens.asScala.toVector map {(_, a.workflowSource)}).toMap
+    val terminalMap = (tokens.asScala.toVector map { (_, a.workflowSource) }).toMap
     val syntaxErrorFormatter = WdlBiscayneSyntaxErrorFormatter(terminalMap)
     parser.parse(tokens, syntaxErrorFormatter).toAst.asInstanceOf[Ast]
   }.toChecked
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/WdlBiscayneSyntaxErrorFormatter.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/WdlBiscayneSyntaxErrorFormatter.scala
index fd8c7120c5e..5946eecba25 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/WdlBiscayneSyntaxErrorFormatter.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/parsing/WdlBiscayneSyntaxErrorFormatter.scala
@@ -13,52 +13,56 @@ case class WdlBiscayneSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSo
     case classicTerminal => terminalMap.get(classicTerminal)
   }
 
-  private def line(t: Terminal): String = getTerminal(t).map(_.split("\n")(t.getLine - 1)).getOrElse(s"Cannot highlight line. It was probably in an imported file.")
+  private def line(t: Terminal): String = getTerminal(t)
+    .map(_.split("\n")(t.getLine - 1))
+    .getOrElse(s"Cannot highlight line. It was probably in an imported file.")
 
-  def unexpectedEof(method: String, expected: java.util.List[TerminalIdentifier], nt_rules: java.util.List[String]): String = "ERROR: Unexpected end of file"
+  def unexpectedEof(method: String,
+                    expected: java.util.List[TerminalIdentifier],
+                    nt_rules: java.util.List[String]
+  ): String = "ERROR: Unexpected end of file"
 
-  def excessTokens(method: String, terminal: Terminal): String = {
+  def excessTokens(method: String, terminal: Terminal): String =
     s"""ERROR: Finished parsing without consuming all tokens.
        |
-        |${pointToSource(terminal)}
+       |${pointToSource(terminal)}
      """.stripMargin
-  }
 
-  def unexpectedSymbol(method: String, actual: Terminal, expected: java.util.List[TerminalIdentifier], rule: String): String = {
+  def unexpectedSymbol(method: String,
+                       actual: Terminal,
+                       expected: java.util.List[TerminalIdentifier],
+                       rule: String
+  ): String = {
     val expectedTokens = expected.asScala.map(_.string).mkString(", ")
     s"""ERROR: Unexpected symbol (line ${actual.getLine}, col ${actual.getColumn}) when parsing '$method'.
        |
-        |Expected $expectedTokens, got "${actual.getSourceString}".
+       |Expected $expectedTokens, got "${actual.getSourceString}".
        |
-        |${pointToSource(actual)}
+       |${pointToSource(actual)}
        |
-        |$rule
+       |$rule
      """.stripMargin
   }
 
-  def noMoreTokens(method: String, expecting: TerminalIdentifier, last: Terminal): String = {
+  def noMoreTokens(method: String, expecting: TerminalIdentifier, last: Terminal): String =
     s"""ERROR: No more tokens.  Expecting ${expecting.string}
        |
-        |${pointToSource(last)}
+       |${pointToSource(last)}
      """.stripMargin
-  }
 
-  def invalidTerminal(method: String, invalid: Terminal): String = {
+  def invalidTerminal(method: String, invalid: Terminal): String =
     s"""ERROR: Invalid symbol ID: ${invalid.getId} (${invalid.getTerminalStr})
        |
-        |${pointToSource(invalid)}
+       |${pointToSource(invalid)}
      """.stripMargin
-  }
 
   // TODO: these next two methods won't be called by the parser because there are no lists in the WDL grammar that
   // cause these to be triggered.  Currently the parser is passing in 'null' for the value of 'last' and when that
   // changes, these errors can be made more helpful.
 
-  def missingListItems(method: String, required: Int, found: Int, last: Terminal): String = {
+  def missingListItems(method: String, required: Int, found: Int, last: Terminal): String =
     s"ERROR: $method requires $required items, but only found $found"
-  }
 
-  def missingTerminator(method: String, terminal: TerminalIdentifier, last: Terminal): String = {
+  def missingTerminator(method: String, terminal: TerminalIdentifier, last: Terminal): String =
     s"ERROR: $method requires a terminator after each element"
-  }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala
index f1fd68f86eb..ef1f719a00e 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala
@@ -3,7 +3,12 @@ package wdl.transforms.biscayne
 import common.transforms.CheckedAtoB
 import wdl.transforms.base.wdlom2wom.TaskDefinitionElementToWomTaskDefinition.TaskDefinitionElementToWomInputs
 import wdl.transforms.base.wdlom2wom.WorkflowDefinitionElementToWomWorkflowDefinition.WorkflowDefinitionConvertInputs
-import wdl.transforms.base.wdlom2wom.{FileElementToWomBundle, FileElementToWomBundleInputs, TaskDefinitionElementToWomTaskDefinition, WorkflowDefinitionElementToWomWorkflowDefinition}
+import wdl.transforms.base.wdlom2wom.{
+  FileElementToWomBundle,
+  FileElementToWomBundleInputs,
+  TaskDefinitionElementToWomTaskDefinition,
+  WorkflowDefinitionElementToWomWorkflowDefinition
+}
 import wom.callable.{CallableTaskDefinition, WorkflowDefinition}
 import wom.executable.WomBundle
 import wdl.transforms.biscayne.linking.expression.consumed._
@@ -12,7 +17,11 @@ import wdl.transforms.biscayne.linking.expression.types._
 import wdl.transforms.biscayne.linking.expression.values._
 
 package object wdlom2wom {
-  val taskDefinitionElementToWomTaskDefinition: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition] = CheckedAtoB.fromErrorOr(TaskDefinitionElementToWomTaskDefinition.convert)
-  val workflowDefinitionElementToWomWorkflowDefinition: CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition] = CheckedAtoB.fromErrorOr(WorkflowDefinitionElementToWomWorkflowDefinition.convert)
-  val fileElementToWomBundle: CheckedAtoB[FileElementToWomBundleInputs, WomBundle] = CheckedAtoB.fromCheck(FileElementToWomBundle.convert)
+  val taskDefinitionElementToWomTaskDefinition: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition] =
+    CheckedAtoB.fromErrorOr(TaskDefinitionElementToWomTaskDefinition.convert)
+  val workflowDefinitionElementToWomWorkflowDefinition
+    : CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition] =
+    CheckedAtoB.fromErrorOr(WorkflowDefinitionElementToWomWorkflowDefinition.convert)
+  val fileElementToWomBundle: CheckedAtoB[FileElementToWomBundleInputs, WomBundle] =
+    CheckedAtoB.fromCheck(FileElementToWomBundle.convert)
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
index e5d7a2f9249..4fde60b1efd 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
@@ -27,14 +27,14 @@ object Ast2WdlomSpec {
   val parser = new WdlParser()
 
   def fromString[A](expression: String,
-                    parseFunction: (util.List[WdlParser.Terminal], SyntaxErrorFormatter) => ParseTree)
-                   (implicit converter: CheckedAtoB[GenericAstNode, A]): Checked[A] = {
+                    parseFunction: (util.List[WdlParser.Terminal], SyntaxErrorFormatter) => ParseTree
+  )(implicit converter: CheckedAtoB[GenericAstNode, A]): Checked[A] = {
 
     // Add the "version development" to force the lexer into "main" mode.
     val versionedExpression = "version development-1.1\n" + expression
     // That "version development" means we'll have 2 unwanted tokens at the start of the list, so drop 'em:
     val tokens = parser.lex(versionedExpression, "string").asScala.drop(2).asJava
-    val terminalMap = (tokens.asScala.toVector map {(_, versionedExpression)}).toMap
+    val terminalMap = (tokens.asScala.toVector map { (_, versionedExpression) }).toMap
     val parseTree = parseFunction(tokens, WdlBiscayneSyntaxErrorFormatter(terminalMap))
     (wrapAstNode andThen converter).run(parseTree.toAst)
   }
@@ -42,18 +42,20 @@ object Ast2WdlomSpec {
 
 class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
-
-
   it should "parse a simple expression" in {
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid Add(PrimitiveLiteralExpressionElement(WomInteger(3)), PrimitiveLiteralExpressionElement(WomInteger(3)))
+    expr shouldBeValid Add(PrimitiveLiteralExpressionElement(WomInteger(3)),
+                           PrimitiveLiteralExpressionElement(WomInteger(3))
+    )
   }
 
   it should "parse a map expression" in {
     val str = "{3: 3}"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid MapLiteral(Map(PrimitiveLiteralExpressionElement(WomInteger(3)) -> PrimitiveLiteralExpressionElement(WomInteger(3))))
+    expr shouldBeValid MapLiteral(
+      Map(PrimitiveLiteralExpressionElement(WomInteger(3)) -> PrimitiveLiteralExpressionElement(WomInteger(3)))
+    )
   }
 
   it should "parse a simple meta section" in {
@@ -65,33 +67,34 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   it should "parse a struct element" in {
     val str = "struct Foo { Int five\n Int six }"
     val struct = fromString[StructElement](str, parser.parse_struct)(astNodeToAst andThen astToStructElement)
-    struct shouldBeValid StructElement("Foo", Seq(
-      StructEntryElement("five", PrimitiveTypeElement(WomIntegerType)),
-      StructEntryElement("six", PrimitiveTypeElement(WomIntegerType)))
+    struct shouldBeValid StructElement("Foo",
+                                       Seq(StructEntryElement("five", PrimitiveTypeElement(WomIntegerType)),
+                                           StructEntryElement("six", PrimitiveTypeElement(WomIntegerType))
+                                       )
     )
   }
 
   it should "parse the new as_map function" in {
     val str = "as_map(some_pairs)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid(AsMap(IdentifierLookup("some_pairs")))
+    expr shouldBeValid (AsMap(IdentifierLookup("some_pairs")))
   }
 
   it should "parse the new as_pairs function" in {
     val str = "as_pairs(some_map)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid(AsPairs(IdentifierLookup("some_map")))
+    expr shouldBeValid (AsPairs(IdentifierLookup("some_map")))
   }
 
   it should "parse the new collect_by_key function" in {
     val str = "collect_by_key(some_map)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid(CollectByKey(IdentifierLookup("some_map")))
+    expr shouldBeValid (CollectByKey(IdentifierLookup("some_map")))
   }
 
   it should "parse the new None keyword" in {
     val str = "None"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid(NoneLiteralElement)
+    expr shouldBeValid NoneLiteralElement
   }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/ast2wdlom/WdlFileToWdlomSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/ast2wdlom/WdlFileToWdlomSpec.scala
index 31e09612000..20e940dab39 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/ast2wdlom/WdlFileToWdlomSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/ast2wdlom/WdlFileToWdlomSpec.scala
@@ -12,7 +12,6 @@ import wom.SourceFileLocation
 import wom.types._
 import wom.values.WomInteger
 
-
 class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "WDL File to WDLOM"
@@ -25,12 +24,11 @@ class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   testCases.list.filter(x => x.isRegularFile && x.extension.contains(".wdl")) foreach { testCase =>
-
     val fileName = testCase.name
     val testName = testCase.name.split("\\.").head
 
     val itShouldString = s"create the correct Element structure for $fileName"
-    val testOrIgnore: (=>Any) => Unit = if (fileName.endsWith(".ignored.wdl")) {
+    val testOrIgnore: (=> Any) => Unit = if (fileName.endsWith(".ignored.wdl")) {
       (it should itShouldString).ignore _
     } else {
       (it should itShouldString).in _
@@ -42,7 +40,8 @@ class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
       fileToFileElement.run(testCase) match {
         case Right(actual) => actual shouldBe expected
         case Left(errors) =>
-          val formattedErrors = errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
+          val formattedErrors =
+            errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
           fail(s"Failed to create WDLOM:$formattedErrors")
       }
 
@@ -57,21 +56,23 @@ object WdlFileToWdlomSpec {
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "no_input_no_output",
-          inputsSection = None,
-          graphElements = Set(
-            CallElement("no_inputs", Some("noi1"), Vector.empty, None, Some(SourceFileLocation(4))),
-            CallElement("no_inputs", None, Vector.empty, None, Some(SourceFileLocation(6))),
-            CallElement("no_inputs", Some("noi2"), Vector.empty, None, Some(SourceFileLocation(8))),
-            CallElement("no_inputs", Some("noi3"), Vector.empty, None, Some(SourceFileLocation(10))),
-            CallElement("no_inputs", Some("noi4"), Vector.empty, None, Some(SourceFileLocation(14))),
-            CallElement("no_inputs", Some("noi5"), Vector.empty, None, Some(SourceFileLocation(18)))
-          ),
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3)))
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "no_input_no_output",
+            inputsSection = None,
+            graphElements = Set(
+              CallElement("no_inputs", Some("noi1"), Vector.empty, None, Some(SourceFileLocation(4))),
+              CallElement("no_inputs", None, Vector.empty, None, Some(SourceFileLocation(6))),
+              CallElement("no_inputs", Some("noi2"), Vector.empty, None, Some(SourceFileLocation(8))),
+              CallElement("no_inputs", Some("noi3"), Vector.empty, None, Some(SourceFileLocation(10))),
+              CallElement("no_inputs", Some("noi4"), Vector.empty, None, Some(SourceFileLocation(14))),
+              CallElement("no_inputs", Some("noi5"), Vector.empty, None, Some(SourceFileLocation(18)))
+            ),
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
         ),
         tasks = Vector(
           TaskDefinitionElement(
@@ -79,7 +80,8 @@ object WdlFileToWdlomSpec {
             inputsSection = None,
             declarations = Vector.empty,
             outputsSection = None,
-            commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(StringCommandPartElement("echo Hello World "))))),
+            commandSection =
+              CommandSectionElement(Vector(CommandSectionLine(Vector(StringCommandPartElement("echo Hello World "))))),
             runtimeSection = None,
             metaSection = None,
             parameterMetaSection = None,
@@ -91,122 +93,280 @@ object WdlFileToWdlomSpec {
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "order",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "n", Some(PrimitiveLiteralExpressionElement(WomInteger(4)))),
-            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", Some(StringLiteral("more")))))),
-          graphElements = Set(CallElement("in_n_out", None, Vector.empty, Some(CallBodyElement(Vector(KvPair("total", IdentifierLookup("n")), KvPair("amount", IdentifierLookup("more"))))), Some(SourceFileLocation(19)))),
-          outputsSection = Some(OutputsSectionElement(Vector(
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "out", IdentifierMemberAccess("in_n_out", "out", List.empty))))),
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(14)))
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "order",
+            inputsSection = Some(
+              InputsSectionElement(
+                Vector(
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                          "n",
+                                          Some(PrimitiveLiteralExpressionElement(WomInteger(4)))
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", Some(StringLiteral("more")))
+                )
+              )
+            ),
+            graphElements = Set(
+              CallElement(
+                "in_n_out",
+                None,
+                Vector.empty,
+                Some(
+                  CallBodyElement(
+                    Vector(KvPair("total", IdentifierLookup("n")), KvPair("amount", IdentifierLookup("more")))
+                  )
+                ),
+                Some(SourceFileLocation(19))
+              )
+            ),
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(
+                  OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                           "out",
+                                           IdentifierMemberAccess("in_n_out", "out", List.empty)
+                  )
+                )
+              )
+            ),
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(14))
+          )
         ),
-        tasks = Vector(TaskDefinitionElement(
-          name = "in_n_out",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "total", None),
-            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "amount", None)))),
-          declarations = Vector.empty,
-          outputsSection = Some(OutputsSectionElement(Vector(
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "out", Add(ReadInt(StdoutElement), PrimitiveLiteralExpressionElement(WomInteger(1))))))),
-          commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(
-            StringCommandPartElement("echo "),
-            PlaceholderCommandPartElement(IdentifierLookup("total"), PlaceholderAttributeSet.empty),
-            StringCommandPartElement(" ")
-          )))),
-          runtimeSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3))
-        ))
+        tasks = Vector(
+          TaskDefinitionElement(
+            name = "in_n_out",
+            inputsSection = Some(
+              InputsSectionElement(
+                Vector(InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "total", None),
+                       InputDeclarationElement(PrimitiveTypeElement(WomStringType), "amount", None)
+                )
+              )
+            ),
+            declarations = Vector.empty,
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(
+                  OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                           "out",
+                                           Add(ReadInt(StdoutElement), PrimitiveLiteralExpressionElement(WomInteger(1)))
+                  )
+                )
+              )
+            ),
+            commandSection = CommandSectionElement(
+              Vector(
+                CommandSectionLine(
+                  Vector(
+                    StringCommandPartElement("echo "),
+                    PlaceholderCommandPartElement(IdentifierLookup("total"), PlaceholderAttributeSet.empty),
+                    StringCommandPartElement(" ")
+                  )
+                )
+              )
+            ),
+            runtimeSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        )
       ),
     "afters" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "afters",
-          inputsSection = None,
-          graphElements = Set(
-            CallElement("foo", None, Vector.empty, Some(CallBodyElement(Vector(KvPair("i", ExpressionElement.PrimitiveLiteralExpressionElement(WomInteger(5)))))),
-                        Some(SourceFileLocation(4))),
-            CallElement("foo", Some("foo2"), Vector("foo"), Some(CallBodyElement(Vector(KvPair("i", ExpressionElement.PrimitiveLiteralExpressionElement(WomInteger(6)))))),
-                        Some(SourceFileLocation(5)))
-          ),
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3)))
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "afters",
+            inputsSection = None,
+            graphElements = Set(
+              CallElement(
+                "foo",
+                None,
+                Vector.empty,
+                Some(
+                  CallBodyElement(
+                    Vector(KvPair("i", ExpressionElement.PrimitiveLiteralExpressionElement(WomInteger(5))))
+                  )
+                ),
+                Some(SourceFileLocation(4))
+              ),
+              CallElement(
+                "foo",
+                Some("foo2"),
+                Vector("foo"),
+                Some(
+                  CallBodyElement(
+                    Vector(KvPair("i", ExpressionElement.PrimitiveLiteralExpressionElement(WomInteger(6))))
+                  )
+                ),
+                Some(SourceFileLocation(5))
+              )
+            ),
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
         ),
-        tasks = Vector(TaskDefinitionElement(
-          name = "foo",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", None)))),
-          declarations = Vector.empty,
-          outputsSection = None,
-          commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(
-            StringCommandPartElement("cat \"hello "),
-            PlaceholderCommandPartElement(IdentifierLookup("i"), PlaceholderAttributeSet.empty),
-            StringCommandPartElement("\" > /tmp/helloFile")
-          )))),
-          runtimeSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(8))
-        ))
+        tasks = Vector(
+          TaskDefinitionElement(
+            name = "foo",
+            inputsSection = Some(
+              InputsSectionElement(Vector(InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", None)))
+            ),
+            declarations = Vector.empty,
+            outputsSection = None,
+            commandSection = CommandSectionElement(
+              Vector(
+                CommandSectionLine(
+                  Vector(
+                    StringCommandPartElement("cat \"hello "),
+                    PlaceholderCommandPartElement(IdentifierLookup("i"), PlaceholderAttributeSet.empty),
+                    StringCommandPartElement("\" > /tmp/helloFile")
+                  )
+                )
+              )
+            ),
+            runtimeSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(8))
+          )
+        )
       ),
     "biscayne_escaping" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "escapes",
-          inputsSection = None,
-          graphElements = Set(
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"backslash",StringExpression(Vector(StringLiteral(" "), BackslashEscape, StringLiteral(" ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"n",StringExpression(Vector(StringLiteral(" "), NewlineEscape, StringLiteral(" ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"t",StringExpression(Vector(StringLiteral(" "), TabEscape, StringLiteral(" ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q1",StringExpression(Vector(StringLiteral("leading text "), DoubleQuoteEscape, StringLiteral(" trailing text")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q2",StringLiteral("\"")),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q3",StringExpression(Vector(StringLiteral("  "), DoubleQuoteEscape, StringLiteral("  ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q4",StringExpression(Vector(StringLiteral("leading text "), SingleQuoteEscape, StringLiteral(" trailing text")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q5",StringLiteral("'")),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q6",StringExpression(Vector(StringLiteral("  "), SingleQuoteEscape, StringLiteral("  ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq1",StringExpression(Vector(StringLiteral("leading text "), DoubleQuoteEscape, StringLiteral(" trailing text")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq2",StringLiteral("\"")),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq3",StringExpression(Vector(StringLiteral("  "), DoubleQuoteEscape, StringLiteral("  ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq4",StringExpression(Vector(StringLiteral("leading text "), SingleQuoteEscape, StringLiteral(" trailing text")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq5",StringLiteral("'")),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq6",StringExpression(Vector(StringLiteral("  "), SingleQuoteEscape, StringLiteral("  ")))),
-            IntermediateValueDeclarationElement(
-              PrimitiveTypeElement(WomStringType),
-              "octal_hello",
-              StringExpression(Vector(UnicodeCharacterEscape(104), UnicodeCharacterEscape(101), UnicodeCharacterEscape(108), UnicodeCharacterEscape(108), UnicodeCharacterEscape(111)))
-            ),
-            IntermediateValueDeclarationElement(
-              PrimitiveTypeElement(WomStringType),
-              "hex_hello",
-              StringExpression(Vector(UnicodeCharacterEscape(104), UnicodeCharacterEscape(101), UnicodeCharacterEscape(108), UnicodeCharacterEscape(108), UnicodeCharacterEscape(111)))
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "escapes",
+            inputsSection = None,
+            graphElements = Set(
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "backslash",
+                StringExpression(Vector(StringLiteral(" "), BackslashEscape, StringLiteral(" ")))
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "n",
+                StringExpression(Vector(StringLiteral(" "), NewlineEscape, StringLiteral(" ")))
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "t",
+                StringExpression(Vector(StringLiteral(" "), TabEscape, StringLiteral(" ")))
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                                  "q1",
+                                                  StringExpression(
+                                                    Vector(StringLiteral("leading text "),
+                                                           DoubleQuoteEscape,
+                                                           StringLiteral(" trailing text")
+                                                    )
+                                                  )
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "q2", StringLiteral("\"")),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "q3",
+                StringExpression(Vector(StringLiteral("  "), DoubleQuoteEscape, StringLiteral("  ")))
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                                  "q4",
+                                                  StringExpression(
+                                                    Vector(StringLiteral("leading text "),
+                                                           SingleQuoteEscape,
+                                                           StringLiteral(" trailing text")
+                                                    )
+                                                  )
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "q5", StringLiteral("'")),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "q6",
+                StringExpression(Vector(StringLiteral("  "), SingleQuoteEscape, StringLiteral("  ")))
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                                  "sq1",
+                                                  StringExpression(
+                                                    Vector(StringLiteral("leading text "),
+                                                           DoubleQuoteEscape,
+                                                           StringLiteral(" trailing text")
+                                                    )
+                                                  )
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "sq2", StringLiteral("\"")),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "sq3",
+                StringExpression(Vector(StringLiteral("  "), DoubleQuoteEscape, StringLiteral("  ")))
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                                  "sq4",
+                                                  StringExpression(
+                                                    Vector(StringLiteral("leading text "),
+                                                           SingleQuoteEscape,
+                                                           StringLiteral(" trailing text")
+                                                    )
+                                                  )
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "sq5", StringLiteral("'")),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "sq6",
+                StringExpression(Vector(StringLiteral("  "), SingleQuoteEscape, StringLiteral("  ")))
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "octal_hello",
+                StringExpression(
+                  Vector(UnicodeCharacterEscape(104),
+                         UnicodeCharacterEscape(101),
+                         UnicodeCharacterEscape(108),
+                         UnicodeCharacterEscape(108),
+                         UnicodeCharacterEscape(111)
+                  )
+                )
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "hex_hello",
+                StringExpression(
+                  Vector(UnicodeCharacterEscape(104),
+                         UnicodeCharacterEscape(101),
+                         UnicodeCharacterEscape(108),
+                         UnicodeCharacterEscape(108),
+                         UnicodeCharacterEscape(111)
+                  )
+                )
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "unicode_hello",
+                StringExpression(
+                  Vector(
+                    UnicodeCharacterEscape(104),
+                    UnicodeCharacterEscape(101),
+                    UnicodeCharacterEscape(108),
+                    UnicodeCharacterEscape(108),
+                    UnicodeCharacterEscape(111)
+                  )
+                )
+              )
             ),
-            IntermediateValueDeclarationElement(
-              PrimitiveTypeElement(WomStringType),
-              "unicode_hello",
-              StringExpression(Vector(
-                UnicodeCharacterEscape(104),
-                UnicodeCharacterEscape(101),
-                UnicodeCharacterEscape(108),
-                UnicodeCharacterEscape(108),
-                UnicodeCharacterEscape(111)
-              ))
-            )
-          ),
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3))
-        )),
-        tasks = Vector.empty)
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        ),
+        tasks = Vector.empty
+      )
   )
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
index 2e1e9a8cb52..11ca72b3a49 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
@@ -17,8 +17,8 @@ class BiscayneExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.expressionConsumedValueHooks should be(Set.empty)
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set.empty)
     }
   }
 
@@ -26,8 +26,8 @@ class BiscayneExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     val str = "3 + three"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("three")))
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("three")))
     }
   }
 
@@ -35,8 +35,8 @@ class BiscayneExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     val str = "as_map(my_task.out)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedCallOutputOrIdentifierAndMemberAccessHook("my_task", "out")))
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedCallOutputOrIdentifierAndMemberAccessHook("my_task", "out")))
     }
   }
 
@@ -44,8 +44,8 @@ class BiscayneExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     val str = "as_pairs(as_map(my_task.out))"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedCallOutputOrIdentifierAndMemberAccessHook("my_task", "out")))
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedCallOutputOrIdentifierAndMemberAccessHook("my_task", "out")))
     }
   }
 
@@ -53,8 +53,8 @@ class BiscayneExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     val str = """ sep(my_separator, ["a", "b", c]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_separator"), UnlinkedIdentifierHook("c")))
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_separator"), UnlinkedIdentifierHook("c")))
     }
   }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
index 35ffa84ca1b..59ebfd18dc4 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
@@ -18,8 +18,8 @@ class BiscayneFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomIntegerType) shouldBeValid Set.empty
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomIntegerType) shouldBeValid Set.empty
     }
   }
 
@@ -27,8 +27,11 @@ class BiscayneFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """as_pairs(read_map("my_map.txt"))"""
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomArrayType(WomPairType(WomStringType, WomStringType))) shouldBeValid Set(WomSingleFile("my_map.txt"))
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty,
+                                     NoIoFunctionSet,
+                                     WomArrayType(WomPairType(WomStringType, WomStringType))
+      ) shouldBeValid Set(WomSingleFile("my_map.txt"))
     }
   }
 
@@ -36,8 +39,10 @@ class BiscayneFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """ sep(' ', read_lines("foo.txt")) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(WomSingleFile("foo.txt"))
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
     }
   }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
index a2b7d60a216..0593605bb2b 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
@@ -15,8 +15,8 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateType(Map.empty) shouldBeValid WomIntegerType
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomIntegerType
     }
   }
 
@@ -24,8 +24,8 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """as_map([(1,2), (3,4)])"""
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateType(Map.empty) shouldBeValid WomMapType(WomIntegerType, WomIntegerType)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomMapType(WomIntegerType, WomIntegerType)
     }
   }
 
@@ -33,8 +33,8 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """as_pairs({ "one": 1, "two": 2, "three": 3 })"""
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomPairType(WomStringType, WomIntegerType))
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomPairType(WomStringType, WomIntegerType))
     }
   }
 
@@ -42,8 +42,8 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """ sep(' ', ["a", "b", "c"]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateType(Map.empty) shouldBeValid WomStringType
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomStringType
     }
   }
 
@@ -51,8 +51,8 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """ sep(' ', prefix("-i ", ["a", "b", "c"])) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateType(Map.empty) shouldBeValid WomStringType
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomStringType
     }
   }
 
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
index 8cab2b627f9..53660a407d9 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
@@ -23,8 +23,8 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomInteger(6), Seq.empty)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomInteger(6), Seq.empty)
     }
   }
 
@@ -32,14 +32,16 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     val str = """ as_map( [("x", 1), ("y", 2), ("z", 3)] ) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    val expectedMap: WomMap = WomMap(Map (
-      WomString("x") -> WomInteger(1),
-      WomString("y") -> WomInteger(2),
-      WomString("z") -> WomInteger(3)
-    ))
+    val expectedMap: WomMap = WomMap(
+      Map(
+        WomString("x") -> WomInteger(1),
+        WomString("y") -> WomInteger(2),
+        WomString("z") -> WomInteger(3)
+      )
+    )
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
     }
   }
 
@@ -50,14 +52,16 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       val expr = fromString[ExpressionElement](str, parser.parse_e)
 
       val inputs = Map("three" -> WomString("three"))
-      val expectedPairs: WomArray = WomArray(Seq(
-        WomPair(WomInteger(1), WomString("one")),
-        WomPair(WomInteger(2), WomString("two")),
-        WomPair(WomInteger(3), WomString("three"))
-      ))
-
-      expr.shouldBeValidPF {
-        case e => e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPairs, Seq.empty)
+      val expectedPairs: WomArray = WomArray(
+        Seq(
+          WomPair(WomInteger(1), WomString("one")),
+          WomPair(WomInteger(2), WomString("two")),
+          WomPair(WomInteger(3), WomString("three"))
+        )
+      )
+
+      expr.shouldBeValidPF { case e =>
+        e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPairs, Seq.empty)
       }
       ()
     }
@@ -73,16 +77,18 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       val str = """ as_pairs(as_map(echo_me)) """
       val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-      val expectedPairs: WomArray = WomArray(Seq(
-        WomPair(WomInteger(1), WomString("one")),
-        WomPair(WomInteger(2), WomString("two")),
-        WomPair(WomInteger(3), WomString("three"))
-      ))
+      val expectedPairs: WomArray = WomArray(
+        Seq(
+          WomPair(WomInteger(1), WomString("one")),
+          WomPair(WomInteger(2), WomString("two")),
+          WomPair(WomInteger(3), WomString("three"))
+        )
+      )
 
       val inputs = Map("echo_me" -> expectedPairs)
 
-      expr.shouldBeValidPF {
-        case e => e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPairs, Seq.empty)
+      expr.shouldBeValidPF { case e =>
+        e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPairs, Seq.empty)
       }
       ()
     }
@@ -95,8 +101,11 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       val str = """ as_map( [("x", 1), ("y", 2), ("x", 3)] ) """
       val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-      expr.shouldBeValidPF {
-        case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None).shouldBeInvalid("""Cannot evaluate 'as_map' with duplicated keys: keys can only appear once but "x" appeared 2 times.""")
+      expr.shouldBeValidPF { case e =>
+        e.evaluateValue(Map.empty, NoIoFunctionSet, None)
+          .shouldBeInvalid(
+            """Cannot evaluate 'as_map' with duplicated keys: keys can only appear once but "x" appeared 2 times."""
+          )
       }
       ()
     }
@@ -109,13 +118,15 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       val str = """ collect_by_key( [("x", 1), ("y", 2), ("x", 3)] ) """
       val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-      val expectedMap: WomMap = WomMap(Map(
-        WomString("x") -> WomArray(Seq(WomInteger(1), WomInteger(3))),
-        WomString("y") -> WomArray(Seq(WomInteger(2)))
-      ))
+      val expectedMap: WomMap = WomMap(
+        Map(
+          WomString("x") -> WomArray(Seq(WomInteger(1), WomInteger(3))),
+          WomString("y") -> WomArray(Seq(WomInteger(2)))
+        )
+      )
 
-      expr.shouldBeValidPF {
-        case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
+      expr.shouldBeValidPF { case e =>
+        e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
       }
       ()
     }
@@ -129,13 +140,16 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     )
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    val expectedMap: WomMap = WomMap(WomMapType(WomStringType, WomOptionalType(WomStringType)), Map (
-      WomString("i") -> WomOptionalValue(WomStringType, Some(WomString("1"))),
-      WomString("s") -> WomOptionalValue(WomStringType, Some(WomString("two")))
-    ))
+    val expectedMap: WomMap = WomMap(
+      WomMapType(WomStringType, WomOptionalType(WomStringType)),
+      Map(
+        WomString("i") -> WomOptionalValue(WomStringType, Some(WomString("1"))),
+        WomString("s") -> WomOptionalValue(WomStringType, Some(WomString("two")))
+      )
+    )
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
     }
   }
 
@@ -158,8 +172,8 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         val expectedEvaluation = WomString(expected)
         val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-        expr.shouldBeValidPF {
-          case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedEvaluation, Seq.empty)
+        expr.shouldBeValidPF { case e =>
+          e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedEvaluation, Seq.empty)
         }
       }
     }
@@ -171,8 +185,8 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
 
     val expectedString: WomString = WomString("a b c")
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
     }
   }
 
@@ -182,8 +196,8 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
 
     val expectedString: WomString = WomString("-i a -i b -i c")
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
     }
   }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
index edcd6204f6c..ba331383e45 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
@@ -3,7 +3,7 @@ package wdl.transforms.cascades.ast2wdlom
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
 import wdl.model.draft3.elements.ExpressionElement
-import wdl.model.draft3.elements.ExpressionElement.{Keys, AsMap, AsPairs, CollectByKey, Min, Max, Sep}
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep}
 import wdl.transforms.base.ast2wdlom.AstNodeToExpressionElement
 
 object AstToNewExpressionElements {
@@ -12,15 +12,20 @@ object AstToNewExpressionElements {
     "as_map" -> AstNodeToExpressionElement.validateOneParamEngineFunction(AsMap, "as_map"),
     "as_pairs" -> AstNodeToExpressionElement.validateOneParamEngineFunction(AsPairs, "as_pairs"),
     "collect_by_key" -> AstNodeToExpressionElement.validateOneParamEngineFunction(CollectByKey, "collect_by_key"),
-
     "min" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Min, "min"),
     "max" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Max, "max"),
-
     "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
-
-    "read_object" -> (_ => "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel),
-    "read_objects" -> (_ => "read_objects is no longer available in this WDL version. Consider using read_json instead".invalidNel),
-    "write_object" -> (_ => "write_object is no longer available in this WDL version. Consider using write_json instead".invalidNel),
-    "write_objects" -> (_ => "write_objects is no longer available in this WDL version. Consider using write_json instead".invalidNel),
+    "read_object" -> (_ =>
+      "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel
+    ),
+    "read_objects" -> (_ =>
+      "read_objects is no longer available in this WDL version. Consider using read_json instead".invalidNel
+    ),
+    "write_object" -> (_ =>
+      "write_object is no longer available in this WDL version. Consider using write_json instead".invalidNel
+    ),
+    "write_objects" -> (_ =>
+      "write_objects is no longer available in this WDL version. Consider using write_json instead".invalidNel
+    )
   )
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/CascadesGenericAstNode.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/CascadesGenericAstNode.scala
index a503ca897be..1eef5176a24 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/CascadesGenericAstNode.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/CascadesGenericAstNode.scala
@@ -5,7 +5,8 @@ import wdl.transforms.base.ast2wdlom.{GenericAst, GenericAstList, GenericAstNode
 import scala.jdk.CollectionConverters._
 
 case class cascadesGenericAst(ast: Ast) extends GenericAst {
-  override def getAttribute(attr: String): GenericAstNode = Option(ast.getAttribute(attr)).map(cascadesGenericAstNode.apply).orNull
+  override def getAttribute(attr: String): GenericAstNode =
+    Option(ast.getAttribute(attr)).map(cascadesGenericAstNode.apply).orNull
   override def getAttributes: Map[String, GenericAstNode] = ast.getAttributes.asScala.toMap collect {
     case (key, value) if value != null => key -> cascadesGenericAstNode(value)
   }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/ast2wdlom.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/ast2wdlom.scala
index 3bda86048ef..5ab621ed5b4 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/ast2wdlom.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/ast2wdlom.scala
@@ -14,50 +14,81 @@ import wom.types.WomUnlistedDirectoryType
 
 package object ast2wdlom {
 
-  val wrapAst: CheckedAtoB[Ast, GenericAst] = CheckedAtoB.fromCheck { a => cascadesGenericAst(a).validNelCheck }
-  val wrapAstNode: CheckedAtoB[AstNode, GenericAstNode] = CheckedAtoB.fromCheck { a => cascadesGenericAstNode(a).validNelCheck }
+  val wrapAst: CheckedAtoB[Ast, GenericAst] = CheckedAtoB.fromCheck(a => cascadesGenericAst(a).validNelCheck)
+  val wrapAstNode: CheckedAtoB[AstNode, GenericAstNode] = CheckedAtoB.fromCheck { a =>
+    cascadesGenericAstNode(a).validNelCheck
+  }
 
-  implicit val astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString] = AstNodeToStaticString.astNodeToStaticStringElement()
+  implicit val astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString] =
+    AstNodeToStaticString.astNodeToStaticStringElement()
 
   // meta sections
   implicit val astNodeToMetaKvPair: CheckedAtoB[GenericAstNode, MetaKvPair] = AstNodeToMetaKvPair.astNodeToMetaKvPair
-  implicit val astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement] = astNodeToAst andThen AstToMetaSectionElement.astToMetaSectionElement
-  implicit val astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement] = astNodeToAst andThen AstToParameterMetaSectionElement.astToParameterMetaSectionElement
+  implicit val astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement] =
+    astNodeToAst andThen AstToMetaSectionElement.astToMetaSectionElement
+  implicit val astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement] =
+    astNodeToAst andThen AstToParameterMetaSectionElement.astToParameterMetaSectionElement
 
-  implicit val astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement] = AstNodeToExpressionElement.astNodeToExpressionElement(customEngineFunctionMakers = AstToNewExpressionElements.newcascadesEngineFunctionMakers)
-  implicit val astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair] = AstNodeToKvPair.astNodeToKvPair(astNodeToExpressionElement)
+  implicit val astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement] =
+    AstNodeToExpressionElement.astNodeToExpressionElement(customEngineFunctionMakers =
+      AstToNewExpressionElements.newcascadesEngineFunctionMakers
+    )
+  implicit val astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair] =
+    AstNodeToKvPair.astNodeToKvPair(astNodeToExpressionElement)
 
-  implicit val astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement] = AstNodeToTypeElement.astNodeToTypeElement(Map("Directory" -> WomUnlistedDirectoryType))
+  implicit val astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement] =
+    AstNodeToTypeElement.astNodeToTypeElement(Map("Directory" -> WomUnlistedDirectoryType))
   implicit val astToStructElement: CheckedAtoB[GenericAst, StructElement] = AstToStructElement.astToStructElement
-  implicit val astNodeToImportElement: CheckedAtoB[GenericAstNode, ImportElement] = astNodeToAst andThen AstToImportElement.astToImportElement
+  implicit val astNodeToImportElement: CheckedAtoB[GenericAstNode, ImportElement] =
+    astNodeToAst andThen AstToImportElement.astToImportElement
 
-  implicit val astNodeToInputDeclarationElement: CheckedAtoB[GenericAstNode, InputDeclarationElement] = astNodeToAst andThen AstToInputDeclarationElement.astToInputDeclarationElement
-  implicit val astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement] = astNodeToAst andThen AstToInputsSectionElement.astToInputsSectionElement
+  implicit val astNodeToInputDeclarationElement: CheckedAtoB[GenericAstNode, InputDeclarationElement] =
+    astNodeToAst andThen AstToInputDeclarationElement.astToInputDeclarationElement
+  implicit val astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement] =
+    astNodeToAst andThen AstToInputsSectionElement.astToInputsSectionElement
 
-  implicit val astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent] = astNodeToAst andThen AstToDeclarationContent.astToDeclarationContent
-  implicit val astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement] = astNodeToAst andThen AstToOutputsSectionElement.astToOutputSectionElement
+  implicit val astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent] =
+    astNodeToAst andThen AstToDeclarationContent.astToDeclarationContent
+  implicit val astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement] =
+    astNodeToAst andThen AstToOutputsSectionElement.astToOutputSectionElement
 
   val astToWorkflowGraphNodeElementConverterMaker = new AstToWorkflowGraphNodeElementConverterMaker()
-  implicit val astNodeToGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement] = astNodeToAst andThen astToWorkflowGraphNodeElementConverterMaker.converter
-  implicit val astNodeToCallElement: CheckedAtoB[GenericAstNode, CallElement] = astNodeToAst andThen AstToCallElement.astToCallElement
-  implicit val astNodeToScatterElement: CheckedAtoB[GenericAstNode, ScatterElement] = astNodeToAst andThen AstToScatterElement.astToScatterElement
-  implicit val astNodeToIfElement: CheckedAtoB[GenericAstNode, IfElement] = astNodeToAst andThen AstToIfElement.astToIfElement
+  implicit val astNodeToGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement] =
+    astNodeToAst andThen astToWorkflowGraphNodeElementConverterMaker.converter
+  implicit val astNodeToCallElement: CheckedAtoB[GenericAstNode, CallElement] =
+    astNodeToAst andThen AstToCallElement.astToCallElement
+  implicit val astNodeToScatterElement: CheckedAtoB[GenericAstNode, ScatterElement] =
+    astNodeToAst andThen AstToScatterElement.astToScatterElement
+  implicit val astNodeToIfElement: CheckedAtoB[GenericAstNode, IfElement] =
+    astNodeToAst andThen AstToIfElement.astToIfElement
   astToWorkflowGraphNodeElementConverterMaker.astNodeToScatterElement = Some(astNodeToScatterElement)
   astToWorkflowGraphNodeElementConverterMaker.astNodeToIfElement = Some(astNodeToIfElement)
   astToWorkflowGraphNodeElementConverterMaker.astNodeToCallElement = Some(astNodeToCallElement)
   astToWorkflowGraphNodeElementConverterMaker.astNodeToDeclarationContent = Some(astNodeToDeclarationContent)
 
-  implicit val astNodeToWorkflowBodyElement: CheckedAtoB[GenericAstNode, WorkflowBodyElement] = astNodeToAst andThen AstToWorkflowBodyElement.astToWorkflowBodyElement
-  implicit val astToWorkflowDefinitionElement: CheckedAtoB[GenericAst, WorkflowDefinitionElement] = AstToWorkflowDefinitionElement.astToWorkflowDefinitionElement
+  implicit val astNodeToWorkflowBodyElement: CheckedAtoB[GenericAstNode, WorkflowBodyElement] =
+    astNodeToAst andThen AstToWorkflowBodyElement.astToWorkflowBodyElement
+  implicit val astToWorkflowDefinitionElement: CheckedAtoB[GenericAst, WorkflowDefinitionElement] =
+    AstToWorkflowDefinitionElement.astToWorkflowDefinitionElement
 
-  implicit val astNodeToPlaceholderAttributeSet: CheckedAtoB[GenericAstNode, PlaceholderAttributeSet] = astNodeToAstList andThen AstNodeToPlaceholderAttributeSet.attributeKvpConverter
-  implicit val astNodeToCommandPartElement: CheckedAtoB[GenericAstNode, CommandPartElement] = AstNodeToCommandPartElement.astNodeToCommandPartElement
-  implicit val astNodeToCommandSectionElement: CheckedAtoB[GenericAstNode, CommandSectionElement] = astNodeToAst andThen AstToCommandSectionElement.astToCommandSectionElement
-  implicit val astNodeToRuntimeAttributesSectionElement: CheckedAtoB[GenericAstNode, RuntimeAttributesSectionElement] = astNodeToAst andThen AstToRuntimeAttributesSectionElement.astToRuntimeSectionElement
-  implicit val astNodeToTaskSectionElement: CheckedAtoB[GenericAstNode, TaskSectionElement] = astNodeToAst andThen AstToTaskSectionElement.astToTaskSectionElement
-  implicit val astToTaskDefinitionElement: CheckedAtoB[GenericAst, TaskDefinitionElement] = AstToTaskDefinitionElement.astToTaskDefinitionElement
+  implicit val astNodeToPlaceholderAttributeSet: CheckedAtoB[GenericAstNode, PlaceholderAttributeSet] =
+    astNodeToAstList andThen AstNodeToPlaceholderAttributeSet.attributeKvpConverter
+  implicit val astNodeToCommandPartElement: CheckedAtoB[GenericAstNode, CommandPartElement] =
+    AstNodeToCommandPartElement.astNodeToCommandPartElement
+  implicit val astNodeToCommandSectionElement: CheckedAtoB[GenericAstNode, CommandSectionElement] =
+    astNodeToAst andThen AstToCommandSectionElement.astToCommandSectionElement
+  implicit val astNodeToRuntimeAttributesSectionElement: CheckedAtoB[GenericAstNode, RuntimeAttributesSectionElement] =
+    astNodeToAst andThen AstToRuntimeAttributesSectionElement.astToRuntimeSectionElement
+  implicit val astNodeToTaskSectionElement: CheckedAtoB[GenericAstNode, TaskSectionElement] =
+    astNodeToAst andThen AstToTaskSectionElement.astToTaskSectionElement
+  implicit val astToTaskDefinitionElement: CheckedAtoB[GenericAst, TaskDefinitionElement] =
+    AstToTaskDefinitionElement.astToTaskDefinitionElement
 
-  implicit val astToFileBodyElement: CheckedAtoB[GenericAstNode, FileBodyElement] = astNodeToAst andThen AstToFileBodyElement.astToFileBodyElement(astToWorkflowDefinitionElement, astToTaskDefinitionElement, astToStructElement)
+  implicit val astToFileBodyElement: CheckedAtoB[GenericAstNode, FileBodyElement] =
+    astNodeToAst andThen AstToFileBodyElement.astToFileBodyElement(astToWorkflowDefinitionElement,
+                                                                   astToTaskDefinitionElement,
+                                                                   astToStructElement
+    )
 
   implicit val astToFileElement: CheckedAtoB[GenericAst, FileElement] = AstToFileElement.astToFileElement
   implicit val fileToFileElement: CheckedAtoB[File, FileElement] = fileToAst andThen wrapAst andThen astToFileElement
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
index 196005fdb84..b4e6c5be1d6 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
@@ -6,52 +6,64 @@ import wdl.model.draft3.graph.{ExpressionValueConsumer, UnlinkedConsumedValueHoo
 
 object cascadesExpressionValueConsumers {
   implicit val keysExpressionValueConsumer: ExpressionValueConsumer[Keys] = new ExpressionValueConsumer[Keys] {
-    override def expressionConsumedValueHooks(a: Keys)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: Keys)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
-    }
   }
 
   implicit val asMapExpressionValueConsumer: ExpressionValueConsumer[AsMap] = new ExpressionValueConsumer[AsMap] {
-    override def expressionConsumedValueHooks(a: AsMap)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: AsMap)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
-    }
   }
 
   implicit val asPairsExpressionValueConsumer: ExpressionValueConsumer[AsPairs] = new ExpressionValueConsumer[AsPairs] {
-    override def expressionConsumedValueHooks(a: AsPairs)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: AsPairs)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
-    }
   }
 
-  implicit val collectByKeyExpressionValueConsumer: ExpressionValueConsumer[CollectByKey] = new ExpressionValueConsumer[CollectByKey] {
-    override def expressionConsumedValueHooks(a: CollectByKey)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
-      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+  implicit val collectByKeyExpressionValueConsumer: ExpressionValueConsumer[CollectByKey] =
+    new ExpressionValueConsumer[CollectByKey] {
+      override def expressionConsumedValueHooks(a: CollectByKey)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
     }
-  }
 
   implicit val minExpressionValueConsumer: ExpressionValueConsumer[Min] = new ExpressionValueConsumer[Min] {
-    override def expressionConsumedValueHooks(a: Min)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
-      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++ expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
-    }
+    override def expressionConsumedValueHooks(
+      a: Min
+    )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++ expressionValueConsumer
+        .expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
   implicit val maxExpressionValueConsumer: ExpressionValueConsumer[Max] = new ExpressionValueConsumer[Max] {
-    override def expressionConsumedValueHooks(a: Max)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
-      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++ expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
-    }
+    override def expressionConsumedValueHooks(
+      a: Max
+    )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++ expressionValueConsumer
+        .expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
   implicit val sepExpressionValueConsumer: ExpressionValueConsumer[Sep] = new ExpressionValueConsumer[Sep] {
-    override def expressionConsumedValueHooks(a: Sep)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: Sep)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++
         expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
-    }
   }
 
-  implicit val noneLiteralExpressionValueConsumer: ExpressionValueConsumer[NoneLiteralElement.type] = new ExpressionValueConsumer[NoneLiteralElement.type] {
-    override def expressionConsumedValueHooks(a: NoneLiteralElement.type)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
-      // None literals consume no values:
-      Set.empty[UnlinkedConsumedValueHook]
+  implicit val noneLiteralExpressionValueConsumer: ExpressionValueConsumer[NoneLiteralElement.type] =
+    new ExpressionValueConsumer[NoneLiteralElement.type] {
+      override def expressionConsumedValueHooks(a: NoneLiteralElement.type)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        // None literals consume no values:
+        Set.empty[UnlinkedConsumedValueHook]
     }
-  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
index d689d2a175a..af54bbbd6a6 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
@@ -14,97 +14,101 @@ import wdl.transforms.cascades.linking.expression.consumed.cascadesExpressionVal
 
 package object consumed {
 
-  implicit val expressionElementUnlinkedValueConsumer: ExpressionValueConsumer[ExpressionElement] = new ExpressionValueConsumer[ExpressionElement] {
-    override def expressionConsumedValueHooks(a: ExpressionElement)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = a match {
-      case _: PrimitiveLiteralExpressionElement | _: StringLiteral => Set.empty[UnlinkedConsumedValueHook]
-      case a: NoneLiteralElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: StringExpression => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ObjectLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: PairLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ArrayLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: MapLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      // Member access:
-      case a: IdentifierLookup => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: IdentifierMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ExpressionMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: IndexAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      // Unary operators:
-      case a: UnaryNegation => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: UnaryPlus => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LogicalNot => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      // Binary operators:
-      case a: LogicalOr => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LogicalAnd => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Equals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: NotEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LessThan => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LessThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: GreaterThan => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: GreaterThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Add => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Subtract => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Multiply => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Divide => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Remainder => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: TernaryIf => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      // Engine functions:
-      case a: StdoutElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: StderrElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: ReadLines => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadMap => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadObject => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadJson => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadInt => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadString => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadFloat => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadBoolean => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteLines => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteMap => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteObject => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteJson => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Range => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Transpose => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Length => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Flatten => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Prefix => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: SelectFirst => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: SelectAll => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Defined => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Floor => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Ceil => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Round => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Glob => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: Size => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Basename => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: Zip => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Cross => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case a: Sub => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      // New WDL biscayne expressions:
-      case a: Keys => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: AsMap => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: AsPairs => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: CollectByKey => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Sep => sepExpressionValueConsumer.expressionConsumedValueHooks(a)(expressionValueConsumer)
-
-      case a: Min => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Max => a.expressionConsumedValueHooks(expressionValueConsumer)
-
-      case other => throw new Exception(s"Cannot generate consumed values for ExpressionElement ${other.getClass.getSimpleName}")
+  implicit val expressionElementUnlinkedValueConsumer: ExpressionValueConsumer[ExpressionElement] =
+    new ExpressionValueConsumer[ExpressionElement] {
+      override def expressionConsumedValueHooks(a: ExpressionElement)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] = a match {
+        case _: PrimitiveLiteralExpressionElement | _: StringLiteral => Set.empty[UnlinkedConsumedValueHook]
+        case a: NoneLiteralElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: StringExpression => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ObjectLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: PairLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ArrayLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: MapLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        // Member access:
+        case a: IdentifierLookup => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: IdentifierMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ExpressionMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: IndexAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        // Unary operators:
+        case a: UnaryNegation => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: UnaryPlus => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LogicalNot => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        // Binary operators:
+        case a: LogicalOr => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LogicalAnd => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Equals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: NotEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LessThan => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LessThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: GreaterThan => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: GreaterThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Add => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Subtract => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Multiply => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Divide => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Remainder => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: TernaryIf => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        // Engine functions:
+        case a: StdoutElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: StderrElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: ReadLines => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadObject => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadJson => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadInt => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadString => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadFloat => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadBoolean => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteLines => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteObject => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteJson => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Range => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Transpose => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Length => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Flatten => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Prefix => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: SelectFirst => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: SelectAll => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Defined => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Floor => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Ceil => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Round => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Glob => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: Size => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Basename => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: Zip => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Cross => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case a: Sub => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        // New WDL biscayne expressions:
+        case a: Keys => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: AsMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: AsPairs => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: CollectByKey => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Sep => sepExpressionValueConsumer.expressionConsumedValueHooks(a)(expressionValueConsumer)
+
+        case a: Min => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Max => a.expressionConsumedValueHooks(expressionValueConsumer)
+
+        case other =>
+          throw new Exception(s"Cannot generate consumed values for ExpressionElement ${other.getClass.getSimpleName}")
+      }
     }
-  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
index f1e63de78cc..3b7b299a090 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
@@ -8,9 +8,12 @@ import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.two
 object cascadesFileEvaluators {
 
   implicit val keysFileEvaluator: FileEvaluator[Keys] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
-  implicit val asMapFileEvaluator: FileEvaluator[AsMap] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
-  implicit val asPairsFileEvaluator: FileEvaluator[AsPairs] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
-  implicit val collectByKeyFileEvaluator: FileEvaluator[CollectByKey] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val asMapFileEvaluator: FileEvaluator[AsMap] =
+    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val asPairsFileEvaluator: FileEvaluator[AsPairs] =
+    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val collectByKeyFileEvaluator: FileEvaluator[CollectByKey] =
+    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
 
   implicit val sepFunctionEvaluator: FileEvaluator[Sep] = twoParameterFunctionPassthroughFileEvaluator[Sep]
 
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
index 1c9da7b2d60..9693cbfaba6 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
@@ -21,82 +21,134 @@ package object files {
 
   implicit val expressionFileEvaluator: FileEvaluator[ExpressionElement] = new FileEvaluator[ExpressionElement] {
 
-    override def predictFilesNeededToEvaluate(a: ExpressionElement, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
-
+    override def predictFilesNeededToEvaluate(a: ExpressionElement,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       a match {
         // Literals:
-        case a: PrimitiveLiteralExpressionElement => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: StringLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ObjectLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: MapLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ArrayLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: PairLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: PrimitiveLiteralExpressionElement =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: StringLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ObjectLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: MapLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ArrayLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: PairLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Lookups and member accesses:
-        case a: IdentifierLookup => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ExpressionMemberAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: IdentifierMemberAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: IndexAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IdentifierLookup =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ExpressionMemberAccess =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IdentifierMemberAccess =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IndexAccess =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Unary operators:
-        case a: UnaryNegation => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: UnaryPlus => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LogicalNot => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: UnaryNegation =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: UnaryPlus =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalNot =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Binary operators (at some point we might want to split these into separate cases):
-        case a: LogicalOr => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LogicalAnd => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalOr =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalAnd =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Equals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: NotEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LessThan => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LessThanOrEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: GreaterThan => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: GreaterThanOrEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: NotEquals =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LessThan =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LessThanOrEquals =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: GreaterThan =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: GreaterThanOrEquals =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Add => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Subtract => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Multiply => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Subtract =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Multiply =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Divide => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Remainder => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Remainder =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
-        case a: TernaryIf => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: TernaryIf =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Engine functions:
-        case StdoutElement => StdoutElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case StderrElement => StderrElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-
-        case a: ReadLines => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadTsv => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadObject => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadObjects => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadJson => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadInt => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadString => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadFloat => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadBoolean => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteLines => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteTsv => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteObject => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteObjects => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteJson => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case StdoutElement =>
+          StdoutElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case StderrElement =>
+          StderrElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+
+        case a: ReadLines =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadTsv =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadMap =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadObject =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadObjects =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadJson =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadInt =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadString =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadFloat =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadBoolean =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteLines =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteTsv =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteMap =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteObject =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteObjects =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteJson =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Range => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Transpose => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Transpose =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Length => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Flatten => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Flatten =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Prefix => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: SelectFirst => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: SelectAll => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Defined => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SelectFirst =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SelectAll =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Defined =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Floor => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Ceil => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Round => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Glob => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: Size => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Basename => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Basename =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: Zip => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Cross => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
@@ -105,8 +157,10 @@ package object files {
 
         case a: Keys => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: AsMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: AsPairs => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: CollectByKey => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: AsPairs =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: CollectByKey =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Sep => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: Min => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
@@ -114,6 +168,5 @@ package object files {
 
         case other => s"No implementation of FileEvaluator[${other.getClass.getSimpleName}]".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
index 4a2e389c25a..e169a561d53 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
@@ -11,59 +11,64 @@ import wom.types._
 
 object cascadesTypeEvaluators {
   implicit val keysFunctionEvaluator: TypeEvaluator[Keys] = new TypeEvaluator[Keys] {
-    override def evaluateType(a: Keys, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Keys, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)) flatMap {
         case WomMapType(keyType, _) => WomArrayType(keyType).validNel
         case other => s"Cannot invoke 'keys' on type '${other.stableName}'. Expected a map".invalidNel
       }
-    }
   }
 
   implicit val asMapFunctionEvaluator: TypeEvaluator[AsMap] = new TypeEvaluator[AsMap] {
-    override def evaluateType(a: AsMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: AsMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
         case WomArrayType(WomPairType(x: WomPrimitiveType, y)) => WomMapType(x, y).validNel
-        case other @ WomArrayType(WomPairType(x, _)) => s"Cannot invoke 'as_map' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
+        case other @ WomArrayType(WomPairType(x, _)) =>
+          s"Cannot invoke 'as_map' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
         case other => s"Cannot invoke 'as_map' on type '${other.stableName}'. Expected an array of pairs".invalidNel
       }
-    }
   }
 
   implicit val asPairsFunctionEvaluator: TypeEvaluator[AsPairs] = new TypeEvaluator[AsPairs] {
-    override def evaluateType(a: AsPairs, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: AsPairs, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)) flatMap {
         case WomMapType(x, y) => WomArrayType(WomPairType(x, y)).validNel
         case other => s"Cannot invoke 'as_pairs' on type '${other.stableName}'. Expected a map".invalidNel
       }
-    }
   }
 
   implicit val collectByKeyFunctionEvaluator: TypeEvaluator[CollectByKey] = new TypeEvaluator[CollectByKey] {
-    override def evaluateType(a: CollectByKey, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: CollectByKey, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
         case WomArrayType(WomPairType(x: WomPrimitiveType, y)) => WomMapType(x, WomArrayType(y)).validNel
-        case other @ WomArrayType(WomPairType(x, _)) => s"Cannot invoke 'collect_by_key' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
-        case other => s"Cannot invoke 'collect_by_key' on type '${other.stableName}'. Expected an array of pairs".invalidNel
+        case other @ WomArrayType(WomPairType(x, _)) =>
+          s"Cannot invoke 'collect_by_key' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
+        case other =>
+          s"Cannot invoke 'collect_by_key' on type '${other.stableName}'. Expected an array of pairs".invalidNel
       }
-    }
   }
 
-  private def resultTypeOfIntVsFloat(functionName: String)(type1: WomType, type2: WomType): ErrorOr[WomType] = (type1, type2) match {
-    case (WomIntegerType, WomIntegerType) => WomIntegerType.validNel
-    case (WomIntegerType, WomFloatType) => WomFloatType.validNel
-    case (WomFloatType, WomIntegerType) => WomFloatType.validNel
-    case (WomFloatType, WomFloatType) => WomFloatType.validNel
-    case (other1, other2) => s"Cannot call '$functionName' with arguments (${other1.friendlyName}, ${other2.friendlyName}). Must be Int or Long.".invalidNel
-  }
+  private def resultTypeOfIntVsFloat(functionName: String)(type1: WomType, type2: WomType): ErrorOr[WomType] =
+    (type1, type2) match {
+      case (WomIntegerType, WomIntegerType) => WomIntegerType.validNel
+      case (WomIntegerType, WomFloatType) => WomFloatType.validNel
+      case (WomFloatType, WomIntegerType) => WomFloatType.validNel
+      case (WomFloatType, WomFloatType) => WomFloatType.validNel
+      case (other1, other2) =>
+        s"Cannot call '$functionName' with arguments (${other1.friendlyName}, ${other2.friendlyName}). Must be Int or Long.".invalidNel
+    }
 
   implicit val minFunctionEvaluator: TypeEvaluator[Min] = new TypeEvaluator[Min] {
-    override def evaluateType(a: Min,
-                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Min, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = {
       val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
       val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
 
@@ -72,9 +77,9 @@ object cascadesTypeEvaluators {
   }
 
   implicit val maxFunctionEvaluator: TypeEvaluator[Max] = new TypeEvaluator[Max] {
-    override def evaluateType(a: Max,
-                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Max, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = {
       val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
       val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
 
@@ -83,15 +88,16 @@ object cascadesTypeEvaluators {
   }
 
   implicit val sepFunctionEvaluator: TypeEvaluator[Sep] = new TypeEvaluator[Sep] {
-    override def evaluateType(a: Sep, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Sep, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.arg2, linkedValues, WomArrayType(WomAnyType)) flatMap {
-        case WomArrayType(WomArrayType(_)) => s"Cannot invoke 'sep' on type 'Array[Array[_]]'. Expected an Array[String].".invalidNel
+        case WomArrayType(WomArrayType(_)) =>
+          s"Cannot invoke 'sep' on type 'Array[Array[_]]'. Expected an Array[String].".invalidNel
         case WomArrayType(_) => WomStringType.validNel
 
         case other => s"Cannot invoke 'sep' on type '${other.stableName}'. Expected an Array[String].".invalidNel
 
       }
-    }
   }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
index 367967b91be..70e6e61a180 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
@@ -18,9 +18,9 @@ import wdl.transforms.biscayne.linking.expression.types.cascadesTypeEvaluators._
 
 package object types {
   implicit val expressionTypeEvaluator: TypeEvaluator[ExpressionElement] = new TypeEvaluator[ExpressionElement] {
-    override def evaluateType(a: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit typeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
-
+    override def evaluateType(a: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit typeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       a match {
         // Literals:
         case a: PrimitiveLiteralExpressionElement => a.evaluateType(linkedValues)(typeEvaluator)
@@ -111,8 +111,8 @@ package object types {
         case a: Min => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Max => a.evaluateType(linkedValues)(typeEvaluator)
 
-        case other => s"Unable to process ${other.getClass.getSimpleName}: No evaluateType exists for that type.".invalidNel
+        case other =>
+          s"Unable to process ${other.getClass.getSimpleName}: No evaluateType exists for that type.".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
index 4a02ed221f1..788f114e181 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
@@ -9,40 +9,54 @@ import common.collections.EnhancedCollections._
 import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement._
 import wdl.model.draft3.graph.expression.{EvaluatedValue, ForCommandInstantiationOptions, ValueEvaluator}
-import wdl.transforms.base.linking.expression.values.EngineFunctionEvaluators.{processValidatedSingleValue, processTwoValidatedValues}
+import wdl.transforms.base.linking.expression.values.EngineFunctionEvaluators.{
+  processTwoValidatedValues,
+  processValidatedSingleValue
+}
 import wom.expression.IoFunctionSet
 import wom.types._
-import wom.values.{WomArray, WomInteger, WomFloat, WomMap, WomOptionalValue, WomPair, WomValue, WomString}
+import wom.values.{WomArray, WomFloat, WomInteger, WomMap, WomOptionalValue, WomPair, WomString, WomValue}
 import wom.types.coercion.defaults._
 
 object cascadesValueEvaluators {
 
-  implicit val noneLiteralEvaluator: ValueEvaluator[NoneLiteralElement.type] = new ValueEvaluator[ExpressionElement.NoneLiteralElement.type] {
-    override def evaluateValue(a: ExpressionElement.NoneLiteralElement.type, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      EvaluatedValue(
-        value = WomOptionalValue(WomNothingType, None),
-        sideEffectFiles = Seq.empty).validNel
+  implicit val noneLiteralEvaluator: ValueEvaluator[NoneLiteralElement.type] =
+    new ValueEvaluator[ExpressionElement.NoneLiteralElement.type] {
+      override def evaluateValue(a: ExpressionElement.NoneLiteralElement.type,
+                                 inputs: Map[String, WomValue],
+                                 ioFunctionSet: IoFunctionSet,
+                                 forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+      )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+        EvaluatedValue(value = WomOptionalValue(WomNothingType, None), sideEffectFiles = Seq.empty).validNel
     }
-  }
 
   implicit val asMapFunctionEvaluator: ValueEvaluator[AsMap] = new ValueEvaluator[AsMap] {
-    override def evaluateValue(a: AsMap, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      processValidatedSingleValue[WomArray, WomMap](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
+    override def evaluateValue(a: AsMap,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+      processValidatedSingleValue[WomArray, WomMap](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) {
         case WomArray(WomArrayType(WomPairType(_: WomPrimitiveType, _)), values) =>
           val validPairs: ErrorOr[List[(WomValue, WomValue)]] = values.toList traverse {
             case WomPair(l, r) => (l, r).validNel
-            case other => s"Unexpected array element. Expected a Pair[X, Y] but array contained ${other.toWomString}]".invalidNel
-          } leftMap {
-            errors => NonEmptyList.fromListUnsafe(errors.toList.distinct)
+            case other =>
+              s"Unexpected array element. Expected a Pair[X, Y] but array contained ${other.toWomString}]".invalidNel
+          } leftMap { errors =>
+            NonEmptyList.fromListUnsafe(errors.toList.distinct)
           }
           validPairs flatMap { pairs =>
             val grouped = pairs.groupBy(_._1)
             val tooManyKeyErrors = grouped collect {
-              case (name, list) if list.length != 1 => s"keys can only appear once but ${name.toWomString} appeared ${list.size} times."
+              case (name, list) if list.length != 1 =>
+                s"keys can only appear once but ${name.toWomString} appeared ${list.size} times."
             }
             if (tooManyKeyErrors.isEmpty) {
-              val pairs = grouped map { case (key, value) => (key -> value.head._2) }
+              val pairs = grouped map { case (key, value) => key -> value.head._2 }
 
               EvaluatedValue(WomMap(pairs), Seq.empty).validNel
             } else {
@@ -50,49 +64,69 @@ object cascadesValueEvaluators {
             }
           }
 
-        case WomArray(womType@WomArrayType(WomPairType(x, _)), _) => s"Cannot evaluate 'as_map' on type ${womType.stableName}. Keys must be primitive but got ${x.stableName}.".invalidNel
-        case other => s"Invalid call of 'as_map' on parameter of type '${other.womType.stableName}' (expected Array[Pair[X, Y]])".invalidNel
-      } (coercer = WomArrayType(WomPairType(WomAnyType, WomAnyType)))
-    }
+        case WomArray(womType @ WomArrayType(WomPairType(x, _)), _) =>
+          s"Cannot evaluate 'as_map' on type ${womType.stableName}. Keys must be primitive but got ${x.stableName}.".invalidNel
+        case other =>
+          s"Invalid call of 'as_map' on parameter of type '${other.womType.stableName}' (expected Array[Pair[X, Y]])".invalidNel
+      }(coercer = WomArrayType(WomPairType(WomAnyType, WomAnyType)))
   }
 
   implicit val keysFunctionEvaluator: ValueEvaluator[Keys] = new ValueEvaluator[Keys] {
     override def evaluateValue(a: Keys,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-
-      processValidatedSingleValue[WomMap, WomArray](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
-        case WomMap(WomMapType(keyType, _), values) => EvaluatedValue(WomArray(WomArrayType(keyType), values.keys.toList), Seq.empty).validNel
-        case other => s"Invalid call of 'keys' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomMap, WomArray](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) {
+        case WomMap(WomMapType(keyType, _), values) =>
+          EvaluatedValue(WomArray(WomArrayType(keyType), values.keys.toList), Seq.empty).validNel
+        case other =>
+          s"Invalid call of 'keys' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
       }
-    }
   }
 
   implicit val asPairsFunctionEvaluator: ValueEvaluator[AsPairs] = new ValueEvaluator[AsPairs] {
-    override def evaluateValue(a: AsPairs, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      processValidatedSingleValue[WomMap, WomArray](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
+    override def evaluateValue(a: AsPairs,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+      processValidatedSingleValue[WomMap, WomArray](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) {
         case WomMap(WomMapType(keyType, valueType), values) =>
-          val validPairs: List[WomPair] = values.toList map {
-            case (l, r) => WomPair(l, r)
+          val validPairs: List[WomPair] = values.toList map { case (l, r) =>
+            WomPair(l, r)
           }
           EvaluatedValue(WomArray(WomArrayType(WomPairType(keyType, valueType)), validPairs), Seq.empty).validNel
 
-        case other => s"Invalid call of 'as_pairs' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
+        case other =>
+          s"Invalid call of 'as_pairs' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
       }
-    }
   }
 
   implicit val collectByKeyFunctionEvaluator: ValueEvaluator[CollectByKey] = new ValueEvaluator[CollectByKey] {
-    override def evaluateValue(a: CollectByKey, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      processValidatedSingleValue[WomArray, WomMap](expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)) {
+    override def evaluateValue(a: CollectByKey,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+      processValidatedSingleValue[WomArray, WomMap](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) {
         case WomArray(WomArrayType(WomPairType(_: WomPrimitiveType, _)), values) =>
           val validPairs: ErrorOr[List[(WomValue, WomValue)]] = values.toList traverse {
             case WomPair(l, r) => (l, r).validNel
-            case other => s"Unexpected array element. Expected a Pair[X, Y] but array contained ${other.toWomString}]".invalidNel
+            case other =>
+              s"Unexpected array element. Expected a Pair[X, Y] but array contained ${other.toWomString}]".invalidNel
           }
           validPairs flatMap { kvpairs =>
             val grouped: Map[WomValue, WomArray] = kvpairs.groupBy(_._1).safeMapValues(v => WomArray(v.map(_._2)))
@@ -100,22 +134,24 @@ object cascadesValueEvaluators {
 
           }
 
-        case WomArray(womType@WomArrayType(WomPairType(x, _)), _) => s"Cannot evaluate 'collect_by_key' on type ${womType.stableName}. Keys must be primitive but got ${x.stableName}.".invalidNel
-        case other => s"Invalid call of 'collect_by_key' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
-      } (coercer = WomArrayType(WomPairType(WomAnyType, WomAnyType)))
-    }
+        case WomArray(womType @ WomArrayType(WomPairType(x, _)), _) =>
+          s"Cannot evaluate 'collect_by_key' on type ${womType.stableName}. Keys must be primitive but got ${x.stableName}.".invalidNel
+        case other =>
+          s"Invalid call of 'collect_by_key' on parameter of type '${other.womType.stableName}' (expected Map[X, Y])".invalidNel
+      }(coercer = WomArrayType(WomPairType(WomAnyType, WomAnyType)))
   }
 
   private def resultOfIntVsFloat(functionName: String,
                                  intFunc: (Int, Int) => Int,
-                                 doubleFunc: (Double, Double) => Double)
-                                (value1: EvaluatedValue[_], value2: EvaluatedValue[_]): ErrorOr[EvaluatedValue[WomValue]] = {
+                                 doubleFunc: (Double, Double) => Double
+  )(value1: EvaluatedValue[_], value2: EvaluatedValue[_]): ErrorOr[EvaluatedValue[WomValue]] = {
     val newValue = (value1.value, value2.value) match {
       case (WomInteger(i1), WomInteger(i2)) => WomInteger(intFunc(i1, i2)).validNel
       case (WomInteger(i1), WomFloat(l2)) => WomFloat(doubleFunc(i1.doubleValue, l2)).validNel
       case (WomFloat(l1), WomInteger(i2)) => WomFloat(doubleFunc(l1, i2.doubleValue)).validNel
       case (WomFloat(l1), WomFloat(l2)) => WomFloat(doubleFunc(l1, l2)).validNel
-      case (other1, other2) => s"Invalid arguments to '$functionName':(${other1.typeName}, ${other2.typeName})".invalidNel
+      case (other1, other2) =>
+        s"Invalid arguments to '$functionName':(${other1.typeName}, ${other2.typeName})".invalidNel
     }
     newValue map { v => EvaluatedValue(v, value1.sideEffectFiles ++ value2.sideEffectFiles) }
   }
@@ -124,10 +160,16 @@ object cascadesValueEvaluators {
     override def evaluateValue(a: Min,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
-      val value1 = expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-      val value2 = expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
+      val value1 =
+        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      val value2 =
+        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
 
       val intFunc = (i1: Int, i2: Int) => Math.min(i1, i2)
       val doubleFunc = (l1: Double, l2: Double) => Math.min(l1, l2)
@@ -140,9 +182,16 @@ object cascadesValueEvaluators {
     override def evaluateValue(a: Max,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
-      val value1 = expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-      val value2 = expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
+      val value1 =
+        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      val value2 =
+        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
 
       val intFunc = (i1: Int, i2: Int) => Math.max(i1, i2)
       val doubleFunc = (l1: Double, l2: Double) => Math.max(l1, l2)
@@ -155,15 +204,17 @@ object cascadesValueEvaluators {
     override def evaluateValue(a: Sep,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] = {
-
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] =
       processTwoValidatedValues[WomString, WomArray, WomString](
-        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator),
-        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        ),
+        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
       ) { (sepvalue, arr) =>
         EvaluatedValue(WomString(arr.value.map(v => v.valueString).mkString(sepvalue.value)), Seq.empty).validNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
index 24b21928f4b..08eb74ac19c 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
@@ -24,94 +24,154 @@ package object values {
     override def evaluateValue(a: ExpressionElement,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
       a match {
         // Literals:
-        case a: PrimitiveLiteralExpressionElement => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: NoneLiteralElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-
-        case a: StringLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: StringExpression => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ObjectLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: MapLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ArrayLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: PairLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: PrimitiveLiteralExpressionElement =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: NoneLiteralElement.type =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: StringLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: StringExpression =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ObjectLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: MapLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ArrayLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: PairLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         // Lookups and member accesses:
-        case a: IdentifierLookup => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ExpressionMemberAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: IdentifierMemberAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: IndexAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: IdentifierLookup =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ExpressionMemberAccess =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: IdentifierMemberAccess =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: IndexAccess =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         // Unary operators:
-        case a: UnaryNegation => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: UnaryPlus => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: LogicalNot => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: UnaryNegation =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: UnaryPlus =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LogicalNot =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         // Binary operators (at some point we might want to split these into separate cases):
-        case a: LogicalOr => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: LogicalAnd => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Equals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: NotEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: LessThan => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: LessThanOrEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: GreaterThan => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: GreaterThanOrEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LogicalOr =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LogicalAnd =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Equals =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: NotEquals =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LessThan =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: LessThanOrEquals =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: GreaterThan =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: GreaterThanOrEquals =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Add => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Subtract => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Multiply => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Divide => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Remainder => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-
-        case a: TernaryIf => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Subtract =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Multiply =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Divide =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Remainder =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: TernaryIf =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         // Engine functions:
-        case a: StdoutElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: StderrElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-
-        case a: ReadLines => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadTsv => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadMap => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadObject => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadObjects => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadJson => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadInt => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadString => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadFloat => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: ReadBoolean => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteLines => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteTsv => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteMap => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteObject => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteObjects => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: WriteJson => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Range => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Transpose => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Length => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Flatten => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Prefix => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: SelectFirst => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: SelectAll => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Defined => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Floor => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: StdoutElement.type =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: StderrElement.type =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+
+        case a: ReadLines =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadTsv =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadMap =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadObject =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadObjects =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadJson =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadInt =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadString =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadFloat =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: ReadBoolean =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteLines =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteTsv =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteMap =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteObject =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteObjects =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: WriteJson =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Range =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Transpose =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Length =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Flatten =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Prefix =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: SelectFirst =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: SelectAll =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Defined =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Floor =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Ceil => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Round => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Round =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Glob => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Size => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Basename => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Basename =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Zip => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: Cross => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Cross =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Sub => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Keys => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: AsMap => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: AsPairs => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-        case a: CollectByKey => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: AsMap =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: AsPairs =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: CollectByKey =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Sep => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Min => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
@@ -119,6 +179,5 @@ package object values {
 
         case other => s"Unable to process ${other.toWdlV1}: No evaluateValue exists for that type in WDL 1.1".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/CascadesParser.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/CascadesParser.scala
index ed0bd20e2e9..dd7b7aef4c7 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/CascadesParser.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/CascadesParser.scala
@@ -15,7 +15,7 @@ object StringParser {
   def convert(a: FileStringParserInput): Checked[Ast] = Try {
     val parser = new WdlParser()
     val tokens = parser.lex(a.workflowSource, a.resource)
-    val terminalMap = (tokens.asScala.toVector map {(_, a.workflowSource)}).toMap
+    val terminalMap = (tokens.asScala.toVector map { (_, a.workflowSource) }).toMap
     val syntaxErrorFormatter = WdlCascadesSyntaxErrorFormatter(terminalMap)
     parser.parse(tokens, syntaxErrorFormatter).toAst.asInstanceOf[Ast]
   }.toChecked
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/WdlCascadesSyntaxErrorFormatter.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/WdlCascadesSyntaxErrorFormatter.scala
index 175adf8f1af..7a24e474a79 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/WdlCascadesSyntaxErrorFormatter.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/parsing/WdlCascadesSyntaxErrorFormatter.scala
@@ -13,52 +13,56 @@ case class WdlCascadesSyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSo
     case classicTerminal => terminalMap.get(classicTerminal)
   }
 
-  private def line(t: Terminal): String = getTerminal(t).map(_.split("\n")(t.getLine - 1)).getOrElse(s"Cannot highlight line. It was probably in an imported file.")
+  private def line(t: Terminal): String = getTerminal(t)
+    .map(_.split("\n")(t.getLine - 1))
+    .getOrElse(s"Cannot highlight line. It was probably in an imported file.")
 
-  def unexpectedEof(method: String, expected: java.util.List[TerminalIdentifier], nt_rules: java.util.List[String]): String = "ERROR: Unexpected end of file"
+  def unexpectedEof(method: String,
+                    expected: java.util.List[TerminalIdentifier],
+                    nt_rules: java.util.List[String]
+  ): String = "ERROR: Unexpected end of file"
 
-  def excessTokens(method: String, terminal: Terminal): String = {
+  def excessTokens(method: String, terminal: Terminal): String =
     s"""ERROR: Finished parsing without consuming all tokens.
        |
-        |${pointToSource(terminal)}
+       |${pointToSource(terminal)}
      """.stripMargin
-  }
 
-  def unexpectedSymbol(method: String, actual: Terminal, expected: java.util.List[TerminalIdentifier], rule: String): String = {
+  def unexpectedSymbol(method: String,
+                       actual: Terminal,
+                       expected: java.util.List[TerminalIdentifier],
+                       rule: String
+  ): String = {
     val expectedTokens = expected.asScala.map(_.string).mkString(", ")
     s"""ERROR: Unexpected symbol (line ${actual.getLine}, col ${actual.getColumn}) when parsing '$method'.
        |
-        |Expected $expectedTokens, got "${actual.getSourceString}".
+       |Expected $expectedTokens, got "${actual.getSourceString}".
        |
-        |${pointToSource(actual)}
+       |${pointToSource(actual)}
        |
-        |$rule
+       |$rule
      """.stripMargin
   }
 
-  def noMoreTokens(method: String, expecting: TerminalIdentifier, last: Terminal): String = {
+  def noMoreTokens(method: String, expecting: TerminalIdentifier, last: Terminal): String =
     s"""ERROR: No more tokens.  Expecting ${expecting.string}
        |
-        |${pointToSource(last)}
+       |${pointToSource(last)}
      """.stripMargin
-  }
 
-  def invalidTerminal(method: String, invalid: Terminal): String = {
+  def invalidTerminal(method: String, invalid: Terminal): String =
     s"""ERROR: Invalid symbol ID: ${invalid.getId} (${invalid.getTerminalStr})
        |
-        |${pointToSource(invalid)}
+       |${pointToSource(invalid)}
      """.stripMargin
-  }
 
   // TODO: these next two methods won't be called by the parser because there are no lists in the WDL grammar that
   // cause these to be triggered.  Currently the parser is passing in 'null' for the value of 'last' and when that
   // changes, these errors can be made more helpful.
 
-  def missingListItems(method: String, required: Int, found: Int, last: Terminal): String = {
+  def missingListItems(method: String, required: Int, found: Int, last: Terminal): String =
     s"ERROR: $method requires $required items, but only found $found"
-  }
 
-  def missingTerminator(method: String, terminal: TerminalIdentifier, last: Terminal): String = {
+  def missingTerminator(method: String, terminal: TerminalIdentifier, last: Terminal): String =
     s"ERROR: $method requires a terminator after each element"
-  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala
index 6f2f084867f..8933a00cb57 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala
@@ -3,7 +3,12 @@ package wdl.transforms.cascades
 import common.transforms.CheckedAtoB
 import wdl.transforms.base.wdlom2wom.TaskDefinitionElementToWomTaskDefinition.TaskDefinitionElementToWomInputs
 import wdl.transforms.base.wdlom2wom.WorkflowDefinitionElementToWomWorkflowDefinition.WorkflowDefinitionConvertInputs
-import wdl.transforms.base.wdlom2wom.{FileElementToWomBundle, FileElementToWomBundleInputs, TaskDefinitionElementToWomTaskDefinition, WorkflowDefinitionElementToWomWorkflowDefinition}
+import wdl.transforms.base.wdlom2wom.{
+  FileElementToWomBundle,
+  FileElementToWomBundleInputs,
+  TaskDefinitionElementToWomTaskDefinition,
+  WorkflowDefinitionElementToWomWorkflowDefinition
+}
 import wom.callable.{CallableTaskDefinition, WorkflowDefinition}
 import wom.executable.WomBundle
 import wdl.transforms.cascades.linking.expression.consumed._
@@ -12,7 +17,11 @@ import wdl.transforms.cascades.linking.expression.types._
 import wdl.transforms.cascades.linking.expression.values._
 
 package object wdlom2wom {
-  val taskDefinitionElementToWomTaskDefinition: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition] = CheckedAtoB.fromErrorOr(TaskDefinitionElementToWomTaskDefinition.convert)
-  val workflowDefinitionElementToWomWorkflowDefinition: CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition] = CheckedAtoB.fromErrorOr(WorkflowDefinitionElementToWomWorkflowDefinition.convert)
-  val fileElementToWomBundle: CheckedAtoB[FileElementToWomBundleInputs, WomBundle] = CheckedAtoB.fromCheck(FileElementToWomBundle.convert)
+  val taskDefinitionElementToWomTaskDefinition: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition] =
+    CheckedAtoB.fromErrorOr(TaskDefinitionElementToWomTaskDefinition.convert)
+  val workflowDefinitionElementToWomWorkflowDefinition
+    : CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition] =
+    CheckedAtoB.fromErrorOr(WorkflowDefinitionElementToWomWorkflowDefinition.convert)
+  val fileElementToWomBundle: CheckedAtoB[FileElementToWomBundleInputs, WomBundle] =
+    CheckedAtoB.fromCheck(FileElementToWomBundle.convert)
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
index 7633624bede..a3a9cd4fb65 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
@@ -27,14 +27,14 @@ object Ast2WdlomSpec {
   val parser = new WdlParser()
 
   def fromString[A](expression: String,
-                    parseFunction: (util.List[WdlParser.Terminal], SyntaxErrorFormatter) => ParseTree)
-                   (implicit converter: CheckedAtoB[GenericAstNode, A]): Checked[A] = {
+                    parseFunction: (util.List[WdlParser.Terminal], SyntaxErrorFormatter) => ParseTree
+  )(implicit converter: CheckedAtoB[GenericAstNode, A]): Checked[A] = {
 
     // Add the "version development" to force the lexer into "main" mode.
     val versionedExpression = "version development\n" + expression
     // That "version development" means we'll have 2 unwanted tokens at the start of the list, so drop 'em:
     val tokens = parser.lex(versionedExpression, "string").asScala.drop(2).asJava
-    val terminalMap = (tokens.asScala.toVector map {(_, versionedExpression)}).toMap
+    val terminalMap = (tokens.asScala.toVector map { (_, versionedExpression) }).toMap
     val parseTree = parseFunction(tokens, WdlCascadesSyntaxErrorFormatter(terminalMap))
     (wrapAstNode andThen converter).run(parseTree.toAst)
   }
@@ -42,18 +42,20 @@ object Ast2WdlomSpec {
 
 class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
-
-
   it should "parse a simple expression" in {
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid Add(PrimitiveLiteralExpressionElement(WomInteger(3)), PrimitiveLiteralExpressionElement(WomInteger(3)))
+    expr shouldBeValid Add(PrimitiveLiteralExpressionElement(WomInteger(3)),
+                           PrimitiveLiteralExpressionElement(WomInteger(3))
+    )
   }
 
   it should "parse a map expression" in {
     val str = "{3: 3}"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid MapLiteral(Map(PrimitiveLiteralExpressionElement(WomInteger(3)) -> PrimitiveLiteralExpressionElement(WomInteger(3))))
+    expr shouldBeValid MapLiteral(
+      Map(PrimitiveLiteralExpressionElement(WomInteger(3)) -> PrimitiveLiteralExpressionElement(WomInteger(3)))
+    )
   }
 
   it should "parse a simple meta section" in {
@@ -65,33 +67,34 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   it should "parse a struct element" in {
     val str = "struct Foo { Int five\n Int six }"
     val struct = fromString[StructElement](str, parser.parse_struct)(astNodeToAst andThen astToStructElement)
-    struct shouldBeValid StructElement("Foo", Seq(
-      StructEntryElement("five", PrimitiveTypeElement(WomIntegerType)),
-      StructEntryElement("six", PrimitiveTypeElement(WomIntegerType)))
+    struct shouldBeValid StructElement("Foo",
+                                       Seq(StructEntryElement("five", PrimitiveTypeElement(WomIntegerType)),
+                                           StructEntryElement("six", PrimitiveTypeElement(WomIntegerType))
+                                       )
     )
   }
 
   it should "parse the new as_map function" in {
     val str = "as_map(some_pairs)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid(AsMap(IdentifierLookup("some_pairs")))
+    expr shouldBeValid (AsMap(IdentifierLookup("some_pairs")))
   }
 
   it should "parse the new as_pairs function" in {
     val str = "as_pairs(some_map)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid(AsPairs(IdentifierLookup("some_map")))
+    expr shouldBeValid (AsPairs(IdentifierLookup("some_map")))
   }
 
   it should "parse the new collect_by_key function" in {
     val str = "collect_by_key(some_map)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid(CollectByKey(IdentifierLookup("some_map")))
+    expr shouldBeValid (CollectByKey(IdentifierLookup("some_map")))
   }
 
   it should "parse the new None keyword" in {
     val str = "None"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid(NoneLiteralElement)
+    expr shouldBeValid NoneLiteralElement
   }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala
index 5d2cb2991e8..0a6a6f0e08e 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala
@@ -12,7 +12,6 @@ import wom.SourceFileLocation
 import wom.types._
 import wom.values.WomInteger
 
-
 class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "WDL File to WDLOM"
@@ -25,12 +24,11 @@ class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   testCases.list.filter(x => x.isRegularFile && x.extension.contains(".wdl")) foreach { testCase =>
-
     val fileName = testCase.name
     val testName = testCase.name.split("\\.").head
 
     val itShouldString = s"create the correct Element structure for $fileName"
-    val testOrIgnore: (=>Any) => Unit = if (fileName.endsWith(".ignored.wdl")) {
+    val testOrIgnore: (=> Any) => Unit = if (fileName.endsWith(".ignored.wdl")) {
       (it should itShouldString).ignore _
     } else {
       (it should itShouldString).in _
@@ -42,7 +40,8 @@ class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
       fileToFileElement.run(testCase) match {
         case Right(actual) => actual shouldBe expected
         case Left(errors) =>
-          val formattedErrors = errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
+          val formattedErrors =
+            errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
           fail(s"Failed to create WDLOM:$formattedErrors")
       }
 
@@ -57,21 +56,23 @@ object WdlFileToWdlomSpec {
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "no_input_no_output",
-          inputsSection = None,
-          graphElements = Set(
-            CallElement("no_inputs", Some("noi1"), Vector.empty, None, Some(SourceFileLocation(7))),
-            CallElement("no_inputs", Some("noi5"), Vector.empty, None, Some(SourceFileLocation(21))),
-            CallElement("no_inputs", Some("noi2"), Vector.empty, None, Some(SourceFileLocation(11))),
-            CallElement("no_inputs", Some("noi3"), Vector.empty, None, Some(SourceFileLocation(13))),
-            CallElement("no_inputs", Some("noi4"), Vector.empty, None, Some(SourceFileLocation(17))),
-            CallElement("no_inputs", None, Vector.empty, None, Some(SourceFileLocation(9)))
-          ),
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(6)))
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "no_input_no_output",
+            inputsSection = None,
+            graphElements = Set(
+              CallElement("no_inputs", Some("noi1"), Vector.empty, None, Some(SourceFileLocation(7))),
+              CallElement("no_inputs", Some("noi5"), Vector.empty, None, Some(SourceFileLocation(21))),
+              CallElement("no_inputs", Some("noi2"), Vector.empty, None, Some(SourceFileLocation(11))),
+              CallElement("no_inputs", Some("noi3"), Vector.empty, None, Some(SourceFileLocation(13))),
+              CallElement("no_inputs", Some("noi4"), Vector.empty, None, Some(SourceFileLocation(17))),
+              CallElement("no_inputs", None, Vector.empty, None, Some(SourceFileLocation(9)))
+            ),
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(6))
+          )
         ),
         tasks = Vector(
           TaskDefinitionElement(
@@ -79,7 +80,8 @@ object WdlFileToWdlomSpec {
             inputsSection = None,
             declarations = Vector.empty,
             outputsSection = None,
-            commandSection = CommandSectionElement(List(CommandSectionLine(Vector(StringCommandPartElement("echo Hello World "))))),
+            commandSection =
+              CommandSectionElement(List(CommandSectionLine(Vector(StringCommandPartElement("echo Hello World "))))),
             runtimeSection = None,
             metaSection = None,
             parameterMetaSection = None,
@@ -91,122 +93,280 @@ object WdlFileToWdlomSpec {
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "order",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "n", Some(PrimitiveLiteralExpressionElement(WomInteger(4)))),
-            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", Some(StringLiteral("more")))))),
-          graphElements = Set(CallElement("in_n_out", None, Vector.empty, Some(CallBodyElement(Vector(KvPair("total", IdentifierLookup("n")), KvPair("amount", IdentifierLookup("more"))))), Some(SourceFileLocation(19)))),
-          outputsSection = Some(OutputsSectionElement(Vector(
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "out", IdentifierMemberAccess("in_n_out", "out", List.empty))))),
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(14)))
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "order",
+            inputsSection = Some(
+              InputsSectionElement(
+                Vector(
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                          "n",
+                                          Some(PrimitiveLiteralExpressionElement(WomInteger(4)))
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", Some(StringLiteral("more")))
+                )
+              )
+            ),
+            graphElements = Set(
+              CallElement(
+                "in_n_out",
+                None,
+                Vector.empty,
+                Some(
+                  CallBodyElement(
+                    Vector(KvPair("total", IdentifierLookup("n")), KvPair("amount", IdentifierLookup("more")))
+                  )
+                ),
+                Some(SourceFileLocation(19))
+              )
+            ),
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(
+                  OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                           "out",
+                                           IdentifierMemberAccess("in_n_out", "out", List.empty)
+                  )
+                )
+              )
+            ),
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(14))
+          )
         ),
-        tasks = Vector(TaskDefinitionElement(
-          name = "in_n_out",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "total", None),
-            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "amount", None)))),
-          declarations = Vector.empty,
-          outputsSection = Some(OutputsSectionElement(Vector(
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "out", Add(ReadInt(StdoutElement), PrimitiveLiteralExpressionElement(WomInteger(1))))))),
-          commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(
-            StringCommandPartElement("echo "),
-            PlaceholderCommandPartElement(IdentifierLookup("total"), PlaceholderAttributeSet.empty),
-            StringCommandPartElement(" ")
-          )))),
-          runtimeSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3))
-        ))
+        tasks = Vector(
+          TaskDefinitionElement(
+            name = "in_n_out",
+            inputsSection = Some(
+              InputsSectionElement(
+                Vector(InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "total", None),
+                       InputDeclarationElement(PrimitiveTypeElement(WomStringType), "amount", None)
+                )
+              )
+            ),
+            declarations = Vector.empty,
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(
+                  OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                           "out",
+                                           Add(ReadInt(StdoutElement), PrimitiveLiteralExpressionElement(WomInteger(1)))
+                  )
+                )
+              )
+            ),
+            commandSection = CommandSectionElement(
+              Vector(
+                CommandSectionLine(
+                  Vector(
+                    StringCommandPartElement("echo "),
+                    PlaceholderCommandPartElement(IdentifierLookup("total"), PlaceholderAttributeSet.empty),
+                    StringCommandPartElement(" ")
+                  )
+                )
+              )
+            ),
+            runtimeSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        )
       ),
     "afters" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "afters",
-          inputsSection = None,
-          graphElements = Set(
-            CallElement("foo", None, Vector.empty, Some(CallBodyElement(Vector(KvPair("i", ExpressionElement.PrimitiveLiteralExpressionElement(WomInteger(5)))))),
-                        Some(SourceFileLocation(4))),
-            CallElement("foo", Some("foo2"), Vector("foo"), Some(CallBodyElement(Vector(KvPair("i", ExpressionElement.PrimitiveLiteralExpressionElement(WomInteger(6)))))),
-                        Some(SourceFileLocation(5)))
-          ),
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3)))
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "afters",
+            inputsSection = None,
+            graphElements = Set(
+              CallElement(
+                "foo",
+                None,
+                Vector.empty,
+                Some(
+                  CallBodyElement(
+                    Vector(KvPair("i", ExpressionElement.PrimitiveLiteralExpressionElement(WomInteger(5))))
+                  )
+                ),
+                Some(SourceFileLocation(4))
+              ),
+              CallElement(
+                "foo",
+                Some("foo2"),
+                Vector("foo"),
+                Some(
+                  CallBodyElement(
+                    Vector(KvPair("i", ExpressionElement.PrimitiveLiteralExpressionElement(WomInteger(6))))
+                  )
+                ),
+                Some(SourceFileLocation(5))
+              )
+            ),
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
         ),
-        tasks = Vector(TaskDefinitionElement(
-          name = "foo",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", None)))),
-          declarations = Vector.empty,
-          outputsSection = None,
-          commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(
-            StringCommandPartElement("cat \"hello "),
-            PlaceholderCommandPartElement(IdentifierLookup("i"), PlaceholderAttributeSet.empty),
-            StringCommandPartElement("\" > /tmp/helloFile")
-          )))),
-          runtimeSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(8))
-        ))
+        tasks = Vector(
+          TaskDefinitionElement(
+            name = "foo",
+            inputsSection = Some(
+              InputsSectionElement(Vector(InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", None)))
+            ),
+            declarations = Vector.empty,
+            outputsSection = None,
+            commandSection = CommandSectionElement(
+              Vector(
+                CommandSectionLine(
+                  Vector(
+                    StringCommandPartElement("cat \"hello "),
+                    PlaceholderCommandPartElement(IdentifierLookup("i"), PlaceholderAttributeSet.empty),
+                    StringCommandPartElement("\" > /tmp/helloFile")
+                  )
+                )
+              )
+            ),
+            runtimeSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(8))
+          )
+        )
       ),
     "cascades_escaping" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "escapes",
-          inputsSection = None,
-          graphElements = Set(
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"backslash",StringExpression(Vector(StringLiteral(" "), BackslashEscape, StringLiteral(" ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"n",StringExpression(Vector(StringLiteral(" "), NewlineEscape, StringLiteral(" ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"t",StringExpression(Vector(StringLiteral(" "), TabEscape, StringLiteral(" ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q1",StringExpression(Vector(StringLiteral("leading text "), DoubleQuoteEscape, StringLiteral(" trailing text")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q2",StringLiteral("\"")),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q3",StringExpression(Vector(StringLiteral("  "), DoubleQuoteEscape, StringLiteral("  ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q4",StringExpression(Vector(StringLiteral("leading text "), SingleQuoteEscape, StringLiteral(" trailing text")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q5",StringLiteral("'")),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"q6",StringExpression(Vector(StringLiteral("  "), SingleQuoteEscape, StringLiteral("  ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq1",StringExpression(Vector(StringLiteral("leading text "), DoubleQuoteEscape, StringLiteral(" trailing text")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq2",StringLiteral("\"")),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq3",StringExpression(Vector(StringLiteral("  "), DoubleQuoteEscape, StringLiteral("  ")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq4",StringExpression(Vector(StringLiteral("leading text "), SingleQuoteEscape, StringLiteral(" trailing text")))),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq5",StringLiteral("'")),
-            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),"sq6",StringExpression(Vector(StringLiteral("  "), SingleQuoteEscape, StringLiteral("  ")))),
-            IntermediateValueDeclarationElement(
-              PrimitiveTypeElement(WomStringType),
-              "octal_hello",
-              StringExpression(Vector(UnicodeCharacterEscape(104), UnicodeCharacterEscape(101), UnicodeCharacterEscape(108), UnicodeCharacterEscape(108), UnicodeCharacterEscape(111)))
-            ),
-            IntermediateValueDeclarationElement(
-              PrimitiveTypeElement(WomStringType),
-              "hex_hello",
-              StringExpression(Vector(UnicodeCharacterEscape(104), UnicodeCharacterEscape(101), UnicodeCharacterEscape(108), UnicodeCharacterEscape(108), UnicodeCharacterEscape(111)))
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "escapes",
+            inputsSection = None,
+            graphElements = Set(
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "backslash",
+                StringExpression(Vector(StringLiteral(" "), BackslashEscape, StringLiteral(" ")))
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "n",
+                StringExpression(Vector(StringLiteral(" "), NewlineEscape, StringLiteral(" ")))
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "t",
+                StringExpression(Vector(StringLiteral(" "), TabEscape, StringLiteral(" ")))
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                                  "q1",
+                                                  StringExpression(
+                                                    Vector(StringLiteral("leading text "),
+                                                           DoubleQuoteEscape,
+                                                           StringLiteral(" trailing text")
+                                                    )
+                                                  )
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "q2", StringLiteral("\"")),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "q3",
+                StringExpression(Vector(StringLiteral("  "), DoubleQuoteEscape, StringLiteral("  ")))
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                                  "q4",
+                                                  StringExpression(
+                                                    Vector(StringLiteral("leading text "),
+                                                           SingleQuoteEscape,
+                                                           StringLiteral(" trailing text")
+                                                    )
+                                                  )
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "q5", StringLiteral("'")),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "q6",
+                StringExpression(Vector(StringLiteral("  "), SingleQuoteEscape, StringLiteral("  ")))
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                                  "sq1",
+                                                  StringExpression(
+                                                    Vector(StringLiteral("leading text "),
+                                                           DoubleQuoteEscape,
+                                                           StringLiteral(" trailing text")
+                                                    )
+                                                  )
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "sq2", StringLiteral("\"")),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "sq3",
+                StringExpression(Vector(StringLiteral("  "), DoubleQuoteEscape, StringLiteral("  ")))
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                                  "sq4",
+                                                  StringExpression(
+                                                    Vector(StringLiteral("leading text "),
+                                                           SingleQuoteEscape,
+                                                           StringLiteral(" trailing text")
+                                                    )
+                                                  )
+              ),
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "sq5", StringLiteral("'")),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "sq6",
+                StringExpression(Vector(StringLiteral("  "), SingleQuoteEscape, StringLiteral("  ")))
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "octal_hello",
+                StringExpression(
+                  Vector(UnicodeCharacterEscape(104),
+                         UnicodeCharacterEscape(101),
+                         UnicodeCharacterEscape(108),
+                         UnicodeCharacterEscape(108),
+                         UnicodeCharacterEscape(111)
+                  )
+                )
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "hex_hello",
+                StringExpression(
+                  Vector(UnicodeCharacterEscape(104),
+                         UnicodeCharacterEscape(101),
+                         UnicodeCharacterEscape(108),
+                         UnicodeCharacterEscape(108),
+                         UnicodeCharacterEscape(111)
+                  )
+                )
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomStringType),
+                "unicode_hello",
+                StringExpression(
+                  Vector(
+                    UnicodeCharacterEscape(104),
+                    UnicodeCharacterEscape(101),
+                    UnicodeCharacterEscape(108),
+                    UnicodeCharacterEscape(108),
+                    UnicodeCharacterEscape(111)
+                  )
+                )
+              )
             ),
-            IntermediateValueDeclarationElement(
-              PrimitiveTypeElement(WomStringType),
-              "unicode_hello",
-              StringExpression(Vector(
-                UnicodeCharacterEscape(104),
-                UnicodeCharacterEscape(101),
-                UnicodeCharacterEscape(108),
-                UnicodeCharacterEscape(108),
-                UnicodeCharacterEscape(111)
-              ))
-            )
-          ),
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3))
-        )),
-        tasks = Vector.empty)
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        ),
+        tasks = Vector.empty
+      )
   )
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
index 4276d882b46..65a03812c25 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
@@ -17,8 +17,8 @@ class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.expressionConsumedValueHooks should be(Set.empty)
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set.empty)
     }
   }
 
@@ -26,8 +26,8 @@ class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     val str = "3 + three"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("three")))
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("three")))
     }
   }
 
@@ -35,8 +35,8 @@ class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     val str = "as_map(my_task.out)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedCallOutputOrIdentifierAndMemberAccessHook("my_task", "out")))
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedCallOutputOrIdentifierAndMemberAccessHook("my_task", "out")))
     }
   }
 
@@ -44,8 +44,8 @@ class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     val str = "as_pairs(as_map(my_task.out))"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedCallOutputOrIdentifierAndMemberAccessHook("my_task", "out")))
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedCallOutputOrIdentifierAndMemberAccessHook("my_task", "out")))
     }
   }
 
@@ -53,8 +53,8 @@ class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     val str = """ sep(my_separator, ["a", "b", c]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_separator"), UnlinkedIdentifierHook("c")))
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_separator"), UnlinkedIdentifierHook("c")))
     }
   }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
index a65bd73c8a9..6e0a828855e 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
@@ -18,8 +18,8 @@ class CascadesFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomIntegerType) shouldBeValid Set.empty
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomIntegerType) shouldBeValid Set.empty
     }
   }
 
@@ -27,8 +27,11 @@ class CascadesFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """as_pairs(read_map("my_map.txt"))"""
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomArrayType(WomPairType(WomStringType, WomStringType))) shouldBeValid Set(WomSingleFile("my_map.txt"))
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty,
+                                     NoIoFunctionSet,
+                                     WomArrayType(WomPairType(WomStringType, WomStringType))
+      ) shouldBeValid Set(WomSingleFile("my_map.txt"))
     }
   }
 
@@ -36,8 +39,10 @@ class CascadesFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """ sep(' ', read_lines("foo.txt")) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(WomSingleFile("foo.txt"))
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
     }
   }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
index b6944e4485a..96c3c51e937 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
@@ -15,8 +15,8 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateType(Map.empty) shouldBeValid WomIntegerType
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomIntegerType
     }
   }
 
@@ -24,8 +24,8 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """as_map([(1,2), (3,4)])"""
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateType(Map.empty) shouldBeValid WomMapType(WomIntegerType, WomIntegerType)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomMapType(WomIntegerType, WomIntegerType)
     }
   }
 
@@ -33,8 +33,8 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """as_pairs({ "one": 1, "two": 2, "three": 3 })"""
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomPairType(WomStringType, WomIntegerType))
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomPairType(WomStringType, WomIntegerType))
     }
   }
 
@@ -42,8 +42,8 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """ sep(' ', ["a", "b", "c"]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateType(Map.empty) shouldBeValid WomStringType
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomStringType
     }
   }
 
@@ -51,8 +51,8 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val str = """ sep(' ', prefix("-i ", ["a", "b", "c"])) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateType(Map.empty) shouldBeValid WomStringType
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomStringType
     }
   }
 
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
index 7055da1c1ae..6dbad32d7d0 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
@@ -23,8 +23,8 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomInteger(6), Seq.empty)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomInteger(6), Seq.empty)
     }
   }
 
@@ -32,14 +32,16 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     val str = """ as_map( [("x", 1), ("y", 2), ("z", 3)] ) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    val expectedMap: WomMap = WomMap(Map (
-      WomString("x") -> WomInteger(1),
-      WomString("y") -> WomInteger(2),
-      WomString("z") -> WomInteger(3)
-    ))
+    val expectedMap: WomMap = WomMap(
+      Map(
+        WomString("x") -> WomInteger(1),
+        WomString("y") -> WomInteger(2),
+        WomString("z") -> WomInteger(3)
+      )
+    )
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
     }
   }
 
@@ -50,14 +52,16 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       val expr = fromString[ExpressionElement](str, parser.parse_e)
 
       val inputs = Map("three" -> WomString("three"))
-      val expectedPairs: WomArray = WomArray(Seq(
-        WomPair(WomInteger(1), WomString("one")),
-        WomPair(WomInteger(2), WomString("two")),
-        WomPair(WomInteger(3), WomString("three"))
-      ))
-
-      expr.shouldBeValidPF {
-        case e => e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPairs, Seq.empty)
+      val expectedPairs: WomArray = WomArray(
+        Seq(
+          WomPair(WomInteger(1), WomString("one")),
+          WomPair(WomInteger(2), WomString("two")),
+          WomPair(WomInteger(3), WomString("three"))
+        )
+      )
+
+      expr.shouldBeValidPF { case e =>
+        e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPairs, Seq.empty)
       }
       ()
     }
@@ -73,16 +77,18 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       val str = """ as_pairs(as_map(echo_me)) """
       val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-      val expectedPairs: WomArray = WomArray(Seq(
-        WomPair(WomInteger(1), WomString("one")),
-        WomPair(WomInteger(2), WomString("two")),
-        WomPair(WomInteger(3), WomString("three"))
-      ))
+      val expectedPairs: WomArray = WomArray(
+        Seq(
+          WomPair(WomInteger(1), WomString("one")),
+          WomPair(WomInteger(2), WomString("two")),
+          WomPair(WomInteger(3), WomString("three"))
+        )
+      )
 
       val inputs = Map("echo_me" -> expectedPairs)
 
-      expr.shouldBeValidPF {
-        case e => e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPairs, Seq.empty)
+      expr.shouldBeValidPF { case e =>
+        e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPairs, Seq.empty)
       }
       ()
     }
@@ -95,8 +101,11 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       val str = """ as_map( [("x", 1), ("y", 2), ("x", 3)] ) """
       val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-      expr.shouldBeValidPF {
-        case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None).shouldBeInvalid("""Cannot evaluate 'as_map' with duplicated keys: keys can only appear once but "x" appeared 2 times.""")
+      expr.shouldBeValidPF { case e =>
+        e.evaluateValue(Map.empty, NoIoFunctionSet, None)
+          .shouldBeInvalid(
+            """Cannot evaluate 'as_map' with duplicated keys: keys can only appear once but "x" appeared 2 times."""
+          )
       }
       ()
     }
@@ -109,13 +118,15 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       val str = """ collect_by_key( [("x", 1), ("y", 2), ("x", 3)] ) """
       val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-      val expectedMap: WomMap = WomMap(Map(
-        WomString("x") -> WomArray(Seq(WomInteger(1), WomInteger(3))),
-        WomString("y") -> WomArray(Seq(WomInteger(2)))
-      ))
+      val expectedMap: WomMap = WomMap(
+        Map(
+          WomString("x") -> WomArray(Seq(WomInteger(1), WomInteger(3))),
+          WomString("y") -> WomArray(Seq(WomInteger(2)))
+        )
+      )
 
-      expr.shouldBeValidPF {
-        case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
+      expr.shouldBeValidPF { case e =>
+        e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
       }
       ()
     }
@@ -129,13 +140,16 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     )
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-    val expectedMap: WomMap = WomMap(WomMapType(WomStringType, WomOptionalType(WomStringType)), Map (
-      WomString("i") -> WomOptionalValue(WomStringType, Some(WomString("1"))),
-      WomString("s") -> WomOptionalValue(WomStringType, Some(WomString("two")))
-    ))
+    val expectedMap: WomMap = WomMap(
+      WomMapType(WomStringType, WomOptionalType(WomStringType)),
+      Map(
+        WomString("i") -> WomOptionalValue(WomStringType, Some(WomString("1"))),
+        WomString("s") -> WomOptionalValue(WomStringType, Some(WomString("two")))
+      )
+    )
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedMap, Seq.empty)
     }
   }
 
@@ -158,8 +172,8 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         val expectedEvaluation = WomString(expected)
         val expr = fromString[ExpressionElement](str, parser.parse_e)
 
-        expr.shouldBeValidPF {
-          case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedEvaluation, Seq.empty)
+        expr.shouldBeValidPF { case e =>
+          e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedEvaluation, Seq.empty)
         }
       }
     }
@@ -171,8 +185,8 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
 
     val expectedString: WomString = WomString("a b c")
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
     }
   }
 
@@ -182,8 +196,8 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
 
     val expectedString: WomString = WomString("-i a -i b -i c")
 
-    expr.shouldBeValidPF {
-      case e => e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
     }
   }
 }
diff --git a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomBundleMakers.scala b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomBundleMakers.scala
index b74e3bbbb34..e2bcb384617 100644
--- a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomBundleMakers.scala
+++ b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomBundleMakers.scala
@@ -5,7 +5,7 @@ import cats.syntax.traverse._
 import cats.instances.list._
 import common.Checked
 import common.validation.ErrorOr.ErrorOr
-import wdl.draft2.model.{WdlNamespace, WdlNamespaceWithWorkflow, WdlNamespaceWithoutWorkflow}
+import wdl.draft2.model.{WdlNamespace, WdlNamespaceWithoutWorkflow, WdlNamespaceWithWorkflow}
 import wom.callable.{TaskDefinition, WorkflowDefinition}
 import wom.executable.WomBundle
 import wom.transforms.WomWorkflowDefinitionMaker.ops._
@@ -16,7 +16,8 @@ object WdlDraft2WomBundleMakers {
 
   implicit val wdlDraft2NamespaceWomBundleMaker: WomBundleMaker[WdlNamespace] = new WomBundleMaker[WdlNamespace] {
     override def toWomBundle(from: WdlNamespace): Checked[WomBundle] = {
-      val workflowsValidation: ErrorOr[List[WorkflowDefinition]] = from.workflows.toList.traverse(_.toWomWorkflowDefinition(isASubworkflow = false))
+      val workflowsValidation: ErrorOr[List[WorkflowDefinition]] =
+        from.workflows.toList.traverse(_.toWomWorkflowDefinition(isASubworkflow = false))
       val tasksValidation: ErrorOr[List[TaskDefinition]] = from.tasks.toList.traverse(_.toWomTaskDefinition)
 
       val errorOr = (workflowsValidation, tasksValidation) mapN { (workflows, tasks) =>
@@ -24,16 +25,21 @@ object WdlDraft2WomBundleMakers {
           if (workflows.size == 1) {
             workflows.headOption
           } else None
-        WomBundle(primary, (tasks ++ workflows).map(c => c.name -> c).toMap, Map.empty, from.resolvedImportRecords) }
+        WomBundle(primary, (tasks ++ workflows).map(c => c.name -> c).toMap, Map.empty, from.resolvedImportRecords)
+      }
       errorOr.toEither
     }
   }
 
-  implicit val wdlDraft2NamespaceWithWorkflowWomBundleMaker: WomBundleMaker[WdlNamespaceWithWorkflow] = new WomBundleMaker[WdlNamespaceWithWorkflow] {
-    override def toWomBundle(a: WdlNamespaceWithWorkflow): Checked[WomBundle] = wdlDraft2NamespaceWomBundleMaker.toWomBundle(a)
-  }
+  implicit val wdlDraft2NamespaceWithWorkflowWomBundleMaker: WomBundleMaker[WdlNamespaceWithWorkflow] =
+    new WomBundleMaker[WdlNamespaceWithWorkflow] {
+      override def toWomBundle(a: WdlNamespaceWithWorkflow): Checked[WomBundle] =
+        wdlDraft2NamespaceWomBundleMaker.toWomBundle(a)
+    }
 
-  implicit val wdlDraft2NamespaceWithoutWorkflowWomBundleMaker: WomBundleMaker[WdlNamespaceWithoutWorkflow] = new WomBundleMaker[WdlNamespaceWithoutWorkflow] {
-    override def toWomBundle(a: WdlNamespaceWithoutWorkflow): Checked[WomBundle] = wdlDraft2NamespaceWomBundleMaker.toWomBundle(a)
-  }
+  implicit val wdlDraft2NamespaceWithoutWorkflowWomBundleMaker: WomBundleMaker[WdlNamespaceWithoutWorkflow] =
+    new WomBundleMaker[WdlNamespaceWithoutWorkflow] {
+      override def toWomBundle(a: WdlNamespaceWithoutWorkflow): Checked[WomBundle] =
+        wdlDraft2NamespaceWomBundleMaker.toWomBundle(a)
+    }
 }
diff --git a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCallNodeMaker.scala b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCallNodeMaker.scala
index 442c938c834..323ab7cd859 100644
--- a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCallNodeMaker.scala
+++ b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCallNodeMaker.scala
@@ -11,16 +11,31 @@ import wdl.draft2.parser.WdlParser.Terminal
 import wom.SourceFileLocation
 import wom.callable.Callable
 import wom.graph.CallNode._
-import wom.callable.Callable.{InputDefinition, OverridableInputDefinitionWithDefault, OptionalInputDefinition, RequiredInputDefinition}
+import wom.callable.Callable.{
+  InputDefinition,
+  OptionalInputDefinition,
+  OverridableInputDefinitionWithDefault,
+  RequiredInputDefinition
+}
 import wom.transforms.WomCallableMaker.ops._
 import wom.graph.CallNode.{InputDefinitionFold, InputDefinitionPointer}
 import wom.graph.GraphNodePort.OutputPort
-import wom.graph.expression.{AnonymousExpressionNode, ExpressionNode, PlainAnonymousExpressionNode, TaskCallInputExpressionNode}
+import wom.graph.expression.{
+  AnonymousExpressionNode,
+  ExpressionNode,
+  PlainAnonymousExpressionNode,
+  TaskCallInputExpressionNode
+}
 import wom.graph._
 import wom.transforms.WomCallNodeMaker
 
 object WdlDraft2WomCallNodeMaker extends WomCallNodeMaker[WdlCall] {
-  override def toWomCallNode(wdlCall: WdlCall, localLookup: Map[String, GraphNodePort.OutputPort], outerLookup: Map[String, GraphNodePort.OutputPort], preserveIndexForOuterLookups: Boolean, inASubworkflow: Boolean): ErrorOr[CallNode.CallNodeAndNewNodes] = {
+  override def toWomCallNode(wdlCall: WdlCall,
+                             localLookup: Map[String, GraphNodePort.OutputPort],
+                             outerLookup: Map[String, GraphNodePort.OutputPort],
+                             preserveIndexForOuterLookups: Boolean,
+                             inASubworkflow: Boolean
+  ): ErrorOr[CallNode.CallNodeAndNewNodes] = {
 
     import common.validation.ErrorOr._
 
@@ -28,68 +43,80 @@ object WdlDraft2WomCallNodeMaker extends WomCallNodeMaker[WdlCall] {
 
     // A validation that all inputs to the call were actually wanted:
     def allInputsWereWantedValidation(callable: Callable): ErrorOr[Unit] = {
-      val callableExpectedInputs = callable.inputs.collect {
-        case r: RequiredInputDefinition => r
-        case o: OptionalInputDefinition => o
-        // Draft 2 values are non-overridable if they have upstream dependencies, so filter for those:
-        case id: OverridableInputDefinitionWithDefault if id.default.inputs.isEmpty => id
-      }.map(_.localName.value)
+      val callableExpectedInputs = callable.inputs
+        .collect {
+          case r: RequiredInputDefinition => r
+          case o: OptionalInputDefinition => o
+          // Draft 2 values are non-overridable if they have upstream dependencies, so filter for those:
+          case id: OverridableInputDefinitionWithDefault if id.default.inputs.isEmpty => id
+        }
+        .map(_.localName.value)
       val unexpectedInputs: Option[NonEmptyList[String]] = NonEmptyList.fromList(wdlCall.inputMappings.toList collect {
         case (inputName, _) if !callableExpectedInputs.contains(inputName) => inputName
       })
 
       unexpectedInputs match {
         case None => ().validNel
-        case Some(unexpectedInputsNel) => (unexpectedInputsNel map { unexpectedInput =>
-          s"Invalid call to '${callable.name}': Didn't expect the input '$unexpectedInput'. Check that this input is declared in the task or workflow. Note that intermediate values (declarations with values that depend on previous values) cannot be overridden."
-        }).invalid
+        case Some(unexpectedInputsNel) =>
+          (unexpectedInputsNel map { unexpectedInput =>
+            s"Invalid call to '${callable.name}': Didn't expect the input '$unexpectedInput'. Check that this input is declared in the task or workflow. Note that intermediate values (declarations with values that depend on previous values) cannot be overridden."
+          }).invalid
       }
     }
 
     /*
-      * Each input mapping gets its own ExpressionNode:
-      *
-      * call my_task { input:
-      *   input1 = "hi!"                -> ExpressionNode with no input port
-      *   input3 = other_task.out + 2   -> ExpressionNode with an input port pointing to the output port of other_task.out
-      * }
+     * Each input mapping gets its own ExpressionNode:
+     *
+     * call my_task { input:
+     *   input1 = "hi!"                -> ExpressionNode with no input port
+     *   input3 = other_task.out + 2   -> ExpressionNode with an input port pointing to the output port of other_task.out
+     * }
      */
     def expressionNodeMappings: ErrorOr[Map[LocalName, AnonymousExpressionNode]] = {
       val precomputedOgins: Map[String, OutputPort] = outerLookup collect {
-        case (name, port) if !localLookup.contains(name) => name -> OuterGraphInputNode(WomIdentifier(name), port, preserveIndexForOuterLookups).singleOutputPort
+        case (name, port) if !localLookup.contains(name) =>
+          name -> OuterGraphInputNode(WomIdentifier(name), port, preserveIndexForOuterLookups).singleOutputPort
       }
       val newLocalLookup = localLookup ++ precomputedOgins
-      wdlCall.inputMappings traverse {
-        case (inputName, wdlExpression) =>
-          val identifier = wdlCall.womIdentifier.combine(inputName)
-          val constructor = wdlCall match {
-            case _: WdlTaskCall => TaskCallInputExpressionNode.apply _
-            case _ => PlainAnonymousExpressionNode.apply _
-          }
-
-          WdlWomExpression.toAnonymousExpressionNode(identifier, WdlWomExpression(wdlExpression, wdlCall), newLocalLookup, Map.empty, preserveIndexForOuterLookups, wdlCall, constructor) map {
-            LocalName(inputName) -> _
-          }
+      wdlCall.inputMappings traverse { case (inputName, wdlExpression) =>
+        val identifier = wdlCall.womIdentifier.combine(inputName)
+        val constructor = wdlCall match {
+          case _: WdlTaskCall => TaskCallInputExpressionNode.apply _
+          case _ => PlainAnonymousExpressionNode.apply _
+        }
+
+        WdlWomExpression.toAnonymousExpressionNode(identifier,
+                                                   WdlWomExpression(wdlExpression, wdlCall),
+                                                   newLocalLookup,
+                                                   Map.empty,
+                                                   preserveIndexForOuterLookups,
+                                                   wdlCall,
+                                                   constructor
+        ) map {
+          LocalName(inputName) -> _
+        }
       }
     }
 
     /*
-      * Fold over the input definitions and
-      * 1) assign each input definition its InputDefinitionPointer
-      * 2) if necessary, create a graph input node and assign its output port to the input definition
-      *
-      * The InputDefinitionFold accumulates the input definition mappings, the create graph input nodes, and the expression nodes.
+     * Fold over the input definitions and
+     * 1) assign each input definition its InputDefinitionPointer
+     * 2) if necessary, create a graph input node and assign its output port to the input definition
+     *
+     * The InputDefinitionFold accumulates the input definition mappings, the create graph input nodes, and the expression nodes.
      */
-    def foldInputDefinitions(expressionNodes: Map[LocalName, ExpressionNode], callable: Callable): InputDefinitionFold = {
+    def foldInputDefinitions(expressionNodes: Map[LocalName, ExpressionNode],
+                             callable: Callable
+    ): InputDefinitionFold = {
       // Updates the fold with a new graph input node. Happens when an optional or required undefined input without an
       // expression node mapping is found
-      def withGraphInputNode(inputDefinition: InputDefinition, graphInputNode: ExternalGraphInputNode) = {
+      def withGraphInputNode(inputDefinition: InputDefinition, graphInputNode: ExternalGraphInputNode) =
         InputDefinitionFold(
-          mappings = List(inputDefinition -> Coproduct[InputDefinitionPointer](graphInputNode.singleOutputPort: OutputPort)),
+          mappings =
+            List(inputDefinition -> Coproduct[InputDefinitionPointer](graphInputNode.singleOutputPort: OutputPort)),
           callInputPorts = Set(callNodeBuilder.makeInputPort(inputDefinition, graphInputNode.singleOutputPort)),
           newGraphInputNodes = Set(graphInputNode)
         )
-      }
 
       callable.inputs.foldMap {
         // If there is an input mapping for this input definition, use that
@@ -103,25 +130,29 @@ object WdlDraft2WomCallNodeMaker extends WomCallNodeMaker[WdlCall] {
           )
 
         // No input mapping, either not an input or in a subworkflow: use the default expression
-        case withDefault@OverridableInputDefinitionWithDefault(_, _, expression, _, _) if inASubworkflow || expression.inputs.nonEmpty =>
+        case withDefault @ OverridableInputDefinitionWithDefault(_, _, expression, _, _)
+            if inASubworkflow || expression.inputs.nonEmpty =>
           InputDefinitionFold(
             mappings = List(withDefault -> Coproduct[InputDefinitionPointer](expression))
           )
 
         // No input mapping and in a top-level workflow: add an input with a default
-        case withDefault@OverridableInputDefinitionWithDefault(n, womType, expression, _, _) =>
+        case withDefault @ OverridableInputDefinitionWithDefault(n, womType, expression, _, _) =>
           val identifier = wdlCall.womIdentifier.combine(n)
-          withGraphInputNode(withDefault, OptionalGraphInputNodeWithDefault(identifier, womType, expression, identifier.fullyQualifiedName.value))
+          withGraphInputNode(
+            withDefault,
+            OptionalGraphInputNodeWithDefault(identifier, womType, expression, identifier.fullyQualifiedName.value)
+          )
 
         // No input mapping, required and we don't have a default value, create a new RequiredGraphInputNode
         // so that it can be satisfied via workflow inputs
-        case required@RequiredInputDefinition(n, womType, _, _) =>
+        case required @ RequiredInputDefinition(n, womType, _, _) =>
           val identifier = wdlCall.womIdentifier.combine(n)
           withGraphInputNode(required, RequiredGraphInputNode(identifier, womType, identifier.fullyQualifiedName.value))
 
         // No input mapping, no default value but optional, create a OptionalGraphInputNode
         // so that it can be satisfied via workflow inputs
-        case optional@OptionalInputDefinition(n, womType, _, _) =>
+        case optional @ OptionalInputDefinition(n, womType, _, _) =>
           val identifier = wdlCall.womIdentifier.combine(n)
           withGraphInputNode(optional, OptionalGraphInputNode(identifier, womType, identifier.fullyQualifiedName.value))
 
@@ -139,11 +170,13 @@ object WdlDraft2WomCallNodeMaker extends WomCallNodeMaker[WdlCall] {
         // Figure out the line number by looking at the AST
         val t: Terminal = AstTools.findTerminals(wdlCall.ast).head
 
-        val callNodeAndNewNodes = callNodeBuilder.build(wdlCall.womIdentifier,
-                                                        callable,
-                                                        foldInputDefinitions(mappings, callable).copy(usedOuterGraphInputNodes = usedOgins),
-                                                        Set.empty,
-                                                        Some(SourceFileLocation(t.getLine)))
+        val callNodeAndNewNodes = callNodeBuilder.build(
+          wdlCall.womIdentifier,
+          callable,
+          foldInputDefinitions(mappings, callable).copy(usedOuterGraphInputNodes = usedOgins),
+          Set.empty,
+          Some(SourceFileLocation(t.getLine))
+        )
 
         // If the created node is a `TaskCallNode` the created input expressions should be `TaskCallInputExpressionNode`s
         // and should be assigned a reference to the `TaskCallNode`. This is used in the `WorkflowExecutionActor` to
diff --git a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCommandTaskDefinitionMaker.scala b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCommandTaskDefinitionMaker.scala
index f23069a1f5b..9d59abfe142 100644
--- a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCommandTaskDefinitionMaker.scala
+++ b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomCommandTaskDefinitionMaker.scala
@@ -5,13 +5,12 @@ import common.validation.ErrorOr.ErrorOr
 import wdl.draft2.model.{AstTools, WdlTask, WdlWomExpression}
 import wdl.draft2.parser.WdlParser.Terminal
 import wom.SourceFileLocation
-import wom.callable.Callable.{OverridableInputDefinitionWithDefault, OptionalInputDefinition, RequiredInputDefinition}
+import wom.callable.Callable.{OptionalInputDefinition, OverridableInputDefinitionWithDefault, RequiredInputDefinition}
 import wom.callable.{Callable, CallableTaskDefinition, CommandTaskDefinition, MetaValueElement}
 import wom.graph.LocalName
 import wom.transforms.WomCommandTaskDefinitionMaker
 import wom.types.WomOptionalType
 
-
 object WdlDraft2WomCommandTaskDefinitionMaker extends WomCommandTaskDefinitionMaker[WdlTask] {
 
   override def toWomTaskDefinition(wdlTask: WdlTask): ErrorOr[CommandTaskDefinition] = {
@@ -22,7 +21,10 @@ object WdlDraft2WomCommandTaskDefinitionMaker extends WomCommandTaskDefinitionMa
       case d if d.expression.isEmpty && d.womType.isInstanceOf[WomOptionalType] =>
         OptionalInputDefinition(LocalName(d.unqualifiedName), d.womType.asInstanceOf[WomOptionalType])
       case d if d.expression.nonEmpty =>
-        OverridableInputDefinitionWithDefault(LocalName(d.unqualifiedName), d.womType, WdlWomExpression(d.expression.get, wdlTask))
+        OverridableInputDefinitionWithDefault(LocalName(d.unqualifiedName),
+                                              d.womType,
+                                              WdlWomExpression(d.expression.get, wdlTask)
+        )
     }).toList
 
     // Figure out the start line of the workflow in the source file
@@ -30,12 +32,10 @@ object WdlDraft2WomCommandTaskDefinitionMaker extends WomCommandTaskDefinitionMa
 
     // Draft-2 only support string values. It does not support composite values, or
     // anything
-    def stringifyMetaValues(meta: Map[String, String]): Map[String, MetaValueElement] = {
-      meta map {
-        case (key, value) =>
-          key -> MetaValueElement.MetaValueElementString(value)
+    def stringifyMetaValues(meta: Map[String, String]): Map[String, MetaValueElement] =
+      meta map { case (key, value) =>
+        key -> MetaValueElement.MetaValueElementString(value)
       }
-    }
 
     CallableTaskDefinition(
       name = wdlTask.fullyQualifiedName,
diff --git a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomConditionalNodeMaker.scala b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomConditionalNodeMaker.scala
index f4303e8ebe5..f26463aa723 100644
--- a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomConditionalNodeMaker.scala
+++ b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomConditionalNodeMaker.scala
@@ -14,39 +14,59 @@ import wom.transforms.WomGraphMaker.ops._
 import wom.types.WomBooleanType
 
 object WdlDraft2WomConditionalNodeMaker extends WomConditionalNodeMaker[If] {
+
   /**
     * @param preserveIndexForOuterLookups When we're evaluating the condition boolean, should we preserve scatter index if we have to use the outerLookup?
     */
-  override def toWomConditionalNode(ifBlock: If, localLookup: Map[String, OutputPort], outerLookup: Map[String, OutputPort], preserveIndexForOuterLookups: Boolean, inASubworkflow: Boolean): ErrorOr[ConditionalNodeWithNewNodes] = {
+  override def toWomConditionalNode(ifBlock: If,
+                                    localLookup: Map[String, OutputPort],
+                                    outerLookup: Map[String, OutputPort],
+                                    preserveIndexForOuterLookups: Boolean,
+                                    inASubworkflow: Boolean
+  ): ErrorOr[ConditionalNodeWithNewNodes] = {
 
     /*
-      * Why? Imagine that we're building three nested levels of a innerGraph.
-      * - Say we're building the middle layer.
-      * - We have a set of OutputPorts in the outer layer that we can make OGINs to if we need them.
-      * - We know that the inner graph might want to make use of those output ports, but we don't know which.
-      * - So, we can make OGINs at this layer for all possible OutputPorts in the outer graph and let the inner graph
-      * use however many of them it needs.
-      */
-    val possiblyNeededNestedOgins: Map[String, OuterGraphInputNode] = outerLookup filterNot { case (name, _) => localLookup.contains(name) } map { case (name, outerPort) =>
+     * Why? Imagine that we're building three nested levels of a innerGraph.
+     * - Say we're building the middle layer.
+     * - We have a set of OutputPorts in the outer layer that we can make OGINs to if we need them.
+     * - We know that the inner graph might want to make use of those output ports, but we don't know which.
+     * - So, we can make OGINs at this layer for all possible OutputPorts in the outer graph and let the inner graph
+     * use however many of them it needs.
+     */
+    val possiblyNeededNestedOgins: Map[String, OuterGraphInputNode] = outerLookup filterNot { case (name, _) =>
+      localLookup.contains(name)
+    } map { case (name, outerPort) =>
       /*
-        * preserveIndexForOuterLookups indicates us whether or not nodes in the outerLookup are in the same scatter inn graph as this node
-        * preserveIndexForOuterLookups = false means the outerLookup nodes are outside a scatter containing this conditional node
-        * preserveIndexForOuterLookups = true means the above predicate does not hold
-        *
-        * When creating OGINs from those outer lookup nodes for the inner graph we want to make sure we set their preserveScatterIndex to preserveIndexForOuterLookups
-        * because they effectively represent the outer lookup nodes inside the conditional. So whether the index must be preserved depends on whether this
-        * conditional node has been asked to "preserveIndexForOuterLookups".
+       * preserveIndexForOuterLookups indicates us whether or not nodes in the outerLookup are in the same scatter inn graph as this node
+       * preserveIndexForOuterLookups = false means the outerLookup nodes are outside a scatter containing this conditional node
+       * preserveIndexForOuterLookups = true means the above predicate does not hold
+       *
+       * When creating OGINs from those outer lookup nodes for the inner graph we want to make sure we set their preserveScatterIndex to preserveIndexForOuterLookups
+       * because they effectively represent the outer lookup nodes inside the conditional. So whether the index must be preserved depends on whether this
+       * conditional node has been asked to "preserveIndexForOuterLookups".
        */
       name -> OuterGraphInputNode(WomIdentifier(name), outerPort, preserveScatterIndex = preserveIndexForOuterLookups)
     }
-    val possiblyNeededNestedOginPorts: Map[String, OutputPort] = possiblyNeededNestedOgins map { case (name: String, ogin: OuterGraphInputNode) => name -> ogin.singleOutputPort }
+    val possiblyNeededNestedOginPorts: Map[String, OutputPort] = possiblyNeededNestedOgins map {
+      case (name: String, ogin: OuterGraphInputNode) => name -> ogin.singleOutputPort
+    }
 
     val ifConditionExpression = WdlWomExpression(ifBlock.condition, ifBlock)
     val ifConditionGraphInputExpressionValidation = WdlWomExpression.toAnonymousExpressionNode(
-      WomIdentifier("conditional"), ifConditionExpression, localLookup ++ possiblyNeededNestedOginPorts, Map.empty, preserveIndexForOuterLookups, ifBlock, PlainAnonymousExpressionNode.apply)
-    val ifConditionTypeValidation = ifConditionExpression.evaluateType((localLookup ++ outerLookup).map { case (k, v) => k -> v.womType }) flatMap {
+      WomIdentifier("conditional"),
+      ifConditionExpression,
+      localLookup ++ possiblyNeededNestedOginPorts,
+      Map.empty,
+      preserveIndexForOuterLookups,
+      ifBlock,
+      PlainAnonymousExpressionNode.apply
+    )
+    val ifConditionTypeValidation = ifConditionExpression.evaluateType((localLookup ++ outerLookup).map { case (k, v) =>
+      k -> v.womType
+    }) flatMap {
       case coerceable if WomBooleanType.isCoerceableFrom(coerceable) => Valid(())
-      case other => s"An if block must be given a boolean expression but instead got '${ifBlock.condition.toWomString}' (a ${other.stableName})".invalidNel
+      case other =>
+        s"An if block must be given a boolean expression but instead got '${ifBlock.condition.toWomString}' (a ${other.stableName})".invalidNel
     }
 
     val innerGraphValidation: ErrorOr[Graph] = (ifBlock: Scope).toWomGraph(
@@ -56,8 +76,9 @@ object WdlDraft2WomConditionalNodeMaker extends WomConditionalNodeMaker[If] {
       inASubworkflow = inASubworkflow
     )
 
-    (ifConditionGraphInputExpressionValidation, ifConditionTypeValidation, innerGraphValidation) mapN { (ifConditionGraphInputExpression, _, innerGraph) =>
-      ConditionalNode.wireInConditional(innerGraph, ifConditionGraphInputExpression)
+    (ifConditionGraphInputExpressionValidation, ifConditionTypeValidation, innerGraphValidation) mapN {
+      (ifConditionGraphInputExpression, _, innerGraph) =>
+        ConditionalNode.wireInConditional(innerGraph, ifConditionGraphInputExpression)
     }
   }
 }
diff --git a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomExecutableMakers.scala b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomExecutableMakers.scala
index 9d68dc33528..3d545ee95b5 100644
--- a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomExecutableMakers.scala
+++ b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomExecutableMakers.scala
@@ -1,7 +1,7 @@
 package wdl.transforms.draft2.wdlom2wom
 
 import common.Checked
-import wdl.draft2.model.{WdlNamespace, WdlNamespaceWithWorkflow, WdlNamespaceWithoutWorkflow}
+import wdl.draft2.model.{WdlNamespace, WdlNamespaceWithoutWorkflow, WdlNamespaceWithWorkflow}
 import wdl.transforms.draft2.wdlom2wom.WdlDraft2WomBundleMakers._
 import wdl.shared.transforms.wdlom2wom.WdlSharedInputParsing
 import wom.core.WorkflowJson
@@ -12,20 +12,33 @@ import wom.transforms.WomBundleMaker.ops._
 
 object WdlDraft2WomExecutableMakers {
   implicit val namespaceWomExecutableMaker: WomExecutableMaker[WdlNamespace] = new WomExecutableMaker[WdlNamespace] {
-    override def toWomExecutable(a: WdlNamespace, inputs: Option[WorkflowJson], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
+    override def toWomExecutable(a: WdlNamespace,
+                                 inputs: Option[WorkflowJson],
+                                 ioFunctions: IoFunctionSet,
+                                 strictValidation: Boolean
+    ): Checked[Executable] =
       a.toWomBundle flatMap { bundle =>
         WdlSharedInputParsing.buildWomExecutable(bundle, inputs, ioFunctions, strictValidation)
       }
-    }
   }
 
-  implicit val namespaceWithWorkflowWomExecutableMaker: WomExecutableMaker[WdlNamespaceWithWorkflow] = new WomExecutableMaker[WdlNamespaceWithWorkflow] {
-    override def toWomExecutable(a: WdlNamespaceWithWorkflow, inputs: Option[WorkflowJson], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] =
-      namespaceWomExecutableMaker.toWomExecutable(a, inputs, ioFunctions, strictValidation)
-  }
+  implicit val namespaceWithWorkflowWomExecutableMaker: WomExecutableMaker[WdlNamespaceWithWorkflow] =
+    new WomExecutableMaker[WdlNamespaceWithWorkflow] {
+      override def toWomExecutable(a: WdlNamespaceWithWorkflow,
+                                   inputs: Option[WorkflowJson],
+                                   ioFunctions: IoFunctionSet,
+                                   strictValidation: Boolean
+      ): Checked[Executable] =
+        namespaceWomExecutableMaker.toWomExecutable(a, inputs, ioFunctions, strictValidation)
+    }
 
-  implicit val namespaceWithoutWorkflowWomExecutableMaker: WomExecutableMaker[WdlNamespaceWithoutWorkflow] = new WomExecutableMaker[WdlNamespaceWithoutWorkflow] {
-    override def toWomExecutable(a: WdlNamespaceWithoutWorkflow, inputs: Option[WorkflowJson], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] =
-      namespaceWomExecutableMaker.toWomExecutable(a, inputs, ioFunctions, strictValidation)
-  }
+  implicit val namespaceWithoutWorkflowWomExecutableMaker: WomExecutableMaker[WdlNamespaceWithoutWorkflow] =
+    new WomExecutableMaker[WdlNamespaceWithoutWorkflow] {
+      override def toWomExecutable(a: WdlNamespaceWithoutWorkflow,
+                                   inputs: Option[WorkflowJson],
+                                   ioFunctions: IoFunctionSet,
+                                   strictValidation: Boolean
+      ): Checked[Executable] =
+        namespaceWomExecutableMaker.toWomExecutable(a, inputs, ioFunctions, strictValidation)
+    }
 }
diff --git a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomGraphMaker.scala b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomGraphMaker.scala
index dc6a66627ff..3f2e837dffe 100644
--- a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomGraphMaker.scala
+++ b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomGraphMaker.scala
@@ -24,7 +24,12 @@ object WdlDraft2WomGraphMaker extends WomGraphMaker[Scope] {
     * - Adds in any extras from 'includeGraphNode' which the call knows should also be in the Graph (eg the Scatter variable's InputGraphNode which this method doesn't know exists)
     * - Builds them all together into a Graph
     */
-  override def toWomGraph(scope: Scope, includeGraphNodes: Set[GraphNode], outerLookup: Map[String, OutputPort], preserveIndexForOuterLookups: Boolean, inASubworkflow: Boolean): ErrorOr[Graph] = {
+  override def toWomGraph(scope: Scope,
+                          includeGraphNodes: Set[GraphNode],
+                          outerLookup: Map[String, OutputPort],
+                          preserveIndexForOuterLookups: Boolean,
+                          inASubworkflow: Boolean
+  ): ErrorOr[Graph] = {
 
     final case class FoldState(nodes: Set[GraphNode], availableInputs: Map[String, GraphNodePort.OutputPort])
 
@@ -36,7 +41,13 @@ object WdlDraft2WomGraphMaker extends WomGraphMaker[Scope] {
     )
 
     def foldFunction(acc: Checked[FoldState], node: WdlGraphNode): Checked[FoldState] = acc flatMap { goodAcc =>
-      buildNode(goodAcc, node).leftMap(errors => errors.map(s"Unable to build WOM node for ${node.getClass.getSimpleName} '${node.womIdentifier.localName.value}': " + _)).toEither
+      buildNode(goodAcc, node)
+        .leftMap(errors =>
+          errors.map(
+            s"Unable to build WOM node for ${node.getClass.getSimpleName} '${node.womIdentifier.localName.value}': " + _
+          )
+        )
+        .toEither
     }
 
     def foldInGeneratedNodeAndNewInputs(acc: FoldState)(gnani: GeneratedNodeAndNewNodes): FoldState = {
@@ -66,37 +77,49 @@ object WdlDraft2WomGraphMaker extends WomGraphMaker[Scope] {
     def buildNode(acc: FoldState, node: WdlGraphNode): ErrorOr[FoldState] = node match {
 
       case wdlCall: WdlCall =>
-        wdlCall.toWomCallNode(acc.availableInputs, outerLookup, preserveIndexForOuterLookups, inASubworkflow) map { cnani: CallNodeAndNewNodes =>
-          foldInGeneratedNodeAndNewInputs(acc)(cnani)
+        wdlCall.toWomCallNode(acc.availableInputs, outerLookup, preserveIndexForOuterLookups, inASubworkflow) map {
+          cnani: CallNodeAndNewNodes =>
+            foldInGeneratedNodeAndNewInputs(acc)(cnani)
         }
 
-      case decl: DeclarationInterface => Declaration.buildWdlDeclarationNode(decl, acc.availableInputs, outerLookup, preserveIndexForOuterLookups) map { wdlDeclNode =>
-        // As with GeneratedNodeAndNewInputs, we might have made some new OuterGraphInputNodes to build this DeclarationNode, so
-        // make sure they get included:
-        val declNode = wdlDeclNode.toGraphNode
-        val newOgins: Set[OuterGraphInputNode] = declNode.upstreamOuterGraphInputNodes
-        val newOginOutputs = newOgins.map(_.nameToPortMapping)
-
-        // Add the output port, but only if the value isn't already available as an input from somewhere else
-        val availableOutputPort: Option[(String, OutputPort)] = if(!acc.availableInputs.contains(wdlDeclNode.localName)) {
-          Option(wdlDeclNode.localName -> wdlDeclNode.singleOutputPort)
-        } else {
-          None
+      case decl: DeclarationInterface =>
+        Declaration.buildWdlDeclarationNode(decl, acc.availableInputs, outerLookup, preserveIndexForOuterLookups) map {
+          wdlDeclNode =>
+            // As with GeneratedNodeAndNewInputs, we might have made some new OuterGraphInputNodes to build this DeclarationNode, so
+            // make sure they get included:
+            val declNode = wdlDeclNode.toGraphNode
+            val newOgins: Set[OuterGraphInputNode] = declNode.upstreamOuterGraphInputNodes
+            val newOginOutputs = newOgins.map(_.nameToPortMapping)
+
+            // Add the output port, but only if the value isn't already available as an input from somewhere else
+            val availableOutputPort: Option[(String, OutputPort)] =
+              if (!acc.availableInputs.contains(wdlDeclNode.localName)) {
+                Option(wdlDeclNode.localName -> wdlDeclNode.singleOutputPort)
+              } else {
+                None
+              }
+
+            FoldState(acc.nodes + declNode ++ newOgins, acc.availableInputs ++ newOginOutputs ++ availableOutputPort)
         }
 
-        FoldState(acc.nodes + declNode ++ newOgins, acc.availableInputs ++ newOginOutputs ++ availableOutputPort)
-      }
-
       case scatter: Scatter =>
-        scatter.toWomScatterNode(acc.availableInputs, outerLookup, preserveIndexForOuterLookups, inASubworkflow) map { foldInGeneratedNodeAndNewInputs(acc)(_) }
+        scatter.toWomScatterNode(acc.availableInputs, outerLookup, preserveIndexForOuterLookups, inASubworkflow) map {
+          foldInGeneratedNodeAndNewInputs(acc)(_)
+        }
       case ifBlock: If =>
-        ifBlock.toWomConditionalNode(acc.availableInputs, outerLookup, preserveIndexForOuterLookups, inASubworkflow) map { foldInGeneratedNodeAndNewInputs(acc)(_) }
+        ifBlock.toWomConditionalNode(acc.availableInputs,
+                                     outerLookup,
+                                     preserveIndexForOuterLookups,
+                                     inASubworkflow
+        ) map { foldInGeneratedNodeAndNewInputs(acc)(_) }
 
       case _ => s"Cannot process WdlGraphNodes of type ${node.getClass.getSimpleName} yet!".invalidNel
     }
 
     val nodeList = scope.childGraphNodesSorted
-    val nodeAccumulator: Checked[FoldState] = nodeList flatMap { _.foldLeft[Checked[FoldState]](Right(initialFoldState))(foldFunction) }
+    val nodeAccumulator: Checked[FoldState] = nodeList flatMap {
+      _.foldLeft[Checked[FoldState]](Right(initialFoldState))(foldFunction)
+    }
 
     def outerLinkInputs(nodes: Set[GraphNode]): Set[OuterGraphInputNode] = nodes flatMap {
       // NB: this curious type annotation just gives intelliJ a hand:
diff --git a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomScatterNodeMaker.scala b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomScatterNodeMaker.scala
index f1f018f2307..cc7ee098774 100644
--- a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomScatterNodeMaker.scala
+++ b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomScatterNodeMaker.scala
@@ -17,32 +17,47 @@ object WdlDraft2WomScatterNodeMaker extends WomScatterNodeMaker[Scatter] {
                                 localLookup: Map[String, GraphNodePort.OutputPort],
                                 outerLookup: Map[String, GraphNodePort.OutputPort],
                                 preserveIndexForOuterLookups: Boolean,
-                                inASubworkflow: Boolean): ErrorOr[ScatterNodeWithNewNodes] = {
+                                inASubworkflow: Boolean
+  ): ErrorOr[ScatterNodeWithNewNodes] = {
 
     /*
-      * Why? Imagine that we're building three nested levels of a innerGraph.
-      * - Say we're building the middle layer.
-      * - We have a set of OutputPorts in the outer layer that we can make OGINs to if we need them.
-      * - We know that the inner graph might want to make use of those output ports, but we don't know which.
-      * - So, we can make OGINs at this layer for all possible OutputPorts in the outer graph and let the inner graph
-      * use however many of them it needs.
-      */
-    val possiblyNeededNestedOgins: Map[String, OuterGraphInputNode] = outerLookup filterNot { case (name, _) => localLookup.contains(name) } map { case (name, outerPort) =>
+     * Why? Imagine that we're building three nested levels of a innerGraph.
+     * - Say we're building the middle layer.
+     * - We have a set of OutputPorts in the outer layer that we can make OGINs to if we need them.
+     * - We know that the inner graph might want to make use of those output ports, but we don't know which.
+     * - So, we can make OGINs at this layer for all possible OutputPorts in the outer graph and let the inner graph
+     * use however many of them it needs.
+     */
+    val possiblyNeededNestedOgins: Map[String, OuterGraphInputNode] = outerLookup filterNot { case (name, _) =>
+      localLookup.contains(name)
+    } map { case (name, outerPort) =>
       /*
-        * preserveScatterIndex = false because in the absence of support of nested scatters,
-        * the index should never be preserved when for nodes coming from outside the scatter.
+       * preserveScatterIndex = false because in the absence of support of nested scatters,
+       * the index should never be preserved when for nodes coming from outside the scatter.
        */
       name -> OuterGraphInputNode(WomIdentifier(name), outerPort, preserveScatterIndex = false)
     }
-    val possiblyNeededNestedOginPorts: Map[String, OutputPort] = possiblyNeededNestedOgins map { case (name: String, ogin: OuterGraphInputNode) => name -> ogin.singleOutputPort }
+    val possiblyNeededNestedOginPorts: Map[String, OutputPort] = possiblyNeededNestedOgins map {
+      case (name: String, ogin: OuterGraphInputNode) => name -> ogin.singleOutputPort
+    }
 
     // Convert the scatter collection WdlExpression to a WdlWomExpression
     val scatterCollectionExpression = WdlWomExpression(scatter.collection, scatter)
     // Generate an ExpressionNode from the WdlWomExpression
     val scatterCollectionExpressionNode =
-      WdlWomExpression.toAnonymousExpressionNode(WomIdentifier(scatter.item), scatterCollectionExpression, localLookup ++ possiblyNeededNestedOginPorts, Map.empty, preserveIndexForOuterLookups, scatter, PlainAnonymousExpressionNode.apply)
+      WdlWomExpression.toAnonymousExpressionNode(
+        WomIdentifier(scatter.item),
+        scatterCollectionExpression,
+        localLookup ++ possiblyNeededNestedOginPorts,
+        Map.empty,
+        preserveIndexForOuterLookups,
+        scatter,
+        PlainAnonymousExpressionNode.apply
+      )
     // Validate the collection evaluates to a traversable type
-    val scatterItemTypeValidation = scatterCollectionExpression.evaluateType((localLookup ++ outerLookup).map { case (k, v) => k -> v.womType }) flatMap {
+    val scatterItemTypeValidation = scatterCollectionExpression.evaluateType((localLookup ++ outerLookup).map {
+      case (k, v) => k -> v.womType
+    }) flatMap {
       case WomArrayType(itemType) => Valid(itemType) // Covers maps because this is a custom unapply (see WdlArrayType)
       case other => s"Cannot scatter over a non-traversable type ${other.stableName}".invalidNel
     }
@@ -52,7 +67,11 @@ object WdlDraft2WomScatterNodeMaker extends WomScatterNodeMaker[Scatter] {
       expressionNode <- scatterCollectionExpressionNode
       // Graph input node for the scatter variable in the inner graph. Note that the type is the array's member type
       womInnerGraphScatterVariableInput = ScatterVariableNode(WomIdentifier(scatter.item), expressionNode, itemType)
-      g <- (scatter: Scope).toWomGraph(Set(womInnerGraphScatterVariableInput), localLookup ++ possiblyNeededNestedOginPorts, preserveIndexForOuterLookups = false, inASubworkflow)
+      g <- (scatter: Scope).toWomGraph(Set(womInnerGraphScatterVariableInput),
+                                       localLookup ++ possiblyNeededNestedOginPorts,
+                                       preserveIndexForOuterLookups = false,
+                                       inASubworkflow
+      )
     } yield ScatterNode.scatterOverGraph(g, womInnerGraphScatterVariableInput)
 
   }
diff --git a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomWorkflowDefinitionMaker.scala b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomWorkflowDefinitionMaker.scala
index 6f52e1a8d7e..08fc5349212 100644
--- a/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomWorkflowDefinitionMaker.scala
+++ b/wdl/transforms/draft2/src/main/scala/wdl/transforms/draft2/wdlom2wom/WdlDraft2WomWorkflowDefinitionMaker.scala
@@ -9,26 +9,31 @@ import wom.transforms.WomGraphMaker.ops._
 import wom.SourceFileLocation
 
 object WdlDraft2WomWorkflowDefinitionMaker extends WomWorkflowDefinitionMaker[WdlWorkflow] {
-  override def toWomWorkflowDefinition(wdlWorkflow: WdlWorkflow, isASubworkflow: Boolean): ErrorOr[WorkflowDefinition] = {
+  override def toWomWorkflowDefinition(wdlWorkflow: WdlWorkflow,
+                                       isASubworkflow: Boolean
+  ): ErrorOr[WorkflowDefinition] = {
     // NB: We don't allow "OuterGraphInputNode"s when building this (the Map is empty), so preserveScatterForExternalLookups isn't ever actually used.
 
     // Figure out the start line of the workflow in the source file
     val t: Terminal = AstTools.findTerminals(wdlWorkflow.ast).head
 
-    def stringifyMetaValues(meta: Map[String, String]): Map[String, MetaValueElement] = {
-      meta map {
-        case (key, value) =>
-          key -> MetaValueElement.MetaValueElementString(value)
+    def stringifyMetaValues(meta: Map[String, String]): Map[String, MetaValueElement] =
+      meta map { case (key, value) =>
+        key -> MetaValueElement.MetaValueElementString(value)
       }
-    }
 
-    (wdlWorkflow: Scope).toWomGraph(Set.empty, Map.empty, preserveIndexForOuterLookups = true, isASubworkflow: Boolean) map { wg =>
+    (wdlWorkflow: Scope).toWomGraph(Set.empty,
+                                    Map.empty,
+                                    preserveIndexForOuterLookups = true,
+                                    isASubworkflow: Boolean
+    ) map { wg =>
       WorkflowDefinition(
         wdlWorkflow.fullyQualifiedName,
         wg,
         stringifyMetaValues(wdlWorkflow.meta),
         stringifyMetaValues(wdlWorkflow.parameterMeta),
-        Some(SourceFileLocation(t.getLine)))
+        Some(SourceFileLocation(t.getLine))
+      )
     }
   }
 }
diff --git a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/Draft2ReadFileLimitsSpec.scala b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/Draft2ReadFileLimitsSpec.scala
index d1d744aeab1..7bae5243f0b 100644
--- a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/Draft2ReadFileLimitsSpec.scala
+++ b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/Draft2ReadFileLimitsSpec.scala
@@ -11,7 +11,7 @@ import scala.concurrent.Future
 
 class Draft2ReadFileLimitsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "ReadLikeFunctions Size Limit Draft 2"
-  
+
   it should "pass correct size limits to the ioFunctions for read_lines" in {
     new WdlWomExpression(WdlExpression.fromString("""read_lines("blah")"""), null)
       .evaluateValue(Map.empty, ioFunctionTester(1, ""))
@@ -75,9 +75,13 @@ class Draft2ReadFileLimitsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
 
 object Draft2ReadFileLimitsSpec {
   def ioFunctionTester(expectedMaxBytes: Int, result: String) = new EmptyIoFunctionSet {
-    override def readFile(path: String, maxBytes: Option[Int] = None, failOnOverflow: Boolean = false) = {
+    override def readFile(path: String, maxBytes: Option[Int] = None, failOnOverflow: Boolean = false) =
       if (maxBytes.contains(expectedMaxBytes)) Future.successful(result)
-      else Future.failed(new Exception(s"readFile was called with a max bytes value of ${maxBytes.getOrElse("No value")} but was expecting $expectedMaxBytes"))
-    }
+      else
+        Future.failed(
+          new Exception(
+            s"readFile was called with a max bytes value of ${maxBytes.getOrElse("No value")} but was expecting $expectedMaxBytes"
+          )
+        )
   }
 }
diff --git a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlAliasWomSpec.scala b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlAliasWomSpec.scala
index 1c70f49b600..b3e1873e193 100644
--- a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlAliasWomSpec.scala
+++ b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlAliasWomSpec.scala
@@ -34,22 +34,29 @@ class WdlAliasWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
     conditionalTestGraph match {
       case Valid(g) => validateGraph(g)
-      case Invalid(errors) => fail(s"Unable to build wom version of conditional foo from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
+      case Invalid(errors) =>
+        fail(s"Unable to build wom version of conditional foo from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
     }
 
     def validateGraph(workflowGraph: Graph) = {
 
       val inputNodes: Set[ExternalGraphInputNode] = workflowGraph.nodes.filterByType[ExternalGraphInputNode]
       inputNodes.map(_.localName) should be(Set("foo1.i", "foo2.i"))
-      inputNodes.map(_.identifier.fullyQualifiedName.value) should be(Set("conditional_test.foo1.i", "conditional_test.foo2.i"))
+      inputNodes.map(_.identifier.fullyQualifiedName.value) should be(
+        Set("conditional_test.foo1.i", "conditional_test.foo2.i")
+      )
 
       val callNodes: Set[CallNode] = workflowGraph.nodes.filterByType[CallNode]
       callNodes.map(_.localName) should be(Set("foo1", "foo2"))
-      callNodes.map(_.identifier.fullyQualifiedName.value) should be(Set("conditional_test.foo1", "conditional_test.foo2"))
+      callNodes.map(_.identifier.fullyQualifiedName.value) should be(
+        Set("conditional_test.foo1", "conditional_test.foo2")
+      )
 
       val outputNodes: Set[GraphOutputNode] = workflowGraph.nodes.filterByType[GraphOutputNode]
       outputNodes.map(_.localName) should be(Set("foo1.out", "foo2.out"))
-      outputNodes.map(_.identifier.fullyQualifiedName.value) should be(Set("conditional_test.foo1.out", "conditional_test.foo2.out"))
+      outputNodes.map(_.identifier.fullyQualifiedName.value) should be(
+        Set("conditional_test.foo1.out", "conditional_test.foo2.out")
+      )
 
       workflowGraph.nodes.size should be(6)
     }
diff --git a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlConditionalWomSpec.scala b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlConditionalWomSpec.scala
index 820bd3bd607..12c5f4e57a3 100644
--- a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlConditionalWomSpec.scala
+++ b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlConditionalWomSpec.scala
@@ -39,66 +39,92 @@ class WdlConditionalWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
 
     conditionalTestGraph match {
       case Valid(g) => validateGraph(g)
-      case Invalid(errors) => fail(s"Unable to build wom version of conditional foo from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
+      case Invalid(errors) =>
+        fail(s"Unable to build wom version of conditional foo from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
     }
 
     def validateGraph(workflowGraph: Graph) = {
 
       case class OuterGraphValidations(conditionalNode: ConditionalNode, foo_i_inputNode: GraphInputNode)
       def validateOuterGraph: OuterGraphValidations = {
-        val conditionalNode = workflowGraph.nodes.firstByType[ConditionalNode].getOrElse(fail("Resulting graph did not contain a ConditionalNode"))
+        val conditionalNode = workflowGraph.nodes
+          .firstByType[ConditionalNode]
+          .getOrElse(fail("Resulting graph did not contain a ConditionalNode"))
 
         val inputNodes: Set[GraphInputNode] = workflowGraph.nodes.filterByType[GraphInputNode]
 
-        val b_inputNode = inputNodes.find(_.localName == "b").getOrElse(fail("Resulting graph did not contain the 'b' GraphInputNode"))
+        val b_inputNode =
+          inputNodes.find(_.localName == "b").getOrElse(fail("Resulting graph did not contain the 'b' GraphInputNode"))
         b_inputNode.womType should be(WomBooleanType)
-        val foo_i_inputNode = inputNodes.find(_.localName == "foo.i").getOrElse(fail("Resulting graph did not contain the 'foo.i' GraphInputNode"))
+        val foo_i_inputNode = inputNodes
+          .find(_.localName == "foo.i")
+          .getOrElse(fail("Resulting graph did not contain the 'foo.i' GraphInputNode"))
         foo_i_inputNode.womType should be(WomIntegerType)
 
-        val foo_out_output = workflowGraph.nodes.collectFirst {
-          case gon: GraphOutputNode if gon.localName == "foo.out" => gon
-        }.getOrElse(fail("Resulting graph did not contain the 'foo.out' GraphOutputNode"))
+        val foo_out_output = workflowGraph.nodes
+          .collectFirst {
+            case gon: GraphOutputNode if gon.localName == "foo.out" => gon
+          }
+          .getOrElse(fail("Resulting graph did not contain the 'foo.out' GraphOutputNode"))
         foo_out_output.womType should be(WomOptionalType(WomStringType))
         foo_out_output.identifier.fullyQualifiedName.value shouldBe "conditional_test.foo.out"
-        
-        val expressionNode = workflowGraph.nodes.collectFirst {
-          case expr: ExpressionNode if expr.localName == "conditional" => expr
-        }.getOrElse(fail("Resulting graph did not contain the 'conditional' ExpressionNode"))
 
-        workflowGraph.nodes should be(Set(conditionalNode, foo_i_inputNode, b_inputNode, foo_out_output, expressionNode))
+        val expressionNode = workflowGraph.nodes
+          .collectFirst {
+            case expr: ExpressionNode if expr.localName == "conditional" => expr
+          }
+          .getOrElse(fail("Resulting graph did not contain the 'conditional' ExpressionNode"))
+
+        workflowGraph.nodes should be(
+          Set(conditionalNode, foo_i_inputNode, b_inputNode, foo_out_output, expressionNode)
+        )
         OuterGraphValidations(conditionalNode, foo_i_inputNode)
       }
 
       case class InnerGraphValidations(foo_out_innerOutput: GraphOutputNode)
       def validateInnerGraph(validatedOuterGraph: OuterGraphValidations): InnerGraphValidations = {
-        val foo_i_innerInput = validatedOuterGraph.conditionalNode.innerGraph.nodes.collectFirst {
-          case gin: ExternalGraphInputNode if gin.identifier.fullyQualifiedName.value == "conditional_test.foo.i" => gin
-        }.getOrElse(fail("Conditional inner graph did not contain a GraphInputNode 'foo.i'"))
-
-        val foo_callNode = validatedOuterGraph.conditionalNode.innerGraph.nodes.collectFirst {
-          case c: CommandCallNode if c.localName == "foo" => c
-        }.getOrElse(fail("Conditional inner graph did not contain a call to 'foo'"))
+        val foo_i_innerInput = validatedOuterGraph.conditionalNode.innerGraph.nodes
+          .collectFirst {
+            case gin: ExternalGraphInputNode if gin.identifier.fullyQualifiedName.value == "conditional_test.foo.i" =>
+              gin
+          }
+          .getOrElse(fail("Conditional inner graph did not contain a GraphInputNode 'foo.i'"))
+
+        val foo_callNode = validatedOuterGraph.conditionalNode.innerGraph.nodes
+          .collectFirst {
+            case c: CommandCallNode if c.localName == "foo" => c
+          }
+          .getOrElse(fail("Conditional inner graph did not contain a call to 'foo'"))
 
         foo_callNode.identifier.fullyQualifiedName.value shouldBe "conditional_test.foo"
 
-        val foo_out_innerOutput = validatedOuterGraph.conditionalNode.innerGraph.nodes.collectFirst {
-          case gon: GraphOutputNode if gon.localName == "foo.out" => gon
-        }.getOrElse(fail("Conditional inner graph did not contain a GraphOutputNode 'foo.out'"))
+        val foo_out_innerOutput = validatedOuterGraph.conditionalNode.innerGraph.nodes
+          .collectFirst {
+            case gon: GraphOutputNode if gon.localName == "foo.out" => gon
+          }
+          .getOrElse(fail("Conditional inner graph did not contain a GraphOutputNode 'foo.out'"))
 
-        validatedOuterGraph.conditionalNode.innerGraph.nodes should be(Set(foo_i_innerInput, foo_callNode, foo_out_innerOutput))
+        validatedOuterGraph.conditionalNode.innerGraph.nodes should be(
+          Set(foo_i_innerInput, foo_callNode, foo_out_innerOutput)
+        )
         InnerGraphValidations(foo_out_innerOutput)
       }
 
-      def validateConnections(validatedOuterGraph: OuterGraphValidations, validatedInnerGraph: InnerGraphValidations) = {
+      def validateConnections(validatedOuterGraph: OuterGraphValidations, validatedInnerGraph: InnerGraphValidations) =
         // The ConditionalNode's output port is correctly associated with the inner graph's GraphOutputNode:
         validatedOuterGraph.conditionalNode.conditionalOutputPorts.toList match {
           case (port @ ConditionalOutputPort(outputToGather, _)) :: Nil =>
             port.name should be("foo.out")
             port.womType should be(WomOptionalType(WomStringType))
             outputToGather eq validatedInnerGraph.foo_out_innerOutput should be(true)
-          case other => fail("Expected exactly one output to be gathered in this conditional but got:" + other.mkString("\n", "\n", "\n"))
+          case other =>
+            fail(
+              "Expected exactly one output to be gathered in this conditional but got:" + other.mkString("\n",
+                                                                                                         "\n",
+                                                                                                         "\n"
+              )
+            )
         }
-      }
 
       val outer = validateOuterGraph
       val inner = validateInnerGraph(outer)
@@ -106,5 +132,4 @@ class WdlConditionalWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
     }
   }
 
-
 }
diff --git a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlInputValidationSpec.scala b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlInputValidationSpec.scala
index 6e5bb2cdb20..cec503bf3de 100644
--- a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlInputValidationSpec.scala
+++ b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlInputValidationSpec.scala
@@ -22,7 +22,12 @@ import wom.transforms.WomWorkflowDefinitionMaker.ops._
 import wom.types._
 import wom.values._
 
-class WdlInputValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with BeforeAndAfterAll with TableDrivenPropertyChecks {
+class WdlInputValidationSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with BeforeAndAfterAll
+    with TableDrivenPropertyChecks {
 
   behavior of "WDL Wom executable"
 
@@ -47,23 +52,41 @@ class WdlInputValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
     """.stripMargin
 
   val namespace = WdlNamespace.loadUsingSource(wdlWorkflow, None, None).get.asInstanceOf[WdlNamespaceWithWorkflow]
-  val graph = namespace.workflow.toWomWorkflowDefinition(isASubworkflow = false)
+  val graph = namespace.workflow
+    .toWomWorkflowDefinition(isASubworkflow = false)
     .valueOr(errors => fail(s"Failed to build a wom definition: ${errors.toList.mkString(", ")}"))
     .graph
 
-  val w1OutputPort = graph.externalInputNodes.find(_.fullyQualifiedName == "w.w1").getOrElse(fail("Failed to find an input node for w1")).singleOutputPort
-  val w2OutputPort = graph.externalInputNodes.find(_.fullyQualifiedName == "w.w2").getOrElse(fail("Failed to find an input node for w2")).singleOutputPort
-  val t1OutputPort = graph.externalInputNodes.find(_.fullyQualifiedName == "w.t.t1").getOrElse(fail("Failed to find an input node for t1")).singleOutputPort
-  val t2OutputPort = graph.externalInputNodes.find(_.fullyQualifiedName == "w.t.t2").getOrElse(fail("Failed to find an input node for t2")).singleOutputPort
-  val u1OutputPort = graph.externalInputNodes.find(_.fullyQualifiedName == "w.u.t1").getOrElse(fail("Failed to find an input node for u1")).singleOutputPort
-  val u2OutputPort = graph.externalInputNodes.find(_.fullyQualifiedName == "w.u.t2").getOrElse(fail("Failed to find an input node for u2")).singleOutputPort
+  val w1OutputPort = graph.externalInputNodes
+    .find(_.fullyQualifiedName == "w.w1")
+    .getOrElse(fail("Failed to find an input node for w1"))
+    .singleOutputPort
+  val w2OutputPort = graph.externalInputNodes
+    .find(_.fullyQualifiedName == "w.w2")
+    .getOrElse(fail("Failed to find an input node for w2"))
+    .singleOutputPort
+  val t1OutputPort = graph.externalInputNodes
+    .find(_.fullyQualifiedName == "w.t.t1")
+    .getOrElse(fail("Failed to find an input node for t1"))
+    .singleOutputPort
+  val t2OutputPort = graph.externalInputNodes
+    .find(_.fullyQualifiedName == "w.t.t2")
+    .getOrElse(fail("Failed to find an input node for t2"))
+    .singleOutputPort
+  val u1OutputPort = graph.externalInputNodes
+    .find(_.fullyQualifiedName == "w.u.t1")
+    .getOrElse(fail("Failed to find an input node for u1"))
+    .singleOutputPort
+  val u2OutputPort = graph.externalInputNodes
+    .find(_.fullyQualifiedName == "w.u.t2")
+    .getOrElse(fail("Failed to find an input node for u2"))
+    .singleOutputPort
 
-  def validate(inputFile: String): Checked[ResolvedExecutableInputs] = {
+  def validate(inputFile: String): Checked[ResolvedExecutableInputs] =
     namespace.toWomExecutable(Option(inputFile), NoIoFunctionSet, strictValidation = true) match {
       case Left(errors) => Left(errors)
       case Right(e) => e.resolvedExecutableInputs.validNelCheck
     }
-  }
 
   val validations: TableFor3[String, String, Checked[ResolvedExecutableInputs]] = Table(
     ("test name", "inputs JSON", "input set"),
@@ -112,18 +135,22 @@ class WdlInputValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
         |{
         |}
       """.stripMargin,
-      NonEmptyList.fromListUnsafe(List(
-        "Required workflow input 'w.t.t1' not specified",
-        "Required workflow input 'w.u.t1' not specified",
-        "Required workflow input 'w.w1' not specified"
-      )).asLeft[ResolvedExecutableInputs]
+      NonEmptyList
+        .fromListUnsafe(
+          List(
+            "Required workflow input 'w.t.t1' not specified",
+            "Required workflow input 'w.u.t1' not specified",
+            "Required workflow input 'w.w1' not specified"
+          )
+        )
+        .asLeft[ResolvedExecutableInputs]
     )
   )
 
   /*
    * Note that we create the graph twice:
-    * once in namespace.workflow.toWomWorkflowDefinition for the expectations
-    * once in namespace.toWomExecutable to validate the actual inputs
+   * once in namespace.workflow.toWomWorkflowDefinition for the expectations
+   * once in namespace.toWomExecutable to validate the actual inputs
    * So the output ports in the map won't be object matches. We just check the name equality.
    */
   private def validateInexactPortEquality(actual: ResolvedExecutableInputs, expected: ResolvedExecutableInputs) = {
@@ -135,13 +162,14 @@ class WdlInputValidationSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
   }
 
   forAll(validations) { (name, inputSource, expectation) =>
-
     it should s"validate $name" in {
       (validate(inputSource), expectation) match {
-        case (Left(actualError), Left(expectedError)) => actualError.toList.toSet -- expectedError.toList.toSet should be(Set.empty)
+        case (Left(actualError), Left(expectedError)) =>
+          actualError.toList.toSet -- expectedError.toList.toSet should be(Set.empty)
         case (Left(actualError), _) => fail(s"Expected success but got errors: ${actualError.toList.mkString(", ")}")
         case (Right(actualInputs), Right(expectedInputs)) => validateInexactPortEquality(actualInputs, expectedInputs)
-        case (_, Left(expectedError)) => fail(s"Expected errors: '${expectedError.toList.mkString(", ")}' but got success ")
+        case (_, Left(expectedError)) =>
+          fail(s"Expected errors: '${expectedError.toList.mkString(", ")}' but got success ")
       }
     }
   }
diff --git a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlNamespaceWomSpec.scala b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlNamespaceWomSpec.scala
index 8761e936ff3..d61a8a336ab 100644
--- a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlNamespaceWomSpec.scala
+++ b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlNamespaceWomSpec.scala
@@ -64,7 +64,8 @@ class WdlNamespaceWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
 
     val workflowGraph = wom3Step match {
       case Valid(g) => g
-      case Invalid(errors) => fail(s"Unable to build wom version of 3step from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
+      case Invalid(errors) =>
+        fail(s"Unable to build wom version of 3step from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
     }
 
     val graphInputNodes = workflowGraph.nodes collect { case gin: ExternalGraphInputNode => gin }
@@ -73,17 +74,27 @@ class WdlNamespaceWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     patternInputNode.localName should be("cgrep.pattern")
     patternInputNode.fullyQualifiedName should be("three_step.cgrep.pattern")
 
-    workflowGraph.nodes collect { case gon: ExpressionBasedGraphOutputNode => gon.localName } should be(Set("wc.count", "cgrep.count", "ps.procs"))
+    workflowGraph.nodes collect { case gon: ExpressionBasedGraphOutputNode => gon.localName } should be(
+      Set("wc.count", "cgrep.count", "ps.procs")
+    )
 
-    val ps: CommandCallNode = workflowGraph.nodes.collectFirst({ case ps: CommandCallNode if ps.localName == "ps" => ps }).get
-    val cgrep: CommandCallNode = workflowGraph.nodes.collectFirst({ case cgrep: CommandCallNode if cgrep.localName == "cgrep" => cgrep }).get
-    val cgrepInFileExpression = {
-      workflowGraph.nodes.collectFirst({ case cgrepInFile: ExpressionNode if cgrepInFile.localName == "cgrep.in_file" => cgrepInFile }).get
-    }
-    val wc: CommandCallNode = workflowGraph.nodes.collectFirst({ case wc: CommandCallNode if wc.localName == "wc" => wc }).get
-    val wcInFileExpression = {
-      workflowGraph.nodes.collectFirst({ case wcInFile: ExpressionNode if wcInFile.localName == "wc.in_file" => wcInFile }).get
-    }
+    val ps: CommandCallNode = workflowGraph.nodes.collectFirst {
+      case ps: CommandCallNode if ps.localName == "ps" => ps
+    }.get
+    val cgrep: CommandCallNode = workflowGraph.nodes.collectFirst {
+      case cgrep: CommandCallNode if cgrep.localName == "cgrep" => cgrep
+    }.get
+    val cgrepInFileExpression =
+      workflowGraph.nodes.collectFirst {
+        case cgrepInFile: ExpressionNode if cgrepInFile.localName == "cgrep.in_file" => cgrepInFile
+      }.get
+    val wc: CommandCallNode = workflowGraph.nodes.collectFirst {
+      case wc: CommandCallNode if wc.localName == "wc" => wc
+    }.get
+    val wcInFileExpression =
+      workflowGraph.nodes.collectFirst {
+        case wcInFile: ExpressionNode if wcInFile.localName == "wc.in_file" => wcInFile
+      }.get
 
     workflowGraph.nodes.filterByType[CallNode] should be(Set(ps, cgrep, wc))
     ps.inputPorts.map(_.name) should be(Set.empty)
@@ -102,10 +113,15 @@ class WdlNamespaceWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     val inFileMapping = cgrepInputs(cgrepFileInputDef)
     inFileMapping.select[OutputPort].isDefined shouldBe true
     // This should be less ugly when we can access a string value from a womexpression
-    inFileMapping.select[OutputPort].get
-      .graphNode.asInstanceOf[ExpressionNode]
-      .womExpression.asInstanceOf[WdlWomExpression]
-      .wdlExpression.valueString shouldBe "ps.procs"
+    inFileMapping
+      .select[OutputPort]
+      .get
+      .graphNode
+      .asInstanceOf[ExpressionNode]
+      .womExpression
+      .asInstanceOf[WdlWomExpression]
+      .wdlExpression
+      .valueString shouldBe "ps.procs"
 
     val cgrepPatternInputDef = cgrep.callable.inputs.find(_.name == "pattern").get
     cgrepInputs(cgrepPatternInputDef).select[OutputPort].get eq patternInputNode.singleOutputPort shouldBe true
diff --git a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlNestedConditionalWomSpec.scala b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlNestedConditionalWomSpec.scala
index 0eeedc5506c..e980c03542a 100644
--- a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlNestedConditionalWomSpec.scala
+++ b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlNestedConditionalWomSpec.scala
@@ -35,7 +35,6 @@ class WdlNestedConditionalWomSpec extends AnyFlatSpec with CromwellTimeoutSpec w
     ("same lookups in if condition, scatter collection, and task calls", sameLookupsInConditionsAndInnerTaskCalls)
   )
 
-
   /*
      NB these tests go as far as "can I make a WOM Graph out of this WDL.
      We don't do anything to check that the WOM Graph is correct"
@@ -51,12 +50,15 @@ class WdlNestedConditionalWomSpec extends AnyFlatSpec with CromwellTimeoutSpec w
 
       // Run each WDL through 20 times because the topological ordering of WdlGraphNodes is sometimes non-deterministic
       // and the order of operations has been known to change whether a bug is expressed or not.
-      val errors = (0 until 20).toList.as(mkTestGraph) collect {
-        case i @ Invalid(_) => i.e.toList
+      val errors = (0 until 20).toList.as(mkTestGraph) collect { case i @ Invalid(_) =>
+        i.e.toList
       }
 
       if (errors.nonEmpty) {
-        fail(s"Unable to build wom version of nested_lookups from WDL ${errors.size * 5}% of the time. First failure was: ${errors.head.mkString("\n", "\n", "\n")}")
+        fail(
+          s"Unable to build wom version of nested_lookups from WDL ${errors.size * 5}% of the time. First failure was: ${errors.head
+              .mkString("\n", "\n", "\n")}"
+        )
       }
 
     }
diff --git a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlScatterWomSpec.scala b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlScatterWomSpec.scala
index 1a2c586e7fd..c302cb87b4a 100644
--- a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlScatterWomSpec.scala
+++ b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlScatterWomSpec.scala
@@ -39,28 +39,36 @@ class WdlScatterWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
 
     scatterTestGraph match {
       case Valid(g) => validateGraph(g)
-      case Invalid(errors) => fail(s"Unable to build wom version of scatter foo from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
+      case Invalid(errors) =>
+        fail(s"Unable to build wom version of scatter foo from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
     }
 
     def validateGraph(workflowGraph: Graph) = {
 
       case class OuterGraphValidations(scatterNode: ScatterNode, xs_inputNode: GraphInputNode)
       def validateOuterGraph: OuterGraphValidations = {
-        val scatterNode = workflowGraph.nodes.firstByType[ScatterNode].getOrElse(fail("Resulting graph did not contain a ScatterNode"))
+        val scatterNode =
+          workflowGraph.nodes.firstByType[ScatterNode].getOrElse(fail("Resulting graph did not contain a ScatterNode"))
 
-        val xs_inputNode = workflowGraph.nodes.collectFirst {
-          case gin: GraphInputNode if gin.localName == "xs" => gin
-        }.getOrElse(fail("Resulting graph did not contain the 'xs' GraphInputNode"))
+        val xs_inputNode = workflowGraph.nodes
+          .collectFirst {
+            case gin: GraphInputNode if gin.localName == "xs" => gin
+          }
+          .getOrElse(fail("Resulting graph did not contain the 'xs' GraphInputNode"))
 
-        val scatterExpressionNode = workflowGraph.nodes.collectFirst {
-          case expr: ExpressionNode if expr.localName == "x" => expr
-        }.getOrElse(fail("Resulting graph did not contain the 'x' ExpressionNode"))
+        val scatterExpressionNode = workflowGraph.nodes
+          .collectFirst {
+            case expr: ExpressionNode if expr.localName == "x" => expr
+          }
+          .getOrElse(fail("Resulting graph did not contain the 'x' ExpressionNode"))
 
         scatterNode.inputPorts.map(_.upstream) shouldBe Set(scatterExpressionNode.singleOutputPort)
 
-        val foo_out_output = workflowGraph.nodes.collectFirst {
-          case gon: GraphOutputNode if gon.localName == "foo.out" => gon
-        }.getOrElse(fail("Resulting graph did not contain the 'foo.out' GraphOutputNode"))
+        val foo_out_output = workflowGraph.nodes
+          .collectFirst {
+            case gon: GraphOutputNode if gon.localName == "foo.out" => gon
+          }
+          .getOrElse(fail("Resulting graph did not contain the 'foo.out' GraphOutputNode"))
         foo_out_output.womType should be(WomArrayType(WomStringType))
         foo_out_output.identifier.fullyQualifiedName.value shouldBe "scatter_test.foo.out"
 
@@ -70,34 +78,49 @@ class WdlScatterWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
 
       case class InnerGraphValidations(x_scatterCollectionInput: GraphInputNode, foo_out_innerOutput: GraphOutputNode)
       def validateInnerGraph(validatedOuterGraph: OuterGraphValidations): InnerGraphValidations = {
-        val x_scatterCollectionInput = validatedOuterGraph.scatterNode.innerGraph.nodes.collectFirst {
-          case gin: GraphInputNode if gin.localName == "x" => gin
-        }.getOrElse(fail("Scatter inner graph did not contain a GraphInputNode 'x'"))
-
-        val foo_callNode = validatedOuterGraph.scatterNode.innerGraph.nodes.collectFirst {
-          case c: CommandCallNode if c.localName == "foo" => c
-        }.getOrElse(fail("Scatter inner graph did not contain a call to 'foo'"))
+        val x_scatterCollectionInput = validatedOuterGraph.scatterNode.innerGraph.nodes
+          .collectFirst {
+            case gin: GraphInputNode if gin.localName == "x" => gin
+          }
+          .getOrElse(fail("Scatter inner graph did not contain a GraphInputNode 'x'"))
+
+        val foo_callNode = validatedOuterGraph.scatterNode.innerGraph.nodes
+          .collectFirst {
+            case c: CommandCallNode if c.localName == "foo" => c
+          }
+          .getOrElse(fail("Scatter inner graph did not contain a call to 'foo'"))
 
         foo_callNode.identifier.fullyQualifiedName.value shouldBe "scatter_test.foo"
 
-        val foo_out_innerOutput = validatedOuterGraph.scatterNode.innerGraph.nodes.collectFirst {
-          case gon: GraphOutputNode if gon.localName == "foo.out" => gon
-        }.getOrElse(fail("Scatter inner graph did not contain a GraphOutputNode 'foo.out'"))
-
-        val foo_out_i_expressionNode = validatedOuterGraph.scatterNode.innerGraph.nodes.collectFirst {
-          case expr: ExpressionNode if expr.localName == "foo.i" => expr
-        }.getOrElse(fail("Scatter inner graph did not contain a ExpressionNode 'scatter_test.foo.i'"))
-
-        validatedOuterGraph.scatterNode.innerGraph.nodes should be(Set(x_scatterCollectionInput, foo_callNode, foo_out_innerOutput, foo_out_i_expressionNode))
+        val foo_out_innerOutput = validatedOuterGraph.scatterNode.innerGraph.nodes
+          .collectFirst {
+            case gon: GraphOutputNode if gon.localName == "foo.out" => gon
+          }
+          .getOrElse(fail("Scatter inner graph did not contain a GraphOutputNode 'foo.out'"))
+
+        val foo_out_i_expressionNode = validatedOuterGraph.scatterNode.innerGraph.nodes
+          .collectFirst {
+            case expr: ExpressionNode if expr.localName == "foo.i" => expr
+          }
+          .getOrElse(fail("Scatter inner graph did not contain a ExpressionNode 'scatter_test.foo.i'"))
+
+        validatedOuterGraph.scatterNode.innerGraph.nodes should be(
+          Set(x_scatterCollectionInput, foo_callNode, foo_out_innerOutput, foo_out_i_expressionNode)
+        )
         InnerGraphValidations(x_scatterCollectionInput, foo_out_innerOutput)
       }
 
-      def validateConnections(validatedOuterGraph: OuterGraphValidations, validatedInnerGraph: InnerGraphValidations) = {
+      def validateConnections(validatedOuterGraph: OuterGraphValidations,
+                              validatedInnerGraph: InnerGraphValidations
+      ) = {
         // The scatter collection links to its predecessor
-        validatedOuterGraph.scatterNode.scatterCollectionExpressionNodes.head.inputPorts.map(_.upstream.graphNode) should be(Set(validatedOuterGraph.xs_inputNode))
+        validatedOuterGraph.scatterNode.scatterCollectionExpressionNodes.head.inputPorts
+          .map(_.upstream.graphNode) should be(Set(validatedOuterGraph.xs_inputNode))
 
         // The ScatterNode's "scatter variable mapping" links to the innerGraph's scatter variable input Node:
-        validatedOuterGraph.scatterNode.scatterVariableInnerGraphInputNodes.head eq validatedInnerGraph.x_scatterCollectionInput should be(true)
+        validatedOuterGraph.scatterNode.scatterVariableInnerGraphInputNodes.head eq validatedInnerGraph.x_scatterCollectionInput should be(
+          true
+        )
 
         // The ScatterNode's output port links to the inner graph's GraphOutputNode:
         validatedOuterGraph.scatterNode.outputMapping.toList match {
@@ -105,7 +128,10 @@ class WdlScatterWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
             port.name should be("foo.out")
             womType should be(WomArrayType(WomStringType))
             outputToGather eq validatedInnerGraph.foo_out_innerOutput should be(true)
-          case other => fail("Expected exactly one output to be gathered in this scatter but got:" + other.mkString("\n", "\n", "\n"))
+          case other =>
+            fail(
+              "Expected exactly one output to be gathered in this scatter but got:" + other.mkString("\n", "\n", "\n")
+            )
         }
       }
 
@@ -140,7 +166,8 @@ class WdlScatterWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
 
     scatterTestGraph match {
       case Valid(g) => validateGraph(g)
-      case Invalid(errors) => fail(s"Unable to build wom version of scatter foo from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
+      case Invalid(errors) =>
+        fail(s"Unable to build wom version of scatter foo from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
     }
 
     def validateGraph(workflowGraph: Graph) = {
@@ -149,10 +176,11 @@ class WdlScatterWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
       workflowGraph.nodes.size should be(7)
 
       // Find that scatter:
-      workflowGraph.nodes.collectFirst {
-        case s: ScatterNode => s
-      }.getOrElse(fail("Resulting graph did not contain a ScatterNode"))
-
+      workflowGraph.nodes
+        .collectFirst { case s: ScatterNode =>
+          s
+        }
+        .getOrElse(fail("Resulting graph did not contain a ScatterNode"))
 
     }
   }
@@ -182,31 +210,38 @@ class WdlScatterWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
 
     scatterTestGraph match {
       case Valid(g) => validateGraph(g)
-      case Invalid(errors) => fail(s"Unable to build wom version of scatter foo from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
+      case Invalid(errors) =>
+        fail(s"Unable to build wom version of scatter foo from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
     }
 
     def validateGraph(workflowGraph: Graph) = {
 
       // Find the inputs:
       val inputNodes = workflowGraph.nodes.filterByType[RequiredGraphInputNode]
-      inputNodes.map {_.localName} should be(Set("foo.j"))
-      inputNodes.map {_.identifier.fullyQualifiedName.value} should be(Set("scatter_test.foo.j"))
+      inputNodes.map(_.localName) should be(Set("foo.j"))
+      inputNodes.map(_.identifier.fullyQualifiedName.value) should be(Set("scatter_test.foo.j"))
 
       // Find that scatter:
-      val scatterNode = workflowGraph.nodes.collectFirst {
-        case s: ScatterNode => s
-      }.getOrElse(fail("Resulting graph did not contain a ScatterNode"))
+      val scatterNode = workflowGraph.nodes
+        .collectFirst { case s: ScatterNode =>
+          s
+        }
+        .getOrElse(fail("Resulting graph did not contain a ScatterNode"))
 
-      val scatterInnerInputs: Set[ExternalGraphInputNode] = scatterNode.innerGraph.nodes.filterByType[ExternalGraphInputNode]
-      scatterInnerInputs map {_.identifier.fullyQualifiedName.value} should be(Set("scatter_test.foo.j"))
-      val scatterInnerItemInput: Set[OuterGraphInputNode] = scatterNode.innerGraph.nodes.filterByType[OuterGraphInputNode]
-      scatterInnerItemInput map {_.localName} should be(Set("s"))
+      val scatterInnerInputs: Set[ExternalGraphInputNode] =
+        scatterNode.innerGraph.nodes.filterByType[ExternalGraphInputNode]
+      scatterInnerInputs map { _.identifier.fullyQualifiedName.value } should be(Set("scatter_test.foo.j"))
+      val scatterInnerItemInput: Set[OuterGraphInputNode] =
+        scatterNode.innerGraph.nodes.filterByType[OuterGraphInputNode]
+      scatterInnerItemInput map { _.localName } should be(Set("s"))
 
       // Find the outputs:
-      val outputNodes = workflowGraph.nodes.collect {
-        case output: GraphOutputNode => output
+      val outputNodes = workflowGraph.nodes.collect { case output: GraphOutputNode =>
+        output
       }
-      outputNodes map { on => (on.localName, on.womType) } should be(Set(("foo.int_out", WomArrayType(WomIntegerType)), ("foo.str_out", WomArrayType(WomStringType))))
+      outputNodes map { on => (on.localName, on.womType) } should be(
+        Set(("foo.int_out", WomArrayType(WomIntegerType)), ("foo.str_out", WomArrayType(WomStringType)))
+      )
 
     }
   }
diff --git a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlSubworkflowWomSpec.scala b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlSubworkflowWomSpec.scala
index fffe841b1be..d41d38c0733 100644
--- a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlSubworkflowWomSpec.scala
+++ b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlSubworkflowWomSpec.scala
@@ -50,19 +50,21 @@ class WdlSubworkflowWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
         |}
       """.stripMargin
 
-
     def innerResolver: Draft2ImportResolver = str => Draft2ResolvedImportBundle(innerWdl, ResolvedImportRecord(str))
 
-    val namespace = WdlNamespace.loadUsingSource(
-      workflowSource = outerWdl,
-      resource = None,
-      importResolver = Some(Seq(innerResolver))).get.asInstanceOf[WdlNamespaceWithWorkflow]
+    val namespace = WdlNamespace
+      .loadUsingSource(workflowSource = outerWdl, resource = None, importResolver = Some(Seq(innerResolver)))
+      .get
+      .asInstanceOf[WdlNamespaceWithWorkflow]
 
     val outerWorkflowGraph = namespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).map(_.graph)
 
     outerWorkflowGraph match {
       case Valid(g) => validateOuter(g)
-      case Invalid(errors) => fail(s"Unable to build wom version of workflow with subworkflow from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
+      case Invalid(errors) =>
+        fail(
+          s"Unable to build wom version of workflow with subworkflow from WDL: ${errors.toList.mkString("\n", "\n", "\n")}"
+        )
     }
 
     def validateOuter(workflowGraph: Graph) = {
@@ -75,7 +77,9 @@ class WdlSubworkflowWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
       val innerCall = calls.head.asInstanceOf[WorkflowCallNode]
       innerCall.localName should be("inner")
       innerCall.identifier.fullyQualifiedName.value should be("outer.inner")
-      innerCall.upstream.head.asInstanceOf[ExpressionNode].inputPorts.map(_.upstream.graphNode) should be(Set(workflowGraph.inputNodes.head))
+      innerCall.upstream.head.asInstanceOf[ExpressionNode].inputPorts.map(_.upstream.graphNode) should be(
+        Set(workflowGraph.inputNodes.head)
+      )
 
       // One output, "out"
       workflowGraph.outputNodes.map(_.localName) should be(Set("out"))
@@ -92,7 +96,9 @@ class WdlSubworkflowWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
       calls.map(_.localName) should be(Set("foo"))
 
       val fooCall = calls.head.asInstanceOf[CommandCallNode]
-      fooCall.upstream.head.asInstanceOf[ExpressionNode].inputPorts.map(_.upstream.graphNode) should be(Set(innerGraph.inputNodes.head))
+      fooCall.upstream.head.asInstanceOf[ExpressionNode].inputPorts.map(_.upstream.graphNode) should be(
+        Set(innerGraph.inputNodes.head)
+      )
 
       innerGraph.outputNodes.map(_.localName) should be(Set("out", "x"))
       innerGraph.outputNodes.map(_.identifier.fullyQualifiedName.value) should be(Set("inner.out", "inner.x"))
@@ -141,26 +147,30 @@ class WdlSubworkflowWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
         |}
       """.stripMargin
 
-
     def innerResolver: Draft2ImportResolver = str => Draft2ResolvedImportBundle(innerWdl, ResolvedImportRecord(str))
 
-    val namespace = WdlNamespace.loadUsingSource(
-      workflowSource = outerWdl,
-      resource = None,
-      importResolver = Some(Seq(innerResolver))).get.asInstanceOf[WdlNamespaceWithWorkflow]
+    val namespace = WdlNamespace
+      .loadUsingSource(workflowSource = outerWdl, resource = None, importResolver = Some(Seq(innerResolver)))
+      .get
+      .asInstanceOf[WdlNamespaceWithWorkflow]
 
     val outerWorkflowGraph = namespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).map(_.graph)
 
     outerWorkflowGraph match {
       case Valid(g) => validateOuter(g)
-      case Invalid(errors) => fail(s"Unable to build wom version of workflow with subworkflow from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
+      case Invalid(errors) =>
+        fail(
+          s"Unable to build wom version of workflow with subworkflow from WDL: ${errors.toList.mkString("\n", "\n", "\n")}"
+        )
     }
 
     def validateOuter(workflowGraph: Graph) = {
       workflowGraph.inputNodes.map(_.localName) should be(Set("xs"))
 
       val scatter = workflowGraph.scatters.head
-      val scatterCollectionNode = workflowGraph.nodes.collectFirst({ case e: ExpressionNode if e.localName == "x" => e }).get
+      val scatterCollectionNode = workflowGraph.nodes.collectFirst {
+        case e: ExpressionNode if e.localName == "x" => e
+      }.get
       scatter.upstream should be(Set(scatterCollectionNode))
       scatter.outputPorts.map(_.name) should be(Set("inner.out"))
       scatter.outputPorts.head.womType should be(WomArrayType(WomStringType))
@@ -206,16 +216,19 @@ class WdlSubworkflowWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
 
     def innerResolver: Draft2ImportResolver = str => Draft2ResolvedImportBundle(innerWdl, ResolvedImportRecord(str))
 
-    val namespace = WdlNamespace.loadUsingSource(
-      workflowSource = outerWdl,
-      resource = None,
-      importResolver = Some(Seq(innerResolver))).get.asInstanceOf[WdlNamespaceWithWorkflow]
+    val namespace = WdlNamespace
+      .loadUsingSource(workflowSource = outerWdl, resource = None, importResolver = Some(Seq(innerResolver)))
+      .get
+      .asInstanceOf[WdlNamespaceWithWorkflow]
 
     val outerWorkflowGraph = namespace.workflow.toWomWorkflowDefinition(isASubworkflow = false).map(_.graph)
 
     outerWorkflowGraph match {
       case Valid(g) => validateOuter(g)
-      case Invalid(errors) => fail(s"Unable to build wom version of workflow with subworkflow from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
+      case Invalid(errors) =>
+        fail(
+          s"Unable to build wom version of workflow with subworkflow from WDL: ${errors.toList.mkString("\n", "\n", "\n")}"
+        )
     }
 
     def validateOuter(workflowGraph: Graph) = {
@@ -250,7 +263,9 @@ class WdlSubworkflowWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Ma
       calls.map(_.localName) should be(Set("foo"))
 
       val fooCall = calls.head.asInstanceOf[CommandCallNode]
-      fooCall.upstream.head.asInstanceOf[ExpressionNode].inputPorts.map(_.upstream.graphNode) should be(Set(innerGraph.inputNodes.head))
+      fooCall.upstream.head.asInstanceOf[ExpressionNode].inputPorts.map(_.upstream.graphNode) should be(
+        Set(innerGraph.inputNodes.head)
+      )
 
       innerGraph.outputNodes.map(_.localName) should be(Set("out"))
       innerGraph.outputNodes.map(_.identifier.fullyQualifiedName.value) should be(Set("twin.out"))
diff --git a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlWomExpressionsAsInputsSpec.scala b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlWomExpressionsAsInputsSpec.scala
index a0d85b969ff..53c750ebf6f 100644
--- a/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlWomExpressionsAsInputsSpec.scala
+++ b/wdl/transforms/draft2/src/test/scala/wdl/transforms/wdlwom/WdlWomExpressionsAsInputsSpec.scala
@@ -35,7 +35,6 @@ object WdlWomExpressionsAsInputsSpec {
     """.stripMargin
 }
 
-
 class WdlWomExpressionsAsInputsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "WdlWomExpressionsAsInputs"
 
@@ -47,7 +46,9 @@ class WdlWomExpressionsAsInputsSpec extends AnyFlatSpec with CromwellTimeoutSpec
       case Invalid(errors) => fail(s"Unable to build wom graph from WDL: ${errors.toList.mkString("\n", "\n", "\n")}")
     }
 
-    val callNodes = workflowGraph.nodes.toList collect { case callNode: CommandCallNode => callNode.localName -> callNode } toMap
+    val callNodes = workflowGraph.nodes.toList collect { case callNode: CommandCallNode =>
+      callNode.localName -> callNode
+    } toMap
 
     val a = callNodes("a")
     val b = callNodes("b")
@@ -56,9 +57,8 @@ class WdlWomExpressionsAsInputsSpec extends AnyFlatSpec with CromwellTimeoutSpec
     val cInputExpressionNode = c.inputPorts.map(_.upstream).head.graphNode.asInstanceOf[ExpressionNode]
     cInputExpressionNode.inputPorts.map(_.upstream) shouldBe a.outputPorts ++ b.outputPorts
 
-    val inputExpression = c.inputDefinitionMappings
-      .head._2.select[OutputPort].get
-      .graphNode.asInstanceOf[ExpressionNode]  
+    val inputExpression =
+      c.inputDefinitionMappings.head._2.select[OutputPort].get.graphNode.asInstanceOf[ExpressionNode]
 
     List("a", "b") foreach { x =>
       val connectedInputPort = inputExpression.inputMapping(s"$x.int_out")
diff --git a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/ast2wdlom/Draft3GenericAstNode.scala b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/ast2wdlom/Draft3GenericAstNode.scala
index 7b0405b473a..1ca48a996bb 100644
--- a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/ast2wdlom/Draft3GenericAstNode.scala
+++ b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/ast2wdlom/Draft3GenericAstNode.scala
@@ -5,7 +5,8 @@ import wdl.transforms.base.ast2wdlom.{GenericAst, GenericAstList, GenericAstNode
 import scala.jdk.CollectionConverters._
 
 case class Draft3GenericAst(ast: Ast) extends GenericAst {
-  override def getAttribute(attr: String): GenericAstNode = Option(ast.getAttribute(attr)).map(Draft3GenericAstNode.apply).orNull
+  override def getAttribute(attr: String): GenericAstNode =
+    Option(ast.getAttribute(attr)).map(Draft3GenericAstNode.apply).orNull
   override def getAttributes: Map[String, GenericAstNode] = ast.getAttributes.asScala.toMap collect {
     case (key, value) if value != null => key -> Draft3GenericAstNode(value)
   }
diff --git a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/ast2wdlom/ast2wdlom.scala b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/ast2wdlom/ast2wdlom.scala
index 7765086a848..eb92bc4855f 100644
--- a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/ast2wdlom/ast2wdlom.scala
+++ b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/ast2wdlom/ast2wdlom.scala
@@ -7,56 +7,117 @@ import common.validation.Checked._
 import wdl.draft3.parser.WdlParser.{Ast, AstNode}
 import wdl.model.draft3.elements.ExpressionElement.KvPair
 import wdl.model.draft3.elements._
-import wdl.transforms.base.ast2wdlom.{AstNodeToCommandPartElement, AstNodeToExpressionElement, AstNodeToKvPair, AstNodeToMetaKvPair, AstNodeToPlaceholderAttributeSet, AstNodeToStaticString, AstNodeToTypeElement, AstToCallElement, AstToCommandSectionElement, AstToDeclarationContent, AstToFileBodyElement, AstToFileElement, AstToIfElement, AstToImportElement, AstToInputDeclarationElement, AstToInputsSectionElement, AstToMetaSectionElement, AstToOutputsSectionElement, AstToParameterMetaSectionElement, AstToRuntimeAttributesSectionElement, AstToScatterElement, AstToStructElement, AstToTaskDefinitionElement, AstToTaskSectionElement, AstToWorkflowBodyElement, AstToWorkflowDefinitionElement, AstToWorkflowGraphNodeElementConverterMaker, GenericAst, GenericAstNode, astNodeToAst, astNodeToAstList}
+import wdl.transforms.base.ast2wdlom.{
+  astNodeToAst,
+  astNodeToAstList,
+  AstNodeToCommandPartElement,
+  AstNodeToExpressionElement,
+  AstNodeToKvPair,
+  AstNodeToMetaKvPair,
+  AstNodeToPlaceholderAttributeSet,
+  AstNodeToStaticString,
+  AstNodeToTypeElement,
+  AstToCallElement,
+  AstToCommandSectionElement,
+  AstToDeclarationContent,
+  AstToFileBodyElement,
+  AstToFileElement,
+  AstToIfElement,
+  AstToImportElement,
+  AstToInputDeclarationElement,
+  AstToInputsSectionElement,
+  AstToMetaSectionElement,
+  AstToOutputsSectionElement,
+  AstToParameterMetaSectionElement,
+  AstToRuntimeAttributesSectionElement,
+  AstToScatterElement,
+  AstToStructElement,
+  AstToTaskDefinitionElement,
+  AstToTaskSectionElement,
+  AstToWorkflowBodyElement,
+  AstToWorkflowDefinitionElement,
+  AstToWorkflowGraphNodeElementConverterMaker,
+  GenericAst,
+  GenericAstNode
+}
 import wdl.draft3.transforms.parsing.fileToAst
 import wom.callable.MetaKvPair
 
 package object ast2wdlom {
 
-  val wrapAst: CheckedAtoB[Ast, GenericAst] = CheckedAtoB.fromCheck { a => Draft3GenericAst(a).validNelCheck }
-  val wrapAstNode: CheckedAtoB[AstNode, GenericAstNode] = CheckedAtoB.fromCheck { a => Draft3GenericAstNode(a).validNelCheck }
+  val wrapAst: CheckedAtoB[Ast, GenericAst] = CheckedAtoB.fromCheck(a => Draft3GenericAst(a).validNelCheck)
+  val wrapAstNode: CheckedAtoB[AstNode, GenericAstNode] = CheckedAtoB.fromCheck { a =>
+    Draft3GenericAstNode(a).validNelCheck
+  }
 
-  implicit val astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString] = AstNodeToStaticString.astNodeToStaticStringElement()
+  implicit val astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString] =
+    AstNodeToStaticString.astNodeToStaticStringElement()
 
   // meta sections
   implicit val astNodeToMetaKvPair: CheckedAtoB[GenericAstNode, MetaKvPair] = AstNodeToMetaKvPair.astNodeToMetaKvPair
-  implicit val astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement] = astNodeToAst andThen AstToMetaSectionElement.astToMetaSectionElement
-  implicit val astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement] = astNodeToAst andThen AstToParameterMetaSectionElement.astToParameterMetaSectionElement
+  implicit val astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement] =
+    astNodeToAst andThen AstToMetaSectionElement.astToMetaSectionElement
+  implicit val astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement] =
+    astNodeToAst andThen AstToParameterMetaSectionElement.astToParameterMetaSectionElement
 
-  implicit val astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement] = AstNodeToExpressionElement.astNodeToExpressionElement(customEngineFunctionMakers = Map.empty)
-  implicit val astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair] = AstNodeToKvPair.astNodeToKvPair(astNodeToExpressionElement)
+  implicit val astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement] =
+    AstNodeToExpressionElement.astNodeToExpressionElement(customEngineFunctionMakers = Map.empty)
+  implicit val astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair] =
+    AstNodeToKvPair.astNodeToKvPair(astNodeToExpressionElement)
 
-  implicit val astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement] = AstNodeToTypeElement.astNodeToTypeElement(Map.empty)
+  implicit val astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement] =
+    AstNodeToTypeElement.astNodeToTypeElement(Map.empty)
   implicit val astToStructElement: CheckedAtoB[GenericAst, StructElement] = AstToStructElement.astToStructElement
-  implicit val astNodeToImportElement: CheckedAtoB[GenericAstNode, ImportElement] = astNodeToAst andThen AstToImportElement.astToImportElement
+  implicit val astNodeToImportElement: CheckedAtoB[GenericAstNode, ImportElement] =
+    astNodeToAst andThen AstToImportElement.astToImportElement
 
-  implicit val astNodeToInputDeclarationElement: CheckedAtoB[GenericAstNode, InputDeclarationElement] = astNodeToAst andThen AstToInputDeclarationElement.astToInputDeclarationElement
-  implicit val astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement] = astNodeToAst andThen AstToInputsSectionElement.astToInputsSectionElement
+  implicit val astNodeToInputDeclarationElement: CheckedAtoB[GenericAstNode, InputDeclarationElement] =
+    astNodeToAst andThen AstToInputDeclarationElement.astToInputDeclarationElement
+  implicit val astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement] =
+    astNodeToAst andThen AstToInputsSectionElement.astToInputsSectionElement
 
-  implicit val astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent] = astNodeToAst andThen AstToDeclarationContent.astToDeclarationContent
-  implicit val astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement] = astNodeToAst andThen AstToOutputsSectionElement.astToOutputSectionElement
+  implicit val astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent] =
+    astNodeToAst andThen AstToDeclarationContent.astToDeclarationContent
+  implicit val astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement] =
+    astNodeToAst andThen AstToOutputsSectionElement.astToOutputSectionElement
 
   val astToWorkflowGraphNodeElementConverterMaker = new AstToWorkflowGraphNodeElementConverterMaker()
-  implicit val astNodeToGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement] = astNodeToAst andThen astToWorkflowGraphNodeElementConverterMaker.converter
-  implicit val astNodeToCallElement: CheckedAtoB[GenericAstNode, CallElement] = astNodeToAst andThen AstToCallElement.astToCallElement
-  implicit val astNodeToScatterElement: CheckedAtoB[GenericAstNode, ScatterElement] = astNodeToAst andThen AstToScatterElement.astToScatterElement
-  implicit val astNodeToIfElement: CheckedAtoB[GenericAstNode, IfElement] = astNodeToAst andThen AstToIfElement.astToIfElement
+  implicit val astNodeToGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement] =
+    astNodeToAst andThen astToWorkflowGraphNodeElementConverterMaker.converter
+  implicit val astNodeToCallElement: CheckedAtoB[GenericAstNode, CallElement] =
+    astNodeToAst andThen AstToCallElement.astToCallElement
+  implicit val astNodeToScatterElement: CheckedAtoB[GenericAstNode, ScatterElement] =
+    astNodeToAst andThen AstToScatterElement.astToScatterElement
+  implicit val astNodeToIfElement: CheckedAtoB[GenericAstNode, IfElement] =
+    astNodeToAst andThen AstToIfElement.astToIfElement
   astToWorkflowGraphNodeElementConverterMaker.astNodeToScatterElement = Some(astNodeToScatterElement)
   astToWorkflowGraphNodeElementConverterMaker.astNodeToIfElement = Some(astNodeToIfElement)
   astToWorkflowGraphNodeElementConverterMaker.astNodeToCallElement = Some(astNodeToCallElement)
   astToWorkflowGraphNodeElementConverterMaker.astNodeToDeclarationContent = Some(astNodeToDeclarationContent)
 
-  implicit val astNodeToWorkflowBodyElement: CheckedAtoB[GenericAstNode, WorkflowBodyElement] = astNodeToAst andThen AstToWorkflowBodyElement.astToWorkflowBodyElement
-  implicit val astToWorkflowDefinitionElement: CheckedAtoB[GenericAst, WorkflowDefinitionElement] = AstToWorkflowDefinitionElement.astToWorkflowDefinitionElement
+  implicit val astNodeToWorkflowBodyElement: CheckedAtoB[GenericAstNode, WorkflowBodyElement] =
+    astNodeToAst andThen AstToWorkflowBodyElement.astToWorkflowBodyElement
+  implicit val astToWorkflowDefinitionElement: CheckedAtoB[GenericAst, WorkflowDefinitionElement] =
+    AstToWorkflowDefinitionElement.astToWorkflowDefinitionElement
 
-  implicit val astNodeToPlaceholderAttributeSet: CheckedAtoB[GenericAstNode, PlaceholderAttributeSet] = astNodeToAstList andThen AstNodeToPlaceholderAttributeSet.attributeKvpConverter
-  implicit val astNodeToCommandPartElement: CheckedAtoB[GenericAstNode, CommandPartElement] = AstNodeToCommandPartElement.astNodeToCommandPartElement
-  implicit val astNodeToCommandSectionElement: CheckedAtoB[GenericAstNode, CommandSectionElement] = astNodeToAst andThen AstToCommandSectionElement.astToCommandSectionElement
-  implicit val astNodeToRuntimeAttributesSectionElement: CheckedAtoB[GenericAstNode, RuntimeAttributesSectionElement] = astNodeToAst andThen AstToRuntimeAttributesSectionElement.astToRuntimeSectionElement
-  implicit val astNodeToTaskSectionElement: CheckedAtoB[GenericAstNode, TaskSectionElement] = astNodeToAst andThen AstToTaskSectionElement.astToTaskSectionElement
-  implicit val astToTaskDefinitionElement: CheckedAtoB[GenericAst, TaskDefinitionElement] = AstToTaskDefinitionElement.astToTaskDefinitionElement
+  implicit val astNodeToPlaceholderAttributeSet: CheckedAtoB[GenericAstNode, PlaceholderAttributeSet] =
+    astNodeToAstList andThen AstNodeToPlaceholderAttributeSet.attributeKvpConverter
+  implicit val astNodeToCommandPartElement: CheckedAtoB[GenericAstNode, CommandPartElement] =
+    AstNodeToCommandPartElement.astNodeToCommandPartElement
+  implicit val astNodeToCommandSectionElement: CheckedAtoB[GenericAstNode, CommandSectionElement] =
+    astNodeToAst andThen AstToCommandSectionElement.astToCommandSectionElement
+  implicit val astNodeToRuntimeAttributesSectionElement: CheckedAtoB[GenericAstNode, RuntimeAttributesSectionElement] =
+    astNodeToAst andThen AstToRuntimeAttributesSectionElement.astToRuntimeSectionElement
+  implicit val astNodeToTaskSectionElement: CheckedAtoB[GenericAstNode, TaskSectionElement] =
+    astNodeToAst andThen AstToTaskSectionElement.astToTaskSectionElement
+  implicit val astToTaskDefinitionElement: CheckedAtoB[GenericAst, TaskDefinitionElement] =
+    AstToTaskDefinitionElement.astToTaskDefinitionElement
 
-  implicit val astToFileBodyElement: CheckedAtoB[GenericAstNode, FileBodyElement] = astNodeToAst andThen AstToFileBodyElement.astToFileBodyElement(astToWorkflowDefinitionElement, astToTaskDefinitionElement, astToStructElement)
+  implicit val astToFileBodyElement: CheckedAtoB[GenericAstNode, FileBodyElement] =
+    astNodeToAst andThen AstToFileBodyElement.astToFileBodyElement(astToWorkflowDefinitionElement,
+                                                                   astToTaskDefinitionElement,
+                                                                   astToStructElement
+    )
 
   implicit val astToFileElement: CheckedAtoB[GenericAst, FileElement] = AstToFileElement.astToFileElement
   implicit val fileToFileElement: CheckedAtoB[File, FileElement] = fileToAst andThen wrapAst andThen astToFileElement
diff --git a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/consumed/package.scala b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/consumed/package.scala
index d63620c4f1f..909937274e4 100644
--- a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/consumed/package.scala
+++ b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/consumed/package.scala
@@ -13,87 +13,91 @@ import wdl.transforms.base.linking.expression.consumed.UnaryOperatorEvaluators._
 
 package object consumed {
 
-  implicit val expressionElementUnlinkedValueConsumer: ExpressionValueConsumer[ExpressionElement] = new ExpressionValueConsumer[ExpressionElement] {
-    override def expressionConsumedValueHooks(a: ExpressionElement)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = a match {
-      case _: PrimitiveLiteralExpressionElement | _: StringLiteral => Set.empty[UnlinkedConsumedValueHook]
-      case a: StringExpression => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ObjectLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: PairLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ArrayLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: MapLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+  implicit val expressionElementUnlinkedValueConsumer: ExpressionValueConsumer[ExpressionElement] =
+    new ExpressionValueConsumer[ExpressionElement] {
+      override def expressionConsumedValueHooks(a: ExpressionElement)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] = a match {
+        case _: PrimitiveLiteralExpressionElement | _: StringLiteral => Set.empty[UnlinkedConsumedValueHook]
+        case a: StringExpression => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ObjectLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: PairLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ArrayLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: MapLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-      // Member access:
-      case a: IdentifierLookup => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: IdentifierMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ExpressionMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: IndexAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+        // Member access:
+        case a: IdentifierLookup => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: IdentifierMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ExpressionMemberAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: IndexAccess => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-      // Unary operators:
-      case a: UnaryNegation => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: UnaryPlus => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LogicalNot => a.expressionConsumedValueHooks(expressionValueConsumer)
+        // Unary operators:
+        case a: UnaryNegation => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: UnaryPlus => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LogicalNot => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-      // Binary operators:
-      case a: LogicalOr => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LogicalAnd => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Equals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: NotEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LessThan => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: LessThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: GreaterThan => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: GreaterThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Add => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Subtract => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Multiply => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Divide => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Remainder => a.expressionConsumedValueHooks(expressionValueConsumer)
+        // Binary operators:
+        case a: LogicalOr => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LogicalAnd => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Equals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: NotEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LessThan => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: LessThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: GreaterThan => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: GreaterThanOrEquals => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Add => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Subtract => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Multiply => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Divide => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Remainder => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-      case a: TernaryIf => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: TernaryIf => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-      // Engine functions:
-      case a: StdoutElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: StderrElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+        // Engine functions:
+        case a: StdoutElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: StderrElement.type => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-      case a: ReadLines => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadMap => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadObject => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadJson => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadInt => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadString => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadFloat => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: ReadBoolean => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteLines => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteMap => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteObject => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: WriteJson => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Range => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Transpose => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Length => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Flatten => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Prefix => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: SelectFirst => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: SelectAll => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Defined => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Floor => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Ceil => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Round => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Glob => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadLines => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadObject => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadJson => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadInt => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadString => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadFloat => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: ReadBoolean => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteLines => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteTsv => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteMap => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteObject => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteObjects => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: WriteJson => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Range => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Transpose => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Length => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Flatten => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Prefix => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: SelectFirst => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: SelectAll => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Defined => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Floor => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Ceil => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Round => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Glob => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-      case a: Size => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Basename => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Size => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Basename => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-      case a: Zip => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Cross => a.expressionConsumedValueHooks(expressionValueConsumer)
-      case a: Sep => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Zip => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Cross => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Sep => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-      case a: Sub => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Sub => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-      // TODO fill in other expression types
-      case other => throw new Exception(s"Cannot generate consumed values for ExpressionElement ${other.getClass.getSimpleName}")
+        // TODO fill in other expression types
+        case other =>
+          throw new Exception(s"Cannot generate consumed values for ExpressionElement ${other.getClass.getSimpleName}")
+      }
     }
-  }
 }
diff --git a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/files/package.scala b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/files/package.scala
index 027fa6efbd2..89d77fd4759 100644
--- a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/files/package.scala
+++ b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/files/package.scala
@@ -20,82 +20,134 @@ package object files {
 
   implicit val expressionFileEvaluator: FileEvaluator[ExpressionElement] = new FileEvaluator[ExpressionElement] {
 
-    override def predictFilesNeededToEvaluate(a: ExpressionElement, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
-
+    override def predictFilesNeededToEvaluate(a: ExpressionElement,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       a match {
         // Literals:
-        case a: PrimitiveLiteralExpressionElement => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: StringLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ObjectLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: MapLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ArrayLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: PairLiteral => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: PrimitiveLiteralExpressionElement =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: StringLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ObjectLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: MapLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ArrayLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: PairLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Lookups and member accesses:
-        case a: IdentifierLookup => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ExpressionMemberAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: IdentifierMemberAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: IndexAccess => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IdentifierLookup =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ExpressionMemberAccess =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IdentifierMemberAccess =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: IndexAccess =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Unary operators:
-        case a: UnaryNegation => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: UnaryPlus => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LogicalNot => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: UnaryNegation =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: UnaryPlus =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalNot =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Binary operators (at some point we might want to split these into separate cases):
-        case a: LogicalOr => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LogicalAnd => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalOr =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LogicalAnd =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Equals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: NotEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LessThan => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: LessThanOrEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: GreaterThan => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: GreaterThanOrEquals => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: NotEquals =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LessThan =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: LessThanOrEquals =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: GreaterThan =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: GreaterThanOrEquals =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Add => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Subtract => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Multiply => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Subtract =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Multiply =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Divide => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Remainder => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Remainder =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
-        case a: TernaryIf => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: TernaryIf =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         // Engine functions:
-        case StdoutElement => StdoutElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case StderrElement => StderrElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case StdoutElement =>
+          StdoutElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case StderrElement =>
+          StderrElement.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
-        case a: ReadLines => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadTsv => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadObject => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadObjects => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadJson => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadInt => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadString => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadFloat => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: ReadBoolean => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteLines => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteTsv => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteObject => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteObjects => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: WriteJson => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadLines =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadTsv =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadMap =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadObject =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadObjects =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadJson =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadInt =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadString =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadFloat =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: ReadBoolean =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteLines =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteTsv =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteMap =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteObject =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteObjects =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: WriteJson =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Range => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Transpose => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Transpose =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Length => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Flatten => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Flatten =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Prefix => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: SelectFirst => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: SelectAll => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Defined => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SelectFirst =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SelectAll =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Defined =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Floor => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Ceil => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Round => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Glob => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: Size => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-        case a: Basename => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Basename =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: Zip => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Cross => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
@@ -104,6 +156,5 @@ package object files {
 
         case other => s"No implementation of FileEvaluator[${other.getClass.getSimpleName}]".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/types/package.scala b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/types/package.scala
index 7da33f63449..4651a0d4c18 100644
--- a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/types/package.scala
+++ b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/types/package.scala
@@ -17,9 +17,9 @@ import wom.types.WomType
 
 package object types {
   implicit val expressionTypeEvaluator: TypeEvaluator[ExpressionElement] = new TypeEvaluator[ExpressionElement] {
-    override def evaluateType(a: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit typeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
-
+    override def evaluateType(a: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit typeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       a match {
         // Literals:
         case a: PrimitiveLiteralExpressionElement => a.evaluateType(linkedValues)(typeEvaluator)
@@ -99,8 +99,8 @@ package object types {
         case a: StdoutElement.type => a.evaluateType(linkedValues)(typeEvaluator)
         case a: StderrElement.type => a.evaluateType(linkedValues)(typeEvaluator)
 
-        case other => s"Unable to process ${other.getClass.getSimpleName}: No evaluateType exists for that type.".invalidNel
+        case other =>
+          s"Unable to process ${other.getClass.getSimpleName}: No evaluateType exists for that type.".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/values/package.scala b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/values/package.scala
index b8da81699e4..65487a16fd8 100644
--- a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/values/package.scala
+++ b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/values/package.scala
@@ -23,23 +23,27 @@ package object values {
     override def evaluateValue(a: ExpressionElement,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
       a match {
         // Literals:
-        case a: PrimitiveLiteralExpressionElement => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
+        case a: PrimitiveLiteralExpressionElement =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: StringLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
-        case a: StringExpression => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
+        case a: StringExpression =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: ObjectLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: MapLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: ArrayLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: PairLiteral => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
 
         // Lookups and member accesses:
-        case a: IdentifierLookup => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
-        case a: ExpressionMemberAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
-        case a: IdentifierMemberAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
+        case a: IdentifierLookup =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
+        case a: ExpressionMemberAccess =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
+        case a: IdentifierMemberAccess =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: IndexAccess => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
 
         // Unary operators:
@@ -53,9 +57,11 @@ package object values {
         case a: Equals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: NotEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: LessThan => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
-        case a: LessThanOrEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
+        case a: LessThanOrEquals =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: GreaterThan => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
-        case a: GreaterThanOrEquals => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
+        case a: GreaterThanOrEquals =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: Add => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: Subtract => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: Multiply => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
@@ -65,8 +71,10 @@ package object values {
         case a: TernaryIf => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
 
         // Engine functions:
-        case a: StdoutElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
-        case a: StderrElement.type => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
+        case a: StdoutElement.type =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
+        case a: StderrElement.type =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
 
         case a: ReadLines => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
         case a: ReadTsv => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(valueEvaluator)
@@ -107,6 +115,5 @@ package object values {
 
         case other => s"Unable to process ${other.toWdlV1}: No evaluateValue exists for that type in WDL 1.0".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/parsing/Draft3Parser.scala b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/parsing/Draft3Parser.scala
index 6f732eda085..450f9f1d0c0 100644
--- a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/parsing/Draft3Parser.scala
+++ b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/parsing/Draft3Parser.scala
@@ -16,7 +16,7 @@ object StringParser {
   def convert(a: FileStringParserInput): Checked[Ast] = Try {
     val parser = new WdlParser()
     val tokens = parser.lex(a.workflowSource, a.resource)
-    val terminalMap = (tokens.asScala.toVector map {(_, a.workflowSource)}).toMap
+    val terminalMap = (tokens.asScala.toVector map { (_, a.workflowSource) }).toMap
     val syntaxErrorFormatter = WdlDraft3SyntaxErrorFormatter(terminalMap)
     parser.parse(tokens, syntaxErrorFormatter).toAst.asInstanceOf[Ast]
   }.toChecked
diff --git a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/parsing/WdlDraft3SyntaxErrorFormatter.scala b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/parsing/WdlDraft3SyntaxErrorFormatter.scala
index acba6e0fb6f..13ebf1f353a 100644
--- a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/parsing/WdlDraft3SyntaxErrorFormatter.scala
+++ b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/parsing/WdlDraft3SyntaxErrorFormatter.scala
@@ -12,52 +12,56 @@ case class WdlDraft3SyntaxErrorFormatter(terminalMap: Map[Terminal, WorkflowSour
     case classicTerminal => terminalMap.get(classicTerminal)
   }
 
-  private def line(t: Terminal): String = getTerminal(t).map(_.split("\n")(t.getLine - 1)).getOrElse(s"Cannot highlight line. It was probably in an imported file.")
+  private def line(t: Terminal): String = getTerminal(t)
+    .map(_.split("\n")(t.getLine - 1))
+    .getOrElse(s"Cannot highlight line. It was probably in an imported file.")
 
-  def unexpectedEof(method: String, expected: java.util.List[TerminalIdentifier], nt_rules: java.util.List[String]): String = "ERROR: Unexpected end of file"
+  def unexpectedEof(method: String,
+                    expected: java.util.List[TerminalIdentifier],
+                    nt_rules: java.util.List[String]
+  ): String = "ERROR: Unexpected end of file"
 
-  def excessTokens(method: String, terminal: Terminal): String = {
+  def excessTokens(method: String, terminal: Terminal): String =
     s"""ERROR: Finished parsing without consuming all tokens.
        |
-        |${pointToSource(terminal)}
+       |${pointToSource(terminal)}
      """.stripMargin
-  }
 
-  def unexpectedSymbol(method: String, actual: Terminal, expected: java.util.List[TerminalIdentifier], rule: String): String = {
+  def unexpectedSymbol(method: String,
+                       actual: Terminal,
+                       expected: java.util.List[TerminalIdentifier],
+                       rule: String
+  ): String = {
     val expectedTokens = expected.asScala.map(_.string).mkString(", ")
     s"""ERROR: Unexpected symbol (line ${actual.getLine}, col ${actual.getColumn}) when parsing '$method'.
        |
-        |Expected $expectedTokens, got "${actual.getSourceString}".
+       |Expected $expectedTokens, got "${actual.getSourceString}".
        |
-        |${pointToSource(actual)}
+       |${pointToSource(actual)}
        |
-        |$rule
+       |$rule
      """.stripMargin
   }
 
-  def noMoreTokens(method: String, expecting: TerminalIdentifier, last: Terminal): String = {
+  def noMoreTokens(method: String, expecting: TerminalIdentifier, last: Terminal): String =
     s"""ERROR: No more tokens.  Expecting ${expecting.string}
        |
-        |${pointToSource(last)}
+       |${pointToSource(last)}
      """.stripMargin
-  }
 
-  def invalidTerminal(method: String, invalid: Terminal): String = {
+  def invalidTerminal(method: String, invalid: Terminal): String =
     s"""ERROR: Invalid symbol ID: ${invalid.getId} (${invalid.getTerminalStr})
        |
-        |${pointToSource(invalid)}
+       |${pointToSource(invalid)}
      """.stripMargin
-  }
 
   // TODO: these next two methods won't be called by the parser because there are no lists in the WDL grammar that
   // cause these to be triggered.  Currently the parser is passing in 'null' for the value of 'last' and when that
   // changes, these errors can be made more helpful.
 
-  def missingListItems(method: String, required: Int, found: Int, last: Terminal): String = {
+  def missingListItems(method: String, required: Int, found: Int, last: Terminal): String =
     s"ERROR: $method requires $required items, but only found $found"
-  }
 
-  def missingTerminator(method: String, terminal: TerminalIdentifier, last: Terminal): String = {
+  def missingTerminator(method: String, terminal: TerminalIdentifier, last: Terminal): String =
     s"ERROR: $method requires a terminator after each element"
-  }
 }
diff --git a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/wdlom2wom/package.scala b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/wdlom2wom/package.scala
index e7fae573d4b..477e31e394e 100644
--- a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/wdlom2wom/package.scala
+++ b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/wdlom2wom/package.scala
@@ -3,7 +3,12 @@ package wdl.draft3.transforms
 import common.transforms.CheckedAtoB
 import wdl.transforms.base.wdlom2wom.TaskDefinitionElementToWomTaskDefinition.TaskDefinitionElementToWomInputs
 import wdl.transforms.base.wdlom2wom.WorkflowDefinitionElementToWomWorkflowDefinition.WorkflowDefinitionConvertInputs
-import wdl.transforms.base.wdlom2wom.{FileElementToWomBundle, FileElementToWomBundleInputs, TaskDefinitionElementToWomTaskDefinition, WorkflowDefinitionElementToWomWorkflowDefinition}
+import wdl.transforms.base.wdlom2wom.{
+  FileElementToWomBundle,
+  FileElementToWomBundleInputs,
+  TaskDefinitionElementToWomTaskDefinition,
+  WorkflowDefinitionElementToWomWorkflowDefinition
+}
 import wom.callable.{CallableTaskDefinition, WorkflowDefinition}
 import wom.executable.WomBundle
 import wdl.draft3.transforms.linking.expression.consumed._
@@ -12,7 +17,11 @@ import wdl.draft3.transforms.linking.expression.types._
 import wdl.draft3.transforms.linking.expression.values._
 
 package object wdlom2wom {
-  val taskDefinitionElementToWomTaskDefinition: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition] = CheckedAtoB.fromErrorOr(TaskDefinitionElementToWomTaskDefinition.convert)
-  val workflowDefinitionElementToWomWorkflowDefinition: CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition] = CheckedAtoB.fromErrorOr(WorkflowDefinitionElementToWomWorkflowDefinition.convert)
-  val fileElementToWomBundle: CheckedAtoB[FileElementToWomBundleInputs, WomBundle] = CheckedAtoB.fromCheck(FileElementToWomBundle.convert)
+  val taskDefinitionElementToWomTaskDefinition: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition] =
+    CheckedAtoB.fromErrorOr(TaskDefinitionElementToWomTaskDefinition.convert)
+  val workflowDefinitionElementToWomWorkflowDefinition
+    : CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition] =
+    CheckedAtoB.fromErrorOr(WorkflowDefinitionElementToWomWorkflowDefinition.convert)
+  val fileElementToWomBundle: CheckedAtoB[FileElementToWomBundleInputs, WomBundle] =
+    CheckedAtoB.fromCheck(FileElementToWomBundle.convert)
 }
diff --git a/wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala b/wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala
index 99731de6aad..0e9cda8c2cf 100644
--- a/wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/AstToWorkflowDefinitionElementSpec.scala
@@ -2,27 +2,57 @@ import cats.data.Validated._
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers._
 import wdl.model.draft3.elements.ExpressionElement._
-import wdl.model.draft3.elements.{InputDeclarationElement, InputsSectionElement, IntermediateValueDeclarationElement, OutputDeclarationElement, OutputsSectionElement, PrimitiveTypeElement}
+import wdl.model.draft3.elements.{
+  InputDeclarationElement,
+  InputsSectionElement,
+  IntermediateValueDeclarationElement,
+  OutputDeclarationElement,
+  OutputsSectionElement,
+  PrimitiveTypeElement
+}
 import wom.types.{WomSingleFileType, WomStringType}
 import wdl.transforms.base.ast2wdlom.AstToWorkflowDefinitionElement._
 
-
-class AstToWorkflowDefinitionElementSpec extends AnyFlatSpec{
+class AstToWorkflowDefinitionElementSpec extends AnyFlatSpec {
   behavior of "Check Stdouts and Stderrs"
 
-  val mockInputSectionStdout = Option(InputsSectionElement(Vector(InputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "i", Some(StdoutElement)))))
-  val mockInputSectionStderr = Option(InputsSectionElement(Vector(InputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "i", Some(StderrElement)))))
-  val mockInputSectionNonStd = Option(InputsSectionElement(Vector(InputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", Some(StringLiteral("more"))))))
-
-
-  val mockIntermediatesStdout = Vector(IntermediateValueDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "y", StdoutElement))
-  val mockIntermediatesStderr = Vector(IntermediateValueDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "y", StderrElement))
-  val mockIntermediatesNonStd = Vector(IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "here", StringLiteral("here")))
+  val mockInputSectionStdout = Option(
+    InputsSectionElement(
+      Vector(InputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "i", Some(StdoutElement)))
+    )
+  )
+  val mockInputSectionStderr = Option(
+    InputsSectionElement(
+      Vector(InputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "i", Some(StderrElement)))
+    )
+  )
+  val mockInputSectionNonStd = Option(
+    InputsSectionElement(
+      Vector(InputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", Some(StringLiteral("more"))))
+    )
+  )
 
-  val mockOutputSectionStdout = Option(OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "s", StdoutElement))))
-  val mockOutputSectionStderr = Option(OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "s", StderrElement))))
-  val mockOutputSectionNonStd = Option(OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", StringLiteral("more")))))
+  val mockIntermediatesStdout = Vector(
+    IntermediateValueDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "y", StdoutElement)
+  )
+  val mockIntermediatesStderr = Vector(
+    IntermediateValueDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "y", StderrElement)
+  )
+  val mockIntermediatesNonStd = Vector(
+    IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "here", StringLiteral("here"))
+  )
 
+  val mockOutputSectionStdout = Option(
+    OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "s", StdoutElement)))
+  )
+  val mockOutputSectionStderr = Option(
+    OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "s", StderrElement)))
+  )
+  val mockOutputSectionNonStd = Option(
+    OutputsSectionElement(
+      Vector(OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", StringLiteral("more")))
+    )
+  )
 
   it should "return an error when there is an stdout in input section" in {
     val testInputs = checkDisallowedInputElement(mockInputSectionStdout, StdoutElement, "stdout")
@@ -75,14 +105,20 @@ class AstToWorkflowDefinitionElementSpec extends AnyFlatSpec{
     val testIntermediates = checkDisallowedIntermediates(mockIntermediatesStdout, StdoutElement, "stdout")
     testIntermediates match {
       case Valid(_) => fail("Intermediate section contained stdout. Should have failed.")
-      case Invalid(e) => e.head should be("Workflow cannot have stdout expression at intermediate declaration section at workflow-level.")
+      case Invalid(e) =>
+        e.head should be(
+          "Workflow cannot have stdout expression at intermediate declaration section at workflow-level."
+        )
     }
   }
   it should "return an error when there is an stderr at intermediate declaration section" in {
     val testIntermediates = checkDisallowedIntermediates(mockIntermediatesStderr, StderrElement, "stderr")
     testIntermediates match {
       case Valid(_) => fail("Intermediate section contained stderr. Should have failed.")
-      case Invalid(e) => e.head should be("Workflow cannot have stderr expression at intermediate declaration section at workflow-level.")
+      case Invalid(e) =>
+        e.head should be(
+          "Workflow cannot have stderr expression at intermediate declaration section at workflow-level."
+        )
     }
   }
 
@@ -90,8 +126,9 @@ class AstToWorkflowDefinitionElementSpec extends AnyFlatSpec{
     val testIntermediates = checkDisallowedIntermediates(mockIntermediatesNonStd, StdoutElement, "non-stdout/stderr")
     testIntermediates match {
       case Valid(_) => // No action
-      case Invalid(_) => fail("Check shouldn't have returned error as intermediate section had non-stdout/stderr intermediates.")
+      case Invalid(_) =>
+        fail("Check shouldn't have returned error as intermediate section had non-stdout/stderr intermediates.")
     }
   }
 
-}
\ No newline at end of file
+}
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
index 035d4e6efa6..7765cac73bc 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
@@ -23,13 +23,13 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   val parser = new WdlParser()
 
   def fromString[A](expression: String,
-                    parseFunction: (util.List[WdlParser.Terminal], SyntaxErrorFormatter) => ParseTree)
-                   (implicit converter: CheckedAtoB[GenericAstNode, A]): Checked[A] = {
+                    parseFunction: (util.List[WdlParser.Terminal], SyntaxErrorFormatter) => ParseTree
+  )(implicit converter: CheckedAtoB[GenericAstNode, A]): Checked[A] = {
     // Add the "version 1.0" to force the lexer into "main" mode.
     val versionedExpression = "version 1.0\n" + expression
     // That "version 1.0" means we'll have 2 unwanted tokens at the start of the list, so drop 'em:
     val tokens = parser.lex(versionedExpression, "string").asScala.drop(2).asJava
-    val terminalMap = (tokens.asScala.toVector map {(_, expression)}).toMap
+    val terminalMap = (tokens.asScala.toVector map { (_, expression) }).toMap
     val parseTree = parseFunction(tokens, WdlDraft3SyntaxErrorFormatter(terminalMap))
     (wrapAstNode andThen converter).run(parseTree.toAst)
   }
@@ -55,6 +55,6 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   it should "parse the (biscayne) None keyword as a plain old identifier" in {
     val str = "None"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
-    expr shouldBeValid(IdentifierLookup("None"))
+    expr shouldBeValid (IdentifierLookup("None"))
   }
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/ExpressionSet.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/ExpressionSet.scala
index dd2a1cd13ab..ee3c178565b 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/ExpressionSet.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/ExpressionSet.scala
@@ -10,7 +10,9 @@ object ExpressionSet {
   val floatLiteral = PrimitiveLiteralExpressionElement(WomFloat(5.5))
   val booleanLiteral = PrimitiveLiteralExpressionElement(WomBoolean(true))
 
-  val stringPlaceholderExpression = StringExpression(Vector(StringLiteral("h"), StringPlaceholder(IdentifierLookup("s")), StringLiteral("o")))
+  val stringPlaceholderExpression = StringExpression(
+    Vector(StringLiteral("h"), StringPlaceholder(IdentifierLookup("s")), StringLiteral("o"))
+  )
 
   val addExpression = Add(intLiteral, intLiteral)
   val subtractExpression = Subtract(intLiteral, intLiteral)
@@ -65,16 +67,20 @@ object ExpressionSet {
   val chainPairAccess = ExpressionMemberAccess(pairExpression, NonEmptyList("a", List("b", "c", "d", "e", "f", "g")))
 
   val arrayOfIs = ArrayLiteral(Vector(intLiteral, Multiply(intLiteral, intLiteral), UnaryNegation(intLiteral)))
-  val objectLiteralExpression = ObjectLiteral(Map(
-    "a" -> intLiteral,
-    "b" -> stringLiteral,
-    "c" -> pairExpression
-  ))
-  val mapLiteralExpression = MapLiteral(Map(
-    StringLiteral("a") -> intLiteral,
-    StringLiteral("b") -> addExpression,
-    StringLiteral("c") -> subtractExpression
-  ))
+  val objectLiteralExpression = ObjectLiteral(
+    Map(
+      "a" -> intLiteral,
+      "b" -> stringLiteral,
+      "c" -> pairExpression
+    )
+  )
+  val mapLiteralExpression = MapLiteral(
+    Map(
+      StringLiteral("a") -> intLiteral,
+      StringLiteral("b") -> addExpression,
+      StringLiteral("c") -> subtractExpression
+    )
+  )
 
   val ternaryIfExpression = TernaryIf(booleanLiteral, intLiteral, intLiteral)
   val zippedExpression = Zip(IdentifierLookup("is"), IdentifierLookup("is"))
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/WdlFileToWdlomSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/WdlFileToWdlomSpec.scala
index 3485bdfa8a3..450e1bebd5d 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/WdlFileToWdlomSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/WdlFileToWdlomSpec.scala
@@ -14,7 +14,6 @@ import wom.values.{WomBoolean, WomFloat, WomInteger}
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "WDL File to WDLOM"
@@ -27,12 +26,11 @@ class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   testCases.list.filter(x => x.isRegularFile && x.extension.contains(".wdl")) foreach { testCase =>
-
     val fileName = testCase.name
     val testName = testCase.name.split("\\.").head
 
     val itShouldString = s"create the correct Element structure for $fileName"
-    val testOrIgnore: (=>Any) => Unit = if (fileName.endsWith(".ignored.wdl")) {
+    val testOrIgnore: (=> Any) => Unit = if (fileName.endsWith(".ignored.wdl")) {
       (it should itShouldString).ignore _
     } else {
       (it should itShouldString).in _
@@ -44,7 +42,8 @@ class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
       fileToFileElement.run(testCase) match {
         case Right(actual) => actual shouldBe expected
         case Left(errors) =>
-          val formattedErrors = errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
+          val formattedErrors =
+            errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
           fail(s"Failed to create WDLOM:$formattedErrors")
       }
 
@@ -59,134 +58,210 @@ object WdlFileToWdlomSpec {
       FileElement(
         imports = List.empty,
         structs = Vector.empty,
-        workflows = List(WorkflowDefinitionElement(
-          name = "empty",
-          inputsSection = None,
-          graphElements = Set.empty,
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3)))),
-        tasks = List.empty),
+        workflows = List(
+          WorkflowDefinitionElement(
+            name = "empty",
+            inputsSection = None,
+            graphElements = Set.empty,
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        ),
+        tasks = List.empty
+      ),
     "struct_definition" -> FileElement(
       imports = Vector(),
-      structs = Vector(StructElement(
-        name = "FooStruct",
-        entries = Vector(
-          StructEntryElement(
-            "simple",
-            PrimitiveTypeElement(WomIntegerType)),
-          StructEntryElement(
-            "complex",
-            PairTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), MapTypeElement(PrimitiveTypeElement(WomStringType), PrimitiveTypeElement(WomBooleanType)))
+      structs = Vector(
+        StructElement(
+          name = "FooStruct",
+          entries = Vector(
+            StructEntryElement("simple", PrimitiveTypeElement(WomIntegerType)),
+            StructEntryElement(
+              "complex",
+              PairTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+                              MapTypeElement(PrimitiveTypeElement(WomStringType), PrimitiveTypeElement(WomBooleanType))
+              )
+            )
           )
         )
-      )),
-      workflows = Vector(WorkflowDefinitionElement(
-        name = "struct_definition",
-        inputsSection = None,
-        graphElements = Set(),
-        outputsSection = Some(OutputsSectionElement(Vector(OutputDeclarationElement(
-          typeElement = TypeAliasElement("FooStruct"),
-          name = "myFoo",
-          expression = ObjectLiteral(Map(
-            "simple" -> PrimitiveLiteralExpressionElement(WomInteger(5)),
-            "complex" -> PairLiteral(ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(5)))), MapLiteral(Map(StringLiteral("t") -> PrimitiveLiteralExpressionElement(WomBoolean(true)))))
-          ))
-        )))),
-        metaSection = None,
-        parameterMetaSection = None,
-        sourceLocation = Some(SourceFileLocation(8)))),
+      ),
+      workflows = Vector(
+        WorkflowDefinitionElement(
+          name = "struct_definition",
+          inputsSection = None,
+          graphElements = Set(),
+          outputsSection = Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(
+                  typeElement = TypeAliasElement("FooStruct"),
+                  name = "myFoo",
+                  expression = ObjectLiteral(
+                    Map(
+                      "simple" -> PrimitiveLiteralExpressionElement(WomInteger(5)),
+                      "complex" -> PairLiteral(
+                        ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(5)))),
+                        MapLiteral(Map(StringLiteral("t") -> PrimitiveLiteralExpressionElement(WomBoolean(true))))
+                      )
+                    )
+                  )
+                )
+              )
+            )
+          ),
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(8))
+        )
+      ),
       tasks = Vector.empty
     ),
     "input_types" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "input_types",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", None),
-            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "s", None),
-            InputDeclarationElement(PrimitiveTypeElement(WomFloatType), "float", None),
-            InputDeclarationElement(PrimitiveTypeElement(WomBooleanType), "b", None),
-            InputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "file", None),
-            InputDeclarationElement(ObjectTypeElement, "o", None),
-            InputDeclarationElement(OptionalTypeElement(PrimitiveTypeElement(WomIntegerType)), "maybe_i", None),
-            InputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomStringType)), "array_s", None),
-            InputDeclarationElement(MapTypeElement(PrimitiveTypeElement(WomIntegerType), PrimitiveTypeElement(WomStringType)), "map_is", None),
-            InputDeclarationElement(
-              ArrayTypeElement(
-                OptionalTypeElement(
-                  PairTypeElement(PrimitiveTypeElement(WomStringType), PrimitiveTypeElement(WomIntegerType)))),
-              "lotsa_nesting_array", None)
-          ))),
-          graphElements = Set.empty,
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3)))),
-        tasks = Vector.empty),
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "input_types",
+            inputsSection = Some(
+              InputsSectionElement(
+                Vector(
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", None),
+                  InputDeclarationElement(PrimitiveTypeElement(WomStringType), "s", None),
+                  InputDeclarationElement(PrimitiveTypeElement(WomFloatType), "float", None),
+                  InputDeclarationElement(PrimitiveTypeElement(WomBooleanType), "b", None),
+                  InputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "file", None),
+                  InputDeclarationElement(ObjectTypeElement, "o", None),
+                  InputDeclarationElement(OptionalTypeElement(PrimitiveTypeElement(WomIntegerType)), "maybe_i", None),
+                  InputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomStringType)), "array_s", None),
+                  InputDeclarationElement(MapTypeElement(PrimitiveTypeElement(WomIntegerType),
+                                                         PrimitiveTypeElement(WomStringType)
+                                          ),
+                                          "map_is",
+                                          None
+                  ),
+                  InputDeclarationElement(
+                    ArrayTypeElement(
+                      OptionalTypeElement(
+                        PairTypeElement(PrimitiveTypeElement(WomStringType), PrimitiveTypeElement(WomIntegerType))
+                      )
+                    ),
+                    "lotsa_nesting_array",
+                    None
+                  )
+                )
+              )
+            ),
+            graphElements = Set.empty,
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        ),
+        tasks = Vector.empty
+      ),
     "input_values" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "input_values",
-          inputsSection = Some(InputsSectionElement(
-            inputDeclarations = Vector(
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", Some(intLiteral)),
-              InputDeclarationElement(PrimitiveTypeElement(WomStringType), "s", Some(stringLiteral)),
-              InputDeclarationElement(PrimitiveTypeElement(WomStringType), "placeholder", Some(stringPlaceholderExpression)),
-              InputDeclarationElement(PrimitiveTypeElement(WomStringType), "placeholder2", Some(stringPlaceholderExpression)),
-              InputDeclarationElement(PrimitiveTypeElement(WomFloatType), "f", Some(floatLiteral)),
-              InputDeclarationElement(PrimitiveTypeElement(WomBooleanType), "b", Some(booleanLiteral))
-            )
-          )),
-          graphElements = Set.empty,
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3)))),
-        tasks = List.empty),
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "input_values",
+            inputsSection = Some(
+              InputsSectionElement(
+                inputDeclarations = Vector(
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", Some(intLiteral)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomStringType), "s", Some(stringLiteral)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                          "placeholder",
+                                          Some(stringPlaceholderExpression)
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                          "placeholder2",
+                                          Some(stringPlaceholderExpression)
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomFloatType), "f", Some(floatLiteral)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomBooleanType), "b", Some(booleanLiteral))
+                )
+              )
+            ),
+            graphElements = Set.empty,
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        ),
+        tasks = List.empty
+      ),
     "input_expressions" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "input_expressions",
-          inputsSection = Some(InputsSectionElement(
-            inputDeclarations = Vector(
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "ten", Some(addExpression)),
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "zero", Some(subtractExpression)),
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "twentyfive", Some(multiplyExpression)),
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "one", Some(divideExpression)),
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "zeroagain", Some(remainderExpression)),
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "tenagain", Some(tenVariableLookup)),
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "pair_expression_member_access", Some(pairExpressionMemberAccess)),
-              InputDeclarationElement(PrimitiveTypeElement(WomBooleanType), "unary_expressions", Some(unaryExpressions)),
-              InputDeclarationElement(PrimitiveTypeElement(WomBooleanType), "comparisons", Some(comparisonExpression)),
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "variableLookupMemberAccesses", Some(chainIdentifierAccess)),
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "expressionMemberAccesses", Some(chainPairAccess)),
-              InputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "is", Some(arrayOfIs)),
-              InputDeclarationElement(ObjectTypeElement, "object_literal", Some(objectLiteralExpression)),
-              InputDeclarationElement(
-                MapTypeElement(PrimitiveTypeElement(WomStringType), PrimitiveTypeElement(WomIntegerType)),
-                "map_literal",
-                Some(mapLiteralExpression)
-              ),
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "ternaryIf", Some(ternaryIfExpression)),
-              InputDeclarationElement(PrimitiveTypeElement(WomStringType), "string_read", Some(ReadString(StdoutElement))),
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "zipped", Some(zippedExpression)),
-              InputDeclarationElement(PrimitiveTypeElement(WomStringType), "subbed", Some(subbedExpression))
-            )
-          )),
-          graphElements = Set.empty,
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(4)))),
-        tasks = Vector.empty),
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "input_expressions",
+            inputsSection = Some(
+              InputsSectionElement(
+                inputDeclarations = Vector(
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "ten", Some(addExpression)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "zero", Some(subtractExpression)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "twentyfive", Some(multiplyExpression)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "one", Some(divideExpression)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "zeroagain", Some(remainderExpression)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "tenagain", Some(tenVariableLookup)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                          "pair_expression_member_access",
+                                          Some(pairExpressionMemberAccess)
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomBooleanType),
+                                          "unary_expressions",
+                                          Some(unaryExpressions)
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomBooleanType),
+                                          "comparisons",
+                                          Some(comparisonExpression)
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                          "variableLookupMemberAccesses",
+                                          Some(chainIdentifierAccess)
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                          "expressionMemberAccesses",
+                                          Some(chainPairAccess)
+                  ),
+                  InputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+                                          "is",
+                                          Some(arrayOfIs)
+                  ),
+                  InputDeclarationElement(ObjectTypeElement, "object_literal", Some(objectLiteralExpression)),
+                  InputDeclarationElement(
+                    MapTypeElement(PrimitiveTypeElement(WomStringType), PrimitiveTypeElement(WomIntegerType)),
+                    "map_literal",
+                    Some(mapLiteralExpression)
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "ternaryIf", Some(ternaryIfExpression)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                          "string_read",
+                                          Some(ReadString(StdoutElement))
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "zipped", Some(zippedExpression)),
+                  InputDeclarationElement(PrimitiveTypeElement(WomStringType), "subbed", Some(subbedExpression))
+                )
+              )
+            ),
+            graphElements = Set.empty,
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(4))
+          )
+        ),
+        tasks = Vector.empty
+      ),
     "passthrough_workflow" ->
       FileElement(
         imports = Vector(),
@@ -194,35 +269,77 @@ object WdlFileToWdlomSpec {
         workflows = Vector(
           WorkflowDefinitionElement(
             name = "foo",
-            inputsSection = Some(InputsSectionElement(Vector(
-              InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "x", None)
-            ))),
-            graphElements = Set(IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "y", IdentifierLookup("x"))),
-            outputsSection = Some(OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "z", IdentifierLookup("y"))))),
+            inputsSection = Some(
+              InputsSectionElement(
+                Vector(
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "x", None)
+                )
+              )
+            ),
+            graphElements = Set(
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "y", IdentifierLookup("x"))
+            ),
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "z", IdentifierLookup("y")))
+              )
+            ),
             metaSection = None,
             parameterMetaSection = None,
-            sourceLocation = Some(SourceFileLocation(3)))),
-        tasks = Vector()),
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        ),
+        tasks = Vector()
+      ),
     "scatter_var_member_access" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
         workflows = Vector(
-          WorkflowDefinitionElement("scatter_var_member_access", None,
-            Set(IntermediateValueDeclarationElement(
-              ArrayTypeElement(PairTypeElement(PrimitiveTypeElement(WomIntegerType), PrimitiveTypeElement(WomIntegerType))),
-              "pairs",
-              ArrayLiteral(Vector(
-                  PairLiteral(PrimitiveLiteralExpressionElement(WomInteger(1)), PrimitiveLiteralExpressionElement(WomInteger(2))),
-                  PairLiteral(PrimitiveLiteralExpressionElement(WomInteger(3)), PrimitiveLiteralExpressionElement(WomInteger(4))),
-                  PairLiteral(PrimitiveLiteralExpressionElement(WomInteger(5)), PrimitiveLiteralExpressionElement(WomInteger(6)))))),
-            ScatterElement("ScatterAt5_12", IdentifierLookup("pairs"), "p",
-                           Vector(IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "x", IdentifierMemberAccess("p", "left", Vector()))), None)),
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3)))),
-        tasks = Vector.empty),
+          WorkflowDefinitionElement(
+            "scatter_var_member_access",
+            None,
+            Set(
+              IntermediateValueDeclarationElement(
+                ArrayTypeElement(
+                  PairTypeElement(PrimitiveTypeElement(WomIntegerType), PrimitiveTypeElement(WomIntegerType))
+                ),
+                "pairs",
+                ArrayLiteral(
+                  Vector(
+                    PairLiteral(PrimitiveLiteralExpressionElement(WomInteger(1)),
+                                PrimitiveLiteralExpressionElement(WomInteger(2))
+                    ),
+                    PairLiteral(PrimitiveLiteralExpressionElement(WomInteger(3)),
+                                PrimitiveLiteralExpressionElement(WomInteger(4))
+                    ),
+                    PairLiteral(PrimitiveLiteralExpressionElement(WomInteger(5)),
+                                PrimitiveLiteralExpressionElement(WomInteger(6))
+                    )
+                  )
+                )
+              ),
+              ScatterElement(
+                "ScatterAt5_12",
+                IdentifierLookup("pairs"),
+                "p",
+                Vector(
+                  IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                      "x",
+                                                      IdentifierMemberAccess("p", "left", Vector())
+                  )
+                ),
+                None
+              )
+            ),
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        ),
+        tasks = Vector.empty
+      ),
     "nested_conditionals" ->
       FileElement(
         imports = Vector.empty,
@@ -232,12 +349,34 @@ object WdlFileToWdlomSpec {
             "Test",
             None,
             Set(
-              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "a", PrimitiveLiteralExpressionElement(WomInteger(5))),
-              IfElement(PrimitiveLiteralExpressionElement(WomBoolean(true)), Vector(
-                IfElement(PrimitiveLiteralExpressionElement(WomBoolean(true)), Vector(
-                  IfElement(PrimitiveLiteralExpressionElement(WomBoolean(true)), Vector(
-                    IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "b", PrimitiveLiteralExpressionElement(WomInteger(5))))))))),
-              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "c", SelectFirst(ArrayLiteral(Vector(IdentifierLookup("a"), IdentifierLookup("b")))))
+              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                  "a",
+                                                  PrimitiveLiteralExpressionElement(WomInteger(5))
+              ),
+              IfElement(
+                PrimitiveLiteralExpressionElement(WomBoolean(true)),
+                Vector(
+                  IfElement(
+                    PrimitiveLiteralExpressionElement(WomBoolean(true)),
+                    Vector(
+                      IfElement(
+                        PrimitiveLiteralExpressionElement(WomBoolean(true)),
+                        Vector(
+                          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                              "b",
+                                                              PrimitiveLiteralExpressionElement(WomInteger(5))
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              IntermediateValueDeclarationElement(
+                PrimitiveTypeElement(WomIntegerType),
+                "c",
+                SelectFirst(ArrayLiteral(Vector(IdentifierLookup("a"), IdentifierLookup("b"))))
+              )
             ),
             None,
             None,
@@ -260,81 +399,165 @@ object WdlFileToWdlomSpec {
               IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "a", intLiteral),
               IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "x", IdentifierLookup("a"))
             ),
-            outputsSection = Some(OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "z", IdentifierLookup("y"))))),
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "z", IdentifierLookup("y")))
+              )
+            ),
             metaSection = None,
             parameterMetaSection = None,
-            sourceLocation = Some(SourceFileLocation(5)))),
-        tasks = Vector()),
+            sourceLocation = Some(SourceFileLocation(5))
+          )
+        ),
+        tasks = Vector()
+      ),
     "simple_first_test" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "order",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "n", Some(PrimitiveLiteralExpressionElement(WomInteger(4)))),
-            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", Some(StringLiteral("more")))))),
-          graphElements = Set(CallElement("in_n_out", None, Vector.empty, Some(CallBodyElement(Vector(KvPair("total", IdentifierLookup("n")), KvPair("amount", IdentifierLookup("more"))))), Some(SourceFileLocation(19)))),
-          outputsSection = Some(OutputsSectionElement(Vector(
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "out", IdentifierMemberAccess("in_n_out", "out", List.empty))))),
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(14)))),
-        tasks = Vector(TaskDefinitionElement(
-          name = "in_n_out",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "total", None),
-            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "amount", None)))),
-          declarations = Vector.empty,
-          outputsSection = Some(OutputsSectionElement(Vector(
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "out", Add(ReadInt(StdoutElement), PrimitiveLiteralExpressionElement(WomInteger(1))))))),
-          commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(
-            StringCommandPartElement("echo "),
-            PlaceholderCommandPartElement(IdentifierLookup("total"), PlaceholderAttributeSet.empty),
-            StringCommandPartElement(" ")
-          )))),
-          runtimeSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3))
-        ))),
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "order",
+            inputsSection = Some(
+              InputsSectionElement(
+                Vector(
+                  InputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                          "n",
+                                          Some(PrimitiveLiteralExpressionElement(WomInteger(4)))
+                  ),
+                  InputDeclarationElement(PrimitiveTypeElement(WomStringType), "more", Some(StringLiteral("more")))
+                )
+              )
+            ),
+            graphElements = Set(
+              CallElement(
+                "in_n_out",
+                None,
+                Vector.empty,
+                Some(
+                  CallBodyElement(
+                    Vector(KvPair("total", IdentifierLookup("n")), KvPair("amount", IdentifierLookup("more")))
+                  )
+                ),
+                Some(SourceFileLocation(19))
+              )
+            ),
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(
+                  OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                           "out",
+                                           IdentifierMemberAccess("in_n_out", "out", List.empty)
+                  )
+                )
+              )
+            ),
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(14))
+          )
+        ),
+        tasks = Vector(
+          TaskDefinitionElement(
+            name = "in_n_out",
+            inputsSection = Some(
+              InputsSectionElement(
+                Vector(InputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "total", None),
+                       InputDeclarationElement(PrimitiveTypeElement(WomStringType), "amount", None)
+                )
+              )
+            ),
+            declarations = Vector.empty,
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(
+                  OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                           "out",
+                                           Add(ReadInt(StdoutElement), PrimitiveLiteralExpressionElement(WomInteger(1)))
+                  )
+                )
+              )
+            ),
+            commandSection = CommandSectionElement(
+              Vector(
+                CommandSectionLine(
+                  Vector(
+                    StringCommandPartElement("echo "),
+                    PlaceholderCommandPartElement(IdentifierLookup("total"), PlaceholderAttributeSet.empty),
+                    StringCommandPartElement(" ")
+                  )
+                )
+              )
+            ),
+            runtimeSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        )
+      ),
     "static_value_workflow" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "foo",
-          inputsSection = None,
-          graphElements = Set.empty,
-          outputsSection = Some(OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "y", PrimitiveLiteralExpressionElement(WomInteger(3)))))),
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3)))),
-        tasks = Vector.empty),
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "foo",
+            inputsSection = None,
+            graphElements = Set.empty,
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(
+                  OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                           "y",
+                                           PrimitiveLiteralExpressionElement(WomInteger(3))
+                  )
+                )
+              )
+            ),
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        ),
+        tasks = Vector.empty
+      ),
     "standalone_task" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement("standalone_task", None, Set.empty,
-                                                     None, None, None,
-                                                     Some(SourceFileLocation(3)))),
+        workflows = Vector(
+          WorkflowDefinitionElement("standalone_task", None, Set.empty, None, None, None, Some(SourceFileLocation(3)))
+        ),
         tasks = Vector(
           TaskDefinitionElement(
             name = "standalone",
-            inputsSection = Some(InputsSectionElement(Vector(InputDeclarationElement(PrimitiveTypeElement(WomStringType), "bar", None)))),
+            inputsSection = Some(
+              InputsSectionElement(Vector(InputDeclarationElement(PrimitiveTypeElement(WomStringType), "bar", None)))
+            ),
             declarations = Vector.empty,
-            outputsSection = Some(OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "out", IdentifierLookup("bar"))))),
-            commandSection = CommandSectionElement(Vector(
-              CommandSectionLine(Vector(
-                StringCommandPartElement("echo "),
-                PlaceholderCommandPartElement(IdentifierLookup("bar"), PlaceholderAttributeSet.empty)
-              ))
-            )),
-            runtimeSection = Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("someFakeDockerRuntime"))))),
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "out", IdentifierLookup("bar")))
+              )
+            ),
+            commandSection = CommandSectionElement(
+              Vector(
+                CommandSectionLine(
+                  Vector(
+                    StringCommandPartElement("echo "),
+                    PlaceholderCommandPartElement(IdentifierLookup("bar"), PlaceholderAttributeSet.empty)
+                  )
+                )
+              )
+            ),
+            runtimeSection =
+              Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("someFakeDockerRuntime"))))),
             metaSection = None,
             parameterMetaSection = None,
             sourceLocation = Some(SourceFileLocation(5))
-            ))
+          )
+        )
       ),
     "task_with_metas" ->
       FileElement(
@@ -347,32 +570,50 @@ object WdlFileToWdlomSpec {
             inputsSection = Some(InputsSectionElement(Vector.empty)),
             declarations = Vector.empty,
             outputsSection = Some(OutputsSectionElement(Vector.empty)),
-            commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(
-              StringCommandPartElement("echo Hello World ")
-            )))),
+            commandSection = CommandSectionElement(
+              Vector(
+                CommandSectionLine(
+                  Vector(
+                    StringCommandPartElement("echo Hello World ")
+                  )
+                )
+              )
+            ),
             runtimeSection = None,
-            metaSection = Some(MetaSectionElement(
-              Map("author" -> MetaValueElementString("John Doe"),
-                "email" -> MetaValueElementString("john.doe@yahoo.com"))
-            )),
-            parameterMetaSection = Some(ParameterMetaSectionElement(
-              Map("a" -> MetaValueElementString("just an integer"),
-                "b" -> MetaValueElementString("an important parameter"),
-                "x" -> MetaValueElementArray(Vector(MetaValueElementString("A"),
-                  MetaValueElementString("B"),
-                  MetaValueElementString("C"))),
-                "y" -> MetaValueElementArray(Vector(MetaValueElementInteger(1),
-                  MetaValueElementInteger(2),
-                  MetaValueElementInteger(3))),
-                "yf" -> MetaValueElementArray(Vector(MetaValueElementFloat(1.1),
-                  MetaValueElementFloat(2.9),
-                  MetaValueElementFloat(3.14))),
-                "z" -> MetaValueElementObject(Map("k1" -> MetaValueElementInteger(1),
-                  "k2" -> MetaValueElementInteger(2),
-                  "k3" -> MetaValueElementInteger(3)))
-              ))),
+            metaSection = Some(
+              MetaSectionElement(
+                Map("author" -> MetaValueElementString("John Doe"),
+                    "email" -> MetaValueElementString("john.doe@yahoo.com")
+                )
+              )
+            ),
+            parameterMetaSection = Some(
+              ParameterMetaSectionElement(
+                Map(
+                  "a" -> MetaValueElementString("just an integer"),
+                  "b" -> MetaValueElementString("an important parameter"),
+                  "x" -> MetaValueElementArray(
+                    Vector(MetaValueElementString("A"), MetaValueElementString("B"), MetaValueElementString("C"))
+                  ),
+                  "y" -> MetaValueElementArray(
+                    Vector(MetaValueElementInteger(1), MetaValueElementInteger(2), MetaValueElementInteger(3))
+                  ),
+                  "yf" -> MetaValueElementArray(
+                    Vector(MetaValueElementFloat(1.1), MetaValueElementFloat(2.9), MetaValueElementFloat(3.14))
+                  ),
+                  "z" -> MetaValueElementObject(
+                    Map("k1" -> MetaValueElementInteger(1),
+                        "k2" -> MetaValueElementInteger(2),
+                        "k3" -> MetaValueElementInteger(3)
+                    )
+                  )
+                )
+              )
+            ),
             sourceLocation = Some(SourceFileLocation(3))
-          ))),
+          )
+        )
+      ),
     "task_with_metas2" ->
       FileElement(
         imports = Vector.empty,
@@ -386,48 +627,58 @@ object WdlFileToWdlomSpec {
             outputsSection = Some(OutputsSectionElement(Vector.empty)),
             commandSection = CommandSectionElement(List.empty),
             runtimeSection = None,
-            metaSection = Some(MetaSectionElement(
-              Map("author" -> MetaValueElementString("John Doe"),
+            metaSection = Some(
+              MetaSectionElement(
+                Map(
+                  "author" -> MetaValueElementString("John Doe"),
                   "email" -> MetaValueElementString("john.doe@yahoo.com"),
                   "b" -> MetaValueElementBoolean(true),
                   "zipcode" -> MetaValueElementInteger(94043),
                   "f" -> MetaValueElementFloat(1.3),
-                  "numbers" -> MetaValueElementArray(Vector(MetaValueElementInteger(1),
-                                                            MetaValueElementInteger(2),
-                                                            MetaValueElementInteger(3))),
+                  "numbers" -> MetaValueElementArray(
+                    Vector(MetaValueElementInteger(1), MetaValueElementInteger(2), MetaValueElementInteger(3))
+                  ),
                   "extras" -> MetaValueElementObject(
-                    Map( "house" -> MetaValueElementString("With porch"),
-                         "cat" -> MetaValueElementString("Lucy")))
-              ))),
+                    Map("house" -> MetaValueElementString("With porch"), "cat" -> MetaValueElementString("Lucy"))
+                  )
+                )
+              )
+            ),
             parameterMetaSection = None,
             sourceLocation = Some(SourceFileLocation(3))
-          ))),
+          )
+        )
+      ),
     "no_input_no_output_workflow" ->
       FileElement(
         imports = Vector.empty,
         structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "no_input_no_output",
-          inputsSection = None,
-          graphElements = Set(
-            CallElement("no_inputs", Some("noi1"), Vector.empty, None, Some(SourceFileLocation(4))),
-            CallElement("no_inputs", None, Vector.empty, None, Some(SourceFileLocation(6))),
-            CallElement("no_inputs", Some("noi2"), Vector.empty, None, Some(SourceFileLocation(8))),
-            CallElement("no_inputs", Some("noi3"), Vector.empty, None, Some(SourceFileLocation(10))),
-            CallElement("no_inputs", Some("noi4"), Vector.empty, None, Some(SourceFileLocation(14))),
-            CallElement("no_inputs", Some("noi5"), Vector.empty, None, Some(SourceFileLocation(18)))
-          ),
-          outputsSection = None,
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(3)))),
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "no_input_no_output",
+            inputsSection = None,
+            graphElements = Set(
+              CallElement("no_inputs", Some("noi1"), Vector.empty, None, Some(SourceFileLocation(4))),
+              CallElement("no_inputs", None, Vector.empty, None, Some(SourceFileLocation(6))),
+              CallElement("no_inputs", Some("noi2"), Vector.empty, None, Some(SourceFileLocation(8))),
+              CallElement("no_inputs", Some("noi3"), Vector.empty, None, Some(SourceFileLocation(10))),
+              CallElement("no_inputs", Some("noi4"), Vector.empty, None, Some(SourceFileLocation(14))),
+              CallElement("no_inputs", Some("noi5"), Vector.empty, None, Some(SourceFileLocation(18)))
+            ),
+            outputsSection = None,
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(3))
+          )
+        ),
         tasks = Vector(
           TaskDefinitionElement(
             name = "no_inputs",
             inputsSection = None,
             declarations = Vector.empty,
             outputsSection = None,
-            commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(StringCommandPartElement("echo Hello World "))))),
+            commandSection =
+              CommandSectionElement(Vector(CommandSectionLine(Vector(StringCommandPartElement("echo Hello World "))))),
             runtimeSection = None,
             metaSection = None,
             parameterMetaSection = None,
@@ -441,297 +692,464 @@ object WdlFileToWdlomSpec {
         structs = Vector(
           StructElement(
             name = "A",
-            entries = Vector(
-              StructEntryElement("i", PrimitiveTypeElement(WomIntegerType)),
-              StructEntryElement("f", PrimitiveTypeElement(WomFloatType)))
+            entries = Vector(StructEntryElement("i", PrimitiveTypeElement(WomIntegerType)),
+                             StructEntryElement("f", PrimitiveTypeElement(WomFloatType))
+            )
           ),
           StructElement(
             name = "B",
             entries = Vector(
               StructEntryElement("a", TypeAliasElement("A")),
               StructEntryElement("i", PrimitiveTypeElement(WomIntegerType)),
-              StructEntryElement("f", PrimitiveTypeElement(WomFloatType)))
-          )),
-        workflows = Vector(WorkflowDefinitionElement(
-          name = "nested_struct",
-          inputsSection = None,
-          graphElements = Set(
-            IntermediateValueDeclarationElement(
-              TypeAliasElement("B"),
-              "b",
-              ObjectLiteral(Map(
-                "a" -> ObjectLiteral(Map(
-                  "i" -> PrimitiveLiteralExpressionElement(WomInteger(5)),
-                  "f" -> PrimitiveLiteralExpressionElement(WomFloat(5.5)))),
-                "i" -> PrimitiveLiteralExpressionElement(WomInteger(6)),
-                "f" -> PrimitiveLiteralExpressionElement(WomFloat(6.6)))))),
-          outputsSection = Some(OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomFloatType), "f", IdentifierMemberAccess("b", "a", Vector("f")))))),
-          metaSection = None,
-          parameterMetaSection = None,
-          sourceLocation = Some(SourceFileLocation(14)))
+              StructEntryElement("f", PrimitiveTypeElement(WomFloatType))
+            )
+          )
+        ),
+        workflows = Vector(
+          WorkflowDefinitionElement(
+            name = "nested_struct",
+            inputsSection = None,
+            graphElements = Set(
+              IntermediateValueDeclarationElement(
+                TypeAliasElement("B"),
+                "b",
+                ObjectLiteral(
+                  Map(
+                    "a" -> ObjectLiteral(
+                      Map("i" -> PrimitiveLiteralExpressionElement(WomInteger(5)),
+                          "f" -> PrimitiveLiteralExpressionElement(WomFloat(5.5))
+                      )
+                    ),
+                    "i" -> PrimitiveLiteralExpressionElement(WomInteger(6)),
+                    "f" -> PrimitiveLiteralExpressionElement(WomFloat(6.6))
+                  )
+                )
+              )
+            ),
+            outputsSection = Some(
+              OutputsSectionElement(
+                Vector(
+                  OutputDeclarationElement(PrimitiveTypeElement(WomFloatType),
+                                           "f",
+                                           IdentifierMemberAccess("b", "a", Vector("f"))
+                  )
+                )
+              )
+            ),
+            metaSection = None,
+            parameterMetaSection = None,
+            sourceLocation = Some(SourceFileLocation(14))
+          )
         ),
         tasks = Vector()
       ),
     "simple_scatter" -> FileElement(
       imports = Vector.empty,
       structs = Vector.empty,
-      workflows = Vector(WorkflowDefinitionElement(
-        name = "simple_scatter",
-        inputsSection = None,
-        graphElements = Set(
-          IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "indices", ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(1)), PrimitiveLiteralExpressionElement(WomInteger(2)), PrimitiveLiteralExpressionElement(WomInteger(3))))),
-          ScatterElement(
-            scatterName = "ScatterAt6_11",
-            scatterExpression = IdentifierLookup("indices"),
-            scatterVariableName = "i",
-            graphElements = Vector(
-              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "j", Add(IdentifierLookup("i"), PrimitiveLiteralExpressionElement(WomInteger(10))))
-            ),
-            sourceLocation = None
-          )
-        ),
-        outputsSection = Some(
-          OutputsSectionElement(Vector(OutputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "js", IdentifierLookup("j"))))
-        ),
-        metaSection = None,
-        parameterMetaSection = None,
-        sourceLocation = Some(SourceFileLocation(3)))
+      workflows = Vector(
+        WorkflowDefinitionElement(
+          name = "simple_scatter",
+          inputsSection = None,
+          graphElements = Set(
+            IntermediateValueDeclarationElement(
+              ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+              "indices",
+              ArrayLiteral(
+                Vector(PrimitiveLiteralExpressionElement(WomInteger(1)),
+                       PrimitiveLiteralExpressionElement(WomInteger(2)),
+                       PrimitiveLiteralExpressionElement(WomInteger(3))
+                )
+              )
+            ),
+            ScatterElement(
+              scatterName = "ScatterAt6_11",
+              scatterExpression = IdentifierLookup("indices"),
+              scatterVariableName = "i",
+              graphElements = Vector(
+                IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                    "j",
+                                                    Add(IdentifierLookup("i"),
+                                                        PrimitiveLiteralExpressionElement(WomInteger(10))
+                                                    )
+                )
+              ),
+              sourceLocation = None
+            )
+          ),
+          outputsSection = Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+                                         "js",
+                                         IdentifierLookup("j")
+                )
+              )
+            )
+          ),
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(3))
+        )
       ),
       tasks = Vector.empty
     ),
     "ogin_scatter" -> FileElement(
       imports = Vector.empty,
       structs = Vector.empty,
-      workflows = Vector(WorkflowDefinitionElement(
-        name = "ogin_scatter",
-        inputsSection = None,
-        graphElements = Set(
-          IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "indices", ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(1)), PrimitiveLiteralExpressionElement(WomInteger(2)), PrimitiveLiteralExpressionElement(WomInteger(3))))),
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "ogin_me", PrimitiveLiteralExpressionElement(WomInteger(10))),
-          ScatterElement(
-            scatterName = "ScatterAt8_11",
-            scatterExpression = IdentifierLookup("indices"),
-            scatterVariableName = "i",
-            graphElements = Vector(
-              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "j", Add(IdentifierLookup("i"), IdentifierLookup("ogin_me")))
-            ),
-            sourceLocation = None
-          )
-        ),
-        outputsSection = Some(
-          OutputsSectionElement(Vector(OutputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "js", IdentifierLookup("j"))))
-        ),
-        metaSection = None,
-        parameterMetaSection = None,
-        sourceLocation = Some(SourceFileLocation(3)))
+      workflows = Vector(
+        WorkflowDefinitionElement(
+          name = "ogin_scatter",
+          inputsSection = None,
+          graphElements = Set(
+            IntermediateValueDeclarationElement(
+              ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+              "indices",
+              ArrayLiteral(
+                Vector(PrimitiveLiteralExpressionElement(WomInteger(1)),
+                       PrimitiveLiteralExpressionElement(WomInteger(2)),
+                       PrimitiveLiteralExpressionElement(WomInteger(3))
+                )
+              )
+            ),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                "ogin_me",
+                                                PrimitiveLiteralExpressionElement(WomInteger(10))
+            ),
+            ScatterElement(
+              scatterName = "ScatterAt8_11",
+              scatterExpression = IdentifierLookup("indices"),
+              scatterVariableName = "i",
+              graphElements = Vector(
+                IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                    "j",
+                                                    Add(IdentifierLookup("i"), IdentifierLookup("ogin_me"))
+                )
+              ),
+              sourceLocation = None
+            )
+          ),
+          outputsSection = Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+                                         "js",
+                                         IdentifierLookup("j")
+                )
+              )
+            )
+          ),
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(3))
+        )
       ),
       tasks = Vector.empty
     ),
     "nested_scatter" -> FileElement(
       Vector(),
       Vector(),
-      Vector(WorkflowDefinitionElement(
-        "nested_scatter",
-        None,
-        Set(
-          IntermediateValueDeclarationElement(
-            ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
-            "indices",
-            ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(1)), PrimitiveLiteralExpressionElement(WomInteger(2)), PrimitiveLiteralExpressionElement(WomInteger(3))))
-          ),
-          IntermediateValueDeclarationElement(
-            PrimitiveTypeElement(WomIntegerType),
-            "y",
-            PrimitiveLiteralExpressionElement(WomInteger(55))
-          ),
-          ScatterElement(
-            scatterName = "ScatterAt8_11",
-            IdentifierLookup("indices"),
-            "a",
-            Vector(
-              ScatterElement(
-                scatterName = "ScatterAt9_13",
-                IdentifierLookup("indices"), "b",
-                Vector(
-                  IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "x", Add(IdentifierLookup("a"), IdentifierLookup("b"))),
-                  ScatterElement(
-                    scatterName = "ScatterAt11_15",
-                    IdentifierLookup("indices"),
-                    "c",
-                    Vector(
-                      IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "j", Add(Add(Add(IdentifierLookup("a"), IdentifierLookup("b")), IdentifierLookup("c")), IdentifierLookup("x")))),
-                    None),
-                  ScatterElement(
-                    scatterName = "ScatterAt14_15",
-                    IdentifierLookup("j"),
-                    "d",
-                    Vector(IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "k", Add(IdentifierLookup("d"), IdentifierLookup("y")))),
-                    None
-                  )
-                ),
-                sourceLocation = None
+      Vector(
+        WorkflowDefinitionElement(
+          "nested_scatter",
+          None,
+          Set(
+            IntermediateValueDeclarationElement(
+              ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+              "indices",
+              ArrayLiteral(
+                Vector(PrimitiveLiteralExpressionElement(WomInteger(1)),
+                       PrimitiveLiteralExpressionElement(WomInteger(2)),
+                       PrimitiveLiteralExpressionElement(WomInteger(3))
+                )
               )
             ),
-            None
-          )
-        ),
-        Some(
-          OutputsSectionElement(Vector(OutputDeclarationElement(ArrayTypeElement(ArrayTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)))), "ks", IdentifierLookup("k"))))
-        ),
-        None,
-        None,
-        Some(SourceFileLocation(3)))
+            IntermediateValueDeclarationElement(
+              PrimitiveTypeElement(WomIntegerType),
+              "y",
+              PrimitiveLiteralExpressionElement(WomInteger(55))
+            ),
+            ScatterElement(
+              scatterName = "ScatterAt8_11",
+              IdentifierLookup("indices"),
+              "a",
+              Vector(
+                ScatterElement(
+                  scatterName = "ScatterAt9_13",
+                  IdentifierLookup("indices"),
+                  "b",
+                  Vector(
+                    IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                        "x",
+                                                        Add(IdentifierLookup("a"), IdentifierLookup("b"))
+                    ),
+                    ScatterElement(
+                      scatterName = "ScatterAt11_15",
+                      IdentifierLookup("indices"),
+                      "c",
+                      Vector(
+                        IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                            "j",
+                                                            Add(Add(Add(IdentifierLookup("a"), IdentifierLookup("b")),
+                                                                    IdentifierLookup("c")
+                                                                ),
+                                                                IdentifierLookup("x")
+                                                            )
+                        )
+                      ),
+                      None
+                    ),
+                    ScatterElement(
+                      scatterName = "ScatterAt14_15",
+                      IdentifierLookup("j"),
+                      "d",
+                      Vector(
+                        IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                            "k",
+                                                            Add(IdentifierLookup("d"), IdentifierLookup("y"))
+                        )
+                      ),
+                      None
+                    )
+                  ),
+                  sourceLocation = None
+                )
+              ),
+              None
+            )
+          ),
+          Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(
+                  ArrayTypeElement(ArrayTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)))),
+                  "ks",
+                  IdentifierLookup("k")
+                )
+              )
+            )
+          ),
+          None,
+          None,
+          Some(SourceFileLocation(3))
+        )
       ),
       Vector()
     ),
     "two_level_scatter" -> FileElement(
-      Vector(),
-      Vector(),
-      Vector(WorkflowDefinitionElement(
-        "two_level_scatter",
-        None,
-        Set(
-          IntermediateValueDeclarationElement(
-            ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
-            "indices",
-            ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(1)), PrimitiveLiteralExpressionElement(WomInteger(2)), PrimitiveLiteralExpressionElement(WomInteger(3))))
-          ),
-          ScatterElement(
-            scatterName = "ScatterAt8_11",
-            IdentifierLookup("indices"),
-            "a",
-            Vector(
-              ScatterElement(
-                scatterName = "ScatterAt9_13",
-                IdentifierLookup("indices"), "b",
-                Vector(
-                  IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "x", Add(IdentifierLookup("a"), IdentifierLookup("b")))),
-                sourceLocation = None
+      Vector(),
+      Vector(),
+      Vector(
+        WorkflowDefinitionElement(
+          "two_level_scatter",
+          None,
+          Set(
+            IntermediateValueDeclarationElement(
+              ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+              "indices",
+              ArrayLiteral(
+                Vector(PrimitiveLiteralExpressionElement(WomInteger(1)),
+                       PrimitiveLiteralExpressionElement(WomInteger(2)),
+                       PrimitiveLiteralExpressionElement(WomInteger(3))
+                )
               )
             ),
-            None
-          )
-        ),
-        None,
-        None,
-        None,
-        Some(SourceFileLocation(3)))
+            ScatterElement(
+              scatterName = "ScatterAt8_11",
+              IdentifierLookup("indices"),
+              "a",
+              Vector(
+                ScatterElement(
+                  scatterName = "ScatterAt9_13",
+                  IdentifierLookup("indices"),
+                  "b",
+                  Vector(
+                    IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                        "x",
+                                                        Add(IdentifierLookup("a"), IdentifierLookup("b"))
+                    )
+                  ),
+                  sourceLocation = None
+                )
+              ),
+              None
+            )
+          ),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(3))
+        )
       ),
       Vector()
     ),
     "simple_conditional" -> FileElement(
       imports = Vector.empty,
       structs = Vector.empty,
-      workflows = Vector(WorkflowDefinitionElement(
-        name = "simple_conditional",
-        inputsSection = None,
-        graphElements = Set(
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomBooleanType), "bool", PrimitiveLiteralExpressionElement(WomBoolean(true))),
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", PrimitiveLiteralExpressionElement(WomInteger(5))),
-          IfElement(
-            conditionExpression = IdentifierLookup("bool"),
-            graphElements = Vector(
-              IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType), "j", Add(IdentifierLookup("i"), PrimitiveLiteralExpressionElement(WomInteger(10))))
+      workflows = Vector(
+        WorkflowDefinitionElement(
+          name = "simple_conditional",
+          inputsSection = None,
+          graphElements = Set(
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomBooleanType),
+                                                "bool",
+                                                PrimitiveLiteralExpressionElement(WomBoolean(true))
+            ),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                "i",
+                                                PrimitiveLiteralExpressionElement(WomInteger(5))
+            ),
+            IfElement(
+              conditionExpression = IdentifierLookup("bool"),
+              graphElements = Vector(
+                IntermediateValueDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                                    "j",
+                                                    Add(IdentifierLookup("i"),
+                                                        PrimitiveLiteralExpressionElement(WomInteger(10))
+                                                    )
+                )
+              )
             )
-          )
-        ),
-        outputsSection = Some(
-          OutputsSectionElement(Vector(OutputDeclarationElement(OptionalTypeElement(PrimitiveTypeElement(WomIntegerType)), "j_maybe", IdentifierLookup("j"))))
-        ),
-        metaSection = None,
-        parameterMetaSection = None,
-        sourceLocation = Some(SourceFileLocation(5)))
+          ),
+          outputsSection = Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(OptionalTypeElement(PrimitiveTypeElement(WomIntegerType)),
+                                         "j_maybe",
+                                         IdentifierLookup("j")
+                )
+              )
+            )
+          ),
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(5))
+        )
       ),
       tasks = Vector.empty
     ),
     "lots_of_nesting" -> FileElement(
       imports = Vector.empty,
       structs = Vector.empty,
-      workflows = Vector(WorkflowDefinitionElement(
-        name = "lots_of_nesting",
-        inputsSection = None,
-        graphElements = Set(
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomBooleanType), "b0", PrimitiveLiteralExpressionElement(WomBoolean(true))),
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomBooleanType), "b1", PrimitiveLiteralExpressionElement(WomBoolean(true))),
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomBooleanType), "b2", PrimitiveLiteralExpressionElement(WomBoolean(true))),
-          IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "i0s", Range(PrimitiveLiteralExpressionElement(WomInteger(2)))),
-          IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "i1s", Range(PrimitiveLiteralExpressionElement(WomInteger(2)))),
-          IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "i2s", Range(PrimitiveLiteralExpressionElement(WomInteger(2)))),
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "s0", StringLiteral("hello")),
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "s1", StringLiteral("world")),
-          IfElement(
-            conditionExpression = IdentifierLookup("b0"),
-            graphElements = Vector(
-              ScatterElement(
-                scatterName = "ScatterAt17_13",
-                scatterExpression = IdentifierLookup("i0s"),
-                scatterVariableName = "i0",
-                graphElements = Vector(
-                  IfElement(
-                    conditionExpression = IdentifierLookup("b1"),
-                    graphElements = Vector(
-                      ScatterElement(
-                        scatterName = "ScatterAt19_17",
-                        scatterExpression = IdentifierLookup("i1s"),
-                        scatterVariableName = "i1",
-                        graphElements = Vector(
-                          IfElement(
-                            conditionExpression = IdentifierLookup("b2"),
-                            graphElements = Vector(
-                              ScatterElement(
-                                "ScatterAt21_21",
-                                IdentifierLookup("i2s"),
-                                "i2",
-                                Vector(
-                                  IntermediateValueDeclarationElement(
-                                    PrimitiveTypeElement(WomStringType),
-                                    "s",
-                                    Add(IdentifierLookup("s0"), IdentifierLookup("s1"))
-                                  )
-                                ),
-                                None
+      workflows = Vector(
+        WorkflowDefinitionElement(
+          name = "lots_of_nesting",
+          inputsSection = None,
+          graphElements = Set(
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomBooleanType),
+                                                "b0",
+                                                PrimitiveLiteralExpressionElement(WomBoolean(true))
+            ),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomBooleanType),
+                                                "b1",
+                                                PrimitiveLiteralExpressionElement(WomBoolean(true))
+            ),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomBooleanType),
+                                                "b2",
+                                                PrimitiveLiteralExpressionElement(WomBoolean(true))
+            ),
+            IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+                                                "i0s",
+                                                Range(PrimitiveLiteralExpressionElement(WomInteger(2)))
+            ),
+            IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+                                                "i1s",
+                                                Range(PrimitiveLiteralExpressionElement(WomInteger(2)))
+            ),
+            IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+                                                "i2s",
+                                                Range(PrimitiveLiteralExpressionElement(WomInteger(2)))
+            ),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "s0", StringLiteral("hello")),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "s1", StringLiteral("world")),
+            IfElement(
+              conditionExpression = IdentifierLookup("b0"),
+              graphElements = Vector(
+                ScatterElement(
+                  scatterName = "ScatterAt17_13",
+                  scatterExpression = IdentifierLookup("i0s"),
+                  scatterVariableName = "i0",
+                  graphElements = Vector(
+                    IfElement(
+                      conditionExpression = IdentifierLookup("b1"),
+                      graphElements = Vector(
+                        ScatterElement(
+                          scatterName = "ScatterAt19_17",
+                          scatterExpression = IdentifierLookup("i1s"),
+                          scatterVariableName = "i1",
+                          graphElements = Vector(
+                            IfElement(
+                              conditionExpression = IdentifierLookup("b2"),
+                              graphElements = Vector(
+                                ScatterElement(
+                                  "ScatterAt21_21",
+                                  IdentifierLookup("i2s"),
+                                  "i2",
+                                  Vector(
+                                    IntermediateValueDeclarationElement(
+                                      PrimitiveTypeElement(WomStringType),
+                                      "s",
+                                      Add(IdentifierLookup("s0"), IdentifierLookup("s1"))
+                                    )
+                                  ),
+                                  None
+                                )
                               )
                             )
-                          )
-                        ),
-                        sourceLocation = None
+                          ),
+                          sourceLocation = None
+                        )
                       )
                     )
-                  )
-                ),
-                sourceLocation = None
+                  ),
+                  sourceLocation = None
+                )
               )
             )
-          )
-        ),
-        outputsSection = Some(OutputsSectionElement(Vector(
-          OutputDeclarationElement(
-            typeElement = OptionalTypeElement(ArrayTypeElement(OptionalTypeElement(ArrayTypeElement(OptionalTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomStringType))))))),
-            name = "s_out",
-            expression = IdentifierLookup("s"))))),
-        metaSection = None,
-        parameterMetaSection = None,
-        sourceLocation = Some(SourceFileLocation(3)))
+          ),
+          outputsSection = Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(
+                  typeElement = OptionalTypeElement(
+                    ArrayTypeElement(
+                      OptionalTypeElement(
+                        ArrayTypeElement(OptionalTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomStringType))))
+                      )
+                    )
+                  ),
+                  name = "s_out",
+                  expression = IdentifierLookup("s")
+                )
+              )
+            )
+          ),
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(3))
+        )
       ),
       tasks = Vector.empty
     ),
     "simple_task" -> FileElement(
-        imports = Vector.empty,
-        structs = Vector.empty,
-        workflows = Vector(WorkflowDefinitionElement("simple_task", None, Set.empty,
-                                                     None, None, None,
-                                                     Some(SourceFileLocation(3)))),
-        tasks = Vector(
-          TaskDefinitionElement(
-            name = "simple",
-            inputsSection = None,
-            declarations = Vector.empty,
-            outputsSection = None,
-            commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(StringCommandPartElement("echo Hello World "))))),
-            runtimeSection = None,
-            metaSection = None,
-            parameterMetaSection = None,
-            sourceLocation = Some(SourceFileLocation(5))))
+      imports = Vector.empty,
+      structs = Vector.empty,
+      workflows = Vector(
+        WorkflowDefinitionElement("simple_task", None, Set.empty, None, None, None, Some(SourceFileLocation(3)))
+      ),
+      tasks = Vector(
+        TaskDefinitionElement(
+          name = "simple",
+          inputsSection = None,
+          declarations = Vector.empty,
+          outputsSection = None,
+          commandSection =
+            CommandSectionElement(Vector(CommandSectionLine(Vector(StringCommandPartElement("echo Hello World "))))),
+          runtimeSection = None,
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(5))
+        )
+      )
     ),
     "default_input_overrides" -> null,
     "nio_file" -> FileElement(
@@ -741,80 +1159,199 @@ object WdlFileToWdlomSpec {
       tasks = Vector(
         TaskDefinitionElement(
           name = "nio_file",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "f", None),
-            InputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "g", Some(IdentifierLookup("f"))),
-            InputDeclarationElement(OptionalTypeElement(PrimitiveTypeElement(WomSingleFileType)), "h", None)
-          ))),
+          inputsSection = Some(
+            InputsSectionElement(
+              Vector(
+                InputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "f", None),
+                InputDeclarationElement(PrimitiveTypeElement(WomSingleFileType), "g", Some(IdentifierLookup("f"))),
+                InputDeclarationElement(OptionalTypeElement(PrimitiveTypeElement(WomSingleFileType)), "h", None)
+              )
+            )
+          ),
           declarations = Vector.empty,
-          outputsSection = Some(OutputsSectionElement(Vector(
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "i", PrimitiveLiteralExpressionElement(WomInteger(5)))
-          ))),
-          commandSection = CommandSectionElement(Vector(CommandSectionLine(Vector(
-            StringCommandPartElement("echo "),
-            PlaceholderCommandPartElement(IdentifierLookup("f"), PlaceholderAttributeSet(None,None,None,None)),
-            StringCommandPartElement(" | cut -c 1-5")
-          )))),
-          runtimeSection = Some(RuntimeAttributesSectionElement(Vector(KvPair("docker",StringLiteral("ubuntu:latest"))))),
+          outputsSection = Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                         "i",
+                                         PrimitiveLiteralExpressionElement(WomInteger(5))
+                )
+              )
+            )
+          ),
+          commandSection = CommandSectionElement(
+            Vector(
+              CommandSectionLine(
+                Vector(
+                  StringCommandPartElement("echo "),
+                  PlaceholderCommandPartElement(IdentifierLookup("f"), PlaceholderAttributeSet(None, None, None, None)),
+                  StringCommandPartElement(" | cut -c 1-5")
+                )
+              )
+            )
+          ),
+          runtimeSection =
+            Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))),
           metaSection = None,
-          parameterMetaSection = Some(ParameterMetaSectionElement(Map(
-            "f" -> MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true))),
-            "g" -> MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true))),
-            "h" -> MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true)))
-          ))),
+          parameterMetaSection = Some(
+            ParameterMetaSectionElement(
+              Map(
+                "f" -> MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true))),
+                "g" -> MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true))),
+                "h" -> MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true)))
+              )
+            )
+          ),
           sourceLocation = Some(SourceFileLocation(3))
         )
       )
-  ),
+    ),
     "taskless_engine_functions" -> FileElement(
       imports = Vector.empty,
       structs = Vector.empty,
-      workflows = Vector(WorkflowDefinitionElement(
-        name = "taskless_engine_functions",
-        inputsSection = None,
-        graphElements = Set(
-          IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "ints", ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(1)), PrimitiveLiteralExpressionElement(WomInteger(2))))),
-          IntermediateValueDeclarationElement(NonEmptyTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType))), "definitelyInts", ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(1)), PrimitiveLiteralExpressionElement(WomInteger(2))))),
-          IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomStringType)), "strings", ArrayLiteral(Vector(StringLiteral("a"), StringLiteral("b")))),
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "filepath", StringLiteral("gs://not/a/real/file.txt")),
-          IntermediateValueDeclarationElement(ArrayTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType))), "matrix",
-            ArrayLiteral(Vector(
-              ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(1)), PrimitiveLiteralExpressionElement(WomInteger(0)))),
-              ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(1)), PrimitiveLiteralExpressionElement(WomInteger(0))))
-            ))
+      workflows = Vector(
+        WorkflowDefinitionElement(
+          name = "taskless_engine_functions",
+          inputsSection = None,
+          graphElements = Set(
+            IntermediateValueDeclarationElement(
+              ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+              "ints",
+              ArrayLiteral(
+                Vector(PrimitiveLiteralExpressionElement(WomInteger(1)),
+                       PrimitiveLiteralExpressionElement(WomInteger(2))
+                )
+              )
+            ),
+            IntermediateValueDeclarationElement(
+              NonEmptyTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType))),
+              "definitelyInts",
+              ArrayLiteral(
+                Vector(PrimitiveLiteralExpressionElement(WomInteger(1)),
+                       PrimitiveLiteralExpressionElement(WomInteger(2))
+                )
+              )
+            ),
+            IntermediateValueDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomStringType)),
+                                                "strings",
+                                                ArrayLiteral(Vector(StringLiteral("a"), StringLiteral("b")))
+            ),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                                "filepath",
+                                                StringLiteral("gs://not/a/real/file.txt")
+            ),
+            IntermediateValueDeclarationElement(
+              ArrayTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType))),
+              "matrix",
+              ArrayLiteral(
+                Vector(
+                  ArrayLiteral(
+                    Vector(PrimitiveLiteralExpressionElement(WomInteger(1)),
+                           PrimitiveLiteralExpressionElement(WomInteger(0))
+                    )
+                  ),
+                  ArrayLiteral(
+                    Vector(PrimitiveLiteralExpressionElement(WomInteger(1)),
+                           PrimitiveLiteralExpressionElement(WomInteger(0))
+                    )
+                  )
+                )
+              )
+            ),
+            IntermediateValueDeclarationElement(
+              ArrayTypeElement(
+                MapTypeElement(PrimitiveTypeElement(WomIntegerType), PrimitiveTypeElement(WomStringType))
+              ),
+              "list_of_maps",
+              ArrayLiteral(
+                Vector(
+                  MapLiteral(
+                    Map(PrimitiveLiteralExpressionElement(WomInteger(1)) -> StringLiteral("one"),
+                        PrimitiveLiteralExpressionElement(WomInteger(2)) -> StringLiteral("two")
+                    )
+                  ),
+                  MapLiteral(
+                    Map(
+                      PrimitiveLiteralExpressionElement(WomInteger(11)) -> StringLiteral("eleven"),
+                      PrimitiveLiteralExpressionElement(WomInteger(22)) -> StringLiteral("twenty-two")
+                    )
+                  )
+                )
+              )
+            ),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomFloatType),
+                                                "f",
+                                                PrimitiveLiteralExpressionElement(WomFloat(1.024))
+            )
           ),
-          IntermediateValueDeclarationElement(ArrayTypeElement(MapTypeElement(PrimitiveTypeElement(WomIntegerType), PrimitiveTypeElement(WomStringType))), "list_of_maps",
-            ArrayLiteral(Vector(
-              MapLiteral(Map(PrimitiveLiteralExpressionElement(WomInteger(1)) -> StringLiteral("one"), PrimitiveLiteralExpressionElement(WomInteger(2)) -> StringLiteral("two"))),
-              MapLiteral(Map(PrimitiveLiteralExpressionElement(WomInteger(11)) -> StringLiteral("eleven"), PrimitiveLiteralExpressionElement(WomInteger(22)) -> StringLiteral("twenty-two")))
-            ))
+          outputsSection = Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(
+                  ArrayTypeElement(
+                    PairTypeElement(PrimitiveTypeElement(WomIntegerType), PrimitiveTypeElement(WomStringType))
+                  ),
+                  "int_cross_string",
+                  Cross(IdentifierLookup("ints"), IdentifierLookup("strings"))
+                ),
+                OutputDeclarationElement(ArrayTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType))),
+                                         "transposed_matrix",
+                                         Transpose(IdentifierLookup("matrix"))
+                ),
+                OutputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+                                         "flattened_matrix",
+                                         Flatten(IdentifierLookup("matrix"))
+                ),
+                OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                         "matrix_length",
+                                         Length(IdentifierLookup("matrix"))
+                ),
+                OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                         "flattened_matrix_length",
+                                         Length(IdentifierLookup("flattened_matrix"))
+                ),
+                OutputDeclarationElement(
+                  ArrayTypeElement(
+                    PairTypeElement(PrimitiveTypeElement(WomIntegerType), PrimitiveTypeElement(WomStringType))
+                  ),
+                  "flattened_map",
+                  Flatten(IdentifierLookup("list_of_maps"))
+                ),
+                OutputDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                         "file_basename",
+                                         Basename(IdentifierLookup("filepath"), None)
+                ),
+                OutputDeclarationElement(PrimitiveTypeElement(WomStringType),
+                                         "file_basename_extensionless",
+                                         Basename(IdentifierLookup("filepath"), Some(StringLiteral(".txt")))
+                ),
+                OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "f_floor", Floor(IdentifierLookup("f"))),
+                OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType),
+                                         "f_ceiling",
+                                         Ceil(IdentifierLookup("f"))
+                ),
+                OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "f_round", Round(IdentifierLookup("f"))),
+                OutputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)),
+                                         "m1",
+                                         IndexAccess(IdentifierLookup("matrix"),
+                                                     PrimitiveLiteralExpressionElement(WomInteger(1))
+                                         )
+                ),
+                OutputDeclarationElement(
+                  PrimitiveTypeElement(WomIntegerType),
+                  "m2",
+                  IndexAccess(IndexAccess(IdentifierLookup("matrix"), PrimitiveLiteralExpressionElement(WomInteger(1))),
+                              PrimitiveLiteralExpressionElement(WomInteger(1))
+                  )
+                )
+              )
+            )
           ),
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomFloatType), "f", PrimitiveLiteralExpressionElement(WomFloat(1.024)))
-        ),
-        outputsSection = Some(
-          OutputsSectionElement(Vector(
-            OutputDeclarationElement(ArrayTypeElement(PairTypeElement(PrimitiveTypeElement(WomIntegerType),PrimitiveTypeElement(WomStringType))), "int_cross_string", Cross(IdentifierLookup("ints"),IdentifierLookup("strings"))),
-            OutputDeclarationElement(ArrayTypeElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType))), "transposed_matrix", Transpose(IdentifierLookup("matrix"))),
-            OutputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "flattened_matrix", Flatten(IdentifierLookup("matrix"))),
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "matrix_length", Length(IdentifierLookup("matrix"))),
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "flattened_matrix_length", Length(IdentifierLookup("flattened_matrix"))),
-            OutputDeclarationElement(ArrayTypeElement(PairTypeElement(PrimitiveTypeElement(WomIntegerType),PrimitiveTypeElement(WomStringType))), "flattened_map", Flatten(IdentifierLookup("list_of_maps"))),
-            OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "file_basename", Basename(IdentifierLookup("filepath"),None)),
-            OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "file_basename_extensionless", Basename(IdentifierLookup("filepath"),Some(StringLiteral(".txt")))),
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "f_floor",Floor(IdentifierLookup("f"))),
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "f_ceiling",Ceil(IdentifierLookup("f"))),
-            OutputDeclarationElement(PrimitiveTypeElement(WomIntegerType), "f_round",Round(IdentifierLookup("f"))),
-            OutputDeclarationElement(
-              ArrayTypeElement(PrimitiveTypeElement(WomIntegerType)), "m1", IndexAccess(IdentifierLookup("matrix"),PrimitiveLiteralExpressionElement(WomInteger(1)))),
-            OutputDeclarationElement(
-              PrimitiveTypeElement(WomIntegerType),"m2", IndexAccess(
-                IndexAccess(IdentifierLookup("matrix"),PrimitiveLiteralExpressionElement(WomInteger(1))),PrimitiveLiteralExpressionElement(WomInteger(1))))
-          ))
-        ),
-        metaSection = None,
-        parameterMetaSection = None,
-        sourceLocation = Some(SourceFileLocation(3))
-      )),
+          metaSection = None,
+          parameterMetaSection = None,
+          sourceLocation = Some(SourceFileLocation(3))
+        )
+      ),
       tasks = Vector.empty
     ),
     "command_syntaxes" -> FileElement(
@@ -824,61 +1361,112 @@ object WdlFileToWdlomSpec {
       tasks = Vector(
         TaskDefinitionElement(
           name = "a",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "world1", Some(StringExpression(Vector(StringLiteral("wo"), StringPlaceholder(IdentifierLookup("rld")))))),
-            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "world2", Some(StringExpression(Vector(StringLiteral("wo"), StringPlaceholder(IdentifierLookup("rld"))))))
-          ))),
+          inputsSection = Some(
+            InputsSectionElement(
+              Vector(
+                InputDeclarationElement(
+                  PrimitiveTypeElement(WomStringType),
+                  "world1",
+                  Some(StringExpression(Vector(StringLiteral("wo"), StringPlaceholder(IdentifierLookup("rld")))))
+                ),
+                InputDeclarationElement(
+                  PrimitiveTypeElement(WomStringType),
+                  "world2",
+                  Some(StringExpression(Vector(StringLiteral("wo"), StringPlaceholder(IdentifierLookup("rld")))))
+                )
+              )
+            )
+          ),
           declarations = Vector(
             IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "rld", StringLiteral("rld"))
           ),
-          outputsSection = Some(OutputsSectionElement(Vector(
-            OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "out", ReadString(StdoutElement))
-          ))),
-          commandSection = CommandSectionElement(Vector(
-            CommandSectionLine(Vector(
-              StringCommandPartElement("echo "),
-              PlaceholderCommandPartElement(StringLiteral("hello"), PlaceholderAttributeSet.empty),
-              StringCommandPartElement(" "),
-              PlaceholderCommandPartElement(IdentifierLookup("world1"), PlaceholderAttributeSet.empty)
-            )),
-            CommandSectionLine(Vector(
-              StringCommandPartElement("echo goodbye "),
-              PlaceholderCommandPartElement(IdentifierLookup("world2"), PlaceholderAttributeSet.empty)
-            )),
-            CommandSectionLine(Vector(
-              StringCommandPartElement("echo "),
-              PlaceholderCommandPartElement(IdentifierLookup("world1"),
-              PlaceholderAttributeSet(Some("foo"), Some("--yes"), Some("--no"), Some(", ")))
-            ))
-          )),
-          runtimeSection = Some(RuntimeAttributesSectionElement(Vector(
-            KvPair("docker", StringLiteral("ubuntu:latest"))
-          ))),
+          outputsSection = Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "out", ReadString(StdoutElement))
+              )
+            )
+          ),
+          commandSection = CommandSectionElement(
+            Vector(
+              CommandSectionLine(
+                Vector(
+                  StringCommandPartElement("echo "),
+                  PlaceholderCommandPartElement(StringLiteral("hello"), PlaceholderAttributeSet.empty),
+                  StringCommandPartElement(" "),
+                  PlaceholderCommandPartElement(IdentifierLookup("world1"), PlaceholderAttributeSet.empty)
+                )
+              ),
+              CommandSectionLine(
+                Vector(
+                  StringCommandPartElement("echo goodbye "),
+                  PlaceholderCommandPartElement(IdentifierLookup("world2"), PlaceholderAttributeSet.empty)
+                )
+              ),
+              CommandSectionLine(
+                Vector(
+                  StringCommandPartElement("echo "),
+                  PlaceholderCommandPartElement(IdentifierLookup("world1"),
+                                                PlaceholderAttributeSet(Some("foo"),
+                                                                        Some("--yes"),
+                                                                        Some("--no"),
+                                                                        Some(", ")
+                                                )
+                  )
+                )
+              )
+            )
+          ),
+          runtimeSection = Some(
+            RuntimeAttributesSectionElement(
+              Vector(
+                KvPair("docker", StringLiteral("ubuntu:latest"))
+              )
+            )
+          ),
           metaSection = None,
           parameterMetaSection = None,
           sourceLocation = Some(SourceFileLocation(3))
         ),
         TaskDefinitionElement(
           name = "b",
-          inputsSection = Some(InputsSectionElement(Vector(
-            InputDeclarationElement(PrimitiveTypeElement(WomStringType), "world", Some(StringLiteral("world")))
-          ))),
+          inputsSection = Some(
+            InputsSectionElement(
+              Vector(
+                InputDeclarationElement(PrimitiveTypeElement(WomStringType), "world", Some(StringLiteral("world")))
+              )
+            )
+          ),
           declarations = Vector.empty,
-          outputsSection = Some(OutputsSectionElement(Vector(
-            OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "out", ReadString(StdoutElement))
-          ))),
-          commandSection = CommandSectionElement(Vector(
-            CommandSectionLine(Vector(
-              StringCommandPartElement("echo hello ${world}")
-            )),
-            CommandSectionLine(Vector(
-              StringCommandPartElement("echo goodbye "),
-              PlaceholderCommandPartElement(IdentifierLookup("world"), PlaceholderAttributeSet.empty)
+          outputsSection = Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "out", ReadString(StdoutElement))
+              )
+            )
+          ),
+          commandSection = CommandSectionElement(
+            Vector(
+              CommandSectionLine(
+                Vector(
+                  StringCommandPartElement("echo hello ${world}")
+                )
+              ),
+              CommandSectionLine(
+                Vector(
+                  StringCommandPartElement("echo goodbye "),
+                  PlaceholderCommandPartElement(IdentifierLookup("world"), PlaceholderAttributeSet.empty)
+                )
+              )
+            )
+          ),
+          runtimeSection = Some(
+            RuntimeAttributesSectionElement(
+              Vector(
+                KvPair("docker", StringLiteral("ubuntu:latest"))
+              )
             )
-            ))),
-          runtimeSection = Some(RuntimeAttributesSectionElement(Vector(
-            KvPair("docker", StringLiteral("ubuntu:latest"))
-          ))),
+          ),
           metaSection = None,
           parameterMetaSection = None,
           sourceLocation = Some(SourceFileLocation(22))
@@ -888,177 +1476,272 @@ object WdlFileToWdlomSpec {
     "gap_in_command" -> FileElement(
       imports = Vector.empty,
       structs = Vector.empty,
-      workflows = Vector(WorkflowDefinitionElement(
-        "my_workflow",
-        None,
-        Set(CallElement("my_task", None, Vector.empty, None, Some(SourceFileLocation(4)))),
-        None,
-        None,
-        None,
-        Some(SourceFileLocation(3))
-      )),
-      tasks = Vector(TaskDefinitionElement(
-        "my_task",
-        None,
-        Vector(),
-        Some(OutputsSectionElement(
-          Vector(OutputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomStringType)),"lines",ReadLines(StdoutElement)))
-        )),
-        CommandSectionElement(Vector(CommandSectionLine(Vector(StringCommandPartElement("""    echo "hi""""))), CommandSectionLine(Vector()), CommandSectionLine(Vector(StringCommandPartElement("""    echo "bye""""))))),
-        None,
-        None,
-        None,
-        Some(SourceFileLocation(7))))
+      workflows = Vector(
+        WorkflowDefinitionElement(
+          "my_workflow",
+          None,
+          Set(CallElement("my_task", None, Vector.empty, None, Some(SourceFileLocation(4)))),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(3))
+        )
+      ),
+      tasks = Vector(
+        TaskDefinitionElement(
+          "my_task",
+          None,
+          Vector(),
+          Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(ArrayTypeElement(PrimitiveTypeElement(WomStringType)),
+                                         "lines",
+                                         ReadLines(StdoutElement)
+                )
+              )
+            )
+          ),
+          CommandSectionElement(
+            Vector(
+              CommandSectionLine(Vector(StringCommandPartElement("""    echo "hi""""))),
+              CommandSectionLine(Vector()),
+              CommandSectionLine(Vector(StringCommandPartElement("""    echo "bye"""")))
+            )
+          ),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(7))
+        )
+      )
     ),
     "same_named_inputs_priority" -> FileElement(
       Vector(),
       Vector(),
-      Vector(WorkflowDefinitionElement(
-        "same_named_inputs_priority",
-        None,
-        Set(
-          CallElement("echo", Some("b"), Vector.empty, Some(CallBodyElement(Vector(KvPair("out", Add(IdentifierLookup("out"), StringLiteral("2")))))), Some(SourceFileLocation(10))),
-          CallElement("echo", Some("a"), Vector.empty, Some(CallBodyElement(Vector(KvPair("out", Add(IdentifierLookup("out"), StringLiteral("1")))))), Some(SourceFileLocation(6))),
-          IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "out", StringLiteral("hello")),
-          CallElement("echo", Some("d"), Vector.empty, Some(CallBodyElement(Vector(KvPair("out", Add(IdentifierLookup("out"), StringLiteral("4")))))), Some(SourceFileLocation(18))),
-          CallElement("echo", Some("c"), Vector.empty, Some(CallBodyElement(Vector(KvPair("out", Add(IdentifierLookup("out"), StringLiteral("3")))))), Some(SourceFileLocation(14)))
-        ),
-        None,
-        None,
-        None,
-        Some(SourceFileLocation(4))
-      )
-    ),
-    Vector(TaskDefinitionElement(
-      "echo",
-      Some(InputsSectionElement(
-        Vector(InputDeclarationElement(PrimitiveTypeElement(WomStringType),"out",None)))),
-      Vector(),
-      Some(OutputsSectionElement(Vector(OutputDeclarationElement(PrimitiveTypeElement(WomStringType),"result",IdentifierLookup("out"))))),
-      CommandSectionElement(
-        Vector(CommandSectionLine(
-          Vector(
-            StringCommandPartElement("echo "),
-            PlaceholderCommandPartElement(IdentifierLookup("out"),
-              PlaceholderAttributeSet(None,None,None,None)))))
+      Vector(
+        WorkflowDefinitionElement(
+          "same_named_inputs_priority",
+          None,
+          Set(
+            CallElement(
+              "echo",
+              Some("b"),
+              Vector.empty,
+              Some(CallBodyElement(Vector(KvPair("out", Add(IdentifierLookup("out"), StringLiteral("2")))))),
+              Some(SourceFileLocation(10))
+            ),
+            CallElement(
+              "echo",
+              Some("a"),
+              Vector.empty,
+              Some(CallBodyElement(Vector(KvPair("out", Add(IdentifierLookup("out"), StringLiteral("1")))))),
+              Some(SourceFileLocation(6))
+            ),
+            IntermediateValueDeclarationElement(PrimitiveTypeElement(WomStringType), "out", StringLiteral("hello")),
+            CallElement(
+              "echo",
+              Some("d"),
+              Vector.empty,
+              Some(CallBodyElement(Vector(KvPair("out", Add(IdentifierLookup("out"), StringLiteral("4")))))),
+              Some(SourceFileLocation(18))
+            ),
+            CallElement(
+              "echo",
+              Some("c"),
+              Vector.empty,
+              Some(CallBodyElement(Vector(KvPair("out", Add(IdentifierLookup("out"), StringLiteral("3")))))),
+              Some(SourceFileLocation(14))
+            )
+          ),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(4))
+        )
       ),
-      Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))), None, None, Some(SourceFileLocation(23))))
+      Vector(
+        TaskDefinitionElement(
+          "echo",
+          Some(InputsSectionElement(Vector(InputDeclarationElement(PrimitiveTypeElement(WomStringType), "out", None)))),
+          Vector(),
+          Some(
+            OutputsSectionElement(
+              Vector(OutputDeclarationElement(PrimitiveTypeElement(WomStringType), "result", IdentifierLookup("out")))
+            )
+          ),
+          CommandSectionElement(
+            Vector(
+              CommandSectionLine(
+                Vector(StringCommandPartElement("echo "),
+                       PlaceholderCommandPartElement(IdentifierLookup("out"),
+                                                     PlaceholderAttributeSet(None, None, None, None)
+                       )
+                )
+              )
+            )
+          ),
+          Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))),
+          None,
+          None,
+          Some(SourceFileLocation(23))
+        )
+      )
     ),
     "cmd_whitespace_spaces" -> FileElement(
       Vector.empty,
       Vector.empty,
-      Vector(WorkflowDefinitionElement(
-        "Test",
-        None,
-        Set(CallElement("Echo", Some("echo"), Vector.empty, None, Some(SourceFileLocation(10)))),
-        None,
-        None,
-        None,
-        Some(SourceFileLocation(8)))
+      Vector(
+        WorkflowDefinitionElement(
+          "Test",
+          None,
+          Set(CallElement("Echo", Some("echo"), Vector.empty, None, Some(SourceFileLocation(10)))),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(8))
+        )
       ),
-      Vector(TaskDefinitionElement(
-        "Echo",
-        None,
-        Vector(),
-        None,
-        CommandSectionElement(List(
-          CommandSectionLine(Vector(StringCommandPartElement("echo \"I am prefixed with spaces\""))))),
-        Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))), None, None,
-        Some(SourceFileLocation(14)))
+      Vector(
+        TaskDefinitionElement(
+          "Echo",
+          None,
+          Vector(),
+          None,
+          CommandSectionElement(
+            List(CommandSectionLine(Vector(StringCommandPartElement("echo \"I am prefixed with spaces\""))))
+          ),
+          Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))),
+          None,
+          None,
+          Some(SourceFileLocation(14))
+        )
       )
     ),
     "cmd_whitespace_none" -> FileElement(
       Vector.empty,
       Vector.empty,
-      Vector(WorkflowDefinitionElement(
-        "Test",
-        None,
-        Set(CallElement("Echo", Some("echo"), Vector.empty, None, Some(SourceFileLocation(5)))),
-        None,
-        None,
-        None,
-        Some(SourceFileLocation(3)))
+      Vector(
+        WorkflowDefinitionElement(
+          "Test",
+          None,
+          Set(CallElement("Echo", Some("echo"), Vector.empty, None, Some(SourceFileLocation(5)))),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(3))
+        )
       ),
-      Vector(TaskDefinitionElement(
-        "Echo",
-        None,
-        Vector(),
-        None,
-        CommandSectionElement(List(
-          CommandSectionLine(Vector(StringCommandPartElement("echo \"I am prefixed with nothing\""))))),
-        Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))), None, None,
-        Some(SourceFileLocation(9)))
+      Vector(
+        TaskDefinitionElement(
+          "Echo",
+          None,
+          Vector(),
+          None,
+          CommandSectionElement(
+            List(CommandSectionLine(Vector(StringCommandPartElement("echo \"I am prefixed with nothing\""))))
+          ),
+          Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))),
+          None,
+          None,
+          Some(SourceFileLocation(9))
+        )
       )
     ),
     "cmd_whitespace_tabs" -> FileElement(
       Vector.empty,
       Vector.empty,
-      Vector(WorkflowDefinitionElement(
-        "Test",
-        None,
-        Set(CallElement("Echo", Some("echo"), Vector.empty, None, Some(SourceFileLocation(5)))),
-        None,
-        None,
-        None,
-        Some(SourceFileLocation(3)))
+      Vector(
+        WorkflowDefinitionElement(
+          "Test",
+          None,
+          Set(CallElement("Echo", Some("echo"), Vector.empty, None, Some(SourceFileLocation(5)))),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(3))
+        )
       ),
-      Vector(TaskDefinitionElement(
-        "Echo",
-        None,
-        Vector(),
-        None,
-        CommandSectionElement(List(
-          CommandSectionLine(Vector(StringCommandPartElement("echo \"I am prefixed with tabs\""))))),
-        Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))), None, None,
-        Some(SourceFileLocation(9)))
+      Vector(
+        TaskDefinitionElement(
+          "Echo",
+          None,
+          Vector(),
+          None,
+          CommandSectionElement(
+            List(CommandSectionLine(Vector(StringCommandPartElement("echo \"I am prefixed with tabs\""))))
+          ),
+          Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))),
+          None,
+          None,
+          Some(SourceFileLocation(9))
+        )
       )
     ),
     "cmd_strip_common_tabs" -> FileElement(
       Vector.empty,
       Vector.empty,
-      Vector(WorkflowDefinitionElement(
-        "Test",
-        None,
-        Set(CallElement("Echo", Some("echo"), Vector.empty, None, Some(SourceFileLocation(5)))),
-        None,
-        None,
-        None,
-        Some(SourceFileLocation(3)))
+      Vector(
+        WorkflowDefinitionElement(
+          "Test",
+          None,
+          Set(CallElement("Echo", Some("echo"), Vector.empty, None, Some(SourceFileLocation(5)))),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(3))
+        )
       ),
-      Vector(TaskDefinitionElement(
-        "Echo",
-        None,
-        Vector(),
-        None,
-        CommandSectionElement(List(
-          CommandSectionLine(Vector(StringCommandPartElement("echo \"I am prefixed with tabs\""))),
-          CommandSectionLine(Vector(StringCommandPartElement("\t\techo \"I am prefixed with even more tabs\""))))),
-        Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))), None, None,
-        Some(SourceFileLocation(9)))
+      Vector(
+        TaskDefinitionElement(
+          "Echo",
+          None,
+          Vector(),
+          None,
+          CommandSectionElement(
+            List(
+              CommandSectionLine(Vector(StringCommandPartElement("echo \"I am prefixed with tabs\""))),
+              CommandSectionLine(Vector(StringCommandPartElement("\t\techo \"I am prefixed with even more tabs\"")))
+            )
+          ),
+          Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))),
+          None,
+          None,
+          Some(SourceFileLocation(9))
+        )
       )
     ),
     "cmd_strip_common_spaces" -> FileElement(
       Vector.empty,
       Vector.empty,
-      Vector(WorkflowDefinitionElement(
-        "Test",
-        None,
-        Set(CallElement("Echo", Some("echo"), Vector.empty, None, Some(SourceFileLocation(5)))),
-        None,
-        None,
-        None,
-        Some(SourceFileLocation(3)))
+      Vector(
+        WorkflowDefinitionElement(
+          "Test",
+          None,
+          Set(CallElement("Echo", Some("echo"), Vector.empty, None, Some(SourceFileLocation(5)))),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(3))
+        )
       ),
-      Vector(TaskDefinitionElement(
-        "Echo",
-        None,
-        Vector(),
-        None,
-        CommandSectionElement(List(
-          CommandSectionLine(Vector(StringCommandPartElement("echo \"I am prefixed with spaces\""))),
-          CommandSectionLine(Vector(StringCommandPartElement("    echo \"I am prefixed with even more spaces\""))))),
-        Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))), None, None,
-        Some(SourceFileLocation(9)))
+      Vector(
+        TaskDefinitionElement(
+          "Echo",
+          None,
+          Vector(),
+          None,
+          CommandSectionElement(
+            List(
+              CommandSectionLine(Vector(StringCommandPartElement("echo \"I am prefixed with spaces\""))),
+              CommandSectionLine(Vector(StringCommandPartElement("    echo \"I am prefixed with even more spaces\"")))
+            )
+          ),
+          Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))),
+          None,
+          None,
+          Some(SourceFileLocation(9))
+        )
       )
     ),
     "string_escaping" -> FileElement(
@@ -1066,7 +1749,9 @@ object WdlFileToWdlomSpec {
       Vector(),
       Vector(
         WorkflowDefinitionElement(
-          "escapes", None, Set(
+          "escapes",
+          None,
+          Set(
             IntermediateValueDeclarationElement(
               PrimitiveTypeElement(WomStringType),
               "backslash",
@@ -1168,9 +1853,12 @@ object WdlFileToWdlomSpec {
               StringLiteral("  \'  ")
             )
           ),
-          None, None, None,
+          None,
+          None,
+          None,
           Some(SourceFileLocation(3))
-        )),
+        )
+      ),
       Vector.empty
     )
   )
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessTypeEvaluatorSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessTypeEvaluatorSpec.scala
index 82826e39139..06bbbc57725 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessTypeEvaluatorSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessTypeEvaluatorSpec.scala
@@ -13,7 +13,6 @@ import wdl.model.draft3.graph.expression.TypeEvaluator.ops._
 import wom.types._
 import wom.values.WomInteger
 
-
 class MemberAccessTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "member access type evaluator"
@@ -47,13 +46,17 @@ class MemberAccessTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec
       ),
       memberAccessTail = NonEmptyList("left", List("right", "right", "left"))
     )
-     nestedPairLookup.evaluateType(Map.empty) shouldBeValid WomPairType(WomIntegerType, WomIntegerType)
+    nestedPairLookup.evaluateType(Map.empty) shouldBeValid WomPairType(WomIntegerType, WomIntegerType)
   }
 
   it should "evaluate a nested member access on a call output" in {
     val callOutputLookup: ExpressionElement = IdentifierMemberAccess("t", "out", List("left", "right"))
     val linkedValues = Map[UnlinkedConsumedValueHook, GeneratedValueHandle](
-      UnlinkedCallOutputOrIdentifierAndMemberAccessHook("t", "out") -> GeneratedCallOutputValueHandle("t", "out", WomPairType(WomPairType(WomIntegerType, WomPairType(WomIntegerType, WomIntegerType)), WomStringType))
+      UnlinkedCallOutputOrIdentifierAndMemberAccessHook("t", "out") -> GeneratedCallOutputValueHandle(
+        "t",
+        "out",
+        WomPairType(WomPairType(WomIntegerType, WomPairType(WomIntegerType, WomIntegerType)), WomStringType)
+      )
     )
 
     callOutputLookup.evaluateType(linkedValues) shouldBeValid WomPairType(WomIntegerType, WomIntegerType)
@@ -64,7 +67,13 @@ class MemberAccessTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec
     val linkedValues = Map[UnlinkedConsumedValueHook, GeneratedValueHandle](
       UnlinkedCallOutputOrIdentifierAndMemberAccessHook("t", "out") -> GeneratedIdentifierValueHandle(
         linkableName = "t",
-        womType = WomCompositeType(Map("out" -> WomPairType(WomPairType(WomIntegerType, WomPairType(WomIntegerType, WomIntegerType)), WomIntegerType)))
+        womType = WomCompositeType(
+          Map(
+            "out" -> WomPairType(WomPairType(WomIntegerType, WomPairType(WomIntegerType, WomIntegerType)),
+                                 WomIntegerType
+            )
+          )
+        )
       )
     )
 
@@ -86,7 +95,10 @@ class MemberAccessTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec
   it should "evaluate an identifier lookup" in {
     val identifierLookup: ExpressionElement = IdentifierLookup("foo")
     val linkedValues = Map[UnlinkedConsumedValueHook, GeneratedValueHandle](
-      UnlinkedIdentifierHook("foo") -> GeneratedIdentifierValueHandle(linkableName = "foo", womType = WomPairType(WomStringType, WomStringType))
+      UnlinkedIdentifierHook("foo") -> GeneratedIdentifierValueHandle(linkableName = "foo",
+                                                                      womType =
+                                                                        WomPairType(WomStringType, WomStringType)
+      )
     )
 
     identifierLookup.evaluateType(linkedValues) shouldBeValid WomPairType(WomStringType, WomStringType)
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessValueEvaluatorSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessValueEvaluatorSpec.scala
index 272a85d38c6..3f90af6c35d 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessValueEvaluatorSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessValueEvaluatorSpec.scala
@@ -13,7 +13,6 @@ import wdl.model.draft3.graph.expression.ValueEvaluator.ops._
 import wom.expression.NoIoFunctionSet
 import wom.values.{WomInteger, WomObject, WomPair, WomString}
 
-
 class MemberAccessValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   val fiveLiteral = PrimitiveLiteralExpressionElement(WomInteger(5))
@@ -48,7 +47,10 @@ class MemberAccessValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpe
       ),
       memberAccessTail = NonEmptyList("left", List("right", "right", "left"))
     )
-     nestedPairLookup.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomPair(womFive, womSix), Seq.empty)
+    nestedPairLookup.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(
+      WomPair(womFive, womSix),
+      Seq.empty
+    )
   }
 
   it should "evaluate a nested member access on a call output" in {
@@ -57,7 +59,9 @@ class MemberAccessValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpe
       "t.out" -> WomPair(WomPair(womFive, WomPair(womFive, womSix)), womFive)
     )
 
-    callOutputLookup.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomPair(womFive, womSix), Seq.empty)
+    callOutputLookup.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomPair(womFive, womSix),
+                                                                                               Seq.empty
+    )
   }
 
   it should "evaluate a nested member access on an object" in {
@@ -66,14 +70,18 @@ class MemberAccessValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpe
       "t" -> WomObject(Map("out" -> WomPair(WomPair(womFive, WomPair(womFive, womSix)), womFive)))
     )
 
-    objectLookup.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomPair(womFive, womSix), Seq.empty)
+    objectLookup.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomPair(womFive, womSix),
+                                                                                           Seq.empty
+    )
   }
 
   it should "evaluate an identifier lookup" in {
     val identifierLookup: ExpressionElement = IdentifierLookup("foo")
     val inputs = Map("foo" -> WomString("foo"))
 
-    identifierLookup.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomString("foo"), Seq.empty)
+    identifierLookup.evaluateValue(inputs, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(WomString("foo"),
+                                                                                               Seq.empty
+    )
   }
 
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/TernaryIfEvaluatorSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/TernaryIfEvaluatorSpec.scala
index 98b2f071b0a..0c9a4323dcc 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/TernaryIfEvaluatorSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/TernaryIfEvaluatorSpec.scala
@@ -16,7 +16,6 @@ import wom.expression.NoIoFunctionSet
 import wom.types.{WomFloatType, WomIntegerType, WomType}
 import wom.values.{WomBoolean, WomFloat, WomInteger, WomValue}
 
-
 /**
   * Checks that the draft3 value evaluators for ExpressionElements are wired to forward values through to the appropriate
   * underlying methods on WomValue.
@@ -43,7 +42,10 @@ class TernaryIfEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
   // Test name, input expression, output type.
   val typeTests: List[(String, ExpressionElement, WomType)] = List(
     ("if true then 5 else 6", TernaryIf(trueLiteral, fiveLiteral, sixLiteral), WomIntegerType),
-    ("if false then 5.5 else 6", TernaryIf(falseLiteral, PrimitiveLiteralExpressionElement(WomFloat(5.5)), sixLiteral), WomFloatType)
+    ("if false then 5.5 else 6",
+     TernaryIf(falseLiteral, PrimitiveLiteralExpressionElement(WomFloat(5.5)), sixLiteral),
+     WomFloatType
+    )
   )
 
   valueTests foreach { case (name, expression, expected) =>
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/UnaryAndBinaryOperatorsEvaluatorSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/UnaryAndBinaryOperatorsEvaluatorSpec.scala
index 76c38f021cc..656e6ae21be 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/UnaryAndBinaryOperatorsEvaluatorSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/UnaryAndBinaryOperatorsEvaluatorSpec.scala
@@ -15,7 +15,6 @@ import wom.expression.NoIoFunctionSet
 import wom.types.{WomBooleanType, WomIntegerType, WomType}
 import wom.values.{WomBoolean, WomInteger, WomValue}
 
-
 /**
   * Checks that the draft3 value evaluators for ExpressionElements are wired to forward values through to the appropriate
   * underlying methods on WomValue.
@@ -41,22 +40,18 @@ class UnaryAndBinaryOperatorsEvaluatorSpec extends AnyFlatSpec with CromwellTime
     ("-(+(-5))", UnaryNegation(UnaryPlus(UnaryNegation(fiveLiteral))), WomInteger(-5), WomIntegerType),
     ("!true", LogicalNot(trueLiteral), WomBoolean(false), WomBooleanType),
     ("!(!true)", LogicalNot(LogicalNot(trueLiteral)), WomBoolean(true), WomBooleanType),
-
     ("true || false", LogicalOr(trueLiteral, falseLiteral), WomBoolean(true), WomBooleanType),
     ("true && false", LogicalAnd(trueLiteral, falseLiteral), WomBoolean(false), WomBooleanType),
     ("true == false", Equals(trueLiteral, falseLiteral), WomBoolean(false), WomBooleanType),
     ("true != false", NotEquals(trueLiteral, falseLiteral), WomBoolean(true), WomBooleanType),
-
     ("5 < 6", LessThan(fiveLiteral, sixLiteral), WomBoolean(true), WomBooleanType),
     ("5 < 5", LessThan(fiveLiteral, fiveLiteral), WomBoolean(false), WomBooleanType),
     ("5 <= 6", LessThanOrEquals(fiveLiteral, sixLiteral), WomBoolean(true), WomBooleanType),
     ("5 <= 5", LessThanOrEquals(fiveLiteral, fiveLiteral), WomBoolean(true), WomBooleanType),
-
     ("6 > 5", GreaterThan(sixLiteral, fiveLiteral), WomBoolean(true), WomBooleanType),
     ("5 > 5", GreaterThan(fiveLiteral, fiveLiteral), WomBoolean(false), WomBooleanType),
     ("6 >= 6", GreaterThanOrEquals(sixLiteral, fiveLiteral), WomBoolean(true), WomBooleanType),
     ("5 >= 5", GreaterThanOrEquals(fiveLiteral, fiveLiteral), WomBoolean(true), WomBooleanType),
-
     ("5 + 5", Add(fiveLiteral, fiveLiteral), WomInteger(10), WomIntegerType),
     ("5 - 5", Subtract(fiveLiteral, fiveLiteral), WomInteger(0), WomIntegerType),
     ("5 * 5", Multiply(fiveLiteral, fiveLiteral), WomInteger(25), WomIntegerType),
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/consumed/ValueConsumerSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/consumed/ValueConsumerSpec.scala
index f2aac51435e..51a352009e3 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/consumed/ValueConsumerSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/consumed/ValueConsumerSpec.scala
@@ -10,7 +10,6 @@ import wdl.model.draft3.graph.ExpressionValueConsumer.ops._
 import wdl.model.draft3.graph.UnlinkedIdentifierHook
 import wom.values.WomInteger
 
-
 class ValueConsumerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   "the glob value consumer" should "find consumed lookup 'x'" in {
     val expr: ExpressionElement = Glob(IdentifierLookup("x"))
@@ -18,7 +17,8 @@ class ValueConsumerSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
   }
 
   "the read_string value consumer" should "find consumed lookup 'x' in read_string(x[0])" in {
-    val expr: ExpressionElement = ReadString(IndexAccess(IdentifierLookup("x"), PrimitiveLiteralExpressionElement(WomInteger(0))))
+    val expr: ExpressionElement =
+      ReadString(IndexAccess(IdentifierLookup("x"), PrimitiveLiteralExpressionElement(WomInteger(0))))
     expr.expressionConsumedValueHooks shouldBe Set(UnlinkedIdentifierHook("x"))
   }
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/values/Draft3ReadFileLimitsSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/values/Draft3ReadFileLimitsSpec.scala
index 11b842f23ed..b856db1c3d7 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/values/Draft3ReadFileLimitsSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/values/Draft3ReadFileLimitsSpec.scala
@@ -13,15 +13,14 @@ import wom.values.WomSingleFile
 
 import scala.concurrent.Future
 
-
 class Draft3ReadFileLimitsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "ReadLikeFunctions Size Limit Draft 3"
-  
+
   it should "pass correct size limits to the ioFunctions for read_lines" in {
-      ReadLines(PrimitiveLiteralExpressionElement(WomSingleFile("blah")))
-        .evaluateValue(Map.empty, ioFunctionTester(1, ""), None)
-        .valueOr(errors => fail(errors.toList.mkString(", ")))
+    ReadLines(PrimitiveLiteralExpressionElement(WomSingleFile("blah")))
+      .evaluateValue(Map.empty, ioFunctionTester(1, ""), None)
+      .valueOr(errors => fail(errors.toList.mkString(", ")))
   }
 
   it should "pass correct size limits to the ioFunctions for read_bool" in {
@@ -82,9 +81,13 @@ class Draft3ReadFileLimitsSpec extends AnyFlatSpec with CromwellTimeoutSpec with
 
 object Draft3ReadFileLimitsSpec {
   def ioFunctionTester(expectedMaxBytes: Int, result: String) = new EmptyIoFunctionSet {
-    override def readFile(path: String, maxBytes: Option[Int] = None, failOnOverflow: Boolean = false) = {
+    override def readFile(path: String, maxBytes: Option[Int] = None, failOnOverflow: Boolean = false) =
       if (maxBytes.contains(expectedMaxBytes)) Future.successful(result)
-      else Future.failed(new Exception(s"readFile was called with a max bytes value of ${maxBytes.getOrElse("No value")} but was expecting $expectedMaxBytes"))
-    }
+      else
+        Future.failed(
+          new Exception(
+            s"readFile was called with a max bytes value of ${maxBytes.getOrElse("No value")} but was expecting $expectedMaxBytes"
+          )
+        )
   }
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/values/Draft3SizeFunctionSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/values/Draft3SizeFunctionSpec.scala
index 41c767d3a80..8fc05adbe0e 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/values/Draft3SizeFunctionSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/values/Draft3SizeFunctionSpec.scala
@@ -18,32 +18,48 @@ import wom.values._
 import scala.concurrent.Future
 import scala.util.{Failure, Success, Try}
 
-
 class Draft3SizeFunctionSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "ReadLikeFunctions.size"
 
   it should "correctly report a 2048 byte file, in bytes by default" in {
-    validate(Size(PrimitiveLiteralExpressionElement(WomSingleFile("blah")), None).evaluateValue(Map.empty, testFunctions(Success(2048L)), None)) {
-      res => assert(res.value == WomFloat(2048d))
+    validate(
+      Size(PrimitiveLiteralExpressionElement(WomSingleFile("blah")), None).evaluateValue(Map.empty,
+                                                                                         testFunctions(Success(2048L)),
+                                                                                         None
+      )
+    ) { res =>
+      assert(res.value == WomFloat(2048d))
     }
   }
 
   it should "correctly report a 2048 byte file, in bytes" in {
-    validate(Size(PrimitiveLiteralExpressionElement(WomSingleFile("blah")), Some(PrimitiveLiteralExpressionElement(WomString("B")))).evaluateValue(Map.empty, testFunctions(Success(2048L)), None)) {
-      res => assert(res.value == WomFloat(2048d))
+    validate(
+      Size(PrimitiveLiteralExpressionElement(WomSingleFile("blah")),
+           Some(PrimitiveLiteralExpressionElement(WomString("B")))
+      ).evaluateValue(Map.empty, testFunctions(Success(2048L)), None)
+    ) { res =>
+      assert(res.value == WomFloat(2048d))
     }
   }
 
   it should "correctly report a 2048 byte file, in KB" in {
-    validate(Size(PrimitiveLiteralExpressionElement(WomSingleFile("blah")), Some(PrimitiveLiteralExpressionElement(WomString("KB")))).evaluateValue(Map.empty, testFunctions(Success(2048L)), None)) {
-      res => assert(res.value == WomFloat(2.0d))
+    validate(
+      Size(PrimitiveLiteralExpressionElement(WomSingleFile("blah")),
+           Some(PrimitiveLiteralExpressionElement(WomString("KB")))
+      ).evaluateValue(Map.empty, testFunctions(Success(2048L)), None)
+    ) { res =>
+      assert(res.value == WomFloat(2.0d))
     }
   }
 
   it should "correctly report a 2048 byte file, in KiB" in {
-    validate(Size(PrimitiveLiteralExpressionElement(WomSingleFile("blah")), Some(PrimitiveLiteralExpressionElement(WomString("KiB")))).evaluateValue(Map.empty, testFunctions(Success(2048L)), None)) {
-      res => assert(res.value == WomFloat(2d))
+    validate(
+      Size(PrimitiveLiteralExpressionElement(WomSingleFile("blah")),
+           Some(PrimitiveLiteralExpressionElement(WomString("KiB")))
+      ).evaluateValue(Map.empty, testFunctions(Success(2048L)), None)
+    ) { res =>
+      assert(res.value == WomFloat(2d))
     }
   }
 
@@ -56,7 +72,9 @@ class Draft3SizeFunctionSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
   }
 
   it should "correctly report the size of a supplied, optional optional, 2048 byte file" in {
-    val value = WomOptionalValue(WomOptionalType(WomSingleFileType), Option(WomOptionalValue(WomSingleFileType, Option(WomSingleFile("blah")))))
+    val value = WomOptionalValue(WomOptionalType(WomSingleFileType),
+                                 Option(WomOptionalValue(WomSingleFileType, Option(WomSingleFile("blah"))))
+    )
 
     validate(Size(IdentifierLookup("x"), None).evaluateValue(Map("x" -> value), testFunctions(Success(2048L)), None)) {
       res => assert(res.value == WomFloat(2048d))
@@ -66,53 +84,90 @@ class Draft3SizeFunctionSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
   it should "correctly report the size of a supplied, optional, 2048 byte file, in MB" in {
     val value = WomOptionalValue(WomSingleFileType, Option(WomSingleFile("blah")))
 
-    validate(Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB")))).evaluateValue(Map("x" -> value), testFunctions(Success(2048L)), None)) {
-      res => assert(res.value == WomFloat(0.001953125d))
+    validate(
+      Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB"))))
+        .evaluateValue(Map("x" -> value), testFunctions(Success(2048L)), None)
+    ) { res =>
+      assert(res.value == WomFloat(0.001953125d))
     }
   }
 
   it should "correctly report that an unsupplied optional file is empty" in {
     val value = WomOptionalValue(WomSingleFileType, None)
 
-    validate(Size(IdentifierLookup("x"), None).evaluateValue(Map("x" -> value), testFunctions(Failure(new Exception("Bad call to size on an empty optional"))), None)) {
-      res => assert(res.value == WomFloat(0d))
+    validate(
+      Size(IdentifierLookup("x"), None).evaluateValue(
+        Map("x" -> value),
+        testFunctions(Failure(new Exception("Bad call to size on an empty optional"))),
+        None
+      )
+    ) { res =>
+      assert(res.value == WomFloat(0d))
     }
   }
 
   it should "correctly report that an unsupplied File?? is empty" in {
-      val value = WomOptionalValue(WomOptionalType(WomSingleFileType), Option(WomOptionalValue(WomSingleFileType, None)))
-
-      validate(Size(IdentifierLookup("x"), None).evaluateValue(Map("x" -> value), testFunctions(Failure(new Exception("Bad call to size on an empty optional"))), None)) {
-        res => assert(res.value == WomFloat(0d))
-      }
+    val value = WomOptionalValue(WomOptionalType(WomSingleFileType), Option(WomOptionalValue(WomSingleFileType, None)))
+
+    validate(
+      Size(IdentifierLookup("x"), None).evaluateValue(
+        Map("x" -> value),
+        testFunctions(Failure(new Exception("Bad call to size on an empty optional"))),
+        None
+      )
+    ) { res =>
+      assert(res.value == WomFloat(0d))
+    }
   }
 
   it should "correctly report that an unsupplied optional file is empty, even in MB" in {
     val value = WomOptionalValue(WomSingleFileType, None)
 
-    validate(Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB")))).evaluateValue(Map("x" -> value), testFunctions(Failure(new Exception("Bad call to size on an empty optional"))), None)) {
-      res => assert(res.value == WomFloat(0d))
+    validate(
+      Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB")))).evaluateValue(
+        Map("x" -> value),
+        testFunctions(Failure(new Exception("Bad call to size on an empty optional"))),
+        None
+      )
+    ) { res =>
+      assert(res.value == WomFloat(0d))
     }
   }
 
   it should "correctly report the size of an array of files, in GiB" in {
     val value = WomArray(Seq(WomSingleFile("blah"), WomSingleFile("blah")))
 
-    validate(Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("GiB")))).evaluateValue(Map("x" -> value), testFunctions(Success(2048L)), None)) {
-      res => assert(res.value == WomFloat(2048d * 2 / 1024 / 1024 / 1024))
+    validate(
+      Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("GiB"))))
+        .evaluateValue(Map("x" -> value), testFunctions(Success(2048L)), None)
+    ) { res =>
+      assert(res.value == WomFloat(2048d * 2 / 1024 / 1024 / 1024))
     }
   }
 
   it should "correctly report that the size of an array of unsupplied optional files is empty, in MB" in {
     val value = WomArray(Seq(WomOptionalValue(WomSingleFileType, None), WomOptionalValue(WomSingleFileType, None)))
 
-    validate(Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB")))).evaluateValue(Map("x" -> value), testFunctions(Failure(new Exception("Bad call to size on an empty optional"))), None)) {
-      res => assert(res.value == WomFloat(0d))
+    validate(
+      Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB")))).evaluateValue(
+        Map("x" -> value),
+        testFunctions(Failure(new Exception("Bad call to size on an empty optional"))),
+        None
+      )
+    ) { res =>
+      assert(res.value == WomFloat(0d))
     }
   }
 
   it should "correctly report the size of a mixed Array[File?] - some supplied and some not" in {
-    val value = WomArray(Seq(WomOptionalValue(WomSingleFileType, Some(WomSingleFile("blah"))), WomOptionalValue(WomSingleFileType, None), WomOptionalValue(WomSingleFileType, Some(WomSingleFile("blah"))), WomOptionalValue(WomSingleFileType, None)))
+    val value = WomArray(
+      Seq(
+        WomOptionalValue(WomSingleFileType, Some(WomSingleFile("blah"))),
+        WomOptionalValue(WomSingleFileType, None),
+        WomOptionalValue(WomSingleFileType, Some(WomSingleFile("blah"))),
+        WomOptionalValue(WomSingleFileType, None)
+      )
+    )
 
     validate(Size(IdentifierLookup("x"), None).evaluateValue(Map("x" -> value), testFunctions(Success(2048L)), None)) {
       res => assert(res.value == WomFloat(2048d * 2))
@@ -121,25 +176,37 @@ class Draft3SizeFunctionSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
   it should "refuse to report file sizes for Ints" in {
     val value = WomInteger(55)
-    val oops = Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB")))).evaluateValue(Map("x" -> value), testFunctions(Failure(new Exception("Bad call to size on an Int"))), None)
+    val oops = Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB"))))
+      .evaluateValue(Map("x" -> value), testFunctions(Failure(new Exception("Bad call to size on an Int"))), None)
     oops match {
       case Valid(x) => fail(s"Expected an Integer to not have a file length but instead got ${x.value.toWomString}")
-      case Invalid(e) => e.head should be("The 'size' method expects a 'File', 'File?', 'Array[File]' or Array[File?] argument but instead got Int.")
+      case Invalid(e) =>
+        e.head should be(
+          "The 'size' method expects a 'File', 'File?', 'Array[File]' or Array[File?] argument but instead got Int."
+        )
     }
   }
 
   it should "refuse to report file sizes for Int?s" in {
     val value = WomOptionalValue(WomIntegerType, Some(WomInteger(55)))
-    val oops = Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB")))).evaluateValue(Map("x" -> value), testFunctions(Failure(new Exception("Bad call to size on an Int?"))), None)
+    val oops = Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB"))))
+      .evaluateValue(Map("x" -> value), testFunctions(Failure(new Exception("Bad call to size on an Int?"))), None)
     oops match {
       case Valid(x) => fail(s"Expected an Int? to not have a file length but instead got ${x.value.toWomString}")
-      case Invalid(e) => e.head should be("The 'size' method expects a 'File', 'File?', 'Array[File]' or Array[File?] argument but instead got Int?.")
+      case Invalid(e) =>
+        e.head should be(
+          "The 'size' method expects a 'File', 'File?', 'Array[File]' or Array[File?] argument but instead got Int?."
+        )
     }
   }
 
   it should "pass on underlying size reading errors" in {
     val value = WomOptionalValue(WomSingleFileType, Some(WomSingleFile("blah")))
-    val oops = Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB")))).evaluateValue(Map("x" -> value), testFunctions(Failure(new Exception("'size' inner exception, expect me to be passed on"))), None)
+    val oops = Size(IdentifierLookup("x"), Some(PrimitiveLiteralExpressionElement(WomString("MB")))).evaluateValue(
+      Map("x" -> value),
+      testFunctions(Failure(new Exception("'size' inner exception, expect me to be passed on"))),
+      None
+    )
     oops match {
       case Valid(x) => fail(s"Expected an Int? to not have a file length but instead got ${x.value.toWomString}")
       case Invalid(e) => e.head should be("'size' inner exception, expect me to be passed on")
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/linking/expression/files/FileEvaluatorSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/linking/expression/files/FileEvaluatorSpec.scala
index 63fbd05ba03..0a9dd40d206 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/linking/expression/files/FileEvaluatorSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/linking/expression/files/FileEvaluatorSpec.scala
@@ -12,7 +12,6 @@ import wom.expression.NoIoFunctionSet
 import wom.types.{WomCompositeType, WomSingleFileType}
 import wom.values.WomSingleFile
 
-
 class FileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "FileEvaluator[ExpressionElement]"
@@ -21,7 +20,10 @@ class FileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     val expressionElement: ExpressionElement = ObjectLiteral(Map("a_file" -> StringLiteral("moo.txt")))
     val structType = WomCompositeType(Map("a_file" -> WomSingleFileType))
 
-    val evaluatedFiles = expressionElement.predictFilesNeededToEvaluate(inputs = Map.empty, ioFunctionSet = NoIoFunctionSet, coerceTo = structType)
+    val evaluatedFiles = expressionElement.predictFilesNeededToEvaluate(inputs = Map.empty,
+                                                                        ioFunctionSet = NoIoFunctionSet,
+                                                                        coerceTo = structType
+    )
     evaluatedFiles shouldBeValid Set(WomSingleFile("moo.txt"))
   }
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wdl/WdlomToWdlFileSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wdl/WdlomToWdlFileSpec.scala
index 2cd9579db0c..88cef1394db 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wdl/WdlomToWdlFileSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wdl/WdlomToWdlFileSpec.scala
@@ -7,7 +7,7 @@ import common.assertion.CromwellTimeoutSpec
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import wdl.draft3.transforms.ast2wdlom._
-import wdl.draft3.transforms.parsing.{FileStringParserInput, fileToAst, stringToAst}
+import wdl.draft3.transforms.parsing.{fileToAst, stringToAst, FileStringParserInput}
 import wdl.model.draft3.elements._
 import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
 import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.fileElementWriter
@@ -20,41 +20,39 @@ class WdlomToWdlFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
 
   assert(testFiles.nonEmpty)
 
-
-  private def stripLocationFromGraphElement(ge : WorkflowGraphElement) : WorkflowGraphElement = {
+  private def stripLocationFromGraphElement(ge: WorkflowGraphElement): WorkflowGraphElement =
     ge match {
       case se: ScatterElement => se.copy(sourceLocation = None)
       case ce: CallElement => ce.copy(sourceLocation = None)
       case _ => ge
     }
-  }
 
-  private def stripLocations(wf: WorkflowDefinitionElement) : WorkflowDefinitionElement = {
+  private def stripLocations(wf: WorkflowDefinitionElement): WorkflowDefinitionElement =
     wf.copy(graphElements = wf.graphElements.map(stripLocationFromGraphElement))
-  }
 
   // Remove the source file information, where it exists.
   //
   // Re-printing does not preserve line numbers at the moment.
-  private def stripSourceLocations(fe : FileElement) : FileElement = {
-    FileElement(fe.imports,
-                fe.structs,
-                fe.workflows.map { case wf =>
-                  val wf2 = stripLocations(wf)
-                  wf2.copy(sourceLocation = None)
-                }.toSeq,
-                fe.tasks.map { case task => task.copy(sourceLocation = None) }.toSeq)
-  }
+  private def stripSourceLocations(fe: FileElement): FileElement =
+    FileElement(
+      fe.imports,
+      fe.structs,
+      fe.workflows.map { case wf =>
+        val wf2 = stripLocations(wf)
+        wf2.copy(sourceLocation = None)
+      }.toSeq,
+      fe.tasks.map { case task => task.copy(sourceLocation = None) }.toSeq
+    )
 
   testFiles.foreach { file =>
-
     it should s"write a file that re-evaluates to the same case classes for ${file.name}" in {
 
       val model: Checked[FileElement] = (fileToAst andThen wrapAst andThen astToFileElement).run(file)
-        model match {
+      model match {
         case Right(wdlModel) =>
-
-          val newModel = (stringToAst andThen wrapAst andThen astToFileElement).run(FileStringParserInput(wdlModel.toWdlV1, file.name))
+          val newModel = (stringToAst andThen wrapAst andThen astToFileElement).run(
+            FileStringParserInput(wdlModel.toWdlV1, file.name)
+          )
 
           // Scala case class deep equality is so nice here
           newModel.map(stripSourceLocations) shouldEqual model.map(stripSourceLocations)
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wom/WdlFileToWomSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wom/WdlFileToWomSpec.scala
index b8a8e2a7a32..d9eb867dd85 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wom/WdlFileToWomSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wom/WdlFileToWomSpec.scala
@@ -33,24 +33,35 @@ class WdlFileToWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
   }
 
   testCases.list.filter(x => x.isRegularFile && x.extension.contains(".wdl")) foreach { testCase =>
-
     val fileName = testCase.name
     val testName = testCase.name.split("\\.").head
 
     val itShouldString = s"create a valid WOM object for $fileName"
-    val testOrIgnore: (=>Any) => Unit = if (testCase.name.endsWith(".ignored.wdl") || testCase.name.endsWith(".nowom.wdl")) {
-      (it should itShouldString).ignore _
-    } else {
-      (it should itShouldString).in _
-    }
+    val testOrIgnore: (=> Any) => Unit =
+      if (testCase.name.endsWith(".ignored.wdl") || testCase.name.endsWith(".nowom.wdl")) {
+        (it should itShouldString).ignore _
+      } else {
+        (it should itShouldString).in _
+      }
 
     testOrIgnore {
-      val converter: CheckedAtoB[File, WomBundle] = fileToAst andThen wrapAst andThen astToFileElement.map(fe => FileElementToWomBundleInputs(fe, "{}", convertNestedScatterToSubworkflow = true, List.empty, List.empty, workflowDefinitionElementToWomWorkflowDefinition, taskDefinitionElementToWomTaskDefinition)) andThen fileElementToWomBundle
+      val converter: CheckedAtoB[File, WomBundle] = fileToAst andThen wrapAst andThen astToFileElement.map(fe =>
+        FileElementToWomBundleInputs(
+          fe,
+          "{}",
+          convertNestedScatterToSubworkflow = true,
+          List.empty,
+          List.empty,
+          workflowDefinitionElementToWomWorkflowDefinition,
+          taskDefinitionElementToWomTaskDefinition
+        )
+      ) andThen fileElementToWomBundle
 
       converter.run(testCase) match {
         case Right(bundle) => validators(testName).apply(bundle)
         case Left(errors) =>
-          val formattedErrors = errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
+          val formattedErrors =
+            errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
           fail(s"Failed to create WOM bundle: $formattedErrors")
       }
     }
@@ -65,7 +76,17 @@ class WdlFileToWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
   // }
   //
   it should "be able to leave nested scatters intact" in {
-    val converter: CheckedAtoB[File, WomBundle] = fileToAst andThen wrapAst andThen astToFileElement.map(fe => FileElementToWomBundleInputs(fe, "{}", convertNestedScatterToSubworkflow = false, List.empty, List.empty, workflowDefinitionElementToWomWorkflowDefinition, taskDefinitionElementToWomTaskDefinition)) andThen fileElementToWomBundle
+    val converter: CheckedAtoB[File, WomBundle] = fileToAst andThen wrapAst andThen astToFileElement.map(fe =>
+      FileElementToWomBundleInputs(
+        fe,
+        "{}",
+        convertNestedScatterToSubworkflow = false,
+        List.empty,
+        List.empty,
+        workflowDefinitionElementToWomWorkflowDefinition,
+        taskDefinitionElementToWomTaskDefinition
+      )
+    ) andThen fileElementToWomBundle
 
     val twoLevelScatterFile = File("wdl/transforms/draft3/src/test/cases/two_level_scatter.wdl")
 
@@ -75,27 +96,37 @@ class WdlFileToWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
         val graph = wf.innerGraph
 
         // get the top scatter node
-        graph.scatters.size shouldBe(1)
-        val topScatter : ScatterNode = graph.scatters.toVector.head
+        graph.scatters.size shouldBe 1
+        val topScatter: ScatterNode = graph.scatters.toVector.head
         val wfCalls = graph.allNodes.filterByType[WorkflowCallNode]
 
         // don't generate any sub-workflows
-        wfCalls.size shouldBe(0)
+        wfCalls.size shouldBe 0
 
         // there should be one scatter inside the top scatter
         val innerGraph = topScatter.innerGraph
-        innerGraph.scatters.size shouldBe(1)
+        innerGraph.scatters.size shouldBe 1
         Succeeded
 
       case Left(errors) =>
-        val formattedErrors = errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
+        val formattedErrors =
+          errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
         fail(s"Failed to create WOM bundle: $formattedErrors")
     }
   }
 
-
   it should "split a nested scatter into a toplevel scatter, and a bottom sub-workflow" in {
-    val converter: CheckedAtoB[File, WomBundle] = fileToAst andThen wrapAst andThen astToFileElement.map(fe => FileElementToWomBundleInputs(fe, "{}", convertNestedScatterToSubworkflow = true, List.empty, List.empty, workflowDefinitionElementToWomWorkflowDefinition, taskDefinitionElementToWomTaskDefinition)) andThen fileElementToWomBundle
+    val converter: CheckedAtoB[File, WomBundle] = fileToAst andThen wrapAst andThen astToFileElement.map(fe =>
+      FileElementToWomBundleInputs(
+        fe,
+        "{}",
+        convertNestedScatterToSubworkflow = true,
+        List.empty,
+        List.empty,
+        workflowDefinitionElementToWomWorkflowDefinition,
+        taskDefinitionElementToWomTaskDefinition
+      )
+    ) andThen fileElementToWomBundle
 
     val twoLevelScatterFile = File("wdl/transforms/draft3/src/test/cases/two_level_scatter.wdl")
 
@@ -105,19 +136,19 @@ class WdlFileToWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
         val graph = wf.innerGraph
 
         // There should be just one scatter.
-        graph.scatters.size shouldBe(1)
+        graph.scatters.size shouldBe 1
         val wfCalls = graph.allNodes.filterByType[WorkflowCallNode]
 
         // There should be a call to a generated sub-workflow in the graph
-        wfCalls.size shouldBe(1)
+        wfCalls.size shouldBe 1
         Succeeded
       case Left(errors) =>
-        val formattedErrors = errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
+        val formattedErrors =
+          errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
         fail(s"Failed to create WOM bundle: $formattedErrors")
     }
   }
 
-
   private val validators: Map[String, WomBundle => Assertion] = Map(
     "declaration_chain" -> anyWomWillDo,
     "empty_workflow" -> anyWomWillDo,
@@ -161,9 +192,11 @@ class WdlFileToWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
   private def anyWomWillDo(b: WomBundle): Assertion = Succeeded
 
   private def validateStructDefinitionWom(b: WomBundle): Assertion = {
-    val wfDef: WorkflowDefinition = (b.allCallables.values.toSet.filterByType[WorkflowDefinition]: Set[WorkflowDefinition]).head
+    val wfDef: WorkflowDefinition =
+      (b.allCallables.values.toSet.filterByType[WorkflowDefinition]: Set[WorkflowDefinition]).head
     b.typeAliases.keySet shouldBe Set("FooStruct")
-    val structOutputType = (wfDef.graph.outputNodes.map(_.womType).filterByType[WomCompositeType]: Set[WomCompositeType]).head
+    val structOutputType =
+      (wfDef.graph.outputNodes.map(_.womType).filterByType[WomCompositeType]: Set[WomCompositeType]).head
 
     structOutputType.typeMap shouldBe Map(
       "simple" -> WomIntegerType,
@@ -172,27 +205,44 @@ class WdlFileToWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
   }
 
   private def validateTaskDefinitionWom(b: WomBundle): Assertion = {
-    val taskDef: CallableTaskDefinition = (b.allCallables.values.toSet.filterByType[CallableTaskDefinition]: Set[CallableTaskDefinition]).head
+    val taskDef: CallableTaskDefinition =
+      (b.allCallables.values.toSet.filterByType[CallableTaskDefinition]: Set[CallableTaskDefinition]).head
     taskDef.name shouldBe "simple"
-    taskDef.commandTemplate(Map.empty) shouldBe List(WdlomWomStringCommandPart(StringCommandPartElement("echo Hello World ")))
+    taskDef.commandTemplate(Map.empty) shouldBe List(
+      WdlomWomStringCommandPart(StringCommandPartElement("echo Hello World "))
+    )
   }
 
   private def validateCommandSyntaxes(b: WomBundle): Assertion = {
     b.allCallables.size should be(2)
-    b.allCallables.get("a")match {
+    b.allCallables.get("a") match {
       case Some(taskA) =>
-        taskA.inputs.filter(_.isInstanceOf[FixedInputDefinitionWithDefault]).map(_.name).toSet should be(Set("rld", "__world1", "__world2"))
-        taskA.inputs.filter(_.isInstanceOf[OptionalInputDefinition]).map(_.name).toSet should be(Set("world1", "world2"))
+        taskA.inputs.filter(_.isInstanceOf[FixedInputDefinitionWithDefault]).map(_.name).toSet should be(
+          Set("rld", "__world1", "__world2")
+        )
+        taskA.inputs.filter(_.isInstanceOf[OptionalInputDefinition]).map(_.name).toSet should be(
+          Set("world1", "world2")
+        )
         taskA.inputs.map(_.name).toSet should be(Set("rld", "__world1", "__world2", "world1", "world2"))
         taskA.outputs.map(_.name).toSet should be(Set("out"))
-        taskA.asInstanceOf[CallableTaskDefinition].runtimeAttributes.attributes("docker").asInstanceOf[WdlomWomExpression].expressionElement should be(StringLiteral("ubuntu:latest"))
+        taskA
+          .asInstanceOf[CallableTaskDefinition]
+          .runtimeAttributes
+          .attributes("docker")
+          .asInstanceOf[WdlomWomExpression]
+          .expressionElement should be(StringLiteral("ubuntu:latest"))
       case None => fail("Expected a task called 'a'")
     }
     b.allCallables.get("b") match {
       case Some(taskB) =>
         taskB.inputs.map(_.name) should be(Seq("world"))
         taskB.outputs.map(_.name) should be(Seq("out"))
-        taskB.asInstanceOf[CallableTaskDefinition].runtimeAttributes.attributes("docker").asInstanceOf[WdlomWomExpression].expressionElement should be(StringLiteral("ubuntu:latest"))
+        taskB
+          .asInstanceOf[CallableTaskDefinition]
+          .runtimeAttributes
+          .attributes("docker")
+          .asInstanceOf[WdlomWomExpression]
+          .expressionElement should be(StringLiteral("ubuntu:latest"))
       case None => fail("Expected a task called 'b'")
     }
   }
@@ -203,11 +253,17 @@ class WdlFileToWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
       case None => fail("No callable found 'nio_file'")
       case Some(nioFileTask) =>
         // Plain old input:
-        nioFileTask.inputs.find(_.name == "f").get.parameterMeta should be(Some(MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true)))))
+        nioFileTask.inputs.find(_.name == "f").get.parameterMeta should be(
+          Some(MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true))))
+        )
         // Input based on upstream:
-        nioFileTask.inputs.find(_.name == "g").get.parameterMeta should be(Some(MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true)))))
+        nioFileTask.inputs.find(_.name == "g").get.parameterMeta should be(
+          Some(MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true))))
+        )
         // Optional input:
-        nioFileTask.inputs.find(_.name == "h").get.parameterMeta should be(Some(MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true)))))
+        nioFileTask.inputs.find(_.name == "h").get.parameterMeta should be(
+          Some(MetaValueElementObject(Map("localization_optional" -> MetaValueElementBoolean(true))))
+        )
     }
   }
 
@@ -231,16 +287,20 @@ class WdlFileToWomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
   private def validateMetaSection(b: WomBundle): Assertion = {
     val task = b.primaryCallable.get.asInstanceOf[CallableTaskDefinition]
 
-    task.meta should be (Map("author" -> MetaValueElementString("John Doe"),
-                             "email" -> MetaValueElementString("john.doe@yahoo.com"),
-                             "b" -> MetaValueElementBoolean(true),
-                             "zipcode" -> MetaValueElementInteger(94043),
-                             "f" -> MetaValueElementFloat(1.3),
-                             "numbers" -> MetaValueElementArray(Vector(MetaValueElementInteger(1),
-                                                                       MetaValueElementInteger(2),
-                                                                       MetaValueElementInteger(3))),
-                             "extras" -> MetaValueElementObject(Map("house" -> MetaValueElementString("With porch"),
-                                                                    "cat" -> MetaValueElementString("Lucy")))
-                         ))
+    task.meta should be(
+      Map(
+        "author" -> MetaValueElementString("John Doe"),
+        "email" -> MetaValueElementString("john.doe@yahoo.com"),
+        "b" -> MetaValueElementBoolean(true),
+        "zipcode" -> MetaValueElementInteger(94043),
+        "f" -> MetaValueElementFloat(1.3),
+        "numbers" -> MetaValueElementArray(
+          Vector(MetaValueElementInteger(1), MetaValueElementInteger(2), MetaValueElementInteger(3))
+        ),
+        "extras" -> MetaValueElementObject(
+          Map("house" -> MetaValueElementString("With porch"), "cat" -> MetaValueElementString("Lucy"))
+        )
+      )
+    )
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToCommandPartElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToCommandPartElement.scala
index 20dc56cd2bc..ef98ac49d8f 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToCommandPartElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToCommandPartElement.scala
@@ -9,15 +9,21 @@ import wdl.model.draft3.elements.{CommandPartElement, ExpressionElement, Placeho
 import wdl.model.draft3.elements.CommandPartElement.{PlaceholderCommandPartElement, StringCommandPartElement}
 
 object AstNodeToCommandPartElement {
-  def astNodeToCommandPartElement(implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement],
-                                  astNodeToPlaceholderAttributeSet: CheckedAtoB[GenericAstNode, PlaceholderAttributeSet]
-                                 ): CheckedAtoB[GenericAstNode, CommandPartElement] = CheckedAtoB.fromErrorOr { a: GenericAstNode => a match {
-    case t: GenericTerminal => astNodeToString(t).toValidated map StringCommandPartElement
-    case a: GenericAst =>
-      val expressionElementV: ErrorOr[ExpressionElement] = a.getAttributeAs[ExpressionElement]("expr").toValidated
-      val attributesV: ErrorOr[PlaceholderAttributeSet] = a.getAttributeAs[PlaceholderAttributeSet]("attributes").toValidated
+  def astNodeToCommandPartElement(implicit
+    astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement],
+    astNodeToPlaceholderAttributeSet: CheckedAtoB[GenericAstNode, PlaceholderAttributeSet]
+  ): CheckedAtoB[GenericAstNode, CommandPartElement] = CheckedAtoB.fromErrorOr { a: GenericAstNode =>
+    a match {
+      case t: GenericTerminal => astNodeToString(t).toValidated map StringCommandPartElement
+      case a: GenericAst =>
+        val expressionElementV: ErrorOr[ExpressionElement] = a.getAttributeAs[ExpressionElement]("expr").toValidated
+        val attributesV: ErrorOr[PlaceholderAttributeSet] =
+          a.getAttributeAs[PlaceholderAttributeSet]("attributes").toValidated
 
-      (expressionElementV, attributesV) mapN { (expressionElement, attributes) => PlaceholderCommandPartElement(expressionElement, attributes) }
-    case other => s"Conversion for $other not supported".invalidNel
-  }}
+        (expressionElementV, attributesV) mapN { (expressionElement, attributes) =>
+          PlaceholderCommandPartElement(expressionElement, attributes)
+        }
+      case other => s"Conversion for $other not supported".invalidNel
+    }
+  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
index e7f5a24d2ee..2a773fd4e23 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
@@ -18,32 +18,39 @@ object AstNodeToExpressionElement {
 
   type EngineFunctionMaker = Vector[ExpressionElement] => ErrorOr[ExpressionElement]
 
-  def astNodeToExpressionElement(customEngineFunctionMakers: Map[String, EngineFunctionMaker]): CheckedAtoB[GenericAstNode, ExpressionElement] = {
+  def astNodeToExpressionElement(
+    customEngineFunctionMakers: Map[String, EngineFunctionMaker]
+  ): CheckedAtoB[GenericAstNode, ExpressionElement] =
     CheckedAtoB.fromErrorOr("parse expression")(convert(customEngineFunctionMakers) _)
-  }
 
-  protected def convert(customEngineFunctionMakers: Map[String, EngineFunctionMaker])(ast: GenericAstNode): ErrorOr[ExpressionElement] = {
+  protected def convert(
+    customEngineFunctionMakers: Map[String, EngineFunctionMaker]
+  )(ast: GenericAstNode): ErrorOr[ExpressionElement] = {
     implicit val recursiveConverter = CheckedAtoB.fromErrorOr(convert(customEngineFunctionMakers) _)
     implicit val recursiveKvConverter = AstNodeToKvPair.astNodeToKvPair
     ast match {
 
-      case t: GenericTerminal if asPrimitive.isDefinedAt((t.getTerminalStr, t.getSourceString)) => asPrimitive((t.getTerminalStr, t.getSourceString)).map(PrimitiveLiteralExpressionElement)
+      case t: GenericTerminal if asPrimitive.isDefinedAt((t.getTerminalStr, t.getSourceString)) =>
+        asPrimitive((t.getTerminalStr, t.getSourceString)).map(PrimitiveLiteralExpressionElement)
       case t: GenericTerminal if t.getTerminalStr == "identifier" => IdentifierLookup(t.getSourceString).validNel
       case t: GenericTerminal if t.getTerminalStr == "none" => NoneLiteralElement.validNel
 
       case a: GenericAst if a.getName == "StringLiteral" => handleStringLiteral(a)
       case a: GenericAst if lhsRhsOperators.contains(a.getName) => useValidatedLhsAndRhs(a, lhsRhsOperators(a.getName))
-      case a: GenericAst if unaryOperators.contains(a.getName) => a.getAttributeAs[ExpressionElement]("expression").map(unaryOperators(a.getName)).toValidated
-      case a: GenericAst if a.getName == "TupleLiteral" => (a.getAttributeAsVector[ExpressionElement]("values") flatMap {
-        case pair if pair.length == 2 => PairLiteral(pair.head, pair(1)).validNelCheck
-        case singleton if singleton.length == 1 => singleton.head.validNelCheck
-        case more => s"No WDL support for ${more.size}-tuples in draft 3".invalidNelCheck
-      }).toValidated
-      case a: GenericAst if a.getName == "ArrayLiteral" => a.getAttributeAsVector[ExpressionElement]("values").toValidated.map(ArrayLiteral)
-      case a: GenericAst if a.getName == "ArrayOrMapLookup" => {
+      case a: GenericAst if unaryOperators.contains(a.getName) =>
+        a.getAttributeAs[ExpressionElement]("expression").map(unaryOperators(a.getName)).toValidated
+      case a: GenericAst if a.getName == "TupleLiteral" =>
+        (a.getAttributeAsVector[ExpressionElement]("values") flatMap {
+          case pair if pair.length == 2 => PairLiteral(pair.head, pair(1)).validNelCheck
+          case singleton if singleton.length == 1 => singleton.head.validNelCheck
+          case more => s"No WDL support for ${more.size}-tuples in draft 3".invalidNelCheck
+        }).toValidated
+      case a: GenericAst if a.getName == "ArrayLiteral" =>
+        a.getAttributeAsVector[ExpressionElement]("values").toValidated.map(ArrayLiteral)
+      case a: GenericAst if a.getName == "ArrayOrMapLookup" =>
         (a.getAttributeAs[ExpressionElement]("lhs").toValidated: ErrorOr[ExpressionElement],
-          a.getAttributeAs[ExpressionElement]("rhs").toValidated: ErrorOr[ExpressionElement]) mapN IndexAccess
-      }
+         a.getAttributeAs[ExpressionElement]("rhs").toValidated: ErrorOr[ExpressionElement]
+        ) mapN IndexAccess
       case a: GenericAst if a.getName == "MemberAccess" => handleMemberAccess(a)
       case a: GenericAst if a.getName == "ObjectLiteral" =>
         (for {
@@ -69,10 +76,13 @@ object AstNodeToExpressionElement {
         val conditionValidation: ErrorOr[ExpressionElement] = a.getAttributeAs[ExpressionElement]("cond").toValidated
         val ifTrueValidation: ErrorOr[ExpressionElement] = a.getAttributeAs[ExpressionElement]("iftrue").toValidated
         val ifFalseValidation: ErrorOr[ExpressionElement] = a.getAttributeAs[ExpressionElement]("iffalse").toValidated
-        (conditionValidation, ifTrueValidation, ifFalseValidation) mapN { (cond, ifTrue, ifFalse) => TernaryIf(cond, ifTrue, ifFalse) }
+        (conditionValidation, ifTrueValidation, ifFalseValidation) mapN { (cond, ifTrue, ifFalse) =>
+          TernaryIf(cond, ifTrue, ifFalse)
+        }
       case a: GenericAst if a.getName == "FunctionCall" =>
         val functionNameValidation: ErrorOr[String] = a.getAttributeAs[String]("name").toValidated
-        val argsValidation: ErrorOr[Vector[ExpressionElement]] = a.getAttributeAsVector[ExpressionElement]("params").toValidated
+        val argsValidation: ErrorOr[Vector[ExpressionElement]] =
+          a.getAttributeAsVector[ExpressionElement]("params").toValidated
 
         val allEngineFunctionMakers = engineFunctionMakers ++ customEngineFunctionMakers
         (functionNameValidation, argsValidation) flatMapN {
@@ -80,9 +90,10 @@ object AstNodeToExpressionElement {
           case (other, _) => s"Unknown engine function: '$other'".invalidNel
         }
 
-
-      case unknownTerminal: GenericTerminal => s"No rule available to create ExpressionElement from terminal: ${unknownTerminal.getTerminalStr} ${unknownTerminal.getSourceString}".invalidNel
-      case unknownAst: GenericAst => s"No rule available to create ExpressionElement from Ast: ${unknownAst.getName}".invalidNel
+      case unknownTerminal: GenericTerminal =>
+        s"No rule available to create ExpressionElement from terminal: ${unknownTerminal.getTerminalStr} ${unknownTerminal.getSourceString}".invalidNel
+      case unknownAst: GenericAst =>
+        s"No rule available to create ExpressionElement from Ast: ${unknownAst.getName}".invalidNel
     }
   }
 
@@ -104,14 +115,19 @@ object AstNodeToExpressionElement {
     "Remainder" -> Remainder.apply
   )
 
-  private def useValidatedLhsAndRhs(a: GenericAst, combiner: BinaryOperatorElementMaker)
-                                   (implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): ErrorOr[ExpressionElement] = {
+  private def useValidatedLhsAndRhs(a: GenericAst, combiner: BinaryOperatorElementMaker)(implicit
+    astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]
+  ): ErrorOr[ExpressionElement] = {
     val lhsValidation: ErrorOr[ExpressionElement] =
-      a.getAttributeAs[ExpressionElement]("lhs").toValidated.contextualizeErrors(s"read left hand side of ${a.getName} expression")
+      a.getAttributeAs[ExpressionElement]("lhs")
+        .toValidated
+        .contextualizeErrors(s"read left hand side of ${a.getName} expression")
     val rhsValidation: ErrorOr[ExpressionElement] =
-      a.getAttributeAs[ExpressionElement]("rhs").toValidated.contextualizeErrors(s"read right-hand side of ${a.getName} expression")
+      a.getAttributeAs[ExpressionElement]("rhs")
+        .toValidated
+        .contextualizeErrors(s"read right-hand side of ${a.getName} expression")
 
-    (lhsValidation, rhsValidation) mapN { combiner }
+    (lhsValidation, rhsValidation) mapN combiner
   }
 
   private type UnaryOperatorElementMaker = ExpressionElement => ExpressionElement
@@ -176,25 +192,28 @@ object AstNodeToExpressionElement {
     "sub" -> validateThreeParamEngineFunction(Sub, "sub")
   )
 
-  private def validateNoParamEngineFunction(element: ExpressionElement, functionName: String)
-                                           (params: Vector[ExpressionElement]): ErrorOr[ExpressionElement] =
+  private def validateNoParamEngineFunction(element: ExpressionElement, functionName: String)(
+    params: Vector[ExpressionElement]
+  ): ErrorOr[ExpressionElement] =
     if (params.isEmpty) {
       element.validNel
     } else {
       s"Function $functionName expects 0 arguments but got ${params.size}".invalidNel
     }
 
-  def validateOneParamEngineFunction(elementMaker: ExpressionElement => ExpressionElement, functionName: String)
-                                            (params: Vector[ExpressionElement]): ErrorOr[ExpressionElement] =
+  def validateOneParamEngineFunction(elementMaker: ExpressionElement => ExpressionElement, functionName: String)(
+    params: Vector[ExpressionElement]
+  ): ErrorOr[ExpressionElement] =
     if (params.size == 1) {
       elementMaker.apply(params.head).validNel
     } else {
       s"Function $functionName expects exactly 1 argument but got ${params.size}".invalidNel
     }
 
-  private def validateOneOrTwoParamEngineFunction(elementMaker: (ExpressionElement, Option[ExpressionElement]) => ExpressionElement,
-                                                  functionName: String)
-                                                 (params: Vector[ExpressionElement]): ErrorOr[ExpressionElement] =
+  private def validateOneOrTwoParamEngineFunction(
+    elementMaker: (ExpressionElement, Option[ExpressionElement]) => ExpressionElement,
+    functionName: String
+  )(params: Vector[ExpressionElement]): ErrorOr[ExpressionElement] =
     if (params.size == 1) {
       elementMaker(params.head, None).validNel
     } else if (params.size == 2) {
@@ -203,30 +222,35 @@ object AstNodeToExpressionElement {
       s"Function $functionName expects 1 or 2 arguments but got ${params.size}".invalidNel
     }
 
-  def validateTwoParamEngineFunction(elementMaker: (ExpressionElement, ExpressionElement) => ExpressionElement, functionName: String)
-                                            (params: Vector[ExpressionElement]): ErrorOr[ExpressionElement] =
+  def validateTwoParamEngineFunction(elementMaker: (ExpressionElement, ExpressionElement) => ExpressionElement,
+                                     functionName: String
+  )(params: Vector[ExpressionElement]): ErrorOr[ExpressionElement] =
     if (params.size == 2) {
       elementMaker.apply(params.head, params(1)).validNel
     } else {
       s"Function $functionName expects exactly 2 arguments but got ${params.size}".invalidNel
     }
 
-  private def validateThreeParamEngineFunction(elementMaker: (ExpressionElement, ExpressionElement, ExpressionElement) => ExpressionElement, functionName: String)
-                                              (params: Vector[ExpressionElement]): ErrorOr[ExpressionElement] =
+  private def validateThreeParamEngineFunction(
+    elementMaker: (ExpressionElement, ExpressionElement, ExpressionElement) => ExpressionElement,
+    functionName: String
+  )(params: Vector[ExpressionElement]): ErrorOr[ExpressionElement] =
     if (params.size == 3) {
       elementMaker.apply(params.head, params(1), params(2)).validNel
     } else {
       s"Function $functionName expects exactly 3 arguments but got ${params.size}".invalidNel
     }
 
-  private def handleMemberAccess(ast: GenericAst)
-                                (implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): ErrorOr[ExpressionElement] = {
+  private def handleMemberAccess(
+    ast: GenericAst
+  )(implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): ErrorOr[ExpressionElement] = {
 
     // Internal simplify method:
     // If the left-hand side is another member access, we can simplify them together.
     // If not, we can build a new member access:
     def simplify(leftExpression: ExpressionElement, suffix: String): ExpressionElement = leftExpression match {
-      case ExpressionMemberAccess(lefterExpression, tail) => ExpressionMemberAccess(lefterExpression, NonEmptyList(tail.head, tail.tail :+ suffix))
+      case ExpressionMemberAccess(lefterExpression, tail) =>
+        ExpressionMemberAccess(lefterExpression, NonEmptyList(tail.head, tail.tail :+ suffix))
       case IdentifierMemberAccess(first, second, tail) => IdentifierMemberAccess(first, second, tail :+ suffix)
       case IdentifierLookup(identifier) => IdentifierMemberAccess(identifier, suffix, Vector.empty)
       case _ => ExpressionMemberAccess(leftExpression, NonEmptyList(suffix, List.empty))
@@ -241,10 +265,12 @@ object AstNodeToExpressionElement {
 
   }
 
-  private def handleStringLiteral(ast: GenericAst)
-                                 (implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): ErrorOr[ExpressionElement] = {
+  private def handleStringLiteral(
+    ast: GenericAst
+  )(implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): ErrorOr[ExpressionElement] = {
 
-    implicit val astNodeToStringPiece: CheckedAtoB[GenericAstNode, StringPiece] = AstNodeToStringPiece.astNodeToStringPiece(Some(astNodeToExpressionElement))
+    implicit val astNodeToStringPiece: CheckedAtoB[GenericAstNode, StringPiece] =
+      AstNodeToStringPiece.astNodeToStringPiece(Some(astNodeToExpressionElement))
     ast.getAttributeAsVector[StringPiece]("pieces").toValidated map { pieces =>
       if (pieces.isEmpty) {
         StringLiteral("")
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToKvPair.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToKvPair.scala
index e26b1194cd3..886fa34735c 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToKvPair.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToKvPair.scala
@@ -9,11 +9,12 @@ import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement.KvPair
 
 object AstNodeToKvPair {
-  def astNodeToKvPair(implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): CheckedAtoB[GenericAstNode, KvPair] = CheckedAtoB.fromErrorOr {
+  def astNodeToKvPair(implicit
+    astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]
+  ): CheckedAtoB[GenericAstNode, KvPair] = CheckedAtoB.fromErrorOr {
     case a: GenericAst if a.getName == "ObjectKV" || a.getName == "MapLiteralKv" || a.getName == "RuntimeAttribute" =>
       val keyValidation: ErrorOr[String] = a.getAttributeAs[String]("key").toValidated
 
-
       val valueValidation: ErrorOr[ExpressionElement] = {
         val validation = a.getAttributeAs[ExpressionElement]("value").toValidated
         val forKeyContext: Option[String] = keyValidation.map(k => s"read value for key '$k'").toOption
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToMetaKvPair.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToMetaKvPair.scala
index c0c3fe90d1f..a306c4ac19d 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToMetaKvPair.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToMetaKvPair.scala
@@ -13,12 +13,14 @@ import wom.callable.{MetaKvPair, MetaValueElement}
 import scala.util.{Failure, Try}
 
 object AstNodeToMetaKvPair {
-  def astNodeToMetaKvPair(implicit astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString]): CheckedAtoB[GenericAstNode, MetaKvPair] = {
+  def astNodeToMetaKvPair(implicit
+    astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString]
+  ): CheckedAtoB[GenericAstNode, MetaKvPair] =
     CheckedAtoB.fromErrorOr("convert AstNode to MetaKvPair")(convertMetaKvPair)
-  }
 
-  private def convertMetaKvPair(astNode: GenericAstNode)
-                               (implicit astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString]): ErrorOr[MetaKvPair] = astNode match {
+  private def convertMetaKvPair(
+    astNode: GenericAstNode
+  )(implicit astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString]): ErrorOr[MetaKvPair] = astNode match {
     case a: GenericAst if a.getName == "MetaKvPair" =>
       val keyValidation: ErrorOr[String] = a.getAttributeAs[String]("key").toValidated
       val valueValidation: ErrorOr[MetaValueElement] = convertMetaValue(a.getAttribute("value"))
@@ -27,8 +29,9 @@ object AstNodeToMetaKvPair {
     case other => s"Expected Ast of type 'MetaKvPair' but got $other".invalidNel
   }
 
-  private def convertMetaValue(astNode: GenericAstNode)
-                              (implicit astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString]): ErrorOr[MetaValueElement] = {
+  private def convertMetaValue(
+    astNode: GenericAstNode
+  )(implicit astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString]): ErrorOr[MetaValueElement] = {
     implicit val recursiveKvPairConversion = CheckedAtoB.fromErrorOr(convertMetaKvPair _)
     astNode match {
       // This is a primitive type, one of {null, boolean, float, int, string}.
@@ -42,10 +45,13 @@ object AstNodeToMetaKvPair {
           case (name, other) => s"No conversion defined for Ast ($name, $other) to MetaValueElement".invalidNel
         }
 
-      case a: GenericAst if a.getName == "StaticString" => astNodeToStaticString(a).toValidated map { staticString => MetaValueElementString.apply(staticString.value) }
+      case a: GenericAst if a.getName == "StaticString" =>
+        astNodeToStaticString(a).toValidated map { staticString => MetaValueElementString.apply(staticString.value) }
 
       case a: GenericAst if a.getName == "MetaArray" =>
-        a.getAttributeAsVectorF[MetaValueElement]("values")(convertMetaValue(_).toEither).toValidated.map(MetaValueElementArray)
+        a.getAttributeAsVectorF[MetaValueElement]("values")(convertMetaValue(_).toEither)
+          .toValidated
+          .map(MetaValueElementArray)
 
       case a: GenericAst if a.getName == "MetaObject" =>
         (for {
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToPlaceholderAttributeSet.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToPlaceholderAttributeSet.scala
index b7e359bb042..26d30b9bef9 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToPlaceholderAttributeSet.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToPlaceholderAttributeSet.scala
@@ -16,7 +16,9 @@ import wdl.model.draft3.elements._
 
 object AstNodeToPlaceholderAttributeSet {
 
-  def attributeKvpConverter(implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): CheckedAtoB[GenericAstList, PlaceholderAttributeSet] = {
+  def attributeKvpConverter(implicit
+    astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]
+  ): CheckedAtoB[GenericAstList, PlaceholderAttributeSet] = {
     val singleElement = astNodeToAst andThen CheckedAtoB.fromErrorOr(convertAttributeKvp _)
 
     def convertAll(as: GenericAstList): ErrorOr[Vector[PlaceholderAttributeElement]] =
@@ -26,40 +28,51 @@ object AstNodeToPlaceholderAttributeSet {
   }
 
   private def validAttributeSet(a: Vector[PlaceholderAttributeElement]): Checked[PlaceholderAttributeSet] = {
-    def foldFunction(acc: (PlaceholderAttributeSet, List[String]), next: PlaceholderAttributeElement): (PlaceholderAttributeSet, List[String]) = {
+    def foldFunction(acc: (PlaceholderAttributeSet, List[String]),
+                     next: PlaceholderAttributeElement
+    ): (PlaceholderAttributeSet, List[String]) =
       (acc, next) match {
-        case ((PlaceholderAttributeSet(None, t, f, s), errors), DefaultAttributeElement(d)) => (PlaceholderAttributeSet(Option(d), t, f, s), errors)
-        case ((pas @ PlaceholderAttributeSet(Some(d1), _, _, _), errors), DefaultAttributeElement(d2)) => (pas, errors :+ s"""Cannot supply 'default="$d2"' because it is already supplied as 'default="$d1"'""")
+        case ((PlaceholderAttributeSet(None, t, f, s), errors), DefaultAttributeElement(d)) =>
+          (PlaceholderAttributeSet(Option(d), t, f, s), errors)
+        case ((pas @ PlaceholderAttributeSet(Some(d1), _, _, _), errors), DefaultAttributeElement(d2)) =>
+          (pas, errors :+ s"""Cannot supply 'default="$d2"' because it is already supplied as 'default="$d1"'""")
 
-        case ((PlaceholderAttributeSet(d, None, f, s), errors), TrueAttributeElement(t)) => (PlaceholderAttributeSet(d, Option(t), f, s), errors)
-        case ((pas @ PlaceholderAttributeSet(_, Some(t1), _, _), errors), TrueAttributeElement(t2)) => (pas, errors :+ s"""Cannot supply 'true="$t2"' because it is already supplied as 'true="$t1"'""")
+        case ((PlaceholderAttributeSet(d, None, f, s), errors), TrueAttributeElement(t)) =>
+          (PlaceholderAttributeSet(d, Option(t), f, s), errors)
+        case ((pas @ PlaceholderAttributeSet(_, Some(t1), _, _), errors), TrueAttributeElement(t2)) =>
+          (pas, errors :+ s"""Cannot supply 'true="$t2"' because it is already supplied as 'true="$t1"'""")
 
-        case ((PlaceholderAttributeSet(d, t, None, s), errors), FalseAttributeElement(f)) => (PlaceholderAttributeSet(d, t, Option(f), s), errors)
-        case ((pas @ PlaceholderAttributeSet(_, _, Some(f1), _), errors), FalseAttributeElement(f2)) => (pas, errors :+ s"""Cannot supply 'false="$f2"' because it is already supplied as 'false="$f1"'""")
+        case ((PlaceholderAttributeSet(d, t, None, s), errors), FalseAttributeElement(f)) =>
+          (PlaceholderAttributeSet(d, t, Option(f), s), errors)
+        case ((pas @ PlaceholderAttributeSet(_, _, Some(f1), _), errors), FalseAttributeElement(f2)) =>
+          (pas, errors :+ s"""Cannot supply 'false="$f2"' because it is already supplied as 'false="$f1"'""")
 
-        case ((PlaceholderAttributeSet(d, t, f, None), errors), SepAttributeElement(s)) => (PlaceholderAttributeSet(d, t, f, Option(s)), errors)
-        case ((pas @ PlaceholderAttributeSet(_, _, _, Some(s1)), errors), SepAttributeElement(s2)) => (pas, errors :+ s"""Cannot supply 'sep="$s2"' because it is already supplied as 'sep="$s1"'""")
+        case ((PlaceholderAttributeSet(d, t, f, None), errors), SepAttributeElement(s)) =>
+          (PlaceholderAttributeSet(d, t, f, Option(s)), errors)
+        case ((pas @ PlaceholderAttributeSet(_, _, _, Some(s1)), errors), SepAttributeElement(s2)) =>
+          (pas, errors :+ s"""Cannot supply 'sep="$s2"' because it is already supplied as 'sep="$s1"'""")
       }
-    }
 
     val folded = a.foldLeft((PlaceholderAttributeSet.empty, List.empty[String]))(foldFunction)
 
     folded match {
       case (_, nel) if nel.nonEmpty => Left(NonEmptyList.fromListUnsafe(nel))
-      case (PlaceholderAttributeSet(_, Some(t), None, _), _) => s"""Cannot specify 'true="$t"' without also having a 'false="..."' attribute""".invalidNelCheck
-      case (PlaceholderAttributeSet(_, None, Some(f), _), _) => s"""Cannot specify 'false="$f"' without also having a 'true="..."' attribute""".invalidNelCheck
+      case (PlaceholderAttributeSet(_, Some(t), None, _), _) =>
+        s"""Cannot specify 'true="$t"' without also having a 'false="..."' attribute""".invalidNelCheck
+      case (PlaceholderAttributeSet(_, None, Some(f), _), _) =>
+        s"""Cannot specify 'false="$f"' without also having a 'true="..."' attribute""".invalidNelCheck
       case (valid, _) => valid.validNelCheck
     }
   }
 
-  private def convertAttributeKvp(a: GenericAst)(implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): ErrorOr[PlaceholderAttributeElement] = {
-    (placeholderAttributeConstructor(a),
-      placeholderAttributeValue(a)) mapN { (constructor, value) =>
+  private def convertAttributeKvp(a: GenericAst)(implicit
+    astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]
+  ): ErrorOr[PlaceholderAttributeElement] =
+    (placeholderAttributeConstructor(a), placeholderAttributeValue(a)) mapN { (constructor, value) =>
       constructor.apply(value)
     }
-  }
 
-  private def placeholderAttributeConstructor(kvpAst: GenericAst): ErrorOr[String => PlaceholderAttributeElement] = {
+  private def placeholderAttributeConstructor(kvpAst: GenericAst): ErrorOr[String => PlaceholderAttributeElement] =
     kvpAst.getAttributeAs[String]("key").toValidated.flatMap {
       case "sep" => (SepAttributeElement.apply _).validNel
       case "default" => (DefaultAttributeElement.apply _).validNel
@@ -67,17 +80,18 @@ object AstNodeToPlaceholderAttributeSet {
       case "false" => (FalseAttributeElement.apply _).validNel
       case other => s"Invalid placeholder attribute: $other".invalidNel
     }
-  }
 
-  private def placeholderAttributeValue(kvpAst: GenericAst)(implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): ErrorOr[String] = {
+  private def placeholderAttributeValue(
+    kvpAst: GenericAst
+  )(implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): ErrorOr[String] =
     kvpAst.getAttributeAs[ExpressionElement]("value").toValidated.flatMap {
       case StringLiteral(literalValue) => literalValue.validNel
-      case StringExpression(pieces) if pieces.length == 1 => pieces.head match {
-        case StringLiteral(literalValue) => literalValue.validNel
-        case other => s"Cannot use $other as a placeholder attribute. Must be a primitive literal".invalidNel
-      }
+      case StringExpression(pieces) if pieces.length == 1 =>
+        pieces.head match {
+          case StringLiteral(literalValue) => literalValue.validNel
+          case other => s"Cannot use $other as a placeholder attribute. Must be a primitive literal".invalidNel
+        }
       case PrimitiveLiteralExpressionElement(primitive) => primitive.valueString.validNel
       case other => s"Cannot use $other as a placeholder attribute. Must be a primitive literal".invalidNel
     }
-  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToStaticString.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToStaticString.scala
index fb3a9ba661a..06e8b640a33 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToStaticString.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToStaticString.scala
@@ -7,39 +7,45 @@ import wdl.model.draft3.elements.ExpressionElement.{StringEscapeSequence, String
 import wdl.model.draft3.elements._
 
 object AstNodeToStringPiece {
-  def astNodeToStringPiece(expressionProcessor: Option[CheckedAtoB[GenericAstNode, ExpressionElement]]): CheckedAtoB[GenericAstNode, StringPiece] = CheckedAtoB.fromCheck("read string piece") {
-
-    case simple: GenericTerminal if simple.getTerminalStr == "string" => StringLiteral(simple.getSourceString).validNelCheck
-    case escape: GenericTerminal if escape.getTerminalStr == "escape" => StringEscapeSequence.parseEscapeSequence(escape.getSourceString).toEither
+  def astNodeToStringPiece(
+    expressionProcessor: Option[CheckedAtoB[GenericAstNode, ExpressionElement]]
+  ): CheckedAtoB[GenericAstNode, StringPiece] = CheckedAtoB.fromCheck("read string piece") {
+
+    case simple: GenericTerminal if simple.getTerminalStr == "string" =>
+      StringLiteral(simple.getSourceString).validNelCheck
+    case escape: GenericTerminal if escape.getTerminalStr == "escape" =>
+      StringEscapeSequence.parseEscapeSequence(escape.getSourceString).toEither
     case expr: GenericAst if expr.getName == "ExpressionPlaceholder" =>
       expressionProcessor match {
-        case Some(processor) => expr.getAttributeAs[ExpressionElement]("expr")(processor) map StringPlaceholder: Checked[StringPlaceholder]
+        case Some(processor) =>
+          expr.getAttributeAs[ExpressionElement]("expr")(processor) map StringPlaceholder: Checked[StringPlaceholder]
         case None => "String placeholders are not allowed in static strings".invalidNelCheck
       }
 
-
-    case otherTerminal: GenericTerminal => s"Unexpected parse tree. Expected string piece but found Terminal '${otherTerminal.getTerminalStr}' (${otherTerminal.getSourceString})".invalidNelCheck
-    case otherAst: GenericAst => s"Unexpected parse tree. Expected string piece but found AST ${otherAst.getName}".invalidNelCheck
+    case otherTerminal: GenericTerminal =>
+      s"Unexpected parse tree. Expected string piece but found Terminal '${otherTerminal.getTerminalStr}' (${otherTerminal.getSourceString})".invalidNelCheck
+    case otherAst: GenericAst =>
+      s"Unexpected parse tree. Expected string piece but found AST ${otherAst.getName}".invalidNelCheck
   }
 }
 
 object AstNodeToStaticString {
-  def astNodeToStaticStringElement(): CheckedAtoB[GenericAstNode, StaticString] = CheckedAtoB.fromCheck("convert AstNode to StaticString") {
-    case a: GenericAst if a.getName == "StaticString" =>
-
-      implicit val astNodeToStringPiece = AstNodeToStringPiece.astNodeToStringPiece(None)
-
-      if (a.getAttributes.contains("value")) {
-        a.getAttributeAsVector[StringPiece]("value") map { pieces =>
-          val unescaped = pieces map {
-            case StringLiteral(s) => s
-            case e: StringEscapeSequence => e.unescape
-            case _: StringPlaceholder => "String placeholders are not allowed in static strings".invalidNelCheck
+  def astNodeToStaticStringElement(): CheckedAtoB[GenericAstNode, StaticString] =
+    CheckedAtoB.fromCheck("convert AstNode to StaticString") {
+      case a: GenericAst if a.getName == "StaticString" =>
+        implicit val astNodeToStringPiece = AstNodeToStringPiece.astNodeToStringPiece(None)
+
+        if (a.getAttributes.contains("value")) {
+          a.getAttributeAsVector[StringPiece]("value") map { pieces =>
+            val unescaped = pieces map {
+              case StringLiteral(s) => s
+              case e: StringEscapeSequence => e.unescape
+              case _: StringPlaceholder => "String placeholders are not allowed in static strings".invalidNelCheck
+            }
+            StaticString(unescaped.mkString(""))
           }
-          StaticString(unescaped.mkString(""))
-        }
-      } else StaticString("").validNelCheck
+        } else StaticString("").validNelCheck
 
-    case other => s"Bad value $other".invalidNelCheck
-  }
+      case other => s"Bad value $other".invalidNelCheck
+    }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToTypeElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToTypeElement.scala
index 5f440cdb323..286f0dfa4fd 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToTypeElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToTypeElement.scala
@@ -10,40 +10,55 @@ import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.typeElementWriter
 
 object AstNodeToTypeElement {
 
-  def astNodeToTypeElement(additionalPrimitiveTypes: Map[String, WomPrimitiveType]): CheckedAtoB[GenericAstNode, TypeElement] =
+  def astNodeToTypeElement(
+    additionalPrimitiveTypes: Map[String, WomPrimitiveType]
+  ): CheckedAtoB[GenericAstNode, TypeElement] =
     CheckedAtoB.fromCheck("convert AstNode to TypeElement") { astNode =>
-
       implicit lazy val astNodeToTypeElementInst = astNodeToTypeElement(additionalPrimitiveTypes)
 
       lazy val fullTypeMap = typeMap ++ additionalPrimitiveTypes
 
       astNode match {
-        case a: GenericAst if a.getName == "OptionalType" => a.getAttributeAs[TypeElement]("innerType") map OptionalTypeElement
-        case a: GenericAst if a.getName == "NonEmptyType" => a.getAttributeAs[TypeElement]("innerType") map NonEmptyTypeElement
+        case a: GenericAst if a.getName == "OptionalType" =>
+          a.getAttributeAs[TypeElement]("innerType") map OptionalTypeElement
+        case a: GenericAst if a.getName == "NonEmptyType" =>
+          a.getAttributeAs[TypeElement]("innerType") map NonEmptyTypeElement
         case a: GenericAst if a.getName == "Type" => compoundType(a)
-        case unknownAst: GenericAst => s"No rule available to create TypeElement from Ast: '${unknownAst.getName}'".invalidNelCheck
-        case t: GenericTerminal if t.getTerminalStr == "type" && fullTypeMap.contains(t.getSourceString) => PrimitiveTypeElement(fullTypeMap(t.getSourceString)).validNelCheck
-        case t: GenericTerminal if t.getTerminalStr == "type" && t.getSourceString == "Object" => ObjectTypeElement.validNelCheck
+        case unknownAst: GenericAst =>
+          s"No rule available to create TypeElement from Ast: '${unknownAst.getName}'".invalidNelCheck
+        case t: GenericTerminal if t.getTerminalStr == "type" && fullTypeMap.contains(t.getSourceString) =>
+          PrimitiveTypeElement(fullTypeMap(t.getSourceString)).validNelCheck
+        case t: GenericTerminal if t.getTerminalStr == "type" && t.getSourceString == "Object" =>
+          ObjectTypeElement.validNelCheck
         case t: GenericTerminal if t.getTerminalStr == "identifier" => TypeAliasElement(t.getSourceString).validNelCheck
-        case t: GenericTerminal => s"No rule available to create TypeElement from '${t.getTerminalStr}' Terminal with value '${t.getSourceString}'".invalidNelCheck
-        case _ => s"No rule available to create TypeElement from AstNode: ${astNode.getClass.getSimpleName}".invalidNelCheck
+        case t: GenericTerminal =>
+          s"No rule available to create TypeElement from '${t.getTerminalStr}' Terminal with value '${t.getSourceString}'".invalidNelCheck
+        case _ =>
+          s"No rule available to create TypeElement from AstNode: ${astNode.getClass.getSimpleName}".invalidNelCheck
       }
     }
 
-  private def compoundType(typeAst: GenericAst)
-                          (implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, TypeElement]): Checked[TypeElement] = typeAst.getAttributeAs[String]("name") flatMap {
-    case "Array" => typeAst.getAttributeAsVector[TypeElement]("subtype") flatMap {
-      case one if one.size == 1 => ArrayTypeElement(one.head).validNelCheck
-      case other => s"Arrays must have exactly one type parameter, but got ${other.map(_.toWdlV1).mkString("[", ",", "]")}".invalidNelCheck
-    }
-    case "Pair" => typeAst.getAttributeAsVector[TypeElement]("subtype") flatMap {
-      case two if two.size == 2 => PairTypeElement(two.head, two(1)).validNelCheck
-      case other => s"Pairs must have exactly two type parameters, but got ${other.map(_.toWdlV1).mkString("[", ",", "]")}".invalidNelCheck
-    }
-    case "Map" => typeAst.getAttributeAsVector[TypeElement]("subtype") flatMap {
-      case two if two.size == 2 => MapTypeElement(two.head, two(1)).validNelCheck
-      case other => s"Maps must have exactly two type parameters, but got ${other.map(_.toWdlV1).mkString("[", ",", "]")}".invalidNelCheck
-    }
+  private def compoundType(typeAst: GenericAst)(implicit
+    astNodeToExpressionElement: CheckedAtoB[GenericAstNode, TypeElement]
+  ): Checked[TypeElement] = typeAst.getAttributeAs[String]("name") flatMap {
+    case "Array" =>
+      typeAst.getAttributeAsVector[TypeElement]("subtype") flatMap {
+        case one if one.size == 1 => ArrayTypeElement(one.head).validNelCheck
+        case other =>
+          s"Arrays must have exactly one type parameter, but got ${other.map(_.toWdlV1).mkString("[", ",", "]")}".invalidNelCheck
+      }
+    case "Pair" =>
+      typeAst.getAttributeAsVector[TypeElement]("subtype") flatMap {
+        case two if two.size == 2 => PairTypeElement(two.head, two(1)).validNelCheck
+        case other =>
+          s"Pairs must have exactly two type parameters, but got ${other.map(_.toWdlV1).mkString("[", ",", "]")}".invalidNelCheck
+      }
+    case "Map" =>
+      typeAst.getAttributeAsVector[TypeElement]("subtype") flatMap {
+        case two if two.size == 2 => MapTypeElement(two.head, two(1)).validNelCheck
+        case other =>
+          s"Maps must have exactly two type parameters, but got ${other.map(_.toWdlV1).mkString("[", ",", "]")}".invalidNelCheck
+      }
     case unknown => s"No rule available to create TypeElement from compound type: $unknown".invalidNelCheck
   }
 
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToCallElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToCallElement.scala
index 99f5e19e63c..31c730c939a 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToCallElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToCallElement.scala
@@ -14,10 +14,11 @@ import wom.SourceFileLocation
 
 object AstToCallElement {
 
-  def astToCallElement(implicit astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair]): CheckedAtoB[GenericAst, CallElement] = CheckedAtoB.fromErrorOr { ast =>
-    def convertBodyElement(a: GenericAst): Checked[CallBodyElement] = {
+  def astToCallElement(implicit
+    astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair]
+  ): CheckedAtoB[GenericAst, CallElement] = CheckedAtoB.fromErrorOr { ast =>
+    def convertBodyElement(a: GenericAst): Checked[CallBodyElement] =
       a.getAttributeAsVector[KvPair]("inputs") map CallBodyElement
-    }
 
     val callableNameValidation: ErrorOr[String] = astNodeToString(ast.getAttribute("task")).toValidated
 
@@ -26,13 +27,16 @@ object AstToCallElement {
       case None => None.validNel
     }
 
-    val afterValidation: ErrorOr[Vector[String]] = ast.getAttributeAsVector[String]("after", optional = true).toValidated
+    val afterValidation: ErrorOr[Vector[String]] =
+      ast.getAttributeAsVector[String]("after", optional = true).toValidated
 
-    implicit val astNodeToCallBodyElement: CheckedAtoB[GenericAstNode, CallBodyElement] = astNodeToAst andThen CheckedAtoB.fromCheck(convertBodyElement _)
+    implicit val astNodeToCallBodyElement: CheckedAtoB[GenericAstNode, CallBodyElement] =
+      astNodeToAst andThen CheckedAtoB.fromCheck(convertBodyElement _)
 
-    val callBodyValidation: ErrorOr[Option[CallBodyElement]] = ast.getAttributeAsOptional[CallBodyElement]("body").toValidated
+    val callBodyValidation: ErrorOr[Option[CallBodyElement]] =
+      ast.getAttributeAsOptional[CallBodyElement]("body").toValidated
 
-    val sourceLocation : Option[SourceFileLocation] = ast.getSourceLine.map(SourceFileLocation(_))
+    val sourceLocation: Option[SourceFileLocation] = ast.getSourceLine.map(SourceFileLocation(_))
 
     // This 'mapN' is split into two so that if we have a call name we can include it in the error message
     (callableNameValidation, aliasValidation) flatMapN { (name, alias) =>
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToCommandSectionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToCommandSectionElement.scala
index c371e050043..f1a682e1850 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToCommandSectionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToCommandSectionElement.scala
@@ -9,9 +9,9 @@ import wdl.model.draft3.elements.CommandPartElement.StringCommandPartElement
 import wdl.model.draft3.elements.{CommandPartElement, CommandSectionElement, CommandSectionLine}
 
 object AstToCommandSectionElement {
-  def astToCommandSectionElement(implicit astNodeToCommandPartElement: CheckedAtoB[GenericAstNode, CommandPartElement]
-                                ): CheckedAtoB[GenericAst, CommandSectionElement] = CheckedAtoB.fromCheck { ast: GenericAst =>
-
+  def astToCommandSectionElement(implicit
+    astNodeToCommandPartElement: CheckedAtoB[GenericAstNode, CommandPartElement]
+  ): CheckedAtoB[GenericAst, CommandSectionElement] = CheckedAtoB.fromCheck { ast: GenericAst =>
     ast.getAttributeAsVector[CommandPartElement]("parts") flatMap { parts =>
       val lines = makeLines(parts)
       val trimmed = trimStartAndEndBlankLines(lines)
@@ -36,9 +36,7 @@ object AstToCommandSectionElement {
       for {
         prefix <- commonPrefix
         lines <- stripStarts(trimmed, prefix)
-      } yield {
-        CommandSectionElement(lines)
-      }
+      } yield CommandSectionElement(lines)
     }
   }
 
@@ -63,9 +61,8 @@ object AstToCommandSectionElement {
     finalAccumulator map dropEmpties
   }
 
-  private def trimStartAndEndBlankLines(elements: Vector[CommandSectionLine]): Vector[CommandSectionLine] = {
+  private def trimStartAndEndBlankLines(elements: Vector[CommandSectionLine]): Vector[CommandSectionLine] =
     elements.dropWhile(allWhitespace).reverse.dropWhile(allWhitespace).reverse
-  }
 
   private def dropEmpties(line: CommandSectionLine): CommandSectionLine = {
     def empty(c: CommandPartElement): Boolean = c match {
@@ -86,19 +83,20 @@ object AstToCommandSectionElement {
     lines.map(leadingWhitespaceForLine(_).getOrElse(""))
   }
 
-  private def stripStarts(lines: Vector[CommandSectionLine], prefix: String): Checked[List[CommandSectionLine]] = {
+  private def stripStarts(lines: Vector[CommandSectionLine], prefix: String): Checked[List[CommandSectionLine]] =
     if (prefix.isEmpty)
       lines.toList.validNelCheck
     else
       lines.toList traverse { line: CommandSectionLine =>
         line.parts.headOption match {
           case Some(StringCommandPartElement(str)) if str.startsWith(prefix) =>
-            CommandSectionLine(Vector(StringCommandPartElement(str.stripPrefix(prefix))) ++ line.parts.tail).validNelCheck
+            CommandSectionLine(
+              Vector(StringCommandPartElement(str.stripPrefix(prefix))) ++ line.parts.tail
+            ).validNelCheck
           case _ =>
             "Failed to strip common whitespace prefix from line.".invalidNelCheck
         }
       }
-  }
 
   private def allWhitespace(s: String): Boolean = s.forall(_.isWhitespace)
   private def allWhitespace(c: CommandPartElement): Boolean = c match {
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToDeclarationContent.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToDeclarationContent.scala
index ad91c5370eb..93d489d10c5 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToDeclarationContent.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToDeclarationContent.scala
@@ -7,17 +7,17 @@ import cats.syntax.either._
 import common.transforms.CheckedAtoB
 
 object AstToDeclarationContent {
-  def astToDeclarationContent(implicit astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement],
-                              astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]
-                             ): CheckedAtoB[GenericAst, DeclarationContent] = CheckedAtoB.fromErrorOr("read declaration") { a =>
-
-
+  def astToDeclarationContent(implicit
+    astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement],
+    astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]
+  ): CheckedAtoB[GenericAst, DeclarationContent] = CheckedAtoB.fromErrorOr("read declaration") { a =>
     val nameValidation: ErrorOr[String] = astNodeToString(a.getAttribute("name")).toValidated
     val outputTypeValidation: ErrorOr[TypeElement] = a.getAttributeAs[TypeElement]("type").toValidated
-    val expressionElementValidation: ErrorOr[ExpressionElement] = a.getAttributeAs[ExpressionElement]("expression").toValidated
+    val expressionElementValidation: ErrorOr[ExpressionElement] =
+      a.getAttributeAs[ExpressionElement]("expression").toValidated
 
-    (nameValidation, outputTypeValidation, expressionElementValidation) mapN {
-      (name, outputType, expression) => DeclarationContent(outputType, name, expression)
+    (nameValidation, outputTypeValidation, expressionElementValidation) mapN { (name, outputType, expression) =>
+      DeclarationContent(outputType, name, expression)
     }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToFileBodyElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToFileBodyElement.scala
index 8a2b2480025..36338b5fabc 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToFileBodyElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToFileBodyElement.scala
@@ -7,17 +7,17 @@ import wdl.model.draft3.elements.{FileBodyElement, StructElement, TaskDefinition
 
 object AstToFileBodyElement {
 
-  def astToFileBodyElement(implicit workflowConverter: CheckedAtoB[GenericAst, WorkflowDefinitionElement],
-                           taskConverter: CheckedAtoB[GenericAst, TaskDefinitionElement],
-                           structConverter: CheckedAtoB[GenericAst, StructElement]): CheckedAtoB[GenericAst, FileBodyElement] = {
+  def astToFileBodyElement(implicit
+    workflowConverter: CheckedAtoB[GenericAst, WorkflowDefinitionElement],
+    taskConverter: CheckedAtoB[GenericAst, TaskDefinitionElement],
+    structConverter: CheckedAtoB[GenericAst, StructElement]
+  ): CheckedAtoB[GenericAst, FileBodyElement] =
     CheckedAtoB.fromCheck(convert(workflowConverter, taskConverter, structConverter))
-  }
 
   def convert(workflowConverter: CheckedAtoB[GenericAst, WorkflowDefinitionElement],
               taskConverter: CheckedAtoB[GenericAst, TaskDefinitionElement],
-              structConverter: CheckedAtoB[GenericAst, StructElement])
-             (ast: GenericAst)
-             : Checked[FileBodyElement] = ast.getName match {
+              structConverter: CheckedAtoB[GenericAst, StructElement]
+  )(ast: GenericAst): Checked[FileBodyElement] = ast.getName match {
     case "Workflow" => workflowConverter.run(ast)
     case "Task" => taskConverter.run(ast)
     case "Struct" => structConverter.run(ast)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToFileElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToFileElement.scala
index 3fcd92c061c..02ed87d0e86 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToFileElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToFileElement.scala
@@ -9,12 +9,14 @@ import wdl.model.draft3.elements._
 
 object AstToFileElement {
 
-  def astToFileElement(implicit astNodeToImportElement: CheckedAtoB[GenericAstNode, ImportElement],
-                       astNodeToFileBodyElement: CheckedAtoB[GenericAstNode, FileBodyElement]
-                      ): CheckedAtoB[GenericAst, FileElement] = CheckedAtoB.fromErrorOr { ast =>
-
-    val validatedImportElements: ErrorOr[Vector[ImportElement]] = ast.getAttributeAsVector[ImportElement]("imports").toValidated
-    val validatedFileBodyElements: ErrorOr[Vector[FileBodyElement]] = ast.getAttributeAsVector[FileBodyElement]("body").toValidated
+  def astToFileElement(implicit
+    astNodeToImportElement: CheckedAtoB[GenericAstNode, ImportElement],
+    astNodeToFileBodyElement: CheckedAtoB[GenericAstNode, FileBodyElement]
+  ): CheckedAtoB[GenericAst, FileElement] = CheckedAtoB.fromErrorOr { ast =>
+    val validatedImportElements: ErrorOr[Vector[ImportElement]] =
+      ast.getAttributeAsVector[ImportElement]("imports").toValidated
+    val validatedFileBodyElements: ErrorOr[Vector[FileBodyElement]] =
+      ast.getAttributeAsVector[FileBodyElement]("body").toValidated
 
     (validatedImportElements, validatedFileBodyElements) mapN { (importElements, fileBodyElements) =>
       val workflowElements: Vector[WorkflowDefinitionElement] = fileBodyElements.filterByType[WorkflowDefinitionElement]
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToIfElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToIfElement.scala
index 45eaa471e33..37cd043e571 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToIfElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToIfElement.scala
@@ -8,12 +8,10 @@ import common.validation.ErrorOr.ErrorOr
 import wdl.model.draft3.elements._
 
 object AstToIfElement {
-  def astToIfElement(implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement],
-                     astNodeToWorkflowGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement]
-
-                    ): CheckedAtoB[GenericAst, IfElement] = CheckedAtoB.fromErrorOr("parse if block") { ast =>
-
-
+  def astToIfElement(implicit
+    astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement],
+    astNodeToWorkflowGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement]
+  ): CheckedAtoB[GenericAst, IfElement] = CheckedAtoB.fromErrorOr("parse if block") { ast =>
     val conditionCollectionExpressionValidation: ErrorOr[ExpressionElement] =
       ast.getAttributeAs[ExpressionElement]("expression").toValidated.contextualizeErrors("parse if (...) condition")
     val bodyValidation: ErrorOr[Vector[WorkflowGraphElement]] =
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToImportElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToImportElement.scala
index ce0042461ed..b3775ed67f9 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToImportElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToImportElement.scala
@@ -9,15 +9,19 @@ import wdl.model.draft3.elements.{ImportElement, LanguageElement, StaticString}
 
 object AstToImportElement {
 
-  def astToImportElement(implicit astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString]): CheckedAtoB[GenericAst, ImportElement] =
+  def astToImportElement(implicit
+    astNodeToStaticString: CheckedAtoB[GenericAstNode, StaticString]
+  ): CheckedAtoB[GenericAst, ImportElement] =
     CheckedAtoB.fromErrorOr("convert Ast to ImportElement") { a =>
-
       val importPath: ErrorOr[String] = a.getAttributeAs[StaticString]("uri").map(_.value).toValidated
       val alias: ErrorOr[Option[String]] = a.getAttributeAsOptional[String]("namespace").toValidated
 
-      val aliasElementMaker: CheckedAtoB[GenericAstNode, ImportStructRenameElement] = astNodeToAst andThen CheckedAtoB.fromErrorOr(convertAliasElement _)
-      val structRenames: ErrorOr[Vector[ImportStructRenameElement]] = a.getAttributeAsVector[ImportStructRenameElement]("aliases")(aliasElementMaker).toValidated
-      val structRenameMap: ErrorOr[Map[String, String]] = structRenames.map(_.map(rename => rename.oldName -> rename.newName).toMap)
+      val aliasElementMaker: CheckedAtoB[GenericAstNode, ImportStructRenameElement] =
+        astNodeToAst andThen CheckedAtoB.fromErrorOr(convertAliasElement _)
+      val structRenames: ErrorOr[Vector[ImportStructRenameElement]] =
+        a.getAttributeAsVector[ImportStructRenameElement]("aliases")(aliasElementMaker).toValidated
+      val structRenameMap: ErrorOr[Map[String, String]] =
+        structRenames.map(_.map(rename => rename.oldName -> rename.newName).toMap)
 
       (importPath, alias, structRenameMap) mapN ImportElement
     }
@@ -29,5 +33,5 @@ object AstToImportElement {
     (oldName, newName) mapN ImportStructRenameElement
   }
 
-  private final case class ImportStructRenameElement(oldName: String, newName: String) extends LanguageElement
+  final private case class ImportStructRenameElement(oldName: String, newName: String) extends LanguageElement
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToInputDeclarationElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToInputDeclarationElement.scala
index b9a54a4b250..193e4aa5a1e 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToInputDeclarationElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToInputDeclarationElement.scala
@@ -9,8 +9,10 @@ import wdl.model.draft3.elements.{ExpressionElement, InputDeclarationElement, Ty
 
 object AstToInputDeclarationElement {
 
-  def astToInputDeclarationElement(implicit astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement],
-                                   astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]): CheckedAtoB[GenericAst, InputDeclarationElement] = CheckedAtoB.fromErrorOr { a: GenericAst =>
+  def astToInputDeclarationElement(implicit
+    astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement],
+    astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement]
+  ): CheckedAtoB[GenericAst, InputDeclarationElement] = CheckedAtoB.fromErrorOr { a: GenericAst =>
     val nameValidation: ErrorOr[String] = astNodeToString(a.getAttribute("name")).toValidated
     val inputTypeValidation: ErrorOr[TypeElement] = astNodeToTypeElement(a.getAttribute("type")).toValidated
     val expressionValidation: ErrorOr[Option[ExpressionElement]] = Option(a.getAttribute("expression")) match {
@@ -18,9 +20,8 @@ object AstToInputDeclarationElement {
       case None => None.validNel
     }
 
-    (nameValidation, inputTypeValidation, expressionValidation) mapN {
-      (name, inputType, expression) =>
-        InputDeclarationElement(inputType, name, expression)
+    (nameValidation, inputTypeValidation, expressionValidation) mapN { (name, inputType, expression) =>
+      InputDeclarationElement(inputType, name, expression)
     }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToInputsSectionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToInputsSectionElement.scala
index fd0774be89d..04f7347a032 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToInputsSectionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToInputsSectionElement.scala
@@ -5,9 +5,9 @@ import wdl.model.draft3.elements.{InputDeclarationElement, InputsSectionElement}
 
 object AstToInputsSectionElement {
 
-  def astToInputsSectionElement(implicit astNodeToInputDeclaration: CheckedAtoB[GenericAstNode, InputDeclarationElement]
-                               ): CheckedAtoB[GenericAst, InputsSectionElement] = CheckedAtoB.fromCheck("convert Ast to Inputs Section") { a =>
-
+  def astToInputsSectionElement(implicit
+    astNodeToInputDeclaration: CheckedAtoB[GenericAstNode, InputDeclarationElement]
+  ): CheckedAtoB[GenericAst, InputsSectionElement] = CheckedAtoB.fromCheck("convert Ast to Inputs Section") { a =>
     a.getAttributeAsVector[InputDeclarationElement]("inputs") map { declarations =>
       InputsSectionElement(declarations)
     }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToMetaSectionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToMetaSectionElement.scala
index 5cda9ade77a..d889ee57b13 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToMetaSectionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToMetaSectionElement.scala
@@ -5,9 +5,9 @@ import wdl.model.draft3.elements.MetaSectionElement
 import wom.callable.MetaKvPair
 
 object AstToMetaSectionElement {
-  def astToMetaSectionElement(implicit astNodeToMetaKvPair: CheckedAtoB[GenericAstNode, MetaKvPair]
-                             ): CheckedAtoB[GenericAst, MetaSectionElement] = CheckedAtoB.fromCheck("convert AST to Meta Section") { ast =>
-
+  def astToMetaSectionElement(implicit
+    astNodeToMetaKvPair: CheckedAtoB[GenericAstNode, MetaKvPair]
+  ): CheckedAtoB[GenericAst, MetaSectionElement] = CheckedAtoB.fromCheck("convert AST to Meta Section") { ast =>
     ast.getAttributeAsVector[MetaKvPair]("map") map { attributes =>
       val asMap = attributes.map(kv => kv.key -> kv.value).toMap
       MetaSectionElement(asMap)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToOutputsSectionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToOutputsSectionElement.scala
index fcac78ec9b1..70f1eb7a605 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToOutputsSectionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToOutputsSectionElement.scala
@@ -4,9 +4,11 @@ import common.transforms.CheckedAtoB
 import wdl.model.draft3.elements.{DeclarationContent, OutputDeclarationElement, OutputsSectionElement}
 
 object AstToOutputsSectionElement {
-  def astToOutputSectionElement(implicit astNodeToMetaKvPair: CheckedAtoB[GenericAstNode, DeclarationContent]
-                             ): CheckedAtoB[GenericAst, OutputsSectionElement] = CheckedAtoB.fromCheck("read outputs section") { a =>
-
-    a.getAttributeAsVector[DeclarationContent]("outputs").map(_.map(OutputDeclarationElement.fromContent)).map(OutputsSectionElement)
+  def astToOutputSectionElement(implicit
+    astNodeToMetaKvPair: CheckedAtoB[GenericAstNode, DeclarationContent]
+  ): CheckedAtoB[GenericAst, OutputsSectionElement] = CheckedAtoB.fromCheck("read outputs section") { a =>
+    a.getAttributeAsVector[DeclarationContent]("outputs")
+      .map(_.map(OutputDeclarationElement.fromContent))
+      .map(OutputsSectionElement)
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToParameterMetaSectionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToParameterMetaSectionElement.scala
index c87a4ef4579..6baa864bcb8 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToParameterMetaSectionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToParameterMetaSectionElement.scala
@@ -5,12 +5,13 @@ import wdl.model.draft3.elements.ParameterMetaSectionElement
 import wom.callable.MetaKvPair
 
 object AstToParameterMetaSectionElement {
-  def astToParameterMetaSectionElement(implicit astNodeToMetaKvPair: CheckedAtoB[GenericAstNode, MetaKvPair]
-                                      ): CheckedAtoB[GenericAst, ParameterMetaSectionElement] = CheckedAtoB.fromCheck("convert AST to parameter_meta section") { ast =>
-
-    ast.getAttributeAsVector[MetaKvPair]("map") map { attributes =>
-      val asMap = attributes.map(kv => kv.key -> kv.value).toMap
-      ParameterMetaSectionElement(asMap)
+  def astToParameterMetaSectionElement(implicit
+    astNodeToMetaKvPair: CheckedAtoB[GenericAstNode, MetaKvPair]
+  ): CheckedAtoB[GenericAst, ParameterMetaSectionElement] =
+    CheckedAtoB.fromCheck("convert AST to parameter_meta section") { ast =>
+      ast.getAttributeAsVector[MetaKvPair]("map") map { attributes =>
+        val asMap = attributes.map(kv => kv.key -> kv.value).toMap
+        ParameterMetaSectionElement(asMap)
+      }
     }
-  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToRuntimeAttributesSectionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToRuntimeAttributesSectionElement.scala
index 1e06f35e225..86dc9e019bd 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToRuntimeAttributesSectionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToRuntimeAttributesSectionElement.scala
@@ -5,11 +5,12 @@ import wdl.model.draft3.elements.ExpressionElement.KvPair
 import wdl.model.draft3.elements.RuntimeAttributesSectionElement
 
 object AstToRuntimeAttributesSectionElement {
-  def astToRuntimeSectionElement(implicit astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair]
-                             ): CheckedAtoB[GenericAst, RuntimeAttributesSectionElement] = CheckedAtoB.fromCheck("convert AST to runtime section") { ast =>
-
-    ast.getAttributeAsVector[KvPair]("map") map { attributes =>
-      RuntimeAttributesSectionElement(attributes)
+  def astToRuntimeSectionElement(implicit
+    astNodeToKvPair: CheckedAtoB[GenericAstNode, KvPair]
+  ): CheckedAtoB[GenericAst, RuntimeAttributesSectionElement] =
+    CheckedAtoB.fromCheck("convert AST to runtime section") { ast =>
+      ast.getAttributeAsVector[KvPair]("map") map { attributes =>
+        RuntimeAttributesSectionElement(attributes)
+      }
     }
-  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToScatterElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToScatterElement.scala
index cee211f86dc..7d265cd7e5e 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToScatterElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToScatterElement.scala
@@ -8,19 +8,22 @@ import wdl.model.draft3.elements._
 import wom.SourceFileLocation
 
 object AstToScatterElement {
-  def astToScatterElement(implicit astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement],
-                          astNodeToWorkflowGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement]
-                         ): CheckedAtoB[GenericAst, ScatterElement] = CheckedAtoB.fromErrorOr("process scatter block") { ast =>
-
+  def astToScatterElement(implicit
+    astNodeToExpressionElement: CheckedAtoB[GenericAstNode, ExpressionElement],
+    astNodeToWorkflowGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement]
+  ): CheckedAtoB[GenericAst, ScatterElement] = CheckedAtoB.fromErrorOr("process scatter block") { ast =>
     val scatterVariableValidation: ErrorOr[GenericTerminal] = ast.getAttributeAs[GenericTerminal]("item").toValidated
 
-    val scatterCollectionExpressionValidation: ErrorOr[ExpressionElement] = ast.getAttributeAs[ExpressionElement]("collection").toValidated
-    val bodyValidation: ErrorOr[Vector[WorkflowGraphElement]] = ast.getAttributeAsVector[WorkflowGraphElement]("body").toValidated
-    val sourceLocation : Option[SourceFileLocation] = ast.getSourceLine.map(SourceFileLocation(_))
+    val scatterCollectionExpressionValidation: ErrorOr[ExpressionElement] =
+      ast.getAttributeAs[ExpressionElement]("collection").toValidated
+    val bodyValidation: ErrorOr[Vector[WorkflowGraphElement]] =
+      ast.getAttributeAsVector[WorkflowGraphElement]("body").toValidated
+    val sourceLocation: Option[SourceFileLocation] = ast.getSourceLine.map(SourceFileLocation(_))
 
-    (scatterVariableValidation, scatterCollectionExpressionValidation, bodyValidation) mapN { (variable, collection, body) =>
-      val scatterName = s"ScatterAt${variable.getLine}_${variable.getColumn}"
-      ScatterElement(scatterName, collection, variable.getSourceString, body, sourceLocation)
+    (scatterVariableValidation, scatterCollectionExpressionValidation, bodyValidation) mapN {
+      (variable, collection, body) =>
+        val scatterName = s"ScatterAt${variable.getLine}_${variable.getColumn}"
+        ScatterElement(scatterName, collection, variable.getSourceString, body, sourceLocation)
     }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToStructElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToStructElement.scala
index 4854c2e7bcf..99c56307aae 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToStructElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToStructElement.scala
@@ -8,9 +8,9 @@ import common.validation.ErrorOr.ErrorOr
 import wdl.model.draft3.elements.{StructElement, StructEntryElement, TypeElement}
 
 object AstToStructElement {
-  def astToStructElement(implicit astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement]
-                         ): CheckedAtoB[GenericAst, StructElement] = CheckedAtoB.fromErrorOr("convert AST to struct definition") { a =>
-
+  def astToStructElement(implicit
+    astNodeToTypeElement: CheckedAtoB[GenericAstNode, TypeElement]
+  ): CheckedAtoB[GenericAst, StructElement] = CheckedAtoB.fromErrorOr("convert AST to struct definition") { a =>
     def convertAstToStructEntry(a: GenericAst): ErrorOr[StructEntryElement] = {
       val name: ErrorOr[String] = a.getAttributeAs[String]("name").toValidated
       val typeElement: ErrorOr[TypeElement] = a.getAttributeAs[TypeElement]("type").toValidated
@@ -18,12 +18,13 @@ object AstToStructElement {
       (name, typeElement).mapN(StructEntryElement.apply)
     }
 
-    implicit val astNodeToStructEntry: CheckedAtoB[GenericAstNode, StructEntryElement] = astNodeToAst andThen CheckedAtoB.fromErrorOr("convert AST to struct entry")(convertAstToStructEntry)
+    implicit val astNodeToStructEntry: CheckedAtoB[GenericAstNode, StructEntryElement] =
+      astNodeToAst andThen CheckedAtoB.fromErrorOr("convert AST to struct entry")(convertAstToStructEntry)
     val nameValidation: ErrorOr[String] = a.getAttributeAs[String]("name").toValidated
-    val entriesValidation: ErrorOr[Vector[StructEntryElement]] = a.getAttributeAsVector[StructEntryElement]("entries").toValidated
+    val entriesValidation: ErrorOr[Vector[StructEntryElement]] =
+      a.getAttributeAsVector[StructEntryElement]("entries").toValidated
 
     (nameValidation, entriesValidation) mapN { (name, entries) => StructElement(name, entries) }
 
-
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToTaskDefinitionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToTaskDefinitionElement.scala
index 2916186c0ef..fdda85254b9 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToTaskDefinitionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToTaskDefinitionElement.scala
@@ -11,14 +11,15 @@ import wom.SourceFileLocation
 
 object AstToTaskDefinitionElement {
 
-  def astToTaskDefinitionElement(implicit astNodeToTaskSectionElement: CheckedAtoB[GenericAstNode, TaskSectionElement]
-                                ): CheckedAtoB[GenericAst, TaskDefinitionElement] = CheckedAtoB.fromErrorOr
-  { a: GenericAst => s"read task definition${a.lineAndColumnString}" }
-  { a =>
-
+  def astToTaskDefinitionElement(implicit
+    astNodeToTaskSectionElement: CheckedAtoB[GenericAstNode, TaskSectionElement]
+  ): CheckedAtoB[GenericAst, TaskDefinitionElement] = CheckedAtoB.fromErrorOr { a: GenericAst =>
+    s"read task definition${a.lineAndColumnString}"
+  } { a =>
     val nameElementValidation: ErrorOr[String] = astNodeToString(a.getAttribute("name")).toValidated
-    val sectionsValidation: ErrorOr[Vector[TaskSectionElement]] = a.getAttributeAsVector[TaskSectionElement]("sections").toValidated
-    val sourceLocation : Option[SourceFileLocation] = a.getSourceLine.map(SourceFileLocation(_))
+    val sectionsValidation: ErrorOr[Vector[TaskSectionElement]] =
+      a.getAttributeAsVector[TaskSectionElement]("sections").toValidated
+    val sourceLocation: Option[SourceFileLocation] = a.getSourceLine.map(SourceFileLocation(_))
 
     (nameElementValidation, sectionsValidation) flatMapN { (nameElement, sections) =>
       combineElements(nameElement, sections, sourceLocation)
@@ -27,19 +28,41 @@ object AstToTaskDefinitionElement {
 
   def combineElements(nameElement: String,
                       bodyElements: Vector[TaskSectionElement],
-                      sourceLocation: Option[SourceFileLocation]) = {
-    val inputsSectionElement: ErrorOr[Option[InputsSectionElement]] = validateOneMax(bodyElements.filterByType[InputsSectionElement], "inputs")
-    val declarations: Vector[IntermediateValueDeclarationElement] = bodyElements.filterByType[IntermediateValueDeclarationElement]
-    val outputsSectionElement: ErrorOr[Option[OutputsSectionElement]] = validateOneMax(bodyElements.filterByType[OutputsSectionElement], "outputs")
-    val commandSectionElement: ErrorOr[CommandSectionElement] = validateExists(bodyElements.filterByType[CommandSectionElement], "command")
-    val runtimeSectionElement: ErrorOr[Option[RuntimeAttributesSectionElement]] = validateOneMax(bodyElements.filterByType[RuntimeAttributesSectionElement], "runtime")
-
-    val metaSectionElement: ErrorOr[Option[MetaSectionElement]] = validateOneMax(bodyElements.filterByType[MetaSectionElement], "meta")
-    val parameterMetaSectionElement: ErrorOr[Option[ParameterMetaSectionElement]] = validateOneMax(bodyElements.filterByType[ParameterMetaSectionElement], "parameterMeta")
-
-    (inputsSectionElement, outputsSectionElement, commandSectionElement, runtimeSectionElement, metaSectionElement, parameterMetaSectionElement) mapN {
-      (inputs, outputs, command, runtime, meta, parameterMeta) =>
-        TaskDefinitionElement(nameElement, inputs, declarations, outputs, command, runtime, meta, parameterMeta, sourceLocation)
+                      sourceLocation: Option[SourceFileLocation]
+  ) = {
+    val inputsSectionElement: ErrorOr[Option[InputsSectionElement]] =
+      validateOneMax(bodyElements.filterByType[InputsSectionElement], "inputs")
+    val declarations: Vector[IntermediateValueDeclarationElement] =
+      bodyElements.filterByType[IntermediateValueDeclarationElement]
+    val outputsSectionElement: ErrorOr[Option[OutputsSectionElement]] =
+      validateOneMax(bodyElements.filterByType[OutputsSectionElement], "outputs")
+    val commandSectionElement: ErrorOr[CommandSectionElement] =
+      validateExists(bodyElements.filterByType[CommandSectionElement], "command")
+    val runtimeSectionElement: ErrorOr[Option[RuntimeAttributesSectionElement]] =
+      validateOneMax(bodyElements.filterByType[RuntimeAttributesSectionElement], "runtime")
+
+    val metaSectionElement: ErrorOr[Option[MetaSectionElement]] =
+      validateOneMax(bodyElements.filterByType[MetaSectionElement], "meta")
+    val parameterMetaSectionElement: ErrorOr[Option[ParameterMetaSectionElement]] =
+      validateOneMax(bodyElements.filterByType[ParameterMetaSectionElement], "parameterMeta")
+
+    (inputsSectionElement,
+     outputsSectionElement,
+     commandSectionElement,
+     runtimeSectionElement,
+     metaSectionElement,
+     parameterMetaSectionElement
+    ) mapN { (inputs, outputs, command, runtime, meta, parameterMeta) =>
+      TaskDefinitionElement(nameElement,
+                            inputs,
+                            declarations,
+                            outputs,
+                            command,
+                            runtime,
+                            meta,
+                            parameterMeta,
+                            sourceLocation
+      )
     }
   }
 
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToTaskSectionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToTaskSectionElement.scala
index f5c724d242d..117a4984b69 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToTaskSectionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToTaskSectionElement.scala
@@ -5,14 +5,15 @@ import common.validation.Checked._
 import wdl.model.draft3.elements._
 
 object AstToTaskSectionElement {
-  def astToTaskSectionElement(implicit astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement],
-                              astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement],
-                              astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent],
-                              astNodeToRuntimeAttributesSectionElement: CheckedAtoB[GenericAstNode, RuntimeAttributesSectionElement],
-                              astNodeToCommandSectionElement: CheckedAtoB[GenericAstNode, CommandSectionElement],
-                              astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement],
-                              astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement]
-                             ): CheckedAtoB[GenericAst, TaskSectionElement] = CheckedAtoB.fromCheck { a: GenericAst =>
+  def astToTaskSectionElement(implicit
+    astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement],
+    astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement],
+    astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent],
+    astNodeToRuntimeAttributesSectionElement: CheckedAtoB[GenericAstNode, RuntimeAttributesSectionElement],
+    astNodeToCommandSectionElement: CheckedAtoB[GenericAstNode, CommandSectionElement],
+    astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement],
+    astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement]
+  ): CheckedAtoB[GenericAst, TaskSectionElement] = CheckedAtoB.fromCheck { a: GenericAst =>
     a.getName match {
       case "Inputs" => astNodeToInputsSectionElement.run(a)
       case "Outputs" => astNodeToOutputsSectionElement(a)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowBodyElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowBodyElement.scala
index 71fd9f78c16..1c213153994 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowBodyElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowBodyElement.scala
@@ -5,17 +5,20 @@ import common.validation.Checked._
 import wdl.model.draft3.elements._
 
 object AstToWorkflowBodyElement {
-  def astToWorkflowBodyElement(implicit astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement],
-                               astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement],
-                               astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement],
-                               astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement],
-                               astNodeToGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement]
-                              ): CheckedAtoB[GenericAst, WorkflowBodyElement] = CheckedAtoB.fromCheck { ast: GenericAst => ast.getName match {
-    case "Inputs" => astNodeToInputsSectionElement(ast)
-    case "Outputs" => astNodeToOutputsSectionElement(ast)
-    case "Meta" => astNodeToMetaSectionElement(ast)
-    case "ParameterMeta" => astNodeToParameterMetaSectionElement(ast)
-    case "Declaration" | "Call" | "Scatter" | "If" => astNodeToGraphElement(ast)
-    case other => s"No conversion defined for Ast with name $other to WorkflowBodyElement".invalidNelCheck
-  }}
+  def astToWorkflowBodyElement(implicit
+    astNodeToInputsSectionElement: CheckedAtoB[GenericAstNode, InputsSectionElement],
+    astNodeToOutputsSectionElement: CheckedAtoB[GenericAstNode, OutputsSectionElement],
+    astNodeToMetaSectionElement: CheckedAtoB[GenericAstNode, MetaSectionElement],
+    astNodeToParameterMetaSectionElement: CheckedAtoB[GenericAstNode, ParameterMetaSectionElement],
+    astNodeToGraphElement: CheckedAtoB[GenericAstNode, WorkflowGraphElement]
+  ): CheckedAtoB[GenericAst, WorkflowBodyElement] = CheckedAtoB.fromCheck { ast: GenericAst =>
+    ast.getName match {
+      case "Inputs" => astNodeToInputsSectionElement(ast)
+      case "Outputs" => astNodeToOutputsSectionElement(ast)
+      case "Meta" => astNodeToMetaSectionElement(ast)
+      case "ParameterMeta" => astNodeToParameterMetaSectionElement(ast)
+      case "Declaration" | "Call" | "Scatter" | "If" => astNodeToGraphElement(ast)
+      case other => s"No conversion defined for Ast with name $other to WorkflowBodyElement".invalidNelCheck
+    }
+  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowDefinitionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowDefinitionElement.scala
index 6b8e7d08dd0..b7128ed7c9e 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowDefinitionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowDefinitionElement.scala
@@ -12,12 +12,14 @@ import wdl.model.draft3.elements.ExpressionElement._
 
 object AstToWorkflowDefinitionElement {
 
-  def astToWorkflowDefinitionElement(implicit astNodeToWorkflowBodyElement: CheckedAtoB[GenericAstNode, WorkflowBodyElement]
-                                    ): CheckedAtoB[GenericAst, WorkflowDefinitionElement] = CheckedAtoB.fromErrorOr { a: GenericAst =>
+  def astToWorkflowDefinitionElement(implicit
+    astNodeToWorkflowBodyElement: CheckedAtoB[GenericAstNode, WorkflowBodyElement]
+  ): CheckedAtoB[GenericAst, WorkflowDefinitionElement] = CheckedAtoB.fromErrorOr { a: GenericAst =>
     val nameElementValidation: ErrorOr[String] = astNodeToString(a.getAttribute("name")).toValidated
 
-    val sourceLocation : Option[SourceFileLocation] = a.getSourceLine.map(SourceFileLocation(_))
-    val bodyElementsValidation: ErrorOr[Vector[WorkflowBodyElement]] = a.getAttributeAsVector[WorkflowBodyElement]("body")(astNodeToWorkflowBodyElement).toValidated
+    val sourceLocation: Option[SourceFileLocation] = a.getSourceLine.map(SourceFileLocation(_))
+    val bodyElementsValidation: ErrorOr[Vector[WorkflowBodyElement]] =
+      a.getAttributeAsVector[WorkflowBodyElement]("body")(astNodeToWorkflowBodyElement).toValidated
     (nameElementValidation, bodyElementsValidation) flatMapN { (name, bodyElements) =>
       combineElements(name, sourceLocation, bodyElements)
     }
@@ -25,35 +27,65 @@ object AstToWorkflowDefinitionElement {
 
   private def combineElements(name: String,
                               sourceLocation: Option[SourceFileLocation],
-                              bodyElements: Vector[WorkflowBodyElement]) = {
+                              bodyElements: Vector[WorkflowBodyElement]
+  ) = {
 
     val inputsSectionValidation: ErrorOr[Option[InputsSectionElement]] = for {
-      inputValidateElement <- validateSize(bodyElements.filterByType[InputsSectionElement], "inputs", 1): ErrorOr[Option[InputsSectionElement]]
+      inputValidateElement <- validateSize(bodyElements.filterByType[InputsSectionElement], "inputs", 1): ErrorOr[
+        Option[InputsSectionElement]
+      ]
       _ <- checkDisallowedInputElement(inputValidateElement, StdoutElement, "stdout")
       _ <- checkDisallowedInputElement(inputValidateElement, StderrElement, "stderr")
     } yield inputValidateElement
 
-    val intermediateValueDeclarationStdoutCheck = checkDisallowedIntermediates(bodyElements.filterByType[IntermediateValueDeclarationElement], StdoutElement, "stdout")
-    val intermediateValueDeclarationStderrCheck = checkDisallowedIntermediates(bodyElements.filterByType[IntermediateValueDeclarationElement], StderrElement, "stderr")
+    val intermediateValueDeclarationStdoutCheck = checkDisallowedIntermediates(
+      bodyElements.filterByType[IntermediateValueDeclarationElement],
+      StdoutElement,
+      "stdout"
+    )
+    val intermediateValueDeclarationStderrCheck = checkDisallowedIntermediates(
+      bodyElements.filterByType[IntermediateValueDeclarationElement],
+      StderrElement,
+      "stderr"
+    )
 
     val outputsSectionValidation: ErrorOr[Option[OutputsSectionElement]] = for {
-      outputValidateElement <- validateSize(bodyElements.filterByType[OutputsSectionElement], "outputs", 1): ErrorOr[Option[OutputsSectionElement]]
+      outputValidateElement <- validateSize(bodyElements.filterByType[OutputsSectionElement], "outputs", 1): ErrorOr[
+        Option[OutputsSectionElement]
+      ]
       _ <- checkDisallowedOutputElement(outputValidateElement, StdoutElement, "stdout")
       _ <- checkDisallowedOutputElement(outputValidateElement, StderrElement, "stderr")
     } yield outputValidateElement
 
     val graphSections: Vector[WorkflowGraphElement] = bodyElements.filterByType[WorkflowGraphElement]
 
-    val metaSectionValidation: ErrorOr[Option[MetaSectionElement]] = validateSize(bodyElements.filterByType[MetaSectionElement], "meta", 1)
-    val parameterMetaSectionValidation: ErrorOr[Option[ParameterMetaSectionElement]] = validateSize(bodyElements.filterByType[ParameterMetaSectionElement], "parameterMeta", 1)
-
-    (inputsSectionValidation, outputsSectionValidation, metaSectionValidation, parameterMetaSectionValidation, intermediateValueDeclarationStdoutCheck, intermediateValueDeclarationStderrCheck) mapN {
-      (validInputs, validOutputs, meta, parameterMeta, _, _) =>
-      WorkflowDefinitionElement(name, validInputs, graphSections.toSet, validOutputs, meta, parameterMeta, sourceLocation)
+    val metaSectionValidation: ErrorOr[Option[MetaSectionElement]] =
+      validateSize(bodyElements.filterByType[MetaSectionElement], "meta", 1)
+    val parameterMetaSectionValidation: ErrorOr[Option[ParameterMetaSectionElement]] =
+      validateSize(bodyElements.filterByType[ParameterMetaSectionElement], "parameterMeta", 1)
+
+    (inputsSectionValidation,
+     outputsSectionValidation,
+     metaSectionValidation,
+     parameterMetaSectionValidation,
+     intermediateValueDeclarationStdoutCheck,
+     intermediateValueDeclarationStderrCheck
+    ) mapN { (validInputs, validOutputs, meta, parameterMeta, _, _) =>
+      WorkflowDefinitionElement(name,
+                                validInputs,
+                                graphSections.toSet,
+                                validOutputs,
+                                meta,
+                                parameterMeta,
+                                sourceLocation
+      )
     }
   }
 
-  def checkDisallowedInputElement(inputSection: Option[InputsSectionElement], expressionType: FunctionCallElement, expressionName: String): ErrorOr[Unit] = {
+  def checkDisallowedInputElement(inputSection: Option[InputsSectionElement],
+                                  expressionType: FunctionCallElement,
+                                  expressionName: String
+  ): ErrorOr[Unit] =
     inputSection match {
       case Some(section) =>
         if (section.inputDeclarations.flatMap(_.expression).exists(_.isInstanceOf[expressionType.type])) {
@@ -61,9 +93,11 @@ object AstToWorkflowDefinitionElement {
         } else ().validNel
       case None => ().validNel
     }
-  }
 
-  def checkDisallowedOutputElement(outputSection: Option[OutputsSectionElement], expressionType: FunctionCallElement, expressionName: String): ErrorOr[Unit] = {
+  def checkDisallowedOutputElement(outputSection: Option[OutputsSectionElement],
+                                   expressionType: FunctionCallElement,
+                                   expressionName: String
+  ): ErrorOr[Unit] =
     outputSection match {
       case Some(section) =>
         if (section.outputs.map(_.expression).exists(_.isInstanceOf[expressionType.type])) {
@@ -71,13 +105,14 @@ object AstToWorkflowDefinitionElement {
         } else ().validNel
       case None => ().validNel
     }
-  }
 
-  def checkDisallowedIntermediates(intermediate: Vector[IntermediateValueDeclarationElement], expressionType: FunctionCallElement, expressionName: String): ErrorOr[Unit] = {
+  def checkDisallowedIntermediates(intermediate: Vector[IntermediateValueDeclarationElement],
+                                   expressionType: FunctionCallElement,
+                                   expressionName: String
+  ): ErrorOr[Unit] =
     if (intermediate.map(_.expression).exists(_.isInstanceOf[expressionType.type])) {
       s"Workflow cannot have $expressionName expression at intermediate declaration section at workflow-level.".invalidNel
     } else ().validNel
-  }
 
   private def validateSize[A](elements: Vector[A], sectionName: String, numExpected: Int): ErrorOr[Option[A]] = {
     val sectionValidation: ErrorOr[Option[A]] = if (elements.size > numExpected) {
@@ -88,4 +123,4 @@ object AstToWorkflowDefinitionElement {
 
     sectionValidation
   }
-}
\ No newline at end of file
+}
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowGraphNodeElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowGraphNodeElement.scala
index 863a72d0e96..e3bf25d3956 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowGraphNodeElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstToWorkflowGraphNodeElement.scala
@@ -7,17 +7,20 @@ import common.validation.Checked._
 import wdl.model.draft3.elements._
 
 object AstToWorkflowGraphNodeElementConverterMaker {
-  private def astToWorkflowGraphNodeElement(astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent],
-                                    astNodeToCallElement: CheckedAtoB[GenericAstNode, CallElement],
-                                    astNodeToScatterElement: CheckedAtoB[GenericAstNode, ScatterElement],
-                                    astNodeToIfElement: CheckedAtoB[GenericAstNode, IfElement]
-                                   ): CheckedAtoB[GenericAst, WorkflowGraphElement] = CheckedAtoB.fromCheck { a: GenericAst => a.getName match {
-    case "Declaration" => astNodeToDeclarationContent(a).map(IntermediateValueDeclarationElement.fromContent)
-    case "Call" => astNodeToCallElement(a)
-    case "Scatter" => astNodeToScatterElement(a)
-    case "If" => astNodeToIfElement(a)
-    case other => s"No conversion defined for Ast with name $other to WorkflowGraphElement".invalidNelCheck
-  }}
+  private def astToWorkflowGraphNodeElement(
+    astNodeToDeclarationContent: CheckedAtoB[GenericAstNode, DeclarationContent],
+    astNodeToCallElement: CheckedAtoB[GenericAstNode, CallElement],
+    astNodeToScatterElement: CheckedAtoB[GenericAstNode, ScatterElement],
+    astNodeToIfElement: CheckedAtoB[GenericAstNode, IfElement]
+  ): CheckedAtoB[GenericAst, WorkflowGraphElement] = CheckedAtoB.fromCheck { a: GenericAst =>
+    a.getName match {
+      case "Declaration" => astNodeToDeclarationContent(a).map(IntermediateValueDeclarationElement.fromContent)
+      case "Call" => astNodeToCallElement(a)
+      case "Scatter" => astNodeToScatterElement(a)
+      case "If" => astNodeToIfElement(a)
+      case other => s"No conversion defined for Ast with name $other to WorkflowGraphElement".invalidNelCheck
+    }
+  }
 }
 
 class AstToWorkflowGraphNodeElementConverterMaker() {
@@ -28,9 +31,10 @@ class AstToWorkflowGraphNodeElementConverterMaker() {
 
   val uninitializedMessage = NonEmptyList.fromListUnsafe(List(""))
 
-  implicit val astNodeToDeclarationContentFixed: CheckedAtoB[GenericAstNode, DeclarationContent] = CheckedAtoB.fromCheck { a =>
-    Either.fromOption(astNodeToDeclarationContent, uninitializedMessage) flatMap { c => c.run(a) }
-  }
+  implicit val astNodeToDeclarationContentFixed: CheckedAtoB[GenericAstNode, DeclarationContent] =
+    CheckedAtoB.fromCheck { a =>
+      Either.fromOption(astNodeToDeclarationContent, uninitializedMessage) flatMap { c => c.run(a) }
+    }
 
   implicit val astNodeToCallElementFixed: CheckedAtoB[GenericAstNode, CallElement] = CheckedAtoB.fromCheck { a =>
     Either.fromOption(astNodeToCallElement, uninitializedMessage) flatMap { c => c.run(a) }
@@ -48,5 +52,6 @@ class AstToWorkflowGraphNodeElementConverterMaker() {
     astNodeToDeclarationContentFixed,
     astNodeToCallElementFixed,
     astNodeToScatterElementFixed,
-    astNodeToIfElementFixed)
+    astNodeToIfElementFixed
+  )
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/GenericAst.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/GenericAst.scala
index 903371b59cd..190c6118feb 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/GenericAst.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/GenericAst.scala
@@ -23,7 +23,8 @@ trait GenericAstNode {
 
   def firstTerminal: Option[GenericTerminal] = {
     def foldFunction(acc: Option[GenericTerminal], next: GenericTerminal): Option[GenericTerminal] = acc match {
-      case Some(t) if t.getLine > next.getLine || (t.getLine == next.getLine && t.getColumn > next.getColumn) => Some(next)
+      case Some(t) if t.getLine > next.getLine || (t.getLine == next.getLine && t.getColumn > next.getColumn) =>
+        Some(next)
       case None => Some(next)
       case _ => acc
     }
@@ -36,11 +37,10 @@ trait GenericAstNode {
   // all the information needed for downstream analysis phases. However, it turns out that
   // getting accurate information out of Hermes is not that simple. For now, we just
   // get the initial source line, which is -more or less- accurate.
-  def getSourceLine: Option[Int] = {
-    firstTerminal map {t => t.getLine }
-  }
+  def getSourceLine: Option[Int] =
+    firstTerminal map { t => t.getLine }
 
-  def lineAndColumnString = firstTerminal map { t => s" at line ${t.getLine} column ${t.getColumn}"} getOrElse("")
+  def lineAndColumnString = firstTerminal map { t => s" at line ${t.getLine} column ${t.getColumn}" } getOrElse ""
 }
 
 trait GenericAst extends GenericAstNode {
@@ -48,13 +48,12 @@ trait GenericAst extends GenericAstNode {
   def getAttributes: Map[String, GenericAstNode]
   def getName: String
 
-  private def getAttributeAsAstNodeVector(attr: String, optional: Boolean): Checked[Vector[GenericAstNode]] = {
+  private def getAttributeAsAstNodeVector(attr: String, optional: Boolean): Checked[Vector[GenericAstNode]] =
     Option(getAttribute(attr)) match {
       case Some(attributeNode) => attributeNode.astListAsVector
       case None if optional => Vector.empty.validNelCheck
       case None => s"No expected attribute '$attr' found".invalidNelCheck
     }
-  }
 
   /**
     * Will get an attribute on this Ast as an AstNode and then convert that into a single element of
@@ -71,7 +70,9 @@ trait GenericAst extends GenericAstNode {
     * Will get an attribute on this Ast as an AstList and then convert that into a vector of Ast
     * @param attr The attribute to read from this Ast
     */
-  def getAttributeAsVector[A](attr: String, optional: Boolean = false)(implicit toA: CheckedAtoB[GenericAstNode, A]): Checked[Vector[A]] = {
+  def getAttributeAsVector[A](attr: String, optional: Boolean = false)(implicit
+    toA: CheckedAtoB[GenericAstNode, A]
+  ): Checked[Vector[A]] =
     for {
       asVector <- getAttributeAsAstNodeVector(attr, optional)
       // This toValidated/toEither dance is necessary to
@@ -79,13 +80,14 @@ trait GenericAst extends GenericAstNode {
       // (2) convert back into a Checked for the flatMap
       result <- asVector.traverse(item => toA.run(item).toValidated).toEither
     } yield result
-  }
 
   /**
     * Will get an attribute on this Ast as an AstList and then convert that into a vector of Ast
     * @param attr The attribute to read from this Ast
     */
-  def getAttributeAsVectorF[A](attr: String, optional: Boolean = false)(toA: GenericAstNode => Checked[A]): Checked[Vector[A]] = {
+  def getAttributeAsVectorF[A](attr: String, optional: Boolean = false)(
+    toA: GenericAstNode => Checked[A]
+  ): Checked[Vector[A]] =
     for {
       asVector <- getAttributeAsAstNodeVector(attr, optional)
       // This toValidated/toEither dance is necessary to
@@ -93,17 +95,15 @@ trait GenericAst extends GenericAstNode {
       // (2) convert back into a Checked for the flatMap
       result <- asVector.traverse(item => toA(item).toValidated).toEither
     } yield result
-  }
 
   /**
     * Gets an attribute on this Ast as an Optional Ast, returns an empty Option if the attribute is empty.
     */
-  def getAttributeAsOptional[A](attr: String)(implicit toA: CheckedAtoB[GenericAstNode, A]): Checked[Option[A]] =  {
+  def getAttributeAsOptional[A](attr: String)(implicit toA: CheckedAtoB[GenericAstNode, A]): Checked[Option[A]] =
     Option(getAttribute(attr)) match {
       case None => None.validNelCheck
       case Some(attribute) => toA.run(attribute).map(Option.apply)
     }
-  }
 }
 
 trait GenericAstList extends GenericAstNode {
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/ast2wdlom.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/ast2wdlom.scala
index 7c7615332be..f9a7085a6fe 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/ast2wdlom.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/ast2wdlom.scala
@@ -20,10 +20,14 @@ package object ast2wdlom {
     case other => s"Cannot convert from AstNode type '${other.getClass.getSimpleName}' into Terminal".invalidNelCheck
   }
 
-  implicit val astNodeToString: CheckedAtoB[GenericAstNode, String] = CheckedAtoB.fromCheck { a: GenericAstNode => a match {
-    case t: GenericTerminal => t.getSourceString.validNelCheck
-    case a: GenericAst => s"Cannot convert Ast of type ${a.getName} into String. Did you want one of its attributes (${a.getAttributes.keys.mkString(", ")})?".invalidNelCheck
-    case other: GenericAstNode => s"Cannot convert ${other.getClass.getSimpleName} into String".invalidNelCheck
-  }}
+  implicit val astNodeToString: CheckedAtoB[GenericAstNode, String] = CheckedAtoB.fromCheck { a: GenericAstNode =>
+    a match {
+      case t: GenericTerminal => t.getSourceString.validNelCheck
+      case a: GenericAst =>
+        s"Cannot convert Ast of type ${a.getName} into String. Did you want one of its attributes (${a.getAttributes.keys
+            .mkString(", ")})?".invalidNelCheck
+      case other: GenericAstNode => s"Cannot convert ${other.getClass.getSimpleName} into String".invalidNelCheck
+    }
+  }
 
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/BinaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/BinaryOperatorEvaluators.scala
index 46ef93f9374..780acd737d4 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/BinaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/BinaryOperatorEvaluators.scala
@@ -22,9 +22,9 @@ object BinaryOperatorEvaluators {
   implicit val remainderEvaluator: ExpressionValueConsumer[Remainder] = forOperation
 
   private def forOperation[A <: BinaryOperation] = new ExpressionValueConsumer[A] {
-    override def expressionConsumedValueHooks(a: A)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: A)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       a.left.expressionConsumedValueHooks ++ a.right.expressionConsumedValueHooks
-    }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/EngineFunctionEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/EngineFunctionEvaluators.scala
index 52c0024f0d4..772e158bc0b 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/EngineFunctionEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/EngineFunctionEvaluators.scala
@@ -7,15 +7,19 @@ import wdl.model.draft3.graph.ExpressionValueConsumer.ops._
 
 object EngineFunctionEvaluators {
 
-  implicit val stdoutElementValueConsumer: ExpressionValueConsumer[StdoutElement.type] = new ExpressionValueConsumer[ExpressionElement.StdoutElement.type] {
-    override def expressionConsumedValueHooks(a: ExpressionElement.StdoutElement.type)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = Set.empty
-  }
+  implicit val stdoutElementValueConsumer: ExpressionValueConsumer[StdoutElement.type] =
+    new ExpressionValueConsumer[ExpressionElement.StdoutElement.type] {
+      override def expressionConsumedValueHooks(a: ExpressionElement.StdoutElement.type)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] = Set.empty
+    }
 
-  implicit val stderrElementValueConsumer: ExpressionValueConsumer[StderrElement.type] = new ExpressionValueConsumer[ExpressionElement.StderrElement.type] {
-    override def expressionConsumedValueHooks(a: ExpressionElement.StderrElement.type)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = Set.empty
-  }
+  implicit val stderrElementValueConsumer: ExpressionValueConsumer[StderrElement.type] =
+    new ExpressionValueConsumer[ExpressionElement.StderrElement.type] {
+      override def expressionConsumedValueHooks(a: ExpressionElement.StderrElement.type)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] = Set.empty
+    }
 
   implicit val readLinesValueConsumer: ExpressionValueConsumer[ReadLines] = forOneParamFunction
   implicit val readTsvValueConsumer: ExpressionValueConsumer[ReadTsv] = forOneParamFunction
@@ -54,29 +58,33 @@ object EngineFunctionEvaluators {
   implicit val joinValueConsumer: ExpressionValueConsumer[Sep] = forTwoParamFunction
 
   implicit val subFunctionValueConsumer: ExpressionValueConsumer[Sub] = new ExpressionValueConsumer[Sub] {
-    override def expressionConsumedValueHooks(a: Sub)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(
+      a: Sub
+    )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
       a.input.expressionConsumedValueHooks ++ a.pattern.expressionConsumedValueHooks ++ a.replace.expressionConsumedValueHooks
-    }
   }
 
-  private def forOneParamFunction[A <: OneParamFunctionCallElement]: ExpressionValueConsumer[A] = new ExpressionValueConsumer[A] {
-    override def expressionConsumedValueHooks(a: A)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = a.param.expressionConsumedValueHooks
-  }
+  private def forOneParamFunction[A <: OneParamFunctionCallElement]: ExpressionValueConsumer[A] =
+    new ExpressionValueConsumer[A] {
+      override def expressionConsumedValueHooks(a: A)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] = a.param.expressionConsumedValueHooks
+    }
 
-  private def forOneOrTwoParamFunction[A <: OneOrTwoParamFunctionCallElement]: ExpressionValueConsumer[A] = new ExpressionValueConsumer[A] {
-    override def expressionConsumedValueHooks(a: A)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
-      a.firstParam.expressionConsumedValueHooks ++
-        a.secondParam.toSet.flatMap { secondParam: ExpressionElement => secondParam.expressionConsumedValueHooks }
+  private def forOneOrTwoParamFunction[A <: OneOrTwoParamFunctionCallElement]: ExpressionValueConsumer[A] =
+    new ExpressionValueConsumer[A] {
+      override def expressionConsumedValueHooks(a: A)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        a.firstParam.expressionConsumedValueHooks ++
+          a.secondParam.toSet.flatMap { secondParam: ExpressionElement => secondParam.expressionConsumedValueHooks }
     }
-  }
 
-  private def forTwoParamFunction[A <: TwoParamFunctionCallElement]: ExpressionValueConsumer[A] = new ExpressionValueConsumer[A] {
-    override def expressionConsumedValueHooks(a: A)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
-      a.arg1.expressionConsumedValueHooks ++ a.arg2.expressionConsumedValueHooks
+  private def forTwoParamFunction[A <: TwoParamFunctionCallElement]: ExpressionValueConsumer[A] =
+    new ExpressionValueConsumer[A] {
+      override def expressionConsumedValueHooks(a: A)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        a.arg1.expressionConsumedValueHooks ++ a.arg2.expressionConsumedValueHooks
     }
-  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/LiteralEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/LiteralEvaluators.scala
index c85a33854d3..e58096c59a0 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/LiteralEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/LiteralEvaluators.scala
@@ -7,47 +7,64 @@ import wdl.model.draft3.graph.{ExpressionValueConsumer, UnlinkedConsumedValueHoo
 
 object LiteralEvaluators {
 
-  implicit val expressionElementSetUnlinkedValueConsumer: ExpressionValueConsumer[Set[ExpressionElement]] = new ExpressionValueConsumer[Set[ExpressionElement]] {
-    override def expressionConsumedValueHooks(elements: Set[ExpressionElement])(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
-      elements.flatMap { e: ExpressionElement => expressionValueConsumer.expressionConsumedValueHooks(e)(expressionValueConsumer) }
-  }
+  implicit val expressionElementSetUnlinkedValueConsumer: ExpressionValueConsumer[Set[ExpressionElement]] =
+    new ExpressionValueConsumer[Set[ExpressionElement]] {
+      override def expressionConsumedValueHooks(
+        elements: Set[ExpressionElement]
+      )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
+        elements.flatMap { e: ExpressionElement =>
+          expressionValueConsumer.expressionConsumedValueHooks(e)(expressionValueConsumer)
+        }
+    }
 
   implicit val kvPairUnlinkedValueConsumer: ExpressionValueConsumer[KvPair] = new ExpressionValueConsumer[KvPair] {
-    override def expressionConsumedValueHooks(a: ExpressionElement.KvPair)(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
+    override def expressionConsumedValueHooks(a: ExpressionElement.KvPair)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       expressionValueConsumer.expressionConsumedValueHooks(a.value)(expressionValueConsumer)
   }
 
-  implicit val objectLiteralUnlinkedValueConsumer: ExpressionValueConsumer[ObjectLiteral] = new ExpressionValueConsumer[ObjectLiteral] {
-    override def expressionConsumedValueHooks(o: ObjectLiteral)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
-      o.elements.values.toSet[ExpressionElement].expressionConsumedValueHooks
-  }
+  implicit val objectLiteralUnlinkedValueConsumer: ExpressionValueConsumer[ObjectLiteral] =
+    new ExpressionValueConsumer[ObjectLiteral] {
+      override def expressionConsumedValueHooks(o: ObjectLiteral)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        o.elements.values.toSet[ExpressionElement].expressionConsumedValueHooks
+    }
 
-  implicit val mapLiteralUnlinkedValueConsumer: ExpressionValueConsumer[MapLiteral] = new ExpressionValueConsumer[MapLiteral] {
-    override def expressionConsumedValueHooks(m: MapLiteral)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
-      m.elements.keys.toSet[ExpressionElement].expressionConsumedValueHooks ++
-        m.elements.values.toSet[ExpressionElement].expressionConsumedValueHooks
-  }
+  implicit val mapLiteralUnlinkedValueConsumer: ExpressionValueConsumer[MapLiteral] =
+    new ExpressionValueConsumer[MapLiteral] {
+      override def expressionConsumedValueHooks(m: MapLiteral)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        m.elements.keys.toSet[ExpressionElement].expressionConsumedValueHooks ++
+          m.elements.values.toSet[ExpressionElement].expressionConsumedValueHooks
+    }
 
-  implicit val pairLiteralUnlinkedValueConsumer: ExpressionValueConsumer[PairLiteral] = new ExpressionValueConsumer[PairLiteral] {
-    override def expressionConsumedValueHooks(p: PairLiteral)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
-      p.left.expressionConsumedValueHooks ++ p.right.expressionConsumedValueHooks
-  }
+  implicit val pairLiteralUnlinkedValueConsumer: ExpressionValueConsumer[PairLiteral] =
+    new ExpressionValueConsumer[PairLiteral] {
+      override def expressionConsumedValueHooks(p: PairLiteral)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        p.left.expressionConsumedValueHooks ++ p.right.expressionConsumedValueHooks
+    }
 
-  implicit val arrayLiteralUnlinkedValueConsumer: ExpressionValueConsumer[ArrayLiteral] = new ExpressionValueConsumer[ArrayLiteral] {
-    override def expressionConsumedValueHooks(a: ArrayLiteral)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
-      a.elements.toSet[ExpressionElement].expressionConsumedValueHooks
-  }
+  implicit val arrayLiteralUnlinkedValueConsumer: ExpressionValueConsumer[ArrayLiteral] =
+    new ExpressionValueConsumer[ArrayLiteral] {
+      override def expressionConsumedValueHooks(a: ArrayLiteral)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        a.elements.toSet[ExpressionElement].expressionConsumedValueHooks
+    }
 
-  implicit val stringExpressionUnlinkedValueConsumer: ExpressionValueConsumer[StringExpression] = new ExpressionValueConsumer[StringExpression] {
-    override def expressionConsumedValueHooks(a: StringExpression)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
-      a.pieces.flatMap {
-        case StringPlaceholder(expr) => expr.expressionConsumedValueHooks.toList
-        case _ => List.empty
-      }.toSet
-  }
+  implicit val stringExpressionUnlinkedValueConsumer: ExpressionValueConsumer[StringExpression] =
+    new ExpressionValueConsumer[StringExpression] {
+      override def expressionConsumedValueHooks(
+        a: StringExpression
+      )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
+        a.pieces.flatMap {
+          case StringPlaceholder(expr) => expr.expressionConsumedValueHooks.toList
+          case _ => List.empty
+        }.toSet
+    }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/LookupEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/LookupEvaluators.scala
index 41b9536f694..24024751adc 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/LookupEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/LookupEvaluators.scala
@@ -3,34 +3,41 @@ package wdl.transforms.base.linking.expression.consumed
 import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement._
 import wdl.model.draft3.graph.ExpressionValueConsumer.ops._
-import wdl.model.draft3.graph.{ExpressionValueConsumer, UnlinkedCallOutputOrIdentifierAndMemberAccessHook, UnlinkedConsumedValueHook, UnlinkedIdentifierHook}
+import wdl.model.draft3.graph.{
+  ExpressionValueConsumer,
+  UnlinkedCallOutputOrIdentifierAndMemberAccessHook,
+  UnlinkedConsumedValueHook,
+  UnlinkedIdentifierHook
+}
 
 object LookupEvaluators {
 
-  implicit val identifierLookupUnlinkedValueConsumer: ExpressionValueConsumer[IdentifierLookup] = new ExpressionValueConsumer[IdentifierLookup] {
-    override def expressionConsumedValueHooks(a: IdentifierLookup)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
-      Set[UnlinkedConsumedValueHook](UnlinkedIdentifierHook(a.identifier))
-  }
+  implicit val identifierLookupUnlinkedValueConsumer: ExpressionValueConsumer[IdentifierLookup] =
+    new ExpressionValueConsumer[IdentifierLookup] {
+      override def expressionConsumedValueHooks(a: IdentifierLookup)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        Set[UnlinkedConsumedValueHook](UnlinkedIdentifierHook(a.identifier))
+    }
 
   implicit val identifierMemberAccessUnlinkedValueConsumer = new ExpressionValueConsumer[IdentifierMemberAccess] {
-    override def expressionConsumedValueHooks(a: IdentifierMemberAccess)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: IdentifierMemberAccess)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       Set[UnlinkedConsumedValueHook](UnlinkedCallOutputOrIdentifierAndMemberAccessHook(a.first, a.second))
-    }
   }
 
   implicit val expressionMemberAccessUnlinkedValueConsumer = new ExpressionValueConsumer[ExpressionMemberAccess] {
-    override def expressionConsumedValueHooks(a: ExpressionMemberAccess)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: ExpressionMemberAccess)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       a.expression.expressionConsumedValueHooks
-    }
   }
 
   implicit val indexAccessUnlinkedValueConsumer = new ExpressionValueConsumer[IndexAccess] {
-    override def expressionConsumedValueHooks(a: IndexAccess)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = {
+    override def expressionConsumedValueHooks(a: IndexAccess)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
       a.expressionElement.expressionConsumedValueHooks ++ a.index.expressionConsumedValueHooks
-    }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/TernaryIfEvaluator.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/TernaryIfEvaluator.scala
index b55d56c76ba..22d7df1a67a 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/TernaryIfEvaluator.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/TernaryIfEvaluator.scala
@@ -7,9 +7,11 @@ import wdl.model.draft3.graph.{ExpressionValueConsumer, UnlinkedConsumedValueHoo
 
 object TernaryIfEvaluator {
 
-  implicit val ternaryIfUnlinkedValueConsumer: ExpressionValueConsumer[TernaryIf] = new ExpressionValueConsumer[TernaryIf] {
-    override def expressionConsumedValueHooks(a: TernaryIf)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
-      a.condition.expressionConsumedValueHooks ++ a.ifTrue.expressionConsumedValueHooks ++ a.ifFalse.expressionConsumedValueHooks
-  }
+  implicit val ternaryIfUnlinkedValueConsumer: ExpressionValueConsumer[TernaryIf] =
+    new ExpressionValueConsumer[TernaryIf] {
+      override def expressionConsumedValueHooks(
+        a: TernaryIf
+      )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] =
+        a.condition.expressionConsumedValueHooks ++ a.ifTrue.expressionConsumedValueHooks ++ a.ifFalse.expressionConsumedValueHooks
+    }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/UnaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/UnaryOperatorEvaluators.scala
index d9ddcbb8495..1f642e43942 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/UnaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/consumed/UnaryOperatorEvaluators.scala
@@ -11,7 +11,8 @@ object UnaryOperatorEvaluators {
   implicit val unaryPlusEvaluator: ExpressionValueConsumer[UnaryPlus] = forOperation
 
   private def forOperation[A <: UnaryOperation] = new ExpressionValueConsumer[A] {
-    override def expressionConsumedValueHooks(a: A)
-                                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): Set[UnlinkedConsumedValueHook] = a.argument.expressionConsumedValueHooks
+    override def expressionConsumedValueHooks(a: A)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] = a.argument.expressionConsumedValueHooks
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/BinaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/BinaryOperatorEvaluators.scala
index b138ed3b0d0..e6ab692f04b 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/BinaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/BinaryOperatorEvaluators.scala
@@ -28,11 +28,16 @@ object BinaryOperatorEvaluators {
   implicit val remainderEvaluator: FileEvaluator[Remainder] = forOperation(_.mod(_))
 
   private def forOperation[A <: BinaryOperation](op: (WomValue, WomValue) => Try[WomValue]) = new FileEvaluator[A] {
-    override def predictFilesNeededToEvaluate(a: A, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+    override def predictFilesNeededToEvaluate(a: A,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       (a.left.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
-        a.right.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)) mapN { _ ++ _ }
-    }
+       a.right.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
+      ) mapN { _ ++ _ }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala
index 498b04dbe87..11c687588a7 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala
@@ -17,13 +17,18 @@ import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.expressionElementWriter
 
 object EngineFunctionEvaluators {
 
-  private def evaluateToFile(forFunction: String, outermostElement: ExpressionElement, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, nestedElement: Option[ExpressionElement] = None)
-                            (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+  private def evaluateToFile(forFunction: String,
+                             outermostElement: ExpressionElement,
+                             inputs: Map[String, WomValue],
+                             ioFunctionSet: IoFunctionSet,
+                             nestedElement: Option[ExpressionElement] = None
+  )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
     // `IndexAccess` `ExpressionElement`s require recursion to look for contained `IdentifierLookup` or `IdentifierMemberAccess`.
     // After all `IndexAccess` elements have been traversed the original `outermostElement` should be evaluated for files.
     val elementToExamine = nestedElement getOrElse outermostElement
     (elementToExamine match {
-      case IndexAccess(expressionElement, _) => evaluateToFile(forFunction, outermostElement, inputs, ioFunctionSet, Option(expressionElement))
+      case IndexAccess(expressionElement, _) =>
+        evaluateToFile(forFunction, outermostElement, inputs, ioFunctionSet, Option(expressionElement))
       // If the specified identifier is not among the inputs there are no files to delocalize from this expression.
       case IdentifierLookup(identifier) if !inputs.contains(identifier) => Set.empty[WomFile].validNel
       case IdentifierMemberAccess(first, _, _) if !inputs.contains(first) => Set.empty[WomFile].validNel
@@ -35,59 +40,90 @@ object EngineFunctionEvaluators {
     }).contextualizeErrors(s"predict files needed to de-localize from '${outermostElement.toWdlV1}' for $forFunction")
   }
 
-  def singleParameterPassthroughFileEvaluator[A <: OneParamFunctionCallElement]: FileEvaluator[A] = new FileEvaluator[A] {
-    override def predictFilesNeededToEvaluate(a: A,
-                                              inputs: Map[String, WomValue],
-                                              ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement], valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
-      a.param.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
+  def singleParameterPassthroughFileEvaluator[A <: OneParamFunctionCallElement]: FileEvaluator[A] =
+    new FileEvaluator[A] {
+      override def predictFilesNeededToEvaluate(a: A,
+                                                inputs: Map[String, WomValue],
+                                                ioFunctionSet: IoFunctionSet,
+                                                coerceTo: WomType
+      )(implicit
+        fileEvaluator: FileEvaluator[ExpressionElement],
+        valueEvaluator: ValueEvaluator[ExpressionElement]
+      ): ErrorOr[Set[WomFile]] =
+        a.param.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
     }
-  }
 
-  def singleParameterEvaluateToFileFileEvaluator[A <: OneParamFunctionCallElement](functionName: String): FileEvaluator[A] = new FileEvaluator[A] {
+  def singleParameterEvaluateToFileFileEvaluator[A <: OneParamFunctionCallElement](
+    functionName: String
+  ): FileEvaluator[A] = new FileEvaluator[A] {
     override def predictFilesNeededToEvaluate(a: A,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement], valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       evaluateToFile(functionName, a.param, inputs, ioFunctionSet)
-    }
   }
 
   implicit val stdoutFunctionEvaluator: FileEvaluator[StdoutElement.type] = new FileEvaluator[StdoutElement.type] {
-    override def predictFilesNeededToEvaluate(a: ExpressionElement.StdoutElement.type, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] =
+    override def predictFilesNeededToEvaluate(a: ExpressionElement.StdoutElement.type,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       Set.empty[WomFile].validNel
   }
 
   implicit val stderrFunctionEvaluator: FileEvaluator[StderrElement.type] = new FileEvaluator[StderrElement.type] {
-    override def predictFilesNeededToEvaluate(a: ExpressionElement.StderrElement.type, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] =
+    override def predictFilesNeededToEvaluate(a: ExpressionElement.StderrElement.type,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       Set.empty[WomFile].validNel
   }
 
-  implicit val readLinesFunctionEvaluator: FileEvaluator[ReadLines] = singleParameterEvaluateToFileFileEvaluator("read_lines")
+  implicit val readLinesFunctionEvaluator: FileEvaluator[ReadLines] = singleParameterEvaluateToFileFileEvaluator(
+    "read_lines"
+  )
 
   implicit val readTsvFunctionEvaluator: FileEvaluator[ReadTsv] = singleParameterEvaluateToFileFileEvaluator("read_tsv")
 
   implicit val readMapFunctionEvaluator: FileEvaluator[ReadMap] = singleParameterEvaluateToFileFileEvaluator("read_map")
 
-  implicit val readObjectFunctionEvaluator: FileEvaluator[ReadObject] = singleParameterEvaluateToFileFileEvaluator("read_object")
+  implicit val readObjectFunctionEvaluator: FileEvaluator[ReadObject] = singleParameterEvaluateToFileFileEvaluator(
+    "read_object"
+  )
 
-  implicit val readObjectsFunctionEvaluator: FileEvaluator[ReadObjects] = singleParameterEvaluateToFileFileEvaluator("read_objects")
+  implicit val readObjectsFunctionEvaluator: FileEvaluator[ReadObjects] = singleParameterEvaluateToFileFileEvaluator(
+    "read_objects"
+  )
 
-  implicit val readJsonFunctionEvaluator: FileEvaluator[ReadJson] = singleParameterEvaluateToFileFileEvaluator("read_json")
+  implicit val readJsonFunctionEvaluator: FileEvaluator[ReadJson] = singleParameterEvaluateToFileFileEvaluator(
+    "read_json"
+  )
 
   implicit val readIntFunctionEvaluator: FileEvaluator[ReadInt] = singleParameterEvaluateToFileFileEvaluator("read_int")
 
-  implicit val readStringFunctionEvaluator: FileEvaluator[ReadString] = singleParameterEvaluateToFileFileEvaluator("read_string")
+  implicit val readStringFunctionEvaluator: FileEvaluator[ReadString] = singleParameterEvaluateToFileFileEvaluator(
+    "read_string"
+  )
 
-  implicit val readFloatFunctionEvaluator: FileEvaluator[ReadFloat] = singleParameterEvaluateToFileFileEvaluator("read_float")
+  implicit val readFloatFunctionEvaluator: FileEvaluator[ReadFloat] = singleParameterEvaluateToFileFileEvaluator(
+    "read_float"
+  )
 
-  implicit val readBooleanFunctionEvaluator: FileEvaluator[ReadBoolean] = singleParameterEvaluateToFileFileEvaluator("read_boolean")
+  implicit val readBooleanFunctionEvaluator: FileEvaluator[ReadBoolean] = singleParameterEvaluateToFileFileEvaluator(
+    "read_boolean"
+  )
 
   implicit val writeLinesFunctionEvaluator: FileEvaluator[WriteLines] = singleParameterPassthroughFileEvaluator
 
@@ -122,28 +158,46 @@ object EngineFunctionEvaluators {
   implicit val roundFunctionEvaluator: FileEvaluator[Round] = singleParameterPassthroughFileEvaluator
 
   implicit val globFunctionEvaluator: FileEvaluator[Glob] = new FileEvaluator[Glob] {
-    override def predictFilesNeededToEvaluate(a: Glob, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+    override def predictFilesNeededToEvaluate(a: Glob,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       a.param.evaluateValue(inputs, ioFunctionSet, None) flatMap {
         case EvaluatedValue(p: WomPrimitive, _) => Set[WomFile](WomGlobFile(p.valueString)).validNel
-        case other => s"Could not predict files to delocalize from '$a' for 'glob'. Expected a primitive but got ${other.getClass.getSimpleName}".invalidNel
+        case other =>
+          s"Could not predict files to delocalize from '$a' for 'glob'. Expected a primitive but got ${other.getClass.getSimpleName}".invalidNel
       }
-    }
   }
 
   implicit val sizeFunctionEvaluator: FileEvaluator[Size] = new FileEvaluator[Size] {
-    override def predictFilesNeededToEvaluate(a: Size, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] =
+    override def predictFilesNeededToEvaluate(a: Size,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       (evaluateToFile("size", a.file, inputs, ioFunctionSet): ErrorOr[Set[WomFile]],
-        a.unit.fold(Set.empty[WomFile].validNel: ErrorOr[Set[WomFile]])(_.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo))) mapN { _ ++ _ }
+       a.unit.fold(Set.empty[WomFile].validNel: ErrorOr[Set[WomFile]])(
+         _.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
+       )
+      ) mapN { _ ++ _ }
   }
 
   implicit val basenameFunctionEvaluator: FileEvaluator[Basename] = new FileEvaluator[Basename] {
-    override def predictFilesNeededToEvaluate(a: Basename, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] =
+    override def predictFilesNeededToEvaluate(a: Basename,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       Set.empty[WomFile].validNel
   }
 
@@ -151,11 +205,14 @@ object EngineFunctionEvaluators {
     override def predictFilesNeededToEvaluate(a: A,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] =
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       (a.arg1.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
-        a.arg2.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)) mapN { _ ++ _ }
+       a.arg2.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
+      ) mapN { _ ++ _ }
   }
 
   implicit val zipFunctionEvaluator: FileEvaluator[Zip] = twoParameterFunctionPassthroughFileEvaluator[Zip]
@@ -163,11 +220,17 @@ object EngineFunctionEvaluators {
   implicit val prefixFunctionEvaluator: FileEvaluator[Prefix] = twoParameterFunctionPassthroughFileEvaluator[Prefix]
 
   implicit val subFunctionEvaluator: FileEvaluator[Sub] = new FileEvaluator[Sub] {
-    override def predictFilesNeededToEvaluate(a: Sub, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] =
+    override def predictFilesNeededToEvaluate(a: Sub,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       (a.pattern.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
-        a.input.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
-        a.replace.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)) mapN { _ ++ _ ++ _ }
+       a.input.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
+       a.replace.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
+      ) mapN { _ ++ _ ++ _ }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/LiteralEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/LiteralEvaluators.scala
index 309ff83b618..db494c27bfa 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/LiteralEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/LiteralEvaluators.scala
@@ -14,22 +14,27 @@ import wom.types.{WomCompositeType, WomSingleFileType, WomType}
 import wom.values.{WomFile, WomSingleFile, WomValue}
 
 object LiteralEvaluators {
-  implicit val primitiveValueEvaluator: FileEvaluator[PrimitiveLiteralExpressionElement] = new FileEvaluator[PrimitiveLiteralExpressionElement] {
-    override def predictFilesNeededToEvaluate(a: PrimitiveLiteralExpressionElement,
-                                              inputs: Map[String, WomValue],
-                                              ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = Set.empty[WomFile].validNel
-  }
+  implicit val primitiveValueEvaluator: FileEvaluator[PrimitiveLiteralExpressionElement] =
+    new FileEvaluator[PrimitiveLiteralExpressionElement] {
+      override def predictFilesNeededToEvaluate(a: PrimitiveLiteralExpressionElement,
+                                                inputs: Map[String, WomValue],
+                                                ioFunctionSet: IoFunctionSet,
+                                                coerceTo: WomType
+      )(implicit
+        fileEvaluator: FileEvaluator[ExpressionElement],
+        valueEvaluator: ValueEvaluator[ExpressionElement]
+      ): ErrorOr[Set[WomFile]] = Set.empty[WomFile].validNel
+    }
 
   implicit val stringLiteralEvaluator: FileEvaluator[StringLiteral] = new FileEvaluator[StringLiteral] {
     override def predictFilesNeededToEvaluate(a: StringLiteral,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = coerceTo match {
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] = coerceTo match {
       case WomSingleFileType => Set[WomFile](WomSingleFile(a.value)).validNel
       case _ => Set.empty[WomFile].validNel
     }
@@ -39,9 +44,11 @@ object LiteralEvaluators {
     override def predictFilesNeededToEvaluate(a: ObjectLiteral,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] = {
       def filesInObjectField(fieldAndWomTypeTuple: (String, WomType)): ErrorOr[Set[WomFile]] = {
         val (field, womType) = fieldAndWomTypeTuple
         a.elements.get(field) match {
@@ -52,7 +59,10 @@ object LiteralEvaluators {
 
       coerceTo match {
         case WomCompositeType(mapping, _) => mapping.toList.traverse(filesInObjectField).map(_.flatten.toSet)
-        case _ => a.elements.values.toList.traverse(_.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)).map(_.toSet.flatten)
+        case _ =>
+          a.elements.values.toList
+            .traverse(_.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo))
+            .map(_.toSet.flatten)
       }
     }
   }
@@ -61,34 +71,40 @@ object LiteralEvaluators {
     override def predictFilesNeededToEvaluate(a: MapLiteral,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
-      a.elements.toList.flatMap { case (x,y) => List(x, y) }.traverse(_.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)).map(_.toSet.flatten)
-    }
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
+      a.elements.toList
+        .flatMap { case (x, y) => List(x, y) }
+        .traverse(_.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo))
+        .map(_.toSet.flatten)
   }
 
   implicit val arrayLiteralEvaluator: FileEvaluator[ArrayLiteral] = new FileEvaluator[ArrayLiteral] {
     override def predictFilesNeededToEvaluate(a: ArrayLiteral,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       a.elements.toList.traverse(_.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)).map(_.toSet.flatten)
-    }
   }
 
   implicit val pairLiteralEvaluator: FileEvaluator[PairLiteral] = new FileEvaluator[PairLiteral] {
     override def predictFilesNeededToEvaluate(a: PairLiteral,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       (a.left.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
-        a.right.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)) mapN { _ ++ _ }
-    }
+       a.right.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
+      ) mapN { _ ++ _ }
   }
 }
-
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/LookupEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/LookupEvaluators.scala
index 586fe7a0cf1..390edda3c9e 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/LookupEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/LookupEvaluators.scala
@@ -17,39 +17,51 @@ object LookupEvaluators {
     override def predictFilesNeededToEvaluate(a: IdentifierLookup,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] =
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       Set.empty[WomFile].validNel
   }
 
-  implicit val expressionMemberAccessEvaluator: FileEvaluator[ExpressionMemberAccess] = new FileEvaluator[ExpressionMemberAccess] {
-    override def predictFilesNeededToEvaluate(a: ExpressionMemberAccess,
-                                              inputs: Map[String, WomValue],
-                                              ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
-      a.expression.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
+  implicit val expressionMemberAccessEvaluator: FileEvaluator[ExpressionMemberAccess] =
+    new FileEvaluator[ExpressionMemberAccess] {
+      override def predictFilesNeededToEvaluate(a: ExpressionMemberAccess,
+                                                inputs: Map[String, WomValue],
+                                                ioFunctionSet: IoFunctionSet,
+                                                coerceTo: WomType
+      )(implicit
+        fileEvaluator: FileEvaluator[ExpressionElement],
+        valueEvaluator: ValueEvaluator[ExpressionElement]
+      ): ErrorOr[Set[WomFile]] =
+        a.expression.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
     }
-  }
 
-  implicit val identifierMemberAccessEvaluator: FileEvaluator[IdentifierMemberAccess] = new FileEvaluator[IdentifierMemberAccess] {
-    override def predictFilesNeededToEvaluate(a: IdentifierMemberAccess,
-                                              inputs: Map[String, WomValue],
-                                              ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] =
-      Set.empty[WomFile].validNel
-  }
+  implicit val identifierMemberAccessEvaluator: FileEvaluator[IdentifierMemberAccess] =
+    new FileEvaluator[IdentifierMemberAccess] {
+      override def predictFilesNeededToEvaluate(a: IdentifierMemberAccess,
+                                                inputs: Map[String, WomValue],
+                                                ioFunctionSet: IoFunctionSet,
+                                                coerceTo: WomType
+      )(implicit
+        fileEvaluator: FileEvaluator[ExpressionElement],
+        valueEvaluator: ValueEvaluator[ExpressionElement]
+      ): ErrorOr[Set[WomFile]] =
+        Set.empty[WomFile].validNel
+    }
 
   implicit val indexAccessFileEvaluator: FileEvaluator[IndexAccess] = new FileEvaluator[IndexAccess] {
-    override def predictFilesNeededToEvaluate(a: IndexAccess, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+    override def predictFilesNeededToEvaluate(a: IndexAccess,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       (a.expressionElement.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
-        a.index.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)) mapN { _ ++ _ }
-    }
+       a.index.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
+      ) mapN { _ ++ _ }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/TernaryIfEvaluator.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/TernaryIfEvaluator.scala
index 6b394abe810..ff42a04522c 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/TernaryIfEvaluator.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/TernaryIfEvaluator.scala
@@ -15,12 +15,14 @@ object TernaryIfEvaluator {
     override def predictFilesNeededToEvaluate(a: TernaryIf,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] = {
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       (a.condition.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
-        a.ifTrue.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
-        a.ifFalse.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)) mapN { _ ++ _ ++ _ }
-    }
+       a.ifTrue.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
+       a.ifFalse.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
+      ) mapN { _ ++ _ ++ _ }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/UnaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/UnaryOperatorEvaluators.scala
index 3a05cb4f1b2..00fde3a1c54 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/UnaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/UnaryOperatorEvaluators.scala
@@ -21,9 +21,11 @@ object UnaryOperatorEvaluators {
     override def predictFilesNeededToEvaluate(a: A,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
-                                              coerceTo: WomType)
-                                             (implicit fileEvaluator: FileEvaluator[ExpressionElement],
-                                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[WomFile]] =
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] =
       a.argument.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/package.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/package.scala
index ebc16cec2af..59f98ee63b5 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/package.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/package.scala
@@ -14,18 +14,22 @@ import wdl.model.draft3.graph.ExpressionValueConsumer.ops._
 
 package object expression {
 
-  implicit def expressionElementToWomExpression(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-                                                fileEvaluator: FileEvaluator[ExpressionElement],
-                                                typeEvaluator: TypeEvaluator[ExpressionElement],
-                                                valueEvaluator: ValueEvaluator[ExpressionElement]): WomExpressionMaker[ExpressionElement] = new WomExpressionMaker[ExpressionElement] {
+  implicit def expressionElementToWomExpression(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): WomExpressionMaker[ExpressionElement] = new WomExpressionMaker[ExpressionElement] {
     override def makeWomExpression(a: ExpressionElement,
                                    typeAliases: Map[String, WomType],
-                                   consumedValueLookup: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]): ErrorOr[WomExpression] = {
+                                   consumedValueLookup: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+    ): ErrorOr[WomExpression] = {
       val consumedValueHooks = a.expressionConsumedValueHooks
 
       val neededLinkedValues = consumedValueHooks.toList.traverse {
         case c if consumedValueLookup.contains(c) => (c -> consumedValueLookup(c)).validNel
-        case missing => s"Could not create WOM expression for '$a': Found no generated value for consumed value $missing".invalidNel
+        case missing =>
+          s"Could not create WOM expression for '$a': Found no generated value for consumed value $missing".invalidNel
       }
 
       neededLinkedValues flatMap { lookup => WdlomWomExpression.make(a, lookup.toMap) }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/BinaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/BinaryOperatorEvaluators.scala
index 03f5d6d77ba..c18a0aadc84 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/BinaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/BinaryOperatorEvaluators.scala
@@ -28,10 +28,11 @@ object BinaryOperatorEvaluators {
   implicit val remainderEvaluator: TypeEvaluator[Remainder] = forOperation(_.mod(_))
 
   private def forOperation[A <: BinaryOperation](op: (WomType, WomType) => Try[WomType]) = new TypeEvaluator[A] {
-    override def evaluateType(a: A, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
-      (a.left.evaluateType(linkedValues),
-        a.right.evaluateType(linkedValues)) flatMapN { (left, right) => op(left, right).toErrorOr }
-    }
+    override def evaluateType(a: A, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      (a.left.evaluateType(linkedValues), a.right.evaluateType(linkedValues)) flatMapN { (left, right) =>
+        op(left, right).toErrorOr
+      }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/EngineFunctionEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/EngineFunctionEvaluators.scala
index 6911708a322..8268cdaac72 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/EngineFunctionEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/EngineFunctionEvaluators.scala
@@ -17,232 +17,241 @@ import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.expressionElementWriter
 
 object EngineFunctionEvaluators {
 
-  implicit val stdoutFunctionEvaluator: TypeEvaluator[StdoutElement.type] = new TypeEvaluator[ExpressionElement.StdoutElement.type] {
-    override def evaluateType(a: ExpressionElement.StdoutElement.type, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
-      WomSingleFileType.validNel
+  implicit val stdoutFunctionEvaluator: TypeEvaluator[StdoutElement.type] =
+    new TypeEvaluator[ExpressionElement.StdoutElement.type] {
+      override def evaluateType(a: ExpressionElement.StdoutElement.type,
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+      )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
+        WomSingleFileType.validNel
     }
-  }
 
-  implicit val stderrFunctionEvaluator: TypeEvaluator[StderrElement.type] = new TypeEvaluator[ExpressionElement.StderrElement.type] {
-    override def evaluateType(a: ExpressionElement.StderrElement.type, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
-      WomSingleFileType.validNel
+  implicit val stderrFunctionEvaluator: TypeEvaluator[StderrElement.type] =
+    new TypeEvaluator[ExpressionElement.StderrElement.type] {
+      override def evaluateType(a: ExpressionElement.StderrElement.type,
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+      )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
+        WomSingleFileType.validNel
     }
-  }
 
   implicit val readLinesFunctionEvaluator: TypeEvaluator[ReadLines] = new TypeEvaluator[ReadLines] {
-    override def evaluateType(a: ReadLines, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ReadLines, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomArrayType(WomStringType))
-    }
   }
 
   implicit val readTsvFunctionEvaluator: TypeEvaluator[ReadTsv] = new TypeEvaluator[ReadTsv] {
-    override def evaluateType(a: ReadTsv, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ReadTsv, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomArrayType(WomArrayType(WomStringType)))
-    }
   }
 
   implicit val readMapFunctionEvaluator: TypeEvaluator[ReadMap] = new TypeEvaluator[ReadMap] {
-    override def evaluateType(a: ReadMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ReadMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomMapType(WomStringType, WomStringType))
-    }
   }
 
   implicit val readObjectFunctionEvaluator: TypeEvaluator[ReadObject] = new TypeEvaluator[ReadObject] {
-    override def evaluateType(a: ReadObject, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ReadObject, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomObjectType)
-    }
   }
 
   implicit val readObjectsFunctionEvaluator: TypeEvaluator[ReadObjects] = new TypeEvaluator[ReadObjects] {
-    override def evaluateType(a: ReadObjects, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ReadObjects, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomArrayType(WomObjectType))
-    }
   }
 
   implicit val readJsonFunctionEvaluator: TypeEvaluator[ReadJson] = new TypeEvaluator[ReadJson] {
-    override def evaluateType(a: ReadJson, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ReadJson, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       // we can't figure out the WomType of data without reading the file hence evaluate it to `WomAnyType`
       validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomAnyType)
-    }
   }
 
   implicit val readIntFunctionEvaluator: TypeEvaluator[ReadInt] = new TypeEvaluator[ReadInt] {
-    override def evaluateType(a: ReadInt, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ReadInt, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomIntegerType)
-    }
   }
 
   implicit val readStringFunctionEvaluator: TypeEvaluator[ReadString] = new TypeEvaluator[ReadString] {
-    override def evaluateType(a: ReadString, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ReadString, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomStringType)
-    }
   }
 
   implicit val readFloatFunctionEvaluator: TypeEvaluator[ReadFloat] = new TypeEvaluator[ReadFloat] {
-    override def evaluateType(a: ReadFloat, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ReadFloat, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomFloatType)
-    }
   }
 
   implicit val readBooleanFunctionEvaluator: TypeEvaluator[ReadBoolean] = new TypeEvaluator[ReadBoolean] {
-    override def evaluateType(a: ReadBoolean, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ReadBoolean, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomBooleanType)
-    }
   }
 
   implicit val writeLinesFunctionEvaluator: TypeEvaluator[WriteLines] = new TypeEvaluator[WriteLines] {
-    override def evaluateType(a: WriteLines, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: WriteLines, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomArrayType(WomStringType)).map(_ => WomSingleFileType)
-    }
   }
 
   implicit val writeTsvFunctionEvaluator: TypeEvaluator[WriteTsv] = new TypeEvaluator[WriteTsv] {
-    override def evaluateType(a: WriteTsv, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: WriteTsv, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomArrayType(WomArrayType(WomStringType))).map(_ => WomSingleFileType)
-    }
   }
 
   implicit val writeMapFunctionEvaluator: TypeEvaluator[WriteMap] = new TypeEvaluator[WriteMap] {
-    override def evaluateType(a: WriteMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: WriteMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)).map(_ => WomSingleFileType)
-    }
   }
 
   implicit val writeObjectFunctionEvaluator: TypeEvaluator[WriteObject] = new TypeEvaluator[WriteObject] {
-    override def evaluateType(a: WriteObject, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: WriteObject, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomObjectType).map(_ => WomSingleFileType)
-    }
   }
 
   implicit val writeObjectsFunctionEvaluator: TypeEvaluator[WriteObjects] = new TypeEvaluator[WriteObjects] {
-    override def evaluateType(a: WriteObjects, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: WriteObjects, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomArrayType(WomObjectType)).map(_ => WomSingleFileType)
-    }
   }
 
   implicit val writeJsonFunctionEvaluator: TypeEvaluator[WriteJson] = new TypeEvaluator[WriteJson] {
-    override def evaluateType(a: WriteJson, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: WriteJson, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       a.param.evaluateType(linkedValues).flatMap {
-        case v if WomBooleanType.isCoerceableFrom(v) ||
-          WomIntegerType.isCoerceableFrom(v) ||
-          WomFloatType.isCoerceableFrom(v) ||
-          WomStringType.isCoerceableFrom(v) ||
-          WomObjectType.isCoerceableFrom(v) ||
-          WomPairType(WomAnyType, WomAnyType).isCoerceableFrom(v) ||
-          WomArrayType(WomAnyType).isCoerceableFrom(v) => WomSingleFileType.validNel
-        case v => (s"Invalid parameter '${a.param}'. Valid input types are 'Boolean', 'String', 'Integer', 'Float', 'Object'," +
-          s" 'Pair[_, _]', 'Map[_, _] or 'Array[_]' but got '${v.friendlyName}'").invalidNel
+        case v
+            if WomBooleanType.isCoerceableFrom(v) ||
+              WomIntegerType.isCoerceableFrom(v) ||
+              WomFloatType.isCoerceableFrom(v) ||
+              WomStringType.isCoerceableFrom(v) ||
+              WomObjectType.isCoerceableFrom(v) ||
+              WomPairType(WomAnyType, WomAnyType).isCoerceableFrom(v) ||
+              WomArrayType(WomAnyType).isCoerceableFrom(v) =>
+          WomSingleFileType.validNel
+        case v =>
+          (s"Invalid parameter '${a.param}'. Valid input types are 'Boolean', 'String', 'Integer', 'Float', 'Object'," +
+            s" 'Pair[_, _]', 'Map[_, _] or 'Array[_]' but got '${v.friendlyName}'").invalidNel
       }
-    }
   }
 
   implicit val rangeFunctionEvaluator: TypeEvaluator[Range] = new TypeEvaluator[Range] {
-    override def evaluateType(a: Range, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Range, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomIntegerType).map(_ => WomArrayType(WomIntegerType))
-    }
   }
 
   implicit val transposeFunctionEvaluator: TypeEvaluator[Transpose] = new TypeEvaluator[Transpose] {
-    override def evaluateType(a: Transpose, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Transpose, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       a.param.evaluateType(linkedValues).flatMap {
         case a @ WomArrayType(WomArrayType(_)) => a.validNel
-        case foundType => s"Invalid parameter '${a.param}'. Expected 'Array[Array[_]]' but got '${foundType.stableName}'".invalidNel
+        case foundType =>
+          s"Invalid parameter '${a.param}'. Expected 'Array[Array[_]]' but got '${foundType.stableName}'".invalidNel
       }
-    }
   }
 
   implicit val lengthFunctionEvaluator: TypeEvaluator[Length] = new TypeEvaluator[Length] {
-    override def evaluateType(a: Length, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Length, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomArrayType(WomAnyType)).map(_ => WomIntegerType)
-    }
   }
 
   implicit val flattenFunctionEvaluator: TypeEvaluator[Flatten] = new TypeEvaluator[Flatten] {
-    override def evaluateType(a: Flatten, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Flatten, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       a.param.evaluateType(linkedValues).flatMap {
         case WomArrayType(inner @ WomArrayType(_)) => inner.validNel
-        case foundType => s"Invalid parameter '${a.param}'. Expected 'Array[Array[_]]' but got '${foundType.stableName}'".invalidNel
+        case foundType =>
+          s"Invalid parameter '${a.param}'. Expected 'Array[Array[_]]' but got '${foundType.stableName}'".invalidNel
       }
-    }
   }
 
   implicit val selectFirstFunctionEvaluator: TypeEvaluator[SelectFirst] = new TypeEvaluator[SelectFirst] {
-    override def evaluateType(a: SelectFirst, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: SelectFirst, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       a.param.evaluateType(linkedValues).flatMap {
         case WomArrayType(WomOptionalType(inner)) => inner.validNel
         case WomArrayType(alreadyNonOptional) => alreadyNonOptional.validNel
-        case foundType => s"Invalid parameter '${a.param}'. Expected an array of optional values (eg 'Array[X?]') but got '${foundType.stableName}'".invalidNel
+        case foundType =>
+          s"Invalid parameter '${a.param}'. Expected an array of optional values (eg 'Array[X?]') but got '${foundType.stableName}'".invalidNel
       }
-    }
   }
 
   implicit val selectAllFunctionEvaluator: TypeEvaluator[SelectAll] = new TypeEvaluator[SelectAll] {
-    override def evaluateType(a: SelectAll, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: SelectAll, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       a.param.evaluateType(linkedValues).flatMap {
         case WomArrayType(WomOptionalType(inner)) => WomArrayType(inner).validNel
         case alreadyNonOptional: WomArrayType => alreadyNonOptional.validNel
-        case foundType => s"Invalid parameter '${a.param}'. Expected an array of optional values (eg 'Array[X?]') but got '${foundType.stableName}'".invalidNel
+        case foundType =>
+          s"Invalid parameter '${a.param}'. Expected an array of optional values (eg 'Array[X?]') but got '${foundType.stableName}'".invalidNel
       }
-    }
   }
 
   implicit val definedFunctionEvaluator: TypeEvaluator[Defined] = new TypeEvaluator[Defined] {
-    override def evaluateType(a: Defined, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Defined, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomOptionalType(WomAnyType)).map(_ => WomBooleanType)
-    }
   }
 
   implicit val floorFunctionEvaluator: TypeEvaluator[Floor] = new TypeEvaluator[Floor] {
-    override def evaluateType(a: Floor, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Floor, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomFloatType).map(_ => WomIntegerType)
-    }
   }
 
   implicit val ceilFunctionEvaluator: TypeEvaluator[Ceil] = new TypeEvaluator[Ceil] {
-    override def evaluateType(a: Ceil, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Ceil, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomFloatType).map(_ => WomIntegerType)
-    }
   }
 
   implicit val roundFunctionEvaluator: TypeEvaluator[Round] = new TypeEvaluator[Round] {
-    override def evaluateType(a: Round, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Round, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomFloatType).map(_ => WomIntegerType)
-    }
   }
 
   implicit val globFunctionTypeEvaluator: TypeEvaluator[Glob] = new TypeEvaluator[Glob] {
-    override def evaluateType(a: Glob, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Glob, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       validateParamType(a.param, linkedValues, WomStringType).map(_ => WomArrayType(WomSingleFileType))
-    }
   }
 
   implicit val sizeFunctionEvaluator: TypeEvaluator[Size] = new TypeEvaluator[Size] {
@@ -253,81 +262,94 @@ object EngineFunctionEvaluators {
       case _ => false
     }
 
-    override def evaluateType(a: Size, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Size, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = {
       val validatedSecondArg: ErrorOr[Unit] = a.secondParam match {
         case None => ().validNel
         case Some(arg) => validateParamType(arg, linkedValues, WomStringType).void
       }
       val validatedFirstArg: ErrorOr[Unit] = a.firstParam.evaluateType(linkedValues).flatMap {
         case t if suitableSizeType(t) => ().validNel
-        case other => s"Invalid first 'size' parameter. Expected File, File? Array[File] or Array[File?] but got ${other.stableName}".invalidNel
+        case other =>
+          s"Invalid first 'size' parameter. Expected File, File? Array[File] or Array[File?] but got ${other.stableName}".invalidNel
       }
       (validatedFirstArg, validatedSecondArg) mapN { (_, _) => WomFloatType }
     }
   }
 
   implicit val basenameFunctionEvaluator: TypeEvaluator[Basename] = new TypeEvaluator[Basename] {
-    override def evaluateType(a: Basename, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Basename, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = {
       val validatedSecondArg: ErrorOr[Unit] = a.secondParam match {
         case None => ().validNel
         case Some(arg) => validateParamType(arg, linkedValues, WomStringType).void
       }
 
-      (validateParamType(a.firstParam, linkedValues, WomSingleFileType),
-        validatedSecondArg) mapN { (_, _) => WomStringType }
+      (validateParamType(a.firstParam, linkedValues, WomSingleFileType), validatedSecondArg) mapN { (_, _) =>
+        WomStringType
+      }
     }
   }
 
-  private def crossOrZipType(arg1: ExpressionElement, arg2: ExpressionElement, linkedValues:  Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                            (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+  private def crossOrZipType(arg1: ExpressionElement,
+                             arg2: ExpressionElement,
+                             linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+  )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
     (arg1.evaluateType(linkedValues), arg2.evaluateType(linkedValues)) match {
       case (Valid(WomArrayType(left)), Valid(WomArrayType(right))) =>
         WomArrayType(WomPairType(left, right)).validNel
-      case (Valid(otherLeft), Valid(WomArrayType(_))) => s"Invalid left parameter '${arg1.toWdlV1}'. Expected Array type but got '${otherLeft.stableName}'".invalidNel
-      case (Valid(WomArrayType(_)), Valid(otherRight)) => s"Invalid right parameter '${arg2.toWdlV1}'. Expected Array type but got '${otherRight.stableName}'".invalidNel
-      case (Valid(otherLeft), Valid(otherRight)) => s"Invalid left and right parameters '(${arg1.toWdlV1}, ${arg2.toWdlV1})'. Expected two Array types but got '(${otherLeft.stableName}, ${otherRight.stableName})'".invalidNel
+      case (Valid(otherLeft), Valid(WomArrayType(_))) =>
+        s"Invalid left parameter '${arg1.toWdlV1}'. Expected Array type but got '${otherLeft.stableName}'".invalidNel
+      case (Valid(WomArrayType(_)), Valid(otherRight)) =>
+        s"Invalid right parameter '${arg2.toWdlV1}'. Expected Array type but got '${otherRight.stableName}'".invalidNel
+      case (Valid(otherLeft), Valid(otherRight)) =>
+        s"Invalid left and right parameters '(${arg1.toWdlV1}, ${arg2.toWdlV1})'. Expected two Array types but got '(${otherLeft.stableName}, ${otherRight.stableName})'".invalidNel
       // One or more are invalid, so mapN function won't actually ever run:
       case (otherLeft, otherRight) => (otherLeft, otherRight) mapN { (_, _) => WomNothingType }
     }
-  }
 
   implicit val zipFunctionEvaluator: TypeEvaluator[Zip] = new TypeEvaluator[Zip] {
-    override def evaluateType(a: Zip, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Zip, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       crossOrZipType(a.arg1, a.arg2, linkedValues)
-    }
   }
   implicit val crossFunctionEvaluator: TypeEvaluator[Cross] = new TypeEvaluator[Cross] {
-    override def evaluateType(a: Cross, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Cross, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       crossOrZipType(a.arg1, a.arg2, linkedValues)
-    }
   }
 
   implicit val prefixFunctionEvaluator: TypeEvaluator[Prefix] = new TypeEvaluator[Prefix] {
-    override def evaluateType(a: Prefix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: Prefix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       (validateParamType(a.prefix, linkedValues, WomStringType),
-        validateParamType(a.array, linkedValues, WomArrayType(WomStringType))
+       validateParamType(a.array, linkedValues, WomArrayType(WomStringType))
       ) mapN { (_, _) => WomArrayType(WomStringType) }
-    }
   }
 
   implicit val subFunctionEvaluator: TypeEvaluator[Sub] = new TypeEvaluator[Sub] {
-    override def evaluateType(a: Sub, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
-
+    override def evaluateType(a: Sub, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       (validateParamType(a.input, linkedValues, WomSingleFileType),
-        validateParamType(a.pattern, linkedValues, WomSingleFileType),
-        validateParamType(a.replace, linkedValues, WomSingleFileType)) mapN { (_, _, _) => WomStringType }
-    }
+       validateParamType(a.pattern, linkedValues, WomSingleFileType),
+       validateParamType(a.replace, linkedValues, WomSingleFileType)
+      ) mapN { (_, _, _) => WomStringType }
   }
 
-  def validateParamType(param: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle], expectedType: WomType)
-                               (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+  def validateParamType(param: ExpressionElement,
+                        linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                        expectedType: WomType
+  )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
     param.evaluateType(linkedValues).flatMap { foundType =>
-      if (expectedType.isCoerceableFrom(foundType)) { foundType.validNel } else { s"Invalid parameter '$param'. Expected '${expectedType.stableName}' but got '${foundType.stableName}'".invalidNel }
+      if (expectedType.isCoerceableFrom(foundType)) { foundType.validNel }
+      else {
+        s"Invalid parameter '$param'. Expected '${expectedType.stableName}' but got '${foundType.stableName}'".invalidNel
+      }
     }
-  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LiteralEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LiteralEvaluators.scala
index c51e106cc46..9e74672f5bc 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LiteralEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LiteralEvaluators.scala
@@ -13,36 +13,44 @@ import wdl.model.draft3.graph.expression.TypeEvaluator.ops._
 import wom.types._
 
 object LiteralEvaluators {
-  implicit val primitiveTypeEvaluator: TypeEvaluator[PrimitiveLiteralExpressionElement] = new TypeEvaluator[PrimitiveLiteralExpressionElement] {
-    override def evaluateType(a: PrimitiveLiteralExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
-      a.value.womType.validNel
-  }
+  implicit val primitiveTypeEvaluator: TypeEvaluator[PrimitiveLiteralExpressionElement] =
+    new TypeEvaluator[PrimitiveLiteralExpressionElement] {
+      override def evaluateType(a: PrimitiveLiteralExpressionElement,
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+      )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
+        a.value.womType.validNel
+    }
 
-  implicit val noneLiteralTypeEvaluator: TypeEvaluator[NoneLiteralElement.type] = new TypeEvaluator[NoneLiteralElement.type] {
-    override def evaluateType(a: NoneLiteralElement.type, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
-      WomOptionalType(WomNothingType).validNel
-  }
+  implicit val noneLiteralTypeEvaluator: TypeEvaluator[NoneLiteralElement.type] =
+    new TypeEvaluator[NoneLiteralElement.type] {
+      override def evaluateType(a: NoneLiteralElement.type,
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+      )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
+        WomOptionalType(WomNothingType).validNel
+    }
 
   implicit val objectLiteralTypeEvaluator: TypeEvaluator[ObjectLiteral] = new TypeEvaluator[ObjectLiteral] {
-    override def evaluateType(a: ObjectLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = WomObjectType.validNel
+    override def evaluateType(a: ObjectLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = WomObjectType.validNel
   }
 
   implicit val stringLiteralTypeEvaluator: TypeEvaluator[StringLiteral] = new TypeEvaluator[StringLiteral] {
-    override def evaluateType(a: StringLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = WomStringType.validNel
+    override def evaluateType(a: StringLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = WomStringType.validNel
   }
 
   implicit val stringExpressionTypeEvaluator: TypeEvaluator[StringExpression] = new TypeEvaluator[StringExpression] {
-    override def evaluateType(a: StringExpression, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = WomStringType.validNel
+    override def evaluateType(a: StringExpression, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = WomStringType.validNel
   }
 
   implicit val mapLiteralTypeEvaluator: TypeEvaluator[MapLiteral] = new TypeEvaluator[MapLiteral] {
-    override def evaluateType(a: MapLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: MapLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = {
 
       val keyTypes = a.elements.keySet.toList.traverse { x: ExpressionElement => x.evaluateType(linkedValues) }
       val commonKeyType: ErrorOr[WomType] = keyTypes.map(WomType.homogeneousTypeFromTypes)
@@ -55,8 +63,9 @@ object LiteralEvaluators {
   }
 
   implicit val arrayLiteralTypeEvaluator: TypeEvaluator[ArrayLiteral] = new TypeEvaluator[ArrayLiteral] {
-    override def evaluateType(a: ArrayLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: ArrayLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = {
 
       val types = a.elements.toList.traverse { x: ExpressionElement => x.evaluateType(linkedValues) }
       val commonType: ErrorOr[WomType] = types.map(WomType.homogeneousTypeFromTypes)
@@ -66,8 +75,9 @@ object LiteralEvaluators {
   }
 
   implicit val pairLiteralTypeEvaluator: TypeEvaluator[PairLiteral] = new TypeEvaluator[PairLiteral] {
-    override def evaluateType(a: PairLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: PairLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] = {
 
       val leftType = a.left.evaluateType(linkedValues)
       val rightType = a.right.evaluateType(linkedValues)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LookupEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LookupEvaluators.scala
index 43a563dd3ee..0221390e8ca 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LookupEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LookupEvaluators.scala
@@ -15,56 +15,72 @@ import wom.types._
 object LookupEvaluators {
 
   implicit val identifierLookupTypeEvaluator: TypeEvaluator[IdentifierLookup] = new TypeEvaluator[IdentifierLookup] {
-    override def evaluateType(a: IdentifierLookup, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: IdentifierLookup, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       linkedValues.collectFirst {
         case (UnlinkedIdentifierHook(id), gen) if a.identifier == id => gen.womType
       } match {
         case Some(womType) => womType.validNel
-        case None => s"Type evaluation failure. No suitable type found for identifier lookup '${a.identifier}' amongst {${linkedValues.map(_._2.linkableName).mkString(", ")}}".invalidNel
+        case None =>
+          s"Type evaluation failure. No suitable type found for identifier lookup '${a.identifier}' amongst {${linkedValues
+              .map(_._2.linkableName)
+              .mkString(", ")}}".invalidNel
       }
-    }
   }
 
-  implicit val expressionMemberAccessEvaluator: TypeEvaluator[ExpressionMemberAccess] = new TypeEvaluator[ExpressionMemberAccess] {
-    override def evaluateType(a: ExpressionMemberAccess, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
-      val baseType = a.expression.evaluateType(linkedValues)
-      baseType flatMap { doLookup(_, a.memberAccessTail) }
+  implicit val expressionMemberAccessEvaluator: TypeEvaluator[ExpressionMemberAccess] =
+    new TypeEvaluator[ExpressionMemberAccess] {
+      override def evaluateType(a: ExpressionMemberAccess,
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+      )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+        val baseType = a.expression.evaluateType(linkedValues)
+        baseType flatMap { doLookup(_, a.memberAccessTail) }
+      }
     }
-  }
 
-  implicit val identifierMemberAccessEvaluator: TypeEvaluator[IdentifierMemberAccess] = new TypeEvaluator[IdentifierMemberAccess] {
-    override def evaluateType(a: IdentifierMemberAccess, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
-      val generatedValueHandle = linkedValues.get(UnlinkedCallOutputOrIdentifierAndMemberAccessHook(a.first, a.second))
+  implicit val identifierMemberAccessEvaluator: TypeEvaluator[IdentifierMemberAccess] =
+    new TypeEvaluator[IdentifierMemberAccess] {
+      override def evaluateType(a: IdentifierMemberAccess,
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+      )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+        val generatedValueHandle =
+          linkedValues.get(UnlinkedCallOutputOrIdentifierAndMemberAccessHook(a.first, a.second))
 
-      generatedValueHandle match {
-        case Some(GeneratedIdentifierValueHandle(a.first, womType)) => doLookup(womType, NonEmptyList(a.second, a.memberAccessTail.toList))
-        case Some(GeneratedCallOutputValueHandle(a.first, a.second, womType)) => NonEmptyList.fromList(a.memberAccessTail.toList) match {
-          case Some(tailList) => doLookup(womType, tailList)
-          case None => womType.validNel
+        generatedValueHandle match {
+          case Some(GeneratedIdentifierValueHandle(a.first, womType)) =>
+            doLookup(womType, NonEmptyList(a.second, a.memberAccessTail.toList))
+          case Some(GeneratedCallOutputValueHandle(a.first, a.second, womType)) =>
+            NonEmptyList.fromList(a.memberAccessTail.toList) match {
+              case Some(tailList) => doLookup(womType, tailList)
+              case None => womType.validNel
+            }
+          case _ =>
+            s"Type evaluation failure. No suitable type found for identifier lookup '${a.first}' or '${a.first}.${a.second}' amongst {${linkedValues
+                .map(_._2.linkableName)
+                .mkString(", ")}}".invalidNel
         }
-        case _ => s"Type evaluation failure. No suitable type found for identifier lookup '${a.first}' or '${a.first}.${a.second}' amongst {${linkedValues.map(_._2.linkableName).mkString(", ")}}".invalidNel
       }
     }
-  }
 
   implicit val indexAccessTypeEvaluator: TypeEvaluator[IndexAccess] = new TypeEvaluator[IndexAccess] {
-    override def evaluateType(a: IndexAccess, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: IndexAccess, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       (a.expressionElement.evaluateType(linkedValues), a.index.evaluateType(linkedValues), a.index.validNel) flatMapN {
         case (a: WomArrayType, WomIntegerType, _) => a.memberType.validNel
-        case (WomMapType(keyType, valueType), lookupType, _) if keyType.isCoerceableFrom(lookupType) => valueType.validNel
-        case (WomCompositeType(typeMap, _), WomStringType, StringLiteral(str)) => typeMap.get(str) match {
-          case Some(innerType) => innerType.validNel
-          case None => s"Type evaluation failed. No such field '$str' for expression $a".invalidNel
-        }
+        case (WomMapType(keyType, valueType), lookupType, _) if keyType.isCoerceableFrom(lookupType) =>
+          valueType.validNel
+        case (WomCompositeType(typeMap, _), WomStringType, StringLiteral(str)) =>
+          typeMap.get(str) match {
+            case Some(innerType) => innerType.validNel
+            case None => s"Type evaluation failed. No such field '$str' for expression $a".invalidNel
+          }
         case (WomObjectType, WomStringType, _) => WomAnyType.validNel
         case (WomAnyType, _, _) => WomAnyType.validNel
-        case (otherObject, otherKey, _) => s"Type evaluation failed for $a. Cannot dereference a ${otherObject.stableName} value using a ${otherKey.stableName} key".invalidNel
+        case (otherObject, otherKey, _) =>
+          s"Type evaluation failed for $a. Cannot dereference a ${otherObject.stableName} value using a ${otherKey.stableName} key".invalidNel
       }
-    }
   }
 
   /**
@@ -81,7 +97,8 @@ object LookupEvaluators {
     val tail = NonEmptyList.fromList(lookupChain.tail)
 
     val thisValue: ErrorOr[WomType] = womType match {
-      case WomCompositeType(typeMap, _) => typeMap.get(key).toErrorOr(s"No such field '$key' on type ${womType.stableName}.")
+      case WomCompositeType(typeMap, _) =>
+        typeMap.get(key).toErrorOr(s"No such field '$key' on type ${womType.stableName}.")
       case WomObjectType => WomAnyType.validNel
       case WomPairType(left, _) if key == "left" => left.validNel
       case WomPairType(_, right) if key == "right" => right.validNel
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/TernaryIfEvaluator.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/TernaryIfEvaluator.scala
index ba90a5c0bf0..ca4b1d61a7f 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/TernaryIfEvaluator.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/TernaryIfEvaluator.scala
@@ -13,14 +13,15 @@ import wom.types.{WomBooleanType, WomType}
 
 object TernaryIfEvaluator {
   implicit val ternaryIfEvaluator: TypeEvaluator[TernaryIf] = new TypeEvaluator[TernaryIf] {
-    override def evaluateType(a: TernaryIf, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: TernaryIf, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       a.condition.evaluateType(linkedValues) flatMap {
         case WomBooleanType =>
           (a.ifTrue.evaluateType(linkedValues): ErrorOr[WomType],
-            a.ifFalse.evaluateType(linkedValues): ErrorOr[WomType]) mapN { (tType, fType) => WomType.homogeneousTypeFromTypes(Seq(tType, fType)) }
+           a.ifFalse.evaluateType(linkedValues): ErrorOr[WomType]
+          ) mapN { (tType, fType) => WomType.homogeneousTypeFromTypes(Seq(tType, fType)) }
         case other => s"Condition should have evaluated to a Boolean but instead got ${other.stableName}".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/UnaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/UnaryOperatorEvaluators.scala
index 70368a692f5..3c2cb62721e 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/UnaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/UnaryOperatorEvaluators.scala
@@ -19,9 +19,9 @@ object UnaryOperatorEvaluators {
   implicit val logicalNotEvaluator: TypeEvaluator[LogicalNot] = forOperation(_.not)
 
   private def forOperation[A <: UnaryOperation](op: WomType => Try[WomType]) = new TypeEvaluator[A] {
-    override def evaluateType(a: A, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                             (implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
+    override def evaluateType(a: A, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
       a.argument.evaluateType(linkedValues) flatMap { op(_).toErrorOr }
-    }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/BinaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/BinaryOperatorEvaluators.scala
index 151ba26a4a6..6f34ed91230 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/BinaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/BinaryOperatorEvaluators.scala
@@ -16,8 +16,10 @@ import wom.values.{WomBoolean, WomOptionalValue, WomValue}
 import scala.util.Try
 
 object BinaryOperatorEvaluators {
-  implicit val logicalOrEvaluator: ValueEvaluator[LogicalOr] = forOperationWithShortCircuit(_.or(_), shortCircuit = { case WomBoolean(true) => WomBoolean(true) })
-  implicit val logicalAndEvaluator: ValueEvaluator[LogicalAnd] = forOperationWithShortCircuit(_.and(_), shortCircuit = { case WomBoolean(false) => WomBoolean(false) })
+  implicit val logicalOrEvaluator: ValueEvaluator[LogicalOr] =
+    forOperationWithShortCircuit(_.or(_), shortCircuit = { case WomBoolean(true) => WomBoolean(true) })
+  implicit val logicalAndEvaluator: ValueEvaluator[LogicalAnd] =
+    forOperationWithShortCircuit(_.and(_), shortCircuit = { case WomBoolean(false) => WomBoolean(false) })
   implicit val equalsEvaluator: ValueEvaluator[Equals] = forOperation(_.equals(_))
   implicit val notEqualsEvaluator: ValueEvaluator[NotEquals] = forOperation(_.notEquals(_))
   implicit val lessThanEvaluator: ValueEvaluator[LessThan] = forOperation(_.lessThan(_))
@@ -33,14 +35,14 @@ object BinaryOperatorEvaluators {
   private def forOperation[A <: BinaryOperation](op: (WomValue, WomValue) => Try[WomValue]): ValueEvaluator[A] =
     forOperationWithShortCircuit(op, PartialFunction.empty[WomValue, WomValue])
 
-
   private def forOperationWithShortCircuit[A <: BinaryOperation](op: (WomValue, WomValue) => Try[WomValue],
-                                                                 shortCircuit: PartialFunction[WomValue, WomValue]) = new ValueEvaluator[A] {
+                                                                 shortCircuit: PartialFunction[WomValue, WomValue]
+  ) = new ValueEvaluator[A] {
     override def evaluateValue(a: A,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
       a.left.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions) flatMap { left =>
         if (shortCircuit.isDefinedAt(left.value)) {
           EvaluatedValue(shortCircuit(left.value), left.sideEffectFiles).validNel
@@ -50,10 +52,13 @@ object BinaryOperatorEvaluators {
 
             // Allow unsupplied optionals, but only if we're instantiating a command:
             val handleOptionals = rawResult.recover {
-              case OptionalNotSuppliedException(_) if forCommandInstantiationOptions.isDefined => WomOptionalValue(WomStringType, None)
+              case OptionalNotSuppliedException(_) if forCommandInstantiationOptions.isDefined =>
+                WomOptionalValue(WomStringType, None)
             }
 
-            handleOptionals.toErrorOr map { newValue => EvaluatedValue(newValue, left.sideEffectFiles ++ right.sideEffectFiles) }
+            handleOptionals.toErrorOr map { newValue =>
+              EvaluatedValue(newValue, left.sideEffectFiles ++ right.sideEffectFiles)
+            }
           }
         }
       }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
index f40c8a9431a..ffaf16ad0d2 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
@@ -16,7 +16,19 @@ import wdl4s.parser.MemoryUnit
 import wom.expression.IoFunctionSet
 import wom.types._
 import wom.values.WomArray.WomArrayLike
-import wom.values.{WomArray, WomBoolean, WomFloat, WomInteger, WomMap, WomObject, WomOptionalValue, WomPair, WomSingleFile, WomString, WomValue}
+import wom.values.{
+  WomArray,
+  WomBoolean,
+  WomFloat,
+  WomInteger,
+  WomMap,
+  WomObject,
+  WomOptionalValue,
+  WomPair,
+  WomSingleFile,
+  WomString,
+  WomValue
+}
 import wom.types.coercion.ops._
 import wom.types.coercion.defaults._
 import wom.types.coercion.WomTypeCoercer
@@ -37,8 +49,8 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: StdoutElement.type,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] =
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] =
       EvaluatedValue(WomSingleFile(ioFunctionSet.pathFunctions.stdout), Seq.empty).validNel
   }
 
@@ -46,123 +58,134 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: StderrElement.type,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] =
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] =
       EvaluatedValue(WomSingleFile(ioFunctionSet.pathFunctions.stderr), Seq.empty).validNel
   }
 
   private val ReadWaitTimeout = 60.seconds
-  private def readFile(fileToRead: WomSingleFile, ioFunctionSet: IoFunctionSet, sizeLimit: Int) = {
-    Try(Await.result(ioFunctionSet.readFile(fileToRead.value, Option(sizeLimit), failOnOverflow = true), ReadWaitTimeout))
-  }
+  private def readFile(fileToRead: WomSingleFile, ioFunctionSet: IoFunctionSet, sizeLimit: Int) =
+    Try(
+      Await.result(ioFunctionSet.readFile(fileToRead.value, Option(sizeLimit), failOnOverflow = true), ReadWaitTimeout)
+    )
 
   implicit val readLinesFunctionEvaluator: ValueEvaluator[ReadLines] = new ValueEvaluator[ReadLines] {
     override def evaluateValue(a: ReadLines,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-      processValidatedSingleValue[WomSingleFile, WomArray](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { fileToRead =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomSingleFile, WomArray](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { fileToRead =>
         val tryResult = for {
-          //validate
+          // validate
           read <- readFile(fileToRead, ioFunctionSet, fileSizeLimitationConfig.readLinesLimit)
           // Users expect an empty file to return zero lines [] not [""]
-          lines = if (read.nonEmpty) {
-            read.split(System.lineSeparator).toList
-          } else {
-            List.empty
-          }
+          lines =
+            if (read.nonEmpty) {
+              read.split(System.lineSeparator).toList
+            } else {
+              List.empty
+            }
         } yield EvaluatedValue(WomArray(lines map WomString.apply), Seq.empty)
         tryResult.toErrorOr.contextualizeErrors(s"""read_lines("${fileToRead.value}")""")
       }
-    }
   }
 
   implicit val readTsvFunctionEvaluator: ValueEvaluator[ReadTsv] = new ValueEvaluator[ReadTsv] {
     override def evaluateValue(a: ReadTsv,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-      processValidatedSingleValue[WomSingleFile, WomArray](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { fileToRead =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomSingleFile, WomArray](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { fileToRead =>
         val tryResult = for {
           read <- readFile(fileToRead, ioFunctionSet, fileSizeLimitationConfig.readTsvLimit)
           tsv <- Try(WomArray.fromTsv(read))
         } yield EvaluatedValue(tsv, Seq.empty)
         tryResult.toErrorOr.contextualizeErrors(s"""read_tsv("${fileToRead.value}")""")
       }
-    }
   }
 
   implicit val readMapFunctionEvaluator: ValueEvaluator[ReadMap] = new ValueEvaluator[ReadMap] {
     override def evaluateValue(a: ReadMap,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomMap]] = {
-      processValidatedSingleValue[WomSingleFile, WomMap](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { fileToRead =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomMap]] =
+      processValidatedSingleValue[WomSingleFile, WomMap](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { fileToRead =>
         val tryResult = for {
           read <- readFile(fileToRead, ioFunctionSet, fileSizeLimitationConfig.readMapLimit)
           map <- WomMap.fromTsv(read)
         } yield EvaluatedValue(map, Seq.empty)
         tryResult.toErrorOr.contextualizeErrors(s"""read_map("${fileToRead.value}")""")
       }
-    }
   }
 
   implicit val readObjectFunctionEvaluator: ValueEvaluator[ReadObject] = new ValueEvaluator[ReadObject] {
     override def evaluateValue(a: ReadObject,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomObject]] = {
-      processValidatedSingleValue[WomSingleFile, WomObject](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { fileToRead =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomObject]] =
+      processValidatedSingleValue[WomSingleFile, WomObject](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { fileToRead =>
         val tryResult = for {
           read <- readFile(fileToRead, ioFunctionSet, fileSizeLimitationConfig.readObjectLimit)
           obj <- WomObject.fromTsv(read)
         } yield obj
         val rightSize: ErrorOr[WomObject] = tryResult.toErrorOr flatMap {
           case oneItem: Array[WomObject] if oneItem.length == 1 => oneItem.head.validNel
-          case other: Array[WomObject] => s"Exactly 1 TSV object expected in input file (ie 2 lines: headers and data), but instead got an array of ${other.length} entries.".invalidNel
+          case other: Array[WomObject] =>
+            s"Exactly 1 TSV object expected in input file (ie 2 lines: headers and data), but instead got an array of ${other.length} entries.".invalidNel
         }
         rightSize.map(EvaluatedValue(_, Seq.empty)).contextualizeErrors(s"""read_object("${fileToRead.value}")""")
       }
-    }
   }
 
   implicit val readObjectsFunctionEvaluator: ValueEvaluator[ReadObjects] = new ValueEvaluator[ReadObjects] {
     override def evaluateValue(a: ReadObjects,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-      processValidatedSingleValue[WomSingleFile, WomArray](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { fileToRead =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomSingleFile, WomArray](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { fileToRead =>
         val tryResult = for {
           read <- readFile(fileToRead, ioFunctionSet, fileSizeLimitationConfig.readObjectLimit)
           objects <- WomObject.fromTsv(read)
         } yield WomArray(objects.toIndexedSeq)
 
-        tryResult.map(EvaluatedValue(_, Seq.empty)).toErrorOr.contextualizeErrors(s"""read_objects("${fileToRead.value}")""")
+        tryResult
+          .map(EvaluatedValue(_, Seq.empty))
+          .toErrorOr
+          .contextualizeErrors(s"""read_objects("${fileToRead.value}")""")
       }
-    }
   }
 
   implicit val readJsonFunctionEvaluator: ValueEvaluator[ReadJson] = new ValueEvaluator[ReadJson] {
     override def evaluateValue(a: ReadJson,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
 
-      def convertJsonToWom(jsValue: JsValue): Try[WomValue] = {
+      def convertJsonToWom(jsValue: JsValue): Try[WomValue] =
         jsValue match {
-          case _: JsNumber => WomIntegerType.coerceRawValue(jsValue).recoverWith { case _ => WomFloatType.coerceRawValue(jsValue) }
+          case _: JsNumber =>
+            WomIntegerType.coerceRawValue(jsValue).recoverWith { case _ => WomFloatType.coerceRawValue(jsValue) }
           case _: JsString => WomStringType.coerceRawValue(jsValue)
           case _: JsBoolean => WomBooleanType.coerceRawValue(jsValue)
           case _: JsArray => WomArrayType(WomAnyType).coerceRawValue(jsValue)
           case _ => WomObjectType.coerceRawValue(jsValue)
         }
-      }
 
       def readJson(fileToRead: WomSingleFile): ErrorOr[EvaluatedValue[WomValue]] = {
         val tryResult: Try[WomValue] = for {
@@ -171,13 +194,15 @@ object EngineFunctionEvaluators {
           womValue <- convertJsonToWom(jsValue)
         } yield womValue
 
-        tryResult.map(EvaluatedValue(_, Seq.empty)).toErrorOr.contextualizeErrors(s"""read_json("${fileToRead.value}")""")
+        tryResult
+          .map(EvaluatedValue(_, Seq.empty))
+          .toErrorOr
+          .contextualizeErrors(s"""read_json("${fileToRead.value}")""")
       }
 
-      def convertToSingleFile(womValue: WomValue): ErrorOr[WomSingleFile] = {
+      def convertToSingleFile(womValue: WomValue): ErrorOr[WomSingleFile] =
         if (womValue.coercionDefined[WomSingleFile]) womValue.coerceToType[WomSingleFile]
         else s"Expected File argument but got ${womValue.womType.stableName}".invalidNel
-      }
 
       for {
         evaluatedValue <- a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
@@ -191,63 +216,79 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: ReadInt,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomInteger]] = {
-      processValidatedSingleValue[WomSingleFile, WomInteger](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { fileToRead =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomInteger]] =
+      processValidatedSingleValue[WomSingleFile, WomInteger](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { fileToRead =>
         val tryResult = for {
           read <- readFile(fileToRead, ioFunctionSet, fileSizeLimitationConfig.readIntLimit)
           asInt <- Try(read.trim.toInt)
         } yield WomInteger(asInt)
-        tryResult.map(EvaluatedValue(_, Seq.empty)).toErrorOr.contextualizeErrors(s"""read_int("${fileToRead.value}")""")
+        tryResult
+          .map(EvaluatedValue(_, Seq.empty))
+          .toErrorOr
+          .contextualizeErrors(s"""read_int("${fileToRead.value}")""")
       }
-    }
   }
 
   implicit val readStringFunctionEvaluator: ValueEvaluator[ReadString] = new ValueEvaluator[ReadString] {
     override def evaluateValue(a: ReadString,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] = {
-      processValidatedSingleValue[WomSingleFile, WomString](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { fileToRead =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] =
+      processValidatedSingleValue[WomSingleFile, WomString](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { fileToRead =>
         val tryResult = for {
           read <- readFile(fileToRead, ioFunctionSet, fileSizeLimitationConfig.readStringLimit)
         } yield WomString(read.trim)
-        tryResult.map(EvaluatedValue(_, Seq.empty)).toErrorOr.contextualizeErrors(s"""read_string("${fileToRead.value}")""")
+        tryResult
+          .map(EvaluatedValue(_, Seq.empty))
+          .toErrorOr
+          .contextualizeErrors(s"""read_string("${fileToRead.value}")""")
       }
-    }
   }
 
   implicit val readFloatFunctionEvaluator: ValueEvaluator[ReadFloat] = new ValueEvaluator[ReadFloat] {
     override def evaluateValue(a: ReadFloat,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomFloat]] = {
-      processValidatedSingleValue[WomSingleFile, WomFloat](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { fileToRead =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomFloat]] =
+      processValidatedSingleValue[WomSingleFile, WomFloat](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { fileToRead =>
         val tryResult = for {
           read <- readFile(fileToRead, ioFunctionSet, fileSizeLimitationConfig.readFloatLimit)
           asFloat <- Try(read.trim.toDouble)
         } yield WomFloat(asFloat)
-        tryResult.map(EvaluatedValue(_, Seq.empty)).toErrorOr.contextualizeErrors(s"""read_float("${fileToRead.value}")""")
+        tryResult
+          .map(EvaluatedValue(_, Seq.empty))
+          .toErrorOr
+          .contextualizeErrors(s"""read_float("${fileToRead.value}")""")
       }
-    }
   }
 
   implicit val readBooleanFunctionEvaluator: ValueEvaluator[ReadBoolean] = new ValueEvaluator[ReadBoolean] {
     override def evaluateValue(a: ReadBoolean,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomBoolean]] = {
-      processValidatedSingleValue[WomSingleFile, WomBoolean](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { fileToRead =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomBoolean]] =
+      processValidatedSingleValue[WomSingleFile, WomBoolean](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { fileToRead =>
         val tryResult = for {
           read <- readFile(fileToRead, ioFunctionSet, fileSizeLimitationConfig.readBoolLimit)
           asBool <- Try(read.trim.toBoolean)
         } yield WomBoolean(asBool)
-        tryResult.map(EvaluatedValue(_, Seq.empty)).toErrorOr.contextualizeErrors(s"""read_boolean("${fileToRead.value}")""")
+        tryResult
+          .map(EvaluatedValue(_, Seq.empty))
+          .toErrorOr
+          .contextualizeErrors(s"""read_boolean("${fileToRead.value}")""")
       }
-    }
   }
 
   private val WriteWaitTimeout = 10.minutes
@@ -260,17 +301,26 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: WriteLines,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
       val functionName = "write_lines"
-      processValidatedSingleValue[WomArray, WomSingleFile](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { stringsToWrite =>
+      processValidatedSingleValue[WomArray, WomSingleFile](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { stringsToWrite =>
         val tryResult = for {
-          serialized <- ValueEvaluation.serializeWomValue(functionName, stringsToWrite, defaultIfOptionalEmpty = WomArray(WomArrayType(WomStringType), Seq.empty))
+          serialized <- ValueEvaluation.serializeWomValue(functionName,
+                                                          stringsToWrite,
+                                                          defaultIfOptionalEmpty =
+                                                            WomArray(WomArrayType(WomStringType), Seq.empty)
+          )
           written <- writeContent(functionName, ioFunctionSet, serialized)
         } yield written
 
-        tryResult.map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v)))).toErrorOr.contextualizeErrors(s"""$functionName(...)""")
-      } (coercer = WomArrayType(WomStringType))
+        tryResult
+          .map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v))))
+          .toErrorOr
+          .contextualizeErrors(s"""$functionName(...)""")
+      }(coercer = WomArrayType(WomStringType))
     }
   }
 
@@ -278,18 +328,26 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: WriteTsv,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
       val functionName = "write_tsv"
-      processValidatedSingleValue[WomArray, WomSingleFile](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { objectToWrite =>
-
+      processValidatedSingleValue[WomArray, WomSingleFile](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { objectToWrite =>
         val tryResult = for {
-          serialized <- ValueEvaluation.serializeWomValue(functionName, objectToWrite, defaultIfOptionalEmpty = WomArray(WomArrayType(WomStringType), List.empty[WomValue]))
+          serialized <- ValueEvaluation.serializeWomValue(functionName,
+                                                          objectToWrite,
+                                                          defaultIfOptionalEmpty =
+                                                            WomArray(WomArrayType(WomStringType), List.empty[WomValue])
+          )
           written <- writeContent(functionName, ioFunctionSet, serialized)
         } yield written
 
-        tryResult.map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v)))).toErrorOr.contextualizeErrors(s"""$functionName(...)""")
-      } (coercer = WomArrayType(WomAnyType))
+        tryResult
+          .map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v))))
+          .toErrorOr
+          .contextualizeErrors(s"""$functionName(...)""")
+      }(coercer = WomArrayType(WomAnyType))
     }
   }
 
@@ -297,16 +355,24 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: WriteMap,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
       val functionName = "write_map"
-      processValidatedSingleValue[WomMap, WomSingleFile](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { mapToWrite: WomMap =>
+      processValidatedSingleValue[WomMap, WomSingleFile](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { mapToWrite: WomMap =>
         val tryResult = for {
-          serialized <- ValueEvaluation.serializeWomValue(functionName, mapToWrite, defaultIfOptionalEmpty = WomMap(Map.empty))
+          serialized <- ValueEvaluation.serializeWomValue(functionName,
+                                                          mapToWrite,
+                                                          defaultIfOptionalEmpty = WomMap(Map.empty)
+          )
           written <- writeContent(functionName, ioFunctionSet, serialized)
         } yield written
 
-        tryResult.map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v)))).toErrorOr.contextualizeErrors(s"""$functionName(...)""")
+        tryResult
+          .map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v))))
+          .toErrorOr
+          .contextualizeErrors(s"""$functionName(...)""")
       }
     }
   }
@@ -315,16 +381,24 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: WriteObject,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
       val functionName = "write_object"
-      processValidatedSingleValue[WomObject, WomSingleFile](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { objectToWrite: WomObject =>
+      processValidatedSingleValue[WomObject, WomSingleFile](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { objectToWrite: WomObject =>
         val tryResult = for {
-          serialized <- ValueEvaluation.serializeWomValue(functionName, objectToWrite, defaultIfOptionalEmpty = WomObject(Map.empty))
+          serialized <- ValueEvaluation.serializeWomValue(functionName,
+                                                          objectToWrite,
+                                                          defaultIfOptionalEmpty = WomObject(Map.empty)
+          )
           written <- writeContent(functionName, ioFunctionSet, serialized)
         } yield written
 
-        tryResult.map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v)))).toErrorOr.contextualizeErrors(s"""$functionName(...)""")
+        tryResult
+          .map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v))))
+          .toErrorOr
+          .contextualizeErrors(s"""$functionName(...)""")
       }
     }
   }
@@ -333,17 +407,25 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: WriteObjects,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
       val functionName = "write_objects"
-      processValidatedSingleValue[WomArray, WomSingleFile](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { objectToWrite =>
+      processValidatedSingleValue[WomArray, WomSingleFile](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { objectToWrite =>
         val tryResult = for {
-          serialized <- ValueEvaluation.serializeWomValue(functionName, objectToWrite, defaultIfOptionalEmpty = WomArray(List(WomObject(Map.empty))))
+          serialized <- ValueEvaluation.serializeWomValue(functionName,
+                                                          objectToWrite,
+                                                          defaultIfOptionalEmpty = WomArray(List(WomObject(Map.empty)))
+          )
           written <- writeContent(functionName, ioFunctionSet, serialized)
         } yield written
 
-        tryResult.map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v)))).toErrorOr.contextualizeErrors(s"""$functionName(...)""")
-      } (coercer = WomArrayType(WomObjectType))
+        tryResult
+          .map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v))))
+          .toErrorOr
+          .contextualizeErrors(s"""$functionName(...)""")
+      }(coercer = WomArrayType(WomObjectType))
     }
   }
 
@@ -351,8 +433,8 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: WriteJson,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] = {
       val functionName = "write_json"
 
       def convertToSingleFile(objectToWrite: WomValue): ErrorOr[EvaluatedValue[WomSingleFile]] = {
@@ -361,26 +443,30 @@ object EngineFunctionEvaluators {
           written <- writeContent(functionName, ioFunctionSet, serialized.compactPrint)
         } yield written
 
-        tryResult.map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v)))).toErrorOr.contextualizeErrors(s"""$functionName(...)""")
+        tryResult
+          .map(v => EvaluatedValue(v, Seq(CommandSetupSideEffectFile(v))))
+          .toErrorOr
+          .contextualizeErrors(s"""$functionName(...)""")
       }
 
-      def evaluateParam(womValue: WomValue): ErrorOr[EvaluatedValue[WomSingleFile]] = {
+      def evaluateParam(womValue: WomValue): ErrorOr[EvaluatedValue[WomSingleFile]] =
         womValue match {
-          case WomBoolean(_) | WomString(_) | WomInteger(_) | WomFloat(_) | WomPair(_, _) => convertToSingleFile(womValue)
+          case WomBoolean(_) | WomString(_) | WomInteger(_) | WomFloat(_) | WomPair(_, _) =>
+            convertToSingleFile(womValue)
           case v if v.coercionDefined[WomObject] => v.coerceToType[WomObject].flatMap(convertToSingleFile)
           case v if v.coercionDefined[WomArray] => v.coerceToType[WomArray].flatMap(convertToSingleFile)
-          case _ => (s"The '$functionName' method expects one of 'Boolean', 'String', 'Integer', 'Float', 'Object', 'Pair[_, _]', " +
-            s"'Map[_, _] or 'Array[_]' argument but instead got '${womValue.womType.friendlyName}'.").invalidNel
+          case _ =>
+            (s"The '$functionName' method expects one of 'Boolean', 'String', 'Integer', 'Float', 'Object', 'Pair[_, _]', " +
+              s"'Map[_, _] or 'Array[_]' argument but instead got '${womValue.womType.friendlyName}'.").invalidNel
         }
-      }
 
       val evaluatedSingleFile: ErrorOr[(EvaluatedValue[WomSingleFile], Seq[CommandSetupSideEffectFile])] = for {
         evaluatedValue <- a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
         evaluatedSingleFile <- evaluateParam(evaluatedValue.value)
       } yield (evaluatedSingleFile, evaluatedValue.sideEffectFiles)
 
-      evaluatedSingleFile map {
-        case (result, previousSideEffectFiles) => result.copy(sideEffectFiles = result.sideEffectFiles ++ previousSideEffectFiles)
+      evaluatedSingleFile map { case (result, previousSideEffectFiles) =>
+        result.copy(sideEffectFiles = result.sideEffectFiles ++ previousSideEffectFiles)
       }
     }
   }
@@ -389,57 +475,62 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: Range,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-      processValidatedSingleValue[WomInteger, WomArray](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { integer =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomInteger, WomArray](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { integer =>
         val array = WomArray(
           womType = WomArrayType(WomIntegerType, guaranteedNonEmpty = integer.value > 0),
           value = (0 until integer.value).map(WomInteger)
         )
         EvaluatedValue(array, Seq.empty).validNel
       }
-    }
   }
 
   implicit val transposeFunctionEvaluator: ValueEvaluator[Transpose] = new ValueEvaluator[Transpose] {
     override def evaluateValue(a: Transpose,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-      processValidatedSingleValue[WomArray, WomArray](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { array =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomArray, WomArray](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { array =>
         EngineFunctions.transpose(array).map(EvaluatedValue(_, Seq.empty)).toErrorOr
       }
-    }
   }
 
   implicit val lengthFunctionEvaluator: ValueEvaluator[Length] = new ValueEvaluator[Length] {
     override def evaluateValue(a: Length,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomInteger]] = {
-      processValidatedSingleValue[WomArray, WomInteger](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { a =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomInteger]] =
+      processValidatedSingleValue[WomArray, WomInteger](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { a =>
         EvaluatedValue(WomInteger(a.value.size), Seq.empty).validNel
       }
-    }
   }
 
   implicit val flattenFunctionEvaluator: ValueEvaluator[Flatten] = new ValueEvaluator[Flatten] {
     override def evaluateValue(a: Flatten,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
       def flatValues(v: WomValue): ErrorOr[Seq[WomValue]] = v match {
         case WomArrayLike(arrayLike) => arrayLike.value.validNel
         case other => s"inner item ${other.toWomString} was not an array-like".invalidNel
       }
 
-      processValidatedSingleValue[WomArray, WomArray](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { array =>
-        val expandedValidation = array.value.toList.traverse{ flatValues }
+      processValidatedSingleValue[WomArray, WomArray](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { array =>
+        val expandedValidation = array.value.toList.traverse(flatValues)
         expandedValidation map { expanded => EvaluatedValue(WomArray(expanded.flatten), Seq.empty) }
-      } (coercer = WomArrayType(WomArrayType(WomAnyType)))
+      }(coercer = WomArrayType(WomArrayType(WomAnyType)))
     }
   }
 
@@ -447,85 +538,93 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: SelectFirst,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] = {
-      processValidatedSingleValue[WomArray, WomValue](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { array =>
-        val firstValue = array.value collectFirst {
-          case WomOptionalValue(_, Some(yay)) => yay
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomValue]] =
+      processValidatedSingleValue[WomArray, WomValue](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { array =>
+        val firstValue = array.value collectFirst { case WomOptionalValue(_, Some(yay)) =>
+          yay
         }
 
         firstValue match {
           case Some(first) => EvaluatedValue(first, Seq.empty).validNel
-          case None => s"select_first was called with ${array.size} empty values. We needed at least one to be filled.".invalidNel
+          case None =>
+            s"select_first was called with ${array.size} empty values. We needed at least one to be filled.".invalidNel
         }
-      } (coercer = WomArrayType(WomOptionalType(WomAnyType)))
-    }
+      }(coercer = WomArrayType(WomOptionalType(WomAnyType)))
   }
 
   implicit val selectAllFunctionEvaluator: ValueEvaluator[SelectAll] = new ValueEvaluator[SelectAll] {
     override def evaluateValue(a: SelectAll,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-      processValidatedSingleValue[WomArray, WomArray](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { array =>
-        val goodValues = array.value.collect {
-          case WomOptionalValue.Flattened(Some(value)) => value
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomArray, WomArray](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { array =>
+        val goodValues = array.value.collect { case WomOptionalValue.Flattened(Some(value)) =>
+          value
         }
         EvaluatedValue(WomArray(goodValues), Seq.empty).validNel
-      } (coercer = WomArrayType(WomOptionalType(WomAnyType)))
-    }
+      }(coercer = WomArrayType(WomOptionalType(WomAnyType)))
   }
 
   implicit val definedFunctionEvaluator: ValueEvaluator[Defined] = new ValueEvaluator[Defined] {
     override def evaluateValue(a: Defined,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomBoolean]] = {
-      processValidatedSingleValue[WomOptionalValue, WomBoolean](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { optionalValue =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomBoolean]] =
+      processValidatedSingleValue[WomOptionalValue, WomBoolean](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { optionalValue =>
         EvaluatedValue(WomBoolean(optionalValue.value.isDefined), Seq.empty).validNel
       }
-    }
   }
 
   implicit val floorFunctionEvaluator: ValueEvaluator[Floor] = new ValueEvaluator[Floor] {
     override def evaluateValue(a: Floor,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomInteger]] = {
-      processValidatedSingleValue[WomFloat, WomInteger](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { float =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomInteger]] =
+      processValidatedSingleValue[WomFloat, WomInteger](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { float =>
         EvaluatedValue(WomInteger(math.floor(float.value).toInt), Seq.empty).validNel
       }
-    }
   }
 
   implicit val ceilFunctionEvaluator: ValueEvaluator[Ceil] = new ValueEvaluator[Ceil] {
     override def evaluateValue(a: Ceil,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomInteger]] = {
-      processValidatedSingleValue[WomFloat, WomInteger](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { float =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomInteger]] =
+      processValidatedSingleValue[WomFloat, WomInteger](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { float =>
         EvaluatedValue(WomInteger(math.ceil(float.value).toInt), Seq.empty).validNel
       }
-    }
   }
 
   implicit val roundFunctionEvaluator: ValueEvaluator[Round] = new ValueEvaluator[Round] {
     override def evaluateValue(a: Round,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomInteger]] = {
-      processValidatedSingleValue[WomFloat, WomInteger](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { float =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomInteger]] =
+      processValidatedSingleValue[WomFloat, WomInteger](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { float =>
         EvaluatedValue(WomInteger(math.round(float.value).toInt), Seq.empty).validNel
       }
-    }
   }
 
   implicit val globFunctionValueEvaluator: ValueEvaluator[Glob] = new ValueEvaluator[Glob] {
+
     /**
       * Evaluate a value from an A
       *
@@ -535,24 +634,28 @@ object EngineFunctionEvaluators {
       * @param forCommandInstantiationOptions Supplied only if we're evaluating this A as part of command instantiation.
       * @return An evaluated value set - the value itself and any files which were produced as part of the evaluation.
       */
-    override def evaluateValue(a: Glob, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      processValidatedSingleValue[WomString, WomArray](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { globString =>
+    override def evaluateValue(a: Glob,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+      processValidatedSingleValue[WomString, WomArray](
+        a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { globString =>
         for {
           globbed <- Try(Await.result(ioFunctionSet.glob(globString.valueString), ReadWaitTimeout)).toErrorOr
           files = globbed map WomSingleFile
           array = WomArray(files)
         } yield EvaluatedValue(array, Seq.empty)
       }
-    }
   }
 
   implicit val sizeFunctionEvaluator: ValueEvaluator[Size] = new ValueEvaluator[Size] {
     override def evaluateValue(a: Size,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomFloat]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomFloat]] = {
       // Inner function: get the memory unit from the second (optional) parameter
       def toUnit(womValue: WomValue): ErrorOr[MemoryUnit] = Try(MemoryUnit.fromSuffix(womValue.valueString)).toErrorOr
 
@@ -566,26 +669,38 @@ object EngineFunctionEvaluators {
       // Inner function: Get the file size, allowing for unpacking of optionals and arrays
       def optionalSafeFileSize(value: WomValue): ErrorOr[Long] = value match {
         case f if f.isInstanceOf[WomSingleFile] || WomSingleFileType.isCoerceableFrom(f.womType) =>
-          f.coerceToType[WomSingleFile] flatMap { file => Try(Await.result(ioFunctionSet.size(file.valueString), Duration.Inf)).toErrorOr }
+          f.coerceToType[WomSingleFile] flatMap { file =>
+            Try(Await.result(ioFunctionSet.size(file.valueString), Duration.Inf)).toErrorOr
+          }
         case WomOptionalValue(f, Some(o)) if isOptionalOfFileType(f) => optionalSafeFileSize(o)
         case WomOptionalValue(f, None) if isOptionalOfFileType(f) => 0L.validNel
-        case WomArray(WomArrayType(womType), values) if isOptionalOfFileType(womType) => values.toList.traverse(optionalSafeFileSize).map(_.sum)
-        case _ => s"The 'size' method expects a 'File', 'File?', 'Array[File]' or Array[File?] argument but instead got ${value.womType.stableName}.".invalidNel
+        case WomArray(WomArrayType(womType), values) if isOptionalOfFileType(womType) =>
+          values.toList.traverse(optionalSafeFileSize).map(_.sum)
+        case _ =>
+          s"The 'size' method expects a 'File', 'File?', 'Array[File]' or Array[File?] argument but instead got ${value.womType.stableName}.".invalidNel
       }
 
       // Inner function: get the file size and convert into the requested memory unit
-      def fileSize(womValue: ErrorOr[EvaluatedValue[_ <: WomValue]], convertToOption: Option[ErrorOr[EvaluatedValue[_ <: WomValue]]]): ErrorOr[EvaluatedValue[WomFloat]] = {
-        val convertTo: ErrorOr[EvaluatedValue[_ <: WomValue]] = convertToOption.getOrElse(EvaluatedValue(WomString("B"), Seq.empty).validNel)
+      def fileSize(womValue: ErrorOr[EvaluatedValue[_ <: WomValue]],
+                   convertToOption: Option[ErrorOr[EvaluatedValue[_ <: WomValue]]]
+      ): ErrorOr[EvaluatedValue[WomFloat]] = {
+        val convertTo: ErrorOr[EvaluatedValue[_ <: WomValue]] =
+          convertToOption.getOrElse(EvaluatedValue(WomString("B"), Seq.empty).validNel)
         for {
           value <- womValue
           evaluatedUnitValue <- convertTo
           convertToUnit <- toUnit(evaluatedUnitValue.value)
           fileSize <- optionalSafeFileSize(value.value)
-        } yield EvaluatedValue(WomFloat(MemorySize(fileSize.toDouble, MemoryUnit.Bytes).to(convertToUnit).amount), value.sideEffectFiles ++ evaluatedUnitValue.sideEffectFiles)
+        } yield EvaluatedValue(WomFloat(MemorySize(fileSize.toDouble, MemoryUnit.Bytes).to(convertToUnit).amount),
+                               value.sideEffectFiles ++ evaluatedUnitValue.sideEffectFiles
+        )
       }
 
-      val evaluatedFileValidation: ErrorOr[EvaluatedValue[_ <: WomValue]] = a.file.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
-      fileSize(evaluatedFileValidation, a.unit map (_.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)))
+      val evaluatedFileValidation: ErrorOr[EvaluatedValue[_ <: WomValue]] =
+        a.file.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      fileSize(evaluatedFileValidation,
+               a.unit map (_.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions))
+      )
     }
   }
 
@@ -593,17 +708,22 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: Basename,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] = {
       def simpleBasename(fileNameAsString: WomString) = fileNameAsString.valueString.split('/').last
 
       a.suffixToRemove match {
-        case None => processValidatedSingleValue[WomString, WomString](a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { str =>
-          EvaluatedValue(WomString(simpleBasename(str)), Seq.empty).validNel
-        }
-        case Some(suffixToRemove) => processTwoValidatedValues[WomString, WomString, WomString](
-          a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
-          suffixToRemove.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { (name, suffix) =>
+        case None =>
+          processValidatedSingleValue[WomString, WomString](
+            a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+          ) { str =>
+            EvaluatedValue(WomString(simpleBasename(str)), Seq.empty).validNel
+          }
+        case Some(suffixToRemove) =>
+          processTwoValidatedValues[WomString, WomString, WomString](
+            a.param.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
+            suffixToRemove.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+          ) { (name, suffix) =>
             EvaluatedValue(WomString(simpleBasename(name).stripSuffix(suffix.valueString)), Seq.empty).validNel
           }
       }
@@ -614,91 +734,127 @@ object EngineFunctionEvaluators {
     override def evaluateValue(a: Zip,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-      processTwoValidatedValues[WomArray, WomArray, WomArray](a.arg1.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions), a.arg2.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { (arr1, arr2) =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processTwoValidatedValues[WomArray, WomArray, WomArray](
+        a.arg1.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
+        a.arg2.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { (arr1, arr2) =>
         if (arr1.size == arr2.size) {
           val pairs = arr1.value.zip(arr2.value) map { case (a, b) => WomPair(a, b) }
-          EvaluatedValue(WomArray(WomArrayType(WomPairType(arr1.arrayType.memberType, arr2.arrayType.memberType)), pairs), Seq.empty).validNel
+          EvaluatedValue(
+            WomArray(WomArrayType(WomPairType(arr1.arrayType.memberType, arr2.arrayType.memberType)), pairs),
+            Seq.empty
+          ).validNel
         } else {
           s"Mismatching array sizes for zip function: ${arr1.size} vs ${arr2.size}".invalidNel
         }
       }
-    }
   }
 
   implicit val crossFunctionEvaluator: ValueEvaluator[Cross] = new ValueEvaluator[Cross] {
     override def evaluateValue(a: Cross,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-      processTwoValidatedValues[WomArray, WomArray, WomArray](a.arg1.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions), a.arg2.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { (arr1, arr2) =>
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processTwoValidatedValues[WomArray, WomArray, WomArray](
+        a.arg1.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
+        a.arg2.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { (arr1, arr2) =>
         val pairs = for {
           a <- arr1.value
           b <- arr2.value
         } yield WomPair(a, b)
-        EvaluatedValue(WomArray(WomArrayType(WomPairType(arr1.arrayType.memberType, arr2.arrayType.memberType)), pairs), Seq.empty).validNel
+        EvaluatedValue(WomArray(WomArrayType(WomPairType(arr1.arrayType.memberType, arr2.arrayType.memberType)), pairs),
+                       Seq.empty
+        ).validNel
       }
-    }
   }
 
   implicit val prefixFunctionEvaluator: ValueEvaluator[Prefix] = new ValueEvaluator[Prefix] {
     override def evaluateValue(a: Prefix,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] = {
-      processTwoValidatedValues[WomString, WomArray, WomArray](a.prefix.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions), a.array.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { (prefix, array) =>
-        EvaluatedValue(WomArray(array.value.map(value => WomString(prefix.value + value.valueString))), Seq.empty).validNel
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processTwoValidatedValues[WomString, WomArray, WomArray](
+        a.prefix.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
+        a.array.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { (prefix, array) =>
+        EvaluatedValue(WomArray(array.value.map(value => WomString(prefix.value + value.valueString))),
+                       Seq.empty
+        ).validNel
       }
-    }
   }
 
   implicit val subFunctionEvaluator: ValueEvaluator[Sub] = new ValueEvaluator[Sub] {
     override def evaluateValue(a: Sub,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] =
       processThreeValidatedValues[WomString, WomString, WomString, WomString](
         a.input.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
         a.pattern.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
-        a.replace.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) { (input, pattern, replace) =>
-        ErrorOr(EvaluatedValue(WomString(pattern.valueString.r.replaceAllIn(input.valueString, replace.valueString)), Seq.empty))
+        a.replace.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) { (input, pattern, replace) =>
+        ErrorOr(
+          EvaluatedValue(WomString(pattern.valueString.r.replaceAllIn(input.valueString, replace.valueString)),
+                         Seq.empty
+          )
+        )
       }
-    }
   }
 
-  def processValidatedSingleValue[A <: WomValue, B <: WomValue](arg: ErrorOr[EvaluatedValue[_]])
-                                                                       (f: A => ErrorOr[EvaluatedValue[B]])
-                                                                       (implicit coercer: WomTypeCoercer[A]): ErrorOr[EvaluatedValue[B]] = {
+  def processValidatedSingleValue[A <: WomValue, B <: WomValue](
+    arg: ErrorOr[EvaluatedValue[_]]
+  )(f: A => ErrorOr[EvaluatedValue[B]])(implicit coercer: WomTypeCoercer[A]): ErrorOr[EvaluatedValue[B]] =
     arg flatMap {
-      case EvaluatedValue(a: WomValue, previousSideEffectFiles) if a.coercionDefined[A] => a.coerceToType[A] flatMap { f.apply } map { result => result.copy(sideEffectFiles = result.sideEffectFiles ++ previousSideEffectFiles) }
+      case EvaluatedValue(a: WomValue, previousSideEffectFiles) if a.coercionDefined[A] =>
+        a.coerceToType[A] flatMap f.apply map { result =>
+          result.copy(sideEffectFiles = result.sideEffectFiles ++ previousSideEffectFiles)
+        }
       case other => s"Expected ${coercer.toDisplayString} argument but got ${other.value.womType.stableName}".invalidNel
     }
-  }
 
-  def processTwoValidatedValues[A <: WomValue, B <: WomValue, R <: WomValue](arg1: ErrorOr[EvaluatedValue[_ <: WomValue]], arg2: ErrorOr[EvaluatedValue[_ <: WomValue]])
-                                                                     (f: (A, B) => ErrorOr[EvaluatedValue[R]])
-                                                                     (implicit coercerA: WomTypeCoercer[A],
-                                                                      coercerB: WomTypeCoercer[B]): ErrorOr[EvaluatedValue[R]] = {
+  def processTwoValidatedValues[A <: WomValue, B <: WomValue, R <: WomValue](
+    arg1: ErrorOr[EvaluatedValue[_ <: WomValue]],
+    arg2: ErrorOr[EvaluatedValue[_ <: WomValue]]
+  )(
+    f: (A, B) => ErrorOr[EvaluatedValue[R]]
+  )(implicit coercerA: WomTypeCoercer[A], coercerB: WomTypeCoercer[B]): ErrorOr[EvaluatedValue[R]] =
     (arg1, arg2) flatMapN {
-      case (EvaluatedValue(a: WomValue, previousSideEffectFilesA), EvaluatedValue(b: WomValue, previousSideEffectFilesB)) if a.coercionDefined[A] && b.coercionDefined[B] =>
-        (a.coerceToType[A], b.coerceToType[B]) flatMapN { f.apply } map { result => result.copy(sideEffectFiles = result.sideEffectFiles ++ previousSideEffectFilesA ++ previousSideEffectFilesB) }
-      case (otherA, otherB) => s"Expected (${coercerA.toDisplayString}, ${coercerB.toDisplayString}) argument but got (${otherA.value.womType.stableName}, ${otherB.value.womType.stableName})".invalidNel
-    }
-  }
-
-  private def processThreeValidatedValues[A <: WomValue, B <: WomValue, C <: WomValue, R <: WomValue](arg1: ErrorOr[EvaluatedValue[_ <: WomValue]], arg2: ErrorOr[EvaluatedValue[_ <: WomValue]], arg3: ErrorOr[EvaluatedValue[_ <: WomValue]])
-                                                                                      (f: (A, B, C) => ErrorOr[EvaluatedValue[R]])
-                                                                                      (implicit coercerA: WomTypeCoercer[A],
-                                                                                       coercerB: WomTypeCoercer[B],
-                                                                                       coercerC: WomTypeCoercer[C]): ErrorOr[EvaluatedValue[R]] = {
+      case (EvaluatedValue(a: WomValue, previousSideEffectFilesA),
+            EvaluatedValue(b: WomValue, previousSideEffectFilesB)
+          ) if a.coercionDefined[A] && b.coercionDefined[B] =>
+        (a.coerceToType[A], b.coerceToType[B]) flatMapN f.apply map { result =>
+          result.copy(sideEffectFiles = result.sideEffectFiles ++ previousSideEffectFilesA ++ previousSideEffectFilesB)
+        }
+      case (otherA, otherB) =>
+        s"Expected (${coercerA.toDisplayString}, ${coercerB.toDisplayString}) argument but got (${otherA.value.womType.stableName}, ${otherB.value.womType.stableName})".invalidNel
+    }
+
+  private def processThreeValidatedValues[A <: WomValue, B <: WomValue, C <: WomValue, R <: WomValue](
+    arg1: ErrorOr[EvaluatedValue[_ <: WomValue]],
+    arg2: ErrorOr[EvaluatedValue[_ <: WomValue]],
+    arg3: ErrorOr[EvaluatedValue[_ <: WomValue]]
+  )(f: (A, B, C) => ErrorOr[EvaluatedValue[R]])(implicit
+    coercerA: WomTypeCoercer[A],
+    coercerB: WomTypeCoercer[B],
+    coercerC: WomTypeCoercer[C]
+  ): ErrorOr[EvaluatedValue[R]] =
     (arg1, arg2, arg3) flatMapN {
-      case (EvaluatedValue(a, previousSideEffectFilesA), EvaluatedValue(b, previousSideEffectFilesB), EvaluatedValue(c, previousSideEffectFilesC)) if a.coercionDefined[A] && b.coercionDefined[B] && c.coercionDefined[C] =>
-        (a.coerceToType[A], b.coerceToType[B], c.coerceToType[C]) flatMapN { f.apply } map { result => result.copy(sideEffectFiles = result.sideEffectFiles ++ previousSideEffectFilesA ++ previousSideEffectFilesB ++ previousSideEffectFilesC) }
-      case (otherA, otherB, otherC) => s"Expected (${coercerA.toDisplayString}, ${coercerB.toDisplayString}, ${coercerB.toDisplayString}) argument but got (${otherA.value.womType.stableName}, ${otherB.value.womType.stableName}, ${otherC.value.womType.stableName})".invalidNel
+      case (EvaluatedValue(a, previousSideEffectFilesA),
+            EvaluatedValue(b, previousSideEffectFilesB),
+            EvaluatedValue(c, previousSideEffectFilesC)
+          ) if a.coercionDefined[A] && b.coercionDefined[B] && c.coercionDefined[C] =>
+        (a.coerceToType[A], b.coerceToType[B], c.coerceToType[C]) flatMapN f.apply map { result =>
+          result.copy(sideEffectFiles =
+            result.sideEffectFiles ++ previousSideEffectFilesA ++ previousSideEffectFilesB ++ previousSideEffectFilesC
+          )
+        }
+      case (otherA, otherB, otherC) =>
+        s"Expected (${coercerA.toDisplayString}, ${coercerB.toDisplayString}, ${coercerB.toDisplayString}) argument but got (${otherA.value.womType.stableName}, ${otherB.value.womType.stableName}, ${otherC.value.womType.stableName})".invalidNel
     }
-  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LiteralEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LiteralEvaluators.scala
index ab2b5c0b448..4831c34e76b 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LiteralEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LiteralEvaluators.scala
@@ -14,32 +14,31 @@ import wom.values.{WomArray, WomMap, WomObject, WomPair, WomString, WomValue}
 
 object LiteralEvaluators {
 
-  implicit val primitiveValueEvaluator: ValueEvaluator[PrimitiveLiteralExpressionElement] = new ValueEvaluator[PrimitiveLiteralExpressionElement] {
-    override def evaluateValue(a: PrimitiveLiteralExpressionElement,
-                               inputs: Map[String, WomValue],
-                               ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      EvaluatedValue(a.value, Seq.empty).validNel
+  implicit val primitiveValueEvaluator: ValueEvaluator[PrimitiveLiteralExpressionElement] =
+    new ValueEvaluator[PrimitiveLiteralExpressionElement] {
+      override def evaluateValue(a: PrimitiveLiteralExpressionElement,
+                                 inputs: Map[String, WomValue],
+                                 ioFunctionSet: IoFunctionSet,
+                                 forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+      )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+        EvaluatedValue(a.value, Seq.empty).validNel
     }
-  }
 
   implicit val stringLiteralEvaluator: ValueEvaluator[StringLiteral] = new ValueEvaluator[StringLiteral] {
     override def evaluateValue(a: StringLiteral,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] =
       EvaluatedValue(WomString(a.value), Seq.empty).validNel
-    }
   }
 
   implicit val stringExpressionEvaluator: ValueEvaluator[StringExpression] = new ValueEvaluator[StringExpression] {
     override def evaluateValue(a: StringExpression,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
       val evaluatedPieces = a.pieces.toList.traverse {
         case e: StringPlaceholder => e.expr.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
         case s: StringLiteral => s.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
@@ -56,8 +55,8 @@ object LiteralEvaluators {
     override def evaluateValue(a: ObjectLiteral,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
 
       val evaluated: ErrorOr[List[(String, EvaluatedValue[_])]] = a.elements.toList traverse { case (key, value) =>
         value.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions).map(key -> _)
@@ -75,12 +74,14 @@ object LiteralEvaluators {
     override def evaluateValue(a: MapLiteral,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-
-      val evaluated: ErrorOr[List[(EvaluatedValue[_], EvaluatedValue[_])]] = a.elements.toList traverse { case (key, value) =>
-        (key.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
-          value.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) mapN { (key, value) => key -> value}
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+
+      val evaluated: ErrorOr[List[(EvaluatedValue[_], EvaluatedValue[_])]] = a.elements.toList traverse {
+        case (key, value) =>
+          (key.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
+           value.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+          ) mapN { (key, value) => key -> value }
       }
 
       evaluated map { kvps =>
@@ -95,8 +96,8 @@ object LiteralEvaluators {
     override def evaluateValue(a: ArrayLiteral,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
 
       val evaluated: ErrorOr[Seq[EvaluatedValue[_]]] = a.elements.toList traverse { entry =>
         entry.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
@@ -114,14 +115,12 @@ object LiteralEvaluators {
     override def evaluateValue(a: PairLiteral,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
       (a.left.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
-        a.right.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) mapN { (left, right) =>
-
+       a.right.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) mapN { (left, right) =>
         EvaluatedValue(WomPair(left.value, right.value), left.sideEffectFiles ++ right.sideEffectFiles)
       }
-    }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LookupEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LookupEvaluators.scala
index 114c4051b93..216673417cf 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LookupEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LookupEvaluators.scala
@@ -14,15 +14,14 @@ import wom.values._
 import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
 import wdl.transforms.base.wdlom2wdl.WdlWriterImpl._
 
-
 object LookupEvaluators {
 
   implicit val identifierLookupEvaluator: ValueEvaluator[IdentifierLookup] = new ValueEvaluator[IdentifierLookup] {
     override def evaluateValue(a: IdentifierLookup,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
       inputs.get(a.identifier) match {
         case Some(value) =>
           val mapped = forCommandInstantiationOptions.fold(value)(_.valueMapper(value))
@@ -30,49 +29,59 @@ object LookupEvaluators {
         case None =>
           s"ValueEvaluator[IdentifierLookup]: No suitable input for '${a.identifier}' amongst {${inputs.keys.mkString(", ")}}".invalidNel
       }
-    }
   }
 
-  implicit val expressionMemberAccessEvaluator: ValueEvaluator[ExpressionMemberAccess] = new ValueEvaluator[ExpressionMemberAccess] {
-    override def evaluateValue(a: ExpressionMemberAccess,
-                               inputs: Map[String, WomValue],
-                               ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      a.expression.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions) flatMap { evaluated =>
-        doLookup(evaluated.value, a.memberAccessTail) map { EvaluatedValue(_, evaluated.sideEffectFiles) }
-      }
+  implicit val expressionMemberAccessEvaluator: ValueEvaluator[ExpressionMemberAccess] =
+    new ValueEvaluator[ExpressionMemberAccess] {
+      override def evaluateValue(a: ExpressionMemberAccess,
+                                 inputs: Map[String, WomValue],
+                                 ioFunctionSet: IoFunctionSet,
+                                 forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+      )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+        a.expression.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions) flatMap { evaluated =>
+          doLookup(evaluated.value, a.memberAccessTail) map { EvaluatedValue(_, evaluated.sideEffectFiles) }
+        }
     }
-  }
-
-  implicit val identifierMemberAccessEvaluator: ValueEvaluator[IdentifierMemberAccess] = new ValueEvaluator[IdentifierMemberAccess] {
-    override def evaluateValue(a: IdentifierMemberAccess,
-                               inputs: Map[String, WomValue],
-                               ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
 
-      // Do the first lookup and decide whether any more lookups are needed:
-      val generatedValueAndLookups: ErrorOr[(WomValue, Seq[String])] = {
-        val callOutputKey = s"${a.first}.${a.second}"
+  implicit val identifierMemberAccessEvaluator: ValueEvaluator[IdentifierMemberAccess] =
+    new ValueEvaluator[IdentifierMemberAccess] {
+      override def evaluateValue(a: IdentifierMemberAccess,
+                                 inputs: Map[String, WomValue],
+                                 ioFunctionSet: IoFunctionSet,
+                                 forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+      )(implicit
+        expressionValueEvaluator: ValueEvaluator[ExpressionElement]
+      ): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+
+        // Do the first lookup and decide whether any more lookups are needed:
+        val generatedValueAndLookups: ErrorOr[(WomValue, Seq[String])] = {
+          val callOutputKey = s"${a.first}.${a.second}"
+
+          if (inputs.keySet.contains(a.first)) { (inputs(a.first), List(a.second) ++ a.memberAccessTail).validNel }
+          else if (inputs.keySet.contains(callOutputKey)) { (inputs(callOutputKey), a.memberAccessTail).validNel }
+          else
+            s"No value found for member access lookup. Report this bug: Insufficient input values supplied by engine. Needed '${a.first}' or '$callOutputKey' but only received: '${inputs.keys
+                .mkString(", ")}'".invalidNel
+        }
 
-        if (inputs.keySet.contains(a.first)) { (inputs(a.first), List(a.second) ++ a.memberAccessTail).validNel }
-        else if (inputs.keySet.contains(callOutputKey)) { (inputs(callOutputKey), a.memberAccessTail).validNel }
-        else
-          s"No value found for member access lookup. Report this bug: Insufficient input values supplied by engine. Needed '${a.first}' or '$callOutputKey' but only received: '${inputs.keys.mkString(", ")}'".invalidNel
+        generatedValueAndLookups flatMap { case (foundValue, lookups) =>
+          NonEmptyList.fromList(lookups.toList) match {
+            case Some(lookupNel) => doLookup(foundValue, lookupNel) map { EvaluatedValue(_, Seq.empty) }
+            case None => EvaluatedValue(foundValue, Seq.empty).validNel
+          }
+        }
       }
-
-      generatedValueAndLookups flatMap { case (foundValue, lookups) => NonEmptyList.fromList(lookups.toList) match {
-        case Some(lookupNel) => doLookup(foundValue, lookupNel) map { EvaluatedValue(_, Seq.empty) }
-        case None => EvaluatedValue(foundValue, Seq.empty).validNel
-      }}
     }
-  }
 
   implicit val indexAccessValueEvaluator: ValueEvaluator[IndexAccess] = new ValueEvaluator[IndexAccess] {
-    override def evaluateValue(a: IndexAccess, inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-      (a.expressionElement.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions), a.index.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)) flatMapN { (lhs, rhs) =>
+    override def evaluateValue(a: IndexAccess,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
+      (a.expressionElement.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions),
+       a.index.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+      ) flatMapN { (lhs, rhs) =>
         val value: ErrorOr[WomValue] = (lhs.value, rhs.value) match {
           case (array: WomArray, WomInteger(index)) =>
             if (array.value.length > index)
@@ -80,12 +89,12 @@ object LookupEvaluators {
             else
               s"Bad array access ${a.toWdlV1}: Array size ${array.value.length} does not have an index value '$index'".invalidNel
           case (WomObject(values, _), WomString(index)) =>
-            if(values.contains(index))
+            if (values.contains(index))
               values(index).validNel
             else
               s"Bad Object access ${a.toWdlV1}: Object with keys [${values.keySet.mkString(", ")}] does not have an index value [$index]".invalidNel
           case (WomMap(mapType, values), index) =>
-            if(values.contains(index))
+            if (values.contains(index))
               values(index).validNel
             else
               s"Bad Map access ${a.toWdlV1}: This ${mapType.stableName} does not have a ${index.womType.stableName} index value [${index.toWomString}]".invalidNel
@@ -95,7 +104,6 @@ object LookupEvaluators {
 
         value map { EvaluatedValue(_, lhs.sideEffectFiles ++ rhs.sideEffectFiles) }
       }
-    }
   }
 
   /**
@@ -113,20 +121,29 @@ object LookupEvaluators {
 
     val thisValue: ErrorOr[WomValue] = womValue match {
       case WomObject(values, _) if values.contains(key) => values(key).validNel
-      case WomObject(_, WomCompositeType(typeMap, _)) if typeMap.contains(key) => typeMap(key) match {
-        case WomOptionalType(innerType) => WomOptionalValue(innerType, None).validNel
-        case other => s"Composite value was unexpectedly missing a field: '$key' (expected type ${other.stableName}). Report this bug! Static validation failed.".invalidNel
-      }
-      case WomObject(_, _: WomCompositeType) => s"No such field '$key' on type ${womValue.womType.stableName}. Report this bug! Static validation failed.".invalidNel
+      case WomObject(_, WomCompositeType(typeMap, _)) if typeMap.contains(key) =>
+        typeMap(key) match {
+          case WomOptionalType(innerType) => WomOptionalValue(innerType, None).validNel
+          case other =>
+            s"Composite value was unexpectedly missing a field: '$key' (expected type ${other.stableName}). Report this bug! Static validation failed.".invalidNel
+        }
+      case WomObject(_, _: WomCompositeType) =>
+        s"No such field '$key' on type ${womValue.womType.stableName}. Report this bug! Static validation failed.".invalidNel
       case WomObject(_, _) => s"'Object'-type value did not contain the field '$key' at runtime".invalidNel
       case p: WomPair if key == "left" => p.left.validNel
       case p: WomPair if key == "right" => p.right.validNel
-      case WomMap(_, value) => Validated.fromOption(
-        o = value.collectFirst {
-          case (k, v) if k.valueString == key => v
-        },
-        ifNone = NonEmptyList(s"Requested key '$key' not found in the Map. Available keys were: ${value.keySet.mkString("[ ", ",", "]")}", Nil))
-      case _ => s"No such field '$key' on type ${womValue.womType.stableName}. Report this bug! Static validation failed.".invalidNel
+      case WomMap(_, value) =>
+        Validated.fromOption(
+          o = value.collectFirst {
+            case (k, v) if k.valueString == key => v
+          },
+          ifNone = NonEmptyList(
+            s"Requested key '$key' not found in the Map. Available keys were: ${value.keySet.mkString("[ ", ",", "]")}",
+            Nil
+          )
+        )
+      case _ =>
+        s"No such field '$key' on type ${womValue.womType.stableName}. Report this bug! Static validation failed.".invalidNel
     }
 
     tail match {
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/TernaryIfEvaluator.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/TernaryIfEvaluator.scala
index da51c3b7120..f07402a1efa 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/TernaryIfEvaluator.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/TernaryIfEvaluator.scala
@@ -14,16 +14,19 @@ object TernaryIfEvaluator {
     override def evaluateValue(a: TernaryIf,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
-
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
       a.condition.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions) flatMap {
         case EvaluatedValue(WomBoolean(true), conditionSideEffectFiles) =>
-          a.ifTrue.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions).map(result => result.copy(sideEffectFiles = result.sideEffectFiles ++ conditionSideEffectFiles))
+          a.ifTrue
+            .evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+            .map(result => result.copy(sideEffectFiles = result.sideEffectFiles ++ conditionSideEffectFiles))
         case EvaluatedValue(WomBoolean(false), conditionSideEffectFiles) =>
-          a.ifFalse.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions).map(result => result.copy(sideEffectFiles = result.sideEffectFiles ++ conditionSideEffectFiles))
-        case other => s"Condition should have evaluated to a Boolean but instead got ${other.value.womType.stableName}".invalidNel
+          a.ifFalse
+            .evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
+            .map(result => result.copy(sideEffectFiles = result.sideEffectFiles ++ conditionSideEffectFiles))
+        case other =>
+          s"Condition should have evaluated to a Boolean but instead got ${other.value.womType.stableName}".invalidNel
       }
-    }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/UnaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/UnaryOperatorEvaluators.scala
index 25395ae9239..b548183a800 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/UnaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/UnaryOperatorEvaluators.scala
@@ -22,13 +22,12 @@ object UnaryOperatorEvaluators {
     override def evaluateValue(a: A,
                                inputs: Map[String, WomValue],
                                ioFunctionSet: IoFunctionSet,
-                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions])
-                              (implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] =
       a.argument.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions) flatMap { arg =>
         op(arg.value).toErrorOr map {
           EvaluatedValue(_, arg.sideEffectFiles)
         }
       }
-    }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/LinkedGraphMaker.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/LinkedGraphMaker.scala
index 22862031a16..01573c30737 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/LinkedGraphMaker.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/LinkedGraphMaker.scala
@@ -20,14 +20,16 @@ object LinkedGraphMaker {
   def make(nodes: Set[WorkflowGraphElement],
            externalHandles: Set[GeneratedValueHandle],
            typeAliases: Map[String, WomType],
-           callables: Map[String, Callable])
-          (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): ErrorOr[LinkedGraph] = {
+           callables: Map[String, Callable]
+  )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): ErrorOr[LinkedGraph] = {
 
-    val generatedValuesByGraphNodeValidation: ErrorOr[Map[WorkflowGraphElement, Set[GeneratedValueHandle]]] = nodes.toList.traverse{ node =>
-      node.generatedValueHandles(typeAliases, callables).map(node -> _)
-    } map (_.toMap)
+    val generatedValuesByGraphNodeValidation: ErrorOr[Map[WorkflowGraphElement, Set[GeneratedValueHandle]]] =
+      nodes.toList.traverse { node =>
+        node.generatedValueHandles(typeAliases, callables).map(node -> _)
+      } map (_.toMap)
 
-    val consumedValuesByGraphNodeValidation: ErrorOr[Map[WorkflowGraphElement, Set[UnlinkedConsumedValueHook]]] = nodes.toList.traverse(n => n.graphElementConsumedValueHooks(typeAliases, callables).map(n -> _)).map(_.toMap)
+    val consumedValuesByGraphNodeValidation: ErrorOr[Map[WorkflowGraphElement, Set[UnlinkedConsumedValueHook]]] =
+      nodes.toList.traverse(n => n.graphElementConsumedValueHooks(typeAliases, callables).map(n -> _)).map(_.toMap)
 
     for {
       generatedValuesByGraphNode <- generatedValuesByGraphNodeValidation
@@ -41,7 +43,8 @@ object LinkedGraphMaker {
 
   def getOrdering(linkedGraph: LinkedGraph): ErrorOr[List[WorkflowGraphElement]] = {
 
-    def nodeName(workflowGraphElement: WorkflowGraphElement): String = workflowGraphElement.toWdlV1.linesIterator.toList.headOption.getOrElse("Unnamed Element").replace("\"", "")
+    def nodeName(workflowGraphElement: WorkflowGraphElement): String =
+      workflowGraphElement.toWdlV1.linesIterator.toList.headOption.getOrElse("Unnamed Element").replace("\"", "")
 
     // Find the topological order in which we must create the graph nodes:
     val edges = linkedGraph.edges map { case LinkedGraphEdge(from, to) => DiEdge(from, to) }
@@ -58,9 +61,9 @@ object LinkedGraphMaker {
             //   c -> a
             //   a -> b
             // we want to start the cycle with the edge "a -> b"
-            val edgeDict : Map[String, String] =
-              cycle.value.edges.map{
-                case graph.EdgeT(from, to) => nodeName(from) -> nodeName(to)
+            val edgeDict: Map[String, String] =
+              cycle.value.edges.map { case graph.EdgeT(from, to) =>
+                nodeName(from) -> nodeName(to)
               }.toMap
             val startPoint = edgeDict.keys.toVector.sorted.head
             var cursor = startPoint
@@ -79,7 +82,9 @@ object LinkedGraphMaker {
                |${cycleReport.mkString(System.lineSeparator)}""".stripMargin.invalidNel
 
           case _ =>
-            val edgeStrings = linkedGraph.edges map { case LinkedGraphEdge(from, to) => s""""${nodeName(from)}" -> "${nodeName(to)}"""" }
+            val edgeStrings = linkedGraph.edges map { case LinkedGraphEdge(from, to) =>
+              s""""${nodeName(from)}" -> "${nodeName(to)}""""
+            }
             // sort the edges for determinism
             val edges = edgeStrings.toVector.sorted
             s"""This workflow contains an elusive cyclic dependency amongst these edges:
@@ -87,14 +92,16 @@ object LinkedGraphMaker {
         }
 
       // This asInstanceOf is not required, but it suppresses an incorrect intelliJ error highlight:
-      case Right(topologicalOrder) => topologicalOrder.toList.map(_.value).asInstanceOf[List[WorkflowGraphElement]].validNel
+      case Right(topologicalOrder) =>
+        topologicalOrder.toList.map(_.value).asInstanceOf[List[WorkflowGraphElement]].validNel
     }
   }
 
   private def makeEdges(elements: Set[WorkflowGraphElement],
-                    consumedValuesByGraphNode: Map[WorkflowGraphElement, Set[UnlinkedConsumedValueHook]],
-                    consumedValueLookup: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
-                    graphElementByGeneratedValueHandle: Map[GeneratedValueHandle, WorkflowGraphElement]): Set[LinkedGraphEdge] = for {
+                        consumedValuesByGraphNode: Map[WorkflowGraphElement, Set[UnlinkedConsumedValueHook]],
+                        consumedValueLookup: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                        graphElementByGeneratedValueHandle: Map[GeneratedValueHandle, WorkflowGraphElement]
+  ): Set[LinkedGraphEdge] = for {
     downstreamElement <- elements
     hook <- consumedValuesByGraphNode(downstreamElement)
     upstreamHandle = consumedValueLookup(hook)
@@ -105,23 +112,36 @@ object LinkedGraphMaker {
                                       typeAliases: Map[String, WomType],
                                       availableHandles: Set[GeneratedValueHandle],
                                       callables: Map[String, Callable]
-                                     )
-                                     (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): ErrorOr[Map[UnlinkedConsumedValueHook, GeneratedValueHandle]] = {
-    val consumedValidation: ErrorOr[Set[UnlinkedConsumedValueHook]] = nodes.toList.traverse(n => n.graphElementConsumedValueHooks(typeAliases, callables)).map(_.toSet.flatten)
+  )(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+  ): ErrorOr[Map[UnlinkedConsumedValueHook, GeneratedValueHandle]] = {
+    val consumedValidation: ErrorOr[Set[UnlinkedConsumedValueHook]] =
+      nodes.toList.traverse(n => n.graphElementConsumedValueHooks(typeAliases, callables)).map(_.toSet.flatten)
 
-    consumedValidation.flatMap { consumed => makeConsumedValueLookup(consumed, availableHandles) }
+    consumedValidation.flatMap(consumed => makeConsumedValueLookup(consumed, availableHandles))
   }
 
-  def makeConsumedValueLookup(consumedValues: Set[UnlinkedConsumedValueHook], availableHandles: Set[GeneratedValueHandle]): ErrorOr[Map[UnlinkedConsumedValueHook, GeneratedValueHandle]] = {
+  def makeConsumedValueLookup(consumedValues: Set[UnlinkedConsumedValueHook],
+                              availableHandles: Set[GeneratedValueHandle]
+  ): ErrorOr[Map[UnlinkedConsumedValueHook, GeneratedValueHandle]] = {
     def isMatch(hook: UnlinkedConsumedValueHook, handle: GeneratedValueHandle): Boolean = (hook, handle) match {
       case (UnlinkedIdentifierHook(id1), GeneratedIdentifierValueHandle(id2, _)) => id1 == id2
-      case (UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first, _), GeneratedIdentifierValueHandle(id2, _)) if first == id2 => true
-      case (UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first1, second1), GeneratedCallOutputValueHandle(first2, second2, _)) if first1 == first2 && second1 == second2 => true
-      case (UnlinkedAfterCallHook(upstreamCallName), GeneratedCallFinishedHandle(finishedCallName)) if finishedCallName == upstreamCallName => true
+      case (UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first, _), GeneratedIdentifierValueHandle(id2, _))
+          if first == id2 =>
+        true
+      case (UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first1, second1),
+            GeneratedCallOutputValueHandle(first2, second2, _)
+          ) if first1 == first2 && second1 == second2 =>
+        true
+      case (UnlinkedAfterCallHook(upstreamCallName), GeneratedCallFinishedHandle(finishedCallName))
+          if finishedCallName == upstreamCallName =>
+        true
       case _ => false
     }
 
-    def findHandle(consumedValueHook: UnlinkedConsumedValueHook): ErrorOr[(UnlinkedConsumedValueHook, GeneratedValueHandle)] = {
+    def findHandle(
+      consumedValueHook: UnlinkedConsumedValueHook
+    ): ErrorOr[(UnlinkedConsumedValueHook, GeneratedValueHandle)] = {
       val maybeFoundHandle = availableHandles collectFirst {
         case handle if isMatch(consumedValueHook, handle) => handle
       }
@@ -129,22 +149,25 @@ object LinkedGraphMaker {
       (maybeFoundHandle, consumedValueHook) match {
         case (Some(handle), hook) => (hook -> handle).validNel
         case (None, UnlinkedAfterCallHook(upstreamCallName)) =>
-            val didYouMean = availableHandles.collect {
-              case after: GeneratedCallFinishedHandle => s"'${after.finishedCallName}'"
-            }.mkString("[", ", ", "]")
-            s"Cannot specify 'after $upstreamCallName': no such call exists. Available calls are: $didYouMean".invalidNel
+          val didYouMean = availableHandles
+            .collect { case after: GeneratedCallFinishedHandle =>
+              s"'${after.finishedCallName}'"
+            }
+            .mkString("[", ", ", "]")
+          s"Cannot specify 'after $upstreamCallName': no such call exists. Available calls are: $didYouMean".invalidNel
         case (None, _) =>
-            val didYouMean = availableHandles.map(h => s"'${h.linkableName}'").mkString("[", ", ", "]")
-            s"Cannot lookup value '${consumedValueHook.linkString}', it is never declared. Available values are: $didYouMean".invalidNel
+          val didYouMean = availableHandles.map(h => s"'${h.linkableName}'").mkString("[", ", ", "]")
+          s"Cannot lookup value '${consumedValueHook.linkString}', it is never declared. Available values are: $didYouMean".invalidNel
       }
     }
 
-
-    consumedValues.toList.traverse { findHandle } map {_.toMap}
+    consumedValues.toList.traverse(findHandle) map { _.toMap }
 
   }
 
-  private def reverseMap(mapping: Map[WorkflowGraphElement, Set[GeneratedValueHandle]]): ErrorOr[Map[GeneratedValueHandle, WorkflowGraphElement]] = {
+  private def reverseMap(
+    mapping: Map[WorkflowGraphElement, Set[GeneratedValueHandle]]
+  ): ErrorOr[Map[GeneratedValueHandle, WorkflowGraphElement]] = {
     val reversed = for {
       nodeAndHandles <- mapping.toList
       node = nodeAndHandles._1
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/package.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/package.scala
index 3a9ccb96900..4a83b19e6cb 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/package.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/package.scala
@@ -18,130 +18,175 @@ import wom.callable.Callable.OutputDefinition
 import wom.types.{WomArrayType, WomOptionalType, WomType}
 
 package object graph {
-  implicit val graphElementUnlinkedValueGenerator: UnlinkedValueGenerator[WorkflowGraphElement] = new UnlinkedValueGenerator[WorkflowGraphElement] {
-
-    override def generatedValueHandles(a: WorkflowGraphElement,
-                                       typeAliases: Map[String, WomType],
-                                       callables: Map[String, Callable]): ErrorOr[Set[GeneratedValueHandle]] = a match {
-      case DeclarationElement(typeElement, name, _) =>
-        typeElement.determineWomType(typeAliases) map { t => Set(GeneratedIdentifierValueHandle(name, t)) }
-      case a: ScatterElement => a.generatedValueHandles(typeAliases, callables)
-      case a: IfElement => a.generatedValueHandles(typeAliases, callables)
-      case a: CallElement => a.generatedValueHandles(typeAliases, callables)
-      case other => s"Cannot generate generated values for WorkflowGraphNodeElement $other".invalidNel
+  implicit val graphElementUnlinkedValueGenerator: UnlinkedValueGenerator[WorkflowGraphElement] =
+    new UnlinkedValueGenerator[WorkflowGraphElement] {
+
+      override def generatedValueHandles(a: WorkflowGraphElement,
+                                         typeAliases: Map[String, WomType],
+                                         callables: Map[String, Callable]
+      ): ErrorOr[Set[GeneratedValueHandle]] = a match {
+        case DeclarationElement(typeElement, name, _) =>
+          typeElement.determineWomType(typeAliases) map { t => Set(GeneratedIdentifierValueHandle(name, t)) }
+        case a: ScatterElement => a.generatedValueHandles(typeAliases, callables)
+        case a: IfElement => a.generatedValueHandles(typeAliases, callables)
+        case a: CallElement => a.generatedValueHandles(typeAliases, callables)
+        case other => s"Cannot generate generated values for WorkflowGraphNodeElement $other".invalidNel
+      }
     }
-  }
-
-  implicit val scatterElementUnlinkedValueGenerator: UnlinkedValueGenerator[ScatterElement] = new UnlinkedValueGenerator[ScatterElement] {
-    override def generatedValueHandles(a: ScatterElement, typeAliases: Map[String, WomType], callables: Map[String, Callable]): ErrorOr[Set[GeneratedValueHandle]] = {
-      a.graphElements.toList.traverse(_.generatedValueHandles(typeAliases, callables)).map(_.toSet.flatten) map { _.map {
-        case GeneratedIdentifierValueHandle(id, womType) => GeneratedIdentifierValueHandle(id, WomArrayType(womType))
-        case GeneratedCallOutputValueHandle(first, second, womType) => GeneratedCallOutputValueHandle(first, second, WomArrayType(womType))
-        case a: GeneratedCallFinishedHandle => a
-      } }
+
+  implicit val scatterElementUnlinkedValueGenerator: UnlinkedValueGenerator[ScatterElement] =
+    new UnlinkedValueGenerator[ScatterElement] {
+      override def generatedValueHandles(a: ScatterElement,
+                                         typeAliases: Map[String, WomType],
+                                         callables: Map[String, Callable]
+      ): ErrorOr[Set[GeneratedValueHandle]] =
+        a.graphElements.toList.traverse(_.generatedValueHandles(typeAliases, callables)).map(_.toSet.flatten) map {
+          _.map {
+            case GeneratedIdentifierValueHandle(id, womType) =>
+              GeneratedIdentifierValueHandle(id, WomArrayType(womType))
+            case GeneratedCallOutputValueHandle(first, second, womType) =>
+              GeneratedCallOutputValueHandle(first, second, WomArrayType(womType))
+            case a: GeneratedCallFinishedHandle => a
+          }
+        }
     }
-  }
-
-  implicit val IfElementUnlinkedValueGenerator: UnlinkedValueGenerator[IfElement] = new UnlinkedValueGenerator[IfElement] {
-    override def generatedValueHandles(a: IfElement, typeAliases: Map[String, WomType], callables: Map[String, Callable]): ErrorOr[Set[GeneratedValueHandle]] = {
-      a.graphElements.toList.traverse(_.generatedValueHandles(typeAliases, callables)).map(_.toSet.flatten) map { _.map {
-        case GeneratedIdentifierValueHandle(id, womType) => GeneratedIdentifierValueHandle(id, WomOptionalType(womType).flatOptionalType)
-        case GeneratedCallOutputValueHandle(first, second, womType) => GeneratedCallOutputValueHandle(first, second, WomOptionalType(womType).flatOptionalType)
-        case a: GeneratedCallFinishedHandle => a
-      } }
+
+  implicit val IfElementUnlinkedValueGenerator: UnlinkedValueGenerator[IfElement] =
+    new UnlinkedValueGenerator[IfElement] {
+      override def generatedValueHandles(a: IfElement,
+                                         typeAliases: Map[String, WomType],
+                                         callables: Map[String, Callable]
+      ): ErrorOr[Set[GeneratedValueHandle]] =
+        a.graphElements.toList.traverse(_.generatedValueHandles(typeAliases, callables)).map(_.toSet.flatten) map {
+          _.map {
+            case GeneratedIdentifierValueHandle(id, womType) =>
+              GeneratedIdentifierValueHandle(id, WomOptionalType(womType).flatOptionalType)
+            case GeneratedCallOutputValueHandle(first, second, womType) =>
+              GeneratedCallOutputValueHandle(first, second, WomOptionalType(womType).flatOptionalType)
+            case a: GeneratedCallFinishedHandle => a
+          }
+        }
     }
-  }
 
-  implicit val callElementUnlinkedValueGenerator: UnlinkedValueGenerator[CallElement] = new UnlinkedValueGenerator[CallElement] {
-    override def generatedValueHandles(a: CallElement, typeAliases: Map[String, WomType], callables: Map[String, Callable]): ErrorOr[Set[GeneratedValueHandle]] = {
-      def callableOutputToHandle(callAlias: String)(callableOutput: OutputDefinition): GeneratedValueHandle = {
-        GeneratedCallOutputValueHandle(callAlias, callableOutput.name, callableOutput.womType)
+  implicit val callElementUnlinkedValueGenerator: UnlinkedValueGenerator[CallElement] =
+    new UnlinkedValueGenerator[CallElement] {
+      override def generatedValueHandles(a: CallElement,
+                                         typeAliases: Map[String, WomType],
+                                         callables: Map[String, Callable]
+      ): ErrorOr[Set[GeneratedValueHandle]] = {
+        def callableOutputToHandle(callAlias: String)(callableOutput: OutputDefinition): GeneratedValueHandle =
+          GeneratedCallOutputValueHandle(callAlias, callableOutput.name, callableOutput.womType)
+
+        callables.get(a.callableReference) match {
+          case Some(callable) =>
+            val callAlias = a.alias.getOrElse(callable.name)
+            val outputs = callable.outputs.map(callableOutputToHandle(callAlias)).toSet
+            (outputs + GeneratedCallFinishedHandle(callAlias)).validNel
+          case None =>
+            s"Cannot generate outputs for 'call ${a.callableReference}'. No such callable exists in [${callables.keySet
+                .mkString(", ")}]".invalidNel
+        }
       }
+    }
 
-      callables.get(a.callableReference) match {
-        case Some(callable) =>
-          val callAlias = a.alias.getOrElse(callable.name)
-          val outputs = callable.outputs.map(callableOutputToHandle(callAlias)).toSet
-          (outputs + GeneratedCallFinishedHandle(callAlias)).validNel
-        case None => s"Cannot generate outputs for 'call ${a.callableReference}'. No such callable exists in [${callables.keySet.mkString(", ")}]".invalidNel
+  implicit val graphElementUnlinkedValueConsumer: GraphElementValueConsumer[WorkflowGraphElement] =
+    new GraphElementValueConsumer[WorkflowGraphElement] {
+      override def graphElementConsumedValueHooks(a: WorkflowGraphElement,
+                                                  typeAliases: Map[String, WomType],
+                                                  callables: Map[String, Callable]
+      )(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): ErrorOr[Set[UnlinkedConsumedValueHook]] = a match {
+        case InputDeclarationElement(_, _, None) => Set.empty[UnlinkedConsumedValueHook].validNel
+        case DeclarationElement(_, _, Some(expr)) => expr.expressionConsumedValueHooks.validNel
+        case a: ScatterElement => a.graphElementConsumedValueHooks(typeAliases, callables)
+        case a: IfElement => a.graphElementConsumedValueHooks(typeAliases, callables)
+        case a: CallElement => a.graphElementConsumedValueHooks(typeAliases, callables)
+        // TODO fill in other expression types
+        case other => throw new Exception(s"Cannot generate consumed values for WorkflowGraphNodeElement $other")
       }
     }
-  }
-
-  implicit val graphElementUnlinkedValueConsumer: GraphElementValueConsumer[WorkflowGraphElement] = new GraphElementValueConsumer[WorkflowGraphElement] {
-    override def graphElementConsumedValueHooks(a: WorkflowGraphElement,
-                                                typeAliases: Map[String, WomType],
-                                                callables: Map[String, Callable])
-                                               (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): ErrorOr[Set[UnlinkedConsumedValueHook]] = a match {
-      case InputDeclarationElement(_, _, None) => Set.empty[UnlinkedConsumedValueHook].validNel
-      case DeclarationElement(_, _, Some(expr)) => expr.expressionConsumedValueHooks.validNel
-      case a: ScatterElement => a.graphElementConsumedValueHooks(typeAliases, callables)
-      case a: IfElement => a.graphElementConsumedValueHooks(typeAliases, callables)
-      case a: CallElement => a.graphElementConsumedValueHooks(typeAliases, callables)
-      // TODO fill in other expression types
-      case other => throw new Exception(s"Cannot generate consumed values for WorkflowGraphNodeElement $other")
-    }
-  }
-
-  implicit val callElementUnlinkedValueConsumer: GraphElementValueConsumer[CallElement] = new GraphElementValueConsumer[CallElement] {
-    override def graphElementConsumedValueHooks(a: CallElement,
-                                                typeAliases: Map[String, WomType],
-                                                callables: Map[String, Callable])
-                                               (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): ErrorOr[Set[UnlinkedConsumedValueHook]] = {
-      import wdl.transforms.base.linking.expression.consumed.LiteralEvaluators.kvPairUnlinkedValueConsumer
-      val consumedByInputSection: Set[UnlinkedConsumedValueHook] = a.body match {
-        case Some(callBodyElement: CallBodyElement) => callBodyElement.inputs.flatMap(_.expressionConsumedValueHooks).toSet
-        case None => Set.empty[UnlinkedConsumedValueHook]
-      }
-
-      val consumedByAfterRequirement: Vector[UnlinkedConsumedValueHook] = a.afters map UnlinkedAfterCallHook.apply
 
-      (consumedByInputSection ++ consumedByAfterRequirement).validNel
-    }
-  }
-
-  implicit val scatterElementUnlinkedValueConsumer: GraphElementValueConsumer[ScatterElement] = new GraphElementValueConsumer[ScatterElement] {
-    override def graphElementConsumedValueHooks(a: ScatterElement,
-                                                typeAliases: Map[String, WomType],
-                                                callables: Map[String, Callable])
-                                               (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): ErrorOr[Set[UnlinkedConsumedValueHook]] = {
-      val bodyConsumedValuesValidation: ErrorOr[Set[UnlinkedConsumedValueHook]] = a.graphElements.toList.traverse(_.graphElementConsumedValueHooks(typeAliases, callables)).map(_.toSet.flatten)
-      val scatterExpressionHooks: Set[UnlinkedConsumedValueHook] = a.scatterExpression.expressionConsumedValueHooks
-
-      val bodyGeneratedValuesValidation: ErrorOr[Set[String]] = a.graphElements.toList.traverse(_.generatedValueHandles(typeAliases, callables)).map(_.toSet.flatten.map(_.linkableName))
-
-      (bodyConsumedValuesValidation, bodyGeneratedValuesValidation) mapN { (bodyConsumedValues, bodyGeneratedValues) =>
-        val unsatisfiedBodyElementHooks = bodyConsumedValues.filterNot {
-          case UnlinkedIdentifierHook(id) => bodyGeneratedValues.contains(id) || id == a.scatterVariableName
-          case UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first, second) =>
-            bodyGeneratedValues.contains(first) || bodyGeneratedValues.contains(s"$first.$second") || a.scatterVariableName == first
-          case after: UnlinkedAfterCallHook => bodyGeneratedValues.contains(after.linkString)
+  implicit val callElementUnlinkedValueConsumer: GraphElementValueConsumer[CallElement] =
+    new GraphElementValueConsumer[CallElement] {
+      override def graphElementConsumedValueHooks(a: CallElement,
+                                                  typeAliases: Map[String, WomType],
+                                                  callables: Map[String, Callable]
+      )(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): ErrorOr[Set[UnlinkedConsumedValueHook]] = {
+        import wdl.transforms.base.linking.expression.consumed.LiteralEvaluators.kvPairUnlinkedValueConsumer
+        val consumedByInputSection: Set[UnlinkedConsumedValueHook] = a.body match {
+          case Some(callBodyElement: CallBodyElement) =>
+            callBodyElement.inputs.flatMap(_.expressionConsumedValueHooks).toSet
+          case None => Set.empty[UnlinkedConsumedValueHook]
         }
 
-        unsatisfiedBodyElementHooks ++ scatterExpressionHooks
+        val consumedByAfterRequirement: Vector[UnlinkedConsumedValueHook] = a.afters map UnlinkedAfterCallHook.apply
+
+        (consumedByInputSection ++ consumedByAfterRequirement).validNel
       }
     }
-  }
-
-  implicit val ifElementUnlinkedValueConsumer: GraphElementValueConsumer[IfElement] = new GraphElementValueConsumer[IfElement] {
-    override def graphElementConsumedValueHooks(a: IfElement,
-                                                typeAliases: Map[String, WomType],
-                                                callables: Map[String, Callable])
-                                               (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): ErrorOr[Set[UnlinkedConsumedValueHook]] = {
-      val bodyConsumedValuesValidation: ErrorOr[Set[UnlinkedConsumedValueHook]] = a.graphElements.toList.traverse(_.graphElementConsumedValueHooks(typeAliases, callables)).map(_.toSet.flatten)
-      val ifExpressionHooks: Set[UnlinkedConsumedValueHook] = a.conditionExpression.expressionConsumedValueHooks
-
-      val bodyGeneratedValuesValidation: ErrorOr[Set[String]] = a.graphElements.toList.traverse(_.generatedValueHandles(typeAliases, callables)).map(_.toSet.flatten.map(_.linkableName))
-
-      (bodyConsumedValuesValidation, bodyGeneratedValuesValidation) mapN { (bodyConsumedValues, bodyGeneratedValues) =>
-        val unsatisfiedBodyElementHooks = bodyConsumedValues.filterNot {
-          case UnlinkedIdentifierHook(id) => bodyGeneratedValues.contains(id)
-          case UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first, second) => bodyGeneratedValues.contains(first) || bodyGeneratedValues.contains(s"$first.$second")
-          case after: UnlinkedAfterCallHook => bodyGeneratedValues.contains(after.linkString)
+
+  implicit val scatterElementUnlinkedValueConsumer: GraphElementValueConsumer[ScatterElement] =
+    new GraphElementValueConsumer[ScatterElement] {
+      override def graphElementConsumedValueHooks(a: ScatterElement,
+                                                  typeAliases: Map[String, WomType],
+                                                  callables: Map[String, Callable]
+      )(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): ErrorOr[Set[UnlinkedConsumedValueHook]] = {
+        val bodyConsumedValuesValidation: ErrorOr[Set[UnlinkedConsumedValueHook]] =
+          a.graphElements.toList.traverse(_.graphElementConsumedValueHooks(typeAliases, callables)).map(_.toSet.flatten)
+        val scatterExpressionHooks: Set[UnlinkedConsumedValueHook] = a.scatterExpression.expressionConsumedValueHooks
+
+        val bodyGeneratedValuesValidation: ErrorOr[Set[String]] = a.graphElements.toList
+          .traverse(_.generatedValueHandles(typeAliases, callables))
+          .map(_.toSet.flatten.map(_.linkableName))
+
+        (bodyConsumedValuesValidation, bodyGeneratedValuesValidation) mapN {
+          (bodyConsumedValues, bodyGeneratedValues) =>
+            val unsatisfiedBodyElementHooks = bodyConsumedValues.filterNot {
+              case UnlinkedIdentifierHook(id) => bodyGeneratedValues.contains(id) || id == a.scatterVariableName
+              case UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first, second) =>
+                bodyGeneratedValues.contains(first) || bodyGeneratedValues.contains(
+                  s"$first.$second"
+                ) || a.scatterVariableName == first
+              case after: UnlinkedAfterCallHook => bodyGeneratedValues.contains(after.linkString)
+            }
+
+            unsatisfiedBodyElementHooks ++ scatterExpressionHooks
         }
+      }
+    }
 
-        unsatisfiedBodyElementHooks ++ ifExpressionHooks
+  implicit val ifElementUnlinkedValueConsumer: GraphElementValueConsumer[IfElement] =
+    new GraphElementValueConsumer[IfElement] {
+      override def graphElementConsumedValueHooks(a: IfElement,
+                                                  typeAliases: Map[String, WomType],
+                                                  callables: Map[String, Callable]
+      )(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): ErrorOr[Set[UnlinkedConsumedValueHook]] = {
+        val bodyConsumedValuesValidation: ErrorOr[Set[UnlinkedConsumedValueHook]] =
+          a.graphElements.toList.traverse(_.graphElementConsumedValueHooks(typeAliases, callables)).map(_.toSet.flatten)
+        val ifExpressionHooks: Set[UnlinkedConsumedValueHook] = a.conditionExpression.expressionConsumedValueHooks
+
+        val bodyGeneratedValuesValidation: ErrorOr[Set[String]] = a.graphElements.toList
+          .traverse(_.generatedValueHandles(typeAliases, callables))
+          .map(_.toSet.flatten.map(_.linkableName))
+
+        (bodyConsumedValuesValidation, bodyGeneratedValuesValidation) mapN {
+          (bodyConsumedValues, bodyGeneratedValues) =>
+            val unsatisfiedBodyElementHooks = bodyConsumedValues.filterNot {
+              case UnlinkedIdentifierHook(id) => bodyGeneratedValues.contains(id)
+              case UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first, second) =>
+                bodyGeneratedValues.contains(first) || bodyGeneratedValues.contains(s"$first.$second")
+              case after: UnlinkedAfterCallHook => bodyGeneratedValues.contains(after.linkString)
+            }
+
+            unsatisfiedBodyElementHooks ++ ifExpressionHooks
+        }
       }
     }
-  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/typemakers/package.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/typemakers/package.scala
index 6213f438089..00f85727f97 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/typemakers/package.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/typemakers/package.scala
@@ -11,51 +11,51 @@ import wdl.model.draft3.graph.expression.WomTypeMaker.ops._
 import wom.types._
 
 package object typemakers {
-  implicit val primitiveTypeElementConverter: WomTypeMaker[PrimitiveTypeElement] = new WomTypeMaker[PrimitiveTypeElement] {
-    override def determineWomType(a: PrimitiveTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] = {
-      a.primitiveType.validNel
+  implicit val primitiveTypeElementConverter: WomTypeMaker[PrimitiveTypeElement] =
+    new WomTypeMaker[PrimitiveTypeElement] {
+      override def determineWomType(a: PrimitiveTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] =
+        a.primitiveType.validNel
     }
-  }
 
   implicit val arrayTypeElementConverter: WomTypeMaker[ArrayTypeElement] = new WomTypeMaker[ArrayTypeElement] {
-    override def determineWomType(a: ArrayTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] = {
+    override def determineWomType(a: ArrayTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] =
       a.inner.determineWomType(availableAliases) map { inner => WomArrayType(inner) }
-    }
   }
 
   implicit val mapTypeElementConverter: WomTypeMaker[MapTypeElement] = new WomTypeMaker[MapTypeElement] {
-    override def determineWomType(a: MapTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] = {
-      (a.keyType.determineWomType(availableAliases),
-        a.valueType.determineWomType(availableAliases)) mapN { (keyType, valueType) => WomMapType(keyType, valueType) }
-    }
+    override def determineWomType(a: MapTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] =
+      (a.keyType.determineWomType(availableAliases), a.valueType.determineWomType(availableAliases)) mapN {
+        (keyType, valueType) => WomMapType(keyType, valueType)
+      }
   }
 
   implicit val optionalTypeElementConverter: WomTypeMaker[OptionalTypeElement] = new WomTypeMaker[OptionalTypeElement] {
-    override def determineWomType(a: OptionalTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] = {
+    override def determineWomType(a: OptionalTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] =
       a.maybeType.determineWomType(availableAliases) map { inner => WomOptionalType(inner) }
-    }
   }
 
   implicit val nonEmptyTypeElementConverter: WomTypeMaker[NonEmptyTypeElement] = new WomTypeMaker[NonEmptyTypeElement] {
-    override def determineWomType(a: NonEmptyTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] = {
+    override def determineWomType(a: NonEmptyTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] =
       a.arrayType.determineWomType(availableAliases) flatMap {
         case WomArrayType(memberType) => WomNonEmptyArrayType(memberType).validNel
         case other: WomType => s"Cannot declare a non-empty $other (+ is only applicable to Array[_] types)".invalidNel
       }
-    }
   }
 
   implicit val pairTypeElementConverter: WomTypeMaker[PairTypeElement] = new WomTypeMaker[PairTypeElement] {
-    override def determineWomType(a: PairTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] = {
-      (a.leftType.determineWomType(availableAliases),
-        a.rightType.determineWomType(availableAliases)) mapN { (keyType, valueType) => WomPairType(keyType, valueType) }
-    }
+    override def determineWomType(a: PairTypeElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] =
+      (a.leftType.determineWomType(availableAliases), a.rightType.determineWomType(availableAliases)) mapN {
+        (keyType, valueType) => WomPairType(keyType, valueType)
+      }
   }
 
   implicit val structTypeElementConverter: WomTypeMaker[TypeAliasElement] = new WomTypeMaker[TypeAliasElement] {
-    override def determineWomType(a: TypeAliasElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] = {
-      availableAliases.get(a.alias).toErrorOr(s"No struct definition for '${a.alias}' found in available structs: [${availableAliases.values.mkString(", ")}]")
-    }
+    override def determineWomType(a: TypeAliasElement, availableAliases: Map[String, WomType]): ErrorOr[WomType] =
+      availableAliases
+        .get(a.alias)
+        .toErrorOr(
+          s"No struct definition for '${a.alias}' found in available structs: [${availableAliases.values.mkString(", ")}]"
+        )
   }
 
   implicit val typeElementToWomType: WomTypeMaker[TypeElement] = new WomTypeMaker[TypeElement] {
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriter.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriter.scala
index 7df0cf44810..01090b1e7cc 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriter.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriter.scala
@@ -10,6 +10,6 @@ trait WdlWriter[A] {
 object WdlWriter {
   // Stolen from WomGraph.scala
   def indent(s: String) = s.linesIterator.map(x => s"  $x").mkString(System.lineSeparator)
-  def combine(ss: Iterable[String]) = ss.mkString(start="", sep=System.lineSeparator, end=System.lineSeparator)
+  def combine(ss: Iterable[String]) = ss.mkString(start = "", sep = System.lineSeparator, end = System.lineSeparator)
   def indentAndCombine(ss: Iterable[String]) = combine(ss.map(indent))
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
index 0597b9c830e..70cc56b5a65 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
@@ -16,15 +16,14 @@ object WdlWriterImpl {
   import WdlWriter.ops._
 
   implicit val ifWriter: WdlWriter[IfElement] = new WdlWriter[IfElement] {
-    override def toWdlV1(a: IfElement) = {
+    override def toWdlV1(a: IfElement) =
       s"""if (${a.conditionExpression.toWdlV1}) {
          |${indentAndCombine(a.graphElements.map(_.toWdlV1))}}""".stripMargin
-    }
   }
 
   implicit val stringPieceWriter: WdlWriter[StringPiece] = new WdlWriter[StringPiece] {
     override def toWdlV1(a: StringPiece): String = a match {
-      case a: StringLiteral     => a.value
+      case a: StringLiteral => a.value
       case a: StringPlaceholder => "~{" + a.expr.toWdlV1 + "}"
       case NewlineEscape => "\\n"
       case TabEscape => "\\t"
@@ -35,7 +34,8 @@ object WdlWriterImpl {
     }
   }
 
-  implicit val indexAccessWriter: WdlWriter[IndexAccess] = a => s"${expressionElementWriter.toWdlV1(a.expressionElement)}[${expressionElementWriter.toWdlV1(a.index)}]"
+  implicit val indexAccessWriter: WdlWriter[IndexAccess] = a =>
+    s"${expressionElementWriter.toWdlV1(a.expressionElement)}[${expressionElementWriter.toWdlV1(a.index)}]"
 
   // Recursive references must be explicit
   implicit val expressionElementWriter: WdlWriter[ExpressionElement] = new WdlWriter[ExpressionElement] {
@@ -45,25 +45,31 @@ object WdlWriterImpl {
       case a: StringExpression => "\"" + a.pieces.map(_.toWdlV1).mkString + "\""
       case a: StringLiteral => "\"" + StringEscapeUtils.escapeJava(a.value) + "\""
       case a: ObjectLiteral =>
-        "object { " + a.elements.map { pair =>
-          pair._1 + ": " + expressionElementWriter.toWdlV1(pair._2)
-        }.mkString(", ") + " }"
+        "object { " + a.elements
+          .map { pair =>
+            pair._1 + ": " + expressionElementWriter.toWdlV1(pair._2)
+          }
+          .mkString(", ") + " }"
       case a: ArrayLiteral =>
         "[" + a.elements.map(expressionElementWriter.toWdlV1).mkString(", ") + "]"
       case a: MapLiteral =>
-        "{ " + a.elements.map { pair =>
-          expressionElementWriter.toWdlV1(pair._1) + ": " + expressionElementWriter.toWdlV1(pair._2)
-        }.mkString(", ") + " }"
+        "{ " + a.elements
+          .map { pair =>
+            expressionElementWriter.toWdlV1(pair._1) + ": " + expressionElementWriter.toWdlV1(pair._2)
+          }
+          .mkString(", ") + " }"
       case a: PairLiteral =>
         s"(${expressionElementWriter.toWdlV1(a.left)}, ${expressionElementWriter.toWdlV1(a.right)})"
       case a: UnaryOperation => a.toWdlV1
       case a: BinaryOperation => a.toWdlV1
       case a: TernaryIf =>
-        s"if ${expressionElementWriter.toWdlV1(a.condition)} then ${expressionElementWriter.toWdlV1(a.ifTrue)} else ${expressionElementWriter.toWdlV1(a.ifFalse)}"
+        s"if ${expressionElementWriter.toWdlV1(a.condition)} then ${expressionElementWriter.toWdlV1(a.ifTrue)} else ${expressionElementWriter
+            .toWdlV1(a.ifFalse)}"
       case a: FunctionCallElement => a.toWdlV1
       case a: IdentifierLookup => a.identifier
       case a: IdentifierMemberAccess => a.toWdlV1
-      case a: ExpressionMemberAccess => s"${expressionElementWriter.toWdlV1(a.expression)}.${a.memberAccessTail.toList.mkString(".")}"
+      case a: ExpressionMemberAccess =>
+        s"${expressionElementWriter.toWdlV1(a.expression)}.${a.memberAccessTail.toList.mkString(".")}"
       case a: IndexAccess => a.toWdlV1
       case a: ExpressionLiteralElement => a.expression
     }
@@ -71,38 +77,37 @@ object WdlWriterImpl {
 
   implicit val unaryOperationWriter: WdlWriter[UnaryOperation] = new WdlWriter[UnaryOperation] {
     override def toWdlV1(a: UnaryOperation): String = a match {
-      case a: LogicalNot    => s"!(${a.argument.toWdlV1})"
+      case a: LogicalNot => s"!(${a.argument.toWdlV1})"
       case a: UnaryNegation => s"-(${a.argument.toWdlV1})"
-      case a: UnaryPlus     => s"+(${a.argument.toWdlV1})"
+      case a: UnaryPlus => s"+(${a.argument.toWdlV1})"
     }
   }
 
   implicit val identifierMemberAccessWriter: WdlWriter[IdentifierMemberAccess] = new WdlWriter[IdentifierMemberAccess] {
-    override def toWdlV1(a: IdentifierMemberAccess): String = {
+    override def toWdlV1(a: IdentifierMemberAccess): String =
       s"${a.first}.${a.second}" + (if (a.memberAccessTail.nonEmpty) {
-        "." + a.memberAccessTail.mkString(".")
-      } else {
-        ""
-      })
-    }
+                                     "." + a.memberAccessTail.mkString(".")
+                                   } else {
+                                     ""
+                                   })
   }
 
   implicit val binaryOperationWriter: WdlWriter[BinaryOperation] = new WdlWriter[BinaryOperation] {
     override def toWdlV1(a: BinaryOperation) = {
       val op = a match {
-        case _: LogicalOr           => "||"
-        case _: LogicalAnd          => "&&"
-        case _: Equals              => "=="
-        case _: NotEquals           => "!="
-        case _: LessThan            => "<"
-        case _: LessThanOrEquals    => "<="
-        case _: GreaterThan         => ">"
+        case _: LogicalOr => "||"
+        case _: LogicalAnd => "&&"
+        case _: Equals => "=="
+        case _: NotEquals => "!="
+        case _: LessThan => "<"
+        case _: LessThanOrEquals => "<="
+        case _: GreaterThan => ">"
         case _: GreaterThanOrEquals => ">="
-        case _: Add                 => "+"
-        case _: Subtract            => "-"
-        case _: Multiply            => "*"
-        case _: Divide              => "/"
-        case _: Remainder           => "%"
+        case _: Add => "+"
+        case _: Subtract => "-"
+        case _: Multiply => "*"
+        case _: Divide => "/"
+        case _: Remainder => "%"
       }
 
       s"(${a.left.toWdlV1} $op ${a.right.toWdlV1})"
@@ -127,14 +132,13 @@ object WdlWriterImpl {
   }
 
   implicit val callBodyElement: WdlWriter[CallBodyElement] = new WdlWriter[CallBodyElement] {
-    override def toWdlV1(a: CallBodyElement): String = {
+    override def toWdlV1(a: CallBodyElement): String =
       if (a.inputs.nonEmpty) {
         s"""input:
            |${indent(indent(a.inputs.map(_.toWdlV1).mkString(",\n")))}""".stripMargin
       } else {
         ""
       }
-    }
   }
 
   object CallElementWriter {
@@ -166,19 +170,22 @@ object WdlWriterImpl {
     }
   }
 
-  implicit val intermediateValueDeclarationElementWriter: WdlWriter[IntermediateValueDeclarationElement] = new WdlWriter[IntermediateValueDeclarationElement] {
-    override def toWdlV1(a: IntermediateValueDeclarationElement) =
-      s"${a.typeElement.toWdlV1} ${a.name} = ${a.expression.toWdlV1}"
-  }
+  implicit val intermediateValueDeclarationElementWriter: WdlWriter[IntermediateValueDeclarationElement] =
+    new WdlWriter[IntermediateValueDeclarationElement] {
+      override def toWdlV1(a: IntermediateValueDeclarationElement) =
+        s"${a.typeElement.toWdlV1} ${a.name} = ${a.expression.toWdlV1}"
+    }
 
   implicit val typeElementWriter: WdlWriter[TypeElement] = new WdlWriter[TypeElement] {
     override def toWdlV1(a: TypeElement) = a match {
       case a: PrimitiveTypeElement => a.primitiveType.toWdlV1
       case a: ArrayTypeElement => s"Array[${typeElementWriter.toWdlV1(a.inner)}]"
-      case a: MapTypeElement => s"Map[${typeElementWriter.toWdlV1(a.keyType)}, ${typeElementWriter.toWdlV1(a.valueType)}]"
+      case a: MapTypeElement =>
+        s"Map[${typeElementWriter.toWdlV1(a.keyType)}, ${typeElementWriter.toWdlV1(a.valueType)}]"
       case a: OptionalTypeElement => s"${typeElementWriter.toWdlV1(a.maybeType)}?"
       case a: NonEmptyTypeElement => s"${typeElementWriter.toWdlV1(a.arrayType)}+"
-      case a: PairTypeElement => s"Pair[${typeElementWriter.toWdlV1(a.leftType)}, ${typeElementWriter.toWdlV1(a.rightType)}]"
+      case a: PairTypeElement =>
+        s"Pair[${typeElementWriter.toWdlV1(a.leftType)}, ${typeElementWriter.toWdlV1(a.rightType)}]"
       case _: ObjectTypeElement.type => "Object"
       case a: TypeAliasElement => a.alias
     }
@@ -188,58 +195,60 @@ object WdlWriterImpl {
     override def toWdlV1(a: WomPrimitiveType) = a.stableName
   }
 
-  implicit val workflowDefinitionElementWriter: WdlWriter[WorkflowDefinitionElement] = new WdlWriter[WorkflowDefinitionElement] {
-    override def toWdlV1(a: WorkflowDefinitionElement) = {
-      val inputs = a.inputsSection match {
-        case Some(i) => i.toWdlV1
-        case None => ""
-      }
-      val outputs = a.outputsSection match {
-        case Some(o) => o.toWdlV1
-        case None => ""
+  implicit val workflowDefinitionElementWriter: WdlWriter[WorkflowDefinitionElement] =
+    new WdlWriter[WorkflowDefinitionElement] {
+      override def toWdlV1(a: WorkflowDefinitionElement) = {
+        val inputs = a.inputsSection match {
+          case Some(i) => i.toWdlV1
+          case None => ""
+        }
+        val outputs = a.outputsSection match {
+          case Some(o) => o.toWdlV1
+          case None => ""
+        }
+
+        // Readability / cosmetic reordering
+        // TODO: use graph ordering
+        // https://github.com/broadinstitute/cromwell/issues/3796
+        val inputDeclarationElements: List[InputDeclarationElement] =
+          a.graphElements.toList.filterByType[InputDeclarationElement]
+        val intermediateValueDeclarationElements: List[IntermediateValueDeclarationElement] =
+          a.graphElements.toList.filterByType[IntermediateValueDeclarationElement]
+        val ifElements: List[IfElement] =
+          a.graphElements.toList.filterByType[IfElement]
+        val scatterElements: List[ScatterElement] =
+          a.graphElements.toList.filterByType[ScatterElement]
+        val callElements: List[CallElement] =
+          a.graphElements.toList.filterByType[CallElement]
+        val outputDeclarationElements: List[OutputDeclarationElement] =
+          a.graphElements.toList.filterByType[OutputDeclarationElement]
+
+        val combined: List[WorkflowGraphElement] = inputDeclarationElements ++
+          intermediateValueDeclarationElements ++
+          ifElements ++
+          scatterElements ++
+          callElements ++
+          outputDeclarationElements
+
+        s"""workflow ${a.name} {
+           |${indent(inputs)}
+           |${indentAndCombine(combined.map(_.toWdlV1))}
+           |${indent(outputs)}
+           |}""".stripMargin
       }
-
-      // Readability / cosmetic reordering
-      // TODO: use graph ordering
-      // https://github.com/broadinstitute/cromwell/issues/3796
-      val inputDeclarationElements: List[InputDeclarationElement] =
-      a.graphElements.toList.filterByType[InputDeclarationElement]
-      val intermediateValueDeclarationElements: List[IntermediateValueDeclarationElement] =
-        a.graphElements.toList.filterByType[IntermediateValueDeclarationElement]
-      val ifElements: List[IfElement] =
-        a.graphElements.toList.filterByType[IfElement]
-      val scatterElements: List[ScatterElement] =
-        a.graphElements.toList.filterByType[ScatterElement]
-      val callElements: List[CallElement] =
-        a.graphElements.toList.filterByType[CallElement]
-      val outputDeclarationElements: List[OutputDeclarationElement] =
-        a.graphElements.toList.filterByType[OutputDeclarationElement]
-
-      val combined: List[WorkflowGraphElement] = inputDeclarationElements ++
-        intermediateValueDeclarationElements ++
-        ifElements ++
-        scatterElements ++
-        callElements ++
-        outputDeclarationElements
-
-      s"""workflow ${a.name} {
-         |${indent(inputs)}
-         |${indentAndCombine(combined.map(_.toWdlV1))}
-         |${indent(outputs)}
-         |}""".stripMargin
     }
-  }
 
-  implicit val runtimeAttributesSectionElementWriter: WdlWriter[RuntimeAttributesSectionElement] = new WdlWriter[RuntimeAttributesSectionElement] {
-    override def toWdlV1(a: RuntimeAttributesSectionElement): String = {
-      val runtimeMap = a.runtimeAttributes map { pair =>
-        s"${pair.key}: ${pair.value.toWdlV1}"
-      }
+  implicit val runtimeAttributesSectionElementWriter: WdlWriter[RuntimeAttributesSectionElement] =
+    new WdlWriter[RuntimeAttributesSectionElement] {
+      override def toWdlV1(a: RuntimeAttributesSectionElement): String = {
+        val runtimeMap = a.runtimeAttributes map { pair =>
+          s"${pair.key}: ${pair.value.toWdlV1}"
+        }
 
-      s"""runtime {
-         |${indentAndCombine(runtimeMap)}}""".stripMargin
+        s"""runtime {
+           |${indentAndCombine(runtimeMap)}}""".stripMargin
+      }
     }
-  }
 
   implicit val metaValueElementWriter: WdlWriter[MetaValueElement] = new WdlWriter[MetaValueElement] {
     override def toWdlV1(a: MetaValueElement): String = a match {
@@ -249,14 +258,15 @@ object WdlWriterImpl {
       case a: MetaValueElementInteger => a.value.toString
       case a: MetaValueElementString => "\"" + a.value + "\""
       case a: MetaValueElementObject =>
-        "{" + a.value.map { pair =>
-          s"${pair._1}: ${metaValueElementWriter.toWdlV1(pair._2)}"
-        }.mkString(", ") + "}"
+        "{" + a.value
+          .map { pair =>
+            s"${pair._1}: ${metaValueElementWriter.toWdlV1(pair._2)}"
+          }
+          .mkString(", ") + "}"
       case a: MetaValueElementArray => "[" + a.value.map(metaValueElementWriter.toWdlV1).mkString(", ") + "]"
     }
   }
 
-
   implicit val metaSectionElementWriter: WdlWriter[MetaSectionElement] = new WdlWriter[MetaSectionElement] {
     override def toWdlV1(a: MetaSectionElement): String = {
       val map = a.meta.map { pair =>
@@ -268,62 +278,62 @@ object WdlWriterImpl {
     }
   }
 
-  implicit val parameterMetaSectionElementWriter: WdlWriter[ParameterMetaSectionElement] = new WdlWriter[ParameterMetaSectionElement] {
-    override def toWdlV1(a: ParameterMetaSectionElement): String = {
-      val map = a.metaAttributes.map { pair =>
-        s"${pair._1}: ${pair._2.toWdlV1}"
+  implicit val parameterMetaSectionElementWriter: WdlWriter[ParameterMetaSectionElement] =
+    new WdlWriter[ParameterMetaSectionElement] {
+      override def toWdlV1(a: ParameterMetaSectionElement): String = {
+        val map = a.metaAttributes.map { pair =>
+          s"${pair._1}: ${pair._2.toWdlV1}"
+        }
+        s"""parameter_meta {
+           |${indentAndCombine(map)}
+           |}""".stripMargin
       }
-      s"""parameter_meta {
-         |${indentAndCombine(map)}
-         |}""".stripMargin
     }
-  }
 
-  implicit val taskDefinitionTypeElementWriter: WdlWriter[TaskDefinitionElement] = new WdlWriter[TaskDefinitionElement] {
-    override def toWdlV1(a: TaskDefinitionElement) = {
-      val inputs = a.inputsSection match {
-        case Some(i) => i.toWdlV1
-        case None => ""
-      }
-      val outputs = a.outputsSection match {
-        case Some(o) => o.toWdlV1
-        case None => ""
-      }
-      val runtime = a.runtimeSection match {
-        case Some(r) => r.toWdlV1
-        case None => ""
-      }
-      val meta = a.metaSection match {
-        case Some(m) => m.toWdlV1
-        case None => ""
-      }
-      val parameterMeta = a.parameterMetaSection match {
-        case Some(p) => p.toWdlV1
-        case None => ""
+  implicit val taskDefinitionTypeElementWriter: WdlWriter[TaskDefinitionElement] =
+    new WdlWriter[TaskDefinitionElement] {
+      override def toWdlV1(a: TaskDefinitionElement) = {
+        val inputs = a.inputsSection match {
+          case Some(i) => i.toWdlV1
+          case None => ""
+        }
+        val outputs = a.outputsSection match {
+          case Some(o) => o.toWdlV1
+          case None => ""
+        }
+        val runtime = a.runtimeSection match {
+          case Some(r) => r.toWdlV1
+          case None => ""
+        }
+        val meta = a.metaSection match {
+          case Some(m) => m.toWdlV1
+          case None => ""
+        }
+        val parameterMeta = a.parameterMetaSection match {
+          case Some(p) => p.toWdlV1
+          case None => ""
+        }
+
+        s"""task ${a.name} {
+           |${indent(inputs)}
+           |${indentAndCombine(a.declarations.map(_.toWdlV1))}
+           |${indent(outputs)}
+           |${a.commandSection.toWdlV1}
+           |${indent(runtime)}
+           |${indent(meta)}
+           |${indent(parameterMeta)}}""".stripMargin
       }
-
-      s"""task ${a.name} {
-         |${indent(inputs)}
-         |${indentAndCombine(a.declarations.map(_.toWdlV1))}
-         |${indent(outputs)}
-         |${a.commandSection.toWdlV1}
-         |${indent(runtime)}
-         |${indent(meta)}
-         |${indent(parameterMeta)}}""".stripMargin
     }
-  }
 
   implicit val commandSectionElementWriter: WdlWriter[CommandSectionElement] = new WdlWriter[CommandSectionElement] {
-    override def toWdlV1(a: CommandSectionElement): String = {
+    override def toWdlV1(a: CommandSectionElement): String =
       s"""  command <<<
          |${combine(a.parts.map(_.toWdlV1))}  >>>""".stripMargin
-    }
   }
 
   implicit val commandSectionLineWriter: WdlWriter[CommandSectionLine] = new WdlWriter[CommandSectionLine] {
-    override def toWdlV1(a: CommandSectionLine): String = {
+    override def toWdlV1(a: CommandSectionLine): String =
       a.parts.map(_.toWdlV1).mkString
-    }
   }
 
   implicit val commandPartElementWriter: WdlWriter[CommandPartElement] = new WdlWriter[CommandPartElement] {
@@ -339,49 +349,49 @@ object WdlWriterImpl {
     }
   }
 
-  implicit val placeholderAttributeSetWriter: WdlWriter[PlaceholderAttributeSet] = new WdlWriter[PlaceholderAttributeSet] {
-    override def toWdlV1(a: PlaceholderAttributeSet): String = {
-      val attrStrings = Map(
-        "sep" -> a.sepAttribute,
-        "true" -> a.trueAttribute,
-        "false" -> a.falseAttribute,
-        "default" -> a.defaultAttribute
-      ).collect({ case (attrKey: String, Some(value)) => attrKey + "=\"" + value + "\"" })
+  implicit val placeholderAttributeSetWriter: WdlWriter[PlaceholderAttributeSet] =
+    new WdlWriter[PlaceholderAttributeSet] {
+      override def toWdlV1(a: PlaceholderAttributeSet): String = {
+        val attrStrings = Map(
+          "sep" -> a.sepAttribute,
+          "true" -> a.trueAttribute,
+          "false" -> a.falseAttribute,
+          "default" -> a.defaultAttribute
+        ).collect { case (attrKey: String, Some(value)) => attrKey + "=\"" + value + "\"" }
 
-      if (attrStrings.isEmpty) "" else attrStrings.mkString(start = "", sep = " ", end = " ")
+        if (attrStrings.isEmpty) "" else attrStrings.mkString(start = "", sep = " ", end = " ")
+      }
     }
-  }
 
   implicit val inputsSectionElementWriter: WdlWriter[InputsSectionElement] = new WdlWriter[InputsSectionElement] {
-    override def toWdlV1(a: InputsSectionElement): String = {
+    override def toWdlV1(a: InputsSectionElement): String =
       s"""input {
          |${indentAndCombine(a.inputDeclarations.map(_.toWdlV1))}}""".stripMargin
-    }
   }
 
-  implicit val inputDeclarationElementWriter: WdlWriter[InputDeclarationElement] = new WdlWriter[InputDeclarationElement] {
-    override def toWdlV1(a: InputDeclarationElement): String = {
-      val expression = a.expression match {
-        case Some(expr) => s" = ${expr.toWdlV1}"
-        case None => ""
-      }
+  implicit val inputDeclarationElementWriter: WdlWriter[InputDeclarationElement] =
+    new WdlWriter[InputDeclarationElement] {
+      override def toWdlV1(a: InputDeclarationElement): String = {
+        val expression = a.expression match {
+          case Some(expr) => s" = ${expr.toWdlV1}"
+          case None => ""
+        }
 
-      s"${a.typeElement.toWdlV1} ${a.name}$expression"
+        s"${a.typeElement.toWdlV1} ${a.name}$expression"
+      }
     }
-  }
 
   implicit val outputsSectionElementWriter: WdlWriter[OutputsSectionElement] = new WdlWriter[OutputsSectionElement] {
-    override def toWdlV1(a: OutputsSectionElement): String = {
+    override def toWdlV1(a: OutputsSectionElement): String =
       s"""output {
          |${indentAndCombine(a.outputs.map(_.toWdlV1))}}""".stripMargin
-    }
   }
 
-  implicit val outputDeclarationElementWriter: WdlWriter[OutputDeclarationElement] = new WdlWriter[OutputDeclarationElement] {
-    override def toWdlV1(a: OutputDeclarationElement): String = {
-      s"${a.typeElement.toWdlV1} ${a.name} = ${a.expression.toWdlV1}"
+  implicit val outputDeclarationElementWriter: WdlWriter[OutputDeclarationElement] =
+    new WdlWriter[OutputDeclarationElement] {
+      override def toWdlV1(a: OutputDeclarationElement): String =
+        s"${a.typeElement.toWdlV1} ${a.name} = ${a.expression.toWdlV1}"
     }
-  }
 
   implicit val functionCallElementWriter: WdlWriter[FunctionCallElement] = new WdlWriter[FunctionCallElement] {
     override def toWdlV1(a: FunctionCallElement): String = a match {
@@ -394,71 +404,73 @@ object WdlWriterImpl {
     }
   }
 
-  implicit val oneParamFunctionCallElementWriter: WdlWriter[OneParamFunctionCallElement] = new WdlWriter[OneParamFunctionCallElement] {
-    override def toWdlV1(a: OneParamFunctionCallElement): String = {
-      val fn = a match {
-        case _: ReadLines    => "read_lines"
-        case _: ReadTsv      => "read_tsv"
-        case _: ReadMap      => "read_map"
-        case _: ReadObject   => "read_object"
-        case _: ReadObjects  => "read_objects"
-        case _: ReadJson     => "read_json"
-        case _: ReadInt      => "read_int"
-        case _: ReadString   => "read_string"
-        case _: ReadFloat    => "read_float"
-        case _: ReadBoolean  => "read_boolean"
-        case _: WriteLines   => "write_lines"
-        case _: WriteTsv     => "write_tsv"
-        case _: WriteMap     => "write_map"
-        case _: WriteObject  => "write_object"
-        case _: WriteObjects => "write_objects"
-        case _: WriteJson    => "write_json"
-        case _: Range        => "range"
-        case _: Transpose    => "transpose"
-        case _: Length       => "length"
-        case _: Flatten      => "flatten"
-        case _: SelectFirst  => "select_first"
-        case _: SelectAll    => "select_all"
-        case _: Defined      => "defined"
-        case _: Floor        => "floor"
-        case _: Ceil         => "ceil"
-        case _: Round        => "round"
-        case _: Glob         => "glob"
-        case _: Keys         => "keys"
-        case _: AsMap        => "as_map"
-        case _: AsPairs      => "as_pairs"
-        case _: CollectByKey => "collect_by_key"
+  implicit val oneParamFunctionCallElementWriter: WdlWriter[OneParamFunctionCallElement] =
+    new WdlWriter[OneParamFunctionCallElement] {
+      override def toWdlV1(a: OneParamFunctionCallElement): String = {
+        val fn = a match {
+          case _: ReadLines => "read_lines"
+          case _: ReadTsv => "read_tsv"
+          case _: ReadMap => "read_map"
+          case _: ReadObject => "read_object"
+          case _: ReadObjects => "read_objects"
+          case _: ReadJson => "read_json"
+          case _: ReadInt => "read_int"
+          case _: ReadString => "read_string"
+          case _: ReadFloat => "read_float"
+          case _: ReadBoolean => "read_boolean"
+          case _: WriteLines => "write_lines"
+          case _: WriteTsv => "write_tsv"
+          case _: WriteMap => "write_map"
+          case _: WriteObject => "write_object"
+          case _: WriteObjects => "write_objects"
+          case _: WriteJson => "write_json"
+          case _: Range => "range"
+          case _: Transpose => "transpose"
+          case _: Length => "length"
+          case _: Flatten => "flatten"
+          case _: SelectFirst => "select_first"
+          case _: SelectAll => "select_all"
+          case _: Defined => "defined"
+          case _: Floor => "floor"
+          case _: Ceil => "ceil"
+          case _: Round => "round"
+          case _: Glob => "glob"
+          case _: Keys => "keys"
+          case _: AsMap => "as_map"
+          case _: AsPairs => "as_pairs"
+          case _: CollectByKey => "collect_by_key"
+        }
+
+        s"$fn(${a.param.toWdlV1})"
       }
-
-      s"$fn(${a.param.toWdlV1})"
     }
-  }
 
-  implicit val oneOrTwoParamFunctionCallElementWriter: WdlWriter[OneOrTwoParamFunctionCallElement] = new WdlWriter[OneOrTwoParamFunctionCallElement] {
-    override def toWdlV1(a: OneOrTwoParamFunctionCallElement): String = {
-      (a, a.secondParam) match {
-        case (_: Size, Some(unit)) => s"size(${a.firstParam.toWdlV1}, ${unit.toWdlV1})"
-        case (_: Size, None) => s"size(${a.firstParam.toWdlV1})"
-        case (_: Basename, Some(suffix)) => s"basename(${a.firstParam.toWdlV1}, ${suffix.toWdlV1})"
-        case (_: Basename, None) => s"basename(${a.firstParam.toWdlV1})"
-      }
+  implicit val oneOrTwoParamFunctionCallElementWriter: WdlWriter[OneOrTwoParamFunctionCallElement] =
+    new WdlWriter[OneOrTwoParamFunctionCallElement] {
+      override def toWdlV1(a: OneOrTwoParamFunctionCallElement): String =
+        (a, a.secondParam) match {
+          case (_: Size, Some(unit)) => s"size(${a.firstParam.toWdlV1}, ${unit.toWdlV1})"
+          case (_: Size, None) => s"size(${a.firstParam.toWdlV1})"
+          case (_: Basename, Some(suffix)) => s"basename(${a.firstParam.toWdlV1}, ${suffix.toWdlV1})"
+          case (_: Basename, None) => s"basename(${a.firstParam.toWdlV1})"
+        }
     }
-  }
 
-  implicit val twoParamFunctionCallElementWriter: WdlWriter[TwoParamFunctionCallElement] = new WdlWriter[TwoParamFunctionCallElement] {
-    override def toWdlV1(a: TwoParamFunctionCallElement): String = {
-      def functionCall(name: String) = s"$name(${a.arg1.toWdlV1}, ${a.arg2.toWdlV1})"
-
-      a match {
-        case _: Zip => functionCall("zip")
-        case _: Cross => functionCall("cross")
-        case _: Prefix => functionCall("prefix")
-        case _: Min => functionCall("min")
-        case _: Max => functionCall("max")
-        case _: Sep => functionCall("sep")
+  implicit val twoParamFunctionCallElementWriter: WdlWriter[TwoParamFunctionCallElement] =
+    new WdlWriter[TwoParamFunctionCallElement] {
+      override def toWdlV1(a: TwoParamFunctionCallElement): String = {
+        def functionCall(name: String) = s"$name(${a.arg1.toWdlV1}, ${a.arg2.toWdlV1})"
+
+        a match {
+          case _: Zip => functionCall("zip")
+          case _: Cross => functionCall("cross")
+          case _: Prefix => functionCall("prefix")
+          case _: Min => functionCall("min")
+          case _: Max => functionCall("max")
+          case _: Sep => functionCall("sep")
+        }
       }
     }
-  }
 
   implicit val structElementWriter: WdlWriter[StructElement] = new WdlWriter[StructElement] {
     override def toWdlV1(a: StructElement): String =
@@ -471,33 +483,33 @@ object WdlWriterImpl {
   }
 
   implicit val importElementWriter: WdlWriter[ImportElement] = new WdlWriter[ImportElement] {
-    override def toWdlV1(a: ImportElement): String = {
+    override def toWdlV1(a: ImportElement): String =
       a.namespace match {
         case Some(namespace) => s"""import "${a.importUrl}" as $namespace"""
-        case None =>            s"""import "${a.importUrl}""""
+        case None => s"""import "${a.importUrl}""""
       }
-    }
   }
 
   implicit val fileElementWriter: WdlWriter[FileElement] = new WdlWriter[FileElement] {
-    override def toWdlV1(a: FileElement) = {
+    override def toWdlV1(a: FileElement) =
       "version 1.0" + System.lineSeparator +
         combine(a.imports.map(_.toWdlV1)) +
         combine(a.structs.map(_.toWdlV1)) +
         combine(a.workflows.map(_.toWdlV1)) +
         combine(a.tasks.map(_.toWdlV1))
-    }
   }
 
   implicit val kvPairWriter: WdlWriter[KvPair] = new WdlWriter[KvPair] {
     override def toWdlV1(a: KvPair): String = s"${a.key} = ${a.value.toWdlV1}"
   }
 
-  implicit val primitiveLiteralExpressionElementWriter: WdlWriter[PrimitiveLiteralExpressionElement] = new WdlWriter[PrimitiveLiteralExpressionElement] {
-    override def toWdlV1(a: PrimitiveLiteralExpressionElement) = a.value.toWomString
-  }
+  implicit val primitiveLiteralExpressionElementWriter: WdlWriter[PrimitiveLiteralExpressionElement] =
+    new WdlWriter[PrimitiveLiteralExpressionElement] {
+      override def toWdlV1(a: PrimitiveLiteralExpressionElement) = a.value.toWomString
+    }
 
-  implicit val noneLiteralExpressionElementWriter: WdlWriter[NoneLiteralElement.type] = new WdlWriter[NoneLiteralElement.type] {
-    override def toWdlV1(a: NoneLiteralElement.type): String = "None"
-  }
+  implicit val noneLiteralExpressionElementWriter: WdlWriter[NoneLiteralElement.type] =
+    new WdlWriter[NoneLiteralElement.type] {
+      override def toWdlV1(a: NoneLiteralElement.type): String = "None"
+    }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala
index 3a34bbefd96..ed12e23c853 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala
@@ -24,13 +24,15 @@ import wdl.transforms.base.wdlom2wdl.WdlWriterImpl._
 object CommandPartElementToWomCommandPart {
   def convert(commandPart: CommandPartElement,
               typeAliases: Map[String, WomType],
-              availableHandles: Set[GeneratedValueHandle])
-             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-              fileEvaluator: FileEvaluator[ExpressionElement],
-              typeEvaluator: TypeEvaluator[ExpressionElement],
-              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[CommandPart] = commandPart match {
+              availableHandles: Set[GeneratedValueHandle]
+  )(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[CommandPart] = commandPart match {
     case s: StringCommandPartElement => WdlomWomStringCommandPart(s).validNel
-    case p: PlaceholderCommandPartElement => {
+    case p: PlaceholderCommandPartElement =>
       val attributes = p.attributes
       val consumedValues = p.expressionElement.expressionConsumedValueHooks
 
@@ -39,10 +41,11 @@ object CommandPartElementToWomCommandPart {
         womExpression <- p.expressionElement.makeWomExpression(typeAliases, consumedValueLookup)
         _ <- validatePlaceholderType(womExpression, attributes)
       } yield WdlomWomPlaceholderCommandPart(attributes, womExpression.asInstanceOf[WdlomWomExpression])
-    }
   }
 
-  private def validatePlaceholderType(womExpression: WomExpression, attributes: PlaceholderAttributeSet): ErrorOr[Unit] = ().validNel
+  private def validatePlaceholderType(womExpression: WomExpression,
+                                      attributes: PlaceholderAttributeSet
+  ): ErrorOr[Unit] = ().validNel
 }
 
 case class WdlomWomStringCommandPart(stringCommandPartElement: StringCommandPartElement) extends CommandPart {
@@ -50,10 +53,12 @@ case class WdlomWomStringCommandPart(stringCommandPartElement: StringCommandPart
   override def instantiate(inputsMap: Map[LocalName, WomValue],
                            functions: IoFunctionSet,
                            valueMapper: WomValue => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] = List(InstantiatedCommand(stringCommandPartElement.value)).validNel
+                           runtimeEnvironment: RuntimeEnvironment
+  ): ErrorOr[List[InstantiatedCommand]] = List(InstantiatedCommand(stringCommandPartElement.value)).validNel
 }
 
-case class WdlomWomPlaceholderCommandPart(attributes: PlaceholderAttributeSet, expression: WdlomWomExpression) extends CommandPart {
+case class WdlomWomPlaceholderCommandPart(attributes: PlaceholderAttributeSet, expression: WdlomWomExpression)
+    extends CommandPart {
   def attributesToString: String = attributes.toWdlV1
   // Yes, it's sad that we need to put ${} here, but otherwise we won't cache hit from draft-2 command sections
   override def toString: String = "${" + s"$attributesToString${expression.expressionElement.toWdlV1}" + "}"
@@ -61,29 +66,44 @@ case class WdlomWomPlaceholderCommandPart(attributes: PlaceholderAttributeSet, e
   override def instantiate(inputsMap: Map[LocalName, WomValue],
                            functions: IoFunctionSet,
                            valueMapper: WomValue => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]] = {
+                           runtimeEnvironment: RuntimeEnvironment
+  ): ErrorOr[List[InstantiatedCommand]] = {
     val inputsValues = inputsMap map { case (localName, value) => localName.value -> value }
-    expression.evaluateValueForPlaceholder(inputsValues, functions, ForCommandInstantiationOptions(valueMapper)) flatMap { evaluatedExpression =>
+    expression.evaluateValueForPlaceholder(inputsValues,
+                                           functions,
+                                           ForCommandInstantiationOptions(valueMapper)
+    ) flatMap { evaluatedExpression =>
       instantiateFromValue(evaluatedExpression, valueMapper).map(List(_))
     }
   }
 
-  private def instantiateFromValue(value: EvaluatedValue[_], valueMapper: WomValue => WomValue): ErrorOr[InstantiatedCommand] = value.value match {
+  private def instantiateFromValue(value: EvaluatedValue[_],
+                                   valueMapper: WomValue => WomValue
+  ): ErrorOr[InstantiatedCommand] = value.value match {
     case WomBoolean(b) if attributes.trueAttribute.isDefined && attributes.falseAttribute.isDefined =>
       InstantiatedCommand(
-        commandString = if (b) { attributes.trueAttribute.get } else { attributes.falseAttribute.get },
+        commandString = if (b) { attributes.trueAttribute.get }
+        else { attributes.falseAttribute.get },
         createdFiles = value.sideEffectFiles.toList
       ).validNel
-    case p: WomPrimitive => InstantiatedCommand(valueMapper(p).valueString, createdFiles = value.sideEffectFiles.toList).validNel
+    case p: WomPrimitive =>
+      InstantiatedCommand(valueMapper(p).valueString, createdFiles = value.sideEffectFiles.toList).validNel
     case WomOptionalValue(_, Some(v)) => instantiateFromValue(value.copy(value = v), valueMapper)
-    case WomOptionalValue(_, None) => attributes.defaultAttribute match {
-      case Some(default) => InstantiatedCommand(commandString = default, createdFiles = value.sideEffectFiles.toList).validNel
-      case None => InstantiatedCommand(commandString = "", createdFiles = value.sideEffectFiles.toList).validNel
-    }
-    case WomArray(WomArrayType(_ : WomPrimitiveType), arrayValue) => attributes.sepAttribute match {
-      case Some(separator) => InstantiatedCommand(commandString = arrayValue.map(valueMapper(_).valueString).mkString(separator), createdFiles = value.sideEffectFiles.toList).validNel
-      case None => "Array value was given but no 'sep' attribute was provided".invalidNel
-    }
-    case other => s"Cannot interpolate ${other.womType.stableName} into a command string with attribute set [$attributes]".invalidNel
+    case WomOptionalValue(_, None) =>
+      attributes.defaultAttribute match {
+        case Some(default) =>
+          InstantiatedCommand(commandString = default, createdFiles = value.sideEffectFiles.toList).validNel
+        case None => InstantiatedCommand(commandString = "", createdFiles = value.sideEffectFiles.toList).validNel
+      }
+    case WomArray(WomArrayType(_: WomPrimitiveType), arrayValue) =>
+      attributes.sepAttribute match {
+        case Some(separator) =>
+          InstantiatedCommand(commandString = arrayValue.map(valueMapper(_).valueString).mkString(separator),
+                              createdFiles = value.sideEffectFiles.toList
+          ).validNel
+        case None => "Array value was given but no 'sep' attribute was provided".invalidNel
+      }
+    case other =>
+      s"Cannot interpolate ${other.womType.stableName} into a command string with attribute set [$attributes]".invalidNel
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/FileElementToWomBundle.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/FileElementToWomBundle.scala
index e92aa2d2784..04f45d1fbab 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/FileElementToWomBundle.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/FileElementToWomBundle.scala
@@ -26,93 +26,110 @@ import wom.types.WomType
 
 object FileElementToWomBundle {
 
-  implicit val fileElementToWomBundle: WomBundleMaker[FileElementToWomBundleInputs] = new WomBundleMaker[FileElementToWomBundleInputs] {
+  implicit val fileElementToWomBundle: WomBundleMaker[FileElementToWomBundleInputs] =
+    new WomBundleMaker[FileElementToWomBundleInputs] {
 
-    override def toWomBundle(a: FileElementToWomBundleInputs): Checked[WomBundle] = {
+      override def toWomBundle(a: FileElementToWomBundleInputs): Checked[WomBundle] = {
 
-      def toWorkflowInner(imports: Vector[WomBundle], tasks: Vector[TaskDefinitionElement], structs: Map[String, WomType]): ErrorOr[WomBundle] = {
+        def toWorkflowInner(imports: Vector[WomBundle],
+                            tasks: Vector[TaskDefinitionElement],
+                            structs: Map[String, WomType]
+        ): ErrorOr[WomBundle] = {
 
-        val allStructs = structs ++ imports.flatMap(_.typeAliases)
+          val allStructs = structs ++ imports.flatMap(_.typeAliases)
 
-        val localTasksValidation: ErrorOr[Map[String, Callable]] = {
-          val validatedTasksVector: ErrorOr[Vector[(String, Callable)]] = tasks.traverse { taskDefinition =>
-            a.taskConverter
-              .run(TaskDefinitionElementToWomInputs(taskDefinition, structs))
-              .map(t => t.name -> t).toValidated
-          }
+          val localTasksValidation: ErrorOr[Map[String, Callable]] = {
+            val validatedTasksVector: ErrorOr[Vector[(String, Callable)]] = tasks.traverse { taskDefinition =>
+              a.taskConverter
+                .run(TaskDefinitionElementToWomInputs(taskDefinition, structs))
+                .map(t => t.name -> t)
+                .toValidated
+            }
 
-          validatedTasksVector flatMap { tasksVector =>
+            validatedTasksVector flatMap { tasksVector =>
+              val duplicateTaskNames = tasksVector.groupBy(_._1).collect { case (x, list) if list.size > 1 => x }
 
-            val duplicateTaskNames = tasksVector.groupBy(_._1).collect { case (x, list) if list.size > 1 => x }
+              NonEmptyList.fromList(duplicateTaskNames.toList) match {
+                case None => tasksVector.toMap.validNel
+                case Some(duplicates) =>
+                  duplicates.map(x => s"Cannot reuse the same task name ('$x') more than once").invalid
 
-            NonEmptyList.fromList(duplicateTaskNames.toList) match {
-              case None => tasksVector.toMap.validNel
-              case Some(duplicates) => duplicates.map { x => s"Cannot reuse the same task name ('$x') more than once" }.invalid
+              }
 
             }
-
           }
-        }
 
-        localTasksValidation flatMap { localTaskMapping =>
-
-          val workflowsValidation: ErrorOr[Vector[WorkflowDefinition]] = {
-            a.fileElement.workflows.toVector.traverse { workflowDefinition =>
-
-              val convertInputs = WorkflowDefinitionConvertInputs(workflowDefinition,
-                                                                  allStructs,
-                                                                  localTaskMapping ++ imports.flatMap(_.allCallables),
-                                                                  a.convertNestedScatterToSubworkflow)
-              a.workflowConverter.run(convertInputs).toValidated
+          localTasksValidation flatMap { localTaskMapping =>
+            val workflowsValidation: ErrorOr[Vector[WorkflowDefinition]] =
+              a.fileElement.workflows.toVector.traverse { workflowDefinition =>
+                val convertInputs = WorkflowDefinitionConvertInputs(workflowDefinition,
+                                                                    allStructs,
+                                                                    localTaskMapping ++ imports.flatMap(_.allCallables),
+                                                                    a.convertNestedScatterToSubworkflow
+                )
+                a.workflowConverter.run(convertInputs).toValidated
+              }
+
+            workflowsValidation map { workflows =>
+              val primary: Option[Callable] =
+                if (workflows.size == 1) {
+                  workflows.headOption
+                } else if (workflows.isEmpty && tasks.size == 1) {
+                  localTaskMapping.headOption map { case (_, callable) => callable }
+                } else None
+
+              val bundledCallableMap = (localTaskMapping.values.toSet ++ workflows).map(c => c.name -> c).toMap
+
+              WomBundle(primary, bundledCallableMap, allStructs, imports.flatMap(_.resolvedImportRecords).toSet)
             }
           }
+        }
 
-          workflowsValidation map { workflows =>
-            val primary: Option[Callable] =
-              if (workflows.size == 1) {
-                workflows.headOption
-              } else if (workflows.isEmpty && tasks.size == 1) {
-                localTaskMapping.headOption map { case (_, callable) => callable }
-              } else None
-
-            val bundledCallableMap = (localTaskMapping.values.toSet ++ workflows).map(c => c.name -> c).toMap
+        val taskDefValidation: ErrorOr[Vector[TaskDefinitionElement]] = a.fileElement.tasks.toVector.validNel
+        val importsValidation: ErrorOr[Vector[WomBundle]] = a.fileElement.imports.toVector.traverse {
+          importWomBundle(_, a.workflowOptionsJson, a.importResolvers, a.languageFactories)
+        }
 
-            WomBundle(primary, bundledCallableMap, allStructs, imports.flatMap(_.resolvedImportRecords).toSet)
+        (importsValidation flatMap { imports =>
+          val structsValidation: ErrorOr[Map[String, WomType]] = StructEvaluation.convert(
+            StructEvaluationInputs(a.fileElement.structs, imports.flatMap(_.typeAliases).toMap)
+          )
+          (taskDefValidation, structsValidation) flatMapN { (tasks, structs) =>
+            toWorkflowInner(imports, tasks, structs)
           }
-        }
+        }).toEither
       }
-
-      val taskDefValidation: ErrorOr[Vector[TaskDefinitionElement]] = a.fileElement.tasks.toVector.validNel
-      val importsValidation: ErrorOr[Vector[WomBundle]] = a.fileElement.imports.toVector.traverse { importWomBundle(_, a.workflowOptionsJson, a.importResolvers, a.languageFactories) }
-
-      (importsValidation flatMap { imports =>
-        val structsValidation: ErrorOr[Map[String, WomType]] = StructEvaluation.convert(StructEvaluationInputs(a.fileElement.structs, imports.flatMap(_.typeAliases).toMap))
-        (taskDefValidation, structsValidation) flatMapN { (tasks, structs) => toWorkflowInner(imports, tasks, structs) }
-      }).toEither
     }
-  }
 
   def convert(a: FileElementToWomBundleInputs): Checked[WomBundle] = a.toWomBundle
 
   private def importWomBundle(importElement: ImportElement,
                               optionsJson: WorkflowOptionsJson,
                               importResolvers: List[ImportResolver],
-                              languageFactories: List[LanguageFactory]): ErrorOr[WomBundle] = {
-    val compoundImportResolver: CheckedAtoB[ImportResolutionRequest, ResolvedImportBundle] = CheckedAtoB.firstSuccess(importResolvers.map(_.resolver), s"resolve import '${importElement.importUrl}'")
+                              languageFactories: List[LanguageFactory]
+  ): ErrorOr[WomBundle] = {
+    val compoundImportResolver: CheckedAtoB[ImportResolutionRequest, ResolvedImportBundle] =
+      CheckedAtoB.firstSuccess(importResolvers.map(_.resolver), s"resolve import '${importElement.importUrl}'")
 
     val languageFactoryKleislis: List[CheckedAtoB[ResolvedImportBundle, WomBundle]] = languageFactories map { factory =>
       CheckedAtoB.fromCheck { resolutionBundle: ResolvedImportBundle =>
-        factory.getWomBundle(resolutionBundle.source, Option(resolutionBundle.resolvedImportRecord), optionsJson, resolutionBundle.newResolvers, languageFactories)
+        factory.getWomBundle(resolutionBundle.source,
+                             Option(resolutionBundle.resolvedImportRecord),
+                             optionsJson,
+                             resolutionBundle.newResolvers,
+                             languageFactories
+        )
       }
     }
-    val compoundLanguageFactory: CheckedAtoB[ResolvedImportBundle, WomBundle] = CheckedAtoB.firstSuccess(languageFactoryKleislis, s"convert imported '${importElement.importUrl}' to WOM")
+    val compoundLanguageFactory: CheckedAtoB[ResolvedImportBundle, WomBundle] =
+      CheckedAtoB.firstSuccess(languageFactoryKleislis, s"convert imported '${importElement.importUrl}' to WOM")
 
     val overallConversion = compoundImportResolver andThen compoundLanguageFactory
 
     overallConversion
       .run(ImportResolutionRequest(importElement.importUrl, importResolvers))
-      .map { applyNamespace(_, importElement) }
-      .flatMap { respectImportRenames(_, importElement.structRenames) }
+      .map(applyNamespace(_, importElement))
+      .flatMap(respectImportRenames(_, importElement.structRenames))
       .contextualizeErrors(s"import '${importElement.importUrl}'")
       .toValidated
   }
@@ -138,16 +155,18 @@ object FileElementToWomBundle {
       }
       womBundle.copy(typeAliases = newStructs).validNelCheck
     } else {
-      s"Cannot import and rename: [${unexpectedAliases.mkString(", ")}] because the set of imported structs was: [${importedStructs.keySet.mkString(", ")}]".invalidNelCheck
+      s"Cannot import and rename: [${unexpectedAliases.mkString(", ")}] because the set of imported structs was: [${importedStructs.keySet
+          .mkString(", ")}]".invalidNelCheck
     }
   }
 }
 
-final case class FileElementToWomBundleInputs(fileElement: FileElement,
-                                              workflowOptionsJson: WorkflowOptionsJson,
-                                              convertNestedScatterToSubworkflow : Boolean,
-                                              importResolvers: List[ImportResolver],
-                                              languageFactories: List[LanguageFactory],
-                                              workflowConverter: CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition],
-                                              taskConverter: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition]
-                                             )
+final case class FileElementToWomBundleInputs(
+  fileElement: FileElement,
+  workflowOptionsJson: WorkflowOptionsJson,
+  convertNestedScatterToSubworkflow: Boolean,
+  importResolvers: List[ImportResolver],
+  languageFactories: List[LanguageFactory],
+  workflowConverter: CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition],
+  taskConverter: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition]
+)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/StructEvaluation.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/StructEvaluation.scala
index da1ccdefb7f..f144a31aad9 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/StructEvaluation.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/StructEvaluation.scala
@@ -13,7 +13,9 @@ import wdl.transforms.base.linking.typemakers._
 object StructEvaluation {
   def convert(a: StructEvaluationInputs): ErrorOr[Map[String, WomType]] = {
 
-    val validKnownAliases: Map[String, ErrorOr[WomType]] = a.knownTypeAliases map { case (key, value) => key -> value.validNel }
+    val validKnownAliases: Map[String, ErrorOr[WomType]] = a.knownTypeAliases map { case (key, value) =>
+      key -> value.validNel
+    }
     val withNewStructs = a.structSections.foldLeft(validKnownAliases)(structFoldFunction)
 
     def unpackMapEntry(entry: (String, ErrorOr[WomType])): ErrorOr[(String, WomType)] = entry._2 map { entry._1 -> _ }
@@ -21,10 +23,12 @@ object StructEvaluation {
     withNewStructs.toList.traverse(unpackMapEntry).map(_.toMap)
   }
 
-  private def structFoldFunction(current: Map[String, ErrorOr[WomType]], next: StructElement): Map[String, ErrorOr[WomType]] = {
+  private def structFoldFunction(current: Map[String, ErrorOr[WomType]],
+                                 next: StructElement
+  ): Map[String, ErrorOr[WomType]] = {
 
-    val currentValid = current collect {
-      case (key, Valid(value)) => key -> value
+    val currentValid = current collect { case (key, Valid(value)) =>
+      key -> value
     }
 
     def convertStructEntryElement(structEntryElement: StructEntryElement): ErrorOr[(String, WomType)] =
@@ -32,9 +36,10 @@ object StructEvaluation {
 
     val elementsValidation: ErrorOr[List[(String, WomType)]] = next.entries.toList.traverse(convertStructEntryElement)
 
-    current + (next.name -> (elementsValidation map { elements => WomCompositeType(elements.toMap, Option(next.name)) } ))
+    current + (next.name -> (elementsValidation map { elements =>
+      WomCompositeType(elements.toMap, Option(next.name))
+    }))
   }
 
   case class StructEvaluationInputs(structSections: Seq[StructElement], knownTypeAliases: Map[String, WomType])
 }
-
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala
index 91a51497b5e..576ce210da5 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala
@@ -28,13 +28,16 @@ import wdl.transforms.base.linking.typemakers._
 
 object TaskDefinitionElementToWomTaskDefinition extends Util {
 
-  final case class TaskDefinitionElementToWomInputs(taskDefinitionElement: TaskDefinitionElement, typeAliases: Map[String, WomType])
-
-  def convert(b: TaskDefinitionElementToWomInputs)
-             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-              fileEvaluator: FileEvaluator[ExpressionElement],
-              typeEvaluator: TypeEvaluator[ExpressionElement],
-              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[CallableTaskDefinition] = {
+  final case class TaskDefinitionElementToWomInputs(taskDefinitionElement: TaskDefinitionElement,
+                                                    typeAliases: Map[String, WomType]
+  )
+
+  def convert(b: TaskDefinitionElementToWomInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[CallableTaskDefinition] = {
     val a = eliminateInputDependencies(b)
     val inputElements = a.taskDefinitionElement.inputsSection.map(_.inputDeclarations).getOrElse(Seq.empty)
 
@@ -42,39 +45,68 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
     val outputElements = a.taskDefinitionElement.outputsSection.map(_.outputs).getOrElse(Seq.empty)
 
     val conversion = (
-      createTaskGraph(inputElements, declarations, outputElements, a.taskDefinitionElement.parameterMetaSection, a.typeAliases),
-      validateParameterMetaEntries(a.taskDefinitionElement.parameterMetaSection, a.taskDefinitionElement.inputsSection, a.taskDefinitionElement.outputsSection)
+      createTaskGraph(inputElements,
+                      declarations,
+                      outputElements,
+                      a.taskDefinitionElement.parameterMetaSection,
+                      a.typeAliases
+      ),
+      validateParameterMetaEntries(a.taskDefinitionElement.parameterMetaSection,
+                                   a.taskDefinitionElement.inputsSection,
+                                   a.taskDefinitionElement.outputsSection
+      )
     ) flatMapN { (taskGraph, _) =>
       val validRuntimeAttributes: ErrorOr[RuntimeAttributes] = a.taskDefinitionElement.runtimeSection match {
         case Some(attributeSection) => createRuntimeAttributes(attributeSection, taskGraph.linkedGraph)
         case None => RuntimeAttributes(Map.empty).validNel
       }
 
-      val validCommand: ErrorOr[Seq[CommandPart]] = {
-        expandLines(a.taskDefinitionElement.commandSection.parts).toList.traverse { parts =>
-          CommandPartElementToWomCommandPart.convert(parts, taskGraph.linkedGraph.typeAliases, taskGraph.linkedGraph.generatedHandles)
-        }.map(_.toSeq)
-      }
+      val validCommand: ErrorOr[Seq[CommandPart]] =
+        expandLines(a.taskDefinitionElement.commandSection.parts).toList
+          .traverse { parts =>
+            CommandPartElementToWomCommandPart.convert(parts,
+                                                       taskGraph.linkedGraph.typeAliases,
+                                                       taskGraph.linkedGraph.generatedHandles
+            )
+          }
+          .map(_.toSeq)
 
-      val (meta, parameterMeta) = processMetaSections(a.taskDefinitionElement.metaSection, a.taskDefinitionElement.parameterMetaSection)
+      val (meta, parameterMeta) =
+        processMetaSections(a.taskDefinitionElement.metaSection, a.taskDefinitionElement.parameterMetaSection)
 
       (validRuntimeAttributes, validCommand) mapN { (runtime, command) =>
-        CallableTaskDefinition(a.taskDefinitionElement.name, Function.const(command.validNel), runtime, meta, parameterMeta, taskGraph.outputs, taskGraph.inputs, Set.empty, Map.empty, sourceLocation = a.taskDefinitionElement.sourceLocation)
+        CallableTaskDefinition(
+          a.taskDefinitionElement.name,
+          Function.const(command.validNel),
+          runtime,
+          meta,
+          parameterMeta,
+          taskGraph.outputs,
+          taskGraph.inputs,
+          Set.empty,
+          Map.empty,
+          sourceLocation = a.taskDefinitionElement.sourceLocation
+        )
       }
     }
 
     conversion.contextualizeErrors(s"process task definition '${b.taskDefinitionElement.name}'")
   }
 
-  private def validateParameterMetaEntries(parameterMetaSectionElement: Option[ParameterMetaSectionElement], inputs: Option[InputsSectionElement], outputs: Option[OutputsSectionElement]): ErrorOr[Unit] = {
-    val validKeys: List[String] = inputs.toList.flatMap(_.inputDeclarations.map(_.name)) ++ outputs.toList.flatMap(_.outputs.map(_.name))
+  private def validateParameterMetaEntries(parameterMetaSectionElement: Option[ParameterMetaSectionElement],
+                                           inputs: Option[InputsSectionElement],
+                                           outputs: Option[OutputsSectionElement]
+  ): ErrorOr[Unit] = {
+    val validKeys: List[String] =
+      inputs.toList.flatMap(_.inputDeclarations.map(_.name)) ++ outputs.toList.flatMap(_.outputs.map(_.name))
     val errors = parameterMetaSectionElement.toList.flatMap { pmse =>
       val keys = pmse.metaAttributes.keySet.toList
       val duplicationErrors = keys.groupBy(identity).collect {
         case (name, list) if list.size > 1 => s"Found ${list.size} parameter meta entries for '$name' (expected 0 or 1)"
       }
       val notValidKeyErrors = keys.collect {
-        case name if !validKeys.contains(name) => s"Invalid parameter_meta entry for '$name': not an input or output parameter"
+        case name if !validKeys.contains(name) =>
+          s"Invalid parameter_meta entry for '$name': not an input or output parameter"
       }
       duplicationErrors.toList ++ notValidKeyErrors
     }
@@ -84,28 +116,40 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
     }
   }
 
-  private def eliminateInputDependencies(a: TaskDefinitionElementToWomInputs)
-                                        (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): TaskDefinitionElementToWomInputs = {
-    case class NewInputElementsSet(original: InputDeclarationElement, newInput: InputDeclarationElement, newDeclaration: IntermediateValueDeclarationElement)
+  private def eliminateInputDependencies(
+    a: TaskDefinitionElementToWomInputs
+  )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): TaskDefinitionElementToWomInputs = {
+    case class NewInputElementsSet(original: InputDeclarationElement,
+                                   newInput: InputDeclarationElement,
+                                   newDeclaration: IntermediateValueDeclarationElement
+    )
 
-    val inputElementsWithUpstreams: Seq[NewInputElementsSet] = a.taskDefinitionElement.inputsSection.map(_.inputDeclarations).getOrElse(Seq.empty) collect {
-      case ide @ InputDeclarationElement(typeElement,name, Some(expression)) if expression.expressionConsumedValueHooks.nonEmpty =>
-        val input = InputDeclarationElement(OptionalTypeElement(typeElement), name, None)
+    val inputElementsWithUpstreams: Seq[NewInputElementsSet] =
+      a.taskDefinitionElement.inputsSection.map(_.inputDeclarations).getOrElse(Seq.empty) collect {
+        case ide @ InputDeclarationElement(typeElement, name, Some(expression))
+            if expression.expressionConsumedValueHooks.nonEmpty =>
+          val input = InputDeclarationElement(OptionalTypeElement(typeElement), name, None)
 
-        val selecterExpression = SelectFirst(ArrayLiteral(Seq(IdentifierLookup(name), expression)))
-        val intermediate = IntermediateValueDeclarationElement(typeElement, s"__$name", selecterExpression)
+          val selecterExpression = SelectFirst(ArrayLiteral(Seq(IdentifierLookup(name), expression)))
+          val intermediate = IntermediateValueDeclarationElement(typeElement, s"__$name", selecterExpression)
 
-        NewInputElementsSet(ide, input, intermediate)
-    }
+          NewInputElementsSet(ide, input, intermediate)
+      }
 
     if (inputElementsWithUpstreams.nonEmpty) {
       val newInputsSection: Option[InputsSectionElement] = a.taskDefinitionElement.inputsSection.map { inputsSection =>
-        InputsSectionElement(inputsSection.inputDeclarations.filterNot(inputElementsWithUpstreams.map(_.original).contains) ++ inputElementsWithUpstreams.map(_.newInput))
+        InputsSectionElement(
+          inputsSection.inputDeclarations.filterNot(
+            inputElementsWithUpstreams.map(_.original).contains
+          ) ++ inputElementsWithUpstreams.map(_.newInput)
+        )
       }
-      val newDeclarationsSection: Seq[IntermediateValueDeclarationElement] = a.taskDefinitionElement.declarations ++ inputElementsWithUpstreams.map(_.newDeclaration)
+      val newDeclarationsSection: Seq[IntermediateValueDeclarationElement] =
+        a.taskDefinitionElement.declarations ++ inputElementsWithUpstreams.map(_.newDeclaration)
 
       val newTaskDefinitionElement = {
-        val withNewInputElements = a.taskDefinitionElement.copy(inputsSection = newInputsSection, declarations = newDeclarationsSection)
+        val withNewInputElements =
+          a.taskDefinitionElement.copy(inputsSection = newInputsSection, declarations = newDeclarationsSection)
         val identifierRenames = inputElementsWithUpstreams.map(ie => ie.original.name -> ie.newDeclaration.name).toMap
         renameIdentifierAccesses(withNewInputElements, identifierRenames)
       }
@@ -117,29 +161,37 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
 
   private def renameIdentifierAccesses(taskDefinitionElement: TaskDefinitionElement, renames: Map[String, String]) = {
 
-    val updatedInputs = taskDefinitionElement.inputsSection.map { inputsSection => InputsSectionElement(
-      inputsSection.inputDeclarations map { id =>
-        id.copy(expression = id.expression.map(_.renameIdentifiers(renames)))
-      }
-    )}
+    val updatedInputs = taskDefinitionElement.inputsSection.map { inputsSection =>
+      InputsSectionElement(
+        inputsSection.inputDeclarations map { id =>
+          id.copy(expression = id.expression.map(_.renameIdentifiers(renames)))
+        }
+      )
+    }
 
-    val updatedOutputs = taskDefinitionElement.outputsSection.map { outputsSection => OutputsSectionElement(
-      outputsSection.outputs map { od =>
-        od.copy(expression = od.expression.renameIdentifiers(renames))
-      }
-    )}
+    val updatedOutputs = taskDefinitionElement.outputsSection.map { outputsSection =>
+      OutputsSectionElement(
+        outputsSection.outputs map { od =>
+          od.copy(expression = od.expression.renameIdentifiers(renames))
+        }
+      )
+    }
 
-    val updatedCommand = CommandSectionElement(
-      taskDefinitionElement.commandSection.parts.map { line => CommandSectionLine(line.parts.map {
+    val updatedCommand = CommandSectionElement(taskDefinitionElement.commandSection.parts.map { line =>
+      CommandSectionLine(line.parts.map {
         case s: StringCommandPartElement => s
-        case p: PlaceholderCommandPartElement => p.copy(expressionElement = p.expressionElement.renameIdentifiers(renames))
-      })})
-
-    val updatedRuntime = taskDefinitionElement.runtimeSection.map { runtimeSection => RuntimeAttributesSectionElement(
-      runtimeSection.runtimeAttributes.map {
-        case KvPair(key, value) => KvPair(key, value.renameIdentifiers(renames))
-      }
-    )}
+        case p: PlaceholderCommandPartElement =>
+          p.copy(expressionElement = p.expressionElement.renameIdentifiers(renames))
+      })
+    })
+
+    val updatedRuntime = taskDefinitionElement.runtimeSection.map { runtimeSection =>
+      RuntimeAttributesSectionElement(
+        runtimeSection.runtimeAttributes.map { case KvPair(key, value) =>
+          KvPair(key, value.renameIdentifiers(renames))
+        }
+      )
+    }
 
     taskDefinitionElement.copy(
       inputsSection = updatedInputs,
@@ -169,35 +221,42 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
     }
   }
 
-  private final case class TaskGraph(inputs: List[Callable.InputDefinition], outputs: List[Callable.OutputDefinition], linkedGraph: LinkedGraph)
+  final private case class TaskGraph(inputs: List[Callable.InputDefinition],
+                                     outputs: List[Callable.OutputDefinition],
+                                     linkedGraph: LinkedGraph
+  )
 
   private def createTaskGraph(inputs: Seq[InputDeclarationElement],
                               declarations: Seq[IntermediateValueDeclarationElement],
                               outputs: Seq[OutputDeclarationElement],
                               parameterMeta: Option[ParameterMetaSectionElement],
-                              typeAliases: Map[String, WomType])
-                             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-                              fileEvaluator: FileEvaluator[ExpressionElement],
-                              typeEvaluator: TypeEvaluator[ExpressionElement],
-                              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[TaskGraph] = {
+                              typeAliases: Map[String, WomType]
+  )(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[TaskGraph] = {
     val combined: Set[WorkflowGraphElement] = (inputs ++ declarations ++ outputs).toSet
     LinkedGraphMaker.make(combined, Set.empty, typeAliases, Map.empty) flatMap { linked =>
       val ordered = LinkedGraphMaker.getOrdering(linked)
 
-      def foldFunction(currentGraphValidation: ErrorOr[TaskGraph], next: WorkflowGraphElement): ErrorOr[TaskGraph] = {
+      def foldFunction(currentGraphValidation: ErrorOr[TaskGraph], next: WorkflowGraphElement): ErrorOr[TaskGraph] =
         currentGraphValidation flatMap { accumulator => addToTaskGraph(next, accumulator) }
-      }
 
       def findParameterMeta(declName: String): Option[MetaValueElement] =
-        parameterMeta.flatMap { _.metaAttributes.get(declName) }
+        parameterMeta.flatMap(_.metaAttributes.get(declName))
 
       def addToTaskGraph(element: WorkflowGraphElement, accumulator: TaskGraph): ErrorOr[TaskGraph] = element match {
         case IntermediateValueDeclarationElement(womTypeElement, name, expression) =>
           val typeValidation = womTypeElement.determineWomType(linked.typeAliases)
-          val expressionValidation: ErrorOr[WomExpression] = expression.makeWomExpression(linked.typeAliases, linked.consumedValueLookup)
+          val expressionValidation: ErrorOr[WomExpression] =
+            expression.makeWomExpression(linked.typeAliases, linked.consumedValueLookup)
 
           (typeValidation, expressionValidation) mapN { (womType, womExpression) =>
-            accumulator.copy(inputs = accumulator.inputs :+ FixedInputDefinitionWithDefault(name, womType, womExpression))
+            accumulator.copy(inputs =
+              accumulator.inputs :+ FixedInputDefinitionWithDefault(name, womType, womExpression)
+            )
           }
         case InputDeclarationElement(womTypeElement, name, None) =>
           womTypeElement.determineWomType(linked.typeAliases) map { womType =>
@@ -207,12 +266,20 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
             }
             accumulator.copy(inputs = accumulator.inputs :+ newInput)
           }
-        case InputDeclarationElement(womTypeElement, name, Some(expression)) if expression.expressionConsumedValueHooks.isEmpty =>
+        case InputDeclarationElement(womTypeElement, name, Some(expression))
+            if expression.expressionConsumedValueHooks.isEmpty =>
           val typeValidation = womTypeElement.determineWomType(linked.typeAliases)
-          val expressionValidation: ErrorOr[WomExpression] = expression.makeWomExpression(linked.typeAliases, linked.consumedValueLookup)
+          val expressionValidation: ErrorOr[WomExpression] =
+            expression.makeWomExpression(linked.typeAliases, linked.consumedValueLookup)
 
           (typeValidation, expressionValidation) mapN { (womType, womExpression) =>
-            accumulator.copy(inputs = accumulator.inputs :+ OverridableInputDefinitionWithDefault(name, womType, womExpression, findParameterMeta(name)))
+            accumulator.copy(inputs =
+              accumulator.inputs :+ OverridableInputDefinitionWithDefault(name,
+                                                                          womType,
+                                                                          womExpression,
+                                                                          findParameterMeta(name)
+              )
+            )
           }
 
         // In this case, the expression has upstream dependencies. Since WOM won't allow that, make this an optional input and fixed declaration pair:
@@ -222,20 +289,23 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
             val newInputType = WomOptionalType(womType).flatOptionalType
             val newInputDefinition = OptionalInputDefinition(newInputName, newInputType, findParameterMeta(name))
 
-            val intermediateExpression: ExpressionElement = SelectFirst(ArrayLiteral(Seq(IdentifierLookup(newInputName), expression)))
+            val intermediateExpression: ExpressionElement =
+              SelectFirst(ArrayLiteral(Seq(IdentifierLookup(newInputName), expression)))
 
-            val intermediateWomExpression: ErrorOr[WomExpression] = intermediateExpression.makeWomExpression(linked.typeAliases, linked.consumedValueLookup)
+            val intermediateWomExpression: ErrorOr[WomExpression] =
+              intermediateExpression.makeWomExpression(linked.typeAliases, linked.consumedValueLookup)
             intermediateWomExpression map { womExpression =>
-              val intermediateDefinition = FixedInputDefinitionWithDefault(name, womType, womExpression, findParameterMeta(name))
+              val intermediateDefinition =
+                FixedInputDefinitionWithDefault(name, womType, womExpression, findParameterMeta(name))
 
               accumulator.copy(inputs = accumulator.inputs :+ newInputDefinition :+ intermediateDefinition)
             }
           }
 
-
         case OutputDeclarationElement(womTypeElement, name, expression) =>
           val typeValidation = womTypeElement.determineWomType(linked.typeAliases)
-          val expressionValidation: ErrorOr[WomExpression] = expression.makeWomExpression(linked.typeAliases, linked.consumedValueLookup)
+          val expressionValidation: ErrorOr[WomExpression] =
+            expression.makeWomExpression(linked.typeAliases, linked.consumedValueLookup)
 
           (typeValidation, expressionValidation) mapN { (womType, womExpression) =>
             accumulator.copy(outputs = accumulator.outputs :+ OutputDefinition(name, womType, womExpression))
@@ -249,19 +319,23 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
     }
   }
 
-  private def createRuntimeAttributes(attributes: RuntimeAttributesSectionElement, linkedGraph: LinkedGraph)
-                                     (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-                                      fileEvaluator: FileEvaluator[ExpressionElement],
-                                      typeEvaluator: TypeEvaluator[ExpressionElement],
-                                      valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[RuntimeAttributes] = {
+  private def createRuntimeAttributes(attributes: RuntimeAttributesSectionElement, linkedGraph: LinkedGraph)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[RuntimeAttributes] = {
 
     def processSingleRuntimeAttribute(kvPair: KvPair): ErrorOr[(String, WomExpression)] = for {
-      consumedValueLookup <- LinkedGraphMaker.makeConsumedValueLookup(kvPair.value.expressionConsumedValueHooks, linkedGraph.generatedHandles)
+      consumedValueLookup <- LinkedGraphMaker.makeConsumedValueLookup(kvPair.value.expressionConsumedValueHooks,
+                                                                      linkedGraph.generatedHandles
+      )
       womExpression <- kvPair.value.makeWomExpression(linkedGraph.typeAliases, consumedValueLookup)
     } yield kvPair.key -> womExpression
 
-
-    attributes.runtimeAttributes.toList.traverse(processSingleRuntimeAttribute).map(atts => RuntimeAttributes(atts.toMap))
+    attributes.runtimeAttributes.toList
+      .traverse(processSingleRuntimeAttribute)
+      .map(atts => RuntimeAttributes(atts.toMap))
   }
 
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/WomBundleToWomExecutable.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/WomBundleToWomExecutable.scala
index 26b40110b8e..11a4a9dadc4 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/WomBundleToWomExecutable.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/WomBundleToWomExecutable.scala
@@ -10,6 +10,10 @@ import wom.transforms.WomExecutableMaker
 object WomBundleToWomExecutable {
 
   implicit val draft3WomBundleToWomExecutable: WomExecutableMaker[WomBundle] = new WomExecutableMaker[WomBundle] {
-    override def toWomExecutable(a: WomBundle, inputs: Option[WorkflowJson], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = WdlSharedInputParsing.buildWomExecutable(a, inputs, ioFunctions, strictValidation)
+    override def toWomExecutable(a: WomBundle,
+                                 inputs: Option[WorkflowJson],
+                                 ioFunctions: IoFunctionSet,
+                                 strictValidation: Boolean
+    ): Checked[Executable] = WdlSharedInputParsing.buildWomExecutable(a, inputs, ioFunctions, strictValidation)
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/WorkflowDefinitionElementToWomWorkflowDefinition.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/WorkflowDefinitionElementToWomWorkflowDefinition.scala
index b1f04d902d8..a7571f9670a 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/WorkflowDefinitionElementToWomWorkflowDefinition.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/WorkflowDefinitionElementToWomWorkflowDefinition.scala
@@ -16,7 +16,7 @@ import wom.callable.MetaValueElement.MetaValueElementBoolean
 import wom.callable.{Callable, WorkflowDefinition}
 import wom.graph.GraphNodePort.OutputPort
 import wom.graph.expression.AnonymousExpressionNode
-import wom.graph.{CallNode, GraphNode, WomIdentifier, Graph => WomGraph}
+import wom.graph.{CallNode, Graph => WomGraph, GraphNode, WomIdentifier}
 import wom.types.WomType
 
 object WorkflowDefinitionElementToWomWorkflowDefinition extends Util {
@@ -24,23 +24,29 @@ object WorkflowDefinitionElementToWomWorkflowDefinition extends Util {
   final case class WorkflowDefinitionConvertInputs(definitionElement: WorkflowDefinitionElement,
                                                    typeAliases: Map[String, WomType],
                                                    callables: Map[String, Callable],
-                                                   convertNestedScatterToSubworkflow : Boolean)
+                                                   convertNestedScatterToSubworkflow: Boolean
+  )
 
-  def convert(b: WorkflowDefinitionConvertInputs)
-             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-              fileEvaluator: FileEvaluator[ExpressionElement],
-              typeEvaluator: TypeEvaluator[ExpressionElement],
-              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[WorkflowDefinition] = {
+  def convert(b: WorkflowDefinitionConvertInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[WorkflowDefinition] = {
 
     val a: WorkflowDefinitionConvertInputs = eliminateInputDependencies(b)
 
-    val (meta, parameterMeta) = processMetaSections(a.definitionElement.metaSection, a.definitionElement.parameterMetaSection)
+    val (meta, parameterMeta) =
+      processMetaSections(a.definitionElement.metaSection, a.definitionElement.parameterMetaSection)
 
-    val allowNestedInputs: Boolean = {
-      meta.get("allowNestedInputs").flatMap {
-        case x: MetaValueElementBoolean => Option(x.value)
-        case _ => None
-      }}.getOrElse(false)
+    val allowNestedInputs: Boolean =
+      meta
+        .get("allowNestedInputs")
+        .flatMap {
+          case x: MetaValueElementBoolean => Option(x.value)
+          case _ => None
+        }
+        .getOrElse(false)
 
     // Make the set of workflow graph elements, including:
     // - Top-level graph elements
@@ -51,11 +57,19 @@ object WorkflowDefinitionElementToWomWorkflowDefinition extends Util {
         a.definitionElement.inputsSection.toSeq.flatMap(_.inputDeclarations) ++
         a.definitionElement.outputsSection.toSeq.flatMap(_.outputs)
 
-    val innerGraph: ErrorOr[WomGraph] = convertGraphElements(GraphLikeConvertInputs(graphNodeElements, Set.empty, Map.empty, a.typeAliases, a.definitionElement.name,
-                                                                                    insideAScatter = false,
-                                                                                    convertNestedScatterToSubworkflow = b.convertNestedScatterToSubworkflow,
-                                                                                    allowNestedInputs = allowNestedInputs,
-                                                                                    a.callables))
+    val innerGraph: ErrorOr[WomGraph] = convertGraphElements(
+      GraphLikeConvertInputs(
+        graphNodeElements,
+        Set.empty,
+        Map.empty,
+        a.typeAliases,
+        a.definitionElement.name,
+        insideAScatter = false,
+        convertNestedScatterToSubworkflow = b.convertNestedScatterToSubworkflow,
+        allowNestedInputs = allowNestedInputs,
+        a.callables
+      )
+    )
     // NB: isEmpty means "not isDefined". We specifically do NOT add defaults if the output section is defined but empty.
     val withDefaultOutputs: ErrorOr[WomGraph] = if (a.definitionElement.outputsSection.isEmpty) {
       innerGraph map { WomGraphMakerTools.addDefaultOutputs(_, Some(WomIdentifier(a.definitionElement.name))) }
@@ -63,8 +77,8 @@ object WorkflowDefinitionElementToWomWorkflowDefinition extends Util {
       innerGraph
     }
 
-    (withDefaultOutputs map {
-      ig => WorkflowDefinition(a.definitionElement.name, ig, meta, parameterMeta, b.definitionElement.sourceLocation)
+    (withDefaultOutputs map { ig =>
+      WorkflowDefinition(a.definitionElement.name, ig, meta, parameterMeta, b.definitionElement.sourceLocation)
     }).contextualizeErrors(s"process workflow definition '${a.definitionElement.name}'")
   }
 
@@ -76,13 +90,15 @@ object WorkflowDefinitionElementToWomWorkflowDefinition extends Util {
                                           insideAScatter: Boolean,
                                           convertNestedScatterToSubworkflow: Boolean,
                                           allowNestedInputs: Boolean,
-                                          callables: Map[String, Callable])
+                                          callables: Map[String, Callable]
+  )
 
-  def convertGraphElements(a: GraphLikeConvertInputs)
-                          (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-                           fileEvaluator: FileEvaluator[ExpressionElement],
-                           typeEvaluator: TypeEvaluator[ExpressionElement],
-                           valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[WomGraph] = {
+  def convertGraphElements(a: GraphLikeConvertInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[WomGraph] = {
 
     val seedGeneratedValueHandles = for {
       seedNode <- a.seedNodes
@@ -92,8 +108,20 @@ object WorkflowDefinitionElementToWomWorkflowDefinition extends Util {
     val finished = a.externalUpstreamCalls map { c => GeneratedCallFinishedHandle(c._2.localName) }
 
     for {
-      linkedGraph <- LinkedGraphMaker.make(nodes = a.graphElements, seedGeneratedValueHandles ++ finished, typeAliases = a.typeAliases, callables = a.callables)
-      womGraph <- makeWomGraph(linkedGraph, a.seedNodes, a.externalUpstreamCalls, a.workflowName, a.insideAScatter, a.convertNestedScatterToSubworkflow, a.allowNestedInputs, a.callables)
+      linkedGraph <- LinkedGraphMaker.make(nodes = a.graphElements,
+                                           seedGeneratedValueHandles ++ finished,
+                                           typeAliases = a.typeAliases,
+                                           callables = a.callables
+      )
+      womGraph <- makeWomGraph(linkedGraph,
+                               a.seedNodes,
+                               a.externalUpstreamCalls,
+                               a.workflowName,
+                               a.insideAScatter,
+                               a.convertNestedScatterToSubworkflow,
+                               a.allowNestedInputs,
+                               a.callables
+      )
     } yield womGraph
   }
 
@@ -102,15 +130,19 @@ object WorkflowDefinitionElementToWomWorkflowDefinition extends Util {
                            externalUpstreamCalls: Map[String, CallNode],
                            workflowName: String,
                            insideAScatter: Boolean,
-                           convertNestedScatterToSubworkflow : Boolean,
+                           convertNestedScatterToSubworkflow: Boolean,
                            allowNestedInputs: Boolean,
-                           callables: Map[String, Callable])
-                          (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-                           fileEvaluator: FileEvaluator[ExpressionElement],
-                           typeEvaluator: TypeEvaluator[ExpressionElement],
-                           valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[WomGraph] = {
-
-    def graphNodeCreationFold(currentValidation: ErrorOr[List[GraphNode]], next: WorkflowGraphElement): ErrorOr[List[GraphNode]] = {
+                           callables: Map[String, Callable]
+  )(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[WomGraph] = {
+
+    def graphNodeCreationFold(currentValidation: ErrorOr[List[GraphNode]],
+                              next: WorkflowGraphElement
+    ): ErrorOr[List[GraphNode]] = {
       def outputName(node: GraphNode, port: OutputPort): String = port.identifier.localName.value
 
       currentValidation flatMap { currentList =>
@@ -129,40 +161,65 @@ object WorkflowDefinitionElementToWomWorkflowDefinition extends Util {
 
         val generatedGraphNodesValidation: ErrorOr[Set[GraphNode]] =
           WorkflowGraphElementToGraphNode.convert(
-            GraphNodeMakerInputs(next, upstreamCallNodes, linkedGraph.consumedValueLookup, availableValues, linkedGraph.typeAliases, workflowName, insideAScatter, convertNestedScatterToSubworkflow, allowNestedInputs, callables))
+            GraphNodeMakerInputs(
+              next,
+              upstreamCallNodes,
+              linkedGraph.consumedValueLookup,
+              availableValues,
+              linkedGraph.typeAliases,
+              workflowName,
+              insideAScatter,
+              convertNestedScatterToSubworkflow,
+              allowNestedInputs,
+              callables
+            )
+          )
         generatedGraphNodesValidation map { nextGraphNodes: Set[GraphNode] => currentList ++ nextGraphNodes }
       }
     }
 
-    val graphNodesValidation = LinkedGraphMaker.getOrdering(linkedGraph) flatMap { ordering: List[WorkflowGraphElement] =>
-      ordering.foldLeft[ErrorOr[List[GraphNode]]](seedNodes.toList.validNel)(graphNodeCreationFold)
+    val graphNodesValidation = LinkedGraphMaker.getOrdering(linkedGraph) flatMap {
+      ordering: List[WorkflowGraphElement] =>
+        ordering.foldLeft[ErrorOr[List[GraphNode]]](seedNodes.toList.validNel)(graphNodeCreationFold)
     }
 
     graphNodesValidation flatMap { graphNodes => WomGraph.validateAndConstruct(graphNodes.toSet) }
   }
 
-  private def eliminateInputDependencies(a: WorkflowDefinitionConvertInputs)
-                                        (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): WorkflowDefinitionConvertInputs = {
-    case class NewInputElementsSet(original: InputDeclarationElement, newInput: InputDeclarationElement, newDeclaration: IntermediateValueDeclarationElement)
+  private def eliminateInputDependencies(
+    a: WorkflowDefinitionConvertInputs
+  )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): WorkflowDefinitionConvertInputs = {
+    case class NewInputElementsSet(original: InputDeclarationElement,
+                                   newInput: InputDeclarationElement,
+                                   newDeclaration: IntermediateValueDeclarationElement
+    )
 
-    val inputElementsWithUpstreams: Seq[NewInputElementsSet] = a.definitionElement.inputsSection.map(_.inputDeclarations).getOrElse(Seq.empty) collect {
-      case ide @ InputDeclarationElement(typeElement,name, Some(expression)) if expression.expressionConsumedValueHooks.nonEmpty =>
-        val input = InputDeclarationElement(OptionalTypeElement(typeElement), name, None)
+    val inputElementsWithUpstreams: Seq[NewInputElementsSet] =
+      a.definitionElement.inputsSection.map(_.inputDeclarations).getOrElse(Seq.empty) collect {
+        case ide @ InputDeclarationElement(typeElement, name, Some(expression))
+            if expression.expressionConsumedValueHooks.nonEmpty =>
+          val input = InputDeclarationElement(OptionalTypeElement(typeElement), name, None)
 
-        val selecterExpression = SelectFirst(ArrayLiteral(Seq(IdentifierLookup(name), expression)))
-        val intermediate = IntermediateValueDeclarationElement(typeElement, s"__$name", selecterExpression)
+          val selecterExpression = SelectFirst(ArrayLiteral(Seq(IdentifierLookup(name), expression)))
+          val intermediate = IntermediateValueDeclarationElement(typeElement, s"__$name", selecterExpression)
 
-        NewInputElementsSet(ide, input, intermediate)
-    }
+          NewInputElementsSet(ide, input, intermediate)
+      }
 
     if (inputElementsWithUpstreams.nonEmpty) {
       val newInputsSection: Option[InputsSectionElement] = a.definitionElement.inputsSection.map { inputsSection =>
-        InputsSectionElement(inputsSection.inputDeclarations.filterNot(inputElementsWithUpstreams.map(_.original).contains) ++ inputElementsWithUpstreams.map(_.newInput))
+        InputsSectionElement(
+          inputsSection.inputDeclarations.filterNot(
+            inputElementsWithUpstreams.map(_.original).contains
+          ) ++ inputElementsWithUpstreams.map(_.newInput)
+        )
       }
-      val newGraphNodeSet: Set[WorkflowGraphElement] = a.definitionElement.graphElements ++ inputElementsWithUpstreams.map(_.newDeclaration)
+      val newGraphNodeSet: Set[WorkflowGraphElement] =
+        a.definitionElement.graphElements ++ inputElementsWithUpstreams.map(_.newDeclaration)
 
       val newWorkflowDefinitionElement: WorkflowDefinitionElement = {
-        val withNewInputElements = a.definitionElement.copy(inputsSection = newInputsSection, graphElements = newGraphNodeSet)
+        val withNewInputElements =
+          a.definitionElement.copy(inputsSection = newInputsSection, graphElements = newGraphNodeSet)
         val identifierRenames = inputElementsWithUpstreams.map(ie => ie.original.name -> ie.newDeclaration.name).toMap
         withNewInputElements.renameIdentifiers(identifierRenames)
       }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/WdlomWomExpression.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/WdlomWomExpression.scala
index 13eff3236ae..f94c15aa7b7 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/WdlomWomExpression.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/WdlomWomExpression.scala
@@ -14,18 +14,23 @@ import wom.expression.{FileEvaluation, IoFunctionSet, WomExpression}
 import wom.types._
 import wom.values.WomValue
 
-final case class WdlomWomExpression private (expressionElement: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-                                            (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-                                             fileEvaluator: FileEvaluator[ExpressionElement],
-                                             typeEvaluator: TypeEvaluator[ExpressionElement],
-                                             valueEvaluator: ValueEvaluator[ExpressionElement]) extends WomExpression {
+final case class WdlomWomExpression private (expressionElement: ExpressionElement,
+                                             linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+)(implicit
+  expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+  fileEvaluator: FileEvaluator[ExpressionElement],
+  typeEvaluator: TypeEvaluator[ExpressionElement],
+  valueEvaluator: ValueEvaluator[ExpressionElement]
+) extends WomExpression {
   override def sourceString: String = expressionElement.toWdlV1
 
-  override def inputs: Set[String] = {
+  override def inputs: Set[String] =
     expressionElement.expressionConsumedValueHooks map { hook => linkedValues(hook).linkableName }
-  }
 
-  def evaluateValueForPlaceholder(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet, forCommandInstantiationOptions: ForCommandInstantiationOptions): ErrorOr[EvaluatedValue[_]] =
+  def evaluateValueForPlaceholder(inputValues: Map[String, WomValue],
+                                  ioFunctionSet: IoFunctionSet,
+                                  forCommandInstantiationOptions: ForCommandInstantiationOptions
+  ): ErrorOr[EvaluatedValue[_]] =
     expressionElement.evaluateValue(inputValues, ioFunctionSet, Option(forCommandInstantiationOptions))
 
   override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] =
@@ -35,20 +40,28 @@ final case class WdlomWomExpression private (expressionElement: ExpressionElemen
   // NB types can be determined using the linked values, so we don't need the inputMap:
   override def evaluateType(inputMap: Map[String, WomType]): ErrorOr[WomType] = evaluatedType
 
-  override def evaluateFiles(inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = {
-    expressionElement.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo) map { _ map {
-      FileEvaluation(_, optional = areAllFileTypesInWomTypeOptional(coerceTo), secondary = false)
-    }}
-  }
+  override def evaluateFiles(inputs: Map[String, WomValue],
+                             ioFunctionSet: IoFunctionSet,
+                             coerceTo: WomType
+  ): ErrorOr[Set[FileEvaluation]] =
+    expressionElement.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo) map {
+      _ map {
+        FileEvaluation(_, optional = areAllFileTypesInWomTypeOptional(coerceTo), secondary = false)
+      }
+    }
 }
 
 object WdlomWomExpression {
-  def make(expressionElement: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])
-          (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-           fileEvaluator: FileEvaluator[ExpressionElement],
-           typeEvaluator: TypeEvaluator[ExpressionElement],
-           valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[WdlomWomExpression] = {
+  def make(expressionElement: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+    implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[WdlomWomExpression] = {
     val candidate = WdlomWomExpression(expressionElement, linkedValues)
-    candidate.evaluatedType.contextualizeErrors(s"process expression '${candidate.sourceString}'") map { _ => candidate }
+    candidate.evaluatedType.contextualizeErrors(s"process expression '${candidate.sourceString}'") map { _ =>
+      candidate
+    }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/BinaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/BinaryOperatorEvaluators.scala
index c862e2abc0e..15fcdac8115 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/BinaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/BinaryOperatorEvaluators.scala
@@ -12,20 +12,23 @@ object BinaryOperatorEvaluators {
   implicit val lessThanEvaluator: IdentifierLookupRenamer[LessThan] = forOperation(LessThan)
   implicit val lessThanOrEqualEvaluator: IdentifierLookupRenamer[LessThanOrEquals] = forOperation(LessThanOrEquals)
   implicit val greaterThanEvaluator: IdentifierLookupRenamer[GreaterThan] = forOperation(GreaterThan)
-  implicit val greaterThanOrEqualEvaluator: IdentifierLookupRenamer[GreaterThanOrEquals] = forOperation(GreaterThanOrEquals)
+  implicit val greaterThanOrEqualEvaluator: IdentifierLookupRenamer[GreaterThanOrEquals] = forOperation(
+    GreaterThanOrEquals
+  )
   implicit val addEvaluator: IdentifierLookupRenamer[Add] = forOperation(Add)
   implicit val subtractEvaluator: IdentifierLookupRenamer[Subtract] = forOperation(Subtract)
   implicit val multiplyEvaluator: IdentifierLookupRenamer[Multiply] = forOperation(Multiply)
   implicit val divideEvaluator: IdentifierLookupRenamer[Divide] = forOperation(Divide)
   implicit val remainderEvaluator: IdentifierLookupRenamer[Remainder] = forOperation(Remainder)
 
-  private def forOperation[A <: BinaryOperation](constructor: (ExpressionElement, ExpressionElement) => A) = new IdentifierLookupRenamer[A] {
-    override def renameIdentifiers(a: A,
-                                   renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): A =
-      constructor.apply(
-        expressionElementRenamer.renameIdentifiers(a.left, renamingMap)(expressionElementRenamer),
-        expressionElementRenamer.renameIdentifiers(a.right, renamingMap)(expressionElementRenamer)
-      )
-  }
+  private def forOperation[A <: BinaryOperation](constructor: (ExpressionElement, ExpressionElement) => A) =
+    new IdentifierLookupRenamer[A] {
+      override def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): A =
+        constructor.apply(
+          expressionElementRenamer.renameIdentifiers(a.left, renamingMap)(expressionElementRenamer),
+          expressionElementRenamer.renameIdentifiers(a.right, renamingMap)(expressionElementRenamer)
+        )
+    }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/EngineFunctionEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/EngineFunctionEvaluators.scala
index 186843b134b..6efcf60cc4f 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/EngineFunctionEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/EngineFunctionEvaluators.scala
@@ -3,7 +3,6 @@ package wdl.transforms.base.wdlom2wom.expression.renaming
 import wdl.model.draft3.elements.ExpressionElement._
 import wdl.model.draft3.elements.ExpressionElement
 
-
 object EngineFunctionEvaluators {
 
   implicit val stdoutRenamer: IdentifierLookupRenamer[StdoutElement.type] = forZeroParamFunction[StdoutElement.type]
@@ -46,51 +45,58 @@ object EngineFunctionEvaluators {
 
   implicit val subRenamer: IdentifierLookupRenamer[Sub] = forThreeParamFunction(Sub)
 
-  private def forZeroParamFunction[A <: ExpressionElement]: IdentifierLookupRenamer[A] = new IdentifierLookupRenamer[A] {
-    override def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): A = a
-  }
+  private def forZeroParamFunction[A <: ExpressionElement]: IdentifierLookupRenamer[A] =
+    new IdentifierLookupRenamer[A] {
+      override def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): A = a
+    }
 
-  private def forOneParamFunction[A <: OneParamFunctionCallElement](constructor: ExpressionElement => A): IdentifierLookupRenamer[A] = new IdentifierLookupRenamer[A] {
-    override def renameIdentifiers(a: A,
-                                   renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): A = {
+  private def forOneParamFunction[A <: OneParamFunctionCallElement](
+    constructor: ExpressionElement => A
+  ): IdentifierLookupRenamer[A] = new IdentifierLookupRenamer[A] {
+    override def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit
+      expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+    ): A =
       constructor.apply(
         expressionElementRenamer.renameIdentifiers(a.param, renamingMap)(expressionElementRenamer)
       )
-    }
   }
 
-  private def forOneOrTwoParamFunction[A <: OneOrTwoParamFunctionCallElement](constructor: (ExpressionElement, Option[ExpressionElement]) => A): IdentifierLookupRenamer[A] = new IdentifierLookupRenamer[A] {
-    override def renameIdentifiers(a: A,
-                                   renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): A = {
+  private def forOneOrTwoParamFunction[A <: OneOrTwoParamFunctionCallElement](
+    constructor: (ExpressionElement, Option[ExpressionElement]) => A
+  ): IdentifierLookupRenamer[A] = new IdentifierLookupRenamer[A] {
+    override def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit
+      expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+    ): A =
       constructor.apply(
         expressionElementRenamer.renameIdentifiers(a.firstParam, renamingMap)(expressionElementRenamer),
         a.secondParam.map(expressionElementRenamer.renameIdentifiers(_, renamingMap)(expressionElementRenamer))
       )
-    }
   }
 
-  private def forTwoParamFunction[A <: TwoParamFunctionCallElement](constructor: (ExpressionElement, ExpressionElement) => A): IdentifierLookupRenamer[A] = new IdentifierLookupRenamer[A] {
-    override def renameIdentifiers(a: A,
-                                   renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): A = {
+  private def forTwoParamFunction[A <: TwoParamFunctionCallElement](
+    constructor: (ExpressionElement, ExpressionElement) => A
+  ): IdentifierLookupRenamer[A] = new IdentifierLookupRenamer[A] {
+    override def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit
+      expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+    ): A =
       constructor.apply(
         expressionElementRenamer.renameIdentifiers(a.arg1, renamingMap)(expressionElementRenamer),
         expressionElementRenamer.renameIdentifiers(a.arg2, renamingMap)(expressionElementRenamer)
       )
-    }
   }
 
-  private def forThreeParamFunction[A <: ThreeParamFunctionCallElement](constructor: (ExpressionElement, ExpressionElement, ExpressionElement) => A): IdentifierLookupRenamer[A] = new IdentifierLookupRenamer[A] {
-    override def renameIdentifiers(a: A,
-                                   renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): A = {
+  private def forThreeParamFunction[A <: ThreeParamFunctionCallElement](
+    constructor: (ExpressionElement, ExpressionElement, ExpressionElement) => A
+  ): IdentifierLookupRenamer[A] = new IdentifierLookupRenamer[A] {
+    override def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit
+      expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+    ): A =
       constructor.apply(
         expressionElementRenamer.renameIdentifiers(a.arg1, renamingMap)(expressionElementRenamer),
         expressionElementRenamer.renameIdentifiers(a.arg2, renamingMap)(expressionElementRenamer),
         expressionElementRenamer.renameIdentifiers(a.arg3, renamingMap)(expressionElementRenamer)
       )
-    }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/IdentifierLookupRenamer.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/IdentifierLookupRenamer.scala
index 0fd301f92f0..c75da3ab685 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/IdentifierLookupRenamer.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/IdentifierLookupRenamer.scala
@@ -5,5 +5,7 @@ import wdl.model.draft3.elements.ExpressionElement
 
 @typeclass
 trait IdentifierLookupRenamer[A <: ExpressionElement] {
-  def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): A
+  def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit
+    expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+  ): A
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/LiteralEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/LiteralEvaluators.scala
index b3158f92f3d..8611caba92e 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/LiteralEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/LiteralEvaluators.scala
@@ -3,56 +3,72 @@ package wdl.transforms.base.wdlom2wom.expression.renaming
 import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement._
 
-
 object LiteralEvaluators {
-  implicit val primitiveIdentifierLookupRenamer: IdentifierLookupRenamer[PrimitiveLiteralExpressionElement] = new IdentifierLookupRenamer[PrimitiveLiteralExpressionElement] {
-    override def renameIdentifiers(a: PrimitiveLiteralExpressionElement, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): PrimitiveLiteralExpressionElement = a
-  }
+  implicit val primitiveIdentifierLookupRenamer: IdentifierLookupRenamer[PrimitiveLiteralExpressionElement] =
+    new IdentifierLookupRenamer[PrimitiveLiteralExpressionElement] {
+      override def renameIdentifiers(a: PrimitiveLiteralExpressionElement, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): PrimitiveLiteralExpressionElement = a
+    }
 
-  implicit val stringLiteralEvaluator: IdentifierLookupRenamer[StringLiteral] = new IdentifierLookupRenamer[StringLiteral] {
-    override def renameIdentifiers(a: StringLiteral, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): StringLiteral = a
-  }
+  implicit val stringLiteralEvaluator: IdentifierLookupRenamer[StringLiteral] =
+    new IdentifierLookupRenamer[StringLiteral] {
+      override def renameIdentifiers(a: StringLiteral, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): StringLiteral = a
+    }
 
-  implicit val stringExpressionEvaluator: IdentifierLookupRenamer[StringExpression] = new IdentifierLookupRenamer[StringExpression] {
-    override def renameIdentifiers(a: StringExpression, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): StringExpression = StringExpression(
-      a.pieces map {
-        case sp: StringPlaceholder => StringPlaceholder(expressionElementRenamer.renameIdentifiers(sp.expr, renamingMap)(expressionElementRenamer))
-        case other => other
-      }
-    )
-  }
+  implicit val stringExpressionEvaluator: IdentifierLookupRenamer[StringExpression] =
+    new IdentifierLookupRenamer[StringExpression] {
+      override def renameIdentifiers(a: StringExpression, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): StringExpression = StringExpression(
+        a.pieces map {
+          case sp: StringPlaceholder =>
+            StringPlaceholder(
+              expressionElementRenamer.renameIdentifiers(sp.expr, renamingMap)(expressionElementRenamer)
+            )
+          case other => other
+        }
+      )
+    }
 
-  implicit val objectLiteralEvaluator: IdentifierLookupRenamer[ObjectLiteral] = new IdentifierLookupRenamer[ObjectLiteral] {
-    override def renameIdentifiers(a: ObjectLiteral, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): ObjectLiteral = ObjectLiteral(
-      a.elements map {
-        case (key, value) => key -> expressionElementRenamer.renameIdentifiers(value, renamingMap)(expressionElementRenamer)
-      }
-    )
-  }
+  implicit val objectLiteralEvaluator: IdentifierLookupRenamer[ObjectLiteral] =
+    new IdentifierLookupRenamer[ObjectLiteral] {
+      override def renameIdentifiers(a: ObjectLiteral, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): ObjectLiteral = ObjectLiteral(
+        a.elements map { case (key, value) =>
+          key -> expressionElementRenamer.renameIdentifiers(value, renamingMap)(expressionElementRenamer)
+        }
+      )
+    }
 
   implicit val mapLiteralEvaluator: IdentifierLookupRenamer[MapLiteral] = new IdentifierLookupRenamer[MapLiteral] {
-    override def renameIdentifiers(a: MapLiteral, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): MapLiteral = MapLiteral(
-      a.elements map {
-        case (key, value) => expressionElementRenamer.renameIdentifiers(key, renamingMap)(expressionElementRenamer) -> expressionElementRenamer.renameIdentifiers(value, renamingMap)(expressionElementRenamer)
+    override def renameIdentifiers(a: MapLiteral, renamingMap: Map[String, String])(implicit
+      expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+    ): MapLiteral = MapLiteral(
+      a.elements map { case (key, value) =>
+        expressionElementRenamer.renameIdentifiers(key, renamingMap)(
+          expressionElementRenamer
+        ) -> expressionElementRenamer.renameIdentifiers(value, renamingMap)(expressionElementRenamer)
       }
     )
   }
 
-  implicit val arrayLiteralEvaluator: IdentifierLookupRenamer[ArrayLiteral] = new IdentifierLookupRenamer[ArrayLiteral] {
-    override def renameIdentifiers(a: ArrayLiteral, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): ArrayLiteral = ArrayLiteral(
-      a.elements map { e => expressionElementRenamer.renameIdentifiers(e, renamingMap)(expressionElementRenamer) }
-    )
-  }
+  implicit val arrayLiteralEvaluator: IdentifierLookupRenamer[ArrayLiteral] =
+    new IdentifierLookupRenamer[ArrayLiteral] {
+      override def renameIdentifiers(a: ArrayLiteral, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): ArrayLiteral = ArrayLiteral(
+        a.elements map { e => expressionElementRenamer.renameIdentifiers(e, renamingMap)(expressionElementRenamer) }
+      )
+    }
 
   implicit val pairLiteralEvaluator: IdentifierLookupRenamer[PairLiteral] = new IdentifierLookupRenamer[PairLiteral] {
-    override def renameIdentifiers(a: PairLiteral, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): PairLiteral = PairLiteral(
+    override def renameIdentifiers(a: PairLiteral, renamingMap: Map[String, String])(implicit
+      expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+    ): PairLiteral = PairLiteral(
       expressionElementRenamer.renameIdentifiers(a.left, renamingMap)(expressionElementRenamer),
       expressionElementRenamer.renameIdentifiers(a.right, renamingMap)(expressionElementRenamer)
     )
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/LookupEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/LookupEvaluators.scala
index f1b2151a8c7..924bde53f80 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/LookupEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/LookupEvaluators.scala
@@ -3,38 +3,48 @@ package wdl.transforms.base.wdlom2wom.expression.renaming
 import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement._
 
-
-
 object LookupEvaluators {
 
-  implicit val identifierLookupEvaluator: IdentifierLookupRenamer[IdentifierLookup] = new IdentifierLookupRenamer[IdentifierLookup] {
-    override def renameIdentifiers(a: IdentifierLookup, renamingMap: Map[String, String])(implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): IdentifierLookup = IdentifierLookup(
-      if (renamingMap.contains(a.identifier))
-        renamingMap(a.identifier)
-      else
-        a.identifier
-    )
-  }
-
-  implicit val expressionMemberAccessEvaluator: IdentifierLookupRenamer[ExpressionMemberAccess] = new IdentifierLookupRenamer[ExpressionMemberAccess] {
-    override def renameIdentifiers(a: ExpressionMemberAccess, renamingMap: Map[String, String])(implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): ExpressionMemberAccess = ExpressionMemberAccess(
-      expressionElementRenamer.renameIdentifiers(a.expression, renamingMap)(expressionElementRenamer),
-      a.memberAccessTail
-    )
-  }
-
-  implicit val identifierMemberAccessEvaluator: IdentifierLookupRenamer[IdentifierMemberAccess] = new IdentifierLookupRenamer[IdentifierMemberAccess] {
-    override def renameIdentifiers(a: IdentifierMemberAccess, renamingMap: Map[String, String])(implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): IdentifierMemberAccess = IdentifierMemberAccess(
-      if (renamingMap.contains(a.first)) renamingMap(a.first) else a.first,
-      a.second,
-      a.memberAccessTail
-    )
-  }
-
-  implicit val indexAccessIdentifierLookupRenamer: IdentifierLookupRenamer[IndexAccess] = new IdentifierLookupRenamer[IndexAccess] {
-    override def renameIdentifiers(a: IndexAccess, renamingMap: Map[String, String])(implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): IndexAccess = IndexAccess(
-      expressionElementRenamer.renameIdentifiers(a.expressionElement, renamingMap)(expressionElementRenamer),
-      expressionElementRenamer.renameIdentifiers(a.index, renamingMap)(expressionElementRenamer)
-    )
-  }
+  implicit val identifierLookupEvaluator: IdentifierLookupRenamer[IdentifierLookup] =
+    new IdentifierLookupRenamer[IdentifierLookup] {
+      override def renameIdentifiers(a: IdentifierLookup, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): IdentifierLookup = IdentifierLookup(
+        if (renamingMap.contains(a.identifier))
+          renamingMap(a.identifier)
+        else
+          a.identifier
+      )
+    }
+
+  implicit val expressionMemberAccessEvaluator: IdentifierLookupRenamer[ExpressionMemberAccess] =
+    new IdentifierLookupRenamer[ExpressionMemberAccess] {
+      override def renameIdentifiers(a: ExpressionMemberAccess, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): ExpressionMemberAccess = ExpressionMemberAccess(
+        expressionElementRenamer.renameIdentifiers(a.expression, renamingMap)(expressionElementRenamer),
+        a.memberAccessTail
+      )
+    }
+
+  implicit val identifierMemberAccessEvaluator: IdentifierLookupRenamer[IdentifierMemberAccess] =
+    new IdentifierLookupRenamer[IdentifierMemberAccess] {
+      override def renameIdentifiers(a: IdentifierMemberAccess, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): IdentifierMemberAccess = IdentifierMemberAccess(
+        if (renamingMap.contains(a.first)) renamingMap(a.first) else a.first,
+        a.second,
+        a.memberAccessTail
+      )
+    }
+
+  implicit val indexAccessIdentifierLookupRenamer: IdentifierLookupRenamer[IndexAccess] =
+    new IdentifierLookupRenamer[IndexAccess] {
+      override def renameIdentifiers(a: IndexAccess, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): IndexAccess = IndexAccess(
+        expressionElementRenamer.renameIdentifiers(a.expressionElement, renamingMap)(expressionElementRenamer),
+        expressionElementRenamer.renameIdentifiers(a.index, renamingMap)(expressionElementRenamer)
+      )
+    }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/TernaryIfEvaluator.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/TernaryIfEvaluator.scala
index a22971854a0..df3b77c3ace 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/TernaryIfEvaluator.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/TernaryIfEvaluator.scala
@@ -5,7 +5,9 @@ import wdl.model.draft3.elements.ExpressionElement._
 
 object TernaryIfEvaluator {
   implicit val ternaryIfEvaluator: IdentifierLookupRenamer[TernaryIf] = new IdentifierLookupRenamer[TernaryIf] {
-    override def renameIdentifiers(a: TernaryIf, renamingMap: Map[String, String])(implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): TernaryIf = TernaryIf(
+    override def renameIdentifiers(a: TernaryIf, renamingMap: Map[String, String])(implicit
+      expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+    ): TernaryIf = TernaryIf(
       expressionElementRenamer.renameIdentifiers(a.condition, renamingMap)(expressionElementRenamer),
       expressionElementRenamer.renameIdentifiers(a.ifTrue, renamingMap)(expressionElementRenamer),
       expressionElementRenamer.renameIdentifiers(a.ifFalse, renamingMap)(expressionElementRenamer)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/UnaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/UnaryOperatorEvaluators.scala
index 9864d239751..71673dd67e2 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/UnaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/UnaryOperatorEvaluators.scala
@@ -10,7 +10,9 @@ object UnaryOperatorEvaluators {
   implicit val logicalNotEvaluator: IdentifierLookupRenamer[LogicalNot] = forOperation(LogicalNot)
 
   private def forOperation[A <: UnaryOperation](constructor: ExpressionElement => A) = new IdentifierLookupRenamer[A] {
-    override def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): A =
+    override def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit
+      expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+    ): A =
       constructor.apply(expressionElementRenamer.renameIdentifiers(a.argument, renamingMap)(expressionElementRenamer))
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/package.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/package.scala
index 2bc9b6b7488..a4fce5d1292 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/package.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/renaming/package.scala
@@ -13,90 +13,89 @@ import wdl.transforms.base.wdlom2wom.expression.renaming.UnaryOperatorEvaluators
 
 package object renaming {
 
-  implicit val expressionEvaluator: IdentifierLookupRenamer[ExpressionElement] = new IdentifierLookupRenamer[ExpressionElement] {
-    override def renameIdentifiers(a: ExpressionElement,
-                                   renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]): ExpressionElement = {
+  implicit val expressionEvaluator: IdentifierLookupRenamer[ExpressionElement] =
+    new IdentifierLookupRenamer[ExpressionElement] {
+      override def renameIdentifiers(a: ExpressionElement, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement]
+      ): ExpressionElement =
+        a match {
+          // Literals:
+          case a: PrimitiveLiteralExpressionElement => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: StringLiteral => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: StringExpression => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ObjectLiteral => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: MapLiteral => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ArrayLiteral => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: PairLiteral => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
 
-      a match {
-        // Literals:
-        case a: PrimitiveLiteralExpressionElement => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: StringLiteral => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: StringExpression => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ObjectLiteral => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: MapLiteral => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ArrayLiteral => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: PairLiteral => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          // Lookups and member accesses:
+          case a: IdentifierLookup => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ExpressionMemberAccess => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: IdentifierMemberAccess => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: IndexAccess => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
 
-        // Lookups and member accesses:
-        case a: IdentifierLookup => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ExpressionMemberAccess => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: IdentifierMemberAccess => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: IndexAccess => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          // Unary operators:
+          case a: UnaryNegation => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: UnaryPlus => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: LogicalNot => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
 
-        // Unary operators:
-        case a: UnaryNegation => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: UnaryPlus => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: LogicalNot => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          // Binary operators (at some point we might want to split these into separate cases):
+          case a: LogicalOr => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: LogicalAnd => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Equals => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: NotEquals => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: LessThan => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: LessThanOrEquals => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: GreaterThan => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: GreaterThanOrEquals => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Add => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Subtract => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Multiply => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Divide => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Remainder => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
 
-        // Binary operators (at some point we might want to split these into separate cases):
-        case a: LogicalOr => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: LogicalAnd => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Equals => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: NotEquals => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: LessThan => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: LessThanOrEquals => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: GreaterThan => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: GreaterThanOrEquals => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Add => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Subtract => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Multiply => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Divide => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Remainder => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: TernaryIf => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
 
-        case a: TernaryIf => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          // Engine functions:
+          case a: StdoutElement.type => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: StderrElement.type => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
 
-        // Engine functions:
-        case a: StdoutElement.type => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: StderrElement.type => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ReadLines => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ReadTsv => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ReadMap => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ReadObject => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ReadObjects => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ReadJson => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ReadInt => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ReadString => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ReadFloat => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: ReadBoolean => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: WriteLines => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: WriteTsv => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: WriteMap => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: WriteObject => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: WriteObjects => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: WriteJson => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Range => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Transpose => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Length => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Flatten => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: SelectFirst => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: SelectAll => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Defined => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Floor => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Ceil => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Round => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Glob => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
 
-        case a: ReadLines => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ReadTsv => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ReadMap => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ReadObject => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ReadObjects => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ReadJson => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ReadInt => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ReadString => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ReadFloat => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: ReadBoolean => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: WriteLines => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: WriteTsv => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: WriteMap => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: WriteObject => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: WriteObjects => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: WriteJson => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Range => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Transpose => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Length => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Flatten => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: SelectFirst => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: SelectAll => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Defined => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Floor => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Ceil => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Round => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Glob => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Size => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Basename => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
 
-        case a: Size => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Basename => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Zip => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Cross => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+          case a: Prefix => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
 
-        case a: Zip => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Cross => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-        case a: Prefix => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-
-        case a: Sub => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
-      }
+          case a: Sub => a.renameIdentifiers(renamingMap)(expressionElementRenamer)
+        }
     }
-  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala
index 322fc5ceba6..6aa36184aef 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala
@@ -16,7 +16,12 @@ import wom.callable.Callable._
 import wom.callable.{Callable, CallableTaskDefinition, TaskDefinition, WorkflowDefinition}
 import wom.graph.CallNode.{CallNodeAndNewNodes, InputDefinitionFold, InputDefinitionPointer}
 import wom.graph.GraphNodePort.OutputPort
-import wom.graph.expression.{AnonymousExpressionNode, ExpressionNode, PlainAnonymousExpressionNode, TaskCallInputExpressionNode}
+import wom.graph.expression.{
+  AnonymousExpressionNode,
+  ExpressionNode,
+  PlainAnonymousExpressionNode,
+  TaskCallInputExpressionNode
+}
 import wom.graph._
 import wom.types.{WomOptionalType, WomType}
 import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
@@ -24,11 +29,12 @@ import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.expressionElementWriter
 import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.CallElementWriter
 
 object CallElementToGraphNode {
-  def convert(a: CallNodeMakerInputs)
-             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-              fileEvaluator: FileEvaluator[ExpressionElement],
-              typeEvaluator: TypeEvaluator[ExpressionElement],
-              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[GraphNode]] = {
+  def convert(a: CallNodeMakerInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[Set[GraphNode]] = {
     val callNodeBuilder = new CallNode.CallNodeBuilder()
 
     val callName = a.node.alias.getOrElse(a.node.callableReference.split("\\.").last)
@@ -41,35 +47,41 @@ object CallElementToGraphNode {
           val unsuppliedInputs = w.inputs.collect {
             case r: RequiredInputDefinition if r.localName.value.contains(".") => r.localName.value
           }
-          val unsuppliedInputsValidation: ErrorOr[Unit] = if (unsuppliedInputs.isEmpty) { ().validNel } else { s"To be called as a sub-workflow it must declare and pass-through the following values via workflow inputs: ${unsuppliedInputs.mkString(", ")}".invalidNel }
+          val unsuppliedInputsValidation: ErrorOr[Unit] = if (unsuppliedInputs.isEmpty) { ().validNel }
+          else {
+            s"To be called as a sub-workflow it must declare and pass-through the following values via workflow inputs: ${unsuppliedInputs
+                .mkString(", ")}".invalidNel
+          }
 
           val unspecifiedOutputs = w.graph.outputNodes.map(_.localName).filter(_.contains("."))
-          val unspecifiedOutputsValidation: ErrorOr[Unit] = if (unspecifiedOutputs.isEmpty) { ().validNel } else { s"To be called as a sub-workflow it must specify all outputs using an output section. This workflow may wish to declare outputs for: ${unspecifiedOutputs.mkString(", ")}".invalidNel }
+          val unspecifiedOutputsValidation: ErrorOr[Unit] = if (unspecifiedOutputs.isEmpty) { ().validNel }
+          else {
+            s"To be called as a sub-workflow it must specify all outputs using an output section. This workflow may wish to declare outputs for: ${unspecifiedOutputs
+                .mkString(", ")}".invalidNel
+          }
 
-          (unsuppliedInputsValidation, unspecifiedOutputsValidation) mapN { (_,_) => w }
+          (unsuppliedInputsValidation, unspecifiedOutputsValidation) mapN { (_, _) => w }
 
         case Some(c: Callable) => c.validNel
         case None => s"Cannot resolve a callable with name ${a.node.callableReference}".invalidNel
       }
 
-    def supplyableInput(definition: Callable.InputDefinition): Boolean = {
-        !definition.isInstanceOf[FixedInputDefinitionWithDefault] &&
-          (!definition.name.contains(".") || a.allowNestedInputs)
-    }
+    def supplyableInput(definition: Callable.InputDefinition): Boolean =
+      !definition.isInstanceOf[FixedInputDefinitionWithDefault] &&
+        (!definition.name.contains(".") || a.allowNestedInputs)
 
-    def validInput(name: String, definition: Callable.InputDefinition): Boolean = {
+    def validInput(name: String, definition: Callable.InputDefinition): Boolean =
       definition.name == name && supplyableInput(definition)
-    }
 
     /*
-      * Each input definition KV pair becomes an entry in map.
-      *
-      * i.e.
-      * call foo {
-      *   input: key = value
-      *
-      * @return ErrorOr of LocalName(key) mapped to ExpressionNode(value).
-      */
+     * Each input definition KV pair becomes an entry in map.
+     *
+     * i.e.
+     * call foo {
+     *   input: key = value
+     *
+     * @return ErrorOr of LocalName(key) mapped to ExpressionNode(value).
+     */
     def expressionNodeMappings(callable: Callable): ErrorOr[Map[LocalName, AnonymousExpressionNode]] = {
 
       def hasDeclaration(callable: Callable, name: String): Boolean = callable match {
@@ -95,8 +107,14 @@ object CallElementToGraphNode {
                     case _ => i.womType
                   }
 
-                  (WorkflowGraphElementToGraphNode.validateAssignmentType(wdlomWomExpression, requiredInputType) flatMap { _ =>
-                    AnonymousExpressionNode.fromInputMapping[AnonymousExpressionNode](identifier, wdlomWomExpression, a.linkablePorts, constructor) map {
+                  (WorkflowGraphElementToGraphNode.validateAssignmentType(wdlomWomExpression,
+                                                                          requiredInputType
+                  ) flatMap { _ =>
+                    AnonymousExpressionNode.fromInputMapping[AnonymousExpressionNode](identifier,
+                                                                                      wdlomWomExpression,
+                                                                                      a.linkablePorts,
+                                                                                      constructor
+                    ) map {
                       LocalName(name) -> _
                     }
                   }).contextualizeErrors(s"supply input $name = ${expression.toWdlV1}")
@@ -116,26 +134,29 @@ object CallElementToGraphNode {
     }
 
     /*
-      * Fold over the input definitions and
-      * 1) assign each input definition its InputDefinitionPointer
-      * 2) if necessary, create a graph input node and assign its output port to the input definition
-      *
-      * @return InputDefinitionFold accumulates the input definition mappings, the create graph input nodes, and the expression nodes.
+     * Fold over the input definitions and
+     * 1) assign each input definition its InputDefinitionPointer
+     * 2) if necessary, create a graph input node and assign its output port to the input definition
+     *
+     * @return InputDefinitionFold accumulates the input definition mappings, the create graph input nodes, and the expression nodes.
      */
-    def foldInputDefinitions(expressionNodes: Map[LocalName, ExpressionNode], callable: Callable): InputDefinitionFold = {
+    def foldInputDefinitions(expressionNodes: Map[LocalName, ExpressionNode],
+                             callable: Callable
+    ): InputDefinitionFold = {
       // Updates the fold with a new graph input node. Happens when an optional or required undefined input without an
       // expression node mapping is found
-      def withGraphInputNode(inputDefinition: InputDefinition, graphInputNode: ExternalGraphInputNode) = {
+      def withGraphInputNode(inputDefinition: InputDefinition, graphInputNode: ExternalGraphInputNode) =
         InputDefinitionFold(
-          mappings = List(inputDefinition -> Coproduct[InputDefinitionPointer](graphInputNode.singleOutputPort: OutputPort)),
+          mappings =
+            List(inputDefinition -> Coproduct[InputDefinitionPointer](graphInputNode.singleOutputPort: OutputPort)),
           callInputPorts = Set(callNodeBuilder.makeInputPort(inputDefinition, graphInputNode.singleOutputPort)),
           newGraphInputNodes = Set(graphInputNode)
         )
-      }
 
       callable.inputs foldMap {
         // If there is an input mapping for this input definition, use that
-        case inputDefinition if expressionNodes.contains(inputDefinition.localName) && supplyableInput(inputDefinition) =>
+        case inputDefinition
+            if expressionNodes.contains(inputDefinition.localName) && supplyableInput(inputDefinition) =>
           val expressionNode = expressionNodes(inputDefinition.localName)
           InputDefinitionFold(
             mappings = List(inputDefinition -> expressionNode.inputDefinitionPointer),
@@ -144,26 +165,30 @@ object CallElementToGraphNode {
           )
 
         // No input mapping, add an optional input using the default expression
-        case withDefault@OverridableInputDefinitionWithDefault(n, womType, expression, _, _) =>
+        case withDefault @ OverridableInputDefinitionWithDefault(n, womType, expression, _, _) =>
           val identifier = WomIdentifier(
             localName = s"$callName.${n.value}",
             fullyQualifiedName = s"${a.workflowName}.$callName.${n.value}"
           )
           if (supplyableInput(withDefault)) {
-            withGraphInputNode(withDefault, OptionalGraphInputNodeWithDefault(identifier, womType, expression, identifier.fullyQualifiedName.value))
+            withGraphInputNode(
+              withDefault,
+              OptionalGraphInputNodeWithDefault(identifier, womType, expression, identifier.fullyQualifiedName.value)
+            )
           } else {
             // We can't supply this from outside so hard code in the default:
             InputDefinitionFold(mappings = List(withDefault -> Coproduct[InputDefinitionPointer](expression)))
           }
 
         // Not an input, use the default expression:
-        case fixedExpression @ FixedInputDefinitionWithDefault(_,_,expression,_, _) => InputDefinitionFold(
-          mappings = List(fixedExpression -> Coproduct[InputDefinitionPointer](expression))
-        )
+        case fixedExpression @ FixedInputDefinitionWithDefault(_, _, expression, _, _) =>
+          InputDefinitionFold(
+            mappings = List(fixedExpression -> Coproduct[InputDefinitionPointer](expression))
+          )
 
         // No input mapping, required and we don't have a default value, create a new RequiredGraphInputNode
         // so that it can be satisfied via workflow inputs
-        case required@RequiredInputDefinition(n, womType, _, _) if supplyableInput(required) =>
+        case required @ RequiredInputDefinition(n, womType, _, _) if supplyableInput(required) =>
           val identifier = WomIdentifier(
             localName = s"$callName.${n.value}",
             fullyQualifiedName = s"${a.workflowName}.$callName.${n.value}"
@@ -173,13 +198,15 @@ object CallElementToGraphNode {
 
         // No input mapping, no default value but optional, create a OptionalGraphInputNode
         // so that it can be satisfied via workflow inputs
-        case optional@OptionalInputDefinition(n, womType, _, _) =>
+        case optional @ OptionalInputDefinition(n, womType, _, _) =>
           val identifier = WomIdentifier(
             localName = s"$callName.${n.value}",
             fullyQualifiedName = s"${a.workflowName}.$callName.${n.value}"
           )
           if (supplyableInput(optional)) {
-            withGraphInputNode(optional, OptionalGraphInputNode(identifier, womType, identifier.fullyQualifiedName.value))
+            withGraphInputNode(optional,
+                               OptionalGraphInputNode(identifier, womType, identifier.fullyQualifiedName.value)
+            )
           } else {
             // Leave it unsupplied:
             InputDefinitionFold()
@@ -188,7 +215,9 @@ object CallElementToGraphNode {
       }
     }
 
-    def updateTaskCallNodeInputs(callNodeAndNewNodes: CallNodeAndNewNodes, mappings: Map[LocalName, AnonymousExpressionNode]): Unit = {
+    def updateTaskCallNodeInputs(callNodeAndNewNodes: CallNodeAndNewNodes,
+                                 mappings: Map[LocalName, AnonymousExpressionNode]
+    ): Unit = {
       for {
         taskCallNode <- List(callNodeAndNewNodes.node) collect { case c: CommandCallNode => c }
         taskCallInputExpression <- mappings.values.toList collect { case t: TaskCallInputExpressionNode => t }
@@ -197,20 +226,27 @@ object CallElementToGraphNode {
       ()
     }
 
-    def findUpstreamCall(callName: String): ErrorOr[GraphNode] = {
-      a.upstreamCalls.get(callName).toErrorOr(s"No such upstream call '$callName' found in available set: [${a.upstreamCalls.keySet.mkString(", ")}]")
-    }
+    def findUpstreamCall(callName: String): ErrorOr[GraphNode] =
+      a.upstreamCalls
+        .get(callName)
+        .toErrorOr(
+          s"No such upstream call '$callName' found in available set: [${a.upstreamCalls.keySet.mkString(", ")}]"
+        )
 
-    def findUpstreamCalls(callNames: List[String]): ErrorOr[Set[GraphNode]] = {
+    def findUpstreamCalls(callNames: List[String]): ErrorOr[Set[GraphNode]] =
       callNames.traverse(findUpstreamCall _).map(_.toSet)
-    }
 
     val result = for {
       callable <- callableValidation
       mappings <- expressionNodeMappings(callable)
       identifier = WomIdentifier(localName = callName, fullyQualifiedName = a.workflowName + "." + callName)
       upstream <- findUpstreamCalls(a.node.afters.toList)
-      result = callNodeBuilder.build(identifier, callable, foldInputDefinitions(mappings, callable), upstream, a.node.sourceLocation)
+      result = callNodeBuilder.build(identifier,
+                                     callable,
+                                     foldInputDefinitions(mappings, callable),
+                                     upstream,
+                                     a.node.sourceLocation
+      )
       _ = updateTaskCallNodeInputs(result, mappings)
     } yield result.nodes
 
@@ -226,4 +262,5 @@ case class CallNodeMakerInputs(node: CallElement,
                                workflowName: String,
                                insideAnotherScatter: Boolean,
                                allowNestedInputs: Boolean,
-                               callables: Map[String, Callable])
+                               callables: Map[String, Callable]
+)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala
index 53742b6be80..7c53c5c0cd6 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala
@@ -23,28 +23,42 @@ import wom.graph.expression.{AnonymousExpressionNode, PlainAnonymousExpressionNo
 import wom.types.{WomAnyType, WomBooleanType, WomType}
 
 object IfElementToGraphNode {
-  def convert(a: ConditionalNodeMakerInputs)
-             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-              fileEvaluator: FileEvaluator[ExpressionElement],
-              typeEvaluator: TypeEvaluator[ExpressionElement],
-              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[GraphNode]] = {
+  def convert(a: ConditionalNodeMakerInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[Set[GraphNode]] = {
     val conditionExpression = a.node.conditionExpression
     val graphElements = a.node.graphElements
 
-    val conditionWomExpressionV: ErrorOr[WdlomWomExpression] = WdlomWomExpression.make(conditionExpression, a.linkableValues)
-    val conditionExpressionNodeValidation: ErrorOr[AnonymousExpressionNode] = conditionWomExpressionV flatMap { conditionWomExpression =>
-      AnonymousExpressionNode.fromInputMapping(WomIdentifier("if_condition"), conditionWomExpression, a.linkablePorts, PlainAnonymousExpressionNode.apply) }
+    val conditionWomExpressionV: ErrorOr[WdlomWomExpression] =
+      WdlomWomExpression.make(conditionExpression, a.linkableValues)
+    val conditionExpressionNodeValidation: ErrorOr[AnonymousExpressionNode] = conditionWomExpressionV flatMap {
+      conditionWomExpression =>
+        AnonymousExpressionNode.fromInputMapping(WomIdentifier("if_condition"),
+                                                 conditionWomExpression,
+                                                 a.linkablePorts,
+                                                 PlainAnonymousExpressionNode.apply
+        )
+    }
 
     val conditionVariableTypeValidation: ErrorOr[Unit] = conditionExpression.evaluateType(a.linkableValues) flatMap {
       case WomBooleanType | WomAnyType => ().validNel
       case other => s"Invalid type for condition variable: ${other.stableName}".invalidNel
     }
 
-    final case class RequiredOuterPorts(valueGeneratorPorts: Map[String, OutputPort], completionPorts: Map[String, CallNode])
+    final case class RequiredOuterPorts(valueGeneratorPorts: Map[String, OutputPort],
+                                        completionPorts: Map[String, CallNode]
+    )
 
     val foundOuterGeneratorsValidation: ErrorOr[RequiredOuterPorts] = {
-      val required: ErrorOr[Set[UnlinkedConsumedValueHook]] = graphElements.toList.traverse { element => element.graphElementConsumedValueHooks(a.availableTypeAliases, a.callables) }.map(_.toSet.flatten)
-      val generated: ErrorOr[Set[GeneratedValueHandle]] = graphElements.toList.traverse { element => element.generatedValueHandles(a.availableTypeAliases, a.callables) }.map(_.toSet.flatten)
+      val required: ErrorOr[Set[UnlinkedConsumedValueHook]] = graphElements.toList
+        .traverse(element => element.graphElementConsumedValueHooks(a.availableTypeAliases, a.callables))
+        .map(_.toSet.flatten)
+      val generated: ErrorOr[Set[GeneratedValueHandle]] = graphElements.toList
+        .traverse(element => element.generatedValueHandles(a.availableTypeAliases, a.callables))
+        .map(_.toSet.flatten)
 
       def makeLink(hook: UnlinkedConsumedValueHook): (String, OutputPort) = {
         val name = a.linkableValues(hook).linkableName
@@ -54,37 +68,49 @@ object IfElementToGraphNode {
 
       (required, generated) mapN { (r, g) =>
         val requiredOuterValues = r collect {
-          case hook@UnlinkedIdentifierHook(id) if !g.exists(_.linkableName == id) => makeLink(hook)
-          case hook@UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first, second) if !g.exists(_.linkableName == first) && !g.exists(_.linkableName == s"$first.$second") => makeLink(hook)
+          case hook @ UnlinkedIdentifierHook(id) if !g.exists(_.linkableName == id) => makeLink(hook)
+          case hook @ UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first, second)
+              if !g.exists(_.linkableName == first) && !g.exists(_.linkableName == s"$first.$second") =>
+            makeLink(hook)
         }
         val requiredCompletionPorts = r collect {
           case UnlinkedAfterCallHook(upstreamCallName) if !g.exists {
-            case GeneratedCallFinishedHandle(`upstreamCallName`) => true
-            case _ => false
-          } => upstreamCallName -> a.upstreamCalls.values.find(_.localName == upstreamCallName).get
+                case GeneratedCallFinishedHandle(`upstreamCallName`) => true
+                case _ => false
+              } =>
+            upstreamCallName -> a.upstreamCalls.values.find(_.localName == upstreamCallName).get
         }
 
         RequiredOuterPorts(requiredOuterValues.toMap, requiredCompletionPorts.toMap)
       }
     }
 
-    (conditionExpressionNodeValidation, conditionVariableTypeValidation, foundOuterGeneratorsValidation) flatMapN { (expressionNode, _, foundOuterGenerators) =>
-      val ogins: Set[GraphNode] = (foundOuterGenerators.valueGeneratorPorts.toList map { case (name: String, port: OutputPort) =>
-        OuterGraphInputNode(WomIdentifier(name), port, preserveScatterIndex = true)
-      }).toSet
+    (conditionExpressionNodeValidation, conditionVariableTypeValidation, foundOuterGeneratorsValidation) flatMapN {
+      (expressionNode, _, foundOuterGenerators) =>
+        val ogins: Set[GraphNode] =
+          (foundOuterGenerators.valueGeneratorPorts.toList map { case (name: String, port: OutputPort) =>
+            OuterGraphInputNode(WomIdentifier(name), port, preserveScatterIndex = true)
+          }).toSet
 
-      val graphLikeConvertInputs = GraphLikeConvertInputs(graphElements.toSet, ogins, foundOuterGenerators.completionPorts, a.availableTypeAliases, a.workflowName,
-                                                          insideAScatter = a.insideAnotherScatter,
-                                                          convertNestedScatterToSubworkflow = a.convertNestedScatterToSubworkflow,
-                                                          allowNestedInputs = a.allowNestedInputs,
-                                                          a.callables)
-      val innerGraph: ErrorOr[Graph] = WorkflowDefinitionElementToWomWorkflowDefinition.convertGraphElements(graphLikeConvertInputs)
+        val graphLikeConvertInputs = GraphLikeConvertInputs(
+          graphElements.toSet,
+          ogins,
+          foundOuterGenerators.completionPorts,
+          a.availableTypeAliases,
+          a.workflowName,
+          insideAScatter = a.insideAnotherScatter,
+          convertNestedScatterToSubworkflow = a.convertNestedScatterToSubworkflow,
+          allowNestedInputs = a.allowNestedInputs,
+          a.callables
+        )
+        val innerGraph: ErrorOr[Graph] =
+          WorkflowDefinitionElementToWomWorkflowDefinition.convertGraphElements(graphLikeConvertInputs)
 
-      innerGraph map { ig =>
-        val withOutputs = WomGraphMakerTools.addDefaultOutputs(ig)
-        val generatedAndNew = ConditionalNode.wireInConditional(withOutputs, expressionNode)
-        generatedAndNew.nodes
-      }
+        innerGraph map { ig =>
+          val withOutputs = WomGraphMakerTools.addDefaultOutputs(ig)
+          val generatedAndNew = ConditionalNode.wireInConditional(withOutputs, expressionNode)
+          generatedAndNew.nodes
+        }
     }
   }
 }
@@ -96,6 +122,7 @@ final case class ConditionalNodeMakerInputs(node: IfElement,
                                             availableTypeAliases: Map[String, WomType],
                                             workflowName: String,
                                             insideAnotherScatter: Boolean,
-                                            convertNestedScatterToSubworkflow : Boolean,
+                                            convertNestedScatterToSubworkflow: Boolean,
                                             allowNestedInputs: Boolean,
-                                            callables: Map[String, Callable])
+                                            callables: Map[String, Callable]
+)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/InputDeclarationElementToGraphNode.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/InputDeclarationElementToGraphNode.scala
index 605131027ba..d70bc22126f 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/InputDeclarationElementToGraphNode.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/InputDeclarationElementToGraphNode.scala
@@ -18,15 +18,17 @@ import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
 import wdl.transforms.base.wdlom2wdl.WdlWriterImpl._
 
 object InputDeclarationElementToGraphNode {
-  def convert(a: GraphInputNodeMakerInputs)
-             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-              fileEvaluator: FileEvaluator[ExpressionElement],
-              typeEvaluator: TypeEvaluator[ExpressionElement],
-              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[GraphNode]] = a.node match {
+  def convert(a: GraphInputNodeMakerInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[Set[GraphNode]] = a.node match {
     case InputDeclarationElement(typeElement, name, None) =>
       val nameInInputSet = s"${a.workflowName}.$name"
       typeElement.determineWomType(a.availableTypeAliases) map {
-        case opt: WomOptionalType => Set(OptionalGraphInputNode(WomIdentifier(name), opt.flatOptionalType, nameInInputSet))
+        case opt: WomOptionalType =>
+          Set(OptionalGraphInputNode(WomIdentifier(name), opt.flatOptionalType, nameInInputSet))
         case womType => Set(RequiredGraphInputNode(WomIdentifier(name), womType, nameInInputSet))
       }
     case InputDeclarationElement(typeElement, name, Some(expr)) =>
@@ -45,7 +47,8 @@ object InputDeclarationElementToGraphNode {
 }
 
 final case class GraphInputNodeMakerInputs(node: InputDeclarationElement,
-                                            linkableValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
-                                            linkablePorts: Map[String, OutputPort],
-                                            availableTypeAliases: Map[String, WomType],
-                                            workflowName: String)
+                                           linkableValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                                           linkablePorts: Map[String, OutputPort],
+                                           availableTypeAliases: Map[String, WomType],
+                                           workflowName: String
+)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala
index 621461559e5..a1a3d5c4d76 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala
@@ -17,7 +17,12 @@ import wdl.model.draft3.elements._
 import wdl.model.draft3.graph._
 import wdl.model.draft3.graph.expression.{FileEvaluator, TypeEvaluator, ValueEvaluator}
 import wdl.shared.transforms.wdlom2wom.WomGraphMakerTools
-import wom.callable.Callable.{InputDefinition, OverridableInputDefinitionWithDefault, OptionalInputDefinition, RequiredInputDefinition}
+import wom.callable.Callable.{
+  InputDefinition,
+  OptionalInputDefinition,
+  OverridableInputDefinitionWithDefault,
+  RequiredInputDefinition
+}
 import wom.callable.{Callable, WorkflowDefinition}
 import wom.graph.CallNode.{CallNodeBuilder, InputDefinitionFold, InputDefinitionPointer}
 import wom.graph.GraphNode.GraphNodeSetter
@@ -27,11 +32,12 @@ import wom.graph.expression.{AnonymousExpressionNode, PlainAnonymousExpressionNo
 import wom.types.{WomAnyType, WomArrayType, WomType}
 
 object ScatterElementToGraphNode {
-  def convert(a: ScatterNodeMakerInputs)
-             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-              fileEvaluator: FileEvaluator[ExpressionElement],
-              typeEvaluator: TypeEvaluator[ExpressionElement],
-              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[GraphNode]] =
+  def convert(a: ScatterNodeMakerInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[Set[GraphNode]] =
     if (a.convertNestedScatterToSubworkflow) {
       // Create a sub-workflow from the inner scatter.
       if (a.insideAnotherScatter) {
@@ -44,18 +50,25 @@ object ScatterElementToGraphNode {
       convertOuterScatter(a)
     }
 
-  def convertOuterScatter(a: ScatterNodeMakerInputs)
-                         (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-                          fileEvaluator: FileEvaluator[ExpressionElement],
-                          typeEvaluator: TypeEvaluator[ExpressionElement],
-                          valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[GraphNode]] = {
+  def convertOuterScatter(a: ScatterNodeMakerInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[Set[GraphNode]] = {
     val scatterExpression = a.node.scatterExpression
     val scatterVariableName = a.node.scatterVariableName
     val graphElements = a.node.graphElements
 
-    val scatterWomExpressionV: ErrorOr[WdlomWomExpression] = WdlomWomExpression.make(scatterExpression, a.linkableValues)
-    val scatterExpressionNodeValidation: ErrorOr[AnonymousExpressionNode] = scatterWomExpressionV flatMap { scatterWomExpression =>
-      AnonymousExpressionNode.fromInputMapping(WomIdentifier(scatterVariableName), scatterWomExpression, a.linkablePorts, PlainAnonymousExpressionNode.apply)
+    val scatterWomExpressionV: ErrorOr[WdlomWomExpression] =
+      WdlomWomExpression.make(scatterExpression, a.linkableValues)
+    val scatterExpressionNodeValidation: ErrorOr[AnonymousExpressionNode] = scatterWomExpressionV flatMap {
+      scatterWomExpression =>
+        AnonymousExpressionNode.fromInputMapping(WomIdentifier(scatterVariableName),
+                                                 scatterWomExpression,
+                                                 a.linkablePorts,
+                                                 PlainAnonymousExpressionNode.apply
+        )
     }
 
     val scatterVariableTypeValidation: ErrorOr[WomType] = scatterExpression.evaluateType(a.linkableValues) flatMap {
@@ -64,11 +77,17 @@ object ScatterElementToGraphNode {
       case other => s"Invalid type for scatter variable '$scatterVariableName': ${other.stableName}".invalidNel
     }
 
-    final case class RequiredOuterPorts(valueGeneratorPorts: Map[String, OutputPort], completionPorts: Map[String, CallNode])
+    final case class RequiredOuterPorts(valueGeneratorPorts: Map[String, OutputPort],
+                                        completionPorts: Map[String, CallNode]
+    )
 
     val foundOuterGeneratorsValidation: ErrorOr[RequiredOuterPorts] = {
-      val required: ErrorOr[Set[UnlinkedConsumedValueHook]] = graphElements.toList.traverse { element => element.graphElementConsumedValueHooks(a.availableTypeAliases, a.callables) }.map(_.toSet.flatten)
-      val generated: ErrorOr[Set[GeneratedValueHandle]] = graphElements.toList.traverse { element => element.generatedValueHandles(a.availableTypeAliases, a.callables) }.map(_.toSet.flatten)
+      val required: ErrorOr[Set[UnlinkedConsumedValueHook]] = graphElements.toList
+        .traverse(element => element.graphElementConsumedValueHooks(a.availableTypeAliases, a.callables))
+        .map(_.toSet.flatten)
+      val generated: ErrorOr[Set[GeneratedValueHandle]] = graphElements.toList
+        .traverse(element => element.generatedValueHandles(a.availableTypeAliases, a.callables))
+        .map(_.toSet.flatten)
 
       def makeLink(hook: UnlinkedConsumedValueHook): (String, OutputPort) = {
         val name = a.linkableValues(hook).linkableName
@@ -78,63 +97,88 @@ object ScatterElementToGraphNode {
 
       (required, generated) mapN { (r, g) =>
         val requiredOuterValues = r collect {
-          case hook@UnlinkedIdentifierHook(id) if id != scatterVariableName && !g.exists(_.linkableName == id) =>
+          case hook @ UnlinkedIdentifierHook(id) if id != scatterVariableName && !g.exists(_.linkableName == id) =>
             makeLink(hook)
-          case hook@UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first, second) if first != scatterVariableName && !g.exists(_.linkableName == first) && !g.exists(_.linkableName == s"$first.$second") =>
+          case hook @ UnlinkedCallOutputOrIdentifierAndMemberAccessHook(first, second)
+              if first != scatterVariableName && !g
+                .exists(_.linkableName == first) && !g.exists(_.linkableName == s"$first.$second") =>
             makeLink(hook)
         }
         val requiredCompletionPorts = r collect {
           case UnlinkedAfterCallHook(upstreamCallName) if !g.exists {
-            case GeneratedCallFinishedHandle(`upstreamCallName`) => true
-            case _ => false
-          } => upstreamCallName -> a.upstreamCalls.values.find(_.localName == upstreamCallName).get
+                case GeneratedCallFinishedHandle(`upstreamCallName`) => true
+                case _ => false
+              } =>
+            upstreamCallName -> a.upstreamCalls.values.find(_.localName == upstreamCallName).get
         }
 
         RequiredOuterPorts(requiredOuterValues.toMap, requiredCompletionPorts.toMap)
       }
     }
 
-    (scatterExpressionNodeValidation, scatterVariableTypeValidation, foundOuterGeneratorsValidation) flatMapN { (expressionNode, scatterVariableType, foundOuterGenerators) =>
-      val womInnerGraphScatterVariableInput = ScatterVariableNode(WomIdentifier(scatterVariableName), expressionNode, scatterVariableType)
-      val ogins: Set[GraphNode] = (foundOuterGenerators.valueGeneratorPorts.toList map { case (name: String, port: OutputPort) =>
-        OuterGraphInputNode(WomIdentifier(name), port, preserveScatterIndex = false)
-      }).toSet
-
-      val graphLikeConvertInputs = GraphLikeConvertInputs(graphElements.toSet, ogins ++ Set(womInnerGraphScatterVariableInput), foundOuterGenerators.completionPorts, a.availableTypeAliases, a.workflowName,
-                                                          insideAScatter = true,
-                                                          convertNestedScatterToSubworkflow = a.convertNestedScatterToSubworkflow,
-                                                          allowNestedInputs = a.allowNestedInputs,
-                                                          a.callables)
-      val innerGraph: ErrorOr[Graph] = WorkflowDefinitionElementToWomWorkflowDefinition.convertGraphElements(graphLikeConvertInputs)
-
-      innerGraph map { ig =>
-        val withOutputs = WomGraphMakerTools.addDefaultOutputs(ig)
-        val generatedAndNew = ScatterNode.scatterOverGraph(withOutputs, womInnerGraphScatterVariableInput)
-        generatedAndNew.nodes
-      }
+    (scatterExpressionNodeValidation, scatterVariableTypeValidation, foundOuterGeneratorsValidation) flatMapN {
+      (expressionNode, scatterVariableType, foundOuterGenerators) =>
+        val womInnerGraphScatterVariableInput =
+          ScatterVariableNode(WomIdentifier(scatterVariableName), expressionNode, scatterVariableType)
+        val ogins: Set[GraphNode] =
+          (foundOuterGenerators.valueGeneratorPorts.toList map { case (name: String, port: OutputPort) =>
+            OuterGraphInputNode(WomIdentifier(name), port, preserveScatterIndex = false)
+          }).toSet
+
+        val graphLikeConvertInputs = GraphLikeConvertInputs(
+          graphElements.toSet,
+          ogins ++ Set(womInnerGraphScatterVariableInput),
+          foundOuterGenerators.completionPorts,
+          a.availableTypeAliases,
+          a.workflowName,
+          insideAScatter = true,
+          convertNestedScatterToSubworkflow = a.convertNestedScatterToSubworkflow,
+          allowNestedInputs = a.allowNestedInputs,
+          a.callables
+        )
+        val innerGraph: ErrorOr[Graph] =
+          WorkflowDefinitionElementToWomWorkflowDefinition.convertGraphElements(graphLikeConvertInputs)
+
+        innerGraph map { ig =>
+          val withOutputs = WomGraphMakerTools.addDefaultOutputs(ig)
+          val generatedAndNew = ScatterNode.scatterOverGraph(withOutputs, womInnerGraphScatterVariableInput)
+          generatedAndNew.nodes
+        }
     }
   }
 
-  def convertInnerScatter(a: ScatterNodeMakerInputs)
-                         (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-                          fileEvaluator: FileEvaluator[ExpressionElement],
-                          typeEvaluator: TypeEvaluator[ExpressionElement],
-                          valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[GraphNode]] = {
+  def convertInnerScatter(a: ScatterNodeMakerInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[Set[GraphNode]] = {
 
-    val requiredOuterValuesValidation: ErrorOr[Set[UnlinkedConsumedValueHook]] = a.node.graphElementConsumedValueHooks(a.availableTypeAliases, a.callables)
+    val requiredOuterValuesValidation: ErrorOr[Set[UnlinkedConsumedValueHook]] =
+      a.node.graphElementConsumedValueHooks(a.availableTypeAliases, a.callables)
 
-    val subWorkflowInputsValidation: ErrorOr[Set[GraphNode]] = requiredOuterValuesValidation map { requiredOuterValues =>
-      val requiredLinkableNames: Set[(String, WomType)] = requiredOuterValues map { hook => (a.linkableValues(hook).linkableName, a.linkableValues(hook).womType) }
-      requiredLinkableNames map { case (name, womType) => RequiredGraphInputNode(WomIdentifier(name), womType, name) }
+    val subWorkflowInputsValidation: ErrorOr[Set[GraphNode]] = requiredOuterValuesValidation map {
+      requiredOuterValues =>
+        val requiredLinkableNames: Set[(String, WomType)] = requiredOuterValues map { hook =>
+          (a.linkableValues(hook).linkableName, a.linkableValues(hook).womType)
+        }
+        requiredLinkableNames map { case (name, womType) => RequiredGraphInputNode(WomIdentifier(name), womType, name) }
     }
 
     val subWorkflowGraphValidation: ErrorOr[Graph] = subWorkflowInputsValidation flatMap { subWorkflowInputs =>
-      val graphLikeConvertInputs = GraphLikeConvertInputs(Set(a.node), subWorkflowInputs, Map.empty, a.availableTypeAliases, a.workflowName,
-                                                          insideAScatter = false,
-                                                          convertNestedScatterToSubworkflow = a.convertNestedScatterToSubworkflow,
-                                                          allowNestedInputs = a.allowNestedInputs,
-                                                          a.callables)
-      val subWorkflowGraph = WorkflowDefinitionElementToWomWorkflowDefinition.convertGraphElements(graphLikeConvertInputs)
+      val graphLikeConvertInputs = GraphLikeConvertInputs(
+        Set(a.node),
+        subWorkflowInputs,
+        Map.empty,
+        a.availableTypeAliases,
+        a.workflowName,
+        insideAScatter = false,
+        convertNestedScatterToSubworkflow = a.convertNestedScatterToSubworkflow,
+        allowNestedInputs = a.allowNestedInputs,
+        a.callables
+      )
+      val subWorkflowGraph =
+        WorkflowDefinitionElementToWomWorkflowDefinition.convertGraphElements(graphLikeConvertInputs)
       subWorkflowGraph map { WomGraphMakerTools.addDefaultOutputs(_) }
     }
 
@@ -152,26 +196,46 @@ object ScatterElementToGraphNode {
       val graphNodeSetter = new GraphNodeSetter[CallNode]
 
       val unsatisfiedInputs = subWorkflowDefinition.inputs filter { i => !a.linkablePorts.contains(i.name) }
-      def inputNodeIdentifier(input: InputDefinition) = WomIdentifier(localName = input.name, fullyQualifiedName = a.workflowName + "." + input.name)
+      def inputNodeIdentifier(input: InputDefinition) =
+        WomIdentifier(localName = input.name, fullyQualifiedName = a.workflowName + "." + input.name)
       val newInputNodes: Map[String, ExternalGraphInputNode] = (unsatisfiedInputs collect {
-        case i: RequiredInputDefinition => i.name -> RequiredGraphInputNode(inputNodeIdentifier(i), i.womType, a.workflowName + "." + i.name, Callable.InputDefinition.IdentityValueMapper)
-        case i: OptionalInputDefinition => i.name -> OptionalGraphInputNode(inputNodeIdentifier(i), i.womType, a.workflowName + "." + i.name, Callable.InputDefinition.IdentityValueMapper)
-        case i: OverridableInputDefinitionWithDefault => i.name -> OptionalGraphInputNodeWithDefault(inputNodeIdentifier(i), i.womType, i.default, a.workflowName + "." + i.name, Callable.InputDefinition.IdentityValueMapper)
+        case i: RequiredInputDefinition =>
+          i.name -> RequiredGraphInputNode(inputNodeIdentifier(i),
+                                           i.womType,
+                                           a.workflowName + "." + i.name,
+                                           Callable.InputDefinition.IdentityValueMapper
+          )
+        case i: OptionalInputDefinition =>
+          i.name -> OptionalGraphInputNode(inputNodeIdentifier(i),
+                                           i.womType,
+                                           a.workflowName + "." + i.name,
+                                           Callable.InputDefinition.IdentityValueMapper
+          )
+        case i: OverridableInputDefinitionWithDefault =>
+          i.name -> OptionalGraphInputNodeWithDefault(inputNodeIdentifier(i),
+                                                      i.womType,
+                                                      i.default,
+                                                      a.workflowName + "." + i.name,
+                                                      Callable.InputDefinition.IdentityValueMapper
+          )
       }).toMap
 
-      val mappingAndPorts: List[((InputDefinition, InputDefinitionPointer), InputPort)] = subWorkflowDefinition.inputs map { i =>
-        val port: OutputPort = a.linkablePorts.getOrElse(i.name, newInputNodes(i.name).singleOutputPort)
-        val pointer = Coproduct[InputDefinitionPointer](port)
-        (i -> pointer, ConnectedInputPort(i.name, i.womType, port, graphNodeSetter.get))
-      }
+      val mappingAndPorts: List[((InputDefinition, InputDefinitionPointer), InputPort)] =
+        subWorkflowDefinition.inputs map { i =>
+          val port: OutputPort = a.linkablePorts.getOrElse(i.name, newInputNodes(i.name).singleOutputPort)
+          val pointer = Coproduct[InputDefinitionPointer](port)
+          (i -> pointer, ConnectedInputPort(i.name, i.womType, port, graphNodeSetter.get))
+        }
       val mapping = mappingAndPorts.map(_._1)
       val inputPorts = mappingAndPorts.map(_._2).toSet
-      val result = callNodeBuilder.build(WomIdentifier(a.node.scatterName),
-                                         subWorkflowDefinition,
-                                         InputDefinitionFold(mappings = mapping, callInputPorts = inputPorts),
-                                         Set.empty,
-                                         a.node.sourceLocation,
-                                         (_, localName) => WomIdentifier(localName))
+      val result = callNodeBuilder.build(
+        WomIdentifier(a.node.scatterName),
+        subWorkflowDefinition,
+        InputDefinitionFold(mappings = mapping, callInputPorts = inputPorts),
+        Set.empty,
+        a.node.sourceLocation,
+        (_, localName) => WomIdentifier(localName)
+      )
       graphNodeSetter._graphNode = result.node
       result.copy(newInputs = result.newInputs ++ newInputNodes.values)
     }
@@ -191,4 +255,5 @@ final case class ScatterNodeMakerInputs(node: ScatterElement,
                                         insideAnotherScatter: Boolean,
                                         convertNestedScatterToSubworkflow: Boolean,
                                         allowNestedInputs: Boolean,
-                                        callables: Map[String, Callable])
+                                        callables: Map[String, Callable]
+)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/WorkflowGraphElementToGraphNode.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/WorkflowGraphElementToGraphNode.scala
index d72fd299dba..56ff7709605 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/WorkflowGraphElementToGraphNode.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/WorkflowGraphElementToGraphNode.scala
@@ -20,13 +20,15 @@ import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
 import wdl.transforms.base.wdlom2wdl.WdlWriterImpl._
 
 object WorkflowGraphElementToGraphNode {
-  def convert(a: GraphNodeMakerInputs)
-             (implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
-              fileEvaluator: FileEvaluator[ExpressionElement],
-              typeEvaluator: TypeEvaluator[ExpressionElement],
-              valueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[Set[GraphNode]] = a.node match {
+  def convert(a: GraphNodeMakerInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[Set[GraphNode]] = a.node match {
     case ie: InputDeclarationElement =>
-      val inputNodeMakerInputs = GraphInputNodeMakerInputs(ie, a.linkableValues, a.linkablePorts, a.availableTypeAliases, a.workflowName)
+      val inputNodeMakerInputs =
+        GraphInputNodeMakerInputs(ie, a.linkableValues, a.linkablePorts, a.availableTypeAliases, a.workflowName)
       InputDeclarationElementToGraphNode.convert(inputNodeMakerInputs)
 
     case DeclarationElement(typeElement, name, Some(expr)) =>
@@ -38,11 +40,19 @@ object WorkflowGraphElementToGraphNode {
 
         val graphNode: ErrorOr[Set[GraphNode]] = a.node match {
           case _: InputDeclarationElement =>
-            Set[GraphNode](OptionalGraphInputNodeWithDefault.apply(WomIdentifier(name), womType, womExpr, name)).validNel
+            Set[GraphNode](
+              OptionalGraphInputNodeWithDefault.apply(WomIdentifier(name), womType, womExpr, name)
+            ).validNel
           case _: IntermediateValueDeclarationElement =>
-            ExposedExpressionNode.fromInputMapping(WomIdentifier(name), womExpr, womType, a.linkablePorts) map { Set(_) }
+            ExposedExpressionNode.fromInputMapping(WomIdentifier(name), womExpr, womType, a.linkablePorts) map {
+              Set(_)
+            }
           case _: OutputDeclarationElement =>
-            ExpressionBasedGraphOutputNode.fromInputMapping(WomIdentifier(name, s"${a.workflowName}.$name"), womExpr, womType, a.linkablePorts) map {Set(_)}
+            ExpressionBasedGraphOutputNode.fromInputMapping(WomIdentifier(name, s"${a.workflowName}.$name"),
+                                                            womExpr,
+                                                            womType,
+                                                            a.linkablePorts
+            ) map { Set(_) }
         }
 
         (correctType, graphNode) mapN { (_, gn) => gn }
@@ -50,15 +60,46 @@ object WorkflowGraphElementToGraphNode {
       result.contextualizeErrors(s"process declaration '${typeElement.toWdlV1} $name = ${expr.toWdlV1}'")
 
     case se: ScatterElement =>
-      val scatterMakerInputs = ScatterNodeMakerInputs(se, a.upstreamCalls, a.linkableValues, a.linkablePorts, a.availableTypeAliases, a.workflowName, a.insideAScatter, a.convertNestedScatterToSubworkflow, a.allowNestedInputs, a.callables)
+      val scatterMakerInputs = ScatterNodeMakerInputs(
+        se,
+        a.upstreamCalls,
+        a.linkableValues,
+        a.linkablePorts,
+        a.availableTypeAliases,
+        a.workflowName,
+        a.insideAScatter,
+        a.convertNestedScatterToSubworkflow,
+        a.allowNestedInputs,
+        a.callables
+      )
       ScatterElementToGraphNode.convert(scatterMakerInputs)
 
     case ie: IfElement =>
-      val ifMakerInputs = ConditionalNodeMakerInputs(ie, a.upstreamCalls, a.linkableValues, a.linkablePorts, a.availableTypeAliases, a.workflowName, a.insideAScatter, a.convertNestedScatterToSubworkflow, a.allowNestedInputs, a.callables)
+      val ifMakerInputs = ConditionalNodeMakerInputs(
+        ie,
+        a.upstreamCalls,
+        a.linkableValues,
+        a.linkablePorts,
+        a.availableTypeAliases,
+        a.workflowName,
+        a.insideAScatter,
+        a.convertNestedScatterToSubworkflow,
+        a.allowNestedInputs,
+        a.callables
+      )
       IfElementToGraphNode.convert(ifMakerInputs)
 
     case ce: CallElement =>
-      val callNodeMakerInputs = CallNodeMakerInputs(ce, a.upstreamCalls, a.linkableValues, a.linkablePorts, a.availableTypeAliases, a.workflowName, a.insideAScatter, a.allowNestedInputs, a.callables)
+      val callNodeMakerInputs = CallNodeMakerInputs(ce,
+                                                    a.upstreamCalls,
+                                                    a.linkableValues,
+                                                    a.linkablePorts,
+                                                    a.availableTypeAliases,
+                                                    a.workflowName,
+                                                    a.insideAScatter,
+                                                    a.allowNestedInputs,
+                                                    a.callables
+      )
       CallElementToGraphNode.convert(callNodeMakerInputs)
   }
 
@@ -80,6 +121,7 @@ final case class GraphNodeMakerInputs(node: WorkflowGraphElement,
                                       availableTypeAliases: Map[String, WomType],
                                       workflowName: String,
                                       insideAScatter: Boolean,
-                                      convertNestedScatterToSubworkflow : Boolean,
+                                      convertNestedScatterToSubworkflow: Boolean,
                                       allowNestedInputs: Boolean,
-                                      callables: Map[String, Callable])
+                                      callables: Map[String, Callable]
+)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/renaming/GraphIdentifierLookupRenamer.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/renaming/GraphIdentifierLookupRenamer.scala
index 7324f320ec6..a1303c8aac4 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/renaming/GraphIdentifierLookupRenamer.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/renaming/GraphIdentifierLookupRenamer.scala
@@ -6,7 +6,8 @@ import wdl.model.draft3.elements.{ExpressionElement, WorkflowGraphElement}
 
 @typeclass
 trait GraphIdentifierLookupRenamer[A] {
-  def renameIdentifiers(a: A, renamingMap: Map[String, String])
-                       (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
-                        graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]): A
+  def renameIdentifiers(a: A, renamingMap: Map[String, String])(implicit
+    expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
+    graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]
+  ): A
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/renaming/package.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/renaming/package.scala
index 731a0996c52..9f2673763c1 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/renaming/package.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/renaming/package.scala
@@ -7,39 +7,36 @@ import wdl.transforms.base.wdlom2wom.expression.renaming.IdentifierLookupRenamer
 
 package object renaming {
 
-  implicit val workflowDefinitionIdentifierRenamer: GraphIdentifierLookupRenamer[WorkflowDefinitionElement] = new GraphIdentifierLookupRenamer[WorkflowDefinitionElement] {
-    override def renameIdentifiers(a: WorkflowDefinitionElement,
-                                   renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
-                                   graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]): WorkflowDefinitionElement = {
-      val newInputsSection = a.inputsSection map { inputSection =>
-        inputSection.copy(inputDeclarations = inputSection.inputDeclarations.map {
-          id =>
+  implicit val workflowDefinitionIdentifierRenamer: GraphIdentifierLookupRenamer[WorkflowDefinitionElement] =
+    new GraphIdentifierLookupRenamer[WorkflowDefinitionElement] {
+      override def renameIdentifiers(a: WorkflowDefinitionElement, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
+        graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]
+      ): WorkflowDefinitionElement = {
+        val newInputsSection = a.inputsSection map { inputSection =>
+          inputSection.copy(inputDeclarations = inputSection.inputDeclarations.map { id =>
             val renamingMapWithoutThisValue = renamingMap.filterNot(_._1 == id.name)
             id.copy(expression = id.expression.map(_.renameIdentifiers(renamingMapWithoutThisValue)))
-        })
-      }
+          })
+        }
 
-      val newGraphElements = a.graphElements map { ge => ge.renameIdentifiers(renamingMap) }
-
-      val newOutputsSection = a.outputsSection map { outputSection =>
-        outputSection.copy(outputs = outputSection.outputs.map {
-          od => od.copy(expression = od.expression.renameIdentifiers(renamingMap))
-        })
-      }
+        val newGraphElements = a.graphElements map { ge => ge.renameIdentifiers(renamingMap) }
 
+        val newOutputsSection = a.outputsSection map { outputSection =>
+          outputSection.copy(outputs = outputSection.outputs.map { od =>
+            od.copy(expression = od.expression.renameIdentifiers(renamingMap))
+          })
+        }
 
-      a.copy(inputsSection = newInputsSection,
-        graphElements = newGraphElements,
-        outputsSection = newOutputsSection)
+        a.copy(inputsSection = newInputsSection, graphElements = newGraphElements, outputsSection = newOutputsSection)
+      }
     }
-  }
 
   implicit val graphElementIdentifierRenamer = new GraphIdentifierLookupRenamer[WorkflowGraphElement] {
-    override def renameIdentifiers(a: WorkflowGraphElement,
-                                   renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
-                                   graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]): WorkflowGraphElement = a match {
+    override def renameIdentifiers(a: WorkflowGraphElement, renamingMap: Map[String, String])(implicit
+      expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
+      graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]
+    ): WorkflowGraphElement = a match {
       case e: ScatterElement => e.renameIdentifiers(renamingMap)
       case e: IfElement => e.renameIdentifiers(renamingMap)
       case e: CallElement => e.renameIdentifiers(renamingMap)
@@ -49,63 +46,74 @@ package object renaming {
     }
   }
 
-  implicit val scatterElementIdentifierRenamer: GraphIdentifierLookupRenamer[ScatterElement] = new GraphIdentifierLookupRenamer[ScatterElement] {
-    override def renameIdentifiers(a: ScatterElement, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
-                                   graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]): ScatterElement = {
-      a.copy(scatterExpression = a.scatterExpression.renameIdentifiers(renamingMap),
-        graphElements = a.graphElements.map(graphIdentifierLookupRenamer.renameIdentifiers(_, renamingMap))
-      )
+  implicit val scatterElementIdentifierRenamer: GraphIdentifierLookupRenamer[ScatterElement] =
+    new GraphIdentifierLookupRenamer[ScatterElement] {
+      override def renameIdentifiers(a: ScatterElement, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
+        graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]
+      ): ScatterElement =
+        a.copy(
+          scatterExpression = a.scatterExpression.renameIdentifiers(renamingMap),
+          graphElements = a.graphElements.map(graphIdentifierLookupRenamer.renameIdentifiers(_, renamingMap))
+        )
     }
-  }
 
-  implicit val ifElementIdentifierRenamer: GraphIdentifierLookupRenamer[IfElement] = new GraphIdentifierLookupRenamer[IfElement] {
-    override def renameIdentifiers(a: IfElement, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
-                                   graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]): IfElement = {
-      a.copy(
-        conditionExpression = a.conditionExpression.renameIdentifiers(renamingMap),
-        graphElements = a.graphElements.map(graphIdentifierLookupRenamer.renameIdentifiers(_, renamingMap))
-      )
+  implicit val ifElementIdentifierRenamer: GraphIdentifierLookupRenamer[IfElement] =
+    new GraphIdentifierLookupRenamer[IfElement] {
+      override def renameIdentifiers(a: IfElement, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
+        graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]
+      ): IfElement =
+        a.copy(
+          conditionExpression = a.conditionExpression.renameIdentifiers(renamingMap),
+          graphElements = a.graphElements.map(graphIdentifierLookupRenamer.renameIdentifiers(_, renamingMap))
+        )
     }
-  }
 
-  implicit val callElementIdentifierRenamer: GraphIdentifierLookupRenamer[CallElement] = new GraphIdentifierLookupRenamer[CallElement] {
-    override def renameIdentifiers(a: CallElement, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
-                                   graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]): CallElement = {
-      a.copy(body = a.body map { bodyElement =>
-        bodyElement.copy(inputs = bodyElement.inputs.map { callInput =>
-          callInput.copy(value = callInput.value.renameIdentifiers(renamingMap))
+  implicit val callElementIdentifierRenamer: GraphIdentifierLookupRenamer[CallElement] =
+    new GraphIdentifierLookupRenamer[CallElement] {
+      override def renameIdentifiers(a: CallElement, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
+        graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]
+      ): CallElement =
+        a.copy(body = a.body map { bodyElement =>
+          bodyElement.copy(inputs = bodyElement.inputs.map { callInput =>
+            callInput.copy(value = callInput.value.renameIdentifiers(renamingMap))
+          })
         })
-      })
     }
-  }
 
-  implicit val inputDeclarationIdentifierRenamer: GraphIdentifierLookupRenamer[InputDeclarationElement] = new GraphIdentifierLookupRenamer[InputDeclarationElement] {
-    override def renameIdentifiers(a: InputDeclarationElement, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
-                                   graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]): InputDeclarationElement = {
-      val renamingMapWithoutThisValue = renamingMap.filterNot(_._2 == a.name)
-      a.copy(expression = a.expression.map(_.renameIdentifiers(renamingMapWithoutThisValue)))
+  implicit val inputDeclarationIdentifierRenamer: GraphIdentifierLookupRenamer[InputDeclarationElement] =
+    new GraphIdentifierLookupRenamer[InputDeclarationElement] {
+      override def renameIdentifiers(a: InputDeclarationElement, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
+        graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]
+      ): InputDeclarationElement = {
+        val renamingMapWithoutThisValue = renamingMap.filterNot(_._2 == a.name)
+        a.copy(expression = a.expression.map(_.renameIdentifiers(renamingMapWithoutThisValue)))
+      }
     }
-  }
 
-  implicit val intermediateDeclarationIdentifierRenamer: GraphIdentifierLookupRenamer[IntermediateValueDeclarationElement] = new GraphIdentifierLookupRenamer[IntermediateValueDeclarationElement] {
-    override def renameIdentifiers(a: IntermediateValueDeclarationElement, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
-                                   graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]): IntermediateValueDeclarationElement = {
-      val renamingMapWithoutThisValue = renamingMap.filterNot(_._2 == a.name)
-      a.copy(expression = a.expression.renameIdentifiers(renamingMapWithoutThisValue))
+  implicit val intermediateDeclarationIdentifierRenamer
+    : GraphIdentifierLookupRenamer[IntermediateValueDeclarationElement] =
+    new GraphIdentifierLookupRenamer[IntermediateValueDeclarationElement] {
+      override def renameIdentifiers(a: IntermediateValueDeclarationElement, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
+        graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]
+      ): IntermediateValueDeclarationElement = {
+        val renamingMapWithoutThisValue = renamingMap.filterNot(_._2 == a.name)
+        a.copy(expression = a.expression.renameIdentifiers(renamingMapWithoutThisValue))
+      }
     }
-  }
 
-  implicit val outputDeclarationIdentifierRenamer: GraphIdentifierLookupRenamer[OutputDeclarationElement] = new GraphIdentifierLookupRenamer[OutputDeclarationElement] {
-    override def renameIdentifiers(a: OutputDeclarationElement, renamingMap: Map[String, String])
-                                  (implicit expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
-                                   graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]): OutputDeclarationElement = {
-      val renamingMapWithoutThisValue = renamingMap.filterNot(_._2 == a.name)
-      a.copy(expression = a.expression.renameIdentifiers(renamingMapWithoutThisValue))
+  implicit val outputDeclarationIdentifierRenamer: GraphIdentifierLookupRenamer[OutputDeclarationElement] =
+    new GraphIdentifierLookupRenamer[OutputDeclarationElement] {
+      override def renameIdentifiers(a: OutputDeclarationElement, renamingMap: Map[String, String])(implicit
+        expressionElementRenamer: IdentifierLookupRenamer[ExpressionElement],
+        graphIdentifierLookupRenamer: GraphIdentifierLookupRenamer[WorkflowGraphElement]
+      ): OutputDeclarationElement = {
+        val renamingMapWithoutThisValue = renamingMap.filterNot(_._2 == a.name)
+        a.copy(expression = a.expression.renameIdentifiers(renamingMapWithoutThisValue))
+      }
     }
-  }
 }
diff --git a/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/evaluation/values/EngineFunctions.scala b/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/evaluation/values/EngineFunctions.scala
index 301f394f45c..4d2b8fa346b 100644
--- a/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/evaluation/values/EngineFunctions.scala
+++ b/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/evaluation/values/EngineFunctions.scala
@@ -9,15 +9,29 @@ object EngineFunctions {
   def transpose(a: WomValue): Try[WomArray] = {
     case class ExpandedTwoDimensionalArray(innerType: WomType, value: Seq[Seq[WomValue]])
     def validateAndExpand(value: WomValue): Try[ExpandedTwoDimensionalArray] = value match {
-      case WomArray(WomArrayType(WomArrayType(innerType)), array: Seq[WomValue]) => expandWdlArray(array) map { ExpandedTwoDimensionalArray(innerType, _) }
-      case WomArray(WomArrayType(nonArrayType), _) => Failure(new IllegalArgumentException(s"Array must be two-dimensional to be transposed but given array of $nonArrayType"))
-      case otherValue => Failure(new IllegalArgumentException(s"Function 'transpose' must be given a two-dimensional array but instead got ${otherValue.typeName}"))
+      case WomArray(WomArrayType(WomArrayType(innerType)), array: Seq[WomValue]) =>
+        expandWdlArray(array) map { ExpandedTwoDimensionalArray(innerType, _) }
+      case WomArray(WomArrayType(nonArrayType), _) =>
+        Failure(
+          new IllegalArgumentException(
+            s"Array must be two-dimensional to be transposed but given array of $nonArrayType"
+          )
+        )
+      case otherValue =>
+        Failure(
+          new IllegalArgumentException(
+            s"Function 'transpose' must be given a two-dimensional array but instead got ${otherValue.typeName}"
+          )
+        )
     }
 
     def expandWdlArray(outerArray: Seq[WomValue]): Try[Seq[Seq[WomValue]]] = Try {
       outerArray map {
         case array: WomArray => array.value
-        case otherValue => throw new IllegalArgumentException(s"Function 'transpose' must be given a two-dimensional array but instead got WdlArray[${otherValue.typeName}]")
+        case otherValue =>
+          throw new IllegalArgumentException(
+            s"Function 'transpose' must be given a two-dimensional array but instead got WdlArray[${otherValue.typeName}]"
+          )
       }
     }
 
diff --git a/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/wdlom2wom/WdlSharedInputParsing.scala b/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/wdlom2wom/WdlSharedInputParsing.scala
index 396198b3c85..5bd7c31e44d 100644
--- a/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/wdlom2wom/WdlSharedInputParsing.scala
+++ b/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/wdlom2wom/WdlSharedInputParsing.scala
@@ -16,18 +16,23 @@ object WdlSharedInputParsing {
     import spray.json._
 
     Try(inputString.parseJson).toErrorOr.toEither flatMap {
-      case JsObject(fields) => fields.map({
-        case (key, jsValue) => key -> { womType: WomType => womType.coerceRawValue(jsValue).toErrorOr }
-      }).validNelCheck
-      case other => s"WDL input file must be a valid Json object. Found a ${other.getClass.getSimpleName}".invalidNelCheck[ParsedInputMap]
+      case JsObject(fields) =>
+        fields.map { case (key, jsValue) =>
+          key -> { womType: WomType => womType.coerceRawValue(jsValue).toErrorOr }
+        }.validNelCheck
+      case other =>
+        s"WDL input file must be a valid Json object. Found a ${other.getClass.getSimpleName}"
+          .invalidNelCheck[ParsedInputMap]
     }
   }
 
-  def buildWomExecutable(bundle: WomBundle, inputs: Option[WorkflowJson], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-
+  def buildWomExecutable(bundle: WomBundle,
+                         inputs: Option[WorkflowJson],
+                         ioFunctions: IoFunctionSet,
+                         strictValidation: Boolean
+  ): Checked[Executable] =
     for {
       ec <- bundle.toExecutableCallable
       executable <- Executable.withInputs(ec, inputCoercionFunction, inputs, ioFunctions, strictValidation)
     } yield executable
-  }
 }
diff --git a/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/wdlom2wom/WomGraphMakerTools.scala b/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/wdlom2wom/WomGraphMakerTools.scala
index c5f4c42e65e..6cb7b3642b5 100644
--- a/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/wdlom2wom/WomGraphMakerTools.scala
+++ b/wdl/transforms/shared/src/main/scala/wdl/shared/transforms/wdlom2wom/WomGraphMakerTools.scala
@@ -17,19 +17,19 @@ object WomGraphMakerTools {
     }
 
     Graph(g.nodes.union((g.nodes collect {
-      case node: CallNode => node.outputPorts.map(op => {
-        val identifier = makeIdentifier(WomIdentifier(op.identifier.localName.value))
-        PortBasedGraphOutputNode(identifier, op.womType, op)
-      })
-      case node: ExposedExpressionNode if forWorkflowOutputs.isEmpty => node.outputPorts.map(op => {
-        PortBasedGraphOutputNode(makeIdentifier(WomIdentifier(op.name)), op.womType, op)
-      })
-      case node: ScatterNode => node.outputMapping.map(op => {
-        PortBasedGraphOutputNode(makeIdentifier(op.identifier), op.womType, op)
-      })
-      case node: ConditionalNode => node.conditionalOutputPorts.map(op => {
-        PortBasedGraphOutputNode(makeIdentifier(op.identifier), op.womType, op)
-      })
+      case node: CallNode =>
+        node.outputPorts.map { op =>
+          val identifier = makeIdentifier(WomIdentifier(op.identifier.localName.value))
+          PortBasedGraphOutputNode(identifier, op.womType, op)
+        }
+      case node: ExposedExpressionNode if forWorkflowOutputs.isEmpty =>
+        node.outputPorts.map(op => PortBasedGraphOutputNode(makeIdentifier(WomIdentifier(op.name)), op.womType, op))
+      case node: ScatterNode =>
+        node.outputMapping.map(op => PortBasedGraphOutputNode(makeIdentifier(op.identifier), op.womType, op))
+      case node: ConditionalNode =>
+        node.conditionalOutputPorts.map { op =>
+          PortBasedGraphOutputNode(makeIdentifier(op.identifier), op.womType, op)
+        }
     }).flatten))
   }
 }
diff --git a/wom/src/main/scala/wdl/util/StringUtil.scala b/wom/src/main/scala/wdl/util/StringUtil.scala
index 871e1842656..f89c4fd73da 100644
--- a/wom/src/main/scala/wdl/util/StringUtil.scala
+++ b/wom/src/main/scala/wdl/util/StringUtil.scala
@@ -50,18 +50,16 @@ object StringUtil {
   def stripAll(s: String, startChars: String, endChars: String): String = {
     /* https://stackoverflow.com/questions/17995260/trimming-strings-in-scala */
     @tailrec
-    def start(n: Int): String = {
+    def start(n: Int): String =
       if (n == s.length) ""
       else if (startChars.indexOf(s.charAt(n).toInt) < 0) end(n, s.length)
       else start(1 + n)
-    }
 
     @tailrec
-    def end(a: Int, n: Int): String = {
+    def end(a: Int, n: Int): String =
       if (n <= a) s.substring(a, n)
       else if (endChars.indexOf(s.charAt(n - 1).toInt) < 0) s.substring(a, n)
       else end(a, n - 1)
-    }
 
     start(0)
   }
diff --git a/wom/src/main/scala/wom/CommandPart.scala b/wom/src/main/scala/wom/CommandPart.scala
index 06279304531..97e661c5b81 100644
--- a/wom/src/main/scala/wom/CommandPart.scala
+++ b/wom/src/main/scala/wom/CommandPart.scala
@@ -10,5 +10,6 @@ trait CommandPart {
   def instantiate(inputsMap: Map[LocalName, WomValue],
                   functions: IoFunctionSet,
                   valueMapper: WomValue => WomValue,
-                  runtimeEnvironment: RuntimeEnvironment): ErrorOr[List[InstantiatedCommand]]
+                  runtimeEnvironment: RuntimeEnvironment
+  ): ErrorOr[List[InstantiatedCommand]]
 }
diff --git a/wom/src/main/scala/wom/RuntimeAttributes.scala b/wom/src/main/scala/wom/RuntimeAttributes.scala
index 853e3145c23..486d69d5e97 100644
--- a/wom/src/main/scala/wom/RuntimeAttributes.scala
+++ b/wom/src/main/scala/wom/RuntimeAttributes.scala
@@ -5,6 +5,7 @@ import wom.expression.WomExpression
 object RuntimeAttributesKeys {
   val DockerKey = "docker"
   val MaxRetriesKey = "maxRetries"
+
   /**
     * Equivalent to CPUMinKey
     */
@@ -12,6 +13,7 @@ object RuntimeAttributesKeys {
   val CpuPlatformKey = "cpuPlatform"
   val CpuMinKey = "cpuMin"
   val CpuMaxKey = "cpuMax"
+
   /**
     * Equivalent to GPUMinKey
     */
@@ -20,6 +22,7 @@ object RuntimeAttributesKeys {
   val GpuMaxKey = "gpuCountMax"
   val GpuTypeKey = "gpuType"
   val DnaNexusInputDirMinKey = "dnaNexusInputDirMin"
+
   /**
     * Equivalent to MemoryMinKey
     */
diff --git a/wom/src/main/scala/wom/WomFileMapper.scala b/wom/src/main/scala/wom/WomFileMapper.scala
index 9d04de3f031..0b04b103537 100644
--- a/wom/src/main/scala/wom/WomFileMapper.scala
+++ b/wom/src/main/scala/wom/WomFileMapper.scala
@@ -8,6 +8,7 @@ import wom.values._
 import scala.util.{Success, Try}
 
 object WomFileMapper {
+
   /**
     * Loops over a WomValue applying the supplied mapper function whenever a WomFile is encountered.
     *
@@ -18,8 +19,7 @@ object WomFileMapper {
     * @see [[wom.values.WomValue.collectAsSeq]]
     * @see [[wom.values.WomFile.mapFile]]
     */
-  def mapWomFiles(mapper: WomFile => WomFile)
-                 (womValue: WomValue): Try[WomValue] = {
+  def mapWomFiles(mapper: WomFile => WomFile)(womValue: WomValue): Try[WomValue] =
     womValue match {
       case file: WomFile => Try(mapper(file))
       case array: WomArray =>
@@ -28,25 +28,27 @@ object WomFileMapper {
           WomArray(array.womType, _)
         }
       case map: WomMap =>
-        val mappedMap = map.value map {
-          case (key, value) => mapWomFiles(mapper)(key) -> mapWomFiles(mapper)(value)
+        val mappedMap = map.value map { case (key, value) =>
+          mapWomFiles(mapper)(key) -> mapWomFiles(mapper)(value)
         }
         TryUtil.sequenceKeyValues(mappedMap) map {
           WomMap(map.womType, _)
         }
       case womObject: WomObjectLike =>
-        val mappedMap = womObject.values map {
-          case (key, value) => key -> mapWomFiles(mapper)(value)
+        val mappedMap = womObject.values map { case (key, value) =>
+          key -> mapWomFiles(mapper)(value)
         }
         TryUtil.sequenceMap(mappedMap).map(WomObject.withTypeUnsafe(_, womObject.womObjectTypeLike))
       case pair: WomPair =>
-        val mappedPair: (Try[WomValue], Try[WomValue]) = (mapWomFiles(mapper)(pair.left), mapWomFiles(mapper)(pair.right))
+        val mappedPair: (Try[WomValue], Try[WomValue]) =
+          (mapWomFiles(mapper)(pair.left), mapWomFiles(mapper)(pair.right))
         TryUtil.sequenceTuple(mappedPair) map {
           (WomPair.apply _).tupled
         }
       case optionalValue: WomOptionalValue =>
         // Build a `WomOptionalValue` from an `Option[WomValue]`.
-        def buildWomOptionalValue(optionalWomValue: Option[WomValue]) = WomOptionalValue(optionalValue.innerType, optionalWomValue)
+        def buildWomOptionalValue(optionalWomValue: Option[WomValue]) =
+          WomOptionalValue(optionalValue.innerType, optionalWomValue)
 
         val mappedOptional: Option[Try[WomValue]] = optionalValue.value.map(mapWomFiles(mapper))
         mappedOptional match {
@@ -57,5 +59,4 @@ object WomFileMapper {
       case coproduct: WomCoproductValue => mapWomFiles(mapper)(coproduct.womValue)
       case other => Success(other)
     }
-  }
 }
diff --git a/wom/src/main/scala/wom/callable/Callable.scala b/wom/src/main/scala/wom/callable/Callable.scala
index 70140cc999f..bb325fa093b 100644
--- a/wom/src/main/scala/wom/callable/Callable.scala
+++ b/wom/src/main/scala/wom/callable/Callable.scala
@@ -16,13 +16,13 @@ trait Callable {
   def inputs: List[_ <: InputDefinition]
   def outputs: List[_ <: OutputDefinition]
 
-  val sourceLocation : Option[SourceFileLocation] = None
+  val sourceLocation: Option[SourceFileLocation] = None
 }
 
 trait ExecutableCallable extends Callable {
   def graph: Graph
-  lazy val taskCallNodes: Set[CommandCallNode] = graph.allNodes collect {
-    case taskNode: CommandCallNode => taskNode
+  lazy val taskCallNodes: Set[CommandCallNode] = graph.allNodes collect { case taskNode: CommandCallNode =>
+    taskNode
   }
 }
 
@@ -48,37 +48,57 @@ object Callable {
   }
 
   object RequiredInputDefinition {
-    def apply(name: String, womType: WomType, valueMapper: InputValueMapper): RequiredInputDefinition = {
+    def apply(name: String, womType: WomType, valueMapper: InputValueMapper): RequiredInputDefinition =
       RequiredInputDefinition(LocalName(name), womType, valueMapper, None)
-    }
-    def apply(name: String, womType: WomType): RequiredInputDefinition = {
+    def apply(name: String, womType: WomType): RequiredInputDefinition =
       RequiredInputDefinition(LocalName(name), womType, InputDefinition.IdentityValueMapper, None)
-    }
-    def apply(name: String, womType: WomType, parameterMeta: Option[MetaValueElement]): RequiredInputDefinition = {
+    def apply(name: String, womType: WomType, parameterMeta: Option[MetaValueElement]): RequiredInputDefinition =
       RequiredInputDefinition(LocalName(name), womType, InputDefinition.IdentityValueMapper, parameterMeta)
-    }
-    def apply(name: String, womType: WomType, valueMapper: InputValueMapper, parameterMeta: Option[MetaValueElement]): RequiredInputDefinition = {
+    def apply(name: String,
+              womType: WomType,
+              valueMapper: InputValueMapper,
+              parameterMeta: Option[MetaValueElement]
+    ): RequiredInputDefinition =
       RequiredInputDefinition(LocalName(name), womType, valueMapper, parameterMeta)
-    }
   }
   final case class RequiredInputDefinition(localName: LocalName,
                                            womType: WomType,
                                            valueMapper: InputValueMapper = InputDefinition.IdentityValueMapper,
-                                           parameterMeta: Option[MetaValueElement] = None) extends InputDefinition
+                                           parameterMeta: Option[MetaValueElement] = None
+  ) extends InputDefinition
 
   object OverridableInputDefinitionWithDefault {
-    def apply(name: String, womType: WomType, default: WomExpression): OverridableInputDefinitionWithDefault = {
-      OverridableInputDefinitionWithDefault(LocalName(name), womType, default, InputDefinition.IdentityValueMapper, None)
-    }
-    def apply(name: String, womType: WomType, default: WomExpression, parameterMeta: Option[MetaValueElement]): OverridableInputDefinitionWithDefault = {
-      OverridableInputDefinitionWithDefault(LocalName(name), womType, default, InputDefinition.IdentityValueMapper, parameterMeta)
-    }
-    def apply(name: String, womType: WomType, default: WomExpression, valueMapper: InputValueMapper): OverridableInputDefinitionWithDefault = {
+    def apply(name: String, womType: WomType, default: WomExpression): OverridableInputDefinitionWithDefault =
+      OverridableInputDefinitionWithDefault(LocalName(name),
+                                            womType,
+                                            default,
+                                            InputDefinition.IdentityValueMapper,
+                                            None
+      )
+    def apply(name: String,
+              womType: WomType,
+              default: WomExpression,
+              parameterMeta: Option[MetaValueElement]
+    ): OverridableInputDefinitionWithDefault =
+      OverridableInputDefinitionWithDefault(LocalName(name),
+                                            womType,
+                                            default,
+                                            InputDefinition.IdentityValueMapper,
+                                            parameterMeta
+      )
+    def apply(name: String,
+              womType: WomType,
+              default: WomExpression,
+              valueMapper: InputValueMapper
+    ): OverridableInputDefinitionWithDefault =
       OverridableInputDefinitionWithDefault(LocalName(name), womType, default, valueMapper, None)
-    }
-    def apply(name: String, womType: WomType, default: WomExpression, valueMapper: InputValueMapper, parameterMeta: Option[MetaValueElement]): OverridableInputDefinitionWithDefault = {
+    def apply(name: String,
+              womType: WomType,
+              default: WomExpression,
+              valueMapper: InputValueMapper,
+              parameterMeta: Option[MetaValueElement]
+    ): OverridableInputDefinitionWithDefault =
       OverridableInputDefinitionWithDefault(LocalName(name), womType, default, valueMapper, parameterMeta)
-    }
   }
 
   sealed trait InputDefinitionWithDefault extends InputDefinition {
@@ -91,16 +111,25 @@ object Callable {
   final case class OverridableInputDefinitionWithDefault(localName: LocalName,
                                                          womType: WomType,
                                                          default: WomExpression,
-                                                         valueMapper: InputValueMapper = InputDefinition.IdentityValueMapper,
-                                                         parameterMeta: Option[MetaValueElement] = None) extends InputDefinitionWithDefault
+                                                         valueMapper: InputValueMapper =
+                                                           InputDefinition.IdentityValueMapper,
+                                                         parameterMeta: Option[MetaValueElement] = None
+  ) extends InputDefinitionWithDefault
 
   object FixedInputDefinitionWithDefault {
-    def apply(name: String, womType: WomType, default: WomExpression): FixedInputDefinitionWithDefault = {
+    def apply(name: String, womType: WomType, default: WomExpression): FixedInputDefinitionWithDefault =
       FixedInputDefinitionWithDefault(LocalName(name), womType, default, InputDefinition.IdentityValueMapper, None)
-    }
-    def apply(name: String, womType: WomType, default: WomExpression, parameterMeta: Option[MetaValueElement]): FixedInputDefinitionWithDefault = {
-      FixedInputDefinitionWithDefault(LocalName(name), womType, default, InputDefinition.IdentityValueMapper, parameterMeta)
-    }
+    def apply(name: String,
+              womType: WomType,
+              default: WomExpression,
+              parameterMeta: Option[MetaValueElement]
+    ): FixedInputDefinitionWithDefault =
+      FixedInputDefinitionWithDefault(LocalName(name),
+                                      womType,
+                                      default,
+                                      InputDefinition.IdentityValueMapper,
+                                      parameterMeta
+      )
   }
 
   /**
@@ -110,25 +139,37 @@ object Callable {
                                                    womType: WomType,
                                                    default: WomExpression,
                                                    valueMapper: InputValueMapper = InputDefinition.IdentityValueMapper,
-                                                   parameterMeta: Option[MetaValueElement] = None) extends InputDefinitionWithDefault
+                                                   parameterMeta: Option[MetaValueElement] = None
+  ) extends InputDefinitionWithDefault
 
   object OptionalInputDefinition {
-    def apply(name: String, womType: WomOptionalType): OptionalInputDefinition = OptionalInputDefinition(LocalName(name), womType, InputDefinition.IdentityValueMapper, None)
-    def apply(name: String, womType: WomOptionalType, parameterMeta: Option[MetaValueElement]): OptionalInputDefinition = OptionalInputDefinition(LocalName(name), womType, InputDefinition.IdentityValueMapper, parameterMeta)
-    def apply(name: String, womType: WomOptionalType, valueMapper: InputValueMapper): OptionalInputDefinition = OptionalInputDefinition(LocalName(name), womType, valueMapper, None)
-    def apply(name: String, womType: WomOptionalType, valueMapper: InputValueMapper, parameterMeta: Option[MetaValueElement]): OptionalInputDefinition = OptionalInputDefinition(LocalName(name), womType, valueMapper, parameterMeta)
+    def apply(name: String, womType: WomOptionalType): OptionalInputDefinition =
+      OptionalInputDefinition(LocalName(name), womType, InputDefinition.IdentityValueMapper, None)
+    def apply(name: String,
+              womType: WomOptionalType,
+              parameterMeta: Option[MetaValueElement]
+    ): OptionalInputDefinition =
+      OptionalInputDefinition(LocalName(name), womType, InputDefinition.IdentityValueMapper, parameterMeta)
+    def apply(name: String, womType: WomOptionalType, valueMapper: InputValueMapper): OptionalInputDefinition =
+      OptionalInputDefinition(LocalName(name), womType, valueMapper, None)
+    def apply(name: String,
+              womType: WomOptionalType,
+              valueMapper: InputValueMapper,
+              parameterMeta: Option[MetaValueElement]
+    ): OptionalInputDefinition = OptionalInputDefinition(LocalName(name), womType, valueMapper, parameterMeta)
   }
   final case class OptionalInputDefinition(localName: LocalName,
                                            womType: WomOptionalType,
                                            valueMapper: InputValueMapper = InputDefinition.IdentityValueMapper,
-                                           parameterMeta: Option[MetaValueElement] = None) extends InputDefinition
+                                           parameterMeta: Option[MetaValueElement] = None
+  ) extends InputDefinition
 
   object OutputDefinition {
-    def apply(name: String, womType: WomType, expression: WomExpression): OutputDefinition = {
+    def apply(name: String, womType: WomType, expression: WomExpression): OutputDefinition =
       OutputDefinition(LocalName(name), womType, expression)
-    }
   }
   final case class OutputDefinition(localName: LocalName, womType: WomType, expression: WomExpression) {
+
     /**
       * Alias for localName.asString
       */
diff --git a/wom/src/main/scala/wom/callable/CommandTaskDefinition.scala b/wom/src/main/scala/wom/callable/CommandTaskDefinition.scala
index 6007fbcf7c9..62531ac5802 100644
--- a/wom/src/main/scala/wom/callable/CommandTaskDefinition.scala
+++ b/wom/src/main/scala/wom/callable/CommandTaskDefinition.scala
@@ -23,21 +23,24 @@ object CommandTaskDefinition {
   type EvaluatedOutputs = Checked[Map[OutputPort, WomValue]]
 
   /*
-    * Result type of the OutputEvaluationFunction. Equivalent to Future[Option[EvaluatedOutputs]]
-    * - Future because it might involve I/O
-    * - Option because it might not return any value (dependent on the task)
-    * - Checked because the evaluation could fail (invalid types, missing values etc...)
-  */
+   * Result type of the OutputEvaluationFunction. Equivalent to Future[Option[EvaluatedOutputs]]
+   * - Future because it might involve I/O
+   * - Option because it might not return any value (dependent on the task)
+   * - Checked because the evaluation could fail (invalid types, missing values etc...)
+   */
   type OutputFunctionResponse = OptionT[Future, EvaluatedOutputs]
 
   // Function definition to evaluate task outputs
-  type OutputEvaluationFunction = (Set[OutputPort], Map[String, WomValue], IoFunctionSet, ExecutionContext) => OutputFunctionResponse
+  type OutputEvaluationFunction =
+    (Set[OutputPort], Map[String, WomValue], IoFunctionSet, ExecutionContext) => OutputFunctionResponse
 
   object OutputEvaluationFunction {
-    val none: OutputEvaluationFunction = { case (_ ,_, _, _) => OptionT[Future, EvaluatedOutputs](Future.successful(None)) }
+    val none: OutputEvaluationFunction = { case (_, _, _, _) =>
+      OptionT[Future, EvaluatedOutputs](Future.successful(None))
+    }
   }
 
-  private implicit val instantiatedCommandMonoid = cats.derived.MkMonoid[InstantiatedCommand]
+  implicit private val instantiatedCommandMonoid = cats.derived.MkMonoid[InstantiatedCommand]
   object CommandTemplateBuilder {
     def fromValues(values: Seq[CommandPart]) = new CommandTemplateBuilder {
       override def build(inputs: WomEvaluatedCallInputs): ErrorOr[Seq[CommandPart]] = values.validNel
@@ -63,11 +66,12 @@ sealed trait TaskDefinition extends Callable {
     * Transform the Callable TaskDefinition to an ExecutableCallable that can be executed on its own.
     */
   def toExecutable: ErrorOr[ExecutableCallable]
+
   /**
     * Provides a custom way to evaluate outputs of the task definition.
     * Return None to leave the evaluation method to the engine.
     */
-  private [wom] def customizedOutputEvaluation: OutputEvaluationFunction
+  private[wom] def customizedOutputEvaluation: OutputEvaluationFunction
 }
 
 /**
@@ -80,7 +84,8 @@ sealed trait CommandTaskDefinition extends TaskDefinition {
   def stderrOverride: Option[WomExpression]
   def commandTemplateBuilder: WomEvaluatedCallInputs => ErrorOr[Seq[CommandPart]]
   // TODO ErrorOrify this ? Throw for now
-  def commandTemplate(taskInputs: WomEvaluatedCallInputs): Seq[CommandPart] = commandTemplateBuilder(taskInputs).toTry("Failed to build command").get
+  def commandTemplate(taskInputs: WomEvaluatedCallInputs): Seq[CommandPart] =
+    commandTemplateBuilder(taskInputs).toTry("Failed to build command").get
   def prefixSeparator: String
   def commandPartSeparator: String
   def stdinRedirection: Option[WomExpression]
@@ -88,18 +93,20 @@ sealed trait CommandTaskDefinition extends TaskDefinition {
   def environmentExpressions: Map[String, WomExpression]
   def additionalGlob: Option[WomGlobFile]
   def homeOverride: Option[RuntimeEnvironment => String]
+
   /**
     * Provides a custom way to evaluate outputs of the task definition.
     * Return None to leave the evaluation method to the engine.
     */
-  private [wom] def customizedOutputEvaluation: OutputEvaluationFunction
+  private[wom] def customizedOutputEvaluation: OutputEvaluationFunction
 
   lazy val unqualifiedName: LocallyQualifiedName = name
 
   def instantiateCommand(taskInputs: WomEvaluatedCallInputs,
                          functions: IoFunctionSet,
                          valueMapper: WomValue => WomValue,
-                         runtimeEnvironment: RuntimeEnvironment): ErrorOr[InstantiatedCommand] = {
+                         runtimeEnvironment: RuntimeEnvironment
+  ): ErrorOr[InstantiatedCommand] = {
 
     val inputsByLocalName = taskInputs map { case (k, v) => k.localName -> v }
     val valueMappedInputsByLocalName = inputsByLocalName map { case (k, v) => k -> valueMapper(v) }
@@ -107,26 +114,30 @@ sealed trait CommandTaskDefinition extends TaskDefinition {
 
     // Just raw command parts, no separators.
     val rawCommandParts: List[ErrorOr[InstantiatedCommand]] =
-      commandTemplate(taskInputs).toList.flatMap({ commandPart =>
+      commandTemplate(taskInputs).toList.flatMap { commandPart =>
         commandPart.instantiate(inputsByLocalName, functions, valueMapper, runtimeEnvironment).sequence
-      })
+      }
 
     // Add separator command parts and monoid smash down to one `ErrorOr[InstantiatedCommand]`.
     val instantiatedCommand: ErrorOr[InstantiatedCommand] =
       rawCommandParts.intercalate(InstantiatedCommand(commandPartSeparator).validNel)
 
     // `normalize` the instantiation (i.e. don't break Python code indentation) and add in the inputs.
-    instantiatedCommand map { c => c.copy(
-      commandString = StringUtil.normalize(c.commandString),
-      preprocessedInputs = inputsByLocalName.toList,
-      valueMappedPreprocessedInputs = valueMappedInputsByLocalName.toList
-    )}
+    instantiatedCommand map { c =>
+      c.copy(
+        commandString = StringUtil.normalize(c.commandString),
+        preprocessedInputs = inputsByLocalName.toList,
+        valueMappedPreprocessedInputs = valueMappedInputsByLocalName.toList
+      )
+    }
   }
 
-  def commandTemplateString(taskInputs: WomEvaluatedCallInputs): String = StringUtil.normalize(commandTemplate(taskInputs).map(_.toString).mkString)
+  def commandTemplateString(taskInputs: WomEvaluatedCallInputs): String =
+    StringUtil.normalize(commandTemplate(taskInputs).map(_.toString).mkString)
 
   override def toString: String = {
-    val template = Try(commandTemplate(Map.empty).toString()).getOrElse("Could not generate command template without inputs")
+    val template =
+      Try(commandTemplate(Map.empty).toString()).getOrElse("Could not generate command template without inputs")
     s"[Task name=$name commandTemplate=$template]"
   }
 }
@@ -150,12 +161,15 @@ final case class CallableTaskDefinition(name: String,
                                         stdoutOverride: Option[WomExpression] = None,
                                         stderrOverride: Option[WomExpression] = None,
                                         additionalGlob: Option[WomGlobFile] = None,
-                                        private [wom] val customizedOutputEvaluation: OutputEvaluationFunction = OutputEvaluationFunction.none,
+                                        private[wom] val customizedOutputEvaluation: OutputEvaluationFunction =
+                                          OutputEvaluationFunction.none,
                                         homeOverride: Option[RuntimeEnvironment => String] = None,
                                         dockerOutputDirectory: Option[String] = None,
-                                        override val sourceLocation : Option[SourceFileLocation]
-                                       ) extends CommandTaskDefinition {
-  def toExecutable: ErrorOr[ExecutableTaskDefinition] = TaskCall.graphFromDefinition(this) map { ExecutableTaskDefinition(this, _) }
+                                        override val sourceLocation: Option[SourceFileLocation]
+) extends CommandTaskDefinition {
+  def toExecutable: ErrorOr[ExecutableTaskDefinition] = TaskCall.graphFromDefinition(this) map {
+    ExecutableTaskDefinition(this, _)
+  }
 }
 
 /**
@@ -164,7 +178,8 @@ final case class CallableTaskDefinition(name: String,
   */
 final case class ExecutableTaskDefinition private (callableTaskDefinition: CallableTaskDefinition,
                                                    override val graph: Graph
-                                                  ) extends CommandTaskDefinition with ExecutableCallable {
+) extends CommandTaskDefinition
+    with ExecutableCallable {
   override def name = callableTaskDefinition.name
   override def inputs = callableTaskDefinition.inputs
   override def outputs = callableTaskDefinition.outputs
@@ -181,7 +196,7 @@ final case class ExecutableTaskDefinition private (callableTaskDefinition: Calla
   override def adHocFileCreation = callableTaskDefinition.adHocFileCreation
   override def environmentExpressions = callableTaskDefinition.environmentExpressions
   override def additionalGlob = callableTaskDefinition.additionalGlob
-  override private [wom]  def customizedOutputEvaluation = callableTaskDefinition.customizedOutputEvaluation
+  override private[wom] def customizedOutputEvaluation = callableTaskDefinition.customizedOutputEvaluation
   override def toExecutable = this.validNel
   override def homeOverride = callableTaskDefinition.homeOverride
   override def dockerOutputDirectory = callableTaskDefinition.dockerOutputDirectory
@@ -191,22 +206,24 @@ sealed trait ExpressionTaskDefinition extends TaskDefinition {
   def evaluate: (Map[String, WomValue], IoFunctionSet, List[OutputPort]) => Checked[Map[OutputPort, WomValue]]
 }
 
-
 /**
   * An expression task definition only.
   * Can be called but cannot be used in an Executable as a standalone execution.
   */
-final case class CallableExpressionTaskDefinition(name: String,
-                                                  evaluate: (Map[String, WomValue], IoFunctionSet, List[OutputPort]) => Checked[Map[OutputPort, WomValue]],
-                                                  runtimeAttributes: RuntimeAttributes,
-                                                  meta: Map[String, MetaValueElement],
-                                                  parameterMeta: Map[String, MetaValueElement],
-                                                  outputs: List[Callable.OutputDefinition],
-                                                  inputs: List[_ <: Callable.InputDefinition],
-                                                  prefixSeparator: String = ".",
-                                                  private [wom] val customizedOutputEvaluation: OutputEvaluationFunction = OutputEvaluationFunction.none
-                                       ) extends ExpressionTaskDefinition {
-  def toExecutable: ErrorOr[ExecutableExpressionTaskDefinition] = TaskCall.graphFromDefinition(this) map { ExecutableExpressionTaskDefinition(this, _) }
+final case class CallableExpressionTaskDefinition(
+  name: String,
+  evaluate: (Map[String, WomValue], IoFunctionSet, List[OutputPort]) => Checked[Map[OutputPort, WomValue]],
+  runtimeAttributes: RuntimeAttributes,
+  meta: Map[String, MetaValueElement],
+  parameterMeta: Map[String, MetaValueElement],
+  outputs: List[Callable.OutputDefinition],
+  inputs: List[_ <: Callable.InputDefinition],
+  prefixSeparator: String = ".",
+  private[wom] val customizedOutputEvaluation: OutputEvaluationFunction = OutputEvaluationFunction.none
+) extends ExpressionTaskDefinition {
+  def toExecutable: ErrorOr[ExecutableExpressionTaskDefinition] = TaskCall.graphFromDefinition(this) map {
+    ExecutableExpressionTaskDefinition(this, _)
+  }
 }
 
 /**
@@ -214,8 +231,9 @@ final case class CallableExpressionTaskDefinition(name: String,
   * Can be called from a workflow but can also be run as a standalone execution.
   */
 final case class ExecutableExpressionTaskDefinition private (callableTaskDefinition: CallableExpressionTaskDefinition,
-                                                   override val graph: Graph
-                                                  ) extends ExpressionTaskDefinition with ExecutableCallable {
+                                                             override val graph: Graph
+) extends ExpressionTaskDefinition
+    with ExecutableCallable {
   override def name = callableTaskDefinition.name
   override def inputs = callableTaskDefinition.inputs
   override def outputs = callableTaskDefinition.outputs
@@ -225,5 +243,5 @@ final case class ExecutableExpressionTaskDefinition private (callableTaskDefinit
   override def meta = callableTaskDefinition.meta
   override def parameterMeta = callableTaskDefinition.parameterMeta
   override def toExecutable = this.validNel
-  override private [wom]  def customizedOutputEvaluation = callableTaskDefinition.customizedOutputEvaluation
+  override private[wom] def customizedOutputEvaluation = callableTaskDefinition.customizedOutputEvaluation
 }
diff --git a/wom/src/main/scala/wom/callable/ContainerizedInputExpression.scala b/wom/src/main/scala/wom/callable/ContainerizedInputExpression.scala
index e77689fbb5b..5293dbcd648 100644
--- a/wom/src/main/scala/wom/callable/ContainerizedInputExpression.scala
+++ b/wom/src/main/scala/wom/callable/ContainerizedInputExpression.scala
@@ -10,7 +10,8 @@ import wom.values.{WomFile, WomValue}
 trait ContainerizedInputExpression {
   def evaluate(hostInputValues: Map[String, WomValue],
                containerizedInputValues: Map[String, WomValue],
-               ioFunctionSet: IoFunctionSet): IOChecked[List[AdHocValue]]
+               ioFunctionSet: IoFunctionSet
+  ): IOChecked[List[AdHocValue]]
 }
 
 final case class AdHocValue(womValue: WomFile, alternativeName: Option[String], inputName: Option[String])
diff --git a/wom/src/main/scala/wom/callable/RuntimeEnvironment.scala b/wom/src/main/scala/wom/callable/RuntimeEnvironment.scala
index a2eb4983788..513516a1af2 100644
--- a/wom/src/main/scala/wom/callable/RuntimeEnvironment.scala
+++ b/wom/src/main/scala/wom/callable/RuntimeEnvironment.scala
@@ -18,5 +18,5 @@ case class RuntimeEnvironment(outputPath: String,
                               cores: Int Refined Positive,
                               ram: Double,
                               outputPathSize: Long,
-                              tempPathSize: Long)
-
+                              tempPathSize: Long
+)
diff --git a/wom/src/main/scala/wom/callable/WorkflowDefinition.scala b/wom/src/main/scala/wom/callable/WorkflowDefinition.scala
index 07f70ebc7e7..102a47ae775 100644
--- a/wom/src/main/scala/wom/callable/WorkflowDefinition.scala
+++ b/wom/src/main/scala/wom/callable/WorkflowDefinition.scala
@@ -8,7 +8,8 @@ final case class WorkflowDefinition(name: String,
                                     innerGraph: Graph,
                                     meta: Map[String, MetaValueElement],
                                     parameterMeta: Map[String, MetaValueElement],
-                                    override val sourceLocation : Option[SourceFileLocation]) extends ExecutableCallable {
+                                    override val sourceLocation: Option[SourceFileLocation]
+) extends ExecutableCallable {
 
   override lazy val toString = s"[Workflow $name]"
   override val graph: Graph = innerGraph
diff --git a/wom/src/main/scala/wom/executable/Executable.scala b/wom/src/main/scala/wom/executable/Executable.scala
index a68c7fc98c2..54da67d0d9c 100644
--- a/wom/src/main/scala/wom/executable/Executable.scala
+++ b/wom/src/main/scala/wom/executable/Executable.scala
@@ -24,66 +24,88 @@ import wom.values.WomValue
 object Executable {
 
   /*
-    * Function provided by each language, that takes the raw input file as a String and returns a Checked[ParsedInputMap]
-    * Each entry of the map is an input found in the file.
-    * The key is a string representation of the input. It must be be equal to the name of the matching GraphInputNode.
-    * The value is a function which given a WomType, attempts to coerce the input value to that type.
-    * Thanks to this level of indirection, the logic that links graph input nodes to input values still resides in WOM,
-    * which 1) abstracts it away and 2) guarantees that the linking mechanism is the same regardless of the language.
-    * At the same time each language can parse the input file however it wants.
+   * Function provided by each language, that takes the raw input file as a String and returns a Checked[ParsedInputMap]
+   * Each entry of the map is an input found in the file.
+   * The key is a string representation of the input. It must be be equal to the name of the matching GraphInputNode.
+   * The value is a function which given a WomType, attempts to coerce the input value to that type.
+   * Thanks to this level of indirection, the logic that links graph input nodes to input values still resides in WOM,
+   * which 1) abstracts it away and 2) guarantees that the linking mechanism is the same regardless of the language.
+   * At the same time each language can parse the input file however it wants.
    */
   type InputParsingFunction = String => Checked[ParsedInputMap]
   type ParsedInputMap = Map[String, DelayedCoercionFunction]
   type DelayedCoercionFunction = WomType => ErrorOr[WomValue]
-  
+
   /*
-    * Maps output ports from graph input nodes to ResolvedExecutableInput
+   * Maps output ports from graph input nodes to ResolvedExecutableInput
    */
   type ResolvedExecutableInputs = Map[OutputPort, ResolvedExecutableInput]
 
-  def withInputs(entryPoint: ExecutableCallable, inputParsingFunction: InputParsingFunction, inputFile: Option[String], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable] = {
-    validateExecutable(entryPoint, inputParsingFunction, parseGraphInputs(strictValidation), inputFile, ioFunctions).toChecked
-  }
+  def withInputs(entryPoint: ExecutableCallable,
+                 inputParsingFunction: InputParsingFunction,
+                 inputFile: Option[String],
+                 ioFunctions: IoFunctionSet,
+                 strictValidation: Boolean
+  ): Checked[Executable] =
+    validateExecutable(entryPoint,
+                       inputParsingFunction,
+                       parseGraphInputs(strictValidation),
+                       inputFile,
+                       ioFunctions
+    ).toChecked
 
   /**
     * Given the graph and the Map[String, DelayedCoercionFunction], attempts to find a value in the map for each ExternalGraphInputNode of the graph
     */
-  private def parseGraphInputs(strictValidation: Boolean)(graph: Graph, inputCoercionMap: Map[String, DelayedCoercionFunction], ioFunctions: IoFunctionSet): IOChecked[ResolvedExecutableInputs] = {
+  private def parseGraphInputs(strictValidation: Boolean)(graph: Graph,
+                                                          inputCoercionMap: Map[String, DelayedCoercionFunction],
+                                                          ioFunctions: IoFunctionSet
+  ): IOChecked[ResolvedExecutableInputs] = {
     import ioFunctions.cs
 
-    def fromInputMapping(gin: ExternalGraphInputNode): Option[IOChecked[ResolvedExecutableInput]] = {
+    def fromInputMapping(gin: ExternalGraphInputNode): Option[IOChecked[ResolvedExecutableInput]] =
       inputCoercionMap
         .get(gin.nameInInputSet)
-        .map { _.apply(gin.womType).toIOChecked
-          .flatMap(gin.valueMapper(ioFunctions)(_))
-          .contextualizeErrors(s"evaluate input '${gin.localName}'")
-          .map(Coproduct[ResolvedExecutableInput](_))
+        .map {
+          _.apply(gin.womType).toIOChecked
+            .flatMap(gin.valueMapper(ioFunctions)(_))
+            .contextualizeErrors(s"evaluate input '${gin.localName}'")
+            .map(Coproduct[ResolvedExecutableInput](_))
         }
-    }
 
     def fallBack(gin: ExternalGraphInputNode): IOChecked[ResolvedExecutableInput] = gin match {
-      case required: RequiredGraphInputNode => s"Required workflow input '${required.nameInInputSet}' not specified".invalidIOChecked
+      case required: RequiredGraphInputNode =>
+        s"Required workflow input '${required.nameInInputSet}' not specified".invalidIOChecked
       case optionalWithDefault: OptionalGraphInputNodeWithDefault =>
         for {
           evaluatedDefault <- optionalWithDefault.default.evaluateValue(Map.empty, ioFunctions).toIOChecked
           mapped <- optionalWithDefault.valueMapper(ioFunctions)(evaluatedDefault)
         } yield Coproduct[ResolvedExecutableInput](mapped)
-      case optional: OptionalGraphInputNode => IOChecked.pure(Coproduct[ResolvedExecutableInput](optional.womType.none: WomValue))
+      case optional: OptionalGraphInputNode =>
+        IOChecked.pure(Coproduct[ResolvedExecutableInput](optional.womType.none: WomValue))
     }
 
-    val providedInputsValidation: IOChecked[ResolvedExecutableInputs] = graph.inputNodes.toList.parTraverse[IOChecked, Option[(OutputPort, ResolvedExecutableInput)]]({
-      case gin: ExternalGraphInputNode =>
-        // The compiler needs the type ascription for some reason
-        fromInputMapping(gin).getOrElse(fallBack(gin)).map((gin.singleOutputPort: OutputPort) -> _).map(Option(_))
-      case _ => Option.empty[(OutputPort, ResolvedExecutableInput)].validIOChecked
-    }).map(_.flatten).map(_.toMap)
+    val providedInputsValidation: IOChecked[ResolvedExecutableInputs] = graph.inputNodes.toList
+      .parTraverse[IOChecked, Option[(OutputPort, ResolvedExecutableInput)]] {
+        case gin: ExternalGraphInputNode =>
+          // The compiler needs the type ascription for some reason
+          fromInputMapping(gin).getOrElse(fallBack(gin)).map((gin.singleOutputPort: OutputPort) -> _).map(Option(_))
+        case _ => Option.empty[(OutputPort, ResolvedExecutableInput)].validIOChecked
+      }
+      .map(_.flatten)
+      .map(_.toMap)
 
     val wantedInputs = graph.externalInputNodes.map(_.nameInInputSet)
     val unwantedInputs = if (strictValidation) inputCoercionMap.keySet.diff(wantedInputs) else Set.empty
 
     val wantedInputsValidation: ErrorOr[Unit] = NonEmptyList.fromList(unwantedInputs.toList) match {
       case None => ().validNel
-      case Some(unwanteds) => Invalid(unwanteds.map(unwanted => s"WARNING: Unexpected input provided: $unwanted (expected inputs: [${wantedInputs.mkString(", ")}])"))
+      case Some(unwanteds) =>
+        Invalid(
+          unwanteds.map(unwanted =>
+            s"WARNING: Unexpected input provided: $unwanted (expected inputs: [${wantedInputs.mkString(", ")}])"
+          )
+        )
     }
 
     (providedInputsValidation, wantedInputsValidation.toIOChecked) mapN { (providedInputs, _) => providedInputs }
diff --git a/wom/src/main/scala/wom/executable/ExecutableValidation.scala b/wom/src/main/scala/wom/executable/ExecutableValidation.scala
index e892b2f2029..4904e41ae69 100644
--- a/wom/src/main/scala/wom/executable/ExecutableValidation.scala
+++ b/wom/src/main/scala/wom/executable/ExecutableValidation.scala
@@ -7,14 +7,21 @@ import wom.executable.Executable.{DelayedCoercionFunction, InputParsingFunction,
 import wom.expression.IoFunctionSet
 import wom.graph.Graph
 
-private [executable] object ExecutableValidation {
+private[executable] object ExecutableValidation {
 
-  private [executable] def validateExecutable(entryPoint: ExecutableCallable,
-                                              inputParsingFunction: InputParsingFunction,
-                                              parseGraphInputs: (Graph, Map[String, DelayedCoercionFunction], IoFunctionSet) => IOChecked[ResolvedExecutableInputs],
-                                              inputFile: Option[String],
-                                              ioFunctions: IoFunctionSet): IOChecked[Executable] = for {
-    parsedInputs <- inputFile.map(inputParsingFunction).map(_.toIOChecked).getOrElse(IOChecked.pure(Map.empty[String, DelayedCoercionFunction]))
+  private[executable] def validateExecutable(entryPoint: ExecutableCallable,
+                                             inputParsingFunction: InputParsingFunction,
+                                             parseGraphInputs: (Graph,
+                                                                Map[String, DelayedCoercionFunction],
+                                                                IoFunctionSet
+                                             ) => IOChecked[ResolvedExecutableInputs],
+                                             inputFile: Option[String],
+                                             ioFunctions: IoFunctionSet
+  ): IOChecked[Executable] = for {
+    parsedInputs <- inputFile
+      .map(inputParsingFunction)
+      .map(_.toIOChecked)
+      .getOrElse(IOChecked.pure(Map.empty[String, DelayedCoercionFunction]))
     validatedInputs <- parseGraphInputs(entryPoint.graph, parsedInputs, ioFunctions)
   } yield Executable(entryPoint, validatedInputs)
 }
diff --git a/wom/src/main/scala/wom/executable/WomBundle.scala b/wom/src/main/scala/wom/executable/WomBundle.scala
index 795df07a258..b3cb11762e4 100644
--- a/wom/src/main/scala/wom/executable/WomBundle.scala
+++ b/wom/src/main/scala/wom/executable/WomBundle.scala
@@ -12,11 +12,13 @@ import wom.types.WomType
 final case class WomBundle(primaryCallable: Option[Callable],
                            allCallables: Map[String, Callable],
                            typeAliases: Map[String, WomType],
-                           resolvedImportRecords: Set[ResolvedImportRecord]) {
+                           resolvedImportRecords: Set[ResolvedImportRecord]
+) {
   def toExecutableCallable: Checked[ExecutableCallable] = primaryCallable match {
     case Some(w: WorkflowDefinition) => w.validNelCheck
     case Some(c: CallableTaskDefinition) => c.toExecutable.toEither
-    case Some(other) => s"Cannot convert WOM bundle to executable. Primary callable was an unknown type ${other.getClass.getSimpleName}.".invalidNelCheck
+    case Some(other) =>
+      s"Cannot convert WOM bundle to executable. Primary callable was an unknown type ${other.getClass.getSimpleName}.".invalidNelCheck
     case None => s"Cannot convert WOM bundle to executable. No primary callable was available.".invalidNelCheck
   }
 
diff --git a/wom/src/main/scala/wom/expression/InputPointerToWomValue.scala b/wom/src/main/scala/wom/expression/InputPointerToWomValue.scala
index 33fa0241127..a95ff619f04 100644
--- a/wom/src/main/scala/wom/expression/InputPointerToWomValue.scala
+++ b/wom/src/main/scala/wom/expression/InputPointerToWomValue.scala
@@ -5,7 +5,7 @@ import common.validation.ErrorOr.ErrorOr
 import common.validation.IOChecked.{IOChecked, _}
 import shapeless.Poly1
 import wom.callable.Callable.InputDefinition.InputValueMapper
-import wom.callable.Callable.{InputDefinition, OverridableInputDefinitionWithDefault, OptionalInputDefinition}
+import wom.callable.Callable.{InputDefinition, OptionalInputDefinition, OverridableInputDefinitionWithDefault}
 import wom.graph.GraphNodePort.OutputPort
 import wom.values.{WomOptionalValue, WomValue}
 
@@ -16,22 +16,28 @@ object InputPointerToWomValue extends Poly1 {
   // Function that can transform any of the coproduct types to an ErrorOr[WomValue]
   type ToWomValueFn = (Map[String, WomValue], IoFunctionSet, OutputPortLookup, InputDefinition) => IOChecked[WomValue]
 
-  def withInitializedValue(ioFunctionSet: IoFunctionSet, womValue: WomValue)(block: WomValue => IOChecked[WomValue]): IOChecked[WomValue] = {
+  def withInitializedValue(ioFunctionSet: IoFunctionSet, womValue: WomValue)(
+    block: WomValue => IOChecked[WomValue]
+  ): IOChecked[WomValue] =
     for {
-      initialized <-  womValue.initialize(ioFunctionSet)
+      initialized <- womValue.initialize(ioFunctionSet)
       evaluated <- block(initialized)
     } yield evaluated
-  }
 
   implicit def fromWomValue: Case.Aux[WomValue, ToWomValueFn] = at[WomValue] {
-    womValue => (_: Map[String, WomValue], ioFunctions: IoFunctionSet, _: OutputPortLookup, inputDefinition: InputDefinition) =>
-      withInitializedValue(ioFunctions, womValue) {
-        inputDefinition.valueMapper(ioFunctions)
-      }
+    womValue =>
+      (_: Map[String, WomValue], ioFunctions: IoFunctionSet, _: OutputPortLookup, inputDefinition: InputDefinition) =>
+        withInitializedValue(ioFunctions, womValue) {
+          inputDefinition.valueMapper(ioFunctions)
+        }
   }
 
   implicit def fromOutputPort: Case.Aux[OutputPort, ToWomValueFn] = at[OutputPort] {
-    port => (knownValues: Map[String, WomValue], ioFunctions: IoFunctionSet, outputPortLookup: OutputPortLookup, inputDefinition: InputDefinition) =>
+    port => (knownValues: Map[String, WomValue],
+             ioFunctions: IoFunctionSet,
+             outputPortLookup: OutputPortLookup,
+             inputDefinition: InputDefinition
+    ) =>
       (outputPortLookup(port), inputDefinition) match {
         case (Valid(womValue), _) if isDefined(womValue) =>
           withInitializedValue(ioFunctions, womValue) {
@@ -39,32 +45,40 @@ object InputPointerToWomValue extends Poly1 {
           }
         case (_, OverridableInputDefinitionWithDefault(_, _, defaultExpression, valueMapper, _)) =>
           evaluateAndMap(defaultExpression, knownValues, valueMapper, ioFunctions)
-        case (_, OptionalInputDefinition(_, optionalType, valueMapper, _)) => valueMapper(ioFunctions)(optionalType.none)
+        case (_, OptionalInputDefinition(_, optionalType, valueMapper, _)) =>
+          valueMapper(ioFunctions)(optionalType.none)
         case _ => s"Failed to lookup input value for required input ${port.internalName}".invalidIOChecked
       }
   }
 
   @tailrec
-  private def isDefined(womValue: WomValue): Boolean = {
+  private def isDefined(womValue: WomValue): Boolean =
     womValue match {
       case WomOptionalValue(_, Some(innerWomValue)) => isDefined(innerWomValue)
       case WomOptionalValue(_, None) => false
       case _ => true
     }
-  }
 
   implicit def fromWomExpression: Case.Aux[WomExpression, ToWomValueFn] = at[WomExpression] {
-    womExpression => (knownValues: Map[String, WomValue], ioFunctions: IoFunctionSet, _: OutputPortLookup, inputDefinition: InputDefinition) =>
+    womExpression => (knownValues: Map[String, WomValue],
+                      ioFunctions: IoFunctionSet,
+                      _: OutputPortLookup,
+                      inputDefinition: InputDefinition
+    ) =>
       evaluateAndMap(womExpression, knownValues, inputDefinition.valueMapper, ioFunctions)
   }
 
-  def evaluate(womExpression: WomExpression, knownValues: Map[String, WomValue], ioFunctions: IoFunctionSet): ErrorOr[WomValue] =
+  def evaluate(womExpression: WomExpression,
+               knownValues: Map[String, WomValue],
+               ioFunctions: IoFunctionSet
+  ): ErrorOr[WomValue] =
     womExpression.evaluateValue(knownValues, ioFunctions)
 
   def evaluateAndMap(womExpression: WomExpression,
                      knownValues: Map[String, WomValue],
                      valueMapper: InputValueMapper,
-                     ioFunctions: IoFunctionSet): IOChecked[WomValue] = for {
+                     ioFunctions: IoFunctionSet
+  ): IOChecked[WomValue] = for {
     evaluated <- evaluate(womExpression, knownValues, ioFunctions).toIOChecked
     mapped <- valueMapper(ioFunctions)(evaluated)
   } yield mapped
diff --git a/wom/src/main/scala/wom/expression/IoFunctionSetAdapter.scala b/wom/src/main/scala/wom/expression/IoFunctionSetAdapter.scala
index 6695113c7de..475d6295045 100644
--- a/wom/src/main/scala/wom/expression/IoFunctionSetAdapter.scala
+++ b/wom/src/main/scala/wom/expression/IoFunctionSetAdapter.scala
@@ -2,7 +2,8 @@ package wom.expression
 
 class IoFunctionSetAdapter(delegate: IoFunctionSet) extends IoFunctionSet {
   override def pathFunctions = delegate.pathFunctions
-  override def readFile(path: String, maxBytes: Option[Int], failOnOverflow: Boolean) = delegate.readFile(path, maxBytes, failOnOverflow)
+  override def readFile(path: String, maxBytes: Option[Int], failOnOverflow: Boolean) =
+    delegate.readFile(path, maxBytes, failOnOverflow)
   override def writeFile(path: String, content: String) = delegate.writeFile(path, content)
   override def createTemporaryDirectory(name: Option[String]) = delegate.createTemporaryDirectory(name)
   override def copyFile(source: String, destination: String) = delegate.copyFile(source, destination)
@@ -11,5 +12,5 @@ class IoFunctionSetAdapter(delegate: IoFunctionSet) extends IoFunctionSet {
   override def listDirectory(path: String)(visited: Vector[String]) = delegate.listDirectory(path)(visited)
   override def isDirectory(path: String) = delegate.isDirectory(path)
   override def size(path: String) = delegate.size(path)
-  override implicit def ec  = delegate.ec
+  implicit override def ec = delegate.ec
 }
diff --git a/wom/src/main/scala/wom/expression/NoIoFunctionSet.scala b/wom/src/main/scala/wom/expression/NoIoFunctionSet.scala
index c10bb74b456..d99a3986b3b 100644
--- a/wom/src/main/scala/wom/expression/NoIoFunctionSet.scala
+++ b/wom/src/main/scala/wom/expression/NoIoFunctionSet.scala
@@ -11,32 +11,41 @@ object EmptyIoFunctionSet {
 }
 
 class EmptyIoFunctionSet extends IoFunctionSet {
-  override def readFile(path: String, maxBytes: Option[Int] = None, failOnOverflow: Boolean = false): Future[String] = Future.failed(new UnsupportedOperationException("readFile is not available here"))
+  override def readFile(path: String, maxBytes: Option[Int] = None, failOnOverflow: Boolean = false): Future[String] =
+    Future.failed(new UnsupportedOperationException("readFile is not available here"))
 
-  override def writeFile(path: String, content: String): Future[WomSingleFile] = {
+  override def writeFile(path: String, content: String): Future[WomSingleFile] =
     Future.failed(new UnsupportedOperationException("writeFile is not available here"))
-  }
 
-  override def copyFile(pathFrom: String, targetName: String): Future[WomSingleFile] = {
+  override def copyFile(pathFrom: String, targetName: String): Future[WomSingleFile] =
     throw new Exception("copyFile is not available here")
-  }
 
-  override def glob(pattern: String): Future[Seq[String]] = throw new UnsupportedOperationException("glob is not available here")
+  override def glob(pattern: String): Future[Seq[String]] = throw new UnsupportedOperationException(
+    "glob is not available here"
+  )
 
   override def listAllFilesUnderDirectory(dirPath: String): Nothing =
     throw new UnsupportedOperationException("listAllFilesUnderDirectory is not available here")
 
-  override def size(path: String): Future[Long] = Future.failed(new UnsupportedOperationException("size is not available here"))
+  override def size(path: String): Future[Long] =
+    Future.failed(new UnsupportedOperationException("size is not available here"))
 
-  override implicit def ec: ExecutionContext = EmptyIoFunctionSet.singleThreadEc
+  implicit override def ec: ExecutionContext = EmptyIoFunctionSet.singleThreadEc
   override def pathFunctions = NoPathFunctionSet
-  override def listDirectory(path: String)(visited: Vector[String] = Vector.empty) = throw new UnsupportedOperationException("listDirectory is not available here")
-  override def isDirectory(path: String): Future[Boolean] = throw new UnsupportedOperationException("isDirectory is not available here")
-  override def createTemporaryDirectory(name: Option[String]) = throw new UnsupportedOperationException("createTemporaryDirectory is not available here")
+  override def listDirectory(path: String)(visited: Vector[String] = Vector.empty) =
+    throw new UnsupportedOperationException("listDirectory is not available here")
+  override def isDirectory(path: String): Future[Boolean] = throw new UnsupportedOperationException(
+    "isDirectory is not available here"
+  )
+  override def createTemporaryDirectory(name: Option[String]) = throw new UnsupportedOperationException(
+    "createTemporaryDirectory is not available here"
+  )
 }
 
 class EmptyPathFunctionSet extends PathFunctionSet {
-  override def sibling(of: String, path: String) = throw new UnsupportedOperationException("sibling is not available here")
+  override def sibling(of: String, path: String) = throw new UnsupportedOperationException(
+    "sibling is not available here"
+  )
   override def isAbsolute(path: String) = false
   override def relativeToHostCallRoot(path: String) = path
   override def name(path: String) = throw new UnsupportedOperationException("name is not available here")
diff --git a/wom/src/main/scala/wom/expression/WomExpression.scala b/wom/src/main/scala/wom/expression/WomExpression.scala
index 50b66d57ebd..db950e654a4 100644
--- a/wom/src/main/scala/wom/expression/WomExpression.scala
+++ b/wom/src/main/scala/wom/expression/WomExpression.scala
@@ -30,7 +30,10 @@ trait WomExpression {
 
   def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType]
 
-  def evaluateFiles(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]]
+  def evaluateFiles(inputValues: Map[String, WomValue],
+                    ioFunctionSet: IoFunctionSet,
+                    coerceTo: WomType
+  ): ErrorOr[Set[FileEvaluation]]
 
   /** Returns `true` if all file types within the specified `WomType` are optional. If not all the file types are
     * optional, return `false` since the current file evaluation structure doesn't allow for mapping individual
@@ -39,10 +42,12 @@ trait WomExpression {
     def innerAreAllFileTypesInWomTypeOptional(womType: WomType): Boolean = womType match {
       case WomOptionalType(_: WomPrimitiveFileType) => true
       case _: WomPrimitiveFileType => false
-      case _: WomPrimitiveType => true // WomPairTypes and WomCompositeTypes may have non-File components here which is fine.
+      case _: WomPrimitiveType =>
+        true // WomPairTypes and WomCompositeTypes may have non-File components here which is fine.
       case WomArrayType(inner) => innerAreAllFileTypesInWomTypeOptional(inner)
       case WomMapType(_, inner) => innerAreAllFileTypesInWomTypeOptional(inner)
-      case WomPairType(leftType, rightType) => innerAreAllFileTypesInWomTypeOptional(leftType) && innerAreAllFileTypesInWomTypeOptional(rightType)
+      case WomPairType(leftType, rightType) =>
+        innerAreAllFileTypesInWomTypeOptional(leftType) && innerAreAllFileTypesInWomTypeOptional(rightType)
       case WomCompositeType(typeMap, _) => typeMap.values.forall(innerAreAllFileTypesInWomTypeOptional)
       case _ => false
     }
@@ -60,9 +65,13 @@ trait WomExpression {
   */
 final case class ValueAsAnExpression(value: WomValue) extends WomExpression {
   override def sourceString: String = value.valueString
-  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] = Valid(value)
+  override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] =
+    Valid(value)
   override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] = Valid(value.womType)
-  override def evaluateFiles(inputTypes: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] = Valid(Set.empty)
+  override def evaluateFiles(inputTypes: Map[String, WomValue],
+                             ioFunctionSet: IoFunctionSet,
+                             coerceTo: WomType
+  ): ErrorOr[Set[FileEvaluation]] = Valid(Set.empty)
   override val inputs: Set[String] = Set.empty
 }
 
@@ -70,6 +79,7 @@ final case class ValueAsAnExpression(value: WomValue) extends WomExpression {
   * Functions only requiring path manipulation and NO I/O
   */
 trait PathFunctionSet {
+
   /**
     * Similar to java.nio.Path.resolveSibling with
     * of == a string representation of a java.nio.Path
@@ -84,7 +94,8 @@ trait PathFunctionSet {
   /**
     * Similar to sibling only if "of" IS an absolute path and "other" IS NOT an absolute path, otherwise return other
     */
-  def absoluteSibling(of: String, other: String): String = if (isAbsolute(of) && !isAbsolute(other)) sibling(of, other) else other
+  def absoluteSibling(of: String, other: String): String =
+    if (isAbsolute(of) && !isAbsolute(other)) sibling(of, other) else other
 
   /**
     * If path is relative, prefix it with the _host_ call root.
@@ -108,6 +119,7 @@ trait PathFunctionSet {
 }
 
 object IoFunctionSet {
+
   /**
     * Simple wrapper class providing information on whether a path is a File or a Directory
     * Avoids repeated calls to isDirectory.
@@ -187,7 +199,7 @@ trait IoFunctionSet {
     * To map/flatMap over IO results
     */
   implicit def ec: ExecutionContext
-  
+
   implicit def cs = IO.contextShift(ec)
 
   /**
diff --git a/wom/src/main/scala/wom/format/MemorySize.scala b/wom/src/main/scala/wom/format/MemorySize.scala
index c9ac793f661..22934ae7cbf 100644
--- a/wom/src/main/scala/wom/format/MemorySize.scala
+++ b/wom/src/main/scala/wom/format/MemorySize.scala
@@ -11,11 +11,10 @@ import wdl4s.parser.MemoryUnit
 import scala.language.postfixOps
 import scala.util.{Failure, Success, Try}
 
-
 object MemorySize {
   val memoryPattern = """(\d+(?:\.\d+)?)\s*(\w+)""".r
 
-  def parse(unparsed: String): Try[MemorySize] = {
+  def parse(unparsed: String): Try[MemorySize] =
     unparsed match {
       case memoryPattern(amountString, unitString) =>
         val amount: ErrorOr[Double] = amountString.parseDouble leftMap {
@@ -31,9 +30,11 @@ object MemorySize {
           case Valid(memorySize) => Success(memorySize)
           case Invalid(nel) => Failure(new UnsupportedOperationException(nel.toList.mkString("\n")))
         }
-      case _ => Failure(new UnsupportedOperationException(s"$unparsed should be of the form 'X Unit' where X is a number, e.g. 8 GB"))
+      case _ =>
+        Failure(
+          new UnsupportedOperationException(s"$unparsed should be of the form 'X Unit' where X is a number, e.g. 8 GB")
+        )
     }
-  }
 }
 
 case class MemorySize(amount: Double, unit: MemoryUnit) {
diff --git a/wom/src/main/scala/wom/graph/CallNode.scala b/wom/src/main/scala/wom/graph/CallNode.scala
index 088b242af1c..2b67229a9fe 100644
--- a/wom/src/main/scala/wom/graph/CallNode.scala
+++ b/wom/src/main/scala/wom/graph/CallNode.scala
@@ -38,44 +38,57 @@ sealed abstract class CallNode extends GraphNode {
   val sourceLocation: Option[SourceFileLocation]
 }
 
-final case class ExpressionCallNode private(override val identifier: WomIdentifier,
-                                            callable: ExpressionTaskDefinition,
-                                            override val inputPorts: Set[GraphNodePort.InputPort],
-                                            inputDefinitionMappings: InputDefinitionMappings,
-                                            outputIdentifierCompoundingFunction: (WomIdentifier, String) => WomIdentifier,
-                                            override val sourceLocation : Option[SourceFileLocation]) extends CallNode with ExpressionNodeLike {
+final case class ExpressionCallNode private (
+  override val identifier: WomIdentifier,
+  callable: ExpressionTaskDefinition,
+  override val inputPorts: Set[GraphNodePort.InputPort],
+  inputDefinitionMappings: InputDefinitionMappings,
+  outputIdentifierCompoundingFunction: (WomIdentifier, String) => WomIdentifier,
+  override val sourceLocation: Option[SourceFileLocation]
+) extends CallNode
+    with ExpressionNodeLike {
   val callType: String = "expression task"
-  lazy val expressionBasedOutputPorts: List[ExpressionBasedOutputPort] = {
-    callable.outputs.map(o => ExpressionBasedOutputPort(outputIdentifierCompoundingFunction(identifier, o.localName.value), o.womType, this, o.expression))
-  }
+  lazy val expressionBasedOutputPorts: List[ExpressionBasedOutputPort] =
+    callable.outputs.map(o =>
+      ExpressionBasedOutputPort(outputIdentifierCompoundingFunction(identifier, o.localName.value),
+                                o.womType,
+                                this,
+                                o.expression
+      )
+    )
 
   override lazy val outputPorts: Set[OutputPort] = expressionBasedOutputPorts.toSet[OutputPort]
 
-  override def evaluate(outputPortLookup: OutputPort => ErrorOr[WomValue], ioFunctionSet: IoFunctionSet) = {
+  override def evaluate(outputPortLookup: OutputPort => ErrorOr[WomValue], ioFunctionSet: IoFunctionSet) =
     for {
       // Evaluate the inputs to get a lookup to evaluate the actual expression
       womEvaluatedInputs <- CallNode.resolveAndEvaluateInputs(this, ioFunctionSet, outputPortLookup).toEither
       // Make a usable lookup
-      lookup = womEvaluatedInputs.map({ case (inputDefinition, value) => inputDefinition.name -> value })
+      lookup = womEvaluatedInputs.map { case (inputDefinition, value) => inputDefinition.name -> value }
       // Evaluate the expression
       evaluated <- callable.evaluate(lookup, ioFunctionSet, expressionBasedOutputPorts)
     } yield evaluated
-  }
 
   override val nonInputBasedPrerequisites = Set.empty
 }
 
-final case class CommandCallNode private(override val identifier: WomIdentifier,
-                                         callable: CommandTaskDefinition,
-                                         override val inputPorts: Set[GraphNodePort.InputPort],
-                                         inputDefinitionMappings: InputDefinitionMappings,
-                                         override val nonInputBasedPrerequisites: Set[GraphNode],
-                                         outputIdentifierCompoundingFunction: (WomIdentifier, String) => WomIdentifier,
-                                         override val sourceLocation : Option[SourceFileLocation]) extends CallNode {
+final case class CommandCallNode private (override val identifier: WomIdentifier,
+                                          callable: CommandTaskDefinition,
+                                          override val inputPorts: Set[GraphNodePort.InputPort],
+                                          inputDefinitionMappings: InputDefinitionMappings,
+                                          override val nonInputBasedPrerequisites: Set[GraphNode],
+                                          outputIdentifierCompoundingFunction: (WomIdentifier, String) => WomIdentifier,
+                                          override val sourceLocation: Option[SourceFileLocation]
+) extends CallNode {
   val callType: String = "task"
-  lazy val expressionBasedOutputPorts: List[ExpressionBasedOutputPort] = {
-    callable.outputs.map(o => ExpressionBasedOutputPort(outputIdentifierCompoundingFunction(identifier, o.localName.value), o.womType, this, o.expression))
-  }
+  lazy val expressionBasedOutputPorts: List[ExpressionBasedOutputPort] =
+    callable.outputs.map(o =>
+      ExpressionBasedOutputPort(outputIdentifierCompoundingFunction(identifier, o.localName.value),
+                                o.womType,
+                                this,
+                                o.expression
+      )
+    )
 
   override lazy val outputPorts: Set[OutputPort] = expressionBasedOutputPorts.toSet[OutputPort]
 
@@ -83,27 +96,30 @@ final case class CommandCallNode private(override val identifier: WomIdentifier,
     * Evaluate outputs using the custom evaluation function of the task definition.
     * An empty return value means the engine should fall back to its default evaluation method.
     */
-  def customOutputEvaluation(inputs: Map[String, WomValue], ioFunctionSet: IoFunctionSet, executionContext: ExecutionContext): OutputFunctionResponse = {
+  def customOutputEvaluation(inputs: Map[String, WomValue],
+                             ioFunctionSet: IoFunctionSet,
+                             executionContext: ExecutionContext
+  ): OutputFunctionResponse =
     callable.customizedOutputEvaluation(outputPorts, inputs, ioFunctionSet, executionContext)
-  }
 }
 
-final case class WorkflowCallNode private (override val identifier: WomIdentifier,
-                                           callable: WorkflowDefinition,
-                                           override val inputPorts: Set[GraphNodePort.InputPort],
-                                           inputDefinitionMappings: InputDefinitionMappings,
-                                           override val nonInputBasedPrerequisites: Set[GraphNode],
-                                           outputIdentifierCompoundingFunction: (WomIdentifier, String) => WomIdentifier,
-                                           override val sourceLocation: Option[SourceFileLocation]) extends CallNode {
+final case class WorkflowCallNode private (
+  override val identifier: WomIdentifier,
+  callable: WorkflowDefinition,
+  override val inputPorts: Set[GraphNodePort.InputPort],
+  inputDefinitionMappings: InputDefinitionMappings,
+  override val nonInputBasedPrerequisites: Set[GraphNode],
+  outputIdentifierCompoundingFunction: (WomIdentifier, String) => WomIdentifier,
+  override val sourceLocation: Option[SourceFileLocation]
+) extends CallNode {
   val callType: String = "workflow"
-  val subworkflowCallOutputPorts: Set[SubworkflowCallOutputPort] = {
-    callable.innerGraph.nodes.collect { case gon: GraphOutputNode => SubworkflowCallOutputPort(outputIdentifierCompoundingFunction(identifier, gon.localName), gon, this) }
-  }
+  val subworkflowCallOutputPorts: Set[SubworkflowCallOutputPort] =
+    callable.innerGraph.nodes.collect { case gon: GraphOutputNode =>
+      SubworkflowCallOutputPort(outputIdentifierCompoundingFunction(identifier, gon.localName), gon, this)
+    }
   override val outputPorts: Set[OutputPort] = subworkflowCallOutputPorts.toSet[OutputPort]
 }
 
-
-
 object TaskCall {
   def graphFromDefinition(taskDefinition: TaskDefinition): ErrorOr[Graph] = {
     val taskDefinitionLocalName = LocalName(taskDefinition.name)
@@ -119,12 +135,14 @@ object TaskCall {
 
     val callNodeBuilder = new CallNodeBuilder()
 
-    val inputDefinitionFold = taskDefinition.inputs.foldMap({ inputDef =>
-    {
+    val inputDefinitionFold = taskDefinition.inputs.foldMap { inputDef =>
       val newNode: Option[ExternalGraphInputNode] = inputDef match {
-        case RequiredInputDefinition(name, womType, valueMapper, _) => Some(RequiredGraphInputNode(identifier(name), womType, name.value, valueMapper))
-        case OverridableInputDefinitionWithDefault(name, womType, default, valueMapper, _) => Some(OptionalGraphInputNodeWithDefault(identifier(name), womType, default, name.value, valueMapper))
-        case OptionalInputDefinition(name, womType, valueMapper, _) => Some(OptionalGraphInputNode(identifier(name), womType, name.value, valueMapper))
+        case RequiredInputDefinition(name, womType, valueMapper, _) =>
+          Some(RequiredGraphInputNode(identifier(name), womType, name.value, valueMapper))
+        case OverridableInputDefinitionWithDefault(name, womType, default, valueMapper, _) =>
+          Some(OptionalGraphInputNodeWithDefault(identifier(name), womType, default, name.value, valueMapper))
+        case OptionalInputDefinition(name, womType, valueMapper, _) =>
+          Some(OptionalGraphInputNode(identifier(name), womType, name.value, valueMapper))
         case _: FixedInputDefinitionWithDefault => None
       }
 
@@ -138,15 +156,26 @@ object TaskCall {
         case None => InputDefinitionFold() // No-op
       }
 
-    }
-    })(inputDefinitionFoldMonoid)
+    }(inputDefinitionFoldMonoid)
 
     val uniqueIdentifier = WomIdentifier(taskDefinition.name)
-    val callWithInputs = callNodeBuilder.build(uniqueIdentifier, taskDefinition, inputDefinitionFold, Set.empty, taskDefinition.sourceLocation)
-
-    val outputNodes: ErrorOr[Seq[GraphOutputNode]] = callWithInputs.node.outputPorts.map(output => PortBasedGraphOutputNode(
-      identifier(LocalName(output.internalName)), output.womType, output
-    )).toList.validNel
+    val callWithInputs = callNodeBuilder.build(uniqueIdentifier,
+                                               taskDefinition,
+                                               inputDefinitionFold,
+                                               Set.empty,
+                                               taskDefinition.sourceLocation
+    )
+
+    val outputNodes: ErrorOr[Seq[GraphOutputNode]] = callWithInputs.node.outputPorts
+      .map(output =>
+        PortBasedGraphOutputNode(
+          identifier(LocalName(output.internalName)),
+          output.womType,
+          output
+        )
+      )
+      .toList
+      .validNel
     val result = for {
       outputs <- outputNodes
       callSet = Set[GraphNode](callWithInputs.node)
@@ -162,30 +191,38 @@ object TaskCall {
 object CallNode {
   def resolveAndEvaluateInputs(callNode: CallNode,
                                expressionLanguageFunctions: IoFunctionSet,
-                               outputStoreLookup: OutputPort => ErrorOr[WomValue]): ErrorOr[WomEvaluatedCallInputs] = {
-    callNode.inputDefinitionMappings.foldLeft(Map.empty[InputDefinition, ErrorOr[WomValue]]) {
-      case (accumulatedInputsSoFar, (inputDefinition, pointer)) =>
-        // We could have a commons method for this kind of "filtering valid values"
-        val validInputsAccumulated: Map[String, WomValue] = accumulatedInputsSoFar.collect({
-          case (input, Valid(errorOrWdlValue)) => input.name -> errorOrWdlValue
-        })
-
-        val coercedValue = pointer.fold(InputPointerToWomValue).apply(
-          validInputsAccumulated, expressionLanguageFunctions, outputStoreLookup, inputDefinition
-        ) flatMap(inputDefinition.womType.coerceRawValue(_).toIOChecked)
-
-        val contextualizedValue = coercedValue.contextualizeErrors(s"evaluate input '${inputDefinition.localName.value}'")
-
-        accumulatedInputsSoFar + (inputDefinition -> contextualizedValue.toErrorOr)
-    }.sequence
-  }
+                               outputStoreLookup: OutputPort => ErrorOr[WomValue]
+  ): ErrorOr[WomEvaluatedCallInputs] =
+    callNode.inputDefinitionMappings
+      .foldLeft(Map.empty[InputDefinition, ErrorOr[WomValue]]) {
+        case (accumulatedInputsSoFar, (inputDefinition, pointer)) =>
+          // We could have a commons method for this kind of "filtering valid values"
+          val validInputsAccumulated: Map[String, WomValue] = accumulatedInputsSoFar.collect {
+            case (input, Valid(errorOrWdlValue)) => input.name -> errorOrWdlValue
+          }
+
+          val coercedValue = pointer
+            .fold(InputPointerToWomValue)
+            .apply(
+              validInputsAccumulated,
+              expressionLanguageFunctions,
+              outputStoreLookup,
+              inputDefinition
+            ) flatMap (inputDefinition.womType.coerceRawValue(_).toIOChecked)
+
+          val contextualizedValue =
+            coercedValue.contextualizeErrors(s"evaluate input '${inputDefinition.localName.value}'")
+
+          accumulatedInputsSoFar + (inputDefinition -> contextualizedValue.toErrorOr)
+      }
+      .sequence
 
   /* A monoid can't be derived automatically for this class because it contains a Map[InputDefinition, InputDefinitionPointer],
    * and there's no monoid defined over InputDefinitionPointer
    */
   implicit val inputDefinitionFoldMonoid = new Monoid[InputDefinitionFold] {
     override def empty: InputDefinitionFold = InputDefinitionFold()
-    override def combine(x: InputDefinitionFold, y: InputDefinitionFold): InputDefinitionFold = {
+    override def combine(x: InputDefinitionFold, y: InputDefinitionFold): InputDefinitionFold =
       InputDefinitionFold(
         mappings = x.mappings ++ y.mappings,
         callInputPorts = x.callInputPorts ++ y.callInputPorts,
@@ -193,14 +230,14 @@ object CallNode {
         newExpressionNodes = x.newExpressionNodes ++ y.newExpressionNodes,
         usedOuterGraphInputNodes = x.usedOuterGraphInputNodes ++ y.usedOuterGraphInputNodes
       )
-    }
   }
 
   final case class InputDefinitionFold(mappings: InputDefinitionMappings = List.empty,
                                        callInputPorts: Set[InputPort] = Set.empty,
                                        newGraphInputNodes: Set[ExternalGraphInputNode] = Set.empty,
                                        newExpressionNodes: Set[ExpressionNode] = Set.empty,
-                                       usedOuterGraphInputNodes: Set[OuterGraphInputNode] = Set.empty)
+                                       usedOuterGraphInputNodes: Set[OuterGraphInputNode] = Set.empty
+  )
 
   type InputDefinitionPointer = OutputPort :+: WomExpression :+: WomValue :+: CNil
   // This is a List rather than Map because the order of 'InputDefinition's is important:
@@ -209,7 +246,8 @@ object CallNode {
   final case class CallNodeAndNewNodes(node: CallNode,
                                        newInputs: Set[ExternalGraphInputNode],
                                        newExpressions: Set[ExpressionNode],
-                                       override val usedOuterGraphInputNodes: Set[OuterGraphInputNode]) extends GeneratedNodeAndNewNodes
+                                       override val usedOuterGraphInputNodes: Set[OuterGraphInputNode]
+  ) extends GeneratedNodeAndNewNodes
 
   /**
     * Don't use this directly; go via callWithInputs to make sure everything's in order when constructing a CallNode.
@@ -220,10 +258,34 @@ object CallNode {
                            inputDefinitionMappings: InputDefinitionMappings,
                            mustFollow: Set[GraphNode],
                            outputIdentifierCompoundingFunction: (WomIdentifier, String) => WomIdentifier,
-                           sourceLocation : Option[SourceFileLocation]): CallNode = callable match {
-    case t: CommandTaskDefinition => CommandCallNode(nodeIdentifier, t, inputPorts, inputDefinitionMappings, mustFollow, outputIdentifierCompoundingFunction, sourceLocation)
-    case w: WorkflowDefinition => WorkflowCallNode(nodeIdentifier, w, inputPorts, inputDefinitionMappings, mustFollow, outputIdentifierCompoundingFunction, sourceLocation)
-    case w: ExpressionTaskDefinition => ExpressionCallNode(nodeIdentifier, w, inputPorts, inputDefinitionMappings, outputIdentifierCompoundingFunction, sourceLocation)
+                           sourceLocation: Option[SourceFileLocation]
+  ): CallNode = callable match {
+    case t: CommandTaskDefinition =>
+      CommandCallNode(nodeIdentifier,
+                      t,
+                      inputPorts,
+                      inputDefinitionMappings,
+                      mustFollow,
+                      outputIdentifierCompoundingFunction,
+                      sourceLocation
+      )
+    case w: WorkflowDefinition =>
+      WorkflowCallNode(nodeIdentifier,
+                       w,
+                       inputPorts,
+                       inputDefinitionMappings,
+                       mustFollow,
+                       outputIdentifierCompoundingFunction,
+                       sourceLocation
+      )
+    case w: ExpressionTaskDefinition =>
+      ExpressionCallNode(nodeIdentifier,
+                         w,
+                         inputPorts,
+                         inputDefinitionMappings,
+                         outputIdentifierCompoundingFunction,
+                         sourceLocation
+      )
   }
 
   /**
@@ -237,24 +299,34 @@ object CallNode {
       * Makes an input port for this call.
       * Ensures that the port will contain the reference to the node when it gets created.
       */
-    def makeInputPort(inputDefinition: InputDefinition, outputPort: OutputPort) = {
+    def makeInputPort(inputDefinition: InputDefinition, outputPort: OutputPort) =
       ConnectedInputPort(inputDefinition.name, inputDefinition.womType, outputPort, graphNodeSetter.get)
-    }
 
     def build(nodeIdentifier: WomIdentifier,
               callable: Callable,
               inputDefinitionFold: InputDefinitionFold,
               mustFollow: Set[GraphNode],
               sourceLocation: Option[SourceFileLocation],
-              outputIdentifierCompoundingFunction: (WomIdentifier, String) => WomIdentifier = defaultOutputIdentifierCompounder
-             ): CallNodeAndNewNodes = {
-      val callNode = CallNode(nodeIdentifier, callable, inputDefinitionFold.callInputPorts, inputDefinitionFold.mappings, mustFollow, outputIdentifierCompoundingFunction, sourceLocation)
+              outputIdentifierCompoundingFunction: (WomIdentifier, String) => WomIdentifier =
+                defaultOutputIdentifierCompounder
+    ): CallNodeAndNewNodes = {
+      val callNode = CallNode(nodeIdentifier,
+                              callable,
+                              inputDefinitionFold.callInputPorts,
+                              inputDefinitionFold.mappings,
+                              mustFollow,
+                              outputIdentifierCompoundingFunction,
+                              sourceLocation
+      )
       graphNodeSetter._graphNode = callNode
-      CallNodeAndNewNodes(callNode, inputDefinitionFold.newGraphInputNodes, inputDefinitionFold.newExpressionNodes, inputDefinitionFold.usedOuterGraphInputNodes)
+      CallNodeAndNewNodes(callNode,
+                          inputDefinitionFold.newGraphInputNodes,
+                          inputDefinitionFold.newExpressionNodes,
+                          inputDefinitionFold.usedOuterGraphInputNodes
+      )
     }
 
-    def defaultOutputIdentifierCompounder(callIdentifier: WomIdentifier, outputName: String): WomIdentifier = {
+    def defaultOutputIdentifierCompounder(callIdentifier: WomIdentifier, outputName: String): WomIdentifier =
       callIdentifier.combine(outputName)
-    }
   }
 }
diff --git a/wom/src/main/scala/wom/graph/ConditionalNode.scala b/wom/src/main/scala/wom/graph/ConditionalNode.scala
index 7faa2c38189..cabf64ff45f 100644
--- a/wom/src/main/scala/wom/graph/ConditionalNode.scala
+++ b/wom/src/main/scala/wom/graph/ConditionalNode.scala
@@ -13,23 +13,29 @@ import common.collections.EnhancedCollections._
   * @param conditionExpression The (boolean) expression on which the conditional is predicated.
   * @param conditionalOutputPorts Output ports for the conditional node which link back to GraphOutputNodes of the inner graph.
   */
-final case class ConditionalNode private(override val innerGraph: Graph,
-                                         conditionExpression: ExpressionNode,
-                                         conditionalOutputPorts: Set[ConditionalOutputPort]) extends GraphNode with GraphNodeWithInnerGraph {
+final case class ConditionalNode private (override val innerGraph: Graph,
+                                          conditionExpression: ExpressionNode,
+                                          conditionalOutputPorts: Set[ConditionalOutputPort]
+) extends GraphNode
+    with GraphNodeWithInnerGraph {
 
   override val identifier: WomIdentifier = WomIdentifier("ConditionalNode")
 
-  override val inputPorts: Set[InputPort] = Set(ConnectedInputPort("condition", WomBooleanType, conditionExpression.singleOutputPort, _ => this))
+  override val inputPorts: Set[InputPort] = Set(
+    ConnectedInputPort("condition", WomBooleanType, conditionExpression.singleOutputPort, _ => this)
+  )
   override val outputPorts: Set[GraphNodePort.OutputPort] = conditionalOutputPorts.toSet[OutputPort]
 }
 
-object ConditionalNode  {
+object ConditionalNode {
 
   final case class ConditionalNodeWithNewNodes(node: ConditionalNode) extends GeneratedNodeAndNewNodes {
     override val newInputs = node.innerGraph.externalInputNodes
     override val usedOuterGraphInputNodes =
       (node.conditionExpression.upstream.filterByType[OuterGraphInputNode]: Set[OuterGraphInputNode]) ++
-        (node.innerGraph.outerGraphInputNodes.map(_.linkToOuterGraphNode).filterByType[OuterGraphInputNode]: Set[OuterGraphInputNode])
+        (node.innerGraph.outerGraphInputNodes
+          .map(_.linkToOuterGraphNode)
+          .filterByType[OuterGraphInputNode]: Set[OuterGraphInputNode])
 
     override val newExpressions = Set(node.conditionExpression)
   }
diff --git a/wom/src/main/scala/wom/graph/Graph.scala b/wom/src/main/scala/wom/graph/Graph.scala
index 8ebf4e9f20e..b5c08ac5e4e 100644
--- a/wom/src/main/scala/wom/graph/Graph.scala
+++ b/wom/src/main/scala/wom/graph/Graph.scala
@@ -53,19 +53,26 @@ object Graph {
 
     def upstreamNodeInGraph(port: InputPort): ErrorOr[Unit] = {
       val upstreamOutputPort = port.upstream
-      boolToErrorOr(nodes.exists(_ eq upstreamOutputPort.graphNode), s"The input link ${port.name} on ${port.graphNode.localName} is linked to a node outside the graph set (${upstreamOutputPort.name})")
+      boolToErrorOr(
+        nodes.exists(_ eq upstreamOutputPort.graphNode),
+        s"The input link ${port.name} on ${port.graphNode.localName} is linked to a node outside the graph set (${upstreamOutputPort.name})"
+      )
     }
 
-    def portProperlyEmbedded(port: GraphNodePort, portFinder: GraphNode => Set[_ <: GraphNodePort]): ErrorOr[Unit] = {
-      boolToErrorOr(portFinder(port.graphNode).exists(_ eq port), s"The port ${port.name} thinks it belongs to a Node (${port.graphNode}), but that Node doesn't think it owns it.")
-    }
+    def portProperlyEmbedded(port: GraphNodePort, portFinder: GraphNode => Set[_ <: GraphNodePort]): ErrorOr[Unit] =
+      boolToErrorOr(
+        portFinder(port.graphNode).exists(_ eq port),
+        s"The port ${port.name} thinks it belongs to a Node (${port.graphNode}), but that Node doesn't think it owns it."
+      )
 
-    def outerGraphInputNodePointsHere(ogin: OuterGraphInputNode): ErrorOr[Unit] = {
-      boolToErrorOr(nodes.contains(ogin.linkToOuterGraph.graphNode), s"The OuterGraphInputNode ${ogin.identifier} does not link into the outer graph")
-    }
+    def outerGraphInputNodePointsHere(ogin: OuterGraphInputNode): ErrorOr[Unit] =
+      boolToErrorOr(nodes.contains(ogin.linkToOuterGraph.graphNode),
+                    s"The OuterGraphInputNode ${ogin.identifier} does not link into the outer graph"
+      )
 
     def validateInnerNodes(node: GraphNode): ErrorOr[Unit] = node match {
-      case g: GraphNodeWithInnerGraph => g.innerGraph.nodes.filterByType[OuterGraphInputNode].toList.traverse(outerGraphInputNodePointsHere).void
+      case g: GraphNodeWithInnerGraph =>
+        g.innerGraph.nodes.filterByType[OuterGraphInputNode].toList.traverse(outerGraphInputNodePointsHere).void
       case _ => ().validNel
     }
 
@@ -77,26 +84,29 @@ object Graph {
       (upstreamNodeValidation, inputPortEmbeddedValidation, upstreamPortEmbeddedValidation).tupled.void
     }
 
-    def validateNode(node: GraphNode): ErrorOr[Unit] = {
+    def validateNode(node: GraphNode): ErrorOr[Unit] =
       (node.inputPorts.toList.traverse(goodLink), validateInnerNodes(node)).tupled.void
-    }
 
     // from https://stackoverflow.com/a/24729587/1498572
     def fqnUniqueness: ErrorOr[Unit] = nodes
-      .collect({
+      .collect {
         case callNode: CallNode => callNode
         case gin: GraphInputNode => gin
         case gon: GraphOutputNode => gon
-      })
+      }
       .toList // Important since nodes is a Set, we don't want duplicates to disappear automatically when mapping to FQN
       .map(_.identifier.fullyQualifiedName)
       .groupBy(identity)
-      .collect({
+      .collect {
         case (fqn, list) if list.lengthCompare(1) > 0 => fqn
-      }).toList match {
+      }
+      .toList match {
       case Nil => ().validNel
       case head :: tail =>
-        NonEmptyList.of(head, tail: _*).map(fqn => s"Two or more nodes have the same FullyQualifiedName: ${fqn.value}").invalid
+        NonEmptyList
+          .of(head, tail: _*)
+          .map(fqn => s"Two or more nodes have the same FullyQualifiedName: ${fqn.value}")
+          .invalid
     }
 
     (fqnUniqueness, nodes.toList.traverse(validateNode)) mapN { case (_, _) =>
diff --git a/wom/src/main/scala/wom/graph/GraphInputNode.scala b/wom/src/main/scala/wom/graph/GraphInputNode.scala
index 211f7ae2202..d6faaa31bf8 100644
--- a/wom/src/main/scala/wom/graph/GraphInputNode.scala
+++ b/wom/src/main/scala/wom/graph/GraphInputNode.scala
@@ -16,6 +16,7 @@ sealed trait GraphInputNode extends GraphNodeWithSingleOutputPort {
 }
 
 sealed trait ExternalGraphInputNode extends GraphInputNode {
+
   /**
     * The fully qualified name should be the same as the one we expect the key in the input file to have.
     * e.g in WDL:
@@ -46,37 +47,49 @@ sealed trait ExternalGraphInputNode extends GraphInputNode {
     * Key that should be looked for in the input set to satisfy this EGIN
     */
   def nameInInputSet: String
-  
+
   def valueMapper: InputValueMapper
 }
 
 final case class RequiredGraphInputNode(override val identifier: WomIdentifier,
                                         womType: WomType,
                                         nameInInputSet: String,
-                                        valueMapper: InputValueMapper = Callable.InputDefinition.IdentityValueMapper) extends ExternalGraphInputNode
+                                        valueMapper: InputValueMapper = Callable.InputDefinition.IdentityValueMapper
+) extends ExternalGraphInputNode
 
 final case class OptionalGraphInputNode(override val identifier: WomIdentifier,
                                         womType: WomOptionalType,
                                         nameInInputSet: String,
-                                        valueMapper: InputValueMapper = Callable.InputDefinition.IdentityValueMapper) extends ExternalGraphInputNode
+                                        valueMapper: InputValueMapper = Callable.InputDefinition.IdentityValueMapper
+) extends ExternalGraphInputNode
 
 // If we want to allow defaults to be "complex" expressions with dependencies we may need to make it an InstantiatedExpression here instead
 final case class OptionalGraphInputNodeWithDefault(override val identifier: WomIdentifier,
                                                    womType: WomType,
                                                    default: WomExpression,
                                                    nameInInputSet: String,
-                                                   valueMapper: InputValueMapper = Callable.InputDefinition.IdentityValueMapper) extends ExternalGraphInputNode
+                                                   valueMapper: InputValueMapper =
+                                                     Callable.InputDefinition.IdentityValueMapper
+) extends ExternalGraphInputNode
 
 object OuterGraphInputNode {
-  def apply(forIdentifier: WomIdentifier, linkToOuterGraph: GraphNodePort.OutputPort, preserveScatterIndex: Boolean): OuterGraphInputNode = {
-    new OuterGraphInputNode(forIdentifier.copy(fullyQualifiedName = forIdentifier.fullyQualifiedName.prefixWith("^")), linkToOuterGraph, preserveScatterIndex)
-  }
+  def apply(forIdentifier: WomIdentifier,
+            linkToOuterGraph: GraphNodePort.OutputPort,
+            preserveScatterIndex: Boolean
+  ): OuterGraphInputNode =
+    new OuterGraphInputNode(forIdentifier.copy(fullyQualifiedName = forIdentifier.fullyQualifiedName.prefixWith("^")),
+                            linkToOuterGraph,
+                            preserveScatterIndex
+    )
 }
 
 /**
   * Used to represent an input to any GraphNode's inner graph which is a link to a value somewhere in the outer graph.
   */
-class OuterGraphInputNode protected(override val identifier: WomIdentifier, val linkToOuterGraph: GraphNodePort.OutputPort, val preserveScatterIndex: Boolean) extends GraphInputNode {
+class OuterGraphInputNode protected (override val identifier: WomIdentifier,
+                                     val linkToOuterGraph: GraphNodePort.OutputPort,
+                                     val preserveScatterIndex: Boolean
+) extends GraphInputNode {
   override def womType: WomType = linkToOuterGraph.womType
   override lazy val singleOutputPort: GraphNodeOutputPort = GraphNodeOutputPort(identifier, womType, this)
   lazy val linkToOuterGraphNode = linkToOuterGraph.graphNode
@@ -92,58 +105,59 @@ class OuterGraphInputNode protected(override val identifier: WomIdentifier, val
   */
 final case class ScatterVariableNode(override val identifier: WomIdentifier,
                                      scatterExpressionNode: ExpressionNode,
-                                     override val womType: WomType) extends OuterGraphInputNode(identifier, scatterExpressionNode.singleOutputPort, preserveScatterIndex = true) {
+                                     override val womType: WomType
+) extends OuterGraphInputNode(identifier, scatterExpressionNode.singleOutputPort, preserveScatterIndex = true) {
   /*
-    * This is the key element of the indexForShard function.
-    * Here is an example:
-    * Let's say we're scattering over 3 arrays of size 2, 3, and 2 respectively, using a cross product.
-    * We will then have 2 * 3 * 2 = 12 shards
-    * 
-    * The possible combinations of input indices are
-    * 
-    * Shard #0: (0, 0, 0)
-    * Shard #1: (0, 0, 1)
-    * Shard #2: (0, 1, 0)
-    * Shard #3: (0, 1, 1)
-    * Shard #4: (0, 2, 0)
-    * Shard #5: (0, 2, 1)
-    * Shard #6: (1, 0, 0)
-    * Shard #7: (1, 0, 1)
-    * Shard #8: (1, 1, 0)
-    * Shard #9: (1, 1, 1)
-    * Shard #10: (1, 2, 0)
-    * Shard #11: (1, 2, 1)
-    * 
-    * We will also have 3 SVNs, one for each array.
-    * Each SVN needs to output one column of the above "matrix", based on the shard number
-    * 
-    * For SVN 1:          For SVN 2:        For SVN 3:
-    *   0 -> 0              0 -> 0            0 -> 0
-    *   1 -> 0              1 -> 0            1 -> 1
-    *   2 -> 0              2 -> 1            2 -> 0
-    *   3 -> 0              3 -> 1            3 -> 1
-    *   4 -> 0              4 -> 2            4 -> 0
-    *   5 -> 0              5 -> 2            5 -> 1
-    *   6 -> 1              6 -> 0            6 -> 0
-    *   7 -> 1              7 -> 0            7 -> 1
-    *   8 -> 1              8 -> 1            8 -> 0
-    *   9 -> 1              9 -> 1            9 -> 1
-    *   10 -> 1             10 -> 2           10 -> 0
-    *   11 -> 1             11 -> 2           11 -> 1
-    *   
-    *  shard / 6         (shard / 2) % 3     shard % 2
-    *  
-    *  This can be generalized to (shard / relativeIndexLength) % arraySize
-    *  where 
-    *   - shard is the shard index as an Int
-    *   - relativeIndexLength is the number of possible combinations for the arrays on the "right" of this variable
-    *   - arraySize is the size of the array for this variable
-    *   
-    * Having a var here is not great as it makes the node mutable, the alternative would be to store this information outside of
-    * the node and make it an argument to indexForShard.
+   * This is the key element of the indexForShard function.
+   * Here is an example:
+   * Let's say we're scattering over 3 arrays of size 2, 3, and 2 respectively, using a cross product.
+   * We will then have 2 * 3 * 2 = 12 shards
+   *
+   * The possible combinations of input indices are
+   *
+   * Shard #0: (0, 0, 0)
+   * Shard #1: (0, 0, 1)
+   * Shard #2: (0, 1, 0)
+   * Shard #3: (0, 1, 1)
+   * Shard #4: (0, 2, 0)
+   * Shard #5: (0, 2, 1)
+   * Shard #6: (1, 0, 0)
+   * Shard #7: (1, 0, 1)
+   * Shard #8: (1, 1, 0)
+   * Shard #9: (1, 1, 1)
+   * Shard #10: (1, 2, 0)
+   * Shard #11: (1, 2, 1)
+   *
+   * We will also have 3 SVNs, one for each array.
+   * Each SVN needs to output one column of the above "matrix", based on the shard number
+   *
+   * For SVN 1:          For SVN 2:        For SVN 3:
+   *   0 -> 0              0 -> 0            0 -> 0
+   *   1 -> 0              1 -> 0            1 -> 1
+   *   2 -> 0              2 -> 1            2 -> 0
+   *   3 -> 0              3 -> 1            3 -> 1
+   *   4 -> 0              4 -> 2            4 -> 0
+   *   5 -> 0              5 -> 2            5 -> 1
+   *   6 -> 1              6 -> 0            6 -> 0
+   *   7 -> 1              7 -> 0            7 -> 1
+   *   8 -> 1              8 -> 1            8 -> 0
+   *   9 -> 1              9 -> 1            9 -> 1
+   *   10 -> 1             10 -> 2           10 -> 0
+   *   11 -> 1             11 -> 2           11 -> 1
+   *
+   *  shard / 6         (shard / 2) % 3     shard % 2
+   *
+   *  This can be generalized to (shard / relativeIndexLength) % arraySize
+   *  where
+   *   - shard is the shard index as an Int
+   *   - relativeIndexLength is the number of possible combinations for the arrays on the "right" of this variable
+   *   - arraySize is the size of the array for this variable
+   *
+   * Having a var here is not great as it makes the node mutable, the alternative would be to store this information outside of
+   * the node and make it an argument to indexForShard.
    */
   private var _relativeIndexLength: Int = 1
-  
+
   def relativeIndexLength = _relativeIndexLength
 
   def withRelativeIndexLength(relativeIndexLength: Int) = this._relativeIndexLength = relativeIndexLength
@@ -152,7 +166,6 @@ final case class ScatterVariableNode(override val identifier: WomIdentifier,
     * Given a shard number, and the total size of the array, returns at which index in the array the value is located.
     */
   // Maybe this whole function should not be hardcoded here but rather defined by the language.. So far it works for all the use cases we have
-  def indexForShard(shardIndex: Int, arraySize: Int) = {
+  def indexForShard(shardIndex: Int, arraySize: Int) =
     (shardIndex / _relativeIndexLength) % arraySize
-  }
 }
diff --git a/wom/src/main/scala/wom/graph/GraphNode.scala b/wom/src/main/scala/wom/graph/GraphNode.scala
index c6be2041097..bd058143bb5 100644
--- a/wom/src/main/scala/wom/graph/GraphNode.scala
+++ b/wom/src/main/scala/wom/graph/GraphNode.scala
@@ -38,12 +38,11 @@ trait GraphNode {
 
   val completionPort = NodeCompletionPort(_ => this)
 
-  def outputByName(name: String): ErrorOr[GraphNodePort.OutputPort] = {
+  def outputByName(name: String): ErrorOr[GraphNodePort.OutputPort] =
     outputPorts.find(_.name == name) match {
       case Some(port) => port.validNel
       case None => s"No such output: $name".invalidNel
     }
-  }
 
   /**
     * The set of all graph nodes which are (transitively) upstream from this one.
@@ -76,7 +75,9 @@ object GraphNode {
 
   def inputPortNamesMatch(required: Set[InputPort], provided: Set[InputPort]): ErrorOr[Unit] = {
     def requiredInputFound(r: InputPort): ErrorOr[Unit] = provided.find(_.name == r.name) match {
-      case Some(p) => if (r.womType.isCoerceableFrom(p.womType)) ().validNel else s"Cannot link a ${p.womType.stableName} to the input ${r.name}: ${r.womType}".invalidNel
+      case Some(p) =>
+        if (r.womType.isCoerceableFrom(p.womType)) ().validNel
+        else s"Cannot link a ${p.womType.stableName} to the input ${r.name}: ${r.womType}".invalidNel
       case None => s"The required input ${r.name}: ${r.womType.stableName} was not provided.".invalidNel
     }
 
@@ -93,7 +94,8 @@ object GraphNode {
     def get: Unit => A = _ => getGraphNode
   }
 
-  private[wom] implicit class EnhancedGraphNodeSet(val nodes: Set[GraphNode]) extends AnyVal {
+  implicit private[wom] class EnhancedGraphNodeSet(val nodes: Set[GraphNode]) extends AnyVal {
+
     /**
       * Interpret this graph's "GraphInputNode"s as "Callable.InputDefinition"s
       */
@@ -103,12 +105,16 @@ object GraphNode {
       case optional: OptionalGraphInputNode =>
         OptionalInputDefinition(optional.identifier.localName, optional.womType)
       case withDefault: OptionalGraphInputNodeWithDefault =>
-        OverridableInputDefinitionWithDefault(withDefault.identifier.localName, withDefault.womType, withDefault.default)
+        OverridableInputDefinitionWithDefault(withDefault.identifier.localName,
+                                              withDefault.womType,
+                                              withDefault.default
+        )
     }
 
     def outputDefinitions: Set[_ <: Callable.OutputDefinition] = nodes collect {
       // TODO: FIXME: Do something for PortBasedGraphOutputNodes
-      case gin: ExpressionBasedGraphOutputNode => OutputDefinition(gin.identifier.localName, gin.womType, gin.womExpression)
+      case gin: ExpressionBasedGraphOutputNode =>
+        OutputDefinition(gin.identifier.localName, gin.womType, gin.womExpression)
     }
   }
 
diff --git a/wom/src/main/scala/wom/graph/GraphNodeInputExpression.scala b/wom/src/main/scala/wom/graph/GraphNodeInputExpression.scala
index 4efbac93783..af5f3d15159 100644
--- a/wom/src/main/scala/wom/graph/GraphNodeInputExpression.scala
+++ b/wom/src/main/scala/wom/graph/GraphNodeInputExpression.scala
@@ -11,7 +11,12 @@ import wom.types.WomType
   * - This one remembers which input the expression is being assigned to.
   * - InstantiatedExpression has created InputPorts for the expression inputs. This one only has references to OutputPorts.
   */
-case class GraphNodeInputExpression(inputName: String, expression: WomExpression, inputMapping: Map[String, OutputPort]) {
+case class GraphNodeInputExpression(inputName: String,
+                                    expression: WomExpression,
+                                    inputMapping: Map[String, OutputPort]
+) {
 
-  private[graph] lazy val evaluateType: ErrorOr[WomType] = expression.evaluateType(inputMapping.map { case (name, port) => (name, port.womType) })
+  private[graph] lazy val evaluateType: ErrorOr[WomType] = expression.evaluateType(inputMapping.map {
+    case (name, port) => (name, port.womType)
+  })
 }
diff --git a/wom/src/main/scala/wom/graph/GraphNodePort.scala b/wom/src/main/scala/wom/graph/GraphNodePort.scala
index d2b2bb3a48f..83cd85d301a 100644
--- a/wom/src/main/scala/wom/graph/GraphNodePort.scala
+++ b/wom/src/main/scala/wom/graph/GraphNodePort.scala
@@ -46,25 +46,38 @@ object GraphNodePort {
     override lazy val graphNode = g.apply(())
   }
 
-  final case class ConnectedInputPort(name: String, womType: WomType, upstream: OutputPort, g: Unit => GraphNode) extends InputPort with DelayedGraphNodePort
+  final case class ConnectedInputPort(name: String, womType: WomType, upstream: OutputPort, g: Unit => GraphNode)
+      extends InputPort
+      with DelayedGraphNodePort
 
   /**
     * For any graph node that uses a declarations to produce outputs (e.g. call, declaration):
     */
   object GraphNodeOutputPort {
-    def apply(name: String, womType: WomType, graphNode: GraphNode): GraphNodeOutputPort = {
-      GraphNodeOutputPort(WomIdentifier(LocalName(name), graphNode.identifier.fullyQualifiedName.combine(name)), womType, graphNode)
-    }
+    def apply(name: String, womType: WomType, graphNode: GraphNode): GraphNodeOutputPort =
+      GraphNodeOutputPort(WomIdentifier(LocalName(name), graphNode.identifier.fullyQualifiedName.combine(name)),
+                          womType,
+                          graphNode
+      )
   }
-  case class GraphNodeOutputPort(override val identifier: WomIdentifier, womType: WomType, graphNode: GraphNode) extends OutputPort
+  case class GraphNodeOutputPort(override val identifier: WomIdentifier, womType: WomType, graphNode: GraphNode)
+      extends OutputPort
 
   object ExpressionBasedOutputPort
-  case class ExpressionBasedOutputPort(override val identifier: WomIdentifier, womType: WomType, graphNode: GraphNode, expression: WomExpression) extends OutputPort
+  case class ExpressionBasedOutputPort(override val identifier: WomIdentifier,
+                                       womType: WomType,
+                                       graphNode: GraphNode,
+                                       expression: WomExpression
+  ) extends OutputPort
 
   /**
     * Represents the gathered output from a call/declaration in a ScatterNode.
     */
-  final case class ScatterGathererPort(womType: WomArrayType, outputToGather: PortBasedGraphOutputNode, g: Unit => GraphNode) extends OutputPort with DelayedGraphNodePort {
+  final case class ScatterGathererPort(womType: WomArrayType,
+                                       outputToGather: PortBasedGraphOutputNode,
+                                       g: Unit => GraphNode
+  ) extends OutputPort
+      with DelayedGraphNodePort {
     // Since this port just wraps a PortBasedGraphOutputNode which itself wraps an output port, we can re-use the same identifier
     override def identifier: WomIdentifier = outputToGather.identifier
   }
@@ -72,7 +85,9 @@ object GraphNodePort {
   /**
     * Represents the conditional output from a call or declaration in a ConditionalNode
     */
-  final case class ConditionalOutputPort(outputToExpose: PortBasedGraphOutputNode, g: Unit => ConditionalNode) extends OutputPort with DelayedGraphNodePort {
+  final case class ConditionalOutputPort(outputToExpose: PortBasedGraphOutputNode, g: Unit => ConditionalNode)
+      extends OutputPort
+      with DelayedGraphNodePort {
     // Since this port just wraps a PortBasedGraphOutputNode which itself wraps an output port, we can re-use the same identifier
     override def identifier: WomIdentifier = outputToExpose.identifier
     override val womType: WomOptionalType = WomOptionalType(outputToExpose.womType).flatOptionalType
@@ -90,7 +105,10 @@ object GraphNodePort {
   /**
     * Represents an output port from a workflow call, based on the output that it exposes.
     */
-  final case class SubworkflowCallOutputPort(identifier: WomIdentifier, outputToExpose: GraphOutputNode, workflowCallNode: WorkflowCallNode) extends OutputPort {
+  final case class SubworkflowCallOutputPort(identifier: WomIdentifier,
+                                             outputToExpose: GraphOutputNode,
+                                             workflowCallNode: WorkflowCallNode
+  ) extends OutputPort {
     override val womType: WomType = outputToExpose.womType
     override val graphNode: GraphNode = workflowCallNode
   }
diff --git a/wom/src/main/scala/wom/graph/GraphNodeWithSingleOutputPort.scala b/wom/src/main/scala/wom/graph/GraphNodeWithSingleOutputPort.scala
index 8f6858e0515..87a985efba8 100644
--- a/wom/src/main/scala/wom/graph/GraphNodeWithSingleOutputPort.scala
+++ b/wom/src/main/scala/wom/graph/GraphNodeWithSingleOutputPort.scala
@@ -6,6 +6,7 @@ import wom.graph.GraphNodePort.OutputPort
 
 trait GraphNodeWithSingleOutputPort extends GraphNode {
   def singleOutputPort: OutputPort
+
   /**
     * Can be used to use this node as an InputDefinitionPointer
     */
diff --git a/wom/src/main/scala/wom/graph/GraphOutputNode.scala b/wom/src/main/scala/wom/graph/GraphOutputNode.scala
index d6c921cd208..dbcf4037bd1 100644
--- a/wom/src/main/scala/wom/graph/GraphOutputNode.scala
+++ b/wom/src/main/scala/wom/graph/GraphOutputNode.scala
@@ -15,7 +15,8 @@ sealed trait GraphOutputNode extends GraphNode {
 /**
   * Exposes an existing output port as a graph output.
   */
-final case class PortBasedGraphOutputNode(override val identifier: WomIdentifier, womType: WomType, source: OutputPort) extends GraphOutputNode {
+final case class PortBasedGraphOutputNode(override val identifier: WomIdentifier, womType: WomType, source: OutputPort)
+    extends GraphOutputNode {
   val singleInputPort: InputPort = ConnectedInputPort(localName, womType, source, _ => this)
   lazy val singleUpstreamNode: GraphNode = singleInputPort.upstream.graphNode
   lazy val singleUpstreamPort: OutputPort = singleInputPort.upstream
@@ -28,14 +29,15 @@ object ExpressionBasedGraphOutputNode {
   def fromInputMapping(identifier: WomIdentifier,
                        expression: WomExpression,
                        explicitWomType: WomType,
-                       inputMapping: Map[String, OutputPort]): ErrorOr[ExpressionBasedGraphOutputNode] = {
+                       inputMapping: Map[String, OutputPort]
+  ): ErrorOr[ExpressionBasedGraphOutputNode] = {
     // This constructor ignores the evaluated type and uses the explicit type instead
     def constructor(identifier: WomIdentifier,
                     expression: WomExpression,
                     evaluatedType: WomType,
-                    inputPorts: Map[String, InputPort]) = {
+                    inputPorts: Map[String, InputPort]
+    ) =
       new ExpressionNode(identifier, expression, explicitWomType, inputPorts) with ExpressionBasedGraphOutputNode
-    }
     buildFromConstructor(constructor)(identifier, expression, inputMapping)
   }
 }
diff --git a/wom/src/main/scala/wom/graph/ScatterNode.scala b/wom/src/main/scala/wom/graph/ScatterNode.scala
index 0240bc11d28..1c534a1a1df 100644
--- a/wom/src/main/scala/wom/graph/ScatterNode.scala
+++ b/wom/src/main/scala/wom/graph/ScatterNode.scala
@@ -16,11 +16,13 @@ import wom.values.{WomArray, WomValue}
   * @param scatterVariableNodes Inner graph nodes for each scatter collection expression being scattered over. WDL uses exactly one, CWL >= 1.
   * @param outputMapping Output ports for the scatter node, which also link back to GraphOutputNodes of the inner graph.
   */
-final case class ScatterNode private(override val innerGraph: Graph,
-                                     scatterVariableNodes: List[ScatterVariableNode],
-                                     outputMapping: Set[ScatterGathererPort],
-                                     scatterProcessingFunction: ScatterProcessingFunction,
-                                     scatterCollectionFunctionBuilder: ScatterCollectionFunctionBuilder) extends GraphNode with GraphNodeWithInnerGraph {
+final case class ScatterNode private (override val innerGraph: Graph,
+                                      scatterVariableNodes: List[ScatterVariableNode],
+                                      outputMapping: Set[ScatterGathererPort],
+                                      scatterProcessingFunction: ScatterProcessingFunction,
+                                      scatterCollectionFunctionBuilder: ScatterCollectionFunctionBuilder
+) extends GraphNode
+    with GraphNodeWithInnerGraph {
 
   override val identifier: WomIdentifier = WomIdentifier("ScatterNode")
 
@@ -29,13 +31,14 @@ final case class ScatterNode private(override val innerGraph: Graph,
 
   // NB if you find yourself calling .filter on this set of inputPorts, you probably just wanted to access either
   // the scatterVariableMapping or otherInputPorts fields directly.
-  override val inputPorts: Set[InputPort] = scatterCollectionExpressionNodes.toSet[ExpressionNode] map { scatterCollectionExpressionNode =>
-    ConnectedInputPort(
-      scatterCollectionExpressionNode.identifier.localName.value,
-      scatterCollectionExpressionNode.womType,
-      scatterCollectionExpressionNode.singleOutputPort,
-      _ => this
-    )
+  override val inputPorts: Set[InputPort] = scatterCollectionExpressionNodes.toSet[ExpressionNode] map {
+    scatterCollectionExpressionNode =>
+      ConnectedInputPort(
+        scatterCollectionExpressionNode.identifier.localName.value,
+        scatterCollectionExpressionNode.womType,
+        scatterCollectionExpressionNode.singleOutputPort,
+        _ => this
+      )
   }
   override val outputPorts: Set[GraphNodePort.OutputPort] = outputMapping.toSet[OutputPort]
 
@@ -44,21 +47,26 @@ final case class ScatterNode private(override val innerGraph: Graph,
 
 object ScatterNode {
   case class ScatterVariableAndValue(scatterVariableNode: ScatterVariableNode, arrayValue: WomArray)
-  
+
   type ScatterProcessingFunction = List[ScatterVariableAndValue] => Checked[Int]
   // Use dot product as the default processing function (works well for single variable scatters too)
   val DefaultScatterProcessingFunction: ScatterProcessingFunction = { nodesAndValues: List[ScatterVariableAndValue] =>
     nodesAndValues.map(_.arrayValue.size).distinct match {
       case head :: Nil => head.validNelCheck
-      case _ => "All arrays must have the same number of element when using the dot product scatter method".invalidNelCheck
+      case _ =>
+        "All arrays must have the same number of element when using the dot product scatter method".invalidNelCheck
     }
   }
-  
+
   type ScatterCollectionFunction = (List[WomValue], WomArrayType) => WomArray
-  val DefaultScatterCollectionFunction: ScatterCollectionFunction = { (shards: List[WomValue], valueType: WomArrayType) => WomArray(valueType, shards) }
-  
+  val DefaultScatterCollectionFunction: ScatterCollectionFunction = {
+    (shards: List[WomValue], valueType: WomArrayType) => WomArray(valueType, shards)
+  }
+
   type ScatterCollectionFunctionBuilder = List[Int] => ScatterCollectionFunction
-  val DefaultScatterCollectionFunctionBuilder: ScatterCollectionFunctionBuilder = { _: List[Int] => DefaultScatterCollectionFunction }
+  val DefaultScatterCollectionFunctionBuilder: ScatterCollectionFunctionBuilder = { _: List[Int] =>
+    DefaultScatterCollectionFunction
+  }
 
   /**
     * Maps from an InstantiatedExpression on the ScatterNode to the GraphInputNode in the innerGraph.
@@ -70,8 +78,13 @@ object ScatterNode {
     override val newExpressions: Set[ExpressionNode] = node.scatterCollectionExpressionNodes.toSet
     override val newInputs: Set[ExternalGraphInputNode] = node.innerGraph.externalInputNodes
     override val usedOuterGraphInputNodes: Set[OuterGraphInputNode] =
-      (node.scatterCollectionExpressionNodes.flatMap(_.upstream).toSet.filterByType[OuterGraphInputNode]: Set[OuterGraphInputNode]) ++
-      (node.innerGraph.outerGraphInputNodes.map(_.linkToOuterGraphNode).filterByType[OuterGraphInputNode]: Set[OuterGraphInputNode])
+      (node.scatterCollectionExpressionNodes
+        .flatMap(_.upstream)
+        .toSet
+        .filterByType[OuterGraphInputNode]: Set[OuterGraphInputNode]) ++
+        (node.innerGraph.outerGraphInputNodes
+          .map(_.linkToOuterGraphNode)
+          .filterByType[OuterGraphInputNode]: Set[OuterGraphInputNode])
   }
 
   /**
@@ -79,17 +92,18 @@ object ScatterNode {
     * Helps making input ports and building the node while making sure node references are set properly.
     */
   def scatterOverGraph(innerGraph: Graph,
-                       scatterVariableInnerGraphInputNode: ScatterVariableNode): ScatterNodeWithNewNodes = {
+                       scatterVariableInnerGraphInputNode: ScatterVariableNode
+  ): ScatterNodeWithNewNodes = {
     val scatterNodeBuilder = new ScatterNodeBuilder
     val outputPorts: Set[ScatterGathererPort] = innerGraph.nodes.collect { case gon: PortBasedGraphOutputNode =>
       scatterNodeBuilder.makeOutputPort(WomArrayType(gon.womType), gon)
     }
 
     scatterNodeBuilder.build(innerGraph,
-      outputPorts,
-      List(scatterVariableInnerGraphInputNode),
-      DefaultScatterProcessingFunction,
-      DefaultScatterCollectionFunctionBuilder
+                             outputPorts,
+                             List(scatterVariableInnerGraphInputNode),
+                             DefaultScatterProcessingFunction,
+                             DefaultScatterCollectionFunctionBuilder
     )
   }
 
@@ -99,16 +113,16 @@ object ScatterNode {
     */
   class ScatterNodeBuilder {
     private val graphNodeSetter = new GraphNode.GraphNodeSetter[ScatterNode]()
-    
-    def makeOutputPort(womType: WomArrayType, nodeToGather: PortBasedGraphOutputNode): ScatterGathererPort = {
+
+    def makeOutputPort(womType: WomArrayType, nodeToGather: PortBasedGraphOutputNode): ScatterGathererPort =
       ScatterGathererPort(womType, nodeToGather, graphNodeSetter.get)
-    }
-    
+
     def build(innerGraph: Graph,
               outputPorts: Set[ScatterGathererPort],
               scatterVariableNodes: List[ScatterVariableNode],
               scatterProcessingFunction: ScatterProcessingFunction,
-              scatterCollectionFunctionBuilder: ScatterCollectionFunctionBuilder) = {
+              scatterCollectionFunctionBuilder: ScatterCollectionFunctionBuilder
+    ) = {
       val scatterNode = ScatterNode(
         innerGraph,
         scatterVariableNodes,
diff --git a/wom/src/main/scala/wom/graph/WomIdentifier.scala b/wom/src/main/scala/wom/graph/WomIdentifier.scala
index 47ff39dbbab..f303c560f8d 100644
--- a/wom/src/main/scala/wom/graph/WomIdentifier.scala
+++ b/wom/src/main/scala/wom/graph/WomIdentifier.scala
@@ -25,14 +25,14 @@ case class FullyQualifiedName(value: String) {
 
 object WomIdentifier {
   def apply(localName: String): WomIdentifier = WomIdentifier(LocalName(localName), FullyQualifiedName(localName))
-  def apply(localName: String, fullyQualifiedName: String): WomIdentifier = WomIdentifier(LocalName(localName), FullyQualifiedName(fullyQualifiedName))
+  def apply(localName: String, fullyQualifiedName: String): WomIdentifier =
+    WomIdentifier(LocalName(localName), FullyQualifiedName(fullyQualifiedName))
 }
 
 case class WomIdentifier(localName: LocalName, fullyQualifiedName: FullyQualifiedName) {
   def combine(other: LocalName): WomIdentifier = combine(other.value)
-  def combine(other: String): WomIdentifier = {
+  def combine(other: String): WomIdentifier =
     WomIdentifier(localName.combineToLocalName(other), fullyQualifiedName.combine(other))
-  }
   def workflowLocalName: String = fullyQualifiedName.value.split("\\.") match {
     case fqn if fqn.length > 1 => fqn.tail.mkString(".")
     case lqn => lqn.head
diff --git a/wom/src/main/scala/wom/graph/expression/AnonymousExpressionNode.scala b/wom/src/main/scala/wom/graph/expression/AnonymousExpressionNode.scala
index bf67bda07ee..20efe665646 100644
--- a/wom/src/main/scala/wom/graph/expression/AnonymousExpressionNode.scala
+++ b/wom/src/main/scala/wom/graph/expression/AnonymousExpressionNode.scala
@@ -13,9 +13,9 @@ object AnonymousExpressionNode {
   def fromInputMapping[T <: AnonymousExpressionNode](identifier: WomIdentifier,
                                                      expression: WomExpression,
                                                      inputMapping: Map[String, OutputPort],
-                                                     constructor: AnonymousExpressionConstructor[T]): ErrorOr[T] = {
+                                                     constructor: AnonymousExpressionConstructor[T]
+  ): ErrorOr[T] =
     ExpressionNode.buildFromConstructor(constructor)(identifier, expression, inputMapping)
-  }
 }
 
 /**
@@ -26,14 +26,17 @@ trait AnonymousExpressionNode extends ExpressionNode
 case class PlainAnonymousExpressionNode(override val identifier: WomIdentifier,
                                         override val womExpression: WomExpression,
                                         override val womType: WomType,
-                                        override val inputMapping: Map[String, InputPort])
-  extends ExpressionNode(identifier, womExpression, womType, inputMapping) with AnonymousExpressionNode
+                                        override val inputMapping: Map[String, InputPort]
+) extends ExpressionNode(identifier, womExpression, womType, inputMapping)
+    with AnonymousExpressionNode
 
 case class TaskCallInputExpressionNode(override val identifier: WomIdentifier,
                                        override val womExpression: WomExpression,
                                        override val womType: WomType,
-                                       override val inputMapping: Map[String, InputPort])
-  extends ExpressionNode(identifier, womExpression, womType, inputMapping) with AnonymousExpressionNode {
+                                       override val inputMapping: Map[String, InputPort]
+) extends ExpressionNode(identifier, womExpression, womType, inputMapping)
+    with AnonymousExpressionNode {
+
   /**
    * The `GraphNodeSetter` that will have a `TaskCallNode` set into it. This is needed in the `WorkflowExecutionActor`
    * to be able to look up backend mapping for the target call in order to have the correct `IoFunctionSet` to
diff --git a/wom/src/main/scala/wom/graph/expression/ExposedExpressionNode.scala b/wom/src/main/scala/wom/graph/expression/ExposedExpressionNode.scala
index 7c88d40490a..8d2778107d3 100644
--- a/wom/src/main/scala/wom/graph/expression/ExposedExpressionNode.scala
+++ b/wom/src/main/scala/wom/graph/expression/ExposedExpressionNode.scala
@@ -10,14 +10,15 @@ object ExposedExpressionNode {
   def fromInputMapping(identifier: WomIdentifier,
                        expression: WomExpression,
                        explicitWomType: WomType,
-                       inputMapping: Map[String, OutputPort]): ErrorOr[ExposedExpressionNode] = {
+                       inputMapping: Map[String, OutputPort]
+  ): ErrorOr[ExposedExpressionNode] = {
     // This constructor ignores the evaluated type and uses the explicit type instead
     def constructor(identifier: WomIdentifier,
                     expression: WomExpression,
                     evaluatedType: WomType,
-                    inputPorts: Map[String, InputPort]) = {
+                    inputPorts: Map[String, InputPort]
+    ) =
       new ExpressionNode(identifier, expression, explicitWomType, inputPorts) with ExposedExpressionNode
-    }
     ExpressionNode.buildFromConstructor(constructor)(identifier, expression, inputMapping)
   }
 }
diff --git a/wom/src/main/scala/wom/graph/expression/ExpressionNode.scala b/wom/src/main/scala/wom/graph/expression/ExpressionNode.scala
index f361315a544..a5e4ace0095 100644
--- a/wom/src/main/scala/wom/graph/expression/ExpressionNode.scala
+++ b/wom/src/main/scala/wom/graph/expression/ExpressionNode.scala
@@ -19,11 +19,13 @@ import scala.util.Try
 abstract class ExpressionNode(override val identifier: WomIdentifier,
                               val womExpression: WomExpression,
                               val womType: WomType,
-                              val inputMapping: Map[String, InputPort]) extends GraphNodeWithSingleOutputPort with ExpressionNodeLike {
+                              val inputMapping: Map[String, InputPort]
+) extends GraphNodeWithSingleOutputPort
+    with ExpressionNodeLike {
   override val singleOutputPort = GraphNodeOutputPort(identifier, womType, this)
   override val outputPorts: Set[GraphNodePort.OutputPort] = Set(singleOutputPort)
   override val inputPorts = inputMapping.values.toSet
-  
+
   // Again an instance of not so pretty flatMapping with mix of ErrorOrs, Eithers and Tries..
   // TODO: This should return an EitherT or whatever we decide we want to use to package Exceptions + Nel[String]
   /**
@@ -34,7 +36,9 @@ abstract class ExpressionNode(override val identifier: WomIdentifier,
     coerced <- womType.coerceRawValue(evaluated).toErrorOr
   } yield coerced).leftMap(_.map(e => s"Evaluating ${womExpression.sourceString} failed: $e")).toEither
 
-  override final def evaluate(outputPortLookup: OutputPort => ErrorOr[WomValue], ioFunctionSet: IoFunctionSet): Checked[Map[OutputPort, WomValue]] = {
+  final override def evaluate(outputPortLookup: OutputPort => ErrorOr[WomValue],
+                              ioFunctionSet: IoFunctionSet
+  ): Checked[Map[OutputPort, WomValue]] = {
     import common.validation.ErrorOr._
     for {
       inputs <- inputMapping.traverseValues(inputPort => outputPortLookup(inputPort.upstream)).toEither
@@ -44,18 +48,21 @@ abstract class ExpressionNode(override val identifier: WomIdentifier,
 }
 
 object ExpressionNode {
+
   /**
     * Constructs an ExpressionNode or a subclass of an expression node.
     * Note: the WomType is the evaluated type derived from the expression.
     */
-  type ExpressionNodeConstructor[E <: ExpressionNode] = (WomIdentifier, WomExpression, WomType, Map[String, InputPort]) => E
+  type ExpressionNodeConstructor[E <: ExpressionNode] =
+    (WomIdentifier, WomExpression, WomType, Map[String, InputPort]) => E
 
   /**
     * Using the passed constructor, attempts to build an expression node from input mappings by linking variable references to other
     * output ports.
     */
-  def buildFromConstructor[E <: ExpressionNode](constructor: ExpressionNodeConstructor[E])
-                                               (identifier: WomIdentifier, expression: WomExpression, inputMapping: Map[String, OutputPort]): ErrorOr[E] = {
+  def buildFromConstructor[E <: ExpressionNode](
+    constructor: ExpressionNodeConstructor[E]
+  )(identifier: WomIdentifier, expression: WomExpression, inputMapping: Map[String, OutputPort]): ErrorOr[E] = {
     val graphNodeSetter = new GraphNode.GraphNodeSetter[ExpressionNode]()
 
     val builtExpressionNode = for {
@@ -65,18 +72,27 @@ object ExpressionNode {
       _ = graphNodeSetter._graphNode = expressionNode
     } yield expressionNode
 
-    def safeSourceString(e: WomExpression) = Try(expression.sourceString).getOrElse("<<expected an expression, none found>>")
+    def safeSourceString(e: WomExpression) =
+      Try(expression.sourceString).getOrElse("<<expected an expression, none found>>")
 
-    builtExpressionNode.leftMap(_.map(e => s"Cannot build expression for '${identifier.fullyQualifiedName.value} = ${safeSourceString(expression)}': $e"))
+    builtExpressionNode.leftMap(
+      _.map(e =>
+        s"Cannot build expression for '${identifier.fullyQualifiedName.value} = ${safeSourceString(expression)}': $e"
+      )
+    )
   }
 
   /**
     * Attempts to find an output port for all referenced variables in the expression, and created input ports to connect them together.
     */
-  private def linkWithInputs(graphNodeSetter: GraphNode.GraphNodeSetter[ExpressionNode], expression: WomExpression, inputMapping: Map[String, OutputPort]): ErrorOr[(WomType, Map[String, InputPort])] = {
+  private def linkWithInputs(graphNodeSetter: GraphNode.GraphNodeSetter[ExpressionNode],
+                             expression: WomExpression,
+                             inputMapping: Map[String, OutputPort]
+  ): ErrorOr[(WomType, Map[String, InputPort])] = {
     def linkInput(input: String): ErrorOr[(String, InputPort)] = inputMapping.get(input) match {
-      case Some(upstreamPort) => (input, ConnectedInputPort(input, upstreamPort.womType, upstreamPort, graphNodeSetter.get)).validNel
-      case None => 
+      case Some(upstreamPort) =>
+        (input, ConnectedInputPort(input, upstreamPort.womType, upstreamPort, graphNodeSetter.get)).validNel
+      case None =>
         s"Expression cannot be connected without the input $input (provided: ${inputMapping.toString})".invalidNel
     }
 
diff --git a/wom/src/main/scala/wom/graph/expression/ExpressionNodeLike.scala b/wom/src/main/scala/wom/graph/expression/ExpressionNodeLike.scala
index f452513b45d..f0cb0d05616 100644
--- a/wom/src/main/scala/wom/graph/expression/ExpressionNodeLike.scala
+++ b/wom/src/main/scala/wom/graph/expression/ExpressionNodeLike.scala
@@ -11,5 +11,7 @@ import wom.values.WomValue
   * Trait for nodes that can be evaluated by the engine
   */
 trait ExpressionNodeLike extends GraphNode {
-  def evaluate(outputPortLookup: OutputPort => ErrorOr[WomValue], ioFunctionSet: IoFunctionSet): Checked[Map[OutputPort, WomValue]]
+  def evaluate(outputPortLookup: OutputPort => ErrorOr[WomValue],
+               ioFunctionSet: IoFunctionSet
+  ): Checked[Map[OutputPort, WomValue]]
 }
diff --git a/wom/src/main/scala/wom/package.scala b/wom/src/main/scala/wom/package.scala
index 3a8188e0060..d05d60df033 100644
--- a/wom/src/main/scala/wom/package.scala
+++ b/wom/src/main/scala/wom/package.scala
@@ -12,7 +12,10 @@ trait TsvSerializable {
 }
 
 class WomExpressionException(message: String = null, cause: Throwable = null) extends RuntimeException(message, cause)
-final case class OptionalNotSuppliedException(operationName: String) extends Exception(s"Sorry! Operation $operationName is not supported on empty optional values. You might resolve this using select_first([optional, default]) to guarantee that you have a filled value.")
+final case class OptionalNotSuppliedException(operationName: String)
+    extends Exception(
+      s"Sorry! Operation $operationName is not supported on empty optional values. You might resolve this using select_first([optional, default]) to guarantee that you have a filled value."
+    )
 
 case class JobOutput(womValue: WomValue)
 
@@ -23,9 +26,11 @@ package object values {
   type WomEvaluatedCallInputs = Map[InputDefinition, WomValue]
 
   implicit class EnhancedWomEvaluatedCallInputs(val inputs: WomEvaluatedCallInputs) extends AnyVal {
-    def prettyString = inputs.map({
-      case (inputDef, womValue) => s"${inputDef.name} -> ${womValue.valueString}"
-    }).mkString(", ")
+    def prettyString = inputs
+      .map { case (inputDef, womValue) =>
+        s"${inputDef.name} -> ${womValue.valueString}"
+      }
+      .mkString(", ")
   }
 
   implicit class HashableString(val value: String) extends AnyVal with Hashable {
@@ -84,7 +89,8 @@ final case class InstantiatedCommand(commandString: String,
                                      evaluatedStdoutOverride: Option[String] = None,
                                      evaluatedStderrOverride: Option[String] = None,
                                      preprocessedInputs: List[(LocalName, WomValue)] = List.empty,
-                                     valueMappedPreprocessedInputs: List[(LocalName, WomValue)] = List.empty)
+                                     valueMappedPreprocessedInputs: List[(LocalName, WomValue)] = List.empty
+)
 
 /**
   * File created as a side effect of instantiating the command.
diff --git a/wom/src/main/scala/wom/runtime/WomOutputRuntimeExtractor.scala b/wom/src/main/scala/wom/runtime/WomOutputRuntimeExtractor.scala
index ce568c6515b..30835df445d 100644
--- a/wom/src/main/scala/wom/runtime/WomOutputRuntimeExtractor.scala
+++ b/wom/src/main/scala/wom/runtime/WomOutputRuntimeExtractor.scala
@@ -7,8 +7,8 @@ import net.ceedubs.ficus.Ficus._
 
 object WomOutputRuntimeExtractor {
   def fromConfig(config: Config) = {
-    val dockerImage = validate { config.getAs[String]("docker-image") }
-    val command = validate { config.as[String]("command") }
+    val dockerImage = validate(config.getAs[String]("docker-image"))
+    val command = validate(config.as[String]("command"))
 
     (dockerImage, command).mapN(WomOutputRuntimeExtractor.apply)
   }
diff --git a/wom/src/main/scala/wom/transforms/WomCallNodeMaker.scala b/wom/src/main/scala/wom/transforms/WomCallNodeMaker.scala
index 03201c77e0c..6bae7aa2a3f 100644
--- a/wom/src/main/scala/wom/transforms/WomCallNodeMaker.scala
+++ b/wom/src/main/scala/wom/transforms/WomCallNodeMaker.scala
@@ -7,5 +7,10 @@ import simulacrum._
 
 @typeclass
 trait WomCallNodeMaker[A] {
-  def toWomCallNode(a: A, localLookup: Map[String, GraphNodePort.OutputPort], outerLookup: Map[String, GraphNodePort.OutputPort], preserveIndexForOuterLookups: Boolean, inASubworkflow: Boolean): ErrorOr[CallNodeAndNewNodes]
+  def toWomCallNode(a: A,
+                    localLookup: Map[String, GraphNodePort.OutputPort],
+                    outerLookup: Map[String, GraphNodePort.OutputPort],
+                    preserveIndexForOuterLookups: Boolean,
+                    inASubworkflow: Boolean
+  ): ErrorOr[CallNodeAndNewNodes]
 }
diff --git a/wom/src/main/scala/wom/transforms/WomConditionalNodeMaker.scala b/wom/src/main/scala/wom/transforms/WomConditionalNodeMaker.scala
index 48a910cc2b4..44ecb63aa8b 100644
--- a/wom/src/main/scala/wom/transforms/WomConditionalNodeMaker.scala
+++ b/wom/src/main/scala/wom/transforms/WomConditionalNodeMaker.scala
@@ -8,5 +8,10 @@ import simulacrum._
 
 @typeclass
 trait WomConditionalNodeMaker[A] {
-  def toWomConditionalNode(a: A, localLookup: Map[String, GraphNodePort.OutputPort], outerLookup: Map[String, OutputPort], preserveIndexForOuterLookups: Boolean, inASubworkflow: Boolean): ErrorOr[ConditionalNodeWithNewNodes]
+  def toWomConditionalNode(a: A,
+                           localLookup: Map[String, GraphNodePort.OutputPort],
+                           outerLookup: Map[String, OutputPort],
+                           preserveIndexForOuterLookups: Boolean,
+                           inASubworkflow: Boolean
+  ): ErrorOr[ConditionalNodeWithNewNodes]
 }
diff --git a/wom/src/main/scala/wom/transforms/WomExecutableMaker.scala b/wom/src/main/scala/wom/transforms/WomExecutableMaker.scala
index d1eed8efd9f..dfb6bcd4c1b 100644
--- a/wom/src/main/scala/wom/transforms/WomExecutableMaker.scala
+++ b/wom/src/main/scala/wom/transforms/WomExecutableMaker.scala
@@ -8,7 +8,11 @@ import wom.expression.IoFunctionSet
 
 @typeclass
 trait WomExecutableMaker[A] {
-  def toWomExecutable(a: A, inputs: Option[WorkflowJson], ioFunctions: IoFunctionSet, strictValidation: Boolean): Checked[Executable]
+  def toWomExecutable(a: A,
+                      inputs: Option[WorkflowJson],
+                      ioFunctions: IoFunctionSet,
+                      strictValidation: Boolean
+  ): Checked[Executable]
 }
 
 @typeclass
diff --git a/wom/src/main/scala/wom/transforms/WomGraphMaker.scala b/wom/src/main/scala/wom/transforms/WomGraphMaker.scala
index 7547c2e548f..f4b2c5edda1 100644
--- a/wom/src/main/scala/wom/transforms/WomGraphMaker.scala
+++ b/wom/src/main/scala/wom/transforms/WomGraphMaker.scala
@@ -6,5 +6,10 @@ import simulacrum._
 
 @typeclass
 trait WomGraphMaker[A] {
-  def toWomGraph(a: A, includeGraphNodes: Set[GraphNode], outerLookup: Map[String, GraphNodePort.OutputPort], preserveIndexForOuterLookups: Boolean, inASubworkflow: Boolean): ErrorOr[Graph]
+  def toWomGraph(a: A,
+                 includeGraphNodes: Set[GraphNode],
+                 outerLookup: Map[String, GraphNodePort.OutputPort],
+                 preserveIndexForOuterLookups: Boolean,
+                 inASubworkflow: Boolean
+  ): ErrorOr[Graph]
 }
diff --git a/wom/src/main/scala/wom/transforms/WomScatterNodeMaker.scala b/wom/src/main/scala/wom/transforms/WomScatterNodeMaker.scala
index 23bcac21176..3355ef0b37e 100644
--- a/wom/src/main/scala/wom/transforms/WomScatterNodeMaker.scala
+++ b/wom/src/main/scala/wom/transforms/WomScatterNodeMaker.scala
@@ -8,5 +8,10 @@ import simulacrum._
 
 @typeclass
 trait WomScatterNodeMaker[A] {
-  def toWomScatterNode(a: A, localLookup: Map[String, GraphNodePort.OutputPort], outerLookup: Map[String, OutputPort], preserveIndexForOuterLookups: Boolean, inASubworkflow: Boolean): ErrorOr[ScatterNodeWithNewNodes]
+  def toWomScatterNode(a: A,
+                       localLookup: Map[String, GraphNodePort.OutputPort],
+                       outerLookup: Map[String, OutputPort],
+                       preserveIndexForOuterLookups: Boolean,
+                       inASubworkflow: Boolean
+  ): ErrorOr[ScatterNodeWithNewNodes]
 }
diff --git a/wom/src/main/scala/wom/types/WomAnyType.scala b/wom/src/main/scala/wom/types/WomAnyType.scala
index 025873e7d0c..6319364887a 100644
--- a/wom/src/main/scala/wom/types/WomAnyType.scala
+++ b/wom/src/main/scala/wom/types/WomAnyType.scala
@@ -44,12 +44,13 @@ case object WomAnyType extends WomType {
   override protected def coercion = {
     case womValue: WomValue => womValue
     case any: Any =>
-
-      def foldFun(acc: Option[WomValue], nextType: WomType): Option[WomValue] = acc.orElse(nextType.coerceRawValue(any).toOption)
+      def foldFun(acc: Option[WomValue], nextType: WomType): Option[WomValue] =
+        acc.orElse(nextType.coerceRawValue(any).toOption)
 
       /* This does throw an exception if it couldn't coerce (.get is intentional) */
-      WomType.womTypeCoercionOrder.foldLeft[Option[WomValue]](None)(foldFun).getOrElse(
-            throw new UnsupportedOperationException(s"Could not coerce $any into a WOM type"))
+      WomType.womTypeCoercionOrder
+        .foldLeft[Option[WomValue]](None)(foldFun)
+        .getOrElse(throw new UnsupportedOperationException(s"Could not coerce $any into a WOM type"))
 //
 //
 //      WomType.womTypeCoercionOrder.map(_.coerceRawValue(any)).find(_.isSuccess).getOrElse(
@@ -57,7 +58,7 @@ case object WomAnyType extends WomType {
 //      ).get
   }
 
-  override final def typeSpecificIsCoerceableFrom(otherType: WomType): Boolean = true
+  final override def typeSpecificIsCoerceableFrom(otherType: WomType): Boolean = true
 
   override def add(rhs: WomType): Try[WomType] = Success(WomAnyType)
   override def subtract(rhs: WomType): Try[WomType] = Success(WomAnyType)
diff --git a/wom/src/main/scala/wom/types/WomArrayType.scala b/wom/src/main/scala/wom/types/WomArrayType.scala
index 86343179ddd..41c3f0cb2db 100644
--- a/wom/src/main/scala/wom/types/WomArrayType.scala
+++ b/wom/src/main/scala/wom/types/WomArrayType.scala
@@ -14,8 +14,8 @@ sealed trait WomArrayType extends WomType {
   val guaranteedNonEmpty: Boolean
 
   private def coerceIterable(values: Seq[Any]): WomArray = values match {
-    case s:Seq[Any] if s.nonEmpty =>
-      val coerced = s.map {memberType.coerceRawValue(_).get}
+    case s: Seq[Any] if s.nonEmpty =>
+      val coerced = s.map(memberType.coerceRawValue(_).get)
       WomArray(this, coerced)
     case _ => WomArray(this, Seq())
   }
@@ -27,18 +27,23 @@ sealed trait WomArrayType extends WomType {
     case javaList: java.util.List[_] if allowEmpty || !javaList.isEmpty => coerceIterable(javaList.asScala.toList)
     case WomArray(WomMaybeEmptyArrayType.EmptyArrayType, _) => WomArray(this, Seq.empty)
     case womArray: WomArray
-      if (allowEmpty || womArray.nonEmpty)
-        && womArray.womType.memberType == WomStringType
-        && memberType == WomSingleFileType =>
+        if (allowEmpty || womArray.nonEmpty)
+          && womArray.womType.memberType == WomStringType
+          && memberType == WomSingleFileType =>
       WomArray(this, womArray.value.map(str => WomSingleFile(str.asInstanceOf[WomString].value)).toList)
-    case womArray: WomArray if (allowEmpty || womArray.nonEmpty) && womArray.womType.memberType == memberType => WomArray(this, womArray.value)
-    case womArray: WomArray if (allowEmpty || womArray.nonEmpty) && womArray.womType.memberType == WomAnyType => coerceIterable(womArray.value)
-    case womArray: WomArray if (allowEmpty || womArray.nonEmpty) && womArray.womType.memberType.isInstanceOf[WomArrayType] && memberType.isInstanceOf[WomArrayType] =>
+    case womArray: WomArray if (allowEmpty || womArray.nonEmpty) && womArray.womType.memberType == memberType =>
+      WomArray(this, womArray.value)
+    case womArray: WomArray if (allowEmpty || womArray.nonEmpty) && womArray.womType.memberType == WomAnyType =>
+      coerceIterable(womArray.value)
+    case womArray: WomArray
+        if (allowEmpty || womArray.nonEmpty) && womArray.womType.memberType.isInstanceOf[WomArrayType] && memberType
+          .isInstanceOf[WomArrayType] =>
       TryUtil.sequence(womArray.value.map(memberType.coerceRawValue)) match {
         case Success(values) => WomArray(this, values)
         case Failure(ex) => throw ex
       }
-    case womArray: WomArray if (allowEmpty || womArray.nonEmpty) && memberType.isCoerceableFrom(womArray.womType.memberType) =>
+    case womArray: WomArray
+        if (allowEmpty || womArray.nonEmpty) && memberType.isCoerceableFrom(womArray.womType.memberType) =>
       womArray.map(v => memberType.coerceRawValue(v).get) // .get because isCoerceableFrom should make it safe
     case WomArrayLike(womArray) if this.isCoerceableFrom(womArray.womType) => coercion.apply(womArray)
   }
@@ -81,11 +86,10 @@ object WomArrayType {
     if (guaranteedNonEmpty) WomNonEmptyArrayType(memberType)
     else WomMaybeEmptyArrayType(memberType)
 
-  def unapply(womType: WomType): Option[WomType] = {
+  def unapply(womType: WomType): Option[WomType] =
     womType match {
       case arrayType: WomArrayType => Option(arrayType.memberType)
       case mapType: WomMapType => Option(mapType.equivalentArrayType.memberType)
       case _ => None
     }
-  }
 }
diff --git a/wom/src/main/scala/wom/types/WomBooleanType.scala b/wom/src/main/scala/wom/types/WomBooleanType.scala
index 46cacb82f36..53d121b50c5 100644
--- a/wom/src/main/scala/wom/types/WomBooleanType.scala
+++ b/wom/src/main/scala/wom/types/WomBooleanType.scala
@@ -19,7 +19,7 @@ case object WomBooleanType extends WomPrimitiveType {
   }
 
   private def comparisonOperator(rhs: WomType, symbol: String): Try[WomType] = rhs match {
-    case wct:WomCoproductType => wct.typeExists(WomStringType)
+    case wct: WomCoproductType => wct.typeExists(WomStringType)
     case WomBooleanType => Success(WomBooleanType)
     case WomOptionalType(memberType) => comparisonOperator(memberType, symbol)
     case _ => invalid(s"$this $symbol $rhs")
diff --git a/wom/src/main/scala/wom/types/WomCompositeType.scala b/wom/src/main/scala/wom/types/WomCompositeType.scala
index b72d3ff6b0e..597b2623a2a 100644
--- a/wom/src/main/scala/wom/types/WomCompositeType.scala
+++ b/wom/src/main/scala/wom/types/WomCompositeType.scala
@@ -7,47 +7,52 @@ import common.validation.Validation._
 import spray.json.JsObject
 import wom.values.{WomMap, WomObject, WomObjectLike, WomValue}
 
-case class WomCompositeType(typeMap: Map[String, WomType], structName: Option[String] = None) extends WomObjectTypeLike {
+case class WomCompositeType(typeMap: Map[String, WomType], structName: Option[String] = None)
+    extends WomObjectTypeLike {
 
-  private def validateType(values: Map[String, Any])(key: String, expectedType: WomType): ErrorOr[(String, WomValue)] = {
+  private def validateType(values: Map[String, Any])(key: String, expectedType: WomType): ErrorOr[(String, WomValue)] =
     (values.get(key), expectedType) match {
       case (Some(value), _) => expectedType.coerceRawValue(value).toErrorOr.map(key -> _)
       case (None, coerceTo: WomOptionalType) => (key -> coerceTo.none).validNel
       case (None, _) =>
         s"No value for field '$key' with non optional type '${expectedType.stableName}' has been provided".invalidNel
     }
-  }
 
-  override def validateAndCoerceValues(values: Map[String, Any]): ErrorOr[Map[String, WomValue]] = {
+  override def validateAndCoerceValues(values: Map[String, Any]): ErrorOr[Map[String, WomValue]] =
     typeMap.toList.traverse(Function.tupled(validateType(values))).map(_.toMap)
-  }
 
   override protected def coercion = {
-    case composite: WomObjectLike if isCoerceableFrom(composite.womType) => WomObject.withTypeUnsafe(composite.values, this)
-    case map: WomMap if WomStringType.isCoerceableFrom(map.womType.keyType) => WomObject.withTypeUnsafe(map.value.map({ case (k, v) => k.valueString -> v }), this)
+    case composite: WomObjectLike if isCoerceableFrom(composite.womType) =>
+      WomObject.withTypeUnsafe(composite.values, this)
+    case map: WomMap if WomStringType.isCoerceableFrom(map.womType.keyType) =>
+      WomObject.withTypeUnsafe(map.value.map { case (k, v) => k.valueString -> v }, this)
     case jsObject: JsObject => WomObject.withTypeUnsafe(jsObject.fields, this)
   }
 
-  override def typeSpecificIsCoerceableFrom(otherType: WomType): Boolean = {
+  override def typeSpecificIsCoerceableFrom(otherType: WomType): Boolean =
     otherType match {
       // This is as good as we can do here without the values
       case mapType: WomMapType if WomStringType.isCoerceableFrom(mapType.keyType) => true
       // Same here, it might not be coerceable but without the values we can't tell
       case WomObjectType => true
-      case compositeType: WomCompositeType if (compositeType.typeMap.size == typeMap.size) &&
-        compositeType.typeMap.forall({ case (key, typeValue) => typeMap.get(key).exists(_.isCoerceableFrom(typeValue)) }) =>
+      case compositeType: WomCompositeType
+          if (compositeType.typeMap.size == typeMap.size) &&
+            compositeType.typeMap.forall { case (key, typeValue) =>
+              typeMap.get(key).exists(_.isCoerceableFrom(typeValue))
+            } =>
         true
 
       case _ => false
     }
-  }
 
   override val friendlyName: String = structName.getOrElse("Object")
 
   override val stableName = {
-    val fieldType = typeMap.map({
-      case (key, value) => s"$key -> ${value.stableName}"
-    }).mkString("\n")
+    val fieldType = typeMap
+      .map { case (key, value) =>
+        s"$key -> ${value.stableName}"
+      }
+      .mkString("\n")
 
     s"WomCompositeType {\n $fieldType \n}"
   }
diff --git a/wom/src/main/scala/wom/types/WomCoproductType.scala b/wom/src/main/scala/wom/types/WomCoproductType.scala
index 9b05ee92f9c..c83a75acd7a 100644
--- a/wom/src/main/scala/wom/types/WomCoproductType.scala
+++ b/wom/src/main/scala/wom/types/WomCoproductType.scala
@@ -19,35 +19,48 @@ case class WomCoproductType(types: NonEmptyList[WomType]) extends WomType {
     * the partial function is not defined are assumed to not be convertible to the target type.
     */
   override def coercion: PartialFunction[Any, WomValue] = {
-    case wct@WomCoproductValue(tpe, _) if (tpe.equalsType(this).isSuccess) => wct
+    case wct @ WomCoproductValue(tpe, _) if tpe.equalsType(this).isSuccess => wct
 
-    //If we can find this type exactly in our coproduct, use that type for the coercion
-    case womValue: WomValue if (types.toList.contains(womValue.womType)) =>
+    // If we can find this type exactly in our coproduct, use that type for the coercion
+    case womValue: WomValue if types.toList.contains(womValue.womType) =>
       val v: Try[WomValue] = womValue.womType.coerceRawValue(womValue)
       WomCoproductValue(this, v.get)
 
-    //If we don't have any information, try to coerce this value one by one, stopping at the first successful try
+    // If we don't have any information, try to coerce this value one by one, stopping at the first successful try
     case any =>
       val triedToCoerce: Try[WomValue] = types.map(_.coerceRawValue(any)).toList.reduce(_ orElse _)
 
-      triedToCoerce.getOrElse(throw new WomTypeException(s"unable to coerce $any to a member of the set of types ${types.toList.mkString(", ")}")) |> (WomCoproductValue(this, _))
+      triedToCoerce.getOrElse(
+        throw new WomTypeException(
+          s"unable to coerce $any to a member of the set of types ${types.toList.mkString(", ")}"
+        )
+      ) |> (WomCoproductValue(this, _))
   }
 
   def typeExists(tpe: WomType): Try[WomBooleanType.type] =
     types.exists(_.equals(tpe)) match {
       case true => Success(WomBooleanType)
-      case _ => Failure(new WomExpressionException(s"Type equality assertion failed because $tpe was not found in the coproduct of ${stableName}"))
+      case _ =>
+        Failure(
+          new WomExpressionException(
+            s"Type equality assertion failed because $tpe was not found in the coproduct of ${stableName}"
+          )
+        )
     }
 
   override def stableName: String =
-    types.map(_.stableName).toList.mkString("Coproduct[",", ", "]")
+    types.map(_.stableName).toList.mkString("Coproduct[", ", ", "]")
 
   override def equalsType(rhs: WomType): Try[WomType] =
     rhs match {
       case WomCoproductType(tpes) if types.equals(tpes) => Success(WomBooleanType)
-      case _ if types.exists(_.equals(rhs)) =>  Success(WomBooleanType)
-      case _ => Failure(new WomExpressionException(s"Type equality could not be asserted because $rhs was found in the coproduct of $stableName"))
+      case _ if types.exists(_.equals(rhs)) => Success(WomBooleanType)
+      case _ =>
+        Failure(
+          new WomExpressionException(
+            s"Type equality could not be asserted because $rhs was found in the coproduct of $stableName"
+          )
+        )
     }
 
-
 }
diff --git a/wom/src/main/scala/wom/types/WomEnumerationType.scala b/wom/src/main/scala/wom/types/WomEnumerationType.scala
index ed9d7ce746c..33a4df63dcc 100644
--- a/wom/src/main/scala/wom/types/WomEnumerationType.scala
+++ b/wom/src/main/scala/wom/types/WomEnumerationType.scala
@@ -4,18 +4,18 @@ import cats.data.NonEmptyList
 import spray.json.JsString
 import wom.values.{WomEnumerationValue, WomValue}
 
-
 /**
   * An enumeration of possible states a value can inhabit.
   */
 case class WomEnumerationType(values: NonEmptyList[String]) extends WomPrimitiveType {
 
   override def coercion: PartialFunction[Any, WomValue] = {
-    case womValue: WomValue if (values.toList.contains(womValue.valueString)) => WomEnumerationValue(this, womValue.valueString)
-    case name: String if (values.toList.contains(name)) => WomEnumerationValue(this, name)
-    case JsString(name)  if (values.toList.contains(name)) => WomEnumerationValue(this, name)
+    case womValue: WomValue if values.toList.contains(womValue.valueString) =>
+      WomEnumerationValue(this, womValue.valueString)
+    case name: String if values.toList.contains(name) => WomEnumerationValue(this, name)
+    case JsString(name) if values.toList.contains(name) => WomEnumerationValue(this, name)
   }
 
   override def stableName: String =
-    values.toList.mkString("Enumeration[",", ", "]")
+    values.toList.mkString("Enumeration[", ", ", "]")
 }
diff --git a/wom/src/main/scala/wom/types/WomFileType.scala b/wom/src/main/scala/wom/types/WomFileType.scala
index ff82a448be8..a31a4e2f535 100644
--- a/wom/src/main/scala/wom/types/WomFileType.scala
+++ b/wom/src/main/scala/wom/types/WomFileType.scala
@@ -52,7 +52,7 @@ case object WomSingleFileType extends WomPrimitiveFileType {
   }
 
   override def equalsType(rhs: WomType): Try[WomType] = rhs match {
-    case wct:WomCoproductType => wct.typeExists(WomStringType)
+    case wct: WomCoproductType => wct.typeExists(WomStringType)
     case WomSingleFileType => Success(WomBooleanType)
     case WomStringType => Success(WomBooleanType)
     case WomOptionalType(memberType) => equalsType(memberType)
@@ -77,7 +77,7 @@ case object WomGlobFileType extends WomPrimitiveFileType {
   }
 
   override def equalsType(rhs: WomType): Try[WomType] = rhs match {
-    case wct:WomCoproductType => wct.typeExists(WomStringType)
+    case wct: WomCoproductType => wct.typeExists(WomStringType)
     case WomGlobFileType => Success(WomBooleanType)
     case WomStringType => Success(WomBooleanType)
     case WomOptionalType(memberType) => equalsType(memberType)
diff --git a/wom/src/main/scala/wom/types/WomFloatType.scala b/wom/src/main/scala/wom/types/WomFloatType.scala
index b7d2d6991b8..f877de38f31 100644
--- a/wom/src/main/scala/wom/types/WomFloatType.scala
+++ b/wom/src/main/scala/wom/types/WomFloatType.scala
@@ -29,7 +29,7 @@ case object WomFloatType extends WomPrimitiveType {
   }
 
   private def comparisonOperator(rhs: WomType, symbol: String): Try[WomType] = rhs match {
-    case wct:WomCoproductType => wct.typeExists(WomStringType)
+    case wct: WomCoproductType => wct.typeExists(WomStringType)
     case WomIntegerType => Success(WomBooleanType)
     case WomFloatType => Success(WomBooleanType)
     case WomOptionalType(memberType) => comparisonOperator(memberType, symbol)
diff --git a/wom/src/main/scala/wom/types/WomIntegerLike.scala b/wom/src/main/scala/wom/types/WomIntegerLike.scala
index 00dce7751bc..6432b9533f7 100644
--- a/wom/src/main/scala/wom/types/WomIntegerLike.scala
+++ b/wom/src/main/scala/wom/types/WomIntegerLike.scala
@@ -1,6 +1,5 @@
 package wom.types
 
-
 object WomIntegerLike {
   implicit class EnhancedLong(val long: Long) extends AnyVal {
     def inIntRange: Boolean = long >= Int.MinValue && long <= Int.MaxValue
diff --git a/wom/src/main/scala/wom/types/WomIntegerType.scala b/wom/src/main/scala/wom/types/WomIntegerType.scala
index a177dd5d924..e5f87c9dfdb 100644
--- a/wom/src/main/scala/wom/types/WomIntegerType.scala
+++ b/wom/src/main/scala/wom/types/WomIntegerType.scala
@@ -14,11 +14,12 @@ case object WomIntegerType extends WomPrimitiveType {
     case n: JsNumber if n.value.isValidInt => WomInteger(n.value.intValue)
     case i: WomInteger => i
     case WomLong(i) if i.inIntRange => WomInteger(i.toInt)
-    case WomLong(i) => throw new RuntimeException(
-      s"Tried to convert a Long value $i into an Int but it was outside the bounds of acceptable Ints, namely ${Int.MinValue} <-> ${Int.MaxValue}")
-    case s: WomString => {
-        WomInteger(s.value.toInt)
-    }
+    case WomLong(i) =>
+      throw new RuntimeException(
+        s"Tried to convert a Long value $i into an Int but it was outside the bounds of acceptable Ints, namely ${Int.MinValue} <-> ${Int.MaxValue}"
+      )
+    case s: WomString =>
+      WomInteger(s.value.toInt)
     case s: String =>
       val bigTry = Try(BigDecimal(s))
       if (bigTry.isSuccess)
@@ -36,14 +37,13 @@ case object WomIntegerType extends WomPrimitiveType {
   }
 
   private def comparisonOperator(rhs: WomType, symbol: String): Try[WomType] = rhs match {
-    case wct:WomCoproductType => wct.typeExists(WomStringType)
+    case wct: WomCoproductType => wct.typeExists(WomStringType)
     case WomIntegerType => Success(WomBooleanType)
     case WomFloatType => Success(WomBooleanType)
     case WomOptionalType(memberType) => comparisonOperator(memberType, symbol)
     case _ => invalid(s"$this $symbol $rhs")
   }
 
-
   override def add(rhs: WomType): Try[WomType] = rhs match {
     case WomStringType => Success(WomStringType)
     case WomOptionalType(memberType) => add(memberType)
diff --git a/wom/src/main/scala/wom/types/WomNothingType.scala b/wom/src/main/scala/wom/types/WomNothingType.scala
index 1c7ec161d77..20d9bcd76a7 100644
--- a/wom/src/main/scala/wom/types/WomNothingType.scala
+++ b/wom/src/main/scala/wom/types/WomNothingType.scala
@@ -7,8 +7,8 @@ import wom.values.{WomOptionalValue, WomValue}
   * (and yet at the same time, most) interesting of all the types, the WomNothingType!
   */
 case object WomNothingType extends WomType {
-  override protected def coercion: PartialFunction[Any, WomValue] = {
-    case WomOptionalValue(WomNothingType, None) => WomOptionalValue(WomNothingType, None)
+  override protected def coercion: PartialFunction[Any, WomValue] = { case WomOptionalValue(WomNothingType, None) =>
+    WomOptionalValue(WomNothingType, None)
   }
   override def stableName: String = "Nothing"
 }
diff --git a/wom/src/main/scala/wom/types/WomObjectType.scala b/wom/src/main/scala/wom/types/WomObjectType.scala
index e1a067eaed9..9d28c84b5b3 100644
--- a/wom/src/main/scala/wom/types/WomObjectType.scala
+++ b/wom/src/main/scala/wom/types/WomObjectType.scala
@@ -10,25 +10,27 @@ import wom.values._
 import scala.util.{Failure, Success, Try}
 
 trait WomObjectTypeLike extends WomType {
+
   /**
     * Validate the values against the WomObjectTypeLike and return a valid map of values if possible.
     * This is an indirection from the usual coercion path but it allows WomObject to validate values against the WomObjectTypeLike at
     * instantiation time and ensure the WomObject is only built if the values match the constraints of the type.
     * See apply method in WomObject.
    */
-  def validateAndCoerceValues(values: Map[String, Any]): ErrorOr[Map[String, WomValue]] = {
-    values.toList.traverse({
-      case (k, v) => WomAnyType.coerceRawValue(v).toErrorOr.map(k -> _)
-    }).map(_.toMap)
-  }
+  def validateAndCoerceValues(values: Map[String, Any]): ErrorOr[Map[String, WomValue]] =
+    values.toList
+      .traverse { case (k, v) =>
+        WomAnyType.coerceRawValue(v).toErrorOr.map(k -> _)
+      }
+      .map(_.toMap)
 }
 
 case object WomObjectType extends WomObjectTypeLike {
   val stableName: String = "Object"
 
   private def handleCoercionFailures(tries: Try[_]*) = {
-    val errorMessages = tries collect {
-      case Failure(f) => f.getMessage
+    val errorMessages = tries collect { case Failure(f) =>
+      f.getMessage
     } mkString ","
 
     throw new UnsupportedOperationException(s"Coercion failed: $errorMessages")
@@ -37,8 +39,8 @@ case object WomObjectType extends WomObjectTypeLike {
   override protected def coercion = {
     case o: WomObjectLike => WomObject(o.values)
     case m: WomMap if isMapCoercable(m) =>
-      val coercedMap = m.value map {
-        case (k, v) => toWomString(k) -> toWomString(v)
+      val coercedMap = m.value map { case (k, v) =>
+        toWomString(k) -> toWomString(v)
       } collect {
         case (Success(k), Success(v)) => k.value -> v
         case (k, v) => handleCoercionFailures(k, v)
@@ -46,7 +48,6 @@ case object WomObjectType extends WomObjectTypeLike {
 
       WomObject(coercedMap)
     case js: JsObject =>
-
       val mapToTry = js.fields map { case (key, value) => key -> WomAnyType.coerceRawValue(value) }
       val mapOfTry = mapToTry map { kvp => kvp._2 map { kvp._1 -> _ } }
       // The TryUtil exception is ignored, we only use it to tell whether it worked or not. We use handleCoercionFailures
@@ -65,6 +66,7 @@ case object WomObjectType extends WomObjectTypeLike {
     case _ => false
   }
 
-  def isMapTypeCoercable(t: WomMapType) = WomStringType.isCoerceableFrom(t.keyType) && WomStringType.isCoerceableFrom(t.valueType)
+  def isMapTypeCoercable(t: WomMapType) =
+    WomStringType.isCoerceableFrom(t.keyType) && WomStringType.isCoerceableFrom(t.valueType)
   def isMapCoercable(m: WomMap) = isMapTypeCoercable(m.womType)
 }
diff --git a/wom/src/main/scala/wom/types/WomOptionalType.scala b/wom/src/main/scala/wom/types/WomOptionalType.scala
index 37b8bcd491a..e1e4e1b5f83 100644
--- a/wom/src/main/scala/wom/types/WomOptionalType.scala
+++ b/wom/src/main/scala/wom/types/WomOptionalType.scala
@@ -11,6 +11,7 @@ case class WomOptionalType(memberType: WomType) extends WomType {
     case recursive: WomOptionalType => 1 + recursive.depth
     case _ => 1
   }
+
   /**
     * Method to be overridden by implementation classes defining a partial function
     * for the conversion of raw input values to specific implementation class value types.
@@ -25,16 +26,19 @@ case class WomOptionalType(memberType: WomType) extends WomType {
     case None => WomOptionalValue(memberType, None)
 
     // Coerce and adjust nesting level of equivalent nested conditionals:
-    case womOptional: WomOptionalValue if baseMemberType.isCoerceableFrom(womOptional.womType.baseMemberType) => womOptional.coerceAndSetNestingLevel(this).get
+    case womOptional: WomOptionalValue if baseMemberType.isCoerceableFrom(womOptional.womType.baseMemberType) =>
+      womOptional.coerceAndSetNestingLevel(this).get
 
     // It's safe to box up values implicitly:
-    case womValue: WomValue if baseMemberType.isCoerceableFrom(womValue.womType) => WomOptionalValue(womValue).coerceAndSetNestingLevel(this).get
+    case womValue: WomValue if baseMemberType.isCoerceableFrom(womValue.womType) =>
+      WomOptionalValue(womValue).coerceAndSetNestingLevel(this).get
 
     case WomOptionalValue(WomNothingType, None) => WomOptionalValue(memberType, None)
 
     case null => WomOptionalValue(memberType, None)
 
-    case coerceable: Any if baseMemberType.coercionDefined(coerceable) => WomOptionalValue(baseMemberType.coerceRawValue(coerceable).get).coerceAndSetNestingLevel(this).get
+    case coerceable: Any if baseMemberType.coercionDefined(coerceable) =>
+      WomOptionalValue(baseMemberType.coerceRawValue(coerceable).get).coerceAndSetNestingLevel(this).get
   }
 
   override def typeSpecificIsCoerceableFrom(otherType: WomType): Boolean = otherType match {
@@ -46,7 +50,8 @@ case class WomOptionalType(memberType: WomType) extends WomType {
     case WomOptionalType(otherMemberType) if memberType.isCoerceableFrom(otherMemberType) => true
 
     // Check flattening:
-    case WomOptionalType(otherMemberType: WomOptionalType) => baseMemberType.isCoerceableFrom(otherMemberType.baseMemberType)
+    case WomOptionalType(otherMemberType: WomOptionalType) =>
+      baseMemberType.isCoerceableFrom(otherMemberType.baseMemberType)
 
     case _ => false
   }
diff --git a/wom/src/main/scala/wom/types/WomPairType.scala b/wom/src/main/scala/wom/types/WomPairType.scala
index fd9bd3ffd3a..69347d291b6 100644
--- a/wom/src/main/scala/wom/types/WomPairType.scala
+++ b/wom/src/main/scala/wom/types/WomPairType.scala
@@ -8,7 +8,8 @@ import scala.util.{Failure, Success, Try}
 case class WomPairType(leftType: WomType, rightType: WomType) extends WomType {
 
   override def typeSpecificIsCoerceableFrom(otherType: WomType): Boolean = otherType match {
-    case WomPairType(otherType1, otherType2) => leftType.isCoerceableFrom(otherType1) && rightType.isCoerceableFrom(otherType2)
+    case WomPairType(otherType1, otherType2) =>
+      leftType.isCoerceableFrom(otherType1) && rightType.isCoerceableFrom(otherType2)
     case _ => false
   }
 
@@ -27,25 +28,34 @@ case class WomPairType(leftType: WomType, rightType: WomType) extends WomType {
 
   def coercePair(m: Map[String, JsValue], womPairType: WomPairType): WomPair = {
 
-    val caseNormalizedMap = m map { case(k, v) => k.toLowerCase.capitalize -> v }
+    val caseNormalizedMap = m map { case (k, v) => k.toLowerCase.capitalize -> v }
 
-    def invalidPair(missingArgs: String*) = Seq(Failure(new IllegalArgumentException(s"Pair ${JsObject(m)} requires for ${missingArgs.mkString("/")} value(s) to be defined.")))
+    def invalidPair(missingArgs: String*) = Seq(
+      Failure(
+        new IllegalArgumentException(
+          s"Pair ${JsObject(m)} requires for ${missingArgs.mkString("/")} value(s) to be defined."
+        )
+      )
+    )
 
     val womPair: Seq[Try[WomValue]] = (caseNormalizedMap.get("Left"), caseNormalizedMap.get("Right")) match {
-      case (Some(leftVal), Some(rightVal)) => Seq(womPairType.leftType.coerceRawValue(leftVal), womPairType.rightType.coerceRawValue(rightVal))
+      case (Some(leftVal), Some(rightVal)) =>
+        Seq(womPairType.leftType.coerceRawValue(leftVal), womPairType.rightType.coerceRawValue(rightVal))
       case (Some(_), _) => invalidPair("Right")
       case (_, Some(_)) => invalidPair("Left")
       case _ => invalidPair("Right", "Left")
     }
 
-    val failures = womPair collect { case f:Failure[_] => f }
+    val failures = womPair collect { case f: Failure[_] => f }
 
     if (failures.isEmpty) {
       womPair match {
         case Seq(Success(left), Success(right)) => WomPair(left, right)
       }
     } else {
-      throw new UnsupportedOperationException(s"Failed to coerce one or more values for creating a ${womPairType.stableName}:\n${failures.toList.mkString("\n")}")
+      throw new UnsupportedOperationException(
+        s"Failed to coerce one or more values for creating a ${womPairType.stableName}:\n${failures.toList.mkString("\n")}"
+      )
     }
   }
 
diff --git a/wom/src/main/scala/wom/types/WomPrimitiveType.scala b/wom/src/main/scala/wom/types/WomPrimitiveType.scala
index 1fc6dabbd59..fe48758b9d6 100644
--- a/wom/src/main/scala/wom/types/WomPrimitiveType.scala
+++ b/wom/src/main/scala/wom/types/WomPrimitiveType.scala
@@ -14,10 +14,9 @@ trait WomPrimitiveType extends WomType {
     WomBooleanType -> Seq(WomStringType, WomBooleanType)
   )
 
-  override def typeSpecificIsCoerceableFrom(otherType: WomType): Boolean = {
+  override def typeSpecificIsCoerceableFrom(otherType: WomType): Boolean =
     coercionMap.get(otherType) match {
       case Some(types) => types contains this
       case None => false
     }
-  }
 }
diff --git a/wom/src/main/scala/wom/types/WomStringType.scala b/wom/src/main/scala/wom/types/WomStringType.scala
index d9ce21007f5..c417ebbaa84 100644
--- a/wom/src/main/scala/wom/types/WomStringType.scala
+++ b/wom/src/main/scala/wom/types/WomStringType.scala
@@ -17,7 +17,7 @@ case object WomStringType extends WomPrimitiveType {
   }
 
   private def comparisonOperator(rhs: WomType, symbol: String): Try[WomType] = rhs match {
-    case wct:WomCoproductType => wct.typeExists(WomStringType)
+    case wct: WomCoproductType => wct.typeExists(WomStringType)
     case WomStringType => Success(WomBooleanType)
     case WomOptionalType(memberType) => comparisonOperator(memberType, symbol)
     case _ => invalid(s"$this $symbol $rhs")
diff --git a/wom/src/main/scala/wom/types/WomType.scala b/wom/src/main/scala/wom/types/WomType.scala
index 47d9f3dab80..71c770ea000 100644
--- a/wom/src/main/scala/wom/types/WomType.scala
+++ b/wom/src/main/scala/wom/types/WomType.scala
@@ -24,19 +24,26 @@ trait WomType {
    * Public interface for a `Try`-wrapped conversion of an input of type `Any` to
    * a `WomValue`.
    */
-  final def coerceRawValue(any: Any): Try[WomValue] = {
+  final def coerceRawValue(any: Any): Try[WomValue] =
     any match {
       case womValue: WomValue if womValue.womType == this => Success(womValue)
       case WomOptionalValue(_, Some(v)) => coerceRawValue(v)
-      case womValue: WomValue if !coercion.isDefinedAt(any) => Failure(new IllegalArgumentException(
-        s"No coercion defined from wom value(s) '${WomValue.takeMaxElements(womValue, 3).toWomString}' of type" +
-          s" '${womValue.womType.stableName}' to '$stableName'."))
-      case _ if !coercion.isDefinedAt(any) => Failure(new IllegalArgumentException(
-        s"No coercion defined from '${ScalaRunTime.stringOf(any, 3)}' of type" +
-          s" '${Option(any.getClass.getCanonicalName).getOrElse(any.getClass.getName)}' to '$stableName'."))
+      case womValue: WomValue if !coercion.isDefinedAt(any) =>
+        Failure(
+          new IllegalArgumentException(
+            s"No coercion defined from wom value(s) '${WomValue.takeMaxElements(womValue, 3).toWomString}' of type" +
+              s" '${womValue.womType.stableName}' to '$stableName'."
+          )
+        )
+      case _ if !coercion.isDefinedAt(any) =>
+        Failure(
+          new IllegalArgumentException(
+            s"No coercion defined from '${ScalaRunTime.stringOf(any, 3)}' of type" +
+              s" '${Option(any.getClass.getCanonicalName).getOrElse(any.getClass.getName)}' to '$stableName'."
+          )
+        )
       case _ => Try(coercion(any))
     }
-  }
 
   final def isCoerceableFrom(otherType: WomType): Boolean = otherType match {
     case WomAnyType => true
@@ -57,28 +64,30 @@ trait WomType {
     */
   def stableName: String
 
-  def invalid(operation: String) = Failure(new WomExpressionException(s"Type evaluation cannot determine type from expression: $operation"))
+  def invalid(operation: String) = Failure(
+    new WomExpressionException(s"Type evaluation cannot determine type from expression: $operation")
+  )
   def add(rhs: WomType): Try[WomType] = invalid(s"$this + $rhs")
   def subtract(rhs: WomType): Try[WomType] = invalid(s"$this - $rhs")
   def multiply(rhs: WomType): Try[WomType] = invalid(s"$this * $rhs")
   def divide(rhs: WomType): Try[WomType] = invalid(s"$this / $rhs")
   def mod(rhs: WomType): Try[WomType] = invalid(s"$this % $rhs")
   def equalsType(rhs: WomType): Try[WomType] =
-    if(this == rhs)
+    if (this == rhs)
       Success(WomBooleanType)
     else
       invalid(s"$this == $rhs")
-  def notEquals(rhs: WomType): Try[WomType] = equalsType(rhs) map { _ => WomBooleanType}
+  def notEquals(rhs: WomType): Try[WomType] = equalsType(rhs) map { _ => WomBooleanType }
   def lessThan(rhs: WomType): Try[WomType] = invalid(s"$this < $rhs")
   def lessThanOrEqual(rhs: WomType): Try[WomType] = (lessThan(rhs), equalsType(rhs)) match {
-    case (Success(b:WomType), _) if b == WomBooleanType => Success(WomBooleanType)
-    case (_, Success(b:WomType)) if b == WomBooleanType => Success(WomBooleanType)
+    case (Success(b: WomType), _) if b == WomBooleanType => Success(WomBooleanType)
+    case (_, Success(b: WomType)) if b == WomBooleanType => Success(WomBooleanType)
     case (_, _) => invalid(s"$this <= $rhs")
   }
   def greaterThan(rhs: WomType): Try[WomType] = invalid(s"$this > $rhs")
   def greaterThanOrEqual(rhs: WomType): Try[WomType] = (greaterThan(rhs), equalsType(rhs)) match {
-    case (Success(b:WomType), _) if b == WomBooleanType => Success(WomBooleanType)
-    case (_, Success(b:WomType)) if b == WomBooleanType => Success(WomBooleanType)
+    case (Success(b: WomType), _) if b == WomBooleanType => Success(WomBooleanType)
+    case (_, Success(b: WomType)) if b == WomBooleanType => Success(WomBooleanType)
     case (_, _) => invalid(s"$this >= $rhs")
   }
   def or(rhs: WomType): Try[WomType] = invalid(s"$this || $rhs")
@@ -91,8 +100,14 @@ trait WomType {
 object WomType {
   /* This is in the order of coercion from non-wom types */
   val womTypeCoercionOrder: Seq[WomType] = Seq(
-    WomStringType, WomIntegerType, WomFloatType, WomPairType(WomAnyType, WomAnyType), WomMapType(WomAnyType, WomAnyType),
-    WomArrayType(WomAnyType), WomBooleanType, WomObjectType,
+    WomStringType,
+    WomIntegerType,
+    WomFloatType,
+    WomPairType(WomAnyType, WomAnyType),
+    WomMapType(WomAnyType, WomAnyType),
+    WomArrayType(WomAnyType),
+    WomBooleanType,
+    WomObjectType,
     // Putting optional type last means we'll only coerce to it for JsNull.
     // That should be OK because every other type X can coerce into X? later if it needs to.
     WomOptionalType(WomAnyType)
@@ -101,13 +116,12 @@ object WomType {
   def homogeneousTypeFromValues(values: Iterable[WomValue]): WomType =
     homogeneousTypeFromTypes(values.map(_.womType))
 
-  def homogeneousTypeFromTypes(types: Iterable[WomType]): WomType = {
+  def homogeneousTypeFromTypes(types: Iterable[WomType]): WomType =
     types.toSet match {
       case s if s.isEmpty => WomNothingType
       case s if s.size == 1 => s.head
       case _ => lowestCommonSubtype(types)
     }
-  }
 
   def lowestCommonSubtype(types: Iterable[WomType]): WomType = types match {
     case e if e.isEmpty => WomNothingType
@@ -121,14 +135,19 @@ object WomType {
   }
 
   private object ListOfPrimitives {
-    def unapply(types: Iterable[WomType]): Option[WomType] = {
+    def unapply(types: Iterable[WomType]): Option[WomType] =
       if (types.forall(_.isInstanceOf[WomPrimitiveType])) {
         firstCommonPrimitive(types)
       } else None
-    }
 
     val coercePriority = List(
-      WomStringType, WomSingleFileType, WomUnlistedDirectoryType, WomFloatType, WomIntegerType, WomBooleanType, WomObjectType
+      WomStringType,
+      WomSingleFileType,
+      WomUnlistedDirectoryType,
+      WomFloatType,
+      WomIntegerType,
+      WomBooleanType,
+      WomObjectType
     )
 
     private def firstCommonPrimitive(types: Iterable[WomType]): Option[WomType] = {
@@ -138,20 +157,18 @@ object WomType {
       // A type not in the incoming list but which everything could coerce to nonetheless:
       lazy val unsuppliedOption: Option[WomType] = coercePriority.find(p => types.forall(p.isCoerceableFrom))
 
-      coercePriority.find { p => suppliedOptions.toList.contains(p) } orElse { unsuppliedOption }
+      coercePriority.find(p => suppliedOptions.toList.contains(p)) orElse unsuppliedOption
     }
   }
 
-
   private object ListOfPairs {
-    def unapply(types: Iterable[WomType]): Option[WomPairType] = {
+    def unapply(types: Iterable[WomType]): Option[WomPairType] =
       if (types.forall(_.isInstanceOf[WomPairType])) {
         val pairs = types.map(_.asInstanceOf[WomPairType])
         val leftType = lowestCommonSubtype(pairs.map(_.leftType))
         val rightType = lowestCommonSubtype(pairs.map(_.rightType))
         Some(WomPairType(leftType, rightType))
       } else None
-    }
   }
 
   private object ListOfOptionals {
@@ -218,7 +235,7 @@ object WomType {
         that cannot be coerced.
 
         Equivalent to logic found in typeSpecificIsCoerceableFrom on WomArrayType.
-        */
+         */
         val memberType = lowestCommonSubtype(arrs.map(_.memberType).filterNot(_.equals(WomNothingType)))
         Some(WomArrayType(memberType))
       } else None
diff --git a/wom/src/main/scala/wom/types/WomTypeJsonFormatter.scala b/wom/src/main/scala/wom/types/WomTypeJsonFormatter.scala
index a8eb4a2905e..28110cf61b7 100644
--- a/wom/src/main/scala/wom/types/WomTypeJsonFormatter.scala
+++ b/wom/src/main/scala/wom/types/WomTypeJsonFormatter.scala
@@ -11,13 +11,11 @@ object WomTypeJsonFormatter extends DefaultJsonProtocol {
   }
 
   implicit object WorkflowInputJsonFormat extends RootJsonFormat[Map[FullyQualifiedName, InputDefinition]] {
-    def write(inputs: Map[FullyQualifiedName, InputDefinition]) = {
+    def write(inputs: Map[FullyQualifiedName, InputDefinition]) =
       JsObject(inputs map { case (fqn, input) =>
         val optional = if (input.optional) "(optional) " else ""
         fqn -> JsString(s"$optional${input.womType.stableName}")
       })
-    }
     def read(value: JsValue) = throw new UnsupportedOperationException
   }
 }
-
diff --git a/wom/src/main/scala/wom/types/coercion/defaults/package.scala b/wom/src/main/scala/wom/types/coercion/defaults/package.scala
index c76417ef385..c792970c2f8 100644
--- a/wom/src/main/scala/wom/types/coercion/defaults/package.scala
+++ b/wom/src/main/scala/wom/types/coercion/defaults/package.scala
@@ -14,20 +14,24 @@ package object defaults {
   implicit val womIntegerCoercer: WomTypeCoercer[WomInteger] = defaultCoercionForType[WomInteger](WomIntegerType)
   implicit val womFloatCoercer: WomTypeCoercer[WomFloat] = defaultCoercionForType[WomFloat](WomFloatType)
   implicit val womStringCoercer: WomTypeCoercer[WomString] = defaultCoercionForType[WomString](WomStringType)
-  implicit val womSingleFileCoercer: WomTypeCoercer[WomSingleFile] = defaultCoercionForType[WomSingleFile](WomSingleFileType)
+  implicit val womSingleFileCoercer: WomTypeCoercer[WomSingleFile] =
+    defaultCoercionForType[WomSingleFile](WomSingleFileType)
   implicit val womObjectCoercer: WomTypeCoercer[WomObject] = defaultCoercionForType[WomObject](WomObjectType)
 
   implicit val womOptionalOfAnyCoercer = defaultCoercionForType[WomOptionalValue](WomOptionalType(WomAnyType))
   implicit val womArrayOfAnyCoercer = defaultCoercionForType[WomArray](WomArrayType(WomAnyType))
   implicit val womMapOfAnyCoercer = defaultCoercionForType[WomMap](WomMapType(WomAnyType, WomAnyType))
-  implicit def womArrayTypeCoercer(arrayType: WomArrayType): WomTypeCoercer[WomArray] = defaultCoercionForType[WomArray](arrayType)
+  implicit def womArrayTypeCoercer(arrayType: WomArrayType): WomTypeCoercer[WomArray] =
+    defaultCoercionForType[WomArray](arrayType)
 
-  private def defaultCoercionForType[A](typeObject: WomType)(implicit classTag: ClassTag[A]): WomTypeCoercer[A] = new WomTypeCoercer[A] {
-    override def coerceToType(any: Any): ErrorOr[A] = typeObject.coerceRawValue(any).toErrorOr flatMap {
-      case womValue: A => womValue.validNel
-      case other => s"Bad coercion in ${getClass.getSimpleName}! Coercion should have created ${typeObject.stableName} but instead created ${other.womType.stableName}".invalidNel
+  private def defaultCoercionForType[A](typeObject: WomType)(implicit classTag: ClassTag[A]): WomTypeCoercer[A] =
+    new WomTypeCoercer[A] {
+      override def coerceToType(any: Any): ErrorOr[A] = typeObject.coerceRawValue(any).toErrorOr flatMap {
+        case womValue: A => womValue.validNel
+        case other =>
+          s"Bad coercion in ${getClass.getSimpleName}! Coercion should have created ${typeObject.stableName} but instead created ${other.womType.stableName}".invalidNel
+      }
+      override def coercionDefined(any: Any): Boolean = typeObject.coercionDefined(any)
+      override def toDisplayString: String = typeObject.stableName
     }
-    override def coercionDefined(any: Any): Boolean = typeObject.coercionDefined(any)
-    override def toDisplayString: String = typeObject.stableName
-  }
 }
diff --git a/wom/src/main/scala/wom/util/YamlUtils.scala b/wom/src/main/scala/wom/util/YamlUtils.scala
index 50dffc0457d..6375006cd7f 100644
--- a/wom/src/main/scala/wom/util/YamlUtils.scala
+++ b/wom/src/main/scala/wom/util/YamlUtils.scala
@@ -36,7 +36,7 @@ object YamlUtils {
   def parse(yaml: String,
             maxNodes: Int Refined NonNegative = defaultMaxNodes,
             maxDepth: Int Refined NonNegative = defaultMaxDepth
-           ): Either[ParsingFailure, Json] = {
+  ): Either[ParsingFailure, Json] =
     try {
       val yamlConstructor = new SafeConstructor(loaderOptions)
       val yamlComposer = new MaxDepthComposer(yaml, maxDepth)
@@ -53,16 +53,14 @@ object YamlUtils {
       case exception: Exception =>
         Left(ParsingFailure(exception.getMessage, exception))
     }
-  }
 
-  private[util] implicit val refinedNonNegativeReader: ValueReader[Int Refined NonNegative] = {
-    (config: Config, path: String) => {
+  implicit private[util] val refinedNonNegativeReader: ValueReader[Int Refined NonNegative] = {
+    (config: Config, path: String) =>
       val int = config.getInt(path)
       refineV[NonNegative](int) match {
         case Left(error) => throw new BadValue(path, error)
         case Right(refinedInt) => refinedInt
       }
-    }
   }
 
   private val yamlConfig = ConfigFactory.load().getConfig("yaml")
@@ -82,11 +80,11 @@ object YamlUtils {
 
   /** Extends SnakeYaml's Composer checking for a maximum depth before a StackOverflowError occurs. */
   private class MaxDepthComposer(yaml: String, maxDepth: Int Refined NonNegative)
-    extends Composer(
-      new ParserImpl(new StreamReader(new StringReader(yaml)), loaderOptions),
-      new Resolver(),
-      loaderOptions
-    ) {
+      extends Composer(
+        new ParserImpl(new StreamReader(new StringReader(yaml)), loaderOptions),
+        new Resolver(),
+        loaderOptions
+      ) {
 
     private val depth = new Counter
 
@@ -99,29 +97,23 @@ object YamlUtils {
       result
     }
 
-    override def composeScalarNode(anchor: String, blockComments: util.List[CommentLine]): Node = {
+    override def composeScalarNode(anchor: String, blockComments: util.List[CommentLine]): Node =
       checkDepth(super.composeScalarNode(anchor, blockComments))
-    }
 
-    override def composeSequenceNode(anchor: String): Node = {
+    override def composeSequenceNode(anchor: String): Node =
       checkDepth(super.composeSequenceNode(anchor))
-    }
 
-    override def composeMappingNode(anchor: String): Node = {
+    override def composeMappingNode(anchor: String): Node =
       checkDepth(super.composeMappingNode(anchor))
-    }
 
-    override def composeMappingChildren(children: util.List[NodeTuple], node: MappingNode): Unit = {
+    override def composeMappingChildren(children: util.List[NodeTuple], node: MappingNode): Unit =
       checkDepth(super.composeMappingChildren(children, node))
-    }
 
-    override def composeKeyNode(node: MappingNode): Node = {
+    override def composeKeyNode(node: MappingNode): Node =
       checkDepth(super.composeKeyNode(node))
-    }
 
-    override def composeValueNode(node: MappingNode): Node = {
+    override def composeValueNode(node: MappingNode): Node =
       checkDepth(super.composeValueNode(node))
-    }
   }
 
   /** A "pointer" reference to a mutable count. */
@@ -147,7 +139,8 @@ object YamlUtils {
   private def searchForOversizedYaml(node: AnyRef,
                                      identitySet: java.util.Set[AnyRef],
                                      maxNodes: Int Refined NonNegative,
-                                     counter: Counter): Unit = {
+                                     counter: Counter
+  ): Unit = {
     if (!identitySet.add(node)) {
       throw new IllegalArgumentException("Loop detected")
     }
@@ -158,15 +151,14 @@ object YamlUtils {
     }
 
     node match {
-      case iterable: java.lang.Iterable[AnyRef]@unchecked =>
+      case iterable: java.lang.Iterable[AnyRef] @unchecked =>
         iterable.asScala foreach {
           searchForOversizedYaml(_, identitySet, maxNodes, counter)
         }
-      case map: java.util.Map[AnyRef, AnyRef]@unchecked =>
-        map.asScala foreach {
-          case (key, value) =>
-            searchForOversizedYaml(key, identitySet, maxNodes, counter)
-            searchForOversizedYaml(value, identitySet, maxNodes, counter)
+      case map: java.util.Map[AnyRef, AnyRef] @unchecked =>
+        map.asScala foreach { case (key, value) =>
+          searchForOversizedYaml(key, identitySet, maxNodes, counter)
+          searchForOversizedYaml(value, identitySet, maxNodes, counter)
         }
       case _ => /* ignore scalars, only loop through Yaml sequences and mappings: https://yaml.org/spec/1.1/#id861435 */
     }
diff --git a/wom/src/main/scala/wom/values/WomArray.scala b/wom/src/main/scala/wom/values/WomArray.scala
index 0fdcde242be..1e4f0d31cc5 100644
--- a/wom/src/main/scala/wom/values/WomArray.scala
+++ b/wom/src/main/scala/wom/values/WomArray.scala
@@ -17,15 +17,19 @@ import scala.util.{Failure, Success, Try}
 object WomArray {
   def empty = WomArray(WomMaybeEmptyArrayType.EmptyArrayType, List.empty)
 
-  def fromTsv(tsv: String): WomArray = {
-    WomArray(WomArrayType(WomArrayType(WomStringType)), tsv.replaceAll("[\r\n]+$", "").split("[\n\r]+").toSeq map { line =>
-      WomArray(WomArrayType(WomStringType), line.split("\t").toSeq.map(WomString))
-    })
-  }
+  def fromTsv(tsv: String): WomArray =
+    WomArray(
+      WomArrayType(WomArrayType(WomStringType)),
+      tsv.replaceAll("[\r\n]+$", "").split("[\n\r]+").toSeq map { line =>
+        WomArray(WomArrayType(WomStringType), line.split("\t").toSeq.map(WomString))
+      }
+    )
 
   def apply(womType: WomArrayType, value: Seq[WomValue]): WomArray = {
     if (womType == WomMaybeEmptyArrayType.EmptyArrayType && value.nonEmpty) {
-      throw new UnsupportedOperationException(s"An ${womType.stableName} must be empty but instead has value: ${value.mkString(", ")}")
+      throw new UnsupportedOperationException(
+        s"An ${womType.stableName} must be empty but instead has value: ${value.mkString(", ")}"
+      )
     }
     if (womType.guaranteedNonEmpty && value.isEmpty) {
       throw new UnsupportedOperationException(s"An ${womType.stableName} must contain at least one element")
@@ -34,11 +38,15 @@ object WomArray {
     val coercedValue = TryUtil.sequence(value map womType.memberType.coerceRawValue)
     coercedValue match {
       case Success(coercedArray) => new WomArray(womType, coercedArray) {}
-      case Failure(f) => throw new UnsupportedOperationException(s"Could not construct array of type $womType with this value: $value", f)
+      case Failure(f) =>
+        throw new UnsupportedOperationException(s"Could not construct array of type $womType with this value: $value",
+                                                f
+        )
     }
   }
 
-  def apply(value: Seq[WomValue]): WomArray = WomArray.apply(WomArrayType(WomType.homogeneousTypeFromValues(value)), value)
+  def apply(value: Seq[WomValue]): WomArray =
+    WomArray.apply(WomArrayType(WomType.homogeneousTypeFromValues(value)), value)
 
   trait WomArrayLike {
     def arrayType: WomArrayType
@@ -53,49 +61,55 @@ object WomArray {
   }
 }
 
-sealed abstract case class WomArray(womType: WomArrayType, value: Seq[WomValue]) extends WomValue with WomArrayLike with TsvSerializable {
+sealed abstract case class WomArray(womType: WomArrayType, value: Seq[WomValue])
+    extends WomValue
+    with WomArrayLike
+    with TsvSerializable {
 
   val nonEmpty = value.nonEmpty
   override def toWomString: String = s"[${value.map(_.toWomString).mkString(", ")}]"
   override def toString = toWomString
 
-  def map[R <: WomValue](f: WomValue => R): WomArray = {
-    value.map{f} match {
+  def map[R <: WomValue](f: WomValue => R): WomArray =
+    value.map(f) match {
       case s: Seq[R] if s.nonEmpty => WomArray(WomArrayType(s.head.womType), s)
       case _ => this
     }
-  }
 
-  def traverse[R <: WomValue, G[_]](f: WomValue => G[R])(implicit applicative: Applicative[G]): G[WomArray] = {
+  def traverse[R <: WomValue, G[_]](f: WomValue => G[R])(implicit applicative: Applicative[G]): G[WomArray] =
     if (value.isEmpty) applicative.pure(this)
     else {
       applicative.map(value.toList.traverse(f)) { mapped =>
         WomArray(WomArrayType(mapped.head.womType), mapped)
       }
     }
-  }
 
-  override def initialize(ioFunctionSet: IoFunctionSet): IOChecked[WomValue] = traverse(_.initialize(ioFunctionSet)).widen
+  override def initialize(ioFunctionSet: IoFunctionSet): IOChecked[WomValue] = traverse(
+    _.initialize(ioFunctionSet)
+  ).widen
 
   def size = value.size
 
-  def tsvSerialize: Try[String] = {
+  def tsvSerialize: Try[String] =
     womType.memberType match {
       case _: WomPrimitiveType => Success(value.map(_.valueString).mkString(start = "", sep = "\n", end = "\n"))
       case WomObjectType => WomObject.tsvSerializeArray(value map { _.asInstanceOf[WomObject] })
       case WomArrayType(_: WomPrimitiveType) =>
-        val tsvString = value.collect({ case a: WomArray => a }) map { a =>
-          a.value.collect({ case p: WomPrimitive => p.valueString }).mkString(start = "", sep = "\t", end = "\n")
+        val tsvString = value.collect { case a: WomArray => a } map { a =>
+          a.value.collect { case p: WomPrimitive => p.valueString }.mkString(start = "", sep = "\t", end = "\n")
         } mkString
 
         Success(tsvString)
-      case _ => Failure(new UnsupportedOperationException(s"Cannot TSV serialize a ${this.womType.stableName} (valid types are Array[Primitive], Array[Array[Primitive]], or Array[Object])"))
+      case _ =>
+        Failure(
+          new UnsupportedOperationException(
+            s"Cannot TSV serialize a ${this.womType.stableName} (valid types are Array[Primitive], Array[Array[Primitive]], or Array[Object])"
+          )
+        )
     }
-  }
 
-  override def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] = {
+  override def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] =
     value flatMap { _.collectAsSeq(filterFn) }
-  }
 
   // For WomArrayLike:
   override val arrayType: WomArrayType = womType
diff --git a/wom/src/main/scala/wom/values/WomBoolean.scala b/wom/src/main/scala/wom/values/WomBoolean.scala
index 1474819436c..f45587ae16f 100644
--- a/wom/src/main/scala/wom/values/WomBoolean.scala
+++ b/wom/src/main/scala/wom/values/WomBoolean.scala
@@ -14,23 +14,23 @@ object WomBoolean {
 /** The constructor is private to force access through the companion
   * object `apply` which ensures the use of one of the canonical instances.
   */
-class WomBoolean private(val value: Boolean) extends WomPrimitive {
+class WomBoolean private (val value: Boolean) extends WomPrimitive {
   val womType = WomBooleanType
 
   override def equals(rhs: WomValue): Try[WomBoolean] = rhs match {
-    case r:WomBoolean => Success(WomBoolean(value == r.value))
+    case r: WomBoolean => Success(WomBoolean(value == r.value))
     case r: WomOptionalValue => evaluateIfDefined("==", r, equals)
     case _ => invalid(s"$value || $rhs")
   }
 
   override def lessThan(rhs: WomValue): Try[WomBoolean] = rhs match {
-    case r:WomBoolean => Success(WomBoolean(value < r.value))
+    case r: WomBoolean => Success(WomBoolean(value < r.value))
     case r: WomOptionalValue => evaluateIfDefined("<", r, lessThan)
     case _ => invalid(s"$value < $rhs")
   }
 
   override def greaterThan(rhs: WomValue): Try[WomBoolean] = rhs match {
-    case r:WomBoolean => Success(WomBoolean(value > r.value))
+    case r: WomBoolean => Success(WomBoolean(value > r.value))
     case r: WomOptionalValue => evaluateIfDefined(">", r, greaterThan)
     case _ => invalid(s"$value > $rhs")
   }
@@ -42,7 +42,7 @@ class WomBoolean private(val value: Boolean) extends WomPrimitive {
   }
 
   override def and(rhs: WomValue): Try[WomBoolean] = rhs match {
-    case r:WomBoolean => Success(WomBoolean(value && r.value))
+    case r: WomBoolean => Success(WomBoolean(value && r.value))
     case r: WomOptionalValue => evaluateIfDefined("&&", r, and)
     case _ => invalid(s"$value && $rhs")
   }
diff --git a/wom/src/main/scala/wom/values/WomCoproductValue.scala b/wom/src/main/scala/wom/values/WomCoproductValue.scala
index 44274dcf5fa..1973a5e363a 100644
--- a/wom/src/main/scala/wom/values/WomCoproductValue.scala
+++ b/wom/src/main/scala/wom/values/WomCoproductValue.scala
@@ -4,7 +4,6 @@ import wom.types.WomCoproductType
 
 case class WomCoproductValue(womType: WomCoproductType, womValue: WomValue) extends WomValue {
 
-  override def toWomString: String = {
+  override def toWomString: String =
     womValue.toWomString
-  }
 }
diff --git a/wom/src/main/scala/wom/values/WomFile.scala b/wom/src/main/scala/wom/values/WomFile.scala
index 4638a712404..bcf7484ef33 100644
--- a/wom/src/main/scala/wom/values/WomFile.scala
+++ b/wom/src/main/scala/wom/values/WomFile.scala
@@ -88,7 +88,7 @@ sealed trait WomFile extends WomValue {
     *
     * WomPrimitiveFile instances return just the instance.
     */
-  def flattenFiles: Seq[WomPrimitiveFile] = {
+  def flattenFiles: Seq[WomPrimitiveFile] =
     this match {
       case womMaybeListedDirectory: WomMaybeListedDirectory =>
         womMaybeListedDirectory.listingOption.getOrElse(Nil).toList match {
@@ -97,24 +97,21 @@ sealed trait WomFile extends WomValue {
         }
       case womMaybePopulatedFile: WomMaybePopulatedFile =>
         val primaryFiles: Seq[WomPrimitiveFile] = womMaybePopulatedFile.valueOption.toList.map(WomSingleFile)
-        womMaybePopulatedFile.secondaryFiles.foldLeft(primaryFiles) {
-          (womFiles, secondaryFile) =>
-            womFiles ++ secondaryFile.flattenFiles
+        womMaybePopulatedFile.secondaryFiles.foldLeft(primaryFiles) { (womFiles, secondaryFile) =>
+          womFiles ++ secondaryFile.flattenFiles
         }
       case womPrimitiveFile: WomPrimitiveFile => List(womPrimitiveFile)
     }
-  }
 
   /**
     * If relevant, load the size of the file.
     */
   def withSize(ioFunctionSet: IoFunctionSet): IO[WomFile] = IO.pure(this)
-  
+
   def sizeOption: Option[Long] = None
 
-  protected def recoverFileNotFound[A](fallback: A)(t: Throwable): IO[A] = {
+  protected def recoverFileNotFound[A](fallback: A)(t: Throwable): IO[A] =
     if (isFileNotFound(t)) IO.pure(fallback) else IO.raiseError(t)
-  }
 
   def isFileNotFound(t: Throwable): Boolean = t match {
     case _: NoSuchFileException | _: FileNotFoundException => true
@@ -124,7 +121,7 @@ sealed trait WomFile extends WomValue {
 }
 
 object WomFile {
-  def apply(fileType: WomFileType, value: String) = {
+  def apply(fileType: WomFileType, value: String) =
     fileType match {
       case WomUnlistedDirectoryType => WomUnlistedDirectory(value)
       case WomSingleFileType => WomSingleFile(value)
@@ -132,7 +129,6 @@ object WomFile {
       case WomMaybeListedDirectoryType => WomMaybeListedDirectory(value)
       case WomMaybePopulatedFileType => WomMaybePopulatedFile(value)
     }
-  }
 }
 
 sealed trait WomPrimitiveFile extends WomFile with WomPrimitive
@@ -163,13 +159,11 @@ final case class WomUnlistedDirectory(value: String) extends WomPrimitiveFile {
     case _ => invalid(s"$value == $rhs")
   }
 
-  override def mapFile(f: String => String): WomUnlistedDirectory = {
+  override def mapFile(f: String => String): WomUnlistedDirectory =
     this.copy(value = f(value))
-  }
 
-  override def collect(f: PartialFunction[WomFile, WomFile]): WomFile = {
+  override def collect(f: PartialFunction[WomFile, WomFile]): WomFile =
     f.applyOrElse[WomFile, WomFile](this, identity)
-  }
 
   override def mapWomFile(f: WomFile => String) = this.copy(value = f(this))
 }
@@ -197,21 +191,18 @@ final case class WomSingleFile(value: String) extends WomPrimitiveFile {
     case _ => invalid(s"$value == $rhs")
   }
 
-  override def mapFile(f: String => String): WomSingleFile = {
+  override def mapFile(f: String => String): WomSingleFile =
     this.copy(value = f(value))
-  }
 
-  override def mapWomFile(f: WomFile => String) = {
+  override def mapWomFile(f: WomFile => String) =
     this.copy(value = f(this))
-  }
 
-  override def collect(f: PartialFunction[WomFile, WomFile]): WomFile = {
+  override def collect(f: PartialFunction[WomFile, WomFile]): WomFile =
     f.applyOrElse[WomFile, WomFile](this, identity)
-  }
 
   override def withSize(ioFunctionSet: IoFunctionSet): IO[WomFile] = {
     implicit def cs = ioFunctionSet.cs
-    IO.fromFuture(IO { ioFunctionSet.size(value)})
+    IO.fromFuture(IO(ioFunctionSet.size(value)))
       .map(Option.apply)
       .handleErrorWith(recoverFileNotFound(None))
       .map(s => WomMaybePopulatedFile(valueOption = Option(value), sizeOption = s))
@@ -250,38 +241,37 @@ final case class WomGlobFile(value: String) extends WomPrimitiveFile {
 
   override def mapWomFile(f: WomFile => String) = this.copy(value = f(this))
 
-  override def collect(f: PartialFunction[WomFile, WomFile]): WomFile = {
+  override def collect(f: PartialFunction[WomFile, WomFile]): WomFile =
     f.applyOrElse[WomFile, WomFile](this, identity)
-  }
 }
 
-
 /**
   * A directory possibly with a listing of other files/directories.
   *
   * @param valueOption   The location of the directory, possibly in the cloud.
   * @param listingOption An optional listing of files/directories, either supplied by a user or generated by the engine.
   */
-case class WomMaybeListedDirectory(valueOption: Option[String] = None,
-                                   listingOption: Option[Seq[WomFile]] = None,
-                                   basename: Option[String] = None,
-                                   initializeFunction: WomMaybeListedDirectory => IoFunctionSet => IOChecked[WomValue] = { dir => _ => IOChecked.pure(dir) }) extends WomFile {
-  override def value: String = {
-    valueOption.getOrElse(throw new UnsupportedOperationException(s"value is not available: $this"))
+case class WomMaybeListedDirectory(
+  valueOption: Option[String] = None,
+  listingOption: Option[Seq[WomFile]] = None,
+  basename: Option[String] = None,
+  initializeFunction: WomMaybeListedDirectory => IoFunctionSet => IOChecked[WomValue] = { dir => _ =>
+    IOChecked.pure(dir)
   }
+) extends WomFile {
+  override def value: String =
+    valueOption.getOrElse(throw new UnsupportedOperationException(s"value is not available: $this"))
 
   override val womFileType: WomFileType = WomMaybeListedDirectoryType
 
   // TODO: WOM: WOMFILE: This isn't even close to a WDL representation (and maybe belongs in WDL?) of this class, but w/o it other areas of the code crash
   override def toWomString = s""""$value""""
 
-  override def mapFile(f: String => String): WomMaybeListedDirectory = {
+  override def mapFile(f: String => String): WomMaybeListedDirectory =
     this.copy(valueOption = valueOption.map(f), listingOption.map(_.map(_.mapFile(f))))
-  }
 
-  override def mapWomFile(f: WomFile => String) = {
+  override def mapWomFile(f: WomFile => String) =
     this.copy(valueOption = Option(f(this)), listingOption.map(_.map(_.mapWomFile(f))))
-  }
 
   override def collect(f: PartialFunction[WomFile, WomFile]): WomFile = {
     val copy = this.copy(listingOption = listingOption.map(_.map(_.collect(f))))
@@ -291,16 +281,17 @@ case class WomMaybeListedDirectory(valueOption: Option[String] = None,
   override def withSize(ioFunctionSet: IoFunctionSet): IO[WomFile] = {
     import ioFunctionSet.cs
 
-    listingOption.map({
-      _.toList
-        .parTraverse[IO, WomFile](_.withSize(ioFunctionSet))
-        .map(listingWithSize => this.copy(listingOption = Option(listingWithSize)))
-    })
+    listingOption
+      .map {
+        _.toList
+          .parTraverse[IO, WomFile](_.withSize(ioFunctionSet))
+          .map(listingWithSize => this.copy(listingOption = Option(listingWithSize)))
+      }
       .getOrElse(IO.pure(this))
   }
 
   override def initialize(ioFunctionSet: IoFunctionSet): IOChecked[WomValue] = initializeFunction(this)(ioFunctionSet)
-  
+
   override def sizeOption = listingOption.map(_.flatMap(_.sizeOption).sum)
 }
 
@@ -324,24 +315,23 @@ case class WomMaybePopulatedFile(valueOption: Option[String] = None,
                                  formatOption: Option[String] = None,
                                  contentsOption: Option[String] = None,
                                  secondaryFiles: Seq[WomFile] = Vector.empty,
-                                 initializeFunction: WomMaybePopulatedFile => IoFunctionSet => IOChecked[WomValue] = { file => _ => IOChecked.pure(file) }
-                                ) extends WomFile {
-  override def value: String = {
+                                 initializeFunction: WomMaybePopulatedFile => IoFunctionSet => IOChecked[WomValue] = {
+                                   file => _ => IOChecked.pure(file)
+                                 }
+) extends WomFile {
+  override def value: String =
     valueOption.getOrElse(throw new UnsupportedOperationException(s"value is not available: $this"))
-  }
 
   override val womFileType: WomFileType = WomMaybePopulatedFileType
 
   // TODO: WOM: WOMFILE: This isn't even close to a WDL representation (and maybe belongs in WDL?) of this class, but w/o it other areas of the code crash
   override def toWomString = s""""$value""""
 
-  override def mapFile(f: String => String): WomMaybePopulatedFile = {
+  override def mapFile(f: String => String): WomMaybePopulatedFile =
     this.copy(valueOption = valueOption.map(f), secondaryFiles = secondaryFiles.map(_.mapFile(f)))
-  }
 
-  override def mapWomFile(f: WomFile => String): WomMaybePopulatedFile = {
+  override def mapWomFile(f: WomFile => String): WomMaybePopulatedFile =
     this.copy(valueOption = Option(f(this)), secondaryFiles = secondaryFiles.map(_.mapWomFile(f)))
-  }
 
   override def collect(f: PartialFunction[WomFile, WomFile]): WomFile = {
     val copy = this.copy(secondaryFiles = secondaryFiles.map(_.collect(f)))
@@ -354,9 +344,12 @@ case class WomMaybePopulatedFile(valueOption: Option[String] = None,
     val ioSize: IO[Option[Long]] = (sizeOption, contentsOption) match {
       case (Some(s), _) => IO.pure(Option(s))
       case (None, Some(contents)) => IO.pure(Option(contents.length.toLong))
-      case _ => IO.fromFuture(IO { ioFunctionSet.size(value) }).map(Option.apply).handleErrorWith(recoverFileNotFound(sizeOption))
+      case _ =>
+        IO.fromFuture(IO(ioFunctionSet.size(value)))
+          .map(Option.apply)
+          .handleErrorWith(recoverFileNotFound(sizeOption))
     }
-    
+
     for {
       size <- ioSize
       secondaryFilesWithSize <- secondaryFiles.toList.parTraverse[IO, WomFile](_.withSize(ioFunctionSet))
diff --git a/wom/src/main/scala/wom/values/WomFloat.scala b/wom/src/main/scala/wom/values/WomFloat.scala
index 08ce5ed912d..74f1dd82fb2 100644
--- a/wom/src/main/scala/wom/values/WomFloat.scala
+++ b/wom/src/main/scala/wom/values/WomFloat.scala
@@ -7,75 +7,67 @@ import scala.util.{Failure, Success, Try}
 
 case class WomFloat(value: Double) extends WomPrimitive {
   val womType = WomFloatType
-  override def add(rhs: WomValue): Try[WomValue] = {
+  override def add(rhs: WomValue): Try[WomValue] =
     rhs match {
-      case r:WomFloat => Success(WomFloat(value + r.value))
-      case r:WomInteger => Success(WomFloat(value + r.value))
-      case r:WomString => Success(WomString(s"$value${r.value}"))
+      case r: WomFloat => Success(WomFloat(value + r.value))
+      case r: WomInteger => Success(WomFloat(value + r.value))
+      case r: WomString => Success(WomString(s"$value${r.value}"))
       case r: WomOptionalValue => evaluateIfDefined("+", r, add)
       case _ => invalid(s"$this + $rhs")
     }
-  }
-  override def subtract(rhs: WomValue): Try[WomValue] = {
+  override def subtract(rhs: WomValue): Try[WomValue] =
     rhs match {
-      case r:WomFloat => Success(WomFloat(value - r.value))
-      case r:WomInteger => Success(WomFloat(value - r.value))
+      case r: WomFloat => Success(WomFloat(value - r.value))
+      case r: WomInteger => Success(WomFloat(value - r.value))
       case r: WomOptionalValue => evaluateIfDefined("-", r, subtract)
       case _ => invalid(s"$this - $rhs")
     }
-  }
-  override def multiply(rhs: WomValue): Try[WomValue] = {
+  override def multiply(rhs: WomValue): Try[WomValue] =
     rhs match {
-      case r:WomFloat => Success(WomFloat(value * r.value))
-      case r:WomInteger => Success(WomFloat(value * r.value))
+      case r: WomFloat => Success(WomFloat(value * r.value))
+      case r: WomInteger => Success(WomFloat(value * r.value))
       case r: WomOptionalValue => evaluateIfDefined("*", r, multiply)
       case _ => invalid(s"$this * $rhs")
     }
-  }
-  override def divide(rhs: WomValue): Try[WomValue] = {
+  override def divide(rhs: WomValue): Try[WomValue] =
     rhs match {
-      case r:WomFloat if r.value == 0.0 => Failure(new WomExpressionException("Divide by zero"))
-      case r:WomFloat => Success(WomFloat(value / r.value))
-      case r:WomInteger if r.value == 0 => Failure(new WomExpressionException("Divide by zero"))
-      case r:WomInteger => Success(WomFloat(value / r.value))
+      case r: WomFloat if r.value == 0.0 => Failure(new WomExpressionException("Divide by zero"))
+      case r: WomFloat => Success(WomFloat(value / r.value))
+      case r: WomInteger if r.value == 0 => Failure(new WomExpressionException("Divide by zero"))
+      case r: WomInteger => Success(WomFloat(value / r.value))
       case r: WomOptionalValue => evaluateIfDefined("/", r, divide)
       case _ => invalid(s"$this / $rhs")
     }
-  }
-  override def mod(rhs: WomValue): Try[WomValue] = {
+  override def mod(rhs: WomValue): Try[WomValue] =
     rhs match {
-      case r:WomFloat if r.value == 0.0 => Failure(new WomExpressionException("Divide by zero"))
-      case r:WomFloat => Success(WomFloat(value % r.value))
-      case r:WomInteger if r.value == 0 => Failure(new WomExpressionException("Divide by zero"))
-      case r:WomInteger => Success(WomFloat(value % r.value))
+      case r: WomFloat if r.value == 0.0 => Failure(new WomExpressionException("Divide by zero"))
+      case r: WomFloat => Success(WomFloat(value % r.value))
+      case r: WomInteger if r.value == 0 => Failure(new WomExpressionException("Divide by zero"))
+      case r: WomInteger => Success(WomFloat(value % r.value))
       case r: WomOptionalValue => evaluateIfDefined("%", r, mod)
       case _ => invalid(s"$this % $rhs")
     }
-  }
-  override def equals(rhs: WomValue): Try[WomBoolean] = {
+  override def equals(rhs: WomValue): Try[WomBoolean] =
     rhs match {
-      case r:WomFloat => Success(WomBoolean(value == r.value))
-      case r:WomInteger => Success(WomBoolean(value == r.value))
+      case r: WomFloat => Success(WomBoolean(value == r.value))
+      case r: WomInteger => Success(WomBoolean(value == r.value))
       case r: WomOptionalValue => evaluateIfDefined("==", r, equals)
       case _ => invalid(s"$this == $rhs")
     }
-  }
-  override def lessThan(rhs: WomValue): Try[WomBoolean] = {
+  override def lessThan(rhs: WomValue): Try[WomBoolean] =
     rhs match {
-      case r:WomFloat => Success(WomBoolean(value < r.value))
-      case r:WomInteger => Success(WomBoolean(value < r.value))
+      case r: WomFloat => Success(WomBoolean(value < r.value))
+      case r: WomInteger => Success(WomBoolean(value < r.value))
       case r: WomOptionalValue => evaluateIfDefined("<", r, lessThan)
       case _ => invalid(s"$this < $rhs")
     }
-  }
-  override def greaterThan(rhs: WomValue): Try[WomBoolean] = {
+  override def greaterThan(rhs: WomValue): Try[WomBoolean] =
     rhs match {
-      case r:WomFloat => Success(WomBoolean(value > r.value))
-      case r:WomInteger => Success(WomBoolean(value > r.value))
+      case r: WomFloat => Success(WomBoolean(value > r.value))
+      case r: WomInteger => Success(WomBoolean(value > r.value))
       case r: WomOptionalValue => evaluateIfDefined(">", r, greaterThan)
       case _ => invalid(s"$this > $rhs")
     }
-  }
   override def unaryPlus: Try[WomValue] = Success(WomFloat(math.abs(value)))
   override def unaryMinus: Try[WomValue] = Success(WomFloat(-value))
   override def toWomString = value.toString
diff --git a/wom/src/main/scala/wom/values/WomInteger.scala b/wom/src/main/scala/wom/values/WomInteger.scala
index 1bcc2e117ac..68e99c93d80 100644
--- a/wom/src/main/scala/wom/values/WomInteger.scala
+++ b/wom/src/main/scala/wom/values/WomInteger.scala
@@ -9,62 +9,64 @@ case class WomInteger(value: Int) extends WomPrimitive {
   val womType = WomIntegerType
 
   override def add(rhs: WomValue): Try[WomValue] = rhs match {
-    case r:WomInteger => Success(WomInteger(value + r.value))
-    case r:WomString => Success(WomString(s"$value${r.value}"))
-    case r:WomFloat => Success(WomFloat(value + r.value))
+    case r: WomInteger => Success(WomInteger(value + r.value))
+    case r: WomString => Success(WomString(s"$value${r.value}"))
+    case r: WomFloat => Success(WomFloat(value + r.value))
     case r: WomOptionalValue => evaluateIfDefined("+", r, add)
     case _ => invalid(s"$value + $rhs")
   }
 
   override def subtract(rhs: WomValue): Try[WomValue] = rhs match {
-    case r:WomInteger => Success(WomInteger(value - r.value))
-    case r:WomFloat => Success(WomFloat(value - r.value))
+    case r: WomInteger => Success(WomInteger(value - r.value))
+    case r: WomFloat => Success(WomFloat(value - r.value))
     case r: WomOptionalValue => evaluateIfDefined("-", r, subtract)
     case _ => invalid(s"$value - $rhs")
   }
 
   override def multiply(rhs: WomValue): Try[WomValue] = rhs match {
-    case r:WomInteger => Success(WomInteger(value * r.value))
-    case r:WomFloat => Success(WomFloat(value * r.value))
+    case r: WomInteger => Success(WomInteger(value * r.value))
+    case r: WomFloat => Success(WomFloat(value * r.value))
     case r: WomOptionalValue => evaluateIfDefined("*", r, multiply)
     case _ => invalid(s"$value * $rhs")
   }
 
   override def divide(rhs: WomValue): Try[WomValue] = rhs match {
-    case r:WomInteger if r.value == 0 => Failure(new WomExpressionException(s"Divide by zero error: $value / $rhs"))
-    case r:WomInteger => Success(WomInteger(value / r.value))
-    case r:WomFloat if r.value == 0.toDouble => Failure(new WomExpressionException(s"Divide by zero error: $value / $rhs"))
-    case r:WomFloat => Success(WomFloat(value / r.value))
+    case r: WomInteger if r.value == 0 => Failure(new WomExpressionException(s"Divide by zero error: $value / $rhs"))
+    case r: WomInteger => Success(WomInteger(value / r.value))
+    case r: WomFloat if r.value == 0.toDouble =>
+      Failure(new WomExpressionException(s"Divide by zero error: $value / $rhs"))
+    case r: WomFloat => Success(WomFloat(value / r.value))
     case r: WomOptionalValue => evaluateIfDefined("/", r, divide)
     case _ => invalid(s"$value / $rhs")
   }
 
   override def mod(rhs: WomValue): Try[WomValue] = rhs match {
-    case r:WomInteger if r.value == 0 => Failure(new WomExpressionException(s"Divide by zero error: $value / $rhs"))
-    case r:WomInteger => Success(WomInteger(value % r.value))
-    case r:WomFloat if r.value == 0.toDouble => Failure(new WomExpressionException(s"Divide by zero error: $value / $rhs"))
-    case r:WomFloat => Success(WomFloat(value % r.value))
+    case r: WomInteger if r.value == 0 => Failure(new WomExpressionException(s"Divide by zero error: $value / $rhs"))
+    case r: WomInteger => Success(WomInteger(value % r.value))
+    case r: WomFloat if r.value == 0.toDouble =>
+      Failure(new WomExpressionException(s"Divide by zero error: $value / $rhs"))
+    case r: WomFloat => Success(WomFloat(value % r.value))
     case r: WomOptionalValue => evaluateIfDefined("%", r, mod)
     case _ => invalid(s"$value % $rhs")
   }
 
   override def equals(rhs: WomValue): Try[WomBoolean] = rhs match {
-    case r:WomInteger => Success(WomBoolean(value == r.value))
-    case r:WomFloat => Success(WomBoolean(value == r.value))
+    case r: WomInteger => Success(WomBoolean(value == r.value))
+    case r: WomFloat => Success(WomBoolean(value == r.value))
     case r: WomOptionalValue => evaluateIfDefined("==", r, equals)
     case _ => invalid(s"$value == $rhs")
   }
 
   override def lessThan(rhs: WomValue): Try[WomBoolean] = rhs match {
-    case r:WomInteger => Success(WomBoolean(value < r.value))
-    case r:WomFloat => Success(WomBoolean(value < r.value))
+    case r: WomInteger => Success(WomBoolean(value < r.value))
+    case r: WomFloat => Success(WomBoolean(value < r.value))
     case r: WomOptionalValue => evaluateIfDefined("<", r, lessThan)
     case _ => invalid(s"$value < $rhs")
   }
 
   override def greaterThan(rhs: WomValue): Try[WomBoolean] = rhs match {
-    case r:WomInteger => Success(WomBoolean(value > r.value))
-    case r:WomFloat => Success(WomBoolean(value > r.value))
+    case r: WomInteger => Success(WomBoolean(value > r.value))
+    case r: WomFloat => Success(WomBoolean(value > r.value))
     case r: WomOptionalValue => evaluateIfDefined(">", r, greaterThan)
     case _ => invalid(s"$value > $rhs")
   }
diff --git a/wom/src/main/scala/wom/values/WomLong.scala b/wom/src/main/scala/wom/values/WomLong.scala
index b9f567a359f..3b8ef661b85 100644
--- a/wom/src/main/scala/wom/values/WomLong.scala
+++ b/wom/src/main/scala/wom/values/WomLong.scala
@@ -1,6 +1,6 @@
 package wom.values
 
-import wom.types.{WomLongType}
+import wom.types.WomLongType
 
 case class WomLong(value: Long) extends WomPrimitive {
   val womType = WomLongType
diff --git a/wom/src/main/scala/wom/values/WomMap.scala b/wom/src/main/scala/wom/values/WomMap.scala
index 5d42b1d3364..97748c8d24a 100644
--- a/wom/src/main/scala/wom/values/WomMap.scala
+++ b/wom/src/main/scala/wom/values/WomMap.scala
@@ -16,11 +16,15 @@ import scala.util.{Failure, Success, Try}
 
 object WomMap {
   def coerceMap(m: Map[_, _], womMapType: WomMapType): WomMap = {
-    val coerced: Map[Try[WomValue], Try[WomValue]] = m map { case(k, v) => womMapType.keyType.coerceRawValue(k) -> womMapType.valueType.coerceRawValue(v) }
-    val failures = coerced flatMap { case(k,v) => Seq(k,v) } collect { case f:Failure[_] => f }
+    val coerced: Map[Try[WomValue], Try[WomValue]] = m map { case (k, v) =>
+      womMapType.keyType.coerceRawValue(k) -> womMapType.valueType.coerceRawValue(v)
+    }
+    val failures = coerced flatMap { case (k, v) => Seq(k, v) } collect { case f: Failure[_] => f }
     failures match {
       case f: Iterable[Failure[_]] if f.nonEmpty =>
-        throw new UnsupportedOperationException(s"Failed to coerce one or more keys or values for creating a ${womMapType.stableName}:\n${TryUtil.stringifyFailures(f)}}")
+        throw new UnsupportedOperationException(
+          s"Failed to coerce one or more keys or values for creating a ${womMapType.stableName}:\n${TryUtil.stringifyFailures(f)}}"
+        )
       case _ =>
         val mapCoerced = coerced map { case (k, v) => k.get -> v.get }
 
@@ -31,14 +35,14 @@ object WomMap {
     }
   }
 
-  def fromTsv(tsv: String, womMapType: WomMapType = WomMapType(WomAnyType, WomAnyType)): Try[WomMap] = {
+  def fromTsv(tsv: String, womMapType: WomMapType = WomMapType(WomAnyType, WomAnyType)): Try[WomMap] =
     FileUtil.parseTsv(tsv) match {
       case Success(table) if table.isEmpty => Success(WomMap(womMapType, Map.empty[WomValue, WomValue]))
-      case Success(table) if table.head.length != 2 => Failure(new UnsupportedOperationException("TSV must be 2 columns to convert to a Map"))
+      case Success(table) if table.head.length != 2 =>
+        Failure(new UnsupportedOperationException("TSV must be 2 columns to convert to a Map"))
       case Success(table) => Try(coerceMap(table.map(row => row(0) -> row(1)).toMap, womMapType))
       case Failure(e) => Failure(e)
     }
-  }
 
   def apply(m: Map[WomValue, WomValue]): WomMap = {
     val keyType = WomType.lowestCommonSubtype(m.keys.map(_.womType))
@@ -47,27 +51,38 @@ object WomMap {
   }
 }
 
-final case class WomMap private(womType: WomMapType, value: Map[WomValue, WomValue]) extends WomValue with WomArrayLike with TsvSerializable {
+final case class WomMap private (womType: WomMapType, value: Map[WomValue, WomValue])
+    extends WomValue
+    with WomArrayLike
+    with TsvSerializable {
   val typesUsedInKey = value.map { case (k, _) => k.womType }.toSet
 
   if (typesUsedInKey.size == 1 && typesUsedInKey.head != womType.keyType)
-    throw new UnsupportedOperationException(s"Could not construct a $womType with map keys of unexpected type: [${value.keys.mkString(", ")}]")
+    throw new UnsupportedOperationException(
+      s"Could not construct a $womType with map keys of unexpected type: [${value.keys.mkString(", ")}]"
+    )
 
   if (typesUsedInKey.size > 1)
-    throw new UnsupportedOperationException(s"Cannot construct $womType with mixed types in map keys: [${value.keys.mkString(", ")}]")
+    throw new UnsupportedOperationException(
+      s"Cannot construct $womType with mixed types in map keys: [${value.keys.mkString(", ")}]"
+    )
 
   val typesUsedInValue = value.map { case (_, v) => v.womType }.toSet
 
   if (typesUsedInValue.size == 1 && typesUsedInValue.head != womType.valueType)
-    throw new UnsupportedOperationException(s"Could not construct a $womType with map values of unexpected type: [${value.values.mkString(", ")}]")
+    throw new UnsupportedOperationException(
+      s"Could not construct a $womType with map values of unexpected type: [${value.values.mkString(", ")}]"
+    )
 
   if (typesUsedInValue.size > 1)
-    throw new UnsupportedOperationException(s"Cannot construct $womType with mixed types in map values: [${value.values.mkString(", ")}]")
+    throw new UnsupportedOperationException(
+      s"Cannot construct $womType with mixed types in map values: [${value.values.mkString(", ")}]"
+    )
 
   override def toWomString: String =
-    "{" + value.map {case (k,v) => s"${k.toWomString}: ${v.toWomString}"}.mkString(", ") + "}"
+    "{" + value.map { case (k, v) => s"${k.toWomString}: ${v.toWomString}" }.mkString(", ") + "}"
 
-  def tsvSerialize: Try[String] = {
+  def tsvSerialize: Try[String] =
     (womType.keyType, womType.valueType) match {
       case (_: WomPrimitiveType, _: WomPrimitiveType) if value.isEmpty =>
         // WDL 1.1 spec on `write_map()` https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#file-write_mapmapstring-string
@@ -76,39 +91,42 @@ final case class WomMap private(womType: WomMapType, value: Map[WomValue, WomVal
         Success("")
       case (_: WomPrimitiveType, _: WomPrimitiveType) =>
         // "All lines are terminated by the newline (\n) character."
-        Success(value.map({case (k, v) => s"${k.valueString}\t${v.valueString}"}).mkString(start="", sep="\n", end="\n"))
+        Success(
+          value
+            .map { case (k, v) => s"${k.valueString}\t${v.valueString}" }
+            .mkString(start = "", sep = "\n", end = "\n")
+        )
       case _ =>
         Failure(new UnsupportedOperationException("Can only TSV serialize a Map[Primitive, Primitive]"))
     }
-  }
 
-  def map(f: PartialFunction[(WomValue, WomValue), (WomValue, WomValue)]): WomMap = {
+  def map(f: PartialFunction[(WomValue, WomValue), (WomValue, WomValue)]): WomMap =
     value map f match {
       case m: Map[WomValue, WomValue] if m.nonEmpty => WomMap(WomMapType(m.head._1.womType, m.head._2.womType), m)
       case _ => this
     }
-  }
 
-  def traverseValues[R <: WomValue, G[_]](f: WomValue => G[R])(implicit applicative: Applicative[G]): G[WomMap] = {
+  def traverseValues[R <: WomValue, G[_]](f: WomValue => G[R])(implicit applicative: Applicative[G]): G[WomMap] =
     if (value.isEmpty) applicative.pure(this)
     else {
-      val traverseFunction: (WomValue, WomValue) => G[(WomValue, R)] = {
-        case (key, v) => applicative.map(f(v)) { key -> _ }
+      val traverseFunction: (WomValue, WomValue) => G[(WomValue, R)] = { case (key, v) =>
+        applicative.map(f(v))(key -> _)
       }
       applicative.map(value.toList.traverse[G, (WomValue, R)](traverseFunction.tupled)) { mapped =>
         WomMap(mapped.toMap)
       }
     }
-  }
 
   override def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] = {
-    val collected = value flatMap {
-      case (k, v) => Seq(k.collectAsSeq(filterFn), v.collectAsSeq(filterFn))
+    val collected = value flatMap { case (k, v) =>
+      Seq(k.collectAsSeq(filterFn), v.collectAsSeq(filterFn))
     }
     collected.flatten.toSeq
   }
 
-  override def initialize(ioFunctionSet: IoFunctionSet): IOChecked[WomValue] = traverseValues(_.initialize(ioFunctionSet)).widen
+  override def initialize(ioFunctionSet: IoFunctionSet): IOChecked[WomValue] = traverseValues(
+    _.initialize(ioFunctionSet)
+  ).widen
 
   // For WomArrayLike:
   override lazy val arrayType: WomArrayType = WomArrayType(WomPairType(womType.keyType, womType.valueType))
diff --git a/wom/src/main/scala/wom/values/WomObject.scala b/wom/src/main/scala/wom/values/WomObject.scala
index 5c4cc1b53e2..4793116a052 100644
--- a/wom/src/main/scala/wom/values/WomObject.scala
+++ b/wom/src/main/scala/wom/values/WomObject.scala
@@ -26,47 +26,51 @@ trait WomObjectLike extends WomValue {
   }
   def womObjectTypeLike: WomObjectTypeLike
 
-  override def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] = {
+  override def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] =
     values.values.toSeq flatMap { _.collectAsSeq(filterFn) }
-  }
 
-  def traverse[R <: WomValue, G[_]](f: WomValue => G[R])(implicit applicative: Applicative[G]): G[WomObjectLike] = {
+  def traverse[R <: WomValue, G[_]](f: WomValue => G[R])(implicit applicative: Applicative[G]): G[WomObjectLike] =
     if (values.isEmpty) applicative.pure(this)
     else {
-      val traverseFunction: (String, WomValue) => G[(String, R)] = {
-        case (key, value) => applicative.map(f(value)) { key -> _ }
+      val traverseFunction: (String, WomValue) => G[(String, R)] = { case (key, value) =>
+        applicative.map(f(value))(key -> _)
       }
       applicative.map(values.toList.traverse[G, (String, R)](traverseFunction.tupled)) { mapped =>
         copyWith(mapped.toMap)
       }
     }
-  }
 
-  override def initialize(ioFunctionSet: IoFunctionSet): IOChecked[WomValue] = traverse(_.initialize(ioFunctionSet)).widen
+  override def initialize(ioFunctionSet: IoFunctionSet): IOChecked[WomValue] = traverse(
+    _.initialize(ioFunctionSet)
+  ).widen
 }
 
 object WomObject {
 
   def coerceObject(m: Map[String, String]): WomObject = {
-    val coerced = WomMap.coerceMap(m, WomMapType(WomStringType, WomAnyType)).value map {
-      case (k, v) => k.valueString -> v
+    val coerced = WomMap.coerceMap(m, WomMapType(WomStringType, WomAnyType)).value map { case (k, v) =>
+      k.valueString -> v
     }
 
     WomObject(coerced)
   }
 
-  def fromTsv(tsv: String): Try[Array[WomObject]] = {
+  def fromTsv(tsv: String): Try[Array[WomObject]] =
     FileUtil.parseTsv(tsv) match {
-      case Success(table) if table.isEmpty => Failure(new UnsupportedOperationException("TSV file was empty or could not be parsed."))
-      case Success(table) if table.length < 2 => Failure(new UnsupportedOperationException("TSV must be 2 rows (or more) to convert to an Object (Array[Object])"))
-      case Success(table) => Try {
-        table.tail map { line => coerceObject((table.head zip line).toMap) }
-      }
+      case Success(table) if table.isEmpty =>
+        Failure(new UnsupportedOperationException("TSV file was empty or could not be parsed."))
+      case Success(table) if table.length < 2 =>
+        Failure(
+          new UnsupportedOperationException("TSV must be 2 rows (or more) to convert to an Object (Array[Object])")
+        )
+      case Success(table) =>
+        Try {
+          table.tail map { line => coerceObject((table.head zip line).toMap) }
+        }
       case Failure(e) => Failure(e)
     }
-  }
 
-  //TODO: Try to stream this out to avoid memory overhead
+  // TODO: Try to stream this out to avoid memory overhead
   def tsvSerializeArray(input: Seq[WomObject]): Try[String] = {
 
     // Validates that all objects have the same attributes.
@@ -86,10 +90,15 @@ object WomObject {
         val attributesLine = attributes.mkString("\t")
         val valuesLines = objects map { obj =>
           attributes map { obj.values(_).valueString } mkString "\t"
-        } mkString(start = "", sep = "\n", end = "\n")
+        } mkString (start = "", sep = "\n", end = "\n")
 
         Success(s"$attributesLine\n$valuesLines")
-      case _ => Failure(new UnsupportedOperationException("Could not serialize array: Objects in the array have different attributes."))
+      case _ =>
+        Failure(
+          new UnsupportedOperationException(
+            "Could not serialize array: Objects in the array have different attributes."
+          )
+        )
     }
   }
 
@@ -100,17 +109,17 @@ object WomObject {
     withTypeErrorOr(values, objectTypeLike).toTry.get
   }
 
-  def withTypeErrorOr(values: Map[String, Any], objectTypeLike: WomObjectTypeLike): ErrorOr[WomObject] = {
+  def withTypeErrorOr(values: Map[String, Any], objectTypeLike: WomObjectTypeLike): ErrorOr[WomObject] =
     objectTypeLike.validateAndCoerceValues(values).map(new WomObject(_, objectTypeLike))
-  }
 
-  def withTypeChecked(values: Map[String, Any], objectTypeLike: WomObjectTypeLike): Checked[WomObject] = {
+  def withTypeChecked(values: Map[String, Any], objectTypeLike: WomObjectTypeLike): Checked[WomObject] =
     withTypeErrorOr(values, objectTypeLike).toEither
-  }
 
 }
 
-case class WomObject private[WomObject] (values: Map[String, WomValue], womType: WomObjectTypeLike) extends WomObjectLike with TsvSerializable {
+case class WomObject private[WomObject] (values: Map[String, WomValue], womType: WomObjectTypeLike)
+    extends WomObjectLike
+    with TsvSerializable {
   lazy val orderedAttributes = values.keySet.toSeq
   lazy val orderedValues = orderedAttributes map { values(_) }
   lazy val womObjectTypeLike = womType
diff --git a/wom/src/main/scala/wom/values/WomOptionalValue.scala b/wom/src/main/scala/wom/values/WomOptionalValue.scala
index d130dda13fa..a8b00264656 100644
--- a/wom/src/main/scala/wom/values/WomOptionalValue.scala
+++ b/wom/src/main/scala/wom/values/WomOptionalValue.scala
@@ -83,9 +83,8 @@ final case class WomOptionalValue(innerType: WomType, value: Option[WomValue]) e
     case None => emptyValueFailure(">")
   }
 
-  override def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] = {
+  override def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] =
     value.toList flatMap { _.collectAsSeq(filterFn) }
-  }
 
   /**
     * Unpack a nested option down to a single layer of optionality
@@ -93,7 +92,8 @@ final case class WomOptionalValue(innerType: WomType, value: Option[WomValue]) e
     */
   @tailrec
   def flattenOptional: WomOptionalValue = this match {
-    case WomOptionalValue(_: WomOptionalType, Some(innerOptionalValue: WomOptionalValue)) => innerOptionalValue.flattenOptional
+    case WomOptionalValue(_: WomOptionalType, Some(innerOptionalValue: WomOptionalValue)) =>
+      innerOptionalValue.flattenOptional
     case WomOptionalValue(innerType: WomOptionalType, None) => WomOptionalValue(innerType.baseMemberType, None)
     case _ => this
   }
@@ -107,7 +107,8 @@ final case class WomOptionalValue(innerType: WomType, value: Option[WomValue]) e
 
     assert(
       targetType.baseMemberTypeIsCompatibleWith(womType.baseMemberType),
-      s"base member type ${targetType.baseMemberType} and womtype ${womType.baseMemberType} are not compatible")
+      s"base member type ${targetType.baseMemberType} and womtype ${womType.baseMemberType} are not compatible"
+    )
     if (womType.depth.equals(targetType.depth)) {
       this
     } else {
@@ -141,7 +142,9 @@ final case class WomOptionalValue(innerType: WomType, value: Option[WomValue]) e
     }
   } getOrElse applicative.pure(this)
 
-  override def initialize(ioFunctionSet: IoFunctionSet): IOChecked[WomValue] = traverse(_.initialize(ioFunctionSet)).widen
+  override def initialize(ioFunctionSet: IoFunctionSet): IOChecked[WomValue] = traverse(
+    _.initialize(ioFunctionSet)
+  ).widen
 }
 
 object WomOptionalValue {
diff --git a/wom/src/main/scala/wom/values/WomPair.scala b/wom/src/main/scala/wom/values/WomPair.scala
index ba9e78def30..bb68e35ca13 100644
--- a/wom/src/main/scala/wom/values/WomPair.scala
+++ b/wom/src/main/scala/wom/values/WomPair.scala
@@ -7,7 +7,6 @@ case class WomPair(left: WomValue, right: WomValue) extends WomValue {
 
   override def toWomString = s"(${left.toWomString}, ${right.toWomString})"
 
-  override def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] = {
+  override def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] =
     left.collectAsSeq(filterFn) ++ right.collectAsSeq(filterFn)
-  }
 }
diff --git a/wom/src/main/scala/wom/values/WomValue.scala b/wom/src/main/scala/wom/values/WomValue.scala
index 45aa88abe12..d1cb620287d 100644
--- a/wom/src/main/scala/wom/values/WomValue.scala
+++ b/wom/src/main/scala/wom/values/WomValue.scala
@@ -15,7 +15,10 @@ trait WomValue {
   def womType: WomType
   def invalid(operation: String) = Failure(new WomExpressionException(s"Cannot perform operation: $operation"))
   def emptyValueFailure(operationName: String) = Failure(OptionalNotSuppliedException(operationName))
-  def evaluateIfDefined[A <: WomValue](operationName: String, optionalValue: WomOptionalValue, operation: WomValue => Try[A]): Try[A] = optionalValue match {
+  def evaluateIfDefined[A <: WomValue](operationName: String,
+                                       optionalValue: WomOptionalValue,
+                                       operation: WomValue => Try[A]
+  ): Try[A] = optionalValue match {
     case WomOptionalValue(_, Some(v)) => operation(v)
     case _ => emptyValueFailure(operationName)
   }
@@ -26,13 +29,13 @@ trait WomValue {
   def divide(rhs: WomValue): Try[WomValue] = invalid(s"$this / $rhs")
   def mod(rhs: WomValue): Try[WomValue] = invalid(s"$this % $rhs")
   def equals(rhs: WomValue): Try[WomBoolean] = invalid(s"$this == $rhs")
-  def notEquals(rhs: WomValue): Try[WomBoolean] = equals(rhs).map{ x => WomBoolean(!x.value)}
+  def notEquals(rhs: WomValue): Try[WomBoolean] = equals(rhs).map(x => WomBoolean(!x.value))
   def lessThan(rhs: WomValue): Try[WomBoolean] = invalid(s"$this < $rhs")
   def lessThanOrEqual(rhs: WomValue): Try[WomBoolean] =
-    Try(WomBoolean(Seq(lessThan _, equals _).exists{ p => p(rhs).get == WomBoolean.True }))
+    Try(WomBoolean(Seq(lessThan _, equals _).exists(p => p(rhs).get == WomBoolean.True)))
   def greaterThan(rhs: WomValue): Try[WomBoolean] = invalid(s"$this > $rhs")
   def greaterThanOrEqual(rhs: WomValue): Try[WomBoolean] =
-    Try(WomBoolean(Seq(greaterThan _, equals _).exists{ p => p(rhs).get == WomBoolean.True }))
+    Try(WomBoolean(Seq(greaterThan _, equals _).exists(p => p(rhs).get == WomBoolean.True)))
   def or(rhs: WomValue): Try[WomBoolean] = invalid(s"$this || $rhs")
   def and(rhs: WomValue): Try[WomBoolean] = invalid(s"$this && $rhs")
   def not: Try[WomValue] = invalid(s"!$this")
@@ -52,9 +55,8 @@ trait WomValue {
    */
   def valueString: String = toWomString
 
-  def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] = {
+  def collectAsSeq[T <: WomValue](filterFn: PartialFunction[WomValue, T]): Seq[T] =
     if (filterFn.isDefinedAt(this)) Seq(filterFn(this)) else Nil
-  }
 
   private def symbolHash(hash: String) = SymbolHash((this.getClass.getCanonicalName + hash).md5Sum)
 
@@ -64,7 +66,7 @@ trait WomValue {
     symbolHash(concatenatedMap)
   }
 
-  def computeHash(implicit hasher: FileHasher): SymbolHash = {
+  def computeHash(implicit hasher: FileHasher): SymbolHash =
     this match {
       case w: WomObject => symbolHash(w.values safeMapValues { _.computeHash(hasher) })
       case w: WomMap => symbolHash(w.value map { case (k, v) => k.computeHash(hasher) -> v.computeHash(hasher) })
@@ -72,7 +74,6 @@ trait WomValue {
       case w: WomFile => hasher(w)
       case w => symbolHash(w.valueString)
     }
-  }
 
   def asWomExpression: ValueAsAnExpression = ValueAsAnExpression(this)
 
@@ -87,6 +88,7 @@ trait WomValue {
 }
 
 object WomValue {
+
   /**
     * Returns the womValue with all collections recursively limited to maximum length `maxElements`.
     *
@@ -95,7 +97,7 @@ object WomValue {
     * @return The womValue with maximum maxElements per collection.
     */
   def takeMaxElements(womValue: WomValue, maxElements: Int): WomValue = {
-    def takeMaxElements(recursiveWomValue: WomValue): WomValue = {
+    def takeMaxElements(recursiveWomValue: WomValue): WomValue =
       recursiveWomValue match {
         case WomArray(womType, values) =>
           val subset = values.take(maxElements)
@@ -104,16 +106,16 @@ object WomValue {
           val subset = values.take(maxElements)
           WomMap(
             womType,
-            subset map {
-              case (mapKey, mapValue) => takeMaxElements(mapKey) -> takeMaxElements(mapValue)
+            subset map { case (mapKey, mapValue) =>
+              takeMaxElements(mapKey) -> takeMaxElements(mapValue)
             }
           )
         case objectLike: WomObjectLike =>
           // First take only a limited number of the top-level elements.
           val shallowSubset = objectLike.values.take(maxElements)
           // Then recursively take only a limited number of elements.
-          val deepSubset = shallowSubset map {
-            case (mapKey, mapValue) => mapKey -> takeMaxElements(mapValue)
+          val deepSubset = shallowSubset map { case (mapKey, mapValue) =>
+            mapKey -> takeMaxElements(mapValue)
           }
           objectLike.copyWith(deepSubset)
         case WomOptionalValue(innerType, valueOption) =>
@@ -121,7 +123,6 @@ object WomValue {
         case WomPair(left, right) => WomPair(takeMaxElements(left), takeMaxElements(right))
         case _ => recursiveWomValue
       }
-    }
 
     takeMaxElements(womValue)
   }
diff --git a/wom/src/main/scala/wom/views/GraphPrint.scala b/wom/src/main/scala/wom/views/GraphPrint.scala
index 6bf146d136a..80d53867174 100644
--- a/wom/src/main/scala/wom/views/GraphPrint.scala
+++ b/wom/src/main/scala/wom/views/GraphPrint.scala
@@ -17,7 +17,7 @@ final class GraphPrint(executableCallable: ExecutableCallable) {
   def dotString: String =
     WorkflowDigraph(
       workflowName = executableCallable.name,
-      digraph = listAllGraphNodes(executableCallable.graph, new AtomicInteger(0), Map.empty),
+      digraph = listAllGraphNodes(executableCallable.graph, new AtomicInteger(0), Map.empty)
     ).dotString
 
   // A "monoid" is just a fancy way of saying "thing you can add together".
@@ -32,20 +32,24 @@ final class GraphPrint(executableCallable: ExecutableCallable) {
    */
   private def listAllGraphNodes(graph: Graph,
                                 clusterCounter: AtomicInteger,
-                                availableScatterVariables: Map[ScatterVariableNode, DotScatterVariableNode]): NodesAndLinks = {
-
+                                availableScatterVariables: Map[ScatterVariableNode, DotScatterVariableNode]
+  ): NodesAndLinks =
     graph.nodes.toList.filter(worthDisplaying).foldMap {
-      case ccn: CommandCallNode => NodesAndLinks(Set(DotCallNode(ccn)), upstreamLinks(ccn, DotCallNode(ccn), availableScatterVariables))
-      case scn: WorkflowCallNode => NodesAndLinks(Set(DotSubworkflowCallNode(scn)), upstreamLinks(scn, DotSubworkflowCallNode(scn), availableScatterVariables))
+      case ccn: CommandCallNode =>
+        NodesAndLinks(Set(DotCallNode(ccn)), upstreamLinks(ccn, DotCallNode(ccn), availableScatterVariables))
+      case scn: WorkflowCallNode =>
+        NodesAndLinks(Set(DotSubworkflowCallNode(scn)),
+                      upstreamLinks(scn, DotSubworkflowCallNode(scn), availableScatterVariables)
+        )
       case s: ScatterNode => handleScatter(s, clusterCounter, availableScatterVariables)
       case c: ConditionalNode => handleConditional(c, clusterCounter, availableScatterVariables)
       case _ => nodeAndLinkMonoid.empty
     }
-  }
 
   def handleScatter(scatterNode: ScatterNode,
                     clusterCounter: AtomicInteger,
-                    knownScatterVariables: Map[ScatterVariableNode, DotScatterVariableNode]): NodesAndLinks = {
+                    knownScatterVariables: Map[ScatterVariableNode, DotScatterVariableNode]
+  ): NodesAndLinks = {
     val clusterNumber = clusterCounter.getAndIncrement()
     val id = s"cluster_$clusterNumber"
 
@@ -65,7 +69,8 @@ final class GraphPrint(executableCallable: ExecutableCallable) {
       svn -> link.get
     }.toMap
 
-    val innerGraphNodesAndLinks = listAllGraphNodes(scatterNode.innerGraph, clusterCounter, knownScatterVariables ++ madeScatterVariableNodes)
+    val innerGraphNodesAndLinks =
+      listAllGraphNodes(scatterNode.innerGraph, clusterCounter, knownScatterVariables ++ madeScatterVariableNodes)
 
     NodesAndLinks(
       nodes = Set(DotScatterNode(id, innerGraphNodesAndLinks.nodes ++ scatterExpressionNodesAndLinks.nodes)),
@@ -75,7 +80,8 @@ final class GraphPrint(executableCallable: ExecutableCallable) {
 
   def handleConditional(conditionalNode: ConditionalNode,
                         clusterCounter: AtomicInteger,
-                        knownScatterVariables: Map[ScatterVariableNode, DotScatterVariableNode]): NodesAndLinks = {
+                        knownScatterVariables: Map[ScatterVariableNode, DotScatterVariableNode]
+  ): NodesAndLinks = {
     val clusterNumber = clusterCounter.getAndIncrement()
     val id = s"cluster_$clusterNumber"
 
@@ -90,7 +96,7 @@ final class GraphPrint(executableCallable: ExecutableCallable) {
     val innerGraphNodesAndLinks = listAllGraphNodes(conditionalNode.innerGraph, clusterCounter, knownScatterVariables)
 
     NodesAndLinks(
-      nodes = Set(DotConditionalNode(id, innerGraphNodesAndLinks.nodes ++ conditionalExpressionNodesAndLinks.nodes)) ,
+      nodes = Set(DotConditionalNode(id, innerGraphNodesAndLinks.nodes ++ conditionalExpressionNodesAndLinks.nodes)),
       links = innerGraphNodesAndLinks.links ++ conditionalExpressionNodesAndLinks.links
     )
   }
@@ -141,24 +147,27 @@ object GraphPrint {
     def dotString = s"""$id [shape="hexagon" label="scatter over ${womType.friendlyName} as $valueName"]"""
   }
   object DotScatterVariableNode {
-    def apply(svn: ScatterVariableNode, clusterNumber: Int): DotScatterVariableNode = DotScatterVariableNode(svn.womType, svn.identifier.localName.value, clusterNumber)
+    def apply(svn: ScatterVariableNode, clusterNumber: Int): DotScatterVariableNode =
+      DotScatterVariableNode(svn.womType, svn.identifier.localName.value, clusterNumber)
   }
 
-  final case class DotConditionalExpressionNode(womType: WomType, expressionString: String, clusterNumber: Int) extends DotNode {
+  final case class DotConditionalExpressionNode(womType: WomType, expressionString: String, clusterNumber: Int)
+      extends DotNode {
     override def id: String = s"CONDITIONAL_${clusterNumber}_EXPRESSION"
     def dotString = s"""$id [shape="hexagon" label="if ($expressionString)" style="dashed" ]"""
   }
   object DotConditionalExpressionNode {
-    def apply(en: ExpressionNode, clusterNumber: Int): DotConditionalExpressionNode = DotConditionalExpressionNode(en.womType, escapeQuotes(en.womExpression.sourceString), clusterNumber)
+    def apply(en: ExpressionNode, clusterNumber: Int): DotConditionalExpressionNode =
+      DotConditionalExpressionNode(en.womType, escapeQuotes(en.womExpression.sourceString), clusterNumber)
   }
 
   final case class DotScatterNode(id: String, nodes: Set[DotNode]) extends DotNode {
     override def dotString: String =
       s"""subgraph $id {
-          |  style="filled,solid";
-          |  fillcolor=white;
-          |  ${nodes.toList.flatMap(_.dotString.linesIterator).mkString(System.lineSeparator() + "  ")}
-          |}""".stripMargin
+         |  style="filled,solid";
+         |  fillcolor=white;
+         |  ${nodes.toList.flatMap(_.dotString.linesIterator).mkString(System.lineSeparator() + "  ")}
+         |}""".stripMargin
   }
 
   final case class DotConditionalNode(id: String, nodes: Set[DotNode]) extends DotNode {
@@ -172,7 +181,8 @@ object GraphPrint {
 
   def upstreamLinks(originNode: GraphNode,
                     origin: DotNode,
-                    availableScatterVariables: Map[ScatterVariableNode, DotScatterVariableNode]): Set[DotLink] = {
+                    availableScatterVariables: Map[ScatterVariableNode, DotScatterVariableNode]
+  ): Set[DotLink] = {
     def relevantAsUpstream(nodeToLink: GraphNode): Set[DotNode] = nodeToLink match {
       case ccn: CommandCallNode => Set(DotCallNode(ccn))
       case scn: WorkflowCallNode => Set(DotSubworkflowCallNode(scn))
@@ -185,7 +195,8 @@ object GraphPrint {
 
     def upstreamPortToRelevantNodes(p: OutputPort) = p match {
       case gatherPort: ScatterGathererPort => relevantAsUpstream(gatherPort.outputToGather.singleUpstreamNode)
-      case conditionalOutputPort: ConditionalOutputPort => relevantAsUpstream(conditionalOutputPort.outputToExpose.singleUpstreamNode)
+      case conditionalOutputPort: ConditionalOutputPort =>
+        relevantAsUpstream(conditionalOutputPort.outputToExpose.singleUpstreamNode)
       case other =>
         relevantAsUpstream(other.graphNode)
     }
diff --git a/wom/src/test/scala/wom/WomMatchers.scala b/wom/src/test/scala/wom/WomMatchers.scala
index ca292662148..863f4ff4c1c 100644
--- a/wom/src/test/scala/wom/WomMatchers.scala
+++ b/wom/src/test/scala/wom/WomMatchers.scala
@@ -4,7 +4,7 @@ import org.scalactic.Equality
 import wom.graph.GraphNode
 
 trait WomMatchers {
-  // This will take precedence when comparing graph nodes or collections of graph nodes 
+  // This will take precedence when comparing graph nodes or collections of graph nodes
   implicit val graphNodeReferenceEquality = new Equality[GraphNode] {
     override def areEqual(left: GraphNode, right: Any): Boolean = right match {
       case node: GraphNode => left eq node
diff --git a/wom/src/test/scala/wom/callable/CommandTaskDefinitionSpec.scala b/wom/src/test/scala/wom/callable/CommandTaskDefinitionSpec.scala
index 29e6fb72cab..39b65bbe586 100644
--- a/wom/src/test/scala/wom/callable/CommandTaskDefinitionSpec.scala
+++ b/wom/src/test/scala/wom/callable/CommandTaskDefinitionSpec.scala
@@ -26,7 +26,9 @@ class CommandTaskDefinitionSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     executableOneInputTask match {
       case Valid(task) =>
         task.graph.nodes.size should be(2)
-        (task.graph.nodes.toList.find(_.isInstanceOf[GraphInputNode]), task.graph.nodes.toList.find(_.isInstanceOf[CallNode])) match {
+        (task.graph.nodes.toList.find(_.isInstanceOf[GraphInputNode]),
+         task.graph.nodes.toList.find(_.isInstanceOf[CallNode])
+        ) match {
           case (Some(inputNode), Some(callNode)) =>
             callNode.inputPorts.size should be(1)
             callNode.inputPorts.head.upstream.graphNode should be(inputNode)
@@ -41,7 +43,9 @@ class CommandTaskDefinitionSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       case Valid(task) =>
         val graph = task.graph
         graph.nodes.size should be(2)
-        (graph.nodes.toList.find(_.isInstanceOf[PortBasedGraphOutputNode]), graph.nodes.toList.find(_.isInstanceOf[CallNode])) match {
+        (graph.nodes.toList.find(_.isInstanceOf[PortBasedGraphOutputNode]),
+         graph.nodes.toList.find(_.isInstanceOf[CallNode])
+        ) match {
           case (Some(outputNode), Some(callNode)) =>
             callNode.outputPorts.size should be(1)
             outputNode.inputPorts.size should be(1)
@@ -74,7 +78,8 @@ object CommandTaskDefinitionSpec {
     inputs = List.empty,
     adHocFileCreation = Set.empty,
     environmentExpressions = Map.empty,
-    sourceLocation = None)
+    sourceLocation = None
+  )
   val executableNoInputsOrOutputsTask = noInputsOrOutputsTask.toExecutable
 
   val oneInputTask = CallableTaskDefinition(
@@ -87,7 +92,8 @@ object CommandTaskDefinitionSpec {
     inputs = List(Callable.RequiredInputDefinition(LocalName("bar"), WomIntegerType)),
     adHocFileCreation = Set.empty,
     environmentExpressions = Map.empty,
-    sourceLocation = None)
+    sourceLocation = None
+  )
   val executableOneInputTask = oneInputTask.toExecutable
 
   val oneOutputTask = CallableTaskDefinition(
@@ -100,7 +106,8 @@ object CommandTaskDefinitionSpec {
     inputs = List.empty,
     adHocFileCreation = Set.empty,
     environmentExpressions = Map.empty,
-    sourceLocation = None)
+    sourceLocation = None
+  )
   val executableOneOutputTask = oneOutputTask.toExecutable
 
   val duplicateFqns = CallableTaskDefinition(
@@ -110,7 +117,9 @@ object CommandTaskDefinitionSpec {
     meta = Map.empty,
     parameterMeta = Map.empty,
     outputs = List(Callable.OutputDefinition(LocalName("bar"), WomStringType, null)),
-    inputs = List(Callable.RequiredInputDefinition(LocalName("bar"), WomStringType), Callable.RequiredInputDefinition(LocalName("bar"), WomStringType)),
+    inputs = List(Callable.RequiredInputDefinition(LocalName("bar"), WomStringType),
+                  Callable.RequiredInputDefinition(LocalName("bar"), WomStringType)
+    ),
     adHocFileCreation = Set.empty,
     environmentExpressions = Map.empty,
     sourceLocation = None
diff --git a/wom/src/test/scala/wom/expression/PlaceholderWomExpression.scala b/wom/src/test/scala/wom/expression/PlaceholderWomExpression.scala
index c3738e6c94a..9206383f1f6 100644
--- a/wom/src/test/scala/wom/expression/PlaceholderWomExpression.scala
+++ b/wom/src/test/scala/wom/expression/PlaceholderWomExpression.scala
@@ -13,15 +13,22 @@ import scala.concurrent.{ExecutionContext, Future}
 final case class PlaceholderWomExpression(inputs: Set[String], fixedWomType: WomType) extends WomExpression {
   override def sourceString: String = "placeholder"
   override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] =
-    Invalid(NonEmptyList.one(s"couldn't evaluate value from inputs $inputs\tfixedWomType\t$fixedWomType\tinputValues\t$inputValues"))
+    Invalid(
+      NonEmptyList.one(
+        s"couldn't evaluate value from inputs $inputs\tfixedWomType\t$fixedWomType\tinputValues\t$inputValues"
+      )
+    )
   override def evaluateType(inputTypes: Map[String, WomType]): ErrorOr[WomType] =
     Valid(fixedWomType)
-  override def evaluateFiles(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet, coerceTo: WomType): ErrorOr[Set[FileEvaluation]] =
+  override def evaluateFiles(inputValues: Map[String, WomValue],
+                             ioFunctionSet: IoFunctionSet,
+                             coerceTo: WomType
+  ): ErrorOr[Set[FileEvaluation]] =
     Valid(Set.empty)
 }
 
 case object DefaultSizeIoFunctionSet extends EmptyIoFunctionSet {
   val DefaultFileSize = -12345L
-  override implicit def ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(1))
+  implicit override def ec: ExecutionContext = ExecutionContext.fromExecutor(Executors.newFixedThreadPool(1))
   override def size(path: String): Future[Long] = Future.successful(DefaultFileSize)
 }
diff --git a/wom/src/test/scala/wom/format/MemorySizeSpec.scala b/wom/src/test/scala/wom/format/MemorySizeSpec.scala
index bcd0ad7396d..af7980d5d33 100644
--- a/wom/src/test/scala/wom/format/MemorySizeSpec.scala
+++ b/wom/src/test/scala/wom/format/MemorySizeSpec.scala
@@ -5,14 +5,15 @@ import wdl4s.parser.MemoryUnit
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 
-
 class MemorySizeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "MemorySize"
-  
+
   it should "provide the rounded up multiple of a number" in {
     MemorySize(2, MemoryUnit.GB).to(MemoryUnit.MB).asRoundedUpMultipleOf(256) shouldBe MemorySize(2048, MemoryUnit.MB)
     MemorySize(2000, MemoryUnit.MB).asRoundedUpMultipleOf(256) shouldBe MemorySize(2048, MemoryUnit.MB)
-    MemorySize(3.75, MemoryUnit.GB).to(MemoryUnit.MB).asRoundedUpMultipleOf(256) shouldBe MemorySize(3840, MemoryUnit.MB)
+    MemorySize(3.75, MemoryUnit.GB).to(MemoryUnit.MB).asRoundedUpMultipleOf(256) shouldBe MemorySize(3840,
+                                                                                                     MemoryUnit.MB
+    )
     assertThrows[IllegalArgumentException](MemorySize(2000, MemoryUnit.MB).asRoundedUpMultipleOf(0))
     assertThrows[IllegalArgumentException](MemorySize(2000, MemoryUnit.MB).asRoundedUpMultipleOf(-5))
   }
diff --git a/wom/src/test/scala/wom/graph/ExpressionAsCallInputSpec.scala b/wom/src/test/scala/wom/graph/ExpressionAsCallInputSpec.scala
index 0075df49bbe..59cfd98980c 100644
--- a/wom/src/test/scala/wom/graph/ExpressionAsCallInputSpec.scala
+++ b/wom/src/test/scala/wom/graph/ExpressionAsCallInputSpec.scala
@@ -37,8 +37,12 @@ class ExpressionAsCallInputSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val ijExpression = PlaceholderWomExpression(Set("i", "j"), WomIntegerType)
 
     // Use that as an input to a one-input task:
-    val expressionNode = AnonymousExpressionNode.fromInputMapping(
-      WomIdentifier("bar"), ijExpression, Map("i" -> iInputNode.singleOutputPort, "j" -> jInputNode.singleOutputPort), TaskCallInputExpressionNode.apply)
+    val expressionNode = AnonymousExpressionNode
+      .fromInputMapping(WomIdentifier("bar"),
+                        ijExpression,
+                        Map("i" -> iInputNode.singleOutputPort, "j" -> jInputNode.singleOutputPort),
+                        TaskCallInputExpressionNode.apply
+      )
       .getOrElse(fail("Failed to build expression node"))
 
     val callNodeBuilder = new CallNodeBuilder()
diff --git a/wom/src/test/scala/wom/graph/ExpressionNodeSpec.scala b/wom/src/test/scala/wom/graph/ExpressionNodeSpec.scala
index 6c3a46864f0..39cd794a2d6 100644
--- a/wom/src/test/scala/wom/graph/ExpressionNodeSpec.scala
+++ b/wom/src/test/scala/wom/graph/ExpressionNodeSpec.scala
@@ -37,7 +37,12 @@ class ExpressionNodeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     // Declare the expression node using both i and j:
     import common.validation.ErrorOr.ShortCircuitingFlatMap
     val graph = for {
-      xDeclarationNode <- AnonymousExpressionNode.fromInputMapping(WomIdentifier("x"), ijExpression, Map("i" -> iInputNode.singleOutputPort, "j" -> jInputNode.singleOutputPort), PlainAnonymousExpressionNode.apply)
+      xDeclarationNode <- AnonymousExpressionNode.fromInputMapping(
+        WomIdentifier("x"),
+        ijExpression,
+        Map("i" -> iInputNode.singleOutputPort, "j" -> jInputNode.singleOutputPort),
+        PlainAnonymousExpressionNode.apply
+      )
       xOutputNode = PortBasedGraphOutputNode(WomIdentifier("x_out"), WomIntegerType, xDeclarationNode.singleOutputPort)
       g <- Graph.validateAndConstruct(Set(iInputNode, jInputNode, xDeclarationNode, xOutputNode))
     } yield g
@@ -48,10 +53,12 @@ class ExpressionNodeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     }
 
     def validate(graph: Graph) = {
-      val x_outGraphOutputNode = graph.nodes.find {
-        case g: GraphOutputNode => g.localName == "x_out"
-        case _ => false
-      }.getOrElse(fail("No 'x_out' GraphOutputNode in the graph"))
+      val x_outGraphOutputNode = graph.nodes
+        .find {
+          case g: GraphOutputNode => g.localName == "x_out"
+          case _ => false
+        }
+        .getOrElse(fail("No 'x_out' GraphOutputNode in the graph"))
 
       x_outGraphOutputNode.upstream.size should be(1)
       val xExpressionNode = x_outGraphOutputNode.upstream.head.asInstanceOf[ExpressionNode]
diff --git a/wom/src/test/scala/wom/graph/GraphOutputNodeSpec.scala b/wom/src/test/scala/wom/graph/GraphOutputNodeSpec.scala
index 5fbb36d4ea0..297ef7a8114 100644
--- a/wom/src/test/scala/wom/graph/GraphOutputNodeSpec.scala
+++ b/wom/src/test/scala/wom/graph/GraphOutputNodeSpec.scala
@@ -7,7 +7,6 @@ import org.scalatest.matchers.should.Matchers
 import wom.expression._
 import wom.types.{WomIntegerType, WomStringType}
 
-
 class GraphOutputNodeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "ExpressionBasedGraphOutputNode"
@@ -24,12 +23,17 @@ class GraphOutputNodeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     val ijExpression = PlaceholderWomExpression(Set("i", "j"), WomIntegerType)
 
     // Declare the expression output using both i and j:
-    val xOutputValidation = ExpressionBasedGraphOutputNode.fromInputMapping(WomIdentifier("x_out"), ijExpression, WomStringType, Map(
-      "i" -> iInputNode.singleOutputPort,
-      "j" -> jInputNode.singleOutputPort))
+    val xOutputValidation = ExpressionBasedGraphOutputNode.fromInputMapping(
+      WomIdentifier("x_out"),
+      ijExpression,
+      WomStringType,
+      Map("i" -> iInputNode.singleOutputPort, "j" -> jInputNode.singleOutputPort)
+    )
 
     import common.validation.ErrorOr.ShortCircuitingFlatMap
-    val graph = xOutputValidation flatMap { xOutput => Graph.validateAndConstruct(Set(iInputNode, jInputNode, jOutput, xOutput)) }
+    val graph = xOutputValidation flatMap { xOutput =>
+      Graph.validateAndConstruct(Set(iInputNode, jInputNode, jOutput, xOutput))
+    }
 
     graph match {
       case Valid(g) => validate(g)
diff --git a/wom/src/test/scala/wom/graph/GraphSpec.scala b/wom/src/test/scala/wom/graph/GraphSpec.scala
index 8cb71a985b0..738e6833ef5 100644
--- a/wom/src/test/scala/wom/graph/GraphSpec.scala
+++ b/wom/src/test/scala/wom/graph/GraphSpec.scala
@@ -12,7 +12,6 @@ import wom.graph.CallNode.{CallNodeAndNewNodes, CallNodeBuilder, InputDefinition
 import wom.graph.GraphNodePort.OutputPort
 import wom.types.{WomIntegerType, WomSingleFileType, WomStringType}
 
-
 class GraphSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "Graph"
 
@@ -64,8 +63,10 @@ class GraphSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
     val psNodeBuilder = new CallNodeBuilder()
 
-    val CallNodeAndNewNodes(psCall, psGraphInputs, _, _) = psNodeBuilder.build(WomIdentifier("ps"), taskDefinition_ps, InputDefinitionFold(), Set.empty, None)
-    val ps_procsOutputPort = psCall.outputByName("ps.procs").getOrElse(fail("Unexpectedly unable to find 'ps.procs' output"))
+    val CallNodeAndNewNodes(psCall, psGraphInputs, _, _) =
+      psNodeBuilder.build(WomIdentifier("ps"), taskDefinition_ps, InputDefinitionFold(), Set.empty, None)
+    val ps_procsOutputPort =
+      psCall.outputByName("ps.procs").getOrElse(fail("Unexpectedly unable to find 'ps.procs' output"))
 
     val cgrepNodeBuilder = new CallNodeBuilder()
     val cgrepInputDefinitionFold = InputDefinitionFold(
@@ -79,8 +80,10 @@ class GraphSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       ),
       Set(workflowInputNode)
     )
-    val CallNodeAndNewNodes(cgrepCall, cgrepGraphInputs, _, _) = cgrepNodeBuilder.build(WomIdentifier("cgrep"), taskDefinition_cgrep, cgrepInputDefinitionFold, Set.empty, None)
-    val cgrep_countOutputPort = cgrepCall.outputByName("cgrep.count").getOrElse(fail("Unexpectedly unable to find 'cgrep.count' output"))
+    val CallNodeAndNewNodes(cgrepCall, cgrepGraphInputs, _, _) =
+      cgrepNodeBuilder.build(WomIdentifier("cgrep"), taskDefinition_cgrep, cgrepInputDefinitionFold, Set.empty, None)
+    val cgrep_countOutputPort =
+      cgrepCall.outputByName("cgrep.count").getOrElse(fail("Unexpectedly unable to find 'cgrep.count' output"))
 
     val wcNodeBuilder = new CallNodeBuilder()
     val wcInputDefinitionFold = InputDefinitionFold(
@@ -93,11 +96,14 @@ class GraphSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       Set.empty
     )
 
-    val CallNodeAndNewNodes(wcCall, wcGraphInputs, _, _) = wcNodeBuilder.build(WomIdentifier("wc"), taskDefinition_wc, wcInputDefinitionFold, Set.empty, None)
-    val wc_countOutputPort = wcCall.outputByName("wc.count").getOrElse(fail("Unexpectedly unable to find 'wc.count' output"))
+    val CallNodeAndNewNodes(wcCall, wcGraphInputs, _, _) =
+      wcNodeBuilder.build(WomIdentifier("wc"), taskDefinition_wc, wcInputDefinitionFold, Set.empty, None)
+    val wc_countOutputPort =
+      wcCall.outputByName("wc.count").getOrElse(fail("Unexpectedly unable to find 'wc.count' output"))
 
     val psProcsOutputNode = PortBasedGraphOutputNode(WomIdentifier("ps.procs"), WomSingleFileType, ps_procsOutputPort)
-    val cgrepCountOutputNode = PortBasedGraphOutputNode(WomIdentifier("cgrep.count"), WomIntegerType, cgrep_countOutputPort)
+    val cgrepCountOutputNode =
+      PortBasedGraphOutputNode(WomIdentifier("cgrep.count"), WomIntegerType, cgrep_countOutputPort)
     val wcCountOutputNode = PortBasedGraphOutputNode(WomIdentifier("wc.count"), WomIntegerType, wc_countOutputPort)
 
     val graphNodes: Set[GraphNode] =
@@ -116,7 +122,9 @@ class GraphSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val workflowGraph = makeThreeStep
 
     workflowGraph.nodes collect { case gin: GraphInputNode => gin.localName } should be(Set("cgrep.pattern"))
-    workflowGraph.nodes collect { case gon: PortBasedGraphOutputNode => gon.localName } should be(Set("wc.count", "cgrep.count", "ps.procs"))
+    workflowGraph.nodes collect { case gon: PortBasedGraphOutputNode => gon.localName } should be(
+      Set("wc.count", "cgrep.count", "ps.procs")
+    )
     workflowGraph.nodes collect { case cn: CallNode => cn.localName } should be(Set("wc", "cgrep", "ps"))
   }
 
@@ -125,27 +133,54 @@ class GraphSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val threeStepWorkflow = WorkflowDefinition("three_step", threeStepGraph, Map.empty, Map.empty, None)
     val threeStepNodeBuilder = new CallNodeBuilder()
 
-    val workflowInputNode = RequiredGraphInputNode(WomIdentifier("three_step.cgrep.pattern"), WomStringType, "three_step.cgrep.pattern")
+    val workflowInputNode =
+      RequiredGraphInputNode(WomIdentifier("three_step.cgrep.pattern"), WomStringType, "three_step.cgrep.pattern")
 
     val inputDefinitionFold = InputDefinitionFold(
       mappings = List.empty,
       Set.empty,
       Set(workflowInputNode)
     )
-    val CallNodeAndNewNodes(threeStepCall, threeStepInputs, _, _) = threeStepNodeBuilder.build(WomIdentifier("three_step"), threeStepWorkflow, inputDefinitionFold, Set.empty, None)
+    val CallNodeAndNewNodes(threeStepCall, threeStepInputs, _, _) =
+      threeStepNodeBuilder.build(WomIdentifier("three_step"), threeStepWorkflow, inputDefinitionFold, Set.empty, None)
 
     // This is painful manually, but it's not up to WOM to decide which subworkflow outputs are forwarded through:
-    val psProcsOutputNode = PortBasedGraphOutputNode(WomIdentifier("three_step.ps.procs"), WomSingleFileType, threeStepCall.outputByName("three_step.ps.procs").getOrElse(fail(s"Subworkflow didn't expose the ps.procs output in ${threeStepCall.outputPorts.map(_.name).mkString(", ")}")))
-    val cgrepCountOutputNode = PortBasedGraphOutputNode(WomIdentifier("three_step.cgrep.count"), WomIntegerType, threeStepCall.outputByName("three_step.cgrep.count").getOrElse(fail("Subworkflow didn't expose the cgrep.count output")))
-    val wcCountOutputNode = PortBasedGraphOutputNode(WomIdentifier("three_step.wc.count"), WomIntegerType, threeStepCall.outputByName("three_step.wc.count").getOrElse(fail("Subworkflow didn't expose the wc.count output")))
+    val psProcsOutputNode = PortBasedGraphOutputNode(
+      WomIdentifier("three_step.ps.procs"),
+      WomSingleFileType,
+      threeStepCall
+        .outputByName("three_step.ps.procs")
+        .getOrElse(
+          fail(
+            s"Subworkflow didn't expose the ps.procs output in ${threeStepCall.outputPorts.map(_.name).mkString(", ")}"
+          )
+        )
+    )
+    val cgrepCountOutputNode = PortBasedGraphOutputNode(
+      WomIdentifier("three_step.cgrep.count"),
+      WomIntegerType,
+      threeStepCall
+        .outputByName("three_step.cgrep.count")
+        .getOrElse(fail("Subworkflow didn't expose the cgrep.count output"))
+    )
+    val wcCountOutputNode = PortBasedGraphOutputNode(
+      WomIdentifier("three_step.wc.count"),
+      WomIntegerType,
+      threeStepCall.outputByName("three_step.wc.count").getOrElse(fail("Subworkflow didn't expose the wc.count output"))
+    )
 
-    val workflowGraph = Graph.validateAndConstruct(Set[GraphNode](threeStepCall, psProcsOutputNode, cgrepCountOutputNode, wcCountOutputNode).union(threeStepInputs.toSet[GraphNode])) match {
+    val workflowGraph = Graph.validateAndConstruct(
+      Set[GraphNode](threeStepCall, psProcsOutputNode, cgrepCountOutputNode, wcCountOutputNode)
+        .union(threeStepInputs.toSet[GraphNode])
+    ) match {
       case Valid(wg) => wg
       case Invalid(errors) => fail(s"Unable to validate graph: ${errors.toList.mkString("\n", "\n", "\n")}")
     }
 
     workflowGraph.nodes collect { case gin: GraphInputNode => gin.localName } should be(Set("three_step.cgrep.pattern"))
-    workflowGraph.nodes collect { case gon: GraphOutputNode => gon.localName } should be(Set("three_step.wc.count", "three_step.cgrep.count", "three_step.ps.procs"))
+    workflowGraph.nodes collect { case gon: GraphOutputNode => gon.localName } should be(
+      Set("three_step.wc.count", "three_step.cgrep.count", "three_step.ps.procs")
+    )
     workflowGraph.nodes collect { case cn: CallNode => cn.localName } should be(Set("three_step"))
   }
 
@@ -157,10 +192,11 @@ class GraphSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
     Graph.validateAndConstruct(Set(nodeA, nodeB, nodeC, nodeD)) match {
       case Valid(_) => fail("Graph should not validate")
-      case Invalid(errors) => errors.toList.toSet shouldBe Set(
-        "Two or more nodes have the same FullyQualifiedName: foo.baz",
-        "Two or more nodes have the same FullyQualifiedName: foo.bar"
-      )
+      case Invalid(errors) =>
+        errors.toList.toSet shouldBe Set(
+          "Two or more nodes have the same FullyQualifiedName: foo.baz",
+          "Two or more nodes have the same FullyQualifiedName: foo.bar"
+        )
     }
   }
 }
diff --git a/wom/src/test/scala/wom/graph/ScatterNodeSpec.scala b/wom/src/test/scala/wom/graph/ScatterNodeSpec.scala
index 0ad865c1f4c..4d8d6455934 100644
--- a/wom/src/test/scala/wom/graph/ScatterNodeSpec.scala
+++ b/wom/src/test/scala/wom/graph/ScatterNodeSpec.scala
@@ -15,7 +15,6 @@ import wom.graph.GraphNodePort.OutputPort
 import wom.graph.expression.{AnonymousExpressionNode, PlainAnonymousExpressionNode}
 import wom.types.{WomArrayType, WomIntegerType, WomStringType}
 
-
 class ScatterNodeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "ScatterNode"
 
@@ -59,7 +58,11 @@ class ScatterNodeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
     val xsExpression = PlaceholderWomExpression(Set("xs"), WomArrayType(WomIntegerType))
     val xsExpressionAsInput = AnonymousExpressionNode
-      .fromInputMapping(WomIdentifier("x"), xsExpression, Map("xs" -> xs_inputNode.singleOutputPort), PlainAnonymousExpressionNode.apply)
+      .fromInputMapping(WomIdentifier("x"),
+                        xsExpression,
+                        Map("xs" -> xs_inputNode.singleOutputPort),
+                        PlainAnonymousExpressionNode.apply
+      )
       .valueOr(failures => fail(s"Failed to create expression node: ${failures.toList.mkString(", ")}"))
 
     val x_inputNode = ScatterVariableNode(WomIdentifier("x"), xsExpressionAsInput, WomArrayType(WomIntegerType))
@@ -73,8 +76,13 @@ class ScatterNodeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
       ),
       newGraphInputNodes = Set.empty
     )
-    val CallNodeAndNewNodes(foo_callNode, _, _, _) = fooNodeBuilder.build(WomIdentifier("foo"), task_foo, fooInputFold, Set.empty, None)
-    val foo_call_outNode = PortBasedGraphOutputNode(WomIdentifier("foo.out"), WomStringType, foo_callNode.outputByName("foo.out").getOrElse(fail("foo CallNode didn't contain the expected 'out' output")))
+    val CallNodeAndNewNodes(foo_callNode, _, _, _) =
+      fooNodeBuilder.build(WomIdentifier("foo"), task_foo, fooInputFold, Set.empty, None)
+    val foo_call_outNode = PortBasedGraphOutputNode(
+      WomIdentifier("foo.out"),
+      WomStringType,
+      foo_callNode.outputByName("foo.out").getOrElse(fail("foo CallNode didn't contain the expected 'out' output"))
+    )
     val scatterGraph = Graph.validateAndConstruct(Set(foo_callNode, x_inputNode, foo_call_outNode)) match {
       case Valid(sg) => sg
       case Invalid(es) => fail("Failed to make scatter graph: " + es.toList.mkString(", "))
@@ -116,7 +124,10 @@ class ScatterNodeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
       finalOutput.inputPorts.head.upstream.name should be("foo.out")
 
       // foo.out links back to the correct output in the inner graph:
-      val innerGraphFooOutNode = scatterNode.outputMapping.find(_.name == "foo.out").getOrElse(fail("Scatter couldn't link back the foo.out output.")).outputToGather
+      val innerGraphFooOutNode = scatterNode.outputMapping
+        .find(_.name == "foo.out")
+        .getOrElse(fail("Scatter couldn't link back the foo.out output."))
+        .outputToGather
       innerGraphFooOutNode.womType should be(WomStringType)
       innerGraphFooOutNode.upstream.size should be(1)
       innerGraphFooOutNode.upstream.head match {
diff --git a/wom/src/test/scala/wom/types/WomArrayTypeSpec.scala b/wom/src/test/scala/wom/types/WomArrayTypeSpec.scala
index c11e2997e2d..3b0ba617c74 100644
--- a/wom/src/test/scala/wom/types/WomArrayTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomArrayTypeSpec.scala
@@ -9,8 +9,7 @@ import wom.values._
 import scala.jdk.CollectionConverters._
 import scala.util.{Failure, Success}
 
-
-class WomArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers  {
+class WomArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   val intArray = WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(1), WomInteger(2), WomInteger(3)))
   "WomArray" should "stringify its value" in {
     intArray.toWomString shouldEqual "[1, 2, 3]"
@@ -42,7 +41,7 @@ class WomArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     }
   }
   "WomArrayType" should "coerce Seq(1,2,3) into a WomArray" in {
-    WomArrayType(WomIntegerType).coerceRawValue(Seq(1,2,3)) match {
+    WomArrayType(WomIntegerType).coerceRawValue(Seq(1, 2, 3)) match {
       case Success(array) => array shouldEqual intArray
       case Failure(f) => fail(s"exception while coercing array: $f")
     }
@@ -54,7 +53,7 @@ class WomArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     }
   }
   it should "coerce a Java List into a WomArray" in {
-    WomArrayType(WomIntegerType).coerceRawValue(List(1,2,3).asJava) match {
+    WomArrayType(WomIntegerType).coerceRawValue(List(1, 2, 3).asJava) match {
       case Success(array) => array shouldEqual intArray
       case Failure(f) => fail(s"exception while coercing Java List: $f")
     }
@@ -62,7 +61,8 @@ class WomArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
   it should "not coerce single values into one-element arrays" in {
     WomArrayType(WomStringType).coerceRawValue(WomString("edamame is tasty")) match {
       case Success(_) => fail("Unexpected success coercing single value to array")
-      case Failure(f) => f.getMessage shouldEqual "No coercion defined from wom value(s) '\"edamame is tasty\"' of type 'String' to 'Array[String]'."
+      case Failure(f) =>
+        f.getMessage shouldEqual "No coercion defined from wom value(s) '\"edamame is tasty\"' of type 'String' to 'Array[String]'."
     }
   }
   it should "stringify its type" in {
@@ -96,7 +96,13 @@ class WomArrayTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matcher
     val map = WomMap(WomMapType(WomIntegerType, WomStringType), Map(WomInteger(1) -> WomString("one")))
     val arrayOfPairsType = WomArrayType(WomPairType(WomIntegerType, WomStringType))
     arrayOfPairsType.isCoerceableFrom(map.womType) should be(true)
-    arrayOfPairsType.coerceRawValue(map) should be(Success(WomArray(WomArrayType(WomPairType(WomIntegerType, WomStringType)), List(WomPair(WomInteger(1), WomString("one"))))))
+    arrayOfPairsType.coerceRawValue(map) should be(
+      Success(
+        WomArray(WomArrayType(WomPairType(WomIntegerType, WomStringType)),
+                 List(WomPair(WomInteger(1), WomString("one")))
+        )
+      )
+    )
 
   }
 }
diff --git a/wom/src/test/scala/wom/types/WomCoercionSpec.scala b/wom/src/test/scala/wom/types/WomCoercionSpec.scala
index 184773ee52c..5011c850565 100644
--- a/wom/src/test/scala/wom/types/WomCoercionSpec.scala
+++ b/wom/src/test/scala/wom/types/WomCoercionSpec.scala
@@ -8,10 +8,12 @@ import wom.values.WomValue
 
 import scala.util.{Failure, Success}
 
-
 abstract class WomCoercionSpec(val goodCoercionTable: TableFor2[_ <: Any, WomValue],
                                val badCoercionTable: TableFor2[_ <: Any, WomType],
-                               val behaviorOf: String) extends AnyFlatSpecLike with CromwellTimeoutSpec with Matchers {
+                               val behaviorOf: String
+) extends AnyFlatSpecLike
+    with CromwellTimeoutSpec
+    with Matchers {
 
   import TableDrivenPropertyChecks._
   import WomCoercionSpec.StringableAny
@@ -19,11 +21,10 @@ abstract class WomCoercionSpec(val goodCoercionTable: TableFor2[_ <: Any, WomVal
   behavior of behaviorOf
 
   forAll(goodCoercionTable) { (fromValue, toValue) =>
-
     it should s"Allow coercion from ${fromValue.displayString} (${fromValue.typeDisplayString}) to ${toValue.toWomString} (${toValue.womType.stableName})" in {
       toValue.womType.coercionDefined(fromValue) should be(true)
       fromValue match {
-        case wv: WomValue => 
+        case wv: WomValue =>
           toValue.womType.isCoerceableFrom(wv.womType) should be(true)
         case _ => // can't test isCoerceableFrom for this fromValue
       }
@@ -35,7 +36,6 @@ abstract class WomCoercionSpec(val goodCoercionTable: TableFor2[_ <: Any, WomVal
   }
 
   forAll(badCoercionTable) { (fromValue, toType) =>
-
     it should s"Not allow coercion from ${fromValue.displayString} to ${toType.stableName}" in {
       toType.coercionDefined(fromValue) should be(false)
       fromValue match {
diff --git a/wom/src/test/scala/wom/types/WomCompositeTypeSpec.scala b/wom/src/test/scala/wom/types/WomCompositeTypeSpec.scala
index 639353ed7ec..d6ec388a83c 100644
--- a/wom/src/test/scala/wom/types/WomCompositeTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomCompositeTypeSpec.scala
@@ -6,8 +6,10 @@ import org.scalatest.prop.{TableDrivenPropertyChecks, TableFor2}
 import wom.types.WomCompositeTypeSpecDefs._
 import wom.values._
 
-
-class WomCompositeTypeSpec() extends WomCoercionSpec(goodCoercionTable, badCoercionTable, behaviorOf) with AnyFlatSpecLike with Matchers {
+class WomCompositeTypeSpec()
+    extends WomCoercionSpec(goodCoercionTable, badCoercionTable, behaviorOf)
+    with AnyFlatSpecLike
+    with Matchers {
 
   "WomObject with composite type" should "fail to build invalid values" in {
     val wrongType = the[Exception] thrownBy {
@@ -45,7 +47,9 @@ private object WomCompositeTypeSpecDefs {
   import spray.json._
   val stringIntCompositeType = WomCompositeType(Map("a" -> WomStringType, "b" -> WomIntegerType))
   val nestedStringIntCompositeType = WomCompositeType(Map("nested_a" -> WomStringType, "nested_b" -> WomIntegerType))
-  val complexNestedCompositeType = WomCompositeType(Map("a" -> WomArrayType(WomStringType), "b" -> nestedStringIntCompositeType))
+  val complexNestedCompositeType = WomCompositeType(
+    Map("a" -> WomArrayType(WomStringType), "b" -> nestedStringIntCompositeType)
+  )
   val simpleCompositeValue = WomObject.withTypeUnsafe(
     Map("a" -> WomString("0"), "b" -> WomInteger(1)),
     stringIntCompositeType
@@ -55,11 +59,13 @@ private object WomCompositeTypeSpecDefs {
       // Field "a" is an array of string
       "a" -> WomArray(WomArrayType(WomStringType), List(WomString("5"))),
       // Field "b" is a composite type itself
-      "b" -> WomObject.withTypeUnsafe(Map("nested_a" -> WomString("8"), "nested_b" -> WomInteger(2)), nestedStringIntCompositeType)
+      "b" -> WomObject.withTypeUnsafe(Map("nested_a" -> WomString("8"), "nested_b" -> WomInteger(2)),
+                                      nestedStringIntCompositeType
+      )
     ),
     complexNestedCompositeType
   )
-  
+
   val simpleCompositeValueAsAMap = WomMap(
     WomMapType(WomStringType, WomIntegerType),
     Map(
@@ -67,7 +73,7 @@ private object WomCompositeTypeSpecDefs {
       WomString("b") -> WomInteger(1)
     )
   )
-  
+
   val goodCoercionTable = Table[Any, WomValue](
     ("fromValue", "toValue"),
     // Identity coercion with simple field types
@@ -78,22 +84,26 @@ private object WomCompositeTypeSpecDefs {
     (simpleCompositeValueAsAMap, simpleCompositeValue),
     // Coercion from untyped WomObject
     (WomObject(
-      Map(
-        "a" -> WomString("0"),
-        "b" -> WomInteger(1)
-      )
-    ), simpleCompositeValue),
+       Map(
+         "a" -> WomString("0"),
+         "b" -> WomInteger(1)
+       )
+     ),
+     simpleCompositeValue
+    ),
     (WomObject(
-      Map(
-        "a" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(5))),
-        "b" -> WomObject(
-          Map(
-            "nested_a" -> WomInteger(8),
-            "nested_b" -> WomInteger(2)
-          )
-        )
-      )
-    ), complexCompositeValue),
+       Map(
+         "a" -> WomArray(WomArrayType(WomIntegerType), List(WomInteger(5))),
+         "b" -> WomObject(
+           Map(
+             "nested_a" -> WomInteger(8),
+             "nested_b" -> WomInteger(2)
+           )
+         )
+       )
+     ),
+     complexCompositeValue
+    ),
     // Coercion from Json
     ("""{ "a": "0", "b": "1" }""".parseJson, simpleCompositeValue),
     ("""{ "a": ["5"], "b": { "nested_a": "8", "nested_b": 2 } }""".parseJson, complexCompositeValue),
@@ -107,7 +117,8 @@ private object WomCompositeTypeSpecDefs {
           "b" -> WomMap(
             WomMapType(WomSingleFileType, WomIntegerType),
             Map(
-              WomSingleFile("nested_a") -> WomInteger(8) , WomSingleFile("nested_b") -> WomInteger(2)
+              WomSingleFile("nested_a") -> WomInteger(8),
+              WomSingleFile("nested_b") -> WomInteger(2)
             )
           )
         ),
@@ -123,7 +134,9 @@ private object WomCompositeTypeSpecDefs {
     // Automatic optional none default
     (
       WomObject.withTypeUnsafe(Map.empty, WomCompositeType(Map("a" -> WomOptionalType(WomStringType)))),
-      WomObject.withTypeUnsafe(Map("a" -> WomOptionalValue.none(WomStringType)), WomCompositeType(Map("a" -> WomOptionalType(WomStringType))))
+      WomObject.withTypeUnsafe(Map("a" -> WomOptionalValue.none(WomStringType)),
+                               WomCompositeType(Map("a" -> WomOptionalType(WomStringType)))
+      )
     )
   )
 
@@ -140,7 +153,8 @@ private object WomCompositeTypeSpecDefs {
         Map(
           "a" -> WomString("0"),
           "b" -> WomBoolean(false)
-        ), WomCompositeType(Map("a" -> WomStringType, "b" -> WomBooleanType))
+        ),
+        WomCompositeType(Map("a" -> WomStringType, "b" -> WomBooleanType))
       ),
       stringIntCompositeType
     ),
diff --git a/wom/src/test/scala/wom/types/WomCoproductSpec.scala b/wom/src/test/scala/wom/types/WomCoproductSpec.scala
index 99a87f85e04..8423c407fba 100644
--- a/wom/src/test/scala/wom/types/WomCoproductSpec.scala
+++ b/wom/src/test/scala/wom/types/WomCoproductSpec.scala
@@ -6,7 +6,6 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import wom.values.{WomBoolean, WomCoproductValue, WomString}
 
-
 class WomCoproductSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "Wom Coproduct Type"
diff --git a/wom/src/test/scala/wom/types/WomFileTypeSpec.scala b/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
index c4a90fadb07..c75b6f4f9ec 100644
--- a/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomFileTypeSpec.scala
@@ -10,51 +10,60 @@ import wom.values.{WomFloat, WomGlobFile, WomSingleFile, WomString, WomUnlistedD
 
 import scala.util.Success
 
-
 class WomFileTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
 
   behavior of "WomFileType"
 
   lazy val coercionTests = Table(
     ("description", "value", "expected"),
-
     ("a string to a dir", "example/string", WomUnlistedDirectory("example/string")),
     ("a string to a file", "example/string", WomSingleFile("example/string")),
     ("a string to a glob", "example/string", WomGlobFile("example/string")),
-
     ("a js string to a dir", JsString("example/js"), WomUnlistedDirectory("example/js")),
     ("a js string to a file", JsString("example/js"), WomSingleFile("example/js")),
     ("a js string to a glob", JsString("example/js"), WomGlobFile("example/js")),
-
     ("a wom string to a dir", WomString("example/wom"), WomUnlistedDirectory("example/wom")),
     ("a wom string to a file", WomString("example/wom"), WomSingleFile("example/wom")),
     ("a wom string to a glob", WomString("example/wom"), WomGlobFile("example/wom")),
-
-    ("a wom dir to a dir", WomUnlistedDirectory("example/dir"),
-      WomUnlistedDirectory("example/dir")),
+    ("a wom dir to a dir", WomUnlistedDirectory("example/dir"), WomUnlistedDirectory("example/dir")),
     ("a wom file to a file", WomSingleFile("example/dir"), WomSingleFile("example/dir")),
     ("a wom glob to a glob", WomGlobFile("example/glob*"), WomGlobFile("example/glob*")),
-
-    ("a string with leading and trailing special symbols to a dir", "  \n\r\t example/string \n\r\t ",
-      WomUnlistedDirectory("example/string")),
-    ("a string with leading and trailing special symbols to a file", "  \n\r\t example/string \n\r\t ",
-      WomSingleFile("example/string")),
-    ("a string with leading and trailing special symbols to a glob", "  \n\r\t example/string \n\r\t ",
-      WomGlobFile("example/string")),
-
-    ("a js string with leading and trailing special symbols to a dir", JsString("  \n\r\t example/js \n\r\t "),
-      WomUnlistedDirectory("example/js")),
-    ("a js string with leading and trailing special symbols to a file", JsString("  \n\r\t example/js \n\r\t "),
-      WomSingleFile("example/js")),
-    ("a js string with leading and trailing special symbols to a glob", JsString("  \n\r\t example/js \n\r\t "),
-      WomGlobFile("example/js")),
-
-    ("a wom string with leading and trailing special symbols to a dir", WomString("  \n\r\t example/wom \n\r\t "),
-      WomUnlistedDirectory("example/wom")),
-    ("a wom string with leading and trailing special symbols to a file", WomString("  \n\r\t example/wom \n\r\t "),
-      WomSingleFile("example/wom")),
-    ("a wom string with leading and trailing special symbols to a glob", WomString("  \n\r\t example/wom \n\r\t "),
-      WomGlobFile("example/wom")),
+    ("a string with leading and trailing special symbols to a dir",
+     "  \n\r\t example/string \n\r\t ",
+     WomUnlistedDirectory("example/string")
+    ),
+    ("a string with leading and trailing special symbols to a file",
+     "  \n\r\t example/string \n\r\t ",
+     WomSingleFile("example/string")
+    ),
+    ("a string with leading and trailing special symbols to a glob",
+     "  \n\r\t example/string \n\r\t ",
+     WomGlobFile("example/string")
+    ),
+    ("a js string with leading and trailing special symbols to a dir",
+     JsString("  \n\r\t example/js \n\r\t "),
+     WomUnlistedDirectory("example/js")
+    ),
+    ("a js string with leading and trailing special symbols to a file",
+     JsString("  \n\r\t example/js \n\r\t "),
+     WomSingleFile("example/js")
+    ),
+    ("a js string with leading and trailing special symbols to a glob",
+     JsString("  \n\r\t example/js \n\r\t "),
+     WomGlobFile("example/js")
+    ),
+    ("a wom string with leading and trailing special symbols to a dir",
+     WomString("  \n\r\t example/wom \n\r\t "),
+     WomUnlistedDirectory("example/wom")
+    ),
+    ("a wom string with leading and trailing special symbols to a file",
+     WomString("  \n\r\t example/wom \n\r\t "),
+     WomSingleFile("example/wom")
+    ),
+    ("a wom string with leading and trailing special symbols to a glob",
+     WomString("  \n\r\t example/wom \n\r\t "),
+     WomGlobFile("example/wom")
+    )
   )
 
   forAll(coercionTests) { (description, value, expected) =>
@@ -67,42 +76,81 @@ class WomFileTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
   lazy val failedCoercionTests = Table[String, WomType, Any, String](
     ("description", "womFileType", "value", "expected"),
-
-    ("a double to a dir", WomUnlistedDirectoryType, 6.28318,
-      "No coercion defined from '6.28318' of type 'java.lang.Double' to 'Directory'."),
-    ("a double to a file", WomSingleFileType, 6.28318,
-      "No coercion defined from '6.28318' of type 'java.lang.Double' to 'File'."),
-    ("a double to a glob", WomGlobFileType, 6.28318,
-      "No coercion defined from '6.28318' of type 'java.lang.Double' to 'Glob'."),
-
-    ("a js number to a dir", WomUnlistedDirectoryType, JsNumber(6.28318),
-      "No coercion defined from '6.28318' of type 'spray.json.JsNumber' to 'Directory'."),
-    ("a js number to a file", WomSingleFileType, JsNumber(6.28318),
-      "No coercion defined from '6.28318' of type 'spray.json.JsNumber' to 'File'."),
-    ("a js number to a glob", WomGlobFileType, JsNumber(6.28318),
-      "No coercion defined from '6.28318' of type 'spray.json.JsNumber' to 'Glob'."),
-
-    ("a wom float to a dir", WomUnlistedDirectoryType, WomFloat(6.28318),
-      "No coercion defined from wom value(s) '6.28318' of type 'Float' to 'Directory'."),
-    ("a wom float to a file", WomSingleFileType, WomFloat(6.28318),
-      "No coercion defined from wom value(s) '6.28318' of type 'Float' to 'File'."),
-    ("a wom float to a glob", WomGlobFileType, WomFloat(6.28318),
-      "No coercion defined from wom value(s) '6.28318' of type 'Float' to 'Glob'."),
-
-    ("a wom file to a dir", WomUnlistedDirectoryType, WomSingleFile("example/file"),
-      """No coercion defined from wom value(s) '"example/file"' of type 'File' to 'Directory'."""),
-    ("a wom glob to a dir", WomUnlistedDirectoryType, WomGlobFile("example/glob*"),
-      """No coercion defined from wom value(s) 'glob("example/glob*")' of type 'Glob' to 'Directory'."""),
-
-    ("a wom dir to a file", WomSingleFileType, WomUnlistedDirectory("example/dir"),
-      """No coercion defined from wom value(s) '"example/dir"' of type 'Directory' to 'File'."""),
-    ("a wom glob to a file", WomSingleFileType, WomGlobFile("example/glob*"),
-      """No coercion defined from wom value(s) 'glob("example/glob*")' of type 'Glob' to 'File'."""),
-
-    ("a wom dir to a glob", WomGlobFileType, WomUnlistedDirectory("example/dir"),
-      """No coercion defined from wom value(s) '"example/dir"' of type 'Directory' to 'Glob'."""),
-    ("a wom file to a glob", WomGlobFileType, WomSingleFile("example/file"),
-      """No coercion defined from wom value(s) '"example/file"' of type 'File' to 'Glob'.""")
+    ("a double to a dir",
+     WomUnlistedDirectoryType,
+     6.28318,
+     "No coercion defined from '6.28318' of type 'java.lang.Double' to 'Directory'."
+    ),
+    ("a double to a file",
+     WomSingleFileType,
+     6.28318,
+     "No coercion defined from '6.28318' of type 'java.lang.Double' to 'File'."
+    ),
+    ("a double to a glob",
+     WomGlobFileType,
+     6.28318,
+     "No coercion defined from '6.28318' of type 'java.lang.Double' to 'Glob'."
+    ),
+    ("a js number to a dir",
+     WomUnlistedDirectoryType,
+     JsNumber(6.28318),
+     "No coercion defined from '6.28318' of type 'spray.json.JsNumber' to 'Directory'."
+    ),
+    ("a js number to a file",
+     WomSingleFileType,
+     JsNumber(6.28318),
+     "No coercion defined from '6.28318' of type 'spray.json.JsNumber' to 'File'."
+    ),
+    ("a js number to a glob",
+     WomGlobFileType,
+     JsNumber(6.28318),
+     "No coercion defined from '6.28318' of type 'spray.json.JsNumber' to 'Glob'."
+    ),
+    ("a wom float to a dir",
+     WomUnlistedDirectoryType,
+     WomFloat(6.28318),
+     "No coercion defined from wom value(s) '6.28318' of type 'Float' to 'Directory'."
+    ),
+    ("a wom float to a file",
+     WomSingleFileType,
+     WomFloat(6.28318),
+     "No coercion defined from wom value(s) '6.28318' of type 'Float' to 'File'."
+    ),
+    ("a wom float to a glob",
+     WomGlobFileType,
+     WomFloat(6.28318),
+     "No coercion defined from wom value(s) '6.28318' of type 'Float' to 'Glob'."
+    ),
+    ("a wom file to a dir",
+     WomUnlistedDirectoryType,
+     WomSingleFile("example/file"),
+     """No coercion defined from wom value(s) '"example/file"' of type 'File' to 'Directory'."""
+    ),
+    ("a wom glob to a dir",
+     WomUnlistedDirectoryType,
+     WomGlobFile("example/glob*"),
+     """No coercion defined from wom value(s) 'glob("example/glob*")' of type 'Glob' to 'Directory'."""
+    ),
+    ("a wom dir to a file",
+     WomSingleFileType,
+     WomUnlistedDirectory("example/dir"),
+     """No coercion defined from wom value(s) '"example/dir"' of type 'Directory' to 'File'."""
+    ),
+    ("a wom glob to a file",
+     WomSingleFileType,
+     WomGlobFile("example/glob*"),
+     """No coercion defined from wom value(s) 'glob("example/glob*")' of type 'Glob' to 'File'."""
+    ),
+    ("a wom dir to a glob",
+     WomGlobFileType,
+     WomUnlistedDirectory("example/dir"),
+     """No coercion defined from wom value(s) '"example/dir"' of type 'Directory' to 'Glob'."""
+    ),
+    ("a wom file to a glob",
+     WomGlobFileType,
+     WomSingleFile("example/file"),
+     """No coercion defined from wom value(s) '"example/file"' of type 'File' to 'Glob'."""
+    )
   )
 
   forAll(failedCoercionTests) { (description, womFileType, value, expected) =>
diff --git a/wom/src/test/scala/wom/types/WomMapTypeSpec.scala b/wom/src/test/scala/wom/types/WomMapTypeSpec.scala
index 214e150f873..1f7391295ba 100644
--- a/wom/src/test/scala/wom/types/WomMapTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomMapTypeSpec.scala
@@ -8,23 +8,29 @@ import wom.values.{WomInteger, WomMap, WomObject, WomString}
 
 import scala.util.{Failure, Success}
 
-
-class WomMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers  {
-  val stringIntMap = WomMap(WomMapType(WomStringType, WomIntegerType), Map(
-    WomString("a") -> WomInteger(1),
-    WomString("b") -> WomInteger(2),
-    WomString("c") -> WomInteger(3)
-  ))
-  val coerceableObject = WomObject(Map(
-    "a" -> WomString("1"),
-    "b" -> WomString("2"),
-    "c" -> WomString("3")
-  ))
-  val coerceableTypedObject = WomObject(Map(
-    "a" -> WomString("1"),
-    "b" -> WomString("2"),
-    "c" -> WomString("3")
-  ), WomCompositeType(Map("a" -> WomStringType, "b" -> WomStringType, "c" -> WomStringType)))
+class WomMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+  val stringIntMap = WomMap(WomMapType(WomStringType, WomIntegerType),
+                            Map(
+                              WomString("a") -> WomInteger(1),
+                              WomString("b") -> WomInteger(2),
+                              WomString("c") -> WomInteger(3)
+                            )
+  )
+  val coerceableObject = WomObject(
+    Map(
+      "a" -> WomString("1"),
+      "b" -> WomString("2"),
+      "c" -> WomString("3")
+    )
+  )
+  val coerceableTypedObject = WomObject(
+    Map(
+      "a" -> WomString("1"),
+      "b" -> WomString("2"),
+      "c" -> WomString("3")
+    ),
+    WomCompositeType(Map("a" -> WomStringType, "b" -> WomStringType, "c" -> WomStringType))
+  )
 
   "WomMap" should "stringify its value" in {
     stringIntMap.toWomString shouldEqual "{\"a\": 1, \"b\": 2, \"c\": 3}"
@@ -36,7 +42,9 @@ class WomMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     }
   }
   it should "coerce a JsObject into a WomMap" in {
-    WomMapType(WomStringType, WomIntegerType).coerceRawValue(JsObject(Map("a" -> JsNumber(1), "b" -> JsNumber(2), "c" -> JsNumber(3)))) match {
+    WomMapType(WomStringType, WomIntegerType).coerceRawValue(
+      JsObject(Map("a" -> JsNumber(1), "b" -> JsNumber(2), "c" -> JsNumber(3)))
+    ) match {
       case Success(array) => array shouldEqual stringIntMap
       case Failure(f) => fail(s"exception while coercing JsObject: $f")
     }
@@ -63,7 +71,9 @@ class WomMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
   it should "detect invalid map construction if there are mixed keys" in {
     try {
-      WomMap(WomMapType(WomStringType, WomStringType), Map(WomInteger(0) -> WomString("foo"), WomString("x") -> WomString("y")))
+      WomMap(WomMapType(WomStringType, WomStringType),
+             Map(WomInteger(0) -> WomString("foo"), WomString("x") -> WomString("y"))
+      )
       fail("Map initialization should have failed")
     } catch {
       case e: UnsupportedOperationException =>
@@ -73,7 +83,9 @@ class WomMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
   it should "detect invalid map construction if there are mixed values" in {
     try {
-      WomMap(WomMapType(WomStringType, WomStringType), Map(WomString("bar") -> WomString("foo"), WomString("x") -> WomInteger(2)))
+      WomMap(WomMapType(WomStringType, WomStringType),
+             Map(WomString("bar") -> WomString("foo"), WomString("x") -> WomInteger(2))
+      )
       fail("Map initialization should have failed")
     } catch {
       case e: UnsupportedOperationException =>
@@ -83,7 +95,9 @@ class WomMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
   it should "detect invalid map construction if the keys are all the wrong type" in {
     try {
-      WomMap(WomMapType(WomStringType, WomStringType), Map(WomInteger(22) -> WomString("foo"), WomInteger(2222) -> WomString("y")))
+      WomMap(WomMapType(WomStringType, WomStringType),
+             Map(WomInteger(22) -> WomString("foo"), WomInteger(2222) -> WomString("y"))
+      )
       fail("Map initialization should have failed")
     } catch {
       case e: UnsupportedOperationException =>
@@ -93,7 +107,9 @@ class WomMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
 
   it should "detect invalid map construction if the values are all the wrong type" in {
     try {
-      WomMap(WomMapType(WomStringType, WomStringType), Map(WomString("bar") -> WomInteger(44), WomString("x") -> WomInteger(4444)))
+      WomMap(WomMapType(WomStringType, WomStringType),
+             Map(WomString("bar") -> WomInteger(44), WomString("x") -> WomInteger(4444))
+      )
       fail("Map initialization should have failed")
     } catch {
       case e: UnsupportedOperationException =>
@@ -113,18 +129,22 @@ class WomMapTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   it should "tsvSerialize non-empty maps correctly and with newlines after every line" in {
     stringIntMap.tsvSerialize shouldEqual Success("a\t1\nb\t2\nc\t3\n")
 
-    val intIntMap = WomMap(WomMapType(WomIntegerType, WomIntegerType), Map(
-      WomInteger(4) -> WomInteger(1),
-      WomInteger(5) -> WomInteger(2),
-      WomInteger(6) -> WomInteger(3),
-    ))
+    val intIntMap = WomMap(WomMapType(WomIntegerType, WomIntegerType),
+                           Map(
+                             WomInteger(4) -> WomInteger(1),
+                             WomInteger(5) -> WomInteger(2),
+                             WomInteger(6) -> WomInteger(3)
+                           )
+    )
     intIntMap.tsvSerialize shouldEqual Success("4\t1\n5\t2\n6\t3\n")
 
-    val stringStringMap = WomMap(WomMapType(WomStringType, WomStringType), Map(
-      WomString("a") -> WomString("x"),
-      WomString("b") -> WomString("y"),
-      WomString("c") -> WomString("z")
-    ))
+    val stringStringMap = WomMap(WomMapType(WomStringType, WomStringType),
+                                 Map(
+                                   WomString("a") -> WomString("x"),
+                                   WomString("b") -> WomString("y"),
+                                   WomString("c") -> WomString("z")
+                                 )
+    )
     stringStringMap.tsvSerialize shouldEqual Success("a\tx\nb\ty\nc\tz\n")
   }
 
diff --git a/wom/src/test/scala/wom/types/WomObjectTypeSpec.scala b/wom/src/test/scala/wom/types/WomObjectTypeSpec.scala
index 7616356f945..376b49b27e8 100644
--- a/wom/src/test/scala/wom/types/WomObjectTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomObjectTypeSpec.scala
@@ -7,37 +7,39 @@ import wom.values.{WomInteger, WomMap, WomObject, WomString}
 
 import scala.util.{Failure, Success}
 
-
 class WomObjectTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-  val abcObject = WomObject(Map(
-    "a" -> WomString("one"),
-    "b" -> WomString("two"),
-    "c" -> WomString("three")
-  ))
+  val abcObject = WomObject(
+    Map(
+      "a" -> WomString("one"),
+      "b" -> WomString("two"),
+      "c" -> WomString("three")
+    )
+  )
 
-  val coerceableMap = WomMap(WomMapType(WomStringType, WomStringType), Map(
-    WomString("a") -> WomString("one"),
-    WomString("b") -> WomString("two"),
-    WomString("c") -> WomString("three"))
+  val coerceableMap = WomMap(
+    WomMapType(WomStringType, WomStringType),
+    Map(WomString("a") -> WomString("one"), WomString("b") -> WomString("two"), WomString("c") -> WomString("three"))
   )
 
-  val abcMixedTypedObject = WomObject(Map(
-    "a" -> WomString("one"),
-    "b" -> WomInteger(2),
-    "c" -> WomString("three")
-  ))
+  val abcMixedTypedObject = WomObject(
+    Map(
+      "a" -> WomString("one"),
+      "b" -> WomInteger(2),
+      "c" -> WomString("three")
+    )
+  )
 
-  val coerceableTypedObject = WomObject.withTypeUnsafe(Map(
-    "a" -> WomString("one"),
-    "b" -> WomInteger(2),
-    "c" -> WomString("three")),
+  val coerceableTypedObject = WomObject.withTypeUnsafe(
+    Map("a" -> WomString("one"), "b" -> WomInteger(2), "c" -> WomString("three")),
     WomCompositeType(Map("a" -> WomStringType, "b" -> WomIntegerType, "c" -> WomStringType))
   )
 
-  val nonCoerceableMap = WomMap(WomMapType(WomStringType, WomObjectType), Map(
-    WomString("a") -> WomObject(Map.empty),
-    WomString("b") -> WomObject(Map.empty),
-    WomString("c") -> WomObject(Map.empty))
+  val nonCoerceableMap = WomMap(
+    WomMapType(WomStringType, WomObjectType),
+    Map(WomString("a") -> WomObject(Map.empty),
+        WomString("b") -> WomObject(Map.empty),
+        WomString("c") -> WomObject(Map.empty)
+    )
   )
 
   "WomObject" should "stringify its value" in {
diff --git a/wom/src/test/scala/wom/types/WomOptionalTypeSpec.scala b/wom/src/test/scala/wom/types/WomOptionalTypeSpec.scala
index df81f5d63d2..c8c80e503f2 100644
--- a/wom/src/test/scala/wom/types/WomOptionalTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomOptionalTypeSpec.scala
@@ -6,8 +6,10 @@ import org.scalatest.prop.{TableDrivenPropertyChecks, TableFor2}
 import wom.types.WomOptionalTypeSpecDefs._
 import wom.values._
 
-
-class WomOptionalTypeSpec() extends WomCoercionSpec(goodCoercionTable, badCoercionTable, behaviorOf) with AnyFlatSpecLike with Matchers {
+class WomOptionalTypeSpec()
+    extends WomCoercionSpec(goodCoercionTable, badCoercionTable, behaviorOf)
+    with AnyFlatSpecLike
+    with Matchers {
 
   import TableDrivenPropertyChecks._
 
@@ -15,7 +17,10 @@ class WomOptionalTypeSpec() extends WomCoercionSpec(goodCoercionTable, badCoerci
     ("optional type", "flat optional type", "base member type"),
     (WomOptionalType(WomIntegerType), WomOptionalType(WomIntegerType), WomIntegerType),
     (WomOptionalType(WomOptionalType(WomIntegerType)), WomOptionalType(WomIntegerType), WomIntegerType),
-    (WomOptionalType(WomOptionalType(WomOptionalType(WomArrayType(WomOptionalType(WomIntegerType))))), WomOptionalType(WomArrayType(WomOptionalType(WomIntegerType))), WomArrayType(WomOptionalType(WomIntegerType)))
+    (WomOptionalType(WomOptionalType(WomOptionalType(WomArrayType(WomOptionalType(WomIntegerType))))),
+     WomOptionalType(WomArrayType(WomOptionalType(WomIntegerType))),
+     WomArrayType(WomOptionalType(WomIntegerType))
+    )
   )
 
   forAll(baseTypes) { (optType, flatOptType, baseType) =>
@@ -42,7 +47,9 @@ private object WomOptionalTypeSpecDefs {
     // Inner coercion defined:
     (WomOptionalValue(WomInteger(4)), WomOptionalValue(WomString("4"))),
     (WomOptionalValue(WomString("a.txt")), WomOptionalValue(WomSingleFile("a.txt"))),
-    (WomOptionalValue(WomOptionalValue(WomString("a.txt"))), WomOptionalValue(WomOptionalValue(WomSingleFile("a.txt")))),
+    (WomOptionalValue(WomOptionalValue(WomString("a.txt"))),
+     WomOptionalValue(WomOptionalValue(WomSingleFile("a.txt")))
+    ),
     (WomOptionalValue(WomIntegerType, None), WomOptionalValue(WomStringType, None)),
 
     // auto-boxing optionals
@@ -57,15 +64,31 @@ private object WomOptionalTypeSpecDefs {
     (WomOptionalValue(WomOptionalValue(WomIntegerType, None)), WomOptionalValue(WomIntegerType, None)),
 
     // flattening and boxing and coercion all at once:
-    (WomOptionalValue(WomOptionalValue(WomOptionalValue(WomInteger(3)))), WomOptionalValue(WomOptionalValue(WomString("3")))),
-    (WomOptionalValue(WomOptionalValue(WomInteger(3))), WomOptionalValue(WomOptionalValue(WomOptionalValue(WomString("3"))))),
-    (WomOptionalValue(WomOptionalValue(WomOptionalValue(WomIntegerType, None))), WomOptionalValue(WomOptionalType(WomStringType), None)),
-    (WomOptionalValue(WomOptionalValue(WomIntegerType, None)), WomOptionalValue(WomOptionalType(WomOptionalType(WomStringType)), None)),
+    (WomOptionalValue(WomOptionalValue(WomOptionalValue(WomInteger(3)))),
+     WomOptionalValue(WomOptionalValue(WomString("3")))
+    ),
+    (WomOptionalValue(WomOptionalValue(WomInteger(3))),
+     WomOptionalValue(WomOptionalValue(WomOptionalValue(WomString("3"))))
+    ),
+    (WomOptionalValue(WomOptionalValue(WomOptionalValue(WomIntegerType, None))),
+     WomOptionalValue(WomOptionalType(WomStringType), None)
+    ),
+    (WomOptionalValue(WomOptionalValue(WomIntegerType, None)),
+     WomOptionalValue(WomOptionalType(WomOptionalType(WomStringType)), None)
+    ),
 
     // Javascript coercions:
     (JsNull, WomOptionalValue.none(WomOptionalType(WomIntegerType))),
-    ("[1, 2, null, 4]".parseJson, WomArray(WomArrayType(WomOptionalType(WomIntegerType)),
-      List(WomOptionalValue(WomInteger(1)), WomOptionalValue(WomInteger(2)), WomOptionalValue.none(WomIntegerType), WomOptionalValue(WomInteger(4))))),
+    ("[1, 2, null, 4]".parseJson,
+     WomArray(
+       WomArrayType(WomOptionalType(WomIntegerType)),
+       List(WomOptionalValue(WomInteger(1)),
+            WomOptionalValue(WomInteger(2)),
+            WomOptionalValue.none(WomIntegerType),
+            WomOptionalValue(WomInteger(4))
+       )
+     )
+    ),
     ("""
        |{
        |  "one": 1,
@@ -73,11 +96,14 @@ private object WomOptionalTypeSpecDefs {
        |  "three": 3
        |}
      """.stripMargin.parseJson,
-      WomMap(WomMapType(WomStringType, WomOptionalType(WomIntegerType)), Map(
-        WomString("one") -> WomOptionalValue(WomInteger(1)),
-        WomString("two") -> WomOptionalValue.none(WomIntegerType),
-        WomString("three") ->WomOptionalValue(WomInteger(3))
-      ))
+     WomMap(
+       WomMapType(WomStringType, WomOptionalType(WomIntegerType)),
+       Map(
+         WomString("one") -> WomOptionalValue(WomInteger(1)),
+         WomString("two") -> WomOptionalValue.none(WomIntegerType),
+         WomString("three") -> WomOptionalValue(WomInteger(3))
+       )
+     )
     )
   )
 
diff --git a/wom/src/test/scala/wom/types/WomTypeSpec.scala b/wom/src/test/scala/wom/types/WomTypeSpec.scala
index 4d3c7befeb5..3a93bf4695c 100644
--- a/wom/src/test/scala/wom/types/WomTypeSpec.scala
+++ b/wom/src/test/scala/wom/types/WomTypeSpec.scala
@@ -12,7 +12,6 @@ import scala.runtime.ScalaRunTime
 import scala.util.Random
 import scala.util.matching.Regex
 
-
 class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   "WomType class" should "stringify WomBoolean to 'Boolean'" in {
     WomBooleanType.stableName shouldEqual "Boolean"
@@ -73,12 +72,15 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
         """ 'wom.types.WomTypeSpec\$\$anon\$\1' to 'Boolean'.""").r
     ),
     (
-      WomArray(WomArrayType(WomOptionalType(WomIntegerType)), Seq(
-        WomOptionalValue(WomInteger(0)),
-        WomOptionalValue(WomInteger(1)),
-        WomOptionalValue(WomInteger(2)),
-        WomOptionalValue(WomInteger(3)),
-        WomOptionalValue(WomInteger(4)))
+      WomArray(
+        WomArrayType(WomOptionalType(WomIntegerType)),
+        Seq(
+          WomOptionalValue(WomInteger(0)),
+          WomOptionalValue(WomInteger(1)),
+          WomOptionalValue(WomInteger(2)),
+          WomOptionalValue(WomInteger(3)),
+          WomOptionalValue(WomInteger(4))
+        )
       ),
       WomOptionalType(WomMaybeEmptyArrayType(WomIntegerType)),
       classOf[IllegalArgumentException],
@@ -98,12 +100,11 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     )
   )
 
-  private def describe(any: Any): String = {
+  private def describe(any: Any): String =
     any match {
       case womValue: WomValue => s"wom value ${womValue.toWomString} of type ${womValue.womType.stableName}"
       case _ => s"scala value ${ScalaRunTime.stringOf(any)}"
     }
-  }
 
   forAll(rawValuesCoercedToType) { (rawValue, womType, exceptionClass, exceptionMessage) =>
     it should s"fail coercing ${womType.stableName} from ${describe(rawValue)}" in {
@@ -117,25 +118,33 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     WomBooleanType.coerceRawValue("true").get shouldEqual WomBoolean.True
     WomBooleanType.coerceRawValue("FALSE").get shouldEqual WomBoolean.False
     WomBooleanType.coerceRawValue(false).get shouldEqual WomBoolean.False
-    WomBooleanType.coerceRawValue(WomOptionalValue(WomBooleanType, Option(WomBoolean(true)))).get shouldEqual WomBoolean.True
+    WomBooleanType
+      .coerceRawValue(WomOptionalValue(WomBooleanType, Option(WomBoolean(true))))
+      .get shouldEqual WomBoolean.True
     WomBooleanType.coerceRawValue("I like turtles").isFailure shouldBe true
   }
 
   "WomString" should "support expected coercions" in {
     WomStringType.coerceRawValue("foo").get shouldEqual WomString("foo")
-    WomStringType.coerceRawValue(WomOptionalValue(WomStringType, Option(WomString("foo")))).get shouldEqual WomString("foo")
+    WomStringType.coerceRawValue(WomOptionalValue(WomStringType, Option(WomString("foo")))).get shouldEqual WomString(
+      "foo"
+    )
     WomStringType.coerceRawValue(-1).isFailure shouldBe true
   }
 
   "WomFile" should "support expected coercions" in {
     WomSingleFileType.coerceRawValue("/etc/passwd").get shouldEqual WomSingleFile("/etc/passwd")
-    WomSingleFileType.coerceRawValue(WomOptionalValue(WomSingleFileType, Option(WomSingleFile("/etc/passwd")))).get shouldEqual WomSingleFile("/etc/passwd")
+    WomSingleFileType
+      .coerceRawValue(WomOptionalValue(WomSingleFileType, Option(WomSingleFile("/etc/passwd"))))
+      .get shouldEqual WomSingleFile("/etc/passwd")
     WomSingleFileType.coerceRawValue(-1).isFailure shouldBe true
   }
 
   "WomInteger" should "support expected coercions" in {
     WomIntegerType.coerceRawValue(42).get shouldEqual WomInteger(42)
-    WomIntegerType.coerceRawValue(WomOptionalValue(WomIntegerType, Option(WomInteger(42)))).get shouldEqual WomInteger(42)
+    WomIntegerType.coerceRawValue(WomOptionalValue(WomIntegerType, Option(WomInteger(42)))).get shouldEqual WomInteger(
+      42
+    )
     WomIntegerType.coerceRawValue("42").get shouldEqual WomInteger(42)
     WomIntegerType.coerceRawValue(JsString("42")).get shouldEqual WomInteger(42)
     WomIntegerType.coerceRawValue("FAIL").isFailure shouldBe true
@@ -167,26 +176,49 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   // Type A in, Type B in, expected results
   val lcsTestCases: List[(List[WomType], WomType)] = List(
     (List(WomIntegerType, WomStringType), WomStringType),
-    (List(WomPairType(WomStringType, WomIntegerType), WomPairType(WomIntegerType, WomStringType)), WomPairType(WomStringType, WomStringType)),
+    (List(WomPairType(WomStringType, WomIntegerType), WomPairType(WomIntegerType, WomStringType)),
+     WomPairType(WomStringType, WomStringType)
+    ),
     (List(WomOptionalType(WomIntegerType), WomOptionalType(WomStringType)), WomOptionalType(WomStringType)),
     (List(WomOptionalType(WomIntegerType), WomStringType), WomOptionalType(WomStringType)),
-    (List(WomArrayType(WomOptionalType(WomIntegerType)), WomArrayType(WomOptionalType(WomStringType))), WomArrayType(WomOptionalType(WomStringType))),
-    (List(WomOptionalType(WomMapType(WomIntegerType, WomStringType)), WomOptionalType(WomMapType(WomStringType, WomIntegerType))), WomOptionalType(WomMapType(WomStringType, WomStringType))),
+    (List(WomArrayType(WomOptionalType(WomIntegerType)), WomArrayType(WomOptionalType(WomStringType))),
+     WomArrayType(WomOptionalType(WomStringType))
+    ),
+    (List(WomOptionalType(WomMapType(WomIntegerType, WomStringType)),
+          WomOptionalType(WomMapType(WomStringType, WomIntegerType))
+     ),
+     WomOptionalType(WomMapType(WomStringType, WomStringType))
+    ),
     (List(
-      WomCompositeType(Map(
-        "i" -> WomIntegerType,
-        "s" -> WomStringType
-      )),
-      WomCompositeType(Map(
-        "a" -> WomStringType,
-        "b" -> WomIntegerType
-      ))
-    ), WomObjectType),
+       WomCompositeType(
+         Map(
+           "i" -> WomIntegerType,
+           "s" -> WomStringType
+         )
+       ),
+       WomCompositeType(
+         Map(
+           "a" -> WomStringType,
+           "b" -> WomIntegerType
+         )
+       )
+     ),
+     WomObjectType
+    ),
     (List(WomIntegerType, WomFloatType), WomFloatType),
     (List(WomIntegerType, WomBooleanType), WomStringType),
-    (List(WomOptionalType(WomMaybeEmptyArrayType(WomSingleFileType)), WomMaybeEmptyArrayType(WomNothingType)), WomOptionalType(WomMaybeEmptyArrayType(WomSingleFileType))),
-    (List(WomMaybeEmptyArrayType(WomSingleFileType), WomMaybeEmptyArrayType(WomNothingType)), WomMaybeEmptyArrayType(WomSingleFileType)),
-    (List(WomMaybeEmptyArrayType(WomStringType), WomMaybeEmptyArrayType(WomIntegerType), WomMaybeEmptyArrayType(WomNothingType)), WomMaybeEmptyArrayType(WomStringType))
+    (List(WomOptionalType(WomMaybeEmptyArrayType(WomSingleFileType)), WomMaybeEmptyArrayType(WomNothingType)),
+     WomOptionalType(WomMaybeEmptyArrayType(WomSingleFileType))
+    ),
+    (List(WomMaybeEmptyArrayType(WomSingleFileType), WomMaybeEmptyArrayType(WomNothingType)),
+     WomMaybeEmptyArrayType(WomSingleFileType)
+    ),
+    (List(WomMaybeEmptyArrayType(WomStringType),
+          WomMaybeEmptyArrayType(WomIntegerType),
+          WomMaybeEmptyArrayType(WomNothingType)
+     ),
+     WomMaybeEmptyArrayType(WomStringType)
+    )
   )
 
   lcsTestCases foreach { case (types, expectedLcs) =>
diff --git a/wom/src/test/scala/wom/util/YamlUtilsSpec.scala b/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
index 03534567f19..986201a2213 100644
--- a/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
+++ b/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
@@ -13,8 +13,12 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks
 
-
-class YamlUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks with EitherValues {
+class YamlUtilsSpec
+    extends AnyFlatSpec
+    with CromwellTimeoutSpec
+    with Matchers
+    with TableDrivenPropertyChecks
+    with EitherValues {
 
   behavior of "YamlUtils"
 
@@ -25,14 +29,14 @@ class YamlUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers w
       "a stackoverflow yaml bomb",
       "{a: &b [*b]}",
       refineMV[NonNegative](10),
-      "Loop detected",
+      "Loop detected"
     ),
     (
       // https://bitbucket.org/asomov/snakeyaml/wiki/Documentation#markdown-header-aliases
       "a recursive yaml example from the snakeyaml wiki",
       "&A [ *A ]",
       refineMV[NonNegative](10),
-      "Loop detected",
+      "Loop detected"
     ),
     (
       "a recursive yaml based on mappings back to the root",
@@ -40,7 +44,7 @@ class YamlUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers w
          |  c: *b
          |""".stripMargin,
       refineMV[NonNegative](10),
-      "Loop detected",
+      "Loop detected"
     ),
     (
       // https://bitbucket.org/asomov/snakeyaml-engine/src/41b3845/src/test/resources/recursive/recursive-set-1.yaml
@@ -54,7 +58,7 @@ class YamlUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers w
          |? *key
          |""".stripMargin,
       refineMV[NonNegative](10),
-      "Loop detected",
+      "Loop detected"
     ),
     (
       // https://en.wikipedia.org/w/index.php?title=Billion_laughs_attack&oldid=871224525#Variations
@@ -70,25 +74,25 @@ class YamlUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers w
          |i: &i [*h,*h,*h,*h,*h,*h,*h,*h,*h]
          |""".stripMargin,
       refineMV[NonNegative](10000),
-      "Loop detection halted at 10000 nodes",
+      "Loop detection halted at 10000 nodes"
     ),
     (
       "a null yaml",
       null,
       refineMV[NonNegative](0),
-      null,
+      null
     ),
     (
       "an empty yaml mapping when limited to zero nodes",
       "{}",
       refineMV[NonNegative](0),
-      "Loop detection halted at 0 nodes",
+      "Loop detection halted at 0 nodes"
     ),
     (
       "an empty yaml sequence when limited to zero nodes",
       "[]",
       refineMV[NonNegative](0),
-      "Loop detection halted at 0 nodes",
+      "Loop detection halted at 0 nodes"
     ),
     (
       "a yaml without a closing brace",
@@ -102,8 +106,8 @@ class YamlUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers w
          | in 'reader', line 1, column 2:
          |    {
          |     ^
-         |""".stripMargin,
-    ),
+         |""".stripMargin
+    )
   )
 
   private val legalYamlTests = Table(
@@ -112,19 +116,19 @@ class YamlUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers w
       "an empty yaml mapping when limited to one node",
       "{}",
       refineMV[NonNegative](1),
-      Json.obj(),
+      Json.obj()
     ),
     (
       "an empty yaml",
       "",
       refineMV[NonNegative](1),
-      Json.False,
+      Json.False
     ),
     (
       "an empty yaml sequence when limited to one node",
       "[]",
       refineMV[NonNegative](1),
-      Json.arr(),
+      Json.arr()
     ),
     (
       "a yaml with the same node for a key and value",
@@ -132,14 +136,14 @@ class YamlUtilsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers w
          |: *a
          |""".stripMargin,
       refineMV[NonNegative](3),
-      Json.obj("b" -> Json.fromString("b")),
+      Json.obj("b" -> Json.fromString("b"))
     ),
     (
       "a yaml with the same nodes in a sequence",
       "[ &a b, *a ]",
       refineMV[NonNegative](3),
-      Json.arr(Json.fromString("b"), Json.fromString("b")),
-    ),
+      Json.arr(Json.fromString("b"), Json.fromString("b"))
+    )
   )
 
   forAll(illegalYamlTests) { (description, yaml, maxNodes, exceptionMessage) =>
diff --git a/wom/src/test/scala/wom/values/WomFileSpec.scala b/wom/src/test/scala/wom/values/WomFileSpec.scala
index 3d4eff63c4c..10409de5730 100644
--- a/wom/src/test/scala/wom/values/WomFileSpec.scala
+++ b/wom/src/test/scala/wom/values/WomFileSpec.scala
@@ -9,7 +9,6 @@ import wom.types._
 
 import scala.util.{Success, Try}
 
-
 class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
 
   behavior of "WomFile"
@@ -39,16 +38,24 @@ class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
   )
   lazy val nestedFilesAndDirs = WomMaybePopulatedFile(
     valueOption = Option(singleFile.value),
-    secondaryFiles = List(WomMaybeListedDirectory(
-      valueOption = Option(listedDir1.value),
-      listingOption = Option(List(WomMaybePopulatedFile(
-        valueOption = Option(secondaryFile1.value),
-        secondaryFiles = List(WomMaybeListedDirectory(
-          valueOption = Option(listedDir2.value),
-          listingOption = Option(List(secondaryFile2))
-        ))
-      )))
-    ))
+    secondaryFiles = List(
+      WomMaybeListedDirectory(
+        valueOption = Option(listedDir1.value),
+        listingOption = Option(
+          List(
+            WomMaybePopulatedFile(
+              valueOption = Option(secondaryFile1.value),
+              secondaryFiles = List(
+                WomMaybeListedDirectory(
+                  valueOption = Option(listedDir2.value),
+                  listingOption = Option(List(secondaryFile2))
+                )
+              )
+            )
+          )
+        )
+      )
+    )
   )
 
   val mapFileTests = Table(
@@ -56,47 +63,62 @@ class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
     ("a single directory", singleDir, WomUnlistedDirectory("prepend/single/dir")),
     ("a single file", singleFile, WomSingleFile("prepend/single/file")),
     ("a glob file", globFile, WomGlobFile("prepend/glob/*")),
-    ("a dir with listed dirs", dirWithListedDirs,
-      WomMaybeListedDirectory(
-        valueOption = Option("prepend/single/dir"),
-        listingOption = Option(List(
-          WomUnlistedDirectory("prepend/listed/dir1"),
-          WomUnlistedDirectory("prepend/listed/dir2")
-        ))
-      )
+    ("a dir with listed dirs",
+     dirWithListedDirs,
+     WomMaybeListedDirectory(
+       valueOption = Option("prepend/single/dir"),
+       listingOption = Option(
+         List(
+           WomUnlistedDirectory("prepend/listed/dir1"),
+           WomUnlistedDirectory("prepend/listed/dir2")
+         )
+       )
+     )
     ),
-    ("a dir with listed files", dirWithListedFiles,
-      WomMaybeListedDirectory(
-        valueOption = Option("prepend/single/dir"),
-        listingOption = Option(List(WomSingleFile("prepend/secondary/file1"), WomSingleFile("prepend/secondary/file2")))
-      )
+    ("a dir with listed files",
+     dirWithListedFiles,
+     WomMaybeListedDirectory(
+       valueOption = Option("prepend/single/dir"),
+       listingOption = Option(List(WomSingleFile("prepend/secondary/file1"), WomSingleFile("prepend/secondary/file2")))
+     )
     ),
-    ("a file with secondary files", fileWithSecondaryFiles,
-      WomMaybePopulatedFile(
-        valueOption = Option("prepend/single/file"),
-        secondaryFiles = List(WomSingleFile("prepend/secondary/file1"), WomSingleFile("prepend/secondary/file2"))
-      )
+    ("a file with secondary files",
+     fileWithSecondaryFiles,
+     WomMaybePopulatedFile(
+       valueOption = Option("prepend/single/file"),
+       secondaryFiles = List(WomSingleFile("prepend/secondary/file1"), WomSingleFile("prepend/secondary/file2"))
+     )
     ),
-    ("a file with secondary dirs", fileWithSecondaryDirs,
-      WomMaybePopulatedFile(
-        valueOption = Option("prepend/single/file"),
-        secondaryFiles = List(WomUnlistedDirectory("prepend/listed/dir1"), WomUnlistedDirectory("prepend/listed/dir2"))
-      )
+    ("a file with secondary dirs",
+     fileWithSecondaryDirs,
+     WomMaybePopulatedFile(
+       valueOption = Option("prepend/single/file"),
+       secondaryFiles = List(WomUnlistedDirectory("prepend/listed/dir1"), WomUnlistedDirectory("prepend/listed/dir2"))
+     )
     ),
-    ("a nested file/dir", nestedFilesAndDirs,
-      WomMaybePopulatedFile(
-        valueOption = Option("prepend/single/file"),
-        secondaryFiles = List(WomMaybeListedDirectory(
-          valueOption = Option("prepend/listed/dir1"),
-          listingOption = Option(List(WomMaybePopulatedFile(
-            valueOption = Option("prepend/secondary/file1"),
-            secondaryFiles = List(WomMaybeListedDirectory(
-              valueOption = Option("prepend/listed/dir2"),
-              listingOption = Option(List(WomSingleFile("prepend/secondary/file2")))
-            ))
-          )))
-        ))
-      )
+    ("a nested file/dir",
+     nestedFilesAndDirs,
+     WomMaybePopulatedFile(
+       valueOption = Option("prepend/single/file"),
+       secondaryFiles = List(
+         WomMaybeListedDirectory(
+           valueOption = Option("prepend/listed/dir1"),
+           listingOption = Option(
+             List(
+               WomMaybePopulatedFile(
+                 valueOption = Option("prepend/secondary/file1"),
+                 secondaryFiles = List(
+                   WomMaybeListedDirectory(
+                     valueOption = Option("prepend/listed/dir2"),
+                     listingOption = Option(List(WomSingleFile("prepend/secondary/file2")))
+                   )
+                 )
+               )
+             )
+           )
+         )
+       )
+     )
     )
   )
 
@@ -117,38 +139,43 @@ class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
     ("a single directory", singleDir, List(WomUnlistedDirectory("single/dir"))),
     ("a single file", singleFile, List(WomSingleFile("single/file"))),
     ("a glob file", globFile, List(WomGlobFile("glob/*"))),
-    ("a dir with listed dirs", dirWithListedDirs,
-      List(
-        WomUnlistedDirectory("listed/dir1"),
-        WomUnlistedDirectory("listed/dir2")
-      )
+    ("a dir with listed dirs",
+     dirWithListedDirs,
+     List(
+       WomUnlistedDirectory("listed/dir1"),
+       WomUnlistedDirectory("listed/dir2")
+     )
     ),
-    ("a dir with listed files", dirWithListedFiles,
-      List(
-        WomSingleFile("secondary/file1"),
-        WomSingleFile("secondary/file2")
-      )
+    ("a dir with listed files",
+     dirWithListedFiles,
+     List(
+       WomSingleFile("secondary/file1"),
+       WomSingleFile("secondary/file2")
+     )
     ),
-    ("a file with secondary files", fileWithSecondaryFiles,
-      List(
-        WomSingleFile("single/file"),
-        WomSingleFile("secondary/file1"),
-        WomSingleFile("secondary/file2")
-      )
+    ("a file with secondary files",
+     fileWithSecondaryFiles,
+     List(
+       WomSingleFile("single/file"),
+       WomSingleFile("secondary/file1"),
+       WomSingleFile("secondary/file2")
+     )
     ),
-    ("a file with secondary dirs", fileWithSecondaryDirs,
-      List(
-        WomSingleFile("single/file"),
-        WomUnlistedDirectory("listed/dir1"),
-        WomUnlistedDirectory("listed/dir2")
-      )
+    ("a file with secondary dirs",
+     fileWithSecondaryDirs,
+     List(
+       WomSingleFile("single/file"),
+       WomUnlistedDirectory("listed/dir1"),
+       WomUnlistedDirectory("listed/dir2")
+     )
     ),
-    ("a nested file/dir", nestedFilesAndDirs,
-      List(
-        WomSingleFile("single/file"),
-        WomSingleFile("secondary/file1"),
-        WomSingleFile("secondary/file2")
-      )
+    ("a nested file/dir",
+     nestedFilesAndDirs,
+     List(
+       WomSingleFile("single/file"),
+       WomSingleFile("secondary/file1"),
+       WomSingleFile("secondary/file2")
+     )
     )
   )
 
@@ -170,7 +197,6 @@ class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
     globFile.toWomString should be("""glob("glob/*")""")
   }
 
-
   val addTests = Table(
     ("description", "womFile", "expectedPrefix", "expectedSuffix"),
     ("a single directory", singleDir, WomString("prefix/single/dir"), WomUnlistedDirectory("single/dir/suffix")),
@@ -235,17 +261,21 @@ class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
 
     it should s"fail to add an optional string prefix to $description" in {
       a[WomExpressionException] should be thrownBy {
-        WomOptionalValue(WomStringType, Option(WomString("prefix/"))).add(
-          WomOptionalValue(womFile.womType, Option(womFile))
-        ).get
+        WomOptionalValue(WomStringType, Option(WomString("prefix/")))
+          .add(
+            WomOptionalValue(womFile.womType, Option(womFile))
+          )
+          .get
       }
     }
 
     it should s"fail to add an optional string suffix to $description" in {
       a[WomExpressionException] should be thrownBy {
-        WomOptionalValue(womFile.womType, Option(womFile)).add(
-          WomOptionalValue(WomStringType, Option(WomString("/suffix")))
-        ).get
+        WomOptionalValue(womFile.womType, Option(womFile))
+          .add(
+            WomOptionalValue(WomStringType, Option(WomString("/suffix")))
+          )
+          .get
       }
     }
   }
@@ -263,9 +293,12 @@ class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
     }
 
     it should s"fail to add an optional int to $description" in {
-      WomOptionalValue(womFile.womType, Option(womFile)).add(
-        WomOptionalValue(WomIntegerType, Option(WomInteger(42)))
-      ).failed.get should have message expected
+      WomOptionalValue(womFile.womType, Option(womFile))
+        .add(
+          WomOptionalValue(WomIntegerType, Option(WomInteger(42)))
+        )
+        .failed
+        .get should have message expected
     }
   }
 
@@ -274,8 +307,11 @@ class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
     ("a single directory matched to a similar directory", singleDir, WomUnlistedDirectory(singleDir.value), true),
     ("a single file matched to a similar file", singleFile, WomSingleFile(singleFile.value), true),
     ("a glob file matched to a similar glob", globFile, WomGlobFile(globFile.value), true),
-    ("a single directory matched to a dissimilar directory", singleDir, WomUnlistedDirectory("should/not/match"),
-      false),
+    ("a single directory matched to a dissimilar directory",
+     singleDir,
+     WomUnlistedDirectory("should/not/match"),
+     false
+    ),
     ("a single file matched to a dissimilar file", singleFile, WomSingleFile("should/not/match"), false),
     ("a glob file matched to a dissimilar glob", globFile, WomGlobFile("should/not/match"), false)
   )
@@ -311,8 +347,10 @@ class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
     ("a single directory matched to a similar glob", singleDir, WomGlobFile(globFile.value)),
     ("a single file matched to a similar glob", singleFile, WomGlobFile(globFile.value)),
     ("a dir with listed dirs matched to a similar directory", dirWithListedDirs, WomUnlistedDirectory(singleDir.value)),
-    ("a dir with listed files matched to a similar directory", dirWithListedFiles,
-      WomUnlistedDirectory(singleDir.value)),
+    ("a dir with listed files matched to a similar directory",
+     dirWithListedFiles,
+     WomUnlistedDirectory(singleDir.value)
+    ),
     ("a file with secondary files matched to a similar file", fileWithSecondaryFiles, WomSingleFile(singleFile.value)),
     ("a file with secondary dirs matched to a similar file", fileWithSecondaryDirs, WomSingleFile(singleFile.value)),
     ("a nested file/dir matched to a similar file", nestedFilesAndDirs, WomSingleFile(singleFile.value))
@@ -333,17 +371,21 @@ class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
 
     it should s"fail comparing (optionally) $description" in {
       a[WomExpressionException] should be thrownBy {
-        WomOptionalValue(womFileA.womType, Option(womFileA)).equals(
-          WomOptionalValue(womFileB.womType, Option(womFileB))
-        ).get
+        WomOptionalValue(womFileA.womType, Option(womFileA))
+          .equals(
+            WomOptionalValue(womFileB.womType, Option(womFileB))
+          )
+          .get
       }
     }
 
     it should s"fail symmetrically comparing (optionally) $description" in {
       a[WomExpressionException] should be thrownBy {
-        WomOptionalValue(womFileB.womType, Option(womFileB)).equals(
-          WomOptionalValue(womFileA.womType, Option(womFileA))
-        ).get
+        WomOptionalValue(womFileB.womType, Option(womFileB))
+          .equals(
+            WomOptionalValue(womFileA.womType, Option(womFileA))
+          )
+          .get
       }
     }
   }
@@ -412,17 +454,21 @@ class WomFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
 
     it should s"expect $expected comparing $description as an optional string" in {
       a[WomExpressionException] should be thrownBy {
-        WomOptionalValue(womFile.womType, Option(womFile)).equals(
-          WomOptionalValue(WomStringType, Option(WomString(string)))
-        ).get
+        WomOptionalValue(womFile.womType, Option(womFile))
+          .equals(
+            WomOptionalValue(WomStringType, Option(WomString(string)))
+          )
+          .get
       }
     }
 
     it should s"expect $expected symmetrically comparing $description as an optional string" in {
       a[WomExpressionException] should be thrownBy {
-        WomOptionalValue(WomStringType, Option(WomString(string))).equals(
-          WomOptionalValue(womFile.womType, Option(womFile))
-        ).get
+        WomOptionalValue(WomStringType, Option(WomString(string)))
+          .equals(
+            WomOptionalValue(womFile.womType, Option(womFile))
+          )
+          .get
       }
     }
   }
diff --git a/wom/src/test/scala/wom/values/WomObjectSpec.scala b/wom/src/test/scala/wom/values/WomObjectSpec.scala
index bed14c9ae46..aa74c1f4c0e 100644
--- a/wom/src/test/scala/wom/values/WomObjectSpec.scala
+++ b/wom/src/test/scala/wom/values/WomObjectSpec.scala
@@ -29,13 +29,13 @@ class WomObjectSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers w
       val array: Array[WomObject] = parsed.success.value
       array should have size 1
 
-      //Attributes
+      // Attributes
       array.head.values should contain key "one"
       array.head.values should contain key "two"
       array.head.values should contain key "three"
       array.head.values should contain key "four"
 
-      //Values
+      // Values
       array.head.values.get("one") shouldBe Some(WomString("one"))
       array.head.values.get("two") shouldBe Some(WomString("four"))
       array.head.values.get("three") shouldBe Some(WomString("nine"))
@@ -73,7 +73,7 @@ class WomObjectSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers w
       val array: Array[WomObject] = parsed.success.value
       array should have size 2
 
-      //Attributes
+      // Attributes
       array foreach { a =>
         a.values should contain key "one"
         a.values should contain key "two"
@@ -81,7 +81,7 @@ class WomObjectSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers w
         a.values should contain key "four"
       }
 
-      //Values
+      // Values
       array.head.values.get("one") shouldBe Some(WomString("one"))
       array.head.values.get("two") shouldBe Some(WomString("four"))
       array.head.values.get("three") shouldBe Some(WomString("nine"))
diff --git a/wom/src/test/scala/wom/values/WomOptionalValueSpec.scala b/wom/src/test/scala/wom/values/WomOptionalValueSpec.scala
index 22dc5afc902..174fc5331ac 100644
--- a/wom/src/test/scala/wom/values/WomOptionalValueSpec.scala
+++ b/wom/src/test/scala/wom/values/WomOptionalValueSpec.scala
@@ -5,7 +5,6 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import wom.types.{WomIntegerType, WomOptionalType}
 
-
 class WomOptionalValueSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   behavior of "WomOptionalValue flattening"
diff --git a/womtool/src/main/scala/womtool/WomtoolMain.scala b/womtool/src/main/scala/womtool/WomtoolMain.scala
index e1fba99d978..6fc1ccb43db 100644
--- a/womtool/src/main/scala/womtool/WomtoolMain.scala
+++ b/womtool/src/main/scala/womtool/WomtoolMain.scala
@@ -62,14 +62,12 @@ object WomtoolMain extends App with StrictLogging {
     case _ => BadUsageTermination(WomtoolCommandLineParser.instance.usage)
   }
 
-
   def highlight(workflowSourcePath: String, mode: HighlightMode): Termination = {
 
-    def highlight(highlighter: SyntaxHighlighter) = {
+    def highlight(highlighter: SyntaxHighlighter) =
       loadWdl(workflowSourcePath) { namespace =>
         SuccessfulTermination(new SyntaxFormatter(highlighter).format(namespace))
       }
-    }
 
     mode match {
       case HtmlHighlighting => highlight(HtmlSyntaxHighlighter)
@@ -78,9 +76,8 @@ object WomtoolMain extends App with StrictLogging {
     }
   }
 
-  def parse(workflowSourcePath: String): Termination = {
+  def parse(workflowSourcePath: String): Termination =
     SuccessfulTermination(AstTools.getAst(Paths.get(workflowSourcePath)).toPrettyString)
-  }
 
   def upgrade(workflowSourcePath: String): Termination = {
     import wdl.draft2.model.Import
@@ -91,20 +88,21 @@ object WomtoolMain extends App with StrictLogging {
       WdlNamespace.loadUsingPath(
         Paths.get(workflowSourcePath),
         None,
-        Option(List(
-          WdlNamespace.directoryResolver(File(workflowSourcePath).parent),
-          WdlNamespace.fileResolver,
-          WdlDraft2LanguageFactory.httpResolver
-        ))
+        Option(
+          List(
+            WdlNamespace.directoryResolver(File(workflowSourcePath).parent),
+            WdlNamespace.fileResolver,
+            WdlDraft2LanguageFactory.httpResolver
+          )
+        )
       )
 
-    def upgradeImport(draft2Import: Import): ImportElement = {
+    def upgradeImport(draft2Import: Import): ImportElement =
       if (draft2Import.namespaceName.nonEmpty)
         // draft-2 does not have structs, so the source WDL will not have any for us to rename
         ImportElement(draft2Import.uri, Option(draft2Import.namespaceName), Map())
       else
         ImportElement(draft2Import.uri, None, Map())
-    }
 
     val maybeWdl: Try[Path] = DefaultPathBuilder.build(workflowSourcePath)
 
@@ -116,13 +114,16 @@ object WomtoolMain extends App with StrictLogging {
             val maybeFileElement = womBundleToFileElement.run(womBundle)
             maybeFileElement match {
               case Right(fileElement) =>
-                SuccessfulTermination(
-                  fileElement.copy(imports = wdlNamespace.imports.map(upgradeImport)).toWdlV1)
+                SuccessfulTermination(fileElement.copy(imports = wdlNamespace.imports.map(upgradeImport)).toWdlV1)
               case Left(errors) =>
-                UnsuccessfulTermination(s"WDL parsing succeeded but could not create WOM: ${errors.toList.mkString("[", ",", "]")}")
+                UnsuccessfulTermination(
+                  s"WDL parsing succeeded but could not create WOM: ${errors.toList.mkString("[", ",", "]")}"
+                )
             }
           case Left(errors) =>
-            UnsuccessfulTermination(s"WDL parsing succeeded but could not create WOM: ${errors.toList.mkString("[", ",", "]")}")
+            UnsuccessfulTermination(
+              s"WDL parsing succeeded but could not create WOM: ${errors.toList.mkString("[", ",", "]")}"
+            )
         }
       case (Failure(throwable), _) =>
         UnsuccessfulTermination(s"Failed to load WDL source: ${throwable.getMessage}")
@@ -131,31 +132,41 @@ object WomtoolMain extends App with StrictLogging {
     }
   }
 
-  def graph(workflowSourcePath: Path): Termination = {
-    WomGraphMaker.getBundle(workflowSourcePath).flatMap(_.toExecutableCallable).contextualizeErrors("create wom bundle") match {
-      case Right(executable) => SuccessfulTermination (new GraphPrint(executable).dotString)
-      case Left(errors) => UnsuccessfulTermination(errors.toList.mkString(System.lineSeparator, System.lineSeparator, System.lineSeparator))
+  def graph(workflowSourcePath: Path): Termination =
+    WomGraphMaker
+      .getBundle(workflowSourcePath)
+      .flatMap(_.toExecutableCallable)
+      .contextualizeErrors("create wom bundle") match {
+      case Right(executable) => SuccessfulTermination(new GraphPrint(executable).dotString)
+      case Left(errors) =>
+        UnsuccessfulTermination(
+          errors.toList.mkString(System.lineSeparator, System.lineSeparator, System.lineSeparator)
+        )
     }
-  }
 
-  def womGraph(workflowSourcePath: Path): Termination = {
-    WomGraphMaker.fromFiles(mainFile = workflowSourcePath, inputs = None).contextualizeErrors("create wom Graph") match {
-      case Right(graphWithImports) => SuccessfulTermination (new WomGraph(graphName = "workflow", graphWithImports.graph).digraphDot)
-      case Left(errors) => UnsuccessfulTermination(errors.toList.mkString(System.lineSeparator, System.lineSeparator, System.lineSeparator))
+  def womGraph(workflowSourcePath: Path): Termination =
+    WomGraphMaker
+      .fromFiles(mainFile = workflowSourcePath, inputs = None)
+      .contextualizeErrors("create wom Graph") match {
+      case Right(graphWithImports) =>
+        SuccessfulTermination(new WomGraph(graphName = "workflow", graphWithImports.graph).digraphDot)
+      case Left(errors) =>
+        UnsuccessfulTermination(
+          errors.toList.mkString(System.lineSeparator, System.lineSeparator, System.lineSeparator)
+        )
     }
-  }
 
-  private[this] def loadWdl(path: String)(f: WdlNamespace => Termination): Termination = {
+  private[this] def loadWdl(path: String)(f: WdlNamespace => Termination): Termination =
     WdlNamespace.loadUsingPath(Paths.get(path), None, None) match {
       case Success(namespace) => f(namespace)
       case Failure(r: RuntimeException) => throw new RuntimeException("Unexpected failure mode", r)
       case Failure(t) => UnsuccessfulTermination(t.getMessage)
     }
-  }
-
 
   def runWomtool(cmdLineArgs: Seq[String]): Termination = {
-    val parsedArgs = WomtoolCommandLineParser.instance.parse(cmdLineArgs, PartialWomtoolCommandLineArguments()) flatMap WomtoolCommandLineParser.validateCommandLine
+    val parsedArgs = WomtoolCommandLineParser.instance.parse(cmdLineArgs,
+                                                             PartialWomtoolCommandLineArguments()
+    ) flatMap WomtoolCommandLineParser.validateCommandLine
 
     parsedArgs match {
       case Some(pa) => dispatchCommand(pa)
diff --git a/womtool/src/main/scala/womtool/cmdline/PartialWomtoolCommandLineArguments.scala b/womtool/src/main/scala/womtool/cmdline/PartialWomtoolCommandLineArguments.scala
index 5e516f7c3a5..af33485e173 100644
--- a/womtool/src/main/scala/womtool/cmdline/PartialWomtoolCommandLineArguments.scala
+++ b/womtool/src/main/scala/womtool/cmdline/PartialWomtoolCommandLineArguments.scala
@@ -8,15 +8,14 @@ final case class PartialWomtoolCommandLineArguments(command: Option[WomtoolComma
                                                     displayOptionalInputs: Option[Boolean] = None,
                                                     highlightMode: Option[HighlightMode] = None,
                                                     listDependencies: Option[Boolean] = None
-                                                   )
+)
 
 sealed trait ValidatedWomtoolCommandLine
 final case class ParseCommandLine(workflowSource: Path) extends ValidatedWomtoolCommandLine
-final case class ValidateCommandLine(workflowSource: Path,
-                                     inputs: Option[Path],
-                                     listDependencies: Boolean) extends ValidatedWomtoolCommandLine
-final case class HighlightCommandLine(workflowSource: Path,
-                                      highlightMode: HighlightMode) extends ValidatedWomtoolCommandLine
+final case class ValidateCommandLine(workflowSource: Path, inputs: Option[Path], listDependencies: Boolean)
+    extends ValidatedWomtoolCommandLine
+final case class HighlightCommandLine(workflowSource: Path, highlightMode: HighlightMode)
+    extends ValidatedWomtoolCommandLine
 final case class InputsCommandLine(workflowSource: Path, showOptionals: Boolean) extends ValidatedWomtoolCommandLine
 final case class OutputsCommandLine(workflowSource: Path) extends ValidatedWomtoolCommandLine
 final case class WomtoolGraphCommandLine(workflowSource: Path) extends ValidatedWomtoolCommandLine
@@ -43,4 +42,3 @@ object HighlightMode {
   case object ConsoleHighlighting extends HighlightMode
   final case class UnrecognizedHighlightingMode(string: String) extends HighlightMode
 }
-
diff --git a/womtool/src/main/scala/womtool/cmdline/WomtoolCommandLineParser.scala b/womtool/src/main/scala/womtool/cmdline/WomtoolCommandLineParser.scala
index 9bdc9ef11a1..8b5801d8a52 100644
--- a/womtool/src/main/scala/womtool/cmdline/WomtoolCommandLineParser.scala
+++ b/womtool/src/main/scala/womtool/cmdline/WomtoolCommandLineParser.scala
@@ -13,14 +13,22 @@ object WomtoolCommandLineParser {
   lazy val instance: scopt.OptionParser[PartialWomtoolCommandLineArguments] = new WomtoolCommandLineParser()
 
   def validateCommandLine(args: PartialWomtoolCommandLineArguments): Option[ValidatedWomtoolCommandLine] = args match {
-    case PartialWomtoolCommandLineArguments(Some(Validate), Some(mainFile), inputs, None, None, listDependencies) => Option(ValidateCommandLine(mainFile, inputs, listDependencies.getOrElse(false)))
-    case PartialWomtoolCommandLineArguments(Some(Inputs), Some(mainFile), None, showOptionals, None, None) => Option(InputsCommandLine(mainFile, !showOptionals.contains(false)))
-    case PartialWomtoolCommandLineArguments(Some(Outputs), Some(mainFile), None, None, None, None) => Option(OutputsCommandLine(mainFile))
-    case PartialWomtoolCommandLineArguments(Some(Parse), Some(mainFile), None, None, None, None) => Option(ParseCommandLine(mainFile))
-    case PartialWomtoolCommandLineArguments(Some(Highlight), Some(mainFile), None, None, Some(mode), None) => Option(HighlightCommandLine(mainFile, mode))
-    case PartialWomtoolCommandLineArguments(Some(Graph), Some(mainFile), None, None, None, None) => Option(WomtoolGraphCommandLine(mainFile))
-    case PartialWomtoolCommandLineArguments(Some(WomGraph), Some(mainFile), None, None, None, None) => Option(WomtoolWomGraphCommandLine(mainFile))
-    case PartialWomtoolCommandLineArguments(Some(Upgrade), Some(mainFile), None, None, None, None) => Option(WomtoolWdlUpgradeCommandLine(mainFile))
+    case PartialWomtoolCommandLineArguments(Some(Validate), Some(mainFile), inputs, None, None, listDependencies) =>
+      Option(ValidateCommandLine(mainFile, inputs, listDependencies.getOrElse(false)))
+    case PartialWomtoolCommandLineArguments(Some(Inputs), Some(mainFile), None, showOptionals, None, None) =>
+      Option(InputsCommandLine(mainFile, !showOptionals.contains(false)))
+    case PartialWomtoolCommandLineArguments(Some(Outputs), Some(mainFile), None, None, None, None) =>
+      Option(OutputsCommandLine(mainFile))
+    case PartialWomtoolCommandLineArguments(Some(Parse), Some(mainFile), None, None, None, None) =>
+      Option(ParseCommandLine(mainFile))
+    case PartialWomtoolCommandLineArguments(Some(Highlight), Some(mainFile), None, None, Some(mode), None) =>
+      Option(HighlightCommandLine(mainFile, mode))
+    case PartialWomtoolCommandLineArguments(Some(Graph), Some(mainFile), None, None, None, None) =>
+      Option(WomtoolGraphCommandLine(mainFile))
+    case PartialWomtoolCommandLineArguments(Some(WomGraph), Some(mainFile), None, None, None, None) =>
+      Option(WomtoolWomGraphCommandLine(mainFile))
+    case PartialWomtoolCommandLineArguments(Some(Upgrade), Some(mainFile), None, None, None, None) =>
+      Option(WomtoolWdlUpgradeCommandLine(mainFile))
     case _ => None
   }
 }
@@ -40,14 +48,18 @@ class WomtoolCommandLineParser extends scopt.OptionParser[PartialWomtoolCommandL
   opt[String]('h', "highlight-mode")
     .text("Highlighting mode, one of 'html', 'console' (used only with 'highlight' command)")
     .optional()
-    .action((s, c) => s match {
-      case "html" => c.copy(highlightMode = Option(HtmlHighlighting))
-      case "console" => c.copy(highlightMode = Option(ConsoleHighlighting))
-      case other => c.copy(highlightMode = Option(UnrecognizedHighlightingMode(other)))
-    })
-
-  opt[Boolean]('o', name="optional-inputs")
-    .text("If set, optional inputs are also included in the inputs set. Default is 'true' (used only with the inputs command)")
+    .action((s, c) =>
+      s match {
+        case "html" => c.copy(highlightMode = Option(HtmlHighlighting))
+        case "console" => c.copy(highlightMode = Option(ConsoleHighlighting))
+        case other => c.copy(highlightMode = Option(UnrecognizedHighlightingMode(other)))
+      }
+    )
+
+  opt[Boolean]('o', name = "optional-inputs")
+    .text(
+      "If set, optional inputs are also included in the inputs set. Default is 'true' (used only with the inputs command)"
+    )
     .optional()
     .action((b, c) => c.copy(displayOptionalInputs = Some(b)))
 
@@ -67,25 +79,29 @@ class WomtoolCommandLineParser extends scopt.OptionParser[PartialWomtoolCommandL
 
   cmd("validate")
     .action((_, c) => c.copy(command = Option(Validate)))
-    .text("Validate a workflow source file. If inputs are provided then 'validate' also checks that the inputs file is a valid set of inputs for the workflow." + System.lineSeparator)
+    .text(
+      "Validate a workflow source file. If inputs are provided then 'validate' also checks that the inputs file is a valid set of inputs for the workflow." + System.lineSeparator
+    )
 
   cmd("inputs")
-    .action((_, c) =>
-      c.copy(command = Option(Inputs)))
+    .action((_, c) => c.copy(command = Option(Inputs)))
     .text("Generate and output a new inputs JSON for this workflow." + System.lineSeparator)
 
   cmd("outputs")
-    .action((_, c) =>
-      c.copy(command = Option(Outputs)))
+    .action((_, c) => c.copy(command = Option(Outputs)))
     .text("Generate and output a list of output types in JSON for this workflow." + System.lineSeparator)
 
   cmd("parse")
     .action((_, c) => c.copy(command = Option(Parse)))
-    .text("(Deprecated; WDL draft 2 only) Print out the Hermes parser's abstract syntax tree for the source file." + System.lineSeparator)
+    .text(
+      "(Deprecated; WDL draft 2 only) Print out the Hermes parser's abstract syntax tree for the source file." + System.lineSeparator
+    )
 
   cmd("highlight")
     .action((_, c) => c.copy(command = Option(Highlight)))
-    .text("(Deprecated; WDL draft 2 only) Print out the Hermes parser's abstract syntax tree for the source file. Requires at least one of 'html' or 'console'" + System.lineSeparator)
+    .text(
+      "(Deprecated; WDL draft 2 only) Print out the Hermes parser's abstract syntax tree for the source file. Requires at least one of 'html' or 'console'" + System.lineSeparator
+    )
 
   cmd("graph")
     .action((_, c) => c.copy(command = Option(Graph)))
@@ -97,6 +113,8 @@ class WomtoolCommandLineParser extends scopt.OptionParser[PartialWomtoolCommandL
 
   cmd("womgraph")
     .action((_, c) => c.copy(command = Option(WomGraph)))
-    .text("(Advanced) Generate and output a graph visualization of Cromwell's internal Workflow Object Model structure for this workflow in .dot format" + System.lineSeparator)
+    .text(
+      "(Advanced) Generate and output a graph visualization of Cromwell's internal Workflow Object Model structure for this workflow in .dot format" + System.lineSeparator
+    )
 
 }
diff --git a/womtool/src/main/scala/womtool/graph/WomGraph.scala b/womtool/src/main/scala/womtool/graph/WomGraph.scala
index b1957a1545c..61c2ac0399b 100644
--- a/womtool/src/main/scala/womtool/graph/WomGraph.scala
+++ b/womtool/src/main/scala/womtool/graph/WomGraph.scala
@@ -29,13 +29,13 @@ import scala.jdk.CollectionConverters._
 class WomGraph(graphName: String, graph: Graph) {
 
   def indent(s: String) = s.linesIterator.map(x => s"  $x").mkString(System.lineSeparator)
-  def combine(ss: Iterable[String]) = ss.mkString(start="", sep=System.lineSeparator, end=System.lineSeparator)
+  def combine(ss: Iterable[String]) = ss.mkString(start = "", sep = System.lineSeparator, end = System.lineSeparator)
   def indentAndCombine(ss: Iterable[String]) = combine(ss.map(indent))
   implicit val monoid = cats.derived.MkMonoid[NodesAndLinks]
 
   val digraphDot: String = {
 
-    val workflowDigraph = WorkflowDigraph (dotSafe(graphName), listAllGraphNodes(graph))
+    val workflowDigraph = WorkflowDigraph(dotSafe(graphName), listAllGraphNodes(graph))
 
     s"""|digraph ${workflowDigraph.workflowName}
         |{
@@ -49,12 +49,12 @@ class WomGraph(graphName: String, graph: Graph) {
 
   private lazy val clusterCount: AtomicInteger = new AtomicInteger(0)
 
-  private[graph] def listAllGraphNodes(graph: Graph): NodesAndLinks = {
+  private[graph] def listAllGraphNodes(graph: Graph): NodesAndLinks =
     graph.nodes.toList foldMap nodesAndLinks
-  }
 
   private def upstreamLinks(graphNode: GraphNode): Set[String] = graphNode match {
-    case ogin: OuterGraphInputNode => Set(s"${ogin.linkToOuterGraph.graphId} -> ${ogin.singleOutputPort.graphId} [style=dashed arrowhead=none]")
+    case ogin: OuterGraphInputNode =>
+      Set(s"${ogin.linkToOuterGraph.graphId} -> ${ogin.singleOutputPort.graphId} [style=dashed arrowhead=none]")
     case _ =>
       for {
         inputPort <- graphNode.inputPorts
@@ -70,13 +70,13 @@ class WomGraph(graphName: String, graph: Graph) {
       // Don't include the scatter expression input port here since they're added later in `internalScatterNodesAndLinks`
       // Round up the gathered output ports so it's obvious they're being gathered.
       s"""
-        |${combine((s.inputPorts -- s.scatterCollectionExpressionNodes.flatMap(_.inputPorts)) map portLine)}
-        |subgraph $nextCluster {
-        |  style=${s.graphStyle};
-        |  fillcolor=${s.graphFillColor}
-        |  "${UUID.randomUUID}" [shape=plaintext label="gather ports"]
-        |${indentAndCombine(s.outputPorts map portLine)}
-        |}
+         |${combine((s.inputPorts -- s.scatterCollectionExpressionNodes.flatMap(_.inputPorts)) map portLine)}
+         |subgraph $nextCluster {
+         |  style=${s.graphStyle};
+         |  fillcolor=${s.graphFillColor}
+         |  "${UUID.randomUUID}" [shape=plaintext label="gather ports"]
+         |${indentAndCombine(s.outputPorts map portLine)}
+         |}
       """.stripMargin
     case _ => combine((graphNode.outputPorts ++ graphNode.inputPorts) map portLine)
   }
@@ -121,7 +121,9 @@ class WomGraph(graphName: String, graph: Graph) {
          |""".stripMargin
     }
 
-    val outputLinks = scatter.outputMapping map { outputPort => s"${outputPort.outputToGather.singleInputPort.graphId} -> ${outputPort.graphId} [style=dashed arrowhead=none]" }
+    val outputLinks = scatter.outputMapping map { outputPort =>
+      s"${outputPort.outputToGather.singleInputPort.graphId} -> ${outputPort.graphId} [style=dashed arrowhead=none]"
+    }
     innerGraph.withLinks(outputLinks)
   }
 
@@ -136,12 +138,13 @@ class WomGraph(graphName: String, graph: Graph) {
          |""".stripMargin
     }
 
-    val outputLinks = conditional.conditionalOutputPorts map { outputPort => s"${outputPort.outputToExpose.singleInputPort.graphId} -> ${outputPort.graphId} [style=dashed arrowhead=none]" }
+    val outputLinks = conditional.conditionalOutputPorts map { outputPort =>
+      s"${outputPort.outputToExpose.singleInputPort.graphId} -> ${outputPort.graphId} [style=dashed arrowhead=none]"
+    }
     innerGraph.withLinks(outputLinks)
   }
 
-  def internalSubworkflowNodesAndLinks(subworkflow: WorkflowCallNode): NodesAndLinks = {
-
+  def internalSubworkflowNodesAndLinks(subworkflow: WorkflowCallNode): NodesAndLinks =
     listAllGraphNodes(subworkflow.callable.innerGraph) wrapNodes { n =>
       s"""
          |subgraph $nextCluster {
@@ -151,7 +154,6 @@ class WomGraph(graphName: String, graph: Graph) {
          |}
          |""".stripMargin
     }
-  }
 
   private def nextCluster: String = "cluster_" + clusterCount.getAndIncrement()
 }
@@ -173,7 +175,8 @@ object WomGraph {
     new WomGraph("workflow", graph)
   }
 
-  private def readFile(filePath: String): String = Files.readAllLines(Paths.get(filePath)).asScala.mkString(System.lineSeparator())
+  private def readFile(filePath: String): String =
+    Files.readAllLines(Paths.get(filePath)).asScala.mkString(System.lineSeparator())
 
   private def womExecutableFromWdl(filePath: String): Graph = {
     val workflowFileString = readFile(filePath)
@@ -183,18 +186,34 @@ object WomGraph {
       firstLine.startsWith("version 1.0")
     }
     val womBundle: Checked[WomBundle] = if (version1) {
-      val converter: CheckedAtoB[File, WomBundle] = fileToAst andThen wrapAst andThen astToFileElement.map(FileElementToWomBundleInputs(_, "{}", convertNestedScatterToSubworkflow = true, List.empty, List.empty, workflowDefinitionElementToWomWorkflowDefinition, taskDefinitionElementToWomTaskDefinition)) andThen fileElementToWomBundle
+      val converter: CheckedAtoB[File, WomBundle] = fileToAst andThen wrapAst andThen astToFileElement.map(
+        FileElementToWomBundleInputs(
+          _,
+          "{}",
+          convertNestedScatterToSubworkflow = true,
+          List.empty,
+          List.empty,
+          workflowDefinitionElementToWomWorkflowDefinition,
+          taskDefinitionElementToWomTaskDefinition
+        )
+      ) andThen fileElementToWomBundle
       converter.run(File(filePath))
     } else {
 
-      WdlNamespaceWithWorkflow.load(readFile(filePath), Seq(WdlNamespace.fileResolver _)).toChecked.flatMap(_.toWomBundle)
+      WdlNamespaceWithWorkflow
+        .load(readFile(filePath), Seq(WdlNamespace.fileResolver _))
+        .toChecked
+        .flatMap(_.toWomBundle)
     }
 
     womBundle match {
-      case Right(wom) if (wom.allCallables.values.toSet.filterByType[WorkflowDefinition]: Set[WorkflowDefinition]).size == 1 => (wom.allCallables.values.toSet.filterByType[WorkflowDefinition]: Set[WorkflowDefinition]).head.graph
+      case Right(wom)
+          if (wom.allCallables.values.toSet.filterByType[WorkflowDefinition]: Set[WorkflowDefinition]).size == 1 =>
+        (wom.allCallables.values.toSet.filterByType[WorkflowDefinition]: Set[WorkflowDefinition]).head.graph
       case Right(_) => throw new Exception("Can only 'wom graph' a WDL with exactly one workflow")
       case Left(errors) =>
-        val formattedErrors = errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
+        val formattedErrors =
+          errors.toList.mkString(System.lineSeparator(), System.lineSeparator(), System.lineSeparator())
         throw new Exception(s"Failed to create WOM: $formattedErrors")
     }
   }
@@ -209,6 +228,7 @@ object WomGraph {
     case _: WomOptionalType => JsNull
     case WomMapType(_, valueType) => JsObject(Map("0" -> fakeInput(valueType)))
     case WomArrayType(innerType) => JsArray(Vector(fakeInput(innerType)))
-    case WomPairType(leftType, rightType) => JsObject(Map("left" -> fakeInput(leftType), "right" -> fakeInput(rightType)))
+    case WomPairType(leftType, rightType) =>
+      JsObject(Map("left" -> fakeInput(leftType), "right" -> fakeInput(rightType)))
   }
 }
diff --git a/womtool/src/main/scala/womtool/graph/package.scala b/womtool/src/main/scala/womtool/graph/package.scala
index e2ae058369c..c20a975e7f3 100644
--- a/womtool/src/main/scala/womtool/graph/package.scala
+++ b/womtool/src/main/scala/womtool/graph/package.scala
@@ -8,7 +8,7 @@ package object graph {
 
   private[graph] def dotSafe(s: String) = s""""${s.replace("\"", "\\\"")}""""
 
-  private[graph] implicit class GraphNodeGraphics(val graphNode: GraphNode) extends AnyVal {
+  implicit private[graph] class GraphNodeGraphics(val graphNode: GraphNode) extends AnyVal {
     def graphFillColor = graphNode match {
       case _: ConditionalNode | _: ScatterNode | _: WorkflowCallNode => "lightgray"
       case _: ExternalGraphInputNode => "lightskyblue1"
@@ -41,7 +41,7 @@ package object graph {
     def graphId: String = dotSafe("NODE" + graphObjectUniqueId(graphNode))
   }
 
-  private[graph] implicit class GraphNodePortGraphics(val graphNodePort: GraphNodePort) extends AnyVal {
+  implicit private[graph] class GraphNodePortGraphics(val graphNodePort: GraphNodePort) extends AnyVal {
     def graphShape = graphNodePort match {
       case _: InputPort => "oval"
       case _: OutputPort => "hexagon"
diff --git a/womtool/src/main/scala/womtool/input/WomGraphMaker.scala b/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
index bd3ef65e09b..65e8d5a522a 100644
--- a/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
+++ b/womtool/src/main/scala/womtool/input/WomGraphMaker.scala
@@ -32,7 +32,8 @@ object WomGraphMaker {
         List(
           new WdlDraft3LanguageFactory(ConfigFactory.empty()),
           new WdlBiscayneLanguageFactory(ConfigFactory.empty()),
-          new WdlCascadesLanguageFactory(ConfigFactory.empty()))
+          new WdlCascadesLanguageFactory(ConfigFactory.empty())
+        )
           .find(_.looksParsable(mainFileContents))
           .getOrElse(new WdlDraft2LanguageFactory(ConfigFactory.empty()))
 
@@ -42,7 +43,7 @@ object WomGraphMaker {
     }
   }
 
-  def fromFiles(mainFile: Path, inputs: Option[Path]): Checked[WomGraphWithResolvedImports] = {
+  def fromFiles(mainFile: Path, inputs: Option[Path]): Checked[WomGraphWithResolvedImports] =
     getBundleAndFactory(mainFile) flatMap { case (womBundle, languageFactory) =>
       inputs match {
         case None =>
@@ -56,11 +57,11 @@ object WomGraphMaker {
           } yield WomGraphWithResolvedImports(validatedWomNamespace.executable.graph, womBundle.resolvedImportRecords)
       }
     }
-  }
 
-  private def readFile(filePath: String): Checked[String] = Try(Files.readAllLines(Paths.get(filePath)).asScala.mkString(System.lineSeparator())).toChecked
+  private def readFile(filePath: String): Checked[String] = Try(
+    Files.readAllLines(Paths.get(filePath)).asScala.mkString(System.lineSeparator())
+  ).toChecked
 
 }
 
-
 case class WomGraphWithResolvedImports(graph: Graph, resolvedImportRecords: Set[ResolvedImportRecord])
diff --git a/womtool/src/main/scala/womtool/inputs/Inputs.scala b/womtool/src/main/scala/womtool/inputs/Inputs.scala
index a983cbd831b..36044358a1a 100644
--- a/womtool/src/main/scala/womtool/inputs/Inputs.scala
+++ b/womtool/src/main/scala/womtool/inputs/Inputs.scala
@@ -3,7 +3,12 @@ package womtool.inputs
 import cromwell.core.path.Path
 import womtool.WomtoolMain.{SuccessfulTermination, Termination, UnsuccessfulTermination}
 import womtool.input.WomGraphMaker
-import wom.graph.{ExternalGraphInputNode, OptionalGraphInputNode, OptionalGraphInputNodeWithDefault, RequiredGraphInputNode}
+import wom.graph.{
+  ExternalGraphInputNode,
+  OptionalGraphInputNode,
+  OptionalGraphInputNodeWithDefault,
+  RequiredGraphInputNode
+}
 import spray.json._
 import spray.json.DefaultJsonProtocol._
 import wom.expression.WomExpression
@@ -12,8 +17,7 @@ import wom.types.{WomCompositeType, WomOptionalType, WomType}
 import scala.util.{Failure, Success, Try}
 
 object Inputs {
-  def inputsJson(main: Path, showOptionals: Boolean): Termination = {
-
+  def inputsJson(main: Path, showOptionals: Boolean): Termination =
     WomGraphMaker.fromFiles(main, inputs = None) match {
       case Right(graphWithImports) =>
         Try(graphWithImports.graph.externalInputNodes.toJson(inputNodeWriter(showOptionals)).prettyPrint) match {
@@ -22,23 +26,25 @@ object Inputs {
         }
       case Left(errors) => UnsuccessfulTermination(errors.toList.mkString(System.lineSeparator))
     }
-  }
 
   private def inputNodeWriter(showOptionals: Boolean): JsonWriter[Set[ExternalGraphInputNode]] = set => {
 
     val valueMap: Seq[(String, JsValue)] = set.toList collect {
       case RequiredGraphInputNode(_, womType, nameInInputSet, _) => nameInInputSet -> womTypeToJson(womType, None)
-      case OptionalGraphInputNode(_, womOptionalType, nameInInputSet, _) if showOptionals => nameInInputSet -> womTypeToJson(womOptionalType, None)
-      case OptionalGraphInputNodeWithDefault(_, womType, default, nameInInputSet, _) if showOptionals => nameInInputSet -> womTypeToJson(womType, Option(default))
+      case OptionalGraphInputNode(_, womOptionalType, nameInInputSet, _) if showOptionals =>
+        nameInInputSet -> womTypeToJson(womOptionalType, None)
+      case OptionalGraphInputNodeWithDefault(_, womType, default, nameInInputSet, _) if showOptionals =>
+        nameInInputSet -> womTypeToJson(womType, Option(default))
     }
 
     valueMap.toMap.toJson
   }
 
   private def womTypeToJson(womType: WomType, default: Option[WomExpression]): JsValue = (womType, default) match {
-    case (WomCompositeType(typeMap, _), _) => JsObject(
-      typeMap.map { case (name, wt) => name -> womTypeToJson(wt, None) }
-    )
+    case (WomCompositeType(typeMap, _), _) =>
+      JsObject(
+        typeMap.map { case (name, wt) => name -> womTypeToJson(wt, None) }
+      )
     case (_, Some(d)) => JsString(s"${womType.stableName} (optional, default = ${d.sourceString})")
     case (_: WomOptionalType, _) => JsString(s"${womType.stableName} (optional)")
     case (_, _) => JsString(s"${womType.stableName}")
diff --git a/womtool/src/main/scala/womtool/outputs/Outputs.scala b/womtool/src/main/scala/womtool/outputs/Outputs.scala
index f08ebbc5d11..34ef4aa9e9d 100644
--- a/womtool/src/main/scala/womtool/outputs/Outputs.scala
+++ b/womtool/src/main/scala/womtool/outputs/Outputs.scala
@@ -11,8 +11,7 @@ import womtool.input.WomGraphMaker
 import scala.util.{Failure, Success, Try}
 
 object Outputs {
-  def outputsJson(main: Path): Termination = {
-
+  def outputsJson(main: Path): Termination =
     WomGraphMaker.fromFiles(main, inputs = None) match {
       case Right(graphWithImports) =>
         Try(graphWithImports.graph.outputNodes.asJson.printWith(sprayLikePrettyPrinter)) match {
@@ -21,20 +20,22 @@ object Outputs {
         }
       case Left(errors) => UnsuccessfulTermination(errors.toList.mkString(System.lineSeparator))
     }
-  }
 
-  private implicit val e: Encoder[Set[GraphOutputNode]] = (set: Set[GraphOutputNode]) => {
-    val valueMap = set.toList.map {
-      node: GraphOutputNode => node.fullyQualifiedName -> womTypeToJson(node.womType)
+  implicit private val e: Encoder[Set[GraphOutputNode]] = (set: Set[GraphOutputNode]) => {
+    val valueMap = set.toList.map { node: GraphOutputNode =>
+      node.fullyQualifiedName -> womTypeToJson(node.womType)
     }
 
     valueMap.toMap.asJson
   }
 
   private def womTypeToJson(womType: WomType): Json = womType match {
-    case WomCompositeType(typeMap, _) => JsonObject.fromMap(
-      typeMap.map { case (name, wt) => name -> womTypeToJson(wt) }
-    ).asJson
+    case WomCompositeType(typeMap, _) =>
+      JsonObject
+        .fromMap(
+          typeMap.map { case (name, wt) => name -> womTypeToJson(wt) }
+        )
+        .asJson
     case _ => womType.stableName.asJson
   }
 
diff --git a/womtool/src/main/scala/womtool/validate/Validate.scala b/womtool/src/main/scala/womtool/validate/Validate.scala
index 79861cae527..b6dd288f396 100644
--- a/womtool/src/main/scala/womtool/validate/Validate.scala
+++ b/womtool/src/main/scala/womtool/validate/Validate.scala
@@ -11,7 +11,8 @@ object Validate {
 
     def workflowDependenciesMsg(workflowResolvedImports: Set[ResolvedImportRecord]) = {
       val msgPrefix = "\nList of Workflow dependencies is:\n"
-      val dependenciesList = if (workflowResolvedImports.nonEmpty) workflowResolvedImports.map(_.importPath).mkString("\n") else "None"
+      val dependenciesList =
+        if (workflowResolvedImports.nonEmpty) workflowResolvedImports.map(_.importPath).mkString("\n") else "None"
 
       msgPrefix + dependenciesList
     }
diff --git a/womtool/src/main/scala/womtool/wom2wdlom/WomToWdlom.scala b/womtool/src/main/scala/womtool/wom2wdlom/WomToWdlom.scala
index 6d7e499e2cd..07382a3ceef 100644
--- a/womtool/src/main/scala/womtool/wom2wdlom/WomToWdlom.scala
+++ b/womtool/src/main/scala/womtool/wom2wdlom/WomToWdlom.scala
@@ -30,19 +30,15 @@ object WomToWdlom {
     s"Value \'$text\' has no representation in the destination format (WDL)".invalidNelCheck
 
   def graphOutputNodeToWorkflowGraphElement: CheckedAtoB[GraphOutputNode, WorkflowGraphElement] =
-    CheckedAtoB.fromCheck { a: GraphOutputNode => a match {
-      case a: ExpressionBasedGraphOutputNode =>
-        for {
-          typeElement <- womTypeToTypeElement(a.womType)
-          expression <- womExpressionToExpressionElement(a.womExpression)
-        } yield {
-          OutputDeclarationElement(
-            typeElement,
-            a.identifier.localName.value,
-            expression)
-        }
-      case _ =>
-        invalidFromString(a.toString)
+    CheckedAtoB.fromCheck { a: GraphOutputNode =>
+      a match {
+        case a: ExpressionBasedGraphOutputNode =>
+          for {
+            typeElement <- womTypeToTypeElement(a.womType)
+            expression <- womExpressionToExpressionElement(a.womExpression)
+          } yield OutputDeclarationElement(typeElement, a.identifier.localName.value, expression)
+        case _ =>
+          invalidFromString(a.toString)
       }
     }
 
@@ -52,16 +48,20 @@ object WomToWdlom {
       val workflows: Iterable[WorkflowDefinition] = a.allCallables.values.filterByType[WorkflowDefinition]
 
       for {
-        workflows <- workflows.map(workflowDefinitionToWorkflowDefinitionElement(_)).toList.sequence[Checked, WorkflowDefinitionElement]
-        tasks <- tasks.map(callableTaskDefinitionToTaskDefinitionElement(_)).toList.sequence[Checked, TaskDefinitionElement]
-      } yield {
-        FileElement(
-          Seq.empty, // Imports do not exist in WOM and cannot sensibly be added at this point
-          Seq.empty, // Structs do not exist in draft-2
-          workflows,
-          tasks
-        )
-      }
+        workflows <- workflows
+          .map(workflowDefinitionToWorkflowDefinitionElement(_))
+          .toList
+          .sequence[Checked, WorkflowDefinitionElement]
+        tasks <- tasks
+          .map(callableTaskDefinitionToTaskDefinitionElement(_))
+          .toList
+          .sequence[Checked, TaskDefinitionElement]
+      } yield FileElement(
+        Seq.empty, // Imports do not exist in WOM and cannot sensibly be added at this point
+        Seq.empty, // Structs do not exist in draft-2
+        workflows,
+        tasks
+      )
     }
 
   def mapToMetaSectionElement: CheckedAtoB[Map[String, MetaValueElement], Option[MetaSectionElement]] =
@@ -72,7 +72,8 @@ object WomToWdlom {
         None.validNelCheck
     }
 
-  def mapToParameterMetaSectionElement: CheckedAtoB[Map[String, MetaValueElement], Option[ParameterMetaSectionElement]] =
+  def mapToParameterMetaSectionElement
+    : CheckedAtoB[Map[String, MetaValueElement], Option[ParameterMetaSectionElement]] =
     CheckedAtoB.fromCheck { a: Map[String, MetaValueElement] =>
       if (a.nonEmpty)
         Some(ParameterMetaSectionElement(a)).validNelCheck
@@ -80,24 +81,21 @@ object WomToWdlom {
         None.validNelCheck
     }
 
-  def runtimeAttributesToRuntimeAttributesSectionElement: CheckedAtoB[RuntimeAttributes, Option[RuntimeAttributesSectionElement]] =
+  def runtimeAttributesToRuntimeAttributesSectionElement
+    : CheckedAtoB[RuntimeAttributes, Option[RuntimeAttributesSectionElement]] =
     CheckedAtoB.fromCheck { a: RuntimeAttributes =>
-      def tupleToKvPair(tuple: (String, WomExpression)): Checked[ExpressionElement.KvPair] = {
+      def tupleToKvPair(tuple: (String, WomExpression)): Checked[ExpressionElement.KvPair] =
         for {
           expressionElement <- womExpressionToExpressionElement(tuple._2)
-        } yield {
-          ExpressionElement.KvPair(tuple._1, expressionElement)
-        }
-      }
+        } yield ExpressionElement.KvPair(tuple._1, expressionElement)
 
       for {
         kvPairs <- (a.attributes map tupleToKvPair).toList.sequence[Checked, ExpressionElement.KvPair]
-      } yield {
+      } yield
         if (kvPairs.nonEmpty)
           Some(RuntimeAttributesSectionElement(kvPairs.toVector))
         else
           None
-      }
     }
 
   def outputDefinitionToOutputDeclarationElement: CheckedAtoB[OutputDefinition, OutputDeclarationElement] =
@@ -105,9 +103,7 @@ object WomToWdlom {
       for {
         typeElement <- womTypeToTypeElement(a.womType)
         expression <- womExpressionToExpressionElement(a.expression)
-      } yield {
-        OutputDeclarationElement(typeElement, a.name, expression)
-      }
+      } yield OutputDeclarationElement(typeElement, a.name, expression)
     }
 
   def inputDefinitionToInputDeclarationElement: CheckedAtoB[InputDefinition, InputDeclarationElement] =
@@ -131,76 +127,83 @@ object WomToWdlom {
     }
 
   def callableTaskDefinitionToTaskDefinitionElement: CheckedAtoB[CallableTaskDefinition, TaskDefinitionElement] =
-    CheckedAtoB.fromCheck {
-      a: CallableTaskDefinition =>
-        val inputs: Checked[List[InputDeclarationElement]] =
-          a.inputs.map(inputDefinitionToInputDeclarationElement(_)).sequence[Checked, InputDeclarationElement]
-        val outputs: Checked[List[OutputDeclarationElement]] =
-          a.outputs.map(outputDefinitionToOutputDeclarationElement(_)).sequence[Checked, OutputDeclarationElement]
+    CheckedAtoB.fromCheck { a: CallableTaskDefinition =>
+      val inputs: Checked[List[InputDeclarationElement]] =
+        a.inputs.map(inputDefinitionToInputDeclarationElement(_)).sequence[Checked, InputDeclarationElement]
+      val outputs: Checked[List[OutputDeclarationElement]] =
+        a.outputs.map(outputDefinitionToOutputDeclarationElement(_)).sequence[Checked, OutputDeclarationElement]
 
-        for {
-          runtime <- runtimeAttributesToRuntimeAttributesSectionElement(a.runtimeAttributes)
-          meta <- mapToMetaSectionElement(a.meta)
-          parameterMeta <- mapToParameterMetaSectionElement(a.parameterMeta)
-          inputs <- inputs
-          outputs <- outputs
-          commands <- a.commandTemplateBuilder(Map()).toEither
-        } yield {
-          val commandLine = CommandSectionLine(commands map {
-            case s: StringCommandPart =>
-              StringCommandPartElement(s.literal)
-            case p: ParameterCommandPart =>
-              val attrs = PlaceholderAttributeSet(
-                defaultAttribute = p.attributes.get("default"),
-                trueAttribute = p.attributes.get("true"),
-                falseAttribute = p.attributes.get("false"),
-                sepAttribute = p.attributes.get("sep")
-              )
-
-              PlaceholderCommandPartElement(ExpressionLiteralElement(p.expression.toWomString), attrs)
-          })
-
-          TaskDefinitionElement(
-            a.name,
-            if (inputs.nonEmpty) Some(InputsSectionElement(inputs)) else None,
-            Seq.empty, // No such thing in draft-2
-            if (outputs.nonEmpty) Some(OutputsSectionElement(outputs)) else None,
-            CommandSectionElement(Seq(commandLine)),
-            runtime,
-            meta,
-            parameterMeta,
-            a.sourceLocation
-          )
-        }
+      for {
+        runtime <- runtimeAttributesToRuntimeAttributesSectionElement(a.runtimeAttributes)
+        meta <- mapToMetaSectionElement(a.meta)
+        parameterMeta <- mapToParameterMetaSectionElement(a.parameterMeta)
+        inputs <- inputs
+        outputs <- outputs
+        commands <- a.commandTemplateBuilder(Map()).toEither
+      } yield {
+        val commandLine = CommandSectionLine(commands map {
+          case s: StringCommandPart =>
+            StringCommandPartElement(s.literal)
+          case p: ParameterCommandPart =>
+            val attrs = PlaceholderAttributeSet(
+              defaultAttribute = p.attributes.get("default"),
+              trueAttribute = p.attributes.get("true"),
+              falseAttribute = p.attributes.get("false"),
+              sepAttribute = p.attributes.get("sep")
+            )
+
+            PlaceholderCommandPartElement(ExpressionLiteralElement(p.expression.toWomString), attrs)
+        })
+
+        TaskDefinitionElement(
+          a.name,
+          if (inputs.nonEmpty) Some(InputsSectionElement(inputs)) else None,
+          Seq.empty, // No such thing in draft-2
+          if (outputs.nonEmpty) Some(OutputsSectionElement(outputs)) else None,
+          CommandSectionElement(Seq(commandLine)),
+          runtime,
+          meta,
+          parameterMeta,
+          a.sourceLocation
+        )
       }
+    }
 
   def workflowDefinitionToWorkflowDefinitionElement: CheckedAtoB[WorkflowDefinition, WorkflowDefinitionElement] =
     CheckedAtoB.fromCheck { a: WorkflowDefinition =>
-        // This is a bit odd, so let's explain. "Real" inputs/outputs that are specified by the WDL's author
-        // cannot have periods in them - period. So any input/output that has a period in it
-        // is an artifact of WOMification and should be dropped
-        val inputs =
-          a.inputs.filter(!_.localName.value.contains(".")).map(inputDefinitionToInputDeclarationElement(_)).sequence[Checked, InputDeclarationElement]
-        val outputs =
-          a.outputs.filter(!_.localName.value.contains(".")).map(outputDefinitionToOutputDeclarationElement(_)).sequence[Checked, OutputDeclarationElement]
+      // This is a bit odd, so let's explain. "Real" inputs/outputs that are specified by the WDL's author
+      // cannot have periods in them - period. So any input/output that has a period in it
+      // is an artifact of WOMification and should be dropped
+      val inputs =
+        a.inputs
+          .filter(!_.localName.value.contains("."))
+          .map(inputDefinitionToInputDeclarationElement(_))
+          .sequence[Checked, InputDeclarationElement]
+      val outputs =
+        a.outputs
+          .filter(!_.localName.value.contains("."))
+          .map(outputDefinitionToOutputDeclarationElement(_))
+          .sequence[Checked, OutputDeclarationElement]
 
-        for {
-          meta <- mapToMetaSectionElement(a.meta)
-          parameterMeta <- mapToParameterMetaSectionElement(a.parameterMeta)
-          inputs <- inputs
-          outputs <- outputs
-          nodes <- selectWdlomRepresentableNodes(a.graph.nodes).map(graphNodeToWorkflowGraphElement(_)).toList.sequence[Checked, WorkflowGraphElement]
-        } yield {
-          WorkflowDefinitionElement(
-            a.name,
-            if (inputs.nonEmpty) Some(InputsSectionElement(inputs)) else None,
-            nodes.toSet,
-            if (outputs.nonEmpty) Some(OutputsSectionElement(outputs)) else None,
-            meta,
-            parameterMeta,
-            a.sourceLocation)
-        }
-      }
+      for {
+        meta <- mapToMetaSectionElement(a.meta)
+        parameterMeta <- mapToParameterMetaSectionElement(a.parameterMeta)
+        inputs <- inputs
+        outputs <- outputs
+        nodes <- selectWdlomRepresentableNodes(a.graph.nodes)
+          .map(graphNodeToWorkflowGraphElement(_))
+          .toList
+          .sequence[Checked, WorkflowGraphElement]
+      } yield WorkflowDefinitionElement(
+        a.name,
+        if (inputs.nonEmpty) Some(InputsSectionElement(inputs)) else None,
+        nodes.toSet,
+        if (outputs.nonEmpty) Some(OutputsSectionElement(outputs)) else None,
+        meta,
+        parameterMeta,
+        a.sourceLocation
+      )
+    }
 
   def expressionNodeLikeToWorkflowGraphElement: CheckedAtoB[ExpressionNodeLike, WorkflowGraphElement] =
     CheckedAtoB.fromCheck {
@@ -208,12 +211,10 @@ object WomToWdlom {
         for {
           typeElement <- womTypeToTypeElement(a.womType)
           expression <- expressionNodeToExpressionElement(a)
-        } yield {
-          IntermediateValueDeclarationElement(
-            typeElement = typeElement,
-            name = a.identifier.localName.value,
-            expression = expression)
-        }
+        } yield IntermediateValueDeclarationElement(typeElement = typeElement,
+                                                    name = a.identifier.localName.value,
+                                                    expression = expression
+        )
       case a: ExpressionCallNode => invalidFromString(a.toString)
     }
 
@@ -236,13 +237,13 @@ object WomToWdlom {
       case a: ConditionalNode =>
         for {
           condition <- expressionNodeToExpressionElement(a.conditionExpression)
-          nodes <- selectWdlomRepresentableNodes(a.innerGraph.nodes).toList.map(graphNodeToWorkflowGraphElement(_)).sequence[Checked, WorkflowGraphElement]
-        } yield {
-          IfElement(
-            conditionExpression = condition,
-            graphElements = nodes
-          )
-        }
+          nodes <- selectWdlomRepresentableNodes(a.innerGraph.nodes).toList
+            .map(graphNodeToWorkflowGraphElement(_))
+            .sequence[Checked, WorkflowGraphElement]
+        } yield IfElement(
+          conditionExpression = condition,
+          graphElements = nodes
+        )
       case a: ExpressionNodeLike =>
         expressionNodeLikeToWorkflowGraphElement(a)
       case a: GraphNodeWithSingleOutputPort =>
@@ -256,37 +257,30 @@ object WomToWdlom {
         else
           for {
             expression <- expressionNodeToExpressionElement(a.scatterCollectionExpressionNodes.head)
-            graph <- selectWdlomRepresentableNodes(a.innerGraph.nodes).toList.map(graphNodeToWorkflowGraphElement(_)).sequence[Checked, WorkflowGraphElement]
-          } yield {
-            ScatterElement(
-              scatterName = a.identifier.localName.value,
-              scatterExpression = expression,
-              scatterVariableName = a.inputPorts.toList.head.name,
-              graphElements = graph,
-              sourceLocation = None
-            )
-          }
-      }
+            graph <- selectWdlomRepresentableNodes(a.innerGraph.nodes).toList
+              .map(graphNodeToWorkflowGraphElement(_))
+              .sequence[Checked, WorkflowGraphElement]
+          } yield ScatterElement(
+            scatterName = a.identifier.localName.value,
+            scatterExpression = expression,
+            scatterVariableName = a.inputPorts.toList.head.name,
+            graphElements = graph,
+            sourceLocation = None
+          )
+    }
 
-  def graphNodeWithSingleOutputPortToWorkflowGraphElement: CheckedAtoB[GraphNodeWithSingleOutputPort, WorkflowGraphElement] =
+  def graphNodeWithSingleOutputPortToWorkflowGraphElement
+    : CheckedAtoB[GraphNodeWithSingleOutputPort, WorkflowGraphElement] =
     CheckedAtoB.fromCheck {
       case a: GraphInputNode =>
         womTypeToTypeElement(a.womType) map { typeElement =>
-          InputDeclarationElement(
-            typeElement,
-            a.identifier.localName.value,
-            None)
+          InputDeclarationElement(typeElement, a.identifier.localName.value, None)
         }
       case a: ExpressionNode =>
         for {
           typeElement <- womTypeToTypeElement(a.womType)
           expression <- womExpressionToExpressionElement(a.womExpression)
-        } yield {
-          IntermediateValueDeclarationElement(
-            typeElement,
-            a.identifier.localName.value,
-            expression)
-        }
+        } yield IntermediateValueDeclarationElement(typeElement, a.identifier.localName.value, expression)
     }
 
   def womTypeToTypeElement: CheckedAtoB[WomType, TypeElement] =
@@ -304,9 +298,7 @@ object WomToWdlom {
         for {
           keyType <- womTypeToTypeElement(a.keyType)
           valueType <- womTypeToTypeElement(a.valueType)
-        } yield {
-          MapTypeElement(keyType, valueType)
-        }
+        } yield MapTypeElement(keyType, valueType)
       case _: WomNothingType.type => invalidFromString("WDL does not have the Nothing type - is this WOM from CWL?")
       case _: WomObjectType.type => ObjectTypeElement.validNelCheck
       case a: WomOptionalType => womOptionalTypeToOptionalTypeElement(a)
@@ -314,9 +306,7 @@ object WomToWdlom {
         for {
           leftType <- womTypeToTypeElement(a.leftType)
           rightType <- womTypeToTypeElement(a.rightType)
-        } yield {
-          PairTypeElement(leftType, rightType)
-        }
+        } yield PairTypeElement(leftType, rightType)
       case a: WomPrimitiveType => womPrimitiveTypeToPrimitiveTypeElement(a)
     }
 
@@ -333,8 +323,8 @@ object WomToWdlom {
     }
 
   def expressionNodeToExpressionElement: CheckedAtoB[ExpressionNode, ExpressionElement] =
-    CheckedAtoB.fromCheck {
-      a: ExpressionNode => womExpressionToExpressionElement(a.womExpression)
+    CheckedAtoB.fromCheck { a: ExpressionNode =>
+      womExpressionToExpressionElement(a.womExpression)
     }
 
   def womExpressionToExpressionElement: CheckedAtoB[WomExpression, ExpressionElement] =
@@ -346,21 +336,22 @@ object WomToWdlom {
   def inputDefinitionPointerToExpressionElement: CheckedAtoB[InputDefinitionPointer, Option[ExpressionElement]] =
     CheckedAtoB.fromCheck {
       // If the input definition is a node containing an expression, it's been declared explicitly
-      case Inl(a: GraphNodeOutputPort) => a.graphNode match {
-        case _: OptionalGraphInputNode =>
-          None.validNelCheck
-        case _: OptionalGraphInputNodeWithDefault =>
-          None.validNelCheck
-        case a: PlainAnonymousExpressionNode =>
-          womExpressionToExpressionElement(a.womExpression) map { expressionElement =>
-            Some(expressionElement)
-          }
-        case a: TaskCallInputExpressionNode =>
-          womExpressionToExpressionElement(a.womExpression) map { expressionElement =>
-            Some(expressionElement)
-          }
-        case _: RequiredGraphInputNode => None.validNelCheck
-      }
+      case Inl(a: GraphNodeOutputPort) =>
+        a.graphNode match {
+          case _: OptionalGraphInputNode =>
+            None.validNelCheck
+          case _: OptionalGraphInputNodeWithDefault =>
+            None.validNelCheck
+          case a: PlainAnonymousExpressionNode =>
+            womExpressionToExpressionElement(a.womExpression) map { expressionElement =>
+              Some(expressionElement)
+            }
+          case a: TaskCallInputExpressionNode =>
+            womExpressionToExpressionElement(a.womExpression) map { expressionElement =>
+              Some(expressionElement)
+            }
+          case _: RequiredGraphInputNode => None.validNelCheck
+        }
       // Input definitions that directly contain expressions are the result of accepting a default input defined by the callable
       case Inr(Inl(_: WomExpression)) => None.validNelCheck
       case Inr(a) =>
@@ -371,22 +362,22 @@ object WomToWdlom {
 
   def callNodeToCallElement: CheckedAtoB[CallNode, CallElement] =
     CheckedAtoB.fromCheck { call: CallNode =>
-      def tupleToKvPair(tuple: (InputDefinition, InputDefinitionPointer)): Option[ExpressionElement.KvPair] = {
+      def tupleToKvPair(tuple: (InputDefinition, InputDefinitionPointer)): Option[ExpressionElement.KvPair] =
         inputDefinitionPointerToExpressionElement(tuple._2) match {
           case Right(Some(value)) => Some(ExpressionElement.KvPair(tuple._1.name, value))
           case _ => None
         }
-      }
 
       val inputs = (call.inputDefinitionMappings flatMap tupleToKvPair).toVector
 
       val callableName = call.callable.name
       val callAlias = call.identifier.localName.value // If no alias, this is just the name; we evaluate for that below
 
-      val maybeAlias = if (callableName != callAlias)
-        Some(callAlias)
-      else
-        None
+      val maybeAlias =
+        if (callableName != callAlias)
+          Some(callAlias)
+        else
+          None
 
       val afters = call.nonInputBasedPrerequisites.map(_.localName).toVector
 
diff --git a/womtool/src/test/scala/womtool/SampleWdl.scala b/womtool/src/test/scala/womtool/SampleWdl.scala
index 54df7953651..a3b00d9bee0 100644
--- a/womtool/src/test/scala/womtool/SampleWdl.scala
+++ b/womtool/src/test/scala/womtool/SampleWdl.scala
@@ -20,8 +20,8 @@ trait SampleWdl {
     def write(x: Any) = x match {
       case n: Int => JsNumber(n)
       case s: String => JsString(s)
-      case b: Boolean => if(b) JsTrue else JsFalse
-      case s: Seq[Any] => JsArray(s map {_.toJson} toVector)
+      case b: Boolean => if (b) JsTrue else JsFalse
+      case s: Seq[Any] => JsArray(s map { _.toJson } toVector)
       case a: WomArray => write(a.value)
       case s: WomString => JsString(s.value)
       case i: WomInteger => JsNumber(i.value)
diff --git a/womtool/src/test/scala/womtool/WomtoolJsonCommandSpec.scala b/womtool/src/test/scala/womtool/WomtoolJsonCommandSpec.scala
index be11acb7ec5..2fe95118094 100644
--- a/womtool/src/test/scala/womtool/WomtoolJsonCommandSpec.scala
+++ b/womtool/src/test/scala/womtool/WomtoolJsonCommandSpec.scala
@@ -41,10 +41,10 @@ abstract class WomtoolJsonCommandSpec extends AnyFlatSpec with CromwellTimeoutSp
         val caseName = validCase.name
 
         // The WDL file is expected to be valid:
-        val wdlFile = mustExist(versionDirectory.path.resolve(s"../../validate/$versionName/valid/$caseName/$caseName.wdl").toFile)
+        val wdlFile =
+          mustExist(versionDirectory.path.resolve(s"../../validate/$versionName/valid/$caseName/$caseName.wdl").toFile)
 
         testDefinitions foreach { definition =>
-
           it should s"validate '${definition.testName}' for $versionName workflow: '$caseName''" in {
             val expectation = expectedJson(versionDirectory, caseName, definition.expectationFilename)
             val fullCommandFormat = definition.commandFormat :+ wdlFile.getAbsolutePath
@@ -57,7 +57,12 @@ abstract class WomtoolJsonCommandSpec extends AnyFlatSpec with CromwellTimeoutSp
                 val unexpected = actualSet.diff(expectedSet)
                 val ungenerated = expectedSet.diff(actualSet)
 
-                assert(actualSet == expectedSet, s"Received lines: $actualContent${System.lineSeparator}with unexpected values: ${unexpected.mkString("[", ",", "]")}${System.lineSeparator}and missing expected values: ${ungenerated.mkString("[", ",", "]")}")
+                assert(
+                  actualSet == expectedSet,
+                  s"Received lines: $actualContent${System.lineSeparator}with unexpected values: ${unexpected
+                      .mkString("[", ",", "]")}${System.lineSeparator}and missing expected values: ${ungenerated
+                      .mkString("[", ",", "]")}"
+                )
 
               case other => fail(s"Expected successful termination but got $other")
             }
@@ -67,9 +72,9 @@ abstract class WomtoolJsonCommandSpec extends AnyFlatSpec with CromwellTimeoutSp
     }
   }
 
-  private def expectedJson(versionDirectory: File, caseName: String, jsonName: String): String = {
+  private def expectedJson(versionDirectory: File, caseName: String, jsonName: String): String =
     File(mustExist(versionDirectory.path.resolve(caseName).resolve(jsonName).toFile).getAbsolutePath).contentAsString
-  }
 
-  private def mustExist(file: java.io.File): java.io.File = if (file.exists) file else fail(s"No such file: ${file.getAbsolutePath}")
+  private def mustExist(file: java.io.File): java.io.File =
+    if (file.exists) file else fail(s"No such file: ${file.getAbsolutePath}")
 }
diff --git a/womtool/src/test/scala/womtool/WomtoolMainSpec.scala b/womtool/src/test/scala/womtool/WomtoolMainSpec.scala
index 048c9408cb8..1a71db15cf3 100644
--- a/womtool/src/test/scala/womtool/WomtoolMainSpec.scala
+++ b/womtool/src/test/scala/womtool/WomtoolMainSpec.scala
@@ -8,7 +8,6 @@ import org.scalatest.matchers.should.Matchers
 import womtool.SampleWdl.{EmptyTask, EmptyWorkflow, ThreeStep}
 import womtool.WomtoolMainSpec._
 
-
 class WomtoolMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with BeforeAndAfterAll {
 
   import WomtoolMain._
@@ -18,8 +17,11 @@ class WomtoolMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   val threeStep = ThreeStep.wdlSource()
 
   it should "print usage" in {
-    WomtoolMain.runWomtool(Seq.empty[String]) match{
-      case BadUsageTermination(msg) => msg should include("Usage: java -jar womtool.jar [validate|inputs|outputs|parse|highlight|graph|upgrade|womgraph] [options] workflow-source")
+    WomtoolMain.runWomtool(Seq.empty[String]) match {
+      case BadUsageTermination(msg) =>
+        msg should include(
+          "Usage: java -jar womtool.jar [validate|inputs|outputs|parse|highlight|graph|upgrade|womgraph] [options] workflow-source"
+        )
       case other => fail(s"Expected BadUsageTermination but got $other")
     }
   }
@@ -59,12 +61,15 @@ class WomtoolMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   it should "not return inputs when there is no workflow" in {
     testWdl(EmptyTask) { wdlAndInputs =>
       val res = WomtoolMain.runWomtool(Seq("inputs", wdlAndInputs.wdl))
-      res should be(UnsuccessfulTermination("Cannot convert WOM bundle to executable. No primary callable was available."))
+      res should be(
+        UnsuccessfulTermination("Cannot convert WOM bundle to executable. No primary callable was available.")
+      )
     }
   }
 }
 
 object WomtoolMainSpec {
+
   /**
     * Tests running a sample wdl, providing the inputs, and cleaning up the temp files only if no exceptions occur.
     *
@@ -168,7 +173,6 @@ object WomtoolMainSpec {
     def deleteTempFiles() = tempFiles.foreach(_.delete(swallowIOExceptions = true))
   }
 
-  def swapExt(filePath: File, oldExt: String, newExt: String): File = {
+  def swapExt(filePath: File, oldExt: String, newExt: String): File =
     File(filePath.toString.stripSuffix(oldExt) + newExt)
-  }
 }
diff --git a/womtool/src/test/scala/womtool/WomtoolValidateSpec.scala b/womtool/src/test/scala/womtool/WomtoolValidateSpec.scala
index d0a68a57640..06c482544ce 100644
--- a/womtool/src/test/scala/womtool/WomtoolValidateSpec.scala
+++ b/womtool/src/test/scala/womtool/WomtoolValidateSpec.scala
@@ -12,7 +12,6 @@ import womtool.WomtoolMain.{SuccessfulTermination, UnsuccessfulTermination}
 import scala.jdk.CollectionConverters._
 import scala.collection.immutable
 
-
 class WomtoolValidateSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   private val presentWorkingDirectoryName = DefaultPathBuilder.get(".").toAbsolutePath.name
@@ -39,7 +38,8 @@ class WomtoolValidateSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     List(validTestCases, invalidTestCases) foreach { path =>
       it should s"be set up for testing $versionName in '${versionDirectory.relativize(path).toString}'" in {
         if (!path.toFile.exists) fail(s"Path doesn't exist: ${path.toAbsolutePath.toString}")
-        if (Option(path.toFile.list).toList.flatten.isEmpty) fail(s"No test cases found in: ${path.toAbsolutePath.toString}")
+        if (Option(path.toFile.list).toList.flatten.isEmpty)
+          fail(s"No test cases found in: ${path.toAbsolutePath.toString}")
         versionDirectory.list.nonEmpty shouldBe true
       }
     }
@@ -59,7 +59,9 @@ class WomtoolValidateSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
       }
 
       it should s"successfully validate $versionName workflow: '$validCase'$withInputsAddition" in {
-        WomtoolMain.runWomtool(Seq("validate", wdl.getAbsolutePath) ++ inputsArgs) should be(SuccessfulTermination("Success!"))
+        WomtoolMain.runWomtool(Seq("validate", wdl.getAbsolutePath) ++ inputsArgs) should be(
+          SuccessfulTermination("Success!")
+        )
       }
 
       if (!knownUngraphableTests.contains(validCase)) {
@@ -70,21 +72,26 @@ class WomtoolValidateSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
 
           WomtoolMain.runWomtool(Seq("graph", wdl.getAbsolutePath)) match {
             case SuccessfulTermination(womtoolGraph) =>
-
               // Check that every call in the WDL is represented in the 'womtool graph' output, and vice versa:
-              val callsInWdl = Files.readAllLines(wdl.toPath).asScala.collect {
-                case WdlCallRegex(taskName, null, null, null, null) => taskName
-                case WdlCallRegex(_, _, taskName, null, null) =>
-                  taskName
-                case WdlCallRegex(_, _, _, _, callAlias) => callAlias
-              }.toSet
+              val callsInWdl = Files
+                .readAllLines(wdl.toPath)
+                .asScala
+                .collect {
+                  case WdlCallRegex(taskName, null, null, null, null) => taskName
+                  case WdlCallRegex(_, _, taskName, null, null) =>
+                    taskName
+                  case WdlCallRegex(_, _, _, _, callAlias) => callAlias
+                }
+                .toSet
 
-              val callsInWomtoolGraph = womtoolGraph.linesIterator.collect {
-                case WomtoolGraphCallRegex(call) => call
+              val callsInWomtoolGraph = womtoolGraph.linesIterator.collect { case WomtoolGraphCallRegex(call) =>
+                call
               }.toSet
 
               if (!callsInWomtoolGraph.exists(_.startsWith("ScatterAt"))) {
-                withClue(s"In WDL not in Graph: ${callsInWdl -- callsInWomtoolGraph}; In Graph not in WDL: ${callsInWomtoolGraph -- callsInWdl}") {
+                withClue(
+                  s"In WDL not in Graph: ${callsInWdl -- callsInWomtoolGraph}; In Graph not in WDL: ${callsInWomtoolGraph -- callsInWdl}"
+                ) {
                   callsInWdl should be(callsInWomtoolGraph)
                 }
               }
@@ -100,7 +107,9 @@ class WomtoolValidateSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
 
       it should s"fail to validate $versionName workflow: '$invalidCase'$withInputsAddition" in {
         val wdl = mustExist(invalidTestCases.resolve(invalidCase).resolve(invalidCase + ".wdl").toFile)
-        val errorFile = ifExists(invalidTestCases.resolve(invalidCase).resolve("error.txt").toFile).map(f => File(f.getAbsolutePath).contentAsString)
+        val errorFile = ifExists(invalidTestCases.resolve(invalidCase).resolve("error.txt").toFile).map(f =>
+          File(f.getAbsolutePath).contentAsString
+        )
         val inputsArgs = inputsFile match {
           case Some(path) => Seq("-i", path.getAbsolutePath)
           case None => Seq.empty[String]
@@ -109,18 +118,20 @@ class WomtoolValidateSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
         val expectedErrorMessage = errorFile map { ef => ef.trim.replace(s"$${PWD_NAME}", presentWorkingDirectoryName) }
 
         WomtoolMain.runWomtool(Seq("validate", wdl.getAbsolutePath) ++ inputsArgs) match {
-          case UnsuccessfulTermination(msg) => expectedErrorMessage match {
-            case Some(expectedError) =>
-              msg should include(expectedError)
-            case None => succeed
-          }
-          case other => fail(s"Expected UnsuccessfulTermination but got $other. Expected error message: ${System.lineSeparator()}${expectedErrorMessage.getOrElse("<<No expected error message specified>>")}")
+          case UnsuccessfulTermination(msg) =>
+            expectedErrorMessage match {
+              case Some(expectedError) =>
+                msg should include(expectedError)
+              case None => succeed
+            }
+          case other =>
+            fail(s"Expected UnsuccessfulTermination but got $other. Expected error message: ${System
+                .lineSeparator()}${expectedErrorMessage.getOrElse("<<No expected error message specified>>")}")
         }
       }
     }
   }
 
-
   behavior of "womtool validate with --list-dependencies flag"
 
   val validationWithImportsTests: File = File("womtool/src/test/resources/validate-with-imports")
@@ -141,12 +152,13 @@ class WomtoolValidateSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
 
     Option(versionDirectory.list).toList.flatten.filterNot(s => s.pathAsString.contains(".DS")) foreach { validCase =>
       val caseName = validCase.name
-      val wdlFile = mustExist(versionDirectory.path.resolve(s"../../validate/$versionName/valid/$caseName/$caseName.wdl").toFile)
-       wdlFile.getAbsolutePath.split("cromwell/womtool")(0)
+      val wdlFile =
+        mustExist(versionDirectory.path.resolve(s"../../validate/$versionName/valid/$caseName/$caseName.wdl").toFile)
+      wdlFile.getAbsolutePath.split("cromwell/womtool")(0)
 
       it should s"successfully validate and print the workflow dependencies for $versionName workflow: '$caseName'" in {
         val rawOutput = expectedOutput(versionDirectory, caseName, "expected_imports.txt")
-        //noinspection RegExpRedundantEscape
+        // noinspection RegExpRedundantEscape
         val importsExpectation = rawOutput.replaceAll("\\{REPLACE_WITH_ROOT_PATH\\}", workingDirectory)
 
         val res = WomtoolMain.runWomtool(Seq("validate", "-l", wdlFile.getAbsolutePath))
@@ -157,14 +169,17 @@ class WomtoolValidateSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
     }
   }
 
-
-  private def mustExist(file: java.io.File): java.io.File = if (file.exists) file else fail(s"No such file: ${file.getAbsolutePath}")
+  private def mustExist(file: java.io.File): java.io.File =
+    if (file.exists) file else fail(s"No such file: ${file.getAbsolutePath}")
   private def ifExists(file: java.io.File): Option[java.io.File] = if (file.exists) Option(file) else None
 
   // The filterNot(_.contains(".DS")) stuff prevents Mac 'Desktop Services' hidden directories from accidentally being picked up:
-  private def listFilesAndFilterDSFile(path: Path): immutable.Seq[String] =  Option(path.toFile.list).toList.flatten.filterNot(_.contains(".DS"))
+  private def listFilesAndFilterDSFile(path: Path): immutable.Seq[String] =
+    Option(path.toFile.list).toList.flatten.filterNot(_.contains(".DS"))
 
-  //noinspection SameParameterValue
+  // noinspection SameParameterValue
   private def expectedOutput(versionDirectory: File, caseName: String, outputTextFileName: String): String =
-    File(mustExist(versionDirectory.path.resolve(caseName).resolve(outputTextFileName).toFile).getAbsolutePath).contentAsString.trim
+    File(
+      mustExist(versionDirectory.path.resolve(caseName).resolve(outputTextFileName).toFile).getAbsolutePath
+    ).contentAsString.trim
 }
diff --git a/womtool/src/test/scala/womtool/graph/ExpressionBasedGraphOutputNodeSpec.scala b/womtool/src/test/scala/womtool/graph/ExpressionBasedGraphOutputNodeSpec.scala
index a34e7c73fa6..70b40cfaff3 100644
--- a/womtool/src/test/scala/womtool/graph/ExpressionBasedGraphOutputNodeSpec.scala
+++ b/womtool/src/test/scala/womtool/graph/ExpressionBasedGraphOutputNodeSpec.scala
@@ -20,12 +20,16 @@ class ExpressionBasedGraphOutputNodeSpec extends WomDotGraphTest {
 
     // Declare the expression output using both i and j:
     val xOutputValidation = ExpressionBasedGraphOutputNode.fromInputMapping(
-      WomIdentifier("x_out"), ijExpression, ijExpression.fixedWomType, Map(
-      "i" -> iInputNode.singleOutputPort,
-      "j" -> jInputNode.singleOutputPort))
+      WomIdentifier("x_out"),
+      ijExpression,
+      ijExpression.fixedWomType,
+      Map("i" -> iInputNode.singleOutputPort, "j" -> jInputNode.singleOutputPort)
+    )
 
     import common.validation.ErrorOr.ShortCircuitingFlatMap
-    val graph = xOutputValidation flatMap { xOutput => Graph.validateAndConstruct(Set(iInputNode, jInputNode, jOutput, xOutput)) }
+    val graph = xOutputValidation flatMap { xOutput =>
+      Graph.validateAndConstruct(Set(iInputNode, jInputNode, jOutput, xOutput))
+    }
 
     graph match {
       case Valid(g) => g
@@ -69,6 +73,8 @@ class ExpressionBasedGraphOutputNodeSpec extends WomDotGraphTest {
       |}
       |""".stripMargin
 
-  override val cases = List(WomDotGraphTestCase("ExpressionBasedGraphOutputNodes", expressionOutputGraph, expressionOutputDot))
+  override val cases = List(
+    WomDotGraphTestCase("ExpressionBasedGraphOutputNodes", expressionOutputGraph, expressionOutputDot)
+  )
   tests()
 }
diff --git a/womtool/src/test/scala/womtool/graph/ExpressionNodeSpec.scala b/womtool/src/test/scala/womtool/graph/ExpressionNodeSpec.scala
index a54a8828fbe..f959385b171 100644
--- a/womtool/src/test/scala/womtool/graph/ExpressionNodeSpec.scala
+++ b/womtool/src/test/scala/womtool/graph/ExpressionNodeSpec.scala
@@ -20,7 +20,11 @@ class ExpressionNodeSpec extends WomDotGraphTest {
     import common.validation.ErrorOr.ShortCircuitingFlatMap
     val graph = for {
       xDeclarationNode <- ExposedExpressionNode.fromInputMapping(
-        WomIdentifier("x"), ijExpression, WomIntegerType, Map("i" -> iInputNode.singleOutputPort, "j" -> jInputNode.singleOutputPort))
+        WomIdentifier("x"),
+        ijExpression,
+        WomIntegerType,
+        Map("i" -> iInputNode.singleOutputPort, "j" -> jInputNode.singleOutputPort)
+      )
       xOutputNode = PortBasedGraphOutputNode(WomIdentifier("x_out"), WomIntegerType, xDeclarationNode.singleOutputPort)
       g <- Graph.validateAndConstruct(Set(iInputNode, jInputNode, xDeclarationNode, xOutputNode))
     } yield g
diff --git a/womtool/src/test/scala/womtool/graph/OutputNameCollisionSpec.scala b/womtool/src/test/scala/womtool/graph/OutputNameCollisionSpec.scala
index 085740def7d..3f38c265584 100644
--- a/womtool/src/test/scala/womtool/graph/OutputNameCollisionSpec.scala
+++ b/womtool/src/test/scala/womtool/graph/OutputNameCollisionSpec.scala
@@ -33,7 +33,8 @@ class OutputNameCollisionSpec extends WomDotGraphTest {
     val namespace = WdlNamespaceWithWorkflow.load(wdl, Seq.empty).get
 
     namespace.toWomBundle match {
-      case Right(bundle) => (bundle.allCallables.values.toSet.filterByType[WorkflowDefinition]: Set[WorkflowDefinition]).head.graph
+      case Right(bundle) =>
+        (bundle.allCallables.values.toSet.filterByType[WorkflowDefinition]: Set[WorkflowDefinition]).head.graph
       case Left(errors) => throw new Exception(errors.toList.mkString(", "))
     }
   }
@@ -61,7 +62,9 @@ class OutputNameCollisionSpec extends WomDotGraphTest {
       |}
       |""".stripMargin
 
-  override val cases = List(WomDotGraphTestCase("non_colliding_output_names", outputCollisionWdlGraph, outputCollisionWdlDot))
+  override val cases = List(
+    WomDotGraphTestCase("non_colliding_output_names", outputCollisionWdlGraph, outputCollisionWdlDot)
+  )
 
   tests()
 }
diff --git a/womtool/src/test/scala/womtool/graph/WomDotGraphTest.scala b/womtool/src/test/scala/womtool/graph/WomDotGraphTest.scala
index c2f6523d10d..0fe7ddc48dc 100644
--- a/womtool/src/test/scala/womtool/graph/WomDotGraphTest.scala
+++ b/womtool/src/test/scala/womtool/graph/WomDotGraphTest.scala
@@ -7,14 +7,13 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import wom.graph.Graph
 
-
 trait WomDotGraphTest extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   def cases: List[WomDotGraphTestCase]
 
   behavior of "womgraph"
 
-  def tests() = {
+  def tests() =
     cases foreach { testCase =>
       it should s"draw the right DOT graph for ${testCase.name}" in {
         val womGraph = new WomGraph(testCase.name, testCase.graph)
@@ -25,15 +24,13 @@ trait WomDotGraphTest extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
         standardResult should be(standardExpectation)
       }
     }
-  }
-  
+
   def standardizifyResult(dot: String) = {
     val regex = "(NODE|PORT)-?[0-9]*".r
     val matches = regex.findAllIn(dot).toList.distinct.map(_.toString)
     val currentMatchId = new AtomicInteger(0)
-    def standardize(m: String) = {
+    def standardize(m: String) =
       m.substring(0, 4) + currentMatchId.getAndIncrement().toString
-    }
     def foldFunction(acc: String, m: String): String = acc.replaceAll(m, standardize(m))
 
     matches.foldLeft(dot)(foldFunction).replaceAll("\n[\\s]*", "\n")
@@ -41,5 +38,4 @@ trait WomDotGraphTest extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
   }
 }
 
-
 final case class WomDotGraphTestCase(name: String, graph: Graph, dotExpectation: String)

From beb86bd997632a354be00abe757ad8cecb483f53 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 4 Dec 2023 20:59:38 -0500
Subject: [PATCH 246/326] WX-1351 Speed up `Centaur Horicromtal PapiV2 Beta`
 (#7329)

---
 core/src/main/resources/reference.conf        |  3 +-
 src/ci/bin/test.inc.sh                        | 39 +++++++++++++++++++
 .../bin/testCentaurHoricromtalPapiV2beta.sh   |  4 +-
 src/ci/bin/testCentaurPapiV2beta.sh           |  2 +
 .../papi_v2beta_horicromtal_application.conf  |  6 +--
 5 files changed, 49 insertions(+), 5 deletions(-)

diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index 6ec05cf6025..3fa11b458ff 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -118,7 +118,8 @@ system {
   max-concurrent-workflows = 5000
 
   # Cromwell will launch up to N submitted workflows at a time, regardless of how many open workflow slots exist
-  max-workflow-launch-count = 50
+  # Deviating from 1 is not recommended for multi-runner setups due to possible deadlocks. [BW-962]
+  max-workflow-launch-count = 1
 
   # Workflows will be grouped by the value of the specified field in their workflow options.
   #
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index eef3a9fab6b..7da8290b9a1 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -1607,6 +1607,45 @@ cromwell::build::generate_code_coverage() {
     fi
 }
 
+cromwell::build::print_workflow_statistics() {
+    echo "Total workflows"
+    mysql --host=127.0.0.1 --user=cromwell --password=test cromwell_test -e \
+        "SELECT COUNT(*) as total_workflows_run FROM WORKFLOW_METADATA_SUMMARY_ENTRY;"
+
+    echo "Late starters"
+    mysql --host=127.0.0.1 --user=cromwell --password=test cromwell_test -e \
+        "SELECT WORKFlOW_NAME as name,
+            TIMESTAMPDIFF(MINUTE, START_TIMESTAMP, END_TIMESTAMP) as runtime_minutes,
+            START_TIMESTAMP as START,
+            END_TIMESTAMP as end
+        FROM WORKFLOW_METADATA_SUMMARY_ENTRY
+            WHERE PARENT_WORKFLOW_EXECUTION_UUID IS NULL # exclude subworkflows
+            ORDER BY START_TIMESTAMP DESC
+            LIMIT 20;"
+
+    echo "Late finishers"
+    mysql --host=127.0.0.1 --user=cromwell --password=test cromwell_test -e \
+        "SELECT WORKFlOW_NAME as name,
+            TIMESTAMPDIFF(MINUTE, START_TIMESTAMP, END_TIMESTAMP) as runtime_minutes,
+            START_TIMESTAMP as start,
+            END_TIMESTAMP as END
+        FROM WORKFLOW_METADATA_SUMMARY_ENTRY
+            WHERE PARENT_WORKFLOW_EXECUTION_UUID IS NULL
+            ORDER BY END_TIMESTAMP DESC
+            LIMIT 20;"
+
+    echo "Long duration"
+    mysql --host=127.0.0.1 --user=cromwell --password=test cromwell_test -e \
+        "SELECT WORKFlOW_NAME as name,
+            TIMESTAMPDIFF(MINUTE, START_TIMESTAMP, END_TIMESTAMP) as RUNTIME_MINUTES,
+            START_TIMESTAMP as start,
+            END_TIMESTAMP as end
+        FROM WORKFLOW_METADATA_SUMMARY_ENTRY
+            WHERE PARENT_WORKFLOW_EXECUTION_UUID IS NULL
+            ORDER BY RUNTIME_MINUTES DESC
+            LIMIT 20;"
+}
+
 cromwell::build::exec_retry_function() {
     local retried_function
     local retry_count
diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
index 9dba2f6f8ce..36b215a2f52 100755
--- a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
+++ b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
@@ -19,7 +19,7 @@ cromwell::build::assemble_jars
 cromwell::build::build_cromwell_docker
 
 cromwell::build::run_centaur \
-    -p 100 \
+    -p 500 \
     -e localdockertest \
     -e relative_output_paths \
     -e relative_output_paths_colliding \
@@ -27,3 +27,5 @@ cromwell::build::run_centaur \
     -e papi_v2alpha1_gcsa \
 
 cromwell::build::generate_code_coverage
+
+cromwell::build::print_workflow_statistics
diff --git a/src/ci/bin/testCentaurPapiV2beta.sh b/src/ci/bin/testCentaurPapiV2beta.sh
index b3a1ef2a61e..43d5a7d62aa 100755
--- a/src/ci/bin/testCentaurPapiV2beta.sh
+++ b/src/ci/bin/testCentaurPapiV2beta.sh
@@ -25,3 +25,5 @@ cromwell::build::run_centaur \
     -e papi_v2alpha1_gcsa \
 
 cromwell::build::generate_code_coverage
+
+cromwell::build::print_workflow_statistics
diff --git a/src/ci/resources/papi_v2beta_horicromtal_application.conf b/src/ci/resources/papi_v2beta_horicromtal_application.conf
index c6bc9176c16..f0f2c45f381 100644
--- a/src/ci/resources/papi_v2beta_horicromtal_application.conf
+++ b/src/ci/resources/papi_v2beta_horicromtal_application.conf
@@ -1,8 +1,8 @@
 include "papi_v2beta_application.conf"
 
-system.max-workflow-launch-count=1
-system.new-workflow-poll-rate=10
-system.max-concurrent-workflows=30
+system.max-workflow-launch-count=10
+system.new-workflow-poll-rate=1
+system.max-concurrent-workflows=500
 system.cromwell_id_random_suffix=false
 
 # Turn off token logging to reduce log volume

From 786d315d99f5361e6a9050f102921516cd785d67 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 4 Dec 2023 22:42:08 -0500
Subject: [PATCH 247/326] WX-1351 CI CWL cleanup (#7327)

---
 src/ci/bin/test.inc.sh                        | 146 +-----------------
 src/ci/bin/testCentaurAws.sh                  |   1 -
 src/ci/bin/testCentaurTes.sh                  |   1 -
 src/ci/bin/testConformanceLocal.sh            |  16 --
 src/ci/bin/testConformancePapiV2alpha1.sh     |  21 ---
 src/ci/bin/testConformancePapiV2beta.sh       |   4 -
 src/ci/bin/testConformanceTesk.sh             |   4 -
 src/ci/bin/test_gcpbatch.inc.sh               |   4 -
 src/ci/bin/test_papi.inc.sh                   |   4 -
 .../centaur_cwl_runner_application.conf       |  44 ------
 src/ci/resources/cwl_conformance_test.wdl     | 136 ----------------
 .../ftp_centaur_cwl_runner.conf.ctmpl         |  16 --
 12 files changed, 2 insertions(+), 395 deletions(-)
 delete mode 100755 src/ci/bin/testConformanceLocal.sh
 delete mode 100755 src/ci/bin/testConformancePapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testConformancePapiV2beta.sh
 delete mode 100755 src/ci/bin/testConformanceTesk.sh
 delete mode 100644 src/ci/resources/centaur_cwl_runner_application.conf
 delete mode 100644 src/ci/resources/cwl_conformance_test.wdl
 delete mode 100644 src/ci/resources/ftp_centaur_cwl_runner.conf.ctmpl

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 7da8290b9a1..6f76ee8c05c 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -355,15 +355,11 @@ cromwell::private::create_build_variables() {
     backend_type="${backend_type#centaurWdlUpgrade}"
     backend_type="${backend_type#centaurHoricromtal}"
     backend_type="${backend_type#centaur}"
-    backend_type="${backend_type#conformance}"
     backend_type="$(echo "${backend_type}" | sed 's/\([A-Z]\)/_\1/g' | tr '[:upper:]' '[:lower:]' | cut -c 2-)"
     CROMWELL_BUILD_BACKEND_TYPE="${backend_type}"
 
-    if [[ "${CROMWELL_BUILD_TYPE}" == conformance* ]]; then
-        CROMWELL_BUILD_SBT_ASSEMBLY_COMMAND="server/assembly centaurCwlRunner/assembly"
-    else
-        CROMWELL_BUILD_SBT_ASSEMBLY_COMMAND="assembly"
-    fi
+    # It may be possible to trim this down to e.g. `server/assembly` for some jobs
+    CROMWELL_BUILD_SBT_ASSEMBLY_COMMAND="assembly"
 
     if [[ "${CROMWELL_BUILD_GENERATE_COVERAGE}" == "true" ]]; then
         CROMWELL_BUILD_SBT_COVERAGE_COMMAND="coverage"
@@ -747,45 +743,6 @@ cromwell::private::create_centaur_variables() {
     export CROMWELL_BUILD_DOCKER_TAG
 }
 
-cromwell::private::create_conformance_variables() {
-    CROMWELL_BUILD_CWL_RUNNER_MODE="${CROMWELL_BUILD_BACKEND_TYPE}"
-    CROMWELL_BUILD_CWL_TOOL_VERSION="3.0.20200724003302"
-    CROMWELL_BUILD_CWL_TEST_VERSION="1.0.20190228134645"
-    CROMWELL_BUILD_CWL_TEST_COMMIT="1f501e38ff692a408e16b246ac7d64d32f0822c2" # use known git hash to avoid changes
-    CROMWELL_BUILD_CWL_TEST_RUNNER="${CROMWELL_BUILD_ROOT_DIRECTORY}/centaurCwlRunner/src/bin/centaur-cwl-runner.bash"
-    CROMWELL_BUILD_CWL_TEST_DIRECTORY="${CROMWELL_BUILD_ROOT_DIRECTORY}/common-workflow-language"
-    CROMWELL_BUILD_CWL_TEST_RESOURCES="${CROMWELL_BUILD_CWL_TEST_DIRECTORY}/v1.0/v1.0"
-    CROMWELL_BUILD_CWL_TEST_WDL="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/cwl_conformance_test.wdl"
-    CROMWELL_BUILD_CWL_TEST_INPUTS="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/cwl_conformance_test.inputs.json"
-    CROMWELL_BUILD_CWL_TEST_OUTPUT="${CROMWELL_BUILD_LOG_DIRECTORY}/cwl_conformance_test.out.txt"
-
-    # Setting CROMWELL_BUILD_CWL_TEST_PARALLELISM too high will cause false negatives due to cromwell server timeouts.
-    case "${CROMWELL_BUILD_TYPE}" in
-        conformanceTesk)
-            # BA-6547: TESK is not currently tested in FC-Jenkins nor Travis
-            CROMWELL_BUILD_CWL_RUNNER_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/ftp_centaur_cwl_runner.conf"
-            CROMWELL_BUILD_CWL_TEST_PARALLELISM=8
-            ;;
-        *)
-            CROMWELL_BUILD_CWL_RUNNER_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/centaur_cwl_runner_application.conf"
-            CROMWELL_BUILD_CWL_TEST_PARALLELISM=10
-            ;;
-    esac
-
-    export CROMWELL_BUILD_CWL_RUNNER_CONFIG
-    export CROMWELL_BUILD_CWL_RUNNER_MODE
-    export CROMWELL_BUILD_CWL_TOOL_VERSION
-    export CROMWELL_BUILD_CWL_TEST_VERSION
-    export CROMWELL_BUILD_CWL_TEST_COMMIT
-    export CROMWELL_BUILD_CWL_TEST_RUNNER
-    export CROMWELL_BUILD_CWL_TEST_DIRECTORY
-    export CROMWELL_BUILD_CWL_TEST_RESOURCES
-    export CROMWELL_BUILD_CWL_TEST_WDL
-    export CROMWELL_BUILD_CWL_TEST_INPUTS
-    export CROMWELL_BUILD_CWL_TEST_OUTPUT
-    export CROMWELL_BUILD_CWL_TEST_PARALLELISM
-}
-
 cromwell::private::verify_secure_build() {
     case "${CROMWELL_BUILD_PROVIDER}" in
         "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
@@ -1032,39 +989,6 @@ cromwell::private::start_docker_databases() {
     fi
 }
 
-cromwell::private::install_cwltest() {
-    # TODO: No clue why these are needed for cwltool. If you know please update this comment.
-    sudo apt-get install procps || true
-    cromwell::private::pip_install cwltool=="${CROMWELL_BUILD_CWL_TOOL_VERSION}" --ignore-installed
-    cromwell::private::pip_install cwltest=="${CROMWELL_BUILD_CWL_TEST_VERSION}"
-}
-
-cromwell::private::checkout_pinned_cwl() {
-    if [[ ! -d "${CROMWELL_BUILD_CWL_TEST_DIRECTORY}" ]]; then
-        git clone \
-            https://github.com/common-workflow-language/common-workflow-language.git \
-            "${CROMWELL_BUILD_CWL_TEST_DIRECTORY}"
-        (
-            pushd "${CROMWELL_BUILD_CWL_TEST_DIRECTORY}" > /dev/null
-            git checkout "${CROMWELL_BUILD_CWL_TEST_COMMIT}"
-            popd > /dev/null
-        )
-    fi
-}
-
-cromwell::private::write_cwl_test_inputs() {
-    cat <<JSON >"${CROMWELL_BUILD_CWL_TEST_INPUTS}"
-{
-    "cwl_conformance_test.cwl_dir": "${CROMWELL_BUILD_CWL_TEST_DIRECTORY}",
-    "cwl_conformance_test.test_result_output": "${CROMWELL_BUILD_CWL_TEST_OUTPUT}",
-    "cwl_conformance_test.centaur_cwl_runner": "${CROMWELL_BUILD_CWL_TEST_RUNNER}",
-    "cwl_conformance_test.conformance_expected_failures":
-        "${CROMWELL_BUILD_RESOURCES_DIRECTORY}/${CROMWELL_BUILD_BACKEND_TYPE}_conformance_expected_failures.txt",
-    "cwl_conformance_test.timeout": 2400
-}
-JSON
-}
-
 cromwell::private::vault_run() {
     if cromwell::private::is_xtrace_enabled; then
         cromwell::private::exec_silent_function cromwell::private::vault_run "$@"
@@ -1267,11 +1191,6 @@ cromwell::private::cat_centaur_log() {
     cat "${CROMWELL_BUILD_CENTAUR_LOG}"
 }
 
-cromwell::private::cat_conformance_log() {
-    echo "CONFORMANCE LOG"
-    cat "${CROMWELL_BUILD_CWL_TEST_OUTPUT}"
-}
-
 cromwell::private::kill_build_heartbeat() {
     if [[ -n "${CROMWELL_BUILD_HEARTBEAT_PID:+set}" ]]; then
         cromwell::private::kill_tree "${CROMWELL_BUILD_HEARTBEAT_PID}"
@@ -1337,47 +1256,6 @@ cromwell::private::kill_tree() {
   kill "${pid}" 2> /dev/null
 }
 
-cromwell::private::start_conformance_cromwell() {
-    # Start the Cromwell server in the directory containing input files so it can access them via their relative path
-    pushd "${CROMWELL_BUILD_CWL_TEST_RESOURCES}" > /dev/null
-
-    # Turn off call caching as hashing doesn't work since it sees local and not GCS paths.
-    # CWL conformance uses alpine images that do not have bash.
-    java \
-        -Xmx2g \
-        -Dconfig.file="${CROMWELL_BUILD_CROMWELL_CONFIG}" \
-        -Dcall-caching.enabled=false \
-        -Dsystem.job-shell=/bin/sh \
-        -jar "${CROMWELL_BUILD_CROMWELL_JAR}" \
-        server &
-
-    CROMWELL_BUILD_CONFORMANCE_CROMWELL_PID=$!
-
-    popd > /dev/null
-
-    cromwell::private::add_exit_function cromwell::private::kill_conformance_cromwell
-}
-
-cromwell::private::kill_conformance_cromwell() {
-    if [[ -n "${CROMWELL_BUILD_CONFORMANCE_CROMWELL_PID+set}" ]]; then
-        cromwell::build::kill_tree "${CROMWELL_BUILD_CONFORMANCE_CROMWELL_PID}"
-    fi
-}
-
-cromwell::private::run_conformance_wdl() {
-    pushd "${CROMWELL_BUILD_CWL_TEST_RESOURCES}" > /dev/null
-
-    CENTAUR_CWL_JAVA_ARGS="-Dconfig.file=${CROMWELL_BUILD_CWL_RUNNER_CONFIG}" \
-        java \
-        -Xmx6g \
-        -Dbackend.providers.Local.config.concurrent-job-limit="${CROMWELL_BUILD_CWL_TEST_PARALLELISM}" \
-        -jar "${CROMWELL_BUILD_CROMWELL_JAR}" \
-        run "${CROMWELL_BUILD_CWL_TEST_WDL}" \
-        -i "${CROMWELL_BUILD_CWL_TEST_INPUTS}"
-
-    popd > /dev/null
-}
-
 cromwell::build::exec_test_script() {
     cromwell::private::create_build_variables
     if [[ "${CROMWELL_BUILD_RUN_TESTS}" == "false" ]]; then
@@ -1458,17 +1336,6 @@ cromwell::build::setup_centaur_environment() {
     fi
 }
 
-cromwell::build::setup_conformance_environment() {
-    cromwell::private::create_centaur_variables
-    cromwell::private::create_conformance_variables
-    if [[ "${CROMWELL_BUILD_IS_CI}" == "true" ]]; then
-        cromwell::private::install_cwltest
-    fi
-    cromwell::private::checkout_pinned_cwl
-    cromwell::private::write_cwl_test_inputs
-    cromwell::private::add_exit_function cromwell::private::cat_conformance_log
-}
-
 cromwell::private::find_or_assemble_cromwell_jar() {
     cromwell::private::find_cromwell_jar
     if [[ "${CROMWELL_BUILD_IS_CI}" == "true" ]] || ! cromwell::private::exists_cromwell_jar; then
@@ -1592,15 +1459,6 @@ cromwell::build::run_centaur() {
         "$@"
 }
 
-cromwell::build::run_conformance() {
-    cromwell::private::start_conformance_cromwell
-
-    # Give cromwell time to start up
-    sleep 30
-
-    cromwell::private::run_conformance_wdl
-}
-
 cromwell::build::generate_code_coverage() {
     if [[ "${CROMWELL_BUILD_GENERATE_COVERAGE}" == "true" ]]; then
         cromwell::private::generate_code_coverage
diff --git a/src/ci/bin/testCentaurAws.sh b/src/ci/bin/testCentaurAws.sh
index 83804005322..f20ebfb9e59 100755
--- a/src/ci/bin/testCentaurAws.sh
+++ b/src/ci/bin/testCentaurAws.sh
@@ -50,7 +50,6 @@ cromwell::build::run_centaur \
 #    -e scatter \
 #    -e long_cmd \
 #    -e runtwiceexpectingcallcaching \
-#    -e cwl_cache_within_workflow \
 #    -e cachewithinwf
 
 cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testCentaurTes.sh b/src/ci/bin/testCentaurTes.sh
index 7cad5b26832..3d3a350cdd6 100755
--- a/src/ci/bin/testCentaurTes.sh
+++ b/src/ci/bin/testCentaurTes.sh
@@ -72,7 +72,6 @@ cromwell::build::run_centaur \
     -e non_root_specified_user \
     -e write_lines_files \
     -e draft3_read_write_functions_local \
-    -e cwl_input_json \
     -e directory_type_local \
 
 cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testConformanceLocal.sh b/src/ci/bin/testConformanceLocal.sh
deleted file mode 100755
index 74e2cabc462..00000000000
--- a/src/ci/bin/testConformanceLocal.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_conformance_environment
-
-cromwell::build::assemble_jars
-
-cromwell::build::run_conformance
-
-cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testConformancePapiV2alpha1.sh b/src/ci/bin/testConformancePapiV2alpha1.sh
deleted file mode 100755
index cb952694b4e..00000000000
--- a/src/ci/bin/testConformancePapiV2alpha1.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test_papi.inc.sh" || source test_papi.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_conformance_environment
-
-cromwell::build::papi::setup_papi_conformance_environment
-
-cromwell::build::assemble_jars
-
-cromwell::build::run_conformance
-
-cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testConformancePapiV2beta.sh b/src/ci/bin/testConformancePapiV2beta.sh
deleted file mode 100755
index 7117a2d78ba..00000000000
--- a/src/ci/bin/testConformancePapiV2beta.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/usr/bin/env bash
-
-echo "Test is temporarily disabled due to ongoing PAPI 503 flakiness."
-exit 0
\ No newline at end of file
diff --git a/src/ci/bin/testConformanceTesk.sh b/src/ci/bin/testConformanceTesk.sh
deleted file mode 100755
index 6f4784888e1..00000000000
--- a/src/ci/bin/testConformanceTesk.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/usr/bin/env bash
-
-echo "$(tput setab 1)$(tput blink)BA-6547: TESK is not currently tested in GOTC-Jenkins, FC-Jenkins, nor Travis... so this 'test' was quick!$(tput sgr 0)"
-exit 0
diff --git a/src/ci/bin/test_gcpbatch.inc.sh b/src/ci/bin/test_gcpbatch.inc.sh
index f75764b6006..1570bdb5f76 100644
--- a/src/ci/bin/test_gcpbatch.inc.sh
+++ b/src/ci/bin/test_gcpbatch.inc.sh
@@ -112,7 +112,3 @@ cromwell::build::batch::setup_batch_centaur_environment() {
     fi
     cromwell::private::batch::setup_batch_service_account
 }
-
-cromwell::build::batch::setup_batch_conformance_environment() {
-    cromwell::private::batch::setup_batch_service_account
-}
diff --git a/src/ci/bin/test_papi.inc.sh b/src/ci/bin/test_papi.inc.sh
index e3c253d7455..98d77820435 100644
--- a/src/ci/bin/test_papi.inc.sh
+++ b/src/ci/bin/test_papi.inc.sh
@@ -122,7 +122,3 @@ cromwell::build::papi::setup_papi_centaur_environment() {
     cromwell::private::papi::setup_papi_service_account
     cromwell::private::papi::setup_papi_endpoint_url
 }
-
-cromwell::build::papi::setup_papi_conformance_environment() {
-    cromwell::private::papi::setup_papi_service_account
-}
diff --git a/src/ci/resources/centaur_cwl_runner_application.conf b/src/ci/resources/centaur_cwl_runner_application.conf
deleted file mode 100644
index 69c63440901..00000000000
--- a/src/ci/resources/centaur_cwl_runner_application.conf
+++ /dev/null
@@ -1,44 +0,0 @@
-include required(classpath("application.conf"))
-
-centaur {
-  cwl-runner {
-    mode = "Error: BA-6546 The environment variable CROMWELL_BUILD_CWL_RUNNER_MODE must be set/export pointing to a valid mode such as 'local'"
-    mode = ${?CROMWELL_BUILD_CWL_RUNNER_MODE}
-
-    papi {
-      default-input-gcs-prefix = "gs://centaur-cwl-conformance-1f501e3/cwl-inputs/"
-    }
-    tesk {
-      default-input-ftp-prefix = "ftp://ftp.hexdump.org/centaur-cwl-conformance/cwl-inputs/"
-    }
-
-    google {
-      application-name = "centaur-cwl-runner"
-      genomics.location = "us-central1"
-      max-attempts = 3
-
-      auth = "Error: BA-6546 The environment variable CROMWELL_BUILD_PAPI_AUTH_MODE must be set/export pointing to a valid mode such as 'application-default'"
-      auth = ${?CROMWELL_BUILD_PAPI_AUTH_MODE}
-      json-dir = "Error: BA-6546 The environment variable CROMWELL_BUILD_RESOURCES_DIRECTORY must be set/export pointing to a valid mode such as 'target/ci/resources'"
-      json-dir = ${?CROMWELL_BUILD_RESOURCES_DIRECTORY}
-
-      genomics {
-        endpoint-url = "Error: BA-6546 The environment variable CROMWELL_BUILD_PAPI_ENDPOINT_URL must be set/export pointing to a valid mode such as 'https://lifesciences.googleapis.com/'"
-        endpoint-url = ${?CROMWELL_BUILD_PAPI_ENDPOINT_URL}
-      }
-
-      auths = [
-        {
-          name = "application-default"
-          scheme = "application_default"
-        }
-        {
-          name = "service-account"
-          scheme = "service_account"
-          json-file = ${centaur.cwl-runner.google.json-dir}/cromwell-centaur-service-account.json
-        }
-      ]
-
-    }
-  }
-}
diff --git a/src/ci/resources/cwl_conformance_test.wdl b/src/ci/resources/cwl_conformance_test.wdl
deleted file mode 100644
index 75b544c9f53..00000000000
--- a/src/ci/resources/cwl_conformance_test.wdl
+++ /dev/null
@@ -1,136 +0,0 @@
-version 1.0
-
-workflow cwl_conformance_test {
-    input {
-        String cwl_dir
-        String test_result_output
-        String centaur_cwl_runner
-        String conformance_expected_failures
-        Int timeout
-    }
-
-    call get_test_count {
-        input:
-            cwl_dir = cwl_dir,
-            centaur_cwl_runner = centaur_cwl_runner
-    }
-
-    scatter (test_index in range(get_test_count.test_count)) {
-        call run_test_index {
-            input:
-                cwl_dir = cwl_dir,
-                centaur_cwl_runner = centaur_cwl_runner,
-                test_index = test_index,
-                timeout = timeout
-        }
-    }
-
-    call make_summary {
-        input:
-            test_count = get_test_count.test_count,
-            test_result_codes = run_test_index.test_result_code,
-            conformance_expected_failures = conformance_expected_failures,
-            test_result_outputs = run_test_index.out,
-            test_result_output = test_result_output
-    }
-
-    output {
-    }
-}
-
-task get_test_count {
-    input {
-        String cwl_dir
-        String centaur_cwl_runner
-    }
-
-    command {
-        cd ~{cwl_dir}
-        ./run_test.sh RUNNER="~{centaur_cwl_runner}" -l | grep -c '^\['
-    }
-
-    output {
-        Int test_count = read_int(stdout())
-    }
-}
-
-task run_test_index {
-    input {
-        String cwl_dir
-        String centaur_cwl_runner
-        Int test_index
-        Int test_number = test_index + 1
-        Int timeout
-    }
-
-    # Weird -n/--timeout format is because ./run_test.sh doesn't pass through the timeout parameter to cwltest.
-    # Test 55 often runs over 10 minutes in Travis/PapiV2 and requires a longer timeout.
-    # So, we use the fact that run_test.sh conveniently doesn't sanitize -n to wire the --timeout _inside_ the -n arg.
-    command {
-        (
-            cd ~{cwl_dir}
-            ./run_test.sh RUNNER="~{centaur_cwl_runner}" -n"~{test_number} --timeout=~{timeout}" 2>&1
-        )
-        echo $? > test_result_code
-    }
-
-    output {
-        Int test_result_code = read_int("test_result_code")
-        File out = stdout()
-    }
-}
-
-task make_summary {
-    input {
-        Int test_count
-        Array[String] test_result_outputs
-        Array[Int] test_result_codes
-        String test_result_output
-        String conformance_expected_failures
-        File test_result_output_lines = write_lines(test_result_outputs)
-        File test_result_code_lines = write_lines(test_result_codes)
-    }
-
-    command <<<
-        TEST_PASSING=0
-        touch unexpected_pass
-        touch unexpected_fail
-
-        for TEST_NUMBER in $(seq ~{test_count}); do
-            # Check if test is supposed to fail
-            grep -q "^${TEST_NUMBER}$" "~{conformance_expected_failures}"
-            TEST_IN_EXPECTED_FAILED=$?
-
-            # Get the test results
-            TEST_RESULT_OUTPUT="$(sed -n ${TEST_NUMBER}p ~{test_result_output_lines})"
-            TEST_RESULT_CODE="$(sed -n ${TEST_NUMBER}p ~{test_result_code_lines})"
-
-            if [ "${TEST_RESULT_CODE}" -eq 0 ]; then
-                TEST_PASSING="$((${TEST_PASSING} + 1))"
-            fi
-
-            # Check for unexpected results
-            if [ "${TEST_IN_EXPECTED_FAILED}" -eq 0 ] && [ "${TEST_RESULT_CODE}" -eq 0 ]; then
-                echo "${TEST_NUMBER}" >> unexpected_pass
-            elif [ "${TEST_IN_EXPECTED_FAILED}" -ne 0 ] && [ "${TEST_RESULT_CODE}" -ne 0 ]; then
-                echo "${TEST_NUMBER}" >> unexpected_fail
-            fi
-
-            cat "$TEST_RESULT_OUTPUT" >> "~{test_result_output}"
-            echo "exited with code ${TEST_RESULT_CODE}" >> "~{test_result_output}"
-        done
-
-        echo "---" >> "~{test_result_output}"
-        echo "Conformance percentage at $(( 100 * ${TEST_PASSING} / ~{test_count} ))%" >> "~{test_result_output}"
-
-        if [ -s unexpected_pass ] || [ -s unexpected_fail ]; then
-            printf "Unexpected passing tests: (%s)\n" "$(paste -s -d ' ' unexpected_pass)" >> "~{test_result_output}"
-            printf "Unexpected failing tests: (%s)\n" "$(paste -s -d ' ' unexpected_fail)" >> "~{test_result_output}"
-            echo "Does ~{conformance_expected_failures} need to be updated?" >> "~{test_result_output}"
-            false
-        fi
-    >>>
-
-    output {
-    }
-}
diff --git a/src/ci/resources/ftp_centaur_cwl_runner.conf.ctmpl b/src/ci/resources/ftp_centaur_cwl_runner.conf.ctmpl
deleted file mode 100644
index 559b9e2f981..00000000000
--- a/src/ci/resources/ftp_centaur_cwl_runner.conf.ctmpl
+++ /dev/null
@@ -1,16 +0,0 @@
-include required(classpath("application.conf"))
-include "centaur_cwl_runner_application.conf"
-
-{{with $cromwellFtp := secret (printf "secret/dsde/cromwell/common/cromwell-ftp")}}
-centaur {
-  cwl-runner {
-    ftp {
-      auth {
-        username = {{$cromwellFtp.Data.username}}
-        password = {{$cromwellFtp.Data.password}}
-      }
-      connection-count-per-user = 1
-    }
-  }
-}
-{{end}}

From bb1e394ed6f537e7f83c4ee5a77e0ae29ea17cd7 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 5 Dec 2023 13:11:44 -0500
Subject: [PATCH 248/326] WX-1351 Remove slow/misbehaving localization test
 (#7330)

---
 .../localize_file_larger_than_disk_space.wdl  | 27 -------------------
 .../localize_file_larger_than_disk_space.test | 17 ------------
 2 files changed, 44 deletions(-)
 delete mode 100644 centaur/src/main/resources/standardTestCases/input_localization/localize_file_larger_than_disk_space.wdl
 delete mode 100644 centaur/src/main/resources/standardTestCases/localize_file_larger_than_disk_space.test

diff --git a/centaur/src/main/resources/standardTestCases/input_localization/localize_file_larger_than_disk_space.wdl b/centaur/src/main/resources/standardTestCases/input_localization/localize_file_larger_than_disk_space.wdl
deleted file mode 100644
index b90c63fe928..00000000000
--- a/centaur/src/main/resources/standardTestCases/input_localization/localize_file_larger_than_disk_space.wdl
+++ /dev/null
@@ -1,27 +0,0 @@
-version 1.0
-
-task localize_file {
-    input {
-        File input_file
-    }
-    command {
-        cat "localizing file over 1 GB"
-    }
-    runtime {
-        docker: "ubuntu:latest"
-        disks: "local-disk 1 HDD"
-    }
-    output {
-        String out = read_string(stdout())
-    }
-}
-
-workflow localize_file_larger_than_disk_space {
-    File wf_input = "gs://cromwell_test_bucket/file_over_1_gb.txt"
-
-    call localize_file { input: input_file = wf_input }
-
-    output {
-        String content = localize_file.out
-    }
-}
diff --git a/centaur/src/main/resources/standardTestCases/localize_file_larger_than_disk_space.test b/centaur/src/main/resources/standardTestCases/localize_file_larger_than_disk_space.test
deleted file mode 100644
index bee99677b01..00000000000
--- a/centaur/src/main/resources/standardTestCases/localize_file_larger_than_disk_space.test
+++ /dev/null
@@ -1,17 +0,0 @@
-name: localize_file_larger_than_disk_space
-testFormat: workflowfailure
-backends: [Papiv2]
-workflowType: WDL
-workflowTypeVersion: 1.0
-tags: ["wdl_1.0"]
-
-files {
-  workflow: input_localization/localize_file_larger_than_disk_space.wdl
-}
-
-metadata {
-  workflowName: localize_file_larger_than_disk_space
-  status: Failed
-  "failures.0.message": "Workflow failed"
-  "failures.0.causedBy.0.message": "Task localize_file_larger_than_disk_space.localize_file:NA:1 failed. The job was stopped before the command finished. PAPI error code 9. Please check the log file for more details: gs://cloud-cromwell-dev-self-cleaning/cromwell_execution/ci/localize_file_larger_than_disk_space/<<UUID>>/call-localize_file/localize_file.log."
-}

From fede8596e6f6b12d7ef5f46db125b996153803b6 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Wed, 6 Dec 2023 15:47:56 -0500
Subject: [PATCH 249/326] WX-1351 Split out restart tests (#7333)

---
 .github/workflows/integration_tests.yml       |  3 +++
 .../failures.restart_while_failing_jes.test   |  1 +
 .../failures.restart_while_failing_local.test |  2 +-
 .../failures.restart_while_failing_tes.test   |  2 +-
 .../bin/testCentaurHoricromtalPapiV2beta.sh   |  1 +
 src/ci/bin/testCentaurPapiV2beta.sh           |  1 +
 src/ci/bin/testCentaurPapiV2betaRestart.sh    | 25 +++++++++++++++++++
 .../papi_v2beta_restart_application.conf      |  1 +
 8 files changed, 34 insertions(+), 2 deletions(-)
 create mode 100755 src/ci/bin/testCentaurPapiV2betaRestart.sh
 create mode 100644 src/ci/resources/papi_v2beta_restart_application.conf

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index ebafe51064c..61ed3c5af41 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -32,6 +32,9 @@ jobs:
           - build_type: centaurPapiV2beta
             build_mysql: 5.7
             friendly_name: Centaur Papi V2 Beta with MySQL 5.7
+          - build_type: centaurPapiV2betaRestart
+            build_mysql: 5.7
+            friendly_name: Centaur Papi V2 Beta (restart)
           - build_type: dbms
             friendly_name: DBMS
           - build_type: centaurTes
diff --git a/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_jes.test b/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_jes.test
index 1ac12322f4f..182a833fbdb 100644
--- a/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_jes.test
+++ b/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_jes.test
@@ -2,6 +2,7 @@ name: failures.restart_while_failing_jes
 testFormat: WorkflowFailureRestartWithRecover
 callMark: restart_while_failing.B1
 backends: [Papi]
+tags: [restart]
 
 files {
   workflow: failures/restart_while_failing/restart_while_failing.wdl
diff --git a/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_local.test b/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_local.test
index f686b16c817..58abbf78245 100644
--- a/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_local.test
+++ b/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_local.test
@@ -3,7 +3,7 @@ testFormat: WorkflowFailureRestartWithRecover
 callMark: restart_while_failing.B1
 backendsMode: "only"
 backends: [Local, LocalNoDocker]
-tags: [localdockertest]
+tags: [localdockertest, restart]
 
 files {
   workflow: failures/restart_while_failing/restart_while_failing.wdl
diff --git a/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_tes.test b/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_tes.test
index 64ea5fd8906..9bb9c1a55d6 100644
--- a/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_tes.test
+++ b/centaur/src/main/resources/standardTestCases/failures.restart_while_failing_tes.test
@@ -2,7 +2,7 @@ name: failures.restart_while_failing_tes
 testFormat: WorkflowFailureRestartWithoutRecover
 callMark: restart_while_failing.B1
 backends: [TES]
-tags: [localdockertest]
+tags: [localdockertest, restart]
 
 files {
   workflow: failures/restart_while_failing/restart_while_failing.wdl
diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
index 36b215a2f52..c894909cd3f 100755
--- a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
+++ b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
@@ -25,6 +25,7 @@ cromwell::build::run_centaur \
     -e relative_output_paths_colliding \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
+    -e restart \
 
 cromwell::build::generate_code_coverage
 
diff --git a/src/ci/bin/testCentaurPapiV2beta.sh b/src/ci/bin/testCentaurPapiV2beta.sh
index 43d5a7d62aa..d66d2a14334 100755
--- a/src/ci/bin/testCentaurPapiV2beta.sh
+++ b/src/ci/bin/testCentaurPapiV2beta.sh
@@ -23,6 +23,7 @@ cromwell::build::run_centaur \
     -e relative_output_paths_colliding \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
+    -e restart \
 
 cromwell::build::generate_code_coverage
 
diff --git a/src/ci/bin/testCentaurPapiV2betaRestart.sh b/src/ci/bin/testCentaurPapiV2betaRestart.sh
new file mode 100755
index 00000000000..e0d50bb18c6
--- /dev/null
+++ b/src/ci/bin/testCentaurPapiV2betaRestart.sh
@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+
+set -o errexit -o nounset -o pipefail
+export CROMWELL_BUILD_REQUIRES_SECURE=true
+# import in shellcheck / CI / IntelliJ compatible ways
+# shellcheck source=/dev/null
+source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
+# shellcheck source=/dev/null
+source "${BASH_SOURCE%/*}/test_papi.inc.sh" || source test_papi.inc.sh
+
+cromwell::build::setup_common_environment
+
+cromwell::build::setup_centaur_environment
+
+cromwell::build::papi::setup_papi_centaur_environment
+
+cromwell::build::assemble_jars
+
+cromwell::build::run_centaur \
+    -p 100 \
+    -i restart \
+
+cromwell::build::generate_code_coverage
+
+cromwell::build::print_workflow_statistics
diff --git a/src/ci/resources/papi_v2beta_restart_application.conf b/src/ci/resources/papi_v2beta_restart_application.conf
new file mode 100644
index 00000000000..2f0bb75860b
--- /dev/null
+++ b/src/ci/resources/papi_v2beta_restart_application.conf
@@ -0,0 +1 @@
+include "papi_v2beta_application.conf"

From f002a9644d7bb0c658151b4a2fe2451b839f6704 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 7 Dec 2023 10:24:59 -0500
Subject: [PATCH 250/326] [WX-1345] Automatic Token Acquisition for TES Config
 (#7256)

---
 .gitignore                                    |  4 +
 project/ContinuousIntegration.scala           | 16 +++-
 ...Repo template_ Cromwell server TES.run.xml | 20 +++++
 ...emplate_ Cromwell server Terra TES.run.xml | 23 ++++++
 src/ci/resources/acquire_b2c_token.sh         | 42 ++++++++++
 .../terra_tes_application.conf.ctmpl          | 80 +++++++++++++++++++
 src/ci/resources/tes_application.conf         | 42 ++++------
 7 files changed, 197 insertions(+), 30 deletions(-)
 create mode 100644 runConfigurations/Repo template_ Cromwell server Terra TES.run.xml
 create mode 100755 src/ci/resources/acquire_b2c_token.sh
 create mode 100644 src/ci/resources/terra_tes_application.conf.ctmpl

diff --git a/.gitignore b/.gitignore
index 250b6aa3c16..94accae9038 100644
--- a/.gitignore
+++ b/.gitignore
@@ -58,6 +58,10 @@ tesk_application.conf
 **/venv/
 exome_germline_single_sample_v1.3/
 **/*.pyc
+src/ci/resources/*.temp
 
 # GHA credentials
 gha-creds-*.json
+
+# jenv
+.java-version
diff --git a/project/ContinuousIntegration.scala b/project/ContinuousIntegration.scala
index d5dd3262f87..f0516150cf5 100644
--- a/project/ContinuousIntegration.scala
+++ b/project/ContinuousIntegration.scala
@@ -9,6 +9,8 @@ object ContinuousIntegration {
   lazy val ciSettings: Seq[Setting[_]] = List(
     srcCiResources := sourceDirectory.value / "ci" / "resources",
     targetCiResources := target.value / "ci" / "resources",
+    envFile := srcCiResources.value / "env.temp", //generated by resources/acquire_b2c_token.sh
+
     vaultToken := userHome / ".vault-token",
     copyCiResources := {
       IO.copyDirectory(srcCiResources.value, targetCiResources.value)
@@ -26,7 +28,12 @@ object ContinuousIntegration {
       if (vaultToken.value.isDirectory) {
         sys.error(s"""The vault token file "${vaultToken.value}" should not be a directory.""")
       }
-      val cmd = List(
+
+      // Only include the local file argument if the file exists (local development w/ acquire_b2c_token.sh)
+      // Don't include it otherwise (CI/CD and other development)
+      val localEnvFileArgs = if(envFile.value.exists()) List("-e", s"ENV_FILE=${envFile.value}") else List()
+
+      val cmd: List[String] = List.concat(List(
         "docker",
         "run",
         "--rm",
@@ -35,7 +42,9 @@ object ContinuousIntegration {
         "-v",
         s"${srcCiResources.value}:${srcCiResources.value}",
         "-v",
-        s"${targetCiResources.value}:${targetCiResources.value}",
+        s"${targetCiResources.value}:${targetCiResources.value}"),
+        localEnvFileArgs,
+        List(
         "-e",
         "ENVIRONMENT=not_used",
         "-e",
@@ -44,7 +53,7 @@ object ContinuousIntegration {
         s"OUT_PATH=${targetCiResources.value}",
         "broadinstitute/dsde-toolbox:dev",
         "render-templates.sh"
-      )
+      ))
       val result = cmd ! log
       if (result != 0) {
         sys.error(
@@ -70,6 +79,7 @@ object ContinuousIntegration {
   private val srcCiResources: SettingKey[File] = settingKey[File]("Source directory for CI resources")
   private val targetCiResources: SettingKey[File] = settingKey[File]("Target directory for CI resources")
   private val vaultToken: SettingKey[File] = settingKey[File]("File with the vault token")
+  private val envFile: SettingKey[File] = settingKey[File]("File with the environment variables needed to render CI resources.")
 
   /**
     * For "reasons" these projects are excluded from the root aggregation in build.sbt.
diff --git a/runConfigurations/Repo template_ Cromwell server TES.run.xml b/runConfigurations/Repo template_ Cromwell server TES.run.xml
index 32127027ecc..192b73735b8 100644
--- a/runConfigurations/Repo template_ Cromwell server TES.run.xml	
+++ b/runConfigurations/Repo template_ Cromwell server TES.run.xml	
@@ -19,4 +19,24 @@
       <option name="RunConfigurationTask" enabled="true" run_configuration_name="renderCiResources" run_configuration_type="SbtRunConfiguration" />
     </method>
   </configuration>
+  <configuration default="false" name="Repo template: Cromwell server TES" type="Application" factoryName="Application">
+    <option name="ALTERNATIVE_JRE_PATH" value="$PROJECT_DIR$/../.sdkman/candidates/java/current" />
+    <envs>
+      <env name="CROMWELL_BUILD_CENTAUR_SLICK_PROFILE" value="slick.jdbc.MySQLProfile$" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_DRIVER" value="com.mysql.cj.jdbc.Driver" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_URL" value="jdbc:mysql://localhost:3306/cromwell_test?allowPublicKeyRetrieval=true&amp;useSSL=false&amp;rewriteBatchedStatements=true&amp;serverTimezone=UTC&amp;useInformationSchema=true" />
+      <env name="CROMWELL_BUILD_RESOURCES_DIRECTORY" value="target/ci/resources" />
+      <env name="CROMWELL_BUILD_PAPI_JSON_FILE" value="target/ci/resources/cromwell-centaur-service-account.json" />
+      <env name="CROMWELL_BUILD_CENTAUR_READ_LINES_LIMIT" value="128000" />
+      <env name="CROMWELL_BUILD_CENTAUR_256_BITS_KEY" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA=" />
+    </envs>
+    <option name="MAIN_CLASS_NAME" value="cromwell.CromwellApp" />
+    <module name="cromwell" />
+    <option name="PROGRAM_PARAMETERS" value="server" />
+    <option name="VM_PARAMETERS" value="-Dconfig.file=target/ci/resources/tes_application.conf" />
+    <method v="2">
+      <option name="Make" enabled="true" />
+      <option name="RunConfigurationTask" enabled="false" run_configuration_name="renderCiResources" run_configuration_type="SbtRunConfiguration" />
+    </method>
+  </configuration>
 </component>
\ No newline at end of file
diff --git a/runConfigurations/Repo template_ Cromwell server Terra TES.run.xml b/runConfigurations/Repo template_ Cromwell server Terra TES.run.xml
new file mode 100644
index 00000000000..d5d7ef07b98
--- /dev/null
+++ b/runConfigurations/Repo template_ Cromwell server Terra TES.run.xml	
@@ -0,0 +1,23 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="Repo template: Cromwell server Terra TES" type="Application" factoryName="Application">
+    <option name="ALTERNATIVE_JRE_PATH" value="$PROJECT_DIR$/../.sdkman/candidates/java/current" />
+    <envs>
+      <env name="CROMWELL_BUILD_CENTAUR_SLICK_PROFILE" value="slick.jdbc.MySQLProfile$" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_DRIVER" value="com.mysql.cj.jdbc.Driver" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_URL" value="jdbc:mysql://localhost:3306/cromwell_test?allowPublicKeyRetrieval=true&amp;useSSL=false&amp;rewriteBatchedStatements=true&amp;serverTimezone=UTC&amp;useInformationSchema=true" />
+      <env name="CROMWELL_BUILD_RESOURCES_DIRECTORY" value="target/ci/resources" />
+      <env name="CROMWELL_BUILD_PAPI_JSON_FILE" value="target/ci/resources/cromwell-centaur-service-account.json" />
+      <env name="CROMWELL_BUILD_CENTAUR_READ_LINES_LIMIT" value="128000" />
+      <env name="CROMWELL_BUILD_CENTAUR_256_BITS_KEY" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA=" />
+    </envs>
+    <option name="MAIN_CLASS_NAME" value="cromwell.CromwellApp" />
+    <module name="cromwell" />
+    <option name="PROGRAM_PARAMETERS" value="server" />
+    <option name="VM_PARAMETERS" value="-Dconfig.file=target/ci/resources/terra_tes_application.conf" />
+    <method v="2">
+      <option name="Make" enabled="true" />
+      <option name="ToolBeforeRunTask" enabled="true" actionId="Tool_External Tools_Acquire Google B2C Token" />
+      <option name="RunConfigurationTask" enabled="true" run_configuration_name="renderCiResources" run_configuration_type="SbtRunConfiguration" />
+    </method>
+  </configuration>
+</component>
\ No newline at end of file
diff --git a/src/ci/resources/acquire_b2c_token.sh b/src/ci/resources/acquire_b2c_token.sh
new file mode 100755
index 00000000000..23eb25461c6
--- /dev/null
+++ b/src/ci/resources/acquire_b2c_token.sh
@@ -0,0 +1,42 @@
+#!/bin/bash
+
+# This script acquires a b2c token using gcloud auth and writes it to a file.
+# This file is used by renderCiResources to populate the CROMWELL_B2C_TOKEN in tes_application.conf.
+# It should be run as a "Before Launch" task in IntelliJ so the token is refreshed regularly.
+
+### Setting up this script for the first time in IntelliJ? 
+### 1. Open the "Run/Debug Configurations" dialog for the TES repo template.
+### 2. Add a new "Before Launch" task, selecting "Run External Tool". 
+###    This task should run BEFORE the renderCiResources task.
+### 3. Configure the new task:
+###   - Name: "Acquire b2c token"
+###   - Program: /full/path/to/src/ci/resources/acquire_b2c_token.sh
+###   - Arguments: ./env.temp
+###   - Working directory: /full/path/to/src/ci/resources
+###   - Advanced Options > Uncheck "Synchronize files after execution"
+### 4. Click "OK" to save the new task. Apply and close the "Run/Debug Configurations" dialog.
+
+# User must provide an output file path as an argument.
+# This can be provided by IntelliJ as a program argument in the run configuration.
+if [ -z "$1" ]; then
+    echo "Error: Must specify an output file path for the environment file."
+    exit 1
+fi
+
+# Acquire a b2c token using gcloud auth.
+# Send stderr to /dev/null so that any gcloud auth errors/update prompts don't pollute the token output.
+echo "Using local gcloud auth to acquire a b2c token..."
+B2C_TOKEN=$(gcloud auth print-access-token 2>/dev/null)
+if [ $? -eq 0 ]; then
+    echo "Acquired b2c token: ${B2C_TOKEN:0:4}****"
+else
+    echo "Failed to acquire b2c token. Is your local shell logged into gcloud?"
+fi
+
+# Create the output directory if it doesn't exist
+output_dir=$(dirname "$1")
+mkdir -p "$output_dir"
+
+# Write the token to the output file. dsde-toolbox will call `source` on this file that we're writing, 
+# so it's expected that this file contains valid bash syntax for setting an environment variable.
+echo "export CROMWELL_B2C_TOKEN=${B2C_TOKEN}" > "$1"
diff --git a/src/ci/resources/terra_tes_application.conf.ctmpl b/src/ci/resources/terra_tes_application.conf.ctmpl
new file mode 100644
index 00000000000..92ae72f9e7a
--- /dev/null
+++ b/src/ci/resources/terra_tes_application.conf.ctmpl
@@ -0,0 +1,80 @@
+include required(classpath("application.conf"))
+include "build_application.inc.conf"
+
+filesystems {
+    blob {
+        class = "cromwell.filesystems.blob.BlobPathBuilderFactory"
+        global {
+            class = "cromwell.filesystems.blob.BlobFileSystemManager"
+            config {
+                workspace-manager: {
+                    # static: Where is WSM Endpoint
+                    url: "https://workspace.dsde-dev.broadinstitute.org"
+                    # See comment in src/ci/resources/acquire_b2c_token.sh for the one-time setup required to automatically acquire this.
+                    # This token can also be manually acquired with gcloud auth print-access-token myAccount@gmail.com
+                    b2cToken: "{{ env "CROMWELL_B2C_TOKEN" }}"
+                }
+            }
+        }
+    }
+}
+
+engine {
+  filesystems {
+    local {
+      enabled: true
+    }
+    http {
+      enabled: true
+    }
+    blob {
+      enabled: true
+    }
+  }
+}
+
+
+backend {
+  default = "TES"
+  providers {
+    TES {
+      actor-factory = "cromwell.backend.impl.tes.TesBackendLifecycleActorFactory"
+      config {
+        # Root of a blob storage container to use
+        # Might look something like: https://lz813a3d637adefec2c6e88f.blob.core.windows.net/sc-d8143fd8-aa07-446d-9ba0-af72203f1794/some/path/"
+        root = ""
+        dockerRoot = "/cromwell-executions"
+        # TES Endpoint for cromwell to use. Might look something like: "https://lz7388ada396994bb48ea5c87a02eed673689c82c2af423d03.servicebus.windows.net/something/tes/v1/tasks
+        endpoint = ""
+        concurrent-job-limit = 1000
+        # Identity to execute the workflow as. Might look something like: "pet-2676571657071603a9eab"
+        workflow-execution-identity = ""
+        # See comment in src/ci/resources/acquire_b2c_token.sh for the one-time setup required to automatically acquire this.
+        # This token can also be manually acquired with gcloud auth print-access-token myAccount@gmail.com
+        bearer-token="Bearer {{ env "CROMWELL_B2C_TOKEN" }}"
+        # Override default polling to make it faster for speedy tests
+        poll-backoff {
+          min: "10 seconds"
+          max: "5 minutes"
+          multiplier: 1.1
+          randomization-factor: 0.5
+        }
+
+        filesystems {
+          blob {
+            enabled: true
+          }
+          local {
+            enabled: false
+          }
+          http {
+            enabled: true
+          }
+        }
+      }
+
+      # Have the engine (maybe) authenticate to docker.io. See BT-141 for more info.
+      include "dockerhub_provider_config_v1.inc.conf"
+    }
+  }
+}
diff --git a/src/ci/resources/tes_application.conf b/src/ci/resources/tes_application.conf
index 5eb812a52d4..29982575eab 100644
--- a/src/ci/resources/tes_application.conf
+++ b/src/ci/resources/tes_application.conf
@@ -2,26 +2,12 @@ include required(classpath("application.conf"))
 include "build_application.inc.conf"
 
 filesystems {
-  blob {
-    class = "cromwell.filesystems.blob.BlobPathBuilderFactory"
-    global {
-      # One BFSM is shared across all BlobPathBuilders
-      class = "cromwell.filesystems.blob.BlobFileSystemManager"
-      config {
-        container: "cromwell"
-        endpoint: "https://<storage-account>.blob.core.windows.net"
-        subscription: "00001111-2222-3333-aaaa-bbbbccccdddd"
-        # WSM config is needed for accessing WSM-managed blob containers
-        # created in Terra workspaces.
-        workspace-manager {
-          url: "https://workspace.dsde-dev.broadinstitute.org"
-          workspace-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
-          container-resource-id: "00001111-2222-3333-aaaa-bbbbccccdddd"
-          b2cToken: "Zardoz"
+    blob {
+        class = "cromwell.filesystems.blob.BlobPathBuilderFactory"
+        global {
+            class = "cromwell.filesystems.blob.BlobFileSystemManager"
         }
-      }
     }
-  }
 }
 
 engine {
@@ -33,7 +19,7 @@ engine {
       enabled: true
     }
     blob {
-      enabled: false
+      enabled: true
     }
   }
 }
@@ -45,27 +31,29 @@ backend {
     TES {
       actor-factory = "cromwell.backend.impl.tes.TesBackendLifecycleActorFactory"
       config {
-        # Use for running on blob storage
-        #root = "https://<storage-account>.blob.core.windows.net/cromwell/cromwell-executions"
-        root = "cromwell-executions"
+        # Root of a blob storage container to use
+        # Might look something like: https://lz813a3d637adefec2c6e88f.blob.core.windows.net/sc-d8143fd8-aa07-446d-9ba0-af72203f1794/some/path/"
+        root = ""
         dockerRoot = "/cromwell-executions"
+        # TES Endpoint for cromwell to use. Might look something like: "https://lz7388ada396994bb48ea5c87a02eed673689c82c2af423d03.servicebus.windows.net/something/tes/v1/tasks
         endpoint = "http://127.0.0.1:9000/v1/tasks"
         concurrent-job-limit = 1000
-
+        # Identity to execute the workflow as. Might look something like: "pet-2676571657071603a9eab"
+        workflow-execution-identity = ""
         # Override default polling to make it faster for speedy tests
         poll-backoff {
-          min: "1 seconds"
+          min: "10 seconds"
           max: "5 minutes"
           multiplier: 1.1
           randomization-factor: 0.5
         }
-        
+
         filesystems {
           blob {
-            enabled: false
+            enabled: true
           }
           local {
-            enabled: true
+            enabled: false
           }
           http {
             enabled: true

From 9c6c43978b72d08996ba183d38120a6b97d0e770 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Thu, 7 Dec 2023 13:47:29 -0500
Subject: [PATCH 251/326] WX-1387 Remove unused case classes (#7334)

---
 .../cromwell/filesystems/blob/BlobPathBuilderFactory.scala     | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
index 2dafa6ab5d2..faa04481316 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilderFactory.scala
@@ -27,8 +27,7 @@ final case class EndpointURL(value: String) {
     sa.toRight(new Exception(s"Storage account name could not be parsed from $value")).toTry
   }
 }
-final case class WorkspaceId(value: UUID) { override def toString: String = value.toString }
-final case class ContainerResourceId(value: UUID) { override def toString: String = value.toString }
+
 final case class WorkspaceManagerURL(value: String) { override def toString: String = value }
 
 final case class BlobPathBuilderFactory(globalConfig: Config, instanceConfig: Config, fsm: BlobFileSystemManager)

From 41ccbc8aa35df0915f84fab05b315e9d2c16893d Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 8 Dec 2023 10:09:25 -0500
Subject: [PATCH 252/326] [WX-1394] Upgrade Logback Core to address
 CVE-2023-6378 (#7332)

---
 project/Dependencies.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 2bc4ec34f00..44dacb56dc7 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -78,7 +78,7 @@ object Dependencies {
   private val kindProjectorV = "0.13.2"
   private val kittensV = "2.3.2"
   private val liquibaseV = "4.8.0"
-  private val logbackV = "1.2.11"
+  private val logbackV = "1.2.13"
   private val lz4JavaV = "1.8.0"
   private val mariadbV = "2.7.4"
   /*

From f9f68474e88adb9d4902080262df2c4677c55446 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 8 Dec 2023 12:02:51 -0500
Subject: [PATCH 253/326] WX-1351 Another round of CI cleanup (#7336)

---
 src/ci/bin/test.inc.sh                        | 381 +-----------------
 .../testCentaurEngineUpgradePapiV2alpha1.sh   |  24 --
 ...aurHoricromtalEngineUpgradePapiV2alpha1.sh |  26 --
 .../bin/testCentaurHoricromtalPapiV2alpha1.sh |  29 --
 .../bin/testCentaurHoricromtalPapiV2beta.sh   |   2 +
 ...taurPapiUpgradeNewWorkflowsPapiV2alpha1.sh |   4 -
 .../bin/testCentaurPapiUpgradePapiV2alpha1.sh |   3 -
 src/ci/bin/testCentaurPapiV2alpha1.sh         |  27 --
 src/ci/bin/testCentaurPapiV2beta.sh           |   2 +
 src/ci/bin/testDockerScripts.sh               |  27 --
 src/ci/bin/testMetadataComparisonPython.sh    |  34 --
 src/ci/bin/test_gcpbatch.inc.sh               |   8 -
 src/ci/bin/test_papi.inc.sh                   |   9 +-
 src/ci/bin/test_unit.inc.sh                   |  12 -
 .../papi_v1_v2alpha1_provider_config.inc.conf |  20 -
 .../resources/papi_v2alpha1_application.conf  |  81 ----
 ...v2alpha1_conformance_expected_failures.txt |  29 --
 ...papi_v2alpha1_horicromtal_application.conf |   9 -
 ...i_v2alpha1_v2beta_upgrade_application.conf |  32 --
 19 files changed, 12 insertions(+), 747 deletions(-)
 delete mode 100755 src/ci/bin/testCentaurEngineUpgradePapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testCentaurHoricromtalEngineUpgradePapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testCentaurHoricromtalPapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testCentaurPapiUpgradeNewWorkflowsPapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testCentaurPapiUpgradePapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testCentaurPapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testDockerScripts.sh
 delete mode 100755 src/ci/bin/testMetadataComparisonPython.sh
 delete mode 100644 src/ci/resources/papi_v1_v2alpha1_provider_config.inc.conf
 delete mode 100644 src/ci/resources/papi_v2alpha1_application.conf
 delete mode 100644 src/ci/resources/papi_v2alpha1_conformance_expected_failures.txt
 delete mode 100644 src/ci/resources/papi_v2alpha1_horicromtal_application.conf
 delete mode 100644 src/ci/resources/papi_v2alpha1_v2beta_upgrade_application.conf

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 6f76ee8c05c..71577ce1e4c 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -45,54 +45,14 @@ cromwell::private::check_debug() {
     fi
 }
 
-cromwell::private::set_variable_if_only_some_files_changed() {
-  files_changed_regex=${1}
-  variable_to_set=${2}
-
-    if [[ "${TRAVIS_EVENT_TYPE:-unset}" != "pull_request" ]]; then
-        export "${variable_to_set}=false"
-    else
-      # Large changesets seem to trigger the situation described in [1] where a `git diff` pipelined to `grep` can cause
-      # `grep` to exit 0 on the first match while `git diff` is still writing to the pipe. When this happens `git diff`
-      # is killed with a SIGPIPE and exits with code 141. With `set -o pipefail` this causes the entire pipeline to exit
-      # with code 141, which sets `$variable_to_set` to `true` when it probably should have been set to `false`.
-      #
-      # Instead of composing these commands into a pipeline write to a temporary file.
-      #
-      # [1] https://stackoverflow.com/a/19120674
-      # [2] https://gist.github.com/mohanpedala/1e2ff5661761d3abd0385e8223e16425#set--o-pipefail
-
-      files_changed_temporary_file=$(mktemp)
-
-      git diff --name-only "origin/${TRAVIS_BRANCH}" > "${files_changed_temporary_file}" 2>&1 && \
-          grep -E -q --invert-match "${files_changed_regex}" "${files_changed_temporary_file}"
-      RESULT=$?
-
-      if [[ $RESULT -eq 0 ]]; then
-        export "${variable_to_set}=false"
-      else
-        export "${variable_to_set}=true"
-      fi
-
-      rm "${files_changed_temporary_file}"
-    fi
-}
-
 # Exports environment variables used for scripts.
 cromwell::private::create_build_variables() {
-    CROMWELL_BUILD_PROVIDER_TRAVIS="travis"
-    CROMWELL_BUILD_PROVIDER_JENKINS="jenkins"
-    CROMWELL_BUILD_PROVIDER_CIRCLE="circle"
     CROMWELL_BUILD_PROVIDER_GITHUB="github"
     CROMWELL_BUILD_PROVIDER_UNKNOWN="unknown"
 
-    if [[ "${TRAVIS-false}" == "true" ]]; then
-        CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_TRAVIS}"
-    elif [[ "${JENKINS-false}" == "true" ]]; then
-        CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_JENKINS}"
-    elif [[ "${CIRCLECI-false}" == "true" ]]; then
-        CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_CIRCLE}"
-    elif [[ "${GITHUB_ACTIONS-false}" == "true" ]]; then
+    # CI providers set an env like `GITHUB_ACTIONS` that indicates to jobs where they're running
+    # https://docs.github.com/en/actions/learn-github-actions/variables#default-environment-variables
+    if [[ "${GITHUB_ACTIONS-false}" == "true" ]]; then
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_GITHUB}"
     else
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_UNKNOWN}"
@@ -157,155 +117,13 @@ cromwell::private::create_build_variables() {
         CROMWELL_BUILD_GIT_HASH_SUFFIX="gUNKNOWN"
     fi
 
-    # Value of the `TRAVIS_BRANCH` variable depends on type of Travis build: if it is pull request build, the value
-    # will be the name of the branch targeted by the pull request, and for push builds it will be the name of the
-    # branch. So, in case of push builds `git diff` will always return empty result. This is why we only use this short
-    # circuiting logic for pull request builds
-
     # PR #6790 disabled the conditional that skips tests for documentation-only PRs, because
     # those PRs (and only those PRs) were uniformly failing tests with a nondescript error.
     # https://broadinstitute.slack.com/archives/GHYJZ2ZE0/p1656625952888149?thread_ts=1656620572.975059&cid=GHYJZ2ZE0
 
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
-            CROMWELL_BUILD_IS_CI=true
-            CROMWELL_BUILD_IS_SECURE="${TRAVIS_SECURE_ENV_VARS}"
-
-            CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
-            CROMWELL_BUILD_BRANCH="${TRAVIS_PULL_REQUEST_BRANCH:-${TRAVIS_BRANCH}}"
-            CROMWELL_BUILD_EVENT="${TRAVIS_EVENT_TYPE}"
-            CROMWELL_BUILD_TAG="${TRAVIS_TAG}"
-            CROMWELL_BUILD_NUMBER="${TRAVIS_JOB_NUMBER}"
-            CROMWELL_BUILD_URL="https://travis-ci.com/${TRAVIS_REPO_SLUG}/jobs/${TRAVIS_JOB_ID}"
-            CROMWELL_BUILD_GIT_USER_EMAIL="travis@travis-ci.com"
-            CROMWELL_BUILD_GIT_USER_NAME="Travis CI"
-            CROMWELL_BUILD_HEARTBEAT_PATTERN="…"
-            CROMWELL_BUILD_GENERATE_COVERAGE=true
-
-            local travis_commit_message
-            local travis_force_tests
-            local travis_minimal_tests
-            if [[ -n "${TRAVIS_COMMIT_RANGE:+set}" ]]; then
-                # The commit message to analyze should be the last one in the commit range.
-                # This works for both pull_request and push builds, unlike using 'git log HEAD' which
-                # gives a merge commit message on pull requests.
-                travis_commit_message="$(git log --reverse "${TRAVIS_COMMIT_RANGE}" | tail -n1 2>/dev/null || true)"
-            fi
-
-            if [[ -z "${travis_commit_message:-}" ]]; then
-                travis_commit_message="$(git log --format=%B --max-count=1 HEAD 2>/dev/null || true)"
-            fi
-
-            if [[ "${travis_commit_message}" == *"[force ci]"* ]]; then
-                travis_force_tests=true
-                travis_minimal_tests=false
-            elif [[ "${travis_commit_message}" == *"[minimal ci]"* ]]; then
-                travis_force_tests=false
-                travis_minimal_tests=true
-            else
-                travis_force_tests=false
-                travis_minimal_tests=false
-            fi
-
-            echo "Building for commit message='${travis_commit_message}' with force=${travis_force_tests} and minimal=${travis_minimal_tests}"
-
-            # For solely documentation updates run only checkPublish. Otherwise always run sbt, even for 'push'.
-            # This allows quick sanity checks before starting PRs *and* publishing after merges into develop.
-            if [[ "${travis_force_tests}" == "true" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=true
-            elif [[ "${travis_minimal_tests}" == "true" ]] && \
-                [[ "${TRAVIS_EVENT_TYPE}" != "push" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=false
-            elif [[ "${TRAVIS_EVENT_TYPE}" == "push" ]] && \
-                [[ "${BUILD_TYPE}" != "sbt" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=false
-            else
-                CROMWELL_BUILD_RUN_TESTS=true
-            fi
-            ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            # External variables must be passed through in the ENVIRONMENT of src/ci/docker-compose/docker-compose.yml
-            CROMWELL_BUILD_IS_CI=true
-            CROMWELL_BUILD_IS_SECURE=true
-            CROMWELL_BUILD_TYPE="${JENKINS_BUILD_TYPE}"
-            CROMWELL_BUILD_BRANCH="${GIT_BRANCH#origin/}"
-            CROMWELL_BUILD_EVENT=""
-            CROMWELL_BUILD_TAG=""
-            CROMWELL_BUILD_NUMBER="${BUILD_NUMBER}"
-            CROMWELL_BUILD_URL="${BUILD_URL}"
-            CROMWELL_BUILD_GIT_USER_EMAIL="jenkins@jenkins.io"
-            CROMWELL_BUILD_GIT_USER_NAME="Jenkins CI"
-            CROMWELL_BUILD_HEARTBEAT_PATTERN="…\n"
-            CROMWELL_BUILD_GENERATE_COVERAGE=false
-            CROMWELL_BUILD_RUN_TESTS=true
-            ;;
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}")
-            CROMWELL_BUILD_IS_CI=true
-            CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
-            CROMWELL_BUILD_NUMBER="${CIRCLE_BUILD_NUM}"
-            CROMWELL_BUILD_URL="${CIRCLE_BUILD_URL}"
-            CROMWELL_BUILD_GIT_USER_EMAIL="builds@circleci.com"
-            CROMWELL_BUILD_GIT_USER_NAME="CircleCI"
-            CROMWELL_BUILD_HEARTBEAT_PATTERN="…"
-            CROMWELL_BUILD_GENERATE_COVERAGE=true
-            CROMWELL_BUILD_BRANCH="${CIRCLE_BRANCH:-${CIRCLE_TAG}}"
-            CROMWELL_BUILD_TAG="${CIRCLE_TAG:-}"
-
-            local circle_github_repository
-            circle_github_repository="${CIRCLE_PROJECT_USERNAME}/${CIRCLE_PROJECT_REPONAME}"
-
-            if [[ "${circle_github_repository}" == "broadinstitute/cromwell" ]]; then
-                CROMWELL_BUILD_IS_SECURE=true
-            else
-                CROMWELL_BUILD_IS_SECURE=false
-            fi
-
-            CROMWELL_BUILD_EVENT="pull_request"
-
-            local circle_commit_message
-            local circle_force_tests
-            local circle_minimal_tests
-            if [[ -n "${CIRCLE_COMMIT_RANGE:+set}" ]]; then
-                # The commit message to analyze should be the last one in the commit range.
-                # This works for both pull_request and push builds, unlike using 'git log HEAD' which
-                # gives a merge commit message on pull requests.
-                circle_commit_message="$(git log --reverse "${CIRCLE_COMMIT_RANGE}" | tail -n1 2>/dev/null || true)"
-            fi
-
-            if [[ -z "${circle_commit_message:-}" ]]; then
-                circle_commit_message="$(git log --format=%B --max-count=1 HEAD 2>/dev/null || true)"
-            fi
-
-            if [[ "${circle_commit_message}" == *"[force ci]"* ]]; then
-                circle_force_tests=true
-                circle_minimal_tests=false
-            elif [[ "${circle_commit_message}" == *"[minimal ci]"* ]]; then
-                circle_force_tests=false
-                circle_minimal_tests=true
-            else
-                circle_force_tests=false
-                circle_minimal_tests=false
-            fi
-
-            echo "Building for commit message='${circle_commit_message}' with force=${circle_force_tests} and minimal=${circle_minimal_tests}"
-
-            # For solely documentation updates run only checkPublish. Otherwise always run sbt, even for 'push'.
-            # This allows quick sanity checks before starting PRs *and* publishing after merges into develop.
-            if [[ "${circle_force_tests}" == "true" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=true
-            elif [[ "${circle_minimal_tests}" == "true" ]] && \
-                [[ "${CROMWELL_BUILD_EVENT}" != "push" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=false
-            elif [[ "${CROMWELL_BUILD_EVENT}" == "push" ]] && \
-                [[ "${BUILD_TYPE}" != "sbt" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=false
-            else
-                CROMWELL_BUILD_RUN_TESTS=true
-            fi
-            ;;
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             CROMWELL_BUILD_IS_CI=true
-            CROMWELL_BUILD_IS_SECURE=true
             CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
             CROMWELL_BUILD_BRANCH="${GITHUB_REF_NAME}"
             CROMWELL_BUILD_EVENT="${GITHUB_EVENT_NAME}"
@@ -320,7 +138,6 @@ cromwell::private::create_build_variables() {
             ;;
         *)
             CROMWELL_BUILD_IS_CI=false
-            CROMWELL_BUILD_IS_SECURE=true
             CROMWELL_BUILD_TYPE="unknown"
             CROMWELL_BUILD_BRANCH="unknown"
             CROMWELL_BUILD_EVENT="unknown"
@@ -371,21 +188,9 @@ cromwell::private::create_build_variables() {
     CROMWELL_BUILD_SBT_EXCLUDE="${BUILD_SBT_EXCLUDE:-}"
 
     case "${CROMWELL_BUILD_TYPE}" in
-        centaurPapiUpgradePapiV2alpha1*)
-            CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2alpha1_v2beta_upgrade_application.conf"
-            ;;
-        centaurPapiUpgradeNewWorkflowsPapiV2alpha1*)
-            CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2alpha1_v2beta_upgrade_application.conf"
-            ;;
-        centaurHoricromtalPapiV2alpha1*)
-            CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2alpha1_horicromtal_application.conf"
-            ;;
         centaurHoricromtalPapiV2beta*)
             CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2beta_horicromtal_application.conf"
             ;;
-        centaurHoricromtalEngineUpgrade*)
-            CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2alpha1_horicromtal_application.conf"
-            ;;
         centaurBlob*)
             CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/centaur_blob_test.conf"
             ;;
@@ -405,7 +210,6 @@ cromwell::private::create_build_variables() {
     CROMWELL_BUILD_DOCKER_TAG="${CROMWELL_BUILD_DOCKER_TAG:0:128}"
     CROMWELL_BUILD_DOCKER_TAG="${CROMWELL_BUILD_DOCKER_TAG//[^a-zA-Z0-9.-]/_}"
 
-    CROMWELL_BUILD_REQUIRES_SECURE="${CROMWELL_BUILD_REQUIRES_SECURE-false}"
     CROMWELL_BUILD_REQUIRES_PRIOR_VERSION="${CROMWELL_BUILD_REQUIRES_PRIOR_VERSION-false}"
 
     local hours_to_minutes
@@ -432,7 +236,6 @@ cromwell::private::create_build_variables() {
     export CROMWELL_BUILD_HOME_DIRECTORY
     export CROMWELL_BUILD_IS_CI
     export CROMWELL_BUILD_IS_HOTFIX
-    export CROMWELL_BUILD_IS_SECURE
     export CROMWELL_BUILD_IS_VIRTUAL_ENV
     export CROMWELL_BUILD_LOG_DIRECTORY
     export CROMWELL_BUILD_NUMBER
@@ -441,9 +244,6 @@ cromwell::private::create_build_variables() {
     export CROMWELL_BUILD_OS_LINUX
     export CROMWELL_BUILD_PRIOR_VERSION_NUMBER
     export CROMWELL_BUILD_PROVIDER
-    export CROMWELL_BUILD_PROVIDER_CIRCLE
-    export CROMWELL_BUILD_PROVIDER_JENKINS
-    export CROMWELL_BUILD_PROVIDER_TRAVIS
     export CROMWELL_BUILD_PROVIDER_UNKNOWN
     export CROMWELL_BUILD_REQUIRES_PRIOR_VERSION
     export CROMWELL_BUILD_REQUIRES_SECURE
@@ -470,8 +270,6 @@ cromwell::private::create_build_variables() {
 
 cromwell::private::echo_build_variables() {
     echo "CROMWELL_BUILD_IS_CI='${CROMWELL_BUILD_IS_CI}'"
-    echo "CROMWELL_BUILD_IS_SECURE='${CROMWELL_BUILD_IS_SECURE}'"
-    echo "CROMWELL_BUILD_REQUIRES_SECURE='${CROMWELL_BUILD_REQUIRES_SECURE}'"
     echo "CROMWELL_BUILD_TYPE='${CROMWELL_BUILD_TYPE}'"
     echo "CROMWELL_BUILD_BRANCH='${CROMWELL_BUILD_BRANCH}'"
     echo "CROMWELL_BUILD_IS_HOTFIX='${CROMWELL_BUILD_IS_HOTFIX}'"
@@ -492,8 +290,6 @@ cromwell::private::create_database_variables() {
     CROMWELL_BUILD_DATABASE_SCHEMA="cromwell_test"
 
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}"|\
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}"|\
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             CROMWELL_BUILD_MARIADB_HOSTNAME="localhost"
             CROMWELL_BUILD_MARIADB_PORT="23306"
@@ -514,29 +310,6 @@ cromwell::private::create_database_variables() {
             CROMWELL_BUILD_POSTGRESQL_LATEST_PORT="15432"
             CROMWELL_BUILD_POSTGRESQL_LATEST_TAG="${BUILD_POSTGRESQL_LATEST-}"
             ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            # NOTE: Jenkins uses src/ci/docker-compose/docker-compose.yml.
-            # We don't define a docker tag because the docker-compose has already spun up the database containers by the
-            # time this script is run. Other variables here must match the database service names and settings the yaml.
-            CROMWELL_BUILD_MARIADB_HOSTNAME="mariadb-db"
-            CROMWELL_BUILD_MARIADB_PORT="3306"
-            CROMWELL_BUILD_MARIADB_DOCKER_TAG=""
-            CROMWELL_BUILD_MARIADB_LATEST_HOSTNAME="mariadb-db-latest"
-            CROMWELL_BUILD_MARIADB_LATEST_PORT="3306"
-            CROMWELL_BUILD_MARIADB_LATEST_TAG=""
-            CROMWELL_BUILD_MYSQL_HOSTNAME="mysql-db"
-            CROMWELL_BUILD_MYSQL_PORT="3306"
-            CROMWELL_BUILD_MYSQL_DOCKER_TAG=""
-            CROMWELL_BUILD_MYSQL_LATEST_HOSTNAME="mysql-db-latest"
-            CROMWELL_BUILD_MYSQL_LATEST_PORT="3306"
-            CROMWELL_BUILD_MYSQL_LATEST_TAG=""
-            CROMWELL_BUILD_POSTGRESQL_HOSTNAME="postgresql-db"
-            CROMWELL_BUILD_POSTGRESQL_PORT="5432"
-            CROMWELL_BUILD_POSTGRESQL_DOCKER_TAG=""
-            CROMWELL_BUILD_POSTGRESQL_LATEST_HOSTNAME="postgresql-db-latest"
-            CROMWELL_BUILD_POSTGRESQL_LATEST_PORT="3306"
-            CROMWELL_BUILD_POSTGRESQL_LATEST_TAG=""
-            ;;
         *)
             if [[ -z "${CROMWELL_BUILD_DOCKER_LOCALHOST-}" ]]; then
                 CROMWELL_BUILD_DOCKER_LOCALHOST="localhost"
@@ -654,8 +427,6 @@ cromwell::private::create_centaur_variables() {
 
     # Pick **one** of the databases to run Centaur against
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}"|\
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}"|\
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
 
             if [[ -n "${CROMWELL_BUILD_MYSQL_DOCKER_TAG:+set}" ]]; then
@@ -681,12 +452,6 @@ cromwell::private::create_centaur_variables() {
 
             CROMWELL_BUILD_CENTAUR_TEST_ADDITIONAL_PARAMETERS=
             ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            CROMWELL_BUILD_CENTAUR_SLICK_PROFILE="slick.jdbc.MySQLProfile$"
-            CROMWELL_BUILD_CENTAUR_JDBC_DRIVER="com.mysql.cj.jdbc.Driver"
-            CROMWELL_BUILD_CENTAUR_JDBC_URL="${mysql_jdbc_url}"
-            CROMWELL_BUILD_CENTAUR_TEST_ADDITIONAL_PARAMETERS="${CENTAUR_TEST_ADDITIONAL_PARAMETERS-}"
-            ;;
         *)
             CROMWELL_BUILD_CENTAUR_SLICK_PROFILE="${CROMWELL_BUILD_CENTAUR_SLICK_PROFILE-slick.jdbc.MySQLProfile\$}"
             CROMWELL_BUILD_CENTAUR_JDBC_DRIVER="${CROMWELL_BUILD_CENTAUR_JDBC_DRIVER-com.mysql.cj.jdbc.Driver}"
@@ -706,19 +471,9 @@ cromwell::private::create_centaur_variables() {
             ;;
     esac
 
-    # When upgrading to the MariaDB driver, start with MySQL then switch to MariaDB.
-    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_TRAVIS}" ]] && \
-        [[ -n "${CROMWELL_BUILD_MARIADB_DOCKER_TAG:+set}" ]]; then
-
-        CROMWELL_BUILD_CENTAUR_PRIOR_SLICK_PROFILE="slick.jdbc.MySQLProfile$"
-        CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_DRIVER="com.mysql.cj.jdbc.Driver"
-        CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_URL="jdbc:mysql://${CROMWELL_BUILD_MARIADB_HOSTNAME}:${CROMWELL_BUILD_MARIADB_PORT}/${CROMWELL_BUILD_DATABASE_SCHEMA}?allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true&serverTimezone=UTC&useInformationSchema=true"
-    else
-
-        CROMWELL_BUILD_CENTAUR_PRIOR_SLICK_PROFILE="${CROMWELL_BUILD_CENTAUR_PRIOR_SLICK_PROFILE-${CROMWELL_BUILD_CENTAUR_SLICK_PROFILE}}"
-        CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_DRIVER="${CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_DRIVER-${CROMWELL_BUILD_CENTAUR_JDBC_DRIVER}}"
-        CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_URL="${CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_URL-${CROMWELL_BUILD_CENTAUR_JDBC_URL}}"
-    fi
+    CROMWELL_BUILD_CENTAUR_PRIOR_SLICK_PROFILE="${CROMWELL_BUILD_CENTAUR_PRIOR_SLICK_PROFILE-${CROMWELL_BUILD_CENTAUR_SLICK_PROFILE}}"
+    CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_DRIVER="${CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_DRIVER-${CROMWELL_BUILD_CENTAUR_JDBC_DRIVER}}"
+    CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_URL="${CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_URL-${CROMWELL_BUILD_CENTAUR_JDBC_URL}}"
 
     CROMWELL_BUILD_CENTAUR_256_BITS_KEY="$(dd bs=1 count=32 if=/dev/urandom 2> /dev/null | base64 | tr -d '\n')"
 
@@ -743,38 +498,12 @@ cromwell::private::create_centaur_variables() {
     export CROMWELL_BUILD_DOCKER_TAG
 }
 
-cromwell::private::verify_secure_build() {
-    case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
-            if [[ "${CROMWELL_BUILD_IS_SECURE}" != "true" ]] && \
-                [[ "${CROMWELL_BUILD_REQUIRES_SECURE}" == "true" ]]; then
-                echo "********************************************************"
-                echo "********************************************************"
-                echo "**                                                    **"
-                echo "**  WARNING: Encrypted keys are unavailable. Exiting. **"
-                echo "**                                                    **"
-                echo "********************************************************"
-                echo "********************************************************"
-                exit 0
-            fi
-            ;;
-        *)
-            ;;
-    esac
-}
-
 cromwell::private::exec_test_script() {
     local upper_build_type
     upper_build_type="$(tr '[:lower:]' '[:upper:]' <<< "${CROMWELL_BUILD_TYPE:0:1}")${CROMWELL_BUILD_TYPE:1}"
     exec "${CROMWELL_BUILD_SCRIPTS_DIRECTORY}/test${upper_build_type}.sh"
 }
 
-cromwell::private::stop_travis_defaults() {
-  # https://stackoverflow.com/questions/27382295/how-to-stop-services-on-travis-ci-running-by-default#answer-27410479
-  sudo /etc/init.d/mysql stop || true
-  sudo /etc/init.d/postgresql stop || true
-}
-
 cromwell::private::delete_boto_config() {
     # https://github.com/travis-ci/travis-ci/issues/7940#issuecomment-310759657
     sudo rm -f /etc/boto.cfg
@@ -788,30 +517,6 @@ cromwell::private::delete_sbt_boot() {
     rm -rf ~/.sbt/boot/
 }
 
-cromwell::private::install_adoptopenjdk() {
-    # https://adoptopenjdk.net/installation.html#linux-pkg-deb
-    sudo apt-get install -y wget apt-transport-https gnupg
-    wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public |
-        sudo apt-key add -
-    echo "deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(
-            grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
-        ) main" |
-        sudo tee /etc/apt/sources.list.d/adoptopenjdk.list
-    sudo apt-get update
-    sudo apt-get install -y adoptopenjdk-11-hotspot
-    sudo update-java-alternatives --set adoptopenjdk-11-hotspot-amd64
-}
-
-cromwell::private::install_sbt_launcher() {
-    # Install sbt launcher
-    # Non-deb package installation instructions adapted from
-    # - https://github.com/sbt/sbt/releases/tag/v1.4.9
-    # - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-    curl --location --fail --silent --show-error "https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz" |
-        sudo tar zxf - -C /usr/share
-    sudo update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1
-}
-
 cromwell::private::install_docker_compose() {
     # Install or upgrade docker-compose so that we get the correct exit codes
     # https://docs.docker.com/compose/release-notes/#1230
@@ -824,12 +529,6 @@ cromwell::private::install_docker_compose() {
     sudo chmod +x /usr/local/bin/docker-compose
 }
 
-cromwell::private::setup_pyenv_python_latest() {
-    # Make `python` whatever the most recent version of python installed
-    # Fixes cases where someone has set pyenv to override `python` to use an older `python2` instead of `python3`
-    pyenv global "$(pyenv versions --bare --skip-aliases | sort -t '.' -k1,1n -k2,2n -k3,3n | tail -n 1)"
-}
-
 cromwell::private::pip_install() {
     local pip_package
     pip_package="${1:?pip_install called without a package}"; shift
@@ -1066,27 +765,7 @@ cromwell::private::render_secure_resources() {
     fi
 }
 
-cromwell::private::copy_all_resources() {
-    # Only copy the CI resources. Secure resources are not rendered.
-    sbt -Dsbt.supershell=false --warn copyCiResources
-}
-
-cromwell::private::setup_secure_resources() {
-    case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            # Jenkins secret resources should have already been rendered outside the CI's docker-compose container.
-            cromwell::private::copy_all_resources
-            ;;
-        *)
-            cromwell::private::render_secure_resources
-            ;;
-    esac
-}
-
 cromwell::private::make_build_directories() {
-    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_JENKINS}" ]]; then
-        sudo chmod -R a+w .
-    fi
     mkdir -p "${CROMWELL_BUILD_LOG_DIRECTORY}"
     mkdir -p "${CROMWELL_BUILD_RESOURCES_DIRECTORY}"
 }
@@ -1269,7 +948,6 @@ cromwell::build::setup_common_environment() {
     cromwell::private::check_debug
     cromwell::private::create_build_variables
     cromwell::private::echo_build_variables
-    cromwell::private::verify_secure_build
     cromwell::private::make_build_directories
     cromwell::private::install_git_secrets
     cromwell::private::install_minnie_kenny
@@ -1277,31 +955,6 @@ cromwell::build::setup_common_environment() {
     cromwell::private::create_database_variables
 
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
-            cromwell::private::stop_travis_defaults
-            # Try to login to vault, and if successful then use vault creds to login to docker.
-            # For those committers with vault access this avoids pull rate limits reported in BT-143.
-            cromwell::private::install_vault
-            cromwell::private::login_vault
-            cromwell::private::login_docker
-            cromwell::private::install_adoptopenjdk
-            cromwell::private::install_sbt_launcher
-            cromwell::private::install_docker_compose
-            cromwell::private::delete_boto_config
-            cromwell::private::delete_sbt_boot
-            cromwell::private::upgrade_pip
-            cromwell::private::start_docker_databases
-            ;;
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}")
-            # Try to login to vault, and if successful then use vault creds to login to docker.
-            # For those committers with vault access this avoids pull rate limits reported in BT-143.
-            cromwell::private::install_vault
-            cromwell::private::login_vault
-            cromwell::private::login_docker
-            cromwell::private::install_adoptopenjdk
-            cromwell::private::setup_pyenv_python_latest
-            cromwell::private::start_docker_databases
-            ;;
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             # Try to login to vault, and if successful then use vault creds to login to docker.
             # For those committers with vault access this avoids pull rate limits reported in BT-143.
@@ -1317,12 +970,11 @@ cromwell::build::setup_common_environment() {
             cromwell::private::upgrade_pip
             cromwell::private::start_docker_databases
             ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}"|\
         *)
             ;;
     esac
 
-    cromwell::private::setup_secure_resources
+    cromwell::private::render_secure_resources
     cromwell::private::start_build_heartbeat
 }
 
@@ -1504,25 +1156,6 @@ cromwell::build::print_workflow_statistics() {
             LIMIT 20;"
 }
 
-cromwell::build::exec_retry_function() {
-    local retried_function
-    local retry_count
-    local attempt
-    local exit_status
-
-    retried_function="${1:?exec_retry_function called without a function}"; shift
-    retry_count="${1:-3}"; shift || true
-    sleep_seconds="${1:-15}"; shift || true
-
-    # https://unix.stackexchange.com/a/82610
-    # https://stackoverflow.com/a/17336953
-    for attempt in $(seq 0 "${retry_count}"); do
-        [[ ${attempt} -gt 0 ]] && sleep "${sleep_seconds}"
-        ${retried_function} && exit_status=0 && break || exit_status=$?
-    done
-    return ${exit_status}
-}
-
 cromwell::build::exec_silent_function() {
     local silent_function
     silent_function="${1:?exec_silent_function called without a function}"; shift
diff --git a/src/ci/bin/testCentaurEngineUpgradePapiV2alpha1.sh b/src/ci/bin/testCentaurEngineUpgradePapiV2alpha1.sh
deleted file mode 100755
index 7a471ce9e34..00000000000
--- a/src/ci/bin/testCentaurEngineUpgradePapiV2alpha1.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-export CROMWELL_BUILD_REQUIRES_PRIOR_VERSION=true
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test_papi.inc.sh" || source test_papi.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_centaur_environment
-
-cromwell::build::papi::setup_papi_centaur_environment
-
-cromwell::build::assemble_jars
-
-cromwell::build::run_centaur \
-    -s "centaur.EngineUpgradeTestCaseSpec" \
-    -e localdockertest \
-
-cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testCentaurHoricromtalEngineUpgradePapiV2alpha1.sh b/src/ci/bin/testCentaurHoricromtalEngineUpgradePapiV2alpha1.sh
deleted file mode 100755
index f4050548f38..00000000000
--- a/src/ci/bin/testCentaurHoricromtalEngineUpgradePapiV2alpha1.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-export CROMWELL_BUILD_REQUIRES_PRIOR_VERSION=true
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test_papi.inc.sh" || source test_papi.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_centaur_environment
-
-cromwell::build::papi::setup_papi_centaur_environment
-
-cromwell::build::assemble_jars
-
-cromwell::build::build_cromwell_docker
-
-cromwell::build::run_centaur \
-    -s "centaur.EngineUpgradeTestCaseSpec" \
-    -e localdockertest
-
-cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2alpha1.sh b/src/ci/bin/testCentaurHoricromtalPapiV2alpha1.sh
deleted file mode 100755
index 3e8453c9d83..00000000000
--- a/src/ci/bin/testCentaurHoricromtalPapiV2alpha1.sh
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test_papi.inc.sh" || source test_papi.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_centaur_environment
-
-cromwell::build::papi::setup_papi_centaur_environment
-
-cromwell::build::assemble_jars
-
-cromwell::build::build_cromwell_docker
-
-cromwell::build::run_centaur \
-    -p 100 \
-    -e localdockertest \
-    -e relative_output_paths \
-    -e relative_output_paths_colliding \
-    -e standard_output_paths_colliding_prevented \
-    -e papi_v2beta_gcsa \
-
-cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
index c894909cd3f..2fac6a6b336 100755
--- a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
+++ b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
@@ -26,6 +26,8 @@ cromwell::build::run_centaur \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
     -e restart \
+    -e lots_of_inputs \
+    # `lots_of_inputs` is redundant to, and a less rigorous version of, `lots_of_inputs_papiv2`
 
 cromwell::build::generate_code_coverage
 
diff --git a/src/ci/bin/testCentaurPapiUpgradeNewWorkflowsPapiV2alpha1.sh b/src/ci/bin/testCentaurPapiUpgradeNewWorkflowsPapiV2alpha1.sh
deleted file mode 100755
index 5b5ffe0ddc3..00000000000
--- a/src/ci/bin/testCentaurPapiUpgradeNewWorkflowsPapiV2alpha1.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/usr/bin/env bash
-
-echo "$(tput setab 1)$(tput blink)BT-81: This sub-build was doing no useful work; it built Cromwell and launched Centaur but never found tests to run. However, tests for functionality implied by this sub-build's name may be desirable, see BT-81 for further information.$(tput sgr 0)"
-exit 0
diff --git a/src/ci/bin/testCentaurPapiUpgradePapiV2alpha1.sh b/src/ci/bin/testCentaurPapiUpgradePapiV2alpha1.sh
deleted file mode 100755
index 8c46a8223e7..00000000000
--- a/src/ci/bin/testCentaurPapiUpgradePapiV2alpha1.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/usr/bin/env bash
-
-echo "$(tput setab 1)$(tput blink)BT-81: This sub-build was doing no useful work; it built Cromwell and launched Centaur but never found tests to run. However, tests for functionality implied by this sub-build's name may be desirable, see BT-81 for further information.$(tput sgr 0)"exit 0
diff --git a/src/ci/bin/testCentaurPapiV2alpha1.sh b/src/ci/bin/testCentaurPapiV2alpha1.sh
deleted file mode 100755
index 706d13c0acb..00000000000
--- a/src/ci/bin/testCentaurPapiV2alpha1.sh
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test_papi.inc.sh" || source test_papi.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_centaur_environment
-
-cromwell::build::papi::setup_papi_centaur_environment
-
-cromwell::build::assemble_jars
-
-cromwell::build::run_centaur \
-    -p 100 \
-    -e localdockertest \
-    -e relative_output_paths \
-    -e relative_output_paths_colliding \
-    -e standard_output_paths_colliding_prevented \
-    -e papi_v2beta_gcsa \
-
-cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testCentaurPapiV2beta.sh b/src/ci/bin/testCentaurPapiV2beta.sh
index d66d2a14334..108c6cca388 100755
--- a/src/ci/bin/testCentaurPapiV2beta.sh
+++ b/src/ci/bin/testCentaurPapiV2beta.sh
@@ -24,6 +24,8 @@ cromwell::build::run_centaur \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
     -e restart \
+    -e lots_of_inputs \
+    # `lots_of_inputs` is redundant to, and a less rigorous version of, `lots_of_inputs_papiv2`
 
 cromwell::build::generate_code_coverage
 
diff --git a/src/ci/bin/testDockerScripts.sh b/src/ci/bin/testDockerScripts.sh
deleted file mode 100755
index e9f670bba54..00000000000
--- a/src/ci/bin/testDockerScripts.sh
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-
-cromwell::build::setup_common_environment
-
-# When running locally, an `ADD .` in the Dockerfile might pull in files the local developer does not expect.
-# Until there is further review of what goes into the docker image (ex: rendered vault secrets!) do not push it yet.
-docker_tag="broadinstitute/cromwell-docker-develop:test-only-do-not-push"
-
-docker build -t "${docker_tag}" scripts/docker-develop
-
-echo "What tests would you like, my dear McMuffins?"
-
-echo "1. Testing for install of sbt"
-docker run --rm "${docker_tag}" which sbt
-
-echo "2. Testing sbt assembly"
-docker run \
-    --rm \
-    --volume "${CROMWELL_BUILD_ROOT_DIRECTORY}:${CROMWELL_BUILD_ROOT_DIRECTORY}" \
-    --workdir "${CROMWELL_BUILD_ROOT_DIRECTORY}" \
-    "${docker_tag}" \
-    sbt -Dsbt.supershell=false --warn assembly
diff --git a/src/ci/bin/testMetadataComparisonPython.sh b/src/ci/bin/testMetadataComparisonPython.sh
deleted file mode 100755
index f12b9ee5fe7..00000000000
--- a/src/ci/bin/testMetadataComparisonPython.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-
-cromwell::build::setup_common_environment
-
-# Our Python scripts can only be run by Python version >= 3.6, because we use string interpolation which was introduced
-# in Python 3.6. But Travis environment is Ubuntu 16.04 Xenial LTS, which officially supports only Python <= 3.5.
-# Thus we have to run Python tests in Docker container.
-GOOGLE_CENTAUR_SERVICE_ACCOUNT_JSON="cromwell-centaur-service-account.json"
-export GOOGLE_APPLICATION_CREDENTIALS="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/${GOOGLE_CENTAUR_SERVICE_ACCOUNT_JSON}"
-export DIGESTER_TEST_GCS=true
-
-docker run -it --rm \
-           -e GOOGLE_APPLICATION_CREDENTIALS \
-           -e DIGESTER_TEST_GCS \
-           -v "${CROMWELL_BUILD_RESOURCES_DIRECTORY}:${CROMWELL_BUILD_RESOURCES_DIRECTORY}" \
-           -v "${CROMWELL_BUILD_ROOT_DIRECTORY}/scripts/metadata_comparison:/metadata_comparison" \
-           python:3 /bin/bash -c "
-
-pip3 install --upgrade requests
-pip3 install --upgrade google-api-python-client
-pip3 install --upgrade google-cloud
-pip3 install --upgrade google-cloud-storage
-pip3 install --upgrade gitpython
-pip3 install --upgrade python-dateutil
-python3 -m unittest discover -v /metadata_comparison
-"
diff --git a/src/ci/bin/test_gcpbatch.inc.sh b/src/ci/bin/test_gcpbatch.inc.sh
index 1570bdb5f76..641cd86d612 100644
--- a/src/ci/bin/test_gcpbatch.inc.sh
+++ b/src/ci/bin/test_gcpbatch.inc.sh
@@ -29,10 +29,6 @@ cromwell::private::batch::setup_batch_gcloud() {
     export CROMWELL_BUILD_BATCH_GCR_IMAGES
     export CROMWELL_BUILD_BATCH_PROJECT_ID
 
-    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_TRAVIS}" ]]; then
-        cromwell::private::batch::install_gcloud
-    fi
-
     # All `gcloud` commands should use this configuration directory.
     # https://stackoverflow.com/questions/34883810/how-to-authenticate-google-apis-with-different-service-account-credentials
     # https://github.com/googleapis/google-auth-library-java/issues/58
@@ -106,9 +102,5 @@ cromwell::private::batch::setup_batch_service_account() {
 
 cromwell::build::batch::setup_batch_centaur_environment() {
     cromwell::private::batch::setup_batch_gcloud
-    if [[ "${CROMWELL_BUILD_PROVIDER}" != "${CROMWELL_BUILD_PROVIDER_JENKINS}" ]]
-    then
-        cromwell::private::batch::setup_batch_gcr
-    fi
     cromwell::private::batch::setup_batch_service_account
 }
diff --git a/src/ci/bin/test_papi.inc.sh b/src/ci/bin/test_papi.inc.sh
index 98d77820435..0b4ed151664 100644
--- a/src/ci/bin/test_papi.inc.sh
+++ b/src/ci/bin/test_papi.inc.sh
@@ -29,10 +29,6 @@ cromwell::private::papi::setup_papi_gcloud() {
     export CROMWELL_BUILD_PAPI_GCR_IMAGES
     export CROMWELL_BUILD_PAPI_PROJECT_ID
 
-    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_TRAVIS}" ]]; then
-        cromwell::private::papi::install_gcloud
-    fi
-
     # All `gcloud` commands should use this configuration directory.
     # https://stackoverflow.com/questions/34883810/how-to-authenticate-google-apis-with-different-service-account-credentials
     # https://github.com/googleapis/google-auth-library-java/issues/58
@@ -115,10 +111,7 @@ cromwell::private::papi::setup_papi_endpoint_url() {
 
 cromwell::build::papi::setup_papi_centaur_environment() {
     cromwell::private::papi::setup_papi_gcloud
-    if [[ "${CROMWELL_BUILD_PROVIDER}" != "${CROMWELL_BUILD_PROVIDER_JENKINS}" ]]
-    then
-        cromwell::private::papi::setup_papi_gcr
-    fi
+    cromwell::private::papi::setup_papi_gcr
     cromwell::private::papi::setup_papi_service_account
     cromwell::private::papi::setup_papi_endpoint_url
 }
diff --git a/src/ci/bin/test_unit.inc.sh b/src/ci/bin/test_unit.inc.sh
index edef0fda323..5ff2b69de3e 100644
--- a/src/ci/bin/test_unit.inc.sh
+++ b/src/ci/bin/test_unit.inc.sh
@@ -18,12 +18,6 @@ source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
 
 cromwell::build::unit::setup_scale_factor() {
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
-            CROMWELL_BUILD_UNIT_SPAN_SCALE_FACTOR=2
-            ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            CROMWELL_BUILD_UNIT_SPAN_SCALE_FACTOR=10
-            ;;
         *)
             CROMWELL_BUILD_UNIT_SPAN_SCALE_FACTOR=1
             ;;
@@ -33,12 +27,6 @@ cromwell::build::unit::setup_scale_factor() {
 
 cromwell::build::unit::setup_exclude_tags() {
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
-            CROMWELL_BUILD_UNIT_EXCLUDE_TAGS="AwsTest,CromwellIntegrationTest,DbmsTest,GcsIntegrationTest"
-            ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            CROMWELL_BUILD_UNIT_EXCLUDE_TAGS="AwsTest,CromwellIntegrationTest,DockerTest,DbmsTest,GcsIntegrationTest"
-            ;;
         *)
             # Use the full list of excludes listed in Testing.scala
             CROMWELL_BUILD_UNIT_EXCLUDE_TAGS=""
diff --git a/src/ci/resources/papi_v1_v2alpha1_provider_config.inc.conf b/src/ci/resources/papi_v1_v2alpha1_provider_config.inc.conf
deleted file mode 100644
index 4b786c6ec2c..00000000000
--- a/src/ci/resources/papi_v1_v2alpha1_provider_config.inc.conf
+++ /dev/null
@@ -1,20 +0,0 @@
-project = "broad-dsde-cromwell-dev"
-root = "gs://cloud-cromwell-dev-self-cleaning/cromwell_execution/ci"
-maximum-polling-interval = 600
-concurrent-job-limit = 1000
-
-genomics {
-  auth = "service_account"
-  endpoint-url = "https://genomics.googleapis.com/"
-}
-
-filesystems {
-  gcs {
-    auth = "service_account"
-    project = "broad-dsde-cromwell-dev"
-  }
-}
-
-slow-job-warning-time: 20 minutes
-
-checkpointing-interval: "10 seconds"
diff --git a/src/ci/resources/papi_v2alpha1_application.conf b/src/ci/resources/papi_v2alpha1_application.conf
deleted file mode 100644
index cc12d36b27d..00000000000
--- a/src/ci/resources/papi_v2alpha1_application.conf
+++ /dev/null
@@ -1,81 +0,0 @@
-include "papi_v2_shared_application.inc.conf"
-
-backend {
-  providers {
-    Papi {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2 {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2USADockerhub {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2NoDockerHubConfig {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2RequesterPays {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-
-        # Need this again (even though it's in the "papiv2_shared" file because the provider_config include overrides it.
-        filesystems.gcs.auth = "requester_pays_service_account"
-      }
-    }
-    Papi-Caching-No-Copy {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2-Virtual-Private-Cloud-Labels {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2-Virtual-Private-Cloud-Literals {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    papi-v2-gcsa {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    papi-v2-usa {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2ParallelCompositeUploads {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2-Reference-Disk-Localization {
-      actor-factory = "cromwell.backend.google.pipelines.v2beta.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v2beta_provider_config.inc.conf"
-      }
-    }
-  }
-}
diff --git a/src/ci/resources/papi_v2alpha1_conformance_expected_failures.txt b/src/ci/resources/papi_v2alpha1_conformance_expected_failures.txt
deleted file mode 100644
index 4caa25c75a6..00000000000
--- a/src/ci/resources/papi_v2alpha1_conformance_expected_failures.txt
+++ /dev/null
@@ -1,29 +0,0 @@
-86
-87
-101
-102
-104
-107
-136
-137
-140
-142
-152
-153
-154
-156
-158
-159
-160
-161
-163
-164
-165
-166
-170
-171
-173
-189
-190
-191
-196
diff --git a/src/ci/resources/papi_v2alpha1_horicromtal_application.conf b/src/ci/resources/papi_v2alpha1_horicromtal_application.conf
deleted file mode 100644
index dacfbd63877..00000000000
--- a/src/ci/resources/papi_v2alpha1_horicromtal_application.conf
+++ /dev/null
@@ -1,9 +0,0 @@
-include "papi_v2alpha1_application.conf"
-
-system.max-workflow-launch-count=1
-system.new-workflow-poll-rate=10
-system.max-concurrent-workflows=30
-system.cromwell_id_random_suffix=false
-
-# Turn off token logging to reduce log volume
-system.hog-safety.token-log-interval-seconds = 0
diff --git a/src/ci/resources/papi_v2alpha1_v2beta_upgrade_application.conf b/src/ci/resources/papi_v2alpha1_v2beta_upgrade_application.conf
deleted file mode 100644
index 6059508a592..00000000000
--- a/src/ci/resources/papi_v2alpha1_v2beta_upgrade_application.conf
+++ /dev/null
@@ -1,32 +0,0 @@
-include required(classpath("application.conf"))
-include "build_application.inc.conf"
-include "papi_application.inc.conf"
-
-# We now have two types of PAPI backend to monitor:
-services.HealthMonitor.config.check-papi-backends: [ Papiv2alpha1, Papiv2beta ]
-
-backend {
-  default = "Papiv2alpha1"
-  enabled = ["Papiv2alpha1", "Papiv2beta"]
-  providers {
-    # Pre-existing PAPI v2alpha1 backend
-    Papiv2alpha1 {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-        include "dockerhub_provider_config_v2.inc.conf"
-        genomics.compute-service-account = "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com"
-        name-for-call-caching-purposes = "Papi"
-      }
-    }
-    Papiv2beta {
-      actor-factory = "cromwell.backend.google.pipelines.v2beta.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v2beta_provider_config.inc.conf"
-        include "dockerhub_provider_config_v2.inc.conf"
-        genomics.compute-service-account = "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com"
-        name-for-call-caching-purposes = "Papi"
-      }
-    }
-  }
-}

From 0b76ae3d0b2ff31fabe6843f1f8e53d56d54cbf0 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 8 Dec 2023 14:59:36 -0500
Subject: [PATCH 254/326] [WX-1395] Scalafmt GitHub Action (#7337)

---
 .github/workflows/scalafmt-check.yml | 31 ++++++++++++++++++
 .github/workflows/scalafmt-fix.yml   | 48 ++++++++++++++++++++++++++++
 project/ContinuousIntegration.scala  | 48 +++++++++++++++-------------
 project/plugins.sbt                  |  1 +
 4 files changed, 106 insertions(+), 22 deletions(-)
 create mode 100644 .github/workflows/scalafmt-check.yml
 create mode 100644 .github/workflows/scalafmt-fix.yml

diff --git a/.github/workflows/scalafmt-check.yml b/.github/workflows/scalafmt-check.yml
new file mode 100644
index 00000000000..2d60b86040b
--- /dev/null
+++ b/.github/workflows/scalafmt-check.yml
@@ -0,0 +1,31 @@
+name: 'Scalafmt'
+
+# This GitHub Action runs the ScalaFmt linting tool on the entire codebase.
+# It fails if any files are not formatted properly.
+# If it is triggered by someone commenting 'scalafmt' on a PR, it will first format, commit, and push formatted code
+# to the branch.
+
+run-name: ${{ format('ScalaFmt Check on {0}', github.ref_name) }}
+
+on:
+  workflow_dispatch:
+  push:
+
+permissions:
+  contents: read
+
+jobs:
+  run-scalafmt-check:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: ${{ inputs.target-branch }}
+      - uses: ./.github/set_up_cromwell_action
+        with:
+          cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+      - name: Run ScalaFmt
+        run: |
+          sbt scalafmtCheckAll
+        working-directory: ${{ github.workspace }}
diff --git a/.github/workflows/scalafmt-fix.yml b/.github/workflows/scalafmt-fix.yml
new file mode 100644
index 00000000000..83e6fb099ed
--- /dev/null
+++ b/.github/workflows/scalafmt-fix.yml
@@ -0,0 +1,48 @@
+name: 'Scalafmt'
+
+# This GitHub Action runs the ScalaFmt linting tool on the entire codebase.
+# It will fix, commit, and push linted code.
+# It will only run when someone comments "scalafmt" on a PR.
+
+run-name: ${{ format('ScalaFmt Fix on {0}', github.ref_name) }}
+
+on:
+  workflow_dispatch:
+  issue_comment:
+    types:
+      - created
+
+jobs:
+  run-scalafmt-fix:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: ${{ inputs.target-branch }}
+      - uses: ./.github/set_up_cromwell_action
+        with:
+          cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+      - name: Check for ScalaFmt Comment
+        id: check-comment
+        run: |
+          if [[ "${{ github.event_name }}" == "issue_comment" && "${{ github.event.comment.body }}" == *"scalafmt"* ]]; then
+            echo "::set-output name=comment-triggered::true"
+            echo "::set-output name=comment-author-email::${{ github.event.comment.user.login }}@users.noreply.github.com"
+            echo "::set-output name=comment-author-name::${{ github.event.comment.user.login }}"
+          else
+            echo "::set-output name=comment-triggered::false"
+          fi
+        shell: bash
+      - name: Run ScalaFmt
+        run: |
+          if [[ ${{ steps.check-comment.outputs.comment-triggered }} == true ]]; then
+            echo "PR Comment Detected. Formatting, committing, and pushing formatted scala code."
+            sbt scalaFmtAll
+            git config --global user.email "${{ steps.check-comment.outputs.comment-author-email }}"
+            git config --global user.name "${{ steps.check-comment.outputs.comment-author-name }}"
+            git add .
+            git commit -m "Auto-format code with ScalaFmt"
+            git push origin ${{ github.ref }}
+          fi
+        working-directory: ${{ github.workspace }}
diff --git a/project/ContinuousIntegration.scala b/project/ContinuousIntegration.scala
index f0516150cf5..aa171a72338 100644
--- a/project/ContinuousIntegration.scala
+++ b/project/ContinuousIntegration.scala
@@ -9,7 +9,7 @@ object ContinuousIntegration {
   lazy val ciSettings: Seq[Setting[_]] = List(
     srcCiResources := sourceDirectory.value / "ci" / "resources",
     targetCiResources := target.value / "ci" / "resources",
-    envFile := srcCiResources.value / "env.temp", //generated by resources/acquire_b2c_token.sh
+    envFile := srcCiResources.value / "env.temp", // generated by resources/acquire_b2c_token.sh
 
     vaultToken := userHome / ".vault-token",
     copyCiResources := {
@@ -31,29 +31,32 @@ object ContinuousIntegration {
 
       // Only include the local file argument if the file exists (local development w/ acquire_b2c_token.sh)
       // Don't include it otherwise (CI/CD and other development)
-      val localEnvFileArgs = if(envFile.value.exists()) List("-e", s"ENV_FILE=${envFile.value}") else List()
+      val localEnvFileArgs = if (envFile.value.exists()) List("-e", s"ENV_FILE=${envFile.value}") else List()
 
-      val cmd: List[String] = List.concat(List(
-        "docker",
-        "run",
-        "--rm",
-        "-v",
-        s"${vaultToken.value}:/root/.vault-token",
-        "-v",
-        s"${srcCiResources.value}:${srcCiResources.value}",
-        "-v",
-        s"${targetCiResources.value}:${targetCiResources.value}"),
+      val cmd: List[String] = List.concat(
+        List(
+          "docker",
+          "run",
+          "--rm",
+          "-v",
+          s"${vaultToken.value}:/root/.vault-token",
+          "-v",
+          s"${srcCiResources.value}:${srcCiResources.value}",
+          "-v",
+          s"${targetCiResources.value}:${targetCiResources.value}"
+        ),
         localEnvFileArgs,
         List(
-        "-e",
-        "ENVIRONMENT=not_used",
-        "-e",
-        s"INPUT_PATH=${srcCiResources.value}",
-        "-e",
-        s"OUT_PATH=${targetCiResources.value}",
-        "broadinstitute/dsde-toolbox:dev",
-        "render-templates.sh"
-      ))
+          "-e",
+          "ENVIRONMENT=not_used",
+          "-e",
+          s"INPUT_PATH=${srcCiResources.value}",
+          "-e",
+          s"OUT_PATH=${targetCiResources.value}",
+          "broadinstitute/dsde-toolbox:dev",
+          "render-templates.sh"
+        )
+      )
       val result = cmd ! log
       if (result != 0) {
         sys.error(
@@ -79,7 +82,8 @@ object ContinuousIntegration {
   private val srcCiResources: SettingKey[File] = settingKey[File]("Source directory for CI resources")
   private val targetCiResources: SettingKey[File] = settingKey[File]("Target directory for CI resources")
   private val vaultToken: SettingKey[File] = settingKey[File]("File with the vault token")
-  private val envFile: SettingKey[File] = settingKey[File]("File with the environment variables needed to render CI resources.")
+  private val envFile: SettingKey[File] =
+    settingKey[File]("File with the environment variables needed to render CI resources.")
 
   /**
     * For "reasons" these projects are excluded from the root aggregation in build.sbt.
diff --git a/project/plugins.sbt b/project/plugins.sbt
index bdb54f675bf..7a0203e08ea 100644
--- a/project/plugins.sbt
+++ b/project/plugins.sbt
@@ -3,4 +3,5 @@ addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.1")
 addSbtPlugin("com.github.sbt" % "sbt-git" % "2.0.0")
 addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.4")
 addSbtPlugin("com.github.cb372" % "sbt-explicit-dependencies" % "0.2.16")
+addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.2")
 addDependencyTreePlugin

From 49438966d397a32c64167d004ecfe143c54caa3d Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 11 Dec 2023 20:54:23 -0500
Subject: [PATCH 255/326] WX-1351 SBT compile speedup (#7339)

---
 project/Settings.scala | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/project/Settings.scala b/project/Settings.scala
index ea775ed2bf5..9a33f663cef 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -77,12 +77,13 @@ object Settings {
     organization := "org.broadinstitute",
     scalaVersion := ScalaVersion,
     resolvers ++= additionalResolvers,
-    // Don't run tasks in parallel, especially helps in low CPU environments like Travis
-    Global / parallelExecution := false,
+    Global / parallelExecution := true,
+    // Seems to cause race conditions in tests, that are not pertinent to what's being tested
+    Test / parallelExecution := false,
     Global / concurrentRestrictions ++= List(
-      // Don't run any other tasks while running tests, especially helps in low CPU environments like Travis
+      // Don't run any other tasks while running tests
       Tags.exclusive(Tags.Test),
-      // Only run tests on one sub-project at a time, especially helps in low CPU environments like Travis
+      // Only run tests on one sub-project at a time
       Tags.limit(Tags.Test, 1)
     ),
     dependencyOverrides ++= cromwellDependencyOverrides,

From 6875c531ed90e17c85c50875b903e67c611e96c6 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 12 Dec 2023 09:33:10 -0500
Subject: [PATCH 256/326] WX-1407 Fix contract tests (#7340)

Co-authored-by: Ivan <ichang@broadinstitute.org>
---
 .github/workflows/consumer_contract_tests.yml | 57 +++++++++++++++----
 pact4s/README.md                              |  3 +-
 .../cromwell/consumer/DrsHubClientSpec.scala  |  6 +-
 project/Dependencies.scala                    |  2 +-
 4 files changed, 52 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/consumer_contract_tests.yml b/.github/workflows/consumer_contract_tests.yml
index 0970e45e863..cce91ff3e2e 100644
--- a/.github/workflows/consumer_contract_tests.yml
+++ b/.github/workflows/consumer_contract_tests.yml
@@ -29,18 +29,25 @@ name: Consumer contract tests
 #     Consumer kicks off can-i-deploy on process to determine if changes can be promoted and used for deployment.
 #
 # NOTE: The publish-contracts workflow will use the latest commit of the branch that triggers this workflow to publish the unique consumer contract version to Pact Broker.
-
 on:
   pull_request:
+    branches:
+      - develop
     paths-ignore:
       - 'README.md'
   push:
+    branches:
+      - develop
     paths-ignore:
       - 'README.md'
   merge_group:
     branches:
       - develop
 
+env:
+  PUBLISH_CONTRACTS_RUN_NAME: 'publish-contracts-${{ github.event.repository.name }}-${{ github.run_id }}-${{ github.run_attempt }}'
+  CAN_I_DEPLOY_RUN_NAME: 'can-i-deploy-${{ github.event.repository.name }}-${{ github.run_id }}-${{ github.run_attempt }}'
+
 jobs:
   init-github-context:
     runs-on: ubuntu-latest
@@ -52,6 +59,23 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      # Construct a version string like `87-9c6c439`. Adapted from `chart_update_on_merge.yml`.
+      - name: Find Cromwell short SHA
+        run: |
+          set -e
+          echo "CROMWELL_SHORT_SHA=`git rev-parse --short $GITHUB_SHA`" >> $GITHUB_ENV
+      - name: Find Cromwell release number
+        run: |
+          set -e
+          previous_version=$(curl -X GET https://api.github.com/repos/broadinstitute/cromwell/releases/latest | jq .tag_name | xargs)
+          if ! [[ "${previous_version}" =~ ^[0-9][0-9]+$ ]]; then
+            exit 1
+          fi
+          echo "CROMWELL_NUMBER=$((previous_version + 1))" >> $GITHUB_ENV
+      - name: Save complete image ID
+        run: |
+          echo "CROMWELL_VERSION=`echo "$CROMWELL_NUMBER-$CROMWELL_SHORT_SHA"`" >> $GITHUB_ENV
+
       - name: Extract branch
         id: extract-branch
         run: |
@@ -70,9 +94,9 @@ jobs:
           fi
           echo "CURRENT_BRANCH=${GITHUB_REF/refs\/heads\//""}" >> $GITHUB_ENV
           echo "CURRENT_SHA=$GITHUB_SHA" >> $GITHUB_ENV
-          
+
           echo "repo-branch=${GITHUB_REF/refs\/heads\//""}" >> $GITHUB_OUTPUT
-          echo "repo-version=${GITHUB_SHA}" >> $GITHUB_OUTPUT
+          echo "repo-version=${CROMWELL_VERSION}" >> $GITHUB_OUTPUT
           echo "fork=${FORK}" >> $GITHUB_OUTPUT
 
       - name: Is PR triggered by forked repo?
@@ -88,7 +112,7 @@ jobs:
           echo "repo-version=${{ steps.extract-branch.outputs.repo-version }}"
           echo "fork=${{ steps.extract-branch.outputs.fork }}"
 
-  cromwell-consumer-contract-tests:
+  cromwell-contract-tests:
     runs-on: ubuntu-latest
     needs: [init-github-context]
     outputs:
@@ -109,7 +133,7 @@ jobs:
         id: encode-pact
         run: |
           cd pact4s
-          NON_BREAKING_B64=$(cat target/pacts/cromwell-consumer-drshub-provider.json | base64 -w 0)
+          NON_BREAKING_B64=$(cat target/pacts/cromwell-drshub.json | base64 -w 0)
           echo "pact-b64=${NON_BREAKING_B64}" >> $GITHUB_OUTPUT
 
   # Prevent untrusted sources from using PRs to publish contracts
@@ -117,16 +141,24 @@ jobs:
   publish-contracts:
     runs-on: ubuntu-latest
     if: ${{ needs.init-github-context.outputs.fork == 'false' ||  needs.init-github-context.outputs.fork == ''}}
-    needs: [init-github-context, cromwell-consumer-contract-tests]
+    needs: [init-github-context, cromwell-contract-tests]
     steps:
       - name: Dispatch to terra-github-workflows
-        uses: broadinstitute/workflow-dispatch@v3
+        uses: broadinstitute/workflow-dispatch@v4.0.0
         with:
+          run-name: "${{ env.PUBLISH_CONTRACTS_RUN_NAME }}"
           workflow: .github/workflows/publish-contracts.yaml
           repo: broadinstitute/terra-github-workflows
           ref: refs/heads/main
           token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # github token for access to kick off a job in the private repo
-          inputs: '{ "pact-b64": "${{ needs.cromwell-consumer-contract-tests.outputs.pact-b64 }}", "repo-owner": "${{ github.repository_owner }}", "repo-name": "${{ github.event.repository.name }}", "repo-branch": "${{ needs.init-github-context.outputs.repo-branch }}" }'
+          inputs: '{
+            "run-name": "${{ env.PUBLISH_CONTRACTS_RUN_NAME }}",
+            "pact-b64": "${{ needs.cromwell-contract-tests.outputs.pact-b64 }}",
+            "repo-owner": "${{ github.repository_owner }}",
+            "repo-name": "${{ github.event.repository.name }}",
+            "repo-branch": "${{ needs.init-github-context.outputs.repo-branch }}",
+            "release-tag": "${{ needs.init-github-context.outputs.repo-version }}"
+          }'
 
   can-i-deploy:
     runs-on: ubuntu-latest
@@ -134,10 +166,15 @@ jobs:
     needs: [ init-github-context, publish-contracts ]
     steps:
       - name: Dispatch to terra-github-workflows
-        uses: broadinstitute/workflow-dispatch@v3
+        uses: broadinstitute/workflow-dispatch@v4.0.0
         with:
+          run-name: "${{ env.CAN_I_DEPLOY_RUN_NAME }}"
           workflow: .github/workflows/can-i-deploy.yaml
           repo: broadinstitute/terra-github-workflows
           ref: refs/heads/main
           token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # github token for access to kick off a job in the private repo
-          inputs: '{ "pacticipant": "cromwell-consumer", "version": "${{ needs.init-github-context.outputs.repo-version }}" }'
+          inputs: '{
+            "run-name": "${{ env.CAN_I_DEPLOY_RUN_NAME }}",
+            "pacticipant": "cromwell",
+            "version": "${{ needs.init-github-context.outputs.repo-version }}"
+          }'
diff --git a/pact4s/README.md b/pact4s/README.md
index d33447f7356..fd3245a877d 100644
--- a/pact4s/README.md
+++ b/pact4s/README.md
@@ -46,6 +46,5 @@ docker run --rm -v $PWD:/working \
 ```
 
 The generated contracts can be found in the `./target/pacts` folder
-- `cromwell-consumer-drshub-provider.json`
-- `cromwell-consumer-fake-provider.json`
+- `cromwell-drshub.json`
 
diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
index ead29c29d4f..5fae4a4bfc5 100644
--- a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
+++ b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
@@ -113,10 +113,10 @@ class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePac
   }.build
 
   val consumerPactBuilder: ConsumerPactBuilder = ConsumerPactBuilder
-    .consumer("cromwell-consumer")
+    .consumer("cromwell")
 
   val pactProvider: PactDslWithProvider = consumerPactBuilder
-    .hasPactWith("drshub-provider")
+    .hasPactWith("drshub")
 
   var pactDslResponse: PactDslResponse = buildInteraction(
     pactProvider,
@@ -134,7 +134,7 @@ class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePac
     uponReceiving = "Request to resolve drs url",
     method = "POST",
     path = "/api/v4/drs/resolve",
-    requestHeaders = Seq("Content-type" -> "application/json"),
+    requestHeaders = Seq("Content-Type" -> "application/json"),
     requestBody = resourceRequestDsl,
     status = 200,
     responseHeaders = Seq(),
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 44dacb56dc7..3e40fc85cdd 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -628,7 +628,7 @@ object Dependencies {
     "org.lz4" % "lz4-java" % lz4JavaV
   )
   val scalaTest = "org.scalatest" %% "scalatest" % scalatestV
-  
+
   val testDependencies: List[ModuleID] = List(
     "org.scalatest" %% "scalatest" % scalatestV,
     // Use mockito Java DSL directly instead of the numerous and often hard to keep updated Scala DSLs.

From 0ecbf53566bc4bbedc6c866aee2eaf044111e66e Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 14 Dec 2023 09:50:46 -0500
Subject: [PATCH 257/326] WX-1409 Java 17 (#7342)

---
 .github/set_up_cromwell_action/action.yml     |  10 +-
 .github/workflows/chart_update_on_merge.yml   |   5 +-
 .github/workflows/docker_build_test.yml       |   5 +-
 .github/workflows/integration_tests.yml       |   8 +
 .github/workflows/trivy.yml                   |   5 +-
 .sdkmanrc                                     |   2 +-
 CHANGELOG.md                                  |   7 +
 .../api/DaemonizedDefaultThreadFactory.scala  |   3 +-
 .../scala/cloud/nio/spi/CloudNioPath.scala    |   2 +-
 .../main/scala/cloud/nio/spi/UnixPath.scala   |   2 +-
 docs/Configuring.md                           |   2 +-
 docs/Releases.md                              |   4 +-
 docs/tutorials/FiveMinuteIntro.md             |   6 +-
 project/Publishing.scala                      |   5 +-
 publish/docker-setup.sh                       |   2 +-
 runConfigurations/renderCiResources.run.xml   |   4 +-
 scripts/docker-compose-mysql/README.md        |   1 -
 .../compose/cromwell/Dockerfile               |   9 -
 .../app-config/cromwell-application.conf      |  61 ---
 .../compose/mysql/init/init_user.sql          |   4 -
 .../docker-compose-mysql/docker-compose.yml   |  22 -
 .../jes-cromwell/docker-compose.yml           |   9 -
 .../jes-cromwell/jes-config/application.conf  |  73 ---
 scripts/docker-develop/Dockerfile             |  64 ---
 scripts/docker-develop/README.md              |  60 ---
 src/ci/bin/test.inc.sh                        |   2 +-
 .../docker-compose/cromwell-test/Dockerfile   |   2 +-
 .../cromwell-test/docker-setup.sh             |  16 +-
 ...haredFileSystemJobExecutionActorSpec.scala | 430 ------------------
 wom/src/main/resources/reference.conf         |   2 +-
 .../test/scala/wom/util/YamlUtilsSpec.scala   |   6 +-
 31 files changed, 57 insertions(+), 776 deletions(-)
 delete mode 100644 scripts/docker-compose-mysql/README.md
 delete mode 100644 scripts/docker-compose-mysql/compose/cromwell/Dockerfile
 delete mode 100644 scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
 delete mode 100644 scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
 delete mode 100644 scripts/docker-compose-mysql/docker-compose.yml
 delete mode 100644 scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
 delete mode 100644 scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
 delete mode 100644 scripts/docker-develop/Dockerfile
 delete mode 100644 scripts/docker-develop/README.md
 delete mode 100644 supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index 13cb11601db..1cbe834d2bd 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -3,7 +3,8 @@
 name: 'Set Up Cromwell Steps'
 description: Specific steps that will set up git secrets, java, sbt, and Cromwell on the local machine. 
 inputs:
-  cromwell_repo_token: #As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell.
+  cromwell_repo_token:
+    description: "As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell."
     required: true
 
 runs:
@@ -12,13 +13,13 @@ runs:
       #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
       - uses: actions/checkout@v3
         name: Checkout Coursier Cache
-      - uses: coursier/cache-action@v6  
+      - uses: coursier/cache-action@v6
         name: Enable Coursier Cache
 
       #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
       - name: Git secrets setup 
         run: |
-          git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
+          git clone --quiet https://github.com/awslabs/git-secrets.git ~/git-secrets
           cd ~/git-secrets
           git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
           sudo make install
@@ -43,5 +44,4 @@ runs:
         uses: actions/setup-java@v3
         with:
           distribution: temurin
-          java-version: 11
-
+          java-version: 17
diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index a2b14f2ec65..b3f7199ab35 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -23,9 +23,10 @@ jobs:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
         path: cromwell
-    - uses: olafurpg/setup-scala@v10
+    - uses: actions/setup-java@v4
       with:
-        java-version: adopt@1.11
+        distribution: 'temurin'
+        java-version: '17'
     - name: Clone Cromwhelm
       uses: actions/checkout@v2
       with:
diff --git a/.github/workflows/docker_build_test.yml b/.github/workflows/docker_build_test.yml
index 01c2ea502c9..a50e39a380f 100644
--- a/.github/workflows/docker_build_test.yml
+++ b/.github/workflows/docker_build_test.yml
@@ -25,9 +25,10 @@ jobs:
           repository: broadinstitute/cromwell
           token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
           path: cromwell
-      - uses: olafurpg/setup-scala@v10
+      - uses: actions/setup-java@v4
         with:
-          java-version: adopt@1.11
+          distribution: 'temurin'
+          java-version: '17'
       # The following invocation should be as similar as possible to the one in chart_update_on_merge.yml
       # To state the obvious: This test should not publish anything. It should simply verify that the build completes.
       - name: Build Cromwell Docker
diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 61ed3c5af41..028b53db130 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -104,6 +104,14 @@ jobs:
         set -e
         echo Running test.sh
         ./src/ci/bin/test.sh
+    # If a build step fails, activate SSH and idle for 60 minutes
+    # - name: Setup tmate session
+    #  if: ${{ failure() }}
+    #  uses: mxschmitt/action-tmate@v3
+    #  timeout-minutes: 60
+    #  with:
+    #    limit-access-to-actor: true
+    #    detached: true
     # always() is some github magic that forces the following step to run, even when the previous fails.
     # Without it, the if statement won't be evaluated on a test failure.
     - uses: ravsamhq/notify-slack-action@v2
diff --git a/.github/workflows/trivy.yml b/.github/workflows/trivy.yml
index b005da65041..69a90937671 100644
--- a/.github/workflows/trivy.yml
+++ b/.github/workflows/trivy.yml
@@ -20,9 +20,10 @@ jobs:
       - uses: actions/checkout@v2
 
       # fetch SBT package
-      - uses: olafurpg/setup-scala@v10
+      - uses: actions/setup-java@v4
         with:
-          java-version: adopt@1.11
+          distribution: 'temurin'
+          java-version: '17'
 
       # set up SBT cache
       - uses: actions/cache@v2
diff --git a/.sdkmanrc b/.sdkmanrc
index 0262a261019..f3b37566860 100644
--- a/.sdkmanrc
+++ b/.sdkmanrc
@@ -1,3 +1,3 @@
 # Enable auto-env through the sdkman_auto_env config
 # Add key=value pairs of SDKs to use below
-java=11.0.11.hs-adpt
+java=17.0.9-tem
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a581852c02e..d670e74a43e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,12 @@
 # Cromwell Change Log
 
+## 87 Release Notes
+
+### Java 17
+
+As of this version, a distribution of Java 17 is required to run Cromwell. Cromwell is developed, tested, and
+containerized using [Eclipse Temurin](https://adoptium.net/temurin/releases/?version=17).
+
 ## 86 Release Notes
 
 ### GCP Batch
diff --git a/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala b/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
index db9eb07d79b..d75299aa590 100644
--- a/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
+++ b/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
@@ -14,8 +14,7 @@ import java.util.concurrent.atomic.AtomicInteger
   * > main thread).
   */
 object DaemonizedDefaultThreadFactory extends ThreadFactory {
-  private val s = System.getSecurityManager
-  private val group = if (s != null) s.getThreadGroup else Thread.currentThread.getThreadGroup
+  private val group = Thread.currentThread.getThreadGroup
   private val threadNumber = new AtomicInteger(1)
   private val namePrefix = "daemonpool-thread-"
 
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
index b6803670d39..530ba5526ef 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
@@ -176,7 +176,7 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
   ): WatchKey = throw new UnsupportedOperationException
 
   override def iterator(): java.util.Iterator[Path] =
-    if (unixPath.isEmpty || unixPath.isRoot) {
+    if (unixPath.izEmpty || unixPath.isRoot) {
       java.util.Collections.emptyIterator()
     } else {
       unixPath.split().to(LazyList).map(part => newPath(UnixPath.getPath(part)).asInstanceOf[Path]).iterator.asJava
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
index b7d9ed02035..7d929d148ab 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
@@ -67,7 +67,7 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
 
   def isAbsolute: Boolean = UnixPath.isAbsolute(path)
 
-  def isEmpty: Boolean = path.isEmpty
+  def izEmpty: Boolean = path.isEmpty
 
   def hasTrailingSeparator: Boolean = UnixPath.hasTrailingSeparator(path)
 
diff --git a/docs/Configuring.md b/docs/Configuring.md
index aa810d19a0c..288ec9723de 100644
--- a/docs/Configuring.md
+++ b/docs/Configuring.md
@@ -689,7 +689,7 @@ This limit may be configured via the configuration value:
 
 ```hocon
 yaml {
-  max-depth = 1000
+  max-depth = 100
 }
 ```
 
diff --git a/docs/Releases.md b/docs/Releases.md
index 9699d7d44bc..a6a709518b9 100644
--- a/docs/Releases.md
+++ b/docs/Releases.md
@@ -19,8 +19,8 @@ Mac users with Homebrew can also get Cromwell with the command `brew install cro
 This documentation frequently refers to a "Cromwell jar" with a name like `cromwell-<version>.jar`. 
 This is the main artifact in Cromwell releases that contains all executable Cromwell code and default configuration.   
 
-A distribution of Java 11 is required to run Cromwell. Cromwell is developed, tested, and containerized using
-[AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/).
+A distribution of Java 17 is required to run Cromwell. Cromwell is developed, tested, and containerized using
+[AdoptOpenJDK 17 HotSpot](https://adoptopenjdk.net/).
 
 For users running a Cromwell server [a docker image](https://hub.docker.com/r/broadinstitute/cromwell) has been made available.
 
diff --git a/docs/tutorials/FiveMinuteIntro.md b/docs/tutorials/FiveMinuteIntro.md
index 1c16a56c606..f15e28087b9 100644
--- a/docs/tutorials/FiveMinuteIntro.md
+++ b/docs/tutorials/FiveMinuteIntro.md
@@ -3,11 +3,11 @@
 ### Prerequisites:
 
 * A Unix-based operating system (yes, that includes Mac!)
-* A Java 11 runtime environment 
+* A Java 17 runtime environment 
     * You can see what you have by running `$ java -version` on a terminal.
     * If not, consider installing via conda or brew [as explained here](../Releases.md).
-    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 11 build of [Temurin](https://adoptium.net/temurin/releases/?version=11)
-      * `sdk install java 11.0.16-tem` as of the time of this writing
+    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 17 build of [Temurin](https://adoptium.net/temurin/releases/?version=17)
+      * `sdk install 17.0.9-tem` as of the time of this writing
     * You might need to update the `export JAVA_HOME` in your bash profile to point to your JAVA install location.
 * A sense of adventure!
 
diff --git a/project/Publishing.scala b/project/Publishing.scala
index 0af27e77147..c8a601a4f0c 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -63,7 +63,7 @@ object Publishing {
       val additionalDockerInstr: Seq[Instruction] = (dockerCustomSettings ?? Nil).value
 
       new Dockerfile {
-        from("us.gcr.io/broad-dsp-gcr-public/base/jre:11-debian")
+        from("us.gcr.io/broad-dsp-gcr-public/base/jre:17-debian")
         expose(8000)
         add(artifact, artifactTargetPath)
         runRaw(s"ln -s $artifactTargetPath /app/$projectName.jar")
@@ -163,8 +163,7 @@ object Publishing {
   val additionalResolvers = List(
     broadArtifactoryResolver,
     broadArtifactoryResolverSnap,
-    Resolver.sonatypeRepo("releases")
-  )
+  ) ++ Resolver.sonatypeOssRepos("releases")
 
   private val artifactoryCredentialsFile =
     file("target/ci/resources/artifactory_credentials.properties").getAbsoluteFile
diff --git a/publish/docker-setup.sh b/publish/docker-setup.sh
index 613d251df96..bc39f31d10a 100755
--- a/publish/docker-setup.sh
+++ b/publish/docker-setup.sh
@@ -20,7 +20,7 @@ mkdir -p /etc/apt/keyrings
 wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
 echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
 apt update
-apt install -y temurin-11-jdk
+apt install -y temurin-17-jdk
 
 # Install jq 1.6 to ensure --rawfile is supported
 curl -L https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 -o /usr/bin/jq
diff --git a/runConfigurations/renderCiResources.run.xml b/runConfigurations/renderCiResources.run.xml
index 2a5ab5e29b8..ef56bf5e4fd 100644
--- a/runConfigurations/renderCiResources.run.xml
+++ b/runConfigurations/renderCiResources.run.xml
@@ -7,8 +7,8 @@
     </option>
     <option name="tasks" value="renderCiResources" />
     <option name="useSbtShell" value="false" />
-    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M -XX:+CMSClassUnloadingEnabled" />
+    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M" />
     <option name="workingDir" value="$PROJECT_DIR$" />
     <method v="2" />
   </configuration>
-</component>
\ No newline at end of file
+</component>
diff --git a/scripts/docker-compose-mysql/README.md b/scripts/docker-compose-mysql/README.md
deleted file mode 100644
index 8fcb404b069..00000000000
--- a/scripts/docker-compose-mysql/README.md
+++ /dev/null
@@ -1 +0,0 @@
-Looking for the MySQL docs? Checkout the [Cromwell documentation](https://cromwell.readthedocs.io/en/develop/Configuring/#database)!
\ No newline at end of file
diff --git a/scripts/docker-compose-mysql/compose/cromwell/Dockerfile b/scripts/docker-compose-mysql/compose/cromwell/Dockerfile
deleted file mode 100644
index 6bf9fd88bf9..00000000000
--- a/scripts/docker-compose-mysql/compose/cromwell/Dockerfile
+++ /dev/null
@@ -1,9 +0,0 @@
-FROM broadinstitute/cromwell:develop
-
-RUN git clone https://github.com/vishnubob/wait-for-it.git
-RUN mkdir cromwell-working-dir
-WORKDIR cromwell-working-dir
-
-COPY ./app-config /app-config
-
-ENTRYPOINT ["/bin/sh", "-c"]
diff --git a/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf b/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
deleted file mode 100644
index a3b8d88ce3d..00000000000
--- a/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
+++ /dev/null
@@ -1,61 +0,0 @@
-include required(classpath("application"))
-
-# Note: If you spot a mistake in this configuration sample, please let us know by making an issue at:
-# https://github.com/broadinstitute/cromwell/issues
-
-call-caching {
-  enabled = false
-}
-
-backend {
-  default = "Local"
-  providers {
-    Local {
-      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
-      config {
-        run-in-background = true
-        runtime-attributes = "String? docker Int? max_runtime = 2"
-        submit = "/bin/bash ${script}"
-        submit-docker = "docker run --rm -v ${cwd}:${docker_cwd} -i ${docker} /bin/bash < ${script}"
-
-        # Root directory where Cromwell writes job results. This directory must be
-        # visible and writeable by the Cromwell process as well as the jobs that Cromwell
-        # launches.
-        root: "cromwell-executions"
-
-        filesystems {
-          local {
-            localization: [
-              "soft-link", "hard-link", "copy"
-            ]
-
-            caching {
-              duplication-strategy: [
-                "soft-link"
-              ]
-
-              # Possible values: file, path
-              # "file" will compute an md5 hash of the file content.
-              # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
-              # in order to allow for the original file path to be hashed.
-              hashing-strategy: "path"
-
-              # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
-              # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
-              check-sibling-md5: false
-            }
-          }
-        }
-      }
-    }
-  }
-}
-
-database {
-  db.url = "jdbc:mysql://mysql-db/cromwell_db?allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true"
-  db.user = "cromwell"
-  db.password = "cromwell"
-  db.driver = "com.mysql.cj.jdbc.Driver"
-  profile = "slick.jdbc.MySQLProfile$"
-  db.connectionTimeout = 15000
-}
diff --git a/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql b/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
deleted file mode 100644
index b07938189e0..00000000000
--- a/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-CREATE USER 'cromwell'@'localhost' IDENTIFIED BY 'cromwell';
-GRANT ALL PRIVILEGES ON cromwell_db.* TO 'cromwell'@'localhost' WITH GRANT OPTION;
-CREATE USER 'cromwell'@'%' IDENTIFIED BY 'cromwell';
-GRANT ALL PRIVILEGES ON cromwell_db.* TO 'cromwell'@'%' WITH GRANT OPTION;
diff --git a/scripts/docker-compose-mysql/docker-compose.yml b/scripts/docker-compose-mysql/docker-compose.yml
deleted file mode 100644
index 3548919eadb..00000000000
--- a/scripts/docker-compose-mysql/docker-compose.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-version: '2'
-services:
-  cromwell:
-    build: 
-      context: ./compose/cromwell
-    volumes:
-      - ./cromwell-executions:/cromwell-working-dir/cromwell-executions
-    command: ["/wait-for-it/wait-for-it.sh mysql-db:3306 -t 120 -- java -Dconfig.file=/app-config/cromwell-application.conf -jar /app/cromwell.jar server"]
-    links:
-      - mysql-db
-    ports:
-      - "80:8000"
-  mysql-db:
-    image: "mysql:5.7"
-    environment:
-      - MYSQL_ROOT_PASSWORD=cromwell
-      - MYSQL_DATABASE=cromwell_db
-    volumes:
-      - ./compose/mysql/init:/docker-entrypoint-initdb.d
-      - ./compose/mysql/data:/var/lib/mysql
-    ports:
-      - "3307:3306"
diff --git a/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml b/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
deleted file mode 100644
index c7f0e1cee01..00000000000
--- a/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-version: '2'
-services:
-  cromwell:
-    volumes:
-      - $HOME/.config/gcloud:/root/.config/gcloud
-      - ./jes-cromwell/jes-config:/app-config
-    environment:
-      - GOOGLE_APPLICATION_CREDENTIALS=/root/.config/gcloud/application_default_credentials.json
-
diff --git a/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf b/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
deleted file mode 100644
index cac33bb42ac..00000000000
--- a/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
+++ /dev/null
@@ -1,73 +0,0 @@
-include required(classpath("application"))
-
-# Note: If you spot a mistake in this configuration sample, please let us know by making an issue at:
-# https://github.com/broadinstitute/cromwell/issues
-
-system.new-workflow-poll-rate=1
-
-google {
-
-  application-name = "cromwell"
-
-  auths = [
-    {
-      name = "application-default"
-      scheme = "application_default"
-    }
-  ]
-}
-
-engine {
-  filesystems {
-     gcs {
-       auth = "application-default"
-     }
-  }
-}
-
-call-caching {
-  enabled = false
-}
-
-backend {
-  default = "Jes"
-  providers {
-    Jes {
-          actor-factory = "cromwell.backend.impl.jes.JesBackendLifecycleActorFactory"
-          config {
-            // Google project
-            project = "broad-dsde-cromwell-dev"
-
-            // Base bucket for workflow executions
-            root = "gs://tjeandet-cromwell-execs"
-
-            // Polling for completion backs-off gradually for slower-running jobs.
-            // This is the maximum polling interval (in seconds):
-            maximum-polling-interval = 600
-
-            genomics {
-              // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
-              // Pipelines and manipulate auth JSONs.
-              auth = "application-default"
-              // Endpoint for APIs, no reason to change this unless directed by Google.
-              endpoint-url = "https://genomics.googleapis.com/"
-            }
-
-            filesystems {
-              gcs {
-                // A reference to a potentially different auth for manipulating files via engine functions.
-                auth = "application-default"
-              }
-            }
-          }
-    }
-  }
-}
-
-database {
-  db.url = "jdbc:mysql://mysql-db/cromwell_db?useSSL=false&rewriteBatchedStatements=true"
-  db.user = "cromwell"
-  db.password = "cromwell"
-  db.driver = "com.mysql.cj.jdbc.Driver"
-  profile = "slick.jdbc.MySQLProfile$"
-}
diff --git a/scripts/docker-develop/Dockerfile b/scripts/docker-develop/Dockerfile
deleted file mode 100644
index 340d7bc00c4..00000000000
--- a/scripts/docker-develop/Dockerfile
+++ /dev/null
@@ -1,64 +0,0 @@
-FROM ubuntu:focal
-
-ARG DEBIAN_FRONTEND=noninteractive
-
-RUN apt-get update -q && \
-    apt-get upgrade -qq && \
-    apt-get install -y curl wget gnupg gnupg2 && \
-    rm -rf /var/lib/apt/lists/*
-
-# docker build -t vanessa/cromwell-dev .
-
-# Development environment for Cromwell that includes:
-#
-#   Scala 2.13
-#   SBT 1.x
-#   Java 11
-#   Git
-
-# Env variables
-ENV SCALA_VERSION 2.13.8
-ENV SBT_VERSION 1.5.5
-
-#
-## AdoptOpenJDK Hotspot
-#
-# https://adoptopenjdk.net/installation.html#linux-pkg-deb
-RUN \
-wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add - && \
-echo \
-"deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2) main" | \
-tee /etc/apt/sources.list.d/adoptopenjdk.list && \
-apt-get update && \
-apt-get install -y adoptopenjdk-11-hotspot
-
-#
-## Scala
-#
-
-RUN mkdir -p /home/pigman && \
-    curl \
-    --location --fail --silent --show-error \
-    https://downloads.typesafe.com/scala/$SCALA_VERSION/scala-$SCALA_VERSION.tgz | tar xfz - -C /opt/ && \
-    echo >> /home/pigman/.bashrc && \
-    echo "export PATH=/opt/scala-$SCALA_VERSION/bin:$PATH" >> /home/pigman/.bashrc
-
-#
-## sbt
-#
-
-# non-deb package installation instructions adapted from
-# - https://github.com/sbt/sbt/releases/tag/v1.4.9
-# - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-RUN curl \
-    --location --fail --silent --show-error \
-    "https://github.com/sbt/sbt/releases/download/v$SBT_VERSION/sbt-$SBT_VERSION.tgz" | \
-    tar zxf - -C /usr/share && \
-    update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1 && \
-    sbt -Dsbt.supershell=false -Dsbt.rootdir=true sbtVersion
-
-# Instruct user to add code here during development
-RUN useradd pigman && \
-    mkdir -p /code
-
-WORKDIR /code
diff --git a/scripts/docker-develop/README.md b/scripts/docker-develop/README.md
deleted file mode 100644
index 20bd1a8203f..00000000000
--- a/scripts/docker-develop/README.md
+++ /dev/null
@@ -1,60 +0,0 @@
-# Cromwell Docker Development
-
-This is a container intended to help with development of Cromwell, in the
-case that you don't want to install the dependencies on your host. It
-includes the required software mentioned in [the developer docs](http://cromwell.readthedocs.io/en/develop/Building/) but with additional instructions to interact with the repository.
-
-As with the build instructions, first start by cloning the Cromwell repository from GitHub:
-
-```bash
-$ git clone git@github.com:broadinstitute/cromwell.git
-```
-
-And change into this directory:
-
-```bash
-$ cd cromwell/scripts/docker-develop
-```
-
-This is where this README.md sits with a [Dockerfile](Dockerfile)
-
-## Step 1. Build the Container
-From this folder with the Dockerfile, build the container. In the command below
-we are calling it `cromwell-dev` and you can choose to change this name if you want.
-
-```bash
-$ docker build -t cromwell-dev .
-```
-
-and change back to the root of the repository
-
-```bash
-cd ../../
-```
-
-## Step 2. Shell into Working Environment
-If you require a specific version of Cromwell as a starting point, do the appropriate `git checkout` now. 
-
-You are next going to want to bind the cromwell
-source code to be somewhere in the container. Actually, we have a `/code` directory
-ready for you to make this easy. Run this command from the base of the repository:
-
-```bash
-$ docker run -v $PWD/:/code -it cromwell-dev bash
-```
-
-## Step 4. The Development Steps
-
-You are going to use the command `sbt assembly` to create a runnable Cromwell JAR. The output
-will be `server/target`. Remember, here we are inside the container with scala and sbt:
-
-
-```bash
-$ sbt assembly
-```
-
-`sbt assembly` will build the runnable Cromwell JAR in `server/target/scala-2.13/` with a name like `cromwell-<VERSION>.jar`.
-
-You can then interact with it in the container, or on your host if you like. Remember that
-you have Java already in the container, so it makes sense to develop there.
-
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 71577ce1e4c..8a9cc27c298 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -746,7 +746,7 @@ cromwell::private::login_docker() {
 
 cromwell::private::render_secure_resources() {
     # Avoid docker output to sbt's stderr by pulling the image here
-    docker pull broadinstitute/dsde-toolbox:dev | cat
+    docker pull --quiet broadinstitute/dsde-toolbox:dev | cat
     # Copy the CI resources, then render the secure resources using Vault
     sbt -Dsbt.supershell=false --warn renderCiResources \
     || if [[ "${CROMWELL_BUILD_IS_CI}" == "true" ]]; then
diff --git a/src/ci/docker-compose/cromwell-test/Dockerfile b/src/ci/docker-compose/cromwell-test/Dockerfile
index 70e2477bb0e..319c462cfbd 100644
--- a/src/ci/docker-compose/cromwell-test/Dockerfile
+++ b/src/ci/docker-compose/cromwell-test/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:focal
+FROM ubuntu:latest
 
 WORKDIR /cromwell-test/
 COPY docker-setup.sh ./
diff --git a/src/ci/docker-compose/cromwell-test/docker-setup.sh b/src/ci/docker-compose/cromwell-test/docker-setup.sh
index c7970c7349b..37e624c6766 100755
--- a/src/ci/docker-compose/cromwell-test/docker-setup.sh
+++ b/src/ci/docker-compose/cromwell-test/docker-setup.sh
@@ -25,13 +25,11 @@ apt-get install -y \
     sudo \
     wget \
 
-# setup install for adoptopenjdk
-# https://adoptopenjdk.net/installation.html#linux-pkg-deb
-wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add -
-echo "deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(
-        grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
-    ) main" |
-    tee /etc/apt/sources.list.d/adoptopenjdk.list
+# setup install for Temurin
+# https://adoptium.net/installation/linux/
+mkdir -p /etc/apt/keyrings
+wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
+echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^UBUNTU_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
 
 # setup install for gcloud
 # https://cloud.google.com/sdk/docs/install#deb
@@ -52,7 +50,7 @@ add-apt-repository \
 # install packages that required setup
 apt-get update
 apt-get install -y \
-    adoptopenjdk-11-hotspot \
+    temurin-17-jdk \
     containerd.io \
     docker-ce \
     docker-ce-cli \
@@ -66,7 +64,7 @@ apt-get clean
 # non-deb package installation instructions adapted from
 # - https://github.com/sbt/sbt/releases/tag/v1.4.9
 # - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-curl -L --silent "https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz" |
+curl -L --silent "https://github.com/sbt/sbt/releases/download/v1.8.1/sbt-1.8.1.tgz" |
     tar zxf - -C /usr/share
 update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1
 
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
deleted file mode 100644
index 5d1b1e02c12..00000000000
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
+++ /dev/null
@@ -1,430 +0,0 @@
-package cromwell.backend.sfs
-
-import _root_.wdl.draft2.model.LocallyQualifiedName
-import akka.testkit.{TestDuration, TestProbe}
-import com.typesafe.config.ConfigFactory
-import common.collections.EnhancedCollections._
-import cromwell.backend.BackendJobExecutionActor.{
-  JobAbortedResponse,
-  JobFailedNonRetryableResponse,
-  JobSucceededResponse,
-  RunOnBackend
-}
-import cromwell.backend.BackendLifecycleActor.AbortJobCommand
-import cromwell.backend._
-import cromwell.backend.async.WrongReturnCode
-import cromwell.backend.io.JobPathsSpecHelper._
-import cromwell.backend.io.TestWorkflows._
-import cromwell.backend.io.{JobPathsWithDocker, TestWorkflows}
-import cromwell.backend.sfs.TestLocalAsyncJobExecutionActor._
-import cromwell.backend.standard.StandardValidatedRuntimeAttributesBuilder
-import cromwell.core.CromwellGraphNode._
-import cromwell.core.Tags._
-import cromwell.core._
-import cromwell.core.callcaching.NoDocker
-import cromwell.core.path.{DefaultPathBuilder, Path}
-import cromwell.services.keyvalue.KeyValueServiceActor._
-import cromwell.util.WomMocks
-import org.scalatest.concurrent.PatienceConfiguration.Timeout
-import org.scalatest.flatspec.AnyFlatSpecLike
-import org.scalatest.prop.TableDrivenPropertyChecks
-import org.scalatest.{Assertion, OptionValues}
-import wom.expression.NoIoFunctionSet
-import wom.graph.{CommandCallNode, WomIdentifier}
-import wom.types._
-import wom.values._
-
-import java.io.FileNotFoundException
-import scala.concurrent.duration._
-import scala.sys.process._
-
-class SharedFileSystemJobExecutionActorSpec
-    extends TestKitSuite
-    with AnyFlatSpecLike
-    with BackendSpec
-    with TableDrivenPropertyChecks
-    with OptionValues {
-
-  behavior of "SharedFileSystemJobExecutionActor"
-
-  lazy val runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition] =
-    StandardValidatedRuntimeAttributesBuilder.default(Some(TestConfig.optionalRuntimeConfig)).definitions.toSet
-
-  private val call = CommandCallNode(WomIdentifier("SfsJEASpec_call"), null, null, null, Set.empty, null, None)
-  private val mockBackendJobDescriptorKey = BackendJobDescriptorKey(call, None, 1)
-
-  def executeSpec(docker: Boolean): Any = {
-    val expectedOutputs: CallOutputs =
-      WomMocks.mockOutputExpectations(Map("hello.salutation" -> WomString("Hello you !")))
-
-    val expectedResponse = JobSucceededResponse(mockBackendJobDescriptorKey,
-                                                Some(0),
-                                                expectedOutputs,
-                                                None,
-                                                Seq.empty,
-                                                None,
-                                                resultGenerationMode = RunOnBackend
-    )
-    val runtime = if (docker) s"""runtime { docker: "$dockerImageUbuntu" }""" else ""
-    val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld, runtime = runtime)
-    val workflow = TestWorkflow(workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor, expectedResponse)
-    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
-                                                                    Map.empty,
-                                                                    WorkflowOptions.empty,
-                                                                    runtimeAttributeDefinitions
-                                ),
-                                workflow.config
-    )
-    testWorkflow(workflow, backend)
-  }
-
-  private val dockerImageUbuntu = "ubuntu:latest"
-
-  it should "docker pull images now so that 'DockerTest' specs below do not timeout" taggedAs DockerTest in {
-    /*
-    This is a poor substitute for `beforeAll()`.
-    If one wants to parallelize the test runs consider using a separate tagged-Suite with a `.beforeAll()`.
-    - https://medium.com/@linda0511ny/tag-whole-test-class-in-scalatest-94cd67fa85a4
-     */
-    List("docker", "pull", dockerImageUbuntu).! should be(0)
-  }
-
-  it should "execute an hello world workflow" in {
-    executeSpec(docker = false)
-  }
-
-  it should "execute an hello world workflow on Docker" taggedAs DockerTest in {
-    executeSpec(docker = true)
-  }
-
-  it should "send back an execution failure if the task fails" in {
-    val expectedResponse =
-      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
-                                    WrongReturnCode("wf_goodbye.goodbye:NA:1", 1, None),
-                                    Option(1)
-      )
-    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(GoodbyeWorld),
-                                TestConfig.backendRuntimeConfigDescriptor,
-                                expectedResponse
-    )
-    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
-                                                                    Map.empty,
-                                                                    WorkflowOptions.empty,
-                                                                    runtimeAttributeDefinitions
-                                ),
-                                workflow.config
-    )
-    testWorkflow(workflow, backend)
-  }
-
-  def localizationSpec(docker: Boolean): Assertion = {
-    def templateConf(localizers: String) = BackendConfigurationDescriptor(
-      ConfigFactory.parseString(s"""|{
-                                    |  root = "local-cromwell-executions"
-                                    |  filesystems {
-                                    |    local {
-                                    |      localization = [
-                                    |        $localizers
-                                    |      ]
-                                    |    }
-                                    |  }
-                                    |  default-runtime-attributes {
-                                    |  cpu: 1
-                                    |  failOnStderr: false
-                                    |  continueOnReturnCode: 0
-                                    |  }
-                                    |}
-                                    |""".stripMargin),
-      ConfigFactory.parseString("{}")
-    )
-
-    val hardConf = templateConf("hard-link")
-    val symConf = templateConf("soft-link")
-    val copyConf = templateConf("copy")
-
-    val jsonInputFile =
-      createCannedFile("localize", "content from json inputs", Option(DefaultPathBuilder.build(".").get))
-    val callInputFile =
-      createCannedFile("localize", "content from call inputs", Option(DefaultPathBuilder.build(".").get))
-    val inputs = Option(s"""{
-      "wf_localize.workflowFile": "${callInputFile.pathAsString}",
-      "wf_localize.localize.inputFileFromJson": "${jsonInputFile.pathAsString}"
-    }""")
-
-    val expectedOutputs: CallOutputs = WomMocks.mockOutputExpectations(
-      Map(
-        "localize.out" -> WomArray(WomArrayType(WomStringType),
-                                   List(WomString("content from json inputs"), WomString("content from call inputs"))
-        )
-      )
-    )
-
-    val confs = List(
-      (hardConf, false),
-      (copyConf, false)
-    ) ++ (if (!docker) List((symConf, true)) else List.empty)
-
-    val localizers = Table(
-      ("conf", "isSymLink"),
-      confs: _*
-    )
-
-    forAll(localizers) { (conf, isSymlink) =>
-      val runtime = if (docker) s"""runtime { docker: "$dockerImageUbuntu" } """ else ""
-      val workflowDescriptor = buildWdlWorkflowDescriptor(InputFiles, inputs, runtime = runtime)
-      val callInputs = Map(
-        "inputFileFromCallInputs" -> workflowDescriptor.knownValues.collectFirst {
-          case (outputPort, resolvedValue) if outputPort.fullyQualifiedName == "wf_localize.workflowFile" =>
-            resolvedValue
-        }.get,
-        "inputFileFromJson" -> workflowDescriptor.knownValues.collectFirst {
-          case (outputPort, resolvedValue)
-              if outputPort.fullyQualifiedName == "wf_localize.localize.inputFileFromJson" =>
-            resolvedValue
-        }.get
-      )
-
-      val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                                      callInputs,
-                                                                      WorkflowOptions.empty,
-                                                                      runtimeAttributeDefinitions
-                                  ),
-                                  conf
-      )
-      val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                                                    callInputs,
-                                                                                    WorkflowOptions.empty,
-                                                                                    runtimeAttributeDefinitions
-      )
-      val expectedResponse = JobSucceededResponse(jobDescriptor.key,
-                                                  Some(0),
-                                                  expectedOutputs,
-                                                  None,
-                                                  Seq.empty,
-                                                  None,
-                                                  resultGenerationMode = RunOnBackend
-      )
-
-      val jobPaths = JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, conf.backendConfig)
-
-      whenReady(backend.execute) { executionResponse =>
-        assertResponse(executionResponse, expectedResponse)
-        val localizedJsonInputFile =
-          DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString,
-                                 jsonInputFile.parent.pathAsString.hashCode.toString + "/" + jsonInputFile.name
-          )
-        val localizedCallInputFile =
-          DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString,
-                                 callInputFile.parent.pathAsString.hashCode.toString + "/" + callInputFile.name
-          )
-
-        localizedJsonInputFile.isSymbolicLink shouldBe isSymlink
-        val realJsonInputFile =
-          if (isSymlink) localizedJsonInputFile.symbolicLink.get else localizedJsonInputFile
-        realJsonInputFile.toFile should exist
-
-        localizedCallInputFile.isSymbolicLink shouldBe isSymlink
-        val realCallInputFile =
-          if (isSymlink) localizedCallInputFile.symbolicLink.get else localizedCallInputFile
-        realCallInputFile.toFile should exist
-      }
-    }
-  }
-
-  it should "execute calls with input files and localize them appropriately" in {
-    localizationSpec(docker = false)
-  }
-
-  it should "execute calls with input files and localize them appropriately (in Docker)" taggedAs DockerTest in {
-    localizationSpec(docker = true)
-  }
-
-  it should "abort a job and kill a process" in {
-    val workflowDescriptor = buildWdlWorkflowDescriptor(Sleep20)
-    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                                                  Map.empty,
-                                                                                  WorkflowOptions.empty,
-                                                                                  runtimeAttributeDefinitions
-    )
-    val backendRef = createBackendRef(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
-    val backend = backendRef.underlyingActor
-
-    val execute = backend.execute
-    backendRef ! AbortJobCommand
-
-    whenReady(execute) { executionResponse =>
-      executionResponse shouldBe a[JobAbortedResponse]
-    }
-  }
-
-  def recoverSpec(completed: Boolean, writeReturnCode: Boolean = true): Assertion = {
-    val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld)
-    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                                                  Map.empty,
-                                                                                  WorkflowOptions.empty,
-                                                                                  runtimeAttributeDefinitions
-    )
-    val backendRef = createBackendRef(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
-    val backend = backendRef.underlyingActor
-
-    val jobPaths = JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, ConfigFactory.empty)
-    jobPaths.callExecutionRoot.createPermissionedDirectories()
-    jobPaths.stdout.write("Hello stubby ! ")
-    jobPaths.stderr.touch()
-
-    val pid =
-      if (completed) {
-        if (writeReturnCode)
-          jobPaths.returnCode.write("0")
-        "0"
-      } else {
-        import sys.process._
-        val proc = Seq("bash", "-c", s"sleep 2; echo 0 > ${jobPaths.returnCode}").run()
-        val pField = proc.getClass.getDeclaredField("p")
-        pField.setAccessible(true)
-        val p = pField.get(proc)
-        val pidField = p.getClass.getDeclaredField("pid")
-        pidField.setAccessible(true)
-        pidField.get(p).toString
-      }
-
-    def execute = backend.recover
-
-    val kvJobKey =
-      KvJobKey(jobDescriptor.key.call.fullyQualifiedName, jobDescriptor.key.index, jobDescriptor.key.attempt)
-    val scopedKey = ScopedKey(workflowDescriptor.id, kvJobKey, SharedFileSystemAsyncJobExecutionActor.JobIdKey)
-    val kvPair = KvPair(scopedKey, pid)
-
-    val previousKvPutter = TestProbe("previousKvPutter")
-    val kvPutReq = KvPut(kvPair)
-    backendRef.underlyingActor.serviceRegistryActor.tell(msg = kvPutReq, sender = previousKvPutter.ref)
-    previousKvPutter.expectMsg(KvPutSuccess(kvPutReq))
-    val outputPort = jobDescriptor.taskCall.outputPorts.head
-    whenReady(execute, Timeout(10.seconds.dilated)) { executionResponse =>
-      if (writeReturnCode) {
-        executionResponse should be(a[JobSucceededResponse])
-        val succeededResponse = executionResponse.asInstanceOf[JobSucceededResponse]
-        succeededResponse.returnCode.value should be(0)
-        succeededResponse.jobOutputs should be(CallOutputs(Map(outputPort -> WomString("Hello stubby !"))))
-      } else {
-        executionResponse should be(a[JobFailedNonRetryableResponse])
-        val failedResponse = executionResponse.asInstanceOf[JobFailedNonRetryableResponse]
-        failedResponse.returnCode should be(empty)
-        failedResponse.throwable should be(a[RuntimeException])
-        failedResponse.throwable.getMessage should startWith("Unable to determine that 0 is alive, and")
-        failedResponse.throwable.getMessage should endWith("call-hello/execution/rc does not exist.")
-      }
-    }
-  }
-
-  it should "recover a job in progress" in {
-    recoverSpec(completed = false)
-  }
-
-  it should "recover a job that already completed" in {
-    recoverSpec(completed = true)
-  }
-
-  it should "not recover a job for a non-existent pid" in {
-    recoverSpec(completed = true, writeReturnCode = false)
-  }
-
-  it should "execute shards from a scatter" in {
-    val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.Scatter)
-
-    val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
-
-    0 to 2 foreach { shard =>
-      // This assumes that engine will give us the evaluated value of the scatter item at the correct index
-      // If this is not the case, more context/logic will need to be moved to the backend so it can figure it out by itself
-      val symbolMaps: Map[LocallyQualifiedName, WomInteger] = Map("intNumber" -> WomInteger(shard))
-
-      val evaluatedAttributes = call.callable.runtimeAttributes.attributes
-        .safeMapValues(_.evaluateValue(Map.empty, NoIoFunctionSet).getOrElse(fail("Can't evaluate runtime attribute")))
-      val runtimeAttributes: Map[LocallyQualifiedName, WomValue] =
-        RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, WorkflowOptions.empty)(
-          evaluatedAttributes
-        )
-
-      val jobDescriptor: BackendJobDescriptor =
-        BackendJobDescriptor(workflowDescriptor,
-                             BackendJobDescriptorKey(call, Option(shard), 1),
-                             runtimeAttributes,
-                             fqnWdlMapToDeclarationMap(symbolMaps),
-                             NoDocker,
-                             None,
-                             Map.empty
-        )
-      val backend = createBackend(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
-      val response =
-        JobSucceededResponse(
-          mockBackendJobDescriptorKey,
-          Some(0),
-          WomMocks.mockOutputExpectations(Map("scattering.out" -> WomInteger(shard))),
-          None,
-          Seq.empty,
-          None,
-          resultGenerationMode = RunOnBackend
-        )
-      executeJobAndAssertOutputs(backend, response)
-    }
-  }
-
-  it should "post process outputs" in {
-    val inputFile = createCannedFile("localize", "content from json inputs").pathAsString
-    val inputs = Option(s"""{
-      "wf_localize.localize.inputFile": "$inputFile"
-    }""")
-    val workflowDescriptor = buildWdlWorkflowDescriptor(OutputProcess, inputs)
-    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                                                  Map.empty,
-                                                                                  WorkflowOptions.empty,
-                                                                                  runtimeAttributeDefinitions
-    )
-    val backend = createBackend(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
-    val jobPaths =
-      JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor.backendConfig)
-    val expectedA = WomSingleFile(jobPaths.callExecutionRoot.resolve("a").toAbsolutePath.pathAsString)
-    val expectedB = WomSingleFile(jobPaths.callExecutionRoot.resolve("dir").toAbsolutePath.resolve("b").pathAsString)
-    val expectedOutputs = WomMocks.mockOutputExpectations(
-      Map(
-        "localize.o1" -> expectedA,
-        "localize.o2" -> WomArray(WomArrayType(WomSingleFileType), Seq(expectedA, expectedB)),
-        "localize.o3" -> WomSingleFile(inputFile)
-      )
-    )
-    val expectedResponse = JobSucceededResponse(jobDescriptor.key,
-                                                Some(0),
-                                                expectedOutputs,
-                                                None,
-                                                Seq.empty,
-                                                None,
-                                                resultGenerationMode = RunOnBackend
-    )
-
-    executeJobAndAssertOutputs(backend, expectedResponse)
-  }
-
-  it should "fail post processing if an output file is not found" in {
-    val expectedResponse =
-      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
-                                    new FileNotFoundException("Could not process output, file not found:"),
-                                    Option(0)
-      )
-    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(MissingOutputProcess),
-                                TestConfig.backendRuntimeConfigDescriptor,
-                                expectedResponse
-    )
-    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
-                                                                    Map.empty,
-                                                                    WorkflowOptions.empty,
-                                                                    runtimeAttributeDefinitions
-                                ),
-                                workflow.config
-    )
-    testWorkflow(workflow, backend)
-  }
-
-  def createCannedFile(prefix: String, contents: String, parent: Option[Path] = None): Path =
-    DefaultPathBuilder.createTempFile(prefix, ".out", parent).write(contents)
-}
diff --git a/wom/src/main/resources/reference.conf b/wom/src/main/resources/reference.conf
index 1907a23eac6..fce1a8e0283 100644
--- a/wom/src/main/resources/reference.conf
+++ b/wom/src/main/resources/reference.conf
@@ -2,7 +2,7 @@ yaml {
   # The maximum number of nodes (scalars + sequences + mappings) that will be parsed in a YAML
   max-nodes = 1000000
   # The maximum nested depth for nodes (sequences + mappings) that will be parsed in a YAML
-  max-depth = 1000
+  max-depth = 100
 }
 
 wom-parse {
diff --git a/wom/src/test/scala/wom/util/YamlUtilsSpec.scala b/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
index 986201a2213..8f5ddd22c95 100644
--- a/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
+++ b/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
@@ -80,7 +80,7 @@ class YamlUtilsSpec
       "a null yaml",
       null,
       refineMV[NonNegative](0),
-      null
+      "Cannot invoke \"String.length()\" because \"s\" is null"
     ),
     (
       "an empty yaml mapping when limited to zero nodes",
@@ -179,14 +179,14 @@ class YamlUtilsSpec
     val nesting = 1000000
     val yaml = ("[" * nesting) + ("]" * nesting)
     val exception: Exception = YamlUtils.parse(yaml).left.value
-    exception should have message "Parsing halted at node depth 1000" // <-- Updating here? Also get the docs too!
+    exception should have message "Parsing halted at node depth 100" // <-- Updating here? Also get the docs too!
   }
 
   it should "fail to parse deeply nested yaml mapping with the default configuration" in {
     val nesting = 1000000
     val yaml = ("{a:" * nesting) + "b" + ("}" * nesting)
     val exception: Exception = YamlUtils.parse(yaml).left.value
-    exception should have message "Parsing halted at node depth 1000" // <-- Updating here? Also get the docs too!
+    exception should have message "Parsing halted at node depth 100" // <-- Updating here? Also get the docs too!
   }
 
   it should "not parse a config with a negative value" in {

From 227778a521e4115fa9f031cdbbaa3dbce432e660 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 14 Dec 2023 10:54:46 -0500
Subject: [PATCH 258/326] Revert "WX-1409 Java 17 (#7342)" (#7343)

---
 .github/set_up_cromwell_action/action.yml     |  10 +-
 .github/workflows/chart_update_on_merge.yml   |   5 +-
 .github/workflows/docker_build_test.yml       |   5 +-
 .github/workflows/integration_tests.yml       |   8 -
 .github/workflows/trivy.yml                   |   5 +-
 .sdkmanrc                                     |   2 +-
 CHANGELOG.md                                  |   7 -
 .../api/DaemonizedDefaultThreadFactory.scala  |   3 +-
 .../scala/cloud/nio/spi/CloudNioPath.scala    |   2 +-
 .../main/scala/cloud/nio/spi/UnixPath.scala   |   2 +-
 docs/Configuring.md                           |   2 +-
 docs/Releases.md                              |   4 +-
 docs/tutorials/FiveMinuteIntro.md             |   6 +-
 project/Publishing.scala                      |   5 +-
 publish/docker-setup.sh                       |   2 +-
 runConfigurations/renderCiResources.run.xml   |   4 +-
 scripts/docker-compose-mysql/README.md        |   1 +
 .../compose/cromwell/Dockerfile               |   9 +
 .../app-config/cromwell-application.conf      |  61 +++
 .../compose/mysql/init/init_user.sql          |   4 +
 .../docker-compose-mysql/docker-compose.yml   |  22 +
 .../jes-cromwell/docker-compose.yml           |   9 +
 .../jes-cromwell/jes-config/application.conf  |  73 +++
 scripts/docker-develop/Dockerfile             |  64 +++
 scripts/docker-develop/README.md              |  60 +++
 src/ci/bin/test.inc.sh                        |   2 +-
 .../docker-compose/cromwell-test/Dockerfile   |   2 +-
 .../cromwell-test/docker-setup.sh             |  16 +-
 ...haredFileSystemJobExecutionActorSpec.scala | 430 ++++++++++++++++++
 wom/src/main/resources/reference.conf         |   2 +-
 .../test/scala/wom/util/YamlUtilsSpec.scala   |   6 +-
 31 files changed, 776 insertions(+), 57 deletions(-)
 create mode 100644 scripts/docker-compose-mysql/README.md
 create mode 100644 scripts/docker-compose-mysql/compose/cromwell/Dockerfile
 create mode 100644 scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
 create mode 100644 scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
 create mode 100644 scripts/docker-compose-mysql/docker-compose.yml
 create mode 100644 scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
 create mode 100644 scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
 create mode 100644 scripts/docker-develop/Dockerfile
 create mode 100644 scripts/docker-develop/README.md
 create mode 100644 supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index 1cbe834d2bd..13cb11601db 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -3,8 +3,7 @@
 name: 'Set Up Cromwell Steps'
 description: Specific steps that will set up git secrets, java, sbt, and Cromwell on the local machine. 
 inputs:
-  cromwell_repo_token:
-    description: "As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell."
+  cromwell_repo_token: #As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell.
     required: true
 
 runs:
@@ -13,13 +12,13 @@ runs:
       #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
       - uses: actions/checkout@v3
         name: Checkout Coursier Cache
-      - uses: coursier/cache-action@v6
+      - uses: coursier/cache-action@v6  
         name: Enable Coursier Cache
 
       #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
       - name: Git secrets setup 
         run: |
-          git clone --quiet https://github.com/awslabs/git-secrets.git ~/git-secrets
+          git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
           cd ~/git-secrets
           git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
           sudo make install
@@ -44,4 +43,5 @@ runs:
         uses: actions/setup-java@v3
         with:
           distribution: temurin
-          java-version: 17
+          java-version: 11
+
diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index b3f7199ab35..a2b14f2ec65 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -23,10 +23,9 @@ jobs:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
         path: cromwell
-    - uses: actions/setup-java@v4
+    - uses: olafurpg/setup-scala@v10
       with:
-        distribution: 'temurin'
-        java-version: '17'
+        java-version: adopt@1.11
     - name: Clone Cromwhelm
       uses: actions/checkout@v2
       with:
diff --git a/.github/workflows/docker_build_test.yml b/.github/workflows/docker_build_test.yml
index a50e39a380f..01c2ea502c9 100644
--- a/.github/workflows/docker_build_test.yml
+++ b/.github/workflows/docker_build_test.yml
@@ -25,10 +25,9 @@ jobs:
           repository: broadinstitute/cromwell
           token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
           path: cromwell
-      - uses: actions/setup-java@v4
+      - uses: olafurpg/setup-scala@v10
         with:
-          distribution: 'temurin'
-          java-version: '17'
+          java-version: adopt@1.11
       # The following invocation should be as similar as possible to the one in chart_update_on_merge.yml
       # To state the obvious: This test should not publish anything. It should simply verify that the build completes.
       - name: Build Cromwell Docker
diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 028b53db130..61ed3c5af41 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -104,14 +104,6 @@ jobs:
         set -e
         echo Running test.sh
         ./src/ci/bin/test.sh
-    # If a build step fails, activate SSH and idle for 60 minutes
-    # - name: Setup tmate session
-    #  if: ${{ failure() }}
-    #  uses: mxschmitt/action-tmate@v3
-    #  timeout-minutes: 60
-    #  with:
-    #    limit-access-to-actor: true
-    #    detached: true
     # always() is some github magic that forces the following step to run, even when the previous fails.
     # Without it, the if statement won't be evaluated on a test failure.
     - uses: ravsamhq/notify-slack-action@v2
diff --git a/.github/workflows/trivy.yml b/.github/workflows/trivy.yml
index 69a90937671..b005da65041 100644
--- a/.github/workflows/trivy.yml
+++ b/.github/workflows/trivy.yml
@@ -20,10 +20,9 @@ jobs:
       - uses: actions/checkout@v2
 
       # fetch SBT package
-      - uses: actions/setup-java@v4
+      - uses: olafurpg/setup-scala@v10
         with:
-          distribution: 'temurin'
-          java-version: '17'
+          java-version: adopt@1.11
 
       # set up SBT cache
       - uses: actions/cache@v2
diff --git a/.sdkmanrc b/.sdkmanrc
index f3b37566860..0262a261019 100644
--- a/.sdkmanrc
+++ b/.sdkmanrc
@@ -1,3 +1,3 @@
 # Enable auto-env through the sdkman_auto_env config
 # Add key=value pairs of SDKs to use below
-java=17.0.9-tem
+java=11.0.11.hs-adpt
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d670e74a43e..a581852c02e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,12 +1,5 @@
 # Cromwell Change Log
 
-## 87 Release Notes
-
-### Java 17
-
-As of this version, a distribution of Java 17 is required to run Cromwell. Cromwell is developed, tested, and
-containerized using [Eclipse Temurin](https://adoptium.net/temurin/releases/?version=17).
-
 ## 86 Release Notes
 
 ### GCP Batch
diff --git a/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala b/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
index d75299aa590..db9eb07d79b 100644
--- a/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
+++ b/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
@@ -14,7 +14,8 @@ import java.util.concurrent.atomic.AtomicInteger
   * > main thread).
   */
 object DaemonizedDefaultThreadFactory extends ThreadFactory {
-  private val group = Thread.currentThread.getThreadGroup
+  private val s = System.getSecurityManager
+  private val group = if (s != null) s.getThreadGroup else Thread.currentThread.getThreadGroup
   private val threadNumber = new AtomicInteger(1)
   private val namePrefix = "daemonpool-thread-"
 
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
index 530ba5526ef..b6803670d39 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
@@ -176,7 +176,7 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
   ): WatchKey = throw new UnsupportedOperationException
 
   override def iterator(): java.util.Iterator[Path] =
-    if (unixPath.izEmpty || unixPath.isRoot) {
+    if (unixPath.isEmpty || unixPath.isRoot) {
       java.util.Collections.emptyIterator()
     } else {
       unixPath.split().to(LazyList).map(part => newPath(UnixPath.getPath(part)).asInstanceOf[Path]).iterator.asJava
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
index 7d929d148ab..b7d9ed02035 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
@@ -67,7 +67,7 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
 
   def isAbsolute: Boolean = UnixPath.isAbsolute(path)
 
-  def izEmpty: Boolean = path.isEmpty
+  def isEmpty: Boolean = path.isEmpty
 
   def hasTrailingSeparator: Boolean = UnixPath.hasTrailingSeparator(path)
 
diff --git a/docs/Configuring.md b/docs/Configuring.md
index 288ec9723de..aa810d19a0c 100644
--- a/docs/Configuring.md
+++ b/docs/Configuring.md
@@ -689,7 +689,7 @@ This limit may be configured via the configuration value:
 
 ```hocon
 yaml {
-  max-depth = 100
+  max-depth = 1000
 }
 ```
 
diff --git a/docs/Releases.md b/docs/Releases.md
index a6a709518b9..9699d7d44bc 100644
--- a/docs/Releases.md
+++ b/docs/Releases.md
@@ -19,8 +19,8 @@ Mac users with Homebrew can also get Cromwell with the command `brew install cro
 This documentation frequently refers to a "Cromwell jar" with a name like `cromwell-<version>.jar`. 
 This is the main artifact in Cromwell releases that contains all executable Cromwell code and default configuration.   
 
-A distribution of Java 17 is required to run Cromwell. Cromwell is developed, tested, and containerized using
-[AdoptOpenJDK 17 HotSpot](https://adoptopenjdk.net/).
+A distribution of Java 11 is required to run Cromwell. Cromwell is developed, tested, and containerized using
+[AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/).
 
 For users running a Cromwell server [a docker image](https://hub.docker.com/r/broadinstitute/cromwell) has been made available.
 
diff --git a/docs/tutorials/FiveMinuteIntro.md b/docs/tutorials/FiveMinuteIntro.md
index f15e28087b9..1c16a56c606 100644
--- a/docs/tutorials/FiveMinuteIntro.md
+++ b/docs/tutorials/FiveMinuteIntro.md
@@ -3,11 +3,11 @@
 ### Prerequisites:
 
 * A Unix-based operating system (yes, that includes Mac!)
-* A Java 17 runtime environment 
+* A Java 11 runtime environment 
     * You can see what you have by running `$ java -version` on a terminal.
     * If not, consider installing via conda or brew [as explained here](../Releases.md).
-    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 17 build of [Temurin](https://adoptium.net/temurin/releases/?version=17)
-      * `sdk install 17.0.9-tem` as of the time of this writing
+    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 11 build of [Temurin](https://adoptium.net/temurin/releases/?version=11)
+      * `sdk install java 11.0.16-tem` as of the time of this writing
     * You might need to update the `export JAVA_HOME` in your bash profile to point to your JAVA install location.
 * A sense of adventure!
 
diff --git a/project/Publishing.scala b/project/Publishing.scala
index c8a601a4f0c..0af27e77147 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -63,7 +63,7 @@ object Publishing {
       val additionalDockerInstr: Seq[Instruction] = (dockerCustomSettings ?? Nil).value
 
       new Dockerfile {
-        from("us.gcr.io/broad-dsp-gcr-public/base/jre:17-debian")
+        from("us.gcr.io/broad-dsp-gcr-public/base/jre:11-debian")
         expose(8000)
         add(artifact, artifactTargetPath)
         runRaw(s"ln -s $artifactTargetPath /app/$projectName.jar")
@@ -163,7 +163,8 @@ object Publishing {
   val additionalResolvers = List(
     broadArtifactoryResolver,
     broadArtifactoryResolverSnap,
-  ) ++ Resolver.sonatypeOssRepos("releases")
+    Resolver.sonatypeRepo("releases")
+  )
 
   private val artifactoryCredentialsFile =
     file("target/ci/resources/artifactory_credentials.properties").getAbsoluteFile
diff --git a/publish/docker-setup.sh b/publish/docker-setup.sh
index bc39f31d10a..613d251df96 100755
--- a/publish/docker-setup.sh
+++ b/publish/docker-setup.sh
@@ -20,7 +20,7 @@ mkdir -p /etc/apt/keyrings
 wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
 echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
 apt update
-apt install -y temurin-17-jdk
+apt install -y temurin-11-jdk
 
 # Install jq 1.6 to ensure --rawfile is supported
 curl -L https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 -o /usr/bin/jq
diff --git a/runConfigurations/renderCiResources.run.xml b/runConfigurations/renderCiResources.run.xml
index ef56bf5e4fd..2a5ab5e29b8 100644
--- a/runConfigurations/renderCiResources.run.xml
+++ b/runConfigurations/renderCiResources.run.xml
@@ -7,8 +7,8 @@
     </option>
     <option name="tasks" value="renderCiResources" />
     <option name="useSbtShell" value="false" />
-    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M" />
+    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M -XX:+CMSClassUnloadingEnabled" />
     <option name="workingDir" value="$PROJECT_DIR$" />
     <method v="2" />
   </configuration>
-</component>
+</component>
\ No newline at end of file
diff --git a/scripts/docker-compose-mysql/README.md b/scripts/docker-compose-mysql/README.md
new file mode 100644
index 00000000000..8fcb404b069
--- /dev/null
+++ b/scripts/docker-compose-mysql/README.md
@@ -0,0 +1 @@
+Looking for the MySQL docs? Checkout the [Cromwell documentation](https://cromwell.readthedocs.io/en/develop/Configuring/#database)!
\ No newline at end of file
diff --git a/scripts/docker-compose-mysql/compose/cromwell/Dockerfile b/scripts/docker-compose-mysql/compose/cromwell/Dockerfile
new file mode 100644
index 00000000000..6bf9fd88bf9
--- /dev/null
+++ b/scripts/docker-compose-mysql/compose/cromwell/Dockerfile
@@ -0,0 +1,9 @@
+FROM broadinstitute/cromwell:develop
+
+RUN git clone https://github.com/vishnubob/wait-for-it.git
+RUN mkdir cromwell-working-dir
+WORKDIR cromwell-working-dir
+
+COPY ./app-config /app-config
+
+ENTRYPOINT ["/bin/sh", "-c"]
diff --git a/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf b/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
new file mode 100644
index 00000000000..a3b8d88ce3d
--- /dev/null
+++ b/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
@@ -0,0 +1,61 @@
+include required(classpath("application"))
+
+# Note: If you spot a mistake in this configuration sample, please let us know by making an issue at:
+# https://github.com/broadinstitute/cromwell/issues
+
+call-caching {
+  enabled = false
+}
+
+backend {
+  default = "Local"
+  providers {
+    Local {
+      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
+      config {
+        run-in-background = true
+        runtime-attributes = "String? docker Int? max_runtime = 2"
+        submit = "/bin/bash ${script}"
+        submit-docker = "docker run --rm -v ${cwd}:${docker_cwd} -i ${docker} /bin/bash < ${script}"
+
+        # Root directory where Cromwell writes job results. This directory must be
+        # visible and writeable by the Cromwell process as well as the jobs that Cromwell
+        # launches.
+        root: "cromwell-executions"
+
+        filesystems {
+          local {
+            localization: [
+              "soft-link", "hard-link", "copy"
+            ]
+
+            caching {
+              duplication-strategy: [
+                "soft-link"
+              ]
+
+              # Possible values: file, path
+              # "file" will compute an md5 hash of the file content.
+              # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
+              # in order to allow for the original file path to be hashed.
+              hashing-strategy: "path"
+
+              # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
+              # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
+              check-sibling-md5: false
+            }
+          }
+        }
+      }
+    }
+  }
+}
+
+database {
+  db.url = "jdbc:mysql://mysql-db/cromwell_db?allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true"
+  db.user = "cromwell"
+  db.password = "cromwell"
+  db.driver = "com.mysql.cj.jdbc.Driver"
+  profile = "slick.jdbc.MySQLProfile$"
+  db.connectionTimeout = 15000
+}
diff --git a/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql b/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
new file mode 100644
index 00000000000..b07938189e0
--- /dev/null
+++ b/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
@@ -0,0 +1,4 @@
+CREATE USER 'cromwell'@'localhost' IDENTIFIED BY 'cromwell';
+GRANT ALL PRIVILEGES ON cromwell_db.* TO 'cromwell'@'localhost' WITH GRANT OPTION;
+CREATE USER 'cromwell'@'%' IDENTIFIED BY 'cromwell';
+GRANT ALL PRIVILEGES ON cromwell_db.* TO 'cromwell'@'%' WITH GRANT OPTION;
diff --git a/scripts/docker-compose-mysql/docker-compose.yml b/scripts/docker-compose-mysql/docker-compose.yml
new file mode 100644
index 00000000000..3548919eadb
--- /dev/null
+++ b/scripts/docker-compose-mysql/docker-compose.yml
@@ -0,0 +1,22 @@
+version: '2'
+services:
+  cromwell:
+    build: 
+      context: ./compose/cromwell
+    volumes:
+      - ./cromwell-executions:/cromwell-working-dir/cromwell-executions
+    command: ["/wait-for-it/wait-for-it.sh mysql-db:3306 -t 120 -- java -Dconfig.file=/app-config/cromwell-application.conf -jar /app/cromwell.jar server"]
+    links:
+      - mysql-db
+    ports:
+      - "80:8000"
+  mysql-db:
+    image: "mysql:5.7"
+    environment:
+      - MYSQL_ROOT_PASSWORD=cromwell
+      - MYSQL_DATABASE=cromwell_db
+    volumes:
+      - ./compose/mysql/init:/docker-entrypoint-initdb.d
+      - ./compose/mysql/data:/var/lib/mysql
+    ports:
+      - "3307:3306"
diff --git a/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml b/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
new file mode 100644
index 00000000000..c7f0e1cee01
--- /dev/null
+++ b/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
@@ -0,0 +1,9 @@
+version: '2'
+services:
+  cromwell:
+    volumes:
+      - $HOME/.config/gcloud:/root/.config/gcloud
+      - ./jes-cromwell/jes-config:/app-config
+    environment:
+      - GOOGLE_APPLICATION_CREDENTIALS=/root/.config/gcloud/application_default_credentials.json
+
diff --git a/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf b/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
new file mode 100644
index 00000000000..cac33bb42ac
--- /dev/null
+++ b/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
@@ -0,0 +1,73 @@
+include required(classpath("application"))
+
+# Note: If you spot a mistake in this configuration sample, please let us know by making an issue at:
+# https://github.com/broadinstitute/cromwell/issues
+
+system.new-workflow-poll-rate=1
+
+google {
+
+  application-name = "cromwell"
+
+  auths = [
+    {
+      name = "application-default"
+      scheme = "application_default"
+    }
+  ]
+}
+
+engine {
+  filesystems {
+     gcs {
+       auth = "application-default"
+     }
+  }
+}
+
+call-caching {
+  enabled = false
+}
+
+backend {
+  default = "Jes"
+  providers {
+    Jes {
+          actor-factory = "cromwell.backend.impl.jes.JesBackendLifecycleActorFactory"
+          config {
+            // Google project
+            project = "broad-dsde-cromwell-dev"
+
+            // Base bucket for workflow executions
+            root = "gs://tjeandet-cromwell-execs"
+
+            // Polling for completion backs-off gradually for slower-running jobs.
+            // This is the maximum polling interval (in seconds):
+            maximum-polling-interval = 600
+
+            genomics {
+              // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
+              // Pipelines and manipulate auth JSONs.
+              auth = "application-default"
+              // Endpoint for APIs, no reason to change this unless directed by Google.
+              endpoint-url = "https://genomics.googleapis.com/"
+            }
+
+            filesystems {
+              gcs {
+                // A reference to a potentially different auth for manipulating files via engine functions.
+                auth = "application-default"
+              }
+            }
+          }
+    }
+  }
+}
+
+database {
+  db.url = "jdbc:mysql://mysql-db/cromwell_db?useSSL=false&rewriteBatchedStatements=true"
+  db.user = "cromwell"
+  db.password = "cromwell"
+  db.driver = "com.mysql.cj.jdbc.Driver"
+  profile = "slick.jdbc.MySQLProfile$"
+}
diff --git a/scripts/docker-develop/Dockerfile b/scripts/docker-develop/Dockerfile
new file mode 100644
index 00000000000..340d7bc00c4
--- /dev/null
+++ b/scripts/docker-develop/Dockerfile
@@ -0,0 +1,64 @@
+FROM ubuntu:focal
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update -q && \
+    apt-get upgrade -qq && \
+    apt-get install -y curl wget gnupg gnupg2 && \
+    rm -rf /var/lib/apt/lists/*
+
+# docker build -t vanessa/cromwell-dev .
+
+# Development environment for Cromwell that includes:
+#
+#   Scala 2.13
+#   SBT 1.x
+#   Java 11
+#   Git
+
+# Env variables
+ENV SCALA_VERSION 2.13.8
+ENV SBT_VERSION 1.5.5
+
+#
+## AdoptOpenJDK Hotspot
+#
+# https://adoptopenjdk.net/installation.html#linux-pkg-deb
+RUN \
+wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add - && \
+echo \
+"deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2) main" | \
+tee /etc/apt/sources.list.d/adoptopenjdk.list && \
+apt-get update && \
+apt-get install -y adoptopenjdk-11-hotspot
+
+#
+## Scala
+#
+
+RUN mkdir -p /home/pigman && \
+    curl \
+    --location --fail --silent --show-error \
+    https://downloads.typesafe.com/scala/$SCALA_VERSION/scala-$SCALA_VERSION.tgz | tar xfz - -C /opt/ && \
+    echo >> /home/pigman/.bashrc && \
+    echo "export PATH=/opt/scala-$SCALA_VERSION/bin:$PATH" >> /home/pigman/.bashrc
+
+#
+## sbt
+#
+
+# non-deb package installation instructions adapted from
+# - https://github.com/sbt/sbt/releases/tag/v1.4.9
+# - https://github.com/broadinstitute/scala-baseimage/pull/4/files
+RUN curl \
+    --location --fail --silent --show-error \
+    "https://github.com/sbt/sbt/releases/download/v$SBT_VERSION/sbt-$SBT_VERSION.tgz" | \
+    tar zxf - -C /usr/share && \
+    update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1 && \
+    sbt -Dsbt.supershell=false -Dsbt.rootdir=true sbtVersion
+
+# Instruct user to add code here during development
+RUN useradd pigman && \
+    mkdir -p /code
+
+WORKDIR /code
diff --git a/scripts/docker-develop/README.md b/scripts/docker-develop/README.md
new file mode 100644
index 00000000000..20bd1a8203f
--- /dev/null
+++ b/scripts/docker-develop/README.md
@@ -0,0 +1,60 @@
+# Cromwell Docker Development
+
+This is a container intended to help with development of Cromwell, in the
+case that you don't want to install the dependencies on your host. It
+includes the required software mentioned in [the developer docs](http://cromwell.readthedocs.io/en/develop/Building/) but with additional instructions to interact with the repository.
+
+As with the build instructions, first start by cloning the Cromwell repository from GitHub:
+
+```bash
+$ git clone git@github.com:broadinstitute/cromwell.git
+```
+
+And change into this directory:
+
+```bash
+$ cd cromwell/scripts/docker-develop
+```
+
+This is where this README.md sits with a [Dockerfile](Dockerfile)
+
+## Step 1. Build the Container
+From this folder with the Dockerfile, build the container. In the command below
+we are calling it `cromwell-dev` and you can choose to change this name if you want.
+
+```bash
+$ docker build -t cromwell-dev .
+```
+
+and change back to the root of the repository
+
+```bash
+cd ../../
+```
+
+## Step 2. Shell into Working Environment
+If you require a specific version of Cromwell as a starting point, do the appropriate `git checkout` now. 
+
+You are next going to want to bind the cromwell
+source code to be somewhere in the container. Actually, we have a `/code` directory
+ready for you to make this easy. Run this command from the base of the repository:
+
+```bash
+$ docker run -v $PWD/:/code -it cromwell-dev bash
+```
+
+## Step 4. The Development Steps
+
+You are going to use the command `sbt assembly` to create a runnable Cromwell JAR. The output
+will be `server/target`. Remember, here we are inside the container with scala and sbt:
+
+
+```bash
+$ sbt assembly
+```
+
+`sbt assembly` will build the runnable Cromwell JAR in `server/target/scala-2.13/` with a name like `cromwell-<VERSION>.jar`.
+
+You can then interact with it in the container, or on your host if you like. Remember that
+you have Java already in the container, so it makes sense to develop there.
+
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 8a9cc27c298..71577ce1e4c 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -746,7 +746,7 @@ cromwell::private::login_docker() {
 
 cromwell::private::render_secure_resources() {
     # Avoid docker output to sbt's stderr by pulling the image here
-    docker pull --quiet broadinstitute/dsde-toolbox:dev | cat
+    docker pull broadinstitute/dsde-toolbox:dev | cat
     # Copy the CI resources, then render the secure resources using Vault
     sbt -Dsbt.supershell=false --warn renderCiResources \
     || if [[ "${CROMWELL_BUILD_IS_CI}" == "true" ]]; then
diff --git a/src/ci/docker-compose/cromwell-test/Dockerfile b/src/ci/docker-compose/cromwell-test/Dockerfile
index 319c462cfbd..70e2477bb0e 100644
--- a/src/ci/docker-compose/cromwell-test/Dockerfile
+++ b/src/ci/docker-compose/cromwell-test/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:latest
+FROM ubuntu:focal
 
 WORKDIR /cromwell-test/
 COPY docker-setup.sh ./
diff --git a/src/ci/docker-compose/cromwell-test/docker-setup.sh b/src/ci/docker-compose/cromwell-test/docker-setup.sh
index 37e624c6766..c7970c7349b 100755
--- a/src/ci/docker-compose/cromwell-test/docker-setup.sh
+++ b/src/ci/docker-compose/cromwell-test/docker-setup.sh
@@ -25,11 +25,13 @@ apt-get install -y \
     sudo \
     wget \
 
-# setup install for Temurin
-# https://adoptium.net/installation/linux/
-mkdir -p /etc/apt/keyrings
-wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
-echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^UBUNTU_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
+# setup install for adoptopenjdk
+# https://adoptopenjdk.net/installation.html#linux-pkg-deb
+wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add -
+echo "deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(
+        grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
+    ) main" |
+    tee /etc/apt/sources.list.d/adoptopenjdk.list
 
 # setup install for gcloud
 # https://cloud.google.com/sdk/docs/install#deb
@@ -50,7 +52,7 @@ add-apt-repository \
 # install packages that required setup
 apt-get update
 apt-get install -y \
-    temurin-17-jdk \
+    adoptopenjdk-11-hotspot \
     containerd.io \
     docker-ce \
     docker-ce-cli \
@@ -64,7 +66,7 @@ apt-get clean
 # non-deb package installation instructions adapted from
 # - https://github.com/sbt/sbt/releases/tag/v1.4.9
 # - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-curl -L --silent "https://github.com/sbt/sbt/releases/download/v1.8.1/sbt-1.8.1.tgz" |
+curl -L --silent "https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz" |
     tar zxf - -C /usr/share
 update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1
 
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
new file mode 100644
index 00000000000..5d1b1e02c12
--- /dev/null
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
@@ -0,0 +1,430 @@
+package cromwell.backend.sfs
+
+import _root_.wdl.draft2.model.LocallyQualifiedName
+import akka.testkit.{TestDuration, TestProbe}
+import com.typesafe.config.ConfigFactory
+import common.collections.EnhancedCollections._
+import cromwell.backend.BackendJobExecutionActor.{
+  JobAbortedResponse,
+  JobFailedNonRetryableResponse,
+  JobSucceededResponse,
+  RunOnBackend
+}
+import cromwell.backend.BackendLifecycleActor.AbortJobCommand
+import cromwell.backend._
+import cromwell.backend.async.WrongReturnCode
+import cromwell.backend.io.JobPathsSpecHelper._
+import cromwell.backend.io.TestWorkflows._
+import cromwell.backend.io.{JobPathsWithDocker, TestWorkflows}
+import cromwell.backend.sfs.TestLocalAsyncJobExecutionActor._
+import cromwell.backend.standard.StandardValidatedRuntimeAttributesBuilder
+import cromwell.core.CromwellGraphNode._
+import cromwell.core.Tags._
+import cromwell.core._
+import cromwell.core.callcaching.NoDocker
+import cromwell.core.path.{DefaultPathBuilder, Path}
+import cromwell.services.keyvalue.KeyValueServiceActor._
+import cromwell.util.WomMocks
+import org.scalatest.concurrent.PatienceConfiguration.Timeout
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.prop.TableDrivenPropertyChecks
+import org.scalatest.{Assertion, OptionValues}
+import wom.expression.NoIoFunctionSet
+import wom.graph.{CommandCallNode, WomIdentifier}
+import wom.types._
+import wom.values._
+
+import java.io.FileNotFoundException
+import scala.concurrent.duration._
+import scala.sys.process._
+
+class SharedFileSystemJobExecutionActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with BackendSpec
+    with TableDrivenPropertyChecks
+    with OptionValues {
+
+  behavior of "SharedFileSystemJobExecutionActor"
+
+  lazy val runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition] =
+    StandardValidatedRuntimeAttributesBuilder.default(Some(TestConfig.optionalRuntimeConfig)).definitions.toSet
+
+  private val call = CommandCallNode(WomIdentifier("SfsJEASpec_call"), null, null, null, Set.empty, null, None)
+  private val mockBackendJobDescriptorKey = BackendJobDescriptorKey(call, None, 1)
+
+  def executeSpec(docker: Boolean): Any = {
+    val expectedOutputs: CallOutputs =
+      WomMocks.mockOutputExpectations(Map("hello.salutation" -> WomString("Hello you !")))
+
+    val expectedResponse = JobSucceededResponse(mockBackendJobDescriptorKey,
+                                                Some(0),
+                                                expectedOutputs,
+                                                None,
+                                                Seq.empty,
+                                                None,
+                                                resultGenerationMode = RunOnBackend
+    )
+    val runtime = if (docker) s"""runtime { docker: "$dockerImageUbuntu" }""" else ""
+    val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld, runtime = runtime)
+    val workflow = TestWorkflow(workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor, expectedResponse)
+    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
+                                                                    Map.empty,
+                                                                    WorkflowOptions.empty,
+                                                                    runtimeAttributeDefinitions
+                                ),
+                                workflow.config
+    )
+    testWorkflow(workflow, backend)
+  }
+
+  private val dockerImageUbuntu = "ubuntu:latest"
+
+  it should "docker pull images now so that 'DockerTest' specs below do not timeout" taggedAs DockerTest in {
+    /*
+    This is a poor substitute for `beforeAll()`.
+    If one wants to parallelize the test runs consider using a separate tagged-Suite with a `.beforeAll()`.
+    - https://medium.com/@linda0511ny/tag-whole-test-class-in-scalatest-94cd67fa85a4
+     */
+    List("docker", "pull", dockerImageUbuntu).! should be(0)
+  }
+
+  it should "execute an hello world workflow" in {
+    executeSpec(docker = false)
+  }
+
+  it should "execute an hello world workflow on Docker" taggedAs DockerTest in {
+    executeSpec(docker = true)
+  }
+
+  it should "send back an execution failure if the task fails" in {
+    val expectedResponse =
+      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
+                                    WrongReturnCode("wf_goodbye.goodbye:NA:1", 1, None),
+                                    Option(1)
+      )
+    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(GoodbyeWorld),
+                                TestConfig.backendRuntimeConfigDescriptor,
+                                expectedResponse
+    )
+    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
+                                                                    Map.empty,
+                                                                    WorkflowOptions.empty,
+                                                                    runtimeAttributeDefinitions
+                                ),
+                                workflow.config
+    )
+    testWorkflow(workflow, backend)
+  }
+
+  def localizationSpec(docker: Boolean): Assertion = {
+    def templateConf(localizers: String) = BackendConfigurationDescriptor(
+      ConfigFactory.parseString(s"""|{
+                                    |  root = "local-cromwell-executions"
+                                    |  filesystems {
+                                    |    local {
+                                    |      localization = [
+                                    |        $localizers
+                                    |      ]
+                                    |    }
+                                    |  }
+                                    |  default-runtime-attributes {
+                                    |  cpu: 1
+                                    |  failOnStderr: false
+                                    |  continueOnReturnCode: 0
+                                    |  }
+                                    |}
+                                    |""".stripMargin),
+      ConfigFactory.parseString("{}")
+    )
+
+    val hardConf = templateConf("hard-link")
+    val symConf = templateConf("soft-link")
+    val copyConf = templateConf("copy")
+
+    val jsonInputFile =
+      createCannedFile("localize", "content from json inputs", Option(DefaultPathBuilder.build(".").get))
+    val callInputFile =
+      createCannedFile("localize", "content from call inputs", Option(DefaultPathBuilder.build(".").get))
+    val inputs = Option(s"""{
+      "wf_localize.workflowFile": "${callInputFile.pathAsString}",
+      "wf_localize.localize.inputFileFromJson": "${jsonInputFile.pathAsString}"
+    }""")
+
+    val expectedOutputs: CallOutputs = WomMocks.mockOutputExpectations(
+      Map(
+        "localize.out" -> WomArray(WomArrayType(WomStringType),
+                                   List(WomString("content from json inputs"), WomString("content from call inputs"))
+        )
+      )
+    )
+
+    val confs = List(
+      (hardConf, false),
+      (copyConf, false)
+    ) ++ (if (!docker) List((symConf, true)) else List.empty)
+
+    val localizers = Table(
+      ("conf", "isSymLink"),
+      confs: _*
+    )
+
+    forAll(localizers) { (conf, isSymlink) =>
+      val runtime = if (docker) s"""runtime { docker: "$dockerImageUbuntu" } """ else ""
+      val workflowDescriptor = buildWdlWorkflowDescriptor(InputFiles, inputs, runtime = runtime)
+      val callInputs = Map(
+        "inputFileFromCallInputs" -> workflowDescriptor.knownValues.collectFirst {
+          case (outputPort, resolvedValue) if outputPort.fullyQualifiedName == "wf_localize.workflowFile" =>
+            resolvedValue
+        }.get,
+        "inputFileFromJson" -> workflowDescriptor.knownValues.collectFirst {
+          case (outputPort, resolvedValue)
+              if outputPort.fullyQualifiedName == "wf_localize.localize.inputFileFromJson" =>
+            resolvedValue
+        }.get
+      )
+
+      val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                      callInputs,
+                                                                      WorkflowOptions.empty,
+                                                                      runtimeAttributeDefinitions
+                                  ),
+                                  conf
+      )
+      val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                    callInputs,
+                                                                                    WorkflowOptions.empty,
+                                                                                    runtimeAttributeDefinitions
+      )
+      val expectedResponse = JobSucceededResponse(jobDescriptor.key,
+                                                  Some(0),
+                                                  expectedOutputs,
+                                                  None,
+                                                  Seq.empty,
+                                                  None,
+                                                  resultGenerationMode = RunOnBackend
+      )
+
+      val jobPaths = JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, conf.backendConfig)
+
+      whenReady(backend.execute) { executionResponse =>
+        assertResponse(executionResponse, expectedResponse)
+        val localizedJsonInputFile =
+          DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString,
+                                 jsonInputFile.parent.pathAsString.hashCode.toString + "/" + jsonInputFile.name
+          )
+        val localizedCallInputFile =
+          DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString,
+                                 callInputFile.parent.pathAsString.hashCode.toString + "/" + callInputFile.name
+          )
+
+        localizedJsonInputFile.isSymbolicLink shouldBe isSymlink
+        val realJsonInputFile =
+          if (isSymlink) localizedJsonInputFile.symbolicLink.get else localizedJsonInputFile
+        realJsonInputFile.toFile should exist
+
+        localizedCallInputFile.isSymbolicLink shouldBe isSymlink
+        val realCallInputFile =
+          if (isSymlink) localizedCallInputFile.symbolicLink.get else localizedCallInputFile
+        realCallInputFile.toFile should exist
+      }
+    }
+  }
+
+  it should "execute calls with input files and localize them appropriately" in {
+    localizationSpec(docker = false)
+  }
+
+  it should "execute calls with input files and localize them appropriately (in Docker)" taggedAs DockerTest in {
+    localizationSpec(docker = true)
+  }
+
+  it should "abort a job and kill a process" in {
+    val workflowDescriptor = buildWdlWorkflowDescriptor(Sleep20)
+    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                  Map.empty,
+                                                                                  WorkflowOptions.empty,
+                                                                                  runtimeAttributeDefinitions
+    )
+    val backendRef = createBackendRef(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
+    val backend = backendRef.underlyingActor
+
+    val execute = backend.execute
+    backendRef ! AbortJobCommand
+
+    whenReady(execute) { executionResponse =>
+      executionResponse shouldBe a[JobAbortedResponse]
+    }
+  }
+
+  def recoverSpec(completed: Boolean, writeReturnCode: Boolean = true): Assertion = {
+    val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld)
+    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                  Map.empty,
+                                                                                  WorkflowOptions.empty,
+                                                                                  runtimeAttributeDefinitions
+    )
+    val backendRef = createBackendRef(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
+    val backend = backendRef.underlyingActor
+
+    val jobPaths = JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, ConfigFactory.empty)
+    jobPaths.callExecutionRoot.createPermissionedDirectories()
+    jobPaths.stdout.write("Hello stubby ! ")
+    jobPaths.stderr.touch()
+
+    val pid =
+      if (completed) {
+        if (writeReturnCode)
+          jobPaths.returnCode.write("0")
+        "0"
+      } else {
+        import sys.process._
+        val proc = Seq("bash", "-c", s"sleep 2; echo 0 > ${jobPaths.returnCode}").run()
+        val pField = proc.getClass.getDeclaredField("p")
+        pField.setAccessible(true)
+        val p = pField.get(proc)
+        val pidField = p.getClass.getDeclaredField("pid")
+        pidField.setAccessible(true)
+        pidField.get(p).toString
+      }
+
+    def execute = backend.recover
+
+    val kvJobKey =
+      KvJobKey(jobDescriptor.key.call.fullyQualifiedName, jobDescriptor.key.index, jobDescriptor.key.attempt)
+    val scopedKey = ScopedKey(workflowDescriptor.id, kvJobKey, SharedFileSystemAsyncJobExecutionActor.JobIdKey)
+    val kvPair = KvPair(scopedKey, pid)
+
+    val previousKvPutter = TestProbe("previousKvPutter")
+    val kvPutReq = KvPut(kvPair)
+    backendRef.underlyingActor.serviceRegistryActor.tell(msg = kvPutReq, sender = previousKvPutter.ref)
+    previousKvPutter.expectMsg(KvPutSuccess(kvPutReq))
+    val outputPort = jobDescriptor.taskCall.outputPorts.head
+    whenReady(execute, Timeout(10.seconds.dilated)) { executionResponse =>
+      if (writeReturnCode) {
+        executionResponse should be(a[JobSucceededResponse])
+        val succeededResponse = executionResponse.asInstanceOf[JobSucceededResponse]
+        succeededResponse.returnCode.value should be(0)
+        succeededResponse.jobOutputs should be(CallOutputs(Map(outputPort -> WomString("Hello stubby !"))))
+      } else {
+        executionResponse should be(a[JobFailedNonRetryableResponse])
+        val failedResponse = executionResponse.asInstanceOf[JobFailedNonRetryableResponse]
+        failedResponse.returnCode should be(empty)
+        failedResponse.throwable should be(a[RuntimeException])
+        failedResponse.throwable.getMessage should startWith("Unable to determine that 0 is alive, and")
+        failedResponse.throwable.getMessage should endWith("call-hello/execution/rc does not exist.")
+      }
+    }
+  }
+
+  it should "recover a job in progress" in {
+    recoverSpec(completed = false)
+  }
+
+  it should "recover a job that already completed" in {
+    recoverSpec(completed = true)
+  }
+
+  it should "not recover a job for a non-existent pid" in {
+    recoverSpec(completed = true, writeReturnCode = false)
+  }
+
+  it should "execute shards from a scatter" in {
+    val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.Scatter)
+
+    val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
+
+    0 to 2 foreach { shard =>
+      // This assumes that engine will give us the evaluated value of the scatter item at the correct index
+      // If this is not the case, more context/logic will need to be moved to the backend so it can figure it out by itself
+      val symbolMaps: Map[LocallyQualifiedName, WomInteger] = Map("intNumber" -> WomInteger(shard))
+
+      val evaluatedAttributes = call.callable.runtimeAttributes.attributes
+        .safeMapValues(_.evaluateValue(Map.empty, NoIoFunctionSet).getOrElse(fail("Can't evaluate runtime attribute")))
+      val runtimeAttributes: Map[LocallyQualifiedName, WomValue] =
+        RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, WorkflowOptions.empty)(
+          evaluatedAttributes
+        )
+
+      val jobDescriptor: BackendJobDescriptor =
+        BackendJobDescriptor(workflowDescriptor,
+                             BackendJobDescriptorKey(call, Option(shard), 1),
+                             runtimeAttributes,
+                             fqnWdlMapToDeclarationMap(symbolMaps),
+                             NoDocker,
+                             None,
+                             Map.empty
+        )
+      val backend = createBackend(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
+      val response =
+        JobSucceededResponse(
+          mockBackendJobDescriptorKey,
+          Some(0),
+          WomMocks.mockOutputExpectations(Map("scattering.out" -> WomInteger(shard))),
+          None,
+          Seq.empty,
+          None,
+          resultGenerationMode = RunOnBackend
+        )
+      executeJobAndAssertOutputs(backend, response)
+    }
+  }
+
+  it should "post process outputs" in {
+    val inputFile = createCannedFile("localize", "content from json inputs").pathAsString
+    val inputs = Option(s"""{
+      "wf_localize.localize.inputFile": "$inputFile"
+    }""")
+    val workflowDescriptor = buildWdlWorkflowDescriptor(OutputProcess, inputs)
+    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                  Map.empty,
+                                                                                  WorkflowOptions.empty,
+                                                                                  runtimeAttributeDefinitions
+    )
+    val backend = createBackend(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
+    val jobPaths =
+      JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor.backendConfig)
+    val expectedA = WomSingleFile(jobPaths.callExecutionRoot.resolve("a").toAbsolutePath.pathAsString)
+    val expectedB = WomSingleFile(jobPaths.callExecutionRoot.resolve("dir").toAbsolutePath.resolve("b").pathAsString)
+    val expectedOutputs = WomMocks.mockOutputExpectations(
+      Map(
+        "localize.o1" -> expectedA,
+        "localize.o2" -> WomArray(WomArrayType(WomSingleFileType), Seq(expectedA, expectedB)),
+        "localize.o3" -> WomSingleFile(inputFile)
+      )
+    )
+    val expectedResponse = JobSucceededResponse(jobDescriptor.key,
+                                                Some(0),
+                                                expectedOutputs,
+                                                None,
+                                                Seq.empty,
+                                                None,
+                                                resultGenerationMode = RunOnBackend
+    )
+
+    executeJobAndAssertOutputs(backend, expectedResponse)
+  }
+
+  it should "fail post processing if an output file is not found" in {
+    val expectedResponse =
+      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
+                                    new FileNotFoundException("Could not process output, file not found:"),
+                                    Option(0)
+      )
+    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(MissingOutputProcess),
+                                TestConfig.backendRuntimeConfigDescriptor,
+                                expectedResponse
+    )
+    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
+                                                                    Map.empty,
+                                                                    WorkflowOptions.empty,
+                                                                    runtimeAttributeDefinitions
+                                ),
+                                workflow.config
+    )
+    testWorkflow(workflow, backend)
+  }
+
+  def createCannedFile(prefix: String, contents: String, parent: Option[Path] = None): Path =
+    DefaultPathBuilder.createTempFile(prefix, ".out", parent).write(contents)
+}
diff --git a/wom/src/main/resources/reference.conf b/wom/src/main/resources/reference.conf
index fce1a8e0283..1907a23eac6 100644
--- a/wom/src/main/resources/reference.conf
+++ b/wom/src/main/resources/reference.conf
@@ -2,7 +2,7 @@ yaml {
   # The maximum number of nodes (scalars + sequences + mappings) that will be parsed in a YAML
   max-nodes = 1000000
   # The maximum nested depth for nodes (sequences + mappings) that will be parsed in a YAML
-  max-depth = 100
+  max-depth = 1000
 }
 
 wom-parse {
diff --git a/wom/src/test/scala/wom/util/YamlUtilsSpec.scala b/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
index 8f5ddd22c95..986201a2213 100644
--- a/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
+++ b/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
@@ -80,7 +80,7 @@ class YamlUtilsSpec
       "a null yaml",
       null,
       refineMV[NonNegative](0),
-      "Cannot invoke \"String.length()\" because \"s\" is null"
+      null
     ),
     (
       "an empty yaml mapping when limited to zero nodes",
@@ -179,14 +179,14 @@ class YamlUtilsSpec
     val nesting = 1000000
     val yaml = ("[" * nesting) + ("]" * nesting)
     val exception: Exception = YamlUtils.parse(yaml).left.value
-    exception should have message "Parsing halted at node depth 100" // <-- Updating here? Also get the docs too!
+    exception should have message "Parsing halted at node depth 1000" // <-- Updating here? Also get the docs too!
   }
 
   it should "fail to parse deeply nested yaml mapping with the default configuration" in {
     val nesting = 1000000
     val yaml = ("{a:" * nesting) + "b" + ("}" * nesting)
     val exception: Exception = YamlUtils.parse(yaml).left.value
-    exception should have message "Parsing halted at node depth 100" // <-- Updating here? Also get the docs too!
+    exception should have message "Parsing halted at node depth 1000" // <-- Updating here? Also get the docs too!
   }
 
   it should "not parse a config with a negative value" in {

From 3d86be853b1234b2c5f8fae99e90316f2bd8f8da Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 14 Dec 2023 15:59:30 -0500
Subject: [PATCH 259/326] WX-1409 Restore Java 17 (#7342) (#7344)

---
 .github/set_up_cromwell_action/action.yml     |  10 +-
 .github/workflows/chart_update_on_merge.yml   |   5 +-
 .github/workflows/docker_build_test.yml       |   5 +-
 .github/workflows/integration_tests.yml       |   8 +
 .github/workflows/trivy.yml                   |   5 +-
 .sdkmanrc                                     |   2 +-
 CHANGELOG.md                                  |   7 +
 .../api/DaemonizedDefaultThreadFactory.scala  |   3 +-
 .../scala/cloud/nio/spi/CloudNioPath.scala    |   2 +-
 .../main/scala/cloud/nio/spi/UnixPath.scala   |   2 +-
 docs/Configuring.md                           |   2 +-
 docs/Releases.md                              |   4 +-
 docs/tutorials/FiveMinuteIntro.md             |   6 +-
 project/Publishing.scala                      |   5 +-
 publish/docker-setup.sh                       |   2 +-
 runConfigurations/renderCiResources.run.xml   |   4 +-
 scripts/docker-compose-mysql/README.md        |   1 -
 .../compose/cromwell/Dockerfile               |   9 -
 .../app-config/cromwell-application.conf      |  61 ---
 .../compose/mysql/init/init_user.sql          |   4 -
 .../docker-compose-mysql/docker-compose.yml   |  22 -
 .../jes-cromwell/docker-compose.yml           |   9 -
 .../jes-cromwell/jes-config/application.conf  |  73 ---
 scripts/docker-develop/Dockerfile             |  64 ---
 scripts/docker-develop/README.md              |  60 ---
 src/ci/bin/test.inc.sh                        |   2 +-
 .../docker-compose/cromwell-test/Dockerfile   |   2 +-
 .../cromwell-test/docker-setup.sh             |  16 +-
 ...haredFileSystemJobExecutionActorSpec.scala | 430 ------------------
 wom/src/main/resources/reference.conf         |   2 +-
 .../test/scala/wom/util/YamlUtilsSpec.scala   |   6 +-
 31 files changed, 57 insertions(+), 776 deletions(-)
 delete mode 100644 scripts/docker-compose-mysql/README.md
 delete mode 100644 scripts/docker-compose-mysql/compose/cromwell/Dockerfile
 delete mode 100644 scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
 delete mode 100644 scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
 delete mode 100644 scripts/docker-compose-mysql/docker-compose.yml
 delete mode 100644 scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
 delete mode 100644 scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
 delete mode 100644 scripts/docker-develop/Dockerfile
 delete mode 100644 scripts/docker-develop/README.md
 delete mode 100644 supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index 13cb11601db..1cbe834d2bd 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -3,7 +3,8 @@
 name: 'Set Up Cromwell Steps'
 description: Specific steps that will set up git secrets, java, sbt, and Cromwell on the local machine. 
 inputs:
-  cromwell_repo_token: #As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell.
+  cromwell_repo_token:
+    description: "As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell."
     required: true
 
 runs:
@@ -12,13 +13,13 @@ runs:
       #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
       - uses: actions/checkout@v3
         name: Checkout Coursier Cache
-      - uses: coursier/cache-action@v6  
+      - uses: coursier/cache-action@v6
         name: Enable Coursier Cache
 
       #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
       - name: Git secrets setup 
         run: |
-          git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
+          git clone --quiet https://github.com/awslabs/git-secrets.git ~/git-secrets
           cd ~/git-secrets
           git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
           sudo make install
@@ -43,5 +44,4 @@ runs:
         uses: actions/setup-java@v3
         with:
           distribution: temurin
-          java-version: 11
-
+          java-version: 17
diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index a2b14f2ec65..b3f7199ab35 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -23,9 +23,10 @@ jobs:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
         path: cromwell
-    - uses: olafurpg/setup-scala@v10
+    - uses: actions/setup-java@v4
       with:
-        java-version: adopt@1.11
+        distribution: 'temurin'
+        java-version: '17'
     - name: Clone Cromwhelm
       uses: actions/checkout@v2
       with:
diff --git a/.github/workflows/docker_build_test.yml b/.github/workflows/docker_build_test.yml
index 01c2ea502c9..a50e39a380f 100644
--- a/.github/workflows/docker_build_test.yml
+++ b/.github/workflows/docker_build_test.yml
@@ -25,9 +25,10 @@ jobs:
           repository: broadinstitute/cromwell
           token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
           path: cromwell
-      - uses: olafurpg/setup-scala@v10
+      - uses: actions/setup-java@v4
         with:
-          java-version: adopt@1.11
+          distribution: 'temurin'
+          java-version: '17'
       # The following invocation should be as similar as possible to the one in chart_update_on_merge.yml
       # To state the obvious: This test should not publish anything. It should simply verify that the build completes.
       - name: Build Cromwell Docker
diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 61ed3c5af41..028b53db130 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -104,6 +104,14 @@ jobs:
         set -e
         echo Running test.sh
         ./src/ci/bin/test.sh
+    # If a build step fails, activate SSH and idle for 60 minutes
+    # - name: Setup tmate session
+    #  if: ${{ failure() }}
+    #  uses: mxschmitt/action-tmate@v3
+    #  timeout-minutes: 60
+    #  with:
+    #    limit-access-to-actor: true
+    #    detached: true
     # always() is some github magic that forces the following step to run, even when the previous fails.
     # Without it, the if statement won't be evaluated on a test failure.
     - uses: ravsamhq/notify-slack-action@v2
diff --git a/.github/workflows/trivy.yml b/.github/workflows/trivy.yml
index b005da65041..69a90937671 100644
--- a/.github/workflows/trivy.yml
+++ b/.github/workflows/trivy.yml
@@ -20,9 +20,10 @@ jobs:
       - uses: actions/checkout@v2
 
       # fetch SBT package
-      - uses: olafurpg/setup-scala@v10
+      - uses: actions/setup-java@v4
         with:
-          java-version: adopt@1.11
+          distribution: 'temurin'
+          java-version: '17'
 
       # set up SBT cache
       - uses: actions/cache@v2
diff --git a/.sdkmanrc b/.sdkmanrc
index 0262a261019..f3b37566860 100644
--- a/.sdkmanrc
+++ b/.sdkmanrc
@@ -1,3 +1,3 @@
 # Enable auto-env through the sdkman_auto_env config
 # Add key=value pairs of SDKs to use below
-java=11.0.11.hs-adpt
+java=17.0.9-tem
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a581852c02e..d670e74a43e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,12 @@
 # Cromwell Change Log
 
+## 87 Release Notes
+
+### Java 17
+
+As of this version, a distribution of Java 17 is required to run Cromwell. Cromwell is developed, tested, and
+containerized using [Eclipse Temurin](https://adoptium.net/temurin/releases/?version=17).
+
 ## 86 Release Notes
 
 ### GCP Batch
diff --git a/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala b/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
index db9eb07d79b..d75299aa590 100644
--- a/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
+++ b/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
@@ -14,8 +14,7 @@ import java.util.concurrent.atomic.AtomicInteger
   * > main thread).
   */
 object DaemonizedDefaultThreadFactory extends ThreadFactory {
-  private val s = System.getSecurityManager
-  private val group = if (s != null) s.getThreadGroup else Thread.currentThread.getThreadGroup
+  private val group = Thread.currentThread.getThreadGroup
   private val threadNumber = new AtomicInteger(1)
   private val namePrefix = "daemonpool-thread-"
 
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
index b6803670d39..530ba5526ef 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
@@ -176,7 +176,7 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
   ): WatchKey = throw new UnsupportedOperationException
 
   override def iterator(): java.util.Iterator[Path] =
-    if (unixPath.isEmpty || unixPath.isRoot) {
+    if (unixPath.izEmpty || unixPath.isRoot) {
       java.util.Collections.emptyIterator()
     } else {
       unixPath.split().to(LazyList).map(part => newPath(UnixPath.getPath(part)).asInstanceOf[Path]).iterator.asJava
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
index b7d9ed02035..7d929d148ab 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
@@ -67,7 +67,7 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
 
   def isAbsolute: Boolean = UnixPath.isAbsolute(path)
 
-  def isEmpty: Boolean = path.isEmpty
+  def izEmpty: Boolean = path.isEmpty
 
   def hasTrailingSeparator: Boolean = UnixPath.hasTrailingSeparator(path)
 
diff --git a/docs/Configuring.md b/docs/Configuring.md
index aa810d19a0c..288ec9723de 100644
--- a/docs/Configuring.md
+++ b/docs/Configuring.md
@@ -689,7 +689,7 @@ This limit may be configured via the configuration value:
 
 ```hocon
 yaml {
-  max-depth = 1000
+  max-depth = 100
 }
 ```
 
diff --git a/docs/Releases.md b/docs/Releases.md
index 9699d7d44bc..a6a709518b9 100644
--- a/docs/Releases.md
+++ b/docs/Releases.md
@@ -19,8 +19,8 @@ Mac users with Homebrew can also get Cromwell with the command `brew install cro
 This documentation frequently refers to a "Cromwell jar" with a name like `cromwell-<version>.jar`. 
 This is the main artifact in Cromwell releases that contains all executable Cromwell code and default configuration.   
 
-A distribution of Java 11 is required to run Cromwell. Cromwell is developed, tested, and containerized using
-[AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/).
+A distribution of Java 17 is required to run Cromwell. Cromwell is developed, tested, and containerized using
+[AdoptOpenJDK 17 HotSpot](https://adoptopenjdk.net/).
 
 For users running a Cromwell server [a docker image](https://hub.docker.com/r/broadinstitute/cromwell) has been made available.
 
diff --git a/docs/tutorials/FiveMinuteIntro.md b/docs/tutorials/FiveMinuteIntro.md
index 1c16a56c606..f15e28087b9 100644
--- a/docs/tutorials/FiveMinuteIntro.md
+++ b/docs/tutorials/FiveMinuteIntro.md
@@ -3,11 +3,11 @@
 ### Prerequisites:
 
 * A Unix-based operating system (yes, that includes Mac!)
-* A Java 11 runtime environment 
+* A Java 17 runtime environment 
     * You can see what you have by running `$ java -version` on a terminal.
     * If not, consider installing via conda or brew [as explained here](../Releases.md).
-    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 11 build of [Temurin](https://adoptium.net/temurin/releases/?version=11)
-      * `sdk install java 11.0.16-tem` as of the time of this writing
+    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 17 build of [Temurin](https://adoptium.net/temurin/releases/?version=17)
+      * `sdk install 17.0.9-tem` as of the time of this writing
     * You might need to update the `export JAVA_HOME` in your bash profile to point to your JAVA install location.
 * A sense of adventure!
 
diff --git a/project/Publishing.scala b/project/Publishing.scala
index 0af27e77147..c8a601a4f0c 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -63,7 +63,7 @@ object Publishing {
       val additionalDockerInstr: Seq[Instruction] = (dockerCustomSettings ?? Nil).value
 
       new Dockerfile {
-        from("us.gcr.io/broad-dsp-gcr-public/base/jre:11-debian")
+        from("us.gcr.io/broad-dsp-gcr-public/base/jre:17-debian")
         expose(8000)
         add(artifact, artifactTargetPath)
         runRaw(s"ln -s $artifactTargetPath /app/$projectName.jar")
@@ -163,8 +163,7 @@ object Publishing {
   val additionalResolvers = List(
     broadArtifactoryResolver,
     broadArtifactoryResolverSnap,
-    Resolver.sonatypeRepo("releases")
-  )
+  ) ++ Resolver.sonatypeOssRepos("releases")
 
   private val artifactoryCredentialsFile =
     file("target/ci/resources/artifactory_credentials.properties").getAbsoluteFile
diff --git a/publish/docker-setup.sh b/publish/docker-setup.sh
index 613d251df96..bc39f31d10a 100755
--- a/publish/docker-setup.sh
+++ b/publish/docker-setup.sh
@@ -20,7 +20,7 @@ mkdir -p /etc/apt/keyrings
 wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
 echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
 apt update
-apt install -y temurin-11-jdk
+apt install -y temurin-17-jdk
 
 # Install jq 1.6 to ensure --rawfile is supported
 curl -L https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 -o /usr/bin/jq
diff --git a/runConfigurations/renderCiResources.run.xml b/runConfigurations/renderCiResources.run.xml
index 2a5ab5e29b8..ef56bf5e4fd 100644
--- a/runConfigurations/renderCiResources.run.xml
+++ b/runConfigurations/renderCiResources.run.xml
@@ -7,8 +7,8 @@
     </option>
     <option name="tasks" value="renderCiResources" />
     <option name="useSbtShell" value="false" />
-    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M -XX:+CMSClassUnloadingEnabled" />
+    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M" />
     <option name="workingDir" value="$PROJECT_DIR$" />
     <method v="2" />
   </configuration>
-</component>
\ No newline at end of file
+</component>
diff --git a/scripts/docker-compose-mysql/README.md b/scripts/docker-compose-mysql/README.md
deleted file mode 100644
index 8fcb404b069..00000000000
--- a/scripts/docker-compose-mysql/README.md
+++ /dev/null
@@ -1 +0,0 @@
-Looking for the MySQL docs? Checkout the [Cromwell documentation](https://cromwell.readthedocs.io/en/develop/Configuring/#database)!
\ No newline at end of file
diff --git a/scripts/docker-compose-mysql/compose/cromwell/Dockerfile b/scripts/docker-compose-mysql/compose/cromwell/Dockerfile
deleted file mode 100644
index 6bf9fd88bf9..00000000000
--- a/scripts/docker-compose-mysql/compose/cromwell/Dockerfile
+++ /dev/null
@@ -1,9 +0,0 @@
-FROM broadinstitute/cromwell:develop
-
-RUN git clone https://github.com/vishnubob/wait-for-it.git
-RUN mkdir cromwell-working-dir
-WORKDIR cromwell-working-dir
-
-COPY ./app-config /app-config
-
-ENTRYPOINT ["/bin/sh", "-c"]
diff --git a/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf b/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
deleted file mode 100644
index a3b8d88ce3d..00000000000
--- a/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
+++ /dev/null
@@ -1,61 +0,0 @@
-include required(classpath("application"))
-
-# Note: If you spot a mistake in this configuration sample, please let us know by making an issue at:
-# https://github.com/broadinstitute/cromwell/issues
-
-call-caching {
-  enabled = false
-}
-
-backend {
-  default = "Local"
-  providers {
-    Local {
-      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
-      config {
-        run-in-background = true
-        runtime-attributes = "String? docker Int? max_runtime = 2"
-        submit = "/bin/bash ${script}"
-        submit-docker = "docker run --rm -v ${cwd}:${docker_cwd} -i ${docker} /bin/bash < ${script}"
-
-        # Root directory where Cromwell writes job results. This directory must be
-        # visible and writeable by the Cromwell process as well as the jobs that Cromwell
-        # launches.
-        root: "cromwell-executions"
-
-        filesystems {
-          local {
-            localization: [
-              "soft-link", "hard-link", "copy"
-            ]
-
-            caching {
-              duplication-strategy: [
-                "soft-link"
-              ]
-
-              # Possible values: file, path
-              # "file" will compute an md5 hash of the file content.
-              # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
-              # in order to allow for the original file path to be hashed.
-              hashing-strategy: "path"
-
-              # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
-              # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
-              check-sibling-md5: false
-            }
-          }
-        }
-      }
-    }
-  }
-}
-
-database {
-  db.url = "jdbc:mysql://mysql-db/cromwell_db?allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true"
-  db.user = "cromwell"
-  db.password = "cromwell"
-  db.driver = "com.mysql.cj.jdbc.Driver"
-  profile = "slick.jdbc.MySQLProfile$"
-  db.connectionTimeout = 15000
-}
diff --git a/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql b/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
deleted file mode 100644
index b07938189e0..00000000000
--- a/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
+++ /dev/null
@@ -1,4 +0,0 @@
-CREATE USER 'cromwell'@'localhost' IDENTIFIED BY 'cromwell';
-GRANT ALL PRIVILEGES ON cromwell_db.* TO 'cromwell'@'localhost' WITH GRANT OPTION;
-CREATE USER 'cromwell'@'%' IDENTIFIED BY 'cromwell';
-GRANT ALL PRIVILEGES ON cromwell_db.* TO 'cromwell'@'%' WITH GRANT OPTION;
diff --git a/scripts/docker-compose-mysql/docker-compose.yml b/scripts/docker-compose-mysql/docker-compose.yml
deleted file mode 100644
index 3548919eadb..00000000000
--- a/scripts/docker-compose-mysql/docker-compose.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-version: '2'
-services:
-  cromwell:
-    build: 
-      context: ./compose/cromwell
-    volumes:
-      - ./cromwell-executions:/cromwell-working-dir/cromwell-executions
-    command: ["/wait-for-it/wait-for-it.sh mysql-db:3306 -t 120 -- java -Dconfig.file=/app-config/cromwell-application.conf -jar /app/cromwell.jar server"]
-    links:
-      - mysql-db
-    ports:
-      - "80:8000"
-  mysql-db:
-    image: "mysql:5.7"
-    environment:
-      - MYSQL_ROOT_PASSWORD=cromwell
-      - MYSQL_DATABASE=cromwell_db
-    volumes:
-      - ./compose/mysql/init:/docker-entrypoint-initdb.d
-      - ./compose/mysql/data:/var/lib/mysql
-    ports:
-      - "3307:3306"
diff --git a/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml b/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
deleted file mode 100644
index c7f0e1cee01..00000000000
--- a/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-version: '2'
-services:
-  cromwell:
-    volumes:
-      - $HOME/.config/gcloud:/root/.config/gcloud
-      - ./jes-cromwell/jes-config:/app-config
-    environment:
-      - GOOGLE_APPLICATION_CREDENTIALS=/root/.config/gcloud/application_default_credentials.json
-
diff --git a/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf b/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
deleted file mode 100644
index cac33bb42ac..00000000000
--- a/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
+++ /dev/null
@@ -1,73 +0,0 @@
-include required(classpath("application"))
-
-# Note: If you spot a mistake in this configuration sample, please let us know by making an issue at:
-# https://github.com/broadinstitute/cromwell/issues
-
-system.new-workflow-poll-rate=1
-
-google {
-
-  application-name = "cromwell"
-
-  auths = [
-    {
-      name = "application-default"
-      scheme = "application_default"
-    }
-  ]
-}
-
-engine {
-  filesystems {
-     gcs {
-       auth = "application-default"
-     }
-  }
-}
-
-call-caching {
-  enabled = false
-}
-
-backend {
-  default = "Jes"
-  providers {
-    Jes {
-          actor-factory = "cromwell.backend.impl.jes.JesBackendLifecycleActorFactory"
-          config {
-            // Google project
-            project = "broad-dsde-cromwell-dev"
-
-            // Base bucket for workflow executions
-            root = "gs://tjeandet-cromwell-execs"
-
-            // Polling for completion backs-off gradually for slower-running jobs.
-            // This is the maximum polling interval (in seconds):
-            maximum-polling-interval = 600
-
-            genomics {
-              // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
-              // Pipelines and manipulate auth JSONs.
-              auth = "application-default"
-              // Endpoint for APIs, no reason to change this unless directed by Google.
-              endpoint-url = "https://genomics.googleapis.com/"
-            }
-
-            filesystems {
-              gcs {
-                // A reference to a potentially different auth for manipulating files via engine functions.
-                auth = "application-default"
-              }
-            }
-          }
-    }
-  }
-}
-
-database {
-  db.url = "jdbc:mysql://mysql-db/cromwell_db?useSSL=false&rewriteBatchedStatements=true"
-  db.user = "cromwell"
-  db.password = "cromwell"
-  db.driver = "com.mysql.cj.jdbc.Driver"
-  profile = "slick.jdbc.MySQLProfile$"
-}
diff --git a/scripts/docker-develop/Dockerfile b/scripts/docker-develop/Dockerfile
deleted file mode 100644
index 340d7bc00c4..00000000000
--- a/scripts/docker-develop/Dockerfile
+++ /dev/null
@@ -1,64 +0,0 @@
-FROM ubuntu:focal
-
-ARG DEBIAN_FRONTEND=noninteractive
-
-RUN apt-get update -q && \
-    apt-get upgrade -qq && \
-    apt-get install -y curl wget gnupg gnupg2 && \
-    rm -rf /var/lib/apt/lists/*
-
-# docker build -t vanessa/cromwell-dev .
-
-# Development environment for Cromwell that includes:
-#
-#   Scala 2.13
-#   SBT 1.x
-#   Java 11
-#   Git
-
-# Env variables
-ENV SCALA_VERSION 2.13.8
-ENV SBT_VERSION 1.5.5
-
-#
-## AdoptOpenJDK Hotspot
-#
-# https://adoptopenjdk.net/installation.html#linux-pkg-deb
-RUN \
-wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add - && \
-echo \
-"deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2) main" | \
-tee /etc/apt/sources.list.d/adoptopenjdk.list && \
-apt-get update && \
-apt-get install -y adoptopenjdk-11-hotspot
-
-#
-## Scala
-#
-
-RUN mkdir -p /home/pigman && \
-    curl \
-    --location --fail --silent --show-error \
-    https://downloads.typesafe.com/scala/$SCALA_VERSION/scala-$SCALA_VERSION.tgz | tar xfz - -C /opt/ && \
-    echo >> /home/pigman/.bashrc && \
-    echo "export PATH=/opt/scala-$SCALA_VERSION/bin:$PATH" >> /home/pigman/.bashrc
-
-#
-## sbt
-#
-
-# non-deb package installation instructions adapted from
-# - https://github.com/sbt/sbt/releases/tag/v1.4.9
-# - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-RUN curl \
-    --location --fail --silent --show-error \
-    "https://github.com/sbt/sbt/releases/download/v$SBT_VERSION/sbt-$SBT_VERSION.tgz" | \
-    tar zxf - -C /usr/share && \
-    update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1 && \
-    sbt -Dsbt.supershell=false -Dsbt.rootdir=true sbtVersion
-
-# Instruct user to add code here during development
-RUN useradd pigman && \
-    mkdir -p /code
-
-WORKDIR /code
diff --git a/scripts/docker-develop/README.md b/scripts/docker-develop/README.md
deleted file mode 100644
index 20bd1a8203f..00000000000
--- a/scripts/docker-develop/README.md
+++ /dev/null
@@ -1,60 +0,0 @@
-# Cromwell Docker Development
-
-This is a container intended to help with development of Cromwell, in the
-case that you don't want to install the dependencies on your host. It
-includes the required software mentioned in [the developer docs](http://cromwell.readthedocs.io/en/develop/Building/) but with additional instructions to interact with the repository.
-
-As with the build instructions, first start by cloning the Cromwell repository from GitHub:
-
-```bash
-$ git clone git@github.com:broadinstitute/cromwell.git
-```
-
-And change into this directory:
-
-```bash
-$ cd cromwell/scripts/docker-develop
-```
-
-This is where this README.md sits with a [Dockerfile](Dockerfile)
-
-## Step 1. Build the Container
-From this folder with the Dockerfile, build the container. In the command below
-we are calling it `cromwell-dev` and you can choose to change this name if you want.
-
-```bash
-$ docker build -t cromwell-dev .
-```
-
-and change back to the root of the repository
-
-```bash
-cd ../../
-```
-
-## Step 2. Shell into Working Environment
-If you require a specific version of Cromwell as a starting point, do the appropriate `git checkout` now. 
-
-You are next going to want to bind the cromwell
-source code to be somewhere in the container. Actually, we have a `/code` directory
-ready for you to make this easy. Run this command from the base of the repository:
-
-```bash
-$ docker run -v $PWD/:/code -it cromwell-dev bash
-```
-
-## Step 4. The Development Steps
-
-You are going to use the command `sbt assembly` to create a runnable Cromwell JAR. The output
-will be `server/target`. Remember, here we are inside the container with scala and sbt:
-
-
-```bash
-$ sbt assembly
-```
-
-`sbt assembly` will build the runnable Cromwell JAR in `server/target/scala-2.13/` with a name like `cromwell-<VERSION>.jar`.
-
-You can then interact with it in the container, or on your host if you like. Remember that
-you have Java already in the container, so it makes sense to develop there.
-
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 71577ce1e4c..8a9cc27c298 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -746,7 +746,7 @@ cromwell::private::login_docker() {
 
 cromwell::private::render_secure_resources() {
     # Avoid docker output to sbt's stderr by pulling the image here
-    docker pull broadinstitute/dsde-toolbox:dev | cat
+    docker pull --quiet broadinstitute/dsde-toolbox:dev | cat
     # Copy the CI resources, then render the secure resources using Vault
     sbt -Dsbt.supershell=false --warn renderCiResources \
     || if [[ "${CROMWELL_BUILD_IS_CI}" == "true" ]]; then
diff --git a/src/ci/docker-compose/cromwell-test/Dockerfile b/src/ci/docker-compose/cromwell-test/Dockerfile
index 70e2477bb0e..319c462cfbd 100644
--- a/src/ci/docker-compose/cromwell-test/Dockerfile
+++ b/src/ci/docker-compose/cromwell-test/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:focal
+FROM ubuntu:latest
 
 WORKDIR /cromwell-test/
 COPY docker-setup.sh ./
diff --git a/src/ci/docker-compose/cromwell-test/docker-setup.sh b/src/ci/docker-compose/cromwell-test/docker-setup.sh
index c7970c7349b..37e624c6766 100755
--- a/src/ci/docker-compose/cromwell-test/docker-setup.sh
+++ b/src/ci/docker-compose/cromwell-test/docker-setup.sh
@@ -25,13 +25,11 @@ apt-get install -y \
     sudo \
     wget \
 
-# setup install for adoptopenjdk
-# https://adoptopenjdk.net/installation.html#linux-pkg-deb
-wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add -
-echo "deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(
-        grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
-    ) main" |
-    tee /etc/apt/sources.list.d/adoptopenjdk.list
+# setup install for Temurin
+# https://adoptium.net/installation/linux/
+mkdir -p /etc/apt/keyrings
+wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
+echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^UBUNTU_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
 
 # setup install for gcloud
 # https://cloud.google.com/sdk/docs/install#deb
@@ -52,7 +50,7 @@ add-apt-repository \
 # install packages that required setup
 apt-get update
 apt-get install -y \
-    adoptopenjdk-11-hotspot \
+    temurin-17-jdk \
     containerd.io \
     docker-ce \
     docker-ce-cli \
@@ -66,7 +64,7 @@ apt-get clean
 # non-deb package installation instructions adapted from
 # - https://github.com/sbt/sbt/releases/tag/v1.4.9
 # - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-curl -L --silent "https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz" |
+curl -L --silent "https://github.com/sbt/sbt/releases/download/v1.8.1/sbt-1.8.1.tgz" |
     tar zxf - -C /usr/share
 update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1
 
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
deleted file mode 100644
index 5d1b1e02c12..00000000000
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
+++ /dev/null
@@ -1,430 +0,0 @@
-package cromwell.backend.sfs
-
-import _root_.wdl.draft2.model.LocallyQualifiedName
-import akka.testkit.{TestDuration, TestProbe}
-import com.typesafe.config.ConfigFactory
-import common.collections.EnhancedCollections._
-import cromwell.backend.BackendJobExecutionActor.{
-  JobAbortedResponse,
-  JobFailedNonRetryableResponse,
-  JobSucceededResponse,
-  RunOnBackend
-}
-import cromwell.backend.BackendLifecycleActor.AbortJobCommand
-import cromwell.backend._
-import cromwell.backend.async.WrongReturnCode
-import cromwell.backend.io.JobPathsSpecHelper._
-import cromwell.backend.io.TestWorkflows._
-import cromwell.backend.io.{JobPathsWithDocker, TestWorkflows}
-import cromwell.backend.sfs.TestLocalAsyncJobExecutionActor._
-import cromwell.backend.standard.StandardValidatedRuntimeAttributesBuilder
-import cromwell.core.CromwellGraphNode._
-import cromwell.core.Tags._
-import cromwell.core._
-import cromwell.core.callcaching.NoDocker
-import cromwell.core.path.{DefaultPathBuilder, Path}
-import cromwell.services.keyvalue.KeyValueServiceActor._
-import cromwell.util.WomMocks
-import org.scalatest.concurrent.PatienceConfiguration.Timeout
-import org.scalatest.flatspec.AnyFlatSpecLike
-import org.scalatest.prop.TableDrivenPropertyChecks
-import org.scalatest.{Assertion, OptionValues}
-import wom.expression.NoIoFunctionSet
-import wom.graph.{CommandCallNode, WomIdentifier}
-import wom.types._
-import wom.values._
-
-import java.io.FileNotFoundException
-import scala.concurrent.duration._
-import scala.sys.process._
-
-class SharedFileSystemJobExecutionActorSpec
-    extends TestKitSuite
-    with AnyFlatSpecLike
-    with BackendSpec
-    with TableDrivenPropertyChecks
-    with OptionValues {
-
-  behavior of "SharedFileSystemJobExecutionActor"
-
-  lazy val runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition] =
-    StandardValidatedRuntimeAttributesBuilder.default(Some(TestConfig.optionalRuntimeConfig)).definitions.toSet
-
-  private val call = CommandCallNode(WomIdentifier("SfsJEASpec_call"), null, null, null, Set.empty, null, None)
-  private val mockBackendJobDescriptorKey = BackendJobDescriptorKey(call, None, 1)
-
-  def executeSpec(docker: Boolean): Any = {
-    val expectedOutputs: CallOutputs =
-      WomMocks.mockOutputExpectations(Map("hello.salutation" -> WomString("Hello you !")))
-
-    val expectedResponse = JobSucceededResponse(mockBackendJobDescriptorKey,
-                                                Some(0),
-                                                expectedOutputs,
-                                                None,
-                                                Seq.empty,
-                                                None,
-                                                resultGenerationMode = RunOnBackend
-    )
-    val runtime = if (docker) s"""runtime { docker: "$dockerImageUbuntu" }""" else ""
-    val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld, runtime = runtime)
-    val workflow = TestWorkflow(workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor, expectedResponse)
-    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
-                                                                    Map.empty,
-                                                                    WorkflowOptions.empty,
-                                                                    runtimeAttributeDefinitions
-                                ),
-                                workflow.config
-    )
-    testWorkflow(workflow, backend)
-  }
-
-  private val dockerImageUbuntu = "ubuntu:latest"
-
-  it should "docker pull images now so that 'DockerTest' specs below do not timeout" taggedAs DockerTest in {
-    /*
-    This is a poor substitute for `beforeAll()`.
-    If one wants to parallelize the test runs consider using a separate tagged-Suite with a `.beforeAll()`.
-    - https://medium.com/@linda0511ny/tag-whole-test-class-in-scalatest-94cd67fa85a4
-     */
-    List("docker", "pull", dockerImageUbuntu).! should be(0)
-  }
-
-  it should "execute an hello world workflow" in {
-    executeSpec(docker = false)
-  }
-
-  it should "execute an hello world workflow on Docker" taggedAs DockerTest in {
-    executeSpec(docker = true)
-  }
-
-  it should "send back an execution failure if the task fails" in {
-    val expectedResponse =
-      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
-                                    WrongReturnCode("wf_goodbye.goodbye:NA:1", 1, None),
-                                    Option(1)
-      )
-    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(GoodbyeWorld),
-                                TestConfig.backendRuntimeConfigDescriptor,
-                                expectedResponse
-    )
-    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
-                                                                    Map.empty,
-                                                                    WorkflowOptions.empty,
-                                                                    runtimeAttributeDefinitions
-                                ),
-                                workflow.config
-    )
-    testWorkflow(workflow, backend)
-  }
-
-  def localizationSpec(docker: Boolean): Assertion = {
-    def templateConf(localizers: String) = BackendConfigurationDescriptor(
-      ConfigFactory.parseString(s"""|{
-                                    |  root = "local-cromwell-executions"
-                                    |  filesystems {
-                                    |    local {
-                                    |      localization = [
-                                    |        $localizers
-                                    |      ]
-                                    |    }
-                                    |  }
-                                    |  default-runtime-attributes {
-                                    |  cpu: 1
-                                    |  failOnStderr: false
-                                    |  continueOnReturnCode: 0
-                                    |  }
-                                    |}
-                                    |""".stripMargin),
-      ConfigFactory.parseString("{}")
-    )
-
-    val hardConf = templateConf("hard-link")
-    val symConf = templateConf("soft-link")
-    val copyConf = templateConf("copy")
-
-    val jsonInputFile =
-      createCannedFile("localize", "content from json inputs", Option(DefaultPathBuilder.build(".").get))
-    val callInputFile =
-      createCannedFile("localize", "content from call inputs", Option(DefaultPathBuilder.build(".").get))
-    val inputs = Option(s"""{
-      "wf_localize.workflowFile": "${callInputFile.pathAsString}",
-      "wf_localize.localize.inputFileFromJson": "${jsonInputFile.pathAsString}"
-    }""")
-
-    val expectedOutputs: CallOutputs = WomMocks.mockOutputExpectations(
-      Map(
-        "localize.out" -> WomArray(WomArrayType(WomStringType),
-                                   List(WomString("content from json inputs"), WomString("content from call inputs"))
-        )
-      )
-    )
-
-    val confs = List(
-      (hardConf, false),
-      (copyConf, false)
-    ) ++ (if (!docker) List((symConf, true)) else List.empty)
-
-    val localizers = Table(
-      ("conf", "isSymLink"),
-      confs: _*
-    )
-
-    forAll(localizers) { (conf, isSymlink) =>
-      val runtime = if (docker) s"""runtime { docker: "$dockerImageUbuntu" } """ else ""
-      val workflowDescriptor = buildWdlWorkflowDescriptor(InputFiles, inputs, runtime = runtime)
-      val callInputs = Map(
-        "inputFileFromCallInputs" -> workflowDescriptor.knownValues.collectFirst {
-          case (outputPort, resolvedValue) if outputPort.fullyQualifiedName == "wf_localize.workflowFile" =>
-            resolvedValue
-        }.get,
-        "inputFileFromJson" -> workflowDescriptor.knownValues.collectFirst {
-          case (outputPort, resolvedValue)
-              if outputPort.fullyQualifiedName == "wf_localize.localize.inputFileFromJson" =>
-            resolvedValue
-        }.get
-      )
-
-      val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                                      callInputs,
-                                                                      WorkflowOptions.empty,
-                                                                      runtimeAttributeDefinitions
-                                  ),
-                                  conf
-      )
-      val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                                                    callInputs,
-                                                                                    WorkflowOptions.empty,
-                                                                                    runtimeAttributeDefinitions
-      )
-      val expectedResponse = JobSucceededResponse(jobDescriptor.key,
-                                                  Some(0),
-                                                  expectedOutputs,
-                                                  None,
-                                                  Seq.empty,
-                                                  None,
-                                                  resultGenerationMode = RunOnBackend
-      )
-
-      val jobPaths = JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, conf.backendConfig)
-
-      whenReady(backend.execute) { executionResponse =>
-        assertResponse(executionResponse, expectedResponse)
-        val localizedJsonInputFile =
-          DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString,
-                                 jsonInputFile.parent.pathAsString.hashCode.toString + "/" + jsonInputFile.name
-          )
-        val localizedCallInputFile =
-          DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString,
-                                 callInputFile.parent.pathAsString.hashCode.toString + "/" + callInputFile.name
-          )
-
-        localizedJsonInputFile.isSymbolicLink shouldBe isSymlink
-        val realJsonInputFile =
-          if (isSymlink) localizedJsonInputFile.symbolicLink.get else localizedJsonInputFile
-        realJsonInputFile.toFile should exist
-
-        localizedCallInputFile.isSymbolicLink shouldBe isSymlink
-        val realCallInputFile =
-          if (isSymlink) localizedCallInputFile.symbolicLink.get else localizedCallInputFile
-        realCallInputFile.toFile should exist
-      }
-    }
-  }
-
-  it should "execute calls with input files and localize them appropriately" in {
-    localizationSpec(docker = false)
-  }
-
-  it should "execute calls with input files and localize them appropriately (in Docker)" taggedAs DockerTest in {
-    localizationSpec(docker = true)
-  }
-
-  it should "abort a job and kill a process" in {
-    val workflowDescriptor = buildWdlWorkflowDescriptor(Sleep20)
-    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                                                  Map.empty,
-                                                                                  WorkflowOptions.empty,
-                                                                                  runtimeAttributeDefinitions
-    )
-    val backendRef = createBackendRef(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
-    val backend = backendRef.underlyingActor
-
-    val execute = backend.execute
-    backendRef ! AbortJobCommand
-
-    whenReady(execute) { executionResponse =>
-      executionResponse shouldBe a[JobAbortedResponse]
-    }
-  }
-
-  def recoverSpec(completed: Boolean, writeReturnCode: Boolean = true): Assertion = {
-    val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld)
-    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                                                  Map.empty,
-                                                                                  WorkflowOptions.empty,
-                                                                                  runtimeAttributeDefinitions
-    )
-    val backendRef = createBackendRef(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
-    val backend = backendRef.underlyingActor
-
-    val jobPaths = JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, ConfigFactory.empty)
-    jobPaths.callExecutionRoot.createPermissionedDirectories()
-    jobPaths.stdout.write("Hello stubby ! ")
-    jobPaths.stderr.touch()
-
-    val pid =
-      if (completed) {
-        if (writeReturnCode)
-          jobPaths.returnCode.write("0")
-        "0"
-      } else {
-        import sys.process._
-        val proc = Seq("bash", "-c", s"sleep 2; echo 0 > ${jobPaths.returnCode}").run()
-        val pField = proc.getClass.getDeclaredField("p")
-        pField.setAccessible(true)
-        val p = pField.get(proc)
-        val pidField = p.getClass.getDeclaredField("pid")
-        pidField.setAccessible(true)
-        pidField.get(p).toString
-      }
-
-    def execute = backend.recover
-
-    val kvJobKey =
-      KvJobKey(jobDescriptor.key.call.fullyQualifiedName, jobDescriptor.key.index, jobDescriptor.key.attempt)
-    val scopedKey = ScopedKey(workflowDescriptor.id, kvJobKey, SharedFileSystemAsyncJobExecutionActor.JobIdKey)
-    val kvPair = KvPair(scopedKey, pid)
-
-    val previousKvPutter = TestProbe("previousKvPutter")
-    val kvPutReq = KvPut(kvPair)
-    backendRef.underlyingActor.serviceRegistryActor.tell(msg = kvPutReq, sender = previousKvPutter.ref)
-    previousKvPutter.expectMsg(KvPutSuccess(kvPutReq))
-    val outputPort = jobDescriptor.taskCall.outputPorts.head
-    whenReady(execute, Timeout(10.seconds.dilated)) { executionResponse =>
-      if (writeReturnCode) {
-        executionResponse should be(a[JobSucceededResponse])
-        val succeededResponse = executionResponse.asInstanceOf[JobSucceededResponse]
-        succeededResponse.returnCode.value should be(0)
-        succeededResponse.jobOutputs should be(CallOutputs(Map(outputPort -> WomString("Hello stubby !"))))
-      } else {
-        executionResponse should be(a[JobFailedNonRetryableResponse])
-        val failedResponse = executionResponse.asInstanceOf[JobFailedNonRetryableResponse]
-        failedResponse.returnCode should be(empty)
-        failedResponse.throwable should be(a[RuntimeException])
-        failedResponse.throwable.getMessage should startWith("Unable to determine that 0 is alive, and")
-        failedResponse.throwable.getMessage should endWith("call-hello/execution/rc does not exist.")
-      }
-    }
-  }
-
-  it should "recover a job in progress" in {
-    recoverSpec(completed = false)
-  }
-
-  it should "recover a job that already completed" in {
-    recoverSpec(completed = true)
-  }
-
-  it should "not recover a job for a non-existent pid" in {
-    recoverSpec(completed = true, writeReturnCode = false)
-  }
-
-  it should "execute shards from a scatter" in {
-    val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.Scatter)
-
-    val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
-
-    0 to 2 foreach { shard =>
-      // This assumes that engine will give us the evaluated value of the scatter item at the correct index
-      // If this is not the case, more context/logic will need to be moved to the backend so it can figure it out by itself
-      val symbolMaps: Map[LocallyQualifiedName, WomInteger] = Map("intNumber" -> WomInteger(shard))
-
-      val evaluatedAttributes = call.callable.runtimeAttributes.attributes
-        .safeMapValues(_.evaluateValue(Map.empty, NoIoFunctionSet).getOrElse(fail("Can't evaluate runtime attribute")))
-      val runtimeAttributes: Map[LocallyQualifiedName, WomValue] =
-        RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, WorkflowOptions.empty)(
-          evaluatedAttributes
-        )
-
-      val jobDescriptor: BackendJobDescriptor =
-        BackendJobDescriptor(workflowDescriptor,
-                             BackendJobDescriptorKey(call, Option(shard), 1),
-                             runtimeAttributes,
-                             fqnWdlMapToDeclarationMap(symbolMaps),
-                             NoDocker,
-                             None,
-                             Map.empty
-        )
-      val backend = createBackend(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
-      val response =
-        JobSucceededResponse(
-          mockBackendJobDescriptorKey,
-          Some(0),
-          WomMocks.mockOutputExpectations(Map("scattering.out" -> WomInteger(shard))),
-          None,
-          Seq.empty,
-          None,
-          resultGenerationMode = RunOnBackend
-        )
-      executeJobAndAssertOutputs(backend, response)
-    }
-  }
-
-  it should "post process outputs" in {
-    val inputFile = createCannedFile("localize", "content from json inputs").pathAsString
-    val inputs = Option(s"""{
-      "wf_localize.localize.inputFile": "$inputFile"
-    }""")
-    val workflowDescriptor = buildWdlWorkflowDescriptor(OutputProcess, inputs)
-    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
-                                                                                  Map.empty,
-                                                                                  WorkflowOptions.empty,
-                                                                                  runtimeAttributeDefinitions
-    )
-    val backend = createBackend(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
-    val jobPaths =
-      JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor.backendConfig)
-    val expectedA = WomSingleFile(jobPaths.callExecutionRoot.resolve("a").toAbsolutePath.pathAsString)
-    val expectedB = WomSingleFile(jobPaths.callExecutionRoot.resolve("dir").toAbsolutePath.resolve("b").pathAsString)
-    val expectedOutputs = WomMocks.mockOutputExpectations(
-      Map(
-        "localize.o1" -> expectedA,
-        "localize.o2" -> WomArray(WomArrayType(WomSingleFileType), Seq(expectedA, expectedB)),
-        "localize.o3" -> WomSingleFile(inputFile)
-      )
-    )
-    val expectedResponse = JobSucceededResponse(jobDescriptor.key,
-                                                Some(0),
-                                                expectedOutputs,
-                                                None,
-                                                Seq.empty,
-                                                None,
-                                                resultGenerationMode = RunOnBackend
-    )
-
-    executeJobAndAssertOutputs(backend, expectedResponse)
-  }
-
-  it should "fail post processing if an output file is not found" in {
-    val expectedResponse =
-      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
-                                    new FileNotFoundException("Could not process output, file not found:"),
-                                    Option(0)
-      )
-    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(MissingOutputProcess),
-                                TestConfig.backendRuntimeConfigDescriptor,
-                                expectedResponse
-    )
-    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
-                                                                    Map.empty,
-                                                                    WorkflowOptions.empty,
-                                                                    runtimeAttributeDefinitions
-                                ),
-                                workflow.config
-    )
-    testWorkflow(workflow, backend)
-  }
-
-  def createCannedFile(prefix: String, contents: String, parent: Option[Path] = None): Path =
-    DefaultPathBuilder.createTempFile(prefix, ".out", parent).write(contents)
-}
diff --git a/wom/src/main/resources/reference.conf b/wom/src/main/resources/reference.conf
index 1907a23eac6..fce1a8e0283 100644
--- a/wom/src/main/resources/reference.conf
+++ b/wom/src/main/resources/reference.conf
@@ -2,7 +2,7 @@ yaml {
   # The maximum number of nodes (scalars + sequences + mappings) that will be parsed in a YAML
   max-nodes = 1000000
   # The maximum nested depth for nodes (sequences + mappings) that will be parsed in a YAML
-  max-depth = 1000
+  max-depth = 100
 }
 
 wom-parse {
diff --git a/wom/src/test/scala/wom/util/YamlUtilsSpec.scala b/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
index 986201a2213..8f5ddd22c95 100644
--- a/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
+++ b/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
@@ -80,7 +80,7 @@ class YamlUtilsSpec
       "a null yaml",
       null,
       refineMV[NonNegative](0),
-      null
+      "Cannot invoke \"String.length()\" because \"s\" is null"
     ),
     (
       "an empty yaml mapping when limited to zero nodes",
@@ -179,14 +179,14 @@ class YamlUtilsSpec
     val nesting = 1000000
     val yaml = ("[" * nesting) + ("]" * nesting)
     val exception: Exception = YamlUtils.parse(yaml).left.value
-    exception should have message "Parsing halted at node depth 1000" // <-- Updating here? Also get the docs too!
+    exception should have message "Parsing halted at node depth 100" // <-- Updating here? Also get the docs too!
   }
 
   it should "fail to parse deeply nested yaml mapping with the default configuration" in {
     val nesting = 1000000
     val yaml = ("{a:" * nesting) + "b" + ("}" * nesting)
     val exception: Exception = YamlUtils.parse(yaml).left.value
-    exception should have message "Parsing halted at node depth 1000" // <-- Updating here? Also get the docs too!
+    exception should have message "Parsing halted at node depth 100" // <-- Updating here? Also get the docs too!
   }
 
   it should "not parse a config with a negative value" in {

From 8b19fee31df056e0470196bdb51ccb4f4b74c4b7 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 15 Dec 2023 10:14:03 -0500
Subject: [PATCH 260/326] Revert "WX-1409 Java 17" (#7346)

---
 .github/set_up_cromwell_action/action.yml     |  10 +-
 .github/workflows/chart_update_on_merge.yml   |   5 +-
 .github/workflows/docker_build_test.yml       |   5 +-
 .github/workflows/integration_tests.yml       |   8 -
 .github/workflows/trivy.yml                   |   5 +-
 .sdkmanrc                                     |   2 +-
 CHANGELOG.md                                  |   7 -
 .../api/DaemonizedDefaultThreadFactory.scala  |   3 +-
 .../scala/cloud/nio/spi/CloudNioPath.scala    |   2 +-
 .../main/scala/cloud/nio/spi/UnixPath.scala   |   2 +-
 docs/Configuring.md                           |   2 +-
 docs/Releases.md                              |   4 +-
 docs/tutorials/FiveMinuteIntro.md             |   6 +-
 project/Publishing.scala                      |   5 +-
 publish/docker-setup.sh                       |   2 +-
 runConfigurations/renderCiResources.run.xml   |   4 +-
 scripts/docker-compose-mysql/README.md        |   1 +
 .../compose/cromwell/Dockerfile               |   9 +
 .../app-config/cromwell-application.conf      |  61 +++
 .../compose/mysql/init/init_user.sql          |   4 +
 .../docker-compose-mysql/docker-compose.yml   |  22 +
 .../jes-cromwell/docker-compose.yml           |   9 +
 .../jes-cromwell/jes-config/application.conf  |  73 +++
 scripts/docker-develop/Dockerfile             |  64 +++
 scripts/docker-develop/README.md              |  60 +++
 src/ci/bin/test.inc.sh                        |   2 +-
 .../docker-compose/cromwell-test/Dockerfile   |   2 +-
 .../cromwell-test/docker-setup.sh             |  16 +-
 ...haredFileSystemJobExecutionActorSpec.scala | 430 ++++++++++++++++++
 wom/src/main/resources/reference.conf         |   2 +-
 .../test/scala/wom/util/YamlUtilsSpec.scala   |   6 +-
 31 files changed, 776 insertions(+), 57 deletions(-)
 create mode 100644 scripts/docker-compose-mysql/README.md
 create mode 100644 scripts/docker-compose-mysql/compose/cromwell/Dockerfile
 create mode 100644 scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
 create mode 100644 scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
 create mode 100644 scripts/docker-compose-mysql/docker-compose.yml
 create mode 100644 scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
 create mode 100644 scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
 create mode 100644 scripts/docker-develop/Dockerfile
 create mode 100644 scripts/docker-develop/README.md
 create mode 100644 supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala

diff --git a/.github/set_up_cromwell_action/action.yml b/.github/set_up_cromwell_action/action.yml
index 1cbe834d2bd..13cb11601db 100644
--- a/.github/set_up_cromwell_action/action.yml
+++ b/.github/set_up_cromwell_action/action.yml
@@ -3,8 +3,7 @@
 name: 'Set Up Cromwell Steps'
 description: Specific steps that will set up git secrets, java, sbt, and Cromwell on the local machine. 
 inputs:
-  cromwell_repo_token:
-    description: "As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell."
+  cromwell_repo_token: #As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell.
     required: true
 
 runs:
@@ -13,13 +12,13 @@ runs:
       #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
       - uses: actions/checkout@v3
         name: Checkout Coursier Cache
-      - uses: coursier/cache-action@v6
+      - uses: coursier/cache-action@v6  
         name: Enable Coursier Cache
 
       #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
       - name: Git secrets setup 
         run: |
-          git clone --quiet https://github.com/awslabs/git-secrets.git ~/git-secrets
+          git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
           cd ~/git-secrets
           git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
           sudo make install
@@ -44,4 +43,5 @@ runs:
         uses: actions/setup-java@v3
         with:
           distribution: temurin
-          java-version: 17
+          java-version: 11
+
diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index b3f7199ab35..a2b14f2ec65 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -23,10 +23,9 @@ jobs:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
         path: cromwell
-    - uses: actions/setup-java@v4
+    - uses: olafurpg/setup-scala@v10
       with:
-        distribution: 'temurin'
-        java-version: '17'
+        java-version: adopt@1.11
     - name: Clone Cromwhelm
       uses: actions/checkout@v2
       with:
diff --git a/.github/workflows/docker_build_test.yml b/.github/workflows/docker_build_test.yml
index a50e39a380f..01c2ea502c9 100644
--- a/.github/workflows/docker_build_test.yml
+++ b/.github/workflows/docker_build_test.yml
@@ -25,10 +25,9 @@ jobs:
           repository: broadinstitute/cromwell
           token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
           path: cromwell
-      - uses: actions/setup-java@v4
+      - uses: olafurpg/setup-scala@v10
         with:
-          distribution: 'temurin'
-          java-version: '17'
+          java-version: adopt@1.11
       # The following invocation should be as similar as possible to the one in chart_update_on_merge.yml
       # To state the obvious: This test should not publish anything. It should simply verify that the build completes.
       - name: Build Cromwell Docker
diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 028b53db130..61ed3c5af41 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -104,14 +104,6 @@ jobs:
         set -e
         echo Running test.sh
         ./src/ci/bin/test.sh
-    # If a build step fails, activate SSH and idle for 60 minutes
-    # - name: Setup tmate session
-    #  if: ${{ failure() }}
-    #  uses: mxschmitt/action-tmate@v3
-    #  timeout-minutes: 60
-    #  with:
-    #    limit-access-to-actor: true
-    #    detached: true
     # always() is some github magic that forces the following step to run, even when the previous fails.
     # Without it, the if statement won't be evaluated on a test failure.
     - uses: ravsamhq/notify-slack-action@v2
diff --git a/.github/workflows/trivy.yml b/.github/workflows/trivy.yml
index 69a90937671..b005da65041 100644
--- a/.github/workflows/trivy.yml
+++ b/.github/workflows/trivy.yml
@@ -20,10 +20,9 @@ jobs:
       - uses: actions/checkout@v2
 
       # fetch SBT package
-      - uses: actions/setup-java@v4
+      - uses: olafurpg/setup-scala@v10
         with:
-          distribution: 'temurin'
-          java-version: '17'
+          java-version: adopt@1.11
 
       # set up SBT cache
       - uses: actions/cache@v2
diff --git a/.sdkmanrc b/.sdkmanrc
index f3b37566860..0262a261019 100644
--- a/.sdkmanrc
+++ b/.sdkmanrc
@@ -1,3 +1,3 @@
 # Enable auto-env through the sdkman_auto_env config
 # Add key=value pairs of SDKs to use below
-java=17.0.9-tem
+java=11.0.11.hs-adpt
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d670e74a43e..a581852c02e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,12 +1,5 @@
 # Cromwell Change Log
 
-## 87 Release Notes
-
-### Java 17
-
-As of this version, a distribution of Java 17 is required to run Cromwell. Cromwell is developed, tested, and
-containerized using [Eclipse Temurin](https://adoptium.net/temurin/releases/?version=17).
-
 ## 86 Release Notes
 
 ### GCP Batch
diff --git a/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala b/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
index d75299aa590..db9eb07d79b 100644
--- a/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
+++ b/centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala
@@ -14,7 +14,8 @@ import java.util.concurrent.atomic.AtomicInteger
   * > main thread).
   */
 object DaemonizedDefaultThreadFactory extends ThreadFactory {
-  private val group = Thread.currentThread.getThreadGroup
+  private val s = System.getSecurityManager
+  private val group = if (s != null) s.getThreadGroup else Thread.currentThread.getThreadGroup
   private val threadNumber = new AtomicInteger(1)
   private val namePrefix = "daemonpool-thread-"
 
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
index 530ba5526ef..b6803670d39 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
@@ -176,7 +176,7 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
   ): WatchKey = throw new UnsupportedOperationException
 
   override def iterator(): java.util.Iterator[Path] =
-    if (unixPath.izEmpty || unixPath.isRoot) {
+    if (unixPath.isEmpty || unixPath.isRoot) {
       java.util.Collections.emptyIterator()
     } else {
       unixPath.split().to(LazyList).map(part => newPath(UnixPath.getPath(part)).asInstanceOf[Path]).iterator.asJava
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
index 7d929d148ab..b7d9ed02035 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
@@ -67,7 +67,7 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
 
   def isAbsolute: Boolean = UnixPath.isAbsolute(path)
 
-  def izEmpty: Boolean = path.isEmpty
+  def isEmpty: Boolean = path.isEmpty
 
   def hasTrailingSeparator: Boolean = UnixPath.hasTrailingSeparator(path)
 
diff --git a/docs/Configuring.md b/docs/Configuring.md
index 288ec9723de..aa810d19a0c 100644
--- a/docs/Configuring.md
+++ b/docs/Configuring.md
@@ -689,7 +689,7 @@ This limit may be configured via the configuration value:
 
 ```hocon
 yaml {
-  max-depth = 100
+  max-depth = 1000
 }
 ```
 
diff --git a/docs/Releases.md b/docs/Releases.md
index a6a709518b9..9699d7d44bc 100644
--- a/docs/Releases.md
+++ b/docs/Releases.md
@@ -19,8 +19,8 @@ Mac users with Homebrew can also get Cromwell with the command `brew install cro
 This documentation frequently refers to a "Cromwell jar" with a name like `cromwell-<version>.jar`. 
 This is the main artifact in Cromwell releases that contains all executable Cromwell code and default configuration.   
 
-A distribution of Java 17 is required to run Cromwell. Cromwell is developed, tested, and containerized using
-[AdoptOpenJDK 17 HotSpot](https://adoptopenjdk.net/).
+A distribution of Java 11 is required to run Cromwell. Cromwell is developed, tested, and containerized using
+[AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/).
 
 For users running a Cromwell server [a docker image](https://hub.docker.com/r/broadinstitute/cromwell) has been made available.
 
diff --git a/docs/tutorials/FiveMinuteIntro.md b/docs/tutorials/FiveMinuteIntro.md
index f15e28087b9..1c16a56c606 100644
--- a/docs/tutorials/FiveMinuteIntro.md
+++ b/docs/tutorials/FiveMinuteIntro.md
@@ -3,11 +3,11 @@
 ### Prerequisites:
 
 * A Unix-based operating system (yes, that includes Mac!)
-* A Java 17 runtime environment 
+* A Java 11 runtime environment 
     * You can see what you have by running `$ java -version` on a terminal.
     * If not, consider installing via conda or brew [as explained here](../Releases.md).
-    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 17 build of [Temurin](https://adoptium.net/temurin/releases/?version=17)
-      * `sdk install 17.0.9-tem` as of the time of this writing
+    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 11 build of [Temurin](https://adoptium.net/temurin/releases/?version=11)
+      * `sdk install java 11.0.16-tem` as of the time of this writing
     * You might need to update the `export JAVA_HOME` in your bash profile to point to your JAVA install location.
 * A sense of adventure!
 
diff --git a/project/Publishing.scala b/project/Publishing.scala
index c8a601a4f0c..0af27e77147 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -63,7 +63,7 @@ object Publishing {
       val additionalDockerInstr: Seq[Instruction] = (dockerCustomSettings ?? Nil).value
 
       new Dockerfile {
-        from("us.gcr.io/broad-dsp-gcr-public/base/jre:17-debian")
+        from("us.gcr.io/broad-dsp-gcr-public/base/jre:11-debian")
         expose(8000)
         add(artifact, artifactTargetPath)
         runRaw(s"ln -s $artifactTargetPath /app/$projectName.jar")
@@ -163,7 +163,8 @@ object Publishing {
   val additionalResolvers = List(
     broadArtifactoryResolver,
     broadArtifactoryResolverSnap,
-  ) ++ Resolver.sonatypeOssRepos("releases")
+    Resolver.sonatypeRepo("releases")
+  )
 
   private val artifactoryCredentialsFile =
     file("target/ci/resources/artifactory_credentials.properties").getAbsoluteFile
diff --git a/publish/docker-setup.sh b/publish/docker-setup.sh
index bc39f31d10a..613d251df96 100755
--- a/publish/docker-setup.sh
+++ b/publish/docker-setup.sh
@@ -20,7 +20,7 @@ mkdir -p /etc/apt/keyrings
 wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
 echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
 apt update
-apt install -y temurin-17-jdk
+apt install -y temurin-11-jdk
 
 # Install jq 1.6 to ensure --rawfile is supported
 curl -L https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 -o /usr/bin/jq
diff --git a/runConfigurations/renderCiResources.run.xml b/runConfigurations/renderCiResources.run.xml
index ef56bf5e4fd..2a5ab5e29b8 100644
--- a/runConfigurations/renderCiResources.run.xml
+++ b/runConfigurations/renderCiResources.run.xml
@@ -7,8 +7,8 @@
     </option>
     <option name="tasks" value="renderCiResources" />
     <option name="useSbtShell" value="false" />
-    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M" />
+    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M -XX:+CMSClassUnloadingEnabled" />
     <option name="workingDir" value="$PROJECT_DIR$" />
     <method v="2" />
   </configuration>
-</component>
+</component>
\ No newline at end of file
diff --git a/scripts/docker-compose-mysql/README.md b/scripts/docker-compose-mysql/README.md
new file mode 100644
index 00000000000..8fcb404b069
--- /dev/null
+++ b/scripts/docker-compose-mysql/README.md
@@ -0,0 +1 @@
+Looking for the MySQL docs? Checkout the [Cromwell documentation](https://cromwell.readthedocs.io/en/develop/Configuring/#database)!
\ No newline at end of file
diff --git a/scripts/docker-compose-mysql/compose/cromwell/Dockerfile b/scripts/docker-compose-mysql/compose/cromwell/Dockerfile
new file mode 100644
index 00000000000..6bf9fd88bf9
--- /dev/null
+++ b/scripts/docker-compose-mysql/compose/cromwell/Dockerfile
@@ -0,0 +1,9 @@
+FROM broadinstitute/cromwell:develop
+
+RUN git clone https://github.com/vishnubob/wait-for-it.git
+RUN mkdir cromwell-working-dir
+WORKDIR cromwell-working-dir
+
+COPY ./app-config /app-config
+
+ENTRYPOINT ["/bin/sh", "-c"]
diff --git a/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf b/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
new file mode 100644
index 00000000000..a3b8d88ce3d
--- /dev/null
+++ b/scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf
@@ -0,0 +1,61 @@
+include required(classpath("application"))
+
+# Note: If you spot a mistake in this configuration sample, please let us know by making an issue at:
+# https://github.com/broadinstitute/cromwell/issues
+
+call-caching {
+  enabled = false
+}
+
+backend {
+  default = "Local"
+  providers {
+    Local {
+      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
+      config {
+        run-in-background = true
+        runtime-attributes = "String? docker Int? max_runtime = 2"
+        submit = "/bin/bash ${script}"
+        submit-docker = "docker run --rm -v ${cwd}:${docker_cwd} -i ${docker} /bin/bash < ${script}"
+
+        # Root directory where Cromwell writes job results. This directory must be
+        # visible and writeable by the Cromwell process as well as the jobs that Cromwell
+        # launches.
+        root: "cromwell-executions"
+
+        filesystems {
+          local {
+            localization: [
+              "soft-link", "hard-link", "copy"
+            ]
+
+            caching {
+              duplication-strategy: [
+                "soft-link"
+              ]
+
+              # Possible values: file, path
+              # "file" will compute an md5 hash of the file content.
+              # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
+              # in order to allow for the original file path to be hashed.
+              hashing-strategy: "path"
+
+              # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
+              # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
+              check-sibling-md5: false
+            }
+          }
+        }
+      }
+    }
+  }
+}
+
+database {
+  db.url = "jdbc:mysql://mysql-db/cromwell_db?allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true"
+  db.user = "cromwell"
+  db.password = "cromwell"
+  db.driver = "com.mysql.cj.jdbc.Driver"
+  profile = "slick.jdbc.MySQLProfile$"
+  db.connectionTimeout = 15000
+}
diff --git a/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql b/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
new file mode 100644
index 00000000000..b07938189e0
--- /dev/null
+++ b/scripts/docker-compose-mysql/compose/mysql/init/init_user.sql
@@ -0,0 +1,4 @@
+CREATE USER 'cromwell'@'localhost' IDENTIFIED BY 'cromwell';
+GRANT ALL PRIVILEGES ON cromwell_db.* TO 'cromwell'@'localhost' WITH GRANT OPTION;
+CREATE USER 'cromwell'@'%' IDENTIFIED BY 'cromwell';
+GRANT ALL PRIVILEGES ON cromwell_db.* TO 'cromwell'@'%' WITH GRANT OPTION;
diff --git a/scripts/docker-compose-mysql/docker-compose.yml b/scripts/docker-compose-mysql/docker-compose.yml
new file mode 100644
index 00000000000..3548919eadb
--- /dev/null
+++ b/scripts/docker-compose-mysql/docker-compose.yml
@@ -0,0 +1,22 @@
+version: '2'
+services:
+  cromwell:
+    build: 
+      context: ./compose/cromwell
+    volumes:
+      - ./cromwell-executions:/cromwell-working-dir/cromwell-executions
+    command: ["/wait-for-it/wait-for-it.sh mysql-db:3306 -t 120 -- java -Dconfig.file=/app-config/cromwell-application.conf -jar /app/cromwell.jar server"]
+    links:
+      - mysql-db
+    ports:
+      - "80:8000"
+  mysql-db:
+    image: "mysql:5.7"
+    environment:
+      - MYSQL_ROOT_PASSWORD=cromwell
+      - MYSQL_DATABASE=cromwell_db
+    volumes:
+      - ./compose/mysql/init:/docker-entrypoint-initdb.d
+      - ./compose/mysql/data:/var/lib/mysql
+    ports:
+      - "3307:3306"
diff --git a/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml b/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
new file mode 100644
index 00000000000..c7f0e1cee01
--- /dev/null
+++ b/scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml
@@ -0,0 +1,9 @@
+version: '2'
+services:
+  cromwell:
+    volumes:
+      - $HOME/.config/gcloud:/root/.config/gcloud
+      - ./jes-cromwell/jes-config:/app-config
+    environment:
+      - GOOGLE_APPLICATION_CREDENTIALS=/root/.config/gcloud/application_default_credentials.json
+
diff --git a/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf b/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
new file mode 100644
index 00000000000..cac33bb42ac
--- /dev/null
+++ b/scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf
@@ -0,0 +1,73 @@
+include required(classpath("application"))
+
+# Note: If you spot a mistake in this configuration sample, please let us know by making an issue at:
+# https://github.com/broadinstitute/cromwell/issues
+
+system.new-workflow-poll-rate=1
+
+google {
+
+  application-name = "cromwell"
+
+  auths = [
+    {
+      name = "application-default"
+      scheme = "application_default"
+    }
+  ]
+}
+
+engine {
+  filesystems {
+     gcs {
+       auth = "application-default"
+     }
+  }
+}
+
+call-caching {
+  enabled = false
+}
+
+backend {
+  default = "Jes"
+  providers {
+    Jes {
+          actor-factory = "cromwell.backend.impl.jes.JesBackendLifecycleActorFactory"
+          config {
+            // Google project
+            project = "broad-dsde-cromwell-dev"
+
+            // Base bucket for workflow executions
+            root = "gs://tjeandet-cromwell-execs"
+
+            // Polling for completion backs-off gradually for slower-running jobs.
+            // This is the maximum polling interval (in seconds):
+            maximum-polling-interval = 600
+
+            genomics {
+              // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
+              // Pipelines and manipulate auth JSONs.
+              auth = "application-default"
+              // Endpoint for APIs, no reason to change this unless directed by Google.
+              endpoint-url = "https://genomics.googleapis.com/"
+            }
+
+            filesystems {
+              gcs {
+                // A reference to a potentially different auth for manipulating files via engine functions.
+                auth = "application-default"
+              }
+            }
+          }
+    }
+  }
+}
+
+database {
+  db.url = "jdbc:mysql://mysql-db/cromwell_db?useSSL=false&rewriteBatchedStatements=true"
+  db.user = "cromwell"
+  db.password = "cromwell"
+  db.driver = "com.mysql.cj.jdbc.Driver"
+  profile = "slick.jdbc.MySQLProfile$"
+}
diff --git a/scripts/docker-develop/Dockerfile b/scripts/docker-develop/Dockerfile
new file mode 100644
index 00000000000..340d7bc00c4
--- /dev/null
+++ b/scripts/docker-develop/Dockerfile
@@ -0,0 +1,64 @@
+FROM ubuntu:focal
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update -q && \
+    apt-get upgrade -qq && \
+    apt-get install -y curl wget gnupg gnupg2 && \
+    rm -rf /var/lib/apt/lists/*
+
+# docker build -t vanessa/cromwell-dev .
+
+# Development environment for Cromwell that includes:
+#
+#   Scala 2.13
+#   SBT 1.x
+#   Java 11
+#   Git
+
+# Env variables
+ENV SCALA_VERSION 2.13.8
+ENV SBT_VERSION 1.5.5
+
+#
+## AdoptOpenJDK Hotspot
+#
+# https://adoptopenjdk.net/installation.html#linux-pkg-deb
+RUN \
+wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add - && \
+echo \
+"deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2) main" | \
+tee /etc/apt/sources.list.d/adoptopenjdk.list && \
+apt-get update && \
+apt-get install -y adoptopenjdk-11-hotspot
+
+#
+## Scala
+#
+
+RUN mkdir -p /home/pigman && \
+    curl \
+    --location --fail --silent --show-error \
+    https://downloads.typesafe.com/scala/$SCALA_VERSION/scala-$SCALA_VERSION.tgz | tar xfz - -C /opt/ && \
+    echo >> /home/pigman/.bashrc && \
+    echo "export PATH=/opt/scala-$SCALA_VERSION/bin:$PATH" >> /home/pigman/.bashrc
+
+#
+## sbt
+#
+
+# non-deb package installation instructions adapted from
+# - https://github.com/sbt/sbt/releases/tag/v1.4.9
+# - https://github.com/broadinstitute/scala-baseimage/pull/4/files
+RUN curl \
+    --location --fail --silent --show-error \
+    "https://github.com/sbt/sbt/releases/download/v$SBT_VERSION/sbt-$SBT_VERSION.tgz" | \
+    tar zxf - -C /usr/share && \
+    update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1 && \
+    sbt -Dsbt.supershell=false -Dsbt.rootdir=true sbtVersion
+
+# Instruct user to add code here during development
+RUN useradd pigman && \
+    mkdir -p /code
+
+WORKDIR /code
diff --git a/scripts/docker-develop/README.md b/scripts/docker-develop/README.md
new file mode 100644
index 00000000000..20bd1a8203f
--- /dev/null
+++ b/scripts/docker-develop/README.md
@@ -0,0 +1,60 @@
+# Cromwell Docker Development
+
+This is a container intended to help with development of Cromwell, in the
+case that you don't want to install the dependencies on your host. It
+includes the required software mentioned in [the developer docs](http://cromwell.readthedocs.io/en/develop/Building/) but with additional instructions to interact with the repository.
+
+As with the build instructions, first start by cloning the Cromwell repository from GitHub:
+
+```bash
+$ git clone git@github.com:broadinstitute/cromwell.git
+```
+
+And change into this directory:
+
+```bash
+$ cd cromwell/scripts/docker-develop
+```
+
+This is where this README.md sits with a [Dockerfile](Dockerfile)
+
+## Step 1. Build the Container
+From this folder with the Dockerfile, build the container. In the command below
+we are calling it `cromwell-dev` and you can choose to change this name if you want.
+
+```bash
+$ docker build -t cromwell-dev .
+```
+
+and change back to the root of the repository
+
+```bash
+cd ../../
+```
+
+## Step 2. Shell into Working Environment
+If you require a specific version of Cromwell as a starting point, do the appropriate `git checkout` now. 
+
+You are next going to want to bind the cromwell
+source code to be somewhere in the container. Actually, we have a `/code` directory
+ready for you to make this easy. Run this command from the base of the repository:
+
+```bash
+$ docker run -v $PWD/:/code -it cromwell-dev bash
+```
+
+## Step 4. The Development Steps
+
+You are going to use the command `sbt assembly` to create a runnable Cromwell JAR. The output
+will be `server/target`. Remember, here we are inside the container with scala and sbt:
+
+
+```bash
+$ sbt assembly
+```
+
+`sbt assembly` will build the runnable Cromwell JAR in `server/target/scala-2.13/` with a name like `cromwell-<VERSION>.jar`.
+
+You can then interact with it in the container, or on your host if you like. Remember that
+you have Java already in the container, so it makes sense to develop there.
+
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 8a9cc27c298..71577ce1e4c 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -746,7 +746,7 @@ cromwell::private::login_docker() {
 
 cromwell::private::render_secure_resources() {
     # Avoid docker output to sbt's stderr by pulling the image here
-    docker pull --quiet broadinstitute/dsde-toolbox:dev | cat
+    docker pull broadinstitute/dsde-toolbox:dev | cat
     # Copy the CI resources, then render the secure resources using Vault
     sbt -Dsbt.supershell=false --warn renderCiResources \
     || if [[ "${CROMWELL_BUILD_IS_CI}" == "true" ]]; then
diff --git a/src/ci/docker-compose/cromwell-test/Dockerfile b/src/ci/docker-compose/cromwell-test/Dockerfile
index 319c462cfbd..70e2477bb0e 100644
--- a/src/ci/docker-compose/cromwell-test/Dockerfile
+++ b/src/ci/docker-compose/cromwell-test/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:latest
+FROM ubuntu:focal
 
 WORKDIR /cromwell-test/
 COPY docker-setup.sh ./
diff --git a/src/ci/docker-compose/cromwell-test/docker-setup.sh b/src/ci/docker-compose/cromwell-test/docker-setup.sh
index 37e624c6766..c7970c7349b 100755
--- a/src/ci/docker-compose/cromwell-test/docker-setup.sh
+++ b/src/ci/docker-compose/cromwell-test/docker-setup.sh
@@ -25,11 +25,13 @@ apt-get install -y \
     sudo \
     wget \
 
-# setup install for Temurin
-# https://adoptium.net/installation/linux/
-mkdir -p /etc/apt/keyrings
-wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
-echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^UBUNTU_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
+# setup install for adoptopenjdk
+# https://adoptopenjdk.net/installation.html#linux-pkg-deb
+wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add -
+echo "deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(
+        grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
+    ) main" |
+    tee /etc/apt/sources.list.d/adoptopenjdk.list
 
 # setup install for gcloud
 # https://cloud.google.com/sdk/docs/install#deb
@@ -50,7 +52,7 @@ add-apt-repository \
 # install packages that required setup
 apt-get update
 apt-get install -y \
-    temurin-17-jdk \
+    adoptopenjdk-11-hotspot \
     containerd.io \
     docker-ce \
     docker-ce-cli \
@@ -64,7 +66,7 @@ apt-get clean
 # non-deb package installation instructions adapted from
 # - https://github.com/sbt/sbt/releases/tag/v1.4.9
 # - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-curl -L --silent "https://github.com/sbt/sbt/releases/download/v1.8.1/sbt-1.8.1.tgz" |
+curl -L --silent "https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz" |
     tar zxf - -C /usr/share
 update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1
 
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
new file mode 100644
index 00000000000..5d1b1e02c12
--- /dev/null
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/SharedFileSystemJobExecutionActorSpec.scala
@@ -0,0 +1,430 @@
+package cromwell.backend.sfs
+
+import _root_.wdl.draft2.model.LocallyQualifiedName
+import akka.testkit.{TestDuration, TestProbe}
+import com.typesafe.config.ConfigFactory
+import common.collections.EnhancedCollections._
+import cromwell.backend.BackendJobExecutionActor.{
+  JobAbortedResponse,
+  JobFailedNonRetryableResponse,
+  JobSucceededResponse,
+  RunOnBackend
+}
+import cromwell.backend.BackendLifecycleActor.AbortJobCommand
+import cromwell.backend._
+import cromwell.backend.async.WrongReturnCode
+import cromwell.backend.io.JobPathsSpecHelper._
+import cromwell.backend.io.TestWorkflows._
+import cromwell.backend.io.{JobPathsWithDocker, TestWorkflows}
+import cromwell.backend.sfs.TestLocalAsyncJobExecutionActor._
+import cromwell.backend.standard.StandardValidatedRuntimeAttributesBuilder
+import cromwell.core.CromwellGraphNode._
+import cromwell.core.Tags._
+import cromwell.core._
+import cromwell.core.callcaching.NoDocker
+import cromwell.core.path.{DefaultPathBuilder, Path}
+import cromwell.services.keyvalue.KeyValueServiceActor._
+import cromwell.util.WomMocks
+import org.scalatest.concurrent.PatienceConfiguration.Timeout
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.prop.TableDrivenPropertyChecks
+import org.scalatest.{Assertion, OptionValues}
+import wom.expression.NoIoFunctionSet
+import wom.graph.{CommandCallNode, WomIdentifier}
+import wom.types._
+import wom.values._
+
+import java.io.FileNotFoundException
+import scala.concurrent.duration._
+import scala.sys.process._
+
+class SharedFileSystemJobExecutionActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with BackendSpec
+    with TableDrivenPropertyChecks
+    with OptionValues {
+
+  behavior of "SharedFileSystemJobExecutionActor"
+
+  lazy val runtimeAttributeDefinitions: Set[RuntimeAttributeDefinition] =
+    StandardValidatedRuntimeAttributesBuilder.default(Some(TestConfig.optionalRuntimeConfig)).definitions.toSet
+
+  private val call = CommandCallNode(WomIdentifier("SfsJEASpec_call"), null, null, null, Set.empty, null, None)
+  private val mockBackendJobDescriptorKey = BackendJobDescriptorKey(call, None, 1)
+
+  def executeSpec(docker: Boolean): Any = {
+    val expectedOutputs: CallOutputs =
+      WomMocks.mockOutputExpectations(Map("hello.salutation" -> WomString("Hello you !")))
+
+    val expectedResponse = JobSucceededResponse(mockBackendJobDescriptorKey,
+                                                Some(0),
+                                                expectedOutputs,
+                                                None,
+                                                Seq.empty,
+                                                None,
+                                                resultGenerationMode = RunOnBackend
+    )
+    val runtime = if (docker) s"""runtime { docker: "$dockerImageUbuntu" }""" else ""
+    val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld, runtime = runtime)
+    val workflow = TestWorkflow(workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor, expectedResponse)
+    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
+                                                                    Map.empty,
+                                                                    WorkflowOptions.empty,
+                                                                    runtimeAttributeDefinitions
+                                ),
+                                workflow.config
+    )
+    testWorkflow(workflow, backend)
+  }
+
+  private val dockerImageUbuntu = "ubuntu:latest"
+
+  it should "docker pull images now so that 'DockerTest' specs below do not timeout" taggedAs DockerTest in {
+    /*
+    This is a poor substitute for `beforeAll()`.
+    If one wants to parallelize the test runs consider using a separate tagged-Suite with a `.beforeAll()`.
+    - https://medium.com/@linda0511ny/tag-whole-test-class-in-scalatest-94cd67fa85a4
+     */
+    List("docker", "pull", dockerImageUbuntu).! should be(0)
+  }
+
+  it should "execute an hello world workflow" in {
+    executeSpec(docker = false)
+  }
+
+  it should "execute an hello world workflow on Docker" taggedAs DockerTest in {
+    executeSpec(docker = true)
+  }
+
+  it should "send back an execution failure if the task fails" in {
+    val expectedResponse =
+      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
+                                    WrongReturnCode("wf_goodbye.goodbye:NA:1", 1, None),
+                                    Option(1)
+      )
+    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(GoodbyeWorld),
+                                TestConfig.backendRuntimeConfigDescriptor,
+                                expectedResponse
+    )
+    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
+                                                                    Map.empty,
+                                                                    WorkflowOptions.empty,
+                                                                    runtimeAttributeDefinitions
+                                ),
+                                workflow.config
+    )
+    testWorkflow(workflow, backend)
+  }
+
+  def localizationSpec(docker: Boolean): Assertion = {
+    def templateConf(localizers: String) = BackendConfigurationDescriptor(
+      ConfigFactory.parseString(s"""|{
+                                    |  root = "local-cromwell-executions"
+                                    |  filesystems {
+                                    |    local {
+                                    |      localization = [
+                                    |        $localizers
+                                    |      ]
+                                    |    }
+                                    |  }
+                                    |  default-runtime-attributes {
+                                    |  cpu: 1
+                                    |  failOnStderr: false
+                                    |  continueOnReturnCode: 0
+                                    |  }
+                                    |}
+                                    |""".stripMargin),
+      ConfigFactory.parseString("{}")
+    )
+
+    val hardConf = templateConf("hard-link")
+    val symConf = templateConf("soft-link")
+    val copyConf = templateConf("copy")
+
+    val jsonInputFile =
+      createCannedFile("localize", "content from json inputs", Option(DefaultPathBuilder.build(".").get))
+    val callInputFile =
+      createCannedFile("localize", "content from call inputs", Option(DefaultPathBuilder.build(".").get))
+    val inputs = Option(s"""{
+      "wf_localize.workflowFile": "${callInputFile.pathAsString}",
+      "wf_localize.localize.inputFileFromJson": "${jsonInputFile.pathAsString}"
+    }""")
+
+    val expectedOutputs: CallOutputs = WomMocks.mockOutputExpectations(
+      Map(
+        "localize.out" -> WomArray(WomArrayType(WomStringType),
+                                   List(WomString("content from json inputs"), WomString("content from call inputs"))
+        )
+      )
+    )
+
+    val confs = List(
+      (hardConf, false),
+      (copyConf, false)
+    ) ++ (if (!docker) List((symConf, true)) else List.empty)
+
+    val localizers = Table(
+      ("conf", "isSymLink"),
+      confs: _*
+    )
+
+    forAll(localizers) { (conf, isSymlink) =>
+      val runtime = if (docker) s"""runtime { docker: "$dockerImageUbuntu" } """ else ""
+      val workflowDescriptor = buildWdlWorkflowDescriptor(InputFiles, inputs, runtime = runtime)
+      val callInputs = Map(
+        "inputFileFromCallInputs" -> workflowDescriptor.knownValues.collectFirst {
+          case (outputPort, resolvedValue) if outputPort.fullyQualifiedName == "wf_localize.workflowFile" =>
+            resolvedValue
+        }.get,
+        "inputFileFromJson" -> workflowDescriptor.knownValues.collectFirst {
+          case (outputPort, resolvedValue)
+              if outputPort.fullyQualifiedName == "wf_localize.localize.inputFileFromJson" =>
+            resolvedValue
+        }.get
+      )
+
+      val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                      callInputs,
+                                                                      WorkflowOptions.empty,
+                                                                      runtimeAttributeDefinitions
+                                  ),
+                                  conf
+      )
+      val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                    callInputs,
+                                                                                    WorkflowOptions.empty,
+                                                                                    runtimeAttributeDefinitions
+      )
+      val expectedResponse = JobSucceededResponse(jobDescriptor.key,
+                                                  Some(0),
+                                                  expectedOutputs,
+                                                  None,
+                                                  Seq.empty,
+                                                  None,
+                                                  resultGenerationMode = RunOnBackend
+      )
+
+      val jobPaths = JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, conf.backendConfig)
+
+      whenReady(backend.execute) { executionResponse =>
+        assertResponse(executionResponse, expectedResponse)
+        val localizedJsonInputFile =
+          DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString,
+                                 jsonInputFile.parent.pathAsString.hashCode.toString + "/" + jsonInputFile.name
+          )
+        val localizedCallInputFile =
+          DefaultPathBuilder.get(jobPaths.callInputsRoot.pathAsString,
+                                 callInputFile.parent.pathAsString.hashCode.toString + "/" + callInputFile.name
+          )
+
+        localizedJsonInputFile.isSymbolicLink shouldBe isSymlink
+        val realJsonInputFile =
+          if (isSymlink) localizedJsonInputFile.symbolicLink.get else localizedJsonInputFile
+        realJsonInputFile.toFile should exist
+
+        localizedCallInputFile.isSymbolicLink shouldBe isSymlink
+        val realCallInputFile =
+          if (isSymlink) localizedCallInputFile.symbolicLink.get else localizedCallInputFile
+        realCallInputFile.toFile should exist
+      }
+    }
+  }
+
+  it should "execute calls with input files and localize them appropriately" in {
+    localizationSpec(docker = false)
+  }
+
+  it should "execute calls with input files and localize them appropriately (in Docker)" taggedAs DockerTest in {
+    localizationSpec(docker = true)
+  }
+
+  it should "abort a job and kill a process" in {
+    val workflowDescriptor = buildWdlWorkflowDescriptor(Sleep20)
+    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                  Map.empty,
+                                                                                  WorkflowOptions.empty,
+                                                                                  runtimeAttributeDefinitions
+    )
+    val backendRef = createBackendRef(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
+    val backend = backendRef.underlyingActor
+
+    val execute = backend.execute
+    backendRef ! AbortJobCommand
+
+    whenReady(execute) { executionResponse =>
+      executionResponse shouldBe a[JobAbortedResponse]
+    }
+  }
+
+  def recoverSpec(completed: Boolean, writeReturnCode: Boolean = true): Assertion = {
+    val workflowDescriptor = buildWdlWorkflowDescriptor(HelloWorld)
+    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                  Map.empty,
+                                                                                  WorkflowOptions.empty,
+                                                                                  runtimeAttributeDefinitions
+    )
+    val backendRef = createBackendRef(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
+    val backend = backendRef.underlyingActor
+
+    val jobPaths = JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, ConfigFactory.empty)
+    jobPaths.callExecutionRoot.createPermissionedDirectories()
+    jobPaths.stdout.write("Hello stubby ! ")
+    jobPaths.stderr.touch()
+
+    val pid =
+      if (completed) {
+        if (writeReturnCode)
+          jobPaths.returnCode.write("0")
+        "0"
+      } else {
+        import sys.process._
+        val proc = Seq("bash", "-c", s"sleep 2; echo 0 > ${jobPaths.returnCode}").run()
+        val pField = proc.getClass.getDeclaredField("p")
+        pField.setAccessible(true)
+        val p = pField.get(proc)
+        val pidField = p.getClass.getDeclaredField("pid")
+        pidField.setAccessible(true)
+        pidField.get(p).toString
+      }
+
+    def execute = backend.recover
+
+    val kvJobKey =
+      KvJobKey(jobDescriptor.key.call.fullyQualifiedName, jobDescriptor.key.index, jobDescriptor.key.attempt)
+    val scopedKey = ScopedKey(workflowDescriptor.id, kvJobKey, SharedFileSystemAsyncJobExecutionActor.JobIdKey)
+    val kvPair = KvPair(scopedKey, pid)
+
+    val previousKvPutter = TestProbe("previousKvPutter")
+    val kvPutReq = KvPut(kvPair)
+    backendRef.underlyingActor.serviceRegistryActor.tell(msg = kvPutReq, sender = previousKvPutter.ref)
+    previousKvPutter.expectMsg(KvPutSuccess(kvPutReq))
+    val outputPort = jobDescriptor.taskCall.outputPorts.head
+    whenReady(execute, Timeout(10.seconds.dilated)) { executionResponse =>
+      if (writeReturnCode) {
+        executionResponse should be(a[JobSucceededResponse])
+        val succeededResponse = executionResponse.asInstanceOf[JobSucceededResponse]
+        succeededResponse.returnCode.value should be(0)
+        succeededResponse.jobOutputs should be(CallOutputs(Map(outputPort -> WomString("Hello stubby !"))))
+      } else {
+        executionResponse should be(a[JobFailedNonRetryableResponse])
+        val failedResponse = executionResponse.asInstanceOf[JobFailedNonRetryableResponse]
+        failedResponse.returnCode should be(empty)
+        failedResponse.throwable should be(a[RuntimeException])
+        failedResponse.throwable.getMessage should startWith("Unable to determine that 0 is alive, and")
+        failedResponse.throwable.getMessage should endWith("call-hello/execution/rc does not exist.")
+      }
+    }
+  }
+
+  it should "recover a job in progress" in {
+    recoverSpec(completed = false)
+  }
+
+  it should "recover a job that already completed" in {
+    recoverSpec(completed = true)
+  }
+
+  it should "not recover a job for a non-existent pid" in {
+    recoverSpec(completed = true, writeReturnCode = false)
+  }
+
+  it should "execute shards from a scatter" in {
+    val workflowDescriptor = buildWdlWorkflowDescriptor(TestWorkflows.Scatter)
+
+    val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
+
+    0 to 2 foreach { shard =>
+      // This assumes that engine will give us the evaluated value of the scatter item at the correct index
+      // If this is not the case, more context/logic will need to be moved to the backend so it can figure it out by itself
+      val symbolMaps: Map[LocallyQualifiedName, WomInteger] = Map("intNumber" -> WomInteger(shard))
+
+      val evaluatedAttributes = call.callable.runtimeAttributes.attributes
+        .safeMapValues(_.evaluateValue(Map.empty, NoIoFunctionSet).getOrElse(fail("Can't evaluate runtime attribute")))
+      val runtimeAttributes: Map[LocallyQualifiedName, WomValue] =
+        RuntimeAttributeDefinition.addDefaultsToAttributes(runtimeAttributeDefinitions, WorkflowOptions.empty)(
+          evaluatedAttributes
+        )
+
+      val jobDescriptor: BackendJobDescriptor =
+        BackendJobDescriptor(workflowDescriptor,
+                             BackendJobDescriptorKey(call, Option(shard), 1),
+                             runtimeAttributes,
+                             fqnWdlMapToDeclarationMap(symbolMaps),
+                             NoDocker,
+                             None,
+                             Map.empty
+        )
+      val backend = createBackend(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
+      val response =
+        JobSucceededResponse(
+          mockBackendJobDescriptorKey,
+          Some(0),
+          WomMocks.mockOutputExpectations(Map("scattering.out" -> WomInteger(shard))),
+          None,
+          Seq.empty,
+          None,
+          resultGenerationMode = RunOnBackend
+        )
+      executeJobAndAssertOutputs(backend, response)
+    }
+  }
+
+  it should "post process outputs" in {
+    val inputFile = createCannedFile("localize", "content from json inputs").pathAsString
+    val inputs = Option(s"""{
+      "wf_localize.localize.inputFile": "$inputFile"
+    }""")
+    val workflowDescriptor = buildWdlWorkflowDescriptor(OutputProcess, inputs)
+    val jobDescriptor: BackendJobDescriptor = jobDescriptorFromSingleCallWorkflow(workflowDescriptor,
+                                                                                  Map.empty,
+                                                                                  WorkflowOptions.empty,
+                                                                                  runtimeAttributeDefinitions
+    )
+    val backend = createBackend(jobDescriptor, TestConfig.backendRuntimeConfigDescriptor)
+    val jobPaths =
+      JobPathsWithDocker(jobDescriptor.key, workflowDescriptor, TestConfig.backendRuntimeConfigDescriptor.backendConfig)
+    val expectedA = WomSingleFile(jobPaths.callExecutionRoot.resolve("a").toAbsolutePath.pathAsString)
+    val expectedB = WomSingleFile(jobPaths.callExecutionRoot.resolve("dir").toAbsolutePath.resolve("b").pathAsString)
+    val expectedOutputs = WomMocks.mockOutputExpectations(
+      Map(
+        "localize.o1" -> expectedA,
+        "localize.o2" -> WomArray(WomArrayType(WomSingleFileType), Seq(expectedA, expectedB)),
+        "localize.o3" -> WomSingleFile(inputFile)
+      )
+    )
+    val expectedResponse = JobSucceededResponse(jobDescriptor.key,
+                                                Some(0),
+                                                expectedOutputs,
+                                                None,
+                                                Seq.empty,
+                                                None,
+                                                resultGenerationMode = RunOnBackend
+    )
+
+    executeJobAndAssertOutputs(backend, expectedResponse)
+  }
+
+  it should "fail post processing if an output file is not found" in {
+    val expectedResponse =
+      JobFailedNonRetryableResponse(mockBackendJobDescriptorKey,
+                                    new FileNotFoundException("Could not process output, file not found:"),
+                                    Option(0)
+      )
+    val workflow = TestWorkflow(buildWdlWorkflowDescriptor(MissingOutputProcess),
+                                TestConfig.backendRuntimeConfigDescriptor,
+                                expectedResponse
+    )
+    val backend = createBackend(jobDescriptorFromSingleCallWorkflow(workflow.workflowDescriptor,
+                                                                    Map.empty,
+                                                                    WorkflowOptions.empty,
+                                                                    runtimeAttributeDefinitions
+                                ),
+                                workflow.config
+    )
+    testWorkflow(workflow, backend)
+  }
+
+  def createCannedFile(prefix: String, contents: String, parent: Option[Path] = None): Path =
+    DefaultPathBuilder.createTempFile(prefix, ".out", parent).write(contents)
+}
diff --git a/wom/src/main/resources/reference.conf b/wom/src/main/resources/reference.conf
index fce1a8e0283..1907a23eac6 100644
--- a/wom/src/main/resources/reference.conf
+++ b/wom/src/main/resources/reference.conf
@@ -2,7 +2,7 @@ yaml {
   # The maximum number of nodes (scalars + sequences + mappings) that will be parsed in a YAML
   max-nodes = 1000000
   # The maximum nested depth for nodes (sequences + mappings) that will be parsed in a YAML
-  max-depth = 100
+  max-depth = 1000
 }
 
 wom-parse {
diff --git a/wom/src/test/scala/wom/util/YamlUtilsSpec.scala b/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
index 8f5ddd22c95..986201a2213 100644
--- a/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
+++ b/wom/src/test/scala/wom/util/YamlUtilsSpec.scala
@@ -80,7 +80,7 @@ class YamlUtilsSpec
       "a null yaml",
       null,
       refineMV[NonNegative](0),
-      "Cannot invoke \"String.length()\" because \"s\" is null"
+      null
     ),
     (
       "an empty yaml mapping when limited to zero nodes",
@@ -179,14 +179,14 @@ class YamlUtilsSpec
     val nesting = 1000000
     val yaml = ("[" * nesting) + ("]" * nesting)
     val exception: Exception = YamlUtils.parse(yaml).left.value
-    exception should have message "Parsing halted at node depth 100" // <-- Updating here? Also get the docs too!
+    exception should have message "Parsing halted at node depth 1000" // <-- Updating here? Also get the docs too!
   }
 
   it should "fail to parse deeply nested yaml mapping with the default configuration" in {
     val nesting = 1000000
     val yaml = ("{a:" * nesting) + "b" + ("}" * nesting)
     val exception: Exception = YamlUtils.parse(yaml).left.value
-    exception should have message "Parsing halted at node depth 100" // <-- Updating here? Also get the docs too!
+    exception should have message "Parsing halted at node depth 1000" // <-- Updating here? Also get the docs too!
   }
 
   it should "not parse a config with a negative value" in {

From e3a923f6bca88cf4aea63b3c0a1ccab586e18e0e Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 19 Dec 2023 08:53:14 -0500
Subject: [PATCH 261/326] [WX-1395] Scala formatter Github Action (#7341)

Co-authored-by: ScalaFmt Fixer <ScalaFmtFixer@fakeDomain.com>
Co-authored-by: Broad Bot <broadbot@broadinstitute.org>
---
 .github/workflows/scalafmt-check.yml |  2 +-
 .github/workflows/scalafmt-fix.yml   | 58 ++++++++++++++++++----------
 2 files changed, 38 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/scalafmt-check.yml b/.github/workflows/scalafmt-check.yml
index 2d60b86040b..3730d2ffc8f 100644
--- a/.github/workflows/scalafmt-check.yml
+++ b/.github/workflows/scalafmt-check.yml
@@ -1,4 +1,4 @@
-name: 'Scalafmt'
+name: 'ScalaFmt Check'
 
 # This GitHub Action runs the ScalaFmt linting tool on the entire codebase.
 # It fails if any files are not formatted properly.
diff --git a/.github/workflows/scalafmt-fix.yml b/.github/workflows/scalafmt-fix.yml
index 83e6fb099ed..a20eab6dbee 100644
--- a/.github/workflows/scalafmt-fix.yml
+++ b/.github/workflows/scalafmt-fix.yml
@@ -1,48 +1,64 @@
-name: 'Scalafmt'
+name: 'ScalaFmt Fix'
 
 # This GitHub Action runs the ScalaFmt linting tool on the entire codebase.
 # It will fix, commit, and push linted code.
 # It will only run when someone comments "scalafmt" on a PR.
 
-run-name: ${{ format('ScalaFmt Fix on {0}', github.ref_name) }}
+run-name: ScalaFmt Fix
 
 on:
-  workflow_dispatch:
   issue_comment:
     types:
       - created
+  workflow_dispatch:
+    branch_name:
+      description: 'Branch to run ScalaFmt against'
+      required: true
+  pull_request_target:
+    types:
+      - opened
+      - synchronize
 
 jobs:
   run-scalafmt-fix:
     runs-on: ubuntu-latest
     timeout-minutes: 20
     steps:
-      - uses: actions/checkout@v3
-        with:
-          ref: ${{ inputs.target-branch }}
-      - uses: ./.github/set_up_cromwell_action
-        with:
-          cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+      - name: Determine Target Branch
+        id: determine-branch
+        run: |
+          if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then
+            echo "::set-output name=target_branch::${{ inputs.branch_name }}"
+          else
+            echo "::set-output name=target_branch::${{ github.event.pull_request.head.ref }}"
+          fi
+        shell: bash
+        env:
+          inputs.branch_name: ${{ inputs.branch_name }}
       - name: Check for ScalaFmt Comment
         id: check-comment
         run: |
           if [[ "${{ github.event_name }}" == "issue_comment" && "${{ github.event.comment.body }}" == *"scalafmt"* ]]; then
             echo "::set-output name=comment-triggered::true"
-            echo "::set-output name=comment-author-email::${{ github.event.comment.user.login }}@users.noreply.github.com"
-            echo "::set-output name=comment-author-name::${{ github.event.comment.user.login }}"
           else
             echo "::set-output name=comment-triggered::false"
           fi
         shell: bash
-      - name: Run ScalaFmt
+      - uses: actions/checkout@v3 # checkout the cromwell repo
+        with:
+         ref: ${{ inputs.target-branch }}
+      - uses: ./.github/set_up_cromwell_action
+        with:
+          cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+      - name: Run ScalaFmt Fixup
+        if: steps.check-comment.outputs.comment-triggered == 'true' || github.event_name == 'workflow_dispatch'
+        env:
+          BROADBOT_GITHUB_TOKEN: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
         run: |
-          if [[ ${{ steps.check-comment.outputs.comment-triggered }} == true ]]; then
-            echo "PR Comment Detected. Formatting, committing, and pushing formatted scala code."
-            sbt scalaFmtAll
-            git config --global user.email "${{ steps.check-comment.outputs.comment-author-email }}"
-            git config --global user.name "${{ steps.check-comment.outputs.comment-author-name }}"
-            git add .
-            git commit -m "Auto-format code with ScalaFmt"
-            git push origin ${{ github.ref }}
-          fi
+          sbt scalafmtAll
+          git config --global user.email "broadbot@broadinstitute.org"
+          git config --global user.name "Broad Bot"
+          git add .
+          git commit -m "ScalaFmt fixup via Broad Bot"
+          git push origin ${{ steps.determine-branch.outputs.target_branch }}
         working-directory: ${{ github.workspace }}

From 6eb71bbcc128de788598f958d4a9a7dd8713b58e Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Fri, 22 Dec 2023 19:18:24 +0100
Subject: [PATCH 262/326] Improved tagging support (#37)

* efs fixes : support paths with over 127 characters, fix delocalization of efs-based globs

* add deployment manual, fix issue with empty disks

* update documentation

* update documentation

* update documentation

* support for tagging instances and volumes used in jobs, some support for spaces in file paths

* corrected workflow id in tagging

* redirect exit code 137 to retry-with-more-memory routine

---------

Co-authored-by: Henrique Ribeiro <henriqueribeiro@users.noreply.github.com>
---
 .../main/scala/cromwell/backend/backend.scala |   2 +
 .../StandardAsyncExecutionActor.scala         |  10 +-
 ...wsBatchAsyncBackendJobExecutionActor.scala |  18 +-
 .../backend/impl/aws/AwsBatchAttributes.scala |  11 +
 .../impl/aws/AwsBatchConfiguration.scala      |   1 +
 .../backend/impl/aws/AwsBatchJob.scala        | 288 ++++++++++++------
 .../impl/aws/AwsBatchJobDefinition.scala      |  25 +-
 .../impl/aws/AwsBatchRuntimeAttributes.scala  |  36 ++-
 .../scala/cromwell/backend/impl/aws/README.md |  30 ++
 .../impl/aws/io/AwsBatchGlobFunctions.scala   |   9 -
 10 files changed, 310 insertions(+), 120 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index 2f18f499f30..a8bb4baaf2f 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -140,10 +140,12 @@ object CommonBackendConfigurationAttributes {
     "default-runtime-attributes.docker",
     "default-runtime-attributes.queueArn",
     "default-runtime-attributes.awsBatchRetryAttempts",
+    "default-runtime-attributes.maxRetries",
     "default-runtime-attributes.awsBatchEvaluateOnExit",
     "default-runtime-attributes.ulimits",
     "default-runtime-attributes.efsDelocalize",
     "default-runtime-attributes.efsMakeMD5",
+    "default-runtime-attributes.tagResources",
     "default-runtime-attributes.failOnStderr",
     "slow-job-warning-time",
     "dockerhub",
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 02c2a2577a2..8acef722f71 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -38,8 +38,9 @@ import wom.callable.{AdHocValue, CommandTaskDefinition, ContainerizedInputExpres
 import wom.expression.WomExpression
 import wom.graph.LocalName
 import wom.values._
+import wom.types._
 import wom.{CommandSetupSideEffectFile, InstantiatedCommand, WomFileMapper}
-
+import java.net.URLDecoder
 import scala.concurrent._
 import scala.concurrent.duration._
 import scala.util.{Failure, Success, Try}
@@ -165,7 +166,12 @@ trait StandardAsyncExecutionActor
         if (inputsToNotLocalize.contains(womFile)) {
           womFile
         } else {
-          mapper(womFile)
+          // resolve
+          val mapped_wom = mapper(womFile)
+          // decode url encoded values generated by the mapper
+          val decoded_womValue = URLDecoder.decode(mapped_wom.valueString,"UTF-8")
+          // convert to womfile again
+          WomFile(WomSingleFileType, decoded_womValue)
         }
     )
   }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 498bd2ec4fe..150d61bef79 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -31,7 +31,7 @@
 
 package cromwell.backend.impl.aws
 
-import java.net.SocketTimeoutException
+import java.net.{SocketTimeoutException, URLDecoder}
 import java.io.FileNotFoundException
 import java.nio.file.Paths
 
@@ -202,7 +202,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       configuration.fsxMntPoint,
       configuration.efsMntPoint,
       Option(runtimeAttributes.efsMakeMD5),
-      Option(runtimeAttributes.efsDelocalize))
+      Option(runtimeAttributes.efsDelocalize),
+      Option(runtimeAttributes.tagResources))
   }
 
   // setup batch client to query job container info
@@ -262,13 +263,13 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         case Success(path: S3Path) =>
           configuration.fileSystem match  {
             case AWSBatchStorageSystems.s3 => 
-                path.pathWithoutScheme
+                URLDecoder.decode(path.pathWithoutScheme,"UTF-8")
             case _ =>  
-                path.toString
+                URLDecoder.decode(path.toString,"UTF-8")
           }
         // non-s3 paths
         case _ => 
-            value
+            URLDecoder.decode(value,"UTF-8")
       }
     )
   }
@@ -421,7 +422,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
             AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), womFile.value, relpath, disk)
         } else {
             // if efs is not enabled, OR efs delocalization IS enabled, keep the s3 path as destination.
-            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), destination, relpath, disk)
+            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), URLDecoder.decode(destination,"UTF-8"), relpath, disk)
         }
     List(output)
   }
@@ -689,7 +690,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       // STATUS LOGIC:
       //   - success : container exit code is zero
       //   - command failure: container exit code > 0, no statusReason in container
-      //   - OOM kill : container exit code > 0, statusReason contains "OutOfMemory"
+      //   - OOM kill : container exit code > 0, statusReason contains "OutOfMemory" OR exit code == 137
       //   - spot kill : no container exit code set. statusReason of ATTEMPT (not container) says "host EC2 (...) terminated"     
       Log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
       val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(job.jobId).build)
@@ -722,6 +723,9 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         case "0" => 
             Log.debug("container exit code was zero. job succeeded")
             false
+        case "137" => 
+            Log.info("Job failed with Container status reason : 'OutOfMemory' (code:137)")
+            true
         case _ => 
             // failed job due to command errors (~ user errors) don't have a container exit reason.
             val containerStatusReason:String = {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index 1119e192262..10e2dddfb98 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -61,6 +61,7 @@ case class AwsBatchAttributes(fileSystem: String,
                               fsxMntPoint: Option[List[String]],
                               efsMntPoint: Option[String],
                               efsMakeMD5: Option[Boolean],
+                              tagResources: Option[Boolean],
                               efsDelocalize: Option[Boolean],
                               globLinkCommand: Option[String],
                               checkSiblingMd5: Option[Boolean]
@@ -91,6 +92,8 @@ object AwsBatchAttributes {
     "ulimits",
     "efsDelocalize",
     "efsMakeMD5",
+    "tagResources",
+    "maxRetries",
     "glob-link-command"
   )
 
@@ -181,6 +184,13 @@ object AwsBatchAttributes {
             case false => None
       }
     }
+    // from config if set: 
+    val tagResources:ErrorOr[Option[Boolean]] = validate {
+        backendConfig.hasPath("default-runtime-attributes.tagResources") match {
+            case true => Some(backendConfig.getBoolean("default-runtime-attributes.tagResources"))
+            case false => None
+      }
+    }
     // from config if set.
     val globLinkCommand:ErrorOr[Option[String]] = validate {
         backendConfig.hasPath("glob-link-command") match {
@@ -207,6 +217,7 @@ object AwsBatchAttributes {
       efsMntPoint,
       efsMakeMD5,
       efsDelocalize,
+      tagResources,
       globLinkCommand,
       checkSiblingMd5
     ).tupled.map((AwsBatchAttributes.apply _).tupled) match {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
index 8a019110509..3ceb1ea3844 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
@@ -60,6 +60,7 @@ class AwsBatchConfiguration(val configurationDescriptor: BackendConfigurationDes
   val efsMntPoint = batchAttributes.efsMntPoint
   val efsMakeMD5 = batchAttributes.efsMakeMD5
   val efsDelocalize = batchAttributes.efsDelocalize
+  val tagResources = batchAttributes.tagResources
   val globLinkCommand = batchAttributes.globLinkCommand
   val checkSiblingMd5 = batchAttributes.checkSiblingMd5
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index d967e26659a..51c5b8080f6 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -87,7 +87,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                              fsxMntPoint: Option[List[String]],
                              efsMntPoint: Option[String],
                              efsMakeMD5: Option[Boolean],
-                             efsDelocalize: Option[Boolean]
+                             efsDelocalize: Option[Boolean],
+                             tagResources: Option[Boolean]
                             ) {
 
 
@@ -131,19 +132,19 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
       case input: AwsBatchFileInput if input.s3key.startsWith("s3://") && input.s3key.endsWith(".tmp") =>
         //we are localizing a tmp file which may contain workdirectory paths that need to be reconfigured
         s"""
-           |_s3_localize_with_retry ${input.s3key} $workDir/${input.local}
-           |sed -i 's#${AwsBatchWorkingDisk.MountPoint.pathAsString}#$workDir#g' $workDir/${input.local}
+           |_s3_localize_with_retry "${input.s3key}" "$workDir/${input.local}"
+           |sed -i 's#${AwsBatchWorkingDisk.MountPoint.pathAsString}#$workDir#g' "$workDir/${input.local}"
            |""".stripMargin
 
       case input: AwsBatchFileInput if input.s3key.startsWith("s3://") => 
         // regular s3 objects : download to working dir.
-        s"_s3_localize_with_retry ${input.s3key} ${input.mount.mountPoint.pathAsString}/${input.local}"
+        s"""_s3_localize_with_retry "${input.s3key}" "${input.mount.mountPoint.pathAsString}/${input.local}" """.stripMargin
           .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
 
       case input: AwsBatchFileInput if efsMntPoint.isDefined && input.s3key.startsWith(efsMntPoint.get) =>  
         // EFS located file : test for presence on provided path.
         Log.debug("EFS input file detected: "+ input.s3key + " / "+ input.local.pathAsString)
-        s"test -e ${input.s3key} || (echo 'input file: ${input.s3key} does not exist' && exit 1)"
+        s"""test -e "${input.s3key}" || (echo 'input file: ${input.s3key} does not exist' && LOCALIZATION_FAILED=1)""".stripMargin
       
       case input: AwsBatchFileInput => 
         // an entry in 'disks' => keep mount as it is.. 
@@ -152,7 +153,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         //  .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
         val filePath = input.local.pathAsString
         Log.debug("input entry in disks detected "+ input.s3key + " / "+ input.local.pathAsString)
-        s"test -e $filePath || (echo 'input file: $filePath does not exist' && exit 1)"
+        s"""test -e "$filePath" || (echo 'input file: $filePath does not exist' && LOCALIZATION_FAILED=1)""".stripMargin
       
       case _ => ""
     }.toList.mkString("\n")
@@ -161,6 +162,17 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     val mp_threshold : Long = if (conf.hasPath("engine.filesystems.s3.MultipartThreshold") ) conf.getMemorySize("engine.filesystems.s3.MultipartThreshold").toBytes() else 5L * 1024L * 1024L * 1024L; 
     Log.debug(s"MultiPart Threshold for delocalizing is $mp_threshold")
 
+    // prepare tags, strip invalid characters
+    val invalidCharsPattern = "[^a-zA-Z0-9_.:/=+-@]+".r
+    Log.debug(s"root workflow id: ${jobDescriptor.workflowDescriptor.rootWorkflowId.toString}")
+    Log.debug(s"root workflow name: ${jobDescriptor.workflowDescriptor.rootWorkflow.name.toString}")
+    
+    
+    val workflowId = invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflowId.toString,"_")
+    val workflowName = invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflow.name.toString,"_")
+    val taskId = invalidCharsPattern.replaceAllIn(jobDescriptor.key.call.fullyQualifiedName + "-" + jobDescriptor.key.index + "-" + jobDescriptor.key.attempt,"_")
+    val doTagging = tagResources.getOrElse(false) // development : always tag resources.
+    //val tags: Map[String,String] = Map("cromwell-workflow-name" -> workflowName, "cromwell-workflow-id" -> workflowId, "cromwell-task-id" -> taskId)
     // this goes at the start of the script after the #!
     val preamble =
       s"""
@@ -168,27 +180,29 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
          |
          |function _s3_localize_with_retry() {
-         |  local s3_path=$$1
+         |  local s3_path="$$1"
          |  # destination must be the path to a file and not just the directory you want the file in
-         |  local destination=$$2
+         |  local destination="$$2"
          |
          |  for i in {1..6};
          |  do
          |    # abort if tries are exhausted
          |    if [ "$$i" -eq 6 ]; then
-         |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts. aborting"
-         |        exit 2
+         |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts."
+         |        LOCALIZATION_FAILED=1
+         |        break
          |    fi
          |    # check validity of source path
-         |    if ! [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
-         |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
-         |      exit 1
+         |    if ! [[ "$$s3_path" =~ s3://([^/]+)/(.+) ]]; then
+         |      echo "$$s3_path is not an S3 path with a bucket and key."
+         |      LOCALIZATION_FAILED=1
+         |      break
          |    fi
          |    # copy
          |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination"  ||
          |        { echo "attempt $$i to copy $$s3_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # check data integrity
-         |    _check_data_integrity $$destination $$s3_path ||
+         |    _check_data_integrity "$$destination" "$$s3_path" || 
          |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # copy succeeded
          |    break
@@ -197,12 +211,19 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |
          |function _s3_delocalize_with_retry() {
          |  # input variables
-         |  local local_path=$$1
+         |  local local_path="$$1"
          |  # destination must be the path to a file and not just the directory you want the file in
-         |  local destination=$$2
+         |  local destination="$$2"
+         |
+         |  # if file/folder does not exist, return immediately
+         |  if [[ ! -e "$$local_path" ]]; then
+         |    echo "$$local_path does not exist. skipping delocalization"
+         |    DELOCALIZATION_FAILED=1
+         |    return
+         |  fi
          |
          |  # get the multipart chunk size
-         |  chunk_size=$$(_get_multipart_chunk_size $$local_path)
+         |  chunk_size=$$(_get_multipart_chunk_size "$$local_path")
          |  local MP_THRESHOLD=${mp_threshold}
          |  # then set them
          |  $awsCmd configure set default.s3.multipart_threshold $$MP_THRESHOLD
@@ -213,31 +234,36 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  do
          |    # if tries exceeded : abort
          |    if [ "$$i" -eq 6 ]; then
-         |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts. aborting"
-         |        exit 2
+         |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts."
+         |        DELOCALIZATION_FAILED=1
+         |        break
          |    fi
          |    # if destination is not a bucket : abort
-         |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then
-         |     echo "$$destination is not an S3 path with a bucket and key. aborting"
-         |      exit 1
+         |    if ! [[ "$$destination" =~ s3://([^/]+)/(.+) ]]; then 
+         |     echo "$$destination is not an S3 path with a bucket and key."
+         |      DELOCALIZATION_FAILED=1
+         |      break
          |    fi
          |    # copy ok or try again.
          |    if [[ -d "$$local_path" ]]; then
          |       # make sure to strip the trailing / in destination
          |       destination=$${destination%/}
          |       # glob directory. do recursive copy
-         |       $awsCmd s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" ||
-         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
-         |       # check integrity for each of the files
-         |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
-         |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE ||
+         |       $awsCmd s3 cp --no-progress "$$local_path" "$$destination" --recursive --exclude "cromwell_glob_control_file" || 
+         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
+         |       # check integrity for each of the files (allow spaces)
+         |       SAVEIFS="$$IFS"
+         |       IFS=$$'\n'
+         |       for FILE in $$(cd "$$local_path" ; ls | grep -v cromwell_glob_control_file); do
+         |           _check_data_integrity "$$local_path/$$FILE" "$$destination/$$FILE" || 
          |               { echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2; }
          |       done
-         |    else
-         |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" ||
-         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+         |       IFS="$$SAVEIFS"
+         |    else 
+         |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" || 
+         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
          |      # check content length for data integrity
-         |      _check_data_integrity $$local_path $$destination ||
+         |      _check_data_integrity "$$local_path" "$$destination" || 
          |         { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    fi
          |    # copy succeeded
@@ -246,9 +272,9 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |}
          |
          |function _get_multipart_chunk_size() {
-         |  local file_path=$$1
+         |  local file_path="$$1"
          |  # file size
-         |  file_size=$$(stat --printf="%s" $$file_path)
+         |  file_size=$$(stat --printf="%s" "$$file_path") 
          |  # chunk_size : you can have at most 10K parts with at least one 5MB part
          |  # this reflects the formula in s3-copy commands of cromwell (S3FileSystemProvider.java)
          |  #   => long partSize = Math.max((objectSize / 10000L) + 1, 5 * 1024 * 1024);
@@ -259,16 +285,16 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |}
          |
          |function _check_data_integrity() {
-         |  local local_path=$$1
-         |  local s3_path=$$2
-         |
+         |  local local_path="$$1"
+         |  local s3_path="$$2"
+         |  
          |  # remote : use content_length
-         |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
+         |  if [[ "$$s3_path" =~ s3://([^/]+)/(.+) ]]; then 
          |        bucket="$${BASH_REMATCH[1]}"
          |        key="$${BASH_REMATCH[2]}"
          |  else
          |      # this is already checked in the caller function
-         |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+         |      echo "$$s3_path is not an S3 path with a bucket and key."
          |      exit 1
          |  fi
          |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') ||
@@ -284,17 +310,70 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  fi
          |}
          |
+         |# function to add tags to instance ands volumes
+         |function _add_tags() {
+         |  local WFID="${workflowId}"
+         |  local TASKID="${taskId}"
+         |  local WFNAME="${workflowName}"
+         |  # see cloud-init docs for how to get instance-id
+         |  INSTANCE_ID=$$(cat /var/lib/cloud/data/instance-id)
+         |  VOLUME_IDS=$$($awsCmd ec2 describe-volumes --filters Name=attachment.instance-id,Values=$$INSTANCE_ID --query 'Volumes[].VolumeId' --output text)
+         |  echo " - Tagging instance $$INSTANCE_ID"
+         |  # add tags. if tag key exists, append tag if value not in comma seperated list yet. 
+         |  # info : tags wfid, taskID cannot have spaces by design. wfName does not allow spaces in WDL spec. 
+         |  WFIDS=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$INSTANCE_ID" "Name=key,Values=cromwell-root-workflow-id" --query 'Tags[].Value' --output text) $$WFID)
+         |  TASKIDS=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$INSTANCE_ID" "Name=key,Values=cromwell-task-id" --query 'Tags[].Value' --output text) $$TASKID)
+         |  WFNAMES=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$INSTANCE_ID" "Name=key,Values=cromwell-root-workflow-name" --query 'Tags[].Value' --output text) $$WFNAME)
+         |  $awsCmd ec2 create-tags --resources $$INSTANCE_ID --tags Key=cromwell-root-workflow-id,Value="$$WFIDS" Key=cromwell-task-id,Value="$$TASKIDS" Key=cromwell-root-workflow-name,Value="$$WFNAMES"
+         |  for VOLUME_ID in $$VOLUME_IDS; do
+         |     echo " - Tagging volume $$VOLUME_ID"
+         |     WFIDS=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$VOLUME_ID" "Name=key,Values=cromwell-root-workflow-id" --query 'Tags[].Value' --output text) $$WFID)
+         |     TASKIDS=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$VOLUME_ID" "Name=key,Values=cromwell-task-id" --query 'Tags[].Value' --output text) $$TASKID)
+         |     WFNAMES=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$VOLUME_ID" "Name=key,Values=cromwell-root-workflow-name" --query 'Tags[].Value' --output text) $$WFNAME)
+         |     $awsCmd ec2 create-tags --resources $$VOLUME_ID --tags Key=cromwell-root-workflow-id,Value="$$WFIDS" Key=cromwell-task-id,Value="$$TASKIDS" Key=cromwell-root-workflow-name,Value="$$WFNAMES"
+         |  done
+         |}
+         |
+         |# function to combine tags into a comma separated list of unique values, trim to 256 characters
+         |function _combine_tags() {
+         |  local TAGS=$$1
+         |  local NEW_TAG=$$2
+         |  if [[ -z "$$TAGS" ]]; then
+         |    # first tag
+         |    echo "$$NEW_TAG"
+         |  elif [[ "$$TAGS" = *$$NEW_TAG* ]]; then
+         |    # tag already exists
+         |    echo "$$TAGS"
+         |  else
+         |    # combine, trim to 256 characters
+         |    echo "$$TAGS;$$NEW_TAG" | cut -c1-256
+         |  fi
+         |}
+         |
          |{
          |set -e
+         |# tag instance and volumes to ensure tags are present in case of failure:
+         |if [[ "${doTagging}" == "true" ]]; then
+         |  echo "*** TAGGING RESOURCES ***"
+         |  _add_tags
+         |fi 
+         |
          |echo '*** LOCALIZING INPUTS ***'
          |if [ ! -d $workDir ]; then mkdir $workDir && chmod 777 $workDir; fi
          |cd $workDir
+         |# make sure localization completes successfully
+         |LOCALIZATION_FAILED=0
          |$inputCopyCommand
-         |echo '*** COMPLETED LOCALIZATION ***'
+         |if [[ $$LOCALIZATION_FAILED -eq 1 ]]; then
+         |  echo '*** LOCALIZATION FAILED ***'
+         |  exit 1
+         |else 
+         |  echo '*** COMPLETED LOCALIZATION ***'
+         |fi
          |set +e
          |}
          |""".stripMargin
-
+    
     // the paths of the stdOut and stdErr
     val stdOut = dockerStdout.replace("/cromwell_root", workDir)
     val stdErr = dockerStderr.replace("/cromwell_root", workDir)
@@ -319,20 +398,23 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                     Log.debug("delocalization on EFS is enabled")
                     Log.debug(s"Delocalizing $globDirectory to $s3GlobOutDirectory\n")
                     s"""
-                        |touch ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}
-                        |_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}
-                        |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi
+                        |touch "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}"
+                        |_s3_delocalize_with_retry "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" "${output.s3key}"
+                        |if [ -e $globDirectory ]; then _s3_delocalize_with_retry "$globDirectory" "$s3GlobOutDirectory" ; fi
                         |""".stripMargin
                 } else {
                     
                     // check file for existence
                     s"""
                         |# test the glob list
-                        |test -e ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && exit 1)
+                        |test -e "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && DELOCALIZATION_FAILED=1)
                         |# test individual files.
-                        |for F in $$(cat ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}); do
-                        |   test -e "${globDirectory}/$$F" || (echo 'globbed file: "${globDirectory}/$$F" does not exist' && exit 1)
+                        |SAVEIFS="$$IFS"
+                        |IFS=$$'\n'
+                        |for F in $$(cat "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}"); do
+                        |   test -e "${globDirectory}/$$F" || (echo 'globbed file: "${globDirectory}/$$F" does not exist' && DELOCALIZATION_FAILED=1 && break)
                         |done
+                        |IFS="$$SAVEIFS"
                         |"""
                 }
            // need to make md5sum? 
@@ -342,15 +424,15 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                     s"""
                         |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
                         |   # the glob list
-                        |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && exit 1 ); 
+                        |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && DELOCALIZATION_FAILED=1 ); 
                         |   # globbed files, using specified number of cpus for parallel processing.
-                        |   cat ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} | xargs -I% -P${runtimeAttributes.cpu.##.toString} bash -c "md5sum ${globDirectory}/% > ${globDirectory}/%.md5"
+                        SAVEIFS="$$IFS"
+                        |IFS=$$'\n'
+                        |   cat "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" | xargs -I% -P${runtimeAttributes.cpu.##.toString} bash -c "md5sum ${globDirectory}/% > ${globDirectory}/%.md5"
                         |fi
+                        |IFS="$$SAVEIFS"
                         |""".stripMargin 
-                } else {
-                    Log.debug("MD5 not enabled: "+efsMakeMD5.get.toString())
-                    ""
-                }
+                } 
            // return combined result
            s"""
           |${test_cmd}
@@ -360,16 +442,16 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
           // default delocalization command.
           Log.debug(s"Delocalize from ${output.name} to ${output.s3key}\n")
           s"""
-             |touch ${output.name}
-             |_s3_delocalize_with_retry ${output.name} ${output.s3key}
-             |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi""".stripMargin
+             |touch "${output.name}"
+             |_s3_delocalize_with_retry "${output.name}" "${output.s3key}"
+             |if [ -e "$globDirectory" ]; then _s3_delocalize_with_retry "$globDirectory" "$s3GlobOutDirectory" ; fi""".stripMargin
         }
 
       // files on /cromwell/ working dir must be delocalized
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
         //output is on working disk mount
         Log.debug("output Data on working disk mount" + output.local.pathAsString)
-        s"""_s3_delocalize_with_retry $workDir/${output.local.pathAsString} ${output.s3key}""".stripMargin
+        s"""_s3_delocalize_with_retry "$workDir/${output.local.pathAsString}" "${output.s3key}" """.stripMargin
 
       // file(name (full path), s3key (delocalized path), local (file basename), mount (disk details))
       // files on EFS mounts are optionally delocalized.
@@ -379,23 +461,22 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         var test_cmd = ""
         if (efsDelocalize.isDefined && efsDelocalize.getOrElse(false)) {
             Log.debug("efs-delocalization enabled")
-            test_cmd = s"_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
+            test_cmd = s"""_s3_delocalize_with_retry "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" "${output.s3key}" """.stripMargin
         } else {
             Log.debug("efs-delocalization disabled")
             // check file for existence
-            test_cmd = s"test -e ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && exit 1)"
+            test_cmd = s"""test -e "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && DELOCALIZATION_FAILED=1)""".stripMargin
         }
         // need to make md5sum?
         var md5_cmd = ""
         if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
             Log.debug("Add cmd to create MD5 sibling.")
             md5_cmd = s"""
-                            |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then
-                            |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && exit 1 );
+                            |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
+                            |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && DELOCALIZATION_FAILED=1 ); 
                             |fi
                             |""".stripMargin
         } else {
-            Log.debug("MD5 not enabled: "+efsMakeMD5.get.toString())
             md5_cmd = ""
         }
         // return combined result
@@ -408,13 +489,13 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         //output on a different mount
         Log.debug("output data on other mount")
         Log.debug(output.toString)
-        s"_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
+        s"""_s3_delocalize_with_retry "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" "${output.s3key}" """.stripMargin
       case _ => ""
     }.mkString("\n") + "\n" +
       s"""
-         |if [ -f $workDir/${jobPaths.returnCodeFilename} ]; then _s3_delocalize_with_retry $workDir/${jobPaths.returnCodeFilename} ${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename} ; fi
-         |if [ -f $stdErr ]; then _s3_delocalize_with_retry $stdErr ${jobPaths.standardPaths.error.pathAsString}; fi
-         |if [ -f $stdOut ]; then _s3_delocalize_with_retry $stdOut ${jobPaths.standardPaths.output.pathAsString}; fi
+         |if [ -f "$workDir/${jobPaths.returnCodeFilename}" ]; then _s3_delocalize_with_retry "$workDir/${jobPaths.returnCodeFilename}" "${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename}" ; fi
+         |if [ -f "$stdErr" ]; then _s3_delocalize_with_retry "$stdErr" "${jobPaths.standardPaths.error.pathAsString}"; fi
+         |if [ -f "$stdOut" ]; then _s3_delocalize_with_retry "$stdOut" "${jobPaths.standardPaths.output.pathAsString}"; fi
          |""".stripMargin
 
 
@@ -423,9 +504,22 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
       s"""
          |{
          |set -e
+         |# (re-)add tags to include added volumes:
+         |if [[ "${doTagging}" == "true" ]]; then
+         |  echo "*** TAGGING RESOURCES ***"
+         |  _add_tags
+         |fi 
+         |
          |echo '*** DELOCALIZING OUTPUTS ***'
+         |DELOCALIZATION_FAILED=0
          |$outputCopyCommand
-         |echo '*** COMPLETED DELOCALIZATION ***'
+         |if [[ $$DELOCALIZATION_FAILED -eq 1 ]]; then
+         |  echo '*** DELOCALIZATION FAILED ***'
+         |  echo '*** EXITING WITH RETURN CODE 1***'
+         |  exit 1
+         |else
+         |  echo '*** COMPLETED DELOCALIZATION ***'
+         |fi
          |echo '*** EXITING WITH RETURN CODE ***'
          |rc=$$(head -n 1 $workDir/${jobPaths.returnCodeFilename})
          |echo $$rc
@@ -471,30 +565,47 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     //calls the client to submit the job
     def callClient(definitionArn: String, awsBatchAttributes: AwsBatchAttributes): Aws[F, SubmitJobResponse] = {
 
+      val workflowId = jobDescriptor.workflowDescriptor.id.toString
+      val workflowName = jobDescriptor.workflowDescriptor.callable.name.toString
+      val rootworkflowId = jobDescriptor.workflowDescriptor.rootWorkflowId.toString
       Log.debug(s"Submitting taskId: $taskId, job definition : $definitionArn, script: $batch_script")
-      Log.info(s"Submitting taskId: $taskId, script: $batch_script")
-
+      Log.info(s"Submitting taskId: $rootworkflowId::$taskId, script: $batch_script")
+      
+      // prepare the job request
+      var submitJobRequest = SubmitJobRequest.builder()
+        .jobName(sanitize(jobDescriptor.taskCall.fullyQualifiedName))
+        .parameters(parameters.collect({ case i: AwsBatchInput => i.toStringString }).toMap.asJava)
+        //provide job environment variables, vcpu and memory
+        .containerOverrides(
+          ContainerOverrides.builder
+            .environment(
+              generateEnvironmentKVPairs(runtimeAttributes.scriptS3BucketName, scriptKeyPrefix, scriptKey): _*
+            )
+            .resourceRequirements(
+              ResourceRequirement.builder().`type`(ResourceType.VCPU).value(runtimeAttributes.cpu.##.toString).build(),
+              ResourceRequirement.builder().`type`(ResourceType.MEMORY).value(runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString).build()
+            )
+            .build()
+        )
+        .jobQueue(runtimeAttributes.queueArn)
+        .jobDefinition(definitionArn)
+      // tagging activated : add to request
+      if (tagResources.getOrElse(false)) {
+          // replace invalid characters in the tags
+          val invalidCharsPattern = "[^a-zA-Z0-9_.:/=+-@]+".r
+          val tags: Map[String,String] = Map(
+            "cromwell-workflow-name" -> invalidCharsPattern.replaceAllIn(workflowName,"_"), 
+            "cromwell-workflow-id" -> invalidCharsPattern.replaceAllIn(workflowId,"_"), 
+            "cromwell-task-id" -> invalidCharsPattern.replaceAllIn(taskId,"_"),
+            "cromwell-root-workflow-name" -> invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflow.name.toString,"_"),
+            "cromwell-root-workflow-id" -> invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflowId.toString,"_")
+            )
+          submitJobRequest = submitJobRequest.tags(tags.asJava).propagateTags(true)
+      }
+      // submit
       val submit: F[SubmitJobResponse] =
         async.delay(batchClient.submitJob(
-          SubmitJobRequest.builder()
-            .jobName(sanitize(jobDescriptor.taskCall.fullyQualifiedName))
-            .parameters(parameters.collect({ case i: AwsBatchInput => i.toStringString }).toMap.asJava)
-
-            //provide job environment variables, vcpu and memory
-            .containerOverrides(
-              ContainerOverrides.builder
-                .environment(
-                  generateEnvironmentKVPairs(runtimeAttributes.scriptS3BucketName, scriptKeyPrefix, scriptKey): _*
-                )
-                .resourceRequirements(
-                  ResourceRequirement.builder().`type`(ResourceType.VCPU).value(runtimeAttributes.cpu.##.toString).build(),
-                  ResourceRequirement.builder().`type`(ResourceType.MEMORY).value(runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString).build()
-                )
-                .build()
-            )
-            .jobQueue(runtimeAttributes.queueArn)
-            .jobDefinition(definitionArn)
-            .build
+            submitJobRequest.build
         ))
 
       ReaderT.liftF(
@@ -584,7 +695,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         fsxMntPoint = fsxMntPoint,
         efsMntPoint = efsMntPoint,
         efsMakeMD5 = efsMakeMD5,
-        efsDelocalize = efsDelocalize
+        efsDelocalize = efsDelocalize,
+        tagResources = tagResources
         )
 
       val jobDefinitionBuilder = StandardAwsBatchJobDefinitionBuilder
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index 792fd6825d0..30148acef87 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -101,6 +101,12 @@ trait AwsBatchJobDefinitionBuilder {
         Volume.builder()
           .name("awsCliHome")
           .host(Host.builder().sourcePath("/usr/local/aws-cli").build())
+          .build(),
+        // the location of the instance-id on the host (set by cloud-init)
+        // https://cloudinit.readthedocs.io/en/23.2.2/reference/faq.html#data
+        Volume.builder()
+          .name("instanceId")
+          .host(Host.builder().sourcePath("/var/lib/cloud/data/instance-id").build())
           .build()
       ) ++ fsx_volumes
     }
@@ -125,7 +131,14 @@ trait AwsBatchJobDefinitionBuilder {
           .sourceVolume("awsCliHome")
           //where the aws-cli will be on the container
           .containerPath("/usr/local/aws-cli")
+          .build(),
+        // the location of the instance-id on the container, used to tag the instance
+        MountPoint.builder()
+          .readOnly(true)
+          .sourceVolume("instanceId")
+          .containerPath("/var/lib/cloud/data/instance-id")
           .build()
+
       ) ++ fsx_disks
     }
 
@@ -140,8 +153,8 @@ trait AwsBatchJobDefinitionBuilder {
       ).toList
     }
 
-    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit], efsDelocalize: Boolean, efsMakeMD5: Boolean): String = {
-      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}"
+    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit], efsDelocalize: Boolean, efsMakeMD5: Boolean, tagResources: Boolean): String = {
+      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}:${tagResources.toString}"
     }
 
     val environment = List.empty[KeyValuePair]
@@ -155,6 +168,7 @@ trait AwsBatchJobDefinitionBuilder {
     val ulimits = buildUlimits( context.runtimeAttributes.ulimits)
     val efsDelocalize = context.runtimeAttributes.efsDelocalize
     val efsMakeMD5 = context.runtimeAttributes.efsMakeMD5
+    val tagResources = context.runtimeAttributes.tagResources
 
     val containerPropsName = buildName(
       context.runtimeAttributes.dockerImage,
@@ -164,7 +178,8 @@ trait AwsBatchJobDefinitionBuilder {
       environment,
       ulimits,
       efsDelocalize,
-      efsMakeMD5
+      efsMakeMD5,
+      tagResources
     )
 
     (ContainerProperties.builder()
@@ -269,7 +284,8 @@ case class AwsBatchJobDefinitionContext(
             fsxMntPoint: Option[List[String]],
             efsMntPoint: Option[String],
             efsMakeMD5: Option[Boolean],
-            efsDelocalize: Option[Boolean]
+            efsDelocalize: Option[Boolean],
+            tagResources: Option[Boolean]
             ) {
 
   override def toString: String = {
@@ -287,6 +303,7 @@ case class AwsBatchJobDefinitionContext(
       .append("efsMntPoint", efsMntPoint)
       .append("efsMakeMD5", efsMakeMD5)
       .append("efsDelocalize", efsDelocalize)
+      .append("tagResources", tagResources)
       .build
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index 13137718354..fc854c1039f 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -71,6 +71,7 @@ import scala.jdk.CollectionConverters._
  * @param ulimits ulimit values to be passed to the container
  * @param efsDelocalize should we delocalize efs files to s3
  * @param efsMakeMD5 should we make a sibling md5 file as part of the job 
+ * @param tagResources should we tag resources
  */
 case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      zones: Vector[String],
@@ -87,7 +88,8 @@ case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      ulimits: Vector[Map[String, String]],
                                      efsDelocalize: Boolean,
                                      efsMakeMD5 : Boolean,
-                                     fileSystem: String= "s3")
+                                     fileSystem: String= "s3",
+                                     tagResources: Boolean = false)
 
 object AwsBatchRuntimeAttributes {
   val Log: Logger = LoggerFactory.getLogger(this.getClass)
@@ -103,7 +105,7 @@ object AwsBatchRuntimeAttributes {
 
   val awsBatchefsDelocalizeKey = "efsDelocalize"
   val awsBatchefsMakeMD5Key = "efsMakeMD5"
-
+  val tagResourcesKey = "tagResources"
   val ZonesKey = "zones"
   private val ZonesDefaultValue = WomString("us-east-1a")
 
@@ -182,6 +184,11 @@ object AwsBatchRuntimeAttributes {
     .configDefaultWomValue(runtimeConfig).getOrElse(WomBoolean(false)))
   }
 
+  private def awsBatchtagResourcesValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = {
+      AwsBatchtagResourcesValidation(AwsBatchRuntimeAttributes.tagResourcesKey).withDefault(AwsBatchtagResourcesValidation(AwsBatchRuntimeAttributes.tagResourcesKey)
+      .configDefaultWomValue(runtimeConfig).getOrElse(WomBoolean(false)))
+  }
+
   private def ulimitsValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[Map[String, String]]] =
    UlimitsValidation.withDefault(UlimitsValidation.configDefaultWomValue(runtimeConfig) getOrElse UlimitsDefaultValue)
 
@@ -197,7 +204,6 @@ object AwsBatchRuntimeAttributes {
     }
     // efs disk configs is set (can be None) in configuration
     val efs_disks = configuration.efsMntPoint.getOrElse("")
-    // TODO : fsx ? 
     // additional disks optionally set as runtime attributes
     val rtc_disks = try {
         rtc.getAnyRef(AwsBatchRuntimeAttributes.DisksKey).asInstanceOf[String] // just to prevent complaints about var/val
@@ -205,9 +211,8 @@ object AwsBatchRuntimeAttributes {
         case _: ConfigException.Missing => 
            "local-disk"
     }
-    // combine and remove empty values
-    val disks = s"${efs_disks},${rtc_disks}".split(",").toSet.filterNot(_.isEmpty).mkString(",")
-    Log.debug(s"Disks: ${disks}")
+    // combine and remove empty values and remove empty values
+    val disks = s"${efs_disks},${rtc_disks}".split(",").toSet.filterNot(_.isEmpty).filterNot(_.isEmpty).mkString(",")
     val runtimeConfig = Some(rtc.withValue(AwsBatchRuntimeAttributes.DisksKey, ConfigValueFactory.fromAnyRef(disks)))
     return runtimeConfig
   }
@@ -229,7 +234,8 @@ object AwsBatchRuntimeAttributes {
                         awsBatchEvaluateOnExitValidation(runtimeConfig),
                         ulimitsValidation(runtimeConfig),
                         awsBatchefsDelocalizeValidation(runtimeConfig),
-                        awsBatchefsMakeMD5Validation(runtimeConfig)
+                        awsBatchefsMakeMD5Validation(runtimeConfig),
+                        awsBatchtagResourcesValidation(runtimeConfig)
                       )
    def validationsLocalBackend  = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
       cpuValidation(runtimeConfig),
@@ -245,7 +251,8 @@ object AwsBatchRuntimeAttributes {
       awsBatchEvaluateOnExitValidation(runtimeConfig),
       ulimitsValidation(runtimeConfig),
       awsBatchefsDelocalizeValidation(runtimeConfig),
-      awsBatchefsMakeMD5Validation(runtimeConfig)
+      awsBatchefsMakeMD5Validation(runtimeConfig),
+      awsBatchtagResourcesValidation(runtimeConfig)
     )
 
     configuration.fileSystem match  {
@@ -275,7 +282,7 @@ object AwsBatchRuntimeAttributes {
     val ulimits: Vector[Map[String, String]] = RuntimeAttributesValidation.extract(ulimitsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val efsDelocalize: Boolean = RuntimeAttributesValidation.extract(awsBatchefsDelocalizeValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
     val efsMakeMD5: Boolean = RuntimeAttributesValidation.extract(awsBatchefsMakeMD5Validation(runtimeAttrsConfig),validatedRuntimeAttributes)
-    
+    val tagResources: Boolean = RuntimeAttributesValidation.extract(awsBatchtagResourcesValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
     new AwsBatchRuntimeAttributes(
       cpu,
       zones,
@@ -292,7 +299,8 @@ object AwsBatchRuntimeAttributes {
       ulimits,
       efsDelocalize,
       efsMakeMD5,
-      fileSystem
+      fileSystem,
+      tagResources
     )
   }
 }
@@ -619,6 +627,14 @@ class AwsBatchefsMakeMD5Validation(key: String) extends BooleanRuntimeAttributes
   override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Boolean"
 }
 
+object AwsBatchtagResourcesValidation {
+  def apply(key: String): AwsBatchtagResourcesValidation = new AwsBatchtagResourcesValidation(key)
+}
+
+class AwsBatchtagResourcesValidation(key: String) extends BooleanRuntimeAttributesValidation(key) {
+  
+  override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be a Boolean"
+}   
 
 object UlimitsValidation
     extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index f9c3670f67b..2c673503c7b 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -507,7 +507,37 @@ task task_three {
 }
 ```
 
+#### TAGGING RESOURCES
+AWS Batch tags jobs and, if configured in the compute environment, instances and volumes with generic tags to track costs.  These tags typically include the job-queue name. To allow more detailed cost tracking, it is possible to enable tagging instances and connected volumes with the following information : 
 
+- *cromwell-workflow-name* : the top-level name of the submitted WDL (eg "workflow myWorkflow {...}")
+- *cromwell-workflow-id* : the identifier assigned to the workflow inside cromwell (eg "2443daac-c232-4e0a-920d-fbf53273e9c5")
+- *cromwell-task-id* : A string consisting of "<workflowName>.<taskName>-<shardIdx>-<attempt>"
+
+In case the same instance is reused for multiple tasks, unique tag values are concatenated up until a maximal length of 255 characters. For example, an instance used for two identical workflows, might be tagged as followes: 
+
+- cromwell-workflow-name : myWorkflow
+- cromwell-workflow-id : 2443daac-c232-4e0a-920d-fbf53273e9c5;df19029e-cc02-41d5-a26d-8d30c0ab05cb
+- cromwell-task-id : myWorkflow.myTask-None-1
+
+To enable tagging, add "tagResources = true" to the default-runtime-attributes section of your configuration: 
+
+```
+backend {
+    providers {
+        AWSBatch {
+            config{
+                
+                default-runtime-attributes {
+                    // enable detailed tagging
+                    tagResources = true
+                }
+            }
+        }
+    }
+}
+
+```
 
 
 AWS Batch
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
index 1706f55370f..ffee6be0918 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
@@ -31,13 +31,6 @@
 package cromwell.backend.impl.aws.io
 
 
-//import cats.implicits._
-//import common.validation.ErrorOr.ErrorOr
-//import cromwell.backend.BackendJobDescriptor
-//import cromwell.core.CallContext
-//import cromwell.core.io.AsyncIoFunctions
-//import wom.expression.{IoFunctionSet, IoFunctionSetAdapter}
-//import wom.graph.CommandCallNode
 import wom.values._
 import cromwell.backend.io._
 import cromwell.backend.standard._
@@ -45,8 +38,6 @@ import scala.concurrent.Future
 import java.nio.file.Paths
 import cromwell.core.path.DefaultPathBuilder
 
-//import cromwell.backend.impl.aws.AwsBatchAttributes
-//import cromwell.backend.impl.aws._
 
 trait AwsBatchGlobFunctions extends GlobFunctions {
     

From b391c0fcf7a3b1a7e1bab3f2b55df4fe10048d58 Mon Sep 17 00:00:00 2001
From: xquek <46759870+xquek@users.noreply.github.com>
Date: Fri, 22 Dec 2023 10:50:52 -0800
Subject: [PATCH 263/326] add gpu count (#41)

* add gpu count

* fix typo

---------

Co-authored-by: quekx <quekx@gene.com>
Co-authored-by: Henrique Ribeiro <henriqueribeiro@users.noreply.github.com>
---
 .../main/scala/cromwell/backend/backend.scala |  1 +
 .../backend/impl/aws/AwsBatchAttributes.scala |  1 +
 .../backend/impl/aws/AwsBatchJob.scala        | 16 ++++++++---
 .../impl/aws/AwsBatchJobDefinition.scala      |  2 ++
 .../impl/aws/AwsBatchRuntimeAttributes.scala  | 28 +++++++++++++++++++
 .../scala/cromwell/backend/impl/aws/README.md | 28 +++++++++++++++++++
 .../backend/impl/aws/AwsBatchJobSpec.scala    | 23 +++++++++++----
 .../aws/AwsBatchRuntimeAttributesSpec.scala   |  4 +--
 8 files changed, 92 insertions(+), 11 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index a8bb4baaf2f..3c5c33ab992 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -136,6 +136,7 @@ object CommonBackendConfigurationAttributes {
     "default-runtime-attributes.zones",
     "default-runtime-attributes.continueOnReturnCode",
     "default-runtime-attributes.cpu",
+    "default-runtime-attributes.gpuCount",
     "default-runtime-attributes.noAddress",
     "default-runtime-attributes.docker",
     "default-runtime-attributes.queueArn",
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index 10e2dddfb98..38f026eadcf 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -90,6 +90,7 @@ object AwsBatchAttributes {
     "awsBatchRetryAttempts",
     "awsBatchEvaluateOnExit",
     "ulimits",
+    "gpuCount",
     "efsDelocalize",
     "efsMakeMD5",
     "tagResources",
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 51c5b8080f6..4cfa08e82a5 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -571,6 +571,17 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
       Log.debug(s"Submitting taskId: $taskId, job definition : $definitionArn, script: $batch_script")
       Log.info(s"Submitting taskId: $rootworkflowId::$taskId, script: $batch_script")
       
+      //provide job environment variables, vcpu and memory
+      var resourceRequirements: Seq[ResourceRequirement] = Seq(
+        ResourceRequirement.builder().`type`(ResourceType.VCPU).value(runtimeAttributes.cpu.##.toString).build(),
+        ResourceRequirement.builder().`type`(ResourceType.MEMORY).value(runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString).build()
+      )
+
+      if (runtimeAttributes.gpuCount > 0) {
+        val gpuRequirement = ResourceRequirement.builder().`type`(ResourceType.GPU).value(runtimeAttributes.gpuCount.toString)
+        resourceRequirements = resourceRequirements :+ gpuRequirement.build()
+      }
+          
       // prepare the job request
       var submitJobRequest = SubmitJobRequest.builder()
         .jobName(sanitize(jobDescriptor.taskCall.fullyQualifiedName))
@@ -581,10 +592,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
             .environment(
               generateEnvironmentKVPairs(runtimeAttributes.scriptS3BucketName, scriptKeyPrefix, scriptKey): _*
             )
-            .resourceRequirements(
-              ResourceRequirement.builder().`type`(ResourceType.VCPU).value(runtimeAttributes.cpu.##.toString).build(),
-              ResourceRequirement.builder().`type`(ResourceType.MEMORY).value(runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString).build()
-            )
+            .resourceRequirements(resourceRequirements.asJava)
             .build()
         )
         .jobQueue(runtimeAttributes.queueArn)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index 30148acef87..f55d3a933f7 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -182,6 +182,8 @@ trait AwsBatchJobDefinitionBuilder {
       tagResources
     )
 
+    // To reuse job definition for gpu and gpu-runs, we will create a job definition that does not gpu requirements
+    // since aws batch does not allow you to set gpu as 0 when you dont need it. you will always need cpu and memory
     (ContainerProperties.builder()
       .image(context.runtimeAttributes.dockerImage)
       .command(packedCommand.asJava)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index fc854c1039f..456355e412c 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -48,6 +48,7 @@ import com.typesafe.config.{ConfigException, ConfigValueFactory}
 
 import scala.util.matching.Regex
 import org.slf4j.{Logger, LoggerFactory}
+import wom.RuntimeAttributesKeys.GpuKey
 
 import scala.util.{Failure, Success, Try}
 import scala.jdk.CollectionConverters._
@@ -56,6 +57,7 @@ import scala.jdk.CollectionConverters._
 /**
  * Attributes that are provided to the job at runtime
  * @param cpu number of vCPU
+ * @param gpuCount number of gpu
  * @param zones the aws availability zones to run in
  * @param memory memory to allocate
  * @param disks a sequence of disk volumes
@@ -74,6 +76,7 @@ import scala.jdk.CollectionConverters._
  * @param tagResources should we tag resources
  */
 case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
+                                     gpuCount: Int,
                                      zones: Vector[String],
                                      memory: MemorySize,
                                      disks: Seq[AwsBatchVolume],
@@ -125,6 +128,10 @@ object AwsBatchRuntimeAttributes {
   private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] = CpuValidation.instance
     .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
+  private def gpuCountValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = {
+    GpuCountValidation(GpuKey).withDefault(GpuCountValidation(GpuKey).configDefaultWomValue(runtimeConfig).getOrElse(WomInteger(0)))
+  }
+
   private def cpuMinValidation(runtimeConfig: Option[Config]):RuntimeAttributesValidation[Int Refined Positive] = CpuValidation.instanceMin
     .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
@@ -222,6 +229,7 @@ object AwsBatchRuntimeAttributes {
     def validationsS3backend = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
                         cpuValidation(runtimeConfig),
                         cpuMinValidation(runtimeConfig),
+                        gpuCountValidation(runtimeConfig),
                         disksValidation(runtimeConfig),
                         zonesValidation(runtimeConfig),
                         memoryValidation(runtimeConfig),
@@ -240,6 +248,7 @@ object AwsBatchRuntimeAttributes {
    def validationsLocalBackend  = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
       cpuValidation(runtimeConfig),
       cpuMinValidation(runtimeConfig),
+      gpuCountValidation(runtimeConfig),
       disksValidation(runtimeConfig),
       zonesValidation(runtimeConfig),
       memoryValidation(runtimeConfig),
@@ -264,6 +273,7 @@ object AwsBatchRuntimeAttributes {
 
   def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes, runtimeAttrsConfig: Option[Config], fileSystem:String): AwsBatchRuntimeAttributes = {
     val cpu: Int Refined Positive = RuntimeAttributesValidation.extract(cpuValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val gpuCount: Int = RuntimeAttributesValidation.extract(gpuCountValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val zones: Vector[String] = RuntimeAttributesValidation.extract(ZonesValidation, validatedRuntimeAttributes)
     val memory: MemorySize = RuntimeAttributesValidation.extract(memoryValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val disks: Seq[AwsBatchVolume] = RuntimeAttributesValidation.extract(disksValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
@@ -285,6 +295,7 @@ object AwsBatchRuntimeAttributes {
     val tagResources: Boolean = RuntimeAttributesValidation.extract(awsBatchtagResourcesValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
     new AwsBatchRuntimeAttributes(
       cpu,
+      gpuCount,
       zones,
       memory,
       disks,
@@ -479,6 +490,23 @@ object DisksValidation extends RuntimeAttributesValidation[Seq[AwsBatchVolume]]
     s"Expecting $key runtime attribute to be a comma separated String or Array[String]"
 }
 
+object GpuCountValidation {
+  def apply(key: String): GpuCountValidation = new GpuCountValidation(key)
+}
+
+class GpuCountValidation(key: String) extends IntRuntimeAttributesValidation(key) {
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[Int]] = {
+    case womValue if WomIntegerType.coerceRawValue(womValue).isSuccess =>
+      WomIntegerType.coerceRawValue(womValue).get match {
+        case WomInteger(value) =>
+          if (value.toInt < 0)
+            s"Expecting $key runtime attribute value greater than or equal to 0".invalidNel
+          else
+            value.toInt.validNel
+      }
+  }
+}
+
 object AwsBatchRetryAttemptsValidation {
   def apply(key: String): AwsBatchRetryAttemptsValidation = new AwsBatchRetryAttemptsValidation(key)
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 2c673503c7b..4b1fd62da2d 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -141,6 +141,34 @@ Parameter description:
   - Type: Integer
   - Required: Yes, when `ulimits` is used.
 
+### GPU support 
+
+Tasks can request GPU by setting `gpuCount` in the task runtime attribute. For instance:
+```
+task gpu_queue_task {
+    input {
+        ...
+    }
+
+    command <<< 
+        ...
+    >>>
+    output {}
+
+    runtime {
+        queueArn: "arn:aws:batch:us-west-2:12345678910:job-queue/quekx-gpu-queue"
+        docker: "xxxx"
+        maxRetries: 1
+        cpu: "1"
+        gpuCount: 1
+        memory: "2 GB"
+    }
+}
+```
+the gpuCount value will be passed to AWS Batch as part of [resourceRequirements](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#ContainerProperties-resourceRequirements).
+You will need to use this feature in conjunction with a aws queue that has GPU instances (see [compute-environment](/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md#compute-environment) for more inforamtion)
+
+
 ### Call Caching with ECR private
 
 AWS ECR is a private container registry, for which access can be regulated using IAM. Call caching is possible by setting up the following configuration:
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index 0c202aa8946..61914626ed7 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -46,12 +46,14 @@ import org.scalatest.PrivateMethodTester
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider
-import software.amazon.awssdk.services.batch.model.{ContainerDetail, EvaluateOnExit, JobDetail, KeyValuePair, RetryAction, RetryStrategy}
+import software.amazon.awssdk.services.batch.model.{ContainerDetail, EvaluateOnExit, JobDetail, KeyValuePair, ResourceRequirement, RetryAction, RetryStrategy}
 import spray.json.{JsObject, JsString}
 import wdl4s.parser.MemoryUnit
 import wom.format.MemorySize
 import wom.graph.CommandCallNode
 
+import scala.jdk.javaapi.CollectionConverters
+
 class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with PrivateMethodTester {
   import AwsBatchTestConfig._
 
@@ -109,6 +111,7 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
   val cpu: Int Refined Positive = 2
   val runtimeAttributes: AwsBatchRuntimeAttributes = new AwsBatchRuntimeAttributes(
       cpu = cpu,
+      gpuCount = 0,
       zones = Vector("us-east-1"),
       memory = MemorySize(2.0, MemoryUnit.GB),
       disks = Seq.empty,
@@ -408,10 +411,8 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     ).build()
 
     val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion.copy(runtimeAttributes = runtime))
-    val jobDefinitionName = jobDefinition.name
     val expected = jobDefinition.retryStrategy
     expected should equal (builder)
-    jobDefinitionName should equal ("cromwell_ubuntu_latest_656d5a7e7cd016d2360b27bc5ee75018d91a777a")
   }
 
   it should "use RetryStrategy evaluateOnExit should be case insensitive" in {
@@ -424,9 +425,21 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     ).build()
 
     val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion.copy(runtimeAttributes = runtime))
-    val jobDefinitionName = jobDefinition.name
     val expected = jobDefinition.retryStrategy
     expected should equal(builder)
-    jobDefinitionName should equal("cromwell_ubuntu_latest_66a335d761780e64e6b154339c5f1db2f0783f96")
   }
+
+  it should "GPU is not set at job definition even if provided" in {
+    val runtime = runtimeAttributes.copy(
+      gpuCount = 1
+    )
+
+    val expected = List(
+      ResourceRequirement.builder().`type`("VCPU").value(s"$cpu").build(),
+      ResourceRequirement.builder().`type`("MEMORY").value("2048").build()
+    )
+
+    val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion.copy(runtimeAttributes = runtime))
+    val actual = jobDefinition.containerProperties.resourceRequirements
+    expected should equal(CollectionConverters.asScala(actual).toSeq)}
 }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
index 944577d229d..a9411b574b5 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
@@ -58,7 +58,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     )))
   }
 
-  val expectedDefaults = new AwsBatchRuntimeAttributes(refineMV[Positive](1), Vector("us-east-1a", "us-east-1b"),
+  val expectedDefaults = new AwsBatchRuntimeAttributes(refineMV[Positive](1), 0, Vector("us-east-1a", "us-east-1b"),
 
     MemorySize(2, MemoryUnit.GB), Vector(AwsBatchWorkingDisk()),
     "ubuntu:latest",
@@ -74,7 +74,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     false
   )
 
-  val expectedDefaultsLocalFS = new AwsBatchRuntimeAttributes(refineMV[Positive](1), Vector("us-east-1a", "us-east-1b"),
+  val expectedDefaultsLocalFS = new AwsBatchRuntimeAttributes(refineMV[Positive](1), 0, Vector("us-east-1a", "us-east-1b"),
 
     MemorySize(2, MemoryUnit.GB), Vector(AwsBatchWorkingDisk()),
     "ubuntu:latest",

From ee2b10f99b3bc4fac58e94d5c2a2b097a57ec416 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Wed, 3 Jan 2024 09:27:12 -0500
Subject: [PATCH 264/326] WX-1385 Reject blob URLs with external SAS tokens as
 unparsable (#7347)

---
 .../filesystems/blob/BlobPathBuilder.scala    | 32 +++++++++++++++----
 .../blob/BlobPathBuilderSpec.scala            | 29 +++++++++++++----
 project/Dependencies.scala                    |  2 +-
 3 files changed, 49 insertions(+), 14 deletions(-)

diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index 22bf6b44742..c0503975b31 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -1,5 +1,6 @@
 package cromwell.filesystems.blob
 
+import akka.http.scaladsl.model.Uri
 import com.azure.storage.blob.nio.AzureBlobFileAttributes
 import com.google.common.net.UrlEscapers
 import cromwell.core.path.{NioPath, Path, PathBuilder}
@@ -21,6 +22,8 @@ object BlobPathBuilder {
     s"Malformed Blob URL for this builder: The endpoint $endpoint doesn't contain the expected host string '{SA}.blob.core.windows.net/'"
   def invalidBlobContainerMessage(endpoint: EndpointURL) =
     s"Malformed Blob URL for this builder: Could not parse container"
+  val externalToken =
+    "Rejecting pre-signed SAS URL so that filesystem selection falls through to HTTP filesystem"
   def parseURI(string: String): Try[URI] = Try(URI.create(UrlEscapers.urlFragmentEscaper().escape(string)))
   def parseStorageAccount(uri: URI): Try[StorageAccountName] = uri.getHost
     .split("\\.")
@@ -50,19 +53,34 @@ object BlobPathBuilder {
   def validateBlobPath(string: String): BlobPathValidation = {
     val blobValidation = for {
       testUri <- parseURI(string)
-      testEndpoint = EndpointURL(testUri.getScheme + "://" + testUri.getHost())
-      testStorageAccount <- parseStorageAccount(testUri)
+      testEndpoint = EndpointURL(testUri.getScheme + "://" + testUri.getHost)
+      _ <- parseStorageAccount(testUri)
       testContainer = testUri.getPath.split("/").find(_.nonEmpty)
-      isBlobHost = testUri.getHost().contains(blobHostnameSuffix) && testUri.getScheme().contains("https")
-      blobPathValidation = (isBlobHost, testContainer) match {
-        case (true, Some(container)) =>
+      isBlobHost = testUri.getHost.contains(blobHostnameSuffix) && testUri.getScheme.contains("https")
+      hasToken = hasSasToken(string)
+      blobPathValidation = (isBlobHost, testContainer, hasToken) match {
+        case (true, Some(container), false) =>
           ValidBlobPath(testUri.getPath.replaceFirst("/" + container, ""), BlobContainerName(container), testEndpoint)
-        case (false, _) => UnparsableBlobPath(new MalformedURLException(invalidBlobHostMessage(testEndpoint)))
-        case (true, None) => UnparsableBlobPath(new MalformedURLException(invalidBlobContainerMessage(testEndpoint)))
+        case (false, _, false) =>
+          UnparsableBlobPath(new MalformedURLException(invalidBlobHostMessage(testEndpoint)))
+        case (true, None, false) =>
+          UnparsableBlobPath(new MalformedURLException(invalidBlobContainerMessage(testEndpoint)))
+        case (_, _, true) =>
+          UnparsableBlobPath(new IllegalArgumentException(externalToken))
       }
     } yield blobPathValidation
     blobValidation recover { case t => UnparsableBlobPath(t) } get
   }
+
+  private def hasSasToken(uri: Uri) = {
+    // These keys are required for all SAS tokens.
+    // https://learn.microsoft.com/en-us/rest/api/storageservices/create-service-sas#construct-a-service-sas
+    val SignedVersionKey = "sv"
+    val SignatureKey = "sig"
+
+    val query = uri.query().toMap
+    query.isDefinedAt(SignedVersionKey) && query.isDefinedAt(SignatureKey)
+  }
 }
 
 class BlobPathBuilder()(private val fsm: BlobFileSystemManager) extends PathBuilder {
diff --git a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
index fbff8e47431..9093141054f 100644
--- a/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
+++ b/filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala
@@ -27,6 +27,23 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     }
   }
 
+  it should "reject a path that is otherwise valid, but has a preexisting SAS token" in {
+    import cromwell.filesystems.blob.BlobPathBuilder.UnparsableBlobPath
+
+    // The `.asInstanceOf[UnparsableBlobPath].errorMessage.getMessage` malarkey is necessary
+    // because Java exceptions compare by reference, while strings are by value
+
+    val sasBlob = "https://lz304a1e79fd7359e5327eda.blob.core.windows.net/sc-705b830a-d699-478e-9da6-49661b326e77" +
+      "?sv=2021-12-02&spr=https&st=2023-12-13T20%3A27%3A55Z&se=2023-12-14T04%3A42%3A55Z&sr=c&sp=racwdlt&sig=blah&rscd=foo"
+    BlobPathBuilder.validateBlobPath(sasBlob).asInstanceOf[UnparsableBlobPath].errorMessage.getMessage should equal(
+      UnparsableBlobPath(
+        new IllegalArgumentException(
+          "Rejecting pre-signed SAS URL so that filesystem selection falls through to HTTP filesystem"
+        )
+      ).errorMessage.getMessage
+    )
+  }
+
   it should "provide a readable error when getting an illegal nioPath" in {
     val endpoint = BlobPathBuilderSpec.buildEndpoint("storageAccount")
     val container = BlobContainerName("container")
@@ -39,8 +56,9 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     testException should contain(exception)
   }
 
-  private def testBlobNioStringCleaning(input: String, expected: String) =
-    BlobPath.cleanedNioPathString(input) shouldBe expected
+  // The following tests use the `centaurtesting` account injected into CI. They depend on access to the
+  // container specified below. You may need to log in to az cli locally to get them to pass.
+  private val subscriptionId: SubscriptionId = SubscriptionId(UUID.fromString("62b22893-6bc1-46d9-8a90-806bb3cce3c9"))
 
   it should "clean the NIO path string when it has a garbled http protocol" in {
     testBlobNioStringCleaning(
@@ -69,10 +87,6 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
       ""
     )
   }
-
-  // The following tests use the `centaurtesting` account injected into CI. They depend on access to the
-  // container specified below. You may need to log in to az cli locally to get them to pass.
-  private val subscriptionId: SubscriptionId = SubscriptionId(UUID.fromString("62b22893-6bc1-46d9-8a90-806bb3cce3c9"))
   private val endpoint: EndpointURL = BlobPathBuilderSpec.buildEndpoint("centaurtesting")
   private val container: BlobContainerName = BlobContainerName("test-blob")
 
@@ -82,6 +96,9 @@ class BlobPathBuilderSpec extends AnyFlatSpec with Matchers with MockSugar {
     new BlobPathBuilder()(fsm)
   }
 
+  private def testBlobNioStringCleaning(input: String, expected: String) =
+    BlobPath.cleanedNioPathString(input) shouldBe expected
+
   it should "read md5 from small files <5g" in {
     val builder = makeBlobPathBuilder()
     val evalPath = "/testRead.txt"
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 3e40fc85cdd..241260329c6 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -499,7 +499,7 @@ object Dependencies {
     List("scalatest", "mysql", "mariadb", "postgresql")
       .map(name => "com.dimafeng" %% s"testcontainers-scala-$name" % testContainersScalaV % Test)
 
-  val blobFileSystemDependencies: List[ModuleID] = azureDependencies ++ wsmDependencies
+  val blobFileSystemDependencies: List[ModuleID] = azureDependencies ++ wsmDependencies ++ akkaHttpDependencies
 
   val s3FileSystemDependencies: List[ModuleID] = junitDependencies
 

From dbd8a2aca7253cecd852b5b44ff199e35cdb81cd Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 4 Jan 2024 11:46:14 -0500
Subject: [PATCH 265/326] WX-1411 Require preinstalled `jq` and `curl` for
 just-in-time SAS feature (#7350)

---
 .../TesAsyncBackendJobExecutionActor.scala    | 28 ++++---------------
 1 file changed, 6 insertions(+), 22 deletions(-)

diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index d7a19685cd8..335ee40b466 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -86,32 +86,16 @@ object TesAsyncBackendJobExecutionActor {
        |  command -v "$$1" > /dev/null 2>&1
        |}
        |
-       |# Check if curl exists; install if not
+       |# Require the user image to pre-install `jq` and `curl` for us. Empirically, we found
+       |# that `apt install` at scale can run into repo outages and flakiness.
        |if ! command_exists curl; then
-       |  if command_exists apt-get; then
-       |    apt-get -y update && apt-get -y install curl
-       |    if [ $$? -ne 0 ]; then
-       |      echo "Error: Failed to install curl via apt-get."
-       |      exit 1
-       |    fi
-       |  else
-       |    echo "Error: apt-get is not available, and curl is not installed."
-       |    exit 1
-       |  fi
+       |  echo "Error: user image must include `curl` for just-in-time SAS token generation, but it is not installed."
+       |  exit 1
        |fi
        |
-       |# Check if jq exists; install if not
        |if ! command_exists jq; then
-       |  if command_exists apt-get; then
-       |    apt-get -y update && apt-get -y install jq
-       |    if [ $$? -ne 0 ]; then
-       |      echo "Error: Failed to install jq via apt-get."
-       |      exit 1
-       |    fi
-       |  else
-       |    echo "Error: apt-get is not available, and jq is not installed."
-       |    exit 1
-       |  fi
+       |  echo "Error: user image must include `jq` for just-in-time SAS token generation, but it is not installed."
+       |  exit 1
        |fi
        |curl --version
        |jq --version

From ecd44b63308cc09896f5440f834787f25c69c367 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 5 Jan 2024 14:23:13 -0500
Subject: [PATCH 266/326] WX-1396 Cromwell client allow additional properties
 (#7352)

---
 scripts/gen_java_client.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/gen_java_client.sh b/scripts/gen_java_client.sh
index beeac43ed2f..7e9f2143749 100755
--- a/scripts/gen_java_client.sh
+++ b/scripts/gen_java_client.sh
@@ -46,7 +46,8 @@ docker run --rm -v ${PWD}:/local ${OPENAPI_DOCKER} generate \
   --http-user-agent "Cromwell-Java-Client/${CROMWELL_HASH}" \
   --skip-validate-spec \
   --api-package ${BASE_PACKAGE}.api \
-  --model-package ${BASE_PACKAGE}.model
+  --model-package ${BASE_PACKAGE}.model \
+  --additional-properties=disallowAdditionalPropertiesIfNotPresent=false
 
 # 2. Remove the generator's build.sbt
 rm codegen_java/build.sbt

From 83ca277933027b01eef6643f86873bea62f8a964 Mon Sep 17 00:00:00 2001
From: Henrique Ribeiro <henriqueribeiro@users.noreply.github.com>
Date: Mon, 8 Jan 2024 09:53:27 +0000
Subject: [PATCH 267/326] Develop AWS (#42)

* 85 release (#28)

* Update cromwell version from 83 to 84

* BW-1255 Implement POST /runs endpoint (#6779)

* Adding route

* Fixing HTTP method error

* All formFields made optional

* A compliling state

* Saving

* Saving

* All three endpoints functioning as expected; updated RESTAPI.md

* Updated response for submission from 200 to 201 to pass tests

* Test submission response

* Moved updated submission response to askSubmit

* test

* updating RESTAPI.md

* saving

* Adding utility file for submitRequest

* cleanup

* Update awssdkv from 2.17.152 to 2.17.194 (#6814)

* BW-1305 Swagger Update (#6818)

* Properly documenting metadataArchiveStatus in WorkflowQueryResult model

* Update docs

* BT-710 Add configs for BlobPathBuilderFactory (#6817)

BT-710 Add configs for BlobPathBuilderFactory

* BW-1305 Make "name" optional in workflow query response (#6821)

* BT-724 Fix BlobPathBuilder failing on retrieving existing filesystem (#6816)

Modify blobPathBuilder to fallback to creating a filesystem if one is not found

* Logging updates: (#6813)

* [BT-698] first pass on BlobTokenGenerator with E2E test (#6824)

* first pass on BlobTokenGenerator with E2E test

* update BlobPathBuilder constructor args in test

* account -> container level client

* [BT-687] specify correct types (#6829)

* specify correct types

* fix test with new type

* remove type declarations in function call

* remove unnecessary sas-token config

* BW-1206 - Combine all Wes Endpoints & add Tests (#6833)

* Add tests, getting frid of WesRunRoutes.scala

* wesWorkflowId fix, ec implicits errors gone

* Refactoring path for GET /runs

* Indentation fix

* Commit to rollback

* Revert "Indentation fix"

This reverts commit 63fc4842c9d4eff68ec9cb7c3ef19e110696598b.

* PR trigger

* Optimize imports

* Missed import

* BW-1354 - Porting CBAS preliminary step (#6837)

* Getting rid of shared utility file; Adding/Updating WES version of submit.

* Edit spec file

* Adding Wes-like error

* BW-1378 Addl CromIAM user enablement checks (#6826)

* Update cromwell version from 84 to 85

* BW-1393 Release doc updates (#6839)

* BT-732 Checksum validation for blobs read by engine (#6838)

* Draft support for optional FileHash

* Draft getMd5 for BlobPath

* Resolve non-parallel IO to fix tests

* Checksum validation for BlobPath

* Nicer error message

* Test for missing Blob hash

* Break attr acquisition into separate method

* Cleanup, comments

* In-progress tests of blob hash command

* Remove test

* Remove unused import

* BT-711 Refresh SAS token for filesystem on expiry (#6831)

* BT-711 Refresh SAS token for filesystem on expiry

* Rough cut of token refresh using exceptions

* Ignore tests, and minor cleanup

* Remove stray line

* Draft of manager class for handling expiring file systems

* Style fixes

* Refactor of blobfilesystemManager and tests covering its functionality

* Refined tests to validate close filesystem as separate unit

* Ignore connected tests

* Clean up of some things

* Refactor BlobFileSystemManager to separate file, and some other cleanup

* Some additional scala-ifying

* Small cleanup

* Correcting imports

* trigger tests

* trigger tests

* Batch 1 of scala steward updates (#6903)

* Batch 1 of scala steward updates

* Rollback snakeYAML

* Attempt 3, with only the passing dependancies

* Revert google API and Big Query udpates

* Winding back other google deps

* rollback remaining google updates

* trigger tests

* trigger tests

* [BW-1398] Migrate PKs to BIGINT (#6907)

* BT-745  Batch 2 of scala steward updates (#6906)

* Update SBT to 2.0.0

* Fix sbt-git import

* Update mouse to 1.0.11

* Update rhino 1.7.14

* SUP-692 Retry with more memory after RC 137 (#6912)

* Reorder execution result checks so 137 can retry with more memory

* Test for memory retry after 137 RC

* Fix test expectations

* Make memory retry checks consistent

* Revert changes to existing test

* Rename retryWithMoreMemory to outOfMemoryDetected

* Scala steward updates batch 3 (#6913)

* Scala steward updates batch 3

* WX-745 Batch 4 scala steward updates (#6916)

* WX-746 Localize all DRS inputs in a single Action (#6914)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* WX-755 Build all images instead of just Cromwell (#6919)

* WX-755 Add `isRelease` option for Docker builds (#6923)

* WX-755 Cromwell/CromIAM automatically board train (#6924)

* WX-755 Fix environment variable syntax (#6926)

* WX-743 Enable TES task creation with BlobPaths (#6921)

* Give blob SAS tokens write permission

* Case class wrapper for subscription id

* Resolve duplicate container name in absolute BlobPath

* Ignored test demonstrating correct absolute path generation

* Update filesystems/blob/src/test/scala/cromwell/filesystems/blob/BlobPathBuilderSpec.scala

Co-authored-by: Brian Reilly <breilly@broadinstitute.org>

* PR feedback

Co-authored-by: Brian Reilly <breilly@broadinstitute.org>

* [WX-765] Update snakeyaml to 1.33 (#6927)

* update snakeyaml to 1.33

* Don't use deprecated no-arg Constructor constructor

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* WM-1414 Refactoring WesRunLog to omit Cromwell's "workflowLog" object (#6925)

* Upgrade Postgres to 42.4.1 (#6932)

* WX-735 Fix incorrect and/or nondeterministic filesystem ordering (#6930)

* WX-772 Update Scala to 2.13.9 (#6928)

* Update Scala to 2.13.9

* Try updating sbt-scoverage

* Does this version exist anywhere we can see?

* This version actually exists

* Update library version to remove conflict

* Codegen version

* Fix fun new 2.13.9 compiler errors

* Resolve warnings

* Newest Scala?

* I guess not

* Does this please Travis?

* force ci

* Back out changes to generated code

Co-authored-by: Adam Nichols <aednichols@gmail.com>

* WX-781 Bump jackson-databind in /CromwellRefdiskManifestCreator (#6935)

Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.13.2.2 to 2.13.4.1.
- [Release notes](https://github.com/FasterXML/jackson/releases)
- [Commits](https://github.com/FasterXML/jackson/commits)

---
updated-dependencies:
- dependency-name: com.fasterxml.jackson.core:jackson-databind
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* WX-808 Host allowlist for HTTP imports (#6938)

* `hostAllowlist` that allows everything

* Refactor

* Stick allow list in HttpResolver

* Better default config

* Allow list tests

* Make it build

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Update commons text to 1.10.0 (#6937)

* WX-751 Token refresh signal for monitoring (#6939)

* Log messages

* `DEBUG` -> `INFO`

* WX-744 Optionally rewrite blob paths to appear as local paths (#6941)

* Modify blob paths for TES

* Make blob transformation configurable

* Update supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Apply PR feedback in second place

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Update changelog for wdl http allow list (#6944)

* WM-1491 Fixing Cromwell-client (#6943)

* More updated client for use in cbas

* Removing excess code

* Fix client build script (#6945)

* WX-837: Remove CWL references from documentation (#6949)

* wx-837 removed cwl references in markdown doc files

* wx-837 removed cwlParsingOverview.md, updated mkdocs.yml

* wx-837 updated cromwell.yaml, generated new RESTAPI file

* WX-728 Add configurable WSM client to Cromwell (#6948)

* Dependencies

* Compiles but no tests

* Formatting

* Moar exclusions

* Update to latest WSM

* Add additional dependency

* We need some UUID here to make the request

* Formatting

* Clarify what is fake

* Formatting

* Use our own version of Jersey and Jackson stuff

* Port-in Khalid's changes (thank you!)

Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>

* Test longevity

Don't break the test if someone decides to add a cert to `ws.org`

* Cleanup

* Cleanup

* Cleanup

* Adjust TES config file for CI

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Khalid Shakir <kshakir@broadinstitute.org>

* CROM-6554: Removed PAPIv1 references from doc (#6950)

* crom-6554 removed references to PAPI v1 from doc

* crom-6554 pr feedback, reworded doc to use example conf as a starting point

* WX-833 Real Azure DRS Credentials (#6952)

* Remove B2C reference from name

* Get token for current user rather than getting from KeyVault

* Remove KeyVault config for engine

* Remove KeyVault config for DRSLocalizer

* Remove KeyVault dependency

* Remove KeyVault support from localizer repo template

* Cleaned up and working Azure token acquisition for engine

* Collapse localizer's AccessTokenStrategy into DrsCredentials

* Cleanup

* WX-853 Remove most CWL (#6955)

* WX-696 Enable getting SAS token from WSM (#6954)

* WX-696 Enable getting SAS token from WSM

* Wire container resource id from config

* Move resource-container-id config path

* First pass at config for WSM

* Remove unused singleton config

* Tests for new config

* Fix config parsing

* Modified b2c token to be provided each time

* Remove singletonConfig arg from factory

* Restore types to factory configs

* Clean up comments and empty token default

* Default to config b2c before searching environment

* Fix token default on api client

* Fix test

* Refactor error handling for when there is no token

* Remove token constructor arg for clientProvider

* Move configs to global singleton config

* Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

* default -> override

* Add override token to test

* Update filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobFileSystemManager.scala

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* Parentheses

* Reduce token timeout

* Move AzureCredentials to separate file

* Make AzureCredentials an object

* WSM token cleanup

* Config refactor (#6960)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Initial blob token documentation

* Refine language in BlobSasTokenGenerator

* Update comment and formatting

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>

* WX-853 Remove CWL language factory, Centaur runner (#6961)

* WX-842 Add Pact Dependency for Cromwell (#6962)

* WX-842 Add Pact Dependency for Cromwell

* Remove incomplete test spec

* Initial Pact Test

* Fix pact so it compiles

* Add breadcrumb comment and clean up

* ID-125 Add support for drshub, rename all the things (#6959)

* Add support for drshub, rename all the things

* fallback to martha if resolver is not in config

* WX-867 Translate crc32c hashes to b64 for getm (#6970)

* Translate crc32c hashes to b64 for getm

* Update tests

* Remove obsolete b64 handling for md5, centralize hex validation

* Restore old test, fix other test

* WX-843 Workflow failure reason should accurately indicate issues opening blob filesystem (#6965)

* WX-859 Accept workflow execution identity in config (#6967)

* WX-892 Trim down `ValueStore` logging to prevent OOMs (#6981)

* Add Nirvana 3.18.1 reference image test, minor cleanup [VS-705] (#6975)

* WX-863 Turn off Azure NIO logging (#6982)

* Turn off Azure NIO logging

* Poke Travis

* WM-1616: Allow repeating attempts at initialization (take 2) (#6985)

* WX-878 Single shared BlobFileSystemManager (#6986)

* Make BlobFileSystemManager shared across all BlobPathBuilders

* Update TES conf file to reflect new singleton config

* Shell escape reference image  files [VS-796] [WX-910] (#6989)

* WX-769 `disks` compatibility for TES backend (#6991)

* Update FiveMinuteIntro.md (#6994)

* WX-906 Sbt Unit Tests as Github Actions (#6992)

* WX-926 Support falling back to OCI Manifest Format (#7003)

* WX-926 Support falling back to OCI Manifest Forma

* Only mount reference disks if requested [WX-925] (#7001)

* [WM-1646] Add missing fields for `WorkflowDescription` for WomTool /describe endpoint to Swagger (#7004)

* WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status (#6980)

* WX-876 Surface TES System Logs to Cromwell when TES backend returns task error status

* Address feedback

* Address feedback (#6997)

* Address additional feedback (#7000)

* Fix copy/paste error (#7005)

* Address additional feedback

* Fix copy/paste error

* Trigger CI

---------

Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>

* Centaur reference image test should validate symlinks [VS-796] (#6996)

* WX-903 Pre-GHA test suite disablement

* WX-877 Update CHANGELOG for release 85 (#7011)

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Co-authored-by: Katrina P <68349264+kpierre13@users.noreply.github.com>
Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Co-authored-by: Christian Freitas <christian.j.freitas@gmail.com>
Co-authored-by: Saloni Shah <salonipshah11@gmail.com>
Co-authored-by: kshakir <kshakir@broadinstitute.org>
Co-authored-by: mspector <michael.l.spector@gmail.com>
Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
Co-authored-by: Brian Reilly <breilly@broadinstitute.org>
Co-authored-by: Adam Nichols <aednichols@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Justin Variath Thomas <JVThomas@users.noreply.github.com>
Co-authored-by: Christian Freitas <cfreitas@broadinstitute.org>
Co-authored-by: Trevyn Langsford <tlangs@broadinstitute.org>
Co-authored-by: Miguel Covarrubias <mcovarr@users.noreply.github.com>
Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com>
Co-authored-by: Tom Wiseman <tom.h.wiseman@gmail.com>
Co-authored-by: Blair Murri <BMurri@users.noreply.github.com>

* Develop aws (#29)

* stuck on globbing

* efs works, no callcaching

* update readme

* extended EFS support

* fix for globbing in nested scatters

* updated config for globbing, to prevent issues with empty folders

* efs fixes : support paths with over 127 characters, fix delocalization of efs-based globs (#32)

* Develop aws (#34)

* efs fixes : support paths with over 127 characters, fix delocalization of efs-based globs

* add deployment manual, fix issue with empty disks

* update documentation

* update documentation

* update documentation

* Options to publish status only (#36)

* add options to publish status only

* updated readme.md

---------

Co-authored-by: quekx <quekx@gene.com>

* Fix aws unit tests (#39)

* checkpoint

* fix ecr and batch tests

* fix AwsBatchJobSpec.scala

---------

Co-authored-by: quekx <quekx@gene.com>

* return bucket directly instead of listing and checking it (#38)

Co-authored-by: quekx <quekx@gene.com>

* Add evaluteOnExit for aws batch retry (#40)

Co-authored-by: quekx <quekx@gene.com>

* Improved tagging support (#37)

* efs fixes : support paths with over 127 characters, fix delocalization of efs-based globs

* add deployment manual, fix issue with empty disks

* update documentation

* update documentation

* update documentation

* support for tagging instances and volumes used in jobs, some support for spaces in file paths

* corrected workflow id in tagging

* redirect exit code 137 to retry-with-more-memory routine

---------

Co-authored-by: Henrique Ribeiro <henriqueribeiro@users.noreply.github.com>

* add gpu count (#41)

* add gpu count

* fix typo

---------

Co-authored-by: quekx <quekx@gene.com>
Co-authored-by: Henrique Ribeiro <henriqueribeiro@users.noreply.github.com>

---------

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Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
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Co-authored-by: Adam Nichols <aednichols@gmail.com>
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Co-authored-by: geertvandeweyer <geertvandeweyer@gmail.com>
Co-authored-by: xquek <46759870+xquek@users.noreply.github.com>
Co-authored-by: quekx <quekx@gene.com>
---
 .../main/scala/cromwell/backend/backend.scala |   4 +
 .../StandardAsyncExecutionActor.scala         |  10 +-
 .../flows/aws/AmazonEcrPublicSpec.scala       |  12 +-
 .../registryv2/flows/aws/AmazonEcrSpec.scala  |  13 +-
 .../main/java/org/lerch/s3fs/S3FileStore.java |   5 +-
 .../impl/aws/SnsMetadataServiceActor.scala    |  12 +-
 ...wsBatchAsyncBackendJobExecutionActor.scala |  18 +-
 .../backend/impl/aws/AwsBatchAttributes.scala |  13 +
 .../impl/aws/AwsBatchConfiguration.scala      |   1 +
 .../backend/impl/aws/AwsBatchJob.scala        | 321 ++++++++++++------
 .../impl/aws/AwsBatchJobDefinition.scala      |  56 ++-
 .../impl/aws/AwsBatchRuntimeAttributes.scala  | 198 ++++++++++-
 .../scala/cromwell/backend/impl/aws/README.md |  93 ++++-
 .../impl/aws/io/AwsBatchGlobFunctions.scala   |   9 -
 ...tchAsyncBackendJobExecutionActorSpec.scala |   3 +-
 .../impl/aws/AwsBatchCallPathsSpec.scala      |   3 +-
 .../backend/impl/aws/AwsBatchJobSpec.scala    | 312 +++++++++++------
 .../aws/AwsBatchRuntimeAttributesSpec.scala   | 117 ++++++-
 .../backend/impl/aws/AwsBatchTestConfig.scala |  90 +++++
 .../impl/aws/AwsBatchWorkflowPathsSpec.scala  |   1 +
 20 files changed, 1004 insertions(+), 287 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index bf9f67e27a1..3c5c33ab992 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -136,13 +136,17 @@ object CommonBackendConfigurationAttributes {
     "default-runtime-attributes.zones",
     "default-runtime-attributes.continueOnReturnCode",
     "default-runtime-attributes.cpu",
+    "default-runtime-attributes.gpuCount",
     "default-runtime-attributes.noAddress",
     "default-runtime-attributes.docker",
     "default-runtime-attributes.queueArn",
     "default-runtime-attributes.awsBatchRetryAttempts",
+    "default-runtime-attributes.maxRetries",
+    "default-runtime-attributes.awsBatchEvaluateOnExit",
     "default-runtime-attributes.ulimits",
     "default-runtime-attributes.efsDelocalize",
     "default-runtime-attributes.efsMakeMD5",
+    "default-runtime-attributes.tagResources",
     "default-runtime-attributes.failOnStderr",
     "slow-job-warning-time",
     "dockerhub",
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 02c2a2577a2..8acef722f71 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -38,8 +38,9 @@ import wom.callable.{AdHocValue, CommandTaskDefinition, ContainerizedInputExpres
 import wom.expression.WomExpression
 import wom.graph.LocalName
 import wom.values._
+import wom.types._
 import wom.{CommandSetupSideEffectFile, InstantiatedCommand, WomFileMapper}
-
+import java.net.URLDecoder
 import scala.concurrent._
 import scala.concurrent.duration._
 import scala.util.{Failure, Success, Try}
@@ -165,7 +166,12 @@ trait StandardAsyncExecutionActor
         if (inputsToNotLocalize.contains(womFile)) {
           womFile
         } else {
-          mapper(womFile)
+          // resolve
+          val mapped_wom = mapper(womFile)
+          // decode url encoded values generated by the mapper
+          val decoded_womValue = URLDecoder.decode(mapped_wom.valueString,"UTF-8")
+          // convert to womfile again
+          WomFile(WomSingleFileType, decoded_womValue)
         }
     )
   }
diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
index 18a0a23232e..f6f1520512f 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrPublicSpec.scala
@@ -1,5 +1,4 @@
 package cromwell.docker.registryv2.flows.aws
-
 import cats.effect.{IO, Resource}
 import cromwell.core.TestKitSuite
 import cromwell.docker.registryv2.DockerRegistryV2Abstract
@@ -12,20 +11,19 @@ import org.mockito.Mockito._
 import org.scalatest.{BeforeAndAfter, PrivateMethodTester}
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
-import org.scalatestplus.mockito.MockitoSugar
 import software.amazon.awssdk.services.ecrpublic.model.{AuthorizationData, GetAuthorizationTokenRequest, GetAuthorizationTokenResponse}
 import software.amazon.awssdk.services.ecrpublic.EcrPublicClient
 
-class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with MockitoSugar with BeforeAndAfter with PrivateMethodTester {
+class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with BeforeAndAfter with PrivateMethodTester {
   behavior of "AmazonEcrPublic"
 
   val goodUri = "public.ecr.aws/amazonlinux/amazonlinux:latest"
   val otherUri = "ubuntu:latest"
 
 
-  val mediaType: MediaType = MediaType.parse(DockerRegistryV2Abstract.ManifestV2MediaType).right.get
+  val mediaType: MediaType = MediaType.parse(DockerRegistryV2Abstract.DockerManifestV2MediaType).getOrElse(fail("Cant parse mediatype"))
   val contentType: Header = `Content-Type`(mediaType)
-  val mockEcrClient: EcrPublicClient = mock[EcrPublicClient]
+  val mockEcrClient: EcrPublicClient = mock(classOf[EcrPublicClient])
   implicit val mockIOClient: Client[IO] = Client({ _: Request[IO] =>
     // This response will have an empty body, so we need to be explicit about the typing:
     Resource.pure[IO, Response[IO]](Response(headers = Headers.of(contentType))) : Resource[IO, Response[IO]]
@@ -44,7 +42,7 @@ class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matcher
   }
 
   it should "have public.ecr.aws as registryHostName" in {
-    val registryHostNameMethod = PrivateMethod[String]('registryHostName)
+    val registryHostNameMethod = PrivateMethod[String](Symbol("registryHostName"))
     registry invokePrivate registryHostNameMethod(DockerImageIdentifier.fromString(goodUri).get) shouldEqual "public.ecr.aws"
   }
 
@@ -63,7 +61,7 @@ class AmazonEcrPublicSpec extends TestKitSuite with AnyFlatSpecLike with Matcher
           .build())
         .build)
 
-    val getTokenMethod = PrivateMethod[IO[Option[String]]]('getToken)
+    val getTokenMethod = PrivateMethod[IO[Option[String]]](Symbol("getToken"))
     registry invokePrivate getTokenMethod(context, mockIOClient) ensuring(io => io.unsafeRunSync().get == token)
   }
 }
diff --git a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala
index 5ddf98c7ffa..c4f121188db 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/registryv2/flows/aws/AmazonEcrSpec.scala
@@ -11,19 +11,18 @@ import org.mockito.Mockito._
 import org.scalatest.{BeforeAndAfter, PrivateMethodTester}
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
-import org.scalatestplus.mockito.MockitoSugar
 import software.amazon.awssdk.services.ecr.EcrClient
 import software.amazon.awssdk.services.ecr.model.{AuthorizationData, GetAuthorizationTokenResponse}
 
-class AmazonEcrSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with MockitoSugar with BeforeAndAfter with PrivateMethodTester{
+class AmazonEcrSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with BeforeAndAfter with PrivateMethodTester{
   behavior of "AmazonEcr"
 
   val goodUri = "123456789012.dkr.ecr.us-east-1.amazonaws.com/amazonlinux/amazonlinux:latest"
   val otherUri = "ubuntu:latest"
 
-  val mediaType: MediaType = MediaType.parse(DockerRegistryV2Abstract.ManifestV2MediaType).right.get
+  val mediaType: MediaType = MediaType.parse(DockerRegistryV2Abstract.DockerManifestV2MediaType).getOrElse(fail("Can't parse media type"))
   val contentType: Header = `Content-Type`(mediaType)
-  val mockEcrClient: EcrClient = mock[EcrClient]
+  val mockEcrClient: EcrClient = mock(classOf[EcrClient])
   implicit val mockIOClient: Client[IO] = Client({ _: Request[IO] =>
     // This response will have an empty body, so we need to be explicit about the typing:
     Resource.pure[IO, Response[IO]](Response(headers = Headers.of(contentType))) : Resource[IO, Response[IO]]
@@ -42,12 +41,12 @@ class AmazonEcrSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with
   }
 
   it should "use Basic Auth Scheme" in {
-    val authSchemeMethod = PrivateMethod[AuthScheme]('authorizationScheme)
+    val authSchemeMethod = PrivateMethod[AuthScheme](Symbol("authorizationScheme"))
     registry invokePrivate authSchemeMethod() shouldEqual AuthScheme.Basic
   }
 
   it should "return 123456789012.dkr.ecr.us-east-1.amazonaws.com as registryHostName" in {
-    val registryHostNameMethod = PrivateMethod[String]('registryHostName)
+    val registryHostNameMethod = PrivateMethod[String](Symbol("registryHostName"))
     registry invokePrivate registryHostNameMethod(DockerImageIdentifier.fromString(goodUri).get) shouldEqual "123456789012.dkr.ecr.us-east-1.amazonaws.com"
   }
 
@@ -66,7 +65,7 @@ class AmazonEcrSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with
           .build())
         .build)
 
-    val getTokenMethod = PrivateMethod[IO[Option[String]]]('getToken)
+    val getTokenMethod = PrivateMethod[IO[Option[String]]](Symbol("getToken"))
     registry invokePrivate getTokenMethod(context, mockIOClient) ensuring(io => io.unsafeRunSync().get == token)
   }
 }
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
index 8e15999180a..5de7e89813b 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
@@ -99,10 +99,7 @@ public Bucket getBucket() {
     }
 
     private Bucket getBucket(String bucketName) {
-        for (Bucket buck : getClient().listBuckets().buckets())
-            if (buck.name().equals(bucketName))
-                return buck;
-        return null;
+        return Bucket.builder().name(bucketName).build();
     }
 
     private boolean hasBucket(String bucketName) {
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
index da66ae4f7f4..4fc9f43328e 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/aws/SnsMetadataServiceActor.scala
@@ -46,7 +46,7 @@ import software.amazon.awssdk.services.sns.model.PublishRequest
 import spray.json.enrichAny
 
 import scala.concurrent.{ExecutionContextExecutor, Future}
-import scala.util.{Failure, Success}
+import scala.util.{Failure, Success, Try}
 
 
 /**
@@ -61,6 +61,10 @@ class AwsSnsMetadataServiceActor(serviceConfig: Config, globalConfig: Config, se
 
   //setup sns client
   val topicArn: String = serviceConfig.getString("aws.topicArn")
+  val publishStatusOnly: Boolean = Try(serviceConfig.getBoolean("aws.publishStatusOnly")) match {
+    case Failure(_) => false
+    case Success(value) => value
+  }
 
   val awsConfig: AwsConfiguration = AwsConfiguration(globalConfig)
   val credentialsProviderChain: AwsCredentialsProviderChain =
@@ -74,7 +78,11 @@ class AwsSnsMetadataServiceActor(serviceConfig: Config, globalConfig: Config, se
   def publishMessages(events: Iterable[MetadataEvent]): Future[Unit] = {
     import AwsSnsMetadataServiceActor.EnhancedMetadataEvents
 
-    val eventsJson = events.toJson
+    val eventsJson = if (publishStatusOnly) {
+      events.filter(_.key.key == "status").toJson
+    } else {
+      events.toJson
+    }
     //if there are no events then don't publish anything
     if( eventsJson.length < 1) { return Future(())}
     log.debug(f"Publishing to $topicArn : $eventsJson")
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 498bd2ec4fe..150d61bef79 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -31,7 +31,7 @@
 
 package cromwell.backend.impl.aws
 
-import java.net.SocketTimeoutException
+import java.net.{SocketTimeoutException, URLDecoder}
 import java.io.FileNotFoundException
 import java.nio.file.Paths
 
@@ -202,7 +202,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       configuration.fsxMntPoint,
       configuration.efsMntPoint,
       Option(runtimeAttributes.efsMakeMD5),
-      Option(runtimeAttributes.efsDelocalize))
+      Option(runtimeAttributes.efsDelocalize),
+      Option(runtimeAttributes.tagResources))
   }
 
   // setup batch client to query job container info
@@ -262,13 +263,13 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         case Success(path: S3Path) =>
           configuration.fileSystem match  {
             case AWSBatchStorageSystems.s3 => 
-                path.pathWithoutScheme
+                URLDecoder.decode(path.pathWithoutScheme,"UTF-8")
             case _ =>  
-                path.toString
+                URLDecoder.decode(path.toString,"UTF-8")
           }
         // non-s3 paths
         case _ => 
-            value
+            URLDecoder.decode(value,"UTF-8")
       }
     )
   }
@@ -421,7 +422,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
             AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), womFile.value, relpath, disk)
         } else {
             // if efs is not enabled, OR efs delocalization IS enabled, keep the s3 path as destination.
-            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), destination, relpath, disk)
+            AwsBatchFileOutput(makeSafeAwsBatchReferenceName(womFile.value), URLDecoder.decode(destination,"UTF-8"), relpath, disk)
         }
     List(output)
   }
@@ -689,7 +690,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       // STATUS LOGIC:
       //   - success : container exit code is zero
       //   - command failure: container exit code > 0, no statusReason in container
-      //   - OOM kill : container exit code > 0, statusReason contains "OutOfMemory"
+      //   - OOM kill : container exit code > 0, statusReason contains "OutOfMemory" OR exit code == 137
       //   - spot kill : no container exit code set. statusReason of ATTEMPT (not container) says "host EC2 (...) terminated"     
       Log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
       val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(job.jobId).build)
@@ -722,6 +723,9 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         case "0" => 
             Log.debug("container exit code was zero. job succeeded")
             false
+        case "137" => 
+            Log.info("Job failed with Container status reason : 'OutOfMemory' (code:137)")
+            true
         case _ => 
             // failed job due to command errors (~ user errors) don't have a container exit reason.
             val containerStatusReason:String = {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
index ecb6c87a457..38f026eadcf 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAttributes.scala
@@ -61,6 +61,7 @@ case class AwsBatchAttributes(fileSystem: String,
                               fsxMntPoint: Option[List[String]],
                               efsMntPoint: Option[String],
                               efsMakeMD5: Option[Boolean],
+                              tagResources: Option[Boolean],
                               efsDelocalize: Option[Boolean],
                               globLinkCommand: Option[String],
                               checkSiblingMd5: Option[Boolean]
@@ -87,9 +88,13 @@ object AwsBatchAttributes {
     "numSubmitAttempts",
     "default-runtime-attributes.scriptBucketName",
     "awsBatchRetryAttempts",
+    "awsBatchEvaluateOnExit",
     "ulimits",
+    "gpuCount",
     "efsDelocalize",
     "efsMakeMD5",
+    "tagResources",
+    "maxRetries",
     "glob-link-command"
   )
 
@@ -180,6 +185,13 @@ object AwsBatchAttributes {
             case false => None
       }
     }
+    // from config if set: 
+    val tagResources:ErrorOr[Option[Boolean]] = validate {
+        backendConfig.hasPath("default-runtime-attributes.tagResources") match {
+            case true => Some(backendConfig.getBoolean("default-runtime-attributes.tagResources"))
+            case false => None
+      }
+    }
     // from config if set.
     val globLinkCommand:ErrorOr[Option[String]] = validate {
         backendConfig.hasPath("glob-link-command") match {
@@ -206,6 +218,7 @@ object AwsBatchAttributes {
       efsMntPoint,
       efsMakeMD5,
       efsDelocalize,
+      tagResources,
       globLinkCommand,
       checkSiblingMd5
     ).tupled.map((AwsBatchAttributes.apply _).tupled) match {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
index 8a019110509..3ceb1ea3844 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchConfiguration.scala
@@ -60,6 +60,7 @@ class AwsBatchConfiguration(val configurationDescriptor: BackendConfigurationDes
   val efsMntPoint = batchAttributes.efsMntPoint
   val efsMakeMD5 = batchAttributes.efsMakeMD5
   val efsDelocalize = batchAttributes.efsDelocalize
+  val tagResources = batchAttributes.tagResources
   val globLinkCommand = batchAttributes.globLinkCommand
   val checkSiblingMd5 = batchAttributes.checkSiblingMd5
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 97302357175..4cfa08e82a5 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -87,7 +87,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                              fsxMntPoint: Option[List[String]],
                              efsMntPoint: Option[String],
                              efsMakeMD5: Option[Boolean],
-                             efsDelocalize: Option[Boolean]
+                             efsDelocalize: Option[Boolean],
+                             tagResources: Option[Boolean]
                             ) {
 
 
@@ -117,7 +118,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     */
   lazy val reconfiguredScript: String = {
     //this is the location of the aws cli mounted into the container by the ec2 launch template
-    val awsCmd = "/usr/local/aws-cli/v2/current/bin/aws "
+    val awsCmd = "/usr/local/aws-cli/v2/current/bin/aws"
     //internal to the container, therefore not mounted
     val workDir = "/tmp/scratch"
     //working in a mount will cause collisions in long running workers
@@ -125,28 +126,25 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     val insertionPoint = replaced.indexOf("\n", replaced.indexOf("#!")) +1 //just after the new line after the shebang!
     // load the config
     val conf : Config = ConfigFactory.load();
-    
+
     /* generate a series of s3 copy statements to copy any s3 files into the container. */
     val inputCopyCommand = inputs.map {
       case input: AwsBatchFileInput if input.s3key.startsWith("s3://") && input.s3key.endsWith(".tmp") =>
         //we are localizing a tmp file which may contain workdirectory paths that need to be reconfigured
         s"""
-           |_s3_localize_with_retry ${input.s3key} $workDir/${input.local}
-           |sed -i 's#${AwsBatchWorkingDisk.MountPoint.pathAsString}#$workDir#g' $workDir/${input.local}
+           |_s3_localize_with_retry "${input.s3key}" "$workDir/${input.local}"
+           |sed -i 's#${AwsBatchWorkingDisk.MountPoint.pathAsString}#$workDir#g' "$workDir/${input.local}"
            |""".stripMargin
 
-      
       case input: AwsBatchFileInput if input.s3key.startsWith("s3://") => 
         // regular s3 objects : download to working dir.
-        s"_s3_localize_with_retry ${input.s3key} ${input.mount.mountPoint.pathAsString}/${input.local}"
+        s"""_s3_localize_with_retry "${input.s3key}" "${input.mount.mountPoint.pathAsString}/${input.local}" """.stripMargin
           .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
 
-      
-       
       case input: AwsBatchFileInput if efsMntPoint.isDefined && input.s3key.startsWith(efsMntPoint.get) =>  
         // EFS located file : test for presence on provided path.
         Log.debug("EFS input file detected: "+ input.s3key + " / "+ input.local.pathAsString)
-        s"test -e ${input.s3key} || (echo 'input file: ${input.s3key} does not exist' && exit 1)"
+        s"""test -e "${input.s3key}" || (echo 'input file: ${input.s3key} does not exist' && LOCALIZATION_FAILED=1)""".stripMargin
       
       case input: AwsBatchFileInput => 
         // an entry in 'disks' => keep mount as it is.. 
@@ -155,7 +153,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         //  .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
         val filePath = input.local.pathAsString
         Log.debug("input entry in disks detected "+ input.s3key + " / "+ input.local.pathAsString)
-        s"test -e $filePath || (echo 'input file: $filePath does not exist' && exit 1)"
+        s"""test -e "$filePath" || (echo 'input file: $filePath does not exist' && LOCALIZATION_FAILED=1)""".stripMargin
       
       case _ => ""
     }.toList.mkString("\n")
@@ -164,6 +162,17 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     val mp_threshold : Long = if (conf.hasPath("engine.filesystems.s3.MultipartThreshold") ) conf.getMemorySize("engine.filesystems.s3.MultipartThreshold").toBytes() else 5L * 1024L * 1024L * 1024L; 
     Log.debug(s"MultiPart Threshold for delocalizing is $mp_threshold")
 
+    // prepare tags, strip invalid characters
+    val invalidCharsPattern = "[^a-zA-Z0-9_.:/=+-@]+".r
+    Log.debug(s"root workflow id: ${jobDescriptor.workflowDescriptor.rootWorkflowId.toString}")
+    Log.debug(s"root workflow name: ${jobDescriptor.workflowDescriptor.rootWorkflow.name.toString}")
+    
+    
+    val workflowId = invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflowId.toString,"_")
+    val workflowName = invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflow.name.toString,"_")
+    val taskId = invalidCharsPattern.replaceAllIn(jobDescriptor.key.call.fullyQualifiedName + "-" + jobDescriptor.key.index + "-" + jobDescriptor.key.attempt,"_")
+    val doTagging = tagResources.getOrElse(false) // development : always tag resources.
+    //val tags: Map[String,String] = Map("cromwell-workflow-name" -> workflowName, "cromwell-workflow-id" -> workflowId, "cromwell-task-id" -> taskId)
     // this goes at the start of the script after the #!
     val preamble =
       s"""
@@ -171,27 +180,29 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
          |
          |function _s3_localize_with_retry() {
-         |  local s3_path=$$1
+         |  local s3_path="$$1"
          |  # destination must be the path to a file and not just the directory you want the file in
-         |  local destination=$$2
+         |  local destination="$$2"
          |
          |  for i in {1..6};
          |  do
          |    # abort if tries are exhausted
          |    if [ "$$i" -eq 6 ]; then
-         |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts. aborting"
-         |        exit 2
+         |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts."
+         |        LOCALIZATION_FAILED=1
+         |        break
          |    fi
          |    # check validity of source path
-         |    if ! [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
-         |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
-         |      exit 1
+         |    if ! [[ "$$s3_path" =~ s3://([^/]+)/(.+) ]]; then
+         |      echo "$$s3_path is not an S3 path with a bucket and key."
+         |      LOCALIZATION_FAILED=1
+         |      break
          |    fi
-         |    # copy  
+         |    # copy
          |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination"  ||
          |        { echo "attempt $$i to copy $$s3_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # check data integrity
-         |    _check_data_integrity $$destination $$s3_path || 
+         |    _check_data_integrity "$$destination" "$$s3_path" || 
          |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # copy succeeded
          |    break
@@ -200,14 +211,21 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |
          |function _s3_delocalize_with_retry() {
          |  # input variables
-         |  local local_path=$$1
+         |  local local_path="$$1"
          |  # destination must be the path to a file and not just the directory you want the file in
-         |  local destination=$$2
+         |  local destination="$$2"
+         |
+         |  # if file/folder does not exist, return immediately
+         |  if [[ ! -e "$$local_path" ]]; then
+         |    echo "$$local_path does not exist. skipping delocalization"
+         |    DELOCALIZATION_FAILED=1
+         |    return
+         |  fi
          |
          |  # get the multipart chunk size
-         |  chunk_size=$$(_get_multipart_chunk_size $$local_path)
+         |  chunk_size=$$(_get_multipart_chunk_size "$$local_path")
          |  local MP_THRESHOLD=${mp_threshold}
-         |  # then set them 
+         |  # then set them
          |  $awsCmd configure set default.s3.multipart_threshold $$MP_THRESHOLD
          |  $awsCmd configure set default.s3.multipart_chunksize $$chunk_size
          |
@@ -216,31 +234,36 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  do
          |    # if tries exceeded : abort
          |    if [ "$$i" -eq 6 ]; then
-         |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts. aborting"
-         |        exit 2
+         |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts."
+         |        DELOCALIZATION_FAILED=1
+         |        break
          |    fi
          |    # if destination is not a bucket : abort
-         |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then 
-         |     echo "$$destination is not an S3 path with a bucket and key. aborting"
-         |      exit 1
+         |    if ! [[ "$$destination" =~ s3://([^/]+)/(.+) ]]; then 
+         |     echo "$$destination is not an S3 path with a bucket and key."
+         |      DELOCALIZATION_FAILED=1
+         |      break
          |    fi
          |    # copy ok or try again.
          |    if [[ -d "$$local_path" ]]; then
-         |       # make sure to strip the trailing / in destination 
+         |       # make sure to strip the trailing / in destination
          |       destination=$${destination%/}
          |       # glob directory. do recursive copy
-         |       $awsCmd s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" || 
+         |       $awsCmd s3 cp --no-progress "$$local_path" "$$destination" --recursive --exclude "cromwell_glob_control_file" || 
          |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
-         |       # check integrity for each of the files
-         |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
-         |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE || 
+         |       # check integrity for each of the files (allow spaces)
+         |       SAVEIFS="$$IFS"
+         |       IFS=$$'\n'
+         |       for FILE in $$(cd "$$local_path" ; ls | grep -v cromwell_glob_control_file); do
+         |           _check_data_integrity "$$local_path/$$FILE" "$$destination/$$FILE" || 
          |               { echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2; }
          |       done
+         |       IFS="$$SAVEIFS"
          |    else 
          |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" || 
          |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
          |      # check content length for data integrity
-         |      _check_data_integrity $$local_path $$destination || 
+         |      _check_data_integrity "$$local_path" "$$destination" || 
          |         { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    fi
          |    # copy succeeded
@@ -249,11 +272,11 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |}
          |
          |function _get_multipart_chunk_size() {
-         |  local file_path=$$1
+         |  local file_path="$$1"
          |  # file size
-         |  file_size=$$(stat --printf="%s" $$file_path) 
+         |  file_size=$$(stat --printf="%s" "$$file_path") 
          |  # chunk_size : you can have at most 10K parts with at least one 5MB part
-         |  # this reflects the formula in s3-copy commands of cromwell (S3FileSystemProvider.java) 
+         |  # this reflects the formula in s3-copy commands of cromwell (S3FileSystemProvider.java)
          |  #   => long partSize = Math.max((objectSize / 10000L) + 1, 5 * 1024 * 1024);
          |  a=$$(( ( file_size / 10000) + 1 ))
          |  b=$$(( 5 * 1024 * 1024 ))
@@ -262,42 +285,95 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |}
          |
          |function _check_data_integrity() {
-         |  local local_path=$$1
-         |  local s3_path=$$2
+         |  local local_path="$$1"
+         |  local s3_path="$$2"
          |  
          |  # remote : use content_length
-         |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then 
+         |  if [[ "$$s3_path" =~ s3://([^/]+)/(.+) ]]; then 
          |        bucket="$${BASH_REMATCH[1]}"
          |        key="$${BASH_REMATCH[2]}"
          |  else
          |      # this is already checked in the caller function
-         |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+         |      echo "$$s3_path is not an S3 path with a bucket and key."
          |      exit 1
          |  fi
-         |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
-         |        { echo "Attempt to get head of object failed for $$s3_path." && return 1 ; }
+         |  s3_content_length=$$($awsCmd s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') ||
+         |        { echo "Attempt to get head of object failed for $$s3_path." && return 1; }
          |  # local
-         |  local_content_length=$$(LC_ALL=C ls -dnL -- "$$local_path" | awk '{print $$5; exit}' ) || 
-         |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }   
+         |  local_content_length=$$(LC_ALL=C ls -dnL -- "$$local_path" | awk '{print $$5; exit}' ) ||
+         |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }
          |  # compare
          |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
          |       true
          |  else
-         |       false  
+         |       false
+         |  fi
+         |}
+         |
+         |# function to add tags to instance ands volumes
+         |function _add_tags() {
+         |  local WFID="${workflowId}"
+         |  local TASKID="${taskId}"
+         |  local WFNAME="${workflowName}"
+         |  # see cloud-init docs for how to get instance-id
+         |  INSTANCE_ID=$$(cat /var/lib/cloud/data/instance-id)
+         |  VOLUME_IDS=$$($awsCmd ec2 describe-volumes --filters Name=attachment.instance-id,Values=$$INSTANCE_ID --query 'Volumes[].VolumeId' --output text)
+         |  echo " - Tagging instance $$INSTANCE_ID"
+         |  # add tags. if tag key exists, append tag if value not in comma seperated list yet. 
+         |  # info : tags wfid, taskID cannot have spaces by design. wfName does not allow spaces in WDL spec. 
+         |  WFIDS=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$INSTANCE_ID" "Name=key,Values=cromwell-root-workflow-id" --query 'Tags[].Value' --output text) $$WFID)
+         |  TASKIDS=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$INSTANCE_ID" "Name=key,Values=cromwell-task-id" --query 'Tags[].Value' --output text) $$TASKID)
+         |  WFNAMES=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$INSTANCE_ID" "Name=key,Values=cromwell-root-workflow-name" --query 'Tags[].Value' --output text) $$WFNAME)
+         |  $awsCmd ec2 create-tags --resources $$INSTANCE_ID --tags Key=cromwell-root-workflow-id,Value="$$WFIDS" Key=cromwell-task-id,Value="$$TASKIDS" Key=cromwell-root-workflow-name,Value="$$WFNAMES"
+         |  for VOLUME_ID in $$VOLUME_IDS; do
+         |     echo " - Tagging volume $$VOLUME_ID"
+         |     WFIDS=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$VOLUME_ID" "Name=key,Values=cromwell-root-workflow-id" --query 'Tags[].Value' --output text) $$WFID)
+         |     TASKIDS=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$VOLUME_ID" "Name=key,Values=cromwell-task-id" --query 'Tags[].Value' --output text) $$TASKID)
+         |     WFNAMES=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$VOLUME_ID" "Name=key,Values=cromwell-root-workflow-name" --query 'Tags[].Value' --output text) $$WFNAME)
+         |     $awsCmd ec2 create-tags --resources $$VOLUME_ID --tags Key=cromwell-root-workflow-id,Value="$$WFIDS" Key=cromwell-task-id,Value="$$TASKIDS" Key=cromwell-root-workflow-name,Value="$$WFNAMES"
+         |  done
+         |}
+         |
+         |# function to combine tags into a comma separated list of unique values, trim to 256 characters
+         |function _combine_tags() {
+         |  local TAGS=$$1
+         |  local NEW_TAG=$$2
+         |  if [[ -z "$$TAGS" ]]; then
+         |    # first tag
+         |    echo "$$NEW_TAG"
+         |  elif [[ "$$TAGS" = *$$NEW_TAG* ]]; then
+         |    # tag already exists
+         |    echo "$$TAGS"
+         |  else
+         |    # combine, trim to 256 characters
+         |    echo "$$TAGS;$$NEW_TAG" | cut -c1-256
          |  fi
          |}
          |
          |{
          |set -e
+         |# tag instance and volumes to ensure tags are present in case of failure:
+         |if [[ "${doTagging}" == "true" ]]; then
+         |  echo "*** TAGGING RESOURCES ***"
+         |  _add_tags
+         |fi 
+         |
          |echo '*** LOCALIZING INPUTS ***'
          |if [ ! -d $workDir ]; then mkdir $workDir && chmod 777 $workDir; fi
          |cd $workDir
+         |# make sure localization completes successfully
+         |LOCALIZATION_FAILED=0
          |$inputCopyCommand
-         |echo '*** COMPLETED LOCALIZATION ***'
+         |if [[ $$LOCALIZATION_FAILED -eq 1 ]]; then
+         |  echo '*** LOCALIZATION FAILED ***'
+         |  exit 1
+         |else 
+         |  echo '*** COMPLETED LOCALIZATION ***'
+         |fi
          |set +e
          |}
          |""".stripMargin
-
+    
     // the paths of the stdOut and stdErr
     val stdOut = dockerStdout.replace("/cromwell_root", workDir)
     val stdErr = dockerStderr.replace("/cromwell_root", workDir)
@@ -322,20 +398,23 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                     Log.debug("delocalization on EFS is enabled")
                     Log.debug(s"Delocalizing $globDirectory to $s3GlobOutDirectory\n")
                     s"""
-                        |touch ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}
-                        |_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}
-                        |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi
+                        |touch "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}"
+                        |_s3_delocalize_with_retry "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" "${output.s3key}"
+                        |if [ -e $globDirectory ]; then _s3_delocalize_with_retry "$globDirectory" "$s3GlobOutDirectory" ; fi
                         |""".stripMargin
                 } else {
                     
                     // check file for existence
                     s"""
                         |# test the glob list
-                        |test -e ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && exit 1)
+                        |test -e "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && DELOCALIZATION_FAILED=1)
                         |# test individual files.
-                        |for F in $$(cat ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}); do
-                        |   test -e "${globDirectory}/$$F" || (echo 'globbed file: "${globDirectory}/$$F" does not exist' && exit 1)
+                        |SAVEIFS="$$IFS"
+                        |IFS=$$'\n'
+                        |for F in $$(cat "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}"); do
+                        |   test -e "${globDirectory}/$$F" || (echo 'globbed file: "${globDirectory}/$$F" does not exist' && DELOCALIZATION_FAILED=1 && break)
                         |done
+                        |IFS="$$SAVEIFS"
                         |"""
                 }
            // need to make md5sum? 
@@ -345,15 +424,15 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                     s"""
                         |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
                         |   # the glob list
-                        |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && exit 1 ); 
+                        |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && DELOCALIZATION_FAILED=1 ); 
                         |   # globbed files, using specified number of cpus for parallel processing.
-                        |   cat ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} | xargs -I% -P${runtimeAttributes.cpu.##.toString} bash -c "md5sum ${globDirectory}/% > ${globDirectory}/%.md5"
+                        SAVEIFS="$$IFS"
+                        |IFS=$$'\n'
+                        |   cat "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" | xargs -I% -P${runtimeAttributes.cpu.##.toString} bash -c "md5sum ${globDirectory}/% > ${globDirectory}/%.md5"
                         |fi
+                        |IFS="$$SAVEIFS"
                         |""".stripMargin 
-                } else {
-                    Log.debug("MD5 not enabled: "+efsMakeMD5.get.toString())
-                    ""
-                }
+                } 
            // return combined result
            s"""
           |${test_cmd}
@@ -363,61 +442,60 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
           // default delocalization command.
           Log.debug(s"Delocalize from ${output.name} to ${output.s3key}\n")
           s"""
-             |touch ${output.name}
-             |_s3_delocalize_with_retry ${output.name} ${output.s3key}
-             |if [ -e $globDirectory ]; then _s3_delocalize_with_retry $globDirectory $s3GlobOutDirectory ; fi""".stripMargin
+             |touch "${output.name}"
+             |_s3_delocalize_with_retry "${output.name}" "${output.s3key}"
+             |if [ -e "$globDirectory" ]; then _s3_delocalize_with_retry "$globDirectory" "$s3GlobOutDirectory" ; fi""".stripMargin
         }
 
       // files on /cromwell/ working dir must be delocalized
       case output: AwsBatchFileOutput if output.s3key.startsWith("s3://") && output.mount.mountPoint.pathAsString == AwsBatchWorkingDisk.MountPoint.pathAsString =>
         //output is on working disk mount
         Log.debug("output Data on working disk mount" + output.local.pathAsString)
-        s"""_s3_delocalize_with_retry $workDir/${output.local.pathAsString} ${output.s3key}""".stripMargin
+        s"""_s3_delocalize_with_retry "$workDir/${output.local.pathAsString}" "${output.s3key}" """.stripMargin
 
       // file(name (full path), s3key (delocalized path), local (file basename), mount (disk details))
-      // files on EFS mounts are optionally delocalized. 
-      case output: AwsBatchFileOutput if efsMntPoint.isDefined && output.mount.mountPoint.pathAsString == efsMntPoint.get =>  
+      // files on EFS mounts are optionally delocalized.
+      case output: AwsBatchFileOutput if efsMntPoint.isDefined && output.mount.mountPoint.pathAsString == efsMntPoint.get =>
         Log.debug("EFS output file detected: "+ output.s3key + s" / ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}")
         // EFS located file : test existence or delocalize.
         var test_cmd = ""
         if (efsDelocalize.isDefined && efsDelocalize.getOrElse(false)) {
             Log.debug("efs-delocalization enabled")
-            test_cmd = s"_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
+            test_cmd = s"""_s3_delocalize_with_retry "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" "${output.s3key}" """.stripMargin
         } else {
             Log.debug("efs-delocalization disabled")
             // check file for existence
-            test_cmd = s"test -e ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && exit 1)"
+            test_cmd = s"""test -e "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" || (echo 'output file: ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} does not exist' && DELOCALIZATION_FAILED=1)""".stripMargin
         }
-        // need to make md5sum? 
+        // need to make md5sum?
         var md5_cmd = ""
         if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
             Log.debug("Add cmd to create MD5 sibling.")
             md5_cmd = s"""
                             |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
-                            |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && exit 1 ); 
+                            |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && DELOCALIZATION_FAILED=1 ); 
                             |fi
-                            |""".stripMargin 
+                            |""".stripMargin
         } else {
-            Log.debug("MD5 not enabled: "+efsMakeMD5.get.toString())
             md5_cmd = ""
-        } 
+        }
         // return combined result
         s"""
           |${test_cmd}
           |${md5_cmd}
           | """.stripMargin
-      
+
       case output: AwsBatchFileOutput =>
         //output on a different mount
         Log.debug("output data on other mount")
         Log.debug(output.toString)
-        s"_s3_delocalize_with_retry ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString} ${output.s3key}"
+        s"""_s3_delocalize_with_retry "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" "${output.s3key}" """.stripMargin
       case _ => ""
     }.mkString("\n") + "\n" +
       s"""
-         |if [ -f $workDir/${jobPaths.returnCodeFilename} ]; then _s3_delocalize_with_retry $workDir/${jobPaths.returnCodeFilename} ${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename} ; fi
-         |if [ -f $stdErr ]; then _s3_delocalize_with_retry $stdErr ${jobPaths.standardPaths.error.pathAsString}; fi
-         |if [ -f $stdOut ]; then _s3_delocalize_with_retry $stdOut ${jobPaths.standardPaths.output.pathAsString}; fi
+         |if [ -f "$workDir/${jobPaths.returnCodeFilename}" ]; then _s3_delocalize_with_retry "$workDir/${jobPaths.returnCodeFilename}" "${jobPaths.callRoot.pathAsString}/${jobPaths.returnCodeFilename}" ; fi
+         |if [ -f "$stdErr" ]; then _s3_delocalize_with_retry "$stdErr" "${jobPaths.standardPaths.error.pathAsString}"; fi
+         |if [ -f "$stdOut" ]; then _s3_delocalize_with_retry "$stdOut" "${jobPaths.standardPaths.output.pathAsString}"; fi
          |""".stripMargin
 
 
@@ -426,9 +504,22 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
       s"""
          |{
          |set -e
+         |# (re-)add tags to include added volumes:
+         |if [[ "${doTagging}" == "true" ]]; then
+         |  echo "*** TAGGING RESOURCES ***"
+         |  _add_tags
+         |fi 
+         |
          |echo '*** DELOCALIZING OUTPUTS ***'
+         |DELOCALIZATION_FAILED=0
          |$outputCopyCommand
-         |echo '*** COMPLETED DELOCALIZATION ***'
+         |if [[ $$DELOCALIZATION_FAILED -eq 1 ]]; then
+         |  echo '*** DELOCALIZATION FAILED ***'
+         |  echo '*** EXITING WITH RETURN CODE 1***'
+         |  exit 1
+         |else
+         |  echo '*** COMPLETED DELOCALIZATION ***'
+         |fi
          |echo '*** EXITING WITH RETURN CODE ***'
          |rc=$$(head -n 1 $workDir/${jobPaths.returnCodeFilename})
          |echo $$rc
@@ -474,30 +565,55 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     //calls the client to submit the job
     def callClient(definitionArn: String, awsBatchAttributes: AwsBatchAttributes): Aws[F, SubmitJobResponse] = {
 
+      val workflowId = jobDescriptor.workflowDescriptor.id.toString
+      val workflowName = jobDescriptor.workflowDescriptor.callable.name.toString
+      val rootworkflowId = jobDescriptor.workflowDescriptor.rootWorkflowId.toString
       Log.debug(s"Submitting taskId: $taskId, job definition : $definitionArn, script: $batch_script")
-      Log.info(s"Submitting taskId: $taskId, script: $batch_script")
-
+      Log.info(s"Submitting taskId: $rootworkflowId::$taskId, script: $batch_script")
+      
+      //provide job environment variables, vcpu and memory
+      var resourceRequirements: Seq[ResourceRequirement] = Seq(
+        ResourceRequirement.builder().`type`(ResourceType.VCPU).value(runtimeAttributes.cpu.##.toString).build(),
+        ResourceRequirement.builder().`type`(ResourceType.MEMORY).value(runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString).build()
+      )
+
+      if (runtimeAttributes.gpuCount > 0) {
+        val gpuRequirement = ResourceRequirement.builder().`type`(ResourceType.GPU).value(runtimeAttributes.gpuCount.toString)
+        resourceRequirements = resourceRequirements :+ gpuRequirement.build()
+      }
+          
+      // prepare the job request
+      var submitJobRequest = SubmitJobRequest.builder()
+        .jobName(sanitize(jobDescriptor.taskCall.fullyQualifiedName))
+        .parameters(parameters.collect({ case i: AwsBatchInput => i.toStringString }).toMap.asJava)
+        //provide job environment variables, vcpu and memory
+        .containerOverrides(
+          ContainerOverrides.builder
+            .environment(
+              generateEnvironmentKVPairs(runtimeAttributes.scriptS3BucketName, scriptKeyPrefix, scriptKey): _*
+            )
+            .resourceRequirements(resourceRequirements.asJava)
+            .build()
+        )
+        .jobQueue(runtimeAttributes.queueArn)
+        .jobDefinition(definitionArn)
+      // tagging activated : add to request
+      if (tagResources.getOrElse(false)) {
+          // replace invalid characters in the tags
+          val invalidCharsPattern = "[^a-zA-Z0-9_.:/=+-@]+".r
+          val tags: Map[String,String] = Map(
+            "cromwell-workflow-name" -> invalidCharsPattern.replaceAllIn(workflowName,"_"), 
+            "cromwell-workflow-id" -> invalidCharsPattern.replaceAllIn(workflowId,"_"), 
+            "cromwell-task-id" -> invalidCharsPattern.replaceAllIn(taskId,"_"),
+            "cromwell-root-workflow-name" -> invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflow.name.toString,"_"),
+            "cromwell-root-workflow-id" -> invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflowId.toString,"_")
+            )
+          submitJobRequest = submitJobRequest.tags(tags.asJava).propagateTags(true)
+      }
+      // submit
       val submit: F[SubmitJobResponse] =
         async.delay(batchClient.submitJob(
-          SubmitJobRequest.builder()
-            .jobName(sanitize(jobDescriptor.taskCall.fullyQualifiedName))
-            .parameters(parameters.collect({ case i: AwsBatchInput => i.toStringString }).toMap.asJava)
-
-            //provide job environment variables, vcpu and memory
-            .containerOverrides(
-              ContainerOverrides.builder
-                .environment(
-                  generateEnvironmentKVPairs(runtimeAttributes.scriptS3BucketName, scriptKeyPrefix, scriptKey): _*
-                )
-                .resourceRequirements(
-                  ResourceRequirement.builder().`type`(ResourceType.VCPU).value(runtimeAttributes.cpu.##.toString).build(),
-                  ResourceRequirement.builder().`type`(ResourceType.MEMORY).value(runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString).build()
-                )
-                .build()
-            )
-            .jobQueue(runtimeAttributes.queueArn)
-            .jobDefinition(definitionArn)
-            .build
+            submitJobRequest.build
         ))
 
       ReaderT.liftF(
@@ -587,7 +703,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         fsxMntPoint = fsxMntPoint,
         efsMntPoint = efsMntPoint,
         efsMakeMD5 = efsMakeMD5,
-        efsDelocalize = efsDelocalize
+        efsDelocalize = efsDelocalize,
+        tagResources = tagResources
         )
 
       val jobDefinitionBuilder = StandardAwsBatchJobDefinitionBuilder
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index e1e5af42539..f55d3a933f7 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -34,7 +34,7 @@ package cromwell.backend.impl.aws
 import scala.collection.mutable.ListBuffer
 import cromwell.backend.BackendJobDescriptor
 import cromwell.backend.io.JobPaths
-import software.amazon.awssdk.services.batch.model.{ContainerProperties, Host, KeyValuePair, MountPoint, ResourceRequirement, ResourceType, RetryStrategy, Ulimit, Volume}
+import software.amazon.awssdk.services.batch.model.{ContainerProperties, EvaluateOnExit, Host, KeyValuePair, MountPoint, ResourceRequirement, ResourceType, RetryAction, RetryStrategy, Ulimit, Volume}
 import cromwell.backend.impl.aws.io.AwsBatchVolume
 
 import scala.jdk.CollectionConverters._
@@ -101,6 +101,12 @@ trait AwsBatchJobDefinitionBuilder {
         Volume.builder()
           .name("awsCliHome")
           .host(Host.builder().sourcePath("/usr/local/aws-cli").build())
+          .build(),
+        // the location of the instance-id on the host (set by cloud-init)
+        // https://cloudinit.readthedocs.io/en/23.2.2/reference/faq.html#data
+        Volume.builder()
+          .name("instanceId")
+          .host(Host.builder().sourcePath("/var/lib/cloud/data/instance-id").build())
           .build()
       ) ++ fsx_volumes
     }
@@ -125,7 +131,14 @@ trait AwsBatchJobDefinitionBuilder {
           .sourceVolume("awsCliHome")
           //where the aws-cli will be on the container
           .containerPath("/usr/local/aws-cli")
+          .build(),
+        // the location of the instance-id on the container, used to tag the instance
+        MountPoint.builder()
+          .readOnly(true)
+          .sourceVolume("instanceId")
+          .containerPath("/var/lib/cloud/data/instance-id")
           .build()
+
       ) ++ fsx_disks
     }
 
@@ -140,8 +153,8 @@ trait AwsBatchJobDefinitionBuilder {
       ).toList
     }
 
-    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit], efsDelocalize: Boolean, efsMakeMD5: Boolean): String = {
-      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}"
+    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit], efsDelocalize: Boolean, efsMakeMD5: Boolean, tagResources: Boolean): String = {
+      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}:${tagResources.toString}"
     }
 
     val environment = List.empty[KeyValuePair]
@@ -155,6 +168,7 @@ trait AwsBatchJobDefinitionBuilder {
     val ulimits = buildUlimits( context.runtimeAttributes.ulimits)
     val efsDelocalize = context.runtimeAttributes.efsDelocalize
     val efsMakeMD5 = context.runtimeAttributes.efsMakeMD5
+    val tagResources = context.runtimeAttributes.tagResources
 
     val containerPropsName = buildName(
       context.runtimeAttributes.dockerImage,
@@ -164,9 +178,12 @@ trait AwsBatchJobDefinitionBuilder {
       environment,
       ulimits,
       efsDelocalize,
-      efsMakeMD5
+      efsMakeMD5,
+      tagResources
     )
 
+    // To reuse job definition for gpu and gpu-runs, we will create a job definition that does not gpu requirements
+    // since aws batch does not allow you to set gpu as 0 when you dont need it. you will always need cpu and memory
     (ContainerProperties.builder()
       .image(context.runtimeAttributes.dockerImage)
       .command(packedCommand.asJava)
@@ -183,9 +200,30 @@ trait AwsBatchJobDefinitionBuilder {
 
   def retryStrategyBuilder(context: AwsBatchJobDefinitionContext): (RetryStrategy.Builder, String) = {
     // We can add here the 'evaluateOnExit' statement
-    (RetryStrategy.builder()
-      .attempts(context.runtimeAttributes.awsBatchRetryAttempts),
-     context.runtimeAttributes.awsBatchRetryAttempts.toString)
+    var builder = RetryStrategy.builder()
+      .attempts(context.runtimeAttributes.awsBatchRetryAttempts)
+
+    var evaluations: Seq[EvaluateOnExit] = Seq()
+    context.runtimeAttributes.awsBatchEvaluateOnExit.foreach(
+      (evaluate) => {
+        val evaluateBuilder = evaluate.foldLeft(EvaluateOnExit.builder()) {
+          case (acc, (k, v)) => (k.toLowerCase, v.toLowerCase) match {
+            case ("action", "retry") => acc.action(RetryAction.RETRY)
+            case ("action", "exit") => acc.action(RetryAction.EXIT)
+            case ("onexitcode", _) => acc.onExitCode(v)
+            case ("onreason", _) => acc.onReason(v)
+            case ("onstatusreason", _) => acc.onStatusReason(v)
+            case _ => acc
+          }
+        }
+        evaluations = evaluations :+ evaluateBuilder.build()
+      }
+    )
+
+    builder = builder.evaluateOnExit(evaluations.asJava)
+
+    (builder,
+     s"${context.runtimeAttributes.awsBatchRetryAttempts.toString}${context.runtimeAttributes.awsBatchEvaluateOnExit.toString}")
   }
 
 
@@ -248,7 +286,8 @@ case class AwsBatchJobDefinitionContext(
             fsxMntPoint: Option[List[String]],
             efsMntPoint: Option[String],
             efsMakeMD5: Option[Boolean],
-            efsDelocalize: Option[Boolean]
+            efsDelocalize: Option[Boolean],
+            tagResources: Option[Boolean]
             ) {
 
   override def toString: String = {
@@ -266,6 +305,7 @@ case class AwsBatchJobDefinitionContext(
       .append("efsMntPoint", efsMntPoint)
       .append("efsMakeMD5", efsMakeMD5)
       .append("efsDelocalize", efsDelocalize)
+      .append("tagResources", tagResources)
       .build
   }
 }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index 235927ab07c..456355e412c 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -44,14 +44,20 @@ import wom.RuntimeAttributesKeys
 import wom.format.MemorySize
 import wom.types._
 import wom.values._
-import com.typesafe.config.{ConfigException,ConfigValueFactory}
+import com.typesafe.config.{ConfigException, ConfigValueFactory}
 
 import scala.util.matching.Regex
 import org.slf4j.{Logger, LoggerFactory}
+import wom.RuntimeAttributesKeys.GpuKey
+
+import scala.util.{Failure, Success, Try}
+import scala.jdk.CollectionConverters._
+
 
 /**
  * Attributes that are provided to the job at runtime
  * @param cpu number of vCPU
+ * @param gpuCount number of gpu
  * @param zones the aws availability zones to run in
  * @param memory memory to allocate
  * @param disks a sequence of disk volumes
@@ -63,11 +69,14 @@ import org.slf4j.{Logger, LoggerFactory}
  * @param scriptS3BucketName the s3 bucket where the execution command or script will be written and, from there, fetched into the container and executed
  * @param fileSystem the filesystem type, default is "s3"
  * @param awsBatchRetryAttempts number of attempts that AWS Batch will retry the task if it fails
+ * @param awsBatchEvaluateOnExit Evaluate on exit strategy setting for AWS batch retry
  * @param ulimits ulimit values to be passed to the container
  * @param efsDelocalize should we delocalize efs files to s3
  * @param efsMakeMD5 should we make a sibling md5 file as part of the job 
+ * @param tagResources should we tag resources
  */
 case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
+                                     gpuCount: Int,
                                      zones: Vector[String],
                                      memory: MemorySize,
                                      disks: Seq[AwsBatchVolume],
@@ -78,10 +87,12 @@ case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      noAddress: Boolean,
                                      scriptS3BucketName: String,
                                      awsBatchRetryAttempts: Int,
+                                     awsBatchEvaluateOnExit: Vector[Map[String, String]],
                                      ulimits: Vector[Map[String, String]],
                                      efsDelocalize: Boolean,
                                      efsMakeMD5 : Boolean,
-                                     fileSystem: String= "s3")
+                                     fileSystem: String= "s3",
+                                     tagResources: Boolean = false)
 
 object AwsBatchRuntimeAttributes {
   val Log: Logger = LoggerFactory.getLogger(this.getClass)
@@ -91,9 +102,13 @@ object AwsBatchRuntimeAttributes {
 
   val awsBatchRetryAttemptsKey = "awsBatchRetryAttempts"
 
+  val awsBatchEvaluateOnExitKey = "awsBatchEvaluateOnExit"
+  private val awsBatchEvaluateOnExitDefault = WomArray(WomArrayType(WomMapType(WomStringType,WomStringType)), Vector(WomMap(Map.empty[WomValue, WomValue])))
+
+
   val awsBatchefsDelocalizeKey = "efsDelocalize"
   val awsBatchefsMakeMD5Key = "efsMakeMD5"
-
+  val tagResourcesKey = "tagResources"
   val ZonesKey = "zones"
   private val ZonesDefaultValue = WomString("us-east-1a")
 
@@ -113,6 +128,10 @@ object AwsBatchRuntimeAttributes {
   private def cpuValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] = CpuValidation.instance
     .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
+  private def gpuCountValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] = {
+    GpuCountValidation(GpuKey).withDefault(GpuCountValidation(GpuKey).configDefaultWomValue(runtimeConfig).getOrElse(WomInteger(0)))
+  }
+
   private def cpuMinValidation(runtimeConfig: Option[Config]):RuntimeAttributesValidation[Int Refined Positive] = CpuValidation.instanceMin
     .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
@@ -157,6 +176,11 @@ object AwsBatchRuntimeAttributes {
     .configDefaultWomValue(runtimeConfig).getOrElse(WomInteger(0)))
   }
 
+  def awsBatchEvaluateOnExitValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[Map[String, String]]] = {
+    AwsBatchEvaluateOnExitValidation
+      .withDefault(AwsBatchEvaluateOnExitValidation.fromConfig(runtimeConfig).getOrElse(awsBatchEvaluateOnExitDefault))
+  }
+
   private def awsBatchefsDelocalizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = {
     AwsBatchefsDelocalizeValidation(awsBatchefsDelocalizeKey).withDefault(AwsBatchefsDelocalizeValidation(awsBatchefsDelocalizeKey)
     .configDefaultWomValue(runtimeConfig).getOrElse(WomBoolean(false)))
@@ -167,6 +191,11 @@ object AwsBatchRuntimeAttributes {
     .configDefaultWomValue(runtimeConfig).getOrElse(WomBoolean(false)))
   }
 
+  private def awsBatchtagResourcesValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = {
+      AwsBatchtagResourcesValidation(AwsBatchRuntimeAttributes.tagResourcesKey).withDefault(AwsBatchtagResourcesValidation(AwsBatchRuntimeAttributes.tagResourcesKey)
+      .configDefaultWomValue(runtimeConfig).getOrElse(WomBoolean(false)))
+  }
+
   private def ulimitsValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Vector[Map[String, String]]] =
    UlimitsValidation.withDefault(UlimitsValidation.configDefaultWomValue(runtimeConfig) getOrElse UlimitsDefaultValue)
 
@@ -182,7 +211,6 @@ object AwsBatchRuntimeAttributes {
     }
     // efs disk configs is set (can be None) in configuration
     val efs_disks = configuration.efsMntPoint.getOrElse("")
-    // TODO : fsx ? 
     // additional disks optionally set as runtime attributes
     val rtc_disks = try {
         rtc.getAnyRef(AwsBatchRuntimeAttributes.DisksKey).asInstanceOf[String] // just to prevent complaints about var/val
@@ -190,19 +218,18 @@ object AwsBatchRuntimeAttributes {
         case _: ConfigException.Missing => 
            "local-disk"
     }
-    // combine and remove empty values
-    val disks = s"${efs_disks},${rtc_disks}".split(",").toSet.filterNot(_.isEmpty).mkString(",")
-    Log.debug(s"Disks: ${disks}")
+    // combine and remove empty values and remove empty values
+    val disks = s"${efs_disks},${rtc_disks}".split(",").toSet.filterNot(_.isEmpty).filterNot(_.isEmpty).mkString(",")
     val runtimeConfig = Some(rtc.withValue(AwsBatchRuntimeAttributes.DisksKey, ConfigValueFactory.fromAnyRef(disks)))
     return runtimeConfig
   }
 
   def runtimeAttributesBuilder(configuration: AwsBatchConfiguration): StandardValidatedRuntimeAttributesBuilder = {
     val runtimeConfig = aggregateDisksInRuntimeConfig(configuration)
-    
     def validationsS3backend = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
                         cpuValidation(runtimeConfig),
                         cpuMinValidation(runtimeConfig),
+                        gpuCountValidation(runtimeConfig),
                         disksValidation(runtimeConfig),
                         zonesValidation(runtimeConfig),
                         memoryValidation(runtimeConfig),
@@ -212,13 +239,16 @@ object AwsBatchRuntimeAttributes {
                         queueArnValidation(runtimeConfig),
                         scriptS3BucketNameValidation(runtimeConfig),
                         awsBatchRetryAttemptsValidation(runtimeConfig),
+                        awsBatchEvaluateOnExitValidation(runtimeConfig),
                         ulimitsValidation(runtimeConfig),
                         awsBatchefsDelocalizeValidation(runtimeConfig),
-                        awsBatchefsMakeMD5Validation(runtimeConfig)
+                        awsBatchefsMakeMD5Validation(runtimeConfig),
+                        awsBatchtagResourcesValidation(runtimeConfig)
                       )
    def validationsLocalBackend  = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
       cpuValidation(runtimeConfig),
       cpuMinValidation(runtimeConfig),
+      gpuCountValidation(runtimeConfig),
       disksValidation(runtimeConfig),
       zonesValidation(runtimeConfig),
       memoryValidation(runtimeConfig),
@@ -227,9 +257,11 @@ object AwsBatchRuntimeAttributes {
       dockerValidation,
       queueArnValidation(runtimeConfig),
       awsBatchRetryAttemptsValidation(runtimeConfig),
+      awsBatchEvaluateOnExitValidation(runtimeConfig),
       ulimitsValidation(runtimeConfig),
       awsBatchefsDelocalizeValidation(runtimeConfig),
-      awsBatchefsMakeMD5Validation(runtimeConfig)
+      awsBatchefsMakeMD5Validation(runtimeConfig),
+      awsBatchtagResourcesValidation(runtimeConfig)
     )
 
     configuration.fileSystem match  {
@@ -241,6 +273,7 @@ object AwsBatchRuntimeAttributes {
 
   def apply(validatedRuntimeAttributes: ValidatedRuntimeAttributes, runtimeAttrsConfig: Option[Config], fileSystem:String): AwsBatchRuntimeAttributes = {
     val cpu: Int Refined Positive = RuntimeAttributesValidation.extract(cpuValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val gpuCount: Int = RuntimeAttributesValidation.extract(gpuCountValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val zones: Vector[String] = RuntimeAttributesValidation.extract(ZonesValidation, validatedRuntimeAttributes)
     val memory: MemorySize = RuntimeAttributesValidation.extract(memoryValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val disks: Seq[AwsBatchVolume] = RuntimeAttributesValidation.extract(disksValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
@@ -254,12 +287,15 @@ object AwsBatchRuntimeAttributes {
        case _ => ""
     }
     val awsBatchRetryAttempts: Int = RuntimeAttributesValidation.extract(awsBatchRetryAttemptsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val awsBatchEvaluateOnExit: Vector[Map[String, String]] = RuntimeAttributesValidation.extract(awsBatchEvaluateOnExitValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+
     val ulimits: Vector[Map[String, String]] = RuntimeAttributesValidation.extract(ulimitsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val efsDelocalize: Boolean = RuntimeAttributesValidation.extract(awsBatchefsDelocalizeValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
     val efsMakeMD5: Boolean = RuntimeAttributesValidation.extract(awsBatchefsMakeMD5Validation(runtimeAttrsConfig),validatedRuntimeAttributes)
-    
+    val tagResources: Boolean = RuntimeAttributesValidation.extract(awsBatchtagResourcesValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
     new AwsBatchRuntimeAttributes(
       cpu,
+      gpuCount,
       zones,
       memory,
       disks,
@@ -270,10 +306,12 @@ object AwsBatchRuntimeAttributes {
       noAddress,
       scriptS3BucketName,
       awsBatchRetryAttempts,
+      awsBatchEvaluateOnExit,
       ulimits,
       efsDelocalize,
       efsMakeMD5,
-      fileSystem
+      fileSystem,
+      tagResources
     )
   }
 }
@@ -452,6 +490,23 @@ object DisksValidation extends RuntimeAttributesValidation[Seq[AwsBatchVolume]]
     s"Expecting $key runtime attribute to be a comma separated String or Array[String]"
 }
 
+object GpuCountValidation {
+  def apply(key: String): GpuCountValidation = new GpuCountValidation(key)
+}
+
+class GpuCountValidation(key: String) extends IntRuntimeAttributesValidation(key) {
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[Int]] = {
+    case womValue if WomIntegerType.coerceRawValue(womValue).isSuccess =>
+      WomIntegerType.coerceRawValue(womValue).get match {
+        case WomInteger(value) =>
+          if (value.toInt < 0)
+            s"Expecting $key runtime attribute value greater than or equal to 0".invalidNel
+          else
+            value.toInt.validNel
+      }
+  }
+}
+
 object AwsBatchRetryAttemptsValidation {
   def apply(key: String): AwsBatchRetryAttemptsValidation = new AwsBatchRetryAttemptsValidation(key)
 }
@@ -473,6 +528,115 @@ class AwsBatchRetryAttemptsValidation(key: String) extends IntRuntimeAttributesV
   override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Integer"
 }
 
+object AwsBatchEvaluateOnExitValidation extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
+
+  val requiredKey = "action"
+  private val acceptedKeys = Set(requiredKey, "onExitCode", "onReason", "onStatusReason")
+
+
+  def fromConfig(runtimeConfig: Option[Config]): Option[WomValue]= {
+    val config = runtimeConfig match {
+      case Some(value) => Try(value.getObjectList(key)) match {
+        case Failure(_) => None
+        case Success(value) => Some(value.asScala.map {
+          _.unwrapped().asScala.toMap
+        }.toList)
+      }
+      case _ => None
+    }
+
+    config match {
+      case Some(value) => Some(AwsBatchEvaluateOnExitValidation
+        .coercion collectFirst {
+        case womType if womType.coerceRawValue(value).isSuccess => womType.coerceRawValue(value).get
+      } getOrElse {
+        BadDefaultAttribute(WomString(value.toString))
+      })
+      case None => None
+    }
+  }
+
+  override def coercion: Iterable[WomType] = {
+    Set(WomStringType, WomArrayType(WomMapType(WomStringType, WomStringType)))
+  }
+
+  override protected def validateValue: PartialFunction[WomValue, ErrorOr[Vector[Map[String, String]]]] = {
+    case WomArray(womType, value)
+      if womType.memberType == WomMapType(WomStringType, WomStringType) =>
+      check_maps(value.toVector)
+    case WomMap(_, _) => "!!! ERROR1".invalidNel
+  }
+
+  private def check_maps(
+                          maps: Vector[WomValue]
+                        ): ErrorOr[Vector[Map[String, String]]] = {
+    val entryNels: Vector[ErrorOr[Map[String, String]]] = maps.map {
+      case WomMap(_, value) => check_keys(value)
+      case _ => "!!! ERROR2".invalidNel
+    }
+    val sequenced: ErrorOr[Vector[Map[String, String]]] = sequenceNels(
+      entryNels
+    )
+    sequenced
+  }
+
+  private def validateActionKey(dict: Map[WomValue, WomValue]): ErrorOr[Map[String, String]] = {
+    val validCondition = Set("retry", "exit")
+    val convertedMap = dict
+      .map { case (WomString(k), WomString(v)) =>
+        (k, v)
+        // case _ => "!!! ERROR3".invalidNel
+      }
+    if (convertedMap.exists {
+      case (key, value) => key.toLowerCase == requiredKey && validCondition.contains(value.toLowerCase)
+    }) {
+      convertedMap.validNel
+    }
+    else {
+      s"Missing or invalid $requiredKey key/value for runtime attribute: $key. Refer to https://docs.aws.amazon.com/batch/latest/APIReference/API_RetryStrategy.html".invalidNel
+    }
+  }
+
+  private def check_keys(
+                          dict: Map[WomValue, WomValue]
+                        ): ErrorOr[Map[String, String]] = {
+    val map_keys = dict.keySet.map(_.valueString.toLowerCase)
+    val unrecognizedKeys =
+      map_keys.diff(acceptedKeys.map(x => x.toLowerCase))
+    if (!dict.nonEmpty) {
+      Map.empty[String, String].validNel
+    }
+    else if (unrecognizedKeys.nonEmpty) {
+      s"Invalid keys in $key runtime attribute: $unrecognizedKeys. Only $acceptedKeys are accepted. Refer to https://docs.aws.amazon.com/batch/latest/APIReference/API_RetryStrategy.html".invalidNel
+    }
+    else {
+      validateActionKey(dict)
+    }
+  }
+
+  private def sequenceNels(
+                            nels: Vector[ErrorOr[Map[String, String]]]
+                          ): ErrorOr[Vector[Map[String, String]]] = {
+    val emptyNel: ErrorOr[Vector[Map[String, String]]] =
+      Vector.empty[Map[String, String]].validNel
+    val seqNel: ErrorOr[Vector[Map[String, String]]] =
+      nels.foldLeft(emptyNel) { (acc, v) =>
+        (acc, v) mapN { (a, v) => a :+ v }
+      }
+    seqNel
+  }
+
+
+  override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be defined"
+
+  /**
+   * Returns the key of the runtime attribute.
+   *
+   * @return The key of the runtime attribute.
+   */
+  override def key: String = AwsBatchRuntimeAttributes.awsBatchEvaluateOnExitKey
+}
+
 object AwsBatchefsDelocalizeValidation {
   def apply(key: String): AwsBatchefsDelocalizeValidation = new AwsBatchefsDelocalizeValidation(key)
 }
@@ -491,6 +655,14 @@ class AwsBatchefsMakeMD5Validation(key: String) extends BooleanRuntimeAttributes
   override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Boolean"
 }
 
+object AwsBatchtagResourcesValidation {
+  def apply(key: String): AwsBatchtagResourcesValidation = new AwsBatchtagResourcesValidation(key)
+}
+
+class AwsBatchtagResourcesValidation(key: String) extends BooleanRuntimeAttributesValidation(key) {
+  
+  override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be a Boolean"
+}   
 
 object UlimitsValidation
     extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
@@ -531,7 +703,7 @@ object UlimitsValidation
       accepted_keys.diff(map_keys) union map_keys.diff(accepted_keys)
 
     if (!dict.nonEmpty){
-      Map.empty[String, String].validNel  
+      Map.empty[String, String].validNel
     }else if (unrecognizedKeys.nonEmpty) {
       s"Invalid keys in $key runtime attribute. Refer to 'ulimits' section on https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#containerProperties".invalidNel
     } else {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 613607da42a..4b1fd62da2d 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -75,6 +75,37 @@ runtime {
 }
 ```
 
+### `awsBatchEvaluteOnExit`
+
+*Default: _[]_* - will always retry 
+
+This runtime attribute sets the `evaluateOnExit` for [*AWS Batch Automated Job Retries*](https://docs.aws.amazon.com/batch/latest/userguide/job_retries.html) and specify the retry condition for a failed job.
+
+This configuration works with `awsBatchRetryAttempts` and is useful if you only want to retry on certain failures. 
+
+For instance, if you will only like to retry during spot termination.
+
+```
+runtime {
+    awsBatchEvaluateOnExit: [
+        {  
+            Action: "RETRY",
+            onStatusReason: "Host EC2*"
+        },
+        {
+            onReason : "*"
+            Action: "EXIT"
+        }
+    ]
+}
+```
+
+For more information on the batch retry strategy, please refer to:
+
+* General Doc: [userguide/job_retries.html](https://docs.aws.amazon.com/batch/latest/userguide/job_retries.html)
+* Blog: [Introducing retry strategies](https://aws.amazon.com/blogs/compute/introducing-retry-strategies-for-aws-batch/)
+
+
 ### `ulimits`
 
 *Default: _empty_*
@@ -110,6 +141,34 @@ Parameter description:
   - Type: Integer
   - Required: Yes, when `ulimits` is used.
 
+### GPU support 
+
+Tasks can request GPU by setting `gpuCount` in the task runtime attribute. For instance:
+```
+task gpu_queue_task {
+    input {
+        ...
+    }
+
+    command <<< 
+        ...
+    >>>
+    output {}
+
+    runtime {
+        queueArn: "arn:aws:batch:us-west-2:12345678910:job-queue/quekx-gpu-queue"
+        docker: "xxxx"
+        maxRetries: 1
+        cpu: "1"
+        gpuCount: 1
+        memory: "2 GB"
+    }
+}
+```
+the gpuCount value will be passed to AWS Batch as part of [resourceRequirements](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#ContainerProperties-resourceRequirements).
+You will need to use this feature in conjunction with a aws queue that has GPU instances (see [compute-environment](/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md#compute-environment) for more inforamtion)
+
+
 ### Call Caching with ECR private
 
 AWS ECR is a private container registry, for which access can be regulated using IAM. Call caching is possible by setting up the following configuration:
@@ -227,6 +286,7 @@ In the AWS backend those notifications can be send to **SNS Topic** or **EventBr
 #### AWS SNS
 
 1. Create an SNS topic, add the following to your `cromwell.conf` file and replace `topicArn` with the topic's ARN you just created:
+2. By default, all cromwell events will be publish to sns. Set `publishStatusOnly = true` if you only publish events that are `status` updates.
 
 ```
 services {
@@ -241,12 +301,13 @@ services {
                 }]
                 region = "us-east-1"
                 topicArn = "<topicARN>"
+                publishStatusOnly = true
             }
         }
     }
 }
 ```
-2. Add `sns:Publish` IAM policy to your Cromwell server IAM role. 
+3. Add `sns:Publish` IAM policy to your Cromwell server IAM role. 
 
 #### AWS EventBridge
 
@@ -474,7 +535,37 @@ task task_three {
 }
 ```
 
+#### TAGGING RESOURCES
+AWS Batch tags jobs and, if configured in the compute environment, instances and volumes with generic tags to track costs.  These tags typically include the job-queue name. To allow more detailed cost tracking, it is possible to enable tagging instances and connected volumes with the following information : 
+
+- *cromwell-workflow-name* : the top-level name of the submitted WDL (eg "workflow myWorkflow {...}")
+- *cromwell-workflow-id* : the identifier assigned to the workflow inside cromwell (eg "2443daac-c232-4e0a-920d-fbf53273e9c5")
+- *cromwell-task-id* : A string consisting of "<workflowName>.<taskName>-<shardIdx>-<attempt>"
+
+In case the same instance is reused for multiple tasks, unique tag values are concatenated up until a maximal length of 255 characters. For example, an instance used for two identical workflows, might be tagged as followes: 
 
+- cromwell-workflow-name : myWorkflow
+- cromwell-workflow-id : 2443daac-c232-4e0a-920d-fbf53273e9c5;df19029e-cc02-41d5-a26d-8d30c0ab05cb
+- cromwell-task-id : myWorkflow.myTask-None-1
+
+To enable tagging, add "tagResources = true" to the default-runtime-attributes section of your configuration: 
+
+```
+backend {
+    providers {
+        AWSBatch {
+            config{
+                
+                default-runtime-attributes {
+                    // enable detailed tagging
+                    tagResources = true
+                }
+            }
+        }
+    }
+}
+
+```
 
 
 AWS Batch
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
index 1706f55370f..ffee6be0918 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
@@ -31,13 +31,6 @@
 package cromwell.backend.impl.aws.io
 
 
-//import cats.implicits._
-//import common.validation.ErrorOr.ErrorOr
-//import cromwell.backend.BackendJobDescriptor
-//import cromwell.core.CallContext
-//import cromwell.core.io.AsyncIoFunctions
-//import wom.expression.{IoFunctionSet, IoFunctionSetAdapter}
-//import wom.graph.CommandCallNode
 import wom.values._
 import cromwell.backend.io._
 import cromwell.backend.standard._
@@ -45,8 +38,6 @@ import scala.concurrent.Future
 import java.nio.file.Paths
 import cromwell.core.path.DefaultPathBuilder
 
-//import cromwell.backend.impl.aws.AwsBatchAttributes
-//import cromwell.backend.impl.aws._
 
 trait AwsBatchGlobFunctions extends GlobFunctions {
     
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
index ba2e5580b3f..98af4f00282 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
@@ -32,7 +32,6 @@
 package cromwell.backend.impl.aws
 
 import java.util.UUID
-
 import akka.actor.{ActorRef, Props}
 import akka.testkit.{ImplicitSender, TestActorRef, TestDuration}
 import common.collections.EnhancedCollections._
@@ -41,7 +40,7 @@ import cromwell.backend._
 import cromwell.backend.async.{ExecutionHandle, FailedNonRetryableExecutionHandle, PendingExecutionHandle}
 import cromwell.backend.impl.aws.AwsBatchAsyncBackendJobExecutionActor.AwsBatchPendingExecutionHandle
 import cromwell.backend.impl.aws.RunStatus.UnsuccessfulRunStatus
-import cromwell.backend.impl.aws.io.AwsBatchWorkingDisk
+import cromwell.backend.impl.aws.io.{AwsBatchWorkflowPaths, AwsBatchWorkingDisk}
 import cromwell.backend.io.JobPathsSpecHelper._
 import cromwell.backend.standard.{DefaultStandardAsyncExecutionActorParams, StandardAsyncExecutionActorParams, StandardAsyncJob, StandardExpressionFunctions, StandardExpressionFunctionsParams}
 import cromwell.cloudsupport.aws.s3.S3Storage
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchCallPathsSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchCallPathsSpec.scala
index b250ab12ed4..131114c8921 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchCallPathsSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchCallPathsSpec.scala
@@ -33,7 +33,8 @@ package cromwell.backend.impl.aws
 
 import common.collections.EnhancedCollections._
 import cromwell.backend.BackendSpec
-import cromwell.backend.io.JobPathsSpecHelper._
+import cromwell.backend.impl.aws.io.{AwsBatchJobPaths, AwsBatchWorkflowPaths}
+import cromwell.backend.io.JobPathsSpecHelper.{EnhancedJobPaths, EnhancedCallContext}
 import org.scalatest.flatspec.AnyFlatSpecLike
 import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider
 import cromwell.core.Tags.AwsTest
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index 0e7172343cd..61914626ed7 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -32,9 +32,9 @@
 package cromwell.backend.impl.aws
 
 import common.collections.EnhancedCollections._
-import cromwell.backend.{BackendJobDescriptorKey, BackendWorkflowDescriptor}
+import cromwell.backend.{BackendJobDescriptor, BackendJobDescriptorKey, BackendWorkflowDescriptor}
 import cromwell.backend.BackendSpec._
-import cromwell.backend.impl.aws.io.AwsBatchWorkingDisk
+import cromwell.backend.impl.aws.io.{AwsBatchJobPaths, AwsBatchWorkflowPaths, AwsBatchWorkingDisk}
 import cromwell.backend.validation.ContinueOnReturnCodeFlag
 import cromwell.core.path.DefaultPathBuilder
 import cromwell.core.TestKitSuite
@@ -46,12 +46,14 @@ import org.scalatest.PrivateMethodTester
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider
-import software.amazon.awssdk.services.batch.model.{ContainerDetail, JobDetail, KeyValuePair}
+import software.amazon.awssdk.services.batch.model.{ContainerDetail, EvaluateOnExit, JobDetail, KeyValuePair, ResourceRequirement, RetryAction, RetryStrategy}
 import spray.json.{JsObject, JsString}
 import wdl4s.parser.MemoryUnit
 import wom.format.MemorySize
 import wom.graph.CommandCallNode
 
+import scala.jdk.javaapi.CollectionConverters
+
 class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with PrivateMethodTester {
   import AwsBatchTestConfig._
 
@@ -100,6 +102,8 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
 
   val call: CommandCallNode = workFlowDescriptor.callable.taskCallNodes.head
   val jobKey: BackendJobDescriptorKey = BackendJobDescriptorKey(call, None, 1)
+  val jobDescriptor: BackendJobDescriptor = BackendJobDescriptor(null, null, null, Map.empty, null, null, null)
+
   val jobPaths: AwsBatchJobPaths = AwsBatchJobPaths(workflowPaths, jobKey)
   val s3Inputs: Set[AwsBatchInput] = Set(AwsBatchFileInput("foo", "s3://bucket/foo", DefaultPathBuilder.get("foo"), AwsBatchWorkingDisk()))
   val s3Outputs: Set[AwsBatchFileOutput] = Set(AwsBatchFileOutput("baa", "s3://bucket/somewhere/baa", DefaultPathBuilder.get("baa"), AwsBatchWorkingDisk()))
@@ -107,6 +111,7 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
   val cpu: Int Refined Positive = 2
   val runtimeAttributes: AwsBatchRuntimeAttributes = new AwsBatchRuntimeAttributes(
       cpu = cpu,
+      gpuCount = 0,
       zones = Vector("us-east-1"),
       memory = MemorySize(2.0, MemoryUnit.GB),
       disks = Seq.empty,
@@ -117,9 +122,19 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
       noAddress = false,
       scriptS3BucketName = "script-bucket",
       awsBatchRetryAttempts = 1,
+      awsBatchEvaluateOnExit = Vector(Map.empty[String, String]),
       ulimits = Vector(Map.empty[String, String]),
+      efsDelocalize = false,
+      efsMakeMD5 = false,
       fileSystem = "s3")
 
+  val batchJobDefintion = AwsBatchJobDefinitionContext(
+    runtimeAttributes = runtimeAttributes,
+    commandText = "", dockerRcPath = "", dockerStdoutPath = "", dockerStderrPath = "", jobDescriptor = jobDescriptor
+    , jobPaths = jobPaths, inputs = Set(), outputs = Set(), fsxMntPoint = None, None, None, None
+
+  )
+
   val containerDetail: ContainerDetail = ContainerDetail.builder().exitCode(0).build()
   val jobDetail: JobDetail = JobDetail.builder().container(containerDetail).build
 
@@ -127,21 +142,21 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       Seq.empty[AwsBatchInput].toSet, Seq.empty[AwsBatchFileOutput].toSet,
-      jobPaths, Seq.empty[AwsBatchParameter], None, None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None)
     job
   }
   private def generateBasicJobForLocalFS: AwsBatchJob = {
     val job = AwsBatchJob(null, runtimeAttributes.copy(fileSystem="local"), "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       Seq.empty[AwsBatchInput].toSet, Seq.empty[AwsBatchFileOutput].toSet,
-      jobPaths, Seq.empty[AwsBatchParameter], None, None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None)
     job
   }
   private def generateJobWithS3InOut: AwsBatchJob = {
     val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       s3Inputs, s3Outputs,
-      jobPaths, Seq.empty[AwsBatchParameter], None, None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None)
     job
   }
 
@@ -180,109 +195,152 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
 
   it should "add s3 localize with retry function to reconfigured script" in {
     val job = generateBasicJob
-    val retryFunctionText = s"""
-                              |export AWS_METADATA_SERVICE_TIMEOUT=10
-                              |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
-                              |
-                              |function _s3_localize_with_retry() {
-                              |  local s3_path=$$1
-                              |  # destination must be the path to a file and not just the directory you want the file in
-                              |  local destination=$$2
-                              |
-                              |  for i in {1..6};
-                              |  do
-                              |    # abort if tries are exhausted
-                              |    if [ "$$i" -eq 6 ]; then
-                              |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts. aborting"
-                              |        exit 2
-                              |    fi
-                              |    # check validity of source path
-                              |    if ! [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
-                              |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
-                              |      exit 1
-                              |    fi
-                              |    # copy  
-                              |    /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$s3_path" "$$destination"  ||
-                              |        ( echo "attempt $$i to copy $$s3_path failed" sleep $$((7 * "$$i")) && continue)
-                              |    # check data integrity
-                              |    _check_data_integrity $$destination $$s3_path || 
-                              |       (echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
-                              |    # copy succeeded
-                              |    break
-                              |  done
-                              |}
-                              |
-                              |function _s3_delocalize_with_retry() {
-                              |  local local_path=$$1
-                              |  # destination must be the path to a file and not just the directory you want the file in
-                              |  local destination=$$2
-                              |
-                              |  for i in {1..6};
-                              |  do
-                              |    # if tries exceeded : abort
-                              |    if [ "$$i" -eq 6 ]; then
-                              |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts. aborting"
-                              |        exit 2
-                              |    fi
-                              |    # if destination is not a bucket : abort
-                              |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then 
-                              |     echo "$$destination is not an S3 path with a bucket and key. aborting"
-                              |      exit 1
-                              |    fi
-                              |    # copy ok or try again.
-                              |    if [[ -d "$$local_path" ]]; then
-                              |       # make sure to strip the trailing / in destination 
-                              |       destination=$${destination%/}
-                              |       # glob directory. do recursive copy
-                              |       /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" || 
-                              |         ( echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
-                              |       # check integrity for each of the files
-                              |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
-                              |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE || 
-                              |               ( echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2)
-                              |       done
-                              |    else 
-                              |      /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$local_path" "$$destination" || 
-                              |         ( echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue) 
-                              |      # check content length for data integrity
-                              |      _check_data_integrity $$local_path $$destination || 
-                              |         ( echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue)
-                              |    fi
-                              |    # copy succeeded
-                              |    break
-                              |  done
-                              |}
-                              |
-                              |function _check_data_integrity() {
-                              |  local local_path=$$1
-                              |  local s3_path=$$2
-                              |  
-                              |  # remote : use content_length
-                              |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then 
-                              |        bucket="$${BASH_REMATCH[1]}"
-                              |        key="$${BASH_REMATCH[2]}"
-                              |  else
-                              |      # this is already checked in the caller function
-                              |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
-                              |      exit 1
-                              |  fi
-                              |  s3_content_length=$$(/usr/local/aws-cli/v2/current/bin/aws s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') || 
-                              |        ( echo "Attempt to get head of object failed for $$s3_path." && return 1 )
-                              |  # local
-                              |  local_content_length=$$(LC_ALL=C ls -dn -- "$$local_path" | awk '{print $$5; exit}' ) || 
-                              |        ( echo "Attempt to get local content length failed for $$_local_path." && return 1 )   
-                              |  # compare
-                              |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
-                              |       true
-                              |  else
-                              |       false  
-                              |  fi
-                              |}
-                              |""".stripMargin
+    val retryFunctionText =
+      s"""
+          |export AWS_METADATA_SERVICE_TIMEOUT=10
+          |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
+          |
+          |function _s3_localize_with_retry() {
+          |  local s3_path=$$1
+          |  # destination must be the path to a file and not just the directory you want the file in
+          |  local destination=$$2
+          |
+          |  for i in {1..6};
+          |  do
+          |    # abort if tries are exhausted
+          |    if [ "$$i" -eq 6 ]; then
+          |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts. aborting"
+          |        exit 2
+          |    fi
+          |    # check validity of source path
+          |    if ! [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
+          |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+          |      exit 1
+          |    fi
+          |    # copy
+          |    /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$s3_path" "$$destination"  ||
+          |        { echo "attempt $$i to copy $$s3_path failed" && sleep $$((7 * "$$i")) && continue; }
+          |    # check data integrity
+          |    _check_data_integrity $$destination $$s3_path ||
+          |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+          |    # copy succeeded
+          |    break
+          |  done
+          |}""".stripMargin
 
     job.reconfiguredScript should include (retryFunctionText)
   }
 
+  it should "s3 delocalization with retry function in reconfigured script" in {
+    val job = generateBasicJob
+    val delocalizeText = s"""
+         |
+         |function _s3_delocalize_with_retry() {
+         |  # input variables
+         |  local local_path=$$1
+         |  # destination must be the path to a file and not just the directory you want the file in
+         |  local destination=$$2
+         |
+         |  # get the multipart chunk size
+         |  chunk_size=$$(_get_multipart_chunk_size $$local_path)
+         |  local MP_THRESHOLD=5368709120
+         |  # then set them
+         |  /usr/local/aws-cli/v2/current/bin/aws configure set default.s3.multipart_threshold $$MP_THRESHOLD
+         |  /usr/local/aws-cli/v2/current/bin/aws configure set default.s3.multipart_chunksize $$chunk_size
+         |
+         |  # try & validate upload 5 times
+         |  for i in {1..6};
+         |  do
+         |    # if tries exceeded : abort
+         |    if [ "$$i" -eq 6 ]; then
+         |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts. aborting"
+         |        exit 2
+         |    fi
+         |    # if destination is not a bucket : abort
+         |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then
+         |     echo "$$destination is not an S3 path with a bucket and key. aborting"
+         |      exit 1
+         |    fi
+         |    # copy ok or try again.
+         |    if [[ -d "$$local_path" ]]; then
+         |       # make sure to strip the trailing / in destination
+         |       destination=$${destination%/}
+         |       # glob directory. do recursive copy
+         |       /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" ||
+         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+         |       # check integrity for each of the files
+         |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
+         |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE ||
+         |               { echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2; }
+         |       done
+         |    else
+         |      /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$local_path" "$$destination" ||
+         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+         |      # check content length for data integrity
+         |      _check_data_integrity $$local_path $$destination ||
+         |         { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
+         |    fi
+         |    # copy succeeded
+         |    break
+         |  done
+         |}""".stripMargin
+    job.reconfiguredScript should include (delocalizeText)
+  }
+
+  it should "generate check data integrity in reconfigured script" in {
+    val job = generateBasicJob
+    val checkDataIntegrityBlock =
+      s"""
+         |function _check_data_integrity() {
+         |  local local_path=$$1
+         |  local s3_path=$$2
+         |
+         |  # remote : use content_length
+         |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
+         |        bucket="$${BASH_REMATCH[1]}"
+         |        key="$${BASH_REMATCH[2]}"
+         |  else
+         |      # this is already checked in the caller function
+         |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+         |      exit 1
+         |  fi
+         |  s3_content_length=$$(/usr/local/aws-cli/v2/current/bin/aws s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') ||
+         |        { echo "Attempt to get head of object failed for $$s3_path." && return 1; }
+         |  # local
+         |  local_content_length=$$(LC_ALL=C ls -dnL -- "$$local_path" | awk '{print $$5; exit}' ) ||
+         |        { echo "Attempt to get local content length failed for $$_local_path." && return 1; }
+         |  # compare
+         |  if [[ "$$s3_content_length" -eq "$$local_content_length" ]]; then
+         |       true
+         |  else
+         |       false
+         |  fi
+         |}
+         |""".stripMargin
+    job.reconfiguredScript should include (checkDataIntegrityBlock)
+  }
+
+  it should "generate get multipart chunk size in script" in {
+    val job = generateBasicJob
+    val getMultiplePartChunkSize =
+      s"""
+         |function _get_multipart_chunk_size() {
+         |  local file_path=$$1
+         |  # file size
+         |  file_size=$$(stat --printf="%s" $$file_path)
+         |  # chunk_size : you can have at most 10K parts with at least one 5MB part
+         |  # this reflects the formula in s3-copy commands of cromwell (S3FileSystemProvider.java)
+         |  #   => long partSize = Math.max((objectSize / 10000L) + 1, 5 * 1024 * 1024);
+         |  a=$$(( ( file_size / 10000) + 1 ))
+         |  b=$$(( 5 * 1024 * 1024 ))
+         |  chunk_size=$$(( a > b ? a : b ))
+         |  echo $$chunk_size
+         |}
+         |""".stripMargin
+
+    job.reconfiguredScript should include (getMultiplePartChunkSize)
+  }
+
   it should "generate postscript with output copy command in reconfigured script" in {
     val job = generateJobWithS3InOut
     val postscript =
@@ -290,13 +348,10 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
          |{
          |set -e
          |echo '*** DELOCALIZING OUTPUTS ***'
-         |
          |_s3_delocalize_with_retry /tmp/scratch/baa s3://bucket/somewhere/baa
          |
-         |
          |if [ -f /tmp/scratch/hello-rc.txt ]; then _s3_delocalize_with_retry /tmp/scratch/hello-rc.txt ${job.jobPaths.returnCode} ; fi
-         |
-         |if [ -f /tmp/scratch/hello-stderr.log ]; then _s3_delocalize_with_retrys /tmp/scratch/hello-stderr.log ${job.jobPaths.standardPaths.error}; fi
+         |if [ -f /tmp/scratch/hello-stderr.log ]; then _s3_delocalize_with_retry /tmp/scratch/hello-stderr.log ${job.jobPaths.standardPaths.error}; fi
          |if [ -f /tmp/scratch/hello-stdout.log ]; then _s3_delocalize_with_retry /tmp/scratch/hello-stdout.log ${job.jobPaths.standardPaths.output}; fi
          |
          |echo '*** COMPLETED DELOCALIZATION ***'
@@ -346,6 +401,45 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     job.rc(jobDetail) should be (0)
   }
 
+  it should "use RetryStrategy" in {
+    val runtime = runtimeAttributes.copy(
+      awsBatchEvaluateOnExit = Vector(Map("action" -> "EXIT", "onStatusReason" -> "Failed")),
+    )
+
+    val builder = RetryStrategy.builder().attempts(1).evaluateOnExit(
+      EvaluateOnExit.builder().onStatusReason("Failed").action(RetryAction.EXIT).build()
+    ).build()
+
+    val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion.copy(runtimeAttributes = runtime))
+    val expected = jobDefinition.retryStrategy
+    expected should equal (builder)
+  }
+
+  it should "use RetryStrategy evaluateOnExit should be case insensitive" in {
+    val runtime = runtimeAttributes.copy(
+      awsBatchEvaluateOnExit = Vector(Map("aCtIoN" -> "EXIT", "onStatusReason" -> "Failed")),
+    )
+
+    val builder = RetryStrategy.builder().attempts(1).evaluateOnExit(
+      EvaluateOnExit.builder().onStatusReason("Failed").action(RetryAction.EXIT).build()
+    ).build()
+
+    val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion.copy(runtimeAttributes = runtime))
+    val expected = jobDefinition.retryStrategy
+    expected should equal(builder)
+  }
+
+  it should "GPU is not set at job definition even if provided" in {
+    val runtime = runtimeAttributes.copy(
+      gpuCount = 1
+    )
 
+    val expected = List(
+      ResourceRequirement.builder().`type`("VCPU").value(s"$cpu").build(),
+      ResourceRequirement.builder().`type`("MEMORY").value("2048").build()
+    )
 
+    val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion.copy(runtimeAttributes = runtime))
+    val actual = jobDefinition.containerProperties.resourceRequirements
+    expected should equal(CollectionConverters.asScala(actual).toSeq)}
 }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
index 3de9cac621b..a9411b574b5 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
@@ -48,6 +48,8 @@ import wom.format.MemorySize
 import wom.types._
 import wom.values._
 
+import scala.util.{Failure, Success, Try}
+
 class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec with Matchers {
 
   def workflowOptionsWithDefaultRA(defaults: Map[String, JsValue]): WorkflowOptions = {
@@ -56,7 +58,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     )))
   }
 
-  val expectedDefaults = new AwsBatchRuntimeAttributes(refineMV[Positive](1), Vector("us-east-1a", "us-east-1b"),
+  val expectedDefaults = new AwsBatchRuntimeAttributes(refineMV[Positive](1), 0, Vector("us-east-1a", "us-east-1b"),
 
     MemorySize(2, MemoryUnit.GB), Vector(AwsBatchWorkingDisk()),
     "ubuntu:latest",
@@ -66,9 +68,13 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     false,
     "my-stuff",
     1,
-    Vector(Map.empty[String, String]))
+    Vector(Map.empty[String, String]),
+    Vector(Map.empty[String, String]),
+    false,
+    false
+  )
 
-  val expectedDefaultsLocalFS = new AwsBatchRuntimeAttributes(refineMV[Positive](1), Vector("us-east-1a", "us-east-1b"),
+  val expectedDefaultsLocalFS = new AwsBatchRuntimeAttributes(refineMV[Positive](1), 0, Vector("us-east-1a", "us-east-1b"),
 
     MemorySize(2, MemoryUnit.GB), Vector(AwsBatchWorkingDisk()),
     "ubuntu:latest",
@@ -79,6 +85,9 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     "",
     1,
     Vector(Map.empty[String, String]),
+    Vector(Map.empty[String, String]),
+    false,
+    false,
     "local")
 
   "AwsBatchRuntimeAttributes" should {
@@ -186,9 +195,9 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
     "validate a valid Filesystem string entry local Filesystem" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),"scriptBucketName" -> WomString(""), "filesystem" -> WomString("local"))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString(""), "filesystem" -> WomString("local"))
       val expectedRuntimeAttributes = expectedDefaultsLocalFS
-      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes,WorkflowOptions.fromMap(Map.empty).get,
+      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes, WorkflowOptions.fromMap(Map.empty).get,
         NonEmptyList.of("us-east-1a", "us-east-1b"), new AwsBatchConfiguration(AwsBatchTestConfigForLocalFS.AwsBatchBackendConfigurationDescriptor))
     }
 
@@ -302,7 +311,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     }
 
     "override config default attributes with default attributes declared in workflow options" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff") )
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"))
 
       val workflowOptionsJson =
         """{
@@ -316,7 +325,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     }
 
     "override config default runtime attributes with task runtime attributes" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"),  "cpu" -> WomInteger(4))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "cpu" -> WomInteger(4))
 
       val workflowOptionsJson =
         """{
@@ -330,7 +339,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     }
 
     "override invalid config default attributes with task runtime attributes" in {
-      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"),"scriptBucketName" -> WomString("my-stuff"),  "cpu" -> WomInteger(4))
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"), "cpu" -> WomInteger(4))
 
       val workflowOptionsJson =
         """{
@@ -369,6 +378,89 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
       val expectedRuntimeAttributes = expectedDefaults.copy(awsBatchRetryAttempts = 0)
       assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
     }
+
+    "validate a valid awsBatchEvaluateOnExit " in {
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "awsBatchRetryAttempts" -> WomInteger(0),
+        "scriptBucketName" -> WomString("my-stuff"),
+        "awsBatchEvaluateOnExit" -> WomArray(
+          Seq(WomMap(Map(WomString("action") -> WomString("RETRY"), WomString("onStatusReason") -> WomString("Host EC2*")))
+          )
+        )
+      )
+
+      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedDefaults.copy(
+        awsBatchRetryAttempts = 0,
+        awsBatchEvaluateOnExit = Vector(Map("action" -> "RETRY", "onStatusReason" -> "Host EC2*"))
+      ))
+    }
+
+    "if awsBatchEvaluteOnExit is empty, do not fail" in {
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "awsBatchRetryAttempts" -> WomInteger(0),
+        "scriptBucketName" -> WomString("my-stuff"),
+        "awsBatchEvaluateOnExit" -> WomArray(WomArrayType(WomMapType(WomStringType,WomStringType)), Vector(WomMap(Map.empty[WomValue, WomValue])))
+      )
+      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedDefaults.copy(
+        awsBatchRetryAttempts = 0,
+      ))
+    }
+
+    "missing or invalid action key result in an invalid awsBatchEvaluateOnExit" in {
+      val invalidEvaluateOnExit = List(
+        // missing action key
+        WomArray(
+          Seq(WomMap(Map(WomString("onStatusReason") -> WomString("Host EC2*")))
+          )
+        ),
+        // invalid value
+        WomArray(
+          Seq(WomMap(Map(WomString("action") -> WomString("TRYAGAIN"), WomString("onStatusReason") -> WomString("Host EC2*")))
+          )
+        )
+      )
+
+      invalidEvaluateOnExit foreach { invalidVal =>
+        val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "awsBatchEvaluateOnExit" -> invalidVal)
+        assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+          "Missing or invalid action key/value for runtime attribute: awsBatchEvaluateOnExit")
+      }
+    }
+  }
+
+  "Unrecognized keys for retry strategy should result in an invalid awsBatchEvaluateOnExit" in {
+    // invalid key
+    val invalidValue = WomArray(
+      Seq(WomMap(Map(WomString("action") -> WomString("RETRY"), WomString("onRandomStatus") -> WomString("Host EC2*")))
+      )
+    )
+    val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "awsBatchEvaluateOnExit" -> invalidValue)
+    assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes,
+      s"""Invalid keys in awsBatchEvaluateOnExit runtime attribute: Set(onrandomstatus).
+         | Only Set(action, onExitCode, onReason, onStatusReason) are accepted.""".stripMargin.replace(
+        "\n", ""))
+  }
+
+  "Config with defined awsBatchEvaluateOnExit works" in {
+    val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "scriptBucketName" -> WomString("my-stuff"),
+    )
+    val batchConfig = new AwsBatchConfiguration(AwsBatchTestWithRetryConfig.AwsBatchBackendConfigurationDescriptor)
+    val workflowOptions = WorkflowOptions.fromMap(Map.empty).get
+    val expectedRuntimeAttributes = expectedDefaults.copy(
+      awsBatchEvaluateOnExit = Vector(
+        Map("Action" -> "RETRY", "onStatusReason" -> "Host EC2*"), Map("Action" -> "EXIT", "onReason" -> "*"))
+    )
+
+    val runtimeAttributesBuilder = AwsBatchRuntimeAttributes.runtimeAttributesBuilder(batchConfig)
+    val defaultedAttributes = RuntimeAttributeDefinition.addDefaultsToAttributes(
+      AwsBatchRuntimeAttributes.runtimeAttributesBuilder(batchConfig).definitions.toSet, workflowOptions)(runtimeAttributes)
+
+    val validatedRuntimeAttributes = runtimeAttributesBuilder.build(defaultedAttributes, NOPLogger.NOP_LOGGER)
+    val actualRuntimeAttributes = AwsBatchRuntimeAttributes(
+      validatedRuntimeAttributes, batchConfig.runtimeConfig, batchConfig.fileSystem)
+    assert(actualRuntimeAttributes == expectedRuntimeAttributes)
   }
 
   private def assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes: Map[String, WomValue],
@@ -388,11 +480,10 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
   private def assertAwsBatchRuntimeAttributesFailedCreation(runtimeAttributes: Map[String, WomValue],
                                                        exMsg: String,
                                                        workflowOptions: WorkflowOptions = emptyWorkflowOptions): Unit = {
-    try {
-      toAwsBatchRuntimeAttributes(runtimeAttributes, workflowOptions, configuration)
-      fail(s"A RuntimeException was expected with message: $exMsg")
-    } catch {
-      case ex: RuntimeException => assert(ex.getMessage.contains(exMsg))
+
+    Try(toAwsBatchRuntimeAttributes(runtimeAttributes, workflowOptions, configuration)) match {
+      case Failure(exception) => assert(exception.getMessage.contains(exMsg))
+      case Success(_) => fail(s"A RuntimeException was expected with message: $exMsg")
     }
     ()
   }
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
index 682714b225c..275f126765b 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
@@ -187,6 +187,96 @@ object AwsBatchTestConfigForLocalFS {
        |
        |""".stripMargin
 
+  val AwsBatchBackendConfig = ConfigFactory.parseString(AwsBatchBackendConfigString)
+  val AwsBatchGlobalConfig = ConfigFactory.parseString(AwsBatchGlobalConfigString)
+  val AwsBatchBackendNoDefaultConfig = ConfigFactory.parseString(NoDefaultsConfigString)
+  val AwsBatchBackendConfigurationDescriptor = BackendConfigurationDescriptor(AwsBatchBackendConfig, AwsBatchGlobalConfig)
+  val NoDefaultsConfigurationDescriptor = BackendConfigurationDescriptor(AwsBatchBackendNoDefaultConfig, AwsBatchGlobalConfig)
+}
+
+object AwsBatchTestWithRetryConfig {
+
+  private val AwsBatchBackendConfigString =
+    """
+      |root = "s3://my-cromwell-workflows-bucket"
+      |
+      |filesystems {
+      |  s3 {
+      |    auth = "default"
+      |  }
+      |}
+      |
+      |auth = "default"
+      |   numSubmitAttempts = 6
+      |   numCreateDefinitionAttempts = 6
+      |
+      |default-runtime-attributes {
+      |    cpu: 1
+      |    failOnStderr: false
+      |    continueOnReturnCode: 0
+      |    docker: "ubuntu:latest"
+      |    memory: "2 GB"
+      |    disks: "local-disk"
+      |    noAddress: false
+      |    zones:["us-east-1a", "us-east-1b"]
+      |    queueArn: "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue"
+      |    scriptBucketName: "my-bucket"
+      |    awsBatchRetryAttempts: 1
+      |    awsBatchEvaluateOnExit: [
+      |     {
+      |       Action: "RETRY",
+      |       onStatusReason: "Host EC2*"
+      |     },
+      |     {
+      |  		  onReason : "*"
+      |       Action: "EXIT"
+      |     }
+      |    ]
+      |}
+      |
+      |""".stripMargin
+
+  private val NoDefaultsConfigString =
+    """
+      |root = "s3://my-cromwell-workflows-bucket"
+      |
+      |auth = "default"
+      |   numSubmitAttempts = 6
+      |   numCreateDefinitionAttempts = 6
+      |
+      |filesystems {
+      |  s3 {
+      |    auth = "default"
+      |  }
+      |}
+      |""".stripMargin
+
+  private val AwsBatchGlobalConfigString =
+    s"""
+       |aws {
+       |  application-name = "cromwell"
+       |  auths = [
+       |    {
+       |      name = "default"
+       |      scheme = "default"
+       |    }
+       |  ]
+       |}
+       |
+       |backend {
+       |  default = "AWS"
+       |  providers {
+       |    AWS {
+       |      actor-factory = "cromwell.backend.impl.aws.AwsBatchBackendLifecycleFactory"
+       |      config {
+       |      $AwsBatchBackendConfigString
+       |      }
+       |    }
+       |  }
+       |}
+       |
+       |""".stripMargin
+
   val AwsBatchBackendConfig = ConfigFactory.parseString(AwsBatchBackendConfigString)
   val AwsBatchGlobalConfig = ConfigFactory.parseString(AwsBatchGlobalConfigString)
   val AwsBatchBackendNoDefaultConfig = ConfigFactory.parseString(NoDefaultsConfigString)
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPathsSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPathsSpec.scala
index 2b2d0ea14d8..09a2223c0ac 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPathsSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchWorkflowPathsSpec.scala
@@ -33,6 +33,7 @@ package cromwell.backend.impl.aws
 
 import common.collections.EnhancedCollections._
 import cromwell.backend.BackendSpec
+import cromwell.backend.impl.aws.io.AwsBatchWorkflowPaths
 import org.scalatest.flatspec.AnyFlatSpecLike
 import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider
 import cromwell.core.Tags.AwsTest

From 225ea5a705afe9e892e7c7a613e97120b9f3da40 Mon Sep 17 00:00:00 2001
From: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Date: Tue, 9 Jan 2024 10:13:13 -0500
Subject: [PATCH 268/326] WM-2428: Include full error context when failing to
 abort TES jobs (#7354)

---
 .../backend/impl/tes/TesAsyncBackendJobExecutionActor.scala     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 335ee40b466..255f9c811dc 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -380,7 +380,7 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
       HttpRequest(method = HttpMethods.POST, uri = s"$tesEndpoint/${job.jobId}:cancel")
     ) onComplete {
       case Success(_) => jobLogger.info("{} Aborted {}", tag: Any, job.jobId)
-      case Failure(ex) => jobLogger.warn("{} Failed to abort {}: {}", tag, job.jobId, ex.getMessage)
+      case Failure(ex) => jobLogger.warn("{} Failed to abort {}", tag, job.jobId, ex)
     }
 
     ()

From ec1f3ac02368249ec0a359ee60bc3b5203feeb92 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 11 Jan 2024 16:45:40 -0500
Subject: [PATCH 269/326] WX-1420 Fix GCP Batch label regex restriction (#7355)

Co-authored-by: Beibei Chen <beibei@formbio.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .../google/batch/models/GcpLabel.scala        | 28 +++++++++++--------
 .../batch/models/GcpBatchLabelSpec.scala      |  3 +-
 2 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala
index 303b2ec85f2..5dabccea425 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpLabel.scala
@@ -18,13 +18,15 @@ final case class GcpLabel(key: String, value: String)
 object GcpLabel {
 
   val MaxLabelLength = 63
-  val GoogleLabelRegexPattern = "[a-z]([-a-z0-9]*[a-z0-9])?"
-  val GoogleLabelRegex = GoogleLabelRegexPattern.r
+  val GoogleLabelKeyRegexPattern = "[a-z]([-a-z_0-9]*[a-z0-9])?" // label key must start with letter
+  val GoogleLabelValueRegexPattern = "[a-z0-9]([-a-z_0-9]*[a-z0-9])?"
+  val GoogleLabelKeyRegex = GoogleLabelKeyRegexPattern.r
+  val GoogleLabelValueRegex = GoogleLabelValueRegexPattern.r
 
-  // This function is used to coerce a string into one that meets the requirements for a label submission to Google Pipelines API.
-  // See 'labels' in https://cloud.google.com/genomics/reference/rpc/google.genomics.v1alpha2#google.genomics.v1alpha2.RunPipelineArgs
+  // This function is used to coerce a string into one that meets the requirements for a label submission to Google Batch API.
+  // https://cloud.google.com/compute/docs/labeling-resources#requirements
   def safeGoogleName(mainText: String, emptyAllowed: Boolean = false): String =
-    validateLabelRegex(mainText) match {
+    validateLabelRegex(mainText, true) match {
       case Valid(labelText) => labelText
       case invalid @ _ if mainText.equals("") && emptyAllowed => mainText
       case invalid @ _ =>
@@ -57,15 +59,19 @@ object GcpLabel {
         }
     }
 
-  def validateLabelRegex(s: String): ErrorOr[String] =
-    (GoogleLabelRegex.pattern.matcher(s).matches, s.length <= MaxLabelLength) match {
+  def validateLabelRegex(s: String, isKey: Boolean): ErrorOr[String] = {
+    val regexPattern = if (isKey) GoogleLabelKeyRegex.pattern else GoogleLabelValueRegex.pattern
+    val field = if (isKey) "label key" else "label value"
+
+    (regexPattern.matcher(s).matches, s.length <= MaxLabelLength) match {
       case (true, true) => s.validNel
       case (false, false) =>
-        s"Invalid label field: `$s` did not match regex '$GoogleLabelRegexPattern' and it is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
-      case (false, _) => s"Invalid label field: `$s` did not match the regex '$GoogleLabelRegexPattern'".invalidNel
+        s"Invalid $field field: `$s` did not match regex '$regexPattern' and it is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
+      case (false, _) => s"Invalid $field field: `$s` did not match the regex '$regexPattern'".invalidNel
       case (_, false) =>
-        s"Invalid label field: `$s` is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
+        s"Invalid $field field: `$s` is ${s.length} characters. The maximum is $MaxLabelLength.".invalidNel
     }
+  }
 
   def safeLabels(values: (String, String)*): Seq[GcpLabel] = {
     def safeGoogleLabel(kvp: (String, String)): GcpLabel =
@@ -74,7 +80,7 @@ object GcpLabel {
   }
 
   def validateLabel(key: String, value: String): ErrorOr[GcpLabel] =
-    (validateLabelRegex(key), validateLabelRegex(value)).mapN { (validKey, validValue) =>
+    (validateLabelRegex(key, true), validateLabelRegex(value, false)).mapN { (validKey, validValue) =>
       GcpLabel(validKey, validValue)
     }
 
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchLabelSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchLabelSpec.scala
index 8ae97f4d0ca..a0dcb31a8b6 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchLabelSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchLabelSpec.scala
@@ -18,14 +18,13 @@ class GcpBatchLabelSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matche
     "cromwell-root-workflow-id-" -> "cromwell-root-workflow-id---x",
     "0-cromwell-root-workflow-id-" -> "x--0-cromwell-root-workflow-id---x",
     "Cromwell-root-workflow-id" -> "cromwell-root-workflow-id",
-    "cromwell_root_workflow_id" -> "cromwell-root-workflow-id",
     "too-long-too-long-too-long-too-long-too-long-too-long-too-long-t" -> "too-long-too-long-too-long-too---g-too-long-too-long-too-long-t",
     "0-too-long-and-invalid-too-long-and-invalid-too-long-and-invali+" -> "x--0-too-long-and-invalid-too----nvalid-too-long-and-invali---x"
   )
 
   googleLabelConversions foreach { case (label: String, conversion: String) =>
     it should s"not validate the bad label key '$label'" in {
-      GcpLabel.validateLabelRegex(label) match {
+      GcpLabel.validateLabelRegex(label, true) match {
         case Invalid(_) => // Good!
         case Valid(_) => fail(s"Label validation succeeded but should have failed.")
       }

From 20b5945d08c2fe475e357ffa101628cd48d12725 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 22 Jan 2024 15:04:12 -0500
Subject: [PATCH 270/326] WX-1385 Remove SAS tokens from TES input log
 printouts (#7358)

---
 .../src/main/scala/common/util/UriUtil.scala  |  7 ++++-
 .../cromwell/backend/impl/tes/TesTask.scala   | 10 ++++++-
 .../backend/impl/tes/TesTaskSpec.scala        | 30 +++++++++++++++++++
 3 files changed, 45 insertions(+), 2 deletions(-)

diff --git a/common/src/main/scala/common/util/UriUtil.scala b/common/src/main/scala/common/util/UriUtil.scala
index 24625be1edb..b2e4a07bced 100644
--- a/common/src/main/scala/common/util/UriUtil.scala
+++ b/common/src/main/scala/common/util/UriUtil.scala
@@ -87,8 +87,13 @@ object UriUtil {
       "signature"
     )
 
+  private val SensitiveKeys =
+    List(
+      "sig"
+    )
+
   private def isSensitiveKey(name: String): Boolean = {
     val lower = name.toLowerCase
-    SensitiveKeyParts.exists(lower.contains(_))
+    SensitiveKeyParts.exists(lower.contains(_)) || SensitiveKeys.exists(lower.equals(_))
   }
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
index 54df895d617..6d45c50f142 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesTask.scala
@@ -367,7 +367,15 @@ final case class Input(name: Option[String],
                        path: String,
                        `type`: Option[String],
                        content: Option[String]
-)
+) {
+  override def toString: String = {
+    import common.util.StringUtil.EnhancedString
+
+    // Mask SAS token signature in query
+    this.getClass.getName + Seq(name, description, url.map(_.maskSensitiveUri), path, `type`, content)
+      .mkString("(", ",", ")")
+  }
+}
 
 final case class Output(name: Option[String],
                         description: Option[String],
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
index 21e818bbc5a..27e7a058d5d 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesTaskSpec.scala
@@ -217,4 +217,34 @@ class TesTaskSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers wit
       "parent_workflow_id" -> Option(subWorkflowId.toString)
     )
   }
+
+  it should "not leak secrets when printing file paths" in {
+    val input = Input(
+      Option("asdf"),
+      Option("asdf"),
+      url = Option(
+        "https://lz304a1e79fd7359e5327eda.blob.core.windows.net/sc-705b830a-d699-478e-9da6-49661b326e77" +
+          "?sv=2021-12-02&spr=https&st=2023-12-13T20%3A27%3A55Z&se=2023-12-14T04%3A42%3A55Z&sr=c&sp=racwdlt&sig=SECRET&rscd=foo"
+      ),
+      "asdf",
+      Option("asdf"),
+      Option("asdf")
+    )
+
+    input.toString shouldBe "cromwell.backend.impl.tes.Input(Some(asdf),Some(asdf),Some(https://lz304a1e79fd7359e5327eda.blob.core.windows.net/sc-705b830a-d699-478e-9da6-49661b326e77" +
+      "?sv=2021-12-02&spr=https&st=2023-12-13T20:27:55Z&se=2023-12-14T04:42:55Z&sr=c&sp=racwdlt&sig=masked&rscd=foo),asdf,Some(asdf),Some(asdf))"
+  }
+
+  it should "not crash if the URL is missing" in {
+    val input = Input(
+      Option("asdf"),
+      Option("asdf"),
+      url = None,
+      "asdf",
+      Option("asdf"),
+      Option("asdf")
+    )
+
+    input.toString shouldBe "cromwell.backend.impl.tes.Input(Some(asdf),Some(asdf),None,asdf,Some(asdf),Some(asdf))"
+  }
 }

From cb53732572e2c41d89260467e58ff6e31ae93f10 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 23 Jan 2024 11:11:01 -0500
Subject: [PATCH 271/326] [WX-1184] PostgreSQL Docker Image for Local Cromwell
 (#7172)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 ...late_ Cromwell server TES Postgres.run.xml | 21 +++++++++++++++++++
 .../postgresql-initdb.d/init.sh               |  5 +++++
 .../postgresql-initdb.d/init.sql              |  1 +
 .../docker-postgres/start_postgres_docker.sh  | 19 +++++++++++++++++
 4 files changed, 46 insertions(+)
 create mode 100644 runConfigurations/Repo template_ Cromwell server TES Postgres.run.xml
 create mode 100755 scripts/docker-postgres/postgresql-initdb.d/init.sh
 create mode 100644 scripts/docker-postgres/postgresql-initdb.d/init.sql
 create mode 100755 scripts/docker-postgres/start_postgres_docker.sh

diff --git a/runConfigurations/Repo template_ Cromwell server TES Postgres.run.xml b/runConfigurations/Repo template_ Cromwell server TES Postgres.run.xml
new file mode 100644
index 00000000000..8cf24e70daa
--- /dev/null
+++ b/runConfigurations/Repo template_ Cromwell server TES Postgres.run.xml	
@@ -0,0 +1,21 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="Repo template: Cromwell server TES Postgres" type="Application" factoryName="Application">
+    <option name="ALTERNATIVE_JRE_PATH" value="$USER_HOME$/.sdkman/candidates/java/current" />
+    <envs>
+      <env name="CROMWELL_BUILD_CENTAUR_256_BITS_KEY" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA=" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_DRIVER" value="org.postgresql.Driver" />
+      <env name="CROMWELL_BUILD_CENTAUR_JDBC_URL" value="jdbc:postgresql://localhost:5432/cromwell_test?reWriteBatchedInserts=true" />
+      <env name="CROMWELL_BUILD_CENTAUR_READ_LINES_LIMIT" value="128000" />
+      <env name="CROMWELL_BUILD_CENTAUR_SLICK_PROFILE" value="slick.jdbc.PostgresProfile$" />
+      <env name="CROMWELL_BUILD_PAPI_JSON_FILE" value="target/ci/resources/cromwell-centaur-service-account.json" />
+      <env name="CROMWELL_BUILD_RESOURCES_DIRECTORY" value="target/ci/resources" />
+    </envs>
+    <option name="MAIN_CLASS_NAME" value="cromwell.CromwellApp" />
+    <module name="cromwell" />
+    <option name="PROGRAM_PARAMETERS" value="server" />
+    <option name="VM_PARAMETERS" value="-Dconfig.file=src/ci/resources/tes_application.conf" />
+    <method v="2">
+      <option name="Make" enabled="true" />
+    </method>
+  </configuration>
+</component>
\ No newline at end of file
diff --git a/scripts/docker-postgres/postgresql-initdb.d/init.sh b/scripts/docker-postgres/postgresql-initdb.d/init.sh
new file mode 100755
index 00000000000..f861d9c4551
--- /dev/null
+++ b/scripts/docker-postgres/postgresql-initdb.d/init.sh
@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+cat << EOF >> /var/lib/postgresql/data/postgresql.conf
+max_connections = 300
+EOF
diff --git a/scripts/docker-postgres/postgresql-initdb.d/init.sql b/scripts/docker-postgres/postgresql-initdb.d/init.sql
new file mode 100644
index 00000000000..8cff561ceee
--- /dev/null
+++ b/scripts/docker-postgres/postgresql-initdb.d/init.sql
@@ -0,0 +1 @@
+create extension lo;
diff --git a/scripts/docker-postgres/start_postgres_docker.sh b/scripts/docker-postgres/start_postgres_docker.sh
new file mode 100755
index 00000000000..93a76108a2b
--- /dev/null
+++ b/scripts/docker-postgres/start_postgres_docker.sh
@@ -0,0 +1,19 @@
+# This script will launch a Postgres 11.3 container with parameters matching the expectations of Cromwell's CI configuration
+# You can run cromwell locally using this container as its DB.
+# Your intelliJ repo template or cromwell config should provide the following environment variables:
+# CROMWELL_BUILD_CENTAUR_JDBC_DRIVER="org.postgresql.Driver"
+# CROMWELL_BUILD_CENTAUR_SLICK_PROFILE="slick.jdbc.PostgresProfile$"
+# CROMWELL_BUILD_CENTAUR_JDBC_URL="jdbc:postgresql://localhost:5432/cromwell_test?reWriteBatchedInserts=true"
+
+set -euo pipefail
+
+CURRENT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+
+docker run \
+    --name=cromwell_postgres_test_db \
+    --env POSTGRES_USER=cromwell \
+    --env POSTGRES_PASSWORD=test \
+    --env POSTGRES_DB=cromwell_test \
+    --volume ${CURRENT_DIR}/postgresql-initdb.d:/docker-entrypoint-initdb.d \
+    --publish 5432:5432 \
+    --rm postgres:14

From b6d1f50febfcc10c91fc5df518feebb7ffab1b7c Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Fri, 26 Jan 2024 09:43:34 -0500
Subject: [PATCH 272/326] WX-1444 Use MySQL LTS in DBMS tests (#7360)

---
 .../test/scala/cromwell/services/database/DatabaseSystem.scala  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/services/src/test/scala/cromwell/services/database/DatabaseSystem.scala b/services/src/test/scala/cromwell/services/database/DatabaseSystem.scala
index 490c7823c20..aa216188167 100644
--- a/services/src/test/scala/cromwell/services/database/DatabaseSystem.scala
+++ b/services/src/test/scala/cromwell/services/database/DatabaseSystem.scala
@@ -53,7 +53,7 @@ case object MysqlEarliestDatabaseSystem extends NetworkDatabaseSystem {
 case object MysqlLatestDatabaseSystem extends NetworkDatabaseSystem {
   override val name: String = "MySQL (latest)"
   override val platform: MysqlDatabasePlatform.type = MysqlDatabasePlatform
-  override val dockerImageVersion: String = "latest"
+  override val dockerImageVersion: String = "8.0"
 }
 
 case object PostgresqlEarliestDatabaseSystem extends NetworkDatabaseSystem {

From 00f840dcb44bcb72dba7d34e9b66a3331f09f886 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Wed, 31 Jan 2024 15:27:09 -0500
Subject: [PATCH 273/326] WX-1449 Add `latest` Docker tag (#7362)

---
 project/Publishing.scala | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/project/Publishing.scala b/project/Publishing.scala
index 0af27e77147..6dd1b281700 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -44,8 +44,8 @@ object Publishing {
           // Tags look like `85`, `85-443a6fc`
           s"$cromwellVersion,${version.value}"
         } else {
-          // Tag looks like `85-443a6fc`
-          version.value
+          // Tag looks like `85-443a6fc`, `latest`
+          s"${version.value},latest"
         }
       }
 

From e74d51b6e56bd8757f38a9b683e5c6b223636f2b Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Wed, 31 Jan 2024 17:17:06 -0500
Subject: [PATCH 274/326] WX-767 Upgrade Cloud SDK to 461.0.0 (#7361)

---
 .../google/batch/runnable/RunnableUtils.scala  | 18 ++----------------
 .../pipelines/common/action/ActionUtils.scala  | 17 +++++------------
 2 files changed, 7 insertions(+), 28 deletions(-)

diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala
index f60baed0608..dbcf1076077 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/runnable/RunnableUtils.scala
@@ -16,30 +16,16 @@ object RunnableUtils {
   /** Port mappings for the ssh container. */
   val sshPortMappings = Map("22" -> Int.box(22))
 
-  /*
-   * At the moment, cloud-sdk (924MB for 276.0.0-slim) and stedolan/jq (182MB) decompressed ~= 1.1 GB
-   */
-  val cromwellImagesSizeRoundedUpInGB = 1
-
   private val config = ConfigFactory.load().getConfig("google")
 
   /**
     * An image with the Google Cloud SDK installed.
     * http://gcr.io/google.com/cloudsdktool/cloud-sdk
     *
-    * FYI additional older versions are available on DockerHub at:
-    * https://hub.docker.com/r/google/cloud-sdk
-    *
-    * When updating this value, also consider updating the CromwellImagesSizeRoundedUpInGB below.
+    * Also update `cromwell.backend.google.pipelines.common.action.ActionUtils`
     */
   val CloudSdkImage: String =
-    // config.getOrElse("cloud-sdk-image-url", "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine")
-    config.getOrElse("cloud-sdk-image-url", "gcr.io/google.com/cloudsdktool/cloud-sdk:434.0.0-alpine")
-  /*
-   * At the moment, cloud-sdk (584MB for 354.0.0-alpine) and stedolan/jq (182MB) decompressed ~= 0.8 GB
-   */
-  val CromwellImagesSizeRoundedUpInGB: Int =
-    config.getOrElse("cloud-sdk-image-size-gb", 1)
+    config.getOrElse("cloud-sdk-image-url", "gcr.io/google.com/cloudsdktool/cloud-sdk:461.0.0-alpine")
 
   /** Quotes a string such that it's compatible as a string argument in the shell. */
   def shellEscaped(any: Any): String = {
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionUtils.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionUtils.scala
index b05971a13ad..642cd48bcd1 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionUtils.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/action/ActionUtils.scala
@@ -15,30 +15,23 @@ object ActionUtils {
   /** Port mappings for the ssh container. */
   val sshPortMappings = Map("22" -> Int.box(22))
 
-  /*
-   * At the moment, cloud-sdk (924MB for 276.0.0-slim) and stedolan/jq (182MB) decompressed ~= 1.1 GB
-   */
-  val cromwellImagesSizeRoundedUpInGB = 1
-
   private val config = ConfigFactory.load().getConfig("google")
 
   /**
     * An image with the Google Cloud SDK installed.
     * http://gcr.io/google.com/cloudsdktool/cloud-sdk
     *
-    * FYI additional older versions are available on DockerHub at:
-    * https://hub.docker.com/r/google/cloud-sdk
+    * When updating this value, also consider updating the `cromwellImagesSizeRoundedUpInGB` below.
     *
-    * When updating this value, also consider updating the CromwellImagesSizeRoundedUpInGB below.
+    * Also update `cromwell.backend.google.batch.runnable.RunnableUtils`
     */
   val CloudSdkImage: String =
-    config.getOrElse("cloud-sdk-image-url", "gcr.io/google.com/cloudsdktool/cloud-sdk:354.0.0-alpine")
+    config.getOrElse("cloud-sdk-image-url", "gcr.io/google.com/cloudsdktool/cloud-sdk:461.0.0-alpine")
 
   /*
-   * At the moment, cloud-sdk (584MB for 354.0.0-alpine) and stedolan/jq (182MB) decompressed ~= 0.8 GB
+   * At the moment, cloud-sdk (955MB for 460.0.0-alpine) ~= 1.0 GB
    */
-  val CromwellImagesSizeRoundedUpInGB: Int =
-    config.getOrElse("cloud-sdk-image-size-gb", 1)
+  val cromwellImagesSizeRoundedUpInGB: Int = config.getOrElse("cloud-sdk-image-size-gb", 1)
 
   /** Quotes a string such that it's compatible as a string argument in the shell. */
   def shellEscaped(any: Any): String = {

From 13236ffd18b243e7d83cf5f8277c84f9e8b42482 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 1 Feb 2024 09:16:24 -0500
Subject: [PATCH 275/326] WX-1443 Adopt `gcloud storage` for localization only
 (#7359)

---
 CHANGELOG.md                                  | 21 ++++++++++++++++
 .../v2beta/src/main/resources/gcs_transfer.sh | 25 ++++++++++---------
 2 files changed, 34 insertions(+), 12 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a581852c02e..9f4d9c30560 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,26 @@
 # Cromwell Change Log
 
+## 87 Release Notes
+
+### Replacement of `gsutil` with `gcloud storage`
+
+In this release, all **localization** functionality on the GCP backend migrates to use the more modern and performant `gcloud storage`. With sufficiently powerful worker VMs, Cromwell can now localize at up to 1200 MB/s [0][1][2].
+
+In a future release, **delocalization** will also migrate to `gcloud storage`. As part of that upcoming change, we are considering turning on [parallel composite uploads](https://cromwell.readthedocs.io/en/stable/backends/Google/#parallel-composite-uploads) by default to maximize performance. Delocalized composite objects will no longer have an md5 checksum in their metadata; refer to the matrix below [3]. If you have compatibility concerns for your workflow, please [submit an issue](https://github.com/broadinstitute/cromwell/issues).
+
+| Delocalization Strategy | Performance   | crc32c | md5 |
+|-------------------------|---------------|--------|-----|
+| Classic                 | Baseline/slow | ✅     | ✅  |
+| Parallel Composite      | Fast          | ✅     | ❌  |
+
+[0] Tested with Intel Ice Lake CPU platform, 16 vCPU, 32 GB RAM, 2500 GB SSD
+
+[1] [Throughput scales with vCPU count](https://cloud.google.com/compute/docs/disks/performance#n2_vms) with a plateau at 16 vCPUs.
+
+[2] [Throughput scales with disk size and type](https://cloud.google.com/compute/docs/disks/performance#throughput_limits_for_zonal) with at a plateau at 2.5 TB SSD. Worked example: 1200 MB/s ÷ 0.48 MB/s per GB = 2500 GB.
+
+[3] Cromwell itself uses crc32c hashes for call caching and is not affected
+
 ## 86 Release Notes
 
 ### GCP Batch
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/resources/gcs_transfer.sh b/supportedBackends/google/pipelines/v2beta/src/main/resources/gcs_transfer.sh
index 47dee2d67df..f729f46bdc0 100755
--- a/supportedBackends/google/pipelines/v2beta/src/main/resources/gcs_transfer.sh
+++ b/supportedBackends/google/pipelines/v2beta/src/main/resources/gcs_transfer.sh
@@ -163,17 +163,18 @@ localize_files() {
   fi
 
   # We need to determine requester pays status of the first file attempting at most `max_attempts` times.
-  NO_REQUESTER_PAYS_COMMAND="mkdir -p '$container_parent' && rm -f "$HOME/.config/gcloud/gce" && gsutil -o 'GSUtil:parallel_thread_count=1' -o 'GSUtil:sliced_object_download_max_components=${num_cpus}' cp '$first_cloud_file' '$container_parent'"
-  REQUESTER_PAYS_COMMAND="rm -f "$HOME/.config/gcloud/gce" && gsutil -o 'GSUtil:parallel_thread_count=1' -o 'GSUtil:sliced_object_download_max_components=${num_cpus}' -u $project cp '$first_cloud_file' '$container_parent'"
+  NO_REQUESTER_PAYS_COMMAND="mkdir -p '$container_parent' && rm -f "$HOME/.config/gcloud/gce" && gcloud storage cp '$first_cloud_file' '$container_parent'"
+  REQUESTER_PAYS_COMMAND="rm -f "$HOME/.config/gcloud/gce" && gcloud storage cp --billing-project $project '$first_cloud_file' '$container_parent'"
 
   basefile=$(basename "$first_cloud_file")
   private::localize_message "$first_cloud_file" "${container_parent}${basefile}"
   private::determine_requester_pays ${max_attempts}
 
   if [[ ${USE_REQUESTER_PAYS} = true ]]; then
-    rpflag="-u $project"
+    # https://cloud.google.com/storage/docs/using-requester-pays#using
+    gcloud_storage_rpflag="--billing-project $project"
   else
-    rpflag=""
+    gcloud_storage_rpflag=""
   fi
 
 
@@ -192,7 +193,7 @@ localize_files() {
     while [[ ${attempt} -le ${max_attempts} ]]; do
       # parallel transfer the remaining files
       rm -f "$HOME/.config/gcloud/gce"
-      if cat files_to_localize.txt | gsutil -o "GSUtil:parallel_thread_count=1" -o "GSUtil:sliced_object_download_max_components=${num_cpus}" -m ${rpflag} cp -I "$container_parent"; then
+      if cat files_to_localize.txt | gcloud storage cp ${gcloud_storage_rpflag} --read-paths-from-stdin "$container_parent"; then
         break
       else
         attempt=$((attempt + 1))
@@ -209,13 +210,13 @@ private::localize_directory() {
   local cloud="$1"
   local container="$2"
   local max_attempts="$3"
-  local rpflag="$4"
+  local gcloud_storage_rpflag="$4"
 
   local attempt=1
   private::localize_message "$cloud" "$container"
   while [[ ${attempt} -lt ${max_attempts} ]]; do
-    # Do not quote rpflag, when that is set it will be -u project which should be two distinct arguments.
-    if mkdir -p "${container}" && rm -f "$HOME/.config/gcloud/gce" && gsutil ${rpflag} -m rsync -r "${cloud}" "${container}" > /dev/null 2>&1; then
+    # Do not quote gcloud_storage_rpflag, when that is set it will be `--billing-project project` which should be two distinct arguments.
+    if mkdir -p "${container}" && rm -f "$HOME/.config/gcloud/gce" && gcloud storage ${gcloud_storage_rpflag} rsync -r "${cloud}" "${container}" > /dev/null 2>&1; then
       break
     else
       attempt=$(($attempt + 1))
@@ -242,21 +243,21 @@ localize_directories() {
 
   BASE_COMMAND="private::localize_directory '${cloud_directory}' '${container_directory}' '${max_attempts}'"
   NO_REQUESTER_PAYS_COMMAND="${BASE_COMMAND} ''"
-  REQUESTER_PAYS_COMMAND="${BASE_COMMAND} '-u $project'"
+  REQUESTER_PAYS_COMMAND="${BASE_COMMAND} '--billing-project $project'"
 
   private::determine_requester_pays ${max_attempts}
 
   if [[ ${USE_REQUESTER_PAYS} = true ]]; then
-    rpflag="-u $project"
+    gcloud_storage_rpflag="--billing-project $project"
   else
-    rpflag=""
+    gcloud_storage_rpflag=""
   fi
 
   while [[ $# -gt 0 ]]; do
     cloud_directory="$1"
     container_directory="$2"
     shift 2
-    private::localize_directory "$cloud_directory" "$container_directory" "$max_attempts" "$rpflag"
+    private::localize_directory "$cloud_directory" "$container_directory" "$max_attempts" "$gcloud_storage_rpflag"
   done
 }
 

From a39eabe7c9f4374e7183ac7d226d608949289520 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 9 Feb 2024 11:06:37 -0500
Subject: [PATCH 276/326] WX-964 suffix() (#7363)

---
 .../biscayne_new_engine_functions.test         |  4 ++++
 .../biscayne_new_engine_functions.wdl          |  8 +++++++-
 .../draft3/elements/ExpressionElement.scala    |  6 ++++++
 .../ast2wdlom/AstToNewExpressionElements.scala |  3 ++-
 .../BiscayneExpressionValueConsumers.scala     |  8 ++++++++
 .../linking/expression/consumed/consumed.scala |  1 +
 .../files/BiscayneFileEvaluators.scala         |  3 ++-
 .../linking/expression/files/files.scala       |  1 +
 .../types/BiscayneTypeEvaluators.scala         | 10 ++++++++++
 .../linking/expression/types/types.scala       |  1 +
 .../values/BiscayneValueEvaluators.scala       | 18 ++++++++++++++++++
 .../linking/expression/values/values.scala     |  2 ++
 .../transforms/biscayne/Ast2WdlomSpec.scala    |  6 ++++++
 .../BiscayneExpressionValueConsumersSpec.scala | 18 ++++++++++++++++++
 .../files/BiscayneFileEvaluatorSpec.scala      | 11 +++++++++++
 .../types/BiscayneTypeEvaluatorSpec.scala      |  8 ++++++++
 .../values/BiscayneValueEvaluatorSpec.scala    | 17 +++++++++++++++++
 .../ast2wdlom/AstToNewExpressionElements.scala |  3 ++-
 .../CascadesExpressionValueConsumers.scala     |  8 ++++++++
 .../linking/expression/consumed/consumed.scala |  1 +
 .../files/CascadesFileEvaluators.scala         |  3 ++-
 .../linking/expression/files/files.scala       |  1 +
 .../types/CascadesTypeEvaluators.scala         | 10 ++++++++++
 .../linking/expression/types/types.scala       |  1 +
 .../values/CascadesValueEvaluators.scala       | 18 ++++++++++++++++++
 .../linking/expression/values/values.scala     |  2 ++
 .../transforms/cascades/Ast2WdlomSpec.scala    |  6 ++++++
 .../CascadesExpressionValueConsumersSpec.scala | 18 ++++++++++++++++++
 .../files/CascadesFileEvaluatorSpec.scala      | 11 +++++++++++
 .../types/CascadesTypeEvaluatorSpec.scala      |  8 ++++++++
 .../values/CascadesValueEvaluatorSpec.scala    | 17 +++++++++++++++++
 .../transforms/ast2wdlom/Ast2WdlomSpec.scala   |  6 ++++++
 .../base/wdlom2wdl/WdlWriterImpl.scala         |  1 +
 33 files changed, 234 insertions(+), 5 deletions(-)

diff --git a/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test b/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
index 184d41b5aeb..6998d4af7e7 100644
--- a/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
+++ b/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
@@ -54,4 +54,8 @@ metadata {
   "outputs.biscayne_new_engine_functions.bigIntFloatComparison": 10.0
   "outputs.biscayne_new_engine_functions.minMaxIntFloatComposition": 1.0
   "outputs.biscayne_new_engine_functions.maxIntVsMaxFloat": 1.79769313E+308
+
+  "outputs.biscayne_new_engine_functions.with_suffixes.0": "aaaS"
+  "outputs.biscayne_new_engine_functions.with_suffixes.1": "bbbS"
+  "outputs.biscayne_new_engine_functions.with_suffixes.2": "cccS"
 }
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
index 220fcb535e5..f7b3d0de7fd 100644
--- a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
@@ -4,7 +4,7 @@ workflow biscayne_new_engine_functions {
 
   meta {
     description: "This test makes sure that these functions work in a real workflow"
-    functions_under_test: [ "keys", "as_map", "as_pairs", "collect_by_key" ]
+    functions_under_test: [ "keys", "as_map", "as_pairs", "collect_by_key", "suffix" ]
   }
 
   Map[String, Int] x_map_in = {"a": 1, "b": 2, "c": 3}
@@ -15,6 +15,8 @@ workflow biscayne_new_engine_functions {
 
   Array[Pair[String,Int]] z_pairs_in = [("a", 1), ("b", 2), ("a", 3)]
 
+  Array[String] some_strings = ["aaa", "bbb", "ccc"]
+
   Int smallestInt = 1
   Float smallFloat = 2.718
   Float bigFloat = 3.141
@@ -48,6 +50,10 @@ workflow biscayne_new_engine_functions {
     Float bigIntFloatComparison = max(bigFloat, biggestInt) # 10.0
     Float minMaxIntFloatComposition = min(max(biggestInt, smallFloat), smallestInt) # 1.0
     Float maxIntVsMaxFloat = max(maxInt, maxFloat)
+
+    # suffix():
+    # =================================================
+    Array[String] with_suffixes = suffix("S", some_strings)
   }
 }
 
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
index a2fc6202193..91f34d064ae 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
@@ -164,6 +164,12 @@ object ExpressionElement {
     override def arg1: ExpressionElement = prefix
     override def arg2: ExpressionElement = array
   }
+
+  final case class Suffix(suffix: ExpressionElement, array: ExpressionElement) extends TwoParamFunctionCallElement {
+    override def arg1: ExpressionElement = suffix
+    override def arg2: ExpressionElement = array
+  }
+
   final case class Min(arg1: ExpressionElement, arg2: ExpressionElement) extends TwoParamFunctionCallElement
   final case class Max(arg1: ExpressionElement, arg2: ExpressionElement) extends TwoParamFunctionCallElement
   final case class Sep(arg1: ExpressionElement, arg2: ExpressionElement) extends TwoParamFunctionCallElement
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
index 52ac86b10a6..5c0c01859c2 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
@@ -3,7 +3,7 @@ package wdl.transforms.biscayne.ast2wdlom
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
 import wdl.model.draft3.elements.ExpressionElement
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep}
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, Suffix}
 import wdl.transforms.base.ast2wdlom.AstNodeToExpressionElement
 
 object AstToNewExpressionElements {
@@ -15,6 +15,7 @@ object AstToNewExpressionElements {
     "min" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Min, "min"),
     "max" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Max, "max"),
     "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
+    "suffix" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Suffix, "suffix"),
     "read_object" -> (_ =>
       "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel
     ),
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
index ad168067177..3c73f8b55cd 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
@@ -58,6 +58,14 @@ object BiscayneExpressionValueConsumers {
         expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
+  implicit val suffixExpressionValueConsumer: ExpressionValueConsumer[Suffix] = new ExpressionValueConsumer[Suffix] {
+    override def expressionConsumedValueHooks(a: Suffix)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++
+        expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
+  }
+
   implicit val noneLiteralExpressionValueConsumer: ExpressionValueConsumer[NoneLiteralElement.type] =
     new ExpressionValueConsumer[NoneLiteralElement.type] {
       override def expressionConsumedValueHooks(a: NoneLiteralElement.type)(implicit
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
index f70c3603b4a..e1121e1d549 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
@@ -81,6 +81,7 @@ package object consumed {
         case a: Length => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Flatten => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Prefix => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Suffix => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: SelectFirst => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: SelectAll => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Defined => a.expressionConsumedValueHooks(expressionValueConsumer)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
index fa968525bbc..6a79d2b3948 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
@@ -1,6 +1,6 @@
 package wdl.transforms.biscayne.linking.expression.files
 
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep}
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, Suffix}
 import wdl.model.draft3.graph.expression.FileEvaluator
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.twoParameterFunctionPassthroughFileEvaluator
@@ -16,6 +16,7 @@ object BiscayneFileEvaluators {
     EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
 
   implicit val sepFunctionEvaluator: FileEvaluator[Sep] = twoParameterFunctionPassthroughFileEvaluator[Sep]
+  implicit val suffixFunctionEvaluator: FileEvaluator[Suffix] = twoParameterFunctionPassthroughFileEvaluator[Suffix]
 
   implicit val minFunctionEvaluator: FileEvaluator[Min] = twoParameterFunctionPassthroughFileEvaluator[Min]
   implicit val maxFunctionEvaluator: FileEvaluator[Max] = twoParameterFunctionPassthroughFileEvaluator[Max]
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
index d143e948272..9dd95e9a0ec 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
@@ -135,6 +135,7 @@ package object files {
         case a: Flatten =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Prefix => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Suffix => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: SelectFirst =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: SelectAll =>
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
index 9a993f6b5b8..1ff5bf71ba4 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
@@ -1,5 +1,6 @@
 package wdl.transforms.biscayne.linking.expression.types
 
+import cats.implicits.catsSyntaxTuple2Semigroupal
 import cats.syntax.validated._
 import common.validation.ErrorOr._
 import wdl.model.draft3.elements.ExpressionElement
@@ -100,4 +101,13 @@ object BiscayneTypeEvaluators {
 
       }
   }
+
+  implicit val suffixFunctionEvaluator: TypeEvaluator[Suffix] = new TypeEvaluator[Suffix] {
+    override def evaluateType(a: Suffix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      (validateParamType(a.suffix, linkedValues, WomStringType),
+       validateParamType(a.array, linkedValues, WomArrayType(WomStringType))
+      ) mapN { (_, _) => WomArrayType(WomStringType) }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
index 0b61f7fd71c..dec2deeb24f 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
@@ -83,6 +83,7 @@ package object types {
         case a: Length => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Flatten => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Prefix => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Suffix => a.evaluateType(linkedValues)(typeEvaluator)
         case a: SelectFirst => a.evaluateType(linkedValues)(typeEvaluator)
         case a: SelectAll => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Defined => a.evaluateType(linkedValues)(typeEvaluator)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
index bdb3516f787..0c4805f0e68 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
@@ -217,4 +217,22 @@ object BiscayneValueEvaluators {
         EvaluatedValue(WomString(arr.value.map(v => v.valueString).mkString(sepvalue.value)), Seq.empty).validNel
       }
   }
+
+  implicit val suffixFunctionEvaluator: ValueEvaluator[Suffix] = new ValueEvaluator[Suffix] {
+    override def evaluateValue(a: Suffix,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processTwoValidatedValues[WomString, WomArray, WomArray](
+        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        ),
+        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) { (suffix, arr) =>
+        EvaluatedValue(WomArray(arr.value.map(v => WomString(v.valueString + suffix.value))), Seq.empty).validNel
+      }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
index 338c8676906..3106ceba428 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
@@ -142,6 +142,8 @@ package object values {
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Prefix =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Suffix =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: SelectFirst =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: SelectAll =>
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
index 4fde60b1efd..a0953cd8397 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
@@ -97,4 +97,10 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val expr = fromString[ExpressionElement](str, parser.parse_e)
     expr shouldBeValid NoneLiteralElement
   }
+
+  it should "parse the new suffix function" in {
+    val str = "suffix(some_str, some_arr)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (Suffix(IdentifierLookup("some_str"), IdentifierLookup("some_arr")))
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
index 11ca72b3a49..76f4a0338e7 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
@@ -57,4 +57,22 @@ class BiscayneExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
       e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_separator"), UnlinkedIdentifierHook("c")))
     }
   }
+
+  it should "discover the variable lookups within a suffix() call" in {
+    val str = """ suffix(my_suffix, ["a", "b", c]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_suffix"), UnlinkedIdentifierHook("c")))
+    }
+  }
+
+  it should "discover an array variable lookup within a suffix() call" in {
+    val str = """ suffix("SFX", my_array) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array")))
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
index 59ebfd18dc4..4a3ed6b63b9 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
@@ -45,4 +45,15 @@ class BiscayneFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       )
     }
   }
+
+  it should "discover the file which would be required to evaluate a suffix() function" in {
+    val str = """ suffix(' # what a line', read_lines("foo.txt")) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
index 0593605bb2b..c8372d36cd1 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
@@ -56,4 +56,12 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
   }
 
+  it should "evaluate the type of a suffix() function as Array[String]" in {
+    val str = """ suffix('S', ["a", "b", "c"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
index 53660a407d9..1487543a838 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
@@ -200,4 +200,21 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
     }
   }
+
+  it should "evaluate a suffix expression correctly" in {
+    val str = """ suffix("S", ["a", "b", "c"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("aS"),
+        WomString("bS"),
+        WomString("cS")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
index ba331383e45..46cd8cb2e60 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
@@ -3,7 +3,7 @@ package wdl.transforms.cascades.ast2wdlom
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
 import wdl.model.draft3.elements.ExpressionElement
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep}
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, Suffix}
 import wdl.transforms.base.ast2wdlom.AstNodeToExpressionElement
 
 object AstToNewExpressionElements {
@@ -15,6 +15,7 @@ object AstToNewExpressionElements {
     "min" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Min, "min"),
     "max" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Max, "max"),
     "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
+    "suffix" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Suffix, "suffix"),
     "read_object" -> (_ =>
       "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel
     ),
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
index b4e6c5be1d6..ebc6d48fba1 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
@@ -58,6 +58,14 @@ object cascadesExpressionValueConsumers {
         expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
+  implicit val suffixExpressionValueConsumer: ExpressionValueConsumer[Suffix] = new ExpressionValueConsumer[Suffix] {
+    override def expressionConsumedValueHooks(a: Suffix)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++
+        expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
+  }
+
   implicit val noneLiteralExpressionValueConsumer: ExpressionValueConsumer[NoneLiteralElement.type] =
     new ExpressionValueConsumer[NoneLiteralElement.type] {
       override def expressionConsumedValueHooks(a: NoneLiteralElement.type)(implicit
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
index af54bbbd6a6..2026aaec010 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
@@ -81,6 +81,7 @@ package object consumed {
         case a: Length => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Flatten => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Prefix => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Suffix => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: SelectFirst => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: SelectAll => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Defined => a.expressionConsumedValueHooks(expressionValueConsumer)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
index 3b7b299a090..32ea447b584 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
@@ -1,6 +1,6 @@
 package wdl.transforms.cascades.linking.expression.files
 
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep}
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, Suffix}
 import wdl.model.draft3.graph.expression.FileEvaluator
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.twoParameterFunctionPassthroughFileEvaluator
@@ -16,6 +16,7 @@ object cascadesFileEvaluators {
     EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
 
   implicit val sepFunctionEvaluator: FileEvaluator[Sep] = twoParameterFunctionPassthroughFileEvaluator[Sep]
+  implicit val suffixFunctionEvaluator: FileEvaluator[Suffix] = twoParameterFunctionPassthroughFileEvaluator[Suffix]
 
   implicit val minFunctionEvaluator: FileEvaluator[Min] = twoParameterFunctionPassthroughFileEvaluator[Min]
   implicit val maxFunctionEvaluator: FileEvaluator[Max] = twoParameterFunctionPassthroughFileEvaluator[Max]
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
index 9693cbfaba6..a53c85b9b89 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
@@ -135,6 +135,7 @@ package object files {
         case a: Flatten =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Prefix => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Suffix => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: SelectFirst =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: SelectAll =>
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
index e169a561d53..180af9eb0d8 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
@@ -1,5 +1,6 @@
 package wdl.transforms.biscayne.linking.expression.types
 
+import cats.implicits.catsSyntaxTuple2Semigroupal
 import cats.syntax.validated._
 import common.validation.ErrorOr._
 import wdl.model.draft3.elements.ExpressionElement
@@ -100,4 +101,13 @@ object cascadesTypeEvaluators {
 
       }
   }
+
+  implicit val suffixFunctionEvaluator: TypeEvaluator[Suffix] = new TypeEvaluator[Suffix] {
+    override def evaluateType(a: Suffix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      (validateParamType(a.suffix, linkedValues, WomStringType),
+       validateParamType(a.array, linkedValues, WomArrayType(WomStringType))
+      ) mapN { (_, _) => WomArrayType(WomStringType) }
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
index 70e6e61a180..4dd7c528e8b 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
@@ -83,6 +83,7 @@ package object types {
         case a: Length => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Flatten => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Prefix => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Suffix => a.evaluateType(linkedValues)(typeEvaluator)
         case a: SelectFirst => a.evaluateType(linkedValues)(typeEvaluator)
         case a: SelectAll => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Defined => a.evaluateType(linkedValues)(typeEvaluator)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
index 788f114e181..db9df85bf06 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
@@ -217,4 +217,22 @@ object cascadesValueEvaluators {
         EvaluatedValue(WomString(arr.value.map(v => v.valueString).mkString(sepvalue.value)), Seq.empty).validNel
       }
   }
+
+  implicit val suffixFunctionEvaluator: ValueEvaluator[Suffix] = new ValueEvaluator[Suffix] {
+    override def evaluateValue(a: Suffix,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processTwoValidatedValues[WomString, WomArray, WomArray](
+        expressionValueEvaluator.evaluateValue(a.arg1, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        ),
+        expressionValueEvaluator.evaluateValue(a.arg2, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) { (suffix, arr) =>
+        EvaluatedValue(WomArray(arr.value.map(v => WomString(v.valueString + suffix.value))), Seq.empty).validNel
+      }
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
index 08eb74ac19c..8850d4371df 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
@@ -142,6 +142,8 @@ package object values {
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Prefix =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Suffix =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: SelectFirst =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: SelectAll =>
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
index a3a9cd4fb65..88b7aff6578 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
@@ -97,4 +97,10 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val expr = fromString[ExpressionElement](str, parser.parse_e)
     expr shouldBeValid NoneLiteralElement
   }
+
+  it should "parse the new suffix function" in {
+    val str = "suffix(some_str, some_arr)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (Suffix(IdentifierLookup("some_str"), IdentifierLookup("some_arr")))
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
index 65a03812c25..57beb7a12a1 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
@@ -57,4 +57,22 @@ class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
       e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_separator"), UnlinkedIdentifierHook("c")))
     }
   }
+
+  it should "discover the variable lookups within a suffix() call" in {
+    val str = """ suffix(my_suffix, ["a", "b", c]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_suffix"), UnlinkedIdentifierHook("c")))
+    }
+  }
+
+  it should "discover an array variable lookup within a suffix() call" in {
+    val str = """ suffix("SFX", my_array) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array")))
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
index 6e0a828855e..5335f7d5f29 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
@@ -45,4 +45,15 @@ class CascadesFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       )
     }
   }
+
+  it should "discover the file which would be required to evaluate a suffix() function" in {
+    val str = """ suffix(' # what a line', read_lines("foo.txt")) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
index 96c3c51e937..954ef0f52f0 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
@@ -56,4 +56,12 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
   }
 
+  it should "evaluate the type of a suffix() function as Array[String]" in {
+    val str = """ suffix('S', ["a", "b", "c"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
index 6dbad32d7d0..bd47a20ca68 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
@@ -200,4 +200,21 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
     }
   }
+
+  it should "evaluate a suffix expression correctly" in {
+    val str = """ suffix("S", ["a", "b", "c"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("aS"),
+        WomString("bS"),
+        WomString("cS")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
index 7765cac73bc..664696ee86d 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
@@ -52,6 +52,12 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     expr shouldBeInvalid "Failed to parse expression (reason 1 of 1): Unknown engine function: 'collect_by_key'"
   }
 
+  it should "not parse the new suffix function" in {
+    val str = "suffix(aStr, anArray)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeInvalid "Failed to parse expression (reason 1 of 1): Unknown engine function: 'suffix'"
+  }
+
   it should "parse the (biscayne) None keyword as a plain old identifier" in {
     val str = "None"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
index 70cc56b5a65..a85f3c34420 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
@@ -465,6 +465,7 @@ object WdlWriterImpl {
           case _: Zip => functionCall("zip")
           case _: Cross => functionCall("cross")
           case _: Prefix => functionCall("prefix")
+          case _: Suffix => functionCall("suffix")
           case _: Min => functionCall("min")
           case _: Max => functionCall("max")
           case _: Sep => functionCall("sep")

From da13c87fdb99cb705ea6d54b205a1f5d076f04cf Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 14 Feb 2024 21:06:07 -0500
Subject: [PATCH 277/326] WX-1417 New database role strategy (#7366)

---
 .../src/main/resources/changelog.xml          |  6 +++
 .../resources/changesets/set_table_role.xml   | 40 +++++++++++++++++++
 .../slick/MetadataSlickDatabase.scala         |  9 +----
 .../database/slick/SlickDatabase.scala        | 25 +++++++++++-
 docs/Configuring.md                           | 28 +++++++++++++
 5 files changed, 100 insertions(+), 8 deletions(-)
 create mode 100644 database/migration/src/main/resources/changesets/set_table_role.xml

diff --git a/database/migration/src/main/resources/changelog.xml b/database/migration/src/main/resources/changelog.xml
index 49d568766b3..cecc4e7b709 100644
--- a/database/migration/src/main/resources/changelog.xml
+++ b/database/migration/src/main/resources/changelog.xml
@@ -90,6 +90,12 @@
     <include file="changesets/enlarge_docker_hash_store_entry_id.xml" relativeToChangelogFile="true" />
     <include file="changesets/enlarge_workflow_store_entry_id.xml" relativeToChangelogFile="true" />
     <include file="changesets/enlarge_sub_workflow_store_entry_id.xml" relativeToChangelogFile="true" />
+    <!-- WARNING!
+      This changeset should always be last.
+      It is always run (and should always run last) to set table ownership correctly.
+      If your changeset adds a new table, make sure it is also owned by the sharedCromwellDbRole.
+    -->
+    <include file="changesets/set_table_role.xml" relativeToChangelogFile="true" />
     <!-- REMINDER!
       Before appending here, did you remember to include the 'objectQuotingStrategy="QUOTE_ALL_OBJECTS"' line in your changeset/xyz.xml...?
     -->
diff --git a/database/migration/src/main/resources/changesets/set_table_role.xml b/database/migration/src/main/resources/changesets/set_table_role.xml
new file mode 100644
index 00000000000..297cf041d95
--- /dev/null
+++ b/database/migration/src/main/resources/changesets/set_table_role.xml
@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog objectQuotingStrategy="QUOTE_ALL_OBJECTS"
+                   xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.3.xsd">
+
+    <!-- The 'engineSharedCromwellDbRole' can be set via JAVA_OPTS if desired (eg -DengineSharedCromwellDbRole=...). -->
+    <property  name="engineSharedCromwellDbRole" value=""/>
+
+    <!--
+        This changeset will be applied whenever the 'sharedCromwellDbRole' property is set.
+        It runs every time to ensure the role is set correctly after all other changesets.
+     -->
+    <changeSet runAlways="true" runOnChange="true" author="jdewar" id="set_table_role" dbms="postgresql">
+        <preConditions onFail="MARK_RAN">
+            <!-- check that 'engineSharedCromwellDbRole' role is set, and matches something in the pg_roles table -->
+            <sqlCheck expectedResult="1">
+                SELECT count(1)
+                FROM pg_roles
+                where '${engineSharedCromwellDbRole}' != '' and pg_roles.rolname = '${engineSharedCromwellDbRole}';
+            </sqlCheck>
+        </preConditions>
+        <sql>
+            ALTER TABLE "CALL_CACHING_AGGREGATION_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "CALL_CACHING_DETRITUS_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "CALL_CACHING_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "CALL_CACHING_HASH_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "CALL_CACHING_SIMPLETON_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "DOCKER_HASH_STORE_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "JOB_KEY_VALUE_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "JOB_STORE_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "JOB_STORE_SIMPLETON_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "SUB_WORKFLOW_STORE_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "WORKFLOW_STORE_ENTRY" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "databasechangelog" OWNER TO ${engineSharedCromwellDbRole};
+            ALTER TABLE "databasechangeloglock" OWNER TO ${engineSharedCromwellDbRole};
+        </sql>
+    </changeSet>
+
+</databaseChangeLog>
diff --git a/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
index c0723af6795..fbab736ae26 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/MetadataSlickDatabase.scala
@@ -14,7 +14,6 @@ import cromwell.database.sql.tables.{
   MetadataEntry,
   WorkflowMetadataSummaryEntry
 }
-import net.ceedubs.ficus.Ficus._
 import slick.basic.DatabasePublisher
 import slick.jdbc.{ResultSetConcurrency, ResultSetType}
 
@@ -76,8 +75,6 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
   import dataAccess.driver.api._
   import MetadataSlickDatabase._
 
-  lazy val pgLargeObjectWriteRole: Option[String] = originalDatabaseConfig.as[Option[String]]("pgLargeObjectWriteRole")
-
   override def existsMetadataEntries()(implicit ec: ExecutionContext): Future[Boolean] = {
     val action = dataAccess.metadataEntriesExists.result
     runTransaction(action)
@@ -106,8 +103,6 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
       labelMetadataKey
     )
 
-    val roleSet = pgLargeObjectWriteRole.map(role => sqlu"""SET ROLE TO "#$role"""")
-
     // These entries also require a write to the summary queue.
     def writeSummarizable(): Future[Unit] = if (partitioned.summarizableMetadata.isEmpty) Future.successful(())
     else {
@@ -116,7 +111,7 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
         val insertMetadata = dataAccess.metadataEntryIdsAutoInc ++= batch
         insertMetadata.flatMap(ids => writeSummaryQueueEntries(ids))
       }
-      runTransaction(DBIO.sequence(roleSet ++ insertActions)).void
+      runTransaction(DBIO.sequence(insertActions)).void
     }
 
     // Non-summarizable metadata that only needs to go to the metadata table can be written much more efficiently
@@ -124,7 +119,7 @@ class MetadataSlickDatabase(originalDatabaseConfig: Config)
     def writeNonSummarizable(): Future[Unit] = if (partitioned.nonSummarizableMetadata.isEmpty) Future.successful(())
     else {
       val action = DBIO.sequence(
-        roleSet ++ partitioned.nonSummarizableMetadata.grouped(insertBatchSize).map(dataAccess.metadataEntries ++= _)
+        partitioned.nonSummarizableMetadata.grouped(insertBatchSize).map(dataAccess.metadataEntries ++= _)
       )
       runLobAction(action).void
     }
diff --git a/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala b/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala
index 55c408f944f..bc9b085b1f1 100644
--- a/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala
+++ b/database/sql/src/main/scala/cromwell/database/slick/SlickDatabase.scala
@@ -72,6 +72,19 @@ abstract class SlickDatabase(override val originalDatabaseConfig: Config) extend
   // NOTE: if you want to refactor database is inner-class type: this.dataAccess.driver.backend.DatabaseFactory
   val database = slickConfig.db
 
+  /*
+  In some cases we want to write Postgres Large Objects (corresponding to Clob/Blob in Slick)
+  with a role other than the database user we are authenticated as. This is important
+  when we want multiple login users to be able to access the records. We can SET ROLE to
+  a role granted to all of them, and they'll all be able to access the Large Objects.
+  This SO thread also has a good explanation:
+  https://dba.stackexchange.com/questions/147607/postgres-large-objects-multiple-users
+   */
+  private lazy val pgLargeObjectWriteRole: Option[String] =
+    originalDatabaseConfig.as[Option[String]]("pgLargeObjectWriteRole")
+  private lazy val roleSetCmd =
+    pgLargeObjectWriteRole.map(role => sqlu"""SET LOCAL ROLE TO "#$role"""")
+
   override lazy val connectionDescription: String = databaseConfig.getString(urlKey)
 
   SlickDatabase.log.info(s"Running with database $urlKey = $connectionDescription")
@@ -167,7 +180,17 @@ abstract class SlickDatabase(override val originalDatabaseConfig: Config) extend
                                         isolationLevel: TransactionIsolation = TransactionIsolation.RepeatableRead,
                                         timeout: Duration = Duration.Inf
   ): Future[R] =
-    runActionInternal(action.transactionally.withTransactionIsolation(isolationLevel), timeout = timeout)
+    runActionInternal(withLobRole(action).transactionally.withTransactionIsolation(isolationLevel), timeout = timeout)
+
+  /*
+  If we're using Postgres and have been configured to do so, set the desired role on the transaction.
+  See comments on `roleSetCmd` above for more information.
+   */
+  private def withLobRole[R](action: DBIO[R]): DBIO[R] =
+    (dataAccess.driver, roleSetCmd) match {
+      case (PostgresProfile, Some(roleSet)) => roleSet.andThen(action)
+      case _ => action
+    }
 
   /* Note that this is only appropriate for actions that do not involve Blob
    * or Clob fields in Postgres, since large object support requires running
diff --git a/docs/Configuring.md b/docs/Configuring.md
index aa810d19a0c..076295d115c 100644
--- a/docs/Configuring.md
+++ b/docs/Configuring.md
@@ -324,6 +324,34 @@ database {
 }
 ```
 
+If you want multiple database users to be able to read Cromwell's data from a Postgresql database, you'll need to create a
+role that all relevant users have access to, and adjust Cromwell to use this role. This is because each Large Object is owned
+by, and only readable by, the role that wrote it.
+
+First, pass these options when executing Cromwell. They will ensure that Cromwell's database tables are 
+owned by the role, not the initial login user.
+ * `-DengineSharedCromwellDbRole=your_role` to control the role that owns the engine tables
+ * `-DsharedCromwellDbRole=your_role` to control the role that owns the metadata tables
+
+Next, use the config key `pgLargeObjectWriteRole` to set the role that should own all large objects, as shown below. 
+This config will have no effect if you aren't using Postgresql. The configured login user can be any user that is
+granted the shared role.
+
+```hocon
+database {
+  profile = "slick.jdbc.PostgresProfile$"
+  pgLargeObjectWriteRole = "your_role"
+  db {
+    driver = "org.postgresql.Driver"
+    url = "jdbc:postgresql://localhost:5432/cromwell"
+    user = "user"
+    password = "pass"
+    port = 5432
+    connectionTimeout = 5000
+  }
+}
+```
+
 **Using Cromwell with file-based database (No server required)**
 
 SQLite is currently not supported. However, HSQLDB does support running with a persistence file.

From f01c1f3fb4e23ee86704d7ff339798298bcb46e1 Mon Sep 17 00:00:00 2001
From: Maria Yazykova <95451512+zykonda@users.noreply.github.com>
Date: Tue, 20 Feb 2024 07:54:50 -0800
Subject: [PATCH 278/326] [WM-2291] Callback API contract tests between
 Cromwell and CBAS (#7251)

Co-authored-by: Chris Llanwarne <cjllanwarne@gmail.com>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .github/workflows/consumer_contract_tests.yml |  30 ++++-
 build.sbt                                     |   2 +
 .../scala/cloud/nio/spi/CloudNioPath.scala    |   2 +-
 .../main/scala/cloud/nio/spi/UnixPath.scala   |   6 +-
 .../finalization/WorkflowCallbackActor.scala  |   6 +-
 pact4s/README.md                              |   2 +
 .../workbench/cromwell/consumer/Helper.scala  |  23 +++-
 .../cromwell/consumer/CbasCallbackSpec.scala  | 118 ++++++++++++++++++
 .../cromwell/consumer/DrsHubClientSpec.scala  |   2 +-
 project/Dependencies.scala                    |   4 +-
 project/Settings.scala                        |   4 -
 11 files changed, 183 insertions(+), 16 deletions(-)
 create mode 100644 pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/CbasCallbackSpec.scala

diff --git a/.github/workflows/consumer_contract_tests.yml b/.github/workflows/consumer_contract_tests.yml
index cce91ff3e2e..4635abaa765 100644
--- a/.github/workflows/consumer_contract_tests.yml
+++ b/.github/workflows/consumer_contract_tests.yml
@@ -116,7 +116,8 @@ jobs:
     runs-on: ubuntu-latest
     needs: [init-github-context]
     outputs:
-      pact-b64: ${{ steps.encode-pact.outputs.pact-b64 }}
+      pact-b64-drshub: ${{ steps.encode-pact.outputs.pact-b64-drshub }}
+      pact-b64-cbas: ${{ steps.encode-pact.outputs.pact-b64-cbas }}
 
     steps:
       - uses: actions/checkout@v3
@@ -132,9 +133,12 @@ jobs:
       - name: Output consumer contract as non-breaking base64 string
         id: encode-pact
         run: |
+          set -e
           cd pact4s
-          NON_BREAKING_B64=$(cat target/pacts/cromwell-drshub.json | base64 -w 0)
-          echo "pact-b64=${NON_BREAKING_B64}" >> $GITHUB_OUTPUT
+          NON_BREAKING_B64_DRSHUB=$(cat target/pacts/cromwell-drshub.json | base64 -w 0)
+          NON_BREAKING_B64_CBAS=$(cat target/pacts/cromwell-cbas.json | base64 -w 0)
+          echo "pact-b64-drshub=${NON_BREAKING_B64_DRSHUB}" >> $GITHUB_OUTPUT
+          echo "pact-b64-cbas=${NON_BREAKING_B64_CBAS}" >> $GITHUB_OUTPUT
 
   # Prevent untrusted sources from using PRs to publish contracts
   # since access to secrets is not allowed.
@@ -143,7 +147,23 @@ jobs:
     if: ${{ needs.init-github-context.outputs.fork == 'false' ||  needs.init-github-context.outputs.fork == ''}}
     needs: [init-github-context, cromwell-contract-tests]
     steps:
-      - name: Dispatch to terra-github-workflows
+      - name: Dispatch drshub to terra-github-workflows
+        uses: broadinstitute/workflow-dispatch@v4.0.0
+        with:
+          run-name: "${{ env.PUBLISH_CONTRACTS_RUN_NAME }}"
+          workflow: .github/workflows/publish-contracts.yaml
+          repo: broadinstitute/terra-github-workflows
+          ref: refs/heads/main
+          token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # github token for access to kick off a job in the private repo
+          inputs: '{
+            "run-name": "${{ env.PUBLISH_CONTRACTS_RUN_NAME }}",
+            "pact-b64": "${{ needs.cromwell-contract-tests.outputs.pact-b64-drshub }}",
+            "repo-owner": "${{ github.repository_owner }}",
+            "repo-name": "${{ github.event.repository.name }}",
+            "repo-branch": "${{ needs.init-github-context.outputs.repo-branch }}",
+            "release-tag": "${{ needs.init-github-context.outputs.repo-version }}"
+          }'
+      - name: Dispatch cbas to terra-github-workflows
         uses: broadinstitute/workflow-dispatch@v4.0.0
         with:
           run-name: "${{ env.PUBLISH_CONTRACTS_RUN_NAME }}"
@@ -153,7 +173,7 @@ jobs:
           token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # github token for access to kick off a job in the private repo
           inputs: '{
             "run-name": "${{ env.PUBLISH_CONTRACTS_RUN_NAME }}",
-            "pact-b64": "${{ needs.cromwell-contract-tests.outputs.pact-b64 }}",
+            "pact-b64": "${{ needs.cromwell-contract-tests.outputs.pact-b64-cbas }}",
             "repo-owner": "${{ github.repository_owner }}",
             "repo-name": "${{ github.event.repository.name }}",
             "repo-branch": "${{ needs.init-github-context.outputs.repo-branch }}",
diff --git a/build.sbt b/build.sbt
index 2c9a8068992..79085e31e92 100644
--- a/build.sbt
+++ b/build.sbt
@@ -399,7 +399,9 @@ lazy val `cromwell-drs-localizer` = project
 
 lazy val pact4s = project.in(file("pact4s"))
   .settings(pact4sSettings)
+  .dependsOn(engine)
   .dependsOn(services)
+  .dependsOn(engine % "test->test")
   .disablePlugins(sbtassembly.AssemblyPlugin)
 
 lazy val server = project
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
index b6803670d39..530ba5526ef 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala
@@ -176,7 +176,7 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
   ): WatchKey = throw new UnsupportedOperationException
 
   override def iterator(): java.util.Iterator[Path] =
-    if (unixPath.isEmpty || unixPath.isRoot) {
+    if (unixPath.izEmpty || unixPath.isRoot) {
       java.util.Collections.emptyIterator()
     } else {
       unixPath.split().to(LazyList).map(part => newPath(UnixPath.getPath(part)).asInstanceOf[Path]).iterator.asJava
diff --git a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
index b7d9ed02035..41d742a4e66 100644
--- a/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
+++ b/cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala
@@ -67,7 +67,11 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
 
   def isAbsolute: Boolean = UnixPath.isAbsolute(path)
 
-  def isEmpty: Boolean = path.isEmpty
+  // Named this way because isEmpty is a name collision new in 17.
+  // The initial compile error is that it needs an override.
+  // Adding the override results in a second error saying it overrides nothing!
+  // So, we just renamed it.
+  def izEmpty: Boolean = path.isEmpty
 
   def hasTrailingSeparator: Boolean = UnixPath.hasTrailingSeparator(path)
 
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
index bd5547e0252..726066b09ee 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/finalization/WorkflowCallbackActor.scala
@@ -11,7 +11,7 @@ import akka.http.scaladsl.model.headers.RawHeader
 import akka.routing.Broadcast
 import akka.util.ByteString
 import cats.data.Validated.{Invalid, Valid}
-import cats.implicits.toTraverseOps
+import cats.implicits.{catsSyntaxValidatedId, toTraverseOps}
 import com.typesafe.config.Config
 import com.typesafe.scalalogging.LazyLogging
 import common.validation.ErrorOr
@@ -50,6 +50,10 @@ object WorkflowCallbackConfig extends LazyLogging {
     override def getAccessToken: ErrorOr.ErrorOr[String] = AzureCredentials.getAccessToken()
   }
 
+  case class StaticTokenAuth(token: String) extends AuthMethod {
+    override def getAccessToken: ErrorOr.ErrorOr[String] = token.validNel
+  }
+
   private lazy val defaultNumThreads = 5
   private lazy val defaultRetryBackoff = SimpleExponentialBackoff(3.seconds, 5.minutes, 1.1)
   private lazy val defaultMaxRetries = 10
diff --git a/pact4s/README.md b/pact4s/README.md
index fd3245a877d..053307943cf 100644
--- a/pact4s/README.md
+++ b/pact4s/README.md
@@ -8,6 +8,7 @@ pact4s is used for contract testing.
   val pact4sDependencies = Seq(
     pact4sScalaTest,
     pact4sCirce,
+    pact4sSpray
     http4sEmberClient,
     http4sDsl,
     http4sEmberServer,
@@ -47,4 +48,5 @@ docker run --rm -v $PWD:/working \
 
 The generated contracts can be found in the `./target/pacts` folder
 - `cromwell-drshub.json`
+- `cromwell-cbas.json`
 
diff --git a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
index 2a63324247a..1405ec20f87 100644
--- a/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
+++ b/pact4s/src/main/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/Helper.scala
@@ -108,7 +108,7 @@ object PactHelper {
                        requestBody: DslPart,
                        status: Int,
                        responseHeaders: Seq[(String, String)],
-                       responsBody: DslPart
+                       responseBody: DslPart
   ): PactDslResponse =
     builder
       .`given`(state, scala.jdk.CollectionConverters.MapHasAsJava(stateParams).asJava)
@@ -120,7 +120,26 @@ object PactHelper {
       .willRespondWith()
       .status(status)
       .headers(scala.jdk.CollectionConverters.MapHasAsJava(responseHeaders.toMap).asJava)
-      .body(responsBody)
+      .body(responseBody)
+
+  def buildInteraction[A](builder: PactDslWithProvider,
+                          state: String,
+                          uponReceiving: String,
+                          method: String,
+                          path: String,
+                          requestHeaders: Seq[(String, String)],
+                          requestBody: A,
+                          status: Int
+  )(implicit ev: PactBodyJsonEncoder[A]): PactDslResponse =
+    builder
+      .`given`(state)
+      .uponReceiving(uponReceiving)
+      .method(method)
+      .path(path)
+      .headers(scala.jdk.CollectionConverters.MapHasAsJava(requestHeaders.toMap).asJava)
+      .body(ev.toJsonString(requestBody))
+      .willRespondWith()
+      .status(status)
 
   def buildInteraction(builder: PactDslResponse,
                        state: String,
diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/CbasCallbackSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/CbasCallbackSpec.scala
new file mode 100644
index 00000000000..e2b353dd70f
--- /dev/null
+++ b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/CbasCallbackSpec.scala
@@ -0,0 +1,118 @@
+package org.broadinstitute.dsde.workbench.cromwell.consumer
+
+import akka.testkit._
+import au.com.dius.pact.consumer.dsl._
+import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
+import au.com.dius.pact.core.model.RequestResponsePact
+import cromwell.core.retry.SimpleExponentialBackoff
+import cromwell.core.{CallOutputs, TestKitSuite, WorkflowId, WorkflowSucceeded}
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackActor.PerformCallbackCommand
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackConfig.StaticTokenAuth
+import cromwell.engine.workflow.lifecycle.finalization.WorkflowCallbackJsonSupport._
+import cromwell.engine.workflow.lifecycle.finalization.{CallbackMessage, WorkflowCallbackActor, WorkflowCallbackConfig}
+import cromwell.services.metadata.MetadataKey
+import cromwell.services.metadata.MetadataService.PutMetadataAction
+import cromwell.util.GracefulShutdownHelper
+import org.broadinstitute.dsde.workbench.cromwell.consumer.PactHelper._
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.matchers.should.Matchers
+import pact4s.scalatest.RequestResponsePactForger
+import pact4s.sprayjson.implicits._
+import wom.graph.GraphNodePort.GraphNodeOutputPort
+import wom.graph.WomIdentifier
+import wom.types.WomStringType
+import wom.values._
+
+import java.net.URI
+import java.util.UUID
+import scala.concurrent.ExecutionContextExecutor
+import scala.concurrent.duration._
+
+class CbasCallbackSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with RequestResponsePactForger {
+
+  implicit val ec: ExecutionContextExecutor = system.dispatcher
+
+  // Akka test setup
+  private val msgWait = 10.second.dilated
+  private val serviceRegistryActor = TestProbe("testServiceRegistryActor")
+  private val deathWatch = TestProbe("deathWatch")
+
+  private val callbackEndpoint = "/api/batch/v1/runs/results"
+  private val bearerToken = "my-token"
+  private val workflowId = WorkflowId(UUID.fromString("12345678-1234-1234-1111-111111111111"))
+  private val basicOutputs = CallOutputs(
+    Map(
+      GraphNodeOutputPort(WomIdentifier("foo", "wf.foo"), WomStringType, null) -> WomString("bar"),
+      GraphNodeOutputPort(WomIdentifier("hello", "wf.hello.hello"), WomStringType, null) -> WomString("Hello")
+    )
+  )
+
+  // This is the message that we expect Cromwell to send CBAS in this test
+  private val expectedCallbackMessage = CallbackMessage(
+    workflowId.toString,
+    "Succeeded",
+    Map(("wf.foo", WomString("bar")), ("wf.hello.hello", WomString("Hello"))),
+    List.empty
+  )
+
+  // Define the folder that the pact contracts get written to upon completion of this test suite.
+  override val pactTestExecutionContext: PactTestExecutionContext =
+    new PactTestExecutionContext(
+      "./target/pacts"
+    )
+
+  val consumerPactBuilder: ConsumerPactBuilder = ConsumerPactBuilder
+    .consumer("cromwell")
+
+  val pactProvider: PactDslWithProvider = consumerPactBuilder
+    .hasPactWith("cbas")
+
+  var pactUpdateCompletedRunDslResponse: PactDslResponse = buildInteraction(
+    pactProvider,
+    state = "post completed workflow results",
+    uponReceiving = "Request to post workflow results",
+    method = "POST",
+    path = callbackEndpoint,
+    requestHeaders = Seq("Authorization" -> "Bearer %s".format(bearerToken), "Content-type" -> "application/json"),
+    requestBody = expectedCallbackMessage,
+    status = 200
+  )
+  override val pact: RequestResponsePact = pactUpdateCompletedRunDslResponse.toPact
+
+  it should "send the right callback to the right URI" in {
+    // Create actor
+    val callbackConfig = WorkflowCallbackConfig.empty
+      .copy(enabled = true)
+      .copy(retryBackoff = SimpleExponentialBackoff(100.millis, 200.millis, 1.1))
+      .copy(authMethod = Option(StaticTokenAuth(bearerToken)))
+      .copy(defaultUri = Option(new URI(mockServer.getUrl + callbackEndpoint)))
+
+    val props = WorkflowCallbackActor.props(
+      serviceRegistryActor.ref,
+      callbackConfig
+    )
+    val workflowCallbackActor = system.actorOf(props, "testWorkflowCallbackActorPact")
+
+    // Send a command to trigger callback
+    val cmd = PerformCallbackCommand(
+      workflowId = workflowId,
+      uri = None,
+      terminalState = WorkflowSucceeded,
+      workflowOutputs = basicOutputs,
+      List.empty
+    )
+    workflowCallbackActor ! cmd
+
+    // Confirm the callback was successful
+    serviceRegistryActor.expectMsgPF(msgWait) {
+      case PutMetadataAction(List(resultEvent, _, _), _) =>
+        resultEvent.key shouldBe MetadataKey(workflowId, None, "workflowCallback", "successful")
+      case _ =>
+    }
+
+    // Shut the actor down
+    deathWatch.watch(workflowCallbackActor)
+    workflowCallbackActor ! GracefulShutdownHelper.ShutdownCommand
+    deathWatch.expectTerminated(workflowCallbackActor, msgWait)
+  }
+}
diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
index 5fae4a4bfc5..bc0155020f1 100644
--- a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
+++ b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/DrsHubClientSpec.scala
@@ -138,7 +138,7 @@ class DrsHubClientSpec extends AnyFlatSpec with Matchers with RequestResponsePac
     requestBody = resourceRequestDsl,
     status = 200,
     responseHeaders = Seq(),
-    responsBody = resourceMetadataResponseDsl
+    responseBody = resourceMetadataResponseDsl
   )
 
   pactDslResponse = buildInteraction(
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 241260329c6..5b073bbdcec 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -839,14 +839,16 @@ object Dependencies {
   val http4sCirce = "org.http4s" %% "http4s-circe" % http4sV
   val pact4sScalaTest = "io.github.jbwheatley" %% "pact4s-scalatest" % pact4sV % Test
   val pact4sCirce = "io.github.jbwheatley" %% "pact4s-circe" % pact4sV
+  val pact4sSpray = "io.github.jbwheatley" %% "pact4s-spray-json" % pact4sV
 
   val pact4sDependencies = Seq(
     pact4sScalaTest,
     pact4sCirce,
+    pact4sSpray,
     http4sEmberClient,
     http4sDsl,
     http4sEmberServer,
     http4sCirce,
     scalaTest,
-  )
+  ) ++ akkaDependencies
 }
diff --git a/project/Settings.scala b/project/Settings.scala
index 9a33f663cef..628a77db4c6 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -101,7 +101,6 @@ object Settings {
 
   val pact4sSettings = sharedSettings ++ List(
     libraryDependencies ++= pact4sDependencies,
-
     /**
       * Invoking pact tests from root project (sbt "project pact" test)
       * will launch tests in a separate JVM context that ensures contracts
@@ -111,9 +110,6 @@ object Settings {
     Test / fork := true
   ) ++ assemblySettings
 
-  lazy val pact4s = project.in(file("pact4s"))
-    .settings(pact4sSettings)
-
   /*
       Docker instructions to install Google Cloud SDK image in docker image. It also installs `crcmod` which
       is needed while downloading large files using `gsutil`.

From 2019b27138c225d2610e26c6a4788baf8e211bfa Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Tue, 20 Feb 2024 16:10:03 -0500
Subject: [PATCH 279/326] WX-1445 Update docker image regex to handle python:3
 correctly (#7367)

---
 .../src/main/scala/cromwell/docker/DockerImageIdentifier.scala  | 2 +-
 .../test/scala/cromwell/docker/DockerImageIdentifierSpec.scala  | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala b/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala
index f34702509db..7c20760b644 100644
--- a/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala
+++ b/dockerHashing/src/main/scala/cromwell/docker/DockerImageIdentifier.scala
@@ -56,7 +56,7 @@ object DockerImageIdentifier {
 
        (                                        # Begin capturing group for name
           [a-z0-9]+(?:[._-][a-z0-9]+)*          # API v2 name component regex - see https://docs.docker.com/registry/spec/api/#/overview
-          (?::[0-9]+)?                          # Optional port
+          (?::[0-9]{4,5}|:443)?                 # Optional port (expect 4 or 5 digits OR :443)
           (?:/[a-z0-9]+(?:[._-][a-z0-9]+)*)*    # Optional additional name components separated by /
        )                                        # End capturing group for name
 
diff --git a/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala b/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala
index 35fe341737b..30c8cb6a010 100644
--- a/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala
+++ b/dockerHashing/src/test/scala/cromwell/docker/DockerImageIdentifierSpec.scala
@@ -41,6 +41,8 @@ class DockerImageIdentifierSpec
        "0.8.1.1--htslib1.5_0"
       ),
       ("terrabatchdev.azurecr.io/postgres:latest", Option("terrabatchdev.azurecr.io"), None, "postgres", "latest"),
+      ("python:3", None, None, "python", "3"),
+      ("localhost:443/ubuntu", Option("localhost:443"), None, "ubuntu", "latest"),
       // Very long tags with trailing spaces cause problems for the re engine
       ("someuser/someimage:supercalifragilisticexpialidociouseventhoughthesoundofitissomethingquiteatrociousifyousayitloudenoughyoullalwayssoundprecocious ",
        None,

From 2a1c4ad2a56ad5922756ff5e28289dd8a781094d Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 22 Feb 2024 21:30:04 -0500
Subject: [PATCH 280/326] =?UTF-8?q?WX-1252=20Runtime=20attributes=20cleanu?=
 =?UTF-8?q?p=20=E2=80=93=20CWL=20runtime=20attributes=20(#7370)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../cromwell/backend/RuntimeEnvironment.scala |  5 +-
 .../backend/validation/CpuValidation.scala    |  4 --
 .../RuntimeAttributesValidationSpec.scala     | 10 ----
 .../impl/aws/AwsBatchRuntimeAttributes.scala  | 15 ------
 ...cpBatchAsyncBackendJobExecutionActor.scala | 28 +----------
 .../batch/api/GcpBatchRequestFactory.scala    |  2 +-
 .../api/GcpBatchRequestFactoryImpl.scala      |  2 +-
 .../batch/io/GcpBatchAttachedDisk.scala       | 11 ----
 .../models/GcpBatchRuntimeAttributes.scala    | 49 +-----------------
 .../google/batch/util/GpuValidation.scala     |  6 +--
 ...tchAsyncBackendJobExecutionActorSpec.scala |  2 -
 .../pipelines/common/GpuValidation.scala      |  6 +--
 ...inesApiAsyncBackendJobExecutionActor.scala | 28 +----------
 .../PipelinesApiRuntimeAttributes.scala       | 50 +------------------
 .../api/PipelinesApiRequestFactory.scala      |  2 +-
 .../common/io/PipelinesApiAttachedDisk.scala  | 12 -----
 ...ApiAsyncBackendJobExecutionActorSpec.scala |  2 -
 .../pipelines/v2alpha1/GenomicsFactory.scala  |  2 +-
 .../v2beta/LifeSciencesFactory.scala          |  2 +-
 .../impl/sfs/config/ConfigConstants.scala     |  4 --
 .../sfs/config/DeclarationValidation.scala    | 14 ------
 .../MemoryDeclarationValidationSpec.scala     | 46 ++---------------
 .../config/DeclarationValidationSpec.scala    |  4 +-
 .../main/scala/wom/RuntimeAttributes.scala    | 20 --------
 24 files changed, 22 insertions(+), 304 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala b/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala
index 40f8f1f7b07..beac15b1610 100644
--- a/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala
+++ b/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala
@@ -3,7 +3,7 @@ package cromwell.backend
 import java.util.UUID
 
 import cromwell.backend.io.JobPaths
-import cromwell.backend.validation.{CpuValidation, MemoryValidation}
+import cromwell.backend.validation.MemoryValidation
 import cromwell.core.path.Path
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
@@ -27,7 +27,8 @@ object RuntimeEnvironmentBuilder {
       callRoot.resolve(s"tmp.$hash").pathAsString
     }
 
-    val cores: Int Refined Positive = CpuValidation.instanceMin.validate(runtimeAttributes).getOrElse(minimums.cores)
+    // This class is going away in https://github.com/broadinstitute/cromwell/pull/7369
+    val cores: Int Refined Positive = minimums.cores
 
     val memoryInMB: Double =
       MemoryValidation
diff --git a/backend/src/main/scala/cromwell/backend/validation/CpuValidation.scala b/backend/src/main/scala/cromwell/backend/validation/CpuValidation.scala
index 0cc06a7dfa4..0038290010c 100644
--- a/backend/src/main/scala/cromwell/backend/validation/CpuValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/CpuValidation.scala
@@ -24,10 +24,6 @@ import wom.values.{WomInteger, WomValue}
 object CpuValidation {
   lazy val instance: RuntimeAttributesValidation[Int Refined Positive] = new CpuValidation(CpuKey)
   lazy val optional: OptionalRuntimeAttributesValidation[Int Refined Positive] = instance.optional
-  lazy val instanceMin: RuntimeAttributesValidation[Int Refined Positive] = new CpuValidation(CpuMinKey)
-  lazy val optionalMin: OptionalRuntimeAttributesValidation[Int Refined Positive] = instanceMin.optional
-  lazy val instanceMax: RuntimeAttributesValidation[Int Refined Positive] = new CpuValidation(CpuMaxKey)
-  lazy val optionalMax: OptionalRuntimeAttributesValidation[Int Refined Positive] = instanceMax.optional
 
   lazy val defaultMin: WomValue = WomInteger(1)
   def configDefaultWomValue(config: Option[Config]): Option[WomValue] = instance.configDefaultWomValue(config)
diff --git a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala
index 6d3bcb6bafa..8f692d6486a 100644
--- a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala
@@ -410,20 +410,10 @@ class RuntimeAttributesValidationSpec
         ConfigFactory.parseString(backendConfigTemplate).getConfig("default-runtime-attributes")
 
       val memoryVal = MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, Some(backendConfig))
-      val memoryMinVal = MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMinKey, Some(backendConfig))
-      val memoryMaxVal = MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMaxKey, Some(backendConfig))
       MemoryValidation
         .withDefaultMemory(RuntimeAttributesKeys.MemoryKey, memoryVal.get)
         .runtimeAttributeDefinition
         .factoryDefault shouldBe Some(WomLong(2147483648L))
-      MemoryValidation
-        .withDefaultMemory(RuntimeAttributesKeys.MemoryMinKey, memoryMinVal.get)
-        .runtimeAttributeDefinition
-        .factoryDefault shouldBe Some(WomLong(322122547L))
-      MemoryValidation
-        .withDefaultMemory(RuntimeAttributesKeys.MemoryMaxKey, memoryMaxVal.get)
-        .runtimeAttributeDefinition
-        .factoryDefault shouldBe Some(WomLong(429496729L))
     }
 
     "shouldn't throw up if the value for a default-runtime-attribute key cannot be coerced into an expected WomType" in {
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index 87f04cc44dc..447f48ae2b9 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -97,10 +97,6 @@ object AwsBatchRuntimeAttributes {
     CpuValidation.instance
       .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
 
-  private def cpuMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] =
-    CpuValidation.instanceMin
-      .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
-
   private def failOnStderrValidation(runtimeConfig: Option[Config]) = FailOnStderrValidation.default(runtimeConfig)
 
   private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) =
@@ -120,13 +116,6 @@ object AwsBatchRuntimeAttributes {
       MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, runtimeConfig) getOrElse MemoryDefaultValue
     )
 
-  private def memoryMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] =
-    MemoryValidation.withDefaultMemory(RuntimeAttributesKeys.MemoryMinKey,
-                                       MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMinKey,
-                                                                            runtimeConfig
-                                       ) getOrElse MemoryDefaultValue
-    )
-
   private def noAddressValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] =
     noAddressValidationInstance
       .withDefault(noAddressValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue)
@@ -152,11 +141,9 @@ object AwsBatchRuntimeAttributes {
       .default(runtimeConfig)
       .withValidation(
         cpuValidation(runtimeConfig),
-        cpuMinValidation(runtimeConfig),
         disksValidation(runtimeConfig),
         zonesValidation(runtimeConfig),
         memoryValidation(runtimeConfig),
-        memoryMinValidation(runtimeConfig),
         noAddressValidation(runtimeConfig),
         dockerValidation,
         queueArnValidation(runtimeConfig),
@@ -166,11 +153,9 @@ object AwsBatchRuntimeAttributes {
       .default(runtimeConfig)
       .withValidation(
         cpuValidation(runtimeConfig),
-        cpuMinValidation(runtimeConfig),
         disksValidation(runtimeConfig),
         zonesValidation(runtimeConfig),
         memoryValidation(runtimeConfig),
-        memoryMinValidation(runtimeConfig),
         noAddressValidation(runtimeConfig),
         dockerValidation,
         queueArnValidation(runtimeConfig)
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
index eba54bdc4c3..dbd63740ad0 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
@@ -48,13 +48,11 @@ import shapeless.Coproduct
 import org.apache.commons.codec.digest.DigestUtils
 import org.apache.commons.csv.{CSVFormat, CSVPrinter}
 import org.apache.commons.io.output.ByteArrayOutputStream
-import wdl4s.parser.MemoryUnit
 import wom.callable.Callable.OutputDefinition
 import wom.callable.MetaValueElement.{MetaValueElementBoolean, MetaValueElementObject}
 import wom.callable.{AdHocValue, RuntimeEnvironment}
 import wom.core.FullyQualifiedName
 import wom.expression.{FileEvaluation, NoIoFunctionSet}
-import wom.format.MemorySize
 import wom.values._
 
 import java.io.OutputStreamWriter
@@ -590,30 +588,6 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
           token <- data.privateDockerEncryptedToken
         } yield CreateBatchDockerKeyAndToken(key, token)
 
-        /*
-         * Right now this doesn't cost anything, because sizeOption returns the size if it was previously already fetched
-         * for some reason (expression evaluation for instance), but otherwise does not retrieve it and returns None.
-         * In CWL-land we tend to be aggressive in pre-fetching the size in order to be able to evaluate JS expressions,
-         * but less in WDL as we can get it last minute and on demand because size is a WDL function, whereas in CWL
-         * we don't inspect the JS to know if size is called and therefore always pre-fetch it.
-         *
-         * We could decide to call withSize before in which case we would retrieve the size for all files and have
-         * a guaranteed more accurate total size, but there might be performance impacts ?
-         */
-        val inputFileSize = Option(callInputFiles.values.flatMap(_.flatMap(_.sizeOption)).sum)
-
-        // Attempt to adjust the disk size by taking into account the size of input files
-        val adjustedSizeDisks =
-          inputFileSize.map(size => MemorySize.apply(size.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB)) map {
-            inputFileSizeInformation =>
-              runtimeAttributes.disks.adjustWorkingDiskWithNewMin(
-                inputFileSizeInformation,
-                jobLogger.info(
-                  s"Adjusted working disk size to ${inputFileSizeInformation.amount} GB to account for input files"
-                )
-              )
-          } getOrElse runtimeAttributes.disks
-
         val inputFilePaths = inputOutputParameters.jobInputParameters.map(_.cloudPath.pathAsString).toSet
 
         val referenceDisksToMount =
@@ -667,7 +641,7 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
           jobShell = batchConfiguration.jobShell,
           privateDockerKeyAndEncryptedToken = dockerKeyAndToken,
           womOutputRuntimeExtractor = jobDescriptor.workflowDescriptor.outputRuntimeExtractor,
-          adjustedSizeDisks = adjustedSizeDisks,
+          disks = runtimeAttributes.disks,
           virtualPrivateCloudConfiguration = batchAttributes.virtualPrivateCloudConfiguration,
           retryWithMoreMemoryKeys = retryWithMoreMemoryKeys,
           fuseEnabled = fuseEnabled(jobDescriptor.workflowDescriptor),
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala
index 3c69c3c8fb4..19421acef8b 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactory.scala
@@ -80,7 +80,7 @@ object GcpBatchRequestFactory {
                                       jobShell: String,
                                       privateDockerKeyAndEncryptedToken: Option[CreateBatchDockerKeyAndToken],
                                       womOutputRuntimeExtractor: Option[WomOutputRuntimeExtractor],
-                                      adjustedSizeDisks: Seq[GcpBatchAttachedDisk],
+                                      disks: Seq[GcpBatchAttachedDisk],
                                       virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
                                       retryWithMoreMemoryKeys: Option[List[String]],
                                       fuseEnabled: Boolean,
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
index a8f6519b7a5..f1f81a6f03b 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/api/GcpBatchRequestFactoryImpl.scala
@@ -161,7 +161,7 @@ class GcpBatchRequestFactoryImpl()(implicit gcsTransferConfiguration: GcsTransfe
     val createParameters = data.createParameters
     val retryCount = data.gcpBatchParameters.runtimeAttributes.preemptible
     val allDisksToBeMounted: Seq[GcpBatchAttachedDisk] =
-      createParameters.adjustedSizeDisks ++ createParameters.referenceDisksForLocalizationOpt.getOrElse(List.empty)
+      createParameters.disks ++ createParameters.referenceDisksForLocalizationOpt.getOrElse(List.empty)
     val gcpBootDiskSizeMb = convertGbToMib(runtimeAttributes)
 
     // set parent for metadata storage of job information
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala
index 50a0704dd4e..d0fc00134d5 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/io/GcpBatchAttachedDisk.scala
@@ -7,8 +7,6 @@ import common.exception.MessageAggregation
 import common.validation.ErrorOr._
 import cromwell.backend.DiskPatterns._
 import cromwell.core.path.{DefaultPathBuilder, Path}
-import wdl4s.parser.MemoryUnit
-import wom.format.MemorySize
 import wom.values._
 
 import scala.util.Try
@@ -58,15 +56,6 @@ object GcpBatchAttachedDisk {
       case _: IllegalArgumentException => s"$value not convertible to a Long".invalidNel
     }
 
-  implicit class EnhancedDisks(val disks: Seq[GcpBatchAttachedDisk]) extends AnyVal {
-    def adjustWorkingDiskWithNewMin(minimum: MemorySize, onAdjustment: => Unit): Seq[GcpBatchAttachedDisk] = disks map {
-      case disk: GcpBatchWorkingDisk
-          if disk == GcpBatchWorkingDisk.Default && disk.sizeGb < minimum.to(MemoryUnit.GB).amount.toInt =>
-        onAdjustment
-        disk.copy(sizeGb = minimum.to(MemoryUnit.GB).amount.toInt)
-      case other => other
-    }
-  }
 }
 
 trait GcpBatchAttachedDisk {
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
index cdf3826f7af..ef9e2389d4b 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
@@ -11,7 +11,6 @@ import cromwell.backend.validation._
 import eu.timepit.refined._
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
-import wdl4s.parser.MemoryUnit
 import wom.RuntimeAttributesKeys
 import wom.format.MemorySize
 import wom.types.{WomArrayType, WomStringType, WomType}
@@ -79,10 +78,6 @@ object GcpBatchRuntimeAttributes {
   val CpuPlatformIntelCascadeLakeValue = "Intel Cascade Lake"
   val CpuPlatformAMDRomeValue = "AMD Rome"
 
-  private def cpuMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] =
-    CpuValidation.instanceMin
-      .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
-
   val UseDockerImageCacheKey = "useDockerImageCache"
   private val useDockerImageCacheValidationInstance = new BooleanRuntimeAttributesValidation(
     UseDockerImageCacheKey
@@ -111,9 +106,6 @@ object GcpBatchRuntimeAttributes {
   private def gpuCountValidation(
     runtimeConfig: Option[Config]
   ): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optional
-  private def gpuMinValidation(
-    runtimeConfig: Option[Config]
-  ): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optionalMin
 
   private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
 
@@ -143,13 +135,6 @@ object GcpBatchRuntimeAttributes {
       MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, runtimeConfig) getOrElse MemoryDefaultValue
     )
 
-  private def memoryMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] =
-    MemoryValidation.withDefaultMemory(
-      RuntimeAttributesKeys.MemoryMinKey,
-      MemoryValidation
-        .configDefaultString(RuntimeAttributesKeys.MemoryMinKey, runtimeConfig) getOrElse MemoryDefaultValue
-    )
-
   private def bootDiskSizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] =
     bootDiskValidationInstance
       .withDefault(bootDiskValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse BootDiskDefaultValue)
@@ -166,15 +151,6 @@ object GcpBatchRuntimeAttributes {
   ): OptionalRuntimeAttributesValidation[Boolean] =
     useDockerImageCacheValidationInstance
 
-  private val outDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
-    InformationValidation.optional(RuntimeAttributesKeys.OutDirMinKey, MemoryUnit.MB, allowZero = true)
-
-  private val tmpDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
-    InformationValidation.optional(RuntimeAttributesKeys.TmpDirMinKey, MemoryUnit.MB, allowZero = true)
-
-  private val inputDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
-    InformationValidation.optional(RuntimeAttributesKeys.DnaNexusInputDirMinKey, MemoryUnit.MB, allowZero = true)
-
   def runtimeAttributesBuilder(batchConfiguration: GcpBatchConfiguration): StandardValidatedRuntimeAttributesBuilder = {
     val runtimeConfig = batchConfiguration.runtimeConfig
     StandardValidatedRuntimeAttributesBuilder
@@ -185,21 +161,15 @@ object GcpBatchRuntimeAttributes {
         gpuDriverValidation(runtimeConfig),
         cpuValidation(runtimeConfig),
         cpuPlatformValidation(runtimeConfig),
-        cpuMinValidation(runtimeConfig),
-        gpuMinValidation(runtimeConfig),
         disksValidation(runtimeConfig),
         noAddressValidation(runtimeConfig),
         zonesValidation(runtimeConfig),
         preemptibleValidation(runtimeConfig),
         memoryValidation(runtimeConfig),
-        memoryMinValidation(runtimeConfig),
         bootDiskSizeValidation(runtimeConfig),
         useDockerImageCacheValidation(runtimeConfig),
         checkpointFileValidationInstance,
-        dockerValidation,
-        outDirMinValidation,
-        tmpDirMinValidation,
-        inputDirMinValidation
+        dockerValidation
       )
   }
 
@@ -257,21 +227,6 @@ object GcpBatchRuntimeAttributes {
       validatedRuntimeAttributes
     )
 
-    val outDirMin: Option[MemorySize] = RuntimeAttributesValidation
-      .extractOption(outDirMinValidation.key, validatedRuntimeAttributes)
-    val tmpDirMin: Option[MemorySize] = RuntimeAttributesValidation
-      .extractOption(tmpDirMinValidation.key, validatedRuntimeAttributes)
-    val inputDirMin: Option[MemorySize] = RuntimeAttributesValidation
-      .extractOption(inputDirMinValidation.key, validatedRuntimeAttributes)
-
-    val totalExecutionDiskSizeBytes = List(inputDirMin.map(_.bytes),
-                                           outDirMin.map(_.bytes),
-                                           tmpDirMin.map(_.bytes)
-    ).flatten.fold(MemorySize(0, MemoryUnit.Bytes).bytes)(_ + _)
-    val totalExecutionDiskSize = MemorySize(totalExecutionDiskSizeBytes, MemoryUnit.Bytes)
-
-    val adjustedDisks = disks.adjustWorkingDiskWithNewMin(totalExecutionDiskSize, ())
-
     new GcpBatchRuntimeAttributes(
       cpu,
       cpuPlatform,
@@ -280,7 +235,7 @@ object GcpBatchRuntimeAttributes {
       preemptible,
       bootDiskSize,
       memory,
-      adjustedDisks,
+      disks,
       docker,
       failOnStderr,
       continueOnReturnCode,
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala
index 51c19813229..001bf0efb84 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/util/GpuValidation.scala
@@ -13,17 +13,13 @@ import cromwell.backend.validation.{
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
 import eu.timepit.refined.refineV
-import wom.RuntimeAttributesKeys.{GpuKey, GpuMaxKey, GpuMinKey}
+import wom.RuntimeAttributesKeys.GpuKey
 import wom.types.WomIntegerType
 import wom.values.{WomInteger, WomValue}
 
 object GpuValidation {
   lazy val instance: RuntimeAttributesValidation[Int Refined Positive] = new GpuValidation(GpuKey)
   lazy val optional: OptionalRuntimeAttributesValidation[Int Refined Positive] = instance.optional
-  lazy val instanceMin: RuntimeAttributesValidation[Int Refined Positive] = new GpuValidation(GpuMinKey)
-  lazy val optionalMin: OptionalRuntimeAttributesValidation[Int Refined Positive] = instanceMin.optional
-  lazy val instanceMax: RuntimeAttributesValidation[Int Refined Positive] = new GpuValidation(GpuMaxKey)
-  lazy val optionalMax: OptionalRuntimeAttributesValidation[Int Refined Positive] = instanceMax.optional
 
   lazy val defaultMin: WomValue = WomInteger(0)
   def configDefaultWomValue(config: Option[Config]): Option[WomValue] = instance.configDefaultWomValue(config)
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
index 4253b1877be..f8d6e071b31 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
@@ -936,12 +936,10 @@ class GcpBatchAsyncBackendJobExecutionActorSpec
         "runtimeAttributes:bootDiskSizeGb" -> "10",
         "runtimeAttributes:continueOnReturnCode" -> "0",
         "runtimeAttributes:cpu" -> "1",
-        "runtimeAttributes:cpuMin" -> "1",
         "runtimeAttributes:disks" -> "local-disk 200 SSD",
         "runtimeAttributes:docker" -> "ubuntu:latest",
         "runtimeAttributes:failOnStderr" -> "false",
         "runtimeAttributes:memory" -> "2 GB",
-        "runtimeAttributes:memoryMin" -> "2 GB",
         "runtimeAttributes:noAddress" -> "false",
         "runtimeAttributes:preemptible" -> "0",
         "runtimeAttributes:zones" -> "us-central1-b,us-central1-a",
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuValidation.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuValidation.scala
index 916410df293..ca21d11b200 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuValidation.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/GpuValidation.scala
@@ -13,17 +13,13 @@ import cromwell.backend.validation.{
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
 import eu.timepit.refined.refineV
-import wom.RuntimeAttributesKeys.{GpuKey, GpuMaxKey, GpuMinKey}
+import wom.RuntimeAttributesKeys.GpuKey
 import wom.types.WomIntegerType
 import wom.values.{WomInteger, WomValue}
 
 object GpuValidation {
   lazy val instance: RuntimeAttributesValidation[Int Refined Positive] = new GpuValidation(GpuKey)
   lazy val optional: OptionalRuntimeAttributesValidation[Int Refined Positive] = instance.optional
-  lazy val instanceMin: RuntimeAttributesValidation[Int Refined Positive] = new GpuValidation(GpuMinKey)
-  lazy val optionalMin: OptionalRuntimeAttributesValidation[Int Refined Positive] = instanceMin.optional
-  lazy val instanceMax: RuntimeAttributesValidation[Int Refined Positive] = new GpuValidation(GpuMaxKey)
-  lazy val optionalMax: OptionalRuntimeAttributesValidation[Int Refined Positive] = instanceMax.optional
 
   lazy val defaultMin: WomValue = WomInteger(0)
   def configDefaultWomValue(config: Option[Config]): Option[WomValue] = instance.configDefaultWomValue(config)
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
index fa079ea86b2..965dc4e1244 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -57,13 +57,11 @@ import cromwell.services.keyvalue.KeyValueServiceActor._
 import cromwell.services.metadata.CallMetadataKeys
 import mouse.all._
 import shapeless.Coproduct
-import wdl4s.parser.MemoryUnit
 import wom.callable.Callable.OutputDefinition
 import wom.callable.MetaValueElement.{MetaValueElementBoolean, MetaValueElementObject}
 import wom.callable.{AdHocValue, RuntimeEnvironment}
 import wom.core.FullyQualifiedName
 import wom.expression.{FileEvaluation, NoIoFunctionSet}
-import wom.format.MemorySize
 import wom.types.{WomArrayType, WomSingleFileType}
 import wom.values._
 
@@ -490,30 +488,6 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
           token <- data.privateDockerEncryptedToken
         } yield CreatePipelineDockerKeyAndToken(key, token)
 
-        /*
-         * Right now this doesn't cost anything, because sizeOption returns the size if it was previously already fetched
-         * for some reason (expression evaluation for instance), but otherwise does not retrieve it and returns None.
-         * In CWL-land we tend to be aggressive in pre-fetching the size in order to be able to evaluate JS expressions,
-         * but less in WDL as we can get it last minute and on demand because size is a WDL function, whereas in CWL
-         * we don't inspect the JS to know if size is called and therefore always pre-fetch it.
-         *
-         * We could decide to call withSize before in which case we would retrieve the size for all files and have
-         * a guaranteed more accurate total size, but there might be performance impacts ?
-         */
-        val inputFileSize = Option(callInputFiles.values.flatMap(_.flatMap(_.sizeOption)).sum)
-
-        // Attempt to adjust the disk size by taking into account the size of input files
-        val adjustedSizeDisks =
-          inputFileSize.map(size => MemorySize.apply(size.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB)) map {
-            inputFileSizeInformation =>
-              runtimeAttributes.disks.adjustWorkingDiskWithNewMin(
-                inputFileSizeInformation,
-                jobLogger.info(
-                  s"Adjusted working disk size to ${inputFileSizeInformation.amount} GB to account for input files"
-                )
-              )
-          } getOrElse runtimeAttributes.disks
-
         val inputFilePaths = inputOutputParameters.jobInputParameters.map(_.cloudPath.pathAsString).toSet
         val referenceDisksToMount =
           if (useReferenceDisks)
@@ -571,7 +545,7 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
           jobShell = pipelinesConfiguration.jobShell,
           privateDockerKeyAndEncryptedToken = dockerKeyAndToken,
           womOutputRuntimeExtractor = jobDescriptor.workflowDescriptor.outputRuntimeExtractor,
-          adjustedSizeDisks = adjustedSizeDisks,
+          disks = runtimeAttributes.disks,
           virtualPrivateCloudConfiguration = jesAttributes.virtualPrivateCloudConfiguration,
           retryWithMoreMemoryKeys = retryWithMoreMemoryKeys,
           fuseEnabled = fuseEnabled(jobDescriptor.workflowDescriptor),
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala
index 3e2ee2446e0..a472007b611 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala
@@ -13,7 +13,6 @@ import cromwell.backend.validation.{BooleanRuntimeAttributesValidation, _}
 import eu.timepit.refined._
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
-import wdl4s.parser.MemoryUnit
 import wom.RuntimeAttributesKeys
 import wom.format.MemorySize
 import wom.types._
@@ -101,10 +100,6 @@ object PipelinesApiRuntimeAttributes {
   private def cpuPlatformValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[String] =
     cpuPlatformValidationInstance
 
-  private def cpuMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int Refined Positive] =
-    CpuValidation.instanceMin
-      .withDefault(CpuValidation.configDefaultWomValue(runtimeConfig) getOrElse CpuValidation.defaultMin)
-
   private def gpuTypeValidation(runtimeConfig: Option[Config]): OptionalRuntimeAttributesValidation[GpuType] =
     GpuTypeValidation.optional
 
@@ -116,10 +111,6 @@ object PipelinesApiRuntimeAttributes {
     runtimeConfig: Option[Config]
   ): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optional
 
-  private def gpuMinValidation(
-    runtimeConfig: Option[Config]
-  ): OptionalRuntimeAttributesValidation[Int Refined Positive] = GpuValidation.optionalMin
-
   private def failOnStderrValidation(runtimeConfig: Option[Config]) = FailOnStderrValidation.default(runtimeConfig)
 
   private def continueOnReturnCodeValidation(runtimeConfig: Option[Config]) =
@@ -144,13 +135,6 @@ object PipelinesApiRuntimeAttributes {
       MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryKey, runtimeConfig) getOrElse MemoryDefaultValue
     )
 
-  private def memoryMinValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] =
-    MemoryValidation.withDefaultMemory(RuntimeAttributesKeys.MemoryMinKey,
-                                       MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMinKey,
-                                                                            runtimeConfig
-                                       ) getOrElse MemoryDefaultValue
-    )
-
   private def bootDiskSizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Int] =
     bootDiskValidationInstance
       .withDefault(bootDiskValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse BootDiskDefaultValue)
@@ -166,15 +150,6 @@ object PipelinesApiRuntimeAttributes {
 
   private val dockerValidation: RuntimeAttributesValidation[String] = DockerValidation.instance
 
-  private val outDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
-    InformationValidation.optional(RuntimeAttributesKeys.OutDirMinKey, MemoryUnit.MB, allowZero = true)
-
-  private val tmpDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
-    InformationValidation.optional(RuntimeAttributesKeys.TmpDirMinKey, MemoryUnit.MB, allowZero = true)
-
-  private val inputDirMinValidation: OptionalRuntimeAttributesValidation[MemorySize] =
-    InformationValidation.optional(RuntimeAttributesKeys.DnaNexusInputDirMinKey, MemoryUnit.MB, allowZero = true)
-
   def runtimeAttributesBuilder(
     jesConfiguration: PipelinesApiConfiguration
   ): StandardValidatedRuntimeAttributesBuilder = {
@@ -186,22 +161,16 @@ object PipelinesApiRuntimeAttributes {
         gpuTypeValidation(runtimeConfig),
         gpuDriverValidation(runtimeConfig),
         cpuValidation(runtimeConfig),
-        cpuMinValidation(runtimeConfig),
-        gpuMinValidation(runtimeConfig),
         disksValidation(runtimeConfig),
         zonesValidation(runtimeConfig),
         preemptibleValidation(runtimeConfig),
         memoryValidation(runtimeConfig),
-        memoryMinValidation(runtimeConfig),
         bootDiskSizeValidation(runtimeConfig),
         noAddressValidation(runtimeConfig),
         cpuPlatformValidation(runtimeConfig),
         useDockerImageCacheValidation(runtimeConfig),
         checkpointFileValidationInstance,
-        dockerValidation,
-        outDirMinValidation,
-        tmpDirMinValidation,
-        inputDirMinValidation
+        dockerValidation
       )
   }
 
@@ -261,21 +230,6 @@ object PipelinesApiRuntimeAttributes {
       validatedRuntimeAttributes
     )
 
-    val outDirMin: Option[MemorySize] =
-      RuntimeAttributesValidation.extractOption(outDirMinValidation.key, validatedRuntimeAttributes)
-    val tmpDirMin: Option[MemorySize] =
-      RuntimeAttributesValidation.extractOption(tmpDirMinValidation.key, validatedRuntimeAttributes)
-    val inputDirMin: Option[MemorySize] =
-      RuntimeAttributesValidation.extractOption(inputDirMinValidation.key, validatedRuntimeAttributes)
-
-    val totalExecutionDiskSizeBytes = List(inputDirMin.map(_.bytes),
-                                           outDirMin.map(_.bytes),
-                                           tmpDirMin.map(_.bytes)
-    ).flatten.fold(MemorySize(0, MemoryUnit.Bytes).bytes)(_ + _)
-    val totalExecutionDiskSize = MemorySize(totalExecutionDiskSizeBytes, MemoryUnit.Bytes)
-
-    val adjustedDisks = disks.adjustWorkingDiskWithNewMin(totalExecutionDiskSize, ())
-
     new PipelinesApiRuntimeAttributes(
       cpu,
       cpuPlatform,
@@ -284,7 +238,7 @@ object PipelinesApiRuntimeAttributes {
       preemptible,
       bootDiskSize,
       memory,
-      adjustedDisks,
+      disks,
       docker,
       failOnStderr,
       continueOnReturnCode,
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestFactory.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestFactory.scala
index 71bc4203b62..188d5a1e9e9 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestFactory.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/api/PipelinesApiRequestFactory.scala
@@ -83,7 +83,7 @@ object PipelinesApiRequestFactory {
                                       jobShell: String,
                                       privateDockerKeyAndEncryptedToken: Option[CreatePipelineDockerKeyAndToken],
                                       womOutputRuntimeExtractor: Option[WomOutputRuntimeExtractor],
-                                      adjustedSizeDisks: Seq[PipelinesApiAttachedDisk],
+                                      disks: Seq[PipelinesApiAttachedDisk],
                                       virtualPrivateCloudConfiguration: VirtualPrivateCloudConfiguration,
                                       retryWithMoreMemoryKeys: Option[List[String]],
                                       fuseEnabled: Boolean,
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/PipelinesApiAttachedDisk.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/PipelinesApiAttachedDisk.scala
index fec1ad22c52..6126384cb27 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/PipelinesApiAttachedDisk.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/io/PipelinesApiAttachedDisk.scala
@@ -7,8 +7,6 @@ import common.exception.MessageAggregation
 import common.validation.ErrorOr._
 import cromwell.backend.DiskPatterns._
 import cromwell.core.path.{DefaultPathBuilder, Path}
-import wdl4s.parser.MemoryUnit
-import wom.format.MemorySize
 import wom.values._
 
 import scala.util.Try
@@ -55,16 +53,6 @@ object PipelinesApiAttachedDisk {
       case _: IllegalArgumentException => s"$value not convertible to a Long".invalidNel
     }
 
-  implicit class EnhancedDisks(val disks: Seq[PipelinesApiAttachedDisk]) extends AnyVal {
-    def adjustWorkingDiskWithNewMin(minimum: MemorySize, onAdjustment: => Unit): Seq[PipelinesApiAttachedDisk] =
-      disks map {
-        case disk: PipelinesApiWorkingDisk
-            if disk == PipelinesApiWorkingDisk.Default && disk.sizeGb < minimum.to(MemoryUnit.GB).amount.toInt =>
-          onAdjustment
-          disk.copy(sizeGb = minimum.to(MemoryUnit.GB).amount.toInt)
-        case other => other
-      }
-  }
 }
 
 trait PipelinesApiAttachedDisk {
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
index 37221ff8534..41e826a4dc2 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActorSpec.scala
@@ -1723,12 +1723,10 @@ class PipelinesApiAsyncBackendJobExecutionActorSpec
         "runtimeAttributes:bootDiskSizeGb" -> "10",
         "runtimeAttributes:continueOnReturnCode" -> "0",
         "runtimeAttributes:cpu" -> "1",
-        "runtimeAttributes:cpuMin" -> "1",
         "runtimeAttributes:disks" -> "local-disk 200 SSD",
         "runtimeAttributes:docker" -> "ubuntu:latest",
         "runtimeAttributes:failOnStderr" -> "false",
         "runtimeAttributes:memory" -> "2 GB",
-        "runtimeAttributes:memoryMin" -> "2 GB",
         "runtimeAttributes:noAddress" -> "false",
         "runtimeAttributes:preemptible" -> "0",
         "runtimeAttributes:zones" -> "us-central1-b,us-central1-a",
diff --git a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
index 3b38f578d6a..2db30f868e6 100644
--- a/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
+++ b/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/GenomicsFactory.scala
@@ -69,7 +69,7 @@ case class GenomicsFactory(applicationName: String, authMode: GoogleAuthMode, en
           case _ => new Network().setUsePrivateAddress(createPipelineParameters.runtimeAttributes.noAddress)
         }
 
-      val allDisksToBeMounted = createPipelineParameters.adjustedSizeDisks ++
+      val allDisksToBeMounted = createPipelineParameters.disks ++
         createPipelineParameters.referenceDisksForLocalizationOpt.getOrElse(List.empty)
 
       // Disks defined in the runtime attributes and reference-files-localization disks
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
index 2c601007e2e..0d4996f63cc 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
@@ -75,7 +75,7 @@ case class LifeSciencesFactory(applicationName: String, authMode: GoogleAuthMode
           case _ => new Network().setUsePrivateAddress(createPipelineParameters.runtimeAttributes.noAddress)
         }
 
-      val allDisksToBeMounted = createPipelineParameters.adjustedSizeDisks ++
+      val allDisksToBeMounted = createPipelineParameters.disks ++
         createPipelineParameters.referenceDisksForLocalizationOpt.getOrElse(List.empty)
 
       // Disks defined in the runtime attributes and reference-files-localization disks
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigConstants.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigConstants.scala
index 1896011fdec..4a697758819 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigConstants.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigConstants.scala
@@ -25,11 +25,7 @@ object ConfigConstants {
   /*
   Runtime attributes that may be specified within the RuntimeAttributesConfig.
    */
-  val DockerRuntimeAttribute = RuntimeAttributesKeys.DockerKey
-  val CpuRuntimeAttribute = RuntimeAttributesKeys.CpuKey
   val MemoryRuntimeAttribute = RuntimeAttributesKeys.MemoryKey
-  val MemoryMinRuntimeAttribute = RuntimeAttributesKeys.MemoryMinKey
-  val MemoryMaxRuntimeAttribute = RuntimeAttributesKeys.MemoryMaxKey
   // See: MemoryDeclarationValidation
   val MemoryRuntimeAttributePrefix = "memory_"
   val MemoryMinRuntimeAttributePrefix = "memoryMin_"
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala
index 7b5bcd4e7fc..87fb72bd240 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/DeclarationValidation.scala
@@ -33,8 +33,6 @@ object DeclarationValidation {
       case name if name == DockerValidation.instance.key =>
         new DeclarationValidation(declaration, DockerValidation.instance, usedInCallCachingOverride = None)
       case RuntimeAttributesKeys.CpuKey => new CpuDeclarationValidation(declaration, CpuValidation.instance)
-      case RuntimeAttributesKeys.CpuMinKey => new CpuDeclarationValidation(declaration, CpuValidation.instanceMin)
-      case RuntimeAttributesKeys.CpuMaxKey => new CpuDeclarationValidation(declaration, CpuValidation.instanceMax)
       // See MemoryDeclarationValidation for more info
       case name
           if MemoryDeclarationValidation.isMemoryDeclaration(name,
@@ -42,18 +40,6 @@ object DeclarationValidation {
                                                              MemoryRuntimeAttributePrefix
           ) =>
         new MemoryDeclarationValidation(declaration, MemoryRuntimeAttribute, MemoryRuntimeAttributePrefix)
-      case name
-          if MemoryDeclarationValidation.isMemoryDeclaration(name,
-                                                             MemoryMinRuntimeAttribute,
-                                                             MemoryRuntimeAttributePrefix
-          ) =>
-        new MemoryDeclarationValidation(declaration, MemoryMinRuntimeAttribute, MemoryMinRuntimeAttributePrefix)
-      case name
-          if MemoryDeclarationValidation.isMemoryDeclaration(name,
-                                                             MemoryMaxRuntimeAttribute,
-                                                             MemoryRuntimeAttributePrefix
-          ) =>
-        new MemoryDeclarationValidation(declaration, MemoryMaxRuntimeAttribute, MemoryMaxRuntimeAttributePrefix)
       case name
           if MemoryDeclarationValidation.isMemoryDeclaration(name, DiskRuntimeAttribute, DiskRuntimeAttributePrefix) =>
         new MemoryDeclarationValidation(declaration, DiskRuntimeAttribute, DiskRuntimeAttributePrefix)
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidationSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidationSpec.scala
index 48722a0dc66..ccc175cbbdb 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidationSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/impl/sfs/config/MemoryDeclarationValidationSpec.scala
@@ -39,48 +39,11 @@ class MemoryDeclarationValidationSpec
     ("Float? memory_gb = 3.0", None, Option(3), None),
     ("Float? memory_gb = 3.0", Option(2), Option(3), Option(WomFloat(2))),
     ("Float? memory_gb = 3", None, Option(3), None),
-    ("Float? memory_gb = 3", Option(2), Option(3), Option(WomFloat(2))),
-    ("Int memoryMin", Option(2), None, Option(WomLong(2L * 1024L * 1024L * 1024L))),
-    ("Int memoryMin_gb", Option(2), None, Option(WomLong(2))),
-    ("Int memoryMin_gb = 3", None, Option(3), None),
-    ("Int memoryMin_gb = 3", Option(2), Option(3), Option(WomLong(2))),
-    ("Int? memoryMin_gb", None, None, None),
-    ("Int? memoryMin_gb", Option(2), None, Option(WomLong(2))),
-    ("Int? memoryMin_gb = 3", None, Option(3), None),
-    ("Int? memoryMin_gb = 3", Option(2), Option(3), Option(WomLong(2))),
-    ("Float memoryMin", Option(2), None, Option(WomFloat(2f * 1024f * 1024f * 1024f))),
-    ("Float memoryMin_gb", Option(2), None, Option(WomFloat(2))),
-    ("Float memoryMin_gb = 3.0", None, Option(3), None),
-    ("Float memoryMin_gb = 3.0", Option(2), Option(3), Option(WomFloat(2))),
-    ("Float? memoryMin_gb", None, None, None),
-    ("Float? memoryMin_gb", Option(2), None, Option(WomFloat(2))),
-    ("Float? memoryMin_gb = 3.0", None, Option(3), None),
-    ("Float? memoryMin_gb = 3.0", Option(2), Option(3), Option(WomFloat(2))),
-    ("Int memoryMax", Option(2), None, Option(WomLong(2L * 1024L * 1024L * 1024L))),
-    ("Int memoryMax_gb", Option(2), None, Option(WomLong(2))),
-    ("Int memoryMax_gb = 3", None, Option(3), None),
-    ("Int memoryMax_gb = 3", Option(2), Option(3), Option(WomLong(2))),
-    ("Int? memoryMax_gb", None, None, None),
-    ("Int? memoryMax_gb", Option(2), None, Option(WomLong(2))),
-    ("Int? memoryMax_gb = 3", None, Option(3), None),
-    ("Int? memoryMax_gb = 3", Option(2), Option(3), Option(WomLong(2))),
-    ("Float memoryMax", Option(2), None, Option(WomFloat(2f * 1024f * 1024f * 1024f))),
-    ("Float memoryMax_gb", Option(2), None, Option(WomFloat(2))),
-    ("Float memoryMax_gb = 3.0", None, Option(3), None),
-    ("Float memoryMax_gb = 3.0", Option(2), Option(3), Option(WomFloat(2))),
-    ("Float? memoryMax_gb", None, None, None),
-    ("Float? memoryMax_gb", Option(2), None, Option(WomFloat(2))),
-    ("Float? memoryMax_gb = 3.0", None, Option(3), None),
-    ("Float? memoryMax_gb = 3.0", Option(2), Option(3), Option(WomFloat(2)))
+    ("Float? memory_gb = 3", Option(2), Option(3), Option(WomFloat(2)))
   )
 
   forAll(validDeclaredAmounts) { (declaration, runtimeAmount, expectedDefaultAmount, expectedExtracted) =>
     it should s"extract memory from declared $declaration with memory set to ${runtimeAmount.getOrElse("none")}" in {
-      val memoryKey =
-        if (declaration.contains("Min")) MemoryMinRuntimeAttribute
-        else if (declaration.contains("Max")) MemoryMaxRuntimeAttribute
-        else MemoryRuntimeAttribute
-
       val memoryPrefix =
         if (declaration.contains("Min")) MemoryMinRuntimeAttributePrefix
         else if (declaration.contains("Max")) MemoryMaxRuntimeAttributePrefix
@@ -92,9 +55,10 @@ class MemoryDeclarationValidationSpec
 
       val configWdlNamespace = new ConfigWdlNamespace(config)
       val runtimeDeclaration = configWdlNamespace.runtimeDeclarations.head
-      val memoryDeclarationValidation = new MemoryDeclarationValidation(runtimeDeclaration, memoryKey, memoryPrefix)
+      val memoryDeclarationValidation =
+        new MemoryDeclarationValidation(runtimeDeclaration, MemoryRuntimeAttribute, memoryPrefix)
       val attributes = runtimeAmount
-        .map(amount => memoryKey -> MemorySize(amount.toDouble, MemoryUnit.GB))
+        .map(amount => MemoryRuntimeAttribute -> MemorySize(amount.toDouble, MemoryUnit.GB))
         .toMap
       val validatedRuntimeAttributes = ValidatedRuntimeAttributes(attributes)
 
@@ -105,7 +69,7 @@ class MemoryDeclarationValidationSpec
         .map(amount => WomLong(MemorySize(amount.toDouble, MemoryUnit.GB).bytes.toLong))
 
       MemoryDeclarationValidation.isMemoryDeclaration(runtimeDeclaration.unqualifiedName,
-                                                      memoryKey,
+                                                      MemoryRuntimeAttribute,
                                                       memoryPrefix
       ) should be(true)
       default should be(expectedDefault)
diff --git a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/DeclarationValidationSpec.scala b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/DeclarationValidationSpec.scala
index 681e4a91baa..265821ad3f8 100644
--- a/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/DeclarationValidationSpec.scala
+++ b/supportedBackends/sfs/src/test/scala/cromwell/backend/sfs/config/DeclarationValidationSpec.scala
@@ -32,9 +32,7 @@ class DeclarationValidationSpec
   it should "validate cpu attributes" in {
     val keys = Table(
       "key",
-      "cpu",
-      "cpuMin",
-      "cpuMax"
+      "cpu"
     )
 
     forAll(keys)(validateCpu)
diff --git a/wom/src/main/scala/wom/RuntimeAttributes.scala b/wom/src/main/scala/wom/RuntimeAttributes.scala
index 486d69d5e97..2c66b6859d3 100644
--- a/wom/src/main/scala/wom/RuntimeAttributes.scala
+++ b/wom/src/main/scala/wom/RuntimeAttributes.scala
@@ -6,33 +6,13 @@ object RuntimeAttributesKeys {
   val DockerKey = "docker"
   val MaxRetriesKey = "maxRetries"
 
-  /**
-    * Equivalent to CPUMinKey
-    */
   val CpuKey = "cpu"
   val CpuPlatformKey = "cpuPlatform"
-  val CpuMinKey = "cpuMin"
-  val CpuMaxKey = "cpuMax"
 
-  /**
-    * Equivalent to GPUMinKey
-    */
   val GpuKey = "gpuCount"
-  val GpuMinKey = "gpuCountMin"
-  val GpuMaxKey = "gpuCountMax"
   val GpuTypeKey = "gpuType"
-  val DnaNexusInputDirMinKey = "dnaNexusInputDirMin"
 
-  /**
-    * Equivalent to MemoryMinKey
-    */
   val MemoryKey = "memory"
-  val MemoryMinKey = "memoryMin"
-  val MemoryMaxKey = "memoryMax"
-  val TmpDirMinKey = "tmpDirMin"
-  val TmpDirMaxKey = "tmpDirMax"
-  val OutDirMinKey = "outDirMin"
-  val OutDirMaxKey = "outDirMax"
   val FailOnStderrKey = "failOnStderr"
   val ContinueOnReturnCodeKey = "continueOnReturnCode"
 }

From f43a5c3970810ab266bcc8beaa2baea30be65051 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 23 Feb 2024 13:43:38 -0500
Subject: [PATCH 281/326] WX-1485 Upgrade postgres lib (#7371)

---
 project/Dependencies.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 5b073bbdcec..6b1e3cc1740 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -100,7 +100,7 @@ object Dependencies {
   private val nettyV = "4.1.72.Final"
   private val owlApiV = "5.1.19"
   private val pact4sV = "0.9.0"
-  private val postgresV = "42.4.1"
+  private val postgresV = "42.4.4"
   private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
   private val refinedV = "0.10.1"

From 84f55958cb2bedf7c93d7079cf72d0b2f133012a Mon Sep 17 00:00:00 2001
From: Chris Llanwarne <cjllanwarne@users.noreply.github.com>
Date: Fri, 23 Feb 2024 17:16:24 -0500
Subject: [PATCH 282/326] WM-2454: Private GitHub support on describe api
 (#7365)

---
 core/src/main/resources/reference.conf        |  14 +-
 .../routes/WomtoolRouteSupport.scala          |  28 ++--
 .../routes/CromwellApiServiceSpec.scala       |   2 +-
 .../languages/util/ImportResolver.scala       |  71 ++++++---
 .../languages/util/ImportResolverSpec.scala   | 137 +++++++++++++++++-
 .../NamespaceCacheSpec.scala                  |   2 +-
 .../services/auth/GithubAuthVending.scala     |  17 +++
 .../auth/GithubAuthVendingSupport.scala       |  45 ++++++
 .../auth/impl/GithubAuthVendingActor.scala    |  33 +++++
 .../cromwell/services/womtool/Describer.scala |   6 +-
 .../womtool/WomtoolServiceMessages.scala      |   4 +-
 .../impl/WomtoolServiceInCromwellActor.scala  |   4 +-
 .../auth/GithubAuthVendingSupportSpec.scala   |  99 +++++++++++++
 .../services/womtool/DescriberSpec.scala      |   2 +-
 .../WomtoolServiceInCromwellActorSpec.scala   |  28 ++--
 src/ci/resources/build_application.inc.conf   |   4 +
 16 files changed, 438 insertions(+), 58 deletions(-)
 create mode 100644 services/src/main/scala/cromwell/services/auth/GithubAuthVending.scala
 create mode 100644 services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala
 create mode 100644 services/src/main/scala/cromwell/services/auth/impl/GithubAuthVendingActor.scala
 create mode 100644 services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala

diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index 3fa11b458ff..c43dbce60ee 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -418,7 +418,7 @@ docker {
       throttle {
         number-of-requests = 1000
         per = 60 seconds
-      }      
+      }
       num-threads = 10
     }
     google {
@@ -524,6 +524,8 @@ backend {
   }
 }
 
+# Note: When adding a new actor that uses service registry pattern make sure that the new actor handles the graceful
+#       shutdown command ('ShutdownCommand'). See https://github.com/broadinstitute/cromwell/issues/2575
 services {
   KeyValue {
     class = "cromwell.services.keyvalue.impl.SqlKeyValueServiceActor"
@@ -571,6 +573,16 @@ services {
     # Default - run within the Cromwell JVM
     class = "cromwell.services.womtool.impl.WomtoolServiceInCromwellActor"
   }
+  GithubAuthVending {
+    class = "cromwell.services.auth.impl.GithubAuthVendingActor"
+    config {
+      enabled = false
+      # Notes:
+      #   - don't include the 'Bearer' before the token
+      #   - this config value should be removed when support for fetching tokens from ECM has been added to Cromwell
+      access-token = "dummy-token"
+    }
+  }
 }
 
 include required(classpath("reference_database.inc.conf"))
diff --git a/engine/src/main/scala/cromwell/webservice/routes/WomtoolRouteSupport.scala b/engine/src/main/scala/cromwell/webservice/routes/WomtoolRouteSupport.scala
index dec26a63dbf..b073c3dae8d 100644
--- a/engine/src/main/scala/cromwell/webservice/routes/WomtoolRouteSupport.scala
+++ b/engine/src/main/scala/cromwell/webservice/routes/WomtoolRouteSupport.scala
@@ -2,12 +2,14 @@ package cromwell.webservice.routes
 
 import akka.actor.{ActorRef, ActorRefFactory}
 import akka.http.scaladsl.model._
+import akka.http.scaladsl.model.headers.OAuth2BearerToken
 import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server.Route
-import akka.pattern.ask
 import akka.stream.ActorMaterializer
 import akka.util.Timeout
 import cromwell.core.{WorkflowOptions, WorkflowSourceFilesCollection}
+import cromwell.languages.util.ImportResolver.ImportAuthProvider
+import cromwell.services.auth.GithubAuthVendingSupport
 import cromwell.services.womtool.WomtoolServiceMessages.{
   DescribeFailure,
   DescribeRequest,
@@ -20,7 +22,7 @@ import cromwell.webservice.WebServiceUtils.EnhancedThrowable
 import scala.concurrent.ExecutionContext
 import scala.util.{Failure, Success}
 
-trait WomtoolRouteSupport extends WebServiceUtils {
+trait WomtoolRouteSupport extends WebServiceUtils with GithubAuthVendingSupport {
 
   implicit def actorRefFactory: ActorRefFactory
   implicit val ec: ExecutionContext
@@ -33,17 +35,25 @@ trait WomtoolRouteSupport extends WebServiceUtils {
     path("womtool" / Segment / "describe") { _ =>
       post {
         entity(as[Multipart.FormData]) { formData: Multipart.FormData =>
-          onComplete(materializeFormData(formData)) {
-            case Success(data) =>
-              validateAndSubmitRequest(data)
-            case Failure(e) =>
-              e.failRequest(StatusCodes.InternalServerError)
+          extractCredentials { creds =>
+            val authProviders: List[ImportAuthProvider] = creds match {
+              case Some(OAuth2BearerToken(token)) => List(importAuthProvider(token))
+              case _ => List.empty
+            }
+            onComplete(materializeFormData(formData)(timeout, materializer, ec)) {
+              case Success(data) =>
+                validateAndSubmitRequest(data, authProviders)
+              case Failure(e) =>
+                e.failRequest(StatusCodes.InternalServerError)
+            }
           }
         }
       }
     }
 
-  private def validateAndSubmitRequest(data: MaterializedFormData): Route = {
+  private def validateAndSubmitRequest(data: MaterializedFormData,
+                                       importAuthProviders: List[ImportAuthProvider]
+  ): Route = {
     // TODO: move constants to WebServiceUtils, adopt in PartialWorkflowSources
     val workflowSource = data.get("workflowSource").map(_.utf8String)
     val workflowUrl = data.get("workflowUrl").map(_.utf8String)
@@ -66,7 +76,7 @@ trait WomtoolRouteSupport extends WebServiceUtils {
       requestedWorkflowId = None
     )
 
-    onComplete(serviceRegistryActor.ask(DescribeRequest(wsfc)).mapTo[DescribeResult]) {
+    onComplete(serviceRegistryActor.ask(DescribeRequest(wsfc, importAuthProviders)).mapTo[DescribeResult]) {
       case Success(response: DescribeSuccess) =>
         import cromwell.services.womtool.models.WorkflowDescription.workflowDescriptionEncoder
         import de.heikoseeberger.akkahttpcirce.ErrorAccumulatingCirceSupport._
diff --git a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
index b7440bbe31c..9088879bc63 100644
--- a/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
+++ b/engine/src/test/scala/cromwell/webservice/routes/CromwellApiServiceSpec.scala
@@ -748,7 +748,7 @@ object CromwellApiServiceSpec {
             )
           case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
         }
-      case DescribeRequest(sourceFiles) =>
+      case DescribeRequest(sourceFiles, _) =>
         sourceFiles.workflowSource match {
           case Some("fail to describe") =>
             sender() ! DescribeFailure("as requested, failing to describe")
diff --git a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
index e3690248b09..bdcd0c8b311 100644
--- a/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
+++ b/languageFactories/language-factory-core/src/main/scala/cromwell/languages/util/ImportResolver.scala
@@ -10,6 +10,7 @@ import cats.syntax.validated._
 import com.softwaremill.sttp._
 import com.softwaremill.sttp.asynchttpclient.cats.AsyncHttpClientCatsBackend
 import com.typesafe.config.ConfigFactory
+import com.typesafe.scalalogging.StrictLogging
 import common.Checked
 import common.transforms.CheckedAtoB
 import common.validation.ErrorOr._
@@ -22,11 +23,11 @@ import java.nio.file.{Path => NioPath}
 import java.security.MessageDigest
 import cromwell.core.WorkflowId
 import wom.ResolvedImportRecord
-import wom.core.WorkflowSource
+import wom.core.{WorkflowSource, WorkflowUrl}
 import wom.values._
 
 import scala.concurrent.duration._
-import scala.concurrent.{Await, ExecutionContext}
+import scala.concurrent.{Await, ExecutionContext, Future}
 import scala.util.{Failure, Success, Try}
 
 object ImportResolver {
@@ -37,6 +38,15 @@ object ImportResolver {
                                   resolvedImportRecord: ResolvedImportRecord
   )
 
+  trait ImportAuthProvider {
+    def validHosts: List[String]
+    def authHeader(): Future[Map[String, String]]
+  }
+
+  trait GithubImportAuthProvider extends ImportAuthProvider {
+    override def validHosts: List[String] = List("github.com", "githubusercontent.com", "raw.githubusercontent.com")
+  }
+
   trait ImportResolver {
     def name: String
     protected def innerResolver(path: String, currentResolvers: List[ImportResolver]): Checked[ResolvedImportBundle]
@@ -179,20 +189,23 @@ object ImportResolver {
     }
   }
 
-  case class HttpResolver(relativeTo: Option[String], headers: Map[String, String], hostAllowlist: Option[List[String]])
-      extends ImportResolver {
+  case class HttpResolver(relativeTo: Option[String],
+                          headers: Map[String, String],
+                          hostAllowlist: Option[List[String]],
+                          authProviders: List[ImportAuthProvider]
+  ) extends ImportResolver
+      with StrictLogging {
     import HttpResolver._
 
     override def name: String = relativeTo match {
       case Some(relativeToPath) => s"http importer (relative to $relativeToPath)"
       case None => "http importer (no 'relative-to' origin)"
-
     }
 
     def newResolverList(newRoot: String): List[ImportResolver] = {
       val rootWithoutFilename = newRoot.split('/').init.mkString("", "/", "/")
       List(
-        HttpResolver(relativeTo = Some(canonicalize(rootWithoutFilename)), headers, hostAllowlist)
+        HttpResolver(relativeTo = Some(canonicalize(rootWithoutFilename)), headers, hostAllowlist, authProviders)
       )
     }
 
@@ -211,8 +224,13 @@ object ImportResolver {
       case None => true
     }
 
+    def fetchAuthHeaders(uri: Uri): Future[Map[String, String]] =
+      authProviders collectFirst {
+        case provider if provider.validHosts.contains(uri.host) => provider.authHeader()
+      } getOrElse Future.successful(Map.empty[String, String])
+
     override def innerResolver(str: String, currentResolvers: List[ImportResolver]): Checked[ResolvedImportBundle] =
-      pathToLookup(str) flatMap { toLookup: WorkflowSource =>
+      pathToLookup(str) flatMap { toLookup: WorkflowUrl =>
         (Try {
           val uri: Uri = uri"$toLookup"
 
@@ -227,21 +245,37 @@ object ImportResolver {
         }).contextualizeErrors(s"download $toLookup")
       }
 
-    private def getUri(toLookup: WorkflowSource): Either[NonEmptyList[WorkflowSource], ResolvedImportBundle] = {
-      implicit val sttpBackend = HttpResolver.sttpBackend()
-      val responseIO: IO[Response[WorkflowSource]] = sttp.get(uri"$toLookup").headers(headers).send()
-
-      // temporary situation to get functionality working before
+    private def getUri(toLookup: WorkflowUrl): Checked[ResolvedImportBundle] = {
+      // Temporary situation to get functionality working before
       // starting in on async-ifying the entire WdlNamespace flow
-      val result: Checked[WorkflowSource] = Await.result(responseIO.unsafeToFuture(), 15.seconds).body.leftMap { e =>
-        NonEmptyList(e.toString.trim, List.empty)
+      // Note: this will cause the calling thread to block for up to 20 seconds
+      // (5 for the auth header lookup, 15 for the http request)
+      val unauthedAttempt = getUriInner(toLookup, Map.empty)
+      val result = if (unauthedAttempt.code == StatusCodes.NotFound) {
+        val authHeaders = Await.result(fetchAuthHeaders(uri"$toLookup"), 5.seconds)
+        if (authHeaders.nonEmpty) {
+          getUriInner(toLookup, authHeaders)
+        } else {
+          unauthedAttempt
+        }
+      } else {
+        unauthedAttempt
       }
 
-      result map {
+      result.body.leftMap { e =>
+        NonEmptyList(e.trim, List.empty)
+      } map {
         ResolvedImportBundle(_, newResolverList(toLookup), ResolvedImportRecord(toLookup))
       }
     }
 
+    protected def getUriInner(toLookup: WorkflowUrl, authHeaders: Map[String, String]): Response[WorkflowSource] = {
+      implicit val sttpBackend = HttpResolver.sttpBackend()
+
+      val responseIO: IO[Response[WorkflowSource]] = sttp.get(uri"$toLookup").headers(headers ++ authHeaders).send()
+      Await.result(responseIO.unsafeToFuture(), 15.seconds)
+    }
+
     override def cleanupIfNecessary(): ErrorOr[Unit] = ().validNel
 
     override def hashKey: ErrorOr[String] = relativeTo.toString.md5Sum.validNel
@@ -252,7 +286,10 @@ object ImportResolver {
     import common.util.IntrospectableLazy
     import common.util.IntrospectableLazy._
 
-    def apply(relativeTo: Option[String] = None, headers: Map[String, String] = Map.empty): HttpResolver = {
+    def apply(relativeTo: Option[String] = None,
+              headers: Map[String, String] = Map.empty,
+              authProviders: List[ImportAuthProvider] = List.empty
+    ): HttpResolver = {
       val config = ConfigFactory.load().getConfig("languages.WDL.http-allow-list")
       val allowListEnabled = config.as[Option[Boolean]]("enabled").getOrElse(false)
       val allowList: Option[List[String]] =
@@ -260,7 +297,7 @@ object ImportResolver {
           config.as[Option[List[String]]]("allowed-http-hosts")
         else None
 
-      new HttpResolver(relativeTo, headers, allowList)
+      new HttpResolver(relativeTo, headers, allowList, authProviders)
     }
 
     val sttpBackend: IntrospectableLazy[SttpBackend[IO, Nothing]] = lazily {
diff --git a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
index 720a7f279af..a451d0c8df6 100644
--- a/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
+++ b/languageFactories/language-factory-core/src/test/scala/cromwell/languages/util/ImportResolverSpec.scala
@@ -7,9 +7,17 @@ import common.assertion.CromwellTimeoutSpec
 import common.assertion.ErrorOrAssertions._
 import cromwell.core.WorkflowId
 import cromwell.core.path.DefaultPath
-import cromwell.languages.util.ImportResolver.{DirectoryResolver, HttpResolver}
+import cromwell.languages.util.ImportResolver.{
+  DirectoryResolver,
+  GithubImportAuthProvider,
+  HttpResolver,
+  ImportAuthProvider
+}
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
+import wom.core.{WorkflowSource, WorkflowUrl}
+
+import scala.concurrent.Future
 
 class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
   behavior of "HttpResolver"
@@ -41,13 +49,13 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   it should "resolve a path from no initial root" in {
-    val resolver = HttpResolver(None, Map.empty, None)
+    val resolver = HttpResolver(None, Map.empty, None, List.empty)
     val toResolve = resolver.pathToLookup("http://abc.com:8000/blah1/blah2.wdl")
     toResolve shouldBeValid "http://abc.com:8000/blah1/blah2.wdl"
   }
 
   it should "resolve a path and store the import in ResolvedImportRecord" in {
-    val resolver = HttpResolver(None, Map.empty, None)
+    val resolver = HttpResolver(None, Map.empty, None, List.empty)
     val importUri =
       "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.wdl"
     val resolvedBundle = resolver.innerResolver(importUri, List(resolver))
@@ -64,14 +72,14 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   val pathEnd = "bob/loblaw/blah/blah.wdl"
 
   it should "allow any import when there is no allow list" in {
-    val resolver = HttpResolver(None, Map.empty, None)
+    val resolver = HttpResolver(None, Map.empty, None, List.empty)
     resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe true
     resolver.isAllowed(uri"http://some-garbage.whatever.eu/$pathEnd") shouldBe true
     resolver.isAllowed(uri"localhost:8080/my/secrets") shouldBe true
   }
 
   it should "allow any import that's on the allow list" in {
-    val resolver = HttpResolver(None, Map.empty, allowList)
+    val resolver = HttpResolver(None, Map.empty, allowList, List.empty)
     resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe true
     resolver.isAllowed(uri"http://anotherwdlsite.org/$pathEnd") shouldBe true
     resolver.isAllowed(uri"https://yetanotherwdlsite.org/$pathEnd") shouldBe false
@@ -81,7 +89,7 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
   }
 
   it should "allow nothing with an empty allow list" in {
-    val resolver = HttpResolver(None, Map.empty, Option(List.empty))
+    val resolver = HttpResolver(None, Map.empty, Option(List.empty), List.empty)
     resolver.isAllowed(uri"https://my.favorite.wdls.com/$pathEnd") shouldBe false
     resolver.isAllowed(uri"http://anotherwdlsite.org/$pathEnd") shouldBe false
     resolver.isAllowed(uri"https://yetanotherwdlsite.org/$pathEnd") shouldBe false
@@ -92,8 +100,9 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
 
   behavior of "HttpResolver with a 'relativeTo' value"
 
-  val relativeHttpResolver = HttpResolver(relativeTo = Some("http://abc.com:8000/blah1/blah2/"), Map.empty, None)
-  val relativeToGithubHttpResolver = HttpResolver(relativeTo = Some(relativeToGithubRoot), Map.empty, None)
+  val relativeHttpResolver =
+    HttpResolver(relativeTo = Some("http://abc.com:8000/blah1/blah2/"), Map.empty, None, List.empty)
+  val relativeToGithubHttpResolver = HttpResolver(relativeTo = Some(relativeToGithubRoot), Map.empty, None, List.empty)
 
   it should "resolve an absolute path from a different initial root" in {
     val pathToLookup = relativeHttpResolver.pathToLookup("http://def.org:8080/blah3.wdl")
@@ -155,6 +164,118 @@ class ImportResolverSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
     }
   }
 
+  behavior of "HttpResolver with an ImportAuthProvider"
+
+  class RecordingHttpResolver(unauthedResponse: Response[String],
+                              authedResponse: Response[String],
+                              authProvider: ImportAuthProvider
+  ) extends HttpResolver(None, Map.empty, None, List(authProvider)) {
+
+    case class RequestRecord(url: WorkflowUrl, headers: Map[String, String], response: Response[String])
+    var requestRecords: List[RequestRecord] = List.empty
+
+    override protected def getUriInner(toLookup: WorkflowUrl,
+                                       authHeaders: Map[String, String]
+    ): Response[WorkflowSource] = {
+      val result =
+        if (
+          Uri.parse(toLookup).get.host == "raw.githubusercontent.com" && authHeaders
+            .get("Authorization")
+            .contains("Bearer 1234")
+        ) {
+          authedResponse
+        } else if (headers.contains("Authorization")) {
+          throw new RuntimeException(s"Unexpected auth header applied")
+        } else {
+          unauthedResponse
+        }
+
+      requestRecords = requestRecords :+ RequestRecord(toLookup, authHeaders, result)
+      result
+    }
+  }
+
+  it should "lookup headers from auth provider after a 404 for valid host" in {
+    val unauthedResponse = new Response[String](Left("Not found or no permissions".getBytes),
+                                                StatusCodes.NotFound,
+                                                "NotFound",
+                                                Nil,
+                                                List.empty
+    )
+    val authedResponse = new Response[String](Right("Hello World"), 200, "OK", Nil, List.empty)
+    val authProvider = new GithubImportAuthProvider {
+      override def authHeader() = Future.successful(Map("Authorization" -> "Bearer 1234"))
+    }
+    val resolver = new RecordingHttpResolver(unauthedResponse, authedResponse, authProvider)
+    val importUri =
+      "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.wdl"
+    val resolvedBundle = resolver.innerResolver(importUri, List(resolver))
+
+    resolvedBundle match {
+      case Left(e) => fail(s"Expected ResolvedImportBundle but got $e")
+      case Right(bundle) =>
+        bundle.resolvedImportRecord.importPath shouldBe importUri
+        bundle.source shouldBe "Hello World"
+
+        resolver.requestRecords.size shouldBe 2
+        resolver.requestRecords.head.url shouldBe importUri
+        resolver.requestRecords.head.headers shouldBe Map.empty
+        resolver.requestRecords(1).url shouldBe importUri
+        resolver.requestRecords(1).headers should be(Map(("Authorization", "Bearer 1234")))
+    }
+  }
+
+  it should "not lookup headers for urls which require no auth" in {
+    val unauthedResponse = new Response[String](Right("Hello World"), 200, "OK", Nil, List.empty)
+    val authedResponse = new Response[String](Left("Shouldn't be authed".getBytes), 500, "BAD", Nil, List.empty)
+    val authProvider = new GithubImportAuthProvider {
+      override def authHeader() = Future.failed(new Exception("Should not be called"))
+    }
+    val resolver = new RecordingHttpResolver(unauthedResponse, authedResponse, authProvider)
+    val importUri =
+      "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.wdl"
+    val resolvedBundle = resolver.innerResolver(importUri, List(resolver))
+
+    resolvedBundle match {
+      case Left(e) => fail(s"Expected ResolvedImportBundle but got $e")
+      case Right(bundle) =>
+        bundle.resolvedImportRecord.importPath shouldBe importUri
+        bundle.source shouldBe "Hello World"
+
+        resolver.requestRecords.size shouldBe 1
+        resolver.requestRecords.head.url shouldBe importUri
+        resolver.requestRecords.head.headers shouldBe Map.empty
+    }
+  }
+
+  it should "not lookup headers for urls which failed with other errors" in {
+    val unauthedResponse = new Response[String](Left("Some other error".getBytes),
+                                                StatusCodes.ServiceUnavailable,
+                                                "ServiceUnavailable",
+                                                Nil,
+                                                List.empty
+    )
+    val authedResponse = new Response[String](Left("Shouldn't be authed".getBytes), 500, "BAD", Nil, List.empty)
+    val authProvider = new GithubImportAuthProvider {
+      override def authHeader() = Future.failed(new Exception("Should not be called"))
+    }
+    val resolver = new RecordingHttpResolver(unauthedResponse, authedResponse, authProvider)
+    val importUri =
+      "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.wdl"
+    val resolvedBundle = resolver.innerResolver(importUri, List(resolver))
+
+    resolvedBundle match {
+      case Left(e) =>
+        e.length should be(1)
+        e.head.contains("Some other error") should be(true)
+        resolver.requestRecords.size shouldBe 1
+        resolver.requestRecords.head.url shouldBe importUri
+        resolver.requestRecords.head.headers shouldBe Map.empty
+      case Right(bundle) =>
+        fail(s"Expected an error but got $bundle")
+    }
+  }
+
   behavior of "directory resolver from root"
 
   val workingDirectory = sys.props("user.dir")
diff --git a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
index eab4163410d..c50fb0df33a 100644
--- a/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
+++ b/languageFactories/wdl-draft2/src/test/scala/languages.wdl.draft2/NamespaceCacheSpec.scala
@@ -61,7 +61,7 @@ class NamespaceCacheSpec extends AnyFlatSpec with CromwellTimeoutSpec with Befor
     )
 
     var lookupCount = 0
-    val countingResolver = new HttpResolver(None, Map.empty, None) {
+    val countingResolver = new HttpResolver(None, Map.empty, None, List.empty) {
       override def pathToLookup(str: String): Checked[String] = {
         lookupCount = lookupCount + 1
         super.pathToLookup(str)
diff --git a/services/src/main/scala/cromwell/services/auth/GithubAuthVending.scala b/services/src/main/scala/cromwell/services/auth/GithubAuthVending.scala
new file mode 100644
index 00000000000..c74df8c947f
--- /dev/null
+++ b/services/src/main/scala/cromwell/services/auth/GithubAuthVending.scala
@@ -0,0 +1,17 @@
+package cromwell.services.auth
+
+import cromwell.services.ServiceRegistryActor.ServiceRegistryMessage
+
+object GithubAuthVending {
+  sealed trait GithubAuthVendingMessage extends ServiceRegistryMessage {
+    override def serviceName: String = "GithubAuthVending"
+  }
+
+  case class GithubAuthRequest(terraToken: String) extends GithubAuthVendingMessage
+
+  sealed trait GithubAuthVendingResponse extends GithubAuthVendingMessage
+  case class GithubAuthTokenResponse(accessToken: String) extends GithubAuthVendingResponse
+  case object NoGithubAuthResponse extends GithubAuthVendingResponse
+  case class GithubAuthVendingFailure(error: Exception) extends GithubAuthVendingResponse
+
+}
diff --git a/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala b/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala
new file mode 100644
index 00000000000..a8d406578ae
--- /dev/null
+++ b/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala
@@ -0,0 +1,45 @@
+package cromwell.services.auth
+
+import akka.actor.ActorRef
+import akka.pattern.{AskSupport, AskTimeoutException}
+import akka.util.Timeout
+import com.typesafe.scalalogging.StrictLogging
+import cromwell.languages.util.ImportResolver.{GithubImportAuthProvider, ImportAuthProvider}
+import cromwell.services.auth.GithubAuthVending.{
+  GithubAuthRequest,
+  GithubAuthTokenResponse,
+  GithubAuthVendingFailure,
+  GithubAuthVendingResponse,
+  NoGithubAuthResponse
+}
+
+import scala.concurrent.{ExecutionContext, Future}
+
+trait GithubAuthVendingSupport extends AskSupport with StrictLogging {
+
+  def serviceRegistryActor: ActorRef
+
+  implicit val timeout: Timeout
+  implicit val ec: ExecutionContext
+
+  def importAuthProvider(token: String): ImportAuthProvider = new GithubImportAuthProvider {
+    override def authHeader(): Future[Map[String, String]] =
+      serviceRegistryActor
+        .ask(GithubAuthRequest(token))
+        .mapTo[GithubAuthVendingResponse]
+        .recoverWith {
+          case e: AskTimeoutException =>
+            Future.failed(new Exception(s"Unable to resolve github auth token within allowed time", e))
+          case e: Throwable =>
+            // This "should" never happen. If it does, let's make it obvious and trigger our alerting:
+            logger.error("Programmer error: Unexpected failure to resolve github auth token", e)
+            Future.failed(new Exception("Failed to resolve github auth token", e))
+        }
+        .flatMap {
+          case GithubAuthTokenResponse(token) => Future.successful(Map("Authorization" -> s"Bearer ${token}"))
+          case NoGithubAuthResponse => Future.successful(Map.empty)
+          case GithubAuthVendingFailure(error) =>
+            Future.failed(new Exception("Failed to resolve github auth token", error))
+        }
+  }
+}
diff --git a/services/src/main/scala/cromwell/services/auth/impl/GithubAuthVendingActor.scala b/services/src/main/scala/cromwell/services/auth/impl/GithubAuthVendingActor.scala
new file mode 100644
index 00000000000..e0f4c9756a0
--- /dev/null
+++ b/services/src/main/scala/cromwell/services/auth/impl/GithubAuthVendingActor.scala
@@ -0,0 +1,33 @@
+package cromwell.services.auth.impl
+
+import akka.actor.{Actor, ActorRef, Props}
+import com.typesafe.config.Config
+import com.typesafe.scalalogging.LazyLogging
+import cromwell.core.Dispatcher.ServiceDispatcher
+import cromwell.services.auth.GithubAuthVending.{GithubAuthRequest, GithubAuthTokenResponse, NoGithubAuthResponse}
+import cromwell.util.GracefulShutdownHelper.ShutdownCommand
+
+class GithubAuthVendingActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
+    extends Actor
+    with LazyLogging {
+
+  lazy val enabled = serviceConfig.getBoolean("enabled")
+
+  override def receive: Receive = {
+    case GithubAuthRequest(_) if enabled =>
+      sender() ! GithubAuthTokenResponse(serviceConfig.getString("access-token"))
+    // This service currently doesn't do any work on shutdown but the service registry pattern requires it
+    // (see https://github.com/broadinstitute/cromwell/issues/2575)
+    case ShutdownCommand => context stop self
+    case _ =>
+      sender() ! NoGithubAuthResponse
+  }
+}
+
+object GithubAuthVendingActor {
+
+  def props(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef): Props =
+    Props(new GithubAuthVendingActor(serviceConfig, globalConfig, serviceRegistryActor))
+      .withDispatcher(ServiceDispatcher)
+
+}
diff --git a/services/src/main/scala/cromwell/services/womtool/Describer.scala b/services/src/main/scala/cromwell/services/womtool/Describer.scala
index 7b8116001da..6263b32c568 100644
--- a/services/src/main/scala/cromwell/services/womtool/Describer.scala
+++ b/services/src/main/scala/cromwell/services/womtool/Describer.scala
@@ -2,7 +2,7 @@ package cromwell.services.womtool
 
 import cats.data.Validated.{Invalid, Valid}
 import cromwell.core.WorkflowSourceFilesCollection
-import cromwell.languages.util.ImportResolver.HttpResolver
+import cromwell.languages.util.ImportResolver.{HttpResolver, ImportAuthProvider, ImportResolver}
 import cromwell.languages.util.{ImportResolver, LanguageFactoryUtil}
 import cromwell.languages.{LanguageFactory, ValidatedWomNamespace}
 import cromwell.services.womtool.WomtoolServiceMessages.{DescribeFailure, DescribeResult, DescribeSuccess}
@@ -13,9 +13,9 @@ import wom.expression.NoIoFunctionSet
 
 object Describer {
 
-  def describeWorkflow(wsfc: WorkflowSourceFilesCollection): DescribeResult = {
+  def describeWorkflow(wsfc: WorkflowSourceFilesCollection, authProviders: List[ImportAuthProvider]): DescribeResult = {
 
-    val initialResolvers = List(HttpResolver(None, Map.empty))
+    val initialResolvers: List[ImportResolver] = List(HttpResolver(None, Map.empty, authProviders))
 
     // The HTTP resolver is used to pull down workflows submitted by URL
     LanguageFactoryUtil.findWorkflowSource(wsfc.workflowSource, wsfc.workflowUrl, initialResolvers) match {
diff --git a/services/src/main/scala/cromwell/services/womtool/WomtoolServiceMessages.scala b/services/src/main/scala/cromwell/services/womtool/WomtoolServiceMessages.scala
index ecbd41d5fc1..d4743cbfe72 100644
--- a/services/src/main/scala/cromwell/services/womtool/WomtoolServiceMessages.scala
+++ b/services/src/main/scala/cromwell/services/womtool/WomtoolServiceMessages.scala
@@ -1,6 +1,7 @@
 package cromwell.services.womtool
 
 import cromwell.core.WorkflowSourceFilesCollection
+import cromwell.languages.util.ImportResolver.ImportAuthProvider
 import cromwell.services.ServiceRegistryActor.ServiceRegistryMessage
 import cromwell.services.womtool.models.WorkflowDescription
 
@@ -12,7 +13,8 @@ object WomtoolServiceMessages {
     override def serviceName: String = WomtoolServiceName
   }
 
-  case class DescribeRequest(filesCollection: WorkflowSourceFilesCollection) extends WomtoolServiceMessage
+  case class DescribeRequest(filesCollection: WorkflowSourceFilesCollection, authProviders: List[ImportAuthProvider])
+      extends WomtoolServiceMessage
 
   sealed trait DescribeResult extends WomtoolServiceMessage
   case class DescribeSuccess(description: WorkflowDescription) extends DescribeResult
diff --git a/services/src/main/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActor.scala b/services/src/main/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActor.scala
index ac1c748281d..d090024e629 100644
--- a/services/src/main/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActor.scala
+++ b/services/src/main/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActor.scala
@@ -18,11 +18,11 @@ class WomtoolServiceInCromwellActor(serviceConfig: Config, globalConfig: Config,
   implicit val ec: ExecutionContext = context.dispatcher
 
   override def receive: Receive = {
-    case DescribeRequest(filesCollection) =>
+    case DescribeRequest(filesCollection, authProviders) =>
       // We are consciously wrapping a Future around the Await.result way down in the HTTP import resolver until we can update the whole call hierarchy to async
       // https://doc.akka.io/docs/akka/2.5.16/actors.html?language=scala#ask-send-and-receive-future
       Future {
-        Describer.describeWorkflow(filesCollection)
+        Describer.describeWorkflow(filesCollection, authProviders)
       } pipeTo sender()
       ()
     case ShutdownCommand =>
diff --git a/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala b/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala
new file mode 100644
index 00000000000..f9bc3e127f4
--- /dev/null
+++ b/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala
@@ -0,0 +1,99 @@
+package cromwell.services.auth
+
+import akka.actor.ActorRef
+import akka.testkit.TestProbe
+import akka.util.Timeout
+import cromwell.core.TestKitSuite
+import cromwell.services.ServiceRegistryActor.ServiceRegistryFailure
+import cromwell.services.auth.GithubAuthVending.GithubAuthRequest
+import cromwell.services.auth.GithubAuthVendingSupportSpec.TestGithubAuthVendingSupport
+import org.scalatest.concurrent.Eventually
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.matchers.should.Matchers
+
+import scala.concurrent.{Await, ExecutionContext, Future}
+import scala.concurrent.duration._
+
+class GithubAuthVendingSupportSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with Eventually {
+
+  behavior of "GithubAuthVendingSupport"
+
+  it should "send a message to the service registry and handle success response" in {
+    val serviceRegistryActor = TestProbe()
+    val testSupport = new TestGithubAuthVendingSupport(serviceRegistryActor.ref)
+    val provider = testSupport.importAuthProvider("user-token")
+    val authHeader: Future[Map[String, String]] = provider.authHeader()
+
+    serviceRegistryActor.expectMsg(GithubAuthRequest("user-token"))
+    serviceRegistryActor.reply(GithubAuthVending.GithubAuthTokenResponse("github-token"))
+
+    Await.result(authHeader, 10.seconds) should be(Map("Authorization" -> "Bearer github-token"))
+  }
+
+  it should "handle 'no auth' responses" in {
+    val serviceRegistryActor = TestProbe()
+    val testSupport = new TestGithubAuthVendingSupport(serviceRegistryActor.ref)
+    val provider = testSupport.importAuthProvider("user-token")
+    val authHeader: Future[Map[String, String]] = provider.authHeader()
+
+    serviceRegistryActor.expectMsg(GithubAuthRequest("user-token"))
+    serviceRegistryActor.reply(GithubAuthVending.NoGithubAuthResponse)
+
+    Await.result(authHeader, 10.seconds) should be(Map.empty)
+  }
+
+  it should "convert error responses in Future failures" in {
+    val serviceRegistryActor = TestProbe()
+    val testSupport = new TestGithubAuthVendingSupport(serviceRegistryActor.ref)
+    val provider = testSupport.importAuthProvider("user-token")
+    val authHeader: Future[Map[String, String]] = provider.authHeader()
+
+    serviceRegistryActor.expectMsg(GithubAuthRequest("user-token"))
+    serviceRegistryActor.reply(GithubAuthVending.GithubAuthVendingFailure(new Exception("BOOM")))
+
+    eventually {
+      authHeader.isCompleted should be(true)
+      authHeader.value.get.failed.get.getMessage should be("Failed to resolve github auth token")
+      authHeader.value.get.failed.get.getCause.getMessage should be("BOOM")
+    }
+  }
+
+  it should "handle timeouts" in {
+    val serviceRegistryActor = TestProbe()
+    val testSupport = new TestGithubAuthVendingSupport(serviceRegistryActor.ref, 1.millisecond)
+    val provider = testSupport.importAuthProvider("user-token")
+    val authHeader: Future[Map[String, String]] = provider.authHeader()
+
+    eventually {
+      authHeader.isCompleted should be(true)
+      authHeader.value.get.failed.get.getMessage should be("Unable to resolve github auth token within allowed time")
+      authHeader.value.get.failed.get.getCause.getMessage should startWith("Ask timed out on")
+    }
+  }
+
+  it should "handle ask failures" in {
+    val serviceRegistryActor = TestProbe()
+    val testSupport = new TestGithubAuthVendingSupport(serviceRegistryActor.ref)
+    val provider = testSupport.importAuthProvider("user-token")
+    val authHeader: Future[Map[String, String]] = provider.authHeader()
+
+    serviceRegistryActor.expectMsg(GithubAuthRequest("user-token"))
+    serviceRegistryActor.reply(ServiceRegistryFailure("GithubAuthVending"))
+
+    eventually {
+      authHeader.isCompleted should be(true)
+      authHeader.value.get.failed.get.getMessage should be("Failed to resolve github auth token")
+      // not the prettiest error message, but at least it should give us something to work with at debug time:
+      authHeader.value.get.failed.get.getCause.getMessage should startWith("Cannot cast")
+    }
+  }
+
+}
+
+object GithubAuthVendingSupportSpec {
+  class TestGithubAuthVendingSupport(val serviceRegistryActor: ActorRef, val timeout: Timeout = 10.seconds)
+      extends GithubAuthVendingSupport {
+    implicit override val ec: ExecutionContext = ExecutionContext.global
+  }
+
+}
diff --git a/services/src/test/scala/cromwell/services/womtool/DescriberSpec.scala b/services/src/test/scala/cromwell/services/womtool/DescriberSpec.scala
index 47fba0684fc..31dcc07934b 100644
--- a/services/src/test/scala/cromwell/services/womtool/DescriberSpec.scala
+++ b/services/src/test/scala/cromwell/services/womtool/DescriberSpec.scala
@@ -73,7 +73,7 @@ class DescriberSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     //
     // N.B. the `asJson` is highly significant as it exercises the entire serialization module and compares
     // the end product instead of an intermediate case class hierarchy
-    Describer.describeWorkflow(wsfc).asInstanceOf[DescribeSuccess].description.asJson shouldBe expectedJson
+    Describer.describeWorkflow(wsfc, List.empty).asInstanceOf[DescribeSuccess].description.asJson shouldBe expectedJson
   }
 }
 
diff --git a/services/src/test/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActorSpec.scala b/services/src/test/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActorSpec.scala
index 08b9955dcc1..29fd4a5970a 100644
--- a/services/src/test/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/womtool/impl/WomtoolServiceInCromwellActorSpec.scala
@@ -137,7 +137,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlValid))
 
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeSuccess(
           description = TestData.successfulDescription
         )
@@ -148,7 +148,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlHttpImportValid))
 
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeSuccess(
           description = TestData.successfulDescription
         )
@@ -160,7 +160,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlValid), inputsJson = TestData.helloWorldInputs)
 
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeSuccess(
           description = TestData.successfulDescription
         )
@@ -172,7 +172,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlValid), inputsJson = TestData.bogusInputs)
 
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeSuccess(
           description = WorkflowDescription(
             valid = false,
@@ -192,7 +192,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlValid), inputsJson = TestData.emptyInputs)
 
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeSuccess(
           description = WorkflowDescription(
             valid = false,
@@ -212,7 +212,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlValidNoInputs), inputsJson = TestData.emptyInputs)
 
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeSuccess(
           description = WorkflowDescription(
             valid = true,
@@ -240,7 +240,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc = wsfcConjurer(workflowSource = Option(TestData.wdlValidNoInputs), inputsJson = TestData.bogusInputs)
 
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeSuccess(
           description = WorkflowDescription(
             valid = false,
@@ -262,7 +262,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
         wsfcConjurer(workflowSource = Option(TestData.wdlValidDraft2NoInputs), inputsJson = TestData.bogusInputs)
 
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeSuccess(
           description = WorkflowDescription(
             valid = true,
@@ -290,7 +290,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc = wsfcConjurer(workflowUrl = Option(TestData.workflowUrlValid))
 
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeSuccess(
           description = WorkflowDescription(
             valid = true,
@@ -317,7 +317,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
 
       val wsfc = wsfcConjurer()
 
-      check(DescribeRequest(wsfc), DescribeFailure("Either workflow source or url has to be supplied"))
+      check(DescribeRequest(wsfc, List.empty), DescribeFailure("Either workflow source or url has to be supplied"))
     }
 
     "return an error when both workflow URL and workflow source specified" in {
@@ -325,7 +325,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc =
         wsfcConjurer(workflowSource = Option(TestData.wdlInvalid), workflowUrl = Option(TestData.workflowUrlValid))
 
-      check(DescribeRequest(wsfc), DescribeFailure("Both workflow source and url can't be supplied"))
+      check(DescribeRequest(wsfc, List.empty), DescribeFailure("Both workflow source and url can't be supplied"))
     }
 
     "return an error when the workflow URL is a 404" in {
@@ -333,7 +333,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
       val wsfc = wsfcConjurer(workflowUrl = Option(TestData.workflowUrlNotFound))
 
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeFailure(
           "Failed to resolve 'https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Failed to download https://raw.githubusercontent.com/broadinstitute/cromwell/develop/my_workflow (reason 1 of 1): 404: Not Found"
         )
@@ -346,7 +346,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
 
       // The error is from the OS network stack and differs between Mac and Linux
       (for {
-        result <- (womtoolActor ? DescribeRequest(wsfc)).mapTo[DescribeResult]
+        result <- (womtoolActor ? DescribeRequest(wsfc, List.empty)).mapTo[DescribeResult]
         _ = result should (
           be(
             DescribeFailure(
@@ -369,7 +369,7 @@ class WomtoolServiceInCromwellActorSpec extends ServicesSpec {
 
       // The HTTP resolver has figured out that you have not given it a URL and assumes it's a relative path
       check(
-        DescribeRequest(wsfc),
+        DescribeRequest(wsfc, List.empty),
         DescribeFailure(
           "Failed to resolve 'Zardoz' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path"
         )
diff --git a/src/ci/resources/build_application.inc.conf b/src/ci/resources/build_application.inc.conf
index 1a8a28857ae..260e0463a14 100644
--- a/src/ci/resources/build_application.inc.conf
+++ b/src/ci/resources/build_application.inc.conf
@@ -59,4 +59,8 @@ services.MetadataService.config.metadata-write-statistics {
   sub-workflow-bundling = true
 }
 
+# Make the shutdown timeout conspicuously long, so that if it hangs, it is an obvious problem in CI.
+# See https://github.com/broadinstitute/cromwell/issues/2575
+akka.coordinated-shutdown.phases.stop-io-activity.timeout = 60 minutes
+
 include "cromwell_database.inc.conf"

From 3713d16f847dca1013707794aa6addafa34cff0c Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 26 Feb 2024 13:11:36 -0500
Subject: [PATCH 283/326] =?UTF-8?q?WX-1252=20Runtime=20attributes=20cleanu?=
 =?UTF-8?q?p=20=E2=80=93=C2=A0CWL=20runtime=20environment=20(#7369)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../main/scala/cromwell/backend/Command.scala | 10 +--
 .../backend/MinimumRuntimeSettings.scala      | 13 ++++
 .../cromwell/backend/RuntimeEnvironment.scala | 64 -------------------
 .../StandardAsyncExecutionActor.scala         | 19 +-----
 docs/tutorials/HPCSlurmWithLocalScratch.md    |  2 +
 ...cpBatchAsyncBackendJobExecutionActor.scala |  8 +--
 ...inesApiAsyncBackendJobExecutionActor.scala |  8 +--
 .../config/ConfigAsyncJobExecutionActor.scala |  5 +-
 .../draft2/model/command/WdlCommandPart.scala |  4 +-
 .../CommandPartElementToWomCommandPart.scala  |  7 +-
 wom/src/main/scala/wom/CommandPart.scala      |  4 +-
 .../wom/callable/CommandTaskDefinition.scala  |  8 +--
 .../wom/callable/RuntimeEnvironment.scala     | 22 -------
 13 files changed, 29 insertions(+), 145 deletions(-)
 create mode 100644 backend/src/main/scala/cromwell/backend/MinimumRuntimeSettings.scala
 delete mode 100644 backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala
 delete mode 100644 wom/src/main/scala/wom/callable/RuntimeEnvironment.scala

diff --git a/backend/src/main/scala/cromwell/backend/Command.scala b/backend/src/main/scala/cromwell/backend/Command.scala
index 3a4eaf3b88a..c523500b7ca 100644
--- a/backend/src/main/scala/cromwell/backend/Command.scala
+++ b/backend/src/main/scala/cromwell/backend/Command.scala
@@ -3,7 +3,6 @@ package cromwell.backend
 import common.validation.ErrorOr._
 import common.validation.Validation._
 import wom.InstantiatedCommand
-import wom.callable.RuntimeEnvironment
 import wom.expression.IoFunctionSet
 import wom.values.{WomEvaluatedCallInputs, WomValue}
 
@@ -26,14 +25,9 @@ object Command {
                   callEngineFunction: IoFunctionSet,
                   inputsPreProcessor: WomEvaluatedCallInputs => Try[WomEvaluatedCallInputs] =
                     (i: WomEvaluatedCallInputs) => Success(i),
-                  valueMapper: WomValue => WomValue,
-                  runtimeEnvironment: RuntimeEnvironment
+                  valueMapper: WomValue => WomValue
   ): ErrorOr[InstantiatedCommand] =
     inputsPreProcessor(jobDescriptor.evaluatedTaskInputs).toErrorOr flatMap { mappedInputs =>
-      jobDescriptor.taskCall.callable.instantiateCommand(mappedInputs,
-                                                         callEngineFunction,
-                                                         valueMapper,
-                                                         runtimeEnvironment
-      )
+      jobDescriptor.taskCall.callable.instantiateCommand(mappedInputs, callEngineFunction, valueMapper)
     }
 }
diff --git a/backend/src/main/scala/cromwell/backend/MinimumRuntimeSettings.scala b/backend/src/main/scala/cromwell/backend/MinimumRuntimeSettings.scala
new file mode 100644
index 00000000000..67c18324ef8
--- /dev/null
+++ b/backend/src/main/scala/cromwell/backend/MinimumRuntimeSettings.scala
@@ -0,0 +1,13 @@
+package cromwell.backend
+
+import eu.timepit.refined.api.Refined
+import eu.timepit.refined.numeric.Positive
+import eu.timepit.refined.refineMV
+import wdl4s.parser.MemoryUnit
+import wom.format.MemorySize
+
+case class MinimumRuntimeSettings(cores: Int Refined Positive = refineMV(1),
+                                  ram: MemorySize = MemorySize(4, MemoryUnit.GB),
+                                  outputPathSize: Long = Long.MaxValue,
+                                  tempPathSize: Long = Long.MaxValue
+)
diff --git a/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala b/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala
deleted file mode 100644
index beac15b1610..00000000000
--- a/backend/src/main/scala/cromwell/backend/RuntimeEnvironment.scala
+++ /dev/null
@@ -1,64 +0,0 @@
-package cromwell.backend
-
-import java.util.UUID
-
-import cromwell.backend.io.JobPaths
-import cromwell.backend.validation.MemoryValidation
-import cromwell.core.path.Path
-import eu.timepit.refined.api.Refined
-import eu.timepit.refined.numeric.Positive
-import eu.timepit.refined.refineMV
-import wdl4s.parser.MemoryUnit
-import wom.callable.RuntimeEnvironment
-import wom.format.MemorySize
-import wom.values.WomValue
-
-object RuntimeEnvironmentBuilder {
-
-  def apply(runtimeAttributes: Map[String, WomValue],
-            callRoot: Path,
-            callExecutionRoot: Path
-  ): MinimumRuntimeSettings => RuntimeEnvironment = { minimums =>
-    val outputPath: String = callExecutionRoot.pathAsString
-
-    val tempPath: String = {
-      val uuid = UUID.randomUUID().toString
-      val hash = uuid.substring(0, uuid.indexOf('-'))
-      callRoot.resolve(s"tmp.$hash").pathAsString
-    }
-
-    // This class is going away in https://github.com/broadinstitute/cromwell/pull/7369
-    val cores: Int Refined Positive = minimums.cores
-
-    val memoryInMB: Double =
-      MemoryValidation
-        .instance()
-        .validate(runtimeAttributes)
-        .map(_.to(MemoryUnit.MB).amount)
-        .getOrElse(minimums.ram.amount)
-
-    // TODO: Read these from somewhere else
-    val outputPathSize: Long = minimums.outputPathSize
-
-    val tempPathSize: Long = minimums.outputPathSize
-
-    RuntimeEnvironment(outputPath, tempPath, cores, memoryInMB, outputPathSize, tempPathSize)
-  }
-
-  /**
-    * Per the spec:
-    *
-    * "For cores, ram, outdirSize and tmpdirSize, if an implementation can't provide the actual number of reserved cores
-    * during the expression evaluation time, it should report back the minimal requested amount."
-    */
-  def apply(runtimeAttributes: Map[String, WomValue],
-            jobPaths: JobPaths
-  ): MinimumRuntimeSettings => RuntimeEnvironment =
-    this.apply(runtimeAttributes, jobPaths.callRoot, jobPaths.callExecutionRoot)
-}
-
-case class MinimumRuntimeSettings(cores: Int Refined Positive = refineMV(1),
-                                  ram: MemorySize = MemorySize(4, MemoryUnit.GB),
-                                  outputPathSize: Long = Long.MaxValue,
-                                  tempPathSize: Long = Long.MaxValue
-)
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 00b5f37513b..1b183a67646 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -37,7 +37,7 @@ import net.ceedubs.ficus.Ficus._
 import org.apache.commons.lang3.StringUtils
 import org.apache.commons.lang3.exception.ExceptionUtils
 import shapeless.Coproduct
-import wom.callable.{AdHocValue, CommandTaskDefinition, ContainerizedInputExpression, RuntimeEnvironment}
+import wom.callable.{AdHocValue, CommandTaskDefinition, ContainerizedInputExpression}
 import wom.expression.WomExpression
 import wom.graph.LocalName
 import wom.values._
@@ -141,7 +141,7 @@ trait StandardAsyncExecutionActor
 
   lazy val temporaryDirectory: String = configurationDescriptor.backendConfig.getOrElse(
     path = "temporary-directory",
-    default = s"""$$(mkdir -p "${runtimeEnvironment.tempPath}" && echo "${runtimeEnvironment.tempPath}")"""
+    default = """$(mktemp -d "$PWD"/tmp.XXXXXX)"""
   )
 
   val logJobIds: Boolean = true
@@ -431,7 +431,6 @@ trait StandardAsyncExecutionActor
       s"""export $k="$v""""
     } mkString ("", "\n", "\n")
 
-    val home = jobDescriptor.taskCall.callable.homeOverride.map(_(runtimeEnvironment)).getOrElse("$HOME")
     val shortId = jobDescriptor.workflowDescriptor.id.shortString
     // Give the out and error FIFO variables names that are unlikely to conflict with anything the user is doing.
     val (out, err) = (s"out$shortId", s"err$shortId")
@@ -479,7 +478,6 @@ trait StandardAsyncExecutionActor
           |$tmpDirPermissionsAdjustment
           |export _JAVA_OPTIONS=-Djava.io.tmpdir="$$tmpDir"
           |export TMPDIR="$$tmpDir"
-          |export HOME="$home"
           |
           |SCRIPT_PREAMBLE
           |
@@ -512,16 +510,6 @@ trait StandardAsyncExecutionActor
     )
   }
 
-  def runtimeEnvironmentPathMapper(env: RuntimeEnvironment): RuntimeEnvironment = {
-    def localize(path: String): String = (WomSingleFile(path) |> commandLineValueMapper).valueString
-    env.copy(outputPath = env.outputPath |> localize, tempPath = env.tempPath |> localize)
-  }
-
-  lazy val runtimeEnvironment: RuntimeEnvironment =
-    RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes, jobPaths)(
-      standardParams.minimumRuntimeSettings
-    ) |> runtimeEnvironmentPathMapper
-
   /**
    * Turns WomFiles into relative paths.  These paths are relative to the working disk.
    *
@@ -685,8 +673,7 @@ trait StandardAsyncExecutionActor
       jobDescriptor,
       backendEngineFunctions,
       mutatingPreProcessor,
-      commandLineValueMapper,
-      runtimeEnvironment
+      commandLineValueMapper
     )
 
     def makeStringKeyedMap(list: List[(LocalName, WomValue)]): Map[String, WomValue] = list.toMap map { case (k, v) =>
diff --git a/docs/tutorials/HPCSlurmWithLocalScratch.md b/docs/tutorials/HPCSlurmWithLocalScratch.md
index 85bed57e531..fb5b95200d9 100644
--- a/docs/tutorials/HPCSlurmWithLocalScratch.md
+++ b/docs/tutorials/HPCSlurmWithLocalScratch.md
@@ -3,6 +3,8 @@
 # Installing the Cromwell To Use Local Scratch Device
 #### These instructions are a community contribution
 
+### In the process of being updated as of 2024-02
+
 In this section we will install the Cromwell Workflow Management system and configure it, so it can use the local scratch device on the compute nodes.
 (these installations are done in a ```centos 8``` enviornment)
 
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
index dbd63740ad0..b9b1a7c0b08 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActor.scala
@@ -50,7 +50,7 @@ import org.apache.commons.csv.{CSVFormat, CSVPrinter}
 import org.apache.commons.io.output.ByteArrayOutputStream
 import wom.callable.Callable.OutputDefinition
 import wom.callable.MetaValueElement.{MetaValueElementBoolean, MetaValueElementObject}
-import wom.callable.{AdHocValue, RuntimeEnvironment}
+import wom.callable.AdHocValue
 import wom.core.FullyQualifiedName
 import wom.expression.{FileEvaluation, NoIoFunctionSet}
 import wom.values._
@@ -992,12 +992,6 @@ class GcpBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff =
     SimpleExponentialBackoff(initialInterval = 5.seconds, maxInterval = 20.seconds, multiplier = 1.1)
 
-  override lazy val runtimeEnvironment: RuntimeEnvironment =
-    RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes,
-                              GcpBatchWorkingDisk.MountPoint,
-                              GcpBatchWorkingDisk.MountPoint
-    )(standardParams.minimumRuntimeSettings)
-
   protected def sendIncrementMetricsForReferenceFiles(referenceInputFilesOpt: Option[Set[GcpBatchInput]]): Unit =
     referenceInputFilesOpt match {
       case Some(referenceInputFiles) =>
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
index 965dc4e1244..f09ebd88bd6 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiAsyncBackendJobExecutionActor.scala
@@ -59,7 +59,7 @@ import mouse.all._
 import shapeless.Coproduct
 import wom.callable.Callable.OutputDefinition
 import wom.callable.MetaValueElement.{MetaValueElementBoolean, MetaValueElementObject}
-import wom.callable.{AdHocValue, RuntimeEnvironment}
+import wom.callable.AdHocValue
 import wom.core.FullyQualifiedName
 import wom.expression.{FileEvaluation, NoIoFunctionSet}
 import wom.types.{WomArrayType, WomSingleFileType}
@@ -146,12 +146,6 @@ class PipelinesApiAsyncBackendJobExecutionActor(override val standardParams: Sta
   override lazy val executeOrRecoverBackOff: SimpleExponentialBackoff =
     SimpleExponentialBackoff(initialInterval = 3 seconds, maxInterval = 20 seconds, multiplier = 1.1)
 
-  override lazy val runtimeEnvironment: RuntimeEnvironment =
-    RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes,
-                              PipelinesApiWorkingDisk.MountPoint,
-                              PipelinesApiWorkingDisk.MountPoint
-    )(standardParams.minimumRuntimeSettings)
-
   protected lazy val cmdInput: PipelinesApiFileInput =
     PipelinesApiFileInput(PipelinesApiJobPaths.JesExecParamName,
                           pipelinesApiCallPaths.script,
diff --git a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala
index 6e8bfba564e..0cdfa77f0dd 100644
--- a/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala
+++ b/supportedBackends/sfs/src/main/scala/cromwell/backend/impl/sfs/config/ConfigAsyncJobExecutionActor.scala
@@ -4,7 +4,6 @@ import java.nio.file.FileAlreadyExistsException
 import java.time.Instant
 
 import common.validation.Validation._
-import cromwell.backend.RuntimeEnvironmentBuilder
 import cromwell.backend.impl.sfs.config.ConfigConstants._
 import cromwell.backend.sfs._
 import cromwell.backend.standard.{StandardAsyncExecutionActorParams, StandardAsyncJob}
@@ -104,10 +103,8 @@ sealed trait ConfigAsyncJobExecutionActor extends SharedFileSystemAsyncJobExecut
       if !inputs.contains(optional.localName.value)
     } yield optional -> WomOptionalValue.none(optional.womType.memberType)
 
-    val runtimeEnvironment =
-      RuntimeEnvironmentBuilder(jobDescriptor.runtimeAttributes, jobPaths)(standardParams.minimumRuntimeSettings)
     val allInputs = providedWomInputs ++ optionalsForciblyInitializedToNone
-    val womInstantiation = taskDefinition.instantiateCommand(allInputs, NoIoFunctionSet, identity, runtimeEnvironment)
+    val womInstantiation = taskDefinition.instantiateCommand(allInputs, NoIoFunctionSet, identity)
 
     val command = womInstantiation.toTry.get.commandString
     jobLogger.info(s"executing: $command")
diff --git a/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/WdlCommandPart.scala b/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/WdlCommandPart.scala
index c2657b2eaf0..bfa836ac413 100644
--- a/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/WdlCommandPart.scala
+++ b/wdl/model/draft2/src/main/scala/wdl/draft2/model/command/WdlCommandPart.scala
@@ -4,7 +4,6 @@ import common.validation.ErrorOr.ErrorOr
 import wdl.draft2.model.Declaration
 import wdl.draft2.model.expression.{WdlFunctions, WdlStandardLibraryFunctions}
 import wdl.shared.FileSizeLimitationConfig
-import wom.callable.RuntimeEnvironment
 import wom.expression.IoFunctionSet
 import wom.graph.LocalName
 import wom.values.WomValue
@@ -20,8 +19,7 @@ trait WdlCommandPart extends CommandPart {
 
   override def instantiate(inputsMap: Map[LocalName, WomValue],
                            functions: IoFunctionSet,
-                           valueMapper: WomValue => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment
+                           valueMapper: WomValue => WomValue
   ): ErrorOr[List[InstantiatedCommand]] = {
     val wdlFunctions =
       WdlStandardLibraryFunctions.fromIoFunctionSet(functions, FileSizeLimitationConfig.fileSizeLimitationConfig)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala
index ed12e23c853..f7062441130 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala
@@ -9,7 +9,6 @@ import wdl.model.draft3.graph.{ExpressionValueConsumer, GeneratedValueHandle}
 import wdl.model.draft3.graph.expression._
 import wdl.transforms.base.linking.graph.LinkedGraphMaker
 import wdl.transforms.base.wdlom2wom.expression.WdlomWomExpression
-import wom.callable.RuntimeEnvironment
 import wom.expression.{IoFunctionSet, WomExpression}
 import wom.graph.LocalName
 import wom.types.{WomArrayType, WomPrimitiveType, WomType}
@@ -52,8 +51,7 @@ case class WdlomWomStringCommandPart(stringCommandPartElement: StringCommandPart
   override def toString: String = stringCommandPartElement.value
   override def instantiate(inputsMap: Map[LocalName, WomValue],
                            functions: IoFunctionSet,
-                           valueMapper: WomValue => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment
+                           valueMapper: WomValue => WomValue
   ): ErrorOr[List[InstantiatedCommand]] = List(InstantiatedCommand(stringCommandPartElement.value)).validNel
 }
 
@@ -65,8 +63,7 @@ case class WdlomWomPlaceholderCommandPart(attributes: PlaceholderAttributeSet, e
 
   override def instantiate(inputsMap: Map[LocalName, WomValue],
                            functions: IoFunctionSet,
-                           valueMapper: WomValue => WomValue,
-                           runtimeEnvironment: RuntimeEnvironment
+                           valueMapper: WomValue => WomValue
   ): ErrorOr[List[InstantiatedCommand]] = {
     val inputsValues = inputsMap map { case (localName, value) => localName.value -> value }
     expression.evaluateValueForPlaceholder(inputsValues,
diff --git a/wom/src/main/scala/wom/CommandPart.scala b/wom/src/main/scala/wom/CommandPart.scala
index 97e661c5b81..f81792f54b7 100644
--- a/wom/src/main/scala/wom/CommandPart.scala
+++ b/wom/src/main/scala/wom/CommandPart.scala
@@ -1,7 +1,6 @@
 package wom
 
 import common.validation.ErrorOr.ErrorOr
-import wom.callable.RuntimeEnvironment
 import wom.expression.IoFunctionSet
 import wom.graph.LocalName
 import wom.values.WomValue
@@ -9,7 +8,6 @@ import wom.values.WomValue
 trait CommandPart {
   def instantiate(inputsMap: Map[LocalName, WomValue],
                   functions: IoFunctionSet,
-                  valueMapper: WomValue => WomValue,
-                  runtimeEnvironment: RuntimeEnvironment
+                  valueMapper: WomValue => WomValue
   ): ErrorOr[List[InstantiatedCommand]]
 }
diff --git a/wom/src/main/scala/wom/callable/CommandTaskDefinition.scala b/wom/src/main/scala/wom/callable/CommandTaskDefinition.scala
index 62531ac5802..ff919602c00 100644
--- a/wom/src/main/scala/wom/callable/CommandTaskDefinition.scala
+++ b/wom/src/main/scala/wom/callable/CommandTaskDefinition.scala
@@ -92,7 +92,6 @@ sealed trait CommandTaskDefinition extends TaskDefinition {
   def adHocFileCreation: Set[ContainerizedInputExpression]
   def environmentExpressions: Map[String, WomExpression]
   def additionalGlob: Option[WomGlobFile]
-  def homeOverride: Option[RuntimeEnvironment => String]
 
   /**
     * Provides a custom way to evaluate outputs of the task definition.
@@ -104,8 +103,7 @@ sealed trait CommandTaskDefinition extends TaskDefinition {
 
   def instantiateCommand(taskInputs: WomEvaluatedCallInputs,
                          functions: IoFunctionSet,
-                         valueMapper: WomValue => WomValue,
-                         runtimeEnvironment: RuntimeEnvironment
+                         valueMapper: WomValue => WomValue
   ): ErrorOr[InstantiatedCommand] = {
 
     val inputsByLocalName = taskInputs map { case (k, v) => k.localName -> v }
@@ -115,7 +113,7 @@ sealed trait CommandTaskDefinition extends TaskDefinition {
     // Just raw command parts, no separators.
     val rawCommandParts: List[ErrorOr[InstantiatedCommand]] =
       commandTemplate(taskInputs).toList.flatMap { commandPart =>
-        commandPart.instantiate(inputsByLocalName, functions, valueMapper, runtimeEnvironment).sequence
+        commandPart.instantiate(inputsByLocalName, functions, valueMapper).sequence
       }
 
     // Add separator command parts and monoid smash down to one `ErrorOr[InstantiatedCommand]`.
@@ -163,7 +161,6 @@ final case class CallableTaskDefinition(name: String,
                                         additionalGlob: Option[WomGlobFile] = None,
                                         private[wom] val customizedOutputEvaluation: OutputEvaluationFunction =
                                           OutputEvaluationFunction.none,
-                                        homeOverride: Option[RuntimeEnvironment => String] = None,
                                         dockerOutputDirectory: Option[String] = None,
                                         override val sourceLocation: Option[SourceFileLocation]
 ) extends CommandTaskDefinition {
@@ -198,7 +195,6 @@ final case class ExecutableTaskDefinition private (callableTaskDefinition: Calla
   override def additionalGlob = callableTaskDefinition.additionalGlob
   override private[wom] def customizedOutputEvaluation = callableTaskDefinition.customizedOutputEvaluation
   override def toExecutable = this.validNel
-  override def homeOverride = callableTaskDefinition.homeOverride
   override def dockerOutputDirectory = callableTaskDefinition.dockerOutputDirectory
 }
 
diff --git a/wom/src/main/scala/wom/callable/RuntimeEnvironment.scala b/wom/src/main/scala/wom/callable/RuntimeEnvironment.scala
deleted file mode 100644
index 513516a1af2..00000000000
--- a/wom/src/main/scala/wom/callable/RuntimeEnvironment.scala
+++ /dev/null
@@ -1,22 +0,0 @@
-package wom.callable
-
-import eu.timepit.refined.api.Refined
-import eu.timepit.refined.numeric.Positive
-
-/**
-  * Parameter documentation quoted from CWL Spec.
-  *
-  * @param outputPath runtime.outdir: an absolute path to the designated output directory
-  * @param tempPath runtime.tmpdir: an absolute path to the designated temporary directory
-  * @param cores runtime.cores: number of CPU cores reserved for the tool process
-  * @param ram runtime.ram: amount of RAM in mebibytes (2**20) reserved for the tool process
-  * @param outputPathSize runtime.outdirSize: reserved storage space available in the designated output directory
-  * @param tempPathSize runtime.tmpdirSize: reserved storage space available in the designated temporary directory
-  */
-case class RuntimeEnvironment(outputPath: String,
-                              tempPath: String,
-                              cores: Int Refined Positive,
-                              ram: Double,
-                              outputPathSize: Long,
-                              tempPathSize: Long
-)

From a29fdf85f1c879a25bb9844686c54eb6c27f76d4 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Tue, 27 Feb 2024 13:03:24 -0500
Subject: [PATCH 284/326] WX-1462 POSIX-flavored sub() (#7374)

---
 .../biscayne_new_engine_functions.test        |  2 +
 .../biscayne_new_engine_functions.wdl         |  7 +++-
 project/Dependencies.scala                    |  4 +-
 .../draft3/elements/ExpressionElement.scala   | 10 +++++
 .../AstToNewExpressionElements.scala          |  3 +-
 .../BiscayneExpressionValueConsumers.scala    | 10 +++++
 .../expression/consumed/consumed.scala        |  2 +-
 .../files/BiscayneFileEvaluators.scala        |  9 +++-
 .../linking/expression/files/files.scala      |  3 +-
 .../types/BiscayneTypeEvaluators.scala        | 12 +++++-
 .../linking/expression/types/types.scala      |  2 +-
 .../values/BiscayneValueEvaluators.scala      | 33 +++++++++++++++
 .../linking/expression/values/values.scala    |  3 +-
 .../transforms/biscayne/Ast2WdlomSpec.scala   |  7 +++-
 ...BiscayneExpressionValueConsumersSpec.scala |  9 ++++
 .../files/BiscayneFileEvaluatorSpec.scala     | 11 +++++
 .../types/BiscayneTypeEvaluatorSpec.scala     |  9 ++++
 .../values/BiscayneValueEvaluatorSpec.scala   | 23 ++++++++++
 .../AstToNewExpressionElements.scala          |  3 +-
 .../CascadesExpressionValueConsumers.scala    | 10 +++++
 .../expression/consumed/consumed.scala        |  2 +-
 .../files/CascadesFileEvaluators.scala        |  9 +++-
 .../linking/expression/files/files.scala      |  3 +-
 .../types/CascadesTypeEvaluators.scala        | 12 +++++-
 .../linking/expression/types/types.scala      |  2 +-
 .../values/CascadesValueEvaluators.scala      | 33 +++++++++++++++
 .../linking/expression/values/values.scala    |  3 +-
 ...CascadesExpressionValueConsumersSpec.scala |  9 ++++
 .../files/CascadesFileEvaluatorSpec.scala     | 11 +++++
 .../types/CascadesTypeEvaluatorSpec.scala     |  9 ++++
 .../values/CascadesValueEvaluatorSpec.scala   | 23 ++++++++++
 .../transforms/ast2wdlom/Ast2WdlomSpec.scala  | 20 +++++++--
 .../values/ValueEvaluatorsSpec.scala          | 42 +++++++++++++++++++
 .../AstNodeToExpressionElement.scala          |  2 +-
 .../files/EngineFunctionEvaluators.scala      | 16 ++++---
 .../values/EngineFunctionEvaluators.scala     |  2 +-
 .../base/wdlom2wdl/WdlWriterImpl.scala        |  1 +
 37 files changed, 340 insertions(+), 31 deletions(-)
 create mode 100644 wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/linking/expression/values/ValueEvaluatorsSpec.scala

diff --git a/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test b/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
index 6998d4af7e7..e05af2f8a2d 100644
--- a/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
+++ b/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
@@ -55,6 +55,8 @@ metadata {
   "outputs.biscayne_new_engine_functions.minMaxIntFloatComposition": 1.0
   "outputs.biscayne_new_engine_functions.maxIntVsMaxFloat": 1.79769313E+308
 
+  "outputs.biscayne_new_engine_functions.substituted": "WATtheWAT"
+
   "outputs.biscayne_new_engine_functions.with_suffixes.0": "aaaS"
   "outputs.biscayne_new_engine_functions.with_suffixes.1": "bbbS"
   "outputs.biscayne_new_engine_functions.with_suffixes.2": "cccS"
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
index f7b3d0de7fd..c4387134421 100644
--- a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
@@ -4,7 +4,7 @@ workflow biscayne_new_engine_functions {
 
   meta {
     description: "This test makes sure that these functions work in a real workflow"
-    functions_under_test: [ "keys", "as_map", "as_pairs", "collect_by_key", "suffix" ]
+    functions_under_test: [ "keys", "as_map", "as_pairs", "collect_by_key", "sub", "suffix" ]
   }
 
   Map[String, Int] x_map_in = {"a": 1, "b": 2, "c": 3}
@@ -51,6 +51,11 @@ workflow biscayne_new_engine_functions {
     Float minMaxIntFloatComposition = min(max(biggestInt, smallFloat), smallestInt) # 1.0
     Float maxIntVsMaxFloat = max(maxInt, maxFloat)
 
+    # sub():
+    # (Exists before Biscayne, but uses different regex flavor here)
+    # =================================================
+    String substituted = sub("AtheZ", "[[:upper:]]", "WAT")
+
     # suffix():
     # =================================================
     Array[String] with_suffixes = suffix("S", some_strings)
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 6b1e3cc1740..30396519016 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -103,6 +103,7 @@ object Dependencies {
   private val postgresV = "42.4.4"
   private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
+  private val re2jV = "1.6"
   private val refinedV = "0.10.1"
   private val rhinoV = "1.7.14"
 
@@ -517,7 +518,8 @@ object Dependencies {
   val wdlDependencies: List[ModuleID] = List(
     "commons-io" % "commons-io" % commonsIoV,
     "org.scala-graph" %% "graph-core" % scalaGraphV,
-    "com.chuusai" %% "shapeless" % shapelessV
+    "com.chuusai" %% "shapeless" % shapelessV,
+    "com.google.re2j" % "re2j" % re2jV,
   ) ++ betterFilesDependencies
 
   val languageFactoryDependencies = List(
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
index 91f34d064ae..23101adfa9e 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
@@ -180,6 +180,8 @@ object ExpressionElement {
     def arg2: ExpressionElement
     def arg3: ExpressionElement
   }
+
+  // Pre-1.1 WDL versions have undefined regex flavor. Cromwell uses the standard Java flavor.
   final case class Sub(input: ExpressionElement, pattern: ExpressionElement, replace: ExpressionElement)
       extends ThreeParamFunctionCallElement {
     override def arg1: ExpressionElement = input
@@ -187,6 +189,14 @@ object ExpressionElement {
     override def arg3: ExpressionElement = replace
   }
 
+  // As of WDL 1.1, WDL regular expressions are expected to be POSIX ERE flavor.
+  final case class SubPosix(input: ExpressionElement, pattern: ExpressionElement, replace: ExpressionElement)
+      extends ThreeParamFunctionCallElement {
+    override def arg1: ExpressionElement = input
+    override def arg2: ExpressionElement = pattern
+    override def arg3: ExpressionElement = replace
+  }
+
   /**
     * A single identifier lookup expression, eg Int x = y
     */
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
index 5c0c01859c2..70ebd4879c3 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
@@ -3,7 +3,7 @@ package wdl.transforms.biscayne.ast2wdlom
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
 import wdl.model.draft3.elements.ExpressionElement
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, Suffix}
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, SubPosix, Suffix}
 import wdl.transforms.base.ast2wdlom.AstNodeToExpressionElement
 
 object AstToNewExpressionElements {
@@ -15,6 +15,7 @@ object AstToNewExpressionElements {
     "min" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Min, "min"),
     "max" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Max, "max"),
     "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
+    "sub" -> AstNodeToExpressionElement.validateThreeParamEngineFunction(SubPosix, "sub"),
     "suffix" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Suffix, "suffix"),
     "read_object" -> (_ =>
       "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
index 3c73f8b55cd..8c5e200e7ee 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
@@ -58,6 +58,16 @@ object BiscayneExpressionValueConsumers {
         expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
+  implicit val subPosixExpressionValueConsumer: ExpressionValueConsumer[SubPosix] =
+    new ExpressionValueConsumer[SubPosix] {
+      override def expressionConsumedValueHooks(a: SubPosix)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++
+          expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer) ++
+          expressionValueConsumer.expressionConsumedValueHooks(a.arg3)(expressionValueConsumer)
+    }
+
   implicit val suffixExpressionValueConsumer: ExpressionValueConsumer[Suffix] = new ExpressionValueConsumer[Suffix] {
     override def expressionConsumedValueHooks(a: Suffix)(implicit
       expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
index e1121e1d549..0016b0c7458 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
@@ -96,7 +96,7 @@ package object consumed {
         case a: Zip => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Cross => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-        case a: Sub => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: SubPosix => a.expressionConsumedValueHooks(expressionValueConsumer)
 
         // New WDL biscayne expressions:
         case a: Keys => a.expressionConsumedValueHooks(expressionValueConsumer)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
index 6a79d2b3948..6d83600ea2b 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
@@ -1,9 +1,12 @@
 package wdl.transforms.biscayne.linking.expression.files
 
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, Suffix}
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, SubPosix, Suffix}
 import wdl.model.draft3.graph.expression.FileEvaluator
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators
-import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.twoParameterFunctionPassthroughFileEvaluator
+import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.{
+  threeParameterFunctionPassthroughFileEvaluator,
+  twoParameterFunctionPassthroughFileEvaluator
+}
 
 object BiscayneFileEvaluators {
 
@@ -16,6 +19,8 @@ object BiscayneFileEvaluators {
     EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
 
   implicit val sepFunctionEvaluator: FileEvaluator[Sep] = twoParameterFunctionPassthroughFileEvaluator[Sep]
+  implicit val subPosixFunctionEvaluator: FileEvaluator[SubPosix] =
+    threeParameterFunctionPassthroughFileEvaluator[SubPosix]
   implicit val suffixFunctionEvaluator: FileEvaluator[Suffix] = twoParameterFunctionPassthroughFileEvaluator[Suffix]
 
   implicit val minFunctionEvaluator: FileEvaluator[Min] = twoParameterFunctionPassthroughFileEvaluator[Min]
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
index 9dd95e9a0ec..e8a8a195289 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
@@ -154,7 +154,8 @@ package object files {
         case a: Zip => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Cross => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
-        case a: Sub => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SubPosix =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: Keys => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: AsMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
index 1ff5bf71ba4..73e01576abe 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
@@ -1,6 +1,6 @@
 package wdl.transforms.biscayne.linking.expression.types
 
-import cats.implicits.catsSyntaxTuple2Semigroupal
+import cats.implicits.{catsSyntaxTuple2Semigroupal, catsSyntaxTuple3Semigroupal}
 import cats.syntax.validated._
 import common.validation.ErrorOr._
 import wdl.model.draft3.elements.ExpressionElement
@@ -102,6 +102,16 @@ object BiscayneTypeEvaluators {
       }
   }
 
+  implicit val subPosixFunctionEvaluator: TypeEvaluator[SubPosix] = new TypeEvaluator[SubPosix] {
+    override def evaluateType(a: SubPosix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      (validateParamType(a.input, linkedValues, WomSingleFileType),
+       validateParamType(a.pattern, linkedValues, WomSingleFileType),
+       validateParamType(a.replace, linkedValues, WomSingleFileType)
+      ) mapN { (_, _, _) => WomStringType }
+  }
+
   implicit val suffixFunctionEvaluator: TypeEvaluator[Suffix] = new TypeEvaluator[Suffix] {
     override def evaluateType(a: Suffix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
index dec2deeb24f..fbcfcd6d339 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
@@ -98,7 +98,7 @@ package object types {
         case a: Zip => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Cross => a.evaluateType(linkedValues)(typeEvaluator)
 
-        case a: Sub => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: SubPosix => a.evaluateType(linkedValues)(typeEvaluator)
 
         case a: StdoutElement.type => a.evaluateType(linkedValues)(typeEvaluator)
         case a: StderrElement.type => a.evaluateType(linkedValues)(typeEvaluator)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
index 0c4805f0e68..0e29f40b2fd 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
@@ -4,12 +4,15 @@ import cats.data.NonEmptyList
 import cats.syntax.validated._
 import cats.syntax.traverse._
 import cats.instances.list._
+import com.google.re2j.{Pattern => RE2JPattern}
 import common.validation.ErrorOr._
 import common.collections.EnhancedCollections._
+import common.validation.ErrorOr
 import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement._
 import wdl.model.draft3.graph.expression.{EvaluatedValue, ForCommandInstantiationOptions, ValueEvaluator}
 import wdl.transforms.base.linking.expression.values.EngineFunctionEvaluators.{
+  processThreeValidatedValues,
   processTwoValidatedValues,
   processValidatedSingleValue
 }
@@ -218,6 +221,36 @@ object BiscayneValueEvaluators {
       }
   }
 
+  implicit val subPosixFunctionEvaluator: ValueEvaluator[SubPosix] = new ValueEvaluator[SubPosix] {
+    override def evaluateValue(a: SubPosix,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] =
+      processThreeValidatedValues[WomString, WomString, WomString, WomString](
+        expressionValueEvaluator.evaluateValue(a.input, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        ),
+        expressionValueEvaluator.evaluateValue(a.pattern, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        ),
+        expressionValueEvaluator.evaluateValue(a.replace, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) { (input, pattern, replace) =>
+        ErrorOr(
+          EvaluatedValue(WomString(
+                           RE2JPattern
+                             .compile(pattern.valueString)
+                             .matcher(input.valueString)
+                             .replaceAll(replace.valueString)
+                         ),
+                         Seq.empty
+          )
+        )
+      }
+  }
+
   implicit val suffixFunctionEvaluator: ValueEvaluator[Suffix] = new ValueEvaluator[Suffix] {
     override def evaluateValue(a: Suffix,
                                inputs: Map[String, WomValue],
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
index 3106ceba428..3a3ba825fe9 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
@@ -165,7 +165,8 @@ package object values {
         case a: Cross =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
-        case a: Sub => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: SubPosix =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Keys => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: AsMap =>
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
index a0953cd8397..b3a28b0d203 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
@@ -1,7 +1,6 @@
 package wdl.transforms.biscayne
 
 import java.util
-
 import common.Checked
 import common.assertion.ErrorOrAssertions._
 import common.transforms.CheckedAtoB
@@ -98,6 +97,12 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     expr shouldBeValid NoneLiteralElement
   }
 
+  it should "get the posix version when parsing the sub function" in {
+    val str = """sub("my input", "[A-Za-z]", "repl")"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (SubPosix(StringLiteral("my input"), StringLiteral("[A-Za-z]"), StringLiteral("repl")))
+  }
+
   it should "parse the new suffix function" in {
     val str = "suffix(some_str, some_arr)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
index 76f4a0338e7..841f283a512 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
@@ -58,6 +58,15 @@ class BiscayneExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     }
   }
 
+  it should "discover the variable lookups within a sub() call" in {
+    val str = """ sub(my_input, "^[A-Z]$", "0") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_input")))
+    }
+  }
+
   it should "discover the variable lookups within a suffix() call" in {
     val str = """ suffix(my_suffix, ["a", "b", c]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
index 4a3ed6b63b9..11affe50c66 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
@@ -46,6 +46,17 @@ class BiscayneFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
   }
 
+  it should "discover the file which would be required to evaluate a sub() function" in {
+    val str = """ sub(read_string("my_nice_file.txt"), "foo", "NEW_VAL") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("my_nice_file.txt")
+      )
+    }
+  }
+
   it should "discover the file which would be required to evaluate a suffix() function" in {
     val str = """ suffix(' # what a line', read_lines("foo.txt")) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
index c8372d36cd1..bea86f6d850 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
@@ -56,6 +56,15 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
   }
 
+  it should "evaluate the type of a sub() function as String" in {
+    val str = """ sub("input", "^pattern$", "s") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomStringType
+    }
+  }
+
   it should "evaluate the type of a suffix() function as Array[String]" in {
     val str = """ suffix('S', ["a", "b", "c"]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
index 1487543a838..66d07e02fe4 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
@@ -201,6 +201,29 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     }
   }
 
+  it should "evaluate a POSIX-flavor regex in a sub expression correctly" in {
+    val str = """ sub("aB", "[[:lower:]]", "9") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedString: WomString = WomString("9B")
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
+    }
+  }
+
+  it should "fail to evaluate a Java-flavor regex in a sub expression" in {
+    val str = """ sub("aB", "\\p{Lower}", "9") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None)
+        .shouldBeInvalid(
+          """error parsing regexp: invalid character class range: `\p{Lower}`"""
+        )
+    }
+  }
+
   it should "evaluate a suffix expression correctly" in {
     val str = """ suffix("S", ["a", "b", "c"]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
index 46cd8cb2e60..c1f36aae542 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
@@ -3,7 +3,7 @@ package wdl.transforms.cascades.ast2wdlom
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
 import wdl.model.draft3.elements.ExpressionElement
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, Suffix}
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, SubPosix, Suffix}
 import wdl.transforms.base.ast2wdlom.AstNodeToExpressionElement
 
 object AstToNewExpressionElements {
@@ -15,6 +15,7 @@ object AstToNewExpressionElements {
     "min" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Min, "min"),
     "max" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Max, "max"),
     "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
+    "sub" -> AstNodeToExpressionElement.validateThreeParamEngineFunction(SubPosix, "sub"),
     "suffix" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Suffix, "suffix"),
     "read_object" -> (_ =>
       "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
index ebc6d48fba1..332550dde47 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
@@ -58,6 +58,16 @@ object cascadesExpressionValueConsumers {
         expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
+  implicit val subPosixExpressionValueConsumer: ExpressionValueConsumer[SubPosix] =
+    new ExpressionValueConsumer[SubPosix] {
+      override def expressionConsumedValueHooks(a: SubPosix)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        expressionValueConsumer.expressionConsumedValueHooks(a.arg1)(expressionValueConsumer) ++
+          expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer) ++
+          expressionValueConsumer.expressionConsumedValueHooks(a.arg3)(expressionValueConsumer)
+    }
+
   implicit val suffixExpressionValueConsumer: ExpressionValueConsumer[Suffix] = new ExpressionValueConsumer[Suffix] {
     override def expressionConsumedValueHooks(a: Suffix)(implicit
       expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
index 2026aaec010..fa6df7e9c97 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
@@ -96,7 +96,7 @@ package object consumed {
         case a: Zip => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Cross => a.expressionConsumedValueHooks(expressionValueConsumer)
 
-        case a: Sub => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: SubPosix => a.expressionConsumedValueHooks(expressionValueConsumer)
 
         // New WDL biscayne expressions:
         case a: Keys => a.expressionConsumedValueHooks(expressionValueConsumer)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
index 32ea447b584..f551359f215 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
@@ -1,9 +1,12 @@
 package wdl.transforms.cascades.linking.expression.files
 
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, Suffix}
+import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, SubPosix, Suffix}
 import wdl.model.draft3.graph.expression.FileEvaluator
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators
-import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.twoParameterFunctionPassthroughFileEvaluator
+import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.{
+  threeParameterFunctionPassthroughFileEvaluator,
+  twoParameterFunctionPassthroughFileEvaluator
+}
 
 object cascadesFileEvaluators {
 
@@ -16,6 +19,8 @@ object cascadesFileEvaluators {
     EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
 
   implicit val sepFunctionEvaluator: FileEvaluator[Sep] = twoParameterFunctionPassthroughFileEvaluator[Sep]
+  implicit val subPosixFunctionEvaluator: FileEvaluator[SubPosix] =
+    threeParameterFunctionPassthroughFileEvaluator[SubPosix]
   implicit val suffixFunctionEvaluator: FileEvaluator[Suffix] = twoParameterFunctionPassthroughFileEvaluator[Suffix]
 
   implicit val minFunctionEvaluator: FileEvaluator[Min] = twoParameterFunctionPassthroughFileEvaluator[Min]
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
index a53c85b9b89..f075f82a4ff 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
@@ -154,7 +154,8 @@ package object files {
         case a: Zip => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Cross => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
-        case a: Sub => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SubPosix =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: Keys => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: AsMap => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
index 180af9eb0d8..7b1b2e45dc5 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
@@ -1,6 +1,6 @@
 package wdl.transforms.biscayne.linking.expression.types
 
-import cats.implicits.catsSyntaxTuple2Semigroupal
+import cats.implicits.{catsSyntaxTuple2Semigroupal, catsSyntaxTuple3Semigroupal}
 import cats.syntax.validated._
 import common.validation.ErrorOr._
 import wdl.model.draft3.elements.ExpressionElement
@@ -102,6 +102,16 @@ object cascadesTypeEvaluators {
       }
   }
 
+  implicit val subPosixFunctionEvaluator: TypeEvaluator[SubPosix] = new TypeEvaluator[SubPosix] {
+    override def evaluateType(a: SubPosix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      (validateParamType(a.input, linkedValues, WomSingleFileType),
+       validateParamType(a.pattern, linkedValues, WomSingleFileType),
+       validateParamType(a.replace, linkedValues, WomSingleFileType)
+      ) mapN { (_, _, _) => WomStringType }
+  }
+
   implicit val suffixFunctionEvaluator: TypeEvaluator[Suffix] = new TypeEvaluator[Suffix] {
     override def evaluateType(a: Suffix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
index 4dd7c528e8b..70cc81ee395 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
@@ -98,7 +98,7 @@ package object types {
         case a: Zip => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Cross => a.evaluateType(linkedValues)(typeEvaluator)
 
-        case a: Sub => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: SubPosix => a.evaluateType(linkedValues)(typeEvaluator)
 
         case a: StdoutElement.type => a.evaluateType(linkedValues)(typeEvaluator)
         case a: StderrElement.type => a.evaluateType(linkedValues)(typeEvaluator)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
index db9df85bf06..7489728980e 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
@@ -4,12 +4,15 @@ import cats.data.NonEmptyList
 import cats.syntax.validated._
 import cats.syntax.traverse._
 import cats.instances.list._
+import com.google.re2j.{Pattern => RE2JPattern}
 import common.validation.ErrorOr._
 import common.collections.EnhancedCollections._
+import common.validation.ErrorOr
 import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement._
 import wdl.model.draft3.graph.expression.{EvaluatedValue, ForCommandInstantiationOptions, ValueEvaluator}
 import wdl.transforms.base.linking.expression.values.EngineFunctionEvaluators.{
+  processThreeValidatedValues,
   processTwoValidatedValues,
   processValidatedSingleValue
 }
@@ -218,6 +221,36 @@ object cascadesValueEvaluators {
       }
   }
 
+  implicit val subPosixFunctionEvaluator: ValueEvaluator[SubPosix] = new ValueEvaluator[SubPosix] {
+    override def evaluateValue(a: SubPosix,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomString]] =
+      processThreeValidatedValues[WomString, WomString, WomString, WomString](
+        expressionValueEvaluator.evaluateValue(a.input, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        ),
+        expressionValueEvaluator.evaluateValue(a.pattern, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        ),
+        expressionValueEvaluator.evaluateValue(a.replace, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) { (input, pattern, replace) =>
+        ErrorOr(
+          EvaluatedValue(WomString(
+                           RE2JPattern
+                             .compile(pattern.valueString)
+                             .matcher(input.valueString)
+                             .replaceAll(replace.valueString)
+                         ),
+                         Seq.empty
+          )
+        )
+      }
+  }
+
   implicit val suffixFunctionEvaluator: ValueEvaluator[Suffix] = new ValueEvaluator[Suffix] {
     override def evaluateValue(a: Suffix,
                                inputs: Map[String, WomValue],
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
index 8850d4371df..d0e2fb8c155 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
@@ -165,7 +165,8 @@ package object values {
         case a: Cross =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
-        case a: Sub => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: SubPosix =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Keys => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: AsMap =>
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
index 57beb7a12a1..49602617a42 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
@@ -58,6 +58,15 @@ class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     }
   }
 
+  it should "discover the variable lookups within a sub() call" in {
+    val str = """ sub(my_input, "^[A-Z]$", "0") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_input")))
+    }
+  }
+
   it should "discover the variable lookups within a suffix() call" in {
     val str = """ suffix(my_suffix, ["a", "b", c]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
index 5335f7d5f29..1733630c121 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
@@ -46,6 +46,17 @@ class CascadesFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
   }
 
+  it should "discover the file which would be required to evaluate a sub() function" in {
+    val str = """ sub(read_string("my_nice_file.txt"), "foo", "NEW_VAL") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("my_nice_file.txt")
+      )
+    }
+  }
+
   it should "discover the file which would be required to evaluate a suffix() function" in {
     val str = """ suffix(' # what a line', read_lines("foo.txt")) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
index 954ef0f52f0..a84adccfa0f 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
@@ -56,6 +56,15 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
   }
 
+  it should "evaluate the type of a sub() function as String" in {
+    val str = """ sub("input", "^pattern$", "s") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomStringType
+    }
+  }
+
   it should "evaluate the type of a suffix() function as Array[String]" in {
     val str = """ suffix('S', ["a", "b", "c"]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
index bd47a20ca68..06ab5818331 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
@@ -201,6 +201,29 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     }
   }
 
+  it should "evaluate a POSIX-flavor regex in a sub expression correctly" in {
+    val str = """ sub("aB", "[[:lower:]]", "9") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedString: WomString = WomString("9B")
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
+    }
+  }
+
+  it should "fail to evaluate a Java-flavor regex in a sub expression" in {
+    val str = """ sub("aB", "\\p{Lower}", "9") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None)
+        .shouldBeInvalid(
+          """error parsing regexp: invalid character class range: `\p{Lower}`"""
+        )
+    }
+  }
+
   it should "evaluate a suffix expression correctly" in {
     val str = """ suffix("S", ["a", "b", "c"]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
index 664696ee86d..d99d3493b60 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
@@ -1,8 +1,8 @@
 package wdl.draft3.transforms.ast2wdlom
 
 import cats.instances.either._
-import java.util
 
+import java.util
 import common.Checked
 import common.assertion.CromwellTimeoutSpec
 import common.assertion.ErrorOrAssertions._
@@ -11,14 +11,15 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import wdl.draft3.parser.WdlParser
 import wdl.draft3.parser.WdlParser.{ParseTree, SyntaxErrorFormatter}
+import wdl.draft3.transforms.ast2wdlom.Ast2WdlomSpec.{fromString, parser}
 import wdl.draft3.transforms.parsing.WdlDraft3SyntaxErrorFormatter
-import wdl.model.draft3.elements.ExpressionElement.IdentifierLookup
+import wdl.model.draft3.elements.ExpressionElement.{IdentifierLookup, StringLiteral, Sub}
 import wdl.model.draft3.elements._
 import wdl.transforms.base.ast2wdlom.GenericAstNode
 
 import scala.jdk.CollectionConverters._
 
-class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+object Ast2WdlomSpec {
 
   val parser = new WdlParser()
 
@@ -29,10 +30,15 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val versionedExpression = "version 1.0\n" + expression
     // That "version 1.0" means we'll have 2 unwanted tokens at the start of the list, so drop 'em:
     val tokens = parser.lex(versionedExpression, "string").asScala.drop(2).asJava
-    val terminalMap = (tokens.asScala.toVector map { (_, expression) }).toMap
+    val terminalMap = (tokens.asScala.toVector map {
+      (_, expression)
+    }).toMap
     val parseTree = parseFunction(tokens, WdlDraft3SyntaxErrorFormatter(terminalMap))
     (wrapAstNode andThen converter).run(parseTree.toAst)
   }
+}
+
+class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   it should "not parse the new as_map function" in {
     val str = "as_map(some_pairs)"
@@ -52,6 +58,12 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     expr shouldBeInvalid "Failed to parse expression (reason 1 of 1): Unknown engine function: 'collect_by_key'"
   }
 
+  it should "get the non-posix version when parsing the sub function" in {
+    val str = """sub("my input", "[A-Za-z]", "repl")"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (Sub(StringLiteral("my input"), StringLiteral("[A-Za-z]"), StringLiteral("repl")))
+  }
+
   it should "not parse the new suffix function" in {
     val str = "suffix(aStr, anArray)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/linking/expression/values/ValueEvaluatorsSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/linking/expression/values/ValueEvaluatorsSpec.scala
new file mode 100644
index 00000000000..013a45308e6
--- /dev/null
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/linking/expression/values/ValueEvaluatorsSpec.scala
@@ -0,0 +1,42 @@
+package wdl.draft3.transforms.linking.expression.values
+
+import common.assertion.CromwellTimeoutSpec
+import common.assertion.ErrorOrAssertions._
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import wdl.draft3.transforms.ast2wdlom.Ast2WdlomSpec.{fromString, parser}
+import wdl.draft3.transforms.ast2wdlom._
+import wdl.model.draft3.elements.ExpressionElement
+import wdl.model.draft3.graph.expression.EvaluatedValue
+import wdl.model.draft3.graph.expression.ValueEvaluator.ops._
+import wom.expression.NoIoFunctionSet
+import wom.values.WomString
+
+class ValueEvaluatorsSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  behavior of "base value evaluator"
+
+  // In pre-1.1 WDL we use Java-flavored regex
+
+  it should "fail to apply a POSIX-flavor sub expression" in {
+    val str = """ sub("aB", "[[:lower:]]", "9") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedString: WomString = WomString("aB") // no substitution
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
+    }
+  }
+
+  it should "evaluate a Java-flavor regex in a sub expression correctly" in {
+    val str = """ sub("aB", "\\p{Lower}", "9") """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedString: WomString = WomString("9B")
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedString, Seq.empty)
+    }
+  }
+}
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
index 2a773fd4e23..407d7f6f96c 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
@@ -231,7 +231,7 @@ object AstNodeToExpressionElement {
       s"Function $functionName expects exactly 2 arguments but got ${params.size}".invalidNel
     }
 
-  private def validateThreeParamEngineFunction(
+  def validateThreeParamEngineFunction(
     elementMaker: (ExpressionElement, ExpressionElement, ExpressionElement) => ExpressionElement,
     functionName: String
   )(params: Vector[ExpressionElement]): ErrorOr[ExpressionElement] =
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala
index 11c687588a7..b8ecf9d764b 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/files/EngineFunctionEvaluators.scala
@@ -219,8 +219,8 @@ object EngineFunctionEvaluators {
   implicit val crossFunctionEvaluator: FileEvaluator[Cross] = twoParameterFunctionPassthroughFileEvaluator[Cross]
   implicit val prefixFunctionEvaluator: FileEvaluator[Prefix] = twoParameterFunctionPassthroughFileEvaluator[Prefix]
 
-  implicit val subFunctionEvaluator: FileEvaluator[Sub] = new FileEvaluator[Sub] {
-    override def predictFilesNeededToEvaluate(a: Sub,
+  def threeParameterFunctionPassthroughFileEvaluator[A <: ThreeParamFunctionCallElement] = new FileEvaluator[A] {
+    override def predictFilesNeededToEvaluate(a: A,
                                               inputs: Map[String, WomValue],
                                               ioFunctionSet: IoFunctionSet,
                                               coerceTo: WomType
@@ -228,9 +228,13 @@ object EngineFunctionEvaluators {
       fileEvaluator: FileEvaluator[ExpressionElement],
       valueEvaluator: ValueEvaluator[ExpressionElement]
     ): ErrorOr[Set[WomFile]] =
-      (a.pattern.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
-       a.input.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
-       a.replace.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
-      ) mapN { _ ++ _ ++ _ }
+      (a.arg1.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
+       a.arg2.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo),
+       a.arg3.evaluateFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)
+      ) mapN {
+        _ ++ _ ++ _
+      }
   }
+
+  implicit val subFunctionEvaluator: FileEvaluator[Sub] = threeParameterFunctionPassthroughFileEvaluator[Sub]
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
index ffaf16ad0d2..58c83c67edc 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
@@ -835,7 +835,7 @@ object EngineFunctionEvaluators {
         s"Expected (${coercerA.toDisplayString}, ${coercerB.toDisplayString}) argument but got (${otherA.value.womType.stableName}, ${otherB.value.womType.stableName})".invalidNel
     }
 
-  private def processThreeValidatedValues[A <: WomValue, B <: WomValue, C <: WomValue, R <: WomValue](
+  def processThreeValidatedValues[A <: WomValue, B <: WomValue, C <: WomValue, R <: WomValue](
     arg1: ErrorOr[EvaluatedValue[_ <: WomValue]],
     arg2: ErrorOr[EvaluatedValue[_ <: WomValue]],
     arg3: ErrorOr[EvaluatedValue[_ <: WomValue]]
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
index a85f3c34420..1df05e48db1 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
@@ -401,6 +401,7 @@ object WdlWriterImpl {
       case a: OneOrTwoParamFunctionCallElement => a.toWdlV1
       case a: TwoParamFunctionCallElement => a.toWdlV1
       case a: Sub => s"sub(${a.input.toWdlV1}, ${a.pattern.toWdlV1}, ${a.replace.toWdlV1})"
+      case a: SubPosix => s"sub(${a.input.toWdlV1}, ${a.pattern.toWdlV1}, ${a.replace.toWdlV1})"
     }
   }
 

From 5e59b02001d32b97c6ae6413cd45d5a4d62a5d71 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 27 Feb 2024 15:40:52 -0500
Subject: [PATCH 285/326] [WX-963] Unzip Engine Function  (#7368)

---
 .../biscayne_new_engine_functions.test        | 15 ++++++
 .../biscayne_new_engine_functions.wdl         | 12 ++++-
 .../draft3/elements/ExpressionElement.scala   |  1 +
 .../AstToNewExpressionElements.scala          | 14 +++++-
 .../BiscayneExpressionValueConsumers.scala    |  7 +++
 .../expression/consumed/consumed.scala        |  1 +
 .../files/BiscayneFileEvaluators.scala        | 15 +++++-
 .../linking/expression/files/files.scala      |  1 +
 .../types/BiscayneTypeEvaluators.scala        | 11 +++++
 .../linking/expression/types/types.scala      |  1 +
 .../values/BiscayneValueEvaluators.scala      | 35 ++++++++++++++
 .../linking/expression/values/values.scala    |  2 +
 .../transforms/biscayne/Ast2WdlomSpec.scala   |  6 +++
 ...BiscayneExpressionValueConsumersSpec.scala |  9 ++++
 .../files/BiscayneFileEvaluatorSpec.scala     | 11 +++++
 .../types/BiscayneTypeEvaluatorSpec.scala     | 22 +++++++++
 .../values/BiscayneValueEvaluatorSpec.scala   | 46 ++++++++++++++++++-
 .../AstToNewExpressionElements.scala          | 14 +++++-
 .../CascadesExpressionValueConsumers.scala    |  7 +++
 .../expression/consumed/consumed.scala        |  1 +
 .../files/CascadesFileEvaluators.scala        | 15 +++++-
 .../linking/expression/files/files.scala      |  1 +
 .../types/CascadesTypeEvaluators.scala        | 11 +++++
 .../linking/expression/types/types.scala      |  1 +
 .../values/CascadesValueEvaluators.scala      | 35 ++++++++++++++
 .../linking/expression/values/values.scala    |  2 +
 .../transforms/cascades/Ast2WdlomSpec.scala   |  6 +++
 ...CascadesExpressionValueConsumersSpec.scala |  9 ++++
 .../files/CascadesFileEvaluatorSpec.scala     | 11 +++++
 .../types/CascadesTypeEvaluatorSpec.scala     | 22 +++++++++
 .../values/CascadesValueEvaluatorSpec.scala   | 46 ++++++++++++++++++-
 .../transforms/ast2wdlom/Ast2WdlomSpec.scala  |  6 +++
 .../AstNodeToExpressionElement.scala          |  2 +-
 .../base/wdlom2wdl/WdlWriterImpl.scala        |  1 +
 34 files changed, 391 insertions(+), 8 deletions(-)

diff --git a/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test b/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
index e05af2f8a2d..3289f2df78c 100644
--- a/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
+++ b/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
@@ -60,4 +60,19 @@ metadata {
   "outputs.biscayne_new_engine_functions.with_suffixes.0": "aaaS"
   "outputs.biscayne_new_engine_functions.with_suffixes.1": "bbbS"
   "outputs.biscayne_new_engine_functions.with_suffixes.2": "cccS"
+
+  "outputs.biscayne_new_engine_functions.unzipped_a.left.0": "A"
+  "outputs.biscayne_new_engine_functions.unzipped_a.right.0": "a"
+
+  "outputs.biscayne_new_engine_functions.unzipped_b.left.0": "A"
+  "outputs.biscayne_new_engine_functions.unzipped_b.left.1": "B"
+  "outputs.biscayne_new_engine_functions.unzipped_b.right.0": "a"
+  "outputs.biscayne_new_engine_functions.unzipped_b.right.1": "b"
+
+  "outputs.biscayne_new_engine_functions.unzipped_c.left.0": "one"
+  "outputs.biscayne_new_engine_functions.unzipped_c.left.1": "two"
+  "outputs.biscayne_new_engine_functions.unzipped_c.left.2": "three"
+  "outputs.biscayne_new_engine_functions.unzipped_c.right.0": 1.0
+  "outputs.biscayne_new_engine_functions.unzipped_c.right.1": 2.0
+  "outputs.biscayne_new_engine_functions.unzipped_c.right.2": 3.0
 }
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
index c4387134421..5c9cb5f8dc4 100644
--- a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
@@ -4,7 +4,7 @@ workflow biscayne_new_engine_functions {
 
   meta {
     description: "This test makes sure that these functions work in a real workflow"
-    functions_under_test: [ "keys", "as_map", "as_pairs", "collect_by_key", "sub", "suffix" ]
+    functions_under_test: [ "keys", "as_map", "as_pairs", "collect_by_key", "suffix", "unzip" ]
   }
 
   Map[String, Int] x_map_in = {"a": 1, "b": 2, "c": 3}
@@ -26,6 +26,10 @@ workflow biscayne_new_engine_functions {
   # max float... near enough:
   Float maxFloat = 179769313000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000.0
 
+  Array[Pair[String,String]] zipped_a = [("A", "a")]
+  Array[Pair[String,String]] zipped_b = [("A", "a"),("B", "b")]
+  Array[Pair[String,Float]] zipped_c = [("one", 1.0),("two", 2.0),("three", 3.0)]
+
   output {
 
     # keys(), as_map(), as_pairs(), collect_by_key():
@@ -59,6 +63,12 @@ workflow biscayne_new_engine_functions {
     # suffix():
     # =================================================
     Array[String] with_suffixes = suffix("S", some_strings)
+
+    # unzip():
+    # =================================================
+    Pair[Array[String], Array[String]] unzipped_a = unzip(zipped_a)
+    Pair[Array[String], Array[String]] unzipped_b = unzip(zipped_b)
+    Pair[Array[String], Array[String]] unzipped_c = unzip(zipped_c)
   }
 }
 
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
index 23101adfa9e..08a89fb2ff0 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
@@ -136,6 +136,7 @@ object ExpressionElement {
   final case class Ceil(param: ExpressionElement) extends OneParamFunctionCallElement
   final case class Round(param: ExpressionElement) extends OneParamFunctionCallElement
   final case class Glob(param: ExpressionElement) extends OneParamFunctionCallElement
+  final case class Unzip(param: ExpressionElement) extends OneParamFunctionCallElement
 
   // 1- or 2-param functions:
   sealed trait OneOrTwoParamFunctionCallElement extends FunctionCallElement {
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
index 70ebd4879c3..f814044d1d0 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
@@ -3,7 +3,18 @@ package wdl.transforms.biscayne.ast2wdlom
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
 import wdl.model.draft3.elements.ExpressionElement
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, SubPosix, Suffix}
+import wdl.model.draft3.elements.ExpressionElement.{
+  AsMap,
+  AsPairs,
+  CollectByKey,
+  Keys,
+  Max,
+  Min,
+  Sep,
+  SubPosix,
+  Suffix,
+  Unzip
+}
 import wdl.transforms.base.ast2wdlom.AstNodeToExpressionElement
 
 object AstToNewExpressionElements {
@@ -17,6 +28,7 @@ object AstToNewExpressionElements {
     "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
     "sub" -> AstNodeToExpressionElement.validateThreeParamEngineFunction(SubPosix, "sub"),
     "suffix" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Suffix, "suffix"),
+    "unzip" -> AstNodeToExpressionElement.validateOneParamEngineFunction(Unzip, "unzip"),
     "read_object" -> (_ =>
       "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel
     ),
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
index 8c5e200e7ee..71ee8a61980 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
@@ -76,6 +76,13 @@ object BiscayneExpressionValueConsumers {
         expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
+  implicit val unzipExpressionValueConsumer: ExpressionValueConsumer[Unzip] = new ExpressionValueConsumer[Unzip] {
+    override def expressionConsumedValueHooks(a: Unzip)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+  }
+
   implicit val noneLiteralExpressionValueConsumer: ExpressionValueConsumer[NoneLiteralElement.type] =
     new ExpressionValueConsumer[NoneLiteralElement.type] {
       override def expressionConsumedValueHooks(a: NoneLiteralElement.type)(implicit
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
index 0016b0c7458..d6cc21f7646 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
@@ -104,6 +104,7 @@ package object consumed {
         case a: AsPairs => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: CollectByKey => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Sep => sepExpressionValueConsumer.expressionConsumedValueHooks(a)(expressionValueConsumer)
+        case a: Unzip => a.expressionConsumedValueHooks(expressionValueConsumer)
 
         case a: Min => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Max => a.expressionConsumedValueHooks(expressionValueConsumer)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
index 6d83600ea2b..89f830f81ab 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
@@ -1,6 +1,17 @@
 package wdl.transforms.biscayne.linking.expression.files
 
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, SubPosix, Suffix}
+import wdl.model.draft3.elements.ExpressionElement.{
+  AsMap,
+  AsPairs,
+  CollectByKey,
+  Keys,
+  Max,
+  Min,
+  Sep,
+  SubPosix,
+  Suffix,
+  Unzip
+}
 import wdl.model.draft3.graph.expression.FileEvaluator
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.{
@@ -26,4 +37,6 @@ object BiscayneFileEvaluators {
   implicit val minFunctionEvaluator: FileEvaluator[Min] = twoParameterFunctionPassthroughFileEvaluator[Min]
   implicit val maxFunctionEvaluator: FileEvaluator[Max] = twoParameterFunctionPassthroughFileEvaluator[Max]
 
+  implicit val unzipFunctionEvaluator: FileEvaluator[Unzip] =
+    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
index e8a8a195289..81f667d80fe 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
@@ -153,6 +153,7 @@ package object files {
 
         case a: Zip => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Cross => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Unzip => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: SubPosix =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
index 73e01576abe..2ea750364e1 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
@@ -120,4 +120,15 @@ object BiscayneTypeEvaluators {
        validateParamType(a.array, linkedValues, WomArrayType(WomStringType))
       ) mapN { (_, _) => WomArrayType(WomStringType) }
   }
+
+  implicit val unzipFunctionEvaluator: TypeEvaluator[Unzip] = new TypeEvaluator[Unzip] {
+    override def evaluateType(a: Unzip, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
+        case WomArrayType(WomNothingType) => WomPairType(WomArrayType(WomAnyType), WomArrayType(WomAnyType)).validNel
+        case WomArrayType(WomPairType(x, y)) => WomPairType(WomArrayType(x), WomArrayType(y)).validNel
+        case other => s"Cannot invoke 'unzip' on type '${other.stableName}'. Expected an array of pairs".invalidNel
+      }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
index fbcfcd6d339..385b4b0c072 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
@@ -97,6 +97,7 @@ package object types {
 
         case a: Zip => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Cross => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Unzip => a.evaluateType(linkedValues)(typeEvaluator)
 
         case a: SubPosix => a.evaluateType(linkedValues)(typeEvaluator)
 
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
index 0e29f40b2fd..8583c9a4af1 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
@@ -268,4 +268,39 @@ object BiscayneValueEvaluators {
         EvaluatedValue(WomArray(arr.value.map(v => WomString(v.valueString + suffix.value))), Seq.empty).validNel
       }
   }
+
+  /**
+   * Unzip: Creates a pair of arrays, the first containing the elements from the left members of an array of pairs,
+   * and the second containing the right members. This is the inverse of the zip function.
+   * https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#-pairarrayx-arrayy-unziparraypairx-y
+   * input: Array[Pair[X,Y]]
+   * output: Pair[Array[X], Array[Y]]
+   */
+  implicit val unzipFunctionEvaluator: ValueEvaluator[Unzip] = new ValueEvaluator[Unzip] {
+    override def evaluateValue(a: Unzip,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomPair]] =
+      processValidatedSingleValue[WomArray, WomPair](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) {
+        case WomArray(WomArrayType(WomAnyType), Seq()) =>
+          EvaluatedValue(
+            WomPair(WomArray(WomArrayType(WomAnyType), Seq.empty), WomArray(WomArrayType(WomAnyType), Seq.empty)),
+            Seq.empty
+          ).validNel
+        case WomArray(WomArrayType(WomPairType(_, _)), values) =>
+          val zippedArrayOfPairs: Seq[(WomValue, WomValue)] = values map { case pair: WomPair =>
+            Tuple2(pair.left, pair.right)
+          }
+          val (left, right) = zippedArrayOfPairs.unzip
+          val unzippedPairOfArrays: WomPair = WomPair(WomArray(left), WomArray(right))
+          EvaluatedValue(unzippedPairOfArrays, Seq.empty).validNel
+        case other =>
+          s"Invalid call of 'unzip' on parameter of type '${other.womType.stableName}' (expected Array[Pair[X, Y]])".invalidNel
+      }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
index 3a3ba825fe9..e7151653258 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
@@ -164,6 +164,8 @@ package object values {
         case a: Zip => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Cross =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Unzip =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: SubPosix =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
index b3a28b0d203..e4f2058edf1 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
@@ -108,4 +108,10 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val expr = fromString[ExpressionElement](str, parser.parse_e)
     expr shouldBeValid (Suffix(IdentifierLookup("some_str"), IdentifierLookup("some_arr")))
   }
+
+  it should "parse the new unzip function" in {
+    val str = "unzip(some_array_of_pairs)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (Unzip(IdentifierLookup("some_array_of_pairs")))
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
index 841f283a512..f8fa6cad40f 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
@@ -84,4 +84,13 @@ class BiscayneExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
       e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array")))
     }
   }
+
+  it should "discover an array variable lookup within a unzip() call" in {
+    val str = """ unzip(my_array_of_pairs) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array_of_pairs")))
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
index 11affe50c66..570d5633d79 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
@@ -67,4 +67,15 @@ class BiscayneFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       )
     }
   }
+
+  it should "discover the file which would be required to evaluate a unzip() function" in {
+    val str = """ unzip(read_lines("foo.txt")) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
index bea86f6d850..dba6da30973 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
@@ -73,4 +73,26 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
     }
   }
+
+  it should "evaluate the type of an unzip() function as Pair[Array[X], Array[Y]]" in {
+    val string_and_int = """ unzip([("one", 1),("two", 2),("three", 3)]) """
+    val string_and_int_expr = fromString[ExpressionElement](string_and_int, parser.parse_e)
+    string_and_int_expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomStringType), WomArrayType(WomIntegerType))
+    }
+
+    val int_and_int = """ unzip([(1,2),(3,4),(5,6)]) """
+    val int_and_int_expr = fromString[ExpressionElement](int_and_int, parser.parse_e)
+    int_and_int_expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomIntegerType), WomArrayType(WomIntegerType))
+    }
+  }
+
+  it should "evaluate the type of an unzip() function on an empty collection as Pair[Array[Any], Array[Any]]" in {
+    val empty = """ unzip([]) """
+    val empty_unzip_expr = fromString[ExpressionElement](empty, parser.parse_e)
+    empty_unzip_expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomAnyType), WomArrayType(WomAnyType))
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
index 66d07e02fe4..bb58ebbe331 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
@@ -11,7 +11,7 @@ import wdl.model.draft3.graph.expression.ValueEvaluator.ops._
 import wdl.transforms.biscayne.Ast2WdlomSpec.{fromString, parser}
 import wdl.transforms.biscayne.ast2wdlom._
 import wom.expression.NoIoFunctionSet
-import wom.types.{WomIntegerType, WomMapType, WomOptionalType, WomStringType}
+import wom.types.{WomAnyType, WomArrayType, WomIntegerType, WomMapType, WomOptionalType, WomStringType}
 import wom.values.{WomArray, WomInteger, WomMap, WomOptionalValue, WomPair, WomString}
 
 class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
@@ -240,4 +240,48 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
     }
   }
+
+  it should "evaluate an unzip expression correctly" in {
+    val str = """ unzip([("one", 1),("two", 2),("three", 3)]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val left: WomArray =
+      WomArray(WomArrayType(WomStringType), Seq(WomString("one"), WomString("two"), WomString("three")))
+    val right: WomArray = WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(1), WomInteger(2), WomInteger(3)))
+    val expectedPair: WomPair = WomPair(left, right)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPair, Seq.empty)
+    }
+  }
+
+  it should "evaluate an unzip on an empty collection correctly" in {
+    val str = """ unzip([])"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val left: WomArray = WomArray(WomArrayType(WomAnyType), Seq())
+    val right: WomArray = WomArray(WomArrayType(WomAnyType), Seq())
+    val expectedPair: WomPair = WomPair(left, right)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPair, Seq.empty)
+    }
+  }
+
+  it should "fail to evaluate unzip on invalid pair" in {
+    val invalidPair = """ unzip([()])"""
+    val invalidPairExpr = fromString[ExpressionElement](invalidPair, parser.parse_e)
+    invalidPairExpr.shouldBeInvalid("Failed to parse expression (reason 1 of 1): No WDL support for 0-tuples")
+  }
+
+  it should "fail to evaluate unzip on heterogeneous pairs" in {
+    val invalidPair = """ unzip([ (1, 11.0), ([1,2,3], 2.0) ])"""
+    val invalidPairExpr = fromString[ExpressionElement](invalidPair, parser.parse_e)
+    invalidPairExpr.map(e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None)
+        .shouldBeInvalid(
+          "Could not construct array of type WomMaybeEmptyArrayType(WomPairType(WomIntegerType,WomFloatType)) with this value: List(WomPair(WomInteger(1),WomFloat(11.0)), WomPair([1, 2, 3],WomFloat(2.0)))"
+        )
+    )
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
index c1f36aae542..1a2ce0d5735 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
@@ -3,7 +3,18 @@ package wdl.transforms.cascades.ast2wdlom
 import cats.syntax.validated._
 import common.validation.ErrorOr.ErrorOr
 import wdl.model.draft3.elements.ExpressionElement
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, SubPosix, Suffix}
+import wdl.model.draft3.elements.ExpressionElement.{
+  AsMap,
+  AsPairs,
+  CollectByKey,
+  Keys,
+  Max,
+  Min,
+  Sep,
+  SubPosix,
+  Suffix,
+  Unzip
+}
 import wdl.transforms.base.ast2wdlom.AstNodeToExpressionElement
 
 object AstToNewExpressionElements {
@@ -17,6 +28,7 @@ object AstToNewExpressionElements {
     "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
     "sub" -> AstNodeToExpressionElement.validateThreeParamEngineFunction(SubPosix, "sub"),
     "suffix" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Suffix, "suffix"),
+    "unzip" -> AstNodeToExpressionElement.validateOneParamEngineFunction(Unzip, "unzip"),
     "read_object" -> (_ =>
       "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel
     ),
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
index 332550dde47..a328b8a4014 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
@@ -84,4 +84,11 @@ object cascadesExpressionValueConsumers {
         // None literals consume no values:
         Set.empty[UnlinkedConsumedValueHook]
     }
+
+  implicit val unzipExpressionValueConsumer: ExpressionValueConsumer[Unzip] = new ExpressionValueConsumer[Unzip] {
+    override def expressionConsumedValueHooks(a: Unzip)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
index fa6df7e9c97..4184595cb72 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
@@ -95,6 +95,7 @@ package object consumed {
 
         case a: Zip => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Cross => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Unzip => a.expressionConsumedValueHooks(expressionValueConsumer)
 
         case a: SubPosix => a.expressionConsumedValueHooks(expressionValueConsumer)
 
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
index f551359f215..7a1114f61b8 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
@@ -1,6 +1,17 @@
 package wdl.transforms.cascades.linking.expression.files
 
-import wdl.model.draft3.elements.ExpressionElement.{AsMap, AsPairs, CollectByKey, Keys, Max, Min, Sep, SubPosix, Suffix}
+import wdl.model.draft3.elements.ExpressionElement.{
+  AsMap,
+  AsPairs,
+  CollectByKey,
+  Keys,
+  Max,
+  Min,
+  Sep,
+  SubPosix,
+  Suffix,
+  Unzip
+}
 import wdl.model.draft3.graph.expression.FileEvaluator
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.{
@@ -17,6 +28,8 @@ object cascadesFileEvaluators {
     EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
   implicit val collectByKeyFileEvaluator: FileEvaluator[CollectByKey] =
     EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val unzipFunctionEvaluator: FileEvaluator[Unzip] =
+    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
 
   implicit val sepFunctionEvaluator: FileEvaluator[Sep] = twoParameterFunctionPassthroughFileEvaluator[Sep]
   implicit val subPosixFunctionEvaluator: FileEvaluator[SubPosix] =
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
index f075f82a4ff..3d96ffcb4d1 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
@@ -153,6 +153,7 @@ package object files {
 
         case a: Zip => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Cross => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Unzip => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
 
         case a: SubPosix =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
index 7b1b2e45dc5..0510a19db30 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
@@ -120,4 +120,15 @@ object cascadesTypeEvaluators {
        validateParamType(a.array, linkedValues, WomArrayType(WomStringType))
       ) mapN { (_, _) => WomArrayType(WomStringType) }
   }
+
+  implicit val unzipFunctionEvaluator: TypeEvaluator[Unzip] = new TypeEvaluator[Unzip] {
+    override def evaluateType(a: Unzip, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
+        case WomArrayType(WomNothingType) => WomPairType(WomArrayType(WomAnyType), WomArrayType(WomAnyType)).validNel
+        case WomArrayType(WomPairType(x, y)) => WomPairType(WomArrayType(x), WomArrayType(y)).validNel
+        case other => s"Cannot invoke 'unzip' on type '${other.stableName}'. Expected an array of pairs".invalidNel
+      }
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
index 70cc81ee395..1a17eeb9d24 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
@@ -97,6 +97,7 @@ package object types {
 
         case a: Zip => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Cross => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Unzip => a.evaluateType(linkedValues)(typeEvaluator)
 
         case a: SubPosix => a.evaluateType(linkedValues)(typeEvaluator)
 
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
index 7489728980e..9152aba2ce9 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
@@ -268,4 +268,39 @@ object cascadesValueEvaluators {
         EvaluatedValue(WomArray(arr.value.map(v => WomString(v.valueString + suffix.value))), Seq.empty).validNel
       }
   }
+
+  /**
+   * Unzip: Creates a pair of arrays, the first containing the elements from the left members of an array of pairs,
+   * and the second containing the right members. This is the inverse of the zip function.
+   * https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#-pairarrayx-arrayy-unziparraypairx-y
+   * input: Array[Pair[X,Y]]
+   * output: Pair[Array[X], Array[Y]]
+   */
+  implicit val unzipFunctionEvaluator: ValueEvaluator[Unzip] = new ValueEvaluator[Unzip] {
+    override def evaluateValue(a: Unzip,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomPair]] =
+      processValidatedSingleValue[WomArray, WomPair](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) {
+        case WomArray(WomArrayType(WomAnyType), Seq()) =>
+          EvaluatedValue(
+            WomPair(WomArray(WomArrayType(WomAnyType), Seq.empty), WomArray(WomArrayType(WomAnyType), Seq.empty)),
+            Seq.empty
+          ).validNel
+        case WomArray(WomArrayType(WomPairType(_, _)), values) =>
+          val zippedArrayOfPairs: Seq[(WomValue, WomValue)] = values map { case pair: WomPair =>
+            Tuple2(pair.left, pair.right)
+          }
+          val (left, right) = zippedArrayOfPairs.unzip
+          val unzippedPairOfArrays: WomPair = WomPair(WomArray(left), WomArray(right))
+          EvaluatedValue(unzippedPairOfArrays, Seq.empty).validNel
+        case other =>
+          s"Invalid call of 'unzip' on parameter of type '${other.womType.stableName}' (expected Array[Pair[X, Y]])".invalidNel
+      }
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
index d0e2fb8c155..f0fcba9ebb6 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
@@ -164,6 +164,8 @@ package object values {
         case a: Zip => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Cross =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Unzip =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: SubPosix =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
index 88b7aff6578..196f7030087 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
@@ -103,4 +103,10 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val expr = fromString[ExpressionElement](str, parser.parse_e)
     expr shouldBeValid (Suffix(IdentifierLookup("some_str"), IdentifierLookup("some_arr")))
   }
+
+  it should "parse the new unzip function" in {
+    val str = "unzip(some_array_of_pairs)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (Unzip(IdentifierLookup("some_array_of_pairs")))
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
index 49602617a42..9ed5933e248 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
@@ -84,4 +84,13 @@ class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
       e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array")))
     }
   }
+
+  it should "discover an array variable lookup within a unzip() call" in {
+    val str = """ unzip(my_array_of_pairs) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array_of_pairs")))
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
index 1733630c121..93a80d195e5 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
@@ -67,4 +67,15 @@ class CascadesFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       )
     }
   }
+
+  it should "discover the file which would be required to evaluate a unzip() function" in {
+    val str = """ unzip(read_lines("foo.txt")) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
index a84adccfa0f..384579e31e7 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
@@ -73,4 +73,26 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
     }
   }
+
+  it should "evaluate the type of an unzip() function as Pair[Array[X], Array[Y]]" in {
+    val string_and_int = """ unzip([("one", 1),("two", 2),("three", 3)]) """
+    val string_and_int_expr = fromString[ExpressionElement](string_and_int, parser.parse_e)
+    string_and_int_expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomStringType), WomArrayType(WomIntegerType))
+    }
+
+    val int_and_int = """ unzip([(1,2),(3,4),(5,6)]) """
+    val int_and_int_expr = fromString[ExpressionElement](int_and_int, parser.parse_e)
+    int_and_int_expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomIntegerType), WomArrayType(WomIntegerType))
+    }
+  }
+
+  it should "evaluate the type of an unzip() function on an empty collection as Pair[Array[Any], Array[Any]]" in {
+    val empty = """ unzip([]) """
+    val empty_unzip_expr = fromString[ExpressionElement](empty, parser.parse_e)
+    empty_unzip_expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomAnyType), WomArrayType(WomAnyType))
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
index 06ab5818331..4c684734f88 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
@@ -11,7 +11,7 @@ import wdl.model.draft3.graph.expression.ValueEvaluator.ops._
 import wdl.transforms.cascades.Ast2WdlomSpec.{fromString, parser}
 import wdl.transforms.cascades.ast2wdlom._
 import wom.expression.NoIoFunctionSet
-import wom.types.{WomIntegerType, WomMapType, WomOptionalType, WomStringType}
+import wom.types.{WomAnyType, WomArrayType, WomIntegerType, WomMapType, WomOptionalType, WomStringType}
 import wom.values.{WomArray, WomInteger, WomMap, WomOptionalValue, WomPair, WomString}
 
 class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
@@ -240,4 +240,48 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
       e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
     }
   }
+
+  it should "evaluate an unzip expression correctly" in {
+    val str = """ unzip([("one", 1),("two", 2),("three", 3)]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val left: WomArray =
+      WomArray(WomArrayType(WomStringType), Seq(WomString("one"), WomString("two"), WomString("three")))
+    val right: WomArray = WomArray(WomArrayType(WomIntegerType), Seq(WomInteger(1), WomInteger(2), WomInteger(3)))
+    val expectedPair: WomPair = WomPair(left, right)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPair, Seq.empty)
+    }
+  }
+
+  it should "evaluate an unzip on an empty collection correctly" in {
+    val str = """ unzip([])"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val left: WomArray = WomArray(WomArrayType(WomAnyType), Seq())
+    val right: WomArray = WomArray(WomArrayType(WomAnyType), Seq())
+    val expectedPair: WomPair = WomPair(left, right)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedPair, Seq.empty)
+    }
+  }
+
+  it should "fail to evaluate unzip on invalid pair" in {
+    val invalidPair = """ unzip([()])"""
+    val invalidPairExpr = fromString[ExpressionElement](invalidPair, parser.parse_e)
+    invalidPairExpr.shouldBeInvalid("Failed to parse expression (reason 1 of 1): No WDL support for 0-tuples")
+  }
+
+  it should "fail to evaluate unzip on heterogeneous pairs" in {
+    val invalidPair = """ unzip([ (1, 11.0), ([1,2,3], 2.0) ])"""
+    val invalidPairExpr = fromString[ExpressionElement](invalidPair, parser.parse_e)
+    invalidPairExpr.map(e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None)
+        .shouldBeInvalid(
+          "Could not construct array of type WomMaybeEmptyArrayType(WomPairType(WomIntegerType,WomFloatType)) with this value: List(WomPair(WomInteger(1),WomFloat(11.0)), WomPair([1, 2, 3],WomFloat(2.0)))"
+        )
+    )
+  }
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
index d99d3493b60..c9e92abb5ed 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
@@ -75,4 +75,10 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val expr = fromString[ExpressionElement](str, parser.parse_e)
     expr shouldBeValid (IdentifierLookup("None"))
   }
+
+  it should "not parse the new unzip function" in {
+    val str = "unzip(some_array_of_pairs)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeInvalid "Failed to parse expression (reason 1 of 1): Unknown engine function: 'unzip'"
+  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
index 407d7f6f96c..acf3eac9f0b 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
@@ -43,7 +43,7 @@ object AstNodeToExpressionElement {
         (a.getAttributeAsVector[ExpressionElement]("values") flatMap {
           case pair if pair.length == 2 => PairLiteral(pair.head, pair(1)).validNelCheck
           case singleton if singleton.length == 1 => singleton.head.validNelCheck
-          case more => s"No WDL support for ${more.size}-tuples in draft 3".invalidNelCheck
+          case more => s"No WDL support for ${more.size}-tuples".invalidNelCheck
         }).toValidated
       case a: GenericAst if a.getName == "ArrayLiteral" =>
         a.getAttributeAsVector[ExpressionElement]("values").toValidated.map(ArrayLiteral)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
index 1df05e48db1..65bae56df2b 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
@@ -440,6 +440,7 @@ object WdlWriterImpl {
           case _: AsMap => "as_map"
           case _: AsPairs => "as_pairs"
           case _: CollectByKey => "collect_by_key"
+          case _: Unzip => "unzip"
         }
 
         s"$fn(${a.param.toWdlV1})"

From e1d5ff488332559ac82c8308b0b893889f1c1da6 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 27 Feb 2024 19:43:47 -0500
Subject: [PATCH 286/326] WX-1489 Hopefully reduce CI flakiness by modernizing
 deadlock test (#7376)

---
 src/ci/docker-compose/deadlock_haproxy.cfg        | 8 ++++++++
 src/ci/docker-compose/docker-compose-deadlock.yml | 3 ++-
 2 files changed, 10 insertions(+), 1 deletion(-)
 create mode 100644 src/ci/docker-compose/deadlock_haproxy.cfg

diff --git a/src/ci/docker-compose/deadlock_haproxy.cfg b/src/ci/docker-compose/deadlock_haproxy.cfg
new file mode 100644
index 00000000000..ef334b51238
--- /dev/null
+++ b/src/ci/docker-compose/deadlock_haproxy.cfg
@@ -0,0 +1,8 @@
+frontend cromwell-cluster
+    bind 0.0.0.0:80
+    default_backend cromwell-servers
+
+backend cromwell-servers
+    balance roundrobin
+    server master cromwell-master:8000
+    server norefresh cromwell-norefresh:8000
diff --git a/src/ci/docker-compose/docker-compose-deadlock.yml b/src/ci/docker-compose/docker-compose-deadlock.yml
index bc809439642..febf23b8153 100644
--- a/src/ci/docker-compose/docker-compose-deadlock.yml
+++ b/src/ci/docker-compose/docker-compose-deadlock.yml
@@ -95,12 +95,13 @@ services:
       cromwell-norefresh:
         condition: service_healthy
   load-balancer:
-    image: dockercloud/haproxy
+    image: haproxy:lts-alpine
     links:
       - cromwell-master
       - cromwell-norefresh
     volumes:
       - /var/run/docker.sock:/var/run/docker.sock
+      - ${CROMWELL_BUILD_DOCKER_DIRECTORY}/deadlock_haproxy.cfg:/usr/local/etc/haproxy/haproxy.cfg:ro
     ports:
       - 8000:80
     depends_on:

From db0dd2d09d164ccac258453f0686fa5ec6dcc057 Mon Sep 17 00:00:00 2001
From: rsaperst <156102201+rsaperst@users.noreply.github.com>
Date: Thu, 29 Feb 2024 11:21:46 -0500
Subject: [PATCH 287/326] [WX-965] quote() and squote() engine functions.
 (#7375)

Co-authored-by: Ryan Saperstein <rsaperst@wmd55-b47.hsd1.ma.comcast.net>
Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .../biscayne_new_engine_functions.test        |  15 ++
 .../biscayne_new_engine_functions.wdl         |  14 +-
 .../draft3/elements/ExpressionElement.scala   |   2 +
 .../AstToNewExpressionElements.scala          |   4 +
 .../BiscayneExpressionValueConsumers.scala    |  14 ++
 .../expression/consumed/consumed.scala        |   2 +
 .../files/BiscayneFileEvaluators.scala        |  20 +-
 .../linking/expression/files/files.scala      |   3 +-
 .../types/BiscayneTypeEvaluators.scala        |  28 +++
 .../linking/expression/types/types.scala      |   3 +-
 .../values/BiscayneValueEvaluators.scala      |  48 ++++
 .../linking/expression/values/values.scala    |   4 +
 .../transforms/biscayne/Ast2WdlomSpec.scala   |  12 +
 ...BiscayneExpressionValueConsumersSpec.scala |  18 ++
 .../files/BiscayneFileEvaluatorSpec.scala     |  22 ++
 .../types/BiscayneTypeEvaluatorSpec.scala     |  36 +++
 .../values/BiscayneValueEvaluatorSpec.scala   | 226 ++++++++++++++++++
 .../AstToNewExpressionElements.scala          |   4 +
 .../CascadesExpressionValueConsumers.scala    |  14 ++
 .../expression/consumed/consumed.scala        |   2 +
 .../files/CascadesFileEvaluators.scala        |   6 +
 .../linking/expression/files/files.scala      |   2 +
 .../types/CascadesTypeEvaluators.scala        |  28 +++
 .../linking/expression/types/types.scala      |   2 +
 .../values/CascadesValueEvaluators.scala      |  42 ++++
 .../linking/expression/values/values.scala    |   4 +
 .../transforms/cascades/Ast2WdlomSpec.scala   |  12 +
 ...CascadesExpressionValueConsumersSpec.scala |  18 ++
 .../files/CascadesFileEvaluatorSpec.scala     |  22 ++
 .../types/CascadesTypeEvaluatorSpec.scala     |  36 +++
 .../values/CascadesValueEvaluatorSpec.scala   | 124 ++++++++++
 .../transforms/ast2wdlom/Ast2WdlomSpec.scala  |  12 +
 .../base/wdlom2wdl/WdlWriterImpl.scala        |   2 +
 33 files changed, 788 insertions(+), 13 deletions(-)

diff --git a/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test b/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
index 3289f2df78c..b9f5430e57b 100644
--- a/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
+++ b/centaur/src/main/resources/standardTestCases/biscayne_new_engine_functions.test
@@ -61,6 +61,21 @@ metadata {
   "outputs.biscayne_new_engine_functions.with_suffixes.1": "bbbS"
   "outputs.biscayne_new_engine_functions.with_suffixes.2": "cccS"
 
+  "outputs.biscayne_new_engine_functions.with_quotes.0": "\"1\""
+  "outputs.biscayne_new_engine_functions.with_quotes.1": "\"2\""
+  "outputs.biscayne_new_engine_functions.with_quotes.2": "\"3\""
+
+  "outputs.biscayne_new_engine_functions.string_with_quotes.0": "\"aaa\""
+  "outputs.biscayne_new_engine_functions.string_with_quotes.1": "\"bbb\""
+  "outputs.biscayne_new_engine_functions.string_with_quotes.2": "\"ccc\""
+
+  "outputs.biscayne_new_engine_functions.with_squotes.0": "'1'"
+  "outputs.biscayne_new_engine_functions.with_squotes.1": "'2'"
+  "outputs.biscayne_new_engine_functions.with_squotes.2": "'3'"
+
+  "outputs.biscayne_new_engine_functions.string_with_squotes.0": "'aaa'"
+  "outputs.biscayne_new_engine_functions.string_with_squotes.1": "'bbb'"
+  "outputs.biscayne_new_engine_functions.string_with_squotes.2": "'ccc'"
   "outputs.biscayne_new_engine_functions.unzipped_a.left.0": "A"
   "outputs.biscayne_new_engine_functions.unzipped_a.right.0": "a"
 
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
index 5c9cb5f8dc4..979af2dc778 100644
--- a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_engine_functions/biscayne_new_engine_functions.wdl
@@ -4,7 +4,7 @@ workflow biscayne_new_engine_functions {
 
   meta {
     description: "This test makes sure that these functions work in a real workflow"
-    functions_under_test: [ "keys", "as_map", "as_pairs", "collect_by_key", "suffix", "unzip" ]
+    functions_under_test: [ "keys", "as_map", "as_pairs", "collect_by_key", "quote", "squote", "sub", "suffix", "unzip" ]
   }
 
   Map[String, Int] x_map_in = {"a": 1, "b": 2, "c": 3}
@@ -17,6 +17,8 @@ workflow biscayne_new_engine_functions {
 
   Array[String] some_strings = ["aaa", "bbb", "ccc"]
 
+  Array[Int] some_ints = [1, 2, 3]
+
   Int smallestInt = 1
   Float smallFloat = 2.718
   Float bigFloat = 3.141
@@ -64,6 +66,16 @@ workflow biscayne_new_engine_functions {
     # =================================================
     Array[String] with_suffixes = suffix("S", some_strings)
 
+    # quote():
+    # =================================================
+    Array[String] with_quotes = quote(some_ints)
+    Array[String] string_with_quotes = quote(some_strings)
+
+    # squote():
+    # =================================================
+    Array[String] with_squotes = squote(some_ints)
+    Array[String] string_with_squotes = squote(some_strings)
+    
     # unzip():
     # =================================================
     Pair[Array[String], Array[String]] unzipped_a = unzip(zipped_a)
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
index 08a89fb2ff0..d6d8948d700 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
@@ -136,6 +136,8 @@ object ExpressionElement {
   final case class Ceil(param: ExpressionElement) extends OneParamFunctionCallElement
   final case class Round(param: ExpressionElement) extends OneParamFunctionCallElement
   final case class Glob(param: ExpressionElement) extends OneParamFunctionCallElement
+  final case class Quote(param: ExpressionElement) extends OneParamFunctionCallElement
+  final case class SQuote(param: ExpressionElement) extends OneParamFunctionCallElement
   final case class Unzip(param: ExpressionElement) extends OneParamFunctionCallElement
 
   // 1- or 2-param functions:
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
index f814044d1d0..fdbfd26dd52 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/ast2wdlom/AstToNewExpressionElements.scala
@@ -10,7 +10,9 @@ import wdl.model.draft3.elements.ExpressionElement.{
   Keys,
   Max,
   Min,
+  Quote,
   Sep,
+  SQuote,
   SubPosix,
   Suffix,
   Unzip
@@ -28,6 +30,8 @@ object AstToNewExpressionElements {
     "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
     "sub" -> AstNodeToExpressionElement.validateThreeParamEngineFunction(SubPosix, "sub"),
     "suffix" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Suffix, "suffix"),
+    "quote" -> AstNodeToExpressionElement.validateOneParamEngineFunction(Quote, "quote"),
+    "squote" -> AstNodeToExpressionElement.validateOneParamEngineFunction(SQuote, "squote"),
     "unzip" -> AstNodeToExpressionElement.validateOneParamEngineFunction(Unzip, "unzip"),
     "read_object" -> (_ =>
       "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
index 71ee8a61980..dd909356ff8 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
@@ -76,6 +76,20 @@ object BiscayneExpressionValueConsumers {
         expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
+  implicit val quoteExpressionValueConsumer: ExpressionValueConsumer[Quote] = new ExpressionValueConsumer[Quote] {
+    override def expressionConsumedValueHooks(a: Quote)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+  }
+
+  implicit val sQuoteExpressionValueConsumer: ExpressionValueConsumer[SQuote] = new ExpressionValueConsumer[SQuote] {
+    override def expressionConsumedValueHooks(a: SQuote)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+  }
+
   implicit val unzipExpressionValueConsumer: ExpressionValueConsumer[Unzip] = new ExpressionValueConsumer[Unzip] {
     override def expressionConsumedValueHooks(a: Unzip)(implicit
       expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
index d6cc21f7646..93df393d4fa 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
@@ -104,6 +104,8 @@ package object consumed {
         case a: AsPairs => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: CollectByKey => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Sep => sepExpressionValueConsumer.expressionConsumedValueHooks(a)(expressionValueConsumer)
+        case a: Quote => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: SQuote => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Unzip => a.expressionConsumedValueHooks(expressionValueConsumer)
 
         case a: Min => a.expressionConsumedValueHooks(expressionValueConsumer)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
index 89f830f81ab..77de240732e 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
@@ -7,36 +7,36 @@ import wdl.model.draft3.elements.ExpressionElement.{
   Keys,
   Max,
   Min,
+  Quote,
   Sep,
+  SQuote,
   SubPosix,
   Suffix,
   Unzip
 }
 import wdl.model.draft3.graph.expression.FileEvaluator
-import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.{
   threeParameterFunctionPassthroughFileEvaluator,
   twoParameterFunctionPassthroughFileEvaluator
 }
+import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
 
 object BiscayneFileEvaluators {
 
-  implicit val keysFileEvaluator: FileEvaluator[Keys] = EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
-  implicit val asMapFileEvaluator: FileEvaluator[AsMap] =
-    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
-  implicit val asPairsFileEvaluator: FileEvaluator[AsPairs] =
-    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
-  implicit val collectByKeyFileEvaluator: FileEvaluator[CollectByKey] =
-    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val keysFileEvaluator: FileEvaluator[Keys] = singleParameterPassthroughFileEvaluator
+  implicit val asMapFileEvaluator: FileEvaluator[AsMap] = singleParameterPassthroughFileEvaluator
+  implicit val asPairsFileEvaluator: FileEvaluator[AsPairs] = singleParameterPassthroughFileEvaluator
+  implicit val collectByKeyFileEvaluator: FileEvaluator[CollectByKey] = singleParameterPassthroughFileEvaluator
 
   implicit val sepFunctionEvaluator: FileEvaluator[Sep] = twoParameterFunctionPassthroughFileEvaluator[Sep]
   implicit val subPosixFunctionEvaluator: FileEvaluator[SubPosix] =
     threeParameterFunctionPassthroughFileEvaluator[SubPosix]
   implicit val suffixFunctionEvaluator: FileEvaluator[Suffix] = twoParameterFunctionPassthroughFileEvaluator[Suffix]
+  implicit val quoteFunctionEvaluator: FileEvaluator[Quote] = singleParameterPassthroughFileEvaluator
+  implicit val sQuoteFunctionEvaluator: FileEvaluator[SQuote] = singleParameterPassthroughFileEvaluator
 
   implicit val minFunctionEvaluator: FileEvaluator[Min] = twoParameterFunctionPassthroughFileEvaluator[Min]
   implicit val maxFunctionEvaluator: FileEvaluator[Max] = twoParameterFunctionPassthroughFileEvaluator[Max]
 
-  implicit val unzipFunctionEvaluator: FileEvaluator[Unzip] =
-    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val unzipFunctionEvaluator: FileEvaluator[Unzip] = singleParameterPassthroughFileEvaluator
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
index 81f667d80fe..40807bf3e58 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
@@ -146,7 +146,8 @@ package object files {
         case a: Ceil => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Round => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Glob => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
-
+        case a: Quote => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SQuote => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Size => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Basename =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
index 2ea750364e1..21f2e9bcc8c 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
@@ -121,6 +121,34 @@ object BiscayneTypeEvaluators {
       ) mapN { (_, _) => WomArrayType(WomStringType) }
   }
 
+  implicit val quoteFunctionEvaluator: TypeEvaluator[Quote] = new TypeEvaluator[Quote] {
+    override def evaluateType(a: Quote, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType)) flatMap {
+        case WomArrayType(WomNothingType) => WomArrayType(WomNothingType).validNel
+        case WomArrayType(_: WomPrimitiveType) => WomArrayType(WomStringType).validNel
+        case other @ WomArrayType(_) =>
+          s"Cannot invoke quote on type Array[${other.stableName}]. Expected an Array of primitive type".invalidNel
+        case other =>
+          s"Cannot invoke quote on type ${other.stableName}. Expected an Array of primitive type".invalidNel
+      }
+  }
+
+  implicit val sQuoteFunctionEvaluator: TypeEvaluator[SQuote] = new TypeEvaluator[SQuote] {
+    override def evaluateType(a: SQuote, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType)) flatMap {
+        case WomArrayType(WomNothingType) => WomArrayType(WomNothingType).validNel
+        case WomArrayType(_: WomPrimitiveType) => WomArrayType(WomStringType).validNel
+        case other @ WomArrayType(_) =>
+          s"Cannot invoke squote on type Array[${other.stableName}]. Expected an Array of primitive type".invalidNel
+        case other =>
+          s"Cannot invoke squote on type ${other.stableName}. Expected an Array of primitive type".invalidNel
+      }
+  }
+
   implicit val unzipFunctionEvaluator: TypeEvaluator[Unzip] = new TypeEvaluator[Unzip] {
     override def evaluateType(a: Unzip, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
index 385b4b0c072..9775cb38970 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
@@ -91,7 +91,8 @@ package object types {
         case a: Ceil => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Round => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Glob => a.evaluateType(linkedValues)(typeEvaluator)
-
+        case a: Quote => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: SQuote => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Size => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Basename => a.evaluateType(linkedValues)(typeEvaluator)
 
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
index 8583c9a4af1..9903313bf00 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
@@ -269,6 +269,54 @@ object BiscayneValueEvaluators {
       }
   }
 
+  /**
+   * Quote: Given an array of primitives, produce a new array in which all elements of the original are in quotes (").
+   * https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#-arraystring-quotearrayp
+   * input: Array[Primitive]
+   * output: Array[String]
+   */
+  implicit val quoteFunctionEvaluator: ValueEvaluator[Quote] = new ValueEvaluator[Quote] {
+    override def evaluateValue(a: Quote,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomArray, WomArray](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) { arr =>
+        EvaluatedValue(
+          WomArray(arr.value.map(v => WomString("\"" + v.valueString.replaceAll(""""""", "\"") + "\""))),
+          Seq.empty
+        ).validNel
+      }
+  }
+
+  /**
+   * SQuote: Given an array of primitives, produce a new array in which all elements of the original are in single quotes (').
+   * https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#-arraystring-squotearrayp
+   * input: Array[Primitive]
+   * output: Array[String]
+   */
+  implicit val sQuoteFunctionEvaluator: ValueEvaluator[SQuote] = new ValueEvaluator[SQuote] {
+    override def evaluateValue(a: SQuote,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomArray, WomArray](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) { arr =>
+        EvaluatedValue(
+          WomArray(arr.value.map(v => WomString("\'" + v.valueString.replaceAll("""'""", "\'") + "\'"))),
+          Seq.empty
+        ).validNel
+      }
+  }
+
   /**
    * Unzip: Creates a pair of arrays, the first containing the elements from the left members of an array of pairs,
    * and the second containing the right members. This is the inverse of the zip function.
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
index e7151653258..eeb5bd1712f 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
@@ -156,6 +156,10 @@ package object values {
         case a: Round =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Glob => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Quote =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: SQuote =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
 
         case a: Size => a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Basename =>
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
index e4f2058edf1..dae69cfdcf8 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
@@ -109,6 +109,18 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     expr shouldBeValid (Suffix(IdentifierLookup("some_str"), IdentifierLookup("some_arr")))
   }
 
+  it should "parse the new quote function" in {
+    val str = "quote(some_arr)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (Quote(IdentifierLookup("some_arr")))
+  }
+
+  it should "parse the new squote function" in {
+    val str = "squote(some_arr)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (SQuote(IdentifierLookup("some_arr")))
+  }
+
   it should "parse the new unzip function" in {
     val str = "unzip(some_array_of_pairs)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
index f8fa6cad40f..b20b844b02e 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
@@ -85,6 +85,24 @@ class BiscayneExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     }
   }
 
+  it should "discover an array variable lookup within a quote() call" in {
+    val str = """ quote(my_array) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array")))
+    }
+  }
+
+  it should "discover an array variable lookup within a squote() call" in {
+    val str = """ squote(my_array) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array")))
+    }
+  }
+
   it should "discover an array variable lookup within a unzip() call" in {
     val str = """ unzip(my_array_of_pairs) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
index 570d5633d79..69ac8a9cfca 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
@@ -68,6 +68,28 @@ class BiscayneFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
   }
 
+  it should "discover the file which would be required to evaluate a quote() function" in {
+    val str = """ quote(read_lines("foo.txt")) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
+    }
+  }
+
+  it should "discover the file which would be required to evaluate a squote() function" in {
+    val str = """ squote(read_lines("foo.txt")) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
+    }
+  }
+
   it should "discover the file which would be required to evaluate a unzip() function" in {
     val str = """ unzip(read_lines("foo.txt")) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
index dba6da30973..a38a80079e5 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
@@ -74,6 +74,42 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
   }
 
+  it should "evaluate the type of a quote() function as Array[String]" in {
+    val str = """ quote([1, 2, 3]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+    }
+  }
+
+  it should "evaluate the type of a quote() function with an empty array as Array[Nothing]" in {
+    val str = """ quote([]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomNothingType)
+    }
+  }
+
+  it should "evaluate the type of a squote() function as Array[String]" in {
+    val str = """ squote([1, 2, 3]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+    }
+  }
+
+  it should "evaluate the type of an squote() function with an empty array as Array[Nothing]" in {
+    val str = """ squote([]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomNothingType)
+    }
+  }
+
   it should "evaluate the type of an unzip() function as Pair[Array[X], Array[Y]]" in {
     val string_and_int = """ unzip([("one", 1),("two", 2),("three", 3)]) """
     val string_and_int_expr = fromString[ExpressionElement](string_and_int, parser.parse_e)
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
index bb58ebbe331..a6d3066b5e9 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
@@ -241,6 +241,232 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     }
   }
 
+  it should "evaluate a quote expression correctly with an empty array" in {
+    val str = """ quote([]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(Seq())
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a quote expression correctly with an array of integers" in {
+    val str = """ quote([1, 2, 3]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\"1\""),
+        WomString("\"2\""),
+        WomString("\"3\"")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a quote expression correctly with an array of booleans" in {
+    val str = """ quote([true, false, true]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\"true\""),
+        WomString("\"false\""),
+        WomString("\"true\"")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a quote expression correctly with an array of floats" in {
+    val str = """ quote([1.1, 2.2, 3]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\"1.1\""),
+        WomString("\"2.2\""),
+        WomString("\"3.0\"")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a quote expression correctly with an array of files" in {
+    val str = """ quote(["/home/someFile.txt", "/rootFile.exe", "./anotherFile.py"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\"/home/someFile.txt\""),
+        WomString("\"/rootFile.exe\""),
+        WomString("\"./anotherFile.py\"")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a quote expression correctly with an array of strings" in {
+    val str = """ quote(["a", "b", "c"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\"a\""),
+        WomString("\"b\""),
+        WomString("\"c\"")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a quote expression correctly with an array of strings that are already in quotes" in {
+    val str = """ quote(["\"a\"", "\"b", "c\""]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\"\"a\"\""),
+        WomString("\"\"b\""),
+        WomString("\"c\"\"")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an empty array" in {
+    val str = """ squote([]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(Seq())
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an array of integers" in {
+    val str = """ squote([1, 2, 3]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\'1\'"),
+        WomString("\'2\'"),
+        WomString("\'3\'")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an array of booleans" in {
+    val str = """ squote([true, false, true]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\'true\'"),
+        WomString("\'false\'"),
+        WomString("\'true\'")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an array of floats" in {
+    val str = """ squote([1.1, 2.2, 3]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\'1.1\'"),
+        WomString("\'2.2\'"),
+        WomString("\'3.0\'")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an array of files" in {
+    val str = """ squote(["/home/someFile.txt", "/rootFile.exe", "./anotherFile.py"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\'/home/someFile.txt\'"),
+        WomString("\'/rootFile.exe\'"),
+        WomString("\'./anotherFile.py\'")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an array of strings" in {
+    val str = """ squote(["a", "b", "c"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\'a\'"),
+        WomString("\'b\'"),
+        WomString("\'c\'")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an array of strings that are already in quotes" in {
+    val str = """ squote(["'a'", "'b", "c'"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("""''a''"""),
+        WomString("""''b'"""),
+        WomString("""'c''""")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
   it should "evaluate an unzip expression correctly" in {
     val str = """ unzip([("one", 1),("two", 2),("three", 3)]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
index 1a2ce0d5735..f4d65d2538b 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/ast2wdlom/AstToNewExpressionElements.scala
@@ -10,7 +10,9 @@ import wdl.model.draft3.elements.ExpressionElement.{
   Keys,
   Max,
   Min,
+  Quote,
   Sep,
+  SQuote,
   SubPosix,
   Suffix,
   Unzip
@@ -28,6 +30,8 @@ object AstToNewExpressionElements {
     "sep" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Sep, "sep"),
     "sub" -> AstNodeToExpressionElement.validateThreeParamEngineFunction(SubPosix, "sub"),
     "suffix" -> AstNodeToExpressionElement.validateTwoParamEngineFunction(Suffix, "suffix"),
+    "quote" -> AstNodeToExpressionElement.validateOneParamEngineFunction(Quote, "quote"),
+    "squote" -> AstNodeToExpressionElement.validateOneParamEngineFunction(SQuote, "squote"),
     "unzip" -> AstNodeToExpressionElement.validateOneParamEngineFunction(Unzip, "unzip"),
     "read_object" -> (_ =>
       "read_object is no longer available in this WDL version. Consider using read_json instead".invalidNel
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
index a328b8a4014..d0faaea154e 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
@@ -76,6 +76,20 @@ object cascadesExpressionValueConsumers {
         expressionValueConsumer.expressionConsumedValueHooks(a.arg2)(expressionValueConsumer)
   }
 
+  implicit val quoteExpressionValueConsumer: ExpressionValueConsumer[Quote] = new ExpressionValueConsumer[Quote] {
+    override def expressionConsumedValueHooks(a: Quote)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+  }
+
+  implicit val sQuoteExpressionValueConsumer: ExpressionValueConsumer[SQuote] = new ExpressionValueConsumer[SQuote] {
+    override def expressionConsumedValueHooks(a: SQuote)(implicit
+      expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+    ): Set[UnlinkedConsumedValueHook] =
+      expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
+  }
+
   implicit val noneLiteralExpressionValueConsumer: ExpressionValueConsumer[NoneLiteralElement.type] =
     new ExpressionValueConsumer[NoneLiteralElement.type] {
       override def expressionConsumedValueHooks(a: NoneLiteralElement.type)(implicit
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
index 4184595cb72..4916a7afd02 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
@@ -82,6 +82,8 @@ package object consumed {
         case a: Flatten => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Prefix => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Suffix => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: Quote => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: SQuote => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: SelectFirst => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: SelectAll => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: Defined => a.expressionConsumedValueHooks(expressionValueConsumer)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
index 7a1114f61b8..2ce3d01b0de 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
@@ -7,7 +7,9 @@ import wdl.model.draft3.elements.ExpressionElement.{
   Keys,
   Max,
   Min,
+  Quote,
   Sep,
+  SQuote,
   SubPosix,
   Suffix,
   Unzip
@@ -35,6 +37,10 @@ object cascadesFileEvaluators {
   implicit val subPosixFunctionEvaluator: FileEvaluator[SubPosix] =
     threeParameterFunctionPassthroughFileEvaluator[SubPosix]
   implicit val suffixFunctionEvaluator: FileEvaluator[Suffix] = twoParameterFunctionPassthroughFileEvaluator[Suffix]
+  implicit val quoteFunctionEvaluator: FileEvaluator[Quote] =
+    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+  implicit val sQuoteFunctionEvaluator: FileEvaluator[SQuote] =
+    EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
 
   implicit val minFunctionEvaluator: FileEvaluator[Min] = twoParameterFunctionPassthroughFileEvaluator[Min]
   implicit val maxFunctionEvaluator: FileEvaluator[Max] = twoParameterFunctionPassthroughFileEvaluator[Max]
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
index 3d96ffcb4d1..f1935603458 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
@@ -136,6 +136,8 @@ package object files {
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Prefix => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: Suffix => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: Quote => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: SQuote => a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: SelectFirst =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: SelectAll =>
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
index 0510a19db30..ba7e9ae8dff 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
@@ -121,6 +121,34 @@ object cascadesTypeEvaluators {
       ) mapN { (_, _) => WomArrayType(WomStringType) }
   }
 
+  implicit val quoteFunctionEvaluator: TypeEvaluator[Quote] = new TypeEvaluator[Quote] {
+    override def evaluateType(a: Quote, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType)) flatMap {
+        case WomArrayType(WomNothingType) => WomArrayType(WomNothingType).validNel
+        case WomArrayType(_: WomPrimitiveType) => WomArrayType(WomStringType).validNel
+        case other @ WomArrayType(_) =>
+          s"Cannot invoke quote on type Array[${other.stableName}]. Expected an Array of primitive type".invalidNel
+        case other =>
+          s"Cannot invoke quote on type ${other.stableName}. Expected an Array of primitive type".invalidNel
+      }
+  }
+
+  implicit val sQuoteFunctionEvaluator: TypeEvaluator[SQuote] = new TypeEvaluator[SQuote] {
+    override def evaluateType(a: SQuote, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType)) flatMap {
+        case WomArrayType(WomNothingType) => WomArrayType(WomNothingType).validNel
+        case WomArrayType(_: WomPrimitiveType) => WomArrayType(WomStringType).validNel
+        case other @ WomArrayType(_) =>
+          s"Cannot invoke quote on type Array[${other.stableName}]. Expected an Array of primitive type".invalidNel
+        case other =>
+          s"Cannot invoke quote on type ${other.stableName}. Expected an Array of primitive type".invalidNel
+      }
+  }
+
   implicit val unzipFunctionEvaluator: TypeEvaluator[Unzip] = new TypeEvaluator[Unzip] {
     override def evaluateType(a: Unzip, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
index 1a17eeb9d24..1a027b745ed 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
@@ -84,6 +84,8 @@ package object types {
         case a: Flatten => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Prefix => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Suffix => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Quote => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: SQuote => a.evaluateType(linkedValues)(typeEvaluator)
         case a: SelectFirst => a.evaluateType(linkedValues)(typeEvaluator)
         case a: SelectAll => a.evaluateType(linkedValues)(typeEvaluator)
         case a: Defined => a.evaluateType(linkedValues)(typeEvaluator)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
index 9152aba2ce9..ee106f2ef6a 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
@@ -269,6 +269,48 @@ object cascadesValueEvaluators {
       }
   }
 
+  /**
+   * Quote: Given an array of primitives, produce a new array in which all elements of the original are in quotes (").
+   * https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#-arraystring-quotearrayp
+   * input: Array[Primitive]
+   * output: Array[String]
+   */
+  implicit val quoteFunctionEvaluator: ValueEvaluator[Quote] = new ValueEvaluator[Quote] {
+    override def evaluateValue(a: Quote,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomArray, WomArray](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) { arr =>
+        EvaluatedValue(WomArray(arr.value.map(v => WomString("\"" + v.valueString + "\""))), Seq.empty).validNel
+      }
+  }
+
+  /**
+   * SQuote: Given an array of primitives, produce a new array in which all elements of the original are in single quotes (').
+   * https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#-arraystring-squotearrayp
+   * input: Array[Primitive]
+   * output: Array[String]
+   */
+  implicit val sQuoteFunctionEvaluator: ValueEvaluator[SQuote] = new ValueEvaluator[SQuote] {
+    override def evaluateValue(a: SQuote,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomArray]] =
+      processValidatedSingleValue[WomArray, WomArray](
+        expressionValueEvaluator.evaluateValue(a.param, inputs, ioFunctionSet, forCommandInstantiationOptions)(
+          expressionValueEvaluator
+        )
+      ) { arr =>
+        EvaluatedValue(WomArray(arr.value.map(v => WomString("\'" + v.valueString + "\'"))), Seq.empty).validNel
+      }
+  }
+
   /**
    * Unzip: Creates a pair of arrays, the first containing the elements from the left members of an array of pairs,
    * and the second containing the right members. This is the inverse of the zip function.
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
index f0fcba9ebb6..3e92a27b2b8 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
@@ -144,6 +144,10 @@ package object values {
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: Suffix =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: Quote =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: SQuote =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: SelectFirst =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: SelectAll =>
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
index 196f7030087..ffc6d3bc131 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
@@ -104,6 +104,18 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     expr shouldBeValid (Suffix(IdentifierLookup("some_str"), IdentifierLookup("some_arr")))
   }
 
+  it should "parse the new quote function" in {
+    val str = "quote(some_arr)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (Quote(IdentifierLookup("some_arr")))
+  }
+
+  it should "parse the new squote function" in {
+    val str = "squote(some_arr)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (SQuote(IdentifierLookup("some_arr")))
+  }
+
   it should "parse the new unzip function" in {
     val str = "unzip(some_array_of_pairs)"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
index 9ed5933e248..9e47424d6c5 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
@@ -85,6 +85,24 @@ class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
     }
   }
 
+  it should "discover an array variable lookup within a quote() call" in {
+    val str = """ quote(my_array) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array")))
+    }
+  }
+
+  it should "discover an array variable lookup within a squote() call" in {
+    val str = """ squote(my_array) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array")))
+    }
+  }
+
   it should "discover an array variable lookup within a unzip() call" in {
     val str = """ unzip(my_array_of_pairs) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
index 93a80d195e5..afc73a56a32 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
@@ -68,6 +68,28 @@ class CascadesFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
   }
 
+  it should "discover the file which would be required to evaluate a quote() function" in {
+    val str = """ quote(read_lines("foo.txt")) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
+    }
+  }
+
+  it should "discover the file which would be required to evaluate a squote() function" in {
+    val str = """ squote(read_lines("foo.txt")) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
+    }
+  }
+
   it should "discover the file which would be required to evaluate a unzip() function" in {
     val str = """ unzip(read_lines("foo.txt")) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
index 384579e31e7..d874fb7e6dd 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
@@ -74,6 +74,42 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     }
   }
 
+  it should "evaluate the type of a quote() function as Array[String]" in {
+    val str = """ quote([1, 2, 3]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+    }
+  }
+
+  it should "evaluate the type of a quote() function with an empty array as Array[Nothing]" in {
+    val str = """ quote([]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomNothingType)
+    }
+  }
+
+  it should "evaluate the type of a squote() function as Array[String]" in {
+    val str = """ squote([1, 2, 3]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+    }
+  }
+
+  it should "evaluate the type of an squote() function with an empty array as Array[Nothing]" in {
+    val str = """ squote([]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomNothingType)
+    }
+  }
+
   it should "evaluate the type of an unzip() function as Pair[Array[X], Array[Y]]" in {
     val string_and_int = """ unzip([("one", 1),("two", 2),("three", 3)]) """
     val string_and_int_expr = fromString[ExpressionElement](string_and_int, parser.parse_e)
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
index 4c684734f88..60215046d05 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
@@ -241,6 +241,130 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
     }
   }
 
+  it should "evaluate a quote expression correctly with an empty array" in {
+    val str = """ quote([]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(Seq())
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a quote expression correctly with an array of integers" in {
+    val str = """ quote([1, 2, 3]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\"1\""),
+        WomString("\"2\""),
+        WomString("\"3\"")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a quote expression correctly with an array of strings" in {
+    val str = """ quote(["a", "b", "c"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\"a\""),
+        WomString("\"b\""),
+        WomString("\"c\"")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a quote expression correctly with an array of strings that are already in quotes" in {
+    val str = """ quote(["\"a\"", "\"b", "c\""]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\"\"a\"\""),
+        WomString("\"\"b\""),
+        WomString("\"c\"\"")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an empty array" in {
+    val str = """ squote([]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(Seq())
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an array of integers" in {
+    val str = """ squote([1, 2, 3]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\'1\'"),
+        WomString("\'2\'"),
+        WomString("\'3\'")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an array of strings" in {
+    val str = """ squote(["a", "b", "c"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\'a\'"),
+        WomString("\'b\'"),
+        WomString("\'c\'")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
+  it should "evaluate a squote expression correctly with an array of strings that are already in quotes" in {
+    val str = """ squote(["\'a\'", "\'b", "c\'"]) """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    val expectedArray: WomArray = WomArray(
+      Seq(
+        WomString("\'\'a\'\'"),
+        WomString("\'\'b\'"),
+        WomString("\'c\'\'")
+      )
+    )
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedArray, Seq.empty)
+    }
+  }
+
   it should "evaluate an unzip expression correctly" in {
     val str = """ unzip([("one", 1),("two", 2),("three", 3)]) """
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
index c9e92abb5ed..d7f507b8343 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
@@ -70,6 +70,18 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     expr shouldBeInvalid "Failed to parse expression (reason 1 of 1): Unknown engine function: 'suffix'"
   }
 
+  it should "not parse the new quote function" in {
+    val str = "quote(anArray)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeInvalid "Failed to parse expression (reason 1 of 1): Unknown engine function: 'quote'"
+  }
+
+  it should "not parse the new squote function" in {
+    val str = "squote(anArray)"
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeInvalid "Failed to parse expression (reason 1 of 1): Unknown engine function: 'squote'"
+  }
+
   it should "parse the (biscayne) None keyword as a plain old identifier" in {
     val str = "None"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
index 65bae56df2b..a09e94534c4 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
@@ -436,6 +436,8 @@ object WdlWriterImpl {
           case _: Ceil => "ceil"
           case _: Round => "round"
           case _: Glob => "glob"
+          case _: Quote => "quote"
+          case _: SQuote => "squote"
           case _: Keys => "keys"
           case _: AsMap => "as_map"
           case _: AsPairs => "as_pairs"

From 82b8dc591c9517a45390d6c40d6fa80db907519d Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 5 Mar 2024 09:15:59 -0500
Subject: [PATCH 288/326] [WX-1317] Remove Akka 'server' header from all HTTP
 responses (#7379)

---
 server/src/main/resources/application.conf | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/server/src/main/resources/application.conf b/server/src/main/resources/application.conf
index e80cd716b4e..3bdacceb8ee 100644
--- a/server/src/main/resources/application.conf
+++ b/server/src/main/resources/application.conf
@@ -8,8 +8,12 @@ akka {
     server {
       request-timeout = 40s
       bind-timeout = 5s
+      # By default, akka includes an HTTP header in responses that looks like:
+      # server=akka-http/10.20.1
+      # For better app sec, we suppress this to make it harder for attackers to learn about our system.
+      # Akka doc: https://doc.akka.io/docs/akka-http/current/configuration.html
+      server-header = ""
     }
-
     client.connecting-timeout = 40s
 
     # Inspired by https://broadworkbench.atlassian.net/browse/CROM-6738

From 79c2bff6644b0f3ee43565ce0deb7c2acdd81ce6 Mon Sep 17 00:00:00 2001
From: Saloni Shah <salonipshah11@gmail.com>
Date: Thu, 7 Mar 2024 14:31:07 -0500
Subject: [PATCH 289/326] WM-2461] Add support for running private workflows on
 Azure (#7373)

---
 core/src/main/resources/reference.conf        |  1 +
 .../MaterializeWorkflowDescriptorActor.scala  | 17 +++++--
 ...terializeWorkflowDescriptorActorSpec.scala | 10 +++-
 .../auth/GithubAuthVendingSupport.scala       | 21 ++++++++-
 .../auth/GithubAuthVendingSupportSpec.scala   | 47 +++++++++++++++++--
 5 files changed, 85 insertions(+), 11 deletions(-)

diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index c43dbce60ee..672d82c8c80 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -577,6 +577,7 @@ services {
     class = "cromwell.services.auth.impl.GithubAuthVendingActor"
     config {
       enabled = false
+      auth.azure = false
       # Notes:
       #   - don't include the 'Bearer' before the token
       #   - this config value should be removed when support for fetching tokens from ECM has been added to Cromwell
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala
index 6b515114149..8e57c77f2de 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/materialization/MaterializeWorkflowDescriptorActor.scala
@@ -2,6 +2,7 @@ package cromwell.engine.workflow.lifecycle.materialization
 
 import akka.actor.{ActorRef, FSM, LoggingFSM, Props, Status}
 import akka.pattern.pipe
+import akka.util.Timeout
 import cats.data.EitherT._
 import cats.data.NonEmptyList
 import cats.data.Validated.{Invalid, Valid}
@@ -36,6 +37,7 @@ import cromwell.filesystems.gcs.batch.GcsBatchCommandBuilder
 import cromwell.languages.util.ImportResolver._
 import cromwell.languages.util.LanguageFactoryUtil
 import cromwell.languages.{LanguageFactory, ValidatedWomNamespace}
+import cromwell.services.auth.GithubAuthVendingSupport
 import cromwell.services.metadata.MetadataService._
 import cromwell.services.metadata.{MetadataEvent, MetadataKey, MetadataValue}
 import eu.timepit.refined.refineV
@@ -50,6 +52,7 @@ import wom.runtime.WomOutputRuntimeExtractor
 import wom.values.{WomString, WomValue}
 
 import scala.concurrent.Future
+import scala.concurrent.duration.DurationInt
 import scala.language.postfixOps
 import scala.util.{Failure, Success, Try}
 
@@ -183,7 +186,7 @@ object MaterializeWorkflowDescriptorActor {
 }
 
 // TODO WOM: need to decide where to draw the line between language specific initialization and WOM
-class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
+class MaterializeWorkflowDescriptorActor(override val serviceRegistryActor: ActorRef,
                                          workflowId: WorkflowId,
                                          cromwellBackends: => CromwellBackends,
                                          importLocalFilesystem: Boolean,
@@ -191,7 +194,8 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
                                          hogGroup: HogGroup
 ) extends LoggingFSM[MaterializeWorkflowDescriptorActorState, Unit]
     with StrictLogging
-    with WorkflowLogging {
+    with WorkflowLogging
+    with GithubAuthVendingSupport {
 
   import MaterializeWorkflowDescriptorActor._
   val tag = self.path.name
@@ -204,6 +208,8 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
 
   protected val pathBuilderFactories: List[PathBuilderFactory] = EngineFilesystems.configuredPathBuilderFactories
 
+  final private val githubAuthVendingTimeout = Timeout(60.seconds)
+
   startWith(ReadyToMaterializeState, ())
 
   when(ReadyToMaterializeState) {
@@ -346,7 +352,12 @@ class MaterializeWorkflowDescriptorActor(serviceRegistryActor: ActorRef,
     for {
       _ <- publishLabelsToMetadata(id, labels.asMap, serviceRegistryActor)
       zippedImportResolver <- zippedResolverCheck
-      importResolvers = zippedImportResolver.toList ++ localFilesystemResolvers :+ HttpResolver(None, Map.empty)
+      importAuthProviderOpt <- importAuthProvider(conf)(githubAuthVendingTimeout).toIOChecked
+      importResolvers = zippedImportResolver.toList ++ localFilesystemResolvers :+ HttpResolver(
+        None,
+        Map.empty,
+        importAuthProviderOpt.toList
+      )
       sourceAndResolvers <- fromEither[IO](
         LanguageFactoryUtil.findWorkflowSource(sourceFiles.workflowSource, sourceFiles.workflowUrl, importResolvers)
       )
diff --git a/server/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala b/server/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala
index 216afa6ee4f..cf845af5d30 100644
--- a/server/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala
+++ b/server/src/test/scala/cromwell/engine/workflow/lifecycle/MaterializeWorkflowDescriptorActorSpec.scala
@@ -1,6 +1,6 @@
 package cromwell.engine.workflow.lifecycle
 
-import akka.actor.Props
+import akka.actor.{ActorRef, Props}
 import akka.testkit.TestDuration
 import cats.data.Validated.{Invalid, Valid}
 import com.typesafe.config.ConfigFactory
@@ -14,6 +14,7 @@ import cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDes
   MaterializeWorkflowDescriptorFailureResponse,
   MaterializeWorkflowDescriptorSuccessResponse
 }
+import cromwell.services.auth.GithubAuthVendingSupport
 import cromwell.util.SampleWdl.HelloWorld
 import cromwell.{CromwellTestKitSpec, CromwellTestKitWordSpec}
 import org.scalatest.BeforeAndAfter
@@ -23,7 +24,10 @@ import wom.values.{WomInteger, WomString}
 
 import scala.concurrent.duration._
 
-class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec with BeforeAndAfter {
+class MaterializeWorkflowDescriptorActorSpec
+    extends CromwellTestKitWordSpec
+    with BeforeAndAfter
+    with GithubAuthVendingSupport {
 
   private val ioActor = system.actorOf(SimpleIoActor.props)
   private val workflowId = WorkflowId.randomId()
@@ -89,6 +93,8 @@ class MaterializeWorkflowDescriptorActorSpec extends CromwellTestKitWordSpec wit
 
   private val fooHogGroup = HogGroup("foo")
 
+  override def serviceRegistryActor: ActorRef = NoBehaviorActor
+
   "MaterializeWorkflowDescriptorActor" should {
     "accept valid WDL, inputs and options files" in {
       val materializeWfActor = system.actorOf(
diff --git a/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala b/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala
index a8d406578ae..63fc9404e07 100644
--- a/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala
+++ b/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala
@@ -3,7 +3,12 @@ package cromwell.services.auth
 import akka.actor.ActorRef
 import akka.pattern.{AskSupport, AskTimeoutException}
 import akka.util.Timeout
+import cats.data.Validated.{Invalid, Valid}
+import cats.implicits.catsSyntaxValidatedId
+import com.typesafe.config.Config
 import com.typesafe.scalalogging.StrictLogging
+import common.validation.ErrorOr.ErrorOr
+import cromwell.cloudsupport.azure.AzureCredentials
 import cromwell.languages.util.ImportResolver.{GithubImportAuthProvider, ImportAuthProvider}
 import cromwell.services.auth.GithubAuthVending.{
   GithubAuthRequest,
@@ -13,16 +18,16 @@ import cromwell.services.auth.GithubAuthVending.{
   NoGithubAuthResponse
 }
 
+import net.ceedubs.ficus.Ficus._
 import scala.concurrent.{ExecutionContext, Future}
 
 trait GithubAuthVendingSupport extends AskSupport with StrictLogging {
 
   def serviceRegistryActor: ActorRef
 
-  implicit val timeout: Timeout
   implicit val ec: ExecutionContext
 
-  def importAuthProvider(token: String): ImportAuthProvider = new GithubImportAuthProvider {
+  def importAuthProvider(token: String)(implicit timeout: Timeout): ImportAuthProvider = new GithubImportAuthProvider {
     override def authHeader(): Future[Map[String, String]] =
       serviceRegistryActor
         .ask(GithubAuthRequest(token))
@@ -42,4 +47,16 @@ trait GithubAuthVendingSupport extends AskSupport with StrictLogging {
             Future.failed(new Exception("Failed to resolve github auth token", error))
         }
   }
+
+  def importAuthProvider(config: Config)(implicit timeout: Timeout): ErrorOr[Option[ImportAuthProvider]] = {
+    val isAuthAzure = config.as[Boolean]("services.GithubAuthVending.config.auth.azure")
+
+    if (isAuthAzure) {
+      val azureToken = AzureCredentials.getAccessToken()
+      azureToken match {
+        case Valid(token) => Option(importAuthProvider(token)).validNel
+        case Invalid(err) => s"Failed to fetch Azure token. Error: ${err.toString}".invalidNel
+      }
+    } else None.validNel
+  }
 }
diff --git a/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala b/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala
index f9bc3e127f4..9a20851ebdd 100644
--- a/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala
+++ b/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala
@@ -3,7 +3,10 @@ package cromwell.services.auth
 import akka.actor.ActorRef
 import akka.testkit.TestProbe
 import akka.util.Timeout
+import cats.data.Validated.{Invalid, Valid}
+import com.typesafe.config.ConfigFactory
 import cromwell.core.TestKitSuite
+import cromwell.languages.util.ImportResolver.GithubImportAuthProvider
 import cromwell.services.ServiceRegistryActor.ServiceRegistryFailure
 import cromwell.services.auth.GithubAuthVending.GithubAuthRequest
 import cromwell.services.auth.GithubAuthVendingSupportSpec.TestGithubAuthVendingSupport
@@ -16,6 +19,21 @@ import scala.concurrent.duration._
 
 class GithubAuthVendingSupportSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with Eventually {
 
+  private def azureGithubAuthVendingConfig(enabled: Boolean = true) = ConfigFactory
+    .parseString(
+      s"""
+         |services {
+         |  GithubAuthVending {
+         |    config {
+         |      auth.azure = ${enabled}
+         |    }
+         |  }
+         |}
+         |""".stripMargin
+    )
+
+  implicit val timeout = Timeout(10.seconds)
+
   behavior of "GithubAuthVendingSupport"
 
   it should "send a message to the service registry and handle success response" in {
@@ -60,8 +78,8 @@ class GithubAuthVendingSupportSpec extends TestKitSuite with AnyFlatSpecLike wit
 
   it should "handle timeouts" in {
     val serviceRegistryActor = TestProbe()
-    val testSupport = new TestGithubAuthVendingSupport(serviceRegistryActor.ref, 1.millisecond)
-    val provider = testSupport.importAuthProvider("user-token")
+    val testSupport = new TestGithubAuthVendingSupport(serviceRegistryActor.ref)
+    val provider = testSupport.importAuthProvider("user-token")(Timeout(1.millisecond))
     val authHeader: Future[Map[String, String]] = provider.authHeader()
 
     eventually {
@@ -88,11 +106,32 @@ class GithubAuthVendingSupportSpec extends TestKitSuite with AnyFlatSpecLike wit
     }
   }
 
+  it should "return Github import auth provider when Azure auth is enabled" in {
+    val serviceRegistryActor = TestProbe()
+    val testSupport = new TestGithubAuthVendingSupport(serviceRegistryActor.ref)
+
+    testSupport.importAuthProvider(azureGithubAuthVendingConfig()) match {
+      case Valid(providerOpt) =>
+        providerOpt.isEmpty shouldBe false
+        providerOpt.get.isInstanceOf[GithubImportAuthProvider] shouldBe true
+        providerOpt.get.validHosts shouldBe List("github.com", "githubusercontent.com", "raw.githubusercontent.com")
+      case Invalid(e) => fail(s"Unexpected failure: $e")
+    }
+  }
+
+  it should "return no import auth provider when Azure auth is disabled" in {
+    val serviceRegistryActor = TestProbe()
+    val testSupport = new TestGithubAuthVendingSupport(serviceRegistryActor.ref)
+
+    testSupport.importAuthProvider(azureGithubAuthVendingConfig(false)) match {
+      case Valid(providerOpt) => providerOpt.isEmpty shouldBe true
+      case Invalid(e) => fail(s"Unexpected failure: $e")
+    }
+  }
 }
 
 object GithubAuthVendingSupportSpec {
-  class TestGithubAuthVendingSupport(val serviceRegistryActor: ActorRef, val timeout: Timeout = 10.seconds)
-      extends GithubAuthVendingSupport {
+  class TestGithubAuthVendingSupport(val serviceRegistryActor: ActorRef) extends GithubAuthVendingSupport {
     implicit override val ec: ExecutionContext = ExecutionContext.global
   }
 

From 6e669cf1f452e837cab3e83a3e67ad2813eac0c0 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 11 Mar 2024 19:09:18 -0400
Subject: [PATCH 290/326] WX-1252 Per-backend runtime attributes (#7380)

---
 .../BackendLifecycleActorFactory.scala        |  5 ++
 .../backend/RuntimeAttributeDefinition.scala  | 49 ++++++++++++++++++-
 .../main/scala/cromwell/backend/backend.scala | 23 +++++++++
 .../it/scala/centaur/CentaurTestSuite.scala   |  3 ++
 ...e_new_runtime_attributes_lifesciences.test | 17 +++++++
 ...biscayne_new_runtime_attributes_local.test | 16 ++++++
 .../biscayne_new_runtime_attributes_tes.test  | 14 ++++++
 .../biscayne_new_runtime_attributes.wdl       | 48 ++++++++++++++++++
 .../test/standard/CentaurTestCase.scala       | 12 +++--
 .../job/preparation/JobPreparationActor.scala |  3 +-
 src/ci/resources/tes_application.conf         |  1 +
 ...AwsBatchBackendLifecycleActorFactory.scala |  6 ++-
 ...GcpBatchBackendLifecycleActorFactory.scala |  6 ++-
 ...linesApiBackendLifecycleActorFactory.scala |  2 +
 .../tes/TesBackendLifecycleActorFactory.scala |  2 +
 .../backend/impl/tes/TesConfiguration.scala   |  4 +-
 16 files changed, 202 insertions(+), 9 deletions(-)
 create mode 100644 centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_lifesciences.test
 create mode 100644 centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_local.test
 create mode 100644 centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_tes.test
 create mode 100644 centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_runtime_attributes/biscayne_new_runtime_attributes.wdl

diff --git a/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala b/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala
index 8be9a7f327c..dc06ec94f09 100644
--- a/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala
+++ b/backend/src/main/scala/cromwell/backend/BackendLifecycleActorFactory.scala
@@ -162,6 +162,11 @@ trait BackendLifecycleActorFactory {
   def dockerHashCredentials(workflowDescriptor: BackendWorkflowDescriptor,
                             initializationDataOption: Option[BackendInitializationData]
   ): List[Any] = List.empty
+
+  /**
+    * Allows Cromwell to self-identify which cloud it's running on for runtime attribute purposes
+    */
+  def platform: Option[Platform] = None
 }
 
 object BackendLifecycleActorFactory {
diff --git a/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala b/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala
index 7e73301af71..37bfa3aa7b8 100644
--- a/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala
+++ b/backend/src/main/scala/cromwell/backend/RuntimeAttributeDefinition.scala
@@ -6,6 +6,7 @@ import cromwell.util.JsonFormatting.WomValueJsonFormatter
 import common.validation.ErrorOr.ErrorOr
 import wom.callable.Callable.InputDefinition
 import wom.expression.IoFunctionSet
+import wom.values.WomObject
 import wom.values.WomValue
 import wom.{RuntimeAttributes, WomExpressionException}
 
@@ -20,13 +21,57 @@ case class RuntimeAttributeDefinition(name: String, factoryDefault: Option[WomVa
 
 object RuntimeAttributeDefinition {
 
+  /**
+    * "Evaluate" means hydrating the runtime attributes with information from the inputs
+    * @param unevaluated WOM expressions that may or may not reference inputs
+    * @param wdlFunctions The set of IO for the current backend
+    * @param evaluatedInputs The inputs
+    * @param platform Optional, directs platform-based prioritization
+    * @return Evaluated
+    */
   def evaluateRuntimeAttributes(unevaluated: RuntimeAttributes,
                                 wdlFunctions: IoFunctionSet,
-                                evaluatedInputs: Map[InputDefinition, WomValue]
+                                evaluatedInputs: Map[InputDefinition, WomValue],
+                                platform: Option[Platform] = None
   ): ErrorOr[Map[String, WomValue]] = {
     import common.validation.ErrorOr._
     val inputsMap = evaluatedInputs map { case (x, y) => x.name -> y }
-    unevaluated.attributes.traverseValues(_.evaluateValue(inputsMap, wdlFunctions))
+    val evaluated = unevaluated.attributes.traverseValues(_.evaluateValue(inputsMap, wdlFunctions))
+
+    // Platform mapping must come after evaluation because we need to evaluate
+    // e.g. `gcp: userDefinedObject` to find out what its runtime value is.
+    // The type system informs us of this because a `WomExpression` in `unevaluated`
+    // cannot be safely read as a `WomObject` with a `values` map until evaluation
+    evaluated.map(e => applyPlatform(e, platform))
+  }
+
+  def applyPlatform(attributes: Map[String, WomValue], maybePlatform: Option[Platform]): Map[String, WomValue] = {
+
+    def extractPlatformAttributes(platform: Platform): Map[String, WomValue] =
+      attributes.get(platform.runtimeKey) match {
+        case Some(obj: WomObject) =>
+          // WDL spec: "Use objects to avoid collisions"
+          // https://github.com/openwdl/wdl/blob/wdl-1.1/SPEC.md#conventions-and-best-practices
+          obj.values
+        case _ =>
+          // A malformed non-object override such as gcp: "banana" is ignored
+          Map.empty
+      }
+
+    val platformAttributes = maybePlatform match {
+      case Some(platform) =>
+        extractPlatformAttributes(platform)
+      case None =>
+        Map.empty
+    }
+
+    // We've scooped our desired platform, now delete "azure", "gcp", etc.
+    val originalAttributesWithoutPlatforms: Map[String, WomValue] =
+      attributes -- Platform.all.map(_.runtimeKey)
+
+    // With `++` keys from the RHS overwrite duplicates in LHS, which is what we want
+    // RHS `Map.empty` is a no-op
+    originalAttributesWithoutPlatforms ++ platformAttributes
   }
 
   def buildMapBasedLookup(evaluatedDeclarations: Map[InputDefinition, Try[WomValue]])(identifier: String): WomValue = {
diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index ab7cdf602b6..be486f977f4 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -155,3 +155,26 @@ object CommonBackendConfigurationAttributes {
 final case class AttemptedLookupResult(name: String, value: Try[WomValue]) {
   def toPair = name -> value
 }
+
+sealed trait Platform {
+  def runtimeKey: String
+}
+
+object Platform {
+  def all: Seq[Platform] = Seq(Gcp, Azure, Aws)
+
+  def apply(str: String): Option[Platform] =
+    all.find(_.runtimeKey == str)
+}
+
+object Gcp extends Platform {
+  override def runtimeKey: String = "gcp"
+}
+
+object Azure extends Platform {
+  override def runtimeKey: String = "azure"
+}
+
+object Aws extends Platform {
+  override def runtimeKey: String = "aws"
+}
diff --git a/centaur/src/it/scala/centaur/CentaurTestSuite.scala b/centaur/src/it/scala/centaur/CentaurTestSuite.scala
index 27cb3e0d01b..20f965ec453 100644
--- a/centaur/src/it/scala/centaur/CentaurTestSuite.scala
+++ b/centaur/src/it/scala/centaur/CentaurTestSuite.scala
@@ -24,6 +24,9 @@ object CentaurTestSuite extends StrictLogging {
     }
 
   val cromwellBackends = CentaurCromwellClient.backends.unsafeRunSync().supportedBackends.map(_.toLowerCase)
+  val defaultBackend = CentaurCromwellClient.backends.unsafeRunSync().defaultBackend.toLowerCase
+  logger.info(s"Cromwell under test configured with backends ${cromwellBackends.mkString(", ")}")
+  logger.info(s"Unless overridden by workflow options file, tests use default backend: $defaultBackend")
 
   def isWdlUpgradeTest(testCase: CentaurTestCase): Boolean = testCase.containsTag("wdl_upgrade")
 
diff --git a/centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_lifesciences.test b/centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_lifesciences.test
new file mode 100644
index 00000000000..7fcb3fb4c28
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_lifesciences.test
@@ -0,0 +1,17 @@
+name: biscayne_new_runtime_attributes_lifesciences
+testFormat: workflowsuccess
+tags: ["wdl_biscayne"]
+
+# Will run on a Cromwell that supports any one of these backends
+backendsMode: any
+backends: [Papi, Papiv2, GCPBatch]
+
+files {
+  workflow: wdl_biscayne/biscayne_new_runtime_attributes/biscayne_new_runtime_attributes.wdl
+}
+
+metadata {
+  "calls.runtime_attributes_wf.runtime_attributes_task.runtimeAttributes.docker": "rockylinux:9",
+  "calls.runtime_attributes_wf.runtime_attributes_task.runtimeAttributes.cpu": 4
+  "calls.runtime_attributes_wf.runtime_attributes_task.runtimeAttributes.memory": "6 GB"
+}
diff --git a/centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_local.test b/centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_local.test
new file mode 100644
index 00000000000..d25d0f7e59b
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_local.test
@@ -0,0 +1,16 @@
+name: biscayne_new_runtime_attributes_local
+testFormat: workflowsuccess
+tags: ["wdl_biscayne"]
+
+# This test should only run in the Local suite, on its default `Local` backend. Unfortunately the `Local` backend
+# leaks into other suites, so require an irrelevant `LocalNoDocker` backend that is only found in Local suite.
+backends: [Local, LocalNoDocker]
+
+files {
+  workflow: wdl_biscayne/biscayne_new_runtime_attributes/biscayne_new_runtime_attributes.wdl
+}
+
+# CPU, memory attributes not applicable for Local backend
+metadata {
+  "calls.runtime_attributes_wf.runtime_attributes_task.runtimeAttributes.docker": "ubuntu:latest",
+}
diff --git a/centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_tes.test b/centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_tes.test
new file mode 100644
index 00000000000..8ee9cf96050
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/biscayne_new_runtime_attributes_tes.test
@@ -0,0 +1,14 @@
+name: biscayne_new_runtime_attributes_tes
+testFormat: workflowsuccess
+tags: ["wdl_biscayne"]
+backends: [TES]
+
+files {
+  workflow: wdl_biscayne/biscayne_new_runtime_attributes/biscayne_new_runtime_attributes.wdl
+}
+
+metadata {
+  "calls.runtime_attributes_wf.runtime_attributes_task.runtimeAttributes.docker": "debian:latest",
+  "calls.runtime_attributes_wf.runtime_attributes_task.runtimeAttributes.cpu": 4
+  "calls.runtime_attributes_wf.runtime_attributes_task.runtimeAttributes.memory": "4 GB"
+}
diff --git a/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_runtime_attributes/biscayne_new_runtime_attributes.wdl b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_runtime_attributes/biscayne_new_runtime_attributes.wdl
new file mode 100644
index 00000000000..1174d5c02d6
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/wdl_biscayne/biscayne_new_runtime_attributes/biscayne_new_runtime_attributes.wdl
@@ -0,0 +1,48 @@
+version development-1.1
+
+workflow runtime_attributes_wf {
+  call runtime_attributes_task
+  output {
+    String out = runtime_attributes_task.out
+  }
+}
+
+task runtime_attributes_task {
+
+  command <<<
+    echo "Zardoz"
+  >>>
+
+  meta {
+    volatile: true
+  }
+
+  runtime {
+    # Meaningless keys are ignored
+    banana: object {
+        cpuPlatform: "Banana Lake"
+    }
+
+    gcp: object {
+        # Platform-specific keys take precedence
+        docker: "rockylinux:9",
+        memory: "6 GB"
+    }
+
+    azure: object {
+        memory: "4 GB",
+        docker: "debian:latest"
+    }
+
+    # Generic keys are ignored in favor of platform ones
+    docker: "ubuntu:latest"
+    memory: "8 GB"
+
+    # We still read generic keys that are not overridden
+    cpu: 4
+  }
+
+  output {
+    String out = read_string(stdout())
+  }
+}
diff --git a/centaur/src/main/scala/centaur/test/standard/CentaurTestCase.scala b/centaur/src/main/scala/centaur/test/standard/CentaurTestCase.scala
index f4ed8a57589..e462ea83c90 100644
--- a/centaur/src/main/scala/centaur/test/standard/CentaurTestCase.scala
+++ b/centaur/src/main/scala/centaur/test/standard/CentaurTestCase.scala
@@ -48,9 +48,15 @@ case class CentaurTestCase(workflow: Workflow,
 
   def isIgnored(supportedBackends: List[String]): Boolean = {
     val backendSupported = workflow.backends match {
-      case AllBackendsRequired(allBackends) => allBackends forall supportedBackends.contains
-      case AnyBackendRequired(anyBackend) => anyBackend exists supportedBackends.contains
-      case OnlyBackendsAllowed(onlyBackends) => supportedBackends forall onlyBackends.contains
+      case AllBackendsRequired(testBackends) =>
+        // Test will run on servers that support all of the test's backends (or more) (default)
+        testBackends forall supportedBackends.contains
+      case AnyBackendRequired(testBackends) =>
+        // Test will run on servers that support at least one of the test's backends (or more)
+        testBackends exists supportedBackends.contains
+      case OnlyBackendsAllowed(testBackends) =>
+        // Test will run on servers that only support backends the test specifies (or fewer)
+        supportedBackends forall testBackends.contains
     }
 
     testOptions.ignore || !backendSupported
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActor.scala
index b621c26ed4d..c39590ebf03 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/preparation/JobPreparationActor.scala
@@ -325,7 +325,8 @@ class JobPreparationActor(workflowDescriptor: EngineWorkflowDescriptor,
     val unevaluatedRuntimeAttributes = jobKey.call.callable.runtimeAttributes
     evaluateRuntimeAttributes(unevaluatedRuntimeAttributes,
                               expressionLanguageFunctions,
-                              inputEvaluation
+                              inputEvaluation,
+                              factory.platform
     ) map curriedAddDefaultsToAttributes
   }
 }
diff --git a/src/ci/resources/tes_application.conf b/src/ci/resources/tes_application.conf
index 29982575eab..c2880dd0400 100644
--- a/src/ci/resources/tes_application.conf
+++ b/src/ci/resources/tes_application.conf
@@ -37,6 +37,7 @@ backend {
         dockerRoot = "/cromwell-executions"
         # TES Endpoint for cromwell to use. Might look something like: "https://lz7388ada396994bb48ea5c87a02eed673689c82c2af423d03.servicebus.windows.net/something/tes/v1/tasks
         endpoint = "http://127.0.0.1:9000/v1/tasks"
+        platform = "azure"
         concurrent-job-limit = 1000
         # Identity to execute the workflow as. Might look something like: "pet-2676571657071603a9eab"
         workflow-execution-identity = ""
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
index 498bee626b1..81f1e0eb8f6 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchBackendLifecycleActorFactory.scala
@@ -33,10 +33,12 @@ package cromwell.backend.impl.aws
 
 import akka.actor.{ActorRef, Props}
 import cromwell.backend.{
+  Aws,
   BackendConfigurationDescriptor,
   BackendInitializationData,
   BackendWorkflowDescriptor,
-  JobExecutionMap
+  JobExecutionMap,
+  Platform
 }
 import cromwell.backend.standard.{
   StandardAsyncExecutionActor,
@@ -106,4 +108,6 @@ case class AwsBatchBackendLifecycleActorFactory(name: String, configurationDescr
 
   override def backendSingletonActorProps(serviceRegistryActor: ActorRef): Option[Props] =
     Option(AwsBatchSingletonActor.props(configuration.awsConfig.region, Option(configuration.awsAuth)))
+
+  override def platform: Option[Platform] = Option(Aws)
 }
diff --git a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala
index 456fd822e7b..14ffbf6af8d 100644
--- a/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala
+++ b/supportedBackends/google/batch/src/main/scala/cromwell/backend/google/batch/GcpBatchBackendLifecycleActorFactory.scala
@@ -18,7 +18,9 @@ import cromwell.backend.{
   BackendConfigurationDescriptor,
   BackendInitializationData,
   BackendWorkflowDescriptor,
-  JobExecutionMap
+  Gcp,
+  JobExecutionMap,
+  Platform
 }
 import cromwell.cloudsupport.gcp.GoogleConfiguration
 import cromwell.core.CallOutputs
@@ -97,6 +99,8 @@ class GcpBatchBackendLifecycleActorFactory(override val name: String,
       GcpBatchBackendSingletonActor.props(requestFactory, serviceRegistryActor = serviceRegistryActor)(requestHandler)
     )
   }
+
+  override def platform: Option[Platform] = Option(Gcp)
 }
 
 object GcpBatchBackendLifecycleActorFactory extends StrictLogging {
diff --git a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactory.scala b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactory.scala
index e993985f985..21bc2e7d2b6 100644
--- a/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactory.scala
+++ b/supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiBackendLifecycleActorFactory.scala
@@ -118,6 +118,8 @@ abstract class PipelinesApiBackendLifecycleActorFactory(
         List(dockerCredentials, googleCredentials).flatten
       case _ => List.empty[Any]
     }
+
+  override def platform: Option[Platform] = Option(Gcp)
 }
 
 object PipelinesApiBackendLifecycleActorFactory extends StrictLogging {
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendLifecycleActorFactory.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendLifecycleActorFactory.scala
index 9cb502ef952..6f3f05706a9 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendLifecycleActorFactory.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesBackendLifecycleActorFactory.scala
@@ -24,4 +24,6 @@ case class TesBackendLifecycleActorFactory(name: String, configurationDescriptor
                                                  restarting: Boolean
   ): StandardInitializationActorParams =
     TesInitializationActorParams(workflowDescriptor, calls, tesConfiguration, serviceRegistryActor)
+
+  override def platform: Option[Platform] = tesConfiguration.platform
 }
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
index b90b406569a..7fabac83685 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesConfiguration.scala
@@ -1,7 +1,7 @@
 package cromwell.backend.impl.tes
 
 import com.typesafe.config.Config
-import cromwell.backend.BackendConfigurationDescriptor
+import cromwell.backend.{BackendConfigurationDescriptor, Platform}
 import cromwell.core.retry.SimpleExponentialBackoff
 import net.ceedubs.ficus.Ficus._
 
@@ -12,6 +12,8 @@ class TesConfiguration(val configurationDescriptor: BackendConfigurationDescript
 
   val endpointURL = configurationDescriptor.backendConfig.getString("endpoint")
   val runtimeConfig = configurationDescriptor.backendRuntimeAttributesConfig
+  val platform: Option[Platform] =
+    configurationDescriptor.backendConfig.as[Option[String]]("platform").flatMap(Platform(_))
   val useBackendParameters =
     configurationDescriptor.backendConfig
       .as[Option[Boolean]](TesConfiguration.useBackendParametersKey)

From 9d71ae214d8cf4cd0a5a8d0bf5bcaeddd7653a13 Mon Sep 17 00:00:00 2001
From: Trevyn Langsford <tlangs@broadinstitute.org>
Date: Tue, 12 Mar 2024 12:40:49 -0400
Subject: [PATCH 291/326] ID-347 Remove Martha References (#7384)

---
 .../cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala     | 3 +--
 docs/filesystems/Filesystems.md                                | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
index ff614646b13..2c19cdabefe 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
@@ -11,8 +11,7 @@ class DrsCloudNioFileSystemProvider(rootConfig: Config,
                                     drsReadInterpreter: DrsReadInterpreter
 ) extends CloudNioFileSystemProvider {
 
-  lazy val drsResolverConfig =
-    if (rootConfig.hasPath("resolver")) rootConfig.getConfig("resolver") else rootConfig.getConfig("martha")
+  lazy val drsResolverConfig = rootConfig.getConfig("resolver")
   lazy val drsConfig: DrsConfig = DrsConfig.fromConfig(drsResolverConfig)
 
   lazy val drsPathResolver: EngineDrsPathResolver =
diff --git a/docs/filesystems/Filesystems.md b/docs/filesystems/Filesystems.md
index 8ca03825c6e..ecde17f89a9 100644
--- a/docs/filesystems/Filesystems.md
+++ b/docs/filesystems/Filesystems.md
@@ -19,7 +19,7 @@ filesystems {
         class = "cromwell.filesystems.drs.DrsFileSystemConfig"
         config {
           resolver {
-            url = "https://martha-url-here or https://drshub-url-here"
+            url = https://drshub-url-here"
             # The number of times to retry failures connecting or HTTP 429 or HTTP 5XX responses, default 3.
             num-retries = 3
             # How long to wait between retrying HTTP 429 or HTTP 5XX responses, default 10 seconds.

From 1049c4e376ce3a5415cf4a0aca540fbe571a745c Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 12 Mar 2024 17:01:16 -0400
Subject: [PATCH 292/326] WX-1461 Remove `womtool upgrade` command (#7382)

---
 CHANGELOG.md                                  |   4 +
 .../centaur/AbstractCentaurTestCaseSpec.scala |  53 ---
 .../it/scala/centaur/CentaurTestSuite.scala   |   2 -
 .../centaur/WdlUpgradeTestCaseSpec.scala      |  15 -
 .../composedenginefunctions.test              |   1 -
 .../conditionals.ifs_in_scatters.test         |   2 +-
 .../conditionals.nested_lookups.test          |   2 +-
 .../conditionals.scatters_in_ifs.test         |   2 +-
 .../conditionals.simple_if.test               |   2 +-
 ...nditionals.simple_if_workflow_outputs.test |   2 +-
 .../standardTestCases/declarations.test       |   1 -
 .../declarations_as_nodes.test                |   1 -
 .../resources/standardTestCases/hello.test    |   1 -
 .../standardTestCases/object_access.test      |   1 -
 .../standardTestCases/scatterchain.test       |   1 -
 .../standardTestCases/scattergather.test      |   1 -
 .../standardTestCases/short_circuit.test      |   2 +-
 .../resources/standardTestCases/square.test   |   1 -
 .../string_interpolation.test                 |   1 -
 .../sub_workflow_hello_world.test             |   2 +-
 .../sub_workflow_var_refs.test                |   2 +-
 .../standardTestCases/valid_labels.test       |   2 +-
 .../standardTestCases/write_lines.test        |   2 -
 docs/developers/Centaur.md                    |   5 +-
 src/ci/bin/test.inc.sh                        |   1 -
 src/ci/bin/testCentaurWdlUpgradeLocal.sh      |  19 -
 .../model/draft3/elements/CallElement.scala   |   7 +-
 .../draft3/elements/DeclarationElement.scala  |  12 +-
 .../wdl/model/draft3/elements/IfElement.scala |   4 +-
 .../draft3/elements/ScatterElement.scala      |   2 +
 .../wdlom2wdl/WdlomToWdlFileSpec.scala        |  63 ---
 .../expression/values/LookupEvaluators.scala  |   2 +-
 .../base/linking/graph/LinkedGraphMaker.scala |   9 +-
 .../base/wdlom2wdl/WdlWriterImpl.scala        | 271 ------------
 .../CommandPartElementToWomCommandPart.scala  |   5 +-
 .../InputDeclarationElementToGraphNode.scala  |   2 +-
 .../WorkflowGraphElementToGraphNode.scala     |   2 +-
 .../src/main/scala/womtool/WomtoolMain.scala  |  63 +--
 .../PartialWomtoolCommandLineArguments.scala  |   2 -
 .../cmdline/WomtoolCommandLineParser.scala    |   6 -
 .../scala/womtool/wom2wdlom/WomToWdlom.scala  | 392 ------------------
 .../biscayne/invalid/after_circle/error.txt   |   4 +-
 .../wdl_draft3/invalid/cycle/error.txt        |   6 +-
 .../test/scala/womtool/WomtoolMainSpec.scala  |   2 +-
 44 files changed, 50 insertions(+), 932 deletions(-)
 delete mode 100644 centaur/src/it/scala/centaur/WdlUpgradeTestCaseSpec.scala
 delete mode 100755 src/ci/bin/testCentaurWdlUpgradeLocal.sh
 delete mode 100644 wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wdl/WdlomToWdlFileSpec.scala
 delete mode 100644 womtool/src/main/scala/womtool/wom2wdlom/WomToWdlom.scala

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9f4d9c30560..aecc6361de4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 ## 87 Release Notes
 
+### `upgrade` command removed from Womtool
+
+Womtool previously supported a `womtool upgrade` command for upgrading draft-2 WDLs to 1.0. With WDL 1.1 soon to become the latest supported version, this functionality is retiring.
+
 ### Replacement of `gsutil` with `gcloud storage`
 
 In this release, all **localization** functionality on the GCP backend migrates to use the more modern and performant `gcloud storage`. With sufficiently powerful worker VMs, Cromwell can now localize at up to 1200 MB/s [0][1][2].
diff --git a/centaur/src/it/scala/centaur/AbstractCentaurTestCaseSpec.scala b/centaur/src/it/scala/centaur/AbstractCentaurTestCaseSpec.scala
index 5a6606bce68..f90fb21e537 100644
--- a/centaur/src/it/scala/centaur/AbstractCentaurTestCaseSpec.scala
+++ b/centaur/src/it/scala/centaur/AbstractCentaurTestCaseSpec.scala
@@ -76,59 +76,6 @@ abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String],
     runOrDont(testCase, tags, isIgnored, retries, runTestAndDeleteZippedImports())
   }
 
-  def executeWdlUpgradeTest(testCase: CentaurTestCase): Unit =
-    executeStandardTest(wdlUpgradeTestWdl(testCase))
-
-  private def wdlUpgradeTestWdl(testCase: CentaurTestCase): CentaurTestCase = {
-    import better.files.File
-    import womtool.WomtoolMain
-
-    // The suffix matters because WomGraphMaker.getBundle() uses it to choose the language factory
-    val rootWorkflowFile = File.newTemporaryFile(suffix = ".wdl").append(testCase.workflow.data.workflowContent.get)
-    val workingDir = File.newTemporaryDirectory()
-    val upgradedImportsDir = File.newTemporaryDirectory()
-    val rootWorkflowFilepath = workingDir / rootWorkflowFile.name
-
-    // Un-upgraded imports go into the working directory
-    testCase.workflow.data.zippedImports match {
-      case Some(importsZip: File) =>
-        importsZip.unzipTo(workingDir)
-      case None => ()
-    }
-
-    // Upgrade the imports and copy to main working dir (precludes transitive imports; no recursion yet)
-    workingDir.list.toList.map { file: File =>
-      val upgradedWdl = WomtoolMain.upgrade(file.pathAsString).stdout.get
-      upgradedImportsDir.createChild(file.name).append(upgradedWdl)
-    }
-
-    // Copy to working directory after we operate on the imports that are in it
-    rootWorkflowFile.copyTo(rootWorkflowFilepath)
-
-    val upgradeResult = WomtoolMain.upgrade(rootWorkflowFilepath.pathAsString)
-
-    upgradeResult.stderr match {
-      case Some(stderr) => println(stderr)
-      case _ => ()
-    }
-
-    val newCase = testCase.copy(
-      workflow = testCase.workflow.copy(
-        testName = testCase.workflow.testName + " (draft-2 to 1.0 upgrade)",
-        data = testCase.workflow.data.copy(
-          workflowContent = Option(upgradeResult.stdout.get), // this '.get' catches an error if upgrade fails
-          zippedImports = Option(upgradedImportsDir.zip())
-        )
-      )
-    )(cromwellTracker) // An empty zip appears to be completely harmless, so no special handling
-
-    rootWorkflowFile.delete(swallowIOExceptions = true)
-    upgradedImportsDir.delete(swallowIOExceptions = true)
-    workingDir.delete(swallowIOExceptions = true)
-
-    newCase
-  }
-
   private def runOrDont(testCase: CentaurTestCase,
                         tags: List[Tag],
                         ignore: Boolean,
diff --git a/centaur/src/it/scala/centaur/CentaurTestSuite.scala b/centaur/src/it/scala/centaur/CentaurTestSuite.scala
index 20f965ec453..c72d774c4e4 100644
--- a/centaur/src/it/scala/centaur/CentaurTestSuite.scala
+++ b/centaur/src/it/scala/centaur/CentaurTestSuite.scala
@@ -28,8 +28,6 @@ object CentaurTestSuite extends StrictLogging {
   logger.info(s"Cromwell under test configured with backends ${cromwellBackends.mkString(", ")}")
   logger.info(s"Unless overridden by workflow options file, tests use default backend: $defaultBackend")
 
-  def isWdlUpgradeTest(testCase: CentaurTestCase): Boolean = testCase.containsTag("wdl_upgrade")
-
   def isEngineUpgradeTest(testCase: CentaurTestCase): Boolean = testCase.containsTag("engine_upgrade")
 
   def isPapiUpgradeTest(testCase: CentaurTestCase): Boolean = testCase.containsTag("papi_upgrade")
diff --git a/centaur/src/it/scala/centaur/WdlUpgradeTestCaseSpec.scala b/centaur/src/it/scala/centaur/WdlUpgradeTestCaseSpec.scala
deleted file mode 100644
index 93f4457d050..00000000000
--- a/centaur/src/it/scala/centaur/WdlUpgradeTestCaseSpec.scala
+++ /dev/null
@@ -1,15 +0,0 @@
-package centaur
-
-import org.scalatest.{DoNotDiscover, ParallelTestExecution}
-
-@DoNotDiscover
-class WdlUpgradeTestCaseSpec(cromwellBackends: List[String])
-    extends AbstractCentaurTestCaseSpec(cromwellBackends)
-    with ParallelTestExecution
-    with CentaurTestSuiteShutdown {
-
-  def this() = this(CentaurTestSuite.cromwellBackends)
-
-  // The WDL version upgrade tests are just regular draft-2 test cases tagged for re-use in testing the upgrade script
-  allTestCases.filter(CentaurTestSuite.isWdlUpgradeTest) foreach executeWdlUpgradeTest
-}
diff --git a/centaur/src/main/resources/standardTestCases/composedenginefunctions.test b/centaur/src/main/resources/standardTestCases/composedenginefunctions.test
index 68628483740..d51f31c9929 100644
--- a/centaur/src/main/resources/standardTestCases/composedenginefunctions.test
+++ b/centaur/src/main/resources/standardTestCases/composedenginefunctions.test
@@ -1,6 +1,5 @@
 name: composedenginefunctions
 testFormat: workflowsuccess
-tags: ["wdl_upgrade"]
 
 files {
   workflow: composedenginefunctions/composedenginefunctions.wdl
diff --git a/centaur/src/main/resources/standardTestCases/conditionals.ifs_in_scatters.test b/centaur/src/main/resources/standardTestCases/conditionals.ifs_in_scatters.test
index 2bd93388199..9d20530291a 100644
--- a/centaur/src/main/resources/standardTestCases/conditionals.ifs_in_scatters.test
+++ b/centaur/src/main/resources/standardTestCases/conditionals.ifs_in_scatters.test
@@ -1,6 +1,6 @@
 name: ifs_in_scatters
 testFormat: workflowsuccess
-tags: [ conditionals, "wdl_upgrade" ]
+tags: [ conditionals ]
 
 files {
   workflow: conditionals_tests/ifs_in_scatters/ifs_in_scatters.wdl
diff --git a/centaur/src/main/resources/standardTestCases/conditionals.nested_lookups.test b/centaur/src/main/resources/standardTestCases/conditionals.nested_lookups.test
index 6f5c0fa2c93..cf4ca22c876 100644
--- a/centaur/src/main/resources/standardTestCases/conditionals.nested_lookups.test
+++ b/centaur/src/main/resources/standardTestCases/conditionals.nested_lookups.test
@@ -1,6 +1,6 @@
 name: nested_lookups
 testFormat: workflowsuccess
-tags: [ conditionals, "wdl_upgrade" ]
+tags: [ conditionals ]
 
 files {
   workflow: conditionals_tests/nested_lookups/nested_lookups.wdl
diff --git a/centaur/src/main/resources/standardTestCases/conditionals.scatters_in_ifs.test b/centaur/src/main/resources/standardTestCases/conditionals.scatters_in_ifs.test
index 8d9cc2193b7..f23865eae67 100644
--- a/centaur/src/main/resources/standardTestCases/conditionals.scatters_in_ifs.test
+++ b/centaur/src/main/resources/standardTestCases/conditionals.scatters_in_ifs.test
@@ -1,6 +1,6 @@
 name: scatters_in_ifs
 testFormat: workflowsuccess
-tags: [ conditionals, "wdl_upgrade" ]
+tags: [ conditionals ]
 
 files {
   workflow: conditionals_tests/scatters_in_ifs/scatters_in_ifs.wdl
diff --git a/centaur/src/main/resources/standardTestCases/conditionals.simple_if.test b/centaur/src/main/resources/standardTestCases/conditionals.simple_if.test
index 82794b863d5..50a1c811892 100644
--- a/centaur/src/main/resources/standardTestCases/conditionals.simple_if.test
+++ b/centaur/src/main/resources/standardTestCases/conditionals.simple_if.test
@@ -1,6 +1,6 @@
 name: simple_if
 testFormat: workflowsuccess
-tags: [ conditionals, "wdl_upgrade" ]
+tags: [ conditionals ]
 
 files {
   workflow: conditionals_tests/simple_if/simple_if.wdl
diff --git a/centaur/src/main/resources/standardTestCases/conditionals.simple_if_workflow_outputs.test b/centaur/src/main/resources/standardTestCases/conditionals.simple_if_workflow_outputs.test
index 3aed74d756b..ede32957e47 100644
--- a/centaur/src/main/resources/standardTestCases/conditionals.simple_if_workflow_outputs.test
+++ b/centaur/src/main/resources/standardTestCases/conditionals.simple_if_workflow_outputs.test
@@ -1,6 +1,6 @@
 name: simple_if_workflow_outputs
 testFormat: workflowsuccess
-tags: [ conditionals, "wdl_upgrade" ]
+tags: [ conditionals ]
 
 files {
   workflow: conditionals_tests/simple_if_workflow_outputs/simple_if_workflow_outputs.wdl
diff --git a/centaur/src/main/resources/standardTestCases/declarations.test b/centaur/src/main/resources/standardTestCases/declarations.test
index 53766678b26..bae479145f0 100644
--- a/centaur/src/main/resources/standardTestCases/declarations.test
+++ b/centaur/src/main/resources/standardTestCases/declarations.test
@@ -2,7 +2,6 @@
 
 name: declarations
 testFormat: workflowsuccess
-tags: ["wdl_upgrade"]
 
 files {
   workflow: declarations/declarations.wdl
diff --git a/centaur/src/main/resources/standardTestCases/declarations_as_nodes.test b/centaur/src/main/resources/standardTestCases/declarations_as_nodes.test
index d18f39677f6..ff1f4416a24 100644
--- a/centaur/src/main/resources/standardTestCases/declarations_as_nodes.test
+++ b/centaur/src/main/resources/standardTestCases/declarations_as_nodes.test
@@ -1,6 +1,5 @@
 name: declarations_as_nodes
 testFormat: workflowsuccess
-tags: ["wdl_upgrade"]
 
 files {
   workflow: declarations_as_nodes/declarations_as_nodes.wdl
diff --git a/centaur/src/main/resources/standardTestCases/hello.test b/centaur/src/main/resources/standardTestCases/hello.test
index 33a49bd4071..2f7fd67087f 100644
--- a/centaur/src/main/resources/standardTestCases/hello.test
+++ b/centaur/src/main/resources/standardTestCases/hello.test
@@ -1,6 +1,5 @@
 name: hello
 testFormat: workflowsuccess
-tags: ["wdl_upgrade"]
 
 files {
   workflow: hello/hello.wdl
diff --git a/centaur/src/main/resources/standardTestCases/object_access.test b/centaur/src/main/resources/standardTestCases/object_access.test
index 1e824f6e78f..84d76d5a893 100644
--- a/centaur/src/main/resources/standardTestCases/object_access.test
+++ b/centaur/src/main/resources/standardTestCases/object_access.test
@@ -1,6 +1,5 @@
 name: object_access
 testFormat: workflowsuccess
-tags: ["wdl_upgrade"]
 
 files {
   workflow: object_access/object_access.wdl
diff --git a/centaur/src/main/resources/standardTestCases/scatterchain.test b/centaur/src/main/resources/standardTestCases/scatterchain.test
index 26fdb95b27b..c1b02be7abe 100644
--- a/centaur/src/main/resources/standardTestCases/scatterchain.test
+++ b/centaur/src/main/resources/standardTestCases/scatterchain.test
@@ -1,6 +1,5 @@
 name: scatterchain
 testFormat: workflowsuccess
-tags: ["wdl_upgrade"]
 
 files {
   workflow: scatter_chain/scatter_chain.wdl
diff --git a/centaur/src/main/resources/standardTestCases/scattergather.test b/centaur/src/main/resources/standardTestCases/scattergather.test
index fad78c0a08c..425be6fd3c4 100644
--- a/centaur/src/main/resources/standardTestCases/scattergather.test
+++ b/centaur/src/main/resources/standardTestCases/scattergather.test
@@ -1,6 +1,5 @@
 name: scattergather
 testFormat: workflowsuccess
-tags: ["wdl_upgrade"]
 
 files {
   workflow: scattergather/scattergather.wdl
diff --git a/centaur/src/main/resources/standardTestCases/short_circuit.test b/centaur/src/main/resources/standardTestCases/short_circuit.test
index a0727dc949f..a961f39071b 100644
--- a/centaur/src/main/resources/standardTestCases/short_circuit.test
+++ b/centaur/src/main/resources/standardTestCases/short_circuit.test
@@ -2,7 +2,7 @@ name: short_circuit
 testFormat: workflowsuccess
 
 backends: [Local]
-tags: [localdockertest, "wdl_upgrade"]
+tags: [localdockertest]
 
 
 files {
diff --git a/centaur/src/main/resources/standardTestCases/square.test b/centaur/src/main/resources/standardTestCases/square.test
index ef0ac9a9ef8..db4e5851ead 100644
--- a/centaur/src/main/resources/standardTestCases/square.test
+++ b/centaur/src/main/resources/standardTestCases/square.test
@@ -1,6 +1,5 @@
 name: square
 testFormat: workflowsuccess
-tags: [ "wdl_upgrade" ]
 
 files {
   workflow: square/square.wdl
diff --git a/centaur/src/main/resources/standardTestCases/string_interpolation.test b/centaur/src/main/resources/standardTestCases/string_interpolation.test
index 7e7e894f9fa..04736e59ea4 100644
--- a/centaur/src/main/resources/standardTestCases/string_interpolation.test
+++ b/centaur/src/main/resources/standardTestCases/string_interpolation.test
@@ -1,6 +1,5 @@
 name: string_interpolation
 testFormat: workflowsuccess
-tags: ["wdl_upgrade"]
 
 files {
   workflow: string_interpolation/string_interpolation.wdl
diff --git a/centaur/src/main/resources/standardTestCases/sub_workflow_hello_world.test b/centaur/src/main/resources/standardTestCases/sub_workflow_hello_world.test
index 4b216940cb2..cc18f753e42 100644
--- a/centaur/src/main/resources/standardTestCases/sub_workflow_hello_world.test
+++ b/centaur/src/main/resources/standardTestCases/sub_workflow_hello_world.test
@@ -1,6 +1,6 @@
 name: sub_workflow_hello_world
 testFormat: workflowsuccess
-tags: [subworkflow, "wdl_upgrade"]
+tags: [subworkflow]
 
 files {
   workflow: sub_workflow_hello_world/sub_workflow_hello_world.wdl
diff --git a/centaur/src/main/resources/standardTestCases/sub_workflow_var_refs.test b/centaur/src/main/resources/standardTestCases/sub_workflow_var_refs.test
index 390c089359b..deca93aa195 100644
--- a/centaur/src/main/resources/standardTestCases/sub_workflow_var_refs.test
+++ b/centaur/src/main/resources/standardTestCases/sub_workflow_var_refs.test
@@ -1,6 +1,6 @@
 name: sub_workflow_var_refs
 testFormat: workflowsuccess
-tags: [subworkflow, "wdl_upgrade"]
+tags: [subworkflow]
 
 files {
   workflow: sub_workflow_var_refs/sub_workflow_var_refs.wdl
diff --git a/centaur/src/main/resources/standardTestCases/valid_labels.test b/centaur/src/main/resources/standardTestCases/valid_labels.test
index 1ab748f8a86..6f7f4e7ceec 100644
--- a/centaur/src/main/resources/standardTestCases/valid_labels.test
+++ b/centaur/src/main/resources/standardTestCases/valid_labels.test
@@ -1,6 +1,6 @@
 name: valid_labels
 testFormat: workflowsuccess
-tags: [ labels, "wdl_upgrade" ]
+tags: [ labels ]
 
 files {
   workflow: hello/hello.wdl
diff --git a/centaur/src/main/resources/standardTestCases/write_lines.test b/centaur/src/main/resources/standardTestCases/write_lines.test
index 977459a50c7..fa0c6edd973 100644
--- a/centaur/src/main/resources/standardTestCases/write_lines.test
+++ b/centaur/src/main/resources/standardTestCases/write_lines.test
@@ -1,6 +1,5 @@
 name: write_lines
 testFormat: workflowsuccess
-tags: ["wdl_upgrade"]
 
 files {
   workflow: write_lines/write_lines.wdl
@@ -13,4 +12,3 @@ metadata {
   "calls.write_lines.f2a.executionStatus": Done
   "outputs.write_lines.a2f_second.x": "a\nb\nc\nd"
 }
-
diff --git a/docs/developers/Centaur.md b/docs/developers/Centaur.md
index 35d2e350e7d..bbbb011ba32 100644
--- a/docs/developers/Centaur.md
+++ b/docs/developers/Centaur.md
@@ -133,7 +133,6 @@ our tests into groups depending on which configuration files they require. Below
 | PAPI Upgrade                  | `PapiUpgradeTestCaseSpec`   | `papiUpgradeTestCases`              |
 | PAPI Upgrade<br>New Workflows | `CentaurTestSuite`          | `papiUpgradeNewWorkflowsTestCases`  |
 | Azure Blob                    | `CentaurTestSuite      `    | `azureBlobTestCases`                |
-| WDL Upgrade                   | `WdlUpgradeTestCaseSpec`    | `standardTestCases`****             |
 | (other)                       | `CentaurTestSuite`          | `standardTestCases`                 |
 
 <small>
@@ -143,9 +142,7 @@ or `papi_v2beta_centaur_application.conf`
 \*\* Cromwell Config overrides
   ([47 link](https://github.com/broadinstitute/cromwell/blob/47/src/ci/bin/test.inc.sh#L213-L221))  
 \*\*\* Test Directory overrides
-  ([47 link](https://github.com/broadinstitute/cromwell/blob/47/src/ci/bin/test.inc.sh#L440-L449))  
-\*\*\*\* Test Directory only tests tagged with `wdl_upgrade`
-  ([47 link](https://github.com/broadinstitute/cromwell/blob/47/centaur/src/main/resources/standardTestCases/write_lines.test#L3))  
+  ([47 link](https://github.com/broadinstitute/cromwell/blob/47/src/ci/bin/test.inc.sh#L440-L449))
 </small>
 
 - Engine Upgrade: Retrieves the [Cromwell Version](https://github.com/broadinstitute/cromwell/blob/47/project/Version.scala#L8) then retrieves the previous jar/docker-image from DockerHub. Centaur starts with the prior version, then restarts with the compiled source code.
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 71577ce1e4c..7aebd3698fb 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -169,7 +169,6 @@ cromwell::private::create_build_variables() {
     backend_type="${CROMWELL_BUILD_TYPE}"
     backend_type="${backend_type#centaurEngineUpgrade}"
     backend_type="${backend_type#centaurPapiUpgrade}"
-    backend_type="${backend_type#centaurWdlUpgrade}"
     backend_type="${backend_type#centaurHoricromtal}"
     backend_type="${backend_type#centaur}"
     backend_type="$(echo "${backend_type}" | sed 's/\([A-Z]\)/_\1/g' | tr '[:upper:]' '[:lower:]' | cut -c 2-)"
diff --git a/src/ci/bin/testCentaurWdlUpgradeLocal.sh b/src/ci/bin/testCentaurWdlUpgradeLocal.sh
deleted file mode 100755
index 31b56ee77d3..00000000000
--- a/src/ci/bin/testCentaurWdlUpgradeLocal.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_centaur_environment
-
-cromwell::build::assemble_jars
-
-# WdlUpgradeTestCaseSpec takes a selection of ordinary draft-2 test cases (tagged as "upgrade"), runs
-# them through the draft-2 to 1.0 upgrade script in Womtool, and runs them against local backend.
-cromwell::build::run_centaur \
-    -s "centaur.WdlUpgradeTestCaseSpec"
-
-cromwell::build::generate_code_coverage
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CallElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CallElement.scala
index 1d4a3e428ca..dbc3685e60d 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CallElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/CallElement.scala
@@ -7,4 +7,9 @@ final case class CallElement(callableReference: String,
                              body: Option[CallBodyElement],
                              override val sourceLocation: Option[SourceFileLocation]
 ) extends LanguageElement
-    with WorkflowGraphElement
+    with WorkflowGraphElement {
+  override def toString: String =
+    s"""Call "$callableReference${alias.map(alias => s" as $alias").getOrElse("")}${afters
+        .map(after => s" after $after")
+        .mkString}""""
+}
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/DeclarationElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/DeclarationElement.scala
index ef85d3973bf..ea05781a59c 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/DeclarationElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/DeclarationElement.scala
@@ -12,7 +12,9 @@ final case class IntermediateValueDeclarationElement(typeElement: TypeElement,
                                                      name: String,
                                                      expression: ExpressionElement
 ) extends WorkflowGraphElement
-    with TaskSectionElement
+    with TaskSectionElement {
+  override def toString: String = s"""Declaration "$name" ($typeElement)"""
+}
 
 object IntermediateValueDeclarationElement {
   def fromContent(content: DeclarationContent): IntermediateValueDeclarationElement =
@@ -24,7 +26,9 @@ object IntermediateValueDeclarationElement {
   */
 final case class OutputDeclarationElement(typeElement: TypeElement, name: String, expression: ExpressionElement)
     extends LanguageElement
-    with WorkflowGraphElement
+    with WorkflowGraphElement {
+  override def toString: String = s"""Output "$name" ($typeElement)"""
+}
 
 object OutputDeclarationElement {
   def fromContent(content: DeclarationContent): OutputDeclarationElement =
@@ -36,7 +40,9 @@ object OutputDeclarationElement {
   */
 final case class InputDeclarationElement(typeElement: TypeElement, name: String, expression: Option[ExpressionElement])
     extends LanguageElement
-    with WorkflowGraphElement
+    with WorkflowGraphElement {
+  override def toString: String = s"""Input "$name" ($typeElement)"""
+}
 
 object DeclarationElement {
   /* Custom unapply so that elsewhere we can do things like this, and otherwise treat all declarations the same:
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/IfElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/IfElement.scala
index 24d851abead..967f220bedc 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/IfElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/IfElement.scala
@@ -1,4 +1,6 @@
 package wdl.model.draft3.elements
 
 final case class IfElement(conditionExpression: ExpressionElement, graphElements: Seq[WorkflowGraphElement])
-    extends WorkflowGraphElement
+    extends WorkflowGraphElement {
+  override def toString: String = s"""Condition "$conditionExpression""""
+}
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ScatterElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ScatterElement.scala
index d9374e4aea9..8e5d77ead52 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ScatterElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ScatterElement.scala
@@ -23,4 +23,6 @@ final case class ScatterElement(scatterName: String,
   // Shorthand to only include certain members for hashing purposes
   // https://stackoverflow.com/a/31915429/818054
   override def hashCode(): Int = (scatterExpression, scatterVariableName, graphElements).##
+
+  override def toString: String = s"""Scatter "$scatterName" ($scatterExpression)"""
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wdl/WdlomToWdlFileSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wdl/WdlomToWdlFileSpec.scala
deleted file mode 100644
index 88cef1394db..00000000000
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/wdlom2wdl/WdlomToWdlFileSpec.scala
+++ /dev/null
@@ -1,63 +0,0 @@
-package wdl.draft3.transforms.wdlom2wdl
-
-import cats.instances.either._
-import better.files.File
-import common.Checked
-import common.assertion.CromwellTimeoutSpec
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-import wdl.draft3.transforms.ast2wdlom._
-import wdl.draft3.transforms.parsing.{fileToAst, stringToAst, FileStringParserInput}
-import wdl.model.draft3.elements._
-import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
-import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.fileElementWriter
-
-class WdlomToWdlFileSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
-
-  val testDirectory = File("wdl/transforms/draft3/src/test/cases")
-
-  val testFiles = testDirectory.list
-
-  assert(testFiles.nonEmpty)
-
-  private def stripLocationFromGraphElement(ge: WorkflowGraphElement): WorkflowGraphElement =
-    ge match {
-      case se: ScatterElement => se.copy(sourceLocation = None)
-      case ce: CallElement => ce.copy(sourceLocation = None)
-      case _ => ge
-    }
-
-  private def stripLocations(wf: WorkflowDefinitionElement): WorkflowDefinitionElement =
-    wf.copy(graphElements = wf.graphElements.map(stripLocationFromGraphElement))
-
-  // Remove the source file information, where it exists.
-  //
-  // Re-printing does not preserve line numbers at the moment.
-  private def stripSourceLocations(fe: FileElement): FileElement =
-    FileElement(
-      fe.imports,
-      fe.structs,
-      fe.workflows.map { case wf =>
-        val wf2 = stripLocations(wf)
-        wf2.copy(sourceLocation = None)
-      }.toSeq,
-      fe.tasks.map { case task => task.copy(sourceLocation = None) }.toSeq
-    )
-
-  testFiles.foreach { file =>
-    it should s"write a file that re-evaluates to the same case classes for ${file.name}" in {
-
-      val model: Checked[FileElement] = (fileToAst andThen wrapAst andThen astToFileElement).run(file)
-      model match {
-        case Right(wdlModel) =>
-          val newModel = (stringToAst andThen wrapAst andThen astToFileElement).run(
-            FileStringParserInput(wdlModel.toWdlV1, file.name)
-          )
-
-          // Scala case class deep equality is so nice here
-          newModel.map(stripSourceLocations) shouldEqual model.map(stripSourceLocations)
-        case Left(_) => fail("Could not load original")
-      }
-    }
-  }
-}
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LookupEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LookupEvaluators.scala
index 216673417cf..1cc006fa261 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LookupEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LookupEvaluators.scala
@@ -12,7 +12,7 @@ import wom.expression.IoFunctionSet
 import wom.types._
 import wom.values._
 import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
-import wdl.transforms.base.wdlom2wdl.WdlWriterImpl._
+import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.indexAccessWriter
 
 object LookupEvaluators {
 
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/LinkedGraphMaker.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/LinkedGraphMaker.scala
index 01573c30737..e99b8799db5 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/LinkedGraphMaker.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/graph/LinkedGraphMaker.scala
@@ -13,8 +13,6 @@ import wom.callable.Callable
 import wom.types.WomType
 import scalax.collection.Graph
 import scalax.collection.GraphEdge.DiEdge
-import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
-import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.graphElementWriter
 
 object LinkedGraphMaker {
   def make(nodes: Set[WorkflowGraphElement],
@@ -43,9 +41,6 @@ object LinkedGraphMaker {
 
   def getOrdering(linkedGraph: LinkedGraph): ErrorOr[List[WorkflowGraphElement]] = {
 
-    def nodeName(workflowGraphElement: WorkflowGraphElement): String =
-      workflowGraphElement.toWdlV1.linesIterator.toList.headOption.getOrElse("Unnamed Element").replace("\"", "")
-
     // Find the topological order in which we must create the graph nodes:
     val edges = linkedGraph.edges map { case LinkedGraphEdge(from, to) => DiEdge(from, to) }
 
@@ -63,7 +58,7 @@ object LinkedGraphMaker {
             // we want to start the cycle with the edge "a -> b"
             val edgeDict: Map[String, String] =
               cycle.value.edges.map { case graph.EdgeT(from, to) =>
-                nodeName(from) -> nodeName(to)
+                from.toString -> to.toString
               }.toMap
             val startPoint = edgeDict.keys.toVector.sorted.head
             var cursor = startPoint
@@ -83,7 +78,7 @@ object LinkedGraphMaker {
 
           case _ =>
             val edgeStrings = linkedGraph.edges map { case LinkedGraphEdge(from, to) =>
-              s""""${nodeName(from)}" -> "${nodeName(to)}""""
+              s""""${from.toString}" -> "${to.toString}""""
             }
             // sort the edges for determinism
             val edges = edgeStrings.toVector.sorted
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
index a09e94534c4..d4a0b043b17 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
@@ -1,13 +1,8 @@
 package wdl.transforms.base.wdlom2wdl
 
-import wdl.model.draft3.elements.CommandPartElement.{PlaceholderCommandPartElement, StringCommandPartElement}
 import wdl.model.draft3.elements.ExpressionElement._
 import wdl.model.draft3.elements._
-import wom.callable.MetaValueElement
-import wom.callable.MetaValueElement._
 import wom.types._
-import WdlWriter._
-import common.collections.EnhancedCollections._
 import org.apache.commons.text.StringEscapeUtils
 
 object WdlWriterImpl {
@@ -15,12 +10,6 @@ object WdlWriterImpl {
   // Auto-generated by simulacrum
   import WdlWriter.ops._
 
-  implicit val ifWriter: WdlWriter[IfElement] = new WdlWriter[IfElement] {
-    override def toWdlV1(a: IfElement) =
-      s"""if (${a.conditionExpression.toWdlV1}) {
-         |${indentAndCombine(a.graphElements.map(_.toWdlV1))}}""".stripMargin
-  }
-
   implicit val stringPieceWriter: WdlWriter[StringPiece] = new WdlWriter[StringPiece] {
     override def toWdlV1(a: StringPiece): String = a match {
       case a: StringLiteral => a.value
@@ -114,33 +103,6 @@ object WdlWriterImpl {
     }
   }
 
-  implicit val graphElementWriter: WdlWriter[WorkflowGraphElement] = new WdlWriter[WorkflowGraphElement] {
-    override def toWdlV1(a: WorkflowGraphElement) = a match {
-      case a: CallElement => a.toWdlV1
-      case a: IntermediateValueDeclarationElement => a.toWdlV1
-      case a: OutputDeclarationElement => a.toWdlV1
-      case a: InputDeclarationElement => a.toWdlV1
-      case a: IfElement => a.toWdlV1
-      case a: ScatterElement => a.toWdlV1
-    }
-  }
-
-  implicit val scatterElementWriter: WdlWriter[ScatterElement] = new WdlWriter[ScatterElement] {
-    override def toWdlV1(a: ScatterElement): String =
-      s"""scatter (${a.scatterVariableName} in ${a.scatterExpression.toWdlV1}) {
-         |${indentAndCombine(a.graphElements.map(_.toWdlV1))}}""".stripMargin
-  }
-
-  implicit val callBodyElement: WdlWriter[CallBodyElement] = new WdlWriter[CallBodyElement] {
-    override def toWdlV1(a: CallBodyElement): String =
-      if (a.inputs.nonEmpty) {
-        s"""input:
-           |${indent(indent(a.inputs.map(_.toWdlV1).mkString(",\n")))}""".stripMargin
-      } else {
-        ""
-      }
-  }
-
   object CallElementWriter {
     def withoutBody(a: CallElement): String = {
       val aliasExpression = a.alias match {
@@ -154,28 +116,6 @@ object WdlWriterImpl {
     }
   }
 
-  implicit val callElementWriter: WdlWriter[CallElement] = new WdlWriter[CallElement] {
-
-    override def toWdlV1(a: CallElement): String = {
-
-      val bodyExpression = a.body match {
-        case Some(body) =>
-          s""" {
-             |  ${body.toWdlV1}
-             |}""".stripMargin
-        case None => ""
-      }
-
-      s"${CallElementWriter.withoutBody(a)}$bodyExpression"
-    }
-  }
-
-  implicit val intermediateValueDeclarationElementWriter: WdlWriter[IntermediateValueDeclarationElement] =
-    new WdlWriter[IntermediateValueDeclarationElement] {
-      override def toWdlV1(a: IntermediateValueDeclarationElement) =
-        s"${a.typeElement.toWdlV1} ${a.name} = ${a.expression.toWdlV1}"
-    }
-
   implicit val typeElementWriter: WdlWriter[TypeElement] = new WdlWriter[TypeElement] {
     override def toWdlV1(a: TypeElement) = a match {
       case a: PrimitiveTypeElement => a.primitiveType.toWdlV1
@@ -195,160 +135,6 @@ object WdlWriterImpl {
     override def toWdlV1(a: WomPrimitiveType) = a.stableName
   }
 
-  implicit val workflowDefinitionElementWriter: WdlWriter[WorkflowDefinitionElement] =
-    new WdlWriter[WorkflowDefinitionElement] {
-      override def toWdlV1(a: WorkflowDefinitionElement) = {
-        val inputs = a.inputsSection match {
-          case Some(i) => i.toWdlV1
-          case None => ""
-        }
-        val outputs = a.outputsSection match {
-          case Some(o) => o.toWdlV1
-          case None => ""
-        }
-
-        // Readability / cosmetic reordering
-        // TODO: use graph ordering
-        // https://github.com/broadinstitute/cromwell/issues/3796
-        val inputDeclarationElements: List[InputDeclarationElement] =
-          a.graphElements.toList.filterByType[InputDeclarationElement]
-        val intermediateValueDeclarationElements: List[IntermediateValueDeclarationElement] =
-          a.graphElements.toList.filterByType[IntermediateValueDeclarationElement]
-        val ifElements: List[IfElement] =
-          a.graphElements.toList.filterByType[IfElement]
-        val scatterElements: List[ScatterElement] =
-          a.graphElements.toList.filterByType[ScatterElement]
-        val callElements: List[CallElement] =
-          a.graphElements.toList.filterByType[CallElement]
-        val outputDeclarationElements: List[OutputDeclarationElement] =
-          a.graphElements.toList.filterByType[OutputDeclarationElement]
-
-        val combined: List[WorkflowGraphElement] = inputDeclarationElements ++
-          intermediateValueDeclarationElements ++
-          ifElements ++
-          scatterElements ++
-          callElements ++
-          outputDeclarationElements
-
-        s"""workflow ${a.name} {
-           |${indent(inputs)}
-           |${indentAndCombine(combined.map(_.toWdlV1))}
-           |${indent(outputs)}
-           |}""".stripMargin
-      }
-    }
-
-  implicit val runtimeAttributesSectionElementWriter: WdlWriter[RuntimeAttributesSectionElement] =
-    new WdlWriter[RuntimeAttributesSectionElement] {
-      override def toWdlV1(a: RuntimeAttributesSectionElement): String = {
-        val runtimeMap = a.runtimeAttributes map { pair =>
-          s"${pair.key}: ${pair.value.toWdlV1}"
-        }
-
-        s"""runtime {
-           |${indentAndCombine(runtimeMap)}}""".stripMargin
-      }
-    }
-
-  implicit val metaValueElementWriter: WdlWriter[MetaValueElement] = new WdlWriter[MetaValueElement] {
-    override def toWdlV1(a: MetaValueElement): String = a match {
-      case _: MetaValueElementNull.type => "null"
-      case a: MetaValueElementBoolean => a.value.toString
-      case a: MetaValueElementFloat => a.value.toString
-      case a: MetaValueElementInteger => a.value.toString
-      case a: MetaValueElementString => "\"" + a.value + "\""
-      case a: MetaValueElementObject =>
-        "{" + a.value
-          .map { pair =>
-            s"${pair._1}: ${metaValueElementWriter.toWdlV1(pair._2)}"
-          }
-          .mkString(", ") + "}"
-      case a: MetaValueElementArray => "[" + a.value.map(metaValueElementWriter.toWdlV1).mkString(", ") + "]"
-    }
-  }
-
-  implicit val metaSectionElementWriter: WdlWriter[MetaSectionElement] = new WdlWriter[MetaSectionElement] {
-    override def toWdlV1(a: MetaSectionElement): String = {
-      val map = a.meta.map { pair =>
-        s"${pair._1}: ${pair._2.toWdlV1}"
-      }
-      s"""meta {
-         |${indentAndCombine(map)}
-         |}""".stripMargin
-    }
-  }
-
-  implicit val parameterMetaSectionElementWriter: WdlWriter[ParameterMetaSectionElement] =
-    new WdlWriter[ParameterMetaSectionElement] {
-      override def toWdlV1(a: ParameterMetaSectionElement): String = {
-        val map = a.metaAttributes.map { pair =>
-          s"${pair._1}: ${pair._2.toWdlV1}"
-        }
-        s"""parameter_meta {
-           |${indentAndCombine(map)}
-           |}""".stripMargin
-      }
-    }
-
-  implicit val taskDefinitionTypeElementWriter: WdlWriter[TaskDefinitionElement] =
-    new WdlWriter[TaskDefinitionElement] {
-      override def toWdlV1(a: TaskDefinitionElement) = {
-        val inputs = a.inputsSection match {
-          case Some(i) => i.toWdlV1
-          case None => ""
-        }
-        val outputs = a.outputsSection match {
-          case Some(o) => o.toWdlV1
-          case None => ""
-        }
-        val runtime = a.runtimeSection match {
-          case Some(r) => r.toWdlV1
-          case None => ""
-        }
-        val meta = a.metaSection match {
-          case Some(m) => m.toWdlV1
-          case None => ""
-        }
-        val parameterMeta = a.parameterMetaSection match {
-          case Some(p) => p.toWdlV1
-          case None => ""
-        }
-
-        s"""task ${a.name} {
-           |${indent(inputs)}
-           |${indentAndCombine(a.declarations.map(_.toWdlV1))}
-           |${indent(outputs)}
-           |${a.commandSection.toWdlV1}
-           |${indent(runtime)}
-           |${indent(meta)}
-           |${indent(parameterMeta)}}""".stripMargin
-      }
-    }
-
-  implicit val commandSectionElementWriter: WdlWriter[CommandSectionElement] = new WdlWriter[CommandSectionElement] {
-    override def toWdlV1(a: CommandSectionElement): String =
-      s"""  command <<<
-         |${combine(a.parts.map(_.toWdlV1))}  >>>""".stripMargin
-  }
-
-  implicit val commandSectionLineWriter: WdlWriter[CommandSectionLine] = new WdlWriter[CommandSectionLine] {
-    override def toWdlV1(a: CommandSectionLine): String =
-      a.parts.map(_.toWdlV1).mkString
-  }
-
-  implicit val commandPartElementWriter: WdlWriter[CommandPartElement] = new WdlWriter[CommandPartElement] {
-    override def toWdlV1(a: CommandPartElement): String = a match {
-      case a: StringCommandPartElement => a.value // .trim?
-      case a: PlaceholderCommandPartElement =>
-        val attributes = a.attributes.toWdlV1
-
-        if (attributes.nonEmpty)
-          s"~{$attributes ${a.expressionElement.toWdlV1}}"
-        else
-          s"~{${a.expressionElement.toWdlV1}}"
-    }
-  }
-
   implicit val placeholderAttributeSetWriter: WdlWriter[PlaceholderAttributeSet] =
     new WdlWriter[PlaceholderAttributeSet] {
       override def toWdlV1(a: PlaceholderAttributeSet): String = {
@@ -363,36 +149,6 @@ object WdlWriterImpl {
       }
     }
 
-  implicit val inputsSectionElementWriter: WdlWriter[InputsSectionElement] = new WdlWriter[InputsSectionElement] {
-    override def toWdlV1(a: InputsSectionElement): String =
-      s"""input {
-         |${indentAndCombine(a.inputDeclarations.map(_.toWdlV1))}}""".stripMargin
-  }
-
-  implicit val inputDeclarationElementWriter: WdlWriter[InputDeclarationElement] =
-    new WdlWriter[InputDeclarationElement] {
-      override def toWdlV1(a: InputDeclarationElement): String = {
-        val expression = a.expression match {
-          case Some(expr) => s" = ${expr.toWdlV1}"
-          case None => ""
-        }
-
-        s"${a.typeElement.toWdlV1} ${a.name}$expression"
-      }
-    }
-
-  implicit val outputsSectionElementWriter: WdlWriter[OutputsSectionElement] = new WdlWriter[OutputsSectionElement] {
-    override def toWdlV1(a: OutputsSectionElement): String =
-      s"""output {
-         |${indentAndCombine(a.outputs.map(_.toWdlV1))}}""".stripMargin
-  }
-
-  implicit val outputDeclarationElementWriter: WdlWriter[OutputDeclarationElement] =
-    new WdlWriter[OutputDeclarationElement] {
-      override def toWdlV1(a: OutputDeclarationElement): String =
-        s"${a.typeElement.toWdlV1} ${a.name} = ${a.expression.toWdlV1}"
-    }
-
   implicit val functionCallElementWriter: WdlWriter[FunctionCallElement] = new WdlWriter[FunctionCallElement] {
     override def toWdlV1(a: FunctionCallElement): String = a match {
       case _: StdoutElement.type => "stdout()"
@@ -477,33 +233,6 @@ object WdlWriterImpl {
       }
     }
 
-  implicit val structElementWriter: WdlWriter[StructElement] = new WdlWriter[StructElement] {
-    override def toWdlV1(a: StructElement): String =
-      s"""struct ${a.name} {
-         |${indentAndCombine(a.entries.map(_.toWdlV1))}}""".stripMargin
-  }
-
-  implicit val structEntryElementWriter: WdlWriter[StructEntryElement] = new WdlWriter[StructEntryElement] {
-    override def toWdlV1(a: StructEntryElement): String = s"${a.typeElement.toWdlV1} ${a.identifier}"
-  }
-
-  implicit val importElementWriter: WdlWriter[ImportElement] = new WdlWriter[ImportElement] {
-    override def toWdlV1(a: ImportElement): String =
-      a.namespace match {
-        case Some(namespace) => s"""import "${a.importUrl}" as $namespace"""
-        case None => s"""import "${a.importUrl}""""
-      }
-  }
-
-  implicit val fileElementWriter: WdlWriter[FileElement] = new WdlWriter[FileElement] {
-    override def toWdlV1(a: FileElement) =
-      "version 1.0" + System.lineSeparator +
-        combine(a.imports.map(_.toWdlV1)) +
-        combine(a.structs.map(_.toWdlV1)) +
-        combine(a.workflows.map(_.toWdlV1)) +
-        combine(a.tasks.map(_.toWdlV1))
-  }
-
   implicit val kvPairWriter: WdlWriter[KvPair] = new WdlWriter[KvPair] {
     override def toWdlV1(a: KvPair): String = s"${a.key} = ${a.value.toWdlV1}"
   }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala
index f7062441130..2ff236f5437 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/CommandPartElementToWomCommandPart.scala
@@ -18,7 +18,7 @@ import wdl.model.draft3.graph.ExpressionValueConsumer.ops._
 import wdl.model.draft3.graph.expression.WomExpressionMaker.ops._
 import wdl.transforms.base.linking.expression._
 import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
-import wdl.transforms.base.wdlom2wdl.WdlWriterImpl._
+import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.{expressionElementWriter, placeholderAttributeSetWriter}
 
 object CommandPartElementToWomCommandPart {
   def convert(commandPart: CommandPartElement,
@@ -57,8 +57,9 @@ case class WdlomWomStringCommandPart(stringCommandPartElement: StringCommandPart
 
 case class WdlomWomPlaceholderCommandPart(attributes: PlaceholderAttributeSet, expression: WdlomWomExpression)
     extends CommandPart {
-  def attributesToString: String = attributes.toWdlV1
+  private def attributesToString: String = attributes.toWdlV1
   // Yes, it's sad that we need to put ${} here, but otherwise we won't cache hit from draft-2 command sections
+  // Re-writes e.g. `echo $((5 + ~{x.a}))` commands to `echo $((5 + ${x.a}))` so they evaluate to equal
   override def toString: String = "${" + s"$attributesToString${expression.expressionElement.toWdlV1}" + "}"
 
   override def instantiate(inputsMap: Map[LocalName, WomValue],
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/InputDeclarationElementToGraphNode.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/InputDeclarationElementToGraphNode.scala
index d70bc22126f..f7e6f107dd7 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/InputDeclarationElementToGraphNode.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/InputDeclarationElementToGraphNode.scala
@@ -15,7 +15,7 @@ import wom.graph.GraphNodePort.OutputPort
 import wom.graph._
 import wom.types.{WomOptionalType, WomType}
 import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
-import wdl.transforms.base.wdlom2wdl.WdlWriterImpl._
+import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.{expressionElementWriter, typeElementWriter}
 
 object InputDeclarationElementToGraphNode {
   def convert(a: GraphInputNodeMakerInputs)(implicit
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/WorkflowGraphElementToGraphNode.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/WorkflowGraphElementToGraphNode.scala
index 56ff7709605..f866fc94644 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/WorkflowGraphElementToGraphNode.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/WorkflowGraphElementToGraphNode.scala
@@ -17,7 +17,7 @@ import wom.graph._
 import wom.graph.expression.ExposedExpressionNode
 import wom.types.WomType
 import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
-import wdl.transforms.base.wdlom2wdl.WdlWriterImpl._
+import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.{expressionElementWriter, typeElementWriter}
 
 object WorkflowGraphElementToGraphNode {
   def convert(a: GraphNodeMakerInputs)(implicit
diff --git a/womtool/src/main/scala/womtool/WomtoolMain.scala b/womtool/src/main/scala/womtool/WomtoolMain.scala
index 6fc1ccb43db..38c586e8bb1 100644
--- a/womtool/src/main/scala/womtool/WomtoolMain.scala
+++ b/womtool/src/main/scala/womtool/WomtoolMain.scala
@@ -2,16 +2,12 @@ package womtool
 
 import java.nio.file.Paths
 
-import better.files.File
 import com.typesafe.scalalogging.StrictLogging
 import common.validation.Validation._
-import cromwell.core.path.{DefaultPathBuilder, Path}
+import cromwell.core.path.Path
 import cromwell.languages.util.ImportResolver.HttpResolver
-import languages.wdl.draft2.WdlDraft2LanguageFactory
 import wdl.draft2.model.formatter.{AnsiSyntaxHighlighter, HtmlSyntaxHighlighter, SyntaxFormatter, SyntaxHighlighter}
 import wdl.draft2.model.{AstTools, WdlNamespace}
-import wdl.transforms.base.wdlom2wdl.WdlWriter.ops._
-import wdl.transforms.base.wdlom2wdl.WdlWriterImpl.fileElementWriter
 import wom.views.GraphPrint
 import womtool.cmdline.HighlightMode.{ConsoleHighlighting, HtmlHighlighting, UnrecognizedHighlightingMode}
 import womtool.cmdline._
@@ -20,9 +16,8 @@ import womtool.input.WomGraphMaker
 import womtool.inputs.Inputs
 import womtool.outputs.Outputs
 import womtool.validate.Validate
-import womtool.wom2wdlom.WomToWdlom.womBundleToFileElement
 
-import scala.util.{Failure, Success, Try}
+import scala.util.{Failure, Success}
 
 object WomtoolMain extends App with StrictLogging {
 
@@ -58,7 +53,6 @@ object WomtoolMain extends App with StrictLogging {
     case o: OutputsCommandLine => Outputs.outputsJson(o.workflowSource)
     case g: WomtoolGraphCommandLine => graph(g.workflowSource)
     case g: WomtoolWomGraphCommandLine => womGraph(g.workflowSource)
-    case u: WomtoolWdlUpgradeCommandLine => upgrade(u.workflowSource.pathAsString)
     case _ => BadUsageTermination(WomtoolCommandLineParser.instance.usage)
   }
 
@@ -79,59 +73,6 @@ object WomtoolMain extends App with StrictLogging {
   def parse(workflowSourcePath: String): Termination =
     SuccessfulTermination(AstTools.getAst(Paths.get(workflowSourcePath)).toPrettyString)
 
-  def upgrade(workflowSourcePath: String): Termination = {
-    import wdl.draft2.model.Import
-    import wdl.model.draft3.elements.ImportElement
-
-    // Get imports directly from WdlNamespace, because they are erased during WOMification
-    val maybeWdlNamespace: Try[WdlNamespace] =
-      WdlNamespace.loadUsingPath(
-        Paths.get(workflowSourcePath),
-        None,
-        Option(
-          List(
-            WdlNamespace.directoryResolver(File(workflowSourcePath).parent),
-            WdlNamespace.fileResolver,
-            WdlDraft2LanguageFactory.httpResolver
-          )
-        )
-      )
-
-    def upgradeImport(draft2Import: Import): ImportElement =
-      if (draft2Import.namespaceName.nonEmpty)
-        // draft-2 does not have structs, so the source WDL will not have any for us to rename
-        ImportElement(draft2Import.uri, Option(draft2Import.namespaceName), Map())
-      else
-        ImportElement(draft2Import.uri, None, Map())
-
-    val maybeWdl: Try[Path] = DefaultPathBuilder.build(workflowSourcePath)
-
-    (maybeWdl, maybeWdlNamespace) match {
-      case (Success(wdl), Success(wdlNamespace)) =>
-        val maybeWomBundle = WomGraphMaker.getBundle(wdl)
-        maybeWomBundle match {
-          case Right(womBundle) =>
-            val maybeFileElement = womBundleToFileElement.run(womBundle)
-            maybeFileElement match {
-              case Right(fileElement) =>
-                SuccessfulTermination(fileElement.copy(imports = wdlNamespace.imports.map(upgradeImport)).toWdlV1)
-              case Left(errors) =>
-                UnsuccessfulTermination(
-                  s"WDL parsing succeeded but could not create WOM: ${errors.toList.mkString("[", ",", "]")}"
-                )
-            }
-          case Left(errors) =>
-            UnsuccessfulTermination(
-              s"WDL parsing succeeded but could not create WOM: ${errors.toList.mkString("[", ",", "]")}"
-            )
-        }
-      case (Failure(throwable), _) =>
-        UnsuccessfulTermination(s"Failed to load WDL source: ${throwable.getMessage}")
-      case (_, Failure(throwable)) =>
-        UnsuccessfulTermination(s"Failed to load WDL source: ${throwable.getMessage}")
-    }
-  }
-
   def graph(workflowSourcePath: Path): Termination =
     WomGraphMaker
       .getBundle(workflowSourcePath)
diff --git a/womtool/src/main/scala/womtool/cmdline/PartialWomtoolCommandLineArguments.scala b/womtool/src/main/scala/womtool/cmdline/PartialWomtoolCommandLineArguments.scala
index af33485e173..d7ec9b4c04e 100644
--- a/womtool/src/main/scala/womtool/cmdline/PartialWomtoolCommandLineArguments.scala
+++ b/womtool/src/main/scala/womtool/cmdline/PartialWomtoolCommandLineArguments.scala
@@ -19,7 +19,6 @@ final case class HighlightCommandLine(workflowSource: Path, highlightMode: Highl
 final case class InputsCommandLine(workflowSource: Path, showOptionals: Boolean) extends ValidatedWomtoolCommandLine
 final case class OutputsCommandLine(workflowSource: Path) extends ValidatedWomtoolCommandLine
 final case class WomtoolGraphCommandLine(workflowSource: Path) extends ValidatedWomtoolCommandLine
-final case class WomtoolWdlUpgradeCommandLine(workflowSource: Path) extends ValidatedWomtoolCommandLine
 final case class WomtoolWomGraphCommandLine(workflowSource: Path) extends ValidatedWomtoolCommandLine
 
 sealed trait WomtoolCommand
@@ -31,7 +30,6 @@ object WomtoolCommand {
   case object Inputs extends WomtoolCommand
   case object Outputs extends WomtoolCommand
   case object Graph extends WomtoolCommand
-  case object Upgrade extends WomtoolCommand
   case object WomGraph extends WomtoolCommand
 }
 
diff --git a/womtool/src/main/scala/womtool/cmdline/WomtoolCommandLineParser.scala b/womtool/src/main/scala/womtool/cmdline/WomtoolCommandLineParser.scala
index 8b5801d8a52..4ca04b5ce55 100644
--- a/womtool/src/main/scala/womtool/cmdline/WomtoolCommandLineParser.scala
+++ b/womtool/src/main/scala/womtool/cmdline/WomtoolCommandLineParser.scala
@@ -27,8 +27,6 @@ object WomtoolCommandLineParser {
       Option(WomtoolGraphCommandLine(mainFile))
     case PartialWomtoolCommandLineArguments(Some(WomGraph), Some(mainFile), None, None, None, None) =>
       Option(WomtoolWomGraphCommandLine(mainFile))
-    case PartialWomtoolCommandLineArguments(Some(Upgrade), Some(mainFile), None, None, None, None) =>
-      Option(WomtoolWdlUpgradeCommandLine(mainFile))
     case _ => None
   }
 }
@@ -107,10 +105,6 @@ class WomtoolCommandLineParser extends scopt.OptionParser[PartialWomtoolCommandL
     .action((_, c) => c.copy(command = Option(Graph)))
     .text("Generate and output a graph visualization of the workflow in .dot format" + System.lineSeparator)
 
-  cmd("upgrade")
-    .action((_, c) => c.copy(command = Option(Upgrade)))
-    .text("Automatically upgrade the WDL to version 1.0 and output the result." + System.lineSeparator)
-
   cmd("womgraph")
     .action((_, c) => c.copy(command = Option(WomGraph)))
     .text(
diff --git a/womtool/src/main/scala/womtool/wom2wdlom/WomToWdlom.scala b/womtool/src/main/scala/womtool/wom2wdlom/WomToWdlom.scala
deleted file mode 100644
index 07382a3ceef..00000000000
--- a/womtool/src/main/scala/womtool/wom2wdlom/WomToWdlom.scala
+++ /dev/null
@@ -1,392 +0,0 @@
-package womtool.wom2wdlom
-
-import cats.syntax.traverse._
-import cats.instances.list._
-import cats.instances.either._
-import common.Checked
-import common.collections.EnhancedCollections._
-import common.transforms.CheckedAtoB
-import common.validation.Checked._
-import shapeless.{Inl, Inr}
-import wdl.draft2.model.command.{ParameterCommandPart, StringCommandPart}
-import wdl.model.draft3.elements._
-import wdl.model.draft3.elements.CommandPartElement.{PlaceholderCommandPartElement, StringCommandPartElement}
-import wdl.model.draft3.elements.ExpressionElement.ExpressionLiteralElement
-import wom.callable.Callable._
-import wom.callable.Callable.OutputDefinition
-import wom.callable.{CallableTaskDefinition, MetaValueElement, WorkflowDefinition}
-import wom.executable.WomBundle
-import wom.expression.WomExpression
-import wom.graph._
-import wom.graph.CallNode.InputDefinitionPointer
-import wom.graph.expression._
-import wom.graph.GraphNodePort.GraphNodeOutputPort
-import wom.RuntimeAttributes
-import wom.types._
-
-object WomToWdlom {
-
-  private def invalidFromString(text: String) =
-    s"Value \'$text\' has no representation in the destination format (WDL)".invalidNelCheck
-
-  def graphOutputNodeToWorkflowGraphElement: CheckedAtoB[GraphOutputNode, WorkflowGraphElement] =
-    CheckedAtoB.fromCheck { a: GraphOutputNode =>
-      a match {
-        case a: ExpressionBasedGraphOutputNode =>
-          for {
-            typeElement <- womTypeToTypeElement(a.womType)
-            expression <- womExpressionToExpressionElement(a.womExpression)
-          } yield OutputDeclarationElement(typeElement, a.identifier.localName.value, expression)
-        case _ =>
-          invalidFromString(a.toString)
-      }
-    }
-
-  def womBundleToFileElement: CheckedAtoB[WomBundle, FileElement] =
-    CheckedAtoB.fromCheck { a: WomBundle =>
-      val tasks: Iterable[CallableTaskDefinition] = a.allCallables.values.filterByType[CallableTaskDefinition]
-      val workflows: Iterable[WorkflowDefinition] = a.allCallables.values.filterByType[WorkflowDefinition]
-
-      for {
-        workflows <- workflows
-          .map(workflowDefinitionToWorkflowDefinitionElement(_))
-          .toList
-          .sequence[Checked, WorkflowDefinitionElement]
-        tasks <- tasks
-          .map(callableTaskDefinitionToTaskDefinitionElement(_))
-          .toList
-          .sequence[Checked, TaskDefinitionElement]
-      } yield FileElement(
-        Seq.empty, // Imports do not exist in WOM and cannot sensibly be added at this point
-        Seq.empty, // Structs do not exist in draft-2
-        workflows,
-        tasks
-      )
-    }
-
-  def mapToMetaSectionElement: CheckedAtoB[Map[String, MetaValueElement], Option[MetaSectionElement]] =
-    CheckedAtoB.fromCheck { a: Map[String, MetaValueElement] =>
-      if (a.nonEmpty)
-        Some(MetaSectionElement(a)).validNelCheck
-      else
-        None.validNelCheck
-    }
-
-  def mapToParameterMetaSectionElement
-    : CheckedAtoB[Map[String, MetaValueElement], Option[ParameterMetaSectionElement]] =
-    CheckedAtoB.fromCheck { a: Map[String, MetaValueElement] =>
-      if (a.nonEmpty)
-        Some(ParameterMetaSectionElement(a)).validNelCheck
-      else
-        None.validNelCheck
-    }
-
-  def runtimeAttributesToRuntimeAttributesSectionElement
-    : CheckedAtoB[RuntimeAttributes, Option[RuntimeAttributesSectionElement]] =
-    CheckedAtoB.fromCheck { a: RuntimeAttributes =>
-      def tupleToKvPair(tuple: (String, WomExpression)): Checked[ExpressionElement.KvPair] =
-        for {
-          expressionElement <- womExpressionToExpressionElement(tuple._2)
-        } yield ExpressionElement.KvPair(tuple._1, expressionElement)
-
-      for {
-        kvPairs <- (a.attributes map tupleToKvPair).toList.sequence[Checked, ExpressionElement.KvPair]
-      } yield
-        if (kvPairs.nonEmpty)
-          Some(RuntimeAttributesSectionElement(kvPairs.toVector))
-        else
-          None
-    }
-
-  def outputDefinitionToOutputDeclarationElement: CheckedAtoB[OutputDefinition, OutputDeclarationElement] =
-    CheckedAtoB.fromCheck { a: OutputDefinition =>
-      for {
-        typeElement <- womTypeToTypeElement(a.womType)
-        expression <- womExpressionToExpressionElement(a.expression)
-      } yield OutputDeclarationElement(typeElement, a.name, expression)
-    }
-
-  def inputDefinitionToInputDeclarationElement: CheckedAtoB[InputDefinition, InputDeclarationElement] =
-    CheckedAtoB.fromCheck { a: InputDefinition =>
-      womTypeToTypeElement(a.womType) flatMap { womType =>
-        a match {
-          case a: RequiredInputDefinition =>
-            InputDeclarationElement(womType, a.localName.value, None).validNelCheck
-          case a: OverridableInputDefinitionWithDefault =>
-            womExpressionToExpressionElement(a.default) map { expression =>
-              InputDeclarationElement(womType, a.localName.value, Some(expression))
-            }
-          case a: FixedInputDefinitionWithDefault =>
-            womExpressionToExpressionElement(a.default) map { expression =>
-              InputDeclarationElement(womType, a.localName.value, Some(expression))
-            }
-          case a: OptionalInputDefinition =>
-            InputDeclarationElement(womType, a.localName.value, None).validNelCheck
-        }
-      }
-    }
-
-  def callableTaskDefinitionToTaskDefinitionElement: CheckedAtoB[CallableTaskDefinition, TaskDefinitionElement] =
-    CheckedAtoB.fromCheck { a: CallableTaskDefinition =>
-      val inputs: Checked[List[InputDeclarationElement]] =
-        a.inputs.map(inputDefinitionToInputDeclarationElement(_)).sequence[Checked, InputDeclarationElement]
-      val outputs: Checked[List[OutputDeclarationElement]] =
-        a.outputs.map(outputDefinitionToOutputDeclarationElement(_)).sequence[Checked, OutputDeclarationElement]
-
-      for {
-        runtime <- runtimeAttributesToRuntimeAttributesSectionElement(a.runtimeAttributes)
-        meta <- mapToMetaSectionElement(a.meta)
-        parameterMeta <- mapToParameterMetaSectionElement(a.parameterMeta)
-        inputs <- inputs
-        outputs <- outputs
-        commands <- a.commandTemplateBuilder(Map()).toEither
-      } yield {
-        val commandLine = CommandSectionLine(commands map {
-          case s: StringCommandPart =>
-            StringCommandPartElement(s.literal)
-          case p: ParameterCommandPart =>
-            val attrs = PlaceholderAttributeSet(
-              defaultAttribute = p.attributes.get("default"),
-              trueAttribute = p.attributes.get("true"),
-              falseAttribute = p.attributes.get("false"),
-              sepAttribute = p.attributes.get("sep")
-            )
-
-            PlaceholderCommandPartElement(ExpressionLiteralElement(p.expression.toWomString), attrs)
-        })
-
-        TaskDefinitionElement(
-          a.name,
-          if (inputs.nonEmpty) Some(InputsSectionElement(inputs)) else None,
-          Seq.empty, // No such thing in draft-2
-          if (outputs.nonEmpty) Some(OutputsSectionElement(outputs)) else None,
-          CommandSectionElement(Seq(commandLine)),
-          runtime,
-          meta,
-          parameterMeta,
-          a.sourceLocation
-        )
-      }
-    }
-
-  def workflowDefinitionToWorkflowDefinitionElement: CheckedAtoB[WorkflowDefinition, WorkflowDefinitionElement] =
-    CheckedAtoB.fromCheck { a: WorkflowDefinition =>
-      // This is a bit odd, so let's explain. "Real" inputs/outputs that are specified by the WDL's author
-      // cannot have periods in them - period. So any input/output that has a period in it
-      // is an artifact of WOMification and should be dropped
-      val inputs =
-        a.inputs
-          .filter(!_.localName.value.contains("."))
-          .map(inputDefinitionToInputDeclarationElement(_))
-          .sequence[Checked, InputDeclarationElement]
-      val outputs =
-        a.outputs
-          .filter(!_.localName.value.contains("."))
-          .map(outputDefinitionToOutputDeclarationElement(_))
-          .sequence[Checked, OutputDeclarationElement]
-
-      for {
-        meta <- mapToMetaSectionElement(a.meta)
-        parameterMeta <- mapToParameterMetaSectionElement(a.parameterMeta)
-        inputs <- inputs
-        outputs <- outputs
-        nodes <- selectWdlomRepresentableNodes(a.graph.nodes)
-          .map(graphNodeToWorkflowGraphElement(_))
-          .toList
-          .sequence[Checked, WorkflowGraphElement]
-      } yield WorkflowDefinitionElement(
-        a.name,
-        if (inputs.nonEmpty) Some(InputsSectionElement(inputs)) else None,
-        nodes.toSet,
-        if (outputs.nonEmpty) Some(OutputsSectionElement(outputs)) else None,
-        meta,
-        parameterMeta,
-        a.sourceLocation
-      )
-    }
-
-  def expressionNodeLikeToWorkflowGraphElement: CheckedAtoB[ExpressionNodeLike, WorkflowGraphElement] =
-    CheckedAtoB.fromCheck {
-      case a: ExpressionNode =>
-        for {
-          typeElement <- womTypeToTypeElement(a.womType)
-          expression <- expressionNodeToExpressionElement(a)
-        } yield IntermediateValueDeclarationElement(typeElement = typeElement,
-                                                    name = a.identifier.localName.value,
-                                                    expression = expression
-        )
-      case a: ExpressionCallNode => invalidFromString(a.toString)
-    }
-
-  // Select only nodes that have a Wdlom representation (i.e. were not synthesized during WOMification)
-  // WOM has some explicit representations that are implicit in WDL; they are necessary for execution,
-  // but do not make sense (or are illegal) in WDL source.
-  private def selectWdlomRepresentableNodes(allNodes: Set[GraphNode]): Set[GraphNode] = {
-    val expressions = allNodes.filterByType[ExposedExpressionNode]
-    val scatters = allNodes.filterByType[ScatterNode]
-    val calls = allNodes.filterByType[CallNode]
-    val conditionals = allNodes.filterByType[ConditionalNode]
-
-    expressions ++ scatters ++ calls ++ conditionals
-  }
-
-  def graphNodeToWorkflowGraphElement: CheckedAtoB[GraphNode, WorkflowGraphElement] =
-    CheckedAtoB.fromCheck {
-      case a: CallNode =>
-        callNodeToCallElement(a)
-      case a: ConditionalNode =>
-        for {
-          condition <- expressionNodeToExpressionElement(a.conditionExpression)
-          nodes <- selectWdlomRepresentableNodes(a.innerGraph.nodes).toList
-            .map(graphNodeToWorkflowGraphElement(_))
-            .sequence[Checked, WorkflowGraphElement]
-        } yield IfElement(
-          conditionExpression = condition,
-          graphElements = nodes
-        )
-      case a: ExpressionNodeLike =>
-        expressionNodeLikeToWorkflowGraphElement(a)
-      case a: GraphNodeWithSingleOutputPort =>
-        graphNodeWithSingleOutputPortToWorkflowGraphElement(a)
-      case a: GraphOutputNode =>
-        graphOutputNodeToWorkflowGraphElement(a)
-      case a: ScatterNode =>
-        // Only CWL has multi-variable scatters
-        if (a.scatterVariableNodes.size != 1)
-          s"In WDL, the scatter node count must be exactly one, was ${a.scatterVariableNodes.size}".invalidNelCheck
-        else
-          for {
-            expression <- expressionNodeToExpressionElement(a.scatterCollectionExpressionNodes.head)
-            graph <- selectWdlomRepresentableNodes(a.innerGraph.nodes).toList
-              .map(graphNodeToWorkflowGraphElement(_))
-              .sequence[Checked, WorkflowGraphElement]
-          } yield ScatterElement(
-            scatterName = a.identifier.localName.value,
-            scatterExpression = expression,
-            scatterVariableName = a.inputPorts.toList.head.name,
-            graphElements = graph,
-            sourceLocation = None
-          )
-    }
-
-  def graphNodeWithSingleOutputPortToWorkflowGraphElement
-    : CheckedAtoB[GraphNodeWithSingleOutputPort, WorkflowGraphElement] =
-    CheckedAtoB.fromCheck {
-      case a: GraphInputNode =>
-        womTypeToTypeElement(a.womType) map { typeElement =>
-          InputDeclarationElement(typeElement, a.identifier.localName.value, None)
-        }
-      case a: ExpressionNode =>
-        for {
-          typeElement <- womTypeToTypeElement(a.womType)
-          expression <- womExpressionToExpressionElement(a.womExpression)
-        } yield IntermediateValueDeclarationElement(typeElement, a.identifier.localName.value, expression)
-    }
-
-  def womTypeToTypeElement: CheckedAtoB[WomType, TypeElement] =
-    CheckedAtoB.fromCheck {
-      case a: WomArrayType =>
-        womTypeToTypeElement(a.memberType) map { typeElement =>
-          if (a.guaranteedNonEmpty)
-            NonEmptyTypeElement(ArrayTypeElement(typeElement))
-          else
-            ArrayTypeElement(typeElement)
-        }
-      case _: WomCoproductType => invalidFromString("WDL does not have coproducts - is this WOM from CWL?")
-      case _: WomFileType => PrimitiveTypeElement(WomSingleFileType).validNelCheck
-      case a: WomMapType =>
-        for {
-          keyType <- womTypeToTypeElement(a.keyType)
-          valueType <- womTypeToTypeElement(a.valueType)
-        } yield MapTypeElement(keyType, valueType)
-      case _: WomNothingType.type => invalidFromString("WDL does not have the Nothing type - is this WOM from CWL?")
-      case _: WomObjectType.type => ObjectTypeElement.validNelCheck
-      case a: WomOptionalType => womOptionalTypeToOptionalTypeElement(a)
-      case a: WomPairType =>
-        for {
-          leftType <- womTypeToTypeElement(a.leftType)
-          rightType <- womTypeToTypeElement(a.rightType)
-        } yield PairTypeElement(leftType, rightType)
-      case a: WomPrimitiveType => womPrimitiveTypeToPrimitiveTypeElement(a)
-    }
-
-  def womOptionalTypeToOptionalTypeElement: CheckedAtoB[WomOptionalType, OptionalTypeElement] =
-    CheckedAtoB.fromCheck { a: WomOptionalType =>
-      womTypeToTypeElement(a.memberType) map { typeElement =>
-        OptionalTypeElement(typeElement)
-      }
-    }
-
-  def womPrimitiveTypeToPrimitiveTypeElement: CheckedAtoB[WomPrimitiveType, PrimitiveTypeElement] =
-    CheckedAtoB.fromCheck { a: WomPrimitiveType =>
-      PrimitiveTypeElement(a).validNelCheck
-    }
-
-  def expressionNodeToExpressionElement: CheckedAtoB[ExpressionNode, ExpressionElement] =
-    CheckedAtoB.fromCheck { a: ExpressionNode =>
-      womExpressionToExpressionElement(a.womExpression)
-    }
-
-  def womExpressionToExpressionElement: CheckedAtoB[WomExpression, ExpressionElement] =
-    CheckedAtoB.fromCheck {
-      case a: WomExpression => ExpressionLiteralElement(a.sourceString).validNelCheck
-      case a => invalidFromString(a.toString)
-    }
-
-  def inputDefinitionPointerToExpressionElement: CheckedAtoB[InputDefinitionPointer, Option[ExpressionElement]] =
-    CheckedAtoB.fromCheck {
-      // If the input definition is a node containing an expression, it's been declared explicitly
-      case Inl(a: GraphNodeOutputPort) =>
-        a.graphNode match {
-          case _: OptionalGraphInputNode =>
-            None.validNelCheck
-          case _: OptionalGraphInputNodeWithDefault =>
-            None.validNelCheck
-          case a: PlainAnonymousExpressionNode =>
-            womExpressionToExpressionElement(a.womExpression) map { expressionElement =>
-              Some(expressionElement)
-            }
-          case a: TaskCallInputExpressionNode =>
-            womExpressionToExpressionElement(a.womExpression) map { expressionElement =>
-              Some(expressionElement)
-            }
-          case _: RequiredGraphInputNode => None.validNelCheck
-        }
-      // Input definitions that directly contain expressions are the result of accepting a default input defined by the callable
-      case Inr(Inl(_: WomExpression)) => None.validNelCheck
-      case Inr(a) =>
-        invalidFromString(a.toString)
-      case a =>
-        invalidFromString(a.toString)
-    }
-
-  def callNodeToCallElement: CheckedAtoB[CallNode, CallElement] =
-    CheckedAtoB.fromCheck { call: CallNode =>
-      def tupleToKvPair(tuple: (InputDefinition, InputDefinitionPointer)): Option[ExpressionElement.KvPair] =
-        inputDefinitionPointerToExpressionElement(tuple._2) match {
-          case Right(Some(value)) => Some(ExpressionElement.KvPair(tuple._1.name, value))
-          case _ => None
-        }
-
-      val inputs = (call.inputDefinitionMappings flatMap tupleToKvPair).toVector
-
-      val callableName = call.callable.name
-      val callAlias = call.identifier.localName.value // If no alias, this is just the name; we evaluate for that below
-
-      val maybeAlias =
-        if (callableName != callAlias)
-          Some(callAlias)
-        else
-          None
-
-      val afters = call.nonInputBasedPrerequisites.map(_.localName).toVector
-
-      CallElement(
-        callableName,
-        maybeAlias,
-        afters,
-        if (inputs.nonEmpty) Some(CallBodyElement(inputs)) else None,
-        call.sourceLocation
-      ).validNelCheck
-    }
-}
diff --git a/womtool/src/test/resources/validate/biscayne/invalid/after_circle/error.txt b/womtool/src/test/resources/validate/biscayne/invalid/after_circle/error.txt
index 3d032e83fac..0930a319d51 100644
--- a/womtool/src/test/resources/validate/biscayne/invalid/after_circle/error.txt
+++ b/womtool/src/test/resources/validate/biscayne/invalid/after_circle/error.txt
@@ -1,3 +1,3 @@
 Failed to process workflow definition 'after_circle' (reason 1 of 1): This workflow contains a cyclic dependency:
-"call foo as foo1 after foo2 {" -> "call foo as foo2 after foo1 {"
-"call foo as foo2 after foo1 {" -> "call foo as foo1 after foo2 {"
+"Call "foo as foo1 after foo2"" -> "Call "foo as foo2 after foo1""
+"Call "foo as foo2 after foo1"" -> "Call "foo as foo1 after foo2""
diff --git a/womtool/src/test/resources/validate/wdl_draft3/invalid/cycle/error.txt b/womtool/src/test/resources/validate/wdl_draft3/invalid/cycle/error.txt
index a24b586cfdc..263b1adc534 100644
--- a/womtool/src/test/resources/validate/wdl_draft3/invalid/cycle/error.txt
+++ b/womtool/src/test/resources/validate/wdl_draft3/invalid/cycle/error.txt
@@ -1,4 +1,4 @@
 Failed to process workflow definition 'cycle' (reason 1 of 1): This workflow contains a cyclic dependency:
-"call mirror as m1 {" -> "call mirror as m2 {"
-"call mirror as m2 {" -> "call mirror as m3 {"
-"call mirror as m3 {" -> "call mirror as m1 {"
+"Call "mirror as m1"" -> "Call "mirror as m2""
+"Call "mirror as m2"" -> "Call "mirror as m3""
+"Call "mirror as m3"" -> "Call "mirror as m1""
diff --git a/womtool/src/test/scala/womtool/WomtoolMainSpec.scala b/womtool/src/test/scala/womtool/WomtoolMainSpec.scala
index 1a71db15cf3..2986d7db759 100644
--- a/womtool/src/test/scala/womtool/WomtoolMainSpec.scala
+++ b/womtool/src/test/scala/womtool/WomtoolMainSpec.scala
@@ -20,7 +20,7 @@ class WomtoolMainSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     WomtoolMain.runWomtool(Seq.empty[String]) match {
       case BadUsageTermination(msg) =>
         msg should include(
-          "Usage: java -jar womtool.jar [validate|inputs|outputs|parse|highlight|graph|upgrade|womgraph] [options] workflow-source"
+          "Usage: java -jar womtool.jar [validate|inputs|outputs|parse|highlight|graph|womgraph] [options] workflow-source"
         )
       case other => fail(s"Expected BadUsageTermination but got $other")
     }

From a8f6e9e095bf2d7bd0876c2eb6d58c4db5fe648d Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 13 Mar 2024 16:24:03 -0400
Subject: [PATCH 293/326] WX-1488 Supply cloud platform when making DRS
 requests (#7381)

---
 build.sbt                                     |  1 +
 .../impl/drs/DrsCloudNioFileProvider.scala    |  2 +-
 .../drs/DrsCloudNioFileSystemProvider.scala   |  3 +-
 .../cloud/nio/impl/drs/DrsCredentials.scala   | 42 ++-----------------
 .../cloud/nio/impl/drs/DrsPathResolver.scala  | 37 +++++++++++++---
 .../nio/impl/drs/EngineDrsPathResolver.scala  |  9 ----
 .../drs/DrsCloudNioFileProviderSpec.scala     |  6 +--
 .../nio/impl/drs/DrsPathResolverSpec.scala    | 15 ++++++-
 .../MockDrsCloudNioFileSystemProvider.scala   | 11 ++---
 ...solver.scala => MockDrsPathResolver.scala} | 11 +++--
 .../DrsLocalizerDrsPathResolver.scala         |  9 ----
 .../drs/localizer/DrsLocalizerMain.scala      | 10 ++---
 .../drs/localizer/DrsLocalizerMainSpec.scala  |  8 ++--
 .../filesystems/drs/DrsReaderSpec.scala       | 10 ++---
 14 files changed, 77 insertions(+), 97 deletions(-)
 delete mode 100644 cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala
 rename cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/{MockEngineDrsPathResolver.scala => MockDrsPathResolver.scala} (86%)
 delete mode 100644 cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala

diff --git a/build.sbt b/build.sbt
index 79085e31e92..a3029d0ab09 100644
--- a/build.sbt
+++ b/build.sbt
@@ -383,6 +383,7 @@ lazy val `cloud-nio-impl-ftp` = (project in cloudNio / "cloud-nio-impl-ftp")
 lazy val `cloud-nio-impl-drs` = (project in cloudNio / "cloud-nio-impl-drs")
   .withLibrarySettings(libraryName = "cloud-nio-impl-drs", dependencies = implDrsDependencies)
   .dependsOn(`cloud-nio-util`)
+  .dependsOn(cloudSupport)
   .dependsOn(common)
   .dependsOn(common % "test->test")
 
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
index 2d3cba53bfc..d4a50238176 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileProvider.scala
@@ -11,7 +11,7 @@ import common.exception._
 import org.apache.commons.lang3.exception.ExceptionUtils
 import org.apache.http.HttpStatus
 
-class DrsCloudNioFileProvider(drsPathResolver: EngineDrsPathResolver, drsReadInterpreter: DrsReadInterpreter)
+class DrsCloudNioFileProvider(drsPathResolver: DrsPathResolver, drsReadInterpreter: DrsReadInterpreter)
     extends CloudNioFileProvider {
 
   private def checkIfPathExistsThroughDrsResolver(drsPath: String): IO[Boolean] =
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
index 2c19cdabefe..216c20524f6 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCloudNioFileSystemProvider.scala
@@ -14,8 +14,7 @@ class DrsCloudNioFileSystemProvider(rootConfig: Config,
   lazy val drsResolverConfig = rootConfig.getConfig("resolver")
   lazy val drsConfig: DrsConfig = DrsConfig.fromConfig(drsResolverConfig)
 
-  lazy val drsPathResolver: EngineDrsPathResolver =
-    EngineDrsPathResolver(drsConfig, drsCredentials)
+  lazy val drsPathResolver: DrsPathResolver = new DrsPathResolver(drsConfig, drsCredentials)
 
   override def config: Config = rootConfig
 
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
index 78b2e9f3503..c8a4fb93743 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsCredentials.scala
@@ -1,17 +1,13 @@
 package cloud.nio.impl.drs
 
 import cats.syntax.validated._
-import com.azure.core.credential.TokenRequestContext
-import com.azure.core.management.AzureEnvironment
-import com.azure.core.management.profile.AzureProfile
-import com.azure.identity.DefaultAzureCredentialBuilder
 import com.google.auth.oauth2.{AccessToken, GoogleCredentials, OAuth2Credentials}
 import com.typesafe.config.Config
 import common.validation.ErrorOr.ErrorOr
 import net.ceedubs.ficus.Ficus._
+import cromwell.cloudsupport.azure.AzureCredentials
 
 import scala.concurrent.duration._
-import scala.jdk.DurationConverters._
 import scala.util.{Failure, Success, Try}
 
 /**
@@ -76,38 +72,6 @@ case object GoogleAppDefaultTokenStrategy extends DrsCredentials {
   * If you need to disambiguate among multiple active user-assigned managed identities, pass
   * in the client id of the identity that should be used.
   */
-case class AzureDrsCredentials(identityClientId: Option[String]) extends DrsCredentials {
-
-  final val tokenAcquisitionTimeout = 5.seconds
-
-  val azureProfile = new AzureProfile(AzureEnvironment.AZURE)
-  val tokenScope = "https://management.azure.com/.default"
-
-  def tokenRequestContext: TokenRequestContext = {
-    val trc = new TokenRequestContext()
-    trc.addScopes(tokenScope)
-    trc
-  }
-
-  def defaultCredentialBuilder: DefaultAzureCredentialBuilder =
-    new DefaultAzureCredentialBuilder()
-      .authorityHost(azureProfile.getEnvironment.getActiveDirectoryEndpoint)
-
-  def getAccessToken: ErrorOr[String] = {
-    val credentials = identityClientId
-      .foldLeft(defaultCredentialBuilder) { (builder, clientId) =>
-        builder.managedIdentityClientId(clientId)
-      }
-      .build()
-
-    Try(
-      credentials
-        .getToken(tokenRequestContext)
-        .block(tokenAcquisitionTimeout.toJava)
-    ) match {
-      case Success(null) => "null token value attempting to obtain access token".invalidNel
-      case Success(token) => token.getToken.validNel
-      case Failure(error) => s"Failed to refresh access token: ${error.getMessage}".invalidNel
-    }
-  }
+case class AzureDrsCredentials(identityClientId: Option[String] = None) extends DrsCredentials {
+  def getAccessToken: ErrorOr[String] = AzureCredentials.getAccessToken(identityClientId)
 }
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
index f8d898a0bcf..028d3ee4849 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/DrsPathResolver.scala
@@ -25,7 +25,7 @@ import java.nio.ByteBuffer
 import java.nio.channels.{Channels, ReadableByteChannel}
 import scala.util.Try
 
-abstract class DrsPathResolver(drsConfig: DrsConfig) {
+class DrsPathResolver(drsConfig: DrsConfig, drsCredentials: DrsCredentials) {
 
   protected lazy val httpClientBuilder: HttpClientBuilder = {
     val clientBuilder = HttpClientBuilder.create()
@@ -38,7 +38,17 @@ abstract class DrsPathResolver(drsConfig: DrsConfig) {
     clientBuilder
   }
 
-  def getAccessToken: ErrorOr[String]
+  def getAccessToken: ErrorOr[String] = drsCredentials.getAccessToken
+
+  private lazy val currentCloudPlatform: Option[DrsCloudPlatform.Value] = drsCredentials match {
+    case _: GoogleOauthDrsCredentials => Option(DrsCloudPlatform.GoogleStorage)
+    case GoogleAppDefaultTokenStrategy => Option(DrsCloudPlatform.GoogleStorage)
+    case _: AzureDrsCredentials => Option(DrsCloudPlatform.Azure)
+    case _ => None
+  }
+
+  def makeDrsResolverRequest(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): DrsResolverRequest =
+    DrsResolverRequest(drsPath, currentCloudPlatform, fields)
 
   private def makeHttpRequestToDrsResolver(drsPath: String,
                                            fields: NonEmptyList[DrsResolverField.Value]
@@ -47,7 +57,7 @@ abstract class DrsPathResolver(drsConfig: DrsConfig) {
       case Valid(token) =>
         IO {
           val postRequest = new HttpPost(drsConfig.drsResolverUrl)
-          val requestJson = DrsResolverRequest(drsPath, fields).asJson.noSpaces
+          val requestJson = makeDrsResolverRequest(drsPath, fields).asJson.noSpaces
           postRequest.setEntity(new StringEntity(requestJson, ContentType.APPLICATION_JSON))
           postRequest.setHeader("Authorization", s"Bearer $token")
           postRequest
@@ -118,7 +128,9 @@ abstract class DrsPathResolver(drsConfig: DrsConfig) {
     * Please note, this method returns an IO that would make a synchronous HTTP request to DRS Resolver when run.
     */
   def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] =
-    rawDrsResolverResponse(drsPath, fields).use(httpResponseToDrsResolverResponse(drsPathForDebugging = drsPath))
+    rawDrsResolverResponse(drsPath, fields).use(
+      httpResponseToDrsResolverResponse(drsPathForDebugging = drsPath)
+    )
 
   def openChannel(accessUrl: AccessUrl): IO[ReadableByteChannel] =
     IO {
@@ -178,7 +190,20 @@ object DrsResolverField extends Enumeration {
   val LocalizationPath: DrsResolverField.Value = Value("localizationPath")
 }
 
-final case class DrsResolverRequest(url: String, fields: NonEmptyList[DrsResolverField.Value])
+// We supply a cloud platform value to the DRS service. In cases where the DRS repository
+// has multiple cloud files associated with a DRS link, it will prefer sending a file on the same
+// platform as this Cromwell instance. That is, if a DRS file has copies on both GCP and Azure,
+// we'll get the GCP one when running on GCP and the Azure one when running on Azure.
+object DrsCloudPlatform extends Enumeration {
+  val GoogleStorage: DrsCloudPlatform.Value = Value("gs")
+  val Azure: DrsCloudPlatform.Value = Value("azure")
+  val AmazonS3: DrsCloudPlatform.Value = Value("s3") // supported by DRSHub but not currently used by us
+}
+
+final case class DrsResolverRequest(url: String,
+                                    cloudPlatform: Option[DrsCloudPlatform.Value],
+                                    fields: NonEmptyList[DrsResolverField.Value]
+)
 
 final case class SADataObject(data: Json)
 
@@ -219,6 +244,8 @@ object DrsResolverResponseSupport {
 
   implicit lazy val drsResolverFieldEncoder: Encoder[DrsResolverField.Value] =
     Encoder.encodeEnumeration(DrsResolverField)
+  implicit lazy val drsResolverCloudPlatformEncoder: Encoder[DrsCloudPlatform.Value] =
+    Encoder.encodeEnumeration(DrsCloudPlatform)
   implicit lazy val drsResolverRequestEncoder: Encoder[DrsResolverRequest] = deriveEncoder
 
   implicit lazy val saDataObjectDecoder: Decoder[SADataObject] = deriveDecoder
diff --git a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala
deleted file mode 100644
index b53ba2cc7d8..00000000000
--- a/cloud-nio/cloud-nio-impl-drs/src/main/scala/cloud/nio/impl/drs/EngineDrsPathResolver.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package cloud.nio.impl.drs
-
-import common.validation.ErrorOr.ErrorOr
-
-case class EngineDrsPathResolver(drsConfig: DrsConfig, drsCredentials: DrsCredentials)
-    extends DrsPathResolver(drsConfig) {
-
-  override def getAccessToken: ErrorOr[String] = drsCredentials.getAccessToken
-}
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
index 5edb8fd6a8b..c3b7cb70349 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsCloudNioFileProviderSpec.scala
@@ -77,7 +77,7 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
   }
 
   it should "return a file provider that can read bytes from gcs" in {
-    val drsPathResolver = new MockEngineDrsPathResolver() {
+    val drsPathResolver = new MockDrsPathResolver() {
       override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] =
         IO(DrsResolverResponse(gsUri = Option("gs://bucket/object/path")))
     }
@@ -99,7 +99,7 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
   }
 
   it should "return a file provider that can read bytes from an access url" in {
-    val drsPathResolver = new MockEngineDrsPathResolver() {
+    val drsPathResolver = new MockDrsPathResolver() {
       override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] =
         IO(DrsResolverResponse(accessUrl = Option(AccessUrl("https://host/object/path", None))))
     }
@@ -121,7 +121,7 @@ class DrsCloudNioFileProviderSpec extends AnyFlatSpecLike with CromwellTimeoutSp
   }
 
   it should "return a file provider that can return file attributes" in {
-    val drsPathResolver = new MockEngineDrsPathResolver() {
+    val drsPathResolver = new MockDrsPathResolver() {
       override def resolveDrs(drsPath: String,
                               fields: NonEmptyList[DrsResolverField.Value]
       ): IO[DrsResolverResponse] = {
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
index 9c6cecd73f1..adbb2adf43b 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/DrsPathResolverSpec.scala
@@ -1,8 +1,9 @@
 package cloud.nio.impl.drs
 
+import cats.data.NonEmptyList
+
 import java.nio.file.attribute.FileTime
 import java.time.OffsetDateTime
-
 import cloud.nio.impl.drs.DrsCloudNioRegularFileAttributes._
 import cloud.nio.spi.{FileHash, HashType}
 import common.assertion.CromwellTimeoutSpec
@@ -157,6 +158,18 @@ class DrsPathResolverSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with
   val responseStatusLine = new BasicStatusLine(new ProtocolVersion("http", 1, 2), 345, "test-reason")
   val testDrsResolverUri = "www.drshub_v4.com"
 
+  it should "construct the right request when using Azure creds" in {
+    val resolver = new MockDrsPathResolver(drsCredentials = AzureDrsCredentials())
+    val drsRequest = resolver.makeDrsResolverRequest(drsPathForDebugging, NonEmptyList.of(DrsResolverField.AccessUrl))
+    drsRequest.cloudPlatform shouldBe Option(DrsCloudPlatform.Azure)
+  }
+
+  it should "construct the right request when using Google creds" in {
+    val resolver = new MockDrsPathResolver()
+    val drsRequest = resolver.makeDrsResolverRequest(drsPathForDebugging, NonEmptyList.of(DrsResolverField.AccessUrl))
+    drsRequest.cloudPlatform shouldBe Option(DrsCloudPlatform.GoogleStorage)
+  }
+
   it should "construct an error message from a populated, well-formed failure response" in {
     val failureResponse = Option(failureResponseJson)
 
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
index 2d0afd33336..5a2ba6172f1 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsCloudNioFileSystemProvider.scala
@@ -7,26 +7,23 @@ import com.google.cloud.NoCredentials
 import com.typesafe.config.{Config, ConfigFactory}
 import org.apache.http.impl.client.HttpClientBuilder
 
-import scala.concurrent.duration.Duration
-
 class MockDrsCloudNioFileSystemProvider(config: Config = mockConfig,
                                         httpClientBuilder: Option[HttpClientBuilder] = None,
                                         drsReadInterpreter: DrsReadInterpreter = (_, _) =>
                                           IO.raiseError(
                                             new UnsupportedOperationException("mock did not specify a read interpreter")
                                           ),
-                                        mockResolver: Option[EngineDrsPathResolver] = None
+                                        mockResolver: Option[DrsPathResolver] = None
 ) extends DrsCloudNioFileSystemProvider(config,
                                         GoogleOauthDrsCredentials(NoCredentials.getInstance, config),
                                         drsReadInterpreter
     ) {
 
-  override lazy val drsPathResolver: EngineDrsPathResolver =
+  override lazy val drsPathResolver: DrsPathResolver =
     mockResolver getOrElse
-      new MockEngineDrsPathResolver(
+      new MockDrsPathResolver(
         drsConfig = drsConfig,
-        httpClientBuilderOverride = httpClientBuilder,
-        accessTokenAcceptableTTL = Duration.Inf
+        httpClientBuilderOverride = httpClientBuilder
       )
 }
 
diff --git a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPathResolver.scala
similarity index 86%
rename from cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
rename to cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPathResolver.scala
index 1aff2f13470..9439c7d94ab 100644
--- a/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockEngineDrsPathResolver.scala
+++ b/cloud-nio/cloud-nio-impl-drs/src/test/scala/cloud/nio/impl/drs/MockDrsPathResolver.scala
@@ -10,12 +10,11 @@ import common.mock.MockSugar
 
 import scala.concurrent.duration.Duration
 
-class MockEngineDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfig,
-                                httpClientBuilderOverride: Option[HttpClientBuilder] = None,
-                                accessTokenAcceptableTTL: Duration = Duration.Inf
-) extends EngineDrsPathResolver(drsConfig,
-                                GoogleOauthDrsCredentials(NoCredentials.getInstance, accessTokenAcceptableTTL)
-    ) {
+class MockDrsPathResolver(drsConfig: DrsConfig = MockDrsPaths.mockDrsConfig,
+                          httpClientBuilderOverride: Option[HttpClientBuilder] = None,
+                          drsCredentials: DrsCredentials =
+                            GoogleOauthDrsCredentials(NoCredentials.getInstance, Duration.Inf)
+) extends DrsPathResolver(drsConfig, drsCredentials) {
 
   override protected lazy val httpClientBuilder: HttpClientBuilder =
     httpClientBuilderOverride getOrElse MockSugar.mock[HttpClientBuilder]
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
deleted file mode 100644
index 94cc30e103c..00000000000
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerDrsPathResolver.scala
+++ /dev/null
@@ -1,9 +0,0 @@
-package drs.localizer
-
-import cloud.nio.impl.drs.{DrsConfig, DrsCredentials, DrsPathResolver}
-import common.validation.ErrorOr.ErrorOr
-
-class DrsLocalizerDrsPathResolver(drsConfig: DrsConfig, drsCredentials: DrsCredentials)
-    extends DrsPathResolver(drsConfig) {
-  override def getAccessToken: ErrorOr[String] = drsCredentials.getAccessToken
-}
diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
index 29ad9d25bd1..64f36239db5 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/DrsLocalizerMain.scala
@@ -144,11 +144,11 @@ class DrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
     }
   }
 
-  def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] =
+  def getDrsPathResolver: IO[DrsPathResolver] =
     IO {
       val drsConfig = DrsConfig.fromEnv(sys.env)
       logger.info(s"Using ${drsConfig.drsResolverUrl} to resolve DRS Objects")
-      new DrsLocalizerDrsPathResolver(drsConfig, drsCredentials)
+      new DrsPathResolver(drsConfig, drsCredentials)
     }
 
   /**
@@ -182,9 +182,7 @@ class DrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
   /**
     * Runs a synchronous HTTP request to resolve the provided DRS URL with the provided resolver.
     */
-  def resolveSingleUrl(resolverObject: DrsLocalizerDrsPathResolver,
-                       drsUrlToResolve: UnresolvedDrsUrl
-  ): IO[ResolvedDrsUrl] = {
+  def resolveSingleUrl(resolverObject: DrsPathResolver, drsUrlToResolve: UnresolvedDrsUrl): IO[ResolvedDrsUrl] = {
     val fields = NonEmptyList.of(DrsResolverField.GsUri,
                                  DrsResolverField.GoogleServiceAccount,
                                  DrsResolverField.AccessUrl,
@@ -213,7 +211,7 @@ class DrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
       }
     }
 
-  def resolveWithRetries(resolverObject: DrsLocalizerDrsPathResolver,
+  def resolveWithRetries(resolverObject: DrsPathResolver,
                          drsUrlToResolve: UnresolvedDrsUrl,
                          resolutionRetries: Int,
                          backoff: Option[CloudNioBackoff],
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
index 1f3bfcfc623..dc06ad21a0c 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/DrsLocalizerMainSpec.scala
@@ -4,7 +4,7 @@ import cats.data.NonEmptyList
 import cats.effect.{ExitCode, IO}
 import cats.syntax.validated._
 import drs.localizer.MockDrsPaths.{fakeAccessUrls, fakeDrsUrlWithGcsResolutionOnly, fakeGoogleUrls}
-import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsCredentials, DrsResolverField, DrsResolverResponse}
+import cloud.nio.impl.drs.{AccessUrl, DrsConfig, DrsCredentials, DrsPathResolver, DrsResolverField, DrsResolverResponse}
 import common.assertion.CromwellTimeoutSpec
 import common.validation.ErrorOr.ErrorOr
 import drs.localizer.MockDrsLocalizerDrsPathResolver.{FakeAccessTokenStrategy, FakeHashes}
@@ -372,11 +372,11 @@ class MockDrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
                            requesterPaysProjectIdOption
     ) {
 
-  override def getDrsPathResolver: IO[DrsLocalizerDrsPathResolver] =
+  override def getDrsPathResolver: IO[DrsPathResolver] =
     IO {
       new MockDrsLocalizerDrsPathResolver(cloud.nio.impl.drs.MockDrsPaths.mockDrsConfig)
     }
-  override def resolveSingleUrl(resolverObject: DrsLocalizerDrsPathResolver,
+  override def resolveSingleUrl(resolverObject: DrsPathResolver,
                                 drsUrlToResolve: UnresolvedDrsUrl
   ): IO[ResolvedDrsUrl] =
     IO {
@@ -391,7 +391,7 @@ class MockDrsLocalizerMain(toResolveAndDownload: IO[List[UnresolvedDrsUrl]],
 }
 
 class MockDrsLocalizerDrsPathResolver(drsConfig: DrsConfig)
-    extends DrsLocalizerDrsPathResolver(drsConfig, FakeAccessTokenStrategy) {
+    extends DrsPathResolver(drsConfig, FakeAccessTokenStrategy) {
 
   override def resolveDrs(drsPath: String, fields: NonEmptyList[DrsResolverField.Value]): IO[DrsResolverResponse] = {
 
diff --git a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
index 2cee6c49b12..c9075333fca 100644
--- a/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
+++ b/filesystems/drs/src/test/scala/cromwell/filesystems/drs/DrsReaderSpec.scala
@@ -1,6 +1,6 @@
 package cromwell.filesystems.drs
 
-import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, DrsResolverResponse, MockEngineDrsPathResolver}
+import cloud.nio.impl.drs.{AccessUrl, DrsPathResolver, DrsResolverResponse, MockDrsPathResolver}
 import common.assertion.CromwellTimeoutSpec
 import cromwell.cloudsupport.gcp.auth.MockAuthMode
 import cromwell.core.WorkflowOptions
@@ -26,7 +26,7 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val googleAuthMode = MockAuthMode("unused")
     val workflowOptions = WorkflowOptions.empty
     val requesterPaysProjectIdOption = None
-    val drsPathResolver = new MockEngineDrsPathResolver()
+    val drsPathResolver = new MockDrsPathResolver()
     val gsUri = "gs://bucket/object"
     val googleServiceAccount = None
     val drsResolverResponse = DrsResolverResponse(gsUri = Option(gsUri), googleServiceAccount = googleServiceAccount)
@@ -46,7 +46,7 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val googleAuthMode = MockAuthMode("unused")
     val workflowOptions = WorkflowOptions.empty
     val requesterPaysProjectIdOption = None
-    val drsPathResolver = new MockEngineDrsPathResolver()
+    val drsPathResolver = new MockDrsPathResolver()
     val accessUrl = AccessUrl("https://host/object/path", Option(Map("hello" -> "world")))
     val drsResolverResponse = DrsResolverResponse(accessUrl = Option(accessUrl))
     val readerIo =
@@ -65,7 +65,7 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val googleAuthMode = MockAuthMode("unused")
     val workflowOptions = WorkflowOptions.empty
     val requesterPaysProjectIdOption = None
-    val drsPathResolver = new MockEngineDrsPathResolver()
+    val drsPathResolver = new MockDrsPathResolver()
     val drsResolverResponse = DrsResolverResponse()
     val readerIo =
       DrsReader.reader(Option(googleAuthMode),
@@ -90,7 +90,7 @@ class DrsReaderSpec extends AnyFlatSpecLike with CromwellTimeoutSpec with Matche
     val httpClientBuilder = mock[HttpClientBuilder]
     httpClientBuilder.build() returns httpClient
 
-    val drsPathResolver = new MockEngineDrsPathResolver(httpClientBuilderOverride = Option(httpClientBuilder))
+    val drsPathResolver = new MockDrsPathResolver(httpClientBuilderOverride = Option(httpClientBuilder))
 
     val accessUrl = AccessUrl("https://host/object/path", Option(Map("hello" -> "world")))
     val drsResolverResponse = DrsResolverResponse(accessUrl = Option(accessUrl))

From b79ead287217948e7333bf15a782ecbbc78800aa Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 14 Mar 2024 09:25:43 -0400
Subject: [PATCH 294/326] WX-757 Fix workflow stuck in aborting after WDL type
 error (#7385)

---
 .../nested_struct_bad_instantiation.inputs    |  4 +++
 .../nested_struct_bad_instantiation.wdl       | 27 +++++++++++++++++++
 .../nested_struct_bad_instantiation.test      | 14 ++++++++++
 .../execution/keys/ExpressionKey.scala        |  4 +--
 .../lifecycle/execution/package.scala         | 10 +++++++
 .../cromwell/SimpleWorkflowActorSpec.scala    |  2 +-
 .../expression/values/LiteralEvaluators.scala | 14 +++++-----
 7 files changed, 66 insertions(+), 9 deletions(-)
 create mode 100644 centaur/src/main/resources/standardTestCases/failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.inputs
 create mode 100644 centaur/src/main/resources/standardTestCases/failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.wdl
 create mode 100644 centaur/src/main/resources/standardTestCases/nested_struct_bad_instantiation.test

diff --git a/centaur/src/main/resources/standardTestCases/failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.inputs b/centaur/src/main/resources/standardTestCases/failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.inputs
new file mode 100644
index 00000000000..6f8cb64990a
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.inputs
@@ -0,0 +1,4 @@
+{
+    "MinimalStructExample.test": "Hello World",
+    "MinimalStructExample.integer": 2
+}
diff --git a/centaur/src/main/resources/standardTestCases/failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.wdl b/centaur/src/main/resources/standardTestCases/failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.wdl
new file mode 100644
index 00000000000..dce55da0bae
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.wdl
@@ -0,0 +1,27 @@
+version 1.0
+
+
+struct firstLayer {
+    String first
+    Int number
+}
+
+struct secondLayer {
+    String second
+    firstLayer lowerLayer
+}
+
+
+workflow MinimalStructExample {
+    input {
+        String test
+        Int integer
+    }
+
+    firstLayer example1 = {"first": test, "number": integer}
+    secondLayer example2 = {"second": test, "lowerLayer": example1}
+
+    output {
+        String example3 = example2.second
+    }
+}
diff --git a/centaur/src/main/resources/standardTestCases/nested_struct_bad_instantiation.test b/centaur/src/main/resources/standardTestCases/nested_struct_bad_instantiation.test
new file mode 100644
index 00000000000..a2608a0262c
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/nested_struct_bad_instantiation.test
@@ -0,0 +1,14 @@
+name: nested_struct_bad_instantiation
+testFormat: workflowfailure
+
+files {
+  workflow: failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.wdl
+  inputs: failures/nested_struct_bad_instantiation/nested_struct_bad_instantiation.inputs
+}
+
+metadata {
+  workflowName: MinimalStructExample
+  status: Failed
+  "failures.0.message": "Workflow failed"
+  "failures.0.causedBy.0.message": "Failed to evaluate 'example2' (reason 1 of 1): Evaluating { \"second\": test, \"lowerLayer\": example1 } failed: Cannot construct WomMapType(WomStringType,WomAnyType) with mixed types in map values: [WomString(Hello World), WomObject(Map(first -> WomString(Hello World), number -> WomInteger(2)),WomCompositeType(Map(first -> WomStringType, number -> WomIntegerType),Some(firstLayer)))]"
+}
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ExpressionKey.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ExpressionKey.scala
index 5fd8e36cac5..51183af9f04 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ExpressionKey.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/keys/ExpressionKey.scala
@@ -6,7 +6,7 @@ import common.validation.ErrorOr._
 import common.validation.Validation._
 import cromwell.core.ExecutionIndex._
 import cromwell.core.{ExecutionStatus, JobKey}
-import cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionDiff
+import cromwell.engine.workflow.lifecycle.execution.{WdlRuntimeException, WorkflowExecutionDiff}
 import cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.{
   ExpressionEvaluationFailedResponse,
   ExpressionEvaluationSucceededResponse
@@ -32,7 +32,7 @@ final case class ExpressionKey(node: ExpressionNodeLike, index: ExecutionIndex)
       .contextualizeErrors(s"evaluate '${node.fullyQualifiedName}'") match {
       case Right(result) => workflowExecutionActor ! ExpressionEvaluationSucceededResponse(this, result)
       case Left(f) =>
-        workflowExecutionActor ! ExpressionEvaluationFailedResponse(this, new RuntimeException(f.toList.mkString(", ")))
+        workflowExecutionActor ! ExpressionEvaluationFailedResponse(this, WdlRuntimeException(f.toList.mkString(", ")))
     }
 
     WorkflowExecutionDiff(Map(this -> ExecutionStatus.Running)).validNel
diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/package.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/package.scala
index 52fbe868f1e..e1695e1d355 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/package.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/package.scala
@@ -5,6 +5,16 @@ package execution {
   import cromwell.core.CallKey
   import wom.values.WomEvaluatedCallInputs
 
+  import scala.util.control.NoStackTrace
+
   final case class JobRunning(key: CallKey, inputs: WomEvaluatedCallInputs)
   final case class JobStarting(callKey: CallKey)
+
+  /**
+    * An exception specific to conditions inside the executing WDL, as opposed to one that is "Cromwell's fault"
+    * @param message Description suitable for user display
+    */
+  final case class WdlRuntimeException(message: String) extends RuntimeException with NoStackTrace {
+    override def getMessage: String = message
+  }
 }
diff --git a/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala b/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
index 4e67ac984a1..266e56060d9 100644
--- a/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
+++ b/server/src/test/scala/cromwell/SimpleWorkflowActorSpec.scala
@@ -192,7 +192,7 @@ class SimpleWorkflowActorSpec extends CromwellTestKitWordSpec with BeforeAndAfte
         workflowActor ! StartWorkflowCommand
       }
       Await.result(promise.future, TestExecutionTimeout)
-      probe.expectTerminated(workflowActor, 2.seconds)
+      probe.expectTerminated(workflowActor, 15.seconds)
       supervisor.expectMsgPF(AwaitAlmostNothing, "parent should get a failed response") {
         case x: WorkflowFailedResponse =>
           x.workflowId should be(workflowId)
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LiteralEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LiteralEvaluators.scala
index 4831c34e76b..e981b103688 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LiteralEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/LiteralEvaluators.scala
@@ -4,7 +4,9 @@ import cats.syntax.apply._
 import cats.syntax.traverse._
 import cats.syntax.validated._
 import cats.instances.list._
+import common.validation.ErrorOr
 import common.validation.ErrorOr.ErrorOr
+import common.validation.ErrorOr.NestedErrorOr
 import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement._
 import wdl.model.draft3.graph.expression.{EvaluatedValue, ForCommandInstantiationOptions, ValueEvaluator}
@@ -84,11 +86,11 @@ object LiteralEvaluators {
           ) mapN { (key, value) => key -> value }
       }
 
-      evaluated map { kvps =>
+      (evaluated map { kvps =>
         val value = kvps.map(entry => entry._1.value -> entry._2.value).toMap
         val sideEffectFiles = kvps.flatMap(entry => entry._1.sideEffectFiles ++ entry._2.sideEffectFiles)
-        EvaluatedValue(WomMap(value.toMap), sideEffectFiles)
-      }
+        ErrorOr(EvaluatedValue(WomMap.apply(value.toMap), sideEffectFiles))
+      }).flatten
     }
   }
 
@@ -103,11 +105,11 @@ object LiteralEvaluators {
         entry.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)
       }
 
-      evaluated map { evaluateds =>
+      (evaluated map { evaluateds =>
         val value = evaluateds.map(_.value)
         val sideEffectFiles = evaluateds.flatMap(_.sideEffectFiles)
-        EvaluatedValue(WomArray(value), sideEffectFiles)
-      }
+        ErrorOr(EvaluatedValue(WomArray.apply(value), sideEffectFiles))
+      }).flatten
     }
   }
 

From cac2b6ff45ffc64eae301381de410e1d73e6a830 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 14 Mar 2024 10:33:50 -0400
Subject: [PATCH 295/326] [WX-1506] Add jobLogger output for subworkflow
 running (with parent and subworkflow ID) (#7388)

Co-authored-by: jlester-msft <47044104+jlester-msft@users.noreply.github.com>
---
 .../lifecycle/execution/SubWorkflowExecutionActor.scala         | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala
index 861989de5f6..75649ebf547 100644
--- a/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala
+++ b/engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/SubWorkflowExecutionActor.scala
@@ -312,6 +312,8 @@ class SubWorkflowExecutionActor(key: SubWorkflowKey,
         }
     }
 
+    jobLogger.info(s"Running subworkflow: ${subWorkflowDescriptor.id}, root: ${parentWorkflow.rootWorkflow.id}")
+
     val workflowRootEvents = buildWorkflowRootMetadataEvents(subWorkflowDescriptor)
 
     serviceRegistryActor ! PutMetadataAction(events ++ inputEvents ++ workflowRootEvents)

From 171f3e9ab4b54515b9d7eb60bfe1677a402cbb45 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 14 Mar 2024 11:47:42 -0400
Subject: [PATCH 296/326] WX-757 Fix `stdout`, `stderr` in workflow body
 causing crashes (#7386)

---
 .../stderr_stdout_workflow_body.wdl                 |  8 ++++++++
 .../stderr_stdout_workflow_body.test                | 13 +++++++++++++
 .../values/EngineFunctionEvaluators.scala           |  4 ++--
 3 files changed, 23 insertions(+), 2 deletions(-)
 create mode 100644 centaur/src/main/resources/standardTestCases/failures/stderr_stdout_workflow_body/stderr_stdout_workflow_body.wdl
 create mode 100644 centaur/src/main/resources/standardTestCases/stderr_stdout_workflow_body.test

diff --git a/centaur/src/main/resources/standardTestCases/failures/stderr_stdout_workflow_body/stderr_stdout_workflow_body.wdl b/centaur/src/main/resources/standardTestCases/failures/stderr_stdout_workflow_body/stderr_stdout_workflow_body.wdl
new file mode 100644
index 00000000000..733d448a5ed
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/failures/stderr_stdout_workflow_body/stderr_stdout_workflow_body.wdl
@@ -0,0 +1,8 @@
+version 1.0
+
+workflow break_with_stderr {
+
+  output {
+    File load_data_csv = select_first([stdout(), stderr()])
+  }
+}
diff --git a/centaur/src/main/resources/standardTestCases/stderr_stdout_workflow_body.test b/centaur/src/main/resources/standardTestCases/stderr_stdout_workflow_body.test
new file mode 100644
index 00000000000..71cd116b44a
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/stderr_stdout_workflow_body.test
@@ -0,0 +1,13 @@
+name: stderr_stdout_workflow_body
+testFormat: workflowfailure
+
+files {
+  workflow: failures/stderr_stdout_workflow_body/stderr_stdout_workflow_body.wdl
+}
+
+metadata {
+  workflowName: break_with_stderr
+  status: Failed
+  "failures.0.message": "Workflow failed"
+  "failures.0.causedBy.0.message": "Failed to evaluate 'break_with_stderr.load_data_csv' (reason 1 of 2): Evaluating select_first([stdout(), stderr()]) failed: stdout is not implemented at the workflow level, Failed to evaluate 'break_with_stderr.load_data_csv' (reason 2 of 2): Evaluating select_first([stdout(), stderr()]) failed: stderr is not implemented at the workflow level"
+}
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
index 58c83c67edc..d539a182ece 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/values/EngineFunctionEvaluators.scala
@@ -51,7 +51,7 @@ object EngineFunctionEvaluators {
                                ioFunctionSet: IoFunctionSet,
                                forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
     )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] =
-      EvaluatedValue(WomSingleFile(ioFunctionSet.pathFunctions.stdout), Seq.empty).validNel
+      ErrorOr(EvaluatedValue(WomSingleFile(ioFunctionSet.pathFunctions.stdout), Seq.empty))
   }
 
   implicit val stderrFunctionEvaluator: ValueEvaluator[StderrElement.type] = new ValueEvaluator[StderrElement.type] {
@@ -60,7 +60,7 @@ object EngineFunctionEvaluators {
                                ioFunctionSet: IoFunctionSet,
                                forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
     )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[WomSingleFile]] =
-      EvaluatedValue(WomSingleFile(ioFunctionSet.pathFunctions.stderr), Seq.empty).validNel
+      ErrorOr(EvaluatedValue(WomSingleFile(ioFunctionSet.pathFunctions.stderr), Seq.empty))
   }
 
   private val ReadWaitTimeout = 60.seconds

From 027de62cf8e37f62330d76dba67ed07cce81a1ba Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Tue, 19 Mar 2024 13:25:14 -0400
Subject: [PATCH 297/326] WX-1519 Stop leaking DRS Localizer images on every CI
 run (#7390)

---
 src/ci/bin/test.inc.sh                                | 2 +-
 src/ci/bin/test_gcpbatch.inc.sh                       | 6 +++---
 src/ci/bin/test_papi.inc.sh                           | 5 ++---
 src/ci/resources/gcp_batch_application.inc.conf.ctmpl | 4 ++--
 4 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 7aebd3698fb..108a3d09843 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -199,7 +199,7 @@ cromwell::private::create_build_variables() {
     esac
 
     if [[ "${CROMWELL_BUILD_IS_CI}" == "true" ]]; then
-        CROMWELL_BUILD_DOCKER_TAG="${CROMWELL_BUILD_PROVIDER}-${CROMWELL_BUILD_NUMBER}"
+        CROMWELL_BUILD_DOCKER_TAG="${CROMWELL_BUILD_PROVIDER}-${CROMWELL_BUILD_TYPE}-${CROMWELL_BUILD_NUMBER}"
     else
         CROMWELL_BUILD_DOCKER_TAG="${CROMWELL_BUILD_PROVIDER}-${CROMWELL_BUILD_TYPE}-${CROMWELL_BUILD_GIT_HASH_SUFFIX}"
     fi
diff --git a/src/ci/bin/test_gcpbatch.inc.sh b/src/ci/bin/test_gcpbatch.inc.sh
index 641cd86d612..0a7c051ccf7 100644
--- a/src/ci/bin/test_gcpbatch.inc.sh
+++ b/src/ci/bin/test_gcpbatch.inc.sh
@@ -67,8 +67,7 @@ cromwell::private::batch::gcr_image_push() {
 
     cromwell::build::build_docker_image "${executable_name}" "${docker_image}"
     echo "${docker_image}" >> "${CROMWELL_BUILD_BATCH_GCR_IMAGES}"
-    # Use cat to quiet docker: https://github.com/moby/moby/issues/36655#issuecomment-375136087
-    docker push "${docker_image}" | cat
+    docker push --quiet "${docker_image}"
 }
 
 cromwell::private::batch::gcr_image_delete() {
@@ -86,7 +85,7 @@ cromwell::private::batch::setup_batch_gcr() {
     elif command -v docker; then
         # Upload images built from this commit
         gcloud auth configure-docker --quiet
-        CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS="gcr.io/${CROMWELL_BUILD_BATCH_PROJECT_ID}/cromwell-drs-localizer:${CROMWELL_BUILD_DOCKER_TAG}-batch"
+        CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS="gcr.io/${CROMWELL_BUILD_BATCH_PROJECT_ID}/cromwell-drs-localizer:${CROMWELL_BUILD_DOCKER_TAG}"
         cromwell::private::batch::gcr_image_push cromwell-drs-localizer "${CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS}"
         export CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS
     else
@@ -102,5 +101,6 @@ cromwell::private::batch::setup_batch_service_account() {
 
 cromwell::build::batch::setup_batch_centaur_environment() {
     cromwell::private::batch::setup_batch_gcloud
+    cromwell::private::batch::setup_batch_gcr
     cromwell::private::batch::setup_batch_service_account
 }
diff --git a/src/ci/bin/test_papi.inc.sh b/src/ci/bin/test_papi.inc.sh
index 0b4ed151664..5c59ee1b38f 100644
--- a/src/ci/bin/test_papi.inc.sh
+++ b/src/ci/bin/test_papi.inc.sh
@@ -66,8 +66,7 @@ cromwell::private::papi::gcr_image_push() {
 
     cromwell::build::build_docker_image "${executable_name}" "${docker_image}"
     echo "${docker_image}" >> "${CROMWELL_BUILD_PAPI_GCR_IMAGES}"
-    # Use cat to quiet docker: https://github.com/moby/moby/issues/36655#issuecomment-375136087
-    docker push "${docker_image}" | cat
+    docker push --quiet "${docker_image}"
 }
 
 cromwell::private::papi::gcr_image_delete() {
@@ -85,7 +84,7 @@ cromwell::private::papi::setup_papi_gcr() {
     elif command -v docker; then
         # Upload images built from this commit
         gcloud auth configure-docker --quiet
-        CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS="gcr.io/${CROMWELL_BUILD_PAPI_PROJECT_ID}/cromwell-drs-localizer:${CROMWELL_BUILD_DOCKER_TAG}-papi"
+        CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS="gcr.io/${CROMWELL_BUILD_PAPI_PROJECT_ID}/cromwell-drs-localizer:${CROMWELL_BUILD_DOCKER_TAG}"
         cromwell::private::papi::gcr_image_push cromwell-drs-localizer "${CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS}"
         export CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS
     else
diff --git a/src/ci/resources/gcp_batch_application.inc.conf.ctmpl b/src/ci/resources/gcp_batch_application.inc.conf.ctmpl
index aebdd7ea377..bedffda63df 100644
--- a/src/ci/resources/gcp_batch_application.inc.conf.ctmpl
+++ b/src/ci/resources/gcp_batch_application.inc.conf.ctmpl
@@ -67,7 +67,7 @@ filesystems.drs.global.config.resolver.url = "https://drshub.dsde-dev.broadinsti
 
 drs {
   localization {
-    docker-image = "Error: BA-6546 The environment variable CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS must be set/export pointing to a valid docker image"
-    docker-image = ${?CROMWELL_BUILD_PAPI_DOCKER_IMAGE_DRS}
+    docker-image = "Error: BA-6546 The environment variable CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS must be set/export pointing to a valid docker image"
+    docker-image = ${?CROMWELL_BUILD_BATCH_DOCKER_IMAGE_DRS}
   }
 }

From 2f8c46dcba0162e2dc91ba06238aea08bd170fde Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Fri, 29 Mar 2024 09:32:45 -0400
Subject: [PATCH 298/326] [WX-1460] WDL 1.1 Struct Literal Parsing (#7391)

Co-authored-by: Janet Gainer-Dewar <jdewar@broadinstitute.org>
---
 .../standardTestCases/struct_literal.test     |   12 +
 .../struct_literal/struct_literal.wdl         |   68 +
 .../draft3/elements/ExpressionElement.scala   |    2 +
 .../java/wdl/biscayne/parser/WdlParser.java   | 1944 +++++++++--------
 .../biscayne/src/main/resources/CHANGELOG.txt |   13 +-
 .../biscayne/src/main/resources/grammar.hgr   |    1 +
 .../BiscayneExpressionValueConsumers.scala    |   10 +
 .../expression/consumed/consumed.scala        |    1 +
 .../files/BiscayneFileEvaluators.scala        |   43 +-
 .../linking/expression/files/files.scala      |    3 +-
 .../types/BiscayneTypeEvaluators.scala        |   12 +
 .../linking/expression/types/types.scala      |    1 +
 .../values/BiscayneValueEvaluators.scala      |   27 +-
 .../linking/expression/values/values.scala    |    3 +-
 .../src/test/cases/struct_literal.wdl         |   39 +
 .../transforms/biscayne/Ast2WdlomSpec.scala   |   11 +-
 .../ast2wdlom/WdlFileToWdlomSpec.scala        |  106 +-
 ...BiscayneExpressionValueConsumersSpec.scala |    9 +
 .../files/BiscayneFileEvaluatorSpec.scala     |   11 +
 .../types/BiscayneTypeEvaluatorSpec.scala     |   10 +
 .../values/BiscayneValueEvaluatorSpec.scala   |   12 +-
 .../java/wdl/cascades/parser/WdlParser.java   | 1942 ++++++++--------
 .../cascades/src/main/resources/CHANGELOG.txt |   13 +-
 .../cascades/src/main/resources/grammar.hgr   |    1 +
 .../CascadesExpressionValueConsumers.scala    |   10 +
 .../expression/consumed/consumed.scala        |    1 +
 .../files/CascadesFileEvaluators.scala        |   42 +-
 .../linking/expression/files/files.scala      |    2 +
 .../types/CascadesTypeEvaluators.scala        |   12 +
 .../linking/expression/types/types.scala      |    1 +
 .../values/CascadesValueEvaluators.scala      |   27 +-
 .../linking/expression/values/values.scala    |    2 +
 .../src/test/cases/struct_literal.wdl         |   39 +
 .../transforms/cascades/Ast2WdlomSpec.scala   |   12 +-
 .../ast2wdlom/WdlFileToWdlomSpec.scala        |  100 +-
 ...CascadesExpressionValueConsumersSpec.scala |    9 +
 .../files/CascadesFileEvaluatorSpec.scala     |   11 +
 .../types/CascadesTypeEvaluatorSpec.scala     |   10 +
 .../values/CascadesValueEvaluatorSpec.scala   |   12 +-
 .../transforms/ast2wdlom/Ast2WdlomSpec.scala  |    8 +
 .../AstNodeToExpressionElement.scala          |    6 +
 .../base/wdlom2wdl/WdlWriterImpl.scala        |    6 +
 42 files changed, 2666 insertions(+), 1938 deletions(-)
 create mode 100644 centaur/src/main/resources/standardTestCases/struct_literal.test
 create mode 100644 centaur/src/main/resources/standardTestCases/struct_literal/struct_literal.wdl
 create mode 100644 wdl/transforms/biscayne/src/test/cases/struct_literal.wdl
 create mode 100644 wdl/transforms/cascades/src/test/cases/struct_literal.wdl

diff --git a/centaur/src/main/resources/standardTestCases/struct_literal.test b/centaur/src/main/resources/standardTestCases/struct_literal.test
new file mode 100644
index 00000000000..72755145a02
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/struct_literal.test
@@ -0,0 +1,12 @@
+name: struct_literal
+testFormat: workflowsuccess
+
+files {
+  workflow: struct_literal/struct_literal.wdl
+}
+
+metadata {
+  workflowName: struct_literal
+  status: Succeeded
+  "outputs.struct_literal.out": 44
+}
diff --git a/centaur/src/main/resources/standardTestCases/struct_literal/struct_literal.wdl b/centaur/src/main/resources/standardTestCases/struct_literal/struct_literal.wdl
new file mode 100644
index 00000000000..215fd40f8d3
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/struct_literal/struct_literal.wdl
@@ -0,0 +1,68 @@
+version development-1.1
+
+struct Plant {
+  String color
+  Int id
+}
+
+struct Fungi {
+    File fungiFile
+}
+
+
+struct Animal {
+  Plant jacket
+  Fungi hat
+}
+
+task a {
+    input {
+      Plant in_plant_literal = Plant{color: "red", id: 44}
+    }
+
+  command {
+    echo "${in_plant_literal.id}"
+  }
+
+  output {
+    Animal out_animal = Animal{jacket: Plant{color: "green", id: 10}, hat: Fungi{fungiFile: stdout()}}
+  }
+
+  runtime {
+    docker: "ubuntu:latest"
+ }
+
+  meta {
+    volatile: true
+  }
+}
+
+task b {
+  input {
+  Animal in_animal
+  }
+
+  command {
+    cat ${in_animal.hat.fungiFile}
+  }
+
+  output {
+    Int out = read_int(stdout())
+  }
+
+  runtime {
+   docker: "ubuntu:latest"
+ }
+
+  meta {
+   volatile: true
+  }
+}
+
+workflow struct_literal {
+  call a
+  call b {input: in_animal=a.out_animal}
+  output {
+    Int out = b.out
+  }
+}
diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
index d6d8948d700..44e4c60a23a 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/elements/ExpressionElement.scala
@@ -33,6 +33,8 @@ object ExpressionElement {
 
   final case class KvPair(key: String, value: ExpressionElement)
   final case class ObjectLiteral(elements: Map[String, ExpressionElement]) extends ExpressionElement
+  final case class StructLiteral(structTypeName: String, elements: Map[String, ExpressionElement])
+      extends ExpressionElement
   final case class ArrayLiteral(elements: Seq[ExpressionElement]) extends ExpressionElement
   final case class MapLiteral(elements: Map[ExpressionElement, ExpressionElement]) extends ExpressionElement
   final case class PairLiteral(left: ExpressionElement, right: ExpressionElement) extends ExpressionElement
diff --git a/wdl/transforms/biscayne/src/main/java/wdl/biscayne/parser/WdlParser.java b/wdl/transforms/biscayne/src/main/java/wdl/biscayne/parser/WdlParser.java
index 26a2ea35d2e..3e4867c7784 100644
--- a/wdl/transforms/biscayne/src/main/java/wdl/biscayne/parser/WdlParser.java
+++ b/wdl/transforms/biscayne/src/main/java/wdl/biscayne/parser/WdlParser.java
@@ -1,9 +1,9 @@
 
 /*
- * This file was generated by Hermes Parser Generator on Wed Mar 22 19:44:20 2023
+ * This file was generated by Hermes Parser Generator on Fri Mar 15 14:50:13 2024
  * 
- * Hermes command: hermes generate resources/grammar.hgr --language=java --directory=./java --name=wdl --java-package=wdl.biscayne.parser --java-use-apache-commons --java-imports=org.apache.commons.lang3.StringEscapeUtils --header
- * Run from: .. (relative to this file)
+ * Hermes command: hermes generate src/main/resources/grammar.hgr --language=java --directory=src/main/java --name=wdl --java-package=wdl.biscayne.parser --java-use-apache-commons --java-imports=org.apache.commons.lang3.StringEscapeUtils --header
+ * Run from: ../../.. (relative to this file)
  * Hermes version: hermes-parser 2.0rc6
  * 
  * !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
@@ -252,12 +252,12 @@ public interface ParseTreeNode {
     }
     public static class Terminal implements AstNode, ParseTreeNode
     {
-        public int id;
-        public String terminal_str;
-        public String source_string;
-        public String resource;
-        public int line;
-        public int col;
+        private int id;
+        private String terminal_str;
+        private String source_string;
+        private String resource;
+        private int line;
+        private int col;
         public Terminal(int id, String terminal_str, String source_string, String resource, int line, int col) {
             this.id = id;
             this.terminal_str = terminal_str;
@@ -516,73 +516,73 @@ public interface TerminalIdentifier {
         public String string();
     }
     public enum WdlTerminalIdentifier implements TerminalIdentifier {
-        TERMINAL_AFTER(23, "after"),
-        TERMINAL_ALIAS(27, "alias"),
-        TERMINAL_AS(10, "as"),
-        TERMINAL_ASTERISK(18, "asterisk"),
-        TERMINAL_BOOLEAN(13, "boolean"),
-        TERMINAL_CALL(60, "call"),
-        TERMINAL_CMD_ATTR_HINT(50, "cmd_attr_hint"),
-        TERMINAL_CMD_PART(11, "cmd_part"),
-        TERMINAL_COLON(28, "colon"),
-        TERMINAL_COMMA(19, "comma"),
-        TERMINAL_DASH(32, "dash"),
-        TERMINAL_DOT(42, "dot"),
-        TERMINAL_DOUBLE_AMPERSAND(29, "double_ampersand"),
-        TERMINAL_DOUBLE_EQUAL(53, "double_equal"),
-        TERMINAL_DOUBLE_PIPE(45, "double_pipe"),
-        TERMINAL_E(22, "e"),
-        TERMINAL_ELSE(57, "else"),
-        TERMINAL_EQUAL(31, "equal"),
-        TERMINAL_ESCAPE(1, "escape"),
-        TERMINAL_EXPRESSION_PLACEHOLDER_END(14, "expression_placeholder_end"),
-        TERMINAL_EXPRESSION_PLACEHOLDER_START(65, "expression_placeholder_start"),
-        TERMINAL_FLOAT(49, "float"),
-        TERMINAL_FQN(34, "fqn"),
-        TERMINAL_GT(2, "gt"),
-        TERMINAL_GTEQ(52, "gteq"),
-        TERMINAL_IDENTIFIER(46, "identifier"),
-        TERMINAL_IF(63, "if"),
-        TERMINAL_IMPORT(55, "import"),
-        TERMINAL_IN(39, "in"),
-        TERMINAL_INPUT(44, "input"),
-        TERMINAL_INTEGER(16, "integer"),
-        TERMINAL_LBRACE(59, "lbrace"),
-        TERMINAL_LPAREN(15, "lparen"),
-        TERMINAL_LSQUARE(17, "lsquare"),
-        TERMINAL_LT(36, "lt"),
-        TERMINAL_LTEQ(40, "lteq"),
-        TERMINAL_META(61, "meta"),
-        TERMINAL_META_VALUE(48, "meta_value"),
-        TERMINAL_NONE(43, "none"),
-        TERMINAL_NOT(12, "not"),
-        TERMINAL_NOT_EQUAL(51, "not_equal"),
-        TERMINAL_NULL(24, "null"),
-        TERMINAL_OBJECT(58, "object"),
-        TERMINAL_OUTPUT(7, "output"),
-        TERMINAL_PARAMETER_META(54, "parameter_meta"),
-        TERMINAL_PERCENT(64, "percent"),
-        TERMINAL_PLUS(33, "plus"),
-        TERMINAL_QMARK(21, "qmark"),
-        TERMINAL_QUOTE(20, "quote"),
-        TERMINAL_RAW_CMD_END(9, "raw_cmd_end"),
-        TERMINAL_RAW_CMD_START(26, "raw_cmd_start"),
-        TERMINAL_RAW_COMMAND(47, "raw_command"),
-        TERMINAL_RBRACE(66, "rbrace"),
-        TERMINAL_RPAREN(6, "rparen"),
-        TERMINAL_RSQUARE(3, "rsquare"),
-        TERMINAL_RUNTIME(8, "runtime"),
-        TERMINAL_SCATTER(62, "scatter"),
-        TERMINAL_SLASH(37, "slash"),
-        TERMINAL_STRING(0, "string"),
-        TERMINAL_STRUCT(5, "struct"),
-        TERMINAL_TASK(56, "task"),
-        TERMINAL_THEN(41, "then"),
-        TERMINAL_TYPE(30, "type"),
-        TERMINAL_TYPE_E(25, "type_e"),
-        TERMINAL_VERSION(4, "version"),
-        TERMINAL_VERSION_NAME(38, "version_name"),
-        TERMINAL_WORKFLOW(35, "workflow"),
+        TERMINAL_AFTER(22, "after"),
+        TERMINAL_ALIAS(60, "alias"),
+        TERMINAL_AS(44, "as"),
+        TERMINAL_ASTERISK(21, "asterisk"),
+        TERMINAL_BOOLEAN(49, "boolean"),
+        TERMINAL_CALL(41, "call"),
+        TERMINAL_CMD_ATTR_HINT(61, "cmd_attr_hint"),
+        TERMINAL_CMD_PART(65, "cmd_part"),
+        TERMINAL_COLON(25, "colon"),
+        TERMINAL_COMMA(46, "comma"),
+        TERMINAL_DASH(42, "dash"),
+        TERMINAL_DOT(45, "dot"),
+        TERMINAL_DOUBLE_AMPERSAND(63, "double_ampersand"),
+        TERMINAL_DOUBLE_EQUAL(56, "double_equal"),
+        TERMINAL_DOUBLE_PIPE(40, "double_pipe"),
+        TERMINAL_E(10, "e"),
+        TERMINAL_ELSE(66, "else"),
+        TERMINAL_EQUAL(51, "equal"),
+        TERMINAL_ESCAPE(35, "escape"),
+        TERMINAL_EXPRESSION_PLACEHOLDER_END(58, "expression_placeholder_end"),
+        TERMINAL_EXPRESSION_PLACEHOLDER_START(7, "expression_placeholder_start"),
+        TERMINAL_FLOAT(17, "float"),
+        TERMINAL_FQN(14, "fqn"),
+        TERMINAL_GT(18, "gt"),
+        TERMINAL_GTEQ(34, "gteq"),
+        TERMINAL_IDENTIFIER(5, "identifier"),
+        TERMINAL_IF(55, "if"),
+        TERMINAL_IMPORT(32, "import"),
+        TERMINAL_IN(4, "in"),
+        TERMINAL_INPUT(33, "input"),
+        TERMINAL_INTEGER(36, "integer"),
+        TERMINAL_LBRACE(3, "lbrace"),
+        TERMINAL_LPAREN(64, "lparen"),
+        TERMINAL_LSQUARE(39, "lsquare"),
+        TERMINAL_LT(57, "lt"),
+        TERMINAL_LTEQ(48, "lteq"),
+        TERMINAL_META(31, "meta"),
+        TERMINAL_META_VALUE(38, "meta_value"),
+        TERMINAL_NONE(24, "none"),
+        TERMINAL_NOT(43, "not"),
+        TERMINAL_NOT_EQUAL(20, "not_equal"),
+        TERMINAL_NULL(9, "null"),
+        TERMINAL_OBJECT(26, "object"),
+        TERMINAL_OUTPUT(54, "output"),
+        TERMINAL_PARAMETER_META(8, "parameter_meta"),
+        TERMINAL_PERCENT(6, "percent"),
+        TERMINAL_PLUS(59, "plus"),
+        TERMINAL_QMARK(1, "qmark"),
+        TERMINAL_QUOTE(28, "quote"),
+        TERMINAL_RAW_CMD_END(62, "raw_cmd_end"),
+        TERMINAL_RAW_CMD_START(50, "raw_cmd_start"),
+        TERMINAL_RAW_COMMAND(23, "raw_command"),
+        TERMINAL_RBRACE(0, "rbrace"),
+        TERMINAL_RPAREN(11, "rparen"),
+        TERMINAL_RSQUARE(47, "rsquare"),
+        TERMINAL_RUNTIME(53, "runtime"),
+        TERMINAL_SCATTER(15, "scatter"),
+        TERMINAL_SLASH(30, "slash"),
+        TERMINAL_STRING(16, "string"),
+        TERMINAL_STRUCT(37, "struct"),
+        TERMINAL_TASK(29, "task"),
+        TERMINAL_THEN(19, "then"),
+        TERMINAL_TYPE(27, "type"),
+        TERMINAL_TYPE_E(13, "type_e"),
+        TERMINAL_VERSION(52, "version"),
+        TERMINAL_VERSION_NAME(12, "version_name"),
+        TERMINAL_WORKFLOW(2, "workflow"),
         END_SENTINAL(-3, "END_SENTINAL");
         private final int id;
         private final String string;
@@ -595,112 +595,112 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
     }
     /* table[nonterminal][terminal] = rule */
     private static final int[][] table = {
+        { -1, -1, -1, -1, -1, 53, -1, -1, -1, -1, -1, -1, -1, 53, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 53, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, 63, -1, -1, 68, -1, -1, -1, -1, 63, -1, 65, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 63, -1, -1, -1, 69, -1, 66, -1, -1, -1, -1, -1, -1, -1, 62, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 67, 64, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { 14, 15, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 84, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, 47, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { 77, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 76, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, 87, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { 52, -1, -1, -1, -1, 52, -1, -1, -1, -1, -1, -1, -1, 52, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 52, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 51, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 34, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 9, -1, -1, -1, -1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, 49, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 80, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
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+        { -1, -1, -1, 44, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 81, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 86, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 88, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, 28, 29, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 32, -1, -1, -1, -1, 32, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 27, -1, 32, 26, -1, -1, -1, -1, -1, -1, 30, -1, -1, -1, -1, -1, -1, 31, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 75, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 23, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 81, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, 38, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 39, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { 16, 16, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 17, -1 },
-        { -1, -1, -1, -1, -1, 19, -1, -1, -1, -1, 18, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 19, -1, -1, -1, -1, -1, -1, -1, 19, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 19, 19, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 39, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 61, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 75, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 25, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 46, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, 67, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 63, -1, -1, -1, -1, 63, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 66, -1, 63, -1, -1, -1, -1, -1, -1, -1, 68, -1, -1, -1, -1, -1, 62, 69, 65, 64, -1, -1, -1 },
-        { -1, -1, -1, -1, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 13, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
-        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 49, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, 61, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
     };
     static {
         Map<Integer, List<TerminalIdentifier>> map = new HashMap<Integer, List<TerminalIdentifier>>();
-        map.put(75, Arrays.asList(new TerminalIdentifier[] {
+        map.put(82, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
         }));
-        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+        map.put(90, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(115, Arrays.asList(new TerminalIdentifier[] {
+        map.put(68, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(68, Arrays.asList(new TerminalIdentifier[] {
+        map.put(101, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(76, Arrays.asList(new TerminalIdentifier[] {
+        map.put(86, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(117, Arrays.asList(new TerminalIdentifier[] {
+        map.put(75, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_EQUAL,
         }));
-        map.put(89, Arrays.asList(new TerminalIdentifier[] {
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+        map.put(115, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -712,27 +712,27 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(79, Arrays.asList(new TerminalIdentifier[] {
+        map.put(103, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(95, Arrays.asList(new TerminalIdentifier[] {
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
         }));
-        map.put(81, Arrays.asList(new TerminalIdentifier[] {
+        map.put(89, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(88, Arrays.asList(new TerminalIdentifier[] {
+        map.put(73, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INPUT,
         }));
-        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(87, Arrays.asList(new TerminalIdentifier[] {
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(91, Arrays.asList(new TerminalIdentifier[] {
+        map.put(102, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_FLOAT,
             WdlTerminalIdentifier.TERMINAL_INTEGER,
@@ -742,15 +742,18 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_NULL,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(110, Arrays.asList(new TerminalIdentifier[] {
+        map.put(109, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(70, Arrays.asList(new TerminalIdentifier[] {
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(108, Arrays.asList(new TerminalIdentifier[] {
+        map.put(80, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(76, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -767,10 +770,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(135, Arrays.asList(new TerminalIdentifier[] {
-            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
-        }));
-        map.put(119, Arrays.asList(new TerminalIdentifier[] {
+        map.put(108, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -787,22 +787,22 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(92, Arrays.asList(new TerminalIdentifier[] {
+        map.put(139, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(114, Arrays.asList(new TerminalIdentifier[] {
+        map.put(70, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+        map.put(100, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(102, Arrays.asList(new TerminalIdentifier[] {
+        map.put(83, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
         }));
-        map.put(104, Arrays.asList(new TerminalIdentifier[] {
+        map.put(88, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -813,44 +813,44 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(140, Arrays.asList(new TerminalIdentifier[] {
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
         }));
-        map.put(109, Arrays.asList(new TerminalIdentifier[] {
+        map.put(104, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
         }));
-        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(124, Arrays.asList(new TerminalIdentifier[] {
+        map.put(137, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
         }));
-        map.put(78, Arrays.asList(new TerminalIdentifier[] {
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
         }));
-        map.put(86, Arrays.asList(new TerminalIdentifier[] {
+        map.put(78, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INPUT,
         }));
-        map.put(118, Arrays.asList(new TerminalIdentifier[] {
+        map.put(117, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(72, Arrays.asList(new TerminalIdentifier[] {
+        map.put(91, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
         }));
-        map.put(99, Arrays.asList(new TerminalIdentifier[] {
+        map.put(95, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
         }));
-        map.put(93, Arrays.asList(new TerminalIdentifier[] {
+        map.put(96, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(138, Arrays.asList(new TerminalIdentifier[] {
+        map.put(97, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_VERSION,
         }));
-        map.put(107, Arrays.asList(new TerminalIdentifier[] {
+        map.put(79, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -867,44 +867,44 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(97, Arrays.asList(new TerminalIdentifier[] {
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
         }));
-        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
         }));
-        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(94, Arrays.asList(new TerminalIdentifier[] {
+        map.put(120, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IF,
         }));
-        map.put(82, Arrays.asList(new TerminalIdentifier[] {
+        map.put(81, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
         }));
-        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+        map.put(85, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
         }));
-        map.put(96, Arrays.asList(new TerminalIdentifier[] {
+        map.put(107, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(83, Arrays.asList(new TerminalIdentifier[] {
+        map.put(67, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+        map.put(105, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(106, Arrays.asList(new TerminalIdentifier[] {
+        map.put(112, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INPUT,
         }));
-        map.put(116, Arrays.asList(new TerminalIdentifier[] {
+        map.put(114, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(100, Arrays.asList(new TerminalIdentifier[] {
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -921,16 +921,16 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+        map.put(106, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_META,
         }));
-        map.put(112, Arrays.asList(new TerminalIdentifier[] {
+        map.put(93, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(141, Arrays.asList(new TerminalIdentifier[] {
+        map.put(77, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(120, Arrays.asList(new TerminalIdentifier[] {
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_FLOAT,
             WdlTerminalIdentifier.TERMINAL_INTEGER,
@@ -940,59 +940,59 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_NULL,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+        map.put(74, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(77, Arrays.asList(new TerminalIdentifier[] {
+        map.put(87, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(84, Arrays.asList(new TerminalIdentifier[] {
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_OUTPUT,
         }));
-        map.put(105, Arrays.asList(new TerminalIdentifier[] {
+        map.put(72, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
         }));
-        map.put(85, Arrays.asList(new TerminalIdentifier[] {
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(80, Arrays.asList(new TerminalIdentifier[] {
+        map.put(84, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RUNTIME,
         }));
-        map.put(121, Arrays.asList(new TerminalIdentifier[] {
+        map.put(116, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_SCATTER,
         }));
-        map.put(101, Arrays.asList(new TerminalIdentifier[] {
+        map.put(113, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_EQUAL,
         }));
-        map.put(98, Arrays.asList(new TerminalIdentifier[] {
+        map.put(99, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(69, Arrays.asList(new TerminalIdentifier[] {
+        map.put(118, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(139, Arrays.asList(new TerminalIdentifier[] {
+        map.put(111, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+        map.put(92, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(74, Arrays.asList(new TerminalIdentifier[] {
+        map.put(94, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
         }));
-        map.put(73, Arrays.asList(new TerminalIdentifier[] {
+        map.put(110, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(113, Arrays.asList(new TerminalIdentifier[] {
+        map.put(138, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_TASK,
         }));
-        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+        map.put(98, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1003,15 +1003,15 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(67, Arrays.asList(new TerminalIdentifier[] {
+        map.put(140, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(71, Arrays.asList(new TerminalIdentifier[] {
+        map.put(121, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_VERSION,
         }));
-        map.put(137, Arrays.asList(new TerminalIdentifier[] {
+        map.put(69, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1023,48 +1023,48 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(103, Arrays.asList(new TerminalIdentifier[] {
+        map.put(71, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_META,
         }));
-        map.put(111, Arrays.asList(new TerminalIdentifier[] {
+        map.put(119, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
         }));
-        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+        map.put(141, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
         nonterminal_first = Collections.unmodifiableMap(map);
     }
     static {
         Map<Integer, List<TerminalIdentifier>> map = new HashMap<Integer, List<TerminalIdentifier>>();
-        map.put(75, Arrays.asList(new TerminalIdentifier[] {
+        map.put(82, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+        map.put(90, Arrays.asList(new TerminalIdentifier[] {
         }));
-        map.put(115, Arrays.asList(new TerminalIdentifier[] {
+        map.put(68, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(68, Arrays.asList(new TerminalIdentifier[] {
+        map.put(101, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(76, Arrays.asList(new TerminalIdentifier[] {
+        map.put(86, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(117, Arrays.asList(new TerminalIdentifier[] {
+        map.put(75, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(89, Arrays.asList(new TerminalIdentifier[] {
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+        map.put(115, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(79, Arrays.asList(new TerminalIdentifier[] {
+        map.put(103, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1078,7 +1078,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(95, Arrays.asList(new TerminalIdentifier[] {
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1092,7 +1092,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(81, Arrays.asList(new TerminalIdentifier[] {
+        map.put(89, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1105,60 +1105,60 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(88, Arrays.asList(new TerminalIdentifier[] {
+        map.put(73, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(87, Arrays.asList(new TerminalIdentifier[] {
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(91, Arrays.asList(new TerminalIdentifier[] {
+        map.put(102, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(110, Arrays.asList(new TerminalIdentifier[] {
+        map.put(109, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(70, Arrays.asList(new TerminalIdentifier[] {
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(108, Arrays.asList(new TerminalIdentifier[] {
+        map.put(80, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(76, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RPAREN,
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(135, Arrays.asList(new TerminalIdentifier[] {
-            WdlTerminalIdentifier.TERMINAL_RBRACE,
-        }));
-        map.put(119, Arrays.asList(new TerminalIdentifier[] {
+        map.put(108, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(92, Arrays.asList(new TerminalIdentifier[] {
+        map.put(139, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(114, Arrays.asList(new TerminalIdentifier[] {
+        map.put(70, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+        map.put(100, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(102, Arrays.asList(new TerminalIdentifier[] {
+        map.put(83, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(104, Arrays.asList(new TerminalIdentifier[] {
+        map.put(88, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(140, Arrays.asList(new TerminalIdentifier[] {
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
         }));
-        map.put(109, Arrays.asList(new TerminalIdentifier[] {
+        map.put(104, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -1175,7 +1175,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1189,7 +1189,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(124, Arrays.asList(new TerminalIdentifier[] {
+        map.put(137, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1202,7 +1202,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(78, Arrays.asList(new TerminalIdentifier[] {
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1217,10 +1217,10 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(86, Arrays.asList(new TerminalIdentifier[] {
+        map.put(78, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(118, Arrays.asList(new TerminalIdentifier[] {
+        map.put(117, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1233,7 +1233,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(72, Arrays.asList(new TerminalIdentifier[] {
+        map.put(91, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1245,12 +1245,12 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(99, Arrays.asList(new TerminalIdentifier[] {
+        map.put(95, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
         }));
-        map.put(93, Arrays.asList(new TerminalIdentifier[] {
+        map.put(96, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1265,9 +1265,9 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(138, Arrays.asList(new TerminalIdentifier[] {
+        map.put(97, Arrays.asList(new TerminalIdentifier[] {
         }));
-        map.put(107, Arrays.asList(new TerminalIdentifier[] {
+        map.put(79, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ASTERISK,
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_CALL,
@@ -1315,7 +1315,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(97, Arrays.asList(new TerminalIdentifier[] {
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
@@ -1323,7 +1323,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
             WdlTerminalIdentifier.TERMINAL_DASH,
@@ -1341,12 +1341,12 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(94, Arrays.asList(new TerminalIdentifier[] {
+        map.put(120, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1359,37 +1359,37 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(82, Arrays.asList(new TerminalIdentifier[] {
+        map.put(81, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+        map.put(85, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(96, Arrays.asList(new TerminalIdentifier[] {
+        map.put(107, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(83, Arrays.asList(new TerminalIdentifier[] {
+        map.put(67, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+        map.put(105, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(106, Arrays.asList(new TerminalIdentifier[] {
+        map.put(112, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1404,15 +1404,15 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(116, Arrays.asList(new TerminalIdentifier[] {
+        map.put(114, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(100, Arrays.asList(new TerminalIdentifier[] {
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+        map.put(106, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1424,12 +1424,12 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(112, Arrays.asList(new TerminalIdentifier[] {
+        map.put(93, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(141, Arrays.asList(new TerminalIdentifier[] {
+        map.put(77, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1444,23 +1444,23 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(120, Arrays.asList(new TerminalIdentifier[] {
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+        map.put(74, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(77, Arrays.asList(new TerminalIdentifier[] {
+        map.put(87, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(84, Arrays.asList(new TerminalIdentifier[] {
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1475,7 +1475,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(105, Arrays.asList(new TerminalIdentifier[] {
+        map.put(72, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1487,7 +1487,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(85, Arrays.asList(new TerminalIdentifier[] {
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1499,7 +1499,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(80, Arrays.asList(new TerminalIdentifier[] {
+        map.put(84, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1511,7 +1511,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(121, Arrays.asList(new TerminalIdentifier[] {
+        map.put(116, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1524,7 +1524,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(101, Arrays.asList(new TerminalIdentifier[] {
+        map.put(113, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1539,7 +1539,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(98, Arrays.asList(new TerminalIdentifier[] {
+        map.put(99, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1550,13 +1550,13 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(69, Arrays.asList(new TerminalIdentifier[] {
+        map.put(118, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(139, Arrays.asList(new TerminalIdentifier[] {
+        map.put(111, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ASTERISK,
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_CALL,
@@ -1604,29 +1604,29 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+        map.put(92, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(74, Arrays.asList(new TerminalIdentifier[] {
+        map.put(94, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(73, Arrays.asList(new TerminalIdentifier[] {
+        map.put(110, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(113, Arrays.asList(new TerminalIdentifier[] {
+        map.put(138, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+        map.put(98, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1638,15 +1638,15 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(67, Arrays.asList(new TerminalIdentifier[] {
+        map.put(140, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(71, Arrays.asList(new TerminalIdentifier[] {
+        map.put(121, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
         }));
-        map.put(137, Arrays.asList(new TerminalIdentifier[] {
+        map.put(69, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1659,7 +1659,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(103, Arrays.asList(new TerminalIdentifier[] {
+        map.put(71, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1672,7 +1672,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(111, Arrays.asList(new TerminalIdentifier[] {
+        map.put(119, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1685,7 +1685,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+        map.put(141, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
@@ -1780,6 +1780,9 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
         map.put(120, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -1796,10 +1799,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(124, Arrays.asList(new TerminalIdentifier[] {
-            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
-        }));
-        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -2104,7 +2104,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -2121,7 +2121,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -2138,46 +2138,49 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
         }));
         map.put(119, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_DASH,
         }));
-        map.put(135, Arrays.asList(new TerminalIdentifier[] {
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_FLOAT,
         }));
-        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
         map.put(121, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IF,
         }));
-        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INTEGER,
         }));
-        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LPAREN,
         }));
-        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LSQUARE,
         }));
-        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+        map.put(137, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_NONE,
         }));
         map.put(117, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_NOT,
         }));
-        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_OBJECT,
         }));
         map.put(118, Arrays.asList(new TerminalIdentifier[] {
@@ -2407,218 +2410,219 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
     }
     static {
         Map<Integer, List<String>> map = new HashMap<Integer, List<String>>();
-        map.put(75, new ArrayList<String>());
-        map.put(128, new ArrayList<String>());
-        map.put(115, new ArrayList<String>());
+        map.put(82, new ArrayList<String>());
+        map.put(90, new ArrayList<String>());
         map.put(68, new ArrayList<String>());
-        map.put(76, new ArrayList<String>());
-        map.put(117, new ArrayList<String>());
-        map.put(89, new ArrayList<String>());
-        map.put(132, new ArrayList<String>());
-        map.put(79, new ArrayList<String>());
-        map.put(95, new ArrayList<String>());
-        map.put(81, new ArrayList<String>());
-        map.put(88, new ArrayList<String>());
+        map.put(101, new ArrayList<String>());
+        map.put(86, new ArrayList<String>());
+        map.put(75, new ArrayList<String>());
         map.put(129, new ArrayList<String>());
-        map.put(87, new ArrayList<String>());
-        map.put(91, new ArrayList<String>());
-        map.put(110, new ArrayList<String>());
-        map.put(70, new ArrayList<String>());
-        map.put(108, new ArrayList<String>());
-        map.put(135, new ArrayList<String>());
-        map.put(119, new ArrayList<String>());
-        map.put(92, new ArrayList<String>());
-        map.put(114, new ArrayList<String>());
+        map.put(115, new ArrayList<String>());
+        map.put(103, new ArrayList<String>());
+        map.put(132, new ArrayList<String>());
+        map.put(89, new ArrayList<String>());
+        map.put(73, new ArrayList<String>());
+        map.put(136, new ArrayList<String>());
         map.put(131, new ArrayList<String>());
         map.put(102, new ArrayList<String>());
-        map.put(104, new ArrayList<String>());
-        map.put(140, new ArrayList<String>());
         map.put(109, new ArrayList<String>());
+        map.put(125, new ArrayList<String>());
+        map.put(80, new ArrayList<String>());
+        map.put(76, new ArrayList<String>());
+        map.put(108, new ArrayList<String>());
+        map.put(139, new ArrayList<String>());
+        map.put(70, new ArrayList<String>());
+        map.put(100, new ArrayList<String>());
+        map.put(83, new ArrayList<String>());
+        map.put(88, new ArrayList<String>());
         map.put(126, new ArrayList<String>());
-        map.put(124, new ArrayList<String>());
+        map.put(104, new ArrayList<String>());
+        map.put(130, new ArrayList<String>());
+        map.put(137, new ArrayList<String>());
+        map.put(127, new ArrayList<String>());
         map.put(78, new ArrayList<String>());
-        map.put(86, new ArrayList<String>());
-        map.put(118, new ArrayList<String>());
-        map.put(72, new ArrayList<String>());
-        map.put(99, new ArrayList<String>());
-        map.put(93, new ArrayList<String>());
-        map.put(138, new ArrayList<String>());
-        map.put(107, new ArrayList<String>());
+        map.put(117, new ArrayList<String>());
+        map.put(91, new ArrayList<String>());
+        map.put(95, new ArrayList<String>());
+        map.put(96, new ArrayList<String>());
         map.put(97, new ArrayList<String>());
+        map.put(79, new ArrayList<String>());
         map.put(133, new ArrayList<String>());
-        map.put(127, new ArrayList<String>());
-        map.put(94, new ArrayList<String>());
-        map.put(82, new ArrayList<String>());
-        map.put(125, new ArrayList<String>());
-        map.put(96, new ArrayList<String>());
-        map.put(83, new ArrayList<String>());
-        map.put(122, new ArrayList<String>());
-        map.put(106, new ArrayList<String>());
-        map.put(116, new ArrayList<String>());
-        map.put(100, new ArrayList<String>());
-        map.put(136, new ArrayList<String>());
-        map.put(112, new ArrayList<String>());
-        map.put(141, new ArrayList<String>());
+        map.put(134, new ArrayList<String>());
+        map.put(123, new ArrayList<String>());
         map.put(120, new ArrayList<String>());
-        map.put(90, new ArrayList<String>());
+        map.put(81, new ArrayList<String>());
+        map.put(85, new ArrayList<String>());
+        map.put(107, new ArrayList<String>());
+        map.put(67, new ArrayList<String>());
+        map.put(105, new ArrayList<String>());
+        map.put(112, new ArrayList<String>());
+        map.put(114, new ArrayList<String>());
+        map.put(124, new ArrayList<String>());
+        map.put(106, new ArrayList<String>());
+        map.put(93, new ArrayList<String>());
         map.put(77, new ArrayList<String>());
+        map.put(135, new ArrayList<String>());
+        map.put(74, new ArrayList<String>());
+        map.put(87, new ArrayList<String>());
+        map.put(122, new ArrayList<String>());
+        map.put(72, new ArrayList<String>());
+        map.put(128, new ArrayList<String>());
         map.put(84, new ArrayList<String>());
-        map.put(105, new ArrayList<String>());
-        map.put(85, new ArrayList<String>());
-        map.put(80, new ArrayList<String>());
-        map.put(121, new ArrayList<String>());
-        map.put(101, new ArrayList<String>());
+        map.put(116, new ArrayList<String>());
+        map.put(113, new ArrayList<String>());
+        map.put(99, new ArrayList<String>());
+        map.put(118, new ArrayList<String>());
+        map.put(111, new ArrayList<String>());
+        map.put(92, new ArrayList<String>());
+        map.put(94, new ArrayList<String>());
+        map.put(110, new ArrayList<String>());
+        map.put(138, new ArrayList<String>());
         map.put(98, new ArrayList<String>());
+        map.put(140, new ArrayList<String>());
+        map.put(121, new ArrayList<String>());
         map.put(69, new ArrayList<String>());
-        map.put(139, new ArrayList<String>());
-        map.put(130, new ArrayList<String>());
-        map.put(74, new ArrayList<String>());
-        map.put(73, new ArrayList<String>());
-        map.put(113, new ArrayList<String>());
-        map.put(123, new ArrayList<String>());
-        map.put(67, new ArrayList<String>());
         map.put(71, new ArrayList<String>());
-        map.put(137, new ArrayList<String>());
-        map.put(103, new ArrayList<String>());
-        map.put(111, new ArrayList<String>());
-        map.put(134, new ArrayList<String>());
-        map.get(75).add("$_gen0 = list($import)");
-        map.get(128).add("$_gen1 = list($file_body_element)");
-        map.get(115).add("$_gen10 = list($input_declaration)");
-        map.get(68).add("$_gen11 = list($kv)");
-        map.get(76).add("$_gen12 = list($meta_kv)");
-        map.get(117).add("$_gen13 = $setter");
-        map.get(117).add("$_gen13 = :_empty");
-        map.get(89).add("$_gen14 = list($output_kv)");
-        map.get(132).add("$_gen15 = list($wf_body_element)");
-        map.get(79).add("$_gen16 = $alias");
-        map.get(79).add("$_gen16 = :_empty");
-        map.get(95).add("$_gen17 = list($call_after)");
-        map.get(81).add("$_gen18 = $call_brace_block");
-        map.get(81).add("$_gen18 = :_empty");
-        map.get(88).add("$_gen19 = $call_body");
-        map.get(88).add("$_gen19 = :_empty");
-        map.get(129).add("$_gen2 = list($struct_declaration)");
-        map.get(87).add("$_gen20 = list($input_kv, :comma)");
-        map.get(91).add("$_gen21 = list($meta_value, :comma)");
-        map.get(110).add("$_gen22 = list($meta_kv, :comma)");
-        map.get(70).add("$_gen23 = list($type_e, :comma)");
-        map.get(108).add("$_gen24 = list($e, :comma)");
-        map.get(135).add("$_gen25 = list($object_kv, :comma)");
-        map.get(119).add("$_gen26 = list($map_kv, :comma)");
-        map.get(92).add("$_gen3 = list($static_string_piece)");
-        map.get(114).add("$_gen4 = list($string_piece)");
-        map.get(131).add("$_gen5 = $import_namespace");
-        map.get(131).add("$_gen5 = :_empty");
-        map.get(102).add("$_gen6 = list($import_alias)");
-        map.get(104).add("$_gen7 = list($task_sections)");
-        map.get(140).add("$_gen8 = list($command_part)");
-        map.get(109).add("$_gen9 = list($expression_placeholder_kv)");
-        map.get(126).add("$alias = :as :identifier -> $1");
-        map.get(124).add("$call = :call :fqn $_gen16 $_gen17 $_gen18 -> Call( task=$1, alias=$2, after=$3, body=$4 )");
-        map.get(78).add("$call_after = :after :identifier -> $1");
-        map.get(86).add("$call_body = :input :colon $_gen20 -> CallBody( inputs=$2 )");
-        map.get(118).add("$call_brace_block = :lbrace $_gen19 :rbrace -> $1");
-        map.get(72).add("$command = :raw_command :raw_cmd_start $_gen8 :raw_cmd_end -> RawCommand( parts=$2 )");
-        map.get(99).add("$command_part = $expression_placeholder");
-        map.get(99).add("$command_part = :cmd_part");
-        map.get(93).add("$declaration = $type_e :identifier $setter -> Declaration( type=$0, name=$1, expression=$2 )");
-        map.get(138).add("$document = $version $_gen0 $_gen1 -> Draft3File( version=$0, imports=$1, body=$2 )");
-        map.get(107).add("$e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :plus $e -> Add( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e :slash $e -> Divide( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
-        map.get(107).add("$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
-        map.get(107).add("$e = $string_literal");
-        map.get(107).add("$e = :boolean");
-        map.get(107).add("$e = :dash $e -> UnaryNegation( expression=$1 )");
-        map.get(107).add("$e = :float");
-        map.get(107).add("$e = :identifier");
-        map.get(107).add("$e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 )");
-        map.get(107).add("$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
-        map.get(107).add("$e = :integer");
-        map.get(107).add("$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
-        map.get(107).add("$e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 )");
-        map.get(107).add("$e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 )");
-        map.get(107).add("$e = :none");
-        map.get(107).add("$e = :not $e -> LogicalNot( expression=$1 )");
-        map.get(107).add("$e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 )");
-        map.get(107).add("$e = :plus $e -> UnaryPlus( expression=$1 )");
-        map.get(97).add("$expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 )");
-        map.get(133).add("$expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 )");
-        map.get(127).add("$file_body_element = $struct");
-        map.get(127).add("$file_body_element = $task");
-        map.get(127).add("$file_body_element = $workflow");
-        map.get(94).add("$if_stmt = :if :lparen $e :rparen :lbrace $_gen15 :rbrace -> If( expression=$2, body=$5 )");
-        map.get(82).add("$import = :import $static_string $_gen5 $_gen6 -> Import( uri=$1, namespace=$2, aliases=$3 )");
-        map.get(125).add("$import_alias = :alias :identifier :as :identifier -> ImportAlias( old_name=$1, new_name=$3 )");
-        map.get(96).add("$import_namespace = :as :identifier -> $1");
-        map.get(83).add("$input_declaration = $type_e :identifier $_gen13 -> InputDeclaration( type=$0, name=$1, expression=$2 )");
-        map.get(122).add("$input_kv = :identifier :equal $e -> ObjectKV( key=$0, value=$2 )");
-        map.get(106).add("$inputs = :input :lbrace $_gen10 :rbrace -> Inputs( inputs=$2 )");
-        map.get(116).add("$kv = :identifier :colon $e -> RuntimeAttribute( key=$0, value=$2 )");
-        map.get(100).add("$map_kv = $e :colon $e -> MapLiteralKv( key=$0, value=$2 )");
-        map.get(136).add("$meta = :meta $meta_map -> Meta( map=$1 )");
-        map.get(112).add("$meta_kv = :identifier :colon $meta_value -> MetaKvPair( key=$0, value=$2 )");
-        map.get(141).add("$meta_map = :lbrace $_gen12 :rbrace -> $1");
-        map.get(120).add("$meta_value = $static_string");
-        map.get(120).add("$meta_value = :boolean");
-        map.get(120).add("$meta_value = :float");
-        map.get(120).add("$meta_value = :integer");
-        map.get(120).add("$meta_value = :lbrace $_gen22 :rbrace -> MetaObject( map=$1 )");
-        map.get(120).add("$meta_value = :lsquare $_gen21 :rsquare -> MetaArray( values=$1 )");
-        map.get(120).add("$meta_value = :null");
-        map.get(90).add("$object_kv = :identifier :colon $e -> ObjectKV( key=$0, value=$2 )");
-        map.get(77).add("$output_kv = $type_e :identifier :equal $e -> Output( type=$0, name=$1, expression=$3 )");
-        map.get(84).add("$outputs = :output :lbrace $_gen14 :rbrace -> Outputs( outputs=$2 )");
-        map.get(105).add("$parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
-        map.get(85).add("$rt_map = :lbrace $_gen11 :rbrace -> $1");
-        map.get(80).add("$runtime = :runtime $rt_map -> Runtime( map=$1 )");
-        map.get(121).add("$scatter = :scatter :lparen :identifier :in $e :rparen :lbrace $_gen15 :rbrace -> Scatter( item=$2, collection=$4, body=$7 )");
-        map.get(101).add("$setter = :equal $e -> $1");
-        map.get(98).add("$static_string = :quote $_gen3 :quote -> StaticString( value=$1 )");
-        map.get(69).add("$static_string_piece = :escape");
-        map.get(69).add("$static_string_piece = :string");
-        map.get(139).add("$string_literal = :quote $_gen4 :quote -> StringLiteral( pieces=$1 )");
-        map.get(130).add("$string_piece = $expression_placeholder");
-        map.get(130).add("$string_piece = $static_string_piece");
-        map.get(74).add("$struct = :struct :identifier :lbrace $_gen2 :rbrace -> Struct( name=$1, entries=$3 )");
-        map.get(73).add("$struct_declaration = $type_e :identifier -> StructEntry( type=$0, name=$1 )");
-        map.get(113).add("$task = :task :identifier :lbrace $_gen7 :rbrace -> Task( name=$1, sections=$3 )");
-        map.get(123).add("$task_sections = $command");
-        map.get(123).add("$task_sections = $declaration");
-        map.get(123).add("$task_sections = $inputs");
-        map.get(123).add("$task_sections = $meta");
-        map.get(123).add("$task_sections = $outputs");
-        map.get(123).add("$task_sections = $parameter_meta");
-        map.get(123).add("$task_sections = $runtime");
-        map.get(67).add("$type_e = :identifier");
-        map.get(67).add("$type_e = :type");
-        map.get(67).add("$type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 )");
-        map.get(67).add("$type_e = :type <=> :plus -> NonEmptyType( innerType=$0 )");
-        map.get(67).add("$type_e = :type <=> :qmark -> OptionalType( innerType=$0 )");
-        map.get(71).add("$version = :version :version_name -> VersionDeclaration( v=$1 )");
-        map.get(137).add("$wf_body_element = $call");
-        map.get(137).add("$wf_body_element = $declaration");
-        map.get(137).add("$wf_body_element = $if_stmt");
-        map.get(137).add("$wf_body_element = $inputs");
-        map.get(137).add("$wf_body_element = $outputs");
-        map.get(137).add("$wf_body_element = $scatter");
-        map.get(137).add("$wf_body_element = $wf_meta");
-        map.get(137).add("$wf_body_element = $wf_parameter_meta");
-        map.get(103).add("$wf_meta = :meta $meta_map -> Meta( map=$1 )");
-        map.get(111).add("$wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
-        map.get(134).add("$workflow = :workflow :identifier :lbrace $_gen15 :rbrace -> Workflow( name=$1, body=$3 )");
+        map.put(119, new ArrayList<String>());
+        map.put(141, new ArrayList<String>());
+        map.get(82).add("$_gen0 = list($import)");
+        map.get(90).add("$_gen1 = list($file_body_element)");
+        map.get(68).add("$_gen10 = list($input_declaration)");
+        map.get(101).add("$_gen11 = list($kv)");
+        map.get(86).add("$_gen12 = list($meta_kv)");
+        map.get(75).add("$_gen13 = $setter");
+        map.get(75).add("$_gen13 = :_empty");
+        map.get(129).add("$_gen14 = list($output_kv)");
+        map.get(115).add("$_gen15 = list($wf_body_element)");
+        map.get(103).add("$_gen16 = $alias");
+        map.get(103).add("$_gen16 = :_empty");
+        map.get(132).add("$_gen17 = list($call_after)");
+        map.get(89).add("$_gen18 = $call_brace_block");
+        map.get(89).add("$_gen18 = :_empty");
+        map.get(73).add("$_gen19 = $call_body");
+        map.get(73).add("$_gen19 = :_empty");
+        map.get(136).add("$_gen2 = list($struct_declaration)");
+        map.get(131).add("$_gen20 = list($input_kv, :comma)");
+        map.get(102).add("$_gen21 = list($meta_value, :comma)");
+        map.get(109).add("$_gen22 = list($meta_kv, :comma)");
+        map.get(125).add("$_gen23 = list($type_e, :comma)");
+        map.get(80).add("$_gen24 = list($object_kv, :comma)");
+        map.get(76).add("$_gen25 = list($e, :comma)");
+        map.get(108).add("$_gen26 = list($map_kv, :comma)");
+        map.get(139).add("$_gen3 = list($static_string_piece)");
+        map.get(70).add("$_gen4 = list($string_piece)");
+        map.get(100).add("$_gen5 = $import_namespace");
+        map.get(100).add("$_gen5 = :_empty");
+        map.get(83).add("$_gen6 = list($import_alias)");
+        map.get(88).add("$_gen7 = list($task_sections)");
+        map.get(126).add("$_gen8 = list($command_part)");
+        map.get(104).add("$_gen9 = list($expression_placeholder_kv)");
+        map.get(130).add("$alias = :as :identifier -> $1");
+        map.get(137).add("$call = :call :fqn $_gen16 $_gen17 $_gen18 -> Call( task=$1, alias=$2, after=$3, body=$4 )");
+        map.get(127).add("$call_after = :after :identifier -> $1");
+        map.get(78).add("$call_body = :input :colon $_gen20 -> CallBody( inputs=$2 )");
+        map.get(117).add("$call_brace_block = :lbrace $_gen19 :rbrace -> $1");
+        map.get(91).add("$command = :raw_command :raw_cmd_start $_gen8 :raw_cmd_end -> RawCommand( parts=$2 )");
+        map.get(95).add("$command_part = $expression_placeholder");
+        map.get(95).add("$command_part = :cmd_part");
+        map.get(96).add("$declaration = $type_e :identifier $setter -> Declaration( type=$0, name=$1, expression=$2 )");
+        map.get(97).add("$document = $version $_gen0 $_gen1 -> Draft3File( version=$0, imports=$1, body=$2 )");
+        map.get(79).add("$e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :plus $e -> Add( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e :slash $e -> Divide( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
+        map.get(79).add("$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
+        map.get(79).add("$e = $string_literal");
+        map.get(79).add("$e = :boolean");
+        map.get(79).add("$e = :dash $e -> UnaryNegation( expression=$1 )");
+        map.get(79).add("$e = :float");
+        map.get(79).add("$e = :identifier");
+        map.get(79).add("$e = :identifier <=> :lbrace $_gen24 :rbrace -> StructLiteral( name=$0, map=$2 )");
+        map.get(79).add("$e = :identifier <=> :lparen $_gen25 :rparen -> FunctionCall( name=$0, params=$2 )");
+        map.get(79).add("$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
+        map.get(79).add("$e = :integer");
+        map.get(79).add("$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
+        map.get(79).add("$e = :lparen $_gen25 :rparen -> TupleLiteral( values=$1 )");
+        map.get(79).add("$e = :lsquare $_gen25 :rsquare -> ArrayLiteral( values=$1 )");
+        map.get(79).add("$e = :none");
+        map.get(79).add("$e = :not $e -> LogicalNot( expression=$1 )");
+        map.get(79).add("$e = :object :lbrace $_gen24 :rbrace -> ObjectLiteral( map=$2 )");
+        map.get(79).add("$e = :plus $e -> UnaryPlus( expression=$1 )");
+        map.get(133).add("$expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 )");
+        map.get(134).add("$expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 )");
+        map.get(123).add("$file_body_element = $struct");
+        map.get(123).add("$file_body_element = $task");
+        map.get(123).add("$file_body_element = $workflow");
+        map.get(120).add("$if_stmt = :if :lparen $e :rparen :lbrace $_gen15 :rbrace -> If( expression=$2, body=$5 )");
+        map.get(81).add("$import = :import $static_string $_gen5 $_gen6 -> Import( uri=$1, namespace=$2, aliases=$3 )");
+        map.get(85).add("$import_alias = :alias :identifier :as :identifier -> ImportAlias( old_name=$1, new_name=$3 )");
+        map.get(107).add("$import_namespace = :as :identifier -> $1");
+        map.get(67).add("$input_declaration = $type_e :identifier $_gen13 -> InputDeclaration( type=$0, name=$1, expression=$2 )");
+        map.get(105).add("$input_kv = :identifier :equal $e -> ObjectKV( key=$0, value=$2 )");
+        map.get(112).add("$inputs = :input :lbrace $_gen10 :rbrace -> Inputs( inputs=$2 )");
+        map.get(114).add("$kv = :identifier :colon $e -> RuntimeAttribute( key=$0, value=$2 )");
+        map.get(124).add("$map_kv = $e :colon $e -> MapLiteralKv( key=$0, value=$2 )");
+        map.get(106).add("$meta = :meta $meta_map -> Meta( map=$1 )");
+        map.get(93).add("$meta_kv = :identifier :colon $meta_value -> MetaKvPair( key=$0, value=$2 )");
+        map.get(77).add("$meta_map = :lbrace $_gen12 :rbrace -> $1");
+        map.get(135).add("$meta_value = $static_string");
+        map.get(135).add("$meta_value = :boolean");
+        map.get(135).add("$meta_value = :float");
+        map.get(135).add("$meta_value = :integer");
+        map.get(135).add("$meta_value = :lbrace $_gen22 :rbrace -> MetaObject( map=$1 )");
+        map.get(135).add("$meta_value = :lsquare $_gen21 :rsquare -> MetaArray( values=$1 )");
+        map.get(135).add("$meta_value = :null");
+        map.get(74).add("$object_kv = :identifier :colon $e -> ObjectKV( key=$0, value=$2 )");
+        map.get(87).add("$output_kv = $type_e :identifier :equal $e -> Output( type=$0, name=$1, expression=$3 )");
+        map.get(122).add("$outputs = :output :lbrace $_gen14 :rbrace -> Outputs( outputs=$2 )");
+        map.get(72).add("$parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
+        map.get(128).add("$rt_map = :lbrace $_gen11 :rbrace -> $1");
+        map.get(84).add("$runtime = :runtime $rt_map -> Runtime( map=$1 )");
+        map.get(116).add("$scatter = :scatter :lparen :identifier :in $e :rparen :lbrace $_gen15 :rbrace -> Scatter( item=$2, collection=$4, body=$7 )");
+        map.get(113).add("$setter = :equal $e -> $1");
+        map.get(99).add("$static_string = :quote $_gen3 :quote -> StaticString( value=$1 )");
+        map.get(118).add("$static_string_piece = :escape");
+        map.get(118).add("$static_string_piece = :string");
+        map.get(111).add("$string_literal = :quote $_gen4 :quote -> StringLiteral( pieces=$1 )");
+        map.get(92).add("$string_piece = $expression_placeholder");
+        map.get(92).add("$string_piece = $static_string_piece");
+        map.get(94).add("$struct = :struct :identifier :lbrace $_gen2 :rbrace -> Struct( name=$1, entries=$3 )");
+        map.get(110).add("$struct_declaration = $type_e :identifier -> StructEntry( type=$0, name=$1 )");
+        map.get(138).add("$task = :task :identifier :lbrace $_gen7 :rbrace -> Task( name=$1, sections=$3 )");
+        map.get(98).add("$task_sections = $command");
+        map.get(98).add("$task_sections = $declaration");
+        map.get(98).add("$task_sections = $inputs");
+        map.get(98).add("$task_sections = $meta");
+        map.get(98).add("$task_sections = $outputs");
+        map.get(98).add("$task_sections = $parameter_meta");
+        map.get(98).add("$task_sections = $runtime");
+        map.get(140).add("$type_e = :identifier");
+        map.get(140).add("$type_e = :type");
+        map.get(140).add("$type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 )");
+        map.get(140).add("$type_e = :type <=> :plus -> NonEmptyType( innerType=$0 )");
+        map.get(140).add("$type_e = :type <=> :qmark -> OptionalType( innerType=$0 )");
+        map.get(121).add("$version = :version :version_name -> VersionDeclaration( v=$1 )");
+        map.get(69).add("$wf_body_element = $call");
+        map.get(69).add("$wf_body_element = $declaration");
+        map.get(69).add("$wf_body_element = $if_stmt");
+        map.get(69).add("$wf_body_element = $inputs");
+        map.get(69).add("$wf_body_element = $outputs");
+        map.get(69).add("$wf_body_element = $scatter");
+        map.get(69).add("$wf_body_element = $wf_meta");
+        map.get(69).add("$wf_body_element = $wf_parameter_meta");
+        map.get(71).add("$wf_meta = :meta $meta_map -> Meta( map=$1 )");
+        map.get(119).add("$wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
+        map.get(141).add("$workflow = :workflow :identifier :lbrace $_gen15 :rbrace -> Workflow( name=$1, body=$3 )");
         nonterminal_rules = Collections.unmodifiableMap(map);
     }
     static {
@@ -2644,9 +2648,9 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
         map.put(new Integer(94), "$_gen21 = list($meta_value, :comma)");
         map.put(new Integer(96), "$_gen22 = list($meta_kv, :comma)");
         map.put(new Integer(98), "$_gen23 = list($type_e, :comma)");
-        map.put(new Integer(120), "$_gen24 = list($e, :comma)");
-        map.put(new Integer(124), "$_gen25 = list($object_kv, :comma)");
-        map.put(new Integer(127), "$_gen26 = list($map_kv, :comma)");
+        map.put(new Integer(120), "$_gen24 = list($object_kv, :comma)");
+        map.put(new Integer(122), "$_gen25 = list($e, :comma)");
+        map.put(new Integer(128), "$_gen26 = list($map_kv, :comma)");
         map.put(new Integer(10), "$_gen3 = list($static_string_piece)");
         map.put(new Integer(12), "$_gen4 = list($string_piece)");
         map.put(new Integer(18), "$_gen5 = $import_namespace");
@@ -2678,22 +2682,23 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
         map.put(new Integer(116), "$e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 )");
         map.put(new Integer(112), "$e = $e :plus $e -> Add( lhs=$0, rhs=$2 )");
         map.put(new Integer(115), "$e = $e :slash $e -> Divide( lhs=$0, rhs=$2 )");
-        map.put(new Integer(123), "$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
-        map.put(new Integer(122), "$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
-        map.put(new Integer(131), "$e = $string_literal");
-        map.put(new Integer(133), "$e = :boolean");
+        map.put(new Integer(125), "$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
+        map.put(new Integer(124), "$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
+        map.put(new Integer(132), "$e = $string_literal");
+        map.put(new Integer(134), "$e = :boolean");
         map.put(new Integer(119), "$e = :dash $e -> UnaryNegation( expression=$1 )");
-        map.put(new Integer(135), "$e = :float");
-        map.put(new Integer(132), "$e = :identifier");
-        map.put(new Integer(121), "$e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 )");
-        map.put(new Integer(130), "$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
-        map.put(new Integer(134), "$e = :integer");
-        map.put(new Integer(128), "$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
-        map.put(new Integer(129), "$e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 )");
-        map.put(new Integer(126), "$e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 )");
-        map.put(new Integer(136), "$e = :none");
+        map.put(new Integer(136), "$e = :float");
+        map.put(new Integer(133), "$e = :identifier");
+        map.put(new Integer(121), "$e = :identifier <=> :lbrace $_gen24 :rbrace -> StructLiteral( name=$0, map=$2 )");
+        map.put(new Integer(123), "$e = :identifier <=> :lparen $_gen25 :rparen -> FunctionCall( name=$0, params=$2 )");
+        map.put(new Integer(131), "$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
+        map.put(new Integer(135), "$e = :integer");
+        map.put(new Integer(129), "$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
+        map.put(new Integer(130), "$e = :lparen $_gen25 :rparen -> TupleLiteral( values=$1 )");
+        map.put(new Integer(127), "$e = :lsquare $_gen25 :rsquare -> ArrayLiteral( values=$1 )");
+        map.put(new Integer(137), "$e = :none");
         map.put(new Integer(117), "$e = :not $e -> LogicalNot( expression=$1 )");
-        map.put(new Integer(125), "$e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 )");
+        map.put(new Integer(126), "$e = :object :lbrace $_gen24 :rbrace -> ObjectLiteral( map=$2 )");
         map.put(new Integer(118), "$e = :plus $e -> UnaryPlus( expression=$1 )");
         map.put(new Integer(38), "$expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 )");
         map.put(new Integer(39), "$expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 )");
@@ -2803,29 +2808,30 @@ private static Terminal expect(ParserContext ctx, TerminalIdentifier expecting)
     private static Map<Integer, Integer> prefix_binding_power_e;
     static {
         Map<Integer, Integer> map = new HashMap<Integer, Integer>();
-        map.put(45, 4000); /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
-        map.put(29, 5000); /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
-        map.put(53, 6000); /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
-        map.put(51, 6000); /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
-        map.put(36, 7000); /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
-        map.put(40, 7000); /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
-        map.put(2, 7000); /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
-        map.put(52, 7000); /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
-        map.put(33, 8000); /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
-        map.put(32, 8000); /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
-        map.put(18, 9000); /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
-        map.put(37, 9000); /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
-        map.put(64, 9000); /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
-        map.put(15, 11000); /* $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall( name=$0, params=$2 ) */
-        map.put(17, 12000); /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
-        map.put(42, 13000); /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
+        map.put(40, 4000); /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
+        map.put(63, 5000); /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
+        map.put(56, 6000); /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
+        map.put(20, 6000); /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
+        map.put(57, 7000); /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
+        map.put(48, 7000); /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
+        map.put(18, 7000); /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
+        map.put(34, 7000); /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
+        map.put(59, 8000); /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
+        map.put(42, 8000); /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
+        map.put(21, 9000); /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
+        map.put(30, 9000); /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
+        map.put(6, 9000); /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
+        map.put(3, 11000); /* $e = :identifier <=> :lbrace list($object_kv, :comma) :rbrace -> StructLiteral( name=$0, map=$2 ) */
+        map.put(64, 12000); /* $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall( name=$0, params=$2 ) */
+        map.put(39, 13000); /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
+        map.put(45, 14000); /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
         infix_binding_power_e = Collections.unmodifiableMap(map);
     }
     static {
         Map<Integer, Integer> map = new HashMap<Integer, Integer>();
-        map.put(12, 10000); /* $e = :not $e -> LogicalNot( expression=$1 ) */
-        map.put(33, 10000); /* $e = :plus $e -> UnaryPlus( expression=$1 ) */
-        map.put(32, 10000); /* $e = :dash $e -> UnaryNegation( expression=$1 ) */
+        map.put(43, 10000); /* $e = :not $e -> LogicalNot( expression=$1 ) */
+        map.put(59, 10000); /* $e = :plus $e -> UnaryPlus( expression=$1 ) */
+        map.put(42, 10000); /* $e = :dash $e -> UnaryNegation( expression=$1 ) */
         prefix_binding_power_e = Collections.unmodifiableMap(map);
     }
     static int get_infix_binding_power_e(int terminal_id) {
@@ -2862,7 +2868,7 @@ public static ParseTree parse_e_internal(ParserContext ctx, int rbp) throws Synt
         return left;
     }
     private static ParseTree nud_e(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(107, "e") );
+        ParseTree tree = new ParseTree( new NonTerminal(79, "e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "e";
         if (current == null) {
@@ -2876,7 +2882,7 @@ else if (rule_first.get(117).contains(terminal_map.get(current.getId()))) {
             tree.setAstTransformation(new AstTransformNodeCreator("LogicalNot", parameters));
             tree.setNudMorphemeCount(2);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NOT));
-            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(12)));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(43)));
             tree.setPrefix(true);
         }
         else if (rule_first.get(118).contains(terminal_map.get(current.getId()))) {
@@ -2887,7 +2893,7 @@ else if (rule_first.get(118).contains(terminal_map.get(current.getId()))) {
             tree.setAstTransformation(new AstTransformNodeCreator("UnaryPlus", parameters));
             tree.setNudMorphemeCount(2);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PLUS));
-            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(33)));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(59)));
             tree.setPrefix(true);
         }
         else if (rule_first.get(119).contains(terminal_map.get(current.getId()))) {
@@ -2898,42 +2904,49 @@ else if (rule_first.get(119).contains(terminal_map.get(current.getId()))) {
             tree.setAstTransformation(new AstTransformNodeCreator("UnaryNegation", parameters));
             tree.setNudMorphemeCount(2);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DASH));
-            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(32)));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(42)));
             tree.setPrefix(true);
         }
         else if (rule_first.get(121).contains(terminal_map.get(current.getId()))) {
-            /* (121) $e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 ) */
+            /* (121) $e = :identifier <=> :lbrace $_gen24 :rbrace -> StructLiteral( name=$0, map=$2 ) */
             ctx.rule = rules.get(121);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
         }
-        else if (rule_first.get(125).contains(terminal_map.get(current.getId()))) {
-            /* (125) $e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 ) */
-            ctx.rule = rules.get(125);
+        else if (rule_first.get(123).contains(terminal_map.get(current.getId()))) {
+            /* (123) $e = :identifier <=> :lparen $_gen25 :rparen -> FunctionCall( name=$0, params=$2 ) */
+            ctx.rule = rules.get(123);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
+        }
+        else if (rule_first.get(126).contains(terminal_map.get(current.getId()))) {
+            /* (126) $e = :object :lbrace $_gen24 :rbrace -> ObjectLiteral( map=$2 ) */
+            ctx.rule = rules.get(126);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("map", 2);
             tree.setAstTransformation(new AstTransformNodeCreator("ObjectLiteral", parameters));
             tree.setNudMorphemeCount(4);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_OBJECT));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE));
-            tree.add(parse__gen25(ctx));
+            tree.add(parse__gen24(ctx));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE));
         }
-        else if (rule_first.get(126).contains(terminal_map.get(current.getId()))) {
-            /* (126) $e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 ) */
-            ctx.rule = rules.get(126);
+        else if (rule_first.get(127).contains(terminal_map.get(current.getId()))) {
+            /* (127) $e = :lsquare $_gen25 :rsquare -> ArrayLiteral( values=$1 ) */
+            ctx.rule = rules.get(127);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("values", 1);
             tree.setAstTransformation(new AstTransformNodeCreator("ArrayLiteral", parameters));
             tree.setNudMorphemeCount(3);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LSQUARE));
-            tree.add(parse__gen24(ctx));
+            tree.add(parse__gen25(ctx));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
         }
-        else if (rule_first.get(128).contains(terminal_map.get(current.getId()))) {
-            /* (128) $e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 ) */
-            ctx.rule = rules.get(128);
+        else if (rule_first.get(129).contains(terminal_map.get(current.getId()))) {
+            /* (129) $e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 ) */
+            ctx.rule = rules.get(129);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("map", 1);
             tree.setAstTransformation(new AstTransformNodeCreator("MapLiteral", parameters));
@@ -2942,20 +2955,20 @@ else if (rule_first.get(128).contains(terminal_map.get(current.getId()))) {
             tree.add(parse__gen26(ctx));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE));
         }
-        else if (rule_first.get(129).contains(terminal_map.get(current.getId()))) {
-            /* (129) $e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 ) */
-            ctx.rule = rules.get(129);
+        else if (rule_first.get(130).contains(terminal_map.get(current.getId()))) {
+            /* (130) $e = :lparen $_gen25 :rparen -> TupleLiteral( values=$1 ) */
+            ctx.rule = rules.get(130);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("values", 1);
             tree.setAstTransformation(new AstTransformNodeCreator("TupleLiteral", parameters));
             tree.setNudMorphemeCount(3);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LPAREN));
-            tree.add(parse__gen24(ctx));
+            tree.add(parse__gen25(ctx));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RPAREN));
         }
-        else if (rule_first.get(130).contains(terminal_map.get(current.getId()))) {
-            /* (130) $e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 ) */
-            ctx.rule = rules.get(130);
+        else if (rule_first.get(131).contains(terminal_map.get(current.getId()))) {
+            /* (131) $e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 ) */
+            ctx.rule = rules.get(131);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("cond", 1);
             parameters.put("iftrue", 3);
@@ -2969,56 +2982,56 @@ else if (rule_first.get(130).contains(terminal_map.get(current.getId()))) {
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_ELSE));
             tree.add(parse_e(ctx));
         }
-        else if (rule_first.get(131).contains(terminal_map.get(current.getId()))) {
-            /* (131) $e = $string_literal */
-            ctx.rule = rules.get(131);
-            tree.setAstTransformation(new AstTransformSubstitution(0));
-            tree.setNudMorphemeCount(1);
-            tree.add(parse_string_literal(ctx));
-        }
         else if (rule_first.get(132).contains(terminal_map.get(current.getId()))) {
-            /* (132) $e = :identifier */
+            /* (132) $e = $string_literal */
             ctx.rule = rules.get(132);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
-            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
+            tree.add(parse_string_literal(ctx));
         }
         else if (rule_first.get(133).contains(terminal_map.get(current.getId()))) {
-            /* (133) $e = :boolean */
+            /* (133) $e = :identifier */
             ctx.rule = rules.get(133);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
-            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_BOOLEAN));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
         }
         else if (rule_first.get(134).contains(terminal_map.get(current.getId()))) {
-            /* (134) $e = :integer */
+            /* (134) $e = :boolean */
             ctx.rule = rules.get(134);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
-            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_INTEGER));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_BOOLEAN));
         }
         else if (rule_first.get(135).contains(terminal_map.get(current.getId()))) {
-            /* (135) $e = :float */
+            /* (135) $e = :integer */
             ctx.rule = rules.get(135);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
-            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_FLOAT));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_INTEGER));
         }
         else if (rule_first.get(136).contains(terminal_map.get(current.getId()))) {
-            /* (136) $e = :none */
+            /* (136) $e = :float */
             ctx.rule = rules.get(136);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_FLOAT));
+        }
+        else if (rule_first.get(137).contains(terminal_map.get(current.getId()))) {
+            /* (137) $e = :none */
+            ctx.rule = rules.get(137);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NONE));
         }
         return tree;
     }
     private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(107, "e") );
+        ParseTree tree = new ParseTree( new NonTerminal(79, "e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "e";
         int modifier;
-        if (current.getId() == 45) {
+        if (current.getId() == 40) {
             /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(104);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3030,10 +3043,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_PIPE));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(45) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(40) - modifier));
             return tree;
         }
-        if (current.getId() == 29) {
+        if (current.getId() == 63) {
             /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(105);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3045,10 +3058,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_AMPERSAND));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(29) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(63) - modifier));
             return tree;
         }
-        if (current.getId() == 53) {
+        if (current.getId() == 56) {
             /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(106);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3060,10 +3073,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_EQUAL));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(53) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(56) - modifier));
             return tree;
         }
-        if (current.getId() == 51) {
+        if (current.getId() == 20) {
             /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(107);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3075,10 +3088,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NOT_EQUAL));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(51) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(20) - modifier));
             return tree;
         }
-        if (current.getId() == 36) {
+        if (current.getId() == 57) {
             /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(108);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3090,10 +3103,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LT));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(36) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(57) - modifier));
             return tree;
         }
-        if (current.getId() == 40) {
+        if (current.getId() == 48) {
             /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(109);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3105,10 +3118,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LTEQ));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(40) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(48) - modifier));
             return tree;
         }
-        if (current.getId() == 2) {
+        if (current.getId() == 18) {
             /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(110);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3120,10 +3133,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_GT));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(2) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(18) - modifier));
             return tree;
         }
-        if (current.getId() == 52) {
+        if (current.getId() == 34) {
             /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(111);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3135,10 +3148,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_GTEQ));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(52) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(34) - modifier));
             return tree;
         }
-        if (current.getId() == 33) {
+        if (current.getId() == 59) {
             /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(112);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3150,10 +3163,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PLUS));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(33) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(59) - modifier));
             return tree;
         }
-        if (current.getId() == 32) {
+        if (current.getId() == 42) {
             /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(113);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3165,10 +3178,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DASH));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(32) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(42) - modifier));
             return tree;
         }
-        if (current.getId() == 18) {
+        if (current.getId() == 21) {
             /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(114);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3180,10 +3193,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_ASTERISK));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(18) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(21) - modifier));
             return tree;
         }
-        if (current.getId() == 37) {
+        if (current.getId() == 30) {
             /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(115);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3195,10 +3208,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_SLASH));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(37) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(30) - modifier));
             return tree;
         }
-        if (current.getId() == 64) {
+        if (current.getId() == 6) {
             /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(116);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3210,25 +3223,38 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PERCENT));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(64) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(6) - modifier));
             return tree;
         }
-        if (current.getId() == 15) {
-            /* $e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 ) */
+        if (current.getId() == 3) {
+            /* $e = :identifier <=> :lbrace $_gen24 :rbrace -> StructLiteral( name=$0, map=$2 ) */
             ctx.rule = rules.get(121);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("name", 0);
+            parameters.put("map", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("StructLiteral", parameters));
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE));
+            tree.add(parse__gen24(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE));
+            return tree;
+        }
+        if (current.getId() == 64) {
+            /* $e = :identifier <=> :lparen $_gen25 :rparen -> FunctionCall( name=$0, params=$2 ) */
+            ctx.rule = rules.get(123);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("name", 0);
             parameters.put("params", 2);
             tree.setAstTransformation(new AstTransformNodeCreator("FunctionCall", parameters));
             tree.add(left);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LPAREN));
-            tree.add(parse__gen24(ctx));
+            tree.add(parse__gen25(ctx));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RPAREN));
             return tree;
         }
-        if (current.getId() == 17) {
+        if (current.getId() == 39) {
             /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
-            ctx.rule = rules.get(122);
+            ctx.rule = rules.get(124);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("lhs", 0);
             parameters.put("rhs", 2);
@@ -3237,13 +3263,13 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(left);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LSQUARE));
             modifier = 0;
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(17) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(39) - modifier));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
             return tree;
         }
-        if (current.getId() == 42) {
+        if (current.getId() == 45) {
             /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
-            ctx.rule = rules.get(123);
+            ctx.rule = rules.get(125);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("value", 0);
             parameters.put("member", 2);
@@ -3300,7 +3326,7 @@ public static ParseTree parse_meta_value_internal(ParserContext ctx, int rbp) th
         return left;
     }
     private static ParseTree nud_meta_value(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(120, "meta_value") );
+        ParseTree tree = new ParseTree( new NonTerminal(135, "meta_value") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "meta_value";
         if (current == null) {
@@ -3366,7 +3392,7 @@ else if (rule_first.get(97).contains(terminal_map.get(current.getId()))) {
         return tree;
     }
     private static ParseTree led_meta_value(ParseTree left, ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(120, "meta_value") );
+        ParseTree tree = new ParseTree( new NonTerminal(135, "meta_value") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "meta_value";
         int modifier;
@@ -3376,9 +3402,9 @@ private static ParseTree led_meta_value(ParseTree left, ParserContext ctx) throw
     private static Map<Integer, Integer> prefix_binding_power_type_e;
     static {
         Map<Integer, Integer> map = new HashMap<Integer, Integer>();
-        map.put(17, 1000); /* $type_e = :type <=> :lsquare list($type_e, :comma) :rsquare -> Type( name=$0, subtype=$2 ) */
-        map.put(21, 2000); /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
-        map.put(33, 3000); /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
+        map.put(39, 1000); /* $type_e = :type <=> :lsquare list($type_e, :comma) :rsquare -> Type( name=$0, subtype=$2 ) */
+        map.put(1, 2000); /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
+        map.put(59, 3000); /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
         infix_binding_power_type_e = Collections.unmodifiableMap(map);
     }
     static {
@@ -3419,7 +3445,7 @@ public static ParseTree parse_type_e_internal(ParserContext ctx, int rbp) throws
         return left;
     }
     private static ParseTree nud_type_e(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(67, "type_e") );
+        ParseTree tree = new ParseTree( new NonTerminal(140, "type_e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "type_e";
         if (current == null) {
@@ -3463,11 +3489,11 @@ else if (rule_first.get(103).contains(terminal_map.get(current.getId()))) {
         return tree;
     }
     private static ParseTree led_type_e(ParseTree left, ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(67, "type_e") );
+        ParseTree tree = new ParseTree( new NonTerminal(140, "type_e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "type_e";
         int modifier;
-        if (current.getId() == 17) {
+        if (current.getId() == 39) {
             /* $type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 ) */
             ctx.rule = rules.get(99);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3480,7 +3506,7 @@ private static ParseTree led_type_e(ParseTree left, ParserContext ctx) throws Sy
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
             return tree;
         }
-        if (current.getId() == 21) {
+        if (current.getId() == 1) {
             /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
             ctx.rule = rules.get(100);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3490,7 +3516,7 @@ private static ParseTree led_type_e(ParseTree left, ParserContext ctx) throws Sy
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_QMARK));
             return tree;
         }
-        if (current.getId() == 33) {
+        if (current.getId() == 59) {
             /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
             ctx.rule = rules.get(101);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3507,12 +3533,12 @@ public ParseTree parse__gen0(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen0(ctx);
     }
     private static ParseTree parse__gen0(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(75, "_gen0"));
+        ParseTree tree = new ParseTree(new NonTerminal(82, "_gen0"));
         tree.setList(true);
         ctx.nonterminal = "_gen0";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(75).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(75).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(82).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(82).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3521,7 +3547,7 @@ private static ParseTree parse__gen0(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(75).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(82).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_import(ctx));
             ctx.nonterminal = "_gen0"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3533,12 +3559,12 @@ public ParseTree parse__gen1(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen1(ctx);
     }
     private static ParseTree parse__gen1(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(128, "_gen1"));
+        ParseTree tree = new ParseTree(new NonTerminal(90, "_gen1"));
         tree.setList(true);
         ctx.nonterminal = "_gen1";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(128).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(128).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(90).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(90).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3547,7 +3573,7 @@ private static ParseTree parse__gen1(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(128).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(90).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_file_body_element(ctx));
             ctx.nonterminal = "_gen1"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3559,12 +3585,12 @@ public ParseTree parse__gen10(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen10(ctx);
     }
     private static ParseTree parse__gen10(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(115, "_gen10"));
+        ParseTree tree = new ParseTree(new NonTerminal(68, "_gen10"));
         tree.setList(true);
         ctx.nonterminal = "_gen10";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(115).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(115).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(68).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(68).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3573,7 +3599,7 @@ private static ParseTree parse__gen10(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(115).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(68).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_input_declaration(ctx));
             ctx.nonterminal = "_gen10"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3585,12 +3611,12 @@ public ParseTree parse__gen11(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen11(ctx);
     }
     private static ParseTree parse__gen11(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(68, "_gen11"));
+        ParseTree tree = new ParseTree(new NonTerminal(101, "_gen11"));
         tree.setList(true);
         ctx.nonterminal = "_gen11";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(68).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(68).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(101).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(101).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3599,7 +3625,7 @@ private static ParseTree parse__gen11(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(68).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(101).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_kv(ctx));
             ctx.nonterminal = "_gen11"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3611,12 +3637,12 @@ public ParseTree parse__gen12(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen12(ctx);
     }
     private static ParseTree parse__gen12(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(76, "_gen12"));
+        ParseTree tree = new ParseTree(new NonTerminal(86, "_gen12"));
         tree.setList(true);
         ctx.nonterminal = "_gen12";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(76).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(76).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(86).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(86).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3625,7 +3651,7 @@ private static ParseTree parse__gen12(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(76).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(86).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_meta_kv(ctx));
             ctx.nonterminal = "_gen12"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3637,12 +3663,12 @@ public ParseTree parse__gen14(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen14(ctx);
     }
     private static ParseTree parse__gen14(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(89, "_gen14"));
+        ParseTree tree = new ParseTree(new NonTerminal(129, "_gen14"));
         tree.setList(true);
         ctx.nonterminal = "_gen14";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(89).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(89).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3651,7 +3677,7 @@ private static ParseTree parse__gen14(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(89).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_output_kv(ctx));
             ctx.nonterminal = "_gen14"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3663,12 +3689,12 @@ public ParseTree parse__gen15(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen15(ctx);
     }
     private static ParseTree parse__gen15(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(132, "_gen15"));
+        ParseTree tree = new ParseTree(new NonTerminal(115, "_gen15"));
         tree.setList(true);
         ctx.nonterminal = "_gen15";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(132).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(132).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(115).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(115).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3677,7 +3703,7 @@ private static ParseTree parse__gen15(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(132).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(115).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_wf_body_element(ctx));
             ctx.nonterminal = "_gen15"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3689,12 +3715,12 @@ public ParseTree parse__gen17(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen17(ctx);
     }
     private static ParseTree parse__gen17(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(95, "_gen17"));
+        ParseTree tree = new ParseTree(new NonTerminal(132, "_gen17"));
         tree.setList(true);
         ctx.nonterminal = "_gen17";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(95).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(95).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(132).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(132).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3703,7 +3729,7 @@ private static ParseTree parse__gen17(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(95).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(132).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_call_after(ctx));
             ctx.nonterminal = "_gen17"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3715,12 +3741,12 @@ public ParseTree parse__gen2(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen2(ctx);
     }
     private static ParseTree parse__gen2(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(129, "_gen2"));
+        ParseTree tree = new ParseTree(new NonTerminal(136, "_gen2"));
         tree.setList(true);
         ctx.nonterminal = "_gen2";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(136).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(136).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3729,7 +3755,7 @@ private static ParseTree parse__gen2(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(136).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_struct_declaration(ctx));
             ctx.nonterminal = "_gen2"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3741,13 +3767,13 @@ public ParseTree parse__gen20(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen20(ctx);
     }
     private static ParseTree parse__gen20(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(87, "_gen20"));
+        ParseTree tree = new ParseTree(new NonTerminal(131, "_gen20"));
         tree.setList(true);
-        tree.setListSeparator(19);
+        tree.setListSeparator(46);
         ctx.nonterminal = "_gen20";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(87).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(87).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(131).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(131).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3756,7 +3782,7 @@ private static ParseTree parse__gen20(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(87).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(131).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_input_kv(ctx));
             ctx.nonterminal = "_gen20"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3782,13 +3808,13 @@ public ParseTree parse__gen21(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen21(ctx);
     }
     private static ParseTree parse__gen21(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(91, "_gen21"));
+        ParseTree tree = new ParseTree(new NonTerminal(102, "_gen21"));
         tree.setList(true);
-        tree.setListSeparator(19);
+        tree.setListSeparator(46);
         ctx.nonterminal = "_gen21";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(91).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(91).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(102).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(102).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3797,7 +3823,7 @@ private static ParseTree parse__gen21(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(91).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(102).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_meta_value(ctx));
             ctx.nonterminal = "_gen21"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3823,13 +3849,13 @@ public ParseTree parse__gen22(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen22(ctx);
     }
     private static ParseTree parse__gen22(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(110, "_gen22"));
+        ParseTree tree = new ParseTree(new NonTerminal(109, "_gen22"));
         tree.setList(true);
-        tree.setListSeparator(19);
+        tree.setListSeparator(46);
         ctx.nonterminal = "_gen22";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(110).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(110).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3838,7 +3864,7 @@ private static ParseTree parse__gen22(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(110).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_meta_kv(ctx));
             ctx.nonterminal = "_gen22"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3864,13 +3890,13 @@ public ParseTree parse__gen23(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen23(ctx);
     }
     private static ParseTree parse__gen23(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(70, "_gen23"));
+        ParseTree tree = new ParseTree(new NonTerminal(125, "_gen23"));
         tree.setList(true);
-        tree.setListSeparator(19);
+        tree.setListSeparator(46);
         ctx.nonterminal = "_gen23";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(70).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(70).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(125).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(125).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3879,7 +3905,7 @@ private static ParseTree parse__gen23(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(70).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(125).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_type_e(ctx));
             ctx.nonterminal = "_gen23"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3905,13 +3931,13 @@ public ParseTree parse__gen24(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen24(ctx);
     }
     private static ParseTree parse__gen24(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(108, "_gen24"));
+        ParseTree tree = new ParseTree(new NonTerminal(80, "_gen24"));
         tree.setList(true);
-        tree.setListSeparator(19);
+        tree.setListSeparator(46);
         ctx.nonterminal = "_gen24";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(108).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(108).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(80).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(80).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3920,8 +3946,8 @@ private static ParseTree parse__gen24(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(108).contains(terminal_map.get(ctx.tokens.current().getId())))) {
-            tree.add(parse_e(ctx));
+               nonterminal_first.get(80).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_object_kv(ctx));
             ctx.nonterminal = "_gen24"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
                 ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
@@ -3946,13 +3972,13 @@ public ParseTree parse__gen25(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen25(ctx);
     }
     private static ParseTree parse__gen25(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(135, "_gen25"));
+        ParseTree tree = new ParseTree(new NonTerminal(76, "_gen25"));
         tree.setList(true);
-        tree.setListSeparator(19);
+        tree.setListSeparator(46);
         ctx.nonterminal = "_gen25";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(135).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(135).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(76).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(76).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3961,8 +3987,8 @@ private static ParseTree parse__gen25(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(135).contains(terminal_map.get(ctx.tokens.current().getId())))) {
-            tree.add(parse_object_kv(ctx));
+               nonterminal_first.get(76).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_e(ctx));
             ctx.nonterminal = "_gen25"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
                 ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
@@ -3987,13 +4013,13 @@ public ParseTree parse__gen26(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen26(ctx);
     }
     private static ParseTree parse__gen26(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(119, "_gen26"));
+        ParseTree tree = new ParseTree(new NonTerminal(108, "_gen26"));
         tree.setList(true);
-        tree.setListSeparator(19);
+        tree.setListSeparator(46);
         ctx.nonterminal = "_gen26";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(119).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(119).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(108).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(108).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4002,7 +4028,7 @@ private static ParseTree parse__gen26(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(119).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(108).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_map_kv(ctx));
             ctx.nonterminal = "_gen26"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -4028,12 +4054,12 @@ public ParseTree parse__gen3(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen3(ctx);
     }
     private static ParseTree parse__gen3(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(92, "_gen3"));
+        ParseTree tree = new ParseTree(new NonTerminal(139, "_gen3"));
         tree.setList(true);
         ctx.nonterminal = "_gen3";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(92).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(92).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(139).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(139).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4042,7 +4068,7 @@ private static ParseTree parse__gen3(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(92).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(139).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_static_string_piece(ctx));
             ctx.nonterminal = "_gen3"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4054,12 +4080,12 @@ public ParseTree parse__gen4(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen4(ctx);
     }
     private static ParseTree parse__gen4(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(114, "_gen4"));
+        ParseTree tree = new ParseTree(new NonTerminal(70, "_gen4"));
         tree.setList(true);
         ctx.nonterminal = "_gen4";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(114).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(114).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(70).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(70).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4068,7 +4094,7 @@ private static ParseTree parse__gen4(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(114).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(70).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_string_piece(ctx));
             ctx.nonterminal = "_gen4"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4080,12 +4106,12 @@ public ParseTree parse__gen6(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen6(ctx);
     }
     private static ParseTree parse__gen6(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(102, "_gen6"));
+        ParseTree tree = new ParseTree(new NonTerminal(83, "_gen6"));
         tree.setList(true);
         ctx.nonterminal = "_gen6";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(102).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(102).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(83).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(83).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4094,7 +4120,7 @@ private static ParseTree parse__gen6(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(102).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(83).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_import_alias(ctx));
             ctx.nonterminal = "_gen6"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4106,12 +4132,12 @@ public ParseTree parse__gen7(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen7(ctx);
     }
     private static ParseTree parse__gen7(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(104, "_gen7"));
+        ParseTree tree = new ParseTree(new NonTerminal(88, "_gen7"));
         tree.setList(true);
         ctx.nonterminal = "_gen7";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(104).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(104).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(88).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(88).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4120,7 +4146,7 @@ private static ParseTree parse__gen7(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(104).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(88).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_task_sections(ctx));
             ctx.nonterminal = "_gen7"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4132,12 +4158,12 @@ public ParseTree parse__gen8(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen8(ctx);
     }
     private static ParseTree parse__gen8(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(140, "_gen8"));
+        ParseTree tree = new ParseTree(new NonTerminal(126, "_gen8"));
         tree.setList(true);
         ctx.nonterminal = "_gen8";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(140).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(140).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(126).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(126).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4146,7 +4172,7 @@ private static ParseTree parse__gen8(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(140).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(126).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_command_part(ctx));
             ctx.nonterminal = "_gen8"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4158,12 +4184,12 @@ public ParseTree parse__gen9(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen9(ctx);
     }
     private static ParseTree parse__gen9(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(109, "_gen9"));
+        ParseTree tree = new ParseTree(new NonTerminal(104, "_gen9"));
         tree.setList(true);
         ctx.nonterminal = "_gen9";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(104).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(104).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4172,7 +4198,7 @@ private static ParseTree parse__gen9(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(104).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_expression_placeholder_kv(ctx));
             ctx.nonterminal = "_gen9"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4187,12 +4213,12 @@ private static ParseTree parse__gen13(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[50][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(117, "_gen13"));
+        int rule = (current != null) ? table[8][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(75, "_gen13"));
         ctx.nonterminal = "_gen13";
         if ( current != null &&
-             !nonterminal_first.get(117).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(117).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(75).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(75).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4216,12 +4242,12 @@ private static ParseTree parse__gen16(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[12][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(79, "_gen16"));
+        int rule = (current != null) ? table[36][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(103, "_gen16"));
         ctx.nonterminal = "_gen16";
         if ( current != null &&
-             !nonterminal_first.get(79).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(79).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(103).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(103).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4245,12 +4271,12 @@ private static ParseTree parse__gen18(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[14][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(81, "_gen18"));
+        int rule = (current != null) ? table[22][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(89, "_gen18"));
         ctx.nonterminal = "_gen18";
         if ( current != null &&
-             !nonterminal_first.get(81).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(81).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(89).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(89).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4274,12 +4300,12 @@ private static ParseTree parse__gen19(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[21][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(88, "_gen19"));
+        int rule = (current != null) ? table[6][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(73, "_gen19"));
         ctx.nonterminal = "_gen19";
         if ( current != null &&
-             !nonterminal_first.get(88).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(88).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(73).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(73).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4303,12 +4329,12 @@ private static ParseTree parse__gen5(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[64][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(131, "_gen5"));
+        int rule = (current != null) ? table[33][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(100, "_gen5"));
         ctx.nonterminal = "_gen5";
         if ( current != null &&
-             !nonterminal_first.get(131).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(131).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(100).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(100).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4332,14 +4358,14 @@ private static ParseTree parse_alias(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[59][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(126, "alias"));
+        int rule = (current != null) ? table[63][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(130, "alias"));
         ctx.nonterminal = "alias";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "alias",
-                nonterminal_first.get(126),
-                nonterminal_rules.get(126)
+                nonterminal_first.get(130),
+                nonterminal_rules.get(130)
             ));
         }
         if (rule == 81) {
@@ -4355,7 +4381,7 @@ private static ParseTree parse_alias(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "alias",
             current,
-            nonterminal_first.get(126),
+            nonterminal_first.get(130),
             rules.get(81)
         ));
     }
@@ -4367,14 +4393,14 @@ private static ParseTree parse_call(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[57][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(124, "call"));
+        int rule = (current != null) ? table[70][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(137, "call"));
         ctx.nonterminal = "call";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call",
-                nonterminal_first.get(124),
-                nonterminal_rules.get(124)
+                nonterminal_first.get(137),
+                nonterminal_rules.get(137)
             ));
         }
         if (rule == 75) {
@@ -4401,7 +4427,7 @@ private static ParseTree parse_call(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call",
             current,
-            nonterminal_first.get(124),
+            nonterminal_first.get(137),
             rules.get(75)
         ));
     }
@@ -4413,14 +4439,14 @@ private static ParseTree parse_call_after(ParserContext ctx) throws SyntaxError
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[11][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(78, "call_after"));
+        int rule = (current != null) ? table[60][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(127, "call_after"));
         ctx.nonterminal = "call_after";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call_after",
-                nonterminal_first.get(78),
-                nonterminal_rules.get(78)
+                nonterminal_first.get(127),
+                nonterminal_rules.get(127)
             ));
         }
         if (rule == 82) {
@@ -4436,7 +4462,7 @@ private static ParseTree parse_call_after(ParserContext ctx) throws SyntaxError
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call_after",
             current,
-            nonterminal_first.get(78),
+            nonterminal_first.get(127),
             rules.get(82)
         ));
     }
@@ -4448,14 +4474,14 @@ private static ParseTree parse_call_body(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[19][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(86, "call_body"));
+        int rule = (current != null) ? table[11][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(78, "call_body"));
         ctx.nonterminal = "call_body";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call_body",
-                nonterminal_first.get(86),
-                nonterminal_rules.get(86)
+                nonterminal_first.get(78),
+                nonterminal_rules.get(78)
             ));
         }
         if (rule == 80) {
@@ -4475,7 +4501,7 @@ private static ParseTree parse_call_body(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call_body",
             current,
-            nonterminal_first.get(86),
+            nonterminal_first.get(78),
             rules.get(80)
         ));
     }
@@ -4487,14 +4513,14 @@ private static ParseTree parse_call_brace_block(ParserContext ctx) throws Syntax
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[51][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(118, "call_brace_block"));
+        int rule = (current != null) ? table[50][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(117, "call_brace_block"));
         ctx.nonterminal = "call_brace_block";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call_brace_block",
-                nonterminal_first.get(118),
-                nonterminal_rules.get(118)
+                nonterminal_first.get(117),
+                nonterminal_rules.get(117)
             ));
         }
         if (rule == 78) {
@@ -4512,7 +4538,7 @@ private static ParseTree parse_call_brace_block(ParserContext ctx) throws Syntax
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call_brace_block",
             current,
-            nonterminal_first.get(118),
+            nonterminal_first.get(117),
             rules.get(78)
         ));
     }
@@ -4524,14 +4550,14 @@ private static ParseTree parse_command(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[5][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(72, "command"));
+        int rule = (current != null) ? table[24][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(91, "command"));
         ctx.nonterminal = "command";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "command",
-                nonterminal_first.get(72),
-                nonterminal_rules.get(72)
+                nonterminal_first.get(91),
+                nonterminal_rules.get(91)
             ));
         }
         if (rule == 34) {
@@ -4553,7 +4579,7 @@ private static ParseTree parse_command(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "command",
             current,
-            nonterminal_first.get(72),
+            nonterminal_first.get(91),
             rules.get(34)
         ));
     }
@@ -4565,14 +4591,14 @@ private static ParseTree parse_command_part(ParserContext ctx) throws SyntaxErro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[32][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(99, "command_part"));
+        int rule = (current != null) ? table[28][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(95, "command_part"));
         ctx.nonterminal = "command_part";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "command_part",
-                nonterminal_first.get(99),
-                nonterminal_rules.get(99)
+                nonterminal_first.get(95),
+                nonterminal_rules.get(95)
             ));
         }
         if (rule == 35) {
@@ -4594,7 +4620,7 @@ else if (rule == 36) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "command_part",
             current,
-            nonterminal_first.get(99),
+            nonterminal_first.get(95),
             rules.get(36)
         ));
     }
@@ -4606,14 +4632,14 @@ private static ParseTree parse_declaration(ParserContext ctx) throws SyntaxError
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[26][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(93, "declaration"));
+        int rule = (current != null) ? table[29][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(96, "declaration"));
         ctx.nonterminal = "declaration";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "declaration",
-                nonterminal_first.get(93),
-                nonterminal_rules.get(93)
+                nonterminal_first.get(96),
+                nonterminal_rules.get(96)
             ));
         }
         if (rule == 54) {
@@ -4635,7 +4661,7 @@ private static ParseTree parse_declaration(ParserContext ctx) throws SyntaxError
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "declaration",
             current,
-            nonterminal_first.get(93),
+            nonterminal_first.get(96),
             rules.get(54)
         ));
     }
@@ -4647,14 +4673,14 @@ private static ParseTree parse_document(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[71][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(138, "document"));
+        int rule = (current != null) ? table[30][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(97, "document"));
         ctx.nonterminal = "document";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "document",
-                nonterminal_first.get(138),
-                nonterminal_rules.get(138)
+                nonterminal_first.get(97),
+                nonterminal_rules.get(97)
             ));
         }
         if (rule == 2) {
@@ -4676,7 +4702,7 @@ private static ParseTree parse_document(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "document",
             current,
-            nonterminal_first.get(138),
+            nonterminal_first.get(97),
             rules.get(2)
         ));
     }
@@ -4688,14 +4714,14 @@ private static ParseTree parse_expression_placeholder(ParserContext ctx) throws
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[30][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(97, "expression_placeholder"));
+        int rule = (current != null) ? table[66][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(133, "expression_placeholder"));
         ctx.nonterminal = "expression_placeholder";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "expression_placeholder",
-                nonterminal_first.get(97),
-                nonterminal_rules.get(97)
+                nonterminal_first.get(133),
+                nonterminal_rules.get(133)
             ));
         }
         if (rule == 38) {
@@ -4718,7 +4744,7 @@ private static ParseTree parse_expression_placeholder(ParserContext ctx) throws
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "expression_placeholder",
             current,
-            nonterminal_first.get(97),
+            nonterminal_first.get(133),
             rules.get(38)
         ));
     }
@@ -4730,14 +4756,14 @@ private static ParseTree parse_expression_placeholder_kv(ParserContext ctx) thro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[66][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(133, "expression_placeholder_kv"));
+        int rule = (current != null) ? table[67][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(134, "expression_placeholder_kv"));
         ctx.nonterminal = "expression_placeholder_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "expression_placeholder_kv",
-                nonterminal_first.get(133),
-                nonterminal_rules.get(133)
+                nonterminal_first.get(134),
+                nonterminal_rules.get(134)
             ));
         }
         if (rule == 39) {
@@ -4760,7 +4786,7 @@ private static ParseTree parse_expression_placeholder_kv(ParserContext ctx) thro
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "expression_placeholder_kv",
             current,
-            nonterminal_first.get(133),
+            nonterminal_first.get(134),
             rules.get(39)
         ));
     }
@@ -4772,14 +4798,14 @@ private static ParseTree parse_file_body_element(ParserContext ctx) throws Synta
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[60][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(127, "file_body_element"));
+        int rule = (current != null) ? table[56][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(123, "file_body_element"));
         ctx.nonterminal = "file_body_element";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "file_body_element",
-                nonterminal_first.get(127),
-                nonterminal_rules.get(127)
+                nonterminal_first.get(123),
+                nonterminal_rules.get(123)
             ));
         }
         if (rule == 3) {
@@ -4809,7 +4835,7 @@ else if (rule == 5) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "file_body_element",
             current,
-            nonterminal_first.get(127),
+            nonterminal_first.get(123),
             rules.get(5)
         ));
     }
@@ -4821,14 +4847,14 @@ private static ParseTree parse_if_stmt(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[27][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(94, "if_stmt"));
+        int rule = (current != null) ? table[53][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(120, "if_stmt"));
         ctx.nonterminal = "if_stmt";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "if_stmt",
-                nonterminal_first.get(94),
-                nonterminal_rules.get(94)
+                nonterminal_first.get(120),
+                nonterminal_rules.get(120)
             ));
         }
         if (rule == 85) {
@@ -4857,7 +4883,7 @@ private static ParseTree parse_if_stmt(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "if_stmt",
             current,
-            nonterminal_first.get(94),
+            nonterminal_first.get(120),
             rules.get(85)
         ));
     }
@@ -4869,14 +4895,14 @@ private static ParseTree parse_import(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[15][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(82, "import"));
+        int rule = (current != null) ? table[14][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(81, "import"));
         ctx.nonterminal = "import";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "import",
-                nonterminal_first.get(82),
-                nonterminal_rules.get(82)
+                nonterminal_first.get(81),
+                nonterminal_rules.get(81)
             ));
         }
         if (rule == 21) {
@@ -4900,7 +4926,7 @@ private static ParseTree parse_import(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "import",
             current,
-            nonterminal_first.get(82),
+            nonterminal_first.get(81),
             rules.get(21)
         ));
     }
@@ -4912,14 +4938,14 @@ private static ParseTree parse_import_alias(ParserContext ctx) throws SyntaxErro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[58][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(125, "import_alias"));
+        int rule = (current != null) ? table[18][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(85, "import_alias"));
         ctx.nonterminal = "import_alias";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "import_alias",
-                nonterminal_first.get(125),
-                nonterminal_rules.get(125)
+                nonterminal_first.get(85),
+                nonterminal_rules.get(85)
             ));
         }
         if (rule == 23) {
@@ -4942,7 +4968,7 @@ private static ParseTree parse_import_alias(ParserContext ctx) throws SyntaxErro
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "import_alias",
             current,
-            nonterminal_first.get(125),
+            nonterminal_first.get(85),
             rules.get(23)
         ));
     }
@@ -4954,14 +4980,14 @@ private static ParseTree parse_import_namespace(ParserContext ctx) throws Syntax
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[29][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(96, "import_namespace"));
+        int rule = (current != null) ? table[40][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(107, "import_namespace"));
         ctx.nonterminal = "import_namespace";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "import_namespace",
-                nonterminal_first.get(96),
-                nonterminal_rules.get(96)
+                nonterminal_first.get(107),
+                nonterminal_rules.get(107)
             ));
         }
         if (rule == 22) {
@@ -4977,7 +5003,7 @@ private static ParseTree parse_import_namespace(ParserContext ctx) throws Syntax
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "import_namespace",
             current,
-            nonterminal_first.get(96),
+            nonterminal_first.get(107),
             rules.get(22)
         ));
     }
@@ -4989,14 +5015,14 @@ private static ParseTree parse_input_declaration(ParserContext ctx) throws Synta
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[16][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(83, "input_declaration"));
+        int rule = (current != null) ? table[0][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(67, "input_declaration"));
         ctx.nonterminal = "input_declaration";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "input_declaration",
-                nonterminal_first.get(83),
-                nonterminal_rules.get(83)
+                nonterminal_first.get(67),
+                nonterminal_rules.get(67)
             ));
         }
         if (rule == 53) {
@@ -5018,7 +5044,7 @@ private static ParseTree parse_input_declaration(ParserContext ctx) throws Synta
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "input_declaration",
             current,
-            nonterminal_first.get(83),
+            nonterminal_first.get(67),
             rules.get(53)
         ));
     }
@@ -5030,14 +5056,14 @@ private static ParseTree parse_input_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[55][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(122, "input_kv"));
+        int rule = (current != null) ? table[38][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(105, "input_kv"));
         ctx.nonterminal = "input_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "input_kv",
-                nonterminal_first.get(122),
-                nonterminal_rules.get(122)
+                nonterminal_first.get(105),
+                nonterminal_rules.get(105)
             ));
         }
         if (rule == 88) {
@@ -5058,7 +5084,7 @@ private static ParseTree parse_input_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "input_kv",
             current,
-            nonterminal_first.get(122),
+            nonterminal_first.get(105),
             rules.get(88)
         ));
     }
@@ -5070,14 +5096,14 @@ private static ParseTree parse_inputs(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[39][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(106, "inputs"));
+        int rule = (current != null) ? table[45][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(112, "inputs"));
         ctx.nonterminal = "inputs";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "inputs",
-                nonterminal_first.get(106),
-                nonterminal_rules.get(106)
+                nonterminal_first.get(112),
+                nonterminal_rules.get(112)
             ));
         }
         if (rule == 41) {
@@ -5099,7 +5125,7 @@ private static ParseTree parse_inputs(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "inputs",
             current,
-            nonterminal_first.get(106),
+            nonterminal_first.get(112),
             rules.get(41)
         ));
     }
@@ -5111,14 +5137,14 @@ private static ParseTree parse_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[49][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(116, "kv"));
+        int rule = (current != null) ? table[47][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(114, "kv"));
         ctx.nonterminal = "kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "kv",
-                nonterminal_first.get(116),
-                nonterminal_rules.get(116)
+                nonterminal_first.get(114),
+                nonterminal_rules.get(114)
             ));
         }
         if (rule == 45) {
@@ -5139,7 +5165,7 @@ private static ParseTree parse_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "kv",
             current,
-            nonterminal_first.get(116),
+            nonterminal_first.get(114),
             rules.get(45)
         ));
     }
@@ -5151,14 +5177,14 @@ private static ParseTree parse_map_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[33][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(100, "map_kv"));
+        int rule = (current != null) ? table[57][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(124, "map_kv"));
         ctx.nonterminal = "map_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "map_kv",
-                nonterminal_first.get(100),
-                nonterminal_rules.get(100)
+                nonterminal_first.get(124),
+                nonterminal_rules.get(124)
             ));
         }
         if (rule == 56) {
@@ -5179,7 +5205,7 @@ private static ParseTree parse_map_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "map_kv",
             current,
-            nonterminal_first.get(100),
+            nonterminal_first.get(124),
             rules.get(56)
         ));
     }
@@ -5191,14 +5217,14 @@ private static ParseTree parse_meta(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[69][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(136, "meta"));
+        int rule = (current != null) ? table[39][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(106, "meta"));
         ctx.nonterminal = "meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "meta",
-                nonterminal_first.get(136),
-                nonterminal_rules.get(136)
+                nonterminal_first.get(106),
+                nonterminal_rules.get(106)
             ));
         }
         if (rule == 46) {
@@ -5216,7 +5242,7 @@ private static ParseTree parse_meta(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "meta",
             current,
-            nonterminal_first.get(136),
+            nonterminal_first.get(106),
             rules.get(46)
         ));
     }
@@ -5228,14 +5254,14 @@ private static ParseTree parse_meta_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[45][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(112, "meta_kv"));
+        int rule = (current != null) ? table[26][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(93, "meta_kv"));
         ctx.nonterminal = "meta_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "meta_kv",
-                nonterminal_first.get(112),
-                nonterminal_rules.get(112)
+                nonterminal_first.get(93),
+                nonterminal_rules.get(93)
             ));
         }
         if (rule == 50) {
@@ -5256,7 +5282,7 @@ private static ParseTree parse_meta_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "meta_kv",
             current,
-            nonterminal_first.get(112),
+            nonterminal_first.get(93),
             rules.get(50)
         ));
     }
@@ -5268,14 +5294,14 @@ private static ParseTree parse_meta_map(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[74][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(141, "meta_map"));
+        int rule = (current != null) ? table[10][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(77, "meta_map"));
         ctx.nonterminal = "meta_map";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "meta_map",
-                nonterminal_first.get(141),
-                nonterminal_rules.get(141)
+                nonterminal_first.get(77),
+                nonterminal_rules.get(77)
             ));
         }
         if (rule == 49) {
@@ -5293,7 +5319,7 @@ private static ParseTree parse_meta_map(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "meta_map",
             current,
-            nonterminal_first.get(141),
+            nonterminal_first.get(77),
             rules.get(49)
         ));
     }
@@ -5305,14 +5331,14 @@ private static ParseTree parse_object_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[23][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(90, "object_kv"));
+        int rule = (current != null) ? table[7][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(74, "object_kv"));
         ctx.nonterminal = "object_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "object_kv",
-                nonterminal_first.get(90),
-                nonterminal_rules.get(90)
+                nonterminal_first.get(74),
+                nonterminal_rules.get(74)
             ));
         }
         if (rule == 87) {
@@ -5333,7 +5359,7 @@ private static ParseTree parse_object_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "object_kv",
             current,
-            nonterminal_first.get(90),
+            nonterminal_first.get(74),
             rules.get(87)
         ));
     }
@@ -5345,14 +5371,14 @@ private static ParseTree parse_output_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[10][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(77, "output_kv"));
+        int rule = (current != null) ? table[20][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(87, "output_kv"));
         ctx.nonterminal = "output_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "output_kv",
-                nonterminal_first.get(77),
-                nonterminal_rules.get(77)
+                nonterminal_first.get(87),
+                nonterminal_rules.get(87)
             ));
         }
         if (rule == 59) {
@@ -5376,7 +5402,7 @@ private static ParseTree parse_output_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "output_kv",
             current,
-            nonterminal_first.get(77),
+            nonterminal_first.get(87),
             rules.get(59)
         ));
     }
@@ -5388,14 +5414,14 @@ private static ParseTree parse_outputs(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[17][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(84, "outputs"));
+        int rule = (current != null) ? table[55][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(122, "outputs"));
         ctx.nonterminal = "outputs";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "outputs",
-                nonterminal_first.get(84),
-                nonterminal_rules.get(84)
+                nonterminal_first.get(122),
+                nonterminal_rules.get(122)
             ));
         }
         if (rule == 58) {
@@ -5417,7 +5443,7 @@ private static ParseTree parse_outputs(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "outputs",
             current,
-            nonterminal_first.get(84),
+            nonterminal_first.get(122),
             rules.get(58)
         ));
     }
@@ -5429,14 +5455,14 @@ private static ParseTree parse_parameter_meta(ParserContext ctx) throws SyntaxEr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[38][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(105, "parameter_meta"));
+        int rule = (current != null) ? table[5][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(72, "parameter_meta"));
         ctx.nonterminal = "parameter_meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "parameter_meta",
-                nonterminal_first.get(105),
-                nonterminal_rules.get(105)
+                nonterminal_first.get(72),
+                nonterminal_rules.get(72)
             ));
         }
         if (rule == 47) {
@@ -5454,7 +5480,7 @@ private static ParseTree parse_parameter_meta(ParserContext ctx) throws SyntaxEr
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "parameter_meta",
             current,
-            nonterminal_first.get(105),
+            nonterminal_first.get(72),
             rules.get(47)
         ));
     }
@@ -5466,14 +5492,14 @@ private static ParseTree parse_rt_map(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[18][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(85, "rt_map"));
+        int rule = (current != null) ? table[61][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(128, "rt_map"));
         ctx.nonterminal = "rt_map";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "rt_map",
-                nonterminal_first.get(85),
-                nonterminal_rules.get(85)
+                nonterminal_first.get(128),
+                nonterminal_rules.get(128)
             ));
         }
         if (rule == 44) {
@@ -5491,7 +5517,7 @@ private static ParseTree parse_rt_map(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "rt_map",
             current,
-            nonterminal_first.get(85),
+            nonterminal_first.get(128),
             rules.get(44)
         ));
     }
@@ -5503,14 +5529,14 @@ private static ParseTree parse_runtime(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[13][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(80, "runtime"));
+        int rule = (current != null) ? table[17][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(84, "runtime"));
         ctx.nonterminal = "runtime";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "runtime",
-                nonterminal_first.get(80),
-                nonterminal_rules.get(80)
+                nonterminal_first.get(84),
+                nonterminal_rules.get(84)
             ));
         }
         if (rule == 42) {
@@ -5528,7 +5554,7 @@ private static ParseTree parse_runtime(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "runtime",
             current,
-            nonterminal_first.get(80),
+            nonterminal_first.get(84),
             rules.get(42)
         ));
     }
@@ -5540,14 +5566,14 @@ private static ParseTree parse_scatter(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[54][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(121, "scatter"));
+        int rule = (current != null) ? table[49][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(116, "scatter"));
         ctx.nonterminal = "scatter";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "scatter",
-                nonterminal_first.get(121),
-                nonterminal_rules.get(121)
+                nonterminal_first.get(116),
+                nonterminal_rules.get(116)
             ));
         }
         if (rule == 86) {
@@ -5581,7 +5607,7 @@ private static ParseTree parse_scatter(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "scatter",
             current,
-            nonterminal_first.get(121),
+            nonterminal_first.get(116),
             rules.get(86)
         ));
     }
@@ -5593,14 +5619,14 @@ private static ParseTree parse_setter(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[34][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(101, "setter"));
+        int rule = (current != null) ? table[46][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(113, "setter"));
         ctx.nonterminal = "setter";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "setter",
-                nonterminal_first.get(101),
-                nonterminal_rules.get(101)
+                nonterminal_first.get(113),
+                nonterminal_rules.get(113)
             ));
         }
         if (rule == 55) {
@@ -5616,7 +5642,7 @@ private static ParseTree parse_setter(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "setter",
             current,
-            nonterminal_first.get(101),
+            nonterminal_first.get(113),
             rules.get(55)
         ));
     }
@@ -5628,14 +5654,14 @@ private static ParseTree parse_static_string(ParserContext ctx) throws SyntaxErr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[31][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(98, "static_string"));
+        int rule = (current != null) ? table[32][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(99, "static_string"));
         ctx.nonterminal = "static_string";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "static_string",
-                nonterminal_first.get(98),
-                nonterminal_rules.get(98)
+                nonterminal_first.get(99),
+                nonterminal_rules.get(99)
             ));
         }
         if (rule == 11) {
@@ -5655,7 +5681,7 @@ private static ParseTree parse_static_string(ParserContext ctx) throws SyntaxErr
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "static_string",
             current,
-            nonterminal_first.get(98),
+            nonterminal_first.get(99),
             rules.get(11)
         ));
     }
@@ -5667,14 +5693,14 @@ private static ParseTree parse_static_string_piece(ParserContext ctx) throws Syn
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[2][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(69, "static_string_piece"));
+        int rule = (current != null) ? table[51][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(118, "static_string_piece"));
         ctx.nonterminal = "static_string_piece";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "static_string_piece",
-                nonterminal_first.get(69),
-                nonterminal_rules.get(69)
+                nonterminal_first.get(118),
+                nonterminal_rules.get(118)
             ));
         }
         if (rule == 14) {
@@ -5696,7 +5722,7 @@ else if (rule == 15) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "static_string_piece",
             current,
-            nonterminal_first.get(69),
+            nonterminal_first.get(118),
             rules.get(15)
         ));
     }
@@ -5708,14 +5734,14 @@ private static ParseTree parse_string_literal(ParserContext ctx) throws SyntaxEr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[72][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(139, "string_literal"));
+        int rule = (current != null) ? table[44][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(111, "string_literal"));
         ctx.nonterminal = "string_literal";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "string_literal",
-                nonterminal_first.get(139),
-                nonterminal_rules.get(139)
+                nonterminal_first.get(111),
+                nonterminal_rules.get(111)
             ));
         }
         if (rule == 13) {
@@ -5735,7 +5761,7 @@ private static ParseTree parse_string_literal(ParserContext ctx) throws SyntaxEr
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "string_literal",
             current,
-            nonterminal_first.get(139),
+            nonterminal_first.get(111),
             rules.get(13)
         ));
     }
@@ -5747,14 +5773,14 @@ private static ParseTree parse_string_piece(ParserContext ctx) throws SyntaxErro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[63][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(130, "string_piece"));
+        int rule = (current != null) ? table[25][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(92, "string_piece"));
         ctx.nonterminal = "string_piece";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "string_piece",
-                nonterminal_first.get(130),
-                nonterminal_rules.get(130)
+                nonterminal_first.get(92),
+                nonterminal_rules.get(92)
             ));
         }
         if (rule == 16) {
@@ -5776,7 +5802,7 @@ else if (rule == 17) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "string_piece",
             current,
-            nonterminal_first.get(130),
+            nonterminal_first.get(92),
             rules.get(17)
         ));
     }
@@ -5788,14 +5814,14 @@ private static ParseTree parse_struct(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[7][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(74, "struct"));
+        int rule = (current != null) ? table[27][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(94, "struct"));
         ctx.nonterminal = "struct";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "struct",
-                nonterminal_first.get(74),
-                nonterminal_rules.get(74)
+                nonterminal_first.get(94),
+                nonterminal_rules.get(94)
             ));
         }
         if (rule == 8) {
@@ -5820,7 +5846,7 @@ private static ParseTree parse_struct(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "struct",
             current,
-            nonterminal_first.get(74),
+            nonterminal_first.get(94),
             rules.get(8)
         ));
     }
@@ -5832,14 +5858,14 @@ private static ParseTree parse_struct_declaration(ParserContext ctx) throws Synt
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[6][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(73, "struct_declaration"));
+        int rule = (current != null) ? table[43][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(110, "struct_declaration"));
         ctx.nonterminal = "struct_declaration";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "struct_declaration",
-                nonterminal_first.get(73),
-                nonterminal_rules.get(73)
+                nonterminal_first.get(110),
+                nonterminal_rules.get(110)
             ));
         }
         if (rule == 9) {
@@ -5858,7 +5884,7 @@ private static ParseTree parse_struct_declaration(ParserContext ctx) throws Synt
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "struct_declaration",
             current,
-            nonterminal_first.get(73),
+            nonterminal_first.get(110),
             rules.get(9)
         ));
     }
@@ -5870,14 +5896,14 @@ private static ParseTree parse_task(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[46][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(113, "task"));
+        int rule = (current != null) ? table[71][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(138, "task"));
         ctx.nonterminal = "task";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "task",
-                nonterminal_first.get(113),
-                nonterminal_rules.get(113)
+                nonterminal_first.get(138),
+                nonterminal_rules.get(138)
             ));
         }
         if (rule == 25) {
@@ -5902,7 +5928,7 @@ private static ParseTree parse_task(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "task",
             current,
-            nonterminal_first.get(113),
+            nonterminal_first.get(138),
             rules.get(25)
         ));
     }
@@ -5914,14 +5940,14 @@ private static ParseTree parse_task_sections(ParserContext ctx) throws SyntaxErr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[56][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(123, "task_sections"));
+        int rule = (current != null) ? table[31][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(98, "task_sections"));
         ctx.nonterminal = "task_sections";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "task_sections",
-                nonterminal_first.get(123),
-                nonterminal_rules.get(123)
+                nonterminal_first.get(98),
+                nonterminal_rules.get(98)
             ));
         }
         if (rule == 26) {
@@ -5983,7 +6009,7 @@ else if (rule == 32) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "task_sections",
             current,
-            nonterminal_first.get(123),
+            nonterminal_first.get(98),
             rules.get(32)
         ));
     }
@@ -5995,14 +6021,14 @@ private static ParseTree parse_version(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[4][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(71, "version"));
+        int rule = (current != null) ? table[54][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(121, "version"));
         ctx.nonterminal = "version";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "version",
-                nonterminal_first.get(71),
-                nonterminal_rules.get(71)
+                nonterminal_first.get(121),
+                nonterminal_rules.get(121)
             ));
         }
         if (rule == 6) {
@@ -6020,7 +6046,7 @@ private static ParseTree parse_version(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "version",
             current,
-            nonterminal_first.get(71),
+            nonterminal_first.get(121),
             rules.get(6)
         ));
     }
@@ -6032,14 +6058,14 @@ private static ParseTree parse_wf_body_element(ParserContext ctx) throws SyntaxE
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[70][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(137, "wf_body_element"));
+        int rule = (current != null) ? table[2][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(69, "wf_body_element"));
         ctx.nonterminal = "wf_body_element";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "wf_body_element",
-                nonterminal_first.get(137),
-                nonterminal_rules.get(137)
+                nonterminal_first.get(69),
+                nonterminal_rules.get(69)
             ));
         }
         if (rule == 62) {
@@ -6109,7 +6135,7 @@ else if (rule == 69) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "wf_body_element",
             current,
-            nonterminal_first.get(137),
+            nonterminal_first.get(69),
             rules.get(69)
         ));
     }
@@ -6121,14 +6147,14 @@ private static ParseTree parse_wf_meta(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[36][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(103, "wf_meta"));
+        int rule = (current != null) ? table[4][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(71, "wf_meta"));
         ctx.nonterminal = "wf_meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "wf_meta",
-                nonterminal_first.get(103),
-                nonterminal_rules.get(103)
+                nonterminal_first.get(71),
+                nonterminal_rules.get(71)
             ));
         }
         if (rule == 84) {
@@ -6146,7 +6172,7 @@ private static ParseTree parse_wf_meta(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "wf_meta",
             current,
-            nonterminal_first.get(103),
+            nonterminal_first.get(71),
             rules.get(84)
         ));
     }
@@ -6158,14 +6184,14 @@ private static ParseTree parse_wf_parameter_meta(ParserContext ctx) throws Synta
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[44][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(111, "wf_parameter_meta"));
+        int rule = (current != null) ? table[52][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(119, "wf_parameter_meta"));
         ctx.nonterminal = "wf_parameter_meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "wf_parameter_meta",
-                nonterminal_first.get(111),
-                nonterminal_rules.get(111)
+                nonterminal_first.get(119),
+                nonterminal_rules.get(119)
             ));
         }
         if (rule == 83) {
@@ -6183,7 +6209,7 @@ private static ParseTree parse_wf_parameter_meta(ParserContext ctx) throws Synta
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "wf_parameter_meta",
             current,
-            nonterminal_first.get(111),
+            nonterminal_first.get(119),
             rules.get(83)
         ));
     }
@@ -6195,14 +6221,14 @@ private static ParseTree parse_workflow(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[67][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(134, "workflow"));
+        int rule = (current != null) ? table[74][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(141, "workflow"));
         ctx.nonterminal = "workflow";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "workflow",
-                nonterminal_first.get(134),
-                nonterminal_rules.get(134)
+                nonterminal_first.get(141),
+                nonterminal_rules.get(141)
             ));
         }
         if (rule == 61) {
@@ -6227,7 +6253,7 @@ private static ParseTree parse_workflow(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "workflow",
             current,
-            nonterminal_first.get(134),
+            nonterminal_first.get(141),
             rules.get(61)
         ));
     }
@@ -6357,9 +6383,6 @@ public void output(LexerContext ctx, TerminalIdentifier terminal, String source_
     default_action(ctx, terminal, source_string, line, col);
 }
     /* END USER CODE */
-    public List<Terminal> post_filter(List<Terminal> terminals) {
-        return terminals;
-    }
     public void destroy(Object context) {
         return;
     }
@@ -7867,8 +7890,7 @@ public List<Terminal> lex(String string, String resource) throws SyntaxError {
             }
         }
         this.destroy(context);
-        List<Terminal> filtered = post_filter(lctx.terminals);
-        return filtered;
+        return lctx.terminals;
     }
     /* Section: Main */
 }
diff --git a/wdl/transforms/biscayne/src/main/resources/CHANGELOG.txt b/wdl/transforms/biscayne/src/main/resources/CHANGELOG.txt
index af2ba7d94e7..d6897aa1358 100644
--- a/wdl/transforms/biscayne/src/main/resources/CHANGELOG.txt
+++ b/wdl/transforms/biscayne/src/main/resources/CHANGELOG.txt
@@ -1,4 +1,15 @@
 2023-03-16
 Synced grammar from OpenWDL `development` version, which is actually development of 2.0. There is no 1.1 Hermes grammar, develop it here.
 Changed version declaration to `development1_1`.
-This disallows `version 1.1` workflows to run with incomplete support. Once development is finished, change to `1.1`.
\ No newline at end of file
+This disallows `version 1.1` workflows to run with incomplete support. Once development is finished, change to `1.1`.
+
+2024-02-28
+When changing the grammar file, generate a new parser by:
+- changing current working directory to cromwell/wdl/transforms/biscayne
+- running: hermes generate src/main/resources/grammar.hgr \
+          --language=java \
+          --directory=src/main/java \
+          --name=wdl \
+          --java-package=wdl.biscayne.parser \
+          --java-use-apache-commons --java-imports=org.apache.commons.lang3.StringEscapeUtils \
+          --header
\ No newline at end of file
diff --git a/wdl/transforms/biscayne/src/main/resources/grammar.hgr b/wdl/transforms/biscayne/src/main/resources/grammar.hgr
index e12ad170e60..451d7e61631 100644
--- a/wdl/transforms/biscayne/src/main/resources/grammar.hgr
+++ b/wdl/transforms/biscayne/src/main/resources/grammar.hgr
@@ -401,6 +401,7 @@ grammar {
       (*:unary) $e = :not $e -> LogicalNot(expression=$1)
       (-:unary) $e = :plus $e -> UnaryPlus(expression=$1)
       (-:unary) $e = :dash $e -> UnaryNegation(expression=$1)
+      (*:left) $e = :identifier <=> :lbrace list($object_kv, :comma) :rbrace -> StructLiteral(name=$0, map=$2)
       (*:left) $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall(name=$0, params=$2)
       (*:left) $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup(lhs=$0, rhs=$2)
       (*:left) $e = $e <=> :dot :identifier -> MemberAccess(value=$0, member=$2)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
index dd909356ff8..58ab50ede6e 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumers.scala
@@ -105,4 +105,14 @@ object BiscayneExpressionValueConsumers {
         // None literals consume no values:
         Set.empty[UnlinkedConsumedValueHook]
     }
+
+  implicit val structLiteralExpressionValueConsumer: ExpressionValueConsumer[StructLiteral] =
+    new ExpressionValueConsumer[StructLiteral] {
+      override def expressionConsumedValueHooks(a: StructLiteral)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        a.elements.values
+          .flatMap(element => expressionValueConsumer.expressionConsumedValueHooks(element)(expressionValueConsumer))
+          .toSet
+    }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
index 93df393d4fa..743f444f998 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/consumed/consumed.scala
@@ -24,6 +24,7 @@ package object consumed {
 
         case a: StringExpression => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: ObjectLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: StructLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: PairLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: ArrayLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: MapLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
index 77de240732e..420c0b5aa21 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluators.scala
@@ -1,5 +1,8 @@
 package wdl.transforms.biscayne.linking.expression.files
 
+import cats.implicits.{catsSyntaxValidatedId, toTraverseOps}
+import common.validation.ErrorOr.ErrorOr
+import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement.{
   AsMap,
   AsPairs,
@@ -10,16 +13,20 @@ import wdl.model.draft3.elements.ExpressionElement.{
   Quote,
   Sep,
   SQuote,
+  StructLiteral,
   SubPosix,
   Suffix,
   Unzip
 }
-import wdl.model.draft3.graph.expression.FileEvaluator
+import wdl.model.draft3.graph.expression.{FileEvaluator, ValueEvaluator}
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.{
   threeParameterFunctionPassthroughFileEvaluator,
   twoParameterFunctionPassthroughFileEvaluator
 }
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.singleParameterPassthroughFileEvaluator
+import wom.expression.IoFunctionSet
+import wom.types.{WomCompositeType, WomType}
+import wom.values.{WomFile, WomValue}
 
 object BiscayneFileEvaluators {
 
@@ -39,4 +46,38 @@ object BiscayneFileEvaluators {
   implicit val maxFunctionEvaluator: FileEvaluator[Max] = twoParameterFunctionPassthroughFileEvaluator[Max]
 
   implicit val unzipFunctionEvaluator: FileEvaluator[Unzip] = singleParameterPassthroughFileEvaluator
+
+  implicit val structLiteralEvaluator: FileEvaluator[StructLiteral] = new FileEvaluator[StructLiteral] {
+    override def predictFilesNeededToEvaluate(a: StructLiteral,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] = {
+      def filesInObjectField(fieldAndWomTypeTuple: (String, WomType)): ErrorOr[Set[WomFile]] = {
+        val (field, womType) = fieldAndWomTypeTuple
+        a.elements.get(field) match {
+          case Some(fieldElement) =>
+            fileEvaluator.predictFilesNeededToEvaluate(fieldElement, inputs, ioFunctionSet, womType)(fileEvaluator,
+                                                                                                     valueEvaluator
+            )
+          case None => s"Invalid assignment to struct. Required field $field was not specified.".invalidNel
+        }
+      }
+
+      coerceTo match {
+        case WomCompositeType(mapping, _) => mapping.toList.traverse(filesInObjectField).map(_.flatten.toSet)
+        case _ =>
+          a.elements.values.toList
+            .traverse(
+              fileEvaluator.evaluateFilesNeededToEvaluate(_, inputs, ioFunctionSet, coerceTo)(fileEvaluator,
+                                                                                              valueEvaluator
+              )
+            )
+            .map(_.toSet.flatten)
+      }
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
index 40807bf3e58..4c224c8c024 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/files/files.scala
@@ -16,7 +16,6 @@ import wom.expression.IoFunctionSet
 import wom.types.WomType
 import wom.values.{WomFile, WomValue}
 import wdl.transforms.biscayne.linking.expression.files.BiscayneFileEvaluators._
-
 package object files {
 
   implicit val expressionFileEvaluator: FileEvaluator[ExpressionElement] = new FileEvaluator[ExpressionElement] {
@@ -37,6 +36,8 @@ package object files {
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: ObjectLiteral =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: StructLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: MapLiteral =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: ArrayLiteral =>
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
index 21f2e9bcc8c..75c6cc297ae 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
@@ -159,4 +159,16 @@ object BiscayneTypeEvaluators {
         case other => s"Cannot invoke 'unzip' on type '${other.stableName}'. Expected an array of pairs".invalidNel
       }
   }
+
+  implicit val structLiteralTypeEvaluator: TypeEvaluator[StructLiteral] = new TypeEvaluator[StructLiteral] {
+    override def evaluateType(a: StructLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      // This works fine, but is not yet a strong enough type check for the WDL 1.1 spec
+      // (i.e. users are able to instantiate struct literals with k/v pairs that aren't actually in the struct definition, without an error being thrown.)
+      // We want to add extra validation here, and return a WomCompositeType that matches the struct definition of everything is OK.
+      // Note that users are allowed to omit optional k/v pairs in their literal.
+      // This requires some extra work to be done in a subsequent PR.
+      WomObjectType.validNel
+  }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
index 9775cb38970..7352c9a1376 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
@@ -29,6 +29,7 @@ package object types {
         case a: StringLiteral => a.evaluateType(linkedValues)(typeEvaluator)
         case a: StringExpression => a.evaluateType(linkedValues)(typeEvaluator)
         case a: ObjectLiteral => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: StructLiteral => a.evaluateType(linkedValues)(typeEvaluator)
         case a: MapLiteral => a.evaluateType(linkedValues)(typeEvaluator)
         case a: ArrayLiteral => a.evaluateType(linkedValues)(typeEvaluator)
         case a: PairLiteral => a.evaluateType(linkedValues)(typeEvaluator)
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
index 9903313bf00..a95a4b2f43c 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluators.scala
@@ -18,7 +18,7 @@ import wdl.transforms.base.linking.expression.values.EngineFunctionEvaluators.{
 }
 import wom.expression.IoFunctionSet
 import wom.types._
-import wom.values.{WomArray, WomFloat, WomInteger, WomMap, WomOptionalValue, WomPair, WomString, WomValue}
+import wom.values.{WomArray, WomFloat, WomInteger, WomMap, WomObject, WomOptionalValue, WomPair, WomString, WomValue}
 import wom.types.coercion.defaults._
 
 object BiscayneValueEvaluators {
@@ -351,4 +351,29 @@ object BiscayneValueEvaluators {
           s"Invalid call of 'unzip' on parameter of type '${other.womType.stableName}' (expected Array[Pair[X, Y]])".invalidNel
       }
   }
+
+  implicit val structLiteralValueEvaluator: ValueEvaluator[StructLiteral] = new ValueEvaluator[StructLiteral] {
+    // This works fine, but is missing a feature from the WDL 1.1 spec: users are allowed to omit optional values from their struct literal.
+    // This requires some extra work to be done in a subsequent PR.
+    // Specifically, make the known struct definitions available to this function so we can populate k/v pairs with None appropriately.
+    override def evaluateValue(a: StructLiteral,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+
+      val evaluated: ErrorOr[List[(String, EvaluatedValue[_])]] = a.elements.toList traverse {
+        case (key: String, value: ExpressionElement) =>
+          expressionValueEvaluator
+            .evaluateValue(value, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+            .map(key -> _)
+      }
+
+      evaluated map { mapping =>
+        val value = mapping.map(entry => entry._1 -> entry._2.value).toMap
+        val sideEffectFiles = mapping.flatMap(entry => entry._2.sideEffectFiles)
+        EvaluatedValue(WomObject(value), sideEffectFiles)
+      }
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
index eeb5bd1712f..3a1db596732 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/values/values.scala
@@ -32,13 +32,14 @@ package object values {
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: NoneLiteralElement.type =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
-
         case a: StringLiteral =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: StringExpression =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: ObjectLiteral =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: StructLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: MapLiteral =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: ArrayLiteral =>
diff --git a/wdl/transforms/biscayne/src/test/cases/struct_literal.wdl b/wdl/transforms/biscayne/src/test/cases/struct_literal.wdl
new file mode 100644
index 00000000000..6251ebf4a58
--- /dev/null
+++ b/wdl/transforms/biscayne/src/test/cases/struct_literal.wdl
@@ -0,0 +1,39 @@
+version development-1.1
+
+struct Plant {
+    String color
+    Boolean tasty
+}
+
+struct Animal {
+    String name
+    Boolean? isGood
+}
+
+task test_struct_parsing {
+    input {
+        Plant standard_plant_input
+        Animal standard_animal_input
+    }
+
+    runtime {
+        docker: "ubuntu:latest"
+    }
+
+    command {
+       echo "all dogs are good"
+    }
+
+    output {
+        Plant standard_plant_forwarded = standard_plant_input
+        Animal standard_animal_forwarded = standard_animal_input
+        Plant plant_output_literal = Plant{color: "red", tasty: true}
+    }
+}
+
+workflow struct_literal {
+    call test_struct_parsing {
+         input: standard_plant_input = Plant{color: "green", tasty: true},
+            standard_animal_input = Animal{name: "mittens", isGood: false}
+         }
+}
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
index dae69cfdcf8..baa70691580 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/Ast2WdlomSpec.scala
@@ -18,7 +18,7 @@ import wdl.transforms.biscayne.ast2wdlom._
 import wdl.transforms.biscayne.parsing.WdlBiscayneSyntaxErrorFormatter
 import wom.callable.MetaValueElement.MetaValueElementInteger
 import wom.types.WomIntegerType
-import wom.values.WomInteger
+import wom.values.{WomBoolean, WomInteger}
 
 import scala.jdk.CollectionConverters._
 
@@ -126,4 +126,13 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val expr = fromString[ExpressionElement](str, parser.parse_e)
     expr shouldBeValid (Unzip(IdentifierLookup("some_array_of_pairs")))
   }
+
+  it should "parse a struct literal" in {
+    val str = """Dog{breed: "fluffy", isGood: true}"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (StructLiteral(
+      "Dog",
+      Map("breed" -> StringLiteral("fluffy"), "isGood" -> PrimitiveLiteralExpressionElement(WomBoolean(true)))
+    ))
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/ast2wdlom/WdlFileToWdlomSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/ast2wdlom/WdlFileToWdlomSpec.scala
index 20e940dab39..0725442f5a5 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/ast2wdlom/WdlFileToWdlomSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/ast2wdlom/WdlFileToWdlomSpec.scala
@@ -6,11 +6,11 @@ import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
 import wdl.model.draft3.elements.CommandPartElement.{PlaceholderCommandPartElement, StringCommandPartElement}
 import wdl.model.draft3.elements.ExpressionElement._
-import wdl.model.draft3.elements._
+import wdl.model.draft3.elements.{CallElement, FileElement, _}
 import wdl.transforms.biscayne.ast2wdlom.WdlFileToWdlomSpec._
 import wom.SourceFileLocation
 import wom.types._
-import wom.values.WomInteger
+import wom.values.{WomBoolean, WomInteger}
 
 class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
@@ -36,7 +36,9 @@ class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Match
 
     testOrIgnore {
 
-      val expected = expectations.getOrElse(testName, fail(s"No Element expectation defined for $testName"))
+      val expected: FileElement =
+        expectations.getOrElse(testName, fail(s"No Element expectation defined for $testName"))
+
       fileToFileElement.run(testCase) match {
         case Right(actual) => actual shouldBe expected
         case Left(errors) =>
@@ -367,6 +369,104 @@ object WdlFileToWdlomSpec {
           )
         ),
         tasks = Vector.empty
+      ),
+    "struct_literal" -> FileElement(
+      imports = Vector(),
+      structs = Vector(
+        StructElement("Plant",
+                      Vector(StructEntryElement("color", PrimitiveTypeElement(WomStringType)),
+                             StructEntryElement("tasty", PrimitiveTypeElement(WomBooleanType))
+                      )
+        ),
+        StructElement(
+          "Animal",
+          Vector(StructEntryElement("name", PrimitiveTypeElement(WomStringType)),
+                 StructEntryElement("isGood", OptionalTypeElement(PrimitiveTypeElement(WomBooleanType)))
+          )
+        )
+      ),
+      workflows = Vector(
+        WorkflowDefinitionElement(
+          "struct_literal",
+          None,
+          Set(
+            CallElement(
+              "test_struct_parsing",
+              None,
+              Vector(),
+              Some(
+                CallBodyElement(
+                  Vector(
+                    KvPair("standard_plant_input",
+                           StructLiteral("Plant",
+                                         Map("color" -> StringLiteral("green"),
+                                             "tasty" -> PrimitiveLiteralExpressionElement(WomBoolean(true))
+                                         )
+                           )
+                    ),
+                    KvPair("standard_animal_input",
+                           StructLiteral("Animal",
+                                         Map("name" -> StringLiteral("mittens"),
+                                             "isGood" -> PrimitiveLiteralExpressionElement(WomBoolean(false))
+                                         )
+                           )
+                    )
+                  )
+                )
+              ),
+              Some(SourceFileLocation(35))
+            )
+          ),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(34))
+        )
+      ),
+      tasks = Vector(
+        TaskDefinitionElement(
+          "test_struct_parsing",
+          Some(
+            InputsSectionElement(
+              Vector(
+                InputDeclarationElement(TypeAliasElement("Plant"), "standard_plant_input", None),
+                InputDeclarationElement(TypeAliasElement("Animal"), "standard_animal_input", None)
+              )
+            )
+          ),
+          Vector(),
+          Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(TypeAliasElement("Plant"),
+                                         "standard_plant_forwarded",
+                                         IdentifierLookup("standard_plant_input")
+                ),
+                OutputDeclarationElement(TypeAliasElement("Animal"),
+                                         "standard_animal_forwarded",
+                                         IdentifierLookup("standard_animal_input")
+                ),
+                OutputDeclarationElement(
+                  TypeAliasElement("Plant"),
+                  "plant_output_literal",
+                  StructLiteral("Plant",
+                                Map("color" -> StringLiteral("red"),
+                                    "tasty" -> PrimitiveLiteralExpressionElement(WomBoolean(true))
+                                )
+                  )
+                )
+              )
+            )
+          ),
+          CommandSectionElement(
+            List(CommandSectionLine(Vector(StringCommandPartElement("""echo "all dogs are good""""))))
+          ),
+          Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))),
+          None,
+          None,
+          Some(SourceFileLocation(13))
+        )
       )
+    )
   )
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
index b20b844b02e..cfa2a609ed4 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/consumed/BiscayneExpressionValueConsumersSpec.scala
@@ -111,4 +111,13 @@ class BiscayneExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
       e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array_of_pairs")))
     }
   }
+
+  it should "discover an array variable lookup within a struct literal member access" in {
+    val str = """ (StructWithAnArray{myArrayMember: arrayToLookup}).myArray """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("arrayToLookup")))
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
index 69ac8a9cfca..31225bb0263 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/files/BiscayneFileEvaluatorSpec.scala
@@ -100,4 +100,15 @@ class BiscayneFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       )
     }
   }
+
+  it should "discover the file which would be required to evaluate a struct literal" in {
+    val str = """ StructWithStringVec{myVec: read_lines("foo.txt")}"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
index a38a80079e5..0c5c158b542 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
@@ -131,4 +131,14 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomAnyType), WomArrayType(WomAnyType))
     }
   }
+
+  it should "evaluate the type of a struct literal" in {
+    // NB: This is not yet strict enough type checking for the WDL 1.1 spec.
+    // In a subsequent branch, we will make this be a WomCompositeType that matches the struct definition.
+    val structLiteral = """ Animal{fur: "fuzzy", isGood: true} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomObjectType
+    }
+  }
 }
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
index a6d3066b5e9..66045fef5ae 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/values/BiscayneValueEvaluatorSpec.scala
@@ -12,7 +12,7 @@ import wdl.transforms.biscayne.Ast2WdlomSpec.{fromString, parser}
 import wdl.transforms.biscayne.ast2wdlom._
 import wom.expression.NoIoFunctionSet
 import wom.types.{WomAnyType, WomArrayType, WomIntegerType, WomMapType, WomOptionalType, WomStringType}
-import wom.values.{WomArray, WomInteger, WomMap, WomOptionalValue, WomPair, WomString}
+import wom.values.{WomArray, WomBoolean, WomInteger, WomMap, WomObject, WomOptionalValue, WomPair, WomString}
 
 class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
@@ -510,4 +510,14 @@ class BiscayneValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         )
     )
   }
+
+  it should "evaluate a struct literal" in {
+    val literal = """ Animal{type: "dog", barks: false}"""
+    val expectedValue = WomObject(Map("type" -> WomString("dog"), "barks" -> WomBoolean(false)))
+    val expr = fromString[ExpressionElement](literal, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedValue, Seq.empty)
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/java/wdl/cascades/parser/WdlParser.java b/wdl/transforms/cascades/src/main/java/wdl/cascades/parser/WdlParser.java
index 678bef21092..fce14da1e72 100644
--- a/wdl/transforms/cascades/src/main/java/wdl/cascades/parser/WdlParser.java
+++ b/wdl/transforms/cascades/src/main/java/wdl/cascades/parser/WdlParser.java
@@ -1,9 +1,9 @@
 
 /*
- * This file was generated by Hermes Parser Generator on Mon Mar 27 20:16:01 2023
+ * This file was generated by Hermes Parser Generator on Tue Mar 26 15:18:16 2024
  * 
- * Hermes command: hermes generate resources/grammar.hgr --language=java --directory=java --name=wdl --java-package=wdl.cascades.parser --java-use-apache-commons --java-imports=org.apache.commons.lang3.StringEscapeUtils --header
- * Run from: .. (relative to this file)
+ * Hermes command: hermes generate src/main/resources/grammar.hgr --language=java --directory=src/main/java --name=wdl --java-package=wdl.cascades.parser --java-use-apache-commons --java-imports=org.apache.commons.lang3.StringEscapeUtils --header
+ * Run from: ../../.. (relative to this file)
  * Hermes version: hermes-parser 2.0rc6
  * 
  * !!! DO NOT CHANGE THIS FILE DIRECTLY !!!
@@ -252,12 +252,12 @@ public interface ParseTreeNode {
     }
     public static class Terminal implements AstNode, ParseTreeNode
     {
-        public int id;
-        public String terminal_str;
-        public String source_string;
-        public String resource;
-        public int line;
-        public int col;
+        private int id;
+        private String terminal_str;
+        private String source_string;
+        private String resource;
+        private int line;
+        private int col;
         public Terminal(int id, String terminal_str, String source_string, String resource, int line, int col) {
             this.id = id;
             this.terminal_str = terminal_str;
@@ -516,73 +516,73 @@ public interface TerminalIdentifier {
         public String string();
     }
     public enum WdlTerminalIdentifier implements TerminalIdentifier {
-        TERMINAL_AFTER(11, "after"),
-        TERMINAL_ALIAS(18, "alias"),
-        TERMINAL_AS(7, "as"),
-        TERMINAL_ASTERISK(3, "asterisk"),
-        TERMINAL_BOOLEAN(30, "boolean"),
-        TERMINAL_CALL(19, "call"),
-        TERMINAL_CMD_ATTR_HINT(33, "cmd_attr_hint"),
-        TERMINAL_CMD_PART(46, "cmd_part"),
-        TERMINAL_COLON(37, "colon"),
-        TERMINAL_COMMA(38, "comma"),
-        TERMINAL_DASH(63, "dash"),
+        TERMINAL_AFTER(47, "after"),
+        TERMINAL_ALIAS(0, "alias"),
+        TERMINAL_AS(36, "as"),
+        TERMINAL_ASTERISK(34, "asterisk"),
+        TERMINAL_BOOLEAN(41, "boolean"),
+        TERMINAL_CALL(57, "call"),
+        TERMINAL_CMD_ATTR_HINT(26, "cmd_attr_hint"),
+        TERMINAL_CMD_PART(7, "cmd_part"),
+        TERMINAL_COLON(58, "colon"),
+        TERMINAL_COMMA(4, "comma"),
+        TERMINAL_DASH(53, "dash"),
         TERMINAL_DOT(62, "dot"),
-        TERMINAL_DOUBLE_AMPERSAND(13, "double_ampersand"),
-        TERMINAL_DOUBLE_EQUAL(24, "double_equal"),
-        TERMINAL_DOUBLE_PIPE(25, "double_pipe"),
-        TERMINAL_E(36, "e"),
-        TERMINAL_ELSE(41, "else"),
-        TERMINAL_EQUAL(53, "equal"),
-        TERMINAL_ESCAPE(31, "escape"),
-        TERMINAL_EXPRESSION_PLACEHOLDER_END(35, "expression_placeholder_end"),
-        TERMINAL_EXPRESSION_PLACEHOLDER_START(42, "expression_placeholder_start"),
-        TERMINAL_FLOAT(56, "float"),
-        TERMINAL_FQN(22, "fqn"),
-        TERMINAL_GT(4, "gt"),
-        TERMINAL_GTEQ(21, "gteq"),
-        TERMINAL_IDENTIFIER(23, "identifier"),
-        TERMINAL_IF(61, "if"),
-        TERMINAL_IMPORT(6, "import"),
-        TERMINAL_IN(17, "in"),
-        TERMINAL_INPUT(49, "input"),
-        TERMINAL_INTEGER(48, "integer"),
-        TERMINAL_LBRACE(32, "lbrace"),
-        TERMINAL_LPAREN(12, "lparen"),
-        TERMINAL_LSQUARE(51, "lsquare"),
-        TERMINAL_LT(65, "lt"),
-        TERMINAL_LTEQ(1, "lteq"),
-        TERMINAL_META(45, "meta"),
+        TERMINAL_DOUBLE_AMPERSAND(8, "double_ampersand"),
+        TERMINAL_DOUBLE_EQUAL(56, "double_equal"),
+        TERMINAL_DOUBLE_PIPE(49, "double_pipe"),
+        TERMINAL_E(44, "e"),
+        TERMINAL_ELSE(35, "else"),
+        TERMINAL_EQUAL(39, "equal"),
+        TERMINAL_ESCAPE(32, "escape"),
+        TERMINAL_EXPRESSION_PLACEHOLDER_END(17, "expression_placeholder_end"),
+        TERMINAL_EXPRESSION_PLACEHOLDER_START(5, "expression_placeholder_start"),
+        TERMINAL_FLOAT(45, "float"),
+        TERMINAL_FQN(18, "fqn"),
+        TERMINAL_GT(2, "gt"),
+        TERMINAL_GTEQ(3, "gteq"),
+        TERMINAL_IDENTIFIER(29, "identifier"),
+        TERMINAL_IF(40, "if"),
+        TERMINAL_IMPORT(31, "import"),
+        TERMINAL_IN(43, "in"),
+        TERMINAL_INPUT(24, "input"),
+        TERMINAL_INTEGER(19, "integer"),
+        TERMINAL_LBRACE(50, "lbrace"),
+        TERMINAL_LPAREN(28, "lparen"),
+        TERMINAL_LSQUARE(61, "lsquare"),
+        TERMINAL_LT(37, "lt"),
+        TERMINAL_LTEQ(11, "lteq"),
+        TERMINAL_META(33, "meta"),
         TERMINAL_META_VALUE(16, "meta_value"),
-        TERMINAL_NONE(44, "none"),
-        TERMINAL_NOT(60, "not"),
-        TERMINAL_NOT_EQUAL(14, "not_equal"),
-        TERMINAL_NULL(40, "null"),
-        TERMINAL_OBJECT(59, "object"),
-        TERMINAL_OUTPUT(28, "output"),
-        TERMINAL_PARAMETER_META(15, "parameter_meta"),
-        TERMINAL_PERCENT(5, "percent"),
-        TERMINAL_PLUS(9, "plus"),
-        TERMINAL_QMARK(57, "qmark"),
-        TERMINAL_QUOTE(50, "quote"),
-        TERMINAL_RAW_CMD_END(58, "raw_cmd_end"),
-        TERMINAL_RAW_CMD_START(27, "raw_cmd_start"),
-        TERMINAL_RAW_COMMAND(39, "raw_command"),
-        TERMINAL_RBRACE(0, "rbrace"),
-        TERMINAL_RPAREN(52, "rparen"),
-        TERMINAL_RSQUARE(8, "rsquare"),
-        TERMINAL_RUNTIME(54, "runtime"),
-        TERMINAL_SCATTER(66, "scatter"),
-        TERMINAL_SLASH(29, "slash"),
-        TERMINAL_STRING(26, "string"),
-        TERMINAL_STRUCT(34, "struct"),
-        TERMINAL_TASK(10, "task"),
-        TERMINAL_THEN(2, "then"),
-        TERMINAL_TYPE(43, "type"),
-        TERMINAL_TYPE_E(20, "type_e"),
-        TERMINAL_VERSION(64, "version"),
-        TERMINAL_VERSION_NAME(55, "version_name"),
-        TERMINAL_WORKFLOW(47, "workflow"),
+        TERMINAL_NONE(54, "none"),
+        TERMINAL_NOT(52, "not"),
+        TERMINAL_NOT_EQUAL(63, "not_equal"),
+        TERMINAL_NULL(51, "null"),
+        TERMINAL_OBJECT(66, "object"),
+        TERMINAL_OUTPUT(60, "output"),
+        TERMINAL_PARAMETER_META(30, "parameter_meta"),
+        TERMINAL_PERCENT(22, "percent"),
+        TERMINAL_PLUS(12, "plus"),
+        TERMINAL_QMARK(9, "qmark"),
+        TERMINAL_QUOTE(14, "quote"),
+        TERMINAL_RAW_CMD_END(10, "raw_cmd_end"),
+        TERMINAL_RAW_CMD_START(15, "raw_cmd_start"),
+        TERMINAL_RAW_COMMAND(27, "raw_command"),
+        TERMINAL_RBRACE(23, "rbrace"),
+        TERMINAL_RPAREN(64, "rparen"),
+        TERMINAL_RSQUARE(42, "rsquare"),
+        TERMINAL_RUNTIME(13, "runtime"),
+        TERMINAL_SCATTER(55, "scatter"),
+        TERMINAL_SLASH(20, "slash"),
+        TERMINAL_STRING(1, "string"),
+        TERMINAL_STRUCT(6, "struct"),
+        TERMINAL_TASK(38, "task"),
+        TERMINAL_THEN(46, "then"),
+        TERMINAL_TYPE(21, "type"),
+        TERMINAL_TYPE_E(48, "type_e"),
+        TERMINAL_VERSION(25, "version"),
+        TERMINAL_VERSION_NAME(59, "version_name"),
+        TERMINAL_WORKFLOW(65, "workflow"),
         END_SENTINAL(-3, "END_SENTINAL");
         private final int id;
         private final String string;
@@ -595,112 +595,112 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
     }
     /* table[nonterminal][terminal] = rule */
     private static final int[][] table = {
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 44, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 84, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 61, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 58, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 78, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
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+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 83, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 55, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 45, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 80, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 56, -1, 56, -1, -1, -1, -1, 56, -1, -1, -1, -1, -1, -1, -1, -1, 56, 56, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 56, 56, -1, -1, 56, 56, -1, -1, -1, -1, 56, -1, 56, 56, 56, -1, -1, -1, -1, -1, -1, 56, -1, -1, -1, -1, 56 },
         { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
+        { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 },
     };
     static {
         Map<Integer, List<TerminalIdentifier>> map = new HashMap<Integer, List<TerminalIdentifier>>();
-        map.put(96, Arrays.asList(new TerminalIdentifier[] {
+        map.put(81, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
         }));
-        map.put(98, Arrays.asList(new TerminalIdentifier[] {
+        map.put(77, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(121, Arrays.asList(new TerminalIdentifier[] {
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(74, Arrays.asList(new TerminalIdentifier[] {
+        map.put(97, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(110, Arrays.asList(new TerminalIdentifier[] {
+        map.put(106, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(70, Arrays.asList(new TerminalIdentifier[] {
+        map.put(101, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_EQUAL,
         }));
-        map.put(67, Arrays.asList(new TerminalIdentifier[] {
+        map.put(119, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+        map.put(98, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -712,27 +712,27 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(81, Arrays.asList(new TerminalIdentifier[] {
+        map.put(95, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
         }));
-        map.put(78, Arrays.asList(new TerminalIdentifier[] {
+        map.put(100, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(117, Arrays.asList(new TerminalIdentifier[] {
+        map.put(107, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INPUT,
         }));
-        map.put(140, Arrays.asList(new TerminalIdentifier[] {
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(119, Arrays.asList(new TerminalIdentifier[] {
+        map.put(110, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(104, Arrays.asList(new TerminalIdentifier[] {
+        map.put(140, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_FLOAT,
             WdlTerminalIdentifier.TERMINAL_INTEGER,
@@ -742,15 +742,18 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_NULL,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(89, Arrays.asList(new TerminalIdentifier[] {
+        map.put(102, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+        map.put(85, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(109, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -767,10 +770,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(80, Arrays.asList(new TerminalIdentifier[] {
-            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
-        }));
-        map.put(92, Arrays.asList(new TerminalIdentifier[] {
+        map.put(118, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -787,22 +787,22 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(109, Arrays.asList(new TerminalIdentifier[] {
+        map.put(74, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(141, Arrays.asList(new TerminalIdentifier[] {
+        map.put(112, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(124, Arrays.asList(new TerminalIdentifier[] {
+        map.put(82, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
         }));
-        map.put(120, Arrays.asList(new TerminalIdentifier[] {
+        map.put(87, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -813,44 +813,44 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(100, Arrays.asList(new TerminalIdentifier[] {
+        map.put(83, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
         }));
-        map.put(73, Arrays.asList(new TerminalIdentifier[] {
+        map.put(75, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
         }));
-        map.put(116, Arrays.asList(new TerminalIdentifier[] {
+        map.put(84, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(75, Arrays.asList(new TerminalIdentifier[] {
+        map.put(104, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
         }));
-        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
         }));
-        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+        map.put(138, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INPUT,
         }));
-        map.put(105, Arrays.asList(new TerminalIdentifier[] {
+        map.put(71, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(95, Arrays.asList(new TerminalIdentifier[] {
+        map.put(113, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RAW_COMMAND,
         }));
-        map.put(88, Arrays.asList(new TerminalIdentifier[] {
+        map.put(91, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
         }));
-        map.put(139, Arrays.asList(new TerminalIdentifier[] {
+        map.put(93, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+        map.put(141, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_VERSION,
         }));
-        map.put(135, Arrays.asList(new TerminalIdentifier[] {
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -867,44 +867,44 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+        map.put(99, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
         }));
-        map.put(87, Arrays.asList(new TerminalIdentifier[] {
+        map.put(92, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
         }));
-        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+        map.put(94, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(69, Arrays.asList(new TerminalIdentifier[] {
+        map.put(103, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IF,
         }));
-        map.put(86, Arrays.asList(new TerminalIdentifier[] {
+        map.put(105, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
         }));
-        map.put(82, Arrays.asList(new TerminalIdentifier[] {
+        map.put(117, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
         }));
-        map.put(91, Arrays.asList(new TerminalIdentifier[] {
+        map.put(88, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
         }));
-        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(76, Arrays.asList(new TerminalIdentifier[] {
+        map.put(72, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(83, Arrays.asList(new TerminalIdentifier[] {
+        map.put(89, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INPUT,
         }));
-        map.put(79, Arrays.asList(new TerminalIdentifier[] {
+        map.put(137, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(85, Arrays.asList(new TerminalIdentifier[] {
+        map.put(139, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -921,16 +921,16 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_META,
         }));
-        map.put(77, Arrays.asList(new TerminalIdentifier[] {
+        map.put(73, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(115, Arrays.asList(new TerminalIdentifier[] {
+        map.put(108, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(113, Arrays.asList(new TerminalIdentifier[] {
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_FLOAT,
             WdlTerminalIdentifier.TERMINAL_INTEGER,
@@ -940,59 +940,59 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_NULL,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(114, Arrays.asList(new TerminalIdentifier[] {
+        map.put(80, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(107, Arrays.asList(new TerminalIdentifier[] {
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(111, Arrays.asList(new TerminalIdentifier[] {
+        map.put(70, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_OUTPUT,
         }));
-        map.put(72, Arrays.asList(new TerminalIdentifier[] {
+        map.put(114, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
         }));
-        map.put(93, Arrays.asList(new TerminalIdentifier[] {
+        map.put(67, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RUNTIME,
         }));
-        map.put(103, Arrays.asList(new TerminalIdentifier[] {
+        map.put(115, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_SCATTER,
         }));
-        map.put(99, Arrays.asList(new TerminalIdentifier[] {
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_EQUAL,
         }));
-        map.put(106, Arrays.asList(new TerminalIdentifier[] {
+        map.put(120, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(118, Arrays.asList(new TerminalIdentifier[] {
+        map.put(111, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(97, Arrays.asList(new TerminalIdentifier[] {
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(102, Arrays.asList(new TerminalIdentifier[] {
+        map.put(86, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+        map.put(76, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
         }));
-        map.put(112, Arrays.asList(new TerminalIdentifier[] {
+        map.put(78, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(68, Arrays.asList(new TerminalIdentifier[] {
+        map.put(121, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_TASK,
         }));
-        map.put(137, Arrays.asList(new TerminalIdentifier[] {
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1003,15 +1003,15 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(101, Arrays.asList(new TerminalIdentifier[] {
+        map.put(79, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(84, Arrays.asList(new TerminalIdentifier[] {
+        map.put(96, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_VERSION,
         }));
-        map.put(71, Arrays.asList(new TerminalIdentifier[] {
+        map.put(116, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1023,48 +1023,48 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(138, Arrays.asList(new TerminalIdentifier[] {
+        map.put(68, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_META,
         }));
-        map.put(108, Arrays.asList(new TerminalIdentifier[] {
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_PARAMETER_META,
         }));
-        map.put(94, Arrays.asList(new TerminalIdentifier[] {
+        map.put(69, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
         nonterminal_first = Collections.unmodifiableMap(map);
     }
     static {
         Map<Integer, List<TerminalIdentifier>> map = new HashMap<Integer, List<TerminalIdentifier>>();
-        map.put(96, Arrays.asList(new TerminalIdentifier[] {
+        map.put(81, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(98, Arrays.asList(new TerminalIdentifier[] {
+        map.put(77, Arrays.asList(new TerminalIdentifier[] {
         }));
-        map.put(121, Arrays.asList(new TerminalIdentifier[] {
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(74, Arrays.asList(new TerminalIdentifier[] {
+        map.put(97, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(110, Arrays.asList(new TerminalIdentifier[] {
+        map.put(106, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(70, Arrays.asList(new TerminalIdentifier[] {
+        map.put(101, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(67, Arrays.asList(new TerminalIdentifier[] {
+        map.put(119, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+        map.put(98, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(81, Arrays.asList(new TerminalIdentifier[] {
+        map.put(95, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1078,7 +1078,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1092,7 +1092,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(78, Arrays.asList(new TerminalIdentifier[] {
+        map.put(100, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1105,60 +1105,60 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(117, Arrays.asList(new TerminalIdentifier[] {
+        map.put(107, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(140, Arrays.asList(new TerminalIdentifier[] {
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(119, Arrays.asList(new TerminalIdentifier[] {
+        map.put(110, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(104, Arrays.asList(new TerminalIdentifier[] {
+        map.put(140, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(89, Arrays.asList(new TerminalIdentifier[] {
+        map.put(102, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+        map.put(85, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_RBRACE,
+        }));
+        map.put(109, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RPAREN,
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(80, Arrays.asList(new TerminalIdentifier[] {
-            WdlTerminalIdentifier.TERMINAL_RBRACE,
-        }));
-        map.put(92, Arrays.asList(new TerminalIdentifier[] {
+        map.put(118, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(109, Arrays.asList(new TerminalIdentifier[] {
+        map.put(74, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(141, Arrays.asList(new TerminalIdentifier[] {
+        map.put(112, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(124, Arrays.asList(new TerminalIdentifier[] {
+        map.put(82, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(120, Arrays.asList(new TerminalIdentifier[] {
+        map.put(87, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(100, Arrays.asList(new TerminalIdentifier[] {
+        map.put(83, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
         }));
-        map.put(73, Arrays.asList(new TerminalIdentifier[] {
+        map.put(75, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -1175,7 +1175,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(116, Arrays.asList(new TerminalIdentifier[] {
+        map.put(84, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1189,7 +1189,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(75, Arrays.asList(new TerminalIdentifier[] {
+        map.put(104, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1202,7 +1202,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AFTER,
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1217,10 +1217,10 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+        map.put(138, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(105, Arrays.asList(new TerminalIdentifier[] {
+        map.put(71, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1233,7 +1233,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(95, Arrays.asList(new TerminalIdentifier[] {
+        map.put(113, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1245,12 +1245,12 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(88, Arrays.asList(new TerminalIdentifier[] {
+        map.put(91, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
         }));
-        map.put(139, Arrays.asList(new TerminalIdentifier[] {
+        map.put(93, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1265,9 +1265,9 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+        map.put(141, Arrays.asList(new TerminalIdentifier[] {
         }));
-        map.put(135, Arrays.asList(new TerminalIdentifier[] {
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ASTERISK,
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_CALL,
@@ -1315,7 +1315,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+        map.put(99, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CMD_PART,
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
@@ -1323,7 +1323,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_RAW_CMD_END,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(87, Arrays.asList(new TerminalIdentifier[] {
+        map.put(92, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_CMD_ATTR_HINT,
             WdlTerminalIdentifier.TERMINAL_DASH,
@@ -1341,12 +1341,12 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+        map.put(94, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(69, Arrays.asList(new TerminalIdentifier[] {
+        map.put(103, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1359,37 +1359,37 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(86, Arrays.asList(new TerminalIdentifier[] {
+        map.put(105, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(82, Arrays.asList(new TerminalIdentifier[] {
+        map.put(117, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(91, Arrays.asList(new TerminalIdentifier[] {
+        map.put(88, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ALIAS,
             WdlTerminalIdentifier.TERMINAL_IMPORT,
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(76, Arrays.asList(new TerminalIdentifier[] {
+        map.put(72, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(83, Arrays.asList(new TerminalIdentifier[] {
+        map.put(89, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1404,15 +1404,15 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(79, Arrays.asList(new TerminalIdentifier[] {
+        map.put(137, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(85, Arrays.asList(new TerminalIdentifier[] {
+        map.put(139, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1424,12 +1424,12 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(77, Arrays.asList(new TerminalIdentifier[] {
+        map.put(73, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(115, Arrays.asList(new TerminalIdentifier[] {
+        map.put(108, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1444,23 +1444,23 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(113, Arrays.asList(new TerminalIdentifier[] {
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(114, Arrays.asList(new TerminalIdentifier[] {
+        map.put(80, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
         }));
-        map.put(107, Arrays.asList(new TerminalIdentifier[] {
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(111, Arrays.asList(new TerminalIdentifier[] {
+        map.put(70, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1475,7 +1475,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(72, Arrays.asList(new TerminalIdentifier[] {
+        map.put(114, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1487,7 +1487,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(93, Arrays.asList(new TerminalIdentifier[] {
+        map.put(67, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1499,7 +1499,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1511,7 +1511,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(103, Arrays.asList(new TerminalIdentifier[] {
+        map.put(115, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1524,7 +1524,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(99, Arrays.asList(new TerminalIdentifier[] {
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1539,7 +1539,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(106, Arrays.asList(new TerminalIdentifier[] {
+        map.put(120, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_AS,
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
@@ -1550,13 +1550,13 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(118, Arrays.asList(new TerminalIdentifier[] {
+        map.put(111, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(97, Arrays.asList(new TerminalIdentifier[] {
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ASTERISK,
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_CALL,
@@ -1604,29 +1604,29 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(102, Arrays.asList(new TerminalIdentifier[] {
+        map.put(86, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_ESCAPE,
             WdlTerminalIdentifier.TERMINAL_EXPRESSION_PLACEHOLDER_START,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
             WdlTerminalIdentifier.TERMINAL_STRING,
         }));
-        map.put(90, Arrays.asList(new TerminalIdentifier[] {
+        map.put(76, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(112, Arrays.asList(new TerminalIdentifier[] {
+        map.put(78, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RBRACE,
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(68, Arrays.asList(new TerminalIdentifier[] {
+        map.put(121, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
         }));
-        map.put(137, Arrays.asList(new TerminalIdentifier[] {
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_INPUT,
             WdlTerminalIdentifier.TERMINAL_META,
@@ -1638,15 +1638,15 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(101, Arrays.asList(new TerminalIdentifier[] {
+        map.put(79, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_COMMA,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_RSQUARE,
         }));
-        map.put(84, Arrays.asList(new TerminalIdentifier[] {
+        map.put(96, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IMPORT,
         }));
-        map.put(71, Arrays.asList(new TerminalIdentifier[] {
+        map.put(116, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1659,7 +1659,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(138, Arrays.asList(new TerminalIdentifier[] {
+        map.put(68, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1672,7 +1672,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(108, Arrays.asList(new TerminalIdentifier[] {
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_CALL,
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
             WdlTerminalIdentifier.TERMINAL_IF,
@@ -1685,7 +1685,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE,
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
-        map.put(94, Arrays.asList(new TerminalIdentifier[] {
+        map.put(69, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_STRUCT,
             WdlTerminalIdentifier.TERMINAL_TASK,
             WdlTerminalIdentifier.TERMINAL_WORKFLOW,
@@ -1780,6 +1780,9 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_TYPE_E,
         }));
         map.put(120, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(122, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -1796,10 +1799,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(124, Arrays.asList(new TerminalIdentifier[] {
-            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
-        }));
-        map.put(127, Arrays.asList(new TerminalIdentifier[] {
+        map.put(128, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -2104,7 +2104,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+        map.put(125, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -2121,7 +2121,7 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(122, Arrays.asList(new TerminalIdentifier[] {
+        map.put(124, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
             WdlTerminalIdentifier.TERMINAL_DASH,
             WdlTerminalIdentifier.TERMINAL_E,
@@ -2138,46 +2138,49 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
             WdlTerminalIdentifier.TERMINAL_PLUS,
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(131, Arrays.asList(new TerminalIdentifier[] {
+        map.put(132, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_QUOTE,
         }));
-        map.put(133, Arrays.asList(new TerminalIdentifier[] {
+        map.put(134, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_BOOLEAN,
         }));
         map.put(119, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_DASH,
         }));
-        map.put(135, Arrays.asList(new TerminalIdentifier[] {
+        map.put(136, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_FLOAT,
         }));
-        map.put(132, Arrays.asList(new TerminalIdentifier[] {
+        map.put(133, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
         map.put(121, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
         }));
-        map.put(130, Arrays.asList(new TerminalIdentifier[] {
+        map.put(123, Arrays.asList(new TerminalIdentifier[] {
+            WdlTerminalIdentifier.TERMINAL_IDENTIFIER,
+        }));
+        map.put(131, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_IF,
         }));
-        map.put(134, Arrays.asList(new TerminalIdentifier[] {
+        map.put(135, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_INTEGER,
         }));
-        map.put(128, Arrays.asList(new TerminalIdentifier[] {
+        map.put(129, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LBRACE,
         }));
-        map.put(129, Arrays.asList(new TerminalIdentifier[] {
+        map.put(130, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LPAREN,
         }));
-        map.put(126, Arrays.asList(new TerminalIdentifier[] {
+        map.put(127, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_LSQUARE,
         }));
-        map.put(136, Arrays.asList(new TerminalIdentifier[] {
+        map.put(137, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_NONE,
         }));
         map.put(117, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_NOT,
         }));
-        map.put(125, Arrays.asList(new TerminalIdentifier[] {
+        map.put(126, Arrays.asList(new TerminalIdentifier[] {
             WdlTerminalIdentifier.TERMINAL_OBJECT,
         }));
         map.put(118, Arrays.asList(new TerminalIdentifier[] {
@@ -2407,218 +2410,219 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
     }
     static {
         Map<Integer, List<String>> map = new HashMap<Integer, List<String>>();
-        map.put(96, new ArrayList<String>());
+        map.put(81, new ArrayList<String>());
+        map.put(77, new ArrayList<String>());
+        map.put(124, new ArrayList<String>());
+        map.put(97, new ArrayList<String>());
+        map.put(106, new ArrayList<String>());
+        map.put(101, new ArrayList<String>());
+        map.put(119, new ArrayList<String>());
         map.put(98, new ArrayList<String>());
-        map.put(121, new ArrayList<String>());
-        map.put(74, new ArrayList<String>());
+        map.put(95, new ArrayList<String>());
+        map.put(135, new ArrayList<String>());
+        map.put(100, new ArrayList<String>());
+        map.put(107, new ArrayList<String>());
+        map.put(131, new ArrayList<String>());
         map.put(110, new ArrayList<String>());
-        map.put(70, new ArrayList<String>());
-        map.put(67, new ArrayList<String>());
-        map.put(123, new ArrayList<String>());
-        map.put(81, new ArrayList<String>());
-        map.put(132, new ArrayList<String>());
-        map.put(78, new ArrayList<String>());
-        map.put(117, new ArrayList<String>());
         map.put(140, new ArrayList<String>());
-        map.put(119, new ArrayList<String>());
+        map.put(102, new ArrayList<String>());
+        map.put(85, new ArrayList<String>());
+        map.put(90, new ArrayList<String>());
+        map.put(109, new ArrayList<String>());
+        map.put(118, new ArrayList<String>());
+        map.put(74, new ArrayList<String>());
+        map.put(112, new ArrayList<String>());
+        map.put(126, new ArrayList<String>());
+        map.put(82, new ArrayList<String>());
+        map.put(87, new ArrayList<String>());
+        map.put(83, new ArrayList<String>());
+        map.put(75, new ArrayList<String>());
+        map.put(84, new ArrayList<String>());
         map.put(104, new ArrayList<String>());
+        map.put(130, new ArrayList<String>());
+        map.put(138, new ArrayList<String>());
+        map.put(71, new ArrayList<String>());
+        map.put(113, new ArrayList<String>());
+        map.put(91, new ArrayList<String>());
+        map.put(93, new ArrayList<String>());
+        map.put(141, new ArrayList<String>());
+        map.put(133, new ArrayList<String>());
+        map.put(99, new ArrayList<String>());
+        map.put(92, new ArrayList<String>());
+        map.put(94, new ArrayList<String>());
+        map.put(103, new ArrayList<String>());
+        map.put(105, new ArrayList<String>());
+        map.put(117, new ArrayList<String>());
+        map.put(88, new ArrayList<String>());
+        map.put(123, new ArrayList<String>());
+        map.put(72, new ArrayList<String>());
         map.put(89, new ArrayList<String>());
+        map.put(137, new ArrayList<String>());
+        map.put(139, new ArrayList<String>());
+        map.put(132, new ArrayList<String>());
+        map.put(73, new ArrayList<String>());
+        map.put(108, new ArrayList<String>());
         map.put(129, new ArrayList<String>());
-        map.put(127, new ArrayList<String>());
         map.put(80, new ArrayList<String>());
-        map.put(92, new ArrayList<String>());
-        map.put(109, new ArrayList<String>());
-        map.put(141, new ArrayList<String>());
-        map.put(122, new ArrayList<String>());
-        map.put(124, new ArrayList<String>());
-        map.put(120, new ArrayList<String>());
-        map.put(100, new ArrayList<String>());
-        map.put(73, new ArrayList<String>());
-        map.put(116, new ArrayList<String>());
-        map.put(75, new ArrayList<String>());
+        map.put(125, new ArrayList<String>());
+        map.put(70, new ArrayList<String>());
+        map.put(114, new ArrayList<String>());
+        map.put(67, new ArrayList<String>());
         map.put(128, new ArrayList<String>());
+        map.put(115, new ArrayList<String>());
         map.put(136, new ArrayList<String>());
-        map.put(105, new ArrayList<String>());
-        map.put(95, new ArrayList<String>());
-        map.put(88, new ArrayList<String>());
-        map.put(139, new ArrayList<String>());
-        map.put(130, new ArrayList<String>());
-        map.put(135, new ArrayList<String>());
-        map.put(133, new ArrayList<String>());
-        map.put(87, new ArrayList<String>());
-        map.put(134, new ArrayList<String>());
-        map.put(69, new ArrayList<String>());
+        map.put(120, new ArrayList<String>());
+        map.put(111, new ArrayList<String>());
+        map.put(127, new ArrayList<String>());
         map.put(86, new ArrayList<String>());
-        map.put(82, new ArrayList<String>());
-        map.put(91, new ArrayList<String>());
-        map.put(125, new ArrayList<String>());
         map.put(76, new ArrayList<String>());
-        map.put(83, new ArrayList<String>());
+        map.put(78, new ArrayList<String>());
+        map.put(121, new ArrayList<String>());
+        map.put(122, new ArrayList<String>());
         map.put(79, new ArrayList<String>());
-        map.put(85, new ArrayList<String>());
-        map.put(126, new ArrayList<String>());
-        map.put(77, new ArrayList<String>());
-        map.put(115, new ArrayList<String>());
-        map.put(113, new ArrayList<String>());
-        map.put(114, new ArrayList<String>());
-        map.put(107, new ArrayList<String>());
-        map.put(111, new ArrayList<String>());
-        map.put(72, new ArrayList<String>());
-        map.put(93, new ArrayList<String>());
-        map.put(131, new ArrayList<String>());
-        map.put(103, new ArrayList<String>());
-        map.put(99, new ArrayList<String>());
-        map.put(106, new ArrayList<String>());
-        map.put(118, new ArrayList<String>());
-        map.put(97, new ArrayList<String>());
-        map.put(102, new ArrayList<String>());
-        map.put(90, new ArrayList<String>());
-        map.put(112, new ArrayList<String>());
+        map.put(96, new ArrayList<String>());
+        map.put(116, new ArrayList<String>());
         map.put(68, new ArrayList<String>());
-        map.put(137, new ArrayList<String>());
-        map.put(101, new ArrayList<String>());
-        map.put(84, new ArrayList<String>());
-        map.put(71, new ArrayList<String>());
-        map.put(138, new ArrayList<String>());
-        map.put(108, new ArrayList<String>());
-        map.put(94, new ArrayList<String>());
-        map.get(96).add("$_gen0 = list($import)");
-        map.get(98).add("$_gen1 = list($file_body_element)");
-        map.get(121).add("$_gen10 = list($input_declaration)");
-        map.get(74).add("$_gen11 = list($kv)");
-        map.get(110).add("$_gen12 = list($meta_kv)");
-        map.get(70).add("$_gen13 = $setter");
-        map.get(70).add("$_gen13 = :_empty");
-        map.get(67).add("$_gen14 = list($output_kv)");
-        map.get(123).add("$_gen15 = list($wf_body_element)");
-        map.get(81).add("$_gen16 = $alias");
-        map.get(81).add("$_gen16 = :_empty");
-        map.get(132).add("$_gen17 = list($call_after)");
-        map.get(78).add("$_gen18 = $call_brace_block");
-        map.get(78).add("$_gen18 = :_empty");
-        map.get(117).add("$_gen19 = $call_body");
-        map.get(117).add("$_gen19 = :_empty");
-        map.get(140).add("$_gen2 = list($struct_declaration)");
-        map.get(119).add("$_gen20 = list($input_kv, :comma)");
-        map.get(104).add("$_gen21 = list($meta_value, :comma)");
-        map.get(89).add("$_gen22 = list($meta_kv, :comma)");
-        map.get(129).add("$_gen23 = list($type_e, :comma)");
-        map.get(127).add("$_gen24 = list($e, :comma)");
-        map.get(80).add("$_gen25 = list($object_kv, :comma)");
-        map.get(92).add("$_gen26 = list($map_kv, :comma)");
-        map.get(109).add("$_gen3 = list($static_string_piece)");
-        map.get(141).add("$_gen4 = list($string_piece)");
-        map.get(122).add("$_gen5 = $import_namespace");
-        map.get(122).add("$_gen5 = :_empty");
-        map.get(124).add("$_gen6 = list($import_alias)");
-        map.get(120).add("$_gen7 = list($task_sections)");
-        map.get(100).add("$_gen8 = list($command_part)");
-        map.get(73).add("$_gen9 = list($expression_placeholder_kv)");
-        map.get(116).add("$alias = :as :identifier -> $1");
-        map.get(75).add("$call = :call :fqn $_gen16 $_gen17 $_gen18 -> Call( task=$1, alias=$2, after=$3, body=$4 )");
-        map.get(128).add("$call_after = :after :identifier -> $1");
-        map.get(136).add("$call_body = :input :colon $_gen20 -> CallBody( inputs=$2 )");
-        map.get(105).add("$call_brace_block = :lbrace $_gen19 :rbrace -> $1");
-        map.get(95).add("$command = :raw_command :raw_cmd_start $_gen8 :raw_cmd_end -> RawCommand( parts=$2 )");
-        map.get(88).add("$command_part = $expression_placeholder");
-        map.get(88).add("$command_part = :cmd_part");
-        map.get(139).add("$declaration = $type_e :identifier $setter -> Declaration( type=$0, name=$1, expression=$2 )");
-        map.get(130).add("$document = $version $_gen0 $_gen1 -> Draft3File( version=$0, imports=$1, body=$2 )");
-        map.get(135).add("$e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :plus $e -> Add( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e :slash $e -> Divide( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
-        map.get(135).add("$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
-        map.get(135).add("$e = $string_literal");
-        map.get(135).add("$e = :boolean");
-        map.get(135).add("$e = :dash $e -> UnaryNegation( expression=$1 )");
-        map.get(135).add("$e = :float");
-        map.get(135).add("$e = :identifier");
-        map.get(135).add("$e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 )");
-        map.get(135).add("$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
-        map.get(135).add("$e = :integer");
-        map.get(135).add("$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
-        map.get(135).add("$e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 )");
-        map.get(135).add("$e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 )");
-        map.get(135).add("$e = :none");
-        map.get(135).add("$e = :not $e -> LogicalNot( expression=$1 )");
-        map.get(135).add("$e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 )");
-        map.get(135).add("$e = :plus $e -> UnaryPlus( expression=$1 )");
-        map.get(133).add("$expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 )");
-        map.get(87).add("$expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 )");
-        map.get(134).add("$file_body_element = $struct");
-        map.get(134).add("$file_body_element = $task");
-        map.get(134).add("$file_body_element = $workflow");
-        map.get(69).add("$if_stmt = :if :lparen $e :rparen :lbrace $_gen15 :rbrace -> If( expression=$2, body=$5 )");
-        map.get(86).add("$import = :import $static_string $_gen5 $_gen6 -> Import( uri=$1, namespace=$2, aliases=$3 )");
-        map.get(82).add("$import_alias = :alias :identifier :as :identifier -> ImportAlias( old_name=$1, new_name=$3 )");
-        map.get(91).add("$import_namespace = :as :identifier -> $1");
-        map.get(125).add("$input_declaration = $type_e :identifier $_gen13 -> InputDeclaration( type=$0, name=$1, expression=$2 )");
-        map.get(76).add("$input_kv = :identifier :equal $e -> ObjectKV( key=$0, value=$2 )");
-        map.get(83).add("$inputs = :input :lbrace $_gen10 :rbrace -> Inputs( inputs=$2 )");
-        map.get(79).add("$kv = :identifier :colon $e -> RuntimeAttribute( key=$0, value=$2 )");
-        map.get(85).add("$map_kv = $e :colon $e -> MapLiteralKv( key=$0, value=$2 )");
-        map.get(126).add("$meta = :meta $meta_map -> Meta( map=$1 )");
-        map.get(77).add("$meta_kv = :identifier :colon $meta_value -> MetaKvPair( key=$0, value=$2 )");
-        map.get(115).add("$meta_map = :lbrace $_gen12 :rbrace -> $1");
-        map.get(113).add("$meta_value = $static_string");
-        map.get(113).add("$meta_value = :boolean");
-        map.get(113).add("$meta_value = :float");
-        map.get(113).add("$meta_value = :integer");
-        map.get(113).add("$meta_value = :lbrace $_gen22 :rbrace -> MetaObject( map=$1 )");
-        map.get(113).add("$meta_value = :lsquare $_gen21 :rsquare -> MetaArray( values=$1 )");
-        map.get(113).add("$meta_value = :null");
-        map.get(114).add("$object_kv = :identifier :colon $e -> ObjectKV( key=$0, value=$2 )");
-        map.get(107).add("$output_kv = $type_e :identifier :equal $e -> Output( type=$0, name=$1, expression=$3 )");
-        map.get(111).add("$outputs = :output :lbrace $_gen14 :rbrace -> Outputs( outputs=$2 )");
-        map.get(72).add("$parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
-        map.get(93).add("$rt_map = :lbrace $_gen11 :rbrace -> $1");
-        map.get(131).add("$runtime = :runtime $rt_map -> Runtime( map=$1 )");
-        map.get(103).add("$scatter = :scatter :lparen :identifier :in $e :rparen :lbrace $_gen15 :rbrace -> Scatter( item=$2, collection=$4, body=$7 )");
-        map.get(99).add("$setter = :equal $e -> $1");
-        map.get(106).add("$static_string = :quote $_gen3 :quote -> StaticString( value=$1 )");
-        map.get(118).add("$static_string_piece = :escape");
-        map.get(118).add("$static_string_piece = :string");
-        map.get(97).add("$string_literal = :quote $_gen4 :quote -> StringLiteral( pieces=$1 )");
-        map.get(102).add("$string_piece = $expression_placeholder");
-        map.get(102).add("$string_piece = $static_string_piece");
-        map.get(90).add("$struct = :struct :identifier :lbrace $_gen2 :rbrace -> Struct( name=$1, entries=$3 )");
-        map.get(112).add("$struct_declaration = $type_e :identifier -> StructEntry( type=$0, name=$1 )");
-        map.get(68).add("$task = :task :identifier :lbrace $_gen7 :rbrace -> Task( name=$1, sections=$3 )");
-        map.get(137).add("$task_sections = $command");
-        map.get(137).add("$task_sections = $declaration");
-        map.get(137).add("$task_sections = $inputs");
-        map.get(137).add("$task_sections = $meta");
-        map.get(137).add("$task_sections = $outputs");
-        map.get(137).add("$task_sections = $parameter_meta");
-        map.get(137).add("$task_sections = $runtime");
-        map.get(101).add("$type_e = :identifier");
-        map.get(101).add("$type_e = :type");
-        map.get(101).add("$type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 )");
-        map.get(101).add("$type_e = :type <=> :plus -> NonEmptyType( innerType=$0 )");
-        map.get(101).add("$type_e = :type <=> :qmark -> OptionalType( innerType=$0 )");
-        map.get(84).add("$version = :version :version_name -> VersionDeclaration( v=$1 )");
-        map.get(71).add("$wf_body_element = $call");
-        map.get(71).add("$wf_body_element = $declaration");
-        map.get(71).add("$wf_body_element = $if_stmt");
-        map.get(71).add("$wf_body_element = $inputs");
-        map.get(71).add("$wf_body_element = $outputs");
-        map.get(71).add("$wf_body_element = $scatter");
-        map.get(71).add("$wf_body_element = $wf_meta");
-        map.get(71).add("$wf_body_element = $wf_parameter_meta");
-        map.get(138).add("$wf_meta = :meta $meta_map -> Meta( map=$1 )");
-        map.get(108).add("$wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
-        map.get(94).add("$workflow = :workflow :identifier :lbrace $_gen15 :rbrace -> Workflow( name=$1, body=$3 )");
+        map.put(134, new ArrayList<String>());
+        map.put(69, new ArrayList<String>());
+        map.get(81).add("$_gen0 = list($import)");
+        map.get(77).add("$_gen1 = list($file_body_element)");
+        map.get(124).add("$_gen10 = list($input_declaration)");
+        map.get(97).add("$_gen11 = list($kv)");
+        map.get(106).add("$_gen12 = list($meta_kv)");
+        map.get(101).add("$_gen13 = $setter");
+        map.get(101).add("$_gen13 = :_empty");
+        map.get(119).add("$_gen14 = list($output_kv)");
+        map.get(98).add("$_gen15 = list($wf_body_element)");
+        map.get(95).add("$_gen16 = $alias");
+        map.get(95).add("$_gen16 = :_empty");
+        map.get(135).add("$_gen17 = list($call_after)");
+        map.get(100).add("$_gen18 = $call_brace_block");
+        map.get(100).add("$_gen18 = :_empty");
+        map.get(107).add("$_gen19 = $call_body");
+        map.get(107).add("$_gen19 = :_empty");
+        map.get(131).add("$_gen2 = list($struct_declaration)");
+        map.get(110).add("$_gen20 = list($input_kv, :comma)");
+        map.get(140).add("$_gen21 = list($meta_value, :comma)");
+        map.get(102).add("$_gen22 = list($meta_kv, :comma)");
+        map.get(85).add("$_gen23 = list($type_e, :comma)");
+        map.get(90).add("$_gen24 = list($object_kv, :comma)");
+        map.get(109).add("$_gen25 = list($e, :comma)");
+        map.get(118).add("$_gen26 = list($map_kv, :comma)");
+        map.get(74).add("$_gen3 = list($static_string_piece)");
+        map.get(112).add("$_gen4 = list($string_piece)");
+        map.get(126).add("$_gen5 = $import_namespace");
+        map.get(126).add("$_gen5 = :_empty");
+        map.get(82).add("$_gen6 = list($import_alias)");
+        map.get(87).add("$_gen7 = list($task_sections)");
+        map.get(83).add("$_gen8 = list($command_part)");
+        map.get(75).add("$_gen9 = list($expression_placeholder_kv)");
+        map.get(84).add("$alias = :as :identifier -> $1");
+        map.get(104).add("$call = :call :fqn $_gen16 $_gen17 $_gen18 -> Call( task=$1, alias=$2, after=$3, body=$4 )");
+        map.get(130).add("$call_after = :after :identifier -> $1");
+        map.get(138).add("$call_body = :input :colon $_gen20 -> CallBody( inputs=$2 )");
+        map.get(71).add("$call_brace_block = :lbrace $_gen19 :rbrace -> $1");
+        map.get(113).add("$command = :raw_command :raw_cmd_start $_gen8 :raw_cmd_end -> RawCommand( parts=$2 )");
+        map.get(91).add("$command_part = $expression_placeholder");
+        map.get(91).add("$command_part = :cmd_part");
+        map.get(93).add("$declaration = $type_e :identifier $setter -> Declaration( type=$0, name=$1, expression=$2 )");
+        map.get(141).add("$document = $version $_gen0 $_gen1 -> Draft3File( version=$0, imports=$1, body=$2 )");
+        map.get(133).add("$e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :plus $e -> Add( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e :slash $e -> Divide( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
+        map.get(133).add("$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
+        map.get(133).add("$e = $string_literal");
+        map.get(133).add("$e = :boolean");
+        map.get(133).add("$e = :dash $e -> UnaryNegation( expression=$1 )");
+        map.get(133).add("$e = :float");
+        map.get(133).add("$e = :identifier");
+        map.get(133).add("$e = :identifier <=> :lbrace $_gen24 :rbrace -> StructLiteral( name=$0, map=$2 )");
+        map.get(133).add("$e = :identifier <=> :lparen $_gen25 :rparen -> FunctionCall( name=$0, params=$2 )");
+        map.get(133).add("$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
+        map.get(133).add("$e = :integer");
+        map.get(133).add("$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
+        map.get(133).add("$e = :lparen $_gen25 :rparen -> TupleLiteral( values=$1 )");
+        map.get(133).add("$e = :lsquare $_gen25 :rsquare -> ArrayLiteral( values=$1 )");
+        map.get(133).add("$e = :none");
+        map.get(133).add("$e = :not $e -> LogicalNot( expression=$1 )");
+        map.get(133).add("$e = :object :lbrace $_gen24 :rbrace -> ObjectLiteral( map=$2 )");
+        map.get(133).add("$e = :plus $e -> UnaryPlus( expression=$1 )");
+        map.get(99).add("$expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 )");
+        map.get(92).add("$expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 )");
+        map.get(94).add("$file_body_element = $struct");
+        map.get(94).add("$file_body_element = $task");
+        map.get(94).add("$file_body_element = $workflow");
+        map.get(103).add("$if_stmt = :if :lparen $e :rparen :lbrace $_gen15 :rbrace -> If( expression=$2, body=$5 )");
+        map.get(105).add("$import = :import $static_string $_gen5 $_gen6 -> Import( uri=$1, namespace=$2, aliases=$3 )");
+        map.get(117).add("$import_alias = :alias :identifier :as :identifier -> ImportAlias( old_name=$1, new_name=$3 )");
+        map.get(88).add("$import_namespace = :as :identifier -> $1");
+        map.get(123).add("$input_declaration = $type_e :identifier $_gen13 -> InputDeclaration( type=$0, name=$1, expression=$2 )");
+        map.get(72).add("$input_kv = :identifier :equal $e -> ObjectKV( key=$0, value=$2 )");
+        map.get(89).add("$inputs = :input :lbrace $_gen10 :rbrace -> Inputs( inputs=$2 )");
+        map.get(137).add("$kv = :identifier :colon $e -> RuntimeAttribute( key=$0, value=$2 )");
+        map.get(139).add("$map_kv = $e :colon $e -> MapLiteralKv( key=$0, value=$2 )");
+        map.get(132).add("$meta = :meta $meta_map -> Meta( map=$1 )");
+        map.get(73).add("$meta_kv = :identifier :colon $meta_value -> MetaKvPair( key=$0, value=$2 )");
+        map.get(108).add("$meta_map = :lbrace $_gen12 :rbrace -> $1");
+        map.get(129).add("$meta_value = $static_string");
+        map.get(129).add("$meta_value = :boolean");
+        map.get(129).add("$meta_value = :float");
+        map.get(129).add("$meta_value = :integer");
+        map.get(129).add("$meta_value = :lbrace $_gen22 :rbrace -> MetaObject( map=$1 )");
+        map.get(129).add("$meta_value = :lsquare $_gen21 :rsquare -> MetaArray( values=$1 )");
+        map.get(129).add("$meta_value = :null");
+        map.get(80).add("$object_kv = :identifier :colon $e -> ObjectKV( key=$0, value=$2 )");
+        map.get(125).add("$output_kv = $type_e :identifier :equal $e -> Output( type=$0, name=$1, expression=$3 )");
+        map.get(70).add("$outputs = :output :lbrace $_gen14 :rbrace -> Outputs( outputs=$2 )");
+        map.get(114).add("$parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
+        map.get(67).add("$rt_map = :lbrace $_gen11 :rbrace -> $1");
+        map.get(128).add("$runtime = :runtime $rt_map -> Runtime( map=$1 )");
+        map.get(115).add("$scatter = :scatter :lparen :identifier :in $e :rparen :lbrace $_gen15 :rbrace -> Scatter( item=$2, collection=$4, body=$7 )");
+        map.get(136).add("$setter = :equal $e -> $1");
+        map.get(120).add("$static_string = :quote $_gen3 :quote -> StaticString( value=$1 )");
+        map.get(111).add("$static_string_piece = :escape");
+        map.get(111).add("$static_string_piece = :string");
+        map.get(127).add("$string_literal = :quote $_gen4 :quote -> StringLiteral( pieces=$1 )");
+        map.get(86).add("$string_piece = $expression_placeholder");
+        map.get(86).add("$string_piece = $static_string_piece");
+        map.get(76).add("$struct = :struct :identifier :lbrace $_gen2 :rbrace -> Struct( name=$1, entries=$3 )");
+        map.get(78).add("$struct_declaration = $type_e :identifier -> StructEntry( type=$0, name=$1 )");
+        map.get(121).add("$task = :task :identifier :lbrace $_gen7 :rbrace -> Task( name=$1, sections=$3 )");
+        map.get(122).add("$task_sections = $command");
+        map.get(122).add("$task_sections = $declaration");
+        map.get(122).add("$task_sections = $inputs");
+        map.get(122).add("$task_sections = $meta");
+        map.get(122).add("$task_sections = $outputs");
+        map.get(122).add("$task_sections = $parameter_meta");
+        map.get(122).add("$task_sections = $runtime");
+        map.get(79).add("$type_e = :identifier");
+        map.get(79).add("$type_e = :type");
+        map.get(79).add("$type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 )");
+        map.get(79).add("$type_e = :type <=> :plus -> NonEmptyType( innerType=$0 )");
+        map.get(79).add("$type_e = :type <=> :qmark -> OptionalType( innerType=$0 )");
+        map.get(96).add("$version = :version :version_name -> VersionDeclaration( v=$1 )");
+        map.get(116).add("$wf_body_element = $call");
+        map.get(116).add("$wf_body_element = $declaration");
+        map.get(116).add("$wf_body_element = $if_stmt");
+        map.get(116).add("$wf_body_element = $inputs");
+        map.get(116).add("$wf_body_element = $outputs");
+        map.get(116).add("$wf_body_element = $scatter");
+        map.get(116).add("$wf_body_element = $wf_meta");
+        map.get(116).add("$wf_body_element = $wf_parameter_meta");
+        map.get(68).add("$wf_meta = :meta $meta_map -> Meta( map=$1 )");
+        map.get(134).add("$wf_parameter_meta = :parameter_meta $meta_map -> ParameterMeta( map=$1 )");
+        map.get(69).add("$workflow = :workflow :identifier :lbrace $_gen15 :rbrace -> Workflow( name=$1, body=$3 )");
         nonterminal_rules = Collections.unmodifiableMap(map);
     }
     static {
@@ -2644,9 +2648,9 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
         map.put(new Integer(94), "$_gen21 = list($meta_value, :comma)");
         map.put(new Integer(96), "$_gen22 = list($meta_kv, :comma)");
         map.put(new Integer(98), "$_gen23 = list($type_e, :comma)");
-        map.put(new Integer(120), "$_gen24 = list($e, :comma)");
-        map.put(new Integer(124), "$_gen25 = list($object_kv, :comma)");
-        map.put(new Integer(127), "$_gen26 = list($map_kv, :comma)");
+        map.put(new Integer(120), "$_gen24 = list($object_kv, :comma)");
+        map.put(new Integer(122), "$_gen25 = list($e, :comma)");
+        map.put(new Integer(128), "$_gen26 = list($map_kv, :comma)");
         map.put(new Integer(10), "$_gen3 = list($static_string_piece)");
         map.put(new Integer(12), "$_gen4 = list($string_piece)");
         map.put(new Integer(18), "$_gen5 = $import_namespace");
@@ -2678,22 +2682,23 @@ public enum WdlTerminalIdentifier implements TerminalIdentifier {
         map.put(new Integer(116), "$e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 )");
         map.put(new Integer(112), "$e = $e :plus $e -> Add( lhs=$0, rhs=$2 )");
         map.put(new Integer(115), "$e = $e :slash $e -> Divide( lhs=$0, rhs=$2 )");
-        map.put(new Integer(123), "$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
-        map.put(new Integer(122), "$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
-        map.put(new Integer(131), "$e = $string_literal");
-        map.put(new Integer(133), "$e = :boolean");
+        map.put(new Integer(125), "$e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 )");
+        map.put(new Integer(124), "$e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 )");
+        map.put(new Integer(132), "$e = $string_literal");
+        map.put(new Integer(134), "$e = :boolean");
         map.put(new Integer(119), "$e = :dash $e -> UnaryNegation( expression=$1 )");
-        map.put(new Integer(135), "$e = :float");
-        map.put(new Integer(132), "$e = :identifier");
-        map.put(new Integer(121), "$e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 )");
-        map.put(new Integer(130), "$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
-        map.put(new Integer(134), "$e = :integer");
-        map.put(new Integer(128), "$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
-        map.put(new Integer(129), "$e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 )");
-        map.put(new Integer(126), "$e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 )");
-        map.put(new Integer(136), "$e = :none");
+        map.put(new Integer(136), "$e = :float");
+        map.put(new Integer(133), "$e = :identifier");
+        map.put(new Integer(121), "$e = :identifier <=> :lbrace $_gen24 :rbrace -> StructLiteral( name=$0, map=$2 )");
+        map.put(new Integer(123), "$e = :identifier <=> :lparen $_gen25 :rparen -> FunctionCall( name=$0, params=$2 )");
+        map.put(new Integer(131), "$e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 )");
+        map.put(new Integer(135), "$e = :integer");
+        map.put(new Integer(129), "$e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 )");
+        map.put(new Integer(130), "$e = :lparen $_gen25 :rparen -> TupleLiteral( values=$1 )");
+        map.put(new Integer(127), "$e = :lsquare $_gen25 :rsquare -> ArrayLiteral( values=$1 )");
+        map.put(new Integer(137), "$e = :none");
         map.put(new Integer(117), "$e = :not $e -> LogicalNot( expression=$1 )");
-        map.put(new Integer(125), "$e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 )");
+        map.put(new Integer(126), "$e = :object :lbrace $_gen24 :rbrace -> ObjectLiteral( map=$2 )");
         map.put(new Integer(118), "$e = :plus $e -> UnaryPlus( expression=$1 )");
         map.put(new Integer(38), "$expression_placeholder = :expression_placeholder_start $_gen9 $e :expression_placeholder_end -> ExpressionPlaceholder( attributes=$1, expr=$2 )");
         map.put(new Integer(39), "$expression_placeholder_kv = :cmd_attr_hint :identifier :equal $e -> ExpressionPlaceholderAttr( key=$1, value=$3 )");
@@ -2803,29 +2808,30 @@ private static Terminal expect(ParserContext ctx, TerminalIdentifier expecting)
     private static Map<Integer, Integer> prefix_binding_power_e;
     static {
         Map<Integer, Integer> map = new HashMap<Integer, Integer>();
-        map.put(25, 4000); /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
-        map.put(13, 5000); /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
-        map.put(24, 6000); /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
-        map.put(14, 6000); /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
-        map.put(65, 7000); /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
-        map.put(1, 7000); /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
-        map.put(4, 7000); /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
-        map.put(21, 7000); /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
-        map.put(9, 8000); /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
-        map.put(63, 8000); /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
-        map.put(3, 9000); /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
-        map.put(29, 9000); /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
-        map.put(5, 9000); /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
-        map.put(12, 11000); /* $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall( name=$0, params=$2 ) */
-        map.put(51, 12000); /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
-        map.put(62, 13000); /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
+        map.put(49, 4000); /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
+        map.put(8, 5000); /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
+        map.put(56, 6000); /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
+        map.put(63, 6000); /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
+        map.put(37, 7000); /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
+        map.put(11, 7000); /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
+        map.put(2, 7000); /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
+        map.put(3, 7000); /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
+        map.put(12, 8000); /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
+        map.put(53, 8000); /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
+        map.put(34, 9000); /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
+        map.put(20, 9000); /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
+        map.put(22, 9000); /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
+        map.put(50, 11000); /* $e = :identifier <=> :lbrace list($object_kv, :comma) :rbrace -> StructLiteral( name=$0, map=$2 ) */
+        map.put(28, 12000); /* $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall( name=$0, params=$2 ) */
+        map.put(61, 13000); /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
+        map.put(62, 14000); /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
         infix_binding_power_e = Collections.unmodifiableMap(map);
     }
     static {
         Map<Integer, Integer> map = new HashMap<Integer, Integer>();
-        map.put(60, 10000); /* $e = :not $e -> LogicalNot( expression=$1 ) */
-        map.put(9, 10000); /* $e = :plus $e -> UnaryPlus( expression=$1 ) */
-        map.put(63, 10000); /* $e = :dash $e -> UnaryNegation( expression=$1 ) */
+        map.put(52, 10000); /* $e = :not $e -> LogicalNot( expression=$1 ) */
+        map.put(12, 10000); /* $e = :plus $e -> UnaryPlus( expression=$1 ) */
+        map.put(53, 10000); /* $e = :dash $e -> UnaryNegation( expression=$1 ) */
         prefix_binding_power_e = Collections.unmodifiableMap(map);
     }
     static int get_infix_binding_power_e(int terminal_id) {
@@ -2862,7 +2868,7 @@ public static ParseTree parse_e_internal(ParserContext ctx, int rbp) throws Synt
         return left;
     }
     private static ParseTree nud_e(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(135, "e") );
+        ParseTree tree = new ParseTree( new NonTerminal(133, "e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "e";
         if (current == null) {
@@ -2876,7 +2882,7 @@ else if (rule_first.get(117).contains(terminal_map.get(current.getId()))) {
             tree.setAstTransformation(new AstTransformNodeCreator("LogicalNot", parameters));
             tree.setNudMorphemeCount(2);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NOT));
-            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(60)));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(52)));
             tree.setPrefix(true);
         }
         else if (rule_first.get(118).contains(terminal_map.get(current.getId()))) {
@@ -2887,7 +2893,7 @@ else if (rule_first.get(118).contains(terminal_map.get(current.getId()))) {
             tree.setAstTransformation(new AstTransformNodeCreator("UnaryPlus", parameters));
             tree.setNudMorphemeCount(2);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PLUS));
-            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(9)));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(12)));
             tree.setPrefix(true);
         }
         else if (rule_first.get(119).contains(terminal_map.get(current.getId()))) {
@@ -2898,42 +2904,49 @@ else if (rule_first.get(119).contains(terminal_map.get(current.getId()))) {
             tree.setAstTransformation(new AstTransformNodeCreator("UnaryNegation", parameters));
             tree.setNudMorphemeCount(2);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DASH));
-            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(63)));
+            tree.add(parse_e_internal(ctx, get_prefix_binding_power_e(53)));
             tree.setPrefix(true);
         }
         else if (rule_first.get(121).contains(terminal_map.get(current.getId()))) {
-            /* (121) $e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 ) */
+            /* (121) $e = :identifier <=> :lbrace $_gen24 :rbrace -> StructLiteral( name=$0, map=$2 ) */
             ctx.rule = rules.get(121);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
         }
-        else if (rule_first.get(125).contains(terminal_map.get(current.getId()))) {
-            /* (125) $e = :object :lbrace $_gen25 :rbrace -> ObjectLiteral( map=$2 ) */
-            ctx.rule = rules.get(125);
+        else if (rule_first.get(123).contains(terminal_map.get(current.getId()))) {
+            /* (123) $e = :identifier <=> :lparen $_gen25 :rparen -> FunctionCall( name=$0, params=$2 ) */
+            ctx.rule = rules.get(123);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
+        }
+        else if (rule_first.get(126).contains(terminal_map.get(current.getId()))) {
+            /* (126) $e = :object :lbrace $_gen24 :rbrace -> ObjectLiteral( map=$2 ) */
+            ctx.rule = rules.get(126);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("map", 2);
             tree.setAstTransformation(new AstTransformNodeCreator("ObjectLiteral", parameters));
             tree.setNudMorphemeCount(4);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_OBJECT));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE));
-            tree.add(parse__gen25(ctx));
+            tree.add(parse__gen24(ctx));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE));
         }
-        else if (rule_first.get(126).contains(terminal_map.get(current.getId()))) {
-            /* (126) $e = :lsquare $_gen24 :rsquare -> ArrayLiteral( values=$1 ) */
-            ctx.rule = rules.get(126);
+        else if (rule_first.get(127).contains(terminal_map.get(current.getId()))) {
+            /* (127) $e = :lsquare $_gen25 :rsquare -> ArrayLiteral( values=$1 ) */
+            ctx.rule = rules.get(127);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("values", 1);
             tree.setAstTransformation(new AstTransformNodeCreator("ArrayLiteral", parameters));
             tree.setNudMorphemeCount(3);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LSQUARE));
-            tree.add(parse__gen24(ctx));
+            tree.add(parse__gen25(ctx));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
         }
-        else if (rule_first.get(128).contains(terminal_map.get(current.getId()))) {
-            /* (128) $e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 ) */
-            ctx.rule = rules.get(128);
+        else if (rule_first.get(129).contains(terminal_map.get(current.getId()))) {
+            /* (129) $e = :lbrace $_gen26 :rbrace -> MapLiteral( map=$1 ) */
+            ctx.rule = rules.get(129);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("map", 1);
             tree.setAstTransformation(new AstTransformNodeCreator("MapLiteral", parameters));
@@ -2942,20 +2955,20 @@ else if (rule_first.get(128).contains(terminal_map.get(current.getId()))) {
             tree.add(parse__gen26(ctx));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE));
         }
-        else if (rule_first.get(129).contains(terminal_map.get(current.getId()))) {
-            /* (129) $e = :lparen $_gen24 :rparen -> TupleLiteral( values=$1 ) */
-            ctx.rule = rules.get(129);
+        else if (rule_first.get(130).contains(terminal_map.get(current.getId()))) {
+            /* (130) $e = :lparen $_gen25 :rparen -> TupleLiteral( values=$1 ) */
+            ctx.rule = rules.get(130);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("values", 1);
             tree.setAstTransformation(new AstTransformNodeCreator("TupleLiteral", parameters));
             tree.setNudMorphemeCount(3);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LPAREN));
-            tree.add(parse__gen24(ctx));
+            tree.add(parse__gen25(ctx));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RPAREN));
         }
-        else if (rule_first.get(130).contains(terminal_map.get(current.getId()))) {
-            /* (130) $e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 ) */
-            ctx.rule = rules.get(130);
+        else if (rule_first.get(131).contains(terminal_map.get(current.getId()))) {
+            /* (131) $e = :if $e :then $e :else $e -> TernaryIf( cond=$1, iftrue=$3, iffalse=$5 ) */
+            ctx.rule = rules.get(131);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("cond", 1);
             parameters.put("iftrue", 3);
@@ -2969,56 +2982,56 @@ else if (rule_first.get(130).contains(terminal_map.get(current.getId()))) {
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_ELSE));
             tree.add(parse_e(ctx));
         }
-        else if (rule_first.get(131).contains(terminal_map.get(current.getId()))) {
-            /* (131) $e = $string_literal */
-            ctx.rule = rules.get(131);
-            tree.setAstTransformation(new AstTransformSubstitution(0));
-            tree.setNudMorphemeCount(1);
-            tree.add(parse_string_literal(ctx));
-        }
         else if (rule_first.get(132).contains(terminal_map.get(current.getId()))) {
-            /* (132) $e = :identifier */
+            /* (132) $e = $string_literal */
             ctx.rule = rules.get(132);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
-            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
+            tree.add(parse_string_literal(ctx));
         }
         else if (rule_first.get(133).contains(terminal_map.get(current.getId()))) {
-            /* (133) $e = :boolean */
+            /* (133) $e = :identifier */
             ctx.rule = rules.get(133);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
-            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_BOOLEAN));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_IDENTIFIER));
         }
         else if (rule_first.get(134).contains(terminal_map.get(current.getId()))) {
-            /* (134) $e = :integer */
+            /* (134) $e = :boolean */
             ctx.rule = rules.get(134);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
-            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_INTEGER));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_BOOLEAN));
         }
         else if (rule_first.get(135).contains(terminal_map.get(current.getId()))) {
-            /* (135) $e = :float */
+            /* (135) $e = :integer */
             ctx.rule = rules.get(135);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
-            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_FLOAT));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_INTEGER));
         }
         else if (rule_first.get(136).contains(terminal_map.get(current.getId()))) {
-            /* (136) $e = :none */
+            /* (136) $e = :float */
             ctx.rule = rules.get(136);
             tree.setAstTransformation(new AstTransformSubstitution(0));
             tree.setNudMorphemeCount(1);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_FLOAT));
+        }
+        else if (rule_first.get(137).contains(terminal_map.get(current.getId()))) {
+            /* (137) $e = :none */
+            ctx.rule = rules.get(137);
+            tree.setAstTransformation(new AstTransformSubstitution(0));
+            tree.setNudMorphemeCount(1);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NONE));
         }
         return tree;
     }
     private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(135, "e") );
+        ParseTree tree = new ParseTree( new NonTerminal(133, "e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "e";
         int modifier;
-        if (current.getId() == 25) {
+        if (current.getId() == 49) {
             /* $e = $e :double_pipe $e -> LogicalOr( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(104);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3030,10 +3043,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_PIPE));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(25) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(49) - modifier));
             return tree;
         }
-        if (current.getId() == 13) {
+        if (current.getId() == 8) {
             /* $e = $e :double_ampersand $e -> LogicalAnd( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(105);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3045,10 +3058,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_AMPERSAND));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(13) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(8) - modifier));
             return tree;
         }
-        if (current.getId() == 24) {
+        if (current.getId() == 56) {
             /* $e = $e :double_equal $e -> Equals( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(106);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3060,10 +3073,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DOUBLE_EQUAL));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(24) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(56) - modifier));
             return tree;
         }
-        if (current.getId() == 14) {
+        if (current.getId() == 63) {
             /* $e = $e :not_equal $e -> NotEquals( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(107);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3075,10 +3088,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_NOT_EQUAL));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(14) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(63) - modifier));
             return tree;
         }
-        if (current.getId() == 65) {
+        if (current.getId() == 37) {
             /* $e = $e :lt $e -> LessThan( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(108);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3090,10 +3103,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LT));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(65) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(37) - modifier));
             return tree;
         }
-        if (current.getId() == 1) {
+        if (current.getId() == 11) {
             /* $e = $e :lteq $e -> LessThanOrEqual( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(109);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3105,10 +3118,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LTEQ));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(1) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(11) - modifier));
             return tree;
         }
-        if (current.getId() == 4) {
+        if (current.getId() == 2) {
             /* $e = $e :gt $e -> GreaterThan( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(110);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3120,10 +3133,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_GT));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(4) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(2) - modifier));
             return tree;
         }
-        if (current.getId() == 21) {
+        if (current.getId() == 3) {
             /* $e = $e :gteq $e -> GreaterThanOrEqual( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(111);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3135,10 +3148,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_GTEQ));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(21) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(3) - modifier));
             return tree;
         }
-        if (current.getId() == 9) {
+        if (current.getId() == 12) {
             /* $e = $e :plus $e -> Add( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(112);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3150,10 +3163,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PLUS));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(9) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(12) - modifier));
             return tree;
         }
-        if (current.getId() == 63) {
+        if (current.getId() == 53) {
             /* $e = $e :dash $e -> Subtract( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(113);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3165,10 +3178,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_DASH));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(63) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(53) - modifier));
             return tree;
         }
-        if (current.getId() == 3) {
+        if (current.getId() == 34) {
             /* $e = $e :asterisk $e -> Multiply( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(114);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3180,10 +3193,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_ASTERISK));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(3) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(34) - modifier));
             return tree;
         }
-        if (current.getId() == 29) {
+        if (current.getId() == 20) {
             /* $e = $e :slash $e -> Divide( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(115);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3195,10 +3208,10 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_SLASH));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(29) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(20) - modifier));
             return tree;
         }
-        if (current.getId() == 5) {
+        if (current.getId() == 22) {
             /* $e = $e :percent $e -> Remainder( lhs=$0, rhs=$2 ) */
             ctx.rule = rules.get(116);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3210,25 +3223,38 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_PERCENT));
             modifier = 0;
             tree.setInfix(true);
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(5) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(22) - modifier));
             return tree;
         }
-        if (current.getId() == 12) {
-            /* $e = :identifier <=> :lparen $_gen24 :rparen -> FunctionCall( name=$0, params=$2 ) */
+        if (current.getId() == 50) {
+            /* $e = :identifier <=> :lbrace $_gen24 :rbrace -> StructLiteral( name=$0, map=$2 ) */
             ctx.rule = rules.get(121);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("name", 0);
+            parameters.put("map", 2);
+            tree.setAstTransformation(new AstTransformNodeCreator("StructLiteral", parameters));
+            tree.add(left);
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LBRACE));
+            tree.add(parse__gen24(ctx));
+            tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RBRACE));
+            return tree;
+        }
+        if (current.getId() == 28) {
+            /* $e = :identifier <=> :lparen $_gen25 :rparen -> FunctionCall( name=$0, params=$2 ) */
+            ctx.rule = rules.get(123);
+            LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
+            parameters.put("name", 0);
             parameters.put("params", 2);
             tree.setAstTransformation(new AstTransformNodeCreator("FunctionCall", parameters));
             tree.add(left);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LPAREN));
-            tree.add(parse__gen24(ctx));
+            tree.add(parse__gen25(ctx));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RPAREN));
             return tree;
         }
-        if (current.getId() == 51) {
+        if (current.getId() == 61) {
             /* $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup( lhs=$0, rhs=$2 ) */
-            ctx.rule = rules.get(122);
+            ctx.rule = rules.get(124);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("lhs", 0);
             parameters.put("rhs", 2);
@@ -3237,13 +3263,13 @@ private static ParseTree led_e(ParseTree left, ParserContext ctx) throws SyntaxE
             tree.add(left);
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_LSQUARE));
             modifier = 0;
-            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(51) - modifier));
+            tree.add(parse_e_internal(ctx, get_infix_binding_power_e(61) - modifier));
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
             return tree;
         }
         if (current.getId() == 62) {
             /* $e = $e <=> :dot :identifier -> MemberAccess( value=$0, member=$2 ) */
-            ctx.rule = rules.get(123);
+            ctx.rule = rules.get(125);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
             parameters.put("value", 0);
             parameters.put("member", 2);
@@ -3300,7 +3326,7 @@ public static ParseTree parse_meta_value_internal(ParserContext ctx, int rbp) th
         return left;
     }
     private static ParseTree nud_meta_value(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(113, "meta_value") );
+        ParseTree tree = new ParseTree( new NonTerminal(129, "meta_value") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "meta_value";
         if (current == null) {
@@ -3366,7 +3392,7 @@ else if (rule_first.get(97).contains(terminal_map.get(current.getId()))) {
         return tree;
     }
     private static ParseTree led_meta_value(ParseTree left, ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(113, "meta_value") );
+        ParseTree tree = new ParseTree( new NonTerminal(129, "meta_value") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "meta_value";
         int modifier;
@@ -3376,9 +3402,9 @@ private static ParseTree led_meta_value(ParseTree left, ParserContext ctx) throw
     private static Map<Integer, Integer> prefix_binding_power_type_e;
     static {
         Map<Integer, Integer> map = new HashMap<Integer, Integer>();
-        map.put(51, 1000); /* $type_e = :type <=> :lsquare list($type_e, :comma) :rsquare -> Type( name=$0, subtype=$2 ) */
-        map.put(57, 2000); /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
-        map.put(9, 3000); /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
+        map.put(61, 1000); /* $type_e = :type <=> :lsquare list($type_e, :comma) :rsquare -> Type( name=$0, subtype=$2 ) */
+        map.put(9, 2000); /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
+        map.put(12, 3000); /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
         infix_binding_power_type_e = Collections.unmodifiableMap(map);
     }
     static {
@@ -3419,7 +3445,7 @@ public static ParseTree parse_type_e_internal(ParserContext ctx, int rbp) throws
         return left;
     }
     private static ParseTree nud_type_e(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(101, "type_e") );
+        ParseTree tree = new ParseTree( new NonTerminal(79, "type_e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "type_e";
         if (current == null) {
@@ -3463,11 +3489,11 @@ else if (rule_first.get(103).contains(terminal_map.get(current.getId()))) {
         return tree;
     }
     private static ParseTree led_type_e(ParseTree left, ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree( new NonTerminal(101, "type_e") );
+        ParseTree tree = new ParseTree( new NonTerminal(79, "type_e") );
         Terminal current = ctx.tokens.current();
         ctx.nonterminal = "type_e";
         int modifier;
-        if (current.getId() == 51) {
+        if (current.getId() == 61) {
             /* $type_e = :type <=> :lsquare $_gen23 :rsquare -> Type( name=$0, subtype=$2 ) */
             ctx.rule = rules.get(99);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3480,7 +3506,7 @@ private static ParseTree led_type_e(ParseTree left, ParserContext ctx) throws Sy
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_RSQUARE));
             return tree;
         }
-        if (current.getId() == 57) {
+        if (current.getId() == 9) {
             /* $type_e = :type <=> :qmark -> OptionalType( innerType=$0 ) */
             ctx.rule = rules.get(100);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3490,7 +3516,7 @@ private static ParseTree led_type_e(ParseTree left, ParserContext ctx) throws Sy
             tree.add(expect(ctx, WdlTerminalIdentifier.TERMINAL_QMARK));
             return tree;
         }
-        if (current.getId() == 9) {
+        if (current.getId() == 12) {
             /* $type_e = :type <=> :plus -> NonEmptyType( innerType=$0 ) */
             ctx.rule = rules.get(101);
             LinkedHashMap<String, Integer> parameters = new LinkedHashMap<String, Integer>();
@@ -3507,12 +3533,12 @@ public ParseTree parse__gen0(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen0(ctx);
     }
     private static ParseTree parse__gen0(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(96, "_gen0"));
+        ParseTree tree = new ParseTree(new NonTerminal(81, "_gen0"));
         tree.setList(true);
         ctx.nonterminal = "_gen0";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(96).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(96).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(81).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(81).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3521,7 +3547,7 @@ private static ParseTree parse__gen0(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(96).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(81).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_import(ctx));
             ctx.nonterminal = "_gen0"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3533,12 +3559,12 @@ public ParseTree parse__gen1(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen1(ctx);
     }
     private static ParseTree parse__gen1(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(98, "_gen1"));
+        ParseTree tree = new ParseTree(new NonTerminal(77, "_gen1"));
         tree.setList(true);
         ctx.nonterminal = "_gen1";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(98).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(98).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(77).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(77).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3547,7 +3573,7 @@ private static ParseTree parse__gen1(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(98).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(77).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_file_body_element(ctx));
             ctx.nonterminal = "_gen1"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3559,12 +3585,12 @@ public ParseTree parse__gen10(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen10(ctx);
     }
     private static ParseTree parse__gen10(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(121, "_gen10"));
+        ParseTree tree = new ParseTree(new NonTerminal(124, "_gen10"));
         tree.setList(true);
         ctx.nonterminal = "_gen10";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(121).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(121).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(124).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(124).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3573,7 +3599,7 @@ private static ParseTree parse__gen10(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(121).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(124).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_input_declaration(ctx));
             ctx.nonterminal = "_gen10"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3585,12 +3611,12 @@ public ParseTree parse__gen11(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen11(ctx);
     }
     private static ParseTree parse__gen11(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(74, "_gen11"));
+        ParseTree tree = new ParseTree(new NonTerminal(97, "_gen11"));
         tree.setList(true);
         ctx.nonterminal = "_gen11";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(74).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(74).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(97).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(97).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3599,7 +3625,7 @@ private static ParseTree parse__gen11(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(74).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(97).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_kv(ctx));
             ctx.nonterminal = "_gen11"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3611,12 +3637,12 @@ public ParseTree parse__gen12(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen12(ctx);
     }
     private static ParseTree parse__gen12(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(110, "_gen12"));
+        ParseTree tree = new ParseTree(new NonTerminal(106, "_gen12"));
         tree.setList(true);
         ctx.nonterminal = "_gen12";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(110).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(110).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(106).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(106).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3625,7 +3651,7 @@ private static ParseTree parse__gen12(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(110).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(106).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_meta_kv(ctx));
             ctx.nonterminal = "_gen12"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3637,12 +3663,12 @@ public ParseTree parse__gen14(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen14(ctx);
     }
     private static ParseTree parse__gen14(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(67, "_gen14"));
+        ParseTree tree = new ParseTree(new NonTerminal(119, "_gen14"));
         tree.setList(true);
         ctx.nonterminal = "_gen14";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(67).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(67).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(119).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(119).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3651,7 +3677,7 @@ private static ParseTree parse__gen14(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(67).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(119).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_output_kv(ctx));
             ctx.nonterminal = "_gen14"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3663,12 +3689,12 @@ public ParseTree parse__gen15(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen15(ctx);
     }
     private static ParseTree parse__gen15(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(123, "_gen15"));
+        ParseTree tree = new ParseTree(new NonTerminal(98, "_gen15"));
         tree.setList(true);
         ctx.nonterminal = "_gen15";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(123).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(123).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(98).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(98).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3677,7 +3703,7 @@ private static ParseTree parse__gen15(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(123).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(98).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_wf_body_element(ctx));
             ctx.nonterminal = "_gen15"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3689,12 +3715,12 @@ public ParseTree parse__gen17(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen17(ctx);
     }
     private static ParseTree parse__gen17(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(132, "_gen17"));
+        ParseTree tree = new ParseTree(new NonTerminal(135, "_gen17"));
         tree.setList(true);
         ctx.nonterminal = "_gen17";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(132).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(132).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(135).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(135).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3703,7 +3729,7 @@ private static ParseTree parse__gen17(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(132).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(135).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_call_after(ctx));
             ctx.nonterminal = "_gen17"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3715,12 +3741,12 @@ public ParseTree parse__gen2(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen2(ctx);
     }
     private static ParseTree parse__gen2(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(140, "_gen2"));
+        ParseTree tree = new ParseTree(new NonTerminal(131, "_gen2"));
         tree.setList(true);
         ctx.nonterminal = "_gen2";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(140).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(140).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(131).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(131).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3729,7 +3755,7 @@ private static ParseTree parse__gen2(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(140).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(131).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_struct_declaration(ctx));
             ctx.nonterminal = "_gen2"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -3741,13 +3767,13 @@ public ParseTree parse__gen20(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen20(ctx);
     }
     private static ParseTree parse__gen20(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(119, "_gen20"));
+        ParseTree tree = new ParseTree(new NonTerminal(110, "_gen20"));
         tree.setList(true);
-        tree.setListSeparator(38);
+        tree.setListSeparator(4);
         ctx.nonterminal = "_gen20";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(119).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(119).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(110).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(110).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3756,7 +3782,7 @@ private static ParseTree parse__gen20(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(119).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(110).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_input_kv(ctx));
             ctx.nonterminal = "_gen20"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3782,13 +3808,13 @@ public ParseTree parse__gen21(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen21(ctx);
     }
     private static ParseTree parse__gen21(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(104, "_gen21"));
+        ParseTree tree = new ParseTree(new NonTerminal(140, "_gen21"));
         tree.setList(true);
-        tree.setListSeparator(38);
+        tree.setListSeparator(4);
         ctx.nonterminal = "_gen21";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(104).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(104).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(140).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(140).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3797,7 +3823,7 @@ private static ParseTree parse__gen21(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(104).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(140).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_meta_value(ctx));
             ctx.nonterminal = "_gen21"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3823,13 +3849,13 @@ public ParseTree parse__gen22(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen22(ctx);
     }
     private static ParseTree parse__gen22(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(89, "_gen22"));
+        ParseTree tree = new ParseTree(new NonTerminal(102, "_gen22"));
         tree.setList(true);
-        tree.setListSeparator(38);
+        tree.setListSeparator(4);
         ctx.nonterminal = "_gen22";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(89).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(89).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(102).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(102).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3838,7 +3864,7 @@ private static ParseTree parse__gen22(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(89).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(102).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_meta_kv(ctx));
             ctx.nonterminal = "_gen22"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3864,13 +3890,13 @@ public ParseTree parse__gen23(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen23(ctx);
     }
     private static ParseTree parse__gen23(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(129, "_gen23"));
+        ParseTree tree = new ParseTree(new NonTerminal(85, "_gen23"));
         tree.setList(true);
-        tree.setListSeparator(38);
+        tree.setListSeparator(4);
         ctx.nonterminal = "_gen23";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(129).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(85).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(85).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3879,7 +3905,7 @@ private static ParseTree parse__gen23(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(129).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(85).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_type_e(ctx));
             ctx.nonterminal = "_gen23"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -3905,13 +3931,13 @@ public ParseTree parse__gen24(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen24(ctx);
     }
     private static ParseTree parse__gen24(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(127, "_gen24"));
+        ParseTree tree = new ParseTree(new NonTerminal(90, "_gen24"));
         tree.setList(true);
-        tree.setListSeparator(38);
+        tree.setListSeparator(4);
         ctx.nonterminal = "_gen24";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(127).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(127).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(90).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(90).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3920,8 +3946,8 @@ private static ParseTree parse__gen24(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(127).contains(terminal_map.get(ctx.tokens.current().getId())))) {
-            tree.add(parse_e(ctx));
+               nonterminal_first.get(90).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_object_kv(ctx));
             ctx.nonterminal = "_gen24"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
                 ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
@@ -3946,13 +3972,13 @@ public ParseTree parse__gen25(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen25(ctx);
     }
     private static ParseTree parse__gen25(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(80, "_gen25"));
+        ParseTree tree = new ParseTree(new NonTerminal(109, "_gen25"));
         tree.setList(true);
-        tree.setListSeparator(38);
+        tree.setListSeparator(4);
         ctx.nonterminal = "_gen25";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(80).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(80).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -3961,8 +3987,8 @@ private static ParseTree parse__gen25(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(80).contains(terminal_map.get(ctx.tokens.current().getId())))) {
-            tree.add(parse_object_kv(ctx));
+               nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+            tree.add(parse_e(ctx));
             ctx.nonterminal = "_gen25"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
                 ctx.tokens.current().getId() == WdlTerminalIdentifier.TERMINAL_COMMA.id()) {
@@ -3987,13 +4013,13 @@ public ParseTree parse__gen26(List<Terminal> tokens, SyntaxErrorFormatter error_
         return parse__gen26(ctx);
     }
     private static ParseTree parse__gen26(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(92, "_gen26"));
+        ParseTree tree = new ParseTree(new NonTerminal(118, "_gen26"));
         tree.setList(true);
-        tree.setListSeparator(38);
+        tree.setListSeparator(4);
         ctx.nonterminal = "_gen26";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(92).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(92).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(118).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(118).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4002,7 +4028,7 @@ private static ParseTree parse__gen26(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(92).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(118).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_map_kv(ctx));
             ctx.nonterminal = "_gen26"; // because parse_* can reset this
             if (ctx.tokens.current() != null &&
@@ -4028,12 +4054,12 @@ public ParseTree parse__gen3(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen3(ctx);
     }
     private static ParseTree parse__gen3(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(109, "_gen3"));
+        ParseTree tree = new ParseTree(new NonTerminal(74, "_gen3"));
         tree.setList(true);
         ctx.nonterminal = "_gen3";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(109).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(74).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(74).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4042,7 +4068,7 @@ private static ParseTree parse__gen3(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(109).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(74).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_static_string_piece(ctx));
             ctx.nonterminal = "_gen3"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4054,12 +4080,12 @@ public ParseTree parse__gen4(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen4(ctx);
     }
     private static ParseTree parse__gen4(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(141, "_gen4"));
+        ParseTree tree = new ParseTree(new NonTerminal(112, "_gen4"));
         tree.setList(true);
         ctx.nonterminal = "_gen4";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(141).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(141).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(112).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(112).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4068,7 +4094,7 @@ private static ParseTree parse__gen4(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(141).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(112).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_string_piece(ctx));
             ctx.nonterminal = "_gen4"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4080,12 +4106,12 @@ public ParseTree parse__gen6(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen6(ctx);
     }
     private static ParseTree parse__gen6(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(124, "_gen6"));
+        ParseTree tree = new ParseTree(new NonTerminal(82, "_gen6"));
         tree.setList(true);
         ctx.nonterminal = "_gen6";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(124).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(124).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(82).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(82).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4094,7 +4120,7 @@ private static ParseTree parse__gen6(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(124).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(82).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_import_alias(ctx));
             ctx.nonterminal = "_gen6"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4106,12 +4132,12 @@ public ParseTree parse__gen7(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen7(ctx);
     }
     private static ParseTree parse__gen7(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(120, "_gen7"));
+        ParseTree tree = new ParseTree(new NonTerminal(87, "_gen7"));
         tree.setList(true);
         ctx.nonterminal = "_gen7";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(120).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(120).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(87).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(87).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4120,7 +4146,7 @@ private static ParseTree parse__gen7(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(120).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(87).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_task_sections(ctx));
             ctx.nonterminal = "_gen7"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4132,12 +4158,12 @@ public ParseTree parse__gen8(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen8(ctx);
     }
     private static ParseTree parse__gen8(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(100, "_gen8"));
+        ParseTree tree = new ParseTree(new NonTerminal(83, "_gen8"));
         tree.setList(true);
         ctx.nonterminal = "_gen8";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(100).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(100).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(83).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(83).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4146,7 +4172,7 @@ private static ParseTree parse__gen8(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(100).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(83).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_command_part(ctx));
             ctx.nonterminal = "_gen8"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4158,12 +4184,12 @@ public ParseTree parse__gen9(List<Terminal> tokens, SyntaxErrorFormatter error_f
         return parse__gen9(ctx);
     }
     private static ParseTree parse__gen9(ParserContext ctx) throws SyntaxError {
-        ParseTree tree = new ParseTree(new NonTerminal(73, "_gen9"));
+        ParseTree tree = new ParseTree(new NonTerminal(75, "_gen9"));
         tree.setList(true);
         ctx.nonterminal = "_gen9";
         if ( ctx.tokens.current() != null &&
-             !nonterminal_first.get(73).contains(terminal_map.get(ctx.tokens.current().getId())) &&
-              nonterminal_follow.get(73).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
+             !nonterminal_first.get(75).contains(terminal_map.get(ctx.tokens.current().getId())) &&
+              nonterminal_follow.get(75).contains(terminal_map.get(ctx.tokens.current().getId())) ) {
             return tree;
         }
         if (ctx.tokens.current() == null) {
@@ -4172,7 +4198,7 @@ private static ParseTree parse__gen9(ParserContext ctx) throws SyntaxError {
         int minimum = 0;
         while (minimum > 0 ||
                (ctx.tokens.current() != null &&
-               nonterminal_first.get(73).contains(terminal_map.get(ctx.tokens.current().getId())))) {
+               nonterminal_first.get(75).contains(terminal_map.get(ctx.tokens.current().getId())))) {
             tree.add(parse_expression_placeholder_kv(ctx));
             ctx.nonterminal = "_gen9"; // because parse_* can reset this
             minimum = Math.max(minimum - 1, 0);
@@ -4187,12 +4213,12 @@ private static ParseTree parse__gen13(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[3][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(70, "_gen13"));
+        int rule = (current != null) ? table[34][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(101, "_gen13"));
         ctx.nonterminal = "_gen13";
         if ( current != null &&
-             !nonterminal_first.get(70).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(70).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(101).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(101).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4216,12 +4242,12 @@ private static ParseTree parse__gen16(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[14][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(81, "_gen16"));
+        int rule = (current != null) ? table[28][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(95, "_gen16"));
         ctx.nonterminal = "_gen16";
         if ( current != null &&
-             !nonterminal_first.get(81).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(81).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(95).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(95).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4245,12 +4271,12 @@ private static ParseTree parse__gen18(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[11][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(78, "_gen18"));
+        int rule = (current != null) ? table[33][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(100, "_gen18"));
         ctx.nonterminal = "_gen18";
         if ( current != null &&
-             !nonterminal_first.get(78).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(78).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(100).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(100).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4274,12 +4300,12 @@ private static ParseTree parse__gen19(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[50][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(117, "_gen19"));
+        int rule = (current != null) ? table[40][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(107, "_gen19"));
         ctx.nonterminal = "_gen19";
         if ( current != null &&
-             !nonterminal_first.get(117).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(117).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(107).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(107).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4303,12 +4329,12 @@ private static ParseTree parse__gen5(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[55][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(122, "_gen5"));
+        int rule = (current != null) ? table[59][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(126, "_gen5"));
         ctx.nonterminal = "_gen5";
         if ( current != null &&
-             !nonterminal_first.get(122).contains(terminal_map.get(current.getId())) &&
-              nonterminal_follow.get(122).contains(terminal_map.get(current.getId())) ) {
+             !nonterminal_first.get(126).contains(terminal_map.get(current.getId())) &&
+              nonterminal_follow.get(126).contains(terminal_map.get(current.getId())) ) {
             return tree;
         }
         if (current == null) {
@@ -4332,14 +4358,14 @@ private static ParseTree parse_alias(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[49][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(116, "alias"));
+        int rule = (current != null) ? table[17][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(84, "alias"));
         ctx.nonterminal = "alias";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "alias",
-                nonterminal_first.get(116),
-                nonterminal_rules.get(116)
+                nonterminal_first.get(84),
+                nonterminal_rules.get(84)
             ));
         }
         if (rule == 81) {
@@ -4355,7 +4381,7 @@ private static ParseTree parse_alias(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "alias",
             current,
-            nonterminal_first.get(116),
+            nonterminal_first.get(84),
             rules.get(81)
         ));
     }
@@ -4367,14 +4393,14 @@ private static ParseTree parse_call(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[8][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(75, "call"));
+        int rule = (current != null) ? table[37][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(104, "call"));
         ctx.nonterminal = "call";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call",
-                nonterminal_first.get(75),
-                nonterminal_rules.get(75)
+                nonterminal_first.get(104),
+                nonterminal_rules.get(104)
             ));
         }
         if (rule == 75) {
@@ -4401,7 +4427,7 @@ private static ParseTree parse_call(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call",
             current,
-            nonterminal_first.get(75),
+            nonterminal_first.get(104),
             rules.get(75)
         ));
     }
@@ -4413,14 +4439,14 @@ private static ParseTree parse_call_after(ParserContext ctx) throws SyntaxError
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[61][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(128, "call_after"));
+        int rule = (current != null) ? table[63][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(130, "call_after"));
         ctx.nonterminal = "call_after";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call_after",
-                nonterminal_first.get(128),
-                nonterminal_rules.get(128)
+                nonterminal_first.get(130),
+                nonterminal_rules.get(130)
             ));
         }
         if (rule == 82) {
@@ -4436,7 +4462,7 @@ private static ParseTree parse_call_after(ParserContext ctx) throws SyntaxError
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call_after",
             current,
-            nonterminal_first.get(128),
+            nonterminal_first.get(130),
             rules.get(82)
         ));
     }
@@ -4448,14 +4474,14 @@ private static ParseTree parse_call_body(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[69][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(136, "call_body"));
+        int rule = (current != null) ? table[71][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(138, "call_body"));
         ctx.nonterminal = "call_body";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call_body",
-                nonterminal_first.get(136),
-                nonterminal_rules.get(136)
+                nonterminal_first.get(138),
+                nonterminal_rules.get(138)
             ));
         }
         if (rule == 80) {
@@ -4475,7 +4501,7 @@ private static ParseTree parse_call_body(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call_body",
             current,
-            nonterminal_first.get(136),
+            nonterminal_first.get(138),
             rules.get(80)
         ));
     }
@@ -4487,14 +4513,14 @@ private static ParseTree parse_call_brace_block(ParserContext ctx) throws Syntax
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[38][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(105, "call_brace_block"));
+        int rule = (current != null) ? table[4][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(71, "call_brace_block"));
         ctx.nonterminal = "call_brace_block";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "call_brace_block",
-                nonterminal_first.get(105),
-                nonterminal_rules.get(105)
+                nonterminal_first.get(71),
+                nonterminal_rules.get(71)
             ));
         }
         if (rule == 78) {
@@ -4512,7 +4538,7 @@ private static ParseTree parse_call_brace_block(ParserContext ctx) throws Syntax
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "call_brace_block",
             current,
-            nonterminal_first.get(105),
+            nonterminal_first.get(71),
             rules.get(78)
         ));
     }
@@ -4524,14 +4550,14 @@ private static ParseTree parse_command(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[28][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(95, "command"));
+        int rule = (current != null) ? table[46][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(113, "command"));
         ctx.nonterminal = "command";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "command",
-                nonterminal_first.get(95),
-                nonterminal_rules.get(95)
+                nonterminal_first.get(113),
+                nonterminal_rules.get(113)
             ));
         }
         if (rule == 34) {
@@ -4553,7 +4579,7 @@ private static ParseTree parse_command(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "command",
             current,
-            nonterminal_first.get(95),
+            nonterminal_first.get(113),
             rules.get(34)
         ));
     }
@@ -4565,14 +4591,14 @@ private static ParseTree parse_command_part(ParserContext ctx) throws SyntaxErro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[21][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(88, "command_part"));
+        int rule = (current != null) ? table[24][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(91, "command_part"));
         ctx.nonterminal = "command_part";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "command_part",
-                nonterminal_first.get(88),
-                nonterminal_rules.get(88)
+                nonterminal_first.get(91),
+                nonterminal_rules.get(91)
             ));
         }
         if (rule == 35) {
@@ -4594,7 +4620,7 @@ else if (rule == 36) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "command_part",
             current,
-            nonterminal_first.get(88),
+            nonterminal_first.get(91),
             rules.get(36)
         ));
     }
@@ -4606,14 +4632,14 @@ private static ParseTree parse_declaration(ParserContext ctx) throws SyntaxError
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[72][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(139, "declaration"));
+        int rule = (current != null) ? table[26][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(93, "declaration"));
         ctx.nonterminal = "declaration";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "declaration",
-                nonterminal_first.get(139),
-                nonterminal_rules.get(139)
+                nonterminal_first.get(93),
+                nonterminal_rules.get(93)
             ));
         }
         if (rule == 54) {
@@ -4635,7 +4661,7 @@ private static ParseTree parse_declaration(ParserContext ctx) throws SyntaxError
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "declaration",
             current,
-            nonterminal_first.get(139),
+            nonterminal_first.get(93),
             rules.get(54)
         ));
     }
@@ -4647,14 +4673,14 @@ private static ParseTree parse_document(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[63][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(130, "document"));
+        int rule = (current != null) ? table[74][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(141, "document"));
         ctx.nonterminal = "document";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "document",
-                nonterminal_first.get(130),
-                nonterminal_rules.get(130)
+                nonterminal_first.get(141),
+                nonterminal_rules.get(141)
             ));
         }
         if (rule == 2) {
@@ -4676,7 +4702,7 @@ private static ParseTree parse_document(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "document",
             current,
-            nonterminal_first.get(130),
+            nonterminal_first.get(141),
             rules.get(2)
         ));
     }
@@ -4688,14 +4714,14 @@ private static ParseTree parse_expression_placeholder(ParserContext ctx) throws
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[66][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(133, "expression_placeholder"));
+        int rule = (current != null) ? table[32][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(99, "expression_placeholder"));
         ctx.nonterminal = "expression_placeholder";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "expression_placeholder",
-                nonterminal_first.get(133),
-                nonterminal_rules.get(133)
+                nonterminal_first.get(99),
+                nonterminal_rules.get(99)
             ));
         }
         if (rule == 38) {
@@ -4718,7 +4744,7 @@ private static ParseTree parse_expression_placeholder(ParserContext ctx) throws
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "expression_placeholder",
             current,
-            nonterminal_first.get(133),
+            nonterminal_first.get(99),
             rules.get(38)
         ));
     }
@@ -4730,14 +4756,14 @@ private static ParseTree parse_expression_placeholder_kv(ParserContext ctx) thro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[20][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(87, "expression_placeholder_kv"));
+        int rule = (current != null) ? table[25][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(92, "expression_placeholder_kv"));
         ctx.nonterminal = "expression_placeholder_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "expression_placeholder_kv",
-                nonterminal_first.get(87),
-                nonterminal_rules.get(87)
+                nonterminal_first.get(92),
+                nonterminal_rules.get(92)
             ));
         }
         if (rule == 39) {
@@ -4760,7 +4786,7 @@ private static ParseTree parse_expression_placeholder_kv(ParserContext ctx) thro
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "expression_placeholder_kv",
             current,
-            nonterminal_first.get(87),
+            nonterminal_first.get(92),
             rules.get(39)
         ));
     }
@@ -4772,14 +4798,14 @@ private static ParseTree parse_file_body_element(ParserContext ctx) throws Synta
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[67][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(134, "file_body_element"));
+        int rule = (current != null) ? table[27][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(94, "file_body_element"));
         ctx.nonterminal = "file_body_element";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "file_body_element",
-                nonterminal_first.get(134),
-                nonterminal_rules.get(134)
+                nonterminal_first.get(94),
+                nonterminal_rules.get(94)
             ));
         }
         if (rule == 3) {
@@ -4809,7 +4835,7 @@ else if (rule == 5) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "file_body_element",
             current,
-            nonterminal_first.get(134),
+            nonterminal_first.get(94),
             rules.get(5)
         ));
     }
@@ -4821,14 +4847,14 @@ private static ParseTree parse_if_stmt(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[2][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(69, "if_stmt"));
+        int rule = (current != null) ? table[36][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(103, "if_stmt"));
         ctx.nonterminal = "if_stmt";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "if_stmt",
-                nonterminal_first.get(69),
-                nonterminal_rules.get(69)
+                nonterminal_first.get(103),
+                nonterminal_rules.get(103)
             ));
         }
         if (rule == 85) {
@@ -4857,7 +4883,7 @@ private static ParseTree parse_if_stmt(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "if_stmt",
             current,
-            nonterminal_first.get(69),
+            nonterminal_first.get(103),
             rules.get(85)
         ));
     }
@@ -4869,14 +4895,14 @@ private static ParseTree parse_import(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[19][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(86, "import"));
+        int rule = (current != null) ? table[38][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(105, "import"));
         ctx.nonterminal = "import";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "import",
-                nonterminal_first.get(86),
-                nonterminal_rules.get(86)
+                nonterminal_first.get(105),
+                nonterminal_rules.get(105)
             ));
         }
         if (rule == 21) {
@@ -4900,7 +4926,7 @@ private static ParseTree parse_import(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "import",
             current,
-            nonterminal_first.get(86),
+            nonterminal_first.get(105),
             rules.get(21)
         ));
     }
@@ -4912,14 +4938,14 @@ private static ParseTree parse_import_alias(ParserContext ctx) throws SyntaxErro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[15][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(82, "import_alias"));
+        int rule = (current != null) ? table[50][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(117, "import_alias"));
         ctx.nonterminal = "import_alias";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "import_alias",
-                nonterminal_first.get(82),
-                nonterminal_rules.get(82)
+                nonterminal_first.get(117),
+                nonterminal_rules.get(117)
             ));
         }
         if (rule == 23) {
@@ -4942,7 +4968,7 @@ private static ParseTree parse_import_alias(ParserContext ctx) throws SyntaxErro
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "import_alias",
             current,
-            nonterminal_first.get(82),
+            nonterminal_first.get(117),
             rules.get(23)
         ));
     }
@@ -4954,14 +4980,14 @@ private static ParseTree parse_import_namespace(ParserContext ctx) throws Syntax
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[24][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(91, "import_namespace"));
+        int rule = (current != null) ? table[21][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(88, "import_namespace"));
         ctx.nonterminal = "import_namespace";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "import_namespace",
-                nonterminal_first.get(91),
-                nonterminal_rules.get(91)
+                nonterminal_first.get(88),
+                nonterminal_rules.get(88)
             ));
         }
         if (rule == 22) {
@@ -4977,7 +5003,7 @@ private static ParseTree parse_import_namespace(ParserContext ctx) throws Syntax
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "import_namespace",
             current,
-            nonterminal_first.get(91),
+            nonterminal_first.get(88),
             rules.get(22)
         ));
     }
@@ -4989,14 +5015,14 @@ private static ParseTree parse_input_declaration(ParserContext ctx) throws Synta
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[58][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(125, "input_declaration"));
+        int rule = (current != null) ? table[56][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(123, "input_declaration"));
         ctx.nonterminal = "input_declaration";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "input_declaration",
-                nonterminal_first.get(125),
-                nonterminal_rules.get(125)
+                nonterminal_first.get(123),
+                nonterminal_rules.get(123)
             ));
         }
         if (rule == 53) {
@@ -5018,7 +5044,7 @@ private static ParseTree parse_input_declaration(ParserContext ctx) throws Synta
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "input_declaration",
             current,
-            nonterminal_first.get(125),
+            nonterminal_first.get(123),
             rules.get(53)
         ));
     }
@@ -5030,14 +5056,14 @@ private static ParseTree parse_input_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[9][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(76, "input_kv"));
+        int rule = (current != null) ? table[5][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(72, "input_kv"));
         ctx.nonterminal = "input_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "input_kv",
-                nonterminal_first.get(76),
-                nonterminal_rules.get(76)
+                nonterminal_first.get(72),
+                nonterminal_rules.get(72)
             ));
         }
         if (rule == 88) {
@@ -5058,7 +5084,7 @@ private static ParseTree parse_input_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "input_kv",
             current,
-            nonterminal_first.get(76),
+            nonterminal_first.get(72),
             rules.get(88)
         ));
     }
@@ -5070,14 +5096,14 @@ private static ParseTree parse_inputs(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[16][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(83, "inputs"));
+        int rule = (current != null) ? table[22][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(89, "inputs"));
         ctx.nonterminal = "inputs";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "inputs",
-                nonterminal_first.get(83),
-                nonterminal_rules.get(83)
+                nonterminal_first.get(89),
+                nonterminal_rules.get(89)
             ));
         }
         if (rule == 41) {
@@ -5099,7 +5125,7 @@ private static ParseTree parse_inputs(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "inputs",
             current,
-            nonterminal_first.get(83),
+            nonterminal_first.get(89),
             rules.get(41)
         ));
     }
@@ -5111,14 +5137,14 @@ private static ParseTree parse_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[12][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(79, "kv"));
+        int rule = (current != null) ? table[70][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(137, "kv"));
         ctx.nonterminal = "kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "kv",
-                nonterminal_first.get(79),
-                nonterminal_rules.get(79)
+                nonterminal_first.get(137),
+                nonterminal_rules.get(137)
             ));
         }
         if (rule == 45) {
@@ -5139,7 +5165,7 @@ private static ParseTree parse_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "kv",
             current,
-            nonterminal_first.get(79),
+            nonterminal_first.get(137),
             rules.get(45)
         ));
     }
@@ -5151,14 +5177,14 @@ private static ParseTree parse_map_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[18][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(85, "map_kv"));
+        int rule = (current != null) ? table[72][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(139, "map_kv"));
         ctx.nonterminal = "map_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "map_kv",
-                nonterminal_first.get(85),
-                nonterminal_rules.get(85)
+                nonterminal_first.get(139),
+                nonterminal_rules.get(139)
             ));
         }
         if (rule == 56) {
@@ -5179,7 +5205,7 @@ private static ParseTree parse_map_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "map_kv",
             current,
-            nonterminal_first.get(85),
+            nonterminal_first.get(139),
             rules.get(56)
         ));
     }
@@ -5191,14 +5217,14 @@ private static ParseTree parse_meta(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[59][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(126, "meta"));
+        int rule = (current != null) ? table[65][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(132, "meta"));
         ctx.nonterminal = "meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "meta",
-                nonterminal_first.get(126),
-                nonterminal_rules.get(126)
+                nonterminal_first.get(132),
+                nonterminal_rules.get(132)
             ));
         }
         if (rule == 46) {
@@ -5216,7 +5242,7 @@ private static ParseTree parse_meta(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "meta",
             current,
-            nonterminal_first.get(126),
+            nonterminal_first.get(132),
             rules.get(46)
         ));
     }
@@ -5228,14 +5254,14 @@ private static ParseTree parse_meta_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[10][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(77, "meta_kv"));
+        int rule = (current != null) ? table[6][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(73, "meta_kv"));
         ctx.nonterminal = "meta_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "meta_kv",
-                nonterminal_first.get(77),
-                nonterminal_rules.get(77)
+                nonterminal_first.get(73),
+                nonterminal_rules.get(73)
             ));
         }
         if (rule == 50) {
@@ -5256,7 +5282,7 @@ private static ParseTree parse_meta_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "meta_kv",
             current,
-            nonterminal_first.get(77),
+            nonterminal_first.get(73),
             rules.get(50)
         ));
     }
@@ -5268,14 +5294,14 @@ private static ParseTree parse_meta_map(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[48][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(115, "meta_map"));
+        int rule = (current != null) ? table[41][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(108, "meta_map"));
         ctx.nonterminal = "meta_map";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "meta_map",
-                nonterminal_first.get(115),
-                nonterminal_rules.get(115)
+                nonterminal_first.get(108),
+                nonterminal_rules.get(108)
             ));
         }
         if (rule == 49) {
@@ -5293,7 +5319,7 @@ private static ParseTree parse_meta_map(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "meta_map",
             current,
-            nonterminal_first.get(115),
+            nonterminal_first.get(108),
             rules.get(49)
         ));
     }
@@ -5305,14 +5331,14 @@ private static ParseTree parse_object_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[47][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(114, "object_kv"));
+        int rule = (current != null) ? table[13][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(80, "object_kv"));
         ctx.nonterminal = "object_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "object_kv",
-                nonterminal_first.get(114),
-                nonterminal_rules.get(114)
+                nonterminal_first.get(80),
+                nonterminal_rules.get(80)
             ));
         }
         if (rule == 87) {
@@ -5333,7 +5359,7 @@ private static ParseTree parse_object_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "object_kv",
             current,
-            nonterminal_first.get(114),
+            nonterminal_first.get(80),
             rules.get(87)
         ));
     }
@@ -5345,14 +5371,14 @@ private static ParseTree parse_output_kv(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[40][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(107, "output_kv"));
+        int rule = (current != null) ? table[58][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(125, "output_kv"));
         ctx.nonterminal = "output_kv";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "output_kv",
-                nonterminal_first.get(107),
-                nonterminal_rules.get(107)
+                nonterminal_first.get(125),
+                nonterminal_rules.get(125)
             ));
         }
         if (rule == 59) {
@@ -5376,7 +5402,7 @@ private static ParseTree parse_output_kv(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "output_kv",
             current,
-            nonterminal_first.get(107),
+            nonterminal_first.get(125),
             rules.get(59)
         ));
     }
@@ -5388,14 +5414,14 @@ private static ParseTree parse_outputs(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[44][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(111, "outputs"));
+        int rule = (current != null) ? table[3][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(70, "outputs"));
         ctx.nonterminal = "outputs";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "outputs",
-                nonterminal_first.get(111),
-                nonterminal_rules.get(111)
+                nonterminal_first.get(70),
+                nonterminal_rules.get(70)
             ));
         }
         if (rule == 58) {
@@ -5417,7 +5443,7 @@ private static ParseTree parse_outputs(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "outputs",
             current,
-            nonterminal_first.get(111),
+            nonterminal_first.get(70),
             rules.get(58)
         ));
     }
@@ -5429,14 +5455,14 @@ private static ParseTree parse_parameter_meta(ParserContext ctx) throws SyntaxEr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[5][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(72, "parameter_meta"));
+        int rule = (current != null) ? table[47][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(114, "parameter_meta"));
         ctx.nonterminal = "parameter_meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "parameter_meta",
-                nonterminal_first.get(72),
-                nonterminal_rules.get(72)
+                nonterminal_first.get(114),
+                nonterminal_rules.get(114)
             ));
         }
         if (rule == 47) {
@@ -5454,7 +5480,7 @@ private static ParseTree parse_parameter_meta(ParserContext ctx) throws SyntaxEr
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "parameter_meta",
             current,
-            nonterminal_first.get(72),
+            nonterminal_first.get(114),
             rules.get(47)
         ));
     }
@@ -5466,14 +5492,14 @@ private static ParseTree parse_rt_map(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[26][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(93, "rt_map"));
+        int rule = (current != null) ? table[0][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(67, "rt_map"));
         ctx.nonterminal = "rt_map";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "rt_map",
-                nonterminal_first.get(93),
-                nonterminal_rules.get(93)
+                nonterminal_first.get(67),
+                nonterminal_rules.get(67)
             ));
         }
         if (rule == 44) {
@@ -5491,7 +5517,7 @@ private static ParseTree parse_rt_map(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "rt_map",
             current,
-            nonterminal_first.get(93),
+            nonterminal_first.get(67),
             rules.get(44)
         ));
     }
@@ -5503,14 +5529,14 @@ private static ParseTree parse_runtime(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[64][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(131, "runtime"));
+        int rule = (current != null) ? table[61][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(128, "runtime"));
         ctx.nonterminal = "runtime";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "runtime",
-                nonterminal_first.get(131),
-                nonterminal_rules.get(131)
+                nonterminal_first.get(128),
+                nonterminal_rules.get(128)
             ));
         }
         if (rule == 42) {
@@ -5528,7 +5554,7 @@ private static ParseTree parse_runtime(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "runtime",
             current,
-            nonterminal_first.get(131),
+            nonterminal_first.get(128),
             rules.get(42)
         ));
     }
@@ -5540,14 +5566,14 @@ private static ParseTree parse_scatter(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[36][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(103, "scatter"));
+        int rule = (current != null) ? table[48][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(115, "scatter"));
         ctx.nonterminal = "scatter";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "scatter",
-                nonterminal_first.get(103),
-                nonterminal_rules.get(103)
+                nonterminal_first.get(115),
+                nonterminal_rules.get(115)
             ));
         }
         if (rule == 86) {
@@ -5581,7 +5607,7 @@ private static ParseTree parse_scatter(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "scatter",
             current,
-            nonterminal_first.get(103),
+            nonterminal_first.get(115),
             rules.get(86)
         ));
     }
@@ -5593,14 +5619,14 @@ private static ParseTree parse_setter(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[32][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(99, "setter"));
+        int rule = (current != null) ? table[69][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(136, "setter"));
         ctx.nonterminal = "setter";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "setter",
-                nonterminal_first.get(99),
-                nonterminal_rules.get(99)
+                nonterminal_first.get(136),
+                nonterminal_rules.get(136)
             ));
         }
         if (rule == 55) {
@@ -5616,7 +5642,7 @@ private static ParseTree parse_setter(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "setter",
             current,
-            nonterminal_first.get(99),
+            nonterminal_first.get(136),
             rules.get(55)
         ));
     }
@@ -5628,14 +5654,14 @@ private static ParseTree parse_static_string(ParserContext ctx) throws SyntaxErr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[39][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(106, "static_string"));
+        int rule = (current != null) ? table[53][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(120, "static_string"));
         ctx.nonterminal = "static_string";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "static_string",
-                nonterminal_first.get(106),
-                nonterminal_rules.get(106)
+                nonterminal_first.get(120),
+                nonterminal_rules.get(120)
             ));
         }
         if (rule == 11) {
@@ -5655,7 +5681,7 @@ private static ParseTree parse_static_string(ParserContext ctx) throws SyntaxErr
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "static_string",
             current,
-            nonterminal_first.get(106),
+            nonterminal_first.get(120),
             rules.get(11)
         ));
     }
@@ -5667,14 +5693,14 @@ private static ParseTree parse_static_string_piece(ParserContext ctx) throws Syn
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[51][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(118, "static_string_piece"));
+        int rule = (current != null) ? table[44][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(111, "static_string_piece"));
         ctx.nonterminal = "static_string_piece";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "static_string_piece",
-                nonterminal_first.get(118),
-                nonterminal_rules.get(118)
+                nonterminal_first.get(111),
+                nonterminal_rules.get(111)
             ));
         }
         if (rule == 14) {
@@ -5696,7 +5722,7 @@ else if (rule == 15) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "static_string_piece",
             current,
-            nonterminal_first.get(118),
+            nonterminal_first.get(111),
             rules.get(15)
         ));
     }
@@ -5708,14 +5734,14 @@ private static ParseTree parse_string_literal(ParserContext ctx) throws SyntaxEr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[30][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(97, "string_literal"));
+        int rule = (current != null) ? table[60][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(127, "string_literal"));
         ctx.nonterminal = "string_literal";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "string_literal",
-                nonterminal_first.get(97),
-                nonterminal_rules.get(97)
+                nonterminal_first.get(127),
+                nonterminal_rules.get(127)
             ));
         }
         if (rule == 13) {
@@ -5735,7 +5761,7 @@ private static ParseTree parse_string_literal(ParserContext ctx) throws SyntaxEr
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "string_literal",
             current,
-            nonterminal_first.get(97),
+            nonterminal_first.get(127),
             rules.get(13)
         ));
     }
@@ -5747,14 +5773,14 @@ private static ParseTree parse_string_piece(ParserContext ctx) throws SyntaxErro
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[35][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(102, "string_piece"));
+        int rule = (current != null) ? table[19][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(86, "string_piece"));
         ctx.nonterminal = "string_piece";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "string_piece",
-                nonterminal_first.get(102),
-                nonterminal_rules.get(102)
+                nonterminal_first.get(86),
+                nonterminal_rules.get(86)
             ));
         }
         if (rule == 16) {
@@ -5776,7 +5802,7 @@ else if (rule == 17) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "string_piece",
             current,
-            nonterminal_first.get(102),
+            nonterminal_first.get(86),
             rules.get(17)
         ));
     }
@@ -5788,14 +5814,14 @@ private static ParseTree parse_struct(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[23][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(90, "struct"));
+        int rule = (current != null) ? table[9][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(76, "struct"));
         ctx.nonterminal = "struct";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "struct",
-                nonterminal_first.get(90),
-                nonterminal_rules.get(90)
+                nonterminal_first.get(76),
+                nonterminal_rules.get(76)
             ));
         }
         if (rule == 8) {
@@ -5820,7 +5846,7 @@ private static ParseTree parse_struct(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "struct",
             current,
-            nonterminal_first.get(90),
+            nonterminal_first.get(76),
             rules.get(8)
         ));
     }
@@ -5832,14 +5858,14 @@ private static ParseTree parse_struct_declaration(ParserContext ctx) throws Synt
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[45][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(112, "struct_declaration"));
+        int rule = (current != null) ? table[11][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(78, "struct_declaration"));
         ctx.nonterminal = "struct_declaration";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "struct_declaration",
-                nonterminal_first.get(112),
-                nonterminal_rules.get(112)
+                nonterminal_first.get(78),
+                nonterminal_rules.get(78)
             ));
         }
         if (rule == 9) {
@@ -5858,7 +5884,7 @@ private static ParseTree parse_struct_declaration(ParserContext ctx) throws Synt
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "struct_declaration",
             current,
-            nonterminal_first.get(112),
+            nonterminal_first.get(78),
             rules.get(9)
         ));
     }
@@ -5870,14 +5896,14 @@ private static ParseTree parse_task(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[1][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(68, "task"));
+        int rule = (current != null) ? table[54][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(121, "task"));
         ctx.nonterminal = "task";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "task",
-                nonterminal_first.get(68),
-                nonterminal_rules.get(68)
+                nonterminal_first.get(121),
+                nonterminal_rules.get(121)
             ));
         }
         if (rule == 25) {
@@ -5902,7 +5928,7 @@ private static ParseTree parse_task(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "task",
             current,
-            nonterminal_first.get(68),
+            nonterminal_first.get(121),
             rules.get(25)
         ));
     }
@@ -5914,14 +5940,14 @@ private static ParseTree parse_task_sections(ParserContext ctx) throws SyntaxErr
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[70][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(137, "task_sections"));
+        int rule = (current != null) ? table[55][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(122, "task_sections"));
         ctx.nonterminal = "task_sections";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "task_sections",
-                nonterminal_first.get(137),
-                nonterminal_rules.get(137)
+                nonterminal_first.get(122),
+                nonterminal_rules.get(122)
             ));
         }
         if (rule == 26) {
@@ -5983,7 +6009,7 @@ else if (rule == 32) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "task_sections",
             current,
-            nonterminal_first.get(137),
+            nonterminal_first.get(122),
             rules.get(32)
         ));
     }
@@ -5995,14 +6021,14 @@ private static ParseTree parse_version(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[17][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(84, "version"));
+        int rule = (current != null) ? table[29][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(96, "version"));
         ctx.nonterminal = "version";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "version",
-                nonterminal_first.get(84),
-                nonterminal_rules.get(84)
+                nonterminal_first.get(96),
+                nonterminal_rules.get(96)
             ));
         }
         if (rule == 6) {
@@ -6020,7 +6046,7 @@ private static ParseTree parse_version(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "version",
             current,
-            nonterminal_first.get(84),
+            nonterminal_first.get(96),
             rules.get(6)
         ));
     }
@@ -6032,14 +6058,14 @@ private static ParseTree parse_wf_body_element(ParserContext ctx) throws SyntaxE
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[4][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(71, "wf_body_element"));
+        int rule = (current != null) ? table[49][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(116, "wf_body_element"));
         ctx.nonterminal = "wf_body_element";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "wf_body_element",
-                nonterminal_first.get(71),
-                nonterminal_rules.get(71)
+                nonterminal_first.get(116),
+                nonterminal_rules.get(116)
             ));
         }
         if (rule == 62) {
@@ -6109,7 +6135,7 @@ else if (rule == 69) {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "wf_body_element",
             current,
-            nonterminal_first.get(71),
+            nonterminal_first.get(116),
             rules.get(69)
         ));
     }
@@ -6121,14 +6147,14 @@ private static ParseTree parse_wf_meta(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[71][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(138, "wf_meta"));
+        int rule = (current != null) ? table[1][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(68, "wf_meta"));
         ctx.nonterminal = "wf_meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "wf_meta",
-                nonterminal_first.get(138),
-                nonterminal_rules.get(138)
+                nonterminal_first.get(68),
+                nonterminal_rules.get(68)
             ));
         }
         if (rule == 84) {
@@ -6146,7 +6172,7 @@ private static ParseTree parse_wf_meta(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "wf_meta",
             current,
-            nonterminal_first.get(138),
+            nonterminal_first.get(68),
             rules.get(84)
         ));
     }
@@ -6158,14 +6184,14 @@ private static ParseTree parse_wf_parameter_meta(ParserContext ctx) throws Synta
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[41][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(108, "wf_parameter_meta"));
+        int rule = (current != null) ? table[67][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(134, "wf_parameter_meta"));
         ctx.nonterminal = "wf_parameter_meta";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "wf_parameter_meta",
-                nonterminal_first.get(108),
-                nonterminal_rules.get(108)
+                nonterminal_first.get(134),
+                nonterminal_rules.get(134)
             ));
         }
         if (rule == 83) {
@@ -6183,7 +6209,7 @@ private static ParseTree parse_wf_parameter_meta(ParserContext ctx) throws Synta
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "wf_parameter_meta",
             current,
-            nonterminal_first.get(108),
+            nonterminal_first.get(134),
             rules.get(83)
         ));
     }
@@ -6195,14 +6221,14 @@ private static ParseTree parse_workflow(ParserContext ctx) throws SyntaxError {
         Terminal current = ctx.tokens.current();
         Terminal next;
         ParseTree subtree;
-        int rule = (current != null) ? table[27][current.getId()] : -1;
-        ParseTree tree = new ParseTree(new NonTerminal(94, "workflow"));
+        int rule = (current != null) ? table[2][current.getId()] : -1;
+        ParseTree tree = new ParseTree(new NonTerminal(69, "workflow"));
         ctx.nonterminal = "workflow";
         if (current == null) {
             throw new SyntaxError(ctx.error_formatter.unexpectedEof(
                 "workflow",
-                nonterminal_first.get(94),
-                nonterminal_rules.get(94)
+                nonterminal_first.get(69),
+                nonterminal_rules.get(69)
             ));
         }
         if (rule == 61) {
@@ -6227,7 +6253,7 @@ private static ParseTree parse_workflow(ParserContext ctx) throws SyntaxError {
         throw new SyntaxError(ctx.error_formatter.unexpectedSymbol(
             "workflow",
             current,
-            nonterminal_first.get(94),
+            nonterminal_first.get(69),
             rules.get(61)
         ));
     }
@@ -6357,9 +6383,6 @@ public void output(LexerContext ctx, TerminalIdentifier terminal, String source_
     default_action(ctx, terminal, source_string, line, col);
 }
     /* END USER CODE */
-    public List<Terminal> post_filter(List<Terminal> terminals) {
-        return terminals;
-    }
     public void destroy(Object context) {
         return;
     }
@@ -7867,8 +7890,7 @@ public List<Terminal> lex(String string, String resource) throws SyntaxError {
             }
         }
         this.destroy(context);
-        List<Terminal> filtered = post_filter(lctx.terminals);
-        return filtered;
+        return lctx.terminals;
     }
     /* Section: Main */
 }
diff --git a/wdl/transforms/cascades/src/main/resources/CHANGELOG.txt b/wdl/transforms/cascades/src/main/resources/CHANGELOG.txt
index b407769cba8..bb8a4687868 100644
--- a/wdl/transforms/cascades/src/main/resources/CHANGELOG.txt
+++ b/wdl/transforms/cascades/src/main/resources/CHANGELOG.txt
@@ -2,4 +2,15 @@
 
 Duplicated Cromwell `biscayne` into `cascades` to serve as new home for OpenWDL `development` version. Grammar synced from OpenWDL.
 Will become WDL 1.2 or 2.0.
-Some Terra users run `version development` WDLs, we don't officially support it, but shouldn't break it too badly if possible.
\ No newline at end of file
+Some Terra users run `version development` WDLs, we don't officially support it, but shouldn't break it too badly if possible.
+
+2024-02-28
+When changing the grammar file, generate a new parser by:
+- changing current working directory to cromwell/wdl/transforms/cascades
+- running: hermes generate src/main/resources/grammar.hgr \
+          --language=java \
+          --directory=src/main/java \
+          --name=wdl \
+          --java-package=wdl.cascades.parser \
+          --java-use-apache-commons --java-imports=org.apache.commons.lang3.StringEscapeUtils \
+          --header
diff --git a/wdl/transforms/cascades/src/main/resources/grammar.hgr b/wdl/transforms/cascades/src/main/resources/grammar.hgr
index 0b17648d925..b5b743b2b06 100644
--- a/wdl/transforms/cascades/src/main/resources/grammar.hgr
+++ b/wdl/transforms/cascades/src/main/resources/grammar.hgr
@@ -401,6 +401,7 @@ grammar {
       (*:unary) $e = :not $e -> LogicalNot(expression=$1)
       (-:unary) $e = :plus $e -> UnaryPlus(expression=$1)
       (-:unary) $e = :dash $e -> UnaryNegation(expression=$1)
+      (*:left) $e = :identifier <=> :lbrace list($object_kv, :comma) :rbrace -> StructLiteral(name=$0, map=$2)
       (*:left) $e = :identifier <=> :lparen list($e, :comma) :rparen -> FunctionCall(name=$0, params=$2)
       (*:left) $e = $e <=> :lsquare $e :rsquare -> ArrayOrMapLookup(lhs=$0, rhs=$2)
       (*:left) $e = $e <=> :dot :identifier -> MemberAccess(value=$0, member=$2)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
index d0faaea154e..1d752645bad 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumers.scala
@@ -105,4 +105,14 @@ object cascadesExpressionValueConsumers {
     ): Set[UnlinkedConsumedValueHook] =
       expressionValueConsumer.expressionConsumedValueHooks(a.param)(expressionValueConsumer)
   }
+
+  implicit val structLiteralExpressionValueConsumer: ExpressionValueConsumer[StructLiteral] =
+    new ExpressionValueConsumer[StructLiteral] {
+      override def expressionConsumedValueHooks(a: StructLiteral)(implicit
+        expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]
+      ): Set[UnlinkedConsumedValueHook] =
+        a.elements.values
+          .flatMap(element => expressionValueConsumer.expressionConsumedValueHooks(element)(expressionValueConsumer))
+          .toSet
+    }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
index 4916a7afd02..18a855e29b8 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/consumed/consumed.scala
@@ -24,6 +24,7 @@ package object consumed {
 
         case a: StringExpression => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: ObjectLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
+        case a: StructLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: PairLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: ArrayLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
         case a: MapLiteral => a.expressionConsumedValueHooks(expressionValueConsumer)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
index 2ce3d01b0de..220049bfca6 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluators.scala
@@ -1,5 +1,8 @@
 package wdl.transforms.cascades.linking.expression.files
 
+import cats.implicits.{catsSyntaxValidatedId, toTraverseOps}
+import common.validation.ErrorOr.ErrorOr
+import wdl.model.draft3.elements.ExpressionElement
 import wdl.model.draft3.elements.ExpressionElement.{
   AsMap,
   AsPairs,
@@ -10,16 +13,20 @@ import wdl.model.draft3.elements.ExpressionElement.{
   Quote,
   Sep,
   SQuote,
+  StructLiteral,
   SubPosix,
   Suffix,
   Unzip
 }
-import wdl.model.draft3.graph.expression.FileEvaluator
+import wdl.model.draft3.graph.expression.{FileEvaluator, ValueEvaluator}
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators
 import wdl.transforms.base.linking.expression.files.EngineFunctionEvaluators.{
   threeParameterFunctionPassthroughFileEvaluator,
   twoParameterFunctionPassthroughFileEvaluator
 }
+import wom.expression.IoFunctionSet
+import wom.types.{WomCompositeType, WomType}
+import wom.values.{WomFile, WomValue}
 
 object cascadesFileEvaluators {
 
@@ -45,4 +52,37 @@ object cascadesFileEvaluators {
   implicit val minFunctionEvaluator: FileEvaluator[Min] = twoParameterFunctionPassthroughFileEvaluator[Min]
   implicit val maxFunctionEvaluator: FileEvaluator[Max] = twoParameterFunctionPassthroughFileEvaluator[Max]
 
+  implicit val structLiteralEvaluator: FileEvaluator[StructLiteral] = new FileEvaluator[StructLiteral] {
+    override def predictFilesNeededToEvaluate(a: StructLiteral,
+                                              inputs: Map[String, WomValue],
+                                              ioFunctionSet: IoFunctionSet,
+                                              coerceTo: WomType
+    )(implicit
+      fileEvaluator: FileEvaluator[ExpressionElement],
+      valueEvaluator: ValueEvaluator[ExpressionElement]
+    ): ErrorOr[Set[WomFile]] = {
+      def filesInObjectField(fieldAndWomTypeTuple: (String, WomType)): ErrorOr[Set[WomFile]] = {
+        val (field, womType) = fieldAndWomTypeTuple
+        a.elements.get(field) match {
+          case Some(fieldElement) =>
+            fileEvaluator.predictFilesNeededToEvaluate(fieldElement, inputs, ioFunctionSet, womType)(fileEvaluator,
+                                                                                                     valueEvaluator
+            )
+          case None => s"Invalid assignment to struct. Required field $field was not specified.".invalidNel
+        }
+      }
+
+      coerceTo match {
+        case WomCompositeType(mapping, _) => mapping.toList.traverse(filesInObjectField).map(_.flatten.toSet)
+        case _ =>
+          a.elements.values.toList
+            .traverse(
+              fileEvaluator.evaluateFilesNeededToEvaluate(_, inputs, ioFunctionSet, coerceTo)(fileEvaluator,
+                                                                                              valueEvaluator
+              )
+            )
+            .map(_.toSet.flatten)
+      }
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
index f1935603458..c770483e4c7 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/files/files.scala
@@ -37,6 +37,8 @@ package object files {
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: ObjectLiteral =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
+        case a: StructLiteral =>
+          a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: MapLiteral =>
           a.predictFilesNeededToEvaluate(inputs, ioFunctionSet, coerceTo)(fileEvaluator, valueEvaluator)
         case a: ArrayLiteral =>
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
index ba7e9ae8dff..137b42128e2 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
@@ -159,4 +159,16 @@ object cascadesTypeEvaluators {
         case other => s"Cannot invoke 'unzip' on type '${other.stableName}'. Expected an array of pairs".invalidNel
       }
   }
+
+  implicit val structLiteralTypeEvaluator: TypeEvaluator[StructLiteral] = new TypeEvaluator[StructLiteral] {
+    override def evaluateType(a: StructLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
+      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      // This works fine, but is not yet a strong enough type check for the WDL 1.1 spec
+      // (i.e. users are able to instantiate struct literals with k/v pairs that aren't actually in the struct definition, without an error being thrown.)
+      // We want to add extra validation here, and return a WomCompositeType that matches the struct definition of everything is OK.
+      // Note that users are allowed to omit optional k/v pairs in their literal.
+      // This requires some extra work to be done in a subsequent PR.
+      WomObjectType.validNel
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
index 1a027b745ed..58e1fe888d7 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
@@ -29,6 +29,7 @@ package object types {
         case a: StringLiteral => a.evaluateType(linkedValues)(typeEvaluator)
         case a: StringExpression => a.evaluateType(linkedValues)(typeEvaluator)
         case a: ObjectLiteral => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: StructLiteral => a.evaluateType(linkedValues)(typeEvaluator)
         case a: MapLiteral => a.evaluateType(linkedValues)(typeEvaluator)
         case a: ArrayLiteral => a.evaluateType(linkedValues)(typeEvaluator)
         case a: PairLiteral => a.evaluateType(linkedValues)(typeEvaluator)
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
index ee106f2ef6a..5df336f062e 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluators.scala
@@ -18,7 +18,7 @@ import wdl.transforms.base.linking.expression.values.EngineFunctionEvaluators.{
 }
 import wom.expression.IoFunctionSet
 import wom.types._
-import wom.values.{WomArray, WomFloat, WomInteger, WomMap, WomOptionalValue, WomPair, WomString, WomValue}
+import wom.values.{WomArray, WomFloat, WomInteger, WomMap, WomObject, WomOptionalValue, WomPair, WomString, WomValue}
 import wom.types.coercion.defaults._
 
 object cascadesValueEvaluators {
@@ -345,4 +345,29 @@ object cascadesValueEvaluators {
           s"Invalid call of 'unzip' on parameter of type '${other.womType.stableName}' (expected Array[Pair[X, Y]])".invalidNel
       }
   }
+
+  implicit val structLiteralValueEvaluator: ValueEvaluator[StructLiteral] = new ValueEvaluator[StructLiteral] {
+    // This works fine, but is missing a feature from the WDL 1.1 spec: users are allowed to omit optional values from their struct literal.
+    // This requires some extra work to be done in a subsequent PR.
+    // Specifically, make the known struct definitions available to this function so we can populate k/v pairs with None appropriately.
+    override def evaluateValue(a: StructLiteral,
+                               inputs: Map[String, WomValue],
+                               ioFunctionSet: IoFunctionSet,
+                               forCommandInstantiationOptions: Option[ForCommandInstantiationOptions]
+    )(implicit expressionValueEvaluator: ValueEvaluator[ExpressionElement]): ErrorOr[EvaluatedValue[_ <: WomValue]] = {
+
+      val evaluated: ErrorOr[List[(String, EvaluatedValue[_])]] = a.elements.toList traverse {
+        case (key: String, value: ExpressionElement) =>
+          expressionValueEvaluator
+            .evaluateValue(value, inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+            .map(key -> _)
+      }
+
+      evaluated map { mapping =>
+        val value = mapping.map(entry => entry._1 -> entry._2.value).toMap
+        val sideEffectFiles = mapping.flatMap(entry => entry._2.sideEffectFiles)
+        EvaluatedValue(WomObject(value), sideEffectFiles)
+      }
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
index 3e92a27b2b8..59d20a381d2 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/values/values.scala
@@ -39,6 +39,8 @@ package object values {
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: ObjectLiteral =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
+        case a: StructLiteral =>
+          a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: MapLiteral =>
           a.evaluateValue(inputs, ioFunctionSet, forCommandInstantiationOptions)(expressionValueEvaluator)
         case a: ArrayLiteral =>
diff --git a/wdl/transforms/cascades/src/test/cases/struct_literal.wdl b/wdl/transforms/cascades/src/test/cases/struct_literal.wdl
new file mode 100644
index 00000000000..b32150d7bd0
--- /dev/null
+++ b/wdl/transforms/cascades/src/test/cases/struct_literal.wdl
@@ -0,0 +1,39 @@
+version development
+
+struct Plant {
+    String color
+    Boolean tasty
+}
+
+struct Animal {
+    String name
+    Boolean? isGood
+}
+
+task test_struct_parsing {
+    input {
+        Plant standard_plant_input
+        Animal standard_animal_input
+    }
+
+    runtime {
+        docker: "ubuntu:latest"
+    }
+
+    command {
+       echo "all dogs are good"
+    }
+
+    output {
+        Plant standard_plant_forwarded = standard_plant_input
+        Animal standard_animal_forwarded = standard_animal_input
+        Plant plant_output_literal = Plant{color: "red", tasty: true}
+    }
+}
+
+workflow struct_literal {
+    call test_struct_parsing {
+         input: standard_plant_input = Plant{color: "green", tasty: true},
+            standard_animal_input = Animal{name: "mittens", isGood: false}
+         }
+}
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
index ffc6d3bc131..971f5d54dc7 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/Ast2WdlomSpec.scala
@@ -1,7 +1,6 @@
 package wdl.transforms.cascades
 
 import java.util
-
 import common.Checked
 import common.assertion.ErrorOrAssertions._
 import common.transforms.CheckedAtoB
@@ -19,7 +18,7 @@ import wdl.transforms.cascades.ast2wdlom._
 import wdl.transforms.cascades.parsing.WdlCascadesSyntaxErrorFormatter
 import wom.callable.MetaValueElement.MetaValueElementInteger
 import wom.types.WomIntegerType
-import wom.values.WomInteger
+import wom.values.{WomBoolean, WomInteger}
 
 import scala.jdk.CollectionConverters._
 
@@ -121,4 +120,13 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val expr = fromString[ExpressionElement](str, parser.parse_e)
     expr shouldBeValid (Unzip(IdentifierLookup("some_array_of_pairs")))
   }
+
+  it should "parse a struct literal" in {
+    val str = """Dog{breed: "fluffy", isGood: true}"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    expr shouldBeValid (StructLiteral(
+      "Dog",
+      Map("breed" -> StringLiteral("fluffy"), "isGood" -> PrimitiveLiteralExpressionElement(WomBoolean(true)))
+    ))
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala
index 0a6a6f0e08e..8a8d691b8d7 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/ast2wdlom/WdlFileToWdlomSpec.scala
@@ -10,7 +10,7 @@ import wdl.model.draft3.elements._
 import wdl.transforms.cascades.ast2wdlom.WdlFileToWdlomSpec._
 import wom.SourceFileLocation
 import wom.types._
-import wom.values.WomInteger
+import wom.values.{WomBoolean, WomInteger}
 
 class WdlFileToWdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
@@ -367,6 +367,104 @@ object WdlFileToWdlomSpec {
           )
         ),
         tasks = Vector.empty
+      ),
+    "struct_literal" -> FileElement(
+      imports = Vector(),
+      structs = Vector(
+        StructElement("Plant",
+                      Vector(StructEntryElement("color", PrimitiveTypeElement(WomStringType)),
+                             StructEntryElement("tasty", PrimitiveTypeElement(WomBooleanType))
+                      )
+        ),
+        StructElement(
+          "Animal",
+          Vector(StructEntryElement("name", PrimitiveTypeElement(WomStringType)),
+                 StructEntryElement("isGood", OptionalTypeElement(PrimitiveTypeElement(WomBooleanType)))
+          )
+        )
+      ),
+      workflows = Vector(
+        WorkflowDefinitionElement(
+          "struct_literal",
+          None,
+          Set(
+            CallElement(
+              "test_struct_parsing",
+              None,
+              Vector(),
+              Some(
+                CallBodyElement(
+                  Vector(
+                    KvPair("standard_plant_input",
+                           StructLiteral("Plant",
+                                         Map("color" -> StringLiteral("green"),
+                                             "tasty" -> PrimitiveLiteralExpressionElement(WomBoolean(true))
+                                         )
+                           )
+                    ),
+                    KvPair("standard_animal_input",
+                           StructLiteral("Animal",
+                                         Map("name" -> StringLiteral("mittens"),
+                                             "isGood" -> PrimitiveLiteralExpressionElement(WomBoolean(false))
+                                         )
+                           )
+                    )
+                  )
+                )
+              ),
+              Some(SourceFileLocation(35))
+            )
+          ),
+          None,
+          None,
+          None,
+          Some(SourceFileLocation(34))
+        )
+      ),
+      tasks = Vector(
+        TaskDefinitionElement(
+          "test_struct_parsing",
+          Some(
+            InputsSectionElement(
+              Vector(
+                InputDeclarationElement(TypeAliasElement("Plant"), "standard_plant_input", None),
+                InputDeclarationElement(TypeAliasElement("Animal"), "standard_animal_input", None)
+              )
+            )
+          ),
+          Vector(),
+          Some(
+            OutputsSectionElement(
+              Vector(
+                OutputDeclarationElement(TypeAliasElement("Plant"),
+                                         "standard_plant_forwarded",
+                                         IdentifierLookup("standard_plant_input")
+                ),
+                OutputDeclarationElement(TypeAliasElement("Animal"),
+                                         "standard_animal_forwarded",
+                                         IdentifierLookup("standard_animal_input")
+                ),
+                OutputDeclarationElement(
+                  TypeAliasElement("Plant"),
+                  "plant_output_literal",
+                  StructLiteral("Plant",
+                                Map("color" -> StringLiteral("red"),
+                                    "tasty" -> PrimitiveLiteralExpressionElement(WomBoolean(true))
+                                )
+                  )
+                )
+              )
+            )
+          ),
+          CommandSectionElement(
+            List(CommandSectionLine(Vector(StringCommandPartElement("""echo "all dogs are good""""))))
+          ),
+          Some(RuntimeAttributesSectionElement(Vector(KvPair("docker", StringLiteral("ubuntu:latest"))))),
+          None,
+          None,
+          Some(SourceFileLocation(13))
+        )
       )
+    )
   )
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
index 9e47424d6c5..2d1f5c0b812 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/consumed/CascadesExpressionValueConsumersSpec.scala
@@ -111,4 +111,13 @@ class CascadesExpressionValueConsumersSpec extends AnyFlatSpec with CromwellTime
       e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("my_array_of_pairs")))
     }
   }
+
+  it should "discover an array variable lookup within a struct literal member access" in {
+    val str = """ (StructWithAnArray{myArrayMember: arrayToLookup}).myArray """
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.expressionConsumedValueHooks should be(Set(UnlinkedIdentifierHook("arrayToLookup")))
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
index afc73a56a32..60ca92d2fc8 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/files/CascadesFileEvaluatorSpec.scala
@@ -100,4 +100,15 @@ class CascadesFileEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       )
     }
   }
+
+  it should "discover the file which would be required to evaluate a struct literal" in {
+    val str = """ StructWithStringVec{myVec: read_lines("foo.txt")}"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.predictFilesNeededToEvaluate(Map.empty, NoIoFunctionSet, WomStringType) shouldBeValid Set(
+        WomSingleFile("foo.txt")
+      )
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
index d874fb7e6dd..0bef2d7a6ef 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
@@ -131,4 +131,14 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
       e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomAnyType), WomArrayType(WomAnyType))
     }
   }
+
+  it should "evaluate the type of a struct literal" in {
+    // NB: This is not yet strict enough type checking for the WDL 1.1 spec.
+    // In a subsequent branch, we will make this be a WomCompositeType that matches the struct definition.
+    val structLiteral = """ Animal{fur: "fuzzy", isGood: true} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty) shouldBeValid WomObjectType
+    }
+  }
 }
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
index 60215046d05..68027a868af 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/values/CascadesValueEvaluatorSpec.scala
@@ -12,7 +12,7 @@ import wdl.transforms.cascades.Ast2WdlomSpec.{fromString, parser}
 import wdl.transforms.cascades.ast2wdlom._
 import wom.expression.NoIoFunctionSet
 import wom.types.{WomAnyType, WomArrayType, WomIntegerType, WomMapType, WomOptionalType, WomStringType}
-import wom.values.{WomArray, WomInteger, WomMap, WomOptionalValue, WomPair, WomString}
+import wom.values.{WomArray, WomBoolean, WomInteger, WomMap, WomObject, WomOptionalValue, WomPair, WomString}
 
 class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
@@ -408,4 +408,14 @@ class CascadesValueEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         )
     )
   }
+
+  it should "evaluate a struct literal" in {
+    val literal = """ Animal{type: "dog", barks: false}"""
+    val expectedValue = WomObject(Map("type" -> WomString("dog"), "barks" -> WomBoolean(false)))
+    val expr = fromString[ExpressionElement](literal, parser.parse_e)
+
+    expr.shouldBeValidPF { case e =>
+      e.evaluateValue(Map.empty, NoIoFunctionSet, None) shouldBeValid EvaluatedValue(expectedValue, Seq.empty)
+    }
+  }
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
index d7f507b8343..2865d977f7d 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/ast2wdlom/Ast2WdlomSpec.scala
@@ -93,4 +93,12 @@ class Ast2WdlomSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     val expr = fromString[ExpressionElement](str, parser.parse_e)
     expr shouldBeInvalid "Failed to parse expression (reason 1 of 1): Unknown engine function: 'unzip'"
   }
+
+  it should "not parse a struct literal" in {
+    val str = """Dog{breed: "fluffy", isGood: true}"""
+    val expr = fromString[ExpressionElement](str, parser.parse_e)
+    // parser interprets "Dog" as an identifier, rather than as part of a struct literal,
+    // since struct literals aren't in WDL 1.0
+    expr shouldBeValid (IdentifierLookup("Dog"))
+  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
index acf3eac9f0b..49bb1c68df6 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/ast2wdlom/AstNodeToExpressionElement.scala
@@ -57,6 +57,12 @@ object AstNodeToExpressionElement {
           objectKvs <- a.getAttributeAsVector[KvPair]("map")
           asMap = objectKvs.map(kv => kv.key -> kv.value).toMap
         } yield ObjectLiteral(asMap)).toValidated
+      case a: GenericAst if a.getName == "StructLiteral" =>
+        (for {
+          objectKvs <- a.getAttributeAsVector[KvPair]("map")
+          asMap = objectKvs.map(kv => kv.key -> kv.value).toMap
+          structTypeName <- a.getAttributeAs[String]("name")
+        } yield StructLiteral(structTypeName, asMap)).toValidated
       case a: GenericAst if a.getName == "MapLiteral" =>
         final case class MapKvPair(key: ExpressionElement, value: ExpressionElement)
         def convertOnePair(astNode: GenericAstNode): ErrorOr[MapKvPair] = astNode match {
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
index d4a0b043b17..ab63d0be7c0 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wdl/WdlWriterImpl.scala
@@ -39,6 +39,12 @@ object WdlWriterImpl {
             pair._1 + ": " + expressionElementWriter.toWdlV1(pair._2)
           }
           .mkString(", ") + " }"
+      case a: StructLiteral =>
+        a.structTypeName + " { " + a.elements
+          .map { pair =>
+            pair._1 + ": " + expressionElementWriter.toWdlV1(pair._2)
+          }
+          .mkString(", ") + " }"
       case a: ArrayLiteral =>
         "[" + a.elements.map(expressionElementWriter.toWdlV1).mkString(", ") + "]"
       case a: MapLiteral =>

From d7def8dc37a937aecfed63bb49ce2392524527c2 Mon Sep 17 00:00:00 2001
From: Saloni Shah <salonipshah11@gmail.com>
Date: Tue, 2 Apr 2024 13:00:27 -0400
Subject: [PATCH 299/326] [WM-2500][WM-2502] Fetch Github token from ECM for
 importing and running private workflows (#7392)

---
 core/src/main/resources/reference.conf        |   6 +-
 project/Dependencies.scala                    |   2 +-
 .../services/auth/GithubAuthVending.scala     |  10 +-
 .../auth/GithubAuthVendingSupport.scala       |  12 +-
 .../services/auth/ecm/EcmConfig.scala         |  10 ++
 .../services/auth/ecm/EcmService.scala        |  58 +++++++++
 .../auth/impl/GithubAuthVendingActor.scala    |  45 +++++--
 .../auth/GithubAuthVendingSupportSpec.scala   |  17 ++-
 .../services/auth/ecm/EcmConfigSpec.scala     |  30 +++++
 .../services/auth/ecm/EcmServiceSpec.scala    |  57 +++++++++
 .../impl/GithubAuthVendingActorSpec.scala     | 112 ++++++++++++++++++
 11 files changed, 330 insertions(+), 29 deletions(-)
 create mode 100644 services/src/main/scala/cromwell/services/auth/ecm/EcmConfig.scala
 create mode 100644 services/src/main/scala/cromwell/services/auth/ecm/EcmService.scala
 create mode 100644 services/src/test/scala/cromwell/services/auth/ecm/EcmConfigSpec.scala
 create mode 100644 services/src/test/scala/cromwell/services/auth/ecm/EcmServiceSpec.scala
 create mode 100644 services/src/test/scala/cromwell/services/auth/impl/GithubAuthVendingActorSpec.scala

diff --git a/core/src/main/resources/reference.conf b/core/src/main/resources/reference.conf
index 672d82c8c80..25fd0e6ac87 100644
--- a/core/src/main/resources/reference.conf
+++ b/core/src/main/resources/reference.conf
@@ -578,10 +578,8 @@ services {
     config {
       enabled = false
       auth.azure = false
-      # Notes:
-      #   - don't include the 'Bearer' before the token
-      #   - this config value should be removed when support for fetching tokens from ECM has been added to Cromwell
-      access-token = "dummy-token"
+      # Set this to the service that Cromwell should retrieve Github access token associated with user's token.
+      # ecm.base-url = ""
     }
   }
 }
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 30396519016..8a12d0e0cc2 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -593,7 +593,7 @@ object Dependencies {
   val servicesDependencies: List[ModuleID] = List(
     "com.google.api" % "gax-grpc" % googleGaxGrpcV,
     "org.apache.commons" % "commons-csv" % commonsCsvV,
-  ) ++ testDatabaseDependencies
+  ) ++ testDatabaseDependencies ++ akkaHttpDependencies
 
   val serverDependencies: List[ModuleID] = slf4jBindingDependencies
 
diff --git a/services/src/main/scala/cromwell/services/auth/GithubAuthVending.scala b/services/src/main/scala/cromwell/services/auth/GithubAuthVending.scala
index c74df8c947f..1d82125c1e1 100644
--- a/services/src/main/scala/cromwell/services/auth/GithubAuthVending.scala
+++ b/services/src/main/scala/cromwell/services/auth/GithubAuthVending.scala
@@ -7,11 +7,15 @@ object GithubAuthVending {
     override def serviceName: String = "GithubAuthVending"
   }
 
-  case class GithubAuthRequest(terraToken: String) extends GithubAuthVendingMessage
+  // types of tokens
+  case class TerraToken(value: String)
+  case class GithubToken(value: String)
+
+  case class GithubAuthRequest(terraToken: TerraToken) extends GithubAuthVendingMessage
 
   sealed trait GithubAuthVendingResponse extends GithubAuthVendingMessage
-  case class GithubAuthTokenResponse(accessToken: String) extends GithubAuthVendingResponse
+  case class GithubAuthTokenResponse(githubAccessToken: GithubToken) extends GithubAuthVendingResponse
   case object NoGithubAuthResponse extends GithubAuthVendingResponse
-  case class GithubAuthVendingFailure(error: Exception) extends GithubAuthVendingResponse
+  case class GithubAuthVendingFailure(errorMsg: String) extends GithubAuthVendingResponse
 
 }
diff --git a/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala b/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala
index 63fc9404e07..4697a741909 100644
--- a/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala
+++ b/services/src/main/scala/cromwell/services/auth/GithubAuthVendingSupport.scala
@@ -15,10 +15,11 @@ import cromwell.services.auth.GithubAuthVending.{
   GithubAuthTokenResponse,
   GithubAuthVendingFailure,
   GithubAuthVendingResponse,
-  NoGithubAuthResponse
+  NoGithubAuthResponse,
+  TerraToken
 }
-
 import net.ceedubs.ficus.Ficus._
+
 import scala.concurrent.{ExecutionContext, Future}
 
 trait GithubAuthVendingSupport extends AskSupport with StrictLogging {
@@ -30,7 +31,7 @@ trait GithubAuthVendingSupport extends AskSupport with StrictLogging {
   def importAuthProvider(token: String)(implicit timeout: Timeout): ImportAuthProvider = new GithubImportAuthProvider {
     override def authHeader(): Future[Map[String, String]] =
       serviceRegistryActor
-        .ask(GithubAuthRequest(token))
+        .ask(GithubAuthRequest(TerraToken(token)))
         .mapTo[GithubAuthVendingResponse]
         .recoverWith {
           case e: AskTimeoutException =>
@@ -41,10 +42,11 @@ trait GithubAuthVendingSupport extends AskSupport with StrictLogging {
             Future.failed(new Exception("Failed to resolve github auth token", e))
         }
         .flatMap {
-          case GithubAuthTokenResponse(token) => Future.successful(Map("Authorization" -> s"Bearer ${token}"))
+          case GithubAuthTokenResponse(githubToken) =>
+            Future.successful(Map("Authorization" -> s"Bearer ${githubToken.value}"))
           case NoGithubAuthResponse => Future.successful(Map.empty)
           case GithubAuthVendingFailure(error) =>
-            Future.failed(new Exception("Failed to resolve github auth token", error))
+            Future.failed(new Exception(s"Failed to resolve GitHub auth token. Error: $error"))
         }
   }
 
diff --git a/services/src/main/scala/cromwell/services/auth/ecm/EcmConfig.scala b/services/src/main/scala/cromwell/services/auth/ecm/EcmConfig.scala
new file mode 100644
index 00000000000..c1f8900d22d
--- /dev/null
+++ b/services/src/main/scala/cromwell/services/auth/ecm/EcmConfig.scala
@@ -0,0 +1,10 @@
+package cromwell.services.auth.ecm
+
+import com.typesafe.config.Config
+import net.ceedubs.ficus.Ficus._
+
+final case class EcmConfig(baseUrl: Option[String])
+
+object EcmConfig {
+  def apply(config: Config): EcmConfig = EcmConfig(config.as[Option[String]]("ecm.base-url"))
+}
diff --git a/services/src/main/scala/cromwell/services/auth/ecm/EcmService.scala b/services/src/main/scala/cromwell/services/auth/ecm/EcmService.scala
new file mode 100644
index 00000000000..b65181d5bda
--- /dev/null
+++ b/services/src/main/scala/cromwell/services/auth/ecm/EcmService.scala
@@ -0,0 +1,58 @@
+package cromwell.services.auth.ecm
+
+import akka.actor.ActorSystem
+import akka.http.scaladsl.Http
+import akka.http.scaladsl.model._
+import akka.http.scaladsl.model.headers.RawHeader
+import akka.util.ByteString
+import cromwell.services.auth.GithubAuthVending.{GithubToken, TerraToken}
+import spray.json._
+
+import scala.concurrent.{ExecutionContext, Future}
+import scala.util.{Success, Try}
+
+class EcmService(baseEcmUrl: String) {
+  private val getGithubAccessTokenApiPath = "api/oauth/v1/github/access-token"
+
+  /*
+     ECM does generally return standard JSON error response, but for 401 status code it seems some other layer in
+     between (like the apache proxies, etc) returns HTML pages. This helper method returns custom error message for 401
+     status code as it contains HTML tags. For all other status code, the response format is generally of ErrorReport
+     schema and this method tries to extract the actual message from the JSON object and return it. In case it fails
+     to parse JSON, it returns the original error response body.
+     ErrorReport schema: {"message":"<actual_error_msg>", "statusCode":<code>}
+   */
+  def extractErrorMessage(errorCode: StatusCode, responseBodyAsStr: String): String =
+    errorCode match {
+      case StatusCodes.Unauthorized => "Invalid or missing authentication credentials."
+      case _ =>
+        Try(responseBodyAsStr.parseJson) match {
+          case Success(JsObject(fields)) =>
+            fields.get("message").map(_.toString().replaceAll("\"", "")).getOrElse(responseBodyAsStr)
+          case _ => responseBodyAsStr
+        }
+    }
+
+  def getGithubAccessToken(
+    userToken: TerraToken
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[GithubToken] = {
+
+    def responseEntityToFutureStr(responseEntity: ResponseEntity): Future[String] =
+      responseEntity.dataBytes.runFold(ByteString(""))(_ ++ _).map(_.utf8String)
+
+    val headers: HttpHeader = RawHeader("Authorization", s"Bearer ${userToken.value}")
+    val httpRequest =
+      HttpRequest(method = HttpMethods.GET, uri = s"$baseEcmUrl/$getGithubAccessTokenApiPath").withHeaders(headers)
+
+    Http()
+      .singleRequest(httpRequest)
+      .flatMap((response: HttpResponse) =>
+        if (response.status.isFailure()) {
+          responseEntityToFutureStr(response.entity) flatMap { errorBody =>
+            val errorMessage = extractErrorMessage(response.status, errorBody)
+            Future.failed(new RuntimeException(s"HTTP ${response.status.value}. $errorMessage"))
+          }
+        } else responseEntityToFutureStr(response.entity).map(GithubToken)
+      )
+  }
+}
diff --git a/services/src/main/scala/cromwell/services/auth/impl/GithubAuthVendingActor.scala b/services/src/main/scala/cromwell/services/auth/impl/GithubAuthVendingActor.scala
index e0f4c9756a0..2cfe51f344b 100644
--- a/services/src/main/scala/cromwell/services/auth/impl/GithubAuthVendingActor.scala
+++ b/services/src/main/scala/cromwell/services/auth/impl/GithubAuthVendingActor.scala
@@ -1,26 +1,57 @@
 package cromwell.services.auth.impl
 
-import akka.actor.{Actor, ActorRef, Props}
+import akka.actor.{Actor, ActorRef, ActorSystem, Props}
 import com.typesafe.config.Config
 import com.typesafe.scalalogging.LazyLogging
+import common.util.StringUtil.EnhancedToStringable
 import cromwell.core.Dispatcher.ServiceDispatcher
-import cromwell.services.auth.GithubAuthVending.{GithubAuthRequest, GithubAuthTokenResponse, NoGithubAuthResponse}
+import cromwell.services.auth.GithubAuthVending.{
+  GithubAuthRequest,
+  GithubAuthTokenResponse,
+  GithubAuthVendingFailure,
+  NoGithubAuthResponse
+}
+import cromwell.services.auth.ecm.{EcmConfig, EcmService}
 import cromwell.util.GracefulShutdownHelper.ShutdownCommand
 
+import scala.concurrent.ExecutionContext
+import scala.util.{Failure, Success}
+
 class GithubAuthVendingActor(serviceConfig: Config, globalConfig: Config, serviceRegistryActor: ActorRef)
     extends Actor
     with LazyLogging {
 
-  lazy val enabled = serviceConfig.getBoolean("enabled")
+  implicit val system: ActorSystem = context.system
+  implicit val ec: ExecutionContext = context.dispatcher
+
+  lazy val enabled: Boolean = serviceConfig.getBoolean("enabled")
+
+  lazy val ecmConfigOpt: EcmConfig = EcmConfig(serviceConfig)
+  lazy val ecmServiceOpt: Option[EcmService] = ecmConfigOpt.baseUrl.map(url => new EcmService(url))
 
   override def receive: Receive = {
-    case GithubAuthRequest(_) if enabled =>
-      sender() ! GithubAuthTokenResponse(serviceConfig.getString("access-token"))
+    case GithubAuthRequest(terraToken) if enabled =>
+      val respondTo = sender()
+      ecmServiceOpt match {
+        case Some(ecmService) =>
+          ecmService.getGithubAccessToken(terraToken) onComplete {
+            case Success(githubToken) => respondTo ! GithubAuthTokenResponse(githubToken)
+            case Failure(e) => respondTo ! GithubAuthVendingFailure(e.getMessage)
+          }
+        case None =>
+          respondTo ! GithubAuthVendingFailure(
+            "Invalid configuration for service 'GithubAuthVending': missing 'ecm.base-url' value."
+          )
+      }
+    case GithubAuthRequest(_) => sender() ! NoGithubAuthResponse
     // This service currently doesn't do any work on shutdown but the service registry pattern requires it
     // (see https://github.com/broadinstitute/cromwell/issues/2575)
     case ShutdownCommand => context stop self
-    case _ =>
-      sender() ! NoGithubAuthResponse
+    case other =>
+      logger.error(
+        s"Programmer Error: Unexpected message ${other.toPrettyElidedString(1000)} received by ${this.self.path.name}."
+      )
+      sender() ! GithubAuthVendingFailure(s"Received unexpected message ${other.toPrettyElidedString(1000)}.")
   }
 }
 
diff --git a/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala b/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala
index 9a20851ebdd..5e62d001e60 100644
--- a/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala
+++ b/services/src/test/scala/cromwell/services/auth/GithubAuthVendingSupportSpec.scala
@@ -8,7 +8,7 @@ import com.typesafe.config.ConfigFactory
 import cromwell.core.TestKitSuite
 import cromwell.languages.util.ImportResolver.GithubImportAuthProvider
 import cromwell.services.ServiceRegistryActor.ServiceRegistryFailure
-import cromwell.services.auth.GithubAuthVending.GithubAuthRequest
+import cromwell.services.auth.GithubAuthVending.{GithubAuthRequest, GithubToken, TerraToken}
 import cromwell.services.auth.GithubAuthVendingSupportSpec.TestGithubAuthVendingSupport
 import org.scalatest.concurrent.Eventually
 import org.scalatest.flatspec.AnyFlatSpecLike
@@ -42,8 +42,8 @@ class GithubAuthVendingSupportSpec extends TestKitSuite with AnyFlatSpecLike wit
     val provider = testSupport.importAuthProvider("user-token")
     val authHeader: Future[Map[String, String]] = provider.authHeader()
 
-    serviceRegistryActor.expectMsg(GithubAuthRequest("user-token"))
-    serviceRegistryActor.reply(GithubAuthVending.GithubAuthTokenResponse("github-token"))
+    serviceRegistryActor.expectMsg(GithubAuthRequest(TerraToken("user-token")))
+    serviceRegistryActor.reply(GithubAuthVending.GithubAuthTokenResponse(GithubToken("github-token")))
 
     Await.result(authHeader, 10.seconds) should be(Map("Authorization" -> "Bearer github-token"))
   }
@@ -54,7 +54,7 @@ class GithubAuthVendingSupportSpec extends TestKitSuite with AnyFlatSpecLike wit
     val provider = testSupport.importAuthProvider("user-token")
     val authHeader: Future[Map[String, String]] = provider.authHeader()
 
-    serviceRegistryActor.expectMsg(GithubAuthRequest("user-token"))
+    serviceRegistryActor.expectMsg(GithubAuthRequest(TerraToken("user-token")))
     serviceRegistryActor.reply(GithubAuthVending.NoGithubAuthResponse)
 
     Await.result(authHeader, 10.seconds) should be(Map.empty)
@@ -66,13 +66,12 @@ class GithubAuthVendingSupportSpec extends TestKitSuite with AnyFlatSpecLike wit
     val provider = testSupport.importAuthProvider("user-token")
     val authHeader: Future[Map[String, String]] = provider.authHeader()
 
-    serviceRegistryActor.expectMsg(GithubAuthRequest("user-token"))
-    serviceRegistryActor.reply(GithubAuthVending.GithubAuthVendingFailure(new Exception("BOOM")))
+    serviceRegistryActor.expectMsg(GithubAuthRequest(TerraToken("user-token")))
+    serviceRegistryActor.reply(GithubAuthVending.GithubAuthVendingFailure("BOOM"))
 
     eventually {
       authHeader.isCompleted should be(true)
-      authHeader.value.get.failed.get.getMessage should be("Failed to resolve github auth token")
-      authHeader.value.get.failed.get.getCause.getMessage should be("BOOM")
+      authHeader.value.get.failed.get.getMessage should be("Failed to resolve GitHub auth token. Error: BOOM")
     }
   }
 
@@ -95,7 +94,7 @@ class GithubAuthVendingSupportSpec extends TestKitSuite with AnyFlatSpecLike wit
     val provider = testSupport.importAuthProvider("user-token")
     val authHeader: Future[Map[String, String]] = provider.authHeader()
 
-    serviceRegistryActor.expectMsg(GithubAuthRequest("user-token"))
+    serviceRegistryActor.expectMsg(GithubAuthRequest(TerraToken("user-token")))
     serviceRegistryActor.reply(ServiceRegistryFailure("GithubAuthVending"))
 
     eventually {
diff --git a/services/src/test/scala/cromwell/services/auth/ecm/EcmConfigSpec.scala b/services/src/test/scala/cromwell/services/auth/ecm/EcmConfigSpec.scala
new file mode 100644
index 00000000000..a666eac9af1
--- /dev/null
+++ b/services/src/test/scala/cromwell/services/auth/ecm/EcmConfigSpec.scala
@@ -0,0 +1,30 @@
+package cromwell.services.auth.ecm
+
+import com.typesafe.config.ConfigFactory
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+class EcmConfigSpec extends AnyFlatSpec with Matchers {
+
+  it should "parse ECM base url when present" in {
+    val config = ConfigFactory.parseString(s"""
+                                              |enabled = true
+                                              |auth.azure = true
+                                              |ecm.base-url = "https://mock-ecm-url.org"
+      """.stripMargin)
+
+    val actualEcmConfig = EcmConfig(config)
+
+    actualEcmConfig.baseUrl shouldBe defined
+    actualEcmConfig.baseUrl.get shouldBe "https://mock-ecm-url.org"
+  }
+
+  it should "return None when ECM base url is absent" in {
+    val config = ConfigFactory.parseString(s"""
+                                              |enabled = true
+                                              |auth.azure = true
+      """.stripMargin)
+
+    EcmConfig(config).baseUrl shouldBe None
+  }
+}
diff --git a/services/src/test/scala/cromwell/services/auth/ecm/EcmServiceSpec.scala b/services/src/test/scala/cromwell/services/auth/ecm/EcmServiceSpec.scala
new file mode 100644
index 00000000000..b1a2442cad9
--- /dev/null
+++ b/services/src/test/scala/cromwell/services/auth/ecm/EcmServiceSpec.scala
@@ -0,0 +1,57 @@
+package cromwell.services.auth.ecm
+
+import akka.http.scaladsl.model.StatusCodes
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.prop.TableDrivenPropertyChecks
+
+class EcmServiceSpec extends AnyFlatSpec with Matchers with TableDrivenPropertyChecks {
+
+  private val ecmService = new EcmService("https://mock-ecm-url.org")
+
+  private val ecm400ErrorMsg = "No enum constant bio.terra.externalcreds.generated.model.Provider.MyOwnProvider"
+  private val ecm404ErrorMsg =
+    "No linked account found for user ID: 123 and provider: github. Please go to the Terra Profile page External Identities tab to link your account for this provider"
+
+  private val testCases = Table(
+    ("test name", "response status code", "response body string", "expected error message"),
+    ("return custom 401 error when status code is 401",
+     StatusCodes.Unauthorized,
+     "<h2>could be anything</h2>",
+     "Invalid or missing authentication credentials."
+    ),
+    ("extract message from valid ErrorReport JSON if status code is 400",
+     StatusCodes.BadRequest,
+     s"""{ "message" : "$ecm400ErrorMsg", "statusCode" : 400}""",
+     ecm400ErrorMsg
+    ),
+    ("extract message from valid ErrorReport JSON if status code is 404",
+     StatusCodes.NotFound,
+     s"""{ "message" : "$ecm404ErrorMsg", "statusCode" : 404}""",
+     ecm404ErrorMsg
+    ),
+    ("extract message from valid ErrorReport JSON if status code is 500",
+     StatusCodes.InternalServerError,
+     """{ "message" : "Internal error", "statusCode" : 500}""",
+     "Internal error"
+    ),
+    ("return response error body if it fails to parse JSON",
+     StatusCodes.InternalServerError,
+     "Response error - not a JSON",
+     "Response error - not a JSON"
+    ),
+    ("return response error body if JSON doesn't contain 'message' key",
+     StatusCodes.BadRequest,
+     """{"non-message-key" : "error message"}""",
+     """{"non-message-key" : "error message"}"""
+    )
+  )
+
+  behavior of "extractErrorMessage in EcmService"
+
+  forAll(testCases) { (testName, statusCode, responseBodyAsStr, expectedErrorMsg) =>
+    it should testName in {
+      assert(ecmService.extractErrorMessage(statusCode, responseBodyAsStr) == expectedErrorMsg)
+    }
+  }
+}
diff --git a/services/src/test/scala/cromwell/services/auth/impl/GithubAuthVendingActorSpec.scala b/services/src/test/scala/cromwell/services/auth/impl/GithubAuthVendingActorSpec.scala
new file mode 100644
index 00000000000..f45c701fa22
--- /dev/null
+++ b/services/src/test/scala/cromwell/services/auth/impl/GithubAuthVendingActorSpec.scala
@@ -0,0 +1,112 @@
+package cromwell.services.auth.impl
+
+import akka.actor.{ActorRef, ActorSystem, Props}
+import akka.testkit.TestProbe
+import com.typesafe.config.{Config, ConfigFactory}
+import cromwell.core.TestKitSuite
+import cromwell.services.auth.GithubAuthVending.{
+  GithubAuthRequest,
+  GithubAuthTokenResponse,
+  GithubAuthVendingFailure,
+  GithubToken,
+  NoGithubAuthResponse,
+  TerraToken
+}
+import cromwell.services.auth.ecm.EcmService
+import cromwell.services.auth.impl.GithubAuthVendingActorSpec.TestGithubAuthVendingActor
+import org.scalatest.concurrent.Eventually
+import org.scalatest.flatspec.AnyFlatSpecLike
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.prop.TableDrivenPropertyChecks
+
+import scala.concurrent.{ExecutionContext, Future}
+
+class GithubAuthVendingActorSpec
+    extends TestKitSuite
+    with AnyFlatSpecLike
+    with Matchers
+    with Eventually
+    with TableDrivenPropertyChecks {
+
+  final private val validUserToken = "valid_user_token"
+  final private val githubAuthEnabledServiceConfig =
+    ConfigFactory.parseString(s"""
+                                 |enabled = true
+                                 |auth.azure = true
+                                 |ecm.base-url = "https://mock-ecm-url.org"
+        """.stripMargin)
+
+  private def githubAuthConfigWithoutEcmUrl(flag: Boolean): Config =
+    ConfigFactory.parseString(s"""
+                                 |enabled = $flag
+                                 |auth.azure = $flag
+        """.stripMargin)
+
+  private val testCases = Table(
+    ("test name", "service config", "use TestEcmService class", "terra token", "response"),
+    ("return NoGithubAuthResponse if GithubAuthVending is disabled",
+     githubAuthConfigWithoutEcmUrl(false),
+     false,
+     validUserToken,
+     NoGithubAuthResponse
+    ),
+    ("return invalid configuration error if no ECM base url is found",
+     githubAuthConfigWithoutEcmUrl(true),
+     false,
+     validUserToken,
+     GithubAuthVendingFailure("Invalid configuration for service 'GithubAuthVending': missing 'ecm.base-url' value.")
+    ),
+    ("return Github token if found",
+     githubAuthEnabledServiceConfig,
+     true,
+     validUserToken,
+     GithubAuthTokenResponse(GithubToken("gha_token"))
+    ),
+    ("return failure message if ECM service returns non-successful response",
+     githubAuthEnabledServiceConfig,
+     true,
+     "invalid_user_token",
+     GithubAuthVendingFailure("Exception thrown for testing purposes")
+    )
+  )
+
+  behavior of "GithubAuthVendingActor"
+
+  forAll(testCases) { (testName, serviceConfig, useTestEcmService, userTerraToken, expectedResponseMsg) =>
+    it should testName in {
+      val serviceRegistryActor = TestProbe()
+      val actor = system.actorOf(
+        Props(new TestGithubAuthVendingActor(serviceConfig, serviceRegistryActor.ref, useTestEcmService))
+      )
+
+      serviceRegistryActor.send(actor, GithubAuthRequest(TerraToken(userTerraToken)))
+      eventually {
+        serviceRegistryActor.expectMsg(expectedResponseMsg)
+      }
+    }
+  }
+}
+
+class TestEcmService(baseUrl: String) extends EcmService(baseUrl) {
+
+  override def getGithubAccessToken(
+    userToken: TerraToken
+  )(implicit actorSystem: ActorSystem, ec: ExecutionContext): Future[GithubToken] =
+    userToken.value match {
+      case "valid_user_token" => Future.successful(GithubToken("gha_token"))
+      case _ => Future.failed(new RuntimeException("Exception thrown for testing purposes"))
+    }
+}
+
+object GithubAuthVendingActorSpec {
+
+  class TestGithubAuthVendingActor(serviceConfig: Config,
+                                   serviceRegistryActor: ActorRef,
+                                   useTestEcmServiceClass: Boolean
+  ) extends GithubAuthVendingActor(serviceConfig, ConfigFactory.parseString(""), serviceRegistryActor) {
+
+    override lazy val ecmServiceOpt: Option[EcmService] =
+      if (useTestEcmServiceClass) Some(new TestEcmService("https://mock-ecm-url.org"))
+      else ecmConfigOpt.baseUrl.map(url => new EcmService(url))
+  }
+}

From 7a03cdace04c2d727aa9d4f6799aa1ce21a23cd1 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Wed, 3 Apr 2024 08:21:06 -0400
Subject: [PATCH 300/326] WX-1542 Fix workflow cancellation (#7398)

---
 .../impl/tes/TesAsyncBackendJobExecutionActor.scala        | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 255f9c811dc..44b24e89980 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -368,9 +368,10 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
 
     val returnCodeTmp = jobPaths.returnCode.plusExt("kill")
     returnCodeTmp.write(s"$SIGTERM\n")
-    try
-      returnCodeTmp.moveTo(jobPaths.returnCode)
-    catch {
+    try {
+      returnCodeTmp.copyTo(jobPaths.returnCode) // Will throw if file exists
+      returnCodeTmp.delete(true)
+    } catch {
       case _: FileAlreadyExistsException =>
         // If the process has already completed, there will be an existing rc file.
         returnCodeTmp.delete(true)

From b8b81ab54e5d85097a0e4731d7336758645aa2aa Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Fri, 5 Apr 2024 13:01:58 -0400
Subject: [PATCH 301/326] WX-1550 Don't pointlessly continue running
 integration tests (#7400)

---
 .github/workflows/integration_tests.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 61ed3c5af41..aca4a2924c0 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -16,6 +16,12 @@ on:
 permissions:
   contents: read
 
+concurrency:
+  # Don't run this workflow concurrently on the same branch
+  group: ${{ github.workflow }}-${{ github.ref }}
+  # For PRs, don't wait for completion of existing runs, cancel them instead
+  cancel-in-progress: ${{ github.ref != 'develop' }}
+
 jobs:
   integration-tests:
     strategy:

From cb7241cb3507a955f8636d5d0f48d449b5e9d42f Mon Sep 17 00:00:00 2001
From: Alexis Hernandez <github@alexitc.com>
Date: Fri, 5 Apr 2024 22:06:04 +0200
Subject: [PATCH 302/326] WX-1557 Fix default values from Configuring.md and
 Scaling.md (#7393)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 docs/Configuring.md | 8 ++++----
 docs/Scaling.md     | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/Configuring.md b/docs/Configuring.md
index 076295d115c..5dc2a43d2ca 100644
--- a/docs/Configuring.md
+++ b/docs/Configuring.md
@@ -134,18 +134,18 @@ system.max-concurrent-workflows = 5000
 
 **New Workflow Poll Rate**
 
-Cromwell will look for new workflows to start on a regular interval, configured as a number of seconds. You can change the polling rate from the default `2` seconds by editing the value:
+Cromwell will look for new workflows to start on a regular interval, configured as a number of seconds. You can change the polling rate from the default `20` seconds by editing the value:
 
 ```hocon
-system.new-workflow-poll-rate = 2
+system.new-workflow-poll-rate = 20
 ```
 
 **Max Workflow Launch Count**
 
-On every poll, Cromwell will take at limited number of new submissions, provided there are new workflows to launch and the `system.max-concurrent-workflows` number has not been reached. While the default is to launch up to `50` workflows, you can override this by setting:
+On every poll, Cromwell will take at limited number of new submissions, provided there are new workflows to launch and the `system.max-concurrent-workflows` number has not been reached. While the default is to launch up to `1` workflow, you can override this by setting:
 
 ```hocon
-system.max-workflow-launch-count = 50
+system.max-workflow-launch-count = 1
 ```
 
 ***Abort configuration***
diff --git a/docs/Scaling.md b/docs/Scaling.md
index beca560212e..6ee7524446c 100644
--- a/docs/Scaling.md
+++ b/docs/Scaling.md
@@ -38,7 +38,7 @@ system {
 
   # Cromwell will launch up to N submitted workflows at a time, regardless of how many open workflow slots exist
   # Set this to 0 for a non-runner.
-  max-workflow-launch-count = 50
+  max-workflow-launch-count = 1
 
   # The maximum number of workflows to run concurrently.
   # Set this to 0 for a non-runner.

From 69d825475e08b4e82c715a170fdacef0b8b6e2bb Mon Sep 17 00:00:00 2001
From: dkj <david.jackson@sanger.ac.uk>
Date: Fri, 5 Apr 2024 21:06:53 +0100
Subject: [PATCH 303/326] WX-1557 Fix actor-factory in Batch101.md (#7377)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 docs/tutorials/Batch101.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/tutorials/Batch101.md b/docs/tutorials/Batch101.md
index 4c31d910ab1..d62a4e9de1a 100644
--- a/docs/tutorials/Batch101.md
+++ b/docs/tutorials/Batch101.md
@@ -122,7 +122,7 @@ backend {
 
   providers {
     batch {
-      actor-factory = "cromwell.backend.google.pipelines.batch.GcpBatchBackendLifecycleActorFactory"
+      actor-factory = "cromwell.backend.google.batch.GcpBatchBackendLifecycleActorFactory"
       config {
         # Google project
         project = "my-cromwell-workflows"

From 6738975f9b47d2f140b937ca13beb513862e9c3a Mon Sep 17 00:00:00 2001
From: Alexis Hernandez <github@alexitc.com>
Date: Fri, 5 Apr 2024 23:44:10 +0200
Subject: [PATCH 304/326] WX-1557 Add more tests to the GCP Batch backend
 (#7394)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 ...tchAsyncBackendJobExecutionActorSpec.scala | 53 +++++++++++++++++++
 .../models/GcpBatchConfigurationSpec.scala    | 15 ++++--
 .../GcpBatchRuntimeAttributesSpec.scala       | 46 +++++++++-------
 3 files changed, 90 insertions(+), 24 deletions(-)

diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
index f8d6e071b31..676a4d025e6 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
@@ -6,8 +6,11 @@ import _root_.wdl.draft2.model._
 import akka.actor.{ActorRef, Props}
 import akka.testkit.{ImplicitSender, TestActorRef, TestDuration, TestProbe}
 import cats.data.NonEmptyList
+import cloud.nio.impl.drs.DrsCloudNioFileProvider.DrsReadInterpreter
+import cloud.nio.impl.drs.{DrsCloudNioFileSystemProvider, GoogleOauthDrsCredentials}
 import com.google.cloud.NoCredentials
 import com.google.cloud.batch.v1.{Job, JobName}
+import com.typesafe.config.{Config, ConfigFactory}
 import common.collections.EnhancedCollections._
 import cromwell.backend.BackendJobExecutionActor.BackendJobExecutionResponse
 import cromwell.backend._
@@ -56,6 +59,7 @@ import scala.concurrent.duration._
 import scala.concurrent.{Await, ExecutionContext, Future, Promise}
 import scala.language.postfixOps
 import common.mock.MockSugar
+import cromwell.filesystems.drs.DrsPathBuilder
 import org.mockito.Mockito._
 
 class GcpBatchAsyncBackendJobExecutionActorSpec
@@ -396,6 +400,55 @@ class GcpBatchAsyncBackendJobExecutionActorSpec
     GcpBatchAsyncBackendJobExecutionActor.groupParametersByGcsBucket(inputs) shouldEqual expected
   }
 
+  it should "generate a CSV manifest for DRS inputs, ignoring non-DRS inputs" in {
+    def makeDrsPathBuilder: DrsPathBuilder = {
+      val drsResolverConfig: Config = ConfigFactory.parseString(
+        """resolver {
+          |   url = "http://drshub-url"
+          |}
+          |""".stripMargin
+      )
+
+      val fakeCredentials = NoCredentials.getInstance
+
+      val drsReadInterpreter: DrsReadInterpreter = (_, _) =>
+        throw new UnsupportedOperationException(
+          "PipelinesApiAsyncBackendJobExecutionActorSpec doesn't need to use drs read interpreter."
+        )
+
+      DrsPathBuilder(
+        new DrsCloudNioFileSystemProvider(drsResolverConfig,
+                                          GoogleOauthDrsCredentials(fakeCredentials, 1.minutes),
+                                          drsReadInterpreter
+        ),
+        None
+      )
+    }
+
+    val mount = GcpBatchWorkingDisk(DiskType.LOCAL, 1)
+
+    def makeDrsInput(name: String, drsUri: String, containerPath: String): GcpBatchFileInput = {
+      val drsPath = makeDrsPathBuilder.build(drsUri).get
+      val containerRelativePath = DefaultPathBuilder.get(containerPath)
+      GcpBatchFileInput(name, drsPath, containerRelativePath, mount)
+    }
+
+    val nonDrsInput: GcpBatchFileInput = GcpBatchFileInput("nnn",
+                                                           DefaultPathBuilder.get("/local/nnn.bai"),
+                                                           DefaultPathBuilder.get("/path/to/nnn.bai"),
+                                                           mount
+    )
+
+    val inputs = List(
+      makeDrsInput("aaa", "drs://drs.example.org/aaa", "path/to/aaa.bai"),
+      nonDrsInput,
+      makeDrsInput("bbb", "drs://drs.example.org/bbb", "path/to/bbb.bai")
+    )
+
+    GcpBatchAsyncBackendJobExecutionActor.generateDrsLocalizerManifest(inputs) shouldEqual
+      "drs://drs.example.org/aaa,/mnt/disks/cromwell_root/path/to/aaa.bai\r\ndrs://drs.example.org/bbb,/mnt/disks/cromwell_root/path/to/bbb.bai\r\n"
+  }
+
   it should "send proper value for \"number of reference files used gauge\" metric, or don't send anything if reference disks feature is disabled" in {
 
     val expectedInput1 = GcpBatchFileInput(name = "testfile1",
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala
index 42ae487b5fb..b65a153fb34 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchConfigurationSpec.scala
@@ -124,9 +124,14 @@ class GcpBatchConfigurationSpec
     ).root shouldBe "gs://my-cromwell-workflows-bucket"
   }
 
-  // it should "have correct docker" in {
-  //  val dockerConf = new GcpBatchConfiguration(BackendConfigurationDescriptor(backendConfig, globalConfig), googleConfiguration, batchAttributes).dockerCredentials
-  //  dockerConf shouldBe defined
-  //  dockerConf.get.token shouldBe "dockerToken"
-  // }
+  it should "have correct docker" in {
+    val dockerConf = new GcpBatchConfiguration(
+      BackendConfigurationDescriptor(backendConfig, globalConfig),
+      googleConfiguration,
+      batchAttributes
+    ).dockerCredentials
+
+    dockerConf shouldBe defined
+    dockerConf.get.token shouldBe "dockerToken"
+  }
 }
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
index beb9b865c1b..110dca0e348 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
@@ -2,10 +2,9 @@ package cromwell.backend.google.batch.models
 
 import cats.data.NonEmptyList
 import cromwell.backend.RuntimeAttributeDefinition
+import cromwell.backend.google.batch.io.{DiskType, GcpBatchAttachedDisk, GcpBatchWorkingDisk}
 import cromwell.backend.google.batch.models.GcpBatchTestConfig._
 import cromwell.backend.validation.ContinueOnReturnCodeSet
-//import cromwell.backend.google.batch.io.{DiskType, GcpBatchAttachedDisk}
-import cromwell.backend.google.batch.io.{DiskType, GcpBatchWorkingDisk}
 import cromwell.core.WorkflowOptions
 import eu.timepit.refined.refineMV
 import org.scalatest.TestSuite
@@ -48,9 +47,8 @@ final class GcpBatchRuntimeAttributesSpec
     }
 
     "fail to validate an invalid Docker entry" in {
-      pending
       val runtimeAttributes = Map("docker" -> WomInteger(1))
-      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting docker runtime attribute to be String")
+      assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting docker runtime attribute to be a String")
     }
 
     "validate a valid failOnStderr entry" in {
@@ -152,21 +150,31 @@ final class GcpBatchRuntimeAttributesSpec
       )
     }
 
-    //    "validate a valid disks entry" in {
-    //      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 20 SSD"))
-    //      val expectedRuntimeAttributes = expectedDefaults.copy(disks = Seq(GcpBatchAttachedDisk.parse("local-disk 20 SSD").get))
-    //      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
-    //    }
-
-    // "fail to validate an invalid disks entry" in {
-    //  val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomInteger(10))
-    //  assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Expecting disks runtime attribute to be a comma separated String or Array[String]")
-    // }
-
-    // "fail to validate a valid disks array entry" in {
-    //  val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomArray(WomArrayType(WomStringType), List(WomString("blah"), WomString("blah blah"))))
-    //  assertBatchRuntimeAttributesFailedCreation(runtimeAttributes, "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE'")
-    // }
+    "validate a valid disks entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomString("local-disk 20 SSD"))
+      val expectedRuntimeAttributes =
+        expectedDefaults.copy(disks = Seq(GcpBatchAttachedDisk.parse("local-disk 20 SSD").get))
+      assertBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes)
+    }
+
+    "fail to validate an invalid disks entry" in {
+      val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "disks" -> WomInteger(10))
+      assertBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Expecting disks runtime attribute to be a comma separated String or Array[String]"
+      )
+    }
+
+    "fail to validate a valid disks array entry" in {
+      val runtimeAttributes =
+        Map("docker" -> WomString("ubuntu:latest"),
+            "disks" -> WomArray(WomArrayType(WomStringType), List(WomString("blah"), WomString("blah blah")))
+        )
+      assertBatchRuntimeAttributesFailedCreation(
+        runtimeAttributes,
+        "Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE'"
+      )
+    }
 
     "validate a valid memory entry" in {
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "memory" -> WomString("1 GB"))

From 3201eb626652fb97c714fc12fdc7c27da4e910f6 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Wed, 10 Apr 2024 17:31:20 -0400
Subject: [PATCH 305/326] [WX-1531] Struct Literal Type Checking (#7402)

---
 .../graph/expression/TypeEvaluator.scala      |   5 +-
 .../types/BiscayneTypeEvaluators.scala        | 222 +++++++++++---
 .../linking/expression/types/types.scala      | 159 +++++-----
 .../types/BiscayneTypeEvaluatorSpec.scala     | 109 +++++--
 .../types/CascadesTypeEvaluators.scala        | 222 +++++++++++---
 .../linking/expression/types/types.scala      | 159 +++++-----
 .../types/CascadesTypeEvaluatorSpec.scala     | 109 +++++--
 .../linking/expression/types/package.scala    | 133 ++++----
 .../MemberAccessTypeEvaluatorSpec.scala       |  14 +-
 .../expression/TernaryIfEvaluatorSpec.scala   |   2 +-
 ...UnaryAndBinaryOperatorsEvaluatorSpec.scala |   2 +-
 .../base/linking/expression/package.scala     |   2 +-
 .../types/BinaryOperatorEvaluators.scala      |  10 +-
 .../types/EngineFunctionEvaluators.scala      | 284 ++++++++++++------
 .../expression/types/LiteralEvaluators.scala  |  62 ++--
 .../expression/types/LookupEvaluators.scala   |  27 +-
 .../expression/types/TernaryIfEvaluator.scala |  11 +-
 .../types/UnaryOperatorEvaluators.scala       |   7 +-
 .../expression/WdlomWomExpression.scala       |  13 +-
 .../graph/CallElementToGraphNode.scala        |   9 +-
 .../graph/IfElementToGraphNode.scala          |  11 +-
 .../graph/ScatterElementToGraphNode.scala     |  13 +-
 22 files changed, 1102 insertions(+), 483 deletions(-)

diff --git a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/TypeEvaluator.scala b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/TypeEvaluator.scala
index b7910478d83..4fc44b7e771 100644
--- a/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/TypeEvaluator.scala
+++ b/wdl/model/draft3/src/main/scala/wdl/model/draft3/graph/expression/TypeEvaluator.scala
@@ -8,7 +8,10 @@ import wom.types.WomType
 
 @typeclass
 trait TypeEvaluator[A] {
-  def evaluateType(a: A, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+  def evaluateType(a: A,
+                   linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                   typeAliases: Map[String, WomType]
+  )(implicit
     expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
   ): ErrorOr[WomType]
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
index 75c6cc297ae..34ea1090d50 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluators.scala
@@ -1,5 +1,6 @@
 package wdl.transforms.biscayne.linking.expression.types
 
+import cats.data.Validated.{Invalid, Valid}
 import cats.implicits.{catsSyntaxTuple2Semigroupal, catsSyntaxTuple3Semigroupal}
 import cats.syntax.validated._
 import common.validation.ErrorOr._
@@ -12,20 +13,26 @@ import wom.types._
 
 object BiscayneTypeEvaluators {
   implicit val keysFunctionEvaluator: TypeEvaluator[Keys] = new TypeEvaluator[Keys] {
-    override def evaluateType(a: Keys, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Keys,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)) flatMap {
+      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType), typeAliases) flatMap {
         case WomMapType(keyType, _) => WomArrayType(keyType).validNel
         case other => s"Cannot invoke 'keys' on type '${other.stableName}'. Expected a map".invalidNel
       }
   }
 
   implicit val asMapFunctionEvaluator: TypeEvaluator[AsMap] = new TypeEvaluator[AsMap] {
-    override def evaluateType(a: AsMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: AsMap,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
+      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType)), typeAliases) flatMap {
         case WomArrayType(WomPairType(x: WomPrimitiveType, y)) => WomMapType(x, y).validNel
         case other @ WomArrayType(WomPairType(x, _)) =>
           s"Cannot invoke 'as_map' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
@@ -34,20 +41,26 @@ object BiscayneTypeEvaluators {
   }
 
   implicit val asPairsFunctionEvaluator: TypeEvaluator[AsPairs] = new TypeEvaluator[AsPairs] {
-    override def evaluateType(a: AsPairs, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: AsPairs,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)) flatMap {
+      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType), typeAliases) flatMap {
         case WomMapType(x, y) => WomArrayType(WomPairType(x, y)).validNel
         case other => s"Cannot invoke 'as_pairs' on type '${other.stableName}'. Expected a map".invalidNel
       }
   }
 
   implicit val collectByKeyFunctionEvaluator: TypeEvaluator[CollectByKey] = new TypeEvaluator[CollectByKey] {
-    override def evaluateType(a: CollectByKey, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: CollectByKey,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
+      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType)), typeAliases) flatMap {
         case WomArrayType(WomPairType(x: WomPrimitiveType, y)) => WomMapType(x, WomArrayType(y)).validNel
         case other @ WomArrayType(WomPairType(x, _)) =>
           s"Cannot invoke 'collect_by_key' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
@@ -67,32 +80,41 @@ object BiscayneTypeEvaluators {
     }
 
   implicit val minFunctionEvaluator: TypeEvaluator[Min] = new TypeEvaluator[Min] {
-    override def evaluateType(a: Min, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Min,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = {
-      val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
-      val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
+      val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues, typeAliases)
+      val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues, typeAliases)
 
       (type1, type2) flatMapN resultTypeOfIntVsFloat("min")
     }
   }
 
   implicit val maxFunctionEvaluator: TypeEvaluator[Max] = new TypeEvaluator[Max] {
-    override def evaluateType(a: Max, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Max,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = {
-      val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
-      val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
+      val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues, typeAliases)
+      val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues, typeAliases)
 
       (type1, type2) flatMapN resultTypeOfIntVsFloat("max")
     }
   }
 
   implicit val sepFunctionEvaluator: TypeEvaluator[Sep] = new TypeEvaluator[Sep] {
-    override def evaluateType(a: Sep, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Sep,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.arg2, linkedValues, WomArrayType(WomAnyType)) flatMap {
+      validateParamType(a.arg2, linkedValues, WomArrayType(WomAnyType), typeAliases) flatMap {
         case WomArrayType(WomArrayType(_)) =>
           s"Cannot invoke 'sep' on type 'Array[Array[_]]'. Expected an Array[String].".invalidNel
         case WomArrayType(_) => WomStringType.validNel
@@ -103,29 +125,38 @@ object BiscayneTypeEvaluators {
   }
 
   implicit val subPosixFunctionEvaluator: TypeEvaluator[SubPosix] = new TypeEvaluator[SubPosix] {
-    override def evaluateType(a: SubPosix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: SubPosix,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      (validateParamType(a.input, linkedValues, WomSingleFileType),
-       validateParamType(a.pattern, linkedValues, WomSingleFileType),
-       validateParamType(a.replace, linkedValues, WomSingleFileType)
+      (validateParamType(a.input, linkedValues, WomSingleFileType, typeAliases),
+       validateParamType(a.pattern, linkedValues, WomSingleFileType, typeAliases),
+       validateParamType(a.replace, linkedValues, WomSingleFileType, typeAliases)
       ) mapN { (_, _, _) => WomStringType }
   }
 
   implicit val suffixFunctionEvaluator: TypeEvaluator[Suffix] = new TypeEvaluator[Suffix] {
-    override def evaluateType(a: Suffix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Suffix,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      (validateParamType(a.suffix, linkedValues, WomStringType),
-       validateParamType(a.array, linkedValues, WomArrayType(WomStringType))
+      (validateParamType(a.suffix, linkedValues, WomStringType, typeAliases),
+       validateParamType(a.array, linkedValues, WomArrayType(WomStringType), typeAliases)
       ) mapN { (_, _) => WomArrayType(WomStringType) }
   }
 
   implicit val quoteFunctionEvaluator: TypeEvaluator[Quote] = new TypeEvaluator[Quote] {
-    override def evaluateType(a: Quote, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Quote,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType)) flatMap {
+      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType), typeAliases) flatMap {
         case WomArrayType(WomNothingType) => WomArrayType(WomNothingType).validNel
         case WomArrayType(_: WomPrimitiveType) => WomArrayType(WomStringType).validNel
         case other @ WomArrayType(_) =>
@@ -136,10 +167,13 @@ object BiscayneTypeEvaluators {
   }
 
   implicit val sQuoteFunctionEvaluator: TypeEvaluator[SQuote] = new TypeEvaluator[SQuote] {
-    override def evaluateType(a: SQuote, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: SQuote,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType)) flatMap {
+      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType), typeAliases) flatMap {
         case WomArrayType(WomNothingType) => WomArrayType(WomNothingType).validNel
         case WomArrayType(_: WomPrimitiveType) => WomArrayType(WomStringType).validNel
         case other @ WomArrayType(_) =>
@@ -150,10 +184,13 @@ object BiscayneTypeEvaluators {
   }
 
   implicit val unzipFunctionEvaluator: TypeEvaluator[Unzip] = new TypeEvaluator[Unzip] {
-    override def evaluateType(a: Unzip, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Unzip,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
+      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType)), typeAliases) flatMap {
         case WomArrayType(WomNothingType) => WomPairType(WomArrayType(WomAnyType), WomArrayType(WomAnyType)).validNel
         case WomArrayType(WomPairType(x, y)) => WomPairType(WomArrayType(x), WomArrayType(y)).validNel
         case other => s"Cannot invoke 'unzip' on type '${other.stableName}'. Expected an array of pairs".invalidNel
@@ -161,14 +198,123 @@ object BiscayneTypeEvaluators {
   }
 
   implicit val structLiteralTypeEvaluator: TypeEvaluator[StructLiteral] = new TypeEvaluator[StructLiteral] {
-    override def evaluateType(a: StructLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+
+    /**
+     * Is the evaluated type allowed to be assigned to the expectedType?
+     */
+    def areTypesAssignable(evaluatedType: WomType, expectedType: WomType): Boolean =
+      // NB: This check is a little looser than we'd like it to be.
+      // For example, String is coercible to Int (Int i = "1" is OK)
+      // It's not until we actually evaluate the value of the string that we can know if that coercion succeeded or not. (Int i = "orange" will fail)
+      // We don't know whether the user has provided "1" or "orange" at this stage.
+      // This is OK as-is because the value evaluators do the coercing and throw meaningful errors if the coercion fails.
+      expectedType.isCoerceableFrom(evaluatedType)
+
+    /**
+     * Helper method to check if something (maybe) found in the struct literal against something (maybe) found in the struct definition.
+     * @return The WomType of the evaluated member. Error if either is not present, or if the types aren't compatible.
+     */
+    def checkIfMemberIsValid(typeName: String,
+                             memberName: String,
+                             evaluatedType: Option[WomType],
+                             expectedType: Option[WomType]
     ): ErrorOr[WomType] =
-      // This works fine, but is not yet a strong enough type check for the WDL 1.1 spec
-      // (i.e. users are able to instantiate struct literals with k/v pairs that aren't actually in the struct definition, without an error being thrown.)
-      // We want to add extra validation here, and return a WomCompositeType that matches the struct definition of everything is OK.
-      // Note that users are allowed to omit optional k/v pairs in their literal.
-      // This requires some extra work to be done in a subsequent PR.
-      WomObjectType.validNel
+      evaluatedType match {
+        case Some(evaluated) =>
+          expectedType match {
+            case Some(expected) =>
+              if (areTypesAssignable(evaluated, expected)) evaluated.validNel
+              else
+                s"$typeName.$memberName expected to be ${expected.friendlyName}. Found ${evaluated.friendlyName}.".invalidNel
+            case None => s"Type $typeName does not have a member called $memberName.".invalidNel
+          }
+        case None => s"Error evaluating the type of ${typeName}.${memberName}.".invalidNel
+      }
+
+    /**
+     * For each member in the literal, check that it exists in the struct definition and is the expected type.
+     * @return The WomCompositeType of the struct literal, as determined from evaluating each member.
+     *         This might not *exactly* match the struct definition due to permitted type coercions.
+     */
+    def checkMembersAgainstDefinition(a: StructLiteral,
+                                      structDefinition: WomCompositeType,
+                                      linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                                      typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomCompositeType] = {
+      val checkedMembers: Map[String, ErrorOr[WomType]] = a.elements.map { case (memberKey, memberExpressionElement) =>
+        val evaluatedType =
+          expressionTypeEvaluator.evaluateType(memberExpressionElement, linkedValues, typeAliases).toOption
+        val expectedType = structDefinition.typeMap.get(memberKey)
+        (memberKey, checkIfMemberIsValid(a.structTypeName, memberKey, evaluatedType, expectedType))
+      }
+
+      val (errors, validatedTypes) = checkedMembers.partition { case (_, errorOr) =>
+        errorOr match {
+          case Invalid(_) => true
+          case Valid(_) => false
+        }
+      }
+
+      if (errors.nonEmpty) {
+        errors.collect { case (_, Invalid(e)) => e.toList.mkString(", ") }.toList.mkString("[ ", ", ", " ]").invalidNel
+      } else {
+        val types = validatedTypes.collect { case (key, Valid(v)) => (key, v) }
+        WomCompositeType(types, Some(a.structTypeName)).validNel
+      }
+    }
+
+    /**
+     * For each member in the struct definition, if that member isn't optional, confirm that it is also in the struct literal.
+     */
+    def checkForMissingMembers(foundMembers: Map[String, WomType],
+                               structDefinition: WomCompositeType
+    ): ErrorOr[Unit] = {
+      val errors: Iterable[String] = structDefinition.typeMap flatMap { case (memberName, memberType) =>
+        memberType match {
+          case WomOptionalType(_) => None
+          case _ =>
+            if (!foundMembers.contains(memberName)) Some(s"Expected member ${memberName} not found. ")
+            else None
+        }
+      }
+      if (errors.nonEmpty) errors.mkString.invalidNel else ().validNel
+    }
+
+    /**
+     * Returns the type of a struct literal, assuming it is compatible with an existing struct definition.
+     * It is required that:
+     *   - a struct definition exist for the literal (looked up the via name of the struct type). This is defined elsewhere in the WDL and is not part of the literal.
+     *   - the struct definition be a WomCompositeType (it's programmer error if it's not)
+     *   - each  member provided in the literal is also in the definition, and is coercible to the defined type.
+     *   - all non-optional members of the definition are present in the literal.
+     * @param a The literal to evaluate
+     * @param linkedValues Used by the expression type evaluator.
+     * @param typeAliases A map containing available struct definitions
+     * @param expressionTypeEvaluator An object capable of evaluating the types of ExpressionElements. Used to evaluate the type of each member provided in the literal.
+     * @return The type of the struct definition (as found in typeAliases) if all goes well. A list of errors otherwise.
+     */
+    override def evaluateType(a: StructLiteral,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      typeAliases.get(a.structTypeName) match {
+        case Some(definition) =>
+          definition match {
+            case compositeType: WomCompositeType =>
+              checkMembersAgainstDefinition(a, compositeType, linkedValues, typeAliases).flatMap { foundMembers =>
+                checkForMissingMembers(foundMembers.typeMap, compositeType) match {
+                  case Invalid(error) => error.invalid
+                  case _ => compositeType.validNel
+                }
+              }
+            case _ =>
+              s"Programmer error: Expected the struct definition of ${a.structTypeName} to be a WomCompositeType".invalidNel
+          }
+        case None => s"Could not find Struct Definition for type ${a.structTypeName}".invalidNel
+      }
   }
 }
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
index 7352c9a1376..ab2f114440a 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/linking/expression/types/types.scala
@@ -18,102 +18,105 @@ import wdl.transforms.biscayne.linking.expression.types.BiscayneTypeEvaluators._
 
 package object types {
   implicit val expressionTypeEvaluator: TypeEvaluator[ExpressionElement] = new TypeEvaluator[ExpressionElement] {
-    override def evaluateType(a: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit typeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: ExpressionElement,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      typeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
       a match {
         // Literals:
-        case a: PrimitiveLiteralExpressionElement => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: NoneLiteralElement.type => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: PrimitiveLiteralExpressionElement => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: NoneLiteralElement.type => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: StringLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: StringExpression => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ObjectLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: StructLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: MapLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ArrayLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: PairLiteral => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: StringLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: StringExpression => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ObjectLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: StructLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: MapLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ArrayLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: PairLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Lookups and member accesses:
-        case a: IdentifierLookup => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ExpressionMemberAccess => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: IdentifierMemberAccess => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: IndexAccess => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: IdentifierLookup => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ExpressionMemberAccess => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: IdentifierMemberAccess => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: IndexAccess => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Unary operators:
-        case a: UnaryNegation => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: UnaryPlus => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LogicalNot => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: UnaryNegation => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: UnaryPlus => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LogicalNot => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Binary operators (at some point we might want to split these into separate cases):
-        case a: LogicalOr => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LogicalAnd => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Equals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: NotEquals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LessThan => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LessThanOrEquals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: GreaterThan => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: GreaterThanOrEquals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Add => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Subtract => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Multiply => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Divide => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Remainder => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: LogicalOr => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LogicalAnd => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Equals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: NotEquals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LessThan => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LessThanOrEquals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: GreaterThan => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: GreaterThanOrEquals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Add => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Subtract => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Multiply => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Divide => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Remainder => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: TernaryIf => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: TernaryIf => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Engine functions:
-        case a: ReadLines => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadTsv => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadMap => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadObject => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadObjects => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadJson => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadInt => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadString => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadFloat => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadBoolean => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteLines => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteTsv => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteMap => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteObject => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteObjects => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteJson => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Range => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Transpose => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Length => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Flatten => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Prefix => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Suffix => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: SelectFirst => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: SelectAll => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Defined => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Floor => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Ceil => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Round => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Glob => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Quote => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: SQuote => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Size => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Basename => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadLines => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadTsv => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadMap => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadObject => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadObjects => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadJson => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadInt => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadString => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadFloat => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadBoolean => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteLines => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteTsv => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteMap => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteObject => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteObjects => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteJson => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Range => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Transpose => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Length => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Flatten => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Prefix => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Suffix => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: SelectFirst => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: SelectAll => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Defined => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Floor => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Ceil => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Round => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Glob => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Quote => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: SQuote => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Size => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Basename => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: Zip => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Cross => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Unzip => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Zip => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Cross => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Unzip => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: SubPosix => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: SubPosix => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: StdoutElement.type => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: StderrElement.type => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: StdoutElement.type => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: StderrElement.type => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: Keys => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: AsMap => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: AsPairs => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: CollectByKey => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Sep => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Keys => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: AsMap => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: AsPairs => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: CollectByKey => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Sep => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: Min => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Max => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Min => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Max => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         case other =>
           s"Unable to process ${other.getClass.getSimpleName}: No evaluateType exists for that type.".invalidNel
diff --git a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
index 0c5c158b542..8c1e95f5523 100644
--- a/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
+++ b/wdl/transforms/biscayne/src/test/scala/wdl/transforms/biscayne/linking/expression/types/BiscayneTypeEvaluatorSpec.scala
@@ -11,12 +11,33 @@ import wdl.transforms.biscayne.ast2wdlom._
 import wom.types._
 
 class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  val plantTypeMap: Map[String, WomType] = Map(
+    "isTasty" -> WomBooleanType,
+    "count" -> WomIntegerType
+  )
+
+  val animalTypeMap: Map[String, WomType] = Map(
+    "isMaybeGood" -> WomOptionalType(WomBooleanType),
+    "hat" -> WomCompositeType(plantTypeMap, Some("Plant"))
+  )
+
+  val bacteriumTypeMap: Map[String, WomType] = Map(
+    "myFile" -> WomSingleFileType
+  )
+
+  val typeAliases: Map[String, WomType] = Map(
+    "Plant" -> WomCompositeType(plantTypeMap, Some("Plant")),
+    "Animal" -> WomCompositeType(animalTypeMap, Some("Animal")),
+    "Bacterium" -> WomCompositeType(bacteriumTypeMap, Some("Bacterium"))
+  )
+
   it should "return nothing from static integer addition" in {
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomIntegerType
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomIntegerType
     }
   }
 
@@ -25,7 +46,7 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomMapType(WomIntegerType, WomIntegerType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomMapType(WomIntegerType, WomIntegerType)
     }
   }
 
@@ -34,7 +55,7 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomPairType(WomStringType, WomIntegerType))
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomPairType(WomStringType, WomIntegerType))
     }
   }
 
@@ -43,7 +64,7 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomStringType
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomStringType
     }
   }
 
@@ -52,7 +73,7 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomStringType
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomStringType
     }
   }
 
@@ -61,7 +82,7 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomStringType
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomStringType
     }
   }
 
@@ -70,7 +91,7 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomStringType)
     }
   }
 
@@ -79,7 +100,7 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomStringType)
     }
   }
 
@@ -88,7 +109,7 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomNothingType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomNothingType)
     }
   }
 
@@ -97,7 +118,7 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomStringType)
     }
   }
 
@@ -106,7 +127,7 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomNothingType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomNothingType)
     }
   }
 
@@ -114,13 +135,17 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val string_and_int = """ unzip([("one", 1),("two", 2),("three", 3)]) """
     val string_and_int_expr = fromString[ExpressionElement](string_and_int, parser.parse_e)
     string_and_int_expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomStringType), WomArrayType(WomIntegerType))
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomPairType(WomArrayType(WomStringType),
+                                                                       WomArrayType(WomIntegerType)
+      )
     }
 
     val int_and_int = """ unzip([(1,2),(3,4),(5,6)]) """
     val int_and_int_expr = fromString[ExpressionElement](int_and_int, parser.parse_e)
     int_and_int_expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomIntegerType), WomArrayType(WomIntegerType))
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomPairType(WomArrayType(WomIntegerType),
+                                                                       WomArrayType(WomIntegerType)
+      )
     }
   }
 
@@ -128,17 +153,67 @@ class BiscayneTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val empty = """ unzip([]) """
     val empty_unzip_expr = fromString[ExpressionElement](empty, parser.parse_e)
     empty_unzip_expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomAnyType), WomArrayType(WomAnyType))
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomPairType(WomArrayType(WomAnyType),
+                                                                       WomArrayType(WomAnyType)
+      )
     }
   }
 
   it should "evaluate the type of a struct literal" in {
-    // NB: This is not yet strict enough type checking for the WDL 1.1 spec.
-    // In a subsequent branch, we will make this be a WomCompositeType that matches the struct definition.
+    val structLiteral = """ Plant{isTasty: true, count: 42} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomCompositeType(plantTypeMap, Some("Plant"))
+    }
+  }
+
+  it should "evaluate the type of a struct literal with a nested struct literal" in {
+    val structLiteral = """ Animal{isMaybeGood: true, hat: Plant{isTasty: true, count: 42}} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomCompositeType(animalTypeMap, Some("Animal"))
+    }
+  }
+
+  it should "fail to evaluate the type of a struct literal with incorrect members" in {
     val structLiteral = """ Animal{fur: "fuzzy", isGood: true} """
     val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
     structExpr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomObjectType
+      e.evaluateType(Map.empty,
+                     typeAliases
+      ) shouldBeInvalid "[ Type Animal does not have a member called fur., Type Animal does not have a member called isGood. ]"
+    }
+  }
+
+  it should "fail to evaluate the type of a struct literal with members that are the wrong type" in {
+    val structLiteral = """ Plant{isTasty: true, count: (0, 1)} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeInvalid "[ Plant.count expected to be Int. Found Pair[Int, Int]. ]"
+    }
+  }
+
+  it should "fail if a struct literal member is missing" in {
+    val structLiteral = """ Plant{count: 4} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeInvalid "Expected member isTasty not found. "
+    }
+  }
+
+  it should "tolerate a missing struct literal optional member" in {
+    val structLiteral = """ Animal{hat: Plant{isTasty: true, count: 42}} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomCompositeType(animalTypeMap, Some("Animal"))
+    }
+  }
+
+  it should "work with file paths in struct literal" in {
+    val structLiteral = """ Bacterium{myFile: "/my/file/path"} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomCompositeType(bacteriumTypeMap, Some("Bacterium"))
     }
   }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
index 137b42128e2..7a49804abb6 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluators.scala
@@ -1,5 +1,6 @@
 package wdl.transforms.biscayne.linking.expression.types
 
+import cats.data.Validated.{Invalid, Valid}
 import cats.implicits.{catsSyntaxTuple2Semigroupal, catsSyntaxTuple3Semigroupal}
 import cats.syntax.validated._
 import common.validation.ErrorOr._
@@ -12,20 +13,26 @@ import wom.types._
 
 object cascadesTypeEvaluators {
   implicit val keysFunctionEvaluator: TypeEvaluator[Keys] = new TypeEvaluator[Keys] {
-    override def evaluateType(a: Keys, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Keys,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)) flatMap {
+      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType), typeAliases) flatMap {
         case WomMapType(keyType, _) => WomArrayType(keyType).validNel
         case other => s"Cannot invoke 'keys' on type '${other.stableName}'. Expected a map".invalidNel
       }
   }
 
   implicit val asMapFunctionEvaluator: TypeEvaluator[AsMap] = new TypeEvaluator[AsMap] {
-    override def evaluateType(a: AsMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: AsMap,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
+      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType)), typeAliases) flatMap {
         case WomArrayType(WomPairType(x: WomPrimitiveType, y)) => WomMapType(x, y).validNel
         case other @ WomArrayType(WomPairType(x, _)) =>
           s"Cannot invoke 'as_map' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
@@ -34,20 +41,26 @@ object cascadesTypeEvaluators {
   }
 
   implicit val asPairsFunctionEvaluator: TypeEvaluator[AsPairs] = new TypeEvaluator[AsPairs] {
-    override def evaluateType(a: AsPairs, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: AsPairs,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)) flatMap {
+      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType), typeAliases) flatMap {
         case WomMapType(x, y) => WomArrayType(WomPairType(x, y)).validNel
         case other => s"Cannot invoke 'as_pairs' on type '${other.stableName}'. Expected a map".invalidNel
       }
   }
 
   implicit val collectByKeyFunctionEvaluator: TypeEvaluator[CollectByKey] = new TypeEvaluator[CollectByKey] {
-    override def evaluateType(a: CollectByKey, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: CollectByKey,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
+      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType)), typeAliases) flatMap {
         case WomArrayType(WomPairType(x: WomPrimitiveType, y)) => WomMapType(x, WomArrayType(y)).validNel
         case other @ WomArrayType(WomPairType(x, _)) =>
           s"Cannot invoke 'collect_by_key' on type ${other.stableName}. Map keys must be primitive but got '${x.stableName}'".invalidNel
@@ -67,32 +80,41 @@ object cascadesTypeEvaluators {
     }
 
   implicit val minFunctionEvaluator: TypeEvaluator[Min] = new TypeEvaluator[Min] {
-    override def evaluateType(a: Min, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Min,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = {
-      val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
-      val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
+      val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues, typeAliases)
+      val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues, typeAliases)
 
       (type1, type2) flatMapN resultTypeOfIntVsFloat("min")
     }
   }
 
   implicit val maxFunctionEvaluator: TypeEvaluator[Max] = new TypeEvaluator[Max] {
-    override def evaluateType(a: Max, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Max,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = {
-      val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
-      val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues)
+      val type1 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues, typeAliases)
+      val type2 = expressionTypeEvaluator.evaluateType(a.arg1, linkedValues, typeAliases)
 
       (type1, type2) flatMapN resultTypeOfIntVsFloat("max")
     }
   }
 
   implicit val sepFunctionEvaluator: TypeEvaluator[Sep] = new TypeEvaluator[Sep] {
-    override def evaluateType(a: Sep, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Sep,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.arg2, linkedValues, WomArrayType(WomAnyType)) flatMap {
+      validateParamType(a.arg2, linkedValues, WomArrayType(WomAnyType), typeAliases) flatMap {
         case WomArrayType(WomArrayType(_)) =>
           s"Cannot invoke 'sep' on type 'Array[Array[_]]'. Expected an Array[String].".invalidNel
         case WomArrayType(_) => WomStringType.validNel
@@ -103,29 +125,38 @@ object cascadesTypeEvaluators {
   }
 
   implicit val subPosixFunctionEvaluator: TypeEvaluator[SubPosix] = new TypeEvaluator[SubPosix] {
-    override def evaluateType(a: SubPosix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: SubPosix,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      (validateParamType(a.input, linkedValues, WomSingleFileType),
-       validateParamType(a.pattern, linkedValues, WomSingleFileType),
-       validateParamType(a.replace, linkedValues, WomSingleFileType)
+      (validateParamType(a.input, linkedValues, WomSingleFileType, typeAliases),
+       validateParamType(a.pattern, linkedValues, WomSingleFileType, typeAliases),
+       validateParamType(a.replace, linkedValues, WomSingleFileType, typeAliases)
       ) mapN { (_, _, _) => WomStringType }
   }
 
   implicit val suffixFunctionEvaluator: TypeEvaluator[Suffix] = new TypeEvaluator[Suffix] {
-    override def evaluateType(a: Suffix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Suffix,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      (validateParamType(a.suffix, linkedValues, WomStringType),
-       validateParamType(a.array, linkedValues, WomArrayType(WomStringType))
+      (validateParamType(a.suffix, linkedValues, WomStringType, typeAliases),
+       validateParamType(a.array, linkedValues, WomArrayType(WomStringType), typeAliases)
       ) mapN { (_, _) => WomArrayType(WomStringType) }
   }
 
   implicit val quoteFunctionEvaluator: TypeEvaluator[Quote] = new TypeEvaluator[Quote] {
-    override def evaluateType(a: Quote, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Quote,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType)) flatMap {
+      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType), typeAliases) flatMap {
         case WomArrayType(WomNothingType) => WomArrayType(WomNothingType).validNel
         case WomArrayType(_: WomPrimitiveType) => WomArrayType(WomStringType).validNel
         case other @ WomArrayType(_) =>
@@ -136,10 +167,13 @@ object cascadesTypeEvaluators {
   }
 
   implicit val sQuoteFunctionEvaluator: TypeEvaluator[SQuote] = new TypeEvaluator[SQuote] {
-    override def evaluateType(a: SQuote, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: SQuote,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType)) flatMap {
+      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType), typeAliases) flatMap {
         case WomArrayType(WomNothingType) => WomArrayType(WomNothingType).validNel
         case WomArrayType(_: WomPrimitiveType) => WomArrayType(WomStringType).validNel
         case other @ WomArrayType(_) =>
@@ -150,10 +184,13 @@ object cascadesTypeEvaluators {
   }
 
   implicit val unzipFunctionEvaluator: TypeEvaluator[Unzip] = new TypeEvaluator[Unzip] {
-    override def evaluateType(a: Unzip, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Unzip,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType))) flatMap {
+      validateParamType(a.param, linkedValues, WomArrayType(WomPairType(WomAnyType, WomAnyType)), typeAliases) flatMap {
         case WomArrayType(WomNothingType) => WomPairType(WomArrayType(WomAnyType), WomArrayType(WomAnyType)).validNel
         case WomArrayType(WomPairType(x, y)) => WomPairType(WomArrayType(x), WomArrayType(y)).validNel
         case other => s"Cannot invoke 'unzip' on type '${other.stableName}'. Expected an array of pairs".invalidNel
@@ -161,14 +198,123 @@ object cascadesTypeEvaluators {
   }
 
   implicit val structLiteralTypeEvaluator: TypeEvaluator[StructLiteral] = new TypeEvaluator[StructLiteral] {
-    override def evaluateType(a: StructLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+
+    /**
+     * Is the evaluated type allowed to be assigned to the expectedType?
+     */
+    def areTypesAssignable(evaluatedType: WomType, expectedType: WomType): Boolean =
+      // NB: This check is a little looser than we'd like it to be.
+      // For example, String is coercible to Int (Int i = "1" is OK)
+      // It's not until we actually evaluate the value of the string that we can know if that coercion succeeded or not. (Int i = "orange" will fail)
+      // We don't know whether the user has provided "1" or "orange" at this stage.
+      // This is OK as-is because the value evaluators do the coercing and throw meaningful errors if the coercion fails.
+      expectedType.isCoerceableFrom(evaluatedType)
+
+    /**
+     * Helper method to check if something (maybe) found in the struct literal against something (maybe) found in the struct definition.
+     * @return The WomType of the evaluated member. Error if either is not present, or if the types aren't compatible.
+     */
+    def checkIfMemberIsValid(typeName: String,
+                             memberName: String,
+                             evaluatedType: Option[WomType],
+                             expectedType: Option[WomType]
     ): ErrorOr[WomType] =
-      // This works fine, but is not yet a strong enough type check for the WDL 1.1 spec
-      // (i.e. users are able to instantiate struct literals with k/v pairs that aren't actually in the struct definition, without an error being thrown.)
-      // We want to add extra validation here, and return a WomCompositeType that matches the struct definition of everything is OK.
-      // Note that users are allowed to omit optional k/v pairs in their literal.
-      // This requires some extra work to be done in a subsequent PR.
-      WomObjectType.validNel
+      evaluatedType match {
+        case Some(evaluated) =>
+          expectedType match {
+            case Some(expected) =>
+              if (areTypesAssignable(evaluated, expected)) evaluated.validNel
+              else
+                s"$typeName.$memberName expected to be ${expected.friendlyName}. Found ${evaluated.friendlyName}.".invalidNel
+            case None => s"Type $typeName does not have a member called $memberName.".invalidNel
+          }
+        case None => s"Error evaluating the type of ${typeName}.${memberName}.".invalidNel
+      }
+
+    /**
+     * For each member in the literal, check that it exists in the struct definition and is the expected type.
+     * @return The WomCompositeType of the struct literal, as determined from evaluating each member.
+     *         This might not *exactly* match the struct definition due to permitted type coercions.
+     */
+    def checkMembersAgainstDefinition(a: StructLiteral,
+                                      structDefinition: WomCompositeType,
+                                      linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                                      typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomCompositeType] = {
+      val checkedMembers: Map[String, ErrorOr[WomType]] = a.elements.map { case (memberKey, memberExpressionElement) =>
+        val evaluatedType =
+          expressionTypeEvaluator.evaluateType(memberExpressionElement, linkedValues, typeAliases).toOption
+        val expectedType = structDefinition.typeMap.get(memberKey)
+        (memberKey, checkIfMemberIsValid(a.structTypeName, memberKey, evaluatedType, expectedType))
+      }
+
+      val (errors, validatedTypes) = checkedMembers.partition { case (_, errorOr) =>
+        errorOr match {
+          case Invalid(_) => true
+          case Valid(_) => false
+        }
+      }
+
+      if (errors.nonEmpty) {
+        errors.collect { case (_, Invalid(e)) => e.toList.mkString(", ") }.toList.mkString("[ ", ", ", " ]").invalidNel
+      } else {
+        val types = validatedTypes.collect { case (key, Valid(v)) => (key, v) }
+        WomCompositeType(types, Some(a.structTypeName)).validNel
+      }
+    }
+
+    /**
+     * For each member in the struct definition, if that member isn't optional, confirm that it is also in the struct literal.
+     */
+    def checkForMissingMembers(foundMembers: Map[String, WomType],
+                               structDefinition: WomCompositeType
+    ): ErrorOr[Unit] = {
+      val errors: Iterable[String] = structDefinition.typeMap flatMap { case (memberName, memberType) =>
+        memberType match {
+          case WomOptionalType(_) => None
+          case _ =>
+            if (!foundMembers.contains(memberName)) Some(s"Expected member ${memberName} not found. ")
+            else None
+        }
+      }
+      if (errors.nonEmpty) errors.mkString.invalidNel else ().validNel
+    }
+
+    /**
+     * Returns the type of a struct literal, assuming it is compatible with an existing struct definition.
+     * It is required that:
+     *   - a struct definition exist for the literal (looked up the via name of the struct type). This is defined elsewhere in the WDL and is not part of the literal.
+     *   - the struct definition be a WomCompositeType (it's programmer error if it's not)
+     *   - each  member provided in the literal is also in the definition, and is coercible to the defined type.
+     *   - all non-optional members of the definition are present in the literal.
+     * @param a The literal to evaluate
+     * @param linkedValues Used by the expression type evaluator.
+     * @param typeAliases A map containing available struct definitions
+     * @param expressionTypeEvaluator An object capable of evaluating the types of ExpressionElements. Used to evaluate the type of each member provided in the literal.
+     * @return The type of the struct definition (as found in typeAliases) if all goes well. A list of errors otherwise.
+     */
+    override def evaluateType(a: StructLiteral,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    ): ErrorOr[WomType] =
+      typeAliases.get(a.structTypeName) match {
+        case Some(definition) =>
+          definition match {
+            case compositeType: WomCompositeType =>
+              checkMembersAgainstDefinition(a, compositeType, linkedValues, typeAliases).flatMap { foundMembers =>
+                checkForMissingMembers(foundMembers.typeMap, compositeType) match {
+                  case Invalid(error) => error.invalid
+                  case _ => compositeType.validNel
+                }
+              }
+            case _ =>
+              s"Programmer error: Expected the struct definition of ${a.structTypeName} to be a WomCompositeType".invalidNel
+          }
+        case None => s"Could not find Struct Definition for type ${a.structTypeName}".invalidNel
+      }
   }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
index 58e1fe888d7..45603ff54e9 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/linking/expression/types/types.scala
@@ -18,103 +18,106 @@ import wdl.transforms.biscayne.linking.expression.types.cascadesTypeEvaluators._
 
 package object types {
   implicit val expressionTypeEvaluator: TypeEvaluator[ExpressionElement] = new TypeEvaluator[ExpressionElement] {
-    override def evaluateType(a: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit typeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: ExpressionElement,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      typeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
       a match {
         // Literals:
-        case a: PrimitiveLiteralExpressionElement => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: NoneLiteralElement.type => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: PrimitiveLiteralExpressionElement => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: NoneLiteralElement.type => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: StringLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: StringExpression => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ObjectLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: StructLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: MapLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ArrayLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: PairLiteral => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: StringLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: StringExpression => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ObjectLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: StructLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: MapLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ArrayLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: PairLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Lookups and member accesses:
-        case a: IdentifierLookup => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ExpressionMemberAccess => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: IdentifierMemberAccess => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: IndexAccess => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: IdentifierLookup => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ExpressionMemberAccess => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: IdentifierMemberAccess => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: IndexAccess => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Unary operators:
-        case a: UnaryNegation => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: UnaryPlus => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LogicalNot => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: UnaryNegation => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: UnaryPlus => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LogicalNot => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Binary operators (at some point we might want to split these into separate cases):
-        case a: LogicalOr => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LogicalAnd => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Equals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: NotEquals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LessThan => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LessThanOrEquals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: GreaterThan => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: GreaterThanOrEquals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Add => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Subtract => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Multiply => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Divide => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Remainder => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: LogicalOr => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LogicalAnd => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Equals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: NotEquals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LessThan => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LessThanOrEquals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: GreaterThan => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: GreaterThanOrEquals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Add => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Subtract => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Multiply => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Divide => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Remainder => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: TernaryIf => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: TernaryIf => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Engine functions:
-        case a: ReadLines => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadTsv => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadMap => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadObject => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadObjects => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadJson => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadInt => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadString => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadFloat => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadBoolean => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteLines => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteTsv => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteMap => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteObject => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteObjects => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteJson => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Range => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Transpose => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Length => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Flatten => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Prefix => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Suffix => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Quote => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: SQuote => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: SelectFirst => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: SelectAll => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Defined => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Floor => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Ceil => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Round => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Glob => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadLines => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadTsv => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadMap => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadObject => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadObjects => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadJson => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadInt => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadString => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadFloat => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadBoolean => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteLines => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteTsv => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteMap => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteObject => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteObjects => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteJson => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Range => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Transpose => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Length => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Flatten => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Prefix => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Suffix => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Quote => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: SQuote => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: SelectFirst => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: SelectAll => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Defined => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Floor => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Ceil => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Round => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Glob => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: Size => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Basename => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Size => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Basename => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: Zip => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Cross => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Unzip => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Zip => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Cross => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Unzip => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: SubPosix => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: SubPosix => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: StdoutElement.type => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: StderrElement.type => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: StdoutElement.type => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: StderrElement.type => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: Keys => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: AsMap => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: AsPairs => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: CollectByKey => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Sep => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Keys => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: AsMap => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: AsPairs => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: CollectByKey => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Sep => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: Min => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Max => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Min => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Max => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         case other =>
           s"Unable to process ${other.getClass.getSimpleName}: No evaluateType exists for that type.".invalidNel
diff --git a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
index 0bef2d7a6ef..b9274d7e866 100644
--- a/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
+++ b/wdl/transforms/cascades/src/test/scala/wdl/transforms/cascades/linking/expression/types/CascadesTypeEvaluatorSpec.scala
@@ -11,12 +11,33 @@ import wdl.transforms.cascades.ast2wdlom._
 import wom.types._
 
 class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
+
+  val plantTypeMap: Map[String, WomType] = Map(
+    "isTasty" -> WomBooleanType,
+    "count" -> WomIntegerType
+  )
+
+  val animalTypeMap: Map[String, WomType] = Map(
+    "isMaybeGood" -> WomOptionalType(WomBooleanType),
+    "hat" -> WomCompositeType(plantTypeMap, Some("Plant"))
+  )
+
+  val bacteriumTypeMap: Map[String, WomType] = Map(
+    "myFile" -> WomSingleFileType
+  )
+
+  val typeAliases: Map[String, WomType] = Map(
+    "Plant" -> WomCompositeType(plantTypeMap, Some("Plant")),
+    "Animal" -> WomCompositeType(animalTypeMap, Some("Animal")),
+    "Bacterium" -> WomCompositeType(bacteriumTypeMap, Some("Bacterium"))
+  )
+
   it should "return nothing from static integer addition" in {
     val str = "3 + 3"
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomIntegerType
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomIntegerType
     }
   }
 
@@ -25,7 +46,7 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomMapType(WomIntegerType, WomIntegerType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomMapType(WomIntegerType, WomIntegerType)
     }
   }
 
@@ -34,7 +55,7 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomPairType(WomStringType, WomIntegerType))
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomPairType(WomStringType, WomIntegerType))
     }
   }
 
@@ -43,7 +64,7 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomStringType
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomStringType
     }
   }
 
@@ -52,7 +73,7 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomStringType
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomStringType
     }
   }
 
@@ -61,7 +82,7 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomStringType
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomStringType
     }
   }
 
@@ -70,7 +91,7 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomStringType)
     }
   }
 
@@ -79,7 +100,7 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomStringType)
     }
   }
 
@@ -88,7 +109,7 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomNothingType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomNothingType)
     }
   }
 
@@ -97,7 +118,7 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomStringType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomStringType)
     }
   }
 
@@ -106,7 +127,7 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val expr = fromString[ExpressionElement](str, parser.parse_e)
 
     expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomArrayType(WomNothingType)
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomArrayType(WomNothingType)
     }
   }
 
@@ -114,13 +135,17 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val string_and_int = """ unzip([("one", 1),("two", 2),("three", 3)]) """
     val string_and_int_expr = fromString[ExpressionElement](string_and_int, parser.parse_e)
     string_and_int_expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomStringType), WomArrayType(WomIntegerType))
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomPairType(WomArrayType(WomStringType),
+                                                                       WomArrayType(WomIntegerType)
+      )
     }
 
     val int_and_int = """ unzip([(1,2),(3,4),(5,6)]) """
     val int_and_int_expr = fromString[ExpressionElement](int_and_int, parser.parse_e)
     int_and_int_expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomIntegerType), WomArrayType(WomIntegerType))
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomPairType(WomArrayType(WomIntegerType),
+                                                                       WomArrayType(WomIntegerType)
+      )
     }
   }
 
@@ -128,17 +153,67 @@ class CascadesTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec wit
     val empty = """ unzip([]) """
     val empty_unzip_expr = fromString[ExpressionElement](empty, parser.parse_e)
     empty_unzip_expr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomPairType(WomArrayType(WomAnyType), WomArrayType(WomAnyType))
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomPairType(WomArrayType(WomAnyType),
+                                                                       WomArrayType(WomAnyType)
+      )
     }
   }
 
   it should "evaluate the type of a struct literal" in {
-    // NB: This is not yet strict enough type checking for the WDL 1.1 spec.
-    // In a subsequent branch, we will make this be a WomCompositeType that matches the struct definition.
+    val structLiteral = """ Plant{isTasty: true, count: 42} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomCompositeType(plantTypeMap, Some("Plant"))
+    }
+  }
+
+  it should "evaluate the type of a struct literal with a nested struct literal" in {
+    val structLiteral = """ Animal{isMaybeGood: true, hat: Plant{isTasty: true, count: 42}} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomCompositeType(animalTypeMap, Some("Animal"))
+    }
+  }
+
+  it should "fail to evaluate the type of a struct literal with incorrect members" in {
     val structLiteral = """ Animal{fur: "fuzzy", isGood: true} """
     val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
     structExpr.shouldBeValidPF { case e =>
-      e.evaluateType(Map.empty) shouldBeValid WomObjectType
+      e.evaluateType(Map.empty,
+                     typeAliases
+      ) shouldBeInvalid "[ Type Animal does not have a member called fur., Type Animal does not have a member called isGood. ]"
+    }
+  }
+
+  it should "fail to evaluate the type of a struct literal with members that are the wrong type" in {
+    val structLiteral = """ Plant{isTasty: true, count: (0, 1)} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeInvalid "[ Plant.count expected to be Int. Found Pair[Int, Int]. ]"
+    }
+  }
+
+  it should "fail if a struct literal member is missing" in {
+    val structLiteral = """ Plant{count: 4} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeInvalid "Expected member isTasty not found. "
+    }
+  }
+
+  it should "tolerate a missing struct literal optional member" in {
+    val structLiteral = """ Animal{hat: Plant{isTasty: true, count: 42}} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomCompositeType(animalTypeMap, Some("Animal"))
+    }
+  }
+
+  it should "work with file paths in struct literal" in {
+    val structLiteral = """ Bacterium{myFile: "/my/file/path"} """
+    val structExpr = fromString[ExpressionElement](structLiteral, parser.parse_e)
+    structExpr.shouldBeValidPF { case e =>
+      e.evaluateType(Map.empty, typeAliases) shouldBeValid WomCompositeType(bacteriumTypeMap, Some("Bacterium"))
     }
   }
 }
diff --git a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/types/package.scala b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/types/package.scala
index 4651a0d4c18..d35685146ac 100644
--- a/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/types/package.scala
+++ b/wdl/transforms/draft3/src/main/scala/wdl/draft3/transforms/linking/expression/types/package.scala
@@ -17,87 +17,90 @@ import wom.types.WomType
 
 package object types {
   implicit val expressionTypeEvaluator: TypeEvaluator[ExpressionElement] = new TypeEvaluator[ExpressionElement] {
-    override def evaluateType(a: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit typeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: ExpressionElement,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      typeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
       a match {
         // Literals:
-        case a: PrimitiveLiteralExpressionElement => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: StringLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: StringExpression => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ObjectLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: MapLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ArrayLiteral => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: PairLiteral => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: PrimitiveLiteralExpressionElement => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: StringLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: StringExpression => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ObjectLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: MapLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ArrayLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: PairLiteral => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Lookups and member accesses:
-        case a: IdentifierLookup => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ExpressionMemberAccess => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: IdentifierMemberAccess => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: IndexAccess => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: IdentifierLookup => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ExpressionMemberAccess => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: IdentifierMemberAccess => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: IndexAccess => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Unary operators:
-        case a: UnaryNegation => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: UnaryPlus => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LogicalNot => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: UnaryNegation => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: UnaryPlus => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LogicalNot => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Binary operators (at some point we might want to split these into separate cases):
-        case a: LogicalOr => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LogicalAnd => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Equals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: NotEquals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LessThan => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: LessThanOrEquals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: GreaterThan => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: GreaterThanOrEquals => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Add => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Subtract => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Multiply => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Divide => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Remainder => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: LogicalOr => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LogicalAnd => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Equals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: NotEquals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LessThan => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: LessThanOrEquals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: GreaterThan => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: GreaterThanOrEquals => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Add => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Subtract => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Multiply => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Divide => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Remainder => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: TernaryIf => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: TernaryIf => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         // Engine functions:
-        case a: ReadLines => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadTsv => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadMap => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadObject => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadObjects => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadJson => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadInt => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadString => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadFloat => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: ReadBoolean => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteLines => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteTsv => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteMap => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteObject => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteObjects => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: WriteJson => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Range => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Transpose => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Length => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Flatten => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Prefix => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: SelectFirst => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: SelectAll => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Defined => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Floor => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Ceil => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Round => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Glob => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: ReadLines => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadTsv => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadMap => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadObject => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadObjects => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadJson => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadInt => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadString => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadFloat => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: ReadBoolean => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteLines => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteTsv => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteMap => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteObject => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteObjects => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: WriteJson => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Range => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Transpose => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Length => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Flatten => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Prefix => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: SelectFirst => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: SelectAll => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Defined => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Floor => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Ceil => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Round => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Glob => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: Size => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Basename => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Size => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Basename => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: Zip => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: Cross => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Zip => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: Cross => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: Sub => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: Sub => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
-        case a: StdoutElement.type => a.evaluateType(linkedValues)(typeEvaluator)
-        case a: StderrElement.type => a.evaluateType(linkedValues)(typeEvaluator)
+        case a: StdoutElement.type => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
+        case a: StderrElement.type => a.evaluateType(linkedValues, typeAliases)(typeEvaluator)
 
         case other =>
           s"Unable to process ${other.getClass.getSimpleName}: No evaluateType exists for that type.".invalidNel
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessTypeEvaluatorSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessTypeEvaluatorSpec.scala
index 06bbbc57725..90bd7cea585 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessTypeEvaluatorSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/MemberAccessTypeEvaluatorSpec.scala
@@ -23,10 +23,10 @@ class MemberAccessTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec
   it should "find the left and right hand sides of a pair expression" in {
     val pair = PairLiteral(fiveLiteral, sixLiteral)
     val leftExpression: ExpressionElement = ExpressionMemberAccess(pair, NonEmptyList("left", List.empty))
-    leftExpression.evaluateType(Map.empty) shouldBeValid WomIntegerType
+    leftExpression.evaluateType(Map.empty, Map.empty) shouldBeValid WomIntegerType
 
     val rightExpression: ExpressionElement = ExpressionMemberAccess(pair, NonEmptyList("right", List.empty))
-    rightExpression.evaluateType(Map.empty) shouldBeValid WomIntegerType
+    rightExpression.evaluateType(Map.empty, Map.empty) shouldBeValid WomIntegerType
   }
 
   it should "find the appropriate value in a deeply nested Pair" in {
@@ -46,7 +46,7 @@ class MemberAccessTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec
       ),
       memberAccessTail = NonEmptyList("left", List("right", "right", "left"))
     )
-    nestedPairLookup.evaluateType(Map.empty) shouldBeValid WomPairType(WomIntegerType, WomIntegerType)
+    nestedPairLookup.evaluateType(Map.empty, Map.empty) shouldBeValid WomPairType(WomIntegerType, WomIntegerType)
   }
 
   it should "evaluate a nested member access on a call output" in {
@@ -59,7 +59,7 @@ class MemberAccessTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec
       )
     )
 
-    callOutputLookup.evaluateType(linkedValues) shouldBeValid WomPairType(WomIntegerType, WomIntegerType)
+    callOutputLookup.evaluateType(linkedValues, Map.empty) shouldBeValid WomPairType(WomIntegerType, WomIntegerType)
   }
 
   it should "evaluate a nested member access on a struct" in {
@@ -77,7 +77,7 @@ class MemberAccessTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec
       )
     )
 
-    objectLookup.evaluateType(linkedValues) shouldBeValid WomPairType(WomIntegerType, WomIntegerType)
+    objectLookup.evaluateType(linkedValues, Map.empty) shouldBeValid WomPairType(WomIntegerType, WomIntegerType)
   }
 
   it should "evaluate a nested member access type on an object" in {
@@ -89,7 +89,7 @@ class MemberAccessTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec
       )
     )
 
-    objectLookup.evaluateType(linkedValues) shouldBeValid WomAnyType
+    objectLookup.evaluateType(linkedValues, Map.empty) shouldBeValid WomAnyType
   }
 
   it should "evaluate an identifier lookup" in {
@@ -101,7 +101,7 @@ class MemberAccessTypeEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec
       )
     )
 
-    identifierLookup.evaluateType(linkedValues) shouldBeValid WomPairType(WomStringType, WomStringType)
+    identifierLookup.evaluateType(linkedValues, Map.empty) shouldBeValid WomPairType(WomStringType, WomStringType)
   }
 
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/TernaryIfEvaluatorSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/TernaryIfEvaluatorSpec.scala
index 0c9a4323dcc..f73f824904f 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/TernaryIfEvaluatorSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/TernaryIfEvaluatorSpec.scala
@@ -56,7 +56,7 @@ class TernaryIfEvaluatorSpec extends AnyFlatSpec with CromwellTimeoutSpec with M
 
   typeTests foreach { case (name, expression, expected) =>
     it should s"evaluate the expression '$name'" in {
-      expression.evaluateType(Map.empty) shouldBeValid expected
+      expression.evaluateType(Map.empty, Map.empty) shouldBeValid expected
     }
   }
 }
diff --git a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/UnaryAndBinaryOperatorsEvaluatorSpec.scala b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/UnaryAndBinaryOperatorsEvaluatorSpec.scala
index 656e6ae21be..23c149a6061 100644
--- a/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/UnaryAndBinaryOperatorsEvaluatorSpec.scala
+++ b/wdl/transforms/draft3/src/test/scala/wdl/draft3/transforms/expression/UnaryAndBinaryOperatorsEvaluatorSpec.scala
@@ -65,7 +65,7 @@ class UnaryAndBinaryOperatorsEvaluatorSpec extends AnyFlatSpec with CromwellTime
     }
 
     it should s"evaluate the type of the expression '$name'" in {
-      expression.evaluateType(Map.empty) shouldBeValid expectedType
+      expression.evaluateType(Map.empty, Map.empty) shouldBeValid expectedType
     }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/package.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/package.scala
index 59f98ee63b5..45d12abd8b2 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/package.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/package.scala
@@ -32,7 +32,7 @@ package object expression {
           s"Could not create WOM expression for '$a': Found no generated value for consumed value $missing".invalidNel
       }
 
-      neededLinkedValues flatMap { lookup => WdlomWomExpression.make(a, lookup.toMap) }
+      neededLinkedValues flatMap { lookup => WdlomWomExpression.make(a, lookup.toMap, typeAliases) }
 
     }
   }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/BinaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/BinaryOperatorEvaluators.scala
index c18a0aadc84..11e9e4b53c5 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/BinaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/BinaryOperatorEvaluators.scala
@@ -28,11 +28,15 @@ object BinaryOperatorEvaluators {
   implicit val remainderEvaluator: TypeEvaluator[Remainder] = forOperation(_.mod(_))
 
   private def forOperation[A <: BinaryOperation](op: (WomType, WomType) => Try[WomType]) = new TypeEvaluator[A] {
-    override def evaluateType(a: A, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: A,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      (a.left.evaluateType(linkedValues), a.right.evaluateType(linkedValues)) flatMapN { (left, right) =>
-        op(left, right).toErrorOr
+      (a.left.evaluateType(linkedValues, typeAliases), a.right.evaluateType(linkedValues, typeAliases)) flatMapN {
+        (left, right) =>
+          op(left, right).toErrorOr
       }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/EngineFunctionEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/EngineFunctionEvaluators.scala
index 8268cdaac72..56d9c59ff72 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/EngineFunctionEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/EngineFunctionEvaluators.scala
@@ -20,7 +20,8 @@ object EngineFunctionEvaluators {
   implicit val stdoutFunctionEvaluator: TypeEvaluator[StdoutElement.type] =
     new TypeEvaluator[ExpressionElement.StdoutElement.type] {
       override def evaluateType(a: ExpressionElement.StdoutElement.type,
-                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                                typeAliases: Map[String, WomType]
       )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
         WomSingleFileType.validNel
     }
@@ -28,122 +29,179 @@ object EngineFunctionEvaluators {
   implicit val stderrFunctionEvaluator: TypeEvaluator[StderrElement.type] =
     new TypeEvaluator[ExpressionElement.StderrElement.type] {
       override def evaluateType(a: ExpressionElement.StderrElement.type,
-                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                                typeAliases: Map[String, WomType]
       )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
         WomSingleFileType.validNel
     }
 
   implicit val readLinesFunctionEvaluator: TypeEvaluator[ReadLines] = new TypeEvaluator[ReadLines] {
-    override def evaluateType(a: ReadLines, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: ReadLines,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomArrayType(WomStringType))
+      validateParamType(a.param, linkedValues, WomSingleFileType, typeAliases).map(_ => WomArrayType(WomStringType))
   }
 
   implicit val readTsvFunctionEvaluator: TypeEvaluator[ReadTsv] = new TypeEvaluator[ReadTsv] {
-    override def evaluateType(a: ReadTsv, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: ReadTsv,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomArrayType(WomArrayType(WomStringType)))
+      validateParamType(a.param, linkedValues, WomSingleFileType, typeAliases).map(_ =>
+        WomArrayType(WomArrayType(WomStringType))
+      )
   }
 
   implicit val readMapFunctionEvaluator: TypeEvaluator[ReadMap] = new TypeEvaluator[ReadMap] {
-    override def evaluateType(a: ReadMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: ReadMap,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomMapType(WomStringType, WomStringType))
+      validateParamType(a.param, linkedValues, WomSingleFileType, typeAliases).map(_ =>
+        WomMapType(WomStringType, WomStringType)
+      )
   }
 
   implicit val readObjectFunctionEvaluator: TypeEvaluator[ReadObject] = new TypeEvaluator[ReadObject] {
-    override def evaluateType(a: ReadObject, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: ReadObject,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomObjectType)
+      validateParamType(a.param, linkedValues, WomSingleFileType, typeAliases).map(_ => WomObjectType)
   }
 
   implicit val readObjectsFunctionEvaluator: TypeEvaluator[ReadObjects] = new TypeEvaluator[ReadObjects] {
-    override def evaluateType(a: ReadObjects, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: ReadObjects,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomArrayType(WomObjectType))
+      validateParamType(a.param, linkedValues, WomSingleFileType, typeAliases).map(_ => WomArrayType(WomObjectType))
   }
 
   implicit val readJsonFunctionEvaluator: TypeEvaluator[ReadJson] = new TypeEvaluator[ReadJson] {
-    override def evaluateType(a: ReadJson, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: ReadJson,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
       // we can't figure out the WomType of data without reading the file hence evaluate it to `WomAnyType`
-      validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomAnyType)
+      validateParamType(a.param, linkedValues, WomSingleFileType, typeAliases).map(_ => WomAnyType)
   }
 
   implicit val readIntFunctionEvaluator: TypeEvaluator[ReadInt] = new TypeEvaluator[ReadInt] {
-    override def evaluateType(a: ReadInt, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: ReadInt,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomIntegerType)
+      validateParamType(a.param, linkedValues, WomSingleFileType, typeAliases).map(_ => WomIntegerType)
   }
 
   implicit val readStringFunctionEvaluator: TypeEvaluator[ReadString] = new TypeEvaluator[ReadString] {
-    override def evaluateType(a: ReadString, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: ReadString,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomStringType)
+      validateParamType(a.param, linkedValues, WomSingleFileType, typeAliases).map(_ => WomStringType)
   }
 
   implicit val readFloatFunctionEvaluator: TypeEvaluator[ReadFloat] = new TypeEvaluator[ReadFloat] {
-    override def evaluateType(a: ReadFloat, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: ReadFloat,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomFloatType)
+      validateParamType(a.param, linkedValues, WomSingleFileType, typeAliases).map(_ => WomFloatType)
   }
 
   implicit val readBooleanFunctionEvaluator: TypeEvaluator[ReadBoolean] = new TypeEvaluator[ReadBoolean] {
-    override def evaluateType(a: ReadBoolean, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: ReadBoolean,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomSingleFileType).map(_ => WomBooleanType)
+      validateParamType(a.param, linkedValues, WomSingleFileType, typeAliases).map(_ => WomBooleanType)
   }
 
   implicit val writeLinesFunctionEvaluator: TypeEvaluator[WriteLines] = new TypeEvaluator[WriteLines] {
-    override def evaluateType(a: WriteLines, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: WriteLines,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomStringType)).map(_ => WomSingleFileType)
+      validateParamType(a.param, linkedValues, WomArrayType(WomStringType), typeAliases).map(_ => WomSingleFileType)
   }
 
   implicit val writeTsvFunctionEvaluator: TypeEvaluator[WriteTsv] = new TypeEvaluator[WriteTsv] {
-    override def evaluateType(a: WriteTsv, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: WriteTsv,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomArrayType(WomStringType))).map(_ => WomSingleFileType)
+      validateParamType(a.param, linkedValues, WomArrayType(WomArrayType(WomStringType)), typeAliases).map(_ =>
+        WomSingleFileType
+      )
   }
 
   implicit val writeMapFunctionEvaluator: TypeEvaluator[WriteMap] = new TypeEvaluator[WriteMap] {
-    override def evaluateType(a: WriteMap, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: WriteMap,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType)).map(_ => WomSingleFileType)
+      validateParamType(a.param, linkedValues, WomMapType(WomAnyType, WomAnyType), typeAliases).map(_ =>
+        WomSingleFileType
+      )
   }
 
   implicit val writeObjectFunctionEvaluator: TypeEvaluator[WriteObject] = new TypeEvaluator[WriteObject] {
-    override def evaluateType(a: WriteObject, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: WriteObject,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomObjectType).map(_ => WomSingleFileType)
+      validateParamType(a.param, linkedValues, WomObjectType, typeAliases).map(_ => WomSingleFileType)
   }
 
   implicit val writeObjectsFunctionEvaluator: TypeEvaluator[WriteObjects] = new TypeEvaluator[WriteObjects] {
-    override def evaluateType(a: WriteObjects, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: WriteObjects,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomObjectType)).map(_ => WomSingleFileType)
+      validateParamType(a.param, linkedValues, WomArrayType(WomObjectType), typeAliases).map(_ => WomSingleFileType)
   }
 
   implicit val writeJsonFunctionEvaluator: TypeEvaluator[WriteJson] = new TypeEvaluator[WriteJson] {
-    override def evaluateType(a: WriteJson, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: WriteJson,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      a.param.evaluateType(linkedValues).flatMap {
+      a.param.evaluateType(linkedValues, typeAliases).flatMap {
         case v
             if WomBooleanType.isCoerceableFrom(v) ||
               WomIntegerType.isCoerceableFrom(v) ||
@@ -160,17 +218,23 @@ object EngineFunctionEvaluators {
   }
 
   implicit val rangeFunctionEvaluator: TypeEvaluator[Range] = new TypeEvaluator[Range] {
-    override def evaluateType(a: Range, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Range,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomIntegerType).map(_ => WomArrayType(WomIntegerType))
+      validateParamType(a.param, linkedValues, WomIntegerType, typeAliases).map(_ => WomArrayType(WomIntegerType))
   }
 
   implicit val transposeFunctionEvaluator: TypeEvaluator[Transpose] = new TypeEvaluator[Transpose] {
-    override def evaluateType(a: Transpose, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Transpose,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      a.param.evaluateType(linkedValues).flatMap {
+      a.param.evaluateType(linkedValues, typeAliases).flatMap {
         case a @ WomArrayType(WomArrayType(_)) => a.validNel
         case foundType =>
           s"Invalid parameter '${a.param}'. Expected 'Array[Array[_]]' but got '${foundType.stableName}'".invalidNel
@@ -178,17 +242,23 @@ object EngineFunctionEvaluators {
   }
 
   implicit val lengthFunctionEvaluator: TypeEvaluator[Length] = new TypeEvaluator[Length] {
-    override def evaluateType(a: Length, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Length,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType)).map(_ => WomIntegerType)
+      validateParamType(a.param, linkedValues, WomArrayType(WomAnyType), typeAliases).map(_ => WomIntegerType)
   }
 
   implicit val flattenFunctionEvaluator: TypeEvaluator[Flatten] = new TypeEvaluator[Flatten] {
-    override def evaluateType(a: Flatten, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Flatten,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      a.param.evaluateType(linkedValues).flatMap {
+      a.param.evaluateType(linkedValues, typeAliases).flatMap {
         case WomArrayType(inner @ WomArrayType(_)) => inner.validNel
         case foundType =>
           s"Invalid parameter '${a.param}'. Expected 'Array[Array[_]]' but got '${foundType.stableName}'".invalidNel
@@ -196,10 +266,13 @@ object EngineFunctionEvaluators {
   }
 
   implicit val selectFirstFunctionEvaluator: TypeEvaluator[SelectFirst] = new TypeEvaluator[SelectFirst] {
-    override def evaluateType(a: SelectFirst, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: SelectFirst,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      a.param.evaluateType(linkedValues).flatMap {
+      a.param.evaluateType(linkedValues, typeAliases).flatMap {
         case WomArrayType(WomOptionalType(inner)) => inner.validNel
         case WomArrayType(alreadyNonOptional) => alreadyNonOptional.validNel
         case foundType =>
@@ -208,10 +281,13 @@ object EngineFunctionEvaluators {
   }
 
   implicit val selectAllFunctionEvaluator: TypeEvaluator[SelectAll] = new TypeEvaluator[SelectAll] {
-    override def evaluateType(a: SelectAll, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: SelectAll,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      a.param.evaluateType(linkedValues).flatMap {
+      a.param.evaluateType(linkedValues, typeAliases).flatMap {
         case WomArrayType(WomOptionalType(inner)) => WomArrayType(inner).validNel
         case alreadyNonOptional: WomArrayType => alreadyNonOptional.validNel
         case foundType =>
@@ -220,38 +296,53 @@ object EngineFunctionEvaluators {
   }
 
   implicit val definedFunctionEvaluator: TypeEvaluator[Defined] = new TypeEvaluator[Defined] {
-    override def evaluateType(a: Defined, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Defined,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomOptionalType(WomAnyType)).map(_ => WomBooleanType)
+      validateParamType(a.param, linkedValues, WomOptionalType(WomAnyType), typeAliases).map(_ => WomBooleanType)
   }
 
   implicit val floorFunctionEvaluator: TypeEvaluator[Floor] = new TypeEvaluator[Floor] {
-    override def evaluateType(a: Floor, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Floor,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomFloatType).map(_ => WomIntegerType)
+      validateParamType(a.param, linkedValues, WomFloatType, typeAliases).map(_ => WomIntegerType)
   }
 
   implicit val ceilFunctionEvaluator: TypeEvaluator[Ceil] = new TypeEvaluator[Ceil] {
-    override def evaluateType(a: Ceil, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Ceil,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomFloatType).map(_ => WomIntegerType)
+      validateParamType(a.param, linkedValues, WomFloatType, typeAliases).map(_ => WomIntegerType)
   }
 
   implicit val roundFunctionEvaluator: TypeEvaluator[Round] = new TypeEvaluator[Round] {
-    override def evaluateType(a: Round, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Round,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomFloatType).map(_ => WomIntegerType)
+      validateParamType(a.param, linkedValues, WomFloatType, typeAliases).map(_ => WomIntegerType)
   }
 
   implicit val globFunctionTypeEvaluator: TypeEvaluator[Glob] = new TypeEvaluator[Glob] {
-    override def evaluateType(a: Glob, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Glob,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      validateParamType(a.param, linkedValues, WomStringType).map(_ => WomArrayType(WomSingleFileType))
+      validateParamType(a.param, linkedValues, WomStringType, typeAliases).map(_ => WomArrayType(WomSingleFileType))
   }
 
   implicit val sizeFunctionEvaluator: TypeEvaluator[Size] = new TypeEvaluator[Size] {
@@ -262,14 +353,17 @@ object EngineFunctionEvaluators {
       case _ => false
     }
 
-    override def evaluateType(a: Size, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Size,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = {
       val validatedSecondArg: ErrorOr[Unit] = a.secondParam match {
         case None => ().validNel
-        case Some(arg) => validateParamType(arg, linkedValues, WomStringType).void
+        case Some(arg) => validateParamType(arg, linkedValues, WomStringType, typeAliases).void
       }
-      val validatedFirstArg: ErrorOr[Unit] = a.firstParam.evaluateType(linkedValues).flatMap {
+      val validatedFirstArg: ErrorOr[Unit] = a.firstParam.evaluateType(linkedValues, typeAliases).flatMap {
         case t if suitableSizeType(t) => ().validNel
         case other =>
           s"Invalid first 'size' parameter. Expected File, File? Array[File] or Array[File?] but got ${other.stableName}".invalidNel
@@ -279,25 +373,30 @@ object EngineFunctionEvaluators {
   }
 
   implicit val basenameFunctionEvaluator: TypeEvaluator[Basename] = new TypeEvaluator[Basename] {
-    override def evaluateType(a: Basename, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Basename,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = {
       val validatedSecondArg: ErrorOr[Unit] = a.secondParam match {
         case None => ().validNel
-        case Some(arg) => validateParamType(arg, linkedValues, WomStringType).void
+        case Some(arg) => validateParamType(arg, linkedValues, WomStringType, typeAliases).void
       }
 
-      (validateParamType(a.firstParam, linkedValues, WomSingleFileType), validatedSecondArg) mapN { (_, _) =>
-        WomStringType
+      (validateParamType(a.firstParam, linkedValues, WomSingleFileType, typeAliases), validatedSecondArg) mapN {
+        (_, _) =>
+          WomStringType
       }
     }
   }
 
   private def crossOrZipType(arg1: ExpressionElement,
                              arg2: ExpressionElement,
-                             linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+                             linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                             typeAliases: Map[String, WomType]
   )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
-    (arg1.evaluateType(linkedValues), arg2.evaluateType(linkedValues)) match {
+    (arg1.evaluateType(linkedValues, typeAliases), arg2.evaluateType(linkedValues, typeAliases)) match {
       case (Valid(WomArrayType(left)), Valid(WomArrayType(right))) =>
         WomArrayType(WomPairType(left, right)).validNel
       case (Valid(otherLeft), Valid(WomArrayType(_))) =>
@@ -311,42 +410,55 @@ object EngineFunctionEvaluators {
     }
 
   implicit val zipFunctionEvaluator: TypeEvaluator[Zip] = new TypeEvaluator[Zip] {
-    override def evaluateType(a: Zip, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Zip,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      crossOrZipType(a.arg1, a.arg2, linkedValues)
+      crossOrZipType(a.arg1, a.arg2, linkedValues, typeAliases)
   }
   implicit val crossFunctionEvaluator: TypeEvaluator[Cross] = new TypeEvaluator[Cross] {
-    override def evaluateType(a: Cross, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Cross,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      crossOrZipType(a.arg1, a.arg2, linkedValues)
+      crossOrZipType(a.arg1, a.arg2, linkedValues, typeAliases)
   }
 
   implicit val prefixFunctionEvaluator: TypeEvaluator[Prefix] = new TypeEvaluator[Prefix] {
-    override def evaluateType(a: Prefix, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Prefix,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      (validateParamType(a.prefix, linkedValues, WomStringType),
-       validateParamType(a.array, linkedValues, WomArrayType(WomStringType))
+      (validateParamType(a.prefix, linkedValues, WomStringType, typeAliases),
+       validateParamType(a.array, linkedValues, WomArrayType(WomStringType), typeAliases)
       ) mapN { (_, _) => WomArrayType(WomStringType) }
   }
 
   implicit val subFunctionEvaluator: TypeEvaluator[Sub] = new TypeEvaluator[Sub] {
-    override def evaluateType(a: Sub, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: Sub,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      (validateParamType(a.input, linkedValues, WomSingleFileType),
-       validateParamType(a.pattern, linkedValues, WomSingleFileType),
-       validateParamType(a.replace, linkedValues, WomSingleFileType)
+      (validateParamType(a.input, linkedValues, WomSingleFileType, typeAliases),
+       validateParamType(a.pattern, linkedValues, WomSingleFileType, typeAliases),
+       validateParamType(a.replace, linkedValues, WomSingleFileType, typeAliases)
       ) mapN { (_, _, _) => WomStringType }
   }
 
   def validateParamType(param: ExpressionElement,
                         linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
-                        expectedType: WomType
+                        expectedType: WomType,
+                        typeAliases: Map[String, WomType]
   )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
-    param.evaluateType(linkedValues).flatMap { foundType =>
+    param.evaluateType(linkedValues, Map()).flatMap { foundType =>
       if (expectedType.isCoerceableFrom(foundType)) { foundType.validNel }
       else {
         s"Invalid parameter '$param'. Expected '${expectedType.stableName}' but got '${foundType.stableName}'".invalidNel
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LiteralEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LiteralEvaluators.scala
index 9e74672f5bc..ff04850866d 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LiteralEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LiteralEvaluators.scala
@@ -16,7 +16,8 @@ object LiteralEvaluators {
   implicit val primitiveTypeEvaluator: TypeEvaluator[PrimitiveLiteralExpressionElement] =
     new TypeEvaluator[PrimitiveLiteralExpressionElement] {
       override def evaluateType(a: PrimitiveLiteralExpressionElement,
-                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                                typeAliases: Map[String, WomType]
       )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
         a.value.womType.validNel
     }
@@ -24,38 +25,55 @@ object LiteralEvaluators {
   implicit val noneLiteralTypeEvaluator: TypeEvaluator[NoneLiteralElement.type] =
     new TypeEvaluator[NoneLiteralElement.type] {
       override def evaluateType(a: NoneLiteralElement.type,
-                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                                typeAliases: Map[String, WomType]
       )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] =
         WomOptionalType(WomNothingType).validNel
     }
 
   implicit val objectLiteralTypeEvaluator: TypeEvaluator[ObjectLiteral] = new TypeEvaluator[ObjectLiteral] {
-    override def evaluateType(a: ObjectLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: ObjectLiteral,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = WomObjectType.validNel
   }
 
   implicit val stringLiteralTypeEvaluator: TypeEvaluator[StringLiteral] = new TypeEvaluator[StringLiteral] {
-    override def evaluateType(a: StringLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: StringLiteral,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = WomStringType.validNel
   }
 
   implicit val stringExpressionTypeEvaluator: TypeEvaluator[StringExpression] = new TypeEvaluator[StringExpression] {
-    override def evaluateType(a: StringExpression, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: StringExpression,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = WomStringType.validNel
   }
 
   implicit val mapLiteralTypeEvaluator: TypeEvaluator[MapLiteral] = new TypeEvaluator[MapLiteral] {
-    override def evaluateType(a: MapLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: MapLiteral,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = {
 
-      val keyTypes = a.elements.keySet.toList.traverse { x: ExpressionElement => x.evaluateType(linkedValues) }
+      val keyTypes = a.elements.keySet.toList.traverse { x: ExpressionElement =>
+        x.evaluateType(linkedValues, typeAliases)
+      }
       val commonKeyType: ErrorOr[WomType] = keyTypes.map(WomType.homogeneousTypeFromTypes)
 
-      val valueTypes = a.elements.values.toList.traverse { y: ExpressionElement => y.evaluateType(linkedValues) }
+      val valueTypes = a.elements.values.toList.traverse { y: ExpressionElement =>
+        y.evaluateType(linkedValues, typeAliases)
+      }
       val commonValueType: ErrorOr[WomType] = valueTypes.map(WomType.homogeneousTypeFromTypes)
 
       (commonKeyType, commonValueType) mapN { (k, v) => WomMapType(k, v) }
@@ -63,11 +81,14 @@ object LiteralEvaluators {
   }
 
   implicit val arrayLiteralTypeEvaluator: TypeEvaluator[ArrayLiteral] = new TypeEvaluator[ArrayLiteral] {
-    override def evaluateType(a: ArrayLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: ArrayLiteral,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = {
 
-      val types = a.elements.toList.traverse { x: ExpressionElement => x.evaluateType(linkedValues) }
+      val types = a.elements.toList.traverse { x: ExpressionElement => x.evaluateType(linkedValues, typeAliases) }
       val commonType: ErrorOr[WomType] = types.map(WomType.homogeneousTypeFromTypes)
 
       commonType.map(WomArrayType.apply(_, guaranteedNonEmpty = a.elements.nonEmpty))
@@ -75,12 +96,15 @@ object LiteralEvaluators {
   }
 
   implicit val pairLiteralTypeEvaluator: TypeEvaluator[PairLiteral] = new TypeEvaluator[PairLiteral] {
-    override def evaluateType(a: PairLiteral, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: PairLiteral,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] = {
 
-      val leftType = a.left.evaluateType(linkedValues)
-      val rightType = a.right.evaluateType(linkedValues)
+      val leftType = a.left.evaluateType(linkedValues, typeAliases: Map[String, WomType])
+      val rightType = a.right.evaluateType(linkedValues, typeAliases: Map[String, WomType])
 
       (leftType, rightType) mapN { (l, r) => WomPairType(l, r) }
     }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LookupEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LookupEvaluators.scala
index 0221390e8ca..1d08616de47 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LookupEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/LookupEvaluators.scala
@@ -15,8 +15,11 @@ import wom.types._
 object LookupEvaluators {
 
   implicit val identifierLookupTypeEvaluator: TypeEvaluator[IdentifierLookup] = new TypeEvaluator[IdentifierLookup] {
-    override def evaluateType(a: IdentifierLookup, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: IdentifierLookup,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
       linkedValues.collectFirst {
         case (UnlinkedIdentifierHook(id), gen) if a.identifier == id => gen.womType
@@ -32,9 +35,10 @@ object LookupEvaluators {
   implicit val expressionMemberAccessEvaluator: TypeEvaluator[ExpressionMemberAccess] =
     new TypeEvaluator[ExpressionMemberAccess] {
       override def evaluateType(a: ExpressionMemberAccess,
-                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                                typeAliases: Map[String, WomType]
       )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
-        val baseType = a.expression.evaluateType(linkedValues)
+        val baseType = a.expression.evaluateType(linkedValues, typeAliases)
         baseType flatMap { doLookup(_, a.memberAccessTail) }
       }
     }
@@ -42,7 +46,8 @@ object LookupEvaluators {
   implicit val identifierMemberAccessEvaluator: TypeEvaluator[IdentifierMemberAccess] =
     new TypeEvaluator[IdentifierMemberAccess] {
       override def evaluateType(a: IdentifierMemberAccess,
-                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+                                linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                                typeAliases: Map[String, WomType]
       )(implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]): ErrorOr[WomType] = {
         val generatedValueHandle =
           linkedValues.get(UnlinkedCallOutputOrIdentifierAndMemberAccessHook(a.first, a.second))
@@ -64,10 +69,16 @@ object LookupEvaluators {
     }
 
   implicit val indexAccessTypeEvaluator: TypeEvaluator[IndexAccess] = new TypeEvaluator[IndexAccess] {
-    override def evaluateType(a: IndexAccess, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-      implicit expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
+    override def evaluateType(a: IndexAccess,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
+      expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      (a.expressionElement.evaluateType(linkedValues), a.index.evaluateType(linkedValues), a.index.validNel) flatMapN {
+      (a.expressionElement.evaluateType(linkedValues, typeAliases),
+       a.index.evaluateType(linkedValues, typeAliases),
+       a.index.validNel
+      ) flatMapN {
         case (a: WomArrayType, WomIntegerType, _) => a.memberType.validNel
         case (WomMapType(keyType, valueType), lookupType, _) if keyType.isCoerceableFrom(lookupType) =>
           valueType.validNel
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/TernaryIfEvaluator.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/TernaryIfEvaluator.scala
index ca4b1d61a7f..3d53d4bc528 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/TernaryIfEvaluator.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/TernaryIfEvaluator.scala
@@ -13,13 +13,16 @@ import wom.types.{WomBooleanType, WomType}
 
 object TernaryIfEvaluator {
   implicit val ternaryIfEvaluator: TypeEvaluator[TernaryIf] = new TypeEvaluator[TernaryIf] {
-    override def evaluateType(a: TernaryIf, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: TernaryIf,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      a.condition.evaluateType(linkedValues) flatMap {
+      a.condition.evaluateType(linkedValues, typeAliases) flatMap {
         case WomBooleanType =>
-          (a.ifTrue.evaluateType(linkedValues): ErrorOr[WomType],
-           a.ifFalse.evaluateType(linkedValues): ErrorOr[WomType]
+          (a.ifTrue.evaluateType(linkedValues, typeAliases): ErrorOr[WomType],
+           a.ifFalse.evaluateType(linkedValues, typeAliases): ErrorOr[WomType]
           ) mapN { (tType, fType) => WomType.homogeneousTypeFromTypes(Seq(tType, fType)) }
         case other => s"Condition should have evaluated to a Boolean but instead got ${other.stableName}".invalidNel
       }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/UnaryOperatorEvaluators.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/UnaryOperatorEvaluators.scala
index 3c2cb62721e..23766b48270 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/UnaryOperatorEvaluators.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/linking/expression/types/UnaryOperatorEvaluators.scala
@@ -19,9 +19,12 @@ object UnaryOperatorEvaluators {
   implicit val logicalNotEvaluator: TypeEvaluator[LogicalNot] = forOperation(_.not)
 
   private def forOperation[A <: UnaryOperation](op: WomType => Try[WomType]) = new TypeEvaluator[A] {
-    override def evaluateType(a: A, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(implicit
+    override def evaluateType(a: A,
+                              linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                              typeAliases: Map[String, WomType]
+    )(implicit
       expressionTypeEvaluator: TypeEvaluator[ExpressionElement]
     ): ErrorOr[WomType] =
-      a.argument.evaluateType(linkedValues) flatMap { op(_).toErrorOr }
+      a.argument.evaluateType(linkedValues, typeAliases) flatMap { op(_).toErrorOr }
   }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/WdlomWomExpression.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/WdlomWomExpression.scala
index f94c15aa7b7..7bfc61907a9 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/WdlomWomExpression.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/expression/WdlomWomExpression.scala
@@ -15,7 +15,8 @@ import wom.types._
 import wom.values.WomValue
 
 final case class WdlomWomExpression private (expressionElement: ExpressionElement,
-                                             linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle]
+                                             linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+                                             typeAliases: Map[String, WomType]
 )(implicit
   expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
   fileEvaluator: FileEvaluator[ExpressionElement],
@@ -36,7 +37,7 @@ final case class WdlomWomExpression private (expressionElement: ExpressionElemen
   override def evaluateValue(inputValues: Map[String, WomValue], ioFunctionSet: IoFunctionSet): ErrorOr[WomValue] =
     expressionElement.evaluateValue(inputValues, ioFunctionSet, None) map { _.value }
 
-  private lazy val evaluatedType = expressionElement.evaluateType(linkedValues)
+  private lazy val evaluatedType = expressionElement.evaluateType(linkedValues, typeAliases)
   // NB types can be determined using the linked values, so we don't need the inputMap:
   override def evaluateType(inputMap: Map[String, WomType]): ErrorOr[WomType] = evaluatedType
 
@@ -52,14 +53,16 @@ final case class WdlomWomExpression private (expressionElement: ExpressionElemen
 }
 
 object WdlomWomExpression {
-  def make(expressionElement: ExpressionElement, linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle])(
-    implicit
+  def make(expressionElement: ExpressionElement,
+           linkedValues: Map[UnlinkedConsumedValueHook, GeneratedValueHandle],
+           typeAliases: Map[String, WomType]
+  )(implicit
     expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
     fileEvaluator: FileEvaluator[ExpressionElement],
     typeEvaluator: TypeEvaluator[ExpressionElement],
     valueEvaluator: ValueEvaluator[ExpressionElement]
   ): ErrorOr[WdlomWomExpression] = {
-    val candidate = WdlomWomExpression(expressionElement, linkedValues)
+    val candidate = WdlomWomExpression(expressionElement, linkedValues, typeAliases)
     candidate.evaluatedType.contextualizeErrors(s"process expression '${candidate.sourceString}'") map { _ =>
       candidate
     }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala
index 6aa36184aef..7e255f27cc9 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/CallElementToGraphNode.scala
@@ -82,7 +82,9 @@ object CallElementToGraphNode {
      *
      * @return ErrorOr of LocalName(key) mapped to ExpressionNode(value).
      */
-    def expressionNodeMappings(callable: Callable): ErrorOr[Map[LocalName, AnonymousExpressionNode]] = {
+    def expressionNodeMappings(callable: Callable,
+                               typeAliases: Map[String, WomType]
+    ): ErrorOr[Map[LocalName, AnonymousExpressionNode]] = {
 
       def hasDeclaration(callable: Callable, name: String): Boolean = callable match {
         case t: TaskDefinition =>
@@ -101,7 +103,8 @@ object CallElementToGraphNode {
                   case _: CallableTaskDefinition => TaskCallInputExpressionNode.apply _
                   case _ => PlainAnonymousExpressionNode.apply _
                 }
-                WdlomWomExpression.make(expression, a.linkableValues) flatMap { wdlomWomExpression =>
+
+                WdlomWomExpression.make(expression, a.linkableValues, typeAliases) flatMap { wdlomWomExpression =>
                   val requiredInputType = i match {
                     case _: OverridableInputDefinitionWithDefault => WomOptionalType(i.womType).flatOptionalType
                     case _ => i.womType
@@ -238,7 +241,7 @@ object CallElementToGraphNode {
 
     val result = for {
       callable <- callableValidation
-      mappings <- expressionNodeMappings(callable)
+      mappings <- expressionNodeMappings(callable, a.availableTypeAliases)
       identifier = WomIdentifier(localName = callName, fullyQualifiedName = a.workflowName + "." + callName)
       upstream <- findUpstreamCalls(a.node.afters.toList)
       result = callNodeBuilder.build(identifier,
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala
index 7c53c5c0cd6..43f18f8754f 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/IfElementToGraphNode.scala
@@ -33,7 +33,7 @@ object IfElementToGraphNode {
     val graphElements = a.node.graphElements
 
     val conditionWomExpressionV: ErrorOr[WdlomWomExpression] =
-      WdlomWomExpression.make(conditionExpression, a.linkableValues)
+      WdlomWomExpression.make(conditionExpression, a.linkableValues, a.availableTypeAliases)
     val conditionExpressionNodeValidation: ErrorOr[AnonymousExpressionNode] = conditionWomExpressionV flatMap {
       conditionWomExpression =>
         AnonymousExpressionNode.fromInputMapping(WomIdentifier("if_condition"),
@@ -43,10 +43,11 @@ object IfElementToGraphNode {
         )
     }
 
-    val conditionVariableTypeValidation: ErrorOr[Unit] = conditionExpression.evaluateType(a.linkableValues) flatMap {
-      case WomBooleanType | WomAnyType => ().validNel
-      case other => s"Invalid type for condition variable: ${other.stableName}".invalidNel
-    }
+    val conditionVariableTypeValidation: ErrorOr[Unit] =
+      conditionExpression.evaluateType(a.linkableValues, a.availableTypeAliases) flatMap {
+        case WomBooleanType | WomAnyType => ().validNel
+        case other => s"Invalid type for condition variable: ${other.stableName}".invalidNel
+      }
 
     final case class RequiredOuterPorts(valueGeneratorPorts: Map[String, OutputPort],
                                         completionPorts: Map[String, CallNode]
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala
index a1a3d5c4d76..126f2b99345 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/graph/ScatterElementToGraphNode.scala
@@ -61,7 +61,7 @@ object ScatterElementToGraphNode {
     val graphElements = a.node.graphElements
 
     val scatterWomExpressionV: ErrorOr[WdlomWomExpression] =
-      WdlomWomExpression.make(scatterExpression, a.linkableValues)
+      WdlomWomExpression.make(scatterExpression, a.linkableValues, a.availableTypeAliases)
     val scatterExpressionNodeValidation: ErrorOr[AnonymousExpressionNode] = scatterWomExpressionV flatMap {
       scatterWomExpression =>
         AnonymousExpressionNode.fromInputMapping(WomIdentifier(scatterVariableName),
@@ -71,11 +71,12 @@ object ScatterElementToGraphNode {
         )
     }
 
-    val scatterVariableTypeValidation: ErrorOr[WomType] = scatterExpression.evaluateType(a.linkableValues) flatMap {
-      case a: WomArrayType => a.memberType.validNel
-      case WomAnyType => WomAnyType.validNel
-      case other => s"Invalid type for scatter variable '$scatterVariableName': ${other.stableName}".invalidNel
-    }
+    val scatterVariableTypeValidation: ErrorOr[WomType] =
+      scatterExpression.evaluateType(a.linkableValues, a.availableTypeAliases) flatMap {
+        case a: WomArrayType => a.memberType.validNel
+        case WomAnyType => WomAnyType.validNel
+        case other => s"Invalid type for scatter variable '$scatterVariableName': ${other.stableName}".invalidNel
+      }
 
     final case class RequiredOuterPorts(valueGeneratorPorts: Map[String, OutputPort],
                                         completionPorts: Map[String, CallNode]

From 3cf06bfbd6b55a2dac674eed4ca53aae38656119 Mon Sep 17 00:00:00 2001
From: rsaperst <156102201+rsaperst@users.noreply.github.com>
Date: Thu, 11 Apr 2024 11:34:36 -0400
Subject: [PATCH 306/326] [WX-1468] Implement `returnCodes` runtime attribute
 (#7389)

Co-authored-by: Ryan Saperstein <rsaperst@wmd55-b47.hsd1.ma.comcast.net>
Co-authored-by: Ryan Saperstein <rsaperst@wmd55-b47.broadinstitute.org>
---
 .../StandardAsyncExecutionActor.scala         |   8 +-
 .../ContinueOnReturnCodeValidation.scala      |  17 ++-
 ...ckendWorkflowInitializationActorSpec.scala |  23 ++-
 ...alidatedRuntimeAttributesBuilderSpec.scala |   6 +-
 .../validation/ContinueOnReturnCodeSpec.scala |   8 +
 .../RuntimeAttributesValidationSpec.scala     |  18 ++-
 .../failing_return_code.test                  |  11 ++
 .../failing_return_code.wdl                   |  20 +++
 ...urn_codes_and_continue_on_return_code.test |  11 ++
 ...turn_codes_and_continue_on_return_code.wdl |  21 +++
 .../standardTestCases/return_codes.test       |  11 ++
 .../return_codes/return_codes.wdl             |  69 +++++++++
 ...turn_codes_invalid_on_old_wdl_version.test |  11 ++
 ...eturn_codes_invalid_on_old_wdl_version.wdl |  18 +++
 ...turn_codes_and_continue_on_return_code.wdl |  55 +++++++
 ...rn_codes_and_continue_on_return_codes.test |  11 ++
 .../aws/AwsBatchRuntimeAttributesSpec.scala   |   3 +-
 .../GcpBatchRuntimeAttributesSpec.scala       |   3 +-
 .../PipelinesApiRuntimeAttributesSpec.scala   |   3 +-
 .../impl/tes/TesRuntimeAttributesSpec.scala   |   3 +-
 .../biscayne/wdlom2wom/package.scala          |  93 +++++++++++-
 .../cascades/wdlom2wom/package.scala          |  93 +++++++++++-
 ...DefinitionElementToWomTaskDefinition.scala | 137 ++++++++++--------
 .../main/scala/wom/RuntimeAttributes.scala    |   4 +
 24 files changed, 575 insertions(+), 82 deletions(-)
 create mode 100644 centaur/src/main/resources/standardTestCases/failing_return_code.test
 create mode 100644 centaur/src/main/resources/standardTestCases/failing_return_code/failing_return_code.wdl
 create mode 100644 centaur/src/main/resources/standardTestCases/invalid_return_codes_and_continue_on_return_code.test
 create mode 100644 centaur/src/main/resources/standardTestCases/invalid_return_codes_and_continue_on_return_code/invalid_return_codes_and_continue_on_return_code.wdl
 create mode 100644 centaur/src/main/resources/standardTestCases/return_codes.test
 create mode 100644 centaur/src/main/resources/standardTestCases/return_codes/return_codes.wdl
 create mode 100644 centaur/src/main/resources/standardTestCases/return_codes_invalid_on_old_wdl_version.test
 create mode 100644 centaur/src/main/resources/standardTestCases/return_codes_invalid_on_old_wdl_version/return_codes_invalid_on_old_wdl_version.wdl
 create mode 100644 centaur/src/main/resources/standardTestCases/valid_return_codes_and_continue_on_return_code/valid_return_codes_and_continue_on_return_code.wdl
 create mode 100644 centaur/src/main/resources/standardTestCases/valid_return_codes_and_continue_on_return_codes.test

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 1b183a67646..bbb796220c4 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -748,10 +748,10 @@ trait StandardAsyncExecutionActor
     RuntimeAttributesValidation.extract(FailOnStderrValidation.instance, validatedRuntimeAttributes)
 
   /**
-    * Returns the behavior for continuing on the return code, obtained by converting `returnCodeContents` to an Int.
-    *
-    * @return the behavior for continuing on the return code.
-    */
+   * Returns the behavior for continuing on the return code, obtained by converting `returnCodeContents` to an Int.
+   *
+   * @return the behavior for continuing on the return code.
+   */
   lazy val continueOnReturnCode: ContinueOnReturnCode =
     RuntimeAttributesValidation.extract(ContinueOnReturnCodeValidation.instance, validatedRuntimeAttributes)
 
diff --git a/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala b/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala
index 14dfb369d77..7573909eb69 100644
--- a/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala
+++ b/backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala
@@ -3,8 +3,8 @@ package cromwell.backend.validation
 import cats.data.Validated.{Invalid, Valid}
 import cats.implicits._
 import com.typesafe.config.Config
-import cromwell.backend.validation.RuntimeAttributesValidation._
 import common.validation.ErrorOr._
+import cromwell.backend.validation.RuntimeAttributesValidation.validateInt
 import wom.RuntimeAttributesKeys
 import wom.types._
 import wom.values._
@@ -23,8 +23,11 @@ import scala.util.Try
   * `default` a validation with the default value specified by the reference.conf file.
   */
 object ContinueOnReturnCodeValidation {
-  lazy val instance: RuntimeAttributesValidation[ContinueOnReturnCode] = new ContinueOnReturnCodeValidation
-  def default(runtimeConfig: Option[Config]): RuntimeAttributesValidation[ContinueOnReturnCode] =
+  lazy val instance: RuntimeAttributesValidation[ContinueOnReturnCode] =
+    new ContinueOnReturnCodeValidation
+  def default(
+    runtimeConfig: Option[Config]
+  ): RuntimeAttributesValidation[ContinueOnReturnCode] =
     instance.withDefault(configDefaultWdlValue(runtimeConfig) getOrElse WomInteger(0))
   def configDefaultWdlValue(runtimeConfig: Option[Config]): Option[WomValue] =
     instance.configDefaultWomValue(runtimeConfig)
@@ -39,6 +42,7 @@ class ContinueOnReturnCodeValidation extends RuntimeAttributesValidation[Continu
   override def validateValue: PartialFunction[WomValue, ErrorOr[ContinueOnReturnCode]] = {
     case WomBoolean(value) => ContinueOnReturnCodeFlag(value).validNel
     case WomString(value) if Try(value.toBoolean).isSuccess => ContinueOnReturnCodeFlag(value.toBoolean).validNel
+    case WomString(value) if value.equals("*") => ContinueOnReturnCodeFlag(true).validNel
     case WomString(value) if Try(value.toInt).isSuccess => ContinueOnReturnCodeSet(Set(value.toInt)).validNel
     case WomInteger(value) => ContinueOnReturnCodeSet(Set(value)).validNel
     case value @ WomArray(_, seq) =>
@@ -47,22 +51,25 @@ class ContinueOnReturnCodeValidation extends RuntimeAttributesValidation[Continu
         case Valid(ints) => ContinueOnReturnCodeSet(ints.toSet).validNel
         case Invalid(_) => invalidValueFailure(value)
       }
+    case value => invalidValueFailure(value)
   }
 
   override def validateExpression: PartialFunction[WomValue, Boolean] = {
     case WomBoolean(_) => true
     case WomString(value) if Try(value.toInt).isSuccess => true
     case WomString(value) if Try(value.toBoolean).isSuccess => true
+    case WomString(value) if value.equals("*") => true
     case WomInteger(_) => true
     case WomArray(WomArrayType(WomStringType), elements) =>
       elements forall { value =>
         Try(value.valueString.toInt).isSuccess
       }
     case WomArray(WomArrayType(WomIntegerType), _) => true
+    case _ => false
   }
 
-  override protected def missingValueMessage: String = s"Expecting $key" +
-    " runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+  override protected def missingValueMessage: String = "Expecting returnCodes/continueOnReturnCode" +
+    " runtime attribute to be either a String '*', 'true', or 'false', a Boolean, or an Array[Int]."
 
   override def usedInCallCaching: Boolean = true
 }
diff --git a/backend/src/test/scala/cromwell/backend/BackendWorkflowInitializationActorSpec.scala b/backend/src/test/scala/cromwell/backend/BackendWorkflowInitializationActorSpec.scala
index 4fc1efd7381..c4688d759f8 100644
--- a/backend/src/test/scala/cromwell/backend/BackendWorkflowInitializationActorSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/BackendWorkflowInitializationActorSpec.scala
@@ -62,6 +62,11 @@ class BackendWorkflowInitializationActorSpec
       "read_int(\"bad file\")"
     )
 
+    val starRow = Table(
+      "value",
+      "*"
+    )
+
     val invalidWdlValueRows = Table(
       "womValue",
       WomString(""),
@@ -201,6 +206,21 @@ class BackendWorkflowInitializationActorSpec
       // NOTE: expressions are never valid to validate
     }
 
+    forAll(starRow) { value =>
+      val womValue = WomString(value)
+      val result = true
+      testContinueOnReturnCode(Option(womValue)) should be(result)
+      ContinueOnReturnCodeValidation.default(optionalConfig).validateOptionalWomValue(Option(womValue)) should be(
+        result
+      )
+      val valid =
+        ContinueOnReturnCodeValidation
+          .default(optionalConfig)
+          .validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
+      valid.isValid should be(result)
+      valid.toEither.toOption.get should be(ContinueOnReturnCodeFlag(true))
+    }
+
     forAll(invalidWdlValueRows) { womValue =>
       val result = false
       testContinueOnReturnCode(Option(womValue)) should be(result)
@@ -213,7 +233,8 @@ class BackendWorkflowInitializationActorSpec
           .validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
       valid.toEither.swap.toOption.get.toList should contain theSameElementsAs List(
-        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+        "Expecting returnCodes/continueOnReturnCode" +
+          " runtime attribute to be either a String '*', 'true', or 'false', a Boolean, or an Array[Int]."
       )
     }
 
diff --git a/backend/src/test/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilderSpec.scala b/backend/src/test/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilderSpec.scala
index bd3024eda9a..35c57983e6e 100644
--- a/backend/src/test/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilderSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilderSpec.scala
@@ -136,7 +136,8 @@ class StandardValidatedRuntimeAttributesBuilderSpec
       val runtimeAttributes = Map("continueOnReturnCode" -> WomString("value"))
       assertRuntimeAttributesFailedCreation(
         runtimeAttributes,
-        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+        "Expecting returnCodes/continueOnReturnCode" +
+          " runtime attribute to be either a String '*', 'true', or 'false', a Boolean, or an Array[Int]."
       )
     }
 
@@ -152,7 +153,6 @@ class StandardValidatedRuntimeAttributesBuilderSpec
                                                 workflowOptions = workflowOptions
       )
     }
-
   }
 
   val defaultLogger: Logger = LoggerFactory.getLogger(classOf[StandardValidatedRuntimeAttributesBuilderSpec])
@@ -188,7 +188,7 @@ class StandardValidatedRuntimeAttributesBuilderSpec
     docker should be(expectedRuntimeAttributes(DockerKey).asInstanceOf[Option[String]])
     failOnStderr should be(expectedRuntimeAttributes(FailOnStderrKey).asInstanceOf[Boolean])
     continueOnReturnCode should be(
-      expectedRuntimeAttributes(ContinueOnReturnCodeKey).asInstanceOf[ContinueOnReturnCode]
+      expectedRuntimeAttributes(ContinueOnReturnCodeKey)
     )
     ()
   }
diff --git a/backend/src/test/scala/cromwell/backend/validation/ContinueOnReturnCodeSpec.scala b/backend/src/test/scala/cromwell/backend/validation/ContinueOnReturnCodeSpec.scala
index e0ff75d3176..bd102bc27c1 100644
--- a/backend/src/test/scala/cromwell/backend/validation/ContinueOnReturnCodeSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/validation/ContinueOnReturnCodeSpec.scala
@@ -37,5 +37,13 @@ class ContinueOnReturnCodeSpec extends AnyWordSpecLike with CromwellTimeoutSpec
         ContinueOnReturnCodeSet(set).continueFor(returnCode) should be(expectedContinue)
       }
     }
+
+    "continue on expected return code string" in {
+      val flagTests = Table(("string", "returnCode", "expectedContinue"), ("*", 0, true), ("*", 1, true))
+
+      forAll(flagTests) { (flag, returnCode, expectedContinue) =>
+        ContinueOnReturnCodeFlag(flag == "*").continueFor(returnCode) should be(expectedContinue)
+      }
+    }
   }
 }
diff --git a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala
index 8f692d6486a..dafca35e1b6 100644
--- a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala
+++ b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala
@@ -184,7 +184,8 @@ class RuntimeAttributesValidationSpec
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) =>
           assert(
-            e.head == "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+            e.head == "Expecting returnCodes/continueOnReturnCode" +
+              " runtime attribute to be either a String '*', 'true', or 'false', a Boolean, or an Array[Int]."
           )
       }
     }
@@ -212,7 +213,8 @@ class RuntimeAttributesValidationSpec
         case Valid(_) => fail("A failure was expected.")
         case Invalid(e) =>
           assert(
-            e.head == "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+            e.head == "Expecting returnCodes/continueOnReturnCode" +
+              " runtime attribute to be either a String '*', 'true', or 'false', a Boolean, or an Array[Int]."
           )
       }
     }
@@ -228,6 +230,18 @@ class RuntimeAttributesValidationSpec
       }
     }
 
+    "return success when tries to validate a valid returnCodes string entry" in {
+      val returnCodesValue = Some(WomString("*"))
+      val result = RuntimeAttributesValidation.validateContinueOnReturnCode(
+        returnCodesValue,
+        "Failed to get return code mandatory key from runtime attributes".invalidNel
+      )
+      result match {
+        case Valid(x) => assert(x == ContinueOnReturnCodeFlag(true))
+        case Invalid(e) => fail(e.toList.mkString(" "))
+      }
+    }
+
     "return success when tries to validate a valid Integer memory entry" in {
       val expectedGb = 1
       val memoryValue = Some(WomInteger(1 << 30))
diff --git a/centaur/src/main/resources/standardTestCases/failing_return_code.test b/centaur/src/main/resources/standardTestCases/failing_return_code.test
new file mode 100644
index 00000000000..163715222cf
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/failing_return_code.test
@@ -0,0 +1,11 @@
+name: failing_return_code
+testFormat: workflowfailure
+
+files {
+  workflow: failing_return_code/failing_return_code.wdl
+}
+
+metadata {
+  workflowName: FailingReturnCode
+  status: Failed
+}
diff --git a/centaur/src/main/resources/standardTestCases/failing_return_code/failing_return_code.wdl b/centaur/src/main/resources/standardTestCases/failing_return_code/failing_return_code.wdl
new file mode 100644
index 00000000000..f393698d2b7
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/failing_return_code/failing_return_code.wdl
@@ -0,0 +1,20 @@
+version development-1.1
+
+workflow FailingReturnCode {
+    call FailingReturnCodeSet
+}
+
+task FailingReturnCodeSet {
+    meta {
+        volatile: true
+    }
+
+    command <<<
+        exit 1
+    >>>
+
+    runtime {
+        returnCodes: [0, 5, 10]
+        docker: "ubuntu:latest"
+    }
+}
diff --git a/centaur/src/main/resources/standardTestCases/invalid_return_codes_and_continue_on_return_code.test b/centaur/src/main/resources/standardTestCases/invalid_return_codes_and_continue_on_return_code.test
new file mode 100644
index 00000000000..8f55af82262
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/invalid_return_codes_and_continue_on_return_code.test
@@ -0,0 +1,11 @@
+name: invalid_return_codes_and_continue_on_return_code
+testFormat: workflowfailure
+
+files {
+  workflow: invalid_return_codes_and_continue_on_return_code/invalid_return_codes_and_continue_on_return_code.wdl
+}
+
+metadata {
+  workflowName: InvalidReturnCodeAndContinueOnReturnCode
+  status: Failed
+}
diff --git a/centaur/src/main/resources/standardTestCases/invalid_return_codes_and_continue_on_return_code/invalid_return_codes_and_continue_on_return_code.wdl b/centaur/src/main/resources/standardTestCases/invalid_return_codes_and_continue_on_return_code/invalid_return_codes_and_continue_on_return_code.wdl
new file mode 100644
index 00000000000..ea2233ab355
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/invalid_return_codes_and_continue_on_return_code/invalid_return_codes_and_continue_on_return_code.wdl
@@ -0,0 +1,21 @@
+version development-1.1
+
+workflow InvalidReturnCodeAndContinueOnReturnCode {
+    call InvalidReturnCodeContinueOnReturnCode
+}
+
+task InvalidReturnCodeContinueOnReturnCode {
+    meta {
+        volatile: true
+    }
+
+    command <<<
+        exit 1
+    >>>
+
+    runtime {
+        docker: "ubuntu:latest"
+        returnCodes: [5, 10, 15]
+        continueOnReturnCode: [1]
+    }
+}
diff --git a/centaur/src/main/resources/standardTestCases/return_codes.test b/centaur/src/main/resources/standardTestCases/return_codes.test
new file mode 100644
index 00000000000..7528064f4c8
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/return_codes.test
@@ -0,0 +1,11 @@
+name: return_codes
+testFormat: workflowsuccess
+
+files {
+  workflow: return_codes/return_codes.wdl
+}
+
+metadata {
+  workflowName: ReturnCodeValidation
+  status: Succeeded
+}
diff --git a/centaur/src/main/resources/standardTestCases/return_codes/return_codes.wdl b/centaur/src/main/resources/standardTestCases/return_codes/return_codes.wdl
new file mode 100644
index 00000000000..21e1da37650
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/return_codes/return_codes.wdl
@@ -0,0 +1,69 @@
+version development-1.1
+
+workflow ReturnCodeValidation {
+    call ReturnCodeSet1
+    call ReturnCodeSet2
+    call ReturnCodeSet3
+    call ReturnCodeString
+}
+
+task ReturnCodeSet1 {
+    meta {
+        volatile: true
+    }
+
+    command <<<
+        exit 1
+    >>>
+
+    runtime {
+        docker: "ubuntu:latest"
+        returnCodes: [1]
+    }
+}
+
+task ReturnCodeSet2 {
+    meta {
+        volatile: true
+    }
+
+    command <<<
+        exit 200
+    >>>
+
+    runtime {
+        docker: "ubuntu:latest"
+        returnCodes: [1, 123, 200]
+    }
+}
+
+task ReturnCodeSet3 {
+    meta {
+        volatile: true
+    }
+
+    command <<<
+        exit 10
+    >>>
+
+    runtime {
+        docker: "ubuntu:latest"
+        returnCodes: 10
+    }
+}
+
+
+task ReturnCodeString {
+    meta {
+        volatile: true
+    }
+
+    command <<<
+        exit 500
+    >>>
+
+    runtime {
+        docker: "ubuntu:latest"
+        returnCodes: "*"
+    }
+}
diff --git a/centaur/src/main/resources/standardTestCases/return_codes_invalid_on_old_wdl_version.test b/centaur/src/main/resources/standardTestCases/return_codes_invalid_on_old_wdl_version.test
new file mode 100644
index 00000000000..20c07a6e051
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/return_codes_invalid_on_old_wdl_version.test
@@ -0,0 +1,11 @@
+name: return_codes_invalid_on_old_wdl_version
+testFormat: workflowfailure
+
+files {
+  workflow: return_codes_invalid_on_old_wdl_version/return_codes_invalid_on_old_wdl_version.wdl
+}
+
+metadata {
+  workflowName: ReturnCodesInvalidOnOldWdl
+  status: Failed
+}
diff --git a/centaur/src/main/resources/standardTestCases/return_codes_invalid_on_old_wdl_version/return_codes_invalid_on_old_wdl_version.wdl b/centaur/src/main/resources/standardTestCases/return_codes_invalid_on_old_wdl_version/return_codes_invalid_on_old_wdl_version.wdl
new file mode 100644
index 00000000000..296dc833f02
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/return_codes_invalid_on_old_wdl_version/return_codes_invalid_on_old_wdl_version.wdl
@@ -0,0 +1,18 @@
+workflow ReturnCodesInvalidOnOldWdl {
+        call ReturnCodesInvalidOnOldWdlTask
+}
+
+task ReturnCodesInvalidOnOldWdlTask {
+    meta {
+        volatile: "true"
+    }
+
+    command <<<
+        exit 5
+    >>>
+
+    runtime {
+        docker: "ubuntu:latest"
+        returnCodes: [5, 10, 15]
+    }
+}
diff --git a/centaur/src/main/resources/standardTestCases/valid_return_codes_and_continue_on_return_code/valid_return_codes_and_continue_on_return_code.wdl b/centaur/src/main/resources/standardTestCases/valid_return_codes_and_continue_on_return_code/valid_return_codes_and_continue_on_return_code.wdl
new file mode 100644
index 00000000000..41acb028221
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/valid_return_codes_and_continue_on_return_code/valid_return_codes_and_continue_on_return_code.wdl
@@ -0,0 +1,55 @@
+version development-1.1
+
+workflow ValidReturnCodeAndContinueOnReturnCode {
+    call ReturnCodeContinueOnReturnCode1
+    call ReturnCodeContinueOnReturnCode2
+    call ReturnCodeContinueOnReturnCode3
+}
+
+task ReturnCodeContinueOnReturnCode1 {
+    meta {
+        volatile: true
+    }
+
+    command <<<
+        exit 1
+    >>>
+
+    runtime {
+        docker: "ubuntu:latest"
+        returnCodes: [1]
+        continueOnReturnCode: [0]
+    }
+}
+
+task ReturnCodeContinueOnReturnCode2 {
+    meta {
+        volatile: true
+    }
+
+    command <<<
+        exit 1
+    >>>
+
+    runtime {
+        docker: "ubuntu:latest"
+        returnCodes: [1]
+        continueOnReturnCode: false
+    }
+}
+
+task ReturnCodeContinueOnReturnCode3 {
+    meta {
+        volatile: true
+    }
+
+    command <<<
+        exit 1
+    >>>
+
+    runtime {
+        docker: "ubuntu:latest"
+        returnCodes: [1, 4, 7]
+        continueOnReturnCode: [1, 3, 5]
+    }
+}
diff --git a/centaur/src/main/resources/standardTestCases/valid_return_codes_and_continue_on_return_codes.test b/centaur/src/main/resources/standardTestCases/valid_return_codes_and_continue_on_return_codes.test
new file mode 100644
index 00000000000..1a8354b9482
--- /dev/null
+++ b/centaur/src/main/resources/standardTestCases/valid_return_codes_and_continue_on_return_codes.test
@@ -0,0 +1,11 @@
+name: valid_return_codes_and_continue_on_return_code
+testFormat: workflowsuccess
+
+files {
+  workflow: valid_return_codes_and_continue_on_return_code/valid_return_codes_and_continue_on_return_code.wdl
+}
+
+metadata {
+  workflowName: ValidReturnCodeAndContinueOnReturnCode
+  status: Succeeded
+}
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
index 957126da9ad..f972f4b6f2e 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
@@ -202,7 +202,8 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
       )
       assertAwsBatchRuntimeAttributesFailedCreation(
         runtimeAttributes,
-        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+        "Expecting returnCodes/continueOnReturnCode" +
+          " runtime attribute to be either a String '*', 'true', or 'false', a Boolean, or an Array[Int]."
       )
     }
 
diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
index 110dca0e348..b1755a5b3b0 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributesSpec.scala
@@ -69,7 +69,8 @@ final class GcpBatchRuntimeAttributesSpec
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomString("value"))
       assertBatchRuntimeAttributesFailedCreation(
         runtimeAttributes,
-        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+        "Expecting returnCodes/continueOnReturnCode" +
+          " runtime attribute to be either a String '*', 'true', or 'false', a Boolean, or an Array[Int]."
       )
     }
 
diff --git a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributesSpec.scala b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributesSpec.scala
index a7a880cb28c..542883743e2 100644
--- a/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributesSpec.scala
+++ b/supportedBackends/google/pipelines/common/src/test/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributesSpec.scala
@@ -99,7 +99,8 @@ final class PipelinesApiRuntimeAttributesSpec
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomString("value"))
       assertPapiRuntimeAttributesFailedCreation(
         runtimeAttributes,
-        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+        "Expecting returnCodes/continueOnReturnCode" +
+          " runtime attribute to be either a String '*', 'true', or 'false', a Boolean, or an Array[Int]."
       )
     }
 
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
index 1fb43503fb6..7189f64a660 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesRuntimeAttributesSpec.scala
@@ -157,7 +157,8 @@ class TesRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeoutSpec
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"), "continueOnReturnCode" -> WomString("value"))
       assertFailure(
         runtimeAttributes,
-        "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
+        "Expecting returnCodes/continueOnReturnCode" +
+          " runtime attribute to be either a String '*', 'true', or 'false', a Boolean, or an Array[Int]."
       )
     }
 
diff --git a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala
index ef1f719a00e..0169ab5af62 100644
--- a/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala
+++ b/wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala
@@ -1,7 +1,16 @@
 package wdl.transforms.biscayne
 
+import cats.implicits.catsSyntaxValidatedId
 import common.transforms.CheckedAtoB
-import wdl.transforms.base.wdlom2wom.TaskDefinitionElementToWomTaskDefinition.TaskDefinitionElementToWomInputs
+import common.validation.ErrorOr.{ErrorOr, ShortCircuitingFlatMapTuple2, _}
+import wdl.model.draft3.elements.{ExpressionElement, RuntimeAttributesSectionElement}
+import wdl.model.draft3.elements.ExpressionElement.{ArrayLiteral, KvPair, PrimitiveLiteralExpressionElement}
+import wdl.model.draft3.graph.ExpressionValueConsumer
+import wdl.model.draft3.graph.expression.{FileEvaluator, TypeEvaluator, ValueEvaluator}
+import wdl.transforms.base.wdlom2wom.TaskDefinitionElementToWomTaskDefinition.{
+  eliminateInputDependencies,
+  TaskDefinitionElementToWomInputs
+}
 import wdl.transforms.base.wdlom2wom.WorkflowDefinitionElementToWomWorkflowDefinition.WorkflowDefinitionConvertInputs
 import wdl.transforms.base.wdlom2wom.{
   FileElementToWomBundle,
@@ -15,13 +24,93 @@ import wdl.transforms.biscayne.linking.expression.consumed._
 import wdl.transforms.biscayne.linking.expression.files._
 import wdl.transforms.biscayne.linking.expression.types._
 import wdl.transforms.biscayne.linking.expression.values._
+import wom.values.WomInteger
+import wom.{RuntimeAttributes, RuntimeAttributesKeys}
 
 package object wdlom2wom {
   val taskDefinitionElementToWomTaskDefinition: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition] =
-    CheckedAtoB.fromErrorOr(TaskDefinitionElementToWomTaskDefinition.convert)
+    CheckedAtoB.fromErrorOr(convert)
   val workflowDefinitionElementToWomWorkflowDefinition
     : CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition] =
     CheckedAtoB.fromErrorOr(WorkflowDefinitionElementToWomWorkflowDefinition.convert)
   val fileElementToWomBundle: CheckedAtoB[FileElementToWomBundleInputs, WomBundle] =
     CheckedAtoB.fromCheck(FileElementToWomBundle.convert)
+
+  private def convert(b: TaskDefinitionElementToWomInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[CallableTaskDefinition] = {
+    val a = eliminateInputDependencies(b)(expressionValueConsumer)
+
+    val conversion =
+      TaskDefinitionElementToWomTaskDefinition.createTaskGraphAndValidateMetadata(a)(expressionValueConsumer,
+                                                                                     fileEvaluator,
+                                                                                     typeEvaluator,
+                                                                                     valueEvaluator
+      ) flatMapN { (taskGraph, _) =>
+        val validRuntimeAttributes: ErrorOr[RuntimeAttributes] = a.taskDefinitionElement.runtimeSection match {
+          case Some(attributeSection) =>
+            TaskDefinitionElementToWomTaskDefinition.createRuntimeAttributes(
+              RuntimeAttributesSectionElement(getFinalRuntimeAttributes(attributeSection)),
+              taskGraph.linkedGraph
+            )(
+              expressionValueConsumer,
+              fileEvaluator,
+              typeEvaluator,
+              valueEvaluator
+            )
+          case None => RuntimeAttributes(Map.empty).validNel
+        }
+
+        TaskDefinitionElementToWomTaskDefinition.createCallableTaskDefinition(a, taskGraph, validRuntimeAttributes)(
+          expressionValueConsumer,
+          fileEvaluator,
+          typeEvaluator,
+          valueEvaluator
+        )
+      }
+
+    conversion.contextualizeErrors(s"process task definition '${b.taskDefinitionElement.name}'")
+  }
+
+  /**
+   * Combine `returnCodes` and `continueOnReturnCode` to be a single attribute. The resulting vector will contain 
+   * `continueOnReturnCode` if either `continueOnReturnCode` or `returnCodes` was in the `attributeSection`, it will 
+   * never contain `returnCodes`. The value for the `continueOnReturnCode` key in the new vector will be the value 
+   * associated with `returnCodes` in the original vector if it exists, else it will be the value associated with 
+   * `continueOnReturnCode` in the original vector.
+   * @param attributeSection list of all runtime attributes and their values
+   * @return A vector of pairs of runtime attribute keys to their respective values
+   */
+  private def getFinalRuntimeAttributes(attributeSection: RuntimeAttributesSectionElement): Vector[KvPair] = {
+    val returnCodesAttribute =
+      attributeSection.runtimeAttributes.toList.find(pair => pair.key.equals(RuntimeAttributesKeys.ReturnCodesKey))
+    val continueOnReturnCodeAttribute =
+      attributeSection.runtimeAttributes.toList.find(pair =>
+        pair.key.equals(RuntimeAttributesKeys.ContinueOnReturnCodeKey)
+      )
+
+    val returnCodesNotUnique = (returnCodesAttribute, continueOnReturnCodeAttribute) match {
+      case (Some(returnCodesValue), Some(continueOnReturnCodeValue)) =>
+        returnCodesValue.value
+          .equals(continueOnReturnCodeValue.value) || returnCodesValue.value.equals(
+          ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(0))))
+        )
+      case _ => false
+    }
+
+    val finalAttributes = (returnCodesAttribute, returnCodesNotUnique) match {
+      case (Some(returnCodesValue), false) =>
+        attributeSection.runtimeAttributes.filterNot(attribute =>
+          attribute.key.equals(RuntimeAttributesKeys.ContinueOnReturnCodeKey)
+        ) ++ Vector(
+          KvPair(RuntimeAttributesKeys.ContinueOnReturnCodeKey, returnCodesValue.value)
+        )
+      case _ => attributeSection.runtimeAttributes
+    }
+
+    finalAttributes.filterNot(attribute => attribute.key.equals(RuntimeAttributesKeys.ReturnCodesKey))
+  }
 }
diff --git a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala
index 8933a00cb57..6441c46f09f 100644
--- a/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala
+++ b/wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala
@@ -1,7 +1,16 @@
 package wdl.transforms.cascades
 
+import cats.implicits.catsSyntaxValidatedId
 import common.transforms.CheckedAtoB
-import wdl.transforms.base.wdlom2wom.TaskDefinitionElementToWomTaskDefinition.TaskDefinitionElementToWomInputs
+import common.validation.ErrorOr.{ErrorOr, ShortCircuitingFlatMapTuple2, _}
+import wdl.model.draft3.elements.ExpressionElement.{ArrayLiteral, KvPair, PrimitiveLiteralExpressionElement}
+import wdl.model.draft3.elements.{ExpressionElement, RuntimeAttributesSectionElement}
+import wdl.model.draft3.graph.ExpressionValueConsumer
+import wdl.model.draft3.graph.expression.{FileEvaluator, TypeEvaluator, ValueEvaluator}
+import wdl.transforms.base.wdlom2wom.TaskDefinitionElementToWomTaskDefinition.{
+  eliminateInputDependencies,
+  TaskDefinitionElementToWomInputs
+}
 import wdl.transforms.base.wdlom2wom.WorkflowDefinitionElementToWomWorkflowDefinition.WorkflowDefinitionConvertInputs
 import wdl.transforms.base.wdlom2wom.{
   FileElementToWomBundle,
@@ -15,13 +24,93 @@ import wdl.transforms.cascades.linking.expression.consumed._
 import wdl.transforms.cascades.linking.expression.files._
 import wdl.transforms.cascades.linking.expression.types._
 import wdl.transforms.cascades.linking.expression.values._
+import wom.values.WomInteger
+import wom.{RuntimeAttributes, RuntimeAttributesKeys}
 
 package object wdlom2wom {
   val taskDefinitionElementToWomTaskDefinition: CheckedAtoB[TaskDefinitionElementToWomInputs, CallableTaskDefinition] =
-    CheckedAtoB.fromErrorOr(TaskDefinitionElementToWomTaskDefinition.convert)
+    CheckedAtoB.fromErrorOr(convert)
   val workflowDefinitionElementToWomWorkflowDefinition
     : CheckedAtoB[WorkflowDefinitionConvertInputs, WorkflowDefinition] =
     CheckedAtoB.fromErrorOr(WorkflowDefinitionElementToWomWorkflowDefinition.convert)
   val fileElementToWomBundle: CheckedAtoB[FileElementToWomBundleInputs, WomBundle] =
     CheckedAtoB.fromCheck(FileElementToWomBundle.convert)
+
+  private def convert(b: TaskDefinitionElementToWomInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[CallableTaskDefinition] = {
+    val a = eliminateInputDependencies(b)(expressionValueConsumer)
+
+    val conversion =
+      TaskDefinitionElementToWomTaskDefinition.createTaskGraphAndValidateMetadata(a)(expressionValueConsumer,
+                                                                                     fileEvaluator,
+                                                                                     typeEvaluator,
+                                                                                     valueEvaluator
+      ) flatMapN { (taskGraph, _) =>
+        val validRuntimeAttributes: ErrorOr[RuntimeAttributes] = a.taskDefinitionElement.runtimeSection match {
+          case Some(attributeSection) =>
+            TaskDefinitionElementToWomTaskDefinition.createRuntimeAttributes(
+              RuntimeAttributesSectionElement(getFinalRuntimeAttributes(attributeSection)),
+              taskGraph.linkedGraph
+            )(
+              expressionValueConsumer,
+              fileEvaluator,
+              typeEvaluator,
+              valueEvaluator
+            )
+          case None => RuntimeAttributes(Map.empty).validNel
+        }
+
+        TaskDefinitionElementToWomTaskDefinition.createCallableTaskDefinition(a, taskGraph, validRuntimeAttributes)(
+          expressionValueConsumer,
+          fileEvaluator,
+          typeEvaluator,
+          valueEvaluator
+        )
+      }
+
+    conversion.contextualizeErrors(s"process task definition '${b.taskDefinitionElement.name}'")
+  }
+
+  /**
+   * Combine `returnCodes` and `continueOnReturnCode` to be a single attribute. The resulting vector will contain 
+   * `continueOnReturnCode` if either `continueOnReturnCode` or `returnCodes` was in the `attributeSection`, it will 
+   * never contain `returnCodes`. The value for the `continueOnReturnCode` key in the new vector will be the value 
+   * associated with `returnCodes` in the original vector if it exists, else it will be the value associated with 
+   * `continueOnReturnCode` in the original vector.
+   * @param attributeSection list of all runtime attributes and their values
+   * @return A vector of pairs of runtime attribute keys to their respective values
+   */
+  private def getFinalRuntimeAttributes(attributeSection: RuntimeAttributesSectionElement): Vector[KvPair] = {
+    val returnCodesAttribute =
+      attributeSection.runtimeAttributes.toList.find(pair => pair.key.equals(RuntimeAttributesKeys.ReturnCodesKey))
+    val continueOnReturnCodeAttribute =
+      attributeSection.runtimeAttributes.toList.find(pair =>
+        pair.key.equals(RuntimeAttributesKeys.ContinueOnReturnCodeKey)
+      )
+
+    val returnCodesNotUnique = (returnCodesAttribute, continueOnReturnCodeAttribute) match {
+      case (Some(returnCodesValue), Some(continueOnReturnCodeValue)) =>
+        returnCodesValue.value
+          .equals(continueOnReturnCodeValue.value) || returnCodesValue.value.equals(
+          ArrayLiteral(Vector(PrimitiveLiteralExpressionElement(WomInteger(0))))
+        )
+      case _ => false
+    }
+
+    val finalAttributes = (returnCodesAttribute, returnCodesNotUnique) match {
+      case (Some(returnCodesValue), false) =>
+        attributeSection.runtimeAttributes.filterNot(attribute =>
+          attribute.key.equals(RuntimeAttributesKeys.ContinueOnReturnCodeKey)
+        ) ++ Vector(
+          KvPair(RuntimeAttributesKeys.ContinueOnReturnCodeKey, returnCodesValue.value)
+        )
+      case _ => attributeSection.runtimeAttributes
+    }
+
+    finalAttributes.filterNot(attribute => attribute.key.equals(RuntimeAttributesKeys.ReturnCodesKey))
+  }
 }
diff --git a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala
index 576ce210da5..d6e0eba7b42 100644
--- a/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala
+++ b/wdl/transforms/new-base/src/main/scala/wdl/transforms/base/wdlom2wom/TaskDefinitionElementToWomTaskDefinition.scala
@@ -2,29 +2,29 @@ package wdl.transforms.base.wdlom2wom
 
 import cats.data.NonEmptyList
 import cats.data.Validated.{Invalid, Valid}
+import cats.instances.list._
 import cats.syntax.apply._
 import cats.syntax.traverse._
 import cats.syntax.validated._
-import cats.instances.list._
 import common.validation.ErrorOr.{ErrorOr, _}
 import wdl.model.draft3.elements.CommandPartElement.{PlaceholderCommandPartElement, StringCommandPartElement}
 import wdl.model.draft3.elements.ExpressionElement.{ArrayLiteral, IdentifierLookup, KvPair, SelectFirst}
 import wdl.model.draft3.elements._
-import wdl.model.draft3.graph.{ExpressionValueConsumer, LinkedGraph}
-import wom.callable.Callable._
-import wom.callable.{Callable, CallableTaskDefinition, MetaValueElement}
-import wom.expression.WomExpression
-import wom.types.{WomOptionalType, WomType}
-import wom.{CommandPart, RuntimeAttributes}
 import wdl.model.draft3.graph.ExpressionValueConsumer.ops._
-import wdl.model.draft3.graph.expression.{FileEvaluator, TypeEvaluator, ValueEvaluator}
 import wdl.model.draft3.graph.expression.WomExpressionMaker.ops._
+import wdl.model.draft3.graph.expression.WomTypeMaker.ops._
+import wdl.model.draft3.graph.expression.{FileEvaluator, TypeEvaluator, ValueEvaluator}
+import wdl.model.draft3.graph.{ExpressionValueConsumer, LinkedGraph}
 import wdl.transforms.base.linking.expression._
 import wdl.transforms.base.linking.graph.LinkedGraphMaker
+import wdl.transforms.base.linking.typemakers._
 import wdl.transforms.base.wdlom2wom.expression.renaming.IdentifierLookupRenamer.ops._
 import wdl.transforms.base.wdlom2wom.expression.renaming.expressionEvaluator
-import wdl.model.draft3.graph.expression.WomTypeMaker.ops._
-import wdl.transforms.base.linking.typemakers._
+import wom.callable.Callable._
+import wom.callable.{Callable, CallableTaskDefinition, MetaValueElement}
+import wom.expression.WomExpression
+import wom.types.{WomOptionalType, WomType}
+import wom.{CommandPart, RuntimeAttributes}
 
 object TaskDefinitionElementToWomTaskDefinition extends Util {
 
@@ -39,60 +39,79 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
     valueEvaluator: ValueEvaluator[ExpressionElement]
   ): ErrorOr[CallableTaskDefinition] = {
     val a = eliminateInputDependencies(b)
-    val inputElements = a.taskDefinitionElement.inputsSection.map(_.inputDeclarations).getOrElse(Seq.empty)
-
-    val declarations = a.taskDefinitionElement.declarations
-    val outputElements = a.taskDefinitionElement.outputsSection.map(_.outputs).getOrElse(Seq.empty)
 
-    val conversion = (
-      createTaskGraph(inputElements,
-                      declarations,
-                      outputElements,
-                      a.taskDefinitionElement.parameterMetaSection,
-                      a.typeAliases
-      ),
-      validateParameterMetaEntries(a.taskDefinitionElement.parameterMetaSection,
-                                   a.taskDefinitionElement.inputsSection,
-                                   a.taskDefinitionElement.outputsSection
-      )
-    ) flatMapN { (taskGraph, _) =>
+    val conversion = createTaskGraphAndValidateMetadata(a) flatMapN { (taskGraph, _) =>
       val validRuntimeAttributes: ErrorOr[RuntimeAttributes] = a.taskDefinitionElement.runtimeSection match {
         case Some(attributeSection) => createRuntimeAttributes(attributeSection, taskGraph.linkedGraph)
         case None => RuntimeAttributes(Map.empty).validNel
       }
-
-      val validCommand: ErrorOr[Seq[CommandPart]] =
-        expandLines(a.taskDefinitionElement.commandSection.parts).toList
-          .traverse { parts =>
-            CommandPartElementToWomCommandPart.convert(parts,
-                                                       taskGraph.linkedGraph.typeAliases,
-                                                       taskGraph.linkedGraph.generatedHandles
-            )
-          }
-          .map(_.toSeq)
-
-      val (meta, parameterMeta) =
-        processMetaSections(a.taskDefinitionElement.metaSection, a.taskDefinitionElement.parameterMetaSection)
-
-      (validRuntimeAttributes, validCommand) mapN { (runtime, command) =>
-        CallableTaskDefinition(
-          a.taskDefinitionElement.name,
-          Function.const(command.validNel),
-          runtime,
-          meta,
-          parameterMeta,
-          taskGraph.outputs,
-          taskGraph.inputs,
-          Set.empty,
-          Map.empty,
-          sourceLocation = a.taskDefinitionElement.sourceLocation
-        )
-      }
+      createCallableTaskDefinition(a, taskGraph, validRuntimeAttributes)
     }
 
     conversion.contextualizeErrors(s"process task definition '${b.taskDefinitionElement.name}'")
   }
 
+  def createTaskGraphAndValidateMetadata(a: TaskDefinitionElementToWomInputs)(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): (ErrorOr[TaskGraph], ErrorOr[Unit]) = {
+    val inputElements = a.taskDefinitionElement.inputsSection.map(_.inputDeclarations).getOrElse(Seq.empty)
+
+    val declarations = a.taskDefinitionElement.declarations
+    val outputElements = a.taskDefinitionElement.outputsSection.map(_.outputs).getOrElse(Seq.empty)
+
+    (createTaskGraph(inputElements,
+                     declarations,
+                     outputElements,
+                     a.taskDefinitionElement.parameterMetaSection,
+                     a.typeAliases
+     ),
+     validateParameterMetaEntries(a.taskDefinitionElement.parameterMetaSection,
+                                  a.taskDefinitionElement.inputsSection,
+                                  a.taskDefinitionElement.outputsSection
+     )
+    )
+  }
+
+  def createCallableTaskDefinition(a: TaskDefinitionElementToWomInputs,
+                                   taskGraph: TaskGraph,
+                                   validRuntimeAttributes: ErrorOr[RuntimeAttributes]
+  )(implicit
+    expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
+    fileEvaluator: FileEvaluator[ExpressionElement],
+    typeEvaluator: TypeEvaluator[ExpressionElement],
+    valueEvaluator: ValueEvaluator[ExpressionElement]
+  ): ErrorOr[CallableTaskDefinition] = {
+    val validCommand: ErrorOr[Seq[CommandPart]] =
+      expandLines(a.taskDefinitionElement.commandSection.parts).toList
+        .traverse { parts =>
+          CommandPartElementToWomCommandPart.convert(parts,
+                                                     taskGraph.linkedGraph.typeAliases,
+                                                     taskGraph.linkedGraph.generatedHandles
+          )
+        }
+        .map(_.toSeq)
+
+    val (meta, parameterMeta) =
+      processMetaSections(a.taskDefinitionElement.metaSection, a.taskDefinitionElement.parameterMetaSection)
+
+    (validRuntimeAttributes, validCommand) mapN { (runtime, command) =>
+      CallableTaskDefinition(
+        a.taskDefinitionElement.name,
+        Function.const(command.validNel),
+        runtime,
+        meta,
+        parameterMeta,
+        taskGraph.outputs,
+        taskGraph.inputs,
+        Set.empty,
+        Map.empty,
+        sourceLocation = a.taskDefinitionElement.sourceLocation
+      )
+    }
+  }
   private def validateParameterMetaEntries(parameterMetaSectionElement: Option[ParameterMetaSectionElement],
                                            inputs: Option[InputsSectionElement],
                                            outputs: Option[OutputsSectionElement]
@@ -116,7 +135,7 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
     }
   }
 
-  private def eliminateInputDependencies(
+  def eliminateInputDependencies(
     a: TaskDefinitionElementToWomInputs
   )(implicit expressionValueConsumer: ExpressionValueConsumer[ExpressionElement]): TaskDefinitionElementToWomInputs = {
     case class NewInputElementsSet(original: InputDeclarationElement,
@@ -221,9 +240,9 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
     }
   }
 
-  final private case class TaskGraph(inputs: List[Callable.InputDefinition],
-                                     outputs: List[Callable.OutputDefinition],
-                                     linkedGraph: LinkedGraph
+  final case class TaskGraph(inputs: List[Callable.InputDefinition],
+                             outputs: List[Callable.OutputDefinition],
+                             linkedGraph: LinkedGraph
   )
 
   private def createTaskGraph(inputs: Seq[InputDeclarationElement],
@@ -319,7 +338,7 @@ object TaskDefinitionElementToWomTaskDefinition extends Util {
     }
   }
 
-  private def createRuntimeAttributes(attributes: RuntimeAttributesSectionElement, linkedGraph: LinkedGraph)(implicit
+  def createRuntimeAttributes(attributes: RuntimeAttributesSectionElement, linkedGraph: LinkedGraph)(implicit
     expressionValueConsumer: ExpressionValueConsumer[ExpressionElement],
     fileEvaluator: FileEvaluator[ExpressionElement],
     typeEvaluator: TypeEvaluator[ExpressionElement],
diff --git a/wom/src/main/scala/wom/RuntimeAttributes.scala b/wom/src/main/scala/wom/RuntimeAttributes.scala
index 2c66b6859d3..216d6404dc5 100644
--- a/wom/src/main/scala/wom/RuntimeAttributes.scala
+++ b/wom/src/main/scala/wom/RuntimeAttributes.scala
@@ -15,6 +15,10 @@ object RuntimeAttributesKeys {
   val MemoryKey = "memory"
   val FailOnStderrKey = "failOnStderr"
   val ContinueOnReturnCodeKey = "continueOnReturnCode"
+
+  // New for WDL 1.1
+  // Semantically, this is the same as continueOnReturnCode as the two attributes are combined at the parsing stage
+  val ReturnCodesKey = "returnCodes"
 }
 
 case class RuntimeAttributes(attributes: Map[String, WomExpression])

From 8e8300a76d7b4bf00445b203a10298bc9460c0d1 Mon Sep 17 00:00:00 2001
From: mspector <michael.l.spector@gmail.com>
Date: Fri, 12 Apr 2024 13:15:56 -0400
Subject: [PATCH 307/326] [WM-2555] Cromwell -> ECM contract test (#7405)

---
 .../consumer/EcmServiceContractSpec.scala     | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/EcmServiceContractSpec.scala

diff --git a/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/EcmServiceContractSpec.scala b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/EcmServiceContractSpec.scala
new file mode 100644
index 00000000000..e8101f66927
--- /dev/null
+++ b/pact4s/src/test/scala/org/broadinstitute/dsde/workbench/cromwell/consumer/EcmServiceContractSpec.scala
@@ -0,0 +1,63 @@
+package org.broadinstitute.dsde.workbench.cromwell.consumer
+
+import au.com.dius.pact.consumer.dsl._
+import au.com.dius.pact.consumer.{ConsumerPactBuilder, PactTestExecutionContext}
+import au.com.dius.pact.core.model.RequestResponsePact
+import cromwell.core.TestKitSuite
+import cromwell.services.auth.GithubAuthVending.{GithubToken, TerraToken}
+import cromwell.services.auth.ecm.EcmService
+import org.scalatest.flatspec.AnyFlatSpecLike
+
+import scala.concurrent.{Await, ExecutionContextExecutor}
+import org.scalatest.matchers.should.Matchers
+import pact4s.scalatest.RequestResponsePactForger
+
+import scala.concurrent.duration.DurationInt
+
+class EcmServiceContractSpec extends TestKitSuite with AnyFlatSpecLike with Matchers with RequestResponsePactForger {
+
+  implicit val ec: ExecutionContextExecutor = system.dispatcher
+
+  /*
+    Define the folder that the pact contracts get written to upon completion of this test suite.
+   */
+  override val pactTestExecutionContext: PactTestExecutionContext =
+    new PactTestExecutionContext(
+      "./target/pacts"
+    )
+
+  val consumerPactBuilder: ConsumerPactBuilder = ConsumerPactBuilder
+    .consumer("cromwell")
+
+  val pactProvider: PactDslWithProvider = consumerPactBuilder
+    .hasPactWith("ecm")
+
+  var testUser: String = "cromwell_test_user@test.com"
+  var testBearerToken: String = "cromwellBearerToken"
+  var testGithubToken: String = "githubToken"
+
+  var pactDslResponse: PactDslResponse = pactProvider
+    .`given`("a user is registered",
+             Map[String, String](
+               "userEmail" -> testUser,
+               "bearerToken" -> testBearerToken
+             )
+    )
+    .uponReceiving("a github token request")
+    .method("GET")
+    .path("/api/oauth/v1/github/access-token")
+    .headers(Map[String, String]("Authorization" -> s"Bearer $testBearerToken"))
+    .willRespondWith()
+    .status(200)
+    .bodyMatchingContentType("text/plain", testGithubToken)
+
+  override val pact: RequestResponsePact = pactDslResponse.toPact
+
+  it should "get a github token" in {
+    Await.result(
+      new EcmService(mockServer.getUrl)
+        .getGithubAccessToken(TerraToken(testBearerToken)),
+      10.seconds
+    ) shouldBe GithubToken(testGithubToken)
+  }
+}

From 04c727dccc46c5128990e413b39fcfbefd04cc25 Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Tue, 16 Apr 2024 10:43:12 -0400
Subject: [PATCH 308/326] [WX-1568] Bump Akka max-response-reason-length limit
 (#7406)

---
 server/src/main/resources/application.conf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/server/src/main/resources/application.conf b/server/src/main/resources/application.conf
index 3bdacceb8ee..90b808b2bf8 100644
--- a/server/src/main/resources/application.conf
+++ b/server/src/main/resources/application.conf
@@ -15,7 +15,9 @@ akka {
       server-header = ""
     }
     client.connecting-timeout = 40s
-
+    // The default limit (64) for this is too low, which makes akka throw an error when a response exceeds this limit.
+    // Bumping higher so that we can accept and log longer error messages that may come back from a server.
+    client.parsing.max-response-reason-length = 1024
     # Inspired by https://broadworkbench.atlassian.net/browse/CROM-6738
     # and copied from https://stackoverflow.com/questions/27910526/logger-log1-slf4jlogger-did-not-respond-within-timeout5000-milliseconds-to-ini
     # This gives the logger a little more than 5 seconds to startup. 5s was *almost* always enough, so a safe 30s should be *plenty* of time:

From 5448b85bf334e0970665a69549e796199acc8bd7 Mon Sep 17 00:00:00 2001
From: Janet Gainer-Dewar <jdewar@broadinstitute.org>
Date: Tue, 16 Apr 2024 13:04:56 -0400
Subject: [PATCH 309/326] WX-1530 Strip pesky URL bits when creating local
 paths for HTTP inputs (#7404)

---
 .../filesystems/http/HttpPathBuilder.scala    |  2 +
 .../TesAsyncBackendJobExecutionActor.scala    | 72 +++++++++++--------
 ...TesAsyncBackendJobExecutionActorSpec.scala | 62 +++++++++++++++-
 3 files changed, 104 insertions(+), 32 deletions(-)

diff --git a/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala b/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala
index fa1861dd81a..29910cd43ac 100644
--- a/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala
+++ b/filesystems/http/src/main/scala/cromwell/filesystems/http/HttpPathBuilder.scala
@@ -55,6 +55,8 @@ case class HttpPath(nioPath: NioPath) extends Path {
 
   override def pathWithoutScheme: String = pathAsString.replaceFirst("http[s]?://", "")
 
+  def pathWithoutSchemeOrQueryOrFragment: String = pathWithoutScheme.split("[?#]").head
+
   def fetchSize(implicit executionContext: ExecutionContext, actorSystem: ActorSystem): Future[Long] =
     Http().singleRequest(HttpRequest(uri = pathAsString, method = HttpMethods.HEAD)).map { response =>
       response.discardEntityBytes()
diff --git a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
index 44b24e89980..f8e0e2044cc 100644
--- a/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/tes/src/main/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActor.scala
@@ -37,6 +37,7 @@ import cromwell.core.retry.Retry._
 import cromwell.core.retry.SimpleExponentialBackoff
 import cromwell.filesystems.blob.{BlobPath, WSMBlobSasTokenGenerator}
 import cromwell.filesystems.drs.{DrsPath, DrsResolver}
+import cromwell.filesystems.http.HttpPath
 import net.ceedubs.ficus.Ficus._
 import wom.values.WomFile
 
@@ -176,6 +177,46 @@ object TesAsyncBackendJobExecutionActor {
         )
       )
   }
+
+  def mapInputPath(path: Path, tesJobPaths: TesJobPaths, commandDirectory: Path): String =
+    path match {
+      case drsPath: DrsPath =>
+        val filepath = DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
+        tesJobPaths.containerExec(commandDirectory, filepath)
+      case httpPath: HttpPath =>
+        // Strip the query params and anything after a # from http paths when turning them into local paths
+        tesJobPaths.callInputsDockerRoot
+          .resolve(httpPath.pathWithoutSchemeOrQueryOrFragment.stripPrefix("/"))
+          .pathAsString
+      case path: Path if path.startsWith(tesJobPaths.workflowPaths.DockerRoot) =>
+        path.pathAsString
+      case path: Path if path.equals(tesJobPaths.callExecutionRoot) =>
+        commandDirectory.pathAsString
+      case path: Path if path.startsWith(tesJobPaths.callExecutionRoot) =>
+        tesJobPaths.containerExec(commandDirectory, path.name)
+      case path: Path if path.startsWith(tesJobPaths.callRoot) =>
+        tesJobPaths.callDockerRoot.resolve(path.name).pathAsString
+      case path: BlobPath if path.startsWith(tesJobPaths.workflowPaths.workflowRoot) =>
+        // Blob paths can get really long, which causes problems for some tools. If this input file
+        // lives in the workflow execution directory, strip off that prefix from the path we're
+        // generating inside `inputs/` to keep the total path length under control.
+        // In Terra on Azure, this saves us 200+ characters.
+        tesJobPaths.callInputsDockerRoot
+          .resolve(
+            path.pathStringWithoutPrefix(tesJobPaths.workflowPaths.workflowRoot)
+          )
+          .pathAsString
+      case path: BlobPath if path.startsWith(tesJobPaths.workflowPaths.executionRoot) =>
+        // See comment above... if this file is in the execution root, strip that off.
+        // In Terra on Azure, this saves us 160+ characters.
+        tesJobPaths.callInputsDockerRoot
+          .resolve(
+            path.pathStringWithoutPrefix(tesJobPaths.workflowPaths.executionRoot)
+          )
+          .pathAsString
+      case _ =>
+        tesJobPaths.callInputsDockerRoot.resolve(path.pathWithoutScheme.stripPrefix("/")).pathAsString
+    }
 }
 
 class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
@@ -262,37 +303,8 @@ class TesAsyncBackendJobExecutionActor(override val standardParams: StandardAsyn
   override def mapCommandLineJobInputWomFile(womFile: WomFile): WomFile =
     womFile.mapFile(value =>
       getPath(value) match {
-        case Success(drsPath: DrsPath) =>
-          val filepath = DrsResolver.getContainerRelativePath(drsPath).unsafeRunSync()
-          tesJobPaths.containerExec(commandDirectory, filepath)
-        case Success(path: Path) if path.startsWith(tesJobPaths.workflowPaths.DockerRoot) =>
-          path.pathAsString
-        case Success(path: Path) if path.equals(tesJobPaths.callExecutionRoot) =>
-          commandDirectory.pathAsString
-        case Success(path: Path) if path.startsWith(tesJobPaths.callExecutionRoot) =>
-          tesJobPaths.containerExec(commandDirectory, path.name)
-        case Success(path: Path) if path.startsWith(tesJobPaths.callRoot) =>
-          tesJobPaths.callDockerRoot.resolve(path.name).pathAsString
-        case Success(path: BlobPath) if path.startsWith(tesJobPaths.workflowPaths.workflowRoot) =>
-          // Blob paths can get really long, which causes problems for some tools. If this input file
-          // lives in the workflow execution directory, strip off that prefix from the path we're
-          // generating inside `inputs/` to keep the total path length under control.
-          // In Terra on Azure, this saves us 200+ characters.
-          tesJobPaths.callInputsDockerRoot
-            .resolve(
-              path.pathStringWithoutPrefix(tesJobPaths.workflowPaths.workflowRoot)
-            )
-            .pathAsString
-        case Success(path: BlobPath) if path.startsWith(tesJobPaths.workflowPaths.executionRoot) =>
-          // See comment above... if this file is in the execution root, strip that off.
-          // In Terra on Azure, this saves us 160+ characters.
-          tesJobPaths.callInputsDockerRoot
-            .resolve(
-              path.pathStringWithoutPrefix(tesJobPaths.workflowPaths.executionRoot)
-            )
-            .pathAsString
         case Success(path: Path) =>
-          tesJobPaths.callInputsDockerRoot.resolve(path.pathWithoutScheme.stripPrefix("/")).pathAsString
+          TesAsyncBackendJobExecutionActor.mapInputPath(path, tesJobPaths, commandDirectory)
         case _ =>
           value
       }
diff --git a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
index 53ba95606d0..f920f3633a7 100644
--- a/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/tes/src/test/scala/cromwell/backend/impl/tes/TesAsyncBackendJobExecutionActorSpec.scala
@@ -1,18 +1,27 @@
 package cromwell.backend.impl.tes
 
 import common.mock.MockSugar
+import cromwell.backend.BackendJobDescriptorKey
+import cromwell.backend.BackendSpec.buildWdlWorkflowDescriptor
 import cromwell.core.logging.JobLogger
-import cromwell.core.path.NioPath
+import cromwell.core.path.{DefaultPathBuilder, NioPath}
 import cromwell.filesystems.blob.{BlobFileSystemManager, BlobPath, WSMBlobSasTokenGenerator}
+import cromwell.filesystems.http.HttpPathBuilder
 import org.mockito.ArgumentMatchers.any
 import org.scalatest.flatspec.AnyFlatSpec
 import org.scalatest.matchers.should.Matchers
+import org.scalatest.prop.TableDrivenPropertyChecks
+import wom.graph.CommandCallNode
 
 import java.time.Duration
 import java.time.temporal.ChronoUnit
 import scala.util.{Failure, Try}
 
-class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers with MockSugar {
+class TesAsyncBackendJobExecutionActorSpec
+    extends AnyFlatSpec
+    with Matchers
+    with MockSugar
+    with TableDrivenPropertyChecks {
   behavior of "TesAsyncBackendJobExecutionActor"
 
   val fullyQualifiedName = "this.name.is.more.than.qualified"
@@ -175,4 +184,53 @@ class TesAsyncBackendJobExecutionActorSpec extends AnyFlatSpec with Matchers wit
     generatedBashScript should include(echoCommandSubstring)
     generatedBashScript should include(exportCommandSubstring)
   }
+
+  private val httpPathTestCases = Table(
+    ("test name", "http path", "local path in input dir"),
+    (
+      "strip simple kv query params",
+      "http://example.com/my_sample.bam?k1=v1&k2=v2",
+      "example.com/my_sample.bam"
+    ),
+    (
+      "handle http paths without query params",
+      "http://example.com/my_sample.bam",
+      "example.com/my_sample.bam"
+    ),
+    (
+      "handle http paths without params but with a ?",
+      "http://example.com/my_sample.bam?",
+      "example.com/my_sample.bam"
+    ),
+    (
+      "handle a blob file with SAS token attached",
+      "https://lzbc096764ae93ffff9f406e.blob.core.windows.net/sc-a7f7a9e0-2dcf-465c-997b-a276090a52da/workspace-services/cbas/terra-app-2f577477-763b-4e27-8e28-b03d91b6f3be/cromwell-workflow-logs/workflow.c621a5df-37f1-422d-b91a-1a65f6112a6a.log?sv=2023-11-03&spr=https&st=2024-04-09T23%3A35%3A37Z&se=2024-04-10T07%3A50%3A37Z&sr=c&sp=racwdlt&sig=REDACTEDS&rscd=100067995116984528334",
+      "lzbc096764ae93ffff9f406e.blob.core.windows.net/sc-a7f7a9e0-2dcf-465c-997b-a276090a52da/workspace-services/cbas/terra-app-2f577477-763b-4e27-8e28-b03d91b6f3be/cromwell-workflow-logs/workflow.c621a5df-37f1-422d-b91a-1a65f6112a6a.log"
+    ),
+    (
+      "handle an http path with fragment",
+      "http://example.com/my_sample.bam#my_favorite_part",
+      "example.com/my_sample.bam"
+    ),
+    (
+      "handle an http path with fragment and query params",
+      "http://example.com/my_sample.bam?k=yourface#my_favorite_part",
+      "example.com/my_sample.bam"
+    )
+  )
+
+  forAll(httpPathTestCases) { (testName, httpPath, localPathInInputDir) =>
+    it should testName in {
+      val wd = buildWdlWorkflowDescriptor(TestWorkflows.HelloWorld)
+      val call: CommandCallNode = wd.callable.taskCallNodes.head
+      val jobKey = BackendJobDescriptorKey(call, None, 1)
+      val jobPaths = TesJobPaths(jobKey, wd, TesTestConfig.backendConfig)
+      val commandDirectory = DefaultPathBuilder.build("/my/command/dir").get
+      val httpBuilder = new HttpPathBuilder()
+
+      val httpPathWithParams = httpBuilder.build(httpPath)
+      val actual = TesAsyncBackendJobExecutionActor.mapInputPath(httpPathWithParams.get, jobPaths, commandDirectory)
+      actual shouldBe s"${jobPaths.callInputsDockerRoot}/$localPathInInputDir"
+    }
+  }
 }

From 0a6ad657febdfc75d42620e7c48b2c1fe472af40 Mon Sep 17 00:00:00 2001
From: Alexis Hernandez <alexis22229@gmail.com>
Date: Wed, 24 Apr 2024 17:25:58 +0200
Subject: [PATCH 310/326] WX-1538 Add more tests to the GCP Batch backend
 (#7410)

---
 ...tchAsyncBackendJobExecutionActorSpec.scala | 469 +++++++++++++++++-
 1 file changed, 465 insertions(+), 4 deletions(-)

diff --git a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
index 676a4d025e6..6ec8bd0053b 100644
--- a/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/google/batch/src/test/scala/cromwell/backend/google/batch/actors/GcpBatchAsyncBackendJobExecutionActorSpec.scala
@@ -12,6 +12,7 @@ import com.google.cloud.NoCredentials
 import com.google.cloud.batch.v1.{Job, JobName}
 import com.typesafe.config.{Config, ConfigFactory}
 import common.collections.EnhancedCollections._
+import common.mock.MockSugar
 import cromwell.backend.BackendJobExecutionActor.BackendJobExecutionResponse
 import cromwell.backend._
 import cromwell.backend.async.AsyncBackendJobExecutionActor.{Execute, ExecutionMode}
@@ -32,6 +33,7 @@ import cromwell.core.callcaching.NoDocker
 import cromwell.core.labels.Labels
 import cromwell.core.logging.JobLogger
 import cromwell.core.path.{DefaultPathBuilder, PathBuilder}
+import cromwell.filesystems.drs.DrsPathBuilder
 import cromwell.filesystems.gcs.{GcsPath, GcsPathBuilder, MockGcsPathBuilder}
 import cromwell.services.instrumentation.InstrumentationService.InstrumentationServiceMessage
 import cromwell.services.instrumentation.{CromwellBucket, CromwellIncrement}
@@ -39,6 +41,7 @@ import cromwell.services.keyvalue.InMemoryKvServiceActor
 import cromwell.services.keyvalue.KeyValueServiceActor.{KvJobKey, KvPair, ScopedKey}
 import cromwell.util.JsonFormatting.WomValueJsonFormatter._
 import cromwell.util.SampleWdl
+import org.mockito.Mockito._
 import org.scalatest._
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
@@ -51,6 +54,7 @@ import wom.expression.NoIoFunctionSet
 import wom.graph.CommandCallNode
 import wom.transforms.WomExecutableMaker.ops._
 import wom.transforms.WomWorkflowDefinitionMaker.ops._
+import wom.types.{WomArrayType, WomMapType, WomSingleFileType, WomStringType}
 import wom.values._
 
 import java.nio.file.Paths
@@ -58,9 +62,7 @@ import java.util.UUID
 import scala.concurrent.duration._
 import scala.concurrent.{Await, ExecutionContext, Future, Promise}
 import scala.language.postfixOps
-import common.mock.MockSugar
-import cromwell.filesystems.drs.DrsPathBuilder
-import org.mockito.Mockito._
+import scala.util.Success
 
 class GcpBatchAsyncBackendJobExecutionActorSpec
     extends TestKitSuite
@@ -677,7 +679,9 @@ class GcpBatchAsyncBackendJobExecutionActorSpec
     wdlNamespace.toWomExecutable(Option(inputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true) match {
       case Right(womExecutable) =>
         val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
-          v.select[WomValue] map { port -> _ }
+          v.select[WomValue] map {
+            port -> _
+          }
         }
 
         val workflowDescriptor = BackendWorkflowDescriptor(
@@ -734,6 +738,463 @@ class GcpBatchAsyncBackendJobExecutionActorSpec
     }
   }
 
+  private val dockerAndDiskMapsWdlNamespace =
+    WdlNamespaceWithWorkflow
+      .load(
+        SampleWdl.CurrentDirectoryMaps.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+        Seq.empty[Draft2ImportResolver]
+      )
+      .get
+
+  private val dockerAndDiskArrayWdlNamespace =
+    WdlNamespaceWithWorkflow
+      .load(
+        SampleWdl.CurrentDirectoryArray.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+        Seq.empty[Draft2ImportResolver]
+      )
+      .get
+
+  private val dockerAndDiskFilesWdlNamespace =
+    WdlNamespaceWithWorkflow
+      .load(
+        SampleWdl.CurrentDirectoryFiles.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+        Seq.empty[Draft2ImportResolver]
+      )
+      .get
+
+  it should "generate correct JesFileInputs from a WdlMap" in {
+    val inputs: Map[String, WomValue] = Map(
+      "stringToFileMap" -> WomMap(
+        WomMapType(WomStringType, WomSingleFileType),
+        Map(
+          WomString("stringTofile1") -> WomSingleFile("gs://path/to/stringTofile1"),
+          WomString("stringTofile2") -> WomSingleFile("gs://path/to/stringTofile2")
+        )
+      ),
+      "fileToStringMap" -> WomMap(
+        WomMapType(WomSingleFileType, WomStringType),
+        Map(
+          WomSingleFile("gs://path/to/fileToString1") -> WomString("fileToString1"),
+          WomSingleFile("gs://path/to/fileToString2") -> WomString("fileToString2")
+        )
+      ),
+      "fileToFileMap" -> WomMap(
+        WomMapType(WomSingleFileType, WomSingleFileType),
+        Map(
+          WomSingleFile("gs://path/to/fileToFile1Key") -> WomSingleFile("gs://path/to/fileToFile1Value"),
+          WomSingleFile("gs://path/to/fileToFile2Key") -> WomSingleFile("gs://path/to/fileToFile2Value")
+        )
+      ),
+      "stringToString" -> WomMap(
+        WomMapType(WomStringType, WomStringType),
+        Map(
+          WomString("stringToString1") -> WomString("path/to/stringToString1"),
+          WomString("stringToString2") -> WomString("path/to/stringToString2")
+        )
+      )
+    )
+
+    val workflowInputs = inputs map { case (key, value) =>
+      (s"wf_whereami.whereami.$key", value)
+    }
+
+    val womWorkflow =
+      dockerAndDiskMapsWdlNamespace.workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    val womExecutableChecked =
+      dockerAndDiskMapsWdlNamespace
+        .toWomExecutable(Option(workflowInputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true)
+    womExecutableChecked match {
+      case Right(womExecutable) =>
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map {
+            port -> _
+          }
+        }
+        val workflowDescriptor = BackendWorkflowDescriptor(
+          WorkflowId.randomId(),
+          womWorkflow,
+          wdlInputs,
+          NoOptions,
+          Labels.empty,
+          HogGroup("foo"),
+          List.empty,
+          None
+        )
+
+        val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
+        val runtimeAttributes = makeRuntimeAttributes(job)
+        val key = BackendJobDescriptorKey(job, None, 1)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
+
+        val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
+        val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
+          props,
+          s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
+
+        val jesInputs = testActorRef.underlyingActor.generateInputs(jobDescriptor)
+        jesInputs should have size 8
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "stringToFileMap",
+            cloudPath = gcsPath("gs://path/to/stringTofile1"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/stringTofile1"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "stringToFileMap",
+            cloudPath = gcsPath("gs://path/to/stringTofile2"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/stringTofile2"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "fileToStringMap",
+            cloudPath = gcsPath("gs://path/to/fileToString1"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToString1"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "fileToStringMap",
+            cloudPath = gcsPath("gs://path/to/fileToString2"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToString2"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "fileToFileMap",
+            cloudPath = gcsPath("gs://path/to/fileToFile1Key"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile1Key"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "fileToFileMap",
+            cloudPath = gcsPath("gs://path/to/fileToFile1Value"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile1Value"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "fileToFileMap",
+            cloudPath = gcsPath("gs://path/to/fileToFile2Key"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile2Key"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "fileToFileMap",
+            cloudPath = gcsPath("gs://path/to/fileToFile2Value"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/fileToFile2Value"),
+            mount = workingDisk
+          )
+        )
+
+      case Left(badness) => fail(badness.toList.mkString(", "))
+    }
+  }
+
+  private def makeJesActorRef(sampleWdl: SampleWdl,
+                              workflowInputs: Map[FullyQualifiedName, WomValue],
+                              callName: LocallyQualifiedName,
+                              callInputs: Map[LocallyQualifiedName, WomValue],
+                              functions: BatchExpressionFunctions = TestableGcpBatchExpressionFunctions
+  ): TestActorRef[TestableGcpBatchJobExecutionActor] = {
+    val wdlNamespaceWithWorkflow =
+      WdlNamespaceWithWorkflow
+        .load(
+          sampleWdl.asWorkflowSources(DockerAndDiskRuntime).workflowSource.get,
+          Seq.empty[Draft2ImportResolver]
+        )
+        .get
+    val womWorkflow =
+      wdlNamespaceWithWorkflow.workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    val womExecutableChecked =
+      wdlNamespaceWithWorkflow
+        .toWomExecutable(
+          Option(workflowInputs.toJson.compactPrint),
+          NoIoFunctionSet,
+          strictValidation = true
+        )
+    womExecutableChecked match {
+      case Right(womExecutable) =>
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map {
+            port -> _
+          }
+        }
+        val workflowDescriptor = BackendWorkflowDescriptor(
+          WorkflowId.randomId(),
+          womWorkflow,
+          wdlInputs,
+          NoOptions,
+          Labels.empty,
+          HogGroup("foo"),
+          List.empty,
+          None
+        )
+
+        val call: CommandCallNode = workflowDescriptor.callable.taskCallNodes.find(_.localName == callName).get
+        val key = BackendJobDescriptorKey(call, None, 1)
+        val runtimeAttributes = makeRuntimeAttributes(call)
+        val jobDescriptor =
+          BackendJobDescriptor(
+            workflowDescriptor = workflowDescriptor,
+            key = key,
+            runtimeAttributes = runtimeAttributes,
+            evaluatedTaskInputs = fqnWdlMapToDeclarationMap(callInputs),
+            maybeCallCachingEligible = NoDocker,
+            dockerSize = None,
+            prefetchedKvStoreEntries = Map.empty
+          )
+
+        val props = Props(
+          new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration, functions)
+        )
+        TestActorRef[TestableGcpBatchJobExecutionActor](
+          props,
+          s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
+      case Left(badness) => fail(badness.toList.mkString(", "))
+    }
+  }
+
+  it should "generate correct JesOutputs" in {
+    val womFile = WomSingleFile("gs://blah/b/c.txt")
+    val workflowInputs = Map("file_passing.f" -> womFile)
+    val callInputs = Map(
+      "in" -> womFile, // how does one programmatically map the wf inputs to the call inputs?
+      "out_name" -> WomString("out") // is it expected that this isn't using the default?
+    )
+    val jesBackend = makeJesActorRef(SampleWdl.FilePassingWorkflow, workflowInputs, "a", callInputs).underlyingActor
+    val jobDescriptor = jesBackend.jobDescriptor
+    val workflowId = jesBackend.workflowId
+    val jesInputs = jesBackend.generateInputs(jobDescriptor)
+    jesInputs should have size 1
+    jesInputs should contain(
+      GcpBatchFileInput(
+        name = "in",
+        cloudPath = gcsPath("gs://blah/b/c.txt"),
+        relativeHostPath = DefaultPathBuilder.get("blah/b/c.txt"),
+        mount = workingDisk
+      )
+    )
+    val jesOutputs = jesBackend.generateOutputs(jobDescriptor)
+    jesOutputs should have size 1
+    jesOutputs should contain(
+      GcpBatchFileOutput(
+        "out",
+        gcsPath(s"gs://my-cromwell-workflows-bucket/file_passing/$workflowId/call-a/out"),
+        DefaultPathBuilder.get("out"),
+        workingDisk,
+        optional = false,
+        secondary = false
+      )
+    )
+  }
+
+  it should "generate correct JesInputs when a command line contains a write_lines call in it" in {
+    val inputs = Map(
+      "strs" -> WomArray(WomArrayType(WomStringType), Seq("A", "B", "C").map(WomString))
+    )
+
+    class TestPipelinesApiExpressionFunctions
+        extends BatchExpressionFunctions(TestableStandardExpressionFunctionsParams) {
+      override def writeFile(path: String, content: String): Future[WomSingleFile] =
+        Future.fromTry(Success(WomSingleFile(s"gs://some/path/file.txt")))
+    }
+
+    val functions = new TestPipelinesApiExpressionFunctions
+    val jesBackend = makeJesActorRef(SampleWdl.ArrayIO, Map.empty, "serialize", inputs, functions).underlyingActor
+    val jobDescriptor = jesBackend.jobDescriptor
+    val jesInputs = jesBackend.generateInputs(jobDescriptor)
+    jesInputs should have size 1
+    jesInputs should contain(
+      GcpBatchFileInput(
+        name = "c35ad8d3",
+        cloudPath = gcsPath("gs://some/path/file.txt"),
+        relativeHostPath = DefaultPathBuilder.get("some/path/file.txt"),
+        mount = workingDisk
+      )
+    )
+    val jesOutputs = jesBackend.generateOutputs(jobDescriptor)
+    jesOutputs should have size 0
+  }
+
+  it should "generate correct JesFileInputs from a WdlArray" in {
+    val inputs: Map[String, WomValue] = Map(
+      "fileArray" ->
+        WomArray(WomArrayType(WomSingleFileType),
+                 Seq(WomSingleFile("gs://path/to/file1"), WomSingleFile("gs://path/to/file2"))
+        )
+    )
+
+    val workflowInputs = inputs map { case (key, value) =>
+      (s"wf_whereami.whereami.$key", value)
+    }
+
+    val womWorkflow =
+      dockerAndDiskArrayWdlNamespace.workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    val womExecutableChecked =
+      dockerAndDiskArrayWdlNamespace
+        .toWomExecutable(Option(workflowInputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true)
+    womExecutableChecked match {
+      case Right(womExecutable) =>
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map {
+            port -> _
+          }
+        }
+        val workflowDescriptor = BackendWorkflowDescriptor(
+          WorkflowId.randomId(),
+          womWorkflow,
+          wdlInputs,
+          NoOptions,
+          Labels.empty,
+          HogGroup("foo"),
+          List.empty,
+          None
+        )
+
+        val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
+        val runtimeAttributes = makeRuntimeAttributes(job)
+        val key = BackendJobDescriptorKey(job, None, 1)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
+
+        val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
+        val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
+          props,
+          s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
+
+        val jesInputs = testActorRef.underlyingActor.generateInputs(jobDescriptor)
+        jesInputs should have size 2
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "fileArray",
+            cloudPath = gcsPath("gs://path/to/file1"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/file1"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "fileArray",
+            cloudPath = gcsPath("gs://path/to/file2"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/file2"),
+            mount = workingDisk
+          )
+        )
+      case Left(badness) => fail(badness.toList.mkString(", "))
+    }
+  }
+
+  it should "generate correct JesFileInputs from a WdlFile" in {
+    val inputs: Map[String, WomValue] = Map(
+      "file1" -> WomSingleFile("gs://path/to/file1"),
+      "file2" -> WomSingleFile("gs://path/to/file2")
+    )
+
+    val workflowInputs = inputs map { case (key, value) =>
+      (s"wf_whereami.whereami.$key", value)
+    }
+
+    val womWorkflow =
+      dockerAndDiskFilesWdlNamespace.workflow
+        .toWomWorkflowDefinition(isASubworkflow = false)
+        .getOrElse(fail("failed to get WomDefinition from WdlWorkflow"))
+    val womExecutableChecked =
+      dockerAndDiskFilesWdlNamespace
+        .toWomExecutable(Option(workflowInputs.toJson.compactPrint), NoIoFunctionSet, strictValidation = true)
+    womExecutableChecked match {
+      case Right(womExecutable) =>
+        val wdlInputs = womExecutable.resolvedExecutableInputs.flatMap { case (port, v) =>
+          v.select[WomValue] map {
+            port -> _
+          }
+        }
+        val workflowDescriptor = BackendWorkflowDescriptor(
+          WorkflowId.randomId(),
+          womWorkflow,
+          wdlInputs,
+          NoOptions,
+          Labels.empty,
+          HogGroup("foo"),
+          List.empty,
+          None
+        )
+
+        val job: CommandCallNode = workflowDescriptor.callable.taskCallNodes.head
+        val runtimeAttributes = makeRuntimeAttributes(job)
+        val key = BackendJobDescriptorKey(job, None, 1)
+        val jobDescriptor = BackendJobDescriptor(workflowDescriptor,
+                                                 key,
+                                                 runtimeAttributes,
+                                                 fqnWdlMapToDeclarationMap(inputs),
+                                                 NoDocker,
+                                                 None,
+                                                 Map.empty
+        )
+
+        val props = Props(new TestableGcpBatchJobExecutionActor(jobDescriptor, Promise(), gcpBatchConfiguration))
+        val testActorRef = TestActorRef[TestableGcpBatchJobExecutionActor](
+          props,
+          s"TestableJesJobExecutionActor-${jobDescriptor.workflowDescriptor.id}"
+        )
+
+        val jesInputs = testActorRef.underlyingActor.generateInputs(jobDescriptor)
+
+        jesInputs should have size 2
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "file1",
+            cloudPath = gcsPath("gs://path/to/file1"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/file1"),
+            mount = workingDisk
+          )
+        )
+        jesInputs should contain(
+          GcpBatchFileInput(
+            name = "file2",
+            cloudPath = gcsPath("gs://path/to/file2"),
+            relativeHostPath = DefaultPathBuilder.get("path/to/file2"),
+            mount = workingDisk
+          )
+        )
+
+      case Left(badness) => fail(badness.toList.mkString(", "))
+    }
+  }
+
   it should "create a GcpBatchFileInput for the monitoring script, when specified" in {
 
     val workflowDescriptor = BackendWorkflowDescriptor(

From f9372f9ba5a6ee1dc8bf45a46810a96493b1833c Mon Sep 17 00:00:00 2001
From: Tom Wiseman <twiseman@broadinstitute.org>
Date: Thu, 2 May 2024 15:32:52 -0400
Subject: [PATCH 311/326] [WX-1605] Fix Codecov Report Uploads (#7418)

---
 .github/workflows/integration_tests.yml | 4 ++++
 src/ci/bin/test.inc.sh                  | 1 -
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index aca4a2924c0..5ff831a4b23 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -110,6 +110,10 @@ jobs:
         set -e
         echo Running test.sh
         ./src/ci/bin/test.sh
+    - uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: false # Tolerate missing codecov reports, since not all suites generate them.
     # always() is some github magic that forces the following step to run, even when the previous fails.
     # Without it, the if statement won't be evaluated on a test failure.
     - uses: ravsamhq/notify-slack-action@v2
diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 108a3d09843..14992929f94 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -834,7 +834,6 @@ cromwell::private::setup_prior_version_resources() {
 cromwell::private::generate_code_coverage() {
     sbt -Dsbt.supershell=false --warn coverageReport
     sbt -Dsbt.supershell=false --warn coverageAggregate
-    bash <(curl -s https://codecov.io/bash) > /dev/null || true
 }
 
 cromwell::private::start_build_heartbeat() {

From 9a411cf26f783b43f1d13f4e371f8b44a29b7b28 Mon Sep 17 00:00:00 2001
From: rsaperst <156102201+rsaperst@users.noreply.github.com>
Date: Thu, 2 May 2024 16:59:07 -0400
Subject: [PATCH 312/326] [WX-1410] Sanitize 4 byte UTF-8 characters before
 inserting into METADATA_ENTRY (#7414)

---
 .../cromwell.examples.conf                    |   5 +
 .../metadata/impl/MetadataServiceActor.scala  |   4 +-
 .../metadata/impl/WriteMetadataActor.scala    |  41 ++++++-
 .../impl/WriteMetadataActorBenchmark.scala    |   2 +-
 .../impl/WriteMetadataActorSpec.scala         | 106 ++++++++++++++++--
 .../v2beta/PipelinesUtilityConversions.scala  |   8 +-
 .../PipelinesUtilityConversionsSpec.scala     |  26 -----
 .../test/scala/wdl/util/StringUtilSpec.scala  |  17 +++
 wom/src/main/scala/wdl/util/StringUtil.scala  |  10 ++
 9 files changed, 172 insertions(+), 47 deletions(-)
 delete mode 100644 supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversionsSpec.scala

diff --git a/cromwell.example.backends/cromwell.examples.conf b/cromwell.example.backends/cromwell.examples.conf
index 4ca250d1202..00f99d2ff5a 100644
--- a/cromwell.example.backends/cromwell.examples.conf
+++ b/cromwell.example.backends/cromwell.examples.conf
@@ -498,6 +498,11 @@ services {
     #   # count against this limit.
     #   metadata-read-row-number-safety-threshold = 1000000
     #
+    #   # Remove any UTF-8 mb4 (4 byte) characters from metadata keys in the list.
+    #   # These characters (namely emojis) will cause metadata writing to fail in database collations
+    #   # that do not support 4 byte UTF-8 characters.
+    #   metadata-keys-to-sanitize-utf8mb4 = ["submittedFiles:workflow", "commandLine"]
+    #
     #  metadata-write-statistics {
     #    # Not strictly necessary since the 'metadata-write-statistics' section itself is enough for statistics to be recorded.
     #    # However, this can be set to 'false' to disable statistics collection without deleting the section.
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala
index 5b45d7bb1e0..bcf6346b601 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/MetadataServiceActor.scala
@@ -110,12 +110,14 @@ case class MetadataServiceActor(serviceConfig: Config, globalConfig: Config, ser
   val metadataWriteStatisticsConfig = MetadataStatisticsRecorderSettings(
     serviceConfig.as[Option[Config]]("metadata-write-statistics")
   )
+  val metadataKeysToClean = serviceConfig.getOrElse[List[String]]("metadata-keys-to-sanitize-utf8mb4", List())
   val writeActor = context.actorOf(
     WriteMetadataActor.props(dbBatchSize,
                              dbFlushRate,
                              serviceRegistryActor,
                              LoadConfig.MetadataWriteThreshold,
-                             metadataWriteStatisticsConfig
+                             metadataWriteStatisticsConfig,
+                             metadataKeysToClean
     ),
     "WriteMetadataActor"
   )
diff --git a/services/src/main/scala/cromwell/services/metadata/impl/WriteMetadataActor.scala b/services/src/main/scala/cromwell/services/metadata/impl/WriteMetadataActor.scala
index 16bf344ac6f..82d2ee2a12f 100644
--- a/services/src/main/scala/cromwell/services/metadata/impl/WriteMetadataActor.scala
+++ b/services/src/main/scala/cromwell/services/metadata/impl/WriteMetadataActor.scala
@@ -6,10 +6,11 @@ import cromwell.core.Dispatcher.ServiceDispatcher
 import cromwell.core.Mailbox.PriorityMailbox
 import cromwell.core.WorkflowId
 import cromwell.core.instrumentation.InstrumentationPrefixes
-import cromwell.services.metadata.MetadataEvent
+import cromwell.services.metadata.{MetadataEvent, MetadataValue}
 import cromwell.services.metadata.MetadataService._
 import cromwell.services.metadata.impl.MetadataStatisticsRecorder.MetadataStatisticsRecorderSettings
 import cromwell.services.{EnhancedBatchActor, MetadataServicesStore}
+import wdl.util.StringUtil
 
 import scala.concurrent.duration._
 import scala.util.{Failure, Success}
@@ -18,7 +19,8 @@ class WriteMetadataActor(override val batchSize: Int,
                          override val flushRate: FiniteDuration,
                          override val serviceRegistryActor: ActorRef,
                          override val threshold: Int,
-                         metadataStatisticsRecorderSettings: MetadataStatisticsRecorderSettings
+                         metadataStatisticsRecorderSettings: MetadataStatisticsRecorderSettings,
+                         metadataKeysToClean: List[String]
 ) extends EnhancedBatchActor[MetadataWriteAction](flushRate, batchSize)
     with ActorLogging
     with MetadataDatabaseAccess
@@ -27,9 +29,10 @@ class WriteMetadataActor(override val batchSize: Int,
   private val statsRecorder = MetadataStatisticsRecorder(metadataStatisticsRecorderSettings)
 
   override def process(e: NonEmptyVector[MetadataWriteAction]) = instrumentedProcess {
+    val cleanedMetadataWriteActions = if (metadataKeysToClean.isEmpty) e else sanitizeInputs(e)
     val empty = (Vector.empty[MetadataEvent], List.empty[(Iterable[MetadataEvent], ActorRef)])
 
-    val (putWithoutResponse, putWithResponse) = e.foldLeft(empty) {
+    val (putWithoutResponse, putWithResponse) = cleanedMetadataWriteActions.foldLeft(empty) {
       case ((putEvents, putAndRespondEvents), action: PutMetadataAction) =>
         (putEvents ++ action.events, putAndRespondEvents)
       case ((putEvents, putAndRespondEvents), action: PutMetadataActionAndRespond) =>
@@ -46,7 +49,7 @@ class WriteMetadataActor(override val batchSize: Int,
       case Success(_) =>
         putWithResponse foreach { case (ev, replyTo) => replyTo ! MetadataWriteSuccess(ev) }
       case Failure(cause) =>
-        val (outOfTries, stillGood) = e.toVector.partition(_.maxAttempts <= 1)
+        val (outOfTries, stillGood) = cleanedMetadataWriteActions.toVector.partition(_.maxAttempts <= 1)
 
         handleOutOfTries(outOfTries, cause)
         handleEventsToReconsider(stillGood)
@@ -55,6 +58,23 @@ class WriteMetadataActor(override val batchSize: Int,
     dbAction.map(_ => allPutEvents.size)
   }
 
+  def sanitizeInputs(
+    metadataWriteActions: NonEmptyVector[MetadataWriteAction]
+  ): NonEmptyVector[MetadataWriteAction] =
+    metadataWriteActions.map { metadataWriteAction =>
+      val metadataEvents =
+        metadataWriteAction.events.map { event =>
+          event.value match {
+            case Some(eventVal) => event.copy(value = Option(MetadataValue(StringUtil.cleanUtf8mb4(eventVal.value))))
+            case None => event
+          }
+        }
+      metadataWriteAction match {
+        case action: PutMetadataAction => action.copy(events = metadataEvents)
+        case actionAndResp: PutMetadataActionAndRespond => actionAndResp.copy(events = metadataEvents)
+      }
+    }
+
   private def countActionsByWorkflow(writeActions: Vector[MetadataWriteAction]): Map[WorkflowId, Int] =
     writeActions.flatMap(_.events).groupBy(_.key.workflowId).map { case (k, v) => k -> v.size }
 
@@ -106,9 +126,18 @@ object WriteMetadataActor {
             flushRate: FiniteDuration,
             serviceRegistryActor: ActorRef,
             threshold: Int,
-            statisticsRecorderSettings: MetadataStatisticsRecorderSettings
+            statisticsRecorderSettings: MetadataStatisticsRecorderSettings,
+            metadataKeysToClean: List[String]
   ): Props =
-    Props(new WriteMetadataActor(dbBatchSize, flushRate, serviceRegistryActor, threshold, statisticsRecorderSettings))
+    Props(
+      new WriteMetadataActor(dbBatchSize,
+                             flushRate,
+                             serviceRegistryActor,
+                             threshold,
+                             statisticsRecorderSettings,
+                             metadataKeysToClean
+      )
+    )
       .withDispatcher(ServiceDispatcher)
       .withMailbox(PriorityMailbox)
 }
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorBenchmark.scala b/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorBenchmark.scala
index 1a4783dee87..fd2fb5b3d4e 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorBenchmark.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorBenchmark.scala
@@ -46,7 +46,7 @@ class WriteMetadataActorBenchmark extends TestKitSuite with AnyFlatSpecLike with
 
   it should "provide good throughput" taggedAs IntegrationTest in {
     val writeActor =
-      TestFSMRef(new WriteMetadataActor(1000, 5.seconds, registry, Int.MaxValue, MetadataStatisticsDisabled) {
+      TestFSMRef(new WriteMetadataActor(1000, 5.seconds, registry, Int.MaxValue, MetadataStatisticsDisabled, List()) {
         override val metadataDatabaseInterface: MetadataSlickDatabase = dataAccess
       })
 
diff --git a/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala b/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala
index 9b9e4f75ccd..f8371928cd0 100644
--- a/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala
+++ b/services/src/test/scala/cromwell/services/metadata/impl/WriteMetadataActorSpec.scala
@@ -38,7 +38,7 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
 
   it should "process jobs in the correct batch sizes" in {
     val registry = TestProbe().ref
-    val writeActor = TestFSMRef(new BatchSizeCountingWriteMetadataActor(10, 10.millis, registry, Int.MaxValue) {
+    val writeActor = TestFSMRef(new BatchSizeCountingWriteMetadataActor(10, 10.millis, registry, Int.MaxValue, List()) {
       override val metadataDatabaseInterface = mockDatabaseInterface(0)
     })
 
@@ -71,9 +71,10 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
   failuresBetweenSuccessValues foreach { failureRate =>
     it should s"succeed metadata writes and respond to all senders even with $failureRate failures between each success" in {
       val registry = TestProbe().ref
-      val writeActor = TestFSMRef(new BatchSizeCountingWriteMetadataActor(10, 10.millis, registry, Int.MaxValue) {
-        override val metadataDatabaseInterface = mockDatabaseInterface(failureRate)
-      })
+      val writeActor =
+        TestFSMRef(new BatchSizeCountingWriteMetadataActor(10, 10.millis, registry, Int.MaxValue, List()) {
+          override val metadataDatabaseInterface = mockDatabaseInterface(failureRate)
+        })
 
       def metadataEvent(index: Int, probe: ActorRef) =
         PutMetadataActionAndRespond(List(
@@ -111,7 +112,7 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
 
   it should s"fail metadata writes and respond to all senders with failures" in {
     val registry = TestProbe().ref
-    val writeActor = TestFSMRef(new BatchSizeCountingWriteMetadataActor(10, 10.millis, registry, Int.MaxValue) {
+    val writeActor = TestFSMRef(new BatchSizeCountingWriteMetadataActor(10, 10.millis, registry, Int.MaxValue, List()) {
       override val metadataDatabaseInterface = mockDatabaseInterface(100)
     })
 
@@ -146,6 +147,90 @@ class WriteMetadataActorSpec extends TestKitSuite with AnyFlatSpecLike with Matc
     writeActor.stop()
   }
 
+  it should s"test removing emojis from metadata works as expected" in {
+    val registry = TestProbe().ref
+    val writeActor =
+      TestFSMRef(new BatchSizeCountingWriteMetadataActor(10, 10.millis, registry, Int.MaxValue, List("metadata_key")) {
+        override val metadataDatabaseInterface = mockDatabaseInterface(100)
+      })
+
+    def metadataEvent(index: Int, probe: ActorRef) = PutMetadataActionAndRespond(
+      List(
+        MetadataEvent(MetadataKey(WorkflowId.randomId(), None, "metadata_key"), MetadataValue(s"🎉_$index"))
+      ),
+      probe
+    )
+
+    val probes = (0 until 43)
+      .map { _ =>
+        val probe = TestProbe()
+        probe
+      }
+      .zipWithIndex
+      .map { case (probe, index) =>
+        probe -> metadataEvent(index, probe.ref)
+      }
+
+    val metadataWriteActions = probes.map(probe => probe._2).toVector
+    val metadataWriteActionNE = NonEmptyVector(metadataWriteActions.head, metadataWriteActions.tail)
+
+    val sanitizedWriteActions = writeActor.underlyingActor.sanitizeInputs(metadataWriteActionNE)
+
+    sanitizedWriteActions.map { writeAction =>
+      writeAction.events.map { event =>
+        if (event.value.getOrElse(fail("Removed value from metadata event")).value.matches("[\\x{10000}-\\x{FFFFF}]")) {
+          fail("Metadata event contains emoji")
+        }
+
+        if (!event.value.getOrElse(fail("Removed value from metadata event")).value.contains("\uFFFD")) {
+          fail("Incorrect character used to replace emoji")
+        }
+      }
+    }
+  }
+
+  it should s"test removing emojis from metadata which doesn't contain emojis returns the string" in {
+    val registry = TestProbe().ref
+    val writeActor =
+      TestFSMRef(new BatchSizeCountingWriteMetadataActor(10, 10.millis, registry, Int.MaxValue, List("metadata_key")) {
+        override val metadataDatabaseInterface = mockDatabaseInterface(100)
+      })
+
+    def metadataEvent(index: Int, probe: ActorRef) = PutMetadataActionAndRespond(
+      List(
+        MetadataEvent(MetadataKey(WorkflowId.randomId(), None, "metadata_key"), MetadataValue(s"hello_$index"))
+      ),
+      probe
+    )
+
+    val probes = (0 until 43)
+      .map { _ =>
+        val probe = TestProbe()
+        probe
+      }
+      .zipWithIndex
+      .map { case (probe, index) =>
+        probe -> metadataEvent(index, probe.ref)
+      }
+
+    val metadataWriteActions = probes.map(probe => probe._2).toVector
+    val metadataWriteActionNE = NonEmptyVector(metadataWriteActions.head, metadataWriteActions.tail)
+
+    val sanitizedWriteActions = writeActor.underlyingActor.sanitizeInputs(metadataWriteActionNE)
+
+    sanitizedWriteActions.map { writeAction =>
+      writeAction.events.map { event =>
+        if (event.value.getOrElse(fail("Removed value from metadata event")).value.matches("[\\x{10000}-\\x{FFFFF}]")) {
+          fail("Metadata event contains emoji")
+        }
+
+        if (event.value.getOrElse(fail("Removed value from metadata event")).value.contains("\uFFFD")) {
+          fail("Incorrectly replaced character in metadata event")
+        }
+      }
+    }
+  }
+
   // Mock database interface.
   // A customizable number of failures occur between each success
   def mockDatabaseInterface(failuresBetweenEachSuccess: Int) = new MetadataSqlDatabase with SqlDatabase {
@@ -382,8 +467,15 @@ object WriteMetadataActorSpec {
   class BatchSizeCountingWriteMetadataActor(override val batchSize: Int,
                                             override val flushRate: FiniteDuration,
                                             override val serviceRegistryActor: ActorRef,
-                                            override val threshold: Int
-  ) extends WriteMetadataActor(batchSize, flushRate, serviceRegistryActor, threshold, MetadataStatisticsDisabled) {
+                                            override val threshold: Int,
+                                            val metadataKeysToClean: List[String]
+  ) extends WriteMetadataActor(batchSize,
+                               flushRate,
+                               serviceRegistryActor,
+                               threshold,
+                               MetadataStatisticsDisabled,
+                               metadataKeysToClean
+      ) {
 
     var batchSizes: Vector[Int] = Vector.empty
     var failureCount: Int = 0
diff --git a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala
index a1e08007b05..486a7ad28b1 100644
--- a/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala
+++ b/supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversions.scala
@@ -8,6 +8,7 @@ import cromwell.core.ExecutionEvent
 import cromwell.core.logging.JobLogger
 import mouse.all._
 import PipelinesUtilityConversions._
+import wdl.util.StringUtil
 
 import scala.language.postfixOps
 
@@ -67,7 +68,7 @@ trait PipelinesUtilityConversions {
     // characters (typically emoji). Some databases have trouble storing these; replace them with the standard
     // "unknown character" unicode symbol.
     val name = Option(event.getContainerStopped) match {
-      case Some(_) => cleanUtf8mb4(event.getDescription)
+      case Some(_) => StringUtil.cleanUtf8mb4(event.getDescription)
       case _ => event.getDescription
     }
 
@@ -101,9 +102,4 @@ object PipelinesUtilityConversions {
         None
       }
   }
-
-  lazy val utf8mb4Regex = "[\\x{10000}-\\x{FFFFF}]"
-  lazy val utf8mb3Replacement = "\uFFFD" // This is the standard char for replacing invalid/unknown unicode chars
-  def cleanUtf8mb4(in: String): String =
-    in.replaceAll(utf8mb4Regex, utf8mb3Replacement)
 }
diff --git a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversionsSpec.scala b/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversionsSpec.scala
deleted file mode 100644
index eeef482a740..00000000000
--- a/supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/PipelinesUtilityConversionsSpec.scala
+++ /dev/null
@@ -1,26 +0,0 @@
-package cromwell.backend.google.pipelines.v2beta
-
-import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.matchers.should.Matchers
-
-class PipelinesUtilityConversionsSpec extends AnyFlatSpec with Matchers {
-  behavior of "PipelinesUtilityConversions"
-
-  it should "not modify strings that contain only ascii characters" in {
-    val input = "hi there!?"
-    PipelinesUtilityConversions.cleanUtf8mb4(input) shouldBe input
-  }
-
-  it should "not modify strings with 3-byte unicode characters" in {
-    val input = "Here is my non-ascii character: \u1234 Do you like it?"
-    PipelinesUtilityConversions.cleanUtf8mb4(input) shouldBe input
-  }
-
-  it should "replace 4-byte unicode characters" in {
-    val cry = new String(Character.toChars(Integer.parseInt("1F62D", 16)))
-    val barf = new String(Character.toChars(Integer.parseInt("1F92E", 16)))
-    val input = s"When I try to put an emoji in the database it $barf and then I $cry"
-    val cleaned = "When I try to put an emoji in the database it \uFFFD and then I \uFFFD"
-    PipelinesUtilityConversions.cleanUtf8mb4(input) shouldBe cleaned
-  }
-}
diff --git a/wdl/model/draft2/src/test/scala/wdl/util/StringUtilSpec.scala b/wdl/model/draft2/src/test/scala/wdl/util/StringUtilSpec.scala
index 7c466aca30e..b3ccadc9fc6 100644
--- a/wdl/model/draft2/src/test/scala/wdl/util/StringUtilSpec.scala
+++ b/wdl/model/draft2/src/test/scala/wdl/util/StringUtilSpec.scala
@@ -70,4 +70,21 @@ class StringUtilSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     }
   }
 
+  it should "not modify strings that contain only ascii characters" in {
+    val input = "hi there!?"
+    StringUtil.cleanUtf8mb4(input) shouldBe input
+  }
+
+  it should "not modify strings with 3-byte unicode characters" in {
+    val input = "Here is my non-ascii character: \u1234 Do you like it?"
+    StringUtil.cleanUtf8mb4(input) shouldBe input
+  }
+
+  it should "replace 4-byte unicode characters" in {
+    val cry = new String(Character.toChars(Integer.parseInt("1F62D", 16)))
+    val barf = new String(Character.toChars(Integer.parseInt("1F92E", 16)))
+    val input = s"When I try to put an emoji in the database it $barf and then I $cry"
+    val cleaned = "When I try to put an emoji in the database it \uFFFD and then I \uFFFD"
+    StringUtil.cleanUtf8mb4(input) shouldBe cleaned
+  }
 }
diff --git a/wom/src/main/scala/wdl/util/StringUtil.scala b/wom/src/main/scala/wdl/util/StringUtil.scala
index f89c4fd73da..03821457be5 100644
--- a/wom/src/main/scala/wdl/util/StringUtil.scala
+++ b/wom/src/main/scala/wdl/util/StringUtil.scala
@@ -8,6 +8,8 @@ import scala.annotation.tailrec
   * WOMmy TaskDefinition. That should get straightened out. */
 object StringUtil {
   val Ws = Pattern.compile("[\\ \\t]+")
+  val utf8mb4Regex = "[\\x{10000}-\\x{FFFFF}]"
+  val utf8mb3Replacement = "\uFFFD" // This is the standard char for replacing
 
   /**
     * 1) Remove all leading newline chars
@@ -63,4 +65,12 @@ object StringUtil {
 
     start(0)
   }
+
+  /**
+   * Remove all utf8mb4 exclusive characters (emoji) from the given string.
+   * @param in String to clean
+   * @return String with all utf8mb4 exclusive characters removed
+   */
+  def cleanUtf8mb4(in: String): String =
+    in.replaceAll(utf8mb4Regex, utf8mb3Replacement)
 }

From 2ebd62bc27a84d89f2dd96aa5968bc332879d6e4 Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Thu, 2 May 2024 18:10:58 -0400
Subject: [PATCH 313/326] WX-1566 Special Docker build for debugging (#7417)

Run `sbt -Dproject.isDebug=true server/docker`
---
 .github/workflows/chart_update_on_merge.yml   |    2 +-
 .github/workflows/docker_build_test.yml       |    8 +-
 .github/workflows/trivy.yml                   |    1 -
 build.sbt                                     |    6 -
 docs/developers/Building.md                   |   23 +-
 perf/src/main/resources/logback.xml           |   29 -
 perf/src/main/scala/cromwell/perf/Call.scala  |   90 -
 .../scala/cromwell/perf/CompareMetadata.scala |  153 --
 .../main/scala/cromwell/perf/Metadata.scala   |   74 -
 project/Dependencies.scala                    |    4 -
 project/Publishing.scala                      |   75 +-
 project/Version.scala                         |   41 +-
 scripts/perf/clone_database/clone_database.sh |   21 -
 .../perf/delete_database/delete_database.sh   |   15 -
 .../delete_horicromtal/delete_horicromtal.sh  |   16 -
 .../perf/delete_instance/delete_instance.sh   |   15 -
 .../deploy_horicromtal/deploy_horicromtal.sh  |   90 -
 .../deploy_horicromtal/run_on_instance.sh     |   78 -
 .../perf/deploy_instance/deploy_instance.sh   |   59 -
 .../perf/deploy_instance/run_on_instance.sh   |   72 -
 scripts/perf/helper.inc.sh                    |  279 ---
 .../create_runner_instance.sh                 |   47 -
 .../test_runner_script.sh                     |   88 -
 scripts/perf/start_database/start_database.sh |    6 -
 scripts/perf/stop_database/stop_database.sh   |    6 -
 .../blacklist_call_caching_stress.test        |   12 -
 .../centaur.conf                              |   18 -
 .../cromwell.conf                             |    9 -
 .../call_caching_stress_lots_of_inputs.test   |   11 -
 .../lots_of_inputs.inputs                     |  804 --------
 .../lots_of_inputs.wdl                        |   28 -
 .../call_caching_stress_no_hint.test          |   12 -
 .../call_caching_stress_no_hint/centaur.conf  |   18 -
 .../call_caching_stress_no_hint/cromwell.conf |    5 -
 .../call_caching_stress_with_hint.test        |   12 -
 .../centaur.conf                              |   18 -
 .../cromwell.conf                             |    5 -
 .../callCachingStress.inputs                  |   14 -
 .../callCachingStress.wdl                     |   32 -
 .../five_dollar_genome.inputs                 |   39 -
 .../five_dollar_genome.test                   |   11 -
 .../five_dollar_genome/five_dollar_genome.wdl |  521 -----
 scripts/perf/test_cases/gary/gary.inputs      |   12 -
 scripts/perf/test_cases/gary/gary.test        |   11 -
 scripts/perf/test_cases/gary/gary.wdl         |   40 -
 scripts/perf/test_cases/hello/hello.test      |   16 -
 scripts/perf/test_cases/reader/cromwell.conf  |    8 -
 scripts/perf/vm_scripts/centaur/centaur.conf  |   17 -
 .../perf/vm_scripts/cromwell-dashboard.json   | 1703 -----------------
 .../perf/vm_scripts/cromwell/cromwell.conf    |   95 -
 scripts/perf/vm_scripts/docker-compose.yml    |   32 -
 .../perf/vm_scripts/statsd-proxy/proxy.conf   |   11 -
 52 files changed, 111 insertions(+), 4701 deletions(-)
 delete mode 100644 perf/src/main/resources/logback.xml
 delete mode 100644 perf/src/main/scala/cromwell/perf/Call.scala
 delete mode 100644 perf/src/main/scala/cromwell/perf/CompareMetadata.scala
 delete mode 100644 perf/src/main/scala/cromwell/perf/Metadata.scala
 delete mode 100755 scripts/perf/clone_database/clone_database.sh
 delete mode 100755 scripts/perf/delete_database/delete_database.sh
 delete mode 100755 scripts/perf/delete_horicromtal/delete_horicromtal.sh
 delete mode 100755 scripts/perf/delete_instance/delete_instance.sh
 delete mode 100755 scripts/perf/deploy_horicromtal/deploy_horicromtal.sh
 delete mode 100644 scripts/perf/deploy_horicromtal/run_on_instance.sh
 delete mode 100755 scripts/perf/deploy_instance/deploy_instance.sh
 delete mode 100644 scripts/perf/deploy_instance/run_on_instance.sh
 delete mode 100644 scripts/perf/helper.inc.sh
 delete mode 100755 scripts/perf/run_centaur_blocking/create_runner_instance.sh
 delete mode 100644 scripts/perf/run_centaur_blocking/test_runner_script.sh
 delete mode 100644 scripts/perf/start_database/start_database.sh
 delete mode 100644 scripts/perf/stop_database/stop_database.sh
 delete mode 100644 scripts/perf/test_cases/blacklist_call_caching_stress/blacklist_call_caching_stress.test
 delete mode 100644 scripts/perf/test_cases/blacklist_call_caching_stress/centaur.conf
 delete mode 100644 scripts/perf/test_cases/blacklist_call_caching_stress/cromwell.conf
 delete mode 100644 scripts/perf/test_cases/call_caching_lots_of_inputs/call_caching_stress_lots_of_inputs.test
 delete mode 100644 scripts/perf/test_cases/call_caching_lots_of_inputs/lots_of_inputs.inputs
 delete mode 100644 scripts/perf/test_cases/call_caching_lots_of_inputs/lots_of_inputs.wdl
 delete mode 100644 scripts/perf/test_cases/call_caching_stress_no_hint/call_caching_stress_no_hint.test
 delete mode 100644 scripts/perf/test_cases/call_caching_stress_no_hint/centaur.conf
 delete mode 100644 scripts/perf/test_cases/call_caching_stress_no_hint/cromwell.conf
 delete mode 100644 scripts/perf/test_cases/call_caching_stress_with_hint/call_caching_stress_with_hint.test
 delete mode 100644 scripts/perf/test_cases/call_caching_stress_with_hint/centaur.conf
 delete mode 100644 scripts/perf/test_cases/call_caching_stress_with_hint/cromwell.conf
 delete mode 100644 scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.inputs
 delete mode 100644 scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.wdl
 delete mode 100644 scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.inputs
 delete mode 100644 scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.test
 delete mode 100644 scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.wdl
 delete mode 100644 scripts/perf/test_cases/gary/gary.inputs
 delete mode 100644 scripts/perf/test_cases/gary/gary.test
 delete mode 100644 scripts/perf/test_cases/gary/gary.wdl
 delete mode 100644 scripts/perf/test_cases/hello/hello.test
 delete mode 100644 scripts/perf/test_cases/reader/cromwell.conf
 delete mode 100644 scripts/perf/vm_scripts/centaur/centaur.conf
 delete mode 100644 scripts/perf/vm_scripts/cromwell-dashboard.json
 delete mode 100644 scripts/perf/vm_scripts/cromwell/cromwell.conf
 delete mode 100644 scripts/perf/vm_scripts/docker-compose.yml
 delete mode 100644 scripts/perf/vm_scripts/statsd-proxy/proxy.conf

diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml
index a2b14f2ec65..a17dd971436 100644
--- a/.github/workflows/chart_update_on_merge.yml
+++ b/.github/workflows/chart_update_on_merge.yml
@@ -60,7 +60,7 @@ jobs:
       run: |
         set -e
         cd cromwell
-        sbt -Dproject.isSnapshot=false -Dproject.isRelease=false dockerBuildAndPush
+        sbt -Dproject.isSnapshot=false dockerBuildAndPush
     - name: Deploy to dev and board release train (Cromwell)
       uses: broadinstitute/repository-dispatch@master
       with:
diff --git a/.github/workflows/docker_build_test.yml b/.github/workflows/docker_build_test.yml
index 01c2ea502c9..b4d373f330e 100644
--- a/.github/workflows/docker_build_test.yml
+++ b/.github/workflows/docker_build_test.yml
@@ -34,4 +34,10 @@ jobs:
         run: |
           set -e
           cd cromwell
-          sbt -Dproject.isSnapshot=false -Dproject.isRelease=false docker
+          sbt -Dproject.isSnapshot=false docker
+      # Rarely used but we really want it always working for emergencies
+      - name: Build Cromwell Debug Docker
+        run: |
+          set -e
+          cd cromwell
+          sbt -Dproject.isDebug=true docker
diff --git a/.github/workflows/trivy.yml b/.github/workflows/trivy.yml
index b005da65041..d353eae4e58 100644
--- a/.github/workflows/trivy.yml
+++ b/.github/workflows/trivy.yml
@@ -12,7 +12,6 @@ jobs:
         project:
         - cromiam
         - cromwell-drs-localizer
-        - perf
         - server
         - womtool
 
diff --git a/build.sbt b/build.sbt
index a3029d0ab09..8e480907c5e 100644
--- a/build.sbt
+++ b/build.sbt
@@ -387,11 +387,6 @@ lazy val `cloud-nio-impl-drs` = (project in cloudNio / "cloud-nio-impl-drs")
   .dependsOn(common)
   .dependsOn(common % "test->test")
 
-lazy val perf = project
-  .withExecutableSettings("perf", dependencies = perfDependencies, pushDocker = false)
-  .dependsOn(common)
-  .dependsOn(common % "test->test")
-
 lazy val `cromwell-drs-localizer` = project
   .withExecutableSettings("cromwell-drs-localizer", drsLocalizerDependencies, drsLocalizerSettings)
   .dependsOn(`cloud-nio-impl-drs`)
@@ -453,7 +448,6 @@ lazy val root = (project in file("."))
   .aggregate(googleBatch)
   .aggregate(httpFileSystem)
   .aggregate(languageFactoryCore)
-  .aggregate(perf)
   .aggregate(server)
   .aggregate(services)
   .aggregate(sfsBackend)
diff --git a/docs/developers/Building.md b/docs/developers/Building.md
index 5c5cc21eaf7..08ffe7a3ddd 100644
--- a/docs/developers/Building.md
+++ b/docs/developers/Building.md
@@ -8,13 +8,6 @@ features or fixes, the following are required to build Cromwell from source:
 * [AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/)
 * [Git](https://git-scm.com/)
 
-You can also use the [development image](https://github.com/broadinstitute/cromwell/tree/develop/scripts/docker-develop), and build a development container to work inside:
-
-```bash
-$ docker build -t cromwell-dev .
-$ docker run -it cromwell-dev bash
-```
-
 First start by cloning the Cromwell repository from GitHub:
 
 ```bash
@@ -35,15 +28,15 @@ Finally build the Cromwell jar:
 $ sbt assembly
 ```
 
-NOTE: This command will run for a long time the first time.  
-NOTE: Compiling will not succeed on directories encrypted with ecryptfs (ubuntu encrypted home dirs for example), due to long file paths.
-
 `sbt assembly` will build the runnable Cromwell JAR in `server/target/scala-2.13/` with a name like `cromwell-<VERSION>.jar`. It will also build a runnable Womtool JAR in `womtool/target/scala-2.13/` with a name like `womtool-<VERSION>.jar`.
 
-To build a [Docker](https://www.docker.com/) image, run:
+## Docker
 
-```bash
-$ sbt server/docker
-```
+The following Docker build configurations are supported. Most users will want Snapshot, resulting in an image like `broadinstitute/cromwell:<VERSION>-SNAP`.
 
-This will build and tag a Docker image with a name like `broadinstitute/cromwell:<VERSION>-SNAP`.
+| Command                                        | Build Type | Debug Tools | Description                          |
+|------------------------------------------------|------------|-------------|--------------------------------------|
+| `sbt server/docker`                            | Snapshot   | No          | Most common local build              |
+| `sbt -Dproject.isDebug=true server/docker`     | Debug      | Yes         | Local build with debugging/profiling |
+| `sbt -Dproject.isSnapshot=false server/docker` | Standard   | No          | Reserved for CI: commit on `develop` |
+| `sbt -Dproject.isRelease=true server/docker`   | Release    | No          | Reserved for CI: numbered release    |
diff --git a/perf/src/main/resources/logback.xml b/perf/src/main/resources/logback.xml
deleted file mode 100644
index 8a90f3ba0ab..00000000000
--- a/perf/src/main/resources/logback.xml
+++ /dev/null
@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<configuration>
-
-    <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender" target="System.out">
-        <filter class="ch.qos.logback.classic.filter.LevelFilter">
-            <level>INFO</level>
-            <onMatch>ACCEPT</onMatch>
-            <onMismatch>DENY</onMismatch>
-        </filter>
-        <encoder>
-            <pattern>%msg%n</pattern>
-        </encoder>
-    </appender>
-
-    <appender name="STDERR" class="ch.qos.logback.core.ConsoleAppender" target="System.err">
-        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
-            <level>ERROR</level>
-        </filter>
-        <encoder>
-            <pattern>%red(%msg%n)</pattern>
-        </encoder>
-    </appender>
-
-    <root level="INFO">
-        <appender-ref ref="STDOUT" />
-        <appender-ref ref="STDERR" />
-    </root>
-
-</configuration>
diff --git a/perf/src/main/scala/cromwell/perf/Call.scala b/perf/src/main/scala/cromwell/perf/Call.scala
deleted file mode 100644
index b8e91589126..00000000000
--- a/perf/src/main/scala/cromwell/perf/Call.scala
+++ /dev/null
@@ -1,90 +0,0 @@
-package cromwell.perf
-
-import java.time.{Duration, OffsetDateTime}
-
-import io.circe.JsonObject
-
-case class CallCaching(hit: Option[Boolean],
-                       result: Option[String],
-                       hitFailures: Option[Seq[Map[String, Seq[JsonObject]]]]
-)
-
-case class ExecutionEvents(startTime: OffsetDateTime, description: String, endTime: OffsetDateTime)
-
-case class Call(shardIndex: Int,
-                start: OffsetDateTime,
-                end: OffsetDateTime,
-                callCaching: Option[CallCaching],
-                executionEvents: Seq[ExecutionEvents]
-) {
-  val callCachingEventStates =
-    List("CheckingCallCache", "FetchingCachedOutputsFromDatabase", "BackendIsCopyingCachedOutputs")
-  val jobPreparationEventStates =
-    List("Pending", "RequestingExecutionToken", "WaitingForValueStore", "PreparingJob", "CheckingJobStore")
-  val cacheCopyingEventStates = List("FetchingCachedOutputsFromDatabase", "BackendIsCopyingCachedOutputs")
-
-  /**
-    * @return Cache copy retries before getting a successful hit or running the job
-    */
-  val cacheCopyRetries: Int = {
-    val numFailures: Option[Int] = for {
-      cachingObject <- callCaching
-      failuresMap <- cachingObject.hitFailures
-    } yield failuresMap.size
-
-    numFailures.getOrElse(0)
-  }
-
-  /***
-    * @return Time (in Duration) job spent in just CheckingCallCache state
-    */
-  val timeInCheckingCallCacheState: Duration = {
-    val eventsRelatedToCC = executionEvents.collect {
-      case event if event.description.equalsIgnoreCase("CheckingCallCache") =>
-        Duration.between(event.startTime, event.endTime)
-    }
-
-    if (eventsRelatedToCC.nonEmpty) eventsRelatedToCC.reduce(_ plus _) else Duration.ZERO
-  }
-
-  /**
-    * @return Time (in Duration) job spent in Call Caching states
-    */
-  val timeInCallCachingState: Duration = {
-    val eventsRelatedToCC =
-      executionEvents.filter(event => callCachingEventStates.exists(state => state.equalsIgnoreCase(event.description)))
-
-    if (eventsRelatedToCC.nonEmpty) {
-      val eventsSortedByStartTime = eventsRelatedToCC.sortBy(_.startTime)
-      Duration.between(eventsSortedByStartTime.head.startTime, eventsSortedByStartTime.last.endTime)
-    } else Duration.ZERO
-  }
-
-  /**
-    * @return Time (in Duration) job spent in job preparation state i.e time between job submission and running it
-    *         (this doesn't consider the time it spent in call caching states
-    */
-  val timeInJobPreparation: Duration = {
-    val durationOfEventsInPreparationState = executionEvents.collect {
-      case event if jobPreparationEventStates.exists(_.equalsIgnoreCase(event.description)) =>
-        Duration.between(event.startTime, event.endTime)
-    }
-
-    if (durationOfEventsInPreparationState.nonEmpty) durationOfEventsInPreparationState.reduce(_ plus _)
-    else Duration.ZERO
-  }
-
-  /**
-    *
-    * @return Time (in Duration) job spent in fetching and copying cache hit(s)
-    */
-  val timeForFetchingAndCopyingCacheHit: Duration = {
-    val durationOfEventsInCacheCopyingState = executionEvents.collect {
-      case event if cacheCopyingEventStates.exists(_.equalsIgnoreCase(event.description)) =>
-        Duration.between(event.startTime, event.endTime)
-    }
-
-    if (durationOfEventsInCacheCopyingState.nonEmpty) durationOfEventsInCacheCopyingState.reduce(_ plus _)
-    else Duration.ZERO
-  }
-}
diff --git a/perf/src/main/scala/cromwell/perf/CompareMetadata.scala b/perf/src/main/scala/cromwell/perf/CompareMetadata.scala
deleted file mode 100644
index 64e49d93807..00000000000
--- a/perf/src/main/scala/cromwell/perf/CompareMetadata.scala
+++ /dev/null
@@ -1,153 +0,0 @@
-package cromwell.perf
-
-import java.io.FileInputStream
-import java.time.{Duration, OffsetDateTime}
-
-import better.files.File
-import cats.data.Validated.{Invalid, Valid}
-import cats.syntax.all._
-import cats.instances.list._
-import com.google.auth.oauth2.GoogleCredentials
-import com.google.cloud.storage.StorageOptions
-import com.typesafe.scalalogging.StrictLogging
-import common.validation.ErrorOr._
-import io.circe._
-import io.circe.generic.semiauto._
-import io.circe.parser._
-
-object CompareMetadata extends App with StrictLogging {
-  private val REGRESSION_CONST = 1.1
-
-  // If removed, IntelliJ (Oct '18) thinks the import isn't used.
-  // Later the compiler fails to find a decoder for OffsetDateTime.
-  lazy val anchorOffsetDateTime: Decoder[OffsetDateTime] = implicitly
-  implicit lazy val decodeCall: Decoder[Call] = deriveDecoder
-  implicit lazy val decodeCallCaching: Decoder[CallCaching] = deriveDecoder
-  implicit lazy val decodeExecutionEvents: Decoder[ExecutionEvents] = deriveDecoder
-  implicit lazy val decodeMetadata: Decoder[Metadata] = deriveDecoder
-
-  def parseMetadataFromLocalFile(filePath: String): Either[Error, Metadata] = {
-    val metadataFile = File(filePath)
-    val metadataFileContent = metadataFile.contentAsString
-
-    decode[Metadata](metadataFileContent)
-  }
-
-  def parseMetadataFromGcsFile(gcsUrl: String, pathToServiceAccount: String): Either[Error, Metadata] = {
-    val gcsUrlArray = gcsUrl.replace("gs://", "").split("/", 2)
-    val Array(gcsBucket, fileToBeLocalized) = gcsUrlArray
-
-    val credentials = GoogleCredentials.fromStream(new FileInputStream(pathToServiceAccount))
-    val storage = StorageOptions.newBuilder().setCredentials(credentials).build().getService
-    val blob = storage.get(gcsBucket, fileToBeLocalized)
-    val metadataFileContent = blob.getContent().map(_.toChar).mkString
-
-    decode[Metadata](metadataFileContent)
-  }
-
-  def parseMetadata(inputFile: String, pathToServiceAccount: String): Either[Error, Metadata] =
-    if (inputFile.startsWith("gs://"))
-      parseMetadataFromGcsFile(inputFile, pathToServiceAccount)
-    else parseMetadataFromLocalFile(inputFile)
-
-  def displayComputedMetrics(metadata: Metadata, displayMsg: String): Unit = {
-    logger.info(displayMsg)
-
-    logger.info(s"Workflow started after: ${metadata.workflowStartedAfter}")
-    logger.info(s"Workflow Running time: ${metadata.workflowRunningTime}")
-    logger.info(s"Total jobs per root workflow: ${metadata.totalJobsPerRootWf}")
-    logger.info(s"Avg cache copy retries: ${metadata.avgCacheRetries}")
-    logger.info(s"Avg time job spent in Call Caching state: ${metadata.avgTimeInCallCachingState}")
-    logger.info(s"Avg time job spent in just CheckingCallCache state: ${metadata.avgTimeInCheckingCallCacheState}")
-    logger.info(s"Avg time job spent in Job Preparation state: ${metadata.avgTimeInJobPreparation}")
-    logger.info(
-      s"Avg time job spent in fetching and copying cache hit(s) state: ${metadata.avgTimeForFetchingAndCopyingCacheHit}"
-    )
-  }
-
-  /***
-    * Compares the metrics in Metadata which have type 'Duration' (mostly the ones related to time metrics)
-    */
-  def compareDurationMetrics(metadataOld: Metadata,
-                             metadataNew: Metadata,
-                             metricFunc: Metadata => Duration,
-                             metricName: String
-  ): ErrorOr[String] =
-    if (metricFunc(metadataNew).toMillis > REGRESSION_CONST * metricFunc(metadataOld).toMillis) {
-      (s"$metricName of new metadata is greater than 10% of old metadata. " +
-        s"New metric value: ${metricFunc(metadataNew)}. " +
-        s"Old metric value: ${metricFunc(metadataOld)}.").invalidNel[String]
-    } else s"$metricName hasn't regressed yet".valid
-
-  /***
-    * Compares the metrics in Metadata which have type 'Int' (mostly the ones related to size metrics)
-    */
-  def compareIntMetrics(metadataOld: Metadata,
-                        metadataNew: Metadata,
-                        metricFunc: Metadata => Int,
-                        metricName: String
-  ): ErrorOr[String] =
-    if (metricFunc(metadataNew) > REGRESSION_CONST * metricFunc(metadataOld)) {
-      (s"$metricName of new metadata is greater than 10% of old metadata. " +
-        s"New metric value: ${metricFunc(metadataNew)}. " +
-        s"Old metric value: ${metricFunc(metadataOld)}.").invalidNel[String]
-    } else s"$metricName hasn't regressed yet".valid
-
-  def compareMetadataMetrics(metadataOld: Metadata, metadataNew: Metadata): ErrorOr[List[String]] = {
-    val durationFuncList: List[(Metadata => Duration, String)] = List(
-      (_.workflowStartedAfter, "workflowStartedAfter"),
-      (_.workflowRunningTime, "workflowRunningTime"),
-      (_.avgTimeInCallCachingState, "avgTimeInCallCachingState"),
-      (_.avgTimeInCheckingCallCacheState, "avgTimeInCheckingCallCacheState"),
-      (_.avgTimeInJobPreparation, "avgTimeInJobPreparation"),
-      (_.avgTimeForFetchingAndCopyingCacheHit, "avgTimeForFetchingAndCopyingCacheHit")
-    )
-
-    val intFuncList: List[(Metadata => Int, String)] =
-      List((_.totalJobsPerRootWf, "totalJobsPerRootWf"), (_.avgCacheRetries, "avgCacheRetries"))
-
-    val durationMetricsComp = durationFuncList.map(x => compareDurationMetrics(metadataOld, metadataNew, x._1, x._2))
-    val intMetricsComp = intFuncList.map(x => compareIntMetrics(metadataOld, metadataNew, x._1, x._2))
-    (durationMetricsComp ::: intMetricsComp).sequence[ErrorOr, String]
-  }
-
-  def printParseErrorToConsoleAndExit(metadataFile: String, error: Error, systemExit: Boolean): Unit = {
-    logger.error(s"Something went wrong while parsing $metadataFile. Error: ${error.getLocalizedMessage}")
-    if (systemExit) System.exit(1)
-  }
-
-  def generateAndCompareMetrics(metadataOldEither: Either[Error, Metadata],
-                                metadataNewEither: Either[Error, Metadata]
-  ): Unit =
-    (metadataOldEither, metadataNewEither) match {
-      case (Right(metadataOld), Right(metadataNew)) =>
-        val metadataOldMsg = s"Metrics for metadata generated from ${args(0)}"
-        val metadataNewMsg = s"\nMetrics for metadata generated from ${args(1)}"
-        displayComputedMetrics(metadataOld, metadataOldMsg)
-        displayComputedMetrics(metadataNew, metadataNewMsg)
-        compareMetadataMetrics(metadataOld, metadataNew) match {
-          case Valid(_) => logger.info("\nYAY!! Metrics from new metadata json haven't regressed!")
-          case Invalid(listOfErrors) =>
-            logger.error("\nBelow metadata metrics have regressed:")
-            logger.error(listOfErrors.toList.mkString("\n"))
-            System.exit(1)
-        }
-      case (Right(_), Left(e)) => printParseErrorToConsoleAndExit(args(1), e, systemExit = true)
-      case (Left(e), Right(_)) => printParseErrorToConsoleAndExit(args(0), e, systemExit = true)
-      case (Left(e1), Left(e2)) =>
-        printParseErrorToConsoleAndExit(args(0), e1, systemExit = false)
-        printParseErrorToConsoleAndExit(args(1), e2, systemExit = true)
-    }
-
-  args.length match {
-    case 2 =>
-      if (args(0).startsWith("gs://") || args(1).startsWith("gs://")) {
-        logger.error("Path to service account is needed to download GCS file. Please pass it as 3rd argument.")
-        System.exit(1)
-      } else generateAndCompareMetrics(parseMetadataFromLocalFile(args(0)), parseMetadataFromLocalFile(args(1)))
-    case 3 => generateAndCompareMetrics(parseMetadata(args(0), args(2)), parseMetadata(args(1), args(2)))
-    case _ =>
-      logger.error("Please pass in 2 file paths!")
-      System.exit(1)
-  }
-}
diff --git a/perf/src/main/scala/cromwell/perf/Metadata.scala b/perf/src/main/scala/cromwell/perf/Metadata.scala
deleted file mode 100644
index b61e88c795a..00000000000
--- a/perf/src/main/scala/cromwell/perf/Metadata.scala
+++ /dev/null
@@ -1,74 +0,0 @@
-package cromwell.perf
-
-import java.time.{Duration, OffsetDateTime}
-
-case class Metadata(id: String,
-                    workflowName: String,
-                    submission: OffsetDateTime,
-                    start: OffsetDateTime,
-                    end: OffsetDateTime,
-                    status: String,
-                    calls: Option[Map[String, Seq[Call]]]
-) {
-
-  private def addInt(x: Int, y: Int): Int = x + y
-
-  private def addDuration(x: Duration, y: Duration): Duration = x.plus(y)
-
-  private def sumElementsInOptionSeq[A](listOption: Option[Iterable[A]], op: (A, A) => A, default: A): A =
-    listOption match {
-      case Some(list) => list.reduce[A]((a, b) => op(a, b))
-      case None => default
-    }
-
-  /**
-    * @return Time between the submission and start of workflow
-    */
-  val workflowStartedAfter: Duration = Duration.between(submission, start)
-
-  val workflowRunningTime: Duration = Duration.between(start, end)
-
-  val totalJobsPerRootWf: Int =
-    sumElementsInOptionSeq(calls.map(taskMap => taskMap.map(callsPerTask => callsPerTask._2.size)), addInt, 0)
-
-  val avgCacheRetries: Int =
-    if (totalJobsPerRootWf > 0) {
-      val cacheRetriesList =
-        calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.cacheCopyRetries)))
-      sumElementsInOptionSeq(cacheRetriesList, addInt, 0) / totalJobsPerRootWf
-    } else 0
-
-  val avgTimeInCallCachingState: Duration =
-    if (totalJobsPerRootWf > 0) {
-      val timeInCallCachingStateList =
-        calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeInCallCachingState)))
-      sumElementsInOptionSeq(timeInCallCachingStateList, addDuration, Duration.ZERO).dividedBy(
-        totalJobsPerRootWf.toLong
-      )
-    } else Duration.ZERO
-
-  val avgTimeInCheckingCallCacheState: Duration =
-    if (totalJobsPerRootWf > 0) {
-      val timeInCheckingCallCacheStateList = calls.map(taskMap =>
-        taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeInCheckingCallCacheState))
-      )
-      sumElementsInOptionSeq(timeInCheckingCallCacheStateList, addDuration, Duration.ZERO).dividedBy(
-        totalJobsPerRootWf.toLong
-      )
-    } else Duration.ZERO
-
-  val avgTimeInJobPreparation: Duration =
-    if (totalJobsPerRootWf > 0) {
-      val timeInJobPreparationList =
-        calls.map(taskMap => taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeInJobPreparation)))
-      sumElementsInOptionSeq(timeInJobPreparationList, addDuration, Duration.ZERO).dividedBy(totalJobsPerRootWf.toLong)
-    } else Duration.ZERO
-
-  val avgTimeForFetchingAndCopyingCacheHit: Duration =
-    if (totalJobsPerRootWf > 0) {
-      val timeInCopyingList = calls.map(taskMap =>
-        taskMap.flatMap(callsPerTask => callsPerTask._2.map(call => call.timeForFetchingAndCopyingCacheHit))
-      )
-      sumElementsInOptionSeq(timeInCopyingList, addDuration, Duration.ZERO).dividedBy(totalJobsPerRootWf.toLong)
-    } else Duration.ZERO
-}
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 8a12d0e0cc2..fc9beae1f12 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -643,9 +643,6 @@ object Dependencies {
   // Version of the swagger UI to write into config files
   val swaggerUiVersion: String = swaggerUiV
 
-  val perfDependencies: List[ModuleID] = circeDependencies ++ betterFilesDependencies ++ commonDependencies ++
-    googleApiClientDependencies ++ googleCloudDependencies
-
   val drsLocalizerDependencies: List[ModuleID] = List(
     "com.google.auth" % "google-auth-library-oauth2-http" % googleOauth2V,
     "com.google.cloud" % "google-cloud-storage" % googleCloudStorageV,
@@ -675,7 +672,6 @@ object Dependencies {
       implDrsDependencies ++
       implFtpDependencies ++
       languageFactoryDependencies ++
-      perfDependencies ++
       serverDependencies ++
       sfsBackendDependencies ++
       spiDependencies ++
diff --git a/project/Publishing.scala b/project/Publishing.scala
index 6dd1b281700..4abc5cc3258 100644
--- a/project/Publishing.scala
+++ b/project/Publishing.scala
@@ -1,4 +1,4 @@
-import Version.cromwellVersion
+import Version.{Debug, Release, Snapshot, Standard, cromwellVersion}
 import org.apache.ivy.Ivy
 import org.apache.ivy.core.IvyPatternHelper
 import org.apache.ivy.core.module.descriptor.{DefaultModuleDescriptor, MDArtifact}
@@ -36,20 +36,26 @@ object Publishing {
       ArrayBuffer(broadinstitute/cromwell:dev, broadinstitute/cromwell:develop)
      */
     dockerTags := {
-      val versionsCsv = if (Version.isSnapshot) {
-        // Tag looks like `85-443a6fc-SNAP`
-        version.value
-      } else {
-        if (Version.isRelease) {
-          // Tags look like `85`, `85-443a6fc`
-          s"$cromwellVersion,${version.value}"
-        } else {
-          // Tag looks like `85-443a6fc`, `latest`
-          s"${version.value},latest"
-        }
+      val tags = Version.buildType match {
+        case Snapshot =>
+          // Ordinary local build
+          // Looks like `85-443a6fc-SNAP`
+          Seq(version.value)
+        case Release =>
+          // Looks like `85`, `85-443a6fc`
+          Seq(cromwellVersion, version.value)
+        case Debug =>
+          // Ordinary local build with debug stuff
+          // Looks like `85-443a6fc-DEBUG`
+          Seq(version.value)
+        case Standard =>
+          // Merge to `develop`
+          // Looks like `85-443a6fc`, `latest`, `develop`
+          // TODO: once we automate releases, `latest` should move to `Release`
+          Seq(version.value, "latest", "develop")
       }
 
-      // Travis applies (as of 10/22) the `dev` and `develop` tags on merge to `develop`
+      val versionsCsv = tags.mkString(",")
       sys.env.getOrElse("CROMWELL_SBT_DOCKER_TAGS", versionsCsv).split(",")
     },
     docker / imageNames := dockerTags.value map { tag =>
@@ -68,6 +74,11 @@ object Publishing {
         add(artifact, artifactTargetPath)
         runRaw(s"ln -s $artifactTargetPath /app/$projectName.jar")
 
+        // Extra tools in debug mode only
+        if (Version.buildType == Debug) {
+          addInstruction(installDebugFacilities)
+        }
+
         /*
         If you use the 'exec' form for an entry point, shell processing is not performed and
         environment variable substitution does not occur.  Thus we have to /bin/bash here
@@ -116,6 +127,44 @@ object Publishing {
     )
   )
 
+  /**
+    * Install packages needed for debugging when shelled in to a running image.
+    *
+    * This includes:
+    * - The JDK, which includes tools like `jstack` not present in the JRE
+    * - The YourKit Java Profiler
+    * - Various Linux system & development utilities
+    *
+    * @return Instruction to run in the build
+    */
+  def installDebugFacilities: Instruction = {
+    import sbtdocker.Instructions
+
+    // It is optimal to use a single `Run` instruction to minimize the number of layers in the image.
+    // Do not be tempted to install the default JDK in the repositories, it's from Oracle.
+    //
+    // Documentation:
+    // - https://www.yourkit.com/docs/java-profiler/2024.3/help/docker_broker.jsp#setup
+    // - https://adoptium.net/installation/linux/#_deb_installation_on_debian_or_ubuntu
+    Instructions.Run(
+      """apt-get update -qq && \
+        |apt-get install -qq --no-install-recommends file gpg htop jq less nload unzip vim && \
+        |wget -qO - https://packages.adoptium.net/artifactory/api/gpg/key/public | gpg --dearmor | \
+        |  tee /etc/apt/trusted.gpg.d/adoptium.gpg > /dev/null && \
+        |echo "deb https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | \
+        |  tee /etc/apt/sources.list.d/adoptium.list && \
+        |apt-get update -qq && \
+        |apt-get install -qq temurin-11-jdk && \
+        |rm -rf /var/lib/apt/lists/* && \
+        |wget -q https://www.yourkit.com/download/docker/YourKit-JavaProfiler-2024.3-docker.zip -P /tmp/docker-build-cache/ && \
+        |unzip /tmp/docker-build-cache/YourKit-JavaProfiler-2024.3-docker.zip -d /tmp/docker-build-cache && \
+        |mkdir -p /usr/local/YourKit-JavaProfiler-2024.3/bin/ && \
+        |cp -R /tmp/docker-build-cache/YourKit-JavaProfiler-2024.3/bin/linux-x86-64/ /usr/local/YourKit-JavaProfiler-2024.3/bin/linux-x86-64/ && \
+        |rm -rf /tmp/docker-build-cache
+        |""".stripMargin
+    )
+  }
+
   def dockerPushSettings(pushEnabled: Boolean): Seq[Setting[_]] =
     if (pushEnabled) {
       List(
diff --git a/project/Version.scala b/project/Version.scala
index e530e54e62e..26b0057eb10 100644
--- a/project/Version.scala
+++ b/project/Version.scala
@@ -8,24 +8,44 @@ object Version {
   // Upcoming release, or current if we're on a master / hotfix branch
   val cromwellVersion = "87"
 
+  sealed trait BuildType
+  case object Snapshot extends BuildType
+  case object Debug extends BuildType
+  case object Release extends BuildType
+  case object Standard extends BuildType
+
+  def buildType: BuildType = {
+    if (isDebug) Debug
+    else if (isRelease) Release
+    else if (isSnapshot) Snapshot
+    else Standard
+  }
+
   /**
     * Returns true if this project should be considered a snapshot.
     *
     * The value is read in directly from the system property `project.isSnapshot` as there were confusing issues with
     * the multi-project and sbt.Keys#isSnapshot().
     *
-    * Default `true`.
+    * This is the default if no arguments are provided.
     */
-  val isSnapshot: Boolean = sys.props.get("project.isSnapshot").forall(_.toBoolean)
+  private lazy val isSnapshot: Boolean = getPropOrDefault("project.isSnapshot", default = true)
 
   /**
-    * Returns `true` if this project should tag a release like `85` in addition to a hash like `85-443a6fc`.
-    *
-    * Has no effect when `isSnapshot` is `true`.
+    * Returns true if this project should be built in the debugging configuration.
     *
-    * Default `true`.
+    * Note that this image is much larger than the default build!
     */
-  val isRelease: Boolean = sys.props.get("project.isRelease").forall(_.toBoolean)
+  private lazy val isDebug: Boolean = getPropOrDefault("project.isDebug")
+
+  /**
+    * Returns `true` if this project should tag a release like `85` in addition to a hash like `85-443a6fc`.
+    */
+  private lazy val isRelease: Boolean = getPropOrDefault("project.isRelease")
+
+  private def getPropOrDefault(prop: String, default: Boolean = false): Boolean = {
+    sys.props.get(prop).map(_.toBoolean).getOrElse(default)
+  }
 
   // Adapted from SbtGit.versionWithGit
   def cromwellVersionWithGit: Seq[Setting[_]] =
@@ -90,6 +110,11 @@ object Version {
     val version = overrideVersion orElse commitVersion getOrElse unknownVersion
 
     // For now, obfuscate SNAPSHOTs from sbt's developers: https://github.com/sbt/sbt/issues/2687#issuecomment-236586241
-    if (isSnapshot) s"$version-SNAP" else version
+    // (by calling it `SNAP` instead of `SNAPSHOT`)
+    buildType match {
+      case Snapshot => s"$version-SNAP"
+      case Debug => s"$version-DEBUG"
+      case _ => version
+    }
   }
 }
diff --git a/scripts/perf/clone_database/clone_database.sh b/scripts/perf/clone_database/clone_database.sh
deleted file mode 100755
index 99240996ff4..00000000000
--- a/scripts/perf/clone_database/clone_database.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-
-source scripts/perf/helper.inc.sh
-
-mkdir -p mnt
-
-# Read the DB password from vault:
-DB_PASS=$(read_path_from_vault_json "secret/dsp/cromwell/perf" '.data.db_pass')
-
-# Read the service account credentials from vault:
-read_service_account_from_vault
-
-# Clone the CloudSQL DB
-# Note: Cloning the same database in parallel doesn't work.
-# By doing it here we can run the jenkins jobs sequentially and ensure the database is cloned once at a time as well
-SQL_OPERATION=$(gcloud_run_as_service_account "perf_sql_create_gcloud_${BUILD_NUMBER}" "gcloud --project broad-dsde-cromwell-perf sql instances clone --async ${CLOUD_SQL_INSTANCE_TO_CLONE} ${CLOUD_SQL_INSTANCE_NEW_NAME} --format='value(name)'" )
-
-gcloud_run_as_service_account "perf_sql_await_gcloud_${BUILD_NUMBER}" "gcloud beta sql operations wait --timeout=900 --project broad-dsde-cromwell-perf ${SQL_OPERATION}"
-
-gcloud_run_as_service_account "perf_sql_user_gcloud_${BUILD_NUMBER}" "gcloud --project broad-dsde-cromwell-perf sql users create cromwell --instance=${CLOUD_SQL_INSTANCE_NEW_NAME} --password=${DB_PASS}"
diff --git a/scripts/perf/delete_database/delete_database.sh b/scripts/perf/delete_database/delete_database.sh
deleted file mode 100755
index a393cac5eb2..00000000000
--- a/scripts/perf/delete_database/delete_database.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-
-source scripts/perf/helper.inc.sh
-
-mkdir -p mnt
-
-# Read the service account credentials from vault:
-read_service_account_from_vault
-
-gcloud_run_as_service_account "perf_sql_delete_gcloud_${BUILD_NUMBER}" " \
-  gcloud \
-      --verbosity info \
-      --project broad-dsde-cromwell-perf \
-      sql instances delete ${CLOUD_SQL_INSTANCE} -q"
diff --git a/scripts/perf/delete_horicromtal/delete_horicromtal.sh b/scripts/perf/delete_horicromtal/delete_horicromtal.sh
deleted file mode 100755
index 807b9c239b0..00000000000
--- a/scripts/perf/delete_horicromtal/delete_horicromtal.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-
-source scripts/perf/helper.inc.sh
-
-mkdir -p mnt
-
-# Read the service account credentials from vault:
-read_service_account_from_vault
-
-for instance in runner101 runner102 reader101
-do
-    gcloud_delete_instance \
-        "perf_delete_gcloud_instance_${BUILD_NUMBER}-${instance}" \
-        "${CROMWELL_INSTANCE_NAME}-${instance}"
-done
diff --git a/scripts/perf/delete_instance/delete_instance.sh b/scripts/perf/delete_instance/delete_instance.sh
deleted file mode 100755
index 29d40ce7fb6..00000000000
--- a/scripts/perf/delete_instance/delete_instance.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-
-source scripts/perf/helper.inc.sh
-
-mkdir -p mnt
-
-# Read the service account credentials from vault:
-read_service_account_from_vault
-
-gcloud_run_as_service_account "perf_delete_gcloud_instance_${BUILD_NUMBER}" " \
-  gcloud \
-    --verbosity info \
-    --project broad-dsde-cromwell-perf \
-    compute instances delete ${CROMWELL_INSTANCE_NAME} --zone=us-central1-c -q"
diff --git a/scripts/perf/deploy_horicromtal/deploy_horicromtal.sh b/scripts/perf/deploy_horicromtal/deploy_horicromtal.sh
deleted file mode 100755
index 6d060996b77..00000000000
--- a/scripts/perf/deploy_horicromtal/deploy_horicromtal.sh
+++ /dev/null
@@ -1,90 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-
-source scripts/perf/helper.inc.sh
-
-DB_PASS=$(read_path_from_vault_json "secret/dsp/cromwell/perf" '.data.db_pass')
-
-read_service_account_from_vault
-
-runner_metadata=(
-  "BUILD_NUMBER=$BUILD_NUMBER"
-  "BUILD_TAG=$BUILD_TAG"
-  "CLEAN_UP=false"
-  "CLOUD_SQL_INSTANCE=$CLOUD_SQL_INSTANCE"
-  "CROMWELL_DB_USER=cromwell"
-  "CROMWELL_DB_PASS=$DB_PASS"
-  "CROMWELL_DOCKER_IMAGE=$CROMWELL_DOCKER_IMAGE"
-  "CROMWELL_PROJECT=broad-dsde-cromwell-perf"
-  "CROMWELL_BUCKET=${CROMWELL_EXECUTION_BUCKET}"
-  "CROMWELL_STATSD_HOST=10.128.0.4"
-  "CROMWELL_STATSD_PORT=8125"
-  "CROMWELL_PERF_SCRIPTS_BRANCH=${REPO_BRANCH}"
-  "GCS_REPORT_PATH=${GCS_REPORT_PATH}"
-  "GCS_REPORT_BUCKET=${GCS_REPORT_BUCKET}"
-  "TEST_CASE_DIRECTORY=${TEST_CASE_DIRECTORY}"
-  "CONFIG_OVERRIDE"="-Dservices.MetadataService.config.metadata-summary-refresh-interval = \"Inf\""
-)
-
-reader_metadata=(
-  "BUILD_NUMBER=$BUILD_NUMBER"
-  "BUILD_TAG=$BUILD_TAG"
-  "CLEAN_UP=false"
-  "CLOUD_SQL_INSTANCE=$CLOUD_SQL_INSTANCE"
-  "CROMWELL_DB_USER=cromwell"
-  "CROMWELL_DB_PASS=$DB_PASS"
-  "CROMWELL_DOCKER_IMAGE=$CROMWELL_DOCKER_IMAGE"
-  "CROMWELL_PROJECT=broad-dsde-cromwell-perf"
-  "CROMWELL_BUCKET=${CROMWELL_EXECUTION_BUCKET}"
-  "CROMWELL_STATSD_HOST=10.128.0.4"
-  "CROMWELL_STATSD_PORT=8125"
-  "CROMWELL_PERF_SCRIPTS_BRANCH=${REPO_BRANCH}"
-  "GCS_REPORT_PATH=${GCS_REPORT_PATH}"
-  "GCS_REPORT_BUCKET=${GCS_REPORT_BUCKET}"
-  "TEST_CASE_DIRECTORY=reader"
-  "CONFIG_OVERRIDE"=""
-)
-
-cp scripts/perf/deploy_instance/run_on_instance.sh mnt/
-
-gcloud_deploy_instance \
-  "perf_deploy_instance_${BUILD_NUMBER}-runner101" \
-   "${CROMWELL_INSTANCE_NAME}-runner101" \
-    "${INSTANCE_TEMPLATE}" \
-     "$(join ${runner_metadata[@]})" | tee runner1.txt
-
-gcloud_deploy_instance \
-  "perf_deploy_instance_${BUILD_NUMBER}-runner102" \
-   "${CROMWELL_INSTANCE_NAME}-runner102" \
-   "${INSTANCE_TEMPLATE}" \
-   "$(join ${runner_metadata[@]})" | tee runner2.txt
-
-# Note: The reader_metadata currently allows the default summarizer to continue running...
-# ... that's fine as long as there's only one reader, but if we add more, we should make the "summarizer" a separate VM.
-
-gcloud_deploy_instance \
-  "perf_deploy_instance_${BUILD_NUMBER}-reader101" \
-   "${CROMWELL_INSTANCE_NAME}-reader101" \
-   "${INSTANCE_TEMPLATE}" \
-   "$(join ${reader_metadata[@]})" | tee reader1.txt
-
-typeset RUNNER_UNDER_TEST_1=$(cat runner1.txt | tail -n1 | awk '{print $5}')
-typeset RUNNER_UNDER_TEST_2=$(cat runner2.txt | tail -n1 | awk '{print $5}')
-
-typeset READER_UNDER_TEST_1=$(cat reader1.txt | tail -n1 | awk '{print $5}')
-typeset CROMWELL_VALUE_TO_RETURN=$(cat reader1.txt | tail -n1 | awk "{print \$${FIELD_NO_TO_RETURN}}" )
-
-if test -z "${RUNNER_UNDER_TEST_1}" -o -z "${RUNNER_UNDER_TEST_2}" -o -z "${READER_UNDER_TEST_1}"
-then
-  echo "One of RUNNER_UNDER_TEST_1 or RUNNER_UNDER_TEST_2 or READER_UNDER_TEST_1 are empty ('${RUNNER_UNDER_TEST_1}', '${RUNNER_UNDER_TEST_2}, ${READER_UNDER_TEST_1}')"
-  exit 1
-else
-  echo "Determined that RUNNER_UNDER_TEST_1=${RUNNER_UNDER_TEST_1}, RUNNER_UNDER_TEST_2=${RUNNER_UNDER_TEST_2}, READER_UNDER_TEST_1=${READER_UNDER_TEST_1}"
-fi
-
-custom_wait_for_cromwell "${RUNNER_UNDER_TEST_1}"
-custom_wait_for_cromwell "${RUNNER_UNDER_TEST_2}"
-custom_wait_for_cromwell "${READER_UNDER_TEST_1}"
-
-mkdir -p output
-echo "CROMWELL_UNDER_TEST=${CROMWELL_VALUE_TO_RETURN}" > output/cromwell.properties
diff --git a/scripts/perf/deploy_horicromtal/run_on_instance.sh b/scripts/perf/deploy_horicromtal/run_on_instance.sh
deleted file mode 100644
index c9420a68ae3..00000000000
--- a/scripts/perf/deploy_horicromtal/run_on_instance.sh
+++ /dev/null
@@ -1,78 +0,0 @@
-#! /bin/bash
-
-set -x
-
-### /!\ This script assumes docker and docker compose are already installed on the host
-
-# Utility function to extract values from instance metadata
-extract_metadata() {
-  curl "http://metadata.google.internal/computeMetadata/v1/instance/attributes/$1" -H "Metadata-Flavor: Google"
-}
-
-# Exports an env var and also adds it to the root bashrc. This way if there is a need to ssh onto the machine
-# for debugging one will have the env variables already set when using root
-addVar() {
-  export $1
-  echo "export $1" >> /root/.bashrc
-}
-
-# Make sure ip forwarding is enabled by default so that docker doesn't lose connectivity
-echo "net.ipv4.ip_forward = 1" > /etc/sysctl.conf
-
-# Set up env variables
-addVar CROMWELL_BRANCH=$(extract_metadata CROMWELL_PERF_SCRIPTS_BRANCH)
-addVar CLOUD_SQL_DB_USER=$(extract_metadata CROMWELL_DB_USER)
-addVar CLOUD_SQL_DB_PASSWORD=$(extract_metadata CROMWELL_DB_PASS)
-addVar CLOUD_SQL_INSTANCE=$(extract_metadata CLOUD_SQL_INSTANCE)
-addVar CROMWELL_DOCKER_IMAGE=$(extract_metadata CROMWELL_DOCKER_IMAGE)
-addVar CROMWELL_PROJECT=$(extract_metadata CROMWELL_PROJECT)
-addVar CROMWELL_EXECUTION_ROOT=$(extract_metadata CROMWELL_BUCKET)
-addVar CROMWELL_STATSD_HOST=$(extract_metadata CROMWELL_STATSD_HOST)
-addVar CROMWELL_STATSD_PORT=$(extract_metadata CROMWELL_STATSD_PORT)
-addVar BUILD_ID=$(extract_metadata BUILD_TAG)
-addVar GCS_REPORT_BUCKET=$(extract_metadata GCS_REPORT_BUCKET)
-addVar GCS_REPORT_PATH=$(extract_metadata GCS_REPORT_PATH)
-addVar TEST_CASE_DIRECTORY=$(extract_metadata TEST_CASE_DIRECTORY)
-addVar CONFIG_OVERRIDE=$(extract_metadata CONFIG_OVERRIDE)
-
-# Use the instance name as statsd prefix to avoid metrics collisions
-addVar CROMWELL_STATSD_PREFIX=${BUILD_ID}
-
-addVar CROMWELL_ROOT=/app
-addVar PERF_ROOT=${CROMWELL_ROOT}/scripts/perf
-addVar TEST_WORKFLOW_ROOT=${PERF_ROOT}/test_cases
-
-# Clone cromwell to get the perf scripts. Use https to avoid ssh fingerprint prompt when the script runs
-git clone -b ${CROMWELL_BRANCH} --depth 1 --single-branch https://github.com/broadinstitute/cromwell.git ${CROMWELL_ROOT}
-
-source ${PERF_ROOT}/helper.inc.sh
-
-if [ -f "${PERF_ROOT}/test_cases/${TEST_CASE_DIRECTORY}/cromwell.conf" ]
-then
-    echo "Using ${PERF_ROOT}/test_cases/${TEST_CASE_DIRECTORY} as the Cromwell configuration directory"
-    addVar CROMWELL_CONF_DIR="${PERF_ROOT}/test_cases/${TEST_CASE_DIRECTORY}"
-
-    # Also copy the default one next to it so we can include it
-    cp ${PERF_ROOT}/vm_scripts/cromwell/cromwell.conf ${CROMWELL_CONF_DIR}/cromwell_default.conf
-else
-    echo "Using ${PERF_ROOT}/vm_scripts/cromwell as the Cromwell configuration directory"
-    addVar CROMWELL_CONF_DIR="${PERF_ROOT}/vm_scripts/cromwell"
-fi
-
-if test -n "${CONFIG_OVERRIDE}"
-then
-    echo "${CONFIG_OVERRIDE}" >> "${CROMWELL_CONF_DIR}/cromwell.conf"
-fi
-
-addVar REPORT_URL="$(strip_trailing_slash "gs://${GCS_REPORT_BUCKET}/${GCS_REPORT_PATH}")"
-
-# Start cromwell and cloud sql proxy
-prepare_statsd_proxy
-docker-compose -f ${PERF_ROOT}/vm_scripts/docker-compose.yml up -d
-
-# Intermittently upload Cromwell logs to the bucket
-while true
-do
-    export_cromwell_logs
-    sleep 60
-done
diff --git a/scripts/perf/deploy_instance/deploy_instance.sh b/scripts/perf/deploy_instance/deploy_instance.sh
deleted file mode 100755
index c1775b8d4b0..00000000000
--- a/scripts/perf/deploy_instance/deploy_instance.sh
+++ /dev/null
@@ -1,59 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-
-source scripts/perf/helper.inc.sh
-
-DB_PASS=$(read_path_from_vault_json "secret/dsp/cromwell/perf" '.data.db_pass')
-
-read_service_account_from_vault
-	
-function join() { local IFS=","; echo "$*"; }
-
-metadata=(
-  "BUILD_NUMBER=$BUILD_NUMBER"
-  "BUILD_TAG=$BUILD_TAG"
-  "CLEAN_UP=false"
-  "CLOUD_SQL_INSTANCE=$CLOUD_SQL_INSTANCE"
-  "CROMWELL_DB_USER=cromwell"
-  "CROMWELL_DB_PASS=$DB_PASS"
-  "CROMWELL_DOCKER_IMAGE=$CROMWELL_DOCKER_IMAGE"
-  "CROMWELL_PROJECT=broad-dsde-cromwell-perf"
-  "CROMWELL_BUCKET=${CROMWELL_EXECUTION_BUCKET}"
-  "CROMWELL_STATSD_HOST=10.128.0.4"
-  "CROMWELL_STATSD_PORT=8125"
-  "CROMWELL_PERF_SCRIPTS_BRANCH=${REPO_BRANCH}"
-  "GCS_REPORT_PATH=${GCS_REPORT_PATH}"
-  "GCS_REPORT_BUCKET=${GCS_REPORT_BUCKET}"
-  "TEST_CASE_DIRECTORY=${TEST_CASE_DIRECTORY}"
-)
-
-cp scripts/perf/deploy_instance/run_on_instance.sh mnt/
-
-gcloud_run_as_service_account "perf_deploy_instance_${BUILD_NUMBER}" \
-  "gcloud \
-    --verbosity info \
-    --project broad-dsde-cromwell-perf \
-    compute \
-    instances \
-    create ${CROMWELL_INSTANCE_NAME} \
-    --zone us-central1-c \
-    --source-instance-template $INSTANCE_TEMPLATE \
-    --metadata-from-file startup-script=$DOCKER_ETC_PATH/run_on_instance.sh \
-    --metadata \
-        $(join ${metadata[@]})" | tee dockerResult.txt
-
-typeset CROMWELL_UNDER_TEST=$(cat dockerResult.txt | tail -n1 | awk '{print $5}' )
-typeset CROMWELL_VALUE_TO_RETURN=$(cat dockerResult.txt | tail -n1 | awk "{print \$${FIELD_NO_TO_RETURN}}" )
-
-if test -z "CROMWELL_UNDER_TEST" -o -z "CROMWELL_VALUE_TO_RETURN"
-then
-  echo "One of CROMWELL_UNDER_TEST or CROMWELL_VALUE_TO_RETURN are empty ('${CROMWELL_UNDER_TEST}', '${CROMWELL_VALUE_TO_RETURN}')"
-  exit 1
-else
-  echo "Determined that CROMWELL_UNDER_TEST=${CROMWELL_UNDER_TEST}, CROMWELL_VALUE_TO_RETURN=${CROMWELL_VALUE_TO_RETURN}"
-fi
-
-custom_wait_for_cromwell "${CROMWELL_UNDER_TEST}"
-
-mkdir -p output
-echo "CROMWELL_UNDER_TEST=${CROMWELL_VALUE_TO_RETURN}" > output/cromwell.properties
diff --git a/scripts/perf/deploy_instance/run_on_instance.sh b/scripts/perf/deploy_instance/run_on_instance.sh
deleted file mode 100644
index 3c5d1e85ed4..00000000000
--- a/scripts/perf/deploy_instance/run_on_instance.sh
+++ /dev/null
@@ -1,72 +0,0 @@
-#! /bin/bash
-
-set -x
-
-### /!\ This script assumes docker and docker compose are already installed on the host
-
-# Utility function to extract values from instance metadata
-extract_metadata() {
-  curl "http://metadata.google.internal/computeMetadata/v1/instance/attributes/$1" -H "Metadata-Flavor: Google"
-}
-
-# Exports an env var and also adds it to the root bashrc. This way if there is a need to ssh onto the machine
-# for debugging one will have the env variables already set when using root
-addVar() {
-  export $1
-  echo "export $1" >> /root/.bashrc
-}
-
-# Make sure ip forwarding is enabled by default so that docker doesn't lose connectivity
-echo "net.ipv4.ip_forward = 1" > /etc/sysctl.conf
-
-# Set up env variables
-addVar CROMWELL_BRANCH=$(extract_metadata CROMWELL_PERF_SCRIPTS_BRANCH)
-addVar CLOUD_SQL_DB_USER=$(extract_metadata CROMWELL_DB_USER)
-addVar CLOUD_SQL_DB_PASSWORD=$(extract_metadata CROMWELL_DB_PASS)
-addVar CLOUD_SQL_INSTANCE=$(extract_metadata CLOUD_SQL_INSTANCE)
-addVar CROMWELL_DOCKER_IMAGE=$(extract_metadata CROMWELL_DOCKER_IMAGE)
-addVar CROMWELL_PROJECT=$(extract_metadata CROMWELL_PROJECT)
-addVar CROMWELL_EXECUTION_ROOT=$(extract_metadata CROMWELL_BUCKET)
-addVar CROMWELL_STATSD_HOST=$(extract_metadata CROMWELL_STATSD_HOST)
-addVar CROMWELL_STATSD_PORT=$(extract_metadata CROMWELL_STATSD_PORT)
-addVar BUILD_ID=$(extract_metadata BUILD_TAG)
-addVar GCS_REPORT_BUCKET=$(extract_metadata GCS_REPORT_BUCKET)
-addVar GCS_REPORT_PATH=$(extract_metadata GCS_REPORT_PATH)
-addVar TEST_CASE_DIRECTORY=$(extract_metadata TEST_CASE_DIRECTORY)
-
-# Use the instance name as statsd prefix to avoid metrics collisions
-addVar CROMWELL_STATSD_PREFIX=${BUILD_ID}
-
-addVar CROMWELL_ROOT=/app
-addVar PERF_ROOT=${CROMWELL_ROOT}/scripts/perf
-addVar TEST_WORKFLOW_ROOT=${PERF_ROOT}/test_cases
-
-# Clone cromwell to get the perf scripts. Use https to avoid ssh fingerprint prompt when the script runs
-git clone -b ${CROMWELL_BRANCH} --depth 1 --single-branch https://github.com/broadinstitute/cromwell.git ${CROMWELL_ROOT}
-
-source ${PERF_ROOT}/helper.inc.sh
-
-if [ -f "${PERF_ROOT}/test_cases/${TEST_CASE_DIRECTORY}/cromwell.conf" ]
-then
-    echo "Using ${PERF_ROOT}/test_cases/${TEST_CASE_DIRECTORY} as the Cromwell configuration directory"
-    addVar CROMWELL_CONF_DIR="${PERF_ROOT}/test_cases/${TEST_CASE_DIRECTORY}"
-
-    # Also copy the default one next to it so we can include it
-    cp ${PERF_ROOT}/vm_scripts/cromwell/cromwell.conf ${CROMWELL_CONF_DIR}/cromwell_default.conf
-else
-    echo "Using ${PERF_ROOT}/vm_scripts/cromwell as the Cromwell configuration directory"
-    addVar CROMWELL_CONF_DIR="${PERF_ROOT}/vm_scripts/cromwell"
-fi
-
-addVar REPORT_URL="$(strip_trailing_slash "gs://${GCS_REPORT_BUCKET}/${GCS_REPORT_PATH}")"
-
-# Start cromwell and cloud sql proxy
-prepare_statsd_proxy
-docker-compose -f ${PERF_ROOT}/vm_scripts/docker-compose.yml up -d
-
-# Intermittently upload Cromwell logs to the bucket
-while true
-do
-    export_cromwell_logs
-    sleep 60
-done
diff --git a/scripts/perf/helper.inc.sh b/scripts/perf/helper.inc.sh
deleted file mode 100644
index aa9e9818c7b..00000000000
--- a/scripts/perf/helper.inc.sh
+++ /dev/null
@@ -1,279 +0,0 @@
-#!/usr/bin/env bash
-
-# Set some global constants:
-typeset CROMWELL_EXECUTION_BUCKET=gs://cromwell-perf-test/
-
-typeset DOCKER_ETC_PATH="/usr/share/etc"
-typeset CROMWELL_PERF_PROJECT=broad-dsde-cromwell-perf
-
-if test -f "/etc/vault-token-dsde"
-then
-  typeset VAULT_TOKEN=$(cat /etc/vault-token-dsde)
-fi
-
-wait_for_cromwell() {
-  git clone https://github.com/vishnubob/wait-for-it.git /wait-for-it
-  chmod u+x /wait-for-it/wait-for-it.sh
-  # Give 5 minutes to cromwell to be online
-
-  echo "[$(date)] Waiting for http://${CROMWELL_UNDER_TEST}:8000/engine/v1/version to appear..."
-  /wait-for-it/wait-for-it.sh ${CROMWELL_UNDER_TEST}:8000 -t 300
-  READY=$?
-  if [ ${READY} -eq 0 ]
-  then
-      # Just wait a bit longer - no rush, this is a chill VM - this is because cromwell responds to requests before being really ready...
-      sleep 30
-    
-      CROMWELL_VERSION=$(curl --silent -X GET "http://${CROMWELL_UNDER_TEST}:8000/engine/v1/version" -H "accept: application/json" | jq -r '.cromwell')
-      if [ -z ${CROMWELL_VERSION} ]
-      then
-        echo "Cromwell was up but failed to return its version, so something went wrong, shutting down"
-        shutdown
-      fi
-      export CROMWELL_VERSION
-  else
-    echo "Cromwell was not ready after 5 minutes, shutting down"
-    shutdown
-  fi
-}
-
-# Waits for Cromwell. Works even from *outside* a google instance
-custom_wait_for_cromwell() {
-
-  set +e
-
-  local cromwell_under_test=$1
-
-  RESULT=1
-  ATTEMPTS=0
-  # increase max tries from 20 to 60 to allow more time for cromwell instance to deploy
-  MAX_ATTEMPTS=60
-
-  while [ "${ATTEMPTS}" -le "${MAX_ATTEMPTS}" -a "${RESULT}" -gt "0" ]
-  do
-    echo "[$(date)] Waiting for Cromwell (http://${cromwell_under_test}:8000/engine/v1/version) to come up (tried ${ATTEMPTS} times so far)"
-    sleep 30
-    ATTEMPTS=$((ATTEMPTS + 1))
-
-    CROMWELL_VERSION_JSON=$(curl --silent -X GET "http://${cromwell_under_test}:8000/engine/v1/version" -H "accept: application/json")
-    RESULT=$?
-
-    CROMWELL_VERSION=$(echo "${CROMWELL_VERSION_JSON}" | jq -r '.cromwell')
-
-    if [ "${RESULT}" -eq "0" -a -z "${CROMWELL_VERSION}" ]
-    then
-      echo "Cromwell was up but failed to return its version, maybe something went wrong? Continuing waiting..."
-      RESULT=1
-    fi
-  done
-
-  if [ "${RESULT}" -gt "0" ]
-  then
-    echo "Cromwell never came up after ${ATTEMPTS} attempts"
-    exit 1
-  else
-    echo "Cromwell came up after ${ATTEMPTS} attempts"
-  fi
-}
-
-export_centaur_logs() {
-    echo "Exporting centaur logs to ${REPORT_URL}"
-
-    # Copy centaur log
-    gsutil -h "Content-Type:text/plain" cp "${CROMWELL_ROOT}/centaur.log" "${REPORT_URL}/centaur.log" || true
-
-    # Copy test_rc.log
-    echo "${TEST_RC}" > test_rc.txt && gsutil -h "Content-Type:text/plain" cp "test_rc.txt" "${REPORT_URL}/test_rc.txt" || true
-}
-
-export_cromwell_logs() {
-    echo "Exporting Cromwell logs to ${REPORT_URL} as $(hostname)"
-
-    # Copy the cromwell container logs
-    gsutil -h "Content-Type:text/plain" cp "$(docker inspect --format='{{.LogPath}}' cromwell)" "${REPORT_URL}/cromwell_$(hostname).log" || true
-    # Copy the docker daemon logs
-    gsutil -h "Content-Type:text/plain" cp "/var/log/daemon.log" "${REPORT_URL}/daemon_$(hostname).log" || true
-}
-
-
-export_logs() {
-    export REPORT_URL="gs://${GCS_REPORT_BUCKET}/${GCS_REPORT_PATH}"
-
-    export_cromwell_logs
-    export_centaur_logs
-}
-
-clean_up() {
-    if [ "${CLEAN_UP}" = true ]
-    then
-        gcloud sql instances delete ${CLOUD_SQL_INSTANCE}
-        self_destruct_instance
-    fi
-}
-
-self_destruct_instance() {
-    gcloud compute instances delete $(curl --silent "http://metadata.google.internal/computeMetadata/v1/instance/name" -H "Metadata-Flavor: Google") --zone=us-central1-c -q
-}
-
-run_test() {
-    cd ${CROMWELL_ROOT}
-
-    if [ -z ${GCS_REPORT_PATH} ]
-    then
-        export GCS_REPORT_PATH="${TEST_CASE_DIRECTORY}/${CROMWELL_VERSION}/${BUILD_ID}"
-    fi
-
-    sbt \
-      --error \
-      -Dconfig.file=${CENTAUR_CONF_DIR}/centaur.conf \
-      -Dcentaur.cromwell.mode="url" \
-      -Dcentaur.cromwell.url="http://${CROMWELL_UNDER_TEST}:8000" \
-      "centaur/it:testOnly centaur.ExternalTestCaseSpec" | tee centaur.log
-    export TEST_RC=$?
-}
-
-shutdown() {
-    export_logs
-    docker-compose -f ${PERF_ROOT}/vm_scripts/docker-compose.yml down
-    clean_up
-}
-
-function join() { local IFS=","; echo "$*"; }
-
-read_path_from_vault_json() {
-  local path=$1
-  local field=$2
-
-  docker run --rm -e VAULT_TOKEN=$VAULT_TOKEN broadinstitute/dsde-toolbox vault read -format=json "${path}" | jq --exit-status -r "${field}"
-}
-
-
-read_service_account_from_vault() {
-  mkdir -p mnt
-  read_path_from_vault_json "secret/dsp/cromwell/perf/service-account-deployer" '.data.service_account' > mnt/sa.json
-}
-
-gcloud_run_as_service_account() {
-  local name="$1"
-  local command="$2"
-  docker run --name ${name} -v "$(pwd)"/mnt:${DOCKER_ETC_PATH} --rm gcr.io/google.com/cloudsdktool/cloud-sdk:slim \
-    /bin/bash -c "\
-    gcloud auth activate-service-account --key-file ${DOCKER_ETC_PATH}/sa.json 2> /dev/null &&\
-    ${command}"
-}
-
-gcloud_get_field_from_instance_describe() {
-  local instance="$1"
-  local field="$2"
-
-  INSTANCE_METADATA=$(gcloud_run_as_service_account "perf_read_field_${field}" \
-   "gcloud \
-     --project broad-dsde-cromwell-perf \
-     compute instances describe \
-     --zone us-central1-c \
-     ${instance}
-   ")
-
-   echo "${INSTANCE_METADATA}" | grep "${field}" | awk '{print $2}'
-}
-
-gcloud_deploy_instance() {
-  local taskname=$1
-  local instance_name=$2
-  local instance_template=$3
-  local joined_metadata_string=$4
-
-  gcloud_run_as_service_account "${taskname}" \
-  "gcloud \
-    --verbosity info \
-    --project broad-dsde-cromwell-perf \
-    compute instances create ${instance_name} \
-      --zone us-central1-c \
-      --source-instance-template ${instance_template} \
-      --metadata-from-file startup-script=$DOCKER_ETC_PATH/run_on_instance.sh \
-      --metadata ${joined_metadata_string}"
-}
-
-gcloud_delete_instance() {
-  local taskname=$1
-  local instance_name=$2
-
-  gcloud_run_as_service_account "${taskname}" " \
-  gcloud \
-    --verbosity info \
-    --project broad-dsde-cromwell-perf \
-    compute instances delete ${instance_name} \
-      --zone=us-central1-c -q"
-}
-
-# Waits for a remote machine to start, and then stop, responding to PINGs
-wait_for_ping_to_start_then_stop() {
-  local address="$1"
-
-  # Turn off "fail on exit code" and "debug logging":
-  set +e
-  set +x
-
-  RESULT=1
-  ATTEMPTS=0
-  MAX_ATTEMPTS=20
-
-  while [ "${ATTEMPTS}" -le "${MAX_ATTEMPTS}" -a "${RESULT}" -gt "0" ]
-  do
-    echo "[$(date)] Waiting for ${address} to respond to pings (tried ${ATTEMPTS} times so far)"
-    sleep 30
-    ATTEMPTS=$((ATTEMPTS + 1))
-
-    ping -c 1 ${address} &> /dev/null
-    RESULT=$?
-  done
-
-  if [ "${RESULT}" -gt "0" ]
-  then
-    echo "[$(date)] ${address} never came up after ${ATTEMPTS} attempts"
-    exit 1
-  else
-    echo "[$(date)] ${address} came up after ${ATTEMPTS} attempts"
-  fi
-
-  while ping -c 1 ${address} &> /dev/null
-  do
-    echo "[$(date)] ${address} is still responding to pings. Pausing before next ping"
-    sleep 30
-  done
-
-  echo "[$(date)] ${address} has stopped responding to pings."
-
-  set -e
-}
-
-strip_trailing_slash() {
-  local path=$1
-  echo "${path}" | sed 's/\/$//'
-}
-
-# Patch the activation policy of the Cloud SQL Instance referenced by $CLOUD_SQL_INSTANCE.
-# In practice used mostly to turn a Cloud SQL instance on or off.
-#
-# Arguments:
-#   `op` - a descriptive term that will appear in the Docker container that runs gcloud.
-#   `policy` - the Cloud SQL activation policy, should be one of ALWAYS, NEVER or ON_DEMAND.
-#              For more details: https://cloud.google.com/sql/docs/mysql/start-stop-restart-instance
-private::patch_cloud_sql_activation_policy() {
-  op="$1"
-  policy="$2"
-
-  mkdir -p mnt
-  # Read the service account credentials from vault:
-  read_service_account_from_vault
-
-  gcloud_run_as_service_account "perf_sql_${op}_gcloud_${BUILD_NUMBER}" "gcloud -q --project broad-dsde-cromwell-perf sql instances patch ${CLOUD_SQL_INSTANCE} --activation-policy ${policy}"
-}
-
-start_cloud_sql() {
-  private::patch_cloud_sql_activation_policy "start" "ALWAYS"
-}
-
-stop_cloud_sql() {
-  private::patch_cloud_sql_activation_policy "stop" "NEVER"
-}
diff --git a/scripts/perf/run_centaur_blocking/create_runner_instance.sh b/scripts/perf/run_centaur_blocking/create_runner_instance.sh
deleted file mode 100755
index 9c0603f5dba..00000000000
--- a/scripts/perf/run_centaur_blocking/create_runner_instance.sh
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/bin/bash
-
-set -euo pipefail
-
-source scripts/perf/helper.inc.sh
-
-# Prepare the startup script to run on new instance
-mkdir -p mnt
-cp scripts/perf/run_centaur_blocking/test_runner_script.sh mnt/
-
-
-read_service_account_from_vault
-
-metadata=(
-  "BUILD_NUMBER=${BUILD_NUMBER}"
-  "BUILD_TAG=${BUILD_TAG}"
-  "CLEAN_UP=true"
-  "CROMWELL_PROJECT=${CROMWELL_PERF_PROJECT}"
-  "CROMWELL_BUCKET=${CROMWELL_EXECUTION_BUCKET}"
-  "CROMWELL_PERF_SCRIPTS_BRANCH=${CROMWELL_BRANCH}"
-  "CROMWELL_UNDER_TEST=${CROMWELL_UNDER_TEST}"
-  "GCS_REPORT_PATH=${GCS_REPORT_PATH}"
-  "GCS_REPORT_BUCKET=${GCS_REPORT_BUCKET}"
-  "TEST_CASE_DIRECTORY=${TEST_CASE_DIRECTORY}"
-)
-
-# NB: The 'cromwell-perf' tag is required to give cromwell the 'perf' firewall rules
-
-gcloud_run_as_service_account "perf_centaur_test_runner_${BUILD_NUMBER}" \
-  "gcloud \
-    --verbosity info \
-    --project ${CROMWELL_PERF_PROJECT} \
-    compute \
-    instances \
-    create ${BUILD_TAG} \
-    --zone us-central1-c \
-    --source-instance-template ${INSTANCE_TEMPLATE} \
-    --tags cromwell-perf \
-    --metadata-from-file startup-script=${DOCKER_ETC_PATH}/test_runner_script.sh \
-    --metadata \
-        $(join ${metadata[@]})"  | tee startupResult.txt
-
-typeset CENTAUR_TEST_RUNNER=$(cat startupResult.txt | tail -n1 | awk '{print $5}' )
-
-echo "Determined that CENTAUR_TEST_RUNNER=${CENTAUR_TEST_RUNNER}"
-
-wait_for_ping_to_start_then_stop ${CENTAUR_TEST_RUNNER}
diff --git a/scripts/perf/run_centaur_blocking/test_runner_script.sh b/scripts/perf/run_centaur_blocking/test_runner_script.sh
deleted file mode 100644
index 0c6baf9a688..00000000000
--- a/scripts/perf/run_centaur_blocking/test_runner_script.sh
+++ /dev/null
@@ -1,88 +0,0 @@
-#! /bin/bash
-
-# Deliberately don't set these options. The script must continue to run (and clean itself up) even if the centaur tests
-# fail.
-#set -euo pipefail
-set +x
-
-### /!\ This script assumes docker and docker compose are already installed on the host
-
-# Utility function to extract values from instance metadata
-extract_metadata() {
-  curl "http://metadata.google.internal/computeMetadata/v1/instance/attributes/$1" -H "Metadata-Flavor: Google"
-}
-
-# Exports an env var and also adds it to the root bashrc. This way if there is a need to ssh onto the machine
-# for debugging one will have the env variables already set when using root
-addVar() {
-  export $1
-  echo "export $1" >> /root/.bashrc
-}
-
-# Make sure ip forwarding is enabled by default so that docker doesn't loses connectivity
-echo "net.ipv4.ip_forward = 1" > /etc/sysctl.conf
-
-# Extract env variables from instance metadata:
-addVar TEST_CASE_DIRECTORY=$(extract_metadata TEST_CASE_DIRECTORY)
-addVar CROMWELL_UNDER_TEST=$(extract_metadata CROMWELL_UNDER_TEST)
-addVar CROMWELL_PROJECT=$(extract_metadata CROMWELL_PROJECT)
-addVar GCS_REPORT_BUCKET=$(extract_metadata GCS_REPORT_BUCKET)
-addVar GCS_REPORT_PATH=$(extract_metadata GCS_REPORT_PATH)
-addVar BUILD_ID=$(extract_metadata BUILD_TAG)
-addVar CROMWELL_PERF_SCRIPTS_BRANCH=$(extract_metadata CROMWELL_PERF_SCRIPTS_BRANCH)
-
-addVar CROMWELL_ROOT=/app
-addVar PERF_ROOT=${CROMWELL_ROOT}/scripts/perf
-
-# Clone cromwell to get the perf scripts. Use https to avoid ssh fingerprint prompt when the script runs
-git clone -b ${CROMWELL_PERF_SCRIPTS_BRANCH} --depth 1 --single-branch https://github.com/broadinstitute/cromwell.git ${CROMWELL_ROOT}
-
-source ${PERF_ROOT}/helper.inc.sh
-
-addVar CLEAN_UP=true
-
-addVar REPORT_BUCKET="cromwell-perf-test-reporting"
-addVar TEST_WORKFLOW_ROOT="${PERF_ROOT}/test_cases"
-addVar REPORT_URL="$(strip_trailing_slash "gs://${GCS_REPORT_BUCKET}/${GCS_REPORT_PATH}")"
-
-if [ -n "${TEST_CASE_DIRECTORY}" ]
-then
-    # Must be a directory
-    TEST_WORKFLOW_DIR=${TEST_WORKFLOW_ROOT}/${TEST_CASE_DIRECTORY}
-    
-    # If it contains a custom cromwell configuration, use that 
-    if [ -f "${TEST_WORKFLOW_DIR}/cromwell.conf" ]
-    then
-        addVar CROMWELL_CONF_DIR=${TEST_WORKFLOW_DIR}
-        # copy the default one next to it so we can include it
-        cp ${PERF_ROOT}/vm_scripts/cromwell/cromwell.conf ${CROMWELL_CONF_DIR}/cromwell_default.conf
-    else
-        # Otherwise use the default one
-        addVar CROMWELL_CONF_DIR=${PERF_ROOT}/vm_scripts/cromwell
-    fi
-    
-    # If it contains a custom centaur configuration, use that 
-    if [ -f "${TEST_WORKFLOW_DIR}/centaur.conf" ]
-    then
-        addVar CENTAUR_CONF_DIR=${TEST_WORKFLOW_DIR}
-        # copy the default one next to it so we can include it
-        cp ${PERF_ROOT}/vm_scripts/centaur/centaur.conf ${CENTAUR_CONF_DIR}/centaur_default.conf
-    else
-        # Otherwise use the default one
-        addVar CENTAUR_CONF_DIR=${PERF_ROOT}/vm_scripts/centaur
-    fi
-    
-    addVar CENTAUR_TEST_FILE=$(ls ${TEST_WORKFLOW_DIR}/*.test | head)
-    sed -i "s/\$BRANCH/${CROMWELL_PERF_SCRIPTS_BRANCH}/" ${CENTAUR_TEST_FILE}
-fi
-
-if [ -n "${CENTAUR_TEST_FILE}" ]
-then
-    wait_for_cromwell
-    run_test
-else
-    echo "No workflow provided, shutting down"
-fi
-
-export_centaur_logs
-self_destruct_instance
diff --git a/scripts/perf/start_database/start_database.sh b/scripts/perf/start_database/start_database.sh
deleted file mode 100644
index 779c6350e77..00000000000
--- a/scripts/perf/start_database/start_database.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-
-source scripts/perf/helper.inc.sh
-
-start_cloud_sql
diff --git a/scripts/perf/stop_database/stop_database.sh b/scripts/perf/stop_database/stop_database.sh
deleted file mode 100644
index 8772f793fa5..00000000000
--- a/scripts/perf/stop_database/stop_database.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-
-source scripts/perf/helper.inc.sh
-
-stop_cloud_sql
diff --git a/scripts/perf/test_cases/blacklist_call_caching_stress/blacklist_call_caching_stress.test b/scripts/perf/test_cases/blacklist_call_caching_stress/blacklist_call_caching_stress.test
deleted file mode 100644
index a00e1fdff3f..00000000000
--- a/scripts/perf/test_cases/blacklist_call_caching_stress/blacklist_call_caching_stress.test
+++ /dev/null
@@ -1,12 +0,0 @@
-name: blacklist_call_caching_stress
-testFormat: workflowsuccess
-
-files {
-  workflow: "https://raw.githubusercontent.com/broadinstitute/cromwell/$BRANCH/scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.wdl"
-  inputs: "https://raw.githubusercontent.com/broadinstitute/cromwell/$BRANCH/scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.inputs"
-  options: "gs://cromwell-perf-test/workflow_related_files/call_caching_sa2_workflow_options.json"
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/scripts/perf/test_cases/blacklist_call_caching_stress/centaur.conf b/scripts/perf/test_cases/blacklist_call_caching_stress/centaur.conf
deleted file mode 100644
index 2b7ce0eed62..00000000000
--- a/scripts/perf/test_cases/blacklist_call_caching_stress/centaur.conf
+++ /dev/null
@@ -1,18 +0,0 @@
-include required("centaur_default.conf")
-
-centaur {
-  metadata-args {
-    includeKey = [
-      "id",
-      "%shardIndex%",
-      "%hitFailures%",
-      "%executionEvents%",
-      "status",
-      "workflowName",
-      "submission",
-      "start",
-      "end",
-      "failures"
-    ]
-  }
-}
diff --git a/scripts/perf/test_cases/blacklist_call_caching_stress/cromwell.conf b/scripts/perf/test_cases/blacklist_call_caching_stress/cromwell.conf
deleted file mode 100644
index 710bfed0fa8..00000000000
--- a/scripts/perf/test_cases/blacklist_call_caching_stress/cromwell.conf
+++ /dev/null
@@ -1,9 +0,0 @@
-include required("cromwell_default.conf")
-
-engine.filesystems.gcs.auth = "user-service-account"
-backend.providers.Papi.config.genomics.auth = "user-service-account"
-backend.providers.Papi.config.filesystems.gcs.auth = "user-service-account"
-
-
-call-caching.blacklist-cache.enabled = true
-call-caching.blacklist-cache.ttl = "3 days"
diff --git a/scripts/perf/test_cases/call_caching_lots_of_inputs/call_caching_stress_lots_of_inputs.test b/scripts/perf/test_cases/call_caching_lots_of_inputs/call_caching_stress_lots_of_inputs.test
deleted file mode 100644
index 8210853b91e..00000000000
--- a/scripts/perf/test_cases/call_caching_lots_of_inputs/call_caching_stress_lots_of_inputs.test
+++ /dev/null
@@ -1,11 +0,0 @@
-name: call_caching_lots_of_inputs
-testFormat: workflowsuccess
-
-files {
-  workflow: "https://raw.githubusercontent.com/broadinstitute/cromwell/$BRANCH/scripts/perf/test_cases/call_caching_lots_of_inputs/lots_of_inputs.wdl"
-  inputs: "https://raw.githubusercontent.com/broadinstitute/cromwell/$BRANCH/scripts/perf/test_cases/call_caching_lots_of_inputs/lots_of_inputs.inputs"
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/scripts/perf/test_cases/call_caching_lots_of_inputs/lots_of_inputs.inputs b/scripts/perf/test_cases/call_caching_lots_of_inputs/lots_of_inputs.inputs
deleted file mode 100644
index 84d05f5842f..00000000000
--- a/scripts/perf/test_cases/call_caching_lots_of_inputs/lots_of_inputs.inputs
+++ /dev/null
@@ -1,804 +0,0 @@
-{
-  "call_cache_read_input_files_perf_test.files" : [
-    "gs://cromwell-perf-testing/lots_of_input_files/input-1",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-2",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-3",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-4",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-5",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-6",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-7",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-8",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-9",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-10",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-11",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-12",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-13",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-14",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-15",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-16",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-17",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-18",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-19",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-20",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-21",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-22",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-23",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-24",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-25",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-26",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-27",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-28",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-29",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-30",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-31",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-32",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-33",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-34",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-35",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-36",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-37",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-38",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-39",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-40",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-41",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-42",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-43",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-44",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-45",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-46",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-47",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-48",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-49",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-50",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-51",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-52",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-53",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-54",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-55",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-56",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-57",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-58",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-59",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-60",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-61",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-62",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-63",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-64",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-65",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-66",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-67",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-68",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-69",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-70",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-71",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-72",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-73",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-74",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-75",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-76",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-77",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-78",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-79",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-80",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-81",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-82",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-83",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-84",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-85",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-86",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-87",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-88",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-89",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-90",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-91",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-92",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-93",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-94",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-95",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-96",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-97",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-98",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-99",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-100",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-101",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-102",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-103",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-104",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-105",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-106",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-107",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-108",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-109",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-110",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-111",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-112",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-113",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-114",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-115",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-116",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-117",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-118",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-119",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-120",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-121",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-122",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-123",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-124",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-125",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-126",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-127",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-128",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-129",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-130",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-131",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-132",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-133",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-134",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-135",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-136",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-137",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-138",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-139",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-140",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-141",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-142",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-143",
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-    "gs://cromwell-perf-testing/lots_of_input_files/input-725",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-726",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-727",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-728",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-729",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-730",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-731",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-732",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-733",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-734",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-735",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-736",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-737",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-738",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-739",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-740",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-741",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-742",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-743",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-744",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-745",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-746",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-747",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-748",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-749",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-750",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-751",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-752",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-753",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-754",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-755",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-756",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-757",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-758",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-759",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-760",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-761",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-762",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-763",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-764",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-765",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-766",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-767",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-768",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-769",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-770",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-771",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-772",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-773",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-774",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-775",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-776",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-777",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-778",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-779",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-780",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-781",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-782",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-783",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-784",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-785",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-786",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-787",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-788",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-789",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-790",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-791",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-792",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-793",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-794",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-795",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-796",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-797",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-798",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-799",
-    "gs://cromwell-perf-testing/lots_of_input_files/input-800"
-  ]
-}
\ No newline at end of file
diff --git a/scripts/perf/test_cases/call_caching_lots_of_inputs/lots_of_inputs.wdl b/scripts/perf/test_cases/call_caching_lots_of_inputs/lots_of_inputs.wdl
deleted file mode 100644
index 961a3b36891..00000000000
--- a/scripts/perf/test_cases/call_caching_lots_of_inputs/lots_of_inputs.wdl
+++ /dev/null
@@ -1,28 +0,0 @@
-version 1.0
-
-task lots_of_inputs {
-    input {
-        Array[File] files
-    }
-    
-    command {
-        echo ~{sep=' ' files}
-    }
-    
-    runtime {
-        docker: "ubuntu@sha256:de774a3145f7ca4f0bd144c7d4ffb2931e06634f11529653b23eba85aef8e378"
-    }
-    
-    output {
-        File out = stdout()
-    }
-}
-
-workflow call_cache_read_input_files_perf_test {
-    input {
-        Array[File] files
-    }
-    scatter(i in range(100)) {
-        call lots_of_inputs { input: files = files }
-    }
-}
diff --git a/scripts/perf/test_cases/call_caching_stress_no_hint/call_caching_stress_no_hint.test b/scripts/perf/test_cases/call_caching_stress_no_hint/call_caching_stress_no_hint.test
deleted file mode 100644
index 41fdcc6858f..00000000000
--- a/scripts/perf/test_cases/call_caching_stress_no_hint/call_caching_stress_no_hint.test
+++ /dev/null
@@ -1,12 +0,0 @@
-name: call_caching_stress_no_hint
-testFormat: workflowsuccess
-
-files {
-  workflow: "../call_caching_stress_workflow/callCachingStress.wdl"
-  inputs: "../call_caching_stress_workflow/callCachingStress.inputs"
-  options: "gs://cromwell-perf-test/workflow_related_files/call_caching_sa2_workflow_options.json"
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/scripts/perf/test_cases/call_caching_stress_no_hint/centaur.conf b/scripts/perf/test_cases/call_caching_stress_no_hint/centaur.conf
deleted file mode 100644
index 2b7ce0eed62..00000000000
--- a/scripts/perf/test_cases/call_caching_stress_no_hint/centaur.conf
+++ /dev/null
@@ -1,18 +0,0 @@
-include required("centaur_default.conf")
-
-centaur {
-  metadata-args {
-    includeKey = [
-      "id",
-      "%shardIndex%",
-      "%hitFailures%",
-      "%executionEvents%",
-      "status",
-      "workflowName",
-      "submission",
-      "start",
-      "end",
-      "failures"
-    ]
-  }
-}
diff --git a/scripts/perf/test_cases/call_caching_stress_no_hint/cromwell.conf b/scripts/perf/test_cases/call_caching_stress_no_hint/cromwell.conf
deleted file mode 100644
index 0ce40f48486..00000000000
--- a/scripts/perf/test_cases/call_caching_stress_no_hint/cromwell.conf
+++ /dev/null
@@ -1,5 +0,0 @@
-include required("cromwell_default.conf")
-
-engine.filesystems.gcs.auth = "user-service-account"
-backend.providers.Papi.config.genomics.auth = "user-service-account"
-backend.providers.Papi.config.filesystems.gcs.auth = "user-service-account"
diff --git a/scripts/perf/test_cases/call_caching_stress_with_hint/call_caching_stress_with_hint.test b/scripts/perf/test_cases/call_caching_stress_with_hint/call_caching_stress_with_hint.test
deleted file mode 100644
index f8a02e989d5..00000000000
--- a/scripts/perf/test_cases/call_caching_stress_with_hint/call_caching_stress_with_hint.test
+++ /dev/null
@@ -1,12 +0,0 @@
-name: call_caching_stress_with_hint
-testFormat: workflowsuccess
-
-files {
-  workflow: "https://raw.githubusercontent.com/broadinstitute/cromwell/$BRANCH/scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.wdl"
-  inputs: "https://raw.githubusercontent.com/broadinstitute/cromwell/$BRANCH/scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.inputs"
-  options: "gs://cromwell-perf-test/workflow_related_files/call_caching_sa2_options_with_cache_hints.json"
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/scripts/perf/test_cases/call_caching_stress_with_hint/centaur.conf b/scripts/perf/test_cases/call_caching_stress_with_hint/centaur.conf
deleted file mode 100644
index 2b7ce0eed62..00000000000
--- a/scripts/perf/test_cases/call_caching_stress_with_hint/centaur.conf
+++ /dev/null
@@ -1,18 +0,0 @@
-include required("centaur_default.conf")
-
-centaur {
-  metadata-args {
-    includeKey = [
-      "id",
-      "%shardIndex%",
-      "%hitFailures%",
-      "%executionEvents%",
-      "status",
-      "workflowName",
-      "submission",
-      "start",
-      "end",
-      "failures"
-    ]
-  }
-}
diff --git a/scripts/perf/test_cases/call_caching_stress_with_hint/cromwell.conf b/scripts/perf/test_cases/call_caching_stress_with_hint/cromwell.conf
deleted file mode 100644
index 0ce40f48486..00000000000
--- a/scripts/perf/test_cases/call_caching_stress_with_hint/cromwell.conf
+++ /dev/null
@@ -1,5 +0,0 @@
-include required("cromwell_default.conf")
-
-engine.filesystems.gcs.auth = "user-service-account"
-backend.providers.Papi.config.genomics.auth = "user-service-account"
-backend.providers.Papi.config.filesystems.gcs.auth = "user-service-account"
diff --git a/scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.inputs b/scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.inputs
deleted file mode 100644
index 281858ee08d..00000000000
--- a/scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.inputs
+++ /dev/null
@@ -1,14 +0,0 @@
-{
-  "callCachingStress.input_files": [
-    "gs://call-caching-testing-sa1/inputs/input1.txt",
-    "gs://call-caching-testing-sa1/inputs/input2.txt",
-    "gs://call-caching-testing-sa1/inputs/input3.txt",
-    "gs://call-caching-testing-sa1/inputs/input4.txt",
-    "gs://call-caching-testing-sa1/inputs/input5.txt",
-    "gs://call-caching-testing-sa1/inputs/input6.txt",
-    "gs://call-caching-testing-sa1/inputs/input7.txt",
-    "gs://call-caching-testing-sa1/inputs/input8.txt",
-    "gs://call-caching-testing-sa1/inputs/input9.txt",
-    "gs://call-caching-testing-sa1/inputs/input10.txt"
-  ]
-}
diff --git a/scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.wdl b/scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.wdl
deleted file mode 100644
index c61f55ecd35..00000000000
--- a/scripts/perf/test_cases/call_caching_stress_workflow/callCachingStress.wdl
+++ /dev/null
@@ -1,32 +0,0 @@
-version 1.0
-
-#NOTE: Please do not change the spelling for 'nb_ouptputs'. This workflow is used for Call Cache test in Perf.
-#      Since there are cache entries inside test db with wrong spelling, correcting the spelling
-#      will fail the test as it won't be call cached anymore!
-task simpleTask {
-    input {
-        Int seed
-        Int nb_ouptputs = 10
-        Array[File] input_files
-    }
-    command {
-        for i in `seq ~{nb_ouptputs}`; do echo $i > $i.txt; done
-    }
-    runtime {
-        docker: "ubuntu@sha256:3f119dc0737f57f704ebecac8a6d8477b0f6ca1ca0332c7ee1395ed2c6a82be7"
-    }
-    output {
-        Array[File] outputs = glob("*.txt")
-    }
-}
-
-workflow callCachingStress {
-    input {
-        Int scatterSize = 1000
-        Array[File] input_files
-    }
-
-    scatter(i in range(scatterSize)) {
-        call simpleTask { input: input_files = input_files, seed = i }
-    }
-}
diff --git a/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.inputs b/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.inputs
deleted file mode 100644
index 31365490649..00000000000
--- a/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.inputs
+++ /dev/null
@@ -1,39 +0,0 @@
-{
-  "germline_single_sample_workflow.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
-  "germline_single_sample_workflow.final_vcf_base_name": "NA12878_small",
-  "germline_single_sample_workflow.skip_QC": "False",
-  "germline_single_sample_workflow.wgs_evaluation_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
-  "germline_single_sample_workflow.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-  "germline_single_sample_workflow.contamination_sites_ud": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.contam.UD",
-  "germline_single_sample_workflow.ref_amb": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb",
-  "germline_single_sample_workflow.sample_name": "NA12878_small",
-  "germline_single_sample_workflow.wgs_calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
-  "germline_single_sample_workflow.agg_preemptible_tries": 3,
-  "germline_single_sample_workflow.dbSNP_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
-  "germline_single_sample_workflow.preemptible_tries": 3,
-  "germline_single_sample_workflow.contamination_sites_mu": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.contam.mu",
-  "germline_single_sample_workflow.base_file_name": "NA12878_small",
-  "germline_single_sample_workflow.contamination_sites_bed": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.contam.bed",
-  "germline_single_sample_workflow.use_gatk4_haplotype_caller": "True",
-  "germline_single_sample_workflow.make_gatk4_single_sample_vcf": "True",
-  "germline_single_sample_workflow.ref_pac": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac",
-  "germline_single_sample_workflow.break_bands_at_multiples_of": 1000000,
-  "germline_single_sample_workflow.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
-  "germline_single_sample_workflow.ref_ann": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
-  "germline_single_sample_workflow.known_indels_sites_VCFs": [
-    "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
-    "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz"
-  ],
-  "germline_single_sample_workflow.ref_alt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt",
-  "germline_single_sample_workflow.flowcell_unmapped_bams_fofn": "gs://gatk-test-data/wgs_ubam/NA12878_24RG/NA12878_24RG_small.txt",
-  "germline_single_sample_workflow.ref_sa": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa",
-  "germline_single_sample_workflow.dbSNP_vcf": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
-  "germline_single_sample_workflow.known_indels_sites_indices": [
-    "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
-    "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
-  ],
-  "germline_single_sample_workflow.wgs_coverage_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_coverage_regions.hg38.interval_list",
-  "germline_single_sample_workflow.ref_bwt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt",
-  "germline_single_sample_workflow.unmapped_bam_suffix": ".unmapped.bam",
-  "germline_single_sample_workflow.haplotype_scatter_count": 50
-}
diff --git a/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.test b/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.test
deleted file mode 100644
index 876f247a045..00000000000
--- a/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.test
+++ /dev/null
@@ -1,11 +0,0 @@
-name: five_dollar_genome
-testFormat: workflowsuccess
-
-files {
-  workflow: "https://raw.githubusercontent.com/broadinstitute/cromwell/$BRANCH/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.wdl"
-  inputs: "https://raw.githubusercontent.com/broadinstitute/cromwell/$BRANCH/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.inputs"
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.wdl b/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.wdl
deleted file mode 100644
index 9d46689650a..00000000000
--- a/scripts/perf/test_cases/five_dollar_genome/five_dollar_genome.wdl
+++ /dev/null
@@ -1,521 +0,0 @@
-## Copyright Broad Institute, 2018 
-## 
-## This WDL pipeline implements data pre-processing and initial variant calling (GVCF 
-## generation) according to the GATK Best Practices (June 2016) for germline SNP and 
-## Indel discovery in human whole-genome sequencing data. 
-## 
-## Requirements/expectations : 
-## - Human whole-genome pair-end sequencing data in unmapped BAM (uBAM) format 
-## - One or more read groups, one per uBAM file, all belonging to a single sample (SM) 
-## - Input uBAM files must additionally comply with the following requirements: 
-## - - filenames all have the same suffix (we use ".unmapped.bam") 
-## - - files must pass validation by ValidateSamFile 
-## - - reads are provided in query-sorted order 
-## - - all reads must have an RG tag 
-## - GVCF output names must end in ".g.vcf.gz" 
-## - Reference genome must be Hg38 with ALT contigs 
-## 
-## Runtime parameters are optimized for Broad's Google Cloud Platform implementation. 
-## For program versions, see docker containers. 
-## 
-## LICENSING : 
-## This script is released under the WDL source code license (BSD-3) (see LICENSE in 
-## https://github.com/broadinstitute/wdl). Note however that the programs it calls may 
-## be subject to different licenses. Users are responsible for checking that they are 
-## authorized to run all programs before running this script. Please see the docker 
-## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed 
-## licensing information pertaining to the included programs. 
- 
-import "https://api.firecloud.org/ga4gh/v1/tools/gatk:alignment/versions/4/plain-WDL/descriptor" as Alignment 
-import "https://api.firecloud.org/ga4gh/v1/tools/gatk:split-large-readgroup/versions/4/plain-WDL/descriptor" as SplitRG 
-import "https://api.firecloud.org/ga4gh/v1/tools/gatk:quality-control/versions/2/plain-WDL/descriptor" as QC 
-import "https://api.firecloud.org/ga4gh/v1/tools/gatk:bam-processing/versions/4/plain-WDL/descriptor" as Processing 
-import "https://api.firecloud.org/ga4gh/v1/tools/gatk:germline-variant-discovery/versions/3/plain-WDL/descriptor" as Calling 
-import "https://api.firecloud.org/ga4gh/v1/tools/gatk:utilities/versions/2/plain-WDL/descriptor" as Utils 
- 
-# WORKFLOW DEFINITION 
-workflow germline_single_sample_workflow { 
- 
-  File flowcell_unmapped_bams_fofn 
-  Array[File] flowcell_unmapped_bams = read_lines(flowcell_unmapped_bams_fofn) 
- 
-  File contamination_sites_ud 
-  File contamination_sites_bed 
-  File contamination_sites_mu 
-  File wgs_evaluation_interval_list 
-  File wgs_coverage_interval_list 
- 
-  String sample_name 
-  String base_file_name 
-  String final_vcf_base_name 
-  String unmapped_bam_suffix 
- 
-  File wgs_calling_interval_list 
-  Int haplotype_scatter_count 
-  Int break_bands_at_multiples_of 
-  Int read_length = 250 
- 
-  File ref_fasta 
-  File ref_fasta_index 
-  File ref_dict 
-  File ref_alt 
-  File ref_bwt 
-  File ref_sa 
-  File ref_amb 
-  File ref_ann 
-  File ref_pac 
- 
-  File dbSNP_vcf 
-  File dbSNP_vcf_index 
-  Array[File] known_indels_sites_VCFs 
-  Array[File] known_indels_sites_indices 
- 
-  Int preemptible_tries 
-  Int agg_preemptible_tries 
- 
-  Boolean skip_QC 
-  Boolean make_gatk4_single_sample_vcf 
-  Boolean use_gatk4_haplotype_caller 
- 
-  Float cutoff_for_large_rg_in_gb = 20.0 
- 
-  String bwa_commandline="bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta" 
- 
-  String recalibrated_bam_basename = base_file_name + ".aligned.duplicates_marked.recalibrated" 
- 
-  Int compression_level = 2 
- 
-  # Get the version of BWA to include in the PG record in the header of the BAM produced 
-  # by MergeBamAlignment. 
-  call Alignment.GetBwaVersion 
- 
-  # Align flowcell-level unmapped input bams in parallel 
-  scatter (unmapped_bam in flowcell_unmapped_bams) { 
- 
-    Float unmapped_bam_size = size(unmapped_bam, "GB") 
- 
-    String unmapped_bam_basename = basename(unmapped_bam, unmapped_bam_suffix) 
- 
-    if (!skip_QC) { 
-      # QC the unmapped BAM 
-      call QC.CollectQualityYieldMetrics as CollectQualityYieldMetrics { 
-        input: 
-          input_bam = unmapped_bam, 
-          metrics_filename = unmapped_bam_basename + ".unmapped.quality_yield_metrics", 
-          preemptible_tries = preemptible_tries 
-      } 
-    } 
- 
-    if (unmapped_bam_size > cutoff_for_large_rg_in_gb) { 
-      # Split bam into multiple smaller bams, 
-      # map reads to reference and recombine into one bam 
-      call SplitRG.split_large_readgroup as SplitRG { 
-        input: 
-          input_bam = unmapped_bam, 
-          bwa_commandline = bwa_commandline, 
-          bwa_version = GetBwaVersion.version, 
-          output_bam_basename = unmapped_bam_basename + ".aligned.unsorted", 
-          ref_fasta = ref_fasta, 
-          ref_fasta_index = ref_fasta_index, 
-          ref_dict = ref_dict, 
-          ref_alt = ref_alt, 
-          ref_amb = ref_amb, 
-          ref_ann = ref_ann, 
-          ref_bwt = ref_bwt, 
-          ref_pac = ref_pac, 
-          ref_sa = ref_sa, 
-          compression_level = compression_level, 
-          preemptible_tries = preemptible_tries 
-      } 
-    } 
- 
-    if (unmapped_bam_size <= cutoff_for_large_rg_in_gb) { 
-      # Map reads to reference 
-      call Alignment.SamToFastqAndBwaMemAndMba as SamToFastqAndBwaMemAndMba { 
-        input: 
-          input_bam = unmapped_bam, 
-          bwa_commandline = bwa_commandline, 
-          output_bam_basename = unmapped_bam_basename + ".aligned.unsorted", 
-          ref_fasta = ref_fasta, 
-          ref_fasta_index = ref_fasta_index, 
-          ref_dict = ref_dict, 
-          ref_alt = ref_alt, 
-          ref_bwt = ref_bwt, 
-          ref_amb = ref_amb, 
-          ref_ann = ref_ann, 
-          ref_pac = ref_pac, 
-          ref_sa = ref_sa, 
-          bwa_version = GetBwaVersion.version, 
-          compression_level = compression_level, 
-          preemptible_tries = preemptible_tries 
-      } 
-    } 
- 
-    File output_aligned_bam = select_first([SamToFastqAndBwaMemAndMba.output_bam, SplitRG.aligned_bam]) 
- 
-    Float mapped_bam_size = size(output_aligned_bam, "GB") 
- 
-    if (!skip_QC) { 
-      # QC the aligned but unsorted readgroup BAM 
-      # no reference as the input here is unsorted, providing a reference would cause an error 
-      call QC.CollectUnsortedReadgroupBamQualityMetrics as CollectUnsortedReadgroupBamQualityMetrics { 
-        input: 
-          input_bam = output_aligned_bam, 
-          output_bam_prefix = unmapped_bam_basename + ".readgroup", 
-          preemptible_tries = preemptible_tries 
-      } 
-    } 
-  } 
- 
-  # Sum the read group bam sizes to approximate the aggregated bam size 
-  call Utils.SumFloats as SumFloats { 
-    input: 
-      sizes = mapped_bam_size, 
-      preemptible_tries = preemptible_tries 
-  } 
- 
-  # Aggregate aligned+merged flowcell BAM files and mark duplicates 
-  # We take advantage of the tool's ability to take multiple BAM inputs and write out a single output 
-  # to avoid having to spend time just merging BAM files. 
-  call Processing.MarkDuplicates as MarkDuplicates { 
-    input: 
-      input_bams = output_aligned_bam, 
-      output_bam_basename = base_file_name + ".aligned.unsorted.duplicates_marked", 
-      metrics_filename = base_file_name + ".duplicate_metrics", 
-      total_input_size = SumFloats.total_size, 
-      compression_level = compression_level, 
-      preemptible_tries = agg_preemptible_tries 
-  } 
- 
-  # Sort aggregated+deduped BAM file 
-  call Processing.SortSam as SortSampleBam { 
-    input: 
-      input_bam = MarkDuplicates.output_bam, 
-      output_bam_basename = base_file_name + ".aligned.duplicate_marked.sorted", 
-      compression_level = compression_level, 
-      preemptible_tries = agg_preemptible_tries 
-  } 
- 
-  # Create list of sequences for scatter-gather parallelization 
-  call Utils.CreateSequenceGroupingTSV as CreateSequenceGroupingTSV { 
-    input: 
-      ref_dict = ref_dict, 
-      preemptible_tries = preemptible_tries 
-  } 
- 
-  # Estimate level of cross-sample contamination 
-  call Processing.CheckContamination as CheckContamination { 
-    input: 
-      input_bam = SortSampleBam.output_bam, 
-      input_bam_index = SortSampleBam.output_bam_index, 
-      contamination_sites_ud = contamination_sites_ud, 
-      contamination_sites_bed = contamination_sites_bed, 
-      contamination_sites_mu = contamination_sites_mu, 
-      ref_fasta = ref_fasta, 
-      ref_fasta_index = ref_fasta_index, 
-      output_prefix = base_file_name + ".preBqsr", 
-      preemptible_tries = agg_preemptible_tries, 
-      contamination_underestimation_factor = 0.75 
-  } 
- 
-  # We need disk to localize the sharded input and output due to the scatter for BQSR. 
-  # If we take the number we are scattering by and reduce by 3 we will have enough disk space 
-  # to account for the fact that the data is not split evenly. 
-  Int num_of_bqsr_scatters = length(CreateSequenceGroupingTSV.sequence_grouping) 
-  Int potential_bqsr_divisor = num_of_bqsr_scatters - 10 
-  Int bqsr_divisor = if potential_bqsr_divisor > 1 then potential_bqsr_divisor else 1 
- 
-  # Perform Base Quality Score Recalibration (BQSR) on the sorted BAM in parallel 
-  scatter (subgroup in CreateSequenceGroupingTSV.sequence_grouping) { 
-    # Generate the recalibration model by interval 
-    call Processing.BaseRecalibrator as BaseRecalibrator { 
-      input: 
-        input_bam = SortSampleBam.output_bam, 
-        recalibration_report_filename = base_file_name + ".recal_data.csv", 
-        sequence_group_interval = subgroup, 
-        dbSNP_vcf = dbSNP_vcf, 
-        dbSNP_vcf_index = dbSNP_vcf_index, 
-        known_indels_sites_VCFs = known_indels_sites_VCFs, 
-        known_indels_sites_indices = known_indels_sites_indices, 
-        ref_dict = ref_dict, 
-        ref_fasta = ref_fasta, 
-        ref_fasta_index = ref_fasta_index, 
-        bqsr_scatter = bqsr_divisor, 
-        preemptible_tries = agg_preemptible_tries 
-    } 
-  } 
- 
-  # Merge the recalibration reports resulting from by-interval recalibration 
-  # The reports are always the same size 
-  call Processing.GatherBqsrReports as GatherBqsrReports { 
-    input: 
-      input_bqsr_reports = BaseRecalibrator.recalibration_report, 
-      output_report_filename = base_file_name + ".recal_data.csv", 
-      preemptible_tries = preemptible_tries 
-  } 
- 
-  scatter (subgroup in CreateSequenceGroupingTSV.sequence_grouping_with_unmapped) { 
-    # Apply the recalibration model by interval 
-    call Processing.ApplyBQSR as ApplyBQSR { 
-      input: 
-        input_bam = SortSampleBam.output_bam, 
-        output_bam_basename = recalibrated_bam_basename, 
-        recalibration_report = GatherBqsrReports.output_bqsr_report, 
-        sequence_group_interval = subgroup, 
-        ref_dict = ref_dict, 
-        ref_fasta = ref_fasta, 
-        ref_fasta_index = ref_fasta_index, 
-        bqsr_scatter = bqsr_divisor, 
-        compression_level = compression_level, 
-        preemptible_tries = agg_preemptible_tries 
-    } 
-  } 
- 
-  Float agg_bam_size = size(SortSampleBam.output_bam, "GB") 
- 
-  # Merge the recalibrated BAM files resulting from by-interval recalibration 
-  call Processing.GatherSortedBamFiles as GatherBamFiles { 
-    input: 
-      input_bams = ApplyBQSR.recalibrated_bam, 
-      output_bam_basename = base_file_name, 
-      total_input_size = agg_bam_size, 
-      compression_level = compression_level, 
-      preemptible_tries = agg_preemptible_tries 
-  } 
- 
-  #BQSR bins the qualities which makes a significantly smaller bam 
-  Float binned_qual_bam_size = size(GatherBamFiles.output_bam, "GB") 
- 
-  File? chimerism_metrics 
- 
-  if (!skip_QC) { 
-    # QC the final BAM (consolidated after scattered BQSR) 
-    call QC.CollectReadgroupBamQualityMetrics as CollectReadgroupBamQualityMetrics { 
-      input: 
-        input_bam = GatherBamFiles.output_bam, 
-        input_bam_index = GatherBamFiles.output_bam_index, 
-        output_bam_prefix = base_file_name + ".readgroup", 
-        ref_dict = ref_dict, 
-        ref_fasta = ref_fasta, 
-        ref_fasta_index = ref_fasta_index, 
-        preemptible_tries = agg_preemptible_tries 
-    } 
- 
-    # QC the final BAM some more (no such thing as too much QC) 
-    call QC.CollectAggregationMetrics as CollectAggregationMetrics { 
-      input: 
-        input_bam = GatherBamFiles.output_bam, 
-        input_bam_index = GatherBamFiles.output_bam_index, 
-        output_bam_prefix = base_file_name, 
-        ref_dict = ref_dict, 
-        ref_fasta = ref_fasta, 
-        ref_fasta_index = ref_fasta_index, 
-        preemptible_tries = agg_preemptible_tries 
-    } 
- 
-    # QC the sample WGS metrics (stringent thresholds) 
-    call QC.CollectWgsMetrics as CollectWgsMetrics { 
-      input: 
-        input_bam = GatherBamFiles.output_bam, 
-        input_bam_index = GatherBamFiles.output_bam_index, 
-        metrics_filename = base_file_name + ".wgs_metrics", 
-        ref_fasta = ref_fasta, 
-        ref_fasta_index = ref_fasta_index, 
-        wgs_coverage_interval_list = wgs_coverage_interval_list, 
-        read_length = read_length, 
-        preemptible_tries = agg_preemptible_tries 
-    } 
- 
-    # QC the sample raw WGS metrics (common thresholds) 
-    call QC.CollectRawWgsMetrics as CollectRawWgsMetrics { 
-      input: 
-        input_bam = GatherBamFiles.output_bam, 
-        input_bam_index = GatherBamFiles.output_bam_index, 
-        metrics_filename = base_file_name + ".raw_wgs_metrics", 
-        ref_fasta = ref_fasta, 
-        ref_fasta_index = ref_fasta_index, 
-        wgs_coverage_interval_list = wgs_coverage_interval_list, 
-        read_length = read_length, 
-        preemptible_tries = agg_preemptible_tries 
-    } 
- 
-    # Generate a checksum per readgroup in the final BAM 
-    call QC.CalculateReadGroupChecksum as CalculateReadGroupChecksum { 
-      input: 
-        input_bam = GatherBamFiles.output_bam, 
-        input_bam_index = GatherBamFiles.output_bam_index, 
-        read_group_md5_filename = recalibrated_bam_basename + ".bam.read_group_md5", 
-        preemptible_tries = agg_preemptible_tries 
-    } 
-  } 
- 
-  # ValidateSamFile runs out of memory in mate validation on crazy edge case data, so we want to skip the mate validation 
-  # in those cases.  These values set the thresholds for what is considered outside the normal realm of "reasonable" data. 
-  Float max_duplication_in_reasonable_sample = 0.30 
-  Float max_chimerism_in_reasonable_sample = 0.15 
- 
-  # Convert the final merged recalibrated BAM file to CRAM format 
-  call Utils.ConvertToCram as ConvertToCram { 
-    input: 
-      input_bam = GatherBamFiles.output_bam, 
-      ref_fasta = ref_fasta, 
-      ref_fasta_index = ref_fasta_index, 
-      output_basename = base_file_name, 
-      preemptible_tries = agg_preemptible_tries 
-  } 
- 
-  if (!skip_QC) { 
-    # Check whether the data has massively high duplication or chimerism rates 
-    call QC.CheckPreValidation as CheckPreValidation { 
-      input: 
-        duplication_metrics = MarkDuplicates.duplicate_metrics, 
-        chimerism_metrics = select_first([CollectAggregationMetrics.alignment_summary_metrics, ""]), 
-        max_duplication_in_reasonable_sample = max_duplication_in_reasonable_sample, 
-        max_chimerism_in_reasonable_sample = max_chimerism_in_reasonable_sample, 
-        preemptible_tries = agg_preemptible_tries 
-    } 
-  } 
- 
-  Boolean is_outlier_data = select_first([CheckPreValidation.is_outlier_data, false]) 
- 
-  # Validate the CRAM file 
-  call QC.ValidateSamFile as ValidateCram { 
-    input: 
-      input_bam = ConvertToCram.output_cram, 
-      input_bam_index = ConvertToCram.output_cram_index, 
-      report_filename = base_file_name + ".cram.validation_report", 
-      ref_dict = ref_dict, 
-      ref_fasta = ref_fasta, 
-      ref_fasta_index = ref_fasta_index, 
-      ignore = ["MISSING_TAG_NM"], 
-      max_output = 1000000000, 
-      is_outlier_data = is_outlier_data, 
-      preemptible_tries = agg_preemptible_tries 
-  } 
- 
-  # Break the calling interval_list into sub-intervals 
-  # Perform variant calling on the sub-intervals, and then gather the results 
-  call Utils.ScatterIntervalList as ScatterIntervalList { 
-    input: 
-      interval_list = wgs_calling_interval_list, 
-      scatter_count = haplotype_scatter_count, 
-      break_bands_at_multiples_of = break_bands_at_multiples_of 
-  } 
- 
-  # We need disk to localize the sharded input and output due to the scatter for HaplotypeCaller. 
-  # If we take the number we are scattering by and reduce by 20 we will have enough disk space 
-  # to account for the fact that the data is quite uneven across the shards. 
-  Int potential_hc_divisor = ScatterIntervalList.interval_count - 20 
-  Int hc_divisor = if potential_hc_divisor > 1 then potential_hc_divisor else 1 
- 
-  # Call variants in parallel over WGS calling intervals 
-  scatter (index in range(ScatterIntervalList.interval_count)) { 
- 
-    if (make_gatk4_single_sample_vcf || use_gatk4_haplotype_caller) { 
-      call Calling.HaplotypeCaller_GATK4_VCF as HaplotypeCaller4 { 
-        input: 
-          contamination = CheckContamination.contamination, 
-          input_bam = GatherBamFiles.output_bam, 
-          interval_list = ScatterIntervalList.out[index], 
-          make_gvcf = !make_gatk4_single_sample_vcf, 
-          vcf_basename = base_file_name, 
-          ref_dict = ref_dict, 
-          ref_fasta = ref_fasta, 
-          ref_fasta_index = ref_fasta_index, 
-          hc_scatter = hc_divisor, 
-          preemptible_tries = agg_preemptible_tries 
-      } 
- 
-      if (make_gatk4_single_sample_vcf) { 
-        call Calling.HardFilterVcf as FilterVcf { 
-          input: 
-            input_vcf = HaplotypeCaller4.output_vcf, 
-            input_vcf_index = HaplotypeCaller4.output_vcf_index, 
-            vcf_basename = base_file_name, 
-            interval_list = ScatterIntervalList.out[index], 
-            preemptible_tries = preemptible_tries 
-        } 
-      } 
-    } 
-    if (!make_gatk4_single_sample_vcf && !use_gatk4_haplotype_caller) { 
-      call Calling.HaplotypeCaller_GATK35_GVCF as HaplotypeCaller3 { 
-        input: 
-          contamination = CheckContamination.contamination, 
-          input_bam = GatherBamFiles.output_bam, 
-          interval_list = ScatterIntervalList.out[index], 
-          gvcf_basename = base_file_name, 
-          ref_dict = ref_dict, 
-          ref_fasta = ref_fasta, 
-          ref_fasta_index = ref_fasta_index, 
-          hc_scatter = hc_divisor, 
-          preemptible_tries = agg_preemptible_tries 
-       } 
-     } 
- 
-     File merge_input = select_first([FilterVcf.output_vcf, HaplotypeCaller4.output_vcf, HaplotypeCaller3.output_gvcf]) 
-     File merge_input_index = select_first([FilterVcf.output_vcf_index, HaplotypeCaller4.output_vcf_index, HaplotypeCaller3.output_gvcf_index]) 
-  } 
- 
-  String name_token = if make_gatk4_single_sample_vcf then ".filtered" else ".g" 
- 
-  # Combine by-interval VCFs into a single sample VCF file 
-  call Calling.MergeVCFs as MergeVCFs { 
-    input: 
-      input_vcfs = merge_input, 
-      input_vcfs_indexes = merge_input_index, 
-      output_vcf_name = final_vcf_base_name + name_token + ".vcf.gz", 
-      preemptible_tries = agg_preemptible_tries 
-  } 
- 
-  # Outputs that will be retained when execution is complete 
-  output { 
-    Array[File?] quality_yield_metrics = CollectQualityYieldMetrics.quality_yield_metrics 
- 
-    Array[File?] unsorted_read_group_base_distribution_by_cycle_pdf = CollectUnsortedReadgroupBamQualityMetrics.base_distribution_by_cycle_pdf 
-    Array[File?] unsorted_read_group_base_distribution_by_cycle_metrics = CollectUnsortedReadgroupBamQualityMetrics.base_distribution_by_cycle_metrics 
-    Array[File?] unsorted_read_group_insert_size_histogram_pdf = CollectUnsortedReadgroupBamQualityMetrics.insert_size_histogram_pdf 
-    Array[File?] unsorted_read_group_insert_size_metrics = CollectUnsortedReadgroupBamQualityMetrics.insert_size_metrics 
-    Array[File?] unsorted_read_group_quality_by_cycle_pdf = CollectUnsortedReadgroupBamQualityMetrics.quality_by_cycle_pdf 
-    Array[File?] unsorted_read_group_quality_by_cycle_metrics = CollectUnsortedReadgroupBamQualityMetrics.quality_by_cycle_metrics 
-    Array[File?] unsorted_read_group_quality_distribution_pdf = CollectUnsortedReadgroupBamQualityMetrics.quality_distribution_pdf 
-    Array[File?] unsorted_read_group_quality_distribution_metrics = CollectUnsortedReadgroupBamQualityMetrics.quality_distribution_metrics 
- 
-    File? read_group_alignment_summary_metrics = CollectReadgroupBamQualityMetrics.alignment_summary_metrics 
-    File? read_group_gc_bias_detail_metrics = CollectReadgroupBamQualityMetrics.gc_bias_detail_metrics 
-    File? read_group_gc_bias_pdf = CollectReadgroupBamQualityMetrics.gc_bias_pdf 
-    File? read_group_gc_bias_summary_metrics = CollectReadgroupBamQualityMetrics.gc_bias_summary_metrics 
- 
-    File selfSM = CheckContamination.selfSM 
-    Float contamination = CheckContamination.contamination 
- 
-    File? calculate_read_group_checksum_md5 = CalculateReadGroupChecksum.md5_file 
- 
-    File? agg_alignment_summary_metrics = CollectAggregationMetrics.alignment_summary_metrics 
-    File? agg_bait_bias_detail_metrics = CollectAggregationMetrics.bait_bias_detail_metrics 
-    File? agg_bait_bias_summary_metrics = CollectAggregationMetrics.bait_bias_summary_metrics 
-    File? agg_gc_bias_detail_metrics = CollectAggregationMetrics.gc_bias_detail_metrics 
-    File? agg_gc_bias_pdf = CollectAggregationMetrics.gc_bias_pdf 
-    File? agg_gc_bias_summary_metrics = CollectAggregationMetrics.gc_bias_summary_metrics 
-    File? agg_insert_size_histogram_pdf = CollectAggregationMetrics.insert_size_histogram_pdf 
-    File? agg_insert_size_metrics = CollectAggregationMetrics.insert_size_metrics 
-    File? agg_pre_adapter_detail_metrics = CollectAggregationMetrics.pre_adapter_detail_metrics 
-    File? agg_pre_adapter_summary_metrics = CollectAggregationMetrics.pre_adapter_summary_metrics 
-    File? agg_quality_distribution_pdf = CollectAggregationMetrics.quality_distribution_pdf 
-    File? agg_quality_distribution_metrics = CollectAggregationMetrics.quality_distribution_metrics 
- 
-    File? wgs_metrics = CollectWgsMetrics.metrics 
-    File? raw_wgs_metrics = CollectRawWgsMetrics.metrics 
- 
-    File duplicate_metrics = MarkDuplicates.duplicate_metrics 
-    File output_bqsr_reports = GatherBqsrReports.output_bqsr_report 
- 
-    File output_cram = ConvertToCram.output_cram 
-    File output_cram_index = ConvertToCram.output_cram_index 
-    File output_cram_md5 = ConvertToCram.output_cram_md5 
- 
-    File validate_cram_file_report = ValidateCram.report 
- 
-    File output_vcf = MergeVCFs.output_vcf 
-    File output_vcf_index = MergeVCFs.output_vcf_index 
-  } 
-}
diff --git a/scripts/perf/test_cases/gary/gary.inputs b/scripts/perf/test_cases/gary/gary.inputs
deleted file mode 100644
index 6c630f09e27..00000000000
--- a/scripts/perf/test_cases/gary/gary.inputs
+++ /dev/null
@@ -1,12 +0,0 @@
-{
-  "echo_strings.echo_files.input1": "gs://debtest3/h.txt",
-  "echo_strings.echo_files.input5": "gs://debtest3/h.txt",
-  "echo_strings.echo_files.input2": "gs://debtest3/h.txt",
-  "echo_strings.echo_files.input10": "gs://debtest3/h.txt",
-  "echo_strings.echo_files.input6": "gs://debtest3/h.txt",
-  "echo_strings.echo_files.input9": "gs://debtest3/h.txt",
-  "echo_strings.echo_files.input3": "gs://debtest3/h.txt",
-  "echo_strings.echo_files.input7": "gs://debtest3/h.txt",
-  "echo_strings.echo_files.input8": "gs://debtest3/h.txt",
-  "echo_strings.echo_files.input4": "gs://debtest3/h.txt"
-}
diff --git a/scripts/perf/test_cases/gary/gary.test b/scripts/perf/test_cases/gary/gary.test
deleted file mode 100644
index 5b1f5783afd..00000000000
--- a/scripts/perf/test_cases/gary/gary.test
+++ /dev/null
@@ -1,11 +0,0 @@
-name: gary
-testFormat: workflowsuccess
-
-files {
-  workflow: "https://raw.githubusercontent.com/broadinstitute/cromwell/$BRANCH/scripts/perf/test_cases/gary/gary.wdl"
-  inputs: "https://raw.githubusercontent.com/broadinstitute/cromwell/$BRANCH/scripts/perf/test_cases/gary/gary.inputs"
-}
-
-metadata {
-  status: Succeeded
-}
diff --git a/scripts/perf/test_cases/gary/gary.wdl b/scripts/perf/test_cases/gary/gary.wdl
deleted file mode 100644
index 57652bb28e4..00000000000
--- a/scripts/perf/test_cases/gary/gary.wdl
+++ /dev/null
@@ -1,40 +0,0 @@
-task echo_files {
-  File input1
-  File input2
-  File input3
-  File input4
-  File input5
-  File input6
-  File input7
-  File input8
-  File input9
-  File input10
-  
-  Float ref_size = size(input1, "GB") + size(input2, "GB") + size(input3, "GB") + size(input4, "GB") + size(input5, "GB") + size(input6, "GB") + size(input7, "GB") + size(input8, "GB") + size(input9, "GB") + size(input10, "GB")
-  
-  output {
-    String out = read_string(stdout())
-  }
-
-  command {
-    # sleep for 1 hour
-    # sleep 3600
-    
-    echo "result: ${ref_size}"
-  }
-
-  runtime {
-    docker: "ubuntu:latest"
-    cpu: "1"
-    memory: "0.1 GB"
-    preemptible: 3
-    disks: "local-disk 1 HDD"
-    bootDiskSizeGb: 10
-  }
-}
-
-workflow echo_strings {
-  scatter (i in range(30)) {
-      call echo_files
-  }
-}
diff --git a/scripts/perf/test_cases/hello/hello.test b/scripts/perf/test_cases/hello/hello.test
deleted file mode 100644
index accd48f9a23..00000000000
--- a/scripts/perf/test_cases/hello/hello.test
+++ /dev/null
@@ -1,16 +0,0 @@
-name: hello
-testFormat: workflowsuccess
-
-files {
-  workflow: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.wdl"
-  inputs: "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/centaur/src/main/resources/standardTestCases/hello/hello.inputs"
-}
-
-metadata {
-  workflowName: wf_hello
-  status: Succeeded
-  "calls.wf_hello.hello.executionStatus": Done
-  "calls.wf_hello.hello.runtimeAttributes.docker": "ubuntu@sha256:71cd81252a3563a03ad8daee81047b62ab5d892ebbfbf71cf53415f29c130950"
-  "outputs.wf_hello.hello.salutation": "Hello m'Lord!"
-  "inputs.wf_hello.hello.addressee": "m'Lord"
-}
diff --git a/scripts/perf/test_cases/reader/cromwell.conf b/scripts/perf/test_cases/reader/cromwell.conf
deleted file mode 100644
index 7a282f4e171..00000000000
--- a/scripts/perf/test_cases/reader/cromwell.conf
+++ /dev/null
@@ -1,8 +0,0 @@
-include required("cromwell_default.conf")
-
-system {
-  cromwell_id = "perf-reader"
-  max-concurrent-workflows = 0
-  max-workflow-launch-count = 0
-  new-workflow-poll-rate = 999999
-}
diff --git a/scripts/perf/vm_scripts/centaur/centaur.conf b/scripts/perf/vm_scripts/centaur/centaur.conf
deleted file mode 100644
index 6f6cbfab9d1..00000000000
--- a/scripts/perf/vm_scripts/centaur/centaur.conf
+++ /dev/null
@@ -1,17 +0,0 @@
-akka.http.client.parsing.max-content-length = 524288000
-
-centaur {
-  error-reporter {
-    retry-attempts: 0
-    providers {
-      gcs {
-        # Reports metadata to gcs for both successes and failures
-        class: "centaur.reporting.GcsReporter"
-        config {
-          report-bucket: ${?GCS_REPORT_BUCKET}
-          report-path: ${?GCS_REPORT_PATH}/metadata.json
-        }
-      }
-    }
-  }
-}
diff --git a/scripts/perf/vm_scripts/cromwell-dashboard.json b/scripts/perf/vm_scripts/cromwell-dashboard.json
deleted file mode 100644
index f11c19a2981..00000000000
--- a/scripts/perf/vm_scripts/cromwell-dashboard.json
+++ /dev/null
@@ -1,1703 +0,0 @@
-{
-  "__inputs": [
-    {
-      "name": "DS_LOCAL_GRAPHITE",
-      "label": "Local Graphite",
-      "description": "",
-      "type": "datasource",
-      "pluginId": "graphite",
-      "pluginName": "Graphite"
-    }
-  ],
-  "__requires": [
-    {
-      "type": "grafana",
-      "id": "grafana",
-      "name": "Grafana",
-      "version": "4.4.3"
-    },
-    {
-      "type": "panel",
-      "id": "graph",
-      "name": "Graph",
-      "version": ""
-    },
-    {
-      "type": "datasource",
-      "id": "graphite",
-      "name": "Graphite",
-      "version": "1.0.0"
-    },
-    {
-      "type": "panel",
-      "id": "singlestat",
-      "name": "Singlestat",
-      "version": ""
-    }
-  ],
-  "annotations": {
-    "list": []
-  },
-  "editable": true,
-  "gnetId": null,
-  "graphTooltip": 0,
-  "hideControls": false,
-  "id": null,
-  "links": [],
-  "refresh": "5s",
-  "rows": [
-    {
-      "collapse": false,
-      "height": 222,
-      "panels": [
-        {
-          "aliasColors": {},
-          "bars": false,
-          "dashLength": 10,
-          "dashes": false,
-          "datasource": "${DS_LOCAL_GRAPHITE}",
-          "fill": 1,
-          "id": 15,
-          "legend": {
-            "avg": false,
-            "current": false,
-            "max": false,
-            "min": false,
-            "show": false,
-            "total": false,
-            "values": false
-          },
-          "lines": true,
-          "linewidth": 1,
-          "links": [],
-          "nullPointMode": "null as zero",
-          "percentage": false,
-          "pointradius": 5,
-          "points": false,
-          "renderer": "flot",
-          "seriesOverrides": [],
-          "spaceLength": 10,
-          "span": 2,
-          "stack": false,
-          "steppedLine": false,
-          "targets": [
-            {
-              "refId": "B",
-              "target": "stats.gauges.cromwell.load.IO"
-            },
-            {
-              "refId": "C",
-              "target": "stats.gauges.cromwell.load.JobStoreReaderActor"
-            },
-            {
-              "refId": "D",
-              "target": "stats.gauges.cromwell.load.JobStoreWriterActor"
-            },
-            {
-              "refId": "E",
-              "target": "stats.gauges.cromwell.load.KvReadActor"
-            },
-            {
-              "refId": "F",
-              "target": "stats.gauges.cromwell.load.KvWriteActor"
-            },
-            {
-              "refId": "G",
-              "target": "stats.gauges.cromwell.load.Memory"
-            },
-            {
-              "refId": "H",
-              "target": "stats.gauges.cromwell.load.PAPIQueryManager"
-            },
-            {
-              "refId": "I",
-              "target": "stats.gauges.cromwell.load.WriteMetadataActor"
-            },
-            {
-              "refId": "J",
-              "target": "maxSeries(stats.gauges.cromwell.load.CallCacheReadActor.*)"
-            },
-            {
-              "refId": "A",
-              "target": "stats.gauges.cromwell.load.CallCacheWriteActor"
-            }
-          ],
-          "thresholds": [],
-          "timeFrom": null,
-          "timeShift": null,
-          "title": "Load Levels",
-          "tooltip": {
-            "msResolution": false,
-            "shared": true,
-            "sort": 0,
-            "value_type": "individual"
-          },
-          "type": "graph",
-          "xaxis": {
-            "buckets": null,
-            "mode": "time",
-            "name": null,
-            "show": true,
-            "values": []
-          },
-          "yaxes": [
-            {
-              "format": "short",
-              "label": null,
-              "logBase": 1,
-              "max": null,
-              "min": null,
-              "show": true
-            },
-            {
-              "format": "short",
-              "label": null,
-              "logBase": 1,
-              "max": null,
-              "min": null,
-              "show": true
-            }
-          ]
-        },
-        {
-          "cacheTimeout": null,
-          "colorBackground": false,
-          "colorValue": true,
-          "colors": [
-            "rgba(50, 172, 45, 0.97)",
-            "rgba(237, 129, 40, 0.89)",
-            "rgba(245, 54, 54, 0.9)"
-          ],
-          "datasource": "${DS_LOCAL_GRAPHITE}",
-          "format": "none",
-          "gauge": {
-            "maxValue": 100,
-            "minValue": 0,
-            "show": false,
-            "thresholdLabels": false,
-            "thresholdMarkers": true
-          },
-          "id": 9,
-          "interval": null,
-          "links": [],
-          "mappingType": 1,
-          "mappingTypes": [
-            {
-              "name": "value to text",
-              "value": 1
-            },
-            {
-              "name": "range to text",
-              "value": 2
-            }
-          ],
-          "maxDataPoints": 100,
-          "nullPointMode": "connected",
-          "nullText": null,
-          "postfix": "",
-          "postfixFontSize": "50%",
-          "prefix": "",
-          "prefixFontSize": "50%",
-          "rangeMaps": [
-            {
-              "from": "null",
-              "text": "N/A",
-              "to": "null"
-            }
-          ],
-          "span": 2,
-          "sparkline": {
-            "fillColor": "rgba(31, 118, 189, 0.18)",
-            "full": false,
-            "lineColor": "rgb(31, 120, 193)",
-            "show": false
-          },
-          "tableColumn": "",
-          "targets": [
-            {
-              "refId": "A",
-              "target": "keepLastValue(stats.gauges.cromwell.load.global, 1)"
-            }
-          ],
-          "thresholds": "1",
-          "title": "Load",
-          "type": "singlestat",
-          "valueFontSize": "80%",
-          "valueMaps": [
-            {
-              "op": "=",
-              "text": "Normal",
-              "value": "0"
-            },
-            {
-              "op": "=",
-              "text": "High",
-              "value": "1"
-            }
-          ],
-          "valueName": "current"
-        },
-        {
-          "cacheTimeout": null,
-          "colorBackground": false,
-          "colorValue": false,
-          "colors": [
-            "rgba(245, 54, 54, 0.9)",
-            "rgba(237, 129, 40, 0.89)",
-            "rgba(50, 172, 45, 0.97)"
-          ],
-          "datasource": "${DS_LOCAL_GRAPHITE}",
-          "editable": true,
-          "error": false,
-          "format": "none",
-          "gauge": {
-            "maxValue": 100,
-            "minValue": 0,
-            "show": false,
-            "thresholdLabels": false,
-            "thresholdMarkers": true
-          },
-          "hideTimeOverride": true,
-          "id": 20,
-          "interval": null,
-          "links": [],
-          "mappingType": 1,
-          "mappingTypes": [
-            {
-              "name": "value to text",
-              "value": 1
-            },
-            {
-              "name": "range to text",
-              "value": 2
-            }
-          ],
-          "maxDataPoints": 100,
-          "nullPointMode": "connected",
-          "nullText": null,
-          "postfix": "",
-          "postfixFontSize": "50%",
-          "prefix": "",
-          "prefixFontSize": "50%",
-          "rangeMaps": [
-            {
-              "from": "null",
-              "text": "N/A",
-              "to": "null"
-            }
-          ],
-          "span": 2,
-          "sparkline": {
-            "fillColor": "rgba(31, 118, 189, 0.18)",
-            "full": false,
-            "lineColor": "rgb(31, 120, 193)",
-            "show": false
-          },
-          "tableColumn": "",
-          "targets": [
-            {
-              "refId": "A",
-              "target": "stats.gauges.cromwell.workflow.Queued"
-            }
-          ],
-          "thresholds": "",
-          "timeFrom": "5m",
-          "timeShift": null,
-          "title": "Workflows Queued",
-          "type": "singlestat",
-          "valueFontSize": "80%",
-          "valueMaps": [
-            {
-              "op": "=",
-              "text": "N/A",
-              "value": "null"
-            }
-          ],
-          "valueName": "current"
-        },
-        {
-          "cacheTimeout": null,
-          "colorBackground": false,
-          "colorValue": false,
-          "colors": [
-            "rgba(245, 54, 54, 0.9)",
-            "rgba(237, 129, 40, 0.89)",
-            "rgba(50, 172, 45, 0.97)"
-          ],
-          "datasource": "${DS_LOCAL_GRAPHITE}",
-          "editable": true,
-          "error": false,
-          "format": "none",
-          "gauge": {
-            "maxValue": 100,
-            "minValue": 0,
-            "show": false,
-            "thresholdLabels": false,
-            "thresholdMarkers": true
-          },
-          "hideTimeOverride": true,
-          "id": 19,
-          "interval": null,
-          "links": [],
-          "mappingType": 1,
-          "mappingTypes": [
-            {
-              "name": "value to text",
-              "value": 1
-            },
-            {
-              "name": "range to text",
-              "value": 2
-            }
-          ],
-          "maxDataPoints": 100,
-          "nullPointMode": "connected",
-          "nullText": null,
-          "postfix": "",
-          "postfixFontSize": "50%",
-          "prefix": "",
-          "prefixFontSize": "50%",
-          "rangeMaps": [
-            {
-              "from": "null",
-              "text": "N/A",
-              "to": "null"
-            }
-          ],
-          "span": 2,
-          "sparkline": {
-            "fillColor": "rgba(31, 118, 189, 0.18)",
-            "full": false,
-            "lineColor": "rgb(31, 120, 193)",
-            "show": false
-          },
-          "tableColumn": "",
-          "targets": [
-            {
-              "refId": "A",
-              "target": "stats.gauges.cromwell.workflow.Running"
-            }
-          ],
-          "thresholds": "",
-          "timeFrom": "5m",
-          "timeShift": null,
-          "title": "Workflows Running",
-          "type": "singlestat",
-          "valueFontSize": "80%",
-          "valueMaps": [
-            {
-              "op": "=",
-              "text": "N/A",
-              "value": "null"
-            }
-          ],
-          "valueName": "current"
-        },
-        {
-          "cacheTimeout": null,
-          "colorBackground": false,
-          "colorValue": false,
-          "colors": [
-            "rgba(50, 172, 45, 0.97)",
-            "rgba(237, 129, 40, 0.89)",
-            "rgba(245, 54, 54, 0.9)"
-          ],
-          "datasource": "${DS_LOCAL_GRAPHITE}",
-          "format": "none",
-          "gauge": {
-            "maxValue": 75000,
-            "minValue": 0,
-            "show": true,
-            "thresholdLabels": false,
-            "thresholdMarkers": false
-          },
-          "hideTimeOverride": true,
-          "id": 12,
-          "interval": null,
-          "links": [],
-          "mappingType": 1,
-          "mappingTypes": [
-            {
-              "name": "value to text",
-              "value": 1
-            },
-            {
-              "name": "range to text",
-              "value": 2
-            }
-          ],
-          "maxDataPoints": "100",
-          "nullPointMode": "connected",
-          "nullText": null,
-          "postfix": "",
-          "postfixFontSize": "50%",
-          "prefix": "",
-          "prefixFontSize": "50%",
-          "rangeMaps": [
-            {
-              "from": "null",
-              "text": "N/A",
-              "to": "null"
-            }
-          ],
-          "span": 2,
-          "sparkline": {
-            "fillColor": "rgba(31, 118, 189, 0.18)",
-            "full": false,
-            "lineColor": "rgb(31, 120, 193)",
-            "show": false
-          },
-          "tableColumn": "",
-          "targets": [
-            {
-              "refId": "A",
-              "target": "keepLastValue(stats.gauges.cromwell.job.Running, 1)"
-            }
-          ],
-          "thresholds": "50000,70000",
-          "timeFrom": "10m",
-          "timeShift": null,
-          "title": "Jobs Running",
-          "type": "singlestat",
-          "valueFontSize": "80%",
-          "valueMaps": [
-            {
-              "op": "=",
-              "text": "N/A",
-              "value": "null"
-            }
-          ],
-          "valueName": "max"
-        },
-        {
-          "cacheTimeout": null,
-          "colorBackground": false,
-          "colorValue": false,
-          "colors": [
-            "rgba(245, 54, 54, 0.9)",
-            "rgba(237, 129, 40, 0.89)",
-            "rgba(50, 172, 45, 0.97)"
-          ],
-          "datasource": "${DS_LOCAL_GRAPHITE}",
-          "editable": true,
-          "error": false,
-          "format": "none",
-          "gauge": {
-            "maxValue": 100,
-            "minValue": 0,
-            "show": false,
-            "thresholdLabels": false,
-            "thresholdMarkers": true
-          },
-          "hideTimeOverride": true,
-          "id": 16,
-          "interval": null,
-          "links": [],
-          "mappingType": 1,
-          "mappingTypes": [
-            {
-              "name": "value to text",
-              "value": 1
-            },
-            {
-              "name": "range to text",
-              "value": 2
-            }
-          ],
-          "maxDataPoints": 100,
-          "nullPointMode": "connected",
-          "nullText": null,
-          "postfix": "",
-          "postfixFontSize": "50%",
-          "prefix": "",
-          "prefixFontSize": "50%",
-          "rangeMaps": [
-            {
-              "from": "null",
-              "text": "N/A",
-              "to": "null"
-            }
-          ],
-          "span": 2,
-          "sparkline": {
-            "fillColor": "rgba(31, 118, 189, 0.18)",
-            "full": false,
-            "lineColor": "rgb(31, 120, 193)",
-            "show": false
-          },
-          "tableColumn": "",
-          "targets": [
-            {
-              "refId": "A",
-              "target": "stats.gauges.cromwell.job.QueuedInCromwell"
-            }
-          ],
-          "thresholds": "",
-          "timeFrom": "5m",
-          "timeShift": null,
-          "title": "Job Queued",
-          "type": "singlestat",
-          "valueFontSize": "80%",
-          "valueMaps": [
-            {
-              "op": "=",
-              "text": "N/A",
-              "value": "null"
-            }
-          ],
-          "valueName": "current"
-        }
-      ],
-      "repeat": null,
-      "repeatIteration": null,
-      "repeatRowId": null,
-      "showTitle": false,
-      "title": "Dashboard Row",
-      "titleSize": "h6"
-    },
-    {
-      "collapse": false,
-      "height": 255,
-      "panels": [
-        {
-          "aliasColors": {},
-          "bars": false,
-          "dashLength": 10,
-          "dashes": false,
-          "datasource": "${DS_LOCAL_GRAPHITE}",
-          "editable": true,
-          "error": false,
-          "fill": 1,
-          "id": 18,
-          "legend": {
-            "avg": false,
-            "current": false,
-            "max": false,
-            "min": false,
-            "show": true,
-            "total": false,
-            "values": false
-          },
-          "lines": true,
-          "linewidth": 1,
-          "links": [],
-          "nullPointMode": "connected",
-          "percentage": false,
-          "pointradius": 5,
-          "points": false,
-          "renderer": "flot",
-          "seriesOverrides": [],
-          "spaceLength": 10,
-          "span": 6,
-          "stack": false,
-          "steppedLine": false,
-          "targets": [
-            {
-              "refId": "A",
-              "target": "alias(scale(stats.gauges.cromwell.workflow.Succeeded.m1_rate, 60), 'Succeeded')"
-            },
-            {
-              "refId": "B",
-              "target": "alias(scale(stats.gauges.cromwell.workflow.Aborted.m1_rate, 60), 'Aborted')"
-            },
-            {
-              "refId": "C",
-              "target": "alias(scale(stats.gauges.cromwell.workflow.Failed.m1_rate, 60), 'Failed')"
-            },
-            {
-              "refId": "D",
-              "target": "alias(scale(stats.gauges.cromwell.workflow.Submitted.m1_rate, 60), 'Submitted')"
-            }
-          ],
-          "thresholds": [],
-          "timeFrom": null,
-          "timeShift": null,
-          "title": "Workflow Throughput",
-          "tooltip": {
-            "msResolution": false,
-            "shared": true,
-            "sort": 0,
-            "value_type": "individual"
-          },
-          "type": "graph",
-          "xaxis": {
-            "buckets": null,
-            "mode": "time",
-            "name": null,
-            "show": true,
-            "values": []
-          },
-          "yaxes": [
-            {
-              "format": "short",
-              "label": "per minute",
-              "logBase": 1,
-              "max": null,
-              "min": null,
-              "show": true
-            },
-            {
-              "format": "short",
-              "label": null,
-              "logBase": 1,
-              "max": null,
-              "min": null,
-              "show": true
-            }
-          ]
-        },
-        {
-          "aliasColors": {},
-          "bars": false,
-          "dashLength": 10,
-          "dashes": false,
-          "datasource": "${DS_LOCAL_GRAPHITE}",
-          "editable": true,
-          "error": false,
-          "fill": 1,
-          "id": 17,
-          "legend": {
-            "avg": false,
-            "current": false,
-            "max": false,
-            "min": false,
-            "show": true,
-            "total": false,
-            "values": false
-          },
-          "lines": true,
-          "linewidth": 1,
-          "links": [],
-          "nullPointMode": "connected",
-          "percentage": false,
-          "pointradius": 5,
-          "points": false,
-          "renderer": "flot",
-          "seriesOverrides": [],
-          "spaceLength": 10,
-          "span": 6,
-          "stack": false,
-          "steppedLine": false,
-          "targets": [
-            {
-              "refId": "A",
-              "target": "stats.gauges.cromwell.workflow.Queued"
-            },
-            {
-              "refId": "B",
-              "target": "stats.gauges.cromwell.workflow.Running"
-            }
-          ],
-          "thresholds": [],
-          "timeFrom": null,
-          "timeShift": null,
-          "title": "Workflows",
-          "tooltip": {
-            "msResolution": false,
-            "shared": true,
-            "sort": 0,
-            "value_type": "individual"
-          },
-          "type": "graph",
-          "xaxis": {
-            "buckets": null,
-            "mode": "time",
-            "name": null,
-            "show": true,
-            "values": []
-          },
-          "yaxes": [
-            {
-              "format": "short",
-              "label": null,
-              "logBase": 1,
-              "max": null,
-              "min": null,
-              "show": true
-            },
-            {
-              "format": "short",
-              "label": null,
-              "logBase": 1,
-              "max": null,
-              "min": null,
-              "show": true
-            }
-          ]
-        }
-      ],
-      "repeat": null,
-      "repeatIteration": null,
-      "repeatRowId": null,
-      "showTitle": false,
-      "title": "Dashboard Row",
-      "titleSize": "h6"
-    },
-    {
-      "collapse": false,
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-              "target": "stats.gauges.cromwell.io.gcs.batch.timing.mean"
-            }
-          ],
-          "thresholds": [],
-          "timeFrom": null,
-          "timeShift": null,
-          "title": "Batch request timing",
-          "tooltip": {
-            "shared": true,
-            "sort": 0,
-            "value_type": "individual"
-          },
-          "type": "graph",
-          "xaxis": {
-            "buckets": null,
-            "mode": "time",
-            "name": null,
-            "show": true,
-            "values": []
-          },
-          "yaxes": [
-            {
-              "format": "short",
-              "label": null,
-              "logBase": 1,
-              "max": null,
-              "min": null,
-              "show": true
-            },
-            {
-              "format": "short",
-              "label": null,
-              "logBase": 1,
-              "max": null,
-              "min": null,
-              "show": true
-            }
-          ]
-        }
-      ],
-      "repeat": null,
-      "repeatIteration": null,
-      "repeatRowId": null,
-      "showTitle": false,
-      "title": "Dashboard Row",
-      "titleSize": "h6"
-    }
-  ],
-  "schemaVersion": 14,
-  "style": "dark",
-  "tags": [],
-  "templating": {
-    "list": []
-  },
-  "time": {
-    "from": "now-15m",
-    "to": "now"
-  },
-  "timepicker": {
-    "refresh_intervals": [
-      "5s",
-      "10s",
-      "30s",
-      "1m",
-      "5m",
-      "15m",
-      "30m",
-      "1h",
-      "2h",
-      "1d"
-    ],
-    "time_options": [
-      "5m",
-      "15m",
-      "1h",
-      "6h",
-      "12h",
-      "24h",
-      "2d",
-      "7d",
-      "30d"
-    ]
-  },
-  "timezone": "browser",
-  "title": "Cromwell",
-  "version": 6
-}
\ No newline at end of file
diff --git a/scripts/perf/vm_scripts/cromwell/cromwell.conf b/scripts/perf/vm_scripts/cromwell/cromwell.conf
deleted file mode 100644
index 9fb29a28b16..00000000000
--- a/scripts/perf/vm_scripts/cromwell/cromwell.conf
+++ /dev/null
@@ -1,95 +0,0 @@
-include required(classpath("application.conf"))
-
-akka.http.server.request-timeout = 600 seconds
-
-google {
-
-  application-name = "cromwell"
-
-  auths = [
-    {
-      name = "application-default"
-      scheme = "application_default"
-    }
-    {
-      name = "user-service-account"
-      scheme = "user_service_account"
-    }
-  ]
-}
-
-engine {
-  filesystems {
-    gcs {
-      auth = "application-default"
-      project = ${?CROMWELL_PROJECT}
-    }
-  }
-}
-
-call-caching {
-  # Allows re-use of existing results for jobs you've already run
-  # (default: false)
-  enabled = true
-
-  # Whether to invalidate a cache result forever if we cannot reuse them. Disable this if you expect some cache copies
-  # to fail for external reasons which should not invalidate the cache (e.g. auth differences between users):
-  # (default: true)
-  invalidate-bad-cache-results = false
-}
-
-system {
-  cromwell_id = "perf-runner"
-  io.number-of-requests = 10240611
-}
-
-backend {
-  default = "Papi"
-  enabled = ["Papi"]
-  providers {
-    Papi {
-      actor-factory = "cromwell.backend.google.pipelines.v1alpha2.PipelinesApiLifecycleActorFactory"
-      config {
-        project = ${?CROMWELL_PROJECT}
-        root = ${?CROMWELL_EXECUTION_ROOT}
-        maximum-polling-interval = 600
-        concurrent-job-limit = 1000
-
-        genomics {
-          auth = "application-default"
-          endpoint-url = "https://genomics.googleapis.com/"
-        }
-
-        filesystems {
-          gcs {
-            auth = "application-default"
-            project = ${?CROMWELL_PROJECT}
-          }
-        }
-      }
-    }
-  }
-}
-
-services {
-  Instrumentation {
-    # Stackdriver - Send metrics to Google's monitoring API
-    class = "cromwell.services.instrumentation.impl.stackdriver.StackdriverInstrumentationServiceActor"
-    config {
-      auth = "application-default"
-      google-project = ${?CROMWELL_PROJECT}
-      # rate at which aggregated metrics will be sent to Stackdriver API, must be 1 minute or more.
-      flush-rate = 1 minute
-      cromwell-perf-test-case = ${?TEST_CASE_DIRECTORY}
-    }
-  }
-}
-
-database {
-  db.url = "jdbc:mysql://cloudsql-db/cromwell?useSSL=true&rewriteBatchedStatements=true"
-  db.user = ${?CLOUD_SQL_DB_USER}
-  db.password = ${?CLOUD_SQL_DB_PASSWORD}
-  db.driver = "com.mysql.cj.jdbc.Driver"
-  db.connectionTimeout=30000
-  profile = "slick.jdbc.MySQLProfile$"
-}
diff --git a/scripts/perf/vm_scripts/docker-compose.yml b/scripts/perf/vm_scripts/docker-compose.yml
deleted file mode 100644
index a6e05ced58c..00000000000
--- a/scripts/perf/vm_scripts/docker-compose.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-version: '2'
-networks:
-   mysql_net:
-     driver: bridge
-services:
-  cromwell:
-    image: "${CROMWELL_DOCKER_IMAGE}"
-    volumes:
-      - ${CROMWELL_CONF_DIR}:/conf
-    environment:
-      - CROMWELL_PROJECT
-      - CROMWELL_EXECUTION_ROOT
-      - CLOUD_SQL_DB_USER
-      - CLOUD_SQL_DB_PASSWORD
-      - TEST_CASE_DIRECTORY
-      - JAVA_OPTS=-Dconfig.file=/conf/cromwell.conf
-    command: ["server"]
-    depends_on:
-      - cloudsql-db
-    ports:
-      - "8000:8000"
-    networks:
-      mysql_net:
-    container_name: cromwell
-  cloudsql-db:
-    image: "gcr.io/cloudsql-docker/gce-proxy:1.11"
-    ports:
-      - "127.0.0.1:3306:3306"
-    container_name: cloudsql-db
-    command: ["/cloud_sql_proxy", "-instances=broad-dsde-cromwell-perf:us-central1:${CLOUD_SQL_INSTANCE}=tcp:0.0.0.0:3306"]
-    networks:
-      mysql_net:
diff --git a/scripts/perf/vm_scripts/statsd-proxy/proxy.conf b/scripts/perf/vm_scripts/statsd-proxy/proxy.conf
deleted file mode 100644
index 900347fa203..00000000000
--- a/scripts/perf/vm_scripts/statsd-proxy/proxy.conf
+++ /dev/null
@@ -1,11 +0,0 @@
-proxy {
-  host = ${?PROXY_HOST}
-  port = ${?PROXY_PORT}
-}
-
-statsd {
-  host = ${?CROMWELL_STATSD_HOST}
-  port = ${?CROMWELL_STATSD_PORT}
-}
-
-output-file = "file:///conf/statsd.log"

From c8e13a8f11a1f3a258bfef2ed05755ea2fd5057f Mon Sep 17 00:00:00 2001
From: rsaperst <156102201+rsaperst@users.noreply.github.com>
Date: Fri, 3 May 2024 09:39:06 -0400
Subject: [PATCH 314/326] [WX-1448] Add verbose logging and timeout for getm
 (#7416)

Co-authored-by: Adam Nichols <anichols@broadinstitute.org>
---
 .../drs/localizer/downloaders/BulkAccessUrlDownloader.scala     | 2 +-
 .../drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
index 00957083bc9..1fd5bc6bf60 100644
--- a/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
+++ b/cromwell-drs-localizer/src/main/scala/drs/localizer/downloaders/BulkAccessUrlDownloader.scala
@@ -75,7 +75,7 @@ case class BulkAccessUrlDownloader(resolvedUrls: List[ResolvedDrsUrl]) extends D
     Files.deleteIfExists(getmManifestPath)
 
   def generateGetmCommand(pathToMainfestJson: Path): String =
-    s"""getm --manifest ${pathToMainfestJson.toString}"""
+    s"""timeout 24h getm --manifest ${pathToMainfestJson.toString} -vv"""
   def runGetm: IO[GetmResult] =
     generateJsonManifest(resolvedUrls).flatMap { manifestPath =>
       val script = generateGetmCommand(manifestPath)
diff --git a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
index 4255b407b1a..6eae90aa842 100644
--- a/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
+++ b/cromwell-drs-localizer/src/test/scala/drs/localizer/downloaders/BulkAccessUrlDownloaderSpec.scala
@@ -80,7 +80,7 @@ class BulkAccessUrlDownloaderSpec extends AnyFlatSpec with CromwellTimeoutSpec w
   it should "properly construct the invocation command" in {
     val downloader = BulkAccessUrlDownloader(oneElement)
     val filepath: Path = downloader.generateJsonManifest(threeElements).unsafeRunSync()
-    val expected = s"""getm --manifest ${filepath.toString}"""
+    val expected = s"""timeout 24h getm --manifest ${filepath.toString} -vv"""
     downloader.generateGetmCommand(filepath) shouldBe expected
   }
 

From 8bdcbb015bad27233e739c0ce570438a9479956c Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 6 May 2024 13:05:17 -0400
Subject: [PATCH 315/326] WX-1566 Fix Morgan's call cache file hash CPU thrash
 Cromwell crash (#7419)

---
 .../cromwell/engine/io/nio/NioFlow.scala      | 56 +----------
 .../cromwell/engine/io/nio/NioHashing.scala   | 92 +++++++++++++++++++
 .../filesystems/blob/BlobPathBuilder.scala    |  4 +-
 3 files changed, 97 insertions(+), 55 deletions(-)
 create mode 100644 engine/src/main/scala/cromwell/engine/io/nio/NioHashing.scala

diff --git a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
index b1fe8b05462..5be9ad36d9c 100644
--- a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
+++ b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
@@ -4,8 +4,7 @@ import akka.actor.ActorSystem
 import akka.stream.scaladsl.Flow
 import cats.effect._
 
-import scala.util.Try
-import cloud.nio.spi.{ChecksumFailure, ChecksumResult, ChecksumSkipped, ChecksumSuccess, FileHash, HashType}
+import cloud.nio.spi.{ChecksumFailure, ChecksumResult, ChecksumSkipped, ChecksumSuccess, FileHash}
 import com.typesafe.config.Config
 import common.util.IORetry
 import cromwell.core.io._
@@ -15,10 +14,7 @@ import cromwell.engine.io.RetryableRequestSupport.{isInfinitelyRetryable, isRetr
 import cromwell.engine.io.{IoAttempts, IoCommandContext, IoCommandStalenessBackpressuring}
 import cromwell.filesystems.blob.BlobPath
 import cromwell.filesystems.drs.DrsPath
-import cromwell.filesystems.gcs.GcsPath
 import cromwell.filesystems.http.HttpPath
-import cromwell.filesystems.s3.S3Path
-import cromwell.util.TryWithResource._
 import net.ceedubs.ficus.Ficus._
 import net.ceedubs.ficus.readers.ValueReader
 
@@ -134,7 +130,7 @@ class NioFlow(parallelism: Int,
 
     def readFileAndChecksum: IO[String] =
       for {
-        fileHash <- getStoredHash(command.file)
+        fileHash <- NioHashing.getStoredHash(command.file)
         uncheckedValue <- readFile
         checksumResult <- fileHash match {
           case Some(hash) => checkHash(uncheckedValue, hash)
@@ -177,31 +173,7 @@ class NioFlow(parallelism: Int,
     }
 
   private def hash(hash: IoHashCommand): IO[String] =
-    // If there is no hash accessible from the file storage system,
-    // we'll read the file and generate the hash ourselves.
-    getStoredHash(hash.file)
-      .flatMap {
-        case Some(storedHash) => IO.pure(storedHash)
-        case None => generateMd5FileHashForPath(hash.file)
-      }
-      .map(_.hash)
-
-  private def getStoredHash(file: Path): IO[Option[FileHash]] =
-    file match {
-      case gcsPath: GcsPath => getFileHashForGcsPath(gcsPath).map(Option(_))
-      case blobPath: BlobPath => getFileHashForBlobPath(blobPath)
-      case drsPath: DrsPath =>
-        IO {
-          // We assume all DRS files have a stored hash; this will throw
-          // if the file does not.
-          drsPath.getFileHash
-        }.map(Option(_))
-      case s3Path: S3Path =>
-        IO {
-          Option(FileHash(HashType.S3Etag, s3Path.eTag))
-        }
-      case _ => IO.pure(None)
-    }
+    NioHashing.hash(hash.file)
 
   private def touch(touch: IoTouchCommand) = IO {
     touch.file.touch()
@@ -222,28 +194,6 @@ class NioFlow(parallelism: Int,
   }
 
   private def createDirectories(path: Path) = path.parent.createDirectories()
-
-  /**
-    * Lazy evaluation of a Try in a delayed IO. This avoids accidentally eagerly evaluating the Try.
-    *
-    * IMPORTANT: Use this instead of IO.fromTry to make sure the Try will be reevaluated if the
-    * IoCommand is retried.
-    */
-  private def delayedIoFromTry[A](t: => Try[A]): IO[A] = IO[A](t.get)
-
-  private def getFileHashForGcsPath(gcsPath: GcsPath): IO[FileHash] = delayedIoFromTry {
-    gcsPath.objectBlobId.map(id => FileHash(HashType.GcsCrc32c, gcsPath.cloudStorage.get(id).getCrc32c))
-  }
-
-  private def getFileHashForBlobPath(blobPath: BlobPath): IO[Option[FileHash]] = delayedIoFromTry {
-    blobPath.md5HexString.map(md5 => md5.map(FileHash(HashType.Md5, _)))
-  }
-
-  private def generateMd5FileHashForPath(path: Path): IO[FileHash] = delayedIoFromTry {
-    tryWithResource(() => path.newInputStream) { inputStream =>
-      FileHash(HashType.Md5, org.apache.commons.codec.digest.DigestUtils.md5Hex(inputStream))
-    }
-  }
 }
 
 object NioFlow {
diff --git a/engine/src/main/scala/cromwell/engine/io/nio/NioHashing.scala b/engine/src/main/scala/cromwell/engine/io/nio/NioHashing.scala
new file mode 100644
index 00000000000..7f371311006
--- /dev/null
+++ b/engine/src/main/scala/cromwell/engine/io/nio/NioHashing.scala
@@ -0,0 +1,92 @@
+package cromwell.engine.io.nio
+
+import cats.effect.IO
+import cloud.nio.spi.{FileHash, HashType}
+import common.util.StringUtil.EnhancedString
+import cromwell.core.path.Path
+import cromwell.filesystems.blob.BlobPath
+import cromwell.filesystems.drs.DrsPath
+import cromwell.filesystems.gcs.GcsPath
+import cromwell.filesystems.http.HttpPath
+import cromwell.filesystems.s3.S3Path
+import cromwell.util.TryWithResource.tryWithResource
+
+import scala.util.Try
+
+object NioHashing {
+
+  def hash(file: Path): IO[String] =
+    // If there is no hash accessible from the file storage system,
+    // we'll read the file and generate the hash ourselves if we can.
+    getStoredHash(file)
+      .flatMap {
+        case Some(storedHash) => IO.pure(storedHash)
+        case None =>
+          if (canHashLocally(file))
+            generateMd5FileHashForPath(file)
+          else
+            IO.raiseError(
+              new Exception(
+                s"File of type ${file.getClass.getSimpleName} requires an associated hash, not present for ${file.pathAsString.maskSensitiveUri}"
+              )
+            )
+      }
+      .map(_.hash)
+
+  def getStoredHash(file: Path): IO[Option[FileHash]] =
+    file match {
+      case gcsPath: GcsPath => getFileHashForGcsPath(gcsPath).map(Option(_))
+      case blobPath: BlobPath => getFileHashForBlobPath(blobPath)
+      case drsPath: DrsPath =>
+        IO {
+          // We assume all DRS files have a stored hash; this will throw
+          // if the file does not.
+          drsPath.getFileHash
+        }.map(Option(_))
+      case s3Path: S3Path =>
+        IO {
+          Option(FileHash(HashType.S3Etag, s3Path.eTag))
+        }
+      case _ => IO.pure(None)
+    }
+
+  /**
+    * In some scenarios like SFS it is appropriate for Cromwell to hash files using its own CPU power.
+    *
+    * In cloud scenarios, we don't want this because the files are huge, downloading them is slow & expensive,
+    * and the extreme CPU usage destabilizes the instance (WX-1566). For more context, see also comments
+    * on `cromwell.filesystems.blob.BlobPath#largeBlobFileMetadataKey()`.
+    *
+    * Cromwell is fundamentally supposed to be a job scheduler, and heavy computation should take place elsewhere.
+    *
+    * @param file The path to consider for local hashing
+    */
+  private def canHashLocally(file: Path) =
+    file match {
+      case _: HttpPath => false
+      case _: BlobPath => false
+      case _ => true
+    }
+
+  private def generateMd5FileHashForPath(path: Path): IO[FileHash] = delayedIoFromTry {
+    tryWithResource(() => path.newInputStream) { inputStream =>
+      FileHash(HashType.Md5, org.apache.commons.codec.digest.DigestUtils.md5Hex(inputStream))
+    }
+  }
+
+  private def getFileHashForGcsPath(gcsPath: GcsPath): IO[FileHash] = delayedIoFromTry {
+    gcsPath.objectBlobId.map(id => FileHash(HashType.GcsCrc32c, gcsPath.cloudStorage.get(id).getCrc32c))
+  }
+
+  private def getFileHashForBlobPath(blobPath: BlobPath): IO[Option[FileHash]] = delayedIoFromTry {
+    blobPath.md5HexString.map(md5 => md5.map(FileHash(HashType.Md5, _)))
+  }
+
+  /**
+    * Lazy evaluation of a Try in a delayed IO. This avoids accidentally eagerly evaluating the Try.
+    *
+    * IMPORTANT: Use this instead of IO.fromTry to make sure the Try will be reevaluated if the
+    * IoCommand is retried.
+    */
+  private def delayedIoFromTry[A](t: => Try[A]): IO[A] = IO[A](t.get)
+}
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
index c0503975b31..3c984d1f2c8 100644
--- a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
+++ b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -110,12 +110,12 @@ object BlobPath {
   // They do this for all files they touch, regardless of size, and the root/metadata property is authoritative over native.
   //
   // N.B. most if not virtually all large files in the wild will NOT have this key populated because they were not created
-  // by TES or its associated upload utility [4].
+  // by TES or its associated upload utility [3].
   //
   // [0] https://learn.microsoft.com/en-us/azure/storage/blobs/scalability-targets
   // [1] https://learn.microsoft.com/en-us/rest/api/storageservices/version-2019-12-12
   // [2] https://github.com/microsoft/ga4gh-tes/blob/03feb746bb961b72fa91266a56db845e3b31be27/src/Tes.Runner/Transfer/BlobBlockApiHttpUtils.cs#L25
-  // [4] https://github.com/microsoft/ga4gh-tes/blob/main/src/Tes.RunnerCLI/scripts/roothash.sh
+  // [3] https://github.com/microsoft/ga4gh-tes/blob/main/src/Tes.RunnerCLI/scripts/roothash.sh
   private val largeBlobFileMetadataKey = "md5_4mib_hashlist_root_hash"
 
   def cleanedNioPathString(nioString: String): String = {

From 32f667c6dcc9bcc4b3cd962ac985b23a89b8306e Mon Sep 17 00:00:00 2001
From: Adam Nichols <anichols@broadinstitute.org>
Date: Mon, 6 May 2024 15:33:31 -0400
Subject: [PATCH 316/326] WX-1566 Fix RTD so this ticket's docs get published
 (#7420)

---
 .readthedocs.yaml     | 14 ++++++++++++++
 docs/set_copyright.py |  3 +++
 mkdocs.yml            |  4 ++--
 3 files changed, 19 insertions(+), 2 deletions(-)
 create mode 100644 .readthedocs.yaml
 create mode 100644 docs/set_copyright.py

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 00000000000..376dcc3a901
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,14 @@
+# Read the Docs configuration file for MkDocs projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+mkdocs:
+  configuration: mkdocs.yml
diff --git a/docs/set_copyright.py b/docs/set_copyright.py
new file mode 100644
index 00000000000..cb0cb6f0718
--- /dev/null
+++ b/docs/set_copyright.py
@@ -0,0 +1,3 @@
+from datetime import datetime
+def on_config(config, **kwargs):
+    config.copyright = f"Copyright © {datetime.now().year} <a href=\"https://broadinstitute.org\">Broad Institute</a>"
diff --git a/mkdocs.yml b/mkdocs.yml
index 4ea08cf6fa8..87d48d3171e 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -110,5 +110,5 @@ extra_css:
 extra_javascript:
     - js/extra.js
 
-copyright: Copyright &copy; 2023 <a href="https://broadinstitute.org">Broad Institute</a>
-# google_analytics: ['identifierID', 'URL.org']
+hooks:
+    - docs/set_copyright.py

From 513af0b353a21ae91ae43ce3d9142c4eadf7136b Mon Sep 17 00:00:00 2001
From: xquek <46759870+xquek@users.noreply.github.com>
Date: Wed, 31 Jul 2024 13:55:54 -0700
Subject: [PATCH 317/326] fix womFileType coercion (#47)

Co-authored-by: quekx <quekx@gene.com>
---
 .../cromwell/backend/standard/StandardAsyncExecutionActor.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 8acef722f71..8ed62d6b2e7 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -171,7 +171,7 @@ trait StandardAsyncExecutionActor
           // decode url encoded values generated by the mapper
           val decoded_womValue = URLDecoder.decode(mapped_wom.valueString,"UTF-8")
           // convert to womfile again
-          WomFile(WomSingleFileType, decoded_womValue)
+          WomFile(womFile.womFileType, decoded_womValue)
         }
     )
   }

From b8c215a24e1cfa658f066075eaf34f9ef6058d1f Mon Sep 17 00:00:00 2001
From: Nathan Thorpe <nathan@techstormpc.com>
Date: Wed, 31 Jul 2024 13:57:25 -0700
Subject: [PATCH 318/326] AWS Batch - add support for custom log group name and
 additional tags (#48)

* implement setting of log group and additional tags

* update tests

* fixes
---
 ...wsBatchAsyncBackendJobExecutionActor.scala | 96 ++++++++++---------
 .../backend/impl/aws/AwsBatchJob.scala        | 89 ++++++++---------
 .../impl/aws/AwsBatchJobDefinition.scala      | 19 +++-
 .../impl/aws/AwsBatchRuntimeAttributes.scala  | 40 ++++++--
 .../backend/impl/aws/AwsBatchJobSpec.scala    |  5 +-
 .../aws/AwsBatchRuntimeAttributesSpec.scala   | 12 ++-
 .../backend/impl/aws/AwsBatchTestConfig.scala |  7 +-
 7 files changed, 162 insertions(+), 106 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 150d61bef79..5582266d1fd 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -47,7 +47,7 @@ import common.util.StringUtil._
 import common.validation.Validation._
 
 import cromwell.backend._
-import cromwell.backend.async._ 
+import cromwell.backend.async._
 import cromwell.backend.impl.aws.IntervalLimitedAwsJobSubmitActor.SubmitAwsJobRequest
 import cromwell.backend.impl.aws.OccasionalStatusPollingActor.{NotifyOfStatus, WhatsMyStatus}
 import cromwell.backend.impl.aws.RunStatus.{Initializing, TerminalRunStatus}
@@ -178,9 +178,9 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
    * commandScriptContents here
    */
 
-   /* part of the full commandScriptContents is overriden here, in the context of mixed S3/EFS support with globbing. 
+   /* part of the full commandScriptContents is overriden here, in the context of mixed S3/EFS support with globbing.
       we'll see how much we need...
-    */ 
+    */
 
   lazy val cmdScript = configuration.fileSystem match {
      case AWSBatchStorageSystems.s3 => commandScriptContents.toEither.toOption.get
@@ -203,7 +203,9 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       configuration.efsMntPoint,
       Option(runtimeAttributes.efsMakeMD5),
       Option(runtimeAttributes.efsDelocalize),
-      Option(runtimeAttributes.tagResources))
+      Option(runtimeAttributes.tagResources),
+      runtimeAttributes.logGroupName,
+      runtimeAttributes.additionalTags)
   }
 
   // setup batch client to query job container info
@@ -247,7 +249,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         }
         Seq(AwsBatchFileInput(s"$namePrefix-$index", remotePath.valueString, DefaultPathBuilder.get(localPathString), workingDisk))
     }
-    
+
   }
 
   /**
@@ -262,13 +264,13 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         // for s3 paths :
         case Success(path: S3Path) =>
           configuration.fileSystem match  {
-            case AWSBatchStorageSystems.s3 => 
+            case AWSBatchStorageSystems.s3 =>
                 URLDecoder.decode(path.pathWithoutScheme,"UTF-8")
-            case _ =>  
+            case _ =>
                 URLDecoder.decode(path.toString,"UTF-8")
           }
         // non-s3 paths
-        case _ => 
+        case _ =>
             URLDecoder.decode(value,"UTF-8")
       }
     )
@@ -301,7 +303,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
           case womFile: WomFile => womFile
         }
     }
-    
+
     val callInputInputs = callInputFiles flatMap {
       case (name, files) => inputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor, true)
     }
@@ -330,7 +332,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         case _ => AwsBatchWorkingDisk.MountPoint.resolve(path)
       }
     }
-    
+
     val absolutePath = DefaultPathBuilder.get(path) match {
       case p if !p.isAbsolute => getAbsolutePath(p)
       case p => p
@@ -369,7 +371,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     }
 
     val additionalGlobOutput = jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateAwsBatchGlobFileOutputs).toSet
-    
+
     outputs.toSet ++ additionalGlobOutput
   }
 
@@ -404,7 +406,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   // used by generateAwsBatchOutputs, could potentially move this def within that function
   private def generateAwsBatchSingleFileOutputs(womFile: WomSingleFile): List[AwsBatchFileOutput] = {
     // rewrite this to create more flexibility
-    // 
+    //
     val destination = configuration.fileSystem match {
       case  AWSBatchStorageSystems.s3 =>  callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
       case _ => DefaultPathBuilder.get(womFile.valueString) match {
@@ -414,8 +416,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
     }
     val (relpath, disk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
-    
-    val output = if (configuration.efsMntPoint.isDefined && 
+
+    val output = if (configuration.efsMntPoint.isDefined &&
                      configuration.efsMntPoint.getOrElse("").equals(disk.toString.split(" ")(1)) &&
                      ! runtimeAttributes.efsDelocalize) {
             // name: String, s3key: String, local: Path, mount: AwsBatchVolume
@@ -426,7 +428,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         }
     List(output)
   }
-  
+
   // get a unique glob name locations & paths.
   //  1. globName :md5 hash of local PATH and WF_ID
   //  2. globbedDir : local path of the directory being globbed.
@@ -445,8 +447,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     // locate the disk where the globbed data resides
     val (_, globDirectoryDisk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
 
-    
-    val (globDirectoryDestinationPath, globListFileDestinationPath) = if (configuration.efsMntPoint.isDefined && 
+
+    val (globDirectoryDestinationPath, globListFileDestinationPath) = if (configuration.efsMntPoint.isDefined &&
                      configuration.efsMntPoint.getOrElse("").equals(globDirectoryDisk.toString.split(" ")(1)) &&
                      ! runtimeAttributes.efsDelocalize) {
                         (globDirectory, globListFile)
@@ -462,11 +464,11 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         globDirectoryDestinationPath.toString,
         globListFileDestinationPath.toString
     )
-    
+
   }
   // used by generateAwsBatchOutputs, could potentially move this def within that function
   private def generateAwsBatchGlobFileOutputs(womFile: WomGlobFile): List[AwsBatchFileOutput] = {
-    
+
     val (globName, globbedDir, globDirectoryDisk, globDirectoryDestinationPath, globListFileDestinationPath) = generateGlobPaths(womFile)
     val (relpathDir,_) = relativePathAndVolume(DefaultPathBuilder.get(globbedDir + "/." + globName + "/" + "*").toString,runtimeAttributes.disks)
     val (relpathList,_) = relativePathAndVolume(DefaultPathBuilder.get(globbedDir + "/." + globName + ".list").toString,runtimeAttributes.disks)
@@ -590,7 +592,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
   override def handleExecutionResult(status: StandardAsyncRunState,
                             oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
-    
+
 
     // get path to sderr
     val stderr = jobPaths.standardPaths.error
@@ -614,8 +616,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
             case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
               val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
               retryElseFail(executionHandle)
-            // job was aborted (cancelled by user?) 
-            // on AWS OOM kill are code 137 : check retryWithMoreMemory here 
+            // job was aborted (cancelled by user?)
+            // on AWS OOM kill are code 137 : check retryWithMoreMemory here
             case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) && !retryWithMoreMemory =>
               jobLogger.debug(s"Job was aborted, code was : '${returnCodeAsString.stripLineEnd}'")
               Future.successful(AbortedExecutionHandle)
@@ -660,14 +662,14 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
           retryElseFail(failureStatus)
         }
     }
-  
-    
+
+
   }
-    
- 
+
+
    // get the exit code of the job.
    def JobExitCode: Future[String] = {
-     
+
      // read if the file exists
      def readRCFile(fileExists: Boolean): Future[String] = {
        if (fileExists)
@@ -684,20 +686,20 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
        jobRC <- readRCFile(fileExists)
      } yield jobRC
    }
-    
-   // new OOM detection 
+
+   // new OOM detection
    def memoryRetryRC(job: StandardAsyncJob): Future[Boolean] = Future {
       // STATUS LOGIC:
       //   - success : container exit code is zero
       //   - command failure: container exit code > 0, no statusReason in container
       //   - OOM kill : container exit code > 0, statusReason contains "OutOfMemory" OR exit code == 137
-      //   - spot kill : no container exit code set. statusReason of ATTEMPT (not container) says "host EC2 (...) terminated"     
+      //   - spot kill : no container exit code set. statusReason of ATTEMPT (not container) says "host EC2 (...) terminated"
       Log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
       val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(job.jobId).build)
       val jobDetail = describeJobsResponse.jobs.get(0) //OrElse(throw new RuntimeException(s"Could not get job details for job '${job.jobId}'"))
       val nrAttempts = jobDetail.attempts.size
-      // if job is terminated/cancelled before starting, there are no attempts. 
-      val lastattempt = 
+      // if job is terminated/cancelled before starting, there are no attempts.
+      val lastattempt =
           try {
               jobDetail.attempts.get(nrAttempts-1)
           } catch {
@@ -706,8 +708,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       if (lastattempt == null ) {
         Log.info(s"No attempts were made for job '${job.jobId}'. no memory-related retry needed.")
         false
-      }     
-      var containerRC = 
+      }
+      var containerRC =
           try {
               lastattempt.container.exitCode
           } catch {
@@ -720,13 +722,13 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       }
       // if not zero => get reason, else set retry to false.
       containerRC.toString() match {
-        case "0" => 
+        case "0" =>
             Log.debug("container exit code was zero. job succeeded")
             false
-        case "137" => 
+        case "137" =>
             Log.info("Job failed with Container status reason : 'OutOfMemory' (code:137)")
             true
-        case _ => 
+        case _ =>
             // failed job due to command errors (~ user errors) don't have a container exit reason.
             val containerStatusReason:String = {
                var lastReason =  lastattempt.container.reason
@@ -745,11 +747,11 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
             Log.debug(s"Retry job based on provided keys : '${retry}'")
             retry
       }
-        
-        
+
+
    }
 
-  
+
 
 
   // Despite being a "runtime" exception, BatchExceptions for 429 (too many requests) are *not* fatal:
@@ -824,7 +826,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       }
     )
   }
-    
+
   override def handleExecutionSuccess(runStatus: StandardAsyncRunState,
                              handle: StandardAsyncPendingExecutionHandle,
                              returnCode: Int)(implicit ec: ExecutionContext): Future[ExecutionHandle] = {
@@ -833,7 +835,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         // Need to make sure the paths are up to date before sending the detritus back in the response
         updateJobPaths()
         // If instance is terminated while copying stdout/stderr : status is failed while jobs outputs are ok
-        //   => Retryable 
+        //   => Retryable
         if (runStatus.toString().equals("Failed")) {
             jobLogger.warn("Got Failed RunStatus for success Execution")
 
@@ -868,8 +870,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     * @return The shell scripting.
     */
   override def globScript(globFile: WomGlobFile): String = {
-    
-    val (globName, globbedDir, _, _, _) = generateGlobPaths(globFile) 
+
+    val (globName, globbedDir, _, _, _) = generateGlobPaths(globFile)
     val controlFileName = "cromwell_glob_control_file"
     val absoluteGlobValue = commandDirectory.resolve(globFile.value).pathAsString
     val globDirectory = globbedDir + "/." + globName + "/"
@@ -882,7 +884,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     }).toString
       .replaceAll("GLOB_PATTERN", absoluteGlobValue)
       .replaceAll("GLOB_DIRECTORY", globDirectory)
-    // if on EFS : remove the globbing dir first, to remove leftover links from previous globs. 
+    // if on EFS : remove the globbing dir first, to remove leftover links from previous globs.
     val mkDirCmd : String = if (configuration.efsMntPoint.isDefined && globDirectory.startsWith(configuration.efsMntPoint.getOrElse(""))) {
         jobLogger.warn("Globbing on EFS has risks.")
         jobLogger.warn(s"The globbing target (${globbedDir}/.${globName}/) will be overwritten when existing!")
@@ -891,13 +893,13 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     } else {
         "mkdir"
     }
- 
+
     val controlFileContent =
       """This file is used by Cromwell to allow for globs that would not match any file.
         |By its presence it works around the limitation of some backends that do not allow empty globs.
         |Regardless of the outcome of the glob, this file will not be part of the final list of globbed files.
       """.stripMargin
-    
+
     s"""|# make the directory which will keep the matching files
         |$mkDirCmd $globDirectory
         |
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 4cfa08e82a5..c846be6ae36 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -88,7 +88,9 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                              efsMntPoint: Option[String],
                              efsMakeMD5: Option[Boolean],
                              efsDelocalize: Option[Boolean],
-                             tagResources: Option[Boolean]
+                             tagResources: Option[Boolean],
+                             logGroupName: String,
+                             additionalTags: Map[String, String]
                             ) {
 
 
@@ -136,38 +138,38 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
            |sed -i 's#${AwsBatchWorkingDisk.MountPoint.pathAsString}#$workDir#g' "$workDir/${input.local}"
            |""".stripMargin
 
-      case input: AwsBatchFileInput if input.s3key.startsWith("s3://") => 
+      case input: AwsBatchFileInput if input.s3key.startsWith("s3://") =>
         // regular s3 objects : download to working dir.
         s"""_s3_localize_with_retry "${input.s3key}" "${input.mount.mountPoint.pathAsString}/${input.local}" """.stripMargin
           .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
 
-      case input: AwsBatchFileInput if efsMntPoint.isDefined && input.s3key.startsWith(efsMntPoint.get) =>  
+      case input: AwsBatchFileInput if efsMntPoint.isDefined && input.s3key.startsWith(efsMntPoint.get) =>
         // EFS located file : test for presence on provided path.
         Log.debug("EFS input file detected: "+ input.s3key + " / "+ input.local.pathAsString)
         s"""test -e "${input.s3key}" || (echo 'input file: ${input.s3key} does not exist' && LOCALIZATION_FAILED=1)""".stripMargin
-      
-      case input: AwsBatchFileInput => 
-        // an entry in 'disks' => keep mount as it is.. 
+
+      case input: AwsBatchFileInput =>
+        // an entry in 'disks' => keep mount as it is..
         //here we don't need a copy command but the centaurTests expect us to verify the existence of the file
         //val filePath = s"${input.mount.mountPoint.pathAsString}/${input.local.pathAsString}"
         //  .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
         val filePath = input.local.pathAsString
         Log.debug("input entry in disks detected "+ input.s3key + " / "+ input.local.pathAsString)
         s"""test -e "$filePath" || (echo 'input file: $filePath does not exist' && LOCALIZATION_FAILED=1)""".stripMargin
-      
+
       case _ => ""
     }.toList.mkString("\n")
 
     // get multipart threshold from config.
-    val mp_threshold : Long = if (conf.hasPath("engine.filesystems.s3.MultipartThreshold") ) conf.getMemorySize("engine.filesystems.s3.MultipartThreshold").toBytes() else 5L * 1024L * 1024L * 1024L; 
+    val mp_threshold : Long = if (conf.hasPath("engine.filesystems.s3.MultipartThreshold") ) conf.getMemorySize("engine.filesystems.s3.MultipartThreshold").toBytes() else 5L * 1024L * 1024L * 1024L;
     Log.debug(s"MultiPart Threshold for delocalizing is $mp_threshold")
 
     // prepare tags, strip invalid characters
     val invalidCharsPattern = "[^a-zA-Z0-9_.:/=+-@]+".r
     Log.debug(s"root workflow id: ${jobDescriptor.workflowDescriptor.rootWorkflowId.toString}")
     Log.debug(s"root workflow name: ${jobDescriptor.workflowDescriptor.rootWorkflow.name.toString}")
-    
-    
+
+
     val workflowId = invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflowId.toString,"_")
     val workflowName = invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflow.name.toString,"_")
     val taskId = invalidCharsPattern.replaceAllIn(jobDescriptor.key.call.fullyQualifiedName + "-" + jobDescriptor.key.index + "-" + jobDescriptor.key.attempt,"_")
@@ -202,7 +204,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |    $awsCmd s3 cp --no-progress "$$s3_path" "$$destination"  ||
          |        { echo "attempt $$i to copy $$s3_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # check data integrity
-         |    _check_data_integrity "$$destination" "$$s3_path" || 
+         |    _check_data_integrity "$$destination" "$$s3_path" ||
          |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    # copy succeeded
          |    break
@@ -239,7 +241,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |        break
          |    fi
          |    # if destination is not a bucket : abort
-         |    if ! [[ "$$destination" =~ s3://([^/]+)/(.+) ]]; then 
+         |    if ! [[ "$$destination" =~ s3://([^/]+)/(.+) ]]; then
          |     echo "$$destination is not an S3 path with a bucket and key."
          |      DELOCALIZATION_FAILED=1
          |      break
@@ -249,21 +251,21 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |       # make sure to strip the trailing / in destination
          |       destination=$${destination%/}
          |       # glob directory. do recursive copy
-         |       $awsCmd s3 cp --no-progress "$$local_path" "$$destination" --recursive --exclude "cromwell_glob_control_file" || 
-         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
+         |       $awsCmd s3 cp --no-progress "$$local_path" "$$destination" --recursive --exclude "cromwell_glob_control_file" ||
+         |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |       # check integrity for each of the files (allow spaces)
          |       SAVEIFS="$$IFS"
          |       IFS=$$'\n'
          |       for FILE in $$(cd "$$local_path" ; ls | grep -v cromwell_glob_control_file); do
-         |           _check_data_integrity "$$local_path/$$FILE" "$$destination/$$FILE" || 
+         |           _check_data_integrity "$$local_path/$$FILE" "$$destination/$$FILE" ||
          |               { echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2; }
          |       done
          |       IFS="$$SAVEIFS"
-         |    else 
-         |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" || 
-         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; } 
+         |    else
+         |      $awsCmd s3 cp --no-progress "$$local_path" "$$destination" ||
+         |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |      # check content length for data integrity
-         |      _check_data_integrity "$$local_path" "$$destination" || 
+         |      _check_data_integrity "$$local_path" "$$destination" ||
          |         { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    fi
          |    # copy succeeded
@@ -274,7 +276,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |function _get_multipart_chunk_size() {
          |  local file_path="$$1"
          |  # file size
-         |  file_size=$$(stat --printf="%s" "$$file_path") 
+         |  file_size=$$(stat --printf="%s" "$$file_path")
          |  # chunk_size : you can have at most 10K parts with at least one 5MB part
          |  # this reflects the formula in s3-copy commands of cromwell (S3FileSystemProvider.java)
          |  #   => long partSize = Math.max((objectSize / 10000L) + 1, 5 * 1024 * 1024);
@@ -287,9 +289,9 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |function _check_data_integrity() {
          |  local local_path="$$1"
          |  local s3_path="$$2"
-         |  
+         |
          |  # remote : use content_length
-         |  if [[ "$$s3_path" =~ s3://([^/]+)/(.+) ]]; then 
+         |  if [[ "$$s3_path" =~ s3://([^/]+)/(.+) ]]; then
          |        bucket="$${BASH_REMATCH[1]}"
          |        key="$${BASH_REMATCH[2]}"
          |  else
@@ -319,8 +321,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |  INSTANCE_ID=$$(cat /var/lib/cloud/data/instance-id)
          |  VOLUME_IDS=$$($awsCmd ec2 describe-volumes --filters Name=attachment.instance-id,Values=$$INSTANCE_ID --query 'Volumes[].VolumeId' --output text)
          |  echo " - Tagging instance $$INSTANCE_ID"
-         |  # add tags. if tag key exists, append tag if value not in comma seperated list yet. 
-         |  # info : tags wfid, taskID cannot have spaces by design. wfName does not allow spaces in WDL spec. 
+         |  # add tags. if tag key exists, append tag if value not in comma seperated list yet.
+         |  # info : tags wfid, taskID cannot have spaces by design. wfName does not allow spaces in WDL spec.
          |  WFIDS=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$INSTANCE_ID" "Name=key,Values=cromwell-root-workflow-id" --query 'Tags[].Value' --output text) $$WFID)
          |  TASKIDS=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$INSTANCE_ID" "Name=key,Values=cromwell-task-id" --query 'Tags[].Value' --output text) $$TASKID)
          |  WFNAMES=$$(_combine_tags $$($awsCmd ec2 describe-tags --filters "Name=resource-id,Values=$$INSTANCE_ID" "Name=key,Values=cromwell-root-workflow-name" --query 'Tags[].Value' --output text) $$WFNAME)
@@ -356,7 +358,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |if [[ "${doTagging}" == "true" ]]; then
          |  echo "*** TAGGING RESOURCES ***"
          |  _add_tags
-         |fi 
+         |fi
          |
          |echo '*** LOCALIZING INPUTS ***'
          |if [ ! -d $workDir ]; then mkdir $workDir && chmod 777 $workDir; fi
@@ -367,13 +369,13 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |if [[ $$LOCALIZATION_FAILED -eq 1 ]]; then
          |  echo '*** LOCALIZATION FAILED ***'
          |  exit 1
-         |else 
+         |else
          |  echo '*** COMPLETED LOCALIZATION ***'
          |fi
          |set +e
          |}
          |""".stripMargin
-    
+
     // the paths of the stdOut and stdErr
     val stdOut = dockerStdout.replace("/cromwell_root", workDir)
     val stdErr = dockerStderr.replace("/cromwell_root", workDir)
@@ -385,7 +387,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
       case output: AwsBatchFileOutput if output.s3key.endsWith(".list") && output.s3key.contains("glob-") =>
         Log.debug("Globbing  : check for EFS settings.")
         val s3GlobOutDirectory = output.s3key.replace(".list", "")
-        // glob paths are not generated with 127 char limit, using generateGlobPaths(). name can be used safely 
+        // glob paths are not generated with 127 char limit, using generateGlobPaths(). name can be used safely
         val globDirectory = output.name.replace(".list", "")
         /*
          * Need to process this list and de-localize each file if the list file actually exists
@@ -403,7 +405,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                         |if [ -e $globDirectory ]; then _s3_delocalize_with_retry "$globDirectory" "$s3GlobOutDirectory" ; fi
                         |""".stripMargin
                 } else {
-                    
+
                     // check file for existence
                     s"""
                         |# test the glob list
@@ -417,22 +419,22 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
                         |IFS="$$SAVEIFS"
                         |"""
                 }
-           // need to make md5sum? 
+           // need to make md5sum?
            val md5_cmd = if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
                     Log.debug("Add cmd to create MD5 sibling.")
-                    // this does NOT regenerate the md5 in case the file is overwritten ! 
+                    // this does NOT regenerate the md5 in case the file is overwritten !
                     s"""
-                        |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
+                        |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then
                         |   # the glob list
-                        |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && DELOCALIZATION_FAILED=1 ); 
+                        |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && DELOCALIZATION_FAILED=1 );
                         |   # globbed files, using specified number of cpus for parallel processing.
                         SAVEIFS="$$IFS"
                         |IFS=$$'\n'
                         |   cat "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" | xargs -I% -P${runtimeAttributes.cpu.##.toString} bash -c "md5sum ${globDirectory}/% > ${globDirectory}/%.md5"
                         |fi
                         |IFS="$$SAVEIFS"
-                        |""".stripMargin 
-                } 
+                        |""".stripMargin
+                }
            // return combined result
            s"""
           |${test_cmd}
@@ -472,8 +474,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
             Log.debug("Add cmd to create MD5 sibling.")
             md5_cmd = s"""
-                            |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
-                            |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && DELOCALIZATION_FAILED=1 ); 
+                            |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then
+                            |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && DELOCALIZATION_FAILED=1 );
                             |fi
                             |""".stripMargin
         } else {
@@ -508,7 +510,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
          |if [[ "${doTagging}" == "true" ]]; then
          |  echo "*** TAGGING RESOURCES ***"
          |  _add_tags
-         |fi 
+         |fi
          |
          |echo '*** DELOCALIZING OUTPUTS ***'
          |DELOCALIZATION_FAILED=0
@@ -570,7 +572,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
       val rootworkflowId = jobDescriptor.workflowDescriptor.rootWorkflowId.toString
       Log.debug(s"Submitting taskId: $taskId, job definition : $definitionArn, script: $batch_script")
       Log.info(s"Submitting taskId: $rootworkflowId::$taskId, script: $batch_script")
-      
+
       //provide job environment variables, vcpu and memory
       var resourceRequirements: Seq[ResourceRequirement] = Seq(
         ResourceRequirement.builder().`type`(ResourceType.VCPU).value(runtimeAttributes.cpu.##.toString).build(),
@@ -581,7 +583,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         val gpuRequirement = ResourceRequirement.builder().`type`(ResourceType.GPU).value(runtimeAttributes.gpuCount.toString)
         resourceRequirements = resourceRequirements :+ gpuRequirement.build()
       }
-          
+
       // prepare the job request
       var submitJobRequest = SubmitJobRequest.builder()
         .jobName(sanitize(jobDescriptor.taskCall.fullyQualifiedName))
@@ -595,6 +597,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
             .resourceRequirements(resourceRequirements.asJava)
             .build()
         )
+        .tags(runtimeAttributes.additionalTags.asJava)
         .jobQueue(runtimeAttributes.queueArn)
         .jobDefinition(definitionArn)
       // tagging activated : add to request
@@ -602,8 +605,8 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
           // replace invalid characters in the tags
           val invalidCharsPattern = "[^a-zA-Z0-9_.:/=+-@]+".r
           val tags: Map[String,String] = Map(
-            "cromwell-workflow-name" -> invalidCharsPattern.replaceAllIn(workflowName,"_"), 
-            "cromwell-workflow-id" -> invalidCharsPattern.replaceAllIn(workflowId,"_"), 
+            "cromwell-workflow-name" -> invalidCharsPattern.replaceAllIn(workflowName,"_"),
+            "cromwell-workflow-id" -> invalidCharsPattern.replaceAllIn(workflowId,"_"),
             "cromwell-task-id" -> invalidCharsPattern.replaceAllIn(taskId,"_"),
             "cromwell-root-workflow-name" -> invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflow.name.toString,"_"),
             "cromwell-root-workflow-id" -> invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflowId.toString,"_")
@@ -816,7 +819,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
   def output(detail: JobDetail): String = {
     val events: Seq[OutputLogEvent] = cloudWatchLogsClient.getLogEvents(GetLogEventsRequest.builder
       // http://aws-java-sdk-javadoc.s3-website-us-west-2.amazonaws.com/latest/software/amazon/awssdk/services/batch/model/ContainerDetail.html#logStreamName--
-      .logGroupName("/aws/batch/job")
+      .logGroupName(runtimeAttributes.logGroupName)
       .logStreamName(detail.container.logStreamName)
       .startFromHead(true)
       .build).events.asScala.toList
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index f55d3a933f7..d4ee0c6c7e6 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -34,7 +34,7 @@ package cromwell.backend.impl.aws
 import scala.collection.mutable.ListBuffer
 import cromwell.backend.BackendJobDescriptor
 import cromwell.backend.io.JobPaths
-import software.amazon.awssdk.services.batch.model.{ContainerProperties, EvaluateOnExit, Host, KeyValuePair, MountPoint, ResourceRequirement, ResourceType, RetryAction, RetryStrategy, Ulimit, Volume}
+import software.amazon.awssdk.services.batch.model.{ContainerProperties, EvaluateOnExit, Host, KeyValuePair, LogConfiguration, MountPoint, ResourceRequirement, ResourceType, RetryAction, RetryStrategy, Ulimit, Volume}
 import cromwell.backend.impl.aws.io.AwsBatchVolume
 
 import scala.jdk.CollectionConverters._
@@ -153,8 +153,8 @@ trait AwsBatchJobDefinitionBuilder {
       ).toList
     }
 
-    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit], efsDelocalize: Boolean, efsMakeMD5: Boolean, tagResources: Boolean): String = {
-      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}:${tagResources.toString}"
+    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit], efsDelocalize: Boolean, efsMakeMD5: Boolean, tagResources: Boolean, logGroupName: String): String = {
+      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}:${tagResources.toString}:$logGroupName"
     }
 
     val environment = List.empty[KeyValuePair]
@@ -165,6 +165,15 @@ trait AwsBatchJobDefinitionBuilder {
     val packedCommand = packCommand("/bin/bash", "-c", cmdName)
     val volumes =  buildVolumes( context.runtimeAttributes.disks, context.fsxMntPoint)
     val mountPoints = buildMountPoints( context.runtimeAttributes.disks, context.fsxMntPoint)
+    val logGroupName = context.runtimeAttributes.logGroupName
+    val logConfiguration = LogConfiguration.builder()
+      .logDriver("awslogs")
+      .options(
+        Map(
+          "awslogs-group" -> logGroupName
+        ).asJava
+      )
+      .build()
     val ulimits = buildUlimits( context.runtimeAttributes.ulimits)
     val efsDelocalize = context.runtimeAttributes.efsDelocalize
     val efsMakeMD5 = context.runtimeAttributes.efsMakeMD5
@@ -179,7 +188,8 @@ trait AwsBatchJobDefinitionBuilder {
       ulimits,
       efsDelocalize,
       efsMakeMD5,
-      tagResources
+      tagResources,
+      logGroupName
     )
 
     // To reuse job definition for gpu and gpu-runs, we will create a job definition that does not gpu requirements
@@ -191,6 +201,7 @@ trait AwsBatchJobDefinitionBuilder {
         ResourceRequirement.builder().`type`(ResourceType.VCPU).value(context.runtimeAttributes.cpu.##.toString).build(),
         ResourceRequirement.builder().`type`(ResourceType.MEMORY).value(context.runtimeAttributes.memory.to(MemoryUnit.MB).amount.toInt.toString).build()
       )
+      .logConfiguration(logConfiguration)
       .volumes(volumes.asJava)
       .mountPoints(mountPoints.asJava)
       .environment(environment.asJava)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index 456355e412c..2a0c52e3916 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -56,6 +56,7 @@ import scala.jdk.CollectionConverters._
 
 /**
  * Attributes that are provided to the job at runtime
+ *
  * @param cpu number of vCPU
  * @param gpuCount number of gpu
  * @param zones the aws availability zones to run in
@@ -72,8 +73,10 @@ import scala.jdk.CollectionConverters._
  * @param awsBatchEvaluateOnExit Evaluate on exit strategy setting for AWS batch retry
  * @param ulimits ulimit values to be passed to the container
  * @param efsDelocalize should we delocalize efs files to s3
- * @param efsMakeMD5 should we make a sibling md5 file as part of the job 
+ * @param efsMakeMD5 should we make a sibling md5 file as part of the job
  * @param tagResources should we tag resources
+ * @param logGroupName the CloudWatch log group name to write logs to
+ * @param additionalTags a map of tags to add to the AWS Batch job submission
  */
 case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      gpuCount: Int,
@@ -91,6 +94,8 @@ case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      ulimits: Vector[Map[String, String]],
                                      efsDelocalize: Boolean,
                                      efsMakeMD5 : Boolean,
+                                     logGroupName: String,
+                                     additionalTags: Map[String, String],
                                      fileSystem: String= "s3",
                                      tagResources: Boolean = false)
 
@@ -122,6 +127,12 @@ object AwsBatchRuntimeAttributes {
 
   private val MemoryDefaultValue = "2 GB"
 
+  private val logGroupNameKey = "logGroupName"
+  private val logGroupNameValidationInstance = new StringRuntimeAttributesValidation(logGroupNameKey)
+  private val LogGroupNameDefaultValue = WomString("/aws/batch/job")
+
+  private val additionalTagsKey = "additionalTags"
+
   val UlimitsKey = "ulimits"
   private val UlimitsDefaultValue = WomArray(WomArrayType(WomMapType(WomStringType,WomStringType)), Vector(WomMap(Map.empty[WomValue, WomValue])))
 
@@ -160,6 +171,9 @@ object AwsBatchRuntimeAttributes {
   private def noAddressValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = noAddressValidationInstance
     .withDefault(noAddressValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue)
 
+  private def logGroupNameValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[String] = logGroupNameValidationInstance
+    .withDefault(logGroupNameValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse LogGroupNameDefaultValue)
+
   private def scriptS3BucketNameValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[String] = {
     ScriptS3BucketNameValidation(scriptS3BucketKey).withDefault(ScriptS3BucketNameValidation(scriptS3BucketKey)
       .configDefaultWomValue(runtimeConfig).getOrElse( throw new RuntimeException( "scriptBucketName is required" )))
@@ -205,7 +219,7 @@ object AwsBatchRuntimeAttributes {
     // get the runtime attributes out of full config
     val rtc: Config = configuration.runtimeConfig match {
         case Some(x) => x
-        case None => 
+        case None =>
             Log.error("aws-batch default runtime attributes not found.")
             throw new RuntimeException("Default runtime attributes not found in config. This should always be present for AWS ! ")
     }
@@ -215,7 +229,7 @@ object AwsBatchRuntimeAttributes {
     val rtc_disks = try {
         rtc.getAnyRef(AwsBatchRuntimeAttributes.DisksKey).asInstanceOf[String] // just to prevent complaints about var/val
     } catch {
-        case _: ConfigException.Missing => 
+        case _: ConfigException.Missing =>
            "local-disk"
     }
     // combine and remove empty values and remove empty values
@@ -238,6 +252,7 @@ object AwsBatchRuntimeAttributes {
                         dockerValidation,
                         queueArnValidation(runtimeConfig),
                         scriptS3BucketNameValidation(runtimeConfig),
+                        logGroupNameValidation(runtimeConfig),
                         awsBatchRetryAttemptsValidation(runtimeConfig),
                         awsBatchEvaluateOnExitValidation(runtimeConfig),
                         ulimitsValidation(runtimeConfig),
@@ -256,6 +271,7 @@ object AwsBatchRuntimeAttributes {
       noAddressValidation(runtimeConfig),
       dockerValidation,
       queueArnValidation(runtimeConfig),
+      logGroupNameValidation(runtimeConfig),
       awsBatchRetryAttemptsValidation(runtimeConfig),
       awsBatchEvaluateOnExitValidation(runtimeConfig),
       ulimitsValidation(runtimeConfig),
@@ -286,6 +302,14 @@ object AwsBatchRuntimeAttributes {
        case AWSBatchStorageSystems.s3 => RuntimeAttributesValidation.extract(scriptS3BucketNameValidation(runtimeAttrsConfig) , validatedRuntimeAttributes)
        case _ => ""
     }
+    val logGroupName: String = RuntimeAttributesValidation.extract(logGroupNameValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val additionalTags: Map[String, String] = runtimeAttrsConfig.collect {
+      case config if config.hasPath(additionalTagsKey) =>
+        config.getObject(additionalTagsKey).entrySet().asScala
+          .map(e => e.getKey -> e.getValue.unwrapped().toString)
+          .toMap
+    }.getOrElse(Map.empty[String, String])
+
     val awsBatchRetryAttempts: Int = RuntimeAttributesValidation.extract(awsBatchRetryAttemptsValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
     val awsBatchEvaluateOnExit: Vector[Map[String, String]] = RuntimeAttributesValidation.extract(awsBatchEvaluateOnExitValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
 
@@ -310,6 +334,8 @@ object AwsBatchRuntimeAttributes {
       ulimits,
       efsDelocalize,
       efsMakeMD5,
+      logGroupName,
+      additionalTags,
       fileSystem,
       tagResources
     )
@@ -642,7 +668,7 @@ object AwsBatchefsDelocalizeValidation {
 }
 
 class AwsBatchefsDelocalizeValidation(key: String) extends BooleanRuntimeAttributesValidation(key) {
-  
+
   override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Boolean"
 }
 
@@ -651,7 +677,7 @@ object AwsBatchefsMakeMD5Validation {
 }
 
 class AwsBatchefsMakeMD5Validation(key: String) extends BooleanRuntimeAttributesValidation(key) {
-  
+
   override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be an Boolean"
 }
 
@@ -660,9 +686,9 @@ object AwsBatchtagResourcesValidation {
 }
 
 class AwsBatchtagResourcesValidation(key: String) extends BooleanRuntimeAttributesValidation(key) {
-  
+
   override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be a Boolean"
-}   
+}
 
 object UlimitsValidation
     extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index 61914626ed7..50aae56b4b4 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -126,7 +126,10 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
       ulimits = Vector(Map.empty[String, String]),
       efsDelocalize = false,
       efsMakeMD5 = false,
-      fileSystem = "s3")
+      fileSystem = "s3",
+      logGroupName = "/aws/batch/job",
+      additionalTags = Map("tag" -> "value")
+  )
 
   val batchJobDefintion = AwsBatchJobDefinitionContext(
     runtimeAttributes = runtimeAttributes,
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
index a9411b574b5..acb87a52cc7 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
@@ -58,8 +58,10 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     )))
   }
 
-  val expectedDefaults = new AwsBatchRuntimeAttributes(refineMV[Positive](1), 0, Vector("us-east-1a", "us-east-1b"),
-
+  val expectedDefaults = new AwsBatchRuntimeAttributes(
+    refineMV[Positive](1),
+    0,
+    Vector("us-east-1a", "us-east-1b"),
     MemorySize(2, MemoryUnit.GB), Vector(AwsBatchWorkingDisk()),
     "ubuntu:latest",
     "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue",
@@ -71,7 +73,9 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     Vector(Map.empty[String, String]),
     Vector(Map.empty[String, String]),
     false,
-    false
+    false,
+    "/Cromwell/job/",
+    Map("tag1" -> "value1")
   )
 
   val expectedDefaultsLocalFS = new AwsBatchRuntimeAttributes(refineMV[Positive](1), 0, Vector("us-east-1a", "us-east-1b"),
@@ -88,6 +92,8 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     Vector(Map.empty[String, String]),
     false,
     false,
+    "/Cromwell/job/",
+    Map(),
     "local")
 
   "AwsBatchRuntimeAttributes" should {
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
index 275f126765b..dafcec8267a 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchTestConfig.scala
@@ -62,6 +62,10 @@ object AwsBatchTestConfig {
       |    queueArn: "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue"
       |    scriptBucketName: "my-bucket"
       |    awsBatchRetryAttempts: 1
+      |    logGroupName: "/Cromwell/job/"
+      |    resourceTags {
+      |       tag1: "value1"
+      |    }
       |}
       |
       |""".stripMargin
@@ -142,6 +146,7 @@ object AwsBatchTestConfigForLocalFS {
       |    queueArn: "arn:aws:batch:us-east-1:111222333444:job-queue/job-queue"
       |    scriptBucketName: ""
       |    awsBatchRetryAttempts: 1
+      |    logGroupName: "/Cromwell/job/"
       |}
       |
       |""".stripMargin
@@ -282,4 +287,4 @@ object AwsBatchTestWithRetryConfig {
   val AwsBatchBackendNoDefaultConfig = ConfigFactory.parseString(NoDefaultsConfigString)
   val AwsBatchBackendConfigurationDescriptor = BackendConfigurationDescriptor(AwsBatchBackendConfig, AwsBatchGlobalConfig)
   val NoDefaultsConfigurationDescriptor = BackendConfigurationDescriptor(AwsBatchBackendNoDefaultConfig, AwsBatchGlobalConfig)
-}
\ No newline at end of file
+}

From a37cb8aec737e3029123136a9ca2f1dcde2ab3ff Mon Sep 17 00:00:00 2001
From: Nathan Thorpe <nathan@techstormpc.com>
Date: Wed, 31 Jul 2024 13:57:44 -0700
Subject: [PATCH 319/326] remove use of S3ClientStore (#49)

---
 .../java/org/lerch/s3fs/AmazonS3Factory.java  |   1 +
 .../main/java/org/lerch/s3fs/S3FileStore.java |  23 ++--
 .../java/org/lerch/s3fs/S3FileSystem.java     |  18 ++--
 .../org/lerch/s3fs/util/S3ClientStore.java    | 100 ------------------
 project/Dependencies.scala                    |   2 +-
 5 files changed, 17 insertions(+), 127 deletions(-)
 delete mode 100644 filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java

diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java b/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
index 08ad1abafa5..4768e6cffcb 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/AmazonS3Factory.java
@@ -71,6 +71,7 @@ public S3Client getS3Client(URI uri, Properties props) {
                .httpClient(httpClient)
                .serviceConfiguration(s3Configuration)
                .overrideConfiguration(clientOverrideConfiguration)
+               .crossRegionAccessEnabled(true)
                .region(region);
 
 
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
index 5de7e89813b..af1d189be74 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileStore.java
@@ -1,17 +1,16 @@
 package org.lerch.s3fs;
 
-import org.lerch.s3fs.util.S3ClientStore;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import software.amazon.awssdk.awscore.exception.AwsServiceException;
-import software.amazon.awssdk.core.exception.SdkClientException;
-import software.amazon.awssdk.regions.Region;
 import software.amazon.awssdk.services.s3.S3Client;
-import software.amazon.awssdk.services.s3.S3Configuration;
-import software.amazon.awssdk.services.s3.model.*;
+import software.amazon.awssdk.services.s3.model.Bucket;
+import software.amazon.awssdk.services.s3.model.GetBucketAclRequest;
+import software.amazon.awssdk.services.s3.model.HeadBucketRequest;
+import software.amazon.awssdk.services.s3.model.ListBucketsRequest;
+import software.amazon.awssdk.services.s3.model.NoSuchBucketException;
+import software.amazon.awssdk.services.s3.model.Owner;
 
 import java.io.IOException;
-import java.net.URI;
 import java.nio.file.FileStore;
 import java.nio.file.attribute.FileAttributeView;
 import java.nio.file.attribute.FileStoreAttributeView;
@@ -24,14 +23,11 @@ public class S3FileStore extends FileStore implements Comparable<S3FileStore> {
 
     private S3FileSystem fileSystem;
     private String name;
-    private S3Client defaultClient;
     private final Logger logger = LoggerFactory.getLogger("S3FileStore");
 
     public S3FileStore(S3FileSystem s3FileSystem, String name) {
         this.fileSystem = s3FileSystem;
         this.name = name;
-        // the default client can be used for getBucketLocation operations
-        this.defaultClient = S3Client.builder().endpointOverride(URI.create("https://s3.us-east-1.amazonaws.com")).region(Region.US_EAST_1).build();
     }
 
     @Override
@@ -127,13 +123,8 @@ public S3Path getRootDirectory() {
         return new S3Path(fileSystem, "/" + this.name());
     }
 
-    /**
-     * Gets a client suitable for this FileStore (bucket) including configuring the correct region endpoint. If no client
-     * exists one will be constructed and cached.
-     * @return a client
-     */
     public S3Client getClient() {
-        return S3ClientStore.getInstance().getClientForBucketName(this.name);
+        return fileSystem.getClient();
     }
 
     public Owner getOwner() {
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystem.java b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystem.java
index 0038a787c64..8a71264a8e3 100644
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystem.java
+++ b/filesystems/s3/src/main/java/org/lerch/s3fs/S3FileSystem.java
@@ -23,7 +23,7 @@ public class S3FileSystem extends FileSystem implements Comparable<S3FileSystem>
     private final String key;
     private final S3Client client;
     private final String endpoint;
-    private int cache;
+    private final int cache;
 
     public S3FileSystem(S3FileSystemProvider provider, String key, S3Client client, String endpoint) {
         this.provider = provider;
@@ -109,15 +109,13 @@ public WatchService newWatchService() throws IOException {
         throw new UnsupportedOperationException();
     }
 
-//    /**
-//     * Deprecated: since SDKv2 many S3 operations need to be signed with a client using the same Region as the location
-//     * of the bucket. Prefer S3Path.client() instead.
-//     * @return
-//     */
-//    @Deprecated
-//    public S3Client getClient() {
-//        return client;
-//    }
+    /**
+     * get the client associated with this fileSystem.
+     * @return S3Client
+     */
+    public S3Client getClient() {
+        return client;
+    }
 
     /**
      * get the endpoint associated with this fileSystem.
diff --git a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java b/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
deleted file mode 100644
index 7cfd648e7a7..00000000000
--- a/filesystems/s3/src/main/java/org/lerch/s3fs/util/S3ClientStore.java
+++ /dev/null
@@ -1,100 +0,0 @@
-package org.lerch.s3fs.util;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import software.amazon.awssdk.regions.Region;
-import software.amazon.awssdk.services.s3.S3Client;
-import software.amazon.awssdk.services.s3.model.HeadBucketResponse;
-import software.amazon.awssdk.services.s3.model.S3Exception;
-
-import java.net.URI;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * A Singleton cache of clients for buckets configured for the region of those buckets
- */
-public class S3ClientStore {
-
-    private static final S3ClientStore instance = new S3ClientStore();
-
-    public static final S3Client DEFAULT_CLIENT = S3Client.builder().endpointOverride(URI.create("https://s3.us-east-1.amazonaws.com")).region(Region.US_EAST_1).build();
-
-    private final Map<String, S3Client> bucketToClientMap = Collections.synchronizedMap(new HashMap<>());
-
-    Logger logger = LoggerFactory.getLogger("S3ClientStore");
-
-
-    private S3ClientStore(){}
-
-    public static S3ClientStore getInstance() { return instance; }
-
-    public S3Client getClientForBucketName( String bucketName ) {
-        logger.debug("obtaining client for bucket '{}'", bucketName);
-        if (bucketName == null || bucketName.trim().equals("")) {
-            return DEFAULT_CLIENT;
-        }
-
-        return bucketToClientMap.computeIfAbsent(bucketName, this::generateClient);
-    }
-
-    /**
-     * Generate a client for the named bucket using a default client to determine the location of the named client
-     * @param bucketName the named of the bucket to make the client for
-     * @return an S3 client appropriate for the region of the named bucket
-     */
-    protected S3Client generateClient(String bucketName){
-        return this.generateClient(bucketName, DEFAULT_CLIENT);
-    }
-
-    /**
-     * Generate a client for the named bucket using a default client to determine the location of the named client
-     * @param bucketName the named of the bucket to make the client for
-     * @param locationClient the client used to determine the location of the named bucket, recommend using DEFAULT_CLIENT
-     * @return an S3 client appropriate for the region of the named bucket
-     */
-    protected S3Client generateClient (String bucketName, S3Client locationClient) {
-        logger.debug("generating client for bucket: '{}'", bucketName);
-        S3Client bucketSpecificClient;
-        try {
-            logger.debug("determining bucket location with getBucketLocation");
-            String bucketLocation = locationClient.getBucketLocation(builder -> builder.bucket(bucketName)).locationConstraintAsString();
-
-            bucketSpecificClient = this.clientForRegion(bucketLocation);
-
-        } catch (S3Exception e) {
-            if(e.statusCode() == 403) {
-                logger.info("Cannot determine location of '{}' bucket directly. Attempting to obtain bucket location with headBucket operation", bucketName);
-                try {
-                    final HeadBucketResponse headBucketResponse = locationClient.headBucket(builder -> builder.bucket(bucketName));
-                    bucketSpecificClient = this.clientForRegion(headBucketResponse.sdkHttpResponse().firstMatchingHeader("x-amz-bucket-region").orElseThrow());
-                } catch (S3Exception e2) {
-                    if (e2.statusCode() == 301) {
-                        bucketSpecificClient = this.clientForRegion(e2.awsErrorDetails().sdkHttpResponse().firstMatchingHeader("x-amz-bucket-region").orElseThrow());
-                    } else {
-                        throw e2;
-                    }
-                }
-            } else {
-                throw e;
-            }
-        }
-
-        if (bucketSpecificClient == null) {
-            logger.warn("Unable to determine the region of bucket: '{}'. Generating a client for the current region.", bucketName);
-            bucketSpecificClient = S3Client.create();
-        }
-
-        return bucketSpecificClient;
-    }
-
-    private S3Client clientForRegion(String regionString){
-        // It may be useful to further cache clients for regions although at some point clients for buckets may need to be
-        // specialized beyond just region end points.
-        Region region = regionString.equals("") ? Region.US_EAST_1 : Region.of(regionString);
-        logger.debug("bucket region is: '{}'", region.id());
-        return S3Client.builder().region(region).build();
-    }
-
-}
diff --git a/project/Dependencies.scala b/project/Dependencies.scala
index 5be942f6d38..10c6b81ec79 100644
--- a/project/Dependencies.scala
+++ b/project/Dependencies.scala
@@ -6,7 +6,7 @@ object Dependencies {
   private val akkaV = "2.5.32" // scala-steward:off (CROM-6637)
   private val ammoniteOpsV = "2.4.1"
   private val apacheHttpClientV = "4.5.13"
-  private val awsSdkV = "2.17.265"
+  private val awsSdkV = "2.26.19"
   // We would like to use the BOM to manage Azure SDK versions, but SBT doesn't support it.
   // https://github.com/Azure/azure-sdk-for-java/tree/main/sdk/boms/azure-sdk-bom
   // https://github.com/sbt/sbt/issues/4531

From 40c62496f30383e49f67b6d7ec350e714b7615e5 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Thu, 17 Oct 2024 09:21:20 +0200
Subject: [PATCH 320/326] PR #44: Multi-aserisk globbing by @kevinRenaersBio. 
 Reapplied selection of changes on aws_develop branch

---
 ...wsBatchAsyncBackendJobExecutionActor.scala | 373 +++++++++++++-----
 .../backend/impl/aws/AwsBatchJob.scala        |  16 +-
 .../impl/aws/io/AwsBatchGlobFunctions.scala   |  35 +-
 3 files changed, 305 insertions(+), 119 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 150d61bef79..5ab504dfa25 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -93,16 +93,21 @@ object AwsBatchAsyncBackendJobExecutionActor {
   type AwsBatchPendingExecutionHandle = PendingExecutionHandle[StandardAsyncJob, AwsBatchJob, RunStatus]
 }
 
-class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: StandardAsyncExecutionActorParams)
-  extends BackendJobLifecycleActor with StandardAsyncExecutionActor with AwsBatchJobCachingActorHelper
-    with KvClient with AskSupport {
-
-  /**
-    * The builder for `IoCommands` to the storage system used by jobs executed by this backend
+class AwsBatchAsyncBackendJobExecutionActor(
+    override val standardParams: StandardAsyncExecutionActorParams
+) extends BackendJobLifecycleActor
+    with StandardAsyncExecutionActor
+    with AwsBatchJobCachingActorHelper
+    with KvClient
+    with AskSupport {
+
+  /** The builder for `IoCommands` to the storage system used by jobs executed
+    * by this backend
     */
-  override lazy val ioCommandBuilder: IoCommandBuilder = configuration.fileSystem match  {
-    case AWSBatchStorageSystems.s3 => S3BatchCommandBuilder
-    case _ =>  DefaultIoCommandBuilder
+  override lazy val ioCommandBuilder: IoCommandBuilder =
+    configuration.fileSystem match {
+      case AWSBatchStorageSystems.s3 => S3BatchCommandBuilder
+      case _                         => DefaultIoCommandBuilder
   }
 
   // the cromwell backend Actor
@@ -193,10 +198,13 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       runtimeAttributes,
       instantiatedCommand.commandString,
       cmdScript,
-      rcPath.toString, executionStdout, executionStderr,
+      rcPath.toString,
+      executionStdout,
+      executionStderr,
       generateAwsBatchInputs(jobDescriptor),
       generateAwsBatchOutputs(jobDescriptor),
-      jobPaths, Seq.empty[AwsBatchParameter],
+      jobPaths,
+      Seq.empty[AwsBatchParameter],
       configuration.awsConfig.region,
       Option(configuration.awsAuth),
       configuration.fsxMntPoint,
@@ -219,9 +227,15 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
    *
    */
   override def tryAbort(job: StandardAsyncJob): Unit = {
-    batchJob.abort(job.jobId) // job.JobId should be the AWS Batch Job Id based on analysis of other backends
-    Log.info(s"Attempted CancelJob operation in AWS Batch for Job ID ${job.jobId}. There were no errors during the operation")
-    Log.info(s"We have normality. Anything you still can't cope with is therefore your own problem")
+    batchJob.abort(
+      job.jobId
+    ) // job.JobId should be the AWS Batch Job Id based on analysis of other backends
+    Log.info(
+      s"Attempted CancelJob operation in AWS Batch for Job ID ${job.jobId}. There were no errors during the operation"
+    )
+    Log.info(
+      s"We have normality. Anything you still can't cope with is therefore your own problem"
+    )
     Log.info(s"https://www.youtube.com/watch?v=YCRxnjE7JVs")
     ()
   }
@@ -231,21 +245,30 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   /**
     * Takes two arrays of remote and local WOM File paths and generates the necessary AwsBatchInputs.
     */
-  private def inputsFromWomFiles(namePrefix: String,
-                                    remotePathArray: Seq[WomFile],
-                                    localPathArray: Seq[WomFile],
-                                    jobDescriptor: BackendJobDescriptor,
-                                    flag: Boolean): Iterable[AwsBatchInput] = {
+  private def inputsFromWomFiles(
+      namePrefix: String,
+      remotePathArray: Seq[WomFile],
+      localPathArray: Seq[WomFile],
+      jobDescriptor: BackendJobDescriptor,
+      flag: Boolean
+  ): Iterable[AwsBatchInput] = {
 
     (remotePathArray zip localPathArray zipWithIndex) flatMap {
       case ((remotePath, localPath), index) =>
         var localPathString = localPath.valueString
-        if (localPathString.startsWith("s3://")){
+        if (localPathString.startsWith("s3://")) {
           localPathString = localPathString.replace("s3://", "")
-        }else if (localPathString.startsWith("s3:/")) {
+        } else if (localPathString.startsWith("s3:/")) {
           localPathString = localPathString.replace("s3:/", "")
         }
-        Seq(AwsBatchFileInput(s"$namePrefix-$index", remotePath.valueString, DefaultPathBuilder.get(localPathString), workingDisk))
+        Seq(
+          AwsBatchFileInput(
+            s"$namePrefix-$index",
+            remotePath.valueString,
+            DefaultPathBuilder.get(localPathString),
+            workingDisk
+          )
+        )
     }
     
   }
@@ -261,15 +284,15 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       getPath(value) match {
         // for s3 paths :
         case Success(path: S3Path) =>
-          configuration.fileSystem match  {
+          configuration.fileSystem match {
             case AWSBatchStorageSystems.s3 => 
-                URLDecoder.decode(path.pathWithoutScheme,"UTF-8")
+                URLDecoder.decode(path.pathWithoutScheme, "UTF-8")
             case _ =>  
                 URLDecoder.decode(path.toString,"UTF-8")
           }
         // non-s3 paths
         case _ => 
-            URLDecoder.decode(value,"UTF-8")
+            URLDecoder.decode(value, "UTF-8")
       }
     )
   }
@@ -279,11 +302,21 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     * @param jobDescriptor the job descriptor from Cromwell
     * @return the inputs derived from the descriptor
     */
-  private[aws] def generateAwsBatchInputs(jobDescriptor: BackendJobDescriptor): Set[AwsBatchInput] = {
-    val writeFunctionFiles = instantiatedCommand.createdFiles map { f => f.file.value.md5SumShort -> List(f) } toMap
-
-    val writeFunctionInputs = writeFunctionFiles flatMap {
-      case (name, files) => inputsFromWomFiles(name, files.map(_.file), files.map(localizationPath), jobDescriptor, false)
+  private[aws] def generateAwsBatchInputs(
+      jobDescriptor: BackendJobDescriptor
+  ): Set[AwsBatchInput] = {
+    val writeFunctionFiles = instantiatedCommand.createdFiles map { f =>
+      f.file.value.md5SumShort -> List(f)
+    } toMap
+
+    val writeFunctionInputs = writeFunctionFiles flatMap { case (name, files) =>
+      inputsFromWomFiles(
+        name,
+        files.map(_.file),
+        files.map(localizationPath),
+        jobDescriptor,
+        false
+      )
     }
 
     // Collect all WomFiles from inputs to the call.
@@ -302,8 +335,14 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         }
     }
     
-    val callInputInputs = callInputFiles flatMap {
-      case (name, files) => inputsFromWomFiles(name, files, files.map(relativeLocalizationPath), jobDescriptor, true)
+    val callInputInputs = callInputFiles flatMap { case (name, files) =>
+      inputsFromWomFiles(
+        name,
+        files,
+        files.map(relativeLocalizationPath),
+        jobDescriptor,
+        true
+      )
     }
     // this is a list : AwsBatchInput(name_in_wf, origin_such_as_s3, target_in_docker_relative, target_in_docker_disk[name mount] )
     val scriptInput: AwsBatchInput = AwsBatchFileInput(
@@ -322,7 +361,10 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     *
     * @throws Exception if the `path` does not live in one of the supplied `disks`
     */
-  private def relativePathAndVolume(path: String, disks: Seq[AwsBatchVolume] ): (Path, AwsBatchVolume) = {
+  private def relativePathAndVolume(
+      path: String,
+      disks: Seq[AwsBatchVolume]
+  ): (Path, AwsBatchVolume) = {
 
     def getAbsolutePath(path: Path) = {
       configuration.fileSystem match {
@@ -351,24 +393,38 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     if (referenceName.length <= 127) referenceName else referenceName.md5Sum
   }
 
-  private[aws] def generateAwsBatchOutputs(jobDescriptor: BackendJobDescriptor): Set[AwsBatchFileOutput] = {
+  private[aws] def generateAwsBatchOutputs(
+      jobDescriptor: BackendJobDescriptor
+  ): Set[AwsBatchFileOutput] = {
     import cats.syntax.validated._
     def evaluateFiles(output: OutputDefinition): List[WomFile] = {
       Try(
-        output.expression.evaluateFiles(jobDescriptor.localInputs, NoIoFunctionSet, output.womType).map(_.toList map { _.file })
+        output.expression
+          .evaluateFiles(
+            jobDescriptor.localInputs,
+            NoIoFunctionSet,
+            output.womType
+          )
+          .map(_.toList map { _.file })
       ).getOrElse(List.empty[WomFile].validNel)
        .getOrElse(List.empty)
     }
-    val womFileOutputs = jobDescriptor.taskCall.callable.outputs.flatMap(evaluateFiles) map relativeLocalizationPath
+    val womFileOutputs = jobDescriptor.taskCall.callable.outputs
+      .flatMap(evaluateFiles) map relativeLocalizationPath
     val outputs: Seq[AwsBatchFileOutput] = womFileOutputs.distinct flatMap {
       _.flattenFiles flatMap {
-        case unlistedDirectory: WomUnlistedDirectory => generateUnlistedDirectoryOutputs(unlistedDirectory)
-        case singleFile: WomSingleFile => generateAwsBatchSingleFileOutputs(singleFile)
+        case unlistedDirectory: WomUnlistedDirectory =>
+          generateUnlistedDirectoryOutputs(unlistedDirectory)
+        case singleFile: WomSingleFile =>
+          generateAwsBatchSingleFileOutputs(singleFile)
         case globFile: WomGlobFile => generateAwsBatchGlobFileOutputs(globFile)
       }
     }
 
-    val additionalGlobOutput = jobDescriptor.taskCall.callable.additionalGlob.toList.flatMap(generateAwsBatchGlobFileOutputs).toSet
+    val additionalGlobOutput =
+      jobDescriptor.taskCall.callable.additionalGlob.toList
+        .flatMap(generateAwsBatchGlobFileOutputs)
+        .toSet
     
     outputs.toSet ++ additionalGlobOutput
   }
@@ -402,13 +458,18 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   }
 
   // used by generateAwsBatchOutputs, could potentially move this def within that function
-  private def generateAwsBatchSingleFileOutputs(womFile: WomSingleFile): List[AwsBatchFileOutput] = {
+  private def generateAwsBatchSingleFileOutputs(
+      womFile: WomSingleFile
+  ): List[AwsBatchFileOutput] = {
     // rewrite this to create more flexibility
-    // 
+    //
     val destination = configuration.fileSystem match {
-      case  AWSBatchStorageSystems.s3 =>  callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
-      case _ => DefaultPathBuilder.get(womFile.valueString) match {
-        case p if !p.isAbsolute =>  callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
+      case AWSBatchStorageSystems.s3 =>
+        callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
+      case _ =>
+        DefaultPathBuilder.get(womFile.valueString) match {
+          case p if !p.isAbsolute =>
+            callRootPath.resolve(womFile.value.stripPrefix("/")).pathAsString
         case p => p.pathAsString
       }
 
@@ -437,7 +498,12 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     // add workflow id to hash for better conflict prevention
     val wfid = standardParams.jobDescriptor.toString.split(":")(0)
     val globName = GlobFunctions.globName(s"${womFile.value}-${wfid}")
-    val globbedDir = Paths.get(womFile.value).getParent.toString
+    var globbedDirPath =
+      Paths.get(womFile.value).getParent()
+    while (globbedDirPath.toString().contains("*")) {
+      globbedDirPath = globbedDirPath.getParent()
+    }
+    val globbedDir: String = globbedDirPath.toString()
     // generalize folder and list file
     val globDirectory = DefaultPathBuilder.get(globbedDir + "/." + globName + "/")
     val globListFile = DefaultPathBuilder.get(globbedDir + "/." + globName + ".list")
@@ -446,14 +512,26 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     val (_, globDirectoryDisk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
 
     
-    val (globDirectoryDestinationPath, globListFileDestinationPath) = if (configuration.efsMntPoint.isDefined && 
-                     configuration.efsMntPoint.getOrElse("").equals(globDirectoryDisk.toString.split(" ")(1)) &&
-                     ! runtimeAttributes.efsDelocalize) {
-                        (globDirectory, globListFile)
-                     } else {
-                        // cannot resolve absolute paths : strip the leading '/'
-                        (callRootPath.resolve(globDirectory.toString.stripPrefix("/")).pathAsString, callRootPath.resolve(globListFile.toString.stripPrefix("/")).pathAsString)
-                     }
+    val (globDirectoryDestinationPath, globListFileDestinationPath) =
+      if (
+        configuration.efsMntPoint.isDefined &&
+        configuration.efsMntPoint
+          .getOrElse("")
+          .equals(globDirectoryDisk.toString.split(" ")(1)) &&
+        !runtimeAttributes.efsDelocalize
+      ) {
+        (globDirectory, globListFile)
+      } else {
+        // cannot resolve absolute paths : strip the leading '/'
+        (
+          callRootPath
+            .resolve(globDirectory.toString.stripPrefix("/"))
+            .pathAsString,
+          callRootPath
+            .resolve(globListFile.toString.stripPrefix("/"))
+            .pathAsString
+        )
+      }
     // return results
     return (
         globName,
@@ -543,8 +621,14 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
 
   override def recoverAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] =  reconnectAsync(jobId)
 
-  override def reconnectAsync(jobId: StandardAsyncJob): Future[ExecutionHandle] = {
-    val handle = PendingExecutionHandle[StandardAsyncJob, StandardAsyncRunInfo, StandardAsyncRunState](jobDescriptor, jobId, Option(batchJob), previousState = None)
+  override def reconnectAsync(
+      jobId: StandardAsyncJob
+  ): Future[ExecutionHandle] = {
+    val handle = PendingExecutionHandle[
+      StandardAsyncJob,
+      StandardAsyncRunInfo,
+      StandardAsyncRunState
+    ](jobDescriptor, jobId, Option(batchJob), previousState = None)
     Future.successful(handle)
   }
 
@@ -588,10 +672,11 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     } yield guaranteedAnswer
   }
 
-  override def handleExecutionResult(status: StandardAsyncRunState,
-                            oldHandle: StandardAsyncPendingExecutionHandle): Future[ExecutionHandle] = {
+  override def handleExecutionResult(
+      status: StandardAsyncRunState,
+      oldHandle: StandardAsyncPendingExecutionHandle
+  ): Future[ExecutionHandle] = {
     
-
     // get path to sderr
     val stderr = jobPaths.standardPaths.error
     lazy val stderrAsOption: Option[Path] = Option(stderr)
@@ -611,44 +696,125 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
         if (isDone(status)) {
           tryReturnCodeAsInt match {
             // stderr not empty : retry
-            case Success(returnCodeAsInt) if failOnStdErr && stderrSize.intValue > 0 =>
-              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(StderrNonEmpty(jobDescriptor.key.tag, stderrSize, stderrAsOption), Option(returnCodeAsInt), None))
+            case Success(returnCodeAsInt)
+                if failOnStdErr && stderrSize.intValue > 0 =>
+              val executionHandle = Future.successful(
+                FailedNonRetryableExecutionHandle(
+                  StderrNonEmpty(
+                    jobDescriptor.key.tag,
+                    stderrSize,
+                    stderrAsOption
+                  ),
+                  Option(returnCodeAsInt),
+                  None
+                )
+              )
               retryElseFail(executionHandle)
             // job was aborted (cancelled by user?) 
             // on AWS OOM kill are code 137 : check retryWithMoreMemory here 
-            case Success(returnCodeAsInt) if isAbort(returnCodeAsInt) && !retryWithMoreMemory =>
-              jobLogger.debug(s"Job was aborted, code was : '${returnCodeAsString.stripLineEnd}'")
+            case Success(returnCodeAsInt)
+                if isAbort(returnCodeAsInt) && !retryWithMoreMemory =>
+              jobLogger.debug(
+                s"Job was aborted, code was : '${returnCodeAsString.stripLineEnd}'"
+              )
               Future.successful(AbortedExecutionHandle)
             // if instance killed after RC.txt creation : edge case with status == Failed AND returnCode == [accepted values] => retry.
-            case Success(returnCodeAsInt) if status.toString() == "Failed" && continueOnReturnCode.continueFor(returnCodeAsInt) =>
-                jobLogger.debug(s"Suspected spot kill due to status/RC mismatch")
-                val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(UnExpectedStatus(jobDescriptor.key.tag, returnCodeAsInt, status.toString(), stderrAsOption), Option(returnCodeAsInt), None))
+           case Success(returnCodeAsInt)
+                if status.toString() == "Failed" && continueOnReturnCode
+                  .continueFor(returnCodeAsInt) =>
+              jobLogger.debug(s"Suspected spot kill due to status/RC mismatch")
+              val executionHandle = Future.successful(
+                FailedNonRetryableExecutionHandle(
+                  UnExpectedStatus(
+                    jobDescriptor.key.tag,
+                    returnCodeAsInt,
+                    status.toString(),
+                    stderrAsOption
+                  ),
+                  Option(returnCodeAsInt),
+                  None
+                )
+              )
                 retryElseFail(executionHandle)
             // job considered ok by accepted exit code
-            case Success(returnCodeAsInt) if continueOnReturnCode.continueFor(returnCodeAsInt) =>
+            case Success(returnCodeAsInt)
+                if continueOnReturnCode.continueFor(returnCodeAsInt) =>
               handleExecutionSuccess(status, oldHandle, returnCodeAsInt)
             // job failed on out-of-memory : retry
-            case Success(returnCodeAsInt) if retryWithMoreMemory  =>
-              jobLogger.info(s"Retrying job due to OOM with exit code : '${returnCodeAsString.stripLineEnd}' ")
-              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
+            case Success(returnCodeAsInt) if retryWithMoreMemory =>
+              jobLogger.info(
+                s"Retrying job due to OOM with exit code : '${returnCodeAsString.stripLineEnd}' "
+              )
+              val executionHandle = Future.successful(
+                FailedNonRetryableExecutionHandle(
+                  RetryWithMoreMemory(
+                    jobDescriptor.key.tag,
+                    stderrAsOption,
+                    memoryRetryErrorKeys,
+                    log
+                  ),
+                  Option(returnCodeAsInt),
+                  None
+                )
+              )
               retryElseFail(executionHandle, retryWithMoreMemory)
             // unaccepted return code : retry.
             case Success(returnCodeAsInt) =>
-              jobLogger.debug(s"Retrying with wrong exit code : '${returnCodeAsString.stripLineEnd}'")
-              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(WrongReturnCode(jobDescriptor.key.tag, returnCodeAsInt, stderrAsOption), Option(returnCodeAsInt), None))
+              jobLogger.debug(
+                s"Retrying with wrong exit code : '${returnCodeAsString.stripLineEnd}'"
+              )
+              val executionHandle = Future.successful(
+                FailedNonRetryableExecutionHandle(
+                  WrongReturnCode(
+                    jobDescriptor.key.tag,
+                    returnCodeAsInt,
+                    stderrAsOption
+                  ),
+                  Option(returnCodeAsInt),
+                  None
+                )
+              )
               retryElseFail(executionHandle)
             case Failure(_) =>
-              jobLogger.warn(s"General failure of job with exit code : '${returnCodeAsString.stripLineEnd}'")
-              Future.successful(FailedNonRetryableExecutionHandle(ReturnCodeIsNotAnInt(jobDescriptor.key.tag, returnCodeAsString, stderrAsOption), kvPairsToSave = None))
+              jobLogger.warn(
+                s"General failure of job with exit code : '${returnCodeAsString.stripLineEnd}'"
+              )
+              Future.successful(
+                FailedNonRetryableExecutionHandle(
+                  ReturnCodeIsNotAnInt(
+                    jobDescriptor.key.tag,
+                    returnCodeAsString,
+                    stderrAsOption
+                  ),
+                  kvPairsToSave = None
+                )
+              )
           }
         } else {
           tryReturnCodeAsInt match {
-            case Success(returnCodeAsInt) if retryWithMoreMemory && !continueOnReturnCode.continueFor(returnCodeAsInt) =>
-              jobLogger.debug(s"job not done but retrying already? : ${status.toString()}")
-              val executionHandle = Future.successful(FailedNonRetryableExecutionHandle(RetryWithMoreMemory(jobDescriptor.key.tag, stderrAsOption, memoryRetryErrorKeys, log), Option(returnCodeAsInt), None))
+            case Success(returnCodeAsInt)
+                if retryWithMoreMemory && !continueOnReturnCode.continueFor(
+                  returnCodeAsInt
+                ) =>
+              jobLogger.debug(
+                s"job not done but retrying already? : ${status.toString()}"
+              )
+              val executionHandle = Future.successful(
+                FailedNonRetryableExecutionHandle(
+                  RetryWithMoreMemory(
+                    jobDescriptor.key.tag,
+                    stderrAsOption,
+                    memoryRetryErrorKeys,
+                    log
+                  ),
+                  Option(returnCodeAsInt),
+                  None
+                )
+              )
               retryElseFail(executionHandle, retryWithMoreMemory)
             case _ =>
-              val failureStatus = handleExecutionFailure(status, tryReturnCodeAsInt.toOption)
+              val failureStatus =
+                handleExecutionFailure(status, tryReturnCodeAsInt.toOption)
               retryElseFail(failureStatus)
           }
         }
@@ -660,8 +826,7 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
           retryElseFail(failureStatus)
         }
     }
-  
-    
+   
   }
     
  
@@ -674,7 +839,6 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
          asyncIo.contentAsStringAsync(jobPaths.returnCode, None, failOnOverflow = false)
        else {
          jobLogger.warn("RC file not found in aws version. Setting job to failed.")
-         //Thread.sleep(300000)
          Future("1")
        }
      }
@@ -694,16 +858,16 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
       //   - spot kill : no container exit code set. statusReason of ATTEMPT (not container) says "host EC2 (...) terminated"     
       Log.debug(s"Looking for memoryRetry in job '${job.jobId}'")
       val describeJobsResponse = batchClient.describeJobs(DescribeJobsRequest.builder.jobs(job.jobId).build)
-      val jobDetail = describeJobsResponse.jobs.get(0) //OrElse(throw new RuntimeException(s"Could not get job details for job '${job.jobId}'"))
+      val jobDetail = describeJobsResponse.jobs.get(0) 
       val nrAttempts = jobDetail.attempts.size
       // if job is terminated/cancelled before starting, there are no attempts. 
       val lastattempt = 
           try {
-              jobDetail.attempts.get(nrAttempts-1)
+              jobDetail.attempts.get(nrAttempts - 1)
           } catch {
-              case _ : Throwable => null
+              case _: Throwable => null
           }
-      if (lastattempt == null ) {
+      if (lastattempt == null) {
         Log.info(s"No attempts were made for job '${job.jobId}'. no memory-related retry needed.")
         false
       }     
@@ -744,14 +908,10 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
             val retry = RetryMemoryKeys.exists(containerStatusReason.contains)
             Log.debug(s"Retry job based on provided keys : '${retry}'")
             retry
-      }
-        
-        
+      }  
    }
 
   
-
-
   // Despite being a "runtime" exception, BatchExceptions for 429 (too many requests) are *not* fatal:
   override def isFatal(throwable: Throwable): Boolean = throwable match {
     case be: BatchException => !be.getMessage.contains("Status Code: 429")
@@ -868,29 +1028,38 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     * @return The shell scripting.
     */
   override def globScript(globFile: WomGlobFile): String = {
-    
     val (globName, globbedDir, _, _, _) = generateGlobPaths(globFile) 
     val controlFileName = "cromwell_glob_control_file"
     val absoluteGlobValue = commandDirectory.resolve(globFile.value).pathAsString
     val globDirectory = globbedDir + "/." + globName + "/"
     val globList = globbedDir + "/." + globName + ".list"
-    val globLinkCommand: String = (if (configuration.globLinkCommand.isDefined) {
+    val globLinkCommand: String =
+      (if (configuration.globLinkCommand.isDefined) {
        "( " + configuration.globLinkCommand.getOrElse("").toString + " )"
 
-    } else {
-        "( ln -L GLOB_PATTERN GLOB_DIRECTORY 2> /dev/null ) || ( ln GLOB_PATTERN GLOB_DIRECTORY )"
-    }).toString
-      .replaceAll("GLOB_PATTERN", absoluteGlobValue)
-      .replaceAll("GLOB_DIRECTORY", globDirectory)
+      } else {
+          "( ln -L GLOB_PATTERN GLOB_DIRECTORY 2> /dev/null ) || ( ln GLOB_PATTERN GLOB_DIRECTORY )"
+      }).toString
+        .replaceAll("GLOB_PATTERN", absoluteGlobValue)
+        .replaceAll("GLOB_DIRECTORY", globDirectory)
     // if on EFS : remove the globbing dir first, to remove leftover links from previous globs. 
-    val mkDirCmd : String = if (configuration.efsMntPoint.isDefined && globDirectory.startsWith(configuration.efsMntPoint.getOrElse(""))) {
+    val mkDirCmd: String =
+      if (
+        configuration.efsMntPoint.isDefined && globDirectory.startsWith(
+          configuration.efsMntPoint.getOrElse("")
+        )
+      ) {
         jobLogger.warn("Globbing on EFS has risks.")
-        jobLogger.warn(s"The globbing target (${globbedDir}/.${globName}/) will be overwritten when existing!")
-        jobLogger.warn("Consider keeping globbed outputs in the cromwell-root folder")
+        jobLogger.warn(
+          s"The globbing target (${globbedDir}/.${globName}/) will be overwritten when existing!"
+        )
+        jobLogger.warn(
+          "Consider keeping globbed outputs in the cromwell-root folder"
+        )
         s"rm -Rf $globDirectory $globList && mkdir"
-    } else {
-        "mkdir"
-    }
+      } else {
+          "mkdir"
+      }
  
     val controlFileContent =
       """This file is used by Cromwell to allow for globs that would not match any file.
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 4cfa08e82a5..f8e3a2d91e2 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -30,7 +30,6 @@
  */
 package cromwell.backend.impl.aws
 
-
 import java.security.MessageDigest
 import java.nio.file.attribute.PosixFilePermission
 
@@ -149,8 +148,6 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
       case input: AwsBatchFileInput => 
         // an entry in 'disks' => keep mount as it is.. 
         //here we don't need a copy command but the centaurTests expect us to verify the existence of the file
-        //val filePath = s"${input.mount.mountPoint.pathAsString}/${input.local.pathAsString}"
-        //  .replace(AwsBatchWorkingDisk.MountPoint.pathAsString, workDir)
         val filePath = input.local.pathAsString
         Log.debug("input entry in disks detected "+ input.s3key + " / "+ input.local.pathAsString)
         s"""test -e "$filePath" || (echo 'input file: $filePath does not exist' && LOCALIZATION_FAILED=1)""".stripMargin
@@ -159,7 +156,10 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     }.toList.mkString("\n")
 
     // get multipart threshold from config.
-    val mp_threshold : Long = if (conf.hasPath("engine.filesystems.s3.MultipartThreshold") ) conf.getMemorySize("engine.filesystems.s3.MultipartThreshold").toBytes() else 5L * 1024L * 1024L * 1024L; 
+    val mp_threshold: Long =
+      if (conf.hasPath("engine.filesystems.s3.MultipartThreshold"))
+        conf.getMemorySize("engine.filesystems.s3.MultipartThreshold").toBytes()
+      else 5L * 1024L * 1024L * 1024L;
     Log.debug(s"MultiPart Threshold for delocalizing is $mp_threshold")
 
     // prepare tags, strip invalid characters
@@ -171,8 +171,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
     val workflowId = invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflowId.toString,"_")
     val workflowName = invalidCharsPattern.replaceAllIn(jobDescriptor.workflowDescriptor.rootWorkflow.name.toString,"_")
     val taskId = invalidCharsPattern.replaceAllIn(jobDescriptor.key.call.fullyQualifiedName + "-" + jobDescriptor.key.index + "-" + jobDescriptor.key.attempt,"_")
-    val doTagging = tagResources.getOrElse(false) // development : always tag resources.
-    //val tags: Map[String,String] = Map("cromwell-workflow-name" -> workflowName, "cromwell-workflow-id" -> workflowId, "cromwell-task-id" -> taskId)
+    val doTagging = tagResources.getOrElse(false) 
     // this goes at the start of the script after the #!
     val preamble =
       s"""
@@ -421,6 +420,7 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
            val md5_cmd = if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
                     Log.debug("Add cmd to create MD5 sibling.")
                     // this does NOT regenerate the md5 in case the file is overwritten ! 
+                    // TODO : Add check for file age => recreate if md5 older than main file
                     s"""
                         |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then 
                         |   # the glob list
@@ -842,7 +842,9 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
       .append("runtimeAttributes", runtimeAttributes)
       .append("commandLine", commandLine)
       .append("commandScript", commandScript)
-      .append("dockerRc", dockerRc).append("dockerStderr", dockerStderr).append("dockerStdout", dockerStdout)
+      .append("dockerRc", dockerRc)
+      .append("dockerStderr", dockerStderr)
+      .append("dockerStdout", dockerStdout)
       .append("inputs", inputs)
       .append("outputs", outputs)
       .append("jobPaths", jobPaths)
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
index ffee6be0918..6c819fe0f84 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
@@ -43,15 +43,14 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
     
   def standardParams: StandardExpressionFunctionsParams
 
-  
-
-  /**
-    * Returns a list of path from the glob.
+  /** Returns a list of path from the glob.
     *
     * The paths are read from a list file based on the pattern.
     *
-    * @param pattern The pattern of the glob. This is the same "glob" passed to globPath().
-    * @return The paths that match the pattern.
+    * @param pattern
+    *   The pattern of the glob. This is the same "glob" passed to globPath().
+    * @return
+    *   The paths that match the pattern.
     */
   override def glob(pattern: String): Future[Seq[String]] = {
     // get access to globName()
@@ -65,13 +64,25 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
     // this function reads in the globfile and locates globbed files : "local" or NIO access is needed to the files. 
     // for now : hard coded as local at mount point /mnt/efs.
     val wfid_regex = ".{8}-.{4}-.{4}-.{4}-.{12}".r
-    val wfid = callContext.root.toString.split("/").toList.filter(element => wfid_regex.pattern.matcher(element).matches()).lastOption.getOrElse("")
+    val wfid = callContext.root.toString
+      .split("/")
+      .toList
+      .filter(element => wfid_regex.pattern.matcher(element).matches())
+      .lastOption
+      .getOrElse("")
     val globPatternName = globName(s"${pattern}-${wfid}")
-    val globbedDir = Paths.get(pattern).getParent.toString
+    var globbedDirPath =
+      Paths.get(pattern).getParent()
+    while (globbedDirPath.toString().contains("*")) {
+      globbedDirPath = globbedDirPath.getParent()
+    }
+    val globbedDir: String = globbedDirPath.toString()
     val listFilePath = if (pattern.startsWith("/mnt/efs/")) {
         DefaultPathBuilder.get(globbedDir + "/." + globPatternName + ".list")
     } else {
-        callContext.root.resolve(s"${globbedDir}/.${globPatternName}.list".stripPrefix("/"))
+        callContext.root.resolve(
+        s"${globbedDir}/.${globPatternName}.list".stripPrefix("/")
+      )
     }
     asyncIo.readLinesAsync(listFilePath.toRealPath()) map { lines =>
       lines.toList map { fileName =>
@@ -79,7 +90,11 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
         if (pattern.startsWith("/mnt/efs/")) {
             s"${globbedDir}/.${globPatternName}/${fileName}"
         } else {
-            callContext.root.resolve(s"${globbedDir}/.${globPatternName}/${fileName}".stripPrefix("/")).pathAsString
+            callContext.root
+            .resolve(
+              s"${globbedDir}/.${globPatternName}/${fileName}".stripPrefix("/")
+            )
+            .pathAsString
         }
       }
     }

From 6560869adb06de31ade3647b5242311707a2bfdb Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Thu, 17 Oct 2024 12:44:50 +0200
Subject: [PATCH 321/326] PR #45 reapplied to aws_develop: support for
 sharedMemory. skipped EFS fixes for now while waiting for feedback

---
 .../main/scala/cromwell/backend/backend.scala |   1 +
 .../StandardAsyncExecutionActor.scala         |   3 +-
 .../impl/aws/AwsBatchJobDefinition.scala      |  27 ++-
 .../impl/aws/AwsBatchRuntimeAttributes.scala  |  27 ++-
 ...tchAsyncBackendJobExecutionActorSpec.scala |   2 +-
 .../backend/impl/aws/AwsBatchJobSpec.scala    | 160 ++++++++++++------
 .../aws/AwsBatchRuntimeAttributesSpec.scala   |  13 ++
 .../main/scala/wom/RuntimeAttributes.scala    |   1 +
 8 files changed, 171 insertions(+), 63 deletions(-)

diff --git a/backend/src/main/scala/cromwell/backend/backend.scala b/backend/src/main/scala/cromwell/backend/backend.scala
index 3c5c33ab992..48212ebd798 100644
--- a/backend/src/main/scala/cromwell/backend/backend.scala
+++ b/backend/src/main/scala/cromwell/backend/backend.scala
@@ -143,6 +143,7 @@ object CommonBackendConfigurationAttributes {
     "default-runtime-attributes.awsBatchRetryAttempts",
     "default-runtime-attributes.maxRetries",
     "default-runtime-attributes.awsBatchEvaluateOnExit",
+    "default-runtime-attributes.sharedMemorySize",
     "default-runtime-attributes.ulimits",
     "default-runtime-attributes.efsDelocalize",
     "default-runtime-attributes.efsMakeMD5",
diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
index 8acef722f71..876473f7bf7 100644
--- a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
+++ b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -38,7 +38,6 @@ import wom.callable.{AdHocValue, CommandTaskDefinition, ContainerizedInputExpres
 import wom.expression.WomExpression
 import wom.graph.LocalName
 import wom.values._
-import wom.types._
 import wom.{CommandSetupSideEffectFile, InstantiatedCommand, WomFileMapper}
 import java.net.URLDecoder
 import scala.concurrent._
@@ -171,7 +170,7 @@ trait StandardAsyncExecutionActor
           // decode url encoded values generated by the mapper
           val decoded_womValue = URLDecoder.decode(mapped_wom.valueString,"UTF-8")
           // convert to womfile again
-          WomFile(WomSingleFileType, decoded_womValue)
+          WomFile(womFile.womFileType, decoded_womValue)
         }
     )
   }
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index d4ee0c6c7e6..197dc2b8069 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -34,7 +34,7 @@ package cromwell.backend.impl.aws
 import scala.collection.mutable.ListBuffer
 import cromwell.backend.BackendJobDescriptor
 import cromwell.backend.io.JobPaths
-import software.amazon.awssdk.services.batch.model.{ContainerProperties, EvaluateOnExit, Host, KeyValuePair, LogConfiguration, MountPoint, ResourceRequirement, ResourceType, RetryAction, RetryStrategy, Ulimit, Volume}
+import software.amazon.awssdk.services.batch.model.{ContainerProperties, EvaluateOnExit, Host, KeyValuePair, LinuxParameters, LogConfiguration, MountPoint, ResourceRequirement, ResourceType, RetryAction, RetryStrategy, Ulimit, Volume}
 import cromwell.backend.impl.aws.io.AwsBatchVolume
 
 import scala.jdk.CollectionConverters._
@@ -153,9 +153,20 @@ trait AwsBatchJobDefinitionBuilder {
       ).toList
     }
 
-    def buildName(imageName: String, packedCommand: String, volumes: List[Volume], mountPoints: List[MountPoint], env: Seq[KeyValuePair], ulimits: List[Ulimit], efsDelocalize: Boolean, efsMakeMD5: Boolean, tagResources: Boolean, logGroupName: String): String = {
-      s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}:${tagResources.toString}:$logGroupName"
-    }
+    def buildName(
+      imageName: String,
+      packedCommand: String,
+      volumes: List[Volume],
+      mountPoints: List[MountPoint],
+      env: Seq[KeyValuePair],
+      ulimits: List[Ulimit],
+      efsDelocalize: Boolean,
+      efsMakeMD5: Boolean,
+      tagResources: Boolean,
+      logGroupName: String,
+      sharedMemorySize: Int): String = {
+        s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}:${tagResources.toString}:$logGroupName"
+      }
 
     val environment = List.empty[KeyValuePair]
     val cmdName = context.runtimeAttributes.fileSystem match {
@@ -189,7 +200,8 @@ trait AwsBatchJobDefinitionBuilder {
       efsDelocalize,
       efsMakeMD5,
       tagResources,
-      logGroupName
+      logGroupName,
+      context.runtimeAttributes.sharedMemorySize.value
     )
 
     // To reuse job definition for gpu and gpu-runs, we will create a job definition that does not gpu requirements
@@ -205,7 +217,10 @@ trait AwsBatchJobDefinitionBuilder {
       .volumes(volumes.asJava)
       .mountPoints(mountPoints.asJava)
       .environment(environment.asJava)
-      .ulimits(ulimits.asJava),
+      .ulimits(ulimits.asJava)
+      .linuxParameters(
+        LinuxParameters.builder().sharedMemorySize(context.runtimeAttributes.sharedMemorySize.##).build()
+      ),
      containerPropsName)
   }
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index 2a0c52e3916..83fab088eaa 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -48,7 +48,7 @@ import com.typesafe.config.{ConfigException, ConfigValueFactory}
 
 import scala.util.matching.Regex
 import org.slf4j.{Logger, LoggerFactory}
-import wom.RuntimeAttributesKeys.GpuKey
+import wom.RuntimeAttributesKeys.{GpuKey, sharedMemoryKey}
 
 import scala.util.{Failure, Success, Try}
 import scala.jdk.CollectionConverters._
@@ -94,6 +94,7 @@ case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      ulimits: Vector[Map[String, String]],
                                      efsDelocalize: Boolean,
                                      efsMakeMD5 : Boolean,
+                                     sharedMemorySize: Int Refined Positive,
                                      logGroupName: String,
                                      additionalTags: Map[String, String],
                                      fileSystem: String= "s3",
@@ -108,6 +109,9 @@ object AwsBatchRuntimeAttributes {
   val awsBatchRetryAttemptsKey = "awsBatchRetryAttempts"
 
   val awsBatchEvaluateOnExitKey = "awsBatchEvaluateOnExit"
+
+  val defaultSharedMemorySize = WomInteger(64)
+
   private val awsBatchEvaluateOnExitDefault = WomArray(WomArrayType(WomMapType(WomStringType,WomStringType)), Vector(WomMap(Map.empty[WomValue, WomValue])))
 
 
@@ -168,6 +172,12 @@ object AwsBatchRuntimeAttributes {
       MemoryValidation.configDefaultString(RuntimeAttributesKeys.MemoryMinKey, runtimeConfig) getOrElse MemoryDefaultValue)
   }
 
+  private def sharedMemorySizeValidation(runtimeConfig: Option[Config]):  RuntimeAttributesValidation[Refined[Int, Positive]] = {
+    SharedMemorySizeValidation(sharedMemoryKey).withDefault(
+      SharedMemorySizeValidation(sharedMemoryKey).configDefaultWomValue(runtimeConfig).getOrElse(defaultSharedMemorySize)
+    )
+  }
+
   private def noAddressValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[Boolean] = noAddressValidationInstance
     .withDefault(noAddressValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue)
 
@@ -258,7 +268,8 @@ object AwsBatchRuntimeAttributes {
                         ulimitsValidation(runtimeConfig),
                         awsBatchefsDelocalizeValidation(runtimeConfig),
                         awsBatchefsMakeMD5Validation(runtimeConfig),
-                        awsBatchtagResourcesValidation(runtimeConfig)
+                        awsBatchtagResourcesValidation(runtimeConfig),
+                        sharedMemorySizeValidation(runtimeConfig),
                       )
    def validationsLocalBackend  = StandardValidatedRuntimeAttributesBuilder.default(runtimeConfig).withValidation(
       cpuValidation(runtimeConfig),
@@ -277,7 +288,8 @@ object AwsBatchRuntimeAttributes {
       ulimitsValidation(runtimeConfig),
       awsBatchefsDelocalizeValidation(runtimeConfig),
       awsBatchefsMakeMD5Validation(runtimeConfig),
-      awsBatchtagResourcesValidation(runtimeConfig)
+      awsBatchtagResourcesValidation(runtimeConfig),
+      sharedMemorySizeValidation(runtimeConfig),
     )
 
     configuration.fileSystem match  {
@@ -317,6 +329,8 @@ object AwsBatchRuntimeAttributes {
     val efsDelocalize: Boolean = RuntimeAttributesValidation.extract(awsBatchefsDelocalizeValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
     val efsMakeMD5: Boolean = RuntimeAttributesValidation.extract(awsBatchefsMakeMD5Validation(runtimeAttrsConfig),validatedRuntimeAttributes)
     val tagResources: Boolean = RuntimeAttributesValidation.extract(awsBatchtagResourcesValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
+    val sharedMemorySize: Int Refined Positive = RuntimeAttributesValidation.extract(sharedMemorySizeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+
     new AwsBatchRuntimeAttributes(
       cpu,
       gpuCount,
@@ -334,6 +348,7 @@ object AwsBatchRuntimeAttributes {
       ulimits,
       efsDelocalize,
       efsMakeMD5,
+      sharedMemorySize,
       logGroupName,
       additionalTags,
       fileSystem,
@@ -690,6 +705,12 @@ class AwsBatchtagResourcesValidation(key: String) extends BooleanRuntimeAttribut
   override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be a Boolean"
 }
 
+object SharedMemorySizeValidation {
+  def apply(key: String): SharedMemorySizeValidation = new SharedMemorySizeValidation(key)
+}
+
+class SharedMemorySizeValidation(key: String) extends PositiveIntRuntimeAttributesValidation(key)
+
 object UlimitsValidation
     extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
   override def key: String = AwsBatchRuntimeAttributes.UlimitsKey
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
index 98af4f00282..15299f9c25c 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActorSpec.scala
@@ -749,7 +749,7 @@ class AwsBatchAsyncBackendJobExecutionActorSpec extends TestKitSuite
         WomSingleFile("/cromwell_root/path/to/file2"), WomSingleFile("/cromwell_root/path/to/file3"))),
       WomMap(WomMapType(WomSingleFileType, WomSingleFileType), Map(
         WomSingleFile("/cromwell_root/path/to/file4") -> WomSingleFile("/cromwell_root/path/to/file5")
-      ))
+      )),
     )
 
     val workflowDescriptor = BackendWorkflowDescriptor(
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index e2ab56d25b7..a91e11ba43a 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -42,11 +42,12 @@ import cromwell.util.SampleWdl
 import eu.timepit.refined.api.Refined
 import eu.timepit.refined.auto._
 import eu.timepit.refined.numeric._
+import eu.timepit.refined.refineMV
 import org.scalatest.PrivateMethodTester
 import org.scalatest.flatspec.AnyFlatSpecLike
 import org.scalatest.matchers.should.Matchers
 import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider
-import software.amazon.awssdk.services.batch.model.{ContainerDetail, EvaluateOnExit, JobDetail, KeyValuePair, ResourceRequirement, RetryAction, RetryStrategy}
+import software.amazon.awssdk.services.batch.model.{ContainerDetail, EvaluateOnExit, JobDetail, KeyValuePair, LinuxParameters, ResourceRequirement, RetryAction, RetryStrategy}
 import spray.json.{JsObject, JsString}
 import wdl4s.parser.MemoryUnit
 import wom.format.MemorySize
@@ -102,13 +103,15 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
 
   val call: CommandCallNode = workFlowDescriptor.callable.taskCallNodes.head
   val jobKey: BackendJobDescriptorKey = BackendJobDescriptorKey(call, None, 1)
-  val jobDescriptor: BackendJobDescriptor = BackendJobDescriptor(null, null, null, Map.empty, null, null, null)
+  val jobDescriptor: BackendJobDescriptor = BackendJobDescriptor(workFlowDescriptor, jobKey, null, Map.empty, null, null, null)
 
-  val jobPaths: AwsBatchJobPaths = AwsBatchJobPaths(workflowPaths, jobKey)
+  val jobPaths: AwsBatchJobPaths = AwsBatchJobPaths(workflowPaths, jobKey) 
   val s3Inputs: Set[AwsBatchInput] = Set(AwsBatchFileInput("foo", "s3://bucket/foo", DefaultPathBuilder.get("foo"), AwsBatchWorkingDisk()))
   val s3Outputs: Set[AwsBatchFileOutput] = Set(AwsBatchFileOutput("baa", "s3://bucket/somewhere/baa", DefaultPathBuilder.get("baa"), AwsBatchWorkingDisk()))
 
   val cpu: Int Refined Positive = 2
+  val sharedMemorySize: Int Refined Positive = 64
+
   val runtimeAttributes: AwsBatchRuntimeAttributes = new AwsBatchRuntimeAttributes(
       cpu = cpu,
       gpuCount = 0,
@@ -127,6 +130,7 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
       efsDelocalize = false,
       efsMakeMD5 = false,
       fileSystem = "s3",
+      sharedMemorySize = sharedMemorySize,
       logGroupName = "/aws/batch/job",
       additionalTags = Map("tag" -> "value")
   )
@@ -134,7 +138,7 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
   val batchJobDefintion = AwsBatchJobDefinitionContext(
     runtimeAttributes = runtimeAttributes,
     commandText = "", dockerRcPath = "", dockerStdoutPath = "", dockerStderrPath = "", jobDescriptor = jobDescriptor
-    , jobPaths = jobPaths, inputs = Set(), outputs = Set(), fsxMntPoint = None, None, None, None
+    , jobPaths = jobPaths, inputs = Set(), outputs = Set(), fsxMntPoint = None, None, None, None, None
 
   )
 
@@ -149,24 +153,24 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
   val jobDetail: JobDetail = JobDetail.builder().container(containerDetail).build
 
   private def generateBasicJob: AwsBatchJob = {
-    val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
+    val job = AwsBatchJob(jobDescriptor, runtimeAttributes, "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       Seq.empty[AwsBatchInput].toSet, Seq.empty[AwsBatchFileOutput].toSet,
-      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None, None)
     job
   }
   private def generateBasicJobForLocalFS: AwsBatchJob = {
-    val job = AwsBatchJob(null, runtimeAttributes.copy(fileSystem="local"), "commandLine", script,
+    val job = AwsBatchJob(jobDescriptor, runtimeAttributes.copy(fileSystem="local"), "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       Seq.empty[AwsBatchInput].toSet, Seq.empty[AwsBatchFileOutput].toSet,
-      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None, None)
     job
   }
   private def generateJobWithS3InOut: AwsBatchJob = {
-    val job = AwsBatchJob(null, runtimeAttributes, "commandLine", script,
+    val job = AwsBatchJob(jobDescriptor, runtimeAttributes, "commandLine", script,
       "/cromwell_root/hello-rc.txt", "/cromwell_root/hello-stdout.log", "/cromwell_root/hello-stderr.log",
       s3Inputs, s3Outputs,
-      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None)
+      jobPaths, Seq.empty[AwsBatchParameter], None, None, None, None, None, None, None)
     job
   }
 
@@ -207,31 +211,30 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     val job = generateBasicJob
     val retryFunctionText =
       s"""
-          |export AWS_METADATA_SERVICE_TIMEOUT=10
-          |export AWS_METADATA_SERVICE_NUM_ATTEMPTS=10
-          |
           |function _s3_localize_with_retry() {
-          |  local s3_path=$$1
+          |  local s3_path="$$1"
           |  # destination must be the path to a file and not just the directory you want the file in
-          |  local destination=$$2
+          |  local destination="$$2"
           |
           |  for i in {1..6};
           |  do
           |    # abort if tries are exhausted
           |    if [ "$$i" -eq 6 ]; then
-          |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts. aborting"
-          |        exit 2
+          |        echo "failed to copy $$s3_path after $$(( $$i - 1 )) attempts."
+          |        LOCALIZATION_FAILED=1
+          |        break
           |    fi
           |    # check validity of source path
-          |    if ! [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
-          |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
-          |      exit 1
+          |    if ! [[ "$$s3_path" =~ s3://([^/]+)/(.+) ]]; then
+          |      echo "$$s3_path is not an S3 path with a bucket and key."
+          |      LOCALIZATION_FAILED=1
+          |      break
           |    fi
           |    # copy
           |    /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$s3_path" "$$destination"  ||
           |        { echo "attempt $$i to copy $$s3_path failed" && sleep $$((7 * "$$i")) && continue; }
           |    # check data integrity
-          |    _check_data_integrity $$destination $$s3_path ||
+          |    _check_data_integrity "$$destination" "$$s3_path" ||
           |       { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
           |    # copy succeeded
           |    break
@@ -244,15 +247,21 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
   it should "s3 delocalization with retry function in reconfigured script" in {
     val job = generateBasicJob
     val delocalizeText = s"""
-         |
          |function _s3_delocalize_with_retry() {
          |  # input variables
-         |  local local_path=$$1
+         |  local local_path="$$1"
          |  # destination must be the path to a file and not just the directory you want the file in
-         |  local destination=$$2
+         |  local destination="$$2"
+         |
+         |  # if file/folder does not exist, return immediately
+         |  if [[ ! -e "$$local_path" ]]; then
+         |    echo "$$local_path does not exist. skipping delocalization"
+         |    DELOCALIZATION_FAILED=1
+         |    return
+         |  fi
          |
          |  # get the multipart chunk size
-         |  chunk_size=$$(_get_multipart_chunk_size $$local_path)
+         |  chunk_size=$$(_get_multipart_chunk_size "$$local_path")
          |  local MP_THRESHOLD=5368709120
          |  # then set them
          |  /usr/local/aws-cli/v2/current/bin/aws configure set default.s3.multipart_threshold $$MP_THRESHOLD
@@ -263,31 +272,37 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
          |  do
          |    # if tries exceeded : abort
          |    if [ "$$i" -eq 6 ]; then
-         |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts. aborting"
-         |        exit 2
+         |        echo "failed to delocalize $$local_path after $$(( $$i - 1 )) attempts."
+         |        DELOCALIZATION_FAILED=1
+         |        break
          |    fi
          |    # if destination is not a bucket : abort
-         |    if ! [[ $$destination =~ s3://([^/]+)/(.+) ]]; then
-         |     echo "$$destination is not an S3 path with a bucket and key. aborting"
-         |      exit 1
+         |    if ! [[ "$$destination" =~ s3://([^/]+)/(.+) ]]; then
+         |     echo "$$destination is not an S3 path with a bucket and key."
+         |      DELOCALIZATION_FAILED=1
+         |      break
          |    fi
          |    # copy ok or try again.
          |    if [[ -d "$$local_path" ]]; then
          |       # make sure to strip the trailing / in destination
          |       destination=$${destination%/}
          |       # glob directory. do recursive copy
-         |       /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress $$local_path $$destination --recursive --exclude "cromwell_glob_control_file" ||
+         |       /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$local_path" "$$destination" --recursive --exclude "cromwell_glob_control_file" ||
          |         { echo "attempt $$i to copy globDir $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
-         |       # check integrity for each of the files
-         |       for FILE in $$(cd $$local_path ; ls | grep -v cromwell_glob_control_file); do
-         |           _check_data_integrity $$local_path/$$FILE $$destination/$$FILE ||
+         |       # check integrity for each of the files (allow spaces)
+         |       SAVEIFS="$$IFS"
+         |       IFS=$$'
+         |'
+         |       for FILE in $$(cd "$$local_path" ; ls | grep -v cromwell_glob_control_file); do
+         |           _check_data_integrity "$$local_path/$$FILE" "$$destination/$$FILE" ||
          |               { echo "data content length difference detected in attempt $$i to copy $$local_path/$$FILE failed" && sleep $$((7 * "$$i")) && continue 2; }
          |       done
+         |       IFS="$$SAVEIFS"
          |    else
          |      /usr/local/aws-cli/v2/current/bin/aws s3 cp --no-progress "$$local_path" "$$destination" ||
          |         { echo "attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |      # check content length for data integrity
-         |      _check_data_integrity $$local_path $$destination ||
+         |      _check_data_integrity "$$local_path" "$$destination" ||
          |         { echo "data content length difference detected in attempt $$i to copy $$local_path failed" && sleep $$((7 * "$$i")) && continue; }
          |    fi
          |    # copy succeeded
@@ -302,16 +317,16 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     val checkDataIntegrityBlock =
       s"""
          |function _check_data_integrity() {
-         |  local local_path=$$1
-         |  local s3_path=$$2
+         |  local local_path="$$1"
+         |  local s3_path="$$2"
          |
          |  # remote : use content_length
-         |  if [[ $$s3_path =~ s3://([^/]+)/(.+) ]]; then
+         |  if [[ "$$s3_path" =~ s3://([^/]+)/(.+) ]]; then
          |        bucket="$${BASH_REMATCH[1]}"
          |        key="$${BASH_REMATCH[2]}"
          |  else
          |      # this is already checked in the caller function
-         |      echo "$$s3_path is not an S3 path with a bucket and key. aborting"
+         |      echo "$$s3_path is not an S3 path with a bucket and key."
          |      exit 1
          |  fi
          |  s3_content_length=$$(/usr/local/aws-cli/v2/current/bin/aws s3api head-object --bucket "$$bucket" --key "$$key" --query 'ContentLength') ||
@@ -325,8 +340,7 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
          |  else
          |       false
          |  fi
-         |}
-         |""".stripMargin
+         |}""".stripMargin
     job.reconfiguredScript should include (checkDataIntegrityBlock)
   }
 
@@ -335,9 +349,9 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     val getMultiplePartChunkSize =
       s"""
          |function _get_multipart_chunk_size() {
-         |  local file_path=$$1
+         |  local file_path="$$1"
          |  # file size
-         |  file_size=$$(stat --printf="%s" $$file_path)
+         |  file_size=$$(stat --printf="%s" "$$file_path")
          |  # chunk_size : you can have at most 10K parts with at least one 5MB part
          |  # this reflects the formula in s3-copy commands of cromwell (S3FileSystemProvider.java)
          |  #   => long partSize = Math.max((objectSize / 10000L) + 1, 5 * 1024 * 1024);
@@ -357,14 +371,27 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
       s"""
          |{
          |set -e
+         |# (re-)add tags to include added volumes:
+         |if [[ "false" == "true" ]]; then
+         |  echo "*** TAGGING RESOURCES ***"
+         |  _add_tags
+         |fi
+         |
          |echo '*** DELOCALIZING OUTPUTS ***'
-         |_s3_delocalize_with_retry /tmp/scratch/baa s3://bucket/somewhere/baa
+         |DELOCALIZATION_FAILED=0
+         |_s3_delocalize_with_retry "/tmp/scratch/baa" "s3://bucket/somewhere/baa"
          |
-         |if [ -f /tmp/scratch/hello-rc.txt ]; then _s3_delocalize_with_retry /tmp/scratch/hello-rc.txt ${job.jobPaths.returnCode} ; fi
-         |if [ -f /tmp/scratch/hello-stderr.log ]; then _s3_delocalize_with_retry /tmp/scratch/hello-stderr.log ${job.jobPaths.standardPaths.error}; fi
-         |if [ -f /tmp/scratch/hello-stdout.log ]; then _s3_delocalize_with_retry /tmp/scratch/hello-stdout.log ${job.jobPaths.standardPaths.output}; fi
+         |if [ -f "/tmp/scratch/hello-rc.txt" ]; then _s3_delocalize_with_retry "/tmp/scratch/hello-rc.txt" "${job.jobPaths.returnCode}" ; fi
+         |if [ -f "/tmp/scratch/hello-stderr.log" ]; then _s3_delocalize_with_retry "/tmp/scratch/hello-stderr.log" "${job.jobPaths.standardPaths.error}"; fi
+         |if [ -f "/tmp/scratch/hello-stdout.log" ]; then _s3_delocalize_with_retry "/tmp/scratch/hello-stdout.log" "${job.jobPaths.standardPaths.output}"; fi
          |
-         |echo '*** COMPLETED DELOCALIZATION ***'
+         |if [[ $$DELOCALIZATION_FAILED -eq 1 ]]; then
+         |  echo '*** DELOCALIZATION FAILED ***'
+         |  echo '*** EXITING WITH RETURN CODE 1***'
+         |  exit 1
+         |else
+         |  echo '*** COMPLETED DELOCALIZATION ***'
+         |fi
          |echo '*** EXITING WITH RETURN CODE ***'
          |rc=$$(head -n 1 /tmp/scratch/hello-rc.txt)
          |echo $$rc
@@ -380,11 +407,24 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
       s"""
          |{
          |set -e
+         |# tag instance and volumes to ensure tags are present in case of failure:
+         |if [[ "false" == "true" ]]; then
+         |  echo "*** TAGGING RESOURCES ***"
+         |  _add_tags
+         |fi
+         |
          |echo '*** LOCALIZING INPUTS ***'
          |if [ ! -d /tmp/scratch ]; then mkdir /tmp/scratch && chmod 777 /tmp/scratch; fi
          |cd /tmp/scratch
-         |_s3_localize_with_retry s3://bucket/foo /tmp/scratch/foo
-         |echo '*** COMPLETED LOCALIZATION ***'
+         |# make sure localization completes successfully
+         |LOCALIZATION_FAILED=0
+         |_s3_localize_with_retry "s3://bucket/foo" "/tmp/scratch/foo"
+         |if [[ $$LOCALIZATION_FAILED -eq 1 ]]; then
+         |  echo '*** LOCALIZATION FAILED ***'
+         |  exit 1
+         |else
+         |  echo '*** COMPLETED LOCALIZATION ***'
+         |fi
          |set +e
          |}
          |""".stripMargin
@@ -452,4 +492,22 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
     val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion.copy(runtimeAttributes = runtime))
     val actual = jobDefinition.containerProperties.resourceRequirements
     expected should equal(CollectionConverters.asScala(actual).toSeq)}
-}
+  }
+
+  it should "use default shared memory size of 64MB" in {
+    val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion)
+    val actual = jobDefinition.containerProperties.linuxParameters()
+    val expected = LinuxParameters.builder().sharedMemorySize(64).build()
+    expected should equal(actual)
+  }
+
+  it should "use user shared memory size if set" in {
+    val runtime = runtimeAttributes.copy(
+      gpuCount = 1,
+      sharedMemorySize = refineMV[Positive](100)
+    )
+    val jobDefinition = StandardAwsBatchJobDefinitionBuilder.build(batchJobDefintion.copy(runtimeAttributes = runtime))
+    val actual = jobDefinition.containerProperties.linuxParameters()
+    val expected = LinuxParameters.builder().sharedMemorySize(100).build()
+    expected should equal(actual)
+  }
\ No newline at end of file
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
index acb87a52cc7..8b6daf7acff 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributesSpec.scala
@@ -74,6 +74,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     Vector(Map.empty[String, String]),
     false,
     false,
+    sharedMemorySize = refineMV[Positive](64),
     "/Cromwell/job/",
     Map("tag1" -> "value1")
   )
@@ -92,6 +93,7 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
     Vector(Map.empty[String, String]),
     false,
     false,
+    refineMV[Positive](64),
     "/Cromwell/job/",
     Map(),
     "local")
@@ -414,6 +416,17 @@ class AwsBatchRuntimeAttributesSpec extends AnyWordSpecLike with CromwellTimeout
       ))
     }
 
+    "if sharedMemorySize is set" in {
+      val runtimeAttributes = Map(
+        "docker" -> WomString("ubuntu:latest"),
+        "scriptBucketName" -> WomString("my-stuff"),
+        "sharedMemorySize" -> WomInteger(10)
+      )
+      assertAwsBatchRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedDefaults.copy(
+        sharedMemorySize = refineMV[Positive](10)
+      ))
+    }
+
     "missing or invalid action key result in an invalid awsBatchEvaluateOnExit" in {
       val invalidEvaluateOnExit = List(
         // missing action key
diff --git a/wom/src/main/scala/wom/RuntimeAttributes.scala b/wom/src/main/scala/wom/RuntimeAttributes.scala
index 853e3145c23..44ba198cf70 100644
--- a/wom/src/main/scala/wom/RuntimeAttributes.scala
+++ b/wom/src/main/scala/wom/RuntimeAttributes.scala
@@ -32,6 +32,7 @@ object RuntimeAttributesKeys {
   val OutDirMaxKey = "outDirMax"
   val FailOnStderrKey = "failOnStderr"
   val ContinueOnReturnCodeKey = "continueOnReturnCode"
+  val sharedMemoryKey = "sharedMemorySize"
 }
 
 case class RuntimeAttributes(attributes: Map[String, WomExpression])

From c07687506a662959729c0af816a70aac5a9f6067 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Thu, 17 Oct 2024 13:40:50 +0200
Subject: [PATCH 322/326] upstream PR #7488 : fix compilation error due to
 swagger2markup

---
 .gitattributes                                |   1 -
 project/GenerateRestApiDocs.scala             | 169 ------------------
 project/Settings.scala                        |   2 -
 project/swagger2markup.sbt                    |  40 -----
 src/ci/bin/testCheckPublish.sh                |   2 +-
 ...wsBatchAsyncBackendJobExecutionActor.scala |   1 -
 .../scala/cromwell/backend/impl/aws/README.md |   8 +
 .../backend/impl/aws/merging_flow.png         | Bin 0 -> 38645 bytes
 8 files changed, 9 insertions(+), 214 deletions(-)
 delete mode 100644 project/GenerateRestApiDocs.scala
 delete mode 100644 project/swagger2markup.sbt
 create mode 100644 supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/merging_flow.png

diff --git a/.gitattributes b/.gitattributes
index d4b49d9edc9..9fcf38aa0a7 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -3,4 +3,3 @@
 *.MD text
 *.java text
 *.html text
-docs/api/RESTAPI.md linguist-generated=true
diff --git a/project/GenerateRestApiDocs.scala b/project/GenerateRestApiDocs.scala
deleted file mode 100644
index 9173a25c3c5..00000000000
--- a/project/GenerateRestApiDocs.scala
+++ /dev/null
@@ -1,169 +0,0 @@
-import io.github.swagger2markup.builder.Swagger2MarkupConfigBuilder
-import io.github.swagger2markup.{MarkupLanguage, Swagger2MarkupConverter}
-import org.apache.commons.lang3.{ClassUtils, StringUtils}
-import sbt.Keys._
-import sbt._
-
-import java.time.OffsetDateTime
-import java.time.format.DateTimeFormatter
-
-/**
-  * Provides a task to generate the REST API markdown from the Swagger YAML.
-  *
-  * Uses imports provided by swagger2markup.sbt.
-  *
-  * Based partially on https://github.com/21re/sbt-swagger-plugin
-  */
-object GenerateRestApiDocs {
-  private lazy val generateRestApiDocs = taskKey[Unit]("Generates the docs/api/RESTAPI.md")
-  private lazy val checkRestApiDocs =
-    taskKey[Unit]("Compares the existing docs/api/RESTAPI.md against the generated version")
-
-  /** Returns a timestamped preamble for the modified markdown output. */
-  private def preamble(): String = {
-    val now = OffsetDateTime.now()
-    s"""|<!--
-        |This file was generated by `sbt generateRestApiDocs` on ${now.format(DateTimeFormatter.RFC_1123_DATE_TIME)}
-        |
-        |!!! DO NOT CHANGE THIS FILE DIRECTLY !!!
-        |
-        |If you wish to change something in this file, either change cromwell.yaml or GenerateRestApiDocs.scala then
-        |regenerate.
-        |-->
-        |""".stripMargin
-  }
-
-  // Path to the input swagger yaml
-  private val SwaggerYamlFile = new File("engine/src/main/resources/swagger/cromwell.yaml")
-
-  // Path to the generated markdown
-  private val RestApiMarkdownFile = new File("docs/api/RESTAPI.md")
-
-  // A regex to locate the collection of swagger paths.
-  private val PathsRegex = "(?s)(.*## Paths)(.*)(## Definitions.*)".r
-  // A regex to locate an individual swagger path within the above collection. Each is turned into "## <original text>"
-  private val PathRegex = "(?s)### (.*)".r
-
-  private val GenericReplacements = List(
-    // Change a few section headers into bolded text.
-    "## Overview" -> "**Overview**  ",
-    "### Version information" -> "**Version information**  ",
-    "### License information" -> "**License information**  ",
-    "### Produces" -> "**Produces**  ",
-    // Since individual paths are moved from "###" to "##" we don't need "Paths" anymore.
-    "<a name=\"paths\"></a>" -> "",
-    "## Paths" -> ""
-  )
-
-  /**
-    * Move contents of the "## Paths" section up a level.
-    *
-    * Each "### example path" will be come "## example path".
-    *
-    * Should be run before `replaceGenerics` as it looks for the string "## Paths".
-    *
-    * @param content The original contents of the RESTAPI.md.
-    * @return The contents with updated paths.
-    */
-  private def replacePaths(content: String): String = {
-    content match {
-      case PathsRegex(start, paths, end) =>
-        val replacedPaths = paths.linesWithSeparators map {
-          case PathRegex(pathDescription) => s"## $pathDescription"
-          case other => other
-        }
-        replacedPaths.mkString(start, "", end)
-      case _ => throw new IllegalArgumentException(
-        "Content did not match expected regex. " +
-          "Did the swagger2markdown format change significantly? " +
-          "If so, a new regex may be required.")
-    }
-  }
-
-  /**
-    * Replaces generic strings in the generated RESTAPI.md.
-    *
-    * @param content The contents of the RESTAPI.md.
-    * @return The contents with generic replacements.
-    */
-  private def replaceGenerics(content: String): String = {
-    GenericReplacements.foldRight(content)(replaceGeneric)
-  }
-
-  /**
-    * Replaces a single generic string in the generated RESTAPI.md.
-    *
-    * @param tokens  The original and replacement strings.
-    * @param content The contents of the RESTAPI.md.
-    * @return The contents with generic replacements.
-    */
-  private def replaceGeneric(tokens: (String, String), content: String): String = {
-    val (original, replacement) = tokens
-    content.replace(original, replacement)
-  }
-
-  /**
-    * Apache commons tries to dynamically load classes from the current thread classloader. Unfortunately the
-    * classloader in the current thread from SBT does NOT have all of the libraries loaded.
-    *
-    * So-- hack in ClassUtils' classloader instead, that has access to all the required libraries including
-    * org.apache.commons.configuration2.PropertiesConfiguration
-    *
-    * Otherwise, a ClassNotFoundException will occur.
-    */
-  private def withPatchedClassLoader[A](block: => A): A = {
-    val classUtilsClassLoader = classOf[ClassUtils].getClassLoader
-    val currentThread = Thread.currentThread
-    val originalThreadClassLoader = currentThread.getContextClassLoader
-    try {
-      currentThread.setContextClassLoader(classUtilsClassLoader)
-      block
-    } finally {
-      currentThread.setContextClassLoader(originalThreadClassLoader)
-    }
-  }
-
-  private def getModifiedMarkdown: String = {
-    withPatchedClassLoader {
-      val config = new Swagger2MarkupConfigBuilder()
-        .withMarkupLanguage(MarkupLanguage.MARKDOWN)
-        .build()
-      val converter = Swagger2MarkupConverter
-        .from(SwaggerYamlFile.toPath)
-        .withConfig(config)
-        .build()
-      val contents = converter.toString
-      replaceGenerics(replacePaths(contents))
-    }
-  }
-
-  /**
-    * Generates the markdown from the swagger YAML, with some Cromwell customizations.
-    */
-  private def writeModifiedMarkdown(): Unit = {
-    val replacedContents = preamble() + getModifiedMarkdown
-    IO.write(RestApiMarkdownFile, replacedContents)
-  }
-
-  /**
-    * Compares the generated markdown against the existing markdown.
-    */
-  private def checkModifiedMarkdown(log: Logger): Unit = {
-    val markdownContents = StringUtils.substringAfter(IO.read(RestApiMarkdownFile), "-->" + System.lineSeparator)
-    val generatedContents = getModifiedMarkdown
-    if (markdownContents != generatedContents) {
-      val message = "The file docs/api/RESTAPI.md is not up to date. Please run: sbt generateRestApiDocs"
-      // Throwing the exception below should log the message... but it doesn't on sbt 1.2.1, so do it here.
-      log.error(message)
-      throw new IllegalStateException(message)
-    } else {
-      log.info("checkRestApiDocs: The file docs/api/RESTAPI.md is up to date.")
-    }
-  }
-
-  // Returns a settings including the `generateRestApiDocs` task.
-  val generateRestApiDocsSettings: Seq[Setting[_]] = List(
-    generateRestApiDocs := writeModifiedMarkdown(),
-    checkRestApiDocs := checkModifiedMarkdown(streams.value.log),
-  )
-}
diff --git a/project/Settings.scala b/project/Settings.scala
index 797d7917dd9..251023c30eb 100644
--- a/project/Settings.scala
+++ b/project/Settings.scala
@@ -1,6 +1,5 @@
 import ContinuousIntegration._
 import Dependencies._
-import GenerateRestApiDocs._
 import Merging._
 import Publishing._
 import Testing._
@@ -208,7 +207,6 @@ object Settings {
         _
           .disablePlugins(AssemblyPlugin)
           .settings(publish := {})
-          .settings(generateRestApiDocsSettings)
           .settings(ciSettings)
           .settings(rootPublishingSettings)
       )
diff --git a/project/swagger2markup.sbt b/project/swagger2markup.sbt
deleted file mode 100644
index 1fa882328f1..00000000000
--- a/project/swagger2markup.sbt
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
-Provides imports used by GenerateRestApiDocs.
-
-Borrowed from https://github.com/21re/sbt-swagger-plugin
-Uses latest (at time of coding) s2m 1.3.1
- */
-val apacheHttpclientV = "4.3.6"
-val asmV = "5.2"
-val commonsCodecV = "1.10"
-val commonsLang3V = "3.5"
-val commonsLoggingV = "1.2"
-val guavaV = "18.0"
-val jacksonV = "2.8.4"
-val javaslangV = "2.0.5"
-val plexusUtilsV = "3.0.22"
-val slf4jV = "1.7.21"
-val swagger2markupV = "1.3.4"
-
-resolvers ++= List(
-  "JCenter" at "https://jcenter.bintray.com"
-)
-
-libraryDependencies ++= List(
-  "io.github.swagger2markup" % "swagger2markup" % swagger2markupV
-)
-
-dependencyOverrides ++= List(
-  "com.fasterxml.jackson.core" % "jackson-annotations" % jacksonV,
-  "com.fasterxml.jackson.core" % "jackson-databind" % jacksonV,
-  "com.google.guava" % "guava" % guavaV,
-  "commons-codec" % "commons-codec" % commonsCodecV,
-  "commons-logging" % "commons-logging" % commonsLoggingV,
-  "io.javaslang" % "javaslang" % javaslangV,
-  "org.apache.commons" % "commons-lang3" % commonsLang3V,
-  "org.apache.httpcomponents" % "httpclient" % apacheHttpclientV,
-  "org.codehaus.plexus" % "plexus-utils" % plexusUtilsV,
-  "org.ow2.asm" % "asm" % asmV,
-  "org.ow2.asm" % "asm-tree" % asmV,
-  "org.slf4j" % "slf4j-api" % slf4jV
-)
diff --git a/src/ci/bin/testCheckPublish.sh b/src/ci/bin/testCheckPublish.sh
index 60989795ed0..46ca9033d9a 100755
--- a/src/ci/bin/testCheckPublish.sh
+++ b/src/ci/bin/testCheckPublish.sh
@@ -10,6 +10,6 @@ cromwell::build::setup_common_environment
 cromwell::build::pip_install mkdocs
 mkdocs build -s
 
-sbt -Dsbt.supershell=false --warn checkRestApiDocs +package assembly dockerPushCheck +doc
+sbt -Dsbt.supershell=false --warn +package assembly dockerPushCheck +doc
 
 git secrets --scan-history
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
index 46a0e8c8aec..4e410b8e77c 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -31,7 +31,6 @@
 
 package cromwell.backend.impl.aws
 
-import java.net.{SocketTimeoutException, URLDecoder}
 import java.net.{SocketTimeoutException, URLDecoder}
 import java.io.FileNotFoundException
 import java.nio.file.Paths
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 4b1fd62da2d..4869dd5e573 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -29,6 +29,14 @@ defined.
 This infrastructure and all the associated configuration still exists; however,
 it is moved out of the Cromwell configuration.
 
+Contributing
+-------------
+
+The aim of this fork is to have better cromwell support on AWS Batch. If you would like to contribute, please fork this repo and submit a pull request against the *aws_develop* branch. We follow the flow below to merge pull requests with upstream code into aws_releases: 
+
+![Merging Flow](merging_flow.png)
+
+
 Deployment
 ----------
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/merging_flow.png b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/merging_flow.png
new file mode 100644
index 0000000000000000000000000000000000000000..8ad6fb0764245c3a05f61fcb5f4dc19144ba0b1f
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literal 0
HcmV?d00001


From b8c16784daa042fd2cc52d931c1f9b10946fffc1 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Mon, 4 Nov 2024 07:34:53 +0100
Subject: [PATCH 323/326] Fix issue with caching on EFS by replacing touch with
 existOrThrow routine

---
 .../cromwell/core/io/DefaultIoCommand.scala   |  4 ++++
 .../scala/cromwell/core/io/IoCommand.scala    |  8 ++++++++
 .../cromwell/core/io/IoCommandBuilder.scala   |  4 ++++
 .../cromwell/engine/io/nio/NioFlow.scala      |  9 +++++++++
 .../s3/batch/S3BatchCommandBuilder.scala      |  4 ++++
 .../s3/batch/S3BatchIoCommand.scala           | 19 +++++++++++++++++++
 .../AwsBatchBackendCacheHitCopyingActor.scala | 11 ++++++-----
 7 files changed, 54 insertions(+), 5 deletions(-)

diff --git a/core/src/main/scala/cromwell/core/io/DefaultIoCommand.scala b/core/src/main/scala/cromwell/core/io/DefaultIoCommand.scala
index 2faf49696ac..44451a1e791 100644
--- a/core/src/main/scala/cromwell/core/io/DefaultIoCommand.scala
+++ b/core/src/main/scala/cromwell/core/io/DefaultIoCommand.scala
@@ -54,6 +54,10 @@ object DefaultIoCommand {
     override def commandDescription: String = s"DefaultIoExistsCommand file '$file'"
   }
 
+  case class DefaultIoExistsOrThrowCommand(override val file: Path) extends IoExistsOrThrowCommand(file) {
+    override def commandDescription: String = s"DefaultIoExistsOrThrowCommand file '$file'"
+  }
+  
   case class DefaultIoReadLinesCommand(override val file: Path) extends IoReadLinesCommand(file) {
     override def commandDescription: String = s"DefaultIoReadLinesCommand file '$file'"
   }
diff --git a/core/src/main/scala/cromwell/core/io/IoCommand.scala b/core/src/main/scala/cromwell/core/io/IoCommand.scala
index 9db50bc2c87..ec90c3b6c5c 100644
--- a/core/src/main/scala/cromwell/core/io/IoCommand.scala
+++ b/core/src/main/scala/cromwell/core/io/IoCommand.scala
@@ -182,6 +182,14 @@ abstract class IoExistsCommand(val file: Path) extends SingleFileIoCommand[Boole
   override lazy val name = "exist"
 }
 
+/**
+  * Check whether a file exists but throw an exception if it doesn't
+  */
+abstract class IoExistsOrThrowCommand(val file: Path) extends SingleFileIoCommand[Boolean] {
+  override def toString = s"Throw error if ${file.pathAsString} does not exist"
+  override lazy val name = "exist"
+}
+
 /**
   * Return the lines of a file in a collection
   */
diff --git a/core/src/main/scala/cromwell/core/io/IoCommandBuilder.scala b/core/src/main/scala/cromwell/core/io/IoCommandBuilder.scala
index c4f5da49959..ae5ef05e252 100644
--- a/core/src/main/scala/cromwell/core/io/IoCommandBuilder.scala
+++ b/core/src/main/scala/cromwell/core/io/IoCommandBuilder.scala
@@ -21,6 +21,7 @@ abstract class PartialIoCommandBuilder {
   def hashCommand: PartialFunction[Path, Try[IoHashCommand]] = PartialFunction.empty
   def touchCommand: PartialFunction[Path, Try[IoTouchCommand]] = PartialFunction.empty
   def existsCommand: PartialFunction[Path, Try[IoExistsCommand]] = PartialFunction.empty
+  def existsOrThrowCommand: PartialFunction[Path, Try[IoExistsOrThrowCommand]] = PartialFunction.empty
   def isDirectoryCommand: PartialFunction[Path, Try[IoIsDirectoryCommand]] = PartialFunction.empty
   def readLinesCommand: PartialFunction[Path, Try[IoReadLinesCommand]] = PartialFunction.empty
 }
@@ -94,6 +95,9 @@ class IoCommandBuilder(partialBuilders: List[PartialIoCommandBuilder] = List.emp
   def existsCommand(file: Path): Try[IoExistsCommand] =
     buildOrDefault(_.existsCommand, file, DefaultIoExistsCommand(file))
 
+  def existsOrThrowCommand(file: Path): Try[IoExistsOrThrowCommand] =
+    buildOrDefault(_.existsOrThrowCommand, file, DefaultIoExistsOrThrowCommand(file))
+    
   def isDirectoryCommand(file: Path): Try[IoIsDirectoryCommand] =
     buildOrDefault(_.isDirectoryCommand, file, DefaultIoIsDirectoryCommand(file))
 
diff --git a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
index 5be9ad36d9c..a2de8303a23 100644
--- a/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
+++ b/engine/src/main/scala/cromwell/engine/io/nio/NioFlow.scala
@@ -20,6 +20,7 @@ import net.ceedubs.ficus.readers.ValueReader
 
 import java.io._
 import java.nio.charset.StandardCharsets
+import java.nio.file.NoSuchFileException
 import scala.concurrent.ExecutionContext
 import scala.concurrent.duration.FiniteDuration
 
@@ -78,6 +79,7 @@ class NioFlow(parallelism: Int,
       case hashCommand: IoHashCommand => hash(hashCommand) map hashCommand.success
       case touchCommand: IoTouchCommand => touch(touchCommand) map touchCommand.success
       case existsCommand: IoExistsCommand => exists(existsCommand) map existsCommand.success
+      case existsOrThrowCommand: IoExistsOrThrowCommand => existsOrThrow(existsOrThrowCommand) map existsOrThrowCommand.success
       case readLinesCommand: IoReadLinesCommand => readLines(readLinesCommand) map readLinesCommand.success
       case isDirectoryCommand: IoIsDirectoryCommand => isDirectory(isDirectoryCommand) map isDirectoryCommand.success
       case _ => IO.raiseError(new UnsupportedOperationException("Method not implemented"))
@@ -183,6 +185,13 @@ class NioFlow(parallelism: Int,
     exists.file.exists
   }
 
+  private def existsOrThrow(exists: IoExistsOrThrowCommand) = IO {
+    exists.file.exists match {
+      case false => throw new NoSuchFileException(exists.file.toString)
+      case true => true
+    }
+  }
+
   private def readLines(exists: IoReadLinesCommand) = IO {
     exists.file.withReader { reader =>
       LazyList.continually(reader.readLine()).takeWhile(_ != null).toList
diff --git a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
index 878b6c5bc26..d41bfd26d67 100644
--- a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
+++ b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchCommandBuilder.scala
@@ -90,6 +90,10 @@ private case object PartialS3BatchCommandBuilder extends PartialIoCommandBuilder
   override def existsCommand: PartialFunction[Path, Try[S3BatchExistsCommand]] = { case path: S3Path =>
     Try(S3BatchExistsCommand(path))
   }
+  
+  override def existsOrThrowCommand: PartialFunction[Path, Try[S3BatchExistsOrThrowCommand]] = { case path: S3Path =>
+    Try(S3BatchExistsOrThrowCommand(path))
+  }
 }
 
 /**
diff --git a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchIoCommand.scala b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchIoCommand.scala
index 696c4d0240c..5a98e46e554 100644
--- a/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchIoCommand.scala
+++ b/filesystems/s3/src/main/scala/cromwell/filesystems/s3/batch/S3BatchIoCommand.scala
@@ -38,12 +38,14 @@ import cromwell.core.io.{
   IoCopyCommand,
   IoDeleteCommand,
   IoExistsCommand,
+  IoExistsOrThrowCommand,
   IoHashCommand,
   IoSizeCommand,
   IoTouchCommand
 }
 
 import cromwell.filesystems.s3.S3Path
+import java.nio.file.NoSuchFileException
 
 /**
   * Io commands with S3 paths and some logic enabling batching of request.
@@ -143,3 +145,20 @@ case class S3BatchExistsCommand(override val file: S3Path)
     }
   override def commandDescription: String = s"S3BatchExistsCommand file '$file'"
 }
+
+/**
+  * `IoCommand` to determine the existence of an object in S3, but throws execption if the object can't be found
+  * @param file the path to the object
+  */
+case class S3BatchExistsOrThrowCommand(override val file: S3Path)
+    extends IoExistsOrThrowCommand(file)
+    with S3BatchHeadCommand[Boolean] {
+  override def mapResponse(response: HeadObjectResponse): Boolean = true
+  override def onFailure(error: SdkException): Option[Left[Boolean, Nothing]] =
+    // If the object can't be found, fail the request and throw an exception
+    error match {
+      case _: NoSuchKeyException => throw new NoSuchFileException(file.toString)
+      case _ => None
+    }
+  override def commandDescription: String = s"S3BatchExistsCommand file '$file'"
+}
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
index b15dc52b364..7610954df3a 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendCacheHitCopyingActor.scala
@@ -36,7 +36,7 @@ import cromwell.backend.impl.aws.{AWSBatchStorageSystems, AwsBatchBackendInitial
 import cromwell.backend.io.JobPaths
 import cromwell.backend.standard.callcaching.{StandardCacheHitCopyingActor, StandardCacheHitCopyingActorParams}
 import cromwell.core.CallOutputs
-import cromwell.core.io.{DefaultIoCommandBuilder, IoCommand, IoCommandBuilder, IoTouchCommand}
+import cromwell.core.io.{DefaultIoCommandBuilder, IoCommand, IoCommandBuilder}
 import cromwell.core.path.Path
 import cromwell.core.simpleton.{WomValueBuilder, WomValueSimpleton}
 import cromwell.filesystems.s3.batch.S3BatchCommandBuilder
@@ -61,10 +61,11 @@ class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyin
                                  sourceCallRootPath: Path
   ): Try[(CallOutputs, Set[IoCommand[_]])] =
     (batchAttributes.fileSystem, cachingStrategy) match {
-      case (AWSBatchStorageSystems.s3, UseOriginalCachedOutputs) =>
-        val touchCommands: Seq[Try[IoTouchCommand]] = womValueSimpletons collect {
+      case (AWSBatchStorageSystems.s3, UseOriginalCachedOutputs) => 
+        val touchCommands: Seq[Try[IoCommand[_]]] = womValueSimpletons collect {
+          // only work on WomFiles, skip others? 
           case WomValueSimpleton(_, wdlFile: WomFile) =>
-            getPath(wdlFile.value) flatMap S3BatchCommandBuilder.touchCommand
+              getPath(wdlFile.value).flatMap(S3BatchCommandBuilder.existsOrThrowCommand)
         }
 
         TryUtil.sequence(touchCommands) map {
@@ -88,7 +89,7 @@ class AwsBatchBackendCacheHitCopyingActor(standardParams: StandardCacheHitCopyin
           Try {
             // PROD-444: Keep It Short and Simple: Throw on the first error and let the outer Try catch-and-re-wrap
             (newDetritus + (JobPaths.CallRootPathKey -> destinationCallRootPath)) ->
-              newDetritus.values.map(S3BatchCommandBuilder.touchCommand(_).get).toSet
+              newDetritus.values.map(S3BatchCommandBuilder.existsOrThrowCommand(_).get).toSet
           }
         }
       case (_, _) => super.processDetritus(sourceJobDetritusFiles)

From bcd4ef932923d633ff5bb803d625041e3aa09210 Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Mon, 4 Nov 2024 07:35:53 +0100
Subject: [PATCH 324/326] make sure that md5 sibling file of EFS data is newer
 than main file to be valid

---
 .../cromwell/backend/impl/aws/AwsBatchJob.scala | 16 +++++++---------
 .../AwsBatchBackendFileHashingActor.scala       | 17 +++++++++++++++--
 2 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
index 15a3fdeff8a..3c5b0acbc72 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJob.scala
@@ -427,18 +427,17 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
            // need to make md5sum?
            val md5_cmd = if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
                     Log.debug("Add cmd to create MD5 sibling.")
-                    // this does NOT regenerate the md5 in case the file is overwritten ! 
-                    // TODO : Add check for file age => recreate if md5 older than main file
+                    // generate MD5 if missing or if local file is newer than sibling md5
                     s"""
-                        |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then
+                        |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' -nt '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]]; then
                         |   # the glob list
                         |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && DELOCALIZATION_FAILED=1 );
                         |   # globbed files, using specified number of cpus for parallel processing.
-                        SAVEIFS="$$IFS"
-                        |IFS=$$'\n'
+                        |   SAVEIFS="$$IFS"
+                        |   IFS=$$'\n'
                         |   cat "${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}" | xargs -I% -P${runtimeAttributes.cpu.##.toString} bash -c "md5sum ${globDirectory}/% > ${globDirectory}/%.md5"
+                        |   IFS="$$SAVEIFS"
                         |fi
-                        |IFS="$$SAVEIFS"
                         |""".stripMargin
                 }
            // return combined result
@@ -461,7 +460,6 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         Log.debug("output Data on working disk mount" + output.local.pathAsString)
         s"""_s3_delocalize_with_retry "$workDir/${output.local.pathAsString}" "${output.s3key}" """.stripMargin
 
-      // file(name (full path), s3key (delocalized path), local (file basename), mount (disk details))
       // files on EFS mounts are optionally delocalized.
       case output: AwsBatchFileOutput if efsMntPoint.isDefined && output.mount.mountPoint.pathAsString == efsMntPoint.get =>
         Log.debug("EFS output file detected: "+ output.s3key + s" / ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}")
@@ -478,9 +476,9 @@ final case class AwsBatchJob(jobDescriptor: BackendJobDescriptor, // WDL/CWL
         // need to make md5sum?
         var md5_cmd = ""
         if (efsMakeMD5.isDefined && efsMakeMD5.getOrElse(false)) {
-            Log.debug("Add cmd to create MD5 sibling.")
+            Log.debug("Add cmd to create MD5 sibling if missing or outdated.")
             md5_cmd = s"""
-                            |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]] ; then
+                            |if [[ ! -f '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' -nt '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' ]]; then
                             |   md5sum '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}' > '${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' || (echo 'Could not generate ${output.mount.mountPoint.pathAsString}/${output.local.pathAsString}.md5' && DELOCALIZATION_FAILED=1 );
                             |fi
                             |""".stripMargin
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
index 5736b6bf130..eb6a9f772e7 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/callcaching/AwsBatchBackendFileHashingActor.scala
@@ -39,10 +39,12 @@ import cromwell.core.io.DefaultIoCommandBuilder
 import scala.util.Try
 import cromwell.backend.standard.callcaching.StandardFileHashingActor.SingleFileHashRequest
 import cromwell.core.path.DefaultPathBuilder
+import org.slf4j.{Logger, LoggerFactory}
 
 class AwsBatchBackendFileHashingActor(standardParams: StandardFileHashingActorParams)
     extends StandardFileHashingActor(standardParams) {
 
+  val Log: Logger = LoggerFactory.getLogger(StandardFileHashingActor.getClass)
   override val ioCommandBuilder = BackendInitializationData
     .as[AwsBatchBackendInitializationData](standardParams.backendInitializationDataOption)
     .configuration
@@ -55,21 +57,32 @@ class AwsBatchBackendFileHashingActor(standardParams: StandardFileHashingActorPa
   val aws_config = BackendInitializationData.as[AwsBatchBackendInitializationData](standardParams.backendInitializationDataOption).configuration
   
   // custom strategy to handle efs (local) files, in case sibling-md5 file is present. 
+  //  if valid md5 is found : return the hash
+  //  if no md5 is found : return None (pass request to parent hashing actor)
+  //  if outdated md5 is found : return invalid string (assume file has been altered after md5 creation)
+  //  if file is missing : return invalid string
   override def customHashStrategy(fileRequest: SingleFileHashRequest): Option[Try[String]] = {
     val file = DefaultPathBuilder.get(fileRequest.file.valueString)
     if (aws_config.efsMntPoint.isDefined && file.toString.startsWith(aws_config.efsMntPoint.getOrElse("--")) && aws_config.checkSiblingMd5.getOrElse(false)) {
             val md5 = file.sibling(s"${file.toString}.md5")
             // check existance of the file : 
             if (!file.exists) {
+                Log.debug(s"File Missing: ${file.toString}")
                 // if missing, cache hit is invalid; return invalid md5
                 Some("File Missing").map(str => Try(str))
             }
-            // check existence of the sibling file
-            else if (md5.exists) {
+            // check existence of the sibling file and make sure it's newer than main file
+            else if (md5.exists && md5.lastModifiedTime.isAfter(file.lastModifiedTime)) {
                 // read the file.
+                Log.debug("Found valid sibling file for " + file.toString)
                 val md5_value: Option[String] = Some(md5.contentAsString.split("\\s+")(0))
                 md5_value.map(str => Try(str))
+            } else if (md5.exists && md5.lastModifiedTime.isBefore(file.lastModifiedTime)) {
+                // sibling file is outdated, return invalid md5
+                Log.debug("Found outdated sibling file for " + file.toString)
+                Some("Checksum File Outdated").map(str => Try(str))
             } else {
+                Log.debug("Found no sibling file for " + file.toString)
                 // File present, but no sibling found, fall back to default.
                 None
             }

From 502b89d2d8d4330420f947957bc98c8cb141e67f Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Mon, 4 Nov 2024 07:37:12 +0100
Subject: [PATCH 325/326] revise sharedmemory attribute to take reguluar GB/MB
 specification

---
 .../impl/aws/AwsBatchJobDefinition.scala      | 12 +++++-----
 .../impl/aws/AwsBatchRuntimeAttributes.scala  | 22 ++++++++-----------
 .../backend/impl/aws/AwsBatchJobSpec.scala    |  2 +-
 3 files changed, 16 insertions(+), 20 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
index 86680f4dcab..7f2cbd1b953 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchJobDefinition.scala
@@ -42,6 +42,7 @@ import java.security.MessageDigest
 import org.apache.commons.lang3.builder.{ToStringBuilder, ToStringStyle}
 import org.slf4j.{Logger, LoggerFactory}
 import wdl4s.parser.MemoryUnit
+import wom.format.MemorySize
 
 /**
   * Responsible for the creation of the job definition.
@@ -164,8 +165,8 @@ trait AwsBatchJobDefinitionBuilder {
       efsMakeMD5: Boolean,
       tagResources: Boolean,
       logGroupName: String,
-      sharedMemorySize: Int): String = {
-        s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}:${tagResources.toString}:$logGroupName"
+      sharedMemorySize: MemorySize): String = {
+        s"$imageName:$packedCommand:${volumes.map(_.toString).mkString(",")}:${mountPoints.map(_.toString).mkString(",")}:${env.map(_.toString).mkString(",")}:${ulimits.map(_.toString).mkString(",")}:${efsDelocalize.toString}:${efsMakeMD5.toString}:${tagResources.toString}:$logGroupName:${sharedMemorySize.to(MemoryUnit.MB).amount.toInt}"
       }
 
     val environment = List.empty[KeyValuePair]
@@ -201,9 +202,8 @@ trait AwsBatchJobDefinitionBuilder {
       efsMakeMD5,
       tagResources,
       logGroupName,
-      context.runtimeAttributes.sharedMemorySize.value
+      context.runtimeAttributes.sharedMemorySize
     )
-
     // To reuse job definition for gpu and gpu-runs, we will create a job definition that does not gpu requirements
     // since aws batch does not allow you to set gpu as 0 when you dont need it. you will always need cpu and memory
     (ContainerProperties.builder()
@@ -219,8 +219,8 @@ trait AwsBatchJobDefinitionBuilder {
       .environment(environment.asJava)
       .ulimits(ulimits.asJava)
       .linuxParameters(
-        LinuxParameters.builder().sharedMemorySize(context.runtimeAttributes.sharedMemorySize.##).build()
-      ),
+      LinuxParameters.builder().sharedMemorySize(context.runtimeAttributes.sharedMemorySize.to(MemoryUnit.MB).amount.toInt).build() // Convert MemorySize to MB
+    ),
      containerPropsName)
   }
 
diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
index fdf4021f257..e90f2feeb78 100755
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchRuntimeAttributes.scala
@@ -42,13 +42,14 @@ import eu.timepit.refined.api.Refined
 import eu.timepit.refined.numeric.Positive
 import wom.RuntimeAttributesKeys
 import wom.format.MemorySize
+import wdl4s.parser.MemoryUnit
 import wom.types._
 import wom.values._
 import com.typesafe.config.{ConfigException, ConfigValueFactory}
 
 import scala.util.matching.Regex
 import org.slf4j.{Logger, LoggerFactory}
-import wom.RuntimeAttributesKeys.{GpuKey, sharedMemoryKey}
+import wom.RuntimeAttributesKeys.{GpuKey } // , sharedMemoryKey}
 
 import scala.util.{Failure, Success, Try}
 import scala.jdk.CollectionConverters._
@@ -94,7 +95,7 @@ case class AwsBatchRuntimeAttributes(cpu: Int Refined Positive,
                                      ulimits: Vector[Map[String, String]],
                                      efsDelocalize: Boolean,
                                      efsMakeMD5 : Boolean,
-                                     sharedMemorySize: Int Refined Positive,
+                                     sharedMemorySize: MemorySize,
                                      logGroupName: String,
                                      additionalTags: Map[String, String],
                                      fileSystem: String= "s3",
@@ -110,7 +111,7 @@ object AwsBatchRuntimeAttributes {
 
   val awsBatchEvaluateOnExitKey = "awsBatchEvaluateOnExit"
 
-  val defaultSharedMemorySize = WomInteger(64)
+  val defaultSharedMemorySize = MemorySize(64, MemoryUnit.MB)
 
   private val awsBatchEvaluateOnExitDefault = WomArray(WomArrayType(WomMapType(WomStringType,WomStringType)), Vector(WomMap(Map.empty[WomValue, WomValue])))
 
@@ -179,9 +180,10 @@ object AwsBatchRuntimeAttributes {
     noAddressValidationInstance
       .withDefault(noAddressValidationInstance.configDefaultWomValue(runtimeConfig) getOrElse NoAddressDefaultValue)
 
-  private def sharedMemorySizeValidation(runtimeConfig: Option[Config]):  RuntimeAttributesValidation[Refined[Int, Positive]] = {
-    SharedMemorySizeValidation(sharedMemoryKey).withDefault(
-      SharedMemorySizeValidation(sharedMemoryKey).configDefaultWomValue(runtimeConfig).getOrElse(defaultSharedMemorySize)
+  private def sharedMemorySizeValidation(runtimeConfig: Option[Config]): RuntimeAttributesValidation[MemorySize] = {
+    MemoryValidation.withDefaultMemory(
+      RuntimeAttributesKeys.sharedMemoryKey,
+      MemoryValidation.configDefaultString(RuntimeAttributesKeys.sharedMemoryKey, runtimeConfig) getOrElse defaultSharedMemorySize.toString
     )
   }
 
@@ -337,7 +339,7 @@ object AwsBatchRuntimeAttributes {
     val efsDelocalize: Boolean = RuntimeAttributesValidation.extract(awsBatchefsDelocalizeValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
     val efsMakeMD5: Boolean = RuntimeAttributesValidation.extract(awsBatchefsMakeMD5Validation(runtimeAttrsConfig),validatedRuntimeAttributes)
     val tagResources: Boolean = RuntimeAttributesValidation.extract(awsBatchtagResourcesValidation(runtimeAttrsConfig),validatedRuntimeAttributes)
-    val sharedMemorySize: Int Refined Positive = RuntimeAttributesValidation.extract(sharedMemorySizeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
+    val sharedMemorySize: MemorySize = RuntimeAttributesValidation.extract(sharedMemorySizeValidation(runtimeAttrsConfig), validatedRuntimeAttributes)
 
     new AwsBatchRuntimeAttributes(
       cpu,
@@ -708,12 +710,6 @@ class AwsBatchtagResourcesValidation(key: String) extends BooleanRuntimeAttribut
   override protected def missingValueMessage: String = s"Expecting $key runtime attribute to be a Boolean"
 }
 
-object SharedMemorySizeValidation {
-  def apply(key: String): SharedMemorySizeValidation = new SharedMemorySizeValidation(key)
-}
-
-class SharedMemorySizeValidation(key: String) extends PositiveIntRuntimeAttributesValidation(key)
-
 object UlimitsValidation
     extends RuntimeAttributesValidation[Vector[Map[String, String]]] {
   override def key: String = AwsBatchRuntimeAttributes.UlimitsKey
diff --git a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
index a91e11ba43a..bbde4840705 100644
--- a/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
+++ b/supportedBackends/aws/src/test/scala/cromwell/backend/impl/aws/AwsBatchJobSpec.scala
@@ -110,7 +110,7 @@ class AwsBatchJobSpec extends TestKitSuite with AnyFlatSpecLike with Matchers wi
   val s3Outputs: Set[AwsBatchFileOutput] = Set(AwsBatchFileOutput("baa", "s3://bucket/somewhere/baa", DefaultPathBuilder.get("baa"), AwsBatchWorkingDisk()))
 
   val cpu: Int Refined Positive = 2
-  val sharedMemorySize: Int Refined Positive = 64
+  val sharedMemorySize: MemorySize = "64 MB"
 
   val runtimeAttributes: AwsBatchRuntimeAttributes = new AwsBatchRuntimeAttributes(
       cpu = cpu,

From 80bcd434dfa6d92d5abfa74c7bb2ab8344522e0e Mon Sep 17 00:00:00 2001
From: geertvandeweyer <geertvandeweyer@gmail.com>
Date: Mon, 4 Nov 2024 07:47:52 +0100
Subject: [PATCH 326/326] updated AWS README file

---
 .../scala/cromwell/backend/impl/aws/README.md | 82 ++++++++++++++++---
 1 file changed, 70 insertions(+), 12 deletions(-)

diff --git a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
index 4869dd5e573..eb998dceb0f 100644
--- a/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
+++ b/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/README.md
@@ -75,7 +75,16 @@ This runtime attribute adds support to [*AWS Batch Automated Job Retries*](https
 
 It takes an Int, between 1 and 10, as a value that indicates the maximum number of times AWS Batch should retry a failed task. If the value 0 is passed, the [*Retry Strategy*](https://docs.aws.amazon.com/batch/latest/userguide/job_definition_parameters.html#retryStrategy) will not be added to the job definiton and the task will run just once.
 
-This configuration should be passed in the `options.json` file when launching the pipeline.
+This configuration should be passed in the `options.json` file when launching the pipeline, as a default_runtime_attribute:
+
+```
+{
+  default_runtime_attribute: {
+    "awsBatchRetryAttempts" : 2
+  }
+}
+```
+Alternatively, it can be provided per task, using the task runtime settings in the WDL:
 
 ```
 runtime {
@@ -83,6 +92,8 @@ runtime {
 }
 ```
 
+_Note: Also see 'MaxRetries' options_
+
 ### `awsBatchEvaluteOnExit`
 
 *Default: _[]_* - will always retry 
@@ -123,14 +134,17 @@ A list of [`ulimits`](https://docs.aws.amazon.com/batch/latest/userguide/job_def
 This configuration should be passed in the `options.json` file when launching the pipeline.
 
 ```
-"ulimits": [
-  {
-    "name": string,
-    "softLimit": integer,
-    "hardLimit": integer
+{
+  default_runtime_attribute: {
+    "ulimits": [
+      {
+        "name": "string",
+        "softLimit": "integer",
+        "hardLimit": "integer"
+      }
+    ]
   }
-  ...
-]
+}
 ```
 Parameter description:
 
@@ -141,12 +155,12 @@ Parameter description:
 
 - `softLimit`
   - The soft limit for the `ulimit` type.
-  - Type: Integer
+  - Type: Integer, but provided as string (with quotes)
   - Required: Yes, when `ulimits` is used.
 
 - `hardLimit`
   - The hard limit for the `ulimit` type.
-  - Type: Integer
+  - Type: Integer, but provided as string (with quotes)
   - Required: Yes, when `ulimits` is used.
 
 ### GPU support 
@@ -177,6 +191,27 @@ the gpuCount value will be passed to AWS Batch as part of [resourceRequirements]
 You will need to use this feature in conjunction with a aws queue that has GPU instances (see [compute-environment](/supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/DEPLOY.md#compute-environment) for more inforamtion)
 
 
+### Shared Memory Support
+
+Tasks can request shared memory by setting `sharedMemorySize` in the task runtime attribute.  This is required to support workflows with tasks that uses SharedMemory for their work, for example in popular ML libraries like PyTorch. The memory is available under /dev/shm in the task.  The value is provided as a Memory value, taking GB/MB suffixes.  For instance, requesting 1Gb of shared memory:
+
+```
+task gpu_queue_task {
+  input {
+    ...
+  } 
+  command <<<
+    ...
+  >>>
+  output {}
+  runtime {
+    sharedMemorySize: "1024 MB"
+  }
+}
+```
+
+
+
 ### Call Caching with ECR private
 
 AWS ECR is a private container registry, for which access can be regulated using IAM. Call caching is possible by setting up the following configuration:
@@ -350,7 +385,7 @@ Cromwell EC2 instances can be equipped with a shared elastic filesystem, termed
 
 Following the [GenomicsWorkFlows](https://docs.opendata.aws/genomics-workflows/orchestration/cromwell/cromwell-overview.html) deployment stack and selecting "Create EFS", you will end up with an EFS filesystem accessible within the provided subnets. It is mounted by default in EC2 workers under /mnt/efs. This is specified in the launch templates USER_DATA if you want to change this. *BEWARE* : For globbing to work on EFS, the mountpoint must be left as "/mnt/efs" ! 
 
-Next, it is recommended to change the EFS setup (in console : select EFS service, then the "SharedDataGenomics" volume, edit). Change performance settings to Enhanced/Elastic, because the bursting throughput is usually insufficient. Optionally set the lifecycle to archive infrequently accessed data and reduce costs. 
+Next, it is recommended to change the EFS setup (in console : select EFS service, then the "SharedDataGenomics" volume, edit). Change performance settings to Enhanced/Elastic, because the bursting throughput is usually insufficient (there can be a significant cost for that!). Optionally set the lifecycle to archive infrequently accessed data and reduce costs. 
 
 2. Set Cromwell Configuration
 
@@ -544,6 +579,7 @@ task task_three {
 ```
 
 #### TAGGING RESOURCES
+
 AWS Batch tags jobs and, if configured in the compute environment, instances and volumes with generic tags to track costs.  These tags typically include the job-queue name. To allow more detailed cost tracking, it is possible to enable tagging instances and connected volumes with the following information : 
 
 - *cromwell-workflow-name* : the top-level name of the submitted WDL (eg "workflow myWorkflow {...}")
@@ -556,7 +592,7 @@ In case the same instance is reused for multiple tasks, unique tag values are co
 - cromwell-workflow-id : 2443daac-c232-4e0a-920d-fbf53273e9c5;df19029e-cc02-41d5-a26d-8d30c0ab05cb
 - cromwell-task-id : myWorkflow.myTask-None-1
 
-To enable tagging, add "tagResources = true" to the default-runtime-attributes section of your configuration: 
+To enable default tagging, add "tagResources = true" to the default-runtime-attributes section of your configuration: 
 
 ```
 backend {
@@ -575,6 +611,28 @@ backend {
 
 ```
 
+Additional, custom tags can be added to jobs, using the "additionalTags" paramter in the "default-runtime-attributes" section of the job definition:
+
+```
+backend {
+    providers {
+        AWSBatch {
+            config{
+                  default-runtime-attributes {
+                      logGroupName: "/Cromwell/job/"
+                      additionalTags {
+                         projectid: "project1"
+                      }
+                  }
+            }
+        }
+    }
+}
+```
+
+The _logGroupName_ enables you to send the logs to a custom log group name and tag the jobs that Cromwell submits.  The _additionalTags_ allows you to specify tags to be added to the jobs as <key> : <value> pairs. 
+
+
 
 AWS Batch
 ---------